Multiple sequence alignment - TraesCS6D01G112600

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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 TraesCS6D01G112600 chr6D 100.000 2879 0 0 1 2879 79155777 79158655 0.000000e+00 5317
1 TraesCS6D01G112600 chr7D 96.034 2143 73 5 748 2879 421782904 421785045 0.000000e+00 3476
2 TraesCS6D01G112600 chr7D 80.845 663 89 31 46 691 16162820 16162179 1.200000e-133 486
3 TraesCS6D01G112600 chr4D 95.695 2137 85 3 748 2877 55373601 55371465 0.000000e+00 3430
4 TraesCS6D01G112600 chr6A 93.762 2132 120 9 746 2869 13093114 13095240 0.000000e+00 3188
5 TraesCS6D01G112600 chr6A 93.420 2143 125 9 746 2877 32325840 32323703 0.000000e+00 3162
6 TraesCS6D01G112600 chr6A 93.340 2132 130 8 746 2869 13151024 13153151 0.000000e+00 3140
7 TraesCS6D01G112600 chr6A 91.076 1143 85 5 1737 2869 136685839 136684704 0.000000e+00 1530
8 TraesCS6D01G112600 chr6A 82.581 620 83 20 90 691 51852910 51852298 9.140000e-145 523
9 TraesCS6D01G112600 chr7A 92.084 2135 136 14 742 2869 643987873 643985765 0.000000e+00 2976
10 TraesCS6D01G112600 chr5D 91.383 2147 158 12 746 2869 379377766 379379908 0.000000e+00 2915
11 TraesCS6D01G112600 chr5D 85.915 568 62 16 90 650 372507335 372507891 8.880000e-165 590
12 TraesCS6D01G112600 chr5B 90.735 2137 182 11 748 2872 32061310 32059178 0.000000e+00 2835
13 TraesCS6D01G112600 chr7B 89.437 2149 197 20 744 2869 613513712 613515853 0.000000e+00 2684
14 TraesCS6D01G112600 chr7B 91.421 1119 87 4 1762 2872 227598508 227597391 0.000000e+00 1526
15 TraesCS6D01G112600 chr2B 82.440 672 79 32 43 690 507809838 507809182 4.190000e-153 551
16 TraesCS6D01G112600 chr2B 80.568 669 93 28 44 690 757331769 757332422 5.580000e-132 481
17 TraesCS6D01G112600 chr6B 82.021 673 80 34 43 690 49354480 49353824 4.220000e-148 534
18 TraesCS6D01G112600 chr6B 82.236 653 83 24 59 693 261845810 261846447 1.520000e-147 532
19 TraesCS6D01G112600 chr6B 81.101 672 87 37 43 690 49360687 49360032 4.280000e-138 501
20 TraesCS6D01G112600 chr5A 84.155 568 64 25 142 690 502645201 502645761 7.070000e-146 527


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 TraesCS6D01G112600 chr6D 79155777 79158655 2878 False 5317 5317 100.000 1 2879 1 chr6D.!!$F1 2878
1 TraesCS6D01G112600 chr7D 421782904 421785045 2141 False 3476 3476 96.034 748 2879 1 chr7D.!!$F1 2131
2 TraesCS6D01G112600 chr7D 16162179 16162820 641 True 486 486 80.845 46 691 1 chr7D.!!$R1 645
3 TraesCS6D01G112600 chr4D 55371465 55373601 2136 True 3430 3430 95.695 748 2877 1 chr4D.!!$R1 2129
4 TraesCS6D01G112600 chr6A 13093114 13095240 2126 False 3188 3188 93.762 746 2869 1 chr6A.!!$F1 2123
5 TraesCS6D01G112600 chr6A 32323703 32325840 2137 True 3162 3162 93.420 746 2877 1 chr6A.!!$R1 2131
6 TraesCS6D01G112600 chr6A 13151024 13153151 2127 False 3140 3140 93.340 746 2869 1 chr6A.!!$F2 2123
7 TraesCS6D01G112600 chr6A 136684704 136685839 1135 True 1530 1530 91.076 1737 2869 1 chr6A.!!$R3 1132
8 TraesCS6D01G112600 chr6A 51852298 51852910 612 True 523 523 82.581 90 691 1 chr6A.!!$R2 601
9 TraesCS6D01G112600 chr7A 643985765 643987873 2108 True 2976 2976 92.084 742 2869 1 chr7A.!!$R1 2127
10 TraesCS6D01G112600 chr5D 379377766 379379908 2142 False 2915 2915 91.383 746 2869 1 chr5D.!!$F2 2123
11 TraesCS6D01G112600 chr5D 372507335 372507891 556 False 590 590 85.915 90 650 1 chr5D.!!$F1 560
12 TraesCS6D01G112600 chr5B 32059178 32061310 2132 True 2835 2835 90.735 748 2872 1 chr5B.!!$R1 2124
13 TraesCS6D01G112600 chr7B 613513712 613515853 2141 False 2684 2684 89.437 744 2869 1 chr7B.!!$F1 2125
14 TraesCS6D01G112600 chr7B 227597391 227598508 1117 True 1526 1526 91.421 1762 2872 1 chr7B.!!$R1 1110
15 TraesCS6D01G112600 chr2B 507809182 507809838 656 True 551 551 82.440 43 690 1 chr2B.!!$R1 647
16 TraesCS6D01G112600 chr2B 757331769 757332422 653 False 481 481 80.568 44 690 1 chr2B.!!$F1 646
17 TraesCS6D01G112600 chr6B 49353824 49354480 656 True 534 534 82.021 43 690 1 chr6B.!!$R1 647
18 TraesCS6D01G112600 chr6B 261845810 261846447 637 False 532 532 82.236 59 693 1 chr6B.!!$F1 634
19 TraesCS6D01G112600 chr6B 49360032 49360687 655 True 501 501 81.101 43 690 1 chr6B.!!$R2 647
