Multiple sequence alignment - TraesCS6B01G161300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G161300 chr6B 100.000 5925 0 0 1 5925 165328495 165334419 0.000000e+00 10942
1 TraesCS6B01G161300 chr6D 89.998 5309 280 94 722 5925 87277852 87283014 0.000000e+00 6630
2 TraesCS6B01G161300 chr6D 84.114 598 59 17 1 576 87276342 87276925 4.040000e-151 545
3 TraesCS6B01G161300 chr6D 82.800 250 38 3 3248 3497 22180094 22180338 1.000000e-52 219
4 TraesCS6B01G161300 chr6D 91.579 95 7 1 618 711 87277446 87277540 4.820000e-26 130
5 TraesCS6B01G161300 chr6A 91.955 3493 165 48 2481 5925 105179944 105183368 0.000000e+00 4787
6 TraesCS6B01G161300 chr6A 87.745 1942 133 53 592 2483 105177990 105179876 0.000000e+00 2170
7 TraesCS6B01G161300 chr6A 82.528 269 24 14 255 510 105177319 105177577 1.290000e-51 215


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G161300 chr6B 165328495 165334419 5924 False 10942.000000 10942 100.000000 1 5925 1 chr6B.!!$F1 5924
1 TraesCS6B01G161300 chr6D 87276342 87283014 6672 False 2435.000000 6630 88.563667 1 5925 3 chr6D.!!$F2 5924
2 TraesCS6B01G161300 chr6A 105177319 105183368 6049 False 2390.666667 4787 87.409333 255 5925 3 chr6A.!!$F1 5670

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
734 1818 0.034670 GCTGCTGTTCTTCTCCCCAT 60.035 55.0 0.0 0.0 0.00 4.00 F
1501 2637 0.234625 TTCGTGATTCGTGTTGCTGC 59.765 50.0 0.0 0.0 40.80 5.25 F
1839 2993 0.250295 TACAGCCTGCACACTCAACC 60.250 55.0 0.0 0.0 0.00 3.77 F
3539 4774 0.185901 AAAGAAGCAGGAGGTTGCCA 59.814 50.0 0.0 0.0 45.18 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 3362 1.091771 ATGTAGTGCGCACATCTGCC 61.092 55.0 39.21 20.48 40.73 4.85 R
3260 4495 0.036732 TCCTGCTTCCATTCACGCTT 59.963 50.0 0.00 0.00 0.00 4.68 R
3616 4851 0.033228 CATTTGCCTTTTCGGTGCCA 59.967 50.0 0.00 0.00 34.25 4.92 R
4996 6254 0.179015 ACCGCACCCAACAACATGTA 60.179 50.0 0.00 0.00 0.00 2.29 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.069331 TGTTGTTGAAAAAGTGGTTATCCTGAT 59.931 33.333 0.00 0.00 34.23 2.90
31 32 6.552008 TGAAAAAGTGGTTATCCTGATCCTT 58.448 36.000 0.00 0.00 34.23 3.36
32 33 6.659242 TGAAAAAGTGGTTATCCTGATCCTTC 59.341 38.462 0.00 0.00 34.23 3.46
33 34 6.394345 AAAAGTGGTTATCCTGATCCTTCT 57.606 37.500 0.00 0.00 34.23 2.85
34 35 5.622346 AAGTGGTTATCCTGATCCTTCTC 57.378 43.478 0.00 0.00 34.23 2.87
61 62 1.238439 CATCGAGGCACAAAACAGGT 58.762 50.000 0.00 0.00 0.00 4.00
63 64 1.873698 TCGAGGCACAAAACAGGTAC 58.126 50.000 0.00 0.00 0.00 3.34
64 65 1.414919 TCGAGGCACAAAACAGGTACT 59.585 47.619 0.00 0.00 43.88 2.73
125 134 2.031012 TTGCAGGACCAGTCAGCG 59.969 61.111 0.00 0.00 35.72 5.18
153 162 1.590147 GTCGGTGTACCCAGTGGAG 59.410 63.158 11.95 3.13 34.81 3.86
165 174 3.209410 CCCAGTGGAGATAAGATTGTGC 58.791 50.000 11.95 0.00 0.00 4.57
181 190 2.416747 TGTGCAATCTATAGCATCGCC 58.583 47.619 0.00 0.00 43.44 5.54
198 207 1.595993 GCCGAGTCACTGACAGCCTA 61.596 60.000 11.80 0.00 34.60 3.93
199 208 0.888619 CCGAGTCACTGACAGCCTAA 59.111 55.000 11.80 0.00 34.60 2.69
200 209 1.478510 CCGAGTCACTGACAGCCTAAT 59.521 52.381 11.80 0.00 34.60 1.73
205 214 5.460419 CGAGTCACTGACAGCCTAATTAATC 59.540 44.000 11.80 0.00 34.60 1.75
211 220 5.819901 ACTGACAGCCTAATTAATCAAGAGC 59.180 40.000 1.25 0.00 0.00 4.09
212 221 5.744171 TGACAGCCTAATTAATCAAGAGCA 58.256 37.500 0.00 0.00 0.00 4.26
214 223 6.094048 TGACAGCCTAATTAATCAAGAGCAAC 59.906 38.462 0.00 0.00 0.00 4.17
216 225 5.357878 CAGCCTAATTAATCAAGAGCAACCA 59.642 40.000 0.00 0.00 0.00 3.67
217 226 5.591877 AGCCTAATTAATCAAGAGCAACCAG 59.408 40.000 0.00 0.00 0.00 4.00
232 241 3.487544 GCAACCAGTGCGATTAAGATTCC 60.488 47.826 0.00 0.00 45.10 3.01
239 248 5.010719 CAGTGCGATTAAGATTCCCTACCTA 59.989 44.000 0.00 0.00 0.00 3.08
276 285 2.550830 AGTCTTCAAAGCGGACACAT 57.449 45.000 0.00 0.00 32.98 3.21
331 342 7.896894 TGTTTGGCGTCACTTTAATTTAAAAC 58.103 30.769 0.00 0.00 0.00 2.43
342 354 1.252215 ATTTAAAACCCGTGGGCCCG 61.252 55.000 19.37 5.74 39.32 6.13
359 371 3.426568 GCTTCCGGTGAGTGCTGC 61.427 66.667 0.00 0.00 0.00 5.25
363 375 2.994387 TTCCGGTGAGTGCTGCACTG 62.994 60.000 37.29 22.77 45.44 3.66
369 381 0.382873 TGAGTGCTGCACTGCAAAAG 59.617 50.000 37.29 0.00 45.44 2.27
370 382 0.383231 GAGTGCTGCACTGCAAAAGT 59.617 50.000 37.29 13.26 45.44 2.66
416 428 3.507103 TGCATTTCATTTCCATCCGTG 57.493 42.857 0.00 0.00 0.00 4.94
417 429 2.824936 TGCATTTCATTTCCATCCGTGT 59.175 40.909 0.00 0.00 0.00 4.49
418 430 4.013050 TGCATTTCATTTCCATCCGTGTA 58.987 39.130 0.00 0.00 0.00 2.90
419 431 4.644234 TGCATTTCATTTCCATCCGTGTAT 59.356 37.500 0.00 0.00 0.00 2.29
420 432 5.825151 TGCATTTCATTTCCATCCGTGTATA 59.175 36.000 0.00 0.00 0.00 1.47
421 433 6.142817 GCATTTCATTTCCATCCGTGTATAC 58.857 40.000 0.00 0.00 0.00 1.47
422 434 6.238621 GCATTTCATTTCCATCCGTGTATACA 60.239 38.462 0.08 0.08 0.00 2.29
424 436 7.689446 TTTCATTTCCATCCGTGTATACAAA 57.311 32.000 7.25 0.00 0.00 2.83
425 437 7.873719 TTCATTTCCATCCGTGTATACAAAT 57.126 32.000 7.25 0.00 0.00 2.32
426 438 8.966069 TTCATTTCCATCCGTGTATACAAATA 57.034 30.769 7.25 0.00 0.00 1.40
427 439 9.567776 TTCATTTCCATCCGTGTATACAAATAT 57.432 29.630 7.25 0.00 0.00 1.28
433 445 9.361315 TCCATCCGTGTATACAAATATATTTCG 57.639 33.333 7.25 6.92 0.00 3.46
