Multiple sequence alignment - TraesCS5A01G325100

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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 TraesCS5A01G325100 chr5A 100.000 3086 0 0 1 3086 535785872 535788957 0.000000e+00 5699.0
1 TraesCS5A01G325100 chr5A 81.850 573 71 20 1272 1818 535671741 535672306 4.690000e-123 451.0
2 TraesCS5A01G325100 chr5A 78.631 482 60 30 996 1448 535778952 535779419 2.340000e-71 279.0
3 TraesCS5A01G325100 chr5A 89.189 185 17 2 1000 1184 535646826 535647007 8.610000e-56 228.0
4 TraesCS5A01G325100 chr5A 88.000 75 9 0 1000 1074 535670777 535670851 4.240000e-14 89.8
5 TraesCS5A01G325100 chr5B 89.134 1270 61 28 868 2127 509470405 509471607 0.000000e+00 1509.0
6 TraesCS5A01G325100 chr5B 79.237 1180 153 64 963 2081 509205966 509207114 0.000000e+00 737.0
7 TraesCS5A01G325100 chr5B 87.521 601 64 8 121 712 509457497 509458095 0.000000e+00 684.0
8 TraesCS5A01G325100 chr5B 79.585 578 91 18 1514 2079 509188391 509188953 3.730000e-104 388.0
9 TraesCS5A01G325100 chr5B 79.691 453 65 21 996 1434 509210058 509210497 5.000000e-78 302.0
10 TraesCS5A01G325100 chr5B 85.714 217 27 3 968 1184 509103852 509104064 3.100000e-55 226.0
11 TraesCS5A01G325100 chr5B 88.827 179 11 3 708 878 509470198 509470375 8.670000e-51 211.0
12 TraesCS5A01G325100 chr5B 94.203 138 6 2 2146 2282 509471661 509471797 3.120000e-50 209.0
13 TraesCS5A01G325100 chr1A 97.540 691 15 2 2397 3086 84485880 84486569 0.000000e+00 1181.0
14 TraesCS5A01G325100 chr1A 97.395 691 17 1 2397 3086 84623081 84623771 0.000000e+00 1175.0
15 TraesCS5A01G325100 chr3A 85.734 708 62 25 2402 3086 713787739 713787048 0.000000e+00 712.0
16 TraesCS5A01G325100 chr3A 82.845 717 53 32 2397 3086 691307742 691308415 2.060000e-161 579.0
17 TraesCS5A01G325100 chr5D 78.901 1147 161 56 1000 2092 422456410 422457529 0.000000e+00 702.0
18 TraesCS5A01G325100 chr5D 82.888 187 19 1 1000 1186 422432418 422432591 4.120000e-34 156.0
19 TraesCS5A01G325100 chr4D 88.257 545 51 6 2398 2939 3423485 3424019 9.330000e-180 640.0
20 TraesCS5A01G325100 chr4D 81.605 598 80 20 5 588 445088998 445089579 4.660000e-128 468.0
21 TraesCS5A01G325100 chr4A 83.567 712 62 31 2397 3086 621688385 621689063 1.570000e-172 616.0
22 TraesCS5A01G325100 chr4A 81.063 602 92 13 1 588 596578901 596578308 7.800000e-126 460.0
23 TraesCS5A01G325100 chr4A 79.427 593 84 22 3 588 660463366 660463927 4.830000e-103 385.0
24 TraesCS5A01G325100 chr7A 83.264 717 50 29 2397 3086 138307101 138306428 2.050000e-166 595.0
25 TraesCS5A01G325100 chr7D 82.471 599 82 14 3 587 233198504 233197915 1.280000e-138 503.0
26 TraesCS5A01G325100 chr7D 83.925 479 40 14 2397 2854 548872631 548873093 1.020000e-114 424.0
27 TraesCS5A01G325100 chr7D 80.713 477 72 12 126 588 148115616 148115146 1.360000e-93 353.0
28 TraesCS5A01G325100 chr7D 89.604 202 13 5 2889 3086 548873087 548873284 1.840000e-62 250.0
29 TraesCS5A01G325100 chr2B 82.581 620 49 29 2397 2994 94177410 94176828 2.760000e-135 492.0
30 TraesCS5A01G325100 chr2B 80.067 597 86 20 3 584 735913602 735914180 2.210000e-111 412.0
31 TraesCS5A01G325100 chr3B 81.987 594 76 19 10 588 270950621 270951198 2.780000e-130 475.0
32 TraesCS5A01G325100 chr3B 81.198 601 88 17 3 588 410065998 410065408 7.800000e-126 460.0
33 TraesCS5A01G325100 chr1B 80.570 597 92 16 3 583 106389092 106388504 3.650000e-119 438.0
34 TraesCS5A01G325100 chr6D 80.496 605 81 23 1 588 138970398 138970982 2.200000e-116 429.0
35 TraesCS5A01G325100 chr3D 79.867 601 92 20 3 588 382980059 382980645 2.210000e-111 412.0
36 TraesCS5A01G325100 chr6B 79.104 603 98 15 3 588 646143352 646142761 1.040000e-104 390.0
37 TraesCS5A01G325100 chr1D 91.509 106 8 1 2397 2501 11731907 11731802 8.920000e-31 145.0


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 TraesCS5A01G325100 chr5A 535785872 535788957 3085 False 5699.0 5699 100.000000 1 3086 1 chr5A.!!$F3 3085
1 TraesCS5A01G325100 chr5A 535670777 535672306 1529 False 270.4 451 84.925000 1000 1818 2 chr5A.!!$F4 818
2 TraesCS5A01G325100 chr5B 509457497 509458095 598 False 684.0 684 87.521000 121 712 1 chr5B.!!$F3 591
3 TraesCS5A01G325100 chr5B 509470198 509471797 1599 False 643.0 1509 90.721333 708 2282 3 chr5B.!!$F5 1574
4 TraesCS5A01G325100 chr5B 509205966 509210497 4531 False 519.5 737 79.464000 963 2081 2 chr5B.!!$F4 1118
5 TraesCS5A01G325100 chr5B 509188391 509188953 562 False 388.0 388 79.585000 1514 2079 1 chr5B.!!$F2 565
6 TraesCS5A01G325100 chr1A 84485880 84486569 689 False 1181.0 1181 97.540000 2397 3086 1 chr1A.!!$F1 689
7 TraesCS5A01G325100 chr1A 84623081 84623771 690 False 1175.0 1175 97.395000 2397 3086 1 chr1A.!!$F2 689
8 TraesCS5A01G325100 chr3A 713787048 713787739 691 True 712.0 712 85.734000 2402 3086 1 chr3A.!!$R1 684
9 TraesCS5A01G325100 chr3A 691307742 691308415 673 False 579.0 579 82.845000 2397 3086 1 chr3A.!!$F1 689
10 TraesCS5A01G325100 chr5D 422456410 422457529 1119 False 702.0 702 78.901000 1000 2092 1 chr5D.!!$F2 1092
