Multiple sequence alignment - TraesCS6D01G102700

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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 TraesCS6D01G102700 chr6D 100.000 5094 0 0 1 5094 65908049 65913142 0.000000e+00 9407.0
1 TraesCS6D01G102700 chr6D 85.393 267 27 11 299 564 431316224 431316479 3.020000e-67 267.0
2 TraesCS6D01G102700 chr6A 92.642 4050 167 36 621 4605 81851780 81847797 0.000000e+00 5707.0
3 TraesCS6D01G102700 chr6A 95.845 361 8 3 4734 5094 81847795 81847442 1.230000e-160 577.0
4 TraesCS6D01G102700 chr6A 98.077 52 1 0 4605 4656 200181382 200181331 1.950000e-14 91.6
5 TraesCS6D01G102700 chr6A 98.077 52 1 0 4605 4656 607959946 607959997 1.950000e-14 91.6
6 TraesCS6D01G102700 chr6A 98.039 51 1 0 4606 4656 15768234 15768184 7.020000e-14 89.8
7 TraesCS6D01G102700 chr6B 96.645 2832 63 15 617 3430 141016808 141019625 0.000000e+00 4674.0
8 TraesCS6D01G102700 chr6B 97.059 1190 24 5 3420 4607 141020408 141021588 0.000000e+00 1993.0
9 TraesCS6D01G102700 chr6B 89.891 366 11 3 4732 5094 141021586 141021928 1.010000e-121 448.0
10 TraesCS6D01G102700 chr6B 90.047 211 19 2 1 209 141015053 141015263 6.500000e-69 272.0
11 TraesCS6D01G102700 chr6B 90.244 82 5 2 4661 4740 270366119 270366039 2.510000e-18 104.0
12 TraesCS6D01G102700 chr3B 90.634 1025 74 13 917 1934 784731434 784732443 0.000000e+00 1341.0
13 TraesCS6D01G102700 chr3B 90.029 1023 84 12 917 1934 784741203 784742212 0.000000e+00 1308.0
14 TraesCS6D01G102700 chr3B 82.857 105 16 2 3233 3335 63412981 63412877 5.430000e-15 93.5
15 TraesCS6D01G102700 chr3A 91.741 448 19 6 2000 2446 735590756 735591186 1.570000e-169 606.0
16 TraesCS6D01G102700 chr3D 85.600 250 23 9 322 565 14079306 14079064 3.050000e-62 250.0
17 TraesCS6D01G102700 chr1A 83.824 272 27 10 298 564 547341277 547341536 5.100000e-60 243.0
18 TraesCS6D01G102700 chr1D 83.088 272 33 10 297 564 461504915 461505177 8.530000e-58 235.0
19 TraesCS6D01G102700 chr1D 91.250 80 3 2 4661 4738 90695862 90695939 6.980000e-19 106.0
20 TraesCS6D01G102700 chr1D 98.039 51 1 0 4606 4656 328237886 328237836 7.020000e-14 89.8
21 TraesCS6D01G102700 chr4A 82.772 267 36 10 298 562 724691689 724691947 3.970000e-56 230.0
22 TraesCS6D01G102700 chr4A 82.156 269 34 11 298 562 724617295 724617553 8.590000e-53 219.0
23 TraesCS6D01G102700 chr5B 81.884 276 32 12 298 564 661525923 661526189 3.090000e-52 217.0
24 TraesCS6D01G102700 chr5B 90.244 82 5 2 4661 4740 253207087 253207167 2.510000e-18 104.0
25 TraesCS6D01G102700 chr5B 83.962 106 13 4 3232 3335 465998062 465997959 1.170000e-16 99.0
26 TraesCS6D01G102700 chr1B 81.818 275 32 12 298 564 634604023 634603759 1.110000e-51 215.0
27 TraesCS6D01G102700 chr4B 79.545 264 42 8 308 562 126602137 126602397 1.460000e-40 178.0
28 TraesCS6D01G102700 chr4B 90.244 82 5 2 4661 4740 282239800 282239880 2.510000e-18 104.0
29 TraesCS6D01G102700 chr4B 98.039 51 1 0 4606 4656 437940463 437940413 7.020000e-14 89.8
30 TraesCS6D01G102700 chr7D 92.308 78 3 2 4661 4736 1299217 1299141 1.940000e-19 108.0
31 TraesCS6D01G102700 chr7D 90.361 83 5 2 4661 4741 47416138 47416057 6.980000e-19 106.0
32 TraesCS6D01G102700 chr4D 91.358 81 4 2 4656 4734 100358741 100358662 1.940000e-19 108.0
33 TraesCS6D01G102700 chr4D 98.039 51 1 0 4606 4656 437508980 437508930 7.020000e-14 89.8
34 TraesCS6D01G102700 chr7B 90.361 83 5 2 4661 4741 462238671 462238752 6.980000e-19 106.0
35 TraesCS6D01G102700 chr2B 85.577 104 10 4 4633 4734 209089621 209089721 2.510000e-18 104.0
36 TraesCS6D01G102700 chr5D 83.962 106 14 3 3232 3335 387623278 387623174 1.170000e-16 99.0
37 TraesCS6D01G102700 chr7A 98.148 54 1 0 4603 4656 573673134 573673081 1.510000e-15 95.3
38 TraesCS6D01G102700 chr2A 96.364 55 2 0 4602 4656 763043567 763043621 1.950000e-14 91.6
39 TraesCS6D01G102700 chrUn 98.039 51 1 0 4606 4656 62690470 62690520 7.020000e-14 89.8


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 TraesCS6D01G102700 chr6D 65908049 65913142 5093 False 9407.00 9407 100.0000 1 5094 1 chr6D.!!$F1 5093
1 TraesCS6D01G102700 chr6A 81847442 81851780 4338 True 3142.00 5707 94.2435 621 5094 2 chr6A.!!$R3 4473
2 TraesCS6D01G102700 chr6B 141015053 141021928 6875 False 1846.75 4674 93.4105 1 5094 4 chr6B.!!$F1 5093
3 TraesCS6D01G102700 chr3B 784731434 784732443 1009 False 1341.00 1341 90.6340 917 1934 1 chr3B.!!$F1 1017
4 TraesCS6D01G102700 chr3B 784741203 784742212 1009 False 1308.00 1308 90.0290 917 1934 1 chr3B.!!$F2 1017

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
419 739 0.112218 TGTTAGTGCCCAACCATGCT 59.888 50.000 0.00 0.00 0.00 3.79 F
451 771 0.321564 TGGGAAACGGAGCATCAGTG 60.322 55.000 0.00 0.00 44.60 3.66 F
452 772 0.321653 GGGAAACGGAGCATCAGTGT 60.322 55.000 0.00 0.00 44.60 3.55 F
1225 2393 1.396301 CTTCAAGTCGATGCTTCTGGC 59.604 52.381 0.00 0.00 42.22 4.85 F
1325 2501 1.504900 CGTGTGCATGCTGATTGCT 59.495 52.632 20.33 0.00 43.37 3.91 F
1488 2674 2.027460 GCACTTTGGCCGGTTGTG 59.973 61.111 1.90 11.88 0.00 3.33 F
