Multiple sequence alignment - TraesCS6A01G053300

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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 TraesCS6A01G053300 chr6A 100.000 2756 0 0 1 2756 27648651 27651406 0.000000e+00 5090
1 TraesCS6A01G053300 chr6A 90.055 362 32 3 1067 1427 27745673 27746031 1.490000e-127 466
2 TraesCS6A01G053300 chr6A 87.258 361 38 5 1067 1426 27699921 27700274 3.300000e-109 405
3 TraesCS6A01G053300 chr6A 90.551 254 19 2 809 1059 27632961 27633212 5.690000e-87 331
4 TraesCS6A01G053300 chr6A 95.890 73 3 0 636 708 107693425 107693353 4.820000e-23 119
5 TraesCS6A01G053300 chrUn 95.759 896 33 4 724 1618 112235664 112236555 0.000000e+00 1439
6 TraesCS6A01G053300 chrUn 94.611 501 24 3 2003 2501 40585367 40585866 0.000000e+00 773
7 TraesCS6A01G053300 chrUn 94.411 501 25 3 2003 2501 215033245 215032746 0.000000e+00 767
8 TraesCS6A01G053300 chrUn 90.377 478 25 1 1 457 112235188 112235665 2.350000e-170 608
9 TraesCS6A01G053300 chrUn 87.368 475 56 4 2029 2501 100223283 100222811 2.410000e-150 542
10 TraesCS6A01G053300 chrUn 89.548 354 33 3 1075 1427 112241703 112242053 1.950000e-121 446
11 TraesCS6A01G053300 chrUn 79.754 568 75 21 1074 1617 112239147 112239698 2.590000e-100 375
12 TraesCS6A01G053300 chrUn 95.475 221 8 2 2537 2756 112236812 112237031 4.370000e-93 351
13 TraesCS6A01G053300 chrUn 92.181 243 14 2 820 1059 112183507 112183747 3.400000e-89 339
14 TraesCS6A01G053300 chrUn 89.121 239 19 5 1641 1877 112236544 112236777 9.660000e-75 291
15 TraesCS6A01G053300 chrUn 91.477 176 14 1 461 636 262705577 262705403 9.860000e-60 241
16 TraesCS6A01G053300 chrUn 88.732 142 11 1 1875 2011 40585261 40585402 4.720000e-38 169
17 TraesCS6A01G053300 chrUn 88.652 141 11 1 1876 2011 215033350 215033210 1.700000e-37 167
18 TraesCS6A01G053300 chrUn 97.183 71 2 0 637 707 32325355 32325425 1.340000e-23 121
19 TraesCS6A01G053300 chr6B 94.038 520 29 2 1100 1618 48479442 48479960 0.000000e+00 787
20 TraesCS6A01G053300 chr6B 92.073 492 36 3 2010 2499 169236716 169237206 0.000000e+00 689
21 TraesCS6A01G053300 chr6B 85.145 552 50 20 1088 1617 48528770 48529311 1.120000e-148 536
22 TraesCS6A01G053300 chr6B 82.422 512 62 19 1067 1569 48538733 48539225 3.280000e-114 422
23 TraesCS6A01G053300 chr6B 95.113 266 10 2 2491 2756 48531052 48531314 1.530000e-112 416
24 TraesCS6A01G053300 chr6B 94.515 237 10 2 1643 1877 48479951 48480186 2.020000e-96 363
25 TraesCS6A01G053300 chr6B 78.623 552 79 25 1074 1590 48536112 48536659 2.050000e-86 329
26 TraesCS6A01G053300 chr6B 91.342 231 14 3 823 1050 48423566 48423793 7.410000e-81 311
27 TraesCS6A01G053300 chr6B 92.935 184 7 3 1065 1245 48493829 48494009 2.100000e-66 263
28 TraesCS6A01G053300 chr6B 91.824 159 11 2 2502 2659 48480194 48480351 1.280000e-53 220
29 TraesCS6A01G053300 chr6B 88.623 167 7 4 1641 1802 48529301 48529460 2.800000e-45 193
30 TraesCS6A01G053300 chr6B 96.262 107 4 0 2650 2756 48481890 48481996 2.820000e-40 176
31 TraesCS6A01G053300 chr5D 95.190 499 21 3 2003 2500 61868560 61868064 0.000000e+00 785
32 TraesCS6A01G053300 chr5D 94.200 500 26 3 2003 2501 325659165 325659662 0.000000e+00 760
33 TraesCS6A01G053300 chr5D 87.158 475 58 3 2029 2501 88473337 88472864 1.120000e-148 536
34 TraesCS6A01G053300 chr5D 90.960 177 15 1 461 637 401323146 401323321 1.280000e-58 237
35 TraesCS6A01G053300 chr5D 88.889 126 9 1 1888 2008 325659072 325659197 1.710000e-32 150
36 TraesCS6A01G053300 chr5D 87.719 114 9 1 1882 1990 61868659 61868546 8.010000e-26 128
37 TraesCS6A01G053300 chr5D 97.222 72 2 0 636 707 110346157 110346086 3.730000e-24 122
38 TraesCS6A01G053300 chr1B 93.613 501 29 3 2003 2501 121842390 121841891 0.000000e+00 745
39 TraesCS6A01G053300 chr1B 88.652 141 11 1 1876 2011 121842495 121842355 1.700000e-37 167
40 TraesCS6A01G053300 chr2B 91.968 498 36 4 2003 2498 153887971 153888466 0.000000e+00 695
41 TraesCS6A01G053300 chr2B 91.954 174 13 1 464 637 600089718 600089890 2.740000e-60 243
42 TraesCS6A01G053300 chr2B 87.234 141 13 1 1876 2011 153887866 153888006 3.670000e-34 156
43 TraesCS6A01G053300 chr4D 82.148 633 77 23 1876 2501 53481155 53480552 6.810000e-141 510
44 TraesCS6A01G053300 chr4D 86.696 451 57 3 2053 2501 380558587 380559036 5.300000e-137 497
45 TraesCS6A01G053300 chr6D 76.971 482 91 19 2029 2499 470970136 470970608 9.790000e-65 257
46 TraesCS6A01G053300 chr6D 97.222 72 2 0 634 705 83174596 83174667 3.730000e-24 122
47 TraesCS6A01G053300 chr7D 92.135 178 13 1 460 637 17234420 17234596 1.640000e-62 250
48 TraesCS6A01G053300 chr7D 90.909 187 15 2 451 637 23526189 23526373 1.640000e-62 250
49 TraesCS6A01G053300 chr7D 97.101 69 2 0 636 704 3867783 3867715 1.730000e-22 117
50 TraesCS6A01G053300 chr5A 91.011 178 15 1 460 637 46367388 46367564 3.550000e-59 239
