Multiple sequence alignment - TraesCS5A01G072200

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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 TraesCS5A01G072200 chr5A 100.000 5688 0 0 1 5688 82981111 82986798 0.000000e+00 10504
1 TraesCS5A01G072200 chr5B 92.873 4027 195 54 1690 5688 95022788 95018826 0.000000e+00 5762
2 TraesCS5A01G072200 chr5B 95.615 1163 41 7 515 1667 95023945 95022783 0.000000e+00 1857
3 TraesCS5A01G072200 chr5B 85.443 474 65 4 1 472 95024668 95024197 1.840000e-134 490
4 TraesCS5A01G072200 chr5D 90.843 3571 261 35 1687 5233 89045858 89049386 0.000000e+00 4723
5 TraesCS5A01G072200 chr5D 91.001 1678 109 20 1 1667 89044220 89045866 0.000000e+00 2224
6 TraesCS5A01G072200 chr5D 83.830 470 26 12 5226 5688 89050827 89051253 8.880000e-108 401
7 TraesCS5A01G072200 chr4A 83.985 537 71 10 1139 1672 546017795 546018319 8.510000e-138 501
8 TraesCS5A01G072200 chr4D 83.654 520 72 8 1142 1657 50977625 50977115 1.430000e-130 477


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 TraesCS5A01G072200 chr5A 82981111 82986798 5687 False 10504.000000 10504 100.000000 1 5688 1 chr5A.!!$F1 5687
1 TraesCS5A01G072200 chr5B 95018826 95024668 5842 True 2703.000000 5762 91.310333 1 5688 3 chr5B.!!$R1 5687
2 TraesCS5A01G072200 chr5D 89044220 89051253 7033 False 2449.333333 4723 88.558000 1 5688 3 chr5D.!!$F1 5687
3 TraesCS5A01G072200 chr4A 546017795 546018319 524 False 501.000000 501 83.985000 1139 1672 1 chr4A.!!$F1 533
4 TraesCS5A01G072200 chr4D 50977115 50977625 510 True 477.000000 477 83.654000 1142 1657 1 chr4D.!!$R1 515

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
497 508 0.250513 GAAGGGAACAGATGAGCGGT 59.749 55.000 0.00 0.0 0.00 5.68 F
2357 2586 1.035139 GGATGGCTTGCATGGGTAAG 58.965 55.000 1.34 0.0 39.45 2.34 F
3370 3602 1.154093 CCATTCAGCGCTTGTGCAG 60.154 57.895 7.50 0.0 39.64 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2621 1.485066 CGTCCCCAGTAAGTTAGCCAT 59.515 52.381 0.00 0.00 0.00 4.40 R
3986 4222 0.745845 ACAGAACATCCGAGCATGCC 60.746 55.000 15.66 4.99 0.00 4.40 R
5266 6966 0.250038 CACCATCCTCCACTATGGCG 60.250 60.000 0.00 0.00 45.53 5.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.410556 ACAATGATTTGTTGTAGATTTTGCTAC 57.589 29.630 0.00 0.00 43.57 3.58
42 43 9.409312 CAATGATTTGTTGTAGATTTTGCTACA 57.591 29.630 0.00 0.00 46.52 2.74
55 56 2.054687 TGCTACAACTGGTAACGACG 57.945 50.000 0.00 0.00 42.51 5.12
57 58 1.336240 GCTACAACTGGTAACGACGGT 60.336 52.381 0.00 0.00 42.51 4.83
95 96 1.575244 CGAATGATGCGACCTGTGAT 58.425 50.000 0.00 0.00 0.00 3.06
115 116 1.953017 CCGCCACCGACAATTTTGA 59.047 52.632 0.00 0.00 36.29 2.69
119 120 1.616620 CCACCGACAATTTTGATGCG 58.383 50.000 0.00 0.00 0.00 4.73
130 131 0.871722 TTTGATGCGACCGTCTTTGG 59.128 50.000 0.00 0.00 0.00 3.28
133 134 1.970917 GATGCGACCGTCTTTGGCAG 61.971 60.000 5.30 0.00 37.01 4.85
146 147 1.515081 TTGGCAGTTGTTACTACCGC 58.485 50.000 0.00 0.00 40.23 5.68
189 190 0.604780 CATGATGATGACCGGAGCCC 60.605 60.000 9.46 0.00 0.00 5.19
196 197 4.493747 GACCGGAGCCCTCGTTCG 62.494 72.222 9.46 0.00 0.00 3.95
223 224 0.881118 CAGGGAAACATTGTGACCGG 59.119 55.000 0.00 0.00 0.00 5.28
224 225 0.476771 AGGGAAACATTGTGACCGGT 59.523 50.000 6.92 6.92 0.00 5.28
225 226 0.596082 GGGAAACATTGTGACCGGTG 59.404 55.000 14.63 0.00 0.00 4.94
266 267 1.000274 GTGGCGCAAAATCCTTCAACT 60.000 47.619 10.83 0.00 0.00 3.16
274 275 4.201822 GCAAAATCCTTCAACTAGCTACGG 60.202 45.833 0.00 0.00 0.00 4.02
288 290 3.619233 GCTACGGAAAAGCTTCAAACA 57.381 42.857 0.00 0.00 37.01 2.83
315 317 1.470112 GCTTGAGCTACGAGGAGAACC 60.470 57.143 0.00 0.00 38.21 3.62
317 319 4.490859 GCTTGAGCTACGAGGAGAACCTA 61.491 52.174 0.00 0.00 41.64 3.08
333 335 4.124351 TACGACCAAGGAGCGCCG 62.124 66.667 2.29 0.00 39.96 6.46
432 435 3.350163 CATGGTGGGAAGGGGGCT 61.350 66.667 0.00 0.00 0.00 5.19
447 450 1.406887 GGGGCTCGTGCTGATTTAAGA 60.407 52.381 9.61 0.00 39.59 2.10
459 462 8.450964 CGTGCTGATTTAAGAAAAAGGAAGATA 58.549 33.333 0.00 0.00 0.00 1.98
489 492 2.133858 AAAGAGGGGAAGGGAACAGA 57.866 50.000 0.00 0.00 0.00 3.41
497 508 0.250513 GAAGGGAACAGATGAGCGGT 59.749 55.000 0.00 0.00 0.00 5.68
502 513 2.418976 GGGAACAGATGAGCGGTTAAAC 59.581 50.000 0.00 0.00 34.99 2.01
519 731 7.273188 GGTTAAACCGCACATTTAAAAGATC 57.727 36.000 0.00 0.00 34.24 2.75
532 744 5.712217 TTAAAAGATCTTGTATCACGCGG 57.288 39.130 12.47 0.00 0.00 6.46
720 941 7.543172 ACATAATAAAGTGCATTGCAAAGACTG 59.457 33.333 13.94 0.00 41.47 3.51
