Multiple sequence alignment - TraesCS6B01G036400

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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 TraesCS6B01G036400 chr6B 100.000 3623 0 0 1 3623 21286863 21283241 0.000000e+00 6691.0
1 TraesCS6B01G036400 chr6B 91.905 630 50 1 1 630 10409593 10408965 0.000000e+00 880.0
2 TraesCS6B01G036400 chr6B 91.746 630 51 1 1 630 10540017 10539389 0.000000e+00 874.0
3 TraesCS6B01G036400 chr6B 91.429 630 52 2 1 630 10474628 10474001 0.000000e+00 863.0
4 TraesCS6B01G036400 chr6D 89.940 2326 110 61 675 2936 11409946 11407681 0.000000e+00 2885.0
5 TraesCS6B01G036400 chr6A 86.777 1384 77 44 685 2028 12838499 12837182 0.000000e+00 1445.0
6 TraesCS6B01G036400 chr6A 95.135 925 24 11 2027 2937 12837139 12836222 0.000000e+00 1439.0
7 TraesCS6B01G036400 chr6A 95.476 641 27 2 1 640 614421733 614422372 0.000000e+00 1022.0
8 TraesCS6B01G036400 chr2B 96.407 668 22 2 2957 3623 646069927 646070593 0.000000e+00 1099.0
9 TraesCS6B01G036400 chr2B 95.678 671 26 3 2954 3623 80052292 80052960 0.000000e+00 1075.0
10 TraesCS6B01G036400 chr7B 96.108 668 23 3 2957 3623 567573252 567573917 0.000000e+00 1086.0
11 TraesCS6B01G036400 chr7B 95.067 669 28 5 2957 3623 43501046 43500381 0.000000e+00 1048.0
12 TraesCS6B01G036400 chr1B 95.802 667 26 2 2957 3623 531390990 531390326 0.000000e+00 1075.0
13 TraesCS6B01G036400 chr1B 95.536 672 27 3 2954 3623 16624766 16624096 0.000000e+00 1072.0
14 TraesCS6B01G036400 chr1B 95.796 666 24 4 2957 3622 616081879 616081218 0.000000e+00 1072.0
15 TraesCS6B01G036400 chr1B 95.509 668 25 5 2957 3623 263931748 263932411 0.000000e+00 1062.0
16 TraesCS6B01G036400 chr1B 96.406 640 23 0 1 640 671269733 671269094 0.000000e+00 1055.0
17 TraesCS6B01G036400 chr4B 95.802 667 22 5 2957 3623 626637137 626636477 0.000000e+00 1072.0
18 TraesCS6B01G036400 chr4B 92.593 54 4 0 675 728 520416042 520415989 1.080000e-10 78.7
19 TraesCS6B01G036400 chr7A 96.417 642 23 0 1 642 484215796 484216437 0.000000e+00 1059.0
20 TraesCS6B01G036400 chr1A 95.462 639 28 1 1 638 72429442 72430080 0.000000e+00 1018.0
21 TraesCS6B01G036400 chr1A 96.078 51 1 1 675 724 285956106 285956156 8.340000e-12 82.4
22 TraesCS6B01G036400 chr5A 94.637 634 34 0 1 634 297714192 297713559 0.000000e+00 983.0
23 TraesCS6B01G036400 chr3A 90.000 590 55 4 1 589 102695099 102695685 0.000000e+00 760.0
24 TraesCS6B01G036400 chr3D 97.872 47 1 0 675 721 390080686 390080640 8.340000e-12 82.4
25 TraesCS6B01G036400 chr3D 97.872 47 1 0 675 721 580128432 580128478 8.340000e-12 82.4
26 TraesCS6B01G036400 chr3D 95.745 47 2 0 675 721 73731595 73731641 3.880000e-10 76.8
27 TraesCS6B01G036400 chr5D 95.745 47 2 0 675 721 203060958 203060912 3.880000e-10 76.8
28 TraesCS6B01G036400 chr5D 95.745 47 2 0 675 721 500452244 500452290 3.880000e-10 76.8
29 TraesCS6B01G036400 chr2D 95.745 47 2 0 675 721 402310900 402310946 3.880000e-10 76.8
30 TraesCS6B01G036400 chr1D 95.745 47 2 0 675 721 221084132 221084178 3.880000e-10 76.8
31 TraesCS6B01G036400 chr3B 89.831 59 3 3 579 636 491531614 491531670 5.020000e-09 73.1


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 TraesCS6B01G036400 chr6B 21283241 21286863 3622 True 6691 6691 100.000 1 3623 1 chr6B.!!$R4 3622
1 TraesCS6B01G036400 chr6B 10408965 10409593 628 True 880 880 91.905 1 630 1 chr6B.!!$R1 629
2 TraesCS6B01G036400 chr6B 10539389 10540017 628 True 874 874 91.746 1 630 1 chr6B.!!$R3 629
3 TraesCS6B01G036400 chr6B 10474001 10474628 627 True 863 863 91.429 1 630 1 chr6B.!!$R2 629
4 TraesCS6B01G036400 chr6D 11407681 11409946 2265 True 2885 2885 89.940 675 2936 1 chr6D.!!$R1 2261
5 TraesCS6B01G036400 chr6A 12836222 12838499 2277 True 1442 1445 90.956 685 2937 2 chr6A.!!$R1 2252
6 TraesCS6B01G036400 chr6A 614421733 614422372 639 False 1022 1022 95.476 1 640 1 chr6A.!!$F1 639
7 TraesCS6B01G036400 chr2B 646069927 646070593 666 False 1099 1099 96.407 2957 3623 1 chr2B.!!$F2 666
8 TraesCS6B01G036400 chr2B 80052292 80052960 668 False 1075 1075 95.678 2954 3623 1 chr2B.!!$F1 669
9 TraesCS6B01G036400 chr7B 567573252 567573917 665 False 1086 1086 96.108 2957 3623 1 chr7B.!!$F1 666
10 TraesCS6B01G036400 chr7B 43500381 43501046 665 True 1048 1048 95.067 2957 3623 1 chr7B.!!$R1 666
11 TraesCS6B01G036400 chr1B 531390326 531390990 664 True 1075 1075 95.802 2957 3623 1 chr1B.!!$R2 666
