Multiple sequence alignment - TraesCS1D01G307500

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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 TraesCS1D01G307500 chr1D 100.000 3528 0 0 2101 5628 403730888 403727361 0.000000e+00 6516
1 TraesCS1D01G307500 chr1D 100.000 1850 0 0 1 1850 403732988 403731139 0.000000e+00 3417
2 TraesCS1D01G307500 chr1D 93.233 133 9 0 5495 5627 411276769 411276901 4.450000e-46 196
3 TraesCS1D01G307500 chr1D 93.130 131 9 0 5497 5627 467604422 467604292 5.750000e-45 193
4 TraesCS1D01G307500 chr1B 94.846 3376 120 23 2101 5439 543181609 543178251 0.000000e+00 5221
5 TraesCS1D01G307500 chr1B 96.418 977 33 2 875 1850 543182637 543181662 0.000000e+00 1609
6 TraesCS1D01G307500 chr1B 83.986 868 64 26 15 835 543183906 543183067 0.000000e+00 763
7 TraesCS1D01G307500 chr1B 93.893 131 8 0 5497 5627 252161795 252161665 1.240000e-46 198
8 TraesCS1D01G307500 chr1B 93.893 131 8 0 5497 5627 642955625 642955755 1.240000e-46 198
9 TraesCS1D01G307500 chr1A 88.661 2972 213 56 2591 5496 499449163 499446250 0.000000e+00 3507
10 TraesCS1D01G307500 chr1A 89.680 1502 91 28 4 1454 499451488 499450000 0.000000e+00 1857
11 TraesCS1D01G307500 chr1A 93.689 206 13 0 1456 1661 499449653 499449448 5.480000e-80 309
12 TraesCS1D01G307500 chr1A 89.796 245 18 4 2101 2345 499449174 499448937 1.970000e-79 307
13 TraesCS1D01G307500 chr1A 93.989 183 11 0 1666 1848 499449409 499449227 1.540000e-70 278
14 TraesCS1D01G307500 chr1A 85.542 166 21 2 2357 2519 285535969 285535804 2.700000e-38 171
15 TraesCS1D01G307500 chr3B 84.917 484 55 9 306 780 583329013 583329487 1.840000e-129 473
16 TraesCS1D01G307500 chr3B 72.854 862 187 33 3407 4245 579452070 579452907 9.360000e-63 252
17 TraesCS1D01G307500 chr4D 83.745 486 62 9 304 780 107281910 107282387 1.440000e-120 444
18 TraesCS1D01G307500 chr4D 93.985 133 8 0 5495 5627 416431720 416431852 9.560000e-48 202
19 TraesCS1D01G307500 chr7D 83.333 486 64 9 304 780 556058195 556057718 3.110000e-117 433
20 TraesCS1D01G307500 chr2D 82.393 443 57 13 305 736 204618033 204618465 3.200000e-97 366
21 TraesCS1D01G307500 chr3A 73.971 680 150 19 3377 4038 583244175 583244845 3.370000e-62 250
22 TraesCS1D01G307500 chr6B 93.893 131 8 0 5497 5627 688594719 688594589 1.240000e-46 198
23 TraesCS1D01G307500 chr3D 93.333 135 5 3 5495 5627 466963087 466963219 4.450000e-46 196
24 TraesCS1D01G307500 chr5B 93.182 132 9 0 5497 5628 320385772 320385641 1.600000e-45 195
25 TraesCS1D01G307500 chr4B 93.130 131 9 0 5497 5627 661374984 661375114 5.750000e-45 193
26 TraesCS1D01G307500 chr4B 85.799 169 16 6 2357 2523 562352646 562352484 7.500000e-39 172
27 TraesCS1D01G307500 chr5A 88.816 152 16 1 629 780 26223066 26222916 9.630000e-43 185
28 TraesCS1D01G307500 chr5A 86.391 169 20 3 2357 2523 382336473 382336306 1.250000e-41 182
29 TraesCS1D01G307500 chr5A 91.597 119 10 0 662 780 504179807 504179689 1.250000e-36 165
30 TraesCS1D01G307500 chr7A 85.380 171 18 6 2357 2523 539543663 539543830 2.700000e-38 171
31 TraesCS1D01G307500 chr7A 84.024 169 24 3 2357 2523 34048560 34048393 5.840000e-35 159
32 TraesCS1D01G307500 chr7A 84.118 170 22 4 2357 2523 175244514 175244681 5.840000e-35 159
33 TraesCS1D01G307500 chr6A 85.714 161 21 2 2364 2523 89893618 89893777 9.700000e-38 169
34 TraesCS1D01G307500 chr6D 85.093 161 23 1 2364 2523 73497235 73497395 4.510000e-36 163


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 TraesCS1D01G307500 chr1D 403727361 403732988 5627 True 4966.5 6516 100.000 1 5628 2 chr1D.!!$R2 5627
1 TraesCS1D01G307500 chr1B 543178251 543183906 5655 True 2531.0 5221 91.750 15 5439 3 chr1B.!!$R2 5424
2 TraesCS1D01G307500 chr1A 499446250 499451488 5238 True 1251.6 3507 91.163 4 5496 5 chr1A.!!$R2 5492
3 TraesCS1D01G307500 chr3B 579452070 579452907 837 False 252.0 252 72.854 3407 4245 1 chr3B.!!$F1 838
4 TraesCS1D01G307500 chr3A 583244175 583244845 670 False 250.0 250 73.971 3377 4038 1 chr3A.!!$F1 661

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
450 494 0.180406 AGAGGTTGCGTGGTTGAGTT 59.820 50.000 0.0 0.0 0.00 3.01 F
685 751 0.461870 TGCCGGTATGCTTGCTGTAG 60.462 55.000 1.9 0.0 0.00 2.74 F
831 902 2.421073 TCTGCAATGAAAATCAGGAGCG 59.579 45.455 0.0 0.0 0.00 5.03 F
1067 1528 2.825836 GGCTGACTTGGCATCCCG 60.826 66.667 0.0 0.0 0.00 5.14 F
1365 1826 3.720601 TGGGCTCGAATGGCTGCT 61.721 61.111 0.0 0.0 0.00 4.24 F
1389 1850 4.606232 CGTGTAAGTTCAGTTTCAAGCTCG 60.606 45.833 0.0 0.0 0.00 5.03 F
3108 3956 3.446310 TGACTGTAAGACGACAAGCAA 57.554 42.857 0.0 0.0 37.43 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 3276 0.033504 ACGCGGAGATTTGTGTCTGT 59.966 50.000 12.47 0.0 0.00 3.41 R
2436 3277 1.990799 TACGCGGAGATTTGTGTCTG 58.009 50.000 12.47 0.0 0.00 3.51 R
2438 3279 3.732943 CTTTTACGCGGAGATTTGTGTC 58.267 45.455 12.47 0.0 0.00 3.67 R
2549 3396 4.202010 GCACAAAAGGTTCTAAGCAAGTGA 60.202 41.667 0.00 0.0 0.00 3.41 R
3108 3956 2.435372 TGCCAGTCAAACAGAAAGGT 57.565 45.000 0.00 0.0 0.00 3.50 R
