Multiple sequence alignment - TraesCS6A01G242200

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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 TraesCS6A01G242200 chr6A 100.000 4804 0 0 1 4804 453907950 453903147 0.000000e+00 8872
1 TraesCS6A01G242200 chr6A 80.195 308 43 11 1668 1961 410325027 410324724 1.050000e-51 215
2 TraesCS6A01G242200 chr6D 94.798 4556 139 37 28 4544 316100663 316096167 0.000000e+00 7011
3 TraesCS6A01G242200 chr6B 94.007 4555 189 36 28 4544 508608132 508612640 0.000000e+00 6822
4 TraesCS6A01G242200 chr2B 93.248 1333 72 5 1249 2567 199221956 199220628 0.000000e+00 1947
5 TraesCS6A01G242200 chr1B 92.718 1332 71 7 1249 2567 342128108 342126790 0.000000e+00 1899
6 TraesCS6A01G242200 chr5B 91.529 1334 90 6 1249 2567 356196768 356198093 0.000000e+00 1816
7 TraesCS6A01G242200 chrUn 97.287 258 7 0 4547 4804 210180193 210180450 5.710000e-119 438
8 TraesCS6A01G242200 chrUn 97.287 258 7 0 4547 4804 210614963 210615220 5.710000e-119 438
9 TraesCS6A01G242200 chrUn 97.287 258 7 0 4547 4804 368233366 368233109 5.710000e-119 438
10 TraesCS6A01G242200 chrUn 97.287 258 7 0 4547 4804 374588237 374588494 5.710000e-119 438
11 TraesCS6A01G242200 chr5A 97.287 258 7 0 4547 4804 29636803 29637060 5.710000e-119 438
12 TraesCS6A01G242200 chr1A 97.287 258 7 0 4547 4804 240674731 240674474 5.710000e-119 438
13 TraesCS6A01G242200 chr4A 96.935 261 7 1 4545 4804 595062908 595062648 2.050000e-118 436
14 TraesCS6A01G242200 chr4A 96.911 259 8 0 4546 4804 36747248 36746990 7.380000e-118 435
15 TraesCS6A01G242200 chr2A 96.911 259 8 0 4546 4804 377816568 377816826 7.380000e-118 435
16 TraesCS6A01G242200 chr7A 81.433 307 39 11 1668 1961 220118965 220118664 8.040000e-58 235
17 TraesCS6A01G242200 chr7A 80.656 305 43 9 1668 1961 121908298 121908597 6.260000e-54 222
18 TraesCS6A01G242200 chr3A 80.921 304 44 8 1668 1961 23263269 23263568 1.350000e-55 228


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 TraesCS6A01G242200 chr6A 453903147 453907950 4803 True 8872 8872 100.000 1 4804 1 chr6A.!!$R2 4803
1 TraesCS6A01G242200 chr6D 316096167 316100663 4496 True 7011 7011 94.798 28 4544 1 chr6D.!!$R1 4516
2 TraesCS6A01G242200 chr6B 508608132 508612640 4508 False 6822 6822 94.007 28 4544 1 chr6B.!!$F1 4516
3 TraesCS6A01G242200 chr2B 199220628 199221956 1328 True 1947 1947 93.248 1249 2567 1 chr2B.!!$R1 1318
4 TraesCS6A01G242200 chr1B 342126790 342128108 1318 True 1899 1899 92.718 1249 2567 1 chr1B.!!$R1 1318
5 TraesCS6A01G242200 chr5B 356196768 356198093 1325 False 1816 1816 91.529 1249 2567 1 chr5B.!!$F1 1318

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
793 811 0.116541 TCTTTCTTCCTCCCCTCCGT 59.883 55.0 0.00 0.0 0.00 4.69 F
1996 2039 0.730840 TGCAGATGCTGAAGAATGCG 59.269 50.0 6.35 0.0 42.66 4.73 F
3291 3338 0.040204 AGCTGGACCTTGGAAATGGG 59.960 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2442 0.297820 CGCTCGATCAACTTTACGCC 59.702 55.0 0.00 0.0 0.0 5.68 R
3719 3766 1.050204 TCCCAGCAAAAGCAGCAAAT 58.950 45.0 0.00 0.0 0.0 2.32 R
4679 4739 0.388520 GTTTCGATTTGGGCCACTGC 60.389 55.0 5.23 0.0 0.0 4.40 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
24 25 5.627135 TCCAGGACCAAGTTTTAAGTTAGG 58.373 41.667 0.00 0.00 0.00 2.69
25 26 4.765339 CCAGGACCAAGTTTTAAGTTAGGG 59.235 45.833 0.00 0.00 0.00 3.53
26 27 5.457052 CCAGGACCAAGTTTTAAGTTAGGGA 60.457 44.000 0.00 0.00 0.00 4.20
68 70 5.635417 AGGCAAAGATTAGCTCTTGTTTC 57.365 39.130 0.00 0.00 43.60 2.78
101 103 2.676342 CAATAACTGGGTCCTACGTTGC 59.324 50.000 0.00 0.00 0.00 4.17
106 108 0.981183 TGGGTCCTACGTTGCTGATT 59.019 50.000 0.00 0.00 0.00 2.57
122 124 4.562789 TGCTGATTTTCTCGTGTCTTATCG 59.437 41.667 0.00 0.00 0.00 2.92
123 125 4.549107 GCTGATTTTCTCGTGTCTTATCGC 60.549 45.833 0.00 0.00 0.00 4.58
160 162 4.859304 TTGAAAACCTCGTCAGCTACTA 57.141 40.909 0.00 0.00 0.00 1.82
221 223 5.631026 ACAATAAGAGCAACAAATACTGCG 58.369 37.500 0.00 0.00 43.51 5.18
270 272 9.113876 GAACGAAAGGGCAAATTATTATAATCG 57.886 33.333 0.00 0.00 0.00 3.34
514 525 1.530293 GCGATTCATCTCCAGTGCATC 59.470 52.381 0.00 0.00 0.00 3.91
515 526 2.141517 CGATTCATCTCCAGTGCATCC 58.858 52.381 0.00 0.00 0.00 3.51
525 539 1.613255 CCAGTGCATCCGGGTAAAAGT 60.613 52.381 0.00 0.00 0.00 2.66
659 675 3.414700 GTGCTGTTCACTCGCGGG 61.415 66.667 3.27 3.27 42.38 6.13
792 810 0.827368 CTCTTTCTTCCTCCCCTCCG 59.173 60.000 0.00 0.00 0.00 4.63
793 811 0.116541 TCTTTCTTCCTCCCCTCCGT 59.883 55.000 0.00 0.00 0.00 4.69
837 855 2.560151 CGAATCGCTGCTCGTCGTC 61.560 63.158 0.00 0.00 39.67 4.20
843 861 1.626388 GCTGCTCGTCGTCGATTTC 59.374 57.895 5.00 0.00 45.21 2.17
848 866 1.194896 CTCGTCGTCGATTTCCGCTC 61.195 60.000 5.00 0.00 45.21 5.03
979 998 1.154197 GGTTTCTTCCCCGTTTCTCG 58.846 55.000 0.00 0.00 39.52 4.04
981 1000 0.947180 TTTCTTCCCCGTTTCTCGCG 60.947 55.000 0.00 0.00 38.35 5.87
993 1012 2.765250 TTCTCGCGTCAGGTTCAGGC 62.765 60.000 5.77 0.00 0.00 4.85
1063 1082 4.065789 CACCTTCCTCTGTAAGTTGTTCC 58.934 47.826 0.00 0.00 33.76 3.62
1073 1092 7.229506 CCTCTGTAAGTTGTTCCTGAGATTTTT 59.770 37.037 0.00 0.00 33.76 1.94
