Multiple sequence alignment - TraesCS7D01G096900

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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 TraesCS7D01G096900 chr7D 100.000 2616 0 0 1 2616 58767356 58769971 0.000000e+00 4831.0
1 TraesCS7D01G096900 chr7D 85.521 739 50 33 778 1485 58863931 58863219 0.000000e+00 719.0
2 TraesCS7D01G096900 chr7D 96.209 422 16 0 1063 1484 73117139 73116718 0.000000e+00 691.0
3 TraesCS7D01G096900 chr4A 89.286 980 72 15 771 1735 675854659 675855620 0.000000e+00 1197.0
4 TraesCS7D01G096900 chr4A 87.580 942 46 29 1709 2616 675855632 675856536 0.000000e+00 1026.0
5 TraesCS7D01G096900 chr4A 78.895 507 56 22 199 681 675854101 675854580 1.970000e-76 296.0
6 TraesCS7D01G096900 chr4A 86.631 187 21 4 17 200 675853880 675854065 1.230000e-48 204.0
7 TraesCS7D01G096900 chr7A 93.909 591 29 3 967 1554 63117624 63118210 0.000000e+00 885.0
8 TraesCS7D01G096900 chr7A 87.278 731 52 22 778 1485 63427883 63427171 0.000000e+00 797.0
9 TraesCS7D01G096900 chr7A 89.537 583 38 12 909 1485 63398899 63398334 0.000000e+00 717.0
10 TraesCS7D01G096900 chr7A 90.698 129 12 0 778 906 63117059 63117187 3.460000e-39 172.0
11 TraesCS7D01G096900 chr5B 85.694 713 51 31 803 1485 339101210 339100519 0.000000e+00 704.0
12 TraesCS7D01G096900 chr5D 92.723 481 22 8 1005 1485 298123725 298124192 0.000000e+00 682.0
13 TraesCS7D01G096900 chrUn 92.593 459 28 6 1028 1484 82565903 82566357 0.000000e+00 654.0
14 TraesCS7D01G096900 chrUn 88.670 406 29 9 771 1172 468331401 468331793 1.820000e-131 479.0
15 TraesCS7D01G096900 chr1D 93.237 414 28 0 1068 1481 369925929 369925516 6.190000e-171 610.0
16 TraesCS7D01G096900 chr1A 78.571 112 19 4 782 891 468599491 468599383 4.670000e-08 69.4
17 TraesCS7D01G096900 chr5A 90.244 41 3 1 583 623 378273265 378273226 5.000000e-03 52.8


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 TraesCS7D01G096900 chr7D 58767356 58769971 2615 False 4831.00 4831 100.0000 1 2616 1 chr7D.!!$F1 2615
1 TraesCS7D01G096900 chr7D 58863219 58863931 712 True 719.00 719 85.5210 778 1485 1 chr7D.!!$R1 707
2 TraesCS7D01G096900 chr4A 675853880 675856536 2656 False 680.75 1197 85.5980 17 2616 4 chr4A.!!$F1 2599
3 TraesCS7D01G096900 chr7A 63427171 63427883 712 True 797.00 797 87.2780 778 1485 1 chr7A.!!$R2 707
4 TraesCS7D01G096900 chr7A 63398334 63398899 565 True 717.00 717 89.5370 909 1485 1 chr7A.!!$R1 576
5 TraesCS7D01G096900 chr7A 63117059 63118210 1151 False 528.50 885 92.3035 778 1554 2 chr7A.!!$F1 776
6 TraesCS7D01G096900 chr5B 339100519 339101210 691 True 704.00 704 85.6940 803 1485 1 chr5B.!!$R1 682

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
263 313 0.109272 TCCATGACGAAGCACGAGAC 60.109 55.0 10.05 2.8 45.77 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2755 0.035317 GAGACACCCAGCACACATCA 59.965 55.0 0.0 0.0 0.0 3.07 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
26 27 2.396590 TCATGTTTCCTTAGGCCGTC 57.603 50.000 0.00 0.00 0.00 4.79
55 56 9.855021 ACTTTATTCATAAAACGGGATGAAAAG 57.145 29.630 1.76 4.96 43.39 2.27
60 61 8.568676 TTCATAAAACGGGATGAAAAGATGTA 57.431 30.769 0.00 0.00 38.73 2.29
65 66 6.683974 AACGGGATGAAAAGATGTATTGAG 57.316 37.500 0.00 0.00 0.00 3.02
68 69 6.884295 ACGGGATGAAAAGATGTATTGAGAAA 59.116 34.615 0.00 0.00 0.00 2.52
70 71 8.408601 CGGGATGAAAAGATGTATTGAGAAAAT 58.591 33.333 0.00 0.00 0.00 1.82
91 95 7.948034 AAATTATCTACTATCTCCTCCTCCG 57.052 40.000 0.00 0.00 0.00 4.63
92 96 6.645884 ATTATCTACTATCTCCTCCTCCGT 57.354 41.667 0.00 0.00 0.00 4.69
102 106 3.024547 CTCCTCCTCCGTTAGAACATGA 58.975 50.000 0.00 0.00 0.00 3.07
109 113 6.103997 TCCTCCGTTAGAACATGAAACATAC 58.896 40.000 0.00 0.00 0.00 2.39
142 146 1.867233 GCACATGTATGACGGGACATC 59.133 52.381 0.00 0.00 34.01 3.06
154 158 4.466370 TGACGGGACATCACTATCTTCTTT 59.534 41.667 0.00 0.00 0.00 2.52
155 159 5.012328 ACGGGACATCACTATCTTCTTTC 57.988 43.478 0.00 0.00 0.00 2.62
156 160 4.712337 ACGGGACATCACTATCTTCTTTCT 59.288 41.667 0.00 0.00 0.00 2.52
158 162 6.380274 ACGGGACATCACTATCTTCTTTCTAA 59.620 38.462 0.00 0.00 0.00 2.10
159 163 7.070074 ACGGGACATCACTATCTTCTTTCTAAT 59.930 37.037 0.00 0.00 0.00 1.73
220 261 2.370189 GCTATCCTAGAACAGGGCATGT 59.630 50.000 0.00 0.00 45.58 3.21
224 265 2.435805 TCCTAGAACAGGGCATGTCATC 59.564 50.000 4.81 0.00 45.58 2.92
240 290 6.624423 GCATGTCATCCCTATACATCATTTGC 60.624 42.308 0.00 0.00 31.60 3.68