1494 1717 3.352338 CTGCCGTGACGAGTACCCC 62.352 68.421 6.54 0.00 0.00 4.95
1632 1855 4.652131 TGGGCCGGCGTTGTCATT 62.652 61.111 22.54 0.00 0.00 2.57
1671 1894 4.657814 AGTTTGGACTCTCTCTCTCTCT 57.342 45.455 0.00 0.00 0.00 3.10
1672 1895 4.589908 AGTTTGGACTCTCTCTCTCTCTC 58.410 47.826 0.00 0.00 0.00 3.20
1673 1896 4.289672 AGTTTGGACTCTCTCTCTCTCTCT 59.710 45.833 0.00 0.00 0.00 3.10
1674 1897 4.487714 TTGGACTCTCTCTCTCTCTCTC 57.512 50.000 0.00 0.00 0.00 3.20
1675 1898 3.724478 TGGACTCTCTCTCTCTCTCTCT 58.276 50.000 0.00 0.00 0.00 3.10
1676 1899 3.706594 TGGACTCTCTCTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
1677 1900 3.964031 GGACTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
1678 1901 4.038642 GGACTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 0.00 3.20
1679 1902 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
1680 1903 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1681 1904 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1682 1905 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1683 1906 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1684 1907 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1685 1908 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1686 1909 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1687 1910 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1688 1911 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1689 1912 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1690 1913 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1691 1914 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1692 1915 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1693 1916 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1694 1917 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1788 2011 9.830975 ATAGTTCCAAAATAAGTTGCTTTTTGT 57.169 25.926 14.27 4.56 38.20 2.83
1789 2012 8.196802 AGTTCCAAAATAAGTTGCTTTTTGTC 57.803 30.769 14.27 8.25 38.20 3.18
1790 2013 8.040727 AGTTCCAAAATAAGTTGCTTTTTGTCT 58.959 29.630 14.27 9.53 38.20 3.41
1791 2014 7.769272 TCCAAAATAAGTTGCTTTTTGTCTG 57.231 32.000 14.27 5.27 38.20 3.51
1792 2015 7.551585 TCCAAAATAAGTTGCTTTTTGTCTGA 58.448 30.769 14.27 6.72 38.20 3.27
1861 2084 2.851263 TTTGTCCCAGTCGTTGCTAT 57.149 45.000 0.00 0.00 0.00 2.97
1871 2094 4.154015 CCAGTCGTTGCTATTGACATTTGA 59.846 41.667 6.35 0.00 35.09 2.69
1932 2155 6.817140 GCTTACTGTTACTGCTTATGGTAGTT 59.183 38.462 0.00 0.00 41.08 2.24
2077 2300 5.738619 TGTACTACCAGTGATGTGACAAT 57.261 39.130 0.00 0.00 0.00 2.71
2081 2304 4.997395 ACTACCAGTGATGTGACAATTGAC 59.003 41.667 13.59 6.72 0.00 3.18
2085 2308 4.154737 CCAGTGATGTGACAATTGACGATT 59.845 41.667 13.59 0.00 0.00 3.34
2103 2326 5.699839 ACGATTTACATTTGGCTCACTTTC 58.300 37.500 0.00 0.00 0.00 2.62
2120 2343 5.415701 TCACTTTCAATTCATTCTGCCCTAC 59.584 40.000 0.00 0.00 0.00 3.18
2170 2393 7.693969 ATTTACCTTCCTTGACAAGAATCTG 57.306 36.000 16.99 0.00 0.00 2.90
2257 2486 5.460646 ACTGTAATTTTCTGAACCATTGCG 58.539 37.500 0.00 0.00 0.00 4.85
2357 2586 1.035139 GGATGGCTTGCATGGGTAAG 58.965 55.000 1.34 0.00 39.45 2.34
2781 3012 5.160607 TCTACGAATGGTCCTTGAATTGT 57.839 39.130 0.00 0.00 0.00 2.71
2788 3019 5.920193 ATGGTCCTTGAATTGTGTATTGG 57.080 39.130 0.00 0.00 0.00 3.16
2799 3030 9.679661 TTGAATTGTGTATTGGTACTGACATAT 57.320 29.630 0.00 0.00 0.00 1.78
3370 3602 1.154093 CCATTCAGCGCTTGTGCAG 60.154 57.895 7.50 0.00 39.64 4.41
3517 3749 7.883217 TCGCTAAAGGATTCTATGGTAGTAAG 58.117 38.462 0.00 0.00 0.00 2.34
3640 3872 2.202623 GCCGGTCAGAGTAGCACG 60.203 66.667 1.90 0.00 0.00 5.34
3709 3941 9.710900 CTAAATTTGAGGTTAAAGAAATGGCTT 57.289 29.630 0.00 0.00 0.00 4.35
3781 4013 5.049167 GCTCTGTTCTTCGATTCATCTGAT 58.951 41.667 0.00 0.00 0.00 2.90
3871 4103 5.729229 TCCTCTGATAACCTTGGTATCCAAA 59.271 40.000 2.85 0.00 43.44 3.28
3892 4124 3.837355 AGAGCAAGTCATGGGAGTTTTT 58.163 40.909 0.00 0.00 34.43 1.94
3923 4158 5.163884 GGTCGTAAAATGCAAGTAAGTCCTC 60.164 44.000 0.00 0.00 0.00 3.71
3924 4159 4.933400 TCGTAAAATGCAAGTAAGTCCTCC 59.067 41.667 0.00 0.00 0.00 4.30
3925 4160 4.935808 CGTAAAATGCAAGTAAGTCCTCCT 59.064 41.667 0.00 0.00 0.00 3.69
3926 4161 5.411669 CGTAAAATGCAAGTAAGTCCTCCTT 59.588 40.000 0.00 0.00 37.17 3.36
3927 4162 6.592607 CGTAAAATGCAAGTAAGTCCTCCTTA 59.407 38.462 0.00 0.00 34.46 2.69
3928 4163 7.118680 CGTAAAATGCAAGTAAGTCCTCCTTAA 59.881 37.037 0.00 0.00 37.39 1.85
3930 4165 4.281898 TGCAAGTAAGTCCTCCTTAACC 57.718 45.455 0.00 0.00 37.39 2.85
