Multiple sequence alignment - TraesCS6B01G409700

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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 TraesCS6B01G409700 chr6B 100.000 5196 0 0 1 5196 684164205 684159010 0.000000e+00 9596.0
1 TraesCS6B01G409700 chr6B 90.969 753 48 8 329 1072 545356410 545357151 0.000000e+00 996.0
2 TraesCS6B01G409700 chr6D 92.783 2896 113 43 1667 4519 450565085 450562243 0.000000e+00 4102.0
3 TraesCS6B01G409700 chr6D 91.005 945 63 13 2 939 450567110 450566181 0.000000e+00 1254.0
4 TraesCS6B01G409700 chr6D 93.243 814 48 5 786 1596 450566182 450565373 0.000000e+00 1192.0
5 TraesCS6B01G409700 chr6D 84.282 439 39 17 4758 5196 450561841 450561433 8.100000e-108 401.0
6 TraesCS6B01G409700 chr6A 95.311 1898 69 12 1732 3622 596087615 596085731 0.000000e+00 2994.0
7 TraesCS6B01G409700 chr6A 86.437 1740 135 45 13 1715 596089429 596087754 0.000000e+00 1812.0
8 TraesCS6B01G409700 chr6A 86.283 904 54 15 3654 4519 596085730 596084859 0.000000e+00 918.0
9 TraesCS6B01G409700 chr6A 86.538 156 11 5 5048 5195 596084228 596084075 4.160000e-36 163.0
10 TraesCS6B01G409700 chr6A 81.410 156 20 5 5048 5195 596079900 596079746 9.140000e-23 119.0
11 TraesCS6B01G409700 chr6A 100.000 50 0 0 1732 1781 596087690 596087641 5.540000e-15 93.5
12 TraesCS6B01G409700 chr6A 86.765 68 3 5 4676 4738 445264041 445263975 2.600000e-08 71.3
13 TraesCS6B01G409700 chr6A 95.455 44 0 2 4698 4740 154043021 154042979 9.340000e-08 69.4
14 TraesCS6B01G409700 chr7A 91.436 794 48 8 329 1113 617839666 617838884 0.000000e+00 1072.0
15 TraesCS6B01G409700 chr3B 90.806 794 53 8 329 1113 190847697 190848479 0.000000e+00 1044.0
16 TraesCS6B01G409700 chr3B 92.308 52 4 0 4676 4727 555269206 555269257 2.010000e-09 75.0
17 TraesCS6B01G409700 chr4A 90.554 794 54 9 329 1113 731522135 731521354 0.000000e+00 1031.0
18 TraesCS6B01G409700 chr3A 88.287 794 47 13 329 1113 709544183 709543427 0.000000e+00 909.0
19 TraesCS6B01G409700 chr4B 90.566 53 3 2 4698 4750 97894911 97894861 9.340000e-08 69.4
20 TraesCS6B01G409700 chr2B 93.333 45 3 0 4698 4742 66994777 66994821 3.360000e-07 67.6
21 TraesCS6B01G409700 chr3D 91.667 48 2 2 4698 4743 300567812 300567765 1.210000e-06 65.8
22 TraesCS6B01G409700 chr1D 84.375 64 8 2 4698 4760 408146092 408146030 1.560000e-05 62.1
23 TraesCS6B01G409700 chrUn 85.246 61 6 3 4698 4756 100780095 100780154 5.620000e-05 60.2
24 TraesCS6B01G409700 chr5A 85.246 61 4 4 4700 4757 662527059 662527117 2.020000e-04 58.4
25 TraesCS6B01G409700 chr5A 100.000 29 0 0 4676 4704 662667706 662667734 3.000000e-03 54.7
26 TraesCS6B01G409700 chr4D 79.775 89 11 6 4937 5020 292906509 292906423 2.020000e-04 58.4
27 TraesCS6B01G409700 chr2D 100.000 28 0 0 4671 4698 537518426 537518399 9.000000e-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 TraesCS6B01G409700 chr6B 684159010 684164205 5195 True 9596.00 9596 100.00000 1 5196 1 chr6B.!!$R1 5195
1 TraesCS6B01G409700 chr6B 545356410 545357151 741 False 996.00 996 90.96900 329 1072 1 chr6B.!!$F1 743
2 TraesCS6B01G409700 chr6D 450561433 450567110 5677 True 1737.25 4102 90.32825 2 5196 4 chr6D.!!$R1 5194
3 TraesCS6B01G409700 chr6A 596084075 596089429 5354 True 1196.10 2994 90.91380 13 5195 5 chr6A.!!$R4 5182
4 TraesCS6B01G409700 chr7A 617838884 617839666 782 True 1072.00 1072 91.43600 329 1113 1 chr7A.!!$R1 784
5 TraesCS6B01G409700 chr3B 190847697 190848479 782 False 1044.00 1044 90.80600 329 1113 1 chr3B.!!$F1 784
6 TraesCS6B01G409700 chr4A 731521354 731522135 781 True 1031.00 1031 90.55400 329 1113 1 chr4A.!!$R1 784
