Multiple sequence alignment - TraesCS2D01G595000

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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 TraesCS2D01G595000 chr2D 100.000 5399 0 0 1 5399 648466048 648471446 0.000000e+00 9971.0
1 TraesCS2D01G595000 chr2D 87.838 666 65 12 3805 4459 648501523 648500863 0.000000e+00 767.0
2 TraesCS2D01G595000 chr2B 91.787 4517 231 73 528 4974 784543726 784548172 0.000000e+00 6157.0
3 TraesCS2D01G595000 chr2B 94.909 275 13 1 1186 1459 766618933 766618659 3.860000e-116 429.0
4 TraesCS2D01G595000 chr2B 83.032 442 36 18 4980 5399 784548422 784548846 1.110000e-96 364.0
5 TraesCS2D01G595000 chrUn 90.375 3148 193 55 603 3672 30832968 30829853 0.000000e+00 4034.0
6 TraesCS2D01G595000 chrUn 91.768 1640 89 19 3782 5399 30829801 30828186 0.000000e+00 2239.0
7 TraesCS2D01G595000 chrUn 90.123 81 7 1 234 314 30833219 30833140 2.660000e-18 104.0
8 TraesCS2D01G595000 chrUn 94.030 67 3 1 317 382 30833097 30833031 3.440000e-17 100.0
9 TraesCS2D01G595000 chrUn 77.833 203 14 18 3 180 30833570 30833374 4.450000e-16 97.1
10 TraesCS2D01G595000 chrUn 97.368 38 1 0 524 561 30833020 30832983 1.260000e-06 65.8
11 TraesCS2D01G595000 chr4A 95.668 277 11 1 1184 1459 667292983 667293259 1.380000e-120 444.0
12 TraesCS2D01G595000 chr4A 93.863 277 16 1 1184 1459 667247395 667247671 3.010000e-112 416.0
13 TraesCS2D01G595000 chr4A 93.141 277 18 1 1184 1459 667269431 667269707 6.510000e-109 405.0
14 TraesCS2D01G595000 chr7A 82.592 517 52 19 1380 1883 729740449 729739958 6.470000e-114 422.0


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 TraesCS2D01G595000 chr2D 648466048 648471446 5398 False 9971.00 9971 100.0000 1 5399 1 chr2D.!!$F1 5398
1 TraesCS2D01G595000 chr2D 648500863 648501523 660 True 767.00 767 87.8380 3805 4459 1 chr2D.!!$R1 654
2 TraesCS2D01G595000 chr2B 784543726 784548846 5120 False 3260.50 6157 87.4095 528 5399 2 chr2B.!!$F1 4871
3 TraesCS2D01G595000 chrUn 30828186 30833570 5384 True 1106.65 4034 90.2495 3 5399 6 chrUn.!!$R1 5396

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
451 615 0.102844 ATGCGCACAAACAAACAGCT 59.897 45.000 14.90 0.0 0.00 4.24 F
457 621 0.531657 ACAAACAAACAGCTGCAGCA 59.468 45.000 38.24 0.0 45.16 4.41 F
1387 1643 0.600255 CCTCAACGACAACGCCTTCT 60.600 55.000 0.00 0.0 43.96 2.85 F
2514 2770 0.774276 TGTTGGCTACCACCATTCCA 59.226 50.000 0.00 0.0 40.13 3.53 F
2787 3043 1.133407 GTTCTTCGTTGTGCCACCAAA 59.867 47.619 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2206 0.105658 AGCCGTTATGGGAGGAGCTA 60.106 55.0 0.00 0.0 38.63 3.32 R
1952 2208 0.533085 GAAGCCGTTATGGGAGGAGC 60.533 60.0 0.00 0.0 38.63 4.70 R
3350 3606 0.523519 GTTGCAGAACTAAGCAGGGC 59.476 55.0 0.00 0.0 42.39 5.19 R
4173 4470 0.680921 ATTTCTCCACCATGGGCACG 60.681 55.0 18.09 1.7 38.32 5.34 R
4528 4833 0.163788 CAAGCACATGGACGACGAAC 59.836 55.0 0.00 0.0 0.00 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.734889 GGTGAACATGGATCCGCTTG 59.265 55.000 7.39 7.41 0.00 4.01
33 34 2.292267 GTGAACATGGATCCGCTTGAT 58.708 47.619 7.39 0.00 36.01 2.57
35 36 2.945008 TGAACATGGATCCGCTTGATTC 59.055 45.455 7.39 10.84 32.41 2.52
36 37 1.586422 ACATGGATCCGCTTGATTCG 58.414 50.000 7.39 0.00 30.71 3.34
37 38 1.138859 ACATGGATCCGCTTGATTCGA 59.861 47.619 7.39 0.00 30.71 3.71
39 40 2.620251 TGGATCCGCTTGATTCGATT 57.380 45.000 7.39 0.00 30.71 3.34
40 41 2.483876 TGGATCCGCTTGATTCGATTC 58.516 47.619 7.39 0.29 30.71 2.52
71 80 6.474140 TTCGATTCATTACCTGCCTAGTAA 57.526 37.500 0.00 0.00 34.38 2.24
72 81 6.085555 TCGATTCATTACCTGCCTAGTAAG 57.914 41.667 0.00 0.00 33.43 2.34
73 82 5.597182 TCGATTCATTACCTGCCTAGTAAGT 59.403 40.000 0.00 0.00 33.43 2.24
74 83 6.774170 TCGATTCATTACCTGCCTAGTAAGTA 59.226 38.462 0.00 0.00 33.43 2.24
77 86 7.670605 TTCATTACCTGCCTAGTAAGTACAT 57.329 36.000 0.00 0.00 33.43 2.29
91 100 5.864986 GTAAGTACATTACGCTGTGCAATT 58.135 37.500 0.00 0.00 34.77 2.32
94 103 6.106877 AGTACATTACGCTGTGCAATTAAG 57.893 37.500 0.00 0.00 34.59 1.85
100 109 1.466167 CGCTGTGCAATTAAGCAGTCT 59.534 47.619 11.18 0.00 46.69 3.24
103 112 4.656041 GCTGTGCAATTAAGCAGTCTTAG 58.344 43.478 6.98 0.00 46.69 2.18
104 113 4.154918 GCTGTGCAATTAAGCAGTCTTAGT 59.845 41.667 6.98 0.00 46.69 2.24
105 114 5.351465 GCTGTGCAATTAAGCAGTCTTAGTA 59.649 40.000 6.98 0.00 46.69 1.82
106 115 6.673316 GCTGTGCAATTAAGCAGTCTTAGTAC 60.673 42.308 6.98 0.00 46.69 2.73
107 116 6.227522 TGTGCAATTAAGCAGTCTTAGTACA 58.772 36.000 0.00 0.00 46.69 2.90
108 117 6.147164 TGTGCAATTAAGCAGTCTTAGTACAC 59.853 38.462 0.00 0.00 46.69 2.90
109 118 5.347635 TGCAATTAAGCAGTCTTAGTACACG 59.652 40.000 0.00 0.00 40.11 4.49
110 119 5.724223 GCAATTAAGCAGTCTTAGTACACGC 60.724 44.000 0.00 0.00 36.27 5.34
116 140 0.179119 GTCTTAGTACACGCCCGCAT 60.179 55.000 0.00 0.00 0.00 4.73
133 157 3.125829 CCGCATGCAGGCAGTAATAATAG 59.874 47.826 24.53 2.25 0.00 1.73
134 158 3.748048 CGCATGCAGGCAGTAATAATAGT 59.252 43.478 24.53 0.00 0.00 2.12
135 159 4.929211 CGCATGCAGGCAGTAATAATAGTA 59.071 41.667 24.53 0.00 0.00 1.82
136 160 5.062683 CGCATGCAGGCAGTAATAATAGTAG 59.937 44.000 24.53 0.00 0.00 2.57