1243 1263 2.760159 ATTTCCATTCCACGGCGCG 61.760 57.895 6.90 0.00 0.00 6.86
1265 1285 2.033194 CGGACTCTGGTTTTCCGCC 61.033 63.158 0.00 0.00 45.35 6.13
1288 1308 1.291877 CGTTCCGGTGAAGCTCTTGG 61.292 60.000 0.00 0.00 0.00 3.61
1320 1340 5.163814 CGAGGTTCAGGTTTGATCAGAATTC 60.164 44.000 0.00 0.00 32.27 2.17
1325 1345 4.388773 TCAGGTTTGATCAGAATTCGTTCG 59.611 41.667 0.00 0.00 0.00 3.95
1421 1453 6.312918 GGATTCTTGCACGATAACAAGTAAGA 59.687 38.462 0.00 0.00 43.05 2.10
1663 1706 6.737720 ATCACTGGTTTCTATGATCTAGCA 57.262 37.500 0.00 0.00 0.00 3.49
1669 1712 4.991056 GGTTTCTATGATCTAGCATCGCAA 59.009 41.667 0.00 0.00 0.00 4.85
1693 1736 9.256477 CAATGTCATCAGAATAAAATGATTGGG 57.744 33.333 0.00 0.00 33.91 4.12
1719 1762 5.505780 TCCACCAACTATATTCCACCTTTG 58.494 41.667 0.00 0.00 0.00 2.77
1746 1789 4.982241 ATTCCTCAGTTCAACAAGGAGA 57.018 40.909 10.62 4.81 39.04 3.71
1808 1851 1.377725 ATTGCCCAGTGGAAGCTCG 60.378 57.895 11.95 0.00 0.00 5.03
1996 2039 0.730840 TGCAGATGCTGAAGAATGCG 59.269 50.000 6.35 0.00 42.66 4.73
2014 2057 1.666189 GCGAGCATTGAAGAGGTAACC 59.334 52.381 0.00 0.00 37.17 2.85
2255 2300 5.558273 CGTTTTTACACTGAGGTAGTTGCTG 60.558 44.000 0.00 0.00 37.60 4.41
2274 2319 7.278868 AGTTGCTGTAGTCTTGCAAATACTATC 59.721 37.037 19.02 14.38 46.22 2.08
2302 2347 9.814899 CTCTCTTAGATTCTTAAATGCAGAAGA 57.185 33.333 4.77 4.77 33.74 2.87
2397 2442 6.454583 GCACCATCAAATCATTGTTGAAATCG 60.455 38.462 2.13 0.00 38.44 3.34
2434 2479 4.113354 GAGCGTGAGAAAAGGTACCTATG 58.887 47.826 16.67 4.83 0.00 2.23
2487 2532 4.431131 ATGCCCAGAAGCCCACGG 62.431 66.667 0.00 0.00 0.00 4.94
2856 2901 1.260561 CAACGTGAACTGGTGCTGTAC 59.739 52.381 0.00 0.00 0.00 2.90
2871 2916 4.036262 GTGCTGTACATTGACCTTTTCACA 59.964 41.667 0.00 0.00 32.26 3.58
2874 2919 5.221048 GCTGTACATTGACCTTTTCACACTT 60.221 40.000 0.00 0.00 32.26 3.16
3173 3218 4.824479 ACCATTTTTCCCTTGCCATAAG 57.176 40.909 0.00 0.00 0.00 1.73
3196 3241 6.970484 AGTTACTTTGTGGATGTTTTAGCAG 58.030 36.000 0.00 0.00 0.00 4.24
3291 3338 0.040204 AGCTGGACCTTGGAAATGGG 59.960 55.000 0.00 0.00 0.00 4.00
3447 3494 6.534079 GCAGTTAATATGGTCACTTTAGACGT 59.466 38.462 0.00 0.00 39.42 4.34
3613 3660 8.683615 CATGAAATGCTGATTGCCTACATATAT 58.316 33.333 0.00 0.00 37.62 0.86
3614 3661 8.047413 TGAAATGCTGATTGCCTACATATATG 57.953 34.615 11.29 11.29 42.00 1.78
3719 3766 2.807967 CGATGCTGGTTTCTCTTTGACA 59.192 45.455 0.00 0.00 0.00 3.58
3761 3808 0.909610 TAGGTCTCCTGGTTGGGCTG 60.910 60.000 0.00 0.00 34.61 4.85
3788 3835 1.009429 AGCCTCATCTTCTCTTCCCCT 59.991 52.381 0.00 0.00 0.00 4.79
3798 3845 0.395862 CTCTTCCCCTCCAGCGACTA 60.396 60.000 0.00 0.00 0.00 2.59
3840 3887 4.342665 AGCCTAGAGTAACAGTATTCAGCC 59.657 45.833 0.00 0.00 0.00 4.85
4096 4144 4.790765 ATGTAAAGGCTGAAAAGGAAGC 57.209 40.909 0.00 0.00 38.76 3.86
4107 4155 5.105997 GCTGAAAAGGAAGCATGTGTTATCT 60.106 40.000 0.00 0.00 39.31 1.98
4228 4287 8.213812 CACGTGTTCAAAAACATATTTTCCATC 58.786 33.333 7.58 0.00 46.58 3.51
4307 4366 8.947055 AGAAAACCAAAATATGAATATGCCAC 57.053 30.769 0.00 0.00 0.00 5.01
4377 4436 1.134995 TGAACTAGCTGACGCATGGAG 60.135 52.381 0.00 0.00 39.10 3.86
4574 4634 6.415798 TTTTAAACAAGGCAAAAGACTTGC 57.584 33.333 10.80 0.78 46.03 4.01
4582 4642 3.110447 GCAAAAGACTTGCCATTTCCA 57.890 42.857 0.00 0.00 39.38 3.53
4583 4643 3.667360 GCAAAAGACTTGCCATTTCCAT 58.333 40.909 0.00 0.00 39.38 3.41
4584 4644 4.067192 GCAAAAGACTTGCCATTTCCATT 58.933 39.130 0.00 0.00 39.38 3.16
4585 4645 4.516321 GCAAAAGACTTGCCATTTCCATTT 59.484 37.500 0.00 0.00 39.38 2.32
4586 4646 5.700373 GCAAAAGACTTGCCATTTCCATTTA 59.300 36.000 0.00 0.00 39.38 1.40
4587 4647 6.204495 GCAAAAGACTTGCCATTTCCATTTAA 59.796 34.615 0.00 0.00 39.38 1.52
4588 4648 7.094677 GCAAAAGACTTGCCATTTCCATTTAAT 60.095 33.333 0.00 0.00 39.38 1.40
4589 4649 9.434420 CAAAAGACTTGCCATTTCCATTTAATA 57.566 29.630 0.00 0.00 0.00 0.98
4591 4651 9.657419 AAAGACTTGCCATTTCCATTTAATAAG 57.343 29.630 0.00 0.00 0.00 1.73
4592 4652 8.593945 AGACTTGCCATTTCCATTTAATAAGA 57.406 30.769 0.00 0.00 0.00 2.10
4593 4653 9.034800 AGACTTGCCATTTCCATTTAATAAGAA 57.965 29.630 0.00 0.00 0.00 2.52
4594 4654 9.305925 GACTTGCCATTTCCATTTAATAAGAAG 57.694 33.333 0.00 0.00 0.00 2.85
4595 4655 9.034800 ACTTGCCATTTCCATTTAATAAGAAGA 57.965 29.630 0.00 0.00 0.00 2.87
4596 4656 9.525409 CTTGCCATTTCCATTTAATAAGAAGAG 57.475 33.333 0.00 0.00 0.00 2.85
4597 4657 8.010733 TGCCATTTCCATTTAATAAGAAGAGG 57.989 34.615 0.00 0.00 0.00 3.69
4598 4658 7.619302 TGCCATTTCCATTTAATAAGAAGAGGT 59.381 33.333 9.32 0.00 0.00 3.85
4599 4659 8.478066 GCCATTTCCATTTAATAAGAAGAGGTT 58.522 33.333 9.32 0.00 0.00 3.50
4610 4670 7.971183 AATAAGAAGAGGTTTCAGAACAGAC 57.029 36.000 0.00 0.00 37.51 3.51
4611 4671 5.359194 AAGAAGAGGTTTCAGAACAGACA 57.641 39.130 0.00 0.00 37.51 3.41
4612 4672 5.559148 AGAAGAGGTTTCAGAACAGACAT 57.441 39.130 0.00 0.00 37.51 3.06
4613 4673 5.546526 AGAAGAGGTTTCAGAACAGACATC 58.453 41.667 0.00 0.00 37.51 3.06
4614 4674 3.919216 AGAGGTTTCAGAACAGACATCG 58.081 45.455 0.00 0.00 37.51 3.84
4615 4675 2.413453 GAGGTTTCAGAACAGACATCGC 59.587 50.000 0.00 0.00 37.51 4.58
