Multiple sequence alignment - TraesCS6D01G256800

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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 TraesCS6D01G256800 chr6D 100.000 3993 0 0 1 3993 363002517 363006509 0.000000e+00 7374.0
1 TraesCS6D01G256800 chr6B 92.273 2226 112 22 664 2858 544629496 544631692 0.000000e+00 3103.0
2 TraesCS6D01G256800 chr6B 85.845 219 19 6 2908 3124 544631841 544632049 5.190000e-54 222.0
3 TraesCS6D01G256800 chr6B 81.057 227 37 3 3572 3792 153353984 153353758 4.100000e-40 176.0
4 TraesCS6D01G256800 chr6B 97.561 41 1 0 839 879 544629749 544629789 1.990000e-08 71.3
5 TraesCS6D01G256800 chr6A 94.678 1071 54 3 698 1766 503484443 503485512 0.000000e+00 1659.0
6 TraesCS6D01G256800 chr6A 87.413 1152 81 28 1855 2977 503485585 503486701 0.000000e+00 1266.0
7 TraesCS6D01G256800 chr6A 83.642 648 87 15 3159 3792 503487494 503488136 3.440000e-165 592.0
8 TraesCS6D01G256800 chr6A 87.243 243 27 3 3554 3792 503525374 503525616 1.410000e-69 274.0
9 TraesCS6D01G256800 chr6A 86.885 244 26 4 3554 3792 503604100 503604342 6.580000e-68 268.0
10 TraesCS6D01G256800 chr6A 86.893 206 21 3 3791 3991 503525898 503526102 4.020000e-55 226.0
11 TraesCS6D01G256800 chr6A 86.538 208 22 3 3789 3991 503604622 503604828 1.440000e-54 224.0
12 TraesCS6D01G256800 chr6A 84.615 117 17 1 3854 3970 503488463 503488578 9.070000e-22 115.0
13 TraesCS6D01G256800 chr1D 97.561 492 9 1 1 492 441647284 441646796 0.000000e+00 839.0
14 TraesCS6D01G256800 chr1D 96.741 491 16 0 1 491 226958772 226959262 0.000000e+00 819.0
15 TraesCS6D01G256800 chr3D 97.358 492 13 0 1 492 553186318 553186809 0.000000e+00 837.0
16 TraesCS6D01G256800 chr3D 95.455 44 2 0 3418 3461 10801581 10801538 1.990000e-08 71.3
17 TraesCS6D01G256800 chr7D 96.945 491 15 0 1 491 169479324 169479814 0.000000e+00 824.0
18 TraesCS6D01G256800 chr7D 96.024 503 17 1 1 500 21765043 21765545 0.000000e+00 815.0
19 TraesCS6D01G256800 chr7D 95.098 510 24 1 1 509 602020819 602020310 0.000000e+00 802.0
20 TraesCS6D01G256800 chr4D 96.945 491 15 0 1 491 51346736 51347226 0.000000e+00 824.0
21 TraesCS6D01G256800 chr4D 83.333 270 30 8 3532 3792 16726479 16726742 6.670000e-58 235.0
22 TraesCS6D01G256800 chr4D 85.281 231 26 5 3549 3779 16671447 16671669 8.630000e-57 231.0
23 TraesCS6D01G256800 chrUn 96.552 493 16 1 1 492 108985746 108986238 0.000000e+00 815.0
24 TraesCS6D01G256800 chrUn 97.222 36 1 0 3418 3453 43589936 43589901 1.200000e-05 62.1
25 TraesCS6D01G256800 chr2B 96.000 500 16 2 1 499 12180934 12180438 0.000000e+00 809.0
26 TraesCS6D01G256800 chr3A 80.808 297 41 10 3503 3791 632771398 632771686 6.720000e-53 219.0
27 TraesCS6D01G256800 chr3A 89.474 76 4 1 3561 3632 581836683 581836608 4.250000e-15 93.5
28 TraesCS6D01G256800 chr3A 95.455 44 2 0 3418 3461 17466047 17466090 1.990000e-08 71.3
29 TraesCS6D01G256800 chr5B 82.819 227 31 4 3546 3766 696724834 696725058 3.150000e-46 196.0
30 TraesCS6D01G256800 chr5B 100.000 28 0 0 3822 3849 132541698 132541725 7.000000e-03 52.8
31 TraesCS6D01G256800 chr3B 81.092 238 40 2 3559 3792 652480951 652481187 6.810000e-43 185.0
32 TraesCS6D01G256800 chr3B 88.235 51 6 0 3427 3477 136452718 136452668 1.200000e-05 62.1
33 TraesCS6D01G256800 chr3B 86.441 59 1 3 3791 3849 578758059 578758008 1.550000e-04 58.4
34 TraesCS6D01G256800 chr4A 80.500 200 31 6 3592 3791 608227229 608227420 3.220000e-31 147.0
35 TraesCS6D01G256800 chr5A 87.654 81 8 2 3850 3929 516798697 516798618 4.250000e-15 93.5
36 TraesCS6D01G256800 chr5A 87.931 58 5 2 3416 3472 524406336 524406280 2.580000e-07 67.6
37 TraesCS6D01G256800 chr5D 86.301 73 10 0 3850 3922 119615912 119615984 3.310000e-11 80.5
38 TraesCS6D01G256800 chr7A 100.000 28 0 0 3822 3849 210262022 210262049 7.000000e-03 52.8


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 TraesCS6D01G256800 chr6D 363002517 363006509 3992 False 7374.0 7374 100.0000 1 3993 1 chr6D.!!$F1 3992
1 TraesCS6D01G256800 chr6B 544629496 544632049 2553 False 1132.1 3103 91.8930 664 3124 3 chr6B.!!$F1 2460
2 TraesCS6D01G256800 chr6A 503484443 503488578 4135 False 908.0 1659 87.5870 698 3970 4 chr6A.!!$F1 3272
3 TraesCS6D01G256800 chr6A 503525374 503526102 728 False 250.0 274 87.0680 3554 3991 2 chr6A.!!$F2 437
4 TraesCS6D01G256800 chr6A 503604100 503604828 728 False 246.0 268 86.7115 3554 3991 2 chr6A.!!$F3 437
5 TraesCS6D01G256800 chr7D 21765043 21765545 502 False 815.0 815 96.0240 1 500 1 chr7D.!!$F1 499
6 TraesCS6D01G256800 chr7D 602020310 602020819 509 True 802.0 802 95.0980 1 509 1 chr7D.!!$R1 508

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
550 554 0.037232 GTGGACCTCTGTGTAGCCAC 60.037 60.0 0.00 0.0 42.19 5.01 F
593 597 0.097674 GCTGAACATGCCACACGATC 59.902 55.0 0.00 0.0 0.00 3.69 F
596 600 0.097674 GAACATGCCACACGATCTGC 59.902 55.0 0.00 0.0 0.00 4.26 F
599 603 0.179181 CATGCCACACGATCTGCAAC 60.179 55.0 0.00 0.0 37.27 4.17 F
1069 1086 0.249197 TGAGAGATGCATCCGCTTCG 60.249 55.0 23.06 0.0 44.80 3.79 F
1778 1811 0.671251 CTGCAACAAGCCCCGTAAAA 59.329 50.0 0.00 0.0 44.83 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1741 0.108615 ATCTCACCGTGGAAAGAGCG 60.109 55.000 0.00 0.0 0.00 5.03 R
