Multiple sequence alignment - TraesCS5B01G087800

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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 TraesCS5B01G087800 chr5B 100.000 2621 0 0 1 2621 112530858 112533478 0.000000e+00 4841.0
1 TraesCS5B01G087800 chr5A 94.536 1281 40 8 727 1983 94799709 94798435 0.000000e+00 1951.0
2 TraesCS5B01G087800 chr5A 88.256 579 41 14 1 571 94800261 94799702 0.000000e+00 667.0
3 TraesCS5B01G087800 chr5A 82.573 482 73 8 2141 2616 94796736 94796260 5.220000e-112 414.0
4 TraesCS5B01G087800 chr5A 86.014 286 35 4 77 360 570317662 570317380 4.240000e-78 302.0
5 TraesCS5B01G087800 chr5D 95.359 1185 27 9 727 1883 103603441 103604625 0.000000e+00 1858.0
6 TraesCS5B01G087800 chr5D 95.294 170 7 1 569 738 115020715 115020547 4.300000e-68 268.0
7 TraesCS5B01G087800 chr5D 91.176 102 9 0 1882 1983 103611297 103611398 3.520000e-29 139.0
8 TraesCS5B01G087800 chr5D 88.462 104 9 2 2000 2100 103611517 103611620 3.540000e-24 122.0
9 TraesCS5B01G087800 chr1B 89.130 276 29 1 74 348 249239323 249239048 2.500000e-90 342.0
10 TraesCS5B01G087800 chr7B 87.943 282 33 1 77 357 712736985 712737266 5.410000e-87 331.0
11 TraesCS5B01G087800 chr7B 87.365 277 32 3 78 353 94700798 94700524 5.450000e-82 315.0
12 TraesCS5B01G087800 chr7B 100.000 28 0 0 2219 2246 672179094 672179121 5.000000e-03 52.8
13 TraesCS5B01G087800 chr7D 87.719 285 32 3 77 360 618322691 618322973 1.940000e-86 329.0
14 TraesCS5B01G087800 chr7D 86.833 281 30 5 81 360 623304219 623304493 9.110000e-80 307.0
15 TraesCS5B01G087800 chr7D 95.833 168 7 0 565 732 484298905 484299072 3.320000e-69 272.0
16 TraesCS5B01G087800 chr2B 86.713 286 33 4 79 362 783944891 783945173 1.960000e-81 313.0
17 TraesCS5B01G087800 chr3D 85.813 289 38 2 75 362 549101995 549101709 1.180000e-78 303.0
18 TraesCS5B01G087800 chr3D 91.018 167 15 0 566 732 357158463 357158629 2.620000e-55 226.0
19 TraesCS5B01G087800 chr3D 88.608 79 8 1 2538 2615 397729842 397729920 7.720000e-16 95.3
20 TraesCS5B01G087800 chr1D 95.732 164 6 1 568 731 469874709 469874871 2.000000e-66 263.0
21 TraesCS5B01G087800 chr1D 95.455 44 2 0 2387 2430 363568087 363568130 1.300000e-08 71.3
22 TraesCS5B01G087800 chr4D 95.152 165 8 0 568 732 481370485 481370321 7.200000e-66 261.0
23 TraesCS5B01G087800 chr2D 94.611 167 9 0 566 732 403487928 403487762 2.590000e-65 259.0
24 TraesCS5B01G087800 chr4B 95.031 161 8 0 583 743 671182344 671182184 1.200000e-63 254.0
25 TraesCS5B01G087800 chr2A 92.814 167 12 0 566 732 102324542 102324376 2.610000e-60 243.0
26 TraesCS5B01G087800 chr2A 94.286 35 2 0 498 532 606818291 606818325 1.000000e-03 54.7
27 TraesCS5B01G087800 chr3A 91.018 167 15 0 566 732 476659458 476659624 2.620000e-55 226.0
28 TraesCS5B01G087800 chr6D 100.000 33 0 0 2220 2252 383698732 383698700 7.830000e-06 62.1
29 TraesCS5B01G087800 chr4A 86.441 59 4 4 2055 2109 375480502 375480560 7.830000e-06 62.1
30 TraesCS5B01G087800 chr6B 97.059 34 1 0 2068 2101 234156211 234156244 1.010000e-04 58.4


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 TraesCS5B01G087800 chr5B 112530858 112533478 2620 False 4841.000000 4841 100.000 1 2621 1 chr5B.!!$F1 2620
1 TraesCS5B01G087800 chr5A 94796260 94800261 4001 True 1010.666667 1951 88.455 1 2616 3 chr5A.!!$R2 2615
2 TraesCS5B01G087800 chr5D 103603441 103604625 1184 False 1858.000000 1858 95.359 727 1883 1 chr5D.!!$F1 1156

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
586 595 0.107017 AGGGCCTGATTGGATTGTCG 60.107 55.0 4.5 0.0 38.35 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 3550 0.039798 CTTCTTCCCGACGTCGACAA 60.04 55.0 37.65 26.0 43.02 3.18 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
42 43 3.314080 CAGTTTGGATGTACGGTGTGTTT 59.686 43.478 0.00 0.00 0.00 2.83
49 50 6.228995 TGGATGTACGGTGTGTTTGTATTTA 58.771 36.000 0.00 0.00 0.00 1.40
59 60 7.519168 CGGTGTGTTTGTATTTAGTCAACATCA 60.519 37.037 0.00 0.00 0.00 3.07
83 91 6.758806 TGTCTTCCCCTTTTTAAGACTACT 57.241 37.500 13.70 0.00 45.98 2.57
84 92 6.766429 TGTCTTCCCCTTTTTAAGACTACTC 58.234 40.000 13.70 0.00 45.98 2.59
112 120 8.791327 AGTGAGGAGTAACTTAGACTAGTAAC 57.209 38.462 0.00 0.00 0.00 2.50
122 130 8.594881 AACTTAGACTAGTAACATGCATATGC 57.405 34.615 21.09 21.09 37.85 3.14
183 191 5.882000 ACATATGTGTAGTGTCATGCAACAT 59.118 36.000 7.78 0.00 36.63 2.71
186 194 5.107109 TGTGTAGTGTCATGCAACATTTC 57.893 39.130 0.00 0.00 0.00 2.17
217 226 6.076981 AGCTTGTAACTCATCTTGTTTTGG 57.923 37.500 0.00 0.00 0.00 3.28
220 229 6.856426 GCTTGTAACTCATCTTGTTTTGGTAC 59.144 38.462 0.00 0.00 0.00 3.34
329 338 5.939764 TGCTGAGTTGGACTCTATGTTAT 57.060 39.130 9.27 0.00 45.27 1.89
332 341 7.847096 TGCTGAGTTGGACTCTATGTTATTAA 58.153 34.615 9.27 0.00 45.27 1.40
348 357 8.747538 ATGTTATTAATGAAGTTACTCCCACC 57.252 34.615 0.00 0.00 0.00 4.61
481 490 1.447099 TAACCAGGGCCAAACACCTA 58.553 50.000 6.18 0.00 34.71 3.08
562 571 7.047271 AGAAAATACTTGGCAAACAAACACAT 58.953 30.769 0.00 0.00 38.91 3.21
563 572 6.843069 AAATACTTGGCAAACAAACACATC 57.157 33.333 0.00 0.00 38.91 3.06
564 573 3.177997 ACTTGGCAAACAAACACATCC 57.822 42.857 0.00 0.00 38.91 3.51
565 574 2.765699 ACTTGGCAAACAAACACATCCT 59.234 40.909 0.00 0.00 38.91 3.24
