Multiple sequence alignment - TraesCS1D01G164800

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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 TraesCS1D01G164800 chr1D 100.000 6796 0 0 1 6796 235679222 235672427 0.000000e+00 12550.0
1 TraesCS1D01G164800 chr1D 100.000 67 0 0 1 67 439321321 439321255 2.570000e-24 124.0
2 TraesCS1D01G164800 chr1D 98.551 69 1 0 1 69 482468524 482468456 9.260000e-24 122.0
3 TraesCS1D01G164800 chr1D 85.714 56 8 0 5010 5065 18070582 18070637 7.360000e-05 60.2
4 TraesCS1D01G164800 chr1B 97.084 4732 73 18 1388 6096 341140085 341135396 0.000000e+00 7914.0
5 TraesCS1D01G164800 chr1B 87.549 763 28 19 580 1298 341141231 341140492 0.000000e+00 821.0
6 TraesCS1D01G164800 chr1B 93.434 198 9 3 68 263 341142800 341142605 2.400000e-74 291.0
7 TraesCS1D01G164800 chr1B 83.750 240 15 9 259 486 341141460 341141233 8.930000e-49 206.0
8 TraesCS1D01G164800 chr1A 92.600 3392 141 41 577 3895 310246545 310249899 0.000000e+00 4772.0
9 TraesCS1D01G164800 chr1A 94.627 2587 91 25 3888 6456 310252755 310255311 0.000000e+00 3964.0
10 TraesCS1D01G164800 chr1A 84.174 436 40 16 73 497 310246132 310246549 4.940000e-106 396.0
11 TraesCS1D01G164800 chr1A 88.387 310 17 5 6490 6796 310255310 310255603 8.380000e-94 355.0
12 TraesCS1D01G164800 chr3B 83.230 161 21 3 5008 5168 526293649 526293495 7.100000e-30 143.0
13 TraesCS1D01G164800 chr7D 98.551 69 1 0 1 69 515167552 515167620 9.260000e-24 122.0
14 TraesCS1D01G164800 chr7A 98.551 69 1 0 1 69 92120143 92120211 9.260000e-24 122.0
15 TraesCS1D01G164800 chr7A 98.551 69 1 0 1 69 499693153 499693085 9.260000e-24 122.0
16 TraesCS1D01G164800 chr7A 78.882 161 32 2 5008 5167 652541907 652541748 2.590000e-19 108.0
17 TraesCS1D01G164800 chr5D 98.551 69 1 0 1 69 403679224 403679292 9.260000e-24 122.0
18 TraesCS1D01G164800 chr4A 96.000 75 2 1 1 74 338991278 338991204 3.330000e-23 121.0
19 TraesCS1D01G164800 chr4A 79.787 188 21 10 5009 5191 379043622 379043447 3.330000e-23 121.0
20 TraesCS1D01G164800 chr5A 94.805 77 3 1 1 76 275523811 275523887 1.200000e-22 119.0
21 TraesCS1D01G164800 chr5A 79.459 185 24 10 5015 5195 410506450 410506276 1.200000e-22 119.0
22 TraesCS1D01G164800 chr3A 94.805 77 2 2 1 75 195884458 195884382 1.200000e-22 119.0
23 TraesCS1D01G164800 chr4D 78.723 188 22 12 5009 5191 211055819 211055645 7.210000e-20 110.0
24 TraesCS1D01G164800 chr4B 78.723 188 22 14 5009 5191 327536094 327535920 7.210000e-20 110.0
25 TraesCS1D01G164800 chr4B 83.036 112 14 4 5080 5189 93286338 93286446 5.610000e-16 97.1
26 TraesCS1D01G164800 chr5B 78.857 175 24 10 5016 5185 364134125 364133959 9.320000e-19 106.0


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 TraesCS1D01G164800 chr1D 235672427 235679222 6795 True 12550.00 12550 100.00000 1 6796 1 chr1D.!!$R1 6795
1 TraesCS1D01G164800 chr1B 341135396 341142800 7404 True 2308.00 7914 90.45425 68 6096 4 chr1B.!!$R1 6028
2 TraesCS1D01G164800 chr1A 310246132 310255603 9471 False 2371.75 4772 89.94700 73 6796 4 chr1A.!!$F1 6723

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
495 1665 0.035152 ACATCAAGCATTCCCGCAGA 60.035 50.000 0.00 0.0 0.00 4.26 F
502 1672 0.169009 GCATTCCCGCAGAACAGTTC 59.831 55.000 5.00 5.0 37.29 3.01 F
1452 3004 0.666913 GCCGTCTCTGGTCGCTAATA 59.333 55.000 0.00 0.0 0.00 0.98 F
2358 3937 1.078848 CTCCTTGCAGGTTCTCCCG 60.079 63.158 0.00 0.0 36.53 5.14 F
2729 4310 0.888736 TGTGCAGGTATGTGTGTGCC 60.889 55.000 0.00 0.0 34.91 5.01 F
4134 8599 2.436646 CCCATGGACACCGACAGC 60.437 66.667 15.22 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 3172 0.456628 CACGCATGCCAATCCATCAA 59.543 50.000 13.15 0.0 0.00 2.57 R
1658 3214 1.063469 CACGTCAAACACCCAGTTCAC 59.937 52.381 0.00 0.0 40.26 3.18 R
2729 4310 1.806542 AGCAACCAAAGTATGACTGCG 59.193 47.619 0.00 0.0 39.80 5.18 R
3618 5201 4.982241 AGGAGTTGGATGTCTTTTCTGA 57.018 40.909 0.00 0.0 0.00 3.27 R
4482 8948 5.503927 ACATGCTTGAATACATCTTCAGGT 58.496 37.500 6.60 0.0 36.55 4.00 R
5803 10271 0.249911 GTCTGTTCGGGTGTGCTTCT 60.250 55.000 0.00 0.0 0.00 2.85 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
20 21 3.306472 TTGGTCAAACTTGCCTAACCT 57.694 42.857 0.00 0.00 0.00 3.50
21 22 3.306472 TGGTCAAACTTGCCTAACCTT 57.694 42.857 0.00 0.00 0.00 3.50
22 23 4.440826 TGGTCAAACTTGCCTAACCTTA 57.559 40.909 0.00 0.00 0.00 2.69
23 24 4.394729 TGGTCAAACTTGCCTAACCTTAG 58.605 43.478 0.00 0.00 0.00 2.18
24 25 4.103469 TGGTCAAACTTGCCTAACCTTAGA 59.897 41.667 0.00 0.00 32.47 2.10
25 26 5.222048 TGGTCAAACTTGCCTAACCTTAGAT 60.222 40.000 0.00 0.00 32.47 1.98
26 27 5.123979 GGTCAAACTTGCCTAACCTTAGATG 59.876 44.000 0.00 0.00 32.47 2.90
27 28 5.705905 GTCAAACTTGCCTAACCTTAGATGT 59.294 40.000 0.00 0.00 32.47 3.06
28 29 5.705441 TCAAACTTGCCTAACCTTAGATGTG 59.295 40.000 0.00 0.00 32.47 3.21
29 30 4.222124 ACTTGCCTAACCTTAGATGTGG 57.778 45.455 0.00 0.00 32.47 4.17
30 31 2.710096 TGCCTAACCTTAGATGTGGC 57.290 50.000 0.00 0.00 39.33 5.01
31 32 1.912731 TGCCTAACCTTAGATGTGGCA 59.087 47.619 0.00 0.00 45.31 4.92
32 33 2.307392 TGCCTAACCTTAGATGTGGCAA 59.693 45.455 0.00 0.00 44.67 4.52
33 34 3.053693 TGCCTAACCTTAGATGTGGCAAT 60.054 43.478 0.00 0.00 44.67 3.56
34 35 3.565902 GCCTAACCTTAGATGTGGCAATC 59.434 47.826 0.00 0.00 38.79 2.67
