Multiple sequence alignment - TraesCS5D01G181500

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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 TraesCS5D01G181500 chr5D 100.000 5633 0 0 1 5633 282156629 282150997 0.000000e+00 10403
1 TraesCS5D01G181500 chr5A 93.133 5388 225 50 11 5314 374650185 374644859 0.000000e+00 7766
2 TraesCS5D01G181500 chr5A 92.063 126 9 1 5494 5619 374639944 374639820 5.800000e-40 176
3 TraesCS5D01G181500 chr5A 88.785 107 8 4 5360 5462 374644848 374644742 1.650000e-25 128
4 TraesCS5D01G181500 chr5B 93.202 4869 222 36 16 4817 320156990 320152164 0.000000e+00 7057
5 TraesCS5D01G181500 chr5B 87.054 672 29 23 4827 5473 320152039 320151401 0.000000e+00 706
6 TraesCS5D01G181500 chr3D 80.374 749 135 10 3633 4375 51682492 51683234 4.930000e-155 558
7 TraesCS5D01G181500 chr3A 80.426 751 131 12 3633 4375 64281497 64282239 4.930000e-155 558
8 TraesCS5D01G181500 chr3B 79.973 749 138 10 3633 4375 82625575 82626317 4.960000e-150 542
9 TraesCS5D01G181500 chr3B 78.468 692 141 8 3641 4328 443806253 443806940 4.000000e-121 446


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 TraesCS5D01G181500 chr5D 282150997 282156629 5632 True 10403.0 10403 100.000 1 5633 1 chr5D.!!$R1 5632
1 TraesCS5D01G181500 chr5A 374644742 374650185 5443 True 3947.0 7766 90.959 11 5462 2 chr5A.!!$R2 5451
2 TraesCS5D01G181500 chr5B 320151401 320156990 5589 True 3881.5 7057 90.128 16 5473 2 chr5B.!!$R1 5457
3 TraesCS5D01G181500 chr3D 51682492 51683234 742 False 558.0 558 80.374 3633 4375 1 chr3D.!!$F1 742
4 TraesCS5D01G181500 chr3A 64281497 64282239 742 False 558.0 558 80.426 3633 4375 1 chr3A.!!$F1 742
5 TraesCS5D01G181500 chr3B 82625575 82626317 742 False 542.0 542 79.973 3633 4375 1 chr3B.!!$F1 742
6 TraesCS5D01G181500 chr3B 443806253 443806940 687 False 446.0 446 78.468 3641 4328 1 chr3B.!!$F2 687

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
382 419 0.107945 AGATTCTGCTGCGAACTCCC 60.108 55.000 8.60 1.55 0.00 4.30 F
384 421 0.107945 ATTCTGCTGCGAACTCCCTC 60.108 55.000 8.60 0.00 0.00 4.30 F
389 426 0.459411 GCTGCGAACTCCCTCTTCTC 60.459 60.000 0.00 0.00 0.00 2.87 F
901 988 0.598065 GACATGTGAAGCCACCCAAC 59.402 55.000 1.15 0.00 42.53 3.77 F
2188 2294 1.153549 GTCGTCAGCACCATCTCCC 60.154 63.158 0.00 0.00 0.00 4.30 F
3201 3307 0.690762 GGTTGTCAGGGCTGGAACTA 59.309 55.000 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1789 1.759445 CCTGAGATCTGGTTCCACGAT 59.241 52.381 0.00 4.39 0.00 3.73 R
2310 2416 2.182842 GCACAGGTCCGGCATGATC 61.183 63.158 15.63 4.86 32.48 2.92 R
2568 2674 4.588899 TGTTGTAGCTTATCACCAGCATT 58.411 39.130 0.00 0.00 39.99 3.56 R
2706 2812 4.124943 AGCTGCAGGATGGCCAGG 62.125 66.667 17.12 1.38 35.86 4.45 R
3972 4078 0.458543 CCTTGTCGTCGTCATGGAGG 60.459 60.000 16.01 6.46 33.67 4.30 R
5314 5577 0.038526 AGTCGCGGAACTGAACGATT 60.039 50.000 6.13 0.00 36.85 3.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.631012 ATTTCCATCCAGCCCCTCGC 62.631 60.000 0.00 0.00 37.98 5.03
123 135 2.438795 CCCCCTTCTTTTCGGGCA 59.561 61.111 0.00 0.00 39.22 5.36
173 185 4.465446 AGGGGAGGCTGCTCGCTA 62.465 66.667 5.84 0.00 39.13 4.26
317 352 1.674764 CCTCGTCCAGCAGCATCTCT 61.675 60.000 0.00 0.00 0.00 3.10
356 393 2.402388 CTGCGATTCTTGCGGCAG 59.598 61.111 1.67 0.00 45.74 4.85
366 403 2.739885 CTTGCGGCAGCTAGATAGAT 57.260 50.000 14.43 0.00 46.63 1.98
367 404 3.037431 CTTGCGGCAGCTAGATAGATT 57.963 47.619 14.43 0.00 46.63 2.40
368 405 2.732412 TGCGGCAGCTAGATAGATTC 57.268 50.000 10.92 0.00 45.42 2.52
369 406 2.242926 TGCGGCAGCTAGATAGATTCT 58.757 47.619 10.92 0.00 45.42 2.40
370 407 2.029560 TGCGGCAGCTAGATAGATTCTG 60.030 50.000 10.92 0.00 45.42 3.02
371 408 2.605030 CGGCAGCTAGATAGATTCTGC 58.395 52.381 7.49 7.49 46.68 4.26
372 409 2.230992 CGGCAGCTAGATAGATTCTGCT 59.769 50.000 13.60 0.00 46.61 4.24
375 412 3.244156 CAGCTAGATAGATTCTGCTGCG 58.756 50.000 9.26 0.00 43.28 5.18
376 413 3.057666 CAGCTAGATAGATTCTGCTGCGA 60.058 47.826 9.26 0.00 43.28 5.10
377 414 3.571828 AGCTAGATAGATTCTGCTGCGAA 59.428 43.478 8.80 8.80 37.41 4.70
378 415 3.672867 GCTAGATAGATTCTGCTGCGAAC 59.327 47.826 8.60 4.72 35.79 3.95
379 416 4.558496 GCTAGATAGATTCTGCTGCGAACT 60.558 45.833 8.60 9.98 35.79 3.01
380 417 3.976169 AGATAGATTCTGCTGCGAACTC 58.024 45.455 8.60 8.05 31.79 3.01
381 418 2.586258 TAGATTCTGCTGCGAACTCC 57.414 50.000 8.60 3.39 0.00 3.85
382 419 0.107945 AGATTCTGCTGCGAACTCCC 60.108 55.000 8.60 1.55 0.00 4.30
383 420 0.107945 GATTCTGCTGCGAACTCCCT 60.108 55.000 8.60 0.00 0.00 4.20
384 421 0.107945 ATTCTGCTGCGAACTCCCTC 60.108 55.000 8.60 0.00 0.00 4.30
385 422 1.188219 TTCTGCTGCGAACTCCCTCT 61.188 55.000 0.00 0.00 0.00 3.69
386 423 1.188219 TCTGCTGCGAACTCCCTCTT 61.188 55.000 0.00 0.00 0.00 2.85
387 424 0.739112 CTGCTGCGAACTCCCTCTTC 60.739 60.000 0.00 0.00 0.00 2.87
388 425 1.188219 TGCTGCGAACTCCCTCTTCT 61.188 55.000 0.00 0.00 0.00 2.85
389 426 0.459411 GCTGCGAACTCCCTCTTCTC 60.459 60.000 0.00 0.00 0.00 2.87
390 427 0.891373 CTGCGAACTCCCTCTTCTCA 59.109 55.000 0.00 0.00 0.00 3.27
403 440 3.245052 CCTCTTCTCAACCTGTGGGATTT 60.245 47.826 0.00 0.00 36.30 2.17
412 449 1.407437 CCTGTGGGATTTCTTCCTCCG 60.407 57.143 0.00 0.00 44.75 4.63
415 452 2.084546 GTGGGATTTCTTCCTCCGTTG 58.915 52.381 0.00 0.00 44.75 4.10
