Multiple sequence alignment - TraesCS3B01G302700

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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 TraesCS3B01G302700 chr3B 100.000 5527 0 0 1 5527 486808592 486814118 0.000000e+00 10207.0
1 TraesCS3B01G302700 chr3A 92.636 2064 67 30 43 2066 494037437 494039455 0.000000e+00 2891.0
2 TraesCS3B01G302700 chr3A 87.206 1618 78 44 3826 5377 494041485 494043039 0.000000e+00 1722.0
3 TraesCS3B01G302700 chr3A 89.420 1087 78 16 2640 3723 494040349 494041401 0.000000e+00 1336.0
4 TraesCS3B01G302700 chr3A 81.405 484 45 15 2084 2534 494039600 494040071 2.450000e-93 353.0
5 TraesCS3B01G302700 chr3A 92.763 152 11 0 5374 5525 494043344 494043495 2.590000e-53 220.0
6 TraesCS3B01G302700 chr3D 92.978 1894 59 23 45 1899 372626077 372627935 0.000000e+00 2693.0
7 TraesCS3B01G302700 chr3D 91.127 1296 54 26 3820 5075 372629933 372631207 0.000000e+00 1700.0
8 TraesCS3B01G302700 chr3D 89.219 1345 84 28 2081 3395 372628143 372629456 0.000000e+00 1624.0
9 TraesCS3B01G302700 chr3D 90.964 332 25 3 3394 3723 372629530 372629858 5.080000e-120 442.0
10 TraesCS3B01G302700 chr3D 85.714 70 10 0 5140 5209 38165645 38165576 2.140000e-09 75.0
11 TraesCS3B01G302700 chr1A 83.897 739 63 27 95 816 58300179 58299480 0.000000e+00 654.0
12 TraesCS3B01G302700 chr1A 93.443 61 3 1 3772 3831 45552554 45552494 7.630000e-14 89.8
13 TraesCS3B01G302700 chr1A 87.324 71 6 3 3754 3822 83824980 83824911 1.650000e-10 78.7
14 TraesCS3B01G302700 chr1B 83.179 755 68 28 82 816 95305021 95304306 2.170000e-178 636.0
15 TraesCS3B01G302700 chr1B 94.737 57 2 1 3766 3822 579608124 579608069 2.740000e-13 87.9
16 TraesCS3B01G302700 chr2B 84.872 390 35 11 43 414 461515291 461514908 6.760000e-99 372.0
17 TraesCS3B01G302700 chr5B 95.312 64 3 0 5320 5383 248759831 248759768 9.800000e-18 102.0
18 TraesCS3B01G302700 chr5B 90.625 64 5 1 3767 3829 550215210 550215273 3.550000e-12 84.2
19 TraesCS3B01G302700 chr5B 79.787 94 17 2 5107 5199 592806832 592806740 3.570000e-07 67.6
20 TraesCS3B01G302700 chr5B 100.000 28 0 0 5385 5412 605760718 605760691 1.000000e-02 52.8
21 TraesCS3B01G302700 chr6D 89.474 76 8 0 5144 5219 159514537 159514462 4.560000e-16 97.1
22 TraesCS3B01G302700 chr5D 98.148 54 1 0 3770 3823 416973236 416973289 1.640000e-15 95.3
23 TraesCS3B01G302700 chr5A 96.296 54 2 0 3769 3822 482768158 482768105 7.630000e-14 89.8
24 TraesCS3B01G302700 chr5A 92.982 57 4 0 5153 5209 661030649 661030705 3.550000e-12 84.2
25 TraesCS3B01G302700 chr5A 81.522 92 16 1 5147 5238 655723154 655723064 2.140000e-09 75.0
26 TraesCS3B01G302700 chr5A 81.522 92 16 1 5147 5238 655794266 655794176 2.140000e-09 75.0
27 TraesCS3B01G302700 chr5A 81.522 92 16 1 5147 5238 655866482 655866392 2.140000e-09 75.0
28 TraesCS3B01G302700 chr2D 91.176 68 3 3 3763 3829 334083040 334082975 7.630000e-14 89.8
29 TraesCS3B01G302700 chr2D 93.333 60 2 2 3764 3822 61804619 61804677 2.740000e-13 87.9
30 TraesCS3B01G302700 chr6A 86.842 76 10 0 5144 5219 584247783 584247858 9.860000e-13 86.1
31 TraesCS3B01G302700 chr7B 89.231 65 5 2 3779 3842 639796240 639796303 4.590000e-11 80.5
32 TraesCS3B01G302700 chr7D 87.500 64 8 0 5147 5210 430114589 430114652 2.140000e-09 75.0
33 TraesCS3B01G302700 chr7D 94.595 37 2 0 5062 5098 613633879 613633915 2.150000e-04 58.4
34 TraesCS3B01G302700 chr7A 94.595 37 2 0 5062 5098 705291854 705291890 2.150000e-04 58.4


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 TraesCS3B01G302700 chr3B 486808592 486814118 5526 False 10207.00 10207 100.000 1 5527 1 chr3B.!!$F1 5526
1 TraesCS3B01G302700 chr3A 494037437 494043495 6058 False 1304.40 2891 88.686 43 5525 5 chr3A.!!$F1 5482
2 TraesCS3B01G302700 chr3D 372626077 372631207 5130 False 1614.75 2693 91.072 45 5075 4 chr3D.!!$F1 5030
3 TraesCS3B01G302700 chr1A 58299480 58300179 699 True 654.00 654 83.897 95 816 1 chr1A.!!$R2 721
4 TraesCS3B01G302700 chr1B 95304306 95305021 715 True 636.00 636 83.179 82 816 1 chr1B.!!$R1 734

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
947 998 0.734889 CAGCGGCTCAGGTTTTATGG 59.265 55.000 0.00 0.0 0.00 2.74 F
1650 1714 0.108520 TGATCGGAAGTTGTACGGGC 60.109 55.000 0.00 0.0 0.00 6.13 F
1830 1895 1.557832 GTGCCCTATCTGTGGTGGTAA 59.442 52.381 0.00 0.0 0.00 2.85 F
2262 2537 1.960689 GGTGTTGTGCACTAATTGGGT 59.039 47.619 19.41 0.0 46.86 4.51 F
3442 3995 1.002366 CTCAGGACTAACATGCACGC 58.998 55.000 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 1992 0.389025 CCCGGCCTTTTCATAATGCC 59.611 55.0 0.00 0.00 38.74 4.40 R
2735 3212 0.608130 TGCTCAGTGCCGAACAGTAT 59.392 50.0 0.00 0.00 42.00 2.12 R
3033 3511 0.682855 ATGCCCACGGTACCATTTGG 60.683 55.0 13.54 14.26 42.17 3.28 R
4097 4688 0.249868 GGCCCTTCTTTGCAAACCAC 60.250 55.0 8.05 0.00 0.00 4.16 R
5299 5952 0.774908 AACCCCCGAATTCAACTGGA 59.225 50.0 6.22 0.00 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.998454 CCACATGTCATTAACTCCAGATC 57.002 43.478 0.00 0.00 0.00 2.75
23 24 5.430886 CCACATGTCATTAACTCCAGATCA 58.569 41.667 0.00 0.00 0.00 2.92
24 25 6.060136 CCACATGTCATTAACTCCAGATCAT 58.940 40.000 0.00 0.00 0.00 2.45
25 26 6.544931 CCACATGTCATTAACTCCAGATCATT 59.455 38.462 0.00 0.00 0.00 2.57
26 27 7.716560 CCACATGTCATTAACTCCAGATCATTA 59.283 37.037 0.00 0.00 0.00 1.90