35 36 4.687219 GCCTAACCTTAGATGTGGCAATCT 60.687 45.833 13.90 13.90 40.12 2.40
36 37 5.440610 CCTAACCTTAGATGTGGCAATCTT 58.559 41.667 14.42 3.22 37.98 2.40
37 38 5.888161 CCTAACCTTAGATGTGGCAATCTTT 59.112 40.000 14.42 7.87 37.98 2.52
38 39 5.649782 AACCTTAGATGTGGCAATCTTTG 57.350 39.130 14.42 9.40 37.98 2.77
39 40 4.019174 ACCTTAGATGTGGCAATCTTTGG 58.981 43.478 14.42 16.41 37.98 3.28
40 41 9.491442 CTAACCTTAGATGTGGCAATCTTTGGC 62.491 44.444 14.42 6.83 43.34 4.52
51 52 4.870363 GCAATCTTTGGCAAAGTTAGTCA 58.130 39.130 32.46 17.32 39.52 3.41
52 53 4.681483 GCAATCTTTGGCAAAGTTAGTCAC 59.319 41.667 32.46 16.68 39.52 3.67
53 54 5.735922 GCAATCTTTGGCAAAGTTAGTCACA 60.736 40.000 32.46 16.01 39.52 3.58
54 55 6.272318 CAATCTTTGGCAAAGTTAGTCACAA 58.728 36.000 32.46 15.37 39.52 3.33
55 56 5.906113 TCTTTGGCAAAGTTAGTCACAAA 57.094 34.783 32.46 12.18 39.52 2.83
56 57 5.646606 TCTTTGGCAAAGTTAGTCACAAAC 58.353 37.500 32.46 0.00 39.52 2.93
57 58 4.379339 TTGGCAAAGTTAGTCACAAACC 57.621 40.909 0.00 0.00 0.00 3.27
58 59 3.357203 TGGCAAAGTTAGTCACAAACCA 58.643 40.909 0.00 0.00 0.00 3.67
59 60 3.764434 TGGCAAAGTTAGTCACAAACCAA 59.236 39.130 0.00 0.00 0.00 3.67
60 61 4.220821 TGGCAAAGTTAGTCACAAACCAAA 59.779 37.500 0.00 0.00 0.00 3.28
61 62 4.565166 GGCAAAGTTAGTCACAAACCAAAC 59.435 41.667 0.00 0.00 0.00 2.93
62 63 5.164954 GCAAAGTTAGTCACAAACCAAACA 58.835 37.500 0.00 0.00 30.35 2.83
63 64 5.288472 GCAAAGTTAGTCACAAACCAAACAG 59.712 40.000 0.00 0.00 30.35 3.16
64 65 4.632538 AGTTAGTCACAAACCAAACAGC 57.367 40.909 0.00 0.00 30.35 4.40
65 66 3.380320 AGTTAGTCACAAACCAAACAGCC 59.620 43.478 0.00 0.00 30.35 4.85
66 67 1.111277 AGTCACAAACCAAACAGCCC 58.889 50.000 0.00 0.00 0.00 5.19
67 68 1.111277 GTCACAAACCAAACAGCCCT 58.889 50.000 0.00 0.00 0.00 5.19
68 69 1.480545 GTCACAAACCAAACAGCCCTT 59.519 47.619 0.00 0.00 0.00 3.95
69 70 1.480137 TCACAAACCAAACAGCCCTTG 59.520 47.619 0.00 0.00 0.00 3.61
74 75 2.819477 CCAAACAGCCCTTGGTTCA 58.181 52.632 1.72 0.00 38.85 3.18
75 76 1.341080 CCAAACAGCCCTTGGTTCAT 58.659 50.000 1.72 0.00 38.85 2.57
76 77 1.001181 CCAAACAGCCCTTGGTTCATG 59.999 52.381 1.72 0.00 38.85 3.07
77 78 1.001181 CAAACAGCCCTTGGTTCATGG 59.999 52.381 0.00 0.00 33.36 3.66
78 79 1.187567 AACAGCCCTTGGTTCATGGC 61.188 55.000 0.00 0.00 44.35 4.40
80 81 3.451894 GCCCTTGGTTCATGGCGG 61.452 66.667 0.00 0.00 33.59 6.13
81 82 3.451894 CCCTTGGTTCATGGCGGC 61.452 66.667 0.00 0.00 0.00 6.53
202 204 1.522668 TTTCTCGCCCAACATGTCAG 58.477 50.000 0.00 0.00 0.00 3.51
300 1458 9.965824 TTTGAAGAGATAAAACATCTTTGGTTC 57.034 29.630 0.00 0.00 33.53 3.62
317 1475 7.780745 TCTTTGGTTCTTTCTTACCCAAATACA 59.219 33.333 0.00 0.00 42.49 2.29
318 1476 6.887626 TGGTTCTTTCTTACCCAAATACAC 57.112 37.500 0.00 0.00 33.34 2.90
319 1477 6.366340 TGGTTCTTTCTTACCCAAATACACA 58.634 36.000 0.00 0.00 33.34 3.72
320 1478 6.263617 TGGTTCTTTCTTACCCAAATACACAC 59.736 38.462 0.00 0.00 33.34 3.82
322 1480 7.201839 GGTTCTTTCTTACCCAAATACACACAA 60.202 37.037 0.00 0.00 0.00 3.33
324 1482 8.472007 TCTTTCTTACCCAAATACACACAAAT 57.528 30.769 0.00 0.00 0.00 2.32
326 1484 9.840427 CTTTCTTACCCAAATACACACAAATAG 57.160 33.333 0.00 0.00 0.00 1.73
384 1553 5.504665 GCGTACATTCAAAGCAGAATAGCAT 60.505 40.000 0.00 0.00 36.13 3.79
390 1559 0.379669 AAGCAGAATAGCATGCACGC 59.620 50.000 21.98 12.16 45.01 5.34
406 1575 4.205584 GCACAAAGCGTCGGTTTC 57.794 55.556 18.86 5.48 30.52 2.78
407 1576 1.721133 GCACAAAGCGTCGGTTTCG 60.721 57.895 18.86 15.87 30.52 3.46
415 1584 2.263540 GTCGGTTTCGCTGGCCTA 59.736 61.111 3.32 0.00 36.13 3.93
416 1585 1.375013 GTCGGTTTCGCTGGCCTAA 60.375 57.895 3.32 0.00 36.13 2.69
417 1586 0.952010 GTCGGTTTCGCTGGCCTAAA 60.952 55.000 3.32 0.00 36.13 1.85
419 1588 0.377203 CGGTTTCGCTGGCCTAAATC 59.623 55.000 3.32 0.00 0.00 2.17
420 1589 0.738975 GGTTTCGCTGGCCTAAATCC 59.261 55.000 3.32 0.00 0.00 3.01
421 1590 0.377203 GTTTCGCTGGCCTAAATCCG 59.623 55.000 3.32 0.00 0.00 4.18
422 1591 0.035820 TTTCGCTGGCCTAAATCCGT 60.036 50.000 3.32 0.00 0.00 4.69
423 1592 0.461339 TTCGCTGGCCTAAATCCGTC 60.461 55.000 3.32 0.00 0.00 4.79
424 1593 2.237751 CGCTGGCCTAAATCCGTCG 61.238 63.158 3.32 0.00 0.00 5.12
425 1594 2.534903 GCTGGCCTAAATCCGTCGC 61.535 63.158 3.32 0.00 0.00 5.19
426 1595 1.153449 CTGGCCTAAATCCGTCGCA 60.153 57.895 3.32 0.00 0.00 5.10
427 1596 0.742990 CTGGCCTAAATCCGTCGCAA 60.743 55.000 3.32 0.00 0.00 4.85
428 1597 1.022451 TGGCCTAAATCCGTCGCAAC 61.022 55.000 3.32 0.00 0.00 4.17
429 1598 0.743345 GGCCTAAATCCGTCGCAACT 60.743 55.000 0.00 0.00 0.00 3.16
430 1599 0.651031 GCCTAAATCCGTCGCAACTC 59.349 55.000 0.00 0.00 0.00 3.01
459 1629 2.753966 GGCACGCGAGATGCACATT 61.754 57.895 15.93 0.00 46.97 2.71
467 1637 0.097674 GAGATGCACATTCGCACCAC 59.902 55.000 0.00 0.00 46.56 4.16
489 1659 3.084039 TCCAGTTGACATCAAGCATTCC 58.916 45.455 0.00 0.00 36.39 3.01
492 1662 0.810648 TTGACATCAAGCATTCCCGC 59.189 50.000 0.00 0.00 0.00 6.13
493 1663 0.322366 TGACATCAAGCATTCCCGCA 60.322 50.000 0.00 0.00 0.00 5.69
494 1664 0.379669 GACATCAAGCATTCCCGCAG 59.620 55.000 0.00 0.00 0.00 5.18
495 1665 0.035152 ACATCAAGCATTCCCGCAGA 60.035 50.000 0.00 0.00 0.00 4.26
496 1666 1.097232 CATCAAGCATTCCCGCAGAA 58.903 50.000 0.00 0.00 39.32 3.02
497 1667 1.098050 ATCAAGCATTCCCGCAGAAC 58.902 50.000 0.00 0.00 37.29 3.01