3005 4231 1.134848 GGCTCTCTCTGATTTCGCTGT 60.135 52.381 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1321 2497 1.821216 GCCAGTAGCAAACCTAGCAA 58.179 50.000 0.00 0.0 42.97 3.91 R
2440 3666 0.252330 TGGGATGGAAGGACACGGTA 60.252 55.000 0.00 0.0 0.00 4.02 R
2475 3701 3.498481 CCACTGTTGATTTCCTCTCCCAA 60.498 47.826 0.00 0.0 0.00 4.12 R
2958 4184 0.937304 GCGAACAGAACAGAAGCACA 59.063 50.000 0.00 0.0 0.00 4.57 R
3005 4231 1.462432 TGGTGAGTTGGCCCCTACA 60.462 57.895 0.00 0.0 0.00 2.74 R
3041 4267 2.383527 GGACAGAGCGGCGAAACAG 61.384 63.158 12.98 0.0 0.00 3.16 R
4718 6743 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.0 0.00 4.37 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
17 18 4.681978 GCTGGAGGGTTGCGTCGT 62.682 66.667 0.00 0.00 0.00 4.34
52 53 0.679960 GGGTTTGGGGGAATCAGACG 60.680 60.000 0.00 0.00 0.00 4.18
87 90 0.170116 CGTGTCAGGAGAGAGAGTGC 59.830 60.000 0.00 0.00 0.00 4.40
122 125 3.520290 TTCGTGCAGTATAGACAAGGG 57.480 47.619 0.00 0.00 0.00 3.95
145 148 7.671495 GGCAATTTTGTCCATCTAAAAACAT 57.329 32.000 0.00 0.00 30.50 2.71
147 150 8.016801 GGCAATTTTGTCCATCTAAAAACATTG 58.983 33.333 0.00 0.00 30.50 2.82
151 154 8.870160 TTTTGTCCATCTAAAAACATTGACAG 57.130 30.769 0.00 0.00 33.54 3.51
152 155 7.581213 TTGTCCATCTAAAAACATTGACAGT 57.419 32.000 0.00 0.00 33.54 3.55
153 156 7.581213 TGTCCATCTAAAAACATTGACAGTT 57.419 32.000 0.00 0.00 0.00 3.16
169 172 7.458409 TTGACAGTTATTAGACGGTAGAAGT 57.542 36.000 0.00 0.00 0.00 3.01
182 185 7.760437 AGACGGTAGAAGTTAATAGAAGTGAC 58.240 38.462 0.00 0.00 0.00 3.67
209 212 9.713713 GAAAGTTTTACAAGGGGCATAAAATTA 57.286 29.630 0.00 0.00 32.16 1.40
300 490 9.902196 AGTTAAAACAATGTTATTTAACGGGAG 57.098 29.630 19.35 0.00 46.47 4.30
301 491 9.896263 GTTAAAACAATGTTATTTAACGGGAGA 57.104 29.630 14.04 0.00 38.78 3.71
303 493 6.753107 AACAATGTTATTTAACGGGAGAGG 57.247 37.500 0.00 0.00 39.00 3.69
304 494 4.638865 ACAATGTTATTTAACGGGAGAGGC 59.361 41.667 0.00 0.00 39.00 4.70
305 495 2.896168 TGTTATTTAACGGGAGAGGCG 58.104 47.619 0.00 0.00 39.00 5.52
306 496 2.234414 TGTTATTTAACGGGAGAGGCGT 59.766 45.455 0.00 0.00 39.00 5.68
309 499 2.259266 TTTAACGGGAGAGGCGTTTT 57.741 45.000 0.00 0.00 0.00 2.43
310 500 1.515081 TTAACGGGAGAGGCGTTTTG 58.485 50.000 0.00 0.00 0.00 2.44
311 501 0.320946 TAACGGGAGAGGCGTTTTGG 60.321 55.000 0.00 0.00 0.00 3.28
319 509 3.267974 GGCGTTTTGGCTCCTGAG 58.732 61.111 0.00 0.00 40.72 3.35
320 510 1.302511 GGCGTTTTGGCTCCTGAGA 60.303 57.895 0.00 0.00 40.72 3.27
321 511 1.301677 GGCGTTTTGGCTCCTGAGAG 61.302 60.000 0.00 0.00 43.57 3.20
339 529 3.631453 GCATATGCTCCCGGATGAA 57.369 52.632 20.64 0.00 38.21 2.57
340 530 2.119801 GCATATGCTCCCGGATGAAT 57.880 50.000 20.64 0.00 38.21 2.57
341 531 3.266510 GCATATGCTCCCGGATGAATA 57.733 47.619 20.64 0.00 38.21 1.75
343 533 3.369892 GCATATGCTCCCGGATGAATAGT 60.370 47.826 20.64 0.00 38.21 2.12
348 668 5.304686 TGCTCCCGGATGAATAGTAAATT 57.695 39.130 0.73 0.00 0.00 1.82
349 669 5.305585 TGCTCCCGGATGAATAGTAAATTC 58.694 41.667 0.73 0.00 0.00 2.17
352 672 6.262273 GCTCCCGGATGAATAGTAAATTCAAA 59.738 38.462 0.73 0.00 40.84 2.69
354 674 8.582657 TCCCGGATGAATAGTAAATTCAAAAA 57.417 30.769 0.73 0.00 40.84 1.94
409 729 6.897259 TTTGTAGATATTCGTGTTAGTGCC 57.103 37.500 0.00 0.00 0.00 5.01
410 730 4.940463 TGTAGATATTCGTGTTAGTGCCC 58.060 43.478 0.00 0.00 0.00 5.36
411 731 4.403113 TGTAGATATTCGTGTTAGTGCCCA 59.597 41.667 0.00 0.00 0.00 5.36
412 732 4.481368 AGATATTCGTGTTAGTGCCCAA 57.519 40.909 0.00 0.00 0.00 4.12
413 733 4.189231 AGATATTCGTGTTAGTGCCCAAC 58.811 43.478 0.00 0.00 0.00 3.77
414 734 1.530323 ATTCGTGTTAGTGCCCAACC 58.470 50.000 0.00 0.00 0.00 3.77
415 735 0.180642 TTCGTGTTAGTGCCCAACCA 59.819 50.000 0.00 0.00 0.00 3.67
416 736 0.398696 TCGTGTTAGTGCCCAACCAT 59.601 50.000 0.00 0.00 0.00 3.55
417 737 0.521291 CGTGTTAGTGCCCAACCATG 59.479 55.000 0.00 0.00 0.00 3.66
418 738 0.243636 GTGTTAGTGCCCAACCATGC 59.756 55.000 0.00 0.00 0.00 4.06
419 739 0.112218 TGTTAGTGCCCAACCATGCT 59.888 50.000 0.00 0.00 0.00 3.79
420 740 1.256812 GTTAGTGCCCAACCATGCTT 58.743 50.000 0.00 0.00 0.00 3.91
421 741 1.067635 GTTAGTGCCCAACCATGCTTG 60.068 52.381 0.00 0.00 0.00 4.01
434 754 2.680841 CCATGCTTGGCAAATTTCATGG 59.319 45.455 23.52 23.52 43.62 3.66
435 755 2.476126 TGCTTGGCAAATTTCATGGG 57.524 45.000 0.00 0.00 34.76 4.00
436 756 1.976404 TGCTTGGCAAATTTCATGGGA 59.024 42.857 0.00 0.00 34.76 4.37
437 757 2.371179 TGCTTGGCAAATTTCATGGGAA 59.629 40.909 0.00 0.00 34.76 3.97
438 758 3.181447 TGCTTGGCAAATTTCATGGGAAA 60.181 39.130 0.00 0.00 40.55 3.13
440 760 3.037431 TGGCAAATTTCATGGGAAACG 57.963 42.857 0.00 0.00 45.22 3.60
441 761 2.289320 TGGCAAATTTCATGGGAAACGG 60.289 45.455 0.00 0.00 45.22 4.44
442 762 2.028567 GGCAAATTTCATGGGAAACGGA 60.029 45.455 0.00 0.00 45.22 4.69
443 763 3.253230 GCAAATTTCATGGGAAACGGAG 58.747 45.455 0.00 0.00 45.22 4.63
444 764 3.253230 CAAATTTCATGGGAAACGGAGC 58.747 45.455 0.00 0.00 45.22 4.70
445 765 2.214376 ATTTCATGGGAAACGGAGCA 57.786 45.000 0.00 0.00 45.22 4.26