434 446 9.361315 CCATCCGTGTATACAAATATATTTCGA 57.639 33.333 7.25 0.00 0.00 3.71
437 449 9.970395 TCCGTGTATACAAATATATTTCGAGTT 57.030 29.630 7.25 0.00 0.00 3.01
475 490 0.679505 TCACAGACAAACGGAGAGGG 59.320 55.000 0.00 0.00 0.00 4.30
480 495 1.004918 ACAAACGGAGAGGGAAGCG 60.005 57.895 0.00 0.00 0.00 4.68
519 815 4.697352 ACAGAAAAGTGATCCCTGAATTCG 59.303 41.667 0.04 0.00 0.00 3.34
523 819 3.268023 AGTGATCCCTGAATTCGTTCC 57.732 47.619 0.04 0.00 0.00 3.62
576 872 8.408043 TGAATCATGGATGTAGAAACACTTTT 57.592 30.769 0.00 0.00 38.78 2.27
577 873 9.513906 TGAATCATGGATGTAGAAACACTTTTA 57.486 29.630 0.00 0.00 38.78 1.52
581 877 9.952030 TCATGGATGTAGAAACACTTTTACATA 57.048 29.630 0.00 0.00 38.78 2.29
584 880 9.173021 TGGATGTAGAAACACTTTTACATATGG 57.827 33.333 7.80 0.00 38.78 2.74
585 881 9.391006 GGATGTAGAAACACTTTTACATATGGA 57.609 33.333 7.80 0.00 38.78 3.41
588 884 8.380099 TGTAGAAACACTTTTACATATGGAGGT 58.620 33.333 7.80 0.00 0.00 3.85
589 885 9.227777 GTAGAAACACTTTTACATATGGAGGTT 57.772 33.333 7.80 0.00 0.00 3.50
590 886 8.110860 AGAAACACTTTTACATATGGAGGTTG 57.889 34.615 7.80 0.00 0.00 3.77
593 1376 7.016153 ACACTTTTACATATGGAGGTTGAGA 57.984 36.000 7.80 0.00 0.00 3.27
613 1396 1.076705 GAAATGGTGGGAGGGAGCC 60.077 63.158 0.00 0.00 0.00 4.70
636 1419 0.321210 CCGTCCACATGGTAACTGCA 60.321 55.000 0.00 0.00 36.34 4.41
683 1467 5.066375 CGGATGTGCATAAATTTCCAAGAGA 59.934 40.000 0.00 0.00 0.00 3.10
734 1818 0.034670 GCTGCTGTTCTTCTCCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
758 1842 5.852282 TTTTTCCTCCAAGAAAACTCCAG 57.148 39.130 0.00 0.00 43.53 3.86
881 1968 1.196012 CTTCTCCACTACCTCCACCC 58.804 60.000 0.00 0.00 0.00 4.61
947 2048 2.644798 CCCTTTTCTCCTCCCTTTCTCA 59.355 50.000 0.00 0.00 0.00 3.27
949 2050 4.268359 CCTTTTCTCCTCCCTTTCTCATG 58.732 47.826 0.00 0.00 0.00 3.07
954 2055 1.283029 TCCTCCCTTTCTCATGCCTTG 59.717 52.381 0.00 0.00 0.00 3.61
955 2056 1.283029 CCTCCCTTTCTCATGCCTTGA 59.717 52.381 0.00 0.00 0.00 3.02
993 2095 4.530857 CCTCCCCACCGCATCGAC 62.531 72.222 0.00 0.00 0.00 4.20
995 2097 3.080765 TCCCCACCGCATCGACAT 61.081 61.111 0.00 0.00 0.00 3.06
1042 2147 0.306533 GCGTAGGCGAAGAGAGAGAG 59.693 60.000 0.00 0.00 41.33 3.20
1043 2148 1.942677 CGTAGGCGAAGAGAGAGAGA 58.057 55.000 0.00 0.00 41.33 3.10
1044 2149 1.864711 CGTAGGCGAAGAGAGAGAGAG 59.135 57.143 0.00 0.00 41.33 3.20
1045 2150 2.482316 CGTAGGCGAAGAGAGAGAGAGA 60.482 54.545 0.00 0.00 41.33 3.10
1046 2151 2.332063 AGGCGAAGAGAGAGAGAGAG 57.668 55.000 0.00 0.00 0.00 3.20
1047 2152 1.837439 AGGCGAAGAGAGAGAGAGAGA 59.163 52.381 0.00 0.00 0.00 3.10
1048 2153 2.158900 AGGCGAAGAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
1049 2154 2.158957 GGCGAAGAGAGAGAGAGAGAGA 60.159 54.545 0.00 0.00 0.00 3.10
1050 2155 3.126831 GCGAAGAGAGAGAGAGAGAGAG 58.873 54.545 0.00 0.00 0.00 3.20
1051 2156 3.181475 GCGAAGAGAGAGAGAGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
1052 2157 4.615949 CGAAGAGAGAGAGAGAGAGAGAG 58.384 52.174 0.00 0.00 0.00 3.20
1053 2158 4.339530 CGAAGAGAGAGAGAGAGAGAGAGA 59.660 50.000 0.00 0.00 0.00 3.10
1054 2159 5.507149 CGAAGAGAGAGAGAGAGAGAGAGAG 60.507 52.000 0.00 0.00 0.00 3.20
1055 2160 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1056 2161 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1057 2162 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1058 2163 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1059 2164 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1060 2165 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1061 2166 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1062 2167 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1063 2168 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1064 2169 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1065 2170 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1130 2238 2.026641 CGGCCATTGGAGATGTTTGAT 58.973 47.619 6.95 0.00 0.00 2.57
1167 2275 4.500716 CCAAGTTCCACAACAAATGGTACC 60.501 45.833 4.43 4.43 38.04 3.34
1168 2276 3.904717 AGTTCCACAACAAATGGTACCA 58.095 40.909 18.99 18.99 38.04 3.25
1171 2279 2.175931 TCCACAACAAATGGTACCACCT 59.824 45.455 19.09 4.35 39.58 4.00
1240 2368 3.441290 GCTCTTGCTGCTGCTGGG 61.441 66.667 17.00 10.38 40.48 4.45
1265 2393 3.262686 GCCCGAAATCGAGCGGTC 61.263 66.667 18.77 4.06 45.85 4.79
1299 2427 3.999229 GATGATTTTTGCTCGTCGACT 57.001 42.857 14.70 0.00 0.00 4.18
1311 2442 2.599281 TCGACTTCTCCGGTGCCA 60.599 61.111 0.00 0.00 0.00 4.92
1349 2480 1.996786 ATTTCTGGATTGCTGCGGCG 61.997 55.000 13.96 0.51 42.25 6.46
1363 2494 3.195698 GGCGGCGGTTCATCTGAC 61.196 66.667 9.78 0.00 0.00 3.51
1399 2534 7.391148 TTCAGTTTCTGAGCTAAAAAGTTGT 57.609 32.000 0.00 0.00 41.75 3.32
1430 2565 1.609208 TTCAAGGGCTGTTTCTCTGC 58.391 50.000 0.00 0.00 39.71 4.26
1438 2573 0.532573 CTGTTTCTCTGCCTCGCCTA 59.467 55.000 0.00 0.00 0.00 3.93
1445 2580 0.249398 TCTGCCTCGCCTACCTTTTC 59.751 55.000 0.00 0.00 0.00 2.29
1467 2603 2.556114 CCCTCTTGTTTGGCTGGAGATT 60.556 50.000 0.00 0.00 0.00 2.40
1468 2604 3.308402 CCCTCTTGTTTGGCTGGAGATTA 60.308 47.826 0.00 0.00 0.00 1.75