27 28 9.112725 CACATGTCATTAACTCCAGATCATTAA 57.887 33.333 0.00 0.00 0.00 1.40
28 29 9.857656 ACATGTCATTAACTCCAGATCATTAAT 57.142 29.630 0.00 0.00 0.00 1.40
31 32 9.904198 TGTCATTAACTCCAGATCATTAATCAA 57.096 29.630 0.00 0.00 36.79 2.57
33 34 9.565090 TCATTAACTCCAGATCATTAATCAAGG 57.435 33.333 0.00 0.00 36.79 3.61
34 35 9.347240 CATTAACTCCAGATCATTAATCAAGGT 57.653 33.333 0.00 0.00 36.79 3.50
35 36 8.964476 TTAACTCCAGATCATTAATCAAGGTC 57.036 34.615 0.00 0.00 36.79 3.85
36 37 6.566079 ACTCCAGATCATTAATCAAGGTCA 57.434 37.500 0.00 0.00 36.79 4.02
37 38 6.962182 ACTCCAGATCATTAATCAAGGTCAA 58.038 36.000 0.00 0.00 36.79 3.18
38 39 7.052873 ACTCCAGATCATTAATCAAGGTCAAG 58.947 38.462 0.00 0.00 36.79 3.02
39 40 7.092712 ACTCCAGATCATTAATCAAGGTCAAGA 60.093 37.037 0.00 0.00 36.79 3.02
40 41 7.809238 TCCAGATCATTAATCAAGGTCAAGAT 58.191 34.615 0.00 0.00 36.79 2.40
41 42 7.718314 TCCAGATCATTAATCAAGGTCAAGATG 59.282 37.037 0.00 0.00 36.79 2.90
57 58 9.851686 AGGTCAAGATGCATGTTAATAATCTTA 57.148 29.630 9.00 0.00 35.85 2.10
89 90 6.969993 ACTCCAAGATATCTCAGTTACTCC 57.030 41.667 5.51 0.00 0.00 3.85
93 94 5.988561 CCAAGATATCTCAGTTACTCCTTGC 59.011 44.000 5.51 0.00 0.00 4.01
120 124 4.068599 GCCTCTAGACCATTAATCAAGGC 58.931 47.826 0.00 0.00 39.90 4.35
438 469 2.212652 CAGGGCATCGAATCGAATCAA 58.787 47.619 10.12 0.00 39.99 2.57
439 470 2.613595 CAGGGCATCGAATCGAATCAAA 59.386 45.455 10.12 0.00 39.99 2.69
440 471 3.251729 CAGGGCATCGAATCGAATCAAAT 59.748 43.478 10.12 0.00 39.99 2.32
441 472 3.499918 AGGGCATCGAATCGAATCAAATC 59.500 43.478 10.12 0.00 39.99 2.17
442 473 3.250762 GGGCATCGAATCGAATCAAATCA 59.749 43.478 10.12 0.00 39.99 2.57
443 474 4.261155 GGGCATCGAATCGAATCAAATCAA 60.261 41.667 10.12 0.00 39.99 2.57
444 475 5.273170 GGCATCGAATCGAATCAAATCAAA 58.727 37.500 10.12 0.00 39.99 2.69
445 476 5.916883 GGCATCGAATCGAATCAAATCAAAT 59.083 36.000 10.12 0.00 39.99 2.32
446 477 6.087291 GGCATCGAATCGAATCAAATCAAATC 59.913 38.462 10.12 0.00 39.99 2.17
447 478 6.634035 GCATCGAATCGAATCAAATCAAATCA 59.366 34.615 10.12 0.00 39.99 2.57
463 494 7.951347 ATCAAATCATATAGCCAAGGGATTC 57.049 36.000 0.00 0.00 0.00 2.52
631 662 4.361253 GCACACCTTCTGCGAGAA 57.639 55.556 0.00 0.00 32.50 2.87
947 998 0.734889 CAGCGGCTCAGGTTTTATGG 59.265 55.000 0.00 0.00 0.00 2.74
1187 1238 2.202623 CTACGCCACCGAGTCAGC 60.203 66.667 0.00 0.00 38.29 4.26
1272 1332 1.878522 GCTGAACGACATCCGCGAT 60.879 57.895 8.23 0.00 43.32 4.58
1588 1652 9.300681 TCATTTCTTTCTTGATTTCCATGTACT 57.699 29.630 0.00 0.00 0.00 2.73
1589 1653 9.350357 CATTTCTTTCTTGATTTCCATGTACTG 57.650 33.333 0.00 0.00 0.00 2.74
1590 1654 8.463930 TTTCTTTCTTGATTTCCATGTACTGT 57.536 30.769 0.00 0.00 0.00 3.55
1591 1655 9.567776 TTTCTTTCTTGATTTCCATGTACTGTA 57.432 29.630 0.00 0.00 0.00 2.74
1592 1656 9.739276 TTCTTTCTTGATTTCCATGTACTGTAT 57.261 29.630 0.00 0.00 0.00 2.29
1594 1658 8.862325 TTTCTTGATTTCCATGTACTGTATGT 57.138 30.769 0.00 0.00 0.00 2.29
1595 1659 7.848223 TCTTGATTTCCATGTACTGTATGTG 57.152 36.000 0.00 0.00 0.00 3.21
1596 1660 6.316140 TCTTGATTTCCATGTACTGTATGTGC 59.684 38.462 0.00 0.00 0.00 4.57
1597 1661 5.744171 TGATTTCCATGTACTGTATGTGCT 58.256 37.500 0.00 0.00 32.31 4.40
1598 1662 5.817296 TGATTTCCATGTACTGTATGTGCTC 59.183 40.000 0.00 0.00 32.31 4.26
1599 1663 5.420725 TTTCCATGTACTGTATGTGCTCT 57.579 39.130 0.00 0.00 32.31 4.09
1600 1664 6.538945 TTTCCATGTACTGTATGTGCTCTA 57.461 37.500 0.00 0.00 32.31 2.43
1601 1665 5.774498 TCCATGTACTGTATGTGCTCTAG 57.226 43.478 0.00 0.00 32.31 2.43
1602 1666 5.201243 TCCATGTACTGTATGTGCTCTAGT 58.799 41.667 0.00 0.00 32.31 2.57
1603 1667 5.656859 TCCATGTACTGTATGTGCTCTAGTT 59.343 40.000 0.00 0.00 32.31 2.24
1604 1668 5.750547 CCATGTACTGTATGTGCTCTAGTTG 59.249 44.000 0.00 0.00 32.31 3.16
1605 1669 5.977489 TGTACTGTATGTGCTCTAGTTGT 57.023 39.130 0.00 0.00 32.31 3.32
1611 1675 3.550437 ATGTGCTCTAGTTGTCATCCC 57.450 47.619 0.00 0.00 0.00 3.85
1634 1698 3.310774 CGAAGGTTGCTTGATTCGATGAT 59.689 43.478 8.38 0.00 45.50 2.45
1637 1701 2.032549 GGTTGCTTGATTCGATGATCGG 60.033 50.000 15.48 0.00 40.88 4.18
1645 1709 5.257082 TGATTCGATGATCGGAAGTTGTA 57.743 39.130 15.48 0.00 40.88 2.41
1650 1714 0.108520 TGATCGGAAGTTGTACGGGC 60.109 55.000 0.00 0.00 0.00 6.13
1659 1723 2.312390 AGTTGTACGGGCCAACATTTT 58.688 42.857 4.39 0.00 43.61 1.82
1666 1730 1.877258 CGGGCCAACATTTTTGCACAT 60.877 47.619 4.39 0.00 26.94 3.21
1684 1748 4.005650 CACATAAGGTGCTTGATCTGTGT 58.994 43.478 0.00 0.00 41.36 3.72
1720 1784 9.353999 GGAGTTCACATATTTTGAATTTACCAC 57.646 33.333 0.84 0.00 35.47 4.16
1809 1874 4.021544 AGGAGTTTCTGACTGAGCTTACTG 60.022 45.833 0.00 0.00 39.19 2.74
1823 1888 2.743183 GCTTACTGGTGCCCTATCTGTG 60.743 54.545 0.00 0.00 0.00 3.66
1830 1895 1.557832 GTGCCCTATCTGTGGTGGTAA 59.442 52.381 0.00 0.00 0.00 2.85
1884 1949 6.688578 TCCTCAGTGTACAACAATAGAACTC 58.311 40.000 0.00 0.00 0.00 3.01
1927 1992 6.058183 AGGCAGCATGAAAGTACCTTAATAG 58.942 40.000 0.00 0.00 39.69 1.73
1941 2006 9.574516 AGTACCTTAATAGGCATTATGAAAAGG 57.425 33.333 0.00 0.00 46.22 3.11
2012 2077 3.056393 TGAGCTTTGAGAAAATGGGCATG 60.056 43.478 0.00 0.00 0.00 4.06
2116 2380 4.159506 GGCTCCTTATCAGCTAGAGTATGG 59.840 50.000 0.00 0.00 37.05 2.74
2171 2435 4.882671 CCAAGATATGTGGCTTGTGTAC 57.117 45.455 0.00 0.00 39.79 2.90
2214 2486 7.699709 TTGGTGGATAAATCTAATAGGTGGA 57.300 36.000 0.00 0.00 0.00 4.02
