Multiple sequence alignment - TraesCS4A01G187400

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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 TraesCS4A01G187400 chr4A 100.000 5981 0 0 1 5981 466637729 466631749 0.000000e+00 11045.0
1 TraesCS4A01G187400 chr4A 85.714 119 16 1 1404 1522 641486878 641486761 2.260000e-24 124.0
2 TraesCS4A01G187400 chr4A 100.000 33 0 0 3794 3826 466633755 466633723 1.800000e-05 62.1
3 TraesCS4A01G187400 chr4A 100.000 33 0 0 3975 4007 466633936 466633904 1.800000e-05 62.1
4 TraesCS4A01G187400 chr4D 95.615 3307 108 18 1972 5265 110084416 110087698 0.000000e+00 5269.0
5 TraesCS4A01G187400 chr4D 89.585 1037 59 27 971 1975 110083370 110084389 0.000000e+00 1271.0
6 TraesCS4A01G187400 chr4D 89.195 472 32 5 1 453 110082038 110082509 6.720000e-159 571.0
7 TraesCS4A01G187400 chr4D 84.967 459 28 24 526 961 110082521 110082961 1.540000e-115 427.0
8 TraesCS4A01G187400 chr4D 78.735 569 97 19 5429 5981 502596352 502596912 5.700000e-95 359.0
9 TraesCS4A01G187400 chr4D 96.512 86 3 0 5252 5337 110093232 110093317 6.250000e-30 143.0
10 TraesCS4A01G187400 chr4D 85.714 98 7 6 4058 4155 43548945 43548855 4.930000e-16 97.1
11 TraesCS4A01G187400 chr4D 100.000 33 0 0 3975 4007 110086220 110086252 1.800000e-05 62.1
12 TraesCS4A01G187400 chr4B 93.875 3363 126 27 2010 5348 171619765 171616459 0.000000e+00 4996.0
13 TraesCS4A01G187400 chr4B 88.583 1524 88 33 497 1975 171621514 171620032 0.000000e+00 1772.0
14 TraesCS4A01G187400 chr4B 88.866 485 34 10 2 467 171621996 171621513 4.020000e-161 579.0
15 TraesCS4A01G187400 chr1D 86.528 579 56 6 5424 5981 204887484 204888061 8.520000e-173 617.0
16 TraesCS4A01G187400 chr1D 79.021 572 87 22 5424 5981 399038048 399038600 1.580000e-95 361.0
17 TraesCS4A01G187400 chr6D 86.111 576 59 8 5427 5981 58746396 58745821 8.580000e-168 601.0
18 TraesCS4A01G187400 chr6D 100.000 29 0 0 2258 2286 468839907 468839935 3.000000e-03 54.7
19 TraesCS4A01G187400 chr5A 84.603 630 63 6 5386 5981 362754718 362755347 3.990000e-166 595.0
20 TraesCS4A01G187400 chr5A 74.576 413 80 17 2367 2778 311977379 311976991 2.230000e-34 158.0
21 TraesCS4A01G187400 chr7D 85.665 579 58 6 5427 5981 494897964 494897387 2.400000e-163 586.0
22 TraesCS4A01G187400 chr7D 84.775 578 65 8 5427 5981 164484860 164484283 5.240000e-155 558.0
23 TraesCS4A01G187400 chr7D 83.938 579 67 12 5427 5981 581492189 581491613 1.140000e-146 531.0
24 TraesCS4A01G187400 chr7D 85.941 441 49 8 5551 5981 635868884 635869321 5.460000e-125 459.0
25 TraesCS4A01G187400 chr3D 86.022 558 56 7 5445 5980 31853299 31853856 4.020000e-161 579.0
26 TraesCS4A01G187400 chr5D 84.896 576 56 13 5427 5981 281222890 281222325 2.440000e-153 553.0
27 TraesCS4A01G187400 chr5D 84.687 431 59 6 5556 5981 520081105 520080677 1.990000e-114 424.0
28 TraesCS4A01G187400 chr5D 75.000 416 74 18 2367 2778 242002615 242002226 1.330000e-36 165.0
29 TraesCS4A01G187400 chr5D 88.889 81 5 3 4057 4135 465200379 465200301 4.930000e-16 97.1
30 TraesCS4A01G187400 chr5D 88.889 81 5 3 4058 4136 465200301 465200379 4.930000e-16 97.1
31 TraesCS4A01G187400 chr7A 83.016 577 75 7 5427 5981 709781060 709780485 8.950000e-138 501.0
32 TraesCS4A01G187400 chr7B 80.763 629 80 15 5391 5981 261980646 261981271 2.540000e-123 453.0
33 TraesCS4A01G187400 chr7B 100.000 29 0 0 2258 2286 652133231 652133203 3.000000e-03 54.7
34 TraesCS4A01G187400 chr2A 80.277 578 89 12 5427 5981 317979739 317979164 4.310000e-111 412.0
35 TraesCS4A01G187400 chr2D 85.085 295 36 6 5427 5715 635091221 635090929 1.630000e-75 294.0
36 TraesCS4A01G187400 chr2D 78.667 225 39 3 5386 5605 268890703 268890923 2.250000e-29 141.0
37 TraesCS4A01G187400 chr5B 74.519 416 72 24 2367 2778 256945275 256944890 3.730000e-32 150.0
38 TraesCS4A01G187400 chr5B 89.623 106 11 0 4381 4486 256943625 256943520 1.050000e-27 135.0
39 TraesCS4A01G187400 chr6A 84.874 119 17 1 1404 1522 530086113 530085996 1.050000e-22 119.0
40 TraesCS4A01G187400 chr6A 94.286 35 2 0 2259 2293 569998870 569998836 3.000000e-03 54.7
41 TraesCS4A01G187400 chr6B 83.333 126 18 3 1402 1527 17384279 17384401 4.900000e-21 113.0
42 TraesCS4A01G187400 chr6B 100.000 29 0 0 2258 2286 714632719 714632747 3.000000e-03 54.7
43 TraesCS4A01G187400 chr2B 88.235 85 7 2 4058 4141 614917141 614917223 1.370000e-16 99.0
44 TraesCS4A01G187400 chr2B 89.024 82 3 2 4058 4135 111604714 111604635 4.930000e-16 97.1
45 TraesCS4A01G187400 chr2B 89.024 82 3 2 4058 4135 111604635 111604714 4.930000e-16 97.1
46 TraesCS4A01G187400 chr1A 86.047 86 8 3 4058 4143 24721260 24721179 8.260000e-14 89.8
47 TraesCS4A01G187400 chr1A 100.000 29 0 0 2258 2286 58191719 58191691 3.000000e-03 54.7


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 TraesCS4A01G187400 chr4A 466631749 466637729 5980 True 11045.00 11045 100.000000 1 5981 1 chr4A.!!$R1 5980
1 TraesCS4A01G187400 chr4D 110082038 110087698 5660 False 1520.02 5269 91.872400 1 5265 5 chr4D.!!$F3 5264
2 TraesCS4A01G187400 chr4D 502596352 502596912 560 False 359.00 359 78.735000 5429 5981 1 chr4D.!!$F2 552
3 TraesCS4A01G187400 chr4B 171616459 171621996 5537 True 2449.00 4996 90.441333 2 5348 3 chr4B.!!$R1 5346
4 TraesCS4A01G187400 chr1D 204887484 204888061 577 False 617.00 617 86.528000 5424 5981 1 chr1D.!!$F1 557