2177 2220 1.152881 AATCATTCTCCAGGCCCGC 60.153 57.895 0.00 0.0 0.00 6.13 R
2396 2443 1.565759 TCCAGCCCTTATCTGCAACAT 59.434 47.619 0.00 0.0 0.00 2.71 R
2786 2837 7.444792 ACAAGTGGACAACCGTATAACAAATTA 59.555 33.333 0.00 0.0 39.42 1.40 R
2837 2889 0.253044 AATCTGCCGTGCACCACTAT 59.747 50.000 12.15 0.0 33.79 2.12 R
3082 3705 0.811219 TCTGATTTGATGCCGCCGAG 60.811 55.000 0.00 0.0 0.00 4.63 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
40 41 7.785028 TCTGTCAGGTTAGTCAATGTATAGGAT 59.215 37.037 0.00 0.00 0.00 3.24
57 58 1.268999 GGATTGCGCTTTTGTGTGTCA 60.269 47.619 9.73 0.00 0.00 3.58
61 62 2.886081 TGCGCTTTTGTGTGTCATTTT 58.114 38.095 9.73 0.00 0.00 1.82
79 80 6.919662 GTCATTTTCTTCAAGCTGTCATTCAA 59.080 34.615 0.00 0.00 0.00 2.69
101 102 1.305718 AAGAGAGGAGCGAGGCCTT 60.306 57.895 6.77 0.00 35.44 4.35
346 350 9.567848 ACGTTTGGTTTTCATAAGCTAATAATG 57.432 29.630 0.00 0.00 0.00 1.90
358 362 9.388506 CATAAGCTAATAATGTATCCCTTCCTG 57.611 37.037 0.00 0.00 0.00 3.86
360 364 6.773638 AGCTAATAATGTATCCCTTCCTGTG 58.226 40.000 0.00 0.00 0.00 3.66
391 395 7.442969 TCCTTTGTGTACCACATTGTAACTAAG 59.557 37.037 0.00 0.00 44.16 2.18
405 409 8.982685 CATTGTAACTAAGCATCTATGTACCAG 58.017 37.037 0.00 0.00 0.00 4.00
406 410 6.513180 TGTAACTAAGCATCTATGTACCAGC 58.487 40.000 0.00 0.00 0.00 4.85
491 495 1.065102 GGCGCAACGAGTCATCTAGTA 59.935 52.381 10.83 0.00 0.00 1.82
492 496 2.376956 GCGCAACGAGTCATCTAGTAG 58.623 52.381 0.30 0.00 0.00 2.57
493 497 2.031807 GCGCAACGAGTCATCTAGTAGA 59.968 50.000 0.30 1.45 0.00 2.59
494 498 3.846744 GCGCAACGAGTCATCTAGTAGAG 60.847 52.174 0.30 0.00 0.00 2.43
495 499 3.310227 CGCAACGAGTCATCTAGTAGAGT 59.690 47.826 5.98 0.00 0.00 3.24
496 500 4.201832 CGCAACGAGTCATCTAGTAGAGTT 60.202 45.833 5.98 0.62 0.00 3.01
497 501 5.006455 CGCAACGAGTCATCTAGTAGAGTTA 59.994 44.000 5.98 0.00 0.00 2.24
498 502 6.456584 CGCAACGAGTCATCTAGTAGAGTTAA 60.457 42.308 5.98 0.00 0.00 2.01
499 503 7.249147 GCAACGAGTCATCTAGTAGAGTTAAA 58.751 38.462 5.98 0.00 0.00 1.52
500 504 7.754027 GCAACGAGTCATCTAGTAGAGTTAAAA 59.246 37.037 5.98 0.00 0.00 1.52
501 505 9.790389 CAACGAGTCATCTAGTAGAGTTAAAAT 57.210 33.333 5.98 0.00 0.00 1.82
503 507 9.175312 ACGAGTCATCTAGTAGAGTTAAAATCA 57.825 33.333 5.98 0.00 0.00 2.57
509 513 9.255304 CATCTAGTAGAGTTAAAATCAAGAGGC 57.745 37.037 5.98 0.00 0.00 4.70
510 514 8.362464 TCTAGTAGAGTTAAAATCAAGAGGCA 57.638 34.615 0.00 0.00 0.00 4.75
511 515 8.251721 TCTAGTAGAGTTAAAATCAAGAGGCAC 58.748 37.037 0.00 0.00 0.00 5.01
513 517 6.876257 AGTAGAGTTAAAATCAAGAGGCACTG 59.124 38.462 0.00 0.00 41.55 3.66
514 518 5.625150 AGAGTTAAAATCAAGAGGCACTGT 58.375 37.500 0.00 0.00 41.55 3.55
515 519 6.769512 AGAGTTAAAATCAAGAGGCACTGTA 58.230 36.000 0.00 0.00 41.55 2.74
516 520 6.876257 AGAGTTAAAATCAAGAGGCACTGTAG 59.124 38.462 0.00 0.00 41.55 2.74
517 521 5.412904 AGTTAAAATCAAGAGGCACTGTAGC 59.587 40.000 0.00 0.00 41.55 3.58
518 522 3.710209 AAATCAAGAGGCACTGTAGCT 57.290 42.857 0.00 0.00 41.55 3.32
519 523 2.977772 ATCAAGAGGCACTGTAGCTC 57.022 50.000 0.00 0.00 41.55 4.09
520 524 0.898320 TCAAGAGGCACTGTAGCTCC 59.102 55.000 0.00 0.00 41.55 4.70
521 525 0.901124 CAAGAGGCACTGTAGCTCCT 59.099 55.000 0.00 0.00 41.55 3.69
522 526 1.134848 CAAGAGGCACTGTAGCTCCTC 60.135 57.143 8.50 8.50 41.55 3.71
523 527 0.040351 AGAGGCACTGTAGCTCCTCA 59.960 55.000 16.76 3.40 45.69 3.86
524 528 0.898320 GAGGCACTGTAGCTCCTCAA 59.102 55.000 11.11 0.00 41.55 3.02
525 529 1.484240 GAGGCACTGTAGCTCCTCAAT 59.516 52.381 11.11 0.00 41.55 2.57
526 530 2.695666 GAGGCACTGTAGCTCCTCAATA 59.304 50.000 11.11 0.00 41.55 1.90
527 531 2.432510 AGGCACTGTAGCTCCTCAATAC 59.567 50.000 0.00 0.00 37.18 1.89
528 532 2.168521 GGCACTGTAGCTCCTCAATACA 59.831 50.000 0.00 0.00 34.17 2.29
529 533 3.369471 GGCACTGTAGCTCCTCAATACAA 60.369 47.826 0.00 0.00 34.17 2.41
530 534 3.868077 GCACTGTAGCTCCTCAATACAAG 59.132 47.826 0.00 0.00 0.00 3.16
531 535 4.437239 CACTGTAGCTCCTCAATACAAGG 58.563 47.826 0.00 0.00 35.05 3.61
532 536 4.081420 CACTGTAGCTCCTCAATACAAGGT 60.081 45.833 0.00 0.00 35.29 3.50
533 537 4.081420 ACTGTAGCTCCTCAATACAAGGTG 60.081 45.833 0.00 0.00 35.29 4.00
534 538 3.197766 TGTAGCTCCTCAATACAAGGTGG 59.802 47.826 0.00 0.00 35.29 4.61
535 539 2.551270 AGCTCCTCAATACAAGGTGGA 58.449 47.619 0.00 0.00 35.29 4.02
536 540 2.237392 AGCTCCTCAATACAAGGTGGAC 59.763 50.000 0.00 0.00 35.29 4.02
537 541 2.681097 GCTCCTCAATACAAGGTGGACC 60.681 54.545 0.00 0.00 35.29 4.46
547 551 2.672414 AGGTGGACCTCTGTGTAGC 58.328 57.895 0.00 0.00 44.77 3.58
548 552 0.905337 AGGTGGACCTCTGTGTAGCC 60.905 60.000 0.00 0.00 44.77 3.93
549 553 1.192146 GGTGGACCTCTGTGTAGCCA 61.192 60.000 0.00 0.00 0.00 4.75
550 554 0.037232 GTGGACCTCTGTGTAGCCAC 60.037 60.000 0.00 0.00 42.19 5.01
551 555 1.215647 GGACCTCTGTGTAGCCACG 59.784 63.158 0.00 0.00 44.92 4.94
552 556 1.446272 GACCTCTGTGTAGCCACGC 60.446 63.158 0.00 0.00 44.92 5.34
553 557 2.154798 GACCTCTGTGTAGCCACGCA 62.155 60.000 0.00 0.00 44.92 5.24
554 558 1.005037 CCTCTGTGTAGCCACGCAA 60.005 57.895 0.00 0.00 44.27 4.85
555 559 1.291877 CCTCTGTGTAGCCACGCAAC 61.292 60.000 0.00 0.00 44.27 4.17
556 560 0.599991 CTCTGTGTAGCCACGCAACA 60.600 55.000 0.00 0.00 44.27 3.33