20 TraesCS6D01G112600 chr5A 502645201 502645761 560 False 527 527 84.155 142 690 1 chr5A.!!$F1 548

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
367 390 0.036448 TCGATCGGGGTAGGCTAGAG 59.964 60.0 16.41 0.0 0.0 2.43 F
553 582 0.038892 TTAACCTCGTGACTCGTGCC 60.039 55.0 0.00 0.0 40.8 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1893 2.118233 GATGATCTCTTCCGGGGGCC 62.118 65.000 0.0 0.0 0.0 5.80 R
1882 1972 2.434331 CAGCCGTTTTGAGGGGGA 59.566 61.111 0.0 0.0 0.0 4.81 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
22 23 5.233957 CACACACACAGAGATAGAGAGAG 57.766 47.826 0.00 0.00 0.00 3.20
23 24 4.940654 CACACACACAGAGATAGAGAGAGA 59.059 45.833 0.00 0.00 0.00 3.10
24 25 5.065090 CACACACACAGAGATAGAGAGAGAG 59.935 48.000 0.00 0.00 0.00 3.20
25 26 5.045942 ACACACACAGAGATAGAGAGAGAGA 60.046 44.000 0.00 0.00 0.00 3.10
26 27 5.525012 CACACACAGAGATAGAGAGAGAGAG 59.475 48.000 0.00 0.00 0.00 3.20
27 28 5.425217 ACACACAGAGATAGAGAGAGAGAGA 59.575 44.000 0.00 0.00 0.00 3.10
28 29 5.987953 CACACAGAGATAGAGAGAGAGAGAG 59.012 48.000 0.00 0.00 0.00 3.20
29 30 5.899547 ACACAGAGATAGAGAGAGAGAGAGA 59.100 44.000 0.00 0.00 0.00 3.10
30 31 6.041409 ACACAGAGATAGAGAGAGAGAGAGAG 59.959 46.154 0.00 0.00 0.00 3.20
31 32 6.266330 CACAGAGATAGAGAGAGAGAGAGAGA 59.734 46.154 0.00 0.00 0.00 3.10
32 33 6.493115 ACAGAGATAGAGAGAGAGAGAGAGAG 59.507 46.154 0.00 0.00 0.00 3.20
33 34 6.718912 CAGAGATAGAGAGAGAGAGAGAGAGA 59.281 46.154 0.00 0.00 0.00 3.10
34 35 6.947733 AGAGATAGAGAGAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
35 36 6.857848 AGATAGAGAGAGAGAGAGAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
36 37 6.947733 AGATAGAGAGAGAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
37 38 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
38 39 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
39 40 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
40 41 4.837860 AGAGAGAGAGAGAGAGAGAGATCC 59.162 50.000 0.00 0.00 0.00 3.36
41 42 3.576118 AGAGAGAGAGAGAGAGAGATCCG 59.424 52.174 0.00 0.00 0.00 4.18
270 286 0.494551 TAGGGTTCTGGTGGGAAGGA 59.505 55.000 0.00 0.00 0.00 3.36
271 287 0.842467 AGGGTTCTGGTGGGAAGGAG 60.842 60.000 0.00 0.00 0.00 3.69
272 288 1.685820 GGTTCTGGTGGGAAGGAGG 59.314 63.158 0.00 0.00 0.00 4.30
273 289 1.685820 GTTCTGGTGGGAAGGAGGG 59.314 63.158 0.00 0.00 0.00 4.30
274 290 0.840722 GTTCTGGTGGGAAGGAGGGA 60.841 60.000 0.00 0.00 0.00 4.20
275 291 0.121197 TTCTGGTGGGAAGGAGGGAT 59.879 55.000 0.00 0.00 0.00 3.85
276 292 0.326618 TCTGGTGGGAAGGAGGGATC 60.327 60.000 0.00 0.00 0.00 3.36
292 309 5.414144 GGAGGGATCTTTCTTTCTCTGTTTG 59.586 44.000 0.00 0.00 0.00 2.93
293 310 5.946486 AGGGATCTTTCTTTCTCTGTTTGT 58.054 37.500 0.00 0.00 0.00 2.83
299 316 9.230932 GATCTTTCTTTCTCTGTTTGTTCTTTG 57.769 33.333 0.00 0.00 0.00 2.77
311 328 7.066525 TCTGTTTGTTCTTTGTACCGAAAATCT 59.933 33.333 0.00 0.00 0.00 2.40
314 331 9.166126 GTTTGTTCTTTGTACCGAAAATCTTAG 57.834 33.333 0.00 0.00 0.00 2.18
315 332 6.894828 TGTTCTTTGTACCGAAAATCTTAGC 58.105 36.000 0.00 0.00 0.00 3.09
316 333 6.072893 TGTTCTTTGTACCGAAAATCTTAGCC 60.073 38.462 0.00 0.00 0.00 3.93
317 334 5.801380 TCTTTGTACCGAAAATCTTAGCCT 58.199 37.500 0.00 0.00 0.00 4.58
318 335 6.938507 TCTTTGTACCGAAAATCTTAGCCTA 58.061 36.000 0.00 0.00 0.00 3.93
319 336 7.039882 TCTTTGTACCGAAAATCTTAGCCTAG 58.960 38.462 0.00 0.00 0.00 3.02
344 367 5.848286 TGGCCTGATACCATTGATAGATT 57.152 39.130 3.32 0.00 30.29 2.40
349 372 7.041107 GCCTGATACCATTGATAGATTCTCTC 58.959 42.308 0.00 0.00 0.00 3.20
356 379 5.339177 CATTGATAGATTCTCTCGATCGGG 58.661 45.833 16.41 13.07 38.46 5.14
367 390 0.036448 TCGATCGGGGTAGGCTAGAG 59.964 60.000 16.41 0.00 0.00 2.43
368 391 0.036448 CGATCGGGGTAGGCTAGAGA 59.964 60.000 7.38 0.00 0.00 3.10
369 392 1.536940 GATCGGGGTAGGCTAGAGAC 58.463 60.000 0.00 0.00 0.00 3.36
377 401 2.550639 GGTAGGCTAGAGACTCCGGTAG 60.551 59.091 0.00 0.00 33.72 3.18
394 418 1.757699 GTAGACCTACCTTCTGGCTGG 59.242 57.143 0.00 0.00 36.63 4.85
397 421 1.997874 CCTACCTTCTGGCTGGGCT 60.998 63.158 0.00 0.00 36.63 5.19
398 422 1.566298 CCTACCTTCTGGCTGGGCTT 61.566 60.000 0.00 0.00 36.63 4.35
