Multiple sequence alignment - TraesCS5B01G389500

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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 TraesCS5B01G389500 chr5B 100.000 2262 0 0 366 2627 568734711 568732450 0.000000e+00 4178.0
1 TraesCS5B01G389500 chr5B 89.271 727 56 7 889 1608 568421246 568420535 0.000000e+00 891.0
2 TraesCS5B01G389500 chr5B 82.743 226 19 8 490 698 568428278 568428056 1.610000e-42 183.0
3 TraesCS5B01G389500 chr5B 86.747 166 18 3 2167 2328 568818557 568818392 5.780000e-42 182.0
4 TraesCS5B01G389500 chr5B 100.000 86 0 0 1 86 568735076 568734991 2.710000e-35 159.0
5 TraesCS5B01G389500 chr5B 94.286 70 4 0 15 84 416417654 416417723 9.940000e-20 108.0
6 TraesCS5B01G389500 chr5B 97.059 34 1 0 2131 2164 568803733 568803700 1.020000e-04 58.4
7 TraesCS5B01G389500 chr5D 93.298 761 41 6 888 1639 462362377 462361618 0.000000e+00 1114.0
8 TraesCS5B01G389500 chr5D 89.011 728 65 10 889 1608 462092580 462091860 0.000000e+00 887.0
9 TraesCS5B01G389500 chr5D 94.822 309 14 2 2319 2627 462356655 462356349 5.090000e-132 481.0
10 TraesCS5B01G389500 chr5D 86.345 476 24 13 433 885 462362914 462362457 5.090000e-132 481.0
11 TraesCS5B01G389500 chr5D 83.411 428 28 20 494 885 462093119 462092699 8.940000e-95 357.0
12 TraesCS5B01G389500 chr5D 79.022 491 43 35 1794 2251 462361517 462361054 5.540000e-72 281.0
13 TraesCS5B01G389500 chr5D 100.000 30 0 0 2134 2163 462352850 462352821 3.650000e-04 56.5
14 TraesCS5B01G389500 chr5A 89.636 714 55 5 899 1608 582401245 582400547 0.000000e+00 891.0
15 TraesCS5B01G389500 chr5A 87.387 777 67 13 889 1649 582608634 582607873 0.000000e+00 863.0
16 TraesCS5B01G389500 chr5A 92.810 459 24 3 2128 2578 582607339 582606882 0.000000e+00 656.0
17 TraesCS5B01G389500 chr5A 81.481 486 35 25 426 885 582609217 582608761 5.380000e-92 348.0
18 TraesCS5B01G389500 chr5A 81.840 424 23 25 494 885 582401760 582401359 9.130000e-80 307.0
19 TraesCS5B01G389500 chr4D 93.151 73 3 2 13 84 12737457 12737386 3.580000e-19 106.0
20 TraesCS5B01G389500 chr2D 100.000 30 0 0 1291 1320 623330308 623330337 3.650000e-04 56.5


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 TraesCS5B01G389500 chr5B 568732450 568735076 2626 True 2168.500000 4178 100.000000 1 2627 2 chr5B.!!$R5 2626
1 TraesCS5B01G389500 chr5B 568420535 568421246 711 True 891.000000 891 89.271000 889 1608 1 chr5B.!!$R1 719
2 TraesCS5B01G389500 chr5D 462361054 462362914 1860 True 625.333333 1114 86.221667 433 2251 3 chr5D.!!$R3 1818
3 TraesCS5B01G389500 chr5D 462091860 462093119 1259 True 622.000000 887 86.211000 494 1608 2 chr5D.!!$R1 1114
4 TraesCS5B01G389500 chr5D 462352821 462356655 3834 True 268.750000 481 97.411000 2134 2627 2 chr5D.!!$R2 493
5 TraesCS5B01G389500 chr5A 582606882 582609217 2335 True 622.333333 863 87.226000 426 2578 3 chr5A.!!$R2 2152
6 TraesCS5B01G389500 chr5A 582400547 582401760 1213 True 599.000000 891 85.738000 494 1608 2 chr5A.!!$R1 1114

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
777 819 0.040067 GACCTGCAGTTTTGGAAGCG 60.04 55.0 13.81 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2006 0.034059 CCTTGTCCTCTCGCTTGTGT 59.966 55.0 0.0 0.0 0.0 3.72 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
27 28 8.500837 TCACTTATTTTCAAAAATGCTACACG 57.499 30.769 10.27 0.00 38.90 4.49
28 29 8.132362 TCACTTATTTTCAAAAATGCTACACGT 58.868 29.630 10.27 0.00 38.90 4.49
29 30 9.388346 CACTTATTTTCAAAAATGCTACACGTA 57.612 29.630 10.27 0.00 38.90 3.57
30 31 9.389570 ACTTATTTTCAAAAATGCTACACGTAC 57.610 29.630 10.27 0.00 38.90 3.67
31 32 6.904954 ATTTTCAAAAATGCTACACGTACG 57.095 33.333 15.01 15.01 37.24 3.67
32 33 4.392619 TTCAAAAATGCTACACGTACGG 57.607 40.909 21.06 11.05 0.00 4.02
33 34 2.158058 TCAAAAATGCTACACGTACGGC 59.842 45.455 21.06 13.52 0.00 5.68
34 35 1.081094 AAAATGCTACACGTACGGCC 58.919 50.000 21.06 0.00 0.00 6.13
35 36 0.248289 AAATGCTACACGTACGGCCT 59.752 50.000 21.06 3.19 0.00 5.19
36 37 0.179119 AATGCTACACGTACGGCCTC 60.179 55.000 21.06 5.12 0.00 4.70
37 38 1.035932 ATGCTACACGTACGGCCTCT 61.036 55.000 21.06 0.00 0.00 3.69
38 39 1.246056 TGCTACACGTACGGCCTCTT 61.246 55.000 21.06 0.00 0.00 2.85
39 40 0.734889 GCTACACGTACGGCCTCTTA 59.265 55.000 21.06 0.40 0.00 2.10
40 41 1.532713 GCTACACGTACGGCCTCTTAC 60.533 57.143 21.06 0.00 0.00 2.34
41 42 0.726827 TACACGTACGGCCTCTTACG 59.273 55.000 21.06 20.65 43.72 3.18
42 43 1.226491 CACGTACGGCCTCTTACGG 60.226 63.158 24.00 13.87 42.84 4.02
43 44 2.409870 ACGTACGGCCTCTTACGGG 61.410 63.158 24.00 1.57 42.84 5.28
44 45 2.810403 GTACGGCCTCTTACGGGG 59.190 66.667 0.00 0.00 0.00 5.73
45 46 3.149648 TACGGCCTCTTACGGGGC 61.150 66.667 0.23 0.23 46.89 5.80
46 47 3.667217 TACGGCCTCTTACGGGGCT 62.667 63.158 10.38 0.00 46.80 5.19
47 48 4.530857 CGGCCTCTTACGGGGCTG 62.531 72.222 10.38 7.39 46.80 4.85
48 49 4.858680 GGCCTCTTACGGGGCTGC 62.859 72.222 10.38 0.00 46.80 5.25
49 50 3.787001 GCCTCTTACGGGGCTGCT 61.787 66.667 2.07 0.00 44.48 4.24
50 51 2.432300 GCCTCTTACGGGGCTGCTA 61.432 63.158 2.07 0.00 44.48 3.49
51 52 1.442148 CCTCTTACGGGGCTGCTAC 59.558 63.158 0.00 0.00 0.00 3.58
52 53 1.327690 CCTCTTACGGGGCTGCTACA 61.328 60.000 0.00 0.00 0.00 2.74
53 54 0.103208 CTCTTACGGGGCTGCTACAG 59.897 60.000 0.00 0.00 34.12 2.74
54 55 0.323999 TCTTACGGGGCTGCTACAGA 60.324 55.000 0.00 0.00 32.44 3.41