5 TraesCS4A01G187400 chr1D 399038048 399038600 552 False 361.00 361 79.021000 5424 5981 1 chr1D.!!$F2 557
6 TraesCS4A01G187400 chr6D 58745821 58746396 575 True 601.00 601 86.111000 5427 5981 1 chr6D.!!$R1 554
7 TraesCS4A01G187400 chr5A 362754718 362755347 629 False 595.00 595 84.603000 5386 5981 1 chr5A.!!$F1 595
8 TraesCS4A01G187400 chr7D 494897387 494897964 577 True 586.00 586 85.665000 5427 5981 1 chr7D.!!$R2 554
9 TraesCS4A01G187400 chr7D 164484283 164484860 577 True 558.00 558 84.775000 5427 5981 1 chr7D.!!$R1 554
10 TraesCS4A01G187400 chr7D 581491613 581492189 576 True 531.00 531 83.938000 5427 5981 1 chr7D.!!$R3 554
11 TraesCS4A01G187400 chr3D 31853299 31853856 557 False 579.00 579 86.022000 5445 5980 1 chr3D.!!$F1 535
12 TraesCS4A01G187400 chr5D 281222325 281222890 565 True 553.00 553 84.896000 5427 5981 1 chr5D.!!$R2 554
13 TraesCS4A01G187400 chr7A 709780485 709781060 575 True 501.00 501 83.016000 5427 5981 1 chr7A.!!$R1 554
14 TraesCS4A01G187400 chr7B 261980646 261981271 625 False 453.00 453 80.763000 5391 5981 1 chr7B.!!$F1 590
15 TraesCS4A01G187400 chr2A 317979164 317979739 575 True 412.00 412 80.277000 5427 5981 1 chr2A.!!$R1 554

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
467 487 0.250793 ATGTATTTCCACCACGCGGA 59.749 50.000 12.47 0.0 35.59 5.54 F
1134 1606 0.105224 TCTCGTGTTTTCTTGGGCGA 59.895 50.000 0.00 0.0 0.00 5.54 F
1139 1611 0.378962 TGTTTTCTTGGGCGACGTTG 59.621 50.000 0.00 0.0 0.00 4.10 F
1142 1614 1.161563 TTTCTTGGGCGACGTTGGTC 61.162 55.000 4.64 0.0 39.89 4.02 F
2098 2843 0.242017 GATTGCTTGCAACCGAGCTT 59.758 50.000 10.37 0.0 46.69 3.74 F
3446 4208 1.202371 GGCATGCCACTGAATGATGTG 60.202 52.381 32.08 0.0 35.81 3.21 F
4840 5621 0.322816 TGTGCAGGGCCAGAAAGATC 60.323 55.000 6.18 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2749 0.030504 CACGCACCAAAGCAACATGA 59.969 50.000 0.0 0.00 0.00 3.07 R
2005 2750 0.248990 ACACGCACCAAAGCAACATG 60.249 50.000 0.0 0.00 0.00 3.21 R
2006 2751 0.459489 AACACGCACCAAAGCAACAT 59.541 45.000 0.0 0.00 0.00 2.71 R
2815 3577 1.047002 CCAAATGTTGAGTGGGCCAA 58.953 50.000 8.4 0.00 0.00 4.52 R
3854 4616 4.396166 CCTTTGAAGTGGGTAGTATGCAAG 59.604 45.833 0.0 0.00 0.00 4.01 R
4944 5725 0.036306 AAGTAGGTTTGTCTGCCCCG 59.964 55.000 0.0 0.00 0.00 5.73 R
5876 6723 0.721718 CAGACGATGCCGGTTCTTTC 59.278 55.000 1.9 0.54 40.78 2.62 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
72 73 5.734498 GCGTGACATCAGCAAAATTAAGTAG 59.266 40.000 0.00 0.00 0.00 2.57
83 84 6.923508 AGCAAAATTAAGTAGGAAAACTGCAC 59.076 34.615 0.00 0.00 33.78 4.57
88 89 4.699925 AAGTAGGAAAACTGCACAGGTA 57.300 40.909 2.21 0.00 33.78 3.08
104 105 6.719370 TGCACAGGTAAGAGTTTATGGAAAAT 59.281 34.615 0.00 0.00 0.00 1.82
170 171 6.820656 ACTATCATGTAAGAACCTCTGCAAAG 59.179 38.462 0.00 0.00 0.00 2.77
173 174 4.008074 TGTAAGAACCTCTGCAAAGGAG 57.992 45.455 14.57 3.48 38.87 3.69
178 179 3.648545 AGAACCTCTGCAAAGGAGTAACT 59.351 43.478 14.57 1.53 38.87 2.24
180 181 2.039084 ACCTCTGCAAAGGAGTAACTGG 59.961 50.000 14.57 0.00 38.87 4.00
215 225 5.108517 CCTCTGAAGTCTGAAACATAGCTC 58.891 45.833 0.00 0.00 0.00 4.09
225 235 5.645067 TCTGAAACATAGCTCATGGAAGTTG 59.355 40.000 0.00 0.00 39.13 3.16
245 255 6.985117 AGTTGAGAGCTCTATCATTCTGATC 58.015 40.000 18.25 0.00 38.26 2.92
247 257 5.643176 TGAGAGCTCTATCATTCTGATCCT 58.357 41.667 18.25 0.00 38.26 3.24
276 286 3.123621 GCTTATAATCCAGGAATGACGCG 59.876 47.826 3.53 3.53 0.00 6.01
387 407 5.523916 TCGATCTGAATTTGCCTTAAGTAGC 59.476 40.000 0.97 0.00 0.00 3.58
389 409 6.183360 CGATCTGAATTTGCCTTAAGTAGCAA 60.183 38.462 13.21 13.21 46.74 3.91
402 422 7.360185 GCCTTAAGTAGCAAGTAAAACAGAGAC 60.360 40.741 0.97 0.00 0.00 3.36
404 424 5.449107 AGTAGCAAGTAAAACAGAGACGA 57.551 39.130 0.00 0.00 0.00 4.20
407 427 2.479275 GCAAGTAAAACAGAGACGACCC 59.521 50.000 0.00 0.00 0.00 4.46
413 433 2.305858 AACAGAGACGACCCTACCTT 57.694 50.000 0.00 0.00 0.00 3.50
414 434 1.546961 ACAGAGACGACCCTACCTTG 58.453 55.000 0.00 0.00 0.00 3.61
420 440 0.896226 ACGACCCTACCTTGAGCTTC 59.104 55.000 0.00 0.00 0.00 3.86
422 442 1.134965 CGACCCTACCTTGAGCTTCAG 60.135 57.143 0.00 0.00 0.00 3.02
462 482 4.096382 AGCATCGAAATGTATTTCCACCAC 59.904 41.667 10.76 0.00 42.34 4.16
465 485 2.780993 GAAATGTATTTCCACCACGCG 58.219 47.619 3.53 3.53 40.10 6.01
466 486 1.091537 AATGTATTTCCACCACGCGG 58.908 50.000 12.47 0.00 38.77 6.46
467 487 0.250793 ATGTATTTCCACCACGCGGA 59.749 50.000 12.47 0.00 35.59 5.54
468 488 0.250793 TGTATTTCCACCACGCGGAT 59.749 50.000 12.47 0.00 35.59 4.18
469 489 1.339247 TGTATTTCCACCACGCGGATT 60.339 47.619 12.47 0.00 35.59 3.01
470 490 1.329599 GTATTTCCACCACGCGGATTC 59.670 52.381 12.47 0.00 35.59 2.52
471 491 0.322098 ATTTCCACCACGCGGATTCA 60.322 50.000 12.47 0.00 35.59 2.57
472 492 1.231958 TTTCCACCACGCGGATTCAC 61.232 55.000 12.47 0.00 35.59 3.18
473 493 2.047274 CCACCACGCGGATTCACT 60.047 61.111 12.47 0.00 35.59 3.41
474 494 2.100631 CCACCACGCGGATTCACTC 61.101 63.158 12.47 0.00 35.59 3.51
475 495 1.374125 CACCACGCGGATTCACTCA 60.374 57.895 12.47 0.00 35.59 3.41
476 496 1.079819 ACCACGCGGATTCACTCAG 60.080 57.895 12.47 0.00 35.59 3.35
477 497 1.079819 CCACGCGGATTCACTCAGT 60.080 57.895 12.47 0.00 0.00 3.41
478 498 1.354337 CCACGCGGATTCACTCAGTG 61.354 60.000 12.47 0.00 35.90 3.66
479 499 1.738099 ACGCGGATTCACTCAGTGC 60.738 57.895 12.47 0.00 33.45 4.40