12 TraesCS6B01G036400 chr1B 16624096 16624766 670 True 1072 1072 95.536 2954 3623 1 chr1B.!!$R1 669
13 TraesCS6B01G036400 chr1B 616081218 616081879 661 True 1072 1072 95.796 2957 3622 1 chr1B.!!$R3 665
14 TraesCS6B01G036400 chr1B 263931748 263932411 663 False 1062 1062 95.509 2957 3623 1 chr1B.!!$F1 666
15 TraesCS6B01G036400 chr1B 671269094 671269733 639 True 1055 1055 96.406 1 640 1 chr1B.!!$R4 639
16 TraesCS6B01G036400 chr4B 626636477 626637137 660 True 1072 1072 95.802 2957 3623 1 chr4B.!!$R2 666
17 TraesCS6B01G036400 chr7A 484215796 484216437 641 False 1059 1059 96.417 1 642 1 chr7A.!!$F1 641
18 TraesCS6B01G036400 chr1A 72429442 72430080 638 False 1018 1018 95.462 1 638 1 chr1A.!!$F1 637
19 TraesCS6B01G036400 chr5A 297713559 297714192 633 True 983 983 94.637 1 634 1 chr5A.!!$R1 633
20 TraesCS6B01G036400 chr3A 102695099 102695685 586 False 760 760 90.000 1 589 1 chr3A.!!$F1 588

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
681 685 0.038251 TGTCTGTGTGTCCTCGATGC 60.038 55.0 0.0 0.0 0.0 3.91 F
1611 1649 0.038801 GCCTCTGTTTCTTGCCTTGC 60.039 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1651 0.034059 CTGAACTGAACGAGCCCTGT 59.966 55.0 0.00 0.0 0.00 4.00 R
2932 3088 0.108804 ATGCACGGGTTCACGACTAG 60.109 55.0 0.34 0.0 37.61 2.57 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
54 55 1.028868 GTCTACTCTACGGTGGCGGT 61.029 60.000 0.00 0.00 0.00 5.68
182 183 3.062763 CTGCCTAGCACTAAATGGATCG 58.937 50.000 0.00 0.00 33.79 3.69
457 458 4.853142 ACCGCTGGATCCGCCCTA 62.853 66.667 18.69 0.00 34.97 3.53
642 646 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
643 647 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
644 648 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
645 649 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
646 650 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
647 651 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
648 652 4.890306 GGGAGGGAGGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
649 653 3.773154 GGAGGGAGGGAGGGAGCT 61.773 72.222 0.00 0.00 0.00 4.09
650 654 2.123033 GAGGGAGGGAGGGAGCTC 60.123 72.222 4.71 4.71 0.00 4.09
651 655 2.955246 AGGGAGGGAGGGAGCTCA 60.955 66.667 17.19 0.00 0.00 4.26
652 656 2.445654 GGGAGGGAGGGAGCTCAG 60.446 72.222 17.19 0.00 0.00 3.35
653 657 2.693017 GGAGGGAGGGAGCTCAGA 59.307 66.667 17.19 0.00 0.00 3.27
654 658 1.002274 GGAGGGAGGGAGCTCAGAA 59.998 63.158 17.19 0.00 0.00 3.02
655 659 0.399806 GGAGGGAGGGAGCTCAGAAT 60.400 60.000 17.19 0.00 0.00 2.40
656 660 1.047801 GAGGGAGGGAGCTCAGAATC 58.952 60.000 17.19 7.08 0.00 2.52
657 661 0.399806 AGGGAGGGAGCTCAGAATCC 60.400 60.000 17.19 15.37 34.64 3.01
658 662 0.399806 GGGAGGGAGCTCAGAATCCT 60.400 60.000 17.19 12.22 35.80 3.24
659 663 1.133009 GGGAGGGAGCTCAGAATCCTA 60.133 57.143 17.19 0.00 35.80 2.94
660 664 2.494439 GGGAGGGAGCTCAGAATCCTAT 60.494 54.545 17.19 0.00 35.80 2.57
661 665 2.566724 GGAGGGAGCTCAGAATCCTATG 59.433 54.545 17.19 0.00 35.80 2.23
662 666 3.238597 GAGGGAGCTCAGAATCCTATGT 58.761 50.000 17.19 0.00 35.80 2.29
663 667 2.971330 AGGGAGCTCAGAATCCTATGTG 59.029 50.000 17.19 0.00 35.80 3.21
664 668 2.703007 GGGAGCTCAGAATCCTATGTGT 59.297 50.000 17.19 0.00 35.80 3.72
665 669 3.244044 GGGAGCTCAGAATCCTATGTGTC 60.244 52.174 17.19 0.00 35.80 3.67
666 670 3.640967 GGAGCTCAGAATCCTATGTGTCT 59.359 47.826 17.19 0.00 32.51 3.41
667 671 4.501229 GGAGCTCAGAATCCTATGTGTCTG 60.501 50.000 17.19 0.00 39.09 3.51
668 672 4.029520 AGCTCAGAATCCTATGTGTCTGT 58.970 43.478 0.00 0.00 38.87 3.41
669 673 4.118410 GCTCAGAATCCTATGTGTCTGTG 58.882 47.826 0.00 0.00 38.87 3.66
670 674 4.382470 GCTCAGAATCCTATGTGTCTGTGT 60.382 45.833 0.00 0.00 38.87 3.72
671 675 5.077134 TCAGAATCCTATGTGTCTGTGTG 57.923 43.478 0.00 0.00 38.87 3.82
672 676 4.528206 TCAGAATCCTATGTGTCTGTGTGT 59.472 41.667 0.00 0.00 38.87 3.72
673 677 4.867047 CAGAATCCTATGTGTCTGTGTGTC 59.133 45.833 0.00 0.00 34.15 3.67
674 678 3.895232 ATCCTATGTGTCTGTGTGTCC 57.105 47.619 0.00 0.00 0.00 4.02
675 679 2.889512 TCCTATGTGTCTGTGTGTCCT 58.110 47.619 0.00 0.00 0.00 3.85
676 680 2.826128 TCCTATGTGTCTGTGTGTCCTC 59.174 50.000 0.00 0.00 0.00 3.71
677 681 2.416027 CCTATGTGTCTGTGTGTCCTCG 60.416 54.545 0.00 0.00 0.00 4.63
678 682 1.328279 ATGTGTCTGTGTGTCCTCGA 58.672 50.000 0.00 0.00 0.00 4.04