55 56 0.179108 CTTACGGGGCTGCTACAGAC 60.179 60.000 0.00 0.00 39.10 3.51
60 61 4.943822 GGCTGCTACAGACCCTTC 57.056 61.111 0.00 0.00 32.43 3.46
61 62 1.222113 GGCTGCTACAGACCCTTCC 59.778 63.158 0.00 0.00 32.43 3.46
62 63 1.553690 GGCTGCTACAGACCCTTCCA 61.554 60.000 0.00 0.00 32.43 3.53
63 64 0.543749 GCTGCTACAGACCCTTCCAT 59.456 55.000 0.00 0.00 32.44 3.41
64 65 1.762957 GCTGCTACAGACCCTTCCATA 59.237 52.381 0.00 0.00 32.44 2.74
65 66 2.170607 GCTGCTACAGACCCTTCCATAA 59.829 50.000 0.00 0.00 32.44 1.90
66 67 3.370527 GCTGCTACAGACCCTTCCATAAA 60.371 47.826 0.00 0.00 32.44 1.40
67 68 4.687219 GCTGCTACAGACCCTTCCATAAAT 60.687 45.833 0.00 0.00 32.44 1.40
68 69 5.036117 TGCTACAGACCCTTCCATAAATC 57.964 43.478 0.00 0.00 0.00 2.17
69 70 4.473196 TGCTACAGACCCTTCCATAAATCA 59.527 41.667 0.00 0.00 0.00 2.57
70 71 5.045213 TGCTACAGACCCTTCCATAAATCAA 60.045 40.000 0.00 0.00 0.00 2.57
71 72 6.064717 GCTACAGACCCTTCCATAAATCAAT 58.935 40.000 0.00 0.00 0.00 2.57
72 73 7.147391 TGCTACAGACCCTTCCATAAATCAATA 60.147 37.037 0.00 0.00 0.00 1.90
73 74 7.719633 GCTACAGACCCTTCCATAAATCAATAA 59.280 37.037 0.00 0.00 0.00 1.40
74 75 9.627123 CTACAGACCCTTCCATAAATCAATAAA 57.373 33.333 0.00 0.00 0.00 1.40
76 77 8.917088 ACAGACCCTTCCATAAATCAATAAATG 58.083 33.333 0.00 0.00 0.00 2.32
77 78 7.869429 CAGACCCTTCCATAAATCAATAAATGC 59.131 37.037 0.00 0.00 0.00 3.56
78 79 7.015584 AGACCCTTCCATAAATCAATAAATGCC 59.984 37.037 0.00 0.00 0.00 4.40
79 80 6.043127 ACCCTTCCATAAATCAATAAATGCCC 59.957 38.462 0.00 0.00 0.00 5.36
80 81 6.466812 CCTTCCATAAATCAATAAATGCCCC 58.533 40.000 0.00 0.00 0.00 5.80
81 82 6.432403 TTCCATAAATCAATAAATGCCCCC 57.568 37.500 0.00 0.00 0.00 5.40
387 388 5.743636 ATTAAAGCCTGCCATTTCAGAAA 57.256 34.783 0.00 0.00 36.19 2.52
388 389 5.743636 TTAAAGCCTGCCATTTCAGAAAT 57.256 34.783 2.20 2.20 36.19 2.17
389 390 3.881937 AAGCCTGCCATTTCAGAAATC 57.118 42.857 5.32 0.00 36.19 2.17
390 391 2.811410 AGCCTGCCATTTCAGAAATCA 58.189 42.857 5.32 1.70 36.19 2.57
391 392 2.494870 AGCCTGCCATTTCAGAAATCAC 59.505 45.455 5.32 2.01 36.19 3.06
392 393 2.417787 GCCTGCCATTTCAGAAATCACC 60.418 50.000 5.32 0.00 36.19 4.02
393 394 2.167075 CCTGCCATTTCAGAAATCACCC 59.833 50.000 5.32 0.00 36.19 4.61
394 395 2.167075 CTGCCATTTCAGAAATCACCCC 59.833 50.000 5.32 0.00 36.19 4.95
395 396 2.225343 TGCCATTTCAGAAATCACCCCT 60.225 45.455 5.32 0.00 0.00 4.79
396 397 2.833943 GCCATTTCAGAAATCACCCCTT 59.166 45.455 5.32 0.00 0.00 3.95
397 398 4.023291 GCCATTTCAGAAATCACCCCTTA 58.977 43.478 5.32 0.00 0.00 2.69
398 399 4.466015 GCCATTTCAGAAATCACCCCTTAA 59.534 41.667 5.32 0.00 0.00 1.85
399 400 5.046663 GCCATTTCAGAAATCACCCCTTAAA 60.047 40.000 5.32 0.00 0.00 1.52
400 401 6.398095 CCATTTCAGAAATCACCCCTTAAAC 58.602 40.000 5.32 0.00 0.00 2.01
401 402 6.211384 CCATTTCAGAAATCACCCCTTAAACT 59.789 38.462 5.32 0.00 0.00 2.66
402 403 6.894339 TTTCAGAAATCACCCCTTAAACTC 57.106 37.500 0.00 0.00 0.00 3.01
403 404 5.576563 TCAGAAATCACCCCTTAAACTCA 57.423 39.130 0.00 0.00 0.00 3.41
404 405 6.139679 TCAGAAATCACCCCTTAAACTCAT 57.860 37.500 0.00 0.00 0.00 2.90
405 406 5.945784 TCAGAAATCACCCCTTAAACTCATG 59.054 40.000 0.00 0.00 0.00 3.07
406 407 5.711976 CAGAAATCACCCCTTAAACTCATGT 59.288 40.000 0.00 0.00 0.00 3.21
407 408 6.884295 CAGAAATCACCCCTTAAACTCATGTA 59.116 38.462 0.00 0.00 0.00 2.29
408 409 7.393234 CAGAAATCACCCCTTAAACTCATGTAA 59.607 37.037 0.00 0.00 0.00 2.41
409 410 7.611855 AGAAATCACCCCTTAAACTCATGTAAG 59.388 37.037 0.00 0.00 0.00 2.34
410 411 5.836024 TCACCCCTTAAACTCATGTAAGT 57.164 39.130 0.00 0.00 0.00 2.24
411 412 5.556915 TCACCCCTTAAACTCATGTAAGTG 58.443 41.667 0.00 0.00 0.00 3.16
412 413 5.072600 TCACCCCTTAAACTCATGTAAGTGT 59.927 40.000 0.00 0.00 0.00 3.55
413 414 5.768164 CACCCCTTAAACTCATGTAAGTGTT 59.232 40.000 0.00 0.00 0.00 3.32
414 415 6.264518 CACCCCTTAAACTCATGTAAGTGTTT 59.735 38.462 0.00 0.00 38.37 2.83
415 416 6.264518 ACCCCTTAAACTCATGTAAGTGTTTG 59.735 38.462 0.00 0.00 36.32 2.93
416 417 6.264518 CCCCTTAAACTCATGTAAGTGTTTGT 59.735 38.462 0.00 0.00 36.32 2.83
417 418 7.446013 CCCCTTAAACTCATGTAAGTGTTTGTA 59.554 37.037 0.00 0.00 36.32 2.41
418 419 9.010029 CCCTTAAACTCATGTAAGTGTTTGTAT 57.990 33.333 0.00 0.00 36.32 2.29
419 420 9.825972 CCTTAAACTCATGTAAGTGTTTGTATG 57.174 33.333 0.00 0.00 36.32 2.39
422 423 8.677148 AAACTCATGTAAGTGTTTGTATGTCT 57.323 30.769 0.00 0.00 34.87 3.41
423 424 9.772973 AAACTCATGTAAGTGTTTGTATGTCTA 57.227 29.630 0.00 0.00 34.87 2.59
424 425 8.988064 ACTCATGTAAGTGTTTGTATGTCTAG 57.012 34.615 0.00 0.00 0.00 2.43
425 426 7.545965 ACTCATGTAAGTGTTTGTATGTCTAGC 59.454 37.037 0.00 0.00 0.00 3.42
426 427 7.382898 TCATGTAAGTGTTTGTATGTCTAGCA 58.617 34.615 0.00 0.00 0.00 3.49
427 428 7.875554 TCATGTAAGTGTTTGTATGTCTAGCAA 59.124 33.333 0.00 0.00 0.00 3.91
428 429 8.503196 CATGTAAGTGTTTGTATGTCTAGCAAA 58.497 33.333 0.00 0.00 0.00 3.68
429 430 8.083462 TGTAAGTGTTTGTATGTCTAGCAAAG 57.917 34.615 0.00 0.00 33.50 2.77
430 431 5.613358 AGTGTTTGTATGTCTAGCAAAGC 57.387 39.130 0.00 0.00 33.50 3.51
431 432 5.308825 AGTGTTTGTATGTCTAGCAAAGCT 58.691 37.500 0.00 0.00 43.41 3.74
469 470 1.318785 CTGTCGACGCTGAATCTTTCG 59.681 52.381 11.62 0.00 0.00 3.46
471 472 1.614385 TCGACGCTGAATCTTTCGAC 58.386 50.000 0.00 0.00 33.95 4.20
480 481 4.084537 GCTGAATCTTTCGACTCGAACAAA 60.085 41.667 13.44 3.00 45.64 2.83