434 471 4.222114 GTTGCTTTCTTGATGAGGTTTCG 58.778 43.478 0.00 0.00 0.00 3.46
436 473 2.162408 GCTTTCTTGATGAGGTTTCGGG 59.838 50.000 0.00 0.00 0.00 5.14
461 498 0.827368 GCACCCTACTTCTCCTCCTG 59.173 60.000 0.00 0.00 0.00 3.86
488 528 0.810031 TGCGCGGCTTTCCTAATCTC 60.810 55.000 8.83 0.00 0.00 2.75
489 529 1.499688 GCGCGGCTTTCCTAATCTCC 61.500 60.000 8.83 0.00 0.00 3.71
492 532 1.132500 CGGCTTTCCTAATCTCCCCT 58.868 55.000 0.00 0.00 0.00 4.79
495 548 3.556999 GGCTTTCCTAATCTCCCCTTTC 58.443 50.000 0.00 0.00 0.00 2.62
502 555 5.880901 TCCTAATCTCCCCTTTCATTATGC 58.119 41.667 0.00 0.00 0.00 3.14
567 620 2.287644 GTGGTTTGAAGGTTGCAATTGC 59.712 45.455 23.69 23.69 42.50 3.56
604 670 2.658422 CCTGGGGCATGTTTGTGC 59.342 61.111 0.00 0.00 44.31 4.57
605 671 2.259204 CTGGGGCATGTTTGTGCG 59.741 61.111 0.00 0.00 45.97 5.34
614 680 2.353030 GTTTGTGCGTTGCGTCCC 60.353 61.111 0.00 0.00 0.00 4.46
616 682 2.829206 TTTGTGCGTTGCGTCCCAG 61.829 57.895 0.00 0.00 0.00 4.45
635 701 4.137543 CCAGTTGGAGCTTGTTTCTTACT 58.862 43.478 0.00 0.00 37.39 2.24
646 712 6.935208 AGCTTGTTTCTTACTAGGATTCGTTT 59.065 34.615 0.00 0.00 31.31 3.60
684 759 3.416414 TTTGGGTTTTGGGGGTTTAGA 57.584 42.857 0.00 0.00 0.00 2.10
710 785 4.284829 TGAATTTGGCCCAAGAATTTCC 57.715 40.909 0.00 0.00 0.00 3.13
722 797 3.188880 AGAATTTCCCATTTGCTCCCA 57.811 42.857 0.00 0.00 0.00 4.37
759 834 1.846439 TCCCCTGCCAAGATTCCTTAG 59.154 52.381 0.00 0.00 0.00 2.18
769 847 5.396884 GCCAAGATTCCTTAGGCTCTCTTTA 60.397 44.000 0.00 0.00 40.37 1.85
791 869 3.579147 TTTGTTCTTTGTACACGAGCG 57.421 42.857 0.00 0.00 0.00 5.03
845 932 5.239306 TGAAGATGAGCTGAAATTTCAACGT 59.761 36.000 20.82 15.45 36.64 3.99
848 935 7.009568 AGATGAGCTGAAATTTCAACGTATC 57.990 36.000 20.82 20.97 36.64 2.24
872 959 1.550072 AGGGAAATTGCGACCCAAATG 59.450 47.619 0.00 0.00 45.43 2.32
901 988 0.598065 GACATGTGAAGCCACCCAAC 59.402 55.000 1.15 0.00 42.53 3.77
1006 1100 3.195698 GACCCGAAGCCATGTCGC 61.196 66.667 0.00 0.00 37.18 5.19
1014 1108 2.045926 GCCATGTCGCCCTTCACT 60.046 61.111 0.00 0.00 0.00 3.41
1025 1131 1.302832 CCTTCACTGCGGGCTTCTT 60.303 57.895 0.00 0.00 0.00 2.52
1257 1363 1.675310 CAACCTCAGCGGCATGGAA 60.675 57.895 1.45 0.00 35.61 3.53
1300 1406 3.075005 CGCTCCTTTCCCTCCCGA 61.075 66.667 0.00 0.00 0.00 5.14
1879 1985 4.467084 GATTGCCGCCGGGTCTCA 62.467 66.667 4.77 0.00 34.97 3.27
1962 2068 1.270147 CCGACCTTCTTCACCGAACTT 60.270 52.381 0.00 0.00 0.00 2.66
2106 2212 2.568090 CCGGCGAGCTTTGCAAAT 59.432 55.556 13.23 0.00 0.00 2.32
2160 2266 1.216710 CCAGCTCTCCGGTGACTTC 59.783 63.158 0.00 0.00 43.75 3.01
2188 2294 1.153549 GTCGTCAGCACCATCTCCC 60.154 63.158 0.00 0.00 0.00 4.30
2289 2395 3.035727 GAGGAGATCGACCTCGGC 58.964 66.667 20.29 0.00 43.25 5.54
2310 2416 1.226156 CAACGAGCTCGACGGAGAG 60.226 63.158 40.58 17.57 43.27 3.20
2517 2623 2.120909 GGTCATGTGGGCGAATGGG 61.121 63.158 0.00 0.00 0.00 4.00
3201 3307 0.690762 GGTTGTCAGGGCTGGAACTA 59.309 55.000 0.00 0.00 0.00 2.24
3210 3316 2.823829 GCTGGAACTAATGGGCGCG 61.824 63.158 0.00 0.00 0.00 6.86
3232 3338 3.576078 TGGACCTGTCAAACAATCACT 57.424 42.857 0.00 0.00 0.00 3.41
3234 3340 3.631686 TGGACCTGTCAAACAATCACTTG 59.368 43.478 0.00 0.00 38.39 3.16
3278 3384 1.648467 GGTGGTCTGCATTTCCTCGC 61.648 60.000 0.00 0.00 0.00 5.03
3283 3389 2.435938 TGCATTTCCTCGCCGACC 60.436 61.111 0.00 0.00 0.00 4.79
3312 3418 1.358759 CAACAACAACCTCACCGGC 59.641 57.895 0.00 0.00 35.61 6.13
3346 3452 2.743928 GCCAGCTCACCACCTTCG 60.744 66.667 0.00 0.00 0.00 3.79
3381 3487 1.609320 GGGAACAACTCTGGTCTCTGC 60.609 57.143 0.00 0.00 36.74 4.26
3972 4078 2.401766 CGGCAGCTTGGACATGGTC 61.402 63.158 0.00 0.00 0.00 4.02
4263 4375 2.345244 CAGAGCTTCCGGTGCACT 59.655 61.111 17.98 17.06 0.00 4.40
4393 4505 0.807496 GCAGATGCTCAAGGACAACC 59.193 55.000 0.00 0.00 38.21 3.77
4394 4506 1.081892 CAGATGCTCAAGGACAACCG 58.918 55.000 0.00 0.00 41.83 4.44
4395 4507 0.976641 AGATGCTCAAGGACAACCGA 59.023 50.000 0.00 0.00 41.83 4.69
4416 4528 0.249657 GCGGCGAGATCTTTGATCCT 60.250 55.000 12.98 0.00 0.00 3.24
4431 4543 1.989966 ATCCTACGCTGACCGACACG 61.990 60.000 0.00 0.00 41.02 4.49
4578 4690 3.441290 AGCGACTTCCTCGACGGG 61.441 66.667 0.00 0.00 46.14 5.28
4584 4696 1.249469 ACTTCCTCGACGGGTTCTCC 61.249 60.000 0.00 0.00 0.00 3.71
4590 4702 1.137086 CTCGACGGGTTCTCCATCAAT 59.863 52.381 0.00 0.00 34.36 2.57
4599 4711 3.308402 GGTTCTCCATCAATTCCTCCACA 60.308 47.826 0.00 0.00 0.00 4.17
4611 4723 5.878406 ATTCCTCCACAATAGACGAATCT 57.122 39.130 0.00 0.00 39.15 2.40
4623 4735 3.443037 AGACGAATCTGCAGAGAAATCG 58.557 45.455 27.83 27.83 42.74 3.34
4754 4878 1.822425 TTCACTGGGGGAGGTTGTAA 58.178 50.000 0.00 0.00 0.00 2.41
4822 4948 4.162509 AGGGACATGAAGGTAGTAGCTTTC 59.837 45.833 15.45 9.05 35.86 2.62
4824 4950 5.396884 GGGACATGAAGGTAGTAGCTTTCAT 60.397 44.000 15.45 15.41 35.86 2.57
4846 5087 6.587226 TCATTTTGCAAGAAAAGGATCAATCG 59.413 34.615 0.00 0.00 0.00 3.34
4854 5095 7.253422 CAAGAAAAGGATCAATCGTATTGCTT 58.747 34.615 0.00 0.00 0.00 3.91
4868 5109 2.404265 TTGCTTGTGTTTCAGCATCG 57.596 45.000 0.00 0.00 37.13 3.84
4908 5149 3.340928 TCAGTTGCATGTCTCAGATTGG 58.659 45.455 0.00 0.00 0.00 3.16
4935 5176 7.549147 TGTGTACTTTTACCTACCAGAATCT 57.451 36.000 0.00 0.00 0.00 2.40
4939 5180 7.876068 TGTACTTTTACCTACCAGAATCTGTTG 59.124 37.037 9.63 0.00 0.00 3.33
4942 5183 7.444487 ACTTTTACCTACCAGAATCTGTTGTTC 59.556 37.037 9.63 0.00 0.00 3.18