51 TraesCS6A01G053300 chr5A 93.750 80 5 0 630 709 691396304 691396225 1.340000e-23 121
52 TraesCS6A01G053300 chr7B 89.831 177 16 2 461 637 12181595 12181421 2.760000e-55 226
53 TraesCS6A01G053300 chr3B 89.831 177 17 1 461 637 226082992 226083167 2.760000e-55 226
54 TraesCS6A01G053300 chr3B 89.385 179 13 2 460 638 125315123 125314951 1.280000e-53 220
55 TraesCS6A01G053300 chr1D 93.671 79 4 1 629 707 296371486 296371563 1.730000e-22 117
56 TraesCS6A01G053300 chr7A 94.595 74 4 0 636 709 353239240 353239313 6.240000e-22 115
57 TraesCS6A01G053300 chr4A 94.521 73 4 0 637 709 18076662 18076734 2.240000e-21 113


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 TraesCS6A01G053300 chr6A 27648651 27651406 2755 False 5090.000000 5090 100.000000 1 2756 1 chr6A.!!$F2 2755
1 TraesCS6A01G053300 chrUn 112235188 112242053 6865 False 585.000000 1439 90.005667 1 2756 6 chrUn.!!$F4 2755
2 TraesCS6A01G053300 chrUn 40585261 40585866 605 False 471.000000 773 91.671500 1875 2501 2 chrUn.!!$F3 626
3 TraesCS6A01G053300 chrUn 215032746 215033350 604 True 467.000000 767 91.531500 1876 2501 2 chrUn.!!$R3 625
4 TraesCS6A01G053300 chr6B 48479442 48481996 2554 False 386.500000 787 94.159750 1100 2756 4 chr6B.!!$F4 1656
5 TraesCS6A01G053300 chr6B 48528770 48531314 2544 False 381.666667 536 89.627000 1088 2756 3 chr6B.!!$F5 1668
6 TraesCS6A01G053300 chr6B 48536112 48539225 3113 False 375.500000 422 80.522500 1067 1590 2 chr6B.!!$F6 523
7 TraesCS6A01G053300 chr5D 61868064 61868659 595 True 456.500000 785 91.454500 1882 2500 2 chr5D.!!$R3 618
8 TraesCS6A01G053300 chr5D 325659072 325659662 590 False 455.000000 760 91.544500 1888 2501 2 chr5D.!!$F2 613
9 TraesCS6A01G053300 chr1B 121841891 121842495 604 True 456.000000 745 91.132500 1876 2501 2 chr1B.!!$R1 625
10 TraesCS6A01G053300 chr2B 153887866 153888466 600 False 425.500000 695 89.601000 1876 2498 2 chr2B.!!$F2 622
11 TraesCS6A01G053300 chr4D 53480552 53481155 603 True 510.000000 510 82.148000 1876 2501 1 chr4D.!!$R1 625

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
666 688 0.179468 AGCTTTCGCCCCGCTTTATA 59.821 50.0 0.0 0.0 36.6 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 3744 0.108992 GGATGGTGCGTCGACAAGTA 60.109 55.0 17.16 0.0 0.0 2.24 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
26 27 1.002069 TTTCTGCATCCTCCCACCAT 58.998 50.000 0.00 0.00 0.00 3.55
43 44 1.399440 CCATTGCTCATTGGACGACAG 59.601 52.381 5.15 0.00 34.61 3.51
55 56 3.006940 TGGACGACAGCCAAATGTATTC 58.993 45.455 0.00 0.00 32.25 1.75
85 86 7.544915 GGTATGTGAAGAAAACACTAGGTACTC 59.455 40.741 0.00 0.00 38.81 2.59
98 99 4.708421 ACTAGGTACTCGCCTAACATTCAA 59.292 41.667 0.00 0.00 40.29 2.69
137 138 2.796032 GCATAAGTGCCTTTTCCGATGC 60.796 50.000 0.00 0.00 45.76 3.91
160 161 1.590591 TTGGGCTGGGTGCTTAGATA 58.409 50.000 0.00 0.00 42.39 1.98
170 171 3.187700 GGTGCTTAGATAACAGACGGTG 58.812 50.000 0.00 0.00 0.00 4.94
188 189 0.829333 TGCACTGGTGGTTTTGCAAT 59.171 45.000 0.00 0.00 41.90 3.56
230 231 1.213275 CATGGCGTGCAATGAAGCA 59.787 52.632 2.97 0.00 43.35 3.91
247 248 6.377327 TGAAGCAAAATATAAGGCACTAGC 57.623 37.500 0.00 0.00 38.49 3.42
307 329 5.241506 ACACATACAAACTCCATGTCTTTGG 59.758 40.000 10.20 0.00 38.18 3.28
308 330 5.473162 CACATACAAACTCCATGTCTTTGGA 59.527 40.000 10.20 4.05 43.56 3.53
356 378 9.473007 TTTATATGAAAATCCAGTGTTCCATGA 57.527 29.630 0.00 0.00 0.00 3.07
400 422 8.454106 AGATCGATTTTCATTTTGTTCGAGAAT 58.546 29.630 0.00 0.00 38.77 2.40
450 472 5.468072 CAGATTTATCCCGTCCAAAGATCAG 59.532 44.000 0.00 0.00 0.00 2.90
457 479 2.417933 CCGTCCAAAGATCAGCTTTCAG 59.582 50.000 0.00 0.00 44.83 3.02
458 480 3.329386 CGTCCAAAGATCAGCTTTCAGA 58.671 45.455 0.00 0.00 44.83 3.27
459 481 3.124297 CGTCCAAAGATCAGCTTTCAGAC 59.876 47.826 5.39 5.39 44.83 3.51
460 482 4.067896 GTCCAAAGATCAGCTTTCAGACA 58.932 43.478 9.31 0.00 44.83 3.41
461 483 4.516698 GTCCAAAGATCAGCTTTCAGACAA 59.483 41.667 9.31 0.00 44.83 3.18
462 484 5.182760 GTCCAAAGATCAGCTTTCAGACAAT 59.817 40.000 9.31 0.00 44.83 2.71
463 485 5.182570 TCCAAAGATCAGCTTTCAGACAATG 59.817 40.000 0.00 0.00 44.83 2.82
464 486 5.182570 CCAAAGATCAGCTTTCAGACAATGA 59.817 40.000 0.00 0.00 44.83 2.57
465 487 6.294342 CCAAAGATCAGCTTTCAGACAATGAA 60.294 38.462 0.00 0.00 44.83 2.57
498 520 4.972514 GCTATAGAAAATAGCATGGCCC 57.027 45.455 3.21 0.00 44.64 5.80
499 521 3.696548 GCTATAGAAAATAGCATGGCCCC 59.303 47.826 3.21 0.00 44.64 5.80
500 522 4.568592 GCTATAGAAAATAGCATGGCCCCT 60.569 45.833 3.21 0.00 44.64 4.79
501 523 2.077687 AGAAAATAGCATGGCCCCTG 57.922 50.000 0.00 0.00 0.00 4.45
502 524 1.570501 AGAAAATAGCATGGCCCCTGA 59.429 47.619 0.00 0.00 0.00 3.86
503 525 2.024080 AGAAAATAGCATGGCCCCTGAA 60.024 45.455 0.00 0.00 0.00 3.02
504 526 2.548464 AAATAGCATGGCCCCTGAAA 57.452 45.000 0.00 0.00 0.00 2.69
505 527 2.548464 AATAGCATGGCCCCTGAAAA 57.452 45.000 0.00 0.00 0.00 2.29
