Time of bloom SSR Results
All SSR results from the Time of bloom experimentation are below.
AT5G24470 (APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 of the Light Signaling pathway) found in Scaffold 00001 (query sequence starts at base 322798)
AT2G46790 (APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 of the Light Signaling pathway) found in Scaffold 00001 (query sequence starts at base 322801)
1) For Primer GTCTTCTTGGCTTTCTCTTCCA - Rev Primer CTTCCACCGCCACTAATATCTC - Repeats (tc) x11 - PCR product = 157 bp - start at base 324273
2) For Primer CGCCTTTTAATTCCTAGTGGTG - Rev Primer TGTTGCCTTATTGTGAGCCTAA - Repeats (tc) x15 - PCR product = 153 bp - start at base 324766
3) For Primer AGCCAATAACCTTTCCTGTTGA - Rev Primer GTGCCTATCAGCCACTCTTTTT - Repeats (tc) x9 - PCR product = 238 bp - start at base 314842
AT4G02560 (LD, LUMINIDEPENDENS of the Autonomous pathway) found in Scaffold 00002 (query sequence starts at base 158601)
1) For Primer ACTGGATCAGTCTCCGACTCTC - Rev Primer GAGTTACGGCTAGGGTTAGGGT - Repeats (tc) x11 - PCR product = 204 bp - start at base 155393
2) For Primer TTTCACTTTTAGCCACCACCTT - Rev Primer CGAATCCATCAGCTAAAAGGAC - Repeats (tc) x11 - PCR product = 190 bp - start at base 166784
3) For Primer GTATGCTGCTGCAAACAATGAT - Rev Primer CTTGGAGAAGTGACAGAAAGCA - Repeats (tc) x44 - PCR product = 236 bp - start at base 341579
AT4G26000 (PEP, PEPPER of the Vernalization pathway) found in Scaffold 00021 (query sequence starts at base 157278)
1) For Primer CACAAGGATGCTCAAACCATAA - Rev Primer AAATGGTTGGATACGAGCTGTT - Repeats (at) x8 - PCR product = 280 bp - start at base 148634
2) For Primer ACGAGGAGTGAGAGAGAAGTGG - Rev Primer CAGACACAAATTGGAGAGCAAG - Repeats (tc) x12 - PCR product = 297 bp - start at base 145700
3) For Primer CTGGGACCAGATAATTCGAAAG - Rev Primer TGACACATGTTGATTGGTCTGA - Repeats (ga) x10 - PCR product = 219 bp - start at base 116906
AT2G18880 (VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 of the Autonomous pathway) found in Scaffold 00026 (query sequence starts at base 369396)
AT5G57380 (VERNALIZATION INSENSITIVE 3, VIN3 of the Autonomous and Vernalization pathways) found in Scaffold 00026 (query sequence starts at base 369405)
AT4G30200 (VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 of the Autonomous and Vernalization pathways) found in Scaffold 00026 (query sequence starts at base 369417)
1) For Primer CGAGTCACCTATCACCAGATCA - Rev Primer TCCTCCAAACCTTACAAAAGGA - Repeats (ta) x10 - PCR product = 244 bp - start at base 362422
2) For Primer AAAAAGGAAGAGGAAGAATCGG - Rev Primer AGCCGACGACGACTCTATCTAA - Repeats (ag) x19 - PCR product = 260 bp - start at base 362158
3) For Primer CTGCTACTGTCACCATCAGAGG - Rev Primer TCTTCCTCTCGTCTCATATGCC - Repeats (ga) x11 - PCR product = 297 bp - start at base 344594
AT2G18915 (ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2 of the Light Signaling pathway) found in Scaffold 00026 (query sequence starts at base 445582)
AT5G57360 (ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL of the Light Signaling pathway) found in Scaffold 00026 (query sequence starts at base 445597)
1) For Primer CAGAGTAAATGGTGTGGACCAA - Rev Primer AAACCGGAACATATCCTCTTCA - Repeats (ga) x10 - PCR product = 200 bp - start at base 441957
2) For Primer GTAGATCAGGGAGAGGAGGGAT - Rev Primer GGTTTATGTGGACCGGAAATAA - Repeats (ag) x11 - PCR product = 250 bp - start at base 429600
3) For Primer TCGCTAAATTGTCTGGGAAAGT - Rev Primer CCTACTTCGGGTAGGTACCTTTA - Repeats (tc) x11 - PCR product = 235 bp - start at base 417206
AT4G00650 (FLA, FLOWERING LOCUS A, FRI, FRIGIDA of the Vernalization pathway) found in Scaffold 00039 (query sequence starts at base 216632)
1) For Primer GGCTCCTTATTTCCCACTCTTT - Rev Primer CAGCATTTCTCATAAGGGAAGG - Repeats (ag) x13 - PCR product = 229 bp - start at base 202952
2) For Primer GGGATTTTGAAGAGTGAAGACG - Rev Primer TCTTCCTCCTCCTATTCCTTCC - Repeats (tc) x10 - PCR product = 297 bp - start at base 235833
3) For Primer CCGTCCAGACAAACTTCTCTTC - Rev Primer GGATTTTAGTATGAGTTCGGCG - Repeats (ctt) x11 - PCR product = 299 bp - start at base 257937
AT1G53160 (FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4 of the Age pathway) found in Scaffold 00062 (query sequence starts at base 412489)
AT2G33810 (SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 of the Age pathway) found in Scaffold 00062 (query sequence starts at base 412489) – CATHERINE D
1) For Primer CCAAACTCCAAGAATGAACTCC - Rev Primer GATCTACGCATTGGAAACATCA - Repeats (ga) x16 - PCR product = 288 bp - start at base 402970
2) For Primer TTTTCTGCTGAAGTGAAGTGGA - Rev Primer TCTTTGTCTGGACATTGTTTGG - Repeats (ga) x10 - PCR product = 180 bp - start at base 392786
3) For Primer AGCGGAAATTATAGGAGGGAAG - Rev Primer GGAGAGAGGAGAGAGAGACGAG - Repeats (tc) x28 - PCR product = 205 bp - start at base 423921
AT3G47500 (CDF3, CYCLING DOF FACTOR 3 of the Light Signaling pathway) found in Scaffold 00079 (query sequence starts at base 68175)
AT1G26790 (of the Light Signaling pathway) found in Scaffold 00079 (query sequence starts at base 69048) – MIKE N
1) For Primer GTTTGACATATCGAGCTTGCAC - Rev Primer TTGGTTGTAGAGGAGTGGGATT - Repeats (aat) x6 - PCR product = 292 bp - start at base 69852
2) For Primer CTCGATCCAATCCATAATCCAT - Rev Primer GATCAAAAGCGCAAGTAGGAGT - Repeats (ag) x8 - PCR product = 270 bp - start at base 71505
3) For Primer TTTGGACTAAAGCGCTACCATT - Rev Primer TACCACCACCCTTTATTTGGAG - Repeats (tcc) x9 - PCR product = 298 bp - start at base 52487
AT1G22770 (FB, GI, GIGANTEA of the Light Signaling pathway) found in Scaffold 00100 (query sequence starts at base 198329) – MIKE N