263 313 0.109272 TCCATGACGAAGCACGAGAC 60.109 55.000 10.05 2.80 45.77 3.36
264 314 0.388520 CCATGACGAAGCACGAGACA 60.389 55.000 10.05 7.42 45.77 3.41
265 315 0.710567 CATGACGAAGCACGAGACAC 59.289 55.000 10.05 0.00 45.77 3.67
266 316 0.598562 ATGACGAAGCACGAGACACT 59.401 50.000 10.05 0.00 45.77 3.55
267 317 0.384309 TGACGAAGCACGAGACACTT 59.616 50.000 10.05 0.00 45.77 3.16
268 318 1.605232 TGACGAAGCACGAGACACTTA 59.395 47.619 10.05 0.00 45.77 2.24
269 319 2.243407 GACGAAGCACGAGACACTTAG 58.757 52.381 10.05 0.00 45.77 2.18
270 320 0.985549 CGAAGCACGAGACACTTAGC 59.014 55.000 0.00 0.00 45.77 3.09
278 328 1.736126 CGAGACACTTAGCTCGTACCA 59.264 52.381 0.00 0.00 46.43 3.25
279 329 2.475852 CGAGACACTTAGCTCGTACCAC 60.476 54.545 0.00 0.00 46.43 4.16
284 334 3.181503 ACACTTAGCTCGTACCACGTATG 60.182 47.826 0.00 0.00 43.14 2.39
288 338 3.079960 AGCTCGTACCACGTATGAATG 57.920 47.619 0.00 0.00 43.14 2.67
296 346 7.034397 TCGTACCACGTATGAATGTTCATTTA 58.966 34.615 12.95 0.00 42.74 1.40
354 405 3.678056 ATACAACTGCGTCCAAAGAGA 57.322 42.857 0.00 0.00 0.00 3.10
389 448 3.564225 GGACACTCAAGGACGAACAATTT 59.436 43.478 0.00 0.00 0.00 1.82
390 449 4.319549 GGACACTCAAGGACGAACAATTTC 60.320 45.833 0.00 0.00 0.00 2.17
401 460 2.244695 GAACAATTTCGGGGTCCCTTT 58.755 47.619 8.15 0.00 0.00 3.11
404 463 2.225267 ACAATTTCGGGGTCCCTTTGAT 60.225 45.455 8.15 0.00 0.00 2.57
408 467 0.610785 TCGGGGTCCCTTTGATTTGC 60.611 55.000 8.15 0.00 0.00 3.68
410 469 0.897621 GGGGTCCCTTTGATTTGCAG 59.102 55.000 8.15 0.00 0.00 4.41
411 470 1.549950 GGGGTCCCTTTGATTTGCAGA 60.550 52.381 8.15 0.00 0.00 4.26
412 471 2.247358 GGGTCCCTTTGATTTGCAGAA 58.753 47.619 0.00 0.00 0.00 3.02
418 477 6.293571 GGTCCCTTTGATTTGCAGAATTTTTG 60.294 38.462 0.00 0.00 0.00 2.44
429 488 8.954950 TTTGCAGAATTTTTGAAATGTAGGAA 57.045 26.923 0.00 0.00 0.00 3.36
466 530 6.594788 AGATTAAAGTGCCATGTCATGTTT 57.405 33.333 11.84 7.95 0.00 2.83
469 533 8.752187 AGATTAAAGTGCCATGTCATGTTTAAT 58.248 29.630 20.79 20.79 34.35 1.40
472 536 3.701040 AGTGCCATGTCATGTTTAATCCC 59.299 43.478 11.84 0.00 0.00 3.85
473 537 2.687425 TGCCATGTCATGTTTAATCCCG 59.313 45.455 11.84 0.00 0.00 5.14
475 539 2.286950 CCATGTCATGTTTAATCCCGCG 60.287 50.000 11.84 0.00 0.00 6.46
477 541 2.701107 TGTCATGTTTAATCCCGCGAA 58.299 42.857 8.23 0.00 0.00 4.70
478 542 2.675844 TGTCATGTTTAATCCCGCGAAG 59.324 45.455 8.23 0.00 0.00 3.79
498 562 2.293170 GCTAGTGAGCCCCAAGAATTC 58.707 52.381 0.00 0.00 43.49 2.17
499 563 2.924421 CTAGTGAGCCCCAAGAATTCC 58.076 52.381 0.65 0.00 0.00 3.01
503 567 0.253327 GAGCCCCAAGAATTCCGAGT 59.747 55.000 0.65 0.00 0.00 4.18
522 586 5.817616 GAGTATTCGACGTCACAGAAAAA 57.182 39.130 17.16 1.78 0.00 1.94
553 617 8.576442 AGACATTGTATAAAAAGGTTTGAGTGG 58.424 33.333 0.00 0.00 0.00 4.00
584 648 8.956446 TTTTTCCCTCTGAAATAGAAAATCCT 57.044 30.769 0.00 0.00 42.38 3.24
600 664 8.863872 AGAAAATCCTAAAAATTCTCGAAGGA 57.136 30.769 0.92 0.92 37.52 3.36
633 697 7.557719 TCCTCCAAAATTCATATGAGGTTTCTC 59.442 37.037 14.71 0.00 40.36 2.87
635 699 8.284945 TCCAAAATTCATATGAGGTTTCTCTG 57.715 34.615 14.71 11.00 40.58 3.35
638 702 9.947669 CAAAATTCATATGAGGTTTCTCTGATC 57.052 33.333 14.71 0.00 40.58 2.92
644 708 9.690913 TCATATGAGGTTTCTCTGATCAAAATT 57.309 29.630 0.00 0.00 40.58 1.82
645 709 9.947669 CATATGAGGTTTCTCTGATCAAAATTC 57.052 33.333 0.00 0.00 40.58 2.17
646 710 6.486253 TGAGGTTTCTCTGATCAAAATTCG 57.514 37.500 0.00 0.00 40.58 3.34
647 711 5.997746 TGAGGTTTCTCTGATCAAAATTCGT 59.002 36.000 0.00 0.00 40.58 3.85
648 712 6.147821 TGAGGTTTCTCTGATCAAAATTCGTC 59.852 38.462 0.00 0.00 40.58 4.20
649 713 6.234177 AGGTTTCTCTGATCAAAATTCGTCT 58.766 36.000 0.00 0.00 0.00 4.18
650 714 6.148480 AGGTTTCTCTGATCAAAATTCGTCTG 59.852 38.462 0.00 0.00 0.00 3.51
651 715 5.536554 TTCTCTGATCAAAATTCGTCTGC 57.463 39.130 0.00 0.00 0.00 4.26
652 716 3.614176 TCTCTGATCAAAATTCGTCTGCG 59.386 43.478 0.00 0.00 39.92 5.18
653 717 3.584834 TCTGATCAAAATTCGTCTGCGA 58.415 40.909 0.00 0.00 46.36 5.10
677 741 4.935352 TTTCCCCACAGAACTGAATTTG 57.065 40.909 8.87 0.00 0.00 2.32
681 745 3.191371 CCCCACAGAACTGAATTTGCTAC 59.809 47.826 8.87 0.00 0.00 3.58
683 747 3.498397 CCACAGAACTGAATTTGCTACGT 59.502 43.478 8.87 0.00 0.00 3.57
684 748 4.688879 CCACAGAACTGAATTTGCTACGTA 59.311 41.667 8.87 0.00 0.00 3.57
685 749 5.389516 CCACAGAACTGAATTTGCTACGTAC 60.390 44.000 8.87 0.00 0.00 3.67
686 750 4.689345 ACAGAACTGAATTTGCTACGTACC 59.311 41.667 8.87 0.00 0.00 3.34
