Multiple sequence alignment - TraesCS1B01G189700

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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 TraesCS1B01G189700 chr1B 100.000 5989 0 0 554 6542 340375892 340369904 0.000000e+00 11060.0
1 TraesCS1B01G189700 chr1B 100.000 301 0 0 1 301 340376445 340376145 2.060000e-154 556.0
2 TraesCS1B01G189700 chr1B 96.591 88 1 1 6455 6542 593597919 593597834 1.900000e-30 145.0
3 TraesCS1B01G189700 chr1B 96.154 52 1 1 6403 6454 338419395 338419445 4.200000e-12 84.2
4 TraesCS1B01G189700 chr1A 94.495 5704 175 45 656 6266 312772250 312777907 0.000000e+00 8665.0
5 TraesCS1B01G189700 chr1A 97.297 185 5 0 90 274 312771721 312771905 1.370000e-81 315.0
6 TraesCS1B01G189700 chr1A 97.727 88 0 1 6455 6542 447735319 447735404 4.090000e-32 150.0
7 TraesCS1B01G189700 chr1A 94.792 96 2 1 1 93 312771593 312771688 5.290000e-31 147.0
8 TraesCS1B01G189700 chr1A 86.207 145 9 7 6277 6413 312779208 312779349 5.290000e-31 147.0
9 TraesCS1B01G189700 chr1A 96.591 88 1 2 6455 6542 109421724 109421809 1.900000e-30 145.0
10 TraesCS1B01G189700 chr1A 97.619 42 0 1 6403 6444 312863804 312863844 3.270000e-08 71.3
11 TraesCS1B01G189700 chr1D 94.427 5652 182 57 680 6266 234743150 234737567 0.000000e+00 8569.0
12 TraesCS1B01G189700 chr1D 93.370 181 7 1 90 270 234743590 234743415 5.030000e-66 263.0
13 TraesCS1B01G189700 chr1D 96.774 93 3 0 1 93 234743707 234743615 8.780000e-34 156.0
14 TraesCS1B01G189700 chr1D 90.351 114 7 4 6302 6415 234721528 234721419 5.290000e-31 147.0
15 TraesCS1B01G189700 chr7B 96.040 909 35 1 1710 2618 64038532 64039439 0.000000e+00 1478.0
16 TraesCS1B01G189700 chr7B 96.800 750 20 2 3319 4066 64039558 64040305 0.000000e+00 1249.0
17 TraesCS1B01G189700 chr7B 95.152 660 25 3 1002 1661 64037886 64038538 0.000000e+00 1035.0
18 TraesCS1B01G189700 chr7B 94.845 97 5 0 3075 3171 64039458 64039554 1.140000e-32 152.0
19 TraesCS1B01G189700 chr7A 96.364 495 14 2 3574 4066 635498627 635498135 0.000000e+00 811.0
20 TraesCS1B01G189700 chr6B 97.753 89 0 1 6454 6542 186695438 186695352 1.140000e-32 152.0
21 TraesCS1B01G189700 chr4B 96.703 91 1 1 6452 6542 97069902 97069990 4.090000e-32 150.0
22 TraesCS1B01G189700 chr2A 95.745 94 2 1 6449 6542 198905243 198905334 4.090000e-32 150.0
23 TraesCS1B01G189700 chr4A 96.629 89 1 1 6454 6542 577759947 577759861 5.290000e-31 147.0
24 TraesCS1B01G189700 chr4A 96.591 88 1 1 6455 6542 527005501 527005416 1.900000e-30 145.0
25 TraesCS1B01G189700 chr3B 95.652 92 2 1 6451 6542 804372705 804372794 5.290000e-31 147.0


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 TraesCS1B01G189700 chr1B 340369904 340376445 6541 True 5808.0 11060 100.00000 1 6542 2 chr1B.!!$R2 6541
1 TraesCS1B01G189700 chr1A 312771593 312779349 7756 False 2318.5 8665 93.19775 1 6413 4 chr1A.!!$F4 6412
2 TraesCS1B01G189700 chr1D 234737567 234743707 6140 True 2996.0 8569 94.85700 1 6266 3 chr1D.!!$R2 6265
3 TraesCS1B01G189700 chr7B 64037886 64040305 2419 False 978.5 1478 95.70925 1002 4066 4 chr7B.!!$F1 3064

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
607 647 0.030773 GTGTGCGTGTGTGAGAGAGA 59.969 55.000 0.00 0.00 0.00 3.10 F
1115 1184 0.036858 GCTCCGGAAGAAGCAGAGTT 60.037 55.000 5.23 0.00 0.00 3.01 F
2630 2735 0.179936 GTTCAGATGGGAGCTCAGGG 59.820 60.000 17.19 0.00 0.00 4.45 F
2771 2876 0.108233 CAGGAAGCTCAGCTCCTGAC 60.108 60.000 28.23 8.19 46.58 3.51 F
2997 3102 1.039785 TGAGAGGGATGCACTCCGAG 61.040 60.000 0.00 0.00 46.01 4.63 F
3804 3909 0.882927 GAACAACGCTACCACTGCCA 60.883 55.000 0.00 0.00 0.00 4.92 F
3866 3971 1.949525 TCTTCTGCTTTCAGTGCCAAC 59.050 47.619 0.00 0.00 41.10 3.77 F
5176 5300 0.179100 AGCGCATCAAGCACGATACT 60.179 50.000 11.47 0.00 46.13 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2435 1.081242 CACGCAGCAAATGTGACCC 60.081 57.895 0.00 0.0 42.31 4.46 R
2771 2876 1.589993 CGACCCATCAGTGCTAGCG 60.590 63.158 10.77 0.0 0.00 4.26 R
3461 3566 2.364324 ACGGTCTTTCTTGTACAGCTCA 59.636 45.455 0.00 0.0 0.00 4.26 R
3581 3686 2.627221 CTGCATCCTTAGCTGCTCTCTA 59.373 50.000 4.91 0.0 39.16 2.43 R
4990 5111 2.239654 CCTCCATTCAAAGCTGTCCCTA 59.760 50.000 0.00 0.0 0.00 3.53 R
5173 5297 0.241749 CGTTACCGGTGCTGACAGTA 59.758 55.000 19.93 0.0 0.00 2.74 R
5397 5524 0.391597 TCGCCTTGTTCGTCTCCTTT 59.608 50.000 0.00 0.0 0.00 3.11 R
6269 6438 0.108520 CAACCAACATGCTCCATGGC 60.109 55.000 6.96 0.0 45.16 4.40 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
31 32 6.037786 TGAATTAGTGGTAGGTCTCAAGTG 57.962 41.667 0.00 0.00 0.00 3.16
194 234 0.261991 ATCCTCCCACCTCGCTCTAA 59.738 55.000 0.00 0.00 0.00 2.10
206 246 6.424207 CCACCTCGCTCTAACTAAATAAATCC 59.576 42.308 0.00 0.00 0.00 3.01
274 314 1.828595 GAACCTTCTCTCTCCCACCTC 59.171 57.143 0.00 0.00 0.00 3.85
275 315 0.041982 ACCTTCTCTCTCCCACCTCC 59.958 60.000 0.00 0.00 0.00 4.30
276 316 0.338120 CCTTCTCTCTCCCACCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