1) For Primer TTTTTGTTGACCCCAAGACTTC - Rev Primer AGCAACTTCCTCATCACAGACA - Repeats (ct) x11 - PCR product = 257 bp - start at base 196803
2) For Primer TTTCGCTCAGTTATCTCTCTCTGA - Rev Primer CCATCTTTAACTGCACAAACCA - Repeats (ta) x12 - PCR product = 225 bp - start at base 207941
3) For Primer TTTCGCTCAGTTATCTCTCTCTGA - Rev Primer CCATCTTTAACTGCACAAACCA - Repeats (ga) x11 - PCR product = 225 bp - start at base 207965
AT3G05120 (ATGID1A, GA INSENSITIVE DWARF1A, GID1A of the Gibberellin pathway) found in Scaffold 00101 (query sequence starts at base 398762)
1) For Primer CATCAATCAACGTAACCACCAT - Rev Primer ATCTGCTGTGAAGTGGAAAGGT - Repeats (gaa) x15 - PCR product = 293 bp - start at base 400426
2) For Primer CTGCTGTGCATATTACCGTTGT - Rev Primer TAATGGTGGAGAATGTGTAGCG - Repeats (ct) x11 - PCR product = 219 bp - start at base 389934
3) For Primer ATGGGTAGTTGCTCCTAATTGC - Rev Primer AACCTCACAACCGAAGAAACAT - Repeats (ct) x10 - PCR product = 279 bp - start at base 420279
AT2G33835 (FES1, FRIGIDA-ESSENTIAL 1 of the Vernalization pathway) found in Scaffold 00102 (query sequence starts at base 88264)
1) For Primer CACCCCTCCATCCATTAGTAAA - Rev Primer ATGGAAAGGACTGGTGGTAAGA - Repeats (tc) x10 - PCR product = 163 bp - start at base 113504
2) For Primer TCTACAGCATCTCTCCCACTCA - Rev Primer CCTCCAAATGATGAACACAAGA - Repeats (tc) x13 - PCR product = 250 bp - start at base 52555
3) For Primer TCTTTGATCCTTCTGGTTTGGT - Rev Primer CAGCTCTCACCTACCTCACTCA - Repeats (ga) x20 - PCR product = 286 bp - start at base 132341
AT4G16280 (FCA of the Ambient Temperature and Autonomous pathways) found in Scaffold 00104 (query sequence starts at base 120318)
1) For Primer CATTCGGATTTCTTATCCATCC - Rev Primer CTCCCTTTCACTGCTCTCTGAT - Repeats (ga) x8 - PCR product = 219 bp - start at base 137168
2) For Primer AACTCAAGCCCATTTACTCCAA - Rev Primer TGTTTGTGACTATGAACCTGGG - Repeats (tc) x10 - PCR product = 209 bp - start at base 150456
3) For Primer ATAAAACCAACACTGACCACCC - Rev Primer TAACCAAAACTCGTCGGAATCT - Repeats (ct) x8 - PCR product = 257 bp - start at base 106905
AT3G15270 (SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5 of the Age pathway) found in Scaffold 00105 (query sequence starts at base 147284)
1) For Primer TCCTCTTGCAAGGAATTGGTAT - Rev Primer CCTAGGGGGAGAATAGTGCTTT - Repeats (ga) x8 - PCR product = 118 bp - start at base 142051
2) For Primer GAGCTTTCGTACCTCCGTAAAA - Rev Primer TGACGTCGTAGAGTTGGTAGGA - Repeats (tc) x13 - PCR product = 299 bp - start at base 139430
3) For Primer TACTGTTATTCAGGGTGGCCTT - Rev Primer AGCCTAGATCGTTTTGCTTCAA - Repeats (ct) x12 - PCR product = 268 bp - start at base 123867
AT1G68050 ("FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1 of the Light Signaling pathway) found in Scaffold 00110 (query sequence starts at base 120279)
1) For Primer ATTCAGATGGCGGATAAAAGAG - Rev Primer CCGCGTTTTCCAGTCTATATTC - Repeats (ag) x8 - PCR product = 242 bp - start at base 126867
2) For Primer GAGGTGAAGTGTAGATGAGGGG - Rev Primer GAGAGAGAGCGACAAGACGAAT - Repeats (ct) x14 - PCR product = 274 bp - start at base 136199
3) For Primer TTTGCGCTCTCTCTCTCTCTCT - Rev Primer GAAACTCGAAATCTTGAAACCG - Repeats (ct) x15 - PCR product = 260 bp - start at base 136377
AT5G02810 (APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7 of the Light Signaling pathway) found in Scaffold 00125 (query sequence starts at base 276518)
1) For Primer TAAGCAAGCTCGAACCCTAATC - Rev Primer CGATGCTGTTAGTTCATTCCAA - Repeats (tc) x11 - PCR product = 263 bp - start at base 278986
2) For Primer GTCATTAGAGCAACAGCAGCAG - Rev Primer TCGTCGTCGTTATCATCATCTC - Repeats (ct) x8 - PCR product = 291 bp - start at base 290380
3) For Primer CCTCAAAACTGGGGAAAATAGA - Rev Primer GGGTATAAAAGGCAAGCAGATG - Repeats (ga) x10 - PCR product = 138 bp - start at base 226349
AT1G27370 (SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 of the Age pathway) found in Scaffold 00127 (query sequence starts at base 165806) – CATHERINE D
1) For Primer CCAGAAATAACCTCGAAACAGC - Rev Primer CCATGATTGATCAAAACAGCTC - Repeats (ga) x12 - PCR product = 281 bp - start at base 169541
2) For Primer AGTTAAGGGAGGCCTAGGGAC - Rev Primer GGTCGCCCTTAGATAAGGATTC - Repeats (at) x11 - PCR product = 298 bp - start at base 176760
3) For Primer CAATTTTGTTCCCACCTCTCTC - Rev Primer AATGAATGTAGCAAATCCCCAC - Repeats (ac) x8 - PCR product = 211 bp - start at base 152171
AT1G66350 (RGA-LIKE 1, RGL, RGL1 of the Gibberellin pathway) found in Scaffold 00134 (query sequence starts at base 174707)
AT3G03450 (RGA-LIKE 2, RGL2 of the Gibberellin pathway) found in Scaffold 00134 (query sequence starts at base 174722)
1) For Primer TGACAAGACGTGCGATATAAGG - Rev Primer TCCTCGTCGAACATCTTTTTG - Repeats (ttc) x5 - PCR product = 250 bp - start at base 174643
2) For Primer TTCACACCAAATGGACTCTGAC - Rev Primer GAGAATAATTTTGTCCCACCCA - Repeats (tc) x9 - PCR product = 237 bp - start at base 135335
3) For Primer AGATCACAATGGGCTTCAAACT - Rev Primer AGGAGGACGTTGGAGACTGTAA - Repeats (ca) x13 - PCR product = 204 bp - start at base 116959
AT1G01060 (LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1 of the Light Signaling pathway) found in Scaffold 00140 (query sequence starts at base 234299)
AT2G46830 (ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 of the Light Signaling pathway) found in Scaffold 00140 (query sequence starts at base 234299)
1) For Primer GAAATTACCCTCTCTGACGTGG - Rev Primer AGAAGATCCAGCTTTGAGTTGC - Repeats (tc) x10 - PCR product = 153 bp - start at base 232252
