Multiple sequence alignment - TraesCS3B01G057700

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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 TraesCS3B01G057700 chr3B 100.000 2768 0 0 2339 5106 30091651 30088884 0.000000e+00 5112.0
1 TraesCS3B01G057700 chr3B 100.000 2060 0 0 1 2060 30093989 30091930 0.000000e+00 3805.0
2 TraesCS3B01G057700 chr3B 91.108 2789 191 27 2341 5106 29592927 29590173 0.000000e+00 3723.0
3 TraesCS3B01G057700 chr3B 95.387 1886 79 6 2801 4681 30409435 30411317 0.000000e+00 2994.0
4 TraesCS3B01G057700 chr3B 94.725 1308 43 8 651 1936 29594581 29593278 0.000000e+00 2010.0
5 TraesCS3B01G057700 chr3B 88.418 1606 130 19 2613 4177 29379793 29381383 0.000000e+00 1884.0
6 TraesCS3B01G057700 chr3B 89.816 1306 83 16 651 1933 30406985 30408263 0.000000e+00 1629.0
7 TraesCS3B01G057700 chr3B 81.423 1265 158 49 3873 5105 29787730 29788949 0.000000e+00 963.0
8 TraesCS3B01G057700 chr3B 86.818 880 68 23 905 1747 29640843 29641711 0.000000e+00 939.0
9 TraesCS3B01G057700 chr3B 93.666 521 29 3 1 521 25732511 25731995 0.000000e+00 776.0
10 TraesCS3B01G057700 chr3B 93.084 535 28 6 1 527 752340315 752340848 0.000000e+00 774.0
11 TraesCS3B01G057700 chr3B 88.819 474 37 4 2374 2834 30408965 30409435 7.420000e-158 568.0
12 TraesCS3B01G057700 chr3B 92.857 392 20 3 1 391 116067146 116066762 3.450000e-156 562.0
13 TraesCS3B01G057700 chr3B 90.411 365 33 2 4742 5106 30411328 30411690 3.580000e-131 479.0
14 TraesCS3B01G057700 chr3B 86.926 283 36 1 3653 3934 29354645 29354363 2.970000e-82 316.0
15 TraesCS3B01G057700 chr3B 94.253 87 5 0 651 737 29640758 29640844 3.210000e-27 134.0
16 TraesCS3B01G057700 chr3B 73.123 413 85 14 1335 1733 29528606 29528206 1.930000e-24 124.0
17 TraesCS3B01G057700 chr3B 100.000 58 0 0 1860 1917 30092056 30091999 1.940000e-19 108.0
18 TraesCS3B01G057700 chr3B 100.000 58 0 0 1934 1991 30092130 30092073 1.940000e-19 108.0
19 TraesCS3B01G057700 chr3B 77.841 176 35 4 4661 4835 29381799 29381971 6.990000e-19 106.0
20 TraesCS3B01G057700 chr3B 96.552 58 1 1 1934 1991 29593353 29593297 1.510000e-15 95.3
21 TraesCS3B01G057700 chr3D 93.075 2787 158 19 2339 5106 18659343 18662113 0.000000e+00 4045.0
22 TraesCS3B01G057700 chr3D 91.601 1905 115 12 2474 4345 18926509 18928401 0.000000e+00 2590.0
23 TraesCS3B01G057700 chr3D 92.552 1262 71 7 651 1890 18657787 18659047 0.000000e+00 1788.0
24 TraesCS3B01G057700 chr3D 90.028 1073 70 8 895 1936 18911019 18912085 0.000000e+00 1354.0
25 TraesCS3B01G057700 chr3D 90.374 561 34 11 2378 2922 18740578 18741134 0.000000e+00 719.0
26 TraesCS3B01G057700 chr3D 93.196 485 30 3 1454 1936 18739710 18740193 0.000000e+00 710.0
27 TraesCS3B01G057700 chr3D 90.249 441 22 7 105 524 581025926 581026366 1.610000e-154 556.0
28 TraesCS3B01G057700 chr3D 96.429 140 5 0 651 790 18910875 18911014 1.110000e-56 231.0
29 TraesCS3B01G057700 chr3D 91.597 119 9 1 523 640 358192169 358192051 4.090000e-36 163.0
30 TraesCS3B01G057700 chr3D 94.737 57 3 0 1934 1990 18912009 18912065 7.040000e-14 89.8
31 TraesCS3B01G057700 chr3D 94.000 50 2 1 2390 2439 508308940 508308892 1.970000e-09 75.0
32 TraesCS3B01G057700 chr3D 91.837 49 4 0 2377 2425 529905230 529905182 9.170000e-08 69.4
33 TraesCS3B01G057700 chr3D 91.489 47 4 0 2377 2423 94034690 94034736 1.190000e-06 65.8
34 TraesCS3B01G057700 chr3D 100.000 31 0 0 1934 1964 18659017 18659047 1.990000e-04 58.4
35 TraesCS3B01G057700 chr3A 92.733 1844 106 11 2392 4217 26195553 26197386 0.000000e+00 2638.0
36 TraesCS3B01G057700 chr3A 89.242 1794 133 36 2613 4359 26141561 26143341 0.000000e+00 2189.0
37 TraesCS3B01G057700 chr3A 91.367 1309 82 11 651 1936 26194144 26195444 0.000000e+00 1762.0
38 TraesCS3B01G057700 chr7D 90.642 545 31 12 1 528 542759783 542759242 0.000000e+00 706.0
39 TraesCS3B01G057700 chr7D 92.500 40 3 0 2382 2421 28560509 28560548 1.990000e-04 58.4
40 TraesCS3B01G057700 chr7B 89.623 530 33 4 1 522 718095941 718096456 0.000000e+00 654.0
41 TraesCS3B01G057700 chr1B 93.462 413 22 2 1 413 675334604 675335011 4.370000e-170 608.0
42 TraesCS3B01G057700 chr1B 90.435 115 11 0 523 637 432380366 432380480 8.850000e-33 152.0
43 TraesCS3B01G057700 chr5D 87.547 530 49 8 1 523 79155591 79156110 9.460000e-167 597.0
44 TraesCS3B01G057700 chr5D 92.982 57 3 1 585 640 559020893 559020949 1.180000e-11 82.4
45 TraesCS3B01G057700 chr6B 92.113 355 26 2 1 355 159185405 159185053 2.750000e-137 499.0
46 TraesCS3B01G057700 chr6B 86.275 51 7 0 2375 2425 683470827 683470777 7.140000e-04 56.5
47 TraesCS3B01G057700 chr2A 88.949 371 34 7 1 367 259119562 259119929 7.800000e-123 451.0
48 TraesCS3B01G057700 chr2A 88.679 371 36 6 1 367 259105310 259105678 1.010000e-121 448.0
49 TraesCS3B01G057700 chr5B 92.593 54 4 0 575 628 488121106 488121053 1.520000e-10 78.7
50 TraesCS3B01G057700 chr5B 97.297 37 1 0 2389 2425 148495722 148495686 4.270000e-06 63.9
51 TraesCS3B01G057700 chr5B 89.091 55 1 4 2374 2425 493132844 493132792 4.270000e-06 63.9
