Multiple sequence alignment - TraesCS7D01G137800

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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 TraesCS7D01G137800 chr7D 100.000 3192 0 0 1 3192 88371618 88368427 0.000000e+00 5895.0
1 TraesCS7D01G137800 chr7D 78.994 895 157 19 826 1707 88133353 88134229 1.650000e-162 582.0
2 TraesCS7D01G137800 chr7D 81.645 681 111 9 826 1503 88180216 88179547 1.290000e-153 553.0
3 TraesCS7D01G137800 chr7D 83.929 560 90 0 843 1402 88078632 88079191 1.300000e-148 536.0
4 TraesCS7D01G137800 chr7D 79.752 726 112 19 829 1535 89232399 89233108 7.950000e-136 494.0
5 TraesCS7D01G137800 chr7B 93.207 1428 88 2 598 2019 38660594 38659170 0.000000e+00 2091.0
6 TraesCS7D01G137800 chr7B 89.404 1425 112 14 603 2019 38782911 38784304 0.000000e+00 1759.0
7 TraesCS7D01G137800 chr7B 93.224 428 26 2 1 425 38661201 38660774 7.520000e-176 627.0
8 TraesCS7D01G137800 chr7B 83.871 589 89 3 832 1414 36991378 36991966 1.000000e-154 556.0
9 TraesCS7D01G137800 chr7B 86.874 419 26 8 2022 2436 38659135 38658742 2.920000e-120 442.0
10 TraesCS7D01G137800 chr7B 81.538 585 46 21 2417 2978 38630929 38630384 2.940000e-115 425.0
11 TraesCS7D01G137800 chr7B 86.667 330 40 3 2647 2976 38624128 38623803 2.340000e-96 363.0
12 TraesCS7D01G137800 chr7B 95.000 180 8 1 2021 2199 38784338 38784517 6.740000e-72 281.0
13 TraesCS7D01G137800 chr7B 100.000 29 0 0 3157 3185 38623754 38623726 2.000000e-03 54.7
14 TraesCS7D01G137800 chr7A 90.197 1418 86 12 603 2019 89974250 89975615 0.000000e+00 1799.0
15 TraesCS7D01G137800 chr7A 88.889 963 61 22 2025 2976 89964033 89963106 0.000000e+00 1144.0
16 TraesCS7D01G137800 chr7A 89.765 850 71 8 1177 2019 89964933 89964093 0.000000e+00 1074.0
17 TraesCS7D01G137800 chr7A 94.937 395 18 2 794 1187 89965818 89965425 4.520000e-173 617.0
18 TraesCS7D01G137800 chr7A 86.898 519 66 2 854 1371 89649553 89650070 5.940000e-162 580.0
19 TraesCS7D01G137800 chr7A 94.403 268 15 0 1609 1876 89947335 89947068 2.290000e-111 412.0
20 TraesCS7D01G137800 chr7A 93.258 178 11 1 2022 2198 89975650 89975827 8.780000e-66 261.0
21 TraesCS7D01G137800 chr7A 86.878 221 20 3 2754 2974 89932745 89932534 4.120000e-59 239.0
22 TraesCS7D01G137800 chr7A 94.231 156 8 1 270 425 89966282 89966128 1.480000e-58 237.0
23 TraesCS7D01G137800 chr7A 85.581 215 15 11 569 782 89965995 89965796 8.970000e-51 211.0
24 TraesCS7D01G137800 chr7A 91.176 136 12 0 2347 2482 89947067 89946932 5.440000e-43 185.0
25 TraesCS7D01G137800 chr7A 82.500 80 13 1 2038 2116 90455266 90455345 5.710000e-08 69.4
26 TraesCS7D01G137800 chr2A 91.822 428 32 3 1 425 50443365 50442938 7.620000e-166 593.0
27 TraesCS7D01G137800 chr2A 84.962 133 9 6 651 782 50442523 50442401 1.200000e-24 124.0
28 TraesCS7D01G137800 chr2A 80.952 84 6 5 3111 3185 50440630 50440548 1.240000e-04 58.4
29 TraesCS7D01G137800 chr6B 84.314 255 20 12 1 255 595205879 595206113 6.890000e-57 231.0
30 TraesCS7D01G137800 chr1D 81.609 261 43 5 2 260 353553882 353553625 8.970000e-51 211.0
31 TraesCS7D01G137800 chr5A 95.385 65 3 0 2442 2506 563176388 563176452 1.570000e-18 104.0
32 TraesCS7D01G137800 chr2D 93.846 65 4 0 2442 2506 200944737 200944673 7.290000e-17 99.0
33 TraesCS7D01G137800 chr2D 93.846 65 4 0 2442 2506 604426696 604426632 7.290000e-17 99.0
34 TraesCS7D01G137800 chrUn 92.308 65 5 0 2442 2506 45089464 45089528 3.390000e-15 93.5
35 TraesCS7D01G137800 chrUn 92.308 65 5 0 2442 2506 171039751 171039815 3.390000e-15 93.5
36 TraesCS7D01G137800 chr4D 92.308 65 5 0 2442 2506 398045325 398045261 3.390000e-15 93.5
37 TraesCS7D01G137800 chr4D 89.286 56 6 0 287 342 30297636 30297691 1.590000e-08 71.3


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 TraesCS7D01G137800 chr7D 88368427 88371618 3191 True 5895.000000 5895 100.000000 1 3192 1 chr7D.!!$R2 3191
1 TraesCS7D01G137800 chr7D 88133353 88134229 876 False 582.000000 582 78.994000 826 1707 1 chr7D.!!$F2 881
2 TraesCS7D01G137800 chr7D 88179547 88180216 669 True 553.000000 553 81.645000 826 1503 1 chr7D.!!$R1 677
3 TraesCS7D01G137800 chr7D 88078632 88079191 559 False 536.000000 536 83.929000 843 1402 1 chr7D.!!$F1 559
4 TraesCS7D01G137800 chr7D 89232399 89233108 709 False 494.000000 494 79.752000 829 1535 1 chr7D.!!$F3 706
5 TraesCS7D01G137800 chr7B 38658742 38661201 2459 True 1053.333333 2091 91.101667 1 2436 3 chr7B.!!$R3 2435
6 TraesCS7D01G137800 chr7B 38782911 38784517 1606 False 1020.000000 1759 92.202000 603 2199 2 chr7B.!!$F2 1596
7 TraesCS7D01G137800 chr7B 36991378 36991966 588 False 556.000000 556 83.871000 832 1414 1 chr7B.!!$F1 582
8 TraesCS7D01G137800 chr7B 38630384 38630929 545 True 425.000000 425 81.538000 2417 2978 1 chr7B.!!$R1 561
9 TraesCS7D01G137800 chr7A 89974250 89975827 1577 False 1030.000000 1799 91.727500 603 2198 2 chr7A.!!$F3 1595
10 TraesCS7D01G137800 chr7A 89963106 89966282 3176 True 656.600000 1144 90.680600 270 2976 5 chr7A.!!$R3 2706
11 TraesCS7D01G137800 chr7A 89649553 89650070 517 False 580.000000 580 86.898000 854 1371 1 chr7A.!!$F1 517