7 TraesCS6B01G409700 chr3A 709543427 709544183 756 True 909.00 909 88.28700 329 1113 1 chr3A.!!$R1 784

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
539 580 0.036306 TTCGGTTCCCTCTTGCCTTC 59.964 55.0 0.0 0.0 0.00 3.46 F
1306 1511 0.678395 CTCGCTGGATGCTACCATCT 59.322 55.0 3.2 0.0 45.73 2.90 F
1652 1867 0.675633 CCACCAAACCTTGCCTTGAG 59.324 55.0 0.0 0.0 0.00 3.02 F
3039 3604 1.305201 TTCTGGGACTTGTGCGTTTC 58.695 50.0 0.0 0.0 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1825 0.251073 ATCTTTGGCATTGCAAGGGC 59.749 50.000 28.32 28.32 41.68 5.19 R
3039 3604 2.483745 CATGCTGTGAAGCCTGCG 59.516 61.111 0.00 0.00 32.52 5.18 R
3634 4201 2.412847 GCAAGCGTTCAACACTCCATAC 60.413 50.000 0.00 0.00 0.00 2.39 R
4961 5884 0.377905 TGAAATCATGCGCATCGGTG 59.622 50.000 22.51 11.63 0.00 4.94 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
175 193 1.757423 GCAGCCATCCTCTCCTCTCC 61.757 65.000 0.00 0.00 0.00 3.71
193 211 4.681978 GCACCTTCAGCCGGACGT 62.682 66.667 5.05 0.00 0.00 4.34
194 212 2.432628 CACCTTCAGCCGGACGTC 60.433 66.667 5.05 7.13 0.00 4.34
195 213 3.692406 ACCTTCAGCCGGACGTCC 61.692 66.667 25.28 25.28 0.00 4.79
196 214 3.382832 CCTTCAGCCGGACGTCCT 61.383 66.667 30.92 11.21 0.00 3.85
197 215 2.182030 CTTCAGCCGGACGTCCTC 59.818 66.667 30.92 21.77 0.00 3.71
198 216 2.282958 TTCAGCCGGACGTCCTCT 60.283 61.111 30.92 23.54 0.00 3.69
199 217 1.878656 CTTCAGCCGGACGTCCTCTT 61.879 60.000 30.92 13.77 0.00 2.85
200 218 1.874345 TTCAGCCGGACGTCCTCTTC 61.874 60.000 30.92 16.69 0.00 2.87
201 219 2.282958 AGCCGGACGTCCTCTTCA 60.283 61.111 30.92 0.00 0.00 3.02
202 220 2.182030 GCCGGACGTCCTCTTCAG 59.818 66.667 30.92 14.85 0.00 3.02
203 221 2.182030 CCGGACGTCCTCTTCAGC 59.818 66.667 30.92 3.55 0.00 4.26
204 222 2.182030 CGGACGTCCTCTTCAGCC 59.818 66.667 30.92 3.41 0.00 4.85
205 223 2.182030 GGACGTCCTCTTCAGCCG 59.818 66.667 27.64 0.00 0.00 5.52
283 324 2.035576 GCATCCTCTGCCCATTCAATTC 59.964 50.000 0.00 0.00 45.66 2.17
321 362 7.442364 TCTTTGTAATGGATGATTACTAGCTGC 59.558 37.037 0.00 0.00 44.80 5.25
433 474 1.474143 GCCAAGATCCCGGAGAAAGAG 60.474 57.143 0.73 0.00 0.00 2.85
521 562 4.675029 CGCAGGTTCGGTCCGGTT 62.675 66.667 12.29 0.00 0.00 4.44
522 563 2.741211 GCAGGTTCGGTCCGGTTC 60.741 66.667 12.29 2.17 0.00 3.62
523 564 2.431942 CAGGTTCGGTCCGGTTCG 60.432 66.667 12.29 7.13 0.00 3.95
539 580 0.036306 TTCGGTTCCCTCTTGCCTTC 59.964 55.000 0.00 0.00 0.00 3.46
540 581 1.377333 CGGTTCCCTCTTGCCTTCC 60.377 63.158 0.00 0.00 0.00 3.46
541 582 1.767692 GGTTCCCTCTTGCCTTCCA 59.232 57.895 0.00 0.00 0.00 3.53
578 619 8.868522 TTCTTGGTGATTTCTCAAGATTACAT 57.131 30.769 13.48 0.00 44.00 2.29
585 626 7.646922 GTGATTTCTCAAGATTACATCATTGGC 59.353 37.037 0.00 0.00 31.85 4.52
652 701 1.813178 TGGCTGTTTTGTTTCGTGTGA 59.187 42.857 0.00 0.00 0.00 3.58
653 702 2.229062 TGGCTGTTTTGTTTCGTGTGAA 59.771 40.909 0.00 0.00 0.00 3.18
656 705 2.851824 CTGTTTTGTTTCGTGTGAAGGC 59.148 45.455 0.00 0.00 35.06 4.35
738 789 7.307692 GCATAAATAAAGGGTGTTTGTTTGGTG 60.308 37.037 3.36 3.87 0.00 4.17
869 920 0.756294 TGGTCGTGTGATCCTTGTGT 59.244 50.000 0.00 0.00 0.00 3.72
903 954 2.369532 AGGTTGTGGATGCTGCAAATTT 59.630 40.909 6.36 0.00 0.00 1.82
1026 1231 0.887836 CTGTGTGCCACATGCTCTGT 60.888 55.000 0.00 0.00 43.71 3.41
1193 1398 0.752054 TTGCTGCCAGGTTTCCAAAG 59.248 50.000 0.00 0.00 0.00 2.77
1217 1422 2.191641 GCCCCTGGAGATGAGCAC 59.808 66.667 0.00 0.00 0.00 4.40
1235 1440 3.142174 GCACTGGAAGGATATTAGCCAC 58.858 50.000 0.02 0.00 39.30 5.01
1239 1444 3.648067 CTGGAAGGATATTAGCCACTGGA 59.352 47.826 0.00 0.00 0.00 3.86