11 TraesCS5A01G325100 chr4D 3423485 3424019 534 False 640.0 640 88.257000 2398 2939 1 chr4D.!!$F1 541
12 TraesCS5A01G325100 chr4D 445088998 445089579 581 False 468.0 468 81.605000 5 588 1 chr4D.!!$F2 583
13 TraesCS5A01G325100 chr4A 621688385 621689063 678 False 616.0 616 83.567000 2397 3086 1 chr4A.!!$F1 689
14 TraesCS5A01G325100 chr4A 596578308 596578901 593 True 460.0 460 81.063000 1 588 1 chr4A.!!$R1 587
15 TraesCS5A01G325100 chr4A 660463366 660463927 561 False 385.0 385 79.427000 3 588 1 chr4A.!!$F2 585
16 TraesCS5A01G325100 chr7A 138306428 138307101 673 True 595.0 595 83.264000 2397 3086 1 chr7A.!!$R1 689
17 TraesCS5A01G325100 chr7D 233197915 233198504 589 True 503.0 503 82.471000 3 587 1 chr7D.!!$R2 584
18 TraesCS5A01G325100 chr7D 548872631 548873284 653 False 337.0 424 86.764500 2397 3086 2 chr7D.!!$F1 689
19 TraesCS5A01G325100 chr2B 94176828 94177410 582 True 492.0 492 82.581000 2397 2994 1 chr2B.!!$R1 597
20 TraesCS5A01G325100 chr2B 735913602 735914180 578 False 412.0 412 80.067000 3 584 1 chr2B.!!$F1 581
21 TraesCS5A01G325100 chr3B 270950621 270951198 577 False 475.0 475 81.987000 10 588 1 chr3B.!!$F1 578
22 TraesCS5A01G325100 chr3B 410065408 410065998 590 True 460.0 460 81.198000 3 588 1 chr3B.!!$R1 585
23 TraesCS5A01G325100 chr1B 106388504 106389092 588 True 438.0 438 80.570000 3 583 1 chr1B.!!$R1 580
24 TraesCS5A01G325100 chr6D 138970398 138970982 584 False 429.0 429 80.496000 1 588 1 chr6D.!!$F1 587
25 TraesCS5A01G325100 chr3D 382980059 382980645 586 False 412.0 412 79.867000 3 588 1 chr3D.!!$F1 585
26 TraesCS5A01G325100 chr6B 646142761 646143352 591 True 390.0 390 79.104000 3 588 1 chr6B.!!$R1 585

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
677 715 0.109532 TCAGCCACGGTGATCCAAAA 59.89 50.0 10.28 0.0 35.04 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 6195 0.033504 GATCGCCCCAATCGCTAAGA 59.966 55.0 0.0 0.0 0.0 2.1 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
41 46 1.504359 GCGTGCGGGCTACATATAAA 58.496 50.000 0.00 0.00 0.00 1.40
42 47 1.868498 GCGTGCGGGCTACATATAAAA 59.132 47.619 0.00 0.00 0.00 1.52
138 143 2.682582 TACCACGTGCAATGGCCACA 62.683 55.000 8.16 0.00 41.31 4.17
197 203 6.127083 TGGTGATGCTGATCTGAATAGTGTAA 60.127 38.462 3.42 0.00 0.00 2.41
275 286 1.370414 AATGTGCTTTCGTGCGTGC 60.370 52.632 0.00 0.00 35.36 5.34
279 290 1.370293 TGCTTTCGTGCGTGCAATG 60.370 52.632 0.00 0.00 35.36 2.82
280 291 1.082169 GCTTTCGTGCGTGCAATGA 60.082 52.632 0.00 0.00 0.00 2.57
282 293 1.253116 CTTTCGTGCGTGCAATGATG 58.747 50.000 0.00 0.00 0.00 3.07
320 337 0.179006 CCCCTTTGCTCCTGCCTATC 60.179 60.000 0.00 0.00 38.71 2.08
323 340 0.533755 CTTTGCTCCTGCCTATCGGG 60.534 60.000 0.00 0.00 42.90 5.14
351 368 3.622060 ATACGGCCAGCCCACACAC 62.622 63.158 2.24 0.00 0.00 3.82
373 390 3.556213 CCGTACAACAACTCATCCTCCAA 60.556 47.826 0.00 0.00 0.00 3.53
490 528 1.405463 TGAAGATCGTCGACATGAGGG 59.595 52.381 17.16 0.00 33.27 4.30
491 529 1.405821 GAAGATCGTCGACATGAGGGT 59.594 52.381 17.16 0.00 33.27 4.34
495 533 0.526211 TCGTCGACATGAGGGTGAAG 59.474 55.000 17.16 0.00 33.27 3.02
496 534 0.243907 CGTCGACATGAGGGTGAAGT 59.756 55.000 17.16 0.00 0.00 3.01
499 537 3.428999 CGTCGACATGAGGGTGAAGTTAT 60.429 47.826 17.16 0.00 0.00 1.89
504 542 4.104086 ACATGAGGGTGAAGTTATCTGGA 58.896 43.478 0.00 0.00 0.00 3.86
544 582 4.694037 GTGGACAACTTTATCGTAAAGGCT 59.306 41.667 16.53 0.00 0.00 4.58
594 632 3.281240 GGCAATGCCTCCACTGTG 58.719 61.111 18.47 0.00 46.69 3.66
595 633 2.345760 GGCAATGCCTCCACTGTGG 61.346 63.158 20.86 20.86 46.69 4.17
596 634 1.604593 GCAATGCCTCCACTGTGGT 60.605 57.895 25.15 3.82 39.03 4.16
597 635 1.589716 GCAATGCCTCCACTGTGGTC 61.590 60.000 25.15 15.84 39.03 4.02
598 636 0.962356 CAATGCCTCCACTGTGGTCC 60.962 60.000 25.15 14.96 39.03 4.46
599 637 2.469465 AATGCCTCCACTGTGGTCCG 62.469 60.000 25.15 14.71 39.03 4.79
600 638 3.311110 GCCTCCACTGTGGTCCGA 61.311 66.667 25.15 6.26 39.03 4.55
601 639 2.879233 GCCTCCACTGTGGTCCGAA 61.879 63.158 25.15 5.88 39.03 4.30
602 640 1.004918 CCTCCACTGTGGTCCGAAC 60.005 63.158 25.15 0.00 39.03 3.95
603 641 1.372997 CTCCACTGTGGTCCGAACG 60.373 63.158 25.15 0.00 39.03 3.95
604 642 2.357034 CCACTGTGGTCCGAACGG 60.357 66.667 18.76 6.94 31.35 4.44
605 643 2.732016 CACTGTGGTCCGAACGGA 59.268 61.111 12.04 12.04 42.90 4.69
620 658 4.235731 GGATACGGGGTTTGCAGG 57.764 61.111 0.00 0.00 0.00 4.85
621 659 1.301954 GGATACGGGGTTTGCAGGT 59.698 57.895 0.00 0.00 0.00 4.00
622 660 0.746923 GGATACGGGGTTTGCAGGTC 60.747 60.000 0.00 0.00 0.00 3.85
623 661 0.746923 GATACGGGGTTTGCAGGTCC 60.747 60.000 0.00 0.00 0.00 4.46
624 662 2.206182 ATACGGGGTTTGCAGGTCCC 62.206 60.000 12.59 12.59 40.41 4.46
626 664 4.280019 GGGGTTTGCAGGTCCCGT 62.280 66.667 13.99 0.00 41.92 5.28
627 665 2.671963 GGGTTTGCAGGTCCCGTC 60.672 66.667 7.08 0.00 0.00 4.79
628 666 3.047877 GGTTTGCAGGTCCCGTCG 61.048 66.667 0.00 0.00 0.00 5.12
629 667 3.723348 GTTTGCAGGTCCCGTCGC 61.723 66.667 0.00 0.00 0.00 5.19
630 668 4.243008 TTTGCAGGTCCCGTCGCA 62.243 61.111 0.00 0.00 0.00 5.10
631 669 4.980805 TTGCAGGTCCCGTCGCAC 62.981 66.667 0.00 0.00 33.29 5.34