52 TraesCS3B01G057700 chr5B 97.222 36 1 0 672 707 28755760 28755795 1.540000e-05 62.1
53 TraesCS3B01G057700 chr5B 100.000 29 0 0 2395 2423 42742477 42742449 3.000000e-03 54.7
54 TraesCS3B01G057700 chr5A 92.453 53 4 0 576 628 669843388 669843440 5.480000e-10 76.8
55 TraesCS3B01G057700 chr4A 88.889 63 6 1 579 640 166302919 166302857 5.480000e-10 76.8
56 TraesCS3B01G057700 chr6D 92.157 51 4 0 2375 2425 450335161 450335111 7.090000e-09 73.1
57 TraesCS3B01G057700 chr2B 95.238 42 2 0 572 613 686832321 686832362 3.300000e-07 67.6
58 TraesCS3B01G057700 chr7A 89.796 49 5 0 2377 2425 32874656 32874704 4.270000e-06 63.9
59 TraesCS3B01G057700 chr2D 95.000 40 2 0 2392 2431 128486567 128486528 4.270000e-06 63.9
60 TraesCS3B01G057700 chr1D 97.222 36 0 1 2388 2423 491705356 491705322 5.520000e-05 60.2
61 TraesCS3B01G057700 chr4B 100.000 29 0 0 2395 2423 75198545 75198517 3.000000e-03 54.7
62 TraesCS3B01G057700 chr4B 100.000 29 0 0 2397 2425 493346607 493346579 3.000000e-03 54.7


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 TraesCS3B01G057700 chr3B 30088884 30093989 5105 True 2283.250000 5112 100.000000 1 5106 4 chr3B.!!$R6 5105
1 TraesCS3B01G057700 chr3B 29590173 29594581 4408 True 1942.766667 3723 94.128333 651 5106 3 chr3B.!!$R5 4455
2 TraesCS3B01G057700 chr3B 30406985 30411690 4705 False 1417.500000 2994 91.108250 651 5106 4 chr3B.!!$F5 4455
3 TraesCS3B01G057700 chr3B 29379793 29381971 2178 False 995.000000 1884 83.129500 2613 4835 2 chr3B.!!$F3 2222
4 TraesCS3B01G057700 chr3B 29787730 29788949 1219 False 963.000000 963 81.423000 3873 5105 1 chr3B.!!$F1 1232
5 TraesCS3B01G057700 chr3B 25731995 25732511 516 True 776.000000 776 93.666000 1 521 1 chr3B.!!$R1 520
6 TraesCS3B01G057700 chr3B 752340315 752340848 533 False 774.000000 774 93.084000 1 527 1 chr3B.!!$F2 526
7 TraesCS3B01G057700 chr3B 29640758 29641711 953 False 536.500000 939 90.535500 651 1747 2 chr3B.!!$F4 1096
8 TraesCS3B01G057700 chr3D 18926509 18928401 1892 False 2590.000000 2590 91.601000 2474 4345 1 chr3D.!!$F1 1871
9 TraesCS3B01G057700 chr3D 18657787 18662113 4326 False 1963.800000 4045 95.209000 651 5106 3 chr3D.!!$F4 4455
10 TraesCS3B01G057700 chr3D 18739710 18741134 1424 False 714.500000 719 91.785000 1454 2922 2 chr3D.!!$F5 1468
11 TraesCS3B01G057700 chr3D 18910875 18912085 1210 False 558.266667 1354 93.731333 651 1990 3 chr3D.!!$F6 1339
12 TraesCS3B01G057700 chr3A 26194144 26197386 3242 False 2200.000000 2638 92.050000 651 4217 2 chr3A.!!$F2 3566
13 TraesCS3B01G057700 chr3A 26141561 26143341 1780 False 2189.000000 2189 89.242000 2613 4359 1 chr3A.!!$F1 1746
14 TraesCS3B01G057700 chr7D 542759242 542759783 541 True 706.000000 706 90.642000 1 528 1 chr7D.!!$R1 527
15 TraesCS3B01G057700 chr7B 718095941 718096456 515 False 654.000000 654 89.623000 1 522 1 chr7B.!!$F1 521
16 TraesCS3B01G057700 chr5D 79155591 79156110 519 False 597.000000 597 87.547000 1 523 1 chr5D.!!$F1 522

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
531 565 0.028242 CTACTAGTGACTGGAGCGCG 59.972 60.0 5.39 0.0 0.00 6.86 F
580 614 0.038892 GCTGTTGAGGGCATGTGTTG 60.039 55.0 0.00 0.0 0.00 3.33 F
587 621 0.109723 AGGGCATGTGTTGTAACGGT 59.890 50.0 0.00 0.0 0.00 4.83 F
2364 2909 0.237235 CAAAACACGTCCGGACCATG 59.763 55.0 28.52 26.5 0.00 3.66 F
3229 3870 0.677731 GCCTACAAGATGGCTGTGCA 60.678 55.0 0.00 0.0 45.26 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2199 0.040958 GAGCGTTCAGTGCCACAAAG 60.041 55.000 0.00 0.0 0.00 2.77 R
1986 2201 0.391228 TAGAGCGTTCAGTGCCACAA 59.609 50.000 1.01 0.0 0.00 3.33 R
2449 2994 0.675837 TCAACATGCCAGCTCAGCTC 60.676 55.000 0.00 0.0 36.40 4.09 R
3637 4278 2.642311 TCCAATGGTACCTCTTGCTTCA 59.358 45.455 14.36 0.0 0.00 3.02 R
4904 5629 0.464554 GCATTCTGGAGCTACCACCC 60.465 60.000 0.00 0.0 44.64 4.61 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
103 106 4.022464 TGTTAGGAAAACAACAAGTGCG 57.978 40.909 0.00 0.00 31.93 5.34
119 122 1.301479 GCGGACTTGGAAACGAGGT 60.301 57.895 0.00 0.00 46.96 3.85
172 175 2.688214 GCTGGAGTAGTGAGAGGATGGA 60.688 54.545 0.00 0.00 0.00 3.41
251 275 5.085275 TGAGGGGTGATTAGAGATGAGAT 57.915 43.478 0.00 0.00 0.00 2.75
421 453 1.706443 GTTCGTGTAAGAACCGGGAG 58.294 55.000 6.32 0.00 43.33 4.30
527 561 5.725362 CCCTTTTTCTACTAGTGACTGGAG 58.275 45.833 5.39 0.00 0.00 3.86
528 562 5.172205 CCTTTTTCTACTAGTGACTGGAGC 58.828 45.833 5.39 0.00 0.00 4.70
529 563 4.436242 TTTTCTACTAGTGACTGGAGCG 57.564 45.455 5.39 0.00 0.00 5.03
530 564 1.380524 TCTACTAGTGACTGGAGCGC 58.619 55.000 5.39 0.00 0.00 5.92
531 565 0.028242 CTACTAGTGACTGGAGCGCG 59.972 60.000 5.39 0.00 0.00 6.86
532 566 1.374343 TACTAGTGACTGGAGCGCGG 61.374 60.000 8.83 0.00 0.00 6.46
533 567 4.129737 TAGTGACTGGAGCGCGGC 62.130 66.667 8.83 0.00 0.00 6.53
555 589 2.736995 CGGTCGGCGTGTGTTGAT 60.737 61.111 6.85 0.00 0.00 2.57
556 590 2.860293 GGTCGGCGTGTGTTGATG 59.140 61.111 6.85 0.00 0.00 3.07
557 591 2.677003 GGTCGGCGTGTGTTGATGG 61.677 63.158 6.85 0.00 0.00 3.51
558 592 1.959226 GTCGGCGTGTGTTGATGGT 60.959 57.895 6.85 0.00 0.00 3.55