566 575 3.197549 ACTTGGCAAACAAACACATCCTT 59.802 39.130 0.00 0.00 38.91 3.36
567 576 4.404073 ACTTGGCAAACAAACACATCCTTA 59.596 37.500 0.00 0.00 38.91 2.69
568 577 4.582701 TGGCAAACAAACACATCCTTAG 57.417 40.909 0.00 0.00 0.00 2.18
569 578 3.320541 TGGCAAACAAACACATCCTTAGG 59.679 43.478 0.00 0.00 0.00 2.69
570 579 3.306019 GGCAAACAAACACATCCTTAGGG 60.306 47.826 0.00 0.00 0.00 3.53
571 580 3.860754 GCAAACAAACACATCCTTAGGGC 60.861 47.826 0.00 0.00 0.00 5.19
572 581 2.215942 ACAAACACATCCTTAGGGCC 57.784 50.000 0.00 0.00 0.00 5.80
573 582 1.710809 ACAAACACATCCTTAGGGCCT 59.289 47.619 12.58 12.58 0.00 5.19
574 583 2.094675 CAAACACATCCTTAGGGCCTG 58.905 52.381 18.53 0.53 0.00 4.85
575 584 1.668826 AACACATCCTTAGGGCCTGA 58.331 50.000 18.53 7.19 0.00 3.86
576 585 1.898863 ACACATCCTTAGGGCCTGAT 58.101 50.000 18.53 7.77 0.00 2.90
577 586 2.208872 ACACATCCTTAGGGCCTGATT 58.791 47.619 18.53 0.00 0.00 2.57
578 587 2.092212 ACACATCCTTAGGGCCTGATTG 60.092 50.000 18.53 12.95 0.00 2.67
579 588 1.496429 ACATCCTTAGGGCCTGATTGG 59.504 52.381 18.53 12.58 39.35 3.16
580 589 1.776667 CATCCTTAGGGCCTGATTGGA 59.223 52.381 18.53 17.44 38.35 3.53
581 590 2.212752 TCCTTAGGGCCTGATTGGAT 57.787 50.000 18.53 0.00 38.35 3.41
582 591 2.502745 TCCTTAGGGCCTGATTGGATT 58.497 47.619 18.53 0.00 38.35 3.01
583 592 2.175499 TCCTTAGGGCCTGATTGGATTG 59.825 50.000 18.53 0.00 38.35 2.67
584 593 2.091665 CCTTAGGGCCTGATTGGATTGT 60.092 50.000 18.53 0.00 38.35 2.71
585 594 3.217626 CTTAGGGCCTGATTGGATTGTC 58.782 50.000 18.53 0.00 38.35 3.18
586 595 0.107017 AGGGCCTGATTGGATTGTCG 60.107 55.000 4.50 0.00 38.35 4.35
587 596 0.394352 GGGCCTGATTGGATTGTCGT 60.394 55.000 0.84 0.00 38.35 4.34
588 597 1.463674 GGCCTGATTGGATTGTCGTT 58.536 50.000 0.00 0.00 38.35 3.85
589 598 1.818674 GGCCTGATTGGATTGTCGTTT 59.181 47.619 0.00 0.00 38.35 3.60
590 599 2.231235 GGCCTGATTGGATTGTCGTTTT 59.769 45.455 0.00 0.00 38.35 2.43
591 600 3.244976 GCCTGATTGGATTGTCGTTTTG 58.755 45.455 0.00 0.00 38.35 2.44
592 601 3.244976 CCTGATTGGATTGTCGTTTTGC 58.755 45.455 0.00 0.00 38.35 3.68
593 602 3.305267 CCTGATTGGATTGTCGTTTTGCA 60.305 43.478 0.00 0.00 38.35 4.08
594 603 3.637432 TGATTGGATTGTCGTTTTGCAC 58.363 40.909 0.00 0.00 0.00 4.57
595 604 3.067320 TGATTGGATTGTCGTTTTGCACA 59.933 39.130 0.00 0.00 0.00 4.57
596 605 2.483583 TGGATTGTCGTTTTGCACAC 57.516 45.000 0.00 0.00 0.00 3.82
597 606 2.020720 TGGATTGTCGTTTTGCACACT 58.979 42.857 0.00 0.00 0.00 3.55
598 607 2.425312 TGGATTGTCGTTTTGCACACTT 59.575 40.909 0.00 0.00 0.00 3.16
599 608 3.119316 TGGATTGTCGTTTTGCACACTTT 60.119 39.130 0.00 0.00 0.00 2.66
600 609 3.862845 GGATTGTCGTTTTGCACACTTTT 59.137 39.130 0.00 0.00 0.00 2.27
601 610 5.038033 GGATTGTCGTTTTGCACACTTTTA 58.962 37.500 0.00 0.00 0.00 1.52
602 611 5.051973 GGATTGTCGTTTTGCACACTTTTAC 60.052 40.000 0.00 0.00 0.00 2.01
603 612 4.421033 TGTCGTTTTGCACACTTTTACA 57.579 36.364 0.00 0.00 0.00 2.41
604 613 4.159857 TGTCGTTTTGCACACTTTTACAC 58.840 39.130 0.00 0.00 0.00 2.90
605 614 3.544682 GTCGTTTTGCACACTTTTACACC 59.455 43.478 0.00 0.00 0.00 4.16
606 615 3.440872 TCGTTTTGCACACTTTTACACCT 59.559 39.130 0.00 0.00 0.00 4.00
607 616 3.545873 CGTTTTGCACACTTTTACACCTG 59.454 43.478 0.00 0.00 0.00 4.00
608 617 4.490743 GTTTTGCACACTTTTACACCTGT 58.509 39.130 0.00 0.00 0.00 4.00
609 618 5.642686 GTTTTGCACACTTTTACACCTGTA 58.357 37.500 0.00 0.00 0.00 2.74
610 619 5.899120 TTTGCACACTTTTACACCTGTAA 57.101 34.783 0.00 0.00 38.60 2.41
611 620 5.899120 TTGCACACTTTTACACCTGTAAA 57.101 34.783 6.54 6.54 45.55 2.01
623 632 7.549147 TTACACCTGTAAAAGATACAGACCT 57.451 36.000 15.31 2.12 45.69 3.85
624 633 6.038997 ACACCTGTAAAAGATACAGACCTC 57.961 41.667 15.31 0.00 45.69 3.85
625 634 5.542635 ACACCTGTAAAAGATACAGACCTCA 59.457 40.000 15.31 0.00 45.69 3.86
626 635 6.042781 ACACCTGTAAAAGATACAGACCTCAA 59.957 38.462 15.31 0.00 45.69 3.02
627 636 7.106239 CACCTGTAAAAGATACAGACCTCAAT 58.894 38.462 15.31 0.00 45.69 2.57
628 637 7.278868 CACCTGTAAAAGATACAGACCTCAATC 59.721 40.741 15.31 0.00 45.69 2.67
629 638 6.477033 CCTGTAAAAGATACAGACCTCAATCG 59.523 42.308 15.31 0.00 45.69 3.34
630 639 6.338146 TGTAAAAGATACAGACCTCAATCGG 58.662 40.000 0.00 0.00 0.00 4.18
631 640 5.422214 AAAAGATACAGACCTCAATCGGT 57.578 39.130 0.00 0.00 40.80 4.69
639 648 2.409975 GACCTCAATCGGTCGTTTTCA 58.590 47.619 0.00 0.00 43.56 2.69
640 649 3.000727 GACCTCAATCGGTCGTTTTCAT 58.999 45.455 0.00 0.00 43.56 2.57
641 650 3.408634 ACCTCAATCGGTCGTTTTCATT 58.591 40.909 0.00 0.00 29.14 2.57
642 651 3.818773 ACCTCAATCGGTCGTTTTCATTT 59.181 39.130 0.00 0.00 29.14 2.32
643 652 4.083484 ACCTCAATCGGTCGTTTTCATTTC 60.083 41.667 0.00 0.00 29.14 2.17
644 653 4.403453 CTCAATCGGTCGTTTTCATTTCC 58.597 43.478 0.00 0.00 0.00 3.13
645 654 3.120477 TCAATCGGTCGTTTTCATTTCCG 60.120 43.478 0.00 0.00 39.40 4.30
646 655 1.149987 TCGGTCGTTTTCATTTCCGG 58.850 50.000 0.00 0.00 38.70 5.14
647 656 0.869730 CGGTCGTTTTCATTTCCGGT 59.130 50.000 0.00 0.00 35.25 5.28
648 657 1.264826 CGGTCGTTTTCATTTCCGGTT 59.735 47.619 0.00 0.00 35.25 4.44
649 658 2.657184 GGTCGTTTTCATTTCCGGTTG 58.343 47.619 0.00 0.00 0.00 3.77
