Multiple sequence alignment - TraesCS6B01G108900

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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 TraesCS6B01G108900 chr6B 100.000 4814 0 0 1 4814 89441035 89436222 0.000000e+00 8890.0
1 TraesCS6B01G108900 chr6A 96.667 4110 131 5 707 4814 49997722 49993617 0.000000e+00 6826.0
2 TraesCS6B01G108900 chrUn 96.576 4089 125 6 728 4814 115033252 115037327 0.000000e+00 6761.0
3 TraesCS6B01G108900 chrUn 78.889 270 32 12 4544 4808 63662831 63663080 4.990000e-35 159.0
4 TraesCS6B01G108900 chr5D 79.116 249 33 13 4564 4808 454809373 454809606 2.320000e-33 154.0
5 TraesCS6B01G108900 chr5B 83.333 120 18 2 4690 4808 556958961 556959079 5.090000e-20 110.0
6 TraesCS6B01G108900 chr2D 89.655 58 4 2 1 58 549862126 549862071 6.680000e-09 73.1


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 TraesCS6B01G108900 chr6B 89436222 89441035 4813 True 8890 8890 100.000 1 4814 1 chr6B.!!$R1 4813
1 TraesCS6B01G108900 chr6A 49993617 49997722 4105 True 6826 6826 96.667 707 4814 1 chr6A.!!$R1 4107
2 TraesCS6B01G108900 chrUn 115033252 115037327 4075 False 6761 6761 96.576 728 4814 1 chrUn.!!$F2 4086

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
666 667 0.092351 GTGCGTACGGTCGACAATTG 59.908 55.0 18.91 3.24 0.00 2.32 F
2052 2054 0.034089 ATGCCAACAGGGTAAGAGCC 60.034 55.0 0.00 0.00 39.65 4.70 F
2298 2300 0.818040 GGTTCGCAGGGACAACACTT 60.818 55.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2585 2587 0.467384 AGCAGGACATCTCCATTCCG 59.533 55.000 0.00 0.00 39.39 4.30 R
3012 3014 2.303890 ACTGCAGTCTGGAATCATGTCA 59.696 45.455 15.25 0.00 0.00 3.58 R
4135 4137 1.847328 TTGCATGAGTACTCCCTCGA 58.153 50.000 20.11 1.12 34.04 4.04 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
24 25 7.656707 ATTCCTGAACAAAATTTGCATACAC 57.343 32.000 5.52 0.00 0.00 2.90
25 26 6.154203 TCCTGAACAAAATTTGCATACACA 57.846 33.333 5.52 0.00 0.00 3.72
26 27 6.215121 TCCTGAACAAAATTTGCATACACAG 58.785 36.000 5.52 6.54 0.00 3.66
27 28 5.984926 CCTGAACAAAATTTGCATACACAGT 59.015 36.000 5.52 0.00 0.00 3.55
28 29 6.479660 CCTGAACAAAATTTGCATACACAGTT 59.520 34.615 5.52 0.00 0.00 3.16
29 30 7.011295 CCTGAACAAAATTTGCATACACAGTTT 59.989 33.333 5.52 0.00 0.00 2.66
30 31 8.261492 TGAACAAAATTTGCATACACAGTTTT 57.739 26.923 5.52 0.00 0.00 2.43
31 32 9.371136 TGAACAAAATTTGCATACACAGTTTTA 57.629 25.926 5.52 0.00 0.00 1.52
47 48 9.915629 ACACAGTTTTATAAAAACTTGTGAACA 57.084 25.926 32.11 6.25 39.17 3.18
61 62 5.830900 TTGTGAACAAGTTTTGAAAACGG 57.169 34.783 14.38 13.01 0.00 4.44
62 63 4.238514 TGTGAACAAGTTTTGAAAACGGG 58.761 39.130 14.38 12.69 0.00 5.28
63 64 4.022242 TGTGAACAAGTTTTGAAAACGGGA 60.022 37.500 14.38 0.00 0.00 5.14
64 65 4.325204 GTGAACAAGTTTTGAAAACGGGAC 59.675 41.667 14.38 9.83 0.00 4.46
65 66 4.022242 TGAACAAGTTTTGAAAACGGGACA 60.022 37.500 14.38 11.74 0.00 4.02
66 67 4.729227 ACAAGTTTTGAAAACGGGACAT 57.271 36.364 14.38 0.00 0.00 3.06
67 68 5.079689 ACAAGTTTTGAAAACGGGACATT 57.920 34.783 14.38 0.63 0.00 2.71
68 69 5.483811 ACAAGTTTTGAAAACGGGACATTT 58.516 33.333 14.38 0.00 0.00 2.32
69 70 5.935206 ACAAGTTTTGAAAACGGGACATTTT 59.065 32.000 14.38 0.00 36.04 1.82
70 71 6.428465 ACAAGTTTTGAAAACGGGACATTTTT 59.572 30.769 14.38 0.00 32.42 1.94
118 119 9.488124 AAAACATGAACAATTTTCGAATTTGTG 57.512 25.926 20.98 13.84 35.74 3.33
119 120 8.417780 AACATGAACAATTTTCGAATTTGTGA 57.582 26.923 20.98 14.10 35.74 3.58
120 121 8.417780 ACATGAACAATTTTCGAATTTGTGAA 57.582 26.923 20.98 14.95 35.74 3.18
121 122 8.327429 ACATGAACAATTTTCGAATTTGTGAAC 58.673 29.630 20.98 16.57 35.74 3.18
122 123 7.818493 TGAACAATTTTCGAATTTGTGAACA 57.182 28.000 20.98 18.11 35.74 3.18
123 124 8.244494 TGAACAATTTTCGAATTTGTGAACAA 57.756 26.923 20.98 2.42 35.74 2.83
124 125 8.877779 TGAACAATTTTCGAATTTGTGAACAAT 58.122 25.926 20.98 9.50 35.74 2.71
125 126 9.701355 GAACAATTTTCGAATTTGTGAACAATT 57.299 25.926 20.98 9.38 35.74 2.32
134 135 9.535270 TCGAATTTGTGAACAATTTTTGAAAAC 57.465 25.926 0.00 0.00 35.55 2.43
135 136 9.322776 CGAATTTGTGAACAATTTTTGAAAACA 57.677 25.926 0.00 0.00 35.55 2.83
137 138 9.623350 AATTTGTGAACAATTTTTGAAAACAGG 57.377 25.926 0.00 0.00 35.55 4.00
138 139 7.969536 TTGTGAACAATTTTTGAAAACAGGA 57.030 28.000 0.00 0.00 0.00 3.86
139 140 7.969536 TGTGAACAATTTTTGAAAACAGGAA 57.030 28.000 0.00 0.00 0.00 3.36
140 141 8.558973 TGTGAACAATTTTTGAAAACAGGAAT 57.441 26.923 0.00 0.00 0.00 3.01
141 142 9.658799 TGTGAACAATTTTTGAAAACAGGAATA 57.341 25.926 0.00 0.00 0.00 1.75
227 228 6.458232 TTTTTGAAACTCCCGAAGAAATGA 57.542 33.333 0.00 0.00 0.00 2.57
228 229 6.458232 TTTTGAAACTCCCGAAGAAATGAA 57.542 33.333 0.00 0.00 0.00 2.57
229 230 6.458232 TTTGAAACTCCCGAAGAAATGAAA 57.542 33.333 0.00 0.00 0.00 2.69
230 231 6.458232 TTGAAACTCCCGAAGAAATGAAAA 57.542 33.333 0.00 0.00 0.00 2.29
231 232 5.827666 TGAAACTCCCGAAGAAATGAAAAC 58.172 37.500 0.00 0.00 0.00 2.43
232 233 5.358442 TGAAACTCCCGAAGAAATGAAAACA 59.642 36.000 0.00 0.00 0.00 2.83
233 234 6.040391 TGAAACTCCCGAAGAAATGAAAACAT 59.960 34.615 0.00 0.00 0.00 2.71
234 235 5.376854 ACTCCCGAAGAAATGAAAACATG 57.623 39.130 0.00 0.00 0.00 3.21
235 236 5.070001 ACTCCCGAAGAAATGAAAACATGA 58.930 37.500 0.00 0.00 0.00 3.07