482 483 4.447724 TGAATCTTTCGACTCGAACAAAGG 59.552 41.667 13.44 2.98 45.64 3.11
483 484 2.750948 TCTTTCGACTCGAACAAAGGG 58.249 47.619 13.44 1.44 45.64 3.95
484 485 1.798813 CTTTCGACTCGAACAAAGGGG 59.201 52.381 13.44 0.00 45.64 4.79
485 486 1.042229 TTCGACTCGAACAAAGGGGA 58.958 50.000 9.86 0.00 41.05 4.81
531 533 2.282180 ACCCAGCACCGCGAATTT 60.282 55.556 8.23 0.00 0.00 1.82
543 557 2.701587 CGAATTTGCGCCTCCCATA 58.298 52.632 4.18 0.00 0.00 2.74
575 589 2.832643 ATCCACCTGCCATTCATCAA 57.167 45.000 0.00 0.00 0.00 2.57
576 590 1.838112 TCCACCTGCCATTCATCAAC 58.162 50.000 0.00 0.00 0.00 3.18
577 591 1.355381 TCCACCTGCCATTCATCAACT 59.645 47.619 0.00 0.00 0.00 3.16
644 662 4.428922 CGTCGCCACACGCACATG 62.429 66.667 0.00 0.00 43.23 3.21
662 680 5.265477 CACATGTACACAAACTCACACAAG 58.735 41.667 0.00 0.00 0.00 3.16
777 819 0.040067 GACCTGCAGTTTTGGAAGCG 60.040 55.000 13.81 0.00 0.00 4.68
778 820 1.372128 CCTGCAGTTTTGGAAGCGC 60.372 57.895 13.81 0.00 0.00 5.92
781 828 2.796617 CAGTTTTGGAAGCGCGCG 60.797 61.111 28.44 28.44 0.00 6.86
798 850 0.529555 GCGCACACAAACCAAACCAT 60.530 50.000 0.30 0.00 0.00 3.55
827 879 0.833834 CAGTGGAGTGTGAGAGGGGT 60.834 60.000 0.00 0.00 0.00 4.95
867 919 3.561313 GCCCTTCTTTAAGATCACCACCA 60.561 47.826 0.00 0.00 34.37 4.17
885 937 3.424105 GCCCCCATTGCCCTCTCT 61.424 66.667 0.00 0.00 0.00 3.10
930 1124 3.222354 AAGCGTCGGGTCCTGTGTC 62.222 63.158 0.00 0.00 0.00 3.67
980 1174 2.850833 TCCAAGGTCCAGGAGATGATT 58.149 47.619 0.00 0.00 0.00 2.57
981 1175 2.507058 TCCAAGGTCCAGGAGATGATTG 59.493 50.000 0.00 0.00 0.00 2.67
1093 1304 1.105167 TGCTTCTGCTGTTGCTGCTT 61.105 50.000 0.00 0.00 40.48 3.91
1098 1309 2.071844 CTGCTGTTGCTGCTTGTGCT 62.072 55.000 0.00 0.00 40.48 4.40
1215 1429 1.548973 CGATGTTCGCCTACGCCATC 61.549 60.000 0.00 0.00 40.73 3.51
1627 1844 1.364626 CTCATCCGCTTGCAGGTGAC 61.365 60.000 11.45 0.00 0.00 3.67
1631 1848 1.005037 CCGCTTGCAGGTGACTACA 60.005 57.895 11.45 0.00 40.21 2.74
1636 1853 0.250124 TTGCAGGTGACTACAACGGG 60.250 55.000 0.00 0.00 38.79 5.28
1637 1854 1.116536 TGCAGGTGACTACAACGGGA 61.117 55.000 0.00 0.00 40.21 5.14
1649 1866 1.692519 ACAACGGGAAAGAGCTACACT 59.307 47.619 0.00 0.00 0.00 3.55
1659 1876 2.125512 GCTACACTCCCACCAGCG 60.126 66.667 0.00 0.00 0.00 5.18
1660 1877 2.943978 GCTACACTCCCACCAGCGT 61.944 63.158 0.00 0.00 0.00 5.07
1661 1878 1.601419 GCTACACTCCCACCAGCGTA 61.601 60.000 0.00 0.00 0.00 4.42
1680 1897 2.655364 CGTACAGCTCATCCGCGG 60.655 66.667 22.12 22.12 34.40 6.46
1682 1899 1.364171 GTACAGCTCATCCGCGGAT 59.636 57.895 34.60 34.60 34.81 4.18
1684 1901 0.823769 TACAGCTCATCCGCGGATCT 60.824 55.000 37.10 27.33 31.62 2.75
1685 1902 1.372748 CAGCTCATCCGCGGATCTC 60.373 63.158 37.10 26.10 31.62 2.75
1687 1904 2.569354 GCTCATCCGCGGATCTCCT 61.569 63.158 37.10 15.82 31.62 3.69
1688 1905 1.288439 CTCATCCGCGGATCTCCTG 59.712 63.158 37.10 26.74 31.62 3.86
1689 1906 1.455773 TCATCCGCGGATCTCCTGT 60.456 57.895 37.10 14.11 31.62 4.00
1691 1908 2.502492 ATCCGCGGATCTCCTGTGG 61.502 63.158 34.60 11.85 39.68 4.17
1692 1909 2.928988 ATCCGCGGATCTCCTGTGGA 62.929 60.000 34.60 18.78 45.66 4.02
1693 1910 2.105128 CGCGGATCTCCTGTGGAC 59.895 66.667 0.00 0.00 0.00 4.02
1694 1911 2.418910 CGCGGATCTCCTGTGGACT 61.419 63.158 0.00 0.00 0.00 3.85
1695 1912 1.142748 GCGGATCTCCTGTGGACTG 59.857 63.158 0.00 0.00 0.00 3.51
1696 1913 1.608717 GCGGATCTCCTGTGGACTGT 61.609 60.000 0.00 0.00 0.00 3.55
1697 1914 0.457851 CGGATCTCCTGTGGACTGTC 59.542 60.000 0.00 0.00 0.00 3.51
1698 1915 1.561643 GGATCTCCTGTGGACTGTCA 58.438 55.000 10.38 0.00 0.00 3.58
1699 1916 2.114616 GGATCTCCTGTGGACTGTCAT 58.885 52.381 10.38 0.00 0.00 3.06
1700 1917 2.158986 GGATCTCCTGTGGACTGTCATG 60.159 54.545 10.38 0.00 0.00 3.07
1703 1920 0.473694 TCCTGTGGACTGTCATGGGT 60.474 55.000 10.38 0.00 0.00 4.51
1704 1921 0.036010 CCTGTGGACTGTCATGGGTC 60.036 60.000 10.38 0.00 0.00 4.46
1705 1922 0.979665 CTGTGGACTGTCATGGGTCT 59.020 55.000 10.38 0.00 33.46 3.85
1706 1923 0.686789 TGTGGACTGTCATGGGTCTG 59.313 55.000 10.38 3.02 33.46 3.51
1707 1924 0.976641 GTGGACTGTCATGGGTCTGA 59.023 55.000 10.38 0.00 33.46 3.27
1708 1925 1.556911 GTGGACTGTCATGGGTCTGAT 59.443 52.381 10.38 0.00 33.46 2.90
1709 1926 2.766263 GTGGACTGTCATGGGTCTGATA 59.234 50.000 10.38 0.00 33.46 2.15
1711 1928 2.366916 GGACTGTCATGGGTCTGATAGG 59.633 54.545 10.38 0.00 38.34 2.57
1714 1931 1.486310 TGTCATGGGTCTGATAGGTGC 59.514 52.381 0.00 0.00 0.00 5.01
1715 1932 1.486310 GTCATGGGTCTGATAGGTGCA 59.514 52.381 0.00 0.00 0.00 4.57
1716 1933 2.105477 GTCATGGGTCTGATAGGTGCAT 59.895 50.000 0.00 0.00 0.00 3.96
1717 1934 2.369860 TCATGGGTCTGATAGGTGCATC 59.630 50.000 0.00 0.00 0.00 3.91
1718 1935 1.878211 TGGGTCTGATAGGTGCATCA 58.122 50.000 0.00 0.00 33.88 3.07
1719 1936 2.195727 TGGGTCTGATAGGTGCATCAA 58.804 47.619 0.00 0.00 34.59 2.57
1720 1937 2.575735 TGGGTCTGATAGGTGCATCAAA 59.424 45.455 0.00 0.00 34.59 2.69
1721 1938 2.945668 GGGTCTGATAGGTGCATCAAAC 59.054 50.000 0.00 0.00 34.59 2.93
1722 1939 3.609853 GGTCTGATAGGTGCATCAAACA 58.390 45.455 0.00 0.00 34.59 2.83
1723 1940 4.202441 GGTCTGATAGGTGCATCAAACAT 58.798 43.478 0.00 0.00 34.59 2.71
1724 1941 4.036027 GGTCTGATAGGTGCATCAAACATG 59.964 45.833 0.00 0.00 34.59 3.21
1725 1942 3.628942 TCTGATAGGTGCATCAAACATGC 59.371 43.478 0.00 0.00 44.76 4.06
1726 1943 2.689471 TGATAGGTGCATCAAACATGCC 59.311 45.455 0.00 0.00 43.94 4.40