447 767 1.750193 TTCATGGGAAACGGAGCATC 58.250 50.000 0.00 0.00 0.00 3.91
448 768 0.617935 TCATGGGAAACGGAGCATCA 59.382 50.000 0.00 0.00 36.25 3.07
449 769 1.019673 CATGGGAAACGGAGCATCAG 58.980 55.000 0.00 0.00 36.25 2.90
451 771 0.321564 TGGGAAACGGAGCATCAGTG 60.322 55.000 0.00 0.00 44.60 3.66
452 772 0.321653 GGGAAACGGAGCATCAGTGT 60.322 55.000 0.00 0.00 44.60 3.55
453 773 1.523758 GGAAACGGAGCATCAGTGTT 58.476 50.000 0.00 0.00 44.60 3.32
454 774 1.880027 GGAAACGGAGCATCAGTGTTT 59.120 47.619 0.00 0.00 44.60 2.83
455 775 2.293399 GGAAACGGAGCATCAGTGTTTT 59.707 45.455 0.00 0.00 44.60 2.43
457 777 1.967319 ACGGAGCATCAGTGTTTTGT 58.033 45.000 0.00 0.00 43.42 2.83
458 778 1.873591 ACGGAGCATCAGTGTTTTGTC 59.126 47.619 0.00 0.00 43.42 3.18
461 781 1.873591 GAGCATCAGTGTTTTGTCGGT 59.126 47.619 0.00 0.00 33.17 4.69
462 782 1.603802 AGCATCAGTGTTTTGTCGGTG 59.396 47.619 0.00 0.00 0.00 4.94
463 783 1.601903 GCATCAGTGTTTTGTCGGTGA 59.398 47.619 0.00 0.00 0.00 4.02
464 784 2.032799 GCATCAGTGTTTTGTCGGTGAA 59.967 45.455 0.00 0.00 0.00 3.18
465 785 3.488384 GCATCAGTGTTTTGTCGGTGAAA 60.488 43.478 0.00 0.00 0.00 2.69
466 786 4.667262 CATCAGTGTTTTGTCGGTGAAAA 58.333 39.130 0.00 0.00 0.00 2.29
467 787 4.768130 TCAGTGTTTTGTCGGTGAAAAA 57.232 36.364 0.00 0.00 0.00 1.94
490 1439 6.880942 AAACAAAATTGGGATGACATTTGG 57.119 33.333 0.00 0.00 33.31 3.28
496 1445 3.805066 TGGGATGACATTTGGTCTTCA 57.195 42.857 11.03 0.00 46.94 3.02
501 1450 5.464168 GGATGACATTTGGTCTTCACTTTG 58.536 41.667 11.03 0.00 46.94 2.77
524 1473 3.351020 TTTTTGCACATGCCAAAATGC 57.649 38.095 19.41 10.27 39.64 3.56
525 1474 2.257691 TTTGCACATGCCAAAATGCT 57.742 40.000 9.05 0.00 41.18 3.79
529 1478 3.065655 TGCACATGCCAAAATGCTTAAC 58.934 40.909 0.49 0.00 41.18 2.01
530 1479 2.416202 GCACATGCCAAAATGCTTAACC 59.584 45.455 0.00 0.00 35.16 2.85
531 1480 3.865684 GCACATGCCAAAATGCTTAACCT 60.866 43.478 0.00 0.00 35.16 3.50
532 1481 4.317488 CACATGCCAAAATGCTTAACCTT 58.683 39.130 0.00 0.00 0.00 3.50
533 1482 4.756135 CACATGCCAAAATGCTTAACCTTT 59.244 37.500 0.00 0.00 0.00 3.11
535 1484 5.827267 ACATGCCAAAATGCTTAACCTTTTT 59.173 32.000 0.00 0.00 0.00 1.94
536 1485 5.747951 TGCCAAAATGCTTAACCTTTTTG 57.252 34.783 11.96 11.96 38.52 2.44
537 1486 4.036144 TGCCAAAATGCTTAACCTTTTTGC 59.964 37.500 12.89 9.82 37.97 3.68
538 1487 4.556501 GCCAAAATGCTTAACCTTTTTGCC 60.557 41.667 12.89 3.17 37.97 4.52
539 1488 4.821260 CCAAAATGCTTAACCTTTTTGCCT 59.179 37.500 12.89 0.00 37.97 4.75
540 1489 5.049474 CCAAAATGCTTAACCTTTTTGCCTC 60.049 40.000 12.89 0.00 37.97 4.70
541 1490 4.953940 AATGCTTAACCTTTTTGCCTCA 57.046 36.364 0.00 0.00 0.00 3.86
542 1491 4.953940 ATGCTTAACCTTTTTGCCTCAA 57.046 36.364 0.00 0.00 0.00 3.02
543 1492 4.744795 TGCTTAACCTTTTTGCCTCAAA 57.255 36.364 0.00 0.00 0.00 2.69
544 1493 5.091261 TGCTTAACCTTTTTGCCTCAAAA 57.909 34.783 1.05 1.05 40.85 2.44
545 1494 5.679601 TGCTTAACCTTTTTGCCTCAAAAT 58.320 33.333 5.68 0.00 41.89 1.82
547 1496 6.601217 TGCTTAACCTTTTTGCCTCAAAATTT 59.399 30.769 5.68 0.00 41.89 1.82
548 1497 6.912051 GCTTAACCTTTTTGCCTCAAAATTTG 59.088 34.615 0.00 0.00 41.89 2.32
549 1498 4.898829 ACCTTTTTGCCTCAAAATTTGC 57.101 36.364 0.00 0.00 41.89 3.68
550 1499 4.268359 ACCTTTTTGCCTCAAAATTTGCA 58.732 34.783 0.00 0.00 41.89 4.08
551 1500 4.336153 ACCTTTTTGCCTCAAAATTTGCAG 59.664 37.500 0.00 0.19 41.89 4.41
554 1503 6.038050 CCTTTTTGCCTCAAAATTTGCAGTTA 59.962 34.615 0.00 0.00 41.89 2.24
555 1504 6.992063 TTTTGCCTCAAAATTTGCAGTTAA 57.008 29.167 0.00 0.00 38.24 2.01
556 1505 5.982465 TTGCCTCAAAATTTGCAGTTAAC 57.018 34.783 0.00 0.00 34.81 2.01
557 1506 5.016051 TGCCTCAAAATTTGCAGTTAACA 57.984 34.783 8.61 0.00 0.00 2.41
561 1510 6.852345 GCCTCAAAATTTGCAGTTAACATTTG 59.148 34.615 8.61 7.39 0.00 2.32
563 1512 7.226325 CCTCAAAATTTGCAGTTAACATTTGGA 59.774 33.333 8.61 6.78 0.00 3.53
564 1513 7.914465 TCAAAATTTGCAGTTAACATTTGGAC 58.086 30.769 8.61 0.00 0.00 4.02
565 1514 7.550551 TCAAAATTTGCAGTTAACATTTGGACA 59.449 29.630 8.61 0.00 0.00 4.02
568 1517 8.449251 AATTTGCAGTTAACATTTGGACATTT 57.551 26.923 8.61 0.00 0.00 2.32
606 1555 2.465813 TGGGCCGAATTGAATTTCCAT 58.534 42.857 0.00 0.00 0.00 3.41
607 1556 2.836981 TGGGCCGAATTGAATTTCCATT 59.163 40.909 0.00 0.00 0.00 3.16
608 1557 4.026744 TGGGCCGAATTGAATTTCCATTA 58.973 39.130 0.00 0.00 0.00 1.90
609 1558 4.653341 TGGGCCGAATTGAATTTCCATTAT 59.347 37.500 0.00 0.00 0.00 1.28
611 1560 5.011023 GGGCCGAATTGAATTTCCATTATCT 59.989 40.000 0.00 0.00 0.00 1.98
613 1562 7.093771 GGGCCGAATTGAATTTCCATTATCTAT 60.094 37.037 0.00 0.00 0.00 1.98
614 1563 8.306761 GGCCGAATTGAATTTCCATTATCTATT 58.693 33.333 0.00 0.00 0.00 1.73
701 1846 2.108976 GCCAATCGAGGATGCCGA 59.891 61.111 0.00 0.81 40.53 5.54
711 1856 4.489771 GATGCCGACCCCACCTGG 62.490 72.222 0.00 0.00 0.00 4.45
772 1932 4.657824 CGCGAACCGACCACACCT 62.658 66.667 0.00 0.00 40.02 4.00
784 1944 4.928140 ACACCTCACCCGTCCCGT 62.928 66.667 0.00 0.00 0.00 5.28
785 1945 4.065281 CACCTCACCCGTCCCGTC 62.065 72.222 0.00 0.00 0.00 4.79