4616 4676 1.464997 GGTTTCAGAACAGACATCGCC 59.535 52.381 0.00 0.00 37.51 5.54
4617 4677 2.143122 GTTTCAGAACAGACATCGCCA 58.857 47.619 0.00 0.00 35.79 5.69
4618 4678 2.542020 TTCAGAACAGACATCGCCAA 57.458 45.000 0.00 0.00 0.00 4.52
4619 4679 2.084610 TCAGAACAGACATCGCCAAG 57.915 50.000 0.00 0.00 0.00 3.61
4620 4680 0.445436 CAGAACAGACATCGCCAAGC 59.555 55.000 0.00 0.00 0.00 4.01
4632 4692 3.669344 CCAAGCGGCGGAAAAGCA 61.669 61.111 9.78 0.00 39.27 3.91
4633 4693 2.334653 CAAGCGGCGGAAAAGCAA 59.665 55.556 9.78 0.00 39.27 3.91
4634 4694 1.299773 CAAGCGGCGGAAAAGCAAA 60.300 52.632 9.78 0.00 39.27 3.68
4635 4695 0.873743 CAAGCGGCGGAAAAGCAAAA 60.874 50.000 9.78 0.00 39.27 2.44
4636 4696 0.874175 AAGCGGCGGAAAAGCAAAAC 60.874 50.000 9.78 0.00 39.27 2.43
4637 4697 1.590259 GCGGCGGAAAAGCAAAACA 60.590 52.632 9.78 0.00 39.27 2.83
4638 4698 1.148759 GCGGCGGAAAAGCAAAACAA 61.149 50.000 9.78 0.00 39.27 2.83
4639 4699 1.496934 CGGCGGAAAAGCAAAACAAT 58.503 45.000 0.00 0.00 39.27 2.71
4640 4700 1.864082 CGGCGGAAAAGCAAAACAATT 59.136 42.857 0.00 0.00 39.27 2.32
4641 4701 3.053455 CGGCGGAAAAGCAAAACAATTA 58.947 40.909 0.00 0.00 39.27 1.40
4642 4702 3.121160 CGGCGGAAAAGCAAAACAATTAC 60.121 43.478 0.00 0.00 39.27 1.89
4643 4703 4.055360 GGCGGAAAAGCAAAACAATTACT 58.945 39.130 0.00 0.00 39.27 2.24
4644 4704 4.149922 GGCGGAAAAGCAAAACAATTACTC 59.850 41.667 0.00 0.00 39.27 2.59
4645 4705 4.982295 GCGGAAAAGCAAAACAATTACTCT 59.018 37.500 0.00 0.00 37.05 3.24
4646 4706 5.117135 GCGGAAAAGCAAAACAATTACTCTC 59.883 40.000 0.00 0.00 37.05 3.20
4647 4707 5.339611 CGGAAAAGCAAAACAATTACTCTCG 59.660 40.000 0.00 0.00 0.00 4.04
4648 4708 5.117135 GGAAAAGCAAAACAATTACTCTCGC 59.883 40.000 0.00 0.00 0.00 5.03
4649 4709 4.829064 AAGCAAAACAATTACTCTCGCA 57.171 36.364 0.00 0.00 0.00 5.10
4650 4710 4.410492 AGCAAAACAATTACTCTCGCAG 57.590 40.909 0.00 0.00 0.00 5.18
4651 4711 3.815401 AGCAAAACAATTACTCTCGCAGT 59.185 39.130 0.00 0.00 39.41 4.40
4652 4712 4.994852 AGCAAAACAATTACTCTCGCAGTA 59.005 37.500 0.00 0.00 36.43 2.74
4653 4713 5.643777 AGCAAAACAATTACTCTCGCAGTAT 59.356 36.000 0.00 0.00 37.44 2.12
4654 4714 6.149474 AGCAAAACAATTACTCTCGCAGTATT 59.851 34.615 0.00 0.00 37.44 1.89
4655 4715 7.333423 AGCAAAACAATTACTCTCGCAGTATTA 59.667 33.333 0.00 0.00 37.44 0.98
4656 4716 7.425595 GCAAAACAATTACTCTCGCAGTATTAC 59.574 37.037 0.00 0.00 37.44 1.89
4657 4717 8.440059 CAAAACAATTACTCTCGCAGTATTACA 58.560 33.333 0.00 0.00 37.44 2.41
4658 4718 8.718102 AAACAATTACTCTCGCAGTATTACAT 57.282 30.769 0.00 0.00 37.44 2.29
4659 4719 8.718102 AACAATTACTCTCGCAGTATTACATT 57.282 30.769 0.00 0.00 37.44 2.71
4660 4720 9.811995 AACAATTACTCTCGCAGTATTACATTA 57.188 29.630 0.00 0.00 37.44 1.90
4661 4721 9.245962 ACAATTACTCTCGCAGTATTACATTAC 57.754 33.333 0.00 0.00 37.44 1.89
4662 4722 8.417928 CAATTACTCTCGCAGTATTACATTACG 58.582 37.037 0.00 0.00 37.44 3.18
4663 4723 4.288531 ACTCTCGCAGTATTACATTACGC 58.711 43.478 0.00 0.00 31.37 4.42
4664 4724 4.201980 ACTCTCGCAGTATTACATTACGCA 60.202 41.667 0.00 0.00 31.37 5.24
4665 4725 4.674475 TCTCGCAGTATTACATTACGCAA 58.326 39.130 0.00 0.00 0.00 4.85
4666 4726 5.103687 TCTCGCAGTATTACATTACGCAAA 58.896 37.500 0.00 0.00 0.00 3.68
4667 4727 5.751509 TCTCGCAGTATTACATTACGCAAAT 59.248 36.000 0.00 0.00 0.00 2.32
4678 4738 2.793946 CGCAAATGCTTAGCGCCT 59.206 55.556 2.29 0.00 45.14 5.52
4679 4739 1.584483 CGCAAATGCTTAGCGCCTG 60.584 57.895 2.29 0.00 45.14 4.85
4680 4740 1.875364 GCAAATGCTTAGCGCCTGC 60.875 57.895 2.29 6.88 38.76 4.85
4681 4741 1.507630 CAAATGCTTAGCGCCTGCA 59.492 52.632 19.03 19.03 46.23 4.41
4682 4742 0.524816 CAAATGCTTAGCGCCTGCAG 60.525 55.000 20.74 6.78 46.23 4.41
4683 4743 0.962356 AAATGCTTAGCGCCTGCAGT 60.962 50.000 20.74 16.91 46.23 4.40
4684 4744 1.651240 AATGCTTAGCGCCTGCAGTG 61.651 55.000 20.74 5.87 46.23 3.66
4685 4745 3.503363 GCTTAGCGCCTGCAGTGG 61.503 66.667 13.81 4.85 46.23 4.00
4692 4752 2.999063 GCCTGCAGTGGCCCAAAT 60.999 61.111 13.81 0.00 46.82 2.32
4693 4753 3.010413 GCCTGCAGTGGCCCAAATC 62.010 63.158 13.81 0.00 46.82 2.17
4694 4754 2.703798 CCTGCAGTGGCCCAAATCG 61.704 63.158 13.81 0.00 40.13 3.34
4695 4755 1.675310 CTGCAGTGGCCCAAATCGA 60.675 57.895 5.25 0.00 40.13 3.59
4696 4756 1.228398 TGCAGTGGCCCAAATCGAA 60.228 52.632 0.00 0.00 40.13 3.71
4697 4757 0.825425 TGCAGTGGCCCAAATCGAAA 60.825 50.000 0.00 0.00 40.13 3.46
4698 4758 0.388520 GCAGTGGCCCAAATCGAAAC 60.389 55.000 0.00 0.00 0.00 2.78
4699 4759 1.247567 CAGTGGCCCAAATCGAAACT 58.752 50.000 0.00 0.00 0.00 2.66
4700 4760 1.613437 CAGTGGCCCAAATCGAAACTT 59.387 47.619 0.00 0.00 0.00 2.66
4701 4761 1.886542 AGTGGCCCAAATCGAAACTTC 59.113 47.619 0.00 0.00 0.00 3.01
4702 4762 1.611491 GTGGCCCAAATCGAAACTTCA 59.389 47.619 0.00 0.00 0.00 3.02
4703 4763 2.231235 GTGGCCCAAATCGAAACTTCAT 59.769 45.455 0.00 0.00 0.00 2.57
4704 4764 2.491693 TGGCCCAAATCGAAACTTCATC 59.508 45.455 0.00 0.00 0.00 2.92
4705 4765 2.755103 GGCCCAAATCGAAACTTCATCT 59.245 45.455 0.00 0.00 0.00 2.90
4706 4766 3.193479 GGCCCAAATCGAAACTTCATCTT 59.807 43.478 0.00 0.00 0.00 2.40
4707 4767 4.321974 GGCCCAAATCGAAACTTCATCTTT 60.322 41.667 0.00 0.00 0.00 2.52
