Multiple sequence alignment - TraesCS1A01G007900

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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 TraesCS1A01G007900 chr1A 100.000 2210 0 0 1 2210 4062197 4064406 0.000000e+00 4082.0
1 TraesCS1A01G007900 chr1D 86.171 1750 110 48 1 1672 112992 111297 0.000000e+00 1770.0
2 TraesCS1A01G007900 chr1D 94.819 193 6 1 2022 2210 111138 110946 4.610000e-77 298.0
3 TraesCS1A01G007900 chr1D 80.451 133 22 4 56 187 189706202 189706073 5.020000e-17 99.0
4 TraesCS1A01G007900 chr1D 97.500 40 0 1 1744 1782 463974377 463974338 1.420000e-07 67.6
5 TraesCS1A01G007900 chr1B 85.049 1438 116 49 180 1558 5509096 5510493 0.000000e+00 1373.0
6 TraesCS1A01G007900 chr1B 93.421 228 15 0 1983 2210 5511280 5511507 2.720000e-89 339.0
7 TraesCS1A01G007900 chr1B 79.298 570 50 20 618 1150 5505751 5506289 9.780000e-89 337.0
8 TraesCS1A01G007900 chr6D 78.947 342 56 13 14 347 139382099 139381766 3.690000e-53 219.0
9 TraesCS1A01G007900 chr6A 76.812 345 68 10 14 354 182316716 182316380 1.350000e-42 183.0
10 TraesCS1A01G007900 chr3D 82.993 147 22 3 43 188 481210723 481210579 1.780000e-26 130.0
11 TraesCS1A01G007900 chr3D 93.478 46 2 1 1738 1782 571897474 571897519 1.420000e-07 67.6
12 TraesCS1A01G007900 chr7D 74.658 292 63 11 62 346 563539026 563539313 3.850000e-23 119.0
13 TraesCS1A01G007900 chr7D 76.757 185 36 4 14 193 422128144 422127962 1.810000e-16 97.1
14 TraesCS1A01G007900 chr5D 72.629 369 86 14 56 415 404479636 404479274 8.340000e-20 108.0
15 TraesCS1A01G007900 chr5D 97.059 34 1 0 1747 1780 398488809 398488842 8.520000e-05 58.4
16 TraesCS1A01G007900 chr3B 85.075 67 6 2 83 147 143584430 143584494 5.090000e-07 65.8
17 TraesCS1A01G007900 chr2A 90.196 51 3 2 1740 1790 2340206 2340254 5.090000e-07 65.8
18 TraesCS1A01G007900 chr2D 92.857 42 2 1 1745 1786 629387916 629387876 2.370000e-05 60.2
19 TraesCS1A01G007900 chr2D 96.875 32 1 0 1751 1782 495841223 495841192 1.000000e-03 54.7
20 TraesCS1A01G007900 chr7A 90.909 44 3 1 1741 1784 267434263 267434305 8.520000e-05 58.4
21 TraesCS1A01G007900 chr3A 100.000 29 0 0 1215 1243 646312065 646312037 1.000000e-03 54.7
22 TraesCS1A01G007900 chr5A 100.000 28 0 0 1756 1783 384427214 384427241 4.000000e-03 52.8


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 TraesCS1A01G007900 chr1A 4062197 4064406 2209 False 4082 4082 100.000000 1 2210 1 chr1A.!!$F1 2209
1 TraesCS1A01G007900 chr1D 110946 112992 2046 True 1034 1770 90.495000 1 2210 2 chr1D.!!$R3 2209
2 TraesCS1A01G007900 chr1B 5505751 5511507 5756 False 683 1373 85.922667 180 2210 3 chr1B.!!$F1 2030

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
924 4147 0.178981 TTGCCTTGCTTTCTCTGCCT 60.179 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 5659 0.026285 GCATGTACGGTTCATCACGC 59.974 55.0 0.0 0.0 0.0 5.34 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
108 109 2.367512 ATCCACCTCCCCTCTGCC 60.368 66.667 0.00 0.00 0.00 4.85
150 151 2.041819 GGAGGGGGATCTCGGTGT 60.042 66.667 0.00 0.00 34.74 4.16
159 160 1.064357 GGATCTCGGTGTCTCGACTTC 59.936 57.143 0.00 0.00 35.18 3.01
162 163 2.504244 CGGTGTCTCGACTTCGGC 60.504 66.667 0.00 0.00 40.29 5.54
245 3413 3.762407 TCATTTCGAGTTGGTCTTCCA 57.238 42.857 0.00 0.00 42.66 3.53
251 3419 2.698797 TCGAGTTGGTCTTCCAGACTTT 59.301 45.455 3.97 0.00 44.46 2.66
262 3430 6.169094 GTCTTCCAGACTTTGATTCTCATCA 58.831 40.000 0.00 0.00 41.88 3.07
275 3443 7.748691 TGATTCTCATCAAGTTTGTTCATCA 57.251 32.000 0.00 0.00 36.41 3.07
285 3453 6.494491 TCAAGTTTGTTCATCAGGATGGATTT 59.506 34.615 9.25 0.00 39.24 2.17
325 3493 2.408271 TCATGATGTCTCCTTGGTGC 57.592 50.000 0.00 0.00 0.00 5.01
337 3505 1.656652 CTTGGTGCGATGAGGTTAGG 58.343 55.000 0.00 0.00 0.00 2.69
345 3513 2.093658 GCGATGAGGTTAGGGTTTCTCA 60.094 50.000 0.00 0.00 40.04 3.27
363 3531 1.666189 TCATTGTTTGTGTGCGACGAA 59.334 42.857 0.00 0.00 0.00 3.85
369 3549 4.487019 TGTTTGTGTGCGACGAATAGATA 58.513 39.130 0.00 0.00 30.24 1.98
405 3585 2.301346 AGGGTTCAATGGCGATGATTC 58.699 47.619 0.00 0.00 0.00 2.52
424 3604 0.747255 CCAGCTCTAGTACGCCACAT 59.253 55.000 0.00 0.00 0.00 3.21
441 3621 1.078426 ATCTTAGGGGCACGTGCAC 60.078 57.895 38.60 36.67 45.53 4.57
450 3630 0.457681 GGCACGTGCACAAACACTTT 60.458 50.000 38.60 0.00 44.36 2.66
453 3633 1.135546 CACGTGCACAAACACTTTCCA 60.136 47.619 18.64 0.00 38.45 3.53
463 3643 4.949856 ACAAACACTTTCCAACTGTCATCT 59.050 37.500 0.00 0.00 0.00 2.90
469 3649 4.989168 ACTTTCCAACTGTCATCTACGAAC 59.011 41.667 0.00 0.00 0.00 3.95
481 3661 1.342174 TCTACGAACTCAAACCGGCTT 59.658 47.619 0.00 0.00 0.00 4.35
499 3681 1.136500 CTTAGGTAGGGGAGCGTCAAC 59.864 57.143 0.00 0.00 0.00 3.18
543 3745 3.754323 TCGGTGGTGCTCGATTTAATTTT 59.246 39.130 0.00 0.00 0.00 1.82
574 3776 6.490040 TGTATATAGGATGCTTTGCCCTTTTC 59.510 38.462 0.00 0.00 0.00 2.29
665 3868 5.864418 AATATTTTCATGCATGGAGCTGT 57.136 34.783 25.97 10.42 45.94 4.40