498 1668 0.250684 TCAAGCATTCCCGCAGAACA 60.251 50.000 0.00 0.00 37.29 3.18
499 1669 0.169672 CAAGCATTCCCGCAGAACAG 59.830 55.000 0.00 0.00 37.29 3.16
500 1670 0.250901 AAGCATTCCCGCAGAACAGT 60.251 50.000 0.00 0.00 37.29 3.55
501 1671 0.250901 AGCATTCCCGCAGAACAGTT 60.251 50.000 0.00 0.00 37.29 3.16
502 1672 0.169009 GCATTCCCGCAGAACAGTTC 59.831 55.000 5.00 5.00 37.29 3.01
503 1673 1.522668 CATTCCCGCAGAACAGTTCA 58.477 50.000 15.85 0.00 37.29 3.18
504 1674 1.879380 CATTCCCGCAGAACAGTTCAA 59.121 47.619 15.85 0.21 37.29 2.69
505 1675 2.045561 TTCCCGCAGAACAGTTCAAA 57.954 45.000 15.85 0.00 0.00 2.69
506 1676 1.305201 TCCCGCAGAACAGTTCAAAC 58.695 50.000 15.85 3.42 0.00 2.93
507 1677 1.021202 CCCGCAGAACAGTTCAAACA 58.979 50.000 15.85 0.00 0.00 2.83
508 1678 1.002468 CCCGCAGAACAGTTCAAACAG 60.002 52.381 15.85 2.33 0.00 3.16
509 1679 1.939934 CCGCAGAACAGTTCAAACAGA 59.060 47.619 15.85 0.00 0.00 3.41
510 1680 2.354510 CCGCAGAACAGTTCAAACAGAA 59.645 45.455 15.85 0.00 0.00 3.02
511 1681 3.181501 CCGCAGAACAGTTCAAACAGAAA 60.182 43.478 15.85 0.00 38.13 2.52
512 1682 4.411327 CGCAGAACAGTTCAAACAGAAAA 58.589 39.130 15.85 0.00 38.13 2.29
513 1683 4.856487 CGCAGAACAGTTCAAACAGAAAAA 59.144 37.500 15.85 0.00 38.13 1.94
536 1706 5.363979 AAAAACCGCAAAAAGAAAAAGCA 57.636 30.435 0.00 0.00 0.00 3.91
537 1707 5.559427 AAAACCGCAAAAAGAAAAAGCAT 57.441 30.435 0.00 0.00 0.00 3.79
538 1708 5.559427 AAACCGCAAAAAGAAAAAGCATT 57.441 30.435 0.00 0.00 0.00 3.56
539 1709 4.794248 ACCGCAAAAAGAAAAAGCATTC 57.206 36.364 0.00 0.00 0.00 2.67
540 1710 3.559655 ACCGCAAAAAGAAAAAGCATTCC 59.440 39.130 0.00 0.00 0.00 3.01
541 1711 3.058983 CCGCAAAAAGAAAAAGCATTCCC 60.059 43.478 0.00 0.00 0.00 3.97
542 1712 3.362888 CGCAAAAAGAAAAAGCATTCCCG 60.363 43.478 0.00 0.00 0.00 5.14
543 1713 3.559655 GCAAAAAGAAAAAGCATTCCCGT 59.440 39.130 0.00 0.00 0.00 5.28
544 1714 4.747605 GCAAAAAGAAAAAGCATTCCCGTA 59.252 37.500 0.00 0.00 0.00 4.02
545 1715 5.107491 GCAAAAAGAAAAAGCATTCCCGTAG 60.107 40.000 0.00 0.00 0.00 3.51
546 1716 6.212955 CAAAAAGAAAAAGCATTCCCGTAGA 58.787 36.000 0.00 0.00 0.00 2.59
547 1717 6.399639 AAAAGAAAAAGCATTCCCGTAGAA 57.600 33.333 0.00 0.00 39.32 2.10
548 1718 5.629079 AAGAAAAAGCATTCCCGTAGAAG 57.371 39.130 0.00 0.00 38.07 2.85
549 1719 4.906618 AGAAAAAGCATTCCCGTAGAAGA 58.093 39.130 0.00 0.00 38.07 2.87
550 1720 5.313712 AGAAAAAGCATTCCCGTAGAAGAA 58.686 37.500 0.00 0.00 38.07 2.52
551 1721 5.946377 AGAAAAAGCATTCCCGTAGAAGAAT 59.054 36.000 0.00 0.00 38.07 2.40
552 1722 7.110155 AGAAAAAGCATTCCCGTAGAAGAATA 58.890 34.615 0.00 0.00 38.07 1.75
553 1723 7.610305 AGAAAAAGCATTCCCGTAGAAGAATAA 59.390 33.333 0.00 0.00 38.07 1.40
554 1724 7.881775 AAAAGCATTCCCGTAGAAGAATAAT 57.118 32.000 0.00 0.00 38.07 1.28
555 1725 8.974060 AAAAGCATTCCCGTAGAAGAATAATA 57.026 30.769 0.00 0.00 38.07 0.98
556 1726 8.974060 AAAGCATTCCCGTAGAAGAATAATAA 57.026 30.769 0.00 0.00 38.07 1.40
557 1727 8.974060 AAGCATTCCCGTAGAAGAATAATAAA 57.026 30.769 0.00 0.00 38.07 1.40
558 1728 8.608844 AGCATTCCCGTAGAAGAATAATAAAG 57.391 34.615 0.00 0.00 38.07 1.85
559 1729 8.211629 AGCATTCCCGTAGAAGAATAATAAAGT 58.788 33.333 0.00 0.00 38.07 2.66
560 1730 8.837389 GCATTCCCGTAGAAGAATAATAAAGTT 58.163 33.333 0.00 0.00 38.07 2.66
644 1825 1.135575 GTGCTCGGCAAATTCCTCTTG 60.136 52.381 0.00 0.00 41.47 3.02
757 1944 4.814294 CTCACCGCCCCGTAGTGC 62.814 72.222 0.00 0.00 0.00 4.40
781 1968 3.716006 CAACACGACCAGCTGGCG 61.716 66.667 33.47 33.47 39.32 5.69
782 1969 4.235762 AACACGACCAGCTGGCGT 62.236 61.111 34.50 34.50 44.39 5.68
791 1978 4.334118 AGCTGGCGTGGCATCACA 62.334 61.111 0.00 0.00 43.79 3.58
903 2106 3.196685 CCCCTTCAAATCTCTCTCTTCGT 59.803 47.826 0.00 0.00 0.00 3.85
966 2177 4.082523 CTCCACCGTGCCGACCAT 62.083 66.667 0.00 0.00 0.00 3.55
1232 2466 0.788391 GACGCGGTTTCAGTTCGATT 59.212 50.000 12.47 0.00 0.00 3.34
1273 2507 4.689549 TTCCCCCTCACGGAGCGA 62.690 66.667 0.00 0.00 0.00 4.93
1352 2586 1.081108 GAGCGCTTCAGTGAGTCGT 60.081 57.895 13.26 5.08 0.00 4.34
1452 3004 0.666913 GCCGTCTCTGGTCGCTAATA 59.333 55.000 0.00 0.00 0.00 0.98
1616 3172 2.438021 TGAGCTCCCACTGTTACAGTTT 59.562 45.455 16.06 0.00 42.59 2.66
1621 3177 4.320494 GCTCCCACTGTTACAGTTTTGATG 60.320 45.833 16.06 3.40 42.59 3.07
1675 3231 2.354821 GTGAGTGAACTGGGTGTTTGAC 59.645 50.000 0.00 0.00 39.30 3.18
1744 3300 4.269183 ACAATATCAAGGATTTCGCACCA 58.731 39.130 0.00 0.00 0.00 4.17
1825 3381 1.883084 CCGCGGGATGTACTTCAGC 60.883 63.158 20.10 12.77 0.00 4.26
2358 3937 1.078848 CTCCTTGCAGGTTCTCCCG 60.079 63.158 0.00 0.00 36.53 5.14
2729 4310 0.888736 TGTGCAGGTATGTGTGTGCC 60.889 55.000 0.00 0.00 34.91 5.01
3395 4978 6.147164 TCAATTTCCACTTTAGTGCTAAGTCG 59.853 38.462 4.34 0.00 44.34 4.18
3932 8385 9.621239 TCCTGATTCCCATATCTAGAAATACTT 57.379 33.333 0.00 0.00 0.00 2.24
4133 8598 3.387716 TCCCATGGACACCGACAG 58.612 61.111 15.22 0.00 0.00 3.51
4134 8599 2.436646 CCCATGGACACCGACAGC 60.437 66.667 15.22 0.00 0.00 4.40
4482 8948 4.645762 TTTTGTTGCAGCTGAATGTACA 57.354 36.364 20.43 5.62 0.00 2.90
4758 9224 5.610398 GGTTTTTGTTTTCACCTGATCCAT 58.390 37.500 0.00 0.00 0.00 3.41
5203 9671 9.080097 GAATGGAGTGAGTAGGTACTAATGTAT 57.920 37.037 0.00 0.00 45.48 2.29
5442 9910 4.947645 TCCTTCAATTTCAAGGTTTGCTG 58.052 39.130 11.26 0.00 41.28 4.41