399 423 0.393537 CTACCTTCTGGCTGGGCTTG 60.394 60.000 0.00 0.00 36.63 4.01
413 437 2.317609 GCTTGCGAGCTCGAACCAA 61.318 57.895 38.74 28.62 45.65 3.67
438 465 0.899717 ATGGTGATGTTGTGGTGGCC 60.900 55.000 0.00 0.00 0.00 5.36
454 482 3.490759 CCGTGATGGCAGTGCGAC 61.491 66.667 9.45 3.50 0.00 5.19
521 550 1.081462 TAGGGATTGTCGGTGGGGT 59.919 57.895 0.00 0.00 0.00 4.95
526 555 0.879090 GATTGTCGGTGGGGTTTGTC 59.121 55.000 0.00 0.00 0.00 3.18
544 573 0.800683 TCGCAGCGATTAACCTCGTG 60.801 55.000 15.11 0.32 40.73 4.35
545 574 0.800683 CGCAGCGATTAACCTCGTGA 60.801 55.000 9.98 0.00 40.73 4.35
546 575 0.645868 GCAGCGATTAACCTCGTGAC 59.354 55.000 0.86 0.00 40.73 3.67
547 576 1.736032 GCAGCGATTAACCTCGTGACT 60.736 52.381 0.86 0.00 40.73 3.41
548 577 2.186076 CAGCGATTAACCTCGTGACTC 58.814 52.381 0.86 0.00 40.73 3.36
549 578 1.189403 GCGATTAACCTCGTGACTCG 58.811 55.000 0.86 0.00 40.73 4.18
550 579 1.467035 GCGATTAACCTCGTGACTCGT 60.467 52.381 0.86 0.00 40.73 4.18
551 580 2.174764 CGATTAACCTCGTGACTCGTG 58.825 52.381 0.00 0.00 40.80 4.35
552 581 1.918609 GATTAACCTCGTGACTCGTGC 59.081 52.381 0.00 0.00 40.80 5.34
553 582 0.038892 TTAACCTCGTGACTCGTGCC 60.039 55.000 0.00 0.00 40.80 5.01
554 583 2.191354 TAACCTCGTGACTCGTGCCG 62.191 60.000 0.00 0.00 40.80 5.69
559 588 4.409218 GTGACTCGTGCCGCGGTA 62.409 66.667 28.70 21.83 41.72 4.02
560 589 4.409218 TGACTCGTGCCGCGGTAC 62.409 66.667 33.25 33.25 41.72 3.34
569 598 4.143333 CCGCGGTACCCACCTCTG 62.143 72.222 19.50 0.00 43.33 3.35
570 599 3.379445 CGCGGTACCCACCTCTGT 61.379 66.667 6.25 0.00 43.33 3.41
571 600 2.939261 CGCGGTACCCACCTCTGTT 61.939 63.158 6.25 0.00 43.33 3.16
572 601 1.373812 GCGGTACCCACCTCTGTTT 59.626 57.895 6.25 0.00 43.33 2.83
573 602 0.953960 GCGGTACCCACCTCTGTTTG 60.954 60.000 6.25 0.00 43.33 2.93
574 603 0.395312 CGGTACCCACCTCTGTTTGT 59.605 55.000 6.25 0.00 43.33 2.83
575 604 1.619827 CGGTACCCACCTCTGTTTGTA 59.380 52.381 6.25 0.00 43.33 2.41
576 605 2.235402 CGGTACCCACCTCTGTTTGTAT 59.765 50.000 6.25 0.00 43.33 2.29
577 606 3.448301 CGGTACCCACCTCTGTTTGTATA 59.552 47.826 6.25 0.00 43.33 1.47
578 607 4.441079 CGGTACCCACCTCTGTTTGTATAG 60.441 50.000 6.25 0.00 43.33 1.31
579 608 3.629142 ACCCACCTCTGTTTGTATAGC 57.371 47.619 0.00 0.00 0.00 2.97
580 609 2.093658 ACCCACCTCTGTTTGTATAGCG 60.094 50.000 0.00 0.00 0.00 4.26
581 610 1.933853 CCACCTCTGTTTGTATAGCGC 59.066 52.381 0.00 0.00 0.00 5.92
582 611 1.588404 CACCTCTGTTTGTATAGCGCG 59.412 52.381 0.00 0.00 0.00 6.86
583 612 1.209128 CCTCTGTTTGTATAGCGCGG 58.791 55.000 8.83 0.00 0.00 6.46
584 613 1.209128 CTCTGTTTGTATAGCGCGGG 58.791 55.000 8.83 0.00 0.00 6.13
585 614 0.533491 TCTGTTTGTATAGCGCGGGT 59.467 50.000 8.83 0.00 0.00 5.28
586 615 0.928229 CTGTTTGTATAGCGCGGGTC 59.072 55.000 8.83 0.00 0.00 4.46
587 616 0.246910 TGTTTGTATAGCGCGGGTCA 59.753 50.000 8.83 0.00 0.00 4.02
588 617 0.648958 GTTTGTATAGCGCGGGTCAC 59.351 55.000 8.83 0.00 0.00 3.67
589 618 0.246910 TTTGTATAGCGCGGGTCACA 59.753 50.000 8.83 0.04 0.00 3.58
590 619 0.179121 TTGTATAGCGCGGGTCACAG 60.179 55.000 8.83 0.00 0.00 3.66
591 620 1.299926 GTATAGCGCGGGTCACAGG 60.300 63.158 8.83 0.00 0.00 4.00
592 621 2.495409 TATAGCGCGGGTCACAGGG 61.495 63.158 8.83 0.00 0.00 4.45
601 630 3.897122 GTCACAGGGGCCCACCAA 61.897 66.667 27.72 4.22 42.91 3.67
602 631 3.897122 TCACAGGGGCCCACCAAC 61.897 66.667 27.72 5.28 42.91 3.77
603 632 4.994756 CACAGGGGCCCACCAACC 62.995 72.222 27.72 4.38 42.91 3.77
605 634 3.996621 CAGGGGCCCACCAACCAT 61.997 66.667 27.72 0.00 42.91 3.55
606 635 2.204385 AGGGGCCCACCAACCATA 60.204 61.111 27.72 0.00 42.91 2.74
607 636 1.625565 AGGGGCCCACCAACCATAT 60.626 57.895 27.72 0.00 42.91 1.78
608 637 1.457455 GGGGCCCACCAACCATATG 60.457 63.158 26.86 0.00 42.91 1.78
609 638 1.618030 GGGCCCACCAACCATATGA 59.382 57.895 19.95 0.00 39.85 2.15
610 639 0.468029 GGGCCCACCAACCATATGAG 60.468 60.000 19.95 0.00 39.85 2.90
611 640 0.468029 GGCCCACCAACCATATGAGG 60.468 60.000 3.65 5.81 35.26 3.86
612 641 0.468029 GCCCACCAACCATATGAGGG 60.468 60.000 3.65 5.06 38.04 4.30
613 642 0.926293 CCCACCAACCATATGAGGGT 59.074 55.000 3.65 5.72 41.41 4.34
618 647 3.924576 AACCATATGAGGGTTGGGC 57.075 52.632 3.65 0.00 46.53 5.36
619 648 0.106719 AACCATATGAGGGTTGGGCG 60.107 55.000 3.65 0.00 46.53 6.13