2) For Primer TTTGTTCCACTTCCCAAGTTCT - Rev Primer GGGGACCATCTTCTTTGCTATT - Repeats (ct) x8 - PCR product = 230 bp - start at base 262342
3) For Primer CTAGGCAAAGCCGCTAATTACA - Rev Primer CCCATGAGATTTCCTTTTGA - Repeats (gaa) x10 - PCR product = 203 bp - start at base 264721
AT3G12810 (CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP of the Vernalization pathway) found in Scaffold 00147 (query sequence starts at base 30164)
1) For Primer GGTTGGATGCTCTGTCACAATA - Rev Primer CCTGCTGTTGTCATTCTCTTTG - Repeats (gt) x14 - PCR product = 195 bp - start at base 36897
2) For Primer GTGTGTGTGTGTGTGTGTGTGA - Rev Primer AATCCTTCGAAAGTATGGCTCA - Repeats (ag) x11 - PCR product = 179 bp - start at base 26112
3) For Primer AGCCAACTACCGTACAAAGACC - Rev Primer AATCCTTCGAAAGTATGGCTCA - Repeats (tg) x15 - PCR product = 239 bp - start at base 26082
AT5G13480 (FY of the Autonomous pathway) found in Scaffold 00166 (query sequence starts at base 74796)
1) For Primer CAGCTACAGCAACACCTTCAAT - Rev Primer AAGGGGGTAAAAGCTGTACCAT - Repeats (caa) x7 - PCR product = 245 bp - start at base 69326
2) For Primer AAACCAATCTTCTCCTTCTCCC - Rev Primer GGTGGTTGTTGTTGTTGTTGTT - Repeats (gca) x6 - PCR product = 282 bp - start at base 69223
3) For Primer GACATGGGAATCTTTGCCTTAG - Rev Primer CACTTCATCAAATAACCAGCCA - Repeats (ag) x19 - PCR product = 266 bp - start at base 119541
AT5G03840 (TERMINAL FLOWER 1, TFL1 of the Ambient Temperature pathway) found in Scaffold 00181 (query sequence starts at base 12825)
1) For Primer TCTAGTAGCTGGGGTGCTTCTC - Rev Primer AGCAGAAGGAAATAGCTCATGC - Repeats (tc) x11 - PCR product = 260 bp - start at base 12778
2) For Primer AGAATCATGCCAACAGAGGTTT - Rev Primer TAGACGGATGGCCTATCAAGTT - Repeats (ct) x9 - PCR product = 111 bp - start at base 13947
3) For Primer TACCAGTTCACGATCTCTCCCT - Rev Primer ACATCAACCCAACAACCTATCC - Repeats (tc) x8 - PCR product = 238 bp - start at base 27256
AT3G10390 (FLD, FLOWERING LOCUS D of the Ambient Temperature and Autonomous pathways) found in Scaffold 00232 (query sequence starts at base 139565)
1) For Primer CATAAACGGTTTTAGCAAGGCT - Rev Primer TCTCTGGGTGACCTTACCATCT - Repeats (ct) x8 - PCR product = 207 bp - start at base 132421
2) For Primer CAGTCCATGGGTATGCTTGATA - Rev Primer TTGCAATGATAAGTACCGCAAG - Repeats (at) x11 - PCR product = 273 bp - start at base 113550
3) For Primer CTTCTTGCTTTGCAGGCTTTAT - Rev Primer TTAGAATGGGGTGTGTGTGTGT - Repeats (tc) x12 - PCR product = 299 bp - start at base 153951
AT3G33520 (ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 of the Ambient Temperature and Vernalization pathways) found in Scaffold 00246 (query sequence starts at base 268521)
1) For Primer CGAGGTCTGGGTTTATGAGGTA - Rev Primer GGGAAACAGAAGTCCAGAGAGA - Repeats (tc) x10 - PCR product = 265 bp - start at base 268979
2) For Primer TTCAACTGAGATGCGTTTAGGA - Rev Primer AAGCAGGTAAATGAGCCCAATA - Repeats (tg) x11 - PCR product = 258 bp - start at base 255772
3) For Primer CACCTTAACAAATGTGGAGCAA - Rev Primer CCCTCATTGATGTGTGTGTTCT - Repeats (tc) x14 - PCR product = 272 bp - start at base 239356
AT4G11880 (AGAMOUS-LIKE 14, AGL14 of the Vernalization pathway) found in Scaffold 00249 (query sequence starts at base 131012)
AT4G22950 (AGAMOUS-LIKE 19, AGL19, GL19 of the Vernalization pathway) found in Scaffold 00249 (query sequence starts at base 131012)
1) For Primer ACACTGTTCAGTTTCAAGGGGT - Rev Primer ACGAAACACATCAAGCTAGCAA - Repeats (at) x9 - PCR product = 285 bp - start at base 132095
2) For Primer TCAAGAACCTGTGAATCTGGAA - Rev Primer TAGGTTTTTCGGGTAACCTTGA - Repeats (ag) x14 - PCR product = 255 bp - start at base 102031
3) For Primer ATTGAACAACAGTTGGAGCAGA - Rev Primer TCAGTGTCGTGTCTATGTCGTG - Repeats (ga) x15 - PCR product = 258 bp - start at base 144337
AT5G11530 (EMBRYONIC FLOWER 1, EMF1 of the Polycomb pathway) found in Scaffold 00253 (query sequence starts at base 11069)
1) For Primer CTCTAACACATTCTGGTTGCCA - Rev Primer TGTATGAAGGTATCCATGCTGC - Repeats (aga) x6 - PCR product = 281 bp - start at base 15630
2) For Primer AAGCTTCACTTGGATTCTCCAC - Rev Primer GCCTTTTATTACAACAAAGCCG - Repeats (ag) x9 - PCR product = 271 bp - start at base 18170
3) For Primer TTTTGATGATGTCAGCAGGTCT - Rev Primer CCACTAGGCCTGATTTTCTCTG - Repeats (ga) x10 - PCR product = 243 bp - start at base 34859
AT2G40080 (EARLY FLOWERING 4, ELF4 of the Light Signaling pathway) found in Scaffold 00254 (query sequence starts at base 228805)
1) For Primer TGACCATCCCTTCTGAATTTCT - Rev Primer TTTCGACAATGCCAACAGATAC - Repeats (ct) x40 - PCR product = 288 bp - start at base 231757
2) For Primer TACACCTCTTCTCTCTCCTGCC - Rev Primer GACTGTTACAACTCCGCTTCCT - Repeats (ca) x12 - PCR product = 216 bp - start at base 233794
3) For Primer CCGTGTATCTATCTCCACTCCC - Rev Primer AGTTTCGAACAGTGCTTTCACA - Repeats (aga) x11 - PCR product = 283 bp - start at base 238558
AT2G34140 (of the Light Signaling pathway) found in Scaffold 00270 (query sequence starts at base 215217)
AT1G29160 (of the Light Signaling pathway) found in Scaffold 00270 (query sequence starts at base 215229)
1) For Primer TGGGACCTGATCTTTTTCTTGT - Rev Primer TGCCCGTTATTGTGTTTGTAAG - Repeats (ga) x18 - PCR product = 226 bp - start at base 215694
2) For Primer CGGATCTTCTCTGTCTGCTTCT - Rev Primer CCCCCTCACCTACTCTTCTTCT - Repeats (ct) x8 - PCR product = 252 bp - start at base 235137
3) For Primer ATTTAACCCCCTCCAACATTCT - Rev Primer GAATTGGCTGGAAATGCATAGT - Repeats (ac) x11 - PCR product = 237 bp - start at base 146669
AT1G31814 (FRIGIDA LIKE 2, FRL2 of the Vernalization pathway) found in Scaffold 00289 (query sequence starts at base 150896)