559 593 1.958715 TCGGCGTGTGTTGATGGTG 60.959 57.895 6.85 0.00 0.00 4.17
560 594 2.255252 GGCGTGTGTTGATGGTGC 59.745 61.111 0.00 0.00 0.00 5.01
561 595 2.127270 GCGTGTGTTGATGGTGCG 60.127 61.111 0.00 0.00 0.00 5.34
562 596 2.127270 CGTGTGTTGATGGTGCGC 60.127 61.111 0.00 0.00 0.00 6.09
563 597 2.606961 CGTGTGTTGATGGTGCGCT 61.607 57.895 9.73 0.00 0.00 5.92
564 598 1.081906 GTGTGTTGATGGTGCGCTG 60.082 57.895 9.73 0.00 0.00 5.18
565 599 1.525765 TGTGTTGATGGTGCGCTGT 60.526 52.632 9.73 0.00 0.00 4.40
566 600 1.100463 TGTGTTGATGGTGCGCTGTT 61.100 50.000 9.73 0.00 0.00 3.16
567 601 0.661187 GTGTTGATGGTGCGCTGTTG 60.661 55.000 9.73 0.00 0.00 3.33
568 602 0.817229 TGTTGATGGTGCGCTGTTGA 60.817 50.000 9.73 0.00 0.00 3.18
569 603 0.110056 GTTGATGGTGCGCTGTTGAG 60.110 55.000 9.73 0.00 0.00 3.02
570 604 1.236616 TTGATGGTGCGCTGTTGAGG 61.237 55.000 9.73 0.00 0.00 3.86
571 605 2.360350 ATGGTGCGCTGTTGAGGG 60.360 61.111 9.73 0.00 35.23 4.30
577 611 2.872557 CGCTGTTGAGGGCATGTG 59.127 61.111 0.00 0.00 0.00 3.21
578 612 1.968017 CGCTGTTGAGGGCATGTGT 60.968 57.895 0.00 0.00 0.00 3.72
579 613 1.518056 CGCTGTTGAGGGCATGTGTT 61.518 55.000 0.00 0.00 0.00 3.32
580 614 0.038892 GCTGTTGAGGGCATGTGTTG 60.039 55.000 0.00 0.00 0.00 3.33
581 615 1.321474 CTGTTGAGGGCATGTGTTGT 58.679 50.000 0.00 0.00 0.00 3.32
582 616 2.503331 CTGTTGAGGGCATGTGTTGTA 58.497 47.619 0.00 0.00 0.00 2.41
583 617 2.884012 CTGTTGAGGGCATGTGTTGTAA 59.116 45.455 0.00 0.00 0.00 2.41
584 618 2.621055 TGTTGAGGGCATGTGTTGTAAC 59.379 45.455 0.00 0.00 0.00 2.50
585 619 1.518325 TGAGGGCATGTGTTGTAACG 58.482 50.000 0.00 0.00 0.00 3.18
586 620 0.802494 GAGGGCATGTGTTGTAACGG 59.198 55.000 0.00 0.00 0.00 4.44
587 621 0.109723 AGGGCATGTGTTGTAACGGT 59.890 50.000 0.00 0.00 0.00 4.83
588 622 0.955905 GGGCATGTGTTGTAACGGTT 59.044 50.000 0.00 0.00 0.00 4.44
589 623 1.338655 GGGCATGTGTTGTAACGGTTT 59.661 47.619 0.00 0.00 0.00 3.27
590 624 2.223852 GGGCATGTGTTGTAACGGTTTT 60.224 45.455 0.00 0.00 0.00 2.43
591 625 3.047093 GGCATGTGTTGTAACGGTTTTC 58.953 45.455 0.00 0.00 0.00 2.29
592 626 2.717011 GCATGTGTTGTAACGGTTTTCG 59.283 45.455 0.00 0.00 45.88 3.46
593 627 2.455295 TGTGTTGTAACGGTTTTCGC 57.545 45.000 0.00 0.00 43.89 4.70
594 628 1.063764 TGTGTTGTAACGGTTTTCGCC 59.936 47.619 0.00 0.00 43.89 5.54
595 629 0.662085 TGTTGTAACGGTTTTCGCCC 59.338 50.000 0.00 0.00 43.89 6.13
601 635 3.270000 CGGTTTTCGCCCGGATTT 58.730 55.556 0.73 0.00 41.78 2.17
602 636 1.582461 CGGTTTTCGCCCGGATTTT 59.418 52.632 0.73 0.00 41.78 1.82
603 637 0.455464 CGGTTTTCGCCCGGATTTTC 60.455 55.000 0.73 0.00 41.78 2.29
604 638 0.455464 GGTTTTCGCCCGGATTTTCG 60.455 55.000 0.73 0.00 0.00 3.46
605 639 0.239082 GTTTTCGCCCGGATTTTCGT 59.761 50.000 0.73 0.00 0.00 3.85
606 640 0.953003 TTTTCGCCCGGATTTTCGTT 59.047 45.000 0.73 0.00 0.00 3.85
607 641 1.805869 TTTCGCCCGGATTTTCGTTA 58.194 45.000 0.73 0.00 0.00 3.18
608 642 1.805869 TTCGCCCGGATTTTCGTTAA 58.194 45.000 0.73 0.00 0.00 2.01
609 643 2.027003 TCGCCCGGATTTTCGTTAAT 57.973 45.000 0.73 0.00 0.00 1.40
610 644 2.358015 TCGCCCGGATTTTCGTTAATT 58.642 42.857 0.73 0.00 0.00 1.40
611 645 3.529533 TCGCCCGGATTTTCGTTAATTA 58.470 40.909 0.73 0.00 0.00 1.40
612 646 3.937706 TCGCCCGGATTTTCGTTAATTAA 59.062 39.130 0.73 0.00 0.00 1.40
613 647 4.030366 CGCCCGGATTTTCGTTAATTAAC 58.970 43.478 16.87 16.87 0.00 2.01
614 648 4.201841 CGCCCGGATTTTCGTTAATTAACT 60.202 41.667 22.57 6.74 34.12 2.24
615 649 5.032220 GCCCGGATTTTCGTTAATTAACTG 58.968 41.667 22.57 16.63 34.12 3.16
616 650 5.575019 CCCGGATTTTCGTTAATTAACTGG 58.425 41.667 22.57 12.05 34.12 4.00
617 651 5.449451 CCCGGATTTTCGTTAATTAACTGGG 60.449 44.000 22.57 16.26 34.12 4.45
618 652 5.032220 CGGATTTTCGTTAATTAACTGGGC 58.968 41.667 22.57 9.47 34.12 5.36
619 653 5.392165 CGGATTTTCGTTAATTAACTGGGCA 60.392 40.000 22.57 6.66 34.12 5.36
620 654 6.391537 GGATTTTCGTTAATTAACTGGGCAA 58.608 36.000 22.57 10.73 34.12 4.52
621 655 6.309494 GGATTTTCGTTAATTAACTGGGCAAC 59.691 38.462 22.57 10.57 34.12 4.17
622 656 6.394025 TTTTCGTTAATTAACTGGGCAACT 57.606 33.333 22.57 0.00 34.12 3.16
623 657 5.616488 TTCGTTAATTAACTGGGCAACTC 57.384 39.130 22.57 0.00 34.12 3.01
624 658 4.901868 TCGTTAATTAACTGGGCAACTCT 58.098 39.130 22.57 0.00 34.12 3.24
625 659 5.310451 TCGTTAATTAACTGGGCAACTCTT 58.690 37.500 22.57 0.00 34.12 2.85
626 660 5.766174 TCGTTAATTAACTGGGCAACTCTTT 59.234 36.000 22.57 0.00 34.12 2.52
627 661 6.263617 TCGTTAATTAACTGGGCAACTCTTTT 59.736 34.615 22.57 0.00 34.12 2.27
628 662 7.444792 TCGTTAATTAACTGGGCAACTCTTTTA 59.555 33.333 22.57 0.00 34.12 1.52
629 663 8.241367 CGTTAATTAACTGGGCAACTCTTTTAT 58.759 33.333 22.57 0.00 34.12 1.40
630 664 9.353999 GTTAATTAACTGGGCAACTCTTTTATG 57.646 33.333 19.07 0.00 33.52 1.90
631 665 3.942130 AACTGGGCAACTCTTTTATGC 57.058 42.857 0.00 0.00 39.33 3.14
632 666 3.160679 ACTGGGCAACTCTTTTATGCT 57.839 42.857 0.00 0.00 39.94 3.79
633 667 3.500343 ACTGGGCAACTCTTTTATGCTT 58.500 40.909 0.00 0.00 39.94 3.91
634 668 4.662278 ACTGGGCAACTCTTTTATGCTTA 58.338 39.130 0.00 0.00 39.94 3.09