236 237 5.534654 ACTCCCGAAGAAATGAAAACATGAA 59.465 36.000 0.00 0.00 0.00 2.57
237 238 5.768317 TCCCGAAGAAATGAAAACATGAAC 58.232 37.500 0.00 0.00 0.00 3.18
238 239 5.300539 TCCCGAAGAAATGAAAACATGAACA 59.699 36.000 0.00 0.00 0.00 3.18
239 240 5.982516 CCCGAAGAAATGAAAACATGAACAA 59.017 36.000 0.00 0.00 0.00 2.83
240 241 6.478344 CCCGAAGAAATGAAAACATGAACAAA 59.522 34.615 0.00 0.00 0.00 2.83
241 242 7.171337 CCCGAAGAAATGAAAACATGAACAAAT 59.829 33.333 0.00 0.00 0.00 2.32
242 243 8.550376 CCGAAGAAATGAAAACATGAACAAATT 58.450 29.630 0.00 0.00 0.00 1.82
243 244 9.919348 CGAAGAAATGAAAACATGAACAAATTT 57.081 25.926 0.00 0.00 0.00 1.82
267 268 9.631452 TTTTGAACAATTTTTGAAAATGGGAAC 57.369 25.926 8.11 1.42 38.53 3.62
287 288 9.672673 TGGGAACATTTTCTAAAATTGTGAAAA 57.327 25.926 12.62 12.62 41.75 2.29
331 332 9.884465 CCAAACAATTTTTGTAAAACAAGAACA 57.116 25.926 10.27 0.00 44.59 3.18
356 357 6.442513 TTTTTGAAATGCCCGAACAATTTT 57.557 29.167 0.00 0.00 0.00 1.82
357 358 6.442513 TTTTGAAATGCCCGAACAATTTTT 57.557 29.167 0.00 0.00 0.00 1.94
358 359 5.415415 TTGAAATGCCCGAACAATTTTTG 57.585 34.783 0.00 0.00 0.00 2.44
359 360 4.697514 TGAAATGCCCGAACAATTTTTGA 58.302 34.783 0.00 0.00 0.00 2.69
360 361 5.118990 TGAAATGCCCGAACAATTTTTGAA 58.881 33.333 0.00 0.00 0.00 2.69
361 362 5.586243 TGAAATGCCCGAACAATTTTTGAAA 59.414 32.000 0.00 0.00 0.00 2.69
362 363 6.094048 TGAAATGCCCGAACAATTTTTGAAAA 59.906 30.769 0.00 0.00 0.00 2.29
363 364 6.442513 AATGCCCGAACAATTTTTGAAAAA 57.557 29.167 5.47 5.47 0.00 1.94
364 365 6.631971 ATGCCCGAACAATTTTTGAAAAAT 57.368 29.167 9.92 9.92 0.00 1.82
365 366 5.814783 TGCCCGAACAATTTTTGAAAAATG 58.185 33.333 15.79 12.16 35.47 2.32
366 367 4.674662 GCCCGAACAATTTTTGAAAAATGC 59.325 37.500 15.79 9.57 33.23 3.56
367 368 5.731686 GCCCGAACAATTTTTGAAAAATGCA 60.732 36.000 15.79 0.00 33.23 3.96
368 369 6.261118 CCCGAACAATTTTTGAAAAATGCAA 58.739 32.000 15.79 0.00 33.23 4.08
369 370 6.749118 CCCGAACAATTTTTGAAAAATGCAAA 59.251 30.769 15.79 0.00 33.23 3.68
370 371 7.253585 CCCGAACAATTTTTGAAAAATGCAAAC 60.254 33.333 15.79 7.06 35.20 2.93
371 372 7.272084 CCGAACAATTTTTGAAAAATGCAAACA 59.728 29.630 15.79 0.00 35.20 2.83
372 373 8.633408 CGAACAATTTTTGAAAAATGCAAACAA 58.367 25.926 15.79 0.00 35.20 2.83
390 391 9.897744 TGCAAACAATTTTTGAATTTGTTAACA 57.102 22.222 3.59 3.59 41.46 2.41
462 463 9.753669 AGAAACACGAACAAATTTTGAAATTTC 57.246 25.926 15.81 11.41 44.38 2.17
463 464 8.888332 AAACACGAACAAATTTTGAAATTTCC 57.112 26.923 15.81 0.00 44.38 3.13
464 465 7.602517 ACACGAACAAATTTTGAAATTTCCA 57.397 28.000 15.81 1.42 44.38 3.53
465 466 8.034058 ACACGAACAAATTTTGAAATTTCCAA 57.966 26.923 15.81 8.13 44.38 3.53
466 467 7.960195 ACACGAACAAATTTTGAAATTTCCAAC 59.040 29.630 15.81 0.00 44.38 3.77
467 468 7.427895 CACGAACAAATTTTGAAATTTCCAACC 59.572 33.333 15.81 0.00 44.38 3.77
468 469 7.119846 ACGAACAAATTTTGAAATTTCCAACCA 59.880 29.630 15.81 0.00 44.38 3.67
469 470 7.965107 CGAACAAATTTTGAAATTTCCAACCAA 59.035 29.630 15.81 0.60 44.38 3.67
470 471 9.800433 GAACAAATTTTGAAATTTCCAACCAAT 57.200 25.926 15.81 4.17 44.38 3.16
485 486 9.672673 TTTCCAACCAATTTTGAAATAAACAGA 57.327 25.926 0.00 0.00 0.00 3.41
486 487 9.672673 TTCCAACCAATTTTGAAATAAACAGAA 57.327 25.926 0.00 0.00 0.00 3.02
487 488 9.672673 TCCAACCAATTTTGAAATAAACAGAAA 57.327 25.926 0.00 0.00 0.00 2.52
534 535 7.812309 AGGAAGAAAAAGAAACAGAAAAACG 57.188 32.000 0.00 0.00 0.00 3.60
535 536 6.811665 AGGAAGAAAAAGAAACAGAAAAACGG 59.188 34.615 0.00 0.00 0.00 4.44
536 537 6.035650 GGAAGAAAAAGAAACAGAAAAACGGG 59.964 38.462 0.00 0.00 0.00 5.28
537 538 6.275494 AGAAAAAGAAACAGAAAAACGGGA 57.725 33.333 0.00 0.00 0.00 5.14
538 539 6.693466 AGAAAAAGAAACAGAAAAACGGGAA 58.307 32.000 0.00 0.00 0.00 3.97
539 540 7.156000 AGAAAAAGAAACAGAAAAACGGGAAA 58.844 30.769 0.00 0.00 0.00 3.13
540 541 7.658167 AGAAAAAGAAACAGAAAAACGGGAAAA 59.342 29.630 0.00 0.00 0.00 2.29
541 542 6.715344 AAAGAAACAGAAAAACGGGAAAAC 57.285 33.333 0.00 0.00 0.00 2.43
542 543 5.394224 AGAAACAGAAAAACGGGAAAACA 57.606 34.783 0.00 0.00 0.00 2.83
543 544 5.407502 AGAAACAGAAAAACGGGAAAACAG 58.592 37.500 0.00 0.00 0.00 3.16
544 545 5.184287 AGAAACAGAAAAACGGGAAAACAGA 59.816 36.000 0.00 0.00 0.00 3.41
545 546 5.394224 AACAGAAAAACGGGAAAACAGAA 57.606 34.783 0.00 0.00 0.00 3.02
546 547 5.394224 ACAGAAAAACGGGAAAACAGAAA 57.606 34.783 0.00 0.00 0.00 2.52
547 548 5.785243 ACAGAAAAACGGGAAAACAGAAAA 58.215 33.333 0.00 0.00 0.00 2.29
548 549 6.224584 ACAGAAAAACGGGAAAACAGAAAAA 58.775 32.000 0.00 0.00 0.00 1.94
571 572 9.605955 AAAAACAAAAAGAAACAGAAAAATCGG 57.394 25.926 0.00 0.00 0.00 4.18
572 573 7.899178 AACAAAAAGAAACAGAAAAATCGGT 57.101 28.000 0.00 0.00 0.00 4.69
573 574 7.520119 ACAAAAAGAAACAGAAAAATCGGTC 57.480 32.000 0.00 0.00 0.00 4.79
574 575 7.093992 ACAAAAAGAAACAGAAAAATCGGTCA 58.906 30.769 0.00 0.00 0.00 4.02
575 576 7.600752 ACAAAAAGAAACAGAAAAATCGGTCAA 59.399 29.630 0.00 0.00 0.00 3.18
576 577 8.439286 CAAAAAGAAACAGAAAAATCGGTCAAA 58.561 29.630 0.00 0.00 0.00 2.69
577 578 8.541133 AAAAGAAACAGAAAAATCGGTCAAAA 57.459 26.923 0.00 0.00 0.00 2.44
578 579 8.541133 AAAGAAACAGAAAAATCGGTCAAAAA 57.459 26.923 0.00 0.00 0.00 1.94
579 580 7.755582 AGAAACAGAAAAATCGGTCAAAAAG 57.244 32.000 0.00 0.00 0.00 2.27