1) For Primer TTAGCAATAATCCACACGATGC - Rev Primer TATGAAATCCCAAACAGGGAAC - Repeats (at) x10 - PCR product = 278 bp - start at base 140291
2) For Primer TACTATTGGGATAGTGGTGGGG - Rev Primer CTTCCTTCATTCTTAGCTTGTTCTG - Repeats (ct) x16 - PCR product = 256 bp - start at base 138109
3) For Primer TATGCATTTGCTAACGGATGTC - Rev Primer GCCTTCTGCGAATAGAAAAGAA - Repeats (gt) x10 - PCR product = 131 bp - start at base 162744
AT4G08920 (ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 of the Light Signaling pathway) found in Scaffold 00331 (query sequence starts at base 124817) – MIKE N
1) For Primer GACATTCAATACGCACCTACCA - Rev Primer AAGGTGCATCGCTTACTACCTC - Repeats (tc) x9 - PCR product = 197 bp - start at base 114263
2) For Primer TTCTCGAACATTATTCCTCTGC - Rev Primer TAGAGAAACCGAGAGAGGATGG - Repeats (ga) x13 - PCR product = 282 bp - start at base 159723
3) For Primer CAGTCGCAAACAAACCTACTCC - Rev Primer TGCCCTAACTTCATTCTCCCTA - Repeats (tcc) x6 - PCR product = 276 bp - start at base 61835
AT2G06255 (ELF4-L3, ELF4-LIKE 3 of the Light Signaling pathway) found in Scaffold 00336 (query sequence starts at base 188137)
1) For Primer AAGTTGGGGTATTCTGTTGTGG - Rev Primer ACTACAATCGTGTAGTGCGGTG - Repeats (ag) x13 - PCR product = 185 bp - start at base 167935
2) For Primer GAAAAACCAAACAAACCTCCAC - Rev Primer CCACAACAGAATACCCCAACTT - Repeats (ga) x10 - PCR product = 277 bp - start at base 167792
3) For Primer AGGTGCAGGGTTCTTACTTGAG - Rev Primer ACAAGCCGAGGTACAAAGAAAA - Repeats (ct) x10 - PCR product = 106 bp - start at base 201634
AT1G30970 (SUF4, SUPPRESSOR OF FRIGIDA4 of the Vernalization pathway) found in Scaffold 00348 (query sequence starts at base 75279)
1) For Primer TTTACGGATATCATCACCCCTC - Rev Primer TGTTTTGCAAGTTCTCCTCTCA - Repeats (tg) x9 - PCR product = 215 bp - start at base 66541
2) For Primer GATGCAGACATGCTAGGGATAC - Rev Primer CAATATGTTGTGGACACCCAAG - Repeats (ca) x10 - PCR product = 297 bp - start at base 65411
3) For Primer GGGTTTATGGTGTTTGTGAAGG - Rev Primer TTTAGAGTGTCTCGGAACACCA - Repeats (ta) x10 - PCR product = 292 bp - start at base 122301
AT2G23380 (CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 of the Autonomous, Polycomb, and Vernalization pathways) found in Scaffold 00354 (query sequence starts at base 64799)
AT4G02020 (EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN of the Autonomous, Polycomb, and Vernalization pathways) found in Scaffold 00354 (query sequence starts at base 64799)
AT1G02580 (EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 of the Polycomb pathway) found in Scaffold 00354 (query sequence starts at base 64805)
1) For Primer TCAGGAACATTGACTATGCAGG - Rev Primer GTTAAAGAAACGATCCGACTGC - Repeats (tc) x8 - PCR product = 285 bp - start at base 53913
2) For Primer ATTTCAACTGATTTAGCTGGGC - Rev Primer CTTGAGTTCAATCCCTCATCTACA - Repeats (ct) x31 - PCR product = 222 bp - start at base 49463
3) For Primer GTTGCCAGCTGAATATCCTTTC - Rev Primer GTGTGTGTGTGTGTGTGTGTGA - Repeats (tc) x14 - PCR product = 163 bp - start at base 81106
AT1G65480 (FLOWERING LOCUS T, FT of the Ambient Temperature pathway) found in Scaffold 00357 (query sequence starts at base 58774)
AT4G20370 (TSF, TWIN SISTER OF FT of the Ambient Temperature pathway) found in Scaffold 00357 (query sequence starts at base 58807) – MIKE N
1) For Primer GCCCACCCTTAGTTATGTTGAC - Rev Primer GAGAGACAGAAGACAGAGAAGAGG - Repeats (ct) x11 - PCR product = 225 bp - start at base 76826
2) For Primer CGCCACGGAAATATATAGGAGA - Rev Primer TGCACGTTTCAAAGTATTGACC - Repeats (at) x10 - PCR product = 221 bp - start at base 29021
3) For Primer GCAATTGCGTAGATGACTTCAG - Rev Primer CTCCAAAGATGTATGCCCTACC - Repeats (tc) x13 - PCR product = 197 bp - start at base 83551
AT2G17770 (ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP of the Ambient Temperature pathway) found in Scaffold 00367 (query sequence starts at base 113139)
AT4G35900 (ATBZIP14, FD, FD-1 of the Ambient Temperature pathway) found in Scaffold 00367 (query sequence starts at base 113139)
1) For Primer GTTTTTGTTGGAGAGGAAGTCG - Rev Primer AGTACCAAATCCCCAAACACAC - Repeats (ag) x9 - PCR product = 188 bp - start at base 113601
2) For Primer GCTTTCTCAGAATGGAGCTGTT - Rev Primer TCAGACAGAGCAGTTGGGTAGA - Repeats (ca) x10 - PCR product = 278 bp - start at base 110027
3) For Primer GATGAAGAGAAGTCTCGGGCTA - Rev Primer GCACCATGCAAGGATTATAACA - Repeats (ct) x10 - PCR product = 243 bp - start at base 100134
AT2G25930 (EARLY FLOWERING 3, ELF3, PYK20 of the Light Signaling pathway) found in Scaffold 00371 (query sequence starts at base 73111)
1) For Primer GTGTGCGTGAGAGAGAGAGAGA - Rev Primer ATCTGAAAAGAAAGGCTTGTGG - Repeats (ag) x18 - PCR product = 245 bp - start at base 71081
2) For Primer ATCCAGTTGAAGGCATCTGATT - Rev Primer GGCAATGCCTTTTCTGTAGTTT - Repeats (ga) x17 - PCR product = 283 bp - start at base 71026
3) For Primer ATCCAGTTGAAGGCATCTGATT - Rev Primer GGCAATGCCTTTTCTGTAGTTT - Repeats (tg) x9 - PCR product = 283 bp - start at base 71005
AT3G24440 (VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 of the Autonomous and Vernalization pathways) found in Scaffold 00396 (query sequence starts at base 73795)
AT2G18870 (VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 of the Autonomous pathway) found in Scaffold 00396 (query sequence starts at base 73810)
1) For Primer CATCGGTCCATAGAGAACACAA - Rev Primer GCAGAGTCGTGTCCTTTCTTTT - Repeats (ag) x9 - PCR product = 232 bp - start at base 82383
2) For Primer GGGGATGGTTACCTGTGAATAA - Rev Primer TGACTCATCAGTCCCTCTCTCA - Repeats (ct) x8 - PCR product = 233 bp - start at base 85845