620 649 1.898574 CCATATGAGGGTTGGGCGC 60.899 63.158 3.65 0.00 0.00 6.53
621 650 1.898574 CATATGAGGGTTGGGCGCC 60.899 63.158 21.18 21.18 0.00 6.53
622 651 3.133365 ATATGAGGGTTGGGCGCCC 62.133 63.158 39.40 39.40 46.43 6.13
638 667 4.161295 CCCCGATCAAGGCGCAGA 62.161 66.667 10.83 3.97 0.00 4.26
639 668 2.109799 CCCGATCAAGGCGCAGAT 59.890 61.111 10.83 9.53 0.00 2.90
640 669 1.958205 CCCGATCAAGGCGCAGATC 60.958 63.158 20.28 20.28 37.79 2.75
641 670 1.068753 CCGATCAAGGCGCAGATCT 59.931 57.895 24.52 6.62 38.75 2.75
642 671 0.315251 CCGATCAAGGCGCAGATCTA 59.685 55.000 24.52 2.78 38.75 1.98
643 672 1.269778 CCGATCAAGGCGCAGATCTAA 60.270 52.381 24.52 3.07 38.75 2.10
644 673 2.057316 CGATCAAGGCGCAGATCTAAG 58.943 52.381 24.52 12.40 38.75 2.18
645 674 2.411904 GATCAAGGCGCAGATCTAAGG 58.588 52.381 21.92 1.87 38.07 2.69
646 675 0.465705 TCAAGGCGCAGATCTAAGGG 59.534 55.000 10.83 0.00 0.00 3.95
647 676 1.147153 AAGGCGCAGATCTAAGGGC 59.853 57.895 10.83 12.19 42.26 5.19
649 678 2.281139 GCGCAGATCTAAGGGCCC 60.281 66.667 16.46 16.46 37.69 5.80
650 679 2.029666 CGCAGATCTAAGGGCCCG 59.970 66.667 18.44 1.51 0.00 6.13
651 680 2.427753 GCAGATCTAAGGGCCCGG 59.572 66.667 18.44 11.27 0.00 5.73
652 681 2.444256 GCAGATCTAAGGGCCCGGT 61.444 63.158 18.44 11.65 0.00 5.28
653 682 1.447643 CAGATCTAAGGGCCCGGTG 59.552 63.158 18.44 10.51 0.00 4.94
654 683 1.766461 AGATCTAAGGGCCCGGTGG 60.766 63.158 18.44 11.09 0.00 4.61
673 702 4.358841 CCATTGGGCCCACACGGA 62.359 66.667 28.70 10.56 0.00 4.69
674 703 2.282816 CATTGGGCCCACACGGAA 60.283 61.111 28.70 9.60 0.00 4.30
675 704 2.035626 ATTGGGCCCACACGGAAG 59.964 61.111 28.70 0.00 0.00 3.46
690 719 3.926616 ACGGAAGTGATCAACCTAACAG 58.073 45.455 0.00 0.00 46.97 3.16
691 720 3.576982 ACGGAAGTGATCAACCTAACAGA 59.423 43.478 0.00 0.00 46.97 3.41
692 721 4.223032 ACGGAAGTGATCAACCTAACAGAT 59.777 41.667 0.00 0.00 46.97 2.90
693 722 5.421056 ACGGAAGTGATCAACCTAACAGATA 59.579 40.000 0.00 0.00 46.97 1.98
694 723 6.070995 ACGGAAGTGATCAACCTAACAGATAA 60.071 38.462 0.00 0.00 46.97 1.75
695 724 6.986817 CGGAAGTGATCAACCTAACAGATAAT 59.013 38.462 0.00 0.00 0.00 1.28
696 725 7.495934 CGGAAGTGATCAACCTAACAGATAATT 59.504 37.037 0.00 0.00 0.00 1.40
697 726 8.616076 GGAAGTGATCAACCTAACAGATAATTG 58.384 37.037 0.00 0.00 0.00 2.32
698 727 9.167311 GAAGTGATCAACCTAACAGATAATTGT 57.833 33.333 0.00 0.00 0.00 2.71
700 729 9.601217 AGTGATCAACCTAACAGATAATTGTAC 57.399 33.333 0.00 0.00 0.00 2.90
701 730 8.540492 GTGATCAACCTAACAGATAATTGTACG 58.460 37.037 0.00 0.00 0.00 3.67
702 731 7.709182 TGATCAACCTAACAGATAATTGTACGG 59.291 37.037 0.00 0.00 0.00 4.02
703 732 7.172868 TCAACCTAACAGATAATTGTACGGA 57.827 36.000 0.00 0.00 0.00 4.69
704 733 7.262772 TCAACCTAACAGATAATTGTACGGAG 58.737 38.462 0.00 0.00 0.00 4.63
705 734 6.158023 ACCTAACAGATAATTGTACGGAGG 57.842 41.667 0.00 0.00 0.00 4.30
706 735 4.989168 CCTAACAGATAATTGTACGGAGGC 59.011 45.833 0.00 0.00 0.00 4.70
707 736 3.093717 ACAGATAATTGTACGGAGGCG 57.906 47.619 0.00 0.00 0.00 5.52
708 737 2.691526 ACAGATAATTGTACGGAGGCGA 59.308 45.455 0.00 0.00 0.00 5.54
709 738 3.321111 ACAGATAATTGTACGGAGGCGAT 59.679 43.478 0.00 0.00 0.00 4.58
710 739 4.521639 ACAGATAATTGTACGGAGGCGATA 59.478 41.667 0.00 0.00 0.00 2.92
711 740 4.857588 CAGATAATTGTACGGAGGCGATAC 59.142 45.833 0.00 0.00 0.00 2.24
712 741 4.521639 AGATAATTGTACGGAGGCGATACA 59.478 41.667 0.00 0.00 0.00 2.29
713 742 2.503920 ATTGTACGGAGGCGATACAC 57.496 50.000 0.00 0.00 0.00 2.90
714 743 0.457035 TTGTACGGAGGCGATACACC 59.543 55.000 0.00 0.00 0.00 4.16
715 744 0.680601 TGTACGGAGGCGATACACCA 60.681 55.000 0.00 0.00 0.00 4.17
716 745 0.457035 GTACGGAGGCGATACACCAA 59.543 55.000 0.00 0.00 0.00 3.67
717 746 1.068127 GTACGGAGGCGATACACCAAT 59.932 52.381 0.00 0.00 0.00 3.16
718 747 0.104304 ACGGAGGCGATACACCAATC 59.896 55.000 0.00 0.00 0.00 2.67
719 748 0.389391 CGGAGGCGATACACCAATCT 59.611 55.000 0.00 0.00 0.00 2.40
720 749 1.603172 CGGAGGCGATACACCAATCTC 60.603 57.143 0.00 0.00 0.00 2.75
721 750 1.689273 GGAGGCGATACACCAATCTCT 59.311 52.381 0.00 0.00 0.00 3.10
722 751 2.288518 GGAGGCGATACACCAATCTCTC 60.289 54.545 0.00 0.00 0.00 3.20