679 683 1.328279 TGTGTCTGTGTGTCCTCGAT 58.672 50.000 0.00 0.00 0.00 3.59
680 684 1.000274 TGTGTCTGTGTGTCCTCGATG 60.000 52.381 0.00 0.00 0.00 3.84
681 685 0.038251 TGTCTGTGTGTCCTCGATGC 60.038 55.000 0.00 0.00 0.00 3.91
682 686 0.038251 GTCTGTGTGTCCTCGATGCA 60.038 55.000 0.00 0.00 0.00 3.96
683 687 0.678950 TCTGTGTGTCCTCGATGCAA 59.321 50.000 0.00 0.00 0.00 4.08
724 738 3.252215 TGCTTTGTACTTCCGGTGATTTG 59.748 43.478 0.00 0.00 0.00 2.32
745 759 8.844441 ATTTGTTTGATCACATTTGCAAAAAG 57.156 26.923 17.19 14.12 32.71 2.27
746 760 7.606858 TTGTTTGATCACATTTGCAAAAAGA 57.393 28.000 17.19 14.13 32.71 2.52
747 761 7.606858 TGTTTGATCACATTTGCAAAAAGAA 57.393 28.000 17.19 3.09 32.71 2.52
748 762 8.037382 TGTTTGATCACATTTGCAAAAAGAAA 57.963 26.923 17.19 5.98 32.71 2.52
749 763 8.675504 TGTTTGATCACATTTGCAAAAAGAAAT 58.324 25.926 17.19 10.34 32.71 2.17
750 764 9.505995 GTTTGATCACATTTGCAAAAAGAAATT 57.494 25.926 17.19 0.00 32.71 1.82
792 806 2.108168 TGGGTTAGAGATGCGCTAAGT 58.892 47.619 9.73 0.00 0.00 2.24
794 808 3.067742 TGGGTTAGAGATGCGCTAAGTAC 59.932 47.826 9.73 0.00 0.00 2.73
813 827 4.741676 AGTACGTCGTTTCACAAGTTAAGG 59.258 41.667 1.78 0.00 0.00 2.69
816 830 4.033243 ACGTCGTTTCACAAGTTAAGGAAC 59.967 41.667 0.00 0.00 35.64 3.62
830 844 7.913674 AGTTAAGGAACAAATAGAGAAGCTG 57.086 36.000 0.00 0.00 38.10 4.24
846 860 2.924185 CTGAGTGGACCAGCACAAG 58.076 57.895 0.00 0.00 0.00 3.16
847 861 0.604780 CTGAGTGGACCAGCACAAGG 60.605 60.000 0.00 0.00 0.00 3.61
848 862 1.302832 GAGTGGACCAGCACAAGGG 60.303 63.158 0.00 0.00 0.00 3.95
894 909 1.730064 ACGACCCGACAAATTCAATCG 59.270 47.619 0.00 0.00 35.62 3.34
952 967 1.439543 AATCTCCCCTATCCCAGCAC 58.560 55.000 0.00 0.00 0.00 4.40
1146 1167 4.816984 GTCGCGAGGAGGGGAGGA 62.817 72.222 10.24 0.00 0.00 3.71
1347 1368 1.021390 ACAAGATGAAGAAGCCGCCG 61.021 55.000 0.00 0.00 0.00 6.46
1371 1392 3.234390 CGCTTCTCGGTGTGTGTG 58.766 61.111 0.00 0.00 33.78 3.82
1372 1393 1.299850 CGCTTCTCGGTGTGTGTGA 60.300 57.895 0.00 0.00 33.78 3.58
1373 1394 0.667487 CGCTTCTCGGTGTGTGTGAT 60.667 55.000 0.00 0.00 33.78 3.06
1374 1395 1.512926 GCTTCTCGGTGTGTGTGATT 58.487 50.000 0.00 0.00 0.00 2.57
1375 1396 1.461127 GCTTCTCGGTGTGTGTGATTC 59.539 52.381 0.00 0.00 0.00 2.52
1376 1397 2.754472 CTTCTCGGTGTGTGTGATTCA 58.246 47.619 0.00 0.00 0.00 2.57
1377 1398 2.438868 TCTCGGTGTGTGTGATTCAG 57.561 50.000 0.00 0.00 0.00 3.02
1378 1399 1.686587 TCTCGGTGTGTGTGATTCAGT 59.313 47.619 0.00 0.00 0.00 3.41
1379 1400 1.794701 CTCGGTGTGTGTGATTCAGTG 59.205 52.381 0.00 0.00 0.00 3.66
1380 1401 1.410882 TCGGTGTGTGTGATTCAGTGA 59.589 47.619 0.00 0.00 0.00 3.41
1381 1402 1.526887 CGGTGTGTGTGATTCAGTGAC 59.473 52.381 0.00 0.00 0.00 3.67
1383 1404 1.873591 GTGTGTGTGATTCAGTGACCC 59.126 52.381 0.00 0.00 0.00 4.46
1386 1407 1.270094 TGTGTGATTCAGTGACCCGAC 60.270 52.381 0.00 0.00 0.00 4.79
1387 1408 0.320374 TGTGATTCAGTGACCCGACC 59.680 55.000 0.00 0.00 0.00 4.79
1388 1409 0.736325 GTGATTCAGTGACCCGACCG 60.736 60.000 0.00 0.00 0.00 4.79
1389 1410 1.153628 GATTCAGTGACCCGACCGG 60.154 63.158 0.00 0.00 37.81 5.28
1390 1411 1.601419 GATTCAGTGACCCGACCGGA 61.601 60.000 9.46 0.00 37.50 5.14
1391 1412 0.976073 ATTCAGTGACCCGACCGGAT 60.976 55.000 9.46 0.00 37.50 4.18
1392 1413 1.601419 TTCAGTGACCCGACCGGATC 61.601 60.000 9.46 2.36 37.50 3.36
1393 1414 2.036731 AGTGACCCGACCGGATCA 59.963 61.111 9.46 5.59 37.50 2.92
1394 1415 2.183555 GTGACCCGACCGGATCAC 59.816 66.667 18.90 18.90 36.31 3.06
1395 1416 2.036731 TGACCCGACCGGATCACT 59.963 61.111 9.46 0.00 37.50 3.41
1396 1417 2.348104 TGACCCGACCGGATCACTG 61.348 63.158 9.46 0.00 37.50 3.66
1397 1418 2.283676 ACCCGACCGGATCACTGT 60.284 61.111 9.46 0.00 37.50 3.55
1398 1419 2.184322 CCCGACCGGATCACTGTG 59.816 66.667 9.46 0.17 37.50 3.66
1399 1420 2.646175 CCCGACCGGATCACTGTGT 61.646 63.158 9.46 0.00 37.50 3.72
1400 1421 1.153823 CCGACCGGATCACTGTGTC 60.154 63.158 9.46 4.93 37.50 3.67
1406 1427 0.163788 CGGATCACTGTGTCGTTTGC 59.836 55.000 7.79 0.00 0.00 3.68
1407 1428 1.225855 GGATCACTGTGTCGTTTGCA 58.774 50.000 7.79 0.00 0.00 4.08
1421 1442 1.541588 GTTTGCAATCGGAGGCTTTCT 59.458 47.619 0.00 0.00 0.00 2.52
1422 1443 1.167851 TTGCAATCGGAGGCTTTCTG 58.832 50.000 0.00 0.00 0.00 3.02
1424 1445 1.277842 TGCAATCGGAGGCTTTCTGTA 59.722 47.619 6.09 0.00 33.64 2.74
1426 1447 2.280628 CAATCGGAGGCTTTCTGTACC 58.719 52.381 0.00 0.00 33.64 3.34