3) For Primer ATTTTTAGAACTGTGCCAAGCC - Rev Primer CCTACTTGAACCGAACTGGTTT - Repeats (tc) x9 - PCR product = 298 bp - start at base 50548
AT3G21320 (of the Light Signaling pathway) found in Scaffold 00509 (query sequence starts at base 181887)
1) For Primer TCACGTAGGCAGTCAAAACAAC - Rev Primer GGCAACATATGTCGGGTAATTT - Repeats (ct) x26 - PCR product = 259 bp - start at base 189409
2) For Primer AGCTCCTCCCATTACAATCTCA - Rev Primer ATGAACTGCTTATGCAATGTGG - Repeats (tg) x12 - PCR product = 272 bp - start at base 169832
3) For Primer GAAATCAATGGAACTACCTCGG - Rev Primer AAATACTACATGGCGCTGTTGA - Repeats (at) x10 - PCR product = 259 bp - start at base 149049
AT1G47250 (20S PROTEASOME ALPHA SUBUNIT F2, PAF2 of the Vernalization pathway) found in Scaffold 00528 (query sequence starts at base 110933)
AT5G42790 (ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 of the Vernalization pathway) found in Scaffold 00528 (query sequence starts at base 110933)
1) For Primer CACGAAAGTAGACGCTGTGAAA - Rev Primer ATTTGAGCTGTCCAAAACACG - Repeats (ata) x9 - PCR product = 248 bp - start at base 108589
2) For Primer ACTTCCCTTAGTGCTGCTTGTC - Rev Primer GGACTAGGTTTTCTTCCCCACT - Repeats (tta) x7 - PCR product = 165 bp - start at base 112665
3) For Primer GAGAGAGACTGTGCATACACGC - Rev Primer AAAGGAAAAGAAGAACAAGGGG - Repeats (ga) x10 - PCR product = 223 bp - start at base 124597
AT5G58230 (ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 of the Autonomous, Polycomb, and Vernalization pathways) found in Scaffold 00615 (query sequence starts at base 161081)
1) For Primer GTGGGATCTTAGCAGGTTTGTC - Rev Primer TACAGTGGGAGGTGGAGTTTTT - Repeats (ct) x10 - PCR product = 128 bp - start at base 163332
2) For Primer AGAACCATAGCATAACGGCCTA - Rev Primer TATGGAGGGAAGAAATTTGGTG - Repeats (tc) x12 - PCR product = 145 bp - start at base 158582
3) For Primer TAGCACAGGCTCCCATTTTTAT - Rev Primer GCTAGTCTGCAGAGCCAAAGAT - Repeats (ag) x8 - PCR product = 219 bp - start at base 120273
AT1G04400 (AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 of the Light Signaling pathway) found in Scaffold 00649 (query sequence starts at base 28296) – MIKE N
1) For Primer TGGTGGTGGTATATGGGTAACA - Rev Primer AATCAACAATCTCACTGCCGTT - Repeats (gtg) x8 - PCR product = 192 bp - start at base 22759
2) For Primer GTAGTGTGATGGTTATGGCGTG - Rev Primer TATACCACCACCACTATTGCCA - Repeats (tgg) x7 - PCR product = 131 bp - start at base 22555
3) For Primer TTGTTTCGCCATTAGGAGAGAT - Rev Primer CCTAAACCCAACTACCACTCCA - Repeats (ga) x10 - PCR product = 139 bp - start at base 49549
AT5G39660 (CDF2, CYCLING DOF FACTOR 2 of the Light Signaling pathway) found in Scaffold 00651 (query sequence starts at base 19066) – MIKE N
1) For Primer AAGTTGGTTTTGTGGCCTTAGA - Rev Primer TTTTTGGGCTAACGAAGAGTGT - Repeats (ct) x7 - PCR product = 295 bp - start at base 22514
2) For Primer TCAAAAGCACACAGAATCAAGC - Rev Primer TGCAAGAGCCAATCTCTCATAA - Repeats (ga) x7 - PCR product = 275 bp - start at base 27722
3) For Primer CCAGTTAGATTGGTGACATTGC - Rev Primer GGACCCATCACTAGATCCTCTG - Repeats (ct) x12 - PCR product = 192 bp - start at base 37067
AT5G23150 (ENHANCER OF AG-4 2, HUA2 of the Vernalization pathway) found in Scaffold 00686 (query sequence starts at base 102689)
1) For Primer GATGAAGAGAAGGCATCAGGTC - Rev Primer AATACCGATGTTTACCGGAGTG - Repeats (ct) x14 - PCR product = 221 bp - start at base 106315
2) For Primer GGATAATCAAAGATGCGAGAGG - Rev Primer ATACACCTTTGGATTCTGTGGG - Repeats (tg) x11 - PCR product = 290 bp - start at base 90834
3) For Primer ACACAACCTGCAATACTCCTCC - Rev Primer TACAAGGTGTGGTGAGTAACGG - Repeats (ta) x12 - PCR product = 284 bp - start at base 117010
AT2G42200 (ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 of the Age pathway) found in Scaffold 00691 (query sequence starts at base 61795) – CATHERINE D
1) For Primer TGTGGACCAACCAACATTAGAG - Rev Primer GAGACTTTTTGTGGTAGGCACC - Repeats (ta) x9 - PCR product = 298 bp - start at base 80542
2) For Primer CACCTTGAGATCTCTCTCTCTCTC - Rev Primer CCCAATCCACATTGAACAGAAT - Repeats (tc) x16 - PCR product = 300 bp - start at base 36515
3) For Primer GCACCATTCTTAATAACATTGCACC - Rev Primer CACGAGAGAGAGAGAGAGAGAGAGA - Repeats (tc) x11 - PCR product = 298 bp - start at base 36283
AT5G17690 (ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2 of the Polycomb pathway) found in Scaffold 00696 (query sequence starts at base 128983)
1) For Primer CCACCTAATCCATTCAAAAAGG - Rev Primer TACCAAATCCCTCAATCCAAAG - Repeats (ag) x9 - PCR product = 293 bp - start at base 127286
2) For Primer GAGAGATGGGGCAACAAAAATA - Rev Primer GCAGGCCTTAATATGCAAGAAC - Repeats (ga) x8 - PCR product = 143 bp - start at base 81894
3) For Primer GCTACAAACCAAAAAGAATCGG - Rev Primer AAAAATCCTCCTTGACTGGGTT - Repeats (ac) x8 - PCR product = 298 bp - start at base 45233
AT2G19520 (ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4 of the Ambient Temperature and Autonomous pathways) found in Scaffold 00728 (query sequence starts at base 8716)
1) For Primer GCAGAAGGAAAACCAAAATCAC - Rev Primer GAGAGGGAGAGAGAGAAGGGAC - Repeats (ga) x11 - PCR product = 263 bp - start at base 2899
2) For Primer TAACCGGTTTTACCGTTTTCC - Rev Primer AGAACCAAGAATTCTGCATTGG - Repeats (tc) x10 - PCR product = 298 bp - start at base 111
3) For Primer CTTTATCATCTGCCTGCCTCTT - Rev Primer CGTAATAAAGAAGGTGGTTCGG - Repeats (tc) x16 - PCR product = 162 bp - start at base 36059
AT2G32950 (ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1 of the Light Signaling pathway) found in Scaffold 00734 (query sequence starts at base 142779)
