Multiple sequence alignment - TraesCS2A01G585700

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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 TraesCS2A01G585700 chr2A 100.000 6206 0 0 1 6206 776224279 776218074 0.000000e+00 11461.0
1 TraesCS2A01G585700 chr1B 92.071 4427 224 57 542 4910 559574960 559579317 0.000000e+00 6113.0
2 TraesCS2A01G585700 chr1B 91.688 397 12 7 5813 6206 559585617 559585995 1.180000e-146 531.0
3 TraesCS2A01G585700 chr1B 89.273 289 20 4 68 346 559574503 559574790 9.900000e-93 351.0
4 TraesCS2A01G585700 chr1B 83.636 220 30 3 5550 5765 559585262 559585479 1.050000e-47 202.0
5 TraesCS2A01G585700 chr2D 89.410 3494 202 66 2786 6206 651414298 651417696 0.000000e+00 4248.0
6 TraesCS2A01G585700 chr2D 92.295 2362 135 27 451 2787 651411855 651414194 0.000000e+00 3310.0
7 TraesCS2A01G585700 chr2D 89.619 289 20 5 68 346 651411454 651411742 5.920000e-95 359.0
8 TraesCS2A01G585700 chr2D 82.000 150 21 5 469 616 609208869 609209014 8.450000e-24 122.0
9 TraesCS2A01G585700 chr2D 80.921 152 21 7 469 616 609218997 609219144 5.080000e-21 113.0
10 TraesCS2A01G585700 chr2D 80.795 151 22 6 469 616 609215342 609215488 1.830000e-20 111.0
11 TraesCS2A01G585700 chr2B 90.018 1683 89 22 3504 5141 780821014 780822662 0.000000e+00 2104.0
12 TraesCS2A01G585700 chr2B 91.129 1488 78 28 2058 3521 780819372 780820829 0.000000e+00 1967.0
13 TraesCS2A01G585700 chr2B 94.366 1278 54 4 798 2075 780818088 780819347 0.000000e+00 1945.0
14 TraesCS2A01G585700 chr2B 93.558 326 15 3 5881 6206 780667771 780667452 1.210000e-131 481.0
15 TraesCS2A01G585700 chr2B 87.279 283 22 12 76 346 780817585 780817865 1.680000e-80 311.0
16 TraesCS2A01G585700 chr2B 82.119 151 20 6 469 616 743233619 743233765 8.450000e-24 122.0
17 TraesCS2A01G585700 chr2B 81.333 150 22 6 469 616 743227494 743227639 3.930000e-22 117.0
18 TraesCS2A01G585700 chr2B 80.263 152 22 7 469 616 743277367 743277514 2.370000e-19 108.0
19 TraesCS2A01G585700 chr2B 100.000 43 0 0 5492 5534 780667827 780667785 5.160000e-11 80.5
20 TraesCS2A01G585700 chr1D 82.969 640 38 20 5576 6206 493954054 493953477 4.290000e-141 512.0
21 TraesCS2A01G585700 chr1D 85.901 383 23 12 4069 4439 493954697 493954334 4.540000e-101 379.0
22 TraesCS2A01G585700 chr3B 94.583 240 11 2 3599 3836 360429163 360428924 2.730000e-98 370.0
23 TraesCS2A01G585700 chr3B 93.519 108 4 2 2595 2699 360429267 360429160 2.320000e-34 158.0
24 TraesCS2A01G585700 chr7B 89.179 268 28 1 5925 6191 586265664 586265397 3.590000e-87 333.0
25 TraesCS2A01G585700 chr7B 87.279 283 32 4 5910 6191 586659728 586660007 2.790000e-83 320.0
26 TraesCS2A01G585700 chr7A 88.806 268 29 1 5925 6191 624966991 624966724 1.670000e-85 327.0
27 TraesCS2A01G585700 chr5D 88.806 268 29 1 5925 6191 400297143 400296876 1.670000e-85 327.0
28 TraesCS2A01G585700 chr5A 88.087 277 31 2 5916 6191 505627932 505627657 1.670000e-85 327.0
29 TraesCS2A01G585700 chr7D 87.912 273 31 2 5917 6188 543602375 543602646 2.790000e-83 320.0
30 TraesCS2A01G585700 chr4D 83.453 139 13 9 505 638 370374544 370374411 3.040000e-23 121.0


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 TraesCS2A01G585700 chr2A 776218074 776224279 6205 True 11461.00 11461 100.000000 1 6206 1 chr2A.!!$R1 6205
1 TraesCS2A01G585700 chr1B 559574503 559579317 4814 False 3232.00 6113 90.672000 68 4910 2 chr1B.!!$F1 4842
2 TraesCS2A01G585700 chr1B 559585262 559585995 733 False 366.50 531 87.662000 5550 6206 2 chr1B.!!$F2 656
3 TraesCS2A01G585700 chr2D 651411454 651417696 6242 False 2639.00 4248 90.441333 68 6206 3 chr2D.!!$F3 6138
4 TraesCS2A01G585700 chr2B 780817585 780822662 5077 False 1581.75 2104 90.698000 76 5141 4 chr2B.!!$F4 5065
5 TraesCS2A01G585700 chr1D 493953477 493954697 1220 True 445.50 512 84.435000 4069 6206 2 chr1D.!!$R1 2137

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
906 1074 0.168788 TCTGTTGCTAAAGCGCATGC 59.831 50.000 11.47 7.91 45.83 4.06 F
1571 1741 1.604378 CGGCTTCTCCTTCACCCAT 59.396 57.895 0.00 0.00 0.00 4.00 F
2464 2695 0.819259 TGGTCCTGTTGTTGAGCTGC 60.819 55.000 0.00 0.00 0.00 5.25 F
3320 3677 0.480690 CTCTCTCTAGCTAGCCCCCA 59.519 60.000 16.35 0.00 0.00 4.96 F
4640 5409 0.179059 TCTGTTTCTGTCTTGGCGCA 60.179 50.000 10.83 0.00 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1909 0.613260 CACGAGGGACATCAAGGGAA 59.387 55.000 0.00 0.00 0.00 3.97 R
3310 3667 0.767375 TCAATGAGATGGGGGCTAGC 59.233 55.000 6.04 6.04 0.00 3.42 R
4144 4744 0.461961 AGCAGTAGGTGGAATCGCTC 59.538 55.000 0.00 0.00 0.00 5.03 R
5138 5936 0.940833 TCTGCAATCACGACGCAAAA 59.059 45.000 0.00 0.00 34.75 2.44 R
5692 6500 1.228925 GGAGGCCTATAGCGAGGGT 60.229 63.158 4.42 0.00 45.17 4.34 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
22 23 4.859400 CGAGAGCCGAGAGACCTA 57.141 61.111 0.00 0.00 41.76 3.08
23 24 3.082165 CGAGAGCCGAGAGACCTAA 57.918 57.895 0.00 0.00 41.76 2.69
24 25 0.658897 CGAGAGCCGAGAGACCTAAC 59.341 60.000 0.00 0.00 41.76 2.34
25 26 1.026584 GAGAGCCGAGAGACCTAACC 58.973 60.000 0.00 0.00 0.00 2.85
26 27 0.331954 AGAGCCGAGAGACCTAACCA 59.668 55.000 0.00 0.00 0.00 3.67
27 28 0.741915 GAGCCGAGAGACCTAACCAG 59.258 60.000 0.00 0.00 0.00 4.00
28 29 1.142097 GCCGAGAGACCTAACCAGC 59.858 63.158 0.00 0.00 0.00 4.85
29 30 1.817209 CCGAGAGACCTAACCAGCC 59.183 63.158 0.00 0.00 0.00 4.85
30 31 0.970937 CCGAGAGACCTAACCAGCCA 60.971 60.000 0.00 0.00 0.00 4.75