1469 2605 3.691609 CCTCTTGTTTGGCTGGAGATTAC 59.308 47.826 0.00 0.00 0.00 1.89
1496 2632 1.355971 CCCGATTCGTGATTCGTGTT 58.644 50.000 5.20 0.00 40.80 3.32
1501 2637 0.234625 TTCGTGATTCGTGTTGCTGC 59.765 50.000 0.00 0.00 40.80 5.25
1525 2661 1.790387 GCATGTGTTCGTCCAGCTC 59.210 57.895 0.00 0.00 0.00 4.09
1584 2722 3.491792 GGGGATTGTTTTGCTTGTTCGAA 60.492 43.478 0.00 0.00 0.00 3.71
1585 2723 4.116238 GGGATTGTTTTGCTTGTTCGAAA 58.884 39.130 0.00 0.00 0.00 3.46
1586 2724 4.568760 GGGATTGTTTTGCTTGTTCGAAAA 59.431 37.500 0.00 0.00 0.00 2.29
1587 2725 5.276820 GGGATTGTTTTGCTTGTTCGAAAAG 60.277 40.000 0.00 7.51 0.00 2.27
1599 2752 0.516877 TCGAAAAGTTGCTGCATCCG 59.483 50.000 1.84 2.04 0.00 4.18
1636 2789 2.804212 GCATTTTGTTCAGGCTGTTGCT 60.804 45.455 15.27 0.00 39.59 3.91
1677 2831 1.131883 GCTGGATTTGCTACTGCTGTG 59.868 52.381 6.48 0.00 40.48 3.66
1839 2993 0.250295 TACAGCCTGCACACTCAACC 60.250 55.000 0.00 0.00 0.00 3.77
1868 3022 6.738200 CGACTTGCACTGTTTACTAATGATTG 59.262 38.462 0.00 0.00 0.00 2.67
1884 3042 6.743575 AATGATTGTTACCAGCAGTACTTC 57.256 37.500 0.00 0.00 0.00 3.01
1887 3045 6.237901 TGATTGTTACCAGCAGTACTTCAAT 58.762 36.000 0.00 0.00 33.53 2.57
1914 3072 2.456989 CAAACAGCTGCACTTTGTCTG 58.543 47.619 15.27 0.00 0.00 3.51
1916 3074 2.620251 ACAGCTGCACTTTGTCTGTA 57.380 45.000 15.27 0.00 36.37 2.74
1917 3075 2.917933 ACAGCTGCACTTTGTCTGTAA 58.082 42.857 15.27 0.00 36.37 2.41
1922 3085 6.039270 ACAGCTGCACTTTGTCTGTAAAAATA 59.961 34.615 15.27 0.00 36.37 1.40
1926 3089 7.594758 GCTGCACTTTGTCTGTAAAAATATTGA 59.405 33.333 0.00 0.00 0.00 2.57
1932 3095 9.844790 CTTTGTCTGTAAAAATATTGAGCATGA 57.155 29.630 0.00 0.00 0.00 3.07
1938 3103 9.661187 CTGTAAAAATATTGAGCATGAGATGTC 57.339 33.333 0.00 0.00 0.00 3.06
1964 3129 5.919348 ATGTGATGGATATTTCCTCCTGT 57.081 39.130 3.72 0.00 43.07 4.00
2088 3253 1.550524 TGCAGAAACAGAGGTATCGCT 59.449 47.619 0.00 0.00 0.00 4.93
2097 3262 5.339008 ACAGAGGTATCGCTGATGTTTAA 57.661 39.130 14.16 0.00 42.31 1.52
2110 3275 5.389859 TGATGTTTAAGCTGGGATTGTTG 57.610 39.130 0.00 0.00 0.00 3.33
2115 3280 5.127845 TGTTTAAGCTGGGATTGTTGACAAA 59.872 36.000 0.10 0.00 39.55 2.83
2197 3362 4.320667 TGTTTCATTCGATTACTGCACG 57.679 40.909 0.00 0.00 0.00 5.34
2243 3408 4.832248 TGGTGTATGAGGTCTTTGTGATC 58.168 43.478 0.00 0.00 0.00 2.92
2255 3420 4.583489 GTCTTTGTGATCTCCTCCCGTATA 59.417 45.833 0.00 0.00 0.00 1.47
2266 3431 5.243954 TCTCCTCCCGTATATGATGTTTCAG 59.756 44.000 0.00 0.00 34.73 3.02
2314 3479 8.804912 ATAGCTTGACTCTCTGAATCATTTTT 57.195 30.769 0.00 0.00 0.00 1.94
2365 3530 6.078202 TGATTGAAAACCTAAAATGACGCA 57.922 33.333 0.00 0.00 0.00 5.24
2377 3542 3.837213 AATGACGCAAATTCCTGTCAG 57.163 42.857 10.91 0.00 43.80 3.51
2435 3600 5.895636 TGTTCTGTAACTATTTGCATGGG 57.104 39.130 0.00 0.00 36.51 4.00
2479 3644 6.106877 TCTCGAAACTGCAAATAAGCATAC 57.893 37.500 0.00 0.00 44.68 2.39
2483 3648 6.592220 TCGAAACTGCAAATAAGCATACACTA 59.408 34.615 0.00 0.00 44.68 2.74
2484 3649 6.901887 CGAAACTGCAAATAAGCATACACTAG 59.098 38.462 0.00 0.00 44.68 2.57
2511 3745 7.532682 TTTTTGCAGAATTGTTCAGTTTACC 57.467 32.000 0.00 0.00 0.00 2.85
2512 3746 6.463995 TTTGCAGAATTGTTCAGTTTACCT 57.536 33.333 0.00 0.00 0.00 3.08
2513 3747 5.437289 TGCAGAATTGTTCAGTTTACCTG 57.563 39.130 0.00 0.00 42.97 4.00
2514 3748 4.278170 TGCAGAATTGTTCAGTTTACCTGG 59.722 41.667 0.00 0.00 41.83 4.45
2526 3760 3.263425 AGTTTACCTGGTCAGTGGGTATG 59.737 47.826 0.63 0.00 35.80 2.39
2527 3761 1.200519 TACCTGGTCAGTGGGTATGC 58.799 55.000 0.63 0.00 34.86 3.14
2528 3762 1.153369 CCTGGTCAGTGGGTATGCG 60.153 63.158 0.00 0.00 0.00 4.73
2578 3812 5.350365 TGTTCGTGTTTTGCTATATCAGTCC 59.650 40.000 0.00 0.00 0.00 3.85
2586 3820 7.720957 TGTTTTGCTATATCAGTCCAGCATATT 59.279 33.333 0.00 0.00 43.13 1.28
2595 3829 4.225942 TCAGTCCAGCATATTCACCTCTTT 59.774 41.667 0.00 0.00 0.00 2.52
2637 3872 6.413892 TCTGGTGCATTCAGTTATGATTACA 58.586 36.000 16.24 0.00 34.73 2.41
2995 4230 6.395426 TGAAGATGTTGCTGAAGAATTTGT 57.605 33.333 0.00 0.00 0.00 2.83
3025 4260 7.364200 CCGTTTAATACCAAGACATTTGAACA 58.636 34.615 0.00 0.00 0.00 3.18
3049 4284 4.950050 CAGATATCTGGTGTACCTCCAAC 58.050 47.826 22.89 0.00 40.20 3.77
3115 4350 7.753580 CCCATCCTTTTTATTAACAACTCGAAC 59.246 37.037 0.00 0.00 0.00 3.95
3131 4366 1.194547 CGAACGGTCATTCACTTGTGG 59.805 52.381 0.00 0.00 0.00 4.17
3137 4372 3.058914 CGGTCATTCACTTGTGGTCTTTC 60.059 47.826 0.64 0.00 0.00 2.62
3154 4389 8.095169 GTGGTCTTTCTTTATCAGGAACTTCTA 58.905 37.037 0.00 0.00 34.60 2.10
3189 4424 0.677842 AACGGCGTAGAGGTTGAAGT 59.322 50.000 15.20 0.00 0.00 3.01
3404 4639 4.603131 ACATTTGGATAGTGATGTGCCTT 58.397 39.130 0.00 0.00 31.94 4.35
3422 4657 1.728971 CTTCTGTGGACATGAAGCGAC 59.271 52.381 0.00 0.00 32.22 5.19
3434 4669 0.652592 GAAGCGACGGAATGGTCATG 59.347 55.000 0.00 0.00 36.73 3.07
3443 4678 3.009033 ACGGAATGGTCATGAAAAGGAGA 59.991 43.478 0.00 0.00 0.00 3.71
3511 4746 3.003027 TGCAGAGGAGCTGGATCTT 57.997 52.632 0.00 0.00 45.03 2.40
3539 4774 0.185901 AAAGAAGCAGGAGGTTGCCA 59.814 50.000 0.00 0.00 45.18 4.92
3620 4855 3.055094 GGTAACTGAGGAGAAAGATGGCA 60.055 47.826 0.00 0.00 0.00 4.92
3631 4866 0.539438 AAGATGGCACCGAAAAGGCA 60.539 50.000 0.00 0.00 46.52 4.75