506 528 2.781403 ATAGCATGGCCCCTGAAAAT 57.219 45.000 0.00 0.00 0.00 1.82
507 529 3.901570 ATAGCATGGCCCCTGAAAATA 57.098 42.857 0.00 0.00 0.00 1.40
508 530 2.781403 AGCATGGCCCCTGAAAATAT 57.219 45.000 0.00 0.00 0.00 1.28
509 531 2.322658 AGCATGGCCCCTGAAAATATG 58.677 47.619 0.00 0.00 0.00 1.78
510 532 1.270465 GCATGGCCCCTGAAAATATGC 60.270 52.381 0.00 0.99 33.64 3.14
511 533 2.322658 CATGGCCCCTGAAAATATGCT 58.677 47.619 0.00 0.00 0.00 3.79
512 534 3.499338 CATGGCCCCTGAAAATATGCTA 58.501 45.455 0.00 0.00 0.00 3.49
513 535 3.901570 TGGCCCCTGAAAATATGCTAT 57.098 42.857 0.00 0.00 0.00 2.97
514 536 4.197559 TGGCCCCTGAAAATATGCTATT 57.802 40.909 0.00 0.00 0.00 1.73
515 537 5.332106 TGGCCCCTGAAAATATGCTATTA 57.668 39.130 0.00 0.00 0.00 0.98
516 538 5.324409 TGGCCCCTGAAAATATGCTATTAG 58.676 41.667 0.00 0.00 0.00 1.73
517 539 4.158579 GGCCCCTGAAAATATGCTATTAGC 59.841 45.833 8.80 8.80 42.82 3.09
518 540 4.142600 GCCCCTGAAAATATGCTATTAGCG 60.143 45.833 10.94 0.00 46.26 4.26
519 541 5.003804 CCCCTGAAAATATGCTATTAGCGT 58.996 41.667 14.53 14.53 46.26 5.07
520 542 5.106555 CCCCTGAAAATATGCTATTAGCGTG 60.107 44.000 18.61 2.19 46.26 5.34
521 543 5.385617 CCTGAAAATATGCTATTAGCGTGC 58.614 41.667 18.61 5.49 46.26 5.34
522 544 5.180117 CCTGAAAATATGCTATTAGCGTGCT 59.820 40.000 18.61 0.00 46.26 4.40
523 545 6.368791 CCTGAAAATATGCTATTAGCGTGCTA 59.631 38.462 18.61 0.00 46.26 3.49
524 546 7.065085 CCTGAAAATATGCTATTAGCGTGCTAT 59.935 37.037 18.61 5.81 46.26 2.97
525 547 8.996024 TGAAAATATGCTATTAGCGTGCTATA 57.004 30.769 18.61 7.66 46.26 1.31
526 548 9.087424 TGAAAATATGCTATTAGCGTGCTATAG 57.913 33.333 18.61 7.85 46.26 1.31
527 549 7.470289 AAATATGCTATTAGCGTGCTATAGC 57.530 36.000 18.18 18.18 46.26 2.97
528 550 3.934457 TGCTATTAGCGTGCTATAGCA 57.066 42.857 23.52 23.52 46.95 3.49
552 574 5.577860 GCTAAAGCGTGCTATTAGTAAGG 57.422 43.478 17.21 0.00 0.00 2.69
553 575 4.084485 GCTAAAGCGTGCTATTAGTAAGGC 60.084 45.833 17.21 4.33 0.00 4.35
554 576 3.536956 AAGCGTGCTATTAGTAAGGCA 57.463 42.857 8.62 8.62 0.00 4.75
555 577 3.753294 AGCGTGCTATTAGTAAGGCAT 57.247 42.857 13.84 0.13 37.05 4.40
556 578 4.073293 AGCGTGCTATTAGTAAGGCATT 57.927 40.909 13.84 0.00 37.05 3.56
557 579 3.809832 AGCGTGCTATTAGTAAGGCATTG 59.190 43.478 13.84 11.37 37.05 2.82
558 580 3.560068 GCGTGCTATTAGTAAGGCATTGT 59.440 43.478 13.84 0.00 37.05 2.71
559 581 4.748102 GCGTGCTATTAGTAAGGCATTGTA 59.252 41.667 13.84 0.00 37.05 2.41
560 582 5.408604 GCGTGCTATTAGTAAGGCATTGTAT 59.591 40.000 13.84 0.00 37.05 2.29
561 583 6.588756 GCGTGCTATTAGTAAGGCATTGTATA 59.411 38.462 13.84 0.00 37.05 1.47
562 584 7.277981 GCGTGCTATTAGTAAGGCATTGTATAT 59.722 37.037 13.84 0.00 37.05 0.86
563 585 9.151471 CGTGCTATTAGTAAGGCATTGTATATT 57.849 33.333 13.84 0.00 37.05 1.28
616 638 1.428448 TAGCAATGCTATTAGCGGCG 58.572 50.000 11.40 0.51 46.26 6.46
617 639 1.441016 GCAATGCTATTAGCGGCGC 60.441 57.895 26.86 26.86 46.26 6.53
618 640 1.845809 GCAATGCTATTAGCGGCGCT 61.846 55.000 37.84 37.84 46.26 5.92
619 641 1.428448 CAATGCTATTAGCGGCGCTA 58.572 50.000 35.39 35.39 46.26 4.26
620 642 2.002586 CAATGCTATTAGCGGCGCTAT 58.997 47.619 38.35 28.53 46.26 2.97
621 643 3.186909 CAATGCTATTAGCGGCGCTATA 58.813 45.455 38.35 28.19 46.26 1.31
622 644 2.561733 TGCTATTAGCGGCGCTATAG 57.438 50.000 38.35 34.01 46.26 1.31
623 645 1.816835 TGCTATTAGCGGCGCTATAGT 59.183 47.619 38.35 28.09 46.26 2.12
624 646 2.186076 GCTATTAGCGGCGCTATAGTG 58.814 52.381 38.35 27.43 41.01 2.74
660 682 2.338620 AAAAAGCTTTCGCCCCGC 59.661 55.556 13.10 0.00 36.60 6.13
661 683 2.200337 AAAAAGCTTTCGCCCCGCT 61.200 52.632 13.10 0.00 36.60 5.52
662 684 1.744320 AAAAAGCTTTCGCCCCGCTT 61.744 50.000 13.10 0.00 45.13 4.68
663 685 2.200337 AAAGCTTTCGCCCCGCTTT 61.200 52.632 5.69 2.93 45.95 3.51
664 686 1.302993 AAGCTTTCGCCCCGCTTTA 60.303 52.632 0.00 0.00 40.82 1.85
665 687 0.679960 AAGCTTTCGCCCCGCTTTAT 60.680 50.000 0.00 0.00 40.82 1.40
666 688 0.179468 AGCTTTCGCCCCGCTTTATA 59.821 50.000 0.00 0.00 36.60 0.98
667 689 1.202770 AGCTTTCGCCCCGCTTTATAT 60.203 47.619 0.00 0.00 36.60 0.86
668 690 1.607148 GCTTTCGCCCCGCTTTATATT 59.393 47.619 0.00 0.00 0.00 1.28
669 691 2.809696 GCTTTCGCCCCGCTTTATATTA 59.190 45.455 0.00 0.00 0.00 0.98
670 692 3.439129 GCTTTCGCCCCGCTTTATATTAT 59.561 43.478 0.00 0.00 0.00 1.28
671 693 4.632688 GCTTTCGCCCCGCTTTATATTATA 59.367 41.667 0.00 0.00 0.00 0.98
672 694 5.122711 GCTTTCGCCCCGCTTTATATTATAA 59.877 40.000 0.00 0.00 0.00 0.98
673 695 6.348704 GCTTTCGCCCCGCTTTATATTATAAA 60.349 38.462 8.26 8.26 0.00 1.40
674 696 6.730960 TTCGCCCCGCTTTATATTATAAAG 57.269 37.500 23.28 23.28 37.53 1.85
684 706 7.759489 CTTTATATTATAAAGCCACTGCCCA 57.241 36.000 18.54 0.00 38.69 5.36
685 707 8.177119 CTTTATATTATAAAGCCACTGCCCAA 57.823 34.615 18.54 0.00 38.69 4.12
686 708 7.759489 TTATATTATAAAGCCACTGCCCAAG 57.241 36.000 0.00 0.00 38.69 3.61