5550 10018 1.472201 CGCAGTATCAGGCACATCACT 60.472 52.381 0.00 0.00 0.00 3.41
5803 10271 4.085466 CGTCAACGACAAATAGTGTTCGAA 60.085 41.667 0.00 0.00 41.96 3.71
5818 10286 0.599204 TCGAAGAAGCACACCCGAAC 60.599 55.000 0.00 0.00 0.00 3.95
5862 10330 9.071276 ACATTTGTTCTGATCAGTGAATACTTT 57.929 29.630 21.92 0.00 34.07 2.66
6016 10484 4.141937 TGAGCTACAGTTATGTCCCATGTC 60.142 45.833 0.00 0.00 41.01 3.06
6089 10557 0.370273 GTTGGCGTATGTCTCTTGCG 59.630 55.000 0.00 0.00 0.00 4.85
6097 10565 0.459899 ATGTCTCTTGCGTCGCCATA 59.540 50.000 15.88 0.00 0.00 2.74
6102 10570 2.361119 TCTCTTGCGTCGCCATAGTTAT 59.639 45.455 15.88 0.00 0.00 1.89
6107 10575 4.834357 TGCGTCGCCATAGTTATACTAA 57.166 40.909 15.88 0.00 33.89 2.24
6137 10605 3.429272 CCGCAAATATTCATGTGGTGCTT 60.429 43.478 10.41 0.00 41.29 3.91
6144 10612 7.944729 AATATTCATGTGGTGCTTTACTCTT 57.055 32.000 0.00 0.00 0.00 2.85
6182 10650 2.659016 CACTCGCCTGGCTTCTCA 59.341 61.111 17.92 0.00 0.00 3.27
6183 10651 1.220206 CACTCGCCTGGCTTCTCAT 59.780 57.895 17.92 0.00 0.00 2.90
6184 10652 0.392193 CACTCGCCTGGCTTCTCATT 60.392 55.000 17.92 0.00 0.00 2.57
6185 10653 0.326264 ACTCGCCTGGCTTCTCATTT 59.674 50.000 17.92 0.00 0.00 2.32
6188 10656 1.812571 TCGCCTGGCTTCTCATTTTTC 59.187 47.619 17.92 0.00 0.00 2.29
6192 10660 4.635223 GCCTGGCTTCTCATTTTTCTTTT 58.365 39.130 12.43 0.00 0.00 2.27
6209 10677 4.678622 TCTTTTTCTTTTGAAACGCCTCC 58.321 39.130 0.00 0.00 46.80 4.30
6210 10678 4.401202 TCTTTTTCTTTTGAAACGCCTCCT 59.599 37.500 0.00 0.00 46.80 3.69
6211 10679 4.729227 TTTTCTTTTGAAACGCCTCCTT 57.271 36.364 0.00 0.00 46.80 3.36
6257 10726 6.155475 TGCAACATAGTTTTACAAAGGCTT 57.845 33.333 0.00 0.00 0.00 4.35
6269 10738 4.081322 ACAAAGGCTTAACCGAAGAAGA 57.919 40.909 0.00 0.00 46.52 2.87
6305 10774 6.097412 GGGCATTCTCAATCTGGATAAGTTTT 59.903 38.462 0.00 0.00 0.00 2.43
6330 10800 4.280174 AGTTTGCTACAGTCTTCTCCGTTA 59.720 41.667 0.00 0.00 0.00 3.18
6339 10809 1.968493 TCTTCTCCGTTAGCTGTGGTT 59.032 47.619 0.00 0.00 0.00 3.67
6343 10813 0.759959 TCCGTTAGCTGTGGTTGGAA 59.240 50.000 0.00 0.00 0.00 3.53
6351 10821 2.024655 AGCTGTGGTTGGAATGGATGAT 60.025 45.455 0.00 0.00 0.00 2.45
6382 10852 1.815817 ATTTGGTTGGGCACGCCTTC 61.816 55.000 8.20 0.00 36.10 3.46
6385 10855 2.676471 GTTGGGCACGCCTTCCAT 60.676 61.111 8.20 0.00 36.10 3.41
6416 10888 0.940991 GAACTTTTTGCAGCGGCCTG 60.941 55.000 6.32 0.00 42.13 4.85
6418 10890 1.372128 CTTTTTGCAGCGGCCTGTC 60.372 57.895 6.32 0.00 41.26 3.51
6437 10909 2.560861 CGTCACCGTTGGCAATGG 59.439 61.111 31.88 31.88 43.45 3.16
6450 10922 1.376424 CAATGGACTCGCTGCCAGT 60.376 57.895 0.00 0.00 37.64 4.00
6468 10940 2.880890 CAGTTTCTGGAGTTCACCTTGG 59.119 50.000 0.00 0.00 0.00 3.61
6469 10941 1.609072 GTTTCTGGAGTTCACCTTGGC 59.391 52.381 0.00 0.00 0.00 4.52
6470 10942 1.140312 TTCTGGAGTTCACCTTGGCT 58.860 50.000 0.00 0.00 0.00 4.75
6471 10943 0.397941 TCTGGAGTTCACCTTGGCTG 59.602 55.000 0.00 0.00 0.00 4.85
6472 10944 1.228245 TGGAGTTCACCTTGGCTGC 60.228 57.895 0.00 0.00 0.00 5.25
6473 10945 1.228245 GGAGTTCACCTTGGCTGCA 60.228 57.895 0.50 0.00 0.00 4.41
6474 10946 0.610232 GGAGTTCACCTTGGCTGCAT 60.610 55.000 0.50 0.00 0.00 3.96
6475 10947 0.524862 GAGTTCACCTTGGCTGCATG 59.475 55.000 0.50 0.00 0.00 4.06
6476 10948 0.896940 AGTTCACCTTGGCTGCATGG 60.897 55.000 0.50 2.52 0.00 3.66
6477 10949 1.153524 TTCACCTTGGCTGCATGGT 59.846 52.632 0.50 3.21 33.52 3.55
6478 10950 0.403655 TTCACCTTGGCTGCATGGTA 59.596 50.000 0.50 0.00 32.25 3.25
6479 10951 0.625316 TCACCTTGGCTGCATGGTAT 59.375 50.000 0.50 0.00 32.25 2.73
6480 10952 1.005805 TCACCTTGGCTGCATGGTATT 59.994 47.619 0.50 0.00 32.25 1.89
6481 10953 1.826720 CACCTTGGCTGCATGGTATTT 59.173 47.619 0.50 0.00 32.25 1.40
6482 10954 1.826720 ACCTTGGCTGCATGGTATTTG 59.173 47.619 0.50 0.00 31.80 2.32
6483 10955 1.137479 CCTTGGCTGCATGGTATTTGG 59.863 52.381 0.50 0.00 0.00 3.28
6484 10956 0.536260 TTGGCTGCATGGTATTTGGC 59.464 50.000 0.50 0.00 0.00 4.52
6485 10957 1.329171 TGGCTGCATGGTATTTGGCC 61.329 55.000 0.50 0.00 38.67 5.36
6486 10958 1.044790 GGCTGCATGGTATTTGGCCT 61.045 55.000 3.32 0.00 35.73 5.19
6487 10959 0.386838 GCTGCATGGTATTTGGCCTC 59.613 55.000 3.32 0.00 0.00 4.70
6488 10960 0.664761 CTGCATGGTATTTGGCCTCG 59.335 55.000 3.32 0.00 0.00 4.63
6489 10961 0.034574 TGCATGGTATTTGGCCTCGT 60.035 50.000 3.32 0.00 0.00 4.18
6490 10962 0.381801 GCATGGTATTTGGCCTCGTG 59.618 55.000 3.32 0.00 0.00 4.35
6491 10963 2.016604 GCATGGTATTTGGCCTCGTGA 61.017 52.381 3.32 0.00 0.00 4.35
6492 10964 2.575532 CATGGTATTTGGCCTCGTGAT 58.424 47.619 3.32 0.00 0.00 3.06
6493 10965 3.738982 CATGGTATTTGGCCTCGTGATA 58.261 45.455 3.32 0.00 0.00 2.15
6494 10966 4.326826 CATGGTATTTGGCCTCGTGATAT 58.673 43.478 3.32 0.00 0.00 1.63
6495 10967 4.431416 TGGTATTTGGCCTCGTGATATT 57.569 40.909 3.32 0.00 0.00 1.28
6496 10968 4.133820 TGGTATTTGGCCTCGTGATATTG 58.866 43.478 3.32 0.00 0.00 1.90
6503 10975 1.772182 CCTCGTGATATTGCTCCGAC 58.228 55.000 0.00 0.00 0.00 4.79
6504 10976 1.067060 CCTCGTGATATTGCTCCGACA 59.933 52.381 0.00 0.00 0.00 4.35
6512 10984 5.294306 GTGATATTGCTCCGACAATCTTTGA 59.706 40.000 2.21 0.00 40.64 2.69
6514 10986 1.808411 TGCTCCGACAATCTTTGACC 58.192 50.000 0.00 0.00 0.00 4.02
6516 10988 1.939838 GCTCCGACAATCTTTGACCGT 60.940 52.381 0.00 0.00 0.00 4.83