688 752 2.613691 ACTGAATTTGCTACGTACCCG 58.386 47.619 0.00 0.00 40.83 5.28
715 779 6.684609 AAAAATAAAAATGAACGCGTCCTC 57.315 33.333 14.44 8.36 0.00 3.71
716 780 3.651562 ATAAAAATGAACGCGTCCTCG 57.348 42.857 14.44 0.00 40.37 4.63
726 790 2.104331 CGTCCTCGCGCAATACCT 59.896 61.111 8.75 0.00 0.00 3.08
761 825 3.267597 AAACGCGCCAGCCAATGAC 62.268 57.895 5.73 0.00 41.18 3.06
767 831 3.057548 CCAGCCAATGACAGCGCA 61.058 61.111 11.47 0.00 0.00 6.09
770 834 4.487412 GCCAATGACAGCGCAGGC 62.487 66.667 11.47 3.55 40.37 4.85
773 837 3.058160 AATGACAGCGCAGGCACC 61.058 61.111 11.83 0.00 43.41 5.01
774 838 3.557903 AATGACAGCGCAGGCACCT 62.558 57.895 11.83 0.00 43.41 4.00
799 895 1.003580 AGCCAATCACGTCACAGGAAT 59.996 47.619 0.00 0.00 0.00 3.01
809 905 1.149174 CACAGGAATCCCCATCCCG 59.851 63.158 0.00 0.00 37.71 5.14
873 971 1.760086 CAGCCGTCCATCTCCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
892 990 0.608035 TGATCCAACGCCCCAAACTC 60.608 55.000 0.00 0.00 0.00 3.01
931 1050 1.984026 CGCCTTCTGCCCCCAAAAT 60.984 57.895 0.00 0.00 36.24 1.82
995 1469 4.742201 CGCCTCACCACCAGACCG 62.742 72.222 0.00 0.00 0.00 4.79
998 1475 2.047844 CTCACCACCAGACCGCAG 60.048 66.667 0.00 0.00 0.00 5.18
1054 1539 0.118346 TCAAACCCTAGCCTCCTCCA 59.882 55.000 0.00 0.00 0.00 3.86
1055 1540 0.253327 CAAACCCTAGCCTCCTCCAC 59.747 60.000 0.00 0.00 0.00 4.02
1061 1546 2.553438 CTAGCCTCCTCCACCCCCTT 62.553 65.000 0.00 0.00 0.00 3.95
1524 2012 3.197766 TCTTGCGATCTGGTTGTAAGGAT 59.802 43.478 6.21 0.00 35.35 3.24
1525 2013 2.905075 TGCGATCTGGTTGTAAGGATG 58.095 47.619 0.00 0.00 0.00 3.51
1531 2023 1.812571 CTGGTTGTAAGGATGTGTGCC 59.187 52.381 0.00 0.00 0.00 5.01
1539 2031 1.602323 GGATGTGTGCCGGGTTTCA 60.602 57.895 2.18 0.00 0.00 2.69
1558 2050 7.201644 GGGTTTCACTGTAGTGTTGATATGATG 60.202 40.741 11.44 0.00 45.76 3.07
1562 2054 8.255394 TCACTGTAGTGTTGATATGATGTTTG 57.745 34.615 11.44 0.00 45.76 2.93
1563 2055 7.334171 TCACTGTAGTGTTGATATGATGTTTGG 59.666 37.037 11.44 0.00 45.76 3.28
1567 2059 6.748333 AGTGTTGATATGATGTTTGGTCTG 57.252 37.500 0.00 0.00 0.00 3.51
1570 2062 5.415389 TGTTGATATGATGTTTGGTCTGGTG 59.585 40.000 0.00 0.00 0.00 4.17
1571 2063 5.434182 TGATATGATGTTTGGTCTGGTGA 57.566 39.130 0.00 0.00 0.00 4.02
1578 2075 4.008074 TGTTTGGTCTGGTGAGATCTTC 57.992 45.455 0.00 0.00 29.65 2.87
1586 2083 1.487976 TGGTGAGATCTTCCCTGATGC 59.512 52.381 13.09 0.00 0.00 3.91
1592 2091 2.170187 AGATCTTCCCTGATGCTGTGAC 59.830 50.000 0.00 0.00 0.00 3.67
1593 2092 0.615331 TCTTCCCTGATGCTGTGACC 59.385 55.000 0.00 0.00 0.00 4.02
1600 2099 2.619849 CCTGATGCTGTGACCCTGAAAT 60.620 50.000 0.00 0.00 0.00 2.17
1602 2101 1.747355 GATGCTGTGACCCTGAAATGG 59.253 52.381 0.00 0.00 0.00 3.16
1606 2105 2.424956 GCTGTGACCCTGAAATGGAATC 59.575 50.000 0.00 0.00 0.00 2.52
1609 2108 0.657840 GACCCTGAAATGGAATCGCG 59.342 55.000 0.00 0.00 0.00 5.87
1620 2119 4.701956 ATGGAATCGCGAATGAAAAGTT 57.298 36.364 15.24 0.00 0.00 2.66
1631 2130 7.329962 TCGCGAATGAAAAGTTCAGTTATCTTA 59.670 33.333 6.20 0.00 43.98 2.10
1632 2131 8.116753 CGCGAATGAAAAGTTCAGTTATCTTAT 58.883 33.333 0.00 0.00 43.98 1.73
1634 2133 9.214953 CGAATGAAAAGTTCAGTTATCTTATGC 57.785 33.333 0.00 0.00 43.98 3.14
1638 2137 9.013229 TGAAAAGTTCAGTTATCTTATGCATGT 57.987 29.630 10.16 0.00 34.08 3.21
1639 2138 9.495754 GAAAAGTTCAGTTATCTTATGCATGTC 57.504 33.333 10.16 0.00 0.00 3.06
1644 2146 6.877236 TCAGTTATCTTATGCATGTCTGTCA 58.123 36.000 10.16 0.00 0.00 3.58
1658 2160 3.565063 TGTCTGTCATGTGGTGTCATTTG 59.435 43.478 0.00 0.00 0.00 2.32
1662 2164 4.930963 TGTCATGTGGTGTCATTTGTTTC 58.069 39.130 0.00 0.00 0.00 2.78
1667 2169 1.336440 TGGTGTCATTTGTTTCCTGCG 59.664 47.619 0.00 0.00 0.00 5.18
1676 2178 6.858993 GTCATTTGTTTCCTGCGTAATTGTTA 59.141 34.615 0.00 0.00 0.00 2.41
1677 2179 7.380065 GTCATTTGTTTCCTGCGTAATTGTTAA 59.620 33.333 0.00 0.00 0.00 2.01
1678 2180 8.085296 TCATTTGTTTCCTGCGTAATTGTTAAT 58.915 29.630 0.00 0.00 0.00 1.40
1684 2186 9.382244 GTTTCCTGCGTAATTGTTAATATCATC 57.618 33.333 0.00 0.00 0.00 2.92
1687 2189 7.602644 TCCTGCGTAATTGTTAATATCATCTCC 59.397 37.037 0.00 0.00 0.00 3.71
1690 2192 7.931407 TGCGTAATTGTTAATATCATCTCCTGT 59.069 33.333 0.00 0.00 0.00 4.00
1707 2209 9.605275 CATCTCCTGTTAATTAGATGACTGAAA 57.395 33.333 7.58 0.00 45.29 2.69
1723 2225 5.163663 TGACTGAAAAACACATGACCTGAAC 60.164 40.000 0.00 0.00 0.00 3.18
1726 2228 6.772716 ACTGAAAAACACATGACCTGAACTAT 59.227 34.615 0.00 0.00 0.00 2.12