12 TraesCS7D01G137800 chr2A 50440548 50443365 2817 True 258.466667 593 85.912000 1 3185 3 chr2A.!!$R1 3184

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
535 620 0.034337 TTACACAGACCCTTCACGGC 59.966 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 3590 1.0756 GCTCTCCTGCTACCCTCCT 60.076 63.158 0.0 0.0 0.0 3.69 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
29 30 9.044150 CATCTTTTCTTGCAAAAGAAACCATTA 57.956 29.630 14.33 0.55 45.37 1.90
33 34 8.553459 TTTCTTGCAAAAGAAACCATTAACAA 57.447 26.923 9.09 0.00 42.10 2.83
36 37 7.491048 TCTTGCAAAAGAAACCATTAACAAGTC 59.509 33.333 0.00 0.00 34.06 3.01
59 61 3.963129 TCATTGGCGGATCTAAAAAGGT 58.037 40.909 0.00 0.00 0.00 3.50
81 83 4.710528 AAGCGAAAAACGTCTCTAAGTG 57.289 40.909 0.00 0.00 44.60 3.16
106 109 7.500227 TGCATTAGGATCTCAAGATTGTAAAGG 59.500 37.037 0.00 0.00 34.37 3.11
130 133 1.409064 CTATGCAGGCTACCAAGACGA 59.591 52.381 0.00 0.00 35.06 4.20
177 180 4.558226 TGATAGCAGGTCTGATTGTGTT 57.442 40.909 1.65 0.00 0.00 3.32
182 185 8.264347 TGATAGCAGGTCTGATTGTGTTATTTA 58.736 33.333 1.65 0.00 0.00 1.40
218 221 2.159572 CCTGCGTGGCAAACTATGTAAC 60.160 50.000 0.00 0.00 38.41 2.50
346 351 2.161855 ACGCTTGATGAGATTTGGCAA 58.838 42.857 0.00 0.00 0.00 4.52
363 368 3.368539 TGGCAAAACGTGTTATAGTAGCG 59.631 43.478 0.00 0.00 0.00 4.26
404 409 7.445121 TGACACTACAGATTTTTCATGAGAGT 58.555 34.615 0.00 0.00 0.00 3.24
405 410 7.933577 TGACACTACAGATTTTTCATGAGAGTT 59.066 33.333 0.00 0.00 0.00 3.01
425 430 2.425143 TTCATTCCAGAGGTGCCATC 57.575 50.000 0.00 0.00 0.00 3.51
426 431 0.178767 TCATTCCAGAGGTGCCATCG 59.821 55.000 0.00 0.00 0.00 3.84
427 432 0.178767 CATTCCAGAGGTGCCATCGA 59.821 55.000 0.00 0.00 0.00 3.59
429 434 1.899437 TTCCAGAGGTGCCATCGACC 61.899 60.000 0.00 0.00 0.00 4.79
430 435 2.659063 CCAGAGGTGCCATCGACCA 61.659 63.158 0.00 0.00 35.76 4.02
431 436 1.296392 CAGAGGTGCCATCGACCAA 59.704 57.895 0.00 0.00 35.76 3.67
432 437 0.107508 CAGAGGTGCCATCGACCAAT 60.108 55.000 0.00 0.00 35.76 3.16
434 439 1.004745 AGAGGTGCCATCGACCAATTT 59.995 47.619 0.00 0.00 35.76 1.82
435 440 1.818674 GAGGTGCCATCGACCAATTTT 59.181 47.619 0.00 0.00 35.76 1.82
466 551 9.862585 AAAACAATATCGAGCAATTTTTGTTTC 57.137 25.926 13.77 0.00 0.00 2.78
487 572 2.360483 CTGATGCAGTGAGTATCGTCCT 59.640 50.000 0.00 0.00 41.68 3.85
499 584 6.418226 GTGAGTATCGTCCTGTAATCACAATC 59.582 42.308 7.76 0.00 42.36 2.67
500 585 6.096282 TGAGTATCGTCCTGTAATCACAATCA 59.904 38.462 0.00 0.00 38.61 2.57
501 586 6.507900 AGTATCGTCCTGTAATCACAATCAG 58.492 40.000 0.00 0.00 33.22 2.90
502 587 3.521560 TCGTCCTGTAATCACAATCAGC 58.478 45.455 0.00 0.00 33.22 4.26
503 588 2.609459 CGTCCTGTAATCACAATCAGCC 59.391 50.000 0.00 0.00 33.22 4.85
504 589 3.679917 CGTCCTGTAATCACAATCAGCCT 60.680 47.826 0.00 0.00 33.22 4.58
505 590 4.265073 GTCCTGTAATCACAATCAGCCTT 58.735 43.478 0.00 0.00 33.22 4.35
506 591 4.333926 GTCCTGTAATCACAATCAGCCTTC 59.666 45.833 0.00 0.00 33.22 3.46
507 592 4.019411 TCCTGTAATCACAATCAGCCTTCA 60.019 41.667 0.00 0.00 33.22 3.02
508 593 4.701651 CCTGTAATCACAATCAGCCTTCAA 59.298 41.667 0.00 0.00 33.22 2.69
509 594 5.183713 CCTGTAATCACAATCAGCCTTCAAA 59.816 40.000 0.00 0.00 33.22 2.69
510 595 6.127535 CCTGTAATCACAATCAGCCTTCAAAT 60.128 38.462 0.00 0.00 33.22 2.32
511 596 6.855836 TGTAATCACAATCAGCCTTCAAATC 58.144 36.000 0.00 0.00 0.00 2.17
512 597 4.627611 ATCACAATCAGCCTTCAAATCG 57.372 40.909 0.00 0.00 0.00 3.34
513 598 3.673902 TCACAATCAGCCTTCAAATCGA 58.326 40.909 0.00 0.00 0.00 3.59
514 599 3.436704 TCACAATCAGCCTTCAAATCGAC 59.563 43.478 0.00 0.00 0.00 4.20
515 600 2.416547 ACAATCAGCCTTCAAATCGACG 59.583 45.455 0.00 0.00 0.00 5.12
516 601 2.386661 ATCAGCCTTCAAATCGACGT 57.613 45.000 0.00 0.00 0.00 4.34
517 602 2.163818 TCAGCCTTCAAATCGACGTT 57.836 45.000 0.00 0.00 0.00 3.99
518 603 3.306917 TCAGCCTTCAAATCGACGTTA 57.693 42.857 0.00 0.00 0.00 3.18
519 604 2.991190 TCAGCCTTCAAATCGACGTTAC 59.009 45.455 0.00 0.00 0.00 2.50
520 605 2.734606 CAGCCTTCAAATCGACGTTACA 59.265 45.455 0.00 0.00 0.00 2.41
521 606 2.735134 AGCCTTCAAATCGACGTTACAC 59.265 45.455 0.00 0.00 0.00 2.90
522 607 2.477375 GCCTTCAAATCGACGTTACACA 59.523 45.455 0.00 0.00 0.00 3.72
523 608 3.423123 GCCTTCAAATCGACGTTACACAG 60.423 47.826 0.00 0.00 0.00 3.66
524 609 3.985279 CCTTCAAATCGACGTTACACAGA 59.015 43.478 0.00 0.00 0.00 3.41
525 610 4.143389 CCTTCAAATCGACGTTACACAGAC 60.143 45.833 0.00 0.00 0.00 3.51
526 611 3.311106 TCAAATCGACGTTACACAGACC 58.689 45.455 0.00 0.00 0.00 3.85
527 612 2.358939 AATCGACGTTACACAGACCC 57.641 50.000 0.00 0.00 0.00 4.46
528 613 1.542492 ATCGACGTTACACAGACCCT 58.458 50.000 0.00 0.00 0.00 4.34
529 614 1.321474 TCGACGTTACACAGACCCTT 58.679 50.000 0.00 0.00 0.00 3.95
530 615 1.267806 TCGACGTTACACAGACCCTTC 59.732 52.381 0.00 0.00 0.00 3.46
531 616 1.001048 CGACGTTACACAGACCCTTCA 60.001 52.381 0.00 0.00 0.00 3.02
532 617 2.401351 GACGTTACACAGACCCTTCAC 58.599 52.381 0.00 0.00 0.00 3.18
535 620 0.034337 TTACACAGACCCTTCACGGC 59.966 55.000 0.00 0.00 0.00 5.68
561 646 3.198872 GGAAAAGAATCCTCTGGTAGCG 58.801 50.000 0.00 0.00 36.50 4.26