650 659 2.291190 GGTCGTTTTCATTTCCGGTTGA 59.709 45.455 0.00 0.35 0.00 3.18
651 660 3.243134 GGTCGTTTTCATTTCCGGTTGAA 60.243 43.478 0.00 7.24 0.00 2.69
652 661 4.352887 GTCGTTTTCATTTCCGGTTGAAA 58.647 39.130 19.08 19.08 46.54 2.69
653 662 4.799428 GTCGTTTTCATTTCCGGTTGAAAA 59.201 37.500 25.01 25.01 45.67 2.29
658 667 7.849804 TTTTCATTTCCGGTTGAAAATCAAA 57.150 28.000 25.01 12.43 45.67 2.69
659 668 6.836577 TTCATTTCCGGTTGAAAATCAAAC 57.163 33.333 0.00 0.00 45.67 2.93
660 669 5.907207 TCATTTCCGGTTGAAAATCAAACA 58.093 33.333 0.00 0.00 44.00 2.83
661 670 6.520272 TCATTTCCGGTTGAAAATCAAACAT 58.480 32.000 0.00 0.00 44.00 2.71
662 671 6.423302 TCATTTCCGGTTGAAAATCAAACATG 59.577 34.615 0.00 4.85 44.00 3.21
663 672 4.250116 TCCGGTTGAAAATCAAACATGG 57.750 40.909 0.00 3.01 44.00 3.66
664 673 2.736192 CCGGTTGAAAATCAAACATGGC 59.264 45.455 8.67 0.00 44.00 4.40
665 674 3.554752 CCGGTTGAAAATCAAACATGGCT 60.555 43.478 8.67 0.00 44.00 4.75
666 675 3.429543 CGGTTGAAAATCAAACATGGCTG 59.570 43.478 8.67 0.00 44.00 4.85
667 676 4.630111 GGTTGAAAATCAAACATGGCTGA 58.370 39.130 3.36 0.00 43.31 4.26
668 677 5.240121 GGTTGAAAATCAAACATGGCTGAT 58.760 37.500 3.36 1.60 43.31 2.90
669 678 5.121142 GGTTGAAAATCAAACATGGCTGATG 59.879 40.000 11.33 0.00 43.31 3.07
670 679 5.725325 TGAAAATCAAACATGGCTGATGA 57.275 34.783 11.33 2.50 35.80 2.92
671 680 6.099159 TGAAAATCAAACATGGCTGATGAA 57.901 33.333 11.33 0.00 35.80 2.57
672 681 6.522946 TGAAAATCAAACATGGCTGATGAAA 58.477 32.000 11.33 0.00 35.80 2.69
673 682 7.162761 TGAAAATCAAACATGGCTGATGAAAT 58.837 30.769 11.33 1.29 35.80 2.17
674 683 8.312564 TGAAAATCAAACATGGCTGATGAAATA 58.687 29.630 11.33 0.00 35.80 1.40
675 684 8.483307 AAAATCAAACATGGCTGATGAAATAC 57.517 30.769 11.33 0.00 35.80 1.89
676 685 6.778834 ATCAAACATGGCTGATGAAATACA 57.221 33.333 10.14 0.00 35.80 2.29
677 686 5.953183 TCAAACATGGCTGATGAAATACAC 58.047 37.500 0.00 0.00 35.80 2.90
678 687 5.711506 TCAAACATGGCTGATGAAATACACT 59.288 36.000 0.00 0.00 35.80 3.55
679 688 6.209192 TCAAACATGGCTGATGAAATACACTT 59.791 34.615 0.00 0.00 35.80 3.16
680 689 5.571784 ACATGGCTGATGAAATACACTTG 57.428 39.130 0.00 0.00 35.80 3.16
681 690 5.012239 ACATGGCTGATGAAATACACTTGT 58.988 37.500 0.00 0.00 35.80 3.16
682 691 6.179756 ACATGGCTGATGAAATACACTTGTA 58.820 36.000 0.00 0.00 35.80 2.41
683 692 6.658816 ACATGGCTGATGAAATACACTTGTAA 59.341 34.615 0.00 0.00 35.80 2.41
684 693 7.176515 ACATGGCTGATGAAATACACTTGTAAA 59.823 33.333 0.00 0.00 35.80 2.01
685 694 7.517614 TGGCTGATGAAATACACTTGTAAAA 57.482 32.000 0.00 0.00 33.76 1.52
686 695 7.592938 TGGCTGATGAAATACACTTGTAAAAG 58.407 34.615 0.00 0.00 33.76 2.27
687 696 7.230510 TGGCTGATGAAATACACTTGTAAAAGT 59.769 33.333 0.00 0.00 33.76 2.66
688 697 8.726988 GGCTGATGAAATACACTTGTAAAAGTA 58.273 33.333 0.00 0.00 33.76 2.24
693 702 9.872757 ATGAAATACACTTGTAAAAGTAACACG 57.127 29.630 0.00 0.00 33.76 4.49
694 703 8.336806 TGAAATACACTTGTAAAAGTAACACGG 58.663 33.333 0.00 0.00 33.76 4.94
695 704 6.790285 ATACACTTGTAAAAGTAACACGGG 57.210 37.500 0.00 0.00 33.76 5.28
696 705 4.516323 ACACTTGTAAAAGTAACACGGGT 58.484 39.130 0.00 0.00 28.77 5.28
697 706 4.333372 ACACTTGTAAAAGTAACACGGGTG 59.667 41.667 0.00 0.00 32.15 4.61
698 707 8.116455 ATACACTTGTAAAAGTAACACGGGTGT 61.116 37.037 0.00 0.00 34.10 4.16
699 708 5.523188 CACTTGTAAAAGTAACACGGGTGTA 59.477 40.000 4.68 0.00 44.13 2.90
700 709 6.203338 CACTTGTAAAAGTAACACGGGTGTAT 59.797 38.462 4.68 0.00 44.13 2.29
701 710 7.384660 CACTTGTAAAAGTAACACGGGTGTATA 59.615 37.037 4.68 0.00 44.13 1.47
702 711 7.930865 ACTTGTAAAAGTAACACGGGTGTATAA 59.069 33.333 4.68 0.00 44.13 0.98
703 712 8.668510 TTGTAAAAGTAACACGGGTGTATAAA 57.331 30.769 4.68 0.00 44.13 1.40
704 713 8.845413 TGTAAAAGTAACACGGGTGTATAAAT 57.155 30.769 4.68 0.00 44.13 1.40
705 714 9.282569 TGTAAAAGTAACACGGGTGTATAAATT 57.717 29.630 4.68 1.99 44.13 1.82
709 718 7.848223 AGTAACACGGGTGTATAAATTTACC 57.152 36.000 4.68 0.00 44.13 2.85
718 727 7.528675 GGGTGTATAAATTTACCCCTATTCCA 58.471 38.462 13.90 0.00 45.65 3.53
719 728 8.005976 GGGTGTATAAATTTACCCCTATTCCAA 58.994 37.037 13.90 0.00 45.65 3.53
720 729 9.074576 GGTGTATAAATTTACCCCTATTCCAAG 57.925 37.037 0.00 0.00 0.00 3.61
721 730 8.573885 GTGTATAAATTTACCCCTATTCCAAGC 58.426 37.037 0.00 0.00 0.00 4.01
722 731 6.894339 ATAAATTTACCCCTATTCCAAGCG 57.106 37.500 0.00 0.00 0.00 4.68
723 732 2.721425 TTTACCCCTATTCCAAGCGG 57.279 50.000 0.00 0.00 0.00 5.52
724 733 0.841289 TTACCCCTATTCCAAGCGGG 59.159 55.000 0.00 0.00 39.85 6.13
810 821 8.239998 ACTTATTTCAGTCTAGCAATTTTGAGC 58.760 33.333 0.00 0.00 0.00 4.26
823 834 1.503818 TTTGAGCGCAGTCCCGAAAC 61.504 55.000 11.47 0.00 0.00 2.78
824 835 2.357034 GAGCGCAGTCCCGAAACA 60.357 61.111 11.47 0.00 0.00 2.83
962 982 1.139058 CCATTACCTTGGACCGGAGAG 59.861 57.143 9.46 0.00 39.25 3.20
963 983 0.831307 ATTACCTTGGACCGGAGAGC 59.169 55.000 9.46 0.00 0.00 4.09
1179 1202 3.050275 GACAAGCCGCTGGACACC 61.050 66.667 0.39 0.00 0.00 4.16
1216 1239 4.722700 AAGATGCAACCGCCGCCT 62.723 61.111 0.00 0.00 37.32 5.52
1395 1421 3.151710 CCGTCCTATCCGGTGCCA 61.152 66.667 0.00 0.00 40.59 4.92
1776 1802 3.519510 ACCTATTGCTTCTGCTACCAAGA 59.480 43.478 0.00 0.00 40.48 3.02
1778 1804 2.479566 TTGCTTCTGCTACCAAGAGG 57.520 50.000 0.00 0.00 40.48 3.69