3217 4068 5.688807 CTCTGGAAGTCCATGGAAATACAT 58.311 41.667 18.20 0.0 46.46 2.29 R
4980 5849 0.105709 CTCCTTCCTCCCTCTCTCCC 60.106 65.000 0.00 0.0 0.00 4.30 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
32 33 2.113986 GCCCAATCCCGATCCAGG 59.886 66.667 0.00 0.00 0.00 4.45
35 36 0.764369 CCCAATCCCGATCCAGGAGA 60.764 60.000 5.45 0.00 36.67 3.71
37 38 1.709578 CAATCCCGATCCAGGAGAGA 58.290 55.000 5.45 0.00 36.67 3.10
139 145 2.502142 GGGTTTTCCGGTCAGGTAAT 57.498 50.000 0.00 0.00 41.82 1.89
303 334 1.667724 CTGTTCCGTGGATTGATCTGC 59.332 52.381 0.00 0.00 0.00 4.26
334 365 1.066716 AGCTGTTCCGCGTAATTACCA 60.067 47.619 10.01 0.52 34.40 3.25
343 376 5.124645 TCCGCGTAATTACCACCAAATAAT 58.875 37.500 10.01 0.00 0.00 1.28
344 377 5.236911 TCCGCGTAATTACCACCAAATAATC 59.763 40.000 10.01 0.00 0.00 1.75
347 380 5.445845 CGTAATTACCACCAAATAATCGGC 58.554 41.667 10.01 0.00 0.00 5.54
366 399 4.927425 TCGGCTAGCTTTGTAGTTTTACTG 59.073 41.667 15.72 0.00 0.00 2.74
368 401 4.435651 GGCTAGCTTTGTAGTTTTACTGCG 60.436 45.833 15.72 0.00 33.27 5.18
426 459 1.068055 TGCTTTCGGGAAGACGTAGAC 60.068 52.381 0.00 0.00 37.57 2.59
448 492 1.284982 CGAGAGGTTGCGTGGTTGAG 61.285 60.000 0.00 0.00 0.00 3.02
450 494 0.180406 AGAGGTTGCGTGGTTGAGTT 59.820 50.000 0.00 0.00 0.00 3.01
451 495 0.586802 GAGGTTGCGTGGTTGAGTTC 59.413 55.000 0.00 0.00 0.00 3.01
462 506 3.364023 GTGGTTGAGTTCGATCGTAGTTG 59.636 47.826 15.94 0.00 0.00 3.16
463 507 3.253921 TGGTTGAGTTCGATCGTAGTTGA 59.746 43.478 15.94 0.00 0.00 3.18
466 510 5.391310 GGTTGAGTTCGATCGTAGTTGAGTA 60.391 44.000 15.94 0.00 0.00 2.59
467 511 5.466432 TGAGTTCGATCGTAGTTGAGTAG 57.534 43.478 15.94 0.00 0.00 2.57
468 512 4.331992 TGAGTTCGATCGTAGTTGAGTAGG 59.668 45.833 15.94 0.00 0.00 3.18
469 513 4.260170 AGTTCGATCGTAGTTGAGTAGGT 58.740 43.478 15.94 0.00 0.00 3.08
470 514 4.699257 AGTTCGATCGTAGTTGAGTAGGTT 59.301 41.667 15.94 0.00 0.00 3.50
471 515 5.877012 AGTTCGATCGTAGTTGAGTAGGTTA 59.123 40.000 15.94 0.00 0.00 2.85
472 516 6.541641 AGTTCGATCGTAGTTGAGTAGGTTAT 59.458 38.462 15.94 0.00 0.00 1.89
475 519 9.710900 TTCGATCGTAGTTGAGTAGGTTATATA 57.289 33.333 15.94 0.00 0.00 0.86
481 527 9.674824 CGTAGTTGAGTAGGTTATATAGGTTTG 57.325 37.037 0.00 0.00 0.00 2.93
486 532 6.094193 AGTAGGTTATATAGGTTTGTCCGC 57.906 41.667 0.00 0.00 41.99 5.54
493 539 1.940883 TAGGTTTGTCCGCGCTCGAT 61.941 55.000 5.56 0.00 41.99 3.59
496 542 0.789383 GTTTGTCCGCGCTCGATTTG 60.789 55.000 5.56 0.00 38.10 2.32
524 570 5.507315 GGAGAAAGTAGCTCTGATCTACTGC 60.507 48.000 18.80 14.46 44.17 4.40
527 573 7.004086 AGAAAGTAGCTCTGATCTACTGCTAT 58.996 38.462 18.80 8.43 44.17 2.97
533 579 6.457355 AGCTCTGATCTACTGCTATTGATTG 58.543 40.000 0.00 0.00 31.71 2.67
535 581 6.416631 TCTGATCTACTGCTATTGATTGCT 57.583 37.500 0.00 0.00 0.00 3.91
557 603 2.231964 TGGCTCGTTACCAAATCGTAGT 59.768 45.455 0.00 0.00 33.12 2.73
558 604 3.256558 GGCTCGTTACCAAATCGTAGTT 58.743 45.455 0.00 0.00 0.00 2.24
619 668 6.519761 GTGTGCAGATTCAAACGTGTTATAAG 59.480 38.462 0.00 0.00 0.00 1.73
622 671 5.508224 GCAGATTCAAACGTGTTATAAGCAC 59.492 40.000 0.00 7.65 0.00 4.40
623 672 6.598525 CAGATTCAAACGTGTTATAAGCACA 58.401 36.000 14.42 0.00 36.71 4.57
624 673 7.075121 CAGATTCAAACGTGTTATAAGCACAA 58.925 34.615 14.42 5.39 36.71 3.33
625 674 7.269084 CAGATTCAAACGTGTTATAAGCACAAG 59.731 37.037 14.42 4.08 36.71 3.16
627 676 5.981174 TCAAACGTGTTATAAGCACAAGAC 58.019 37.500 14.42 0.00 36.71 3.01
628 677 5.756347 TCAAACGTGTTATAAGCACAAGACT 59.244 36.000 14.42 0.00 36.71 3.24
630 679 7.601130 TCAAACGTGTTATAAGCACAAGACTAT 59.399 33.333 14.42 0.00 36.71 2.12
631 680 7.900782 AACGTGTTATAAGCACAAGACTATT 57.099 32.000 14.42 0.00 36.71 1.73
632 681 7.290857 ACGTGTTATAAGCACAAGACTATTG 57.709 36.000 14.42 0.00 36.71 1.90
633 682 7.094631 ACGTGTTATAAGCACAAGACTATTGA 58.905 34.615 14.42 0.00 36.71 2.57
634 683 7.063074 ACGTGTTATAAGCACAAGACTATTGAC 59.937 37.037 14.42 0.00 36.71 3.18
637 686 9.151471 TGTTATAAGCACAAGACTATTGACTTC 57.849 33.333 0.00 0.00 0.00 3.01
664 727 7.660185 GTGAAATCACCTCGATGCTCTCGTA 62.660 48.000 2.04 0.00 43.10 3.43
685 751 0.461870 TGCCGGTATGCTTGCTGTAG 60.462 55.000 1.90 0.00 0.00 2.74
702 768 3.146066 TGTAGTAAGGCAGTTGCTTTGG 58.854 45.455 11.20 0.00 40.66 3.28
831 902 2.421073 TCTGCAATGAAAATCAGGAGCG 59.579 45.455 0.00 0.00 0.00 5.03
888 1349 7.540400 CACGCCTATTGATGTATTTTTCACAAA 59.460 33.333 0.00 0.00 0.00 2.83
891 1352 7.540745 GCCTATTGATGTATTTTTCACAAACGT 59.459 33.333 0.00 0.00 0.00 3.99
1067 1528 2.825836 GGCTGACTTGGCATCCCG 60.826 66.667 0.00 0.00 0.00 5.14
1329 1790 5.760743 GGAGAACCTAATCATTAAGCTCCAC 59.239 44.000 0.00 0.00 39.27 4.02
1365 1826 3.720601 TGGGCTCGAATGGCTGCT 61.721 61.111 0.00 0.00 0.00 4.24
1389 1850 4.606232 CGTGTAAGTTCAGTTTCAAGCTCG 60.606 45.833 0.00 0.00 0.00 5.03
1438 1899 4.997905 TTTTGTTCTCATGCTTCTCTCG 57.002 40.909 0.00 0.00 0.00 4.04
1555 2361 5.941733 TCATGATATTTTGCGTGATATGCC 58.058 37.500 0.00 0.00 0.00 4.40
1718 2558 7.434492 ACATAGGTATTAGTTTCAGACATCGG 58.566 38.462 0.00 0.00 0.00 4.18