AT2G46340 (SPA1, SUPPRESSOR OF PHYA-105 1 of the Light Signaling pathway) found in Scaffold 00734 (query sequence starts at base 142779)
AT1G53090 (SPA1-RELATED 4, SPA4 of the Light Signaling pathway) found in Scaffold 00734 (query sequence starts at base 143450)
AT3G15354 (SPA1-RELATED 3, SPA3 of the Light Signaling pathway) found in Scaffold 00734 (query sequence starts at base 143450)
1) For Primer GGAGGGGAAACAAGGATAGAAC - Rev Primer ATATTGAGGCTGTGGTCGTCTT - Repeats (aag) x8 - PCR product = 186 bp - start at base 148205
2) For Primer TTACCCCCTCTCTCTCTCATACC - Rev Primer AAACATCTTCAATCATGCTCCC - Repeats (tc) x15 - PCR product = 298 bp - start at base 136748
3) For Primer CCACAAAACAGCAGTAACCAAA - Rev Primer TACGGTATGAGAGAGAGAGGGG - Repeats (ga) x10 - PCR product = 122 bp - start at base 136457
AT2G18790 (HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B of the Light Signaling pathway) found in Scaffold 00751 (query sequence starts at base 83698)
AT4G16250 (PHYD, PHYTOCHROME D of the Light Signaling pathway) found in Scaffold 00751 (query sequence starts at base 83707)
AT4G18130 (PHYE, PHYTOCHROME E of the Light Signaling pathway) found in Scaffold 00751 (query sequence starts at base 83749) – MIKE N
1) For Primer CCCGAAAATACCCTTTCTCTCT - Rev Primer GGCAATTACCAATTACGTGTCA - Repeats (aga) x8 - PCR product = 265 bp - start at base 81899
2) For Primer AAGAGGGGTAGACCAAAATTGA - Rev Primer AATTTCACTCCAACCAAGAAGG - Repeats (ag) x10 - PCR product = 262 bp - start at base 92356
3) For Primer TCTCTCATGCATGGATGGTTAT - Rev Primer CATTGAACATCTACCTGTGGGA - Repeats (ct) x10 - PCR product = 298 bp - start at base 73385
AT5G61380 (APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1 of the Light Signaling pathway) found in Scaffold 00753 (query sequence starts at base 70468)
1) For Primer CACTACATCCAAACAAAACCCA - Rev Primer TGCGTGCGATAATGGAGTATTA - Repeats (gt) x11 - PCR product = 284 bp - start at base 98714
2) For Primer CCTCGTGCACATACGAAAATTA - Rev Primer TACGTTGCACATTTTTCTCCAC - Repeats (ta) x8 - PCR product = 266 bp - start at base 52292
3) For Primer ATTTCTACCCTGTCCACCAAGA - Rev Primer GAGACAGAAGTGGCATCTGTGA - Repeats (ga) x17 - PCR product = 168 bp - start at base 102220
AT3G18990 (REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1 of the Vernalization pathway) found in Scaffold 00811 (query sequence starts at base 96661)
1) For Primer ACAGACCCTCCTGCCTTCAC - Rev Primer TCTGAACTGCTCATACCCTGAA - Repeats (ag) x21 - PCR product = 251 bp - start at base 89371
2) For Primer TAAGGAGTGGGCACGGTATATT - Rev Primer AATGTTTTGAGGTCTCTGGGAA - Repeats (tc) x8 - PCR product = 260 bp - start at base 100084
3) For Primer GACTTAACAGCAGCCTGGTACA - Rev Primer AGTACCAATAAGTACCGCGTCG - Repeats (ag) x8 - PCR product = 112 bp - start at base 100915
AT3G07650 (B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 of the Light Signaling pathway) found in Scaffold 00832 (query sequence starts at base 89599)
1) For Primer TTATATGGTCGCTGATCCCTTT - Rev Primer TGAAGGGGAGAAATAGCACCTA - Repeats (tc) x7 - PCR product = 233 bp - start at base 58681
2) For Primer GACCCTGTTCAAATTTTGCTTC - Rev Primer TCAAAGGAGCGGAGAAGAATAG - Repeats (ga) x9 - PCR product = 212 bp - start at base 21272
3) For Primer GACCCTGTTCAAATTTTGCTTC - Rev Primer TCAAAGGAGCGGAGAAGAATAG - Repeats (ca) x8 - PCR product = 212 bp - start at base 21256
AT5G51230 (ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2 of the Polycomb pathway) found in Scaffold 00857 (query sequence starts at base 44887)
AT4G16845 (REDUCED VERNALIZATION RESPONSE 2, VRN2 of the Autonomous, Polycomb, and Vernalization pathways) found in Scaffold 00857 (query sequence starts at base 55203)
AT2G35670 (FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2 of the Polycomb pathway) found in Scaffold 00857 (query sequence starts at base 55565)
1) For Primer CATGTGTGTGTGATCAAAGGTG - Rev Primer ACGTATGACAGACGCAAAACAC - Repeats (tc) x9 - PCR product = 274 bp - start at base 67373
2) For Primer CCAAAGCCTTAAAAACGACACT - Rev Primer ATGATTGGAAAGAAGGGAGTGA - Repeats (ct) x11 - PCR product = 204 bp - start at base 113486
3) For Primer CCCCCTCTATATATCCACCACA - Rev Primer GAGGGTACTGGTGATGAAGGAG - Repeats (cac) x8 - PCR product = 214 bp - start at base 125050
AT1G77300 (ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8 of the Vernalization pathway) found in Scaffold 00894 (query sequence starts at base 89213)
1) For Primer GTAAAAGCGTTCGTATTTGCCT - Rev Primer TTAAGGGTGGCTCTGATACCAT - Repeats (ct) x10 - PCR product = 295 bp - start at base 77010
2) For Primer AAACTGCTTACTTTCCGTTTGC - Rev Primer TCATGTGCTGACCTACAAATCC - Repeats (tag) x10 - PCR product = 254 bp - start at base 71796
3) For Primer AAAGAAGCACCGAACTGGATAG - Rev Primer CGGTTCCGGGTACATATAAAAA - Repeats (ga) x10 - PCR product = 293 bp - start at base 92614
AT5G37055 (ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING of the Vernalization pathway) found in Scaffold 00925 (query sequence starts at base 38143)
1) For Primer GCCTGATAGAAGGGACGTACAC - Rev Primer TGCTGGATGTATCCTTCATTTG - Repeats (ctt) x8 - PCR product = 286 bp - start at base 45585
2) For Primer GAATGGCGACATTGTTAGATCA - Rev Primer TAGAAATCCCACGATACGAAGG - Repeats (tg) x11 - PCR product = 173 bp - start at base 17776
3) For Primer CTTTCAGGATTCATTTTCCAGC - Rev Primer TGTTGGCTTCACTCCATGTATC - Repeats (ag) x8 - PCR product = 204 bp - start at base 5444
AT3G25730 (EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 of the Light Signaling pathway) found in Scaffold 00930 (query sequence starts at base 63060)