723 752 2.362397 GAGGCGATACACCAATCTCTCA 59.638 50.000 0.00 0.00 30.67 3.27
724 753 2.968574 AGGCGATACACCAATCTCTCAT 59.031 45.455 0.00 0.00 0.00 2.90
725 754 3.006323 AGGCGATACACCAATCTCTCATC 59.994 47.826 0.00 0.00 0.00 2.92
726 755 3.006323 GGCGATACACCAATCTCTCATCT 59.994 47.826 0.00 0.00 0.00 2.90
727 756 4.233789 GCGATACACCAATCTCTCATCTC 58.766 47.826 0.00 0.00 0.00 2.75
728 757 4.261783 GCGATACACCAATCTCTCATCTCA 60.262 45.833 0.00 0.00 0.00 3.27
729 758 5.566429 GCGATACACCAATCTCTCATCTCAT 60.566 44.000 0.00 0.00 0.00 2.90
730 759 6.349694 GCGATACACCAATCTCTCATCTCATA 60.350 42.308 0.00 0.00 0.00 2.15
731 760 7.630297 GCGATACACCAATCTCTCATCTCATAT 60.630 40.741 0.00 0.00 0.00 1.78
732 761 7.914871 CGATACACCAATCTCTCATCTCATATC 59.085 40.741 0.00 0.00 0.00 1.63
733 762 6.357579 ACACCAATCTCTCATCTCATATCC 57.642 41.667 0.00 0.00 0.00 2.59
734 763 6.083383 ACACCAATCTCTCATCTCATATCCT 58.917 40.000 0.00 0.00 0.00 3.24
735 764 6.558014 ACACCAATCTCTCATCTCATATCCTT 59.442 38.462 0.00 0.00 0.00 3.36
736 765 7.732140 ACACCAATCTCTCATCTCATATCCTTA 59.268 37.037 0.00 0.00 0.00 2.69
737 766 8.591940 CACCAATCTCTCATCTCATATCCTTAA 58.408 37.037 0.00 0.00 0.00 1.85
738 767 8.592809 ACCAATCTCTCATCTCATATCCTTAAC 58.407 37.037 0.00 0.00 0.00 2.01
739 768 8.814931 CCAATCTCTCATCTCATATCCTTAACT 58.185 37.037 0.00 0.00 0.00 2.24
833 865 2.050351 ATCGATCGCCGGCTAACG 60.050 61.111 26.68 24.17 43.80 3.18
921 957 2.154854 TCTTGTGCTGTTTCCTCGAG 57.845 50.000 5.13 5.13 0.00 4.04
1076 1113 4.828387 AGAAGAAGAGGTGAAGAAGTACGT 59.172 41.667 0.00 0.00 0.00 3.57
1081 1118 3.825014 AGAGGTGAAGAAGTACGTAGCAA 59.175 43.478 0.00 0.00 0.00 3.91
1254 1312 2.440409 CTGGGTGATTGGAAGAAGGTG 58.560 52.381 0.00 0.00 0.00 4.00
1651 1726 1.451927 GAGGAATGCGGTGATGGCA 60.452 57.895 0.00 0.00 45.71 4.92
1727 1805 2.530151 ACCTCAGGAGCAGCCCAA 60.530 61.111 0.00 0.00 37.37 4.12
1815 1893 2.022129 AGAGCGTCGCCAAAACTCG 61.022 57.895 14.86 0.00 32.60 4.18
1882 1972 1.115467 GAGGAGGACGATGTGACCAT 58.885 55.000 0.00 0.00 34.56 3.55
1996 2095 2.119484 TTGATGGTTCGGTCGGGCTT 62.119 55.000 0.00 0.00 0.00 4.35
2148 2265 7.120285 CCTTAAAGAAGAGCAATGACAAGATGA 59.880 37.037 0.00 0.00 34.25 2.92
2344 2506 3.261137 AGGGTCTTCGTTCTTCTTTAGGG 59.739 47.826 0.00 0.00 0.00 3.53
2623 2792 5.265350 TCAATGAGATCTTGAGAGCTGAG 57.735 43.478 3.13 0.00 41.40 3.35
2790 2959 0.526662 CGTCTGGACCGAGCTTTAGT 59.473 55.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.940654 TCTCTCTCTATCTCTGTGTGTGTG 59.059 45.833 0.00 0.00 0.00 3.82
1 2 5.045942 TCTCTCTCTCTATCTCTGTGTGTGT 60.046 44.000 0.00 0.00 0.00 3.72
2 3 5.427378 TCTCTCTCTCTATCTCTGTGTGTG 58.573 45.833 0.00 0.00 0.00 3.82
3 4 5.425217 TCTCTCTCTCTCTATCTCTGTGTGT 59.575 44.000 0.00 0.00 0.00 3.72
4 5 5.917462 TCTCTCTCTCTCTATCTCTGTGTG 58.083 45.833 0.00 0.00 0.00 3.82
5 6 5.899547 TCTCTCTCTCTCTCTATCTCTGTGT 59.100 44.000 0.00 0.00 0.00 3.72
6 7 6.266330 TCTCTCTCTCTCTCTCTATCTCTGTG 59.734 46.154 0.00 0.00 0.00 3.66
7 8 6.377080 TCTCTCTCTCTCTCTCTATCTCTGT 58.623 44.000 0.00 0.00 0.00 3.41
8 9 6.718912 TCTCTCTCTCTCTCTCTCTATCTCTG 59.281 46.154 0.00 0.00 0.00 3.35
9 10 6.857848 TCTCTCTCTCTCTCTCTCTATCTCT 58.142 44.000 0.00 0.00 0.00 3.10
10 11 6.945435 TCTCTCTCTCTCTCTCTCTCTATCTC 59.055 46.154 0.00 0.00 0.00 2.75
11 12 6.857848 TCTCTCTCTCTCTCTCTCTCTATCT 58.142 44.000 0.00 0.00 0.00 1.98
12 13 6.945435 TCTCTCTCTCTCTCTCTCTCTCTATC 59.055 46.154 0.00 0.00 0.00 2.08
13 14 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
14 15 6.267492 TCTCTCTCTCTCTCTCTCTCTCTA 57.733 45.833 0.00 0.00 0.00 2.43
15 16 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
16 17 5.047377 GGATCTCTCTCTCTCTCTCTCTCTC 60.047 52.000 0.00 0.00 0.00 3.20
17 18 4.837860 GGATCTCTCTCTCTCTCTCTCTCT 59.162 50.000 0.00 0.00 0.00 3.10
18 19 4.321601 CGGATCTCTCTCTCTCTCTCTCTC 60.322 54.167 0.00 0.00 0.00 3.20
19 20 3.576118 CGGATCTCTCTCTCTCTCTCTCT 59.424 52.174 0.00 0.00 0.00 3.10
20 21 3.306364 CCGGATCTCTCTCTCTCTCTCTC 60.306 56.522 0.00 0.00 0.00 3.20
21 22 2.634940 CCGGATCTCTCTCTCTCTCTCT 59.365 54.545 0.00 0.00 0.00 3.10
22 23 2.872038 GCCGGATCTCTCTCTCTCTCTC 60.872 59.091 5.05 0.00 0.00 3.20
23 24 1.072331 GCCGGATCTCTCTCTCTCTCT 59.928 57.143 5.05 0.00 0.00 3.10