1727 1944 1.093972 TAGGTGCATCAAACATGCCG 58.906 50.000 0.00 0.00 43.94 5.69
1728 1945 0.608856 AGGTGCATCAAACATGCCGA 60.609 50.000 0.00 0.00 43.94 5.54
1729 1946 0.243365 GGTGCATCAAACATGCCGAA 59.757 50.000 4.18 0.00 43.94 4.30
1731 1948 0.243365 TGCATCAAACATGCCGAACC 59.757 50.000 4.18 0.00 43.94 3.62
1733 1950 1.733389 GCATCAAACATGCCGAACCAG 60.733 52.381 0.00 0.00 39.01 4.00
1734 1951 1.135315 CATCAAACATGCCGAACCAGG 60.135 52.381 0.00 0.00 0.00 4.45
1742 1959 4.452733 CCGAACCAGGCCGTCTCC 62.453 72.222 0.00 0.00 0.00 3.71
1743 1960 4.452733 CGAACCAGGCCGTCTCCC 62.453 72.222 0.00 0.00 0.00 4.30
1744 1961 3.319198 GAACCAGGCCGTCTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
1745 1962 3.316573 GAACCAGGCCGTCTCCCAG 62.317 68.421 0.00 0.00 0.00 4.45
1746 1963 4.640690 ACCAGGCCGTCTCCCAGT 62.641 66.667 0.00 0.00 0.00 4.00
1747 1964 3.322466 CCAGGCCGTCTCCCAGTT 61.322 66.667 0.00 0.00 0.00 3.16
1748 1965 1.987855 CCAGGCCGTCTCCCAGTTA 60.988 63.158 0.00 0.00 0.00 2.24
1749 1966 1.338136 CCAGGCCGTCTCCCAGTTAT 61.338 60.000 0.00 0.00 0.00 1.89
1750 1967 0.541863 CAGGCCGTCTCCCAGTTATT 59.458 55.000 0.00 0.00 0.00 1.40
1751 1968 1.760613 CAGGCCGTCTCCCAGTTATTA 59.239 52.381 0.00 0.00 0.00 0.98
1752 1969 2.169769 CAGGCCGTCTCCCAGTTATTAA 59.830 50.000 0.00 0.00 0.00 1.40
1753 1970 2.169978 AGGCCGTCTCCCAGTTATTAAC 59.830 50.000 0.00 0.00 0.00 2.01
1754 1971 2.558378 GCCGTCTCCCAGTTATTAACC 58.442 52.381 2.92 0.00 0.00 2.85
1755 1972 2.744166 GCCGTCTCCCAGTTATTAACCC 60.744 54.545 2.92 0.00 0.00 4.11
1756 1973 2.482490 CCGTCTCCCAGTTATTAACCCG 60.482 54.545 2.92 0.00 0.00 5.28
1757 1974 2.428171 CGTCTCCCAGTTATTAACCCGA 59.572 50.000 2.92 0.00 0.00 5.14
1758 1975 3.490419 CGTCTCCCAGTTATTAACCCGAG 60.490 52.174 2.92 6.03 0.00 4.63
1759 1976 2.433239 TCTCCCAGTTATTAACCCGAGC 59.567 50.000 2.92 0.00 0.00 5.03
1760 1977 1.487558 TCCCAGTTATTAACCCGAGCC 59.512 52.381 2.92 0.00 0.00 4.70
1761 1978 1.489230 CCCAGTTATTAACCCGAGCCT 59.511 52.381 2.92 0.00 0.00 4.58
1762 1979 2.484947 CCCAGTTATTAACCCGAGCCTC 60.485 54.545 2.92 0.00 0.00 4.70
1763 1980 2.169769 CCAGTTATTAACCCGAGCCTCA 59.830 50.000 2.92 0.00 0.00 3.86
1764 1981 3.370103 CCAGTTATTAACCCGAGCCTCAA 60.370 47.826 2.92 0.00 0.00 3.02
1765 1982 4.451900 CAGTTATTAACCCGAGCCTCAAT 58.548 43.478 2.92 0.00 0.00 2.57
1775 1992 1.063616 CGAGCCTCAATGCACAAGATG 59.936 52.381 0.00 0.00 0.00 2.90
1786 2003 2.791383 CACAAGATGCCGGTGAAAAA 57.209 45.000 1.90 0.00 34.52 1.94
1787 2004 2.664916 CACAAGATGCCGGTGAAAAAG 58.335 47.619 1.90 0.00 34.52 2.27
1789 2006 2.955660 ACAAGATGCCGGTGAAAAAGAA 59.044 40.909 1.90 0.00 0.00 2.52
1790 2007 3.243401 ACAAGATGCCGGTGAAAAAGAAC 60.243 43.478 1.90 0.00 0.00 3.01
1792 2009 2.293399 AGATGCCGGTGAAAAAGAACAC 59.707 45.455 1.90 0.00 36.44 3.32
1793 2010 1.464734 TGCCGGTGAAAAAGAACACA 58.535 45.000 1.90 0.00 38.57 3.72
1794 2011 1.819288 TGCCGGTGAAAAAGAACACAA 59.181 42.857 1.90 0.00 38.57 3.33
1795 2012 2.159310 TGCCGGTGAAAAAGAACACAAG 60.159 45.455 1.90 0.00 38.57 3.16
1796 2013 2.459934 CCGGTGAAAAAGAACACAAGC 58.540 47.619 0.00 0.00 38.57 4.01
1802 2105 3.312421 TGAAAAAGAACACAAGCGAGAGG 59.688 43.478 0.00 0.00 0.00 3.69
1821 2124 6.394345 AGAGGACAAGGAAGGAATGTATTT 57.606 37.500 0.00 0.00 0.00 1.40
1823 2126 7.569240 AGAGGACAAGGAAGGAATGTATTTAG 58.431 38.462 0.00 0.00 0.00 1.85
1858 2161 2.081462 AGGTTCGGCTACCATTTTTCG 58.919 47.619 8.16 0.00 40.82 3.46
1862 2165 1.801771 TCGGCTACCATTTTTCGTGTG 59.198 47.619 0.00 0.00 0.00 3.82
1863 2166 1.801771 CGGCTACCATTTTTCGTGTGA 59.198 47.619 0.00 0.00 0.00 3.58
1864 2167 2.418628 CGGCTACCATTTTTCGTGTGAT 59.581 45.455 0.00 0.00 0.00 3.06
1865 2168 3.485216 CGGCTACCATTTTTCGTGTGATC 60.485 47.826 0.00 0.00 0.00 2.92
1867 2170 3.181500 GCTACCATTTTTCGTGTGATCCC 60.181 47.826 0.00 0.00 0.00 3.85
1868 2171 2.870175 ACCATTTTTCGTGTGATCCCA 58.130 42.857 0.00 0.00 0.00 4.37
1870 2173 3.193267 ACCATTTTTCGTGTGATCCCATG 59.807 43.478 0.00 0.00 0.00 3.66
1872 2175 4.414852 CATTTTTCGTGTGATCCCATGAC 58.585 43.478 0.00 0.00 30.30 3.06
1873 2176 2.849294 TTTCGTGTGATCCCATGACA 57.151 45.000 0.00 0.00 30.30 3.58
1874 2177 3.348647 TTTCGTGTGATCCCATGACAT 57.651 42.857 0.00 0.00 30.30 3.06
1887 2190 2.679837 CCATGACATGGTGACTGCTTAC 59.320 50.000 24.15 0.00 45.54 2.34
1903 2206 0.245539 TTACGCTAGCCGCTTCAGTT 59.754 50.000 9.66 0.00 41.76 3.16
1963 2266 3.144506 AGCTGTGACTTGGAATGTTGAG 58.855 45.455 0.00 0.00 0.00 3.02
1974 2277 6.207417 ACTTGGAATGTTGAGTTTGTCCTATG 59.793 38.462 0.00 0.00 0.00 2.23
1980 2283 6.012658 TGTTGAGTTTGTCCTATGCAAATC 57.987 37.500 0.00 0.00 38.00 2.17
2023 2326 4.141367 TGGTGTGAGTTGGGTTGAATCTAA 60.141 41.667 0.00 0.00 0.00 2.10
2025 2328 5.300792 GGTGTGAGTTGGGTTGAATCTAAAA 59.699 40.000 0.00 0.00 0.00 1.52
2033 2370 9.108284 AGTTGGGTTGAATCTAAAACAAAATTG 57.892 29.630 0.00 0.00 0.00 2.32
2062 2399 1.454653 CGAGTTCGTTTCTTCGGGAAC 59.545 52.381 0.00 0.00 39.16 3.62
2072 2412 3.876589 TTCGGGAACTGCTGCGTCC 62.877 63.158 7.98 7.98 32.53 4.79
2092 2432 2.464459 CCCTGATTGCTTCGCCGTC 61.464 63.158 0.00 0.00 0.00 4.79
2093 2433 2.697425 CTGATTGCTTCGCCGTCG 59.303 61.111 0.00 0.00 0.00 5.12
2094 2434 3.425938 CTGATTGCTTCGCCGTCGC 62.426 63.158 0.00 0.00 35.26 5.19
2112 2452 4.213700 GATCTCGTCGACGGATGC 57.786 61.111 35.05 22.68 40.29 3.91