AT1G13260 (EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1 of the Light Signaling pathway) found in Scaffold 00930 (query sequence starts at base 63069)
AT1G25560 (EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1 of the Light Signaling pathway) found in Scaffold 00930 (query sequence starts at base 63096)
AT1G68840 (ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2 of the Light Signaling pathway) found in Scaffold 00930 (query sequence starts at base 63096)
1) For Primer ATTATGTGGAAAGCAAACCGAC - Rev Primer TAGTTTGTGGCAAATGAGGATG - Repeats (ct) x11 - PCR product = 189 bp - start at base 62365
2) For Primer CCATGTGAAAAGGGATAAGCAT - Rev Primer TTGTTTGGTGCTCCTCTACTCA - Repeats (gat) x9 - PCR product = 158 bp - start at base 57313
3) For Primer NGTTGCATGCTAATCTCTTTGG - Rev Primer ATGAAATGTGGGACTCTGTTCC - Repeats (ta) x11 - PCR product = 214 bp - start at base 54197
AT5G08330 (CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 of the Light Signaling pathway) found in Scaffold 00993 (query sequence starts at base 294)
1) For Primer ATCCACTCGATTGAAGCAAGAT - Rev Primer GGTTTCTTCACAGTTAGGGCTC - Repeats (aac) x7 - PCR product = 190 bp - start at base 261
2) For Primer CCTCTTGCTGGTAAGCACTCTT - Rev Primer ATGGTCTAGAACCAAACATGGG - Repeats (gt) x11 - PCR product = 208 bp - start at base 13096
3) For Primer ACATGTTCCAAACAAACCCTTC - Rev Primer GCGTCTCCTCTCTCTCTCTCTC - Repeats (ag) x12 - PCR product = 292 bp - start at base 18424
AT4G11110 (SPA1-RELATED 2, SPA2 of the Light Signaling pathway) found in Scaffold 01034 (query sequence starts at base 19205)
1) For Primer CGGCCTAAAACACTTATCGAAC - Rev Primer AACGGGCTTCCTCTACATACAA - Repeats (ag) x9 - PCR product = 222 bp - start at base 14166
2) For Primer CACGCCTCTCTCTCTCTCTCTC - Rev Primer CTACAAAAGTCTCCAAACCCCA - Repeats (ct) x20 - PCR product = 180 bp - start at base 3833
3) For Primer ACTTCTTGTTTTGAGGGGGAAT - Rev Primer TAGGTAACTCATGCTCTGGGGT - Repeats (ct) x11 - PCR product = 157 bp - start at base 34735
AT2G47700 (RED AND FAR-RED INSENSITIVE 2, RFI2 of the Light Signaling pathway) found in Scaffold 01059 (query sequence starts at base 96557)
1) For Primer TAACAGGAGCACAATGATCCAA - Rev Primer TCTCTCTCCCTCTCTCGCTCTA - Repeats (ga) x8 - PCR product = 247 bp - start at base 73538
2) For Primer ACACATGGCTTGATCTACTTCG - Rev Primer GCGAGGTAAGAGAGAAGGACAA - Repeats (tc) x28 - PCR product = 300 bp - start at base 62959
3) For Primer CCTCTCCAGTATTACTCACCCG - Rev Primer TAAGAAAGGAACGAACCTTGGA - Repeats (tc) x8 - PCR product = 294 bp - start at base 54451
AT5G35840 (PHYC, PHYTOCHROME C of the Light Signaling pathway) found in Scaffold 01070 (query sequence starts at base 75395)
1) For Primer TGAACGGGTCCAGTCTATTCTT - Rev Primer TTTGGTGTCTCTTCTGGGTTTT - Repeats (ag) x14 - PCR product = 182 bp - start at base 56787
2) For Primer AATCCCATGTCGACACCTATTC - Rev Primer TGCCTTCAAATCAGACTAAGCA - Repeats (gca) x6 - PCR product = 186 bp - start at base 97674
3) For Primer GGGAGGAAATCCACTAAAAAGG - Rev Primer CCTGTTGGTGGTCTTGCATATT - Repeats (tg) x17 - PCR product = 298 bp - start at base 16459
AT5G62430 (CDF1, CYCLING DOF FACTOR 1 of the Light Signaling pathway) found in Scaffold 01102 (query sequence starts at base 51435) – MIKE N
1) For Primer AGGATGAGTGAAAGAGCGTACC - Rev Primer CCAGATTTTTCAGAGAATTGGC - Repeats (ag) x12 - PCR product = 253 bp - start at base 45392
2) For Primer TTCTCCATCTTTAACGTCAGCA - Rev Primer GATTGCACGTACTTCACCAAGA - Repeats (ga) x32 - PCR product = 260 bp - start at base 78317
3) For Primer GTGTGTAATGGGACAAGCCTTT - Rev Primer GCTAAAATAGGCCCAGTAGGCT - Repeats (ac) x11 - PCR product = 289 bp - start at base 81642
AT3G46640 (LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1 of the Light Signaling pathway) found in Scaffold 01150 (query sequence starts at base 80272)
1) For Primer CCTTGTCTGCACACTTAGCATC - Rev Primer AAATTGAGTGAGATAAGCCCCA - Repeats (gaa) x8 - PCR product = 197 bp - start at base 72111
2) For Primer ACATATGGTTTCTATGTGCCCC - Rev Primer TTGTTCGATTACAGGAGCAGAA - Repeats (ga) x9 - PCR product = 277 bp - start at base 64622
3) For Primer CTTTCAGCAACTTCTCCTTCGT - Rev Primer TGAGATCCCAACCACAATGTTA - Repeats (tc) x18 - PCR product = 242 bp - start at base 30081
AT2G22540 (AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP of the Ambient Temperature and Vernalization pathways) found in Scaffold 01187 (query sequence starts at base 47701)
AT4G24540 (AGAMOUS-LIKE 24, AGL24 of the Vernalization pathway) found in Scaffold 01187 (query sequence starts at base 47701)
1) For Primer CAAATGGTGATAGCAAACATGG - Rev Primer CTCAAAGAAAATTCCCAAGACG - Repeats (tta) x7 - PCR product = 274 bp - start at base 57880
2) For Primer GCTACTGTTCTCGTCTCCTCGT - Rev Primer TCAATAGAACCTTCCACCGACT - Repeats (ct) x13 - PCR product = 116 bp - start at base 78977
3) For Primer AATGTTTTGTGTCTCCCAATCC - Rev Primer GGCACAACGCTAGTTGATAAAG - Repeats (ga) x12 - PCR product = 275 bp - start at base 95120
AT4G34530 (CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 of the Light Signaling pathway) found in Scaffold 01322 (query sequence starts at base 82955)
1) For Primer ACCTTTTCCCGGAACTATGATT - Rev Primer GGTTAAAACCGTAAACGACAGC - Repeats (gt) x20 - PCR product = 243 bp - start at base 88042
2) For Primer AAGATGGAGATAAGCAGGTCCC - Rev Primer TTCTAGTCTTAGCGTGGATGGC - Repeats (ag) x11 - PCR product = 290 bp - start at base 75518
3) For Primer TCAAAGAGCTTGTTCTGCTGTG - Rev Primer CCCTCAACCCTCTTCTTCTTTT - Repeats (ga) x9 - PCR product = 143 bp - start at base 61574
AT1G14920 (GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2 of the Gibberellin pathway) found in Scaffold 01360 (query sequence starts at base 51382)