137 161 5.934625 GCATGCAGGCAGTAATAATAGTAGT 59.065 40.000 20.11 0.00 0.00 2.73
140 164 6.675026 TGCAGGCAGTAATAATAGTAGTACG 58.325 40.000 2.57 0.28 36.20 3.67
141 165 6.263842 TGCAGGCAGTAATAATAGTAGTACGT 59.736 38.462 2.57 0.00 36.20 3.57
142 166 6.581542 GCAGGCAGTAATAATAGTAGTACGTG 59.418 42.308 0.00 3.52 36.20 4.49
166 190 1.455383 ATTGCCCGCGGATTGGATTC 61.455 55.000 30.73 5.24 0.00 2.52
172 196 1.217001 CGCGGATTGGATTCGATTCA 58.783 50.000 9.36 0.00 0.00 2.57
207 320 4.806342 GCGGATATTTTCACCGTGTATT 57.194 40.909 0.00 0.00 46.95 1.89
210 323 5.464389 GCGGATATTTTCACCGTGTATTAGT 59.536 40.000 0.00 0.00 46.95 2.24
212 325 7.330208 GCGGATATTTTCACCGTGTATTAGTAT 59.670 37.037 0.00 0.00 46.95 2.12
213 326 9.199982 CGGATATTTTCACCGTGTATTAGTATT 57.800 33.333 0.00 0.00 41.47 1.89
238 362 7.054491 ACCTATTATTTTTGCATGGATGGAC 57.946 36.000 0.00 0.00 0.00 4.02
242 366 2.142356 TTTTGCATGGATGGACGGAT 57.858 45.000 0.00 0.00 0.00 4.18
255 379 3.696045 TGGACGGATGGAAATGAAATGT 58.304 40.909 0.00 0.00 0.00 2.71
256 380 3.443329 TGGACGGATGGAAATGAAATGTG 59.557 43.478 0.00 0.00 0.00 3.21
258 382 4.201950 GGACGGATGGAAATGAAATGTGAG 60.202 45.833 0.00 0.00 0.00 3.51
290 414 2.729360 ACGGCGCTTTAAAGATTTTTGC 59.271 40.909 19.48 10.89 0.00 3.68
298 422 5.385509 TTTAAAGATTTTTGCCTCCTCCG 57.614 39.130 0.00 0.00 0.00 4.63
312 437 1.428370 CCTCCGTGTGTGTGTGTGTG 61.428 60.000 0.00 0.00 0.00 3.82
313 438 0.739462 CTCCGTGTGTGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
314 439 1.016653 TCCGTGTGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
315 440 1.295357 CCGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
390 554 4.087892 CCCGCCCCTGACTGACAG 62.088 72.222 0.00 0.00 45.36 3.51
391 555 3.314331 CCGCCCCTGACTGACAGT 61.314 66.667 8.12 8.12 44.40 3.55
392 556 2.047844 CGCCCCTGACTGACAGTG 60.048 66.667 14.14 0.00 44.40 3.66
393 557 2.872388 CGCCCCTGACTGACAGTGT 61.872 63.158 14.14 0.00 44.40 3.55
394 558 1.302033 GCCCCTGACTGACAGTGTG 60.302 63.158 14.14 5.17 44.40 3.82
395 559 1.302033 CCCCTGACTGACAGTGTGC 60.302 63.158 14.14 0.00 44.40 4.57
396 560 1.302033 CCCTGACTGACAGTGTGCC 60.302 63.158 14.14 0.00 44.40 5.01
397 561 1.665916 CCTGACTGACAGTGTGCCG 60.666 63.158 14.14 0.00 44.40 5.69
398 562 2.280119 TGACTGACAGTGTGCCGC 60.280 61.111 14.14 0.00 0.00 6.53
399 563 3.044305 GACTGACAGTGTGCCGCC 61.044 66.667 14.14 0.00 0.00 6.13
400 564 4.969196 ACTGACAGTGTGCCGCCG 62.969 66.667 7.47 0.00 0.00 6.46
401 565 4.969196 CTGACAGTGTGCCGCCGT 62.969 66.667 0.00 0.00 0.00 5.68
423 587 2.761559 TGGACACACCAGTACAAATCG 58.238 47.619 0.00 0.00 44.64 3.34
424 588 2.073816 GGACACACCAGTACAAATCGG 58.926 52.381 0.00 0.00 38.79 4.18
425 589 2.289195 GGACACACCAGTACAAATCGGA 60.289 50.000 0.00 0.00 38.79 4.55
426 590 3.596214 GACACACCAGTACAAATCGGAT 58.404 45.455 0.00 0.00 0.00 4.18
427 591 4.000988 GACACACCAGTACAAATCGGATT 58.999 43.478 0.00 0.00 0.00 3.01
428 592 3.751175 ACACACCAGTACAAATCGGATTG 59.249 43.478 3.59 1.78 36.37 2.67
429 593 4.000325 CACACCAGTACAAATCGGATTGA 59.000 43.478 3.59 0.00 34.38 2.57
430 594 4.454161 CACACCAGTACAAATCGGATTGAA 59.546 41.667 3.59 0.00 34.38 2.69
431 595 4.454504 ACACCAGTACAAATCGGATTGAAC 59.545 41.667 3.59 3.51 34.38 3.18
432 596 4.454161 CACCAGTACAAATCGGATTGAACA 59.546 41.667 3.59 0.00 34.38 3.18
433 597 5.123820 CACCAGTACAAATCGGATTGAACAT 59.876 40.000 3.59 0.00 34.38 2.71
434 598 5.123820 ACCAGTACAAATCGGATTGAACATG 59.876 40.000 3.59 1.08 34.38 3.21
435 599 5.030295 CAGTACAAATCGGATTGAACATGC 58.970 41.667 3.59 0.00 34.38 4.06
436 600 3.135414 ACAAATCGGATTGAACATGCG 57.865 42.857 3.59 0.00 34.38 4.73
437 601 1.847999 CAAATCGGATTGAACATGCGC 59.152 47.619 0.00 0.00 32.85 6.09
438 602 1.093972 AATCGGATTGAACATGCGCA 58.906 45.000 14.96 14.96 32.85 6.09
439 603 0.378257 ATCGGATTGAACATGCGCAC 59.622 50.000 14.90 0.00 32.85 5.34
440 604 0.952984 TCGGATTGAACATGCGCACA 60.953 50.000 14.90 2.35 32.85 4.57
441 605 0.109827 CGGATTGAACATGCGCACAA 60.110 50.000 14.90 13.57 0.00 3.33
442 606 1.665448 CGGATTGAACATGCGCACAAA 60.665 47.619 14.90 3.06 0.00 2.83
443 607 1.720852 GGATTGAACATGCGCACAAAC 59.279 47.619 14.90 11.26 0.00 2.93
444 608 2.392821 GATTGAACATGCGCACAAACA 58.607 42.857 14.90 8.78 0.00 2.83
445 609 2.284263 TTGAACATGCGCACAAACAA 57.716 40.000 14.90 14.71 0.00 2.83
446 610 2.284263 TGAACATGCGCACAAACAAA 57.716 40.000 14.90 0.00 0.00 2.83
447 611 1.923204 TGAACATGCGCACAAACAAAC 59.077 42.857 14.90 0.00 0.00 2.93
448 612 1.923204 GAACATGCGCACAAACAAACA 59.077 42.857 14.90 0.00 0.00 2.83
449 613 1.558741 ACATGCGCACAAACAAACAG 58.441 45.000 14.90 0.00 0.00 3.16
450 614 0.230260 CATGCGCACAAACAAACAGC 59.770 50.000 14.90 0.00 0.00 4.40
451 615 0.102844 ATGCGCACAAACAAACAGCT 59.897 45.000 14.90 0.00 0.00 4.24
452 616 0.801451 TGCGCACAAACAAACAGCTG 60.801 50.000 13.48 13.48 0.00 4.24
453 617 1.919340 CGCACAAACAAACAGCTGC 59.081 52.632 15.27 0.00 0.00 5.25
454 618 0.801451 CGCACAAACAAACAGCTGCA 60.801 50.000 15.27 0.00 0.00 4.41
455 619 0.925466 GCACAAACAAACAGCTGCAG 59.075 50.000 15.27 10.11 0.00 4.41