2113 2453 1.370657 GATCTCGTCGACGGATGCC 60.371 63.158 35.05 20.36 40.29 4.40
2175 2528 0.041312 CAAGGTTCGTTTCCGTGCAG 60.041 55.000 0.00 0.00 35.01 4.41
2296 2656 2.254546 ATATTTTCCAGCGATCGCCA 57.745 45.000 34.89 17.70 43.17 5.69
2305 2665 1.016130 AGCGATCGCCAGTTTGTCTG 61.016 55.000 34.89 0.00 43.17 3.51
2316 2676 3.249799 CCAGTTTGTCTGCATTTCGTACA 59.750 43.478 0.00 0.00 42.38 2.90
2325 2685 4.864806 TCTGCATTTCGTACATCAGAGTTC 59.135 41.667 0.00 0.00 0.00 3.01
2331 2691 7.571244 GCATTTCGTACATCAGAGTTCAGAAAA 60.571 37.037 0.00 0.00 0.00 2.29
2333 2693 7.962964 TTCGTACATCAGAGTTCAGAAAATT 57.037 32.000 0.00 0.00 0.00 1.82
2334 2694 7.351414 TCGTACATCAGAGTTCAGAAAATTG 57.649 36.000 0.00 0.00 0.00 2.32
2335 2695 6.929049 TCGTACATCAGAGTTCAGAAAATTGT 59.071 34.615 0.00 0.00 0.00 2.71
2336 2696 7.441157 TCGTACATCAGAGTTCAGAAAATTGTT 59.559 33.333 0.00 0.00 0.00 2.83
2397 2757 3.183775 CCGCGGAATTTATCCTTCTTACG 59.816 47.826 24.07 0.00 46.98 3.18
2399 2759 4.317839 CGCGGAATTTATCCTTCTTACGTG 60.318 45.833 0.00 0.00 46.98 4.49
2455 2815 8.908903 ACAAAGTTGTGTTTGACAATAATAGGA 58.091 29.630 3.44 0.00 46.34 2.94
2475 2835 3.573967 GGATCAACTGACCCATGTGTTTT 59.426 43.478 0.00 0.00 0.00 2.43
2520 2880 7.715657 TGGTTACATGATTGAAATATCTTGCC 58.284 34.615 0.00 0.00 34.66 4.52
2556 2917 1.079875 TAAAGCGAATGACGACCGGC 61.080 55.000 0.00 0.00 45.77 6.13
2584 2945 2.772568 TGTTGAACATGTTGCGAAGG 57.227 45.000 17.58 0.00 0.00 3.46
2616 2977 1.135315 GTTGCGCATGGATGTCAACAT 60.135 47.619 12.75 0.00 40.09 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.132362 ACGTGTAGCATTTTTGAAAATAAGTGA 58.868 29.630 1.69 0.00 36.52 3.41
3 4 8.280909 ACGTGTAGCATTTTTGAAAATAAGTG 57.719 30.769 1.69 0.00 36.52 3.16
4 5 9.389570 GTACGTGTAGCATTTTTGAAAATAAGT 57.610 29.630 0.00 0.00 36.52 2.24
5 6 8.563949 CGTACGTGTAGCATTTTTGAAAATAAG 58.436 33.333 7.22 0.00 36.52 1.73
8 9 5.854338 CCGTACGTGTAGCATTTTTGAAAAT 59.146 36.000 15.21 0.00 39.07 1.82
9 10 5.206299 CCGTACGTGTAGCATTTTTGAAAA 58.794 37.500 15.21 0.00 0.00 2.29
10 11 4.774586 CCGTACGTGTAGCATTTTTGAAA 58.225 39.130 15.21 0.00 0.00 2.69
13 14 2.501881 GCCGTACGTGTAGCATTTTTG 58.498 47.619 15.21 0.00 0.00 2.44
14 15 1.465777 GGCCGTACGTGTAGCATTTTT 59.534 47.619 15.21 0.00 0.00 1.94
15 16 1.081094 GGCCGTACGTGTAGCATTTT 58.919 50.000 15.21 0.00 0.00 1.82
16 17 0.248289 AGGCCGTACGTGTAGCATTT 59.752 50.000 15.21 0.00 0.00 2.32
17 18 0.179119 GAGGCCGTACGTGTAGCATT 60.179 55.000 15.21 2.63 0.00 3.56
18 19 1.035932 AGAGGCCGTACGTGTAGCAT 61.036 55.000 15.21 7.86 0.00 3.79
19 20 1.246056 AAGAGGCCGTACGTGTAGCA 61.246 55.000 15.21 0.00 0.00 3.49
20 21 0.734889 TAAGAGGCCGTACGTGTAGC 59.265 55.000 15.21 10.07 0.00 3.58
21 22 1.267732 CGTAAGAGGCCGTACGTGTAG 60.268 57.143 21.46 0.00 42.78 2.74
22 23 0.726827 CGTAAGAGGCCGTACGTGTA 59.273 55.000 21.46 0.00 42.78 2.90
23 24 1.503542 CGTAAGAGGCCGTACGTGT 59.496 57.895 21.46 0.00 42.78 4.49
24 25 1.226491 CCGTAAGAGGCCGTACGTG 60.226 63.158 25.15 16.98 45.03 4.49
25 26 2.409870 CCCGTAAGAGGCCGTACGT 61.410 63.158 25.15 11.75 45.03 3.57
26 27 2.410469 CCCGTAAGAGGCCGTACG 59.590 66.667 22.31 22.31 45.70 3.67
27 28 2.810403 CCCCGTAAGAGGCCGTAC 59.190 66.667 0.00 0.21 43.02 3.67
28 29 3.149648 GCCCCGTAAGAGGCCGTA 61.150 66.667 0.00 0.00 43.76 4.02
33 34 1.327690 TGTAGCAGCCCCGTAAGAGG 61.328 60.000 0.00 0.00 43.02 3.69
34 35 0.103208 CTGTAGCAGCCCCGTAAGAG 59.897 60.000 0.00 0.00 43.02 2.85
35 36 0.323999 TCTGTAGCAGCCCCGTAAGA 60.324 55.000 0.00 0.00 43.02 2.10
36 37 0.179108 GTCTGTAGCAGCCCCGTAAG 60.179 60.000 0.00 0.00 0.00 2.34
37 38 1.610554 GGTCTGTAGCAGCCCCGTAA 61.611 60.000 0.00 0.00 0.00 3.18
38 39 2.056223 GGTCTGTAGCAGCCCCGTA 61.056 63.158 0.00 0.00 0.00 4.02
39 40 3.391382 GGTCTGTAGCAGCCCCGT 61.391 66.667 0.00 0.00 0.00 5.28
40 41 4.162690 GGGTCTGTAGCAGCCCCG 62.163 72.222 13.83 0.00 39.95 5.73
42 43 1.222113 GAAGGGTCTGTAGCAGCCC 59.778 63.158 15.81 15.81 43.30 5.19
43 44 1.222113 GGAAGGGTCTGTAGCAGCC 59.778 63.158 0.00 0.00 0.00 4.85
44 45 0.543749 ATGGAAGGGTCTGTAGCAGC 59.456 55.000 0.00 0.00 0.00 5.25
45 46 4.487714 TTTATGGAAGGGTCTGTAGCAG 57.512 45.455 0.00 0.00 0.00 4.24
46 47 4.473196 TGATTTATGGAAGGGTCTGTAGCA 59.527 41.667 0.00 0.00 0.00 3.49
47 48 5.036117 TGATTTATGGAAGGGTCTGTAGC 57.964 43.478 0.00 0.00 0.00 3.58
48 49 9.627123 TTTATTGATTTATGGAAGGGTCTGTAG 57.373 33.333 0.00 0.00 0.00 2.74
50 51 8.917088 CATTTATTGATTTATGGAAGGGTCTGT 58.083 33.333 0.00 0.00 0.00 3.41
51 52 7.869429 GCATTTATTGATTTATGGAAGGGTCTG 59.131 37.037 0.00 0.00 0.00 3.51
52 53 7.015584 GGCATTTATTGATTTATGGAAGGGTCT 59.984 37.037 0.00 0.00 0.00 3.85
53 54 7.154656 GGCATTTATTGATTTATGGAAGGGTC 58.845 38.462 0.00 0.00 0.00 4.46
54 55 6.043127 GGGCATTTATTGATTTATGGAAGGGT 59.957 38.462 0.00 0.00 0.00 4.34
55 56 6.466812 GGGCATTTATTGATTTATGGAAGGG 58.533 40.000 0.00 0.00 0.00 3.95
56 57 6.466812 GGGGCATTTATTGATTTATGGAAGG 58.533 40.000 0.00 0.00 0.00 3.46
57 58 6.466812 GGGGGCATTTATTGATTTATGGAAG 58.533 40.000 0.00 0.00 0.00 3.46
58 59 6.432403 GGGGGCATTTATTGATTTATGGAA 57.568 37.500 0.00 0.00 0.00 3.53
365 366 5.743636 TTTCTGAAATGGCAGGCTTTAAT 57.256 34.783 0.00 0.00 36.55 1.40
366 367 5.245751 TGATTTCTGAAATGGCAGGCTTTAA 59.754 36.000 19.59 0.00 36.55 1.52
367 368 4.771577 TGATTTCTGAAATGGCAGGCTTTA 59.228 37.500 19.59 0.00 36.55 1.85
368 369 3.579586 TGATTTCTGAAATGGCAGGCTTT 59.420 39.130 19.59 0.00 36.55 3.51