24 25 1.523758 GCCGGATCTCTCTCTCTCTC 58.476 60.000 5.05 0.00 0.00 3.20
25 26 0.250295 CGCCGGATCTCTCTCTCTCT 60.250 60.000 5.05 0.00 0.00 3.10
26 27 1.234615 CCGCCGGATCTCTCTCTCTC 61.235 65.000 5.05 0.00 0.00 3.20
27 28 1.228124 CCGCCGGATCTCTCTCTCT 60.228 63.158 5.05 0.00 0.00 3.10
28 29 2.914908 GCCGCCGGATCTCTCTCTC 61.915 68.421 7.68 0.00 0.00 3.20
29 30 2.909965 GCCGCCGGATCTCTCTCT 60.910 66.667 7.68 0.00 0.00 3.10
30 31 4.335584 CGCCGCCGGATCTCTCTC 62.336 72.222 7.68 0.00 0.00 3.20
55 56 3.494254 ACACCGGCAAAGGGGTCA 61.494 61.111 0.00 0.00 46.93 4.02
224 231 6.042437 ACAGGGCAAAGAAATCTCAAAGAAAT 59.958 34.615 0.00 0.00 0.00 2.17
260 276 1.213182 GAAAGATCCCTCCTTCCCACC 59.787 57.143 0.00 0.00 0.00 4.61
261 277 2.200955 AGAAAGATCCCTCCTTCCCAC 58.799 52.381 0.00 0.00 0.00 4.61
270 286 5.946486 ACAAACAGAGAAAGAAAGATCCCT 58.054 37.500 0.00 0.00 0.00 4.20
271 287 6.488344 AGAACAAACAGAGAAAGAAAGATCCC 59.512 38.462 0.00 0.00 0.00 3.85
272 288 7.503521 AGAACAAACAGAGAAAGAAAGATCC 57.496 36.000 0.00 0.00 0.00 3.36
273 289 9.230932 CAAAGAACAAACAGAGAAAGAAAGATC 57.769 33.333 0.00 0.00 0.00 2.75
274 290 8.743714 ACAAAGAACAAACAGAGAAAGAAAGAT 58.256 29.630 0.00 0.00 0.00 2.40
275 291 8.110860 ACAAAGAACAAACAGAGAAAGAAAGA 57.889 30.769 0.00 0.00 0.00 2.52
276 292 9.278734 GTACAAAGAACAAACAGAGAAAGAAAG 57.721 33.333 0.00 0.00 0.00 2.62
292 309 6.148976 AGGCTAAGATTTTCGGTACAAAGAAC 59.851 38.462 0.00 0.00 0.00 3.01
293 310 6.235664 AGGCTAAGATTTTCGGTACAAAGAA 58.764 36.000 0.00 0.00 0.00 2.52
299 316 4.690122 TGCTAGGCTAAGATTTTCGGTAC 58.310 43.478 0.00 0.00 0.00 3.34
315 332 1.059098 TGGTATCAGGCCATGCTAGG 58.941 55.000 5.01 0.00 0.00 3.02
316 333 3.079578 CAATGGTATCAGGCCATGCTAG 58.920 50.000 5.01 0.00 45.21 3.42
317 334 2.710471 TCAATGGTATCAGGCCATGCTA 59.290 45.455 5.01 0.00 45.21 3.49
318 335 1.496001 TCAATGGTATCAGGCCATGCT 59.504 47.619 5.01 0.00 45.21 3.79
319 336 1.985473 TCAATGGTATCAGGCCATGC 58.015 50.000 5.01 0.00 45.21 4.06
349 372 0.036448 TCTCTAGCCTACCCCGATCG 59.964 60.000 8.51 8.51 0.00 3.69
356 379 0.183252 ACCGGAGTCTCTAGCCTACC 59.817 60.000 9.46 0.00 0.00 3.18
377 401 1.908483 CCCAGCCAGAAGGTAGGTC 59.092 63.158 0.00 0.00 37.19 3.85
397 421 1.221466 CTGTTGGTTCGAGCTCGCAA 61.221 55.000 30.97 24.44 39.60 4.85
398 422 1.664649 CTGTTGGTTCGAGCTCGCA 60.665 57.895 30.97 19.02 39.60 5.10
399 423 3.016474 GCTGTTGGTTCGAGCTCGC 62.016 63.158 30.97 17.74 39.60 5.03
413 437 1.250328 CACAACATCACCATGGCTGT 58.750 50.000 13.04 10.53 33.82 4.40
438 465 3.842126 CGTCGCACTGCCATCACG 61.842 66.667 0.00 0.00 0.00 4.35
521 550 1.730064 GAGGTTAATCGCTGCGACAAA 59.270 47.619 28.41 20.39 39.18 2.83
526 555 0.800683 TCACGAGGTTAATCGCTGCG 60.801 55.000 17.25 17.25 46.60 5.18
557 586 4.439968 GCTATACAAACAGAGGTGGGTAC 58.560 47.826 0.00 0.00 0.00 3.34
558 587 3.131577 CGCTATACAAACAGAGGTGGGTA 59.868 47.826 0.00 0.00 0.00 3.69
559 588 2.093658 CGCTATACAAACAGAGGTGGGT 60.094 50.000 0.00 0.00 0.00 4.51
560 589 2.550978 CGCTATACAAACAGAGGTGGG 58.449 52.381 0.00 0.00 0.00 4.61
561 590 1.933853 GCGCTATACAAACAGAGGTGG 59.066 52.381 0.00 0.00 0.00 4.61
562 591 1.588404 CGCGCTATACAAACAGAGGTG 59.412 52.381 5.56 0.00 0.00 4.00
563 592 1.470979 CCGCGCTATACAAACAGAGGT 60.471 52.381 5.56 0.00 0.00 3.85
564 593 1.209128 CCGCGCTATACAAACAGAGG 58.791 55.000 5.56 0.00 0.00 3.69
565 594 1.209128 CCCGCGCTATACAAACAGAG 58.791 55.000 5.56 0.00 0.00 3.35
566 595 0.533491 ACCCGCGCTATACAAACAGA 59.467 50.000 5.56 0.00 0.00 3.41
567 596 0.928229 GACCCGCGCTATACAAACAG 59.072 55.000 5.56 0.00 0.00 3.16
568 597 0.246910 TGACCCGCGCTATACAAACA 59.753 50.000 5.56 0.00 0.00 2.83
569 598 0.648958 GTGACCCGCGCTATACAAAC 59.351 55.000 5.56 0.00 0.00 2.93
570 599 0.246910 TGTGACCCGCGCTATACAAA 59.753 50.000 5.56 0.00 0.00 2.83
571 600 0.179121 CTGTGACCCGCGCTATACAA 60.179 55.000 5.56 0.00 0.00 2.41
572 601 1.435925 CTGTGACCCGCGCTATACA 59.564 57.895 5.56 2.25 0.00 2.29
573 602 1.299926 CCTGTGACCCGCGCTATAC 60.300 63.158 5.56 0.00 0.00 1.47
574 603 2.495409 CCCTGTGACCCGCGCTATA 61.495 63.158 5.56 0.00 0.00 1.31
575 604 3.849951 CCCTGTGACCCGCGCTAT 61.850 66.667 5.56 0.00 0.00 2.97
