Multiple sequence alignment - TraesCS3D01G047200

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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 TraesCS3D01G047200 chr3D 100.000 2732 0 0 1 2732 17655166 17652435 0.000000e+00 5046.0
1 TraesCS3D01G047200 chrUn 88.084 1049 92 8 666 1688 282457886 282456845 0.000000e+00 1214.0
2 TraesCS3D01G047200 chrUn 88.084 1049 92 8 666 1688 308580936 308581977 0.000000e+00 1214.0
3 TraesCS3D01G047200 chrUn 89.841 315 27 5 2360 2672 346501690 346501379 1.520000e-107 399.0
4 TraesCS3D01G047200 chr3A 87.428 1042 91 17 790 1815 25949162 25948145 0.000000e+00 1162.0
5 TraesCS3D01G047200 chr3A 92.279 531 27 8 2205 2732 25947579 25947060 0.000000e+00 741.0
6 TraesCS3D01G047200 chr3A 83.544 395 36 12 1842 2210 25948162 25947771 2.610000e-90 342.0
7 TraesCS3D01G047200 chr3A 84.932 292 28 8 2395 2672 19290045 19290334 5.760000e-72 281.0
8 TraesCS3D01G047200 chr3A 75.462 595 127 13 1092 1681 26410591 26411171 3.470000e-69 272.0
9 TraesCS3D01G047200 chr3A 75.645 349 66 9 1338 1681 26446398 26446732 3.640000e-34 156.0
10 TraesCS3D01G047200 chr3A 74.581 358 62 18 1336 1683 25954013 25953675 2.210000e-26 130.0
11 TraesCS3D01G047200 chr3A 82.353 85 13 2 1361 1444 25959144 25959061 3.770000e-09 73.1
12 TraesCS3D01G047200 chr7B 91.282 585 41 7 29 612 665605382 665605957 0.000000e+00 789.0
13 TraesCS3D01G047200 chr4A 84.859 601 66 16 24 614 543573146 543573731 1.410000e-162 582.0
14 TraesCS3D01G047200 chr4A 80.504 595 85 20 30 610 702919297 702918720 6.990000e-116 427.0
15 TraesCS3D01G047200 chr1B 88.320 488 52 4 27 514 605266522 605266040 5.070000e-162 580.0
16 TraesCS3D01G047200 chr1B 90.667 75 4 3 14 87 486541248 486541176 2.240000e-16 97.1
17 TraesCS3D01G047200 chr5B 84.041 589 75 16 28 607 393987456 393988034 1.430000e-152 549.0
18 TraesCS3D01G047200 chr7A 82.828 594 84 13 28 608 721887448 721886860 1.450000e-142 516.0
19 TraesCS3D01G047200 chr4B 87.615 436 48 6 173 607 536305065 536305495 4.060000e-138 501.0
20 TraesCS3D01G047200 chr4B 81.683 606 78 20 29 612 568443375 568442781 8.850000e-130 473.0
21 TraesCS3D01G047200 chr2B 85.207 338 48 1 275 612 649450596 649450931 2.010000e-91 346.0
22 TraesCS3D01G047200 chr2B 90.411 73 5 2 28 99 649450402 649450473 8.050000e-16 95.3
23 TraesCS3D01G047200 chr5A 85.987 157 19 3 29 182 590293749 590293905 6.050000e-37 165.0
24 TraesCS3D01G047200 chr3B 74.528 424 71 26 1336 1754 24933671 24934062 1.690000e-32 150.0
25 TraesCS3D01G047200 chr3B 81.818 143 23 2 1542 1681 29757632 29757774 1.720000e-22 117.0
26 TraesCS3D01G047200 chr5D 90.667 75 5 2 28 100 45599091 45599017 6.230000e-17 99.0


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 TraesCS3D01G047200 chr3D 17652435 17655166 2731 True 5046.000000 5046 100.000000 1 2732 1 chr3D.!!$R1 2731
1 TraesCS3D01G047200 chrUn 282456845 282457886 1041 True 1214.000000 1214 88.084000 666 1688 1 chrUn.!!$R1 1022
2 TraesCS3D01G047200 chrUn 308580936 308581977 1041 False 1214.000000 1214 88.084000 666 1688 1 chrUn.!!$F1 1022
3 TraesCS3D01G047200 chr3A 25947060 25949162 2102 True 748.333333 1162 87.750333 790 2732 3 chr3A.!!$R3 1942
4 TraesCS3D01G047200 chr3A 26410591 26411171 580 False 272.000000 272 75.462000 1092 1681 1 chr3A.!!$F2 589
5 TraesCS3D01G047200 chr7B 665605382 665605957 575 False 789.000000 789 91.282000 29 612 1 chr7B.!!$F1 583
6 TraesCS3D01G047200 chr4A 543573146 543573731 585 False 582.000000 582 84.859000 24 614 1 chr4A.!!$F1 590
7 TraesCS3D01G047200 chr4A 702918720 702919297 577 True 427.000000 427 80.504000 30 610 1 chr4A.!!$R1 580
8 TraesCS3D01G047200 chr5B 393987456 393988034 578 False 549.000000 549 84.041000 28 607 1 chr5B.!!$F1 579
9 TraesCS3D01G047200 chr7A 721886860 721887448 588 True 516.000000 516 82.828000 28 608 1 chr7A.!!$R1 580
10 TraesCS3D01G047200 chr4B 568442781 568443375 594 True 473.000000 473 81.683000 29 612 1 chr4B.!!$R1 583
11 TraesCS3D01G047200 chr2B 649450402 649450931 529 False 220.650000 346 87.809000 28 612 2 chr2B.!!$F1 584

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