480 500 1.737735 CGCGGATTCACTCAGTGCA 60.738 57.895 0.00 0.00 32.98 4.57
481 501 1.690283 CGCGGATTCACTCAGTGCAG 61.690 60.000 0.00 0.00 32.98 4.41
482 502 0.390340 GCGGATTCACTCAGTGCAGA 60.390 55.000 0.00 0.00 32.98 4.26
483 503 1.638133 CGGATTCACTCAGTGCAGAG 58.362 55.000 0.00 1.57 41.44 3.35
484 504 1.367659 GGATTCACTCAGTGCAGAGC 58.632 55.000 0.00 0.00 39.26 4.09
485 505 1.066286 GGATTCACTCAGTGCAGAGCT 60.066 52.381 0.00 0.00 39.26 4.09
486 506 2.614987 GGATTCACTCAGTGCAGAGCTT 60.615 50.000 0.00 0.00 39.26 3.74
487 507 1.875009 TTCACTCAGTGCAGAGCTTG 58.125 50.000 0.00 0.00 39.26 4.01
517 537 2.569404 GGGGAGAGAGAGAAGCAAGAAA 59.431 50.000 0.00 0.00 0.00 2.52
519 539 4.505742 GGGGAGAGAGAGAAGCAAGAAAAA 60.506 45.833 0.00 0.00 0.00 1.94
520 540 5.252547 GGGAGAGAGAGAAGCAAGAAAAAT 58.747 41.667 0.00 0.00 0.00 1.82
521 541 5.353956 GGGAGAGAGAGAAGCAAGAAAAATC 59.646 44.000 0.00 0.00 0.00 2.17
522 542 5.353956 GGAGAGAGAGAAGCAAGAAAAATCC 59.646 44.000 0.00 0.00 0.00 3.01
528 548 5.939296 AGAGAAGCAAGAAAAATCCTCAGAG 59.061 40.000 0.00 0.00 0.00 3.35
570 590 2.203728 TGGTCGCCACTGTAGGGT 60.204 61.111 0.00 0.00 0.00 4.34
571 591 1.077086 TGGTCGCCACTGTAGGGTA 59.923 57.895 0.00 0.00 0.00 3.69
596 616 1.383248 AGGTAGGCGGAAGATGGCT 60.383 57.895 0.00 0.00 45.16 4.75
607 627 0.916358 AAGATGGCTGGGCTGGTAGT 60.916 55.000 0.00 0.00 0.00 2.73
608 628 1.153086 GATGGCTGGGCTGGTAGTG 60.153 63.158 0.00 0.00 0.00 2.74
609 629 2.615227 GATGGCTGGGCTGGTAGTGG 62.615 65.000 0.00 0.00 0.00 4.00
610 630 3.330720 GGCTGGGCTGGTAGTGGT 61.331 66.667 0.00 0.00 0.00 4.16
611 631 1.993391 GGCTGGGCTGGTAGTGGTA 60.993 63.158 0.00 0.00 0.00 3.25
612 632 1.522569 GCTGGGCTGGTAGTGGTAG 59.477 63.158 0.00 0.00 0.00 3.18
624 644 3.006728 TGGTAGGGAAGGTGCCGG 61.007 66.667 0.00 0.00 30.73 6.13
698 730 3.564218 GGGGCGCAGATGGGAGAT 61.564 66.667 10.83 0.00 0.00 2.75
699 731 2.217038 GGGGCGCAGATGGGAGATA 61.217 63.158 10.83 0.00 0.00 1.98
700 732 1.294780 GGGCGCAGATGGGAGATAG 59.705 63.158 10.83 0.00 0.00 2.08
730 762 2.325082 GCAACTCCGGCAATGTCGT 61.325 57.895 6.48 0.00 0.00 4.34
761 793 3.071479 GTTACCACAAATGCGAGGAAGA 58.929 45.455 0.00 0.00 0.00 2.87
802 848 4.884257 GCTTGACGGGCCGCGATA 62.884 66.667 28.71 6.91 0.00 2.92
810 856 2.995258 GACGGGCCGCGATAAATAAATA 59.005 45.455 28.71 0.00 0.00 1.40
811 857 3.602483 ACGGGCCGCGATAAATAAATAT 58.398 40.909 28.71 0.00 0.00 1.28
926 988 1.447317 CCGCCGCCAATTAATCTGCT 61.447 55.000 7.36 0.00 0.00 4.24
954 1016 1.913762 CCTCCAACTCCGACCACCT 60.914 63.158 0.00 0.00 0.00 4.00
957 1019 2.663196 CAACTCCGACCACCTCCC 59.337 66.667 0.00 0.00 0.00 4.30
961 1023 4.393778 TCCGACCACCTCCCCCTC 62.394 72.222 0.00 0.00 0.00 4.30
966 1028 4.825679 CCACCTCCCCCTCCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
967 1029 3.700350 CACCTCCCCCTCCCCTCT 61.700 72.222 0.00 0.00 0.00 3.69
968 1030 3.369388 ACCTCCCCCTCCCCTCTC 61.369 72.222 0.00 0.00 0.00 3.20
969 1031 3.039526 CCTCCCCCTCCCCTCTCT 61.040 72.222 0.00 0.00 0.00 3.10
970 1032 2.612251 CTCCCCCTCCCCTCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
971 1033 3.036959 TCCCCCTCCCCTCTCTCC 61.037 72.222 0.00 0.00 0.00 3.71
972 1034 4.548513 CCCCCTCCCCTCTCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
1080 1543 1.287730 CCGCAGCGGCTCATCTTATC 61.288 60.000 23.64 0.00 41.17 1.75
1116 1588 8.128322 TCACTATGATAAGCTCTCCCTAATTC 57.872 38.462 0.00 0.00 0.00 2.17
1134 1606 0.105224 TCTCGTGTTTTCTTGGGCGA 59.895 50.000 0.00 0.00 0.00 5.54
1139 1611 0.378962 TGTTTTCTTGGGCGACGTTG 59.621 50.000 0.00 0.00 0.00 4.10
1142 1614 1.161563 TTTCTTGGGCGACGTTGGTC 61.162 55.000 4.64 0.00 39.89 4.02
1147 1619 2.737376 GGCGACGTTGGTCTGGTC 60.737 66.667 4.64 0.00 41.16 4.02
1183 1655 2.800985 GCTGATGCTTCATCGTCTGCTA 60.801 50.000 2.33 0.00 43.14 3.49
1220 1692 3.646715 TCCGGCAAAGGTGAGGGG 61.647 66.667 0.00 0.00 0.00 4.79
1221 1693 4.740822 CCGGCAAAGGTGAGGGGG 62.741 72.222 0.00 0.00 0.00 5.40
1283 1767 4.321008 GGATTGGTTCGAGCGTATAGATGA 60.321 45.833 0.00 0.00 0.00 2.92
1290 1774 1.267261 GAGCGTATAGATGACTGCCGT 59.733 52.381 0.00 0.00 0.00 5.68
1293 1777 2.351835 GCGTATAGATGACTGCCGTGAT 60.352 50.000 0.00 0.00 0.00 3.06
1294 1778 3.857383 GCGTATAGATGACTGCCGTGATT 60.857 47.826 0.00 0.00 0.00 2.57
1295 1779 4.615223 GCGTATAGATGACTGCCGTGATTA 60.615 45.833 0.00 0.00 0.00 1.75
1296 1780 5.089411 CGTATAGATGACTGCCGTGATTAG 58.911 45.833 0.00 0.00 0.00 1.73
1297 1781 5.334957 CGTATAGATGACTGCCGTGATTAGT 60.335 44.000 0.00 0.00 0.00 2.24
1298 1782 3.895232 AGATGACTGCCGTGATTAGTT 57.105 42.857 0.00 0.00 0.00 2.24
1344 1852 5.745312 TTCCTTCTGTTCTCATGCTAAGA 57.255 39.130 0.00 0.00 0.00 2.10
1351 1859 6.647229 TCTGTTCTCATGCTAAGAATGATGT 58.353 36.000 0.00 0.00 35.35 3.06
1352 1860 6.537660 TCTGTTCTCATGCTAAGAATGATGTG 59.462 38.462 0.00 0.00 35.35 3.21
1362 1870 6.939730 TGCTAAGAATGATGTGGAAAACTGTA 59.060 34.615 0.00 0.00 0.00 2.74
1554 2062 2.514824 GGGAGGCATCCTTCGTGC 60.515 66.667 18.35 0.00 45.85 5.34
1570 2078 5.637810 CCTTCGTGCTGTAATTTCAGACTAA 59.362 40.000 15.52 8.21 37.61 2.24
1696 2205 1.569479 GCTGGAACTCAGGTTGCGTC 61.569 60.000 0.00 0.00 44.92 5.19
1704 2213 2.027625 CAGGTTGCGTCCCGTCTTC 61.028 63.158 0.00 0.00 0.00 2.87
1711 2220 1.374252 CGTCCCGTCTTCACCCTTG 60.374 63.158 0.00 0.00 0.00 3.61