580 581 6.756542 AGAAACAGAAAAATCGGTCAAAAAGG 59.243 34.615 0.00 0.00 0.00 3.11
581 582 5.845391 ACAGAAAAATCGGTCAAAAAGGA 57.155 34.783 0.00 0.00 0.00 3.36
582 583 6.215495 ACAGAAAAATCGGTCAAAAAGGAA 57.785 33.333 0.00 0.00 0.00 3.36
583 584 6.635755 ACAGAAAAATCGGTCAAAAAGGAAA 58.364 32.000 0.00 0.00 0.00 3.13
584 585 7.100409 ACAGAAAAATCGGTCAAAAAGGAAAA 58.900 30.769 0.00 0.00 0.00 2.29
585 586 7.604545 ACAGAAAAATCGGTCAAAAAGGAAAAA 59.395 29.630 0.00 0.00 0.00 1.94
614 615 2.963548 GGAACCTTCTAGAAGACCGG 57.036 55.000 30.17 18.38 40.79 5.28
615 616 1.134759 GGAACCTTCTAGAAGACCGGC 60.135 57.143 30.17 15.33 40.79 6.13
616 617 1.826096 GAACCTTCTAGAAGACCGGCT 59.174 52.381 30.17 8.89 40.79 5.52
617 618 1.187087 ACCTTCTAGAAGACCGGCTG 58.813 55.000 30.17 15.60 40.79 4.85
618 619 1.272536 ACCTTCTAGAAGACCGGCTGA 60.273 52.381 30.17 0.00 40.79 4.26
619 620 1.135333 CCTTCTAGAAGACCGGCTGAC 59.865 57.143 30.17 0.00 40.79 3.51
620 621 2.096248 CTTCTAGAAGACCGGCTGACT 58.904 52.381 25.55 6.27 40.79 3.41
621 622 3.280295 CTTCTAGAAGACCGGCTGACTA 58.720 50.000 25.55 7.05 40.79 2.59
622 623 2.920524 TCTAGAAGACCGGCTGACTAG 58.079 52.381 20.60 20.60 36.56 2.57
623 624 6.273509 CTTCTAGAAGACCGGCTGACTAGC 62.274 54.167 25.55 0.00 43.81 3.42
634 635 3.810310 GCTGACTAGCTCTGGTACAAT 57.190 47.619 0.00 0.00 46.57 2.71
635 636 3.452474 GCTGACTAGCTCTGGTACAATG 58.548 50.000 0.00 0.00 46.57 2.82
636 637 3.739519 GCTGACTAGCTCTGGTACAATGG 60.740 52.174 0.00 0.00 46.57 3.16
637 638 2.766263 TGACTAGCTCTGGTACAATGGG 59.234 50.000 0.00 0.00 38.70 4.00
638 639 1.486726 ACTAGCTCTGGTACAATGGGC 59.513 52.381 0.00 0.00 38.70 5.36
639 640 0.837272 TAGCTCTGGTACAATGGGCC 59.163 55.000 0.00 0.00 38.70 5.80
640 641 1.819632 GCTCTGGTACAATGGGCCG 60.820 63.158 0.00 0.00 38.70 6.13
641 642 1.153168 CTCTGGTACAATGGGCCGG 60.153 63.158 0.00 0.00 38.70 6.13
642 643 2.828549 CTGGTACAATGGGCCGGC 60.829 66.667 21.18 21.18 38.70 6.13
643 644 4.434354 TGGTACAATGGGCCGGCC 62.434 66.667 38.57 38.57 31.92 6.13
661 662 3.170585 GCTGTGCGTACGGTCGAC 61.171 66.667 18.39 7.13 35.54 4.20
662 663 2.253154 CTGTGCGTACGGTCGACA 59.747 61.111 18.91 2.62 0.00 4.35
663 664 1.370778 CTGTGCGTACGGTCGACAA 60.371 57.895 18.91 0.00 0.00 3.18
664 665 0.731514 CTGTGCGTACGGTCGACAAT 60.732 55.000 18.91 6.97 0.00 2.71
665 666 0.318869 TGTGCGTACGGTCGACAATT 60.319 50.000 18.91 2.83 0.00 2.32
666 667 0.092351 GTGCGTACGGTCGACAATTG 59.908 55.000 18.91 3.24 0.00 2.32
667 668 1.009903 TGCGTACGGTCGACAATTGG 61.010 55.000 18.91 4.36 0.00 3.16
668 669 0.733566 GCGTACGGTCGACAATTGGA 60.734 55.000 18.91 0.00 0.00 3.53
669 670 1.265568 CGTACGGTCGACAATTGGAG 58.734 55.000 18.91 3.21 0.00 3.86
670 671 1.636988 GTACGGTCGACAATTGGAGG 58.363 55.000 18.91 0.00 0.00 4.30
671 672 0.108520 TACGGTCGACAATTGGAGGC 60.109 55.000 18.91 4.44 0.00 4.70
672 673 1.375396 CGGTCGACAATTGGAGGCA 60.375 57.895 18.91 0.00 0.00 4.75
673 674 0.953471 CGGTCGACAATTGGAGGCAA 60.953 55.000 18.91 0.00 0.00 4.52
674 675 1.243902 GGTCGACAATTGGAGGCAAA 58.756 50.000 18.91 0.00 0.00 3.68
675 676 1.200020 GGTCGACAATTGGAGGCAAAG 59.800 52.381 18.91 0.00 0.00 2.77
676 677 2.151202 GTCGACAATTGGAGGCAAAGA 58.849 47.619 11.55 0.00 0.00 2.52
677 678 2.160417 GTCGACAATTGGAGGCAAAGAG 59.840 50.000 11.55 0.00 0.00 2.85
678 679 1.135575 CGACAATTGGAGGCAAAGAGC 60.136 52.381 10.83 0.00 44.65 4.09
684 685 4.883026 GAGGCAAAGAGCGTCGTA 57.117 55.556 0.00 0.00 46.68 3.43
685 686 3.347411 GAGGCAAAGAGCGTCGTAT 57.653 52.632 0.00 0.00 46.68 3.06
686 687 2.486951 GAGGCAAAGAGCGTCGTATA 57.513 50.000 0.00 0.00 46.68 1.47
687 688 2.386249 GAGGCAAAGAGCGTCGTATAG 58.614 52.381 0.00 0.00 46.68 1.31
688 689 2.859032 GAGGCAAAGAGCGTCGTATAGG 60.859 54.545 0.00 0.00 46.68 2.57
689 690 1.488527 GCAAAGAGCGTCGTATAGGG 58.511 55.000 0.00 0.00 0.00 3.53
690 691 1.202382 GCAAAGAGCGTCGTATAGGGT 60.202 52.381 0.00 0.00 0.00 4.34
691 692 2.737679 GCAAAGAGCGTCGTATAGGGTT 60.738 50.000 0.00 0.00 0.00 4.11
692 693 3.518590 CAAAGAGCGTCGTATAGGGTTT 58.481 45.455 0.00 0.00 0.00 3.27
693 694 3.881937 AAGAGCGTCGTATAGGGTTTT 57.118 42.857 0.00 0.00 0.00 2.43
694 695 3.433513 AGAGCGTCGTATAGGGTTTTC 57.566 47.619 0.00 0.00 0.00 2.29
695 696 2.100418 AGAGCGTCGTATAGGGTTTTCC 59.900 50.000 0.00 0.00 39.75 3.13
705 706 4.494515 GGTTTTCCCGCTCCTTGT 57.505 55.556 0.00 0.00 0.00 3.16
711 712 3.495434 TTTCCCGCTCCTTGTTCTAAA 57.505 42.857 0.00 0.00 0.00 1.85
719 720 4.750098 CGCTCCTTGTTCTAAAAGACTTCA 59.250 41.667 0.00 0.00 0.00 3.02
733 734 9.760660 CTAAAAGACTTCAATGTACAGTATTGC 57.239 33.333 0.33 0.00 35.90 3.56
734 735 7.744087 AAAGACTTCAATGTACAGTATTGCA 57.256 32.000 0.33 0.00 35.90 4.08
741 742 5.064579 TCAATGTACAGTATTGCATTCCGTG 59.935 40.000 0.33 0.00 35.90 4.94
749 750 2.264005 TTGCATTCCGTGTGGTTAGT 57.736 45.000 0.00 0.00 36.30 2.24
771 773 3.320541 TGGCCGGCCTTATTGAATTTATG 59.679 43.478 43.34 0.00 36.94 1.90
786 788 2.932569 TTATGACGGGCCGGGCTAGA 62.933 60.000 31.78 9.94 0.00 2.43
795 797 2.111878 CGGGCTAGATTGGGCCTG 59.888 66.667 4.53 1.15 46.80 4.85
802 804 0.178068 TAGATTGGGCCTGACTTCGC 59.822 55.000 4.53 0.00 0.00 4.70
812 814 1.178276 CTGACTTCGCTGACCTACCT 58.822 55.000 0.00 0.00 0.00 3.08