5158 5421 1.676916 CCGATGGTGCTGATGTCAGTT 60.677 52.381 11.35 0.00 45.45 3.16
5199 5462 0.732538 GGCGTTGAAAAATCCAGCCG 60.733 55.000 0.00 0.00 33.43 5.52
5222 5485 4.202202 GCTAGATCTTGTGGACAGTAGCAT 60.202 45.833 0.00 0.00 33.52 3.79
5223 5486 5.010112 GCTAGATCTTGTGGACAGTAGCATA 59.990 44.000 0.00 0.00 33.52 3.14
5224 5487 5.528043 AGATCTTGTGGACAGTAGCATAG 57.472 43.478 0.00 0.00 0.00 2.23
5225 5488 3.526931 TCTTGTGGACAGTAGCATAGC 57.473 47.619 0.00 0.00 0.00 2.97
5226 5489 2.831526 TCTTGTGGACAGTAGCATAGCA 59.168 45.455 0.00 0.00 0.00 3.49
5274 5537 4.696455 CCAGGTTTTGATTTGTCTGCTTT 58.304 39.130 0.00 0.00 0.00 3.51
5288 5551 4.155462 TGTCTGCTTTCTGAATGATTGCTC 59.845 41.667 7.40 0.00 0.00 4.26
5291 5554 4.329392 TGCTTTCTGAATGATTGCTCTGA 58.671 39.130 7.40 0.00 0.00 3.27
5310 5573 1.127582 GATGACGAAGCTGAGCAACAC 59.872 52.381 7.39 0.00 0.00 3.32
5314 5577 1.742831 ACGAAGCTGAGCAACACAAAA 59.257 42.857 7.39 0.00 0.00 2.44
5316 5579 3.181487 ACGAAGCTGAGCAACACAAAAAT 60.181 39.130 7.39 0.00 0.00 1.82
5317 5580 3.423206 CGAAGCTGAGCAACACAAAAATC 59.577 43.478 7.39 0.00 0.00 2.17
5327 5597 4.026886 GCAACACAAAAATCGTTCAGTTCC 60.027 41.667 0.00 0.00 0.00 3.62
5335 5605 2.087009 CGTTCAGTTCCGCGACTCC 61.087 63.158 8.23 0.00 0.00 3.85
5336 5606 2.087009 GTTCAGTTCCGCGACTCCG 61.087 63.158 8.23 0.00 39.16 4.63
5343 5613 3.020627 CCGCGACTCCGGTACTAG 58.979 66.667 8.23 0.00 43.24 2.57
5344 5614 1.817099 CCGCGACTCCGGTACTAGT 60.817 63.158 8.23 0.00 43.24 2.57
5345 5615 0.530650 CCGCGACTCCGGTACTAGTA 60.531 60.000 8.23 0.00 43.24 1.82
5346 5616 0.579156 CGCGACTCCGGTACTAGTAC 59.421 60.000 22.53 22.53 36.06 2.73
5347 5617 1.804372 CGCGACTCCGGTACTAGTACT 60.804 57.143 27.71 11.54 36.36 2.73
5348 5618 2.543861 CGCGACTCCGGTACTAGTACTA 60.544 54.545 27.71 15.20 36.36 1.82
5349 5619 3.458189 GCGACTCCGGTACTAGTACTAA 58.542 50.000 27.71 14.89 36.36 2.24
5350 5620 3.871594 GCGACTCCGGTACTAGTACTAAA 59.128 47.826 27.71 14.60 36.36 1.85
5351 5621 4.260415 GCGACTCCGGTACTAGTACTAAAC 60.260 50.000 27.71 13.37 36.36 2.01
5352 5622 5.112686 CGACTCCGGTACTAGTACTAAACT 58.887 45.833 27.71 11.55 42.62 2.66
5353 5623 5.233263 CGACTCCGGTACTAGTACTAAACTC 59.767 48.000 27.71 17.13 39.80 3.01
5354 5624 5.432645 ACTCCGGTACTAGTACTAAACTCC 58.567 45.833 27.71 12.07 39.80 3.85
5360 5630 5.295540 GGTACTAGTACTAAACTCCCTCGTG 59.704 48.000 27.71 0.00 39.80 4.35
5473 5748 7.441017 AGCAGAAGATAAGGTCTGAATCATAC 58.559 38.462 4.89 0.00 43.32 2.39
5474 5749 7.070447 AGCAGAAGATAAGGTCTGAATCATACA 59.930 37.037 4.89 0.00 43.32 2.29
5475 5750 7.384660 GCAGAAGATAAGGTCTGAATCATACAG 59.615 40.741 4.89 0.00 43.32 2.74
5476 5751 8.420222 CAGAAGATAAGGTCTGAATCATACAGT 58.580 37.037 1.30 0.00 43.32 3.55
5477 5752 9.647918 AGAAGATAAGGTCTGAATCATACAGTA 57.352 33.333 1.30 0.00 37.23 2.74
5499 5774 9.926751 CAGTATACTGCACATTTTTCTTCTATG 57.073 33.333 19.55 0.00 37.15 2.23
5500 5775 9.113838 AGTATACTGCACATTTTTCTTCTATGG 57.886 33.333 4.10 0.00 0.00 2.74
5501 5776 5.064441 ACTGCACATTTTTCTTCTATGGC 57.936 39.130 0.00 0.00 0.00 4.40
5502 5777 4.768968 ACTGCACATTTTTCTTCTATGGCT 59.231 37.500 0.00 0.00 0.00 4.75
5503 5778 5.063180 TGCACATTTTTCTTCTATGGCTG 57.937 39.130 0.00 0.00 0.00 4.85
5504 5779 3.861689 GCACATTTTTCTTCTATGGCTGC 59.138 43.478 0.00 0.00 0.00 5.25
5505 5780 4.618927 GCACATTTTTCTTCTATGGCTGCA 60.619 41.667 0.50 0.00 0.00 4.41
5506 5781 5.657474 CACATTTTTCTTCTATGGCTGCAT 58.343 37.500 0.50 0.00 0.00 3.96
5507 5782 5.518847 CACATTTTTCTTCTATGGCTGCATG 59.481 40.000 0.50 0.00 0.00 4.06
5508 5783 5.419788 ACATTTTTCTTCTATGGCTGCATGA 59.580 36.000 0.50 0.00 0.00 3.07
5509 5784 5.571784 TTTTTCTTCTATGGCTGCATGAG 57.428 39.130 0.50 0.00 0.00 2.90
5510 5785 2.924757 TCTTCTATGGCTGCATGAGG 57.075 50.000 0.50 0.00 0.00 3.86
5529 5804 2.273538 GCAGGATTGGCATCTCATCT 57.726 50.000 0.00 0.00 0.00 2.90
5530 5805 2.584236 GCAGGATTGGCATCTCATCTT 58.416 47.619 0.00 0.00 0.00 2.40
5531 5806 2.957006 GCAGGATTGGCATCTCATCTTT 59.043 45.455 0.00 0.00 0.00 2.52
5532 5807 3.383825 GCAGGATTGGCATCTCATCTTTT 59.616 43.478 0.00 0.00 0.00 2.27
5533 5808 4.499357 GCAGGATTGGCATCTCATCTTTTC 60.499 45.833 0.00 0.00 0.00 2.29
5534 5809 4.888239 CAGGATTGGCATCTCATCTTTTCT 59.112 41.667 0.00 0.00 0.00 2.52
5535 5810 5.008811 CAGGATTGGCATCTCATCTTTTCTC 59.991 44.000 0.00 0.00 0.00 2.87
5536 5811 5.104024 AGGATTGGCATCTCATCTTTTCTCT 60.104 40.000 0.00 0.00 0.00 3.10
5537 5812 5.008811 GGATTGGCATCTCATCTTTTCTCTG 59.991 44.000 0.00 0.00 0.00 3.35
5538 5813 3.882444 TGGCATCTCATCTTTTCTCTGG 58.118 45.455 0.00 0.00 0.00 3.86
5539 5814 3.520721 TGGCATCTCATCTTTTCTCTGGA 59.479 43.478 0.00 0.00 0.00 3.86
5540 5815 4.128643 GGCATCTCATCTTTTCTCTGGAG 58.871 47.826 0.00 0.00 0.00 3.86
5541 5816 3.560896 GCATCTCATCTTTTCTCTGGAGC 59.439 47.826 0.00 0.00 0.00 4.70
5542 5817 4.683942 GCATCTCATCTTTTCTCTGGAGCT 60.684 45.833 0.00 0.00 0.00 4.09
5543 5818 5.430007 CATCTCATCTTTTCTCTGGAGCTT 58.570 41.667 0.00 0.00 0.00 3.74
5544 5819 4.829968 TCTCATCTTTTCTCTGGAGCTTG 58.170 43.478 0.00 0.00 0.00 4.01
5545 5820 3.940221 CTCATCTTTTCTCTGGAGCTTGG 59.060 47.826 0.00 0.00 0.00 3.61
5546 5821 2.191128 TCTTTTCTCTGGAGCTTGGC 57.809 50.000 0.00 0.00 0.00 4.52
5547 5822 1.421268 TCTTTTCTCTGGAGCTTGGCA 59.579 47.619 0.00 0.00 0.00 4.92