1245 1450 2.684001 TATTAGCCACTGGAACACCG 57.316 50.000 0.00 0.00 0.00 4.94
1247 1452 2.741486 TTAGCCACTGGAACACCGCC 62.741 60.000 0.00 0.00 0.00 6.13
1306 1511 0.678395 CTCGCTGGATGCTACCATCT 59.322 55.000 3.20 0.00 45.73 2.90
1309 1514 1.336702 CGCTGGATGCTACCATCTCTC 60.337 57.143 3.20 0.00 45.73 3.20
1416 1621 5.753921 GGTGCCTGTATCTAGTGTCATAAAC 59.246 44.000 0.00 0.00 0.00 2.01
1419 1624 8.361139 GTGCCTGTATCTAGTGTCATAAACTAT 58.639 37.037 0.00 0.00 30.00 2.12
1447 1652 3.071479 GTTTGAGTCATGGAGGCGTTTA 58.929 45.455 0.00 0.00 0.00 2.01
1448 1653 2.380084 TGAGTCATGGAGGCGTTTAC 57.620 50.000 0.00 0.00 0.00 2.01
1449 1654 1.899814 TGAGTCATGGAGGCGTTTACT 59.100 47.619 0.00 0.00 0.00 2.24
1450 1655 2.301870 TGAGTCATGGAGGCGTTTACTT 59.698 45.455 0.00 0.00 0.00 2.24
1451 1656 2.930682 GAGTCATGGAGGCGTTTACTTC 59.069 50.000 0.00 0.00 0.00 3.01
1452 1657 2.567615 AGTCATGGAGGCGTTTACTTCT 59.432 45.455 0.00 0.00 0.00 2.85
1453 1658 3.008049 AGTCATGGAGGCGTTTACTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
1454 1659 3.371285 GTCATGGAGGCGTTTACTTCTTC 59.629 47.826 0.00 0.00 0.00 2.87
1467 1672 6.816640 CGTTTACTTCTTCACATCTTCCCATA 59.183 38.462 0.00 0.00 0.00 2.74
1498 1712 4.610945 CTTGCTCTTTTAGGTTGTGTTGG 58.389 43.478 0.00 0.00 0.00 3.77
1525 1739 9.097257 CGTGCCTAATTTTGGAAATGAATTAAT 57.903 29.630 0.73 0.00 0.00 1.40
1555 1769 2.358898 GCATGTCTGAGGTGTTGTTTGT 59.641 45.455 0.00 0.00 0.00 2.83
1565 1780 6.925211 TGAGGTGTTGTTTGTCATTTTGTTA 58.075 32.000 0.00 0.00 0.00 2.41
1600 1815 6.472887 TGATTCTCGTTCCTTTATTGACCTT 58.527 36.000 0.00 0.00 0.00 3.50
1652 1867 0.675633 CCACCAAACCTTGCCTTGAG 59.324 55.000 0.00 0.00 0.00 3.02
1653 1868 0.675633 CACCAAACCTTGCCTTGAGG 59.324 55.000 0.00 0.00 40.24 3.86
1670 1885 2.885113 GGGGGCTCGACAAAATGC 59.115 61.111 0.00 0.00 0.00 3.56
1678 2110 4.688413 GGGCTCGACAAAATGCATTTTTAA 59.312 37.500 30.13 16.46 37.86 1.52
1715 2147 5.111989 CAGAAGTTCAGTGTGAGAGTTTGA 58.888 41.667 5.50 0.00 0.00 2.69
1717 2149 5.757320 AGAAGTTCAGTGTGAGAGTTTGATG 59.243 40.000 5.50 0.00 0.00 3.07
1718 2150 5.028549 AGTTCAGTGTGAGAGTTTGATGT 57.971 39.130 0.00 0.00 0.00 3.06
1719 2151 6.161855 AGTTCAGTGTGAGAGTTTGATGTA 57.838 37.500 0.00 0.00 0.00 2.29
1722 2154 6.101650 TCAGTGTGAGAGTTTGATGTACAT 57.898 37.500 8.43 8.43 0.00 2.29
1726 2158 8.939929 CAGTGTGAGAGTTTGATGTACATAAAT 58.060 33.333 8.71 0.00 0.00 1.40
1798 2352 4.953667 TCAGATGGATGATTGTAGACTGC 58.046 43.478 0.00 0.00 0.00 4.40
1873 2427 9.529325 GTTGCAGATAATCACACAGTATAGTAA 57.471 33.333 0.00 0.00 0.00 2.24
1932 2489 5.358160 AGATGTGTAGTGATCGAGATGTTCA 59.642 40.000 0.00 0.00 0.00 3.18
1943 2500 6.363357 TGATCGAGATGTTCATATAGCGTTTG 59.637 38.462 0.00 0.00 0.00 2.93
1944 2501 5.588240 TCGAGATGTTCATATAGCGTTTGT 58.412 37.500 0.00 0.00 0.00 2.83
2091 2650 7.324178 AGGCTCATATAATGATTCGTTAGTCC 58.676 38.462 4.74 0.00 38.85 3.85
2105 2664 3.927142 CGTTAGTCCATCTTCAACCTGTC 59.073 47.826 0.00 0.00 0.00 3.51
2120 2679 1.418373 CTGTCGCGAAGATGAACACA 58.582 50.000 12.06 0.00 0.00 3.72
2134 2693 7.984422 AGATGAACACAATAACATGAGTTGA 57.016 32.000 0.00 0.00 38.69 3.18
2526 3090 4.190772 GAGAGCTAGCTTTTCTGCTGATT 58.809 43.478 20.42 0.00 43.87 2.57
2596 3160 9.646427 AAGTAGCACTACTCTCTTTTCTATTTG 57.354 33.333 10.64 0.00 44.96 2.32
2646 3210 9.981114 CCAATCTTTTTAACCTACATCTGTTTT 57.019 29.630 0.00 0.00 0.00 2.43
2648 3212 9.981114 AATCTTTTTAACCTACATCTGTTTTGG 57.019 29.630 0.00 0.00 0.00 3.28
2806 3371 9.045745 ACAGTATGGAAATACAAATGGGAAATT 57.954 29.630 0.00 0.00 43.62 1.82