563 648 4.504858 GAAAAGAATCCTCTGGTAGCGAA 58.495 43.478 0.00 0.00 30.03 4.70
565 650 3.528597 AGAATCCTCTGGTAGCGAAAC 57.471 47.619 0.00 0.00 0.00 2.78
575 660 0.796927 GTAGCGAAACCACAGCCTTC 59.203 55.000 0.00 0.00 0.00 3.46
591 676 4.213270 CAGCCTTCAAATCGACTTTACACA 59.787 41.667 0.00 0.00 0.00 3.72
604 689 3.883489 ACTTTACACAGACCCTTCAAAGC 59.117 43.478 0.00 0.00 0.00 3.51
620 705 2.359230 GCAGTCCACCAGCCTGTC 60.359 66.667 0.00 0.00 0.00 3.51
626 711 2.047061 GTCCACCAGCCTGTCCATATA 58.953 52.381 0.00 0.00 0.00 0.86
786 1097 3.873679 TACCGCCGTCCACCAGAGT 62.874 63.158 0.00 0.00 0.00 3.24
788 1099 3.680786 CGCCGTCCACCAGAGTCA 61.681 66.667 0.00 0.00 0.00 3.41
789 1100 2.982130 GCCGTCCACCAGAGTCAT 59.018 61.111 0.00 0.00 0.00 3.06
802 1113 3.857854 GTCATGCCGACGCTGCTG 61.858 66.667 0.00 0.00 34.19 4.41
1521 2803 1.384525 CCTCTGCTCGTACTAGTGCT 58.615 55.000 5.39 0.00 0.00 4.40
1563 2845 0.276277 ATCCCCCTCATCCCCAAGAT 59.724 55.000 0.00 0.00 34.66 2.40
1767 3085 4.475135 GCCAACGAGGAGGAGGGC 62.475 72.222 2.86 0.00 41.22 5.19
1898 3240 3.314331 CGGCACAGACTGGGAGGT 61.314 66.667 9.48 0.00 0.00 3.85
2019 3361 2.114616 CTCCAGGTATGCCAGAGAACT 58.885 52.381 12.72 0.00 38.80 3.01
2194 3590 3.755628 GTGCCGCGGAGGTAGTCA 61.756 66.667 33.48 12.98 43.70 3.41
2195 3591 3.449227 TGCCGCGGAGGTAGTCAG 61.449 66.667 33.48 0.00 43.70 3.51
2215 3646 1.452145 GAGGGTAGCAGGAGAGCGAG 61.452 65.000 0.00 0.00 40.15 5.03
2288 3722 3.611766 ATCGAGTGATCCGTTTCCTTT 57.388 42.857 0.00 0.00 0.00 3.11
2320 3754 7.577107 CGAGACTCGTTATCTAAGATTCATCA 58.423 38.462 16.83 0.00 34.72 3.07
2336 3770 1.898472 CATCAGTGACCTCTGGAGTGT 59.102 52.381 0.00 0.00 36.25 3.55
2395 3829 9.096823 TCTTTCCATAAACTAAGAAGACCTACA 57.903 33.333 0.00 0.00 0.00 2.74
2407 3841 9.442047 CTAAGAAGACCTACAAATTGTCATCTT 57.558 33.333 15.04 15.04 44.49 2.40
2413 3847 6.068010 ACCTACAAATTGTCATCTTTGGTGA 58.932 36.000 0.22 0.00 36.81 4.02
2472 3974 5.981174 TCGTCTTTTGAATTGGAACTAACG 58.019 37.500 0.00 0.00 0.00 3.18
2517 4019 4.993705 TTCTAGTTTGGGACATGGAGTT 57.006 40.909 0.00 0.00 39.30 3.01
2518 4020 4.993705 TCTAGTTTGGGACATGGAGTTT 57.006 40.909 0.00 0.00 39.30 2.66
2519 4021 4.906618 TCTAGTTTGGGACATGGAGTTTC 58.093 43.478 0.00 0.00 39.30 2.78
2520 4022 3.884037 AGTTTGGGACATGGAGTTTCT 57.116 42.857 0.00 0.00 39.30 2.52
2521 4023 4.993705 AGTTTGGGACATGGAGTTTCTA 57.006 40.909 0.00 0.00 39.30 2.10
2527 4029 4.010349 GGGACATGGAGTTTCTAGTTTGG 58.990 47.826 0.00 0.00 0.00 3.28
2563 4065 2.821969 ACTCGCAAATTCAAATGCTCCT 59.178 40.909 0.00 0.00 40.39 3.69
2575 4077 6.258230 TCAAATGCTCCTTCATAAACAGTG 57.742 37.500 0.00 0.00 0.00 3.66
2645 4170 6.507900 ACATTCATGAACCGTCTACATAGAG 58.492 40.000 11.07 0.00 32.01 2.43
2668 4193 8.564370 AGAGATTCCTAAATCCTCTGGAAAAAT 58.436 33.333 0.00 0.00 41.97 1.82
2691 4216 5.486526 TGTCAATGCTCCAAAAACACTTTT 58.513 33.333 0.00 0.00 35.02 2.27
2774 4299 7.066887 TCACGGAAATTTGCATGTATGTAGAAT 59.933 33.333 10.49 0.00 0.00 2.40
2900 4425 2.034558 CACTTTCGTTCCAGTTTGCCAT 59.965 45.455 0.00 0.00 0.00 4.40
2934 4459 4.457257 CCACTTGGATTTTCAGAGGAGAAC 59.543 45.833 0.00 0.00 37.39 3.01
2995 4520 4.775440 TTTTTAATATGGTACCGACGCG 57.225 40.909 3.53 3.53 0.00 6.01
3006 4531 3.017314 CGACGCGGACGCTCATAC 61.017 66.667 12.47 1.12 45.53 2.39
3007 4532 2.101575 GACGCGGACGCTCATACA 59.898 61.111 12.47 0.00 45.53 2.29
3008 4533 2.202570 ACGCGGACGCTCATACAC 60.203 61.111 12.47 0.00 45.53 2.90
3009 4534 2.202557 CGCGGACGCTCATACACA 60.203 61.111 15.11 0.00 39.32 3.72
3010 4535 2.505498 CGCGGACGCTCATACACAC 61.505 63.158 15.11 0.00 39.32 3.82
3011 4536 1.445410 GCGGACGCTCATACACACA 60.445 57.895 9.76 0.00 38.26 3.72
3012 4537 1.683790 GCGGACGCTCATACACACAC 61.684 60.000 9.76 0.00 38.26 3.82
3013 4538 0.388006 CGGACGCTCATACACACACA 60.388 55.000 0.00 0.00 0.00 3.72
3014 4539 1.735700 CGGACGCTCATACACACACAT 60.736 52.381 0.00 0.00 0.00 3.21
3015 4540 2.478879 CGGACGCTCATACACACACATA 60.479 50.000 0.00 0.00 0.00 2.29
3016 4541 2.858344 GGACGCTCATACACACACATAC 59.142 50.000 0.00 0.00 0.00 2.39
3017 4542 3.507786 GACGCTCATACACACACATACA 58.492 45.455 0.00 0.00 0.00 2.29
3018 4543 3.250744 ACGCTCATACACACACATACAC 58.749 45.455 0.00 0.00 0.00 2.90
3019 4544 3.056821 ACGCTCATACACACACATACACT 60.057 43.478 0.00 0.00 0.00 3.55
3020 4545 3.547868 CGCTCATACACACACATACACTC 59.452 47.826 0.00 0.00 0.00 3.51
3021 4546 4.494484 GCTCATACACACACATACACTCA 58.506 43.478 0.00 0.00 0.00 3.41
3022 4547 4.327357 GCTCATACACACACATACACTCAC 59.673 45.833 0.00 0.00 0.00 3.51
3023 4548 4.816392 TCATACACACACATACACTCACC 58.184 43.478 0.00 0.00 0.00 4.02
3024 4549 2.543777 ACACACACATACACTCACCC 57.456 50.000 0.00 0.00 0.00 4.61
3025 4550 1.071699 ACACACACATACACTCACCCC 59.928 52.381 0.00 0.00 0.00 4.95
3026 4551 0.690762 ACACACATACACTCACCCCC 59.309 55.000 0.00 0.00 0.00 5.40
3027 4552 0.984230 CACACATACACTCACCCCCT 59.016 55.000 0.00 0.00 0.00 4.79
3028 4553 2.184533 CACACATACACTCACCCCCTA 58.815 52.381 0.00 0.00 0.00 3.53
3029 4554 2.771943 CACACATACACTCACCCCCTAT 59.228 50.000 0.00 0.00 0.00 2.57