1437 1458 4.327680 GCTTTCTGTACCCTGTTTCTGAT 58.672 43.478 0.00 0.00 0.00 2.90
1439 1460 3.981071 TCTGTACCCTGTTTCTGATGG 57.019 47.619 0.00 0.00 0.00 3.51
1440 1461 3.516586 TCTGTACCCTGTTTCTGATGGA 58.483 45.455 0.00 0.00 0.00 3.41
1441 1462 4.104086 TCTGTACCCTGTTTCTGATGGAT 58.896 43.478 0.00 0.00 0.00 3.41
1442 1463 4.162320 TCTGTACCCTGTTTCTGATGGATC 59.838 45.833 0.00 0.00 0.00 3.36
1543 1580 4.717629 TTCGACGCCGTGCTGGAG 62.718 66.667 0.00 0.00 44.31 3.86
1579 1616 1.516386 CGACGCCGTCAAGTATGCT 60.516 57.895 18.40 0.00 32.09 3.79
1584 1621 0.179134 GCCGTCAAGTATGCTCGACT 60.179 55.000 0.29 0.00 0.00 4.18
1592 1630 1.133982 AGTATGCTCGACTGACAGCTG 59.866 52.381 13.48 13.48 36.53 4.24
1606 1644 0.240411 CAGCTGCCTCTGTTTCTTGC 59.760 55.000 0.00 0.00 0.00 4.01
1608 1646 0.892814 GCTGCCTCTGTTTCTTGCCT 60.893 55.000 0.00 0.00 0.00 4.75
1609 1647 1.613836 CTGCCTCTGTTTCTTGCCTT 58.386 50.000 0.00 0.00 0.00 4.35
1611 1649 0.038801 GCCTCTGTTTCTTGCCTTGC 60.039 55.000 0.00 0.00 0.00 4.01
1612 1650 0.600057 CCTCTGTTTCTTGCCTTGCC 59.400 55.000 0.00 0.00 0.00 4.52
1613 1651 1.321474 CTCTGTTTCTTGCCTTGCCA 58.679 50.000 0.00 0.00 0.00 4.92
1614 1652 1.000938 CTCTGTTTCTTGCCTTGCCAC 60.001 52.381 0.00 0.00 0.00 5.01
1615 1653 0.746063 CTGTTTCTTGCCTTGCCACA 59.254 50.000 0.00 0.00 0.00 4.17
1616 1654 0.746063 TGTTTCTTGCCTTGCCACAG 59.254 50.000 0.00 0.00 0.00 3.66
1618 1656 1.114722 TTTCTTGCCTTGCCACAGGG 61.115 55.000 0.00 0.00 34.01 4.45
1630 1668 0.951040 CCACAGGGCTCGTTCAGTTC 60.951 60.000 0.00 0.00 0.00 3.01
1631 1669 0.249868 CACAGGGCTCGTTCAGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
1632 1670 0.034059 ACAGGGCTCGTTCAGTTCAG 59.966 55.000 0.00 0.00 0.00 3.02
1633 1671 0.318441 CAGGGCTCGTTCAGTTCAGA 59.682 55.000 0.00 0.00 0.00 3.27
1634 1672 0.605589 AGGGCTCGTTCAGTTCAGAG 59.394 55.000 0.00 0.00 0.00 3.35
1635 1673 0.318762 GGGCTCGTTCAGTTCAGAGT 59.681 55.000 0.00 0.00 33.57 3.24
1636 1674 1.270358 GGGCTCGTTCAGTTCAGAGTT 60.270 52.381 0.00 0.00 33.57 3.01
1637 1675 2.062519 GGCTCGTTCAGTTCAGAGTTC 58.937 52.381 0.00 0.00 33.57 3.01
1638 1676 2.545952 GGCTCGTTCAGTTCAGAGTTCA 60.546 50.000 0.00 0.00 33.57 3.18
1639 1677 2.728839 GCTCGTTCAGTTCAGAGTTCAG 59.271 50.000 0.00 0.00 33.57 3.02
1640 1678 3.551046 GCTCGTTCAGTTCAGAGTTCAGA 60.551 47.826 0.00 0.00 33.57 3.27
1641 1679 3.966154 TCGTTCAGTTCAGAGTTCAGAC 58.034 45.455 0.00 0.00 0.00 3.51
1642 1680 3.632604 TCGTTCAGTTCAGAGTTCAGACT 59.367 43.478 0.00 0.00 39.32 3.24
1643 1681 4.098044 TCGTTCAGTTCAGAGTTCAGACTT 59.902 41.667 0.00 0.00 35.88 3.01
1644 1682 4.208047 CGTTCAGTTCAGAGTTCAGACTTG 59.792 45.833 0.00 0.00 35.88 3.16
1645 1683 5.352284 GTTCAGTTCAGAGTTCAGACTTGA 58.648 41.667 0.00 0.00 35.88 3.02
1646 1684 4.938080 TCAGTTCAGAGTTCAGACTTGAC 58.062 43.478 0.00 0.00 35.88 3.18
1647 1685 4.402474 TCAGTTCAGAGTTCAGACTTGACA 59.598 41.667 0.00 0.00 35.88 3.58
1648 1686 4.744137 CAGTTCAGAGTTCAGACTTGACAG 59.256 45.833 0.00 0.00 35.88 3.51
1649 1687 3.377346 TCAGAGTTCAGACTTGACAGC 57.623 47.619 0.00 0.00 35.88 4.40
1650 1688 2.695147 TCAGAGTTCAGACTTGACAGCA 59.305 45.455 0.00 0.00 35.88 4.41
1651 1689 3.132824 TCAGAGTTCAGACTTGACAGCAA 59.867 43.478 0.00 0.00 35.88 3.91
1652 1690 4.063689 CAGAGTTCAGACTTGACAGCAAT 58.936 43.478 0.00 0.00 35.88 3.56
1653 1691 4.152045 CAGAGTTCAGACTTGACAGCAATC 59.848 45.833 0.00 0.00 35.88 2.67
1654 1692 3.406764 AGTTCAGACTTGACAGCAATCC 58.593 45.455 0.00 0.00 32.68 3.01
1655 1693 3.141398 GTTCAGACTTGACAGCAATCCA 58.859 45.455 0.00 0.00 32.68 3.41
1656 1694 3.490439 TCAGACTTGACAGCAATCCAA 57.510 42.857 0.00 0.00 32.68 3.53
1657 1695 4.025040 TCAGACTTGACAGCAATCCAAT 57.975 40.909 0.00 0.00 32.68 3.16
1658 1696 3.754850 TCAGACTTGACAGCAATCCAATG 59.245 43.478 0.00 0.00 32.68 2.82
1669 1707 4.004982 AGCAATCCAATGTGATTTTTGGC 58.995 39.130 0.00 0.00 41.78 4.52
1745 1783 4.615815 ATCAGCAGCGCCGGGATC 62.616 66.667 2.29 0.00 0.00 3.36
1787 1825 1.301954 GCACGTGGAGGGGGTAATT 59.698 57.895 18.88 0.00 0.00 1.40
1788 1826 1.029947 GCACGTGGAGGGGGTAATTG 61.030 60.000 18.88 0.00 0.00 2.32
1792 1830 1.680860 CGTGGAGGGGGTAATTGTTCC 60.681 57.143 0.00 0.00 0.00 3.62
1793 1831 1.356398 GTGGAGGGGGTAATTGTTCCA 59.644 52.381 0.00 0.00 32.62 3.53
1796 1834 2.243736 GGAGGGGGTAATTGTTCCATCA 59.756 50.000 8.78 0.00 32.38 3.07
1797 1835 3.288092 GAGGGGGTAATTGTTCCATCAC 58.712 50.000 0.00 0.00 31.25 3.06