6540 11012 3.304057 CCTGAAAGAAAAACTGCTCGGTC 60.304 47.826 0.00 0.00 34.07 4.79
6551 11023 1.270550 CTGCTCGGTCCAAAAAGCATT 59.729 47.619 5.89 0.00 43.30 3.56
6571 11043 5.771666 GCATTGGATAGGAAATTCTGGATCA 59.228 40.000 0.00 0.00 0.00 2.92
6631 11103 2.908073 GCAATTCGCCGGCCTATGG 61.908 63.158 23.46 13.12 32.94 2.74
6685 11157 8.298854 CAAGATGTCAAGGACACAATTAAATGA 58.701 33.333 0.49 0.00 45.65 2.57
6692 11165 8.134895 TCAAGGACACAATTAAATGAAACTCAC 58.865 33.333 0.00 0.00 0.00 3.51
6721 11194 1.599542 GGATGTACATTGCTTCCTCGC 59.400 52.381 10.30 0.00 0.00 5.03
6729 11202 0.036388 TTGCTTCCTCGCCCTACAAG 60.036 55.000 0.00 0.00 0.00 3.16
6730 11203 0.902984 TGCTTCCTCGCCCTACAAGA 60.903 55.000 0.00 0.00 0.00 3.02
6731 11204 0.466124 GCTTCCTCGCCCTACAAGAT 59.534 55.000 0.00 0.00 0.00 2.40
6732 11205 1.808133 GCTTCCTCGCCCTACAAGATG 60.808 57.143 0.00 0.00 0.00 2.90
6733 11206 0.178068 TTCCTCGCCCTACAAGATGC 59.822 55.000 0.00 0.00 0.00 3.91
6734 11207 0.975556 TCCTCGCCCTACAAGATGCA 60.976 55.000 0.00 0.00 0.00 3.96
6735 11208 0.107703 CCTCGCCCTACAAGATGCAA 60.108 55.000 0.00 0.00 0.00 4.08
6736 11209 1.475751 CCTCGCCCTACAAGATGCAAT 60.476 52.381 0.00 0.00 0.00 3.56
6737 11210 2.292267 CTCGCCCTACAAGATGCAATT 58.708 47.619 0.00 0.00 0.00 2.32
6738 11211 2.288666 TCGCCCTACAAGATGCAATTC 58.711 47.619 0.00 0.00 0.00 2.17
6749 11222 0.184451 ATGCAATTCGAGGGCCTCAT 59.816 50.000 31.69 16.85 0.00 2.90
6755 11228 0.830648 TTCGAGGGCCTCATTACCTG 59.169 55.000 31.69 14.51 34.02 4.00
6768 11241 4.352893 TCATTACCTGAGACATGGTGAGA 58.647 43.478 0.00 0.00 37.74 3.27
6769 11242 4.964897 TCATTACCTGAGACATGGTGAGAT 59.035 41.667 0.00 0.00 37.74 2.75
6770 11243 6.136155 TCATTACCTGAGACATGGTGAGATA 58.864 40.000 0.00 0.00 37.74 1.98
6771 11244 5.854010 TTACCTGAGACATGGTGAGATAC 57.146 43.478 0.00 0.00 37.74 2.24
6772 11245 2.690497 ACCTGAGACATGGTGAGATACG 59.310 50.000 0.00 0.00 34.90 3.06
6773 11246 2.952310 CCTGAGACATGGTGAGATACGA 59.048 50.000 0.00 0.00 0.00 3.43
6774 11247 3.381590 CCTGAGACATGGTGAGATACGAA 59.618 47.826 0.00 0.00 0.00 3.85
6786 11259 4.092091 GTGAGATACGAAGTCTTTGCTTGG 59.908 45.833 0.00 0.00 43.93 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.705441 CACATCTAAGGTTAGGCAAGTTTGA 59.295 40.000 0.00 0.00 0.00 2.69
5 6 5.106157 CCACATCTAAGGTTAGGCAAGTTTG 60.106 44.000 0.00 0.00 0.00 2.93
6 7 5.010282 CCACATCTAAGGTTAGGCAAGTTT 58.990 41.667 0.00 0.00 0.00 2.66
8 9 3.622455 GCCACATCTAAGGTTAGGCAAGT 60.622 47.826 0.00 0.00 40.29 3.16
9 10 2.945668 GCCACATCTAAGGTTAGGCAAG 59.054 50.000 0.00 0.00 40.29 4.01
10 11 2.307392 TGCCACATCTAAGGTTAGGCAA 59.693 45.455 0.00 0.00 46.55 4.52
11 12 2.710096 GCCACATCTAAGGTTAGGCA 57.290 50.000 0.00 0.00 40.29 4.75
13 14 5.041191 AGATTGCCACATCTAAGGTTAGG 57.959 43.478 0.00 0.00 0.00 2.69
15 16 5.652014 CCAAAGATTGCCACATCTAAGGTTA 59.348 40.000 0.00 0.00 0.00 2.85
16 17 4.463891 CCAAAGATTGCCACATCTAAGGTT 59.536 41.667 0.00 0.00 0.00 3.50
17 18 4.019174 CCAAAGATTGCCACATCTAAGGT 58.981 43.478 0.00 0.00 0.00 3.50
18 19 3.181483 GCCAAAGATTGCCACATCTAAGG 60.181 47.826 0.00 0.00 0.00 2.69
19 20 3.444742 TGCCAAAGATTGCCACATCTAAG 59.555 43.478 0.00 0.00 0.00 2.18
20 21 3.429492 TGCCAAAGATTGCCACATCTAA 58.571 40.909 0.00 0.00 0.00 2.10
21 22 3.084536 TGCCAAAGATTGCCACATCTA 57.915 42.857 0.00 0.00 0.00 1.98
22 23 1.927487 TGCCAAAGATTGCCACATCT 58.073 45.000 0.00 0.00 0.00 2.90
23 24 2.747396 TTGCCAAAGATTGCCACATC 57.253 45.000 0.00 0.00 0.00 3.06
24 25 2.369532 ACTTTGCCAAAGATTGCCACAT 59.630 40.909 23.32 0.00 41.02 3.21
25 26 1.761784 ACTTTGCCAAAGATTGCCACA 59.238 42.857 23.32 0.00 41.02 4.17
26 27 2.531522 ACTTTGCCAAAGATTGCCAC 57.468 45.000 23.32 0.00 41.02 5.01
27 28 3.640967 ACTAACTTTGCCAAAGATTGCCA 59.359 39.130 23.32 0.00 41.02 4.92
28 29 4.237724 GACTAACTTTGCCAAAGATTGCC 58.762 43.478 23.32 1.98 41.02 4.52
29 30 4.681483 GTGACTAACTTTGCCAAAGATTGC 59.319 41.667 23.32 9.44 41.02 3.56
30 31 5.830912 TGTGACTAACTTTGCCAAAGATTG 58.169 37.500 23.32 14.58 41.02 2.67
31 32 6.463995 TTGTGACTAACTTTGCCAAAGATT 57.536 33.333 23.32 14.98 41.02 2.40
32 33 6.273071 GTTTGTGACTAACTTTGCCAAAGAT 58.727 36.000 23.32 14.26 41.02 2.40
33 34 5.393678 GGTTTGTGACTAACTTTGCCAAAGA 60.394 40.000 23.32 1.30 41.02 2.52
34 35 4.803613 GGTTTGTGACTAACTTTGCCAAAG 59.196 41.667 15.47 15.47 44.10 2.77
35 36 4.220821 TGGTTTGTGACTAACTTTGCCAAA 59.779 37.500 9.55 0.00 0.00 3.28
36 37 3.764434 TGGTTTGTGACTAACTTTGCCAA 59.236 39.130 9.55 0.00 0.00 4.52
37 38 3.357203 TGGTTTGTGACTAACTTTGCCA 58.643 40.909 9.55 0.00 0.00 4.92
38 39 4.379339 TTGGTTTGTGACTAACTTTGCC 57.621 40.909 9.55 0.00 0.00 4.52
39 40 5.164954 TGTTTGGTTTGTGACTAACTTTGC 58.835 37.500 9.55 0.62 0.00 3.68
40 41 5.288472 GCTGTTTGGTTTGTGACTAACTTTG 59.712 40.000 9.55 0.00 0.00 2.77
41 42 5.407502 GCTGTTTGGTTTGTGACTAACTTT 58.592 37.500 9.55 0.00 0.00 2.66
42 43 4.142249 GGCTGTTTGGTTTGTGACTAACTT 60.142 41.667 9.55 0.00 0.00 2.66
43 44 3.380320 GGCTGTTTGGTTTGTGACTAACT 59.620 43.478 9.55 0.00 0.00 2.24
44 45 3.490249 GGGCTGTTTGGTTTGTGACTAAC 60.490 47.826 1.25 1.25 0.00 2.34
45 46 2.691011 GGGCTGTTTGGTTTGTGACTAA 59.309 45.455 0.00 0.00 0.00 2.24
46 47 2.092103 AGGGCTGTTTGGTTTGTGACTA 60.092 45.455 0.00 0.00 0.00 2.59
47 48 1.111277 GGGCTGTTTGGTTTGTGACT 58.889 50.000 0.00 0.00 0.00 3.41