687 709 1.762708 TATAAAGCCACTGCCCAAGC 58.237 50.000 0.00 0.00 38.69 4.01
688 710 0.972471 ATAAAGCCACTGCCCAAGCC 60.972 55.000 0.00 0.00 38.69 4.35
689 711 2.364722 TAAAGCCACTGCCCAAGCCA 62.365 55.000 0.00 0.00 38.69 4.75
690 712 3.754586 AAGCCACTGCCCAAGCCAA 62.755 57.895 0.00 0.00 38.69 4.52
691 713 3.233231 GCCACTGCCCAAGCCAAA 61.233 61.111 0.00 0.00 38.69 3.28
692 714 2.586293 GCCACTGCCCAAGCCAAAT 61.586 57.895 0.00 0.00 38.69 2.32
693 715 1.257055 GCCACTGCCCAAGCCAAATA 61.257 55.000 0.00 0.00 38.69 1.40
694 716 1.488390 CCACTGCCCAAGCCAAATAT 58.512 50.000 0.00 0.00 38.69 1.28
695 717 1.410153 CCACTGCCCAAGCCAAATATC 59.590 52.381 0.00 0.00 38.69 1.63
696 718 1.410153 CACTGCCCAAGCCAAATATCC 59.590 52.381 0.00 0.00 38.69 2.59
697 719 1.006998 ACTGCCCAAGCCAAATATCCA 59.993 47.619 0.00 0.00 38.69 3.41
698 720 2.109774 CTGCCCAAGCCAAATATCCAA 58.890 47.619 0.00 0.00 38.69 3.53
699 721 1.830477 TGCCCAAGCCAAATATCCAAC 59.170 47.619 0.00 0.00 38.69 3.77
700 722 1.830477 GCCCAAGCCAAATATCCAACA 59.170 47.619 0.00 0.00 0.00 3.33
701 723 2.235898 GCCCAAGCCAAATATCCAACAA 59.764 45.455 0.00 0.00 0.00 2.83
702 724 3.679639 GCCCAAGCCAAATATCCAACAAG 60.680 47.826 0.00 0.00 0.00 3.16
703 725 3.118665 CCCAAGCCAAATATCCAACAAGG 60.119 47.826 0.00 0.00 39.47 3.61
704 726 3.515104 CCAAGCCAAATATCCAACAAGGT 59.485 43.478 0.00 0.00 39.02 3.50
705 727 4.020307 CCAAGCCAAATATCCAACAAGGTT 60.020 41.667 0.00 0.00 39.02 3.50
706 728 5.170748 CAAGCCAAATATCCAACAAGGTTC 58.829 41.667 0.00 0.00 39.02 3.62
707 729 4.415596 AGCCAAATATCCAACAAGGTTCA 58.584 39.130 0.00 0.00 39.02 3.18
708 730 4.220602 AGCCAAATATCCAACAAGGTTCAC 59.779 41.667 0.00 0.00 39.02 3.18
709 731 4.220602 GCCAAATATCCAACAAGGTTCACT 59.779 41.667 0.00 0.00 39.02 3.41
710 732 5.417580 GCCAAATATCCAACAAGGTTCACTA 59.582 40.000 0.00 0.00 39.02 2.74
711 733 6.071616 GCCAAATATCCAACAAGGTTCACTAA 60.072 38.462 0.00 0.00 39.02 2.24
712 734 7.524698 GCCAAATATCCAACAAGGTTCACTAAA 60.525 37.037 0.00 0.00 39.02 1.85
713 735 8.028938 CCAAATATCCAACAAGGTTCACTAAAG 58.971 37.037 0.00 0.00 39.02 1.85
714 736 6.759497 ATATCCAACAAGGTTCACTAAAGC 57.241 37.500 0.00 0.00 39.02 3.51
715 737 3.219281 TCCAACAAGGTTCACTAAAGCC 58.781 45.455 0.00 0.00 39.02 4.35
716 738 3.117663 TCCAACAAGGTTCACTAAAGCCT 60.118 43.478 0.00 0.00 39.02 4.58
717 739 3.636764 CCAACAAGGTTCACTAAAGCCTT 59.363 43.478 0.00 0.00 41.55 4.35
720 742 1.911057 AGGTTCACTAAAGCCTTGCC 58.089 50.000 0.00 0.00 35.94 4.52
721 743 0.888619 GGTTCACTAAAGCCTTGCCC 59.111 55.000 0.00 0.00 0.00 5.36
722 744 1.616159 GTTCACTAAAGCCTTGCCCA 58.384 50.000 0.00 0.00 0.00 5.36
723 745 1.269723 GTTCACTAAAGCCTTGCCCAC 59.730 52.381 0.00 0.00 0.00 4.61
724 746 0.476338 TCACTAAAGCCTTGCCCACA 59.524 50.000 0.00 0.00 0.00 4.17
725 747 1.133637 TCACTAAAGCCTTGCCCACAA 60.134 47.619 0.00 0.00 0.00 3.33
763 785 1.774110 TTGCCCACAAGAAGCTTTGA 58.226 45.000 0.00 0.00 0.00 2.69
770 792 3.251972 CCACAAGAAGCTTTGAGGAGTTC 59.748 47.826 8.47 0.00 40.07 3.01
790 812 6.978338 AGTTCAGACGTAATCTCAACTTGTA 58.022 36.000 0.00 0.00 45.78 2.41
804 826 3.857157 ACTTGTACAGTTGTGATGGGT 57.143 42.857 0.00 0.00 27.32 4.51
849 871 5.355350 GTGGGCAATATACTTGGCTCATATC 59.645 44.000 15.72 4.88 43.51 1.63
915 937 8.197592 TGTAACCTTCCTTGTATTCTCTACAA 57.802 34.615 0.00 0.00 36.20 2.41
916 938 8.822805 TGTAACCTTCCTTGTATTCTCTACAAT 58.177 33.333 0.00 0.00 36.90 2.71
1024 1046 2.791501 TAAACCAACGCGGGCTCTCC 62.792 60.000 12.47 0.00 40.22 3.71
1027 1049 4.379243 CAACGCGGGCTCTCCACT 62.379 66.667 12.47 0.00 34.36 4.00
1052 1074 1.590238 GTTGAGACGCTTGGATCATCG 59.410 52.381 0.00 0.00 0.00 3.84
1063 1085 3.348647 TGGATCATCGTCCACACATTT 57.651 42.857 0.00 0.00 43.20 2.32
1120 1142 1.077930 GAAGCAGCAGATGGAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
1366 1415 1.969085 CAGCAAGCTGGGCATCAAA 59.031 52.632 14.10 0.00 40.17 2.69
1606 1674 1.065272 GCCCGTACCAATTAACCTCCA 60.065 52.381 0.00 0.00 0.00 3.86
1607 1675 2.618559 GCCCGTACCAATTAACCTCCAA 60.619 50.000 0.00 0.00 0.00 3.53
1608 1676 3.275999 CCCGTACCAATTAACCTCCAAG 58.724 50.000 0.00 0.00 0.00 3.61
1609 1677 2.681344 CCGTACCAATTAACCTCCAAGC 59.319 50.000 0.00 0.00 0.00 4.01
1610 1678 3.606687 CGTACCAATTAACCTCCAAGCT 58.393 45.455 0.00 0.00 0.00 3.74
1611 1679 3.374058 CGTACCAATTAACCTCCAAGCTG 59.626 47.826 0.00 0.00 0.00 4.24
1612 1680 2.171003 ACCAATTAACCTCCAAGCTGC 58.829 47.619 0.00 0.00 0.00 5.25
1613 1681 2.225117 ACCAATTAACCTCCAAGCTGCT 60.225 45.455 0.00 0.00 0.00 4.24
1614 1682 2.424956 CCAATTAACCTCCAAGCTGCTC 59.575 50.000 1.00 0.00 0.00 4.26
1615 1683 2.424956 CAATTAACCTCCAAGCTGCTCC 59.575 50.000 1.00 0.00 0.00 4.70
1616 1684 0.036388 TTAACCTCCAAGCTGCTCCG 60.036 55.000 1.00 0.00 0.00 4.63
1617 1685 1.899437 TAACCTCCAAGCTGCTCCGG 61.899 60.000 1.00 7.21 0.00 5.14
1618 1686 4.479993 CCTCCAAGCTGCTCCGGG 62.480 72.222 15.67 12.02 0.00 5.73