31 32 0.457851 CGAGAGACCTAACCAGCCAG 59.542 60.000 0.00 0.00 0.00 4.85
32 33 0.827368 GAGAGACCTAACCAGCCAGG 59.173 60.000 0.00 0.00 45.67 4.45
33 34 0.413832 AGAGACCTAACCAGCCAGGA 59.586 55.000 0.00 0.00 41.22 3.86
34 35 0.827368 GAGACCTAACCAGCCAGGAG 59.173 60.000 0.00 0.00 41.22 3.69
35 36 1.222113 GACCTAACCAGCCAGGAGC 59.778 63.158 0.00 0.00 41.22 4.70
36 37 2.258748 GACCTAACCAGCCAGGAGCC 62.259 65.000 0.00 0.00 45.47 4.70
37 38 2.300967 CCTAACCAGCCAGGAGCCA 61.301 63.158 0.00 0.00 45.47 4.75
38 39 1.222936 CTAACCAGCCAGGAGCCAG 59.777 63.158 0.00 0.00 45.47 4.85
39 40 2.883267 CTAACCAGCCAGGAGCCAGC 62.883 65.000 0.00 0.00 45.47 4.85
109 110 4.653888 CCCTTCCCGCCACCGTTT 62.654 66.667 0.00 0.00 0.00 3.60
273 294 1.074167 CTCCAGCCTCCACCCCTAT 60.074 63.158 0.00 0.00 0.00 2.57
348 477 2.687935 TGAGTTGTTTCTCTGTTTGCCC 59.312 45.455 0.00 0.00 35.68 5.36
364 493 5.163280 TGTTTGCCCAACTGTTAGTACTACT 60.163 40.000 0.91 0.00 36.21 2.57
367 496 7.959658 TTGCCCAACTGTTAGTACTACTATA 57.040 36.000 0.91 0.00 29.64 1.31
368 497 7.959658 TGCCCAACTGTTAGTACTACTATAA 57.040 36.000 0.91 0.00 29.64 0.98
369 498 8.543293 TGCCCAACTGTTAGTACTACTATAAT 57.457 34.615 0.91 0.00 29.64 1.28
371 500 8.419442 GCCCAACTGTTAGTACTACTATAATGT 58.581 37.037 0.91 0.00 29.64 2.71
382 511 8.162085 AGTACTACTATAATGTACTAGCCAGCA 58.838 37.037 0.00 0.00 43.20 4.41
389 518 1.553248 TGTACTAGCCAGCAACCGATT 59.447 47.619 0.00 0.00 0.00 3.34
391 520 1.453155 ACTAGCCAGCAACCGATTTG 58.547 50.000 0.00 0.00 38.37 2.32
423 552 2.030007 TGCAAGACAGCAATTTAGCCAC 60.030 45.455 0.00 0.00 42.46 5.01
424 553 2.229784 GCAAGACAGCAATTTAGCCACT 59.770 45.455 0.00 0.00 34.23 4.00
425 554 3.829948 CAAGACAGCAATTTAGCCACTG 58.170 45.455 0.00 0.00 34.23 3.66
426 555 2.440409 AGACAGCAATTTAGCCACTGG 58.560 47.619 0.00 0.00 34.23 4.00
427 556 2.162681 GACAGCAATTTAGCCACTGGT 58.837 47.619 0.00 0.00 34.23 4.00
428 557 2.558359 GACAGCAATTTAGCCACTGGTT 59.442 45.455 0.00 0.00 34.23 3.67
429 558 2.965147 ACAGCAATTTAGCCACTGGTTT 59.035 40.909 0.00 0.00 34.23 3.27
430 559 4.148838 ACAGCAATTTAGCCACTGGTTTA 58.851 39.130 0.00 0.00 34.23 2.01
431 560 4.022329 ACAGCAATTTAGCCACTGGTTTAC 60.022 41.667 0.00 0.00 34.23 2.01
432 561 4.218417 CAGCAATTTAGCCACTGGTTTACT 59.782 41.667 0.00 0.00 34.23 2.24
433 562 4.218417 AGCAATTTAGCCACTGGTTTACTG 59.782 41.667 0.00 0.00 34.23 2.74
434 563 4.485163 CAATTTAGCCACTGGTTTACTGC 58.515 43.478 0.00 0.00 0.00 4.40
435 564 3.502123 TTTAGCCACTGGTTTACTGCT 57.498 42.857 0.00 0.00 0.00 4.24
436 565 3.502123 TTAGCCACTGGTTTACTGCTT 57.498 42.857 0.00 0.00 0.00 3.91
437 566 4.627284 TTAGCCACTGGTTTACTGCTTA 57.373 40.909 0.00 0.00 0.00 3.09
438 567 3.502123 AGCCACTGGTTTACTGCTTAA 57.498 42.857 0.00 0.00 0.00 1.85
439 568 4.034285 AGCCACTGGTTTACTGCTTAAT 57.966 40.909 0.00 0.00 0.00 1.40
440 569 3.758554 AGCCACTGGTTTACTGCTTAATG 59.241 43.478 0.00 0.00 0.00 1.90
441 570 3.673323 GCCACTGGTTTACTGCTTAATGC 60.673 47.826 0.00 0.00 43.25 3.56
442 571 3.758554 CCACTGGTTTACTGCTTAATGCT 59.241 43.478 0.00 0.00 43.37 3.79
443 572 4.218417 CCACTGGTTTACTGCTTAATGCTT 59.782 41.667 0.00 0.00 43.37 3.91
444 573 5.414454 CCACTGGTTTACTGCTTAATGCTTA 59.586 40.000 0.00 0.00 43.37 3.09
445 574 6.095440 CCACTGGTTTACTGCTTAATGCTTAT 59.905 38.462 0.00 0.00 43.37 1.73
446 575 7.282224 CCACTGGTTTACTGCTTAATGCTTATA 59.718 37.037 0.00 0.00 43.37 0.98
447 576 8.840321 CACTGGTTTACTGCTTAATGCTTATAT 58.160 33.333 0.00 0.00 43.37 0.86
484 613 4.632688 GCCATTGAATTGTGGAATTTGGAG 59.367 41.667 5.52 0.00 37.72 3.86
495 624 7.548196 TGTGGAATTTGGAGTATATTTCGTC 57.452 36.000 0.00 0.00 0.00 4.20
501 630 7.948278 ATTTGGAGTATATTTCGTCAGCTAC 57.052 36.000 0.00 0.00 0.00 3.58
506 635 6.924060 GGAGTATATTTCGTCAGCTACAATGT 59.076 38.462 0.00 0.00 0.00 2.71
507 636 7.438459 GGAGTATATTTCGTCAGCTACAATGTT 59.562 37.037 0.00 0.00 0.00 2.71
508 637 8.131455 AGTATATTTCGTCAGCTACAATGTTG 57.869 34.615 0.00 0.00 0.00 3.33
509 638 6.985188 ATATTTCGTCAGCTACAATGTTGT 57.015 33.333 3.64 3.64 44.86 3.32
510 639 4.466567 TTTCGTCAGCTACAATGTTGTG 57.533 40.909 8.57 0.84 42.31 3.33
511 640 3.378911 TCGTCAGCTACAATGTTGTGA 57.621 42.857 8.57 0.00 42.31 3.58
512 641 3.317150 TCGTCAGCTACAATGTTGTGAG 58.683 45.455 8.57 4.01 42.31 3.51
513 642 3.005367 TCGTCAGCTACAATGTTGTGAGA 59.995 43.478 8.57 0.00 42.31 3.27
514 643 3.121944 CGTCAGCTACAATGTTGTGAGAC 59.878 47.826 8.57 9.23 42.31 3.36
515 644 4.310769 GTCAGCTACAATGTTGTGAGACT 58.689 43.478 8.57 0.00 42.31 3.24
516 645 4.752101 GTCAGCTACAATGTTGTGAGACTT 59.248 41.667 8.57 0.00 42.31 3.01
517 646 4.751600 TCAGCTACAATGTTGTGAGACTTG 59.248 41.667 8.57 0.23 42.31 3.16
518 647 4.751600 CAGCTACAATGTTGTGAGACTTGA 59.248 41.667 8.57 0.00 42.31 3.02
519 648 5.410746 CAGCTACAATGTTGTGAGACTTGAT 59.589 40.000 8.57 0.00 42.31 2.57
520 649 6.000219 AGCTACAATGTTGTGAGACTTGATT 59.000 36.000 8.57 0.00 42.31 2.57
521 650 6.072838 AGCTACAATGTTGTGAGACTTGATTG 60.073 38.462 8.57 0.00 42.31 2.67
522 651 6.073058 GCTACAATGTTGTGAGACTTGATTGA 60.073 38.462 8.57 0.00 42.31 2.57
523 652 6.309712 ACAATGTTGTGAGACTTGATTGAG 57.690 37.500 0.00 0.00 40.49 3.02
524 653 5.152097 CAATGTTGTGAGACTTGATTGAGC 58.848 41.667 0.00 0.00 0.00 4.26
525 654 4.077300 TGTTGTGAGACTTGATTGAGCT 57.923 40.909 0.00 0.00 0.00 4.09
526 655 5.213891 TGTTGTGAGACTTGATTGAGCTA 57.786 39.130 0.00 0.00 0.00 3.32