48 49 1.111277 AGGGCTGTTTGGTTTGTGAC 58.889 50.000 0.00 0.00 0.00 3.67
49 50 1.480137 CAAGGGCTGTTTGGTTTGTGA 59.520 47.619 0.00 0.00 0.00 3.58
50 51 1.473080 CCAAGGGCTGTTTGGTTTGTG 60.473 52.381 7.50 0.00 40.15 3.33
51 52 0.829990 CCAAGGGCTGTTTGGTTTGT 59.170 50.000 7.50 0.00 40.15 2.83
52 53 3.684693 CCAAGGGCTGTTTGGTTTG 57.315 52.632 7.50 0.00 40.15 2.93
57 58 1.001181 CCATGAACCAAGGGCTGTTTG 59.999 52.381 0.00 0.00 0.00 2.93
58 59 1.341080 CCATGAACCAAGGGCTGTTT 58.659 50.000 0.00 0.00 0.00 2.83
59 60 1.187567 GCCATGAACCAAGGGCTGTT 61.188 55.000 0.00 0.00 43.09 3.16
60 61 1.607467 GCCATGAACCAAGGGCTGT 60.607 57.895 0.00 0.00 43.09 4.40
61 62 2.703798 CGCCATGAACCAAGGGCTG 61.704 63.158 0.00 0.00 44.23 4.85
62 63 2.361610 CGCCATGAACCAAGGGCT 60.362 61.111 0.00 0.00 44.23 5.19
63 64 3.451894 CCGCCATGAACCAAGGGC 61.452 66.667 0.00 0.00 42.98 5.19
64 65 3.451894 GCCGCCATGAACCAAGGG 61.452 66.667 0.00 0.00 0.00 3.95
65 66 3.814268 CGCCGCCATGAACCAAGG 61.814 66.667 0.00 0.00 0.00 3.61
66 67 3.814268 CCGCCGCCATGAACCAAG 61.814 66.667 0.00 0.00 0.00 3.61
67 68 4.652131 ACCGCCGCCATGAACCAA 62.652 61.111 0.00 0.00 0.00 3.67
70 71 4.778143 AGGACCGCCGCCATGAAC 62.778 66.667 0.00 0.00 39.96 3.18
71 72 3.561120 AAAGGACCGCCGCCATGAA 62.561 57.895 0.00 0.00 39.96 2.57
72 73 3.969250 GAAAGGACCGCCGCCATGA 62.969 63.158 0.00 0.00 39.96 3.07
73 74 3.508840 GAAAGGACCGCCGCCATG 61.509 66.667 0.00 0.00 39.96 3.66
74 75 4.796495 GGAAAGGACCGCCGCCAT 62.796 66.667 0.00 0.00 39.96 4.40
102 103 0.179103 AACTGTTCGGAACCGTTCGT 60.179 50.000 20.44 4.10 34.35 3.85
300 1458 9.840427 CTATTTGTGTGTATTTGGGTAAGAAAG 57.160 33.333 0.00 0.00 0.00 2.62
317 1475 7.318141 ACATGTTACGCTAGTACTATTTGTGT 58.682 34.615 2.33 7.47 31.60 3.72
318 1476 7.305247 CGACATGTTACGCTAGTACTATTTGTG 60.305 40.741 2.33 1.48 31.60 3.33
319 1477 6.690098 CGACATGTTACGCTAGTACTATTTGT 59.310 38.462 2.33 5.21 31.60 2.83
320 1478 7.078926 CGACATGTTACGCTAGTACTATTTG 57.921 40.000 2.33 0.00 31.60 2.32
390 1559 4.489683 CGAAACCGACGCTTTGTG 57.510 55.556 0.00 0.00 0.00 3.33
401 1570 0.738975 GGATTTAGGCCAGCGAAACC 59.261 55.000 5.01 0.00 0.00 3.27
404 1573 0.461339 GACGGATTTAGGCCAGCGAA 60.461 55.000 5.01 0.00 0.00 4.70
405 1574 1.143183 GACGGATTTAGGCCAGCGA 59.857 57.895 5.01 0.00 0.00 4.93
406 1575 2.237751 CGACGGATTTAGGCCAGCG 61.238 63.158 5.01 0.00 0.00 5.18
407 1576 2.534903 GCGACGGATTTAGGCCAGC 61.535 63.158 5.01 0.00 0.00 4.85
408 1577 0.742990 TTGCGACGGATTTAGGCCAG 60.743 55.000 5.01 0.00 0.00 4.85
409 1578 1.022451 GTTGCGACGGATTTAGGCCA 61.022 55.000 5.01 0.00 0.00 5.36
411 1580 0.651031 GAGTTGCGACGGATTTAGGC 59.349 55.000 0.00 0.00 0.00 3.93
412 1581 0.921347 CGAGTTGCGACGGATTTAGG 59.079 55.000 0.00 0.00 44.57 2.69
413 1582 0.297820 GCGAGTTGCGACGGATTTAG 59.702 55.000 0.00 0.00 44.57 1.85
414 1583 2.365823 GCGAGTTGCGACGGATTTA 58.634 52.632 0.00 0.00 44.57 1.40
415 1584 3.165498 GCGAGTTGCGACGGATTT 58.835 55.556 0.00 0.00 44.57 2.17
459 1629 1.069090 GTCAACTGGAGTGGTGCGA 59.931 57.895 0.00 0.00 0.00 5.10
467 1637 3.128242 GGAATGCTTGATGTCAACTGGAG 59.872 47.826 0.00 0.00 0.00 3.86
489 1659 1.939934 TCTGTTTGAACTGTTCTGCGG 59.060 47.619 20.18 14.34 0.00 5.69
514 1684 5.363979 TGCTTTTTCTTTTTGCGGTTTTT 57.636 30.435 0.00 0.00 0.00 1.94
515 1685 5.559427 ATGCTTTTTCTTTTTGCGGTTTT 57.441 30.435 0.00 0.00 0.00 2.43
516 1686 5.448496 GGAATGCTTTTTCTTTTTGCGGTTT 60.448 36.000 0.00 0.00 0.00 3.27
517 1687 4.035091 GGAATGCTTTTTCTTTTTGCGGTT 59.965 37.500 0.00 0.00 0.00 4.44
518 1688 3.559655 GGAATGCTTTTTCTTTTTGCGGT 59.440 39.130 0.00 0.00 0.00 5.68
519 1689 3.058983 GGGAATGCTTTTTCTTTTTGCGG 60.059 43.478 0.00 0.00 0.00 5.69
520 1690 3.362888 CGGGAATGCTTTTTCTTTTTGCG 60.363 43.478 0.00 0.00 0.00 4.85
521 1691 3.559655 ACGGGAATGCTTTTTCTTTTTGC 59.440 39.130 0.00 0.00 0.00 3.68
522 1692 6.212955 TCTACGGGAATGCTTTTTCTTTTTG 58.787 36.000 0.00 0.00 0.00 2.44
523 1693 6.399639 TCTACGGGAATGCTTTTTCTTTTT 57.600 33.333 0.00 0.00 0.00 1.94
524 1694 6.264518 TCTTCTACGGGAATGCTTTTTCTTTT 59.735 34.615 0.00 0.00 33.01 2.27
525 1695 5.768164 TCTTCTACGGGAATGCTTTTTCTTT 59.232 36.000 0.00 0.00 33.01 2.52
526 1696 5.313712 TCTTCTACGGGAATGCTTTTTCTT 58.686 37.500 0.00 0.00 33.01 2.52
527 1697 4.906618 TCTTCTACGGGAATGCTTTTTCT 58.093 39.130 0.00 0.00 33.01 2.52
528 1698 5.622770 TTCTTCTACGGGAATGCTTTTTC 57.377 39.130 0.00 0.00 33.01 2.29
529 1699 7.696992 TTATTCTTCTACGGGAATGCTTTTT 57.303 32.000 0.00 0.00 34.52 1.94
530 1700 7.881775 ATTATTCTTCTACGGGAATGCTTTT 57.118 32.000 0.00 0.00 34.52 2.27
531 1701 8.974060 TTATTATTCTTCTACGGGAATGCTTT 57.026 30.769 0.00 0.00 34.52 3.51
532 1702 8.974060 TTTATTATTCTTCTACGGGAATGCTT 57.026 30.769 0.00 0.00 34.52 3.91
533 1703 8.211629 ACTTTATTATTCTTCTACGGGAATGCT 58.788 33.333 0.00 0.00 34.52 3.79
534 1704 8.379457 ACTTTATTATTCTTCTACGGGAATGC 57.621 34.615 0.00 0.00 34.52 3.56
560 1730 4.343811 TTTCTGTCGCGTCAAAGAAAAA 57.656 36.364 18.56 8.58 36.10 1.94
561 1731 4.343811 TTTTCTGTCGCGTCAAAGAAAA 57.656 36.364 23.53 23.53 43.03 2.29
562 1732 4.343811 TTTTTCTGTCGCGTCAAAGAAA 57.656 36.364 17.61 17.61 36.98 2.52
598 1768 2.125147 CGGATCTCCTTTGCGCCA 60.125 61.111 4.18 0.00 0.00 5.69
757 1944 1.654220 CTGGTCGTGTTGGCTTTGG 59.346 57.895 0.00 0.00 0.00 3.28