667 3870 3.306917 TTTTCATGCATGGAGCTGTTG 57.693 42.857 25.97 0.00 45.94 3.33
680 3883 7.173907 GCATGGAGCTGTTGACAGTATATAATT 59.826 37.037 12.32 0.00 45.45 1.40
744 3952 6.307155 CAAAAGGCGTGACTAGAAAATACAG 58.693 40.000 0.00 0.00 0.00 2.74
746 3954 2.608090 GGCGTGACTAGAAAATACAGGC 59.392 50.000 0.00 0.00 40.17 4.85
768 3976 4.556699 GCGCAAAAGGTGTGACTAGAAAAT 60.557 41.667 0.30 0.00 40.42 1.82
770 3978 5.277779 CGCAAAAGGTGTGACTAGAAAATGA 60.278 40.000 0.00 0.00 40.42 2.57
817 4025 1.442184 CGAGACGTCACCAACCGAG 60.442 63.158 19.50 0.00 0.00 4.63
878 4086 2.362736 CACAATCACACCATCCTCCTG 58.637 52.381 0.00 0.00 0.00 3.86
880 4088 0.257039 AATCACACCATCCTCCTGCC 59.743 55.000 0.00 0.00 0.00 4.85
890 4113 4.486503 CTCCTGCCCTGCTCCTGC 62.487 72.222 0.00 0.00 40.20 4.85
912 4135 0.963856 TGCTCTGCTCCATTGCCTTG 60.964 55.000 0.00 0.00 0.00 3.61
924 4147 0.178981 TTGCCTTGCTTTCTCTGCCT 60.179 50.000 0.00 0.00 0.00 4.75
925 4148 0.892358 TGCCTTGCTTTCTCTGCCTG 60.892 55.000 0.00 0.00 0.00 4.85
926 4149 1.881602 CCTTGCTTTCTCTGCCTGC 59.118 57.895 0.00 0.00 0.00 4.85
927 4150 1.593296 CCTTGCTTTCTCTGCCTGCC 61.593 60.000 0.00 0.00 0.00 4.85
928 4151 0.608582 CTTGCTTTCTCTGCCTGCCT 60.609 55.000 0.00 0.00 0.00 4.75
945 4172 1.816183 GCCTCGAGGAGCTAGCTAGAA 60.816 57.143 35.69 0.87 37.39 2.10
948 4175 5.155332 CCTCGAGGAGCTAGCTAGAAAGC 62.155 56.522 28.21 11.74 43.12 3.51
960 4187 4.329296 GCTAGAAAGCGAGAAAGAAACC 57.671 45.455 0.00 0.00 39.39 3.27
1015 4242 2.687566 GGATGTCGGACTGGGGGT 60.688 66.667 9.88 0.00 0.00 4.95
1180 4407 0.867329 CATCGCGCTCTTCGTCATCA 60.867 55.000 5.56 0.00 41.07 3.07
1211 4438 2.029020 TGCACATCACCACTGACTAGAC 60.029 50.000 0.00 0.00 0.00 2.59
1265 4492 3.883669 CTCCAATTAAGCTGCTCTTCCT 58.116 45.455 1.00 0.00 36.25 3.36
1318 4559 5.343249 CCTCTCTGTTTTGTTTTGTTCTGG 58.657 41.667 0.00 0.00 0.00 3.86
1348 4589 4.988540 TGCTTGCAAGTACTTGTAGTAGTG 59.011 41.667 30.90 17.74 42.31 2.74
1349 4590 4.989168 GCTTGCAAGTACTTGTAGTAGTGT 59.011 41.667 30.90 0.00 42.31 3.55
1363 4604 8.926715 TTGTAGTAGTGTATGTGATCATGTTC 57.073 34.615 0.00 0.00 35.70 3.18
1372 4613 4.891627 TGTGATCATGTTCGTTTGTTGT 57.108 36.364 0.00 0.00 0.00 3.32
1374 4615 4.219033 GTGATCATGTTCGTTTGTTGTCC 58.781 43.478 0.00 0.00 0.00 4.02
1376 4617 4.578516 TGATCATGTTCGTTTGTTGTCCTT 59.421 37.500 0.00 0.00 0.00 3.36
1377 4618 4.285807 TCATGTTCGTTTGTTGTCCTTG 57.714 40.909 0.00 0.00 0.00 3.61
1386 4627 7.330900 TCGTTTGTTGTCCTTGGTAATTAAA 57.669 32.000 0.00 0.00 0.00 1.52
1404 4645 0.866061 AACTCGCGCGTATGTAGCTG 60.866 55.000 30.98 11.45 0.00 4.24
1406 4647 3.692367 CGCGCGTATGTAGCTGCC 61.692 66.667 24.19 0.00 33.18 4.85
1408 4649 1.883084 GCGCGTATGTAGCTGCCTT 60.883 57.895 8.43 0.00 0.00 4.35
1443 4686 7.557719 AGAGATGTGTACTTAATTTTCCATGGG 59.442 37.037 13.02 0.00 0.00 4.00
1453 4696 0.187117 TTTCCATGGGAGTGGCACAA 59.813 50.000 21.41 2.44 44.16 3.33
1469 4713 6.861055 AGTGGCACAAACAAGTTATTTAATCG 59.139 34.615 21.41 0.00 44.16 3.34
1489 4733 6.952773 ATCGTCTGAAGCTCTAGATTAACT 57.047 37.500 0.00 0.00 0.00 2.24
1500 4744 6.836527 AGCTCTAGATTAACTGGTAGATGTGT 59.163 38.462 0.00 0.00 0.00 3.72
1501 4745 7.999545 AGCTCTAGATTAACTGGTAGATGTGTA 59.000 37.037 0.00 0.00 0.00 2.90
1540 4790 3.878699 CCCATTTTTCTTGCAAAGCAACT 59.121 39.130 0.00 0.00 45.70 3.16
1558 4808 4.998033 GCAACTACCTTCTTTTCAGCTACT 59.002 41.667 0.00 0.00 0.00 2.57
1559 4809 5.120986 GCAACTACCTTCTTTTCAGCTACTC 59.879 44.000 0.00 0.00 0.00 2.59
1561 4811 5.088026 ACTACCTTCTTTTCAGCTACTCCT 58.912 41.667 0.00 0.00 0.00 3.69
1562 4812 6.254522 ACTACCTTCTTTTCAGCTACTCCTA 58.745 40.000 0.00 0.00 0.00 2.94
1563 4813 5.408880 ACCTTCTTTTCAGCTACTCCTAC 57.591 43.478 0.00 0.00 0.00 3.18
1564 4814 4.838986 ACCTTCTTTTCAGCTACTCCTACA 59.161 41.667 0.00 0.00 0.00 2.74
1565 4815 5.307196 ACCTTCTTTTCAGCTACTCCTACAA 59.693 40.000 0.00 0.00 0.00 2.41
1566 4816 5.639931 CCTTCTTTTCAGCTACTCCTACAAC 59.360 44.000 0.00 0.00 0.00 3.32
1567 4817 4.806330 TCTTTTCAGCTACTCCTACAACG 58.194 43.478 0.00 0.00 0.00 4.10
1568 4818 2.649331 TTCAGCTACTCCTACAACGC 57.351 50.000 0.00 0.00 0.00 4.84
1569 4819 0.450583 TCAGCTACTCCTACAACGCG 59.549 55.000 3.53 3.53 0.00 6.01
1570 4820 1.139095 AGCTACTCCTACAACGCGC 59.861 57.895 5.73 0.00 0.00 6.86
1571 4821 1.153901 GCTACTCCTACAACGCGCA 60.154 57.895 5.73 0.00 0.00 6.09
1572 4822 0.527817 GCTACTCCTACAACGCGCAT 60.528 55.000 5.73 0.00 0.00 4.73
1573 4823 1.200483 CTACTCCTACAACGCGCATG 58.800 55.000 5.73 8.75 0.00 4.06
1574 4824 0.812549 TACTCCTACAACGCGCATGA 59.187 50.000 18.09 0.86 0.00 3.07
1575 4825 0.037697 ACTCCTACAACGCGCATGAA 60.038 50.000 18.09 0.00 0.00 2.57
1576 4826 1.075542 CTCCTACAACGCGCATGAAA 58.924 50.000 18.09 5.97 0.00 2.69
1584 4834 1.696988 ACGCGCATGAAATTTCAACC 58.303 45.000 23.91 15.98 41.13 3.77
1591 4841 3.617288 GCATGAAATTTCAACCACCCCTC 60.617 47.826 23.91 3.37 41.13 4.30