456 620 0.925466 CACAAACAAACAGCTGCAGC 59.075 50.000 31.53 31.53 42.49 5.25
457 621 0.531657 ACAAACAAACAGCTGCAGCA 59.468 45.000 38.24 0.00 45.16 4.41
458 622 1.205657 CAAACAAACAGCTGCAGCAG 58.794 50.000 38.24 32.87 45.16 4.24
476 640 7.992180 GCAGCAGCACTAATTTAATTGTAAT 57.008 32.000 0.00 0.00 41.58 1.89
477 641 8.411318 GCAGCAGCACTAATTTAATTGTAATT 57.589 30.769 0.00 5.89 41.58 1.40
478 642 9.515020 GCAGCAGCACTAATTTAATTGTAATTA 57.485 29.630 0.00 0.00 41.58 1.40
504 668 6.689554 AGGAGTAAGTAAGTAAGTGAACAGC 58.310 40.000 0.00 0.00 0.00 4.40
505 669 5.868258 GGAGTAAGTAAGTAAGTGAACAGCC 59.132 44.000 0.00 0.00 0.00 4.85
506 670 5.791666 AGTAAGTAAGTAAGTGAACAGCCC 58.208 41.667 0.00 0.00 0.00 5.19
507 671 4.699925 AAGTAAGTAAGTGAACAGCCCA 57.300 40.909 0.00 0.00 0.00 5.36
508 672 4.004196 AGTAAGTAAGTGAACAGCCCAC 57.996 45.455 0.00 0.00 34.89 4.61
509 673 3.389983 AGTAAGTAAGTGAACAGCCCACA 59.610 43.478 0.00 0.00 37.01 4.17
510 674 2.256117 AGTAAGTGAACAGCCCACAC 57.744 50.000 0.00 0.00 37.01 3.82
511 675 1.488812 AGTAAGTGAACAGCCCACACA 59.511 47.619 0.00 0.00 37.01 3.72
512 676 1.602377 GTAAGTGAACAGCCCACACAC 59.398 52.381 0.00 0.00 37.01 3.82
513 677 1.095228 AAGTGAACAGCCCACACACG 61.095 55.000 0.00 0.00 37.01 4.49
514 678 2.899838 TGAACAGCCCACACACGC 60.900 61.111 0.00 0.00 0.00 5.34
515 679 3.660111 GAACAGCCCACACACGCC 61.660 66.667 0.00 0.00 0.00 5.68
516 680 4.189580 AACAGCCCACACACGCCT 62.190 61.111 0.00 0.00 0.00 5.52
517 681 4.626081 ACAGCCCACACACGCCTC 62.626 66.667 0.00 0.00 0.00 4.70
520 684 4.980805 GCCCACACACGCCTCGAA 62.981 66.667 0.00 0.00 0.00 3.71
521 685 2.280524 CCCACACACGCCTCGAAA 60.281 61.111 0.00 0.00 0.00 3.46
522 686 2.317609 CCCACACACGCCTCGAAAG 61.318 63.158 0.00 0.00 0.00 2.62
530 694 1.535462 CACGCCTCGAAAGACCAAAAT 59.465 47.619 0.00 0.00 35.39 1.82
569 733 2.617274 AACGAAAAGCAGCCGAGGC 61.617 57.895 5.89 5.89 42.33 4.70
580 744 4.465446 CCGAGGCTGGGAGAGGGA 62.465 72.222 10.44 0.00 0.00 4.20
581 745 2.837291 CGAGGCTGGGAGAGGGAG 60.837 72.222 0.00 0.00 0.00 4.30
582 746 2.445654 GAGGCTGGGAGAGGGAGG 60.446 72.222 0.00 0.00 0.00 4.30
583 747 4.101077 AGGCTGGGAGAGGGAGGG 62.101 72.222 0.00 0.00 0.00 4.30
584 748 4.095400 GGCTGGGAGAGGGAGGGA 62.095 72.222 0.00 0.00 0.00 4.20
585 749 2.445654 GCTGGGAGAGGGAGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
586 750 2.285180 CTGGGAGAGGGAGGGAGG 59.715 72.222 0.00 0.00 0.00 4.30
587 751 3.368501 TGGGAGAGGGAGGGAGGG 61.369 72.222 0.00 0.00 0.00 4.30
588 752 3.036959 GGGAGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
589 753 2.284151 GGAGAGGGAGGGAGGGAC 59.716 72.222 0.00 0.00 0.00 4.46
671 849 1.402787 AAAGGCTGTGGTTTCACTGG 58.597 50.000 0.00 0.00 43.94 4.00
704 882 0.892814 AAACAGAGGAGCAAGCCAGC 60.893 55.000 0.00 0.00 0.00 4.85
793 1001 2.199652 CCACGCACCCACACCATTT 61.200 57.895 0.00 0.00 0.00 2.32
812 1020 2.198827 TGACACCCACATCACATTCC 57.801 50.000 0.00 0.00 0.00 3.01
839 1049 4.969196 ACACTGCCGACCACAGCG 62.969 66.667 0.00 0.00 38.79 5.18
899 1121 2.601299 GCTTATCCCCACCCCCAC 59.399 66.667 0.00 0.00 0.00 4.61
930 1152 2.670148 CCTTCCTTCCTCCCCACCG 61.670 68.421 0.00 0.00 0.00 4.94
953 1190 3.680786 GCAAACCCAACTCCGGCC 61.681 66.667 0.00 0.00 0.00 6.13
1042 1280 1.456518 CTCATCCTCCTCCTCGCCA 60.457 63.158 0.00 0.00 0.00 5.69
1043 1281 0.831288 CTCATCCTCCTCCTCGCCAT 60.831 60.000 0.00 0.00 0.00 4.40
1049 1290 4.271816 CCTCCTCGCCATCGTCGG 62.272 72.222 0.00 0.00 36.96 4.79
1312 1568 1.079543 CTCAGCCTCCAGACCAACG 60.080 63.158 0.00 0.00 0.00 4.10
1313 1569 2.743928 CAGCCTCCAGACCAACGC 60.744 66.667 0.00 0.00 0.00 4.84
1387 1643 0.600255 CCTCAACGACAACGCCTTCT 60.600 55.000 0.00 0.00 43.96 2.85
1388 1644 0.784778 CTCAACGACAACGCCTTCTC 59.215 55.000 0.00 0.00 43.96 2.87
1621 1877 1.621072 CCCTCTCCTACAACAGGCTCT 60.621 57.143 0.00 0.00 45.10 4.09
1686 1942 1.954528 CTGGCTCAACAACCAGCTG 59.045 57.895 6.78 6.78 46.50 4.24
1693 1949 2.818169 AACAACCAGCTGGGCGAGA 61.818 57.895 35.42 0.00 42.05 4.04
1950 2206 2.048603 GCTCAAGGCCGGCAATCTT 61.049 57.895 30.85 19.65 34.27 2.40
1952 2208 1.303309 CTCAAGGCCGGCAATCTTAG 58.697 55.000 30.85 15.77 0.00 2.18
2196 2452 2.124693 CCTCGGAGACCTCTCTGCC 61.125 68.421 6.58 0.00 46.39 4.85
2334 2590 2.126031 GCCTTCAGACCGGACGTC 60.126 66.667 9.46 7.13 42.32 4.34
2350 2606 3.325870 GACGTCAATGTCATTCTCACCA 58.674 45.455 11.55 0.00 38.75 4.17
2370 2626 1.963515 AGCAATCCCAACTTCAACACC 59.036 47.619 0.00 0.00 0.00 4.16
2407 2663 4.020617 CTGCTCCCAAGGACGCCA 62.021 66.667 0.00 0.00 0.00 5.69
2514 2770 0.774276 TGTTGGCTACCACCATTCCA 59.226 50.000 0.00 0.00 40.13 3.53
2544 2800 2.359230 GTGGTGGCTCTGCTGTCC 60.359 66.667 0.00 0.00 0.00 4.02
2586 2842 2.293122 CTGCAAGAAAAATGGGTCGTCA 59.707 45.455 0.00 0.00 34.07 4.35
2787 3043 1.133407 GTTCTTCGTTGTGCCACCAAA 59.867 47.619 0.00 0.00 0.00 3.28
3018 3274 3.549794 GAATGAAAGGCTGCTGGTCTAT 58.450 45.455 0.00 0.00 0.00 1.98
3090 3346 2.364842 GAGCTGGAGCCCCTCTCA 60.365 66.667 0.00 0.00 43.70 3.27
3252 3508 2.885266 GGATTTCGGGCTCCTTAAATCC 59.115 50.000 19.72 19.72 41.68 3.01