369 370 3.056322 GTGATTTCTGAAATGGCAGGCTT 60.056 43.478 19.59 0.00 36.55 4.35
370 371 2.494870 GTGATTTCTGAAATGGCAGGCT 59.505 45.455 19.59 0.00 36.55 4.58
371 372 2.417787 GGTGATTTCTGAAATGGCAGGC 60.418 50.000 19.59 5.49 36.55 4.85
372 373 2.167075 GGGTGATTTCTGAAATGGCAGG 59.833 50.000 19.59 0.00 36.55 4.85
373 374 2.167075 GGGGTGATTTCTGAAATGGCAG 59.833 50.000 19.59 0.00 37.24 4.85
374 375 2.178580 GGGGTGATTTCTGAAATGGCA 58.821 47.619 19.59 9.90 0.00 4.92
375 376 2.460669 AGGGGTGATTTCTGAAATGGC 58.539 47.619 19.59 11.48 0.00 4.40
376 377 6.211384 AGTTTAAGGGGTGATTTCTGAAATGG 59.789 38.462 19.59 0.00 0.00 3.16
377 378 7.039784 TGAGTTTAAGGGGTGATTTCTGAAATG 60.040 37.037 19.59 0.00 0.00 2.32
378 379 7.010160 TGAGTTTAAGGGGTGATTTCTGAAAT 58.990 34.615 15.09 15.09 0.00 2.17
379 380 6.369629 TGAGTTTAAGGGGTGATTTCTGAAA 58.630 36.000 5.15 5.15 0.00 2.69
380 381 5.947663 TGAGTTTAAGGGGTGATTTCTGAA 58.052 37.500 0.00 0.00 0.00 3.02
381 382 5.576563 TGAGTTTAAGGGGTGATTTCTGA 57.423 39.130 0.00 0.00 0.00 3.27
382 383 5.711976 ACATGAGTTTAAGGGGTGATTTCTG 59.288 40.000 0.00 0.00 0.00 3.02
383 384 5.892348 ACATGAGTTTAAGGGGTGATTTCT 58.108 37.500 0.00 0.00 0.00 2.52
384 385 7.393515 ACTTACATGAGTTTAAGGGGTGATTTC 59.606 37.037 0.00 0.00 30.73 2.17
385 386 7.176690 CACTTACATGAGTTTAAGGGGTGATTT 59.823 37.037 0.00 0.00 30.73 2.17
386 387 6.659242 CACTTACATGAGTTTAAGGGGTGATT 59.341 38.462 0.00 0.00 30.73 2.57
387 388 6.180472 CACTTACATGAGTTTAAGGGGTGAT 58.820 40.000 0.00 0.00 30.73 3.06
388 389 5.072600 ACACTTACATGAGTTTAAGGGGTGA 59.927 40.000 0.00 0.00 33.64 4.02
389 390 5.313712 ACACTTACATGAGTTTAAGGGGTG 58.686 41.667 0.00 0.00 33.64 4.61
390 391 5.578157 ACACTTACATGAGTTTAAGGGGT 57.422 39.130 0.00 0.00 33.64 4.95
391 392 6.264518 ACAAACACTTACATGAGTTTAAGGGG 59.735 38.462 0.00 0.00 33.64 4.79
392 393 7.272037 ACAAACACTTACATGAGTTTAAGGG 57.728 36.000 0.00 0.12 35.23 3.95
393 394 9.825972 CATACAAACACTTACATGAGTTTAAGG 57.174 33.333 0.00 0.00 33.30 2.69
396 397 9.772973 AGACATACAAACACTTACATGAGTTTA 57.227 29.630 0.00 0.00 33.30 2.01
397 398 8.677148 AGACATACAAACACTTACATGAGTTT 57.323 30.769 0.00 0.00 34.78 2.66
398 399 9.424319 CTAGACATACAAACACTTACATGAGTT 57.576 33.333 0.00 0.00 0.00 3.01
399 400 7.545965 GCTAGACATACAAACACTTACATGAGT 59.454 37.037 0.00 0.00 0.00 3.41
400 401 7.545615 TGCTAGACATACAAACACTTACATGAG 59.454 37.037 0.00 0.00 0.00 2.90
401 402 7.382898 TGCTAGACATACAAACACTTACATGA 58.617 34.615 0.00 0.00 0.00 3.07
402 403 7.595311 TGCTAGACATACAAACACTTACATG 57.405 36.000 0.00 0.00 0.00 3.21
403 404 8.615878 TTTGCTAGACATACAAACACTTACAT 57.384 30.769 0.00 0.00 0.00 2.29
404 405 7.307751 GCTTTGCTAGACATACAAACACTTACA 60.308 37.037 0.00 0.00 0.00 2.41
405 406 7.015877 GCTTTGCTAGACATACAAACACTTAC 58.984 38.462 0.00 0.00 0.00 2.34
406 407 6.934645 AGCTTTGCTAGACATACAAACACTTA 59.065 34.615 0.00 0.00 36.99 2.24
407 408 5.765182 AGCTTTGCTAGACATACAAACACTT 59.235 36.000 0.00 0.00 36.99 3.16
408 409 5.308825 AGCTTTGCTAGACATACAAACACT 58.691 37.500 0.00 0.00 36.99 3.55
409 410 5.613358 AGCTTTGCTAGACATACAAACAC 57.387 39.130 0.00 0.00 36.99 3.32
410 411 4.388773 CGAGCTTTGCTAGACATACAAACA 59.611 41.667 0.00 0.00 39.88 2.83
411 412 4.725169 GCGAGCTTTGCTAGACATACAAAC 60.725 45.833 4.76 0.00 39.88 2.93
412 413 3.370978 GCGAGCTTTGCTAGACATACAAA 59.629 43.478 4.76 0.00 39.88 2.83
413 414 2.930040 GCGAGCTTTGCTAGACATACAA 59.070 45.455 4.76 0.00 39.88 2.41
414 415 2.166459 AGCGAGCTTTGCTAGACATACA 59.834 45.455 12.22 0.00 41.87 2.29
415 416 2.815478 AGCGAGCTTTGCTAGACATAC 58.185 47.619 12.22 0.00 41.87 2.39
416 417 3.526931 AAGCGAGCTTTGCTAGACATA 57.473 42.857 13.96 0.00 43.14 2.29
417 418 2.393271 AAGCGAGCTTTGCTAGACAT 57.607 45.000 13.96 0.00 43.14 3.06
418 419 3.526931 ATAAGCGAGCTTTGCTAGACA 57.473 42.857 15.90 0.00 43.14 3.41
419 420 4.866682 AAATAAGCGAGCTTTGCTAGAC 57.133 40.909 15.90 0.00 43.14 2.59
420 421 5.880054 AAAAATAAGCGAGCTTTGCTAGA 57.120 34.783 15.90 6.81 43.14 2.43
446 447 0.171455 AGATTCAGCGTCGACAGACC 59.829 55.000 17.16 0.30 44.28 3.85
469 470 0.036294 CCCTCCCCTTTGTTCGAGTC 60.036 60.000 0.00 0.00 0.00 3.36
471 472 1.299976 CCCCTCCCCTTTGTTCGAG 59.700 63.158 0.00 0.00 0.00 4.04
491 492 6.583806 GGTCACACAAGATTTCAATCATTGAC 59.416 38.462 0.00 11.29 39.87 3.18
502 503 1.956477 GTGCTGGGTCACACAAGATTT 59.044 47.619 0.00 0.00 36.77 2.17
541 555 2.420129 GGTGGATTTGCTGTCGACCTAT 60.420 50.000 14.12 0.00 40.20 2.57
543 557 0.321653 GGTGGATTTGCTGTCGACCT 60.322 55.000 14.12 0.00 40.20 3.85
575 589 1.485066 GACGGATTCCATGGGTGTAGT 59.515 52.381 13.02 7.34 0.00 2.73
576 590 1.202651 GGACGGATTCCATGGGTGTAG 60.203 57.143 13.02 3.92 45.10 2.74
577 591 0.834612 GGACGGATTCCATGGGTGTA 59.165 55.000 13.02 0.00 45.10 2.90
638 656 3.064682 TGTGTGAGTTTGTGTACATGTGC 59.935 43.478 9.11 8.01 0.00 4.57
639 657 4.873768 TGTGTGAGTTTGTGTACATGTG 57.126 40.909 9.11 0.00 0.00 3.21
644 662 5.500290 CGTCTTCTTGTGTGAGTTTGTGTAC 60.500 44.000 0.00 0.00 0.00 2.90
662 680 4.821589 CTGGGCCTCGGCGTCTTC 62.822 72.222 6.85 0.00 43.06 2.87
777 819 2.580867 TTTGGTTTGTGTGCGCGC 60.581 55.556 27.26 27.26 0.00 6.86
778 820 2.227568 GGTTTGGTTTGTGTGCGCG 61.228 57.895 0.00 0.00 0.00 6.86
781 828 1.066303 TCGATGGTTTGGTTTGTGTGC 59.934 47.619 0.00 0.00 0.00 4.57
798 850 2.094545 CACACTCCACTGATGTCATCGA 60.095 50.000 8.29 0.00 0.00 3.59