5548 5823 2.040813 TCTTTTCTCTGGAGCTTGGCAT 59.959 45.455 0.00 0.00 0.00 4.40
5549 5824 2.592102 TTTCTCTGGAGCTTGGCATT 57.408 45.000 0.00 0.00 0.00 3.56
5550 5825 2.592102 TTCTCTGGAGCTTGGCATTT 57.408 45.000 0.00 0.00 0.00 2.32
5551 5826 1.830279 TCTCTGGAGCTTGGCATTTG 58.170 50.000 0.00 0.00 0.00 2.32
5552 5827 1.352017 TCTCTGGAGCTTGGCATTTGA 59.648 47.619 0.00 0.00 0.00 2.69
5553 5828 2.025605 TCTCTGGAGCTTGGCATTTGAT 60.026 45.455 0.00 0.00 0.00 2.57
5554 5829 3.200605 TCTCTGGAGCTTGGCATTTGATA 59.799 43.478 0.00 0.00 0.00 2.15
5555 5830 4.141321 TCTCTGGAGCTTGGCATTTGATAT 60.141 41.667 0.00 0.00 0.00 1.63
5556 5831 4.539726 TCTGGAGCTTGGCATTTGATATT 58.460 39.130 0.00 0.00 0.00 1.28
5557 5832 4.581824 TCTGGAGCTTGGCATTTGATATTC 59.418 41.667 0.00 0.00 0.00 1.75
5558 5833 4.539726 TGGAGCTTGGCATTTGATATTCT 58.460 39.130 0.00 0.00 0.00 2.40
5559 5834 5.693961 TGGAGCTTGGCATTTGATATTCTA 58.306 37.500 0.00 0.00 0.00 2.10
5560 5835 5.532406 TGGAGCTTGGCATTTGATATTCTAC 59.468 40.000 0.00 0.00 0.00 2.59
5561 5836 5.532406 GGAGCTTGGCATTTGATATTCTACA 59.468 40.000 0.00 0.00 0.00 2.74
5562 5837 6.208204 GGAGCTTGGCATTTGATATTCTACAT 59.792 38.462 0.00 0.00 0.00 2.29
5563 5838 6.978338 AGCTTGGCATTTGATATTCTACATG 58.022 36.000 0.00 0.00 0.00 3.21
5564 5839 6.015688 AGCTTGGCATTTGATATTCTACATGG 60.016 38.462 0.00 0.00 0.00 3.66
5565 5840 6.016024 GCTTGGCATTTGATATTCTACATGGA 60.016 38.462 0.00 0.00 0.00 3.41
5566 5841 7.470424 GCTTGGCATTTGATATTCTACATGGAA 60.470 37.037 0.00 0.00 0.00 3.53
5567 5842 7.275888 TGGCATTTGATATTCTACATGGAAC 57.724 36.000 0.00 0.00 0.00 3.62
5568 5843 6.265196 TGGCATTTGATATTCTACATGGAACC 59.735 38.462 0.00 0.00 0.00 3.62
5569 5844 6.491403 GGCATTTGATATTCTACATGGAACCT 59.509 38.462 0.00 0.00 0.00 3.50
5570 5845 7.014615 GGCATTTGATATTCTACATGGAACCTT 59.985 37.037 0.00 0.00 0.00 3.50
5571 5846 8.078596 GCATTTGATATTCTACATGGAACCTTC 58.921 37.037 0.00 0.00 0.00 3.46
5587 5862 7.754851 GGAACCTTCCTATTGTTTTGTAAGA 57.245 36.000 0.00 0.00 44.11 2.10
5588 5863 7.591165 GGAACCTTCCTATTGTTTTGTAAGAC 58.409 38.462 0.00 0.00 44.11 3.01
5589 5864 7.309012 GGAACCTTCCTATTGTTTTGTAAGACC 60.309 40.741 0.00 0.00 44.11 3.85
5590 5865 6.607019 ACCTTCCTATTGTTTTGTAAGACCA 58.393 36.000 0.00 0.00 0.00 4.02
5591 5866 7.238710 ACCTTCCTATTGTTTTGTAAGACCAT 58.761 34.615 0.00 0.00 0.00 3.55
5592 5867 8.387813 ACCTTCCTATTGTTTTGTAAGACCATA 58.612 33.333 0.00 0.00 0.00 2.74
5593 5868 9.408648 CCTTCCTATTGTTTTGTAAGACCATAT 57.591 33.333 0.00 0.00 0.00 1.78
5596 5871 9.403583 TCCTATTGTTTTGTAAGACCATATTCC 57.596 33.333 0.00 0.00 0.00 3.01
5597 5872 9.408648 CCTATTGTTTTGTAAGACCATATTCCT 57.591 33.333 0.00 0.00 0.00 3.36
5599 5874 7.696992 TTGTTTTGTAAGACCATATTCCTCC 57.303 36.000 0.00 0.00 0.00 4.30
5600 5875 7.027874 TGTTTTGTAAGACCATATTCCTCCT 57.972 36.000 0.00 0.00 0.00 3.69
5601 5876 7.110155 TGTTTTGTAAGACCATATTCCTCCTC 58.890 38.462 0.00 0.00 0.00 3.71
5602 5877 7.037586 TGTTTTGTAAGACCATATTCCTCCTCT 60.038 37.037 0.00 0.00 0.00 3.69
5603 5878 7.510675 TTTGTAAGACCATATTCCTCCTCTT 57.489 36.000 0.00 0.00 0.00 2.85
5604 5879 7.510675 TTGTAAGACCATATTCCTCCTCTTT 57.489 36.000 0.00 0.00 0.00 2.52
5605 5880 7.125792 TGTAAGACCATATTCCTCCTCTTTC 57.874 40.000 0.00 0.00 0.00 2.62
5606 5881 6.672218 TGTAAGACCATATTCCTCCTCTTTCA 59.328 38.462 0.00 0.00 0.00 2.69
5607 5882 6.642733 AAGACCATATTCCTCCTCTTTCAA 57.357 37.500 0.00 0.00 0.00 2.69
5608 5883 6.642733 AGACCATATTCCTCCTCTTTCAAA 57.357 37.500 0.00 0.00 0.00 2.69
5609 5884 6.657875 AGACCATATTCCTCCTCTTTCAAAG 58.342 40.000 0.00 0.00 0.00 2.77
5610 5885 6.445139 AGACCATATTCCTCCTCTTTCAAAGA 59.555 38.462 0.00 0.00 35.87 2.52
5611 5886 6.418946 ACCATATTCCTCCTCTTTCAAAGAC 58.581 40.000 0.00 0.00 33.12 3.01
5612 5887 5.825151 CCATATTCCTCCTCTTTCAAAGACC 59.175 44.000 0.00 0.00 33.12 3.85
5613 5888 6.353429 CCATATTCCTCCTCTTTCAAAGACCT 60.353 42.308 0.00 0.00 33.12 3.85
5614 5889 4.357918 TTCCTCCTCTTTCAAAGACCTG 57.642 45.455 0.00 0.00 33.12 4.00
5615 5890 3.587498 TCCTCCTCTTTCAAAGACCTGA 58.413 45.455 0.00 0.00 33.12 3.86
5616 5891 3.580458 TCCTCCTCTTTCAAAGACCTGAG 59.420 47.826 0.00 3.08 33.12 3.35
5617 5892 3.307339 CCTCCTCTTTCAAAGACCTGAGG 60.307 52.174 16.04 16.04 41.57 3.86
5618 5893 2.039084 TCCTCTTTCAAAGACCTGAGGC 59.961 50.000 0.00 0.00 40.42 4.70
5619 5894 2.431454 CTCTTTCAAAGACCTGAGGCC 58.569 52.381 0.00 0.00 33.12 5.19
5620 5895 1.774254 TCTTTCAAAGACCTGAGGCCA 59.226 47.619 5.01 0.00 31.20 5.36
5621 5896 2.174639 TCTTTCAAAGACCTGAGGCCAA 59.825 45.455 5.01 0.00 31.20 4.52
5622 5897 1.981256 TTCAAAGACCTGAGGCCAAC 58.019 50.000 5.01 0.00 0.00 3.77
5623 5898 1.140312 TCAAAGACCTGAGGCCAACT 58.860 50.000 5.01 0.00 0.00 3.16
5624 5899 1.072331 TCAAAGACCTGAGGCCAACTC 59.928 52.381 5.01 0.00 46.78 3.01
5625 5900 0.402121 AAAGACCTGAGGCCAACTCC 59.598 55.000 5.01 0.00 46.01 3.85
5626 5901 0.768221 AAGACCTGAGGCCAACTCCA 60.768 55.000 5.01 0.00 46.01 3.86
5627 5902 1.003233 GACCTGAGGCCAACTCCAC 60.003 63.158 5.01 0.00 46.01 4.02
5628 5903 2.352805 CCTGAGGCCAACTCCACC 59.647 66.667 5.01 0.00 46.01 4.61
5629 5904 2.046892 CTGAGGCCAACTCCACCG 60.047 66.667 5.01 0.00 46.01 4.94
5630 5905 4.329545 TGAGGCCAACTCCACCGC 62.330 66.667 5.01 0.00 46.01 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.243636 GGAAATGGTTTGGGTGCTCG 59.756 55.000 0.00 0.00 0.00 5.03