1767 2607 8.439971 TGAAGGTATTGTCCATTATATGAAGCT 58.560 33.333 0.00 0.00 0.00 3.74
2253 3094 5.739752 TGTCAGTTCTGTGACTTGAATTG 57.260 39.130 5.65 7.60 46.06 2.32
2345 3186 7.853524 TCGATGTTGTTACGAAAACATAGTTT 58.146 30.769 8.50 0.00 44.83 2.66
2367 3208 9.911788 AGTTTGATACCAATTCATCTAGATGTT 57.088 29.630 27.80 15.79 34.89 2.71
2372 3213 9.213799 GATACCAATTCATCTAGATGTTCCTTC 57.786 37.037 27.80 14.06 39.72 3.46
2397 3238 6.090763 CGTTATTGCACATCTAAGTGACTCAA 59.909 38.462 0.00 0.00 42.05 3.02
2627 3474 7.615582 TCTACTTGGATTTGTGCTGATTAAG 57.384 36.000 0.00 0.00 0.00 1.85
2654 3501 8.854614 ATATCAGGCTTATTGACCTACATTTC 57.145 34.615 0.00 0.00 33.38 2.17
2674 3521 7.068226 ACATTTCGCCTAGTATTATTTGCCTTT 59.932 33.333 0.00 0.00 0.00 3.11
2763 3610 5.744666 TGCTAGTTTTGTGGTACTGTTTC 57.255 39.130 0.00 0.00 0.00 2.78
2784 3631 7.816995 TGTTTCACAACAAAGCTGTTAGATTTT 59.183 29.630 0.00 0.00 44.15 1.82
2785 3632 8.655970 GTTTCACAACAAAGCTGTTAGATTTTT 58.344 29.630 0.00 0.00 44.15 1.94
2903 3750 7.575414 TCAGTTTCCTGTTAAAAATGCTACA 57.425 32.000 0.00 0.00 39.82 2.74
3088 3936 5.068987 ACATTGTGGTTTCAACTGCAACTAT 59.931 36.000 0.00 0.00 0.00 2.12
3108 3956 3.446310 TGACTGTAAGACGACAAGCAA 57.554 42.857 0.00 0.00 37.43 3.91
3379 4230 8.632679 TGCATTTCTTCTCTTTAATTGTCACTT 58.367 29.630 0.00 0.00 0.00 3.16
3685 4536 3.057033 CCCAGCTTCCAGATGTTTCTTTG 60.057 47.826 0.00 0.00 27.62 2.77
3709 4560 5.246307 AGCAATTTACCTGGTCTGTACTTC 58.754 41.667 0.63 0.00 0.00 3.01
3981 4840 1.561542 CTTCTAGGCCCATGACTGGTT 59.438 52.381 0.00 0.00 41.37 3.67
4100 4959 3.344215 GATCCCTGCATGCGCTCG 61.344 66.667 14.09 0.00 39.64 5.03
4419 5278 8.960591 CATCTGGTTAGTGATTACTCCATTTTT 58.039 33.333 0.00 0.00 38.36 1.94
4477 5336 6.968904 CCGAGATTTCACTGGTTTAATCAATG 59.031 38.462 0.00 0.00 31.12 2.82
4483 5342 6.198650 TCACTGGTTTAATCAATGCTGATG 57.801 37.500 0.00 0.00 41.66 3.07
4487 5346 6.379133 ACTGGTTTAATCAATGCTGATGTCAT 59.621 34.615 0.00 0.00 41.66 3.06
4535 5394 1.745087 CAGATGAACCAACAATCCCCG 59.255 52.381 0.00 0.00 0.00 5.73
4543 5402 1.937899 CCAACAATCCCCGAATACGAC 59.062 52.381 0.00 0.00 42.66 4.34
4664 5523 1.537814 TACAGTGGTGCAGGTACCGG 61.538 60.000 7.81 7.81 43.87 5.28
4718 5577 0.587768 TGCATTTGACTGACACGCTG 59.412 50.000 0.00 0.00 0.00 5.18
4813 5672 6.410540 CCTCCAATAAAGCTGTAGAAGAGTT 58.589 40.000 0.00 0.00 0.00 3.01
4814 5673 7.556844 CCTCCAATAAAGCTGTAGAAGAGTTA 58.443 38.462 0.00 0.00 0.00 2.24
4823 5692 5.929415 AGCTGTAGAAGAGTTAGTTCTTTGC 59.071 40.000 0.00 0.00 37.53 3.68
4833 5702 7.051000 AGAGTTAGTTCTTTGCTCCATTATCC 58.949 38.462 0.00 0.00 0.00 2.59
4834 5703 6.963322 AGTTAGTTCTTTGCTCCATTATCCT 58.037 36.000 0.00 0.00 0.00 3.24
4853 5722 2.678336 CCTGAGTAAAATTCCCTCGTGC 59.322 50.000 0.00 0.00 0.00 5.34
4856 5725 2.603560 GAGTAAAATTCCCTCGTGCTCG 59.396 50.000 0.81 0.81 38.55 5.03
4857 5726 2.232941 AGTAAAATTCCCTCGTGCTCGA 59.767 45.455 10.80 10.80 44.12 4.04
4868 5737 1.672356 GTGCTCGACCAACCTGCAT 60.672 57.895 0.00 0.00 36.04 3.96
4893 5762 1.738099 CTCACTTCGGCCGTCCTTG 60.738 63.158 27.15 17.57 0.00 3.61
4905 5774 0.243636 CGTCCTTGAAAATGCCCACC 59.756 55.000 0.00 0.00 0.00 4.61
4919 5788 2.291282 TGCCCACCCAACTATGTAAAGG 60.291 50.000 0.00 0.00 0.00 3.11
4930 5799 6.127730 CCAACTATGTAAAGGGGTTCATTGTC 60.128 42.308 0.00 0.00 0.00 3.18
4948 5817 1.007964 CGTCCAAACATGCGCCAAA 60.008 52.632 4.18 0.00 0.00 3.28
4980 5849 4.651867 CCCACCTGGCATCTTCTG 57.348 61.111 0.00 0.00 0.00 3.02
5007 5877 1.621672 GGGAGGAAGGAGAGCACCTG 61.622 65.000 0.00 0.00 40.49 4.00
5054 5924 3.646162 TGGTAGCTTTGACTCTTTCTCCA 59.354 43.478 0.00 0.00 0.00 3.86
5080 5950 0.743701 CCAGCAGGATGTCAGTGAGC 60.744 60.000 0.00 0.00 39.31 4.26
5081 5951 0.036671 CAGCAGGATGTCAGTGAGCA 60.037 55.000 0.00 0.00 39.31 4.26
5132 6017 4.728772 TGTTTGAATGAGTTGGATGGACT 58.271 39.130 0.00 0.00 0.00 3.85
5134 6019 5.241506 TGTTTGAATGAGTTGGATGGACTTC 59.758 40.000 0.00 0.00 0.00 3.01
5199 6096 6.399639 GTGGTTTCACTCCCATTTTTCTTA 57.600 37.500 0.00 0.00 40.58 2.10
5204 6101 7.598869 GGTTTCACTCCCATTTTTCTTAATCAC 59.401 37.037 0.00 0.00 0.00 3.06
5306 6204 1.080974 GTAGCACGGCTGTACACGT 60.081 57.895 5.75 5.75 45.25 4.49
5332 6230 4.022589 CCAGCATGTTGTGATGTTCTTTCT 60.023 41.667 8.84 0.00 42.62 2.52
5333 6231 4.915667 CAGCATGTTGTGATGTTCTTTCTG 59.084 41.667 0.65 0.00 39.36 3.02
5334 6232 4.823442 AGCATGTTGTGATGTTCTTTCTGA 59.177 37.500 0.00 0.00 0.00 3.27
5336 6234 5.696822 CATGTTGTGATGTTCTTTCTGAGG 58.303 41.667 0.00 0.00 0.00 3.86
5340 6238 6.152661 TGTTGTGATGTTCTTTCTGAGGTTTT 59.847 34.615 0.00 0.00 0.00 2.43
5341 6239 7.338196 TGTTGTGATGTTCTTTCTGAGGTTTTA 59.662 33.333 0.00 0.00 0.00 1.52
5342 6240 8.352942 GTTGTGATGTTCTTTCTGAGGTTTTAT 58.647 33.333 0.00 0.00 0.00 1.40
5343 6241 9.567776 TTGTGATGTTCTTTCTGAGGTTTTATA 57.432 29.630 0.00 0.00 0.00 0.98
5344 6242 9.739276 TGTGATGTTCTTTCTGAGGTTTTATAT 57.261 29.630 0.00 0.00 0.00 0.86
5345 6243 9.994432 GTGATGTTCTTTCTGAGGTTTTATATG 57.006 33.333 0.00 0.00 0.00 1.78