3931 4166 3.908103 TGCAAGTAAGTCCTCCTTAACCT 59.092 43.478 0.00 0.00 37.39 3.50
3932 4167 4.020485 TGCAAGTAAGTCCTCCTTAACCTC 60.020 45.833 0.00 0.00 37.39 3.85
3933 4168 4.020485 GCAAGTAAGTCCTCCTTAACCTCA 60.020 45.833 0.00 0.00 37.39 3.86
3934 4169 5.725362 CAAGTAAGTCCTCCTTAACCTCAG 58.275 45.833 0.00 0.00 37.39 3.35
3935 4170 5.013258 AGTAAGTCCTCCTTAACCTCAGT 57.987 43.478 0.00 0.00 37.39 3.41
3980 4216 9.995003 TTTTTCTTCATAATTGTGCACCTTTAT 57.005 25.926 15.69 14.01 0.00 1.40
4008 4244 2.079158 CATGCTCGGATGTTCTGTGTT 58.921 47.619 0.00 0.00 0.00 3.32
4009 4245 2.254546 TGCTCGGATGTTCTGTGTTT 57.745 45.000 0.00 0.00 0.00 2.83
4030 4269 2.024176 AGCATTTACCTAGCCACACG 57.976 50.000 0.00 0.00 0.00 4.49
4048 4287 3.576118 ACACGATATTCTCTGGAGGGATG 59.424 47.826 0.00 0.00 0.00 3.51
4053 4292 5.420421 CGATATTCTCTGGAGGGATGTATGT 59.580 44.000 0.00 0.00 0.00 2.29
4059 4298 6.889198 TCTCTGGAGGGATGTATGTTTTAAG 58.111 40.000 0.00 0.00 0.00 1.85
4076 4315 7.035004 TGTTTTAAGATTATTCATGTGCAGGC 58.965 34.615 0.00 0.00 0.00 4.85
4096 4335 6.518369 GCAGGCCTGTTTCTAGGTTAAAAATT 60.518 38.462 32.81 0.00 40.11 1.82
4100 4339 7.255836 GGCCTGTTTCTAGGTTAAAAATTCTGT 60.256 37.037 0.00 0.00 40.11 3.41
4109 4348 7.713764 AGGTTAAAAATTCTGTCACATTTGC 57.286 32.000 0.00 0.00 0.00 3.68
4147 4386 1.813513 CTGTAGCCAGTGTTCCCTTG 58.186 55.000 0.00 0.00 33.80 3.61
4162 4409 4.222124 TCCCTTGTGGAAATTCTAGAGC 57.778 45.455 0.00 0.00 41.40 4.09
4167 4414 5.104735 CCTTGTGGAAATTCTAGAGCCTAGT 60.105 44.000 8.51 0.00 34.57 2.57
4172 4419 5.119694 GGAAATTCTAGAGCCTAGTTGTGG 58.880 45.833 8.51 0.00 0.00 4.17
4179 4426 6.875076 TCTAGAGCCTAGTTGTGGTATTTTC 58.125 40.000 8.51 0.00 0.00 2.29
4205 4452 5.351465 GGTTCACGATTCTAGATTTTGCTGA 59.649 40.000 0.00 0.00 0.00 4.26
4225 4474 5.823209 TGAAATTCAGATGTAGGTGCATG 57.177 39.130 0.00 0.00 0.00 4.06
4226 4475 5.255687 TGAAATTCAGATGTAGGTGCATGT 58.744 37.500 0.00 0.00 0.00 3.21
4229 4478 6.594788 AATTCAGATGTAGGTGCATGTTTT 57.405 33.333 0.00 0.00 0.00 2.43
4230 4479 5.375417 TTCAGATGTAGGTGCATGTTTTG 57.625 39.130 0.00 0.00 0.00 2.44
4239 4488 2.287644 GGTGCATGTTTTGACAAAAGCC 59.712 45.455 13.59 4.19 0.00 4.35
4242 4491 3.132646 TGCATGTTTTGACAAAAGCCTCT 59.867 39.130 13.59 0.00 0.00 3.69
4243 4492 3.492011 GCATGTTTTGACAAAAGCCTCTG 59.508 43.478 13.59 8.11 0.00 3.35
4245 4494 2.159114 TGTTTTGACAAAAGCCTCTGCC 60.159 45.455 13.59 0.77 38.69 4.85
4253 4502 3.903714 ACAAAAGCCTCTGCCCTAAATTT 59.096 39.130 0.00 0.00 38.69 1.82
4259 4508 5.073428 AGCCTCTGCCCTAAATTTATAAGC 58.927 41.667 0.00 3.22 38.69 3.09
4262 4511 5.241728 CCTCTGCCCTAAATTTATAAGCCAC 59.758 44.000 0.00 0.00 0.00 5.01
4263 4512 6.013554 TCTGCCCTAAATTTATAAGCCACT 57.986 37.500 0.00 0.00 0.00 4.00
4264 4513 5.827797 TCTGCCCTAAATTTATAAGCCACTG 59.172 40.000 0.00 0.00 0.00 3.66
4265 4514 4.892934 TGCCCTAAATTTATAAGCCACTGG 59.107 41.667 0.00 0.00 0.00 4.00
4266 4515 4.893524 GCCCTAAATTTATAAGCCACTGGT 59.106 41.667 0.00 0.00 0.00 4.00
4267 4516 5.362717 GCCCTAAATTTATAAGCCACTGGTT 59.637 40.000 0.00 0.00 35.99 3.67
4268 4517 6.127168 GCCCTAAATTTATAAGCCACTGGTTT 60.127 38.462 2.38 2.38 33.46 3.27
4269 4518 7.068962 GCCCTAAATTTATAAGCCACTGGTTTA 59.931 37.037 6.82 6.82 33.24 2.01
4270 4519 9.143155 CCCTAAATTTATAAGCCACTGGTTTAT 57.857 33.333 18.21 18.21 40.98 1.40
4271 4520 9.965824 CCTAAATTTATAAGCCACTGGTTTATG 57.034 33.333 21.57 7.73 39.00 1.90
4283 4532 9.695155 AGCCACTGGTTTATGTATTTAGTTAAT 57.305 29.630 0.00 0.00 0.00 1.40
4312 4561 2.975489 AGCACTATCTTATCCCCAGTGG 59.025 50.000 0.63 0.63 37.63 4.00
4317 4566 6.465894 GCACTATCTTATCCCCAGTGGTTATT 60.466 42.308 8.74 0.00 37.63 1.40
4334 4583 8.755028 AGTGGTTATTTGTTTTTGTAGGACTTT 58.245 29.630 0.00 0.00 0.00 2.66
4376 4627 6.869913 ACTAAATCATCATTTGCACAACCTTG 59.130 34.615 0.00 0.00 33.95 3.61
4390 4641 4.761739 CACAACCTTGTAATGTGATCACCT 59.238 41.667 22.85 10.76 45.61 4.00
4391 4642 4.761739 ACAACCTTGTAATGTGATCACCTG 59.238 41.667 22.85 3.16 40.16 4.00
4392 4643 4.908601 ACCTTGTAATGTGATCACCTGA 57.091 40.909 22.85 3.52 0.00 3.86
4394 4645 5.003804 ACCTTGTAATGTGATCACCTGAAC 58.996 41.667 22.85 15.12 0.00 3.18
4396 4647 5.649395 CCTTGTAATGTGATCACCTGAACAT 59.351 40.000 22.85 5.92 34.79 2.71
4407 4658 8.180267 GTGATCACCTGAACATTATTTTCTCTG 58.820 37.037 15.31 0.00 0.00 3.35
4414 4665 5.044476 TGAACATTATTTTCTCTGGCCCCTA 60.044 40.000 0.00 0.00 0.00 3.53
4415 4666 5.466127 ACATTATTTTCTCTGGCCCCTAA 57.534 39.130 0.00 0.00 0.00 2.69