4708 4768 4.622740 GCCCAAATCGAAACTTCATCTTTG 59.377 41.667 0.00 0.00 0.00 2.77
4709 4769 5.564651 GCCCAAATCGAAACTTCATCTTTGA 60.565 40.000 4.39 0.00 0.00 2.69
4710 4770 6.624423 CCCAAATCGAAACTTCATCTTTGAT 58.376 36.000 4.39 0.00 0.00 2.57
4711 4771 6.529125 CCCAAATCGAAACTTCATCTTTGATG 59.471 38.462 4.39 1.45 34.15 3.07
4712 4772 6.034256 CCAAATCGAAACTTCATCTTTGATGC 59.966 38.462 4.39 0.00 31.80 3.91
4713 4773 4.326413 TCGAAACTTCATCTTTGATGCG 57.674 40.909 2.93 0.95 31.80 4.73
4714 4774 3.745975 TCGAAACTTCATCTTTGATGCGT 59.254 39.130 2.93 0.91 31.80 5.24
4715 4775 4.084507 CGAAACTTCATCTTTGATGCGTC 58.915 43.478 0.00 0.00 31.80 5.19
4716 4776 4.377328 CGAAACTTCATCTTTGATGCGTCA 60.377 41.667 3.97 3.97 31.80 4.35
4717 4777 4.410492 AACTTCATCTTTGATGCGTCAC 57.590 40.909 8.48 0.00 33.11 3.67
4718 4778 3.402110 ACTTCATCTTTGATGCGTCACA 58.598 40.909 8.48 0.45 33.11 3.58
4719 4779 4.005650 ACTTCATCTTTGATGCGTCACAT 58.994 39.130 8.48 0.00 43.54 3.21
4720 4780 4.142752 ACTTCATCTTTGATGCGTCACATG 60.143 41.667 8.48 11.12 39.84 3.21
4721 4781 3.598299 TCATCTTTGATGCGTCACATGA 58.402 40.909 8.48 13.17 39.84 3.07
4722 4782 3.371898 TCATCTTTGATGCGTCACATGAC 59.628 43.478 8.48 1.70 39.84 3.06
4723 4783 2.765122 TCTTTGATGCGTCACATGACA 58.235 42.857 8.48 0.00 44.99 3.58
4724 4784 3.137533 TCTTTGATGCGTCACATGACAA 58.862 40.909 8.48 0.00 44.99 3.18
4725 4785 3.752747 TCTTTGATGCGTCACATGACAAT 59.247 39.130 8.48 5.07 44.99 2.71
4726 4786 3.745332 TTGATGCGTCACATGACAATC 57.255 42.857 8.48 13.21 44.99 2.67
4727 4787 1.660104 TGATGCGTCACATGACAATCG 59.340 47.619 3.97 0.00 44.99 3.34
4728 4788 0.374758 ATGCGTCACATGACAATCGC 59.625 50.000 12.32 9.71 44.99 4.58
4729 4789 1.060937 GCGTCACATGACAATCGCC 59.939 57.895 12.32 0.00 44.99 5.54
4730 4790 1.634757 GCGTCACATGACAATCGCCA 61.635 55.000 12.32 0.00 44.99 5.69
4731 4791 0.095245 CGTCACATGACAATCGCCAC 59.905 55.000 12.32 0.00 44.99 5.01
4732 4792 0.447801 GTCACATGACAATCGCCACC 59.552 55.000 7.15 0.00 44.18 4.61
4733 4793 1.018752 TCACATGACAATCGCCACCG 61.019 55.000 0.00 0.00 0.00 4.94
4734 4794 1.745115 ACATGACAATCGCCACCGG 60.745 57.895 0.00 0.00 34.56 5.28
4735 4795 2.824041 ATGACAATCGCCACCGGC 60.824 61.111 0.00 0.00 46.75 6.13
4752 4812 3.049674 CGCCGCTTTGCTCCTGAA 61.050 61.111 0.00 0.00 0.00 3.02
4753 4813 2.873288 GCCGCTTTGCTCCTGAAG 59.127 61.111 0.00 0.00 0.00 3.02
4754 4814 1.672356 GCCGCTTTGCTCCTGAAGA 60.672 57.895 0.00 0.00 0.00 2.87
4755 4815 1.916697 GCCGCTTTGCTCCTGAAGAC 61.917 60.000 0.00 0.00 0.00 3.01
4756 4816 0.603707 CCGCTTTGCTCCTGAAGACA 60.604 55.000 0.00 0.00 0.00 3.41
4757 4817 0.514691 CGCTTTGCTCCTGAAGACAC 59.485 55.000 0.00 0.00 0.00 3.67
4758 4818 0.514691 GCTTTGCTCCTGAAGACACG 59.485 55.000 0.00 0.00 0.00 4.49
4759 4819 1.873903 GCTTTGCTCCTGAAGACACGA 60.874 52.381 0.00 0.00 0.00 4.35
4760 4820 2.064762 CTTTGCTCCTGAAGACACGAG 58.935 52.381 0.00 0.00 34.13 4.18
4761 4821 4.177229 GCTCCTGAAGACACGAGC 57.823 61.111 0.00 0.00 43.53 5.03
4762 4822 1.290324 GCTCCTGAAGACACGAGCA 59.710 57.895 13.24 0.00 46.51 4.26
4763 4823 0.108424 GCTCCTGAAGACACGAGCAT 60.108 55.000 13.24 0.00 46.51 3.79
4764 4824 1.674221 GCTCCTGAAGACACGAGCATT 60.674 52.381 13.24 0.00 46.51 3.56
4765 4825 2.266554 CTCCTGAAGACACGAGCATTC 58.733 52.381 0.00 0.00 0.00 2.67
4766 4826 1.066858 TCCTGAAGACACGAGCATTCC 60.067 52.381 0.00 0.00 0.00 3.01
4767 4827 1.066573 CCTGAAGACACGAGCATTCCT 60.067 52.381 0.00 0.00 0.00 3.36
4768 4828 2.613977 CCTGAAGACACGAGCATTCCTT 60.614 50.000 0.00 0.00 0.00 3.36
4769 4829 3.070018 CTGAAGACACGAGCATTCCTTT 58.930 45.455 0.00 0.00 0.00 3.11
4770 4830 3.067106 TGAAGACACGAGCATTCCTTTC 58.933 45.455 0.00 0.00 0.00 2.62
4771 4831 2.839486 AGACACGAGCATTCCTTTCA 57.161 45.000 0.00 0.00 0.00 2.69
4772 4832 3.340814 AGACACGAGCATTCCTTTCAT 57.659 42.857 0.00 0.00 0.00 2.57
4773 4833 3.679389 AGACACGAGCATTCCTTTCATT 58.321 40.909 0.00 0.00 0.00 2.57
4774 4834 3.686726 AGACACGAGCATTCCTTTCATTC 59.313 43.478 0.00 0.00 0.00 2.67
4775 4835 2.749621 ACACGAGCATTCCTTTCATTCC 59.250 45.455 0.00 0.00 0.00 3.01
4776 4836 2.749076 CACGAGCATTCCTTTCATTCCA 59.251 45.455 0.00 0.00 0.00 3.53
4777 4837 3.379372 CACGAGCATTCCTTTCATTCCAT 59.621 43.478 0.00 0.00 0.00 3.41
4778 4838 4.576053 CACGAGCATTCCTTTCATTCCATA 59.424 41.667 0.00 0.00 0.00 2.74
4779 4839 5.240183 CACGAGCATTCCTTTCATTCCATAT 59.760 40.000 0.00 0.00 0.00 1.78
4780 4840 5.471456 ACGAGCATTCCTTTCATTCCATATC 59.529 40.000 0.00 0.00 0.00 1.63
4781 4841 5.704515 CGAGCATTCCTTTCATTCCATATCT 59.295 40.000 0.00 0.00 0.00 1.98
4782 4842 6.128336 CGAGCATTCCTTTCATTCCATATCTC 60.128 42.308 0.00 0.00 0.00 2.75
4783 4843 6.008960 AGCATTCCTTTCATTCCATATCTCC 58.991 40.000 0.00 0.00 0.00 3.71
4784 4844 5.184671 GCATTCCTTTCATTCCATATCTCCC 59.815 44.000 0.00 0.00 0.00 4.30
4785 4845 5.992564 TTCCTTTCATTCCATATCTCCCA 57.007 39.130 0.00 0.00 0.00 4.37
4786 4846 6.535161 TTCCTTTCATTCCATATCTCCCAT 57.465 37.500 0.00 0.00 0.00 4.00
4787 4847 6.131972 TCCTTTCATTCCATATCTCCCATC 57.868 41.667 0.00 0.00 0.00 3.51
4788 4848 5.014544 TCCTTTCATTCCATATCTCCCATCC 59.985 44.000 0.00 0.00 0.00 3.51
