Multiple sequence alignment - TraesCS3D01G061300

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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 TraesCS3D01G061300 chr3D 100.000 2735 0 0 1 2735 26644084 26641350 0.000000e+00 5051.0
1 TraesCS3D01G061300 chr3D 80.723 83 16 0 2155 2237 26640855 26640937 6.320000e-07 65.8
2 TraesCS3D01G061300 chr3B 93.964 878 49 4 765 1641 44857818 44856944 0.000000e+00 1325.0
3 TraesCS3D01G061300 chr3B 86.873 937 90 17 721 1641 45272021 45271102 0.000000e+00 1018.0
4 TraesCS3D01G061300 chr3B 82.713 833 107 18 780 1604 44848407 44847604 0.000000e+00 706.0
5 TraesCS3D01G061300 chr3B 88.277 563 40 15 1 559 44905264 44904724 0.000000e+00 651.0
6 TraesCS3D01G061300 chr3B 90.400 125 6 3 627 746 44904589 44904466 2.820000e-35 159.0
7 TraesCS3D01G061300 chr6A 91.787 901 37 7 1643 2529 581842769 581843646 0.000000e+00 1219.0
8 TraesCS3D01G061300 chr6A 95.872 218 7 2 2520 2735 34036524 34036741 4.330000e-93 351.0
9 TraesCS3D01G061300 chr6B 91.676 901 38 7 1643 2529 207241591 207242468 0.000000e+00 1214.0
10 TraesCS3D01G061300 chr1B 89.033 693 63 8 932 1618 636680045 636679360 0.000000e+00 846.0
11 TraesCS3D01G061300 chr1B 97.248 218 4 2 2520 2735 52692286 52692069 4.300000e-98 368.0
12 TraesCS3D01G061300 chr1B 88.673 309 16 7 403 693 636685248 636684941 2.590000e-95 359.0
13 TraesCS3D01G061300 chr1B 80.090 442 79 9 1644 2080 664416079 664415642 1.220000e-83 320.0
14 TraesCS3D01G061300 chr1B 81.308 214 15 3 688 900 636680236 636680047 1.700000e-32 150.0
15 TraesCS3D01G061300 chr1B 95.652 69 3 0 688 756 636663382 636663314 8.010000e-21 111.0
16 TraesCS3D01G061300 chrUn 84.048 840 113 14 780 1609 38808428 38809256 0.000000e+00 789.0
17 TraesCS3D01G061300 chr2D 95.316 491 19 1 1669 2159 427332416 427332902 0.000000e+00 776.0
18 TraesCS3D01G061300 chr2D 94.932 296 7 2 2234 2529 427332905 427333192 8.930000e-125 457.0
19 TraesCS3D01G061300 chr3A 84.091 396 52 7 1220 1607 36678718 36678326 3.330000e-99 372.0
20 TraesCS3D01G061300 chr3A 76.584 363 62 14 1964 2312 696126220 696125867 7.780000e-41 178.0
21 TraesCS3D01G061300 chr1A 87.781 311 36 2 1309 1618 553903117 553902808 2.000000e-96 363.0
22 TraesCS3D01G061300 chr1A 81.910 199 13 7 696 893 553903891 553903715 2.190000e-31 147.0
23 TraesCS3D01G061300 chr7D 96.330 218 6 2 2520 2735 634755570 634755353 9.310000e-95 357.0
24 TraesCS3D01G061300 chr6D 96.330 218 6 2 2520 2735 353103421 353103638 9.310000e-95 357.0
25 TraesCS3D01G061300 chr5A 96.330 218 6 2 2520 2735 394749210 394749427 9.310000e-95 357.0
26 TraesCS3D01G061300 chr5A 95.872 218 7 2 2520 2735 35738764 35738981 4.330000e-93 351.0
27 TraesCS3D01G061300 chr7B 95.872 218 7 2 2520 2735 672785404 672785187 4.330000e-93 351.0
28 TraesCS3D01G061300 chr4B 95.872 218 7 2 2520 2735 186604255 186604472 4.330000e-93 351.0
29 TraesCS3D01G061300 chr4A 95.872 218 7 2 2520 2735 740747483 740747700 4.330000e-93 351.0
30 TraesCS3D01G061300 chr2B 80.320 437 63 12 1644 2077 545224941 545225357 2.650000e-80 309.0


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 TraesCS3D01G061300 chr3D 26641350 26644084 2734 True 5051.0 5051 100.0000 1 2735 1 chr3D.!!$R1 2734
1 TraesCS3D01G061300 chr3B 44856944 44857818 874 True 1325.0 1325 93.9640 765 1641 1 chr3B.!!$R2 876
2 TraesCS3D01G061300 chr3B 45271102 45272021 919 True 1018.0 1018 86.8730 721 1641 1 chr3B.!!$R3 920
3 TraesCS3D01G061300 chr3B 44847604 44848407 803 True 706.0 706 82.7130 780 1604 1 chr3B.!!$R1 824
4 TraesCS3D01G061300 chr3B 44904466 44905264 798 True 405.0 651 89.3385 1 746 2 chr3B.!!$R4 745
5 TraesCS3D01G061300 chr6A 581842769 581843646 877 False 1219.0 1219 91.7870 1643 2529 1 chr6A.!!$F2 886
6 TraesCS3D01G061300 chr6B 207241591 207242468 877 False 1214.0 1214 91.6760 1643 2529 1 chr6B.!!$F1 886
7 TraesCS3D01G061300 chr1B 636679360 636680236 876 True 498.0 846 85.1705 688 1618 2 chr1B.!!$R5 930
8 TraesCS3D01G061300 chrUn 38808428 38809256 828 False 789.0 789 84.0480 780 1609 1 chrUn.!!$F1 829
9 TraesCS3D01G061300 chr2D 427332416 427333192 776 False 616.5 776 95.1240 1669 2529 2 chr2D.!!$F1 860
10 TraesCS3D01G061300 chr1A 553902808 553903891 1083 True 255.0 363 84.8455 696 1618 2 chr1A.!!$R1 922

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
59 60 0.039437 GTCAGTGACGAGGCGAAAGA 60.039 55.0 7.68 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2314 0.747255 GGAGCTCATAGGCGAAGTCA 59.253 55.0 17.19 0.0 37.29 3.41 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
59 60 0.039437 GTCAGTGACGAGGCGAAAGA 60.039 55.000 7.68 0.00 0.00 2.52
71 72 5.047847 CGAGGCGAAAGATGGAACTTATAA 58.952 41.667 0.00 0.00 0.00 0.98
89 90 6.888088 ACTTATAACAAGGTATGGGTTCAACC 59.112 38.462 0.00 0.00 37.60 3.77
101 102 1.401905 GGTTCAACCCATCGATGCTTC 59.598 52.381 20.25 5.38 30.04 3.86
142 144 9.435688 AAAATCCTAAAGAATATTGGTTGCAAC 57.564 29.630 21.59 21.59 0.00 4.17
180 182 8.527810 ACAAATGAGAAAAGTGAACCAGTAAAA 58.472 29.630 0.00 0.00 0.00 1.52
210 212 9.924010 AGAGATTAGTAGTACAGTAGATGGTTT 57.076 33.333 2.52 0.00 0.00 3.27
222 224 8.306313 ACAGTAGATGGTTTATCATGTCAGTA 57.694 34.615 0.00 0.00 38.31 2.74
243 245 9.958180 TCAGTAAAATAGAACCTGAATCATTCA 57.042 29.630 0.00 0.00 38.17 2.57