1594 4844 2.309136 AATTTCAACCACCCCTCCAG 57.691 50.000 0.00 0.00 0.00 3.86
1596 4846 1.650242 TTTCAACCACCCCTCCAGCA 61.650 55.000 0.00 0.00 0.00 4.41
1597 4847 1.434513 TTCAACCACCCCTCCAGCAT 61.435 55.000 0.00 0.00 0.00 3.79
1604 4854 1.228510 CCCCTCCAGCATTCCCTTC 59.771 63.158 0.00 0.00 0.00 3.46
1614 4864 4.070716 CAGCATTCCCTTCTGATATCCAC 58.929 47.826 0.00 0.00 0.00 4.02
1660 4913 0.251698 TGCCCATGTGCATTCTTGGA 60.252 50.000 0.00 0.00 36.04 3.53
1668 4921 4.707030 TGTGCATTCTTGGATTCATGAC 57.293 40.909 0.00 0.00 0.00 3.06
1672 4925 5.819379 GTGCATTCTTGGATTCATGACTCTA 59.181 40.000 12.29 4.11 0.00 2.43
1673 4926 6.317140 GTGCATTCTTGGATTCATGACTCTAA 59.683 38.462 12.29 11.46 0.00 2.10
1676 4929 6.932356 TTCTTGGATTCATGACTCTAATGC 57.068 37.500 11.42 1.21 0.00 3.56
1677 4930 5.993055 TCTTGGATTCATGACTCTAATGCA 58.007 37.500 11.42 3.73 0.00 3.96
1678 4931 6.053650 TCTTGGATTCATGACTCTAATGCAG 58.946 40.000 11.42 1.93 33.38 4.41
1680 4933 4.141551 TGGATTCATGACTCTAATGCAGCT 60.142 41.667 12.29 0.00 0.00 4.24
1682 4935 5.407995 GGATTCATGACTCTAATGCAGCTAC 59.592 44.000 12.29 0.00 0.00 3.58
1683 4936 5.604758 TTCATGACTCTAATGCAGCTACT 57.395 39.130 0.00 0.00 0.00 2.57
1685 4938 6.324561 TCATGACTCTAATGCAGCTACTAG 57.675 41.667 0.00 0.00 0.00 2.57
1688 4941 5.895928 TGACTCTAATGCAGCTACTAGTTG 58.104 41.667 0.00 0.00 0.00 3.16
1691 5041 5.600484 ACTCTAATGCAGCTACTAGTTGGAT 59.400 40.000 0.00 0.00 38.98 3.41
1696 5046 7.559590 AATGCAGCTACTAGTTGGATTTTAG 57.440 36.000 12.12 0.00 42.77 1.85
1705 5055 9.444600 CTACTAGTTGGATTTTAGCCAAGTAAA 57.555 33.333 0.00 4.00 45.67 2.01
1716 5066 9.981114 ATTTTAGCCAAGTAAATATGCAATACC 57.019 29.630 0.00 0.00 0.00 2.73
1718 5068 5.454062 AGCCAAGTAAATATGCAATACCCA 58.546 37.500 0.00 0.00 0.00 4.51
1733 5474 9.816354 ATGCAATACCCAATCAATTAAAACTAC 57.184 29.630 0.00 0.00 0.00 2.73
1734 5475 9.030452 TGCAATACCCAATCAATTAAAACTACT 57.970 29.630 0.00 0.00 0.00 2.57
1737 5478 8.762481 ATACCCAATCAATTAAAACTACTCCC 57.238 34.615 0.00 0.00 0.00 4.30
1740 5481 6.663523 CCCAATCAATTAAAACTACTCCCTGT 59.336 38.462 0.00 0.00 0.00 4.00
1741 5482 7.832187 CCCAATCAATTAAAACTACTCCCTGTA 59.168 37.037 0.00 0.00 0.00 2.74
1742 5483 9.238368 CCAATCAATTAAAACTACTCCCTGTAA 57.762 33.333 0.00 0.00 0.00 2.41
1754 5495 8.375493 ACTACTCCCTGTAATGATCTAAAACA 57.625 34.615 0.00 0.00 0.00 2.83
1756 5497 9.838339 CTACTCCCTGTAATGATCTAAAACAAT 57.162 33.333 0.00 0.00 0.00 2.71
1759 5500 9.401058 CTCCCTGTAATGATCTAAAACAATCTT 57.599 33.333 0.00 0.00 0.00 2.40
1787 5528 6.687081 TTCTTTACAGAGAGAGTAGCTAGC 57.313 41.667 6.62 6.62 0.00 3.42
1788 5529 5.996644 TCTTTACAGAGAGAGTAGCTAGCT 58.003 41.667 23.12 23.12 0.00 3.32
1789 5530 7.127012 TCTTTACAGAGAGAGTAGCTAGCTA 57.873 40.000 20.67 20.67 0.00 3.32
1790 5531 7.741785 TCTTTACAGAGAGAGTAGCTAGCTAT 58.258 38.462 26.59 15.56 0.00 2.97
1791 5532 7.659799 TCTTTACAGAGAGAGTAGCTAGCTATG 59.340 40.741 26.59 19.89 0.00 2.23
1792 5533 5.304686 ACAGAGAGAGTAGCTAGCTATGT 57.695 43.478 26.59 20.50 0.00 2.29
1793 5534 6.428083 ACAGAGAGAGTAGCTAGCTATGTA 57.572 41.667 26.59 4.06 0.00 2.29
1794 5535 7.016153 ACAGAGAGAGTAGCTAGCTATGTAT 57.984 40.000 26.59 14.74 0.00 2.29
1795 5536 8.141298 ACAGAGAGAGTAGCTAGCTATGTATA 57.859 38.462 26.59 2.81 0.00 1.47
1800 5541 9.802039 AGAGAGTAGCTAGCTATGTATACTTTT 57.198 33.333 26.59 12.75 0.00 2.27
1803 5544 9.834628 GAGTAGCTAGCTATGTATACTTTTCAG 57.165 37.037 26.59 0.00 0.00 3.02
1808 5549 7.386299 GCTAGCTATGTATACTTTTCAGCACAT 59.614 37.037 7.70 0.00 0.00 3.21
1827 5568 9.983804 CAGCACATATAATACATGCTTGATTAG 57.016 33.333 6.60 0.00 44.01 1.73
1846 5587 2.951269 TCGAACTGCCGACCTAGAA 58.049 52.632 0.00 0.00 33.14 2.10
1847 5588 0.809385 TCGAACTGCCGACCTAGAAG 59.191 55.000 0.00 0.00 33.14 2.85
1848 5589 0.802607 CGAACTGCCGACCTAGAAGC 60.803 60.000 0.00 0.00 0.00 3.86
1849 5590 0.246635 GAACTGCCGACCTAGAAGCA 59.753 55.000 0.00 0.00 0.00 3.91
1850 5591 0.037232 AACTGCCGACCTAGAAGCAC 60.037 55.000 0.00 0.00 0.00 4.40
1851 5592 1.517257 CTGCCGACCTAGAAGCACG 60.517 63.158 0.00 0.00 0.00 5.34
1852 5593 2.886124 GCCGACCTAGAAGCACGC 60.886 66.667 0.00 0.00 0.00 5.34
1853 5594 2.579787 CCGACCTAGAAGCACGCG 60.580 66.667 3.53 3.53 0.00 6.01
1854 5595 3.248171 CGACCTAGAAGCACGCGC 61.248 66.667 5.73 0.00 38.99 6.86
1855 5596 2.126071 GACCTAGAAGCACGCGCA 60.126 61.111 5.73 0.00 42.27 6.09
1858 5599 4.196826 CTAGAAGCACGCGCACGC 62.197 66.667 5.73 9.41 45.53 5.34
1865 5606 3.327754 CACGCGCACGCCCTATAC 61.328 66.667 5.73 0.00 45.53 1.47
1866 5607 3.829044 ACGCGCACGCCCTATACA 61.829 61.111 5.73 0.00 45.53 2.29
1869 5610 2.279918 CGCACGCCCTATACACCC 60.280 66.667 0.00 0.00 0.00 4.61
1870 5611 2.279918 GCACGCCCTATACACCCG 60.280 66.667 0.00 0.00 0.00 5.28
1872 5613 1.362717 CACGCCCTATACACCCGAG 59.637 63.158 0.00 0.00 0.00 4.63
1874 5615 1.105759 ACGCCCTATACACCCGAGAC 61.106 60.000 0.00 0.00 0.00 3.36