635 669 5.076873 ACTGGGCAACTCTTTTATGCTTAA 58.923 37.500 0.00 0.00 39.94 1.85
636 670 5.716703 ACTGGGCAACTCTTTTATGCTTAAT 59.283 36.000 0.00 0.00 39.94 1.40
637 671 6.889722 ACTGGGCAACTCTTTTATGCTTAATA 59.110 34.615 0.00 0.00 39.94 0.98
638 672 7.396055 ACTGGGCAACTCTTTTATGCTTAATAA 59.604 33.333 0.00 0.00 39.94 1.40
639 673 8.305046 TGGGCAACTCTTTTATGCTTAATAAT 57.695 30.769 0.00 0.00 39.94 1.28
640 674 8.757877 TGGGCAACTCTTTTATGCTTAATAATT 58.242 29.630 0.00 0.00 39.94 1.40
762 796 3.266636 ACAACAACCGCGATATCATCAA 58.733 40.909 8.23 0.00 0.00 2.57
805 839 3.211865 CTTGATGTGCAGCCACTCATAT 58.788 45.455 0.00 0.00 42.54 1.78
812 846 1.268234 GCAGCCACTCATATTTGCGTC 60.268 52.381 0.00 0.00 0.00 5.19
867 901 4.457466 ACAGAGTTCCCATGTTAAACGTT 58.543 39.130 0.00 0.00 0.00 3.99
870 904 3.731089 AGTTCCCATGTTAAACGTTCGA 58.269 40.909 0.00 0.00 0.00 3.71
871 905 3.495753 AGTTCCCATGTTAAACGTTCGAC 59.504 43.478 0.00 4.06 0.00 4.20
872 906 3.109044 TCCCATGTTAAACGTTCGACA 57.891 42.857 16.04 16.04 0.00 4.35
873 907 3.464907 TCCCATGTTAAACGTTCGACAA 58.535 40.909 17.19 1.65 0.00 3.18
874 908 3.495377 TCCCATGTTAAACGTTCGACAAG 59.505 43.478 17.19 13.69 0.00 3.16
875 909 3.249080 CCCATGTTAAACGTTCGACAAGT 59.751 43.478 17.19 3.44 0.00 3.16
876 910 4.448395 CCCATGTTAAACGTTCGACAAGTA 59.552 41.667 17.19 0.00 0.00 2.24
877 911 5.121142 CCCATGTTAAACGTTCGACAAGTAT 59.879 40.000 17.19 2.57 0.00 2.12
878 912 6.013085 CCATGTTAAACGTTCGACAAGTATG 58.987 40.000 17.19 12.01 0.00 2.39
879 913 6.128769 CCATGTTAAACGTTCGACAAGTATGA 60.129 38.462 17.19 0.00 0.00 2.15
880 914 6.442487 TGTTAAACGTTCGACAAGTATGAG 57.558 37.500 12.58 0.00 0.00 2.90
881 915 6.207928 TGTTAAACGTTCGACAAGTATGAGA 58.792 36.000 12.58 0.00 0.00 3.27
882 916 6.864685 TGTTAAACGTTCGACAAGTATGAGAT 59.135 34.615 12.58 0.00 0.00 2.75
883 917 5.763444 AAACGTTCGACAAGTATGAGATG 57.237 39.130 0.00 0.00 0.00 2.90
884 918 3.770666 ACGTTCGACAAGTATGAGATGG 58.229 45.455 0.00 0.00 0.00 3.51
885 919 3.192844 ACGTTCGACAAGTATGAGATGGT 59.807 43.478 0.00 0.00 0.00 3.55
886 920 4.174009 CGTTCGACAAGTATGAGATGGTT 58.826 43.478 0.00 0.00 0.00 3.67
887 921 4.265556 CGTTCGACAAGTATGAGATGGTTC 59.734 45.833 0.00 0.00 0.00 3.62
888 922 4.386867 TCGACAAGTATGAGATGGTTCC 57.613 45.455 0.00 0.00 0.00 3.62
889 923 3.767131 TCGACAAGTATGAGATGGTTCCA 59.233 43.478 0.00 0.00 0.00 3.53
890 924 4.405680 TCGACAAGTATGAGATGGTTCCAT 59.594 41.667 3.80 3.80 0.00 3.41
891 925 5.104941 TCGACAAGTATGAGATGGTTCCATT 60.105 40.000 5.77 0.00 0.00 3.16
892 926 5.235186 CGACAAGTATGAGATGGTTCCATTC 59.765 44.000 5.77 6.47 0.00 2.67
893 927 5.440610 ACAAGTATGAGATGGTTCCATTCC 58.559 41.667 5.77 2.39 0.00 3.01
894 928 4.713792 AGTATGAGATGGTTCCATTCCC 57.286 45.455 5.77 0.18 0.00 3.97
895 929 4.047166 AGTATGAGATGGTTCCATTCCCA 58.953 43.478 5.77 5.30 34.66 4.37
954 1015 4.378666 GCATGATCACCAATTTTGTTTGCC 60.379 41.667 0.00 0.00 0.00 4.52
1009 1070 4.080863 AGTCTTGTATTTCGATGGCTCCTT 60.081 41.667 0.00 0.00 0.00 3.36
1144 1205 1.759445 CCATCTCTGATCCGTTCTGGT 59.241 52.381 0.00 0.00 39.52 4.00
1170 1231 0.904865 ACACAGAGGCGGGAAGATCA 60.905 55.000 0.00 0.00 0.00 2.92
1180 1241 2.872038 GCGGGAAGATCATGTGGTATCC 60.872 54.545 0.00 0.00 0.00 2.59
1312 1402 2.796383 CGAGTAGTTGATGAAGCCTCCG 60.796 54.545 0.00 0.00 0.00 4.63
1375 1465 1.336887 ACACCCAGTTCAAGATCGACG 60.337 52.381 0.00 0.00 0.00 5.12
1409 1499 7.201794 CCTGAATCTCATCTTGTACAATTGCAT 60.202 37.037 9.13 3.64 0.00 3.96
1410 1500 7.700505 TGAATCTCATCTTGTACAATTGCATC 58.299 34.615 9.13 7.13 0.00 3.91
1750 1856 3.515502 AGCTACAATAGGACAAGCAGTGA 59.484 43.478 0.00 0.00 35.63 3.41
1769 1875 5.396362 CAGTGACTAATTTGTTTGCACTTCG 59.604 40.000 9.18 0.00 33.29 3.79
1775 1881 7.145323 ACTAATTTGTTTGCACTTCGCTAATT 58.855 30.769 0.00 0.00 43.06 1.40
1784 1890 3.188460 GCACTTCGCTAATTGAACCAAGA 59.812 43.478 0.00 0.00 37.77 3.02
1814 1921 6.414408 GTCATGTCAGTGACTTATCCTTTG 57.586 41.667 23.29 8.63 43.96 2.77
1824 1931 9.219603 CAGTGACTTATCCTTTGATTCACTAAA 57.780 33.333 7.63 0.00 41.41 1.85
1838 1945 3.682696 TCACTAAACTCTCTAGGCGTGA 58.317 45.455 0.00 0.00 0.00 4.35
1936 2151 7.425577 TTGTGAAATGATATGATGACGGATC 57.574 36.000 0.00 0.00 0.00 3.36
1937 2152 5.934043 TGTGAAATGATATGATGACGGATCC 59.066 40.000 0.00 0.00 0.00 3.36
1938 2153 5.352569 GTGAAATGATATGATGACGGATCCC 59.647 44.000 6.06 0.00 0.00 3.85
1941 2156 3.247162 TGATATGATGACGGATCCCCAA 58.753 45.455 6.06 0.00 0.00 4.12
1942 2157 3.845992 TGATATGATGACGGATCCCCAAT 59.154 43.478 6.06 0.00 0.00 3.16
1944 2159 3.600448 ATGATGACGGATCCCCAATTT 57.400 42.857 6.06 0.00 0.00 1.82
1945 2160 2.653726 TGATGACGGATCCCCAATTTG 58.346 47.619 6.06 0.00 0.00 2.32
1947 2162 2.418368 TGACGGATCCCCAATTTGAG 57.582 50.000 6.06 0.00 0.00 3.02
1948 2163 1.912731 TGACGGATCCCCAATTTGAGA 59.087 47.619 6.06 0.00 0.00 3.27
1949 2164 2.509548 TGACGGATCCCCAATTTGAGAT 59.490 45.455 6.06 0.00 0.00 2.75
1950 2165 3.053693 TGACGGATCCCCAATTTGAGATT 60.054 43.478 6.06 0.00 0.00 2.40
1951 2166 4.165180 TGACGGATCCCCAATTTGAGATTA 59.835 41.667 6.06 0.00 0.00 1.75