1619 1687 4.479993 CTCCAAGCTGCTCCGGGG 62.480 72.222 15.67 0.00 0.00 5.73
1634 1702 3.495729 GGGGTGAGCCTCCTTCAA 58.504 61.111 0.00 0.00 34.45 2.69
1635 1703 1.767692 GGGGTGAGCCTCCTTCAAA 59.232 57.895 0.00 0.00 34.45 2.69
1636 1704 0.112412 GGGGTGAGCCTCCTTCAAAA 59.888 55.000 0.00 0.00 34.45 2.44
1637 1705 1.480498 GGGGTGAGCCTCCTTCAAAAA 60.480 52.381 0.00 0.00 34.45 1.94
1689 1762 8.820933 AGAAAAAGATTTGAAAAGCTAGTTTGC 58.179 29.630 7.13 0.08 32.73 3.68
1690 1763 8.722480 AAAAAGATTTGAAAAGCTAGTTTGCT 57.278 26.923 0.00 0.00 46.40 3.91
1870 3470 3.849708 GTCTTTTTGCGACGAAAAAGTGT 59.150 39.130 26.23 0.00 46.36 3.55
1903 3503 6.500684 TTTCGAAAGTACGTCTAGGTGTAT 57.499 37.500 6.47 0.00 34.70 2.29
1950 3555 7.544622 AGTTACAAGAAACTATACTCATCGCA 58.455 34.615 0.00 0.00 37.93 5.10
1997 3602 0.527565 CCCAAGCCAATCCAAAGACG 59.472 55.000 0.00 0.00 0.00 4.18
1998 3603 0.527565 CCAAGCCAATCCAAAGACGG 59.472 55.000 0.00 0.00 0.00 4.79
1999 3604 0.109132 CAAGCCAATCCAAAGACGGC 60.109 55.000 0.00 0.00 42.04 5.68
2000 3605 1.250840 AAGCCAATCCAAAGACGGCC 61.251 55.000 0.00 0.00 42.49 6.13
2001 3606 1.976474 GCCAATCCAAAGACGGCCA 60.976 57.895 2.24 0.00 37.77 5.36
2002 3607 1.531739 GCCAATCCAAAGACGGCCAA 61.532 55.000 2.24 0.00 37.77 4.52
2003 3608 0.243636 CCAATCCAAAGACGGCCAAC 59.756 55.000 2.24 0.00 0.00 3.77
2004 3609 0.958091 CAATCCAAAGACGGCCAACA 59.042 50.000 2.24 0.00 0.00 3.33
2005 3610 0.958822 AATCCAAAGACGGCCAACAC 59.041 50.000 2.24 0.00 0.00 3.32
2006 3611 0.893727 ATCCAAAGACGGCCAACACC 60.894 55.000 2.24 0.00 0.00 4.16
2007 3612 1.826054 CCAAAGACGGCCAACACCA 60.826 57.895 2.24 0.00 0.00 4.17
2008 3613 1.358759 CAAAGACGGCCAACACCAC 59.641 57.895 2.24 0.00 0.00 4.16
2009 3614 1.077357 AAAGACGGCCAACACCACA 60.077 52.632 2.24 0.00 0.00 4.17
2010 3615 0.681564 AAAGACGGCCAACACCACAA 60.682 50.000 2.24 0.00 0.00 3.33
2011 3616 1.101049 AAGACGGCCAACACCACAAG 61.101 55.000 2.24 0.00 0.00 3.16
2012 3617 3.194272 GACGGCCAACACCACAAGC 62.194 63.158 2.24 0.00 0.00 4.01
2013 3618 3.977244 CGGCCAACACCACAAGCC 61.977 66.667 2.24 0.00 40.33 4.35
2014 3619 2.837291 GGCCAACACCACAAGCCA 60.837 61.111 0.00 0.00 43.32 4.75
2015 3620 2.430610 GGCCAACACCACAAGCCAA 61.431 57.895 0.00 0.00 43.32 4.52
2016 3621 1.747774 GCCAACACCACAAGCCAAT 59.252 52.632 0.00 0.00 0.00 3.16
2017 3622 0.319813 GCCAACACCACAAGCCAATC 60.320 55.000 0.00 0.00 0.00 2.67
2018 3623 0.318120 CCAACACCACAAGCCAATCC 59.682 55.000 0.00 0.00 0.00 3.01
2019 3624 1.039068 CAACACCACAAGCCAATCCA 58.961 50.000 0.00 0.00 0.00 3.41
2020 3625 1.411977 CAACACCACAAGCCAATCCAA 59.588 47.619 0.00 0.00 0.00 3.53
2021 3626 1.786937 ACACCACAAGCCAATCCAAA 58.213 45.000 0.00 0.00 0.00 3.28
2022 3627 1.688197 ACACCACAAGCCAATCCAAAG 59.312 47.619 0.00 0.00 0.00 2.77
2023 3628 1.962807 CACCACAAGCCAATCCAAAGA 59.037 47.619 0.00 0.00 0.00 2.52
2024 3629 1.963515 ACCACAAGCCAATCCAAAGAC 59.036 47.619 0.00 0.00 0.00 3.01
2035 3640 2.561037 CCAAAGACGGCCAACACCC 61.561 63.158 2.24 0.00 0.00 4.61
2075 3680 1.529226 AGAGCCTATCCTCATCGACG 58.471 55.000 0.00 0.00 34.26 5.12
2086 3692 2.028484 ATCGACGCACAACACCGT 59.972 55.556 0.00 0.00 40.85 4.83
2102 3708 1.008194 CGTGTCTCGACCGAAACCA 60.008 57.895 0.00 0.00 42.86 3.67
2138 3744 1.134175 CACCAACTTCCGCAACACTTT 59.866 47.619 0.00 0.00 0.00 2.66
2199 3807 0.036875 GCAAGTGGGTAGCAGGACTT 59.963 55.000 0.00 0.00 0.00 3.01
2255 3864 1.300620 GCGACGGGCATACATAGCA 60.301 57.895 0.00 0.00 42.87 3.49
2269 3878 0.390860 ATAGCACCGCAGAGGATCAC 59.609 55.000 0.00 0.00 45.00 3.06
2281 3890 2.050350 GGATCACGGAGGACCACGA 61.050 63.158 14.50 0.00 35.59 4.35
2286 3895 1.975407 ACGGAGGACCACGACGAAT 60.975 57.895 14.50 0.00 35.59 3.34
2428 4038 1.392589 CACCACAACTCCAAGCAAGT 58.607 50.000 0.00 0.00 0.00 3.16
2459 4069 1.659335 GAACACGCCTCAACGACGA 60.659 57.895 0.00 0.00 36.70 4.20
2558 4168 1.545582 TGTTAGCCAAGCCATTGAAGC 59.454 47.619 0.00 0.00 38.83 3.86
2601 4211 9.442047 GATCAGAGAAAGGAGAAAAGATAACAA 57.558 33.333 0.00 0.00 0.00 2.83
2607 4218 7.449704 AGAAAGGAGAAAAGATAACAAGCACAT 59.550 33.333 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.681243 GGTGGGAGGATGCAGAAACC 60.681 60.000 0.00 0.00 0.00 3.27
26 27 0.955428 GGCTGTCGTCCAATGAGCAA 60.955 55.000 0.00 0.00 0.00 3.91
43 44 5.822519 TCACATACCTCAGAATACATTTGGC 59.177 40.000 0.00 0.00 0.00 4.52
55 56 6.591834 CCTAGTGTTTTCTTCACATACCTCAG 59.408 42.308 0.00 0.00 38.16 3.35
85 86 9.003658 AGAGGATAATTTATTGAATGTTAGGCG 57.996 33.333 0.00 0.00 0.00 5.52
98 99 9.862371 CACTTATGCGAGTAGAGGATAATTTAT 57.138 33.333 0.00 0.00 32.81 1.40
160 161 1.523711 CACCAGTGCACCGTCTGTT 60.524 57.895 14.63 0.00 0.00 3.16
170 171 1.952193 AATTGCAAAACCACCAGTGC 58.048 45.000 1.71 0.00 37.51 4.40
196 197 3.368323 CGCCATGAAATTAAGTTTGGGCT 60.368 43.478 17.82 0.00 36.61 5.19
230 231 7.111247 TGCATTTGCTAGTGCCTTATATTTT 57.889 32.000 12.62 0.00 40.56 1.82