1875 5616 1.803366 CGCCCTATACACCCGAGACC 61.803 65.000 0.00 0.00 0.00 3.85
1876 5617 0.757935 GCCCTATACACCCGAGACCA 60.758 60.000 0.00 0.00 0.00 4.02
1877 5618 1.329256 CCCTATACACCCGAGACCAG 58.671 60.000 0.00 0.00 0.00 4.00
1878 5619 1.133575 CCCTATACACCCGAGACCAGA 60.134 57.143 0.00 0.00 0.00 3.86
1879 5620 2.231529 CCTATACACCCGAGACCAGAG 58.768 57.143 0.00 0.00 0.00 3.35
1880 5621 2.231529 CTATACACCCGAGACCAGAGG 58.768 57.143 0.00 0.00 0.00 3.69
1886 5627 2.796500 CCGAGACCAGAGGGAGTAC 58.204 63.158 0.00 0.00 38.05 2.73
1887 5628 1.096386 CCGAGACCAGAGGGAGTACG 61.096 65.000 0.00 0.00 38.05 3.67
1888 5629 0.392729 CGAGACCAGAGGGAGTACGT 60.393 60.000 0.00 0.00 38.05 3.57
1889 5630 1.096416 GAGACCAGAGGGAGTACGTG 58.904 60.000 0.00 0.00 38.05 4.49
1890 5631 0.404812 AGACCAGAGGGAGTACGTGT 59.595 55.000 0.00 0.00 38.05 4.49
1891 5632 1.632409 AGACCAGAGGGAGTACGTGTA 59.368 52.381 0.00 0.00 38.05 2.90
1892 5633 1.742268 GACCAGAGGGAGTACGTGTAC 59.258 57.143 0.00 1.90 38.05 2.90
1893 5634 1.074405 ACCAGAGGGAGTACGTGTACA 59.926 52.381 12.32 0.00 36.71 2.90
1894 5635 2.165167 CCAGAGGGAGTACGTGTACAA 58.835 52.381 12.32 0.00 38.48 2.41
1895 5636 2.094854 CCAGAGGGAGTACGTGTACAAC 60.095 54.545 12.32 6.02 38.48 3.32
1896 5637 2.555325 CAGAGGGAGTACGTGTACAACA 59.445 50.000 12.32 0.00 38.48 3.33
1897 5638 3.192844 CAGAGGGAGTACGTGTACAACAT 59.807 47.826 12.32 2.53 38.48 2.71
1898 5639 3.830755 AGAGGGAGTACGTGTACAACATT 59.169 43.478 12.32 0.00 38.48 2.71
1899 5640 4.282703 AGAGGGAGTACGTGTACAACATTT 59.717 41.667 12.32 0.00 38.48 2.32
1900 5641 4.964593 AGGGAGTACGTGTACAACATTTT 58.035 39.130 12.32 0.00 38.48 1.82
1901 5642 4.992951 AGGGAGTACGTGTACAACATTTTC 59.007 41.667 12.32 0.00 38.48 2.29
1902 5643 4.751098 GGGAGTACGTGTACAACATTTTCA 59.249 41.667 12.32 0.00 38.48 2.69
1903 5644 5.236911 GGGAGTACGTGTACAACATTTTCAA 59.763 40.000 12.32 0.00 38.48 2.69
1904 5645 6.238429 GGGAGTACGTGTACAACATTTTCAAA 60.238 38.462 12.32 0.00 38.48 2.69
1905 5646 6.630045 GGAGTACGTGTACAACATTTTCAAAC 59.370 38.462 12.32 0.00 38.48 2.93
1906 5647 6.488817 AGTACGTGTACAACATTTTCAAACC 58.511 36.000 12.32 0.00 38.48 3.27
1907 5648 4.344448 ACGTGTACAACATTTTCAAACCG 58.656 39.130 0.00 0.00 0.00 4.44
1908 5649 3.726730 CGTGTACAACATTTTCAAACCGG 59.273 43.478 0.00 0.00 0.00 5.28
1909 5650 3.487942 GTGTACAACATTTTCAAACCGGC 59.512 43.478 0.00 0.00 0.00 6.13
1910 5651 2.969628 ACAACATTTTCAAACCGGCA 57.030 40.000 0.00 0.00 0.00 5.69
1911 5652 2.820330 ACAACATTTTCAAACCGGCAG 58.180 42.857 0.00 0.00 0.00 4.85
1912 5653 2.167487 ACAACATTTTCAAACCGGCAGT 59.833 40.909 0.00 0.00 0.00 4.40
1913 5654 3.381908 ACAACATTTTCAAACCGGCAGTA 59.618 39.130 0.00 0.00 0.00 2.74
1914 5655 3.915437 ACATTTTCAAACCGGCAGTAG 57.085 42.857 0.00 0.00 0.00 2.57
1915 5656 3.482436 ACATTTTCAAACCGGCAGTAGA 58.518 40.909 0.00 0.00 0.00 2.59
1916 5657 3.886505 ACATTTTCAAACCGGCAGTAGAA 59.113 39.130 0.00 0.00 0.00 2.10
1917 5658 4.339814 ACATTTTCAAACCGGCAGTAGAAA 59.660 37.500 0.00 2.53 33.35 2.52
1918 5659 4.561735 TTTTCAAACCGGCAGTAGAAAG 57.438 40.909 0.00 0.00 35.38 2.62
1919 5660 1.519408 TCAAACCGGCAGTAGAAAGC 58.481 50.000 0.00 0.00 0.00 3.51
1920 5661 0.165944 CAAACCGGCAGTAGAAAGCG 59.834 55.000 0.00 0.00 0.00 4.68
1921 5662 0.250166 AAACCGGCAGTAGAAAGCGT 60.250 50.000 0.00 0.00 0.00 5.07
1922 5663 0.949105 AACCGGCAGTAGAAAGCGTG 60.949 55.000 0.00 0.00 0.00 5.34
1923 5664 1.080093 CCGGCAGTAGAAAGCGTGA 60.080 57.895 0.00 0.00 0.00 4.35
1924 5665 0.460284 CCGGCAGTAGAAAGCGTGAT 60.460 55.000 0.00 0.00 0.00 3.06
1925 5666 0.647410 CGGCAGTAGAAAGCGTGATG 59.353 55.000 0.00 0.00 0.00 3.07
1926 5667 1.735700 CGGCAGTAGAAAGCGTGATGA 60.736 52.381 0.00 0.00 0.00 2.92
1927 5668 2.346803 GGCAGTAGAAAGCGTGATGAA 58.653 47.619 0.00 0.00 0.00 2.57
1928 5669 2.094417 GGCAGTAGAAAGCGTGATGAAC 59.906 50.000 0.00 0.00 0.00 3.18
1929 5670 2.094417 GCAGTAGAAAGCGTGATGAACC 59.906 50.000 0.00 0.00 0.00 3.62
1930 5671 2.345641 CAGTAGAAAGCGTGATGAACCG 59.654 50.000 0.00 0.00 0.00 4.44
1931 5672 2.029290 AGTAGAAAGCGTGATGAACCGT 60.029 45.455 0.00 0.00 0.00 4.83
1932 5673 2.736144 AGAAAGCGTGATGAACCGTA 57.264 45.000 0.00 0.00 0.00 4.02
1933 5674 2.334838 AGAAAGCGTGATGAACCGTAC 58.665 47.619 0.00 0.00 0.00 3.67
1934 5675 2.063266 GAAAGCGTGATGAACCGTACA 58.937 47.619 0.00 0.00 0.00 2.90
1935 5676 2.380084 AAGCGTGATGAACCGTACAT 57.620 45.000 0.00 0.00 0.00 2.29
1936 5677 1.640428 AGCGTGATGAACCGTACATG 58.360 50.000 0.00 0.00 0.00 3.21
1937 5678 0.026285 GCGTGATGAACCGTACATGC 59.974 55.000 0.00 0.00 37.93 4.06
1938 5679 1.355005 CGTGATGAACCGTACATGCA 58.645 50.000 0.00 0.00 0.00 3.96
1939 5680 1.324435 CGTGATGAACCGTACATGCAG 59.676 52.381 0.00 0.00 0.00 4.41
1940 5681 2.346803 GTGATGAACCGTACATGCAGT 58.653 47.619 0.00 0.00 0.00 4.40
1941 5682 2.094258 GTGATGAACCGTACATGCAGTG 59.906 50.000 0.00 0.00 0.00 3.66
1942 5683 2.289382 TGATGAACCGTACATGCAGTGT 60.289 45.455 0.00 0.00 44.95 3.55