1 2 1.337118 TGGAAATGGTTTGGGTGCTC 58.663 50.000 0.00 0.00 0.00 4.26
2 3 1.901833 GATGGAAATGGTTTGGGTGCT 59.098 47.619 0.00 0.00 0.00 4.40
3 4 1.066215 GGATGGAAATGGTTTGGGTGC 60.066 52.381 0.00 0.00 0.00 5.01
4 5 2.234414 CTGGATGGAAATGGTTTGGGTG 59.766 50.000 0.00 0.00 0.00 4.61
5 6 2.539302 CTGGATGGAAATGGTTTGGGT 58.461 47.619 0.00 0.00 0.00 4.51
6 7 1.207811 GCTGGATGGAAATGGTTTGGG 59.792 52.381 0.00 0.00 0.00 4.12
7 8 1.207811 GGCTGGATGGAAATGGTTTGG 59.792 52.381 0.00 0.00 0.00 3.28
8 9 1.207811 GGGCTGGATGGAAATGGTTTG 59.792 52.381 0.00 0.00 0.00 2.93
9 10 1.571955 GGGCTGGATGGAAATGGTTT 58.428 50.000 0.00 0.00 0.00 3.27
33 34 0.033090 GGGTAATTACTCGGCCTCGG 59.967 60.000 15.05 0.00 36.95 4.63
39 40 3.943381 GGTTTCCAAGGGTAATTACTCGG 59.057 47.826 15.05 9.03 0.00 4.63
74 75 2.300850 TTATTCGCGGGAGAACGGGG 62.301 60.000 6.13 0.00 45.42 5.73
75 76 0.460635 TTTATTCGCGGGAGAACGGG 60.461 55.000 6.13 0.00 46.53 5.28
76 77 0.648958 GTTTATTCGCGGGAGAACGG 59.351 55.000 6.13 0.00 32.39 4.44
77 78 1.352114 TGTTTATTCGCGGGAGAACG 58.648 50.000 6.13 0.00 32.39 3.95
78 79 2.740447 AGTTGTTTATTCGCGGGAGAAC 59.260 45.455 6.13 9.82 32.39 3.01
79 80 2.997986 GAGTTGTTTATTCGCGGGAGAA 59.002 45.455 6.13 0.00 34.31 2.87
80 81 2.613691 GAGTTGTTTATTCGCGGGAGA 58.386 47.619 6.13 0.00 0.00 3.71
81 82 1.323534 CGAGTTGTTTATTCGCGGGAG 59.676 52.381 6.13 0.00 0.00 4.30
82 83 1.352114 CGAGTTGTTTATTCGCGGGA 58.648 50.000 6.13 0.00 0.00 5.14
173 185 3.439129 GCTACTCAACCGCCATTAGTTTT 59.561 43.478 0.00 0.00 0.00 2.43
317 352 1.657804 GAGGACAAGGGAAGGGAAGA 58.342 55.000 0.00 0.00 0.00 2.87
356 393 3.567576 TCGCAGCAGAATCTATCTAGC 57.432 47.619 0.00 0.00 36.32 3.42
363 400 0.107945 GGGAGTTCGCAGCAGAATCT 60.108 55.000 0.00 0.00 32.25 2.40
364 401 0.107945 AGGGAGTTCGCAGCAGAATC 60.108 55.000 0.00 0.00 32.25 2.52
365 402 0.107945 GAGGGAGTTCGCAGCAGAAT 60.108 55.000 0.00 0.00 32.25 2.40
366 403 1.188219 AGAGGGAGTTCGCAGCAGAA 61.188 55.000 0.00 0.00 0.00 3.02
367 404 1.188219 AAGAGGGAGTTCGCAGCAGA 61.188 55.000 0.00 0.00 0.00 4.26
368 405 0.739112 GAAGAGGGAGTTCGCAGCAG 60.739 60.000 0.00 0.00 0.00 4.24
369 406 1.188219 AGAAGAGGGAGTTCGCAGCA 61.188 55.000 0.00 0.00 0.00 4.41
370 407 0.459411 GAGAAGAGGGAGTTCGCAGC 60.459 60.000 0.00 0.00 0.00 5.25
371 408 0.891373 TGAGAAGAGGGAGTTCGCAG 59.109 55.000 0.00 0.00 31.19 5.18
372 409 1.000955 GTTGAGAAGAGGGAGTTCGCA 59.999 52.381 0.00 0.00 32.67 5.10
373 410 1.673329 GGTTGAGAAGAGGGAGTTCGC 60.673 57.143 0.00 0.00 0.00 4.70
374 411 1.896465 AGGTTGAGAAGAGGGAGTTCG 59.104 52.381 0.00 0.00 0.00 3.95
375 412 2.635427 ACAGGTTGAGAAGAGGGAGTTC 59.365 50.000 0.00 0.00 0.00 3.01
376 413 2.370189 CACAGGTTGAGAAGAGGGAGTT 59.630 50.000 0.00 0.00 0.00 3.01
377 414 1.974236 CACAGGTTGAGAAGAGGGAGT 59.026 52.381 0.00 0.00 0.00 3.85
378 415 1.277557 CCACAGGTTGAGAAGAGGGAG 59.722 57.143 0.00 0.00 0.00 4.30
379 416 1.352083 CCACAGGTTGAGAAGAGGGA 58.648 55.000 0.00 0.00 0.00 4.20
380 417 0.326264 CCCACAGGTTGAGAAGAGGG 59.674 60.000 0.00 0.00 0.00 4.30
381 418 1.352083 TCCCACAGGTTGAGAAGAGG 58.648 55.000 0.00 0.00 0.00 3.69
382 419 3.710209 AATCCCACAGGTTGAGAAGAG 57.290 47.619 0.00 0.00 0.00 2.85
383 420 3.652869 AGAAATCCCACAGGTTGAGAAGA 59.347 43.478 0.00 0.00 0.00 2.87
384 421 4.026356 AGAAATCCCACAGGTTGAGAAG 57.974 45.455 0.00 0.00 0.00 2.85
385 422 4.398319 GAAGAAATCCCACAGGTTGAGAA 58.602 43.478 0.00 0.00 0.00 2.87
386 423 3.244911 GGAAGAAATCCCACAGGTTGAGA 60.245 47.826 0.00 0.00 43.00 3.27
387 424 3.084786 GGAAGAAATCCCACAGGTTGAG 58.915 50.000 0.00 0.00 43.00 3.02
388 425 3.154827 GGAAGAAATCCCACAGGTTGA 57.845 47.619 0.00 0.00 43.00 3.18
403 440 2.104111 TCAAGAAAGCAACGGAGGAAGA 59.896 45.455 0.00 0.00 0.00 2.87
412 449 4.222114 CGAAACCTCATCAAGAAAGCAAC 58.778 43.478 0.00 0.00 0.00 4.17
415 452 2.162408 CCCGAAACCTCATCAAGAAAGC 59.838 50.000 0.00 0.00 0.00 3.51
436 473 1.066071 GGAGAAGTAGGGTGCCTGAAC 60.066 57.143 0.00 0.00 34.61 3.18
473 510 1.132500 AGGGGAGATTAGGAAAGCCG 58.868 55.000 0.00 0.00 39.96 5.52
475 512 4.236527 TGAAAGGGGAGATTAGGAAAGC 57.763 45.455 0.00 0.00 0.00 3.51
488 528 3.294214 AGAAGCAGCATAATGAAAGGGG 58.706 45.455 0.00 0.00 0.00 4.79
489 529 4.441079 CCAAGAAGCAGCATAATGAAAGGG 60.441 45.833 0.00 0.00 0.00 3.95
492 532 5.726980 AACCAAGAAGCAGCATAATGAAA 57.273 34.783 0.00 0.00 0.00 2.69
495 548 4.100529 CGAAACCAAGAAGCAGCATAATG 58.899 43.478 0.00 0.00 0.00 1.90
502 555 1.065401 TGCAACGAAACCAAGAAGCAG 59.935 47.619 0.00 0.00 0.00 4.24
540 593 3.244561 TGCAACCTTCAAACCACCAAAAA 60.245 39.130 0.00 0.00 0.00 1.94
593 659 1.865149 GACGCAACGCACAAACATGC 61.865 55.000 0.00 0.00 42.48 4.06
604 670 2.280524 TCCAACTGGGACGCAACG 60.281 61.111 0.00 0.00 42.15 4.10
605 671 2.617274 GCTCCAACTGGGACGCAAC 61.617 63.158 0.00 0.00 42.15 4.17
614 680 5.409826 CCTAGTAAGAAACAAGCTCCAACTG 59.590 44.000 0.00 0.00 0.00 3.16
616 682 5.548406 TCCTAGTAAGAAACAAGCTCCAAC 58.452 41.667 0.00 0.00 0.00 3.77
635 701 4.837093 AGAACCCATGAAACGAATCCTA 57.163 40.909 0.00 0.00 0.00 2.94
646 712 4.006989 CCAAAACGTGATAGAACCCATGA 58.993 43.478 0.00 0.00 0.00 3.07
684 759 2.676748 TCTTGGGCCAAATTCAACACT 58.323 42.857 21.28 0.00 0.00 3.55
710 785 3.592059 CAAGAACAATGGGAGCAAATGG 58.408 45.455 0.00 0.00 0.00 3.16
722 797 1.000274 GGGAAAGCACGCAAGAACAAT 60.000 47.619 0.00 0.00 43.62 2.71