723 768 0.034896 GTTCCAGTCACATCACGGGT 59.965 55.0 0.0 0.0 33.61 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2672 2986 0.036388 TGAACGATGAAGGGAGGCAC 60.036 55.0 0.0 0.0 0.0 5.01 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
22 23 2.937469 TTACATGCCAATTGCGAAGG 57.063 45.000 0.00 0.00 45.60 3.46
23 24 1.832883 TACATGCCAATTGCGAAGGT 58.167 45.000 0.00 0.00 45.60 3.50
24 25 0.968405 ACATGCCAATTGCGAAGGTT 59.032 45.000 0.00 0.00 45.60 3.50
25 26 1.337074 ACATGCCAATTGCGAAGGTTG 60.337 47.619 0.00 0.00 45.60 3.77
26 27 0.390209 ATGCCAATTGCGAAGGTTGC 60.390 50.000 0.00 0.00 45.60 4.17
166 185 7.096477 CGAAGACAAGCAAGGAAATAAAAACAG 60.096 37.037 0.00 0.00 0.00 3.16
186 207 0.690762 GGGAGGCCACTGTCTAACAA 59.309 55.000 5.01 0.00 0.00 2.83
211 234 4.280174 AGGCACTCGAACTACTTCTAAACA 59.720 41.667 0.00 0.00 0.00 2.83
212 235 4.621886 GGCACTCGAACTACTTCTAAACAG 59.378 45.833 0.00 0.00 0.00 3.16
213 236 5.221130 GCACTCGAACTACTTCTAAACAGT 58.779 41.667 0.00 0.00 0.00 3.55
237 269 2.753009 CTTAGCAGCACACCCAGGCA 62.753 60.000 0.00 0.00 0.00 4.75
241 273 2.044555 CAGCACACCCAGGCATCAG 61.045 63.158 0.00 0.00 0.00 2.90
246 278 1.226542 CACCCAGGCATCAGCATCT 59.773 57.895 0.00 0.00 44.61 2.90
258 294 2.747436 TCAGCATCTTGATCCGATTCG 58.253 47.619 0.00 0.00 0.00 3.34
364 407 1.180907 TGCTCGATGAGTCTTGCTCT 58.819 50.000 0.00 0.00 44.41 4.09
446 490 5.759273 CCAACCACACATCATTTTCACAATT 59.241 36.000 0.00 0.00 0.00 2.32
464 508 7.178573 TCACAATTTCCATTGGGTCAGTAATA 58.821 34.615 2.09 0.00 43.50 0.98
465 509 7.838696 TCACAATTTCCATTGGGTCAGTAATAT 59.161 33.333 2.09 0.00 43.50 1.28
466 510 8.477256 CACAATTTCCATTGGGTCAGTAATATT 58.523 33.333 2.09 0.00 43.82 1.28
544 588 4.804261 GCTGAAGTACCAACCAAGATCAGT 60.804 45.833 0.00 0.00 36.36 3.41
614 659 7.502226 AGTCACTGAGATCTCTAGGAGTATTTG 59.498 40.741 22.95 10.76 0.00 2.32
615 660 7.284489 GTCACTGAGATCTCTAGGAGTATTTGT 59.716 40.741 22.95 3.21 0.00 2.83
616 661 7.284261 TCACTGAGATCTCTAGGAGTATTTGTG 59.716 40.741 22.95 12.85 0.00 3.33
617 662 7.284261 CACTGAGATCTCTAGGAGTATTTGTGA 59.716 40.741 22.95 0.00 0.00 3.58
618 663 7.836685 ACTGAGATCTCTAGGAGTATTTGTGAA 59.163 37.037 22.95 0.00 0.00 3.18
619 664 8.231692 TGAGATCTCTAGGAGTATTTGTGAAG 57.768 38.462 22.95 0.00 0.00 3.02
620 665 7.286546 TGAGATCTCTAGGAGTATTTGTGAAGG 59.713 40.741 22.95 0.00 0.00 3.46
621 666 7.129425 AGATCTCTAGGAGTATTTGTGAAGGT 58.871 38.462 0.00 0.00 0.00 3.50
622 667 7.621683 AGATCTCTAGGAGTATTTGTGAAGGTT 59.378 37.037 0.00 0.00 0.00 3.50
623 668 6.936279 TCTCTAGGAGTATTTGTGAAGGTTG 58.064 40.000 0.00 0.00 0.00 3.77
624 669 6.497259 TCTCTAGGAGTATTTGTGAAGGTTGT 59.503 38.462 0.00 0.00 0.00 3.32
625 670 7.672660 TCTCTAGGAGTATTTGTGAAGGTTGTA 59.327 37.037 0.00 0.00 0.00 2.41
626 671 7.609056 TCTAGGAGTATTTGTGAAGGTTGTAC 58.391 38.462 0.00 0.00 0.00 2.90
627 672 6.182507 AGGAGTATTTGTGAAGGTTGTACA 57.817 37.500 0.00 0.00 0.00 2.90
628 673 6.597562 AGGAGTATTTGTGAAGGTTGTACAA 58.402 36.000 3.59 3.59 32.93 2.41
629 674 7.057894 AGGAGTATTTGTGAAGGTTGTACAAA 58.942 34.615 10.51 0.00 45.12 2.83
630 675 7.228706 AGGAGTATTTGTGAAGGTTGTACAAAG 59.771 37.037 10.51 0.00 44.51 2.77
631 676 7.227910 GGAGTATTTGTGAAGGTTGTACAAAGA 59.772 37.037 10.51 0.00 44.51 2.52
632 677 8.691661 AGTATTTGTGAAGGTTGTACAAAGAT 57.308 30.769 10.51 0.00 44.51 2.40
633 678 8.784043 AGTATTTGTGAAGGTTGTACAAAGATC 58.216 33.333 10.51 9.06 44.51 2.75
634 679 7.581213 ATTTGTGAAGGTTGTACAAAGATCA 57.419 32.000 10.51 11.49 44.51 2.92
635 680 7.581213 TTTGTGAAGGTTGTACAAAGATCAT 57.419 32.000 10.51 0.00 38.83 2.45
636 681 8.684386 TTTGTGAAGGTTGTACAAAGATCATA 57.316 30.769 10.51 9.92 38.83 2.15
637 682 8.684386 TTGTGAAGGTTGTACAAAGATCATAA 57.316 30.769 10.51 14.68 31.95 1.90
638 683 8.862325 TGTGAAGGTTGTACAAAGATCATAAT 57.138 30.769 10.51 0.00 0.00 1.28
639 684 8.946085 TGTGAAGGTTGTACAAAGATCATAATC 58.054 33.333 10.51 4.10 0.00 1.75
640 685 8.946085 GTGAAGGTTGTACAAAGATCATAATCA 58.054 33.333 10.51 2.81 34.07 2.57
641 686 9.513906 TGAAGGTTGTACAAAGATCATAATCAA 57.486 29.630 10.51 0.00 34.07 2.57