1943 5684 3.056465 TGATGAACCGTACATGCAGTGTA 60.056 43.478 0.00 0.00 42.29 2.90
1952 5693 1.800586 ACATGCAGTGTACAAGCTTCG 59.199 47.619 18.84 11.34 39.91 3.79
1953 5694 1.800586 CATGCAGTGTACAAGCTTCGT 59.199 47.619 18.84 1.07 0.00 3.85
1954 5695 1.497991 TGCAGTGTACAAGCTTCGTC 58.502 50.000 18.84 0.00 0.00 4.20
1955 5696 1.202475 TGCAGTGTACAAGCTTCGTCA 60.202 47.619 18.84 0.00 0.00 4.35
1956 5697 2.069273 GCAGTGTACAAGCTTCGTCAT 58.931 47.619 12.85 0.00 0.00 3.06
1960 5701 5.518847 GCAGTGTACAAGCTTCGTCATAATA 59.481 40.000 12.85 0.00 0.00 0.98
1964 5705 9.162764 AGTGTACAAGCTTCGTCATAATAAAAT 57.837 29.630 0.00 0.00 0.00 1.82
1971 5712 8.620533 AGCTTCGTCATAATAAAATTTTGAGC 57.379 30.769 13.76 2.83 0.00 4.26
1972 5713 7.702348 AGCTTCGTCATAATAAAATTTTGAGCC 59.298 33.333 13.76 0.00 0.00 4.70
1977 5718 9.658475 CGTCATAATAAAATTTTGAGCCGATAA 57.342 29.630 13.76 0.00 0.00 1.75
1995 5740 8.618677 AGCCGATAAAAGGTTAATTAGCTAAAC 58.381 33.333 10.85 4.22 33.29 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 1.834822 CGAGATCCCCCTCCCTCAC 60.835 68.421 0.00 0.00 0.00 3.51
131 132 3.036959 ACCGAGATCCCCCTCCCT 61.037 66.667 0.00 0.00 0.00 4.20
150 151 2.687700 ACTACTAGCCGAAGTCGAGA 57.312 50.000 1.43 0.00 43.02 4.04
159 160 5.526506 ACCATAACCTAAACTACTAGCCG 57.473 43.478 0.00 0.00 0.00 5.52
200 3368 1.523938 GCCATCTACCTGAACGCCC 60.524 63.158 0.00 0.00 0.00 6.13
262 3430 6.494491 TCAAATCCATCCTGATGAACAAACTT 59.506 34.615 8.69 0.00 41.20 2.66
270 3438 4.748857 GCTCCATCAAATCCATCCTGATGA 60.749 45.833 8.69 0.00 46.14 2.92
275 3443 2.107901 GGAGCTCCATCAAATCCATCCT 59.892 50.000 28.43 0.00 35.64 3.24
285 3453 0.033503 TCTACACCGGAGCTCCATCA 60.034 55.000 31.67 10.99 35.14 3.07
325 3493 3.887621 TGAGAAACCCTAACCTCATCG 57.112 47.619 0.00 0.00 31.45 3.84
337 3505 2.788786 CGCACACAAACAATGAGAAACC 59.211 45.455 0.00 0.00 0.00 3.27
345 3513 3.743911 TCTATTCGTCGCACACAAACAAT 59.256 39.130 0.00 0.00 0.00 2.71
393 3573 0.763652 AGAGCTGGAATCATCGCCAT 59.236 50.000 0.00 0.00 32.89 4.40
405 3585 0.747255 ATGTGGCGTACTAGAGCTGG 59.253 55.000 0.00 0.00 0.00 4.85
424 3604 2.046009 TTGTGCACGTGCCCCTAAGA 62.046 55.000 35.72 14.25 41.18 2.10
445 3625 4.988540 TTCGTAGATGACAGTTGGAAAGTG 59.011 41.667 0.00 0.00 45.54 3.16
450 3630 3.824443 TGAGTTCGTAGATGACAGTTGGA 59.176 43.478 0.00 0.00 35.04 3.53
453 3633 4.989168 GGTTTGAGTTCGTAGATGACAGTT 59.011 41.667 0.00 0.00 35.04 3.16
463 3643 2.353011 CCTAAGCCGGTTTGAGTTCGTA 60.353 50.000 14.54 0.00 0.00 3.43
469 3649 1.134491 CCCTACCTAAGCCGGTTTGAG 60.134 57.143 14.54 7.18 38.49 3.02
481 3661 0.040058 TGTTGACGCTCCCCTACCTA 59.960 55.000 0.00 0.00 0.00 3.08
543 3745 9.627123 GGGCAAAGCATCCTATATACATAATAA 57.373 33.333 0.00 0.00 0.00 1.40
574 3776 6.649557 ACCTAGATCTTTTACAAAGGTTCGTG 59.350 38.462 0.00 0.00 31.95 4.35
694 3899 6.417635 CACTTGCGCTTCAGAAAAGAAAATAA 59.582 34.615 9.73 0.00 0.00 1.40
696 3901 4.741676 CACTTGCGCTTCAGAAAAGAAAAT 59.258 37.500 9.73 0.00 0.00 1.82
744 3952 0.517316 CTAGTCACACCTTTTGCGCC 59.483 55.000 4.18 0.00 0.00 6.53
746 3954 4.545823 TTTTCTAGTCACACCTTTTGCG 57.454 40.909 0.00 0.00 0.00 4.85
817 4025 0.740737 CCTTTCATCGCCATTCCCAC 59.259 55.000 0.00 0.00 0.00 4.61
880 4088 2.187424 GAGCAGAGCAGGAGCAGG 59.813 66.667 0.00 0.00 45.49 4.85
890 4113 1.096386 GGCAATGGAGCAGAGCAGAG 61.096 60.000 0.00 0.00 35.83 3.35
912 4135 2.105466 CGAGGCAGGCAGAGAAAGC 61.105 63.158 0.00 0.00 0.00 3.51
924 4147 0.536233 CTAGCTAGCTCCTCGAGGCA 60.536 60.000 27.39 14.38 34.44 4.75
925 4148 0.250553 TCTAGCTAGCTCCTCGAGGC 60.251 60.000 27.39 16.00 34.44 4.70
926 4149 2.264005 TTCTAGCTAGCTCCTCGAGG 57.736 55.000 26.32 26.32 0.00 4.63
927 4150 2.031157 GCTTTCTAGCTAGCTCCTCGAG 60.031 54.545 23.26 13.01 44.27 4.04
928 4151 1.950909 GCTTTCTAGCTAGCTCCTCGA 59.049 52.381 23.26 10.96 44.27 4.04
945 4172 1.235281 GGCGGGTTTCTTTCTCGCTT 61.235 55.000 9.86 0.00 44.88 4.68
948 4175 2.388232 CCGGCGGGTTTCTTTCTCG 61.388 63.158 20.56 0.00 0.00 4.04
949 4176 2.687805 GCCGGCGGGTTTCTTTCTC 61.688 63.158 29.48 2.10 34.97 2.87
969 4196 1.001760 TCCCCTTCCTCTTCTCCGG 59.998 63.158 0.00 0.00 0.00 5.14
974 4201 0.340208 TCTCCCTCCCCTTCCTCTTC 59.660 60.000 0.00 0.00 0.00 2.87
975 4202 0.341609 CTCTCCCTCCCCTTCCTCTT 59.658 60.000 0.00 0.00 0.00 2.85
976 4203 1.598856 CCTCTCCCTCCCCTTCCTCT 61.599 65.000 0.00 0.00 0.00 3.69
977 4204 1.074850 CCTCTCCCTCCCCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
978 4205 2.652113 CCCTCTCCCTCCCCTTCCT 61.652 68.421 0.00 0.00 0.00 3.36
979 4206 2.040359 CCCTCTCCCTCCCCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
1015 4242 4.429212 CACCGCGATCACCACCGA 62.429 66.667 8.23 0.00 0.00 4.69
1074 4301 4.660938 AAGTGGTGCTTCCCGGGC 62.661 66.667 18.49 4.56 30.06 6.13
1180 4407 1.153389 TGATGTGCACGCCGATGAT 60.153 52.632 13.13 0.00 0.00 2.45
1211 4438 2.202987 GATGGAGCTCAGCCGGTG 60.203 66.667 17.19 0.00 0.00 4.94