4427 4678 5.646215 TCTGGCCCCTAAGTTTAAATTTCA 58.354 37.500 0.00 0.00 0.00 2.69
4502 4753 2.670934 CCTGGACAGTGGCTGCAC 60.671 66.667 0.50 0.00 34.37 4.57
4546 4797 5.815233 ATCTCTTGTTGGACTTCTTCTCA 57.185 39.130 0.00 0.00 0.00 3.27
4576 4827 0.535335 GAGGTCCATTGTACGGCTCA 59.465 55.000 0.00 0.00 0.00 4.26
4577 4828 0.981183 AGGTCCATTGTACGGCTCAA 59.019 50.000 0.00 0.00 0.00 3.02
4586 4837 1.275010 TGTACGGCTCAATTCTCTGCA 59.725 47.619 0.00 0.00 0.00 4.41
4639 4890 2.270205 CTCATTCTGCGGGGCACT 59.730 61.111 0.00 0.00 33.79 4.40
4660 4911 5.651139 CACTGAAATCTCCAACCAGATGATT 59.349 40.000 0.00 0.00 33.13 2.57
4663 4914 6.720309 TGAAATCTCCAACCAGATGATTGTA 58.280 36.000 0.00 0.00 33.13 2.41
4666 4917 3.519107 TCTCCAACCAGATGATTGTAGCA 59.481 43.478 0.00 0.00 0.00 3.49
4678 4929 4.754322 TGATTGTAGCAATACGCAAGAGA 58.246 39.130 0.00 0.00 46.13 3.10
4708 4959 4.808364 TGACAGCTGTAACAAAATTTTGCC 59.192 37.500 26.94 16.80 41.79 4.52
4734 4985 7.711339 CCTCTTATTACACAACCATAACCTCTC 59.289 40.741 0.00 0.00 0.00 3.20
4735 4986 8.141298 TCTTATTACACAACCATAACCTCTCA 57.859 34.615 0.00 0.00 0.00 3.27
4772 5023 2.900546 TCTCTTCCAAGAACAGAGACCC 59.099 50.000 0.00 0.00 38.51 4.46
4773 5024 2.634940 CTCTTCCAAGAACAGAGACCCA 59.365 50.000 0.00 0.00 36.88 4.51
4775 5026 2.398754 TCCAAGAACAGAGACCCAGA 57.601 50.000 0.00 0.00 0.00 3.86
4784 5035 2.182827 CAGAGACCCAGAGATCCACAA 58.817 52.381 0.00 0.00 0.00 3.33
4811 5063 5.640732 ACAGTGACATTGAGTTGTTGAAAC 58.359 37.500 4.78 0.00 0.00 2.78
4817 5069 4.949856 ACATTGAGTTGTTGAAACAGACCT 59.050 37.500 0.00 0.00 40.50 3.85
4823 5075 3.358111 TGTTGAAACAGACCTGAACCA 57.642 42.857 3.76 0.00 34.30 3.67
4846 5098 4.278419 ACTGTTGAATTTGGTTGTAGCTCC 59.722 41.667 0.00 0.00 0.00 4.70
4847 5099 3.572255 TGTTGAATTTGGTTGTAGCTCCC 59.428 43.478 0.00 0.00 0.00 4.30
4853 5105 1.729586 TGGTTGTAGCTCCCTGACTT 58.270 50.000 0.00 0.00 0.00 3.01
4857 5109 2.300437 GTTGTAGCTCCCTGACTTGTCT 59.700 50.000 0.00 0.00 0.00 3.41
4858 5110 3.451402 TGTAGCTCCCTGACTTGTCTA 57.549 47.619 0.00 0.00 0.00 2.59
4866 5118 2.559931 CCCTGACTTGTCTAGAAGGGGA 60.560 54.545 14.90 0.00 42.72 4.81
4869 5121 3.699038 CTGACTTGTCTAGAAGGGGAGAG 59.301 52.174 0.00 0.00 0.00 3.20
5025 5277 8.948631 TCTTATCCTTCATCTGTACATGAAAC 57.051 34.615 11.89 0.00 41.28 2.78
5028 5280 6.065976 TCCTTCATCTGTACATGAAACCAT 57.934 37.500 11.89 0.00 41.28 3.55
5036 5288 9.726232 CATCTGTACATGAAACCATTTTCTATG 57.274 33.333 0.00 4.24 41.64 2.23
5085 5337 6.403333 TCTGACTATTGTTTGTACGATTGC 57.597 37.500 0.00 0.00 30.81 3.56
5137 5389 5.067413 CGTCGGTGCTGGGAATATACTATAT 59.933 44.000 0.00 0.00 0.00 0.86
5219 5471 5.610338 GCTTTTGCTGTGCGAAAATAAGAAC 60.610 40.000 6.45 0.00 40.76 3.01
5269 6969 1.066430 TCCTGAAACTGTCATACCGCC 60.066 52.381 0.00 0.00 35.07 6.13
5300 7003 7.035612 GGAGGATGGTGATGAACAAAATAAAC 58.964 38.462 0.00 0.00 0.00 2.01
5304 7007 4.979197 TGGTGATGAACAAAATAAACACGC 59.021 37.500 0.00 0.00 0.00 5.34
5308 7011 7.394872 GTGATGAACAAAATAAACACGCAAAA 58.605 30.769 0.00 0.00 0.00 2.44
5313 7016 6.576551 ACAAAATAAACACGCAAAAATCGT 57.423 29.167 0.00 0.00 41.28 3.73
5407 7118 2.203401 CTACGAGGACGGTCTCTGTAG 58.797 57.143 8.23 12.39 44.46 2.74
5435 7146 1.208358 CACTGATGTTGCGTGCCTG 59.792 57.895 0.00 0.00 0.00 4.85
5489 7200 0.463474 GGCCATCTCCTGTCAGCTTC 60.463 60.000 0.00 0.00 0.00 3.86
5495 7206 2.881734 TCTCCTGTCAGCTTCAGAGAA 58.118 47.619 14.92 2.72 35.20 2.87
5520 7231 1.610522 GAACCTGCTGTTGTCTGCATT 59.389 47.619 0.00 0.00 44.85 3.56
5526 7237 4.637534 CCTGCTGTTGTCTGCATTAGTAAT 59.362 41.667 0.00 0.00 44.85 1.89
5527 7238 5.448225 CCTGCTGTTGTCTGCATTAGTAATG 60.448 44.000 17.09 17.09 44.85 1.90
5528 7239 5.003160 TGCTGTTGTCTGCATTAGTAATGT 58.997 37.500 21.15 0.00 42.06 2.71
5529 7240 5.122239 TGCTGTTGTCTGCATTAGTAATGTC 59.878 40.000 21.15 14.71 42.06 3.06
5530 7241 5.352569 GCTGTTGTCTGCATTAGTAATGTCT 59.647 40.000 21.15 0.00 41.01 3.41
5531 7242 6.674037 GCTGTTGTCTGCATTAGTAATGTCTG 60.674 42.308 21.15 16.56 41.01 3.51
5532 7243 5.122239 TGTTGTCTGCATTAGTAATGTCTGC 59.878 40.000 21.15 11.12 41.01 4.26
5533 7244 4.831107 TGTCTGCATTAGTAATGTCTGCA 58.169 39.130 21.15 14.63 41.01 4.41
5534 7245 5.430886 TGTCTGCATTAGTAATGTCTGCAT 58.569 37.500 21.15 0.00 41.55 3.96
5535 7246 5.525012 TGTCTGCATTAGTAATGTCTGCATC 59.475 40.000 21.15 12.12 41.55 3.91
5536 7247 5.525012 GTCTGCATTAGTAATGTCTGCATCA 59.475 40.000 21.15 9.83 41.55 3.07
5537 7248 5.756833 TCTGCATTAGTAATGTCTGCATCAG 59.243 40.000 21.15 17.02 41.55 2.90