3380 3636 6.633234 GCTTAGTTCTGCAACTTCTGTTTTAC 59.367 38.462 0.00 0.00 40.16 2.01
3471 3758 8.856153 TTGCTGTGTAAATAACCTCATTTAGA 57.144 30.769 0.00 0.00 32.44 2.10
3472 3759 9.461312 TTGCTGTGTAAATAACCTCATTTAGAT 57.539 29.630 0.00 0.00 32.44 1.98
3473 3760 9.461312 TGCTGTGTAAATAACCTCATTTAGATT 57.539 29.630 0.00 0.00 32.44 2.40
3509 3796 6.111382 TGAAAAACTGAATTGATGTGGCAAA 58.889 32.000 0.00 0.00 0.00 3.68
3577 3864 7.036220 CCAGTGTAAGTAACCTCATGTAAGAG 58.964 42.308 0.00 0.00 35.39 2.85
3627 3914 8.641541 ACATTGGAAATGTTTGATGAACTAGTT 58.358 29.630 8.13 8.13 39.08 2.24
3689 3979 5.432885 ACTGCACAAGTTTATACACCAAC 57.567 39.130 0.00 0.00 34.57 3.77
3723 4013 8.946085 TCAATAGAACATGTATCTTTGTCCAAC 58.054 33.333 13.40 0.00 0.00 3.77
3743 4033 4.385358 ACATTGTGAAGTTTGAACCACC 57.615 40.909 0.00 0.00 0.00 4.61
3755 4045 1.421268 TGAACCACCTTCTGATGCAGT 59.579 47.619 0.00 0.00 32.61 4.40
3757 4047 3.264193 TGAACCACCTTCTGATGCAGTAT 59.736 43.478 0.00 0.00 32.61 2.12
3762 4052 7.136822 ACCACCTTCTGATGCAGTATATAAA 57.863 36.000 0.00 0.00 32.61 1.40
3766 4056 7.443575 CACCTTCTGATGCAGTATATAAAAGCT 59.556 37.037 0.00 0.00 32.61 3.74
3772 4062 8.102800 TGATGCAGTATATAAAAGCTTCCATG 57.897 34.615 0.00 0.00 0.00 3.66
3843 4139 7.120579 TGTTATTATGGTTCCTGAATGTGTGTC 59.879 37.037 0.00 0.00 0.00 3.67
3891 4188 1.399727 GCAGTGACCGGAAAAATCACG 60.400 52.381 9.46 8.81 45.97 4.35
3894 4191 1.136446 GTGACCGGAAAAATCACGACG 60.136 52.381 9.46 0.00 33.94 5.12
4423 4728 4.326548 CCTTGATCATCATCATCGTCATCG 59.673 45.833 0.00 0.00 38.89 3.84
4424 4729 3.248266 TGATCATCATCATCGTCATCGC 58.752 45.455 0.00 0.00 33.80 4.58
4485 4790 1.228124 CTCCCCTGTTTCGGCACAA 60.228 57.895 0.00 0.00 0.00 3.33
4486 4791 1.228124 TCCCCTGTTTCGGCACAAG 60.228 57.895 0.00 0.00 0.00 3.16
4488 4793 2.252260 CCTGTTTCGGCACAAGCG 59.748 61.111 0.00 0.00 43.41 4.68
4490 4795 1.355210 CTGTTTCGGCACAAGCGTT 59.645 52.632 0.00 0.00 43.41 4.84
4491 4796 0.657368 CTGTTTCGGCACAAGCGTTC 60.657 55.000 0.00 0.00 43.41 3.95
4492 4797 1.721133 GTTTCGGCACAAGCGTTCG 60.721 57.895 0.00 0.00 43.41 3.95
4494 4799 1.707239 TTTCGGCACAAGCGTTCGTT 61.707 50.000 0.00 0.00 43.41 3.85
4498 4803 1.011574 GCACAAGCGTTCGTTTCGT 60.012 52.632 0.00 0.00 0.00 3.85
4520 4825 6.930722 TCGTTCTTGTAGGTAAAGTAAAAGGG 59.069 38.462 0.00 0.00 0.00 3.95
4523 4828 6.536447 TCTTGTAGGTAAAGTAAAAGGGGTG 58.464 40.000 0.00 0.00 0.00 4.61
4526 4831 2.107031 AGGTAAAGTAAAAGGGGTGCGT 59.893 45.455 0.00 0.00 0.00 5.24
4527 4832 2.485426 GGTAAAGTAAAAGGGGTGCGTC 59.515 50.000 0.00 0.00 0.00 5.19
4528 4833 1.232119 AAAGTAAAAGGGGTGCGTCG 58.768 50.000 0.00 0.00 0.00 5.12
4529 4834 0.107268 AAGTAAAAGGGGTGCGTCGT 59.893 50.000 0.00 0.00 0.00 4.34
4550 4855 1.207593 GTCGTCCATGTGCTTGTGC 59.792 57.895 0.00 0.00 40.20 4.57
4618 4929 0.250124 TGTTCAACTGGGTGCTACCG 60.250 55.000 0.00 0.00 39.83 4.02
4641 4959 0.109342 GATGGATGGATTGGTCGCCT 59.891 55.000 0.00 0.00 0.00 5.52
4705 5023 9.859427 CTTTACCTAGCAATCAAATCAAATCAA 57.141 29.630 0.00 0.00 0.00 2.57
4765 5083 3.440522 CCTGGAACCGAATTTTCTCCTTC 59.559 47.826 0.00 0.00 0.00 3.46
4766 5084 4.327680 CTGGAACCGAATTTTCTCCTTCT 58.672 43.478 0.00 0.00 0.00 2.85
4770 5089 6.150318 GGAACCGAATTTTCTCCTTCTTTTC 58.850 40.000 0.00 0.00 0.00 2.29
4808 5133 1.134159 GCATCTGGTTCCTCATGCTCT 60.134 52.381 14.13 0.00 38.89 4.09
4813 5138 1.034292 GGTTCCTCATGCTCTTGGCC 61.034 60.000 0.00 0.00 40.92 5.36
4814 5139 0.034670 GTTCCTCATGCTCTTGGCCT 60.035 55.000 3.32 0.00 40.92 5.19
4815 5140 0.254178 TTCCTCATGCTCTTGGCCTC 59.746 55.000 3.32 0.00 40.92 4.70
4816 5141 0.911045 TCCTCATGCTCTTGGCCTCA 60.911 55.000 3.32 0.00 40.92 3.86
4817 5142 0.183014 CCTCATGCTCTTGGCCTCAT 59.817 55.000 3.32 0.00 40.92 2.90
4818 5143 1.309950 CTCATGCTCTTGGCCTCATG 58.690 55.000 3.32 9.84 40.92 3.07
4819 5144 0.106868 TCATGCTCTTGGCCTCATGG 60.107 55.000 3.32 0.00 40.92 3.66
4917 5242 2.044946 GGGGGCAGCAAGTACCAG 60.045 66.667 0.00 0.00 0.00 4.00
4933 5258 1.970114 CAGTCCAGGCTTGCACCAG 60.970 63.158 0.00 0.00 0.00 4.00
4935 5260 1.968540 GTCCAGGCTTGCACCAGTC 60.969 63.158 0.00 0.00 0.00 3.51
4974 5303 0.479815 TGATCTCCCATGCCCCATTC 59.520 55.000 0.00 0.00 0.00 2.67
4976 5305 0.776176 ATCTCCCATGCCCCATTCTC 59.224 55.000 0.00 0.00 0.00 2.87
5135 5727 6.344500 TGATCTTTATGCAGGTTCTCTTCTC 58.656 40.000 0.00 0.00 0.00 2.87
5136 5728 6.155910 TGATCTTTATGCAGGTTCTCTTCTCT 59.844 38.462 0.00 0.00 0.00 3.10
5137 5729 5.728471 TCTTTATGCAGGTTCTCTTCTCTG 58.272 41.667 0.00 0.00 0.00 3.35
5139 5731 2.015456 TGCAGGTTCTCTTCTCTGGA 57.985 50.000 0.00 0.00 0.00 3.86
5140 5732 1.898472 TGCAGGTTCTCTTCTCTGGAG 59.102 52.381 0.00 0.00 0.00 3.86
5141 5733 1.899142 GCAGGTTCTCTTCTCTGGAGT 59.101 52.381 0.00 0.00 33.06 3.85
5228 5823 3.144506 GCTGTGGCTCACTTGCATATAT 58.855 45.455 13.90 0.00 35.77 0.86
5229 5824 3.058432 GCTGTGGCTCACTTGCATATATG 60.058 47.826 8.45 8.45 35.77 1.78
5308 5914 3.575687 CTCCAGTGATGGCCTTTTTCTTT 59.424 43.478 3.32 0.00 0.00 2.52
5325 5931 1.334869 CTTTTCTGTGGCGCTGAAAGT 59.665 47.619 25.15 0.00 42.92 2.66