277 317 1.687996 CCTTCTCTCTCCCACCTCCTC 60.688 61.905 0.00 0.00 0.00 3.71
278 318 1.287739 CTTCTCTCTCCCACCTCCTCT 59.712 57.143 0.00 0.00 0.00 3.69
279 319 0.923358 TCTCTCTCCCACCTCCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
280 320 0.926293 CTCTCTCCCACCTCCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
281 321 0.923358 TCTCTCCCACCTCCTCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
282 322 0.926293 CTCTCCCACCTCCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
283 323 1.287739 CTCTCCCACCTCCTCTCTCTT 59.712 57.143 0.00 0.00 0.00 2.85
284 324 1.719378 TCTCCCACCTCCTCTCTCTTT 59.281 52.381 0.00 0.00 0.00 2.52
285 325 2.107366 CTCCCACCTCCTCTCTCTTTC 58.893 57.143 0.00 0.00 0.00 2.62
286 326 1.719378 TCCCACCTCCTCTCTCTTTCT 59.281 52.381 0.00 0.00 0.00 2.52
287 327 2.112691 TCCCACCTCCTCTCTCTTTCTT 59.887 50.000 0.00 0.00 0.00 2.52
288 328 2.909662 CCCACCTCCTCTCTCTTTCTTT 59.090 50.000 0.00 0.00 0.00 2.52
289 329 3.055458 CCCACCTCCTCTCTCTTTCTTTC 60.055 52.174 0.00 0.00 0.00 2.62
290 330 3.837731 CCACCTCCTCTCTCTTTCTTTCT 59.162 47.826 0.00 0.00 0.00 2.52
291 331 4.081697 CCACCTCCTCTCTCTTTCTTTCTC 60.082 50.000 0.00 0.00 0.00 2.87
292 332 4.772100 CACCTCCTCTCTCTTTCTTTCTCT 59.228 45.833 0.00 0.00 0.00 3.10
293 333 5.016831 ACCTCCTCTCTCTTTCTTTCTCTC 58.983 45.833 0.00 0.00 0.00 3.20
294 334 5.222337 ACCTCCTCTCTCTTTCTTTCTCTCT 60.222 44.000 0.00 0.00 0.00 3.10
295 335 5.358160 CCTCCTCTCTCTTTCTTTCTCTCTC 59.642 48.000 0.00 0.00 0.00 3.20
296 336 5.261216 TCCTCTCTCTTTCTTTCTCTCTCC 58.739 45.833 0.00 0.00 0.00 3.71
297 337 4.402474 CCTCTCTCTTTCTTTCTCTCTCCC 59.598 50.000 0.00 0.00 0.00 4.30
298 338 4.349365 TCTCTCTTTCTTTCTCTCTCCCC 58.651 47.826 0.00 0.00 0.00 4.81
299 339 3.445987 TCTCTTTCTTTCTCTCTCCCCC 58.554 50.000 0.00 0.00 0.00 5.40
574 614 4.574674 AGAGAGAGAGAGAGAGAGCAAA 57.425 45.455 0.00 0.00 0.00 3.68
575 615 4.521146 AGAGAGAGAGAGAGAGAGCAAAG 58.479 47.826 0.00 0.00 0.00 2.77
576 616 3.019564 AGAGAGAGAGAGAGAGCAAAGC 58.980 50.000 0.00 0.00 0.00 3.51
577 617 2.754552 GAGAGAGAGAGAGAGCAAAGCA 59.245 50.000 0.00 0.00 0.00 3.91
578 618 2.756760 AGAGAGAGAGAGAGCAAAGCAG 59.243 50.000 0.00 0.00 0.00 4.24
579 619 2.754552 GAGAGAGAGAGAGCAAAGCAGA 59.245 50.000 0.00 0.00 0.00 4.26
580 620 2.756760 AGAGAGAGAGAGCAAAGCAGAG 59.243 50.000 0.00 0.00 0.00 3.35
581 621 1.205417 AGAGAGAGAGCAAAGCAGAGC 59.795 52.381 0.00 0.00 0.00 4.09
582 622 0.249955 AGAGAGAGCAAAGCAGAGCC 59.750 55.000 0.00 0.00 0.00 4.70
583 623 1.079266 AGAGAGCAAAGCAGAGCCG 60.079 57.895 0.00 0.00 0.00 5.52
584 624 1.375268 GAGAGCAAAGCAGAGCCGT 60.375 57.895 0.00 0.00 0.00 5.68
585 625 0.108615 GAGAGCAAAGCAGAGCCGTA 60.109 55.000 0.00 0.00 0.00 4.02
586 626 0.108424 AGAGCAAAGCAGAGCCGTAG 60.108 55.000 0.00 0.00 0.00 3.51
587 627 0.390472 GAGCAAAGCAGAGCCGTAGT 60.390 55.000 0.00 0.00 0.00 2.73
588 628 0.671781 AGCAAAGCAGAGCCGTAGTG 60.672 55.000 0.00 0.00 0.00 2.74
589 629 0.951040 GCAAAGCAGAGCCGTAGTGT 60.951 55.000 0.00 0.00 0.00 3.55
590 630 0.792640 CAAAGCAGAGCCGTAGTGTG 59.207 55.000 0.00 0.00 0.00 3.82
591 631 0.393077 AAAGCAGAGCCGTAGTGTGT 59.607 50.000 0.00 0.00 0.00 3.72
592 632 0.319900 AAGCAGAGCCGTAGTGTGTG 60.320 55.000 0.00 0.00 0.00 3.82
593 633 2.383527 GCAGAGCCGTAGTGTGTGC 61.384 63.158 0.00 0.00 0.00 4.57
594 634 2.088763 CAGAGCCGTAGTGTGTGCG 61.089 63.158 0.00 0.00 0.00 5.34
595 635 2.049433 GAGCCGTAGTGTGTGCGT 60.049 61.111 0.00 0.00 31.27 5.24
596 636 2.355837 AGCCGTAGTGTGTGCGTG 60.356 61.111 0.00 0.00 31.27 5.34
597 637 2.660552 GCCGTAGTGTGTGCGTGT 60.661 61.111 0.00 0.00 31.27 4.49
598 638 2.938823 GCCGTAGTGTGTGCGTGTG 61.939 63.158 0.00 0.00 31.27 3.82
599 639 1.590525 CCGTAGTGTGTGCGTGTGT 60.591 57.895 0.00 0.00 31.27 3.72
600 640 1.557907 CGTAGTGTGTGCGTGTGTG 59.442 57.895 0.00 0.00 0.00 3.82
601 641 0.868177 CGTAGTGTGTGCGTGTGTGA 60.868 55.000 0.00 0.00 0.00 3.58
602 642 0.852777 GTAGTGTGTGCGTGTGTGAG 59.147 55.000 0.00 0.00 0.00 3.51
603 643 0.741915 TAGTGTGTGCGTGTGTGAGA 59.258 50.000 0.00 0.00 0.00 3.27
604 644 0.528466 AGTGTGTGCGTGTGTGAGAG 60.528 55.000 0.00 0.00 0.00 3.20
605 645 0.527600 GTGTGTGCGTGTGTGAGAGA 60.528 55.000 0.00 0.00 0.00 3.10
606 646 0.249031 TGTGTGCGTGTGTGAGAGAG 60.249 55.000 0.00 0.00 0.00 3.20
607 647 0.030773 GTGTGCGTGTGTGAGAGAGA 59.969 55.000 0.00 0.00 0.00 3.10
608 648 0.312102 TGTGCGTGTGTGAGAGAGAG 59.688 55.000 0.00 0.00 0.00 3.20
609 649 1.006314 GTGCGTGTGTGAGAGAGAGC 61.006 60.000 0.00 0.00 0.00 4.09
610 650 1.175347 TGCGTGTGTGAGAGAGAGCT 61.175 55.000 0.00 0.00 0.00 4.09
611 651 0.455972 GCGTGTGTGAGAGAGAGCTC 60.456 60.000 5.27 5.27 41.62 4.09
612 652 0.877743 CGTGTGTGAGAGAGAGCTCA 59.122 55.000 17.77 0.00 43.81 4.26
613 653 1.135717 CGTGTGTGAGAGAGAGCTCAG 60.136 57.143 17.77 0.00 44.92 3.35
614 654 0.887247 TGTGTGAGAGAGAGCTCAGC 59.113 55.000 17.77 7.53 44.92 4.26