642 687 9.774742 GAAGGTTGTACAAAGATCATAATCAAC 57.225 33.333 10.51 3.68 34.07 3.18
643 688 9.520515 AAGGTTGTACAAAGATCATAATCAACT 57.479 29.630 10.51 0.00 34.87 3.16
644 689 9.167311 AGGTTGTACAAAGATCATAATCAACTC 57.833 33.333 10.51 0.00 34.87 3.01
645 690 8.398665 GGTTGTACAAAGATCATAATCAACTCC 58.601 37.037 10.51 0.00 34.87 3.85
646 691 9.167311 GTTGTACAAAGATCATAATCAACTCCT 57.833 33.333 10.51 0.00 34.07 3.69
647 692 9.739276 TTGTACAAAGATCATAATCAACTCCTT 57.261 29.630 5.64 0.00 34.07 3.36
650 695 8.443953 ACAAAGATCATAATCAACTCCTTAGC 57.556 34.615 0.00 0.00 34.07 3.09
651 696 8.049117 ACAAAGATCATAATCAACTCCTTAGCA 58.951 33.333 0.00 0.00 34.07 3.49
652 697 8.896744 CAAAGATCATAATCAACTCCTTAGCAA 58.103 33.333 0.00 0.00 34.07 3.91
653 698 9.466497 AAAGATCATAATCAACTCCTTAGCAAA 57.534 29.630 0.00 0.00 34.07 3.68
654 699 8.443953 AGATCATAATCAACTCCTTAGCAAAC 57.556 34.615 0.00 0.00 34.07 2.93
655 700 8.049117 AGATCATAATCAACTCCTTAGCAAACA 58.951 33.333 0.00 0.00 34.07 2.83
656 701 7.994425 TCATAATCAACTCCTTAGCAAACAA 57.006 32.000 0.00 0.00 0.00 2.83
657 702 8.044060 TCATAATCAACTCCTTAGCAAACAAG 57.956 34.615 0.00 0.00 0.00 3.16
658 703 7.882791 TCATAATCAACTCCTTAGCAAACAAGA 59.117 33.333 0.00 0.00 0.00 3.02
659 704 6.566197 AATCAACTCCTTAGCAAACAAGAG 57.434 37.500 0.00 0.00 0.00 2.85
660 705 4.389374 TCAACTCCTTAGCAAACAAGAGG 58.611 43.478 0.00 0.00 0.00 3.69
661 706 3.425162 ACTCCTTAGCAAACAAGAGGG 57.575 47.619 0.00 0.00 0.00 4.30
662 707 2.087646 CTCCTTAGCAAACAAGAGGGC 58.912 52.381 0.00 0.00 0.00 5.19
663 708 1.423541 TCCTTAGCAAACAAGAGGGCA 59.576 47.619 0.00 0.00 0.00 5.36
664 709 2.158534 TCCTTAGCAAACAAGAGGGCAA 60.159 45.455 0.00 0.00 0.00 4.52
671 716 2.887152 CAAACAAGAGGGCAAAGTAGCT 59.113 45.455 0.00 0.00 34.17 3.32
672 717 2.481289 ACAAGAGGGCAAAGTAGCTC 57.519 50.000 0.00 0.00 34.37 4.09
680 725 2.354403 GGGCAAAGTAGCTCGAACCTAA 60.354 50.000 0.00 0.00 34.17 2.69
681 726 3.332034 GGCAAAGTAGCTCGAACCTAAA 58.668 45.455 0.00 0.00 34.17 1.85
689 734 5.749109 AGTAGCTCGAACCTAAAAATGATCG 59.251 40.000 0.00 0.00 0.00 3.69
691 736 3.002348 GCTCGAACCTAAAAATGATCGGG 59.998 47.826 0.00 0.00 34.09 5.14
693 738 2.680841 CGAACCTAAAAATGATCGGGCA 59.319 45.455 0.00 0.00 0.00 5.36
696 741 5.474825 GAACCTAAAAATGATCGGGCAAAA 58.525 37.500 0.00 0.00 0.00 2.44
697 742 4.816392 ACCTAAAAATGATCGGGCAAAAC 58.184 39.130 0.00 0.00 0.00 2.43
706 751 0.178975 TCGGGCAAAACATCCTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
707 752 0.243636 CGGGCAAAACATCCTGGTTC 59.756 55.000 0.00 0.00 0.00 3.62
723 768 0.034896 GTTCCAGTCACATCACGGGT 59.965 55.000 0.00 0.00 33.61 5.28
729 774 1.086696 GTCACATCACGGGTTCATGG 58.913 55.000 0.00 0.00 0.00 3.66
731 776 1.903183 TCACATCACGGGTTCATGGTA 59.097 47.619 0.00 0.00 0.00 3.25
763 808 1.429463 GCTCAATCCGTCAAAGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
891 962 2.936498 CAAATGTTCCGGCCACTAGTAG 59.064 50.000 2.24 0.00 0.00 2.57
894 965 1.272313 TGTTCCGGCCACTAGTAGTCT 60.272 52.381 2.24 0.00 0.00 3.24
895 966 2.025981 TGTTCCGGCCACTAGTAGTCTA 60.026 50.000 2.24 0.00 0.00 2.59
896 967 2.617774 GTTCCGGCCACTAGTAGTCTAG 59.382 54.545 2.24 1.37 46.43 2.43
905 976 1.189884 CTAGTAGTCTAGTCGTCGCGC 59.810 57.143 0.00 0.00 38.91 6.86
906 977 0.459934 AGTAGTCTAGTCGTCGCGCT 60.460 55.000 5.56 0.00 0.00 5.92
907 978 0.315220 GTAGTCTAGTCGTCGCGCTG 60.315 60.000 5.56 0.00 0.00 5.18
951 1022 1.891150 CTTCCACCACGTAGTACACCT 59.109 52.381 0.38 0.00 41.61 4.00
988 1059 3.306294 GCCCTTTGTCCATCTTCCAAAAG 60.306 47.826 0.00 0.00 0.00 2.27
1035 1106 0.178990 GGTTCTTCCTGGCCTTGTGT 60.179 55.000 3.32 0.00 0.00 3.72
1040 1111 1.347707 CTTCCTGGCCTTGTGTCTACA 59.652 52.381 3.32 0.00 34.31 2.74
1087 1158 1.748500 GAGCAAGGAGAAGGCTGCC 60.749 63.158 11.65 11.65 38.15 4.85
1223 1294 1.394917 CTTCACCGGATTTGCTTCTCG 59.605 52.381 9.46 0.00 0.00 4.04
1232 1303 3.119602 GGATTTGCTTCTCGGGTTTTACC 60.120 47.826 0.00 0.00 37.60 2.85
1272 1343 1.166531 ACGGCTTTGCAGTCCTCAAC 61.167 55.000 0.00 0.00 29.95 3.18
1389 1460 3.056328 GTCAAACTGCGGCCCTCC 61.056 66.667 0.00 0.00 0.00 4.30