5538 7249 5.430886 TGCATTAGTAATGTCTGCATCAGT 58.569 37.500 21.15 0.00 41.01 3.41
5539 7250 6.581712 TGCATTAGTAATGTCTGCATCAGTA 58.418 36.000 21.15 0.00 41.01 2.74
5540 7251 7.047271 TGCATTAGTAATGTCTGCATCAGTAA 58.953 34.615 21.15 0.00 41.01 2.24
5541 7252 7.716560 TGCATTAGTAATGTCTGCATCAGTAAT 59.283 33.333 21.15 0.00 41.01 1.89
5581 7292 4.160329 AGTGGACCATGTTCTCTCTAACA 58.840 43.478 0.00 0.00 43.16 2.41
5603 7316 0.872021 GGTGATAGCGTTCTCTGCGG 60.872 60.000 0.00 0.00 37.44 5.69
5653 7366 2.912956 ACCAGCTAGAGGATTCCAAACA 59.087 45.455 5.29 0.00 0.00 2.83
5654 7367 3.525199 ACCAGCTAGAGGATTCCAAACAT 59.475 43.478 5.29 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.233848 GCAACCGTCGTTACCAGTTG 59.766 55.000 5.70 5.70 38.50 3.16
42 43 0.105408 AGCAACCGTCGTTACCAGTT 59.895 50.000 0.00 0.00 0.00 3.16
44 45 1.336148 TGTAGCAACCGTCGTTACCAG 60.336 52.381 0.00 0.00 0.00 4.00
48 49 1.068281 TGGTTGTAGCAACCGTCGTTA 59.932 47.619 21.46 4.88 43.15 3.18
55 56 3.508744 CCATGAATGGTTGTAGCAACC 57.491 47.619 20.54 20.54 43.05 3.77
95 96 2.196925 AAAATTGTCGGTGGCGGCA 61.197 52.632 7.97 7.97 0.00 5.69
115 116 2.031919 TGCCAAAGACGGTCGCAT 59.968 55.556 1.89 0.00 0.00 4.73
119 120 1.021968 AACAACTGCCAAAGACGGTC 58.978 50.000 0.00 0.00 0.00 4.79
130 131 0.388907 TCGGCGGTAGTAACAACTGC 60.389 55.000 7.21 0.00 46.42 4.40
133 134 0.109781 TCGTCGGCGGTAGTAACAAC 60.110 55.000 10.62 0.00 38.89 3.32
146 147 1.127951 GGTTGTAGCAATTGTCGTCGG 59.872 52.381 7.40 0.00 0.00 4.79
196 197 3.674753 CACAATGTTTCCCTGATTTTCGC 59.325 43.478 0.00 0.00 0.00 4.70
199 200 4.261994 CGGTCACAATGTTTCCCTGATTTT 60.262 41.667 0.00 0.00 0.00 1.82
223 224 3.609853 TGTCATAGCTTCCCATGAACAC 58.390 45.455 0.00 0.00 33.15 3.32
224 225 3.998913 TGTCATAGCTTCCCATGAACA 57.001 42.857 0.00 0.00 33.15 3.18
225 226 4.036027 CACATGTCATAGCTTCCCATGAAC 59.964 45.833 17.10 6.26 37.07 3.18
274 275 2.202295 TGCGGTGTTTGAAGCTTTTC 57.798 45.000 0.00 0.00 0.00 2.29
315 317 2.202756 GGCGCTCCTTGGTCGTAG 60.203 66.667 7.64 0.00 0.00 3.51
324 326 4.514577 CGATTGGTCGGCGCTCCT 62.515 66.667 7.64 3.24 44.00 3.69
366 368 3.299977 CTTGCTGCCCTGCTTGCA 61.300 61.111 0.00 0.00 37.09 4.08
411 414 2.438434 CCCTTCCCACCATGCGTC 60.438 66.667 0.00 0.00 0.00 5.19
412 415 4.047125 CCCCTTCCCACCATGCGT 62.047 66.667 0.00 0.00 0.00 5.24
416 419 3.023735 GAGCCCCCTTCCCACCAT 61.024 66.667 0.00 0.00 0.00 3.55
432 435 6.485313 TCTTCCTTTTTCTTAAATCAGCACGA 59.515 34.615 0.00 0.00 0.00 4.35
475 478 0.106967 GCTCATCTGTTCCCTTCCCC 60.107 60.000 0.00 0.00 0.00 4.81
476 479 0.462759 CGCTCATCTGTTCCCTTCCC 60.463 60.000 0.00 0.00 0.00 3.97
477 480 0.462759 CCGCTCATCTGTTCCCTTCC 60.463 60.000 0.00 0.00 0.00 3.46
478 481 0.250513 ACCGCTCATCTGTTCCCTTC 59.749 55.000 0.00 0.00 0.00 3.46
482 485 2.418976 GGTTTAACCGCTCATCTGTTCC 59.581 50.000 0.00 0.00 0.00 3.62
483 486 3.741805 GGTTTAACCGCTCATCTGTTC 57.258 47.619 0.00 0.00 0.00 3.18
497 508 8.138712 ACAAGATCTTTTAAATGTGCGGTTTAA 58.861 29.630 4.86 0.00 31.26 1.52
502 513 7.429340 GTGATACAAGATCTTTTAAATGTGCGG 59.571 37.037 4.86 0.00 0.00 5.69
509 520 5.640357 ACCGCGTGATACAAGATCTTTTAAA 59.360 36.000 4.86 0.00 0.00 1.52
511 522 4.565166 CACCGCGTGATACAAGATCTTTTA 59.435 41.667 4.86 4.30 35.23 1.52
519 731 0.992072 CACTCACCGCGTGATACAAG 59.008 55.000 4.92 0.00 41.94 3.16
532 744 2.359230 GCTGGTGGCCTCACTCAC 60.359 66.667 3.32 0.00 43.17 3.51
625 839 6.298441 TGATCCATGTGACTCTTGTATGAA 57.702 37.500 0.00 0.00 0.00 2.57
690 910 7.758613 TTGCAATGCACTTTATTATGTCATG 57.241 32.000 7.72 0.00 38.71 3.07
844 1066 6.183360 GGACCCTTTTATAGTAGTACGCTTGA 60.183 42.308 0.00 0.00 0.00 3.02
1413 1636 3.073735 AGGAGCTGCACGAGGAGG 61.074 66.667 8.35 0.00 33.18 4.30
1470 1693 2.673341 TCGTCACGGCAGAGCTCT 60.673 61.111 11.45 11.45 0.00 4.09
1482 1705 1.676635 CCAGTCGGGGTACTCGTCA 60.677 63.158 8.49 0.00 0.00 4.35
1632 1855 1.534476 TCACCAGTCCAAGGCGGTA 60.534 57.895 0.00 0.00 35.57 4.02
1667 1890 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1668 1891 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1669 1892 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1670 1893 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1671 1894 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1672 1895 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1673 1896 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1674 1897 5.804944 ATGAGAGAGAGAGAGAGAGAGAG 57.195 47.826 0.00 0.00 0.00 3.20