527 656 5.798132 TGTTGTGAGACTTGATTGAGCTAT 58.202 37.500 0.00 0.00 0.00 2.97
528 657 6.233434 TGTTGTGAGACTTGATTGAGCTATT 58.767 36.000 0.00 0.00 0.00 1.73
529 658 6.712095 TGTTGTGAGACTTGATTGAGCTATTT 59.288 34.615 0.00 0.00 0.00 1.40
530 659 6.732531 TGTGAGACTTGATTGAGCTATTTG 57.267 37.500 0.00 0.00 0.00 2.32
531 660 6.233434 TGTGAGACTTGATTGAGCTATTTGT 58.767 36.000 0.00 0.00 0.00 2.83
532 661 6.712095 TGTGAGACTTGATTGAGCTATTTGTT 59.288 34.615 0.00 0.00 0.00 2.83
533 662 7.229306 TGTGAGACTTGATTGAGCTATTTGTTT 59.771 33.333 0.00 0.00 0.00 2.83
534 663 7.536622 GTGAGACTTGATTGAGCTATTTGTTTG 59.463 37.037 0.00 0.00 0.00 2.93
535 664 7.229306 TGAGACTTGATTGAGCTATTTGTTTGT 59.771 33.333 0.00 0.00 0.00 2.83
536 665 8.621532 AGACTTGATTGAGCTATTTGTTTGTA 57.378 30.769 0.00 0.00 0.00 2.41
537 666 9.236006 AGACTTGATTGAGCTATTTGTTTGTAT 57.764 29.630 0.00 0.00 0.00 2.29
538 667 9.846248 GACTTGATTGAGCTATTTGTTTGTATT 57.154 29.630 0.00 0.00 0.00 1.89
634 797 3.695606 TCCGCCACTGCCTCTGAC 61.696 66.667 0.00 0.00 0.00 3.51
685 848 2.704572 GCTGCAGTGTATTCTTCCTGT 58.295 47.619 16.64 0.00 0.00 4.00
691 854 4.275936 GCAGTGTATTCTTCCTGTTTGTGT 59.724 41.667 0.00 0.00 0.00 3.72
699 862 9.048446 GTATTCTTCCTGTTTGTGTTGTTACTA 57.952 33.333 0.00 0.00 0.00 1.82
709 872 8.658609 TGTTTGTGTTGTTACTAGTGTTAGAAC 58.341 33.333 5.39 1.90 32.14 3.01
763 926 5.181245 TGTTTTCCTAGTTGCTATGTCTTGC 59.819 40.000 0.00 0.00 0.00 4.01
770 933 3.054802 AGTTGCTATGTCTTGCTAAGCCT 60.055 43.478 0.00 0.00 32.14 4.58
780 943 4.390297 GTCTTGCTAAGCCTCACTTTACAG 59.610 45.833 0.00 0.00 39.97 2.74
896 1064 7.282585 AGGCAGATTTATTATGTCTGTTGCTA 58.717 34.615 3.86 0.00 41.04 3.49
906 1074 0.168788 TCTGTTGCTAAAGCGCATGC 59.831 50.000 11.47 7.91 45.83 4.06
927 1095 4.176271 GCTGTTTACATGGGAAGATTTGC 58.824 43.478 0.00 0.00 0.00 3.68
936 1104 2.028839 TGGGAAGATTTGCATGCAGTTG 60.029 45.455 21.50 0.00 0.00 3.16
1033 1203 2.432510 GTCTCAGTTGGATAGGGACAGG 59.567 54.545 0.00 0.00 0.00 4.00
1053 1223 6.872920 ACAGGCTTGAATAAGAGAGAAGTAG 58.127 40.000 1.40 0.00 35.92 2.57
1133 1303 2.091885 TCTTCTGAAGGCTGGTTTTGGT 60.092 45.455 16.83 0.00 0.00 3.67
1385 1555 3.650942 ACTCATCCTTGTTACTGGTGGAA 59.349 43.478 0.00 0.00 0.00 3.53
1463 1633 3.067320 AGTTTGGCTTCAACTCTCTTTGC 59.933 43.478 0.00 0.00 0.00 3.68
1469 1639 1.953559 TCAACTCTCTTTGCGTTGCT 58.046 45.000 0.00 0.00 40.18 3.91
1571 1741 1.604378 CGGCTTCTCCTTCACCCAT 59.396 57.895 0.00 0.00 0.00 4.00
1859 2029 8.810990 TTTTTGTTTAAGGTTAGAGTCTGGAA 57.189 30.769 1.86 0.00 0.00 3.53
1868 2038 6.784031 AGGTTAGAGTCTGGAACAATTTCAT 58.216 36.000 1.86 0.00 38.70 2.57
1980 2150 6.509418 TTGAGCAACAAACCTAACCATATC 57.491 37.500 0.00 0.00 35.39 1.63
1995 2165 4.841422 ACCATATCTGCTGATAGAATGGC 58.159 43.478 23.60 0.00 38.05 4.40
2145 2360 4.862641 AATGCCTGGATACTTGGTTAGT 57.137 40.909 0.00 0.00 41.04 2.24
2174 2389 7.148457 GGTTGTAGACTTTAGTAGAATGGTTGC 60.148 40.741 0.00 0.00 0.00 4.17
2206 2421 4.260170 AGCTTCAAACAGAGATGGCTAAG 58.740 43.478 0.00 0.00 0.00 2.18
2224 2439 7.506114 TGGCTAAGAAAATTATCCGACTGTAT 58.494 34.615 0.00 0.00 0.00 2.29
2328 2549 3.496160 GGCCTAGAGTTGGTTTCAGTTGA 60.496 47.826 0.00 0.00 0.00 3.18
2363 2584 7.537715 CAAATGCAAGATCACCATGTACTTAA 58.462 34.615 0.00 0.00 0.00 1.85
2375 2596 6.036517 CACCATGTACTTAAGAGTCTGAATGC 59.963 42.308 10.09 0.00 37.33 3.56
2376 2597 6.108687 CCATGTACTTAAGAGTCTGAATGCA 58.891 40.000 10.09 0.00 37.33 3.96
2377 2598 6.595326 CCATGTACTTAAGAGTCTGAATGCAA 59.405 38.462 10.09 0.00 37.33 4.08
2378 2599 7.201591 CCATGTACTTAAGAGTCTGAATGCAAG 60.202 40.741 10.09 0.00 37.33 4.01
2379 2600 6.993079 TGTACTTAAGAGTCTGAATGCAAGA 58.007 36.000 10.09 0.00 37.33 3.02
2380 2601 7.615403 TGTACTTAAGAGTCTGAATGCAAGAT 58.385 34.615 10.09 0.00 37.33 2.40
2381 2602 7.761704 TGTACTTAAGAGTCTGAATGCAAGATC 59.238 37.037 10.09 0.00 37.33 2.75
2383 2604 6.593382 ACTTAAGAGTCTGAATGCAAGATCAC 59.407 38.462 10.09 0.00 0.00 3.06
2384 2605 3.871485 AGAGTCTGAATGCAAGATCACC 58.129 45.455 0.00 0.00 0.00 4.02
2385 2606 3.262660 AGAGTCTGAATGCAAGATCACCA 59.737 43.478 0.00 0.00 0.00 4.17
2386 2607 4.080469 AGAGTCTGAATGCAAGATCACCAT 60.080 41.667 0.00 0.00 0.00 3.55
2389 2610 4.877823 GTCTGAATGCAAGATCACCATGTA 59.122 41.667 0.00 0.00 0.00 2.29
2390 2611 4.877823 TCTGAATGCAAGATCACCATGTAC 59.122 41.667 0.00 0.00 0.00 2.90
2409 2637 7.042187 CCATGTACTTGAGAAGATATGACAAGC 60.042 40.741 10.20 0.00 40.72 4.01
2427 2658 2.799017 AGCAATGACTGATCCTTTGCA 58.201 42.857 17.30 0.00 41.77 4.08
2451 2682 1.985159 TGAATAGCTGGTTGTGGTCCT 59.015 47.619 0.00 0.00 0.00 3.85
2464 2695 0.819259 TGGTCCTGTTGTTGAGCTGC 60.819 55.000 0.00 0.00 0.00 5.25
2527 2759 9.468532 AAGCAAAGTCAAATTTGATTAAGAGTC 57.531 29.630 23.05 8.38 44.48 3.36
2651 2887 9.162793 GCTCATTATGTTTGACATTCGAAATAG 57.837 33.333 0.00 0.00 39.88 1.73
2940 3288 1.518929 GATGAAGCACGTCGATACTGC 59.481 52.381 0.00 0.00 32.94 4.40
3071 3419 7.656542 TGTTACATGTCGAATGTTACTTGGTAA 59.343 33.333 20.13 7.33 34.01 2.85
3299 3656 5.041191 AGGACTCTGAATCTCTCTCTCTC 57.959 47.826 0.00 0.00 0.00 3.20
3300 3657 4.723789 AGGACTCTGAATCTCTCTCTCTCT 59.276 45.833 0.00 0.00 0.00 3.10
3303 3660 5.923204 ACTCTGAATCTCTCTCTCTCTCTC 58.077 45.833 0.00 0.00 0.00 3.20
3304 3661 5.664908 ACTCTGAATCTCTCTCTCTCTCTCT 59.335 44.000 0.00 0.00 0.00 3.10
3305 3662 6.166984 TCTGAATCTCTCTCTCTCTCTCTC 57.833 45.833 0.00 0.00 0.00 3.20