584 613 3.897122 TTGGTGGGCCCCTGTGAC 61.897 66.667 22.27 10.43 0.00 3.67
585 614 3.897122 GTTGGTGGGCCCCTGTGA 61.897 66.667 22.27 0.00 0.00 3.58
586 615 4.994756 GGTTGGTGGGCCCCTGTG 62.995 72.222 22.27 0.00 0.00 3.66
588 617 1.948403 ATATGGTTGGTGGGCCCCTG 61.948 60.000 22.27 0.00 0.00 4.45
589 618 1.625565 ATATGGTTGGTGGGCCCCT 60.626 57.895 22.27 0.00 0.00 4.79
590 619 1.457455 CATATGGTTGGTGGGCCCC 60.457 63.158 22.27 10.91 0.00 5.80
591 620 0.468029 CTCATATGGTTGGTGGGCCC 60.468 60.000 17.59 17.59 0.00 5.80
592 621 0.468029 CCTCATATGGTTGGTGGGCC 60.468 60.000 2.13 0.00 0.00 5.80
593 622 0.468029 CCCTCATATGGTTGGTGGGC 60.468 60.000 2.13 0.00 0.00 5.36
594 623 0.926293 ACCCTCATATGGTTGGTGGG 59.074 55.000 2.13 7.82 37.06 4.61
595 624 2.826674 AACCCTCATATGGTTGGTGG 57.173 50.000 2.13 0.00 44.30 4.61
600 629 0.106719 CGCCCAACCCTCATATGGTT 60.107 55.000 2.13 0.00 46.92 3.67
601 630 1.531748 CGCCCAACCCTCATATGGT 59.468 57.895 2.13 0.00 37.85 3.55
602 631 1.898574 GCGCCCAACCCTCATATGG 60.899 63.158 2.13 0.00 0.00 2.74
603 632 1.898574 GGCGCCCAACCCTCATATG 60.899 63.158 18.11 0.00 0.00 1.78
604 633 2.515901 GGCGCCCAACCCTCATAT 59.484 61.111 18.11 0.00 0.00 1.78
605 634 3.804329 GGGCGCCCAACCCTCATA 61.804 66.667 40.73 0.00 44.68 2.15
621 650 3.466791 ATCTGCGCCTTGATCGGGG 62.467 63.158 4.18 3.46 39.79 5.73
622 651 1.958205 GATCTGCGCCTTGATCGGG 60.958 63.158 4.18 0.70 31.29 5.14
623 652 0.315251 TAGATCTGCGCCTTGATCGG 59.685 55.000 21.11 0.00 42.62 4.18
624 653 2.057316 CTTAGATCTGCGCCTTGATCG 58.943 52.381 21.11 10.00 42.62 3.69
625 654 2.411904 CCTTAGATCTGCGCCTTGATC 58.588 52.381 20.32 20.32 39.32 2.92
626 655 1.071385 CCCTTAGATCTGCGCCTTGAT 59.929 52.381 4.18 6.11 0.00 2.57
627 656 0.465705 CCCTTAGATCTGCGCCTTGA 59.534 55.000 4.18 0.26 0.00 3.02
628 657 1.162800 GCCCTTAGATCTGCGCCTTG 61.163 60.000 4.18 0.00 0.00 3.61
629 658 1.147153 GCCCTTAGATCTGCGCCTT 59.853 57.895 4.18 0.00 0.00 4.35
630 659 2.812619 GGCCCTTAGATCTGCGCCT 61.813 63.158 4.18 0.00 33.50 5.52
631 660 2.281139 GGCCCTTAGATCTGCGCC 60.281 66.667 4.18 6.95 0.00 6.53
632 661 2.281139 GGGCCCTTAGATCTGCGC 60.281 66.667 17.04 0.00 0.00 6.09
633 662 2.029666 CGGGCCCTTAGATCTGCG 59.970 66.667 22.43 0.00 0.00 5.18
634 663 2.427753 CCGGGCCCTTAGATCTGC 59.572 66.667 22.43 0.00 0.00 4.26
635 664 1.447643 CACCGGGCCCTTAGATCTG 59.552 63.158 22.43 0.22 0.00 2.90
636 665 1.766461 CCACCGGGCCCTTAGATCT 60.766 63.158 22.43 0.00 0.00 2.75
637 666 2.819284 CCCACCGGGCCCTTAGATC 61.819 68.421 22.43 0.00 35.35 2.75
638 667 2.772622 CCCACCGGGCCCTTAGAT 60.773 66.667 22.43 0.00 35.35 1.98
656 685 3.877344 TTCCGTGTGGGCCCAATGG 62.877 63.158 30.64 28.30 35.24 3.16
657 686 2.282816 TTCCGTGTGGGCCCAATG 60.283 61.111 30.64 21.01 35.24 2.82
658 687 2.035626 CTTCCGTGTGGGCCCAAT 59.964 61.111 30.64 0.00 35.24 3.16
659 688 3.494254 ACTTCCGTGTGGGCCCAA 61.494 61.111 30.64 14.78 35.24 4.12
660 689 4.263572 CACTTCCGTGTGGGCCCA 62.264 66.667 24.45 24.45 36.39 5.36
661 690 3.268103 ATCACTTCCGTGTGGGCCC 62.268 63.158 17.59 17.59 41.89 5.80
662 691 1.745489 GATCACTTCCGTGTGGGCC 60.745 63.158 0.00 0.00 41.89 5.80
663 692 0.605319 TTGATCACTTCCGTGTGGGC 60.605 55.000 0.00 0.00 41.89 5.36
664 693 1.156736 GTTGATCACTTCCGTGTGGG 58.843 55.000 0.00 0.00 41.89 4.61
665 694 1.156736 GGTTGATCACTTCCGTGTGG 58.843 55.000 0.00 0.00 41.89 4.17
666 695 2.169832 AGGTTGATCACTTCCGTGTG 57.830 50.000 0.00 0.00 41.89 3.82
667 696 3.070446 TGTTAGGTTGATCACTTCCGTGT 59.930 43.478 0.00 0.00 41.89 4.49
668 697 3.659786 TGTTAGGTTGATCACTTCCGTG 58.340 45.455 0.00 0.00 42.59 4.94
669 698 3.576982 TCTGTTAGGTTGATCACTTCCGT 59.423 43.478 0.00 0.00 0.00 4.69
670 699 4.188247 TCTGTTAGGTTGATCACTTCCG 57.812 45.455 0.00 0.00 0.00 4.30
671 700 8.616076 CAATTATCTGTTAGGTTGATCACTTCC 58.384 37.037 0.00 0.00 0.00 3.46
672 701 9.167311 ACAATTATCTGTTAGGTTGATCACTTC 57.833 33.333 0.00 0.00 0.00 3.01
674 703 9.601217 GTACAATTATCTGTTAGGTTGATCACT 57.399 33.333 0.00 0.00 0.00 3.41
675 704 8.540492 CGTACAATTATCTGTTAGGTTGATCAC 58.460 37.037 0.00 0.00 0.00 3.06
676 705 7.709182 CCGTACAATTATCTGTTAGGTTGATCA 59.291 37.037 0.00 0.00 0.00 2.92
677 706 7.924412 TCCGTACAATTATCTGTTAGGTTGATC 59.076 37.037 0.00 0.00 0.00 2.92