615 655 1.176527 GTGTGAGAGAGAGCTCAGCT 58.823 55.000 17.77 12.75 44.92 4.24
616 656 1.135315 GTGTGAGAGAGAGCTCAGCTG 60.135 57.143 17.77 7.63 44.92 4.24
617 657 0.457035 GTGAGAGAGAGCTCAGCTGG 59.543 60.000 17.77 5.82 44.92 4.85
618 658 0.683828 TGAGAGAGAGCTCAGCTGGG 60.684 60.000 17.77 12.70 43.81 4.45
619 659 0.684153 GAGAGAGAGCTCAGCTGGGT 60.684 60.000 16.66 11.02 43.81 4.51
620 660 0.252193 AGAGAGAGCTCAGCTGGGTT 60.252 55.000 16.66 9.69 43.81 4.11
621 661 0.175531 GAGAGAGCTCAGCTGGGTTC 59.824 60.000 21.86 21.86 39.88 3.62
622 662 1.220477 GAGAGCTCAGCTGGGTTCC 59.780 63.158 25.09 13.82 39.88 3.62
623 663 1.229464 AGAGCTCAGCTGGGTTCCT 60.229 57.895 25.09 9.41 39.88 3.36
624 664 0.839853 AGAGCTCAGCTGGGTTCCTT 60.840 55.000 25.09 6.60 39.88 3.36
625 665 0.037447 GAGCTCAGCTGGGTTCCTTT 59.963 55.000 19.06 0.00 39.88 3.11
626 666 0.037447 AGCTCAGCTGGGTTCCTTTC 59.963 55.000 16.66 0.00 37.57 2.62
627 667 0.037447 GCTCAGCTGGGTTCCTTTCT 59.963 55.000 16.66 0.00 0.00 2.52
628 668 1.948144 GCTCAGCTGGGTTCCTTTCTC 60.948 57.143 16.66 0.00 0.00 2.87
629 669 1.627834 CTCAGCTGGGTTCCTTTCTCT 59.372 52.381 15.13 0.00 0.00 3.10
630 670 1.625818 TCAGCTGGGTTCCTTTCTCTC 59.374 52.381 15.13 0.00 0.00 3.20
631 671 1.349026 CAGCTGGGTTCCTTTCTCTCA 59.651 52.381 5.57 0.00 0.00 3.27
632 672 1.349357 AGCTGGGTTCCTTTCTCTCAC 59.651 52.381 0.00 0.00 0.00 3.51
633 673 1.349357 GCTGGGTTCCTTTCTCTCACT 59.651 52.381 0.00 0.00 0.00 3.41
634 674 2.567615 GCTGGGTTCCTTTCTCTCACTA 59.432 50.000 0.00 0.00 0.00 2.74
635 675 3.368948 GCTGGGTTCCTTTCTCTCACTAG 60.369 52.174 0.00 0.00 0.00 2.57
636 676 4.090090 CTGGGTTCCTTTCTCTCACTAGA 58.910 47.826 0.00 0.00 0.00 2.43
637 677 4.689062 TGGGTTCCTTTCTCTCACTAGAT 58.311 43.478 0.00 0.00 0.00 1.98
638 678 4.712337 TGGGTTCCTTTCTCTCACTAGATC 59.288 45.833 0.00 0.00 0.00 2.75
639 679 4.959839 GGGTTCCTTTCTCTCACTAGATCT 59.040 45.833 0.00 0.00 0.00 2.75
640 680 5.163457 GGGTTCCTTTCTCTCACTAGATCTG 60.163 48.000 5.18 0.00 0.00 2.90
641 681 5.348164 GTTCCTTTCTCTCACTAGATCTGC 58.652 45.833 5.18 0.00 0.00 4.26
642 682 3.957497 TCCTTTCTCTCACTAGATCTGCC 59.043 47.826 5.18 0.00 0.00 4.85
643 683 3.069443 CCTTTCTCTCACTAGATCTGCCC 59.931 52.174 5.18 0.00 0.00 5.36
644 684 3.388552 TTCTCTCACTAGATCTGCCCA 57.611 47.619 5.18 0.00 0.00 5.36
645 685 2.660572 TCTCTCACTAGATCTGCCCAC 58.339 52.381 5.18 0.00 0.00 4.61
646 686 2.243478 TCTCTCACTAGATCTGCCCACT 59.757 50.000 5.18 0.00 0.00 4.00
647 687 2.361757 CTCTCACTAGATCTGCCCACTG 59.638 54.545 5.18 0.00 0.00 3.66
648 688 1.411977 CTCACTAGATCTGCCCACTGG 59.588 57.143 5.18 0.00 0.00 4.00
649 689 1.198713 CACTAGATCTGCCCACTGGT 58.801 55.000 5.18 0.00 0.00 4.00
650 690 1.134580 CACTAGATCTGCCCACTGGTG 60.135 57.143 5.18 0.00 36.96 4.17
684 724 3.305516 CCTTTGCCCAAAGCCGCT 61.306 61.111 13.83 0.00 44.76 5.52
754 809 0.106469 TCCCTCTCTATGCGTGCTCT 60.106 55.000 0.00 0.00 0.00 4.09
896 965 2.184579 GTGACGGACTAGCCAGCC 59.815 66.667 0.00 0.00 35.94 4.85
897 966 3.449227 TGACGGACTAGCCAGCCG 61.449 66.667 11.94 11.94 43.08 5.52
898 967 4.208686 GACGGACTAGCCAGCCGG 62.209 72.222 16.27 0.00 42.29 6.13
1115 1184 0.036858 GCTCCGGAAGAAGCAGAGTT 60.037 55.000 5.23 0.00 0.00 3.01
1132 1203 4.332819 CAGAGTTTTCGTCTTGGTTCTTGT 59.667 41.667 0.00 0.00 0.00 3.16
1789 1866 2.656069 GGAGGTAGGTCGCCTTGCA 61.656 63.158 3.71 0.00 36.29 4.08
1828 1905 0.727398 GTTTAGACACATCCGCTGCC 59.273 55.000 0.00 0.00 0.00 4.85
1990 2086 2.997986 GTGCATTTGCTTTGATTCAGGG 59.002 45.455 3.94 0.00 42.66 4.45
2008 2104 3.195396 CAGGGGTTGATTGTGTAATTGGG 59.805 47.826 0.00 0.00 0.00 4.12
2026 2122 4.640771 TGGGTACTGATTCTTGCTCTTT 57.359 40.909 0.00 0.00 0.00 2.52
2052 2148 2.022129 CAGTGAGAACGGCGACACC 61.022 63.158 16.62 0.00 34.33 4.16
2338 2435 4.137116 TGTCTAGTTGATCATTTCGGGG 57.863 45.455 0.00 0.00 0.00 5.73
2431 2528 2.624316 AGAACTGAACAATGCATGCG 57.376 45.000 14.09 0.76 0.00 4.73
2444 2541 1.869132 TGCATGCGCTATGTCATCTTC 59.131 47.619 14.09 0.00 39.08 2.87
2630 2735 0.179936 GTTCAGATGGGAGCTCAGGG 59.820 60.000 17.19 0.00 0.00 4.45
2771 2876 0.108233 CAGGAAGCTCAGCTCCTGAC 60.108 60.000 28.23 8.19 46.58 3.51
2924 3029 5.277974 GCAGACACTCAGAAAGCAAATTGTA 60.278 40.000 0.00 0.00 0.00 2.41
2942 3047 3.428532 TGTAAAAGAGAGTAGGCGAGGT 58.571 45.455 0.00 0.00 0.00 3.85
2948 3053 1.402613 GAGAGTAGGCGAGGTCAAGAC 59.597 57.143 0.00 0.00 0.00 3.01
2997 3102 1.039785 TGAGAGGGATGCACTCCGAG 61.040 60.000 0.00 0.00 46.01 4.63
3350 3455 4.978099 AGATGGACATGTCTGAAACAAGT 58.022 39.130 24.50 0.75 42.25 3.16
3428 3533 1.929836 GGCATCGCTAGTTCTGAACTG 59.070 52.381 28.46 19.70 42.84 3.16
3461 3566 8.632906 AGATTCTTGAACTGAGTGATGAAATT 57.367 30.769 0.00 0.00 0.00 1.82
3581 3686 2.427095 GAGGCTGGAACAAACACAACTT 59.573 45.455 0.00 0.00 38.70 2.66
3804 3909 0.882927 GAACAACGCTACCACTGCCA 60.883 55.000 0.00 0.00 0.00 4.92
3866 3971 1.949525 TCTTCTGCTTTCAGTGCCAAC 59.050 47.619 0.00 0.00 41.10 3.77