1783 1809 0.252239 TCTGCTACCAAGAGGCCAGA 60.252 55.000 5.01 0.00 39.06 3.86
1785 1811 1.153269 GCTACCAAGAGGCCAGAGC 60.153 63.158 5.01 0.00 39.06 4.09
1886 1927 3.008049 AGAATTGCTTCGAGTGGTTAGGT 59.992 43.478 0.00 0.00 36.45 3.08
1908 1949 1.977293 GAATCCCCTCTCGCAAGGCT 61.977 60.000 0.00 0.00 34.88 4.58
1909 1950 2.262774 AATCCCCTCTCGCAAGGCTG 62.263 60.000 0.00 0.00 34.88 4.85
1928 1969 4.487948 GCTGCTGTTGAATATTTGAGCAA 58.512 39.130 10.81 0.00 36.09 3.91
1951 1992 9.815936 GCAATTTTTCATGAAGTTTAATTCAGG 57.184 29.630 8.41 0.00 42.20 3.86
1998 2077 5.784750 TCAAAACTAGTCATGCAATCGAG 57.215 39.130 0.00 0.00 0.00 4.04
2002 2081 4.456280 ACTAGTCATGCAATCGAGAACA 57.544 40.909 0.00 0.00 0.00 3.18
2006 2085 5.039480 AGTCATGCAATCGAGAACAAAAG 57.961 39.130 0.00 0.00 0.00 2.27
2008 2087 3.191162 TCATGCAATCGAGAACAAAAGGG 59.809 43.478 0.00 0.00 0.00 3.95
2016 2095 8.188139 GCAATCGAGAACAAAAGGGATAAATAA 58.812 33.333 0.00 0.00 0.00 1.40
2024 3504 9.394477 GAACAAAAGGGATAAATAATCATACGC 57.606 33.333 0.00 0.00 36.20 4.42
2026 3506 7.039993 ACAAAAGGGATAAATAATCATACGCCC 60.040 37.037 0.00 0.00 36.20 6.13
2034 3514 2.799126 AATCATACGCCCCAACAGAA 57.201 45.000 0.00 0.00 0.00 3.02
2047 3527 4.423732 CCCAACAGAAGAAGTGTTTGTTG 58.576 43.478 8.29 8.29 44.92 3.33
2050 3530 4.600012 ACAGAAGAAGTGTTTGTTGTCG 57.400 40.909 0.00 0.00 0.00 4.35
2069 3549 0.588252 GCAGCGTCATGTTGTGAAGT 59.412 50.000 0.00 0.00 38.90 3.01
2070 3550 1.002468 GCAGCGTCATGTTGTGAAGTT 60.002 47.619 0.00 0.00 38.90 2.66
2071 3551 2.541588 GCAGCGTCATGTTGTGAAGTTT 60.542 45.455 0.00 0.00 38.90 2.66
2075 3558 3.279950 CGTCATGTTGTGAAGTTTGTCG 58.720 45.455 0.00 0.00 38.90 4.35
2089 3572 0.039798 TTGTCGACGTCGGGAAGAAG 60.040 55.000 35.05 7.30 40.29 2.85
2092 3575 4.454554 GACGTCGGGAAGAAGTCG 57.545 61.111 0.00 0.00 45.47 4.18
2094 3577 0.454117 GACGTCGGGAAGAAGTCGTC 60.454 60.000 0.00 0.00 45.47 4.20
2107 3590 0.748450 AGTCGTCGTTGGGAAACTCA 59.252 50.000 0.00 0.00 0.00 3.41
2109 3592 1.459592 GTCGTCGTTGGGAAACTCATG 59.540 52.381 0.00 0.00 0.00 3.07
2114 3597 1.165270 GTTGGGAAACTCATGGTCCG 58.835 55.000 0.00 0.00 31.73 4.79
2116 3599 1.646912 TGGGAAACTCATGGTCCGTA 58.353 50.000 0.00 0.00 31.73 4.02
2137 3620 1.611491 GGCACGGTGAAGAAAATCCAA 59.389 47.619 13.29 0.00 0.00 3.53
2138 3621 2.231235 GGCACGGTGAAGAAAATCCAAT 59.769 45.455 13.29 0.00 0.00 3.16
2139 3622 3.244976 GCACGGTGAAGAAAATCCAATG 58.755 45.455 13.29 0.00 0.00 2.82
2140 3623 3.244976 CACGGTGAAGAAAATCCAATGC 58.755 45.455 0.74 0.00 0.00 3.56
2141 3624 2.231235 ACGGTGAAGAAAATCCAATGCC 59.769 45.455 0.00 0.00 0.00 4.40
2142 3625 2.731968 CGGTGAAGAAAATCCAATGCCG 60.732 50.000 0.00 0.00 0.00 5.69
2144 3627 3.428045 GGTGAAGAAAATCCAATGCCGAG 60.428 47.826 0.00 0.00 0.00 4.63
2146 3629 4.078537 TGAAGAAAATCCAATGCCGAGAA 58.921 39.130 0.00 0.00 0.00 2.87
2148 3631 2.424956 AGAAAATCCAATGCCGAGAAGC 59.575 45.455 0.00 0.00 0.00 3.86
2149 3632 0.734889 AAATCCAATGCCGAGAAGCG 59.265 50.000 0.00 0.00 40.47 4.68
2150 3633 0.107703 AATCCAATGCCGAGAAGCGA 60.108 50.000 0.00 0.00 44.57 4.93
2152 3635 1.153568 CCAATGCCGAGAAGCGAGA 60.154 57.895 0.00 0.00 44.57 4.04
2153 3636 0.531532 CCAATGCCGAGAAGCGAGAT 60.532 55.000 0.00 0.00 44.57 2.75
2157 3741 1.141881 GCCGAGAAGCGAGATGGAA 59.858 57.895 0.00 0.00 44.57 3.53
2175 3759 2.720561 AAAACGTTAGGCGGCGCAAC 62.721 55.000 34.36 26.85 46.52 4.17
2197 3784 0.955428 TTGGAATCAGGCACTCACGC 60.955 55.000 0.00 0.00 34.60 5.34
2254 3841 2.582978 GTGGAGTACCCGCCTTCC 59.417 66.667 3.32 0.00 39.55 3.46
2257 3844 1.684734 GGAGTACCCGCCTTCCTGA 60.685 63.158 0.00 0.00 0.00 3.86
2262 3849 2.798445 TACCCGCCTTCCTGAGCTCA 62.798 60.000 17.19 17.19 0.00 4.26
2265 3852 1.519246 CGCCTTCCTGAGCTCATCA 59.481 57.895 18.63 3.48 36.21 3.07
2271 3858 0.911045 TCCTGAGCTCATCAAGGGCA 60.911 55.000 18.63 2.30 37.52 5.36
2275 3862 1.101331 GAGCTCATCAAGGGCAAAGG 58.899 55.000 9.40 0.00 0.00 3.11
2292 3879 4.097361 GGAGCCTCCCAACCGTCC 62.097 72.222 0.00 0.00 0.00 4.79
2293 3880 4.452733 GAGCCTCCCAACCGTCCG 62.453 72.222 0.00 0.00 0.00 4.79
2295 3882 4.324991 GCCTCCCAACCGTCCGTT 62.325 66.667 0.00 0.00 33.90 4.44
2301 3888 4.025401 CAACCGTCCGTTGCCAGC 62.025 66.667 0.00 0.00 45.16 4.85
2345 3932 2.985512 GAAGCCGATGCGAGCCATCT 62.986 60.000 0.00 0.00 46.61 2.90
2346 3933 3.344215 GCCGATGCGAGCCATCTG 61.344 66.667 0.00 0.00 46.61 2.90
2351 3938 1.430479 GATGCGAGCCATCTGATCTG 58.570 55.000 0.00 0.00 45.58 2.90
2359 3946 1.689243 CCATCTGATCTGCCCGGACA 61.689 60.000 0.73 0.00 0.00 4.02
2363 3950 2.249413 CTGATCTGCCCGGACAGCTT 62.249 60.000 13.73 2.58 37.59 3.74
2365 3952 2.244117 GATCTGCCCGGACAGCTTGA 62.244 60.000 13.73 6.43 37.59 3.02
2366 3953 1.841302 ATCTGCCCGGACAGCTTGAA 61.841 55.000 13.73 0.00 37.59 2.69
2371 3958 1.672356 CCGGACAGCTTGAACCCTG 60.672 63.158 0.00 0.00 35.26 4.45
2376 3963 1.377725 CAGCTTGAACCCTGGCGAT 60.378 57.895 0.00 0.00 0.00 4.58
2377 3964 1.078143 AGCTTGAACCCTGGCGATC 60.078 57.895 0.00 0.00 0.00 3.69
2378 3965 1.078143 GCTTGAACCCTGGCGATCT 60.078 57.895 0.00 0.00 0.00 2.75
2390 3977 0.308376 GGCGATCTGACTCGTAGGTC 59.692 60.000 9.87 0.00 40.73 3.85