1740 2280 4.530388 CTGAACTATTGTTGCACACTGTG 58.470 43.478 6.19 6.19 36.39 3.66
1754 2294 1.270550 CACTGTGGCTTGGATTTGGTC 59.729 52.381 0.00 0.00 0.00 4.02
1764 2304 5.393461 GGCTTGGATTTGGTCATTCTGTTAG 60.393 44.000 0.00 0.00 0.00 2.34
1770 2310 3.334583 TGGTCATTCTGTTAGTCTGCC 57.665 47.619 0.00 0.00 0.00 4.85
1775 2315 3.055819 TCATTCTGTTAGTCTGCCCTGTC 60.056 47.826 0.00 0.00 0.00 3.51
1805 2345 2.497138 TGGTTGCTGTGAGATTCAGTG 58.503 47.619 0.00 0.00 35.60 3.66
1808 2348 3.557054 GGTTGCTGTGAGATTCAGTGGTA 60.557 47.826 0.00 0.00 35.60 3.25
1821 2361 9.396022 GAGATTCAGTGGTATTTTTCCTATCAA 57.604 33.333 0.00 0.00 0.00 2.57
1854 2394 4.910195 ACACTATGAAAGGCAGATTGTCA 58.090 39.130 0.00 0.00 26.84 3.58
1865 2405 5.021458 AGGCAGATTGTCATTCCATTTTCT 58.979 37.500 0.00 0.00 0.00 2.52
1866 2406 6.189859 AGGCAGATTGTCATTCCATTTTCTA 58.810 36.000 0.00 0.00 0.00 2.10
1868 2408 6.268566 GCAGATTGTCATTCCATTTTCTACC 58.731 40.000 0.00 0.00 0.00 3.18
1871 2411 7.121759 CAGATTGTCATTCCATTTTCTACCTGT 59.878 37.037 0.00 0.00 0.00 4.00
1872 2412 6.817765 TTGTCATTCCATTTTCTACCTGTC 57.182 37.500 0.00 0.00 0.00 3.51
1873 2413 4.935205 TGTCATTCCATTTTCTACCTGTCG 59.065 41.667 0.00 0.00 0.00 4.35
1874 2414 5.175859 GTCATTCCATTTTCTACCTGTCGA 58.824 41.667 0.00 0.00 0.00 4.20
1875 2415 5.292101 GTCATTCCATTTTCTACCTGTCGAG 59.708 44.000 0.00 0.00 0.00 4.04
1876 2416 5.186992 TCATTCCATTTTCTACCTGTCGAGA 59.813 40.000 0.00 0.00 0.00 4.04
1877 2417 5.477607 TTCCATTTTCTACCTGTCGAGAA 57.522 39.130 0.00 0.00 0.00 2.87
1878 2418 5.073311 TCCATTTTCTACCTGTCGAGAAG 57.927 43.478 0.00 0.00 33.38 2.85
1879 2419 4.081642 TCCATTTTCTACCTGTCGAGAAGG 60.082 45.833 11.72 11.72 40.93 3.46
1880 2420 3.314541 TTTTCTACCTGTCGAGAAGGC 57.685 47.619 12.97 0.00 38.48 4.35
1881 2421 1.919240 TTCTACCTGTCGAGAAGGCA 58.081 50.000 12.97 0.97 38.48 4.75
1882 2422 1.919240 TCTACCTGTCGAGAAGGCAA 58.081 50.000 12.97 2.65 38.48 4.52
1883 2423 1.819288 TCTACCTGTCGAGAAGGCAAG 59.181 52.381 12.97 10.92 38.48 4.01
1884 2424 1.819288 CTACCTGTCGAGAAGGCAAGA 59.181 52.381 12.97 0.00 38.48 3.02
1885 2425 0.605589 ACCTGTCGAGAAGGCAAGAG 59.394 55.000 12.97 0.00 38.48 2.85
1886 2426 0.108424 CCTGTCGAGAAGGCAAGAGG 60.108 60.000 1.24 0.00 31.91 3.69
1887 2427 0.108424 CTGTCGAGAAGGCAAGAGGG 60.108 60.000 0.00 0.00 31.91 4.30
1888 2428 1.448717 GTCGAGAAGGCAAGAGGGC 60.449 63.158 0.00 0.00 43.80 5.19
1897 2437 2.035312 CAAGAGGGCTTGGCTGCT 59.965 61.111 0.00 0.00 46.13 4.24
1898 2438 1.605738 CAAGAGGGCTTGGCTGCTT 60.606 57.895 0.00 0.00 46.13 3.91
1899 2439 1.605738 AAGAGGGCTTGGCTGCTTG 60.606 57.895 0.00 0.00 31.83 4.01
1900 2440 2.034687 GAGGGCTTGGCTGCTTGA 59.965 61.111 0.00 0.00 0.00 3.02
1921 2461 2.045524 GGCAGGATGAGAAGGAGATGA 58.954 52.381 0.00 0.00 39.69 2.92
1923 2463 3.118112 GGCAGGATGAGAAGGAGATGAAA 60.118 47.826 0.00 0.00 39.69 2.69
1927 2467 4.104420 AGGATGAGAAGGAGATGAAATGGG 59.896 45.833 0.00 0.00 0.00 4.00
1953 2493 2.228582 TGATCTGTTGAAACCATTGCCG 59.771 45.455 0.00 0.00 0.00 5.69
1982 2522 0.385974 GGCAATGAACACGAGCACAC 60.386 55.000 0.00 0.00 0.00 3.82
1993 2535 3.056536 ACACGAGCACACTGTCTGATATT 60.057 43.478 0.00 0.00 0.00 1.28
2054 2596 6.018098 CCTTGCTTTGCAGTTCTATAGAGATG 60.018 42.308 2.02 7.15 40.61 2.90
2091 2633 6.070596 TCAGATCTCTTTCAGTTTAGGCATCA 60.071 38.462 0.00 0.00 0.00 3.07
2093 2635 7.282675 CAGATCTCTTTCAGTTTAGGCATCAAT 59.717 37.037 0.00 0.00 0.00 2.57
2099 2641 4.870636 TCAGTTTAGGCATCAATGGGAAT 58.129 39.130 0.00 0.00 0.00 3.01
2101 2643 4.646040 CAGTTTAGGCATCAATGGGAATGA 59.354 41.667 0.00 0.00 0.00 2.57
2118 2660 5.107133 GGAATGATCAGAAACAATTGCCTG 58.893 41.667 5.05 10.59 0.00 4.85
2133 2675 7.370383 ACAATTGCCTGTTCATAACTTTACTG 58.630 34.615 5.05 0.00 0.00 2.74
2145 2687 1.073763 ACTTTACTGGCAGTGCATGGA 59.926 47.619 29.65 5.87 0.00 3.41
2160 2702 0.625091 ATGGATTTGGGTCCCGGGTA 60.625 55.000 22.86 4.13 37.48 3.69
2232 2775 0.322975 GATGTGTGCTGGGTGTCTCT 59.677 55.000 0.00 0.00 0.00 3.10
2233 2776 0.035881 ATGTGTGCTGGGTGTCTCTG 59.964 55.000 0.00 0.00 0.00 3.35
2261 2804 4.411256 TGATATGATGCTTGCTGTCTGA 57.589 40.909 0.00 0.00 0.00 3.27
2299 2848 3.758023 TGACGATGAAATGAAGTGGCAAT 59.242 39.130 0.00 0.00 0.00 3.56
2305 2854 6.183360 CGATGAAATGAAGTGGCAATGAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
2314 2863 4.646492 AGTGGCAATGAAAAGTTCAGTTCT 59.354 37.500 0.00 0.00 43.98 3.01
2352 2901 2.290367 TCTGTGGTCTCATTTGTTTGCG 59.710 45.455 0.00 0.00 0.00 4.85