633 671 4.681978 GCAGGTCCCGTCGCACTT 62.682 66.667 0.00 0.00 0.00 3.16
634 672 2.967397 CAGGTCCCGTCGCACTTA 59.033 61.111 0.00 0.00 0.00 2.24
635 673 1.290955 CAGGTCCCGTCGCACTTAA 59.709 57.895 0.00 0.00 0.00 1.85
636 674 0.320073 CAGGTCCCGTCGCACTTAAA 60.320 55.000 0.00 0.00 0.00 1.52
637 675 0.611714 AGGTCCCGTCGCACTTAAAT 59.388 50.000 0.00 0.00 0.00 1.40
638 676 1.004595 GGTCCCGTCGCACTTAAATC 58.995 55.000 0.00 0.00 0.00 2.17
639 677 1.004595 GTCCCGTCGCACTTAAATCC 58.995 55.000 0.00 0.00 0.00 3.01
640 678 0.458889 TCCCGTCGCACTTAAATCCG 60.459 55.000 0.00 0.00 0.00 4.18
641 679 0.458889 CCCGTCGCACTTAAATCCGA 60.459 55.000 0.00 0.00 0.00 4.55
642 680 1.567504 CCGTCGCACTTAAATCCGAT 58.432 50.000 0.00 0.00 31.96 4.18
643 681 1.931172 CCGTCGCACTTAAATCCGATT 59.069 47.619 0.00 0.00 31.96 3.34
644 682 2.350498 CCGTCGCACTTAAATCCGATTT 59.650 45.455 11.09 11.09 36.29 2.17
645 683 3.342269 CGTCGCACTTAAATCCGATTTG 58.658 45.455 15.37 3.60 33.82 2.32
646 684 3.680789 GTCGCACTTAAATCCGATTTGG 58.319 45.455 15.37 10.59 40.09 3.28
647 685 3.126343 GTCGCACTTAAATCCGATTTGGT 59.874 43.478 15.37 11.13 39.52 3.67
648 686 4.330620 GTCGCACTTAAATCCGATTTGGTA 59.669 41.667 15.37 1.92 39.52 3.25
649 687 4.330620 TCGCACTTAAATCCGATTTGGTAC 59.669 41.667 15.37 8.55 39.52 3.34
650 688 4.093703 CGCACTTAAATCCGATTTGGTACA 59.906 41.667 15.37 0.00 39.52 2.90
651 689 9.414312 GTCGCACTTAAATCCGATTTGGTACAA 62.414 40.741 15.37 2.06 36.21 2.41
664 702 2.827755 TGGTACAATACTCCTCAGCCA 58.172 47.619 0.00 0.00 31.92 4.75
665 703 2.500098 TGGTACAATACTCCTCAGCCAC 59.500 50.000 0.00 0.00 31.92 5.01
666 704 2.481449 GGTACAATACTCCTCAGCCACG 60.481 54.545 0.00 0.00 0.00 4.94
667 705 0.537188 ACAATACTCCTCAGCCACGG 59.463 55.000 0.00 0.00 0.00 4.94
668 706 0.537188 CAATACTCCTCAGCCACGGT 59.463 55.000 0.00 0.00 0.00 4.83
669 707 0.537188 AATACTCCTCAGCCACGGTG 59.463 55.000 0.00 0.00 0.00 4.94
670 708 0.324368 ATACTCCTCAGCCACGGTGA 60.324 55.000 10.28 0.00 37.74 4.02
671 709 0.324368 TACTCCTCAGCCACGGTGAT 60.324 55.000 10.28 0.00 39.36 3.06
672 710 1.142748 CTCCTCAGCCACGGTGATC 59.857 63.158 10.28 0.87 39.36 2.92
673 711 2.187946 CCTCAGCCACGGTGATCC 59.812 66.667 10.28 0.00 39.36 3.36
674 712 2.659063 CCTCAGCCACGGTGATCCA 61.659 63.158 10.28 0.00 39.36 3.41
675 713 1.296392 CTCAGCCACGGTGATCCAA 59.704 57.895 10.28 0.00 39.36 3.53
676 714 0.321564 CTCAGCCACGGTGATCCAAA 60.322 55.000 10.28 0.00 39.36 3.28
677 715 0.109532 TCAGCCACGGTGATCCAAAA 59.890 50.000 10.28 0.00 35.04 2.44
678 716 0.958091 CAGCCACGGTGATCCAAAAA 59.042 50.000 10.28 0.00 32.22 1.94
701 739 7.739498 AAAATACAACAATCCAACGTAGAGT 57.261 32.000 0.00 0.00 0.00 3.24
702 740 6.963049 AATACAACAATCCAACGTAGAGTC 57.037 37.500 0.00 0.00 0.00 3.36
703 741 4.602340 ACAACAATCCAACGTAGAGTCT 57.398 40.909 0.00 0.00 0.00 3.24
704 742 4.557205 ACAACAATCCAACGTAGAGTCTC 58.443 43.478 0.00 0.00 0.00 3.36
705 743 4.281182 ACAACAATCCAACGTAGAGTCTCT 59.719 41.667 7.68 7.68 0.00 3.10
706 744 5.221461 ACAACAATCCAACGTAGAGTCTCTT 60.221 40.000 7.89 0.00 0.00 2.85
740 778 2.618053 CGGTACAGATGGGACTGAAAC 58.382 52.381 0.00 0.00 40.63 2.78
742 780 3.446161 CGGTACAGATGGGACTGAAACTA 59.554 47.826 0.00 0.00 40.63 2.24
744 782 5.360591 GGTACAGATGGGACTGAAACTATG 58.639 45.833 0.00 0.00 40.63 2.23
747 785 5.491982 ACAGATGGGACTGAAACTATGAAC 58.508 41.667 0.00 0.00 40.63 3.18
775 813 4.201792 GCATAGCAACAGAATCACTCAGTG 60.202 45.833 0.00 0.00 34.45 3.66
780 818 4.122046 CAACAGAATCACTCAGTGTGTGA 58.878 43.478 25.52 25.52 46.58 3.58
782 820 4.122776 ACAGAATCACTCAGTGTGTGAAC 58.877 43.478 26.67 22.32 45.82 3.18
804 843 1.881252 CGGCGAATGGGTACTTCCG 60.881 63.158 0.00 0.00 37.00 4.30
822 861 0.459237 CGGGTCAAGTCAGCTAGCAG 60.459 60.000 18.83 9.54 0.00 4.24
858 904 3.058501 CACGCCAAGTTTTCCGTATTTCT 60.059 43.478 0.00 0.00 32.05 2.52
893 978 9.862371 ATATCCAATTTAATTAACACACGCAAA 57.138 25.926 0.00 0.00 0.00 3.68
969 1054 3.747976 GGCGGCGGCTTCACAAAT 61.748 61.111 27.22 0.00 39.81 2.32
970 1055 2.202479 GCGGCGGCTTCACAAATC 60.202 61.111 9.78 0.00 35.83 2.17
971 1056 2.485122 CGGCGGCTTCACAAATCC 59.515 61.111 7.61 0.00 0.00 3.01
972 1057 2.331893 CGGCGGCTTCACAAATCCA 61.332 57.895 7.61 0.00 0.00 3.41
973 1058 1.212751 GGCGGCTTCACAAATCCAC 59.787 57.895 0.00 0.00 0.00 4.02
995 1080 4.580551 CGATCCCCCGTACCGTGC 62.581 72.222 0.00 0.00 0.00 5.34
996 1081 3.463585 GATCCCCCGTACCGTGCA 61.464 66.667 0.00 0.00 0.00 4.57
997 1082 2.766651 ATCCCCCGTACCGTGCAT 60.767 61.111 0.00 0.00 0.00 3.96
998 1083 2.989055 GATCCCCCGTACCGTGCATG 62.989 65.000 0.00 0.00 0.00 4.06
1089 1816 4.324991 GGGCCCCTCGACAACGTT 62.325 66.667 12.23 0.00 40.69 3.99
1192 1919 1.385409 CGCACGGCATATACATGTACG 59.615 52.381 7.96 9.38 39.19 3.67
1195 1922 3.121279 GCACGGCATATACATGTACGAAG 59.879 47.826 16.80 10.82 37.77 3.79
1258 2035 2.701780 CGGCCGTACTGCAGAGACT 61.702 63.158 23.35 0.00 0.00 3.24
1290 2073 0.458543 CCGTCAAGACCGTCATGGAG 60.459 60.000 4.03 0.00 42.00 3.86
1329 2112 2.936570 GCGCATCATCGGAAGCTCG 61.937 63.158 0.30 0.00 35.65 5.03