2404 3991 1.033746 TAGGTCGATGACGGGTGGAC 61.034 60.000 0.00 0.00 40.21 4.02
2432 4019 0.936764 CGCGATCGCTACAATCAGCT 60.937 55.000 34.69 0.00 39.51 4.24
2433 4020 0.506080 GCGATCGCTACAATCAGCTG 59.494 55.000 31.94 7.63 39.51 4.24
2434 4021 1.865655 GCGATCGCTACAATCAGCTGA 60.866 52.381 31.94 20.79 39.51 4.26
2435 4022 1.783711 CGATCGCTACAATCAGCTGAC 59.216 52.381 20.97 3.90 39.51 3.51
2437 4024 2.741759 TCGCTACAATCAGCTGACAA 57.258 45.000 20.97 3.72 39.51 3.18
2440 4027 2.346847 CGCTACAATCAGCTGACAAGTC 59.653 50.000 20.97 6.12 39.51 3.01
2443 4030 3.325293 ACAATCAGCTGACAAGTCGAT 57.675 42.857 20.97 0.00 0.00 3.59
2446 4033 3.815856 ATCAGCTGACAAGTCGATGAT 57.184 42.857 20.97 14.96 35.84 2.45
2452 4039 2.669924 CTGACAAGTCGATGATGTGTGG 59.330 50.000 5.57 0.00 0.00 4.17
2481 4068 1.516386 CGCGATTGCTACAGTCGGT 60.516 57.895 0.00 0.00 42.37 4.69
2547 4134 0.181350 CTTCCTGGGTGATGGCCTAC 59.819 60.000 3.32 0.00 0.00 3.18
2550 4137 0.394352 CCTGGGTGATGGCCTACAAC 60.394 60.000 3.32 6.78 0.00 3.32
2564 4151 4.201950 GGCCTACAACTGCACATGATTTAG 60.202 45.833 0.00 0.00 0.00 1.85
2571 4158 6.902341 CAACTGCACATGATTTAGTTGTAGT 58.098 36.000 19.14 10.26 41.82 2.73
2576 4163 8.795786 TGCACATGATTTAGTTGTAGTTTTTC 57.204 30.769 0.00 0.00 0.00 2.29
2577 4164 7.589587 TGCACATGATTTAGTTGTAGTTTTTCG 59.410 33.333 0.00 0.00 0.00 3.46
2580 4168 9.878599 ACATGATTTAGTTGTAGTTTTTCGAAG 57.121 29.630 0.00 0.00 0.00 3.79
2596 4184 7.941795 TTTTCGAAGTAAGAATATCGATCCC 57.058 36.000 0.00 0.00 43.04 3.85
2599 4187 4.852104 CGAAGTAAGAATATCGATCCCACG 59.148 45.833 0.00 0.00 37.48 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.552687 GGGAAGACATGATGTTGACTAAATACA 59.447 37.037 0.00 0.00 0.00 2.29
49 50 2.915604 AGGGGAAGACATGATGTTGACT 59.084 45.455 0.00 0.00 0.00 3.41
65 66 7.676893 TCACTATGAGTAGTCTTAAAAAGGGGA 59.323 37.037 0.00 0.00 39.12 4.81
83 91 8.770322 ACTAGTCTAAGTTACTCCTCACTATGA 58.230 37.037 0.00 0.00 0.00 2.15
84 92 8.967664 ACTAGTCTAAGTTACTCCTCACTATG 57.032 38.462 0.00 0.00 0.00 2.23
152 160 7.492669 GCATGACACTACACATATGTTACTCTT 59.507 37.037 5.37 0.00 40.48 2.85
153 161 6.980978 GCATGACACTACACATATGTTACTCT 59.019 38.462 5.37 0.00 40.48 3.24
167 175 8.915871 ATAAATGAAATGTTGCATGACACTAC 57.084 30.769 0.00 0.00 31.30 2.73
169 177 9.577110 CTAATAAATGAAATGTTGCATGACACT 57.423 29.630 0.00 0.00 31.30 3.55
205 214 4.804608 TCACACGTACCAAAACAAGATG 57.195 40.909 0.00 0.00 0.00 2.90
211 220 4.319694 GGGTAACATCACACGTACCAAAAC 60.320 45.833 2.56 0.00 39.74 2.43
213 222 3.181457 TGGGTAACATCACACGTACCAAA 60.181 43.478 2.56 0.00 39.74 3.28
217 226 5.002464 ACTATGGGTAACATCACACGTAC 57.998 43.478 0.00 0.00 41.03 3.67
220 229 5.838529 TCATACTATGGGTAACATCACACG 58.161 41.667 0.00 0.00 41.03 4.49
276 285 8.959548 TGCTTATGTGACAATGATTTAATGAGT 58.040 29.630 0.00 0.00 0.00 3.41
277 286 9.791820 TTGCTTATGTGACAATGATTTAATGAG 57.208 29.630 0.00 0.00 0.00 2.90
300 309 3.311966 GAGTCCAACTCAGCAAATTTGC 58.688 45.455 31.36 31.36 44.45 3.68
329 338 5.505780 CCATGGTGGGAGTAACTTCATTAA 58.494 41.667 2.57 0.00 32.67 1.40
332 341 3.652057 CCATGGTGGGAGTAACTTCAT 57.348 47.619 2.57 0.00 32.67 2.57
452 461 6.126739 TGTTTGGCCCTGGTTAAAATTTTAGT 60.127 34.615 10.40 0.00 0.00 2.24
525 534 9.877178 TGCCAAGTATTTTCTTAAGTTTTTCAA 57.123 25.926 1.63 0.00 0.00 2.69
546 555 3.902881 AAGGATGTGTTTGTTTGCCAA 57.097 38.095 0.00 0.00 0.00 4.52
562 571 2.175499 CAATCCAATCAGGCCCTAAGGA 59.825 50.000 0.00 0.76 37.29 3.36
563 572 2.091665 ACAATCCAATCAGGCCCTAAGG 60.092 50.000 0.00 0.00 37.29 2.69
564 573 3.217626 GACAATCCAATCAGGCCCTAAG 58.782 50.000 0.00 0.00 37.29 2.18
565 574 2.421388 CGACAATCCAATCAGGCCCTAA 60.421 50.000 0.00 0.00 37.29 2.69
566 575 1.140852 CGACAATCCAATCAGGCCCTA 59.859 52.381 0.00 0.00 37.29 3.53
567 576 0.107017 CGACAATCCAATCAGGCCCT 60.107 55.000 0.00 0.00 37.29 5.19
568 577 0.394352 ACGACAATCCAATCAGGCCC 60.394 55.000 0.00 0.00 37.29 5.80
569 578 1.463674 AACGACAATCCAATCAGGCC 58.536 50.000 0.00 0.00 37.29 5.19
570 579 3.244976 CAAAACGACAATCCAATCAGGC 58.755 45.455 0.00 0.00 37.29 4.85
571 580 3.244976 GCAAAACGACAATCCAATCAGG 58.755 45.455 0.00 0.00 39.47 3.86
572 581 3.670055 GTGCAAAACGACAATCCAATCAG 59.330 43.478 0.00 0.00 0.00 2.90
573 582 3.067320 TGTGCAAAACGACAATCCAATCA 59.933 39.130 0.00 0.00 0.00 2.57
574 583 3.425193 GTGTGCAAAACGACAATCCAATC 59.575 43.478 0.00 0.00 0.00 2.67
575 584 3.068024 AGTGTGCAAAACGACAATCCAAT 59.932 39.130 0.00 0.00 0.00 3.16
576 585 2.425312 AGTGTGCAAAACGACAATCCAA 59.575 40.909 0.00 0.00 0.00 3.53
577 586 2.020720 AGTGTGCAAAACGACAATCCA 58.979 42.857 0.00 0.00 0.00 3.41
578 587 2.774439 AGTGTGCAAAACGACAATCC 57.226 45.000 0.00 0.00 0.00 3.01
579 588 5.513495 TGTAAAAGTGTGCAAAACGACAATC 59.487 36.000 0.00 0.00 0.00 2.67
580 589 5.287513 GTGTAAAAGTGTGCAAAACGACAAT 59.712 36.000 0.00 0.00 0.00 2.71
581 590 4.617645 GTGTAAAAGTGTGCAAAACGACAA 59.382 37.500 0.00 0.00 0.00 3.18
582 591 4.159857 GTGTAAAAGTGTGCAAAACGACA 58.840 39.130 0.00 0.00 0.00 4.35
583 592 3.544682 GGTGTAAAAGTGTGCAAAACGAC 59.455 43.478 0.00 0.00 0.00 4.34
584 593 3.440872 AGGTGTAAAAGTGTGCAAAACGA 59.559 39.130 0.00 0.00 0.00 3.85
585 594 3.545873 CAGGTGTAAAAGTGTGCAAAACG 59.454 43.478 0.00 0.00 0.00 3.60