2215 2487 7.699709 TGGTGGATAAATCTAATAGGTGGAA 57.300 36.000 0.00 0.00 0.00 3.53
2228 2503 6.808321 AATAGGTGGAACTGTGCTAATCTA 57.192 37.500 0.00 0.00 36.74 1.98
2262 2537 1.960689 GGTGTTGTGCACTAATTGGGT 59.039 47.619 19.41 0.00 46.86 4.51
2356 2631 4.162698 TGCGAAGGAAACCTAGGCTTATAA 59.837 41.667 9.30 0.00 34.44 0.98
2480 2781 6.888105 TCAAAGAAGTATCATATGTGGCAGA 58.112 36.000 1.90 0.00 0.00 4.26
2481 2782 6.988580 TCAAAGAAGTATCATATGTGGCAGAG 59.011 38.462 1.90 0.00 0.00 3.35
2562 2949 5.931441 AATAGAACATGCCGATTTCTAGC 57.069 39.130 8.26 0.00 35.76 3.42
2568 2955 4.986622 ACATGCCGATTTCTAGCTTTTTC 58.013 39.130 0.00 0.00 0.00 2.29
2577 2964 8.906693 CCGATTTCTAGCTTTTTCTTTTCTTTC 58.093 33.333 0.00 0.00 0.00 2.62
2624 3011 8.863049 CACAAAAAGAACATGCCATATTCTTAC 58.137 33.333 11.13 0.00 40.85 2.34
2667 3144 6.989169 AGCATAAGACCTAGTAAAGCATCAAG 59.011 38.462 0.00 0.00 0.00 3.02
2708 3185 8.481492 AATTGCATCTATCATATGTTCCCAAA 57.519 30.769 1.90 0.00 0.00 3.28
2735 3212 4.930696 TCAGGAGGTACTGTGAAGTGATA 58.069 43.478 0.00 0.00 41.55 2.15
2788 3265 8.634475 ACTTTCTGTTTGCTTTACAATCTTTC 57.366 30.769 0.00 0.00 38.31 2.62
2797 3274 7.004555 TGCTTTACAATCTTTCAGTCTCCTA 57.995 36.000 0.00 0.00 0.00 2.94
2817 3294 9.699410 TCTCCTAAAATTGTATTCCAACATGAT 57.301 29.630 0.00 0.00 35.44 2.45
2864 3342 5.300034 AGTTCATGCAGTGATTGTTTTCAGA 59.700 36.000 0.00 0.00 36.54 3.27
2926 3404 8.121305 ACTTCAACATCTACAAAATAATGGCA 57.879 30.769 0.00 0.00 0.00 4.92
2930 3408 9.941325 TCAACATCTACAAAATAATGGCAAAAT 57.059 25.926 0.00 0.00 0.00 1.82
2956 3434 5.168647 TGTATTCGTTTGGGTAACTGGAT 57.831 39.130 0.00 0.00 34.46 3.41
3163 3641 6.183360 CCTCTGAATTGATCACAATGAAGACC 60.183 42.308 0.00 0.00 44.67 3.85
3267 3745 2.026641 CAGGATACAAGTGCCATTGGG 58.973 52.381 4.53 0.00 41.41 4.12
3300 3778 2.158519 GGATGGGATTCGGTTAATGGGT 60.159 50.000 0.00 0.00 0.00 4.51
3333 3811 6.821665 CAGAAGAAATCAAATGGCCAATTCAT 59.178 34.615 10.96 0.00 0.00 2.57
3433 3986 6.253758 TCAAGTACTCCATTCTCAGGACTAA 58.746 40.000 0.00 0.00 32.10 2.24
3442 3995 1.002366 CTCAGGACTAACATGCACGC 58.998 55.000 0.00 0.00 0.00 5.34
3454 4007 2.009051 CATGCACGCTTTCATAGTCCA 58.991 47.619 0.00 0.00 0.00 4.02
3470 4023 6.368791 TCATAGTCCAATTCTGTTCAGTTTCG 59.631 38.462 0.00 0.00 0.00 3.46
3475 4028 4.213270 CCAATTCTGTTCAGTTTCGTGCTA 59.787 41.667 0.00 0.00 0.00 3.49
3483 4036 1.660607 CAGTTTCGTGCTACATGCGAT 59.339 47.619 0.00 0.00 46.63 4.58
3523 4076 1.663695 AAATGTATCTGTTCCGCCGG 58.336 50.000 0.00 0.00 0.00 6.13
3622 4176 6.743110 TGCTTGCAATCATGTTTAGTACAAA 58.257 32.000 0.00 0.00 40.89 2.83
3628 4182 9.225436 TGCAATCATGTTTAGTACAAATAGTGA 57.775 29.630 0.00 0.00 40.89 3.41
3651 4205 4.583871 CTCTTTTGTAGAGGCAATGAGGT 58.416 43.478 0.00 0.00 45.61 3.85
3724 4280 2.781945 GCATGTGCCCAACTAATAGC 57.218 50.000 0.00 0.00 34.31 2.97
3725 4281 1.338020 GCATGTGCCCAACTAATAGCC 59.662 52.381 0.00 0.00 34.31 3.93
3730 4320 1.765904 TGCCCAACTAATAGCCGATGA 59.234 47.619 0.00 0.00 0.00 2.92
3741 4331 2.254546 AGCCGATGACAGTGACAAAA 57.745 45.000 0.00 0.00 0.00 2.44
3772 4362 6.254157 CCAGCATGATTTTACTTGCAATGTAC 59.746 38.462 0.00 0.00 41.33 2.90
3773 4363 7.031372 CAGCATGATTTTACTTGCAATGTACT 58.969 34.615 0.00 0.00 41.33 2.73
3774 4364 7.219535 CAGCATGATTTTACTTGCAATGTACTC 59.780 37.037 0.00 3.39 41.33 2.59
3775 4365 6.473455 GCATGATTTTACTTGCAATGTACTCC 59.527 38.462 0.00 0.00 39.58 3.85
3776 4366 6.509418 TGATTTTACTTGCAATGTACTCCC 57.491 37.500 0.00 0.00 0.00 4.30
3777 4367 6.245408 TGATTTTACTTGCAATGTACTCCCT 58.755 36.000 0.00 0.00 0.00 4.20
3778 4368 6.374333 TGATTTTACTTGCAATGTACTCCCTC 59.626 38.462 0.00 0.00 0.00 4.30
3779 4369 5.499004 TTTACTTGCAATGTACTCCCTCT 57.501 39.130 0.00 0.00 0.00 3.69
3780 4370 3.340814 ACTTGCAATGTACTCCCTCTG 57.659 47.619 0.00 0.00 0.00 3.35
3781 4371 2.639839 ACTTGCAATGTACTCCCTCTGT 59.360 45.455 0.00 0.00 0.00 3.41
3782 4372 3.838317 ACTTGCAATGTACTCCCTCTGTA 59.162 43.478 0.00 0.00 0.00 2.74
3783 4373 4.081420 ACTTGCAATGTACTCCCTCTGTAG 60.081 45.833 0.00 0.00 0.00 2.74
3784 4374 3.441101 TGCAATGTACTCCCTCTGTAGT 58.559 45.455 0.00 0.00 0.00 2.73
3785 4375 3.195610 TGCAATGTACTCCCTCTGTAGTG 59.804 47.826 0.00 0.00 0.00 2.74
3786 4376 3.447586 GCAATGTACTCCCTCTGTAGTGA 59.552 47.826 0.00 0.00 0.00 3.41
3787 4377 4.100189 GCAATGTACTCCCTCTGTAGTGAT 59.900 45.833 0.00 0.00 0.00 3.06
3788 4378 5.737635 GCAATGTACTCCCTCTGTAGTGATC 60.738 48.000 0.00 0.00 0.00 2.92
3789 4379 4.864483 TGTACTCCCTCTGTAGTGATCT 57.136 45.455 0.00 0.00 0.00 2.75
3790 4380 5.970501 TGTACTCCCTCTGTAGTGATCTA 57.029 43.478 0.00 0.00 0.00 1.98
3791 4381 6.323210 TGTACTCCCTCTGTAGTGATCTAA 57.677 41.667 0.00 0.00 0.00 2.10
3792 4382 6.728411 TGTACTCCCTCTGTAGTGATCTAAA 58.272 40.000 0.00 0.00 0.00 1.85
3793 4383 6.602406 TGTACTCCCTCTGTAGTGATCTAAAC 59.398 42.308 0.00 0.00 0.00 2.01
3794 4384 4.641094 ACTCCCTCTGTAGTGATCTAAACG 59.359 45.833 0.00 0.00 0.00 3.60
3795 4385 3.380637 TCCCTCTGTAGTGATCTAAACGC 59.619 47.826 0.00 0.00 0.00 4.84
3796 4386 3.381908 CCCTCTGTAGTGATCTAAACGCT 59.618 47.826 0.00 0.00 0.00 5.07
3797 4387 4.498345 CCCTCTGTAGTGATCTAAACGCTC 60.498 50.000 0.00 0.00 0.00 5.03
3798 4388 4.336993 CCTCTGTAGTGATCTAAACGCTCT 59.663 45.833 0.00 0.00 0.00 4.09