3666 4901 3.047807 ATCGGACCCACATGGCTGG 62.048 63.158 0.00 0.00 37.83 4.85
3748 4983 2.555757 GCAAGAAACTGAATCAGCTGGT 59.444 45.455 15.13 2.68 34.37 4.00
3814 5049 0.733729 CTAAGCCGTACAGAGCGACT 59.266 55.000 0.00 0.00 0.00 4.18
3873 5108 2.678580 TCGGGCACGACATCTGGA 60.679 61.111 7.15 0.00 45.59 3.86
4130 5371 0.454196 ACCAACACACGGTTCTTTGC 59.546 50.000 0.00 0.00 37.72 3.68
4164 5405 5.507149 CGACCAATGATGAAAAGGTGACAAA 60.507 40.000 0.00 0.00 31.57 2.83
4264 5505 2.985282 AGGCGTAACGGGTCGACA 60.985 61.111 18.91 0.00 37.57 4.35
4324 5565 1.001378 ACTGCGATTGACTTTGGCAAC 60.001 47.619 0.00 0.00 32.59 4.17
4327 5568 1.401539 GCGATTGACTTTGGCAACCTC 60.402 52.381 0.00 0.00 0.00 3.85
4399 5640 4.047059 GGAGGGCACGACGACGAA 62.047 66.667 15.32 0.00 42.66 3.85
4426 5667 5.153675 AGGATGATGGATAAGCTTCTGAGA 58.846 41.667 0.00 0.00 0.00 3.27
4558 5802 1.484240 CCCAGTCATCCAGAGAGAACC 59.516 57.143 0.00 0.00 0.00 3.62
4560 5804 0.820871 AGTCATCCAGAGAGAACCGC 59.179 55.000 0.00 0.00 0.00 5.68
4609 5853 2.364448 GGGAGGACGAAGGCTCCT 60.364 66.667 0.00 0.00 41.18 3.69
4626 5870 3.901797 CTGCCCCTGTTCGGTCCAC 62.902 68.421 0.00 0.00 0.00 4.02
4690 5934 1.011968 TGCCGGATTTCGACGAACTG 61.012 55.000 10.38 4.95 42.43 3.16
4696 5940 0.602638 ATTTCGACGAACTGGCTGCA 60.603 50.000 10.38 0.00 0.00 4.41
4786 6030 2.680841 GTGTGTTCTACCACAGCAACAA 59.319 45.455 0.00 0.00 45.45 2.83
4861 6118 2.283173 CTTGGACCTTGGTGGCCC 60.283 66.667 0.00 0.00 39.04 5.80
4867 6124 0.759060 GACCTTGGTGGCCCTGTTTT 60.759 55.000 0.00 0.00 40.22 2.43
4875 6132 3.576550 TGGTGGCCCTGTTTTAATCTTTC 59.423 43.478 0.00 0.00 0.00 2.62
4919 6176 0.178995 TTGCATTGCTCCCTGTGTGA 60.179 50.000 10.49 0.00 0.00 3.58
4920 6177 0.038599 TGCATTGCTCCCTGTGTGAT 59.961 50.000 10.49 0.00 0.00 3.06
4921 6178 0.454600 GCATTGCTCCCTGTGTGATG 59.545 55.000 0.16 0.00 0.00 3.07
4923 6180 1.741706 CATTGCTCCCTGTGTGATGTC 59.258 52.381 0.00 0.00 0.00 3.06
4925 6182 1.937191 TGCTCCCTGTGTGATGTCTA 58.063 50.000 0.00 0.00 0.00 2.59
4926 6183 1.827344 TGCTCCCTGTGTGATGTCTAG 59.173 52.381 0.00 0.00 0.00 2.43
4927 6184 1.137872 GCTCCCTGTGTGATGTCTAGG 59.862 57.143 0.00 0.00 0.00 3.02
4929 6186 0.179000 CCCTGTGTGATGTCTAGGGC 59.821 60.000 0.00 0.00 41.44 5.19
4952 6210 4.015084 AGAGAGCATTGGTTGGAGAATTG 58.985 43.478 0.00 0.00 0.00 2.32
4975 6233 4.218312 GAGTGGGCAATTTGATAGGGAAT 58.782 43.478 0.00 0.00 0.00 3.01
4976 6234 5.385198 GAGTGGGCAATTTGATAGGGAATA 58.615 41.667 0.00 0.00 0.00 1.75
4977 6235 5.388654 AGTGGGCAATTTGATAGGGAATAG 58.611 41.667 0.00 0.00 0.00 1.73
5029 6292 0.030504 TGCGGTTGTTTGATGTGCTG 59.969 50.000 0.00 0.00 0.00 4.41
5039 6302 4.161333 GTTTGATGTGCTGATGTGCTTAC 58.839 43.478 0.00 0.00 0.00 2.34
5044 6307 1.466167 GTGCTGATGTGCTTACCTGTG 59.534 52.381 0.00 0.00 0.00 3.66
5062 6329 4.037565 CCTGTGAGTGTATAGATGCCGTTA 59.962 45.833 0.00 0.00 0.00 3.18
5063 6330 5.279006 CCTGTGAGTGTATAGATGCCGTTAT 60.279 44.000 0.00 0.00 0.00 1.89
5084 6353 8.276325 CGTTATTGAGGCTATACTGAAAATGAC 58.724 37.037 0.00 0.00 0.00 3.06
5087 6356 5.348986 TGAGGCTATACTGAAAATGACGAC 58.651 41.667 0.00 0.00 0.00 4.34
5093 6363 6.199342 GCTATACTGAAAATGACGACTCTTCC 59.801 42.308 0.00 0.00 0.00 3.46
5136 6406 5.339177 TGTGTGCATGTGAGTTTTAAGTTG 58.661 37.500 0.00 0.00 0.00 3.16
5143 6413 6.676950 CATGTGAGTTTTAAGTTGGTATGCA 58.323 36.000 0.00 0.00 0.00 3.96
5144 6414 6.067263 TGTGAGTTTTAAGTTGGTATGCAC 57.933 37.500 0.00 0.00 0.00 4.57
5170 6440 5.984926 TGACATTTCAACCTTGAATTTCTGC 59.015 36.000 1.35 0.00 45.65 4.26
5172 6442 5.163322 ACATTTCAACCTTGAATTTCTGCCA 60.163 36.000 1.35 0.00 45.65 4.92
5180 6450 4.482386 CTTGAATTTCTGCCACATGACAG 58.518 43.478 0.00 4.21 35.15 3.51
5185 6455 1.913778 TCTGCCACATGACAGCATTT 58.086 45.000 0.00 0.00 35.64 2.32
5186 6456 2.241160 TCTGCCACATGACAGCATTTT 58.759 42.857 0.00 0.00 35.64 1.82
5225 6495 3.418619 CACGTTGAGTCGAAGCATTTTTG 59.581 43.478 0.00 0.00 34.70 2.44
5244 6514 0.875059 GGGTTGTTTCTCGCAGGAAG 59.125 55.000 0.00 0.00 0.00 3.46
5246 6516 0.238553 GTTGTTTCTCGCAGGAAGGC 59.761 55.000 0.00 0.00 0.00 4.35
5324 6605 6.157994 ACTTCCTGGCCTAACAATAATCTACA 59.842 38.462 3.32 0.00 0.00 2.74
5383 6669 5.635417 GGTCAGTACCGAACTAAACTACT 57.365 43.478 0.00 0.00 35.76 2.57
5387 6673 7.413548 GGTCAGTACCGAACTAAACTACTACTC 60.414 44.444 0.00 0.00 35.76 2.59
5389 6675 4.954092 ACCGAACTAAACTACTACTCCG 57.046 45.455 0.00 0.00 0.00 4.63
5391 6677 5.003804 ACCGAACTAAACTACTACTCCGAA 58.996 41.667 0.00 0.00 0.00 4.30
5414 6700 2.191128 ATAGAAATCTGATGCCGGCC 57.809 50.000 26.77 10.34 0.00 6.13
5484 6773 1.763546 GCTAGCCCAGGGACCTCATC 61.764 65.000 10.89 0.00 0.00 2.92
5694 6983 2.270205 AGGAGACCCTGCGCATTG 59.730 61.111 12.24 7.79 42.42 2.82
5695 6984 2.825836 GGAGACCCTGCGCATTGG 60.826 66.667 21.00 21.00 0.00 3.16
5696 6985 2.268920 GAGACCCTGCGCATTGGA 59.731 61.111 27.31 0.00 0.00 3.53
5697 6986 1.153086 GAGACCCTGCGCATTGGAT 60.153 57.895 27.31 17.13 0.00 3.41
5698 6987 1.442526 GAGACCCTGCGCATTGGATG 61.443 60.000 27.31 10.87 0.00 3.51
5699 6988 2.440796 ACCCTGCGCATTGGATGG 60.441 61.111 27.31 17.01 0.00 3.51
5700 6989 2.124193 CCCTGCGCATTGGATGGA 60.124 61.111 12.24 0.00 0.00 3.41