3947 4052 4.816385 CAGTTGGAAGAGTTACTGCAGAAA 59.184 41.667 23.35 4.90 32.53 2.52
4242 4349 3.640498 TGCAAATGGTGAAAAGGACATGA 59.360 39.130 0.00 0.00 0.00 3.07
4261 4368 4.572985 TGATCTTGCAAGACAAAACTGG 57.427 40.909 30.66 0.00 37.96 4.00
4391 4498 7.054751 AGACAATAGGGAAGCTACAAATAACC 58.945 38.462 0.00 0.00 0.00 2.85
4657 4773 5.046529 AGCTTTCTCTCATATGCGTAACAG 58.953 41.667 0.00 0.00 0.00 3.16
4862 4983 3.131933 CCATGAGTTTGTGGGTTGTCAAA 59.868 43.478 0.00 0.00 0.00 2.69
4869 4990 6.702329 AGTTTGTGGGTTGTCAAAACAAATA 58.298 32.000 18.19 3.23 46.56 1.40
4986 5107 2.028020 GCTGTACAACCTGCTTCCTAGT 60.028 50.000 0.00 0.00 0.00 2.57
4990 5111 2.269940 ACAACCTGCTTCCTAGTGGAT 58.730 47.619 0.00 0.00 42.81 3.41
5173 5297 1.717937 GAAGCGCATCAAGCACGAT 59.282 52.632 11.47 0.00 46.13 3.73
5176 5300 0.179100 AGCGCATCAAGCACGATACT 60.179 50.000 11.47 0.00 46.13 2.12
5227 5351 2.331451 GCCAACGGACACAGCAAC 59.669 61.111 0.00 0.00 0.00 4.17
5252 5376 3.108881 CACGACACGAGGTTATCATCTG 58.891 50.000 0.00 0.00 0.00 2.90
5311 5438 6.761099 ACTCCAGTTATACATATAGGAGCG 57.239 41.667 0.00 0.00 43.76 5.03
5315 5442 6.722590 TCCAGTTATACATATAGGAGCGGAAA 59.277 38.462 0.00 0.00 0.00 3.13
5327 5454 3.197766 AGGAGCGGAAATGACTGACATAA 59.802 43.478 0.00 0.00 38.38 1.90
5397 5524 3.360867 CTCAAAGGAGCTGGAGTCTCTA 58.639 50.000 0.00 0.00 33.67 2.43
5712 5855 3.655211 CAGAGGCCAGGCAAGGGT 61.655 66.667 15.19 0.00 0.00 4.34
5815 5958 0.758123 TGTGTGCAGGATGTGTCAGA 59.242 50.000 0.00 0.00 39.31 3.27
5844 5987 0.336392 TGCCTCTAGAGAGAGCCCAA 59.664 55.000 21.76 0.00 46.97 4.12
5856 5999 1.419762 AGAGCCCAATGTGTGTGTGTA 59.580 47.619 0.00 0.00 0.00 2.90
5876 6026 9.151471 GTGTGTATGTGTGTTGTATAATTCTCT 57.849 33.333 0.00 0.00 0.00 3.10
5916 6066 6.348376 GCTGGAAGAAAGAAAAGTGAGAGATG 60.348 42.308 0.00 0.00 34.07 2.90
5964 6114 4.805719 CCTTTTCTTTTGAAGCAACTGACC 59.194 41.667 0.00 0.00 39.88 4.02
5981 6131 4.136796 CTGACCATTTGAACTTGGACTCA 58.863 43.478 0.73 0.00 36.79 3.41
5986 6136 1.581934 TTGAACTTGGACTCACAGCG 58.418 50.000 0.00 0.00 0.00 5.18
6023 6173 4.389576 CTGGCCGAAGTTGCACGC 62.390 66.667 0.00 0.00 0.00 5.34
6196 6365 2.690778 GGCAGATCACCACGGTTGC 61.691 63.158 2.58 2.58 0.00 4.17
6246 6415 1.285578 GCTCTTGCGTCTCATCTTCC 58.714 55.000 0.00 0.00 0.00 3.46
6261 6430 3.309436 TTCCGTCATCCCAGGTGCG 62.309 63.158 0.00 0.00 0.00 5.34
6266 6435 1.021390 GTCATCCCAGGTGCGAGTTG 61.021 60.000 0.00 0.00 0.00 3.16
6268 6437 0.249120 CATCCCAGGTGCGAGTTGTA 59.751 55.000 0.00 0.00 0.00 2.41
6269 6438 0.537188 ATCCCAGGTGCGAGTTGTAG 59.463 55.000 0.00 0.00 0.00 2.74
6270 6439 1.741770 CCCAGGTGCGAGTTGTAGC 60.742 63.158 0.00 0.00 0.00 3.58
6271 6440 1.741770 CCAGGTGCGAGTTGTAGCC 60.742 63.158 0.00 0.00 0.00 3.93
6272 6441 1.005037 CAGGTGCGAGTTGTAGCCA 60.005 57.895 0.00 0.00 0.00 4.75
6274 6443 0.391661 AGGTGCGAGTTGTAGCCATG 60.392 55.000 0.00 0.00 0.00 3.66
6275 6444 1.369091 GGTGCGAGTTGTAGCCATGG 61.369 60.000 7.63 7.63 0.00 3.66
6293 7752 4.372384 CATGGAGCATGTTGGTTGTACCA 61.372 47.826 0.00 0.00 40.28 3.25
6310 7771 0.320073 CCAGCAGTGGTGGCATTTTG 60.320 55.000 27.35 3.32 44.28 2.44
6320 7781 3.006752 TGGTGGCATTTTGTCATTTCCTC 59.993 43.478 0.00 0.00 33.03 3.71
6348 7809 4.285863 AGGAATTGTGTGAAAACCCTTGA 58.714 39.130 0.00 0.00 0.00 3.02
6355 7816 6.385649 TGTGTGAAAACCCTTGAATCTAAC 57.614 37.500 0.00 0.00 0.00 2.34
6367 7828 6.349611 CCCTTGAATCTAACTTCATGTGTTGG 60.350 42.308 14.01 11.91 35.20 3.77
6370 7831 6.295249 TGAATCTAACTTCATGTGTTGGACA 58.705 36.000 17.01 11.60 37.64 4.02
6373 7834 5.063204 TCTAACTTCATGTGTTGGACAAGG 58.937 41.667 13.07 0.00 38.36 3.61
6402 7869 1.493950 CGCTCATGCATCGTCCCTTC 61.494 60.000 0.00 0.00 39.64 3.46
6403 7870 0.179062 GCTCATGCATCGTCCCTTCT 60.179 55.000 0.00 0.00 39.41 2.85
6404 7871 1.745141 GCTCATGCATCGTCCCTTCTT 60.745 52.381 0.00 0.00 39.41 2.52
6405 7872 2.208431 CTCATGCATCGTCCCTTCTTC 58.792 52.381 0.00 0.00 0.00 2.87
6406 7873 1.554617 TCATGCATCGTCCCTTCTTCA 59.445 47.619 0.00 0.00 0.00 3.02
6411 7878 3.826157 TGCATCGTCCCTTCTTCATTTTT 59.174 39.130 0.00 0.00 0.00 1.94
6426 7893 3.757836 TTTTTCGGGGGAAAGGGAG 57.242 52.632 0.00 0.00 0.00 4.30
6427 7894 0.541063 TTTTTCGGGGGAAAGGGAGC 60.541 55.000 0.00 0.00 0.00 4.70
6428 7895 1.432023 TTTTCGGGGGAAAGGGAGCT 61.432 55.000 0.00 0.00 0.00 4.09
6429 7896 1.432023 TTTCGGGGGAAAGGGAGCTT 61.432 55.000 0.00 0.00 0.00 3.74
6430 7897 0.548197 TTCGGGGGAAAGGGAGCTTA 60.548 55.000 0.00 0.00 0.00 3.09
6431 7898 0.327191 TCGGGGGAAAGGGAGCTTAT 60.327 55.000 0.00 0.00 0.00 1.73
6432 7899 1.061967 TCGGGGGAAAGGGAGCTTATA 60.062 52.381 0.00 0.00 0.00 0.98
6433 7900 1.985895 CGGGGGAAAGGGAGCTTATAT 59.014 52.381 0.00 0.00 0.00 0.86
6434 7901 2.375509 CGGGGGAAAGGGAGCTTATATT 59.624 50.000 0.00 0.00 0.00 1.28
6435 7902 3.585732 CGGGGGAAAGGGAGCTTATATTA 59.414 47.826 0.00 0.00 0.00 0.98
6436 7903 4.042435 CGGGGGAAAGGGAGCTTATATTAA 59.958 45.833 0.00 0.00 0.00 1.40