869 2029 3.368501 CCCCTCTCCCCTCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
1147 2314 3.441290 CTCTCCCCGTTCTCGCGT 61.441 66.667 5.77 0.00 35.54 6.01
1225 2393 1.396301 CTTCAAGTCGATGCTTCTGGC 59.604 52.381 0.00 0.00 42.22 4.85
1256 2424 2.520979 CTCGGATCTGTCGTTTCAGAC 58.479 52.381 0.42 0.00 45.40 3.51
1323 2499 4.066769 GCGTGTGCATGCTGATTG 57.933 55.556 20.33 6.22 42.15 2.67
1324 2500 2.156446 GCGTGTGCATGCTGATTGC 61.156 57.895 20.33 12.48 42.15 3.56
1325 2501 1.504900 CGTGTGCATGCTGATTGCT 59.495 52.632 20.33 0.00 43.37 3.91
1488 2674 2.027460 GCACTTTGGCCGGTTGTG 59.973 61.111 1.90 11.88 0.00 3.33
1567 2753 5.309638 TGGTTGTTACTTAGCTTGCATGTA 58.690 37.500 0.00 0.00 0.00 2.29
1596 2782 6.861065 TTTCTGTCATGTCTTAAACAGGTC 57.139 37.500 9.38 0.05 42.37 3.85
2235 3461 5.172934 TGACCAGTATTAACGGCAAGTAAG 58.827 41.667 0.00 0.00 0.00 2.34
2236 3462 5.156608 ACCAGTATTAACGGCAAGTAAGT 57.843 39.130 0.00 0.00 0.00 2.24
2237 3463 6.071447 TGACCAGTATTAACGGCAAGTAAGTA 60.071 38.462 0.00 0.00 0.00 2.24
2238 3464 6.700352 ACCAGTATTAACGGCAAGTAAGTAA 58.300 36.000 0.00 0.00 0.00 2.24
2367 3593 4.698583 ATTCAGACATTTCTTGCAGCTC 57.301 40.909 0.00 0.00 0.00 4.09
2440 3666 5.074515 TCCCACCTATTTTGGAAGAAGAACT 59.925 40.000 0.00 0.00 36.02 3.01
2499 3725 3.263425 GGGAGAGGAAATCAACAGTGGTA 59.737 47.826 0.00 0.00 0.00 3.25
2958 4184 2.047061 TGTAGAAGGTGAGCCAGTTGT 58.953 47.619 0.00 0.00 37.19 3.32
3005 4231 1.134848 GGCTCTCTCTGATTTCGCTGT 60.135 52.381 0.00 0.00 0.00 4.40
3041 4267 0.895559 CACAAAGTCCTCCAAGGCCC 60.896 60.000 0.00 0.00 34.61 5.80
3170 4398 2.230266 AGGTCAAAGTGTTTTGTTGCGT 59.770 40.909 0.56 0.00 43.33 5.24
3261 4489 6.405953 CCTCCATAACTGTACTCTGTTAGGTG 60.406 46.154 13.21 12.25 39.82 4.00
3651 5674 7.222000 AGTTTTTGTTTGGTCTGTTGTCTAA 57.778 32.000 0.00 0.00 0.00 2.10
3676 5699 1.203162 TGAGCATGATTGGGTTGGGTT 60.203 47.619 0.00 0.00 0.00 4.11
3762 5785 8.694540 TGACATATAACCCCATCATTTTCTTTG 58.305 33.333 0.00 0.00 0.00 2.77
3765 5788 4.890158 AACCCCATCATTTTCTTTGTCC 57.110 40.909 0.00 0.00 0.00 4.02
3921 5944 2.540931 CACCAGAAAGCACACAAAATGC 59.459 45.455 0.00 0.00 43.74 3.56
4106 6129 2.069273 CGTGGTGACAAATCTGGAGAC 58.931 52.381 0.00 0.00 46.06 3.36
4164 6189 6.237154 AGGATGAAGAAATTCCTATAGCTGC 58.763 40.000 0.00 0.00 38.11 5.25
4167 6192 3.797559 AGAAATTCCTATAGCTGCCCC 57.202 47.619 0.00 0.00 0.00 5.80
4545 6570 4.886247 GAGCTCAACTCGTATGTACTCT 57.114 45.455 9.40 0.00 35.18 3.24
4604 6629 9.798994 ACGTCTTATACTGTTTATTTACAGAGG 57.201 33.333 10.46 0.00 46.72 3.69
4605 6630 9.798994 CGTCTTATACTGTTTATTTACAGAGGT 57.201 33.333 10.46 0.00 46.72 3.85
4619 6644 2.688538 AGGTACTCCCTCCGTCCC 59.311 66.667 0.00 0.00 40.71 4.46
4620 6645 2.243888 AGGTACTCCCTCCGTCCCA 61.244 63.158 0.00 0.00 40.71 4.37
4621 6646 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
4622 6647 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
4623 6648 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
4624 6649 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
4625 6650 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
4626 6651 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4627 6652 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4628 6653 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
4629 6654 3.961408 CTCCCTCCGTCCCATAATATAGG 59.039 52.174 0.00 0.00 0.00 2.57
4630 6655 3.599240 TCCCTCCGTCCCATAATATAGGA 59.401 47.826 0.00 0.00 0.00 2.94
4631 6656 3.705072 CCCTCCGTCCCATAATATAGGAC 59.295 52.174 7.65 7.65 45.49 3.85
4663 6688 3.277715 ACTAGCGTAGTGTCCTTAGTCC 58.722 50.000 0.00 0.00 37.69 3.85
4664 6689 1.472188 AGCGTAGTGTCCTTAGTCCC 58.528 55.000 0.00 0.00 0.00 4.46
4665 6690 1.180029 GCGTAGTGTCCTTAGTCCCA 58.820 55.000 0.00 0.00 0.00 4.37
4666 6691 1.547372 GCGTAGTGTCCTTAGTCCCAA 59.453 52.381 0.00 0.00 0.00 4.12
4667 6692 2.028748 GCGTAGTGTCCTTAGTCCCAAA 60.029 50.000 0.00 0.00 0.00 3.28
4668 6693 3.555586 GCGTAGTGTCCTTAGTCCCAAAA 60.556 47.826 0.00 0.00 0.00 2.44
4669 6694 4.828829 CGTAGTGTCCTTAGTCCCAAAAT 58.171 43.478 0.00 0.00 0.00 1.82
4670 6695 5.625197 GCGTAGTGTCCTTAGTCCCAAAATA 60.625 44.000 0.00 0.00 0.00 1.40
4671 6696 6.579865 CGTAGTGTCCTTAGTCCCAAAATAT 58.420 40.000 0.00 0.00 0.00 1.28
4672 6697 7.685155 GCGTAGTGTCCTTAGTCCCAAAATATA 60.685 40.741 0.00 0.00 0.00 0.86
4673 6698 7.866393 CGTAGTGTCCTTAGTCCCAAAATATAG 59.134 40.741 0.00 0.00 0.00 1.31
4674 6699 7.138054 AGTGTCCTTAGTCCCAAAATATAGG 57.862 40.000 0.00 0.00 0.00 2.57
4675 6700 6.906901 AGTGTCCTTAGTCCCAAAATATAGGA 59.093 38.462 0.00 0.00 0.00 2.94
4706 6731 3.312421 TGACACTAGTGCTGTCAAAAAGC 59.688 43.478 22.90 0.00 43.99 3.51
4707 6732 2.287915 ACACTAGTGCTGTCAAAAAGCG 59.712 45.455 22.90 0.00 43.88 4.68
4708 6733 2.287915 CACTAGTGCTGTCAAAAAGCGT 59.712 45.455 10.54 0.00 43.88 5.07
4709 6734 2.544267 ACTAGTGCTGTCAAAAAGCGTC 59.456 45.455 0.00 0.00 43.88 5.19
4710 6735 1.668419 AGTGCTGTCAAAAAGCGTCT 58.332 45.000 0.00 0.00 43.88 4.18