3030 4555 2.771943 ACACATACACTCACCCCCTATG 59.228 50.000 0.00 0.00 0.00 2.23
3031 4556 3.038280 CACATACACTCACCCCCTATGA 58.962 50.000 0.00 0.00 0.00 2.15
3032 4557 3.454447 CACATACACTCACCCCCTATGAA 59.546 47.826 0.00 0.00 0.00 2.57
3033 4558 3.454812 ACATACACTCACCCCCTATGAAC 59.545 47.826 0.00 0.00 0.00 3.18
3034 4559 2.038863 ACACTCACCCCCTATGAACA 57.961 50.000 0.00 0.00 0.00 3.18
3035 4560 1.628846 ACACTCACCCCCTATGAACAC 59.371 52.381 0.00 0.00 0.00 3.32
3036 4561 1.628340 CACTCACCCCCTATGAACACA 59.372 52.381 0.00 0.00 0.00 3.72
3037 4562 1.628846 ACTCACCCCCTATGAACACAC 59.371 52.381 0.00 0.00 0.00 3.82
3038 4563 1.628340 CTCACCCCCTATGAACACACA 59.372 52.381 0.00 0.00 0.00 3.72
3039 4564 1.349688 TCACCCCCTATGAACACACAC 59.650 52.381 0.00 0.00 0.00 3.82
3040 4565 1.073125 CACCCCCTATGAACACACACA 59.927 52.381 0.00 0.00 0.00 3.72
3041 4566 1.992557 ACCCCCTATGAACACACACAT 59.007 47.619 0.00 0.00 0.00 3.21
3042 4567 3.054728 CACCCCCTATGAACACACACATA 60.055 47.826 0.00 0.00 0.00 2.29
3043 4568 3.054655 ACCCCCTATGAACACACACATAC 60.055 47.826 0.00 0.00 0.00 2.39
3044 4569 3.054728 CCCCCTATGAACACACACATACA 60.055 47.826 0.00 0.00 0.00 2.29
3045 4570 3.938963 CCCCTATGAACACACACATACAC 59.061 47.826 0.00 0.00 0.00 2.90
3046 4571 4.323485 CCCCTATGAACACACACATACACT 60.323 45.833 0.00 0.00 0.00 3.55
3047 4572 4.870426 CCCTATGAACACACACATACACTC 59.130 45.833 0.00 0.00 0.00 3.51
3048 4573 5.478407 CCTATGAACACACACATACACTCA 58.522 41.667 0.00 0.00 0.00 3.41
3049 4574 5.348724 CCTATGAACACACACATACACTCAC 59.651 44.000 0.00 0.00 0.00 3.51
3050 4575 3.462982 TGAACACACACATACACTCACC 58.537 45.455 0.00 0.00 0.00 4.02
3051 4576 2.543777 ACACACACATACACTCACCC 57.456 50.000 0.00 0.00 0.00 4.61
3052 4577 1.071699 ACACACACATACACTCACCCC 59.928 52.381 0.00 0.00 0.00 4.95
3053 4578 1.347707 CACACACATACACTCACCCCT 59.652 52.381 0.00 0.00 0.00 4.79
3054 4579 2.054799 ACACACATACACTCACCCCTT 58.945 47.619 0.00 0.00 0.00 3.95
3055 4580 3.007506 CACACACATACACTCACCCCTTA 59.992 47.826 0.00 0.00 0.00 2.69
3056 4581 3.844211 ACACACATACACTCACCCCTTAT 59.156 43.478 0.00 0.00 0.00 1.73
3057 4582 4.191544 CACACATACACTCACCCCTTATG 58.808 47.826 0.00 0.00 0.00 1.90
3058 4583 4.081142 CACACATACACTCACCCCTTATGA 60.081 45.833 0.00 0.00 0.00 2.15
3059 4584 4.534500 ACACATACACTCACCCCTTATGAA 59.466 41.667 0.00 0.00 0.00 2.57
3060 4585 4.876107 CACATACACTCACCCCTTATGAAC 59.124 45.833 0.00 0.00 0.00 3.18
3061 4586 4.534500 ACATACACTCACCCCTTATGAACA 59.466 41.667 0.00 0.00 0.00 3.18
3062 4587 3.418684 ACACTCACCCCTTATGAACAC 57.581 47.619 0.00 0.00 0.00 3.32
3063 4588 2.708861 ACACTCACCCCTTATGAACACA 59.291 45.455 0.00 0.00 0.00 3.72
3064 4589 3.074412 CACTCACCCCTTATGAACACAC 58.926 50.000 0.00 0.00 0.00 3.82
3065 4590 2.708861 ACTCACCCCTTATGAACACACA 59.291 45.455 0.00 0.00 0.00 3.72
3066 4591 3.074412 CTCACCCCTTATGAACACACAC 58.926 50.000 0.00 0.00 0.00 3.82
3067 4592 2.439880 TCACCCCTTATGAACACACACA 59.560 45.455 0.00 0.00 0.00 3.72
3068 4593 3.073798 TCACCCCTTATGAACACACACAT 59.926 43.478 0.00 0.00 0.00 3.21
3069 4594 3.191162 CACCCCTTATGAACACACACATG 59.809 47.826 0.00 0.00 0.00 3.21
3070 4595 2.164219 CCCCTTATGAACACACACATGC 59.836 50.000 0.00 0.00 0.00 4.06
3071 4596 2.819019 CCCTTATGAACACACACATGCA 59.181 45.455 0.00 0.00 0.00 3.96
3072 4597 3.366273 CCCTTATGAACACACACATGCAC 60.366 47.826 0.00 0.00 0.00 4.57
3073 4598 3.252944 CCTTATGAACACACACATGCACA 59.747 43.478 0.00 0.00 0.00 4.57
3074 4599 4.082625 CCTTATGAACACACACATGCACAT 60.083 41.667 0.00 0.00 0.00 3.21
3075 4600 3.564235 ATGAACACACACATGCACATC 57.436 42.857 0.00 0.00 0.00 3.06
3076 4601 1.263752 TGAACACACACATGCACATCG 59.736 47.619 0.00 0.00 0.00 3.84
3077 4602 1.264020 GAACACACACATGCACATCGT 59.736 47.619 0.00 0.00 0.00 3.73
3078 4603 2.162319 ACACACACATGCACATCGTA 57.838 45.000 0.00 0.00 0.00 3.43
3079 4604 1.798223 ACACACACATGCACATCGTAC 59.202 47.619 0.00 0.00 0.00 3.67
3080 4605 1.128507 CACACACATGCACATCGTACC 59.871 52.381 0.00 0.00 0.00 3.34
3081 4606 0.726827 CACACATGCACATCGTACCC 59.273 55.000 0.00 0.00 0.00 3.69
3082 4607 0.613260 ACACATGCACATCGTACCCT 59.387 50.000 0.00 0.00 0.00 4.34
3083 4608 1.003118 ACACATGCACATCGTACCCTT 59.997 47.619 0.00 0.00 0.00 3.95
3084 4609 2.235155 ACACATGCACATCGTACCCTTA 59.765 45.455 0.00 0.00 0.00 2.69
3085 4610 3.118408 ACACATGCACATCGTACCCTTAT 60.118 43.478 0.00 0.00 0.00 1.73
3086 4611 4.100344 ACACATGCACATCGTACCCTTATA 59.900 41.667 0.00 0.00 0.00 0.98
3087 4612 5.053811 CACATGCACATCGTACCCTTATAA 58.946 41.667 0.00 0.00 0.00 0.98
3088 4613 5.177511 CACATGCACATCGTACCCTTATAAG 59.822 44.000 5.43 5.43 0.00 1.73
3089 4614 3.724374 TGCACATCGTACCCTTATAAGC 58.276 45.455 6.99 0.00 0.00 3.09
3090 4615 3.133183 TGCACATCGTACCCTTATAAGCA 59.867 43.478 6.99 0.00 0.00 3.91
3091 4616 3.493503 GCACATCGTACCCTTATAAGCAC 59.506 47.826 6.99 3.93 0.00 4.40
3092 4617 4.056050 CACATCGTACCCTTATAAGCACC 58.944 47.826 6.99 0.00 0.00 5.01
3093 4618 3.965347 ACATCGTACCCTTATAAGCACCT 59.035 43.478 6.99 0.00 0.00 4.00
3094 4619 4.407945 ACATCGTACCCTTATAAGCACCTT 59.592 41.667 6.99 0.00 0.00 3.50