6437 7904 5.457052 CGGGGGAAAGGGAGCTTATATTAAA 60.457 44.000 0.00 0.00 0.00 1.52
6438 7905 6.562228 GGGGGAAAGGGAGCTTATATTAAAT 58.438 40.000 0.00 0.00 0.00 1.40
6439 7906 7.016914 GGGGGAAAGGGAGCTTATATTAAATT 58.983 38.462 0.00 0.00 0.00 1.82
6440 7907 8.174757 GGGGGAAAGGGAGCTTATATTAAATTA 58.825 37.037 0.00 0.00 0.00 1.40
6441 7908 9.244292 GGGGAAAGGGAGCTTATATTAAATTAG 57.756 37.037 0.00 0.00 0.00 1.73
6442 7909 9.244292 GGGAAAGGGAGCTTATATTAAATTAGG 57.756 37.037 0.00 0.00 0.00 2.69
6443 7910 9.244292 GGAAAGGGAGCTTATATTAAATTAGGG 57.756 37.037 0.00 0.00 0.00 3.53
6444 7911 9.809395 GAAAGGGAGCTTATATTAAATTAGGGT 57.191 33.333 0.00 0.00 0.00 4.34
6445 7912 9.588096 AAAGGGAGCTTATATTAAATTAGGGTG 57.412 33.333 0.00 0.00 0.00 4.61
6446 7913 7.699878 AGGGAGCTTATATTAAATTAGGGTGG 58.300 38.462 0.00 0.00 0.00 4.61
6447 7914 6.890268 GGGAGCTTATATTAAATTAGGGTGGG 59.110 42.308 0.00 0.00 0.00 4.61
6448 7915 7.257272 GGGAGCTTATATTAAATTAGGGTGGGA 60.257 40.741 0.00 0.00 0.00 4.37
6449 7916 8.168058 GGAGCTTATATTAAATTAGGGTGGGAA 58.832 37.037 0.00 0.00 0.00 3.97
6450 7917 9.755122 GAGCTTATATTAAATTAGGGTGGGAAT 57.245 33.333 0.00 0.00 0.00 3.01
6454 7921 9.523168 TTATATTAAATTAGGGTGGGAATTCGG 57.477 33.333 0.00 0.00 0.00 4.30
6455 7922 5.453866 TTAAATTAGGGTGGGAATTCGGA 57.546 39.130 0.00 0.00 0.00 4.55
6456 7923 3.577805 AATTAGGGTGGGAATTCGGAG 57.422 47.619 0.00 0.00 0.00 4.63
6457 7924 1.961133 TTAGGGTGGGAATTCGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
6458 7925 1.200519 TAGGGTGGGAATTCGGAGTG 58.799 55.000 0.00 0.00 0.00 3.51
6459 7926 1.749258 GGGTGGGAATTCGGAGTGC 60.749 63.158 0.00 0.00 0.00 4.40
6460 7927 2.106683 GGTGGGAATTCGGAGTGCG 61.107 63.158 0.00 0.00 0.00 5.34
6461 7928 2.106683 GTGGGAATTCGGAGTGCGG 61.107 63.158 3.57 0.00 0.00 5.69
6462 7929 3.202706 GGGAATTCGGAGTGCGGC 61.203 66.667 3.57 0.00 0.00 6.53
6463 7930 3.564027 GGAATTCGGAGTGCGGCG 61.564 66.667 0.51 0.51 0.00 6.46
6464 7931 2.813908 GAATTCGGAGTGCGGCGT 60.814 61.111 9.37 0.00 0.00 5.68
6465 7932 2.358247 AATTCGGAGTGCGGCGTT 60.358 55.556 9.37 0.00 0.00 4.84
6466 7933 1.908066 GAATTCGGAGTGCGGCGTTT 61.908 55.000 9.37 0.00 0.00 3.60
6467 7934 1.908066 AATTCGGAGTGCGGCGTTTC 61.908 55.000 9.37 3.75 0.00 2.78
6471 7938 4.072088 GAGTGCGGCGTTTCGGTG 62.072 66.667 9.37 0.00 0.00 4.94
6496 7963 3.667087 GCATCTGCACCCGTTCAA 58.333 55.556 0.00 0.00 41.59 2.69
6497 7964 1.956043 GCATCTGCACCCGTTCAAA 59.044 52.632 0.00 0.00 41.59 2.69
6498 7965 0.313672 GCATCTGCACCCGTTCAAAA 59.686 50.000 0.00 0.00 41.59 2.44
6499 7966 1.269517 GCATCTGCACCCGTTCAAAAA 60.270 47.619 0.00 0.00 41.59 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.729838 GTGGACGTGTGAGCGACTC 60.730 63.158 0.00 0.00 35.59 3.36
194 234 9.209048 GAAAAGGGTAATGGGGATTTATTTAGT 57.791 33.333 0.00 0.00 0.00 2.24
206 246 2.632763 TTGGGGAAAAGGGTAATGGG 57.367 50.000 0.00 0.00 0.00 4.00
274 314 4.402474 GGGAGAGAGAAAGAAAGAGAGAGG 59.598 50.000 0.00 0.00 0.00 3.69
275 315 4.402474 GGGGAGAGAGAAAGAAAGAGAGAG 59.598 50.000 0.00 0.00 0.00 3.20
276 316 4.349365 GGGGAGAGAGAAAGAAAGAGAGA 58.651 47.826 0.00 0.00 0.00 3.10
277 317 3.450817 GGGGGAGAGAGAAAGAAAGAGAG 59.549 52.174 0.00 0.00 0.00 3.20
278 318 3.445987 GGGGGAGAGAGAAAGAAAGAGA 58.554 50.000 0.00 0.00 0.00 3.10
279 319 3.904800 GGGGGAGAGAGAAAGAAAGAG 57.095 52.381 0.00 0.00 0.00 2.85
553 593 4.521146 CTTTGCTCTCTCTCTCTCTCTCT 58.479 47.826 0.00 0.00 0.00 3.10
554 594 3.065925 GCTTTGCTCTCTCTCTCTCTCTC 59.934 52.174 0.00 0.00 0.00 3.20
555 595 3.019564 GCTTTGCTCTCTCTCTCTCTCT 58.980 50.000 0.00 0.00 0.00 3.10
556 596 2.754552 TGCTTTGCTCTCTCTCTCTCTC 59.245 50.000 0.00 0.00 0.00 3.20
557 597 2.756760 CTGCTTTGCTCTCTCTCTCTCT 59.243 50.000 0.00 0.00 0.00 3.10
558 598 2.754552 TCTGCTTTGCTCTCTCTCTCTC 59.245 50.000 0.00 0.00 0.00 3.20
559 599 2.756760 CTCTGCTTTGCTCTCTCTCTCT 59.243 50.000 0.00 0.00 0.00 3.10
560 600 2.736400 GCTCTGCTTTGCTCTCTCTCTC 60.736 54.545 0.00 0.00 0.00 3.20
561 601 1.205417 GCTCTGCTTTGCTCTCTCTCT 59.795 52.381 0.00 0.00 0.00 3.10
562 602 1.643880 GCTCTGCTTTGCTCTCTCTC 58.356 55.000 0.00 0.00 0.00 3.20
563 603 0.249955 GGCTCTGCTTTGCTCTCTCT 59.750 55.000 0.00 0.00 0.00 3.10
564 604 1.083242 CGGCTCTGCTTTGCTCTCTC 61.083 60.000 0.00 0.00 0.00 3.20
565 605 1.079266 CGGCTCTGCTTTGCTCTCT 60.079 57.895 0.00 0.00 0.00 3.10
566 606 0.108615 TACGGCTCTGCTTTGCTCTC 60.109 55.000 0.00 0.00 0.00 3.20
567 607 0.108424 CTACGGCTCTGCTTTGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
568 608 0.390472 ACTACGGCTCTGCTTTGCTC 60.390 55.000 0.00 0.00 0.00 4.26
569 609 0.671781 CACTACGGCTCTGCTTTGCT 60.672 55.000 0.00 0.00 0.00 3.91
570 610 0.951040 ACACTACGGCTCTGCTTTGC 60.951 55.000 0.00 0.00 0.00 3.68
571 611 0.792640 CACACTACGGCTCTGCTTTG 59.207 55.000 0.00 0.00 0.00 2.77
572 612 0.393077 ACACACTACGGCTCTGCTTT 59.607 50.000 0.00 0.00 0.00 3.51
573 613 0.319900 CACACACTACGGCTCTGCTT 60.320 55.000 0.00 0.00 0.00 3.91