3799 4389 5.163602 CCTCTGTAGTGATCTAAACGCTCTT 60.164 44.000 0.00 0.00 0.00 2.85
3800 4390 6.038382 CCTCTGTAGTGATCTAAACGCTCTTA 59.962 42.308 0.00 0.00 0.00 2.10
3801 4391 7.255312 CCTCTGTAGTGATCTAAACGCTCTTAT 60.255 40.741 0.00 0.00 0.00 1.73
3802 4392 8.672823 TCTGTAGTGATCTAAACGCTCTTATA 57.327 34.615 0.00 0.00 0.00 0.98
3803 4393 9.286170 TCTGTAGTGATCTAAACGCTCTTATAT 57.714 33.333 0.00 0.00 0.00 0.86
3804 4394 9.900710 CTGTAGTGATCTAAACGCTCTTATATT 57.099 33.333 0.00 0.00 0.00 1.28
3817 4407 9.930693 AACGCTCTTATATTTCTTTATAGAGGG 57.069 33.333 0.00 0.00 38.95 4.30
3818 4408 9.310449 ACGCTCTTATATTTCTTTATAGAGGGA 57.690 33.333 16.73 0.00 37.30 4.20
3819 4409 9.796120 CGCTCTTATATTTCTTTATAGAGGGAG 57.204 37.037 0.00 0.00 36.40 4.30
3917 4508 2.371841 AGGTCAGCTGTGAACATTGGTA 59.628 45.455 14.67 0.00 43.64 3.25
3939 4530 7.936847 TGGTACTGTGGATTGGATTTGATATAC 59.063 37.037 0.00 0.00 0.00 1.47
3972 4563 6.889722 TCAAATTTCACGAATCCCTTCCTAAT 59.110 34.615 0.00 0.00 0.00 1.73
4085 4676 1.531602 GCTTGGGTTCAGGGCACTT 60.532 57.895 0.00 0.00 0.00 3.16
4097 4688 5.384367 TCAGGGCACTTCTCAAACCTGAG 62.384 52.174 7.10 0.00 46.79 3.35
4132 4723 1.683938 GGGCCGCCTTATACCAAAAGT 60.684 52.381 9.86 0.00 0.00 2.66
4354 4945 3.634910 ACCGGGCATTTATAACAATCACC 59.365 43.478 6.32 0.00 0.00 4.02
4362 4953 6.914757 GCATTTATAACAATCACCTGCTCTTC 59.085 38.462 0.00 0.00 0.00 2.87
4373 4964 1.346068 CCTGCTCTTCCCTATAGGTGC 59.654 57.143 17.72 12.85 36.75 5.01
4430 5021 0.304705 GCTACGCGGGAATGACATTG 59.695 55.000 12.47 0.00 0.00 2.82
4439 5030 4.256920 CGGGAATGACATTGTCTTCTTCT 58.743 43.478 17.26 0.00 33.15 2.85
4497 5088 4.164604 TGGCGGGTAAAATATCCTGTAACT 59.835 41.667 0.00 0.00 33.07 2.24
4527 5141 6.471976 TGAGAGATCAGTTCATTGTTTTCG 57.528 37.500 0.00 0.00 0.00 3.46
4563 5196 8.097662 ACTTTTTCTCTAGGACAATACTTCAGG 58.902 37.037 0.00 0.00 0.00 3.86
4650 5288 4.508662 AGGAGCGTCTATCAAAAAGGAAG 58.491 43.478 0.00 0.00 0.00 3.46
4653 5291 5.411669 GGAGCGTCTATCAAAAAGGAAGAAA 59.588 40.000 0.00 0.00 0.00 2.52
4687 5334 0.251916 TGACCCCAATAGCCAACGAG 59.748 55.000 0.00 0.00 0.00 4.18
4697 5344 2.750350 CCAACGAGCCTTCCCTGT 59.250 61.111 0.00 0.00 0.00 4.00
4698 5345 1.073199 CCAACGAGCCTTCCCTGTT 59.927 57.895 0.00 0.00 0.00 3.16
4735 5385 1.431496 GCCACGAGCATTGCAAATTT 58.569 45.000 11.91 0.00 42.97 1.82
4736 5386 2.605030 GCCACGAGCATTGCAAATTTA 58.395 42.857 11.91 0.00 42.97 1.40
4737 5387 2.992543 GCCACGAGCATTGCAAATTTAA 59.007 40.909 11.91 0.00 42.97 1.52
4738 5388 3.431572 GCCACGAGCATTGCAAATTTAAA 59.568 39.130 11.91 0.00 42.97 1.52
4739 5389 4.084118 GCCACGAGCATTGCAAATTTAAAA 60.084 37.500 11.91 0.00 42.97 1.52
4740 5390 5.373262 CCACGAGCATTGCAAATTTAAAAC 58.627 37.500 11.91 0.00 0.00 2.43
4741 5391 5.050499 CCACGAGCATTGCAAATTTAAAACA 60.050 36.000 11.91 0.00 0.00 2.83
4742 5392 6.066410 CACGAGCATTGCAAATTTAAAACAG 58.934 36.000 11.91 0.00 0.00 3.16
4743 5393 5.074791 CGAGCATTGCAAATTTAAAACAGC 58.925 37.500 11.91 0.00 0.00 4.40
4744 5394 5.333187 CGAGCATTGCAAATTTAAAACAGCA 60.333 36.000 11.91 7.46 0.00 4.41
4767 5417 4.392921 AGTTAGCGAGCATGACAACTAT 57.607 40.909 0.00 0.00 0.00 2.12
4800 5450 9.727627 GTTTTGTTTTTCATCATAAAATTGCCA 57.272 25.926 0.00 0.00 0.00 4.92
4842 5492 1.479323 CATCTTTGCCCATCCTTGTGG 59.521 52.381 0.00 0.00 39.05 4.17
4893 5543 2.270434 TGCCACCCTTCCTAGAGAAT 57.730 50.000 0.00 0.00 32.82 2.40
4906 5556 2.215907 AGAGAATCGTCCGCTGAATG 57.784 50.000 0.00 0.00 42.67 2.67
5043 5695 8.903820 GGGGCGATATCTTTAGCAATTTATTAT 58.096 33.333 0.34 0.00 0.00 1.28
5100 5753 0.544223 TGGTTACATGCATACCCGCT 59.456 50.000 13.42 0.00 0.00 5.52
5107 5760 0.681733 ATGCATACCCGCTAGACCAG 59.318 55.000 0.00 0.00 0.00 4.00
5108 5761 0.686441 TGCATACCCGCTAGACCAGT 60.686 55.000 0.00 0.00 0.00 4.00
5109 5762 1.325355 GCATACCCGCTAGACCAGTA 58.675 55.000 0.00 0.00 0.00 2.74
5110 5763 1.684983 GCATACCCGCTAGACCAGTAA 59.315 52.381 0.00 0.00 0.00 2.24
5111 5764 2.101917 GCATACCCGCTAGACCAGTAAA 59.898 50.000 0.00 0.00 0.00 2.01
5112 5765 3.431207 GCATACCCGCTAGACCAGTAAAA 60.431 47.826 0.00 0.00 0.00 1.52
5113 5766 4.742743 GCATACCCGCTAGACCAGTAAAAT 60.743 45.833 0.00 0.00 0.00 1.82
5114 5767 3.994931 ACCCGCTAGACCAGTAAAATT 57.005 42.857 0.00 0.00 0.00 1.82
5115 5768 3.606687 ACCCGCTAGACCAGTAAAATTG 58.393 45.455 0.00 0.00 0.00 2.32
5116 5769 2.943033 CCCGCTAGACCAGTAAAATTGG 59.057 50.000 0.00 0.00 41.60 3.16
5169 5822 9.797556 AAATTTTAGGGTATTAAACTTGATCGC 57.202 29.630 0.00 0.00 0.00 4.58
5196 5849 2.288961 ACTCACGTGTGAAGTTTCGT 57.711 45.000 23.32 0.00 39.39 3.85
5220 5873 7.224557 CGTGAAGAAATGACATATGTGGTATCA 59.775 37.037 14.43 4.78 0.00 2.15
5228 5881 5.759763 TGACATATGTGGTATCATGAGCAAC 59.240 40.000 14.43 1.08 0.00 4.17
5238 5891 7.326063 GTGGTATCATGAGCAACAAAAAGTAAC 59.674 37.037 0.09 0.00 0.00 2.50
5240 5893 5.493133 TCATGAGCAACAAAAAGTAACGT 57.507 34.783 0.00 0.00 0.00 3.99
5241 5894 5.885881 TCATGAGCAACAAAAAGTAACGTT 58.114 33.333 5.88 5.88 0.00 3.99
5243 5896 6.908284 TCATGAGCAACAAAAAGTAACGTTAC 59.092 34.615 27.23 27.23 0.00 2.50
5246 5899 5.334319 AGCAACAAAAAGTAACGTTACACC 58.666 37.500 33.43 12.89 36.12 4.16
5251 5904 7.109006 ACAAAAAGTAACGTTACACCTATCG 57.891 36.000 33.43 19.71 36.12 2.92
5263 5916 6.205464 CGTTACACCTATCGTAAGGGATCTTA 59.795 42.308 9.98 0.00 41.32 2.10