1453 2238 4.711949 CCGGCAAGCAGCTCTGGT 62.712 66.667 0.00 0.00 44.79 4.00
1536 2333 4.760047 ACCCACGCCGTGATGCTC 62.760 66.667 20.57 0.00 35.23 4.26
1639 2442 3.088789 AGTACCTGGACGTCATCTTCT 57.911 47.619 18.91 5.32 0.00 2.85
1647 2453 2.100989 GACGTCATCTTCTACAGGGGT 58.899 52.381 11.55 0.00 0.00 4.95
1670 2476 1.546476 CTTCTACACGGTCAGCTCCTT 59.454 52.381 0.00 0.00 0.00 3.36
1693 2499 4.619227 AGGTGAACGCGTGGGTGG 62.619 66.667 14.98 0.00 0.00 4.61
1774 2587 4.778415 CCGTGCTCACCGAGTCCG 62.778 72.222 0.00 0.00 31.39 4.79
1779 2592 2.567049 CTCACCGAGTCCGTGTCC 59.433 66.667 10.76 0.00 0.00 4.02
1831 2644 4.547905 CGCGCGACCACGATACCT 62.548 66.667 28.94 0.00 42.66 3.08
1835 2648 0.379669 CGCGACCACGATACCTACTT 59.620 55.000 0.00 0.00 42.66 2.24
1837 2650 2.225019 CGCGACCACGATACCTACTTAT 59.775 50.000 0.00 0.00 42.66 1.73
1838 2651 3.666374 CGCGACCACGATACCTACTTATC 60.666 52.174 0.00 0.00 42.66 1.75
1840 2653 4.023365 GCGACCACGATACCTACTTATCTT 60.023 45.833 0.00 0.00 42.66 2.40
1847 2672 7.309867 CCACGATACCTACTTATCTTATGGCTT 60.310 40.741 0.00 0.00 0.00 4.35
1849 2674 7.093858 ACGATACCTACTTATCTTATGGCTTCC 60.094 40.741 0.00 0.00 0.00 3.46
1916 2748 2.747686 GCTTCCCGTGGAGAACCA 59.252 61.111 0.00 0.00 44.76 3.67
2070 2902 2.000447 CCTTACGTTGCAAGGCTAGAC 59.000 52.381 18.61 0.00 36.41 2.59
2111 2947 1.674441 TCATCCATGTCGACCGTAGAC 59.326 52.381 14.12 4.93 38.98 2.59
2127 2963 3.487574 CGTAGACTCGATTCATTTCCAGC 59.512 47.826 5.50 0.00 0.00 4.85
2138 3237 1.605710 CATTTCCAGCTTAGGGCATCG 59.394 52.381 0.00 0.00 44.79 3.84
2139 3238 0.107214 TTTCCAGCTTAGGGCATCGG 60.107 55.000 0.00 0.00 44.79 4.18
2160 3274 4.655921 TTGGGCGCCAAGATTAGG 57.344 55.556 30.85 0.00 38.75 2.69
2201 3315 2.813754 CGCAAGATTGTTTCTCTTCCCA 59.186 45.455 0.00 0.00 43.02 4.37
2261 3375 2.740714 CGCCTGCCGTTGTAAGCTC 61.741 63.158 0.00 0.00 0.00 4.09
2268 3382 1.738099 CGTTGTAAGCTCAGGCGCT 60.738 57.895 7.64 0.00 44.37 5.92
2270 3384 0.670546 GTTGTAAGCTCAGGCGCTGA 60.671 55.000 7.64 8.39 44.37 4.26
2315 3429 6.844097 AAACTTATTTATTTTCCGCCTCCA 57.156 33.333 0.00 0.00 0.00 3.86
2316 3430 5.830000 ACTTATTTATTTTCCGCCTCCAC 57.170 39.130 0.00 0.00 0.00 4.02
2317 3431 5.258051 ACTTATTTATTTTCCGCCTCCACA 58.742 37.500 0.00 0.00 0.00 4.17
2318 3432 5.712917 ACTTATTTATTTTCCGCCTCCACAA 59.287 36.000 0.00 0.00 0.00 3.33
2319 3433 6.209788 ACTTATTTATTTTCCGCCTCCACAAA 59.790 34.615 0.00 0.00 0.00 2.83
2320 3434 3.926821 TTATTTTCCGCCTCCACAAAC 57.073 42.857 0.00 0.00 0.00 2.93
2321 3435 0.596082 ATTTTCCGCCTCCACAAACG 59.404 50.000 0.00 0.00 0.00 3.60
2322 3436 0.748729 TTTTCCGCCTCCACAAACGT 60.749 50.000 0.00 0.00 0.00 3.99
2323 3437 1.161563 TTTCCGCCTCCACAAACGTC 61.162 55.000 0.00 0.00 0.00 4.34
2324 3438 2.030562 CCGCCTCCACAAACGTCT 59.969 61.111 0.00 0.00 0.00 4.18
2325 3439 1.180456 TCCGCCTCCACAAACGTCTA 61.180 55.000 0.00 0.00 0.00 2.59
2326 3440 1.012486 CCGCCTCCACAAACGTCTAC 61.012 60.000 0.00 0.00 0.00 2.59
2327 3441 1.012486 CGCCTCCACAAACGTCTACC 61.012 60.000 0.00 0.00 0.00 3.18
2328 3442 1.012486 GCCTCCACAAACGTCTACCG 61.012 60.000 0.00 0.00 44.03 4.02
2351 3465 1.923899 TTTTTCCCGGCAAAAACGTC 58.076 45.000 12.05 0.00 31.65 4.34
2352 3466 1.104630 TTTTCCCGGCAAAAACGTCT 58.895 45.000 0.00 0.00 0.00 4.18
2353 3467 1.964552 TTTCCCGGCAAAAACGTCTA 58.035 45.000 0.00 0.00 0.00 2.59
2354 3468 1.228533 TTCCCGGCAAAAACGTCTAC 58.771 50.000 0.00 0.00 0.00 2.59
2355 3469 0.603439 TCCCGGCAAAAACGTCTACC 60.603 55.000 0.00 0.00 0.00 3.18
2356 3470 1.494189 CCGGCAAAAACGTCTACCG 59.506 57.895 8.06 8.06 44.03 4.02
2367 3481 0.719465 CGTCTACCGTTGTTGATGCC 59.281 55.000 0.00 0.00 0.00 4.40
2368 3482 1.084289 GTCTACCGTTGTTGATGCCC 58.916 55.000 0.00 0.00 0.00 5.36
2369 3483 0.035820 TCTACCGTTGTTGATGCCCC 60.036 55.000 0.00 0.00 0.00 5.80
2370 3484 0.322098 CTACCGTTGTTGATGCCCCA 60.322 55.000 0.00 0.00 0.00 4.96
2371 3485 0.322098 TACCGTTGTTGATGCCCCAG 60.322 55.000 0.00 0.00 0.00 4.45
2372 3486 2.568090 CGTTGTTGATGCCCCAGC 59.432 61.111 0.00 0.00 40.48 4.85
2382 3496 4.440145 GCCCCAGCAAAGATTCCA 57.560 55.556 0.00 0.00 39.53 3.53
2383 3497 2.196319 GCCCCAGCAAAGATTCCAG 58.804 57.895 0.00 0.00 39.53 3.86
2384 3498 1.953231 GCCCCAGCAAAGATTCCAGC 61.953 60.000 0.00 0.00 39.53 4.85
2385 3499 0.612732 CCCCAGCAAAGATTCCAGCA 60.613 55.000 0.00 0.00 0.00 4.41
2386 3500 0.815734 CCCAGCAAAGATTCCAGCAG 59.184 55.000 0.00 0.00 0.00 4.24
2387 3501 1.615116 CCCAGCAAAGATTCCAGCAGA 60.615 52.381 0.00 0.00 0.00 4.26
2388 3502 1.471684 CCAGCAAAGATTCCAGCAGAC 59.528 52.381 0.00 0.00 0.00 3.51
2389 3503 2.156917 CAGCAAAGATTCCAGCAGACA 58.843 47.619 0.00 0.00 0.00 3.41
2390 3504 2.555325 CAGCAAAGATTCCAGCAGACAA 59.445 45.455 0.00 0.00 0.00 3.18
2391 3505 3.005050 CAGCAAAGATTCCAGCAGACAAA 59.995 43.478 0.00 0.00 0.00 2.83
2392 3506 3.830755 AGCAAAGATTCCAGCAGACAAAT 59.169 39.130 0.00 0.00 0.00 2.32
2393 3507 3.924686 GCAAAGATTCCAGCAGACAAATG 59.075 43.478 0.00 0.00 0.00 2.32
2394 3508 4.491676 CAAAGATTCCAGCAGACAAATGG 58.508 43.478 0.00 0.00 35.30 3.16