5356 5962 1.338389 ACCGGGGTTAATCAAGTGTCG 60.338 52.381 6.32 0.00 0.00 4.35
5370 5976 1.067776 AGTGTCGTTGTCGAGGAATCC 60.068 52.381 0.00 0.00 46.96 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153706 GTTCACCATGCATGCCAGC 60.154 57.895 21.69 5.12 0.00 4.85
1 2 0.821517 ATGTTCACCATGCATGCCAG 59.178 50.000 21.69 12.41 30.69 4.85
2 3 0.533032 CATGTTCACCATGCATGCCA 59.467 50.000 21.69 11.58 44.21 4.92
3 4 3.355816 CATGTTCACCATGCATGCC 57.644 52.632 21.69 6.41 44.21 4.40
15 16 2.032549 CGAATCAAGCGGATCCATGTTC 60.033 50.000 13.41 11.64 34.28 3.18
21 22 1.457303 CGAATCGAATCAAGCGGATCC 59.543 52.381 0.00 0.00 34.28 3.36
40 41 5.666427 GCAGGTAATGAATCGAATCGAATCG 60.666 44.000 16.66 16.66 38.45 3.34
71 80 5.447279 GCTTAATTGCACAGCGTAATGTACT 60.447 40.000 0.00 0.00 29.40 2.73
72 81 4.728608 GCTTAATTGCACAGCGTAATGTAC 59.271 41.667 0.00 0.00 29.40 2.90
73 82 4.393371 TGCTTAATTGCACAGCGTAATGTA 59.607 37.500 0.00 0.00 38.12 2.29
74 83 3.190327 TGCTTAATTGCACAGCGTAATGT 59.810 39.130 0.00 0.00 38.12 2.71
77 86 2.811431 ACTGCTTAATTGCACAGCGTAA 59.189 40.909 0.00 0.00 38.12 3.18
83 92 6.147164 GTGTACTAAGACTGCTTAATTGCACA 59.853 38.462 0.00 0.00 36.44 4.57
91 100 2.165030 GGGCGTGTACTAAGACTGCTTA 59.835 50.000 0.00 0.00 35.56 3.09
94 103 0.801067 CGGGCGTGTACTAAGACTGC 60.801 60.000 0.00 0.00 0.00 4.40
100 109 1.812093 GCATGCGGGCGTGTACTAA 60.812 57.895 13.83 0.00 35.52 2.24
103 112 3.864686 CTGCATGCGGGCGTGTAC 61.865 66.667 19.33 0.00 35.52 2.90
110 119 0.534877 TATTACTGCCTGCATGCGGG 60.535 55.000 36.88 36.88 45.07 6.13
116 140 6.263842 ACGTACTACTATTATTACTGCCTGCA 59.736 38.462 0.00 0.00 0.00 4.41
133 157 2.538449 CGGGCAATCAATCACGTACTAC 59.462 50.000 0.00 0.00 0.00 2.73
134 158 2.816689 CGGGCAATCAATCACGTACTA 58.183 47.619 0.00 0.00 0.00 1.82
135 159 1.651987 CGGGCAATCAATCACGTACT 58.348 50.000 0.00 0.00 0.00 2.73
136 160 0.027586 GCGGGCAATCAATCACGTAC 59.972 55.000 0.00 0.00 0.00 3.67
137 161 1.425267 CGCGGGCAATCAATCACGTA 61.425 55.000 0.00 0.00 0.00 3.57
140 164 1.447317 ATCCGCGGGCAATCAATCAC 61.447 55.000 27.83 0.00 0.00 3.06
141 165 0.751277 AATCCGCGGGCAATCAATCA 60.751 50.000 27.83 0.77 0.00 2.57
142 166 0.318107 CAATCCGCGGGCAATCAATC 60.318 55.000 27.83 0.00 0.00 2.67
172 196 4.789075 CCGCGTGACCCGTCGATT 62.789 66.667 4.92 0.00 37.98 3.34
176 200 0.529119 AAATATCCGCGTGACCCGTC 60.529 55.000 4.92 0.00 39.32 4.79
177 201 0.108041 AAAATATCCGCGTGACCCGT 60.108 50.000 4.92 0.00 39.32 5.28
178 202 0.580104 GAAAATATCCGCGTGACCCG 59.420 55.000 4.92 0.00 40.40 5.28
179 203 1.329599 GTGAAAATATCCGCGTGACCC 59.670 52.381 4.92 0.00 0.00 4.46
182 206 1.282817 CGGTGAAAATATCCGCGTGA 58.717 50.000 4.92 1.95 37.90 4.35
183 207 1.003851 ACGGTGAAAATATCCGCGTG 58.996 50.000 4.92 0.00 46.92 5.34
186 210 4.806342 AATACACGGTGAAAATATCCGC 57.194 40.909 16.29 0.00 46.92 5.54
212 325 8.637986 GTCCATCCATGCAAAAATAATAGGTAA 58.362 33.333 0.00 0.00 0.00 2.85
213 326 7.040755 CGTCCATCCATGCAAAAATAATAGGTA 60.041 37.037 0.00 0.00 0.00 3.08
214 327 6.239008 CGTCCATCCATGCAAAAATAATAGGT 60.239 38.462 0.00 0.00 0.00 3.08
215 328 6.151691 CGTCCATCCATGCAAAAATAATAGG 58.848 40.000 0.00 0.00 0.00 2.57
216 329 6.016360 TCCGTCCATCCATGCAAAAATAATAG 60.016 38.462 0.00 0.00 0.00 1.73
217 330 5.830457 TCCGTCCATCCATGCAAAAATAATA 59.170 36.000 0.00 0.00 0.00 0.98
218 331 4.648762 TCCGTCCATCCATGCAAAAATAAT 59.351 37.500 0.00 0.00 0.00 1.28
219 332 4.019858 TCCGTCCATCCATGCAAAAATAA 58.980 39.130 0.00 0.00 0.00 1.40
220 333 3.625853 TCCGTCCATCCATGCAAAAATA 58.374 40.909 0.00 0.00 0.00 1.40
221 334 2.455557 TCCGTCCATCCATGCAAAAAT 58.544 42.857 0.00 0.00 0.00 1.82
222 335 1.916506 TCCGTCCATCCATGCAAAAA 58.083 45.000 0.00 0.00 0.00 1.94
223 336 1.750206 CATCCGTCCATCCATGCAAAA 59.250 47.619 0.00 0.00 0.00 2.44
224 337 1.391577 CATCCGTCCATCCATGCAAA 58.608 50.000 0.00 0.00 0.00 3.68
225 338 0.466007 CCATCCGTCCATCCATGCAA 60.466 55.000 0.00 0.00 0.00 4.08
227 340 0.179020 TTCCATCCGTCCATCCATGC 60.179 55.000 0.00 0.00 0.00 4.06
228 341 2.346766 TTTCCATCCGTCCATCCATG 57.653 50.000 0.00 0.00 0.00 3.66
238 362 3.699067 GCTCACATTTCATTTCCATCCG 58.301 45.455 0.00 0.00 0.00 4.18
242 366 1.202114 GGCGCTCACATTTCATTTCCA 59.798 47.619 7.64 0.00 0.00 3.53
290 414 1.300931 CACACACACACGGAGGAGG 60.301 63.158 0.00 0.00 0.00 4.30
298 422 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
330 493 2.045045 CCGGAGATGGCTGCCAAA 60.045 61.111 27.24 2.61 36.95 3.28
382 546 3.044305 GGCGGCACACTGTCAGTC 61.044 66.667 3.07 0.00 0.00 3.51
383 547 4.969196 CGGCGGCACACTGTCAGT 62.969 66.667 10.53 0.00 0.00 3.41
401 565 3.472652 GATTTGTACTGGTGTGTCCACA 58.527 45.455 0.00 0.00 43.71 4.17
402 566 2.478894 CGATTTGTACTGGTGTGTCCAC 59.521 50.000 0.00 0.00 41.93 4.02
403 567 2.549134 CCGATTTGTACTGGTGTGTCCA 60.549 50.000 0.00 0.00 45.01 4.02
404 568 2.073816 CCGATTTGTACTGGTGTGTCC 58.926 52.381 0.00 0.00 0.00 4.02
405 569 3.034721 TCCGATTTGTACTGGTGTGTC 57.965 47.619 0.00 0.00 0.00 3.67
406 570 3.695830 ATCCGATTTGTACTGGTGTGT 57.304 42.857 0.00 0.00 0.00 3.72
407 571 4.000325 TCAATCCGATTTGTACTGGTGTG 59.000 43.478 0.00 0.00 0.00 3.82