1720 2230 5.219633 CCGTCTTCACCCTTGTAAAATTTG 58.780 41.667 0.00 0.00 0.00 2.32
1731 2241 5.466393 CCTTGTAAAATTTGCACAGAAAGGG 59.534 40.000 0.00 6.07 0.00 3.95
1791 2302 2.549754 AGTTCATTTCTGTTCTGCCACG 59.450 45.455 0.00 0.00 0.00 4.94
1805 2316 3.258372 TCTGCCACGTAGAGATGAGTTTT 59.742 43.478 0.00 0.00 0.00 2.43
1808 2319 5.109210 TGCCACGTAGAGATGAGTTTTATG 58.891 41.667 0.00 0.00 0.00 1.90
1890 2401 5.453648 GTGCCTACTCATGTATACTTCTCG 58.546 45.833 4.17 0.00 0.00 4.04
1893 2404 5.618195 GCCTACTCATGTATACTTCTCGAGC 60.618 48.000 7.81 0.00 0.00 5.03
1899 2410 4.983671 TGTATACTTCTCGAGCATGTGT 57.016 40.909 7.81 7.11 0.00 3.72
2003 2748 5.068987 GGATGCTTGCTCCCATTTATAACAA 59.931 40.000 0.00 0.00 0.00 2.83
2004 2749 6.239402 GGATGCTTGCTCCCATTTATAACAAT 60.239 38.462 0.00 0.00 0.00 2.71
2005 2750 6.147864 TGCTTGCTCCCATTTATAACAATC 57.852 37.500 0.00 0.00 0.00 2.67
2006 2751 5.655974 TGCTTGCTCCCATTTATAACAATCA 59.344 36.000 0.00 0.00 0.00 2.57
2067 2812 9.627123 TTATTACAGCTTCAATATGTAAGGCTT 57.373 29.630 4.58 4.58 41.32 4.35
2098 2843 0.242017 GATTGCTTGCAACCGAGCTT 59.758 50.000 10.37 0.00 46.69 3.74
2103 2848 1.799258 CTTGCAACCGAGCTTGGCTT 61.799 55.000 20.81 10.62 39.88 4.35
2134 2879 8.902540 TGTTAAGCTTTAAGAATGAGACTCAA 57.097 30.769 9.70 0.00 0.00 3.02
2140 2885 8.150945 AGCTTTAAGAATGAGACTCAACTAACA 58.849 33.333 9.70 0.00 0.00 2.41
2202 2947 7.362920 GGTGGAATGTCAAGTAATTAGTGCATT 60.363 37.037 13.36 13.36 0.00 3.56
2231 2976 9.797556 AAGAAAGTTTTGATACTTGTTTACCAC 57.202 29.630 0.00 0.00 38.33 4.16
2255 3000 4.605640 ACTACCTAAACTGCCAAACGTA 57.394 40.909 0.00 0.00 0.00 3.57
2281 3026 8.671384 TCCCAAACGTCTTATATTTAGGAATG 57.329 34.615 0.00 0.00 0.00 2.67
2282 3027 7.717875 TCCCAAACGTCTTATATTTAGGAATGG 59.282 37.037 0.00 0.00 0.00 3.16
2283 3028 7.717875 CCCAAACGTCTTATATTTAGGAATGGA 59.282 37.037 0.00 0.00 0.00 3.41
2313 3075 8.505625 GGTAGTATGTTTCATTTACGTTTCCAA 58.494 33.333 0.00 0.00 0.00 3.53
2314 3076 9.321590 GTAGTATGTTTCATTTACGTTTCCAAC 57.678 33.333 0.00 0.00 0.00 3.77
2315 3077 7.932335 AGTATGTTTCATTTACGTTTCCAACA 58.068 30.769 0.00 0.00 0.00 3.33
2316 3078 8.407064 AGTATGTTTCATTTACGTTTCCAACAA 58.593 29.630 0.00 0.00 0.00 2.83
2317 3079 9.021863 GTATGTTTCATTTACGTTTCCAACAAA 57.978 29.630 0.00 0.00 0.00 2.83
2318 3080 8.655651 ATGTTTCATTTACGTTTCCAACAAAT 57.344 26.923 0.00 0.00 0.00 2.32
2319 3081 9.751542 ATGTTTCATTTACGTTTCCAACAAATA 57.248 25.926 0.00 0.00 0.00 1.40
2320 3082 9.021863 TGTTTCATTTACGTTTCCAACAAATAC 57.978 29.630 0.00 0.00 0.00 1.89
2321 3083 7.839438 TTCATTTACGTTTCCAACAAATACG 57.161 32.000 0.00 0.00 38.14 3.06
2322 3084 6.957150 TCATTTACGTTTCCAACAAATACGT 58.043 32.000 0.00 0.00 45.96 3.57
2323 3085 7.416022 TCATTTACGTTTCCAACAAATACGTT 58.584 30.769 0.00 0.00 42.10 3.99
2324 3086 7.914346 TCATTTACGTTTCCAACAAATACGTTT 59.086 29.630 0.00 0.00 42.10 3.60
2325 3087 7.662182 TTTACGTTTCCAACAAATACGTTTC 57.338 32.000 0.00 0.00 42.10 2.78
2326 3088 4.600032 ACGTTTCCAACAAATACGTTTCC 58.400 39.130 0.00 0.00 42.10 3.13
2327 3089 4.096081 ACGTTTCCAACAAATACGTTTCCA 59.904 37.500 0.00 0.00 42.10 3.53
2328 3090 4.438471 CGTTTCCAACAAATACGTTTCCAC 59.562 41.667 0.00 0.00 0.00 4.02
2329 3091 5.341617 GTTTCCAACAAATACGTTTCCACA 58.658 37.500 0.00 0.00 0.00 4.17
2330 3092 5.776173 TTCCAACAAATACGTTTCCACAT 57.224 34.783 0.00 0.00 0.00 3.21
2336 3098 7.114247 CCAACAAATACGTTTCCACATAGTTTG 59.886 37.037 0.00 0.00 0.00 2.93
2337 3099 6.146898 ACAAATACGTTTCCACATAGTTTGC 58.853 36.000 0.00 0.00 0.00 3.68
2406 3168 4.218417 GCTCCATGGAATTATATTGGCGTT 59.782 41.667 17.00 0.00 0.00 4.84
2439 3201 2.739913 CAACATAAACGGGAAGAAGCGA 59.260 45.455 0.00 0.00 0.00 4.93
2534 3296 6.987403 AGAGGAGGAAACTAATGAGGATAC 57.013 41.667 0.00 0.00 44.43 2.24
2810 3572 7.990314 GGCTCTCATTTCTCTTTATTTACTCCT 59.010 37.037 0.00 0.00 0.00 3.69
2815 3577 8.383175 TCATTTCTCTTTATTTACTCCTGTGGT 58.617 33.333 0.00 0.00 0.00 4.16
3232 3994 4.527944 TCCTCAGATATGTTCTCTCGTGT 58.472 43.478 0.00 0.00 29.93 4.49
3446 4208 1.202371 GGCATGCCACTGAATGATGTG 60.202 52.381 32.08 0.00 35.81 3.21
3455 4217 7.678837 TGCCACTGAATGATGTGTCATATATA 58.321 34.615 0.00 0.00 44.20 0.86
3602 4364 5.280011 GGATGTTAGGACAGAGAAGAAACCA 60.280 44.000 0.00 0.00 39.58 3.67
3854 4616 6.648725 AGTACATTTTTCTATGCTCGTCAC 57.351 37.500 0.00 0.00 0.00 3.67
3925 4687 7.448748 TTTCTGATTTGTACTTTAGGCTTCC 57.551 36.000 0.00 0.00 0.00 3.46
4083 4854 3.006967 CCCTCCGTCCCATAATGTAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
4084 4855 3.895656 CCTCCGTCCCATAATGTAAGAGA 59.104 47.826 0.00 0.00 0.00 3.10
4213 4988 2.717580 TCACTGCAGTTACACTACCG 57.282 50.000 18.94 2.28 0.00 4.02
4420 5199 2.166254 CCACAAGCACCCAATTACATCC 59.834 50.000 0.00 0.00 0.00 3.51
4490 5269 2.654749 TCATCAACTCACGTAGCTGG 57.345 50.000 0.00 0.00 0.00 4.85
4508 5287 3.635591 CTGGCCCTCCTATCATTTTGTT 58.364 45.455 0.00 0.00 0.00 2.83
4535 5314 8.579850 TTGTTTTTGAAGTGCTGATATCCTAT 57.420 30.769 0.00 0.00 0.00 2.57
4569 5348 2.038952 TCTCTTGCTGTAACATGCTGGT 59.961 45.455 0.00 0.00 0.00 4.00
4611 5390 6.345096 TGGGATCTTTCATTGGAAAAAGAC 57.655 37.500 0.05 0.00 42.52 3.01
4680 5459 0.749454 CTCCTGAAGATTTGCCCCCG 60.749 60.000 0.00 0.00 0.00 5.73
4758 5537 8.674263 TTAATTTCCATTCTTTTGCATGTGTT 57.326 26.923 0.00 0.00 0.00 3.32
4786 5565 1.826385 AGCCACATGTGTAAAGAGCC 58.174 50.000 23.79 4.86 0.00 4.70