1406 1477 2.058595 CCTTCAGGATCGACCCCGT 61.059 63.158 0.00 0.00 40.05 5.28
1437 1508 3.265791 CCTCATCTTCTACAACTGCACC 58.734 50.000 0.00 0.00 0.00 5.01
1446 1517 2.032681 AACTGCACCGAGAAGGCC 59.967 61.111 0.00 0.00 46.52 5.19
1507 1578 4.373116 CGACGGTGAGGTGTGGGG 62.373 72.222 0.00 0.00 0.00 4.96
1539 1610 2.126228 CTTGTTCGCGCGGGAGTA 60.126 61.111 31.69 15.62 0.00 2.59
1545 1616 1.386525 TTCGCGCGGGAGTACCTTAT 61.387 55.000 31.69 0.00 36.97 1.73
1549 1620 0.031721 CGCGGGAGTACCTTATGACC 59.968 60.000 0.00 0.00 36.97 4.02
1555 1626 2.664015 GAGTACCTTATGACCCGACCT 58.336 52.381 0.00 0.00 0.00 3.85
1556 1627 3.029570 GAGTACCTTATGACCCGACCTT 58.970 50.000 0.00 0.00 0.00 3.50
1670 1744 2.124570 CATCAGGGGTGGCTTCCG 60.125 66.667 0.00 0.00 0.00 4.30
1692 1766 0.392863 TGACATGGCATGAACCTCCG 60.393 55.000 32.74 5.02 0.00 4.63
1730 1804 2.761767 TCACCCGACGGATCATCTTTTA 59.238 45.455 17.49 0.00 0.00 1.52
1731 1805 3.123804 CACCCGACGGATCATCTTTTAG 58.876 50.000 17.49 0.00 0.00 1.85
1739 1813 6.090898 CGACGGATCATCTTTTAGTCAAGTTT 59.909 38.462 0.00 0.00 0.00 2.66
1754 1828 4.330347 GTCAAGTTTGTAGCTTAGCTAGGC 59.670 45.833 19.53 19.53 42.11 3.93
1774 1857 0.041684 CCCTTGCTTGGATTTCCCCT 59.958 55.000 0.00 0.00 34.29 4.79
1784 1867 3.989056 TGGATTTCCCCTTTATTGACCC 58.011 45.455 0.00 0.00 34.29 4.46
1797 1882 2.601240 TTGACCCAAGCCATCAATCA 57.399 45.000 0.00 0.00 0.00 2.57
1798 1883 2.832643 TGACCCAAGCCATCAATCAT 57.167 45.000 0.00 0.00 0.00 2.45
1799 1884 2.380941 TGACCCAAGCCATCAATCATG 58.619 47.619 0.00 0.00 0.00 3.07
1800 1885 1.068127 GACCCAAGCCATCAATCATGC 59.932 52.381 0.00 0.00 0.00 4.06
1801 1886 1.116308 CCCAAGCCATCAATCATGCA 58.884 50.000 0.00 0.00 0.00 3.96
1802 1887 1.691976 CCCAAGCCATCAATCATGCAT 59.308 47.619 0.00 0.00 0.00 3.96
1803 1888 2.288825 CCCAAGCCATCAATCATGCATC 60.289 50.000 0.00 0.00 0.00 3.91
1804 1889 2.364002 CCAAGCCATCAATCATGCATCA 59.636 45.455 0.00 0.00 0.00 3.07
1805 1890 3.006859 CCAAGCCATCAATCATGCATCAT 59.993 43.478 0.00 0.00 0.00 2.45
1806 1891 3.942130 AGCCATCAATCATGCATCATG 57.058 42.857 0.00 0.00 42.60 3.07
1807 1892 2.029020 AGCCATCAATCATGCATCATGC 60.029 45.455 1.35 1.35 45.29 4.06
1822 1907 1.045407 CATGCATTCATGGGAAGGGG 58.955 55.000 0.00 0.00 44.84 4.79
1823 1908 0.638292 ATGCATTCATGGGAAGGGGT 59.362 50.000 0.00 0.00 35.43 4.95
1824 1909 0.324552 TGCATTCATGGGAAGGGGTG 60.325 55.000 0.00 0.00 35.43 4.61
1825 1910 0.324645 GCATTCATGGGAAGGGGTGT 60.325 55.000 0.00 0.00 35.43 4.16
1826 1911 1.477553 CATTCATGGGAAGGGGTGTG 58.522 55.000 0.00 0.00 36.25 3.82
1827 1912 1.084018 ATTCATGGGAAGGGGTGTGT 58.916 50.000 0.00 0.00 36.25 3.72
1828 1913 0.112218 TTCATGGGAAGGGGTGTGTG 59.888 55.000 0.00 0.00 0.00 3.82
1829 1914 1.978617 CATGGGAAGGGGTGTGTGC 60.979 63.158 0.00 0.00 0.00 4.57
1830 1915 3.224007 ATGGGAAGGGGTGTGTGCC 62.224 63.158 0.00 0.00 0.00 5.01
1838 1923 4.572571 GGTGTGTGCCCGGTTGGA 62.573 66.667 0.00 0.00 37.49 3.53
1839 1924 2.517402 GTGTGTGCCCGGTTGGAA 60.517 61.111 0.00 0.00 37.49 3.53
1840 1925 2.122167 GTGTGTGCCCGGTTGGAAA 61.122 57.895 0.00 0.00 37.49 3.13
1916 2017 2.831742 CCGGGCAGCGAGGTACTA 60.832 66.667 0.00 0.00 41.55 1.82
1917 2018 2.722487 CGGGCAGCGAGGTACTAG 59.278 66.667 0.00 0.00 41.55 2.57
1931 2032 1.555533 GTACTAGCTTCCTGCCCAAGT 59.444 52.381 0.00 0.00 44.23 3.16
1988 2089 5.046231 GCCAAATTGGTATAACCCCTTTTCA 60.046 40.000 14.17 0.00 40.46 2.69
1990 2091 7.454225 CCAAATTGGTATAACCCCTTTTCAAA 58.546 34.615 3.34 0.00 37.50 2.69
2046 2148 2.680805 CGGCACTATGGCATATTAGGGG 60.681 54.545 7.81 0.00 43.94 4.79
2053 2155 2.187958 TGGCATATTAGGGGATCTCCG 58.812 52.381 5.81 0.00 36.71 4.63
2057 2159 3.368531 GCATATTAGGGGATCTCCGACAC 60.369 52.174 5.81 0.00 36.71 3.67
2064 2166 1.404315 GGGATCTCCGACACAAGTCAC 60.404 57.143 0.00 0.00 45.23 3.67
2065 2167 1.546476 GGATCTCCGACACAAGTCACT 59.454 52.381 0.00 0.00 45.23 3.41
2066 2168 2.600731 GATCTCCGACACAAGTCACTG 58.399 52.381 0.00 0.00 45.23 3.66
2087 2189 0.473694 ATCTCCCCCATATGTCCGCA 60.474 55.000 1.24 0.00 0.00 5.69
2116 2231 6.849588 AAAAACTGGCTCATCAAATTTGTC 57.150 33.333 17.47 3.94 0.00 3.18