231 232 6.713762 TGCATTTGCTAGTGCCTTATATTT 57.286 33.333 12.62 0.00 40.56 1.40
247 248 3.358707 TTGAGTCAGCTGTTGCATTTG 57.641 42.857 14.67 0.00 42.74 2.32
307 329 8.894768 AAATAGTAGCACCAAGATTATCACTC 57.105 34.615 0.00 0.00 0.00 3.51
356 378 7.348080 TCGATCTCAATATGTTTAGTCCTGT 57.652 36.000 0.00 0.00 0.00 4.00
385 407 5.455392 AGCAACTCATTCTCGAACAAAATG 58.545 37.500 0.00 0.00 0.00 2.32
414 436 7.491682 ACGGGATAAATCTGATTTTCAATTGG 58.508 34.615 19.68 7.55 33.82 3.16
421 443 6.889722 TCTTTGGACGGGATAAATCTGATTTT 59.110 34.615 19.68 8.77 33.82 1.82
477 499 3.696548 GGGGCCATGCTATTTTCTATAGC 59.303 47.826 4.39 9.29 45.28 2.97
478 500 4.946157 CAGGGGCCATGCTATTTTCTATAG 59.054 45.833 4.75 0.00 0.00 1.31
479 501 4.601420 TCAGGGGCCATGCTATTTTCTATA 59.399 41.667 14.54 0.00 0.00 1.31
480 502 3.398967 TCAGGGGCCATGCTATTTTCTAT 59.601 43.478 14.54 0.00 0.00 1.98
481 503 2.782925 TCAGGGGCCATGCTATTTTCTA 59.217 45.455 14.54 0.00 0.00 2.10
482 504 1.570501 TCAGGGGCCATGCTATTTTCT 59.429 47.619 14.54 0.00 0.00 2.52
483 505 2.071778 TCAGGGGCCATGCTATTTTC 57.928 50.000 14.54 0.00 0.00 2.29
484 506 2.548464 TTCAGGGGCCATGCTATTTT 57.452 45.000 14.54 0.00 0.00 1.82
485 507 2.548464 TTTCAGGGGCCATGCTATTT 57.452 45.000 14.54 0.00 0.00 1.40
486 508 2.548464 TTTTCAGGGGCCATGCTATT 57.452 45.000 14.54 0.00 0.00 1.73
487 509 2.781403 ATTTTCAGGGGCCATGCTAT 57.219 45.000 14.54 3.51 0.00 2.97
488 510 3.499338 CATATTTTCAGGGGCCATGCTA 58.501 45.455 14.54 0.43 0.00 3.49
489 511 2.322658 CATATTTTCAGGGGCCATGCT 58.677 47.619 14.54 0.45 0.00 3.79
490 512 1.270465 GCATATTTTCAGGGGCCATGC 60.270 52.381 14.54 9.41 0.00 4.06
491 513 2.322658 AGCATATTTTCAGGGGCCATG 58.677 47.619 12.97 12.97 0.00 3.66
492 514 2.781403 AGCATATTTTCAGGGGCCAT 57.219 45.000 4.39 0.00 0.00 4.40
493 515 3.901570 ATAGCATATTTTCAGGGGCCA 57.098 42.857 4.39 0.00 0.00 5.36
494 516 4.158579 GCTAATAGCATATTTTCAGGGGCC 59.841 45.833 7.49 0.00 41.89 5.80
495 517 4.142600 CGCTAATAGCATATTTTCAGGGGC 60.143 45.833 13.15 0.00 42.58 5.80
496 518 5.003804 ACGCTAATAGCATATTTTCAGGGG 58.996 41.667 13.15 0.00 42.58 4.79
497 519 5.617751 GCACGCTAATAGCATATTTTCAGGG 60.618 44.000 13.15 0.00 42.58 4.45
498 520 5.180117 AGCACGCTAATAGCATATTTTCAGG 59.820 40.000 13.15 0.00 42.58 3.86
499 521 6.233430 AGCACGCTAATAGCATATTTTCAG 57.767 37.500 13.15 0.00 42.58 3.02
500 522 7.905604 ATAGCACGCTAATAGCATATTTTCA 57.094 32.000 13.15 0.00 42.58 2.69
501 523 8.058915 GCTATAGCACGCTAATAGCATATTTTC 58.941 37.037 20.01 0.00 40.38 2.29
502 524 7.910304 GCTATAGCACGCTAATAGCATATTTT 58.090 34.615 20.01 0.00 40.38 1.82
503 525 7.470289 GCTATAGCACGCTAATAGCATATTT 57.530 36.000 20.01 0.00 40.38 1.40
530 552 4.084485 GCCTTACTAATAGCACGCTTTAGC 60.084 45.833 15.08 0.00 37.78 3.09
531 553 5.047847 TGCCTTACTAATAGCACGCTTTAG 58.952 41.667 0.00 7.90 0.00 1.85
532 554 5.013568 TGCCTTACTAATAGCACGCTTTA 57.986 39.130 0.00 0.00 0.00 1.85
533 555 3.869065 TGCCTTACTAATAGCACGCTTT 58.131 40.909 0.00 0.00 0.00 3.51
534 556 3.536956 TGCCTTACTAATAGCACGCTT 57.463 42.857 0.00 0.00 0.00 4.68
535 557 3.753294 ATGCCTTACTAATAGCACGCT 57.247 42.857 0.00 0.00 38.21 5.07
536 558 3.560068 ACAATGCCTTACTAATAGCACGC 59.440 43.478 0.00 0.00 38.21 5.34
537 559 8.703604 ATATACAATGCCTTACTAATAGCACG 57.296 34.615 0.00 0.00 38.21 5.34
595 617 7.398380 TAGCGCCGCTAATAGCATTGCTATA 62.398 44.000 27.00 15.90 44.05 1.31
596 618 6.703043 TAGCGCCGCTAATAGCATTGCTAT 62.703 45.833 22.60 22.60 45.34 2.97
597 619 1.428448 CGCCGCTAATAGCATTGCTA 58.572 50.000 20.06 20.06 45.55 3.49
598 620 1.845809 GCGCCGCTAATAGCATTGCT 61.846 55.000 16.63 16.63 42.58 3.91
599 621 1.441016 GCGCCGCTAATAGCATTGC 60.441 57.895 13.15 10.20 42.58 3.56
600 622 1.428448 TAGCGCCGCTAATAGCATTG 58.572 50.000 17.75 1.92 42.58 2.82
601 623 2.386661 ATAGCGCCGCTAATAGCATT 57.613 45.000 23.98 1.03 44.62 3.56
602 624 2.427453 ACTATAGCGCCGCTAATAGCAT 59.573 45.455 23.98 9.03 44.62 3.79
603 625 1.816835 ACTATAGCGCCGCTAATAGCA 59.183 47.619 23.98 0.09 44.62 3.49
604 626 2.186076 CACTATAGCGCCGCTAATAGC 58.814 52.381 23.98 1.41 44.62 2.97
605 627 2.186076 GCACTATAGCGCCGCTAATAG 58.814 52.381 23.98 23.03 44.62 1.73
606 628 2.273370 GCACTATAGCGCCGCTAATA 57.727 50.000 23.98 14.06 44.62 0.98
607 629 3.123674 GCACTATAGCGCCGCTAAT 57.876 52.632 23.98 13.68 44.62 1.73
608 630 4.647654 GCACTATAGCGCCGCTAA 57.352 55.556 23.98 11.35 44.62 3.09
649 671 6.730960 TTATAATATAAAGCGGGGCGAAAG 57.269 37.500 0.00 0.00 0.00 2.62
650 672 6.348704 GCTTTATAATATAAAGCGGGGCGAAA 60.349 38.462 30.20 0.57 46.31 3.46
651 673 5.122711 GCTTTATAATATAAAGCGGGGCGAA 59.877 40.000 30.20 0.00 46.31 4.70
652 674 4.632688 GCTTTATAATATAAAGCGGGGCGA 59.367 41.667 30.20 0.05 46.31 5.54
653 675 4.905269 GCTTTATAATATAAAGCGGGGCG 58.095 43.478 30.20 10.34 46.31 6.13
660 682 7.759489 TGGGCAGTGGCTTTATAATATAAAG 57.241 36.000 22.11 22.11 40.87 1.85