2358 2907 3.119495 GGTCTCATTTGTTTGCGGCTTAT 60.119 43.478 0.00 0.00 0.00 1.73
2442 2992 6.426633 TGTTGTACAGATGGTATTGAACACTG 59.573 38.462 0.00 0.00 33.76 3.66
2446 2996 8.151596 TGTACAGATGGTATTGAACACTGTTAA 58.848 33.333 0.00 0.00 38.49 2.01
2448 2998 7.871853 ACAGATGGTATTGAACACTGTTAAAC 58.128 34.615 0.00 0.00 36.11 2.01
2449 2999 7.040686 ACAGATGGTATTGAACACTGTTAAACC 60.041 37.037 0.00 1.72 36.11 3.27
2452 3002 7.648039 TGGTATTGAACACTGTTAAACCTTT 57.352 32.000 12.29 0.00 0.00 3.11
2454 3004 7.339721 TGGTATTGAACACTGTTAAACCTTTGA 59.660 33.333 12.29 0.00 0.00 2.69
2467 3036 9.137459 TGTTAAACCTTTGATTTGGTGATTCTA 57.863 29.630 0.00 0.00 36.57 2.10
2486 3055 8.874156 TGATTCTATTGGTCTGCTCTGTTATAT 58.126 33.333 0.00 0.00 0.00 0.86
2487 3056 9.717942 GATTCTATTGGTCTGCTCTGTTATATT 57.282 33.333 0.00 0.00 0.00 1.28
2528 3097 8.156820 TGATATTCAGTTGTCTTTTCTCCTTCA 58.843 33.333 0.00 0.00 0.00 3.02
2543 3112 8.575649 TTTCTCCTTCAGGAAAATTATGTACC 57.424 34.615 0.00 0.00 44.91 3.34
2558 3127 0.458716 GTACCTGCGACTCAGAAGCC 60.459 60.000 0.00 0.00 45.72 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.462483 GGCCTAAGGAAACATGATTTGTGA 59.538 41.667 0.00 0.00 38.99 3.58
1 2 4.675146 CGGCCTAAGGAAACATGATTTGTG 60.675 45.833 0.00 0.00 38.99 3.33
2 3 3.443681 CGGCCTAAGGAAACATGATTTGT 59.556 43.478 0.00 0.00 41.53 2.83
3 4 3.443681 ACGGCCTAAGGAAACATGATTTG 59.556 43.478 0.00 0.00 0.00 2.32
4 5 3.694566 GACGGCCTAAGGAAACATGATTT 59.305 43.478 0.00 0.00 0.00 2.17
5 6 3.054361 AGACGGCCTAAGGAAACATGATT 60.054 43.478 0.00 0.00 0.00 2.57
6 7 2.505819 AGACGGCCTAAGGAAACATGAT 59.494 45.455 0.00 0.00 0.00 2.45
7 8 1.906574 AGACGGCCTAAGGAAACATGA 59.093 47.619 0.00 0.00 0.00 3.07
8 9 2.009774 CAGACGGCCTAAGGAAACATG 58.990 52.381 0.00 0.00 0.00 3.21
9 10 1.906574 TCAGACGGCCTAAGGAAACAT 59.093 47.619 0.00 0.00 0.00 2.71
10 11 1.001633 GTCAGACGGCCTAAGGAAACA 59.998 52.381 0.00 0.00 0.00 2.83
11 12 1.275573 AGTCAGACGGCCTAAGGAAAC 59.724 52.381 0.00 0.00 0.00 2.78
12 13 1.640917 AGTCAGACGGCCTAAGGAAA 58.359 50.000 0.00 0.00 0.00 3.13
13 14 1.640917 AAGTCAGACGGCCTAAGGAA 58.359 50.000 0.00 0.00 0.00 3.36
14 15 1.640917 AAAGTCAGACGGCCTAAGGA 58.359 50.000 0.00 0.00 0.00 3.36
15 16 3.821421 ATAAAGTCAGACGGCCTAAGG 57.179 47.619 0.00 0.00 0.00 2.69
26 27 8.208718 TCATCCCGTTTTATGAATAAAGTCAG 57.791 34.615 0.00 0.00 34.13 3.51
65 66 8.463607 CGGAGGAGGAGATAGTAGATAATTTTC 58.536 40.741 0.00 0.00 0.00 2.29
68 69 7.034967 ACGGAGGAGGAGATAGTAGATAATT 57.965 40.000 0.00 0.00 0.00 1.40
70 71 6.451292 AACGGAGGAGGAGATAGTAGATAA 57.549 41.667 0.00 0.00 0.00 1.75
84 85 4.566004 TGTTTCATGTTCTAACGGAGGAG 58.434 43.478 0.00 0.00 0.00 3.69
91 95 6.304683 GCAAACCGTATGTTTCATGTTCTAAC 59.695 38.462 0.00 0.00 45.35 2.34
92 96 6.375377 GCAAACCGTATGTTTCATGTTCTAA 58.625 36.000 0.00 0.00 45.35 2.10
122 126 1.867233 GATGTCCCGTCATACATGTGC 59.133 52.381 9.11 0.00 36.48 4.57
135 139 9.620259 AAATTAGAAAGAAGATAGTGATGTCCC 57.380 33.333 0.00 0.00 0.00 4.46
207 248 0.257039 GGGATGACATGCCCTGTTCT 59.743 55.000 14.83 0.00 41.31 3.01
220 261 7.231317 GGAAAAGCAAATGATGTATAGGGATGA 59.769 37.037 0.00 0.00 0.00 2.92
224 265 6.713762 TGGAAAAGCAAATGATGTATAGGG 57.286 37.500 0.00 0.00 0.00 3.53
233 274 4.797471 CTTCGTCATGGAAAAGCAAATGA 58.203 39.130 0.00 0.00 0.00 2.57
240 290 1.798223 TCGTGCTTCGTCATGGAAAAG 59.202 47.619 0.00 0.00 40.80 2.27
263 313 3.064408 TCATACGTGGTACGAGCTAAGTG 59.936 47.826 8.48 0.00 46.05 3.16
264 314 3.273434 TCATACGTGGTACGAGCTAAGT 58.727 45.455 8.48 0.00 46.05 2.24
265 315 3.957671 TCATACGTGGTACGAGCTAAG 57.042 47.619 8.48 0.00 46.05 2.18
266 316 4.096833 ACATTCATACGTGGTACGAGCTAA 59.903 41.667 8.48 0.00 46.05 3.09
267 317 3.628942 ACATTCATACGTGGTACGAGCTA 59.371 43.478 8.48 0.00 46.05 3.32
268 318 2.426024 ACATTCATACGTGGTACGAGCT 59.574 45.455 8.48 0.00 46.05 4.09
269 319 2.805845 ACATTCATACGTGGTACGAGC 58.194 47.619 8.48 0.00 46.05 5.03
270 320 4.417506 TGAACATTCATACGTGGTACGAG 58.582 43.478 8.48 0.00 36.56 4.18
278 328 9.773328 CACTTGAATAAATGAACATTCATACGT 57.227 29.630 7.52 0.00 46.60 3.57
279 329 9.225201 CCACTTGAATAAATGAACATTCATACG 57.775 33.333 7.52 0.00 46.60 3.06
318 369 6.215845 CAGTTGTATTTCTTTCCCTGGTTTG 58.784 40.000 0.00 0.00 0.00 2.93
354 405 6.013379 TCCTTGAGTGTCCAGAGATACATTTT 60.013 38.462 0.00 0.00 36.63 1.82
389 448 0.610785 GCAAATCAAAGGGACCCCGA 60.611 55.000 7.00 1.61 41.95 5.14