3306 3663 5.901853 TCTGAATCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
3307 3664 6.041409 TCTGAATCTCTCTCTCTCTCTCTCTC 59.959 46.154 0.00 0.00 0.00 3.20
3308 3665 5.901853 TGAATCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
3309 3666 7.069344 TGAATCTCTCTCTCTCTCTCTCTCTA 58.931 42.308 0.00 0.00 0.00 2.43
3310 3667 7.232330 TGAATCTCTCTCTCTCTCTCTCTCTAG 59.768 44.444 0.00 0.00 0.00 2.43
3311 3668 4.830046 TCTCTCTCTCTCTCTCTCTCTAGC 59.170 50.000 0.00 0.00 0.00 3.42
3312 3669 4.809193 TCTCTCTCTCTCTCTCTCTAGCT 58.191 47.826 0.00 0.00 0.00 3.32
3313 3670 5.953571 TCTCTCTCTCTCTCTCTCTAGCTA 58.046 45.833 0.00 0.00 0.00 3.32
3314 3671 6.007076 TCTCTCTCTCTCTCTCTCTAGCTAG 58.993 48.000 15.01 15.01 0.00 3.42
3315 3672 4.524714 TCTCTCTCTCTCTCTCTAGCTAGC 59.475 50.000 16.35 6.62 0.00 3.42
3320 3677 0.480690 CTCTCTCTAGCTAGCCCCCA 59.519 60.000 16.35 0.00 0.00 4.96
3535 4105 4.739228 TCATTGAAACGCTGTCAAAATGTG 59.261 37.500 0.78 0.00 38.44 3.21
3565 4135 8.310122 ACTTCCATTGCATTAAACTGGATAAT 57.690 30.769 0.00 0.00 35.99 1.28
3593 4163 4.261801 CCTTGGGACCTTACATGTTACAG 58.738 47.826 2.30 0.00 0.00 2.74
3622 4193 6.474427 CAGGCTTTGCATTTTGATACATACTG 59.526 38.462 0.00 0.00 0.00 2.74
3664 4235 4.019174 ACATTTGGTGGGATGAATCAGAC 58.981 43.478 0.00 0.00 0.00 3.51
3713 4284 8.506083 AGAAGGATAGACAATTTGAATATGGGT 58.494 33.333 2.79 0.00 0.00 4.51
3742 4313 3.195396 TGCTTGTTCAGAAAATATGGGGC 59.805 43.478 0.00 0.00 0.00 5.80
3812 4391 5.147032 TGTTCTCCCAAATTTTGATGGACT 58.853 37.500 10.72 0.00 39.12 3.85
3813 4392 5.010922 TGTTCTCCCAAATTTTGATGGACTG 59.989 40.000 10.72 0.35 39.12 3.51
3836 4421 5.470098 TGCAAAACAGTCTGTCTTATCCTTC 59.530 40.000 5.82 0.00 0.00 3.46
3855 4440 4.884164 CCTTCTCTTCTGTCCAAAAAGTGT 59.116 41.667 0.00 0.00 0.00 3.55
3891 4477 4.488790 CAGGTGCTCTGCCAAAGT 57.511 55.556 0.00 0.00 36.60 2.66
3892 4478 1.954528 CAGGTGCTCTGCCAAAGTG 59.045 57.895 0.00 0.00 36.60 3.16
3893 4479 1.900498 AGGTGCTCTGCCAAAGTGC 60.900 57.895 0.00 0.00 44.13 4.40
3894 4480 2.647297 GTGCTCTGCCAAAGTGCC 59.353 61.111 0.00 0.00 43.39 5.01
3895 4481 2.195411 TGCTCTGCCAAAGTGCCA 59.805 55.556 0.00 0.00 43.39 4.92
3896 4482 1.900016 TGCTCTGCCAAAGTGCCAG 60.900 57.895 0.00 0.00 43.39 4.85
3966 4554 8.873830 TCTTTTCAATTTATCTCTCTACAAGCG 58.126 33.333 0.00 0.00 0.00 4.68
4008 4596 9.196552 GTTCTATTTTCCTTCTGTTTCCATTTG 57.803 33.333 0.00 0.00 0.00 2.32
4025 4613 9.672673 TTTCCATTTGTTTCCACTCAAATTTAA 57.327 25.926 0.00 0.00 40.70 1.52
4034 4622 7.945033 TTCCACTCAAATTTAACTTTGATGC 57.055 32.000 18.07 0.00 42.54 3.91
4061 4649 9.956640 ATTTTGGATCAGATGGATAGAATAGAC 57.043 33.333 0.00 0.00 36.00 2.59
4125 4725 6.402983 GCTGAATGACTGTCAGGATAAAGTTG 60.403 42.308 16.46 0.18 42.36 3.16
4144 4744 3.921119 TGATTTGTGCAAGTTAGCAGG 57.079 42.857 0.00 0.00 46.69 4.85
4489 5254 6.613755 TTTCTGTAGGAAAAGTAACAGTGC 57.386 37.500 0.00 0.00 40.51 4.40
4500 5265 4.946478 AGTAACAGTGCTATCTCCCATC 57.054 45.455 0.00 0.00 0.00 3.51
4501 5267 4.290093 AGTAACAGTGCTATCTCCCATCA 58.710 43.478 0.00 0.00 0.00 3.07
4640 5409 0.179059 TCTGTTTCTGTCTTGGCGCA 60.179 50.000 10.83 0.00 0.00 6.09
4645 5414 0.737367 TTCTGTCTTGGCGCATCTCG 60.737 55.000 10.83 0.00 42.12 4.04
4855 5630 6.094742 CACTGAAGAGTTGCTCAGTAGATAGA 59.905 42.308 4.51 0.00 40.94 1.98
4868 5643 7.040340 GCTCAGTAGATAGAACAATGTAGCCTA 60.040 40.741 0.00 0.00 0.00 3.93
4894 5669 2.165030 AGATGGCATGTTTAGCAAGTGC 59.835 45.455 3.81 0.00 42.49 4.40
4909 5684 0.466189 AGTGCCATGCGAATTAGGGG 60.466 55.000 0.00 0.00 0.00 4.79
4914 5689 1.409521 CCATGCGAATTAGGGGGTTCA 60.410 52.381 0.00 0.00 0.00 3.18
4919 5694 3.288092 GCGAATTAGGGGGTTCATCTTT 58.712 45.455 0.00 0.00 0.00 2.52
4922 5697 4.947388 CGAATTAGGGGGTTCATCTTTTGA 59.053 41.667 0.00 0.00 0.00 2.69
4972 5747 9.545105 TTGAACTAGACAAATTTAACTAACGGA 57.455 29.630 0.00 0.00 0.00 4.69
5030 5828 3.186909 CATGCATGCAGATCAACTTTGG 58.813 45.455 26.69 0.00 0.00 3.28
5053 5851 3.843422 TGAATGGATTCAGTTGTGGGTT 58.157 40.909 0.00 0.00 41.51 4.11
5105 5903 1.762957 TCCTGAGGATTTTCTAGCCGG 59.237 52.381 0.00 0.00 0.00 6.13
5123 5921 0.247460 GGCCTTTGCATGAACCTTCC 59.753 55.000 0.00 0.00 40.13 3.46
5128 5926 3.321682 CCTTTGCATGAACCTTCCTTGAA 59.678 43.478 0.00 0.00 0.00 2.69
5135 5933 5.047802 GCATGAACCTTCCTTGAATTGAGAA 60.048 40.000 0.00 0.00 0.00 2.87
5138 5936 7.601705 TGAACCTTCCTTGAATTGAGAAAAT 57.398 32.000 0.00 0.00 0.00 1.82
5143 5941 7.227314 ACCTTCCTTGAATTGAGAAAATTTTGC 59.773 33.333 8.47 0.84 0.00 3.68
5160 5958 0.512518 TGCGTCGTGATTGCAGAAAG 59.487 50.000 0.00 0.00 34.03 2.62
5184 5982 2.752903 AGTTCGTGAAGTTTGGCTGTTT 59.247 40.909 0.00 0.00 0.00 2.83
5195 5993 9.039870 TGAAGTTTGGCTGTTTAAATAACAATG 57.960 29.630 0.00 0.00 0.00 2.82
5201 5999 9.553064 TTGGCTGTTTAAATAACAATGTGAAAT 57.447 25.926 0.00 0.00 0.00 2.17
5203 6001 9.810231 GGCTGTTTAAATAACAATGTGAAATTG 57.190 29.630 0.00 0.00 35.29 2.32
5225 6024 4.821805 TGATGTCAACAACCTTCTTTCTCC 59.178 41.667 0.00 0.00 0.00 3.71
5270 6069 5.705441 GTGGTGTCCTTGAAATTCAGTGATA 59.295 40.000 0.00 0.00 0.00 2.15
5272 6071 5.163854 GGTGTCCTTGAAATTCAGTGATACG 60.164 44.000 13.26 0.00 0.00 3.06
5280 6079 4.406648 AATTCAGTGATACGCTCCATCA 57.593 40.909 0.00 0.00 0.00 3.07
5282 6081 2.379005 TCAGTGATACGCTCCATCAGT 58.621 47.619 0.00 0.00 36.68 3.41
5296 6095 0.033011 ATCAGTCCTCCTGCGTACCT 60.033 55.000 0.00 0.00 41.25 3.08
5312 6113 7.280205 CCTGCGTACCTTAAATTCAAAGTAGAT 59.720 37.037 0.00 0.00 0.00 1.98