2395 3509 3.726557 AGATTCCAGCAGACAAATGGA 57.273 42.857 0.00 0.00 41.33 3.41
2450 4327 1.343075 TGCCTCTACCTTACCCCTCAG 60.343 57.143 0.00 0.00 0.00 3.35
2540 6051 0.539438 ATCAAAACGAAGCCAGCCCA 60.539 50.000 0.00 0.00 0.00 5.36
2656 6195 2.166664 GGGTTCTCATCTCAGTTAGCGT 59.833 50.000 0.00 0.00 0.00 5.07
2657 6196 3.440228 GGTTCTCATCTCAGTTAGCGTC 58.560 50.000 0.00 0.00 0.00 5.19
2658 6197 3.129638 GGTTCTCATCTCAGTTAGCGTCT 59.870 47.826 0.00 0.00 0.00 4.18
2659 6198 4.381079 GGTTCTCATCTCAGTTAGCGTCTT 60.381 45.833 0.00 0.00 0.00 3.01
2660 6199 5.163642 GGTTCTCATCTCAGTTAGCGTCTTA 60.164 44.000 0.00 0.00 0.00 2.10
2661 6200 5.743026 TCTCATCTCAGTTAGCGTCTTAG 57.257 43.478 0.00 0.00 0.00 2.18
2662 6201 4.035792 TCTCATCTCAGTTAGCGTCTTAGC 59.964 45.833 0.00 0.00 37.41 3.09
2663 6202 2.826979 TCTCAGTTAGCGTCTTAGCG 57.173 50.000 0.00 0.00 43.00 4.26
2688 6484 2.867855 GCGATCATCGGGGTGCCTA 61.868 63.158 9.59 0.00 40.84 3.93
2727 6523 1.139095 GTCCTAGTTGAGCGTCGGG 59.861 63.158 0.00 0.00 0.00 5.14
2812 6612 6.420913 AACAGAGACTGCCTAGTTTTTAGA 57.579 37.500 0.00 0.00 37.25 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 46 7.064609 CGTTCACTCAATGTTGGTCTACATATT 59.935 37.037 0.00 0.00 37.76 1.28
42 47 6.535150 CGTTCACTCAATGTTGGTCTACATAT 59.465 38.462 0.00 0.00 37.76 1.78
138 143 1.429463 GTTCGTCAACTCGAGGCAAT 58.571 50.000 18.41 0.00 40.86 3.56
171 177 4.510711 CACTATTCAGATCAGCATCACCAC 59.489 45.833 0.00 0.00 0.00 4.16
197 203 1.884579 AGGTCGTTGTCGTATCACTGT 59.115 47.619 0.00 0.00 38.33 3.55
275 286 1.655484 TCTGGCAGCGTACATCATTG 58.345 50.000 10.34 0.00 0.00 2.82
279 290 2.682893 CCTTCTGGCAGCGTACATC 58.317 57.895 10.34 0.00 0.00 3.06
280 291 4.941609 CCTTCTGGCAGCGTACAT 57.058 55.556 10.34 0.00 0.00 2.29
343 360 0.658897 GTTGTTGTACGGTGTGTGGG 59.341 55.000 0.00 0.00 0.00 4.61
351 368 2.028476 TGGAGGATGAGTTGTTGTACGG 60.028 50.000 0.00 0.00 0.00 4.02
354 371 5.624509 CGATCTTGGAGGATGAGTTGTTGTA 60.625 44.000 0.00 0.00 0.00 2.41
473 510 0.741326 CACCCTCATGTCGACGATCT 59.259 55.000 11.62 0.00 0.00 2.75
490 528 6.543831 AGCCATTTGTATCCAGATAACTTCAC 59.456 38.462 0.00 0.00 0.00 3.18
491 529 6.662755 AGCCATTTGTATCCAGATAACTTCA 58.337 36.000 0.00 0.00 0.00 3.02
495 533 7.040409 CCCTAAAGCCATTTGTATCCAGATAAC 60.040 40.741 0.00 0.00 0.00 1.89
496 534 7.004086 CCCTAAAGCCATTTGTATCCAGATAA 58.996 38.462 0.00 0.00 0.00 1.75
499 537 4.229582 ACCCTAAAGCCATTTGTATCCAGA 59.770 41.667 0.00 0.00 0.00 3.86
504 542 4.264172 TGTCCACCCTAAAGCCATTTGTAT 60.264 41.667 0.00 0.00 0.00 2.29
516 554 4.895668 ACGATAAAGTTGTCCACCCTAA 57.104 40.909 0.00 0.00 0.00 2.69
588 626 0.528924 TATCCGTTCGGACCACAGTG 59.471 55.000 16.22 0.00 37.10 3.66
589 627 0.529378 GTATCCGTTCGGACCACAGT 59.471 55.000 16.22 2.26 37.10 3.55
590 628 0.524816 CGTATCCGTTCGGACCACAG 60.525 60.000 16.22 9.60 37.10 3.66
591 629 1.507630 CGTATCCGTTCGGACCACA 59.492 57.895 16.22 0.00 37.10 4.17
592 630 4.389772 CGTATCCGTTCGGACCAC 57.610 61.111 16.22 14.93 37.10 4.16
597 635 1.085501 CAAACCCCGTATCCGTTCGG 61.086 60.000 4.74 4.74 45.42 4.30
598 636 1.698714 GCAAACCCCGTATCCGTTCG 61.699 60.000 0.00 0.00 0.00 3.95
599 637 0.674269 TGCAAACCCCGTATCCGTTC 60.674 55.000 0.00 0.00 0.00 3.95
600 638 0.675522 CTGCAAACCCCGTATCCGTT 60.676 55.000 0.00 0.00 0.00 4.44
601 639 1.078708 CTGCAAACCCCGTATCCGT 60.079 57.895 0.00 0.00 0.00 4.69
602 640 1.817941 CCTGCAAACCCCGTATCCG 60.818 63.158 0.00 0.00 0.00 4.18
603 641 0.746923 GACCTGCAAACCCCGTATCC 60.747 60.000 0.00 0.00 0.00 2.59
604 642 0.746923 GGACCTGCAAACCCCGTATC 60.747 60.000 0.00 0.00 0.00 2.24
605 643 1.301954 GGACCTGCAAACCCCGTAT 59.698 57.895 0.00 0.00 0.00 3.06
606 644 2.751688 GGACCTGCAAACCCCGTA 59.248 61.111 0.00 0.00 0.00 4.02
607 645 4.280019 GGGACCTGCAAACCCCGT 62.280 66.667 10.35 0.00 37.85 5.28
609 647 4.280019 ACGGGACCTGCAAACCCC 62.280 66.667 14.31 10.77 40.43 4.95
610 648 2.671963 GACGGGACCTGCAAACCC 60.672 66.667 0.00 11.17 40.17 4.11
611 649 3.047877 CGACGGGACCTGCAAACC 61.048 66.667 0.00 0.00 0.00 3.27
612 650 3.723348 GCGACGGGACCTGCAAAC 61.723 66.667 0.00 0.00 0.00 2.93
613 651 4.243008 TGCGACGGGACCTGCAAA 62.243 61.111 0.00 0.00 33.80 3.68
614 652 4.980805 GTGCGACGGGACCTGCAA 62.981 66.667 0.00 0.00 39.34 4.08
616 654 2.775032 TTAAGTGCGACGGGACCTGC 62.775 60.000 0.00 0.00 34.61 4.85
617 655 0.320073 TTTAAGTGCGACGGGACCTG 60.320 55.000 0.00 0.00 34.61 4.00
618 656 0.611714 ATTTAAGTGCGACGGGACCT 59.388 50.000 0.00 0.00 34.61 3.85
619 657 1.004595 GATTTAAGTGCGACGGGACC 58.995 55.000 0.00 0.00 34.61 4.46
620 658 1.004595 GGATTTAAGTGCGACGGGAC 58.995 55.000 0.00 0.00 34.21 4.46
621 659 0.458889 CGGATTTAAGTGCGACGGGA 60.459 55.000 5.98 0.00 34.67 5.14
622 660 0.458889 TCGGATTTAAGTGCGACGGG 60.459 55.000 10.43 0.00 37.03 5.28
623 661 1.567504 ATCGGATTTAAGTGCGACGG 58.432 50.000 16.29 0.00 44.53 4.79
624 662 3.342269 CAAATCGGATTTAAGTGCGACG 58.658 45.455 16.29 5.27 44.53 5.12
625 663 3.126343 ACCAAATCGGATTTAAGTGCGAC 59.874 43.478 16.29 0.00 44.53 5.19
626 664 3.340034 ACCAAATCGGATTTAAGTGCGA 58.660 40.909 16.29 16.29 45.75 5.10