4789 4849 4.934797 TTCATTCCATATCTCCCATCCC 57.065 45.455 0.00 0.00 0.00 3.85
4790 4850 3.885669 TCATTCCATATCTCCCATCCCA 58.114 45.455 0.00 0.00 0.00 4.37
4791 4851 3.588842 TCATTCCATATCTCCCATCCCAC 59.411 47.826 0.00 0.00 0.00 4.61
4792 4852 2.813338 TCCATATCTCCCATCCCACA 57.187 50.000 0.00 0.00 0.00 4.17
4793 4853 3.073411 TCCATATCTCCCATCCCACAA 57.927 47.619 0.00 0.00 0.00 3.33
4794 4854 2.981784 TCCATATCTCCCATCCCACAAG 59.018 50.000 0.00 0.00 0.00 3.16
4795 4855 2.981784 CCATATCTCCCATCCCACAAGA 59.018 50.000 0.00 0.00 0.00 3.02
4796 4856 3.395607 CCATATCTCCCATCCCACAAGAA 59.604 47.826 0.00 0.00 0.00 2.52
4797 4857 4.506271 CCATATCTCCCATCCCACAAGAAG 60.506 50.000 0.00 0.00 0.00 2.85
4798 4858 2.044793 TCTCCCATCCCACAAGAAGT 57.955 50.000 0.00 0.00 0.00 3.01
4799 4859 3.199442 TCTCCCATCCCACAAGAAGTA 57.801 47.619 0.00 0.00 0.00 2.24
4800 4860 3.526899 TCTCCCATCCCACAAGAAGTAA 58.473 45.455 0.00 0.00 0.00 2.24
4801 4861 3.263425 TCTCCCATCCCACAAGAAGTAAC 59.737 47.826 0.00 0.00 0.00 2.50
4802 4862 2.983192 TCCCATCCCACAAGAAGTAACA 59.017 45.455 0.00 0.00 0.00 2.41
4803 4863 3.009033 TCCCATCCCACAAGAAGTAACAG 59.991 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.246163 CCTAACTTAAAACTTGGTCCTGGAT 58.754 40.000 0.00 0.00 0.00 3.41
1 2 5.457052 CCCTAACTTAAAACTTGGTCCTGGA 60.457 44.000 0.00 0.00 0.00 3.86
2 3 4.765339 CCCTAACTTAAAACTTGGTCCTGG 59.235 45.833 0.00 0.00 0.00 4.45
3 4 5.627135 TCCCTAACTTAAAACTTGGTCCTG 58.373 41.667 0.00 0.00 0.00 3.86
4 5 5.917545 TCCCTAACTTAAAACTTGGTCCT 57.082 39.130 0.00 0.00 0.00 3.85
5 6 6.548622 ACTTTCCCTAACTTAAAACTTGGTCC 59.451 38.462 0.00 0.00 0.00 4.46
6 7 7.578310 ACTTTCCCTAACTTAAAACTTGGTC 57.422 36.000 0.00 0.00 0.00 4.02
7 8 7.966339 AACTTTCCCTAACTTAAAACTTGGT 57.034 32.000 0.00 0.00 0.00 3.67
8 9 9.961265 CTAAACTTTCCCTAACTTAAAACTTGG 57.039 33.333 0.00 0.00 0.00 3.61
9 10 9.459640 GCTAAACTTTCCCTAACTTAAAACTTG 57.540 33.333 0.00 0.00 0.00 3.16
10 11 9.417561 AGCTAAACTTTCCCTAACTTAAAACTT 57.582 29.630 0.00 0.00 0.00 2.66
11 12 8.991783 AGCTAAACTTTCCCTAACTTAAAACT 57.008 30.769 0.00 0.00 0.00 2.66
12 13 9.064706 AGAGCTAAACTTTCCCTAACTTAAAAC 57.935 33.333 0.00 0.00 0.00 2.43
13 14 9.636789 AAGAGCTAAACTTTCCCTAACTTAAAA 57.363 29.630 0.00 0.00 0.00 1.52
16 17 9.939802 CTTAAGAGCTAAACTTTCCCTAACTTA 57.060 33.333 0.00 0.00 0.00 2.24
17 18 7.390996 GCTTAAGAGCTAAACTTTCCCTAACTT 59.609 37.037 6.67 0.00 45.65 2.66
18 19 6.879993 GCTTAAGAGCTAAACTTTCCCTAACT 59.120 38.462 6.67 0.00 45.65 2.24
19 20 7.074507 GCTTAAGAGCTAAACTTTCCCTAAC 57.925 40.000 6.67 0.00 45.65 2.34
48 49 8.970691 TTAATGAAACAAGAGCTAATCTTTGC 57.029 30.769 0.00 0.00 46.49 3.68
68 70 5.723295 ACCCAGTTATTGCTTGCTTTAATG 58.277 37.500 0.00 0.00 0.00 1.90
101 103 4.800993 AGCGATAAGACACGAGAAAATCAG 59.199 41.667 0.00 0.00 0.00 2.90
106 108 4.093514 CGTTAGCGATAAGACACGAGAAA 58.906 43.478 0.00 0.00 41.33 2.52
122 124 3.398954 TCAATCATTTTCGCCGTTAGC 57.601 42.857 0.00 0.00 38.52 3.09
123 125 5.060446 GGTTTTCAATCATTTTCGCCGTTAG 59.940 40.000 0.00 0.00 0.00 2.34
160 162 4.526650 CCCTACCCAACAAAAATTGCTAGT 59.473 41.667 0.00 0.00 0.00 2.57
221 223 4.743644 CGGTACTCTTCCCAACGAATAATC 59.256 45.833 0.00 0.00 0.00 1.75
233 235 2.603953 CCTTTCGTTCGGTACTCTTCC 58.396 52.381 0.00 0.00 0.00 3.46
270 272 4.563786 GGGATCGGAAGGATATTCTTGTCC 60.564 50.000 0.00 3.65 34.82 4.02
336 339 7.875327 AAACGTAAAAGGCCATAGTGATTAT 57.125 32.000 5.01 0.00 0.00 1.28
399 404 5.573669 AGAAAAATTCGAGCGTAAGAGAGAC 59.426 40.000 0.00 0.00 34.78 3.36
465 476 8.087750 GCTCTCTCAAGCAAATCTATATACTGT 58.912 37.037 0.00 0.00 42.05 3.55
466 477 8.464770 GCTCTCTCAAGCAAATCTATATACTG 57.535 38.462 0.00 0.00 42.05 2.74
481 492 2.614779 TGAATCGCTTGCTCTCTCAAG 58.385 47.619 0.00 0.00 44.63 3.02
496 507 2.141517 CGGATGCACTGGAGATGAATC 58.858 52.381 0.00 0.00 32.00 2.52
514 525 2.563297 GGGAGCAACTTTTACCCGG 58.437 57.895 0.00 0.00 0.00 5.73
525 539 5.713792 TTTTTATCATGTTTCGGGAGCAA 57.286 34.783 0.00 0.00 0.00 3.91
622 638 7.147408 ACAGCACTCCTCCTTTATCTAATCATT 60.147 37.037 0.00 0.00 0.00 2.57
671 687 1.335051 GGCAGTTTGCGTTTTCCTCTC 60.335 52.381 0.00 0.00 46.21 3.20
672 688 0.668535 GGCAGTTTGCGTTTTCCTCT 59.331 50.000 0.00 0.00 46.21 3.69
792 810 2.569373 AATGGGGAGGGAGGGAGGAC 62.569 65.000 0.00 0.00 0.00 3.85
793 811 1.848835 AAATGGGGAGGGAGGGAGGA 61.849 60.000 0.00 0.00 0.00 3.71
870 888 0.974383 TCGTCCCAACCTTTCTCTCC 59.026 55.000 0.00 0.00 0.00 3.71
873 891 1.555533 AGGATCGTCCCAACCTTTCTC 59.444 52.381 1.06 0.00 37.19 2.87
957 976 0.956633 GAAACGGGGAAGAAACCACC 59.043 55.000 0.00 0.00 0.00 4.61
1011 1030 1.008309 GTAGACCGAGATCAGCGCC 60.008 63.158 2.29 0.00 0.00 6.53
1063 1082 4.906423 CAGAATGCGGAGAAAAATCTCAG 58.094 43.478 8.01 5.09 38.44 3.35
1115 1135 4.202010 ACAAGAATTCAGTTCAACCAACGG 60.202 41.667 8.44 0.00 40.32 4.44
1243 1263 0.321387 GGAAAACCAGAGTCCGTCCC 60.321 60.000 0.00 0.00 0.00 4.46
1273 1293 0.321671 TTCTCCAAGAGCTTCACCGG 59.678 55.000 0.00 0.00 0.00 5.28
1288 1308 3.878160 AACCTGAACCTCGATCTTCTC 57.122 47.619 0.00 0.00 0.00 2.87
1320 1340 3.604392 GTCTTGACCTGAAAAACGAACG 58.396 45.455 0.00 0.00 0.00 3.95