257 259 7.748691 TGAATCATTCAGTCTTTCATGTCAA 57.251 32.000 0.00 0.00 34.08 3.18
258 260 7.813645 TGAATCATTCAGTCTTTCATGTCAAG 58.186 34.615 0.00 0.00 34.08 3.02
259 261 6.754702 ATCATTCAGTCTTTCATGTCAAGG 57.245 37.500 7.33 0.00 0.00 3.61
262 264 3.819368 TCAGTCTTTCATGTCAAGGCAA 58.181 40.909 12.53 0.95 0.00 4.52
263 265 3.817084 TCAGTCTTTCATGTCAAGGCAAG 59.183 43.478 12.53 6.50 0.00 4.01
264 266 3.567164 CAGTCTTTCATGTCAAGGCAAGT 59.433 43.478 12.53 0.00 0.00 3.16
265 267 3.567164 AGTCTTTCATGTCAAGGCAAGTG 59.433 43.478 12.53 0.00 0.00 3.16
266 268 2.294233 TCTTTCATGTCAAGGCAAGTGC 59.706 45.455 0.00 0.00 41.14 4.40
270 272 1.542472 CATGTCAAGGCAAGTGCATCA 59.458 47.619 5.52 0.00 44.36 3.07
271 273 1.913778 TGTCAAGGCAAGTGCATCAT 58.086 45.000 5.52 0.00 44.36 2.45
272 274 3.070476 TGTCAAGGCAAGTGCATCATA 57.930 42.857 5.52 0.00 44.36 2.15
273 275 3.623703 TGTCAAGGCAAGTGCATCATAT 58.376 40.909 5.52 0.00 44.36 1.78
274 276 4.779696 TGTCAAGGCAAGTGCATCATATA 58.220 39.130 5.52 0.00 44.36 0.86
275 277 5.379187 TGTCAAGGCAAGTGCATCATATAT 58.621 37.500 5.52 0.00 44.36 0.86
276 278 5.829391 TGTCAAGGCAAGTGCATCATATATT 59.171 36.000 5.52 0.00 44.36 1.28
277 279 6.016860 TGTCAAGGCAAGTGCATCATATATTC 60.017 38.462 5.52 0.00 44.36 1.75
278 280 6.016860 GTCAAGGCAAGTGCATCATATATTCA 60.017 38.462 5.52 0.00 44.36 2.57
279 281 6.717997 TCAAGGCAAGTGCATCATATATTCAT 59.282 34.615 5.52 0.00 44.36 2.57
280 282 7.884354 TCAAGGCAAGTGCATCATATATTCATA 59.116 33.333 5.52 0.00 44.36 2.15
281 283 8.683615 CAAGGCAAGTGCATCATATATTCATAT 58.316 33.333 5.52 0.00 44.36 1.78
282 284 8.221965 AGGCAAGTGCATCATATATTCATATG 57.778 34.615 5.52 0.00 42.75 1.78
283 285 7.832685 AGGCAAGTGCATCATATATTCATATGT 59.167 33.333 5.52 0.00 42.41 2.29
284 286 8.464404 GGCAAGTGCATCATATATTCATATGTT 58.536 33.333 5.52 0.00 42.41 2.71
285 287 9.850628 GCAAGTGCATCATATATTCATATGTTT 57.149 29.630 1.90 0.00 41.50 2.83
329 331 1.466360 GCAACAGCTGGTATGAAAGCG 60.466 52.381 19.93 0.00 44.34 4.68
335 337 3.496130 CAGCTGGTATGAAAGCGAATAGG 59.504 47.826 5.57 0.00 44.34 2.57
348 350 4.270834 AGCGAATAGGTAGAGAGAACACA 58.729 43.478 0.00 0.00 0.00 3.72
350 352 4.734108 GCGAATAGGTAGAGAGAACACACC 60.734 50.000 0.00 0.00 0.00 4.16
369 371 3.433615 CACCAAGAAGAAAAGTCTAGCCG 59.566 47.826 0.00 0.00 32.16 5.52
387 389 3.140141 CGCAAATGCCCGGGTCAT 61.140 61.111 24.63 22.24 37.91 3.06
471 473 9.809096 TGATGAAGTACTTTAAATTGCAACAAA 57.191 25.926 10.02 1.82 0.00 2.83
559 562 1.128200 ATGGGTCGTAGCATAGGCAA 58.872 50.000 0.67 0.00 44.61 4.52
560 563 0.906066 TGGGTCGTAGCATAGGCAAA 59.094 50.000 0.67 0.00 44.61 3.68
561 564 1.279558 TGGGTCGTAGCATAGGCAAAA 59.720 47.619 0.67 0.00 44.61 2.44
563 566 2.290641 GGGTCGTAGCATAGGCAAAATG 59.709 50.000 0.67 0.00 44.61 2.32
565 568 3.202906 GTCGTAGCATAGGCAAAATGGA 58.797 45.455 0.67 0.00 44.61 3.41
568 571 3.242739 CGTAGCATAGGCAAAATGGACAC 60.243 47.826 0.67 0.00 44.61 3.67
569 572 1.745087 AGCATAGGCAAAATGGACACG 59.255 47.619 0.67 0.00 44.61 4.49
570 573 1.472480 GCATAGGCAAAATGGACACGT 59.528 47.619 0.00 0.00 40.72 4.49
572 575 3.486875 GCATAGGCAAAATGGACACGTAC 60.487 47.826 0.00 0.00 40.72 3.67
573 576 2.264005 AGGCAAAATGGACACGTACA 57.736 45.000 0.00 0.00 0.00 2.90
574 577 2.151202 AGGCAAAATGGACACGTACAG 58.849 47.619 0.00 0.00 0.00 2.74
575 578 1.877443 GGCAAAATGGACACGTACAGT 59.123 47.619 0.00 0.00 0.00 3.55
576 579 3.068560 GGCAAAATGGACACGTACAGTA 58.931 45.455 0.00 0.00 0.00 2.74
577 580 3.124636 GGCAAAATGGACACGTACAGTAG 59.875 47.826 0.00 0.00 0.00 2.57
578 581 3.424433 GCAAAATGGACACGTACAGTAGC 60.424 47.826 0.00 0.00 0.00 3.58
579 582 3.671008 AAATGGACACGTACAGTAGCA 57.329 42.857 0.00 0.00 0.00 3.49
580 583 3.887621 AATGGACACGTACAGTAGCAT 57.112 42.857 0.00 0.00 0.00 3.79
581 584 4.994907 AATGGACACGTACAGTAGCATA 57.005 40.909 0.00 0.00 0.00 3.14
582 585 4.569761 ATGGACACGTACAGTAGCATAG 57.430 45.455 0.00 0.00 0.00 2.23
583 586 2.686405 TGGACACGTACAGTAGCATAGG 59.314 50.000 0.00 0.00 0.00 2.57
584 587 2.543238 GGACACGTACAGTAGCATAGGC 60.543 54.545 0.00 0.00 41.61 3.93
585 588 2.097036 ACACGTACAGTAGCATAGGCA 58.903 47.619 0.67 0.00 44.61 4.75
586 589 2.693591 ACACGTACAGTAGCATAGGCAT 59.306 45.455 0.67 0.00 44.61 4.40
587 590 3.132289 ACACGTACAGTAGCATAGGCATT 59.868 43.478 0.67 0.00 44.61 3.56
588 591 3.736252 CACGTACAGTAGCATAGGCATTC 59.264 47.826 0.67 0.00 44.61 2.67
589 592 3.383505 ACGTACAGTAGCATAGGCATTCA 59.616 43.478 0.67 0.00 44.61 2.57
590 593 3.736252 CGTACAGTAGCATAGGCATTCAC 59.264 47.826 0.67 0.00 44.61 3.18
591 594 2.826428 ACAGTAGCATAGGCATTCACG 58.174 47.619 0.67 0.00 44.61 4.35
592 595 2.168521 ACAGTAGCATAGGCATTCACGT 59.831 45.455 0.67 0.00 44.61 4.49
593 596 2.797156 CAGTAGCATAGGCATTCACGTC 59.203 50.000 0.67 0.00 44.61 4.34
594 597 1.787155 GTAGCATAGGCATTCACGTCG 59.213 52.381 0.67 0.00 44.61 5.12
595 598 0.175760 AGCATAGGCATTCACGTCGT 59.824 50.000 0.67 0.00 44.61 4.34
596 599 1.407618 AGCATAGGCATTCACGTCGTA 59.592 47.619 0.67 0.00 44.61 3.43
597 600 1.521423 GCATAGGCATTCACGTCGTAC 59.479 52.381 0.00 0.00 40.72 3.67
598 601 2.804647 CATAGGCATTCACGTCGTACA 58.195 47.619 0.00 0.00 0.00 2.90
599 602 3.381045 CATAGGCATTCACGTCGTACAT 58.619 45.455 0.00 0.00 0.00 2.29
600 603 1.640428 AGGCATTCACGTCGTACATG 58.360 50.000 0.00 4.60 0.00 3.21