1798 1836 2.024369 AGGGGGTAATTGTTCCATCACC 60.024 50.000 0.00 0.00 0.00 4.02
1799 1837 2.021457 GGGGTAATTGTTCCATCACCG 58.979 52.381 0.00 0.00 0.00 4.94
1800 1838 2.021457 GGGTAATTGTTCCATCACCGG 58.979 52.381 0.00 0.00 0.00 5.28
1805 1856 2.189521 GTTCCATCACCGGCCGAT 59.810 61.111 30.73 6.36 0.00 4.18
1818 1869 1.737236 CGGCCGATCAATGTTCTTTGA 59.263 47.619 24.07 4.16 39.77 2.69
1826 1877 5.796935 CGATCAATGTTCTTTGATTGGTCAC 59.203 40.000 15.20 4.42 44.35 3.67
1828 1879 5.830912 TCAATGTTCTTTGATTGGTCACAC 58.169 37.500 0.00 0.00 33.11 3.82
1835 1898 2.672996 ATTGGTCACACGCAGCCC 60.673 61.111 0.00 0.00 0.00 5.19
1853 1916 1.486310 CCCGTCATCCTGAATTCCTGA 59.514 52.381 2.27 0.00 0.00 3.86
1854 1917 2.105477 CCCGTCATCCTGAATTCCTGAT 59.895 50.000 2.27 2.08 0.00 2.90
1856 1919 3.812053 CCGTCATCCTGAATTCCTGATTC 59.188 47.826 2.27 0.97 43.67 2.52
2015 2089 9.742552 GTTCTTCGACAGTAAGTAAAAATCATC 57.257 33.333 0.00 0.00 0.00 2.92
2018 2092 7.827819 TCGACAGTAAGTAAAAATCATCCTG 57.172 36.000 0.00 0.00 0.00 3.86
2023 2097 5.817816 AGTAAGTAAAAATCATCCTGCCTCG 59.182 40.000 0.00 0.00 0.00 4.63
2038 2156 5.652014 TCCTGCCTCGATCACAAATTAATTT 59.348 36.000 7.64 7.64 0.00 1.82
2040 2158 5.890334 TGCCTCGATCACAAATTAATTTCC 58.110 37.500 10.53 0.00 0.00 3.13
2044 2162 6.907212 CCTCGATCACAAATTAATTTCCTTCG 59.093 38.462 10.53 15.00 0.00 3.79
2133 2277 0.671472 TGCAGCTGACCAACATCTCG 60.671 55.000 20.43 0.00 0.00 4.04
2638 2789 2.742204 GCCTAGGAATGTTCGTCCTTCC 60.742 54.545 14.75 3.67 43.26 3.46
2783 2939 2.033049 GCCTGATGCAAGTAGCTGAATG 59.967 50.000 0.00 0.00 45.94 2.67
2784 2940 2.033049 CCTGATGCAAGTAGCTGAATGC 59.967 50.000 11.22 11.22 45.94 3.56
2785 2941 2.019249 TGATGCAAGTAGCTGAATGCC 58.981 47.619 14.36 3.84 45.94 4.40
2786 2942 2.295885 GATGCAAGTAGCTGAATGCCT 58.704 47.619 14.36 6.88 45.94 4.75
2787 2943 1.456296 TGCAAGTAGCTGAATGCCTG 58.544 50.000 14.36 0.00 45.94 4.85
2788 2944 1.003464 TGCAAGTAGCTGAATGCCTGA 59.997 47.619 14.36 0.00 45.94 3.86
2869 3025 2.607631 AGGAAGGTTCAAACGAACGA 57.392 45.000 0.14 0.00 43.16 3.85
2870 3026 2.908916 AGGAAGGTTCAAACGAACGAA 58.091 42.857 0.14 0.00 43.16 3.85
2871 3027 3.272581 AGGAAGGTTCAAACGAACGAAA 58.727 40.909 0.14 0.00 43.16 3.46
2905 3061 0.531974 ATATAGGCAACCACACGGCG 60.532 55.000 4.80 4.80 34.57 6.46
2913 3069 0.461339 AACCACACGGCGGATATGTC 60.461 55.000 13.24 0.00 34.57 3.06
2935 3091 9.698309 ATGTCATTTCGATTATGTTAGGACTAG 57.302 33.333 7.62 0.00 0.00 2.57
2936 3092 8.692710 TGTCATTTCGATTATGTTAGGACTAGT 58.307 33.333 0.00 0.00 0.00 2.57
2937 3093 9.182933 GTCATTTCGATTATGTTAGGACTAGTC 57.817 37.037 14.87 14.87 0.00 2.59
2938 3094 8.074370 TCATTTCGATTATGTTAGGACTAGTCG 58.926 37.037 16.56 1.50 0.00 4.18
2939 3095 6.932356 TTCGATTATGTTAGGACTAGTCGT 57.068 37.500 20.89 20.89 0.00 4.34
2940 3096 6.296365 TCGATTATGTTAGGACTAGTCGTG 57.704 41.667 24.71 7.67 0.00 4.35
2941 3097 6.051074 TCGATTATGTTAGGACTAGTCGTGA 58.949 40.000 24.71 15.91 0.00 4.35
2942 3098 6.539826 TCGATTATGTTAGGACTAGTCGTGAA 59.460 38.462 24.71 12.29 0.00 3.18
2943 3099 6.632035 CGATTATGTTAGGACTAGTCGTGAAC 59.368 42.308 24.71 21.41 0.00 3.18
2944 3100 4.715527 ATGTTAGGACTAGTCGTGAACC 57.284 45.455 24.71 8.03 0.00 3.62
2945 3101 2.821969 TGTTAGGACTAGTCGTGAACCC 59.178 50.000 24.71 7.32 0.00 4.11
2946 3102 1.742761 TAGGACTAGTCGTGAACCCG 58.257 55.000 24.71 0.00 0.00 5.28
2947 3103 0.251077 AGGACTAGTCGTGAACCCGT 60.251 55.000 16.96 0.00 0.00 5.28
2948 3104 0.109412 GGACTAGTCGTGAACCCGTG 60.109 60.000 16.56 0.00 0.00 4.94
2949 3105 0.731855 GACTAGTCGTGAACCCGTGC 60.732 60.000 7.22 0.00 0.00 5.34
2950 3106 1.287815 CTAGTCGTGAACCCGTGCA 59.712 57.895 0.00 0.00 0.00 4.57
2951 3107 0.108804 CTAGTCGTGAACCCGTGCAT 60.109 55.000 0.00 0.00 0.00 3.96
2952 3108 0.319083 TAGTCGTGAACCCGTGCATT 59.681 50.000 0.00 0.00 0.00 3.56
2953 3109 0.949105 AGTCGTGAACCCGTGCATTC 60.949 55.000 0.00 0.00 0.00 2.67
2954 3110 2.024868 TCGTGAACCCGTGCATTCG 61.025 57.895 0.00 0.00 0.00 3.34
2955 3111 2.175811 GTGAACCCGTGCATTCGC 59.824 61.111 0.00 0.00 39.24 4.70
3155 3314 2.043953 GTGGGCTGATTGGGTCCC 60.044 66.667 0.00 0.00 39.22 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.105577 AGTAGACTGTAGAGACCCTCTCA 58.894 47.826 0.00 0.00 45.73 3.27
54 55 2.032528 CTTCCGTTGCCTCAGCCA 59.967 61.111 0.00 0.00 38.69 4.75
