Multiple sequence alignment - TraesCS2B01G498900

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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 TraesCS2B01G498900 chr2B 100.000 4516 0 0 1 4516 695173192 695168677 0.000000e+00 8340
1 TraesCS2B01G498900 chr2B 84.211 1615 194 34 2779 4367 695108949 695110528 0.000000e+00 1513
2 TraesCS2B01G498900 chr2B 85.026 1349 146 21 1076 2405 695379983 695378672 0.000000e+00 1321
3 TraesCS2B01G498900 chr2B 84.370 1350 157 22 1076 2402 695106859 695108177 0.000000e+00 1275
4 TraesCS2B01G498900 chr2B 81.992 1305 192 25 1076 2354 695508139 695509426 0.000000e+00 1068
5 TraesCS2B01G498900 chr2B 91.405 605 42 6 1 598 512059350 512058749 0.000000e+00 821
6 TraesCS2B01G498900 chr2B 79.143 887 148 25 1059 1922 695414347 695413475 3.030000e-161 579
7 TraesCS2B01G498900 chr2B 86.667 390 42 6 2870 3256 695377747 695377365 1.500000e-114 424
8 TraesCS2B01G498900 chr2D 95.710 3636 114 16 772 4380 577535897 577539517 0.000000e+00 5812
9 TraesCS2B01G498900 chr2D 84.756 1581 159 35 2822 4366 577579902 577578368 0.000000e+00 1509
10 TraesCS2B01G498900 chr2D 85.320 1342 170 18 1076 2405 577802846 577801520 0.000000e+00 1362
11 TraesCS2B01G498900 chr2D 84.821 1344 160 16 1076 2405 577581911 577580598 0.000000e+00 1312
12 TraesCS2B01G498900 chr2D 85.274 1168 129 19 1255 2405 577440836 577441977 0.000000e+00 1164
13 TraesCS2B01G498900 chr2D 88.080 646 66 9 2830 3468 577442759 577443400 0.000000e+00 756
14 TraesCS2B01G498900 chr2D 85.486 689 80 14 2734 3405 577800845 577800160 0.000000e+00 701
15 TraesCS2B01G498900 chr2A 94.213 1970 69 14 790 2724 715918284 715916325 0.000000e+00 2964
16 TraesCS2B01G498900 chr2A 96.562 1629 44 6 2760 4380 715916321 715914697 0.000000e+00 2687
17 TraesCS2B01G498900 chr2A 84.676 1390 157 23 1043 2405 715951255 715949895 0.000000e+00 1336
18 TraesCS2B01G498900 chr2A 85.314 1035 131 11 1076 2104 715880631 715881650 0.000000e+00 1050
19 TraesCS2B01G498900 chr2A 87.179 936 93 14 2822 3735 715890501 715891431 0.000000e+00 1038
20 TraesCS2B01G498900 chr2A 82.927 779 75 23 2721 3480 715949210 715948471 0.000000e+00 649
21 TraesCS2B01G498900 chr2A 81.979 283 26 8 2132 2405 715881651 715881917 2.740000e-52 217
22 TraesCS2B01G498900 chr2A 81.979 283 26 6 2132 2405 715887429 715887695 2.740000e-52 217
23 TraesCS2B01G498900 chr7A 92.953 596 37 3 1 591 156611 157206 0.000000e+00 863
24 TraesCS2B01G498900 chr7B 92.893 591 34 4 7 591 216950621 216950033 0.000000e+00 852
25 TraesCS2B01G498900 chr4B 92.931 580 36 5 19 593 389486128 389486707 0.000000e+00 839
26 TraesCS2B01G498900 chr4B 92.256 594 41 3 1 589 389499135 389499728 0.000000e+00 837
27 TraesCS2B01G498900 chr6B 91.919 594 43 3 1 589 439791363 439791956 0.000000e+00 826
28 TraesCS2B01G498900 chr3B 92.061 592 40 3 6 591 572021651 572021061 0.000000e+00 826
29 TraesCS2B01G498900 chrUn 91.779 596 44 3 1 592 4573048 4573642 0.000000e+00 824
30 TraesCS2B01G498900 chrUn 91.611 596 45 3 1 592 131600720 131600126 0.000000e+00 819


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 TraesCS2B01G498900 chr2B 695168677 695173192 4515 True 8340.0 8340 100.0000 1 4516 1 chr2B.!!$R2 4515
1 TraesCS2B01G498900 chr2B 695106859 695110528 3669 False 1394.0 1513 84.2905 1076 4367 2 chr2B.!!$F2 3291
2 TraesCS2B01G498900 chr2B 695508139 695509426 1287 False 1068.0 1068 81.9920 1076 2354 1 chr2B.!!$F1 1278
3 TraesCS2B01G498900 chr2B 695377365 695379983 2618 True 872.5 1321 85.8465 1076 3256 2 chr2B.!!$R4 2180
4 TraesCS2B01G498900 chr2B 512058749 512059350 601 True 821.0 821 91.4050 1 598 1 chr2B.!!$R1 597
5 TraesCS2B01G498900 chr2B 695413475 695414347 872 True 579.0 579 79.1430 1059 1922 1 chr2B.!!$R3 863
6 TraesCS2B01G498900 chr2D 577535897 577539517 3620 False 5812.0 5812 95.7100 772 4380 1 chr2D.!!$F1 3608
7 TraesCS2B01G498900 chr2D 577578368 577581911 3543 True 1410.5 1509 84.7885 1076 4366 2 chr2D.!!$R1 3290
8 TraesCS2B01G498900 chr2D 577800160 577802846 2686 True 1031.5 1362 85.4030 1076 3405 2 chr2D.!!$R2 2329
9 TraesCS2B01G498900 chr2D 577440836 577443400 2564 False 960.0 1164 86.6770 1255 3468 2 chr2D.!!$F2 2213
10 TraesCS2B01G498900 chr2A 715914697 715918284 3587 True 2825.5 2964 95.3875 790 4380 2 chr2A.!!$R1 3590
11 TraesCS2B01G498900 chr2A 715948471 715951255 2784 True 992.5 1336 83.8015 1043 3480 2 chr2A.!!$R2 2437
12 TraesCS2B01G498900 chr2A 715880631 715881917 1286 False 633.5 1050 83.6465 1076 2405 2 chr2A.!!$F1 1329
13 TraesCS2B01G498900 chr2A 715887429 715891431 4002 False 627.5 1038 84.5790 2132 3735 2 chr2A.!!$F2 1603
14 TraesCS2B01G498900 chr7A 156611 157206 595 False 863.0 863 92.9530 1 591 1 chr7A.!!$F1 590
15 TraesCS2B01G498900 chr7B 216950033 216950621 588 True 852.0 852 92.8930 7 591 1 chr7B.!!$R1 584
16 TraesCS2B01G498900 chr4B 389486128 389486707 579 False 839.0 839 92.9310 19 593 1 chr4B.!!$F1 574