1675 1898 5.163269 CCAATGAGAGAGAGAGAGAGAGAGA 60.163 48.000 0.00 0.00 0.00 3.10
1676 1899 5.061853 CCAATGAGAGAGAGAGAGAGAGAG 58.938 50.000 0.00 0.00 0.00 3.20
1677 1900 4.686944 GCCAATGAGAGAGAGAGAGAGAGA 60.687 50.000 0.00 0.00 0.00 3.10
1678 1901 3.567164 GCCAATGAGAGAGAGAGAGAGAG 59.433 52.174 0.00 0.00 0.00 3.20
1679 1902 3.202818 AGCCAATGAGAGAGAGAGAGAGA 59.797 47.826 0.00 0.00 0.00 3.10
1680 1903 3.317149 CAGCCAATGAGAGAGAGAGAGAG 59.683 52.174 0.00 0.00 0.00 3.20
1681 1904 3.289836 CAGCCAATGAGAGAGAGAGAGA 58.710 50.000 0.00 0.00 0.00 3.10
1682 1905 3.025978 ACAGCCAATGAGAGAGAGAGAG 58.974 50.000 0.00 0.00 0.00 3.20
1683 1906 3.098774 ACAGCCAATGAGAGAGAGAGA 57.901 47.619 0.00 0.00 0.00 3.10
1684 1907 3.891422 AACAGCCAATGAGAGAGAGAG 57.109 47.619 0.00 0.00 0.00 3.20
1685 1908 4.774726 ACTAAACAGCCAATGAGAGAGAGA 59.225 41.667 0.00 0.00 0.00 3.10
1686 1909 5.083533 ACTAAACAGCCAATGAGAGAGAG 57.916 43.478 0.00 0.00 0.00 3.20
1687 1910 5.489792 AACTAAACAGCCAATGAGAGAGA 57.510 39.130 0.00 0.00 0.00 3.10
1688 1911 6.566197 AAAACTAAACAGCCAATGAGAGAG 57.434 37.500 0.00 0.00 0.00 3.20
1689 1912 6.959639 AAAAACTAAACAGCCAATGAGAGA 57.040 33.333 0.00 0.00 0.00 3.10
1780 2003 6.309737 CCTAATGCTGATTTCAGACAAAAAGC 59.690 38.462 11.70 0.00 46.59 3.51
1787 2010 6.705863 AAATCCCTAATGCTGATTTCAGAC 57.294 37.500 11.70 3.84 46.59 3.51
1788 2011 7.722949 AAAAATCCCTAATGCTGATTTCAGA 57.277 32.000 11.70 0.00 46.59 3.27
1813 2036 2.894763 TCCGGTTTCTCGTCTTTTGA 57.105 45.000 0.00 0.00 0.00 2.69
1821 2044 4.483476 AAATCACTTTTCCGGTTTCTCG 57.517 40.909 0.00 0.00 0.00 4.04
1861 2084 6.601613 ACACTAAAACCTCACTCAAATGTCAA 59.398 34.615 0.00 0.00 0.00 3.18
1871 2094 7.233757 ACTGAGATCTAACACTAAAACCTCACT 59.766 37.037 0.00 0.00 0.00 3.41
1932 2155 4.651778 CTGGGTCCTCAAACTAATGTGAA 58.348 43.478 0.00 0.00 0.00 3.18
2019 2242 8.530804 AAAAGATCAAGCATTCCTATAGCTTT 57.469 30.769 0.00 0.00 45.57 3.51
2077 2300 4.759693 AGTGAGCCAAATGTAAATCGTCAA 59.240 37.500 0.00 0.00 0.00 3.18
2081 2304 5.698832 TGAAAGTGAGCCAAATGTAAATCG 58.301 37.500 0.00 0.00 0.00 3.34
2085 2308 7.048629 TGAATTGAAAGTGAGCCAAATGTAA 57.951 32.000 0.00 0.00 0.00 2.41
2103 2326 3.797039 TCTCGTAGGGCAGAATGAATTG 58.203 45.455 0.00 0.00 39.69 2.32
2120 2343 2.101415 TGTCTGCAACCCTCATATCTCG 59.899 50.000 0.00 0.00 0.00 4.04
2232 2461 7.081349 CGCAATGGTTCAGAAAATTACAGTTA 58.919 34.615 0.00 0.00 0.00 2.24
2257 2486 6.625873 ACAAACTTCTCTGATCTTTTCACC 57.374 37.500 0.00 0.00 0.00 4.02
2357 2586 3.592059 TGATTACTACTTGGTTCGGTGC 58.408 45.455 0.00 0.00 0.00 5.01
2392 2621 1.485066 CGTCCCCAGTAAGTTAGCCAT 59.515 52.381 0.00 0.00 0.00 4.40
2567 2797 4.541085 TGTCAGCAGCATTAATTCATCG 57.459 40.909 0.00 0.00 0.00 3.84
2753 2984 5.419542 TCAAGGACCATTCGTAGAATTCTG 58.580 41.667 18.47 2.20 45.90 3.02
2822 3054 8.025445 ACAAATGAATAGTTCTGAATTGTGAGC 58.975 33.333 0.00 0.00 0.00 4.26
2892 3124 2.117156 CATCCAGGCCCAAAGCGAG 61.117 63.158 0.00 0.00 45.17 5.03
3170 3402 7.180229 TCTGTGAGATCCTTACCAATTAACAGA 59.820 37.037 0.00 0.00 37.42 3.41
3370 3602 5.952526 TTTTTGGGTCTATTTTCCTCGAC 57.047 39.130 0.00 0.00 0.00 4.20
3445 3677 4.256110 TCATGAAGGATATAGCCAATGCG 58.744 43.478 10.21 0.00 44.33 4.73
3517 3749 2.280186 CCGATACTGCCGGCTTCC 60.280 66.667 29.70 11.13 40.54 3.46
3640 3872 3.802685 GTCCAGCATACGTTCCTGTTATC 59.197 47.826 0.00 0.00 0.00 1.75
3709 3941 1.833630 CTTCTGGTGATCAGTGCCCTA 59.166 52.381 0.00 0.00 43.76 3.53
3715 3947 2.376808 CGAAGCTTCTGGTGATCAGT 57.623 50.000 23.50 0.00 43.76 3.41
3781 4013 5.181811 CCACTCATTTAGAACATCAAGTGCA 59.818 40.000 0.00 0.00 33.30 4.57
3871 4103 3.515602 AAAACTCCCATGACTTGCTCT 57.484 42.857 0.00 0.00 0.00 4.09
3892 4124 9.309516 CTTACTTGCATTTTACGACCTATTCTA 57.690 33.333 0.00 0.00 0.00 2.10
3923 4158 7.189079 AGAAGGATTAGAACTGAGGTTAAGG 57.811 40.000 0.00 0.00 35.58 2.69
3924 4159 7.125053 AGGAGAAGGATTAGAACTGAGGTTAAG 59.875 40.741 0.00 0.00 35.58 1.85
3925 4160 6.960542 AGGAGAAGGATTAGAACTGAGGTTAA 59.039 38.462 0.00 0.00 35.58 2.01
3926 4161 6.381420 CAGGAGAAGGATTAGAACTGAGGTTA 59.619 42.308 0.00 0.00 35.58 2.85
3927 4162 5.188751 CAGGAGAAGGATTAGAACTGAGGTT 59.811 44.000 0.00 0.00 38.52 3.50
3928 4163 4.714308 CAGGAGAAGGATTAGAACTGAGGT 59.286 45.833 0.00 0.00 0.00 3.85
3930 4165 5.930837 ACAGGAGAAGGATTAGAACTGAG 57.069 43.478 0.00 0.00 0.00 3.35
3931 4166 6.688073 AAACAGGAGAAGGATTAGAACTGA 57.312 37.500 0.00 0.00 0.00 3.41
3932 4167 7.751768 AAAAACAGGAGAAGGATTAGAACTG 57.248 36.000 0.00 0.00 0.00 3.16