5725 7014 3.321968 ACCCAAGAAGAAATCAGCAAACC 59.678 43.478 0.00 0.00 0.00 3.27
5727 7016 4.202243 CCCAAGAAGAAATCAGCAAACCAA 60.202 41.667 0.00 0.00 0.00 3.67
5735 7026 1.686355 TCAGCAAACCAACCAACGAT 58.314 45.000 0.00 0.00 0.00 3.73
5753 7044 2.476619 CGATCAGAAACAGAGCACGTTT 59.523 45.455 0.00 4.44 39.23 3.60
5754 7045 3.673338 CGATCAGAAACAGAGCACGTTTA 59.327 43.478 0.00 0.00 36.72 2.01
5755 7046 4.327357 CGATCAGAAACAGAGCACGTTTAT 59.673 41.667 0.00 0.41 36.72 1.40
5759 7050 5.404366 TCAGAAACAGAGCACGTTTATACAC 59.596 40.000 0.00 0.00 36.72 2.90
5760 7051 5.176774 CAGAAACAGAGCACGTTTATACACA 59.823 40.000 0.00 0.00 36.72 3.72
5761 7052 5.405571 AGAAACAGAGCACGTTTATACACAG 59.594 40.000 0.00 0.00 36.72 3.66
5762 7053 4.252971 ACAGAGCACGTTTATACACAGT 57.747 40.909 0.00 0.00 0.00 3.55
5763 7054 5.381174 ACAGAGCACGTTTATACACAGTA 57.619 39.130 0.00 0.00 0.00 2.74
5764 7055 5.775686 ACAGAGCACGTTTATACACAGTAA 58.224 37.500 0.00 0.00 0.00 2.24
5765 7056 6.218019 ACAGAGCACGTTTATACACAGTAAA 58.782 36.000 0.00 0.00 0.00 2.01
5829 7124 0.035439 ATCGCATGGTCTTCCGGTTT 60.035 50.000 0.00 0.00 36.30 3.27
5830 7125 0.250553 TCGCATGGTCTTCCGGTTTT 60.251 50.000 0.00 0.00 36.30 2.43
5831 7126 0.109781 CGCATGGTCTTCCGGTTTTG 60.110 55.000 0.00 0.00 36.30 2.44
5877 7178 5.117355 TCGGTAGATATACCTTTTCTGCG 57.883 43.478 14.43 0.00 37.96 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.323412 GCCTCGATGCTTCTAGGAGA 58.677 55.000 20.59 0.18 37.05 3.71
32 33 1.035923 TGCCTCGATGCTTCTAGGAG 58.964 55.000 20.59 9.41 37.05 3.69
33 34 0.747255 GTGCCTCGATGCTTCTAGGA 59.253 55.000 20.59 6.36 37.05 2.94
34 35 0.461548 TGTGCCTCGATGCTTCTAGG 59.538 55.000 13.93 14.05 37.77 3.02
48 49 5.240844 ACTGATTTAGTACCTGTTTTGTGCC 59.759 40.000 0.00 0.00 38.04 5.01
93 102 3.312404 GCAAGACTGCTCCAGTGAA 57.688 52.632 2.12 0.00 45.44 3.18
117 126 1.261619 GACCAGACAAAACGCTGACTG 59.738 52.381 0.00 5.61 38.37 3.51
125 134 1.869132 GGTACACCGACCAGACAAAAC 59.131 52.381 0.00 0.00 39.51 2.43
165 174 3.175152 GACTCGGCGATGCTATAGATTG 58.825 50.000 11.27 0.00 0.00 2.67
172 181 1.029947 TCAGTGACTCGGCGATGCTA 61.030 55.000 11.27 0.00 0.00 3.49
173 182 2.182791 CAGTGACTCGGCGATGCT 59.817 61.111 11.27 3.35 0.00 3.79
177 186 2.954611 CTGTCAGTGACTCGGCGA 59.045 61.111 23.29 10.14 33.15 5.54
179 188 1.595993 TAGGCTGTCAGTGACTCGGC 61.596 60.000 23.29 23.02 33.15 5.54
181 190 2.949451 ATTAGGCTGTCAGTGACTCG 57.051 50.000 23.29 15.13 33.15 4.18
211 220 3.065371 GGGAATCTTAATCGCACTGGTTG 59.935 47.826 0.00 0.00 0.00 3.77
212 221 3.054361 AGGGAATCTTAATCGCACTGGTT 60.054 43.478 0.00 0.00 32.60 3.67
214 223 3.199880 AGGGAATCTTAATCGCACTGG 57.800 47.619 0.00 0.00 32.60 4.00
216 225 3.967987 AGGTAGGGAATCTTAATCGCACT 59.032 43.478 0.00 0.00 32.60 4.40
217 226 4.338379 AGGTAGGGAATCTTAATCGCAC 57.662 45.455 0.00 0.00 32.60 5.34
220 229 6.323266 CGTGATAGGTAGGGAATCTTAATCG 58.677 44.000 0.00 0.00 0.00 3.34
226 235 3.897657 TCCGTGATAGGTAGGGAATCT 57.102 47.619 0.00 0.00 0.00 2.40
232 241 5.243060 TCACATGTAATCCGTGATAGGTAGG 59.757 44.000 0.00 0.00 34.83 3.18
239 248 5.344743 AGACTTCACATGTAATCCGTGAT 57.655 39.130 0.00 0.00 39.29 3.06
276 285 0.885150 TTTGTGCGTCGCCACCAATA 60.885 50.000 15.88 4.06 34.85 1.90
308 319 6.479331 GGGTTTTAAATTAAAGTGACGCCAAA 59.521 34.615 0.00 0.00 0.00 3.28
342 354 3.426568 GCAGCACTCACCGGAAGC 61.427 66.667 9.46 4.17 0.00 3.86
345 357 3.233980 AGTGCAGCACTCACCGGA 61.234 61.111 23.11 0.00 41.21 5.14
363 375 0.941542 TCCACGCAGTACACTTTTGC 59.058 50.000 0.00 0.00 41.61 3.68
369 381 0.460311 ATAGGCTCCACGCAGTACAC 59.540 55.000 0.00 0.00 41.61 2.90
370 382 0.744874 GATAGGCTCCACGCAGTACA 59.255 55.000 0.00 0.00 41.61 2.90
372 384 0.744874 GTGATAGGCTCCACGCAGTA 59.255 55.000 0.00 0.00 41.61 2.74
374 386 1.032794 TAGTGATAGGCTCCACGCAG 58.967 55.000 12.38 0.00 41.67 5.18
375 387 1.480789 TTAGTGATAGGCTCCACGCA 58.519 50.000 12.38 4.51 41.67 5.24
376 388 2.596904 TTTAGTGATAGGCTCCACGC 57.403 50.000 12.38 3.42 38.26 5.34
451 463 4.275936 CCTCTCCGTTTGTCTGTGATTTTT 59.724 41.667 0.00 0.00 0.00 1.94
475 490 1.211190 CTTTTGGGCAGCTCGCTTC 59.789 57.895 7.85 0.00 41.91 3.86
498 523 4.911390 ACGAATTCAGGGATCACTTTTCT 58.089 39.130 6.22 0.00 0.00 2.52
505 801 2.837591 TCTGGAACGAATTCAGGGATCA 59.162 45.455 6.22 0.00 36.46 2.92
564 860 9.226606 CAACCTCCATATGTAAAAGTGTTTCTA 57.773 33.333 1.24 0.00 0.00 2.10
576 872 7.147320 ACCATTTCATCTCAACCTCCATATGTA 60.147 37.037 1.24 0.00 0.00 2.29
577 873 6.066690 CCATTTCATCTCAACCTCCATATGT 58.933 40.000 1.24 0.00 0.00 2.29
581 877 4.275810 CACCATTTCATCTCAACCTCCAT 58.724 43.478 0.00 0.00 0.00 3.41
582 878 3.561960 CCACCATTTCATCTCAACCTCCA 60.562 47.826 0.00 0.00 0.00 3.86
583 879 3.019564 CCACCATTTCATCTCAACCTCC 58.980 50.000 0.00 0.00 0.00 4.30
584 880 3.019564 CCCACCATTTCATCTCAACCTC 58.980 50.000 0.00 0.00 0.00 3.85
585 881 2.649312 TCCCACCATTTCATCTCAACCT 59.351 45.455 0.00 0.00 0.00 3.50
586 882 3.019564 CTCCCACCATTTCATCTCAACC 58.980 50.000 0.00 0.00 0.00 3.77
588 884 2.025037 CCCTCCCACCATTTCATCTCAA 60.025 50.000 0.00 0.00 0.00 3.02
589 885 1.565759 CCCTCCCACCATTTCATCTCA 59.434 52.381 0.00 0.00 0.00 3.27
590 886 1.846439 TCCCTCCCACCATTTCATCTC 59.154 52.381 0.00 0.00 0.00 2.75