574 614 1.290324 CACACACTACGGCTCTGCT 59.710 57.895 0.00 0.00 0.00 4.24
575 615 2.383527 GCACACACTACGGCTCTGC 61.384 63.158 0.00 0.00 0.00 4.26
576 616 2.088763 CGCACACACTACGGCTCTG 61.089 63.158 0.00 0.00 0.00 3.35
577 617 2.258591 CGCACACACTACGGCTCT 59.741 61.111 0.00 0.00 0.00 4.09
578 618 2.049433 ACGCACACACTACGGCTC 60.049 61.111 0.00 0.00 0.00 4.70
579 619 2.355837 CACGCACACACTACGGCT 60.356 61.111 0.00 0.00 0.00 5.52
580 620 2.660552 ACACGCACACACTACGGC 60.661 61.111 0.00 0.00 0.00 5.68
581 621 1.590525 ACACACGCACACACTACGG 60.591 57.895 0.00 0.00 0.00 4.02
582 622 0.868177 TCACACACGCACACACTACG 60.868 55.000 0.00 0.00 0.00 3.51
583 623 0.852777 CTCACACACGCACACACTAC 59.147 55.000 0.00 0.00 0.00 2.73
584 624 0.741915 TCTCACACACGCACACACTA 59.258 50.000 0.00 0.00 0.00 2.74
585 625 0.528466 CTCTCACACACGCACACACT 60.528 55.000 0.00 0.00 0.00 3.55
586 626 0.527600 TCTCTCACACACGCACACAC 60.528 55.000 0.00 0.00 0.00 3.82
587 627 0.249031 CTCTCTCACACACGCACACA 60.249 55.000 0.00 0.00 0.00 3.72
588 628 0.030773 TCTCTCTCACACACGCACAC 59.969 55.000 0.00 0.00 0.00 3.82
589 629 0.312102 CTCTCTCTCACACACGCACA 59.688 55.000 0.00 0.00 0.00 4.57
590 630 1.006314 GCTCTCTCTCACACACGCAC 61.006 60.000 0.00 0.00 0.00 5.34
591 631 1.175347 AGCTCTCTCTCACACACGCA 61.175 55.000 0.00 0.00 0.00 5.24
592 632 0.455972 GAGCTCTCTCTCACACACGC 60.456 60.000 6.43 0.00 36.42 5.34
593 633 0.877743 TGAGCTCTCTCTCACACACG 59.122 55.000 16.19 0.00 38.11 4.49
594 634 1.402720 GCTGAGCTCTCTCTCACACAC 60.403 57.143 16.19 0.00 38.11 3.82
595 635 0.887247 GCTGAGCTCTCTCTCACACA 59.113 55.000 16.19 0.00 38.11 3.72
596 636 1.135315 CAGCTGAGCTCTCTCTCACAC 60.135 57.143 16.19 0.00 38.11 3.82
597 637 1.175654 CAGCTGAGCTCTCTCTCACA 58.824 55.000 16.19 0.00 38.11 3.58
598 638 0.457035 CCAGCTGAGCTCTCTCTCAC 59.543 60.000 17.39 0.00 38.11 3.51
599 639 0.683828 CCCAGCTGAGCTCTCTCTCA 60.684 60.000 17.39 0.00 40.50 3.27
600 640 0.684153 ACCCAGCTGAGCTCTCTCTC 60.684 60.000 17.39 0.00 36.40 3.20
601 641 0.252193 AACCCAGCTGAGCTCTCTCT 60.252 55.000 17.39 6.22 36.40 3.10
602 642 0.175531 GAACCCAGCTGAGCTCTCTC 59.824 60.000 17.39 3.85 36.40 3.20
603 643 1.264045 GGAACCCAGCTGAGCTCTCT 61.264 60.000 17.39 9.20 36.40 3.10
604 644 1.220477 GGAACCCAGCTGAGCTCTC 59.780 63.158 17.39 6.86 36.40 3.20
605 645 0.839853 AAGGAACCCAGCTGAGCTCT 60.840 55.000 17.39 3.00 36.40 4.09
606 646 0.037447 AAAGGAACCCAGCTGAGCTC 59.963 55.000 17.39 6.82 36.40 4.09
607 647 0.037447 GAAAGGAACCCAGCTGAGCT 59.963 55.000 17.39 0.00 40.77 4.09
608 648 0.037447 AGAAAGGAACCCAGCTGAGC 59.963 55.000 17.39 0.00 0.00 4.26
609 649 1.627834 AGAGAAAGGAACCCAGCTGAG 59.372 52.381 17.39 3.79 0.00 3.35
610 650 1.625818 GAGAGAAAGGAACCCAGCTGA 59.374 52.381 17.39 0.00 0.00 4.26
611 651 1.349026 TGAGAGAAAGGAACCCAGCTG 59.651 52.381 6.78 6.78 0.00 4.24
612 652 1.349357 GTGAGAGAAAGGAACCCAGCT 59.651 52.381 0.00 0.00 0.00 4.24
613 653 1.349357 AGTGAGAGAAAGGAACCCAGC 59.651 52.381 0.00 0.00 0.00 4.85
614 654 4.090090 TCTAGTGAGAGAAAGGAACCCAG 58.910 47.826 0.00 0.00 0.00 4.45
615 655 4.127918 TCTAGTGAGAGAAAGGAACCCA 57.872 45.455 0.00 0.00 0.00 4.51
616 656 4.959839 AGATCTAGTGAGAGAAAGGAACCC 59.040 45.833 0.00 0.00 34.35 4.11
617 657 5.681179 GCAGATCTAGTGAGAGAAAGGAACC 60.681 48.000 0.00 0.00 34.35 3.62
618 658 5.348164 GCAGATCTAGTGAGAGAAAGGAAC 58.652 45.833 0.00 0.00 34.35 3.62
619 659 4.404073 GGCAGATCTAGTGAGAGAAAGGAA 59.596 45.833 0.00 0.00 34.35 3.36
620 660 3.957497 GGCAGATCTAGTGAGAGAAAGGA 59.043 47.826 0.00 0.00 34.35 3.36
621 661 3.069443 GGGCAGATCTAGTGAGAGAAAGG 59.931 52.174 0.00 0.00 34.35 3.11
622 662 3.703556 TGGGCAGATCTAGTGAGAGAAAG 59.296 47.826 0.00 0.00 34.35 2.62
623 663 3.449018 GTGGGCAGATCTAGTGAGAGAAA 59.551 47.826 0.00 0.00 34.35 2.52
624 664 3.027412 GTGGGCAGATCTAGTGAGAGAA 58.973 50.000 0.00 0.00 34.35 2.87
625 665 2.243478 AGTGGGCAGATCTAGTGAGAGA 59.757 50.000 0.00 0.00 34.35 3.10
626 666 2.361757 CAGTGGGCAGATCTAGTGAGAG 59.638 54.545 0.00 0.00 34.35 3.20
627 667 2.382882 CAGTGGGCAGATCTAGTGAGA 58.617 52.381 0.00 0.00 35.71 3.27
628 668 1.411977 CCAGTGGGCAGATCTAGTGAG 59.588 57.143 0.00 0.00 0.00 3.51
629 669 1.273267 ACCAGTGGGCAGATCTAGTGA 60.273 52.381 15.21 0.00 37.90 3.41
630 670 1.134580 CACCAGTGGGCAGATCTAGTG 60.135 57.143 15.21 0.00 37.90 2.74
631 671 1.198713 CACCAGTGGGCAGATCTAGT 58.801 55.000 15.21 0.00 37.90 2.57
632 672 0.467384 CCACCAGTGGGCAGATCTAG 59.533 60.000 15.21 0.00 46.81 2.43
633 673 2.607811 CCACCAGTGGGCAGATCTA 58.392 57.895 15.21 0.00 46.81 1.98
634 674 3.408229 CCACCAGTGGGCAGATCT 58.592 61.111 15.21 0.00 46.81 2.75
644 684 3.889692 CAGGGGCACACCACCAGT 61.890 66.667 0.00 0.00 42.21 4.00
648 688 4.603535 AAGGCAGGGGCACACCAC 62.604 66.667 1.41 0.00 43.71 4.16
649 689 4.601794 CAAGGCAGGGGCACACCA 62.602 66.667 1.41 0.00 43.71 4.17
654 694 4.238062 AAAGGCAAGGCAGGGGCA 62.238 61.111 0.00 0.00 43.71 5.36