1952 2167 4.718961 ACGGATCCCCAATTTGAGATTAG 58.281 43.478 6.06 2.04 0.00 1.73
1953 2168 4.166144 ACGGATCCCCAATTTGAGATTAGT 59.834 41.667 6.06 2.56 0.00 2.24
1954 2169 5.368523 ACGGATCCCCAATTTGAGATTAGTA 59.631 40.000 6.06 0.00 0.00 1.82
1955 2170 5.701290 CGGATCCCCAATTTGAGATTAGTAC 59.299 44.000 6.06 0.00 0.00 2.73
1956 2171 6.601332 GGATCCCCAATTTGAGATTAGTACA 58.399 40.000 0.00 0.00 0.00 2.90
1957 2172 7.234355 GGATCCCCAATTTGAGATTAGTACAT 58.766 38.462 0.00 0.00 0.00 2.29
1958 2173 7.175641 GGATCCCCAATTTGAGATTAGTACATG 59.824 40.741 0.00 0.00 0.00 3.21
1959 2174 7.206789 TCCCCAATTTGAGATTAGTACATGA 57.793 36.000 0.00 0.00 0.00 3.07
1960 2175 7.815383 TCCCCAATTTGAGATTAGTACATGAT 58.185 34.615 0.00 0.00 0.00 2.45
1961 2176 8.281531 TCCCCAATTTGAGATTAGTACATGATT 58.718 33.333 0.00 0.00 0.00 2.57
1962 2177 8.917088 CCCCAATTTGAGATTAGTACATGATTT 58.083 33.333 0.00 0.00 0.00 2.17
1970 2185 8.668353 TGAGATTAGTACATGATTTTGACTTGC 58.332 33.333 0.00 0.00 0.00 4.01
1971 2186 8.798859 AGATTAGTACATGATTTTGACTTGCT 57.201 30.769 0.00 0.00 0.00 3.91
1972 2187 8.887717 AGATTAGTACATGATTTTGACTTGCTC 58.112 33.333 0.00 0.00 0.00 4.26
1973 2188 7.977789 TTAGTACATGATTTTGACTTGCTCA 57.022 32.000 0.00 0.00 0.00 4.26
1974 2189 6.882610 AGTACATGATTTTGACTTGCTCAA 57.117 33.333 0.00 0.00 37.08 3.02
1975 2190 7.458409 AGTACATGATTTTGACTTGCTCAAT 57.542 32.000 0.00 0.00 38.74 2.57
1976 2191 7.310664 AGTACATGATTTTGACTTGCTCAATG 58.689 34.615 0.00 0.00 38.74 2.82
1977 2192 4.927425 ACATGATTTTGACTTGCTCAATGC 59.073 37.500 0.00 0.00 38.74 3.56
1978 2193 3.567530 TGATTTTGACTTGCTCAATGCG 58.432 40.909 0.00 0.00 46.63 4.73
1979 2194 3.004629 TGATTTTGACTTGCTCAATGCGT 59.995 39.130 0.00 0.00 46.63 5.24
1980 2195 3.435105 TTTTGACTTGCTCAATGCGTT 57.565 38.095 0.00 0.00 46.63 4.84
1981 2196 2.404265 TTGACTTGCTCAATGCGTTG 57.596 45.000 12.66 12.66 46.63 4.10
1982 2197 1.308047 TGACTTGCTCAATGCGTTGT 58.692 45.000 17.94 0.00 46.63 3.32
1983 2198 1.002576 TGACTTGCTCAATGCGTTGTG 60.003 47.619 17.94 16.32 46.63 3.33
1986 2201 4.950744 GCTCAATGCGTTGTGCTT 57.049 50.000 29.34 0.00 46.17 3.91
2020 2235 3.826754 CTAGAGCGGCGCTGACCA 61.827 66.667 41.51 19.22 39.88 4.02
2024 2239 4.626081 AGCGGCGCTGACCACTTT 62.626 61.111 36.00 6.04 37.57 2.66
2053 2296 4.451150 GGCGCGGGATGTCAGACA 62.451 66.667 8.83 5.50 0.00 3.41
2363 2908 1.512156 GCAAAACACGTCCGGACCAT 61.512 55.000 28.52 14.60 0.00 3.55
2364 2909 0.237235 CAAAACACGTCCGGACCATG 59.763 55.000 28.52 26.50 0.00 3.66
2365 2910 1.512156 AAAACACGTCCGGACCATGC 61.512 55.000 28.52 3.72 0.00 4.06
2366 2911 2.668185 AAACACGTCCGGACCATGCA 62.668 55.000 28.52 0.00 0.00 3.96
2367 2912 2.815211 CACGTCCGGACCATGCAG 60.815 66.667 28.52 15.62 0.00 4.41
2368 2913 3.311110 ACGTCCGGACCATGCAGT 61.311 61.111 28.52 16.30 0.00 4.40
2369 2914 2.509336 CGTCCGGACCATGCAGTC 60.509 66.667 28.52 0.46 35.95 3.51
2375 2920 2.662596 GACCATGCAGTCCGGACA 59.337 61.111 35.00 16.62 0.00 4.02
2388 2933 2.753043 GGACAGTCCGGACGGCTA 60.753 66.667 31.17 0.00 36.20 3.93
2428 2973 1.543429 CGTTGGAGATGCCCTTATCCC 60.543 57.143 0.00 0.00 34.97 3.85
2434 2979 3.593780 GGAGATGCCCTTATCCCCTTTAT 59.406 47.826 0.00 0.00 0.00 1.40
2435 2980 4.044698 GGAGATGCCCTTATCCCCTTTATT 59.955 45.833 0.00 0.00 0.00 1.40
2438 2983 5.840693 AGATGCCCTTATCCCCTTTATTTTG 59.159 40.000 0.00 0.00 0.00 2.44
2449 2994 7.617041 TCCCCTTTATTTTGTTTGTTTGTTG 57.383 32.000 0.00 0.00 0.00 3.33
2460 3005 1.311859 TGTTTGTTGAGCTGAGCTGG 58.688 50.000 13.71 0.00 39.88 4.85
2491 3036 6.183361 TGAGAGATGCTGCTATTTTGACCTAT 60.183 38.462 0.00 0.00 0.00 2.57
2502 3047 9.851686 TGCTATTTTGACCTATATGACATCTTT 57.148 29.630 0.00 0.00 0.00 2.52
2535 3080 5.171476 AGTTTTGATGTGATGTCGGTCTAG 58.829 41.667 0.00 0.00 0.00 2.43
2571 3116 9.669353 CCATTCGAGTTAAAATATTTGATCTGG 57.331 33.333 0.39 0.81 0.00 3.86
2625 3175 3.196254 GGATGTCAAATTGCCATGGTTCT 59.804 43.478 14.67 0.00 0.00 3.01
2782 3347 8.465999 ACATGATACTTTGTCACAAACTTTGAA 58.534 29.630 8.55 0.00 0.00 2.69
2818 3394 7.707774 GCAAACTGCCAAGTCTAAAATTAAA 57.292 32.000 0.00 0.00 37.42 1.52
3151 3792 7.217200 ACAAGTACTCAGAGCTGAAACAAATA 58.783 34.615 0.00 0.00 39.39 1.40
3229 3870 0.677731 GCCTACAAGATGGCTGTGCA 60.678 55.000 0.00 0.00 45.26 4.57
3358 3999 5.048991 CGGTTTTTGCTTAGAAGGAGCTAAA 60.049 40.000 0.00 2.50 40.97 1.85
3415 4056 8.258708 GGTTCACTGGAGAAGTATATTTACACT 58.741 37.037 0.00 0.00 36.83 3.55
3516 4157 3.777465 TCAAGGATGTAGTACTCGCAC 57.223 47.619 0.00 0.00 0.00 5.34
3559 4200 9.545928 AAGCCTCAGAATATACTTCTAGATCAT 57.454 33.333 0.00 0.00 0.00 2.45
3637 4278 1.885887 GATAGCATCCTCTCTGTCGCT 59.114 52.381 0.00 0.00 0.00 4.93
3697 4338 7.317722 AGTATTCTGTAGAGGTTTTGGAGTT 57.682 36.000 0.00 0.00 0.00 3.01
3839 4480 8.147058 ACAGGATTTATGACAGTATAGCAGAAG 58.853 37.037 0.00 0.00 0.00 2.85
3862 4503 6.357367 AGAGGTACAAACTTGTGAAGTCATT 58.643 36.000 5.34 0.00 41.91 2.57
3970 4611 4.641989 AGCAAGGTGATTGATATGTTGGAC 59.358 41.667 0.00 0.00 41.83 4.02
4091 4732 0.685097 GTATTGCTCCGCATCCCCTA 59.315 55.000 0.00 0.00 38.76 3.53