1325 1345 2.606272 ACGTCGTCTTGACCTGAAAAAC 59.394 45.455 0.00 0.00 45.23 2.43
1638 1676 6.988580 TGCTAGATCATAGAAACCAGTGATTG 59.011 38.462 0.00 0.00 31.86 2.67
1663 1706 7.933396 TCATTTTATTCTGATGACATTGCGAT 58.067 30.769 0.00 0.00 0.00 4.58
1669 1712 8.771521 TCCCAATCATTTTATTCTGATGACAT 57.228 30.769 0.00 0.00 33.08 3.06
1693 1736 5.941788 AGGTGGAATATAGTTGGTGGAATC 58.058 41.667 0.00 0.00 0.00 2.52
1719 1762 7.103641 TCCTTGTTGAACTGAGGAATACATAC 58.896 38.462 15.33 0.00 35.45 2.39
1746 1789 6.962182 TCATTTCCTCAATCACCTTATCAGT 58.038 36.000 0.00 0.00 0.00 3.41
1808 1851 2.492484 AGATGTAACACCAGAGTCGTCC 59.508 50.000 0.00 0.00 0.00 4.79
1936 1979 7.429636 TGTGAAATACAGTTAGCCTTTGTAC 57.570 36.000 0.00 0.00 33.42 2.90
1996 2039 2.280628 CGGGTTACCTCTTCAATGCTC 58.719 52.381 0.00 0.00 33.28 4.26
2014 2057 5.567138 AAATTTCTGTTTGGATAGAGCGG 57.433 39.130 0.00 0.00 0.00 5.52
2238 2283 3.231818 ACTACAGCAACTACCTCAGTGT 58.768 45.455 0.00 0.00 37.63 3.55
2255 2300 8.846211 AGAGAGAGATAGTATTTGCAAGACTAC 58.154 37.037 19.79 13.71 0.00 2.73
2274 2319 9.814899 TTCTGCATTTAAGAATCTAAGAGAGAG 57.185 33.333 0.00 0.00 37.70 3.20
2351 2396 5.048083 GTGCTTGAACATTGTCCTATTTCCA 60.048 40.000 0.00 0.00 0.00 3.53
2397 2442 0.297820 CGCTCGATCAACTTTACGCC 59.702 55.000 0.00 0.00 0.00 5.68
2434 2479 2.252072 TATGACACCGGCCTGGAAGC 62.252 60.000 18.74 8.43 42.00 3.86
2618 2663 8.869109 ACACTTTAGAATCATGATTTTTGGGAA 58.131 29.630 21.57 5.26 0.00 3.97
2619 2664 8.306038 CACACTTTAGAATCATGATTTTTGGGA 58.694 33.333 21.57 6.27 0.00 4.37
2620 2665 8.090214 ACACACTTTAGAATCATGATTTTTGGG 58.910 33.333 21.57 14.07 0.00 4.12
2856 2901 5.835257 ACATGAAGTGTGAAAAGGTCAATG 58.165 37.500 0.00 0.00 40.28 2.82
2871 2916 5.221263 ACAGTGAGTAGAAACGACATGAAGT 60.221 40.000 0.00 0.00 0.00 3.01
2874 2919 4.848562 ACAGTGAGTAGAAACGACATGA 57.151 40.909 0.00 0.00 0.00 3.07
3039 3084 8.025243 ACATATTCTTTTGCATTTGCTCAAAG 57.975 30.769 15.81 15.81 42.66 2.77
3173 3218 6.966021 TCTGCTAAAACATCCACAAAGTAAC 58.034 36.000 0.00 0.00 0.00 2.50
3291 3338 2.423577 ACGCCATAGTGACTTGGTTTC 58.576 47.619 12.93 0.35 35.34 2.78
3396 3443 5.205565 GCAGAAAAAGAACGAAACAGTAGG 58.794 41.667 0.00 0.00 0.00 3.18
3613 3660 7.103641 GGATAAATCCAATATAAGCGAGGACA 58.896 38.462 4.04 0.00 46.38 4.02
3614 3661 7.541122 GGATAAATCCAATATAAGCGAGGAC 57.459 40.000 4.04 0.00 46.38 3.85
3719 3766 1.050204 TCCCAGCAAAAGCAGCAAAT 58.950 45.000 0.00 0.00 0.00 2.32
3788 3835 1.681793 GGCATCTAAGTAGTCGCTGGA 59.318 52.381 0.00 0.00 0.00 3.86
3798 3845 3.950395 GGCTTCAATCTTGGCATCTAAGT 59.050 43.478 0.00 0.00 0.00 2.24
3840 3887 1.180029 CCCAAGCATCTGGAAACTGG 58.820 55.000 1.29 0.00 38.96 4.00
4096 4144 6.495181 AGGGTCACTAGGATAGATAACACATG 59.505 42.308 0.00 0.00 42.77 3.21
4107 4155 6.945636 TTTTGAAAGAGGGTCACTAGGATA 57.054 37.500 0.00 0.00 0.00 2.59
4137 4185 8.677300 TGATCAAAGTCTAGGAACAAAATATGC 58.323 33.333 0.00 0.00 0.00 3.14
4298 4357 5.319453 CCCAAGTCAGATATGTGGCATATT 58.681 41.667 7.27 0.00 0.00 1.28
4299 4358 4.263639 CCCCAAGTCAGATATGTGGCATAT 60.264 45.833 7.27 1.41 0.00 1.78
4300 4359 3.072915 CCCCAAGTCAGATATGTGGCATA 59.927 47.826 7.27 0.00 0.00 3.14
4301 4360 2.158564 CCCCAAGTCAGATATGTGGCAT 60.159 50.000 7.27 0.00 0.00 4.40
4302 4361 1.212688 CCCCAAGTCAGATATGTGGCA 59.787 52.381 7.27 0.00 0.00 4.92
4303 4362 1.477558 CCCCCAAGTCAGATATGTGGC 60.478 57.143 0.00 0.00 0.00 5.01
4304 4363 2.105477 CTCCCCCAAGTCAGATATGTGG 59.895 54.545 0.00 0.00 0.00 4.17
4307 4366 4.656112 AGTTACTCCCCCAAGTCAGATATG 59.344 45.833 0.00 0.00 0.00 1.78
4310 4369 3.207044 AGTTACTCCCCCAAGTCAGAT 57.793 47.619 0.00 0.00 0.00 2.90
4316 4375 6.548251 TGTTTTCTTAAAGTTACTCCCCCAAG 59.452 38.462 0.00 0.00 0.00 3.61
4349 4408 6.144078 TGCGTCAGCTAGTTCATTAGATTA 57.856 37.500 0.00 0.00 45.42 1.75
4377 4436 6.874288 ATGAGGCTCTAAACATAAGAATGC 57.126 37.500 16.72 0.00 36.50 3.56
4550 4610 6.836953 GCAAGTCTTTTGCCTTGTTTAAAAA 58.163 32.000 0.54 0.00 40.13 1.94
4551 4611 6.415798 GCAAGTCTTTTGCCTTGTTTAAAA 57.584 33.333 0.54 0.00 40.13 1.52
4562 4622 3.110447 TGGAAATGGCAAGTCTTTTGC 57.890 42.857 3.39 3.39 44.22 3.68
4563 4623 7.727331 TTAAATGGAAATGGCAAGTCTTTTG 57.273 32.000 0.00 0.00 0.00 2.44
4565 4625 9.657419 CTTATTAAATGGAAATGGCAAGTCTTT 57.343 29.630 0.00 0.00 0.00 2.52
4566 4626 9.034800 TCTTATTAAATGGAAATGGCAAGTCTT 57.965 29.630 0.00 0.00 0.00 3.01
4567 4627 8.593945 TCTTATTAAATGGAAATGGCAAGTCT 57.406 30.769 0.00 0.00 0.00 3.24
4568 4628 9.305925 CTTCTTATTAAATGGAAATGGCAAGTC 57.694 33.333 0.00 0.00 0.00 3.01
4569 4629 9.034800 TCTTCTTATTAAATGGAAATGGCAAGT 57.965 29.630 0.00 0.00 0.00 3.16
4570 4630 9.525409 CTCTTCTTATTAAATGGAAATGGCAAG 57.475 33.333 0.00 0.00 0.00 4.01
4571 4631 8.477256 CCTCTTCTTATTAAATGGAAATGGCAA 58.523 33.333 0.00 0.00 0.00 4.52
4572 4632 7.619302 ACCTCTTCTTATTAAATGGAAATGGCA 59.381 33.333 0.00 0.00 0.00 4.92
4573 4633 8.011844 ACCTCTTCTTATTAAATGGAAATGGC 57.988 34.615 0.00 0.00 0.00 4.40
4584 4644 9.490379 GTCTGTTCTGAAACCTCTTCTTATTAA 57.510 33.333 0.00 0.00 34.28 1.40
4585 4645 8.647796 TGTCTGTTCTGAAACCTCTTCTTATTA 58.352 33.333 0.00 0.00 34.28 0.98