2811 3376 8.614469 TGGAAATACAAATGGGAAATTTTGAC 57.386 30.769 0.00 0.00 36.54 3.18
2933 3498 3.591196 TTGGCTGGAAAAATTGATCCG 57.409 42.857 5.56 2.75 38.63 4.18
3014 3579 6.687604 TGAAAAGTTCTGTATGATCTCGTCA 58.312 36.000 0.00 0.00 42.06 4.35
3039 3604 1.305201 TTCTGGGACTTGTGCGTTTC 58.695 50.000 0.00 0.00 0.00 2.78
3088 3653 1.676529 TGTGCTAGAGTACCGCAGATC 59.323 52.381 0.00 0.00 33.84 2.75
3403 3969 7.617723 TGGTAAGTTGGAATAGTTGGCAATAAT 59.382 33.333 1.92 0.00 0.00 1.28
3464 4030 9.607988 TTTTCAGTCTGATGTTACTGTCTAAAA 57.392 29.630 2.68 0.00 42.96 1.52
3614 4181 6.970043 TGGTTTTGTTCATCAAGTTTTACTCG 59.030 34.615 0.00 0.00 37.35 4.18
3631 4198 3.671716 ACTCGTATGTGAAACTTTCCCC 58.328 45.455 0.00 0.00 38.04 4.81
3634 4201 4.069304 TCGTATGTGAAACTTTCCCCTTG 58.931 43.478 0.00 0.00 38.04 3.61
3803 4372 4.340381 AGCTGTTTCTGATTTGCTTCTTGT 59.660 37.500 0.00 0.00 0.00 3.16
3804 4373 4.443394 GCTGTTTCTGATTTGCTTCTTGTG 59.557 41.667 0.00 0.00 0.00 3.33
3824 4393 5.063204 TGTGACAAGCTAAACTGCTGTATT 58.937 37.500 0.00 0.00 43.24 1.89
3825 4394 5.049474 TGTGACAAGCTAAACTGCTGTATTG 60.049 40.000 0.00 1.15 43.24 1.90
3826 4395 5.049405 GTGACAAGCTAAACTGCTGTATTGT 60.049 40.000 0.00 4.16 43.24 2.71
3946 4554 7.147976 AGTTTAAGTTGATTTGGAAGATGCAC 58.852 34.615 0.00 0.00 0.00 4.57
4062 4670 4.164843 TGTTTTCCCTTTGCTGTACTCT 57.835 40.909 0.00 0.00 0.00 3.24
4063 4671 4.532834 TGTTTTCCCTTTGCTGTACTCTT 58.467 39.130 0.00 0.00 0.00 2.85
4084 4692 0.612174 TCTGGACCCTCCTTGACTCG 60.612 60.000 0.00 0.00 37.46 4.18
4167 4775 0.179163 GCGATGTACCAAAAGCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
4198 4806 9.952030 AAGAAAGGGAAGAAAGAAGAGTAATAG 57.048 33.333 0.00 0.00 0.00 1.73
4205 4813 0.032267 AGAAGAGTAATAGGGCGCGC 59.968 55.000 25.94 25.94 0.00 6.86
4207 4815 3.403881 GAGTAATAGGGCGCGCGC 61.404 66.667 44.40 44.40 41.06 6.86
4230 4838 3.665190 AGAAACGACATGAGGTTCTTCC 58.335 45.455 16.49 4.75 0.00 3.46
4244 4852 3.146847 GTTCTTCCTGGTGGGTTTACAG 58.853 50.000 0.00 0.00 36.25 2.74
4250 4858 3.053544 TCCTGGTGGGTTTACAGTTTTGA 60.054 43.478 0.00 0.00 36.25 2.69
4283 4891 7.201767 GCTATTCTATTCTTGGAGCAACATTGT 60.202 37.037 0.00 0.00 0.00 2.71
4306 4914 1.344438 CACTTACCTGCAGACCTCACA 59.656 52.381 17.39 0.00 0.00 3.58
4307 4915 1.344763 ACTTACCTGCAGACCTCACAC 59.655 52.381 17.39 0.00 0.00 3.82
4314 4922 1.016130 GCAGACCTCACACCATGACG 61.016 60.000 0.00 0.00 32.37 4.35
4361 4970 5.142265 CAGACTTGTGTGATGATGAAAACG 58.858 41.667 0.00 0.00 0.00 3.60
4411 5020 7.742963 TTTTTCGAAGTATCGTAAAATGACTGC 59.257 33.333 10.34 0.00 46.40 4.40
4431 5041 3.636300 TGCTTGTGTAGTTTCAATTGCCT 59.364 39.130 0.00 0.00 0.00 4.75
4442 5052 2.446435 TCAATTGCCTCCTTGGTTAGC 58.554 47.619 0.00 0.00 38.35 3.09
4453 5063 3.901844 TCCTTGGTTAGCTTACTCTGTGT 59.098 43.478 2.46 0.00 0.00 3.72
4457 5067 5.143376 TGGTTAGCTTACTCTGTGTAACC 57.857 43.478 2.46 1.95 36.33 2.85
4533 5143 4.699925 TGTTGTTACACTTTAGCCTCCT 57.300 40.909 0.00 0.00 0.00 3.69
4534 5144 5.043737 TGTTGTTACACTTTAGCCTCCTT 57.956 39.130 0.00 0.00 0.00 3.36
4535 5145 5.442391 TGTTGTTACACTTTAGCCTCCTTT 58.558 37.500 0.00 0.00 0.00 3.11
4536 5146 5.298276 TGTTGTTACACTTTAGCCTCCTTTG 59.702 40.000 0.00 0.00 0.00 2.77
4541 5151 4.278310 ACACTTTAGCCTCCTTTGTTTGT 58.722 39.130 0.00 0.00 0.00 2.83
4544 5154 4.953579 ACTTTAGCCTCCTTTGTTTGTTGA 59.046 37.500 0.00 0.00 0.00 3.18
4546 5156 5.452078 TTAGCCTCCTTTGTTTGTTGATG 57.548 39.130 0.00 0.00 0.00 3.07
4548 5158 3.571401 AGCCTCCTTTGTTTGTTGATGAG 59.429 43.478 0.00 0.00 0.00 2.90