4840 5621 0.322816 TGTGCAGGGCCAGAAAGATC 60.323 55.000 6.18 0.00 0.00 2.75
4890 5671 1.135139 CCTGGAATGATCGTGTCGACT 59.865 52.381 17.92 0.00 39.18 4.18
4896 5677 2.500442 GATCGTGTCGACTGCAGCG 61.500 63.158 15.27 18.19 39.18 5.18
4944 5725 3.065371 GCAACATAGACACAACCATAGCC 59.935 47.826 0.00 0.00 0.00 3.93
5057 5838 7.539366 GCGAGTATCTATCTGTTTTCAGTATCC 59.461 40.741 0.00 0.00 46.98 2.59
5082 5877 9.965824 CCTGTATTTTATGTTTCTCTGTTTTGT 57.034 29.630 0.00 0.00 0.00 2.83
5088 5883 9.567848 TTTTATGTTTCTCTGTTTTGTGAAGAC 57.432 29.630 0.00 0.00 0.00 3.01
5089 5884 5.216566 TGTTTCTCTGTTTTGTGAAGACG 57.783 39.130 0.00 0.00 0.00 4.18
5093 5888 2.198406 TCTGTTTTGTGAAGACGACCG 58.802 47.619 0.00 0.00 0.00 4.79
5164 5959 5.456921 ACTCACCAAATTACCTGATCCAT 57.543 39.130 0.00 0.00 0.00 3.41
5184 5979 4.576463 CCATATGCTCTACTTTTGACACCC 59.424 45.833 0.00 0.00 0.00 4.61
5232 6027 3.780804 TGAGCTTTGTTAGGGCAACTA 57.219 42.857 0.00 0.00 38.05 2.24
5233 6028 4.093472 TGAGCTTTGTTAGGGCAACTAA 57.907 40.909 0.00 0.00 39.31 2.24
5270 6065 1.212751 GCCAGCAATTGTTCCGACC 59.787 57.895 7.40 0.00 0.00 4.79
5309 6104 8.445493 CAAAATTCCATAAATCAGAACCAAAGC 58.555 33.333 0.00 0.00 0.00 3.51
5336 6131 1.379146 GTTTGGGGGAGTCTGGACC 59.621 63.158 0.00 0.00 0.00 4.46
5337 6132 2.221299 TTTGGGGGAGTCTGGACCG 61.221 63.158 0.00 0.00 0.00 4.79
5338 6133 2.976284 TTTGGGGGAGTCTGGACCGT 62.976 60.000 0.00 0.00 0.00 4.83
5339 6134 3.075641 GGGGGAGTCTGGACCGTC 61.076 72.222 0.00 0.00 0.00 4.79
5340 6135 2.283676 GGGGAGTCTGGACCGTCA 60.284 66.667 0.00 0.00 0.00 4.35
5341 6136 1.686110 GGGGAGTCTGGACCGTCAT 60.686 63.158 0.00 0.00 0.00 3.06
5342 6137 1.517832 GGGAGTCTGGACCGTCATG 59.482 63.158 0.00 0.00 0.00 3.07
5343 6138 1.258445 GGGAGTCTGGACCGTCATGT 61.258 60.000 0.00 0.00 0.00 3.21
5345 6140 1.822990 GGAGTCTGGACCGTCATGTTA 59.177 52.381 0.00 0.00 0.00 2.41
5346 6141 2.159226 GGAGTCTGGACCGTCATGTTAG 60.159 54.545 0.00 0.00 0.00 2.34
5347 6142 2.753452 GAGTCTGGACCGTCATGTTAGA 59.247 50.000 0.00 0.00 0.00 2.10
5348 6143 2.755655 AGTCTGGACCGTCATGTTAGAG 59.244 50.000 0.00 0.00 0.00 2.43
5349 6144 1.476891 TCTGGACCGTCATGTTAGAGC 59.523 52.381 0.00 0.00 0.00 4.09
5351 6146 1.831106 TGGACCGTCATGTTAGAGCAT 59.169 47.619 0.00 0.00 0.00 3.79
5352 6147 2.159099 TGGACCGTCATGTTAGAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
5363 6158 2.203181 GAGCATCTCCAGCCAGGC 60.203 66.667 1.84 1.84 37.29 4.85
5364 6159 3.771110 GAGCATCTCCAGCCAGGCC 62.771 68.421 8.22 0.00 37.29 5.19
5365 6160 4.891037 GCATCTCCAGCCAGGCCC 62.891 72.222 8.22 0.00 37.29 5.80
5366 6161 4.201122 CATCTCCAGCCAGGCCCC 62.201 72.222 8.22 0.00 37.29 5.80
5367 6162 4.765970 ATCTCCAGCCAGGCCCCA 62.766 66.667 8.22 0.00 37.29 4.96
5379 6174 4.408378 GCCCCAGGCGACTTTTTA 57.592 55.556 0.00 0.00 39.62 1.52
5380 6175 2.882170 GCCCCAGGCGACTTTTTAT 58.118 52.632 0.00 0.00 39.62 1.40
5381 6176 0.455815 GCCCCAGGCGACTTTTTATG 59.544 55.000 0.00 0.00 39.62 1.90
5382 6177 0.455815 CCCCAGGCGACTTTTTATGC 59.544 55.000 0.00 0.00 40.21 3.14
5383 6178 0.098728 CCCAGGCGACTTTTTATGCG 59.901 55.000 0.00 0.00 40.21 4.73
5496 6302 1.920272 GCGAAAAGTCAAGTCAACCGC 60.920 52.381 0.00 0.00 0.00 5.68
5510 6331 3.234730 CCGCCTAGATTCGCCCCT 61.235 66.667 0.00 0.00 0.00 4.79
5538 6359 1.296715 GGTCGTCACCCTGCTGATT 59.703 57.895 0.00 0.00 36.54 2.57
5544 6365 1.555075 GTCACCCTGCTGATTCTGGTA 59.445 52.381 0.00 0.00 0.00 3.25
5549 6370 1.066143 CCTGCTGATTCTGGTACCGTT 60.066 52.381 7.57 0.00 0.00 4.44
5553 6375 2.353803 GCTGATTCTGGTACCGTTCACT 60.354 50.000 7.57 0.00 0.00 3.41
5562 6384 1.485294 TACCGTTCACTGCCCACCAT 61.485 55.000 0.00 0.00 0.00 3.55
5565 6387 0.677731 CGTTCACTGCCCACCATCAT 60.678 55.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.377766 TCCTACTTAATTTTGCTGATGTCAC 57.622 36.000 0.00 0.00 0.00 3.67
72 73 3.477530 ACTCTTACCTGTGCAGTTTTCC 58.522 45.455 0.00 0.00 0.00 3.13
160 161 2.704572 CCAGTTACTCCTTTGCAGAGG 58.295 52.381 17.22 17.22 35.58 3.69
161 162 2.079925 GCCAGTTACTCCTTTGCAGAG 58.920 52.381 0.00 0.00 37.39 3.35
170 171 3.437049 GTCAGATGTTTGCCAGTTACTCC 59.563 47.826 0.00 0.00 0.00 3.85
173 174 3.412386 AGGTCAGATGTTTGCCAGTTAC 58.588 45.455 0.00 0.00 0.00 2.50
178 179 1.699083 TCAGAGGTCAGATGTTTGCCA 59.301 47.619 0.00 0.00 0.00 4.92
180 181 3.406764 ACTTCAGAGGTCAGATGTTTGC 58.593 45.455 0.00 0.00 0.00 3.68
215 225 5.273674 TGATAGAGCTCTCAACTTCCATG 57.726 43.478 22.17 0.00 0.00 3.66
276 286 3.877508 GGAGGTTGTATGATTGGTAGTGC 59.122 47.826 0.00 0.00 0.00 4.40
333 353 1.270785 TGGATGTGCTCGCTTTCTTCA 60.271 47.619 0.00 0.00 0.00 3.02
387 407 3.991367 AGGGTCGTCTCTGTTTTACTTG 58.009 45.455 0.00 0.00 0.00 3.16
389 409 3.509184 GGTAGGGTCGTCTCTGTTTTACT 59.491 47.826 0.00 0.00 0.00 2.24
402 422 0.895530 TGAAGCTCAAGGTAGGGTCG 59.104 55.000 0.00 0.00 0.00 4.79
404 424 2.327325 TCTGAAGCTCAAGGTAGGGT 57.673 50.000 0.00 0.00 0.00 4.34
407 427 3.871485 AGCATTCTGAAGCTCAAGGTAG 58.129 45.455 8.05 0.00 36.00 3.18
413 433 8.959548 TCAAAATTATTAGCATTCTGAAGCTCA 58.040 29.630 14.62 7.55 42.05 4.26
414 434 9.448294 CTCAAAATTATTAGCATTCTGAAGCTC 57.552 33.333 14.62 0.00 42.05 4.09
462 482 1.690283 CTGCACTGAGTGAATCCGCG 61.690 60.000 18.18 0.00 35.23 6.46
465 485 1.066286 AGCTCTGCACTGAGTGAATCC 60.066 52.381 18.18 0.00 35.23 3.01