3095 4620 4.395959 TCGTACCCTTATAAGCACCTTG 57.604 45.455 6.99 0.00 0.00 3.61
3096 4621 3.133362 TCGTACCCTTATAAGCACCTTGG 59.867 47.826 6.99 4.51 0.00 3.61
3097 4622 3.133362 CGTACCCTTATAAGCACCTTGGA 59.867 47.826 6.99 0.00 0.00 3.53
3098 4623 3.933861 ACCCTTATAAGCACCTTGGAG 57.066 47.619 6.99 0.00 0.00 3.86
3099 4624 3.460825 ACCCTTATAAGCACCTTGGAGA 58.539 45.455 6.99 0.00 0.00 3.71
3100 4625 3.850173 ACCCTTATAAGCACCTTGGAGAA 59.150 43.478 6.99 0.00 0.00 2.87
3101 4626 4.291249 ACCCTTATAAGCACCTTGGAGAAA 59.709 41.667 6.99 0.00 0.00 2.52
3102 4627 4.640647 CCCTTATAAGCACCTTGGAGAAAC 59.359 45.833 6.99 0.00 0.00 2.78
3103 4628 4.332819 CCTTATAAGCACCTTGGAGAAACG 59.667 45.833 6.99 0.00 0.00 3.60
3104 4629 2.178912 TAAGCACCTTGGAGAAACGG 57.821 50.000 0.00 0.00 0.00 4.44
3105 4630 0.472471 AAGCACCTTGGAGAAACGGA 59.528 50.000 0.00 0.00 0.00 4.69
3106 4631 0.035458 AGCACCTTGGAGAAACGGAG 59.965 55.000 0.00 0.00 0.00 4.63
3108 4633 1.512926 CACCTTGGAGAAACGGAGTG 58.487 55.000 0.00 0.00 45.00 3.51
3109 4634 0.396811 ACCTTGGAGAAACGGAGTGG 59.603 55.000 0.00 0.00 45.00 4.00
3110 4635 0.396811 CCTTGGAGAAACGGAGTGGT 59.603 55.000 0.00 0.00 45.00 4.16
3111 4636 1.621814 CCTTGGAGAAACGGAGTGGTA 59.378 52.381 0.00 0.00 45.00 3.25
3112 4637 2.236395 CCTTGGAGAAACGGAGTGGTAT 59.764 50.000 0.00 0.00 45.00 2.73
3113 4638 3.449737 CCTTGGAGAAACGGAGTGGTATA 59.550 47.826 0.00 0.00 45.00 1.47
3114 4639 4.101119 CCTTGGAGAAACGGAGTGGTATAT 59.899 45.833 0.00 0.00 45.00 0.86
3115 4640 5.396436 CCTTGGAGAAACGGAGTGGTATATT 60.396 44.000 0.00 0.00 45.00 1.28
3122 4647 5.978934 AACGGAGTGGTATATTTAAAGCG 57.021 39.130 0.00 0.00 45.00 4.68
3138 4663 2.505628 AGCGTCAGTCTATGCATCAG 57.494 50.000 0.19 0.00 33.64 2.90
3142 4667 3.774066 CGTCAGTCTATGCATCAGTTGA 58.226 45.455 0.19 0.84 0.00 3.18
3143 4668 4.366586 CGTCAGTCTATGCATCAGTTGAT 58.633 43.478 0.19 0.00 34.56 2.57
3148 4673 5.628606 CAGTCTATGCATCAGTTGATAGTCG 59.371 44.000 0.19 0.00 32.63 4.18
3150 4675 5.627367 GTCTATGCATCAGTTGATAGTCGTC 59.373 44.000 0.19 0.00 32.63 4.20
3185 4719 8.954950 TTTCCAAAATGCTTTACTCAAATGAA 57.045 26.923 0.00 0.00 0.00 2.57
3186 4720 8.592105 TTCCAAAATGCTTTACTCAAATGAAG 57.408 30.769 0.00 0.00 0.00 3.02
3187 4721 7.153985 TCCAAAATGCTTTACTCAAATGAAGG 58.846 34.615 0.00 0.00 0.00 3.46
3188 4722 7.015098 TCCAAAATGCTTTACTCAAATGAAGGA 59.985 33.333 0.00 0.00 0.00 3.36
3189 4723 7.330208 CCAAAATGCTTTACTCAAATGAAGGAG 59.670 37.037 0.00 0.00 37.18 3.69
3190 4724 7.530426 AAATGCTTTACTCAAATGAAGGAGT 57.470 32.000 0.00 0.00 45.72 3.85
3191 4725 8.635765 AAATGCTTTACTCAAATGAAGGAGTA 57.364 30.769 0.00 0.00 42.30 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.270352 TCCGCCAATGAAGACTTGTT 57.730 45.000 0.00 0.00 0.00 2.83
33 34 4.487714 TTTAGATCCGCCAATGAAGACT 57.512 40.909 0.00 0.00 0.00 3.24
36 37 4.399303 ACCTTTTTAGATCCGCCAATGAAG 59.601 41.667 0.00 0.00 0.00 3.02
42 43 3.275999 GCTTACCTTTTTAGATCCGCCA 58.724 45.455 0.00 0.00 0.00 5.69
59 61 4.149396 GCACTTAGAGACGTTTTTCGCTTA 59.851 41.667 0.00 0.00 44.19 3.09
81 83 7.500559 ACCTTTACAATCTTGAGATCCTAATGC 59.499 37.037 0.00 0.00 32.75 3.56
106 109 1.672881 CTTGGTAGCCTGCATAGCAAC 59.327 52.381 11.08 1.63 38.41 4.17
130 133 7.088589 AGCTAAATTTTGTAATCTCATGCGT 57.911 32.000 0.00 0.00 0.00 5.24
177 180 7.429636 GCAGGGCGAAACACTATTATAAATA 57.570 36.000 0.00 0.00 0.00 1.40
218 221 8.874745 AATAACAATGTTCTTACAATCGTTCG 57.125 30.769 0.22 0.00 37.91 3.95
264 267 3.679502 GCAGGCAGCGAAACATTTTATTT 59.320 39.130 0.00 0.00 0.00 1.40
265 268 3.253230 GCAGGCAGCGAAACATTTTATT 58.747 40.909 0.00 0.00 0.00 1.40
267 270 2.346099 GCAGGCAGCGAAACATTTTA 57.654 45.000 0.00 0.00 0.00 1.52
346 351 3.119388 TGAGCCGCTACTATAACACGTTT 60.119 43.478 0.00 0.00 0.00 3.60
363 368 3.817647 AGTGTCATGTTCTTTTCTGAGCC 59.182 43.478 0.00 0.00 0.00 4.70
404 409 2.673775 TGGCACCTCTGGAATGAAAA 57.326 45.000 0.00 0.00 0.00 2.29
405 410 2.726821 GATGGCACCTCTGGAATGAAA 58.273 47.619 0.00 0.00 0.00 2.69
441 446 9.260002 AGAAACAAAAATTGCTCGATATTGTTT 57.740 25.926 17.46 17.46 46.28 2.83
443 448 8.081633 TCAGAAACAAAAATTGCTCGATATTGT 58.918 29.630 0.00 0.00 0.00 2.71
444 449 8.451687 TCAGAAACAAAAATTGCTCGATATTG 57.548 30.769 0.00 0.00 0.00 1.90
466 551 2.360483 AGGACGATACTCACTGCATCAG 59.640 50.000 0.00 0.00 37.52 2.90
487 572 6.403527 CGATTTGAAGGCTGATTGTGATTACA 60.404 38.462 0.00 0.00 34.31 2.41
499 584 2.734606 TGTAACGTCGATTTGAAGGCTG 59.265 45.455 0.00 0.00 0.00 4.85
500 585 2.735134 GTGTAACGTCGATTTGAAGGCT 59.265 45.455 0.00 0.00 0.00 4.58
501 586 2.477375 TGTGTAACGTCGATTTGAAGGC 59.523 45.455 0.00 0.00 42.39 4.35
502 587 3.985279 TCTGTGTAACGTCGATTTGAAGG 59.015 43.478 0.00 0.00 42.39 3.46
503 588 4.143389 GGTCTGTGTAACGTCGATTTGAAG 60.143 45.833 0.00 0.00 42.39 3.02
504 589 3.737266 GGTCTGTGTAACGTCGATTTGAA 59.263 43.478 0.00 0.00 42.39 2.69
505 590 3.311106 GGTCTGTGTAACGTCGATTTGA 58.689 45.455 0.00 0.00 42.39 2.69
506 591 2.410730 GGGTCTGTGTAACGTCGATTTG 59.589 50.000 0.00 0.00 42.39 2.32
507 592 2.298163 AGGGTCTGTGTAACGTCGATTT 59.702 45.455 0.00 0.00 42.39 2.17