601 604 1.203758 AGGCATTCACGTCGTACATGA 59.796 47.619 16.45 0.38 0.00 3.07
602 605 1.588404 GGCATTCACGTCGTACATGAG 59.412 52.381 16.45 0.00 0.00 2.90
603 606 1.005975 GCATTCACGTCGTACATGAGC 60.006 52.381 16.45 5.78 0.00 4.26
604 607 2.258755 CATTCACGTCGTACATGAGCA 58.741 47.619 0.00 0.00 0.00 4.26
605 608 2.647529 TTCACGTCGTACATGAGCAT 57.352 45.000 0.00 0.00 0.00 3.79
606 609 3.768468 TTCACGTCGTACATGAGCATA 57.232 42.857 0.00 0.00 0.00 3.14
607 610 3.060978 TCACGTCGTACATGAGCATAC 57.939 47.619 0.00 0.00 0.00 2.39
618 621 3.689649 ACATGAGCATACGGGAGAAAAAC 59.310 43.478 0.00 0.00 0.00 2.43
650 756 5.916661 ACATACGTAGAGATGAAACCAGT 57.083 39.130 0.08 0.00 0.00 4.00
665 771 9.346725 GATGAAACCAGTTGTTAGATTGAAATC 57.653 33.333 0.00 0.00 35.67 2.17
685 791 2.171870 TCTGACGGGGTGAAAGAAAAGT 59.828 45.455 0.00 0.00 0.00 2.66
800 912 7.701539 TTGTAAACACTCATTTATGCTGGAT 57.298 32.000 0.00 0.00 0.00 3.41
818 930 7.228314 GCTGGATATACGGCATATAATCCTA 57.772 40.000 14.29 0.00 42.32 2.94
889 1007 7.863901 ATGTTTGAGATATAGGCTTCCTAGT 57.136 36.000 0.00 0.00 39.70 2.57
990 1335 3.900966 ACCCCGTTAAGGTGAACTATC 57.099 47.619 0.00 0.00 35.85 2.08
996 1341 5.581085 CCCGTTAAGGTGAACTATCAAGAAG 59.419 44.000 0.00 0.00 37.30 2.85
998 1343 6.531948 CCGTTAAGGTGAACTATCAAGAAGAG 59.468 42.308 0.00 0.00 37.30 2.85
999 1344 7.313646 CGTTAAGGTGAACTATCAAGAAGAGA 58.686 38.462 0.00 0.00 37.30 3.10
1000 1345 7.273815 CGTTAAGGTGAACTATCAAGAAGAGAC 59.726 40.741 0.00 0.00 37.30 3.36
1145 1507 4.162690 ACGGCGGATCAAGCTCCC 62.163 66.667 13.24 0.00 34.52 4.30
1210 1572 2.126189 GACCACTACGTCACGCCC 60.126 66.667 0.00 0.00 32.74 6.13
1218 1580 1.304509 TACGTCACGCCCGACATGTA 61.305 55.000 0.00 0.00 35.54 2.29
1609 1976 1.444553 CGTCGACTGGGTGAAGCTC 60.445 63.158 14.70 0.00 0.00 4.09
1739 2106 1.762370 ACCCCCTGAACTTTGCAAAAG 59.238 47.619 13.84 7.45 0.00 2.27
1798 2165 7.499895 AGAATTGAAGGTGGTTTTCGTACTAAA 59.500 33.333 0.00 0.00 0.00 1.85
1799 2166 6.998968 TTGAAGGTGGTTTTCGTACTAAAA 57.001 33.333 1.41 1.41 0.00 1.52
1892 2259 3.531538 TCAGCAACGTCTTTTTGTCTCT 58.468 40.909 0.00 0.00 0.00 3.10
1896 2263 4.156008 AGCAACGTCTTTTTGTCTCTGTTT 59.844 37.500 0.00 0.00 0.00 2.83
1939 2306 3.177884 ACCACTGCAGCTTCCCCA 61.178 61.111 15.27 0.00 0.00 4.96
1959 2326 2.797278 CCGCCCTGACTTCGCCTAT 61.797 63.158 0.00 0.00 0.00 2.57
2029 2396 2.261671 CACCTGTAGCGTCGCCTT 59.738 61.111 14.86 0.00 0.00 4.35
2159 2526 2.933287 TGGTCCTTCCATGGCCGT 60.933 61.111 6.96 0.00 41.93 5.68
2160 2527 2.438434 GGTCCTTCCATGGCCGTG 60.438 66.667 18.73 18.73 35.97 4.94
2162 2529 3.329889 TCCTTCCATGGCCGTGCT 61.330 61.111 20.27 0.00 0.00 4.40
2163 2530 2.361610 CCTTCCATGGCCGTGCTT 60.362 61.111 20.27 0.00 0.00 3.91
2164 2531 1.978617 CCTTCCATGGCCGTGCTTT 60.979 57.895 20.27 0.00 0.00 3.51
2165 2532 1.535204 CCTTCCATGGCCGTGCTTTT 61.535 55.000 20.27 0.00 0.00 2.27
2172 2553 4.445545 GCCGTGCTTTTCCGAGCG 62.446 66.667 0.00 0.00 45.64 5.03
2185 2566 1.139734 CGAGCGCTGCTTTCCTAGA 59.860 57.895 18.48 0.00 39.88 2.43
2278 2659 1.332195 GGCCTCTTCCTTTTGCAACT 58.668 50.000 0.00 0.00 0.00 3.16
2349 2730 3.475566 TCCATAGGATTTGGAAGAGCG 57.524 47.619 0.00 0.00 40.29 5.03
2419 2800 1.669604 CGAGAGTCTCTCATCCCGAA 58.330 55.000 25.91 0.00 43.55 4.30
2436 2817 1.673168 GAAGGCCATTACTGCTCCTG 58.327 55.000 5.01 0.00 0.00 3.86
2489 2870 4.932591 GAGATGCACATGCGCGCG 62.933 66.667 28.44 28.44 45.83 6.86
2529 2910 3.944015 GCTCACTGATTAGGAATGCAAGT 59.056 43.478 0.00 0.00 0.00 3.16
2530 2911 4.034975 GCTCACTGATTAGGAATGCAAGTC 59.965 45.833 0.00 0.00 0.00 3.01
2531 2912 5.164620 TCACTGATTAGGAATGCAAGTCA 57.835 39.130 0.00 0.00 28.43 3.41
2532 2913 5.748402 TCACTGATTAGGAATGCAAGTCAT 58.252 37.500 0.00 0.00 36.87 3.06
2533 2914 5.587443 TCACTGATTAGGAATGCAAGTCATG 59.413 40.000 0.00 0.00 35.13 3.07
2545 2926 4.192000 GTCATGCCTGACCGACAG 57.808 61.111 10.74 3.25 45.06 3.51
2556 2937 2.261671 CCGACAGGTGCTACGCTT 59.738 61.111 0.00 0.00 0.00 4.68
2557 2938 1.374252 CCGACAGGTGCTACGCTTT 60.374 57.895 0.00 0.00 0.00 3.51
2558 2939 1.626654 CCGACAGGTGCTACGCTTTG 61.627 60.000 0.00 0.00 0.00 2.77
2559 2940 0.944311 CGACAGGTGCTACGCTTTGT 60.944 55.000 0.00 0.00 0.00 2.83
2560 2941 0.790814 GACAGGTGCTACGCTTTGTC 59.209 55.000 0.00 0.00 31.47 3.18
2561 2942 0.105964 ACAGGTGCTACGCTTTGTCA 59.894 50.000 0.00 0.00 0.00 3.58
2562 2943 1.270839 ACAGGTGCTACGCTTTGTCAT 60.271 47.619 0.00 0.00 0.00 3.06
2563 2944 1.129251 CAGGTGCTACGCTTTGTCATG 59.871 52.381 0.00 0.00 0.00 3.07
2564 2945 0.179189 GGTGCTACGCTTTGTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
2565 2946 0.179189 GTGCTACGCTTTGTCATGCC 60.179 55.000 0.00 0.00 0.00 4.40
2566 2947 0.321564 TGCTACGCTTTGTCATGCCT 60.322 50.000 0.00 0.00 0.00 4.75
2567 2948 1.066502 TGCTACGCTTTGTCATGCCTA 60.067 47.619 0.00 0.00 0.00 3.93
2568 2949 1.594862 GCTACGCTTTGTCATGCCTAG 59.405 52.381 0.00 0.00 0.00 3.02
2569 2950 2.893637 CTACGCTTTGTCATGCCTAGT 58.106 47.619 0.00 0.00 0.00 2.57
2570 2951 1.726853 ACGCTTTGTCATGCCTAGTC 58.273 50.000 0.00 0.00 0.00 2.59
2571 2952 0.647410 CGCTTTGTCATGCCTAGTCG 59.353 55.000 0.00 0.00 0.00 4.18
2572 2953 1.009829 GCTTTGTCATGCCTAGTCGG 58.990 55.000 0.00 0.00 0.00 4.79
2581 2962 3.935024 CCTAGTCGGCAGGTGCTA 58.065 61.111 1.26 0.00 41.70 3.49