408 572 4.280436 TCAATCCGATTTGTACTGGTGT 57.720 40.909 0.00 0.00 0.00 4.16
409 573 4.454161 TGTTCAATCCGATTTGTACTGGTG 59.546 41.667 0.00 0.00 30.76 4.17
410 574 4.647611 TGTTCAATCCGATTTGTACTGGT 58.352 39.130 0.00 0.00 30.76 4.00
411 575 5.572211 CATGTTCAATCCGATTTGTACTGG 58.428 41.667 0.00 0.00 30.76 4.00
412 576 5.030295 GCATGTTCAATCCGATTTGTACTG 58.970 41.667 0.00 5.87 30.76 2.74
413 577 4.201812 CGCATGTTCAATCCGATTTGTACT 60.202 41.667 0.00 0.00 30.76 2.73
414 578 4.028383 CGCATGTTCAATCCGATTTGTAC 58.972 43.478 0.00 0.00 0.00 2.90
415 579 3.486708 GCGCATGTTCAATCCGATTTGTA 60.487 43.478 0.30 0.00 0.00 2.41
416 580 2.731968 GCGCATGTTCAATCCGATTTGT 60.732 45.455 0.30 0.00 0.00 2.83
417 581 1.847999 GCGCATGTTCAATCCGATTTG 59.152 47.619 0.30 0.00 0.00 2.32
418 582 1.472082 TGCGCATGTTCAATCCGATTT 59.528 42.857 5.66 0.00 0.00 2.17
419 583 1.093972 TGCGCATGTTCAATCCGATT 58.906 45.000 5.66 0.00 0.00 3.34
420 584 0.378257 GTGCGCATGTTCAATCCGAT 59.622 50.000 15.91 0.00 0.00 4.18
421 585 0.952984 TGTGCGCATGTTCAATCCGA 60.953 50.000 15.91 0.00 0.00 4.55
422 586 0.109827 TTGTGCGCATGTTCAATCCG 60.110 50.000 15.91 0.00 0.00 4.18
423 587 1.720852 GTTTGTGCGCATGTTCAATCC 59.279 47.619 15.91 3.27 0.00 3.01
424 588 2.392821 TGTTTGTGCGCATGTTCAATC 58.607 42.857 15.91 12.55 0.00 2.67
425 589 2.505628 TGTTTGTGCGCATGTTCAAT 57.494 40.000 15.91 0.00 0.00 2.57
426 590 2.284263 TTGTTTGTGCGCATGTTCAA 57.716 40.000 15.91 10.62 0.00 2.69
427 591 1.923204 GTTTGTTTGTGCGCATGTTCA 59.077 42.857 15.91 3.18 0.00 3.18
428 592 1.923204 TGTTTGTTTGTGCGCATGTTC 59.077 42.857 15.91 0.00 0.00 3.18
429 593 1.925847 CTGTTTGTTTGTGCGCATGTT 59.074 42.857 15.91 0.00 0.00 2.71
430 594 1.558741 CTGTTTGTTTGTGCGCATGT 58.441 45.000 15.91 0.00 0.00 3.21
431 595 0.230260 GCTGTTTGTTTGTGCGCATG 59.770 50.000 15.91 0.00 0.00 4.06
432 596 0.102844 AGCTGTTTGTTTGTGCGCAT 59.897 45.000 15.91 0.00 0.00 4.73
433 597 0.801451 CAGCTGTTTGTTTGTGCGCA 60.801 50.000 5.66 5.66 0.00 6.09
434 598 1.919340 CAGCTGTTTGTTTGTGCGC 59.081 52.632 5.25 0.00 0.00 6.09
435 599 0.801451 TGCAGCTGTTTGTTTGTGCG 60.801 50.000 16.64 0.00 33.52 5.34
436 600 0.925466 CTGCAGCTGTTTGTTTGTGC 59.075 50.000 16.64 0.00 0.00 4.57
437 601 0.925466 GCTGCAGCTGTTTGTTTGTG 59.075 50.000 31.33 0.00 38.21 3.33
438 602 0.531657 TGCTGCAGCTGTTTGTTTGT 59.468 45.000 36.61 0.00 42.66 2.83
439 603 1.205657 CTGCTGCAGCTGTTTGTTTG 58.794 50.000 36.61 12.99 42.66 2.93
440 604 3.654178 CTGCTGCAGCTGTTTGTTT 57.346 47.368 36.61 0.00 42.66 2.83
452 616 7.992180 ATTACAATTAAATTAGTGCTGCTGC 57.008 32.000 8.89 8.89 40.20 5.25
478 642 7.656542 GCTGTTCACTTACTTACTTACTCCTTT 59.343 37.037 0.00 0.00 0.00 3.11
479 643 7.153315 GCTGTTCACTTACTTACTTACTCCTT 58.847 38.462 0.00 0.00 0.00 3.36
480 644 6.295180 GGCTGTTCACTTACTTACTTACTCCT 60.295 42.308 0.00 0.00 0.00 3.69
481 645 5.868258 GGCTGTTCACTTACTTACTTACTCC 59.132 44.000 0.00 0.00 0.00 3.85
482 646 5.868258 GGGCTGTTCACTTACTTACTTACTC 59.132 44.000 0.00 0.00 0.00 2.59
483 647 5.306160 TGGGCTGTTCACTTACTTACTTACT 59.694 40.000 0.00 0.00 0.00 2.24
484 648 5.407691 GTGGGCTGTTCACTTACTTACTTAC 59.592 44.000 0.00 0.00 32.78 2.34
485 649 5.070714 TGTGGGCTGTTCACTTACTTACTTA 59.929 40.000 0.00 0.00 36.21 2.24
486 650 4.141574 TGTGGGCTGTTCACTTACTTACTT 60.142 41.667 0.00 0.00 36.21 2.24
487 651 3.389983 TGTGGGCTGTTCACTTACTTACT 59.610 43.478 0.00 0.00 36.21 2.24
488 652 3.497262 GTGTGGGCTGTTCACTTACTTAC 59.503 47.826 0.00 0.00 36.21 2.34
489 653 3.134985 TGTGTGGGCTGTTCACTTACTTA 59.865 43.478 0.00 0.00 36.21 2.24
490 654 2.092646 TGTGTGGGCTGTTCACTTACTT 60.093 45.455 0.00 0.00 36.21 2.24
491 655 1.488812 TGTGTGGGCTGTTCACTTACT 59.511 47.619 0.00 0.00 36.21 2.24
492 656 1.602377 GTGTGTGGGCTGTTCACTTAC 59.398 52.381 0.00 0.00 36.21 2.34
493 657 1.808512 CGTGTGTGGGCTGTTCACTTA 60.809 52.381 0.00 0.00 36.21 2.24
494 658 1.095228 CGTGTGTGGGCTGTTCACTT 61.095 55.000 0.00 0.00 36.21 3.16
495 659 1.523711 CGTGTGTGGGCTGTTCACT 60.524 57.895 0.00 0.00 36.21 3.41
496 660 3.022287 CGTGTGTGGGCTGTTCAC 58.978 61.111 0.00 0.00 35.82 3.18
497 661 2.899838 GCGTGTGTGGGCTGTTCA 60.900 61.111 0.00 0.00 0.00 3.18
498 662 3.660111 GGCGTGTGTGGGCTGTTC 61.660 66.667 0.00 0.00 0.00 3.18
499 663 4.189580 AGGCGTGTGTGGGCTGTT 62.190 61.111 0.00 0.00 39.05 3.16
500 664 4.626081 GAGGCGTGTGTGGGCTGT 62.626 66.667 0.00 0.00 40.78 4.40
503 667 4.980805 TTCGAGGCGTGTGTGGGC 62.981 66.667 0.00 0.00 0.00 5.36
504 668 2.280524 TTTCGAGGCGTGTGTGGG 60.281 61.111 0.00 0.00 0.00 4.61
505 669 1.300620 TCTTTCGAGGCGTGTGTGG 60.301 57.895 0.00 0.00 0.00 4.17
506 670 1.557443 GGTCTTTCGAGGCGTGTGTG 61.557 60.000 0.00 0.00 0.00 3.82
507 671 1.300697 GGTCTTTCGAGGCGTGTGT 60.301 57.895 0.00 0.00 0.00 3.72
508 672 0.878523 TTGGTCTTTCGAGGCGTGTG 60.879 55.000 0.00 0.00 0.00 3.82
509 673 0.179067 TTTGGTCTTTCGAGGCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
510 674 0.941542 TTTTGGTCTTTCGAGGCGTG 59.058 50.000 0.00 0.00 0.00 5.34
511 675 1.892209 ATTTTGGTCTTTCGAGGCGT 58.108 45.000 0.00 0.00 0.00 5.68