5353 6154 7.406031 TTTGGTATAAGAGACGAGATGACTT 57.594 36.000 0.00 0.00 0.00 3.01
5356 6157 5.048573 GGTATAAGAGACGAGATGACTTCCC 60.049 48.000 0.00 0.00 0.00 3.97
5368 6169 2.938838 TGACTTCCCGAATTTTGGTGT 58.061 42.857 1.96 0.00 0.00 4.16
5369 6170 2.882137 TGACTTCCCGAATTTTGGTGTC 59.118 45.455 1.96 7.55 0.00 3.67
5370 6171 3.146847 GACTTCCCGAATTTTGGTGTCT 58.853 45.455 1.96 0.00 0.00 3.41
5371 6172 2.884639 ACTTCCCGAATTTTGGTGTCTG 59.115 45.455 1.96 0.00 0.00 3.51
5372 6173 2.940994 TCCCGAATTTTGGTGTCTGA 57.059 45.000 1.96 0.00 0.00 3.27
5373 6174 3.216187 TCCCGAATTTTGGTGTCTGAA 57.784 42.857 1.96 0.00 0.00 3.02
5374 6175 3.556999 TCCCGAATTTTGGTGTCTGAAA 58.443 40.909 1.96 0.00 0.00 2.69
5375 6176 4.148838 TCCCGAATTTTGGTGTCTGAAAT 58.851 39.130 1.96 0.00 0.00 2.17
5376 6177 4.586841 TCCCGAATTTTGGTGTCTGAAATT 59.413 37.500 1.96 0.00 36.12 1.82
5377 6178 4.685628 CCCGAATTTTGGTGTCTGAAATTG 59.314 41.667 1.96 0.00 34.22 2.32
5379 6180 5.752955 CCGAATTTTGGTGTCTGAAATTGTT 59.247 36.000 0.00 0.00 34.22 2.83
5380 6181 6.257630 CCGAATTTTGGTGTCTGAAATTGTTT 59.742 34.615 0.00 0.00 34.22 2.83
5381 6182 7.201600 CCGAATTTTGGTGTCTGAAATTGTTTT 60.202 33.333 0.00 0.00 34.22 2.43
5437 6245 7.981789 TGTGAGAGAATTCATACATGTAACCTC 59.018 37.037 10.14 9.73 0.00 3.85
5447 6255 1.818674 CATGTAACCTCCAAAGTGGGC 59.181 52.381 0.00 0.00 38.32 5.36
5456 6264 1.153756 CAAAGTGGGCCCAGGAACT 59.846 57.895 29.55 16.90 43.88 3.01
5476 6284 9.264719 AGGAACTGATTCTTTTATTTTTGCAAG 57.735 29.630 0.00 0.00 37.18 4.01
5477 6285 9.045223 GGAACTGATTCTTTTATTTTTGCAAGT 57.955 29.630 0.00 0.00 34.98 3.16
5479 6287 9.598517 AACTGATTCTTTTATTTTTGCAAGTCA 57.401 25.926 0.00 0.00 0.00 3.41
5480 6288 9.252962 ACTGATTCTTTTATTTTTGCAAGTCAG 57.747 29.630 0.00 0.00 34.58 3.51
5481 6289 8.592105 TGATTCTTTTATTTTTGCAAGTCAGG 57.408 30.769 0.00 0.00 0.00 3.86
5482 6290 8.420222 TGATTCTTTTATTTTTGCAAGTCAGGA 58.580 29.630 0.00 0.00 0.00 3.86
5483 6291 9.260002 GATTCTTTTATTTTTGCAAGTCAGGAA 57.740 29.630 0.00 0.00 0.00 3.36
5484 6292 8.419076 TTCTTTTATTTTTGCAAGTCAGGAAC 57.581 30.769 0.00 0.00 0.00 3.62
5485 6293 7.781056 TCTTTTATTTTTGCAAGTCAGGAACT 58.219 30.769 0.00 0.00 41.10 3.01
5503 6311 7.365497 AGGAACTGATTCTTTTTGTTGGAAT 57.635 32.000 0.00 0.00 37.18 3.01
5512 6320 6.816134 TCTTTTTGTTGGAATCATGATCGA 57.184 33.333 9.06 0.00 0.00 3.59
5515 6323 5.956068 TTTGTTGGAATCATGATCGAACA 57.044 34.783 20.72 20.72 41.66 3.18
5516 6324 6.513806 TTTGTTGGAATCATGATCGAACAT 57.486 33.333 22.99 1.78 42.47 2.71
5517 6325 5.739752 TGTTGGAATCATGATCGAACATC 57.260 39.130 20.72 11.01 39.54 3.06
5518 6326 4.576053 TGTTGGAATCATGATCGAACATCC 59.424 41.667 20.72 17.43 39.54 3.51
5692 6500 1.081041 CCGATTCGTCCACGTCACA 60.081 57.895 5.20 0.00 40.80 3.58
5701 6509 2.632544 CCACGTCACACCCTCGCTA 61.633 63.158 0.00 0.00 0.00 4.26
5758 6575 0.806868 CCTCGTCCTGCAACGTACTA 59.193 55.000 10.50 0.00 43.08 1.82
5759 6576 1.467035 CCTCGTCCTGCAACGTACTAC 60.467 57.143 10.50 0.00 43.08 2.73
5760 6577 1.467734 CTCGTCCTGCAACGTACTACT 59.532 52.381 10.50 0.00 43.08 2.57
5765 6582 2.029649 TCCTGCAACGTACTACTTGGAC 60.030 50.000 0.00 0.00 0.00 4.02
5775 6592 1.477295 ACTACTTGGACCTAGCTTCGC 59.523 52.381 2.53 0.00 0.00 4.70
5899 6805 4.840005 GGCGGCGAAGGAGAAGGG 62.840 72.222 12.98 0.00 0.00 3.95
5901 6807 3.775654 CGGCGAAGGAGAAGGGCT 61.776 66.667 0.00 0.00 0.00 5.19
5902 6808 2.188207 GGCGAAGGAGAAGGGCTC 59.812 66.667 0.00 0.00 43.17 4.70
5963 6869 1.682684 CCTGGGCACGACCTACTCT 60.683 63.158 0.00 0.00 39.10 3.24
6050 6956 2.203788 TCCTGGGTCGCCTTCACT 60.204 61.111 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.199190 CTCTCGGCTCTCGCTCGT 61.199 66.667 0.00 0.00 39.05 4.18
1 2 2.892914 TCTCTCGGCTCTCGCTCG 60.893 66.667 0.00 0.00 39.05 5.03
2 3 2.713154 GTCTCTCGGCTCTCGCTC 59.287 66.667 0.00 0.00 39.05 5.03
3 4 1.973816 TAGGTCTCTCGGCTCTCGCT 61.974 60.000 0.00 0.00 39.05 4.93
4 5 1.096386 TTAGGTCTCTCGGCTCTCGC 61.096 60.000 0.00 0.00 39.05 5.03
5 6 0.658897 GTTAGGTCTCTCGGCTCTCG 59.341 60.000 0.00 0.00 40.90 4.04
7 8 0.331954 TGGTTAGGTCTCTCGGCTCT 59.668 55.000 0.00 0.00 0.00 4.09
8 9 0.741915 CTGGTTAGGTCTCTCGGCTC 59.258 60.000 0.00 0.00 0.00 4.70
9 10 1.324005 GCTGGTTAGGTCTCTCGGCT 61.324 60.000 0.00 0.00 0.00 5.52
10 11 1.142097 GCTGGTTAGGTCTCTCGGC 59.858 63.158 0.00 0.00 0.00 5.54
11 12 0.970937 TGGCTGGTTAGGTCTCTCGG 60.971 60.000 0.00 0.00 0.00 4.63
12 13 0.457851 CTGGCTGGTTAGGTCTCTCG 59.542 60.000 0.00 0.00 0.00 4.04
13 14 0.827368 CCTGGCTGGTTAGGTCTCTC 59.173 60.000 1.62 0.00 0.00 3.20
14 15 0.413832 TCCTGGCTGGTTAGGTCTCT 59.586 55.000 10.44 0.00 35.54 3.10
15 16 0.827368 CTCCTGGCTGGTTAGGTCTC 59.173 60.000 10.44 0.00 35.54 3.36
16 17 1.268283 GCTCCTGGCTGGTTAGGTCT 61.268 60.000 10.44 0.00 38.06 3.85
17 18 1.222113 GCTCCTGGCTGGTTAGGTC 59.778 63.158 10.44 0.00 38.06 3.85
18 19 2.301738 GGCTCCTGGCTGGTTAGGT 61.302 63.158 10.44 0.00 41.46 3.08
19 20 2.262774 CTGGCTCCTGGCTGGTTAGG 62.263 65.000 10.44 0.00 41.46 2.69
20 21 1.222936 CTGGCTCCTGGCTGGTTAG 59.777 63.158 10.44 2.64 41.46 2.34
21 22 2.971598 GCTGGCTCCTGGCTGGTTA 61.972 63.158 10.44 0.00 41.46 2.85
22 23 4.357279 GCTGGCTCCTGGCTGGTT 62.357 66.667 10.44 0.00 41.46 3.67
58 59 4.500116 GACAGGGAGACGGCGAGC 62.500 72.222 16.62 4.95 0.00 5.03
59 60 4.180946 CGACAGGGAGACGGCGAG 62.181 72.222 16.62 0.00 0.00 5.03