17 TraesCS2B01G498900 chr4B 389499135 389499728 593 False 837.0 837 92.2560 1 589 1 chr4B.!!$F2 588
18 TraesCS2B01G498900 chr6B 439791363 439791956 593 False 826.0 826 91.9190 1 589 1 chr6B.!!$F1 588
19 TraesCS2B01G498900 chr3B 572021061 572021651 590 True 826.0 826 92.0610 6 591 1 chr3B.!!$R1 585
20 TraesCS2B01G498900 chrUn 4573048 4573642 594 False 824.0 824 91.7790 1 592 1 chrUn.!!$F1 591
21 TraesCS2B01G498900 chrUn 131600126 131600720 594 True 819.0 819 91.6110 1 592 1 chrUn.!!$R1 591

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
599 606 0.030195 TATCCTCATCAGTGGGCCCA 60.030 55.000 24.45 24.45 0.00 5.36 F
1598 1686 0.034616 CCGAAGATGATCAGAGGCCC 59.965 60.000 0.00 0.00 0.00 5.80 F
1671 1759 0.895530 TGTCTTCTCATCGGACACCC 59.104 55.000 0.00 0.00 35.44 4.61 F
1855 1943 1.068753 CTCGAATGGATCTGCCGCT 59.931 57.895 0.00 0.00 40.66 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1882 0.713883 AGCACGAAAATGTACTCGCG 59.286 50.000 0.0 0.0 38.64 5.87 R
2623 4320 2.147958 GGATACAAACACAAGGCGACA 58.852 47.619 0.0 0.0 0.00 4.35 R
3199 5914 3.671433 CGTCCTCAATGTCAATGCAAAGG 60.671 47.826 0.0 0.0 0.00 3.11 R
3848 6594 0.379669 GGCCGCTTGATCACATTCAG 59.620 55.000 0.0 0.0 0.00 3.02 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
31 32 0.889186 GCCAACTGTCGTGGTTCCAT 60.889 55.000 0.84 0.00 0.00 3.41
75 76 3.663198 AGGTATGGAGAGGCAAGATCTT 58.337 45.455 0.88 0.88 0.00 2.40
175 177 1.439353 CGGAGGCGGTCAATTGGATG 61.439 60.000 5.42 0.00 0.00 3.51
189 191 7.445096 GGTCAATTGGATGATGTGTGTGATATA 59.555 37.037 5.42 0.00 0.00 0.86
190 192 8.501580 GTCAATTGGATGATGTGTGTGATATAG 58.498 37.037 5.42 0.00 0.00 1.31
193 197 4.907269 TGGATGATGTGTGTGATATAGGGT 59.093 41.667 0.00 0.00 0.00 4.34
242 249 4.502604 GGTGGCTTATATAGAGTTCGCCAA 60.503 45.833 1.22 0.00 46.30 4.52
301 308 3.244284 ACATAAAGTGGTGGCGTTACTGA 60.244 43.478 0.00 0.00 0.00 3.41
345 352 9.220767 GCTATTAATGACCTTAAAGACTATGGG 57.779 37.037 0.00 0.00 33.15 4.00
389 396 3.601435 CTGAGTGACTCCTAGTCTTCGA 58.399 50.000 10.52 0.00 45.27 3.71
397 404 1.134461 TCCTAGTCTTCGAGAGGTCGG 60.134 57.143 0.00 0.00 46.80 4.79
439 446 3.334280 AGTGACAGTAGGTAGGGAGACTT 59.666 47.826 0.00 0.00 0.00 3.01
456 463 3.259374 AGACTTCCGAGTGACATGATGTT 59.741 43.478 0.00 0.00 35.88 2.71
539 546 2.507407 TTTGGATAGTGACCTTGGGC 57.493 50.000 0.00 0.00 0.00 5.36
595 602 2.366916 GGTCTGTATCCTCATCAGTGGG 59.633 54.545 0.00 0.00 0.00 4.61
597 604 1.071385 CTGTATCCTCATCAGTGGGCC 59.929 57.143 0.00 0.00 0.00 5.80
598 605 0.398318 GTATCCTCATCAGTGGGCCC 59.602 60.000 17.59 17.59 0.00 5.80
599 606 0.030195 TATCCTCATCAGTGGGCCCA 60.030 55.000 24.45 24.45 0.00 5.36
600 607 0.700269 ATCCTCATCAGTGGGCCCAT 60.700 55.000 31.45 14.68 0.00 4.00
601 608 0.920763 TCCTCATCAGTGGGCCCATT 60.921 55.000 31.45 23.46 0.00 3.16
602 609 0.466922 CCTCATCAGTGGGCCCATTC 60.467 60.000 31.45 17.11 0.00 2.67
603 610 0.549950 CTCATCAGTGGGCCCATTCT 59.450 55.000 31.45 19.49 0.00 2.40
604 611 0.548031 TCATCAGTGGGCCCATTCTC 59.452 55.000 31.45 15.79 0.00 2.87
605 612 0.466922 CATCAGTGGGCCCATTCTCC 60.467 60.000 31.45 15.35 0.00 3.71
606 613 1.649271 ATCAGTGGGCCCATTCTCCC 61.649 60.000 31.45 14.48 42.93 4.30
607 614 3.023735 AGTGGGCCCATTCTCCCC 61.024 66.667 31.45 13.62 41.92 4.81
608 615 4.143301 GTGGGCCCATTCTCCCCC 62.143 72.222 31.45 8.65 41.92 5.40
609 616 4.386100 TGGGCCCATTCTCCCCCT 62.386 66.667 24.45 0.00 41.92 4.79
610 617 3.029981 GGGCCCATTCTCCCCCTT 61.030 66.667 19.95 0.00 36.50 3.95
611 618 1.699930 GGGCCCATTCTCCCCCTTA 60.700 63.158 19.95 0.00 36.50 2.69
612 619 1.293683 GGGCCCATTCTCCCCCTTAA 61.294 60.000 19.95 0.00 36.50 1.85
613 620 0.860457 GGCCCATTCTCCCCCTTAAT 59.140 55.000 0.00 0.00 0.00 1.40
614 621 1.220493 GGCCCATTCTCCCCCTTAATT 59.780 52.381 0.00 0.00 0.00 1.40
615 622 2.360316 GGCCCATTCTCCCCCTTAATTT 60.360 50.000 0.00 0.00 0.00 1.82
616 623 3.384168 GCCCATTCTCCCCCTTAATTTT 58.616 45.455 0.00 0.00 0.00 1.82
617 624 3.388024 GCCCATTCTCCCCCTTAATTTTC 59.612 47.826 0.00 0.00 0.00 2.29
618 625 4.619679 CCCATTCTCCCCCTTAATTTTCA 58.380 43.478 0.00 0.00 0.00 2.69
619 626 5.029474 CCCATTCTCCCCCTTAATTTTCAA 58.971 41.667 0.00 0.00 0.00 2.69
620 627 5.667172 CCCATTCTCCCCCTTAATTTTCAAT 59.333 40.000 0.00 0.00 0.00 2.57
621 628 6.158520 CCCATTCTCCCCCTTAATTTTCAATT 59.841 38.462 0.00 0.00 0.00 2.32
622 629 7.346960 CCCATTCTCCCCCTTAATTTTCAATTA 59.653 37.037 0.00 0.00 0.00 1.40
623 630 8.767436 CCATTCTCCCCCTTAATTTTCAATTAA 58.233 33.333 2.51 2.51 0.00 1.40
627 634 8.598916 TCTCCCCCTTAATTTTCAATTAAAACC 58.401 33.333 3.84 0.00 39.82 3.27
628 635 7.691213 TCCCCCTTAATTTTCAATTAAAACCC 58.309 34.615 3.84 0.00 39.82 4.11
629 636 7.294958 TCCCCCTTAATTTTCAATTAAAACCCA 59.705 33.333 3.84 0.00 39.82 4.51
630 637 7.392113 CCCCCTTAATTTTCAATTAAAACCCAC 59.608 37.037 3.84 0.00 39.82 4.61
631 638 7.392113 CCCCTTAATTTTCAATTAAAACCCACC 59.608 37.037 3.84 0.00 39.82 4.61