557 561 0.599991 TCTGTGTAGCCACGCAACAG 60.600 55.000 0.00 0.00 44.27 3.16
558 562 0.880278 CTGTGTAGCCACGCAACAGT 60.880 55.000 0.00 0.00 44.27 3.55
559 563 1.157257 TGTGTAGCCACGCAACAGTG 61.157 55.000 0.00 0.00 44.92 3.66
571 575 2.160822 CAACAGTGCTACACTCAGCT 57.839 50.000 0.00 0.00 43.43 4.24
572 576 2.064762 CAACAGTGCTACACTCAGCTC 58.935 52.381 0.00 0.00 43.43 4.09
573 577 0.242286 ACAGTGCTACACTCAGCTCG 59.758 55.000 0.00 0.00 43.43 5.03
574 578 0.457509 CAGTGCTACACTCAGCTCGG 60.458 60.000 0.00 0.00 43.43 4.63
575 579 1.807573 GTGCTACACTCAGCTCGGC 60.808 63.158 0.00 0.00 42.30 5.54
576 580 1.979155 TGCTACACTCAGCTCGGCT 60.979 57.895 0.00 0.00 42.30 5.52
585 589 2.437359 AGCTCGGCTGAACATGCC 60.437 61.111 0.00 0.00 46.42 4.40
591 595 3.654201 GCTGAACATGCCACACGA 58.346 55.556 0.00 0.00 0.00 4.35
592 596 2.174334 GCTGAACATGCCACACGAT 58.826 52.632 0.00 0.00 0.00 3.73
593 597 0.097674 GCTGAACATGCCACACGATC 59.902 55.000 0.00 0.00 0.00 3.69
594 598 1.730501 CTGAACATGCCACACGATCT 58.269 50.000 0.00 0.00 0.00 2.75
595 599 1.395954 CTGAACATGCCACACGATCTG 59.604 52.381 0.00 0.00 0.00 2.90
596 600 0.097674 GAACATGCCACACGATCTGC 59.902 55.000 0.00 0.00 0.00 4.26
597 601 0.606130 AACATGCCACACGATCTGCA 60.606 50.000 0.00 0.00 38.23 4.41
598 602 0.606130 ACATGCCACACGATCTGCAA 60.606 50.000 0.00 0.00 37.27 4.08
599 603 0.179181 CATGCCACACGATCTGCAAC 60.179 55.000 0.00 0.00 37.27 4.17
600 604 0.321919 ATGCCACACGATCTGCAACT 60.322 50.000 0.00 0.00 37.27 3.16
601 605 0.950555 TGCCACACGATCTGCAACTC 60.951 55.000 0.00 0.00 0.00 3.01
602 606 1.959899 GCCACACGATCTGCAACTCG 61.960 60.000 14.16 14.16 40.62 4.18
603 607 0.388520 CCACACGATCTGCAACTCGA 60.389 55.000 20.64 0.20 38.24 4.04
604 608 1.633561 CACACGATCTGCAACTCGAT 58.366 50.000 20.64 5.31 38.24 3.59
605 609 1.995484 CACACGATCTGCAACTCGATT 59.005 47.619 20.64 7.08 38.24 3.34
606 610 3.179048 CACACGATCTGCAACTCGATTA 58.821 45.455 20.64 0.00 38.24 1.75
607 611 3.798878 CACACGATCTGCAACTCGATTAT 59.201 43.478 20.64 0.00 38.24 1.28
608 612 3.798878 ACACGATCTGCAACTCGATTATG 59.201 43.478 20.64 12.31 38.24 1.90
609 613 3.798878 CACGATCTGCAACTCGATTATGT 59.201 43.478 20.64 3.78 38.24 2.29
610 614 4.976116 CACGATCTGCAACTCGATTATGTA 59.024 41.667 20.64 0.00 38.24 2.29
611 615 5.116225 CACGATCTGCAACTCGATTATGTAG 59.884 44.000 20.64 0.00 38.24 2.74
612 616 5.215903 CGATCTGCAACTCGATTATGTAGT 58.784 41.667 11.12 0.00 37.05 2.73
613 617 5.340932 CGATCTGCAACTCGATTATGTAGTC 59.659 44.000 11.12 6.57 37.05 2.59
614 618 4.933330 TCTGCAACTCGATTATGTAGTCC 58.067 43.478 9.12 0.00 0.00 3.85
615 619 4.401202 TCTGCAACTCGATTATGTAGTCCA 59.599 41.667 9.12 0.00 0.00 4.02
616 620 5.069119 TCTGCAACTCGATTATGTAGTCCAT 59.931 40.000 9.12 0.00 37.58 3.41
617 621 5.049828 TGCAACTCGATTATGTAGTCCATG 58.950 41.667 0.00 0.00 34.86 3.66
618 622 5.163457 TGCAACTCGATTATGTAGTCCATGA 60.163 40.000 0.00 0.00 34.86 3.07
619 623 5.753438 GCAACTCGATTATGTAGTCCATGAA 59.247 40.000 0.00 0.00 34.86 2.57
620 624 6.425114 GCAACTCGATTATGTAGTCCATGAAT 59.575 38.462 0.00 0.00 34.86 2.57
621 625 7.598869 GCAACTCGATTATGTAGTCCATGAATA 59.401 37.037 0.00 0.00 34.86 1.75
622 626 9.476202 CAACTCGATTATGTAGTCCATGAATAA 57.524 33.333 0.00 0.00 34.86 1.40
623 627 9.477484 AACTCGATTATGTAGTCCATGAATAAC 57.523 33.333 0.00 0.00 34.86 1.89
624 628 8.861086 ACTCGATTATGTAGTCCATGAATAACT 58.139 33.333 0.00 0.00 34.86 2.24
627 631 9.077674 CGATTATGTAGTCCATGAATAACTAGC 57.922 37.037 0.00 0.00 34.86 3.42
630 634 7.847711 ATGTAGTCCATGAATAACTAGCTCT 57.152 36.000 0.00 0.00 30.69 4.09
631 635 7.661536 TGTAGTCCATGAATAACTAGCTCTT 57.338 36.000 0.00 0.00 0.00 2.85
632 636 8.762481 TGTAGTCCATGAATAACTAGCTCTTA 57.238 34.615 0.00 0.00 0.00 2.10
633 637 8.851145 TGTAGTCCATGAATAACTAGCTCTTAG 58.149 37.037 0.00 0.00 35.39 2.18
634 638 6.754193 AGTCCATGAATAACTAGCTCTTAGC 58.246 40.000 0.00 0.00 42.84 3.09
635 639 6.325028 AGTCCATGAATAACTAGCTCTTAGCA 59.675 38.462 0.00 0.00 45.56 3.49
636 640 7.016072 AGTCCATGAATAACTAGCTCTTAGCAT 59.984 37.037 0.00 0.00 45.56 3.79
637 641 7.330700 GTCCATGAATAACTAGCTCTTAGCATC 59.669 40.741 0.00 0.00 45.56 3.91
638 642 7.234371 TCCATGAATAACTAGCTCTTAGCATCT 59.766 37.037 0.00 0.00 45.56 2.90
639 643 7.877097 CCATGAATAACTAGCTCTTAGCATCTT 59.123 37.037 0.00 0.00 45.56 2.40
640 644 9.920133 CATGAATAACTAGCTCTTAGCATCTTA 57.080 33.333 0.00 0.00 45.56 2.10
680 687 5.982890 AAGTCCCAAACCACATAAATCAG 57.017 39.130 0.00 0.00 0.00 2.90
683 690 5.476945 AGTCCCAAACCACATAAATCAGTTC 59.523 40.000 0.00 0.00 0.00 3.01
684 691 5.242838 GTCCCAAACCACATAAATCAGTTCA 59.757 40.000 0.00 0.00 0.00 3.18
693 700 9.295825 ACCACATAAATCAGTTCATCTAAACAA 57.704 29.630 0.00 0.00 0.00 2.83
704 711 7.536622 CAGTTCATCTAAACAAAGAAGCATGAC 59.463 37.037 0.00 0.00 0.00 3.06
709 716 6.054941 TCTAAACAAAGAAGCATGACTGACA 58.945 36.000 0.00 0.00 0.00 3.58
764 771 5.398169 TGTAAAATGCTCAAATAAGCCGTG 58.602 37.500 0.00 0.00 41.77 4.94
767 774 1.448985 TGCTCAAATAAGCCGTGGAC 58.551 50.000 0.00 0.00 41.77 4.02
773 780 4.138290 TCAAATAAGCCGTGGACAAAAGA 58.862 39.130 0.00 0.00 0.00 2.52
809 816 0.467290 GCAGTTGGTTTCCCCTCACA 60.467 55.000 0.00 0.00 0.00 3.58