197 198 1.026182 TCCAGCAATCGCGCAAGAAT 61.026 50.000 8.75 0.00 45.49 2.40
457 458 0.833949 GCCCGAAAAGGAGGAGATCT 59.166 55.000 0.00 0.00 45.00 2.75
642 646 2.971330 CACATAGGATTCTGAGCTCCCT 59.029 50.000 12.15 12.30 31.49 4.20
643 647 2.703007 ACACATAGGATTCTGAGCTCCC 59.297 50.000 12.15 4.40 31.49 4.30
644 648 3.640967 AGACACATAGGATTCTGAGCTCC 59.359 47.826 12.15 0.00 0.00 4.70
645 649 4.099266 ACAGACACATAGGATTCTGAGCTC 59.901 45.833 6.82 6.82 38.19 4.09
646 650 4.029520 ACAGACACATAGGATTCTGAGCT 58.970 43.478 14.16 0.00 38.19 4.09
647 651 4.118410 CACAGACACATAGGATTCTGAGC 58.882 47.826 14.16 0.00 38.19 4.26
648 652 5.107824 CACACAGACACATAGGATTCTGAG 58.892 45.833 14.16 10.01 38.19 3.35
649 653 4.528206 ACACACAGACACATAGGATTCTGA 59.472 41.667 14.16 0.00 38.19 3.27
650 654 4.825422 ACACACAGACACATAGGATTCTG 58.175 43.478 7.99 7.99 41.14 3.02
651 655 4.081420 GGACACACAGACACATAGGATTCT 60.081 45.833 0.00 0.00 0.00 2.40
652 656 4.081420 AGGACACACAGACACATAGGATTC 60.081 45.833 0.00 0.00 0.00 2.52
653 657 3.840666 AGGACACACAGACACATAGGATT 59.159 43.478 0.00 0.00 0.00 3.01
654 658 3.445008 AGGACACACAGACACATAGGAT 58.555 45.455 0.00 0.00 0.00 3.24
655 659 2.826128 GAGGACACACAGACACATAGGA 59.174 50.000 0.00 0.00 0.00 2.94
656 660 2.416027 CGAGGACACACAGACACATAGG 60.416 54.545 0.00 0.00 0.00 2.57
657 661 2.488153 TCGAGGACACACAGACACATAG 59.512 50.000 0.00 0.00 0.00 2.23
658 662 2.510613 TCGAGGACACACAGACACATA 58.489 47.619 0.00 0.00 0.00 2.29
659 663 1.328279 TCGAGGACACACAGACACAT 58.672 50.000 0.00 0.00 0.00 3.21
660 664 1.000274 CATCGAGGACACACAGACACA 60.000 52.381 0.00 0.00 0.00 3.72
661 665 1.702886 CATCGAGGACACACAGACAC 58.297 55.000 0.00 0.00 0.00 3.67
662 666 0.038251 GCATCGAGGACACACAGACA 60.038 55.000 0.00 0.00 0.00 3.41
663 667 0.038251 TGCATCGAGGACACACAGAC 60.038 55.000 0.00 0.00 0.00 3.51
664 668 0.678950 TTGCATCGAGGACACACAGA 59.321 50.000 0.00 0.00 0.00 3.41
665 669 1.730501 ATTGCATCGAGGACACACAG 58.269 50.000 0.00 0.00 0.00 3.66
666 670 2.183478 AATTGCATCGAGGACACACA 57.817 45.000 0.00 0.00 0.00 3.72
667 671 3.559238 AAAATTGCATCGAGGACACAC 57.441 42.857 0.00 0.00 0.00 3.82
668 672 5.895636 ATAAAAATTGCATCGAGGACACA 57.104 34.783 0.00 0.00 0.00 3.72
669 673 7.915397 ACATAATAAAAATTGCATCGAGGACAC 59.085 33.333 0.00 0.00 0.00 3.67
670 674 7.995289 ACATAATAAAAATTGCATCGAGGACA 58.005 30.769 0.00 0.00 0.00 4.02
671 675 8.856490 AACATAATAAAAATTGCATCGAGGAC 57.144 30.769 0.00 0.00 0.00 3.85
672 676 9.299963 CAAACATAATAAAAATTGCATCGAGGA 57.700 29.630 0.00 0.00 0.00 3.71
673 677 9.299963 TCAAACATAATAAAAATTGCATCGAGG 57.700 29.630 0.00 0.00 0.00 4.63
679 683 9.656040 AGCATCTCAAACATAATAAAAATTGCA 57.344 25.926 0.00 0.00 0.00 4.08
724 738 9.505995 AATTTCTTTTTGCAAATGTGATCAAAC 57.494 25.926 13.65 0.00 0.00 2.93
748 762 9.958180 CCATTCCCCAAATTTAGTTTCTTTAAT 57.042 29.630 0.00 0.00 0.00 1.40
749 763 8.379331 CCCATTCCCCAAATTTAGTTTCTTTAA 58.621 33.333 0.00 0.00 0.00 1.52
750 764 7.514473 ACCCATTCCCCAAATTTAGTTTCTTTA 59.486 33.333 0.00 0.00 0.00 1.85
751 765 6.331572 ACCCATTCCCCAAATTTAGTTTCTTT 59.668 34.615 0.00 0.00 0.00 2.52
766 780 1.543429 CGCATCTCTAACCCATTCCCC 60.543 57.143 0.00 0.00 0.00 4.81
792 806 4.930963 TCCTTAACTTGTGAAACGACGTA 58.069 39.130 0.00 0.00 42.39 3.57
794 808 4.033129 TGTTCCTTAACTTGTGAAACGACG 59.967 41.667 0.00 0.00 36.58 5.12
813 827 5.350091 GTCCACTCAGCTTCTCTATTTGTTC 59.650 44.000 0.00 0.00 0.00 3.18
816 830 4.187694 GGTCCACTCAGCTTCTCTATTTG 58.812 47.826 0.00 0.00 0.00 2.32
830 844 1.302832 CCCTTGTGCTGGTCCACTC 60.303 63.158 0.00 0.00 36.68 3.51
860 875 0.530870 GGTCGTTGATGGCCTAGAGC 60.531 60.000 3.32 0.27 42.60 4.09
894 909 1.571460 GCCATGTGCGCTATGCTAC 59.429 57.895 9.73 0.00 46.63 3.58
1200 1221 0.784778 CGACCAGCACGTTCTTCTTC 59.215 55.000 0.00 0.00 0.00 2.87
1365 1386 1.148310 CGGGTCACTGAATCACACAC 58.852 55.000 0.00 0.00 0.00 3.82
1366 1387 1.044611 TCGGGTCACTGAATCACACA 58.955 50.000 0.00 0.00 0.00 3.72
1368 1389 0.320374 GGTCGGGTCACTGAATCACA 59.680 55.000 0.00 0.00 32.79 3.58
1369 1390 0.736325 CGGTCGGGTCACTGAATCAC 60.736 60.000 0.00 0.00 32.79 3.06
1370 1391 1.589630 CGGTCGGGTCACTGAATCA 59.410 57.895 0.00 0.00 32.79 2.57
1371 1392 1.153628 CCGGTCGGGTCACTGAATC 60.154 63.158 0.74 0.00 32.79 2.52
1372 1393 0.976073 ATCCGGTCGGGTCACTGAAT 60.976 55.000 9.68 0.00 37.00 2.57
1373 1394 1.601419 GATCCGGTCGGGTCACTGAA 61.601 60.000 16.81 0.00 44.55 3.02