2582 2963 2.431023 CCTAGTCGGCAGGTGCTAT 58.569 57.895 1.26 0.00 41.70 2.97
2583 2964 0.032678 CCTAGTCGGCAGGTGCTATG 59.967 60.000 1.26 0.00 41.70 2.23
2584 2965 0.598680 CTAGTCGGCAGGTGCTATGC 60.599 60.000 1.26 0.45 43.09 3.14
2585 2966 1.326951 TAGTCGGCAGGTGCTATGCA 61.327 55.000 1.26 0.00 45.68 3.96
2586 2967 1.524621 GTCGGCAGGTGCTATGCAT 60.525 57.895 3.79 3.79 45.68 3.96
2587 2968 1.524393 TCGGCAGGTGCTATGCATG 60.524 57.895 10.16 0.26 45.68 4.06
2588 2969 1.524393 CGGCAGGTGCTATGCATGA 60.524 57.895 10.16 0.00 45.68 3.07
2589 2970 1.779025 CGGCAGGTGCTATGCATGAC 61.779 60.000 10.16 3.09 45.68 3.06
2590 2971 0.749091 GGCAGGTGCTATGCATGACA 60.749 55.000 10.16 4.24 45.68 3.58
2591 2972 0.661552 GCAGGTGCTATGCATGACAG 59.338 55.000 10.16 0.00 41.91 3.51
2592 2973 1.744798 GCAGGTGCTATGCATGACAGA 60.745 52.381 10.16 0.00 41.91 3.41
2593 2974 2.847441 CAGGTGCTATGCATGACAGAT 58.153 47.619 10.16 0.00 41.91 2.90
2594 2975 2.806818 CAGGTGCTATGCATGACAGATC 59.193 50.000 10.16 0.81 41.91 2.75
2595 2976 2.704596 AGGTGCTATGCATGACAGATCT 59.295 45.455 10.16 0.00 41.91 2.75
2596 2977 3.136077 AGGTGCTATGCATGACAGATCTT 59.864 43.478 10.16 0.00 41.91 2.40
2597 2978 3.881688 GGTGCTATGCATGACAGATCTTT 59.118 43.478 10.16 0.00 41.91 2.52
2598 2979 4.024218 GGTGCTATGCATGACAGATCTTTC 60.024 45.833 10.16 1.70 41.91 2.62
2599 2980 4.573607 GTGCTATGCATGACAGATCTTTCA 59.426 41.667 13.75 13.75 41.91 2.69
2600 2981 5.065602 GTGCTATGCATGACAGATCTTTCAA 59.934 40.000 15.24 0.13 41.91 2.69
2601 2982 5.648960 TGCTATGCATGACAGATCTTTCAAA 59.351 36.000 15.24 5.39 31.71 2.69
2602 2983 6.183360 TGCTATGCATGACAGATCTTTCAAAG 60.183 38.462 15.24 11.80 31.71 2.77
2603 2984 6.037940 GCTATGCATGACAGATCTTTCAAAGA 59.962 38.462 15.24 1.30 42.69 2.52
2604 2985 5.618056 TGCATGACAGATCTTTCAAAGAC 57.382 39.130 15.24 6.32 41.01 3.01
2605 2986 5.311265 TGCATGACAGATCTTTCAAAGACT 58.689 37.500 15.24 0.00 41.01 3.24
2606 2987 5.766670 TGCATGACAGATCTTTCAAAGACTT 59.233 36.000 15.24 0.00 41.01 3.01
2607 2988 6.072838 TGCATGACAGATCTTTCAAAGACTTC 60.073 38.462 15.24 0.00 41.01 3.01
2608 2989 6.072838 GCATGACAGATCTTTCAAAGACTTCA 60.073 38.462 15.24 3.41 41.01 3.02
2609 2990 7.521099 GCATGACAGATCTTTCAAAGACTTCAA 60.521 37.037 15.24 0.00 41.01 2.69
2610 2991 7.488187 TGACAGATCTTTCAAAGACTTCAAG 57.512 36.000 9.14 0.00 41.01 3.02
2611 2992 6.017605 TGACAGATCTTTCAAAGACTTCAAGC 60.018 38.462 9.14 0.00 41.01 4.01
2612 2993 6.060788 ACAGATCTTTCAAAGACTTCAAGCT 58.939 36.000 0.68 0.00 41.01 3.74
2613 2994 6.017275 ACAGATCTTTCAAAGACTTCAAGCTG 60.017 38.462 0.68 0.00 41.01 4.24
2614 2995 6.017275 CAGATCTTTCAAAGACTTCAAGCTGT 60.017 38.462 0.68 0.00 41.01 4.40
2615 2996 5.490139 TCTTTCAAAGACTTCAAGCTGTG 57.510 39.130 0.00 0.00 31.20 3.66
2616 2997 4.943705 TCTTTCAAAGACTTCAAGCTGTGT 59.056 37.500 0.00 0.00 31.20 3.72
2617 2998 4.882671 TTCAAAGACTTCAAGCTGTGTC 57.117 40.909 0.00 0.00 0.00 3.67
2618 2999 2.866156 TCAAAGACTTCAAGCTGTGTCG 59.134 45.455 0.00 0.00 34.92 4.35
2619 3000 1.871080 AAGACTTCAAGCTGTGTCGG 58.129 50.000 0.00 0.00 34.92 4.79
2620 3001 0.601311 AGACTTCAAGCTGTGTCGGC 60.601 55.000 0.00 0.00 34.92 5.54
2622 3003 0.882042 ACTTCAAGCTGTGTCGGCTG 60.882 55.000 3.78 0.00 46.32 4.85
2623 3004 0.601046 CTTCAAGCTGTGTCGGCTGA 60.601 55.000 3.78 0.00 46.32 4.26
2624 3005 0.035317 TTCAAGCTGTGTCGGCTGAT 59.965 50.000 0.00 0.00 46.32 2.90
2625 3006 0.671472 TCAAGCTGTGTCGGCTGATG 60.671 55.000 0.00 0.56 46.32 3.07
2626 3007 1.376424 AAGCTGTGTCGGCTGATGG 60.376 57.895 0.00 0.00 46.32 3.51
2627 3008 2.046892 GCTGTGTCGGCTGATGGT 60.047 61.111 0.00 0.00 32.24 3.55
2628 3009 1.218047 GCTGTGTCGGCTGATGGTA 59.782 57.895 0.00 0.00 32.24 3.25
2629 3010 1.084370 GCTGTGTCGGCTGATGGTAC 61.084 60.000 0.00 0.00 32.24 3.34
2630 3011 0.532573 CTGTGTCGGCTGATGGTACT 59.467 55.000 0.00 0.00 0.00 2.73
2631 3012 0.973632 TGTGTCGGCTGATGGTACTT 59.026 50.000 0.00 0.00 0.00 2.24
2632 3013 1.337728 TGTGTCGGCTGATGGTACTTG 60.338 52.381 0.00 0.00 0.00 3.16
2633 3014 0.249120 TGTCGGCTGATGGTACTTGG 59.751 55.000 0.00 0.00 0.00 3.61
2634 3015 1.090052 GTCGGCTGATGGTACTTGGC 61.090 60.000 0.00 0.00 0.00 4.52
2635 3016 1.078497 CGGCTGATGGTACTTGGCA 60.078 57.895 0.00 0.00 0.00 4.92
2636 3017 1.091771 CGGCTGATGGTACTTGGCAG 61.092 60.000 0.00 0.00 0.00 4.85
2637 3018 2.101700 GCTGATGGTACTTGGCAGC 58.898 57.895 12.25 12.25 44.11 5.25
2638 3019 3.556817 CTGATGGTACTTGGCAGCA 57.443 52.632 0.00 0.00 0.00 4.41
2639 3020 2.048444 CTGATGGTACTTGGCAGCAT 57.952 50.000 0.00 0.00 36.85 3.79
2640 3021 1.674441 CTGATGGTACTTGGCAGCATG 59.326 52.381 0.00 0.00 34.41 4.06
2641 3022 1.027357 GATGGTACTTGGCAGCATGG 58.973 55.000 0.00 0.00 34.41 3.66
2642 3023 0.332632 ATGGTACTTGGCAGCATGGT 59.667 50.000 0.00 0.00 35.86 3.55
2643 3024 0.608856 TGGTACTTGGCAGCATGGTG 60.609 55.000 20.52 20.52 35.86 4.17
2644 3025 1.508088 GTACTTGGCAGCATGGTGC 59.492 57.895 35.86 35.86 45.46 5.01
2654 3035 3.483954 GCATGGTGCTGAGGTGTAT 57.516 52.632 0.00 0.00 40.96 2.29
2655 3036 1.303309 GCATGGTGCTGAGGTGTATC 58.697 55.000 0.00 0.00 40.96 2.24
2656 3037 1.407299 GCATGGTGCTGAGGTGTATCA 60.407 52.381 0.00 0.00 40.96 2.15
2658 3039 1.644509 TGGTGCTGAGGTGTATCAGT 58.355 50.000 5.69 0.00 46.93 3.41
2659 3040 1.276138 TGGTGCTGAGGTGTATCAGTG 59.724 52.381 5.69 0.00 46.93 3.66