632 639 8.160765 CCCTTAATTTTCAATTAAAACCCACCT 58.839 33.333 3.84 0.00 39.82 4.00
633 640 9.567776 CCTTAATTTTCAATTAAAACCCACCTT 57.432 29.630 3.84 0.00 39.82 3.50
644 651 9.496873 AATTAAAACCCACCTTTATGTAAAAGC 57.503 29.630 0.00 0.00 0.00 3.51
645 652 6.740944 AAAACCCACCTTTATGTAAAAGCT 57.259 33.333 0.00 0.00 0.00 3.74
646 653 6.740944 AAACCCACCTTTATGTAAAAGCTT 57.259 33.333 0.00 0.00 0.00 3.74
647 654 5.722021 ACCCACCTTTATGTAAAAGCTTG 57.278 39.130 0.00 0.00 0.00 4.01
648 655 5.144832 ACCCACCTTTATGTAAAAGCTTGT 58.855 37.500 0.00 0.00 0.00 3.16
649 656 6.308566 ACCCACCTTTATGTAAAAGCTTGTA 58.691 36.000 0.00 0.00 0.00 2.41
650 657 6.951778 ACCCACCTTTATGTAAAAGCTTGTAT 59.048 34.615 0.00 0.00 0.00 2.29
651 658 7.122204 ACCCACCTTTATGTAAAAGCTTGTATC 59.878 37.037 0.00 0.00 0.00 2.24
652 659 7.416326 CCCACCTTTATGTAAAAGCTTGTATCC 60.416 40.741 0.00 0.00 0.00 2.59
653 660 7.339466 CCACCTTTATGTAAAAGCTTGTATCCT 59.661 37.037 0.00 0.00 0.00 3.24
654 661 8.739972 CACCTTTATGTAAAAGCTTGTATCCTT 58.260 33.333 0.00 0.00 0.00 3.36
655 662 9.309224 ACCTTTATGTAAAAGCTTGTATCCTTT 57.691 29.630 0.00 0.00 32.98 3.11
662 669 9.127277 TGTAAAAGCTTGTATCCTTTTGTAAGT 57.873 29.630 0.00 0.00 40.40 2.24
667 674 8.664211 AGCTTGTATCCTTTTGTAAGTATAGC 57.336 34.615 0.00 0.00 0.00 2.97
668 675 8.265055 AGCTTGTATCCTTTTGTAAGTATAGCA 58.735 33.333 0.00 0.00 0.00 3.49
669 676 9.057089 GCTTGTATCCTTTTGTAAGTATAGCAT 57.943 33.333 0.00 0.00 0.00 3.79
675 682 9.740710 ATCCTTTTGTAAGTATAGCATTATCCC 57.259 33.333 0.00 0.00 0.00 3.85
676 683 8.161425 TCCTTTTGTAAGTATAGCATTATCCCC 58.839 37.037 0.00 0.00 0.00 4.81
677 684 7.393515 CCTTTTGTAAGTATAGCATTATCCCCC 59.606 40.741 0.00 0.00 0.00 5.40
678 685 7.642094 TTTGTAAGTATAGCATTATCCCCCT 57.358 36.000 0.00 0.00 0.00 4.79
679 686 6.869206 TGTAAGTATAGCATTATCCCCCTC 57.131 41.667 0.00 0.00 0.00 4.30
680 687 5.724854 TGTAAGTATAGCATTATCCCCCTCC 59.275 44.000 0.00 0.00 0.00 4.30
681 688 3.737263 AGTATAGCATTATCCCCCTCCC 58.263 50.000 0.00 0.00 0.00 4.30
682 689 1.987080 ATAGCATTATCCCCCTCCCC 58.013 55.000 0.00 0.00 0.00 4.81
683 690 0.178843 TAGCATTATCCCCCTCCCCC 60.179 60.000 0.00 0.00 0.00 5.40
684 691 2.907179 GCATTATCCCCCTCCCCCG 61.907 68.421 0.00 0.00 0.00 5.73
685 692 2.531942 ATTATCCCCCTCCCCCGC 60.532 66.667 0.00 0.00 0.00 6.13
704 711 2.663196 GGTCTCTCCCCCAACACG 59.337 66.667 0.00 0.00 0.00 4.49
705 712 2.047179 GTCTCTCCCCCAACACGC 60.047 66.667 0.00 0.00 0.00 5.34
706 713 2.525629 TCTCTCCCCCAACACGCA 60.526 61.111 0.00 0.00 0.00 5.24
707 714 2.046892 CTCTCCCCCAACACGCAG 60.047 66.667 0.00 0.00 0.00 5.18
743 750 4.578898 CGCACCTGCCCGCGTATA 62.579 66.667 4.92 0.00 46.23 1.47
744 751 2.030562 GCACCTGCCCGCGTATAT 59.969 61.111 4.92 0.00 34.31 0.86
745 752 2.317609 GCACCTGCCCGCGTATATG 61.318 63.158 4.92 0.00 34.31 1.78
746 753 1.069090 CACCTGCCCGCGTATATGT 59.931 57.895 4.92 0.00 0.00 2.29
747 754 0.944311 CACCTGCCCGCGTATATGTC 60.944 60.000 4.92 0.00 0.00 3.06
748 755 1.733041 CCTGCCCGCGTATATGTCG 60.733 63.158 4.92 0.00 0.00 4.35
749 756 1.007734 CTGCCCGCGTATATGTCGT 60.008 57.895 4.92 0.00 0.00 4.34
750 757 1.275471 CTGCCCGCGTATATGTCGTG 61.275 60.000 4.92 8.14 38.32 4.35
751 758 1.299620 GCCCGCGTATATGTCGTGT 60.300 57.895 4.92 0.00 37.14 4.49
752 759 0.872881 GCCCGCGTATATGTCGTGTT 60.873 55.000 4.92 0.00 37.14 3.32
753 760 1.126079 CCCGCGTATATGTCGTGTTC 58.874 55.000 4.92 0.00 37.14 3.18
754 761 1.268896 CCCGCGTATATGTCGTGTTCT 60.269 52.381 4.92 0.00 37.14 3.01
755 762 1.779157 CCGCGTATATGTCGTGTTCTG 59.221 52.381 4.92 0.00 37.14 3.02
756 763 2.447250 CGCGTATATGTCGTGTTCTGT 58.553 47.619 0.00 0.00 34.71 3.41
757 764 2.850060 CGCGTATATGTCGTGTTCTGTT 59.150 45.455 0.00 0.00 34.71 3.16
758 765 3.302434 CGCGTATATGTCGTGTTCTGTTT 59.698 43.478 0.00 0.00 34.71 2.83
759 766 4.201551 CGCGTATATGTCGTGTTCTGTTTT 60.202 41.667 0.00 0.00 34.71 2.43
760 767 5.003684 CGCGTATATGTCGTGTTCTGTTTTA 59.996 40.000 0.00 0.00 34.71 1.52
761 768 6.291427 CGCGTATATGTCGTGTTCTGTTTTAT 60.291 38.462 0.00 0.00 34.71 1.40
762 769 7.096925 CGCGTATATGTCGTGTTCTGTTTTATA 60.097 37.037 0.00 0.00 34.71 0.98
763 770 8.205948 GCGTATATGTCGTGTTCTGTTTTATAG 58.794 37.037 0.00 0.00 0.00 1.31
764 771 8.688184 CGTATATGTCGTGTTCTGTTTTATAGG 58.312 37.037 0.00 0.00 0.00 2.57
765 772 5.796350 ATGTCGTGTTCTGTTTTATAGGC 57.204 39.130 0.00 0.00 0.00 3.93
766 773 4.890088 TGTCGTGTTCTGTTTTATAGGCT 58.110 39.130 0.00 0.00 0.00 4.58
767 774 4.927425 TGTCGTGTTCTGTTTTATAGGCTC 59.073 41.667 0.00 0.00 0.00 4.70
768 775 5.169295 GTCGTGTTCTGTTTTATAGGCTCT 58.831 41.667 0.00 0.00 0.00 4.09
769 776 5.288952 GTCGTGTTCTGTTTTATAGGCTCTC 59.711 44.000 0.00 0.00 0.00 3.20
770 777 5.047590 TCGTGTTCTGTTTTATAGGCTCTCA 60.048 40.000 0.00 0.00 0.00 3.27
771 778 5.062308 CGTGTTCTGTTTTATAGGCTCTCAC 59.938 44.000 0.00 0.00 0.00 3.51
772 779 5.062308 GTGTTCTGTTTTATAGGCTCTCACG 59.938 44.000 0.00 0.00 0.00 4.35