4549 5159 3.305608 GCCTCCTTTGTTTGTTGATGAGG 60.306 47.826 0.00 0.00 40.83 3.86
4550 5160 3.891366 CCTCCTTTGTTTGTTGATGAGGT 59.109 43.478 0.00 0.00 34.73 3.85
4551 5161 4.342092 CCTCCTTTGTTTGTTGATGAGGTT 59.658 41.667 0.00 0.00 34.73 3.50
4552 5162 5.163416 CCTCCTTTGTTTGTTGATGAGGTTT 60.163 40.000 0.00 0.00 34.73 3.27
4553 5163 5.659463 TCCTTTGTTTGTTGATGAGGTTTG 58.341 37.500 0.00 0.00 0.00 2.93
4554 5164 5.186797 TCCTTTGTTTGTTGATGAGGTTTGT 59.813 36.000 0.00 0.00 0.00 2.83
4555 5165 5.291614 CCTTTGTTTGTTGATGAGGTTTGTG 59.708 40.000 0.00 0.00 0.00 3.33
4556 5166 5.398603 TTGTTTGTTGATGAGGTTTGTGT 57.601 34.783 0.00 0.00 0.00 3.72
4557 5167 4.992688 TGTTTGTTGATGAGGTTTGTGTC 58.007 39.130 0.00 0.00 0.00 3.67
4584 5357 0.889186 TCGGCTGCTTTCTTCCAACC 60.889 55.000 0.00 0.00 0.00 3.77
4585 5358 1.172180 CGGCTGCTTTCTTCCAACCA 61.172 55.000 0.00 0.00 0.00 3.67
4586 5359 1.039856 GGCTGCTTTCTTCCAACCAA 58.960 50.000 0.00 0.00 0.00 3.67
4587 5360 1.269778 GGCTGCTTTCTTCCAACCAAC 60.270 52.381 0.00 0.00 0.00 3.77
4600 5373 4.984295 TCCAACCAACTGATGAGATTCAA 58.016 39.130 0.00 0.00 0.00 2.69
4650 5459 1.340017 CGTCCAACATCACCCCAAGAT 60.340 52.381 0.00 0.00 0.00 2.40
4651 5460 2.807676 GTCCAACATCACCCCAAGATT 58.192 47.619 0.00 0.00 0.00 2.40
4674 5483 5.337578 TTTTCTTTCTCCAACCCAACTTG 57.662 39.130 0.00 0.00 0.00 3.16
4677 5486 4.457466 TCTTTCTCCAACCCAACTTGTAC 58.543 43.478 0.00 0.00 0.00 2.90
4678 5487 4.165372 TCTTTCTCCAACCCAACTTGTACT 59.835 41.667 0.00 0.00 0.00 2.73
4679 5488 3.764237 TCTCCAACCCAACTTGTACTC 57.236 47.619 0.00 0.00 0.00 2.59
4680 5489 2.370849 TCTCCAACCCAACTTGTACTCC 59.629 50.000 0.00 0.00 0.00 3.85
4681 5490 1.422402 TCCAACCCAACTTGTACTCCC 59.578 52.381 0.00 0.00 0.00 4.30
4683 5492 2.552373 CCAACCCAACTTGTACTCCCTC 60.552 54.545 0.00 0.00 0.00 4.30
4684 5493 1.359168 ACCCAACTTGTACTCCCTCC 58.641 55.000 0.00 0.00 0.00 4.30
4685 5494 0.249398 CCCAACTTGTACTCCCTCCG 59.751 60.000 0.00 0.00 0.00 4.63
4686 5495 0.974383 CCAACTTGTACTCCCTCCGT 59.026 55.000 0.00 0.00 0.00 4.69
4687 5496 1.346722 CCAACTTGTACTCCCTCCGTT 59.653 52.381 0.00 0.00 0.00 4.44
4688 5497 2.612221 CCAACTTGTACTCCCTCCGTTC 60.612 54.545 0.00 0.00 0.00 3.95
4689 5498 2.299297 CAACTTGTACTCCCTCCGTTCT 59.701 50.000 0.00 0.00 0.00 3.01
4690 5499 3.446442 ACTTGTACTCCCTCCGTTCTA 57.554 47.619 0.00 0.00 0.00 2.10
4691 5500 3.771216 ACTTGTACTCCCTCCGTTCTAA 58.229 45.455 0.00 0.00 0.00 2.10
4692 5501 4.154942 ACTTGTACTCCCTCCGTTCTAAA 58.845 43.478 0.00 0.00 0.00 1.85
4693 5502 4.590222 ACTTGTACTCCCTCCGTTCTAAAA 59.410 41.667 0.00 0.00 0.00 1.52
4694 5503 5.247792 ACTTGTACTCCCTCCGTTCTAAAAT 59.752 40.000 0.00 0.00 0.00 1.82
4695 5504 6.438425 ACTTGTACTCCCTCCGTTCTAAAATA 59.562 38.462 0.00 0.00 0.00 1.40
4696 5505 7.125356 ACTTGTACTCCCTCCGTTCTAAAATAT 59.875 37.037 0.00 0.00 0.00 1.28
4697 5506 8.537728 TTGTACTCCCTCCGTTCTAAAATATA 57.462 34.615 0.00 0.00 0.00 0.86
4698 5507 8.537728 TGTACTCCCTCCGTTCTAAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
4699 5508 8.636213 TGTACTCCCTCCGTTCTAAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
4700 5509 7.909485 ACTCCCTCCGTTCTAAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4701 5510 7.724287 ACTCCCTCCGTTCTAAAATATAAGAC 58.276 38.462 0.00 0.00 0.00 3.01
4702 5511 7.564292 ACTCCCTCCGTTCTAAAATATAAGACT 59.436 37.037 0.00 0.00 0.00 3.24
4703 5512 8.315220 TCCCTCCGTTCTAAAATATAAGACTT 57.685 34.615 0.00 0.00 0.00 3.01
4704 5513 9.425248 TCCCTCCGTTCTAAAATATAAGACTTA 57.575 33.333 0.00 0.00 0.00 2.24