817 819 2.028930 ACTTCGCTGACCTACCTCAAAG 60.029 50.000 0.00 0.00 0.00 2.77
818 820 1.629043 TCGCTGACCTACCTCAAAGT 58.371 50.000 0.00 0.00 0.00 2.66
821 823 1.066071 GCTGACCTACCTCAAAGTCCC 60.066 57.143 0.00 0.00 0.00 4.46
822 824 2.257207 CTGACCTACCTCAAAGTCCCA 58.743 52.381 0.00 0.00 0.00 4.37
823 825 2.637872 CTGACCTACCTCAAAGTCCCAA 59.362 50.000 0.00 0.00 0.00 4.12
824 826 3.050089 TGACCTACCTCAAAGTCCCAAA 58.950 45.455 0.00 0.00 0.00 3.28
826 828 2.107726 ACCTACCTCAAAGTCCCAAACC 59.892 50.000 0.00 0.00 0.00 3.27
827 829 2.554564 CCTACCTCAAAGTCCCAAACCC 60.555 54.545 0.00 0.00 0.00 4.11
828 830 0.187606 ACCTCAAAGTCCCAAACCCC 59.812 55.000 0.00 0.00 0.00 4.95
829 831 0.187361 CCTCAAAGTCCCAAACCCCA 59.813 55.000 0.00 0.00 0.00 4.96
830 832 1.328279 CTCAAAGTCCCAAACCCCAC 58.672 55.000 0.00 0.00 0.00 4.61
859 861 2.037527 ACCCCTCTCGTCCTGTCC 59.962 66.667 0.00 0.00 0.00 4.02
992 994 2.417516 CGCCACATACCTCTCCGG 59.582 66.667 0.00 0.00 39.35 5.14
1005 1007 0.546122 TCTCCGGCCAATACATGCTT 59.454 50.000 2.24 0.00 0.00 3.91
1122 1124 2.430921 GCGACCGACACCACTCTG 60.431 66.667 0.00 0.00 0.00 3.35
1311 1313 3.826754 CTCGCTCACGCCCAGCTA 61.827 66.667 0.00 0.00 39.84 3.32
1420 1422 2.124996 CCCTCTTCCCCCACCTCA 59.875 66.667 0.00 0.00 0.00 3.86
1443 1445 3.256136 CCGAGGTGTACAAAGACTTCTCT 59.744 47.826 0.00 0.00 0.00 3.10
1449 1451 6.098409 AGGTGTACAAAGACTTCTCTTTCTCA 59.902 38.462 0.00 0.00 43.70 3.27
1535 1537 1.665679 CGTGTTCGATGAAATGGGGAG 59.334 52.381 0.00 0.00 39.71 4.30
1611 1613 4.052518 GCTGGGGATGTGGGCACT 62.053 66.667 0.00 0.00 0.00 4.40
1647 1649 3.104766 CAGATGCGGTGTGATGGC 58.895 61.111 0.00 0.00 0.00 4.40
1814 1816 2.628657 GGTATTGCGGAGTAGGACAGAT 59.371 50.000 0.00 0.00 0.00 2.90
1815 1817 3.069729 GGTATTGCGGAGTAGGACAGATT 59.930 47.826 0.00 0.00 0.00 2.40
1857 1859 1.205893 CTGTCACTGGAGTCTAAGGGC 59.794 57.143 0.00 0.00 0.00 5.19
1875 1877 0.889186 GCCTGTCACCGAATGTGGTT 60.889 55.000 0.00 0.00 45.48 3.67
1941 1943 1.920835 GGAGGCTGAGAGGGTGGTT 60.921 63.158 0.00 0.00 0.00 3.67
1947 1949 1.972207 GCTGAGAGGGTGGTTAGGGAT 60.972 57.143 0.00 0.00 0.00 3.85
1968 1970 9.571816 AGGGATATGAAAGAAAATGAGAAGATC 57.428 33.333 0.00 0.00 0.00 2.75
1995 1997 0.686441 ACGAGGTAGCCTATGGTGCA 60.686 55.000 0.00 0.00 31.76 4.57
2052 2054 0.034089 ATGCCAACAGGGTAAGAGCC 60.034 55.000 0.00 0.00 39.65 4.70
2227 2229 5.536916 ACTCTAGTAGATGGGTATTGCAGAC 59.463 44.000 0.00 0.00 0.00 3.51
2229 2231 4.679373 AGTAGATGGGTATTGCAGACAG 57.321 45.455 3.54 0.00 0.00 3.51
2241 2243 1.144708 TGCAGACAGGGTTCCATGAAA 59.855 47.619 10.49 0.00 0.00 2.69
2252 2254 4.504689 GGGTTCCATGAAAAAGGCATTTGA 60.505 41.667 0.00 0.00 0.00 2.69
2298 2300 0.818040 GGTTCGCAGGGACAACACTT 60.818 55.000 0.00 0.00 0.00 3.16
2301 2303 1.045407 TCGCAGGGACAACACTTACT 58.955 50.000 0.00 0.00 0.00 2.24
2307 2309 5.815740 CGCAGGGACAACACTTACTTATAAT 59.184 40.000 0.00 0.00 0.00 1.28
2309 2311 7.656137 CGCAGGGACAACACTTACTTATAATAT 59.344 37.037 0.00 0.00 0.00 1.28
2313 2315 8.774586 GGGACAACACTTACTTATAATATGCTG 58.225 37.037 0.00 0.00 0.00 4.41
2436 2438 3.057736 CACTGCTGGATGGTTTCTTCAAG 60.058 47.826 0.00 0.00 0.00 3.02
2585 2587 4.591072 AGAGGAGCTATTTGGTAGGATGAC 59.409 45.833 0.00 0.00 0.00 3.06
2677 2679 6.168270 ACCTGGATAGAGCTACTCAAATTC 57.832 41.667 0.00 0.00 32.06 2.17
2756 2758 6.880484 TCATAACCGGATTCTTTGTAGCTAA 58.120 36.000 9.46 0.00 0.00 3.09
2772 2774 1.068264 GCTAAGCAAAGTGGCAAGGTC 60.068 52.381 0.00 0.00 35.83 3.85
2886 2888 7.541162 GCAATCTGCATGATGCCTATAATTTA 58.459 34.615 15.70 0.00 44.23 1.40
3006 3008 2.937469 TGGTGTTGCAAGAACTTGTG 57.063 45.000 13.37 0.00 42.31 3.33
3012 3014 2.949644 GTTGCAAGAACTTGTGGGTACT 59.050 45.455 14.62 0.00 42.31 2.73
3156 3158 3.343617 GCTGTGCAAATTGGGTAGAGTA 58.656 45.455 0.00 0.00 0.00 2.59
3262 3264 1.815408 GCTCTGCCTCAGGTTTTGTCA 60.815 52.381 0.00 0.00 31.51 3.58
3470 3472 5.704354 TGGACATTGCAAGGATGGTAATAT 58.296 37.500 19.41 0.00 0.00 1.28
3518 3520 3.906998 AGATGATCGAGCAAGGTATTCG 58.093 45.455 7.76 0.00 35.76 3.34
3690 3692 6.513180 TCGGTGTGGTAATATGAAAGAGATC 58.487 40.000 0.00 0.00 0.00 2.75
4135 4137 8.522830 CACACATTATCCTTTTTGTCCTACAAT 58.477 33.333 0.00 0.00 38.00 2.71
4257 4259 3.269178 CAGTCAAGAAGAGGATGAAGGC 58.731 50.000 0.00 0.00 0.00 4.35
4326 4329 8.956446 TGGGTGATAGTCTTTCATATAGATGA 57.044 34.615 0.00 0.00 40.45 2.92
4626 4629 6.233905 ACCTGGGGCATGTTTTATTTTATC 57.766 37.500 0.00 0.00 0.00 1.75
4634 4637 9.952188 GGGCATGTTTTATTTTATCTCTCTAAC 57.048 33.333 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.215789 TGTGTATGCAAATTTTGTTCAGGAAT 58.784 30.769 10.65 0.00 0.00 3.01
1 2 6.577103 TGTGTATGCAAATTTTGTTCAGGAA 58.423 32.000 10.65 0.00 0.00 3.36
2 3 6.154203 TGTGTATGCAAATTTTGTTCAGGA 57.846 33.333 10.65 0.00 0.00 3.86
3 4 5.984926 ACTGTGTATGCAAATTTTGTTCAGG 59.015 36.000 10.65 4.67 0.00 3.86
4 5 7.467557 AACTGTGTATGCAAATTTTGTTCAG 57.532 32.000 10.65 11.21 0.00 3.02
5 6 7.840342 AAACTGTGTATGCAAATTTTGTTCA 57.160 28.000 10.65 1.99 0.00 3.18
21 22 9.915629 TGTTCACAAGTTTTTATAAAACTGTGT 57.084 25.926 26.78 19.99 40.10 3.72
39 40 4.686554 CCCGTTTTCAAAACTTGTTCACAA 59.313 37.500 11.23 0.00 0.00 3.33