512 676 4.156182 GTTTATTTTGGTCTTTCGAGGCG 58.844 43.478 0.00 0.00 0.00 5.52
513 677 5.116069 TGTTTATTTTGGTCTTTCGAGGC 57.884 39.130 0.00 0.00 0.00 4.70
514 678 7.326063 GTGATTGTTTATTTTGGTCTTTCGAGG 59.674 37.037 0.00 0.00 0.00 4.63
515 679 7.059488 CGTGATTGTTTATTTTGGTCTTTCGAG 59.941 37.037 0.00 0.00 0.00 4.04
516 680 6.853872 CGTGATTGTTTATTTTGGTCTTTCGA 59.146 34.615 0.00 0.00 0.00 3.71
517 681 6.635239 ACGTGATTGTTTATTTTGGTCTTTCG 59.365 34.615 0.00 0.00 0.00 3.46
518 682 7.924103 ACGTGATTGTTTATTTTGGTCTTTC 57.076 32.000 0.00 0.00 0.00 2.62
519 683 7.976734 TGAACGTGATTGTTTATTTTGGTCTTT 59.023 29.630 0.00 0.00 30.75 2.52
520 684 7.434013 GTGAACGTGATTGTTTATTTTGGTCTT 59.566 33.333 0.00 0.00 30.75 3.01
521 685 6.915843 GTGAACGTGATTGTTTATTTTGGTCT 59.084 34.615 0.00 0.00 30.75 3.85
522 686 6.693545 TGTGAACGTGATTGTTTATTTTGGTC 59.306 34.615 0.00 0.00 30.75 4.02
530 694 5.333513 GTTGGTTGTGAACGTGATTGTTTA 58.666 37.500 0.00 0.00 30.75 2.01
569 733 2.285180 CCTCCCTCCCTCTCCCAG 59.715 72.222 0.00 0.00 0.00 4.45
570 734 3.368501 CCCTCCCTCCCTCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
575 739 0.326618 TGATTGTCCCTCCCTCCCTC 60.327 60.000 0.00 0.00 0.00 4.30
577 741 0.999712 TTTGATTGTCCCTCCCTCCC 59.000 55.000 0.00 0.00 0.00 4.30
578 742 2.621668 CCTTTTGATTGTCCCTCCCTCC 60.622 54.545 0.00 0.00 0.00 4.30
579 743 2.728007 CCTTTTGATTGTCCCTCCCTC 58.272 52.381 0.00 0.00 0.00 4.30
580 744 1.272704 GCCTTTTGATTGTCCCTCCCT 60.273 52.381 0.00 0.00 0.00 4.20
581 745 1.186200 GCCTTTTGATTGTCCCTCCC 58.814 55.000 0.00 0.00 0.00 4.30
582 746 0.811281 CGCCTTTTGATTGTCCCTCC 59.189 55.000 0.00 0.00 0.00 4.30
583 747 1.821216 TCGCCTTTTGATTGTCCCTC 58.179 50.000 0.00 0.00 0.00 4.30
584 748 2.286365 TTCGCCTTTTGATTGTCCCT 57.714 45.000 0.00 0.00 0.00 4.20
585 749 2.556622 TCTTTCGCCTTTTGATTGTCCC 59.443 45.455 0.00 0.00 0.00 4.46
586 750 3.826466 CTCTTTCGCCTTTTGATTGTCC 58.174 45.455 0.00 0.00 0.00 4.02
587 751 3.237628 GCTCTTTCGCCTTTTGATTGTC 58.762 45.455 0.00 0.00 0.00 3.18
588 752 2.350772 CGCTCTTTCGCCTTTTGATTGT 60.351 45.455 0.00 0.00 0.00 2.71
589 753 2.245096 CGCTCTTTCGCCTTTTGATTG 58.755 47.619 0.00 0.00 0.00 2.67
671 849 6.436843 TCCTCTGTTTTCACTTGAGTTTTC 57.563 37.500 0.00 0.00 0.00 2.29
704 882 2.037251 TCTCCTTTTTGTCTCCTCGTGG 59.963 50.000 0.00 0.00 0.00 4.94
775 975 2.199652 AAATGGTGTGGGTGCGTGG 61.200 57.895 0.00 0.00 0.00 4.94
781 981 0.469144 GGGTGTCAAATGGTGTGGGT 60.469 55.000 0.00 0.00 0.00 4.51
782 982 0.468958 TGGGTGTCAAATGGTGTGGG 60.469 55.000 0.00 0.00 0.00 4.61
784 984 1.397672 TGTGGGTGTCAAATGGTGTG 58.602 50.000 0.00 0.00 0.00 3.82
785 985 2.238521 GATGTGGGTGTCAAATGGTGT 58.761 47.619 0.00 0.00 0.00 4.16
786 986 2.030007 GTGATGTGGGTGTCAAATGGTG 60.030 50.000 0.00 0.00 0.00 4.17
789 997 4.487948 GAATGTGATGTGGGTGTCAAATG 58.512 43.478 0.00 0.00 0.00 2.32
793 1001 1.271871 GGGAATGTGATGTGGGTGTCA 60.272 52.381 0.00 0.00 0.00 3.58
843 1056 1.139947 CCTTCCCTTCGAGTCGCTC 59.860 63.158 7.92 0.00 0.00 5.03
870 1092 1.734137 GATAAGCGGCGAGGTGAGA 59.266 57.895 12.98 0.00 0.00 3.27
899 1121 2.778717 GAAGGGAGGGGATGGGGG 60.779 72.222 0.00 0.00 0.00 5.40
930 1152 3.207547 GAGTTGGGTTTGCGGTGGC 62.208 63.158 0.00 0.00 40.52 5.01
932 1154 2.903547 CGGAGTTGGGTTTGCGGTG 61.904 63.158 0.00 0.00 0.00 4.94
933 1155 2.593436 CGGAGTTGGGTTTGCGGT 60.593 61.111 0.00 0.00 0.00 5.68
936 1158 3.680786 GGCCGGAGTTGGGTTTGC 61.681 66.667 5.05 0.00 0.00 3.68
937 1159 3.361977 CGGCCGGAGTTGGGTTTG 61.362 66.667 20.10 0.00 0.00 2.93
1224 1480 1.522580 GCCGATGCTCTTGAGGTCC 60.523 63.158 0.00 0.00 33.53 4.46
1260 1516 2.042435 AGGGAGGAGAAGGAGGCG 60.042 66.667 0.00 0.00 0.00 5.52
1387 1643 2.284405 GTCGTTGGGGAGGGAGGA 60.284 66.667 0.00 0.00 0.00 3.71
1388 1644 1.900545 GAAGTCGTTGGGGAGGGAGG 61.901 65.000 0.00 0.00 0.00 4.30
1650 1906 3.708220 GAGCTTCTGGACGCCGGAG 62.708 68.421 5.05 3.72 40.34 4.63
1686 1942 2.185608 GAGAGCTTGGTCTCGCCC 59.814 66.667 13.03 0.00 38.12 6.13
1693 1949 4.379243 CGTGCCGGAGAGCTTGGT 62.379 66.667 5.05 0.00 0.00 3.67
1950 2206 0.105658 AGCCGTTATGGGAGGAGCTA 60.106 55.000 0.00 0.00 38.63 3.32
1952 2208 0.533085 GAAGCCGTTATGGGAGGAGC 60.533 60.000 0.00 0.00 38.63 4.70
2121 2377 1.079503 GATTGAGCACCGACACCTTC 58.920 55.000 0.00 0.00 0.00 3.46
2196 2452 3.862775 ATCAAGCCTGATGTCCGAGAGG 61.863 54.545 0.00 0.00 46.80 3.69
2334 2590 4.439700 GGATTGCTGGTGAGAATGACATTG 60.440 45.833 5.14 0.00 0.00 2.82
2350 2606 1.963515 GGTGTTGAAGTTGGGATTGCT 59.036 47.619 0.00 0.00 0.00 3.91
2407 2663 0.951558 GGCGTTGTTGGTGAATGAGT 59.048 50.000 0.00 0.00 0.00 3.41
2514 2770 4.373116 ACCACGCCGATCGCAACT 62.373 61.111 10.32 0.00 43.23 3.16
2544 2800 4.275508 AGCACCACAGCACCCAGG 62.276 66.667 0.00 0.00 36.85 4.45
2694 2950 2.042831 GCTGCTGGTTCCGCTTGAT 61.043 57.895 0.00 0.00 0.00 2.57
2787 3043 2.034558 CACATTGTCCGGAGCAAAGTTT 59.965 45.455 18.54 5.36 0.00 2.66
2973 3229 1.078709 CGATGCCGTAGCCCATTATG 58.921 55.000 0.00 0.00 38.69 1.90
3018 3274 1.951895 GCTCCATTGGACATGTGCTCA 60.952 52.381 18.75 5.61 0.00 4.26
3090 3346 4.015084 CAATGTTCAGCCTCTTCTTCCAT 58.985 43.478 0.00 0.00 0.00 3.41