2122 2237 2.159379 GCTCATCAAATTTGTCCGGACC 60.159 50.000 31.19 14.15 0.00 4.46
2132 2247 0.106369 TGTCCGGACCGTATGGATCT 60.106 55.000 31.19 0.00 39.21 2.75
2149 2264 1.675641 CTCCTTGTTCGCCCCCAAG 60.676 63.158 0.00 0.00 38.21 3.61
2173 2288 2.525629 GGAGCTCTAGGGGAGGCC 60.526 72.222 14.64 0.00 42.08 5.19
2174 2289 2.283809 GAGCTCTAGGGGAGGCCA 59.716 66.667 5.01 0.00 42.08 5.36
2182 2297 2.856039 TAGGGGAGGCCAGACAGTCG 62.856 65.000 5.01 0.00 0.00 4.18
2183 2298 2.680352 GGGAGGCCAGACAGTCGA 60.680 66.667 5.01 0.00 0.00 4.20
2188 2303 2.126424 GCCAGACAGTCGACGGAC 60.126 66.667 22.71 16.02 43.76 4.79
2210 2325 1.068588 CCGTCAACTCAGTCTTGGACA 59.931 52.381 0.52 0.00 34.60 4.02
2230 2542 5.453198 GGACACCATCACAAATCCACTTTTT 60.453 40.000 0.00 0.00 0.00 1.94
2286 2598 8.547967 TTGCTATTACTAAGTTGGTTGAGAAG 57.452 34.615 0.00 0.00 0.00 2.85
2289 2601 9.649167 GCTATTACTAAGTTGGTTGAGAAGTTA 57.351 33.333 0.00 0.00 0.00 2.24
2298 2610 9.750125 AAGTTGGTTGAGAAGTTATGATTTTTC 57.250 29.630 0.00 0.00 0.00 2.29
2305 2617 9.985730 TTGAGAAGTTATGATTTTTCAAATGCT 57.014 25.926 0.00 0.00 27.58 3.79
2310 2622 8.707938 AGTTATGATTTTTCAAATGCTAAGGC 57.292 30.769 0.00 0.00 39.26 4.35
2312 2624 9.154847 GTTATGATTTTTCAAATGCTAAGGCTT 57.845 29.630 4.58 4.58 39.59 4.35
2376 2688 2.154462 GCTGTTATCTGCCAAGTGTGT 58.846 47.619 0.00 0.00 33.40 3.72
2378 2690 3.372206 GCTGTTATCTGCCAAGTGTGTAG 59.628 47.826 0.00 0.00 33.40 2.74
2394 2706 5.412594 AGTGTGTAGGTTGCACAAATATCAG 59.587 40.000 1.60 0.00 46.65 2.90
2409 2721 8.710551 CACAAATATCAGAATCTACTCATCAGC 58.289 37.037 0.00 0.00 0.00 4.26
2431 2743 1.897560 ACAAGAGCACAAAGTAGGCC 58.102 50.000 0.00 0.00 0.00 5.19
2456 2768 6.017605 CGAACTTAAATGATCAGGCTAAGCAT 60.018 38.462 15.85 9.05 0.00 3.79
2461 2773 3.920231 TGATCAGGCTAAGCATTCTGT 57.080 42.857 0.00 0.00 0.00 3.41
2464 2776 4.637534 TGATCAGGCTAAGCATTCTGTTTC 59.362 41.667 0.00 0.00 0.00 2.78
2530 2844 2.285141 CGTCAAAGTCGTTACACGCAAA 60.285 45.455 0.00 0.00 42.21 3.68
2561 2875 2.498167 CATGGCTTACTAGTCCATGGC 58.502 52.381 24.69 13.52 44.08 4.40
2569 2883 5.784177 CTTACTAGTCCATGGCGTCATTAT 58.216 41.667 6.96 0.00 0.00 1.28
2623 2937 1.263217 CCGTTTGCAGTCAACTGTACC 59.737 52.381 11.55 0.62 45.45 3.34
2634 2948 2.202570 CTGTACCCCGCTCGTTCG 60.203 66.667 0.00 0.00 0.00 3.95
2672 2986 2.724977 TCAAGCTTCGACCACAGTAG 57.275 50.000 0.00 0.00 0.00 2.57
2683 2997 0.250513 CCACAGTAGTGCCTCCCTTC 59.749 60.000 0.00 0.00 44.53 3.46
2710 3024 2.912295 TCATTCACCACAATCTCTCCCA 59.088 45.455 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.584325 ACCTTCGCAATTGGCATGTAATAT 59.416 37.500 7.72 0.00 45.17 1.28
2 3 2.760092 ACCTTCGCAATTGGCATGTAAT 59.240 40.909 7.72 0.00 45.17 1.89
5 6 0.968405 AACCTTCGCAATTGGCATGT 59.032 45.000 7.72 0.00 45.17 3.21
6 7 1.352114 CAACCTTCGCAATTGGCATG 58.648 50.000 7.72 0.00 45.17 4.06
7 8 0.390209 GCAACCTTCGCAATTGGCAT 60.390 50.000 7.72 0.00 45.17 4.40
8 9 1.006337 GCAACCTTCGCAATTGGCA 60.006 52.632 7.72 0.00 45.17 4.92
9 10 0.319813 AAGCAACCTTCGCAATTGGC 60.320 50.000 7.72 0.00 39.90 4.52
10 11 2.153366 AAAGCAACCTTCGCAATTGG 57.847 45.000 7.72 0.00 0.00 3.16
166 185 1.198759 TGTTAGACAGTGGCCTCCCC 61.199 60.000 3.32 0.00 0.00 4.81
186 207 6.152323 TGTTTAGAAGTAGTTCGAGTGCCTAT 59.848 38.462 4.65 0.00 37.79 2.57
229 261 0.395311 CAAGATGCTGATGCCTGGGT 60.395 55.000 0.00 0.00 38.71 4.51
237 269 3.324117 CGAATCGGATCAAGATGCTGAT 58.676 45.455 0.00 2.54 38.79 2.90
241 273 0.514691 GGCGAATCGGATCAAGATGC 59.485 55.000 4.35 1.81 0.00 3.91
246 278 2.677836 CTCTTTTGGCGAATCGGATCAA 59.322 45.455 4.35 0.00 0.00 2.57
258 294 4.757799 GAAGGAAGTCTTCTCTTTTGGC 57.242 45.455 12.31 0.28 46.30 4.52
283 326 0.602638 TGGCGTGCTTCGAATTCAGT 60.603 50.000 6.22 0.00 42.86 3.41
364 407 4.698780 CAGAGGAAAGAATGTTGATGCTGA 59.301 41.667 0.00 0.00 0.00 4.26
614 659 8.946085 TGATTATGATCTTTGTACAACCTTCAC 58.054 33.333 8.07 0.00 33.28 3.18
615 660 9.513906 TTGATTATGATCTTTGTACAACCTTCA 57.486 29.630 8.07 11.28 33.28 3.02
616 661 9.774742 GTTGATTATGATCTTTGTACAACCTTC 57.225 33.333 8.07 5.91 33.28 3.46