390 449 0.897863 TGCAAATCAAAGGGACCCCG 60.898 55.000 7.00 0.00 41.95 5.73
391 450 0.897621 CTGCAAATCAAAGGGACCCC 59.102 55.000 7.00 1.17 0.00 4.95
401 460 8.991026 CCTACATTTCAAAAATTCTGCAAATCA 58.009 29.630 0.00 0.00 0.00 2.57
404 463 8.954950 TTCCTACATTTCAAAAATTCTGCAAA 57.045 26.923 0.00 0.00 0.00 3.68
432 491 9.643693 CATGGCACTTTAATCTTGTATTTTTCT 57.356 29.630 0.00 0.00 0.00 2.52
466 530 1.337071 CTCACTAGCTTCGCGGGATTA 59.663 52.381 6.13 0.00 0.00 1.75
469 533 3.064987 GCTCACTAGCTTCGCGGGA 62.065 63.158 6.13 0.00 45.85 5.14
492 556 3.376234 TGACGTCGAATACTCGGAATTCT 59.624 43.478 11.62 0.00 45.49 2.40
493 557 3.481388 GTGACGTCGAATACTCGGAATTC 59.519 47.826 11.62 0.00 45.49 2.17
498 562 1.395954 TCTGTGACGTCGAATACTCGG 59.604 52.381 11.62 1.00 45.49 4.63
499 563 2.800694 TCTGTGACGTCGAATACTCG 57.199 50.000 11.62 0.00 46.87 4.18
526 590 9.965824 CACTCAAACCTTTTTATACAATGTCTT 57.034 29.630 0.00 0.00 0.00 3.01
527 591 8.576442 CCACTCAAACCTTTTTATACAATGTCT 58.424 33.333 0.00 0.00 0.00 3.41
528 592 8.573035 TCCACTCAAACCTTTTTATACAATGTC 58.427 33.333 0.00 0.00 0.00 3.06
529 593 8.472007 TCCACTCAAACCTTTTTATACAATGT 57.528 30.769 0.00 0.00 0.00 2.71
530 594 9.357652 CATCCACTCAAACCTTTTTATACAATG 57.642 33.333 0.00 0.00 0.00 2.82
605 669 8.613922 AAACCTCATATGAATTTTGGAGGATT 57.386 30.769 13.39 4.07 43.58 3.01
611 675 8.284945 TCAGAGAAACCTCATATGAATTTTGG 57.715 34.615 13.44 10.17 33.16 3.28
626 690 6.310197 CAGACGAATTTTGATCAGAGAAACC 58.690 40.000 0.00 0.00 0.00 3.27
627 691 5.792468 GCAGACGAATTTTGATCAGAGAAAC 59.208 40.000 0.00 0.00 0.00 2.78
645 709 0.168128 GTGGGGAAAATTCGCAGACG 59.832 55.000 11.62 0.00 41.42 4.18
646 710 1.200020 CTGTGGGGAAAATTCGCAGAC 59.800 52.381 11.62 8.11 40.32 3.51
647 711 1.073125 TCTGTGGGGAAAATTCGCAGA 59.927 47.619 11.62 3.86 43.15 4.26
648 712 1.533625 TCTGTGGGGAAAATTCGCAG 58.466 50.000 11.62 0.00 41.42 5.18
649 713 1.611491 GTTCTGTGGGGAAAATTCGCA 59.389 47.619 11.62 0.00 41.42 5.10
650 714 1.886542 AGTTCTGTGGGGAAAATTCGC 59.113 47.619 1.88 1.88 39.19 4.70
651 715 3.146066 TCAGTTCTGTGGGGAAAATTCG 58.854 45.455 0.00 0.00 0.00 3.34
652 716 5.728637 ATTCAGTTCTGTGGGGAAAATTC 57.271 39.130 0.00 0.00 0.00 2.17
653 717 6.290605 CAAATTCAGTTCTGTGGGGAAAATT 58.709 36.000 0.00 0.00 0.00 1.82
654 718 5.742838 GCAAATTCAGTTCTGTGGGGAAAAT 60.743 40.000 0.00 0.00 0.00 1.82
655 719 4.442753 GCAAATTCAGTTCTGTGGGGAAAA 60.443 41.667 0.00 0.00 0.00 2.29
659 723 2.242043 AGCAAATTCAGTTCTGTGGGG 58.758 47.619 0.00 0.00 0.00 4.96
692 756 5.341196 CGAGGACGCGTTCATTTTTATTTTT 59.659 36.000 21.79 0.00 0.00 1.94
693 757 4.849383 CGAGGACGCGTTCATTTTTATTTT 59.151 37.500 21.79 0.00 0.00 1.82
694 758 4.399978 CGAGGACGCGTTCATTTTTATTT 58.600 39.130 21.79 0.00 0.00 1.40
695 759 3.998522 CGAGGACGCGTTCATTTTTATT 58.001 40.909 21.79 0.00 0.00 1.40
696 760 3.651562 CGAGGACGCGTTCATTTTTAT 57.348 42.857 21.79 0.00 0.00 1.40
709 773 2.104331 AGGTATTGCGCGAGGACG 59.896 61.111 12.10 0.00 42.93 4.79
710 774 2.526120 GCAGGTATTGCGCGAGGAC 61.526 63.158 12.10 3.57 44.09 3.85
711 775 2.202878 GCAGGTATTGCGCGAGGA 60.203 61.111 12.10 0.00 44.09 3.71
719 783 1.369091 GCACACTCGGGCAGGTATTG 61.369 60.000 0.00 0.00 0.00 1.90
720 784 1.078426 GCACACTCGGGCAGGTATT 60.078 57.895 0.00 0.00 0.00 1.89
721 785 2.290287 TGCACACTCGGGCAGGTAT 61.290 57.895 0.00 0.00 34.58 2.73
722 786 2.920384 TGCACACTCGGGCAGGTA 60.920 61.111 0.00 0.00 34.58 3.08
723 787 4.626081 GTGCACACTCGGGCAGGT 62.626 66.667 13.17 0.00 41.35 4.00
731 795 2.248431 GCGTTTCGGTGCACACTC 59.752 61.111 20.43 0.00 0.00 3.51
732 796 3.636043 CGCGTTTCGGTGCACACT 61.636 61.111 20.43 0.00 33.78 3.55
750 814 3.047718 CTGCGCTGTCATTGGCTGG 62.048 63.158 9.73 0.00 0.00 4.85
751 815 2.483745 CTGCGCTGTCATTGGCTG 59.516 61.111 9.73 0.00 0.00 4.85
752 816 2.749044 CCTGCGCTGTCATTGGCT 60.749 61.111 9.73 0.00 0.00 4.75
753 817 4.487412 GCCTGCGCTGTCATTGGC 62.487 66.667 9.73 7.22 0.00 4.52
754 818 3.057548 TGCCTGCGCTGTCATTGG 61.058 61.111 9.73 0.53 35.36 3.16
755 819 2.177531 GTGCCTGCGCTGTCATTG 59.822 61.111 9.73 0.00 35.36 2.82
756 820 3.058160 GGTGCCTGCGCTGTCATT 61.058 61.111 9.73 0.00 35.36 2.57
770 834 2.046023 TGATTGGCTGGCGAGGTG 60.046 61.111 0.00 0.00 0.00 4.00
773 837 2.434884 ACGTGATTGGCTGGCGAG 60.435 61.111 0.00 0.00 0.00 5.03
774 838 2.434185 GACGTGATTGGCTGGCGA 60.434 61.111 0.00 0.00 0.00 5.54
873 971 0.608035 GAGTTTGGGGCGTTGGATCA 60.608 55.000 0.00 0.00 0.00 2.92