3171 3427 2.237143 TGCTGACTTAAGATCCCTGTGG 59.763 50.000 10.09 0.00 0.00 4.17
3189 3445 2.778299 TCGCCAAGTAGAATGTTTGCT 58.222 42.857 0.00 0.00 0.00 3.91
3252 3508 4.675029 AAGTTCCCGTCCGGTGCG 62.675 66.667 0.00 7.83 0.00 5.34
3350 3606 0.523519 GTTGCAGAACTAAGCAGGGC 59.476 55.000 0.00 0.00 42.39 5.19
3475 3762 8.964476 TCAATTCAGTTTTTCAGTTCTCTACT 57.036 30.769 0.00 0.00 37.68 2.57
3476 3763 9.604626 CATCAATTCAGTTTTTCAGTTCTCTAC 57.395 33.333 0.00 0.00 0.00 2.59
3577 3864 7.171508 TGTCATTATCAAATCAACTCGGCTATC 59.828 37.037 0.00 0.00 0.00 2.08
3627 3914 4.224370 GTCACAGGGTTCCCAGTTAGAATA 59.776 45.833 10.73 0.00 0.00 1.75
3723 4013 4.654091 AGGTGGTTCAAACTTCACAATG 57.346 40.909 0.00 0.00 32.29 2.82
3743 4033 8.502387 GGAAGCTTTTATATACTGCATCAGAAG 58.498 37.037 0.00 0.00 35.18 2.85
3762 4052 7.951347 AGTAAATTTCTCATCATGGAAGCTT 57.049 32.000 0.00 0.00 0.00 3.74
3766 4056 9.177608 CTTGGTAGTAAATTTCTCATCATGGAA 57.822 33.333 0.00 0.00 0.00 3.53
3816 4111 7.094377 ACACACATTCAGGAACCATAATAACAC 60.094 37.037 0.00 0.00 0.00 3.32
3827 4123 1.195448 CAGCGACACACATTCAGGAAC 59.805 52.381 0.00 0.00 0.00 3.62
3882 4179 4.024048 ACATCTGCTTTCGTCGTGATTTTT 60.024 37.500 0.00 0.00 0.00 1.94
3891 4188 3.229552 GCTGAAAACATCTGCTTTCGTC 58.770 45.455 2.63 0.00 46.29 4.20
4173 4470 0.680921 ATTTCTCCACCATGGGCACG 60.681 55.000 18.09 1.70 38.32 5.34
4402 4699 3.676646 GCGATGACGATGATGATGATCAA 59.323 43.478 0.00 0.00 39.81 2.57
4423 4728 7.843490 TGTACTTATTTCTTGTAGACATGGC 57.157 36.000 0.00 0.00 0.00 4.40
4485 4790 1.283736 ACAAGAACGAAACGAACGCT 58.716 45.000 0.00 0.00 0.00 5.07
4486 4791 2.409371 CCTACAAGAACGAAACGAACGC 60.409 50.000 0.00 0.00 0.00 4.84
4488 4793 5.888412 TTACCTACAAGAACGAAACGAAC 57.112 39.130 0.00 0.00 0.00 3.95
4490 4795 5.591099 ACTTTACCTACAAGAACGAAACGA 58.409 37.500 0.00 0.00 0.00 3.85
4491 4796 5.895216 ACTTTACCTACAAGAACGAAACG 57.105 39.130 0.00 0.00 0.00 3.60
4492 4797 9.642312 CTTTTACTTTACCTACAAGAACGAAAC 57.358 33.333 0.00 0.00 0.00 2.78
4494 4799 7.442062 CCCTTTTACTTTACCTACAAGAACGAA 59.558 37.037 0.00 0.00 0.00 3.85
4498 4803 6.999871 CACCCCTTTTACTTTACCTACAAGAA 59.000 38.462 0.00 0.00 0.00 2.52
4520 4825 3.456039 GACGACGAACGACGCACC 61.456 66.667 16.85 5.34 46.94 5.01
4523 4828 2.503375 ATGGACGACGAACGACGC 60.503 61.111 16.85 10.60 46.94 5.19
4526 4831 1.731613 GCACATGGACGACGAACGA 60.732 57.895 0.00 0.00 45.77 3.85
4528 4833 0.163788 CAAGCACATGGACGACGAAC 59.836 55.000 0.00 0.00 0.00 3.95
4529 4834 0.249699 ACAAGCACATGGACGACGAA 60.250 50.000 0.00 0.00 0.00 3.85
4550 4855 2.359214 TGTCTATCTACAGCGGCAGAAG 59.641 50.000 1.45 0.00 0.00 2.85
4612 4923 1.629043 TCCATCCATCCTACGGTAGC 58.371 55.000 9.70 0.00 0.00 3.58
4618 4929 2.872038 GCGACCAATCCATCCATCCTAC 60.872 54.545 0.00 0.00 0.00 3.18
4629 4947 1.253100 TGGAAAAAGGCGACCAATCC 58.747 50.000 0.00 0.00 0.00 3.01
4631 4949 5.395214 GGAATAATGGAAAAAGGCGACCAAT 60.395 40.000 0.00 0.00 36.00 3.16
4641 4959 8.110860 GTCTCAAGACTGGAATAATGGAAAAA 57.889 34.615 2.86 0.00 41.65 1.94
4705 5023 9.168451 GATCAATCAGAGAAGCATGATATGATT 57.832 33.333 0.00 2.48 42.31 2.57
4713 5031 4.273724 CAGTGGATCAATCAGAGAAGCATG 59.726 45.833 0.00 0.00 0.00 4.06
4819 5144 2.344872 CCCTTTGGCCTTTGCAGC 59.655 61.111 3.32 0.00 40.13 5.25
4820 5145 2.586293 CCCCCTTTGGCCTTTGCAG 61.586 63.158 3.32 0.00 40.13 4.41
4821 5146 2.526375 CCCCCTTTGGCCTTTGCA 60.526 61.111 3.32 0.00 40.13 4.08
4822 5147 2.203773 TCCCCCTTTGGCCTTTGC 60.204 61.111 3.32 0.00 0.00 3.68
4823 5148 0.545071 ATGTCCCCCTTTGGCCTTTG 60.545 55.000 3.32 0.00 0.00 2.77
4824 5149 0.252239 GATGTCCCCCTTTGGCCTTT 60.252 55.000 3.32 0.00 0.00 3.11
4825 5150 1.388133 GATGTCCCCCTTTGGCCTT 59.612 57.895 3.32 0.00 0.00 4.35
4917 5242 1.968540 GACTGGTGCAAGCCTGGAC 60.969 63.158 0.00 0.00 42.85 4.02
4933 5258 2.823154 AGTGTGTAGAGCCTGAGAAGAC 59.177 50.000 0.00 0.00 0.00 3.01
4935 5260 3.256879 TCAAGTGTGTAGAGCCTGAGAAG 59.743 47.826 0.00 0.00 0.00 2.85
5029 5605 1.270550 CTTGCTTCAATGGTGGTGGTC 59.729 52.381 0.00 0.00 0.00 4.02
5121 5713 1.899142 ACTCCAGAGAAGAGAACCTGC 59.101 52.381 0.70 0.00 35.27 4.85
5135 5727 6.587990 CACTTGTCAGATAACTACAACTCCAG 59.412 42.308 0.00 0.00 0.00 3.86
5136 5728 6.455647 CACTTGTCAGATAACTACAACTCCA 58.544 40.000 0.00 0.00 0.00 3.86
5137 5729 5.869888 CCACTTGTCAGATAACTACAACTCC 59.130 44.000 0.00 0.00 0.00 3.85
5139 5731 5.238583 GCCACTTGTCAGATAACTACAACT 58.761 41.667 0.00 0.00 0.00 3.16
5140 5732 4.091509 CGCCACTTGTCAGATAACTACAAC 59.908 45.833 0.00 0.00 0.00 3.32
5141 5733 4.242475 CGCCACTTGTCAGATAACTACAA 58.758 43.478 0.00 0.00 0.00 2.41
5228 5823 2.829720 ACGTCAGTGGTTAATAGGAGCA 59.170 45.455 0.00 0.00 0.00 4.26
5229 5824 3.521947 ACGTCAGTGGTTAATAGGAGC 57.478 47.619 0.00 0.00 0.00 4.70
5308 5914 0.179059 TCACTTTCAGCGCCACAGAA 60.179 50.000 2.29 0.21 0.00 3.02
5325 5931 5.189342 TGATTAACCCCGGTAATTACACTCA 59.811 40.000 17.16 2.58 0.00 3.41
5370 5976 1.262417 CAAATCATCGATGCCGTGGAG 59.738 52.381 20.81 2.96 37.05 3.86


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

AutoCloner maintained by Alex Coulton.