759 1946 1.152963 AGCTGGTCGTGTTGGCTTT 60.153 52.632 0.00 0.00 0.00 3.51
781 1968 1.089920 GGAGTGTGATGTGATGCCAC 58.910 55.000 0.00 0.00 43.46 5.01
782 1969 0.035152 GGGAGTGTGATGTGATGCCA 60.035 55.000 0.00 0.00 0.00 4.92
789 1976 4.760047 GCGGCGGGAGTGTGATGT 62.760 66.667 9.78 0.00 0.00 3.06
791 1978 4.760047 GTGCGGCGGGAGTGTGAT 62.760 66.667 9.78 0.00 0.00 3.06
813 2002 2.284995 AGGACAGGACAGGAGGCC 60.285 66.667 0.00 0.00 0.00 5.19
1041 2252 4.436998 GACGTGGACAGGAGCCGG 62.437 72.222 0.00 0.00 0.00 6.13
1131 2342 0.759812 TGTTGTACCAGGGGTCGTGA 60.760 55.000 0.00 0.00 37.09 4.35
1312 2546 1.010935 ACTGCTGCTCGAACGACATG 61.011 55.000 0.00 0.00 0.00 3.21
1452 3004 0.457509 CAACTCAGAGCGCTCACGAT 60.458 55.000 36.87 18.18 43.93 3.73
1581 3137 2.766828 GGAGCTCACCCTGTAGTACAAT 59.233 50.000 17.19 0.00 0.00 2.71
1616 3172 0.456628 CACGCATGCCAATCCATCAA 59.543 50.000 13.15 0.00 0.00 2.57
1621 3177 2.869233 AAATACACGCATGCCAATCC 57.131 45.000 13.15 0.00 0.00 3.01
1658 3214 1.063469 CACGTCAAACACCCAGTTCAC 59.937 52.381 0.00 0.00 40.26 3.18
1675 3231 3.340034 ACCATACCACCACAAATACACG 58.660 45.455 0.00 0.00 0.00 4.49
1741 3297 6.014840 CGACAGTAGGGGTGTATATTATTGGT 60.015 42.308 0.00 0.00 0.00 3.67
1744 3300 5.046807 GCCGACAGTAGGGGTGTATATTATT 60.047 44.000 1.37 0.00 0.00 1.40
1825 3381 2.710096 TCTCCCCTTTATCCTTTGCG 57.290 50.000 0.00 0.00 0.00 4.85
1994 3553 8.965986 AAAAGACAAACAACTAGAGAACAAAC 57.034 30.769 0.00 0.00 0.00 2.93
2034 3593 6.430925 GGCAATTCACATGGATATAGCTACAA 59.569 38.462 0.00 0.00 0.00 2.41
2097 3656 3.627577 ACAAAGCAAGTTCAGTACAGGTG 59.372 43.478 0.00 0.00 0.00 4.00
2358 3937 3.006940 TGTTCCCACGTCAAGCATTATC 58.993 45.455 0.00 0.00 0.00 1.75
2551 4132 4.459337 AGGCATTTACTCCAAACAGTAAGC 59.541 41.667 0.00 0.00 39.49 3.09
2729 4310 1.806542 AGCAACCAAAGTATGACTGCG 59.193 47.619 0.00 0.00 39.80 5.18
3395 4978 6.743575 ACCTATTGTGCACTTAGAAATCAC 57.256 37.500 19.41 0.00 0.00 3.06
3618 5201 4.982241 AGGAGTTGGATGTCTTTTCTGA 57.018 40.909 0.00 0.00 0.00 3.27
4131 8596 5.555017 AGTATACATATTTGAGGCTGGCTG 58.445 41.667 9.06 0.00 0.00 4.85
4132 8597 5.832539 AGTATACATATTTGAGGCTGGCT 57.167 39.130 2.24 2.24 0.00 4.75
4133 8598 6.712547 AGAAAGTATACATATTTGAGGCTGGC 59.287 38.462 5.50 0.00 0.00 4.85
4134 8599 7.716998 ACAGAAAGTATACATATTTGAGGCTGG 59.283 37.037 5.50 0.00 0.00 4.85
4175 8640 7.609097 ATGCTATAGATCAAGAAAGGAGACA 57.391 36.000 3.21 0.00 0.00 3.41
4482 8948 5.503927 ACATGCTTGAATACATCTTCAGGT 58.496 37.500 6.60 0.00 36.55 4.00
5203 9671 2.687935 GTTTTGCACTTTGTCTCCCAGA 59.312 45.455 0.00 0.00 0.00 3.86
5442 9910 2.163818 TGACACGAGTTGGGTCATTC 57.836 50.000 11.68 0.00 36.69 2.67
5613 10081 1.437986 GTCCCGAGGATCCAAGTCG 59.562 63.158 15.82 14.47 32.73 4.18
5803 10271 0.249911 GTCTGTTCGGGTGTGCTTCT 60.250 55.000 0.00 0.00 0.00 2.85
5818 10286 3.436700 TGTATGTGCCTGATACGTCTG 57.563 47.619 0.00 0.00 0.00 3.51
5862 10330 2.936498 GAGCAGCTAAACCGAAATAGCA 59.064 45.455 0.00 0.00 45.48 3.49
6016 10484 7.492669 ACATCTGACATTTATTCAAGTCCTACG 59.507 37.037 0.00 0.00 0.00 3.51
6089 10557 8.485591 GTGTTTGATTAGTATAACTATGGCGAC 58.514 37.037 0.00 0.00 29.64 5.19
6097 10565 7.675962 TTTGCGGTGTTTGATTAGTATAACT 57.324 32.000 0.00 0.00 0.00 2.24
6102 10570 8.270080 TGAATATTTGCGGTGTTTGATTAGTA 57.730 30.769 0.00 0.00 0.00 1.82
6107 10575 5.806502 CACATGAATATTTGCGGTGTTTGAT 59.193 36.000 0.00 0.00 0.00 2.57
6124 10592 6.109156 TCTAAGAGTAAAGCACCACATGAA 57.891 37.500 0.00 0.00 0.00 2.57
6137 10605 7.997773 TGAACTAGTGAGCTTCTAAGAGTAA 57.002 36.000 0.00 0.00 0.00 2.24
6144 10612 6.188407 AGTGGTATGAACTAGTGAGCTTCTA 58.812 40.000 0.00 0.00 0.00 2.10
6182 10650 8.039603 AGGCGTTTCAAAAGAAAAAGAAAAAT 57.960 26.923 0.00 0.00 32.44 1.82
6183 10651 7.360522 GGAGGCGTTTCAAAAGAAAAAGAAAAA 60.361 33.333 0.00 0.00 32.44 1.94
6184 10652 6.091577 GGAGGCGTTTCAAAAGAAAAAGAAAA 59.908 34.615 0.00 0.00 32.44 2.29
6185 10653 5.579119 GGAGGCGTTTCAAAAGAAAAAGAAA 59.421 36.000 0.00 0.00 0.00 2.52
6188 10656 4.682787 AGGAGGCGTTTCAAAAGAAAAAG 58.317 39.130 0.00 0.00 0.00 2.27
6192 10660 5.533154 TCAATAAGGAGGCGTTTCAAAAGAA 59.467 36.000 0.00 0.00 0.00 2.52
6257 10726 4.360951 AACCACCATTCTTCTTCGGTTA 57.639 40.909 0.00 0.00 33.62 2.85
6269 10738 1.901833 GAGAATGCCCAAACCACCATT 59.098 47.619 0.00 0.00 0.00 3.16
6305 10774 4.280174 ACGGAGAAGACTGTAGCAAACTTA 59.720 41.667 0.00 0.00 0.00 2.24
6330 10800 1.355381 TCATCCATTCCAACCACAGCT 59.645 47.619 0.00 0.00 0.00 4.24
6339 10809 2.785269 AGGCTTGGTATCATCCATTCCA 59.215 45.455 0.00 0.00 37.33 3.53
6343 10813 4.736611 ATCAAGGCTTGGTATCATCCAT 57.263 40.909 25.92 6.91 37.33 3.41
6382 10852 5.880054 AAAAGTTCAGTCGTTATCCATGG 57.120 39.130 4.97 4.97 0.00 3.66
6385 10855 4.576873 TGCAAAAAGTTCAGTCGTTATCCA 59.423 37.500 0.00 0.00 0.00 3.41
6437 10909 1.294659 CCAGAAACTGGCAGCGAGTC 61.295 60.000 15.89 6.81 45.13 3.36
6450 10922 1.494721 AGCCAAGGTGAACTCCAGAAA 59.505 47.619 0.00 0.00 0.00 2.52
6456 10928 0.524862 CATGCAGCCAAGGTGAACTC 59.475 55.000 0.00 0.00 32.22 3.01
6457 10929 0.896940 CCATGCAGCCAAGGTGAACT 60.897 55.000 0.00 0.00 32.22 3.01
6458 10930 1.181098 ACCATGCAGCCAAGGTGAAC 61.181 55.000 0.00 0.00 41.24 3.18
6461 10933 1.477553 AATACCATGCAGCCAAGGTG 58.522 50.000 10.02 0.00 42.61 4.00
6462 10934 1.826720 CAAATACCATGCAGCCAAGGT 59.173 47.619 5.89 5.89 44.62 3.50