4586 4646 7.509546 TGTCTGTTCTGAAACCTCTTCTTATT 58.490 34.615 0.00 0.00 34.28 1.40
4587 4647 7.067496 TGTCTGTTCTGAAACCTCTTCTTAT 57.933 36.000 0.00 0.00 34.28 1.73
4588 4648 6.479972 TGTCTGTTCTGAAACCTCTTCTTA 57.520 37.500 0.00 0.00 34.28 2.10
4589 4649 5.359194 TGTCTGTTCTGAAACCTCTTCTT 57.641 39.130 0.00 0.00 34.28 2.52
4590 4650 5.546526 GATGTCTGTTCTGAAACCTCTTCT 58.453 41.667 0.00 0.00 34.28 2.85
4591 4651 4.387256 CGATGTCTGTTCTGAAACCTCTTC 59.613 45.833 0.00 0.00 34.28 2.87
4592 4652 4.310769 CGATGTCTGTTCTGAAACCTCTT 58.689 43.478 0.00 0.00 34.28 2.85
4593 4653 3.862642 GCGATGTCTGTTCTGAAACCTCT 60.863 47.826 0.00 0.00 34.28 3.69
4594 4654 2.413453 GCGATGTCTGTTCTGAAACCTC 59.587 50.000 0.00 0.00 34.28 3.85
4595 4655 2.417719 GCGATGTCTGTTCTGAAACCT 58.582 47.619 0.00 0.00 34.28 3.50
4596 4656 1.464997 GGCGATGTCTGTTCTGAAACC 59.535 52.381 0.00 0.00 34.28 3.27
4597 4657 2.143122 TGGCGATGTCTGTTCTGAAAC 58.857 47.619 0.00 0.00 35.85 2.78
4598 4658 2.542020 TGGCGATGTCTGTTCTGAAA 57.458 45.000 0.00 0.00 0.00 2.69
4599 4659 2.416747 CTTGGCGATGTCTGTTCTGAA 58.583 47.619 0.00 0.00 0.00 3.02
4600 4660 1.941209 GCTTGGCGATGTCTGTTCTGA 60.941 52.381 0.00 0.00 0.00 3.27
4601 4661 0.445436 GCTTGGCGATGTCTGTTCTG 59.555 55.000 0.00 0.00 0.00 3.02
4602 4662 2.846371 GCTTGGCGATGTCTGTTCT 58.154 52.632 0.00 0.00 0.00 3.01
4615 4675 2.691674 TTTGCTTTTCCGCCGCTTGG 62.692 55.000 0.00 0.00 0.00 3.61
4616 4676 0.873743 TTTTGCTTTTCCGCCGCTTG 60.874 50.000 0.00 0.00 0.00 4.01
4617 4677 0.874175 GTTTTGCTTTTCCGCCGCTT 60.874 50.000 0.00 0.00 0.00 4.68
4618 4678 1.299850 GTTTTGCTTTTCCGCCGCT 60.300 52.632 0.00 0.00 0.00 5.52
4619 4679 1.148759 TTGTTTTGCTTTTCCGCCGC 61.149 50.000 0.00 0.00 0.00 6.53
4620 4680 1.496934 ATTGTTTTGCTTTTCCGCCG 58.503 45.000 0.00 0.00 0.00 6.46
4621 4681 4.055360 AGTAATTGTTTTGCTTTTCCGCC 58.945 39.130 0.00 0.00 0.00 6.13
4622 4682 4.982295 AGAGTAATTGTTTTGCTTTTCCGC 59.018 37.500 0.00 0.00 0.00 5.54
4623 4683 5.339611 CGAGAGTAATTGTTTTGCTTTTCCG 59.660 40.000 0.00 0.00 0.00 4.30
4624 4684 5.117135 GCGAGAGTAATTGTTTTGCTTTTCC 59.883 40.000 0.00 0.00 0.00 3.13
4625 4685 5.685511 TGCGAGAGTAATTGTTTTGCTTTTC 59.314 36.000 0.00 0.00 0.00 2.29
4626 4686 5.587289 TGCGAGAGTAATTGTTTTGCTTTT 58.413 33.333 0.00 0.00 0.00 2.27
4627 4687 5.181690 TGCGAGAGTAATTGTTTTGCTTT 57.818 34.783 0.00 0.00 0.00 3.51
4628 4688 4.275936 ACTGCGAGAGTAATTGTTTTGCTT 59.724 37.500 0.00 0.00 30.86 3.91
4629 4689 3.815401 ACTGCGAGAGTAATTGTTTTGCT 59.185 39.130 0.00 0.00 30.86 3.91
4630 4690 4.147219 ACTGCGAGAGTAATTGTTTTGC 57.853 40.909 0.00 0.00 30.86 3.68
4631 4691 8.440059 TGTAATACTGCGAGAGTAATTGTTTTG 58.560 33.333 0.00 0.00 40.67 2.44
4632 4692 8.542497 TGTAATACTGCGAGAGTAATTGTTTT 57.458 30.769 0.00 0.00 40.67 2.43
4633 4693 8.718102 ATGTAATACTGCGAGAGTAATTGTTT 57.282 30.769 0.00 0.00 40.67 2.83
4634 4694 8.718102 AATGTAATACTGCGAGAGTAATTGTT 57.282 30.769 0.00 0.00 40.67 2.83
4635 4695 9.245962 GTAATGTAATACTGCGAGAGTAATTGT 57.754 33.333 0.00 0.00 40.67 2.71
4636 4696 8.417928 CGTAATGTAATACTGCGAGAGTAATTG 58.582 37.037 0.00 0.00 40.67 2.32
4637 4697 7.114529 GCGTAATGTAATACTGCGAGAGTAATT 59.885 37.037 0.00 0.00 40.67 1.40
4638 4698 6.581542 GCGTAATGTAATACTGCGAGAGTAAT 59.418 38.462 0.00 0.00 40.67 1.89
4639 4699 5.911280 GCGTAATGTAATACTGCGAGAGTAA 59.089 40.000 0.00 0.00 40.67 2.24
4640 4700 5.007921 TGCGTAATGTAATACTGCGAGAGTA 59.992 40.000 0.00 0.00 41.57 2.59
4641 4701 4.201980 TGCGTAATGTAATACTGCGAGAGT 60.202 41.667 0.00 0.00 38.88 3.24
4642 4702 4.287720 TGCGTAATGTAATACTGCGAGAG 58.712 43.478 0.00 0.00 32.10 3.20
4643 4703 4.295857 TGCGTAATGTAATACTGCGAGA 57.704 40.909 0.00 0.00 32.10 4.04
4644 4704 5.383984 TTTGCGTAATGTAATACTGCGAG 57.616 39.130 0.00 0.00 32.10 5.03
4645 4705 5.733299 CATTTGCGTAATGTAATACTGCGA 58.267 37.500 3.81 0.00 39.05 5.10
4646 4706 4.375698 GCATTTGCGTAATGTAATACTGCG 59.624 41.667 11.56 0.00 44.52 5.18
4647 4707 5.789774 GCATTTGCGTAATGTAATACTGC 57.210 39.130 11.56 0.00 44.52 4.40
4669 4729 3.503363 GCCACTGCAGGCGCTAAG 61.503 66.667 19.93 2.31 46.12 2.18
4676 4736 2.703798 CGATTTGGGCCACTGCAGG 61.704 63.158 19.93 2.55 40.13 4.85
4677 4737 1.243342 TTCGATTTGGGCCACTGCAG 61.243 55.000 13.48 13.48 40.13 4.41
4678 4738 0.825425 TTTCGATTTGGGCCACTGCA 60.825 50.000 5.23 0.00 40.13 4.41
4679 4739 0.388520 GTTTCGATTTGGGCCACTGC 60.389 55.000 5.23 0.00 0.00 4.40
4680 4740 1.247567 AGTTTCGATTTGGGCCACTG 58.752 50.000 5.23 0.00 0.00 3.66
4681 4741 1.886542 GAAGTTTCGATTTGGGCCACT 59.113 47.619 5.23 0.00 0.00 4.00
4682 4742 1.611491 TGAAGTTTCGATTTGGGCCAC 59.389 47.619 5.23 0.00 0.00 5.01
4683 4743 1.988293 TGAAGTTTCGATTTGGGCCA 58.012 45.000 0.00 0.00 0.00 5.36
4684 4744 2.755103 AGATGAAGTTTCGATTTGGGCC 59.245 45.455 0.00 0.00 0.00 5.80
4685 4745 4.440839 AAGATGAAGTTTCGATTTGGGC 57.559 40.909 0.00 0.00 0.00 5.36
4686 4746 6.012658 TCAAAGATGAAGTTTCGATTTGGG 57.987 37.500 12.33 0.00 32.28 4.12
4687 4747 6.034256 GCATCAAAGATGAAGTTTCGATTTGG 59.966 38.462 10.95 4.09 39.49 3.28
4688 4748 6.237123 CGCATCAAAGATGAAGTTTCGATTTG 60.237 38.462 10.95 8.65 39.49 2.32