508 593 1.891150 AGGGTCTGTGTAACGTCGATT 59.109 47.619 0.00 0.00 42.39 3.34
509 594 1.542492 AGGGTCTGTGTAACGTCGAT 58.458 50.000 0.00 0.00 42.39 3.59
510 595 1.267806 GAAGGGTCTGTGTAACGTCGA 59.732 52.381 0.00 0.00 42.39 4.20
511 596 1.001048 TGAAGGGTCTGTGTAACGTCG 60.001 52.381 0.00 0.00 42.39 5.12
512 597 2.401351 GTGAAGGGTCTGTGTAACGTC 58.599 52.381 0.00 0.00 42.39 4.34
513 598 1.269413 CGTGAAGGGTCTGTGTAACGT 60.269 52.381 0.00 0.00 42.39 3.99
514 599 1.415374 CGTGAAGGGTCTGTGTAACG 58.585 55.000 0.00 0.00 42.39 3.18
515 600 1.792006 CCGTGAAGGGTCTGTGTAAC 58.208 55.000 0.00 0.00 35.97 2.50
516 601 0.034337 GCCGTGAAGGGTCTGTGTAA 59.966 55.000 0.00 0.00 41.48 2.41
517 602 1.116536 TGCCGTGAAGGGTCTGTGTA 61.117 55.000 0.00 0.00 41.48 2.90
518 603 2.383245 CTGCCGTGAAGGGTCTGTGT 62.383 60.000 0.00 0.00 41.48 3.72
519 604 1.669115 CTGCCGTGAAGGGTCTGTG 60.669 63.158 0.00 0.00 41.48 3.66
520 605 1.407656 TTCTGCCGTGAAGGGTCTGT 61.408 55.000 0.00 0.00 41.48 3.41
521 606 0.671781 CTTCTGCCGTGAAGGGTCTG 60.672 60.000 0.00 0.00 39.62 3.51
522 607 1.674057 CTTCTGCCGTGAAGGGTCT 59.326 57.895 0.00 0.00 39.62 3.85
523 608 4.285851 CTTCTGCCGTGAAGGGTC 57.714 61.111 0.00 0.00 39.62 4.46
527 612 2.494059 TCTTTTCCTTCTGCCGTGAAG 58.506 47.619 0.00 0.00 42.10 3.02
528 613 2.631160 TCTTTTCCTTCTGCCGTGAA 57.369 45.000 0.00 0.00 0.00 3.18
529 614 2.631160 TTCTTTTCCTTCTGCCGTGA 57.369 45.000 0.00 0.00 0.00 4.35
530 615 2.162408 GGATTCTTTTCCTTCTGCCGTG 59.838 50.000 0.00 0.00 32.68 4.94
531 616 2.040412 AGGATTCTTTTCCTTCTGCCGT 59.960 45.455 0.00 0.00 43.88 5.68
532 617 2.680339 GAGGATTCTTTTCCTTCTGCCG 59.320 50.000 0.00 0.00 46.35 5.69
535 620 4.916183 ACCAGAGGATTCTTTTCCTTCTG 58.084 43.478 10.47 10.47 46.35 3.02
555 640 0.605589 AAGGCTGTGGTTTCGCTACC 60.606 55.000 0.00 0.00 38.73 3.18
558 643 0.465460 TTGAAGGCTGTGGTTTCGCT 60.465 50.000 0.00 0.00 0.00 4.93
559 644 0.383949 TTTGAAGGCTGTGGTTTCGC 59.616 50.000 0.00 0.00 0.00 4.70
560 645 2.665519 CGATTTGAAGGCTGTGGTTTCG 60.666 50.000 0.00 0.00 0.00 3.46
561 646 2.552315 TCGATTTGAAGGCTGTGGTTTC 59.448 45.455 0.00 0.00 0.00 2.78
563 648 1.880027 GTCGATTTGAAGGCTGTGGTT 59.120 47.619 0.00 0.00 0.00 3.67
565 650 1.813513 AGTCGATTTGAAGGCTGTGG 58.186 50.000 0.00 0.00 0.00 4.17
575 660 4.315803 AGGGTCTGTGTAAAGTCGATTTG 58.684 43.478 0.00 0.00 32.01 2.32
591 676 1.140312 TGGACTGCTTTGAAGGGTCT 58.860 50.000 0.00 0.00 0.00 3.85
620 705 6.101650 TGTTGGAGTACAGCAGATATATGG 57.898 41.667 0.00 0.00 35.22 2.74
691 969 1.771854 GGAGGAAGGGGAGGAAGAATC 59.228 57.143 0.00 0.00 0.00 2.52
734 1012 3.998672 GGTCGGAGGTGGCGACAA 61.999 66.667 0.00 0.00 46.06 3.18
735 1013 4.988716 AGGTCGGAGGTGGCGACA 62.989 66.667 0.00 0.00 34.69 4.35
779 1090 2.573869 CGTCGGCATGACTCTGGT 59.426 61.111 0.00 0.00 45.87 4.00
782 1093 2.182791 CAGCGTCGGCATGACTCT 59.817 61.111 0.00 1.47 43.30 3.24
1248 2307 0.703488 TGATGGAATCTGGCAACCCA 59.297 50.000 0.00 0.00 45.81 4.51
1521 2803 4.339872 TCAGCGTTTACCTTTGGAACTA 57.660 40.909 0.00 0.00 0.00 2.24
1563 2845 3.744559 GCTGCACGAAACTTGGGA 58.255 55.556 0.00 0.00 0.00 4.37
1767 3085 2.682494 TCCGAAGAAGGGGGACGG 60.682 66.667 0.00 0.00 44.09 4.79
2133 3529 1.220477 GTCTCCTCCAGCTGCTTCC 59.780 63.158 8.66 0.00 0.00 3.46
2194 3590 1.075600 GCTCTCCTGCTACCCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
2195 3591 2.494530 CGCTCTCCTGCTACCCTCC 61.495 68.421 0.00 0.00 0.00 4.30
2215 3646 4.530857 CGCCCCATGTCCTCCGTC 62.531 72.222 0.00 0.00 0.00 4.79
2318 3752 2.088104 AACACTCCAGAGGTCACTGA 57.912 50.000 0.00 0.00 39.94 3.41
2319 3753 2.918712 AAACACTCCAGAGGTCACTG 57.081 50.000 0.00 0.00 37.61 3.66
2320 3754 3.244249 GCTTAAACACTCCAGAGGTCACT 60.244 47.826 0.00 0.00 0.00 3.41
2336 3770 6.767524 ATTTGAATGGTGATACCGCTTAAA 57.232 33.333 0.00 0.00 42.58 1.52
2388 3822 6.206634 TCACCAAAGATGACAATTTGTAGGTC 59.793 38.462 1.15 1.65 35.16 3.85
2395 3829 9.829507 TTGTTAAATCACCAAAGATGACAATTT 57.170 25.926 0.00 0.00 29.26 1.82
2472 3974 6.901081 TCCTTCTTTTCTTTTCCCTTCATC 57.099 37.500 0.00 0.00 0.00 2.92
2517 4019 4.993705 AACTCCATGTCCCAAACTAGAA 57.006 40.909 0.00 0.00 0.00 2.10
2518 4020 4.597507 AGAAACTCCATGTCCCAAACTAGA 59.402 41.667 0.00 0.00 0.00 2.43
2519 4021 4.911390 AGAAACTCCATGTCCCAAACTAG 58.089 43.478 0.00 0.00 0.00 2.57
2520 4022 4.993705 AGAAACTCCATGTCCCAAACTA 57.006 40.909 0.00 0.00 0.00 2.24
2521 4023 3.884037 AGAAACTCCATGTCCCAAACT 57.116 42.857 0.00 0.00 0.00 2.66
2575 4077 7.750903 GGTGTGCTAGATTTGTCACTATTTTTC 59.249 37.037 0.00 0.00 0.00 2.29
2645 4170 8.298729 ACATTTTTCCAGAGGATTTAGGAATC 57.701 34.615 0.00 0.00 39.67 2.52
2668 4193 4.734398 AAGTGTTTTTGGAGCATTGACA 57.266 36.364 0.00 0.00 0.00 3.58
2691 4216 6.827762 ACCATTTCTTCAAAATGCTTGGAAAA 59.172 30.769 5.22 0.00 36.56 2.29
2695 4220 5.528320 ACAACCATTTCTTCAAAATGCTTGG 59.472 36.000 16.72 5.42 37.45 3.61
2934 4459 9.160496 AGCTAAATGTAGAATTTTGAGACTCTG 57.840 33.333 3.68 0.00 0.00 3.35
2977 4502 2.420628 CCGCGTCGGTACCATATTAA 57.579 50.000 13.54 0.00 42.73 1.40
2993 4518 1.445410 TGTGTGTATGAGCGTCCGC 60.445 57.895 2.94 2.94 42.33 5.54