759 834 8.349983 TGTACAAAGAACAAAATAAAGAGAGCC 58.650 33.333 0.00 0.00 0.00 4.70
769 847 4.271533 TCGCTCGTGTACAAAGAACAAAAT 59.728 37.500 10.03 0.00 0.00 1.82
791 869 2.488153 ACAAGCTTAGCCCGAACAATTC 59.512 45.455 0.00 0.00 0.00 2.17
804 882 5.818678 TCTTCACTAGGGAAACAAGCTTA 57.181 39.130 9.13 0.00 0.00 3.09
845 932 2.288666 GTCGCAATTTCCCTGCAGATA 58.711 47.619 17.39 0.00 39.91 1.98
848 935 1.508088 GGTCGCAATTTCCCTGCAG 59.492 57.895 6.78 6.78 39.91 4.41
872 959 1.986378 CTTCACATGTCGACGGAGAAC 59.014 52.381 11.62 0.00 0.00 3.01
901 988 4.249020 TTGCGTGCTGCCGTGTTG 62.249 61.111 11.14 0.00 45.60 3.33
1014 1108 1.237285 GCAAGAAGAAGAAGCCCGCA 61.237 55.000 0.00 0.00 0.00 5.69
1019 1113 1.136113 GCACGAGCAAGAAGAAGAAGC 60.136 52.381 0.00 0.00 41.58 3.86
1025 1131 0.668706 GAGCAGCACGAGCAAGAAGA 60.669 55.000 7.77 0.00 45.49 2.87
1237 1343 2.401766 CCATGCCGCTGAGGTTGAC 61.402 63.158 0.00 0.00 43.70 3.18
1683 1789 1.759445 CCTGAGATCTGGTTCCACGAT 59.241 52.381 0.00 4.39 0.00 3.73
2106 2212 2.604686 ACCTCGAGGGAGCTGCAA 60.605 61.111 34.04 0.00 39.06 4.08
2289 2395 2.202492 CCGTCGAGCTCGTTGGAG 60.202 66.667 33.33 20.17 43.46 3.86
2310 2416 2.182842 GCACAGGTCCGGCATGATC 61.183 63.158 15.63 4.86 32.48 2.92
2568 2674 4.588899 TGTTGTAGCTTATCACCAGCATT 58.411 39.130 0.00 0.00 39.99 3.56
2706 2812 4.124943 AGCTGCAGGATGGCCAGG 62.125 66.667 17.12 1.38 35.86 4.45
3182 3288 0.690762 TAGTTCCAGCCCTGACAACC 59.309 55.000 0.00 0.00 0.00 3.77
3183 3289 2.561478 TTAGTTCCAGCCCTGACAAC 57.439 50.000 0.00 0.20 0.00 3.32
3186 3292 1.408822 CCCATTAGTTCCAGCCCTGAC 60.409 57.143 0.00 0.00 0.00 3.51
3201 3307 3.797353 AGGTCCATCGCGCCCATT 61.797 61.111 0.00 0.00 0.00 3.16
3210 3316 4.074970 AGTGATTGTTTGACAGGTCCATC 58.925 43.478 0.00 0.00 0.00 3.51
3232 3338 2.361865 GGGTATGCCGCCAACCAA 60.362 61.111 12.04 0.00 34.83 3.67
3234 3340 2.516225 GAGGGTATGCCGCCAACC 60.516 66.667 3.17 3.17 34.97 3.77
3262 3368 2.464459 CGGCGAGGAAATGCAGACC 61.464 63.158 0.00 0.00 0.00 3.85
3264 3370 1.447838 GTCGGCGAGGAAATGCAGA 60.448 57.895 11.20 0.00 32.93 4.26
3278 3384 2.330372 TTGGAGACGTCGAGGTCGG 61.330 63.158 27.13 0.00 41.81 4.79
3283 3389 1.521423 GTTGTTGTTGGAGACGTCGAG 59.479 52.381 10.46 0.00 0.00 4.04
3558 3664 0.688087 ACCCGGTTCTGATCTCCTCC 60.688 60.000 0.00 0.00 0.00 4.30
3630 3736 1.145819 GATGCTCAGTGGCTCCTCC 59.854 63.158 5.39 0.00 0.00 4.30
3972 4078 0.458543 CCTTGTCGTCGTCATGGAGG 60.459 60.000 16.01 6.46 33.67 4.30
4263 4375 0.608856 TGTAGACGTCGCCCTTGGTA 60.609 55.000 10.46 0.00 0.00 3.25
4393 4505 2.105128 AAAGATCTCGCCGCCTCG 59.895 61.111 0.00 0.00 0.00 4.63
4394 4506 0.249657 ATCAAAGATCTCGCCGCCTC 60.250 55.000 0.00 0.00 0.00 4.70
4395 4507 0.249657 GATCAAAGATCTCGCCGCCT 60.250 55.000 0.00 0.00 0.00 5.52
4416 4528 1.208358 CTTCGTGTCGGTCAGCGTA 59.792 57.895 0.00 0.00 0.00 4.42
4578 4690 3.955471 TGTGGAGGAATTGATGGAGAAC 58.045 45.455 0.00 0.00 0.00 3.01
4584 4696 5.359756 TCGTCTATTGTGGAGGAATTGATG 58.640 41.667 0.00 0.00 0.00 3.07
4590 4702 4.680708 GCAGATTCGTCTATTGTGGAGGAA 60.681 45.833 0.00 0.00 40.30 3.36
4599 4711 5.689514 CGATTTCTCTGCAGATTCGTCTATT 59.310 40.000 18.63 0.00 33.25 1.73
4611 4723 0.240145 ACGACGACGATTTCTCTGCA 59.760 50.000 15.32 0.00 42.66 4.41
4623 4735 5.982324 AGAAAAGGAAAACATTACGACGAC 58.018 37.500 0.00 0.00 0.00 4.34
4666 4785 0.312416 CTCGCTGTTCTATCCCTCCG 59.688 60.000 0.00 0.00 0.00 4.63
4822 4948 6.366877 ACGATTGATCCTTTTCTTGCAAAATG 59.633 34.615 0.00 0.00 0.00 2.32
4824 4950 5.841810 ACGATTGATCCTTTTCTTGCAAAA 58.158 33.333 0.00 0.00 0.00 2.44
4846 5087 3.848019 CGATGCTGAAACACAAGCAATAC 59.152 43.478 0.96 0.00 36.70 1.89
4854 5095 2.160219 GCAAGATCGATGCTGAAACACA 59.840 45.455 16.39 0.00 40.64 3.72
4908 5149 5.484715 TCTGGTAGGTAAAAGTACACATGC 58.515 41.667 0.00 0.00 31.21 4.06
4935 5176 2.546368 CGGTCAATTCTTCCGAACAACA 59.454 45.455 6.63 0.00 46.05 3.33
4939 5180 2.140717 ACACGGTCAATTCTTCCGAAC 58.859 47.619 16.06 0.00 46.05 3.95
4955 5199 3.370978 ACAAGACAGTCAAGAACAACACG 59.629 43.478 2.66 0.00 0.00 4.49
5101 5364 1.070776 GTCAAGGAAAGACGACAACGC 60.071 52.381 0.00 0.00 43.96 4.84
5158 5421 2.124736 GCCGGCATTCCTGTGCTA 60.125 61.111 24.80 0.00 44.45 3.49
5199 5462 3.131223 TGCTACTGTCCACAAGATCTAGC 59.869 47.826 0.00 0.00 0.00 3.42
5222 5485 2.195727 TCCATGATTCAGGTGGTGCTA 58.804 47.619 6.26 0.00 34.61 3.49
5223 5486 0.994247 TCCATGATTCAGGTGGTGCT 59.006 50.000 6.26 0.00 34.61 4.40
5224 5487 1.679680 CATCCATGATTCAGGTGGTGC 59.320 52.381 6.26 0.00 34.61 5.01
5225 5488 3.008835 ACATCCATGATTCAGGTGGTG 57.991 47.619 6.26 6.71 34.61 4.17
5226 5489 3.782523 AGTACATCCATGATTCAGGTGGT 59.217 43.478 6.26 6.50 34.61 4.16
5274 5537 4.117685 CGTCATCAGAGCAATCATTCAGA 58.882 43.478 0.00 0.00 0.00 3.27
5288 5551 1.392853 GTTGCTCAGCTTCGTCATCAG 59.607 52.381 0.00 0.00 0.00 2.90
5291 5554 1.151668 GTGTTGCTCAGCTTCGTCAT 58.848 50.000 0.00 0.00 0.00 3.06
5310 5573 1.969256 CGCGGAACTGAACGATTTTTG 59.031 47.619 0.00 0.00 0.00 2.44
5314 5577 0.038526 AGTCGCGGAACTGAACGATT 60.039 50.000 6.13 0.00 36.85 3.34
5316 5579 1.081641 GAGTCGCGGAACTGAACGA 60.082 57.895 6.13 0.00 0.00 3.85
5317 5580 2.087009 GGAGTCGCGGAACTGAACG 61.087 63.158 6.13 0.00 0.00 3.95
5327 5597 0.579156 GTACTAGTACCGGAGTCGCG 59.421 60.000 20.47 0.00 34.56 5.87
5335 5605 4.509600 CGAGGGAGTTTAGTACTAGTACCG 59.490 50.000 25.97 15.49 37.17 4.02