586 595 4.490743 ACAGGTGTAAAAGTGTGCAAAAC 58.509 39.130 0.00 0.00 0.00 2.43
587 596 4.792521 ACAGGTGTAAAAGTGTGCAAAA 57.207 36.364 0.00 0.00 0.00 2.44
588 597 5.899120 TTACAGGTGTAAAAGTGTGCAAA 57.101 34.783 0.00 0.00 37.54 3.68
589 598 5.899120 TTTACAGGTGTAAAAGTGTGCAA 57.101 34.783 11.96 0.00 44.63 4.08
598 607 7.970102 AGGTCTGTATCTTTTACAGGTGTAAA 58.030 34.615 10.59 10.59 45.55 2.01
599 608 7.233962 TGAGGTCTGTATCTTTTACAGGTGTAA 59.766 37.037 11.65 0.00 43.67 2.41
600 609 6.722590 TGAGGTCTGTATCTTTTACAGGTGTA 59.277 38.462 11.65 0.00 43.67 2.90
601 610 5.542635 TGAGGTCTGTATCTTTTACAGGTGT 59.457 40.000 11.65 0.00 43.67 4.16
602 611 6.037786 TGAGGTCTGTATCTTTTACAGGTG 57.962 41.667 11.65 0.00 43.67 4.00
603 612 6.681729 TTGAGGTCTGTATCTTTTACAGGT 57.318 37.500 11.65 0.00 43.67 4.00
604 613 6.477033 CGATTGAGGTCTGTATCTTTTACAGG 59.523 42.308 11.65 0.00 43.67 4.00
605 614 6.477033 CCGATTGAGGTCTGTATCTTTTACAG 59.523 42.308 6.45 6.45 44.56 2.74
606 615 6.070995 ACCGATTGAGGTCTGTATCTTTTACA 60.071 38.462 0.00 0.00 41.46 2.41
607 616 6.338937 ACCGATTGAGGTCTGTATCTTTTAC 58.661 40.000 0.00 0.00 41.46 2.01
608 617 6.540438 ACCGATTGAGGTCTGTATCTTTTA 57.460 37.500 0.00 0.00 41.46 1.52
609 618 5.422214 ACCGATTGAGGTCTGTATCTTTT 57.578 39.130 0.00 0.00 41.46 2.27
621 630 4.403453 GAAATGAAAACGACCGATTGAGG 58.597 43.478 0.00 0.00 37.30 3.86
622 631 4.403453 GGAAATGAAAACGACCGATTGAG 58.597 43.478 0.00 0.00 0.00 3.02
623 632 3.120477 CGGAAATGAAAACGACCGATTGA 60.120 43.478 0.00 0.00 42.40 2.57
624 633 3.160545 CGGAAATGAAAACGACCGATTG 58.839 45.455 0.00 0.00 42.40 2.67
625 634 2.160813 CCGGAAATGAAAACGACCGATT 59.839 45.455 0.00 0.00 42.40 3.34
626 635 1.735571 CCGGAAATGAAAACGACCGAT 59.264 47.619 0.00 0.00 42.40 4.18
627 636 1.149987 CCGGAAATGAAAACGACCGA 58.850 50.000 0.00 0.00 42.40 4.69
628 637 0.869730 ACCGGAAATGAAAACGACCG 59.130 50.000 9.46 0.00 40.03 4.79
629 638 2.291190 TCAACCGGAAATGAAAACGACC 59.709 45.455 9.46 0.00 0.00 4.79
630 639 3.612472 TCAACCGGAAATGAAAACGAC 57.388 42.857 9.46 0.00 0.00 4.34
631 640 4.634184 TTTCAACCGGAAATGAAAACGA 57.366 36.364 22.94 8.85 41.26 3.85
635 644 6.818644 TGTTTGATTTTCAACCGGAAATGAAA 59.181 30.769 22.00 22.00 44.59 2.69
636 645 6.341316 TGTTTGATTTTCAACCGGAAATGAA 58.659 32.000 9.46 13.16 44.59 2.57
637 646 5.907207 TGTTTGATTTTCAACCGGAAATGA 58.093 33.333 9.46 6.88 44.59 2.57
638 647 6.347563 CCATGTTTGATTTTCAACCGGAAATG 60.348 38.462 9.46 4.12 44.59 2.32
639 648 5.700373 CCATGTTTGATTTTCAACCGGAAAT 59.300 36.000 9.46 2.89 44.59 2.17
640 649 5.053145 CCATGTTTGATTTTCAACCGGAAA 58.947 37.500 9.46 0.00 43.59 3.13
641 650 4.626042 CCATGTTTGATTTTCAACCGGAA 58.374 39.130 9.46 0.00 35.89 4.30
642 651 3.553922 GCCATGTTTGATTTTCAACCGGA 60.554 43.478 9.46 0.00 35.89 5.14
643 652 2.736192 GCCATGTTTGATTTTCAACCGG 59.264 45.455 0.00 0.00 35.89 5.28
644 653 3.429543 CAGCCATGTTTGATTTTCAACCG 59.570 43.478 0.00 0.00 35.89 4.44
645 654 4.630111 TCAGCCATGTTTGATTTTCAACC 58.370 39.130 0.00 0.00 35.89 3.77
646 655 5.927689 TCATCAGCCATGTTTGATTTTCAAC 59.072 36.000 6.48 0.00 35.89 3.18
647 656 6.099159 TCATCAGCCATGTTTGATTTTCAA 57.901 33.333 6.48 0.00 34.03 2.69
648 657 5.725325 TCATCAGCCATGTTTGATTTTCA 57.275 34.783 6.48 0.00 31.91 2.69
649 658 7.605410 ATTTCATCAGCCATGTTTGATTTTC 57.395 32.000 6.48 0.00 31.91 2.29
650 659 8.095792 TGTATTTCATCAGCCATGTTTGATTTT 58.904 29.630 6.48 0.00 31.91 1.82
651 660 7.546667 GTGTATTTCATCAGCCATGTTTGATTT 59.453 33.333 6.48 0.00 31.91 2.17
652 661 7.037438 GTGTATTTCATCAGCCATGTTTGATT 58.963 34.615 6.48 0.00 31.91 2.57
653 662 6.379133 AGTGTATTTCATCAGCCATGTTTGAT 59.621 34.615 3.95 3.95 34.48 2.57
654 663 5.711506 AGTGTATTTCATCAGCCATGTTTGA 59.288 36.000 0.00 0.00 33.66 2.69
655 664 5.957798 AGTGTATTTCATCAGCCATGTTTG 58.042 37.500 0.00 0.00 33.66 2.93
656 665 6.015180 ACAAGTGTATTTCATCAGCCATGTTT 60.015 34.615 0.00 0.00 33.66 2.83
657 666 5.477984 ACAAGTGTATTTCATCAGCCATGTT 59.522 36.000 0.00 0.00 33.66 2.71
658 667 5.012239 ACAAGTGTATTTCATCAGCCATGT 58.988 37.500 0.00 0.00 33.66 3.21
659 668 5.571784 ACAAGTGTATTTCATCAGCCATG 57.428 39.130 0.00 0.00 0.00 3.66
660 669 7.701539 TTTACAAGTGTATTTCATCAGCCAT 57.298 32.000 0.00 0.00 0.00 4.40
661 670 7.230510 ACTTTTACAAGTGTATTTCATCAGCCA 59.769 33.333 0.00 0.00 42.05 4.75
662 671 7.593825 ACTTTTACAAGTGTATTTCATCAGCC 58.406 34.615 0.00 0.00 42.05 4.85
667 676 9.872757 CGTGTTACTTTTACAAGTGTATTTCAT 57.127 29.630 4.49 0.00 43.54 2.57
668 677 8.336806 CCGTGTTACTTTTACAAGTGTATTTCA 58.663 33.333 4.49 0.00 43.54 2.69
669 678 7.799914 CCCGTGTTACTTTTACAAGTGTATTTC 59.200 37.037 4.49 0.00 43.54 2.17
670 679 7.282901 ACCCGTGTTACTTTTACAAGTGTATTT 59.717 33.333 4.49 0.00 43.54 1.40
671 680 6.767423 ACCCGTGTTACTTTTACAAGTGTATT 59.233 34.615 4.49 0.00 43.54 1.89
672 681 6.203338 CACCCGTGTTACTTTTACAAGTGTAT 59.797 38.462 4.49 0.00 43.54 2.29
673 682 5.523188 CACCCGTGTTACTTTTACAAGTGTA 59.477 40.000 4.49 0.00 43.54 2.90
674 683 4.333372 CACCCGTGTTACTTTTACAAGTGT 59.667 41.667 4.49 0.00 43.54 3.55
675 684 4.333372 ACACCCGTGTTACTTTTACAAGTG 59.667 41.667 4.49 0.00 40.39 3.16
676 685 4.516323 ACACCCGTGTTACTTTTACAAGT 58.484 39.130 0.00 0.00 41.83 3.16