892 990 3.151022 GCTGGAGGAGGGAGACGG 61.151 72.222 0.00 0.00 0.00 4.79
918 1016 1.357137 GGGAAAATTTTGGGGGCAGA 58.643 50.000 8.47 0.00 0.00 4.26
920 1018 0.401979 TGGGGAAAATTTTGGGGGCA 60.402 50.000 8.47 0.00 0.00 5.36
921 1019 0.998928 ATGGGGAAAATTTTGGGGGC 59.001 50.000 8.47 0.00 0.00 5.80
927 1046 1.578897 CGGGGGATGGGGAAAATTTT 58.421 50.000 2.28 2.28 0.00 1.82
931 1050 4.068887 GGCGGGGGATGGGGAAAA 62.069 66.667 0.00 0.00 0.00 2.29
959 1078 1.880646 CGCGGGGTTAAATAGATGGGG 60.881 57.143 0.00 0.00 0.00 4.96
963 1082 0.763035 AGGCGCGGGGTTAAATAGAT 59.237 50.000 8.83 0.00 0.00 1.98
964 1083 0.105408 GAGGCGCGGGGTTAAATAGA 59.895 55.000 8.83 0.00 0.00 1.98
995 1469 1.509923 GGGATTTGAGCTGTGCTGC 59.490 57.895 0.00 0.00 39.88 5.25
998 1475 1.304381 TGGGGGATTTGAGCTGTGC 60.304 57.895 0.00 0.00 0.00 4.57
1031 1508 0.253327 GGAGGCTAGGGTTTGAGTGG 59.747 60.000 0.00 0.00 0.00 4.00
1054 1539 2.041265 ATCGGAGCTGAAGGGGGT 59.959 61.111 0.00 0.00 0.00 4.95
1055 1540 2.507944 CATCGGAGCTGAAGGGGG 59.492 66.667 0.00 0.00 0.00 5.40
1524 2012 1.821759 CAGTGAAACCCGGCACACA 60.822 57.895 11.77 0.00 37.80 3.72
1525 2013 0.533308 TACAGTGAAACCCGGCACAC 60.533 55.000 11.77 10.50 37.80 3.82
1539 2031 7.168219 ACCAAACATCATATCAACACTACAGT 58.832 34.615 0.00 0.00 0.00 3.55
1558 2050 3.339141 GGAAGATCTCACCAGACCAAAC 58.661 50.000 12.28 0.00 0.00 2.93
1562 2054 1.484240 CAGGGAAGATCTCACCAGACC 59.516 57.143 15.67 3.20 0.00 3.85
1563 2055 2.461695 TCAGGGAAGATCTCACCAGAC 58.538 52.381 15.67 3.11 0.00 3.51
1567 2059 1.767681 AGCATCAGGGAAGATCTCACC 59.232 52.381 0.00 1.08 0.00 4.02
1570 2062 2.433604 TCACAGCATCAGGGAAGATCTC 59.566 50.000 0.00 0.00 0.00 2.75
1571 2063 2.170187 GTCACAGCATCAGGGAAGATCT 59.830 50.000 0.00 0.00 0.00 2.75
1578 2075 1.077930 CAGGGTCACAGCATCAGGG 60.078 63.158 0.00 0.00 0.00 4.45
1586 2083 2.679837 CGATTCCATTTCAGGGTCACAG 59.320 50.000 0.00 0.00 0.00 3.66
1592 2091 1.378531 TTCGCGATTCCATTTCAGGG 58.621 50.000 10.88 0.00 0.00 4.45
1593 2092 2.613595 TCATTCGCGATTCCATTTCAGG 59.386 45.455 10.88 0.00 0.00 3.86
1600 2099 3.500299 TGAACTTTTCATTCGCGATTCCA 59.500 39.130 10.88 0.00 34.08 3.53
1602 2101 4.712763 ACTGAACTTTTCATTCGCGATTC 58.287 39.130 10.88 8.84 39.30 2.52
1606 2105 5.858475 AGATAACTGAACTTTTCATTCGCG 58.142 37.500 0.00 0.00 39.30 5.87
1620 2119 6.877236 TGACAGACATGCATAAGATAACTGA 58.123 36.000 0.00 0.00 0.00 3.41
1635 2134 3.708403 ATGACACCACATGACAGACAT 57.292 42.857 0.00 0.00 36.41 3.06
1636 2135 3.490439 AATGACACCACATGACAGACA 57.510 42.857 0.00 0.00 36.41 3.41
1637 2136 3.565482 ACAAATGACACCACATGACAGAC 59.435 43.478 0.00 0.00 36.41 3.51
1638 2137 3.819368 ACAAATGACACCACATGACAGA 58.181 40.909 0.00 0.00 36.41 3.41
1639 2138 4.572985 AACAAATGACACCACATGACAG 57.427 40.909 0.00 0.00 36.41 3.51
1644 2146 3.243839 GCAGGAAACAAATGACACCACAT 60.244 43.478 0.00 0.00 0.00 3.21
1658 2160 9.382244 GATGATATTAACAATTACGCAGGAAAC 57.618 33.333 0.00 0.00 0.00 2.78
1662 2164 7.604164 AGGAGATGATATTAACAATTACGCAGG 59.396 37.037 0.00 0.00 0.00 4.85
1692 2194 8.299570 GGTCATGTGTTTTTCAGTCATCTAATT 58.700 33.333 0.00 0.00 0.00 1.40
1701 2203 4.949856 AGTTCAGGTCATGTGTTTTTCAGT 59.050 37.500 0.00 0.00 0.00 3.41
1702 2204 5.505173 AGTTCAGGTCATGTGTTTTTCAG 57.495 39.130 0.00 0.00 0.00 3.02
1707 2209 6.735694 GCAACAATAGTTCAGGTCATGTGTTT 60.736 38.462 0.00 0.00 35.28 2.83
1740 2280 2.827921 ACAGAATGACCAAATCCAAGCC 59.172 45.455 0.00 0.00 39.69 4.35
1754 2294 3.265791 GACAGGGCAGACTAACAGAATG 58.734 50.000 0.00 0.00 46.00 2.67
1764 2304 3.064900 AGAAGAAATGACAGGGCAGAC 57.935 47.619 0.00 0.00 0.00 3.51
1770 2310 3.571401 AGCAACCAAGAAGAAATGACAGG 59.429 43.478 0.00 0.00 0.00 4.00
1775 2315 4.276678 TCTCACAGCAACCAAGAAGAAATG 59.723 41.667 0.00 0.00 0.00 2.32
1821 2361 8.630054 TGCCTTTCATAGTGTACAAAATTACT 57.370 30.769 0.00 0.00 0.00 2.24
1840 2380 5.750352 AAATGGAATGACAATCTGCCTTT 57.250 34.783 0.00 0.00 0.00 3.11
1854 2394 5.677319 TCTCGACAGGTAGAAAATGGAAT 57.323 39.130 0.00 0.00 0.00 3.01
1865 2405 1.819288 CTCTTGCCTTCTCGACAGGTA 59.181 52.381 7.58 0.82 33.40 3.08
1866 2406 0.605589 CTCTTGCCTTCTCGACAGGT 59.394 55.000 7.58 0.00 33.40 4.00
1868 2408 0.108424 CCCTCTTGCCTTCTCGACAG 60.108 60.000 0.00 0.00 0.00 3.51
1871 2411 1.194781 AAGCCCTCTTGCCTTCTCGA 61.195 55.000 0.00 0.00 0.00 4.04
1872 2412 1.023513 CAAGCCCTCTTGCCTTCTCG 61.024 60.000 0.00 0.00 42.66 4.04
1873 2413 0.679321 CCAAGCCCTCTTGCCTTCTC 60.679 60.000 0.00 0.00 46.38 2.87