817 824 2.509964 GGTTTCCCCTCACATCACCTAT 59.490 50.000 0.00 0.00 0.00 2.57
834 841 9.739276 CATCACCTATAAGAAGGCCATTATAAA 57.261 33.333 5.01 0.00 40.62 1.40
835 842 9.965902 ATCACCTATAAGAAGGCCATTATAAAG 57.034 33.333 5.01 7.76 40.62 1.85
837 844 9.442047 CACCTATAAGAAGGCCATTATAAAGAG 57.558 37.037 5.01 1.31 40.62 2.85
902 909 3.261580 CACAAAGTGTCGCCTCATCATA 58.738 45.455 0.00 0.00 0.00 2.15
910 917 0.532862 CGCCTCATCATACCACCCAC 60.533 60.000 0.00 0.00 0.00 4.61
922 930 1.694169 CACCCACATAGCCCCTCCT 60.694 63.158 0.00 0.00 0.00 3.69
1010 1027 2.157738 CTCTCAAGCCAACCAAGGAAG 58.842 52.381 0.00 0.00 0.00 3.46
1016 1033 1.152567 CCAACCAAGGAAGCCACCA 60.153 57.895 0.00 0.00 0.00 4.17
1069 1086 0.249197 TGAGAGATGCATCCGCTTCG 60.249 55.000 23.06 0.00 44.80 3.79
1099 1116 4.835891 CCTCCTCTACGGGGCGGT 62.836 72.222 0.00 0.00 0.00 5.68
1100 1117 3.217743 CTCCTCTACGGGGCGGTC 61.218 72.222 0.00 0.00 0.00 4.79
1146 1163 4.476410 CCTACTGCGCTGCGTCGA 62.476 66.667 24.04 7.12 0.00 4.20
1334 1351 3.753434 CTGTCCTCCTGCGACGCT 61.753 66.667 22.08 0.00 32.68 5.07
1724 1741 4.704833 TGCTCCAAGTGCCTCCGC 62.705 66.667 0.00 0.00 0.00 5.54
1778 1811 0.671251 CTGCAACAAGCCCCGTAAAA 59.329 50.000 0.00 0.00 44.83 1.52
1780 1813 1.689273 TGCAACAAGCCCCGTAAAAAT 59.311 42.857 0.00 0.00 44.83 1.82
1792 1825 7.853299 AGCCCCGTAAAAATAACCATTTTAAT 58.147 30.769 0.00 0.00 42.29 1.40
1809 1842 9.421806 CCATTTTAATTGTCAATTACTGCTTCA 57.578 29.630 16.03 0.00 33.32 3.02
1829 1862 5.233957 TCAGTCGGCAACATTTATCAATG 57.766 39.130 0.00 0.00 44.90 2.82
1868 1901 2.093816 TCAGCTCGCAATCTTGATCTGT 60.094 45.455 0.00 0.00 0.00 3.41
1873 1906 4.201891 GCTCGCAATCTTGATCTGTGAAAT 60.202 41.667 0.00 0.00 0.00 2.17
1936 1970 2.869636 GCACACTCCCTGAGAACTTGAG 60.870 54.545 0.00 0.00 33.32 3.02
1937 1971 2.366916 CACACTCCCTGAGAACTTGAGT 59.633 50.000 0.00 0.00 36.77 3.41
1938 1972 3.574396 CACACTCCCTGAGAACTTGAGTA 59.426 47.826 0.00 0.00 34.68 2.59
1953 1987 9.376075 AGAACTTGAGTAGTATTTCATCACATG 57.624 33.333 0.00 0.00 35.54 3.21
2160 2203 5.233902 CACGAAATGATCAGATCTCAAGTCC 59.766 44.000 11.83 0.00 0.00 3.85
2161 2204 4.443725 CGAAATGATCAGATCTCAAGTCCG 59.556 45.833 11.83 3.15 0.00 4.79
2162 2205 4.333913 AATGATCAGATCTCAAGTCCGG 57.666 45.455 11.83 0.00 0.00 5.14
2163 2206 2.034878 TGATCAGATCTCAAGTCCGGG 58.965 52.381 11.83 0.00 0.00 5.73
2164 2207 0.755686 ATCAGATCTCAAGTCCGGGC 59.244 55.000 0.00 0.00 0.00 6.13
2165 2208 1.144936 CAGATCTCAAGTCCGGGCC 59.855 63.158 0.08 0.00 0.00 5.80
2166 2209 1.002274 AGATCTCAAGTCCGGGCCT 59.998 57.895 0.08 0.00 0.00 5.19
2167 2210 1.144936 GATCTCAAGTCCGGGCCTG 59.855 63.158 0.08 3.88 0.00 4.85
2168 2211 1.613630 ATCTCAAGTCCGGGCCTGT 60.614 57.895 11.58 0.00 0.00 4.00
2169 2212 1.617947 ATCTCAAGTCCGGGCCTGTC 61.618 60.000 11.58 3.21 0.00 3.51
2170 2213 3.649277 CTCAAGTCCGGGCCTGTCG 62.649 68.421 11.58 1.15 0.00 4.35
2276 2319 0.992802 GTCCTTTCAGCGCTAAGACG 59.007 55.000 19.27 3.42 0.00 4.18
2297 2340 4.466370 ACGGAATCATTAGTTCTCTGGACA 59.534 41.667 0.00 0.00 0.00 4.02
2317 2360 3.509575 ACAAAGTAGGAGAGCAGAGTGAG 59.490 47.826 0.00 0.00 0.00 3.51
2362 2409 1.002576 TGCATTTCACGTGTGCAAGAG 60.003 47.619 24.77 10.98 44.99 2.85
2396 2443 4.142881 CGACTGATGAGAGTACGTCTTGAA 60.143 45.833 0.00 0.00 34.71 2.69
2409 2456 5.536554 ACGTCTTGAATGTTGCAGATAAG 57.463 39.130 0.00 0.00 0.00 1.73
2413 2460 3.370840 TGAATGTTGCAGATAAGGGCT 57.629 42.857 0.00 0.00 0.00 5.19
2837 2889 1.370778 CGGTGCGTTACGTGTGAGA 60.371 57.895 6.63 0.00 0.00 3.27
2849 2991 1.350193 GTGTGAGATAGTGGTGCACG 58.650 55.000 11.45 0.00 39.64 5.34
2853 2995 0.807667 GAGATAGTGGTGCACGGCAG 60.808 60.000 11.45 0.00 40.08 4.85
2866 3008 0.327924 ACGGCAGATTCCATGGTTCA 59.672 50.000 12.58 0.00 0.00 3.18
2874 3016 6.491403 GGCAGATTCCATGGTTCATTAATACT 59.509 38.462 12.58 0.65 0.00 2.12
2917 3075 1.863454 GTGATCGCGATTCAGCTGATT 59.137 47.619 24.55 14.60 33.23 2.57
2929 3087 4.767578 TCAGCTGATTAGGAGCAAGAAT 57.232 40.909 13.74 0.00 39.05 2.40
2931 3089 3.493877 CAGCTGATTAGGAGCAAGAATCG 59.506 47.826 8.42 0.00 39.05 3.34
2932 3090 2.805099 GCTGATTAGGAGCAAGAATCGG 59.195 50.000 0.00 0.00 38.47 4.18
2941 3099 0.804989 GCAAGAATCGGACCAGGTTG 59.195 55.000 0.00 0.00 0.00 3.77
2968 3127 4.489679 AACTCAGAAAGAAAATGGCGTC 57.510 40.909 0.00 0.00 0.00 5.19
3026 3648 2.159114 ACCAACCAAACATGTTGTGCTC 60.159 45.455 12.82 0.00 41.13 4.26
3027 3649 2.101249 CCAACCAAACATGTTGTGCTCT 59.899 45.455 12.82 0.00 41.13 4.09
3028 3650 3.374745 CAACCAAACATGTTGTGCTCTC 58.625 45.455 12.82 0.00 38.58 3.20
3030 3652 2.233271 CCAAACATGTTGTGCTCTCCT 58.767 47.619 12.82 0.00 0.00 3.69
3031 3653 2.624838 CCAAACATGTTGTGCTCTCCTT 59.375 45.455 12.82 0.00 0.00 3.36
3032 3654 3.820467 CCAAACATGTTGTGCTCTCCTTA 59.180 43.478 12.82 0.00 0.00 2.69
3034 3656 4.357918 AACATGTTGTGCTCTCCTTAGT 57.642 40.909 11.07 0.00 0.00 2.24
3043 3665 2.040939 GCTCTCCTTAGTCCTTACCCC 58.959 57.143 0.00 0.00 0.00 4.95
3050 3672 5.167921 TCCTTAGTCCTTACCCCTTTCTTT 58.832 41.667 0.00 0.00 0.00 2.52
3056 3678 5.609708 AGTCCTTACCCCTTTCTTTAGAACA 59.390 40.000 0.00 0.00 33.13 3.18
3082 3705 6.044682 CCCTTCTTGGCATTTCATTCATTAC 58.955 40.000 0.00 0.00 0.00 1.89