2660 3041 1.406069 GGTGCTGAGGTGTATCAGTGG 60.406 57.143 5.69 0.00 46.93 4.00
2661 3042 0.250234 TGCTGAGGTGTATCAGTGGC 59.750 55.000 5.69 0.00 46.93 5.01
2662 3043 0.807667 GCTGAGGTGTATCAGTGGCG 60.808 60.000 5.69 0.00 46.93 5.69
2663 3044 0.817654 CTGAGGTGTATCAGTGGCGA 59.182 55.000 0.00 0.00 41.52 5.54
2664 3045 0.530744 TGAGGTGTATCAGTGGCGAC 59.469 55.000 0.00 0.00 0.00 5.19
2665 3046 0.179108 GAGGTGTATCAGTGGCGACC 60.179 60.000 0.00 0.00 0.00 4.79
2666 3047 1.518572 GGTGTATCAGTGGCGACCG 60.519 63.158 0.00 0.00 0.00 4.79
2667 3048 2.165301 GTGTATCAGTGGCGACCGC 61.165 63.158 5.75 5.75 41.06 5.68
2668 3049 2.954868 GTATCAGTGGCGACCGCG 60.955 66.667 8.36 0.00 43.06 6.46
2669 3050 3.135457 TATCAGTGGCGACCGCGA 61.135 61.111 8.23 1.16 43.06 5.87
2678 3059 4.813526 CGACCGCGACGTCCTCAG 62.814 72.222 8.23 0.00 40.82 3.35
2679 3060 3.429141 GACCGCGACGTCCTCAGA 61.429 66.667 8.23 0.00 0.00 3.27
2680 3061 2.750637 ACCGCGACGTCCTCAGAT 60.751 61.111 8.23 0.00 0.00 2.90
2681 3062 2.278206 CCGCGACGTCCTCAGATG 60.278 66.667 8.23 0.00 34.96 2.90
2682 3063 2.485582 CGCGACGTCCTCAGATGT 59.514 61.111 10.58 0.00 45.16 3.06
2683 3064 1.154016 CGCGACGTCCTCAGATGTT 60.154 57.895 10.58 0.00 42.46 2.71
2684 3065 0.732880 CGCGACGTCCTCAGATGTTT 60.733 55.000 10.58 0.00 42.46 2.83
2685 3066 0.716108 GCGACGTCCTCAGATGTTTG 59.284 55.000 10.58 0.00 42.46 2.93
2686 3067 0.716108 CGACGTCCTCAGATGTTTGC 59.284 55.000 10.58 0.00 42.46 3.68
2687 3068 0.716108 GACGTCCTCAGATGTTTGCG 59.284 55.000 3.51 0.00 42.46 4.85
2688 3069 1.291877 ACGTCCTCAGATGTTTGCGC 61.292 55.000 0.00 0.00 39.27 6.09
2689 3070 1.421485 GTCCTCAGATGTTTGCGCG 59.579 57.895 0.00 0.00 0.00 6.86
2690 3071 2.099062 CCTCAGATGTTTGCGCGC 59.901 61.111 27.26 27.26 0.00 6.86
2691 3072 2.679934 CCTCAGATGTTTGCGCGCA 61.680 57.895 33.09 33.09 0.00 6.09
2692 3073 1.225936 CTCAGATGTTTGCGCGCAG 60.226 57.895 34.25 20.50 0.00 5.18
2693 3074 2.202388 CAGATGTTTGCGCGCAGG 60.202 61.111 34.25 14.32 0.00 4.85
2694 3075 3.434319 AGATGTTTGCGCGCAGGG 61.434 61.111 34.25 0.00 46.11 4.45
2695 3076 3.430862 GATGTTTGCGCGCAGGGA 61.431 61.111 34.25 21.12 46.37 4.20
2696 3077 3.386867 GATGTTTGCGCGCAGGGAG 62.387 63.158 34.25 0.00 46.37 4.30
2707 3088 3.322466 CAGGGAGGAGGTGCCGTT 61.322 66.667 0.00 0.00 43.04 4.44
2708 3089 3.322466 AGGGAGGAGGTGCCGTTG 61.322 66.667 0.00 0.00 43.04 4.10
2709 3090 4.410400 GGGAGGAGGTGCCGTTGG 62.410 72.222 0.00 0.00 43.43 3.77
2710 3091 4.410400 GGAGGAGGTGCCGTTGGG 62.410 72.222 0.00 0.00 43.43 4.12
2731 3112 4.771356 CGTGGTGGCGTCGACGAT 62.771 66.667 39.74 0.00 40.81 3.73
2732 3113 2.486504 GTGGTGGCGTCGACGATA 59.513 61.111 39.74 24.35 43.02 2.92
2733 3114 1.585521 GTGGTGGCGTCGACGATAG 60.586 63.158 39.74 13.08 43.02 2.08
2734 3115 2.654404 GGTGGCGTCGACGATAGC 60.654 66.667 39.74 29.51 43.02 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.181517 CGTCACTGACCATATTGCACTTG 60.182 47.826 3.50 0.00 0.00 3.16
33 34 2.205074 GCCTCGTCACTGACCATATTG 58.795 52.381 3.50 0.00 0.00 1.90
59 60 7.220890 ACCCATACCTTGTTATAAGTTCCAT 57.779 36.000 0.00 0.00 0.00 3.41
180 182 9.938280 CATCTACTGTACTACTAATCTCTAGCT 57.062 37.037 0.00 0.00 0.00 3.32
198 200 9.599866 TTTACTGACATGATAAACCATCTACTG 57.400 33.333 0.00 0.00 34.46 2.74
243 245 3.567164 CACTTGCCTTGACATGAAAGACT 59.433 43.478 0.00 0.00 0.00 3.24
251 253 1.913778 TGATGCACTTGCCTTGACAT 58.086 45.000 0.00 0.00 41.18 3.06
254 256 6.063404 TGAATATATGATGCACTTGCCTTGA 58.937 36.000 0.00 0.00 41.18 3.02
255 257 6.321848 TGAATATATGATGCACTTGCCTTG 57.678 37.500 0.00 0.00 41.18 3.61
256 258 8.683615 CATATGAATATATGATGCACTTGCCTT 58.316 33.333 0.00 0.00 45.92 4.35
257 259 7.832685 ACATATGAATATATGATGCACTTGCCT 59.167 33.333 10.38 0.00 45.92 4.75
258 260 7.993101 ACATATGAATATATGATGCACTTGCC 58.007 34.615 10.38 0.00 45.92 4.52
259 261 9.850628 AAACATATGAATATATGATGCACTTGC 57.149 29.630 10.38 0.00 45.92 4.01
315 317 3.467803 ACCTATTCGCTTTCATACCAGC 58.532 45.455 0.00 0.00 0.00 4.85
329 331 5.916661 TGGTGTGTTCTCTCTACCTATTC 57.083 43.478 0.00 0.00 32.68 1.75
335 337 5.455056 TCTTCTTGGTGTGTTCTCTCTAC 57.545 43.478 0.00 0.00 0.00 2.59
348 350 3.665190 CGGCTAGACTTTTCTTCTTGGT 58.335 45.455 0.00 0.00 32.75 3.67
350 352 2.092838 CGCGGCTAGACTTTTCTTCTTG 59.907 50.000 0.00 0.00 32.75 3.02
412 414 9.934784 AATATGGCAGACATCTATCTATCTACT 57.065 33.333 0.00 0.00 41.03 2.57
471 473 8.962884 AAAATCTTCCAGCACTTAAACAAAAT 57.037 26.923 0.00 0.00 0.00 1.82
536 539 2.036733 GCCTATGCTACGACCCATTACA 59.963 50.000 0.00 0.00 33.53 2.41
545 548 3.202906 GTCCATTTTGCCTATGCTACGA 58.797 45.455 0.00 0.00 38.71 3.43
559 562 3.671008 TGCTACTGTACGTGTCCATTT 57.329 42.857 0.00 0.00 0.00 2.32
560 563 3.887621 ATGCTACTGTACGTGTCCATT 57.112 42.857 0.00 0.00 0.00 3.16
561 564 3.318275 CCTATGCTACTGTACGTGTCCAT 59.682 47.826 0.00 0.00 0.00 3.41
563 566 2.543238 GCCTATGCTACTGTACGTGTCC 60.543 54.545 0.00 0.00 33.53 4.02
565 568 2.097036 TGCCTATGCTACTGTACGTGT 58.903 47.619 0.00 0.00 38.71 4.49
568 571 3.736252 GTGAATGCCTATGCTACTGTACG 59.264 47.826 0.00 0.00 38.71 3.67
569 572 3.736252 CGTGAATGCCTATGCTACTGTAC 59.264 47.826 0.00 0.00 38.71 2.90
570 573 3.383505 ACGTGAATGCCTATGCTACTGTA 59.616 43.478 0.00 0.00 38.71 2.74
572 575 2.797156 GACGTGAATGCCTATGCTACTG 59.203 50.000 0.00 0.00 38.71 2.74