661 683 7.255801 GCTTGGGCAGTGGCTTTATAATATAAA 60.256 37.037 17.16 5.46 40.87 1.40
662 684 6.208599 GCTTGGGCAGTGGCTTTATAATATAA 59.791 38.462 17.16 0.00 40.87 0.98
663 685 5.710099 GCTTGGGCAGTGGCTTTATAATATA 59.290 40.000 17.16 0.00 40.87 0.86
664 686 4.524328 GCTTGGGCAGTGGCTTTATAATAT 59.476 41.667 17.16 0.00 40.87 1.28
665 687 3.888930 GCTTGGGCAGTGGCTTTATAATA 59.111 43.478 17.16 0.00 40.87 0.98
666 688 2.695147 GCTTGGGCAGTGGCTTTATAAT 59.305 45.455 17.16 0.00 40.87 1.28
667 689 2.099405 GCTTGGGCAGTGGCTTTATAA 58.901 47.619 17.16 4.09 40.87 0.98
668 690 1.684869 GGCTTGGGCAGTGGCTTTATA 60.685 52.381 17.16 0.00 40.87 0.98
669 691 0.972471 GGCTTGGGCAGTGGCTTTAT 60.972 55.000 17.16 0.00 40.87 1.40
670 692 1.606313 GGCTTGGGCAGTGGCTTTA 60.606 57.895 17.16 0.67 40.87 1.85
671 693 2.919328 GGCTTGGGCAGTGGCTTT 60.919 61.111 17.16 0.00 40.87 3.51
672 694 3.754586 TTGGCTTGGGCAGTGGCTT 62.755 57.895 17.16 0.00 39.75 4.35
673 695 3.640881 TATTTGGCTTGGGCAGTGGCT 62.641 52.381 17.16 0.00 39.75 4.75
674 696 1.257055 TATTTGGCTTGGGCAGTGGC 61.257 55.000 8.47 8.47 39.75 5.01
675 697 1.410153 GATATTTGGCTTGGGCAGTGG 59.590 52.381 0.00 0.00 39.75 4.00
676 698 1.410153 GGATATTTGGCTTGGGCAGTG 59.590 52.381 0.00 0.00 39.75 3.66
677 699 1.006998 TGGATATTTGGCTTGGGCAGT 59.993 47.619 0.00 0.00 39.75 4.40
678 700 1.779221 TGGATATTTGGCTTGGGCAG 58.221 50.000 0.00 0.00 39.75 4.85
679 701 1.830477 GTTGGATATTTGGCTTGGGCA 59.170 47.619 0.00 0.00 40.87 5.36
680 702 1.830477 TGTTGGATATTTGGCTTGGGC 59.170 47.619 0.00 0.00 37.82 5.36
681 703 3.118665 CCTTGTTGGATATTTGGCTTGGG 60.119 47.826 0.00 0.00 38.35 4.12
682 704 3.515104 ACCTTGTTGGATATTTGGCTTGG 59.485 43.478 0.00 0.00 39.71 3.61
683 705 4.806640 ACCTTGTTGGATATTTGGCTTG 57.193 40.909 0.00 0.00 39.71 4.01
684 706 4.837860 TGAACCTTGTTGGATATTTGGCTT 59.162 37.500 0.00 0.00 39.71 4.35
685 707 4.220602 GTGAACCTTGTTGGATATTTGGCT 59.779 41.667 0.00 0.00 39.71 4.75
686 708 4.220602 AGTGAACCTTGTTGGATATTTGGC 59.779 41.667 0.00 0.00 39.71 4.52
687 709 5.982890 AGTGAACCTTGTTGGATATTTGG 57.017 39.130 0.00 0.00 39.71 3.28
688 710 7.542130 GCTTTAGTGAACCTTGTTGGATATTTG 59.458 37.037 0.00 0.00 39.71 2.32
689 711 7.309805 GGCTTTAGTGAACCTTGTTGGATATTT 60.310 37.037 0.00 0.00 39.71 1.40
690 712 6.152831 GGCTTTAGTGAACCTTGTTGGATATT 59.847 38.462 0.00 0.00 39.71 1.28
691 713 5.652452 GGCTTTAGTGAACCTTGTTGGATAT 59.348 40.000 0.00 0.00 39.71 1.63
692 714 5.007682 GGCTTTAGTGAACCTTGTTGGATA 58.992 41.667 0.00 0.00 39.71 2.59
693 715 3.826729 GGCTTTAGTGAACCTTGTTGGAT 59.173 43.478 0.00 0.00 39.71 3.41
694 716 3.117663 AGGCTTTAGTGAACCTTGTTGGA 60.118 43.478 0.00 0.00 39.71 3.53
695 717 3.222603 AGGCTTTAGTGAACCTTGTTGG 58.777 45.455 0.00 0.00 42.93 3.77
696 718 4.918810 AAGGCTTTAGTGAACCTTGTTG 57.081 40.909 0.00 0.00 40.97 3.33
700 722 2.239400 GGCAAGGCTTTAGTGAACCTT 58.761 47.619 0.00 0.00 43.28 3.50
701 723 1.547901 GGGCAAGGCTTTAGTGAACCT 60.548 52.381 0.00 0.00 0.00 3.50
702 724 0.888619 GGGCAAGGCTTTAGTGAACC 59.111 55.000 0.00 0.00 0.00 3.62
703 725 1.269723 GTGGGCAAGGCTTTAGTGAAC 59.730 52.381 0.00 0.00 0.00 3.18
704 726 1.133637 TGTGGGCAAGGCTTTAGTGAA 60.134 47.619 0.00 0.00 0.00 3.18
705 727 0.476338 TGTGGGCAAGGCTTTAGTGA 59.524 50.000 0.00 0.00 0.00 3.41
706 728 1.270550 CTTGTGGGCAAGGCTTTAGTG 59.729 52.381 0.00 0.00 46.17 2.74
707 729 1.620822 CTTGTGGGCAAGGCTTTAGT 58.379 50.000 0.00 0.00 46.17 2.24
721 743 7.253422 CAAGGCTTTAGTAAATCCATCTTGTG 58.747 38.462 15.98 2.99 0.00 3.33
722 744 6.127619 GCAAGGCTTTAGTAAATCCATCTTGT 60.128 38.462 15.98 0.00 0.00 3.16
723 745 6.268566 GCAAGGCTTTAGTAAATCCATCTTG 58.731 40.000 15.98 12.55 0.00 3.02
724 746 5.360999 GGCAAGGCTTTAGTAAATCCATCTT 59.639 40.000 15.98 1.57 0.00 2.40
725 747 4.889995 GGCAAGGCTTTAGTAAATCCATCT 59.110 41.667 15.98 0.09 0.00 2.90
726 748 4.038042 GGGCAAGGCTTTAGTAAATCCATC 59.962 45.833 15.98 5.94 0.00 3.51
763 785 5.061920 GTTGAGATTACGTCTGAACTCCT 57.938 43.478 0.00 0.00 44.58 3.69
770 792 6.150318 ACTGTACAAGTTGAGATTACGTCTG 58.850 40.000 10.54 0.00 34.15 3.51
790 812 1.425066 ACATCCACCCATCACAACTGT 59.575 47.619 0.00 0.00 0.00 3.55
804 826 6.764085 CCCACTAATATTACGTTCAACATCCA 59.236 38.462 0.00 0.00 0.00 3.41
874 896 7.607991 GGAAGGTTACAATCAGAAGAAATCTCA 59.392 37.037 0.00 0.00 35.73 3.27
915 937 9.258629 CAAGGGAAATCAGAGAGAGAGATATAT 57.741 37.037 0.00 0.00 0.00 0.86
916 938 8.452056 TCAAGGGAAATCAGAGAGAGAGATATA 58.548 37.037 0.00 0.00 0.00 0.86
955 977 6.127925 CCATCAGCGCATACATATTTGGTTAT 60.128 38.462 11.47 0.00 0.00 1.89
964 986 4.758688 CTTATCCCATCAGCGCATACATA 58.241 43.478 11.47 0.00 0.00 2.29
1001 1023 1.529865 GAGCCCGCGTTGGTTTATATC 59.470 52.381 4.92 0.00 35.15 1.63
1004 1026 0.743345 GAGAGCCCGCGTTGGTTTAT 60.743 55.000 4.92 0.00 35.15 1.40
1024 1046 2.989840 CCAAGCGTCTCAACTCTTAGTG 59.010 50.000 0.00 0.00 29.48 2.74