3099 3722 0.176910 TACTCGGCGGCATCAAATCA 59.823 50.000 10.53 0.00 0.00 2.57
3116 3739 3.802948 ATCAGATCGTACAGGGTCAAC 57.197 47.619 0.00 0.00 0.00 3.18
3119 3742 2.993899 CAGATCGTACAGGGTCAACAAC 59.006 50.000 0.00 0.00 0.00 3.32
3122 3745 3.263489 TCGTACAGGGTCAACAACAAA 57.737 42.857 0.00 0.00 0.00 2.83
3147 3770 7.830099 AAAAGGAATCACTCAATCTGTTTCT 57.170 32.000 0.00 0.00 0.00 2.52
3148 3771 7.830099 AAAGGAATCACTCAATCTGTTTCTT 57.170 32.000 0.00 0.00 0.00 2.52
3149 3772 7.830099 AAGGAATCACTCAATCTGTTTCTTT 57.170 32.000 0.00 0.00 0.00 2.52
3150 3773 7.830099 AGGAATCACTCAATCTGTTTCTTTT 57.170 32.000 0.00 0.00 0.00 2.27
3151 3774 8.242729 AGGAATCACTCAATCTGTTTCTTTTT 57.757 30.769 0.00 0.00 0.00 1.94
3291 4065 4.916183 TGTTCATGTGTTATGGATGTGGA 58.084 39.130 0.00 0.00 0.00 4.02
3298 4075 9.199645 TCATGTGTTATGGATGTGGATATTTTT 57.800 29.630 0.00 0.00 0.00 1.94
3322 4099 8.825667 TTAAGATAAAATTGGTCAAACCTTGC 57.174 30.769 0.00 0.00 39.58 4.01
3386 4165 2.417379 CGGAGGGAGTACATCACAACAG 60.417 54.545 0.00 0.00 31.63 3.16
3387 4166 2.567615 GGAGGGAGTACATCACAACAGT 59.432 50.000 0.00 0.00 31.63 3.55
3396 4175 3.211045 ACATCACAACAGTTTTAGCCGT 58.789 40.909 0.00 0.00 0.00 5.68
3400 4179 1.951602 ACAACAGTTTTAGCCGTTCCC 59.048 47.619 0.00 0.00 0.00 3.97
3401 4180 2.227194 CAACAGTTTTAGCCGTTCCCT 58.773 47.619 0.00 0.00 0.00 4.20
3404 4183 4.296621 ACAGTTTTAGCCGTTCCCTTAT 57.703 40.909 0.00 0.00 0.00 1.73
3460 4240 6.324254 CCCCTATAATTTAGAGGAGGATACGG 59.676 46.154 16.93 5.54 39.53 4.02
3462 4242 6.608002 CCTATAATTTAGAGGAGGATACGGCT 59.392 42.308 10.99 0.00 39.53 5.52
3469 4249 4.020543 AGAGGAGGATACGGCTGAATATC 58.979 47.826 0.00 0.00 46.39 1.63
3473 4253 5.308237 AGGAGGATACGGCTGAATATCTTTT 59.692 40.000 0.00 0.00 46.39 2.27
3474 4254 6.497259 AGGAGGATACGGCTGAATATCTTTTA 59.503 38.462 0.00 0.00 46.39 1.52
3478 4258 6.311690 GGATACGGCTGAATATCTTTTAGAGC 59.688 42.308 0.00 0.00 0.00 4.09
3483 4263 5.472820 GGCTGAATATCTTTTAGAGCAGCAT 59.527 40.000 0.00 0.00 46.70 3.79
3491 4271 4.864806 TCTTTTAGAGCAGCATAAGTGACG 59.135 41.667 0.00 0.00 0.00 4.35
3495 4275 2.996621 AGAGCAGCATAAGTGACGTTTC 59.003 45.455 0.00 0.00 0.00 2.78
3603 4383 9.800433 TTTACACACATATTAAATCCAAGCATG 57.200 29.630 0.00 0.00 0.00 4.06
3623 4407 9.716507 AAGCATGATAATTAACGTACAATTCAC 57.283 29.630 10.39 7.63 0.00 3.18
3700 4484 7.230712 ACGAAAGGGTTCAAATGAAGTAAAGAT 59.769 33.333 0.00 0.00 34.27 2.40
3753 4537 1.442526 GATGCCAGGGATGCTCAACG 61.443 60.000 0.00 0.00 0.00 4.10
3761 4545 2.141517 GGGATGCTCAACGAGATCATG 58.858 52.381 0.00 0.00 33.44 3.07
3804 4871 3.645884 TCGGTTCTCTTGTTACCTTTCG 58.354 45.455 0.00 0.00 0.00 3.46
3806 4873 3.072211 GGTTCTCTTGTTACCTTTCGGG 58.928 50.000 0.00 0.00 41.89 5.14
3810 4877 2.235536 CTTGTTACCTTTCGGGCGCG 62.236 60.000 18.21 18.21 39.10 6.86
3848 4915 0.615544 ACAAATGTGGCCCATGGAGG 60.616 55.000 15.22 0.00 32.82 4.30
3899 4970 2.596346 TCACAACATGGTTGCAAGGAT 58.404 42.857 0.00 0.00 0.00 3.24
3933 5004 1.154093 CAAGCCTAGCGAACGACGA 60.154 57.895 0.00 0.00 45.77 4.20
3944 5015 2.244436 GAACGACGACGACGGGATCA 62.244 60.000 22.36 0.00 44.46 2.92
3982 5053 0.824109 TGGAGCTCGATTCCAACGAT 59.176 50.000 14.49 0.00 41.61 3.73
3983 5054 1.212616 GGAGCTCGATTCCAACGATG 58.787 55.000 7.83 0.00 39.02 3.84
3992 5063 2.895372 CCAACGATGGTAGCGGCC 60.895 66.667 3.02 0.00 42.18 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.619801 ACATTGACTAACCTGACAGAAAAC 57.380 37.500 3.32 0.00 0.00 2.43
40 41 2.575694 AATGACACACAAAAGCGCAA 57.424 40.000 11.47 0.00 0.00 4.85
57 58 7.230108 TCTCTTGAATGACAGCTTGAAGAAAAT 59.770 33.333 0.00 0.00 0.00 1.82
61 62 5.219343 TCTCTTGAATGACAGCTTGAAGA 57.781 39.130 0.00 0.00 0.00 2.87
79 80 0.751643 GCCTCGCTCCTCTCTTCTCT 60.752 60.000 0.00 0.00 0.00 3.10
101 102 1.063341 CCTCCTCCTGAGTCTGGATCA 60.063 57.143 18.17 7.82 39.65 2.92
346 350 4.031611 AGGAAGTACACAGGAAGGGATAC 58.968 47.826 0.00 0.00 0.00 2.24
391 395 5.463724 GTCTTTACTGCTGGTACATAGATGC 59.536 44.000 0.00 0.00 38.20 3.91
405 409 2.808543 CAGACACCCAAGTCTTTACTGC 59.191 50.000 0.00 0.00 46.26 4.40
406 410 4.336889 TCAGACACCCAAGTCTTTACTG 57.663 45.455 0.00 0.00 46.26 2.74
491 495 5.625150 ACAGTGCCTCTTGATTTTAACTCT 58.375 37.500 0.00 0.00 0.00 3.24
492 496 5.948992 ACAGTGCCTCTTGATTTTAACTC 57.051 39.130 0.00 0.00 0.00 3.01
493 497 5.412904 GCTACAGTGCCTCTTGATTTTAACT 59.587 40.000 0.00 0.00 0.00 2.24
494 498 5.412904 AGCTACAGTGCCTCTTGATTTTAAC 59.587 40.000 0.00 0.00 0.00 2.01
495 499 5.560724 AGCTACAGTGCCTCTTGATTTTAA 58.439 37.500 0.00 0.00 0.00 1.52
496 500 5.165961 AGCTACAGTGCCTCTTGATTTTA 57.834 39.130 0.00 0.00 0.00 1.52
497 501 4.006319 GAGCTACAGTGCCTCTTGATTTT 58.994 43.478 0.00 0.00 0.00 1.82
498 502 3.604582 GAGCTACAGTGCCTCTTGATTT 58.395 45.455 0.00 0.00 0.00 2.17
499 503 2.093235 GGAGCTACAGTGCCTCTTGATT 60.093 50.000 0.00 0.00 0.00 2.57
500 504 1.484240 GGAGCTACAGTGCCTCTTGAT 59.516 52.381 0.00 0.00 0.00 2.57
501 505 0.898320 GGAGCTACAGTGCCTCTTGA 59.102 55.000 0.00 0.00 0.00 3.02
502 506 0.901124 AGGAGCTACAGTGCCTCTTG 59.099 55.000 0.00 0.00 0.00 3.02
503 507 1.190643 GAGGAGCTACAGTGCCTCTT 58.809 55.000 9.16 0.00 42.81 2.85
504 508 0.040351 TGAGGAGCTACAGTGCCTCT 59.960 55.000 15.68 0.00 45.58 3.69