573 576 2.543861 CGACGTGAATGCCTATGCTACT 60.544 50.000 0.00 0.00 38.71 2.57
574 577 1.787155 CGACGTGAATGCCTATGCTAC 59.213 52.381 0.00 0.00 38.71 3.58
575 578 1.407618 ACGACGTGAATGCCTATGCTA 59.592 47.619 0.00 0.00 38.71 3.49
576 579 0.175760 ACGACGTGAATGCCTATGCT 59.824 50.000 0.00 0.00 38.71 3.79
577 580 1.521423 GTACGACGTGAATGCCTATGC 59.479 52.381 11.56 0.00 38.26 3.14
578 581 2.804647 TGTACGACGTGAATGCCTATG 58.195 47.619 11.56 0.00 0.00 2.23
579 582 3.067601 TCATGTACGACGTGAATGCCTAT 59.932 43.478 11.56 0.00 40.82 2.57
580 583 2.424246 TCATGTACGACGTGAATGCCTA 59.576 45.455 11.56 0.00 40.82 3.93
581 584 1.203758 TCATGTACGACGTGAATGCCT 59.796 47.619 11.56 0.00 40.82 4.75
582 585 1.588404 CTCATGTACGACGTGAATGCC 59.412 52.381 11.56 0.00 42.90 4.40
583 586 1.005975 GCTCATGTACGACGTGAATGC 60.006 52.381 11.56 3.94 42.90 3.56
584 587 2.258755 TGCTCATGTACGACGTGAATG 58.741 47.619 11.56 13.71 42.90 2.67
585 588 2.647529 TGCTCATGTACGACGTGAAT 57.352 45.000 11.56 0.77 42.90 2.57
586 589 2.647529 ATGCTCATGTACGACGTGAA 57.352 45.000 11.56 0.00 42.90 3.18
587 590 2.538132 CGTATGCTCATGTACGACGTGA 60.538 50.000 11.56 0.00 44.67 4.35
588 591 1.773525 CGTATGCTCATGTACGACGTG 59.226 52.381 11.56 0.00 44.67 4.49
589 592 1.268386 CCGTATGCTCATGTACGACGT 60.268 52.381 13.43 5.52 44.67 4.34
590 593 1.395670 CCGTATGCTCATGTACGACG 58.604 55.000 13.43 10.14 44.67 5.12
591 594 1.335810 TCCCGTATGCTCATGTACGAC 59.664 52.381 13.43 0.59 44.67 4.34
592 595 1.607148 CTCCCGTATGCTCATGTACGA 59.393 52.381 13.43 0.00 44.67 3.43
593 596 1.607148 TCTCCCGTATGCTCATGTACG 59.393 52.381 6.62 6.62 42.32 3.67
594 597 3.728076 TTCTCCCGTATGCTCATGTAC 57.272 47.619 0.00 0.00 0.00 2.90
595 598 4.746535 TTTTCTCCCGTATGCTCATGTA 57.253 40.909 0.00 0.00 0.00 2.29
596 599 3.627395 TTTTCTCCCGTATGCTCATGT 57.373 42.857 0.00 0.00 0.00 3.21
597 600 3.242413 CGTTTTTCTCCCGTATGCTCATG 60.242 47.826 0.00 0.00 0.00 3.07
598 601 2.936498 CGTTTTTCTCCCGTATGCTCAT 59.064 45.455 0.00 0.00 0.00 2.90
599 602 2.289195 ACGTTTTTCTCCCGTATGCTCA 60.289 45.455 0.00 0.00 32.22 4.26
600 603 2.093783 CACGTTTTTCTCCCGTATGCTC 59.906 50.000 0.00 0.00 32.81 4.26
601 604 2.073816 CACGTTTTTCTCCCGTATGCT 58.926 47.619 0.00 0.00 32.81 3.79
602 605 2.070783 TCACGTTTTTCTCCCGTATGC 58.929 47.619 0.00 0.00 32.81 3.14
603 606 4.390603 TCAATCACGTTTTTCTCCCGTATG 59.609 41.667 0.00 0.00 32.81 2.39
604 607 4.571919 TCAATCACGTTTTTCTCCCGTAT 58.428 39.130 0.00 0.00 32.81 3.06
605 608 3.992643 TCAATCACGTTTTTCTCCCGTA 58.007 40.909 0.00 0.00 32.81 4.02
606 609 2.841215 TCAATCACGTTTTTCTCCCGT 58.159 42.857 0.00 0.00 34.71 5.28
607 610 3.889196 TTCAATCACGTTTTTCTCCCG 57.111 42.857 0.00 0.00 0.00 5.14
618 621 6.691388 TCATCTCTACGTATGTTTCAATCACG 59.309 38.462 0.00 0.00 38.52 4.35
650 756 4.941263 CCCCGTCAGATTTCAATCTAACAA 59.059 41.667 1.64 0.00 43.65 2.83
665 771 2.290641 CACTTTTCTTTCACCCCGTCAG 59.709 50.000 0.00 0.00 0.00 3.51
671 777 7.739498 TGTATTAGTCACTTTTCTTTCACCC 57.261 36.000 0.00 0.00 0.00 4.61
703 809 1.180029 GTGCCTCATGTGCCTGATTT 58.820 50.000 7.37 0.00 0.00 2.17
756 867 6.114221 ACAACTTTACATACACACACACAC 57.886 37.500 0.00 0.00 0.00 3.82
757 868 7.845066 TTACAACTTTACATACACACACACA 57.155 32.000 0.00 0.00 0.00 3.72
758 869 8.176365 TGTTTACAACTTTACATACACACACAC 58.824 33.333 0.00 0.00 0.00 3.82
759 870 8.176365 GTGTTTACAACTTTACATACACACACA 58.824 33.333 0.00 0.00 35.82 3.72
760 871 8.392612 AGTGTTTACAACTTTACATACACACAC 58.607 33.333 0.00 0.00 37.64 3.82
761 872 8.495361 AGTGTTTACAACTTTACATACACACA 57.505 30.769 0.00 0.00 37.64 3.72
762 873 8.605746 TGAGTGTTTACAACTTTACATACACAC 58.394 33.333 0.00 0.00 37.64 3.82
763 874 8.719560 TGAGTGTTTACAACTTTACATACACA 57.280 30.769 0.00 0.00 37.64 3.72
808 920 7.589958 ATCGCCGAAGATCTTAGGATTATAT 57.410 36.000 31.85 16.30 37.51 0.86
955 1300 2.367567 ACGGGGTGGTGTATCATATCAC 59.632 50.000 0.00 0.00 0.00 3.06
970 1315 3.175594 TGATAGTTCACCTTAACGGGGT 58.824 45.455 0.00 0.00 37.50 4.95
990 1335 2.224621 TGCCCTCCTTTGTCTCTTCTTG 60.225 50.000 0.00 0.00 0.00 3.02
996 1341 1.743252 CGCTGCCCTCCTTTGTCTC 60.743 63.158 0.00 0.00 0.00 3.36
998 1343 2.747855 CCGCTGCCCTCCTTTGTC 60.748 66.667 0.00 0.00 0.00 3.18
999 1344 4.351054 CCCGCTGCCCTCCTTTGT 62.351 66.667 0.00 0.00 0.00 2.83
1000 1345 3.984193 CTCCCGCTGCCCTCCTTTG 62.984 68.421 0.00 0.00 0.00 2.77
1368 1730 1.796796 GACCGCATGACCTTCTTGC 59.203 57.895 0.00 4.40 42.15 4.01
1609 1976 5.812127 TGAATGAATTCAGTGACCGATACTG 59.188 40.000 14.00 0.00 45.30 2.74
1641 2008 8.071854 TCAGGGGGAGAAATATACTTTCTTCTA 58.928 37.037 12.11 0.00 38.73 2.10
1739 2106 1.134220 TCTGGGGTGACATTTATCCGC 60.134 52.381 0.00 0.00 0.00 5.54
1798 2165 5.500234 TCATTAACAGCCTAGTCAGCATTT 58.500 37.500 0.00 0.00 0.00 2.32
1799 2166 5.102953 TCATTAACAGCCTAGTCAGCATT 57.897 39.130 0.00 0.00 0.00 3.56
1947 2314 0.747255 GGAGCTCATAGGCGAAGTCA 59.253 55.000 17.19 0.00 37.29 3.41
1959 2326 4.373116 GCGTTCACCCGGAGCTCA 62.373 66.667 17.19 0.00 0.00 4.26
1989 2356 0.820871 GGATCAGACGAGGAAGCAGT 59.179 55.000 0.00 0.00 0.00 4.40
2121 2488 1.502231 CGTGTGAGAGAGGTTGGTTG 58.498 55.000 0.00 0.00 0.00 3.77
2122 2489 0.249911 GCGTGTGAGAGAGGTTGGTT 60.250 55.000 0.00 0.00 0.00 3.67
2123 2490 1.115930 AGCGTGTGAGAGAGGTTGGT 61.116 55.000 0.00 0.00 0.00 3.67