1293 4534 3.420839 ACAAAACAAAACAGAGAGGCG 57.579 42.857 0.00 0.00 0.00 5.52
1334 4575 9.452065 CATGATCACATACACTACTACAAGTAC 57.548 37.037 0.00 0.00 35.09 2.73
1348 4589 6.370593 ACAACAAACGAACATGATCACATAC 58.629 36.000 0.00 0.00 35.09 2.39
1349 4590 6.348132 GGACAACAAACGAACATGATCACATA 60.348 38.462 0.00 0.00 35.09 2.29
1363 4604 7.197703 AGTTTAATTACCAAGGACAACAAACG 58.802 34.615 0.00 0.00 0.00 3.60
1372 4613 2.674357 GCGCGAGTTTAATTACCAAGGA 59.326 45.455 12.10 0.00 0.00 3.36
1374 4615 2.093152 ACGCGCGAGTTTAATTACCAAG 59.907 45.455 39.36 0.21 0.00 3.61
1376 4617 1.712401 ACGCGCGAGTTTAATTACCA 58.288 45.000 39.36 0.00 0.00 3.25
1377 4618 3.243643 ACATACGCGCGAGTTTAATTACC 59.756 43.478 39.36 0.00 0.00 2.85
1386 4627 1.298413 CAGCTACATACGCGCGAGT 60.298 57.895 39.36 30.25 0.00 4.18
1430 4673 3.096092 GTGCCACTCCCATGGAAAATTA 58.904 45.455 15.22 0.00 43.02 1.40
1443 4686 7.060633 CGATTAAATAACTTGTTTGTGCCACTC 59.939 37.037 0.00 0.00 0.00 3.51
1453 4696 8.324163 AGCTTCAGACGATTAAATAACTTGTT 57.676 30.769 0.00 0.00 0.00 2.83
1469 4713 6.215495 ACCAGTTAATCTAGAGCTTCAGAC 57.785 41.667 0.00 0.00 0.00 3.51
1540 4790 6.014647 TGTAGGAGTAGCTGAAAAGAAGGTA 58.985 40.000 0.00 0.00 0.00 3.08
1558 4808 1.732941 ATTTCATGCGCGTTGTAGGA 58.267 45.000 8.43 0.00 0.00 2.94
1559 4809 2.542766 AATTTCATGCGCGTTGTAGG 57.457 45.000 8.43 0.00 0.00 3.18
1561 4811 3.544356 TGAAATTTCATGCGCGTTGTA 57.456 38.095 16.91 0.00 31.01 2.41
1562 4812 2.414058 TGAAATTTCATGCGCGTTGT 57.586 40.000 16.91 0.00 31.01 3.32
1563 4813 2.159986 GGTTGAAATTTCATGCGCGTTG 60.160 45.455 21.10 6.40 37.00 4.10
1564 4814 2.058057 GGTTGAAATTTCATGCGCGTT 58.942 42.857 21.10 0.00 37.00 4.84
1565 4815 1.000827 TGGTTGAAATTTCATGCGCGT 60.001 42.857 21.10 0.00 37.00 6.01
1566 4816 1.386412 GTGGTTGAAATTTCATGCGCG 59.614 47.619 21.10 0.00 37.00 6.86
1567 4817 1.726248 GGTGGTTGAAATTTCATGCGC 59.274 47.619 21.10 0.00 37.00 6.09
1568 4818 2.336667 GGGTGGTTGAAATTTCATGCG 58.663 47.619 21.10 0.00 37.00 4.73
1569 4819 2.302733 AGGGGTGGTTGAAATTTCATGC 59.697 45.455 21.10 15.99 37.00 4.06
1570 4820 3.055891 GGAGGGGTGGTTGAAATTTCATG 60.056 47.826 21.10 0.00 37.00 3.07
1571 4821 3.173151 GGAGGGGTGGTTGAAATTTCAT 58.827 45.455 21.10 4.09 37.00 2.57
1572 4822 2.091055 TGGAGGGGTGGTTGAAATTTCA 60.091 45.455 16.91 16.91 34.92 2.69
1573 4823 2.562738 CTGGAGGGGTGGTTGAAATTTC 59.437 50.000 11.41 11.41 0.00 2.17
1574 4824 2.608623 CTGGAGGGGTGGTTGAAATTT 58.391 47.619 0.00 0.00 0.00 1.82
1575 4825 1.827245 GCTGGAGGGGTGGTTGAAATT 60.827 52.381 0.00 0.00 0.00 1.82
1576 4826 0.251787 GCTGGAGGGGTGGTTGAAAT 60.252 55.000 0.00 0.00 0.00 2.17
1584 4834 1.867595 AAGGGAATGCTGGAGGGGTG 61.868 60.000 0.00 0.00 0.00 4.61
1591 4841 3.073503 TGGATATCAGAAGGGAATGCTGG 59.926 47.826 4.83 0.00 0.00 4.85
1594 4844 4.070716 CTGTGGATATCAGAAGGGAATGC 58.929 47.826 4.83 0.00 35.20 3.56
1596 4846 7.013823 CATACTGTGGATATCAGAAGGGAAT 57.986 40.000 4.83 0.00 36.81 3.01
1597 4847 6.425210 CATACTGTGGATATCAGAAGGGAA 57.575 41.667 4.83 0.00 36.81 3.97
1630 4880 1.674441 CACATGGGCAGCTACTGATTG 59.326 52.381 0.00 0.00 32.44 2.67
1660 4913 6.172136 AGTAGCTGCATTAGAGTCATGAAT 57.828 37.500 4.12 0.00 0.00 2.57
1668 4921 5.521906 TCCAACTAGTAGCTGCATTAGAG 57.478 43.478 4.12 0.00 0.00 2.43
1672 4925 6.038714 GCTAAAATCCAACTAGTAGCTGCATT 59.961 38.462 4.12 0.00 32.94 3.56
1673 4926 5.529060 GCTAAAATCCAACTAGTAGCTGCAT 59.471 40.000 4.12 0.00 32.94 3.96
1676 4929 5.428253 TGGCTAAAATCCAACTAGTAGCTG 58.572 41.667 9.27 0.00 35.42 4.24
1677 4930 5.693769 TGGCTAAAATCCAACTAGTAGCT 57.306 39.130 9.27 0.00 35.42 3.32
1678 4931 5.880887 ACTTGGCTAAAATCCAACTAGTAGC 59.119 40.000 0.00 0.00 38.57 3.58
1680 4933 9.969001 ATTTACTTGGCTAAAATCCAACTAGTA 57.031 29.630 0.00 0.00 38.57 1.82
1685 4938 7.978975 TGCATATTTACTTGGCTAAAATCCAAC 59.021 33.333 0.00 0.00 38.57 3.77
1691 5041 8.417884 GGGTATTGCATATTTACTTGGCTAAAA 58.582 33.333 0.00 0.00 0.00 1.52
1696 5046 5.782893 TGGGTATTGCATATTTACTTGGC 57.217 39.130 0.00 0.00 0.00 4.52
1716 5066 7.703058 ACAGGGAGTAGTTTTAATTGATTGG 57.297 36.000 0.00 0.00 0.00 3.16
1728 5469 8.822805 TGTTTTAGATCATTACAGGGAGTAGTT 58.177 33.333 0.00 0.00 33.43 2.24
1729 5470 8.375493 TGTTTTAGATCATTACAGGGAGTAGT 57.625 34.615 0.00 0.00 33.43 2.73
1730 5471 9.838339 ATTGTTTTAGATCATTACAGGGAGTAG 57.162 33.333 0.00 0.00 33.43 2.57
1731 5472 9.832445 GATTGTTTTAGATCATTACAGGGAGTA 57.168 33.333 0.00 0.00 0.00 2.59
1732 5473 8.552296 AGATTGTTTTAGATCATTACAGGGAGT 58.448 33.333 0.00 0.00 0.00 3.85
1733 5474 8.970859 AGATTGTTTTAGATCATTACAGGGAG 57.029 34.615 0.00 0.00 0.00 4.30
1761 5502 8.842280 GCTAGCTACTCTCTCTGTAAAGAAATA 58.158 37.037 7.70 0.00 0.00 1.40
1762 5503 7.559897 AGCTAGCTACTCTCTCTGTAAAGAAAT 59.440 37.037 17.69 0.00 0.00 2.17
1763 5504 6.887545 AGCTAGCTACTCTCTCTGTAAAGAAA 59.112 38.462 17.69 0.00 0.00 2.52
1764 5505 6.419791 AGCTAGCTACTCTCTCTGTAAAGAA 58.580 40.000 17.69 0.00 0.00 2.52