5271 5924 3.075866 GTAAGGGATCTTACGTGACCG 57.924 52.381 0.00 0.00 43.79 4.79
5280 5933 2.756207 TCTTACGTGACCGATTGGATGA 59.244 45.455 5.81 0.00 39.21 2.92
5283 5936 2.985896 ACGTGACCGATTGGATGAAAT 58.014 42.857 5.81 0.00 39.21 2.17
5285 5938 3.198068 CGTGACCGATTGGATGAAATCT 58.802 45.455 5.81 0.00 39.03 2.40
5286 5939 3.001634 CGTGACCGATTGGATGAAATCTG 59.998 47.826 5.81 0.00 39.03 2.90
5295 5948 1.697284 GATGAAATCTGGGAAGGGGC 58.303 55.000 0.00 0.00 41.17 5.80
5304 5957 3.023735 GGAAGGGGCCCATCCAGT 61.024 66.667 36.14 9.53 36.21 4.00
5305 5958 2.626467 GGAAGGGGCCCATCCAGTT 61.626 63.158 36.14 16.81 36.21 3.16
5306 5959 1.380380 GAAGGGGCCCATCCAGTTG 60.380 63.158 27.72 0.00 36.21 3.16
5307 5960 1.856873 AAGGGGCCCATCCAGTTGA 60.857 57.895 27.72 0.00 36.21 3.18
5308 5961 1.442886 AAGGGGCCCATCCAGTTGAA 61.443 55.000 27.72 0.00 36.21 2.69
5309 5962 1.224003 AGGGGCCCATCCAGTTGAAT 61.224 55.000 27.72 0.00 36.21 2.57
5310 5963 0.325577 GGGGCCCATCCAGTTGAATT 60.326 55.000 26.86 0.00 36.21 2.17
5311 5964 1.114627 GGGCCCATCCAGTTGAATTC 58.885 55.000 19.95 0.00 36.21 2.17
5312 5965 0.740737 GGCCCATCCAGTTGAATTCG 59.259 55.000 0.04 0.00 34.01 3.34
5317 5970 0.999712 ATCCAGTTGAATTCGGGGGT 59.000 50.000 0.04 0.00 0.00 4.95
5345 5998 1.913419 TGGTTAGGGATGGAAGGTCAC 59.087 52.381 0.00 0.00 0.00 3.67
5346 5999 1.134491 GGTTAGGGATGGAAGGTCACG 60.134 57.143 0.00 0.00 0.00 4.35
5383 6344 4.100498 CCCCTTCGTAGGTCTAGCATTTTA 59.900 45.833 7.37 0.00 40.19 1.52
5384 6345 5.395990 CCCCTTCGTAGGTCTAGCATTTTAA 60.396 44.000 7.37 0.00 40.19 1.52
5408 6369 1.113517 GTCTACCCGGCTGGAGCATA 61.114 60.000 15.09 0.00 44.36 3.14
5476 6437 3.412879 GAGTCAGTACCGGCCGAGC 62.413 68.421 30.73 16.14 0.00 5.03
5515 6476 1.601419 CTCCCTCTCGTTTGCCCGTA 61.601 60.000 0.00 0.00 0.00 4.02
5525 6486 2.147958 GTTTGCCCGTACAGTGATGAA 58.852 47.619 0.00 0.00 0.00 2.57
5526 6487 2.550606 GTTTGCCCGTACAGTGATGAAA 59.449 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.430886 TGATCTGGAGTTAATGACATGTGG 58.569 41.667 1.15 0.00 0.00 4.17
1 2 7.563888 AATGATCTGGAGTTAATGACATGTG 57.436 36.000 1.15 0.00 0.00 3.21
2 3 9.857656 ATTAATGATCTGGAGTTAATGACATGT 57.142 29.630 0.00 0.00 0.00 3.21
5 6 9.904198 TTGATTAATGATCTGGAGTTAATGACA 57.096 29.630 0.00 0.00 35.69 3.58
7 8 9.565090 CCTTGATTAATGATCTGGAGTTAATGA 57.435 33.333 0.00 0.00 35.69 2.57
8 9 9.347240 ACCTTGATTAATGATCTGGAGTTAATG 57.653 33.333 0.00 0.00 35.69 1.90
9 10 9.566432 GACCTTGATTAATGATCTGGAGTTAAT 57.434 33.333 0.00 0.00 35.69 1.40
10 11 8.548025 TGACCTTGATTAATGATCTGGAGTTAA 58.452 33.333 0.00 0.00 35.69 2.01
11 12 8.089625 TGACCTTGATTAATGATCTGGAGTTA 57.910 34.615 0.00 0.00 35.69 2.24
12 13 6.962182 TGACCTTGATTAATGATCTGGAGTT 58.038 36.000 0.00 0.00 35.69 3.01
13 14 6.566079 TGACCTTGATTAATGATCTGGAGT 57.434 37.500 0.00 0.00 35.69 3.85
14 15 7.278135 TCTTGACCTTGATTAATGATCTGGAG 58.722 38.462 0.00 0.00 35.69 3.86
15 16 7.199167 TCTTGACCTTGATTAATGATCTGGA 57.801 36.000 0.00 0.00 35.69 3.86
16 17 7.521748 GCATCTTGACCTTGATTAATGATCTGG 60.522 40.741 0.00 0.00 35.69 3.86
17 18 7.012989 TGCATCTTGACCTTGATTAATGATCTG 59.987 37.037 0.00 0.00 35.69 2.90
18 19 7.058525 TGCATCTTGACCTTGATTAATGATCT 58.941 34.615 0.00 0.00 35.69 2.75
19 20 7.268199 TGCATCTTGACCTTGATTAATGATC 57.732 36.000 0.00 0.00 35.21 2.92
20 21 7.287005 ACATGCATCTTGACCTTGATTAATGAT 59.713 33.333 0.00 0.00 0.00 2.45
21 22 6.604396 ACATGCATCTTGACCTTGATTAATGA 59.396 34.615 0.00 0.00 0.00 2.57
22 23 6.802608 ACATGCATCTTGACCTTGATTAATG 58.197 36.000 0.00 0.00 0.00 1.90
23 24 7.414222 AACATGCATCTTGACCTTGATTAAT 57.586 32.000 0.00 0.00 0.00 1.40
24 25 6.839124 AACATGCATCTTGACCTTGATTAA 57.161 33.333 0.00 0.00 0.00 1.40
25 26 7.936496 TTAACATGCATCTTGACCTTGATTA 57.064 32.000 0.00 0.00 0.00 1.75
26 27 6.839124 TTAACATGCATCTTGACCTTGATT 57.161 33.333 0.00 0.00 0.00 2.57
27 28 8.523915 TTATTAACATGCATCTTGACCTTGAT 57.476 30.769 0.00 0.00 0.00 2.57
28 29 7.936496 TTATTAACATGCATCTTGACCTTGA 57.064 32.000 0.00 0.00 0.00 3.02
29 30 8.627403 AGATTATTAACATGCATCTTGACCTTG 58.373 33.333 0.00 0.00 0.00 3.61
30 31 8.757982 AGATTATTAACATGCATCTTGACCTT 57.242 30.769 0.00 0.00 0.00 3.50
31 32 8.757982 AAGATTATTAACATGCATCTTGACCT 57.242 30.769 0.00 0.00 33.78 3.85
57 58 9.427821 ACTGAGATATCTTGGAGTATTACACTT 57.572 33.333 6.70 0.00 37.72 3.16
71 72 5.663106 TGGCAAGGAGTAACTGAGATATCTT 59.337 40.000 6.70 0.00 0.00 2.40
89 90 0.249657 GGTCTAGAGGCGATGGCAAG 60.250 60.000 1.01 0.00 42.47 4.01
93 94 4.021104 TGATTAATGGTCTAGAGGCGATGG 60.021 45.833 0.00 0.00 0.00 3.51
161 177 9.982651 GAGCAGATGGTACTGTAGATTTATTTA 57.017 33.333 0.00 0.00 39.73 1.40
162 178 7.934120 GGAGCAGATGGTACTGTAGATTTATTT 59.066 37.037 0.00 0.00 39.73 1.40
163 179 7.445945 GGAGCAGATGGTACTGTAGATTTATT 58.554 38.462 0.00 0.00 39.73 1.40
164 180 6.294787 CGGAGCAGATGGTACTGTAGATTTAT 60.295 42.308 0.00 0.00 39.73 1.40
165 181 5.009710 CGGAGCAGATGGTACTGTAGATTTA 59.990 44.000 0.00 0.00 39.73 1.40
166 182 4.202161 CGGAGCAGATGGTACTGTAGATTT 60.202 45.833 0.00 0.00 39.73 2.17
167 183 3.319405 CGGAGCAGATGGTACTGTAGATT 59.681 47.826 0.00 0.00 39.73 2.40
303 333 4.177026 GCGCTTCTCAAAGTTCATCTCTA 58.823 43.478 0.00 0.00 34.79 2.43
438 469 7.121759 CGAATCCCTTGGCTATATGATTTGATT 59.878 37.037 0.00 0.00 0.00 2.57
439 470 6.600822 CGAATCCCTTGGCTATATGATTTGAT 59.399 38.462 0.00 0.00 0.00 2.57