627 665 3.757745 ACCAAATCGGATTTAAGTGCG 57.242 42.857 15.13 5.51 38.63 5.34
628 666 5.554822 TGTACCAAATCGGATTTAAGTGC 57.445 39.130 15.13 17.22 38.63 4.40
629 667 8.889717 AGTATTGTACCAAATCGGATTTAAGTG 58.110 33.333 15.13 4.62 38.63 3.16
630 668 9.106070 GAGTATTGTACCAAATCGGATTTAAGT 57.894 33.333 15.13 16.45 38.63 2.24
631 669 8.557029 GGAGTATTGTACCAAATCGGATTTAAG 58.443 37.037 15.13 12.08 38.63 1.85
632 670 8.269317 AGGAGTATTGTACCAAATCGGATTTAA 58.731 33.333 15.13 6.82 38.63 1.52
633 671 7.798071 AGGAGTATTGTACCAAATCGGATTTA 58.202 34.615 15.13 0.12 38.63 1.40
634 672 6.659824 AGGAGTATTGTACCAAATCGGATTT 58.340 36.000 10.11 10.11 38.63 2.17
635 673 6.126883 TGAGGAGTATTGTACCAAATCGGATT 60.127 38.462 0.00 0.00 38.63 3.01
636 674 5.365605 TGAGGAGTATTGTACCAAATCGGAT 59.634 40.000 0.00 0.00 38.63 4.18
637 675 4.712829 TGAGGAGTATTGTACCAAATCGGA 59.287 41.667 0.00 0.00 38.63 4.55
638 676 5.018539 TGAGGAGTATTGTACCAAATCGG 57.981 43.478 0.00 0.00 42.50 4.18
639 677 4.508124 GCTGAGGAGTATTGTACCAAATCG 59.492 45.833 0.00 0.00 0.00 3.34
640 678 4.816925 GGCTGAGGAGTATTGTACCAAATC 59.183 45.833 0.00 0.00 0.00 2.17
641 679 4.227300 TGGCTGAGGAGTATTGTACCAAAT 59.773 41.667 0.00 0.00 0.00 2.32
642 680 3.585289 TGGCTGAGGAGTATTGTACCAAA 59.415 43.478 0.00 0.00 0.00 3.28
643 681 3.055385 GTGGCTGAGGAGTATTGTACCAA 60.055 47.826 0.00 0.00 0.00 3.67
644 682 2.500098 GTGGCTGAGGAGTATTGTACCA 59.500 50.000 0.00 0.00 0.00 3.25
645 683 2.481449 CGTGGCTGAGGAGTATTGTACC 60.481 54.545 0.00 0.00 0.00 3.34
646 684 2.481449 CCGTGGCTGAGGAGTATTGTAC 60.481 54.545 0.00 0.00 0.00 2.90
647 685 1.754803 CCGTGGCTGAGGAGTATTGTA 59.245 52.381 0.00 0.00 0.00 2.41
648 686 0.537188 CCGTGGCTGAGGAGTATTGT 59.463 55.000 0.00 0.00 0.00 2.71
649 687 0.537188 ACCGTGGCTGAGGAGTATTG 59.463 55.000 0.84 0.00 0.00 1.90
650 688 0.537188 CACCGTGGCTGAGGAGTATT 59.463 55.000 0.00 0.00 0.00 1.89
651 689 0.324368 TCACCGTGGCTGAGGAGTAT 60.324 55.000 0.00 0.00 0.00 2.12
652 690 0.324368 ATCACCGTGGCTGAGGAGTA 60.324 55.000 0.00 0.00 0.00 2.59
653 691 1.608717 GATCACCGTGGCTGAGGAGT 61.609 60.000 0.00 0.00 0.00 3.85
654 692 1.142748 GATCACCGTGGCTGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69
655 693 2.359169 GGATCACCGTGGCTGAGGA 61.359 63.158 0.00 0.00 0.00 3.71
656 694 2.184020 TTGGATCACCGTGGCTGAGG 62.184 60.000 0.00 0.00 39.42 3.86
657 695 0.321564 TTTGGATCACCGTGGCTGAG 60.322 55.000 0.00 0.00 39.42 3.35
658 696 0.109532 TTTTGGATCACCGTGGCTGA 59.890 50.000 0.00 0.00 39.42 4.26
659 697 0.958091 TTTTTGGATCACCGTGGCTG 59.042 50.000 0.00 0.00 39.42 4.85
660 698 3.430473 TTTTTGGATCACCGTGGCT 57.570 47.368 0.00 0.00 39.42 4.75
676 714 8.161699 ACTCTACGTTGGATTGTTGTATTTTT 57.838 30.769 0.00 0.00 0.00 1.94
677 715 7.660208 AGACTCTACGTTGGATTGTTGTATTTT 59.340 33.333 0.00 0.00 0.00 1.82
678 716 7.159372 AGACTCTACGTTGGATTGTTGTATTT 58.841 34.615 0.00 0.00 0.00 1.40
679 717 6.698380 AGACTCTACGTTGGATTGTTGTATT 58.302 36.000 0.00 0.00 0.00 1.89
680 718 6.153000 AGAGACTCTACGTTGGATTGTTGTAT 59.847 38.462 2.19 0.00 0.00 2.29
681 719 5.475909 AGAGACTCTACGTTGGATTGTTGTA 59.524 40.000 2.19 0.00 0.00 2.41
682 720 4.281182 AGAGACTCTACGTTGGATTGTTGT 59.719 41.667 2.19 0.00 0.00 3.32
683 721 4.810790 AGAGACTCTACGTTGGATTGTTG 58.189 43.478 2.19 0.00 0.00 3.33
684 722 5.470047 AAGAGACTCTACGTTGGATTGTT 57.530 39.130 5.14 0.00 0.00 2.83
685 723 5.470047 AAAGAGACTCTACGTTGGATTGT 57.530 39.130 5.14 0.00 0.00 2.71
686 724 6.531948 CCTAAAAGAGACTCTACGTTGGATTG 59.468 42.308 5.14 0.00 0.00 2.67
687 725 6.351117 CCCTAAAAGAGACTCTACGTTGGATT 60.351 42.308 5.14 0.00 0.00 3.01
688 726 5.127356 CCCTAAAAGAGACTCTACGTTGGAT 59.873 44.000 5.14 0.00 0.00 3.41
689 727 4.461781 CCCTAAAAGAGACTCTACGTTGGA 59.538 45.833 5.14 0.00 0.00 3.53
690 728 4.461781 TCCCTAAAAGAGACTCTACGTTGG 59.538 45.833 5.14 4.82 0.00 3.77
691 729 5.640189 TCCCTAAAAGAGACTCTACGTTG 57.360 43.478 5.14 0.00 0.00 4.10
692 730 9.810870 ATATATCCCTAAAAGAGACTCTACGTT 57.189 33.333 5.14 3.55 0.00 3.99
693 731 9.452287 GATATATCCCTAAAAGAGACTCTACGT 57.548 37.037 5.14 0.00 0.00 3.57
694 732 8.895737 GGATATATCCCTAAAAGAGACTCTACG 58.104 40.741 19.69 0.00 41.20 3.51
695 733 8.895737 CGGATATATCCCTAAAAGAGACTCTAC 58.104 40.741 23.44 0.00 44.24 2.59
696 734 8.053963 CCGGATATATCCCTAAAAGAGACTCTA 58.946 40.741 23.44 0.00 44.24 2.43
697 735 6.893005 CCGGATATATCCCTAAAAGAGACTCT 59.107 42.308 23.44 0.00 44.24 3.24
698 736 6.664384 ACCGGATATATCCCTAAAAGAGACTC 59.336 42.308 23.44 0.00 44.24 3.36
699 737 6.563163 ACCGGATATATCCCTAAAAGAGACT 58.437 40.000 23.44 0.00 44.24 3.24
700 738 6.854091 ACCGGATATATCCCTAAAAGAGAC 57.146 41.667 23.44 0.00 44.24 3.36
701 739 7.472741 TGTACCGGATATATCCCTAAAAGAGA 58.527 38.462 23.44 1.29 44.24 3.10
702 740 7.614583 TCTGTACCGGATATATCCCTAAAAGAG 59.385 40.741 23.44 13.18 44.24 2.85
703 741 7.472741 TCTGTACCGGATATATCCCTAAAAGA 58.527 38.462 23.44 17.66 44.24 2.52
704 742 7.713734 TCTGTACCGGATATATCCCTAAAAG 57.286 40.000 23.44 15.99 44.24 2.27