677 686 6.790285 ATACACCCGTGTTACTTTTACAAG 57.210 37.500 5.69 0.00 41.83 3.16
678 687 8.668510 TTTATACACCCGTGTTACTTTTACAA 57.331 30.769 5.69 0.00 41.83 2.41
679 688 8.845413 ATTTATACACCCGTGTTACTTTTACA 57.155 30.769 5.69 0.00 41.83 2.41
683 692 8.729756 GGTAAATTTATACACCCGTGTTACTTT 58.270 33.333 5.69 3.25 41.83 2.66
684 693 7.336679 GGGTAAATTTATACACCCGTGTTACTT 59.663 37.037 10.47 0.00 41.83 2.24
685 694 6.823182 GGGTAAATTTATACACCCGTGTTACT 59.177 38.462 10.47 0.00 41.83 2.24
686 695 7.015226 GGGTAAATTTATACACCCGTGTTAC 57.985 40.000 10.47 1.07 41.83 2.50
695 704 8.573885 GCTTGGAATAGGGGTAAATTTATACAC 58.426 37.037 0.31 0.00 0.00 2.90
696 705 7.446013 CGCTTGGAATAGGGGTAAATTTATACA 59.554 37.037 0.31 0.00 0.00 2.29
697 706 7.094506 CCGCTTGGAATAGGGGTAAATTTATAC 60.095 40.741 0.31 0.00 41.86 1.47
698 707 6.943718 CCGCTTGGAATAGGGGTAAATTTATA 59.056 38.462 0.31 0.00 41.86 0.98
699 708 5.773176 CCGCTTGGAATAGGGGTAAATTTAT 59.227 40.000 0.31 0.00 41.86 1.40
700 709 5.134661 CCGCTTGGAATAGGGGTAAATTTA 58.865 41.667 0.00 0.00 41.86 1.40
701 710 3.958147 CCGCTTGGAATAGGGGTAAATTT 59.042 43.478 0.00 0.00 41.86 1.82
702 711 3.562182 CCGCTTGGAATAGGGGTAAATT 58.438 45.455 0.00 0.00 41.86 1.82
703 712 2.158519 CCCGCTTGGAATAGGGGTAAAT 60.159 50.000 0.00 0.00 44.46 1.40
704 713 1.213430 CCCGCTTGGAATAGGGGTAAA 59.787 52.381 0.00 0.00 44.46 2.01
705 714 0.841289 CCCGCTTGGAATAGGGGTAA 59.159 55.000 0.00 0.00 44.46 2.85
706 715 2.535224 CCCGCTTGGAATAGGGGTA 58.465 57.895 0.00 0.00 44.46 3.69
707 716 3.331293 CCCGCTTGGAATAGGGGT 58.669 61.111 0.00 0.00 44.46 4.95
709 718 2.203351 GCCCCGCTTGGAATAGGG 60.203 66.667 0.00 0.00 43.41 3.53
710 719 2.203351 GGCCCCGCTTGGAATAGG 60.203 66.667 0.00 0.00 35.39 2.57
711 720 0.472471 TAAGGCCCCGCTTGGAATAG 59.528 55.000 0.00 0.00 35.39 1.73
712 721 0.472471 CTAAGGCCCCGCTTGGAATA 59.528 55.000 0.00 0.00 35.39 1.75
713 722 1.227383 CTAAGGCCCCGCTTGGAAT 59.773 57.895 0.00 0.00 35.39 3.01
714 723 2.674754 CTAAGGCCCCGCTTGGAA 59.325 61.111 0.00 0.00 35.39 3.53
715 724 3.407967 CCTAAGGCCCCGCTTGGA 61.408 66.667 0.00 0.00 35.39 3.53
716 725 4.506255 CCCTAAGGCCCCGCTTGG 62.506 72.222 0.00 0.00 0.00 3.61
717 726 4.506255 CCCCTAAGGCCCCGCTTG 62.506 72.222 0.00 0.00 0.00 4.01
721 730 1.564483 TAAACACCCCTAAGGCCCCG 61.564 60.000 0.00 0.00 40.58 5.73
722 731 0.705842 TTAAACACCCCTAAGGCCCC 59.294 55.000 0.00 0.00 40.58 5.80
723 732 2.840640 ATTAAACACCCCTAAGGCCC 57.159 50.000 0.00 0.00 40.58 5.80
724 733 4.090819 TCAAATTAAACACCCCTAAGGCC 58.909 43.478 0.00 0.00 40.58 5.19
725 734 5.731957 TTCAAATTAAACACCCCTAAGGC 57.268 39.130 0.00 0.00 40.58 4.35
763 772 3.570212 AAGCTGGGCCAACCGACT 61.570 61.111 8.04 0.00 44.64 4.18
810 821 1.128692 GAGAAATGTTTCGGGACTGCG 59.871 52.381 0.24 0.00 41.92 5.18
823 834 4.232221 GTCACATGCACTTTGGAGAAATG 58.768 43.478 0.00 0.00 0.00 2.32
824 835 3.058016 CGTCACATGCACTTTGGAGAAAT 60.058 43.478 0.00 0.00 0.00 2.17
962 982 3.859411 TTTCTCTTTCCTCTCTCTCGC 57.141 47.619 0.00 0.00 0.00 5.03
963 983 6.978080 CCTTATTTTCTCTTTCCTCTCTCTCG 59.022 42.308 0.00 0.00 0.00 4.04
1043 1066 1.743252 GCTCTTGGGCTCTTGGACG 60.743 63.158 0.00 0.00 0.00 4.79
1071 1094 2.360475 GTGTGGAGGAGCAAGGGC 60.360 66.667 0.00 0.00 41.61 5.19
1179 1202 2.215478 CTTGTTTGGTCTCGAGCGCG 62.215 60.000 7.81 2.41 39.35 6.86
1743 1769 6.528423 GCAGAAGCAATAGGTATCTATACACG 59.472 42.308 0.00 0.00 41.58 4.49
1778 1804 3.224007 TTTTCCCCTGGGCTCTGGC 62.224 63.158 7.39 0.00 34.68 4.85
1783 1809 2.121042 TCCCTTTTCCCCTGGGCT 60.121 61.111 7.39 0.00 40.69 5.19
1785 1811 0.413434 AATGTCCCTTTTCCCCTGGG 59.587 55.000 5.50 5.50 42.20 4.45
1786 1812 1.901833 CAAATGTCCCTTTTCCCCTGG 59.098 52.381 0.00 0.00 0.00 4.45
1787 1813 2.608623 ACAAATGTCCCTTTTCCCCTG 58.391 47.619 0.00 0.00 0.00 4.45
1886 1927 0.826715 CTTGCGAGAGGGGATTCAGA 59.173 55.000 0.00 0.00 0.00 3.27
1908 1949 7.966246 AAAATTGCTCAAATATTCAACAGCA 57.034 28.000 6.52 6.52 35.11 4.41
1909 1950 8.497554 TGAAAAATTGCTCAAATATTCAACAGC 58.502 29.630 0.00 0.00 34.11 4.40
1988 2067 3.420893 TCCCTTTTGTTCTCGATTGCAT 58.579 40.909 0.00 0.00 0.00 3.96
1998 2077 9.394477 GCGTATGATTATTTATCCCTTTTGTTC 57.606 33.333 0.00 0.00 31.87 3.18
2002 2081 6.436218 GGGGCGTATGATTATTTATCCCTTTT 59.564 38.462 0.00 0.00 31.87 2.27
2006 2085 4.850680 TGGGGCGTATGATTATTTATCCC 58.149 43.478 0.00 0.00 31.87 3.85
2008 2087 6.653320 TCTGTTGGGGCGTATGATTATTTATC 59.347 38.462 0.00 0.00 0.00 1.75
2016 2095 1.837439 TCTTCTGTTGGGGCGTATGAT 59.163 47.619 0.00 0.00 0.00 2.45
2017 2096 1.271856 TCTTCTGTTGGGGCGTATGA 58.728 50.000 0.00 0.00 0.00 2.15
2018 2097 2.009774 CTTCTTCTGTTGGGGCGTATG 58.990 52.381 0.00 0.00 0.00 2.39
2024 3504 3.023832 ACAAACACTTCTTCTGTTGGGG 58.976 45.455 0.00 0.00 32.07 4.96
2034 3514 1.064060 GCTGCGACAACAAACACTTCT 59.936 47.619 0.00 0.00 0.00 2.85
2047 3527 1.154599 CACAACATGACGCTGCGAC 60.155 57.895 30.47 23.37 0.00 5.19
2050 3530 0.588252 ACTTCACAACATGACGCTGC 59.412 50.000 0.00 0.00 36.92 5.25
2069 3549 0.385029 TTCTTCCCGACGTCGACAAA 59.615 50.000 37.65 24.73 43.02 2.83
2070 3550 0.039798 CTTCTTCCCGACGTCGACAA 60.040 55.000 37.65 26.00 43.02 3.18
2071 3551 1.168407 ACTTCTTCCCGACGTCGACA 61.168 55.000 37.65 21.01 43.02 4.35