593 1376 0.259938 GCTCCCTCCCACCATTTCAT 59.740 55.000 0.00 0.00 0.00 2.57
613 1396 1.209504 AGTTACCATGTGGACGGATGG 59.790 52.381 5.96 0.00 44.23 3.51
614 1397 2.279741 CAGTTACCATGTGGACGGATG 58.720 52.381 5.96 0.00 38.94 3.51
615 1398 1.406887 GCAGTTACCATGTGGACGGAT 60.407 52.381 5.96 0.00 38.94 4.18
616 1399 0.036765 GCAGTTACCATGTGGACGGA 60.037 55.000 5.96 0.00 38.94 4.69
619 1402 1.165270 GGTGCAGTTACCATGTGGAC 58.835 55.000 5.96 0.00 40.54 4.02
636 1419 4.522789 GTCCAGTTATTGTCCATTTGTGGT 59.477 41.667 0.00 0.00 0.00 4.16
698 1490 2.586425 CAGCTTCTAGAGAGAGAGGGG 58.414 57.143 0.00 0.00 31.77 4.79
700 1492 2.620115 CAGCAGCTTCTAGAGAGAGAGG 59.380 54.545 0.00 0.00 31.77 3.69
754 1838 0.677731 CGCAGGAGAAATTGGCTGGA 60.678 55.000 0.00 0.00 0.00 3.86
758 1842 2.100991 CGCGCAGGAGAAATTGGC 59.899 61.111 8.75 0.00 0.00 4.52
881 1968 1.999634 GATGGAGATGGTGGGGTGGG 62.000 65.000 0.00 0.00 0.00 4.61
949 2050 2.568090 CAATGGTGGCGTCAAGGC 59.432 61.111 0.00 0.00 46.95 4.35
976 2078 4.530857 GTCGATGCGGTGGGGAGG 62.531 72.222 0.00 0.00 0.00 4.30
983 2085 1.736586 GAGGAGATGTCGATGCGGT 59.263 57.895 0.00 0.00 0.00 5.68
984 2086 1.006805 GGAGGAGATGTCGATGCGG 60.007 63.158 0.00 0.00 0.00 5.69
986 2088 1.663074 GCGGAGGAGATGTCGATGC 60.663 63.158 0.00 0.00 0.00 3.91
988 2090 2.556459 CGGCGGAGGAGATGTCGAT 61.556 63.158 0.00 0.00 0.00 3.59
989 2091 3.209812 CGGCGGAGGAGATGTCGA 61.210 66.667 0.00 0.00 0.00 4.20
991 2093 4.593864 GGCGGCGGAGGAGATGTC 62.594 72.222 9.78 0.00 0.00 3.06
1042 2147 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1043 2148 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1044 2149 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1045 2150 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1046 2151 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1047 2152 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1048 2153 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1049 2154 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1050 2155 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
1051 2156 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1052 2157 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
1053 2158 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
1054 2159 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
1055 2160 4.574674 TTTGCTCTCTCTCTCTCTCTCT 57.425 45.455 0.00 0.00 0.00 3.10
1056 2161 5.643379 TTTTTGCTCTCTCTCTCTCTCTC 57.357 43.478 0.00 0.00 0.00 3.20
1057 2162 4.082026 GCTTTTTGCTCTCTCTCTCTCTCT 60.082 45.833 0.00 0.00 38.95 3.10
1058 2163 4.176271 GCTTTTTGCTCTCTCTCTCTCTC 58.824 47.826 0.00 0.00 38.95 3.20
1059 2164 3.367292 CGCTTTTTGCTCTCTCTCTCTCT 60.367 47.826 0.00 0.00 40.11 3.10
1060 2165 2.923020 CGCTTTTTGCTCTCTCTCTCTC 59.077 50.000 0.00 0.00 40.11 3.20
1061 2166 2.353605 CCGCTTTTTGCTCTCTCTCTCT 60.354 50.000 0.00 0.00 40.11 3.10
1062 2167 1.999024 CCGCTTTTTGCTCTCTCTCTC 59.001 52.381 0.00 0.00 40.11 3.20
1063 2168 1.943507 GCCGCTTTTTGCTCTCTCTCT 60.944 52.381 0.00 0.00 40.11 3.10
1064 2169 0.445829 GCCGCTTTTTGCTCTCTCTC 59.554 55.000 0.00 0.00 40.11 3.20
1065 2170 1.294659 CGCCGCTTTTTGCTCTCTCT 61.295 55.000 0.00 0.00 40.11 3.10
1130 2238 3.403038 GAACTTGGAGTTGAGCAAGCTA 58.597 45.455 0.00 0.00 38.80 3.32
1167 2275 1.348775 GGAGGGAGGGATCCAAGGTG 61.349 65.000 15.23 0.00 35.54 4.00
1168 2276 1.004891 GGAGGGAGGGATCCAAGGT 59.995 63.158 15.23 0.00 35.54 3.50
1171 2279 1.318380 GGAGGAGGGAGGGATCCAA 59.682 63.158 15.23 0.00 38.12 3.53
1240 2368 3.577313 GATTTCGGGCTGGCTCGC 61.577 66.667 10.21 0.00 40.19 5.03
1265 2393 2.160822 ATCATCGCCAGAAATCCTCG 57.839 50.000 0.00 0.00 0.00 4.63
1274 2402 1.131126 ACGAGCAAAAATCATCGCCAG 59.869 47.619 0.00 0.00 38.71 4.85
1297 2425 4.379243 CGCTGGCACCGGAGAAGT 62.379 66.667 9.46 0.00 0.00 3.01
1311 2442 3.302344 AAACAAATGCCGGCCGCT 61.302 55.556 26.77 5.57 38.78 5.52
1349 2480 1.810030 GGACGTCAGATGAACCGCC 60.810 63.158 18.91 0.00 0.00 6.13
1376 2511 7.391148 AACAACTTTTTAGCTCAGAAACTGA 57.609 32.000 0.00 0.00 38.25 3.41
1384 2519 3.630312 AGGCGAAACAACTTTTTAGCTCA 59.370 39.130 0.00 0.00 37.29 4.26
1390 2525 7.835634 TGAATTAAAGGCGAAACAACTTTTT 57.164 28.000 0.00 0.00 36.07 1.94
1399 2534 3.056891 CAGCCCTTGAATTAAAGGCGAAA 60.057 43.478 15.56 0.00 44.69 3.46
1430 2565 1.223763 GGGGAAAAGGTAGGCGAGG 59.776 63.158 0.00 0.00 0.00 4.63
1438 2573 2.677914 CCAAACAAGAGGGGAAAAGGT 58.322 47.619 0.00 0.00 0.00 3.50
1445 2580 0.610232 CTCCAGCCAAACAAGAGGGG 60.610 60.000 0.00 0.00 0.00 4.79
1467 2603 0.396139 ACGAATCGGGCCTGGTAGTA 60.396 55.000 12.87 0.00 0.00 1.82
1468 2604 1.684734 ACGAATCGGGCCTGGTAGT 60.685 57.895 12.87 5.84 0.00 2.73
1469 2605 1.227263 CACGAATCGGGCCTGGTAG 60.227 63.158 12.87 5.11 0.00 3.18
1501 2637 1.417592 GACGAACACATGCGAGCAG 59.582 57.895 3.58 0.00 0.00 4.24
1525 2661 1.207570 AGACCATCAGAGAGCAAGCAG 59.792 52.381 0.00 0.00 0.00 4.24
1584 2722 1.308069 ATCGCGGATGCAGCAACTTT 61.308 50.000 6.13 0.00 42.97 2.66
1585 2723 1.308069 AATCGCGGATGCAGCAACTT 61.308 50.000 6.13 0.00 42.97 2.66
1586 2724 1.308069 AAATCGCGGATGCAGCAACT 61.308 50.000 6.13 0.00 42.97 3.16