678 707 7.788026 TCCGTACAATTATCTGTTAGGTTGAT 58.212 34.615 0.00 0.00 0.00 2.57
679 708 7.172868 TCCGTACAATTATCTGTTAGGTTGA 57.827 36.000 0.00 0.00 0.00 3.18
680 709 6.479001 CCTCCGTACAATTATCTGTTAGGTTG 59.521 42.308 0.00 0.00 0.00 3.77
681 710 6.579865 CCTCCGTACAATTATCTGTTAGGTT 58.420 40.000 0.00 0.00 0.00 3.50
682 711 5.452917 GCCTCCGTACAATTATCTGTTAGGT 60.453 44.000 0.00 0.00 0.00 3.08
683 712 4.989168 GCCTCCGTACAATTATCTGTTAGG 59.011 45.833 0.00 0.00 0.00 2.69
684 713 4.680110 CGCCTCCGTACAATTATCTGTTAG 59.320 45.833 0.00 0.00 0.00 2.34
685 714 4.338964 TCGCCTCCGTACAATTATCTGTTA 59.661 41.667 0.00 0.00 35.54 2.41
686 715 3.131577 TCGCCTCCGTACAATTATCTGTT 59.868 43.478 0.00 0.00 35.54 3.16
687 716 2.691526 TCGCCTCCGTACAATTATCTGT 59.308 45.455 0.00 0.00 35.54 3.41
688 717 3.364889 TCGCCTCCGTACAATTATCTG 57.635 47.619 0.00 0.00 35.54 2.90
689 718 4.521639 TGTATCGCCTCCGTACAATTATCT 59.478 41.667 0.00 0.00 32.32 1.98
690 719 4.620184 GTGTATCGCCTCCGTACAATTATC 59.380 45.833 0.00 0.00 34.90 1.75
691 720 4.553323 GTGTATCGCCTCCGTACAATTAT 58.447 43.478 0.00 0.00 34.90 1.28
692 721 3.243501 GGTGTATCGCCTCCGTACAATTA 60.244 47.826 0.00 0.00 34.90 1.40
693 722 2.482490 GGTGTATCGCCTCCGTACAATT 60.482 50.000 0.00 0.00 34.90 2.32
694 723 1.068127 GGTGTATCGCCTCCGTACAAT 59.932 52.381 0.00 0.00 34.90 2.71
695 724 0.457035 GGTGTATCGCCTCCGTACAA 59.543 55.000 0.00 0.00 34.90 2.41
696 725 0.680601 TGGTGTATCGCCTCCGTACA 60.681 55.000 0.00 0.00 34.70 2.90
697 726 0.457035 TTGGTGTATCGCCTCCGTAC 59.543 55.000 1.15 0.00 34.70 3.67
698 727 1.338973 GATTGGTGTATCGCCTCCGTA 59.661 52.381 1.15 0.00 34.70 4.02
699 728 0.104304 GATTGGTGTATCGCCTCCGT 59.896 55.000 1.15 0.00 34.70 4.69
700 729 0.389391 AGATTGGTGTATCGCCTCCG 59.611 55.000 1.15 0.00 34.70 4.63
701 730 1.689273 AGAGATTGGTGTATCGCCTCC 59.311 52.381 1.15 0.00 34.70 4.30
702 731 2.362397 TGAGAGATTGGTGTATCGCCTC 59.638 50.000 1.15 0.00 34.70 4.70
703 732 2.388735 TGAGAGATTGGTGTATCGCCT 58.611 47.619 1.15 0.00 34.70 5.52
704 733 2.890808 TGAGAGATTGGTGTATCGCC 57.109 50.000 0.00 0.00 34.12 5.54
705 734 4.233789 GAGATGAGAGATTGGTGTATCGC 58.766 47.826 0.00 0.00 0.00 4.58
706 735 5.444663 TGAGATGAGAGATTGGTGTATCG 57.555 43.478 0.00 0.00 0.00 2.92
707 736 8.196771 GGATATGAGATGAGAGATTGGTGTATC 58.803 40.741 0.00 0.00 0.00 2.24
708 737 7.900246 AGGATATGAGATGAGAGATTGGTGTAT 59.100 37.037 0.00 0.00 0.00 2.29
709 738 7.244558 AGGATATGAGATGAGAGATTGGTGTA 58.755 38.462 0.00 0.00 0.00 2.90
710 739 6.083383 AGGATATGAGATGAGAGATTGGTGT 58.917 40.000 0.00 0.00 0.00 4.16
711 740 6.608539 AGGATATGAGATGAGAGATTGGTG 57.391 41.667 0.00 0.00 0.00 4.17
712 741 8.592809 GTTAAGGATATGAGATGAGAGATTGGT 58.407 37.037 0.00 0.00 0.00 3.67
713 742 8.814931 AGTTAAGGATATGAGATGAGAGATTGG 58.185 37.037 0.00 0.00 0.00 3.16
767 796 4.473520 CCGCCGCCAGAGGTGAAT 62.474 66.667 2.24 0.00 44.18 2.57
833 865 0.881118 TTTCAACGAGGATTGGCAGC 59.119 50.000 0.00 0.00 0.00 5.25
839 871 0.958876 GGCGGGTTTCAACGAGGATT 60.959 55.000 0.00 0.00 0.00 3.01
921 957 1.226888 CTAGGTTACAGCGGCGACC 60.227 63.158 12.98 9.17 0.00 4.79
983 1019 4.104738 TCAACATCTCCTCCAGGTTTTTCT 59.895 41.667 0.00 0.00 36.34 2.52
1076 1113 1.672363 CAAGCCATCTCGCATTTGCTA 59.328 47.619 0.51 0.00 39.32 3.49
1081 1118 0.816825 ATCGCAAGCCATCTCGCATT 60.817 50.000 0.00 0.00 37.18 3.56
1651 1726 4.803452 TGTTTGTTCTTCTCCTCCCAAAT 58.197 39.130 0.00 0.00 0.00 2.32
1815 1893 2.118233 GATGATCTCTTCCGGGGGCC 62.118 65.000 0.00 0.00 0.00 5.80
1882 1972 2.434331 CAGCCGTTTTGAGGGGGA 59.566 61.111 0.00 0.00 0.00 4.81
1996 2095 3.455910 AGCCTCAGGTGATATTGCTGTAA 59.544 43.478 0.00 0.00 0.00 2.41
2148 2265 4.778143 GGAGCCCGCCAATGTCGT 62.778 66.667 0.00 0.00 0.00 4.34
2275 2434 9.924650 TGAGTTTCTACTAAACAAAGGATAGAC 57.075 33.333 3.70 0.00 33.84 2.59
2344 2506 5.292345 ACCAACGCCAAAACTAAAATCAAAC 59.708 36.000 0.00 0.00 0.00 2.93
2623 2792 3.713826 TCCTTAGGACCATGTTGTTCC 57.286 47.619 0.00 0.00 0.00 3.62
2641 2810 1.204146 TCTGGGCACTATCCTGTTCC 58.796 55.000 0.00 0.00 0.00 3.62
2790 2959 0.836606 TCCTGACCAACAAGCTGTCA 59.163 50.000 4.03 4.03 37.45 3.58


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

AutoCloner maintained by Alex Coulton.