4711 6736 2.017049 AGTGCTGTCAAAAAGCGTCTT 58.983 42.857 0.00 0.00 43.88 3.01
4712 6737 3.202906 AGTGCTGTCAAAAAGCGTCTTA 58.797 40.909 0.00 0.00 43.88 2.10
4713 6738 3.002348 AGTGCTGTCAAAAAGCGTCTTAC 59.998 43.478 0.00 0.00 43.88 2.34
4714 6739 2.939756 TGCTGTCAAAAAGCGTCTTACA 59.060 40.909 0.00 0.00 43.88 2.41
4715 6740 3.563808 TGCTGTCAAAAAGCGTCTTACAT 59.436 39.130 0.00 0.00 43.88 2.29
4716 6741 4.036262 TGCTGTCAAAAAGCGTCTTACATT 59.964 37.500 0.00 0.00 43.88 2.71
4717 6742 5.237561 TGCTGTCAAAAAGCGTCTTACATTA 59.762 36.000 0.00 0.00 43.88 1.90
4718 6743 6.072728 TGCTGTCAAAAAGCGTCTTACATTAT 60.073 34.615 0.00 0.00 43.88 1.28
4719 6744 6.249260 GCTGTCAAAAAGCGTCTTACATTATG 59.751 38.462 0.00 0.00 0.00 1.90
4720 6745 6.607689 TGTCAAAAAGCGTCTTACATTATGG 58.392 36.000 0.00 0.00 0.00 2.74
4721 6746 6.027749 GTCAAAAAGCGTCTTACATTATGGG 58.972 40.000 0.00 0.00 0.00 4.00
4722 6747 5.941058 TCAAAAAGCGTCTTACATTATGGGA 59.059 36.000 0.00 0.00 0.00 4.37
4723 6748 5.813080 AAAAGCGTCTTACATTATGGGAC 57.187 39.130 0.00 1.75 0.00 4.46
4725 6750 2.132762 GCGTCTTACATTATGGGACGG 58.867 52.381 25.20 14.78 46.26 4.79
4726 6751 2.223876 GCGTCTTACATTATGGGACGGA 60.224 50.000 25.20 5.94 46.26 4.69
4727 6752 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
4728 6753 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
4729 6754 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4730 6755 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4849 6874 2.683152 GCCTCTGCACAATCTGATTCCT 60.683 50.000 0.00 0.00 37.47 3.36
4851 6876 3.377485 CCTCTGCACAATCTGATTCCTTG 59.623 47.826 0.00 0.00 0.00 3.61
4998 7026 1.451028 GCTGTGCCATCAGTCTCCC 60.451 63.158 0.00 0.00 37.70 4.30
5090 7118 3.191162 GGTGTGTTTGATAGCTTGCATCA 59.809 43.478 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.078285 ACGACTCGTCTCTCTCCCC 60.078 63.158 0.00 0.00 33.69 4.81
74 75 0.968393 GAACCGGCACTCTCTCTCCT 60.968 60.000 0.00 0.00 0.00 3.69
75 76 1.513622 GAACCGGCACTCTCTCTCC 59.486 63.158 0.00 0.00 0.00 3.71
122 125 8.772705 TCAATGTTTTTAGATGGACAAAATTGC 58.227 29.630 0.00 0.00 0.00 3.56
145 148 7.458409 ACTTCTACCGTCTAATAACTGTCAA 57.542 36.000 0.00 0.00 0.00 3.18
158 161 6.686253 CGTCACTTCTATTAACTTCTACCGTC 59.314 42.308 0.00 0.00 0.00 4.79
174 177 5.296035 CCCTTGTAAAACTTTCGTCACTTCT 59.704 40.000 0.00 0.00 0.00 2.85
182 185 3.934457 ATGCCCCTTGTAAAACTTTCG 57.066 42.857 0.00 0.00 0.00 3.46
231 421 9.710900 ATTTGACACTGGAAATTTATTTCTTCC 57.289 29.630 13.27 1.10 44.21 3.46
246 436 8.870160 TGTTTCTTTATTTGATTTGACACTGG 57.130 30.769 0.00 0.00 0.00 4.00
275 465 9.896263 TCTCCCGTTAAATAACATTGTTTTAAC 57.104 29.630 18.50 18.50 40.16 2.01
281 471 4.638865 GCCTCTCCCGTTAAATAACATTGT 59.361 41.667 4.37 0.00 35.99 2.71
282 472 4.260620 CGCCTCTCCCGTTAAATAACATTG 60.261 45.833 4.37 0.00 35.99 2.82
283 473 3.875134 CGCCTCTCCCGTTAAATAACATT 59.125 43.478 4.37 0.00 35.99 2.71
284 474 3.118519 ACGCCTCTCCCGTTAAATAACAT 60.119 43.478 4.37 0.00 34.96 2.71
285 475 2.234414 ACGCCTCTCCCGTTAAATAACA 59.766 45.455 4.37 0.00 34.96 2.41
286 476 2.897436 ACGCCTCTCCCGTTAAATAAC 58.103 47.619 0.00 0.00 34.96 1.89
287 477 3.615224 AACGCCTCTCCCGTTAAATAA 57.385 42.857 0.00 0.00 45.89 1.40
289 479 2.484742 AAACGCCTCTCCCGTTAAAT 57.515 45.000 0.00 0.00 46.90 1.40
290 480 1.874872 CAAAACGCCTCTCCCGTTAAA 59.125 47.619 0.00 0.00 46.90 1.52
291 481 1.515081 CAAAACGCCTCTCCCGTTAA 58.485 50.000 0.00 0.00 46.90 2.01
292 482 0.320946 CCAAAACGCCTCTCCCGTTA 60.321 55.000 0.00 0.00 46.90 3.18
294 484 2.032071 CCAAAACGCCTCTCCCGT 59.968 61.111 0.00 0.00 41.24 5.28
295 485 3.431725 GCCAAAACGCCTCTCCCG 61.432 66.667 0.00 0.00 0.00 5.14
296 486 2.034221 AGCCAAAACGCCTCTCCC 59.966 61.111 0.00 0.00 0.00 4.30
297 487 2.041115 GGAGCCAAAACGCCTCTCC 61.041 63.158 0.00 0.00 36.86 3.71
299 489 1.302832 CAGGAGCCAAAACGCCTCT 60.303 57.895 0.00 0.00 37.82 3.69
300 490 1.301677 CTCAGGAGCCAAAACGCCTC 61.302 60.000 0.00 0.00 37.82 4.70
301 491 1.302832 CTCAGGAGCCAAAACGCCT 60.303 57.895 0.00 0.00 40.95 5.52
302 492 1.301677 CTCTCAGGAGCCAAAACGCC 61.302 60.000 0.00 0.00 32.43 5.68
303 493 2.166270 CTCTCAGGAGCCAAAACGC 58.834 57.895 0.00 0.00 32.43 4.84
321 511 2.119801 ATTCATCCGGGAGCATATGC 57.880 50.000 20.36 20.36 42.49 3.14
322 512 4.478206 ACTATTCATCCGGGAGCATATG 57.522 45.455 0.00 0.00 0.00 1.78
323 513 6.620877 TTTACTATTCATCCGGGAGCATAT 57.379 37.500 0.00 0.00 0.00 1.78
325 515 4.974645 TTTACTATTCATCCGGGAGCAT 57.025 40.909 0.00 0.00 0.00 3.79
327 517 5.305585 TGAATTTACTATTCATCCGGGAGC 58.694 41.667 0.00 0.00 33.55 4.70
328 518 7.801716 TTTGAATTTACTATTCATCCGGGAG 57.198 36.000 0.00 0.00 37.79 4.30
329 519 8.582657 TTTTTGAATTTACTATTCATCCGGGA 57.417 30.769 0.00 0.00 37.79 5.14
384 704 7.148373 GGGCACTAACACGAATATCTACAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
387 707 5.105269 TGGGCACTAACACGAATATCTACAA 60.105 40.000 0.00 0.00 0.00 2.41
388 708 4.403113 TGGGCACTAACACGAATATCTACA 59.597 41.667 0.00 0.00 0.00 2.74