4721 5530 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4722 5531 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4723 5532 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4724 5533 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
4725 5534 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
4730 5539 3.967467 AGGAACGGAGGGAGTAGATAA 57.033 47.619 0.00 0.00 0.00 1.75
4739 5548 5.486526 GGAGGGAGTAGATAAGATTGCATG 58.513 45.833 0.00 0.00 0.00 4.06
4741 5550 6.070309 GGAGGGAGTAGATAAGATTGCATGAT 60.070 42.308 0.00 0.00 0.00 2.45
4771 5580 8.672823 ACTAATTTCAAGTAGGTTCTCGTTTT 57.327 30.769 0.00 0.00 31.28 2.43
4773 5582 9.382244 CTAATTTCAAGTAGGTTCTCGTTTTTG 57.618 33.333 0.00 0.00 0.00 2.44
4774 5583 5.744666 TTCAAGTAGGTTCTCGTTTTTGG 57.255 39.130 0.00 0.00 0.00 3.28
4775 5584 3.562557 TCAAGTAGGTTCTCGTTTTTGGC 59.437 43.478 0.00 0.00 0.00 4.52
4776 5585 2.501261 AGTAGGTTCTCGTTTTTGGCC 58.499 47.619 0.00 0.00 0.00 5.36
4777 5586 1.538512 GTAGGTTCTCGTTTTTGGCCC 59.461 52.381 0.00 0.00 0.00 5.80
4778 5587 1.170290 AGGTTCTCGTTTTTGGCCCG 61.170 55.000 0.00 0.00 0.00 6.13
4779 5588 1.167781 GGTTCTCGTTTTTGGCCCGA 61.168 55.000 0.00 0.00 0.00 5.14
4780 5589 0.040692 GTTCTCGTTTTTGGCCCGAC 60.041 55.000 0.00 0.00 0.00 4.79
4794 5632 2.543238 GGCCCGACGTATCTAACTCTTG 60.543 54.545 0.00 0.00 0.00 3.02
4796 5634 3.428589 GCCCGACGTATCTAACTCTTGTT 60.429 47.826 0.00 0.00 39.98 2.83
4820 5658 4.384940 GAGCATCTCTAACCAATCCCTTC 58.615 47.826 0.00 0.00 0.00 3.46
4823 5661 4.949856 GCATCTCTAACCAATCCCTTCAAA 59.050 41.667 0.00 0.00 0.00 2.69
4825 5663 6.071391 GCATCTCTAACCAATCCCTTCAAAAA 60.071 38.462 0.00 0.00 0.00 1.94
4826 5664 6.894339 TCTCTAACCAATCCCTTCAAAAAC 57.106 37.500 0.00 0.00 0.00 2.43
4829 5667 7.563556 TCTCTAACCAATCCCTTCAAAAACTTT 59.436 33.333 0.00 0.00 0.00 2.66
4830 5668 7.722363 TCTAACCAATCCCTTCAAAAACTTTC 58.278 34.615 0.00 0.00 0.00 2.62
4846 5684 9.706846 CAAAAACTTTCAATTCCTCATTTTGAC 57.293 29.630 0.00 0.00 37.40 3.18
4847 5685 9.447157 AAAAACTTTCAATTCCTCATTTTGACA 57.553 25.926 0.00 0.00 0.00 3.58
4864 5702 5.362105 TTGACAAGTTAACCACACCTAGT 57.638 39.130 0.88 0.00 0.00 2.57
4914 5837 8.968242 GTAAAAATTGTAAGTCTGCCTCAAAAG 58.032 33.333 0.00 0.00 0.00 2.27
4929 5852 0.977395 AAAAGGCAGCTACTCGACCT 59.023 50.000 0.00 0.00 0.00 3.85
4933 5856 1.144093 AGGCAGCTACTCGACCTATCT 59.856 52.381 0.00 0.00 0.00 1.98
4934 5857 1.268352 GGCAGCTACTCGACCTATCTG 59.732 57.143 0.00 0.00 0.00 2.90
4948 5871 1.137086 CTATCTGTCACCACTTCCCGG 59.863 57.143 0.00 0.00 0.00 5.73
4974 5897 3.879682 CCACCACCGATGCGCATG 61.880 66.667 30.76 17.30 0.00 4.06
4975 5898 2.819154 CACCACCGATGCGCATGA 60.819 61.111 30.76 0.00 0.00 3.07
4976 5899 2.182181 CACCACCGATGCGCATGAT 61.182 57.895 30.76 9.92 0.00 2.45
4977 5900 1.451927 ACCACCGATGCGCATGATT 60.452 52.632 30.76 3.52 0.00 2.57
4978 5901 1.031571 ACCACCGATGCGCATGATTT 61.032 50.000 30.76 3.00 0.00 2.17
4979 5902 0.317269 CCACCGATGCGCATGATTTC 60.317 55.000 30.76 13.25 0.00 2.17
4980 5903 0.377905 CACCGATGCGCATGATTTCA 59.622 50.000 30.76 0.00 0.00 2.69
4981 5904 0.659427 ACCGATGCGCATGATTTCAG 59.341 50.000 30.76 8.76 0.00 3.02
4982 5905 0.659417 CCGATGCGCATGATTTCAGC 60.659 55.000 30.76 9.64 0.00 4.26
5001 5924 2.780595 CGGAATGGAACCGCAAGAT 58.219 52.632 0.00 0.00 43.74 2.40
5067 5990 0.251341 CACCAAGGAAGAGGTTGGGG 60.251 60.000 6.10 0.00 46.53 4.96
5069 5992 1.002857 CCAAGGAAGAGGTTGGGGAT 58.997 55.000 0.00 0.00 39.76 3.85
5073 5996 4.510205 CCAAGGAAGAGGTTGGGGATAAAA 60.510 45.833 0.00 0.00 39.76 1.52