5336 5606 5.295540 CACGAGGGAGTTTAGTACTAGTACC 59.704 48.000 25.97 12.94 37.17 3.34
5337 5607 5.877564 ACACGAGGGAGTTTAGTACTAGTAC 59.122 44.000 23.03 23.03 37.17 2.73
5338 5608 6.054860 ACACGAGGGAGTTTAGTACTAGTA 57.945 41.667 2.23 0.00 37.17 1.82
5339 5609 4.916183 ACACGAGGGAGTTTAGTACTAGT 58.084 43.478 0.00 0.00 37.17 2.57
5340 5610 5.647225 AGAACACGAGGGAGTTTAGTACTAG 59.353 44.000 2.23 0.00 37.17 2.57
5341 5611 5.413833 CAGAACACGAGGGAGTTTAGTACTA 59.586 44.000 0.00 0.00 37.17 1.82
5342 5612 4.217983 CAGAACACGAGGGAGTTTAGTACT 59.782 45.833 0.00 0.00 40.71 2.73
5343 5613 4.022503 ACAGAACACGAGGGAGTTTAGTAC 60.023 45.833 0.00 0.00 0.00 2.73
5344 5614 4.147321 ACAGAACACGAGGGAGTTTAGTA 58.853 43.478 0.00 0.00 0.00 1.82
5345 5615 2.963782 ACAGAACACGAGGGAGTTTAGT 59.036 45.455 0.00 0.00 0.00 2.24
5346 5616 3.256136 AGACAGAACACGAGGGAGTTTAG 59.744 47.826 0.00 0.00 0.00 1.85
5347 5617 3.005472 CAGACAGAACACGAGGGAGTTTA 59.995 47.826 0.00 0.00 0.00 2.01
5348 5618 2.040178 AGACAGAACACGAGGGAGTTT 58.960 47.619 0.00 0.00 0.00 2.66
5349 5619 1.341531 CAGACAGAACACGAGGGAGTT 59.658 52.381 0.00 0.00 0.00 3.01
5350 5620 0.962489 CAGACAGAACACGAGGGAGT 59.038 55.000 0.00 0.00 0.00 3.85
5351 5621 0.389166 GCAGACAGAACACGAGGGAG 60.389 60.000 0.00 0.00 0.00 4.30
5352 5622 0.827925 AGCAGACAGAACACGAGGGA 60.828 55.000 0.00 0.00 0.00 4.20
5353 5623 0.668706 CAGCAGACAGAACACGAGGG 60.669 60.000 0.00 0.00 0.00 4.30
5354 5624 0.315251 TCAGCAGACAGAACACGAGG 59.685 55.000 0.00 0.00 0.00 4.63
5473 5748 9.926751 CATAGAAGAAAAATGTGCAGTATACTG 57.073 33.333 25.68 25.68 46.40 2.74
5474 5749 9.113838 CCATAGAAGAAAAATGTGCAGTATACT 57.886 33.333 0.00 0.00 0.00 2.12
5475 5750 7.857885 GCCATAGAAGAAAAATGTGCAGTATAC 59.142 37.037 0.00 0.00 0.00 1.47
5476 5751 7.775093 AGCCATAGAAGAAAAATGTGCAGTATA 59.225 33.333 0.00 0.00 0.00 1.47
5477 5752 6.604795 AGCCATAGAAGAAAAATGTGCAGTAT 59.395 34.615 0.00 0.00 0.00 2.12
5478 5753 5.945784 AGCCATAGAAGAAAAATGTGCAGTA 59.054 36.000 0.00 0.00 0.00 2.74
5479 5754 4.768968 AGCCATAGAAGAAAAATGTGCAGT 59.231 37.500 0.00 0.00 0.00 4.40
5480 5755 5.100259 CAGCCATAGAAGAAAAATGTGCAG 58.900 41.667 0.00 0.00 0.00 4.41
5481 5756 4.618927 GCAGCCATAGAAGAAAAATGTGCA 60.619 41.667 0.00 0.00 0.00 4.57
5482 5757 3.861689 GCAGCCATAGAAGAAAAATGTGC 59.138 43.478 0.00 0.00 0.00 4.57
5483 5758 5.063180 TGCAGCCATAGAAGAAAAATGTG 57.937 39.130 0.00 0.00 0.00 3.21
5484 5759 5.419788 TCATGCAGCCATAGAAGAAAAATGT 59.580 36.000 0.00 0.00 0.00 2.71
5485 5760 5.898174 TCATGCAGCCATAGAAGAAAAATG 58.102 37.500 0.00 0.00 0.00 2.32
5486 5761 5.068723 CCTCATGCAGCCATAGAAGAAAAAT 59.931 40.000 0.00 0.00 0.00 1.82
5487 5762 4.400251 CCTCATGCAGCCATAGAAGAAAAA 59.600 41.667 0.00 0.00 0.00 1.94
5488 5763 3.949754 CCTCATGCAGCCATAGAAGAAAA 59.050 43.478 0.00 0.00 0.00 2.29
5489 5764 3.548770 CCTCATGCAGCCATAGAAGAAA 58.451 45.455 0.00 0.00 0.00 2.52
5490 5765 2.747467 GCCTCATGCAGCCATAGAAGAA 60.747 50.000 0.00 0.00 40.77 2.52
5491 5766 1.202734 GCCTCATGCAGCCATAGAAGA 60.203 52.381 0.00 0.00 40.77 2.87
5492 5767 1.236628 GCCTCATGCAGCCATAGAAG 58.763 55.000 0.00 0.00 40.77 2.85
5493 5768 3.409201 GCCTCATGCAGCCATAGAA 57.591 52.632 0.00 0.00 40.77 2.10
5503 5778 1.113517 ATGCCAATCCTGCCTCATGC 61.114 55.000 0.00 0.00 41.77 4.06
5504 5779 0.959553 GATGCCAATCCTGCCTCATG 59.040 55.000 0.00 0.00 0.00 3.07
5505 5780 0.851469 AGATGCCAATCCTGCCTCAT 59.149 50.000 0.00 0.00 32.77 2.90
5506 5781 0.182061 GAGATGCCAATCCTGCCTCA 59.818 55.000 0.00 0.00 32.77 3.86
5507 5782 0.182061 TGAGATGCCAATCCTGCCTC 59.818 55.000 0.00 0.00 32.77 4.70
5508 5783 0.851469 ATGAGATGCCAATCCTGCCT 59.149 50.000 0.00 0.00 32.77 4.75
5509 5784 1.202903 AGATGAGATGCCAATCCTGCC 60.203 52.381 0.00 0.00 32.77 4.85
5510 5785 2.273538 AGATGAGATGCCAATCCTGC 57.726 50.000 0.00 0.00 32.77 4.85
5511 5786 4.888239 AGAAAAGATGAGATGCCAATCCTG 59.112 41.667 0.00 0.00 32.77 3.86
5512 5787 5.104024 AGAGAAAAGATGAGATGCCAATCCT 60.104 40.000 0.00 0.00 32.77 3.24
5513 5788 5.008811 CAGAGAAAAGATGAGATGCCAATCC 59.991 44.000 0.00 0.00 32.77 3.01
5514 5789 5.008811 CCAGAGAAAAGATGAGATGCCAATC 59.991 44.000 0.00 0.00 0.00 2.67
5515 5790 4.888239 CCAGAGAAAAGATGAGATGCCAAT 59.112 41.667 0.00 0.00 0.00 3.16
5516 5791 4.019051 TCCAGAGAAAAGATGAGATGCCAA 60.019 41.667 0.00 0.00 0.00 4.52
5517 5792 3.520721 TCCAGAGAAAAGATGAGATGCCA 59.479 43.478 0.00 0.00 0.00 4.92
5518 5793 4.128643 CTCCAGAGAAAAGATGAGATGCC 58.871 47.826 0.00 0.00 0.00 4.40
5519 5794 3.560896 GCTCCAGAGAAAAGATGAGATGC 59.439 47.826 0.00 0.00 0.00 3.91
5520 5795 5.026038 AGCTCCAGAGAAAAGATGAGATG 57.974 43.478 0.00 0.00 0.00 2.90
5521 5796 5.430007 CAAGCTCCAGAGAAAAGATGAGAT 58.570 41.667 0.00 0.00 0.00 2.75
5522 5797 4.323333 CCAAGCTCCAGAGAAAAGATGAGA 60.323 45.833 0.00 0.00 0.00 3.27
5523 5798 3.940221 CCAAGCTCCAGAGAAAAGATGAG 59.060 47.826 0.00 0.00 0.00 2.90
5524 5799 3.871463 GCCAAGCTCCAGAGAAAAGATGA 60.871 47.826 0.00 0.00 0.00 2.92
5525 5800 2.422832 GCCAAGCTCCAGAGAAAAGATG 59.577 50.000 0.00 0.00 0.00 2.90
5526 5801 2.040813 TGCCAAGCTCCAGAGAAAAGAT 59.959 45.455 0.00 0.00 0.00 2.40
5527 5802 1.421268 TGCCAAGCTCCAGAGAAAAGA 59.579 47.619 0.00 0.00 0.00 2.52
5528 5803 1.901591 TGCCAAGCTCCAGAGAAAAG 58.098 50.000 0.00 0.00 0.00 2.27
5529 5804 2.592102 ATGCCAAGCTCCAGAGAAAA 57.408 45.000 0.00 0.00 0.00 2.29