5346 6244 9.958180 TGATGTTCTTTCTGAGGTTTTATATGA 57.042 29.630 0.00 0.00 0.00 2.15
5439 6357 3.988976 TCACATGGAAGGAAGAGAAGG 57.011 47.619 0.00 0.00 0.00 3.46
5446 6364 4.090090 TGGAAGGAAGAGAAGGTCAGTAG 58.910 47.826 0.00 0.00 0.00 2.57
5448 6366 4.158949 GGAAGGAAGAGAAGGTCAGTAGTC 59.841 50.000 0.00 0.00 0.00 2.59
5457 6375 3.300239 AGGTCAGTAGTCTAGCGGAAT 57.700 47.619 0.00 0.00 0.00 3.01
5458 6376 3.633418 AGGTCAGTAGTCTAGCGGAATT 58.367 45.455 0.00 0.00 0.00 2.17
5483 6401 2.681848 CAGCAAGAGATCCGCATCTTTT 59.318 45.455 0.00 0.00 39.71 2.27
5496 6414 5.762711 TCCGCATCTTTTATTATGCTGCTAA 59.237 36.000 0.00 0.00 45.03 3.09
5497 6415 6.430925 TCCGCATCTTTTATTATGCTGCTAAT 59.569 34.615 0.00 5.53 45.03 1.73
5498 6416 7.606073 TCCGCATCTTTTATTATGCTGCTAATA 59.394 33.333 0.00 4.61 45.03 0.98
5499 6417 8.236586 CCGCATCTTTTATTATGCTGCTAATAA 58.763 33.333 14.61 14.61 45.03 1.40
5500 6418 9.611284 CGCATCTTTTATTATGCTGCTAATAAA 57.389 29.630 20.52 20.52 45.03 1.40
5531 6449 9.683069 ATTTTCATCATATGCCTATTTCGTTTC 57.317 29.630 0.00 0.00 0.00 2.78
5532 6450 7.800155 TTCATCATATGCCTATTTCGTTTCA 57.200 32.000 0.00 0.00 0.00 2.69
5533 6451 7.189693 TCATCATATGCCTATTTCGTTTCAC 57.810 36.000 0.00 0.00 0.00 3.18
5534 6452 6.765512 TCATCATATGCCTATTTCGTTTCACA 59.234 34.615 0.00 0.00 0.00 3.58
5535 6453 6.993786 TCATATGCCTATTTCGTTTCACAA 57.006 33.333 0.00 0.00 0.00 3.33
5536 6454 7.384439 TCATATGCCTATTTCGTTTCACAAA 57.616 32.000 0.00 0.00 0.00 2.83
5537 6455 7.247728 TCATATGCCTATTTCGTTTCACAAAC 58.752 34.615 0.00 0.00 38.02 2.93
5538 6456 4.902443 TGCCTATTTCGTTTCACAAACA 57.098 36.364 0.40 0.00 41.44 2.83
5539 6457 5.446143 TGCCTATTTCGTTTCACAAACAT 57.554 34.783 0.40 0.00 41.44 2.71
5540 6458 5.457140 TGCCTATTTCGTTTCACAAACATC 58.543 37.500 0.40 0.00 41.44 3.06
5541 6459 4.553429 GCCTATTTCGTTTCACAAACATCG 59.447 41.667 0.40 0.00 41.44 3.84
5542 6460 5.615984 GCCTATTTCGTTTCACAAACATCGA 60.616 40.000 0.00 0.00 41.44 3.59
5543 6461 6.542852 CCTATTTCGTTTCACAAACATCGAT 58.457 36.000 0.00 0.00 41.44 3.59
5544 6462 7.675403 GCCTATTTCGTTTCACAAACATCGATA 60.675 37.037 0.00 0.00 41.44 2.92
5545 6463 8.335356 CCTATTTCGTTTCACAAACATCGATAT 58.665 33.333 0.00 0.00 41.44 1.63
5553 6471 9.885743 GTTTCACAAACATCGATATATTTTTGC 57.114 29.630 0.00 0.00 41.04 3.68
5554 6472 9.631452 TTTCACAAACATCGATATATTTTTGCA 57.369 25.926 0.00 0.00 0.00 4.08
5555 6473 8.613613 TCACAAACATCGATATATTTTTGCAC 57.386 30.769 0.00 0.00 0.00 4.57
5556 6474 8.239998 TCACAAACATCGATATATTTTTGCACA 58.760 29.630 0.00 0.00 0.00 4.57
5557 6475 8.858186 CACAAACATCGATATATTTTTGCACAA 58.142 29.630 0.00 0.00 0.00 3.33
5558 6476 9.416794 ACAAACATCGATATATTTTTGCACAAA 57.583 25.926 0.00 0.00 0.00 2.83
5559 6477 9.674208 CAAACATCGATATATTTTTGCACAAAC 57.326 29.630 0.00 0.00 0.00 2.93
5560 6478 9.638239 AAACATCGATATATTTTTGCACAAACT 57.362 25.926 0.00 0.00 0.00 2.66
5561 6479 8.841444 ACATCGATATATTTTTGCACAAACTC 57.159 30.769 0.00 0.00 0.00 3.01
5562 6480 7.639850 ACATCGATATATTTTTGCACAAACTCG 59.360 33.333 0.00 7.44 0.00 4.18
5563 6481 6.482835 TCGATATATTTTTGCACAAACTCGG 58.517 36.000 15.38 1.49 0.00 4.63
5564 6482 6.092944 TCGATATATTTTTGCACAAACTCGGT 59.907 34.615 15.38 0.00 0.00 4.69
5565 6483 6.410914 CGATATATTTTTGCACAAACTCGGTC 59.589 38.462 0.00 0.00 0.00 4.79
5566 6484 3.791973 ATTTTTGCACAAACTCGGTCA 57.208 38.095 0.00 0.00 0.00 4.02
5567 6485 3.577649 TTTTTGCACAAACTCGGTCAA 57.422 38.095 0.00 0.00 0.00 3.18
5568 6486 3.577649 TTTTGCACAAACTCGGTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
5569 6487 2.553079 TTGCACAAACTCGGTCAAAC 57.447 45.000 0.00 0.00 0.00 2.93
5570 6488 0.375454 TGCACAAACTCGGTCAAACG 59.625 50.000 0.00 0.00 0.00 3.60
5571 6489 0.375803 GCACAAACTCGGTCAAACGT 59.624 50.000 0.00 0.00 34.94 3.99
5572 6490 1.202098 GCACAAACTCGGTCAAACGTT 60.202 47.619 0.00 0.00 34.94 3.99
5573 6491 2.030701 GCACAAACTCGGTCAAACGTTA 59.969 45.455 0.00 0.00 34.94 3.18
5574 6492 3.303526 GCACAAACTCGGTCAAACGTTAT 60.304 43.478 0.00 0.00 34.94 1.89
5575 6493 4.208355 CACAAACTCGGTCAAACGTTATG 58.792 43.478 0.00 2.59 34.94 1.90
5576 6494 4.025563 CACAAACTCGGTCAAACGTTATGA 60.026 41.667 0.00 5.15 34.94 2.15
5577 6495 4.753107 ACAAACTCGGTCAAACGTTATGAT 59.247 37.500 0.00 0.00 34.94 2.45
5578 6496 5.927689 ACAAACTCGGTCAAACGTTATGATA 59.072 36.000 0.00 0.00 34.94 2.15
5579 6497 6.090358 ACAAACTCGGTCAAACGTTATGATAG 59.910 38.462 0.00 9.22 34.94 2.08
5580 6498 5.320549 ACTCGGTCAAACGTTATGATAGT 57.679 39.130 0.00 9.75 34.94 2.12
5581 6499 5.717119 ACTCGGTCAAACGTTATGATAGTT 58.283 37.500 0.00 0.00 34.94 2.24
5582 6500 6.161381 ACTCGGTCAAACGTTATGATAGTTT 58.839 36.000 0.00 0.00 38.46 2.66
5589 6507 6.980051 AAACGTTATGATAGTTTGACCCTC 57.020 37.500 0.00 0.00 36.81 4.30
5590 6508 5.019785 ACGTTATGATAGTTTGACCCTCC 57.980 43.478 0.00 0.00 0.00 4.30
5591 6509 4.468510 ACGTTATGATAGTTTGACCCTCCA 59.531 41.667 0.00 0.00 0.00 3.86
5592 6510 5.046159 ACGTTATGATAGTTTGACCCTCCAA 60.046 40.000 0.00 0.00 0.00 3.53
5593 6511 5.293569 CGTTATGATAGTTTGACCCTCCAAC 59.706 44.000 0.00 0.00 0.00 3.77