389 709 4.940463 TGGGCACTAACACGAATATCTAC 58.060 43.478 0.00 0.00 0.00 2.59
391 711 4.481368 TTGGGCACTAACACGAATATCT 57.519 40.909 0.00 0.00 0.00 1.98
402 722 1.255882 CAAGCATGGTTGGGCACTAA 58.744 50.000 26.36 0.00 0.00 2.24
404 724 1.909781 CCAAGCATGGTTGGGCACT 60.910 57.895 37.95 2.91 43.02 4.40
414 734 2.680841 CCCATGAAATTTGCCAAGCATG 59.319 45.455 0.00 1.91 38.76 4.06
415 735 2.572556 TCCCATGAAATTTGCCAAGCAT 59.427 40.909 0.00 0.00 38.76 3.79
416 736 1.976404 TCCCATGAAATTTGCCAAGCA 59.024 42.857 0.00 0.00 36.47 3.91
417 737 2.766345 TCCCATGAAATTTGCCAAGC 57.234 45.000 0.00 0.00 0.00 4.01
418 738 3.432933 CGTTTCCCATGAAATTTGCCAAG 59.567 43.478 0.00 0.00 42.20 3.61
419 739 3.397482 CGTTTCCCATGAAATTTGCCAA 58.603 40.909 0.00 0.00 42.20 4.52
420 740 2.289320 CCGTTTCCCATGAAATTTGCCA 60.289 45.455 0.00 0.00 42.20 4.92
421 741 2.028567 TCCGTTTCCCATGAAATTTGCC 60.029 45.455 0.00 0.00 42.20 4.52
422 742 3.253230 CTCCGTTTCCCATGAAATTTGC 58.747 45.455 0.00 0.00 42.20 3.68
423 743 3.253230 GCTCCGTTTCCCATGAAATTTG 58.747 45.455 0.00 0.00 42.20 2.32
424 744 2.896685 TGCTCCGTTTCCCATGAAATTT 59.103 40.909 0.00 0.00 42.20 1.82
425 745 2.524306 TGCTCCGTTTCCCATGAAATT 58.476 42.857 0.00 0.00 42.20 1.82
426 746 2.214376 TGCTCCGTTTCCCATGAAAT 57.786 45.000 0.00 0.00 42.20 2.17
427 747 2.091541 GATGCTCCGTTTCCCATGAAA 58.908 47.619 0.00 0.00 38.14 2.69
428 748 1.004161 TGATGCTCCGTTTCCCATGAA 59.996 47.619 0.00 0.00 0.00 2.57
430 750 1.019673 CTGATGCTCCGTTTCCCATG 58.980 55.000 0.00 0.00 0.00 3.66
431 751 0.620556 ACTGATGCTCCGTTTCCCAT 59.379 50.000 0.00 0.00 0.00 4.00
433 753 0.321653 ACACTGATGCTCCGTTTCCC 60.322 55.000 0.00 0.00 0.00 3.97
434 754 1.523758 AACACTGATGCTCCGTTTCC 58.476 50.000 0.00 0.00 0.00 3.13
435 755 3.243068 ACAAAACACTGATGCTCCGTTTC 60.243 43.478 0.00 0.00 0.00 2.78
436 756 2.687935 ACAAAACACTGATGCTCCGTTT 59.312 40.909 0.00 0.00 0.00 3.60
437 757 2.290641 GACAAAACACTGATGCTCCGTT 59.709 45.455 0.00 0.00 0.00 4.44
438 758 1.873591 GACAAAACACTGATGCTCCGT 59.126 47.619 0.00 0.00 0.00 4.69
440 760 1.197721 CCGACAAAACACTGATGCTCC 59.802 52.381 0.00 0.00 0.00 4.70
441 761 1.873591 ACCGACAAAACACTGATGCTC 59.126 47.619 0.00 0.00 0.00 4.26
442 762 1.603802 CACCGACAAAACACTGATGCT 59.396 47.619 0.00 0.00 0.00 3.79
443 763 1.601903 TCACCGACAAAACACTGATGC 59.398 47.619 0.00 0.00 0.00 3.91
444 764 3.961477 TTCACCGACAAAACACTGATG 57.039 42.857 0.00 0.00 0.00 3.07
445 765 4.974368 TTTTCACCGACAAAACACTGAT 57.026 36.364 0.00 0.00 0.00 2.90
465 785 7.341512 ACCAAATGTCATCCCAATTTTGTTTTT 59.658 29.630 0.00 0.00 0.00 1.94
466 786 6.832900 ACCAAATGTCATCCCAATTTTGTTTT 59.167 30.769 0.00 0.00 0.00 2.43
467 787 6.363882 ACCAAATGTCATCCCAATTTTGTTT 58.636 32.000 0.00 0.00 0.00 2.83
468 788 5.939447 ACCAAATGTCATCCCAATTTTGTT 58.061 33.333 0.00 0.00 0.00 2.83
469 789 5.550290 GACCAAATGTCATCCCAATTTTGT 58.450 37.500 0.00 0.00 43.85 2.83
508 1457 3.065655 GTTAAGCATTTTGGCATGTGCA 58.934 40.909 17.59 0.00 44.36 4.57
509 1458 2.416202 GGTTAAGCATTTTGGCATGTGC 59.584 45.455 10.20 10.20 41.14 4.57
510 1459 3.929094 AGGTTAAGCATTTTGGCATGTG 58.071 40.909 7.52 0.00 35.83 3.21
511 1460 4.622260 AAGGTTAAGCATTTTGGCATGT 57.378 36.364 7.52 0.00 35.83 3.21
512 1461 5.945466 AAAAGGTTAAGCATTTTGGCATG 57.055 34.783 7.52 0.00 39.28 4.06
516 1465 4.821260 AGGCAAAAAGGTTAAGCATTTTGG 59.179 37.500 32.21 21.37 39.75 3.28
517 1466 5.526846 TGAGGCAAAAAGGTTAAGCATTTTG 59.473 36.000 29.68 29.68 39.75 2.44
518 1467 5.679601 TGAGGCAAAAAGGTTAAGCATTTT 58.320 33.333 13.24 13.24 42.05 1.82
519 1468 5.289083 TGAGGCAAAAAGGTTAAGCATTT 57.711 34.783 7.52 4.69 31.84 2.32
520 1469 4.953940 TGAGGCAAAAAGGTTAAGCATT 57.046 36.364 7.52 0.00 0.00 3.56
522 1471 4.744795 TTTGAGGCAAAAAGGTTAAGCA 57.255 36.364 7.52 0.00 29.89 3.91
523 1472 6.618287 AATTTTGAGGCAAAAAGGTTAAGC 57.382 33.333 9.10 0.00 44.68 3.09
524 1473 6.912051 GCAAATTTTGAGGCAAAAAGGTTAAG 59.088 34.615 13.26 0.00 44.68 1.85
525 1474 6.375455 TGCAAATTTTGAGGCAAAAAGGTTAA 59.625 30.769 13.26 0.00 44.68 2.01
529 1478 4.336153 ACTGCAAATTTTGAGGCAAAAAGG 59.664 37.500 13.26 4.09 44.68 3.11
530 1479 5.488645 ACTGCAAATTTTGAGGCAAAAAG 57.511 34.783 13.26 5.01 44.68 2.27
531 1480 5.893897 AACTGCAAATTTTGAGGCAAAAA 57.106 30.435 13.26 1.32 44.68 1.94
532 1481 6.372659 TGTTAACTGCAAATTTTGAGGCAAAA 59.627 30.769 13.26 7.66 45.41 2.44
533 1482 5.877012 TGTTAACTGCAAATTTTGAGGCAAA 59.123 32.000 13.26 0.00 35.59 3.68
535 1484 5.016051 TGTTAACTGCAAATTTTGAGGCA 57.984 34.783 13.26 3.17 34.66 4.75
536 1485 6.544038 AATGTTAACTGCAAATTTTGAGGC 57.456 33.333 13.26 0.00 0.00 4.70
537 1486 7.226325 TCCAAATGTTAACTGCAAATTTTGAGG 59.774 33.333 13.26 6.75 0.00 3.86
538 1487 8.063630 GTCCAAATGTTAACTGCAAATTTTGAG 58.936 33.333 13.26 9.47 0.00 3.02
539 1488 7.550551 TGTCCAAATGTTAACTGCAAATTTTGA 59.449 29.630 13.26 3.17 0.00 2.69
540 1489 7.692088 TGTCCAAATGTTAACTGCAAATTTTG 58.308 30.769 7.22 4.72 0.00 2.44
541 1490 7.856145 TGTCCAAATGTTAACTGCAAATTTT 57.144 28.000 7.22 0.00 0.00 1.82