2994 4519 0.388006 TGTGTGTGTATGAGCGTCCG 60.388 55.000 0.00 0.00 0.00 4.79
2995 4520 2.010145 ATGTGTGTGTATGAGCGTCC 57.990 50.000 0.00 0.00 0.00 4.79
2996 4521 3.303495 GTGTATGTGTGTGTATGAGCGTC 59.697 47.826 0.00 0.00 0.00 5.19
2997 4522 3.056821 AGTGTATGTGTGTGTATGAGCGT 60.057 43.478 0.00 0.00 0.00 5.07
2998 4523 3.511699 AGTGTATGTGTGTGTATGAGCG 58.488 45.455 0.00 0.00 0.00 5.03
2999 4524 4.327357 GTGAGTGTATGTGTGTGTATGAGC 59.673 45.833 0.00 0.00 0.00 4.26
3000 4525 4.864806 GGTGAGTGTATGTGTGTGTATGAG 59.135 45.833 0.00 0.00 0.00 2.90
3001 4526 4.322424 GGGTGAGTGTATGTGTGTGTATGA 60.322 45.833 0.00 0.00 0.00 2.15
3002 4527 3.932710 GGGTGAGTGTATGTGTGTGTATG 59.067 47.826 0.00 0.00 0.00 2.39
3003 4528 3.055385 GGGGTGAGTGTATGTGTGTGTAT 60.055 47.826 0.00 0.00 0.00 2.29
3004 4529 2.300723 GGGGTGAGTGTATGTGTGTGTA 59.699 50.000 0.00 0.00 0.00 2.90
3005 4530 1.071699 GGGGTGAGTGTATGTGTGTGT 59.928 52.381 0.00 0.00 0.00 3.72
3006 4531 1.610624 GGGGGTGAGTGTATGTGTGTG 60.611 57.143 0.00 0.00 0.00 3.82
3007 4532 0.690762 GGGGGTGAGTGTATGTGTGT 59.309 55.000 0.00 0.00 0.00 3.72
3008 4533 0.984230 AGGGGGTGAGTGTATGTGTG 59.016 55.000 0.00 0.00 0.00 3.82
3009 4534 2.634639 TAGGGGGTGAGTGTATGTGT 57.365 50.000 0.00 0.00 0.00 3.72
3010 4535 3.038280 TCATAGGGGGTGAGTGTATGTG 58.962 50.000 0.00 0.00 0.00 3.21
3011 4536 3.414759 TCATAGGGGGTGAGTGTATGT 57.585 47.619 0.00 0.00 0.00 2.29
3012 4537 3.454447 TGTTCATAGGGGGTGAGTGTATG 59.546 47.826 0.00 0.00 0.00 2.39
3013 4538 3.454812 GTGTTCATAGGGGGTGAGTGTAT 59.545 47.826 0.00 0.00 0.00 2.29
3014 4539 2.835764 GTGTTCATAGGGGGTGAGTGTA 59.164 50.000 0.00 0.00 0.00 2.90
3015 4540 1.628846 GTGTTCATAGGGGGTGAGTGT 59.371 52.381 0.00 0.00 0.00 3.55
3016 4541 1.628340 TGTGTTCATAGGGGGTGAGTG 59.372 52.381 0.00 0.00 0.00 3.51
3017 4542 1.628846 GTGTGTTCATAGGGGGTGAGT 59.371 52.381 0.00 0.00 0.00 3.41
3018 4543 1.628340 TGTGTGTTCATAGGGGGTGAG 59.372 52.381 0.00 0.00 0.00 3.51
3019 4544 1.349688 GTGTGTGTTCATAGGGGGTGA 59.650 52.381 0.00 0.00 0.00 4.02
3020 4545 1.073125 TGTGTGTGTTCATAGGGGGTG 59.927 52.381 0.00 0.00 0.00 4.61
3021 4546 1.440618 TGTGTGTGTTCATAGGGGGT 58.559 50.000 0.00 0.00 0.00 4.95
3022 4547 2.806945 ATGTGTGTGTTCATAGGGGG 57.193 50.000 0.00 0.00 0.00 5.40
3023 4548 3.938963 GTGTATGTGTGTGTTCATAGGGG 59.061 47.826 0.00 0.00 0.00 4.79
3024 4549 4.832248 AGTGTATGTGTGTGTTCATAGGG 58.168 43.478 0.00 0.00 0.00 3.53
3025 4550 5.348724 GTGAGTGTATGTGTGTGTTCATAGG 59.651 44.000 0.00 0.00 0.00 2.57
3026 4551 5.348724 GGTGAGTGTATGTGTGTGTTCATAG 59.651 44.000 0.00 0.00 0.00 2.23
3027 4552 5.234752 GGTGAGTGTATGTGTGTGTTCATA 58.765 41.667 0.00 0.00 0.00 2.15
3028 4553 4.065088 GGTGAGTGTATGTGTGTGTTCAT 58.935 43.478 0.00 0.00 0.00 2.57
3029 4554 3.462982 GGTGAGTGTATGTGTGTGTTCA 58.537 45.455 0.00 0.00 0.00 3.18
3030 4555 2.806244 GGGTGAGTGTATGTGTGTGTTC 59.194 50.000 0.00 0.00 0.00 3.18
3031 4556 2.486548 GGGGTGAGTGTATGTGTGTGTT 60.487 50.000 0.00 0.00 0.00 3.32
3032 4557 1.071699 GGGGTGAGTGTATGTGTGTGT 59.928 52.381 0.00 0.00 0.00 3.72
3033 4558 1.347707 AGGGGTGAGTGTATGTGTGTG 59.652 52.381 0.00 0.00 0.00 3.82
3034 4559 1.729586 AGGGGTGAGTGTATGTGTGT 58.270 50.000 0.00 0.00 0.00 3.72
3035 4560 2.859165 AAGGGGTGAGTGTATGTGTG 57.141 50.000 0.00 0.00 0.00 3.82
3036 4561 4.101114 TCATAAGGGGTGAGTGTATGTGT 58.899 43.478 0.00 0.00 0.00 3.72
3037 4562 4.753516 TCATAAGGGGTGAGTGTATGTG 57.246 45.455 0.00 0.00 0.00 3.21
3038 4563 4.534500 TGTTCATAAGGGGTGAGTGTATGT 59.466 41.667 0.00 0.00 0.00 2.29
3039 4564 4.876107 GTGTTCATAAGGGGTGAGTGTATG 59.124 45.833 0.00 0.00 0.00 2.39
3040 4565 4.534500 TGTGTTCATAAGGGGTGAGTGTAT 59.466 41.667 0.00 0.00 0.00 2.29
3041 4566 3.904965 TGTGTTCATAAGGGGTGAGTGTA 59.095 43.478 0.00 0.00 0.00 2.90
3042 4567 2.708861 TGTGTTCATAAGGGGTGAGTGT 59.291 45.455 0.00 0.00 0.00 3.55
3043 4568 3.074412 GTGTGTTCATAAGGGGTGAGTG 58.926 50.000 0.00 0.00 0.00 3.51
3044 4569 2.708861 TGTGTGTTCATAAGGGGTGAGT 59.291 45.455 0.00 0.00 0.00 3.41
3045 4570 3.074412 GTGTGTGTTCATAAGGGGTGAG 58.926 50.000 0.00 0.00 0.00 3.51
3046 4571 2.439880 TGTGTGTGTTCATAAGGGGTGA 59.560 45.455 0.00 0.00 0.00 4.02
3047 4572 2.857483 TGTGTGTGTTCATAAGGGGTG 58.143 47.619 0.00 0.00 0.00 4.61
3048 4573 3.420893 CATGTGTGTGTTCATAAGGGGT 58.579 45.455 0.00 0.00 0.00 4.95
3049 4574 2.164219 GCATGTGTGTGTTCATAAGGGG 59.836 50.000 0.00 0.00 0.00 4.79
3050 4575 2.819019 TGCATGTGTGTGTTCATAAGGG 59.181 45.455 0.00 0.00 0.00 3.95
3051 4576 3.252944 TGTGCATGTGTGTGTTCATAAGG 59.747 43.478 0.00 0.00 0.00 2.69
3052 4577 4.486574 TGTGCATGTGTGTGTTCATAAG 57.513 40.909 0.00 0.00 0.00 1.73
3053 4578 4.378253 CGATGTGCATGTGTGTGTTCATAA 60.378 41.667 0.00 0.00 0.00 1.90
3054 4579 3.124976 CGATGTGCATGTGTGTGTTCATA 59.875 43.478 0.00 0.00 0.00 2.15
3055 4580 2.095617 CGATGTGCATGTGTGTGTTCAT 60.096 45.455 0.00 0.00 0.00 2.57
3056 4581 1.263752 CGATGTGCATGTGTGTGTTCA 59.736 47.619 0.00 0.00 0.00 3.18
3057 4582 1.264020 ACGATGTGCATGTGTGTGTTC 59.736 47.619 0.00 0.00 0.00 3.18
3058 4583 1.308047 ACGATGTGCATGTGTGTGTT 58.692 45.000 0.00 0.00 0.00 3.32