5594 6512 4.927267 ATGATAGTTTGACCCTCCAACA 57.073 40.909 0.00 0.00 0.00 3.33
5595 6513 4.715534 TGATAGTTTGACCCTCCAACAA 57.284 40.909 0.00 0.00 0.00 2.83
5596 6514 5.055265 TGATAGTTTGACCCTCCAACAAA 57.945 39.130 0.00 0.00 0.00 2.83
5597 6515 5.070001 TGATAGTTTGACCCTCCAACAAAG 58.930 41.667 0.00 0.00 34.86 2.77
5598 6516 3.382083 AGTTTGACCCTCCAACAAAGT 57.618 42.857 0.00 0.00 34.86 2.66
5599 6517 3.708451 AGTTTGACCCTCCAACAAAGTT 58.292 40.909 0.00 0.00 34.79 2.66
5600 6518 3.447229 AGTTTGACCCTCCAACAAAGTTG 59.553 43.478 3.00 3.00 34.79 3.16
5601 6519 2.065899 TGACCCTCCAACAAAGTTGG 57.934 50.000 20.09 20.09 40.87 3.77
5602 6520 1.566703 TGACCCTCCAACAAAGTTGGA 59.433 47.619 25.17 25.17 45.61 3.53
5603 6521 2.024846 TGACCCTCCAACAAAGTTGGAA 60.025 45.455 26.25 12.88 46.85 3.53
5604 6522 2.623416 GACCCTCCAACAAAGTTGGAAG 59.377 50.000 26.25 21.51 46.85 3.46
5605 6523 2.024369 ACCCTCCAACAAAGTTGGAAGT 60.024 45.455 26.25 22.95 46.85 3.01
5606 6524 3.203487 ACCCTCCAACAAAGTTGGAAGTA 59.797 43.478 26.25 9.67 46.85 2.24
5607 6525 3.568430 CCCTCCAACAAAGTTGGAAGTAC 59.432 47.826 26.25 0.00 46.85 2.73
5608 6526 4.204012 CCTCCAACAAAGTTGGAAGTACA 58.796 43.478 26.25 8.75 46.85 2.90
5609 6527 4.036380 CCTCCAACAAAGTTGGAAGTACAC 59.964 45.833 26.25 0.00 46.85 2.90
5610 6528 4.850680 TCCAACAAAGTTGGAAGTACACT 58.149 39.130 24.83 0.00 44.90 3.55
5611 6529 4.879545 TCCAACAAAGTTGGAAGTACACTC 59.120 41.667 24.83 0.00 44.90 3.51
5612 6530 4.881850 CCAACAAAGTTGGAAGTACACTCT 59.118 41.667 21.24 0.00 42.06 3.24
5613 6531 5.357032 CCAACAAAGTTGGAAGTACACTCTT 59.643 40.000 21.24 0.00 42.06 2.85
5614 6532 6.127730 CCAACAAAGTTGGAAGTACACTCTTT 60.128 38.462 21.24 0.00 42.06 2.52
5615 6533 7.066525 CCAACAAAGTTGGAAGTACACTCTTTA 59.933 37.037 21.24 0.00 42.06 1.85
5616 6534 8.455682 CAACAAAGTTGGAAGTACACTCTTTAA 58.544 33.333 2.05 0.00 0.00 1.52
5617 6535 8.570068 ACAAAGTTGGAAGTACACTCTTTAAA 57.430 30.769 0.00 0.00 0.00 1.52
5618 6536 8.674607 ACAAAGTTGGAAGTACACTCTTTAAAG 58.325 33.333 9.04 9.04 0.00 1.85
5619 6537 8.889717 CAAAGTTGGAAGTACACTCTTTAAAGA 58.110 33.333 16.85 16.85 0.00 2.52
5620 6538 9.457436 AAAGTTGGAAGTACACTCTTTAAAGAA 57.543 29.630 18.25 1.42 34.03 2.52
5621 6539 8.434733 AGTTGGAAGTACACTCTTTAAAGAAC 57.565 34.615 18.25 13.23 34.03 3.01
5622 6540 7.224167 AGTTGGAAGTACACTCTTTAAAGAACG 59.776 37.037 18.25 13.97 34.03 3.95
5623 6541 5.987347 TGGAAGTACACTCTTTAAAGAACGG 59.013 40.000 18.25 12.59 34.03 4.44
5624 6542 6.183360 TGGAAGTACACTCTTTAAAGAACGGA 60.183 38.462 18.25 6.84 34.03 4.69
5625 6543 6.365518 GGAAGTACACTCTTTAAAGAACGGAG 59.634 42.308 18.25 9.21 34.03 4.63
5626 6544 5.780984 AGTACACTCTTTAAAGAACGGAGG 58.219 41.667 18.25 8.55 34.03 4.30
5627 6545 4.950205 ACACTCTTTAAAGAACGGAGGA 57.050 40.909 18.25 0.00 34.03 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 103 3.417779 GGCTGGGGGAGGGGTAAC 61.418 72.222 0.00 0.00 0.00 2.50
98 104 3.961651 TGGCTGGGGGAGGGGTAA 61.962 66.667 0.00 0.00 0.00 2.85
99 105 4.431524 CTGGCTGGGGGAGGGGTA 62.432 72.222 0.00 0.00 0.00 3.69
303 334 0.371645 GGAACAGCTCTCGCAATTCG 59.628 55.000 0.00 0.00 39.10 3.34
334 365 4.270008 ACAAAGCTAGCCGATTATTTGGT 58.730 39.130 21.73 7.17 33.14 3.67
343 376 4.927425 CAGTAAAACTACAAAGCTAGCCGA 59.073 41.667 12.13 0.00 0.00 5.54
344 377 4.435651 GCAGTAAAACTACAAAGCTAGCCG 60.436 45.833 12.13 2.68 0.00 5.52
347 380 5.840940 ACGCAGTAAAACTACAAAGCTAG 57.159 39.130 0.00 0.00 41.94 3.42
408 441 3.436496 GATGTCTACGTCTTCCCGAAAG 58.564 50.000 0.00 0.00 36.22 2.62
426 459 0.670546 AACCACGCAACCTCTCGATG 60.671 55.000 0.00 0.00 0.00 3.84
448 492 4.612932 ACCTACTCAACTACGATCGAAC 57.387 45.455 24.34 0.00 0.00 3.95
450 494 9.363763 CTATATAACCTACTCAACTACGATCGA 57.636 37.037 24.34 4.52 0.00 3.59
451 495 8.602328 CCTATATAACCTACTCAACTACGATCG 58.398 40.741 14.88 14.88 0.00 3.69
462 506 6.155136 GCGGACAAACCTATATAACCTACTC 58.845 44.000 0.00 0.00 36.31 2.59
463 507 5.278660 CGCGGACAAACCTATATAACCTACT 60.279 44.000 0.00 0.00 36.31 2.57
466 510 3.801293 GCGCGGACAAACCTATATAACCT 60.801 47.826 8.83 0.00 36.31 3.50
467 511 2.477754 GCGCGGACAAACCTATATAACC 59.522 50.000 8.83 0.00 36.31 2.85
468 512 3.387397 AGCGCGGACAAACCTATATAAC 58.613 45.455 8.83 0.00 36.31 1.89
469 513 3.645884 GAGCGCGGACAAACCTATATAA 58.354 45.455 8.83 0.00 36.31 0.98
470 514 2.351060 CGAGCGCGGACAAACCTATATA 60.351 50.000 8.83 0.00 36.31 0.86
471 515 1.602165 CGAGCGCGGACAAACCTATAT 60.602 52.381 8.83 0.00 36.31 0.86
472 516 0.248743 CGAGCGCGGACAAACCTATA 60.249 55.000 8.83 0.00 36.31 1.31
475 519 2.781595 AATCGAGCGCGGACAAACCT 62.782 55.000 10.69 0.00 38.28 3.50
481 527 3.564027 CCCAAATCGAGCGCGGAC 61.564 66.667 10.69 0.00 38.28 4.79
482 528 4.830765 CCCCAAATCGAGCGCGGA 62.831 66.667 10.69 3.79 38.28 5.54
524 570 4.260784 GGTAACGAGCCAAGCAATCAATAG 60.261 45.833 0.00 0.00 0.00 1.73
527 573 1.810151 GGTAACGAGCCAAGCAATCAA 59.190 47.619 0.00 0.00 0.00 2.57
533 579 1.202031 CGATTTGGTAACGAGCCAAGC 60.202 52.381 9.23 6.36 45.47 4.01