6463 10935 1.137479 CCAAATACCATGCAGCCAAGG 59.863 52.381 0.00 0.00 35.94 3.61
6464 10936 1.472026 GCCAAATACCATGCAGCCAAG 60.472 52.381 0.00 0.00 0.00 3.61
6465 10937 0.536260 GCCAAATACCATGCAGCCAA 59.464 50.000 0.00 0.00 0.00 4.52
6466 10938 1.329171 GGCCAAATACCATGCAGCCA 61.329 55.000 0.00 0.00 38.79 4.75
6467 10939 1.044790 AGGCCAAATACCATGCAGCC 61.045 55.000 5.01 0.00 39.25 4.85
6468 10940 0.386838 GAGGCCAAATACCATGCAGC 59.613 55.000 5.01 0.00 0.00 5.25
6469 10941 0.664761 CGAGGCCAAATACCATGCAG 59.335 55.000 5.01 0.00 0.00 4.41
6470 10942 0.034574 ACGAGGCCAAATACCATGCA 60.035 50.000 5.01 0.00 0.00 3.96
6471 10943 0.381801 CACGAGGCCAAATACCATGC 59.618 55.000 5.01 0.00 0.00 4.06
6472 10944 2.036958 TCACGAGGCCAAATACCATG 57.963 50.000 5.01 0.00 0.00 3.66
6473 10945 4.640771 ATATCACGAGGCCAAATACCAT 57.359 40.909 5.01 0.00 0.00 3.55
6474 10946 4.133820 CAATATCACGAGGCCAAATACCA 58.866 43.478 5.01 0.00 0.00 3.25
6475 10947 3.058224 GCAATATCACGAGGCCAAATACC 60.058 47.826 5.01 0.00 0.00 2.73
6476 10948 3.815401 AGCAATATCACGAGGCCAAATAC 59.185 43.478 5.01 0.00 0.00 1.89
6477 10949 4.065088 GAGCAATATCACGAGGCCAAATA 58.935 43.478 5.01 0.00 0.00 1.40
6478 10950 2.880890 GAGCAATATCACGAGGCCAAAT 59.119 45.455 5.01 0.00 0.00 2.32
6479 10951 2.288666 GAGCAATATCACGAGGCCAAA 58.711 47.619 5.01 0.00 0.00 3.28
6480 10952 1.475034 GGAGCAATATCACGAGGCCAA 60.475 52.381 5.01 0.00 0.00 4.52
6481 10953 0.106708 GGAGCAATATCACGAGGCCA 59.893 55.000 5.01 0.00 0.00 5.36
6482 10954 0.946221 CGGAGCAATATCACGAGGCC 60.946 60.000 0.00 0.00 0.00 5.19
6483 10955 0.032130 TCGGAGCAATATCACGAGGC 59.968 55.000 0.00 0.00 0.00 4.70
6484 10956 1.067060 TGTCGGAGCAATATCACGAGG 59.933 52.381 0.00 0.00 33.92 4.63
6485 10957 2.492019 TGTCGGAGCAATATCACGAG 57.508 50.000 0.00 0.00 33.92 4.18
6486 10958 2.951457 TTGTCGGAGCAATATCACGA 57.049 45.000 0.00 0.00 0.00 4.35
6487 10959 3.384668 AGATTGTCGGAGCAATATCACG 58.615 45.455 6.01 0.00 38.98 4.35
6488 10960 5.294306 TCAAAGATTGTCGGAGCAATATCAC 59.706 40.000 6.01 0.00 38.98 3.06
6489 10961 5.294306 GTCAAAGATTGTCGGAGCAATATCA 59.706 40.000 6.01 0.00 38.98 2.15
6490 10962 5.277538 GGTCAAAGATTGTCGGAGCAATATC 60.278 44.000 6.01 0.00 38.98 1.63
6491 10963 4.576463 GGTCAAAGATTGTCGGAGCAATAT 59.424 41.667 6.01 1.86 38.98 1.28
6492 10964 3.938963 GGTCAAAGATTGTCGGAGCAATA 59.061 43.478 6.01 0.00 38.98 1.90
6493 10965 2.749621 GGTCAAAGATTGTCGGAGCAAT 59.250 45.455 5.79 5.79 41.28 3.56
6494 10966 2.151202 GGTCAAAGATTGTCGGAGCAA 58.849 47.619 0.00 0.00 0.00 3.91
6495 10967 1.808411 GGTCAAAGATTGTCGGAGCA 58.192 50.000 0.00 0.00 0.00 4.26
6496 10968 0.721718 CGGTCAAAGATTGTCGGAGC 59.278 55.000 0.00 0.00 0.00 4.70
6503 10975 2.472695 TCAGGGACGGTCAAAGATTG 57.527 50.000 10.76 0.00 0.00 2.67
6504 10976 3.072476 TCTTTCAGGGACGGTCAAAGATT 59.928 43.478 14.02 0.00 29.99 2.40
6512 10984 2.949644 CAGTTTTTCTTTCAGGGACGGT 59.050 45.455 0.00 0.00 0.00 4.83
6514 10986 2.618709 AGCAGTTTTTCTTTCAGGGACG 59.381 45.455 0.00 0.00 0.00 4.79
6516 10988 2.878406 CGAGCAGTTTTTCTTTCAGGGA 59.122 45.455 0.00 0.00 0.00 4.20
6540 11012 7.279313 CAGAATTTCCTATCCAATGCTTTTTGG 59.721 37.037 7.17 7.17 46.28 3.28
6571 11043 7.972277 GTGAAACTCATGCTCATGTCAATTTAT 59.028 33.333 9.41 0.00 39.72 1.40
6659 11131 8.298854 TCATTTAATTGTGTCCTTGACATCTTG 58.701 33.333 0.00 0.00 44.63 3.02
6685 11157 2.379907 ACATCCCATCCTTGGTGAGTTT 59.620 45.455 0.00 0.00 41.91 2.66
6692 11165 2.624838 GCAATGTACATCCCATCCTTGG 59.375 50.000 9.23 0.00 43.23 3.61
6706 11179 1.138266 GTAGGGCGAGGAAGCAATGTA 59.862 52.381 0.00 0.00 39.27 2.29
6709 11182 0.618458 TTGTAGGGCGAGGAAGCAAT 59.382 50.000 0.00 0.00 39.27 3.56
6721 11194 2.874701 CCTCGAATTGCATCTTGTAGGG 59.125 50.000 0.00 0.00 0.00 3.53
6729 11202 0.464373 TGAGGCCCTCGAATTGCATC 60.464 55.000 6.21 7.84 36.43 3.91
6730 11203 0.184451 ATGAGGCCCTCGAATTGCAT 59.816 50.000 6.21 0.00 32.35 3.96
6731 11204 0.034186 AATGAGGCCCTCGAATTGCA 60.034 50.000 6.21 0.00 32.35 4.08
6732 11205 1.604278 GTAATGAGGCCCTCGAATTGC 59.396 52.381 6.21 1.31 32.35 3.56
6733 11206 2.158755 AGGTAATGAGGCCCTCGAATTG 60.159 50.000 6.21 0.00 32.35 2.32
6734 11207 2.127708 AGGTAATGAGGCCCTCGAATT 58.872 47.619 6.21 3.94 32.35 2.17
6735 11208 1.417890 CAGGTAATGAGGCCCTCGAAT 59.582 52.381 6.21 0.00 32.35 3.34
6736 11209 0.830648 CAGGTAATGAGGCCCTCGAA 59.169 55.000 6.21 0.00 32.35 3.71
6737 11210 0.032515 TCAGGTAATGAGGCCCTCGA 60.033 55.000 6.21 0.00 32.77 4.04
6738 11211 2.516448 TCAGGTAATGAGGCCCTCG 58.484 57.895 6.21 0.00 32.77 4.63
6749 11222 4.338400 CGTATCTCACCATGTCTCAGGTAA 59.662 45.833 0.00 0.00 36.07 2.85
6755 11228 4.336993 AGACTTCGTATCTCACCATGTCTC 59.663 45.833 0.00 0.00 0.00 3.36
6768 11241 2.744202 CAGCCAAGCAAAGACTTCGTAT 59.256 45.455 0.00 0.00 0.00 3.06
6769 11242 2.143122 CAGCCAAGCAAAGACTTCGTA 58.857 47.619 0.00 0.00 0.00 3.43
6770 11243 0.947244 CAGCCAAGCAAAGACTTCGT 59.053 50.000 0.00 0.00 0.00 3.85
6771 11244 0.239347 CCAGCCAAGCAAAGACTTCG 59.761 55.000 0.00 0.00 0.00 3.79
6772 11245 1.322442 ACCAGCCAAGCAAAGACTTC 58.678 50.000 0.00 0.00 0.00 3.01
6773 11246 2.656947 TACCAGCCAAGCAAAGACTT 57.343 45.000 0.00 0.00 0.00 3.01
6774 11247 2.656947 TTACCAGCCAAGCAAAGACT 57.343 45.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.