3059 4584 1.798223 GTACGATGTGCATGTGTGTGT 59.202 47.619 0.00 0.00 0.00 3.72
3060 4585 1.128507 GGTACGATGTGCATGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
3061 4586 1.438651 GGTACGATGTGCATGTGTGT 58.561 50.000 0.00 0.00 0.00 3.72
3062 4587 0.726827 GGGTACGATGTGCATGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
3063 4588 0.613260 AGGGTACGATGTGCATGTGT 59.387 50.000 0.00 0.00 0.00 3.72
3064 4589 1.737838 AAGGGTACGATGTGCATGTG 58.262 50.000 0.00 0.00 0.00 3.21
3065 4590 3.838244 ATAAGGGTACGATGTGCATGT 57.162 42.857 0.00 0.00 0.00 3.21
3066 4591 4.152402 GCTTATAAGGGTACGATGTGCATG 59.848 45.833 14.28 0.00 0.00 4.06
3067 4592 4.202315 TGCTTATAAGGGTACGATGTGCAT 60.202 41.667 14.28 0.00 0.00 3.96
3068 4593 3.133183 TGCTTATAAGGGTACGATGTGCA 59.867 43.478 14.28 0.00 0.00 4.57
3069 4594 3.493503 GTGCTTATAAGGGTACGATGTGC 59.506 47.826 14.28 0.00 0.00 4.57
3070 4595 4.056050 GGTGCTTATAAGGGTACGATGTG 58.944 47.826 14.28 0.00 0.00 3.21
3071 4596 3.965347 AGGTGCTTATAAGGGTACGATGT 59.035 43.478 14.28 0.00 0.00 3.06
3072 4597 4.602340 AGGTGCTTATAAGGGTACGATG 57.398 45.455 14.28 0.00 0.00 3.84
3073 4598 4.202326 CCAAGGTGCTTATAAGGGTACGAT 60.202 45.833 14.28 0.00 0.00 3.73
3074 4599 3.133362 CCAAGGTGCTTATAAGGGTACGA 59.867 47.826 14.28 0.00 0.00 3.43
3075 4600 3.133362 TCCAAGGTGCTTATAAGGGTACG 59.867 47.826 14.28 0.00 0.00 3.67
3076 4601 4.407945 TCTCCAAGGTGCTTATAAGGGTAC 59.592 45.833 14.28 0.00 0.00 3.34
3077 4602 4.627015 TCTCCAAGGTGCTTATAAGGGTA 58.373 43.478 14.28 0.00 0.00 3.69
3078 4603 3.460825 TCTCCAAGGTGCTTATAAGGGT 58.539 45.455 14.28 0.00 0.00 4.34
3079 4604 4.503714 TTCTCCAAGGTGCTTATAAGGG 57.496 45.455 14.28 5.83 0.00 3.95
3080 4605 4.332819 CGTTTCTCCAAGGTGCTTATAAGG 59.667 45.833 14.28 0.00 0.00 2.69
3081 4606 4.332819 CCGTTTCTCCAAGGTGCTTATAAG 59.667 45.833 8.20 8.20 0.00 1.73
3082 4607 4.020039 TCCGTTTCTCCAAGGTGCTTATAA 60.020 41.667 0.00 0.00 0.00 0.98
3083 4608 3.516300 TCCGTTTCTCCAAGGTGCTTATA 59.484 43.478 0.00 0.00 0.00 0.98
3084 4609 2.304761 TCCGTTTCTCCAAGGTGCTTAT 59.695 45.455 0.00 0.00 0.00 1.73
3085 4610 1.695242 TCCGTTTCTCCAAGGTGCTTA 59.305 47.619 0.00 0.00 0.00 3.09
3086 4611 0.472471 TCCGTTTCTCCAAGGTGCTT 59.528 50.000 0.00 0.00 0.00 3.91
3087 4612 0.035458 CTCCGTTTCTCCAAGGTGCT 59.965 55.000 0.00 0.00 0.00 4.40
3088 4613 0.250338 ACTCCGTTTCTCCAAGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
3089 4614 1.512926 CACTCCGTTTCTCCAAGGTG 58.487 55.000 0.00 0.00 0.00 4.00
3090 4615 0.396811 CCACTCCGTTTCTCCAAGGT 59.603 55.000 0.00 0.00 0.00 3.50
3091 4616 0.396811 ACCACTCCGTTTCTCCAAGG 59.603 55.000 0.00 0.00 0.00 3.61
3092 4617 3.611766 ATACCACTCCGTTTCTCCAAG 57.388 47.619 0.00 0.00 0.00 3.61
3093 4618 5.687166 AATATACCACTCCGTTTCTCCAA 57.313 39.130 0.00 0.00 0.00 3.53
3094 4619 5.687166 AAATATACCACTCCGTTTCTCCA 57.313 39.130 0.00 0.00 0.00 3.86
3095 4620 7.254692 GCTTTAAATATACCACTCCGTTTCTCC 60.255 40.741 0.00 0.00 0.00 3.71
3096 4621 7.516312 CGCTTTAAATATACCACTCCGTTTCTC 60.516 40.741 0.00 0.00 0.00 2.87
3097 4622 6.257193 CGCTTTAAATATACCACTCCGTTTCT 59.743 38.462 0.00 0.00 0.00 2.52
3098 4623 6.036408 ACGCTTTAAATATACCACTCCGTTTC 59.964 38.462 0.00 0.00 0.00 2.78
3099 4624 5.876460 ACGCTTTAAATATACCACTCCGTTT 59.124 36.000 0.00 0.00 0.00 3.60
3100 4625 5.422145 ACGCTTTAAATATACCACTCCGTT 58.578 37.500 0.00 0.00 0.00 4.44
3101 4626 5.014808 ACGCTTTAAATATACCACTCCGT 57.985 39.130 0.00 0.00 0.00 4.69
3102 4627 5.045215 TGACGCTTTAAATATACCACTCCG 58.955 41.667 0.00 0.00 0.00 4.63
3103 4628 6.047231 ACTGACGCTTTAAATATACCACTCC 58.953 40.000 0.00 0.00 0.00 3.85
3104 4629 6.979238 AGACTGACGCTTTAAATATACCACTC 59.021 38.462 0.00 0.00 0.00 3.51
3105 4630 6.875076 AGACTGACGCTTTAAATATACCACT 58.125 36.000 0.00 0.00 0.00 4.00
3106 4631 8.700644 CATAGACTGACGCTTTAAATATACCAC 58.299 37.037 0.00 0.00 0.00 4.16
3107 4632 7.384115 GCATAGACTGACGCTTTAAATATACCA 59.616 37.037 0.00 0.00 0.00 3.25
3108 4633 7.384115 TGCATAGACTGACGCTTTAAATATACC 59.616 37.037 0.00 0.00 0.00 2.73
3109 4634 8.294341 TGCATAGACTGACGCTTTAAATATAC 57.706 34.615 0.00 0.00 0.00 1.47
3110 4635 9.140286 GATGCATAGACTGACGCTTTAAATATA 57.860 33.333 0.00 0.00 0.00 0.86
3111 4636 7.657354 TGATGCATAGACTGACGCTTTAAATAT 59.343 33.333 0.00 0.00 0.00 1.28
3112 4637 6.983890 TGATGCATAGACTGACGCTTTAAATA 59.016 34.615 0.00 0.00 0.00 1.40
3113 4638 5.817296 TGATGCATAGACTGACGCTTTAAAT 59.183 36.000 0.00 0.00 0.00 1.40
3114 4639 5.175127 TGATGCATAGACTGACGCTTTAAA 58.825 37.500 0.00 0.00 0.00 1.52
3115 4640 4.754322 TGATGCATAGACTGACGCTTTAA 58.246 39.130 0.00 0.00 0.00 1.52
3122 4647 6.511416 ACTATCAACTGATGCATAGACTGAC 58.489 40.000 0.00 0.00 36.05 3.51
3138 4663 8.902735 GGAAAAATGAAAAAGACGACTATCAAC 58.097 33.333 0.00 0.00 0.00 3.18
3142 4667 9.810545 TTTTGGAAAAATGAAAAAGACGACTAT 57.189 25.926 0.00 0.00 0.00 2.12
3143 4668 9.810545 ATTTTGGAAAAATGAAAAAGACGACTA 57.189 25.926 0.00 0.00 0.00 2.59
3148 4673 9.571810 AAAGCATTTTGGAAAAATGAAAAAGAC 57.428 25.926 23.07 8.47 39.36 3.01


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

AutoCloner maintained by Alex Coulton.