3986 4222 0.745845 ACAGAACATCCGAGCATGCC 60.746 55.000 15.66 4.99 0.00 4.40
4008 4244 3.936453 CGTGTGGCTAGGTAAATGCTTAA 59.064 43.478 0.00 0.00 0.00 1.85
4009 4245 3.196039 TCGTGTGGCTAGGTAAATGCTTA 59.804 43.478 0.00 0.00 0.00 3.09
4030 4269 6.865834 ACATACATCCCTCCAGAGAATATC 57.134 41.667 0.00 0.00 0.00 1.63
4053 4292 6.380846 AGGCCTGCACATGAATAATCTTAAAA 59.619 34.615 3.11 0.00 0.00 1.52
4059 4298 2.954318 ACAGGCCTGCACATGAATAATC 59.046 45.455 33.06 0.00 0.00 1.75
4074 4313 7.090808 CAGAATTTTTAACCTAGAAACAGGCC 58.909 38.462 0.00 0.00 39.53 5.19
4076 4315 8.846211 TGACAGAATTTTTAACCTAGAAACAGG 58.154 33.333 0.00 0.00 41.87 4.00
4096 4335 3.797451 TTTGCAAGCAAATGTGACAGA 57.203 38.095 15.59 0.00 40.51 3.41
4133 4372 1.150536 TCCACAAGGGAACACTGGC 59.849 57.895 0.00 0.00 44.80 4.85
4147 4386 5.582665 CACAACTAGGCTCTAGAATTTCCAC 59.417 44.000 14.03 0.00 0.00 4.02
4156 4403 6.758886 CAGAAAATACCACAACTAGGCTCTAG 59.241 42.308 0.00 7.46 0.00 2.43
4162 4409 6.001460 TGAACCAGAAAATACCACAACTAGG 58.999 40.000 0.00 0.00 0.00 3.02
4167 4414 4.452825 TCGTGAACCAGAAAATACCACAA 58.547 39.130 0.00 0.00 0.00 3.33
4172 4419 8.649973 ATCTAGAATCGTGAACCAGAAAATAC 57.350 34.615 0.00 0.00 0.00 1.89
4179 4426 5.352569 AGCAAAATCTAGAATCGTGAACCAG 59.647 40.000 0.00 0.00 0.00 4.00
4205 4452 6.594788 AAACATGCACCTACATCTGAATTT 57.405 33.333 0.00 0.00 0.00 1.82
4213 4462 5.528043 TTTGTCAAAACATGCACCTACAT 57.472 34.783 0.00 0.00 34.73 2.29
4215 4464 4.209080 GCTTTTGTCAAAACATGCACCTAC 59.791 41.667 6.65 0.00 34.73 3.18
4225 4474 2.473816 GGCAGAGGCTTTTGTCAAAAC 58.526 47.619 6.65 4.74 40.87 2.43
4226 4475 1.412343 GGGCAGAGGCTTTTGTCAAAA 59.588 47.619 10.27 10.27 40.87 2.44
4229 4478 1.064003 TAGGGCAGAGGCTTTTGTCA 58.936 50.000 6.84 0.00 40.87 3.58
4230 4479 2.200373 TTAGGGCAGAGGCTTTTGTC 57.800 50.000 0.00 0.00 40.87 3.18
4239 4488 6.016777 CAGTGGCTTATAAATTTAGGGCAGAG 60.017 42.308 18.18 12.77 0.00 3.35
4242 4491 4.892934 CCAGTGGCTTATAAATTTAGGGCA 59.107 41.667 15.56 15.56 0.00 5.36
4243 4492 4.893524 ACCAGTGGCTTATAAATTTAGGGC 59.106 41.667 9.78 9.02 0.00 5.19
4245 4494 9.965824 CATAAACCAGTGGCTTATAAATTTAGG 57.034 33.333 15.83 6.28 0.00 2.69
4281 4530 8.763601 GGGGATAAGATAGTGCTCACTTATATT 58.236 37.037 7.92 6.31 42.54 1.28
4283 4532 7.246027 TGGGGATAAGATAGTGCTCACTTATA 58.754 38.462 7.92 0.00 42.54 0.98
4284 4533 6.084738 TGGGGATAAGATAGTGCTCACTTAT 58.915 40.000 7.92 0.00 42.54 1.73
4288 4537 3.643792 ACTGGGGATAAGATAGTGCTCAC 59.356 47.826 0.00 0.00 0.00 3.51
4295 4544 7.518188 ACAAATAACCACTGGGGATAAGATAG 58.482 38.462 1.10 0.00 41.15 2.08
4299 4548 6.850752 AAACAAATAACCACTGGGGATAAG 57.149 37.500 1.10 0.00 41.15 1.73
4302 4551 5.368230 ACAAAAACAAATAACCACTGGGGAT 59.632 36.000 1.10 0.00 41.15 3.85
4305 4554 6.041069 TCCTACAAAAACAAATAACCACTGGG 59.959 38.462 0.00 0.00 41.29 4.45
4360 4611 5.068329 TCACATTACAAGGTTGTGCAAATGA 59.932 36.000 17.68 8.33 42.31 2.57
4372 4623 5.003160 TGTTCAGGTGATCACATTACAAGG 58.997 41.667 26.47 7.50 0.00 3.61
4390 4641 4.023291 GGGGCCAGAGAAAATAATGTTCA 58.977 43.478 4.39 0.00 0.00 3.18
4391 4642 4.281657 AGGGGCCAGAGAAAATAATGTTC 58.718 43.478 4.39 0.00 0.00 3.18
4392 4643 4.337264 AGGGGCCAGAGAAAATAATGTT 57.663 40.909 4.39 0.00 0.00 2.71
4394 4645 5.449553 ACTTAGGGGCCAGAGAAAATAATG 58.550 41.667 4.39 0.00 0.00 1.90
4396 4647 5.530176 AACTTAGGGGCCAGAGAAAATAA 57.470 39.130 4.39 0.00 0.00 1.40
4403 4654 5.714806 TGAAATTTAAACTTAGGGGCCAGAG 59.285 40.000 4.39 1.75 0.00 3.35
4407 4658 5.731957 TGTGAAATTTAAACTTAGGGGCC 57.268 39.130 0.00 0.00 0.00 5.80
4427 4678 5.702670 AGAACGTCATCATCTTGAACAATGT 59.297 36.000 0.00 0.00 0.00 2.71
4546 4797 5.359194 ACAATGGACCTCGTATTTCAGAT 57.641 39.130 0.00 0.00 0.00 2.90
4600 4851 4.098349 AGGTACAATACGAATGAGGCGTAA 59.902 41.667 0.00 0.00 45.84 3.18
4639 4890 5.573219 ACAATCATCTGGTTGGAGATTTCA 58.427 37.500 7.99 0.00 29.72 2.69
4660 4911 4.503910 ACAATCTCTTGCGTATTGCTACA 58.496 39.130 0.00 0.00 46.63 2.74
4663 4914 3.599343 TGACAATCTCTTGCGTATTGCT 58.401 40.909 0.00 0.00 46.63 3.91
4666 4917 5.178061 TGTCATGACAATCTCTTGCGTATT 58.822 37.500 26.02 0.00 38.56 1.89
4678 4929 6.389830 TTTTGTTACAGCTGTCATGACAAT 57.610 33.333 27.63 17.16 41.33 2.71
4708 4959 7.565680 AGAGGTTATGGTTGTGTAATAAGAGG 58.434 38.462 0.00 0.00 0.00 3.69
4734 4985 6.052360 GGAAGAGAAGCCTTCTATAGGTTTG 58.948 44.000 7.02 0.00 46.32 2.93
4759 5010 3.103742 GGATCTCTGGGTCTCTGTTCTT 58.896 50.000 0.00 0.00 0.00 2.52