1374 1395 2.036731 ATCCGGTCGGGTCACTGA 59.963 61.111 9.68 0.00 37.00 3.41
1375 1396 2.494918 GATCCGGTCGGGTCACTG 59.505 66.667 16.81 0.00 44.55 3.66
1379 1400 2.348888 ACAGTGATCCGGTCGGGTC 61.349 63.158 15.10 15.10 45.36 4.46
1380 1401 2.283676 ACAGTGATCCGGTCGGGT 60.284 61.111 9.68 1.38 37.00 5.28
1381 1402 2.184322 CACAGTGATCCGGTCGGG 59.816 66.667 9.68 0.00 35.59 5.14
1383 1404 1.514228 CGACACAGTGATCCGGTCG 60.514 63.158 7.81 0.69 44.13 4.79
1386 1407 0.790207 CAAACGACACAGTGATCCGG 59.210 55.000 7.81 0.00 0.00 5.14
1387 1408 0.163788 GCAAACGACACAGTGATCCG 59.836 55.000 7.81 10.03 0.00 4.18
1388 1409 1.225855 TGCAAACGACACAGTGATCC 58.774 50.000 7.81 0.00 0.00 3.36
1389 1410 3.482786 GATTGCAAACGACACAGTGATC 58.517 45.455 7.81 0.30 0.00 2.92
1390 1411 2.096268 CGATTGCAAACGACACAGTGAT 60.096 45.455 22.96 0.00 0.00 3.06
1391 1412 1.260297 CGATTGCAAACGACACAGTGA 59.740 47.619 22.96 0.00 0.00 3.41
1392 1413 1.660052 CCGATTGCAAACGACACAGTG 60.660 52.381 27.99 7.66 0.00 3.66
1393 1414 0.586319 CCGATTGCAAACGACACAGT 59.414 50.000 27.99 0.00 0.00 3.55
1394 1415 0.865111 TCCGATTGCAAACGACACAG 59.135 50.000 27.99 12.45 0.00 3.66
1395 1416 0.865111 CTCCGATTGCAAACGACACA 59.135 50.000 27.99 9.62 0.00 3.72
1396 1417 0.165944 CCTCCGATTGCAAACGACAC 59.834 55.000 27.99 4.25 0.00 3.67
1397 1418 1.573829 GCCTCCGATTGCAAACGACA 61.574 55.000 27.99 14.14 0.00 4.35
1398 1419 1.134694 GCCTCCGATTGCAAACGAC 59.865 57.895 27.99 12.01 0.00 4.34
1399 1420 0.605319 AAGCCTCCGATTGCAAACGA 60.605 50.000 27.99 14.13 0.00 3.85
1400 1421 0.240945 AAAGCCTCCGATTGCAAACG 59.759 50.000 20.82 20.82 0.00 3.60
1406 1427 2.280628 GGTACAGAAAGCCTCCGATTG 58.719 52.381 0.00 0.00 0.00 2.67
1407 1428 1.209747 GGGTACAGAAAGCCTCCGATT 59.790 52.381 0.00 0.00 34.08 3.34
1421 1442 3.199946 GGATCCATCAGAAACAGGGTACA 59.800 47.826 6.95 0.00 0.00 2.90
1422 1443 3.456277 AGGATCCATCAGAAACAGGGTAC 59.544 47.826 15.82 0.00 0.00 3.34
1424 1445 2.240667 CAGGATCCATCAGAAACAGGGT 59.759 50.000 15.82 0.00 0.00 4.34
1426 1447 3.276857 CACAGGATCCATCAGAAACAGG 58.723 50.000 15.82 0.00 0.00 4.00
1533 1570 2.317609 CCGTTGTTCTCCAGCACGG 61.318 63.158 0.00 0.00 0.00 4.94
1543 1580 1.566018 CGAGGTCCTTGCCGTTGTTC 61.566 60.000 0.00 0.00 0.00 3.18
1579 1616 1.604879 AGAGGCAGCTGTCAGTCGA 60.605 57.895 22.50 0.00 0.00 4.20
1592 1630 0.038801 GCAAGGCAAGAAACAGAGGC 60.039 55.000 0.00 0.00 0.00 4.70
1611 1649 0.951040 GAACTGAACGAGCCCTGTGG 60.951 60.000 0.00 0.00 0.00 4.17
1612 1650 0.249868 TGAACTGAACGAGCCCTGTG 60.250 55.000 0.00 0.00 0.00 3.66
1613 1651 0.034059 CTGAACTGAACGAGCCCTGT 59.966 55.000 0.00 0.00 0.00 4.00
1614 1652 0.318441 TCTGAACTGAACGAGCCCTG 59.682 55.000 0.00 0.00 0.00 4.45
1615 1653 0.605589 CTCTGAACTGAACGAGCCCT 59.394 55.000 0.00 0.00 0.00 5.19
1616 1654 0.318762 ACTCTGAACTGAACGAGCCC 59.681 55.000 0.00 0.00 0.00 5.19
1618 1656 2.728839 CTGAACTCTGAACTGAACGAGC 59.271 50.000 0.00 0.00 0.00 5.03
1619 1657 3.978217 GTCTGAACTCTGAACTGAACGAG 59.022 47.826 0.00 0.00 0.00 4.18
1620 1658 3.632604 AGTCTGAACTCTGAACTGAACGA 59.367 43.478 0.00 0.00 0.00 3.85
1621 1659 3.971150 AGTCTGAACTCTGAACTGAACG 58.029 45.455 0.00 0.00 0.00 3.95
1622 1660 5.233263 GTCAAGTCTGAACTCTGAACTGAAC 59.767 44.000 0.00 0.00 33.48 3.18
1623 1661 5.105351 TGTCAAGTCTGAACTCTGAACTGAA 60.105 40.000 0.00 0.00 33.48 3.02
1624 1662 4.402474 TGTCAAGTCTGAACTCTGAACTGA 59.598 41.667 0.00 0.00 33.48 3.41
1625 1663 4.686972 TGTCAAGTCTGAACTCTGAACTG 58.313 43.478 0.00 0.00 33.48 3.16
1626 1664 4.739137 GCTGTCAAGTCTGAACTCTGAACT 60.739 45.833 0.00 0.00 33.48 3.01
1630 1668 3.103447 TGCTGTCAAGTCTGAACTCTG 57.897 47.619 0.00 0.00 33.48 3.35
1631 1669 3.827008 TTGCTGTCAAGTCTGAACTCT 57.173 42.857 0.00 0.00 33.48 3.24
1632 1670 3.434984 GGATTGCTGTCAAGTCTGAACTC 59.565 47.826 0.00 0.00 35.37 3.01
1633 1671 3.181451 TGGATTGCTGTCAAGTCTGAACT 60.181 43.478 0.00 0.00 35.37 3.01
1634 1672 3.141398 TGGATTGCTGTCAAGTCTGAAC 58.859 45.455 0.00 0.00 35.37 3.18
1635 1673 3.490439 TGGATTGCTGTCAAGTCTGAA 57.510 42.857 0.00 0.00 35.37 3.02
1636 1674 3.490439 TTGGATTGCTGTCAAGTCTGA 57.510 42.857 0.00 0.00 35.37 3.27
1637 1675 3.504906 ACATTGGATTGCTGTCAAGTCTG 59.495 43.478 0.00 0.00 35.37 3.51
1638 1676 3.504906 CACATTGGATTGCTGTCAAGTCT 59.495 43.478 0.00 0.00 35.37 3.24
1639 1677 3.503363 TCACATTGGATTGCTGTCAAGTC 59.497 43.478 0.00 0.00 35.37 3.01