1765 5506 5.996644 AGCTAGCTACTCTCTCTGTAAAGA 58.003 41.667 17.69 0.00 0.00 2.52
1767 5508 7.284074 ACATAGCTAGCTACTCTCTCTGTAAA 58.716 38.462 26.41 1.24 0.00 2.01
1769 5510 6.428083 ACATAGCTAGCTACTCTCTCTGTA 57.572 41.667 26.41 1.95 0.00 2.74
1770 5511 5.304686 ACATAGCTAGCTACTCTCTCTGT 57.695 43.478 26.41 20.31 0.00 3.41
1771 5512 8.258007 AGTATACATAGCTAGCTACTCTCTCTG 58.742 40.741 26.41 19.68 0.00 3.35
1772 5513 8.375493 AGTATACATAGCTAGCTACTCTCTCT 57.625 38.462 26.41 16.83 0.00 3.10
1773 5514 9.444600 AAAGTATACATAGCTAGCTACTCTCTC 57.555 37.037 26.41 15.06 0.00 3.20
1774 5515 9.802039 AAAAGTATACATAGCTAGCTACTCTCT 57.198 33.333 26.41 15.89 0.00 3.10
1776 5517 9.575868 TGAAAAGTATACATAGCTAGCTACTCT 57.424 33.333 26.41 13.63 0.00 3.24
1777 5518 9.834628 CTGAAAAGTATACATAGCTAGCTACTC 57.165 37.037 26.41 12.56 0.00 2.59
1778 5519 8.301002 GCTGAAAAGTATACATAGCTAGCTACT 58.699 37.037 26.41 17.30 0.00 2.57
1779 5520 8.082852 TGCTGAAAAGTATACATAGCTAGCTAC 58.917 37.037 26.41 15.24 0.00 3.58
1780 5521 8.082852 GTGCTGAAAAGTATACATAGCTAGCTA 58.917 37.037 26.09 26.09 0.00 3.32
1781 5522 6.926272 GTGCTGAAAAGTATACATAGCTAGCT 59.074 38.462 23.12 23.12 0.00 3.32
1782 5523 6.701841 TGTGCTGAAAAGTATACATAGCTAGC 59.298 38.462 6.62 6.62 0.00 3.42
1783 5524 8.824159 ATGTGCTGAAAAGTATACATAGCTAG 57.176 34.615 5.50 0.00 0.00 3.42
1794 5535 9.559732 AGCATGTATTATATGTGCTGAAAAGTA 57.440 29.630 11.59 0.00 43.84 2.24
1795 5536 8.455903 AGCATGTATTATATGTGCTGAAAAGT 57.544 30.769 11.59 0.00 43.84 2.66
1800 5541 8.625786 AATCAAGCATGTATTATATGTGCTGA 57.374 30.769 12.64 12.10 44.66 4.26
1803 5544 9.979270 GACTAATCAAGCATGTATTATATGTGC 57.021 33.333 0.00 4.39 36.11 4.57
1830 5571 0.246635 TGCTTCTAGGTCGGCAGTTC 59.753 55.000 0.00 0.00 0.00 3.01
1833 5574 1.517257 CGTGCTTCTAGGTCGGCAG 60.517 63.158 0.00 0.00 35.29 4.85
1848 5589 3.327754 GTATAGGGCGTGCGCGTG 61.328 66.667 22.18 0.00 43.06 5.34
1849 5590 3.829044 TGTATAGGGCGTGCGCGT 61.829 61.111 22.18 3.77 43.06 6.01
1850 5591 3.327754 GTGTATAGGGCGTGCGCG 61.328 66.667 16.86 16.86 43.06 6.86
1851 5592 2.965462 GGTGTATAGGGCGTGCGC 60.965 66.667 8.17 8.17 41.06 6.09
1852 5593 2.279918 GGGTGTATAGGGCGTGCG 60.280 66.667 0.00 0.00 0.00 5.34
1853 5594 2.279918 CGGGTGTATAGGGCGTGC 60.280 66.667 0.00 0.00 0.00 5.34
1854 5595 1.105167 TCTCGGGTGTATAGGGCGTG 61.105 60.000 0.00 0.00 0.00 5.34
1855 5596 1.105759 GTCTCGGGTGTATAGGGCGT 61.106 60.000 0.00 0.00 0.00 5.68
1857 5598 0.757935 TGGTCTCGGGTGTATAGGGC 60.758 60.000 0.00 0.00 0.00 5.19
1858 5599 1.133575 TCTGGTCTCGGGTGTATAGGG 60.134 57.143 0.00 0.00 0.00 3.53
1859 5600 2.231529 CTCTGGTCTCGGGTGTATAGG 58.768 57.143 0.00 0.00 0.00 2.57
1860 5601 2.231529 CCTCTGGTCTCGGGTGTATAG 58.768 57.143 0.00 0.00 0.00 1.31
1862 5603 0.397254 CCCTCTGGTCTCGGGTGTAT 60.397 60.000 0.00 0.00 33.16 2.29
1863 5604 1.000019 CCCTCTGGTCTCGGGTGTA 60.000 63.158 0.00 0.00 33.16 2.90
1864 5605 2.283966 CCCTCTGGTCTCGGGTGT 60.284 66.667 0.00 0.00 33.16 4.16
1865 5606 2.037367 TCCCTCTGGTCTCGGGTG 59.963 66.667 0.00 0.00 39.10 4.61
1866 5607 1.212934 TACTCCCTCTGGTCTCGGGT 61.213 60.000 0.00 0.00 39.10 5.28
1869 5610 0.392729 ACGTACTCCCTCTGGTCTCG 60.393 60.000 0.00 0.00 0.00 4.04
1870 5611 1.096416 CACGTACTCCCTCTGGTCTC 58.904 60.000 0.00 0.00 0.00 3.36
1872 5613 1.742268 GTACACGTACTCCCTCTGGTC 59.258 57.143 0.00 0.00 33.45 4.02
1874 5615 1.830279 TGTACACGTACTCCCTCTGG 58.170 55.000 8.69 0.00 37.00 3.86
1875 5616 2.555325 TGTTGTACACGTACTCCCTCTG 59.445 50.000 8.69 0.00 37.00 3.35
1876 5617 2.867624 TGTTGTACACGTACTCCCTCT 58.132 47.619 8.69 0.00 37.00 3.69
1877 5618 3.863142 ATGTTGTACACGTACTCCCTC 57.137 47.619 8.69 0.00 37.00 4.30
1878 5619 4.612264 AAATGTTGTACACGTACTCCCT 57.388 40.909 8.69 0.00 37.00 4.20
1879 5620 4.751098 TGAAAATGTTGTACACGTACTCCC 59.249 41.667 8.69 0.00 37.00 4.30
1880 5621 5.910637 TGAAAATGTTGTACACGTACTCC 57.089 39.130 8.69 0.56 37.00 3.85
1881 5622 6.630045 GGTTTGAAAATGTTGTACACGTACTC 59.370 38.462 8.69 3.34 37.00 2.59
1882 5623 6.488817 GGTTTGAAAATGTTGTACACGTACT 58.511 36.000 8.69 0.00 37.00 2.73
1883 5624 5.393163 CGGTTTGAAAATGTTGTACACGTAC 59.607 40.000 0.00 0.22 36.63 3.67
1884 5625 5.499935 CGGTTTGAAAATGTTGTACACGTA 58.500 37.500 0.00 0.00 0.00 3.57
1885 5626 4.344448 CGGTTTGAAAATGTTGTACACGT 58.656 39.130 0.00 0.00 0.00 4.49
1886 5627 3.726730 CCGGTTTGAAAATGTTGTACACG 59.273 43.478 0.00 0.00 0.00 4.49
1887 5628 3.487942 GCCGGTTTGAAAATGTTGTACAC 59.512 43.478 1.90 0.00 0.00 2.90
1888 5629 3.130516 TGCCGGTTTGAAAATGTTGTACA 59.869 39.130 1.90 0.00 0.00 2.90
1889 5630 3.707793 TGCCGGTTTGAAAATGTTGTAC 58.292 40.909 1.90 0.00 0.00 2.90
1890 5631 3.381908 ACTGCCGGTTTGAAAATGTTGTA 59.618 39.130 1.90 0.00 0.00 2.41
1891 5632 2.167487 ACTGCCGGTTTGAAAATGTTGT 59.833 40.909 1.90 0.00 0.00 3.32
1892 5633 2.820330 ACTGCCGGTTTGAAAATGTTG 58.180 42.857 1.90 0.00 0.00 3.33