5169 6100 2.367377 CCTCCCCTGCTCCATCCA 60.367 66.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 207 2.182030 CCGGCTGAAGAGGACGTC 59.818 66.667 7.13 7.13 0.00 4.34
190 208 3.382832 CCCGGCTGAAGAGGACGT 61.383 66.667 0.00 0.00 0.00 4.34
191 209 3.068691 TCCCGGCTGAAGAGGACG 61.069 66.667 0.00 0.00 0.00 4.79
192 210 2.896443 CTCCCGGCTGAAGAGGAC 59.104 66.667 0.00 0.00 0.00 3.85
193 211 3.077556 GCTCCCGGCTGAAGAGGA 61.078 66.667 12.74 2.03 38.06 3.71
194 212 4.168291 GGCTCCCGGCTGAAGAGG 62.168 72.222 12.74 0.00 41.46 3.69
195 213 4.168291 GGGCTCCCGGCTGAAGAG 62.168 72.222 0.00 7.90 41.46 2.85
197 215 3.764160 GATGGGCTCCCGGCTGAAG 62.764 68.421 0.00 0.00 41.46 3.02
198 216 3.797353 GATGGGCTCCCGGCTGAA 61.797 66.667 0.00 0.00 41.46 3.02
283 324 9.784680 CATCCATTACAAAGATCAGAAGAAAAG 57.215 33.333 0.00 0.00 0.00 2.27
303 344 5.758790 ATCTGCAGCTAGTAATCATCCAT 57.241 39.130 9.47 0.00 0.00 3.41
321 362 2.621998 GCCAATCTCCACATCCAATCTG 59.378 50.000 0.00 0.00 0.00 2.90
524 565 1.821136 CAATGGAAGGCAAGAGGGAAC 59.179 52.381 0.00 0.00 0.00 3.62
525 566 1.892329 GCAATGGAAGGCAAGAGGGAA 60.892 52.381 0.00 0.00 0.00 3.97
526 567 0.323725 GCAATGGAAGGCAAGAGGGA 60.324 55.000 0.00 0.00 0.00 4.20
527 568 1.325476 GGCAATGGAAGGCAAGAGGG 61.325 60.000 0.00 0.00 0.00 4.30
528 569 0.324091 AGGCAATGGAAGGCAAGAGG 60.324 55.000 0.00 0.00 0.00 3.69
529 570 0.815734 CAGGCAATGGAAGGCAAGAG 59.184 55.000 0.00 0.00 0.00 2.85
530 571 0.405198 TCAGGCAATGGAAGGCAAGA 59.595 50.000 0.00 0.00 0.00 3.02
531 572 1.067354 GTTCAGGCAATGGAAGGCAAG 60.067 52.381 0.00 0.00 0.00 4.01
539 580 2.629617 ACCAAGAAAGTTCAGGCAATGG 59.370 45.455 3.31 0.00 0.00 3.16
540 581 3.318839 TCACCAAGAAAGTTCAGGCAATG 59.681 43.478 3.31 0.00 0.00 2.82
541 582 3.565307 TCACCAAGAAAGTTCAGGCAAT 58.435 40.909 3.31 0.00 0.00 3.56
578 619 0.828022 CTACTACGGGTGGCCAATGA 59.172 55.000 7.24 0.00 0.00 2.57
585 626 4.056050 GCACAATAATCTACTACGGGTGG 58.944 47.826 0.00 0.00 0.00 4.61
652 701 3.953775 CTCACACCCACCCGCCTT 61.954 66.667 0.00 0.00 0.00 4.35
653 702 4.954118 TCTCACACCCACCCGCCT 62.954 66.667 0.00 0.00 0.00 5.52
656 705 1.990060 ATCCTCTCACACCCACCCG 60.990 63.158 0.00 0.00 0.00 5.28
825 876 4.209080 GGAGCAAACAAACAAAGAATTCCG 59.791 41.667 0.65 0.00 0.00 4.30
869 920 5.100344 TCCACAACCTACACACTAACAAA 57.900 39.130 0.00 0.00 0.00 2.83
1147 1352 1.988107 TCCTGTTGAAGGCTTCCTCAT 59.012 47.619 23.68 0.00 46.92 2.90
1193 1398 0.394899 CATCTCCAGGGGCTCCAAAC 60.395 60.000 4.79 0.00 34.83 2.93
1201 1406 1.525923 CAGTGCTCATCTCCAGGGG 59.474 63.158 0.00 0.00 0.00 4.79
1217 1422 3.648067 TCCAGTGGCTAATATCCTTCCAG 59.352 47.826 3.51 0.00 0.00 3.86
1235 1440 0.168128 GATTTTCGGCGGTGTTCCAG 59.832 55.000 7.21 0.00 0.00 3.86
1329 1534 2.618709 CCCAAGGACTGTTGACAAGAAC 59.381 50.000 0.00 0.00 0.00 3.01
1416 1621 7.439655 GCCTCCATGACTCAAACTAGTTTATAG 59.560 40.741 20.15 20.33 0.00 1.31
1419 1624 5.488341 GCCTCCATGACTCAAACTAGTTTA 58.512 41.667 20.15 5.41 0.00 2.01
1447 1652 4.225942 TGCTATGGGAAGATGTGAAGAAGT 59.774 41.667 0.00 0.00 0.00 3.01
1448 1653 4.774124 TGCTATGGGAAGATGTGAAGAAG 58.226 43.478 0.00 0.00 0.00 2.85
1449 1654 4.384537 CCTGCTATGGGAAGATGTGAAGAA 60.385 45.833 0.00 0.00 0.00 2.52
1450 1655 3.135348 CCTGCTATGGGAAGATGTGAAGA 59.865 47.826 0.00 0.00 0.00 2.87
1451 1656 3.135348 TCCTGCTATGGGAAGATGTGAAG 59.865 47.826 0.00 0.00 0.00 3.02
1452 1657 3.114606 TCCTGCTATGGGAAGATGTGAA 58.885 45.455 0.00 0.00 0.00 3.18
1453 1658 2.763039 TCCTGCTATGGGAAGATGTGA 58.237 47.619 0.00 0.00 0.00 3.58
1454 1659 3.565764 TTCCTGCTATGGGAAGATGTG 57.434 47.619 0.00 0.00 37.86 3.21
1498 1712 3.843999 TCATTTCCAAAATTAGGCACGC 58.156 40.909 0.00 0.00 0.00 5.34