1587 2725 1.135699 CAAATCGCGGATGCAGCAAC 61.136 55.000 6.13 0.00 42.97 4.17
1839 2993 1.263217 GTAAACAGTGCAAGTCGGTGG 59.737 52.381 0.00 0.00 0.00 4.61
1868 3022 5.240844 ACCAAATTGAAGTACTGCTGGTAAC 59.759 40.000 10.18 0.00 34.21 2.50
1884 3042 1.262151 GCAGCTGTTTGCACCAAATTG 59.738 47.619 16.64 0.00 45.94 2.32
1887 3045 4.831698 GCAGCTGTTTGCACCAAA 57.168 50.000 16.64 0.00 45.94 3.28
1906 3064 9.844790 TCATGCTCAATATTTTTACAGACAAAG 57.155 29.630 0.00 0.00 0.00 2.77
1910 3068 9.661187 CATCTCATGCTCAATATTTTTACAGAC 57.339 33.333 0.00 0.00 0.00 3.51
1922 3085 7.904205 TCACATATAGACATCTCATGCTCAAT 58.096 34.615 0.00 0.00 0.00 2.57
1926 3089 6.439692 TCCATCACATATAGACATCTCATGCT 59.560 38.462 0.00 0.00 0.00 3.79
1964 3129 2.423803 CCCTTCCATCTGCATTCCATCA 60.424 50.000 0.00 0.00 0.00 3.07
2088 3253 5.048083 GTCAACAATCCCAGCTTAAACATCA 60.048 40.000 0.00 0.00 0.00 3.07
2097 3262 2.158475 TCCTTTGTCAACAATCCCAGCT 60.158 45.455 0.00 0.00 35.55 4.24
2110 3275 2.163818 TGACCGACATGTCCTTTGTC 57.836 50.000 20.03 19.00 40.06 3.18
2115 3280 2.426522 CAACATTGACCGACATGTCCT 58.573 47.619 20.03 5.31 34.25 3.85
2197 3362 1.091771 ATGTAGTGCGCACATCTGCC 61.092 55.000 39.21 20.48 40.73 4.85
2207 3372 4.629634 TCATACACCAGAAAATGTAGTGCG 59.370 41.667 0.00 0.00 34.88 5.34
2243 3408 5.243954 TCTGAAACATCATATACGGGAGGAG 59.756 44.000 0.00 0.00 0.00 3.69
2255 3420 7.889469 ACTAAGCAACAATTCTGAAACATCAT 58.111 30.769 0.00 0.00 0.00 2.45
2266 3431 4.858935 TGCTGTCAACTAAGCAACAATTC 58.141 39.130 0.00 0.00 46.06 2.17
2363 3528 4.773323 AGCTAAACTGACAGGAATTTGC 57.227 40.909 7.51 10.85 0.00 3.68
2365 3530 8.515414 GTTGATTAGCTAAACTGACAGGAATTT 58.485 33.333 10.85 1.25 0.00 1.82
2435 3600 7.172703 TCGAGATCCTCTAAAACTTTGGAAAAC 59.827 37.037 0.00 0.00 0.00 2.43
2507 3741 1.557832 GCATACCCACTGACCAGGTAA 59.442 52.381 0.00 0.00 39.50 2.85
2508 3742 1.200519 GCATACCCACTGACCAGGTA 58.799 55.000 0.00 0.00 40.32 3.08
2509 3743 1.899437 CGCATACCCACTGACCAGGT 61.899 60.000 0.00 0.00 37.69 4.00
2510 3744 1.153369 CGCATACCCACTGACCAGG 60.153 63.158 1.82 0.00 0.00 4.45
2511 3745 1.815421 GCGCATACCCACTGACCAG 60.815 63.158 0.30 0.00 0.00 4.00
2512 3746 2.267642 GCGCATACCCACTGACCA 59.732 61.111 0.30 0.00 0.00 4.02
2513 3747 2.513897 GGCGCATACCCACTGACC 60.514 66.667 10.83 0.00 0.00 4.02
2526 3760 1.138266 TCTAGTATGGAAGTTGGGCGC 59.862 52.381 0.00 0.00 0.00 6.53
2527 3761 3.069586 TCATCTAGTATGGAAGTTGGGCG 59.930 47.826 0.00 0.00 0.00 6.13
2528 3762 4.101741 ACTCATCTAGTATGGAAGTTGGGC 59.898 45.833 0.00 0.00 36.36 5.36
2637 3872 8.140112 AGTGATCAACTATAGAAGGAAGTTGT 57.860 34.615 6.78 2.94 46.49 3.32
2899 4134 2.140717 CAAACTGTCCACGTAAGGGTC 58.859 52.381 0.00 0.00 41.30 4.46
2995 4230 5.423704 TGTCTTGGTATTAAACGGGATCA 57.576 39.130 0.00 0.00 0.00 2.92
3025 4260 4.620723 TGGAGGTACACCAGATATCTGTT 58.379 43.478 27.03 14.10 46.01 3.16
3115 4350 2.169832 AGACCACAAGTGAATGACCG 57.830 50.000 0.94 0.00 0.00 4.79
3154 4389 2.296190 GCCGTTGAATGAACCCTTCTTT 59.704 45.455 0.00 0.00 0.00 2.52
3189 4424 0.463654 GTGTCCATTGCGCCCTGATA 60.464 55.000 4.18 0.00 0.00 2.15
3260 4495 0.036732 TCCTGCTTCCATTCACGCTT 59.963 50.000 0.00 0.00 0.00 4.68
3261 4496 0.036732 TTCCTGCTTCCATTCACGCT 59.963 50.000 0.00 0.00 0.00 5.07
3310 4545 5.630121 ACTTGACCAATGTAATCAGGAACA 58.370 37.500 0.00 0.00 0.00 3.18
3404 4639 0.388520 CGTCGCTTCATGTCCACAGA 60.389 55.000 0.00 0.00 0.00 3.41
3422 4657 3.609853 TCTCCTTTTCATGACCATTCCG 58.390 45.455 0.00 0.00 0.00 4.30
3434 4669 4.315803 TCGTCCTTGTTGATCTCCTTTTC 58.684 43.478 0.00 0.00 0.00 2.29
3443 4678 3.821033 CCCTTTTTCTCGTCCTTGTTGAT 59.179 43.478 0.00 0.00 0.00 2.57
3511 4746 3.614092 CTCCTGCTTCTTTGAGCCATTA 58.386 45.455 0.00 0.00 42.01 1.90
3539 4774 6.409524 TTCTCTTTGAACAGATTTTGCCAT 57.590 33.333 0.00 0.00 0.00 4.40
3600 4835 3.055094 GGTGCCATCTTTCTCCTCAGTTA 60.055 47.826 0.00 0.00 0.00 2.24
3608 4843 2.162408 CCTTTTCGGTGCCATCTTTCTC 59.838 50.000 0.00 0.00 0.00 2.87
3616 4851 0.033228 CATTTGCCTTTTCGGTGCCA 59.967 50.000 0.00 0.00 34.25 4.92
3620 4855 0.755686 TTGCCATTTGCCTTTTCGGT 59.244 45.000 0.00 0.00 40.16 4.69
3666 4901 2.292267 CCCAGTTATGATCAGTGCCAC 58.708 52.381 0.09 0.00 0.00 5.01
3748 4983 2.228545 TGCCATTGCCATTCAAGGTA 57.771 45.000 0.00 0.00 38.22 3.08
3814 5049 4.158579 TCTTCTTCAGCAGATTTCTCGCTA 59.841 41.667 4.83 0.00 33.82 4.26
3823 5058 9.638176 AAACCATTATTATCTTCTTCAGCAGAT 57.362 29.630 0.00 0.00 32.92 2.90
3859 5094 0.247736 ACTCTTCCAGATGTCGTGCC 59.752 55.000 0.00 0.00 0.00 5.01
3865 5100 3.808618 GCTGTCCAAACTCTTCCAGATGT 60.809 47.826 0.00 0.00 0.00 3.06
3869 5104 1.528129 GGCTGTCCAAACTCTTCCAG 58.472 55.000 0.00 0.00 0.00 3.86
3873 5108 0.535102 CACCGGCTGTCCAAACTCTT 60.535 55.000 0.00 0.00 0.00 2.85
4130 5371 2.126071 ATTGGTCGCCTCGTCGTG 60.126 61.111 0.00 0.00 0.00 4.35
4264 5505 1.185618 TCTGGTAGTCACTGCCGCTT 61.186 55.000 7.52 0.00 39.12 4.68
4345 5586 2.125350 CTCCTGCTCCGGTGCTTC 60.125 66.667 27.24 1.43 0.00 3.86
4399 5640 5.246656 CAGAAGCTTATCCATCATCCTCTCT 59.753 44.000 0.00 0.00 0.00 3.10
4426 5667 1.729586 TCCCCTTCTTGCTGTAGTGT 58.270 50.000 0.00 0.00 0.00 3.55
4531 5775 3.785859 GGATGACTGGGCGCTCCA 61.786 66.667 3.94 11.40 44.79 3.86