617 662 9.520515 AGTTGATTATGATCTTTGTACAACCTT 57.479 29.630 8.07 0.00 36.71 3.50
618 663 9.167311 GAGTTGATTATGATCTTTGTACAACCT 57.833 33.333 8.07 0.00 36.71 3.50
619 664 8.398665 GGAGTTGATTATGATCTTTGTACAACC 58.601 37.037 8.07 0.00 36.71 3.77
620 665 9.167311 AGGAGTTGATTATGATCTTTGTACAAC 57.833 33.333 8.07 0.00 36.43 3.32
621 666 9.739276 AAGGAGTTGATTATGATCTTTGTACAA 57.261 29.630 3.59 3.59 33.28 2.41
624 669 9.547753 GCTAAGGAGTTGATTATGATCTTTGTA 57.452 33.333 0.00 0.00 33.28 2.41
625 670 8.049117 TGCTAAGGAGTTGATTATGATCTTTGT 58.951 33.333 0.00 0.00 33.28 2.83
626 671 8.442632 TGCTAAGGAGTTGATTATGATCTTTG 57.557 34.615 0.00 0.00 33.28 2.77
627 672 9.466497 TTTGCTAAGGAGTTGATTATGATCTTT 57.534 29.630 0.00 0.00 33.28 2.52
628 673 8.897752 GTTTGCTAAGGAGTTGATTATGATCTT 58.102 33.333 0.00 0.00 33.28 2.40
629 674 8.049117 TGTTTGCTAAGGAGTTGATTATGATCT 58.951 33.333 0.00 0.00 33.28 2.75
630 675 8.213518 TGTTTGCTAAGGAGTTGATTATGATC 57.786 34.615 0.00 0.00 0.00 2.92
631 676 8.579850 TTGTTTGCTAAGGAGTTGATTATGAT 57.420 30.769 0.00 0.00 0.00 2.45
632 677 7.882791 TCTTGTTTGCTAAGGAGTTGATTATGA 59.117 33.333 0.00 0.00 0.00 2.15
633 678 8.044060 TCTTGTTTGCTAAGGAGTTGATTATG 57.956 34.615 0.00 0.00 0.00 1.90
634 679 7.337942 CCTCTTGTTTGCTAAGGAGTTGATTAT 59.662 37.037 0.00 0.00 0.00 1.28
635 680 6.655003 CCTCTTGTTTGCTAAGGAGTTGATTA 59.345 38.462 0.00 0.00 0.00 1.75
636 681 5.474876 CCTCTTGTTTGCTAAGGAGTTGATT 59.525 40.000 0.00 0.00 0.00 2.57
637 682 5.006386 CCTCTTGTTTGCTAAGGAGTTGAT 58.994 41.667 0.00 0.00 0.00 2.57
638 683 4.389374 CCTCTTGTTTGCTAAGGAGTTGA 58.611 43.478 0.00 0.00 0.00 3.18
639 684 3.503748 CCCTCTTGTTTGCTAAGGAGTTG 59.496 47.826 0.00 0.00 0.00 3.16
640 685 3.756117 CCCTCTTGTTTGCTAAGGAGTT 58.244 45.455 0.00 0.00 0.00 3.01
641 686 2.553247 GCCCTCTTGTTTGCTAAGGAGT 60.553 50.000 0.00 0.00 0.00 3.85
642 687 2.087646 GCCCTCTTGTTTGCTAAGGAG 58.912 52.381 0.00 0.00 0.00 3.69
643 688 1.423541 TGCCCTCTTGTTTGCTAAGGA 59.576 47.619 0.00 0.00 0.00 3.36
644 689 1.909700 TGCCCTCTTGTTTGCTAAGG 58.090 50.000 0.00 0.00 0.00 2.69
645 690 3.319122 ACTTTGCCCTCTTGTTTGCTAAG 59.681 43.478 0.00 0.00 40.66 2.18
646 691 3.295973 ACTTTGCCCTCTTGTTTGCTAA 58.704 40.909 0.00 0.00 0.00 3.09
647 692 2.944129 ACTTTGCCCTCTTGTTTGCTA 58.056 42.857 0.00 0.00 0.00 3.49
648 693 1.780503 ACTTTGCCCTCTTGTTTGCT 58.219 45.000 0.00 0.00 0.00 3.91
649 694 2.608016 GCTACTTTGCCCTCTTGTTTGC 60.608 50.000 0.00 0.00 0.00 3.68
650 695 2.887152 AGCTACTTTGCCCTCTTGTTTG 59.113 45.455 0.00 0.00 0.00 2.93
651 696 3.149981 GAGCTACTTTGCCCTCTTGTTT 58.850 45.455 0.00 0.00 0.00 2.83
652 697 2.784347 GAGCTACTTTGCCCTCTTGTT 58.216 47.619 0.00 0.00 0.00 2.83
653 698 1.338200 CGAGCTACTTTGCCCTCTTGT 60.338 52.381 0.00 0.00 0.00 3.16
654 699 1.066858 TCGAGCTACTTTGCCCTCTTG 60.067 52.381 0.00 0.00 0.00 3.02
655 700 1.267121 TCGAGCTACTTTGCCCTCTT 58.733 50.000 0.00 0.00 0.00 2.85
656 701 1.066787 GTTCGAGCTACTTTGCCCTCT 60.067 52.381 0.00 0.00 0.00 3.69
657 702 1.360820 GTTCGAGCTACTTTGCCCTC 58.639 55.000 0.00 0.00 0.00 4.30
658 703 0.036294 GGTTCGAGCTACTTTGCCCT 60.036 55.000 0.00 0.00 0.00 5.19
659 704 0.036294 AGGTTCGAGCTACTTTGCCC 60.036 55.000 0.00 0.00 0.00 5.36
660 705 2.667473 TAGGTTCGAGCTACTTTGCC 57.333 50.000 0.00 0.00 0.00 4.52
661 706 5.352643 TTTTTAGGTTCGAGCTACTTTGC 57.647 39.130 0.00 0.00 0.00 3.68
662 707 7.129109 TCATTTTTAGGTTCGAGCTACTTTG 57.871 36.000 0.00 0.00 0.00 2.77
663 708 7.201530 CGATCATTTTTAGGTTCGAGCTACTTT 60.202 37.037 0.00 0.00 0.00 2.66
664 709 6.255887 CGATCATTTTTAGGTTCGAGCTACTT 59.744 38.462 0.00 0.00 0.00 2.24
671 716 2.940410 GCCCGATCATTTTTAGGTTCGA 59.060 45.455 0.00 0.00 0.00 3.71
672 717 2.680841 TGCCCGATCATTTTTAGGTTCG 59.319 45.455 0.00 0.00 0.00 3.95
680 725 3.515104 AGGATGTTTTGCCCGATCATTTT 59.485 39.130 0.00 0.00 0.00 1.82
681 726 3.099141 AGGATGTTTTGCCCGATCATTT 58.901 40.909 0.00 0.00 0.00 2.32
689 734 0.608130 GGAACCAGGATGTTTTGCCC 59.392 55.000 0.00 0.00 0.00 5.36
691 736 2.730550 CTGGAACCAGGATGTTTTGC 57.269 50.000 12.54 0.00 40.17 3.68
706 751 0.320374 GAACCCGTGATGTGACTGGA 59.680 55.000 0.00 0.00 0.00 3.86