40 41 4.022242 TCCCGTTTTCAAAACTTGTTCACA 60.022 37.500 11.23 0.00 0.00 3.58
41 42 4.325204 GTCCCGTTTTCAAAACTTGTTCAC 59.675 41.667 11.23 0.00 0.00 3.18
42 43 4.022242 TGTCCCGTTTTCAAAACTTGTTCA 60.022 37.500 11.23 2.02 0.00 3.18
43 44 4.487019 TGTCCCGTTTTCAAAACTTGTTC 58.513 39.130 11.23 0.00 0.00 3.18
44 45 4.522722 TGTCCCGTTTTCAAAACTTGTT 57.477 36.364 11.23 0.00 0.00 2.83
45 46 4.729227 ATGTCCCGTTTTCAAAACTTGT 57.271 36.364 11.23 0.00 0.00 3.16
46 47 6.415798 AAAATGTCCCGTTTTCAAAACTTG 57.584 33.333 11.23 2.34 27.83 3.16
92 93 9.488124 CACAAATTCGAAAATTGTTCATGTTTT 57.512 25.926 22.65 4.77 35.27 2.43
93 94 8.877779 TCACAAATTCGAAAATTGTTCATGTTT 58.122 25.926 22.65 4.94 35.27 2.83
94 95 8.417780 TCACAAATTCGAAAATTGTTCATGTT 57.582 26.923 22.65 4.79 35.27 2.71
95 96 8.327429 GTTCACAAATTCGAAAATTGTTCATGT 58.673 29.630 22.65 5.34 35.27 3.21
96 97 8.326713 TGTTCACAAATTCGAAAATTGTTCATG 58.673 29.630 22.65 14.96 35.27 3.07
97 98 8.417780 TGTTCACAAATTCGAAAATTGTTCAT 57.582 26.923 22.65 6.17 35.27 2.57
98 99 7.818493 TGTTCACAAATTCGAAAATTGTTCA 57.182 28.000 22.65 18.97 35.27 3.18
99 100 9.701355 AATTGTTCACAAATTCGAAAATTGTTC 57.299 25.926 22.65 17.41 39.55 3.18
108 109 9.535270 GTTTTCAAAAATTGTTCACAAATTCGA 57.465 25.926 0.00 0.00 39.55 3.71
109 110 9.322776 TGTTTTCAAAAATTGTTCACAAATTCG 57.677 25.926 0.00 0.00 39.55 3.34
111 112 9.623350 CCTGTTTTCAAAAATTGTTCACAAATT 57.377 25.926 0.00 0.00 39.55 1.82
112 113 9.007901 TCCTGTTTTCAAAAATTGTTCACAAAT 57.992 25.926 0.00 0.00 39.55 2.32
113 114 8.383318 TCCTGTTTTCAAAAATTGTTCACAAA 57.617 26.923 0.00 0.00 39.55 2.83
114 115 7.969536 TCCTGTTTTCAAAAATTGTTCACAA 57.030 28.000 0.00 0.00 40.51 3.33
115 116 7.969536 TTCCTGTTTTCAAAAATTGTTCACA 57.030 28.000 0.00 0.00 0.00 3.58
204 205 6.458232 TCATTTCTTCGGGAGTTTCAAAAA 57.542 33.333 0.00 0.00 0.00 1.94
205 206 6.458232 TTCATTTCTTCGGGAGTTTCAAAA 57.542 33.333 0.00 0.00 0.00 2.44
206 207 6.458232 TTTCATTTCTTCGGGAGTTTCAAA 57.542 33.333 0.00 0.00 0.00 2.69
207 208 6.127591 TGTTTTCATTTCTTCGGGAGTTTCAA 60.128 34.615 0.00 0.00 0.00 2.69
208 209 5.358442 TGTTTTCATTTCTTCGGGAGTTTCA 59.642 36.000 0.00 0.00 0.00 2.69
209 210 5.827666 TGTTTTCATTTCTTCGGGAGTTTC 58.172 37.500 0.00 0.00 0.00 2.78
210 211 5.845391 TGTTTTCATTTCTTCGGGAGTTT 57.155 34.783 0.00 0.00 0.00 2.66
211 212 5.534654 TCATGTTTTCATTTCTTCGGGAGTT 59.465 36.000 0.00 0.00 38.64 3.01
212 213 5.070001 TCATGTTTTCATTTCTTCGGGAGT 58.930 37.500 0.00 0.00 38.64 3.85
213 214 5.627499 TCATGTTTTCATTTCTTCGGGAG 57.373 39.130 0.00 0.00 38.64 4.30
214 215 5.300539 TGTTCATGTTTTCATTTCTTCGGGA 59.699 36.000 0.00 0.00 38.64 5.14
215 216 5.527951 TGTTCATGTTTTCATTTCTTCGGG 58.472 37.500 0.00 0.00 38.64 5.14
216 217 7.462109 TTTGTTCATGTTTTCATTTCTTCGG 57.538 32.000 0.00 0.00 38.64 4.30
217 218 9.919348 AAATTTGTTCATGTTTTCATTTCTTCG 57.081 25.926 0.00 0.00 38.64 3.79
241 242 9.631452 GTTCCCATTTTCAAAAATTGTTCAAAA 57.369 25.926 0.00 0.00 36.52 2.44
242 243 8.796475 TGTTCCCATTTTCAAAAATTGTTCAAA 58.204 25.926 0.00 0.00 36.52 2.69
243 244 8.340618 TGTTCCCATTTTCAAAAATTGTTCAA 57.659 26.923 0.00 0.00 36.52 2.69
244 245 7.928307 TGTTCCCATTTTCAAAAATTGTTCA 57.072 28.000 0.00 0.00 36.52 3.18
245 246 9.800433 AAATGTTCCCATTTTCAAAAATTGTTC 57.200 25.926 0.00 0.00 46.61 3.18
259 260 9.844257 TTCACAATTTTAGAAAATGTTCCCATT 57.156 25.926 1.10 0.00 43.14 3.16
260 261 9.844257 TTTCACAATTTTAGAAAATGTTCCCAT 57.156 25.926 1.10 0.00 38.53 4.00
261 262 9.672673 TTTTCACAATTTTAGAAAATGTTCCCA 57.327 25.926 1.10 0.00 38.53 4.37
305 306 9.884465 TGTTCTTGTTTTACAAAAATTGTTTGG 57.116 25.926 4.39 0.00 42.22 3.28
333 334 6.442513 AAAATTGTTCGGGCATTTCAAAAA 57.557 29.167 0.00 0.00 0.00 1.94
334 335 6.094048 TCAAAAATTGTTCGGGCATTTCAAAA 59.906 30.769 0.00 0.00 0.00 2.44
335 336 5.586243 TCAAAAATTGTTCGGGCATTTCAAA 59.414 32.000 0.00 0.00 0.00 2.69
336 337 5.118990 TCAAAAATTGTTCGGGCATTTCAA 58.881 33.333 0.00 0.00 0.00 2.69
337 338 4.697514 TCAAAAATTGTTCGGGCATTTCA 58.302 34.783 0.00 0.00 0.00 2.69
338 339 5.665381 TTCAAAAATTGTTCGGGCATTTC 57.335 34.783 0.00 0.00 0.00 2.17
339 340 6.442513 TTTTCAAAAATTGTTCGGGCATTT 57.557 29.167 0.00 0.00 0.00 2.32
340 341 6.442513 TTTTTCAAAAATTGTTCGGGCATT 57.557 29.167 0.00 0.00 0.00 3.56
341 342 6.437094 CATTTTTCAAAAATTGTTCGGGCAT 58.563 32.000 5.29 0.00 0.00 4.40
342 343 5.731686 GCATTTTTCAAAAATTGTTCGGGCA 60.732 36.000 5.29 0.00 33.86 5.36
343 344 4.674662 GCATTTTTCAAAAATTGTTCGGGC 59.325 37.500 5.29 1.25 33.86 6.13
344 345 5.814783 TGCATTTTTCAAAAATTGTTCGGG 58.185 33.333 5.29 0.00 33.86 5.14
345 346 7.272084 TGTTTGCATTTTTCAAAAATTGTTCGG 59.728 29.630 5.29 0.00 35.49 4.30
346 347 8.154868 TGTTTGCATTTTTCAAAAATTGTTCG 57.845 26.923 5.29 0.00 35.49 3.95
364 365 9.897744 TGTTAACAAATTCAAAAATTGTTTGCA 57.102 22.222 5.64 7.75 35.27 4.08
436 437 9.753669 GAAATTTCAAAATTTGTTCGTGTTTCT 57.246 25.926 16.03 0.00 45.70 2.52
437 438 8.994881 GGAAATTTCAAAATTTGTTCGTGTTTC 58.005 29.630 19.49 8.61 45.70 2.78
438 439 8.507249 TGGAAATTTCAAAATTTGTTCGTGTTT 58.493 25.926 19.49 1.09 45.70 2.83
439 440 8.034058 TGGAAATTTCAAAATTTGTTCGTGTT 57.966 26.923 19.49 0.00 45.70 3.32
440 441 7.602517 TGGAAATTTCAAAATTTGTTCGTGT 57.397 28.000 19.49 0.00 45.70 4.49