773 780 5.169295 GTTCTGTTTTATAGGCTCTCACGT 58.831 41.667 0.00 0.00 0.00 4.49
774 781 4.744570 TCTGTTTTATAGGCTCTCACGTG 58.255 43.478 9.94 9.94 0.00 4.49
775 782 4.219944 TCTGTTTTATAGGCTCTCACGTGT 59.780 41.667 16.51 0.00 0.00 4.49
776 783 5.416639 TCTGTTTTATAGGCTCTCACGTGTA 59.583 40.000 16.51 4.28 0.00 2.90
777 784 6.028146 TGTTTTATAGGCTCTCACGTGTAA 57.972 37.500 16.51 3.92 0.00 2.41
778 785 5.865552 TGTTTTATAGGCTCTCACGTGTAAC 59.134 40.000 16.51 3.83 0.00 2.50
779 786 5.909621 TTTATAGGCTCTCACGTGTAACT 57.090 39.130 16.51 10.28 31.75 2.24
780 787 5.496133 TTATAGGCTCTCACGTGTAACTC 57.504 43.478 16.51 4.29 31.75 3.01
781 788 1.912417 AGGCTCTCACGTGTAACTCT 58.088 50.000 16.51 6.55 31.75 3.24
782 789 1.813786 AGGCTCTCACGTGTAACTCTC 59.186 52.381 16.51 1.10 31.75 3.20
783 790 1.540267 GGCTCTCACGTGTAACTCTCA 59.460 52.381 16.51 0.00 31.75 3.27
784 791 2.586900 GCTCTCACGTGTAACTCTCAC 58.413 52.381 16.51 0.00 31.75 3.51
785 792 2.668834 GCTCTCACGTGTAACTCTCACC 60.669 54.545 16.51 0.00 32.86 4.02
786 793 2.552743 CTCTCACGTGTAACTCTCACCA 59.447 50.000 16.51 0.00 32.86 4.17
795 802 7.841245 CGTGTAACTCTCACCAGTACATGGG 62.841 52.000 13.68 6.52 45.16 4.00
834 843 1.962807 TGCAATACAAGCAGCCAAACT 59.037 42.857 0.00 0.00 37.02 2.66
945 957 0.464452 CCGCCGGAAGTTTATCTCCT 59.536 55.000 5.05 0.00 0.00 3.69
996 1022 1.551430 TCTCTTCTCTCGTCGACTCCT 59.449 52.381 14.70 0.00 0.00 3.69
999 1025 2.496871 TCTTCTCTCGTCGACTCCTACT 59.503 50.000 14.70 0.00 0.00 2.57
1007 1033 2.159128 CGTCGACTCCTACTCTACTCCA 60.159 54.545 14.70 0.00 0.00 3.86
1340 1398 2.158534 ACACACAATAACTGCCTTCCCA 60.159 45.455 0.00 0.00 0.00 4.37
1341 1399 3.091545 CACACAATAACTGCCTTCCCAT 58.908 45.455 0.00 0.00 0.00 4.00
1342 1400 3.511146 CACACAATAACTGCCTTCCCATT 59.489 43.478 0.00 0.00 0.00 3.16
1343 1401 3.763897 ACACAATAACTGCCTTCCCATTC 59.236 43.478 0.00 0.00 0.00 2.67
1344 1402 3.131046 CACAATAACTGCCTTCCCATTCC 59.869 47.826 0.00 0.00 0.00 3.01
1345 1403 2.348411 ATAACTGCCTTCCCATTCCG 57.652 50.000 0.00 0.00 0.00 4.30
1396 1457 0.176680 CCCCTCCAAGACGATGACAG 59.823 60.000 0.00 0.00 0.00 3.51
1520 1608 0.321564 TGATGGCACTGTTTCTCCGG 60.322 55.000 0.00 0.00 0.00 5.14
1598 1686 0.034616 CCGAAGATGATCAGAGGCCC 59.965 60.000 0.00 0.00 0.00 5.80
1615 1703 1.449601 CCTCCCGTGTGGTATGTGC 60.450 63.158 0.00 0.00 34.77 4.57
1671 1759 0.895530 TGTCTTCTCATCGGACACCC 59.104 55.000 0.00 0.00 35.44 4.61
1855 1943 1.068753 CTCGAATGGATCTGCCGCT 59.931 57.895 0.00 0.00 40.66 5.52
2276 2372 8.774586 CCTTTTATGAAATACATCTCGGTAAGG 58.225 37.037 0.00 0.00 40.07 2.69
2357 2458 9.295825 GGTCCATAAATTGTATCCAATGATGTA 57.704 33.333 5.81 0.00 40.42 2.29
2413 2562 9.631452 GGTTTTAGTCAAAGTAACTCGTAGTAT 57.369 33.333 0.00 0.00 0.00 2.12
2428 2579 4.102210 TCGTAGTATAGGACCTAGCAGTGT 59.898 45.833 7.43 0.00 29.31 3.55
2443 3081 5.113502 AGCAGTGTTATTCAACTCTTTGC 57.886 39.130 0.00 0.00 36.58 3.68
2590 3779 7.921786 TTACAATTGGATAGAGGAGTTTGTG 57.078 36.000 10.83 0.00 0.00 3.33
2655 4533 9.831737 CTTGTGTTTGTATCCAAAGATTTCTAG 57.168 33.333 0.00 0.00 41.09 2.43
2735 5380 7.921786 TTCACCACTCATTAACTCCATAAAG 57.078 36.000 0.00 0.00 0.00 1.85
2916 5628 6.765989 TGGCAGTGGTGTATCAGTAATTTATC 59.234 38.462 0.00 0.00 0.00 1.75
3075 5787 6.262273 TCAAAATCTGAGGTTACTGGAAACAC 59.738 38.462 0.00 0.00 35.60 3.32
3199 5914 1.618343 GCAGAGATAGAGGCCTTCTCC 59.382 57.143 23.64 10.28 43.44 3.71
3232 5947 3.574396 ACATTGAGGACGAGAAGAACTCA 59.426 43.478 0.00 0.00 45.14 3.41
3325 6040 1.079543 CCCTGAACTCGCAGACTGG 60.080 63.158 4.26 0.00 38.14 4.00
3486 6219 1.098050 GGTTCTGTGATGATGGTGCC 58.902 55.000 0.00 0.00 0.00 5.01
3656 6394 5.664262 CGAGCGAGTTTGAAGATCATATTG 58.336 41.667 0.00 0.00 0.00 1.90
3682 6424 0.961019 GTGGCCATTCTCTGTTGCAA 59.039 50.000 9.72 0.00 0.00 4.08
3870 6616 0.608856 AATGTGATCAAGCGGCCACA 60.609 50.000 2.24 10.61 42.71 4.17
3871 6617 1.308069 ATGTGATCAAGCGGCCACAC 61.308 55.000 2.24 7.99 41.56 3.82
3969 6716 3.190744 CAGTCATGTTGCAATTCTGAGCT 59.809 43.478 0.59 0.00 0.00 4.09
4035 6800 4.978863 TTGTGCGGCGCTGCTACA 62.979 61.111 38.42 33.53 35.36 2.74
4102 6867 0.036732 ATGGACACGACAACATGGCT 59.963 50.000 0.00 0.00 0.00 4.75
4312 7087 6.432581 AGGGTATTTTCAGGGGAAACTTATC 58.567 40.000 0.00 0.00 42.48 1.75
4357 7132 9.296400 GTCTGTTAGATGAGAGAAATAGTGAAC 57.704 37.037 0.00 0.00 0.00 3.18
4380 7155 5.296035 ACTGAGTTGTTTAAGCACACTAACC 59.704 40.000 0.00 0.00 0.00 2.85
4381 7156 4.271533 TGAGTTGTTTAAGCACACTAACCG 59.728 41.667 0.00 0.00 0.00 4.44
4382 7157 4.444536 AGTTGTTTAAGCACACTAACCGA 58.555 39.130 0.00 0.00 0.00 4.69
4383 7158 5.061179 AGTTGTTTAAGCACACTAACCGAT 58.939 37.500 0.00 0.00 0.00 4.18
4384 7159 6.225318 AGTTGTTTAAGCACACTAACCGATA 58.775 36.000 0.00 0.00 0.00 2.92
4385 7160 6.367969 AGTTGTTTAAGCACACTAACCGATAG 59.632 38.462 0.00 0.00 37.66 2.08
4386 7161 5.786311 TGTTTAAGCACACTAACCGATAGT 58.214 37.500 0.00 0.00 45.95 2.12
4395 7170 3.353557 ACTAACCGATAGTGCTCACTCA 58.646 45.455 5.72 0.00 43.33 3.41