61 62 4.477975 GACGACAGGGAGACGGCG 62.478 72.222 4.80 4.80 39.69 6.46
62 63 4.131088 GGACGACAGGGAGACGGC 62.131 72.222 0.00 0.00 42.82 5.68
63 64 3.812019 CGGACGACAGGGAGACGG 61.812 72.222 0.00 0.00 39.69 4.79
64 65 3.812019 CCGGACGACAGGGAGACG 61.812 72.222 0.00 0.00 41.15 4.18
65 66 4.131088 GCCGGACGACAGGGAGAC 62.131 72.222 5.05 0.00 32.13 3.36
94 95 3.361977 CCAAACGGTGGCGGGAAG 61.362 66.667 0.00 0.00 41.72 3.46
283 304 1.972660 AATGGCTAGAGCGGTGGGTC 61.973 60.000 0.00 0.00 43.26 4.46
292 313 2.286872 CCTTGCTGTGAATGGCTAGAG 58.713 52.381 0.00 0.00 34.29 2.43
364 493 4.585581 TCGGTTGCTGGCTAGTACATTATA 59.414 41.667 0.00 0.00 0.00 0.98
367 496 1.553248 TCGGTTGCTGGCTAGTACATT 59.447 47.619 0.00 0.00 0.00 2.71
368 497 1.191535 TCGGTTGCTGGCTAGTACAT 58.808 50.000 0.00 0.00 0.00 2.29
369 498 1.191535 ATCGGTTGCTGGCTAGTACA 58.808 50.000 0.00 0.00 0.00 2.90
371 500 2.235155 TCAAATCGGTTGCTGGCTAGTA 59.765 45.455 0.00 0.00 37.13 1.82
372 501 1.003118 TCAAATCGGTTGCTGGCTAGT 59.997 47.619 0.00 0.00 37.13 2.57
373 502 1.737838 TCAAATCGGTTGCTGGCTAG 58.262 50.000 0.00 0.00 37.13 3.42
374 503 2.418368 ATCAAATCGGTTGCTGGCTA 57.582 45.000 0.00 0.00 37.13 3.93
375 504 1.203052 CAATCAAATCGGTTGCTGGCT 59.797 47.619 0.00 0.00 37.13 4.75
376 505 1.202114 TCAATCAAATCGGTTGCTGGC 59.798 47.619 0.00 0.00 37.13 4.85
377 506 3.574284 TTCAATCAAATCGGTTGCTGG 57.426 42.857 0.00 0.00 37.13 4.85
382 511 5.722263 TGCATCAATTCAATCAAATCGGTT 58.278 33.333 0.00 0.00 0.00 4.44
389 518 5.165676 GCTGTCTTGCATCAATTCAATCAA 58.834 37.500 0.00 0.00 0.00 2.57
391 520 4.740268 TGCTGTCTTGCATCAATTCAATC 58.260 39.130 0.00 0.00 38.12 2.67
448 577 9.051679 CACAATTCAATGGCATCAATCAATTAT 57.948 29.630 0.00 0.00 0.00 1.28
449 578 7.496263 CCACAATTCAATGGCATCAATCAATTA 59.504 33.333 0.00 0.00 0.00 1.40
457 586 5.423704 AATTCCACAATTCAATGGCATCA 57.576 34.783 0.00 0.00 35.81 3.07
484 613 7.846107 CACAACATTGTAGCTGACGAAATATAC 59.154 37.037 0.00 0.00 39.91 1.47
495 624 4.751600 TCAAGTCTCACAACATTGTAGCTG 59.248 41.667 0.00 0.00 39.91 4.24
501 630 5.048921 AGCTCAATCAAGTCTCACAACATTG 60.049 40.000 0.00 0.00 0.00 2.82
506 635 6.712095 ACAAATAGCTCAATCAAGTCTCACAA 59.288 34.615 0.00 0.00 0.00 3.33
507 636 6.233434 ACAAATAGCTCAATCAAGTCTCACA 58.767 36.000 0.00 0.00 0.00 3.58
508 637 6.734104 ACAAATAGCTCAATCAAGTCTCAC 57.266 37.500 0.00 0.00 0.00 3.51
509 638 7.229306 ACAAACAAATAGCTCAATCAAGTCTCA 59.771 33.333 0.00 0.00 0.00 3.27
510 639 7.588512 ACAAACAAATAGCTCAATCAAGTCTC 58.411 34.615 0.00 0.00 0.00 3.36
511 640 7.516198 ACAAACAAATAGCTCAATCAAGTCT 57.484 32.000 0.00 0.00 0.00 3.24
512 641 9.846248 AATACAAACAAATAGCTCAATCAAGTC 57.154 29.630 0.00 0.00 0.00 3.01
634 797 5.835113 AAATCCTTGAACCCAATCGTATG 57.165 39.130 0.00 0.00 0.00 2.39
685 848 8.774890 TGTTCTAACACTAGTAACAACACAAA 57.225 30.769 5.82 0.00 33.17 2.83
699 862 8.303156 CAGCAGCTAGATATATGTTCTAACACT 58.697 37.037 0.00 0.00 42.51 3.55
709 872 6.865726 ACGAAGTTTCAGCAGCTAGATATATG 59.134 38.462 0.00 0.00 37.78 1.78
763 926 6.146347 GTGAGAAACTGTAAAGTGAGGCTTAG 59.854 42.308 0.00 0.00 36.17 2.18
770 933 3.724374 CCGGTGAGAAACTGTAAAGTGA 58.276 45.455 0.00 0.00 32.74 3.41
780 943 0.036388 TCATGGAGCCGGTGAGAAAC 60.036 55.000 1.90 0.00 0.00 2.78
906 1074 5.389859 TGCAAATCTTCCCATGTAAACAG 57.610 39.130 0.00 0.00 0.00 3.16
927 1095 5.865013 TGATAAATTGCTCAACAACTGCATG 59.135 36.000 0.00 0.00 42.27 4.06
936 1104 6.638468 GGGATCGATTTGATAAATTGCTCAAC 59.362 38.462 0.00 0.00 37.47 3.18
1033 1203 6.255453 CACTGCTACTTCTCTCTTATTCAAGC 59.745 42.308 0.00 0.00 0.00 4.01
1053 1223 2.097466 CCGTCATGTAAAATCCCACTGC 59.903 50.000 0.00 0.00 0.00 4.40
1133 1303 1.619432 GCAATTGGATCCTTGTCCCCA 60.619 52.381 14.23 0.00 37.48 4.96
1385 1555 0.036010 CTGGAGGATTGAACTGCGGT 60.036 55.000 0.00 0.00 0.00 5.68
1469 1639 1.671742 GACAAGGGAAGGAGCGTCA 59.328 57.895 0.00 0.00 0.00 4.35
1571 1741 2.525629 TGAAGGACAGGGGACGCA 60.526 61.111 0.00 0.00 0.00 5.24
1739 1909 0.613260 CACGAGGGACATCAAGGGAA 59.387 55.000 0.00 0.00 0.00 3.97
1835 2005 7.830201 TGTTCCAGACTCTAACCTTAAACAAAA 59.170 33.333 0.00 0.00 0.00 2.44
1881 2051 6.479972 TCCATACGAAGGTCACATCTTAAT 57.520 37.500 0.00 0.00 0.00 1.40
1886 2056 4.567159 GTCTTTCCATACGAAGGTCACATC 59.433 45.833 0.00 0.00 0.00 3.06
1969 2139 7.046652 CCATTCTATCAGCAGATATGGTTAGG 58.953 42.308 9.97 1.56 36.21 2.69
1980 2150 2.634815 AGGTGCCATTCTATCAGCAG 57.365 50.000 0.00 0.00 35.56 4.24
1995 2165 7.957002 AGATACAGAACATAGTTCCATAGGTG 58.043 38.462 6.29 0.71 0.00 4.00
2145 2360 7.453752 ACCATTCTACTAAAGTCTACAACCTGA 59.546 37.037 0.00 0.00 0.00 3.86
2174 2389 6.042777 TCTCTGTTTGAAGCTATCATAACCG 58.957 40.000 0.00 0.00 38.03 4.44
2224 2439 3.205338 GCATGAGTGTGTGCATATGGTA 58.795 45.455 4.56 0.00 40.94 3.25
2296 2512 6.763715 ACCAACTCTAGGCCATAATATTCA 57.236 37.500 5.01 0.00 0.00 2.57
2297 2513 7.719633 TGAAACCAACTCTAGGCCATAATATTC 59.280 37.037 5.01 0.00 0.00 1.75
2328 2549 5.922544 GTGATCTTGCATTTGCTTAGTTTGT 59.077 36.000 3.94 0.00 42.66 2.83
2363 2584 3.262660 TGGTGATCTTGCATTCAGACTCT 59.737 43.478 0.00 0.00 0.00 3.24
2375 2596 6.401394 TCTTCTCAAGTACATGGTGATCTTG 58.599 40.000 0.00 4.72 35.17 3.02
2376 2597 6.611613 TCTTCTCAAGTACATGGTGATCTT 57.388 37.500 0.00 0.00 0.00 2.40
2377 2598 6.805016 ATCTTCTCAAGTACATGGTGATCT 57.195 37.500 0.00 0.00 0.00 2.75
2378 2599 8.363390 TCATATCTTCTCAAGTACATGGTGATC 58.637 37.037 0.00 0.00 0.00 2.92