466 486 2.383368 AGCTCTGCACTGAGTGAATC 57.617 50.000 18.18 0.00 35.23 2.52
467 487 2.424557 CAAGCTCTGCACTGAGTGAAT 58.575 47.619 18.18 0.00 35.23 2.57
468 488 1.875009 CAAGCTCTGCACTGAGTGAA 58.125 50.000 18.18 4.53 35.23 3.18
469 489 3.601277 CAAGCTCTGCACTGAGTGA 57.399 52.632 18.18 0.55 35.23 3.41
479 499 2.415608 CCCAGGCATGCAAGCTCTG 61.416 63.158 21.36 19.22 34.59 3.35
480 500 2.044252 CCCAGGCATGCAAGCTCT 60.044 61.111 21.36 6.49 34.17 4.09
481 501 3.145551 CCCCAGGCATGCAAGCTC 61.146 66.667 21.36 4.12 34.17 4.09
482 502 4.772231 CCCCCAGGCATGCAAGCT 62.772 66.667 21.36 4.35 34.17 3.74
483 503 4.764771 TCCCCCAGGCATGCAAGC 62.765 66.667 21.36 5.09 0.00 4.01
484 504 2.441532 CTCCCCCAGGCATGCAAG 60.442 66.667 21.36 10.90 0.00 4.01
485 505 2.940467 TCTCCCCCAGGCATGCAA 60.940 61.111 21.36 0.00 0.00 4.08
486 506 3.414193 CTCTCCCCCAGGCATGCA 61.414 66.667 21.36 0.00 0.00 3.96
487 507 3.092511 TCTCTCCCCCAGGCATGC 61.093 66.667 9.90 9.90 0.00 4.06
488 508 1.383664 TCTCTCTCCCCCAGGCATG 60.384 63.158 0.00 0.00 0.00 4.06
489 509 1.074623 CTCTCTCTCCCCCAGGCAT 60.075 63.158 0.00 0.00 0.00 4.40
490 510 1.815384 TTCTCTCTCTCCCCCAGGCA 61.815 60.000 0.00 0.00 0.00 4.75
491 511 1.002274 TTCTCTCTCTCCCCCAGGC 59.998 63.158 0.00 0.00 0.00 4.85
492 512 1.048160 GCTTCTCTCTCTCCCCCAGG 61.048 65.000 0.00 0.00 0.00 4.45
493 513 0.325110 TGCTTCTCTCTCTCCCCCAG 60.325 60.000 0.00 0.00 0.00 4.45
494 514 0.117140 TTGCTTCTCTCTCTCCCCCA 59.883 55.000 0.00 0.00 0.00 4.96
495 515 0.829990 CTTGCTTCTCTCTCTCCCCC 59.170 60.000 0.00 0.00 0.00 5.40
517 537 5.707066 ATCTTGGTTAGCTCTGAGGATTT 57.293 39.130 6.83 0.00 0.00 2.17
519 539 5.707066 AAATCTTGGTTAGCTCTGAGGAT 57.293 39.130 6.83 0.00 0.00 3.24
520 540 5.721960 ACTAAATCTTGGTTAGCTCTGAGGA 59.278 40.000 6.83 0.00 32.74 3.71
521 541 5.983540 ACTAAATCTTGGTTAGCTCTGAGG 58.016 41.667 6.83 0.00 32.74 3.86
522 542 6.872920 AGACTAAATCTTGGTTAGCTCTGAG 58.127 40.000 0.00 0.00 31.62 3.35
528 548 6.045955 CCTCTGAGACTAAATCTTGGTTAGC 58.954 44.000 6.17 0.00 38.00 3.09
566 586 1.075450 CCTACCTCCGGCTTACCCT 60.075 63.158 0.00 0.00 0.00 4.34
570 590 2.836360 CCGCCTACCTCCGGCTTA 60.836 66.667 0.00 0.00 45.37 3.09
571 591 4.772231 TCCGCCTACCTCCGGCTT 62.772 66.667 0.00 0.00 45.37 4.35
596 616 1.306654 CCCTACCACTACCAGCCCA 60.307 63.158 0.00 0.00 0.00 5.36
607 627 3.006728 CCGGCACCTTCCCTACCA 61.007 66.667 0.00 0.00 0.00 3.25
608 628 3.793888 CCCGGCACCTTCCCTACC 61.794 72.222 0.00 0.00 0.00 3.18
609 629 4.484872 GCCCGGCACCTTCCCTAC 62.485 72.222 3.91 0.00 0.00 3.18
691 723 3.606662 GCTCGCCGCTATCTCCCA 61.607 66.667 0.00 0.00 35.14 4.37
692 724 3.606662 TGCTCGCCGCTATCTCCC 61.607 66.667 0.00 0.00 40.11 4.30
693 725 2.355244 GTGCTCGCCGCTATCTCC 60.355 66.667 0.00 0.00 40.11 3.71
694 726 1.659954 CAGTGCTCGCCGCTATCTC 60.660 63.158 0.00 0.00 40.11 2.75
695 727 2.415010 CAGTGCTCGCCGCTATCT 59.585 61.111 0.00 0.00 40.11 1.98
696 728 3.333969 GCAGTGCTCGCCGCTATC 61.334 66.667 8.18 0.00 40.11 2.08
697 729 3.664025 TTGCAGTGCTCGCCGCTAT 62.664 57.895 17.60 0.00 40.11 2.97
698 730 4.371590 TTGCAGTGCTCGCCGCTA 62.372 61.111 17.60 0.00 40.11 4.26
730 762 4.424566 GTGGTAACCTCGCGCCGA 62.425 66.667 0.00 1.17 0.00 5.54
734 766 0.179200 GCATTTGTGGTAACCTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
761 793 1.611673 CCTCGTCAGAAACATGGGCTT 60.612 52.381 0.00 0.00 0.00 4.35
802 848 5.612688 TGGGCTCTGAGGAGGATATTTATTT 59.387 40.000 6.83 0.00 39.80 1.40
810 856 1.760086 CGTGGGCTCTGAGGAGGAT 60.760 63.158 6.83 0.00 39.80 3.24
811 857 2.363018 CGTGGGCTCTGAGGAGGA 60.363 66.667 6.83 0.00 39.80 3.71
926 988 0.323542 GAGTTGGAGGAGACGGAGGA 60.324 60.000 0.00 0.00 0.00 3.71
954 1016 3.036959 GGAGAGAGGGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
961 1023 3.151022 GTCTGCCGGAGAGAGGGG 61.151 72.222 5.05 0.00 0.00 4.79
962 1024 3.151022 GGTCTGCCGGAGAGAGGG 61.151 72.222 5.05 0.00 0.00 4.30
963 1025 2.043450 AGGTCTGCCGGAGAGAGG 60.043 66.667 5.05 0.00 40.50 3.69
964 1026 1.379176 TGAGGTCTGCCGGAGAGAG 60.379 63.158 5.05 0.00 40.50 3.20
965 1027 1.379176 CTGAGGTCTGCCGGAGAGA 60.379 63.158 5.05 1.66 40.50 3.10
966 1028 3.074999 GCTGAGGTCTGCCGGAGAG 62.075 68.421 5.05 0.00 40.50 3.20
967 1029 3.071206 GCTGAGGTCTGCCGGAGA 61.071 66.667 5.05 1.90 40.50 3.71
1073 1536 9.218525 TCATAGTGAGAAAAAGGGAGATAAGAT 57.781 33.333 0.00 0.00 0.00 2.40
1080 1543 7.278875 AGCTTATCATAGTGAGAAAAAGGGAG 58.721 38.462 0.00 0.00 26.13 4.30
1116 1588 0.234884 GTCGCCCAAGAAAACACGAG 59.765 55.000 0.00 0.00 0.00 4.18
1134 1606 1.458777 TCCCTGACCAGACCAACGT 60.459 57.895 0.00 0.00 0.00 3.99
1139 1611 2.232298 CTTCGCTCCCTGACCAGACC 62.232 65.000 0.00 0.00 0.00 3.85
1142 1614 0.108424 CTTCTTCGCTCCCTGACCAG 60.108 60.000 0.00 0.00 0.00 4.00
1147 1619 1.449246 CAGCCTTCTTCGCTCCCTG 60.449 63.158 0.00 0.00 33.17 4.45
1220 1692 4.759516 TTGAAACGAAAGATTAGTGCCC 57.240 40.909 0.00 0.00 0.00 5.36
1221 1693 4.558860 GCATTGAAACGAAAGATTAGTGCC 59.441 41.667 0.00 0.00 0.00 5.01
1253 1725 2.420022 CGCTCGAACCAATCCAAGAATT 59.580 45.455 0.00 0.00 0.00 2.17
1254 1726 2.009774 CGCTCGAACCAATCCAAGAAT 58.990 47.619 0.00 0.00 0.00 2.40
1260 1736 3.637998 TCTATACGCTCGAACCAATCC 57.362 47.619 0.00 0.00 0.00 3.01
1266 1750 2.974536 GCAGTCATCTATACGCTCGAAC 59.025 50.000 0.00 0.00 0.00 3.95
1269 1753 1.726251 CGGCAGTCATCTATACGCTCG 60.726 57.143 0.00 0.00 0.00 5.03