441 442 7.427895 GGTTGGAAATTTCAAAATTTGTTCGTG 59.572 33.333 19.49 0.00 45.70 4.35
442 443 7.119846 TGGTTGGAAATTTCAAAATTTGTTCGT 59.880 29.630 19.49 0.00 45.70 3.85
443 444 7.467623 TGGTTGGAAATTTCAAAATTTGTTCG 58.532 30.769 19.49 0.00 45.70 3.95
444 445 9.800433 ATTGGTTGGAAATTTCAAAATTTGTTC 57.200 25.926 19.49 2.39 45.70 3.18
459 460 9.672673 TCTGTTTATTTCAAAATTGGTTGGAAA 57.327 25.926 0.00 0.00 29.80 3.13
460 461 9.672673 TTCTGTTTATTTCAAAATTGGTTGGAA 57.327 25.926 0.00 0.00 30.56 3.53
461 462 9.672673 TTTCTGTTTATTTCAAAATTGGTTGGA 57.327 25.926 0.00 0.00 0.00 3.53
508 509 8.708742 CGTTTTTCTGTTTCTTTTTCTTCCTTT 58.291 29.630 0.00 0.00 0.00 3.11
509 510 7.330946 CCGTTTTTCTGTTTCTTTTTCTTCCTT 59.669 33.333 0.00 0.00 0.00 3.36
510 511 6.811665 CCGTTTTTCTGTTTCTTTTTCTTCCT 59.188 34.615 0.00 0.00 0.00 3.36
511 512 6.035650 CCCGTTTTTCTGTTTCTTTTTCTTCC 59.964 38.462 0.00 0.00 0.00 3.46
512 513 6.809689 TCCCGTTTTTCTGTTTCTTTTTCTTC 59.190 34.615 0.00 0.00 0.00 2.87
513 514 6.693466 TCCCGTTTTTCTGTTTCTTTTTCTT 58.307 32.000 0.00 0.00 0.00 2.52
514 515 6.275494 TCCCGTTTTTCTGTTTCTTTTTCT 57.725 33.333 0.00 0.00 0.00 2.52
515 516 6.954616 TTCCCGTTTTTCTGTTTCTTTTTC 57.045 33.333 0.00 0.00 0.00 2.29
516 517 7.226918 TGTTTTCCCGTTTTTCTGTTTCTTTTT 59.773 29.630 0.00 0.00 0.00 1.94
517 518 6.706716 TGTTTTCCCGTTTTTCTGTTTCTTTT 59.293 30.769 0.00 0.00 0.00 2.27
518 519 6.224584 TGTTTTCCCGTTTTTCTGTTTCTTT 58.775 32.000 0.00 0.00 0.00 2.52
519 520 5.785243 TGTTTTCCCGTTTTTCTGTTTCTT 58.215 33.333 0.00 0.00 0.00 2.52
520 521 5.184287 TCTGTTTTCCCGTTTTTCTGTTTCT 59.816 36.000 0.00 0.00 0.00 2.52
521 522 5.404096 TCTGTTTTCCCGTTTTTCTGTTTC 58.596 37.500 0.00 0.00 0.00 2.78
522 523 5.394224 TCTGTTTTCCCGTTTTTCTGTTT 57.606 34.783 0.00 0.00 0.00 2.83
523 524 5.394224 TTCTGTTTTCCCGTTTTTCTGTT 57.606 34.783 0.00 0.00 0.00 3.16
524 525 5.394224 TTTCTGTTTTCCCGTTTTTCTGT 57.606 34.783 0.00 0.00 0.00 3.41
525 526 6.713792 TTTTTCTGTTTTCCCGTTTTTCTG 57.286 33.333 0.00 0.00 0.00 3.02
545 546 9.605955 CCGATTTTTCTGTTTCTTTTTGTTTTT 57.394 25.926 0.00 0.00 0.00 1.94
546 547 8.779303 ACCGATTTTTCTGTTTCTTTTTGTTTT 58.221 25.926 0.00 0.00 0.00 2.43
547 548 8.317891 ACCGATTTTTCTGTTTCTTTTTGTTT 57.682 26.923 0.00 0.00 0.00 2.83
548 549 7.600752 TGACCGATTTTTCTGTTTCTTTTTGTT 59.399 29.630 0.00 0.00 0.00 2.83
549 550 7.093992 TGACCGATTTTTCTGTTTCTTTTTGT 58.906 30.769 0.00 0.00 0.00 2.83
550 551 7.518731 TGACCGATTTTTCTGTTTCTTTTTG 57.481 32.000 0.00 0.00 0.00 2.44
551 552 8.541133 TTTGACCGATTTTTCTGTTTCTTTTT 57.459 26.923 0.00 0.00 0.00 1.94
552 553 8.541133 TTTTGACCGATTTTTCTGTTTCTTTT 57.459 26.923 0.00 0.00 0.00 2.27
553 554 8.541133 TTTTTGACCGATTTTTCTGTTTCTTT 57.459 26.923 0.00 0.00 0.00 2.52
554 555 7.277760 CCTTTTTGACCGATTTTTCTGTTTCTT 59.722 33.333 0.00 0.00 0.00 2.52
555 556 6.756542 CCTTTTTGACCGATTTTTCTGTTTCT 59.243 34.615 0.00 0.00 0.00 2.52
556 557 6.754675 TCCTTTTTGACCGATTTTTCTGTTTC 59.245 34.615 0.00 0.00 0.00 2.78
557 558 6.635755 TCCTTTTTGACCGATTTTTCTGTTT 58.364 32.000 0.00 0.00 0.00 2.83
558 559 6.215495 TCCTTTTTGACCGATTTTTCTGTT 57.785 33.333 0.00 0.00 0.00 3.16
559 560 5.845391 TCCTTTTTGACCGATTTTTCTGT 57.155 34.783 0.00 0.00 0.00 3.41
560 561 7.532682 TTTTCCTTTTTGACCGATTTTTCTG 57.467 32.000 0.00 0.00 0.00 3.02
589 590 4.322877 GGTCTTCTAGAAGGTTCCCTGAAC 60.323 50.000 28.09 16.69 41.32 3.18
590 591 3.838903 GGTCTTCTAGAAGGTTCCCTGAA 59.161 47.826 28.09 6.64 38.88 3.02
591 592 3.442076 GGTCTTCTAGAAGGTTCCCTGA 58.558 50.000 28.09 7.56 38.88 3.86
592 593 2.166664 CGGTCTTCTAGAAGGTTCCCTG 59.833 54.545 28.09 14.15 38.88 4.45
593 594 2.458620 CGGTCTTCTAGAAGGTTCCCT 58.541 52.381 28.09 0.00 38.88 4.20
594 595 1.481363 CCGGTCTTCTAGAAGGTTCCC 59.519 57.143 28.09 20.90 38.88 3.97
595 596 1.134759 GCCGGTCTTCTAGAAGGTTCC 60.135 57.143 28.09 24.13 38.88 3.62
596 597 1.826096 AGCCGGTCTTCTAGAAGGTTC 59.174 52.381 28.09 18.95 38.88 3.62
597 598 1.550976 CAGCCGGTCTTCTAGAAGGTT 59.449 52.381 28.09 11.57 38.88 3.50
598 599 1.187087 CAGCCGGTCTTCTAGAAGGT 58.813 55.000 28.09 9.71 38.88 3.50
599 600 1.135333 GTCAGCCGGTCTTCTAGAAGG 59.865 57.143 28.09 16.50 38.88 3.46
600 601 2.096248 AGTCAGCCGGTCTTCTAGAAG 58.904 52.381 24.10 24.10 39.71 2.85
601 602 2.217510 AGTCAGCCGGTCTTCTAGAA 57.782 50.000 1.90 4.81 0.00 2.10
602 603 2.920524 CTAGTCAGCCGGTCTTCTAGA 58.079 52.381 18.72 0.00 32.85 2.43
603 604 1.335496 GCTAGTCAGCCGGTCTTCTAG 59.665 57.143 18.95 18.95 42.37 2.43
604 605 1.390565 GCTAGTCAGCCGGTCTTCTA 58.609 55.000 1.90 5.56 42.37 2.10
605 606 2.194460 GCTAGTCAGCCGGTCTTCT 58.806 57.895 1.90 4.70 42.37 2.85
606 607 4.816990 GCTAGTCAGCCGGTCTTC 57.183 61.111 1.90 0.00 42.37 2.87
615 616 3.181471 CCCATTGTACCAGAGCTAGTCAG 60.181 52.174 0.00 0.00 0.00 3.51
616 617 2.766263 CCCATTGTACCAGAGCTAGTCA 59.234 50.000 0.00 0.00 0.00 3.41
617 618 2.483889 GCCCATTGTACCAGAGCTAGTC 60.484 54.545 0.00 0.00 0.00 2.59
618 619 1.486726 GCCCATTGTACCAGAGCTAGT 59.513 52.381 0.00 0.00 0.00 2.57
619 620 1.202698 GGCCCATTGTACCAGAGCTAG 60.203 57.143 0.00 0.00 0.00 3.42
620 621 0.837272 GGCCCATTGTACCAGAGCTA 59.163 55.000 0.00 0.00 0.00 3.32
621 622 1.609783 GGCCCATTGTACCAGAGCT 59.390 57.895 0.00 0.00 0.00 4.09