2379 2600 8.147058 GTCATATCTTCTCAAGTACATGGTGAT 58.853 37.037 0.00 1.07 0.00 3.06
2380 2601 7.124147 TGTCATATCTTCTCAAGTACATGGTGA 59.876 37.037 0.00 0.00 0.00 4.02
2381 2602 7.267857 TGTCATATCTTCTCAAGTACATGGTG 58.732 38.462 0.00 0.00 0.00 4.17
2383 2604 7.042187 GCTTGTCATATCTTCTCAAGTACATGG 60.042 40.741 0.00 0.00 38.09 3.66
2384 2605 7.493645 TGCTTGTCATATCTTCTCAAGTACATG 59.506 37.037 0.00 0.00 38.09 3.21
2385 2606 7.559486 TGCTTGTCATATCTTCTCAAGTACAT 58.441 34.615 0.00 0.00 38.09 2.29
2386 2607 6.935167 TGCTTGTCATATCTTCTCAAGTACA 58.065 36.000 0.00 0.00 38.09 2.90
2389 2610 7.065563 GTCATTGCTTGTCATATCTTCTCAAGT 59.934 37.037 0.00 0.00 38.09 3.16
2390 2611 7.280428 AGTCATTGCTTGTCATATCTTCTCAAG 59.720 37.037 0.00 0.00 38.60 3.02
2427 2658 2.639839 ACCACAACCAGCTATTCAGACT 59.360 45.455 0.00 0.00 0.00 3.24
2451 2682 1.068588 AGTACTCGCAGCTCAACAACA 59.931 47.619 0.00 0.00 0.00 3.33
2464 2695 9.516314 TCACATTCATTAATTACTCAGTACTCG 57.484 33.333 0.00 0.00 0.00 4.18
2501 2733 9.468532 GACTCTTAATCAAATTTGACTTTGCTT 57.531 29.630 22.71 14.04 40.49 3.91
2527 2759 9.358872 GCTCCAAAGGAAAATTTAAAGTATGAG 57.641 33.333 0.00 0.00 0.00 2.90
2531 2763 7.507616 TCCAGCTCCAAAGGAAAATTTAAAGTA 59.492 33.333 0.00 0.00 0.00 2.24
2536 2769 5.144100 TGTCCAGCTCCAAAGGAAAATTTA 58.856 37.500 0.00 0.00 32.30 1.40
2543 2776 0.979665 CTCTGTCCAGCTCCAAAGGA 59.020 55.000 0.00 0.00 0.00 3.36
2546 2779 4.033009 TGATATCTCTGTCCAGCTCCAAA 58.967 43.478 3.98 0.00 0.00 3.28
2583 2816 9.703892 TTCAACCAATCAACCAACTAATAAATG 57.296 29.630 0.00 0.00 0.00 2.32
2589 2822 6.549364 AGATGTTCAACCAATCAACCAACTAA 59.451 34.615 0.00 0.00 0.00 2.24
2651 2887 3.042887 GGCGAAACAGTGTGATCAAAAC 58.957 45.455 0.00 0.00 0.00 2.43
2716 2959 5.021033 TGGTGCTTGAAAAACACAATGAT 57.979 34.783 0.00 0.00 36.00 2.45
2940 3288 1.898472 TCTCCTTCAACAGGCAGAGAG 59.102 52.381 0.00 0.00 43.55 3.20
3074 3422 9.520204 CTGCAAATTAAAATTCCGTTAGATGAT 57.480 29.630 0.00 0.00 0.00 2.45
3075 3423 7.973388 CCTGCAAATTAAAATTCCGTTAGATGA 59.027 33.333 0.00 0.00 0.00 2.92
3076 3424 7.973388 TCCTGCAAATTAAAATTCCGTTAGATG 59.027 33.333 0.00 0.00 0.00 2.90
3077 3425 8.062065 TCCTGCAAATTAAAATTCCGTTAGAT 57.938 30.769 0.00 0.00 0.00 1.98
3092 3440 4.067192 GTCAAGGCAAATTCCTGCAAATT 58.933 39.130 4.59 0.00 44.52 1.82
3096 3444 0.968405 GGTCAAGGCAAATTCCTGCA 59.032 50.000 4.59 0.00 44.52 4.41
3282 3639 5.901853 AGAGAGAGAGAGAGAGAGATTCAGA 59.098 44.000 0.00 0.00 0.00 3.27
3299 3656 1.271926 GGGGGCTAGCTAGAGAGAGAG 60.272 61.905 25.15 0.00 0.00 3.20
3300 3657 0.774908 GGGGGCTAGCTAGAGAGAGA 59.225 60.000 25.15 0.00 0.00 3.10
3303 3660 1.077005 AGATGGGGGCTAGCTAGAGAG 59.923 57.143 25.15 0.02 0.00 3.20
3304 3661 1.076350 GAGATGGGGGCTAGCTAGAGA 59.924 57.143 25.15 2.70 0.00 3.10
3305 3662 1.203112 TGAGATGGGGGCTAGCTAGAG 60.203 57.143 25.15 1.31 0.00 2.43
3306 3663 0.860457 TGAGATGGGGGCTAGCTAGA 59.140 55.000 25.15 3.01 0.00 2.43
3307 3664 1.949799 ATGAGATGGGGGCTAGCTAG 58.050 55.000 16.84 16.84 0.00 3.42
3308 3665 1.980765 CAATGAGATGGGGGCTAGCTA 59.019 52.381 15.72 0.00 0.00 3.32
3309 3666 0.769873 CAATGAGATGGGGGCTAGCT 59.230 55.000 15.72 0.00 0.00 3.32
3310 3667 0.767375 TCAATGAGATGGGGGCTAGC 59.233 55.000 6.04 6.04 0.00 3.42
3311 3668 2.333069 TCTCAATGAGATGGGGGCTAG 58.667 52.381 9.18 0.00 33.35 3.42
3312 3669 2.494888 TCTCAATGAGATGGGGGCTA 57.505 50.000 9.18 0.00 33.35 3.93
3313 3670 1.830486 ATCTCAATGAGATGGGGGCT 58.170 50.000 23.51 0.00 46.21 5.19
3474 3840 5.068855 TCAGACATTGTGGAATGCAGAAAAA 59.931 36.000 0.00 0.00 42.54 1.94
3488 3854 4.644234 TCACCACACATTTTCAGACATTGT 59.356 37.500 0.00 0.00 0.00 2.71
3565 4135 3.033659 TGTAAGGTCCCAAGGCAAAAA 57.966 42.857 0.00 0.00 0.00 1.94
3622 4193 3.394606 TGTATTTTCTAGGATGCCCTCCC 59.605 47.826 0.00 0.00 46.27 4.30
3812 4391 4.973168 AGGATAAGACAGACTGTTTTGCA 58.027 39.130 18.94 3.18 0.00 4.08
3813 4392 5.703130 AGAAGGATAAGACAGACTGTTTTGC 59.297 40.000 18.94 11.63 0.00 3.68
3825 4404 5.923733 TGGACAGAAGAGAAGGATAAGAC 57.076 43.478 0.00 0.00 0.00 3.01
3889 4475 5.204292 TCTCTATCTACATGAACTGGCACT 58.796 41.667 0.00 0.00 0.00 4.40
3890 4476 5.521906 TCTCTATCTACATGAACTGGCAC 57.478 43.478 0.00 0.00 0.00 5.01
3891 4477 6.544928 TTTCTCTATCTACATGAACTGGCA 57.455 37.500 0.00 0.00 0.00 4.92
3892 4478 7.212976 TCATTTCTCTATCTACATGAACTGGC 58.787 38.462 0.00 0.00 0.00 4.85
3893 4479 9.605275 TTTCATTTCTCTATCTACATGAACTGG 57.395 33.333 0.00 0.00 31.89 4.00
3957 4545 5.079689 TCATGATTGGTAACGCTTGTAGA 57.920 39.130 0.00 0.00 42.51 2.59
3991 4579 4.959210 TGGAAACAAATGGAAACAGAAGGA 59.041 37.500 0.00 0.00 40.96 3.36
4025 4613 5.988310 TCTGATCCAAAATGCATCAAAGT 57.012 34.783 0.00 0.00 0.00 2.66
4034 4622 9.955102 TCTATTCTATCCATCTGATCCAAAATG 57.045 33.333 0.00 0.00 34.76 2.32
4125 4725 3.671702 GCTCCTGCTAACTTGCACAAATC 60.672 47.826 0.00 0.00 38.12 2.17
4144 4744 0.461961 AGCAGTAGGTGGAATCGCTC 59.538 55.000 0.00 0.00 0.00 5.03
4481 5246 4.030216 TGTGATGGGAGATAGCACTGTTA 58.970 43.478 0.00 0.00 35.60 2.41
4489 5254 3.004210 CAGACTCGTGTGATGGGAGATAG 59.996 52.174 0.00 0.00 0.00 2.08
4640 5409 1.993370 GCGTTAGTGAACAAGCGAGAT 59.007 47.619 0.00 0.00 35.06 2.75
4645 5414 2.480419 ACATGAGCGTTAGTGAACAAGC 59.520 45.455 0.00 0.00 35.06 4.01
4648 5417 1.798223 GCACATGAGCGTTAGTGAACA 59.202 47.619 0.00 0.00 35.06 3.18
4745 5520 1.338136 ACTCGAAATCGGGGCTGGAT 61.338 55.000 7.70 0.00 45.75 3.41