542 1491 8.449251 AATGTCCAAATGTTAACTGCAAATTT 57.551 26.923 7.22 1.38 0.00 1.82
543 1492 8.449251 AAATGTCCAAATGTTAACTGCAAATT 57.551 26.923 7.22 0.00 0.00 1.82
544 1493 8.449251 AAAATGTCCAAATGTTAACTGCAAAT 57.551 26.923 7.22 0.00 0.00 2.32
545 1494 7.856145 AAAATGTCCAAATGTTAACTGCAAA 57.144 28.000 7.22 0.00 0.00 3.68
582 1531 4.068599 GGAAATTCAATTCGGCCCAAAAA 58.931 39.130 0.00 0.00 0.00 1.94
583 1532 3.071602 TGGAAATTCAATTCGGCCCAAAA 59.928 39.130 0.00 0.00 0.00 2.44
584 1533 2.634940 TGGAAATTCAATTCGGCCCAAA 59.365 40.909 0.00 0.00 0.00 3.28
586 1535 1.930251 TGGAAATTCAATTCGGCCCA 58.070 45.000 0.00 0.00 0.00 5.36
587 1536 3.541996 AATGGAAATTCAATTCGGCCC 57.458 42.857 0.00 0.00 0.00 5.80
588 1537 6.089249 AGATAATGGAAATTCAATTCGGCC 57.911 37.500 0.00 0.00 0.00 6.13
609 1558 9.959721 AAGCACAAGAAAGTTCCTTATAATAGA 57.040 29.630 0.00 0.00 0.00 1.98
613 1562 9.528018 CAAAAAGCACAAGAAAGTTCCTTATAA 57.472 29.630 0.00 0.00 0.00 0.98
614 1563 8.691797 ACAAAAAGCACAAGAAAGTTCCTTATA 58.308 29.630 0.00 0.00 0.00 0.98
615 1564 7.555965 ACAAAAAGCACAAGAAAGTTCCTTAT 58.444 30.769 0.00 0.00 0.00 1.73
616 1565 6.930731 ACAAAAAGCACAAGAAAGTTCCTTA 58.069 32.000 0.00 0.00 0.00 2.69
617 1566 5.793817 ACAAAAAGCACAAGAAAGTTCCTT 58.206 33.333 0.00 0.00 0.00 3.36
618 1567 5.405935 ACAAAAAGCACAAGAAAGTTCCT 57.594 34.783 0.00 0.00 0.00 3.36
619 1568 4.265320 CGACAAAAAGCACAAGAAAGTTCC 59.735 41.667 0.00 0.00 0.00 3.62
620 1569 4.259411 GCGACAAAAAGCACAAGAAAGTTC 60.259 41.667 0.00 0.00 0.00 3.01
622 1571 3.179048 GCGACAAAAAGCACAAGAAAGT 58.821 40.909 0.00 0.00 0.00 2.66
623 1572 3.178267 TGCGACAAAAAGCACAAGAAAG 58.822 40.909 0.00 0.00 38.59 2.62
701 1846 3.637273 GTCGCTTCCAGGTGGGGT 61.637 66.667 0.00 0.00 37.22 4.95
711 1856 4.329545 TGGTGGGGCTGTCGCTTC 62.330 66.667 0.00 0.00 36.09 3.86
784 1944 1.770927 TTGGTTTGAGGGGACGGGA 60.771 57.895 0.00 0.00 0.00 5.14
785 1945 1.602605 GTTGGTTTGAGGGGACGGG 60.603 63.158 0.00 0.00 0.00 5.28
786 1946 1.964373 CGTTGGTTTGAGGGGACGG 60.964 63.158 0.00 0.00 0.00 4.79
787 1947 2.613506 GCGTTGGTTTGAGGGGACG 61.614 63.158 0.00 0.00 0.00 4.79
788 1948 1.527380 TGCGTTGGTTTGAGGGGAC 60.527 57.895 0.00 0.00 0.00 4.46
934 2096 4.951963 GGGGCTCGCTCGAATCGG 62.952 72.222 1.76 0.00 0.00 4.18
945 2107 4.610714 GGATTCCTCGCGGGGCTC 62.611 72.222 23.67 19.33 35.33 4.70
1147 2314 2.263852 CTCGAGCAAGCAGAGGCA 59.736 61.111 0.00 0.00 44.61 4.75
1319 2495 2.356069 GCCAGTAGCAAACCTAGCAATC 59.644 50.000 0.00 0.00 42.97 2.67
1320 2496 2.369394 GCCAGTAGCAAACCTAGCAAT 58.631 47.619 0.00 0.00 42.97 3.56
1321 2497 1.821216 GCCAGTAGCAAACCTAGCAA 58.179 50.000 0.00 0.00 42.97 3.91
1322 2498 3.551259 GCCAGTAGCAAACCTAGCA 57.449 52.632 0.00 0.00 42.97 3.49
1488 2674 5.007626 TCACAGTAGAAGCACAACATCAAAC 59.992 40.000 0.00 0.00 0.00 2.93
1567 2753 8.450578 TGTTTAAGACATGACAGAAATGAAGT 57.549 30.769 0.00 0.00 32.00 3.01
1665 2851 7.039714 AGGTTTATTCATCAAACAAAGGAGTCC 60.040 37.037 0.00 0.00 37.57 3.85
1773 2989 4.326058 GCGATGAACTGAAACGCG 57.674 55.556 3.53 3.53 39.90 6.01
2235 3461 8.283291 GCATATGCACTTCCTAATGTAACTTAC 58.717 37.037 22.84 0.00 41.59 2.34
2236 3462 8.210946 AGCATATGCACTTCCTAATGTAACTTA 58.789 33.333 28.62 0.00 45.16 2.24
2237 3463 7.012704 CAGCATATGCACTTCCTAATGTAACTT 59.987 37.037 28.62 0.00 45.16 2.66
2238 3464 6.484643 CAGCATATGCACTTCCTAATGTAACT 59.515 38.462 28.62 0.00 45.16 2.24
2440 3666 0.252330 TGGGATGGAAGGACACGGTA 60.252 55.000 0.00 0.00 0.00 4.02
2475 3701 3.498481 CCACTGTTGATTTCCTCTCCCAA 60.498 47.826 0.00 0.00 0.00 4.12
2499 3725 4.352009 TCTTCCACAATGGGCATGTTAAT 58.648 39.130 0.00 0.00 38.32 1.40
2958 4184 0.937304 GCGAACAGAACAGAAGCACA 59.063 50.000 0.00 0.00 0.00 4.57
3005 4231 1.462432 TGGTGAGTTGGCCCCTACA 60.462 57.895 0.00 0.00 0.00 2.74
3041 4267 2.383527 GGACAGAGCGGCGAAACAG 61.384 63.158 12.98 0.00 0.00 3.16
3170 4398 6.160576 TGTTCATATGCACTAGCTACATGA 57.839 37.500 7.03 0.00 42.74 3.07
3261 4489 2.409870 CGCAGGGTGCCTCATTTCC 61.410 63.158 0.00 0.00 41.12 3.13
3651 5674 3.007182 CCAACCCAATCATGCTCAAAGTT 59.993 43.478 0.00 0.00 0.00 2.66
3676 5699 1.139455 AGGAAGGTTGTCGAAAACGGA 59.861 47.619 12.26 0.00 0.00 4.69
3762 5785 4.221703 TGAAAGGTTGATCTGAGAGAGGAC 59.778 45.833 0.00 0.00 0.00 3.85
3765 5788 6.404708 TGATTGAAAGGTTGATCTGAGAGAG 58.595 40.000 0.00 0.00 0.00 3.20
3921 5944 0.392193 AGCGTCCATTGGCTCTTCAG 60.392 55.000 0.00 0.00 33.32 3.02
4120 6145 3.386486 CTTCGTGTGTAAGTAACCTGCA 58.614 45.455 0.00 0.00 0.00 4.41
4348 6373 2.047655 CGCCAACAGTAAGCCGGA 60.048 61.111 5.05 0.00 0.00 5.14
4545 6570 7.877612 TCACTGTCTTGCATTTATTTACAGAGA 59.122 33.333 0.00 0.00 37.04 3.10
4604 6629 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
4605 6630 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4606 6631 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4607 6632 3.961408 CCTATATTATGGGACGGAGGGAG 59.039 52.174 0.00 0.00 31.57 4.30
4608 6633 3.599240 TCCTATATTATGGGACGGAGGGA 59.401 47.826 4.74 0.00 34.71 4.20
4609 6634 3.990369 TCCTATATTATGGGACGGAGGG 58.010 50.000 4.74 0.00 34.71 4.30