622 623 1.819632 CGGCCCATTGTACCAGAGC 60.820 63.158 0.00 0.00 0.00 4.09
623 624 1.153168 CCGGCCCATTGTACCAGAG 60.153 63.158 0.00 0.00 0.00 3.35
624 625 2.994699 CCGGCCCATTGTACCAGA 59.005 61.111 0.00 0.00 0.00 3.86
625 626 2.828549 GCCGGCCCATTGTACCAG 60.829 66.667 18.11 0.00 0.00 4.00
626 627 4.434354 GGCCGGCCCATTGTACCA 62.434 66.667 36.64 0.00 0.00 3.25
644 645 3.170585 GTCGACCGTACGCACAGC 61.171 66.667 10.49 0.00 0.00 4.40
645 646 0.731514 ATTGTCGACCGTACGCACAG 60.732 55.000 14.12 0.00 0.00 3.66
646 647 0.318869 AATTGTCGACCGTACGCACA 60.319 50.000 14.12 6.61 0.00 4.57
647 648 0.092351 CAATTGTCGACCGTACGCAC 59.908 55.000 14.12 4.80 0.00 5.34
648 649 1.009903 CCAATTGTCGACCGTACGCA 61.010 55.000 14.12 0.00 0.00 5.24
649 650 0.733566 TCCAATTGTCGACCGTACGC 60.734 55.000 14.12 0.00 0.00 4.42
650 651 1.265568 CTCCAATTGTCGACCGTACG 58.734 55.000 14.12 8.69 0.00 3.67
651 652 1.636988 CCTCCAATTGTCGACCGTAC 58.363 55.000 14.12 0.00 0.00 3.67
652 653 0.108520 GCCTCCAATTGTCGACCGTA 60.109 55.000 14.12 0.00 0.00 4.02
653 654 1.375523 GCCTCCAATTGTCGACCGT 60.376 57.895 14.12 0.00 0.00 4.83
654 655 0.953471 TTGCCTCCAATTGTCGACCG 60.953 55.000 14.12 0.00 0.00 4.79
655 656 1.200020 CTTTGCCTCCAATTGTCGACC 59.800 52.381 14.12 0.00 0.00 4.79
656 657 2.151202 TCTTTGCCTCCAATTGTCGAC 58.849 47.619 9.11 9.11 0.00 4.20
657 658 2.426522 CTCTTTGCCTCCAATTGTCGA 58.573 47.619 4.43 0.00 0.00 4.20
658 659 1.135575 GCTCTTTGCCTCCAATTGTCG 60.136 52.381 4.43 0.00 35.15 4.35
659 660 1.135575 CGCTCTTTGCCTCCAATTGTC 60.136 52.381 4.43 0.00 38.78 3.18
660 661 0.883833 CGCTCTTTGCCTCCAATTGT 59.116 50.000 4.43 0.00 38.78 2.71
661 662 0.883833 ACGCTCTTTGCCTCCAATTG 59.116 50.000 0.00 0.00 38.78 2.32
662 663 1.168714 GACGCTCTTTGCCTCCAATT 58.831 50.000 0.00 0.00 38.78 2.32
663 664 1.021390 CGACGCTCTTTGCCTCCAAT 61.021 55.000 0.00 0.00 38.78 3.16
664 665 1.667830 CGACGCTCTTTGCCTCCAA 60.668 57.895 0.00 0.00 38.78 3.53
665 666 1.529152 TACGACGCTCTTTGCCTCCA 61.529 55.000 0.00 0.00 38.78 3.86
666 667 0.179108 ATACGACGCTCTTTGCCTCC 60.179 55.000 0.00 0.00 38.78 4.30
667 668 2.386249 CTATACGACGCTCTTTGCCTC 58.614 52.381 0.00 0.00 38.78 4.70
668 669 1.067212 CCTATACGACGCTCTTTGCCT 59.933 52.381 0.00 0.00 38.78 4.75
669 670 1.488527 CCTATACGACGCTCTTTGCC 58.511 55.000 0.00 0.00 38.78 4.52
670 671 1.202382 ACCCTATACGACGCTCTTTGC 60.202 52.381 0.00 0.00 38.57 3.68
671 672 2.865343 ACCCTATACGACGCTCTTTG 57.135 50.000 0.00 0.00 0.00 2.77
672 673 3.881937 AAACCCTATACGACGCTCTTT 57.118 42.857 0.00 0.00 0.00 2.52
673 674 3.429960 GGAAAACCCTATACGACGCTCTT 60.430 47.826 0.00 0.00 0.00 2.85
674 675 2.100418 GGAAAACCCTATACGACGCTCT 59.900 50.000 0.00 0.00 0.00 4.09
675 676 2.467838 GGAAAACCCTATACGACGCTC 58.532 52.381 0.00 0.00 0.00 5.03
676 677 1.137675 GGGAAAACCCTATACGACGCT 59.862 52.381 0.00 0.00 34.51 5.07
677 678 1.575244 GGGAAAACCCTATACGACGC 58.425 55.000 0.00 0.00 34.51 5.19
678 679 1.843992 CGGGAAAACCCTATACGACG 58.156 55.000 0.00 0.00 34.99 5.12
679 680 1.137675 AGCGGGAAAACCCTATACGAC 59.862 52.381 0.00 0.00 34.99 4.34
680 681 1.410153 GAGCGGGAAAACCCTATACGA 59.590 52.381 0.00 0.00 34.99 3.43
681 682 1.539712 GGAGCGGGAAAACCCTATACG 60.540 57.143 0.00 0.00 34.99 3.06
682 683 1.767088 AGGAGCGGGAAAACCCTATAC 59.233 52.381 0.00 0.00 34.99 1.47
683 684 2.171870 CAAGGAGCGGGAAAACCCTATA 59.828 50.000 0.00 0.00 34.99 1.31
684 685 1.064685 CAAGGAGCGGGAAAACCCTAT 60.065 52.381 0.00 0.00 34.99 2.57
685 686 0.326927 CAAGGAGCGGGAAAACCCTA 59.673 55.000 0.00 0.00 34.99 3.53
686 687 1.074951 CAAGGAGCGGGAAAACCCT 59.925 57.895 0.00 0.00 34.99 4.34
687 688 0.826256 AACAAGGAGCGGGAAAACCC 60.826 55.000 0.00 0.00 34.99 4.11
688 689 0.596577 GAACAAGGAGCGGGAAAACC 59.403 55.000 0.00 0.00 0.00 3.27
689 690 1.605753 AGAACAAGGAGCGGGAAAAC 58.394 50.000 0.00 0.00 0.00 2.43
690 691 3.495434 TTAGAACAAGGAGCGGGAAAA 57.505 42.857 0.00 0.00 0.00 2.29
691 692 3.495434 TTTAGAACAAGGAGCGGGAAA 57.505 42.857 0.00 0.00 0.00 3.13
692 693 3.071892 TCTTTTAGAACAAGGAGCGGGAA 59.928 43.478 0.00 0.00 0.00 3.97
693 694 2.635915 TCTTTTAGAACAAGGAGCGGGA 59.364 45.455 0.00 0.00 0.00 5.14
694 695 2.742589 GTCTTTTAGAACAAGGAGCGGG 59.257 50.000 0.00 0.00 0.00 6.13
695 696 3.665190 AGTCTTTTAGAACAAGGAGCGG 58.335 45.455 0.00 0.00 0.00 5.52
696 697 4.750098 TGAAGTCTTTTAGAACAAGGAGCG 59.250 41.667 0.00 0.00 0.00 5.03
697 698 6.619801 TTGAAGTCTTTTAGAACAAGGAGC 57.380 37.500 0.00 0.00 0.00 4.70
698 699 8.159344 ACATTGAAGTCTTTTAGAACAAGGAG 57.841 34.615 0.00 0.00 0.00 3.69
699 700 9.052759 GTACATTGAAGTCTTTTAGAACAAGGA 57.947 33.333 0.00 0.00 0.00 3.36
700 701 8.836413 TGTACATTGAAGTCTTTTAGAACAAGG 58.164 33.333 0.00 0.00 0.00 3.61
701 702 9.869844 CTGTACATTGAAGTCTTTTAGAACAAG 57.130 33.333 0.00 0.00 0.00 3.16
702 703 9.391006 ACTGTACATTGAAGTCTTTTAGAACAA 57.609 29.630 0.00 0.00 0.00 2.83
703 704 8.958119 ACTGTACATTGAAGTCTTTTAGAACA 57.042 30.769 0.00 0.00 0.00 3.18
711 712 7.928307 ATGCAATACTGTACATTGAAGTCTT 57.072 32.000 11.06 0.00 35.77 3.01
719 720 4.941263 ACACGGAATGCAATACTGTACATT 59.059 37.500 0.00 0.00 35.52 2.71
733 734 0.802494 GCCACTAACCACACGGAATG 59.198 55.000 0.00 0.00 35.59 2.67