2124 2491 0.668706 CAGCGTGTGAGAGAGGTTGG 60.669 60.000 0.00 0.00 0.00 3.77
2159 2526 3.726517 GCAGCGCTCGGAAAAGCA 61.727 61.111 7.13 0.00 42.62 3.91
2160 2527 2.463675 AAAGCAGCGCTCGGAAAAGC 62.464 55.000 7.13 6.17 38.25 3.51
2162 2529 1.574428 GAAAGCAGCGCTCGGAAAA 59.426 52.632 7.13 0.00 38.25 2.29
2163 2530 2.325082 GGAAAGCAGCGCTCGGAAA 61.325 57.895 7.13 0.00 38.25 3.13
2164 2531 1.884075 TAGGAAAGCAGCGCTCGGAA 61.884 55.000 7.13 0.00 38.25 4.30
2165 2532 2.284798 CTAGGAAAGCAGCGCTCGGA 62.285 60.000 7.13 0.00 38.25 4.55
2172 2553 1.086634 CGCCAGTCTAGGAAAGCAGC 61.087 60.000 0.00 0.00 0.00 5.25
2210 2591 2.218603 ACCACGAACATGAACTTGACC 58.781 47.619 0.00 0.00 0.00 4.02
2278 2659 2.355837 GCTTCTGCGTGACGGACA 60.356 61.111 7.25 0.00 31.67 4.02
2399 2780 0.816018 TCGGGATGAGAGACTCTCGC 60.816 60.000 24.09 18.66 46.25 5.03
2400 2781 1.601903 CTTCGGGATGAGAGACTCTCG 59.398 57.143 24.09 14.46 46.25 4.04
2401 2782 1.953686 CCTTCGGGATGAGAGACTCTC 59.046 57.143 23.28 23.28 39.66 3.20
2402 2783 2.026905 GCCTTCGGGATGAGAGACTCT 61.027 57.143 4.14 4.14 37.25 3.24
2403 2784 0.387565 GCCTTCGGGATGAGAGACTC 59.612 60.000 0.00 0.00 37.25 3.36
2404 2785 1.045911 GGCCTTCGGGATGAGAGACT 61.046 60.000 0.00 0.00 37.25 3.24
2405 2786 1.330655 TGGCCTTCGGGATGAGAGAC 61.331 60.000 3.32 0.00 37.25 3.36
2419 2800 0.995024 AACAGGAGCAGTAATGGCCT 59.005 50.000 3.32 0.00 0.00 5.19
2436 2817 5.612351 CTTCAATAAGGGTAGGGAGCTAAC 58.388 45.833 0.00 0.00 0.00 2.34
2535 2916 1.154016 CGTAGCACCTGTCGGTCAG 60.154 63.158 0.00 0.00 43.24 3.51
2536 2917 2.959372 CGTAGCACCTGTCGGTCA 59.041 61.111 0.00 0.00 43.24 4.02
2550 2931 2.734175 CGACTAGGCATGACAAAGCGTA 60.734 50.000 0.00 5.80 0.00 4.42
2551 2932 1.726853 GACTAGGCATGACAAAGCGT 58.273 50.000 0.00 4.28 0.00 5.07
2552 2933 0.647410 CGACTAGGCATGACAAAGCG 59.353 55.000 0.00 2.58 0.00 4.68
2553 2934 1.009829 CCGACTAGGCATGACAAAGC 58.990 55.000 0.00 0.00 0.00 3.51
2564 2945 0.032678 CATAGCACCTGCCGACTAGG 59.967 60.000 0.00 0.00 43.38 3.02
2565 2946 0.598680 GCATAGCACCTGCCGACTAG 60.599 60.000 0.00 0.00 43.38 2.57
2566 2947 1.326951 TGCATAGCACCTGCCGACTA 61.327 55.000 3.19 0.00 43.38 2.59
2567 2948 1.976132 ATGCATAGCACCTGCCGACT 61.976 55.000 0.00 0.00 43.04 4.18
2568 2949 1.524621 ATGCATAGCACCTGCCGAC 60.525 57.895 0.00 0.00 43.04 4.79
2569 2950 1.524393 CATGCATAGCACCTGCCGA 60.524 57.895 0.00 0.00 43.04 5.54
2570 2951 1.524393 TCATGCATAGCACCTGCCG 60.524 57.895 0.00 0.00 43.04 5.69
2571 2952 0.749091 TGTCATGCATAGCACCTGCC 60.749 55.000 0.00 0.00 43.04 4.85
2572 2953 0.661552 CTGTCATGCATAGCACCTGC 59.338 55.000 0.00 0.00 43.04 4.85
2573 2954 2.320745 TCTGTCATGCATAGCACCTG 57.679 50.000 0.00 0.00 43.04 4.00
2574 2955 2.704596 AGATCTGTCATGCATAGCACCT 59.295 45.455 0.00 0.00 43.04 4.00
2575 2956 3.123157 AGATCTGTCATGCATAGCACC 57.877 47.619 0.00 0.00 43.04 5.01
2576 2957 4.573607 TGAAAGATCTGTCATGCATAGCAC 59.426 41.667 11.81 0.00 43.04 4.40
2577 2958 4.773013 TGAAAGATCTGTCATGCATAGCA 58.227 39.130 11.81 0.05 44.86 3.49
2578 2959 5.746307 TTGAAAGATCTGTCATGCATAGC 57.254 39.130 16.48 0.00 0.00 2.97
2579 2960 7.280428 AGTCTTTGAAAGATCTGTCATGCATAG 59.720 37.037 16.48 9.10 40.18 2.23
2580 2961 7.108194 AGTCTTTGAAAGATCTGTCATGCATA 58.892 34.615 16.48 0.00 40.18 3.14
2581 2962 5.944599 AGTCTTTGAAAGATCTGTCATGCAT 59.055 36.000 16.48 0.00 40.18 3.96
2582 2963 5.311265 AGTCTTTGAAAGATCTGTCATGCA 58.689 37.500 16.48 0.00 40.18 3.96
2583 2964 5.876612 AGTCTTTGAAAGATCTGTCATGC 57.123 39.130 16.48 7.28 40.18 4.06
2584 2965 7.430992 TGAAGTCTTTGAAAGATCTGTCATG 57.569 36.000 16.48 12.18 40.18 3.07
2585 2966 7.308469 GCTTGAAGTCTTTGAAAGATCTGTCAT 60.308 37.037 16.48 0.06 40.18 3.06
2586 2967 6.017605 GCTTGAAGTCTTTGAAAGATCTGTCA 60.018 38.462 11.81 11.81 40.18 3.58
2587 2968 6.204495 AGCTTGAAGTCTTTGAAAGATCTGTC 59.796 38.462 11.20 5.89 40.18 3.51
2588 2969 6.017275 CAGCTTGAAGTCTTTGAAAGATCTGT 60.017 38.462 11.20 0.00 40.18 3.41
2589 2970 6.017275 ACAGCTTGAAGTCTTTGAAAGATCTG 60.017 38.462 11.20 11.18 40.18 2.90
2590 2971 6.017275 CACAGCTTGAAGTCTTTGAAAGATCT 60.017 38.462 11.20 7.44 40.18 2.75
2591 2972 6.141462 CACAGCTTGAAGTCTTTGAAAGATC 58.859 40.000 11.20 6.27 40.18 2.75
2592 2973 5.591877 ACACAGCTTGAAGTCTTTGAAAGAT 59.408 36.000 11.20 0.00 40.18 2.40
2593 2974 4.943705 ACACAGCTTGAAGTCTTTGAAAGA 59.056 37.500 3.02 3.02 34.51 2.52
2594 2975 5.240713 ACACAGCTTGAAGTCTTTGAAAG 57.759 39.130 0.00 0.00 0.00 2.62
2595 2976 4.201812 CGACACAGCTTGAAGTCTTTGAAA 60.202 41.667 8.87 0.00 0.00 2.69
2596 2977 3.309682 CGACACAGCTTGAAGTCTTTGAA 59.690 43.478 8.87 0.00 0.00 2.69
2597 2978 2.866156 CGACACAGCTTGAAGTCTTTGA 59.134 45.455 8.87 0.00 0.00 2.69
2598 2979 2.032549 CCGACACAGCTTGAAGTCTTTG 60.033 50.000 0.00 0.00 0.00 2.77
2599 2980 2.213499 CCGACACAGCTTGAAGTCTTT 58.787 47.619 0.00 0.00 0.00 2.52
2600 2981 1.871080 CCGACACAGCTTGAAGTCTT 58.129 50.000 0.00 0.00 0.00 3.01
2601 2982 0.601311 GCCGACACAGCTTGAAGTCT 60.601 55.000 0.00 0.00 0.00 3.24
2602 2983 0.601311 AGCCGACACAGCTTGAAGTC 60.601 55.000 0.00 0.00 37.24 3.01
2603 2984 0.882042 CAGCCGACACAGCTTGAAGT 60.882 55.000 0.00 0.00 38.95 3.01
2604 2985 0.601046 TCAGCCGACACAGCTTGAAG 60.601 55.000 3.37 0.00 38.95 3.02