4396 7171 2.656560 AACCGATAGTGCTCACTCAC 57.343 50.000 5.72 1.72 42.54 3.51
4397 7172 1.545841 ACCGATAGTGCTCACTCACA 58.454 50.000 5.72 0.00 42.54 3.58
4398 7173 2.103373 ACCGATAGTGCTCACTCACAT 58.897 47.619 5.72 0.00 42.54 3.21
4399 7174 2.099921 ACCGATAGTGCTCACTCACATC 59.900 50.000 5.72 3.87 42.54 3.06
4400 7175 2.099756 CCGATAGTGCTCACTCACATCA 59.900 50.000 5.72 0.00 42.54 3.07
4401 7176 3.111838 CGATAGTGCTCACTCACATCAC 58.888 50.000 5.72 0.00 42.54 3.06
4402 7177 3.181492 CGATAGTGCTCACTCACATCACT 60.181 47.826 5.72 0.00 42.54 3.41
4403 7178 4.035675 CGATAGTGCTCACTCACATCACTA 59.964 45.833 5.72 0.00 42.28 2.74
4404 7179 3.865011 AGTGCTCACTCACATCACTAG 57.135 47.619 0.00 0.00 36.92 2.57
4405 7180 3.161067 AGTGCTCACTCACATCACTAGT 58.839 45.455 0.00 0.00 36.92 2.57
4406 7181 3.576118 AGTGCTCACTCACATCACTAGTT 59.424 43.478 0.00 0.00 36.92 2.24
4407 7182 4.039730 AGTGCTCACTCACATCACTAGTTT 59.960 41.667 0.00 0.00 36.92 2.66
4408 7183 4.752101 GTGCTCACTCACATCACTAGTTTT 59.248 41.667 0.00 0.00 36.97 2.43
4409 7184 5.237344 GTGCTCACTCACATCACTAGTTTTT 59.763 40.000 0.00 0.00 36.97 1.94
4427 7202 2.843401 TTTTCCATTCGTTCCTCCGA 57.157 45.000 0.00 0.00 34.52 4.55
4449 7224 2.938956 AAAACTAGCAGCCAGTGACT 57.061 45.000 0.00 0.00 0.00 3.41
4450 7225 2.464157 AAACTAGCAGCCAGTGACTC 57.536 50.000 0.00 0.00 0.00 3.36
4451 7226 0.244994 AACTAGCAGCCAGTGACTCG 59.755 55.000 0.00 0.00 0.00 4.18
4452 7227 0.609406 ACTAGCAGCCAGTGACTCGA 60.609 55.000 0.00 0.00 0.00 4.04
4453 7228 0.528017 CTAGCAGCCAGTGACTCGAA 59.472 55.000 0.00 0.00 0.00 3.71
4454 7229 0.966179 TAGCAGCCAGTGACTCGAAA 59.034 50.000 0.00 0.00 0.00 3.46
4455 7230 0.320247 AGCAGCCAGTGACTCGAAAG 60.320 55.000 0.00 0.00 0.00 2.62
4456 7231 0.319900 GCAGCCAGTGACTCGAAAGA 60.320 55.000 0.00 0.00 39.12 2.52
4457 7232 1.873903 GCAGCCAGTGACTCGAAAGAA 60.874 52.381 0.00 0.00 41.32 2.52
4458 7233 2.483876 CAGCCAGTGACTCGAAAGAAA 58.516 47.619 0.00 0.00 41.32 2.52
4459 7234 2.872245 CAGCCAGTGACTCGAAAGAAAA 59.128 45.455 0.00 0.00 41.32 2.29
4460 7235 3.312421 CAGCCAGTGACTCGAAAGAAAAA 59.688 43.478 0.00 0.00 41.32 1.94
4461 7236 4.023707 CAGCCAGTGACTCGAAAGAAAAAT 60.024 41.667 0.00 0.00 41.32 1.82
4462 7237 4.023707 AGCCAGTGACTCGAAAGAAAAATG 60.024 41.667 0.00 0.00 41.32 2.32
4463 7238 4.024048 GCCAGTGACTCGAAAGAAAAATGA 60.024 41.667 0.00 0.00 41.32 2.57
4464 7239 5.683859 CCAGTGACTCGAAAGAAAAATGAG 58.316 41.667 0.00 0.00 41.32 2.90
4465 7240 5.237344 CCAGTGACTCGAAAGAAAAATGAGT 59.763 40.000 0.00 0.00 42.25 3.41
4466 7241 6.423905 CCAGTGACTCGAAAGAAAAATGAGTA 59.576 38.462 0.00 0.00 39.83 2.59
4467 7242 7.284351 CAGTGACTCGAAAGAAAAATGAGTAC 58.716 38.462 0.00 0.00 39.83 2.73
4468 7243 6.984474 AGTGACTCGAAAGAAAAATGAGTACA 59.016 34.615 0.00 0.00 39.83 2.90
4469 7244 7.657761 AGTGACTCGAAAGAAAAATGAGTACAT 59.342 33.333 0.00 0.00 39.83 2.29
4470 7245 7.952637 GTGACTCGAAAGAAAAATGAGTACATC 59.047 37.037 0.00 0.00 39.83 3.06
4471 7246 7.117812 TGACTCGAAAGAAAAATGAGTACATCC 59.882 37.037 0.00 0.00 39.83 3.51
4472 7247 7.162082 ACTCGAAAGAAAAATGAGTACATCCT 58.838 34.615 0.00 0.00 41.32 3.24
4473 7248 7.661847 ACTCGAAAGAAAAATGAGTACATCCTT 59.338 33.333 0.00 0.00 41.32 3.36
4474 7249 8.391075 TCGAAAGAAAAATGAGTACATCCTTT 57.609 30.769 0.00 0.00 37.03 3.11
4475 7250 8.504005 TCGAAAGAAAAATGAGTACATCCTTTC 58.496 33.333 0.00 0.00 37.87 2.62
4476 7251 8.507249 CGAAAGAAAAATGAGTACATCCTTTCT 58.493 33.333 0.00 0.00 43.01 2.52
4477 7252 9.617975 GAAAGAAAAATGAGTACATCCTTTCTG 57.382 33.333 14.78 0.00 41.86 3.02
4478 7253 8.924511 AAGAAAAATGAGTACATCCTTTCTGA 57.075 30.769 14.78 0.00 41.86 3.27
4479 7254 9.525826 AAGAAAAATGAGTACATCCTTTCTGAT 57.474 29.630 14.78 4.84 41.86 2.90
4486 7261 9.775854 ATGAGTACATCCTTTCTGATAGATTTG 57.224 33.333 0.00 0.00 29.98 2.32
4487 7262 8.981659 TGAGTACATCCTTTCTGATAGATTTGA 58.018 33.333 0.00 0.00 0.00 2.69
4488 7263 9.995003 GAGTACATCCTTTCTGATAGATTTGAT 57.005 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.257207 CCCCCTTTCTACTGTCAGTCA 58.743 52.381 9.26 0.00 0.00 3.41
75 76 2.100252 GTGTACACCTTCGCCATAGCTA 59.900 50.000 15.42 0.00 36.60 3.32
167 169 6.944290 CCCTATATCACACACATCATCCAATT 59.056 38.462 0.00 0.00 0.00 2.32
175 177 4.380531 CACCACCCTATATCACACACATC 58.619 47.826 0.00 0.00 0.00 3.06
193 197 2.904866 GCACAAGGGTTCGCACCA 60.905 61.111 6.56 0.00 46.43 4.17
242 249 4.467107 GGAGGGCGGGAGAGGTCT 62.467 72.222 0.00 0.00 0.00 3.85
271 278 7.724305 ACGCCACCACTTTATGTATATTAAG 57.276 36.000 0.00 0.00 0.00 1.85
277 284 4.873827 CAGTAACGCCACCACTTTATGTAT 59.126 41.667 0.00 0.00 0.00 2.29
301 308 3.067684 AGCACTTAAGGTTGGCGTTAT 57.932 42.857 7.53 0.00 0.00 1.89
345 352 0.040425 GCAACGGACACACATTCACC 60.040 55.000 0.00 0.00 0.00 4.02
381 388 0.961358 CACCCGACCTCTCGAAGACT 60.961 60.000 0.00 0.00 43.06 3.24
389 396 1.827969 CAAGAGAATCACCCGACCTCT 59.172 52.381 0.00 0.00 37.82 3.69