4126 4772 5.682234 AGCCAAAAGGAAGATTAATTGGG 57.318 39.130 4.69 0.00 38.17 4.12
4151 4797 6.529829 GCAAATGTAAATTCGAATTGCCACTA 59.470 34.615 23.38 9.36 36.57 2.74
4666 5372 3.914364 CGCACTGAATTTTTACCTTGCTC 59.086 43.478 0.00 0.00 0.00 4.26
4673 5379 4.790765 ATTTTTACCTTGCTCCTCTTGC 57.209 40.909 0.00 0.00 0.00 4.01
4674 5380 2.949177 TTTACCTTGCTCCTCTTGCA 57.051 45.000 0.00 0.00 38.80 4.08
4794 5500 0.458025 GCCGTTACTCTCCCTCAACG 60.458 60.000 0.00 0.00 42.46 4.10
4892 5617 2.891882 AGCTGAGAGGCTCTTCGC 59.108 61.111 19.80 21.99 38.24 4.70
4917 5642 1.612442 GGTCAGGGTGGTAGCTCCA 60.612 63.158 14.51 0.00 45.01 3.86
4979 5704 2.513897 GGCGTGGGAAATCGAGGG 60.514 66.667 0.00 0.00 0.00 4.30
5082 5811 0.313987 CCTTTTTCCCGTTCACTGCC 59.686 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 106 3.672767 TTCTACCTCGTTTCCAAGTCC 57.327 47.619 0.00 0.00 0.00 3.85
119 122 6.038356 CGCTTAACTTTCGGGTTCTATTCTA 58.962 40.000 0.00 0.00 0.00 2.10
172 175 2.816411 TCTAACTTCCCGGACAGTCAT 58.184 47.619 0.73 0.00 0.00 3.06
343 375 0.399075 CCACCTTTAGTCCCGGTTGT 59.601 55.000 0.00 0.00 0.00 3.32
421 453 3.118112 GGTACTAAAGCCTCCCCCTTTAC 60.118 52.174 0.00 0.00 34.58 2.01
538 572 2.736995 ATCAACACACGCCGACCG 60.737 61.111 0.00 0.00 44.21 4.79
539 573 2.677003 CCATCAACACACGCCGACC 61.677 63.158 0.00 0.00 0.00 4.79
540 574 1.959226 ACCATCAACACACGCCGAC 60.959 57.895 0.00 0.00 0.00 4.79
541 575 1.958715 CACCATCAACACACGCCGA 60.959 57.895 0.00 0.00 0.00 5.54
542 576 2.555782 CACCATCAACACACGCCG 59.444 61.111 0.00 0.00 0.00 6.46
543 577 2.255252 GCACCATCAACACACGCC 59.745 61.111 0.00 0.00 0.00 5.68
544 578 2.127270 CGCACCATCAACACACGC 60.127 61.111 0.00 0.00 0.00 5.34
545 579 2.127270 GCGCACCATCAACACACG 60.127 61.111 0.30 0.00 0.00 4.49
546 580 1.081906 CAGCGCACCATCAACACAC 60.082 57.895 11.47 0.00 0.00 3.82
547 581 1.100463 AACAGCGCACCATCAACACA 61.100 50.000 11.47 0.00 0.00 3.72
548 582 0.661187 CAACAGCGCACCATCAACAC 60.661 55.000 11.47 0.00 0.00 3.32
549 583 0.817229 TCAACAGCGCACCATCAACA 60.817 50.000 11.47 0.00 0.00 3.33
550 584 0.110056 CTCAACAGCGCACCATCAAC 60.110 55.000 11.47 0.00 0.00 3.18
551 585 1.236616 CCTCAACAGCGCACCATCAA 61.237 55.000 11.47 0.00 0.00 2.57
552 586 1.672030 CCTCAACAGCGCACCATCA 60.672 57.895 11.47 0.00 0.00 3.07
553 587 2.401766 CCCTCAACAGCGCACCATC 61.402 63.158 11.47 0.00 0.00 3.51
554 588 2.360350 CCCTCAACAGCGCACCAT 60.360 61.111 11.47 0.00 0.00 3.55
557 591 3.058160 ATGCCCTCAACAGCGCAC 61.058 61.111 11.47 0.00 33.31 5.34
558 592 3.057548 CATGCCCTCAACAGCGCA 61.058 61.111 11.47 0.00 35.35 6.09
559 593 3.058160 ACATGCCCTCAACAGCGC 61.058 61.111 0.00 0.00 0.00 5.92
560 594 1.518056 AACACATGCCCTCAACAGCG 61.518 55.000 0.00 0.00 0.00 5.18
561 595 0.038892 CAACACATGCCCTCAACAGC 60.039 55.000 0.00 0.00 0.00 4.40
562 596 1.321474 ACAACACATGCCCTCAACAG 58.679 50.000 0.00 0.00 0.00 3.16
563 597 2.621055 GTTACAACACATGCCCTCAACA 59.379 45.455 0.00 0.00 0.00 3.33
564 598 2.350388 CGTTACAACACATGCCCTCAAC 60.350 50.000 0.00 0.00 0.00 3.18
565 599 1.876799 CGTTACAACACATGCCCTCAA 59.123 47.619 0.00 0.00 0.00 3.02
566 600 1.518325 CGTTACAACACATGCCCTCA 58.482 50.000 0.00 0.00 0.00 3.86
567 601 0.802494 CCGTTACAACACATGCCCTC 59.198 55.000 0.00 0.00 0.00 4.30
568 602 0.109723 ACCGTTACAACACATGCCCT 59.890 50.000 0.00 0.00 0.00 5.19
569 603 0.955905 AACCGTTACAACACATGCCC 59.044 50.000 0.00 0.00 0.00 5.36
570 604 2.785713 AAACCGTTACAACACATGCC 57.214 45.000 0.00 0.00 0.00 4.40
571 605 2.717011 CGAAAACCGTTACAACACATGC 59.283 45.455 0.00 0.00 0.00 4.06
572 606 2.717011 GCGAAAACCGTTACAACACATG 59.283 45.455 0.00 0.00 41.15 3.21
573 607 2.287129 GGCGAAAACCGTTACAACACAT 60.287 45.455 0.00 0.00 41.15 3.21
574 608 1.063764 GGCGAAAACCGTTACAACACA 59.936 47.619 0.00 0.00 41.15 3.72
575 609 1.597690 GGGCGAAAACCGTTACAACAC 60.598 52.381 0.00 0.00 41.15 3.32
576 610 0.662085 GGGCGAAAACCGTTACAACA 59.338 50.000 0.00 0.00 41.15 3.33
577 611 0.384601 CGGGCGAAAACCGTTACAAC 60.385 55.000 0.00 0.00 46.03 3.32
578 612 1.940334 CGGGCGAAAACCGTTACAA 59.060 52.632 0.00 0.00 46.03 2.41
579 613 3.640231 CGGGCGAAAACCGTTACA 58.360 55.556 0.00 0.00 46.03 2.41
585 619 0.455464 CGAAAATCCGGGCGAAAACC 60.455 55.000 0.00 0.00 0.00 3.27
586 620 0.239082 ACGAAAATCCGGGCGAAAAC 59.761 50.000 0.00 0.00 0.00 2.43
587 621 0.953003 AACGAAAATCCGGGCGAAAA 59.047 45.000 0.00 0.00 0.00 2.29
588 622 1.805869 TAACGAAAATCCGGGCGAAA 58.194 45.000 0.00 0.00 0.00 3.46
589 623 1.805869 TTAACGAAAATCCGGGCGAA 58.194 45.000 0.00 0.00 0.00 4.70
590 624 2.027003 ATTAACGAAAATCCGGGCGA 57.973 45.000 0.00 0.00 0.00 5.54
591 625 2.836479 AATTAACGAAAATCCGGGCG 57.164 45.000 0.00 0.50 0.00 6.13
592 626 5.032220 CAGTTAATTAACGAAAATCCGGGC 58.968 41.667 19.92 0.00 40.96 6.13
593 627 5.449451 CCCAGTTAATTAACGAAAATCCGGG 60.449 44.000 19.92 15.77 40.96 5.73
594 628 5.575019 CCCAGTTAATTAACGAAAATCCGG 58.425 41.667 19.92 0.00 40.96 5.14
595 629 5.032220 GCCCAGTTAATTAACGAAAATCCG 58.968 41.667 19.92 6.72 40.96 4.18
596 630 5.956642 TGCCCAGTTAATTAACGAAAATCC 58.043 37.500 19.92 8.75 40.96 3.01