4642 6667 3.277715 GGACTAAGGACACTACGCTAGT 58.722 50.000 0.00 0.00 40.28 2.57
4643 6668 2.617774 GGGACTAAGGACACTACGCTAG 59.382 54.545 0.00 0.00 0.00 3.42
4644 6669 2.025981 TGGGACTAAGGACACTACGCTA 60.026 50.000 0.00 0.00 0.00 4.26
4645 6670 1.272313 TGGGACTAAGGACACTACGCT 60.272 52.381 0.00 0.00 0.00 5.07
4646 6671 1.180029 TGGGACTAAGGACACTACGC 58.820 55.000 0.00 0.00 0.00 4.42
4647 6672 3.947910 TTTGGGACTAAGGACACTACG 57.052 47.619 0.00 0.00 0.00 3.51
4648 6673 8.148999 CCTATATTTTGGGACTAAGGACACTAC 58.851 40.741 0.00 0.00 0.00 2.73
4649 6674 8.069356 TCCTATATTTTGGGACTAAGGACACTA 58.931 37.037 0.00 0.00 0.00 2.74
4650 6675 6.906901 TCCTATATTTTGGGACTAAGGACACT 59.093 38.462 0.00 0.00 0.00 3.55
4651 6676 7.133133 TCCTATATTTTGGGACTAAGGACAC 57.867 40.000 0.00 0.00 0.00 3.67
4653 6678 6.183360 ACGTCCTATATTTTGGGACTAAGGAC 60.183 42.308 7.89 7.89 45.08 3.85
4654 6679 5.901276 ACGTCCTATATTTTGGGACTAAGGA 59.099 40.000 7.78 0.00 45.08 3.36
4655 6680 6.170846 ACGTCCTATATTTTGGGACTAAGG 57.829 41.667 7.78 0.00 45.08 2.69
4656 6681 8.502105 AAAACGTCCTATATTTTGGGACTAAG 57.498 34.615 7.78 0.00 45.08 2.18
4657 6682 8.866970 AAAAACGTCCTATATTTTGGGACTAA 57.133 30.769 7.78 0.00 45.08 2.24
4685 6710 3.604772 CGCTTTTTGACAGCACTAGTGTC 60.605 47.826 23.44 15.50 43.97 3.67
4686 6711 2.287915 CGCTTTTTGACAGCACTAGTGT 59.712 45.455 23.44 8.30 37.07 3.55
4687 6712 2.287915 ACGCTTTTTGACAGCACTAGTG 59.712 45.455 18.93 18.93 37.07 2.74
4688 6713 2.544267 GACGCTTTTTGACAGCACTAGT 59.456 45.455 0.00 0.00 37.07 2.57
4689 6714 2.802816 AGACGCTTTTTGACAGCACTAG 59.197 45.455 0.00 0.00 37.07 2.57
4690 6715 2.833794 AGACGCTTTTTGACAGCACTA 58.166 42.857 0.00 0.00 37.07 2.74
4691 6716 1.668419 AGACGCTTTTTGACAGCACT 58.332 45.000 0.00 0.00 37.07 4.40
4692 6717 2.475200 AAGACGCTTTTTGACAGCAC 57.525 45.000 0.00 0.00 37.07 4.40
4693 6718 2.939756 TGTAAGACGCTTTTTGACAGCA 59.060 40.909 0.00 0.00 37.07 4.41
4694 6719 3.602390 TGTAAGACGCTTTTTGACAGC 57.398 42.857 0.00 0.00 0.00 4.40
4695 6720 6.742718 CCATAATGTAAGACGCTTTTTGACAG 59.257 38.462 0.00 0.00 0.00 3.51
4696 6721 6.348950 CCCATAATGTAAGACGCTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
4697 6722 6.027749 CCCATAATGTAAGACGCTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
4698 6723 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
4699 6724 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
4700 6725 5.163794 CGTCCCATAATGTAAGACGCTTTTT 60.164 40.000 0.00 0.00 43.07 1.94
4701 6726 4.331717 CGTCCCATAATGTAAGACGCTTTT 59.668 41.667 0.00 0.00 43.07 2.27
4702 6727 3.869246 CGTCCCATAATGTAAGACGCTTT 59.131 43.478 0.00 0.00 43.07 3.51
4703 6728 3.454375 CGTCCCATAATGTAAGACGCTT 58.546 45.455 0.00 0.00 43.07 4.68
4704 6729 2.223971 CCGTCCCATAATGTAAGACGCT 60.224 50.000 5.39 0.00 46.66 5.07
4705 6730 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
4707 6732 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4708 6733 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4709 6734 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
4710 6735 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
4711 6736 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
4712 6737 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
4713 6738 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
4714 6739 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
4715 6740 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
4716 6741 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
4717 6742 1.133544 GTACTACTCCCTCCGTCCCAT 60.134 57.143 0.00 0.00 0.00 4.00
4718 6743 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
4719 6744 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
4720 6745 2.361643 ATGTACTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
4721 6746 3.698040 TGAAATGTACTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
4722 6747 3.705051 TGAAATGTACTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
4723 6748 4.341235 TGATGAAATGTACTACTCCCTCCG 59.659 45.833 0.00 0.00 0.00 4.63
4724 6749 5.871396 TGATGAAATGTACTACTCCCTCC 57.129 43.478 0.00 0.00 0.00 4.30
4725 6750 5.755861 GCTTGATGAAATGTACTACTCCCTC 59.244 44.000 0.00 0.00 0.00 4.30
4726 6751 5.426833 AGCTTGATGAAATGTACTACTCCCT 59.573 40.000 0.00 0.00 0.00 4.20
4727 6752 5.675538 AGCTTGATGAAATGTACTACTCCC 58.324 41.667 0.00 0.00 0.00 4.30
4728 6753 6.457528 GCAAGCTTGATGAAATGTACTACTCC 60.458 42.308 30.39 1.48 0.00 3.85
4729 6754 6.092670 TGCAAGCTTGATGAAATGTACTACTC 59.907 38.462 30.39 6.25 0.00 2.59
4730 6755 5.939883 TGCAAGCTTGATGAAATGTACTACT 59.060 36.000 30.39 0.00 0.00 2.57
4849 6874 2.192979 GGCTCATCCGATGGCCAA 59.807 61.111 24.74 0.00 42.51 4.52
4880 6908 2.046892 GAGAAGGGCTTGCGCTGA 60.047 61.111 9.73 0.00 36.09 4.26
4998 7026 2.985896 AGTTGGATGTGGTTCATACGG 58.014 47.619 0.00 0.00 40.12 4.02


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

AutoCloner maintained by Alex Coulton.