397 404 4.859798 CACTCGACTAACAAGAGAATCACC 59.140 45.833 0.00 0.00 37.82 4.02
439 446 2.562738 ACTCAACATCATGTCACTCGGA 59.437 45.455 0.00 0.00 0.00 4.55
497 504 2.708325 AGGCAAGAAGGTCAAGAGACTT 59.292 45.455 0.00 0.00 44.36 3.01
539 546 0.674534 GGCCTGACCTATACGTCCTG 59.325 60.000 0.00 0.00 34.51 3.86
595 602 2.775490 AATTAAGGGGGAGAATGGGC 57.225 50.000 0.00 0.00 0.00 5.36
597 604 6.813293 ATTGAAAATTAAGGGGGAGAATGG 57.187 37.500 0.00 0.00 0.00 3.16
601 608 8.598916 GGTTTTAATTGAAAATTAAGGGGGAGA 58.401 33.333 0.00 0.00 39.22 3.71
602 609 7.827236 GGGTTTTAATTGAAAATTAAGGGGGAG 59.173 37.037 0.00 0.00 39.22 4.30
603 610 7.294958 TGGGTTTTAATTGAAAATTAAGGGGGA 59.705 33.333 0.00 0.00 39.22 4.81
604 611 7.392113 GTGGGTTTTAATTGAAAATTAAGGGGG 59.608 37.037 0.00 0.00 39.22 5.40
605 612 7.392113 GGTGGGTTTTAATTGAAAATTAAGGGG 59.608 37.037 0.00 0.00 39.22 4.79
606 613 8.160765 AGGTGGGTTTTAATTGAAAATTAAGGG 58.839 33.333 0.00 0.00 39.22 3.95
607 614 9.567776 AAGGTGGGTTTTAATTGAAAATTAAGG 57.432 29.630 0.00 0.00 39.22 2.69
618 625 9.496873 GCTTTTACATAAAGGTGGGTTTTAATT 57.503 29.630 0.00 0.00 0.00 1.40
619 626 8.876181 AGCTTTTACATAAAGGTGGGTTTTAAT 58.124 29.630 1.59 0.00 36.71 1.40
620 627 8.252624 AGCTTTTACATAAAGGTGGGTTTTAA 57.747 30.769 1.59 0.00 36.71 1.52
621 628 7.842887 AGCTTTTACATAAAGGTGGGTTTTA 57.157 32.000 1.59 0.00 36.71 1.52
622 629 6.740944 AGCTTTTACATAAAGGTGGGTTTT 57.259 33.333 1.59 0.00 36.71 2.43
623 630 6.099125 ACAAGCTTTTACATAAAGGTGGGTTT 59.901 34.615 0.00 0.00 37.93 3.27
624 631 5.600898 ACAAGCTTTTACATAAAGGTGGGTT 59.399 36.000 0.00 0.00 37.93 4.11
625 632 5.144832 ACAAGCTTTTACATAAAGGTGGGT 58.855 37.500 0.00 5.45 37.93 4.51
626 633 5.722021 ACAAGCTTTTACATAAAGGTGGG 57.278 39.130 0.00 4.97 37.93 4.61
627 634 7.339466 AGGATACAAGCTTTTACATAAAGGTGG 59.661 37.037 0.00 3.08 37.93 4.61
628 635 8.281212 AGGATACAAGCTTTTACATAAAGGTG 57.719 34.615 0.00 1.68 37.93 4.00
629 636 8.879427 AAGGATACAAGCTTTTACATAAAGGT 57.121 30.769 0.00 0.00 39.38 3.50
636 643 9.127277 ACTTACAAAAGGATACAAGCTTTTACA 57.873 29.630 0.00 0.00 37.01 2.41
641 648 9.110502 GCTATACTTACAAAAGGATACAAGCTT 57.889 33.333 0.00 0.00 37.46 3.74
642 649 8.265055 TGCTATACTTACAAAAGGATACAAGCT 58.735 33.333 5.59 0.00 36.61 3.74
643 650 8.433421 TGCTATACTTACAAAAGGATACAAGC 57.567 34.615 0.00 0.00 37.46 4.01
649 656 9.740710 GGGATAATGCTATACTTACAAAAGGAT 57.259 33.333 0.00 0.00 39.70 3.24
650 657 8.161425 GGGGATAATGCTATACTTACAAAAGGA 58.839 37.037 0.00 0.00 37.01 3.36
651 658 7.393515 GGGGGATAATGCTATACTTACAAAAGG 59.606 40.741 0.00 0.00 37.01 3.11
652 659 8.164070 AGGGGGATAATGCTATACTTACAAAAG 58.836 37.037 0.00 0.00 38.77 2.27
653 660 8.052621 AGGGGGATAATGCTATACTTACAAAA 57.947 34.615 0.00 0.00 0.00 2.44
654 661 7.256908 GGAGGGGGATAATGCTATACTTACAAA 60.257 40.741 0.00 0.00 0.00 2.83
655 662 6.214819 GGAGGGGGATAATGCTATACTTACAA 59.785 42.308 0.00 0.00 0.00 2.41
656 663 5.724854 GGAGGGGGATAATGCTATACTTACA 59.275 44.000 0.00 0.00 0.00 2.41
657 664 5.130643 GGGAGGGGGATAATGCTATACTTAC 59.869 48.000 0.00 0.00 0.00 2.34
658 665 5.286221 GGGAGGGGGATAATGCTATACTTA 58.714 45.833 0.00 0.00 0.00 2.24
659 666 4.112331 GGGAGGGGGATAATGCTATACTT 58.888 47.826 0.00 0.00 0.00 2.24
660 667 3.571259 GGGGAGGGGGATAATGCTATACT 60.571 52.174 0.00 0.00 0.00 2.12
661 668 2.778270 GGGGAGGGGGATAATGCTATAC 59.222 54.545 0.00 0.00 0.00 1.47
662 669 2.294263 GGGGGAGGGGGATAATGCTATA 60.294 54.545 0.00 0.00 0.00 1.31
663 670 1.560551 GGGGGAGGGGGATAATGCTAT 60.561 57.143 0.00 0.00 0.00 2.97
664 671 0.178843 GGGGGAGGGGGATAATGCTA 60.179 60.000 0.00 0.00 0.00 3.49
665 672 1.466186 GGGGGAGGGGGATAATGCT 60.466 63.158 0.00 0.00 0.00 3.79
666 673 2.907179 CGGGGGAGGGGGATAATGC 61.907 68.421 0.00 0.00 0.00 3.56
667 674 2.907179 GCGGGGGAGGGGGATAATG 61.907 68.421 0.00 0.00 0.00 1.90
668 675 2.531942 GCGGGGGAGGGGGATAAT 60.532 66.667 0.00 0.00 0.00 1.28
687 694 2.663196 CGTGTTGGGGGAGAGACC 59.337 66.667 0.00 0.00 38.08 3.85
688 695 2.047179 GCGTGTTGGGGGAGAGAC 60.047 66.667 0.00 0.00 0.00 3.36
689 696 2.525629 TGCGTGTTGGGGGAGAGA 60.526 61.111 0.00 0.00 0.00 3.10
690 697 2.046892 CTGCGTGTTGGGGGAGAG 60.047 66.667 0.00 0.00 0.00 3.20
691 698 2.847234 ACTGCGTGTTGGGGGAGA 60.847 61.111 0.00 0.00 0.00 3.71
692 699 2.669569 CACTGCGTGTTGGGGGAG 60.670 66.667 1.24 0.00 0.00 4.30
693 700 4.947147 GCACTGCGTGTTGGGGGA 62.947 66.667 9.76 0.00 35.75 4.81
727 734 2.030562 ATATACGCGGGCAGGTGC 59.969 61.111 12.47 0.00 41.14 5.01
728 735 0.944311 GACATATACGCGGGCAGGTG 60.944 60.000 12.47 3.94 0.00 4.00
729 736 1.366366 GACATATACGCGGGCAGGT 59.634 57.895 12.47 1.43 0.00 4.00
730 737 1.733041 CGACATATACGCGGGCAGG 60.733 63.158 12.47 0.00 0.00 4.85
731 738 1.007734 ACGACATATACGCGGGCAG 60.008 57.895 12.47 0.00 0.00 4.85
732 739 1.299544 CACGACATATACGCGGGCA 60.300 57.895 12.47 0.00 0.00 5.36
733 740 0.872881 AACACGACATATACGCGGGC 60.873 55.000 12.47 0.00 30.18 6.13