597 631 7.088272 AGTTGCCCAGTTAATTAACGAAAATC 58.912 34.615 19.92 10.55 40.96 2.17
598 632 6.988522 AGTTGCCCAGTTAATTAACGAAAAT 58.011 32.000 19.92 6.23 40.96 1.82
599 633 6.263617 AGAGTTGCCCAGTTAATTAACGAAAA 59.736 34.615 19.92 10.43 40.96 2.29
600 634 5.766174 AGAGTTGCCCAGTTAATTAACGAAA 59.234 36.000 19.92 6.82 40.96 3.46
601 635 5.310451 AGAGTTGCCCAGTTAATTAACGAA 58.690 37.500 19.92 8.53 40.96 3.85
602 636 4.901868 AGAGTTGCCCAGTTAATTAACGA 58.098 39.130 19.92 3.58 40.96 3.85
603 637 5.622770 AAGAGTTGCCCAGTTAATTAACG 57.377 39.130 19.92 15.03 40.96 3.18
604 638 9.353999 CATAAAAGAGTTGCCCAGTTAATTAAC 57.646 33.333 18.77 18.77 36.46 2.01
605 639 8.032451 GCATAAAAGAGTTGCCCAGTTAATTAA 58.968 33.333 0.00 0.00 0.00 1.40
606 640 7.396055 AGCATAAAAGAGTTGCCCAGTTAATTA 59.604 33.333 0.00 0.00 37.07 1.40
607 641 6.211384 AGCATAAAAGAGTTGCCCAGTTAATT 59.789 34.615 0.00 0.00 37.07 1.40
608 642 5.716703 AGCATAAAAGAGTTGCCCAGTTAAT 59.283 36.000 0.00 0.00 37.07 1.40
609 643 5.076873 AGCATAAAAGAGTTGCCCAGTTAA 58.923 37.500 0.00 0.00 37.07 2.01
610 644 4.662278 AGCATAAAAGAGTTGCCCAGTTA 58.338 39.130 0.00 0.00 37.07 2.24
611 645 3.500343 AGCATAAAAGAGTTGCCCAGTT 58.500 40.909 0.00 0.00 37.07 3.16
612 646 3.160679 AGCATAAAAGAGTTGCCCAGT 57.839 42.857 0.00 0.00 37.07 4.00
613 647 5.643379 TTAAGCATAAAAGAGTTGCCCAG 57.357 39.130 0.00 0.00 37.07 4.45
614 648 7.710676 TTATTAAGCATAAAAGAGTTGCCCA 57.289 32.000 0.00 0.00 37.07 5.36
660 694 6.375736 TGAACAACACACTATTTCCACTTGAA 59.624 34.615 0.00 0.00 0.00 2.69
762 796 1.202818 GGGTGCAGGACTTTTCAGACT 60.203 52.381 0.00 0.00 0.00 3.24
805 839 1.072505 GGAAGACCTGGGACGCAAA 59.927 57.895 0.00 0.00 0.00 3.68
862 896 4.174009 CCATCTCATACTTGTCGAACGTT 58.826 43.478 0.00 0.00 0.00 3.99
867 901 3.767131 TGGAACCATCTCATACTTGTCGA 59.233 43.478 0.00 0.00 0.00 4.20
870 904 5.440610 GGAATGGAACCATCTCATACTTGT 58.559 41.667 6.81 0.00 35.31 3.16
871 905 4.823989 GGGAATGGAACCATCTCATACTTG 59.176 45.833 6.81 0.00 35.31 3.16
872 906 4.478317 TGGGAATGGAACCATCTCATACTT 59.522 41.667 6.81 0.00 35.31 2.24
873 907 4.047166 TGGGAATGGAACCATCTCATACT 58.953 43.478 6.81 0.00 35.31 2.12
874 908 4.437682 TGGGAATGGAACCATCTCATAC 57.562 45.455 6.81 0.00 35.31 2.39
875 909 4.386312 GGTTGGGAATGGAACCATCTCATA 60.386 45.833 6.81 0.00 41.24 2.15
876 910 3.628257 GGTTGGGAATGGAACCATCTCAT 60.628 47.826 6.81 0.00 41.24 2.90
877 911 2.291540 GGTTGGGAATGGAACCATCTCA 60.292 50.000 6.81 4.64 41.24 3.27
878 912 2.291540 TGGTTGGGAATGGAACCATCTC 60.292 50.000 6.81 7.02 45.37 2.75
879 913 1.715931 TGGTTGGGAATGGAACCATCT 59.284 47.619 6.81 0.00 45.37 2.90
880 914 2.230130 TGGTTGGGAATGGAACCATC 57.770 50.000 6.81 1.61 45.37 3.51
883 917 3.826729 GCTATATGGTTGGGAATGGAACC 59.173 47.826 0.00 0.00 41.85 3.62
884 918 4.469657 TGCTATATGGTTGGGAATGGAAC 58.530 43.478 0.00 0.00 0.00 3.62
885 919 4.805140 TGCTATATGGTTGGGAATGGAA 57.195 40.909 0.00 0.00 0.00 3.53
886 920 4.263905 GGATGCTATATGGTTGGGAATGGA 60.264 45.833 0.00 0.00 0.00 3.41
887 921 4.019174 GGATGCTATATGGTTGGGAATGG 58.981 47.826 0.00 0.00 0.00 3.16
888 922 3.691118 CGGATGCTATATGGTTGGGAATG 59.309 47.826 0.00 0.00 0.00 2.67
889 923 3.330701 ACGGATGCTATATGGTTGGGAAT 59.669 43.478 0.00 0.00 0.00 3.01
890 924 2.708861 ACGGATGCTATATGGTTGGGAA 59.291 45.455 0.00 0.00 0.00 3.97
891 925 2.334977 ACGGATGCTATATGGTTGGGA 58.665 47.619 0.00 0.00 0.00 4.37
892 926 2.859165 ACGGATGCTATATGGTTGGG 57.141 50.000 0.00 0.00 0.00 4.12
893 927 4.008074 AGAACGGATGCTATATGGTTGG 57.992 45.455 0.00 0.00 0.00 3.77
894 928 5.751680 CAAAGAACGGATGCTATATGGTTG 58.248 41.667 0.00 0.00 0.00 3.77
895 929 4.275936 GCAAAGAACGGATGCTATATGGTT 59.724 41.667 0.00 0.00 37.12 3.67
954 1015 1.142870 TCAACAAGACACAGAAGGGGG 59.857 52.381 0.00 0.00 0.00 5.40
1009 1070 6.127703 CCGATGAAGACTAAGAACCAGTAGAA 60.128 42.308 0.00 0.00 0.00 2.10
1144 1205 2.031012 CGCCTCTGTGTCAGCCAA 59.969 61.111 0.00 0.00 0.00 4.52
1170 1231 3.200825 CCTTGAAGTCCAGGATACCACAT 59.799 47.826 0.00 0.00 37.17 3.21
1312 1402 1.724582 ATCTTTATGCCGCAACCGCC 61.725 55.000 0.00 0.00 33.11 6.13
1375 1465 1.936547 GATGAGATTCAGGTTGCCGAC 59.063 52.381 0.00 0.00 0.00 4.79
1409 1499 4.735132 CCACCGCGCTTTCCTCGA 62.735 66.667 5.56 0.00 0.00 4.04
1687 1793 9.892130 AAAAATAATTTGGTGGTTGAACTTACA 57.108 25.926 0.00 0.00 0.00 2.41
1715 1821 7.491696 GTCCTATTGTAGCTACGAACTTGATTT 59.508 37.037 17.76 1.66 0.00 2.17
1735 1841 6.476378 ACAAATTAGTCACTGCTTGTCCTAT 58.524 36.000 0.00 0.00 0.00 2.57
1769 1875 9.860898 ATGACTAATTTTCTTGGTTCAATTAGC 57.139 29.630 9.43 5.00 40.57 3.09
1775 1881 7.502226 ACTGACATGACTAATTTTCTTGGTTCA 59.498 33.333 0.00 0.00 0.00 3.18
1814 1921 5.038033 CACGCCTAGAGAGTTTAGTGAATC 58.962 45.833 0.00 0.00 0.00 2.52
1824 1931 1.474879 GAGCTTTCACGCCTAGAGAGT 59.525 52.381 0.00 0.00 0.00 3.24
1838 1945 6.095160 GGATCTCAATTGATTGACAGAGCTTT 59.905 38.462 8.96 0.00 41.51 3.51
1936 2151 8.469309 AATCATGTACTAATCTCAAATTGGGG 57.531 34.615 0.00 0.00 0.00 4.96
1944 2159 8.668353 GCAAGTCAAAATCATGTACTAATCTCA 58.332 33.333 0.00 0.00 0.00 3.27