754 809 4.051167 CACATGGAGGCAGGGGCA 62.051 66.667 0.00 0.00 43.71 5.36
775 830 1.533547 GGTTAGTTAGAGCGGCGAGAC 60.534 57.143 12.98 0.00 0.00 3.36
787 842 0.035176 GTGCGGGTGGTGGTTAGTTA 59.965 55.000 0.00 0.00 0.00 2.24
897 966 4.742201 TGCTTGCTCGTCTCGGCC 62.742 66.667 0.00 0.00 0.00 6.13
898 967 2.734673 CTTGCTTGCTCGTCTCGGC 61.735 63.158 0.00 0.00 0.00 5.54
899 968 0.459237 ATCTTGCTTGCTCGTCTCGG 60.459 55.000 0.00 0.00 0.00 4.63
900 969 1.354040 AATCTTGCTTGCTCGTCTCG 58.646 50.000 0.00 0.00 0.00 4.04
901 970 2.222685 CGAAATCTTGCTTGCTCGTCTC 60.223 50.000 0.00 0.00 0.00 3.36
902 971 1.728971 CGAAATCTTGCTTGCTCGTCT 59.271 47.619 0.00 0.00 0.00 4.18
903 972 1.461127 ACGAAATCTTGCTTGCTCGTC 59.539 47.619 0.00 0.00 34.68 4.20
904 973 1.461127 GACGAAATCTTGCTTGCTCGT 59.539 47.619 5.31 5.31 41.80 4.18
905 974 1.728971 AGACGAAATCTTGCTTGCTCG 59.271 47.619 0.00 0.00 31.62 5.03
906 975 2.159599 CCAGACGAAATCTTGCTTGCTC 60.160 50.000 0.00 0.00 34.41 4.26
907 976 1.808945 CCAGACGAAATCTTGCTTGCT 59.191 47.619 0.00 0.00 34.41 3.91
908 977 1.537202 ACCAGACGAAATCTTGCTTGC 59.463 47.619 0.00 0.00 34.41 4.01
909 978 3.499918 AGAACCAGACGAAATCTTGCTTG 59.500 43.478 0.00 0.00 34.41 4.01
992 1061 3.039202 GACTTGAACATGCCGGCGG 62.039 63.158 24.35 24.35 0.00 6.13
1041 1110 2.203195 TGCAGCTTGAACACGGCT 60.203 55.556 0.00 0.00 36.70 5.52
1115 1184 5.090083 CGAAAAACAAGAACCAAGACGAAA 58.910 37.500 0.00 0.00 0.00 3.46
1789 1866 2.093658 ACTAATCTCCAACCAACGCGAT 60.094 45.455 15.93 0.00 0.00 4.58
1828 1905 6.652481 TGATCTCTTAAAGCTCAAACCAGAAG 59.348 38.462 0.00 0.00 27.33 2.85
1990 2086 5.708230 TCAGTACCCAATTACACAATCAACC 59.292 40.000 0.00 0.00 0.00 3.77
2008 2104 3.181516 CCGCAAAGAGCAAGAATCAGTAC 60.182 47.826 0.00 0.00 46.13 2.73
2026 2122 2.355837 GTTCTCACTGTCGCCGCA 60.356 61.111 0.00 0.00 0.00 5.69
2052 2148 4.776953 CGCGGCGAAGACTTTGCG 62.777 66.667 19.16 15.30 41.10 4.85
2338 2435 1.081242 CACGCAGCAAATGTGACCC 60.081 57.895 0.00 0.00 42.31 4.46
2431 2528 4.899352 ACATAGGGGAAGATGACATAGC 57.101 45.455 0.00 0.00 0.00 2.97
2444 2541 7.233553 TCAGTTACTATCTGATGAACATAGGGG 59.766 40.741 0.00 0.00 37.07 4.79
2630 2735 3.503748 CACTGGTTTTGGGAGTGAATCTC 59.496 47.826 0.00 0.00 39.64 2.75
2771 2876 1.589993 CGACCCATCAGTGCTAGCG 60.590 63.158 10.77 0.00 0.00 4.26
2924 3029 2.526432 TGACCTCGCCTACTCTCTTTT 58.474 47.619 0.00 0.00 0.00 2.27
2997 3102 3.432890 CCTCTAAGGCCTTCACATTCTCC 60.433 52.174 24.49 0.00 0.00 3.71
3350 3455 4.276678 TCGTCTTCTTTCTCTTGGTACGAA 59.723 41.667 0.00 0.00 34.32 3.85
3461 3566 2.364324 ACGGTCTTTCTTGTACAGCTCA 59.636 45.455 0.00 0.00 0.00 4.26
3581 3686 2.627221 CTGCATCCTTAGCTGCTCTCTA 59.373 50.000 4.91 0.00 39.16 2.43
3804 3909 2.979240 GAATTCCTCCTGAAGTCGCTT 58.021 47.619 0.00 0.00 38.19 4.68
4242 4349 3.953612 TCACCAGTTTTGTCTTGCAAGAT 59.046 39.130 30.65 12.15 38.47 2.40
4391 4498 3.753272 ACTGGAGTTTCAACGATCCAATG 59.247 43.478 0.00 0.00 41.17 2.82
4862 4983 6.826741 ACACAGTGACACCTACTTTATTTGTT 59.173 34.615 7.81 0.00 0.00 2.83
4869 4990 5.138276 TCTCTACACAGTGACACCTACTTT 58.862 41.667 7.81 0.00 0.00 2.66
4986 5107 3.371917 CCATTCAAAGCTGTCCCTATCCA 60.372 47.826 0.00 0.00 0.00 3.41
4990 5111 2.239654 CCTCCATTCAAAGCTGTCCCTA 59.760 50.000 0.00 0.00 0.00 3.53
5173 5297 0.241749 CGTTACCGGTGCTGACAGTA 59.758 55.000 19.93 0.00 0.00 2.74
5227 5351 2.552585 ATAACCTCGTGTCGTGGCCG 62.553 60.000 0.00 0.00 43.18 6.13
5311 5438 5.517770 GCAGCAAATTATGTCAGTCATTTCC 59.482 40.000 0.00 0.00 37.91 3.13
5315 5442 4.703575 ACAGCAGCAAATTATGTCAGTCAT 59.296 37.500 0.00 0.00 40.25 3.06
5327 5454 4.682860 CGAGAAAAATCAACAGCAGCAAAT 59.317 37.500 0.00 0.00 0.00 2.32
5397 5524 0.391597 TCGCCTTGTTCGTCTCCTTT 59.608 50.000 0.00 0.00 0.00 3.11
5405 5532 2.099062 GCTGCATCGCCTTGTTCG 59.901 61.111 0.00 0.00 0.00 3.95
5567 5695 2.337583 CTACATGTGGGTGAGTGAACG 58.662 52.381 9.11 0.00 0.00 3.95
5569 5697 1.977854 AGCTACATGTGGGTGAGTGAA 59.022 47.619 13.53 0.00 0.00 3.18
5625 5754 4.014406 CGCCTATACAAAACCCTCCTTTT 58.986 43.478 0.00 0.00 0.00 2.27
5712 5855 1.555075 GTATTGTGACAGGCCAGAGGA 59.445 52.381 5.01 0.00 0.00 3.71
5815 5958 0.608130 TCTAGAGGCACGCACAACAT 59.392 50.000 0.00 0.00 0.00 2.71
5844 5987 3.944650 ACAACACACATACACACACACAT 59.055 39.130 0.00 0.00 0.00 3.21
5856 5999 9.453572 ACATCAAGAGAATTATACAACACACAT 57.546 29.630 0.00 0.00 0.00 3.21
5876 6026 0.675083 CCAGCACAGCCAAACATCAA 59.325 50.000 0.00 0.00 0.00 2.57
5916 6066 7.171508 GGTTCAAATTGTCCCTTCATTTCTTTC 59.828 37.037 0.00 0.00 0.00 2.62
5964 6114 3.607775 CGCTGTGAGTCCAAGTTCAAATG 60.608 47.826 0.00 0.00 0.00 2.32
5981 6131 1.476891 ACAGGAACATCGATACGCTGT 59.523 47.619 0.00 6.25 37.82 4.40
5986 6136 5.704888 CCAGATAGACAGGAACATCGATAC 58.295 45.833 0.00 0.00 0.00 2.24
6023 6173 1.750778 CCAGGGGTGATCCGAAATTTG 59.249 52.381 0.00 0.00 36.01 2.32
6238 6407 1.123077 CCTGGGATGACGGAAGATGA 58.877 55.000 0.00 0.00 0.00 2.92