707 752 0.034756 TGAACCCGTGATGTGACTGG 59.965 55.000 0.00 0.00 0.00 4.00
729 774 2.988010 TGAGCCATGACCATGACTAC 57.012 50.000 11.28 1.48 41.20 2.73
731 776 2.422519 GGATTGAGCCATGACCATGACT 60.423 50.000 11.28 5.07 41.20 3.41
747 792 4.048820 GTGTAACGACTTTGACGGATTG 57.951 45.455 0.00 0.00 34.93 2.67
763 808 2.203308 TTTTGCGGGGCCGTGTAA 60.203 55.556 0.00 0.00 42.09 2.41
802 861 1.076513 TGGACTGGTAGGCAGTGACTA 59.923 52.381 0.01 0.01 32.33 2.59
812 871 3.771577 ACTGAAACCTTGGACTGGTAG 57.228 47.619 0.00 0.00 36.69 3.18
891 962 2.277373 CCAGCGCGACGACTAGAC 60.277 66.667 12.10 0.00 0.00 2.59
905 976 1.198713 AGATATATGGAGGCGCCCAG 58.801 55.000 26.15 0.00 39.97 4.45
906 977 1.555075 GAAGATATATGGAGGCGCCCA 59.445 52.381 26.15 16.30 41.05 5.36
907 978 1.134371 GGAAGATATATGGAGGCGCCC 60.134 57.143 26.15 15.07 34.97 6.13
951 1022 0.838987 AGGGCTACGGGGACTTTTGA 60.839 55.000 0.00 0.00 0.00 2.69
988 1059 1.427592 GCAGACATCGGAGCAGAAGC 61.428 60.000 0.00 0.00 42.56 3.86
1025 1096 1.813862 GCAGTTGTAGACACAAGGCCA 60.814 52.381 5.01 0.00 45.18 5.36
1035 1106 0.038251 CCACGAGCAGCAGTTGTAGA 60.038 55.000 0.00 0.00 0.00 2.59
1071 1142 2.753446 GGGCAGCCTTCTCCTTGC 60.753 66.667 12.43 0.00 35.87 4.01
1120 1191 2.048503 CCAGAACGGGTCGGACAC 60.049 66.667 10.76 5.20 0.00 3.67
1223 1294 0.935196 CATAGCGCTCGGTAAAACCC 59.065 55.000 16.34 0.00 33.75 4.11
1333 1404 0.467844 ACATGGCAGCTGTTGGTGAA 60.468 50.000 16.64 0.00 43.76 3.18
1336 1407 2.567497 GCACATGGCAGCTGTTGGT 61.567 57.895 16.64 6.12 43.97 3.67
1389 1460 1.320344 TGACGGGGTCGATCCTGAAG 61.320 60.000 30.50 13.71 40.11 3.02
1406 1477 4.838423 TGTAGAAGATGAGGTTCAGGTTGA 59.162 41.667 0.00 0.00 0.00 3.18
1458 1529 3.179265 CGATCACGACGTGCCACC 61.179 66.667 22.99 10.22 42.66 4.61
1507 1578 1.374758 CAAGCACCTCCCACTCGTC 60.375 63.158 0.00 0.00 0.00 4.20
1539 1610 1.946984 TCAAGGTCGGGTCATAAGGT 58.053 50.000 0.00 0.00 0.00 3.50
1545 1616 0.599558 CGTAGTTCAAGGTCGGGTCA 59.400 55.000 0.00 0.00 0.00 4.02
1549 1620 1.804326 CGCCGTAGTTCAAGGTCGG 60.804 63.158 0.00 0.00 43.37 4.79
1555 1626 1.153978 CGTAGCCGCCGTAGTTCAA 60.154 57.895 0.00 0.00 0.00 2.69
1556 1627 2.486504 CGTAGCCGCCGTAGTTCA 59.513 61.111 0.00 0.00 0.00 3.18
1670 1744 1.133790 GAGGTTCATGCCATGTCAAGC 59.866 52.381 4.31 2.57 0.00 4.01
1692 1766 3.624831 GAACTTACGTGCACGGCGC 62.625 63.158 39.21 19.84 44.95 6.53
1718 1792 8.178313 GCTACAAACTTGACTAAAAGATGATCC 58.822 37.037 0.00 0.00 0.00 3.36
1730 1804 5.725362 CCTAGCTAAGCTACAAACTTGACT 58.275 41.667 0.00 0.00 40.44 3.41
1731 1805 4.330347 GCCTAGCTAAGCTACAAACTTGAC 59.670 45.833 7.10 0.00 40.44 3.18
1739 1813 0.264955 AGGGGCCTAGCTAAGCTACA 59.735 55.000 13.88 0.00 40.44 2.74
1754 1828 0.977627 GGGGAAATCCAAGCAAGGGG 60.978 60.000 1.22 0.00 37.91 4.79
1774 1857 5.022122 TGATTGATGGCTTGGGTCAATAAA 58.978 37.500 0.00 0.00 41.30 1.40
1784 1867 3.726291 TGATGCATGATTGATGGCTTG 57.274 42.857 2.46 0.00 31.99 4.01
1804 1889 0.638292 ACCCCTTCCCATGAATGCAT 59.362 50.000 0.00 0.00 34.29 3.96
1805 1890 0.324552 CACCCCTTCCCATGAATGCA 60.325 55.000 0.00 0.00 0.00 3.96
1806 1891 0.324645 ACACCCCTTCCCATGAATGC 60.325 55.000 0.00 0.00 0.00 3.56
1807 1892 1.272648 ACACACCCCTTCCCATGAATG 60.273 52.381 0.00 0.00 0.00 2.67
1808 1893 1.084018 ACACACCCCTTCCCATGAAT 58.916 50.000 0.00 0.00 0.00 2.57
1809 1894 0.112218 CACACACCCCTTCCCATGAA 59.888 55.000 0.00 0.00 0.00 2.57
1810 1895 1.767036 CACACACCCCTTCCCATGA 59.233 57.895 0.00 0.00 0.00 3.07
1811 1896 1.978617 GCACACACCCCTTCCCATG 60.979 63.158 0.00 0.00 0.00 3.66
1812 1897 2.440599 GCACACACCCCTTCCCAT 59.559 61.111 0.00 0.00 0.00 4.00
1813 1898 3.897122 GGCACACACCCCTTCCCA 61.897 66.667 0.00 0.00 0.00 4.37
1814 1899 4.678743 GGGCACACACCCCTTCCC 62.679 72.222 0.00 0.00 45.00 3.97
1821 1906 4.572571 TCCAACCGGGCACACACC 62.573 66.667 6.32 0.00 36.21 4.16
1822 1907 1.668101 TTTTCCAACCGGGCACACAC 61.668 55.000 6.32 0.00 36.21 3.82
1823 1908 0.757188 ATTTTCCAACCGGGCACACA 60.757 50.000 6.32 0.00 36.21 3.72
1824 1909 0.319469 CATTTTCCAACCGGGCACAC 60.319 55.000 6.32 0.00 36.21 3.82