505 509 0.898320 TTGAGGAGCTACAGTGCCTC 59.102 55.000 9.44 9.44 45.59 4.70
506 510 1.577736 ATTGAGGAGCTACAGTGCCT 58.422 50.000 0.00 0.00 0.00 4.75
507 511 2.168521 TGTATTGAGGAGCTACAGTGCC 59.831 50.000 0.00 0.00 0.00 5.01
508 512 3.526931 TGTATTGAGGAGCTACAGTGC 57.473 47.619 0.00 0.00 0.00 4.40
509 513 4.081420 ACCTTGTATTGAGGAGCTACAGTG 60.081 45.833 0.00 0.00 37.72 3.66
510 514 4.081420 CACCTTGTATTGAGGAGCTACAGT 60.081 45.833 0.00 0.00 37.72 3.55
511 515 4.437239 CACCTTGTATTGAGGAGCTACAG 58.563 47.826 0.00 0.00 37.72 2.74
512 516 3.197766 CCACCTTGTATTGAGGAGCTACA 59.802 47.826 0.00 0.00 37.72 2.74
513 517 3.451178 TCCACCTTGTATTGAGGAGCTAC 59.549 47.826 0.00 0.00 37.72 3.58
514 518 3.451178 GTCCACCTTGTATTGAGGAGCTA 59.549 47.826 0.00 0.00 37.72 3.32
515 519 2.237392 GTCCACCTTGTATTGAGGAGCT 59.763 50.000 0.00 0.00 37.72 4.09
516 520 2.633488 GTCCACCTTGTATTGAGGAGC 58.367 52.381 0.00 0.00 37.72 4.70
517 521 2.840651 AGGTCCACCTTGTATTGAGGAG 59.159 50.000 0.00 0.00 46.09 3.69
518 522 2.915869 AGGTCCACCTTGTATTGAGGA 58.084 47.619 0.00 0.00 46.09 3.71
530 534 1.192146 TGGCTACACAGAGGTCCACC 61.192 60.000 0.00 0.00 0.00 4.61
531 535 0.037232 GTGGCTACACAGAGGTCCAC 60.037 60.000 0.00 0.00 46.90 4.02
532 536 2.362242 GTGGCTACACAGAGGTCCA 58.638 57.895 0.00 0.00 46.90 4.02
541 545 1.569493 CACTGTTGCGTGGCTACAC 59.431 57.895 0.00 0.00 39.07 2.90
542 546 2.250939 GCACTGTTGCGTGGCTACA 61.251 57.895 0.00 4.93 41.31 2.74
543 547 2.556287 GCACTGTTGCGTGGCTAC 59.444 61.111 0.00 0.00 39.50 3.58
551 555 0.514691 GCTGAGTGTAGCACTGTTGC 59.485 55.000 6.50 4.64 45.44 4.17
552 556 2.064762 GAGCTGAGTGTAGCACTGTTG 58.935 52.381 6.50 0.00 45.44 3.33
553 557 1.336332 CGAGCTGAGTGTAGCACTGTT 60.336 52.381 6.50 0.00 45.44 3.16
554 558 0.242286 CGAGCTGAGTGTAGCACTGT 59.758 55.000 6.50 0.00 45.44 3.55
555 559 0.457509 CCGAGCTGAGTGTAGCACTG 60.458 60.000 6.50 0.00 45.44 3.66
557 561 1.807573 GCCGAGCTGAGTGTAGCAC 60.808 63.158 0.00 0.00 46.07 4.40
558 562 1.979155 AGCCGAGCTGAGTGTAGCA 60.979 57.895 0.00 0.00 46.07 3.49
559 563 2.888863 AGCCGAGCTGAGTGTAGC 59.111 61.111 0.00 0.00 44.01 3.58
568 572 2.437359 GGCATGTTCAGCCGAGCT 60.437 61.111 0.00 0.00 43.15 4.09
574 578 0.097674 GATCGTGTGGCATGTTCAGC 59.902 55.000 0.00 0.00 0.00 4.26
575 579 1.395954 CAGATCGTGTGGCATGTTCAG 59.604 52.381 0.00 0.00 0.00 3.02
576 580 1.441738 CAGATCGTGTGGCATGTTCA 58.558 50.000 0.00 0.00 0.00 3.18
577 581 0.097674 GCAGATCGTGTGGCATGTTC 59.902 55.000 0.00 0.00 0.00 3.18
578 582 0.606130 TGCAGATCGTGTGGCATGTT 60.606 50.000 0.00 0.00 0.00 2.71
579 583 0.606130 TTGCAGATCGTGTGGCATGT 60.606 50.000 0.00 0.00 35.98 3.21
580 584 0.179181 GTTGCAGATCGTGTGGCATG 60.179 55.000 0.00 0.00 35.98 4.06
581 585 0.321919 AGTTGCAGATCGTGTGGCAT 60.322 50.000 0.00 0.00 35.98 4.40
582 586 0.950555 GAGTTGCAGATCGTGTGGCA 60.951 55.000 0.00 0.00 0.00 4.92
583 587 1.790387 GAGTTGCAGATCGTGTGGC 59.210 57.895 0.00 0.00 0.00 5.01
584 588 0.388520 TCGAGTTGCAGATCGTGTGG 60.389 55.000 18.47 0.00 39.86 4.17
585 589 1.633561 ATCGAGTTGCAGATCGTGTG 58.366 50.000 18.47 0.00 39.86 3.82
586 590 2.370281 AATCGAGTTGCAGATCGTGT 57.630 45.000 18.47 9.05 39.86 4.49
587 591 3.798878 ACATAATCGAGTTGCAGATCGTG 59.201 43.478 18.47 13.16 39.86 4.35
588 592 4.046938 ACATAATCGAGTTGCAGATCGT 57.953 40.909 18.47 6.72 39.86 3.73
589 593 5.215903 ACTACATAATCGAGTTGCAGATCG 58.784 41.667 14.48 14.48 40.26 3.69
590 594 5.631512 GGACTACATAATCGAGTTGCAGATC 59.368 44.000 0.00 0.00 0.00 2.75
591 595 5.069119 TGGACTACATAATCGAGTTGCAGAT 59.931 40.000 0.00 0.00 0.00 2.90
592 596 4.401202 TGGACTACATAATCGAGTTGCAGA 59.599 41.667 0.00 0.00 0.00 4.26
593 597 4.682787 TGGACTACATAATCGAGTTGCAG 58.317 43.478 0.00 0.00 0.00 4.41
594 598 4.729227 TGGACTACATAATCGAGTTGCA 57.271 40.909 0.00 0.00 0.00 4.08
595 599 5.289595 TCATGGACTACATAATCGAGTTGC 58.710 41.667 0.00 0.00 37.84 4.17
596 600 7.953158 ATTCATGGACTACATAATCGAGTTG 57.047 36.000 0.00 0.00 37.84 3.16
597 601 9.477484 GTTATTCATGGACTACATAATCGAGTT 57.523 33.333 0.00 0.00 37.84 3.01
598 602 8.861086 AGTTATTCATGGACTACATAATCGAGT 58.139 33.333 0.00 0.00 37.84 4.18
601 605 9.077674 GCTAGTTATTCATGGACTACATAATCG 57.922 37.037 0.00 0.00 37.84 3.34
604 608 9.368416 AGAGCTAGTTATTCATGGACTACATAA 57.632 33.333 0.00 0.00 37.84 1.90
605 609 8.941995 AGAGCTAGTTATTCATGGACTACATA 57.058 34.615 0.00 0.00 37.84 2.29
606 610 7.847711 AGAGCTAGTTATTCATGGACTACAT 57.152 36.000 0.00 0.00 41.57 2.29
607 611 7.661536 AAGAGCTAGTTATTCATGGACTACA 57.338 36.000 0.00 0.00 0.00 2.74
608 612 7.810759 GCTAAGAGCTAGTTATTCATGGACTAC 59.189 40.741 0.00 0.00 38.45 2.73
609 613 7.505923 TGCTAAGAGCTAGTTATTCATGGACTA 59.494 37.037 0.00 0.00 42.97 2.59
610 614 6.325028 TGCTAAGAGCTAGTTATTCATGGACT 59.675 38.462 0.00 0.00 42.97 3.85
611 615 6.516718 TGCTAAGAGCTAGTTATTCATGGAC 58.483 40.000 0.00 0.00 42.97 4.02
612 616 6.731292 TGCTAAGAGCTAGTTATTCATGGA 57.269 37.500 0.00 0.00 42.97 3.41
613 617 7.385267 AGATGCTAAGAGCTAGTTATTCATGG 58.615 38.462 0.00 0.00 42.97 3.66
614 618 8.830201 AAGATGCTAAGAGCTAGTTATTCATG 57.170 34.615 0.00 0.00 42.97 3.07
643 647 9.136323 GGTTTGGGACTTTAGATGATATCAATT 57.864 33.333 9.99 3.61 0.00 2.32