705 743 7.125204 CCATCTGTACCGGATATATCCCTAAAA 59.875 40.741 23.44 8.20 44.24 1.52
706 744 6.610020 CCATCTGTACCGGATATATCCCTAAA 59.390 42.308 23.44 9.31 44.24 1.85
740 778 7.662604 TCTGTTGCTATGCATATGTTCATAG 57.337 36.000 18.75 18.75 42.95 2.23
742 780 6.947644 TTCTGTTGCTATGCATATGTTCAT 57.052 33.333 6.92 2.99 38.76 2.57
744 782 6.854892 GTGATTCTGTTGCTATGCATATGTTC 59.145 38.462 6.92 0.08 38.76 3.18
747 785 6.204108 TGAGTGATTCTGTTGCTATGCATATG 59.796 38.462 6.92 0.00 38.76 1.78
804 843 0.107945 CCTGCTAGCTGACTTGACCC 60.108 60.000 21.96 0.00 0.00 4.46
822 861 3.666253 CGTGCCCCCAACGAAACC 61.666 66.667 0.00 0.00 0.00 3.27
873 958 8.831550 ACCAAATTTGCGTGTGTTAATTAAATT 58.168 25.926 12.92 0.00 0.00 1.82
952 1037 3.683587 GATTTGTGAAGCCGCCGCC 62.684 63.158 0.00 0.00 34.57 6.13
953 1038 2.202479 GATTTGTGAAGCCGCCGC 60.202 61.111 0.00 0.00 0.00 6.53
954 1039 2.331893 TGGATTTGTGAAGCCGCCG 61.332 57.895 0.00 0.00 44.36 6.46
955 1040 1.212751 GTGGATTTGTGAAGCCGCC 59.787 57.895 0.00 0.00 44.36 6.13
956 1041 4.868195 GTGGATTTGTGAAGCCGC 57.132 55.556 0.00 0.00 44.36 6.53
957 1042 1.176527 ATGGTGGATTTGTGAAGCCG 58.823 50.000 0.00 0.00 44.36 5.52
958 1043 2.415893 CGAATGGTGGATTTGTGAAGCC 60.416 50.000 0.00 0.00 41.76 4.35
959 1044 2.487762 TCGAATGGTGGATTTGTGAAGC 59.512 45.455 0.00 0.00 0.00 3.86
960 1045 4.201950 GGATCGAATGGTGGATTTGTGAAG 60.202 45.833 0.00 0.00 0.00 3.02
961 1046 3.694072 GGATCGAATGGTGGATTTGTGAA 59.306 43.478 0.00 0.00 0.00 3.18
962 1047 3.278574 GGATCGAATGGTGGATTTGTGA 58.721 45.455 0.00 0.00 0.00 3.58
963 1048 2.358898 GGGATCGAATGGTGGATTTGTG 59.641 50.000 0.00 0.00 0.00 3.33
964 1049 2.654863 GGGATCGAATGGTGGATTTGT 58.345 47.619 0.00 0.00 0.00 2.83
965 1050 1.956477 GGGGATCGAATGGTGGATTTG 59.044 52.381 0.00 0.00 0.00 2.32
966 1051 1.133482 GGGGGATCGAATGGTGGATTT 60.133 52.381 0.00 0.00 0.00 2.17
967 1052 0.478507 GGGGGATCGAATGGTGGATT 59.521 55.000 0.00 0.00 0.00 3.01
968 1053 1.768684 CGGGGGATCGAATGGTGGAT 61.769 60.000 0.00 0.00 0.00 3.41
969 1054 2.439960 CGGGGGATCGAATGGTGGA 61.440 63.158 0.00 0.00 0.00 4.02
970 1055 1.404479 TACGGGGGATCGAATGGTGG 61.404 60.000 0.00 0.00 0.00 4.61
971 1056 0.249741 GTACGGGGGATCGAATGGTG 60.250 60.000 0.00 0.00 0.00 4.17
972 1057 1.405272 GGTACGGGGGATCGAATGGT 61.405 60.000 0.00 0.00 0.00 3.55
973 1058 1.370064 GGTACGGGGGATCGAATGG 59.630 63.158 0.00 0.00 0.00 3.16
1177 1904 3.659786 TGCCTTCGTACATGTATATGCC 58.340 45.455 9.18 0.00 37.85 4.40
1182 1909 5.348986 CAGTAACTGCCTTCGTACATGTAT 58.651 41.667 9.18 0.00 0.00 2.29
1192 1919 2.355209 CCTCCTTCCAGTAACTGCCTTC 60.355 54.545 0.00 0.00 0.00 3.46
1195 1922 0.253327 CCCTCCTTCCAGTAACTGCC 59.747 60.000 0.00 0.00 0.00 4.85
1233 1989 3.760035 CAGTACGGCCGGCTGACT 61.760 66.667 41.14 31.94 32.39 3.41
1329 2112 2.126189 GTGACGACCCAGCCGTAC 60.126 66.667 0.00 0.00 40.67 3.67
1522 2319 2.887568 GAGGAGCATCACGGCGTG 60.888 66.667 32.75 32.75 39.27 5.34
1639 2442 1.272807 GTGTAGAAGGCACCCCTGTA 58.727 55.000 0.00 0.00 41.90 2.74
1647 2453 1.185618 AGCTGACCGTGTAGAAGGCA 61.186 55.000 0.00 0.00 0.00 4.75
1826 2639 6.154706 CCGGAAGCCATAAGATAAGTAGGTAT 59.845 42.308 0.00 0.00 0.00 2.73
1831 2644 3.644265 TGCCGGAAGCCATAAGATAAGTA 59.356 43.478 5.05 0.00 42.71 2.24
1835 2648 2.805295 CGTTGCCGGAAGCCATAAGATA 60.805 50.000 5.05 0.00 42.71 1.98
1837 2650 0.742990 CGTTGCCGGAAGCCATAAGA 60.743 55.000 5.05 0.00 42.71 2.10
1838 2651 0.742990 TCGTTGCCGGAAGCCATAAG 60.743 55.000 5.05 0.00 42.71 1.73
1840 2653 1.448893 GTCGTTGCCGGAAGCCATA 60.449 57.895 5.05 0.00 42.71 2.74
1847 2672 1.287815 CTGTACTGTCGTTGCCGGA 59.712 57.895 5.05 0.00 33.95 5.14
1849 2674 1.736645 CCCTGTACTGTCGTTGCCG 60.737 63.158 0.00 0.00 0.00 5.69
1916 2748 1.751351 TCGTCATTTCCTCGAGCTCAT 59.249 47.619 15.40 0.00 0.00 2.90
2111 2947 3.812053 CCCTAAGCTGGAAATGAATCGAG 59.188 47.826 0.00 0.00 0.00 4.04
2127 2963 2.203070 AAGCGCCGATGCCCTAAG 60.203 61.111 2.29 0.00 34.65 2.18
2143 3242 0.329931 TTCCTAATCTTGGCGCCCAA 59.670 50.000 26.77 17.05 41.69 4.12
2144 3243 0.550914 ATTCCTAATCTTGGCGCCCA 59.449 50.000 26.77 13.22 0.00 5.36
2160 3274 1.983972 CCGACGCTATAGCCAGATTC 58.016 55.000 19.00 6.95 37.91 2.52
2289 3403 8.973182 TGGAGGCGGAAAATAAATAAGTTTTAT 58.027 29.630 0.00 0.00 0.00 1.40
2290 3404 8.245491 GTGGAGGCGGAAAATAAATAAGTTTTA 58.755 33.333 0.00 0.00 0.00 1.52
2291 3405 7.094631 GTGGAGGCGGAAAATAAATAAGTTTT 58.905 34.615 0.00 0.00 0.00 2.43
2292 3406 6.209788 TGTGGAGGCGGAAAATAAATAAGTTT 59.790 34.615 0.00 0.00 0.00 2.66
2293 3407 5.712917 TGTGGAGGCGGAAAATAAATAAGTT 59.287 36.000 0.00 0.00 0.00 2.66
2294 3408 5.258051 TGTGGAGGCGGAAAATAAATAAGT 58.742 37.500 0.00 0.00 0.00 2.24
2295 3409 5.828299 TGTGGAGGCGGAAAATAAATAAG 57.172 39.130 0.00 0.00 0.00 1.73
2296 3410 6.391537 GTTTGTGGAGGCGGAAAATAAATAA 58.608 36.000 0.00 0.00 0.00 1.40
2297 3411 5.392165 CGTTTGTGGAGGCGGAAAATAAATA 60.392 40.000 0.00 0.00 0.00 1.40
2298 3412 4.617298 CGTTTGTGGAGGCGGAAAATAAAT 60.617 41.667 0.00 0.00 0.00 1.40
2299 3413 3.304794 CGTTTGTGGAGGCGGAAAATAAA 60.305 43.478 0.00 0.00 0.00 1.40