AT2G01570 (REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1 of the Gibberellin pathway) found in Scaffold 01360 (query sequence starts at base 51382)
1) For Primer CCCTCTCCCTCATTCTAACCTT - Rev Primer GTGCCTTAGGGTACCAAATCAA - Repeats (tc) x11 - PCR product = 252 bp - start at base 68499
2) For Primer ACCCACTTTCAGAGAAATTCCA - Rev Primer ACGGAGTCTTTATCGGTTGAAA - Repeats (ct) x18 - PCR product = 267 bp - start at base 39593
3) For Primer TTCTAGTACCGCGCTTTTTCTC - Rev Primer ATCAACAAAGGGTTTCAGGCTA - Repeats (tc) x17 - PCR product = 286 bp - start at base 75242
AT3G04610 (FLK, FLOWERING LOCUS KH DOMAIN of the Autonomous pathway) found in Scaffold 01384 (query sequence starts at base 28309)
1) For Primer GCAAAAATGGGTAGGTCTTCTG - Rev Primer CCACGTGTTACATTTGTCTTGG - Repeats (ag) x9 - PCR product = 226 bp - start at base 27550
2) For Primer GGAATTGGGATGAAATGAGAAG - Rev Primer CGGAACAATTATCTTCCTCGTC - Repeats (ta) x10 - PCR product = 258 bp - start at base 46362
3) For Primer CGAGTAATATTTCCGAAGCACA - Rev Primer ATTAAAAGCGTGAGAGGCAGAG - Repeats (aat) x10 - PCR product = 266 bp - start at base 49252
AT3G20740 (FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3 of the Autonomous, Polycomb, and Vernalization pathways) found in Scaffold 01670 (query sequence starts at base 9836)
1) For Primer CCTCTCCCTCAATTCTCTCTCA - Rev Primer CTTGTTCTCGTTGTCGAGTTTG - Repeats (cgg) x5 - PCR product = 287 bp - start at base 4993
2) For Primer GCGATGCAGAAGTTGTTGATAG - Rev Primer ACACCTTACCGATTCAAGTGCT - Repeats (ta) x6 - PCR product = 223 bp - start at base 31113
3) For Primer GCAATTTCATCTTCGCTCTCTT - Rev Primer GAGCGTTTGTATGGAGTGAATG - Repeats (ct) x5 - PCR product = 298 bp - start at base 59874
AT2G43410 (FPA of the Autonomous pathway) found in Scaffold 01689 (query sequence starts at base 47663)
1) For Primer AGAATTTAAGGGGGTTTGGTGT - Rev Primer CGTGTAAACTGTAAAGTAGTTGGG - Repeats (ac) x10 - PCR product = 111 bp - start at base 45530
2) For Primer TACGGCGAAGACCAGATTTATT - Rev Primer AAAAACTTGGGGTCTGTAGGGT - Repeats (ct) x9 - PCR product = 135 bp - start at base 25148
3) For Primer TATGGGCCAGCGTTTACTTACT - Rev Primer CAGTTCCTGCTTGTCAAGTGTC - Repeats (gt) x14 - PCR product = 255 bp - start at base 10708
AT3G02380 (ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 of the Light Signaling pathway) found in Scaffold 01843 (query sequence starts at base 40767)
AT5G15840 (B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG of the Light Signaling pathway) found in Scaffold 01843 (query sequence starts at base 40767)
AT5G15850 (ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 of the Light Signaling pathway) found in Scaffold 01843 (query sequence starts at base 40767) – MIKE N
1) For Primer GAAACAGATGGCATGGTGAGTA - Rev Primer CTCCAAAACCCTATGAAAGTGC - Repeats (tc) x11 - PCR product = 275 bp - start at base 48319
2) For Primer GTCATCCTCGAAGAAAGACACC - Rev Primer TCGACTGGAATTGTCTCCCTAT - Repeats (ct) x7 - PCR product = 287 bp - start at base 48872
3) For Primer AGGGAAGTAGCAGCAAAGACAT - Rev Primer AGAACCCTGATGAGTTGAGGAA - Repeats (ca) x11 - PCR product = 133 bp - start at base 18196
AT5G60100 (APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 of the Light Signaling pathway) found in Scaffold 02075 (query sequence starts at base 14139)
1) For Primer GCATGTTAAAAGGTGCTGTTGA - Rev Primer ACTTCGACTTTCTCTTGTTCCG - Repeats (ct) x7 - PCR product = 238 bp - start at base 14277
2) For Primer GATCACCATTTCACAAGCTGAG - Rev Primer ATACATTTCAGATATGCGCGTG - Repeats (ga) x7 - PCR product = 263 bp - start at base 14887
3) For Primer CCTTTCTCTTATTCTCTCGCCA - Rev Primer AGCCATAGAGTGAGGACGGTTA - Repeats (ct) x8 - PCR product = 293 bp - start at base 20948
AT1G20330 (COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 of the Vernalization pathway) found in Scaffold 02142 (query sequence starts at base 24743)
1) For Primer TATCAGAAGACGTCCCAGAGGT - Rev Primer GGTCGAGATGCACAATTAGACA - Repeats (ct) x10 - PCR product = 182 bp - start at base 35782
2) For Primer CGTTTTGGGTGAGTACAAGTGA - Rev Primer CCACATTCCCGATCTTATTGTT - Repeats (tc) x6 - PCR product = 235 bp - start at base 23016
3) For Primer CGAATCTTGTTGTCGTATTGGA - Rev Primer ATCAGCACATTCTCAGAAAGCA - Repeats (ct) x5 - PCR product = 252 bp - start at base 22648
AT1G09570 (ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A of the Light Signaling pathway) found in Scaffold 03861 (query sequence starts at base 3771) – MIKE N
No adequate SSRs could be found
AT5G65060 (AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 639)
AT5G65080 (AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 699)
AT5G10140 (AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 708)
AT5G65050 (AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 723)
AT5G65070 (AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 723)
AT1G77080 (AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 of the Ambient Temperature and Vernalization pathways) found in Scaffold 10765 (query sequence starts at base 744)
No adequate SSRs could be found
AT5G24930 (ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 of the Light Signaling pathway) found in Scaffold 11225 (query sequence starts at base 2816)
AT5G57660 (ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 of the Light Signaling pathway) found in Scaffold 11225 (query sequence starts at base 2816)
1) For Primer CTCCGTTCCAAAATAAGTGTCC - Rev Primer ACGTACTACTCCCTCCATTCCA - Repeats (ag) x5 - PCR product = 240 bp - start at base 442
Only one adequate SSR could be found