440 471 5.939883 CGAATCCCTTGGCTATATGATTTGA 59.060 40.000 0.00 0.00 0.00 2.69
441 472 5.392380 GCGAATCCCTTGGCTATATGATTTG 60.392 44.000 0.00 0.00 33.71 2.32
442 473 4.702131 GCGAATCCCTTGGCTATATGATTT 59.298 41.667 0.00 0.00 33.71 2.17
443 474 4.263462 TGCGAATCCCTTGGCTATATGATT 60.263 41.667 0.00 0.00 37.05 2.57
444 475 3.264193 TGCGAATCCCTTGGCTATATGAT 59.736 43.478 0.00 0.00 37.05 2.45
445 476 2.637382 TGCGAATCCCTTGGCTATATGA 59.363 45.455 0.00 0.00 37.05 2.15
446 477 3.057969 TGCGAATCCCTTGGCTATATG 57.942 47.619 0.00 0.00 37.05 1.78
447 478 5.371526 CATATGCGAATCCCTTGGCTATAT 58.628 41.667 0.00 0.00 37.05 0.86
463 494 1.228063 AGAGGCAAGCCCATATGCG 60.228 57.895 7.62 0.00 43.47 4.73
699 730 2.513204 TCCTACCCTCTCGTCGCG 60.513 66.667 0.00 0.00 0.00 5.87
706 737 0.336737 CTGTCCACCTCCTACCCTCT 59.663 60.000 0.00 0.00 0.00 3.69
819 851 4.023291 GCACCCAAAAATCCTAATCCTCA 58.977 43.478 0.00 0.00 0.00 3.86
947 998 0.108520 TAGAATGGACGGTTCCGTGC 60.109 55.000 24.61 24.61 46.37 5.34
1017 1068 1.287815 CAACATGGCTGCTGTGGTG 59.712 57.895 8.07 8.07 0.00 4.17
1018 1069 2.567497 GCAACATGGCTGCTGTGGT 61.567 57.895 13.24 0.00 36.84 4.16
1019 1070 2.260434 GCAACATGGCTGCTGTGG 59.740 61.111 13.24 0.00 36.84 4.17
1562 1626 9.300681 AGTACATGGAAATCAAGAAAGAAATGA 57.699 29.630 0.00 0.00 0.00 2.57
1563 1627 9.350357 CAGTACATGGAAATCAAGAAAGAAATG 57.650 33.333 0.00 0.00 0.00 2.32
1564 1628 9.082313 ACAGTACATGGAAATCAAGAAAGAAAT 57.918 29.630 0.00 0.00 0.00 2.17
1567 1631 9.166173 CATACAGTACATGGAAATCAAGAAAGA 57.834 33.333 0.00 0.00 0.00 2.52
1568 1632 8.950210 ACATACAGTACATGGAAATCAAGAAAG 58.050 33.333 0.00 0.00 0.00 2.62
1571 1635 6.316140 GCACATACAGTACATGGAAATCAAGA 59.684 38.462 0.00 0.00 0.00 3.02
1576 1640 5.994250 AGAGCACATACAGTACATGGAAAT 58.006 37.500 0.00 0.00 0.00 2.17
1587 1651 5.046529 GGATGACAACTAGAGCACATACAG 58.953 45.833 0.00 0.00 0.00 2.74
1588 1652 4.141937 GGGATGACAACTAGAGCACATACA 60.142 45.833 0.00 0.00 0.00 2.29
1589 1653 4.372656 GGGATGACAACTAGAGCACATAC 58.627 47.826 0.00 0.00 0.00 2.39
1590 1654 3.388024 GGGGATGACAACTAGAGCACATA 59.612 47.826 0.00 0.00 0.00 2.29
1591 1655 2.171448 GGGGATGACAACTAGAGCACAT 59.829 50.000 0.00 0.00 0.00 3.21
1592 1656 1.555075 GGGGATGACAACTAGAGCACA 59.445 52.381 0.00 0.00 0.00 4.57
1594 1658 0.824109 CGGGGATGACAACTAGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
1595 1659 1.112113 TCGGGGATGACAACTAGAGC 58.888 55.000 0.00 0.00 0.00 4.09
1596 1660 2.101582 CCTTCGGGGATGACAACTAGAG 59.898 54.545 0.00 0.00 37.23 2.43
1597 1661 2.108168 CCTTCGGGGATGACAACTAGA 58.892 52.381 0.00 0.00 37.23 2.43
1598 1662 1.831736 ACCTTCGGGGATGACAACTAG 59.168 52.381 2.52 0.00 40.03 2.57
1599 1663 1.946984 ACCTTCGGGGATGACAACTA 58.053 50.000 2.52 0.00 40.03 2.24
1600 1664 1.064825 AACCTTCGGGGATGACAACT 58.935 50.000 2.52 0.00 40.03 3.16
1601 1665 1.165270 CAACCTTCGGGGATGACAAC 58.835 55.000 2.52 0.00 39.87 3.32
1602 1666 0.608035 GCAACCTTCGGGGATGACAA 60.608 55.000 9.08 0.00 39.87 3.18
1603 1667 1.002624 GCAACCTTCGGGGATGACA 60.003 57.895 9.08 0.00 39.87 3.58
1604 1668 0.322546 AAGCAACCTTCGGGGATGAC 60.323 55.000 9.08 2.55 39.87 3.06
1605 1669 0.322456 CAAGCAACCTTCGGGGATGA 60.322 55.000 9.08 0.00 39.87 2.92
1611 1675 1.438651 TCGAATCAAGCAACCTTCGG 58.561 50.000 10.28 0.00 40.52 4.30
1634 1698 1.756408 TTGGCCCGTACAACTTCCGA 61.756 55.000 0.00 0.00 0.00 4.55
1637 1701 1.530323 ATGTTGGCCCGTACAACTTC 58.470 50.000 0.00 0.00 46.28 3.01
1645 1709 0.531753 GTGCAAAAATGTTGGCCCGT 60.532 50.000 0.00 0.00 32.01 5.28
1650 1714 5.594724 CACCTTATGTGCAAAAATGTTGG 57.405 39.130 0.00 0.00 38.34 3.77
1666 1730 4.202357 ACAGAACACAGATCAAGCACCTTA 60.202 41.667 0.00 0.00 0.00 2.69
1684 1748 0.176910 TGTGAACTCCGTGCACAGAA 59.823 50.000 18.64 0.00 45.95 3.02
1720 1784 1.488527 GTAGCACTCGGAATAAGCGG 58.511 55.000 0.00 0.00 0.00 5.52
1790 1855 3.743396 CACCAGTAAGCTCAGTCAGAAAC 59.257 47.826 0.00 0.00 0.00 2.78
1823 1888 2.754002 AGCTCGTCTAAGAGTTACCACC 59.246 50.000 0.00 0.00 40.26 4.61
1830 1895 3.074675 TCCAGAAGCTCGTCTAAGAGT 57.925 47.619 0.00 0.00 40.26 3.24
1884 1949 4.574013 TGCCTTTTGCCATTTTTAACACAG 59.426 37.500 0.00 0.00 40.16 3.66
1927 1992 0.389025 CCCGGCCTTTTCATAATGCC 59.611 55.000 0.00 0.00 38.74 4.40
1941 2006 1.947456 GTGAAAATCCACTATCCCGGC 59.053 52.381 0.00 0.00 34.38 6.13
1999 2064 2.519771 TCTCAGCATGCCCATTTTCT 57.480 45.000 15.66 0.00 34.76 2.52
2000 2065 4.098349 TGTTATCTCAGCATGCCCATTTTC 59.902 41.667 15.66 0.04 34.76 2.29
2012 2077 6.736123 TCGGTACTTTCTATGTTATCTCAGC 58.264 40.000 0.00 0.00 0.00 4.26
2116 2380 3.819564 TCCACCACTGCTCACATATAC 57.180 47.619 0.00 0.00 0.00 1.47
2171 2435 3.052036 CAAAGTTTGGCGACCAATTCAG 58.948 45.455 7.78 0.25 43.55 3.02
2202 2474 6.611642 AGATTAGCACAGTTCCACCTATTAGA 59.388 38.462 0.00 0.00 0.00 2.10
2203 2475 6.821388 AGATTAGCACAGTTCCACCTATTAG 58.179 40.000 0.00 0.00 0.00 1.73
2208 2480 5.045578 ACAATAGATTAGCACAGTTCCACCT 60.046 40.000 0.00 0.00 0.00 4.00
2214 2486 7.766278 CAGGTCTTACAATAGATTAGCACAGTT 59.234 37.037 0.00 0.00 0.00 3.16
2215 2487 7.124298 TCAGGTCTTACAATAGATTAGCACAGT 59.876 37.037 0.00 0.00 0.00 3.55
2228 2503 4.389374 CACAACACCTCAGGTCTTACAAT 58.611 43.478 0.00 0.00 31.02 2.71
2262 2537 9.276590 CTGTAATAGATATGTCCAAAATCAGCA 57.723 33.333 0.00 0.00 0.00 4.41