2605 2986 0.035317 ATCAGCCGACACAGCTTGAA 59.965 50.000 3.37 0.00 38.95 2.69
2606 2987 0.671472 CATCAGCCGACACAGCTTGA 60.671 55.000 3.37 0.00 38.95 3.02
2607 2988 1.642037 CCATCAGCCGACACAGCTTG 61.642 60.000 0.00 0.00 38.95 4.01
2608 2989 1.376424 CCATCAGCCGACACAGCTT 60.376 57.895 0.00 0.00 38.95 3.74
2609 2990 1.257750 TACCATCAGCCGACACAGCT 61.258 55.000 0.00 0.00 42.70 4.24
2610 2991 1.084370 GTACCATCAGCCGACACAGC 61.084 60.000 0.00 0.00 0.00 4.40
2611 2992 0.532573 AGTACCATCAGCCGACACAG 59.467 55.000 0.00 0.00 0.00 3.66
2612 2993 0.973632 AAGTACCATCAGCCGACACA 59.026 50.000 0.00 0.00 0.00 3.72
2613 2994 1.359848 CAAGTACCATCAGCCGACAC 58.640 55.000 0.00 0.00 0.00 3.67
2614 2995 0.249120 CCAAGTACCATCAGCCGACA 59.751 55.000 0.00 0.00 0.00 4.35
2615 2996 1.090052 GCCAAGTACCATCAGCCGAC 61.090 60.000 0.00 0.00 0.00 4.79
2616 2997 1.220749 GCCAAGTACCATCAGCCGA 59.779 57.895 0.00 0.00 0.00 5.54
2617 2998 1.078497 TGCCAAGTACCATCAGCCG 60.078 57.895 0.00 0.00 0.00 5.52
2618 2999 1.379642 GCTGCCAAGTACCATCAGCC 61.380 60.000 13.01 0.82 42.98 4.85
2619 3000 2.101700 GCTGCCAAGTACCATCAGC 58.898 57.895 10.01 10.01 42.46 4.26
2620 3001 1.674441 CATGCTGCCAAGTACCATCAG 59.326 52.381 0.00 0.00 0.00 2.90
2621 3002 1.682702 CCATGCTGCCAAGTACCATCA 60.683 52.381 0.00 0.00 0.00 3.07
2622 3003 1.027357 CCATGCTGCCAAGTACCATC 58.973 55.000 0.00 0.00 0.00 3.51
2623 3004 0.332632 ACCATGCTGCCAAGTACCAT 59.667 50.000 0.00 0.00 0.00 3.55
2624 3005 0.608856 CACCATGCTGCCAAGTACCA 60.609 55.000 0.00 0.00 0.00 3.25
2625 3006 1.937546 GCACCATGCTGCCAAGTACC 61.938 60.000 1.22 0.00 40.96 3.34
2626 3007 1.508088 GCACCATGCTGCCAAGTAC 59.492 57.895 1.22 0.00 40.96 2.73
2627 3008 4.001248 GCACCATGCTGCCAAGTA 57.999 55.556 1.22 0.00 40.96 2.24
2636 3017 1.303309 GATACACCTCAGCACCATGC 58.697 55.000 0.00 0.00 45.46 4.06
2637 3018 2.093288 ACTGATACACCTCAGCACCATG 60.093 50.000 1.14 0.00 45.37 3.66
2638 3019 2.093288 CACTGATACACCTCAGCACCAT 60.093 50.000 1.14 0.00 45.37 3.55
2639 3020 1.276138 CACTGATACACCTCAGCACCA 59.724 52.381 1.14 0.00 45.37 4.17
2640 3021 1.406069 CCACTGATACACCTCAGCACC 60.406 57.143 1.14 0.00 45.37 5.01
2641 3022 2.009042 GCCACTGATACACCTCAGCAC 61.009 57.143 1.14 0.00 45.37 4.40
2642 3023 0.250234 GCCACTGATACACCTCAGCA 59.750 55.000 1.14 0.00 45.37 4.41
2643 3024 0.807667 CGCCACTGATACACCTCAGC 60.808 60.000 1.14 0.00 45.37 4.26
2644 3025 0.817654 TCGCCACTGATACACCTCAG 59.182 55.000 0.00 0.00 46.59 3.35
2645 3026 0.530744 GTCGCCACTGATACACCTCA 59.469 55.000 0.00 0.00 0.00 3.86
2646 3027 0.179108 GGTCGCCACTGATACACCTC 60.179 60.000 0.00 0.00 0.00 3.85
2647 3028 1.898154 GGTCGCCACTGATACACCT 59.102 57.895 0.00 0.00 0.00 4.00
2648 3029 1.518572 CGGTCGCCACTGATACACC 60.519 63.158 0.00 0.00 0.00 4.16
2649 3030 2.165301 GCGGTCGCCACTGATACAC 61.165 63.158 3.73 0.00 34.56 2.90
2650 3031 2.183300 GCGGTCGCCACTGATACA 59.817 61.111 3.73 0.00 34.56 2.29
2651 3032 2.954868 CGCGGTCGCCACTGATAC 60.955 66.667 9.85 0.00 37.98 2.24
2652 3033 3.135457 TCGCGGTCGCCACTGATA 61.135 61.111 6.13 0.00 37.98 2.15
2653 3034 4.796231 GTCGCGGTCGCCACTGAT 62.796 66.667 6.13 0.00 37.98 2.90
2661 3042 4.813526 CTGAGGACGTCGCGGTCG 62.814 72.222 19.12 19.12 37.82 4.79
2662 3043 2.762234 ATCTGAGGACGTCGCGGTC 61.762 63.158 9.92 6.62 36.18 4.79
2663 3044 2.750637 ATCTGAGGACGTCGCGGT 60.751 61.111 9.92 0.00 0.00 5.68
2664 3045 2.278206 CATCTGAGGACGTCGCGG 60.278 66.667 9.92 9.38 0.00 6.46
2665 3046 0.732880 AAACATCTGAGGACGTCGCG 60.733 55.000 9.92 0.00 0.00 5.87
2666 3047 0.716108 CAAACATCTGAGGACGTCGC 59.284 55.000 9.92 4.73 0.00 5.19
2667 3048 0.716108 GCAAACATCTGAGGACGTCG 59.284 55.000 9.92 0.00 0.00 5.12
2668 3049 0.716108 CGCAAACATCTGAGGACGTC 59.284 55.000 7.13 7.13 0.00 4.34
2669 3050 1.291877 GCGCAAACATCTGAGGACGT 61.292 55.000 0.30 0.00 0.00 4.34
2670 3051 1.421485 GCGCAAACATCTGAGGACG 59.579 57.895 0.30 0.00 0.00 4.79
2671 3052 1.421485 CGCGCAAACATCTGAGGAC 59.579 57.895 8.75 0.00 0.00 3.85
2672 3053 2.390599 GCGCGCAAACATCTGAGGA 61.391 57.895 29.10 0.00 0.00 3.71
2673 3054 2.099062 GCGCGCAAACATCTGAGG 59.901 61.111 29.10 0.00 0.00 3.86
2674 3055 1.225936 CTGCGCGCAAACATCTGAG 60.226 57.895 35.50 16.11 0.00 3.35
2675 3056 2.679934 CCTGCGCGCAAACATCTGA 61.680 57.895 35.50 8.69 0.00 3.27
2676 3057 2.202388 CCTGCGCGCAAACATCTG 60.202 61.111 35.50 20.72 0.00 2.90
2677 3058 3.434319 CCCTGCGCGCAAACATCT 61.434 61.111 35.50 0.00 0.00 2.90
2678 3059 3.386867 CTCCCTGCGCGCAAACATC 62.387 63.158 35.50 2.41 0.00 3.06
2679 3060 3.434319 CTCCCTGCGCGCAAACAT 61.434 61.111 35.50 0.00 0.00 2.71
2690 3071 3.322466 AACGGCACCTCCTCCCTG 61.322 66.667 0.00 0.00 0.00 4.45
2691 3072 3.322466 CAACGGCACCTCCTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
2692 3073 4.410400 CCAACGGCACCTCCTCCC 62.410 72.222 0.00 0.00 0.00 4.30
2693 3074 4.410400 CCCAACGGCACCTCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
2714 3095 3.385440 TATCGTCGACGCCACCACG 62.385 63.158 32.19 7.94 39.60 4.94
2715 3096 1.585521 CTATCGTCGACGCCACCAC 60.586 63.158 32.19 0.00 39.60 4.16
2716 3097 2.795973 CTATCGTCGACGCCACCA 59.204 61.111 32.19 15.92 39.60 4.17
2717 3098 2.654404 GCTATCGTCGACGCCACC 60.654 66.667 32.19 16.46 39.60 4.61


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

AutoCloner maintained by Alex Coulton.