644 648 8.281531 TGGTTTGGGACTTTAGATGATATCAAT 58.718 33.333 9.99 4.30 0.00 2.57
645 649 7.556275 GTGGTTTGGGACTTTAGATGATATCAA 59.444 37.037 9.99 0.00 0.00 2.57
646 650 7.054124 GTGGTTTGGGACTTTAGATGATATCA 58.946 38.462 8.10 8.10 0.00 2.15
647 651 7.054124 TGTGGTTTGGGACTTTAGATGATATC 58.946 38.462 0.00 0.00 0.00 1.63
648 652 6.969043 TGTGGTTTGGGACTTTAGATGATAT 58.031 36.000 0.00 0.00 0.00 1.63
649 653 6.381498 TGTGGTTTGGGACTTTAGATGATA 57.619 37.500 0.00 0.00 0.00 2.15
650 654 5.255397 TGTGGTTTGGGACTTTAGATGAT 57.745 39.130 0.00 0.00 0.00 2.45
651 655 4.715534 TGTGGTTTGGGACTTTAGATGA 57.284 40.909 0.00 0.00 0.00 2.92
652 656 7.461182 TTTATGTGGTTTGGGACTTTAGATG 57.539 36.000 0.00 0.00 0.00 2.90
653 657 7.893302 TGATTTATGTGGTTTGGGACTTTAGAT 59.107 33.333 0.00 0.00 0.00 1.98
654 658 7.235079 TGATTTATGTGGTTTGGGACTTTAGA 58.765 34.615 0.00 0.00 0.00 2.10
655 659 7.176690 ACTGATTTATGTGGTTTGGGACTTTAG 59.823 37.037 0.00 0.00 0.00 1.85
656 660 7.007723 ACTGATTTATGTGGTTTGGGACTTTA 58.992 34.615 0.00 0.00 0.00 1.85
657 661 5.838521 ACTGATTTATGTGGTTTGGGACTTT 59.161 36.000 0.00 0.00 0.00 2.66
658 662 5.393866 ACTGATTTATGTGGTTTGGGACTT 58.606 37.500 0.00 0.00 0.00 3.01
659 663 4.998051 ACTGATTTATGTGGTTTGGGACT 58.002 39.130 0.00 0.00 0.00 3.85
660 664 5.242838 TGAACTGATTTATGTGGTTTGGGAC 59.757 40.000 0.00 0.00 0.00 4.46
661 665 5.389520 TGAACTGATTTATGTGGTTTGGGA 58.610 37.500 0.00 0.00 0.00 4.37
662 666 5.720371 TGAACTGATTTATGTGGTTTGGG 57.280 39.130 0.00 0.00 0.00 4.12
680 687 7.536622 CAGTCATGCTTCTTTGTTTAGATGAAC 59.463 37.037 0.00 0.00 0.00 3.18
683 690 7.020010 GTCAGTCATGCTTCTTTGTTTAGATG 58.980 38.462 0.00 0.00 0.00 2.90
684 691 6.712095 TGTCAGTCATGCTTCTTTGTTTAGAT 59.288 34.615 0.00 0.00 0.00 1.98
691 698 5.117355 ACAATGTCAGTCATGCTTCTTTG 57.883 39.130 0.00 3.07 36.81 2.77
693 700 5.300034 TCAAACAATGTCAGTCATGCTTCTT 59.700 36.000 0.00 0.00 36.81 2.52
694 701 4.823442 TCAAACAATGTCAGTCATGCTTCT 59.177 37.500 0.00 0.00 36.81 2.85
695 702 4.913924 GTCAAACAATGTCAGTCATGCTTC 59.086 41.667 0.00 0.00 36.81 3.86
764 771 2.774439 TCGCAAAGCTTCTTTTGTCC 57.226 45.000 0.00 0.00 39.62 4.02
767 774 2.219445 GCCTTTCGCAAAGCTTCTTTTG 59.781 45.455 0.00 0.00 40.25 2.44
773 780 1.006922 GCAGCCTTTCGCAAAGCTT 60.007 52.632 0.00 0.00 41.38 3.74
809 816 9.965902 CTTTATAATGGCCTTCTTATAGGTGAT 57.034 33.333 3.32 0.00 37.63 3.06
817 824 6.260700 TGGCTCTTTATAATGGCCTTCTTA 57.739 37.500 21.01 0.00 42.84 2.10
834 841 0.778083 ATGCATGATGGGATGGCTCT 59.222 50.000 0.00 0.00 0.00 4.09
835 842 1.174783 GATGCATGATGGGATGGCTC 58.825 55.000 2.46 0.00 0.00 4.70
837 844 0.251653 AGGATGCATGATGGGATGGC 60.252 55.000 2.46 0.00 0.00 4.40
888 895 0.464036 GGTGGTATGATGAGGCGACA 59.536 55.000 0.00 0.00 0.00 4.35
890 897 0.689412 TGGGTGGTATGATGAGGCGA 60.689 55.000 0.00 0.00 0.00 5.54
892 899 0.546122 TGTGGGTGGTATGATGAGGC 59.454 55.000 0.00 0.00 0.00 4.70
902 909 2.001269 GAGGGGCTATGTGGGTGGT 61.001 63.158 0.00 0.00 0.00 4.16
910 917 1.006043 TCGGAGATAGGAGGGGCTATG 59.994 57.143 0.00 0.00 0.00 2.23
1069 1086 3.223589 GGAGGAGGAGAGAGCGGC 61.224 72.222 0.00 0.00 0.00 6.53
1109 1126 2.720758 CGGCGAGAACAGCAAGACG 61.721 63.158 0.00 0.00 36.08 4.18
1110 1127 2.383527 CCGGCGAGAACAGCAAGAC 61.384 63.158 9.30 0.00 36.08 3.01
1119 1136 4.143333 GCAGTAGGCCGGCGAGAA 62.143 66.667 22.54 1.89 36.11 2.87
1131 1148 2.812542 AATGTCGACGCAGCGCAGTA 62.813 55.000 16.61 3.71 0.00 2.74
1139 1156 3.657448 ATCCGGCAATGTCGACGCA 62.657 57.895 9.51 0.00 29.41 5.24
1142 1159 2.237751 CGGATCCGGCAATGTCGAC 61.238 63.158 26.95 9.11 35.56 4.20
1724 1741 0.108615 ATCTCACCGTGGAAAGAGCG 60.109 55.000 0.00 0.00 0.00 5.03
1792 1825 3.745975 CCGACTGAAGCAGTAATTGACAA 59.254 43.478 0.00 0.00 45.44 3.18
1809 1842 4.269183 TCCATTGATAAATGTTGCCGACT 58.731 39.130 2.00 0.00 0.00 4.18
1829 1862 4.616953 GCTGAGAGCTAACTAGTGAATCC 58.383 47.826 0.00 0.00 38.45 3.01
1853 1886 5.263948 CAGATTTCACAGATCAAGATTGCG 58.736 41.667 0.00 0.00 0.00 4.85
1890 1923 1.864862 CTTCACTTCAGCACTGCCG 59.135 57.895 0.00 0.00 0.00 5.69
1995 2037 7.486647 TGTCTAAAATCTTATCTGACCGTACC 58.513 38.462 0.00 0.00 0.00 3.34
2173 2216 3.714078 ATTCTCCAGGCCCGCCCTA 62.714 63.158 0.00 0.00 44.09 3.53
2175 2218 4.883354 CATTCTCCAGGCCCGCCC 62.883 72.222 0.00 0.00 36.58 6.13
2176 2219 2.631012 AATCATTCTCCAGGCCCGCC 62.631 60.000 0.00 0.00 0.00 6.13
2177 2220 1.152881 AATCATTCTCCAGGCCCGC 60.153 57.895 0.00 0.00 0.00 6.13
2276 2319 6.881602 ACTTTGTCCAGAGAACTAATGATTCC 59.118 38.462 0.00 0.00 0.00 3.01
2297 2340 2.495669 GCTCACTCTGCTCTCCTACTTT 59.504 50.000 0.00 0.00 0.00 2.66
2336 2379 2.605338 GCACACGTGAAATGCAAGATGT 60.605 45.455 25.01 0.00 39.23 3.06
2344 2387 2.545526 ACTCTCTTGCACACGTGAAATG 59.454 45.455 25.01 11.66 0.00 2.32
2362 2409 3.124806 TCTCATCAGTCGTCGTGTAACTC 59.875 47.826 0.00 0.00 31.75 3.01
2396 2443 1.565759 TCCAGCCCTTATCTGCAACAT 59.434 47.619 0.00 0.00 0.00 2.71
2786 2837 7.444792 ACAAGTGGACAACCGTATAACAAATTA 59.555 33.333 0.00 0.00 39.42 1.40
2833 2885 1.218047 GCCGTGCACCACTATCTCA 59.782 57.895 12.15 0.00 31.34 3.27
2837 2889 0.253044 AATCTGCCGTGCACCACTAT 59.747 50.000 12.15 0.00 33.79 2.12
2849 2991 5.796424 ATTAATGAACCATGGAATCTGCC 57.204 39.130 21.47 0.00 0.00 4.85