1893 5634 3.886505 TCTACTGCCGGTTTGAAAATGTT 59.113 39.130 1.90 0.00 0.00 2.71
1894 5635 3.482436 TCTACTGCCGGTTTGAAAATGT 58.518 40.909 1.90 0.00 0.00 2.71
1895 5636 4.497473 TTCTACTGCCGGTTTGAAAATG 57.503 40.909 1.90 0.00 0.00 2.32
1896 5637 4.558697 GCTTTCTACTGCCGGTTTGAAAAT 60.559 41.667 1.90 0.00 32.92 1.82
1897 5638 3.243267 GCTTTCTACTGCCGGTTTGAAAA 60.243 43.478 1.90 0.00 32.92 2.29
1898 5639 2.292292 GCTTTCTACTGCCGGTTTGAAA 59.708 45.455 1.90 6.34 32.61 2.69
1899 5640 1.877443 GCTTTCTACTGCCGGTTTGAA 59.123 47.619 1.90 0.00 0.00 2.69
1900 5641 1.519408 GCTTTCTACTGCCGGTTTGA 58.481 50.000 1.90 0.00 0.00 2.69
1901 5642 0.165944 CGCTTTCTACTGCCGGTTTG 59.834 55.000 1.90 0.00 0.00 2.93
1902 5643 0.250166 ACGCTTTCTACTGCCGGTTT 60.250 50.000 1.90 0.00 0.00 3.27
1903 5644 0.949105 CACGCTTTCTACTGCCGGTT 60.949 55.000 1.90 0.00 0.00 4.44
1904 5645 1.374252 CACGCTTTCTACTGCCGGT 60.374 57.895 1.90 0.00 0.00 5.28
1905 5646 0.460284 ATCACGCTTTCTACTGCCGG 60.460 55.000 0.00 0.00 0.00 6.13
1906 5647 0.647410 CATCACGCTTTCTACTGCCG 59.353 55.000 0.00 0.00 0.00 5.69
1907 5648 2.010145 TCATCACGCTTTCTACTGCC 57.990 50.000 0.00 0.00 0.00 4.85
1908 5649 2.094417 GGTTCATCACGCTTTCTACTGC 59.906 50.000 0.00 0.00 0.00 4.40
1909 5650 2.345641 CGGTTCATCACGCTTTCTACTG 59.654 50.000 0.00 0.00 0.00 2.74
1910 5651 2.029290 ACGGTTCATCACGCTTTCTACT 60.029 45.455 0.00 0.00 0.00 2.57
1911 5652 2.334838 ACGGTTCATCACGCTTTCTAC 58.665 47.619 0.00 0.00 0.00 2.59
1912 5653 2.736144 ACGGTTCATCACGCTTTCTA 57.264 45.000 0.00 0.00 0.00 2.10
1913 5654 2.288579 TGTACGGTTCATCACGCTTTCT 60.289 45.455 0.00 0.00 0.00 2.52
1914 5655 2.063266 TGTACGGTTCATCACGCTTTC 58.937 47.619 0.00 0.00 0.00 2.62
1915 5656 2.157834 TGTACGGTTCATCACGCTTT 57.842 45.000 0.00 0.00 0.00 3.51
1916 5657 1.999735 CATGTACGGTTCATCACGCTT 59.000 47.619 0.00 0.00 0.00 4.68
1917 5658 1.640428 CATGTACGGTTCATCACGCT 58.360 50.000 0.00 0.00 0.00 5.07
1918 5659 0.026285 GCATGTACGGTTCATCACGC 59.974 55.000 0.00 0.00 0.00 5.34
1919 5660 1.324435 CTGCATGTACGGTTCATCACG 59.676 52.381 0.00 0.00 0.00 4.35
1920 5661 2.094258 CACTGCATGTACGGTTCATCAC 59.906 50.000 0.00 0.00 0.00 3.06
1921 5662 2.289382 ACACTGCATGTACGGTTCATCA 60.289 45.455 0.00 0.00 40.88 3.07
1922 5663 2.346803 ACACTGCATGTACGGTTCATC 58.653 47.619 0.00 0.00 40.88 2.92
1923 5664 2.472695 ACACTGCATGTACGGTTCAT 57.527 45.000 0.00 0.00 40.88 2.57
1924 5665 3.999821 ACACTGCATGTACGGTTCA 57.000 47.368 0.00 0.00 40.88 3.18
1931 5672 2.993220 CGAAGCTTGTACACTGCATGTA 59.007 45.455 18.52 5.28 43.19 2.29
1932 5673 1.800586 CGAAGCTTGTACACTGCATGT 59.199 47.619 18.52 6.93 46.06 3.21
1933 5674 1.800586 ACGAAGCTTGTACACTGCATG 59.199 47.619 18.52 11.46 0.00 4.06
1934 5675 2.069273 GACGAAGCTTGTACACTGCAT 58.931 47.619 18.52 9.46 0.00 3.96
1935 5676 1.202475 TGACGAAGCTTGTACACTGCA 60.202 47.619 18.52 0.00 0.00 4.41
1936 5677 1.497991 TGACGAAGCTTGTACACTGC 58.502 50.000 2.10 10.97 0.00 4.40
1937 5678 7.520119 TTATTATGACGAAGCTTGTACACTG 57.480 36.000 2.10 0.00 0.00 3.66
1938 5679 8.542497 TTTTATTATGACGAAGCTTGTACACT 57.458 30.769 2.10 0.00 0.00 3.55
1939 5680 9.769093 AATTTTATTATGACGAAGCTTGTACAC 57.231 29.630 2.10 0.00 0.00 2.90
1943 5684 9.906660 TCAAAATTTTATTATGACGAAGCTTGT 57.093 25.926 2.10 1.92 0.00 3.16
1945 5686 9.076596 GCTCAAAATTTTATTATGACGAAGCTT 57.923 29.630 0.00 0.00 0.00 3.74
1946 5687 7.702348 GGCTCAAAATTTTATTATGACGAAGCT 59.298 33.333 2.44 0.00 0.00 3.74
1947 5688 7.305418 CGGCTCAAAATTTTATTATGACGAAGC 60.305 37.037 2.44 0.00 0.00 3.86
1948 5689 7.908082 TCGGCTCAAAATTTTATTATGACGAAG 59.092 33.333 2.44 0.00 0.00 3.79
1949 5690 7.753659 TCGGCTCAAAATTTTATTATGACGAA 58.246 30.769 2.44 0.00 0.00 3.85
1950 5691 7.310072 TCGGCTCAAAATTTTATTATGACGA 57.690 32.000 2.44 8.50 0.00 4.20
1951 5692 9.658475 TTATCGGCTCAAAATTTTATTATGACG 57.342 29.630 2.44 6.44 0.00 4.35
1960 5701 9.719355 ATTAACCTTTTATCGGCTCAAAATTTT 57.281 25.926 0.00 0.00 0.00 1.82
1964 5705 7.971722 GCTAATTAACCTTTTATCGGCTCAAAA 59.028 33.333 0.00 0.00 0.00 2.44
1970 5711 8.618677 AGTTTAGCTAATTAACCTTTTATCGGC 58.381 33.333 7.08 0.00 0.00 5.54
1971 5712 9.931210 CAGTTTAGCTAATTAACCTTTTATCGG 57.069 33.333 7.08 0.00 0.00 4.18
1995 5740 7.172190 AGTCGCCATAATGAATCTTGTTATCAG 59.828 37.037 0.00 0.00 0.00 2.90
1998 5743 7.807977 AAGTCGCCATAATGAATCTTGTTAT 57.192 32.000 0.00 0.00 0.00 1.89
2002 5747 6.324819 ACAAAAGTCGCCATAATGAATCTTG 58.675 36.000 0.00 0.00 0.00 3.02
2003 5748 6.515272 ACAAAAGTCGCCATAATGAATCTT 57.485 33.333 0.00 0.00 0.00 2.40
2009 5754 5.354234 AGGACTAACAAAAGTCGCCATAATG 59.646 40.000 0.00 0.00 45.69 1.90
2010 5755 5.354234 CAGGACTAACAAAAGTCGCCATAAT 59.646 40.000 0.00 0.00 45.69 1.28
2016 5761 2.349532 GCACAGGACTAACAAAAGTCGC 60.350 50.000 0.00 0.00 45.69 5.19
2153 5902 0.539438 TGATTGGTGTGGGACTTGGC 60.539 55.000 0.00 0.00 0.00 4.52
2156 5905 2.039746 TCGATTGATTGGTGTGGGACTT 59.960 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.