2319 2594 5.957842 TCCTTCGCAAACAAATATCAAGT 57.042 34.783 0.00 0.00 0.00 3.16
2335 2610 8.897872 TTAATTATAAGCCTAGGTTTCCTTCG 57.102 34.615 14.89 0.00 34.61 3.79
2401 2677 7.606456 CCAAATAGTCCACACTGTACTAACATT 59.394 37.037 0.00 0.00 34.37 2.71
2411 2687 1.812571 GGCACCAAATAGTCCACACTG 59.187 52.381 0.00 0.00 33.62 3.66
2416 2692 0.398696 ACACGGCACCAAATAGTCCA 59.601 50.000 0.00 0.00 0.00 4.02
2417 2693 1.530323 AACACGGCACCAAATAGTCC 58.470 50.000 0.00 0.00 0.00 3.85
2515 2816 6.579666 AAAATATTCTTGCAGTGCTCTTCA 57.420 33.333 17.60 0.00 0.00 3.02
2553 2940 9.973450 AGGAAAGAAAAGAAAAAGCTAGAAATC 57.027 29.630 0.00 0.00 0.00 2.17
2557 2944 9.803315 GAAAAGGAAAGAAAAGAAAAAGCTAGA 57.197 29.630 0.00 0.00 0.00 2.43
2561 2948 8.256611 ACAGAAAAGGAAAGAAAAGAAAAAGC 57.743 30.769 0.00 0.00 0.00 3.51
2577 2964 7.439157 TGTGAGTCAATATGAACAGAAAAGG 57.561 36.000 0.00 0.00 0.00 3.11
2591 2978 5.163426 TGGCATGTTCTTTTTGTGAGTCAAT 60.163 36.000 0.00 0.00 35.84 2.57
2592 2979 4.159321 TGGCATGTTCTTTTTGTGAGTCAA 59.841 37.500 0.00 0.00 0.00 3.18
2735 3212 0.608130 TGCTCAGTGCCGAACAGTAT 59.392 50.000 0.00 0.00 42.00 2.12
2787 3264 8.160765 TGTTGGAATACAATTTTAGGAGACTGA 58.839 33.333 0.00 0.00 40.97 3.41
2788 3265 8.335532 TGTTGGAATACAATTTTAGGAGACTG 57.664 34.615 0.00 0.00 40.97 3.51
2817 3294 7.462590 ACTAGCAGAGATAGGTACATCACATA 58.537 38.462 0.00 0.00 0.00 2.29
2864 3342 6.767456 TGGATCAAATAGCAACCACAATTTT 58.233 32.000 0.00 0.00 0.00 1.82
2922 3400 6.238484 CCCAAACGAATACAAAAATTTTGCCA 60.238 34.615 17.39 7.03 0.00 4.92
2923 3401 6.139435 CCCAAACGAATACAAAAATTTTGCC 58.861 36.000 17.39 4.91 0.00 4.52
2926 3404 9.602568 AGTTACCCAAACGAATACAAAAATTTT 57.397 25.926 0.00 0.00 43.29 1.82
2930 3408 6.320672 TCCAGTTACCCAAACGAATACAAAAA 59.679 34.615 0.00 0.00 43.29 1.94
2941 3419 5.010617 ACAATGAACATCCAGTTACCCAAAC 59.989 40.000 0.00 0.00 41.51 2.93
2956 3434 7.384439 TGTTGAACAAGTTCTACAATGAACA 57.616 32.000 21.72 14.67 46.50 3.18
3032 3510 4.329831 CCCACGGTACCATTTGGG 57.670 61.111 22.82 22.82 42.92 4.12
3033 3511 0.682855 ATGCCCACGGTACCATTTGG 60.683 55.000 13.54 14.26 42.17 3.28
3041 3519 1.138069 CATCACACTATGCCCACGGTA 59.862 52.381 0.00 0.00 0.00 4.02
3045 3523 1.745087 CCAACATCACACTATGCCCAC 59.255 52.381 0.00 0.00 0.00 4.61
3100 3578 4.259690 GCATTGATGAGCTTCGCAATTTTC 60.260 41.667 6.25 0.00 0.00 2.29
3163 3641 3.340814 AATGACTGCAGTACCTTCAGG 57.659 47.619 21.73 0.00 42.17 3.86
3185 3663 9.730420 GAAAACAGAAACATAGCTAGTTCAAAA 57.270 29.630 13.92 0.00 0.00 2.44
3267 3745 6.127451 ACCGAATCCCATCCTTTATTTGTTTC 60.127 38.462 0.00 0.00 0.00 2.78
3300 3778 2.542020 TGATTTCTTCTGCACCACGA 57.458 45.000 0.00 0.00 0.00 4.35
3333 3811 1.079543 GCTTCTGCTTGCCTCGAGA 60.080 57.895 15.71 0.00 36.03 4.04
3415 3968 4.383552 GCATGTTAGTCCTGAGAATGGAGT 60.384 45.833 0.00 0.00 40.14 3.85
3433 3986 2.009774 GGACTATGAAAGCGTGCATGT 58.990 47.619 7.93 0.00 0.00 3.21
3442 3995 7.678947 ACTGAACAGAATTGGACTATGAAAG 57.321 36.000 8.87 0.00 0.00 2.62
3454 4007 4.814234 TGTAGCACGAAACTGAACAGAATT 59.186 37.500 8.87 3.52 0.00 2.17
3470 4023 5.651172 TTATGTGTTATCGCATGTAGCAC 57.349 39.130 9.60 0.00 46.13 4.40
3475 4028 6.036626 TGTTCGAATTATGTGTTATCGCATGT 59.963 34.615 0.00 0.00 43.46 3.21
3595 4149 8.049655 TGTACTAAACATGATTGCAAGCAATA 57.950 30.769 22.73 11.29 38.78 1.90
3651 4205 6.964807 TTACTACACTCACAGTTGGAACTA 57.035 37.500 0.00 0.00 37.08 2.24
3741 4331 5.469760 GCAAGTAAAATCATGCTGGGTTTTT 59.530 36.000 4.84 2.20 35.93 1.94
3746 4336 3.872511 TGCAAGTAAAATCATGCTGGG 57.127 42.857 0.00 0.00 39.49 4.45
3748 4338 7.031372 AGTACATTGCAAGTAAAATCATGCTG 58.969 34.615 4.94 0.00 39.49 4.41
3772 4362 4.498345 GCGTTTAGATCACTACAGAGGGAG 60.498 50.000 0.00 0.00 38.94 4.30
3773 4363 3.380637 GCGTTTAGATCACTACAGAGGGA 59.619 47.826 0.00 0.00 40.22 4.20
3774 4364 3.381908 AGCGTTTAGATCACTACAGAGGG 59.618 47.826 0.00 0.00 0.00 4.30
3775 4365 4.336993 AGAGCGTTTAGATCACTACAGAGG 59.663 45.833 0.00 0.00 37.82 3.69
3776 4366 5.493133 AGAGCGTTTAGATCACTACAGAG 57.507 43.478 0.00 0.00 37.82 3.35
3777 4367 5.899120 AAGAGCGTTTAGATCACTACAGA 57.101 39.130 0.00 0.00 37.82 3.41
3778 4368 9.900710 AATATAAGAGCGTTTAGATCACTACAG 57.099 33.333 0.00 0.00 37.82 2.74
3791 4381 9.930693 CCCTCTATAAAGAAATATAAGAGCGTT 57.069 33.333 0.00 0.00 0.00 4.84
3792 4382 9.310449 TCCCTCTATAAAGAAATATAAGAGCGT 57.690 33.333 0.00 0.00 0.00 5.07
3793 4383 9.796120 CTCCCTCTATAAAGAAATATAAGAGCG 57.204 37.037 0.00 0.00 0.00 5.03
3876 4467 7.913789 TGACCTAGTATGTGTAACCATTCTTT 58.086 34.615 0.00 0.00 34.36 2.52
3917 4508 9.730705 CATAGTATATCAAATCCAATCCACAGT 57.269 33.333 0.00 0.00 0.00 3.55
3939 4530 8.840321 AGGGATTCGTGAAATTTGAATACATAG 58.160 33.333 11.88 0.00 35.14 2.23
3947 4538 4.662278 AGGAAGGGATTCGTGAAATTTGA 58.338 39.130 0.00 0.00 0.00 2.69
3955 4546 5.590259 ACATTTGATTAGGAAGGGATTCGTG 59.410 40.000 0.00 0.00 0.00 4.35
3972 4563 7.363705 CCTTGATACCTGCCAATTTACATTTGA 60.364 37.037 0.00 0.00 0.00 2.69
4097 4688 0.249868 GGCCCTTCTTTGCAAACCAC 60.250 55.000 8.05 0.00 0.00 4.16
4341 4932 5.191722 AGGGAAGAGCAGGTGATTGTTATAA 59.808 40.000 0.00 0.00 0.00 0.98
4354 4945 2.042464 TGCACCTATAGGGAAGAGCAG 58.958 52.381 22.91 3.60 40.27 4.24
4362 4953 3.480470 CACAAGGAATGCACCTATAGGG 58.520 50.000 22.91 12.53 39.62 3.53
4430 5021 2.300437 ACTACTGCCACCAGAAGAAGAC 59.700 50.000 0.00 0.00 41.77 3.01