734 735 0.322187 GGCCACTAACCACACGGAAT 60.322 55.000 0.00 0.00 35.59 3.01
741 742 2.187896 TAAGGCCGGCCACTAACCAC 62.188 60.000 45.13 17.02 38.92 4.16
749 750 1.859302 AAATTCAATAAGGCCGGCCA 58.141 45.000 45.13 28.44 38.92 5.36
771 773 3.547513 AATCTAGCCCGGCCCGTC 61.548 66.667 5.55 0.00 0.00 4.79
786 788 1.377725 CAGCGAAGTCAGGCCCAAT 60.378 57.895 0.00 0.00 0.00 3.16
795 797 1.174783 TGAGGTAGGTCAGCGAAGTC 58.825 55.000 0.00 0.00 0.00 3.01
802 804 2.257207 TGGGACTTTGAGGTAGGTCAG 58.743 52.381 0.00 0.00 0.00 3.51
812 814 0.930726 AGTGGGGTTTGGGACTTTGA 59.069 50.000 0.00 0.00 0.00 2.69
817 819 0.185175 AGTGAAGTGGGGTTTGGGAC 59.815 55.000 0.00 0.00 0.00 4.46
818 820 1.702957 CTAGTGAAGTGGGGTTTGGGA 59.297 52.381 0.00 0.00 0.00 4.37
821 823 1.534729 GGCTAGTGAAGTGGGGTTTG 58.465 55.000 0.00 0.00 0.00 2.93
822 824 0.404426 GGGCTAGTGAAGTGGGGTTT 59.596 55.000 0.00 0.00 0.00 3.27
823 825 0.770557 TGGGCTAGTGAAGTGGGGTT 60.771 55.000 0.00 0.00 0.00 4.11
824 826 1.151899 TGGGCTAGTGAAGTGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
826 828 1.299976 GGTGGGCTAGTGAAGTGGG 59.700 63.158 0.00 0.00 0.00 4.61
827 829 1.299976 GGGTGGGCTAGTGAAGTGG 59.700 63.158 0.00 0.00 0.00 4.00
828 830 1.201429 AGGGGTGGGCTAGTGAAGTG 61.201 60.000 0.00 0.00 0.00 3.16
829 831 0.910088 GAGGGGTGGGCTAGTGAAGT 60.910 60.000 0.00 0.00 0.00 3.01
830 832 0.618968 AGAGGGGTGGGCTAGTGAAG 60.619 60.000 0.00 0.00 0.00 3.02
859 861 2.280552 TGGTCGGAGAAGAACGGGG 61.281 63.158 0.00 0.00 39.69 5.73
976 978 2.109181 GCCGGAGAGGTATGTGGC 59.891 66.667 5.05 0.00 43.70 5.01
992 994 3.304525 GCATCTCTGAAGCATGTATTGGC 60.305 47.826 0.00 0.00 0.00 4.52
1005 1007 1.751351 CGGAGTAAGTGGCATCTCTGA 59.249 52.381 12.19 0.00 35.93 3.27
1122 1124 4.803426 CGAGTGAGACGGCCCAGC 62.803 72.222 0.00 0.00 0.00 4.85
1299 1301 2.283604 TGGAGTAGCTGGGCGTGA 60.284 61.111 0.00 0.00 0.00 4.35
1311 1313 2.284625 TGGGCGAGGATGTGGAGT 60.285 61.111 0.00 0.00 0.00 3.85
1420 1422 2.963782 AGAAGTCTTTGTACACCTCGGT 59.036 45.455 0.00 0.00 0.00 4.69
1443 1445 1.296715 GAAGGAGGCGGCTGAGAAA 59.703 57.895 19.63 0.00 0.00 2.52
1611 1613 2.124529 TCAAACACAGCCACCGCA 60.125 55.556 0.00 0.00 37.52 5.69
1647 1649 2.022129 GAACTCGTCCGGCAGTGTG 61.022 63.158 0.00 0.00 0.00 3.82
1783 1785 1.072173 TCCGCAATACCCATCCATCAG 59.928 52.381 0.00 0.00 0.00 2.90
1785 1787 1.072331 ACTCCGCAATACCCATCCATC 59.928 52.381 0.00 0.00 0.00 3.51
1814 1816 1.768684 AACCCTTCTCGCAGCCTCAA 61.769 55.000 0.00 0.00 0.00 3.02
1815 1817 1.768684 AAACCCTTCTCGCAGCCTCA 61.769 55.000 0.00 0.00 0.00 3.86
1947 1949 7.824289 ACCACGATCTTCTCATTTTCTTTCATA 59.176 33.333 0.00 0.00 0.00 2.15
2052 2054 3.048501 CAGTCCGACATCAATCATCTCG 58.951 50.000 0.40 0.00 0.00 4.04
2227 2229 1.969923 TGCCTTTTTCATGGAACCCTG 59.030 47.619 0.00 0.00 0.00 4.45
2229 2231 3.701205 AATGCCTTTTTCATGGAACCC 57.299 42.857 0.00 0.00 0.00 4.11
2241 2243 4.961438 ATCACAGGTTTCAAATGCCTTT 57.039 36.364 0.00 0.00 0.00 3.11
2252 2254 6.575244 TCCTTACCATCATATCACAGGTTT 57.425 37.500 0.00 0.00 33.91 3.27
2307 2309 5.689514 CGAACAAAAACCATTCAACAGCATA 59.310 36.000 0.00 0.00 0.00 3.14
2309 2311 3.862267 CGAACAAAAACCATTCAACAGCA 59.138 39.130 0.00 0.00 0.00 4.41
2313 2315 4.032331 CCACACGAACAAAAACCATTCAAC 59.968 41.667 0.00 0.00 0.00 3.18
2328 2330 3.326836 TCATCAATAGCACCACACGAA 57.673 42.857 0.00 0.00 0.00 3.85
2436 2438 1.450025 CCTTCTCGGTTTTACCTGCC 58.550 55.000 0.00 0.00 35.66 4.85
2585 2587 0.467384 AGCAGGACATCTCCATTCCG 59.533 55.000 0.00 0.00 39.39 4.30
2677 2679 3.128589 CCTAAATGTTCCATGTCAACCCG 59.871 47.826 0.00 0.00 0.00 5.28
2756 2758 1.342174 CATTGACCTTGCCACTTTGCT 59.658 47.619 0.00 0.00 0.00 3.91
2772 2774 7.044510 GCAGTCATTTCAACAACGATATCATTG 60.045 37.037 9.88 9.88 0.00 2.82
2886 2888 7.611855 AGACCTTTCTCGACCATTTCAAAATAT 59.388 33.333 0.00 0.00 0.00 1.28
2998 3000 4.002906 TCATGTCAGTACCCACAAGTTC 57.997 45.455 0.00 0.00 0.00 3.01
3000 3002 4.565652 GGAATCATGTCAGTACCCACAAGT 60.566 45.833 0.00 0.00 0.00 3.16
3006 3008 3.452627 AGTCTGGAATCATGTCAGTACCC 59.547 47.826 0.00 0.00 0.00 3.69
3012 3014 2.303890 ACTGCAGTCTGGAATCATGTCA 59.696 45.455 15.25 0.00 0.00 3.58
3156 3158 7.613022 TCCTCAAACAAATTTCTAGCATCTGAT 59.387 33.333 0.00 0.00 0.00 2.90
3262 3264 2.450476 CCTCAGGCCAAAAGCTACATT 58.550 47.619 5.01 0.00 43.05 2.71
3352 3354 2.821969 CCCTTTGAACATTCCCAGACTG 59.178 50.000 0.00 0.00 0.00 3.51
3470 3472 7.633193 TGTTTTAACTTGAAGGCTTCAGTTA 57.367 32.000 28.58 28.58 41.38 2.24
3518 3520 9.819267 GTATAGAATAGGTGAATACATTAGGCC 57.181 37.037 0.00 0.00 0.00 5.19
3690 3692 4.397103 TGCATCTCATTGTAAAGCTTGGAG 59.603 41.667 0.00 1.18 0.00 3.86
4045 4047 5.036117 ACCTTTGAAGCTTCTGACTGTAA 57.964 39.130 26.09 8.40 0.00 2.41
4050 4052 4.249661 CCTAGACCTTTGAAGCTTCTGAC 58.750 47.826 26.09 12.47 0.00 3.51
4135 4137 1.847328 TTGCATGAGTACTCCCTCGA 58.153 50.000 20.11 1.12 34.04 4.04
4626 4629 5.916883 CACCAAAGCAATTGTTGTTAGAGAG 59.083 40.000 7.40 0.00 37.32 3.20
4634 4637 6.607735 ATTTCTTCACCAAAGCAATTGTTG 57.392 33.333 7.40 4.63 37.32 3.33
4643 4646 7.249186 TGCATTGAAAATTTCTTCACCAAAG 57.751 32.000 7.29 0.00 35.07 2.77


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

AutoCloner maintained by Alex Coulton.