5530 5805 2.559668 CAAATGCCAAGCTCCAGAGAAA 59.440 45.455 0.00 0.00 0.00 2.52
5531 5806 2.165167 CAAATGCCAAGCTCCAGAGAA 58.835 47.619 0.00 0.00 0.00 2.87
5532 5807 1.352017 TCAAATGCCAAGCTCCAGAGA 59.648 47.619 0.00 0.00 0.00 3.10
5533 5808 1.830279 TCAAATGCCAAGCTCCAGAG 58.170 50.000 0.00 0.00 0.00 3.35
5534 5809 2.519771 ATCAAATGCCAAGCTCCAGA 57.480 45.000 0.00 0.00 0.00 3.86
5535 5810 4.583489 AGAATATCAAATGCCAAGCTCCAG 59.417 41.667 0.00 0.00 0.00 3.86
5536 5811 4.539726 AGAATATCAAATGCCAAGCTCCA 58.460 39.130 0.00 0.00 0.00 3.86
5537 5812 5.532406 TGTAGAATATCAAATGCCAAGCTCC 59.468 40.000 0.00 0.00 0.00 4.70
5538 5813 6.624352 TGTAGAATATCAAATGCCAAGCTC 57.376 37.500 0.00 0.00 0.00 4.09
5539 5814 6.015688 CCATGTAGAATATCAAATGCCAAGCT 60.016 38.462 0.00 0.00 0.00 3.74
5540 5815 6.016024 TCCATGTAGAATATCAAATGCCAAGC 60.016 38.462 0.00 0.00 0.00 4.01
5541 5816 7.514784 TCCATGTAGAATATCAAATGCCAAG 57.485 36.000 0.00 0.00 0.00 3.61
5542 5817 7.201902 GGTTCCATGTAGAATATCAAATGCCAA 60.202 37.037 0.00 0.00 0.00 4.52
5543 5818 6.265196 GGTTCCATGTAGAATATCAAATGCCA 59.735 38.462 0.00 0.00 0.00 4.92
5544 5819 6.491403 AGGTTCCATGTAGAATATCAAATGCC 59.509 38.462 0.00 0.00 0.00 4.40
5545 5820 7.516198 AGGTTCCATGTAGAATATCAAATGC 57.484 36.000 0.00 0.00 0.00 3.56
5546 5821 8.571336 GGAAGGTTCCATGTAGAATATCAAATG 58.429 37.037 3.73 0.00 46.76 2.32
5547 5822 8.697507 GGAAGGTTCCATGTAGAATATCAAAT 57.302 34.615 3.73 0.00 46.76 2.32
5564 5839 7.229907 TGGTCTTACAAAACAATAGGAAGGTTC 59.770 37.037 0.00 0.00 0.00 3.62
5565 5840 7.064229 TGGTCTTACAAAACAATAGGAAGGTT 58.936 34.615 0.00 0.00 0.00 3.50
5566 5841 6.607019 TGGTCTTACAAAACAATAGGAAGGT 58.393 36.000 0.00 0.00 0.00 3.50
5567 5842 7.703058 ATGGTCTTACAAAACAATAGGAAGG 57.297 36.000 0.00 0.00 0.00 3.46
5570 5845 9.403583 GGAATATGGTCTTACAAAACAATAGGA 57.596 33.333 0.00 0.00 0.00 2.94
5571 5846 9.408648 AGGAATATGGTCTTACAAAACAATAGG 57.591 33.333 0.00 0.00 0.00 2.57
5573 5848 9.403583 GGAGGAATATGGTCTTACAAAACAATA 57.596 33.333 0.00 0.00 0.00 1.90
5574 5849 8.116026 AGGAGGAATATGGTCTTACAAAACAAT 58.884 33.333 0.00 0.00 0.00 2.71
5575 5850 7.466804 AGGAGGAATATGGTCTTACAAAACAA 58.533 34.615 0.00 0.00 0.00 2.83
5576 5851 7.027874 AGGAGGAATATGGTCTTACAAAACA 57.972 36.000 0.00 0.00 0.00 2.83
5577 5852 7.339482 AGAGGAGGAATATGGTCTTACAAAAC 58.661 38.462 0.00 0.00 0.00 2.43
5578 5853 7.510675 AGAGGAGGAATATGGTCTTACAAAA 57.489 36.000 0.00 0.00 0.00 2.44
5579 5854 7.510675 AAGAGGAGGAATATGGTCTTACAAA 57.489 36.000 0.00 0.00 0.00 2.83
5580 5855 7.182026 TGAAAGAGGAGGAATATGGTCTTACAA 59.818 37.037 0.00 0.00 0.00 2.41
5581 5856 6.672218 TGAAAGAGGAGGAATATGGTCTTACA 59.328 38.462 0.00 0.00 0.00 2.41
5582 5857 7.125792 TGAAAGAGGAGGAATATGGTCTTAC 57.874 40.000 0.00 0.00 0.00 2.34
5583 5858 7.749377 TTGAAAGAGGAGGAATATGGTCTTA 57.251 36.000 0.00 0.00 0.00 2.10
5584 5859 6.642733 TTGAAAGAGGAGGAATATGGTCTT 57.357 37.500 0.00 0.00 0.00 3.01
5585 5860 6.445139 TCTTTGAAAGAGGAGGAATATGGTCT 59.555 38.462 3.02 0.00 32.71 3.85
5586 5861 6.540551 GTCTTTGAAAGAGGAGGAATATGGTC 59.459 42.308 8.06 0.00 38.41 4.02
5587 5862 6.418946 GTCTTTGAAAGAGGAGGAATATGGT 58.581 40.000 8.06 0.00 38.41 3.55
5588 5863 5.825151 GGTCTTTGAAAGAGGAGGAATATGG 59.175 44.000 8.06 0.00 38.41 2.74
5589 5864 6.541641 CAGGTCTTTGAAAGAGGAGGAATATG 59.458 42.308 8.06 0.00 38.41 1.78
5590 5865 6.445139 TCAGGTCTTTGAAAGAGGAGGAATAT 59.555 38.462 8.06 0.00 38.41 1.28
5591 5866 5.785423 TCAGGTCTTTGAAAGAGGAGGAATA 59.215 40.000 8.06 0.00 38.41 1.75
5592 5867 4.599241 TCAGGTCTTTGAAAGAGGAGGAAT 59.401 41.667 8.06 0.00 38.41 3.01
5593 5868 3.973973 TCAGGTCTTTGAAAGAGGAGGAA 59.026 43.478 8.06 0.00 38.41 3.36
5594 5869 3.580458 CTCAGGTCTTTGAAAGAGGAGGA 59.420 47.826 8.06 3.53 38.41 3.71
5595 5870 3.307339 CCTCAGGTCTTTGAAAGAGGAGG 60.307 52.174 23.95 23.95 44.12 4.30
5596 5871 3.867984 GCCTCAGGTCTTTGAAAGAGGAG 60.868 52.174 8.06 14.18 44.12 3.69
5597 5872 2.039084 GCCTCAGGTCTTTGAAAGAGGA 59.961 50.000 8.06 5.88 44.12 3.71
5598 5873 2.431454 GCCTCAGGTCTTTGAAAGAGG 58.569 52.381 8.06 6.82 44.19 3.69
5599 5874 2.224621 TGGCCTCAGGTCTTTGAAAGAG 60.225 50.000 8.06 0.00 38.41 2.85
5600 5875 1.774254 TGGCCTCAGGTCTTTGAAAGA 59.226 47.619 3.32 3.02 34.51 2.52
5601 5876 2.276732 TGGCCTCAGGTCTTTGAAAG 57.723 50.000 3.32 0.00 0.00 2.62
5602 5877 2.091885 AGTTGGCCTCAGGTCTTTGAAA 60.092 45.455 3.32 0.00 0.00 2.69
5603 5878 1.494721 AGTTGGCCTCAGGTCTTTGAA 59.505 47.619 3.32 0.00 0.00 2.69
5604 5879 1.072331 GAGTTGGCCTCAGGTCTTTGA 59.928 52.381 3.32 0.00 40.17 2.69
5605 5880 1.528129 GAGTTGGCCTCAGGTCTTTG 58.472 55.000 3.32 0.00 40.17 2.77
5606 5881 0.402121 GGAGTTGGCCTCAGGTCTTT 59.598 55.000 3.32 0.00 42.40 2.52
5607 5882 0.768221 TGGAGTTGGCCTCAGGTCTT 60.768 55.000 3.32 0.00 42.40 3.01
5608 5883 1.152030 TGGAGTTGGCCTCAGGTCT 60.152 57.895 3.32 0.00 42.40 3.85
5609 5884 1.003233 GTGGAGTTGGCCTCAGGTC 60.003 63.158 3.32 0.00 42.40 3.85
5610 5885 2.529744 GGTGGAGTTGGCCTCAGGT 61.530 63.158 3.32 0.00 42.40 4.00
5611 5886 2.352805 GGTGGAGTTGGCCTCAGG 59.647 66.667 3.32 0.00 42.40 3.86
5612 5887 2.046892 CGGTGGAGTTGGCCTCAG 60.047 66.667 3.32 0.00 42.40 3.35
5613 5888 4.329545 GCGGTGGAGTTGGCCTCA 62.330 66.667 3.32 0.00 42.40 3.86


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

AutoCloner maintained by Alex Coulton.