1283 1767 5.393896 GGAGTAACTAACTAATCACGGCAGT 60.394 44.000 0.00 0.00 39.07 4.40
1324 1832 6.111382 TCATTCTTAGCATGAGAACAGAAGG 58.889 40.000 0.00 0.00 36.08 3.46
1366 1874 9.827198 ATCCACCATTTACATATGTAATTCCAT 57.173 29.630 25.09 14.73 39.89 3.41
1546 2054 3.997021 AGTCTGAAATTACAGCACGAAGG 59.003 43.478 0.00 0.00 37.75 3.46
1547 2055 6.586463 TCTTAGTCTGAAATTACAGCACGAAG 59.414 38.462 0.00 0.00 37.75 3.79
1570 2078 7.875041 TGAAATCGTTGAGAAGAGAGAATTTCT 59.125 33.333 0.00 0.00 39.43 2.52
1611 2120 5.117355 AGTTGATCTTGCACAACATCAAG 57.883 39.130 17.21 0.00 45.70 3.02
1696 2205 2.554370 TTTACAAGGGTGAAGACGGG 57.446 50.000 0.00 0.00 0.00 5.28
1704 2213 4.942852 TCTGTGCAAATTTTACAAGGGTG 58.057 39.130 0.00 0.00 0.00 4.61
1711 2220 4.631131 AGCCCTTTCTGTGCAAATTTTAC 58.369 39.130 0.00 0.00 0.00 2.01
1720 2230 2.185004 TGAAGTAGCCCTTTCTGTGC 57.815 50.000 0.00 0.00 32.03 4.57
1731 2241 5.672321 GCTGTAAGACAAAGCATGAAGTAGC 60.672 44.000 0.00 0.00 36.91 3.58
1791 2302 9.606631 ATTTGAGACCATAAAACTCATCTCTAC 57.393 33.333 0.00 0.00 39.78 2.59
1890 2401 4.510340 CGGTAAATACCCTAACACATGCTC 59.490 45.833 4.07 0.00 43.51 4.26
1893 2404 4.773013 ACCGGTAAATACCCTAACACATG 58.227 43.478 4.49 0.00 43.51 3.21
1899 2410 3.106054 TGCAGACCGGTAAATACCCTAA 58.894 45.455 7.34 0.00 43.51 2.69
2003 2748 0.961019 ACGCACCAAAGCAACATGAT 59.039 45.000 0.00 0.00 0.00 2.45
2004 2749 0.030504 CACGCACCAAAGCAACATGA 59.969 50.000 0.00 0.00 0.00 3.07
2005 2750 0.248990 ACACGCACCAAAGCAACATG 60.249 50.000 0.00 0.00 0.00 3.21
2006 2751 0.459489 AACACGCACCAAAGCAACAT 59.541 45.000 0.00 0.00 0.00 2.71
2067 2812 3.909587 AGCAATCATAGCTTGGCCA 57.090 47.368 0.00 0.00 39.87 5.36
2098 2843 6.717540 TCTTAAAGCTTAACAATACCAAGCCA 59.282 34.615 0.00 0.00 44.57 4.75
2103 2848 9.733556 TCTCATTCTTAAAGCTTAACAATACCA 57.266 29.630 0.00 0.00 0.00 3.25
2134 2879 3.826729 GGAGCACAAAAATCCCTGTTAGT 59.173 43.478 0.00 0.00 0.00 2.24
2140 2885 3.243359 TCTTGGAGCACAAAAATCCCT 57.757 42.857 0.00 0.00 38.91 4.20
2231 2976 4.992951 ACGTTTGGCAGTTTAGGTAGTAAG 59.007 41.667 0.00 0.00 0.00 2.34
2255 3000 9.284968 CATTCCTAAATATAAGACGTTTGGGAT 57.715 33.333 0.58 0.00 40.60 3.85
2281 3026 6.700520 CGTAAATGAAACATACTACCTCCTCC 59.299 42.308 0.00 0.00 0.00 4.30
2282 3027 7.263496 ACGTAAATGAAACATACTACCTCCTC 58.737 38.462 0.00 0.00 0.00 3.71
2283 3028 7.179076 ACGTAAATGAAACATACTACCTCCT 57.821 36.000 0.00 0.00 0.00 3.69
2313 3075 6.146898 GCAAACTATGTGGAAACGTATTTGT 58.853 36.000 0.00 0.00 0.00 2.83
2314 3076 5.571357 GGCAAACTATGTGGAAACGTATTTG 59.429 40.000 0.00 0.00 0.00 2.32
2315 3077 5.475564 AGGCAAACTATGTGGAAACGTATTT 59.524 36.000 0.00 0.00 0.00 1.40
2316 3078 5.007682 AGGCAAACTATGTGGAAACGTATT 58.992 37.500 0.00 0.00 0.00 1.89
2317 3079 4.585879 AGGCAAACTATGTGGAAACGTAT 58.414 39.130 0.00 0.00 0.00 3.06
2318 3080 4.010667 AGGCAAACTATGTGGAAACGTA 57.989 40.909 0.00 0.00 0.00 3.57
2319 3081 2.858745 AGGCAAACTATGTGGAAACGT 58.141 42.857 0.00 0.00 0.00 3.99
2320 3082 4.876107 AGATAGGCAAACTATGTGGAAACG 59.124 41.667 0.00 0.00 42.43 3.60
2321 3083 7.859325 TTAGATAGGCAAACTATGTGGAAAC 57.141 36.000 0.00 0.00 42.43 2.78
2322 3084 9.474313 AATTTAGATAGGCAAACTATGTGGAAA 57.526 29.630 0.00 0.00 42.43 3.13
2327 3089 9.574516 CCCTTAATTTAGATAGGCAAACTATGT 57.425 33.333 0.00 0.00 42.43 2.29
2328 3090 8.515414 GCCCTTAATTTAGATAGGCAAACTATG 58.485 37.037 5.63 0.00 42.43 2.23
2329 3091 8.448816 AGCCCTTAATTTAGATAGGCAAACTAT 58.551 33.333 11.25 0.00 45.03 2.12
2330 3092 7.812306 AGCCCTTAATTTAGATAGGCAAACTA 58.188 34.615 11.25 0.00 41.45 2.24
2336 3098 6.418946 AGCATAGCCCTTAATTTAGATAGGC 58.581 40.000 2.98 2.98 39.25 3.93
2337 3099 8.103305 TGAAGCATAGCCCTTAATTTAGATAGG 58.897 37.037 0.00 0.00 0.00 2.57
2406 3168 5.285651 CCGTTTATGTTGGAAAGCTTGAAA 58.714 37.500 0.00 0.00 0.00 2.69
2439 3201 8.383175 TCAACTTTTGAAGATGGTATAGGTTCT 58.617 33.333 0.00 0.00 36.59 3.01
2534 3296 4.464008 ACATACATGTAGGATGGGCTTTG 58.536 43.478 23.38 9.06 39.68 2.77
2815 3577 1.047002 CCAAATGTTGAGTGGGCCAA 58.953 50.000 8.40 0.00 0.00 4.52
2942 3704 7.514721 ATGTTCCTTACAAGTTCCTAAGAACA 58.485 34.615 6.97 0.00 45.53 3.18
3232 3994 9.359653 TGATCTATGAATACATGACAGAGAGAA 57.640 33.333 0.00 0.00 35.81 2.87
3287 4049 5.959618 ACATTAAACTGGTCTAAGCCAAC 57.040 39.130 0.00 0.00 38.18 3.77
3455 4217 7.050493 ACATATCCAGAGGACATAGGAGTAT 57.950 40.000 0.00 0.00 32.98 2.12
3602 4364 7.173907 GCATTGTGAGCCTTAATAGACATACAT 59.826 37.037 0.00 0.00 0.00 2.29
3854 4616 4.396166 CCTTTGAAGTGGGTAGTATGCAAG 59.604 45.833 0.00 0.00 0.00 4.01
3997 4759 9.884465 AAATTTTCATCAACTAGAAGACGAAAG 57.116 29.630 0.00 0.00 0.00 2.62
3998 4760 9.663904 CAAATTTTCATCAACTAGAAGACGAAA 57.336 29.630 0.00 1.63 0.00 3.46
3999 4761 8.289618 CCAAATTTTCATCAACTAGAAGACGAA 58.710 33.333 0.00 0.00 0.00 3.85
4000 4762 7.573096 GCCAAATTTTCATCAACTAGAAGACGA 60.573 37.037 0.00 0.00 0.00 4.20
4001 4763 6.524586 GCCAAATTTTCATCAACTAGAAGACG 59.475 38.462 0.00 0.00 0.00 4.18
4003 4765 7.523293 TGCCAAATTTTCATCAACTAGAAGA 57.477 32.000 0.00 0.00 0.00 2.87
4005 4767 7.669427 ACATGCCAAATTTTCATCAACTAGAA 58.331 30.769 0.00 0.00 0.00 2.10
4006 4768 7.230849 ACATGCCAAATTTTCATCAACTAGA 57.769 32.000 0.00 0.00 0.00 2.43
4007 4769 7.894376 AACATGCCAAATTTTCATCAACTAG 57.106 32.000 0.00 0.00 0.00 2.57