4772 5023 4.867047 GTCACTGTACATTGTGGATCTCTG 59.133 45.833 12.40 0.00 35.15 3.35
4773 5024 4.528206 TGTCACTGTACATTGTGGATCTCT 59.472 41.667 12.40 0.00 35.15 3.10
4775 5026 4.890158 TGTCACTGTACATTGTGGATCT 57.110 40.909 12.40 0.00 35.15 2.75
4784 5035 6.054941 TCAACAACTCAATGTCACTGTACAT 58.945 36.000 0.00 0.00 41.87 2.29
4811 5063 2.620251 TCAACAGTGGTTCAGGTCTG 57.380 50.000 0.00 0.00 34.21 3.51
4823 5075 4.278419 GGAGCTACAACCAAATTCAACAGT 59.722 41.667 0.00 0.00 0.00 3.55
4846 5098 2.763448 CTCCCCTTCTAGACAAGTCAGG 59.237 54.545 2.72 0.00 0.00 3.86
4847 5099 3.699038 CTCTCCCCTTCTAGACAAGTCAG 59.301 52.174 2.72 0.00 0.00 3.51
4853 5105 5.838955 TGTAAATCTCTCCCCTTCTAGACA 58.161 41.667 0.00 0.00 0.00 3.41
4857 5109 4.557705 CCCTGTAAATCTCTCCCCTTCTA 58.442 47.826 0.00 0.00 0.00 2.10
4858 5110 3.388913 CCCTGTAAATCTCTCCCCTTCT 58.611 50.000 0.00 0.00 0.00 2.85
4866 5118 4.851639 ATTCACTGCCCTGTAAATCTCT 57.148 40.909 0.00 0.00 0.00 3.10
4869 5121 3.763897 ACCAATTCACTGCCCTGTAAATC 59.236 43.478 0.00 0.00 0.00 2.17
5025 5277 3.270027 TCGCTGTCCACATAGAAAATGG 58.730 45.455 0.00 0.00 34.58 3.16
5028 5280 4.154015 CACATTCGCTGTCCACATAGAAAA 59.846 41.667 2.44 0.00 35.29 2.29
5036 5288 1.394917 GTCATCACATTCGCTGTCCAC 59.605 52.381 0.00 0.00 35.29 4.02
5085 5337 5.805486 CCGTACCAATAACATATCATCGAGG 59.195 44.000 0.00 0.00 0.00 4.63
5114 5366 4.803098 ATAGTATATTCCCAGCACCGAC 57.197 45.455 0.00 0.00 0.00 4.79
5188 5440 1.802136 CGCACAGCAAAAGCTTCCAAA 60.802 47.619 0.00 0.00 0.00 3.28
5219 5471 2.947652 CCACCAGGCATCAAAGTATCTG 59.052 50.000 0.00 0.00 0.00 2.90
5266 6966 0.250038 CACCATCCTCCACTATGGCG 60.250 60.000 0.00 0.00 45.53 5.69
5269 6969 4.141642 TGTTCATCACCATCCTCCACTATG 60.142 45.833 0.00 0.00 0.00 2.23
5283 6986 6.503616 TTGCGTGTTTATTTTGTTCATCAC 57.496 33.333 0.00 0.00 0.00 3.06
5300 7003 3.804688 TGTACATGACGATTTTTGCGTG 58.195 40.909 0.00 0.00 42.77 5.34
5304 7007 4.393062 AGAGGCTGTACATGACGATTTTTG 59.607 41.667 0.00 0.00 0.00 2.44
5308 7011 3.895232 AAGAGGCTGTACATGACGATT 57.105 42.857 0.00 0.00 0.00 3.34
5313 7016 3.411446 CCACAAAAGAGGCTGTACATGA 58.589 45.455 0.00 0.00 0.00 3.07
5354 7065 2.425592 CACCTGACCGTGCTGGAA 59.574 61.111 2.38 0.00 42.00 3.53
5355 7066 3.625897 CCACCTGACCGTGCTGGA 61.626 66.667 2.38 0.00 42.00 3.86
5356 7067 3.625897 TCCACCTGACCGTGCTGG 61.626 66.667 0.00 0.00 46.41 4.85
5357 7068 2.357517 GTCCACCTGACCGTGCTG 60.358 66.667 0.00 0.00 38.09 4.41
5358 7069 2.383245 CTTGTCCACCTGACCGTGCT 62.383 60.000 0.00 0.00 43.78 4.40
5376 7087 0.259065 TCCTCGTAGGGCACTGATCT 59.741 55.000 0.00 0.00 35.59 2.75
5407 7118 1.580845 AACATCAGTGAAGCGCAGGC 61.581 55.000 11.47 0.00 40.37 4.85
5489 7200 3.737850 ACAGCAGGTTCTCTTTTCTCTG 58.262 45.455 0.00 0.00 0.00 3.35
5495 7206 3.209410 CAGACAACAGCAGGTTCTCTTT 58.791 45.455 0.00 0.00 37.72 2.52
5520 7231 6.447162 CCGATTACTGATGCAGACATTACTA 58.553 40.000 0.82 0.00 36.35 1.82
5526 7237 1.831106 ACCCGATTACTGATGCAGACA 59.169 47.619 0.82 0.00 35.18 3.41
5527 7238 2.205074 CACCCGATTACTGATGCAGAC 58.795 52.381 0.82 0.00 35.18 3.51
5528 7239 1.831106 ACACCCGATTACTGATGCAGA 59.169 47.619 0.82 0.00 35.18 4.26
5529 7240 2.315925 ACACCCGATTACTGATGCAG 57.684 50.000 0.00 0.00 37.52 4.41
5530 7241 3.028130 TCTACACCCGATTACTGATGCA 58.972 45.455 0.00 0.00 0.00 3.96
5531 7242 3.728076 TCTACACCCGATTACTGATGC 57.272 47.619 0.00 0.00 0.00 3.91
5532 7243 5.043903 CAGTTCTACACCCGATTACTGATG 58.956 45.833 0.00 0.00 34.87 3.07
5533 7244 4.954202 TCAGTTCTACACCCGATTACTGAT 59.046 41.667 0.00 0.00 36.54 2.90
5534 7245 4.338012 TCAGTTCTACACCCGATTACTGA 58.662 43.478 0.00 0.00 38.44 3.41
5535 7246 4.713824 TCAGTTCTACACCCGATTACTG 57.286 45.455 0.00 0.00 34.38 2.74
5536 7247 5.014858 TCTTCAGTTCTACACCCGATTACT 58.985 41.667 0.00 0.00 0.00 2.24
5537 7248 5.105837 ACTCTTCAGTTCTACACCCGATTAC 60.106 44.000 0.00 0.00 0.00 1.89
5538 7249 5.014858 ACTCTTCAGTTCTACACCCGATTA 58.985 41.667 0.00 0.00 0.00 1.75
5539 7250 3.833070 ACTCTTCAGTTCTACACCCGATT 59.167 43.478 0.00 0.00 0.00 3.34
5540 7251 3.193691 CACTCTTCAGTTCTACACCCGAT 59.806 47.826 0.00 0.00 0.00 4.18
5541 7252 2.557056 CACTCTTCAGTTCTACACCCGA 59.443 50.000 0.00 0.00 0.00 5.14
5581 7292 1.134965 GCAGAGAACGCTATCACCAGT 60.135 52.381 0.00 0.00 0.00 4.00
5603 7316 0.823356 TGCCTCTCACTTTGGTTGGC 60.823 55.000 0.00 0.00 39.33 4.52
5653 7366 1.886542 GTCGAAGGGTGAGGCAAAAAT 59.113 47.619 0.00 0.00 0.00 1.82
5654 7367 1.314730 GTCGAAGGGTGAGGCAAAAA 58.685 50.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.