867 919 3.424105 GAGAGGGCAATGGGGGCT 61.424 66.667 0.00 0.00 0.00 5.19
885 937 2.386661 GGAAAGAACCGATCAGCAGA 57.613 50.000 0.00 0.00 0.00 4.26
930 1124 1.376942 CAAGAGCCAGCCTGACAGG 60.377 63.158 17.83 17.83 38.80 4.00
980 1174 0.252284 GGACCTGGACTTCCTCCTCA 60.252 60.000 0.00 0.00 40.26 3.86
981 1175 0.252284 TGGACCTGGACTTCCTCCTC 60.252 60.000 0.00 0.00 40.26 3.71
1078 1283 2.027325 CACAAGCAGCAACAGCAGA 58.973 52.632 0.00 0.00 0.00 4.26
1502 1716 2.805353 CGTCGTTGTCCTCCGCTG 60.805 66.667 0.00 0.00 0.00 5.18
1503 1717 2.981909 TCGTCGTTGTCCTCCGCT 60.982 61.111 0.00 0.00 0.00 5.52
1508 1722 4.353437 GCCCGTCGTCGTTGTCCT 62.353 66.667 0.71 0.00 35.01 3.85
1572 1789 1.354337 CGAAGATGTGCACCGTCCTG 61.354 60.000 15.69 2.05 0.00 3.86
1627 1844 3.056749 AGTGTAGCTCTTTCCCGTTGTAG 60.057 47.826 0.00 0.00 0.00 2.74
1631 1848 1.275573 GGAGTGTAGCTCTTTCCCGTT 59.724 52.381 0.00 0.00 43.62 4.44
1636 1853 1.623811 TGGTGGGAGTGTAGCTCTTTC 59.376 52.381 0.00 0.00 43.62 2.62
1637 1854 1.625818 CTGGTGGGAGTGTAGCTCTTT 59.374 52.381 0.00 0.00 43.62 2.52
1649 1866 2.361483 TACGCTACGCTGGTGGGA 60.361 61.111 0.00 0.00 0.00 4.37
1652 1869 2.158959 GCTGTACGCTACGCTGGTG 61.159 63.158 2.99 0.00 35.14 4.17
1663 1880 2.407846 ATCCGCGGATGAGCTGTACG 62.408 60.000 38.62 1.24 32.98 3.67
1664 1881 0.664767 GATCCGCGGATGAGCTGTAC 60.665 60.000 43.46 23.00 34.60 2.90
1665 1882 0.823769 AGATCCGCGGATGAGCTGTA 60.824 55.000 43.46 13.24 34.60 2.74
1666 1883 2.081425 GAGATCCGCGGATGAGCTGT 62.081 60.000 43.46 20.71 34.60 4.40
1668 1885 2.569354 GGAGATCCGCGGATGAGCT 61.569 63.158 43.46 32.69 34.60 4.09
1669 1886 2.048690 GGAGATCCGCGGATGAGC 60.049 66.667 43.46 28.70 34.60 4.26
1670 1887 1.288439 CAGGAGATCCGCGGATGAG 59.712 63.158 43.46 23.21 42.08 2.90
1671 1888 1.455773 ACAGGAGATCCGCGGATGA 60.456 57.895 43.46 17.62 42.08 2.92
1674 1891 3.147595 CCACAGGAGATCCGCGGA 61.148 66.667 33.12 33.12 42.08 5.54
1675 1892 3.147595 TCCACAGGAGATCCGCGG 61.148 66.667 22.12 22.12 42.08 6.46
1676 1893 2.105128 GTCCACAGGAGATCCGCG 59.895 66.667 0.00 0.00 42.08 6.46
1677 1894 1.142748 CAGTCCACAGGAGATCCGC 59.857 63.158 0.00 0.00 42.08 5.54
1680 1897 2.158986 CCATGACAGTCCACAGGAGATC 60.159 54.545 0.00 0.00 29.39 2.75
1682 1899 1.269958 CCATGACAGTCCACAGGAGA 58.730 55.000 0.00 0.00 29.39 3.71
1684 1901 0.473694 ACCCATGACAGTCCACAGGA 60.474 55.000 0.00 0.00 0.00 3.86
1685 1902 0.036010 GACCCATGACAGTCCACAGG 60.036 60.000 0.00 0.00 0.00 4.00
1687 1904 0.686789 CAGACCCATGACAGTCCACA 59.313 55.000 0.00 0.00 33.29 4.17
1688 1905 0.976641 TCAGACCCATGACAGTCCAC 59.023 55.000 0.00 0.00 33.29 4.02
1689 1906 1.956869 ATCAGACCCATGACAGTCCA 58.043 50.000 0.00 0.00 33.29 4.02
1691 1908 3.034635 ACCTATCAGACCCATGACAGTC 58.965 50.000 0.00 0.00 30.46 3.51
1692 1909 2.768527 CACCTATCAGACCCATGACAGT 59.231 50.000 0.00 0.00 30.46 3.55
1693 1910 2.484417 GCACCTATCAGACCCATGACAG 60.484 54.545 0.00 0.00 30.46 3.51
1694 1911 1.486310 GCACCTATCAGACCCATGACA 59.514 52.381 0.00 0.00 30.46 3.58
1695 1912 1.486310 TGCACCTATCAGACCCATGAC 59.514 52.381 0.00 0.00 30.46 3.06
1696 1913 1.878211 TGCACCTATCAGACCCATGA 58.122 50.000 0.00 0.00 0.00 3.07
1697 1914 2.105306 TGATGCACCTATCAGACCCATG 59.895 50.000 0.00 0.00 32.39 3.66
1698 1915 2.411583 TGATGCACCTATCAGACCCAT 58.588 47.619 0.00 0.00 32.39 4.00
1699 1916 1.878211 TGATGCACCTATCAGACCCA 58.122 50.000 0.00 0.00 32.39 4.51
1700 1917 2.945668 GTTTGATGCACCTATCAGACCC 59.054 50.000 0.00 0.00 38.25 4.46
1703 1920 3.628942 GCATGTTTGATGCACCTATCAGA 59.371 43.478 0.00 0.00 44.00 3.27
1704 1921 3.243301 GGCATGTTTGATGCACCTATCAG 60.243 47.826 8.78 0.00 46.21 2.90
1705 1922 2.689471 GGCATGTTTGATGCACCTATCA 59.311 45.455 8.78 0.00 46.21 2.15
1706 1923 2.287188 CGGCATGTTTGATGCACCTATC 60.287 50.000 8.78 0.00 46.21 2.08
1707 1924 1.677576 CGGCATGTTTGATGCACCTAT 59.322 47.619 8.78 0.00 46.21 2.57
1708 1925 1.093972 CGGCATGTTTGATGCACCTA 58.906 50.000 8.78 0.00 46.21 3.08
1709 1926 0.608856 TCGGCATGTTTGATGCACCT 60.609 50.000 8.78 0.00 46.21 4.00
1711 1928 1.339711 GTTCGGCATGTTTGATGCAC 58.660 50.000 8.78 0.00 46.21 4.57
1714 1931 1.135315 CCTGGTTCGGCATGTTTGATG 60.135 52.381 0.00 0.00 0.00 3.07
1715 1932 1.176527 CCTGGTTCGGCATGTTTGAT 58.823 50.000 0.00 0.00 0.00 2.57
1716 1933 2.639970 CCTGGTTCGGCATGTTTGA 58.360 52.632 0.00 0.00 0.00 2.69
1725 1942 4.452733 GGAGACGGCCTGGTTCGG 62.453 72.222 0.00 0.00 0.00 4.30
1726 1943 4.452733 GGGAGACGGCCTGGTTCG 62.453 72.222 0.00 9.37 0.00 3.95
1727 1944 3.316573 CTGGGAGACGGCCTGGTTC 62.317 68.421 0.00 0.00 0.00 3.62
1728 1945 3.322466 CTGGGAGACGGCCTGGTT 61.322 66.667 0.00 0.00 0.00 3.67
1729 1946 2.741878 TAACTGGGAGACGGCCTGGT 62.742 60.000 0.00 0.00 0.00 4.00
1731 1948 0.541863 AATAACTGGGAGACGGCCTG 59.458 55.000 0.00 0.00 0.00 4.85
1733 1950 2.558378 GTTAATAACTGGGAGACGGCC 58.442 52.381 0.00 0.00 0.00 6.13
1734 1951 2.558378 GGTTAATAACTGGGAGACGGC 58.442 52.381 2.96 0.00 0.00 5.68
1735 1952 2.482490 CGGGTTAATAACTGGGAGACGG 60.482 54.545 2.96 0.00 0.00 4.79
1736 1953 2.428171 TCGGGTTAATAACTGGGAGACG 59.572 50.000 2.96 0.00 0.00 4.18
1737 1954 3.740452 GCTCGGGTTAATAACTGGGAGAC 60.740 52.174 16.55 8.63 0.00 3.36
1738 1955 2.433239 GCTCGGGTTAATAACTGGGAGA 59.567 50.000 16.55 5.30 0.00 3.71
1739 1956 2.484947 GGCTCGGGTTAATAACTGGGAG 60.485 54.545 2.96 8.24 0.00 4.30