4585 5829 4.626402 TTCGTCCTCCCCACCGGT 62.626 66.667 0.00 0.00 0.00 5.28
4609 5853 3.948719 GTGGACCGAACAGGGGCA 61.949 66.667 0.00 0.00 46.96 5.36
4612 5856 2.663196 GAGGTGGACCGAACAGGG 59.337 66.667 0.00 0.00 46.96 4.45
4617 5861 4.373116 GCAGCGAGGTGGACCGAA 62.373 66.667 4.40 0.00 42.08 4.30
4626 5870 4.383861 TGTCCTGCTGCAGCGAGG 62.384 66.667 33.67 33.67 45.83 4.63
4696 5940 1.522355 CTTCATGGCGCTGATCCGT 60.522 57.895 7.64 0.00 0.00 4.69
4786 6030 0.318191 CGATCGCCGTCATGAGATGT 60.318 55.000 0.26 0.00 0.00 3.06
4861 6118 6.816136 ACCACCAAAGGAAAGATTAAAACAG 58.184 36.000 0.00 0.00 0.00 3.16
4867 6124 7.338449 GCAAGTATACCACCAAAGGAAAGATTA 59.662 37.037 0.00 0.00 0.00 1.75
4875 6132 4.677779 GCAATGCAAGTATACCACCAAAGG 60.678 45.833 0.00 0.00 0.00 3.11
4919 6176 2.100128 ATGCTCTCTGCCCTAGACAT 57.900 50.000 0.00 0.00 42.00 3.06
4920 6177 1.483827 CAATGCTCTCTGCCCTAGACA 59.516 52.381 0.00 0.00 42.00 3.41
4921 6178 1.202627 CCAATGCTCTCTGCCCTAGAC 60.203 57.143 0.00 0.00 42.00 2.59
4923 6180 0.835941 ACCAATGCTCTCTGCCCTAG 59.164 55.000 0.00 0.00 42.00 3.02
4925 6182 0.323178 CAACCAATGCTCTCTGCCCT 60.323 55.000 0.00 0.00 42.00 5.19
4926 6183 1.318158 CCAACCAATGCTCTCTGCCC 61.318 60.000 0.00 0.00 42.00 5.36
4927 6184 0.322816 TCCAACCAATGCTCTCTGCC 60.323 55.000 0.00 0.00 42.00 4.85
4929 6186 2.775911 TCTCCAACCAATGCTCTCTG 57.224 50.000 0.00 0.00 0.00 3.35
4952 6210 2.091885 TCCCTATCAAATTGCCCACTCC 60.092 50.000 0.00 0.00 0.00 3.85
4992 6250 2.158841 CGCACCCAACAACATGTACTAC 59.841 50.000 0.00 0.00 0.00 2.73
4993 6251 2.418692 CGCACCCAACAACATGTACTA 58.581 47.619 0.00 0.00 0.00 1.82
4994 6252 1.234821 CGCACCCAACAACATGTACT 58.765 50.000 0.00 0.00 0.00 2.73
4995 6253 0.239879 CCGCACCCAACAACATGTAC 59.760 55.000 0.00 0.00 0.00 2.90
4996 6254 0.179015 ACCGCACCCAACAACATGTA 60.179 50.000 0.00 0.00 0.00 2.29
4997 6255 1.040339 AACCGCACCCAACAACATGT 61.040 50.000 0.00 0.00 0.00 3.21
5029 6292 3.045601 ACACTCACAGGTAAGCACATC 57.954 47.619 0.00 0.00 0.00 3.06
5039 6302 2.362397 ACGGCATCTATACACTCACAGG 59.638 50.000 0.00 0.00 0.00 4.00
5044 6307 5.864474 CCTCAATAACGGCATCTATACACTC 59.136 44.000 0.00 0.00 0.00 3.51
5062 6329 6.480320 GTCGTCATTTTCAGTATAGCCTCAAT 59.520 38.462 0.00 0.00 0.00 2.57
5063 6330 5.810587 GTCGTCATTTTCAGTATAGCCTCAA 59.189 40.000 0.00 0.00 0.00 3.02
5080 6349 4.608948 AACAAGAAGGAAGAGTCGTCAT 57.391 40.909 8.37 0.00 0.00 3.06
5084 6353 4.372656 ACAGAAACAAGAAGGAAGAGTCG 58.627 43.478 0.00 0.00 0.00 4.18
5087 6356 4.884164 ACCAACAGAAACAAGAAGGAAGAG 59.116 41.667 0.00 0.00 0.00 2.85
5093 6363 3.129287 ACAGCACCAACAGAAACAAGAAG 59.871 43.478 0.00 0.00 0.00 2.85
5136 6406 4.218417 AGGTTGAAATGTCAAGTGCATACC 59.782 41.667 0.00 0.00 44.44 2.73
5170 6440 7.537715 TGACTAATAAAAATGCTGTCATGTGG 58.462 34.615 0.00 0.00 32.23 4.17
5172 6442 8.454106 GTCTGACTAATAAAAATGCTGTCATGT 58.546 33.333 0.00 0.00 33.42 3.21
5180 6450 5.125417 TGGCCAGTCTGACTAATAAAAATGC 59.875 40.000 10.47 2.72 0.00 3.56
5185 6455 3.259876 ACGTGGCCAGTCTGACTAATAAA 59.740 43.478 5.11 0.00 0.00 1.40
5186 6456 2.829720 ACGTGGCCAGTCTGACTAATAA 59.170 45.455 5.11 0.00 0.00 1.40
5225 6495 0.875059 CTTCCTGCGAGAAACAACCC 59.125 55.000 0.00 0.00 0.00 4.11
5324 6605 0.384309 TCTGAAGAGAACGTGCGTGT 59.616 50.000 0.00 0.00 0.00 4.49
5381 6667 8.693120 TCAGATTTCTATATGTTCGGAGTAGT 57.307 34.615 0.00 0.00 0.00 2.73
5382 6668 9.566530 CATCAGATTTCTATATGTTCGGAGTAG 57.433 37.037 0.00 0.00 0.00 2.57
5383 6669 8.029522 GCATCAGATTTCTATATGTTCGGAGTA 58.970 37.037 0.00 0.00 0.00 2.59
5387 6673 5.062683 CGGCATCAGATTTCTATATGTTCGG 59.937 44.000 0.00 0.00 0.00 4.30
5389 6675 5.163814 GCCGGCATCAGATTTCTATATGTTC 60.164 44.000 24.80 0.00 0.00 3.18
5391 6677 4.256920 GCCGGCATCAGATTTCTATATGT 58.743 43.478 24.80 0.00 0.00 2.29
5399 6685 0.323725 AGTTGGCCGGCATCAGATTT 60.324 50.000 30.85 1.40 0.00 2.17
5484 6773 2.390288 CATTTCGTCGTCGGCGTG 59.610 61.111 19.81 6.53 39.49 5.34
5691 6980 4.750941 TCTTCTTGGGTTTTCCATCCAAT 58.249 39.130 0.00 0.00 46.52 3.16
5692 6981 4.191804 TCTTCTTGGGTTTTCCATCCAA 57.808 40.909 0.00 0.00 46.52 3.53
5693 6982 3.893753 TCTTCTTGGGTTTTCCATCCA 57.106 42.857 0.00 0.00 46.52 3.41
5694 6983 5.245977 TGATTTCTTCTTGGGTTTTCCATCC 59.754 40.000 0.00 0.00 46.52 3.51
5695 6984 6.345096 TGATTTCTTCTTGGGTTTTCCATC 57.655 37.500 0.00 0.00 46.52 3.51
5696 6985 5.279657 GCTGATTTCTTCTTGGGTTTTCCAT 60.280 40.000 0.00 0.00 46.52 3.41
5697 6986 4.039124 GCTGATTTCTTCTTGGGTTTTCCA 59.961 41.667 0.00 0.00 45.43 3.53
5698 6987 4.039124 TGCTGATTTCTTCTTGGGTTTTCC 59.961 41.667 0.00 0.00 39.75 3.13
5699 6988 5.200368 TGCTGATTTCTTCTTGGGTTTTC 57.800 39.130 0.00 0.00 0.00 2.29
5700 6989 5.612725 TTGCTGATTTCTTCTTGGGTTTT 57.387 34.783 0.00 0.00 0.00 2.43
5725 7014 3.364366 GCTCTGTTTCTGATCGTTGGTTG 60.364 47.826 0.00 0.00 0.00 3.77
5727 7016 2.224281 TGCTCTGTTTCTGATCGTTGGT 60.224 45.455 0.00 0.00 0.00 3.67
5735 7026 5.404366 GTGTATAAACGTGCTCTGTTTCTGA 59.596 40.000 10.44 0.00 39.96 3.27
5819 7114 1.302192 CGGAGGCAAAACCGGAAGA 60.302 57.895 9.46 0.00 46.52 2.87
5877 7178 2.558380 AAATCGGCCCCAGGAGAAGC 62.558 60.000 0.00 0.00 0.00 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.