4855 5630 7.277174 GCCATCTAAAATAGGCTACATTGTT 57.723 36.000 0.00 0.00 43.70 2.83
4868 5643 7.037438 CACTTGCTAAACATGCCATCTAAAAT 58.963 34.615 0.00 0.00 0.00 1.82
4894 5669 1.318576 GAACCCCCTAATTCGCATGG 58.681 55.000 0.00 0.00 0.00 3.66
4949 5724 8.943002 CCATCCGTTAGTTAAATTTGTCTAGTT 58.057 33.333 0.00 0.00 0.00 2.24
4980 5762 3.464720 AGAGAACCTCTGGTCTCATGA 57.535 47.619 10.02 0.00 39.62 3.07
4989 5771 1.407989 GCATGGGGAAGAGAACCTCTG 60.408 57.143 0.00 0.00 40.28 3.35
4997 5779 3.127099 ATGCATGCATGGGGAAGAG 57.873 52.632 31.74 0.11 35.03 2.85
5030 5828 4.019174 ACCCACAACTGAATCCATTCATC 58.981 43.478 2.45 0.00 44.92 2.92
5053 5851 2.840511 TCCCAGTAGCTAAATCCACCA 58.159 47.619 0.00 0.00 0.00 4.17
5105 5903 1.260544 AGGAAGGTTCATGCAAAGGC 58.739 50.000 0.00 0.00 41.68 4.35
5123 5921 6.074888 ACGACGCAAAATTTTCTCAATTCAAG 60.075 34.615 0.00 0.00 0.00 3.02
5128 5926 4.854399 TCACGACGCAAAATTTTCTCAAT 58.146 34.783 0.00 0.00 0.00 2.57
5135 5933 2.725723 CTGCAATCACGACGCAAAATTT 59.274 40.909 0.00 0.00 34.75 1.82
5138 5936 0.940833 TCTGCAATCACGACGCAAAA 59.059 45.000 0.00 0.00 34.75 2.44
5143 5941 1.792367 TCACTTTCTGCAATCACGACG 59.208 47.619 0.00 0.00 0.00 5.12
5160 5958 1.940613 AGCCAAACTTCACGAACTCAC 59.059 47.619 0.00 0.00 0.00 3.51
5195 5993 6.507023 AGAAGGTTGTTGACATCAATTTCAC 58.493 36.000 18.59 4.18 38.24 3.18
5201 5999 5.299279 GGAGAAAGAAGGTTGTTGACATCAA 59.701 40.000 0.00 0.00 0.00 2.57
5203 6001 4.821805 TGGAGAAAGAAGGTTGTTGACATC 59.178 41.667 0.00 0.00 0.00 3.06
5204 6002 4.792068 TGGAGAAAGAAGGTTGTTGACAT 58.208 39.130 0.00 0.00 0.00 3.06
5208 6006 4.144297 TGGATGGAGAAAGAAGGTTGTTG 58.856 43.478 0.00 0.00 0.00 3.33
5211 6009 4.584325 TGTTTGGATGGAGAAAGAAGGTTG 59.416 41.667 0.00 0.00 0.00 3.77
5225 6024 2.157668 CGTCGAAAGAGGTGTTTGGATG 59.842 50.000 0.00 0.00 43.49 3.51
5270 6069 1.000993 AGGAGGACTGATGGAGCGT 59.999 57.895 0.00 0.00 0.00 5.07
5280 6079 2.226962 TTAAGGTACGCAGGAGGACT 57.773 50.000 0.00 0.00 0.00 3.85
5282 6081 3.516300 TGAATTTAAGGTACGCAGGAGGA 59.484 43.478 0.00 0.00 0.00 3.71
5353 6154 2.940994 TCAGACACCAAAATTCGGGA 57.059 45.000 2.58 0.00 0.00 5.14
5356 6157 6.826893 AACAATTTCAGACACCAAAATTCG 57.173 33.333 0.00 0.00 31.91 3.34
5368 6169 7.496747 CCCAAGAGGTTAAAAACAATTTCAGA 58.503 34.615 0.00 0.00 0.00 3.27
5369 6170 7.713764 CCCAAGAGGTTAAAAACAATTTCAG 57.286 36.000 0.00 0.00 0.00 3.02
5423 6231 4.640201 CCCACTTTGGAGGTTACATGTATG 59.360 45.833 6.36 0.00 40.96 2.39
5437 6245 1.908299 GTTCCTGGGCCCACTTTGG 60.908 63.158 24.45 21.64 37.25 3.28
5447 6255 7.118245 GCAAAAATAAAAGAATCAGTTCCTGGG 59.882 37.037 0.00 0.00 34.81 4.45
5456 6264 8.420222 TCCTGACTTGCAAAAATAAAAGAATCA 58.580 29.630 0.00 0.00 0.00 2.57
5457 6265 8.816640 TCCTGACTTGCAAAAATAAAAGAATC 57.183 30.769 0.00 0.00 0.00 2.52
5458 6266 9.045223 GTTCCTGACTTGCAAAAATAAAAGAAT 57.955 29.630 0.00 0.00 0.00 2.40
5459 6267 8.257306 AGTTCCTGACTTGCAAAAATAAAAGAA 58.743 29.630 0.00 0.00 33.92 2.52
5460 6268 7.706179 CAGTTCCTGACTTGCAAAAATAAAAGA 59.294 33.333 0.00 0.00 36.10 2.52
5461 6269 7.706179 TCAGTTCCTGACTTGCAAAAATAAAAG 59.294 33.333 0.00 0.00 35.39 2.27
5462 6270 7.551585 TCAGTTCCTGACTTGCAAAAATAAAA 58.448 30.769 0.00 0.00 35.39 1.52
5463 6271 7.106439 TCAGTTCCTGACTTGCAAAAATAAA 57.894 32.000 0.00 0.00 35.39 1.40
5464 6272 6.707440 TCAGTTCCTGACTTGCAAAAATAA 57.293 33.333 0.00 0.00 35.39 1.40
5465 6273 6.899393 ATCAGTTCCTGACTTGCAAAAATA 57.101 33.333 0.00 0.00 43.63 1.40
5466 6274 5.796424 ATCAGTTCCTGACTTGCAAAAAT 57.204 34.783 0.00 0.00 43.63 1.82
5467 6275 5.360714 AGAATCAGTTCCTGACTTGCAAAAA 59.639 36.000 0.00 0.00 43.63 1.94
5468 6276 4.889409 AGAATCAGTTCCTGACTTGCAAAA 59.111 37.500 0.00 0.00 43.63 2.44
5469 6277 4.464008 AGAATCAGTTCCTGACTTGCAAA 58.536 39.130 0.00 0.00 43.63 3.68
5470 6278 4.090761 AGAATCAGTTCCTGACTTGCAA 57.909 40.909 0.00 0.00 43.63 4.08
5471 6279 3.777106 AGAATCAGTTCCTGACTTGCA 57.223 42.857 0.00 0.00 43.63 4.08
5472 6280 5.444663 AAAAGAATCAGTTCCTGACTTGC 57.555 39.130 0.00 0.00 43.63 4.01
5473 6281 6.799512 ACAAAAAGAATCAGTTCCTGACTTG 58.200 36.000 0.00 0.00 43.63 3.16
5474 6282 7.260603 CAACAAAAAGAATCAGTTCCTGACTT 58.739 34.615 0.00 0.00 43.63 3.01
5475 6283 6.183360 CCAACAAAAAGAATCAGTTCCTGACT 60.183 38.462 0.00 0.00 43.63 3.41
5476 6284 5.979517 CCAACAAAAAGAATCAGTTCCTGAC 59.020 40.000 0.00 0.00 43.63 3.51
5477 6285 5.890985 TCCAACAAAAAGAATCAGTTCCTGA 59.109 36.000 0.00 0.00 44.99 3.86
5478 6286 6.147864 TCCAACAAAAAGAATCAGTTCCTG 57.852 37.500 0.00 0.00 34.81 3.86
5479 6287 6.790232 TTCCAACAAAAAGAATCAGTTCCT 57.210 33.333 0.00 0.00 34.81 3.36
5480 6288 7.209475 TGATTCCAACAAAAAGAATCAGTTCC 58.791 34.615 9.88 0.00 46.68 3.62
5498 6306 4.694760 AGGATGTTCGATCATGATTCCA 57.305 40.909 19.35 10.76 0.00 3.53
5499 6307 4.818546 ACAAGGATGTTCGATCATGATTCC 59.181 41.667 13.57 11.38 35.91 3.01
5500 6308 5.998454 ACAAGGATGTTCGATCATGATTC 57.002 39.130 13.57 1.89 35.91 2.52
5503 6311 4.631377 GTCAACAAGGATGTTCGATCATGA 59.369 41.667 13.57 0.00 46.78 3.07
5600 6408 1.644786 CGATCTGGGCCGTTGGTTTC 61.645 60.000 0.00 0.00 0.00 2.78
5692 6500 1.228925 GGAGGCCTATAGCGAGGGT 60.229 63.158 4.42 0.00 45.17 4.34
5701 6509 3.930012 GCGCGAAGGGAGGCCTAT 61.930 66.667 12.10 0.00 46.37 2.57
5835 6738 4.742201 GAGGAGCAGCACCGCGAA 62.742 66.667 8.23 0.00 36.85 4.70


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

AutoCloner maintained by Alex Coulton.