1825 1910 2.045280 CATTTTCCAACCGGGCACA 58.955 52.632 6.32 0.00 36.21 4.57
1826 1911 1.374125 GCATTTTCCAACCGGGCAC 60.374 57.895 6.32 0.00 36.21 5.01
1827 1912 1.190833 ATGCATTTTCCAACCGGGCA 61.191 50.000 6.32 1.87 36.21 5.36
1828 1913 0.460109 GATGCATTTTCCAACCGGGC 60.460 55.000 6.32 0.00 36.21 6.13
1829 1914 0.894141 TGATGCATTTTCCAACCGGG 59.106 50.000 6.32 0.00 38.37 5.73
1830 1915 2.542597 CATGATGCATTTTCCAACCGG 58.457 47.619 0.00 0.00 0.00 5.28
1831 1916 1.928503 GCATGATGCATTTTCCAACCG 59.071 47.619 13.36 0.00 44.26 4.44
1912 2013 1.952621 ACTTGGGCAGGAAGCTAGTA 58.047 50.000 0.00 0.00 44.79 1.82
1916 2017 0.825010 CACAACTTGGGCAGGAAGCT 60.825 55.000 0.00 0.00 44.79 3.74
1917 2018 1.662044 CACAACTTGGGCAGGAAGC 59.338 57.895 0.00 0.00 44.65 3.86
1931 2032 0.899720 GGTCGTCTATCACCCCACAA 59.100 55.000 0.00 0.00 0.00 3.33
1969 2070 8.499288 TCTTTTTGAAAAGGGGTTATACCAAT 57.501 30.769 14.33 0.00 44.22 3.16
1973 2074 9.826574 AACTTTCTTTTTGAAAAGGGGTTATAC 57.173 29.630 14.33 0.00 44.22 1.47
2023 2125 2.615240 CCTAATATGCCATAGTGCCGCA 60.615 50.000 0.00 0.00 36.84 5.69
2024 2126 2.009774 CCTAATATGCCATAGTGCCGC 58.990 52.381 0.00 0.00 0.00 6.53
2030 2132 4.039730 CGGAGATCCCCTAATATGCCATAG 59.960 50.000 0.00 0.00 0.00 2.23
2032 2134 2.774234 CGGAGATCCCCTAATATGCCAT 59.226 50.000 0.00 0.00 0.00 4.40
2046 2148 2.229062 TCAGTGACTTGTGTCGGAGATC 59.771 50.000 0.00 0.00 45.70 2.75
2053 2155 3.330267 GGGAGATTCAGTGACTTGTGTC 58.670 50.000 0.00 0.00 43.20 3.67
2057 2159 1.630369 TGGGGGAGATTCAGTGACTTG 59.370 52.381 0.00 0.00 0.00 3.16
2064 2166 2.027745 CGGACATATGGGGGAGATTCAG 60.028 54.545 7.80 0.00 0.00 3.02
2065 2167 1.977854 CGGACATATGGGGGAGATTCA 59.022 52.381 7.80 0.00 0.00 2.57
2066 2168 1.339151 GCGGACATATGGGGGAGATTC 60.339 57.143 7.80 0.00 0.00 2.52
2097 2199 2.489329 CGGACAAATTTGATGAGCCAGT 59.511 45.455 24.64 0.00 0.00 4.00
2098 2200 2.159338 CCGGACAAATTTGATGAGCCAG 60.159 50.000 24.64 11.90 0.00 4.85
2116 2231 0.539901 AGGAGATCCATACGGTCCGG 60.540 60.000 17.28 0.00 38.89 5.14
2122 2237 2.128035 GCGAACAAGGAGATCCATACG 58.872 52.381 0.92 1.42 38.89 3.06
2132 2247 2.406002 GACTTGGGGGCGAACAAGGA 62.406 60.000 15.56 0.00 46.29 3.36
2149 2264 1.529713 CCCTAGAGCTCCTCCCGAC 60.530 68.421 10.93 0.00 0.00 4.79
2173 2288 1.081376 GGTGTCCGTCGACTGTCTG 60.081 63.158 14.70 0.00 39.94 3.51
2174 2289 2.614446 CGGTGTCCGTCGACTGTCT 61.614 63.158 14.70 0.00 42.73 3.41
2188 2303 1.068588 TCCAAGACTGAGTTGACGGTG 59.931 52.381 0.00 0.00 0.00 4.94
2198 2313 2.046292 TGTGATGGTGTCCAAGACTGA 58.954 47.619 0.00 0.00 36.95 3.41
2199 2314 2.549064 TGTGATGGTGTCCAAGACTG 57.451 50.000 0.00 0.00 36.95 3.51
2286 2598 8.707938 AGCCTTAGCATTTGAAAAATCATAAC 57.292 30.769 0.00 0.00 43.56 1.89
2289 2601 7.388437 TCAAGCCTTAGCATTTGAAAAATCAT 58.612 30.769 0.00 0.00 43.56 2.45
2343 2655 4.407296 CAGATAACAGCCCTCTAACCTTCT 59.593 45.833 0.00 0.00 0.00 2.85
2347 2659 2.485657 GGCAGATAACAGCCCTCTAACC 60.486 54.545 0.00 0.00 41.84 2.85
2376 2688 8.486210 AGTAGATTCTGATATTTGTGCAACCTA 58.514 33.333 0.00 0.00 34.36 3.08
2378 2690 7.280876 TGAGTAGATTCTGATATTTGTGCAACC 59.719 37.037 0.00 0.00 34.36 3.77
2394 2706 6.456718 GCTCTTGTTTGCTGATGAGTAGATTC 60.457 42.308 0.00 0.00 0.00 2.52
2409 2721 3.550842 GGCCTACTTTGTGCTCTTGTTTG 60.551 47.826 0.00 0.00 0.00 2.93
2431 2743 5.294306 TGCTTAGCCTGATCATTTAAGTTCG 59.706 40.000 0.29 0.00 0.00 3.95
2456 2768 4.780815 AGTGATGTGACTTGGAAACAGAA 58.219 39.130 0.00 0.00 44.54 3.02
2461 2773 4.346709 TGGACTAGTGATGTGACTTGGAAA 59.653 41.667 0.00 0.00 0.00 3.13
2464 2776 3.589988 GTGGACTAGTGATGTGACTTGG 58.410 50.000 0.00 0.00 0.00 3.61
2561 2875 5.411361 TCCAGGAAGTTTCACAATAATGACG 59.589 40.000 0.00 0.00 0.00 4.35
2569 2883 1.210967 ACCGTCCAGGAAGTTTCACAA 59.789 47.619 1.32 0.00 45.00 3.33
2643 2957 3.063997 GGTCGAAGCTTGAACCACATATG 59.936 47.826 17.93 0.00 0.00 1.78
2672 2986 0.036388 TGAACGATGAAGGGAGGCAC 60.036 55.000 0.00 0.00 0.00 5.01
2683 2997 4.633126 AGAGATTGTGGTGAATGAACGATG 59.367 41.667 0.00 0.00 0.00 3.84
2710 3024 2.354203 GGAGACATCGGAGCAGAAGTTT 60.354 50.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.