1874 2414 1.381851 CCAAGCCCTCTTGCCTTCT 59.618 57.895 0.00 0.00 46.38 2.85
1875 2415 2.346541 GCCAAGCCCTCTTGCCTTC 61.347 63.158 0.00 0.00 46.38 3.46
1876 2416 2.283460 GCCAAGCCCTCTTGCCTT 60.283 61.111 0.00 0.00 46.38 4.35
1877 2417 3.263259 AGCCAAGCCCTCTTGCCT 61.263 61.111 0.00 0.00 46.38 4.75
1878 2418 3.066814 CAGCCAAGCCCTCTTGCC 61.067 66.667 0.00 0.00 46.38 4.52
1879 2419 3.756727 GCAGCCAAGCCCTCTTGC 61.757 66.667 0.00 0.00 46.38 4.01
1881 2421 1.605738 CAAGCAGCCAAGCCCTCTT 60.606 57.895 0.00 0.00 34.23 2.85
1882 2422 2.035312 CAAGCAGCCAAGCCCTCT 59.965 61.111 0.00 0.00 34.23 3.69
1883 2423 2.034687 TCAAGCAGCCAAGCCCTC 59.965 61.111 0.00 0.00 34.23 4.30
1884 2424 2.035312 CTCAAGCAGCCAAGCCCT 59.965 61.111 0.00 0.00 34.23 5.19
1885 2425 3.066814 CCTCAAGCAGCCAAGCCC 61.067 66.667 0.00 0.00 34.23 5.19
1886 2426 3.756727 GCCTCAAGCAGCCAAGCC 61.757 66.667 0.00 0.00 42.97 4.35
1895 2435 1.666054 CTTCTCATCCTGCCTCAAGC 58.334 55.000 0.00 0.00 44.14 4.01
1896 2436 1.836166 TCCTTCTCATCCTGCCTCAAG 59.164 52.381 0.00 0.00 0.00 3.02
1897 2437 1.836166 CTCCTTCTCATCCTGCCTCAA 59.164 52.381 0.00 0.00 0.00 3.02
1898 2438 1.007600 TCTCCTTCTCATCCTGCCTCA 59.992 52.381 0.00 0.00 0.00 3.86
1899 2439 1.786937 TCTCCTTCTCATCCTGCCTC 58.213 55.000 0.00 0.00 0.00 4.70
1900 2440 2.048601 CATCTCCTTCTCATCCTGCCT 58.951 52.381 0.00 0.00 0.00 4.75
1907 2447 5.444176 GAACCCATTTCATCTCCTTCTCAT 58.556 41.667 0.00 0.00 33.94 2.90
1921 2461 4.387026 TCAACAGATCAGGAACCCATTT 57.613 40.909 0.00 0.00 0.00 2.32
1923 2463 4.082125 GTTTCAACAGATCAGGAACCCAT 58.918 43.478 0.00 0.00 0.00 4.00
1927 2467 5.464168 CAATGGTTTCAACAGATCAGGAAC 58.536 41.667 0.00 0.00 0.00 3.62
1974 2514 4.045104 GGTAATATCAGACAGTGTGCTCG 58.955 47.826 0.00 0.00 0.00 5.03
1982 2522 6.644347 AGTTCACCTTGGTAATATCAGACAG 58.356 40.000 0.00 0.00 0.00 3.51
1993 2535 5.801380 GGATACAAGAAGTTCACCTTGGTA 58.199 41.667 5.50 0.00 42.86 3.25
2054 2596 4.399004 AGAGATCTGATTGCCACTGTAC 57.601 45.455 0.00 0.00 0.00 2.90
2091 2633 6.110707 GCAATTGTTTCTGATCATTCCCATT 58.889 36.000 7.40 0.00 0.00 3.16
2093 2635 4.081531 GGCAATTGTTTCTGATCATTCCCA 60.082 41.667 7.40 0.00 0.00 4.37
2099 2641 4.583907 TGAACAGGCAATTGTTTCTGATCA 59.416 37.500 21.75 21.75 41.15 2.92
2101 2643 5.733620 ATGAACAGGCAATTGTTTCTGAT 57.266 34.783 22.75 15.55 41.15 2.90
2118 2660 4.215399 TGCACTGCCAGTAAAGTTATGAAC 59.785 41.667 0.00 0.00 0.00 3.18
2133 2675 1.259840 ACCCAAATCCATGCACTGCC 61.260 55.000 0.00 0.00 0.00 4.85
2145 2687 0.625091 TCCATACCCGGGACCCAAAT 60.625 55.000 32.02 4.78 0.00 2.32
2160 2702 7.405292 TGATCCTTTGACTAGACAAAATCCAT 58.595 34.615 18.57 9.69 38.90 3.41
2212 2755 0.035317 GAGACACCCAGCACACATCA 59.965 55.000 0.00 0.00 0.00 3.07
2232 2775 5.295045 CAGCAAGCATCATATCAACACTACA 59.705 40.000 0.00 0.00 0.00 2.74
2233 2776 5.295292 ACAGCAAGCATCATATCAACACTAC 59.705 40.000 0.00 0.00 0.00 2.73
2261 2804 1.464608 CGTCACAACGCAGGAAATCAT 59.535 47.619 0.00 0.00 42.82 2.45
2282 2831 6.527423 ACTTTTCATTGCCACTTCATTTCAT 58.473 32.000 0.00 0.00 0.00 2.57
2299 2848 7.509141 TGCATCATAAGAACTGAACTTTTCA 57.491 32.000 0.00 0.00 38.17 2.69
2330 2879 3.607775 CGCAAACAAATGAGACCACAGAG 60.608 47.826 0.00 0.00 0.00 3.35
2331 2880 2.290367 CGCAAACAAATGAGACCACAGA 59.710 45.455 0.00 0.00 0.00 3.41
2336 2885 0.598065 AGCCGCAAACAAATGAGACC 59.402 50.000 0.00 0.00 0.00 3.85
2446 2996 7.235399 ACCAATAGAATCACCAAATCAAAGGTT 59.765 33.333 0.00 0.00 35.52 3.50
2448 2998 7.123247 AGACCAATAGAATCACCAAATCAAAGG 59.877 37.037 0.00 0.00 0.00 3.11
2449 2999 7.972277 CAGACCAATAGAATCACCAAATCAAAG 59.028 37.037 0.00 0.00 0.00 2.77
2452 3002 5.357878 GCAGACCAATAGAATCACCAAATCA 59.642 40.000 0.00 0.00 0.00 2.57
2454 3004 5.513233 AGCAGACCAATAGAATCACCAAAT 58.487 37.500 0.00 0.00 0.00 2.32
2467 3036 7.944729 ACAAAATATAACAGAGCAGACCAAT 57.055 32.000 0.00 0.00 0.00 3.16
2469 3038 7.309133 CCAAACAAAATATAACAGAGCAGACCA 60.309 37.037 0.00 0.00 0.00 4.02
2486 3055 4.870123 ATATCACAGCAGCCAAACAAAA 57.130 36.364 0.00 0.00 0.00 2.44
2487 3056 4.280425 TGAATATCACAGCAGCCAAACAAA 59.720 37.500 0.00 0.00 0.00 2.83
2528 3097 5.099042 AGTCGCAGGTACATAATTTTCCT 57.901 39.130 0.00 0.00 0.00 3.36
2543 3112 2.200067 CTATTGGCTTCTGAGTCGCAG 58.800 52.381 0.00 0.00 46.31 5.18
2558 3127 0.879400 CCCGAGCTCTGCTGCTATTG 60.879 60.000 12.85 0.00 44.17 1.90
2592 3161 3.110705 ACAGCAGGAATCCACTACTCAT 58.889 45.455 0.61 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.