4439 5030 2.986492 GGAGGTACTACTGCCACCA 58.014 57.895 0.00 0.00 41.55 4.17
4478 5069 8.803397 AAAGACAGTTACAGGATATTTTACCC 57.197 34.615 0.00 0.00 0.00 3.69
4497 5088 6.994496 ACAATGAACTGATCTCTCAAAAGACA 59.006 34.615 0.00 0.00 0.00 3.41
4563 5196 5.294552 GTCCTATAGTGTTTGGCAGACATTC 59.705 44.000 14.37 2.46 0.00 2.67
4627 5260 4.553330 TCCTTTTTGATAGACGCTCCTT 57.447 40.909 0.00 0.00 0.00 3.36
4628 5261 4.223032 TCTTCCTTTTTGATAGACGCTCCT 59.777 41.667 0.00 0.00 0.00 3.69
4629 5262 4.504858 TCTTCCTTTTTGATAGACGCTCC 58.495 43.478 0.00 0.00 0.00 4.70
4631 5264 6.877611 TTTTCTTCCTTTTTGATAGACGCT 57.122 33.333 0.00 0.00 0.00 5.07
4664 5302 3.137544 TCGTTGGCTATTGGGGTCATTAT 59.862 43.478 0.00 0.00 0.00 1.28
4732 5382 6.093495 TGCTCGCTAACTATGCTGTTTTAAAT 59.907 34.615 0.00 0.00 0.00 1.40
4735 5385 4.500127 TGCTCGCTAACTATGCTGTTTTA 58.500 39.130 0.00 0.00 0.00 1.52
4736 5386 3.334691 TGCTCGCTAACTATGCTGTTTT 58.665 40.909 0.00 0.00 0.00 2.43
4737 5387 2.972625 TGCTCGCTAACTATGCTGTTT 58.027 42.857 0.00 0.00 0.00 2.83
4738 5388 2.672961 TGCTCGCTAACTATGCTGTT 57.327 45.000 0.00 0.00 0.00 3.16
4739 5389 2.101415 TCATGCTCGCTAACTATGCTGT 59.899 45.455 0.00 0.00 0.00 4.40
4740 5390 2.474359 GTCATGCTCGCTAACTATGCTG 59.526 50.000 0.00 0.00 0.00 4.41
4741 5391 2.101415 TGTCATGCTCGCTAACTATGCT 59.899 45.455 0.00 0.00 0.00 3.79
4742 5392 2.473816 TGTCATGCTCGCTAACTATGC 58.526 47.619 0.00 0.00 0.00 3.14
4743 5393 4.115516 AGTTGTCATGCTCGCTAACTATG 58.884 43.478 0.00 0.00 0.00 2.23
4744 5394 4.392921 AGTTGTCATGCTCGCTAACTAT 57.607 40.909 0.00 0.00 0.00 2.12
4767 5417 9.809096 TTTATGATGAAAAACAAAACTACAGCA 57.191 25.926 0.00 0.00 0.00 4.41
4800 5450 5.527951 TGACGATTTAAATTTGCAAGCACT 58.472 33.333 1.43 0.00 0.00 4.40
4842 5492 8.587952 AACATTTTGATGGCAACTTTAGTTAC 57.412 30.769 0.00 0.00 36.32 2.50
4893 5543 2.536365 GTAATGTCATTCAGCGGACGA 58.464 47.619 0.07 0.00 36.83 4.20
4906 5556 4.076394 TGTGCTAAAACCAGGGTAATGTC 58.924 43.478 0.00 0.00 0.00 3.06
5043 5695 7.857456 TCTTGTCCCATTACTTATGCTCTTTA 58.143 34.615 0.00 0.00 32.60 1.85
5044 5696 6.721318 TCTTGTCCCATTACTTATGCTCTTT 58.279 36.000 0.00 0.00 32.60 2.52
5047 5699 7.500559 AGAATTCTTGTCCCATTACTTATGCTC 59.499 37.037 0.88 0.00 32.60 4.26
5092 5745 5.365619 CAATTTTACTGGTCTAGCGGGTAT 58.634 41.667 0.00 0.00 0.00 2.73
5096 5749 3.606687 ACCAATTTTACTGGTCTAGCGG 58.393 45.455 0.00 0.00 44.05 5.52
5151 5804 3.547746 TGGGCGATCAAGTTTAATACCC 58.452 45.455 0.00 0.00 35.29 3.69
5196 5849 9.059260 CATGATACCACATATGTCATTTCTTCA 57.941 33.333 5.07 3.94 0.00 3.02
5212 5865 5.772521 ACTTTTTGTTGCTCATGATACCAC 58.227 37.500 0.00 0.00 0.00 4.16
5220 5873 6.689669 GTGTAACGTTACTTTTTGTTGCTCAT 59.310 34.615 32.10 0.00 34.77 2.90
5228 5881 7.109006 ACGATAGGTGTAACGTTACTTTTTG 57.891 36.000 32.10 20.01 34.27 2.44
5238 5891 4.518211 AGATCCCTTACGATAGGTGTAACG 59.482 45.833 0.00 0.00 38.12 3.18
5240 5893 7.516198 GTAAGATCCCTTACGATAGGTGTAA 57.484 40.000 0.00 0.00 43.49 2.41
5263 5916 2.465860 TTTCATCCAATCGGTCACGT 57.534 45.000 0.00 0.00 41.85 4.49
5264 5917 3.001634 CAGATTTCATCCAATCGGTCACG 59.998 47.826 0.00 0.00 38.10 4.35
5271 5924 3.893813 CCCTTCCCAGATTTCATCCAATC 59.106 47.826 0.00 0.00 33.87 2.67
5280 5933 3.109596 GGGCCCCTTCCCAGATTT 58.890 61.111 12.23 0.00 45.82 2.17
5286 5939 3.825623 CTGGATGGGCCCCTTCCC 61.826 72.222 29.26 20.58 44.37 3.97
5295 5948 1.392589 CCCGAATTCAACTGGATGGG 58.607 55.000 6.22 1.35 0.00 4.00
5298 5951 0.999712 ACCCCCGAATTCAACTGGAT 59.000 50.000 6.22 0.00 0.00 3.41
5299 5952 0.774908 AACCCCCGAATTCAACTGGA 59.225 50.000 6.22 0.00 0.00 3.86
5302 5955 6.097696 CCAATAAATAACCCCCGAATTCAACT 59.902 38.462 6.22 0.00 0.00 3.16
5303 5956 6.127281 ACCAATAAATAACCCCCGAATTCAAC 60.127 38.462 6.22 0.00 0.00 3.18
5304 5957 5.958987 ACCAATAAATAACCCCCGAATTCAA 59.041 36.000 6.22 0.00 0.00 2.69
5305 5958 5.520751 ACCAATAAATAACCCCCGAATTCA 58.479 37.500 6.22 0.00 0.00 2.57
5306 5959 6.474140 AACCAATAAATAACCCCCGAATTC 57.526 37.500 0.00 0.00 0.00 2.17
5307 5960 6.551975 CCTAACCAATAAATAACCCCCGAATT 59.448 38.462 0.00 0.00 0.00 2.17
5308 5961 6.072649 CCTAACCAATAAATAACCCCCGAAT 58.927 40.000 0.00 0.00 0.00 3.34
5309 5962 5.447757 CCTAACCAATAAATAACCCCCGAA 58.552 41.667 0.00 0.00 0.00 4.30
5310 5963 4.141205 CCCTAACCAATAAATAACCCCCGA 60.141 45.833 0.00 0.00 0.00 5.14
5311 5964 4.141205 TCCCTAACCAATAAATAACCCCCG 60.141 45.833 0.00 0.00 0.00 5.73
5312 5965 5.406570 TCCCTAACCAATAAATAACCCCC 57.593 43.478 0.00 0.00 0.00 5.40
5317 5970 7.889178 ACCTTCCATCCCTAACCAATAAATAA 58.111 34.615 0.00 0.00 0.00 1.40
5345 5998 1.102222 AGGGGCTACGAAGAGCTACG 61.102 60.000 8.26 6.01 42.43 3.51
5346 5999 1.067364 GAAGGGGCTACGAAGAGCTAC 59.933 57.143 8.26 3.30 42.43 3.58
5383 6344 3.081409 AGCCGGGTAGACGCCATT 61.081 61.111 3.10 0.00 0.00 3.16
5384 6345 3.849951 CAGCCGGGTAGACGCCAT 61.850 66.667 5.47 0.00 0.00 4.40
5415 6376 4.410228 TCAAAATCATAGTAGCAGGCTCCT 59.590 41.667 0.00 0.00 0.00 3.69
5417 6378 6.874288 AATCAAAATCATAGTAGCAGGCTC 57.126 37.500 0.00 0.00 0.00 4.70
5458 6419 2.799371 CTCGGCCGGTACTGACTC 59.201 66.667 27.83 0.00 0.00 3.36
5476 6437 0.951040 AGCGACGCTTTCCTTCAAGG 60.951 55.000 18.46 0.00 33.89 3.61


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

AutoCloner maintained by Alex Coulton.