1945 2160 8.887717 AGCAAGTCAAAATCATGTACTAATCTC 58.112 33.333 0.00 0.00 0.00 2.75
1947 2162 8.668353 TGAGCAAGTCAAAATCATGTACTAATC 58.332 33.333 0.00 0.00 29.64 1.75
1948 2163 8.565896 TGAGCAAGTCAAAATCATGTACTAAT 57.434 30.769 0.00 0.00 29.64 1.73
1949 2164 7.977789 TGAGCAAGTCAAAATCATGTACTAA 57.022 32.000 0.00 0.00 29.64 2.24
1950 2165 7.977789 TTGAGCAAGTCAAAATCATGTACTA 57.022 32.000 0.00 0.00 42.49 1.82
1951 2166 6.882610 TTGAGCAAGTCAAAATCATGTACT 57.117 33.333 0.00 0.00 42.49 2.73
1963 2178 1.002576 CACAACGCATTGAGCAAGTCA 60.003 47.619 0.00 0.00 46.13 3.41
1964 2179 1.678360 CACAACGCATTGAGCAAGTC 58.322 50.000 0.00 0.00 46.13 3.01
1965 2180 3.851620 CACAACGCATTGAGCAAGT 57.148 47.368 0.00 0.00 46.13 3.16
1973 2188 0.875474 GCCACAAAGCACAACGCATT 60.875 50.000 0.00 0.00 46.13 3.56
1974 2189 1.300080 GCCACAAAGCACAACGCAT 60.300 52.632 0.00 0.00 46.13 4.73
1975 2190 2.103934 GCCACAAAGCACAACGCA 59.896 55.556 0.00 0.00 46.13 5.24
1976 2191 2.103934 TGCCACAAAGCACAACGC 59.896 55.556 0.00 0.00 38.00 4.84
1982 2197 1.726865 CGTTCAGTGCCACAAAGCA 59.273 52.632 0.00 0.00 41.46 3.91
1983 2198 1.658409 GCGTTCAGTGCCACAAAGC 60.658 57.895 0.00 0.00 0.00 3.51
1984 2199 0.040958 GAGCGTTCAGTGCCACAAAG 60.041 55.000 0.00 0.00 0.00 2.77
1985 2200 0.463654 AGAGCGTTCAGTGCCACAAA 60.464 50.000 1.01 0.00 0.00 2.83
1986 2201 0.391228 TAGAGCGTTCAGTGCCACAA 59.609 50.000 1.01 0.00 0.00 3.33
2020 2235 1.001269 GCCCTTTCCCGCCTAAAGT 60.001 57.895 0.00 0.00 33.05 2.66
2343 2888 1.890510 GGTCCGGACGTGTTTTGCT 60.891 57.895 27.68 0.00 0.00 3.91
2371 2916 2.753043 TAGCCGTCCGGACTGTCC 60.753 66.667 30.92 16.99 37.50 4.02
2372 2917 2.488820 GTAGCCGTCCGGACTGTC 59.511 66.667 30.92 19.74 37.50 3.51
2388 2933 4.324991 GACCCTCAAACCGCCCGT 62.325 66.667 0.00 0.00 0.00 5.28
2428 2973 7.904461 CAGCTCAACAAACAAACAAAATAAAGG 59.096 33.333 0.00 0.00 0.00 3.11
2434 2979 4.388469 GCTCAGCTCAACAAACAAACAAAA 59.612 37.500 0.00 0.00 0.00 2.44
2435 2980 3.925913 GCTCAGCTCAACAAACAAACAAA 59.074 39.130 0.00 0.00 0.00 2.83
2438 2983 3.111098 CAGCTCAGCTCAACAAACAAAC 58.889 45.455 0.00 0.00 36.40 2.93
2449 2994 0.675837 TCAACATGCCAGCTCAGCTC 60.676 55.000 0.00 0.00 36.40 4.09
2460 3005 1.380524 AGCAGCATCTCTCAACATGC 58.619 50.000 0.00 0.00 44.96 4.06
2502 3047 8.902540 ACATCACATCAAAACTAGTAGTTTCA 57.097 30.769 24.84 16.35 46.78 2.69
2511 3056 5.147330 AGACCGACATCACATCAAAACTA 57.853 39.130 0.00 0.00 0.00 2.24
2512 3057 4.008074 AGACCGACATCACATCAAAACT 57.992 40.909 0.00 0.00 0.00 2.66
2535 3080 6.737254 TTTAACTCGAATGGGAAAGATCAC 57.263 37.500 0.00 0.00 0.00 3.06
2565 3110 8.940952 GCTATTAGAAATGGACATAACCAGATC 58.059 37.037 0.00 0.00 43.49 2.75
2835 3444 9.834628 TCTTCCAATTTCACGTCATTAAATTAC 57.165 29.630 6.96 0.00 32.89 1.89
2857 3485 9.436957 TTCTAATATAGCCATTTCGGAATCTTC 57.563 33.333 0.00 0.00 36.56 2.87
3151 3792 7.391833 CCAAGTTTATCCTTGAAAGAGCTAGTT 59.608 37.037 2.62 0.00 43.65 2.24
3358 3999 6.096987 CCATATACTCATATACAAGGGCTCGT 59.903 42.308 0.00 0.00 0.00 4.18
3370 4011 9.051259 AGTGAACCATTAGCCATATACTCATAT 57.949 33.333 0.00 0.00 0.00 1.78
3425 4066 7.213178 ACTTGTCCCATCCAATAACTAGATT 57.787 36.000 0.00 0.00 0.00 2.40
3516 4157 3.449737 AGGCTTGATGTCAAAATGGATGG 59.550 43.478 0.00 0.00 35.15 3.51
3637 4278 2.642311 TCCAATGGTACCTCTTGCTTCA 59.358 45.455 14.36 0.00 0.00 3.02
3681 4322 6.764560 TGTAGAAACAACTCCAAAACCTCTAC 59.235 38.462 0.00 0.00 35.43 2.59
3839 4480 6.619801 AATGACTTCACAAGTTTGTACCTC 57.380 37.500 0.00 0.00 43.03 3.85
3970 4611 3.686241 TCTCCAATTCGTTGATGCTCTTG 59.314 43.478 0.00 0.00 0.00 3.02
4091 4732 5.850013 TCCTTTTGGCTATGGTAACGGAGT 61.850 45.833 0.00 0.00 41.53 3.85
4126 4772 5.348451 AGTGGCAATTCGAATTTACATTTGC 59.652 36.000 20.56 18.93 37.76 3.68
4360 5049 9.448438 TCTATGACTTAGGTACTACAACGTTTA 57.552 33.333 0.00 0.00 42.67 2.01
4362 5051 7.391554 TGTCTATGACTTAGGTACTACAACGTT 59.608 37.037 0.00 0.00 42.67 3.99
4367 5056 9.610705 CTACTTGTCTATGACTTAGGTACTACA 57.389 37.037 0.00 0.00 42.67 2.74
4673 5379 3.553511 GTGCTATTCGATTGAGTGGTCTG 59.446 47.826 0.00 0.00 0.00 3.51
4674 5380 3.430929 GGTGCTATTCGATTGAGTGGTCT 60.431 47.826 0.00 0.00 0.00 3.85
4723 5429 1.676635 GGCTCTGATTGCTGGCACA 60.677 57.895 0.00 0.00 0.00 4.57
4725 5431 1.273986 TAGGGCTCTGATTGCTGGCA 61.274 55.000 0.00 0.00 0.00 4.92
4734 5440 1.381872 GCCAGGAGTAGGGCTCTGA 60.382 63.158 0.00 0.00 46.74 3.27
4768 5474 1.358046 GAGAGTAACGGCGCGGTAT 59.642 57.895 21.59 13.36 29.80 2.73
4814 5520 1.152830 GGTGGTCAGGGCAGGAAAA 59.847 57.895 0.00 0.00 0.00 2.29
4892 5617 4.802051 CCACCCTGACCCGCATGG 62.802 72.222 0.00 0.00 38.18 3.66
4894 5619 2.285069 TACCACCCTGACCCGCAT 60.285 61.111 0.00 0.00 0.00 4.73
4904 5629 0.464554 GCATTCTGGAGCTACCACCC 60.465 60.000 0.00 0.00 44.64 4.61
4969 5694 2.557920 ATCTGCCATCCCTCGATTTC 57.442 50.000 0.00 0.00 0.00 2.17
4970 5695 2.954318 CAAATCTGCCATCCCTCGATTT 59.046 45.455 0.00 0.00 35.39 2.17
4979 5704 2.162208 TGCTCGAAACAAATCTGCCATC 59.838 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.