2874 3016 5.822519 ACTGCAAAAGTGTTCAGAGTTCATA 59.177 36.000 0.00 0.00 37.88 2.15
2889 3040 2.159667 TGAATCGCGATCACTGCAAAAG 60.160 45.455 23.92 0.00 0.00 2.27
2890 3041 1.803555 TGAATCGCGATCACTGCAAAA 59.196 42.857 23.92 0.22 0.00 2.44
2894 3052 1.150567 AGCTGAATCGCGATCACTGC 61.151 55.000 30.54 30.54 34.40 4.40
2903 3061 1.797635 GCTCCTAATCAGCTGAATCGC 59.202 52.381 22.50 13.37 33.75 4.58
2917 3075 1.757118 CTGGTCCGATTCTTGCTCCTA 59.243 52.381 0.00 0.00 0.00 2.94
2932 3090 2.618709 CTGAGTTTTGGACAACCTGGTC 59.381 50.000 0.00 0.00 37.04 4.02
2941 3099 5.463392 GCCATTTTCTTTCTGAGTTTTGGAC 59.537 40.000 0.00 0.00 0.00 4.02
2968 3127 2.346244 AGAAATGCATTTTCATTGCGCG 59.654 40.909 24.81 0.00 45.19 6.86
2977 3136 7.864379 CCAAATCGAGCTATAGAAATGCATTTT 59.136 33.333 24.81 16.47 0.00 1.82
2980 3139 5.413833 CCCAAATCGAGCTATAGAAATGCAT 59.586 40.000 3.21 0.00 0.00 3.96
3026 3648 4.363573 AGAAAGGGGTAAGGACTAAGGAG 58.636 47.826 0.00 0.00 0.00 3.69
3027 3649 4.431158 AGAAAGGGGTAAGGACTAAGGA 57.569 45.455 0.00 0.00 0.00 3.36
3028 3650 5.516059 AAAGAAAGGGGTAAGGACTAAGG 57.484 43.478 0.00 0.00 0.00 2.69
3030 3652 7.293062 TGTTCTAAAGAAAGGGGTAAGGACTAA 59.707 37.037 0.00 0.00 35.58 2.24
3031 3653 6.788957 TGTTCTAAAGAAAGGGGTAAGGACTA 59.211 38.462 0.00 0.00 35.58 2.59
3032 3654 5.609708 TGTTCTAAAGAAAGGGGTAAGGACT 59.390 40.000 0.00 0.00 35.58 3.85
3034 3656 5.514310 GCTGTTCTAAAGAAAGGGGTAAGGA 60.514 44.000 0.00 0.00 35.58 3.36
3043 3665 5.048434 CCAAGAAGGGCTGTTCTAAAGAAAG 60.048 44.000 3.56 0.00 35.65 2.62
3069 3692 2.290641 GCCGCCGAGTAATGAATGAAAT 59.709 45.455 0.00 0.00 0.00 2.17
3082 3705 0.811219 TCTGATTTGATGCCGCCGAG 60.811 55.000 0.00 0.00 0.00 4.63
3099 3722 2.631062 TGTTGTTGACCCTGTACGATCT 59.369 45.455 0.00 0.00 0.00 2.75
3122 3745 8.242729 AGAAACAGATTGAGTGATTCCTTTTT 57.757 30.769 0.00 0.00 29.35 1.94
3268 4042 5.320277 TCCACATCCATAACACATGAACAA 58.680 37.500 0.00 0.00 0.00 2.83
3270 4044 7.750229 ATATCCACATCCATAACACATGAAC 57.250 36.000 0.00 0.00 0.00 3.18
3272 4046 8.765488 AAAATATCCACATCCATAACACATGA 57.235 30.769 0.00 0.00 0.00 3.07
3298 4075 8.189119 AGCAAGGTTTGACCAATTTTATCTTA 57.811 30.769 0.00 0.00 41.95 2.10
3307 4084 6.825610 TCAAATTAAGCAAGGTTTGACCAAT 58.174 32.000 0.00 0.00 41.95 3.16
3309 4086 5.860941 TCAAATTAAGCAAGGTTTGACCA 57.139 34.783 0.00 0.00 41.95 4.02
3338 4115 7.624360 TTTTTACTCCGCATATCAAACTCAT 57.376 32.000 0.00 0.00 0.00 2.90
3363 4140 1.933021 TGTGATGTACTCCCTCCGTT 58.067 50.000 0.00 0.00 0.00 4.44
3365 4142 1.548719 TGTTGTGATGTACTCCCTCCG 59.451 52.381 0.00 0.00 0.00 4.63
3366 4143 2.567615 ACTGTTGTGATGTACTCCCTCC 59.432 50.000 0.00 0.00 0.00 4.30
3367 4144 3.963428 ACTGTTGTGATGTACTCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
3379 4158 2.287368 GGGAACGGCTAAAACTGTTGTG 60.287 50.000 0.00 0.00 39.25 3.33
3426 4206 9.548631 TCCTCTAAATTATAGGGGATCAGTTAG 57.451 37.037 10.51 0.00 39.19 2.34
3427 4207 9.548631 CTCCTCTAAATTATAGGGGATCAGTTA 57.451 37.037 13.44 0.00 42.86 2.24
3431 4211 7.128567 TCCTCCTCTAAATTATAGGGGATCA 57.871 40.000 13.44 4.66 42.86 2.92
3448 4228 4.020543 AGATATTCAGCCGTATCCTCCTC 58.979 47.826 0.00 0.00 0.00 3.71
3460 4240 5.998454 TGCTGCTCTAAAAGATATTCAGC 57.002 39.130 0.00 0.00 44.07 4.26
3462 4242 9.049523 CACTTATGCTGCTCTAAAAGATATTCA 57.950 33.333 0.00 0.00 0.00 2.57
3469 4249 4.627467 ACGTCACTTATGCTGCTCTAAAAG 59.373 41.667 0.00 0.37 0.00 2.27
3473 4253 3.868757 AACGTCACTTATGCTGCTCTA 57.131 42.857 0.00 0.00 0.00 2.43
3474 4254 2.751166 AACGTCACTTATGCTGCTCT 57.249 45.000 0.00 0.00 0.00 4.09
3478 4258 7.060600 TCAATTAGAAACGTCACTTATGCTG 57.939 36.000 0.00 0.00 0.00 4.41
3483 4263 6.110707 GGGGATCAATTAGAAACGTCACTTA 58.889 40.000 0.00 0.00 0.00 2.24
3527 4307 8.956426 ACACTAGAACAAGATTTGACAAAGAAA 58.044 29.630 6.77 0.00 0.00 2.52
3529 4309 9.042008 GTACACTAGAACAAGATTTGACAAAGA 57.958 33.333 6.77 0.00 0.00 2.52
3530 4310 8.826710 TGTACACTAGAACAAGATTTGACAAAG 58.173 33.333 6.77 0.00 0.00 2.77
3599 4379 8.059502 TCGTGAATTGTACGTTAATTATCATGC 58.940 33.333 9.56 0.28 41.91 4.06
3652 4436 9.521503 TTCGTGTGTTTGAATTTGAATAATTCA 57.478 25.926 8.43 8.43 42.82 2.57
3727 4511 1.074405 GCATCCCTGGCATCTCCATAA 59.926 52.381 0.00 0.00 45.50 1.90
3746 4530 2.094894 CACCAACATGATCTCGTTGAGC 59.905 50.000 21.95 0.00 44.20 4.26
3753 4537 2.795329 ACCCAACACCAACATGATCTC 58.205 47.619 0.00 0.00 0.00 2.75
3761 4545 2.817844 GAGGTTCATACCCAACACCAAC 59.182 50.000 0.00 0.00 46.28 3.77
3804 4871 2.961669 AAACGACAATCACGCGCCC 61.962 57.895 5.73 0.00 0.00 6.13
3806 4873 1.052768 GACAAACGACAATCACGCGC 61.053 55.000 5.73 0.00 0.00 6.86
3810 4877 4.530094 TGTCAAGACAAACGACAATCAC 57.470 40.909 0.00 0.00 38.56 3.06
3899 4970 1.159285 CTTGTTGCCGAAGATGCTCA 58.841 50.000 0.00 0.00 0.00 4.26
3933 5004 2.202878 CCGCATTGATCCCGTCGT 60.203 61.111 0.00 0.00 0.00 4.34
3944 5015 2.369257 ATCTCCATCGTCGCCGCATT 62.369 55.000 0.00 0.00 0.00 3.56
3956 5027 1.622811 GGAATCGAGCTCCATCTCCAT 59.377 52.381 8.47 0.00 32.77 3.41
3957 5028 1.043816 GGAATCGAGCTCCATCTCCA 58.956 55.000 8.47 0.00 32.77 3.86


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

AutoCloner maintained by Alex Coulton.