1027 1049 3.509967 TGATCCAAGCGTCTCAACTCTTA 59.490 43.478 0.00 0.00 29.48 2.10
1052 1074 3.012518 CAGGATCAGGAAATGTGTGGAC 58.987 50.000 0.00 0.00 0.00 4.02
1063 1085 4.081198 GCTTCTTCTTCTTCAGGATCAGGA 60.081 45.833 0.00 0.00 0.00 3.86
1358 1407 0.526954 CAGCCGCAGATTTTGATGCC 60.527 55.000 0.00 0.00 39.30 4.40
1360 1409 0.813184 ACCAGCCGCAGATTTTGATG 59.187 50.000 0.00 0.00 0.00 3.07
1389 1438 0.242825 CGACGTCTTCTTACCAGCCA 59.757 55.000 14.70 0.00 0.00 4.75
1393 1442 0.883833 GGTCCGACGTCTTCTTACCA 59.116 55.000 14.70 0.00 30.46 3.25
1419 1468 7.172190 TCAACTCATCAAGAAGAAGAATGTGAC 59.828 37.037 0.00 0.00 0.00 3.67
1579 1643 1.319614 AATTGGTACGGGCCATGTGC 61.320 55.000 4.39 5.93 38.48 4.57
1615 1683 3.787001 GAAGGAGGCTCACCCCCG 61.787 72.222 17.69 0.00 36.11 5.73
1616 1684 1.789576 TTTGAAGGAGGCTCACCCCC 61.790 60.000 17.69 0.00 36.11 5.40
1617 1685 0.112412 TTTTGAAGGAGGCTCACCCC 59.888 55.000 17.69 0.00 36.11 4.95
1618 1686 1.995376 TTTTTGAAGGAGGCTCACCC 58.005 50.000 17.69 0.00 36.11 4.61
1637 1705 1.886542 CCTAAACCGGAGCAGCTTTTT 59.113 47.619 9.46 0.00 0.00 1.94
1638 1706 1.073284 TCCTAAACCGGAGCAGCTTTT 59.927 47.619 9.46 0.00 0.00 2.27
1639 1707 0.690762 TCCTAAACCGGAGCAGCTTT 59.309 50.000 9.46 0.00 0.00 3.51
1678 1747 3.054139 TCCCATGATCAGCAAACTAGCTT 60.054 43.478 0.09 0.00 43.70 3.74
1729 1802 3.209410 GCTGCTACAATCATAGCCACTT 58.791 45.455 2.51 0.00 45.95 3.16
1886 3486 6.297582 AGCTATGATACACCTAGACGTACTT 58.702 40.000 0.00 0.00 0.00 2.24
1940 3545 2.875317 TGCTTGTTGTTTGCGATGAGTA 59.125 40.909 0.00 0.00 0.00 2.59
1950 3555 4.566360 GTGTTTGTGCTATGCTTGTTGTTT 59.434 37.500 0.00 0.00 0.00 2.83
1997 3602 1.757423 ATTGGCTTGTGGTGTTGGCC 61.757 55.000 0.00 0.00 42.73 5.36
1998 3603 0.319813 GATTGGCTTGTGGTGTTGGC 60.320 55.000 0.00 0.00 0.00 4.52
1999 3604 0.318120 GGATTGGCTTGTGGTGTTGG 59.682 55.000 0.00 0.00 0.00 3.77
2000 3605 1.039068 TGGATTGGCTTGTGGTGTTG 58.961 50.000 0.00 0.00 0.00 3.33
2001 3606 1.786937 TTGGATTGGCTTGTGGTGTT 58.213 45.000 0.00 0.00 0.00 3.32
2002 3607 1.688197 CTTTGGATTGGCTTGTGGTGT 59.312 47.619 0.00 0.00 0.00 4.16
2003 3608 1.962807 TCTTTGGATTGGCTTGTGGTG 59.037 47.619 0.00 0.00 0.00 4.17
2004 3609 1.963515 GTCTTTGGATTGGCTTGTGGT 59.036 47.619 0.00 0.00 0.00 4.16
2005 3610 1.068333 CGTCTTTGGATTGGCTTGTGG 60.068 52.381 0.00 0.00 0.00 4.17
2006 3611 1.068333 CCGTCTTTGGATTGGCTTGTG 60.068 52.381 0.00 0.00 0.00 3.33
2007 3612 1.247567 CCGTCTTTGGATTGGCTTGT 58.752 50.000 0.00 0.00 0.00 3.16
2008 3613 0.109132 GCCGTCTTTGGATTGGCTTG 60.109 55.000 0.00 0.00 40.44 4.01
2009 3614 1.250840 GGCCGTCTTTGGATTGGCTT 61.251 55.000 1.20 0.00 42.06 4.35
2010 3615 1.678970 GGCCGTCTTTGGATTGGCT 60.679 57.895 1.20 0.00 42.06 4.75
2011 3616 1.531739 TTGGCCGTCTTTGGATTGGC 61.532 55.000 0.00 0.00 41.83 4.52
2012 3617 0.243636 GTTGGCCGTCTTTGGATTGG 59.756 55.000 0.00 0.00 0.00 3.16
2013 3618 0.958091 TGTTGGCCGTCTTTGGATTG 59.042 50.000 0.00 0.00 0.00 2.67
2014 3619 0.958822 GTGTTGGCCGTCTTTGGATT 59.041 50.000 0.00 0.00 0.00 3.01
2015 3620 0.893727 GGTGTTGGCCGTCTTTGGAT 60.894 55.000 0.00 0.00 0.00 3.41
2016 3621 1.527380 GGTGTTGGCCGTCTTTGGA 60.527 57.895 0.00 0.00 0.00 3.53
2017 3622 2.561037 GGGTGTTGGCCGTCTTTGG 61.561 63.158 0.00 0.00 0.00 3.28
2018 3623 2.561037 GGGGTGTTGGCCGTCTTTG 61.561 63.158 0.00 0.00 0.00 2.77
2019 3624 2.203437 GGGGTGTTGGCCGTCTTT 60.203 61.111 0.00 0.00 0.00 2.52
2020 3625 2.575455 TTTGGGGTGTTGGCCGTCTT 62.575 55.000 0.00 0.00 0.00 3.01
2021 3626 2.976494 CTTTGGGGTGTTGGCCGTCT 62.976 60.000 0.00 0.00 0.00 4.18
2022 3627 2.519780 TTTGGGGTGTTGGCCGTC 60.520 61.111 0.00 0.00 0.00 4.79
2023 3628 2.520741 CTTTGGGGTGTTGGCCGT 60.521 61.111 0.00 0.00 0.00 5.68
2024 3629 3.989787 GCTTTGGGGTGTTGGCCG 61.990 66.667 0.00 0.00 0.00 6.13
2075 3680 1.590525 TCGAGACACGGTGTTGTGC 60.591 57.895 15.94 2.28 43.74 4.57
2086 3692 1.134759 TGTTTGGTTTCGGTCGAGACA 60.135 47.619 14.33 3.71 31.75 3.41
2102 3708 3.485463 TGGTGTTCTTCGGAGATGTTT 57.515 42.857 0.00 0.00 35.04 2.83
2138 3744 0.108992 GGATGGTGCGTCGACAAGTA 60.109 55.000 17.16 0.00 0.00 2.24
2199 3807 1.409064 CATCTTCCTCGAACCGGATCA 59.591 52.381 9.46 0.00 0.00 2.92
2255 3864 2.362503 TCCGTGATCCTCTGCGGT 60.363 61.111 0.00 0.00 44.07 5.68
2269 3878 0.248377 GTATTCGTCGTGGTCCTCCG 60.248 60.000 0.00 0.00 36.30 4.63
2281 3890 1.445716 CGCTCTCCTCCGGTATTCGT 61.446 60.000 0.00 0.00 37.11 3.85
2286 3895 2.513204 CGTCGCTCTCCTCCGGTA 60.513 66.667 0.00 0.00 0.00 4.02
2428 4038 1.003839 GTGTTCGGCATGTCCCTCA 60.004 57.895 0.00 0.00 0.00 3.86
2459 4069 1.290134 GTCATTCCCCTCCTTGGAGT 58.710 55.000 14.77 0.00 38.35 3.85
2532 4142 2.300956 TGGCTTGGCTAACATTTGGA 57.699 45.000 0.00 0.00 0.00 3.53
2601 4211 4.676196 GCAATGCTACTTTGCTTATGTGCT 60.676 41.667 0.00 0.00 44.71 4.40


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

AutoCloner maintained by Alex Coulton.