535 581 2.172851 ACGATTTGGTAACGAGCCAA 57.827 45.000 0.00 0.00 43.51 4.52
565 612 2.141517 CATAGCTGAAGCATCGGAAGG 58.858 52.381 0.99 0.00 45.16 3.46
619 668 4.153117 CACAGGAAGTCAATAGTCTTGTGC 59.847 45.833 2.78 0.00 40.85 4.57
622 671 7.388776 TGATTTCACAGGAAGTCAATAGTCTTG 59.611 37.037 0.89 0.00 43.94 3.02
623 672 7.389053 GTGATTTCACAGGAAGTCAATAGTCTT 59.611 37.037 5.84 0.00 46.93 3.01
624 673 6.876257 GTGATTTCACAGGAAGTCAATAGTCT 59.124 38.462 5.84 0.00 46.93 3.24
625 674 6.092807 GGTGATTTCACAGGAAGTCAATAGTC 59.907 42.308 12.43 0.00 46.93 2.59
627 676 6.176183 AGGTGATTTCACAGGAAGTCAATAG 58.824 40.000 12.43 0.00 46.93 1.73
628 677 6.126863 AGGTGATTTCACAGGAAGTCAATA 57.873 37.500 12.43 0.00 46.93 1.90
630 679 4.389374 GAGGTGATTTCACAGGAAGTCAA 58.611 43.478 12.43 0.00 46.93 3.18
637 686 6.713893 AGAGCATCGAGGTGATTTCACAGG 62.714 50.000 12.43 1.66 44.62 4.00
664 727 0.680921 ACAGCAAGCATACCGGCAAT 60.681 50.000 0.00 0.00 35.83 3.56
685 751 1.069227 CGACCAAAGCAACTGCCTTAC 60.069 52.381 0.00 0.00 43.38 2.34
702 768 0.889306 AGGAACACACTCCTAGCGAC 59.111 55.000 0.00 0.00 44.43 5.19
761 827 0.249741 GTTACCACACTCAGGCACGT 60.250 55.000 0.00 0.00 0.00 4.49
865 936 7.540745 ACGTTTGTGAAAAATACATCAATAGGC 59.459 33.333 0.00 0.00 0.00 3.93
888 1349 4.527509 AGACATGAATGAGACAGAACGT 57.472 40.909 0.00 0.00 0.00 3.99
891 1352 5.233083 ACCAAGACATGAATGAGACAGAA 57.767 39.130 0.00 0.00 0.00 3.02
971 1432 1.877637 ACACGTTGCTGAGTTATGCA 58.122 45.000 0.00 0.00 37.42 3.96
985 1446 3.365465 CGAGTCATCTCTCAGAAACACGT 60.365 47.826 0.00 0.00 38.45 4.49
1025 1486 4.554036 GACCAGGCATCTCCCGGC 62.554 72.222 0.00 0.00 34.51 6.13
1067 1528 1.409227 CCTCGCGCTATCATCATCGC 61.409 60.000 5.56 0.00 43.62 4.58
1329 1790 3.706086 CCCACTTATTCCCCATTTTGGAG 59.294 47.826 0.00 0.00 40.96 3.86
1365 1826 4.439057 AGCTTGAAACTGAACTTACACGA 58.561 39.130 0.00 0.00 0.00 4.35
1389 1850 7.315142 TGATGAATGCTGAACCTGAAAAATAC 58.685 34.615 0.00 0.00 0.00 1.89
1534 2340 5.942236 AGAGGCATATCACGCAAAATATCAT 59.058 36.000 0.00 0.00 0.00 2.45
1555 2361 5.123936 TCCATGCATGAGAAGATCAAAGAG 58.876 41.667 28.31 5.90 42.53 2.85
1767 2607 6.100404 AGGTTGCAGCAAGAAAATAATCAA 57.900 33.333 8.49 0.00 0.00 2.57
1782 2622 7.448748 AGTTTGGTACTTTATTAGGTTGCAG 57.551 36.000 0.00 0.00 31.29 4.41
2253 3094 2.450160 CACAAAACTCGCAAGGAACAC 58.550 47.619 0.00 0.00 38.47 3.32
2320 3161 7.410800 AACTATGTTTTCGTAACAACATCGA 57.589 32.000 9.28 0.00 41.67 3.59
2345 3186 8.267620 AGGAACATCTAGATGAATTGGTATCA 57.732 34.615 34.16 0.00 41.20 2.15
2367 3208 5.580691 CACTTAGATGTGCAATAACGAAGGA 59.419 40.000 0.00 0.00 0.00 3.36
2372 3213 5.576774 TGAGTCACTTAGATGTGCAATAACG 59.423 40.000 0.00 0.00 37.81 3.18
2434 3275 1.271379 ACGCGGAGATTTGTGTCTGTA 59.729 47.619 12.47 0.00 0.00 2.74
2435 3276 0.033504 ACGCGGAGATTTGTGTCTGT 59.966 50.000 12.47 0.00 0.00 3.41
2436 3277 1.990799 TACGCGGAGATTTGTGTCTG 58.009 50.000 12.47 0.00 0.00 3.51
2438 3279 3.732943 CTTTTACGCGGAGATTTGTGTC 58.267 45.455 12.47 0.00 0.00 3.67
2521 3368 7.385267 AGCAGGAAATAAACATTATTTGTGCA 58.615 30.769 24.19 0.00 38.99 4.57
2549 3396 4.202010 GCACAAAAGGTTCTAAGCAAGTGA 60.202 41.667 0.00 0.00 0.00 3.41
2627 3474 9.726438 AAATGTAGGTCAATAAGCCTGATATAC 57.274 33.333 0.00 0.00 36.38 1.47
2674 3521 8.586570 AGTAATCGTGCAAAATGAATGAAAAA 57.413 26.923 0.00 0.00 0.00 1.94
2784 3631 6.829298 TGTTGGGTAACAGTCACTAAATGAAA 59.171 34.615 0.00 0.00 41.66 2.69
2785 3632 6.358178 TGTTGGGTAACAGTCACTAAATGAA 58.642 36.000 0.00 0.00 41.66 2.57
2804 3651 8.506168 ACAGTATTGTTATCCAGTTATGTTGG 57.494 34.615 0.00 0.00 32.28 3.77
2844 3691 8.790718 CCAAGGAAATTTGATAGGATGTATCAG 58.209 37.037 0.00 0.00 35.62 2.90
3088 3936 3.120792 GTTGCTTGTCGTCTTACAGTCA 58.879 45.455 0.00 0.00 0.00 3.41
3108 3956 2.435372 TGCCAGTCAAACAGAAAGGT 57.565 45.000 0.00 0.00 0.00 3.50
3217 4068 5.688807 CTCTGGAAGTCCATGGAAATACAT 58.311 41.667 18.20 0.00 46.46 2.29
3379 4230 6.353323 TGTTCTGAAGGTTAGTGACAATGAA 58.647 36.000 0.00 0.00 0.00 2.57
3685 4536 4.833390 AGTACAGACCAGGTAAATTGCTC 58.167 43.478 0.00 0.00 0.00 4.26
3981 4840 0.692419 GGGAGCTCCATCTTCCAGGA 60.692 60.000 33.29 0.00 37.91 3.86
4081 4940 2.515523 AGCGCATGCAGGGATCAC 60.516 61.111 19.57 0.00 46.23 3.06
4100 4959 2.332362 CTGATGCCATTGCCGCTGAC 62.332 60.000 0.00 0.00 36.33 3.51
4307 5166 2.870411 GTTGACAAGAGCGTACAGGTTT 59.130 45.455 0.00 0.00 0.00 3.27
4477 5336 2.062087 GCTGCTGCAAATGACATCAGC 61.062 52.381 16.77 16.77 46.25 4.26
4483 5342 1.513586 GCTCGCTGCTGCAAATGAC 60.514 57.895 16.29 0.00 39.64 3.06
4487 5346 4.648626 AGGGCTCGCTGCTGCAAA 62.649 61.111 16.29 2.03 42.39 3.68
4535 5394 6.251549 GCAAGAGAAATCCTTTGTCGTATTC 58.748 40.000 0.00 0.00 37.93 1.75
4543 5402 4.097589 GGATGAGGCAAGAGAAATCCTTTG 59.902 45.833 0.00 0.00 32.52 2.77
4777 5636 0.329596 ATTGGAGGCCAGTTGGAGAC 59.670 55.000 5.01 0.00 37.39 3.36
4813 5672 6.156949 ACTCAGGATAATGGAGCAAAGAACTA 59.843 38.462 0.00 0.00 31.88 2.24
4814 5673 5.045286 ACTCAGGATAATGGAGCAAAGAACT 60.045 40.000 0.00 0.00 31.88 3.01