4083 4854 5.356882 TTTCCGACATGTCAGAAAATGTC 57.643 39.130 27.24 13.99 46.01 3.06
4084 4855 5.766150 TTTTCCGACATGTCAGAAAATGT 57.234 34.783 31.95 0.00 39.60 2.71
4091 4862 7.361201 AATGTAAGACATTTTCCGACATGTCAG 60.361 37.037 24.93 14.62 45.80 3.51
4102 4873 6.540914 TCCGTCCCATAATGTAAGACATTTTC 59.459 38.462 9.92 0.00 45.80 2.29
4313 5088 5.305585 AGAGTTGACGTGAACATACCATTT 58.694 37.500 20.00 0.00 0.00 2.32
4490 5269 5.793817 ACAAAAACAAAATGATAGGAGGGC 58.206 37.500 0.00 0.00 0.00 5.19
4508 5287 7.725251 AGGATATCAGCACTTCAAAAACAAAA 58.275 30.769 4.83 0.00 0.00 2.44
4535 5314 2.297315 AGCAAGAGAACTCGACATGTCA 59.703 45.455 24.93 11.49 34.09 3.58
4569 5348 8.485392 AGATCCCAAATTCTGAAGAAAAACAAA 58.515 29.630 0.00 0.00 37.61 2.83
4611 5390 2.021355 ATTCAGCTTCCTCTTCTGCG 57.979 50.000 0.00 0.00 0.00 5.18
4680 5459 3.243201 CCTGGTGAACAAAGAGAAGTTGC 60.243 47.826 0.00 0.00 0.00 4.17
4770 5549 4.688879 TCTTTACGGCTCTTTACACATGTG 59.311 41.667 24.25 24.25 0.00 3.21
4786 5565 6.531594 TCATCACATCTACTTGCTTCTTTACG 59.468 38.462 0.00 0.00 0.00 3.18
4866 5647 3.383505 TCGACACGATCATTCCAGGTATT 59.616 43.478 0.00 0.00 0.00 1.89
4896 5677 0.955428 TCAGCACGTTGAAGCCATCC 60.955 55.000 0.00 0.00 0.00 3.51
4944 5725 0.036306 AAGTAGGTTTGTCTGCCCCG 59.964 55.000 0.00 0.00 0.00 5.73
5075 5870 1.928503 GACGGTCGTCTTCACAAAACA 59.071 47.619 15.25 0.00 41.57 2.83
5076 5871 2.640375 GACGGTCGTCTTCACAAAAC 57.360 50.000 15.25 0.00 41.57 2.43
5086 5881 1.986378 CATGAAACTGAGACGGTCGTC 59.014 52.381 14.79 14.79 44.86 4.20
5087 5882 1.340248 ACATGAAACTGAGACGGTCGT 59.660 47.619 0.00 0.00 0.00 4.34
5088 5883 2.065993 ACATGAAACTGAGACGGTCG 57.934 50.000 0.00 0.00 0.00 4.79
5089 5884 6.561614 TCTATTACATGAAACTGAGACGGTC 58.438 40.000 0.00 0.00 0.00 4.79
5093 5888 9.469807 CCACTATCTATTACATGAAACTGAGAC 57.530 37.037 0.00 0.00 0.00 3.36
5164 5959 4.901197 TGGGTGTCAAAAGTAGAGCATA 57.099 40.909 0.00 0.00 0.00 3.14
5217 6012 3.633065 AGCGTTTTAGTTGCCCTAACAAA 59.367 39.130 0.00 0.00 41.88 2.83
5232 6027 3.119495 GGCTATTTGGTGATCAGCGTTTT 60.119 43.478 19.36 7.42 32.97 2.43
5233 6028 2.423538 GGCTATTTGGTGATCAGCGTTT 59.576 45.455 19.36 9.07 32.97 3.60
5270 6065 1.784283 GAATTTTGCACGTCCAAACCG 59.216 47.619 3.62 0.00 34.68 4.44
5336 6131 3.379240 CTGGAGATGCTCTAACATGACG 58.621 50.000 0.00 0.00 0.00 4.35
5337 6132 3.129871 GCTGGAGATGCTCTAACATGAC 58.870 50.000 0.00 0.00 0.00 3.06
5338 6133 2.103771 GGCTGGAGATGCTCTAACATGA 59.896 50.000 0.00 0.00 0.00 3.07
5339 6134 2.158856 TGGCTGGAGATGCTCTAACATG 60.159 50.000 0.00 0.00 0.00 3.21
5340 6135 2.104451 CTGGCTGGAGATGCTCTAACAT 59.896 50.000 0.00 0.00 0.00 2.71
5341 6136 1.483827 CTGGCTGGAGATGCTCTAACA 59.516 52.381 0.00 0.00 0.00 2.41
5342 6137 1.202627 CCTGGCTGGAGATGCTCTAAC 60.203 57.143 4.05 0.00 38.35 2.34
5343 6138 1.126488 CCTGGCTGGAGATGCTCTAA 58.874 55.000 4.05 0.00 38.35 2.10
5345 6140 2.744243 GCCTGGCTGGAGATGCTCT 61.744 63.158 15.36 0.00 38.35 4.09
5346 6141 2.203181 GCCTGGCTGGAGATGCTC 60.203 66.667 15.36 0.00 38.35 4.26
5347 6142 3.806667 GGCCTGGCTGGAGATGCT 61.807 66.667 19.68 0.00 38.35 3.79
5348 6143 4.891037 GGGCCTGGCTGGAGATGC 62.891 72.222 19.68 0.00 38.35 3.91
5349 6144 4.201122 GGGGCCTGGCTGGAGATG 62.201 72.222 19.68 0.00 38.35 2.90
5362 6157 0.455815 CATAAAAAGTCGCCTGGGGC 59.544 55.000 5.77 0.00 46.75 5.80
5363 6158 0.455815 GCATAAAAAGTCGCCTGGGG 59.544 55.000 4.03 4.03 0.00 4.96
5364 6159 0.098728 CGCATAAAAAGTCGCCTGGG 59.901 55.000 0.00 0.00 0.00 4.45
5365 6160 0.523335 GCGCATAAAAAGTCGCCTGG 60.523 55.000 0.30 0.00 41.53 4.45
5366 6161 2.930168 GCGCATAAAAAGTCGCCTG 58.070 52.632 0.30 0.00 41.53 4.85
5369 6164 1.582680 CCGGCGCATAAAAAGTCGC 60.583 57.895 10.83 0.00 45.99 5.19
5370 6165 1.582680 GCCGGCGCATAAAAAGTCG 60.583 57.895 12.58 0.00 34.03 4.18
5371 6166 1.504446 TGCCGGCGCATAAAAAGTC 59.496 52.632 23.90 0.00 41.12 3.01
5372 6167 3.674906 TGCCGGCGCATAAAAAGT 58.325 50.000 23.90 0.00 41.12 2.66
5380 6175 3.243274 CTAAAAACGTGCCGGCGCA 62.243 57.895 36.82 17.40 44.78 6.09
5381 6176 2.501008 CTAAAAACGTGCCGGCGC 60.501 61.111 30.11 30.11 34.88 6.53
5382 6177 2.174835 CCTAAAAACGTGCCGGCG 59.825 61.111 23.90 11.34 37.94 6.46
5383 6178 2.126618 GCCTAAAAACGTGCCGGC 60.127 61.111 22.73 22.73 0.00 6.13
5384 6179 1.500396 GAGCCTAAAAACGTGCCGG 59.500 57.895 0.00 0.00 0.00 6.13
5389 6184 0.390735 ATCGCCGAGCCTAAAAACGT 60.391 50.000 0.00 0.00 0.00 3.99
5496 6302 2.340443 GCGAGGGGCGAATCTAGG 59.660 66.667 0.00 0.00 44.57 3.02
5525 6346 1.555075 GTACCAGAATCAGCAGGGTGA 59.445 52.381 3.41 3.41 33.14 4.02
5538 6359 1.669440 GGCAGTGAACGGTACCAGA 59.331 57.895 13.54 0.00 0.00 3.86
5544 6365 2.748058 GATGGTGGGCAGTGAACGGT 62.748 60.000 0.00 0.00 0.00 4.83
5549 6370 2.195727 TCTAATGATGGTGGGCAGTGA 58.804 47.619 0.00 0.00 0.00 3.41
5553 6375 3.326521 ACCTATCTAATGATGGTGGGCA 58.673 45.455 0.00 0.00 34.86 5.36
5562 6384 4.489737 ACGGGGAATGACCTATCTAATGA 58.510 43.478 0.00 0.00 38.98 2.57
5565 6387 2.889045 CGACGGGGAATGACCTATCTAA 59.111 50.000 0.00 0.00 38.98 2.10
5616 6438 2.656069 CCCGAACGGTGGTGGAGAT 61.656 63.158 12.23 0.00 0.00 2.75
5862 6709 1.074951 CTTTCCTTTCACCCGCCCT 59.925 57.895 0.00 0.00 0.00 5.19
5876 6723 0.721718 CAGACGATGCCGGTTCTTTC 59.278 55.000 1.90 0.54 40.78 2.62


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

AutoCloner maintained by Alex Coulton.