2300 3414 2.226912 CGTTTGTGGAGGCGGAAAATAA 59.773 45.455 0.00 0.00 0.00 1.40
2301 3415 1.807742 CGTTTGTGGAGGCGGAAAATA 59.192 47.619 0.00 0.00 0.00 1.40
2302 3416 0.596082 CGTTTGTGGAGGCGGAAAAT 59.404 50.000 0.00 0.00 0.00 1.82
2303 3417 0.748729 ACGTTTGTGGAGGCGGAAAA 60.749 50.000 0.00 0.00 0.00 2.29
2304 3418 1.153127 ACGTTTGTGGAGGCGGAAA 60.153 52.632 0.00 0.00 0.00 3.13
2305 3419 1.595929 GACGTTTGTGGAGGCGGAA 60.596 57.895 0.00 0.00 0.00 4.30
2306 3420 1.180456 TAGACGTTTGTGGAGGCGGA 61.180 55.000 0.00 0.00 0.00 5.54
2307 3421 1.012486 GTAGACGTTTGTGGAGGCGG 61.012 60.000 0.00 0.00 0.00 6.13
2308 3422 1.012486 GGTAGACGTTTGTGGAGGCG 61.012 60.000 0.00 0.00 0.00 5.52
2309 3423 1.012486 CGGTAGACGTTTGTGGAGGC 61.012 60.000 0.00 0.00 37.93 4.70
2310 3424 3.117589 CGGTAGACGTTTGTGGAGG 57.882 57.895 0.00 0.00 37.93 4.30
2332 3446 1.477295 AGACGTTTTTGCCGGGAAAAA 59.523 42.857 34.33 34.33 33.42 1.94
2333 3447 1.104630 AGACGTTTTTGCCGGGAAAA 58.895 45.000 27.64 27.64 0.00 2.29
2334 3448 1.603326 GTAGACGTTTTTGCCGGGAAA 59.397 47.619 18.09 18.09 0.00 3.13
2335 3449 1.228533 GTAGACGTTTTTGCCGGGAA 58.771 50.000 3.37 3.37 0.00 3.97
2336 3450 0.603439 GGTAGACGTTTTTGCCGGGA 60.603 55.000 2.18 0.00 0.00 5.14
2337 3451 1.871077 GGTAGACGTTTTTGCCGGG 59.129 57.895 2.18 0.00 0.00 5.73
2338 3452 1.494189 CGGTAGACGTTTTTGCCGG 59.506 57.895 14.25 0.00 38.65 6.13
2349 3463 1.084289 GGGCATCAACAACGGTAGAC 58.916 55.000 0.00 0.00 0.00 2.59
2350 3464 0.035820 GGGGCATCAACAACGGTAGA 60.036 55.000 0.00 0.00 0.00 2.59
2351 3465 0.322098 TGGGGCATCAACAACGGTAG 60.322 55.000 0.00 0.00 0.00 3.18
2352 3466 0.322098 CTGGGGCATCAACAACGGTA 60.322 55.000 0.00 0.00 0.00 4.02
2353 3467 1.603455 CTGGGGCATCAACAACGGT 60.603 57.895 0.00 0.00 0.00 4.83
2354 3468 2.993471 GCTGGGGCATCAACAACGG 61.993 63.158 0.00 0.00 38.54 4.44
2355 3469 2.267351 TGCTGGGGCATCAACAACG 61.267 57.895 0.00 0.00 44.28 4.10
2356 3470 3.776158 TGCTGGGGCATCAACAAC 58.224 55.556 0.00 0.00 44.28 3.32
2365 3479 1.953231 GCTGGAATCTTTGCTGGGGC 61.953 60.000 0.00 0.00 39.26 5.80
2366 3480 0.612732 TGCTGGAATCTTTGCTGGGG 60.613 55.000 0.00 0.00 0.00 4.96
2367 3481 0.815734 CTGCTGGAATCTTTGCTGGG 59.184 55.000 0.00 0.00 0.00 4.45
2368 3482 1.471684 GTCTGCTGGAATCTTTGCTGG 59.528 52.381 0.00 0.00 0.00 4.85
2369 3483 2.156917 TGTCTGCTGGAATCTTTGCTG 58.843 47.619 0.00 0.00 0.00 4.41
2370 3484 2.574006 TGTCTGCTGGAATCTTTGCT 57.426 45.000 0.00 0.00 0.00 3.91
2371 3485 3.648339 TTTGTCTGCTGGAATCTTTGC 57.352 42.857 0.00 0.00 0.00 3.68
2372 3486 4.219070 TCCATTTGTCTGCTGGAATCTTTG 59.781 41.667 0.00 0.00 36.15 2.77
2373 3487 4.410099 TCCATTTGTCTGCTGGAATCTTT 58.590 39.130 0.00 0.00 36.15 2.52
2374 3488 4.015084 CTCCATTTGTCTGCTGGAATCTT 58.985 43.478 0.00 0.00 38.55 2.40
2375 3489 3.618351 CTCCATTTGTCTGCTGGAATCT 58.382 45.455 0.00 0.00 38.55 2.40
2376 3490 2.686915 CCTCCATTTGTCTGCTGGAATC 59.313 50.000 0.00 0.00 38.55 2.52
2377 3491 2.622452 CCCTCCATTTGTCTGCTGGAAT 60.622 50.000 0.00 0.00 38.55 3.01
2378 3492 1.272092 CCCTCCATTTGTCTGCTGGAA 60.272 52.381 0.00 0.00 38.55 3.53
2379 3493 0.329261 CCCTCCATTTGTCTGCTGGA 59.671 55.000 0.00 0.00 37.50 3.86
2380 3494 1.318158 GCCCTCCATTTGTCTGCTGG 61.318 60.000 0.00 0.00 0.00 4.85
2381 3495 1.651240 CGCCCTCCATTTGTCTGCTG 61.651 60.000 0.00 0.00 0.00 4.41
2382 3496 1.377725 CGCCCTCCATTTGTCTGCT 60.378 57.895 0.00 0.00 0.00 4.24
2383 3497 3.056313 GCGCCCTCCATTTGTCTGC 62.056 63.158 0.00 0.00 0.00 4.26
2384 3498 1.651240 CTGCGCCCTCCATTTGTCTG 61.651 60.000 4.18 0.00 0.00 3.51
2385 3499 1.377725 CTGCGCCCTCCATTTGTCT 60.378 57.895 4.18 0.00 0.00 3.41
2386 3500 0.749454 ATCTGCGCCCTCCATTTGTC 60.749 55.000 4.18 0.00 0.00 3.18
2387 3501 0.323725 AATCTGCGCCCTCCATTTGT 60.324 50.000 4.18 0.00 0.00 2.83
2388 3502 0.383231 GAATCTGCGCCCTCCATTTG 59.617 55.000 4.18 0.00 0.00 2.32
2389 3503 0.257039 AGAATCTGCGCCCTCCATTT 59.743 50.000 4.18 0.00 0.00 2.32
2390 3504 0.179034 GAGAATCTGCGCCCTCCATT 60.179 55.000 4.18 0.00 0.00 3.16
2391 3505 1.449353 GAGAATCTGCGCCCTCCAT 59.551 57.895 4.18 0.00 0.00 3.41
2392 3506 2.903357 GAGAATCTGCGCCCTCCA 59.097 61.111 4.18 0.00 0.00 3.86
2450 4327 0.181350 ATCAGAAACGGAGGGCATCC 59.819 55.000 8.44 8.44 45.64 3.51
2540 6051 2.778270 GGTCCTCTAACTGGGCCTTTAT 59.222 50.000 4.53 0.00 45.46 1.40
2656 6195 0.033504 GATCGCCCCAATCGCTAAGA 59.966 55.000 0.00 0.00 0.00 2.10
2657 6196 0.249868 TGATCGCCCCAATCGCTAAG 60.250 55.000 0.00 0.00 0.00 2.18
2658 6197 0.396435 ATGATCGCCCCAATCGCTAA 59.604 50.000 0.00 0.00 0.00 3.09
2659 6198 0.037326 GATGATCGCCCCAATCGCTA 60.037 55.000 0.00 0.00 0.00 4.26
2660 6199 1.302033 GATGATCGCCCCAATCGCT 60.302 57.895 0.00 0.00 0.00 4.93
2661 6200 2.671177 CGATGATCGCCCCAATCGC 61.671 63.158 0.41 0.00 31.14 4.58
2662 6201 2.029288 CCGATGATCGCCCCAATCG 61.029 63.158 9.74 4.37 38.82 3.34
2663 6202 1.672356 CCCGATGATCGCCCCAATC 60.672 63.158 9.74 0.00 38.82 2.67
2812 6612 0.892755 TAGGCGACTCGGACACAAAT 59.107 50.000 0.00 0.00 43.67 2.32


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

AutoCloner maintained by Alex Coulton.