4689 4749 5.796935 CGCATCAAAGATGAAGTTTCGATTT 59.203 36.000 10.95 0.00 39.49 2.17
4690 4750 5.106555 ACGCATCAAAGATGAAGTTTCGATT 60.107 36.000 10.95 0.00 39.49 3.34
4691 4751 4.393062 ACGCATCAAAGATGAAGTTTCGAT 59.607 37.500 10.95 0.00 39.49 3.59
4692 4752 3.745975 ACGCATCAAAGATGAAGTTTCGA 59.254 39.130 10.95 0.00 39.49 3.71
4693 4753 4.070581 ACGCATCAAAGATGAAGTTTCG 57.929 40.909 10.95 6.14 39.49 3.46
4694 4754 4.848299 GTGACGCATCAAAGATGAAGTTTC 59.152 41.667 10.95 4.37 39.49 2.78
4695 4755 4.275689 TGTGACGCATCAAAGATGAAGTTT 59.724 37.500 10.95 0.00 39.49 2.66
4696 4756 3.814842 TGTGACGCATCAAAGATGAAGTT 59.185 39.130 10.95 0.00 39.49 2.66
4697 4757 3.402110 TGTGACGCATCAAAGATGAAGT 58.598 40.909 10.95 9.17 39.49 3.01
4698 4758 4.093850 TCATGTGACGCATCAAAGATGAAG 59.906 41.667 10.95 6.33 39.49 3.02
4699 4759 4.002316 TCATGTGACGCATCAAAGATGAA 58.998 39.130 10.95 0.00 39.49 2.57
4700 4760 3.371898 GTCATGTGACGCATCAAAGATGA 59.628 43.478 10.95 0.00 36.31 2.92
4701 4761 3.677601 GTCATGTGACGCATCAAAGATG 58.322 45.455 0.00 2.71 36.31 2.90
4713 4773 0.447801 GGTGGCGATTGTCATGTGAC 59.552 55.000 6.21 6.21 44.97 3.67
4714 4774 1.018752 CGGTGGCGATTGTCATGTGA 61.019 55.000 0.00 0.00 28.63 3.58
4715 4775 1.425031 CGGTGGCGATTGTCATGTG 59.575 57.895 0.00 0.00 28.63 3.21
4716 4776 1.745115 CCGGTGGCGATTGTCATGT 60.745 57.895 0.00 0.00 28.63 3.21
4717 4777 3.101209 CCGGTGGCGATTGTCATG 58.899 61.111 0.00 0.00 28.63 3.07
4718 4778 2.824041 GCCGGTGGCGATTGTCAT 60.824 61.111 1.90 0.00 39.62 3.06
4735 4795 3.031964 CTTCAGGAGCAAAGCGGCG 62.032 63.158 0.51 0.51 39.27 6.46
4736 4796 1.672356 TCTTCAGGAGCAAAGCGGC 60.672 57.895 0.00 0.00 0.00 6.53
4737 4797 0.603707 TGTCTTCAGGAGCAAAGCGG 60.604 55.000 0.00 0.00 0.00 5.52
4738 4798 0.514691 GTGTCTTCAGGAGCAAAGCG 59.485 55.000 0.00 0.00 0.00 4.68
4739 4799 0.514691 CGTGTCTTCAGGAGCAAAGC 59.485 55.000 0.00 0.00 0.00 3.51
4740 4800 2.064762 CTCGTGTCTTCAGGAGCAAAG 58.935 52.381 5.28 0.00 45.25 2.77
4741 4801 2.154854 CTCGTGTCTTCAGGAGCAAA 57.845 50.000 5.28 0.00 45.25 3.68
4742 4802 3.894257 CTCGTGTCTTCAGGAGCAA 57.106 52.632 5.28 0.00 45.25 3.91
4746 4806 1.066858 GGAATGCTCGTGTCTTCAGGA 60.067 52.381 0.00 0.00 37.04 3.86
4747 4807 1.066573 AGGAATGCTCGTGTCTTCAGG 60.067 52.381 0.00 0.00 0.00 3.86
4748 4808 2.376808 AGGAATGCTCGTGTCTTCAG 57.623 50.000 0.00 0.00 0.00 3.02
4749 4809 2.839486 AAGGAATGCTCGTGTCTTCA 57.161 45.000 0.00 0.00 0.00 3.02
4750 4810 3.067106 TGAAAGGAATGCTCGTGTCTTC 58.933 45.455 0.00 0.00 0.00 2.87
4751 4811 3.126001 TGAAAGGAATGCTCGTGTCTT 57.874 42.857 0.00 0.00 0.00 3.01
4752 4812 2.839486 TGAAAGGAATGCTCGTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
4753 4813 3.181506 GGAATGAAAGGAATGCTCGTGTC 60.182 47.826 0.00 0.00 0.00 3.67
4754 4814 2.749621 GGAATGAAAGGAATGCTCGTGT 59.250 45.455 0.00 0.00 0.00 4.49
4755 4815 2.749076 TGGAATGAAAGGAATGCTCGTG 59.251 45.455 0.00 0.00 0.00 4.35
4756 4816 3.071874 TGGAATGAAAGGAATGCTCGT 57.928 42.857 0.00 0.00 0.00 4.18
4757 4817 5.704515 AGATATGGAATGAAAGGAATGCTCG 59.295 40.000 0.00 0.00 0.00 5.03
4758 4818 6.150809 GGAGATATGGAATGAAAGGAATGCTC 59.849 42.308 0.00 0.00 0.00 4.26
4759 4819 6.008960 GGAGATATGGAATGAAAGGAATGCT 58.991 40.000 0.00 0.00 0.00 3.79
4760 4820 5.184671 GGGAGATATGGAATGAAAGGAATGC 59.815 44.000 0.00 0.00 0.00 3.56
4761 4821 6.309357 TGGGAGATATGGAATGAAAGGAATG 58.691 40.000 0.00 0.00 0.00 2.67
4762 4822 6.535161 TGGGAGATATGGAATGAAAGGAAT 57.465 37.500 0.00 0.00 0.00 3.01
4763 4823 5.992564 TGGGAGATATGGAATGAAAGGAA 57.007 39.130 0.00 0.00 0.00 3.36
4764 4824 5.014544 GGATGGGAGATATGGAATGAAAGGA 59.985 44.000 0.00 0.00 0.00 3.36
4765 4825 5.259632 GGATGGGAGATATGGAATGAAAGG 58.740 45.833 0.00 0.00 0.00 3.11
4766 4826 5.222192 TGGGATGGGAGATATGGAATGAAAG 60.222 44.000 0.00 0.00 0.00 2.62
4767 4827 4.669290 TGGGATGGGAGATATGGAATGAAA 59.331 41.667 0.00 0.00 0.00 2.69
4768 4828 4.043310 GTGGGATGGGAGATATGGAATGAA 59.957 45.833 0.00 0.00 0.00 2.57
4769 4829 3.588842 GTGGGATGGGAGATATGGAATGA 59.411 47.826 0.00 0.00 0.00 2.57
4770 4830 3.331591 TGTGGGATGGGAGATATGGAATG 59.668 47.826 0.00 0.00 0.00 2.67
4771 4831 3.612458 TGTGGGATGGGAGATATGGAAT 58.388 45.455 0.00 0.00 0.00 3.01
4772 4832 3.073411 TGTGGGATGGGAGATATGGAA 57.927 47.619 0.00 0.00 0.00 3.53
4773 4833 2.813338 TGTGGGATGGGAGATATGGA 57.187 50.000 0.00 0.00 0.00 3.41
4774 4834 2.981784 TCTTGTGGGATGGGAGATATGG 59.018 50.000 0.00 0.00 0.00 2.74
4775 4835 4.103785 ACTTCTTGTGGGATGGGAGATATG 59.896 45.833 0.00 0.00 0.00 1.78
4776 4836 4.310740 ACTTCTTGTGGGATGGGAGATAT 58.689 43.478 0.00 0.00 0.00 1.63
4777 4837 3.736094 ACTTCTTGTGGGATGGGAGATA 58.264 45.455 0.00 0.00 0.00 1.98
4778 4838 2.566746 ACTTCTTGTGGGATGGGAGAT 58.433 47.619 0.00 0.00 0.00 2.75
4779 4839 2.044793 ACTTCTTGTGGGATGGGAGA 57.955 50.000 0.00 0.00 0.00 3.71
4780 4840 3.009033 TGTTACTTCTTGTGGGATGGGAG 59.991 47.826 0.00 0.00 0.00 4.30
4781 4841 2.983192 TGTTACTTCTTGTGGGATGGGA 59.017 45.455 0.00 0.00 0.00 4.37
4782 4842 3.347216 CTGTTACTTCTTGTGGGATGGG 58.653 50.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.