1740 1957 1.487558 GGCTCGGGTTAATAACTGGGA 59.512 52.381 2.96 0.00 0.00 4.37
1742 1959 2.169769 TGAGGCTCGGGTTAATAACTGG 59.830 50.000 10.42 0.00 0.00 4.00
1743 1960 3.536956 TGAGGCTCGGGTTAATAACTG 57.463 47.619 10.42 0.00 0.00 3.16
1744 1961 4.451900 CATTGAGGCTCGGGTTAATAACT 58.548 43.478 10.42 0.00 0.00 2.24
1745 1962 3.003378 GCATTGAGGCTCGGGTTAATAAC 59.997 47.826 10.42 0.00 0.00 1.89
1746 1963 3.211045 GCATTGAGGCTCGGGTTAATAA 58.789 45.455 10.42 0.00 0.00 1.40
1747 1964 2.171659 TGCATTGAGGCTCGGGTTAATA 59.828 45.455 10.42 0.00 34.04 0.98
1748 1965 1.064758 TGCATTGAGGCTCGGGTTAAT 60.065 47.619 10.42 0.42 34.04 1.40
1749 1966 0.326595 TGCATTGAGGCTCGGGTTAA 59.673 50.000 10.42 0.00 34.04 2.01
1750 1967 0.392461 GTGCATTGAGGCTCGGGTTA 60.392 55.000 10.42 0.00 34.04 2.85
1751 1968 1.675641 GTGCATTGAGGCTCGGGTT 60.676 57.895 10.42 0.00 34.04 4.11
1752 1969 2.045926 GTGCATTGAGGCTCGGGT 60.046 61.111 10.42 0.00 34.04 5.28
1753 1970 1.651240 CTTGTGCATTGAGGCTCGGG 61.651 60.000 10.42 2.74 34.04 5.14
1754 1971 0.674581 TCTTGTGCATTGAGGCTCGG 60.675 55.000 10.42 3.12 34.04 4.63
1755 1972 1.063616 CATCTTGTGCATTGAGGCTCG 59.936 52.381 10.42 0.00 34.04 5.03
1756 1973 2.846039 CATCTTGTGCATTGAGGCTC 57.154 50.000 7.79 7.79 34.04 4.70
1775 1992 2.459934 CTTGTGTTCTTTTTCACCGGC 58.540 47.619 0.00 0.00 34.14 6.13
1784 2001 2.158957 TGTCCTCTCGCTTGTGTTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
1786 2003 1.040646 TGTCCTCTCGCTTGTGTTCT 58.959 50.000 0.00 0.00 0.00 3.01
1787 2004 1.795286 CTTGTCCTCTCGCTTGTGTTC 59.205 52.381 0.00 0.00 0.00 3.18
1789 2006 0.034059 CCTTGTCCTCTCGCTTGTGT 59.966 55.000 0.00 0.00 0.00 3.72
1790 2007 0.318441 TCCTTGTCCTCTCGCTTGTG 59.682 55.000 0.00 0.00 0.00 3.33
1792 2009 1.674221 CCTTCCTTGTCCTCTCGCTTG 60.674 57.143 0.00 0.00 0.00 4.01
1793 2010 0.610687 CCTTCCTTGTCCTCTCGCTT 59.389 55.000 0.00 0.00 0.00 4.68
1794 2011 0.251832 TCCTTCCTTGTCCTCTCGCT 60.252 55.000 0.00 0.00 0.00 4.93
1795 2012 0.608640 TTCCTTCCTTGTCCTCTCGC 59.391 55.000 0.00 0.00 0.00 5.03
1796 2013 2.234908 ACATTCCTTCCTTGTCCTCTCG 59.765 50.000 0.00 0.00 0.00 4.04
1821 2124 6.395629 CCGAACCTACTCTGACAATTTTCTA 58.604 40.000 0.00 0.00 0.00 2.10
1823 2126 4.142881 GCCGAACCTACTCTGACAATTTTC 60.143 45.833 0.00 0.00 0.00 2.29
1867 2170 2.349580 CGTAAGCAGTCACCATGTCATG 59.650 50.000 5.79 5.79 0.00 3.07
1868 2171 2.621338 CGTAAGCAGTCACCATGTCAT 58.379 47.619 0.00 0.00 0.00 3.06
1903 2206 2.430546 AAAAACATCGCGGCATTTCA 57.569 40.000 6.13 0.00 0.00 2.69
1930 2233 3.931578 AGTCACAGCTCACAGATTTACC 58.068 45.455 0.00 0.00 0.00 2.85
1937 2240 2.245159 TTCCAAGTCACAGCTCACAG 57.755 50.000 0.00 0.00 0.00 3.66
1963 2266 4.794169 ACAACGATTTGCATAGGACAAAC 58.206 39.130 0.00 0.00 39.65 2.93
1974 2277 4.083537 TGGTGTAGATCAACAACGATTTGC 60.084 41.667 0.00 0.00 41.17 3.68
2023 2326 6.560253 ACTCGTCTGATAGCAATTTTGTTT 57.440 33.333 0.00 0.00 0.00 2.83
2025 2328 5.163953 CGAACTCGTCTGATAGCAATTTTGT 60.164 40.000 0.00 0.00 34.11 2.83
2056 2393 4.379243 AGGACGCAGCAGTTCCCG 62.379 66.667 0.00 0.00 0.00 5.14
2058 2395 2.435059 GGAGGACGCAGCAGTTCC 60.435 66.667 0.00 0.00 0.00 3.62
2062 2399 2.249413 AATCAGGGAGGACGCAGCAG 62.249 60.000 0.00 0.00 0.00 4.24
2095 2435 1.370657 GGCATCCGTCGACGAGATC 60.371 63.158 37.65 25.29 43.02 2.75
2096 2436 2.722487 GGCATCCGTCGACGAGAT 59.278 61.111 37.65 30.82 43.02 2.75
2097 2437 3.872728 CGGCATCCGTCGACGAGA 61.873 66.667 37.65 30.11 45.23 4.04
2107 2447 2.046285 CAAAGGGACCACGGCATCC 61.046 63.158 0.00 0.00 0.00 3.51
2108 2448 2.700773 GCAAAGGGACCACGGCATC 61.701 63.158 0.00 0.00 0.00 3.91
2109 2449 2.676471 GCAAAGGGACCACGGCAT 60.676 61.111 0.00 0.00 0.00 4.40
2110 2450 4.966787 GGCAAAGGGACCACGGCA 62.967 66.667 0.00 0.00 0.00 5.69
2112 2452 4.636435 ACGGCAAAGGGACCACGG 62.636 66.667 0.00 0.00 0.00 4.94
2113 2453 3.353836 CACGGCAAAGGGACCACG 61.354 66.667 0.00 0.00 0.00 4.94
2114 2454 1.303317 ATCACGGCAAAGGGACCAC 60.303 57.895 0.00 0.00 0.00 4.16
2115 2455 1.002624 GATCACGGCAAAGGGACCA 60.003 57.895 0.00 0.00 0.00 4.02
2116 2456 0.744771 GAGATCACGGCAAAGGGACC 60.745 60.000 0.00 0.00 0.00 4.46
2175 2528 1.060713 CGTCACGTTGAGACCATCAC 58.939 55.000 0.00 0.00 37.77 3.06
2259 2619 8.180920 GGAAAATATTCTTCTCTGTTTGAGAGC 58.819 37.037 0.00 0.00 41.09 4.09
2296 2656 4.754618 TGATGTACGAAATGCAGACAAACT 59.245 37.500 0.00 0.00 0.00 2.66
2305 2665 4.864806 TCTGAACTCTGATGTACGAAATGC 59.135 41.667 0.00 0.00 0.00 3.56
2316 2676 8.868522 TGGATAACAATTTTCTGAACTCTGAT 57.131 30.769 0.00 0.00 0.00 2.90
2325 2685 3.768757 TGGCCCTGGATAACAATTTTCTG 59.231 43.478 0.00 0.00 0.00 3.02
2331 2691 1.134098 CGTCTGGCCCTGGATAACAAT 60.134 52.381 0.00 0.00 0.00 2.71
2333 2693 1.622607 CCGTCTGGCCCTGGATAACA 61.623 60.000 0.00 0.00 0.00 2.41
2334 2694 1.146263 CCGTCTGGCCCTGGATAAC 59.854 63.158 0.00 0.00 0.00 1.89
2335 2695 1.002403 TCCGTCTGGCCCTGGATAA 59.998 57.895 0.00 0.00 34.14 1.75
2336 2696 1.457643 CTCCGTCTGGCCCTGGATA 60.458 63.158 0.00 0.00 34.14 2.59
2397 2757 8.261522 AGTTTTCAGATAGGGTTCTTATCTCAC 58.738 37.037 0.00 0.00 0.00 3.51
2455 2815 3.321682 CCAAAACACATGGGTCAGTTGAT 59.678 43.478 16.62 0.00 34.15 2.57
2520 2880 6.212955 TCGCTTTATTCTTCCTTGGTTTTTG 58.787 36.000 0.00 0.00 0.00 2.44
2584 2945 0.944386 TGCGCAACTTTGAAGACCTC 59.056 50.000 8.16 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.