2075 3558 0.454117 GACGACTTCTTCCCGACGTC 60.454 60.000 5.18 5.18 39.94 4.34
2089 3572 1.459592 CATGAGTTTCCCAACGACGAC 59.540 52.381 0.00 0.00 38.03 4.34
2092 3575 1.804748 GACCATGAGTTTCCCAACGAC 59.195 52.381 0.00 0.00 38.03 4.34
2094 3577 1.165270 GGACCATGAGTTTCCCAACG 58.835 55.000 0.00 0.00 38.03 4.10
2114 3597 2.418976 GGATTTTCTTCACCGTGCCTAC 59.581 50.000 0.00 0.00 0.00 3.18
2116 3599 1.202879 TGGATTTTCTTCACCGTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
2118 3601 3.244976 CATTGGATTTTCTTCACCGTGC 58.755 45.455 0.00 0.00 0.00 5.34
2137 3620 1.068753 CCATCTCGCTTCTCGGCAT 59.931 57.895 0.00 0.00 39.05 4.40
2138 3621 1.604147 TTCCATCTCGCTTCTCGGCA 61.604 55.000 0.00 0.00 39.05 5.69
2139 3622 0.460284 TTTCCATCTCGCTTCTCGGC 60.460 55.000 0.00 0.00 39.05 5.54
2140 3623 1.661112 GTTTTCCATCTCGCTTCTCGG 59.339 52.381 0.00 0.00 39.05 4.63
2141 3624 1.321743 CGTTTTCCATCTCGCTTCTCG 59.678 52.381 0.00 0.00 40.15 4.04
2142 3625 2.338500 ACGTTTTCCATCTCGCTTCTC 58.662 47.619 0.00 0.00 0.00 2.87
2144 3627 3.062234 CCTAACGTTTTCCATCTCGCTTC 59.938 47.826 5.91 0.00 0.00 3.86
2146 3629 2.618053 CCTAACGTTTTCCATCTCGCT 58.382 47.619 5.91 0.00 0.00 4.93
2148 3631 1.323534 CGCCTAACGTTTTCCATCTCG 59.676 52.381 5.91 0.00 36.87 4.04
2149 3632 1.664151 CCGCCTAACGTTTTCCATCTC 59.336 52.381 5.91 0.00 41.42 2.75
2150 3633 1.734163 CCGCCTAACGTTTTCCATCT 58.266 50.000 5.91 0.00 41.42 2.90
2152 3635 1.641123 CGCCGCCTAACGTTTTCCAT 61.641 55.000 5.91 0.00 41.42 3.41
2153 3636 2.319096 CGCCGCCTAACGTTTTCCA 61.319 57.895 5.91 0.00 41.42 3.53
2157 3741 2.973600 TTGCGCCGCCTAACGTTT 60.974 55.556 5.91 0.00 41.42 3.60
2175 3759 0.674581 TGAGTGCCTGATTCCAAGCG 60.675 55.000 0.00 0.00 32.49 4.68
2181 3765 1.364626 CCAGCGTGAGTGCCTGATTC 61.365 60.000 0.00 0.00 34.65 2.52
2197 3784 5.776173 ATATGTTACTTCGTCTCTCCCAG 57.224 43.478 0.00 0.00 0.00 4.45
2248 3835 1.666054 CTTGATGAGCTCAGGAAGGC 58.334 55.000 22.96 7.44 32.85 4.35
2249 3836 1.134159 CCCTTGATGAGCTCAGGAAGG 60.134 57.143 31.97 31.97 37.66 3.46
2254 3841 1.743958 CTTTGCCCTTGATGAGCTCAG 59.256 52.381 22.96 8.16 34.68 3.35
2257 3844 0.324091 CCCTTTGCCCTTGATGAGCT 60.324 55.000 0.00 0.00 0.00 4.09
2262 3849 1.000866 GGCTCCCTTTGCCCTTGAT 59.999 57.895 0.00 0.00 44.32 2.57
2275 3862 4.097361 GGACGGTTGGGAGGCTCC 62.097 72.222 25.80 25.80 35.23 4.70
2327 3914 2.590007 GATGGCTCGCATCGGCTT 60.590 61.111 0.00 0.00 38.10 4.35
2328 3915 3.544607 AGATGGCTCGCATCGGCT 61.545 61.111 0.00 0.00 38.10 5.52
2332 3919 1.430479 CAGATCAGATGGCTCGCATC 58.570 55.000 0.00 0.00 0.00 3.91
2333 3920 0.603172 GCAGATCAGATGGCTCGCAT 60.603 55.000 0.00 0.00 0.00 4.73
2342 3929 2.037620 GCTGTCCGGGCAGATCAGAT 62.038 60.000 39.44 0.00 38.70 2.90
2345 3932 2.293318 AAGCTGTCCGGGCAGATCA 61.293 57.895 39.44 0.31 38.70 2.92
2346 3933 1.817099 CAAGCTGTCCGGGCAGATC 60.817 63.158 39.44 22.38 38.70 2.75
2351 3938 3.056328 GGTTCAAGCTGTCCGGGC 61.056 66.667 0.00 0.00 0.00 6.13
2359 3946 1.078143 GATCGCCAGGGTTCAAGCT 60.078 57.895 0.00 0.00 0.00 3.74
2363 3950 0.904865 AGTCAGATCGCCAGGGTTCA 60.905 55.000 0.00 0.00 0.00 3.18
2365 3952 1.901085 GAGTCAGATCGCCAGGGTT 59.099 57.895 0.00 0.00 0.00 4.11
2366 3953 2.418910 CGAGTCAGATCGCCAGGGT 61.419 63.158 0.00 0.00 35.66 4.34
2371 3958 0.308376 GACCTACGAGTCAGATCGCC 59.692 60.000 0.00 0.00 46.60 5.54
2426 4013 3.118847 ACATCATCGACTTGTCAGCTGAT 60.119 43.478 21.47 2.86 0.00 2.90
2427 4014 2.232208 ACATCATCGACTTGTCAGCTGA 59.768 45.455 13.74 13.74 0.00 4.26
2429 4016 2.028658 ACACATCATCGACTTGTCAGCT 60.029 45.455 0.00 0.00 0.00 4.24
2432 4019 2.298729 TCCACACATCATCGACTTGTCA 59.701 45.455 0.00 0.00 0.00 3.58
2433 4020 2.926200 CTCCACACATCATCGACTTGTC 59.074 50.000 0.00 0.00 0.00 3.18
2434 4021 2.932622 GCTCCACACATCATCGACTTGT 60.933 50.000 0.00 0.00 0.00 3.16
2435 4022 1.662629 GCTCCACACATCATCGACTTG 59.337 52.381 0.00 0.00 0.00 3.16
2437 4024 0.179127 CGCTCCACACATCATCGACT 60.179 55.000 0.00 0.00 0.00 4.18
2440 4027 0.873312 CCTCGCTCCACACATCATCG 60.873 60.000 0.00 0.00 0.00 3.84
2443 4030 2.981302 CCCTCGCTCCACACATCA 59.019 61.111 0.00 0.00 0.00 3.07
2466 4053 3.782046 ACATGTACCGACTGTAGCAATC 58.218 45.455 0.00 0.00 0.00 2.67
2469 4056 1.475280 GGACATGTACCGACTGTAGCA 59.525 52.381 0.00 0.00 0.00 3.49
2481 4068 0.539518 CCACCCGTCATGGACATGTA 59.460 55.000 11.66 0.00 42.00 2.29
2503 4090 2.815211 CACCACATGGCCGTCTCG 60.815 66.667 0.00 0.00 39.32 4.04
2504 4091 2.436646 CCACCACATGGCCGTCTC 60.437 66.667 0.00 0.00 43.24 3.36
2516 4103 4.974438 AGGAAGGCGGGTCCACCA 62.974 66.667 7.51 0.00 40.22 4.17
2550 4137 8.801715 AAAAACTACAACTAAATCATGTGCAG 57.198 30.769 0.00 0.00 0.00 4.41
2571 4158 7.982919 TGGGATCGATATTCTTACTTCGAAAAA 59.017 33.333 0.00 0.00 43.04 1.94
2576 4163 4.852104 CGTGGGATCGATATTCTTACTTCG 59.148 45.833 0.00 0.00 0.00 3.79
2577 4164 5.162075 CCGTGGGATCGATATTCTTACTTC 58.838 45.833 0.00 0.00 0.00 3.01
2580 4168 3.846360 CCCGTGGGATCGATATTCTTAC 58.154 50.000 0.00 0.00 37.50 2.34
2596 4184 0.810648 CAATTCATGTGGTCCCCGTG 59.189 55.000 0.00 0.00 0.00 4.94
2599 4187 2.514458 ACTCAATTCATGTGGTCCCC 57.486 50.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.