4823 5692 7.521669 AGGGAATTTTACTCAGGATAATGGAG 58.478 38.462 0.00 0.00 34.85 3.86
4833 5702 3.600388 AGCACGAGGGAATTTTACTCAG 58.400 45.455 0.00 0.00 0.00 3.35
4834 5703 3.596214 GAGCACGAGGGAATTTTACTCA 58.404 45.455 0.00 0.00 0.00 3.41
4853 5722 1.012086 CATCATGCAGGTTGGTCGAG 58.988 55.000 0.00 0.00 0.00 4.04
4868 5737 1.375908 GGCCGAAGTGAGTGCATCA 60.376 57.895 0.00 0.00 34.79 3.07
4874 5743 2.207924 AAGGACGGCCGAAGTGAGT 61.208 57.895 35.90 7.12 39.96 3.41
4882 5751 1.154035 GCATTTTCAAGGACGGCCG 60.154 57.895 26.86 26.86 39.96 6.13
4893 5762 2.831526 ACATAGTTGGGTGGGCATTTTC 59.168 45.455 0.00 0.00 0.00 2.29
4905 5774 5.714806 ACAATGAACCCCTTTACATAGTTGG 59.285 40.000 0.00 0.00 0.00 3.77
4919 5788 1.950909 TGTTTGGACGACAATGAACCC 59.049 47.619 0.00 0.00 39.21 4.11
4930 5799 1.007964 TTTGGCGCATGTTTGGACG 60.008 52.632 10.83 0.00 0.00 4.79
4948 5817 2.993264 GGGCAGCAATGTGGCAGT 60.993 61.111 10.33 0.00 44.72 4.40
4976 5845 1.007721 CTTCCTCCCTCTCTCCCAGAA 59.992 57.143 0.00 0.00 0.00 3.02
4978 5847 0.398381 CCTTCCTCCCTCTCTCCCAG 60.398 65.000 0.00 0.00 0.00 4.45
4979 5848 0.855855 TCCTTCCTCCCTCTCTCCCA 60.856 60.000 0.00 0.00 0.00 4.37
4980 5849 0.105709 CTCCTTCCTCCCTCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
5007 5877 4.907457 CCCATGTGGCATCCTACC 57.093 61.111 0.00 0.00 0.00 3.18
5031 5901 4.249661 GGAGAAAGAGTCAAAGCTACCAG 58.750 47.826 0.00 0.00 0.00 4.00
5090 5968 3.133003 ACAAGAGGATCAATACGGTCCAG 59.867 47.826 0.00 0.00 37.82 3.86
5132 6017 2.288666 AGCGCTCACTTTGTTGAAGAA 58.711 42.857 2.64 0.00 38.77 2.52
5134 6019 2.378806 CAAGCGCTCACTTTGTTGAAG 58.621 47.619 12.06 0.00 41.32 3.02
5306 6204 1.330234 ACATCACAACATGCTGGCAA 58.670 45.000 0.45 0.00 0.00 4.52
5342 6240 9.290483 GTCTTCGATTTCGCAGATATAATCATA 57.710 33.333 5.66 0.00 42.83 2.15
5343 6241 7.276658 GGTCTTCGATTTCGCAGATATAATCAT 59.723 37.037 5.66 0.00 42.83 2.45
5344 6242 6.586463 GGTCTTCGATTTCGCAGATATAATCA 59.414 38.462 5.66 0.00 42.83 2.57
5345 6243 6.586463 TGGTCTTCGATTTCGCAGATATAATC 59.414 38.462 5.66 0.00 42.83 1.75
5346 6244 6.455647 TGGTCTTCGATTTCGCAGATATAAT 58.544 36.000 5.66 0.00 42.83 1.28
5347 6245 5.838529 TGGTCTTCGATTTCGCAGATATAA 58.161 37.500 5.66 0.00 42.83 0.98
5399 6316 2.040442 TCCCGGATCTCCCAAGCA 59.960 61.111 0.73 0.00 34.14 3.91
5406 6323 1.202580 CCATGTGAACTCCCGGATCTC 60.203 57.143 0.73 0.00 0.00 2.75
5439 6357 3.117046 GCAATTCCGCTAGACTACTGAC 58.883 50.000 0.00 0.00 0.00 3.51
5446 6364 0.375106 GCTGTGCAATTCCGCTAGAC 59.625 55.000 0.00 0.00 0.00 2.59
5448 6366 0.804364 TTGCTGTGCAATTCCGCTAG 59.196 50.000 0.45 0.00 43.99 3.42
5457 6375 1.300971 GCGGATCTCTTGCTGTGCAA 61.301 55.000 4.87 4.87 46.80 4.08
5458 6376 1.742880 GCGGATCTCTTGCTGTGCA 60.743 57.895 0.00 0.00 36.47 4.57
5467 6385 6.734104 GCATAATAAAAGATGCGGATCTCT 57.266 37.500 20.43 12.62 38.03 3.10
5505 6423 9.683069 GAAACGAAATAGGCATATGATGAAAAT 57.317 29.630 6.97 0.00 0.00 1.82
5506 6424 8.681806 TGAAACGAAATAGGCATATGATGAAAA 58.318 29.630 6.97 0.00 0.00 2.29
5507 6425 8.128582 GTGAAACGAAATAGGCATATGATGAAA 58.871 33.333 6.97 0.00 0.00 2.69
5508 6426 7.281999 TGTGAAACGAAATAGGCATATGATGAA 59.718 33.333 6.97 0.00 42.39 2.57
5509 6427 6.765512 TGTGAAACGAAATAGGCATATGATGA 59.234 34.615 6.97 0.00 42.39 2.92
5510 6428 6.958255 TGTGAAACGAAATAGGCATATGATG 58.042 36.000 6.97 0.00 42.39 3.07
5511 6429 7.566760 TTGTGAAACGAAATAGGCATATGAT 57.433 32.000 6.97 0.00 42.39 2.45
5512 6430 6.993786 TTGTGAAACGAAATAGGCATATGA 57.006 33.333 6.97 0.00 42.39 2.15
5513 6431 7.026562 TGTTTGTGAAACGAAATAGGCATATG 58.973 34.615 0.00 0.00 42.99 1.78
5514 6432 7.151999 TGTTTGTGAAACGAAATAGGCATAT 57.848 32.000 0.00 0.00 42.99 1.78
5515 6433 6.561737 TGTTTGTGAAACGAAATAGGCATA 57.438 33.333 0.00 0.00 42.99 3.14
5516 6434 5.446143 TGTTTGTGAAACGAAATAGGCAT 57.554 34.783 0.00 0.00 42.99 4.40
5517 6435 4.902443 TGTTTGTGAAACGAAATAGGCA 57.098 36.364 0.00 0.00 42.99 4.75
5518 6436 4.553429 CGATGTTTGTGAAACGAAATAGGC 59.447 41.667 0.00 0.00 42.99 3.93
5519 6437 5.922546 TCGATGTTTGTGAAACGAAATAGG 58.077 37.500 0.00 0.00 42.99 2.57
5527 6445 9.885743 GCAAAAATATATCGATGTTTGTGAAAC 57.114 29.630 18.98 0.00 34.74 2.78
5528 6446 9.631452 TGCAAAAATATATCGATGTTTGTGAAA 57.369 25.926 18.98 9.16 34.74 2.69
5529 6447 9.071221 GTGCAAAAATATATCGATGTTTGTGAA 57.929 29.630 18.98 10.99 34.74 3.18
5530 6448 8.239998 TGTGCAAAAATATATCGATGTTTGTGA 58.760 29.630 18.98 8.03 34.74 3.58
5531 6449 8.392124 TGTGCAAAAATATATCGATGTTTGTG 57.608 30.769 8.54 12.16 35.50 3.33
5532 6450 8.978564 TTGTGCAAAAATATATCGATGTTTGT 57.021 26.923 8.54 0.00 0.00 2.83
5533 6451 9.674208 GTTTGTGCAAAAATATATCGATGTTTG 57.326 29.630 8.54 11.04 31.33 2.93
5534 6452 9.638239 AGTTTGTGCAAAAATATATCGATGTTT 57.362 25.926 8.54 3.93 31.33 2.83
5535 6453 9.289303 GAGTTTGTGCAAAAATATATCGATGTT 57.711 29.630 8.54 0.00 31.33 2.71
5536 6454 7.639850 CGAGTTTGTGCAAAAATATATCGATGT 59.360 33.333 17.34 3.54 31.33 3.06
5537 6455 7.112009 CCGAGTTTGTGCAAAAATATATCGATG 59.888 37.037 21.09 9.25 31.33 3.84