1640 1678 3.489355 TCACATTGGATTGCTGTCAAGT 58.511 40.909 0.00 0.00 35.37 3.16
1641 1679 4.713824 ATCACATTGGATTGCTGTCAAG 57.286 40.909 0.00 0.00 35.37 3.02
1642 1680 5.471556 AAATCACATTGGATTGCTGTCAA 57.528 34.783 0.00 0.00 37.55 3.18
1643 1681 5.471556 AAAATCACATTGGATTGCTGTCA 57.528 34.783 0.00 0.00 37.55 3.58
1644 1682 6.160664 CAAAAATCACATTGGATTGCTGTC 57.839 37.500 0.00 0.00 37.55 3.51
1654 1692 2.156117 CACGCAGCCAAAAATCACATTG 59.844 45.455 0.00 0.00 0.00 2.82
1655 1693 2.406130 CACGCAGCCAAAAATCACATT 58.594 42.857 0.00 0.00 0.00 2.71
1656 1694 1.936203 GCACGCAGCCAAAAATCACAT 60.936 47.619 0.00 0.00 37.23 3.21
1657 1695 0.597118 GCACGCAGCCAAAAATCACA 60.597 50.000 0.00 0.00 37.23 3.58
1658 1696 0.597118 TGCACGCAGCCAAAAATCAC 60.597 50.000 0.00 0.00 44.83 3.06
1745 1783 1.347320 GCTCGTCGGTTTGAAGGTAG 58.653 55.000 0.00 0.00 0.00 3.18
1788 1826 1.887707 GATCGGCCGGTGATGGAAC 60.888 63.158 27.83 0.00 0.00 3.62
1792 1830 0.815213 ACATTGATCGGCCGGTGATG 60.815 55.000 27.83 24.89 0.00 3.07
1793 1831 0.107214 AACATTGATCGGCCGGTGAT 60.107 50.000 27.83 12.13 0.00 3.06
1796 1834 0.035439 AAGAACATTGATCGGCCGGT 60.035 50.000 27.83 21.57 0.00 5.28
1797 1835 1.094785 AAAGAACATTGATCGGCCGG 58.905 50.000 27.83 10.66 0.00 6.13
1798 1836 1.737236 TCAAAGAACATTGATCGGCCG 59.263 47.619 22.12 22.12 34.50 6.13
1799 1837 4.107622 CAATCAAAGAACATTGATCGGCC 58.892 43.478 5.89 0.00 46.57 6.13
1800 1838 4.107622 CCAATCAAAGAACATTGATCGGC 58.892 43.478 5.89 0.00 46.57 5.54
1805 1856 5.505489 CGTGTGACCAATCAAAGAACATTGA 60.505 40.000 0.00 0.00 43.03 2.57
1818 1869 2.672996 GGGCTGCGTGTGACCAAT 60.673 61.111 0.00 0.00 0.00 3.16
1826 1877 4.457496 AGGATGACGGGCTGCGTG 62.457 66.667 0.00 0.00 0.00 5.34
1828 1879 4.147449 TCAGGATGACGGGCTGCG 62.147 66.667 0.00 0.00 42.56 5.18
1853 1916 1.369692 TTCACGGCGTCCTGTGAAT 59.630 52.632 10.85 0.00 46.86 2.57
1856 1919 2.738521 CCTTCACGGCGTCCTGTG 60.739 66.667 10.85 0.00 37.44 3.66
1857 1920 2.915659 TCCTTCACGGCGTCCTGT 60.916 61.111 10.85 0.00 0.00 4.00
2015 2089 5.505173 AATTAATTTGTGATCGAGGCAGG 57.495 39.130 0.00 0.00 0.00 4.85
2018 2092 6.136541 AGGAAATTAATTTGTGATCGAGGC 57.863 37.500 17.98 0.00 0.00 4.70
2023 2097 7.461107 TCGACGAAGGAAATTAATTTGTGATC 58.539 34.615 17.98 9.52 0.00 2.92
2038 2156 5.641636 TCATTTCATTTCAATCGACGAAGGA 59.358 36.000 0.00 0.00 0.00 3.36
2040 2158 7.780253 TTTCATTTCATTTCAATCGACGAAG 57.220 32.000 0.00 0.00 0.00 3.79
2044 2162 6.237915 GCCCATTTCATTTCATTTCAATCGAC 60.238 38.462 0.00 0.00 0.00 4.20
2783 2939 4.451774 GCAGAAGTGATCAGATATTCAGGC 59.548 45.833 0.00 3.74 0.00 4.85
2784 2940 5.608449 TGCAGAAGTGATCAGATATTCAGG 58.392 41.667 0.00 0.00 0.00 3.86
2785 2941 9.438228 AATATGCAGAAGTGATCAGATATTCAG 57.562 33.333 0.00 0.00 0.00 3.02
2786 2942 9.788889 AAATATGCAGAAGTGATCAGATATTCA 57.211 29.630 0.00 0.00 0.00 2.57
2826 2982 8.889717 CCTTCTGTATAAAATAATCACAACGGT 58.110 33.333 0.00 0.00 0.00 4.83
2896 3052 0.249868 ATGACATATCCGCCGTGTGG 60.250 55.000 0.00 0.00 38.77 4.17
2905 3061 9.653287 TCCTAACATAATCGAAATGACATATCC 57.347 33.333 15.72 0.00 0.00 2.59
2913 3069 7.861372 ACGACTAGTCCTAACATAATCGAAATG 59.139 37.037 17.23 9.02 0.00 2.32
2932 3088 0.108804 ATGCACGGGTTCACGACTAG 60.109 55.000 0.34 0.00 37.61 2.57
2933 3089 0.319083 AATGCACGGGTTCACGACTA 59.681 50.000 0.34 0.00 37.61 2.59
2934 3090 0.949105 GAATGCACGGGTTCACGACT 60.949 55.000 0.34 0.00 37.61 4.18
2935 3091 1.495951 GAATGCACGGGTTCACGAC 59.504 57.895 0.34 0.00 37.61 4.34
2936 3092 2.024868 CGAATGCACGGGTTCACGA 61.025 57.895 0.34 0.00 37.61 4.35
2937 3093 2.474266 CGAATGCACGGGTTCACG 59.526 61.111 0.00 0.00 40.31 4.35
2938 3094 2.175811 GCGAATGCACGGGTTCAC 59.824 61.111 0.00 0.00 42.15 3.18
2939 3095 3.418913 CGCGAATGCACGGGTTCA 61.419 61.111 0.00 0.00 42.97 3.18
2940 3096 4.811761 GCGCGAATGCACGGGTTC 62.812 66.667 12.10 2.10 45.42 3.62
2941 3097 3.943479 TAGCGCGAATGCACGGGTT 62.943 57.895 12.10 10.98 45.42 4.11
2942 3098 3.943479 TTAGCGCGAATGCACGGGT 62.943 57.895 12.10 5.67 45.42 5.28
2943 3099 2.047151 AATTAGCGCGAATGCACGGG 62.047 55.000 16.69 9.09 46.17 5.28
2944 3100 0.248054 AAATTAGCGCGAATGCACGG 60.248 50.000 16.69 0.00 42.97 4.94
2945 3101 1.534028 AAAATTAGCGCGAATGCACG 58.466 45.000 16.69 0.00 42.97 5.34
3465 3629 5.870706 TGTCACCAACTCACCAACATAATA 58.129 37.500 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.