734 741 1.126079 GAACACGACATATACGCGGG 58.874 55.000 12.47 0.00 0.00 6.13
735 742 1.779157 CAGAACACGACATATACGCGG 59.221 52.381 12.47 0.00 0.00 6.46
736 743 2.447250 ACAGAACACGACATATACGCG 58.553 47.619 3.53 3.53 0.00 6.01
737 744 4.835199 AAACAGAACACGACATATACGC 57.165 40.909 0.00 0.00 0.00 4.42
738 745 8.688184 CCTATAAAACAGAACACGACATATACG 58.312 37.037 0.00 0.00 0.00 3.06
739 746 8.485591 GCCTATAAAACAGAACACGACATATAC 58.514 37.037 0.00 0.00 0.00 1.47
740 747 8.418662 AGCCTATAAAACAGAACACGACATATA 58.581 33.333 0.00 0.00 0.00 0.86
741 748 7.272978 AGCCTATAAAACAGAACACGACATAT 58.727 34.615 0.00 0.00 0.00 1.78
742 749 6.636705 AGCCTATAAAACAGAACACGACATA 58.363 36.000 0.00 0.00 0.00 2.29
743 750 5.488341 AGCCTATAAAACAGAACACGACAT 58.512 37.500 0.00 0.00 0.00 3.06
744 751 4.890088 AGCCTATAAAACAGAACACGACA 58.110 39.130 0.00 0.00 0.00 4.35
745 752 5.169295 AGAGCCTATAAAACAGAACACGAC 58.831 41.667 0.00 0.00 0.00 4.34
746 753 5.047590 TGAGAGCCTATAAAACAGAACACGA 60.048 40.000 0.00 0.00 0.00 4.35
747 754 5.062308 GTGAGAGCCTATAAAACAGAACACG 59.938 44.000 0.00 0.00 0.00 4.49
748 755 5.062308 CGTGAGAGCCTATAAAACAGAACAC 59.938 44.000 0.00 0.00 0.00 3.32
749 756 5.168569 CGTGAGAGCCTATAAAACAGAACA 58.831 41.667 0.00 0.00 0.00 3.18
750 757 5.062308 CACGTGAGAGCCTATAAAACAGAAC 59.938 44.000 10.90 0.00 0.00 3.01
751 758 5.168569 CACGTGAGAGCCTATAAAACAGAA 58.831 41.667 10.90 0.00 0.00 3.02
752 759 4.219944 ACACGTGAGAGCCTATAAAACAGA 59.780 41.667 25.01 0.00 0.00 3.41
753 760 4.495422 ACACGTGAGAGCCTATAAAACAG 58.505 43.478 25.01 0.00 0.00 3.16
754 761 4.530710 ACACGTGAGAGCCTATAAAACA 57.469 40.909 25.01 0.00 0.00 2.83
755 762 6.098017 AGTTACACGTGAGAGCCTATAAAAC 58.902 40.000 25.01 8.14 0.00 2.43
756 763 6.152323 AGAGTTACACGTGAGAGCCTATAAAA 59.848 38.462 25.01 0.00 0.00 1.52
757 764 5.651139 AGAGTTACACGTGAGAGCCTATAAA 59.349 40.000 25.01 0.00 0.00 1.40
758 765 5.191426 AGAGTTACACGTGAGAGCCTATAA 58.809 41.667 25.01 4.66 0.00 0.98
759 766 4.778579 AGAGTTACACGTGAGAGCCTATA 58.221 43.478 25.01 0.00 0.00 1.31
760 767 3.622630 AGAGTTACACGTGAGAGCCTAT 58.377 45.455 25.01 4.77 0.00 2.57
761 768 3.008330 GAGAGTTACACGTGAGAGCCTA 58.992 50.000 25.01 0.00 0.00 3.93
762 769 1.813786 GAGAGTTACACGTGAGAGCCT 59.186 52.381 25.01 12.95 0.00 4.58
763 770 1.540267 TGAGAGTTACACGTGAGAGCC 59.460 52.381 25.01 8.16 0.00 4.70
764 771 2.586900 GTGAGAGTTACACGTGAGAGC 58.413 52.381 25.01 11.57 0.00 4.09
765 772 2.552743 TGGTGAGAGTTACACGTGAGAG 59.447 50.000 25.01 0.00 38.90 3.20
766 773 2.552743 CTGGTGAGAGTTACACGTGAGA 59.447 50.000 25.01 6.70 38.90 3.27
767 774 2.293677 ACTGGTGAGAGTTACACGTGAG 59.706 50.000 25.01 6.75 38.90 3.51
768 775 2.304092 ACTGGTGAGAGTTACACGTGA 58.696 47.619 25.01 2.68 38.90 4.35
769 776 2.795175 ACTGGTGAGAGTTACACGTG 57.205 50.000 15.48 15.48 38.90 4.49
770 777 3.216800 TGTACTGGTGAGAGTTACACGT 58.783 45.455 0.00 0.00 38.90 4.49
771 778 3.909776 TGTACTGGTGAGAGTTACACG 57.090 47.619 0.00 0.00 38.90 4.49
772 779 4.495422 CCATGTACTGGTGAGAGTTACAC 58.505 47.826 0.00 0.00 40.49 2.90
773 780 3.513912 CCCATGTACTGGTGAGAGTTACA 59.486 47.826 9.57 0.00 44.30 2.41
774 781 3.679083 GCCCATGTACTGGTGAGAGTTAC 60.679 52.174 9.57 0.00 44.30 2.50
775 782 2.500098 GCCCATGTACTGGTGAGAGTTA 59.500 50.000 9.57 0.00 44.30 2.24
776 783 1.279271 GCCCATGTACTGGTGAGAGTT 59.721 52.381 9.57 0.00 44.30 3.01
777 784 0.905357 GCCCATGTACTGGTGAGAGT 59.095 55.000 9.57 0.00 44.30 3.24
778 785 1.198713 AGCCCATGTACTGGTGAGAG 58.801 55.000 9.57 0.00 44.30 3.20
779 786 1.656587 AAGCCCATGTACTGGTGAGA 58.343 50.000 9.57 0.00 44.30 3.27
780 787 3.845781 ATAAGCCCATGTACTGGTGAG 57.154 47.619 9.57 0.00 44.30 3.51
781 788 4.584638 AAATAAGCCCATGTACTGGTGA 57.415 40.909 9.57 0.00 44.30 4.02
782 789 5.296780 CACTAAATAAGCCCATGTACTGGTG 59.703 44.000 9.57 0.07 44.30 4.17
783 790 5.437060 CACTAAATAAGCCCATGTACTGGT 58.563 41.667 9.57 0.00 44.30 4.00
784 791 4.821805 CCACTAAATAAGCCCATGTACTGG 59.178 45.833 0.00 0.00 45.51 4.00
785 792 5.680619 TCCACTAAATAAGCCCATGTACTG 58.319 41.667 0.00 0.00 0.00 2.74
786 793 5.163195 CCTCCACTAAATAAGCCCATGTACT 60.163 44.000 0.00 0.00 0.00 2.73
945 957 4.021229 TGTGTTAGCGAGATAGAGGGAAA 58.979 43.478 0.00 0.00 0.00 3.13
996 1022 3.170991 AGTGGTTGCTGGAGTAGAGTA 57.829 47.619 0.00 0.00 0.00 2.59
999 1025 1.623811 GGAAGTGGTTGCTGGAGTAGA 59.376 52.381 0.00 0.00 0.00 2.59
1007 1033 3.706086 ACTTTGAAATGGAAGTGGTTGCT 59.294 39.130 0.00 0.00 34.96 3.91
1310 1359 4.697352 GCAGTTATTGTGTGTGAGAGGAAT 59.303 41.667 0.00 0.00 0.00 3.01
1396 1457 0.036306 ATTGACCACCCACTCGGAAC 59.964 55.000 0.00 0.00 34.64 3.62
1508 1596 1.073199 CTTGGGCCGGAGAAACAGT 59.927 57.895 5.05 0.00 0.00 3.55
1520 1608 4.329545 TCGTGGTGCTCCTTGGGC 62.330 66.667 6.34 0.00 34.23 5.36
1560 1648 1.351017 GGAGGAGAATGTGTGGAACCA 59.649 52.381 0.00 0.00 34.36 3.67
1598 1686 1.449601 GGCACATACCACACGGGAG 60.450 63.158 0.00 0.00 41.15 4.30
1615 1703 1.134075 CGTGAGTAGTCGTGACGGG 59.866 63.158 4.70 0.00 36.20 5.28