6246 6415 2.202797 CTCGCACCTGGGATGACG 60.203 66.667 0.00 0.00 36.39 4.35
6261 6430 1.945394 CATGCTCCATGGCTACAACTC 59.055 52.381 6.96 0.00 38.11 3.01
6266 6435 1.027357 CCAACATGCTCCATGGCTAC 58.973 55.000 6.96 0.00 45.16 3.58
6268 6437 0.251922 AACCAACATGCTCCATGGCT 60.252 50.000 6.96 0.00 45.16 4.75
6269 6438 0.108520 CAACCAACATGCTCCATGGC 60.109 55.000 6.96 0.00 45.16 4.40
6270 6439 1.259609 ACAACCAACATGCTCCATGG 58.740 50.000 4.97 4.97 45.16 3.66
6271 6440 2.164219 GGTACAACCAACATGCTCCATG 59.836 50.000 3.80 3.80 41.75 3.66
6272 6441 2.446435 GGTACAACCAACATGCTCCAT 58.554 47.619 0.00 0.00 38.42 3.41
6293 7752 0.675633 GACAAAATGCCACCACTGCT 59.324 50.000 0.00 0.00 0.00 4.24
6295 7754 3.389925 AATGACAAAATGCCACCACTG 57.610 42.857 0.00 0.00 0.00 3.66
6296 7755 3.244181 GGAAATGACAAAATGCCACCACT 60.244 43.478 0.00 0.00 0.00 4.00
6297 7756 3.066380 GGAAATGACAAAATGCCACCAC 58.934 45.455 0.00 0.00 0.00 4.16
6298 7757 2.971330 AGGAAATGACAAAATGCCACCA 59.029 40.909 0.00 0.00 0.00 4.17
6299 7758 3.588955 GAGGAAATGACAAAATGCCACC 58.411 45.455 0.00 0.00 0.00 4.61
6301 7760 2.352617 GCGAGGAAATGACAAAATGCCA 60.353 45.455 0.00 0.00 0.00 4.92
6302 7761 2.262211 GCGAGGAAATGACAAAATGCC 58.738 47.619 0.00 0.00 0.00 4.40
6320 7781 0.871722 TTCACACAATTCCTTCCGCG 59.128 50.000 0.00 0.00 0.00 6.46
6348 7809 6.207417 CCTTGTCCAACACATGAAGTTAGATT 59.793 38.462 0.00 0.00 33.90 2.40
6355 7816 3.743521 TCTCCTTGTCCAACACATGAAG 58.256 45.455 0.00 0.00 33.90 3.02
6367 7828 2.094494 TGAGCGTCTTCATCTCCTTGTC 60.094 50.000 0.00 0.00 0.00 3.18
6370 7831 2.741228 GCATGAGCGTCTTCATCTCCTT 60.741 50.000 0.00 0.00 35.67 3.36
6373 7834 1.931906 TGCATGAGCGTCTTCATCTC 58.068 50.000 0.00 0.00 46.23 2.75
6411 7878 0.548197 TAAGCTCCCTTTCCCCCGAA 60.548 55.000 0.00 0.00 32.47 4.30
6412 7879 0.327191 ATAAGCTCCCTTTCCCCCGA 60.327 55.000 0.00 0.00 32.47 5.14
6413 7880 1.430992 TATAAGCTCCCTTTCCCCCG 58.569 55.000 0.00 0.00 32.47 5.73
6414 7881 5.594199 TTAATATAAGCTCCCTTTCCCCC 57.406 43.478 0.00 0.00 32.47 5.40
6415 7882 9.244292 CTAATTTAATATAAGCTCCCTTTCCCC 57.756 37.037 0.00 0.00 32.47 4.81
6416 7883 9.244292 CCTAATTTAATATAAGCTCCCTTTCCC 57.756 37.037 0.00 0.00 32.47 3.97
6417 7884 9.244292 CCCTAATTTAATATAAGCTCCCTTTCC 57.756 37.037 0.00 0.00 32.47 3.13
6418 7885 9.809395 ACCCTAATTTAATATAAGCTCCCTTTC 57.191 33.333 0.00 0.00 32.47 2.62
6419 7886 9.588096 CACCCTAATTTAATATAAGCTCCCTTT 57.412 33.333 0.00 0.00 32.47 3.11
6420 7887 8.170730 CCACCCTAATTTAATATAAGCTCCCTT 58.829 37.037 0.00 0.00 35.05 3.95
6421 7888 7.257419 CCCACCCTAATTTAATATAAGCTCCCT 60.257 40.741 0.00 0.00 0.00 4.20
6422 7889 6.890268 CCCACCCTAATTTAATATAAGCTCCC 59.110 42.308 0.00 0.00 0.00 4.30
6423 7890 7.696017 TCCCACCCTAATTTAATATAAGCTCC 58.304 38.462 0.00 0.00 0.00 4.70
6424 7891 9.755122 ATTCCCACCCTAATTTAATATAAGCTC 57.245 33.333 0.00 0.00 0.00 4.09
6428 7895 9.523168 CCGAATTCCCACCCTAATTTAATATAA 57.477 33.333 0.00 0.00 0.00 0.98
6429 7896 8.892530 TCCGAATTCCCACCCTAATTTAATATA 58.107 33.333 0.00 0.00 0.00 0.86
6430 7897 7.761608 TCCGAATTCCCACCCTAATTTAATAT 58.238 34.615 0.00 0.00 0.00 1.28
6431 7898 7.147266 ACTCCGAATTCCCACCCTAATTTAATA 60.147 37.037 0.00 0.00 0.00 0.98
6432 7899 6.020881 TCCGAATTCCCACCCTAATTTAAT 57.979 37.500 0.00 0.00 0.00 1.40
6433 7900 5.044698 ACTCCGAATTCCCACCCTAATTTAA 60.045 40.000 0.00 0.00 0.00 1.52
6434 7901 4.475747 ACTCCGAATTCCCACCCTAATTTA 59.524 41.667 0.00 0.00 0.00 1.40
6435 7902 3.268595 ACTCCGAATTCCCACCCTAATTT 59.731 43.478 0.00 0.00 0.00 1.82
6436 7903 2.850568 ACTCCGAATTCCCACCCTAATT 59.149 45.455 0.00 0.00 0.00 1.40
6437 7904 2.172717 CACTCCGAATTCCCACCCTAAT 59.827 50.000 0.00 0.00 0.00 1.73
6438 7905 1.557832 CACTCCGAATTCCCACCCTAA 59.442 52.381 0.00 0.00 0.00 2.69
6439 7906 1.200519 CACTCCGAATTCCCACCCTA 58.799 55.000 0.00 0.00 0.00 3.53
6440 7907 1.991230 CACTCCGAATTCCCACCCT 59.009 57.895 0.00 0.00 0.00 4.34
6441 7908 1.749258 GCACTCCGAATTCCCACCC 60.749 63.158 0.00 0.00 0.00 4.61
6442 7909 2.106683 CGCACTCCGAATTCCCACC 61.107 63.158 0.00 0.00 40.02 4.61
6443 7910 2.106683 CCGCACTCCGAATTCCCAC 61.107 63.158 0.00 0.00 40.02 4.61
6444 7911 2.267642 CCGCACTCCGAATTCCCA 59.732 61.111 0.00 0.00 40.02 4.37
6445 7912 3.202706 GCCGCACTCCGAATTCCC 61.203 66.667 0.00 0.00 40.02 3.97
6446 7913 3.564027 CGCCGCACTCCGAATTCC 61.564 66.667 0.00 0.00 40.02 3.01
6447 7914 1.908066 AAACGCCGCACTCCGAATTC 61.908 55.000 0.00 0.00 40.02 2.17
6448 7915 1.908066 GAAACGCCGCACTCCGAATT 61.908 55.000 0.00 0.00 40.02 2.17
6449 7916 2.358247 AAACGCCGCACTCCGAAT 60.358 55.556 0.00 0.00 40.02 3.34
6450 7917 3.039588 GAAACGCCGCACTCCGAA 61.040 61.111 0.00 0.00 40.02 4.30
6454 7921 4.072088 CACCGAAACGCCGCACTC 62.072 66.667 0.00 0.00 0.00 3.51
6479 7946 0.313672 TTTTGAACGGGTGCAGATGC 59.686 50.000 0.00 0.00 42.50 3.91
6480 7947 2.791383 TTTTTGAACGGGTGCAGATG 57.209 45.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.