5538 6456 7.132213 CCGAGTTTGTGCAAAAATATATCGAT 58.868 34.615 21.09 2.16 31.33 3.59
5539 6457 6.092944 ACCGAGTTTGTGCAAAAATATATCGA 59.907 34.615 21.09 0.00 31.33 3.59
5540 6458 6.255215 ACCGAGTTTGTGCAAAAATATATCG 58.745 36.000 5.11 12.38 31.33 2.92
5541 6459 7.247728 TGACCGAGTTTGTGCAAAAATATATC 58.752 34.615 5.11 1.66 31.33 1.63
5542 6460 7.151999 TGACCGAGTTTGTGCAAAAATATAT 57.848 32.000 5.11 0.00 31.33 0.86
5543 6461 6.561737 TGACCGAGTTTGTGCAAAAATATA 57.438 33.333 5.11 0.00 31.33 0.86
5544 6462 5.446143 TGACCGAGTTTGTGCAAAAATAT 57.554 34.783 5.11 0.00 31.33 1.28
5545 6463 4.902443 TGACCGAGTTTGTGCAAAAATA 57.098 36.364 5.11 0.00 31.33 1.40
5546 6464 3.791973 TGACCGAGTTTGTGCAAAAAT 57.208 38.095 5.11 0.00 31.33 1.82
5547 6465 3.577649 TTGACCGAGTTTGTGCAAAAA 57.422 38.095 0.00 0.00 31.33 1.94
5548 6466 3.246619 GTTTGACCGAGTTTGTGCAAAA 58.753 40.909 0.00 0.00 31.33 2.44
5549 6467 2.729467 CGTTTGACCGAGTTTGTGCAAA 60.729 45.455 0.00 0.00 0.00 3.68
5550 6468 1.202087 CGTTTGACCGAGTTTGTGCAA 60.202 47.619 0.00 0.00 0.00 4.08
5551 6469 0.375454 CGTTTGACCGAGTTTGTGCA 59.625 50.000 0.00 0.00 0.00 4.57
5552 6470 0.375803 ACGTTTGACCGAGTTTGTGC 59.624 50.000 0.00 0.00 0.00 4.57
5553 6471 2.817538 AACGTTTGACCGAGTTTGTG 57.182 45.000 0.00 0.00 0.00 3.33
5554 6472 4.121317 TCATAACGTTTGACCGAGTTTGT 58.879 39.130 5.91 0.00 0.00 2.83
5555 6473 4.718858 TCATAACGTTTGACCGAGTTTG 57.281 40.909 5.91 0.00 0.00 2.93
5556 6474 6.161381 ACTATCATAACGTTTGACCGAGTTT 58.839 36.000 5.91 0.00 0.00 2.66
5557 6475 5.717119 ACTATCATAACGTTTGACCGAGTT 58.283 37.500 5.91 0.00 0.00 3.01
5558 6476 5.320549 ACTATCATAACGTTTGACCGAGT 57.679 39.130 5.91 11.07 0.00 4.18
5559 6477 6.309494 TCAAACTATCATAACGTTTGACCGAG 59.691 38.462 5.91 10.53 46.60 4.63
5560 6478 6.157904 TCAAACTATCATAACGTTTGACCGA 58.842 36.000 5.91 0.00 46.60 4.69
5561 6479 6.397831 TCAAACTATCATAACGTTTGACCG 57.602 37.500 5.91 7.50 46.60 4.79
5565 6483 6.183360 GGAGGGTCAAACTATCATAACGTTTG 60.183 42.308 5.91 5.11 45.29 2.93
5566 6484 5.878669 GGAGGGTCAAACTATCATAACGTTT 59.121 40.000 5.91 0.00 0.00 3.60
5567 6485 5.046159 TGGAGGGTCAAACTATCATAACGTT 60.046 40.000 5.88 5.88 0.00 3.99
5568 6486 4.468510 TGGAGGGTCAAACTATCATAACGT 59.531 41.667 0.00 0.00 0.00 3.99
5569 6487 5.018539 TGGAGGGTCAAACTATCATAACG 57.981 43.478 0.00 0.00 0.00 3.18
5570 6488 6.177610 TGTTGGAGGGTCAAACTATCATAAC 58.822 40.000 0.00 0.00 0.00 1.89
5571 6489 6.381498 TGTTGGAGGGTCAAACTATCATAA 57.619 37.500 0.00 0.00 0.00 1.90
5572 6490 6.381498 TTGTTGGAGGGTCAAACTATCATA 57.619 37.500 0.00 0.00 0.00 2.15
5573 6491 4.927267 TGTTGGAGGGTCAAACTATCAT 57.073 40.909 0.00 0.00 0.00 2.45
5574 6492 4.715534 TTGTTGGAGGGTCAAACTATCA 57.284 40.909 0.00 0.00 0.00 2.15
5575 6493 5.070685 ACTTTGTTGGAGGGTCAAACTATC 58.929 41.667 0.00 0.00 0.00 2.08
5576 6494 5.061721 ACTTTGTTGGAGGGTCAAACTAT 57.938 39.130 0.00 0.00 0.00 2.12
5577 6495 4.513406 ACTTTGTTGGAGGGTCAAACTA 57.487 40.909 0.00 0.00 0.00 2.24
5578 6496 3.382083 ACTTTGTTGGAGGGTCAAACT 57.618 42.857 0.00 0.00 0.00 2.66
5579 6497 3.430236 CCAACTTTGTTGGAGGGTCAAAC 60.430 47.826 21.06 0.00 42.06 2.93
5580 6498 2.763448 CCAACTTTGTTGGAGGGTCAAA 59.237 45.455 21.06 0.00 42.06 2.69
5581 6499 2.024846 TCCAACTTTGTTGGAGGGTCAA 60.025 45.455 23.38 4.76 43.17 3.18
5582 6500 1.566703 TCCAACTTTGTTGGAGGGTCA 59.433 47.619 23.38 5.39 43.17 4.02
5583 6501 2.358322 TCCAACTTTGTTGGAGGGTC 57.642 50.000 23.38 0.00 43.17 4.46
5588 6506 4.850680 AGTGTACTTCCAACTTTGTTGGA 58.149 39.130 23.38 23.38 46.08 3.53
5589 6507 4.881850 AGAGTGTACTTCCAACTTTGTTGG 59.118 41.667 19.97 19.97 40.87 3.77
5590 6508 6.436843 AAGAGTGTACTTCCAACTTTGTTG 57.563 37.500 3.69 3.69 0.00 3.33
5591 6509 8.570068 TTAAAGAGTGTACTTCCAACTTTGTT 57.430 30.769 0.00 0.00 31.02 2.83
5592 6510 8.570068 TTTAAAGAGTGTACTTCCAACTTTGT 57.430 30.769 0.00 0.00 31.02 2.83
5593 6511 8.889717 TCTTTAAAGAGTGTACTTCCAACTTTG 58.110 33.333 13.99 0.00 31.02 2.77
5594 6512 9.457436 TTCTTTAAAGAGTGTACTTCCAACTTT 57.543 29.630 17.05 0.00 36.22 2.66
5595 6513 8.890718 GTTCTTTAAAGAGTGTACTTCCAACTT 58.109 33.333 17.05 0.00 36.22 2.66
5596 6514 7.224167 CGTTCTTTAAAGAGTGTACTTCCAACT 59.776 37.037 17.05 0.00 36.22 3.16
5597 6515 7.342942 CGTTCTTTAAAGAGTGTACTTCCAAC 58.657 38.462 17.05 7.83 36.22 3.77
5598 6516 6.480981 CCGTTCTTTAAAGAGTGTACTTCCAA 59.519 38.462 17.05 0.00 36.22 3.53
5599 6517 5.987347 CCGTTCTTTAAAGAGTGTACTTCCA 59.013 40.000 17.05 0.00 36.22 3.53
5600 6518 6.218746 TCCGTTCTTTAAAGAGTGTACTTCC 58.781 40.000 17.05 0.00 36.22 3.46
5601 6519 6.365518 CCTCCGTTCTTTAAAGAGTGTACTTC 59.634 42.308 17.05 3.05 36.22 3.01
5602 6520 6.041296 TCCTCCGTTCTTTAAAGAGTGTACTT 59.959 38.462 17.05 0.00 36.22 2.24
5603 6521 5.537674 TCCTCCGTTCTTTAAAGAGTGTACT 59.462 40.000 17.05 0.00 36.22 2.73
5604 6522 5.776744 TCCTCCGTTCTTTAAAGAGTGTAC 58.223 41.667 17.05 11.81 36.22 2.90
5606 6524 4.950205 TCCTCCGTTCTTTAAAGAGTGT 57.050 40.909 17.05 0.00 36.22 3.55


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

AutoCloner maintained by Alex Coulton.