1671 1759 1.246737 GGGAAAAGCTGCCACTCCAG 61.247 60.000 12.01 0.00 35.04 3.86
1794 1882 0.713883 AGCACGAAAATGTACTCGCG 59.286 50.000 0.00 0.00 38.64 5.87
1976 2064 4.565022 TGTGCAACACAAATCTCTCGATA 58.435 39.130 0.00 0.00 45.67 2.92
2276 2372 2.426522 TCACACACAAGAATAGGCTGC 58.573 47.619 0.00 0.00 0.00 5.25
2413 2562 5.720041 AGTTGAATAACACTGCTAGGTCCTA 59.280 40.000 0.00 0.00 39.30 2.94
2428 2579 9.520515 AAGAGATTAAGGCAAAGAGTTGAATAA 57.479 29.630 0.00 0.00 36.83 1.40
2623 4320 2.147958 GGATACAAACACAAGGCGACA 58.852 47.619 0.00 0.00 0.00 4.35
2916 5628 7.848716 CTTTTACAGAAGCAATGAAAGTGAG 57.151 36.000 0.00 0.00 30.28 3.51
3075 5787 3.857549 TCTCAGAACCATCTTCGACAG 57.142 47.619 0.00 0.00 32.03 3.51
3199 5914 3.671433 CGTCCTCAATGTCAATGCAAAGG 60.671 47.826 0.00 0.00 0.00 3.11
3232 5947 3.771216 AGCCATGATTTTCCTCACAAGT 58.229 40.909 0.00 0.00 0.00 3.16
3325 6040 8.447053 GTTTTGATCTTCTGTCTGTAGAATTCC 58.553 37.037 0.65 0.00 36.21 3.01
3486 6219 6.207417 ACCATCAGTGTTTATTCAGAAACCTG 59.793 38.462 8.23 8.23 38.33 4.00
3710 6452 4.079253 AGCATCACGGTGTAAGGAAAATT 58.921 39.130 8.17 0.00 0.00 1.82
3848 6594 0.379669 GGCCGCTTGATCACATTCAG 59.620 55.000 0.00 0.00 0.00 3.02
3930 6676 0.518636 CTGATATTGCGGCCGGATTG 59.481 55.000 29.38 4.68 0.00 2.67
3969 6716 1.224069 GCTGACAAGCTGCTCGTTCA 61.224 55.000 1.00 5.17 46.60 3.18
4079 6844 0.391130 ATGTTGTCGTGTCCATCCGG 60.391 55.000 0.00 0.00 0.00 5.14
4080 6845 0.721154 CATGTTGTCGTGTCCATCCG 59.279 55.000 0.00 0.00 0.00 4.18
4102 6867 2.822255 GGGCGCCGATACTGCAAA 60.822 61.111 22.54 0.00 0.00 3.68
4208 6983 2.887568 GCTGTCAGCTATGCGCGT 60.888 61.111 17.89 7.55 45.59 6.01
4357 7132 5.558273 CGGTTAGTGTGCTTAAACAACTCAG 60.558 44.000 0.00 0.00 0.00 3.35
4380 7155 3.111838 GTGATGTGAGTGAGCACTATCG 58.888 50.000 2.65 0.00 42.66 2.92
4381 7156 4.383850 AGTGATGTGAGTGAGCACTATC 57.616 45.455 2.65 4.30 42.66 2.08
4382 7157 4.952957 ACTAGTGATGTGAGTGAGCACTAT 59.047 41.667 2.65 0.00 42.66 2.12
4383 7158 4.336280 ACTAGTGATGTGAGTGAGCACTA 58.664 43.478 2.65 0.00 42.66 2.74
4384 7159 3.161067 ACTAGTGATGTGAGTGAGCACT 58.839 45.455 2.20 2.20 45.84 4.40
4385 7160 3.584406 ACTAGTGATGTGAGTGAGCAC 57.416 47.619 0.00 0.00 39.22 4.40
4386 7161 4.607293 AAACTAGTGATGTGAGTGAGCA 57.393 40.909 0.00 0.00 0.00 4.26
4387 7162 5.931441 AAAAACTAGTGATGTGAGTGAGC 57.069 39.130 0.00 0.00 0.00 4.26
4407 7182 3.128852 TCGGAGGAACGAATGGAAAAA 57.871 42.857 0.00 0.00 40.34 1.94
4408 7183 2.843401 TCGGAGGAACGAATGGAAAA 57.157 45.000 0.00 0.00 40.34 2.29
4409 7184 2.843401 TTCGGAGGAACGAATGGAAA 57.157 45.000 0.00 0.00 46.68 3.13
4429 7204 3.142174 GAGTCACTGGCTGCTAGTTTTT 58.858 45.455 16.47 4.45 0.00 1.94
4430 7205 2.772287 GAGTCACTGGCTGCTAGTTTT 58.228 47.619 16.47 4.81 0.00 2.43
4431 7206 1.337260 CGAGTCACTGGCTGCTAGTTT 60.337 52.381 16.47 5.17 0.00 2.66
4432 7207 0.244994 CGAGTCACTGGCTGCTAGTT 59.755 55.000 16.47 1.92 0.00 2.24
4433 7208 0.609406 TCGAGTCACTGGCTGCTAGT 60.609 55.000 13.27 13.27 0.00 2.57
4434 7209 0.528017 TTCGAGTCACTGGCTGCTAG 59.472 55.000 11.77 11.77 0.00 3.42
4435 7210 0.966179 TTTCGAGTCACTGGCTGCTA 59.034 50.000 0.00 0.00 0.00 3.49
4436 7211 0.320247 CTTTCGAGTCACTGGCTGCT 60.320 55.000 0.00 0.00 0.00 4.24
4437 7212 0.319900 TCTTTCGAGTCACTGGCTGC 60.320 55.000 0.00 0.00 0.00 5.25
4438 7213 2.154854 TTCTTTCGAGTCACTGGCTG 57.845 50.000 0.00 0.00 0.00 4.85
4439 7214 2.910688 TTTCTTTCGAGTCACTGGCT 57.089 45.000 0.00 0.00 0.00 4.75
4440 7215 3.963383 TTTTTCTTTCGAGTCACTGGC 57.037 42.857 0.00 0.00 0.00 4.85
4441 7216 5.237344 ACTCATTTTTCTTTCGAGTCACTGG 59.763 40.000 0.00 0.00 31.39 4.00
4442 7217 6.292389 ACTCATTTTTCTTTCGAGTCACTG 57.708 37.500 0.00 0.00 31.39 3.66
4443 7218 6.984474 TGTACTCATTTTTCTTTCGAGTCACT 59.016 34.615 0.00 0.00 37.98 3.41
4444 7219 7.173863 TGTACTCATTTTTCTTTCGAGTCAC 57.826 36.000 0.00 0.00 37.98 3.67
4445 7220 7.117812 GGATGTACTCATTTTTCTTTCGAGTCA 59.882 37.037 0.00 0.00 37.98 3.41
4446 7221 7.332182 AGGATGTACTCATTTTTCTTTCGAGTC 59.668 37.037 0.00 0.00 37.98 3.36
4447 7222 7.162082 AGGATGTACTCATTTTTCTTTCGAGT 58.838 34.615 0.00 0.00 40.03 4.18
4448 7223 7.602517 AGGATGTACTCATTTTTCTTTCGAG 57.397 36.000 0.00 0.00 34.06 4.04
4449 7224 7.979444 AAGGATGTACTCATTTTTCTTTCGA 57.021 32.000 0.00 0.00 34.06 3.71
4450 7225 8.507249 AGAAAGGATGTACTCATTTTTCTTTCG 58.493 33.333 0.00 0.00 40.74 3.46
4451 7226 9.617975 CAGAAAGGATGTACTCATTTTTCTTTC 57.382 33.333 13.54 0.00 41.12 2.62
4452 7227 9.354673 TCAGAAAGGATGTACTCATTTTTCTTT 57.645 29.630 13.54 0.00 41.12 2.52
4453 7228 8.924511 TCAGAAAGGATGTACTCATTTTTCTT 57.075 30.769 13.54 0.00 41.12 2.52
4460 7235 9.775854 CAAATCTATCAGAAAGGATGTACTCAT 57.224 33.333 0.00 0.00 36.95 2.90
4461 7236 8.981659 TCAAATCTATCAGAAAGGATGTACTCA 58.018 33.333 0.00 0.00 0.00 3.41
4462 7237 9.995003 ATCAAATCTATCAGAAAGGATGTACTC 57.005 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.