1525 1739 3.133542 CACCTCAGACATGCCTTCATCTA 59.866 47.826 0.00 0.00 0.00 1.98
1565 1780 6.180472 AGGAACGAGAATCATGTTAAACCAT 58.820 36.000 0.00 0.00 33.17 3.55
1600 1815 4.402851 GCAAGGGCAGATGACACA 57.597 55.556 0.00 0.00 40.72 3.72
1610 1825 0.251073 ATCTTTGGCATTGCAAGGGC 59.749 50.000 28.32 28.32 41.68 5.19
1653 1868 1.322538 ATGCATTTTGTCGAGCCCCC 61.323 55.000 0.00 0.00 0.00 5.40
1678 2110 8.671921 CACTGAACTTCTGCAATACTCATAAAT 58.328 33.333 0.00 0.00 0.00 1.40
1798 2352 4.744795 AATCTGTCAGGCAGGTTACTAG 57.255 45.455 0.00 0.00 46.01 2.57
1889 2443 9.671279 ACACATCTTGACATGATACTCATAAAA 57.329 29.630 0.00 0.00 34.28 1.52
1893 2447 7.924947 CACTACACATCTTGACATGATACTCAT 59.075 37.037 0.00 0.00 37.65 2.90
1932 2489 5.820423 TCAGCACCATAAACAAACGCTATAT 59.180 36.000 0.00 0.00 0.00 0.86
1943 2500 2.813754 TCAGCAGTTCAGCACCATAAAC 59.186 45.455 0.00 0.00 36.85 2.01
1944 2501 3.138884 TCAGCAGTTCAGCACCATAAA 57.861 42.857 0.00 0.00 36.85 1.40
2035 2593 8.902540 TTCCACAGGCTTTTATATACAGTATG 57.097 34.615 3.03 0.00 46.00 2.39
2048 2606 3.026694 GCCTCATAATTCCACAGGCTTT 58.973 45.455 9.38 0.00 45.40 3.51
2091 2650 1.391485 CTTCGCGACAGGTTGAAGATG 59.609 52.381 9.15 0.00 40.12 2.90
2105 2664 4.320667 TGTTATTGTGTTCATCTTCGCG 57.679 40.909 0.00 0.00 0.00 5.87
2120 2679 9.388506 CTTATGAAGACCTCAACTCATGTTATT 57.611 33.333 0.00 0.00 37.67 1.40
2134 2693 6.882768 AAATCACCTCTCTTATGAAGACCT 57.117 37.500 0.00 0.00 33.12 3.85
2526 3090 6.126409 ACATTAGGTCAAAGACAAACCTTGA 58.874 36.000 0.00 0.00 40.53 3.02
2596 3160 6.130058 GCGAATAGTTTCTATGCAGCTTTAC 58.870 40.000 0.00 0.00 0.00 2.01
2646 3210 5.412640 CAATCAAGATAATTGCTGCAACCA 58.587 37.500 18.51 8.71 0.00 3.67
2648 3212 5.653507 TCCAATCAAGATAATTGCTGCAAC 58.346 37.500 18.51 4.85 33.65 4.17
2726 3290 4.927267 TTCCTGGACAACAAGGATACAT 57.073 40.909 0.00 0.00 41.41 2.29
2806 3371 6.757897 ACTGAAACTGAGTGATTTGTCAAA 57.242 33.333 0.00 0.00 0.00 2.69
2811 3376 7.251704 AGTGTTACTGAAACTGAGTGATTTG 57.748 36.000 0.00 0.00 38.99 2.32
2933 3498 9.639601 CTTACATAAAGGATTTCAAAAAGACCC 57.360 33.333 0.00 0.00 40.09 4.46
3014 3579 2.679059 CGCACAAGTCCCAGAATCAGAT 60.679 50.000 0.00 0.00 0.00 2.90
3039 3604 2.483745 CATGCTGTGAAGCCTGCG 59.516 61.111 0.00 0.00 32.52 5.18
3088 3653 4.226761 GCCGTACTGTGAAATTTTTCCAG 58.773 43.478 14.59 14.59 39.36 3.86
3430 3996 5.972107 ACATCAGACTGAAAAGGAAATGG 57.028 39.130 9.70 0.00 0.00 3.16
3464 4030 8.782339 ATTAACGGTGCTAATACTGTTTAGTT 57.218 30.769 8.23 0.00 45.33 2.24
3506 4073 7.835682 TCAAGTCATCAACCATATTCTTTGGAT 59.164 33.333 0.00 0.00 37.69 3.41
3614 4181 6.127730 CCATACAAGGGGAAAGTTTCACATAC 60.128 42.308 19.28 2.52 33.74 2.39
3631 4198 3.067106 AGCGTTCAACACTCCATACAAG 58.933 45.455 0.00 0.00 0.00 3.16
3634 4201 2.412847 GCAAGCGTTCAACACTCCATAC 60.413 50.000 0.00 0.00 0.00 2.39
3803 4372 5.049474 CACAATACAGCAGTTTAGCTTGTCA 60.049 40.000 0.00 0.00 43.70 3.58
3804 4373 5.049405 ACACAATACAGCAGTTTAGCTTGTC 60.049 40.000 0.00 0.00 43.70 3.18
3847 4428 7.165485 ACTGGTTATGCACAAGTAGAAATACA 58.835 34.615 0.00 0.00 37.98 2.29
3855 4436 3.868369 GCTGGACTGGTTATGCACAAGTA 60.868 47.826 0.00 0.00 40.14 2.24
3856 4437 2.783135 CTGGACTGGTTATGCACAAGT 58.217 47.619 0.00 0.00 43.15 3.16
3946 4554 8.694975 ATTCTTTCGATAATCCACGATATCTG 57.305 34.615 0.34 0.00 38.30 2.90
4028 4636 6.610075 AAGGGAAAACAAATACTGCATCAT 57.390 33.333 0.00 0.00 0.00 2.45
4062 4670 1.150135 AGTCAAGGAGGGTCCAGAGAA 59.850 52.381 0.00 0.00 39.61 2.87
4063 4671 0.787084 AGTCAAGGAGGGTCCAGAGA 59.213 55.000 0.00 0.00 39.61 3.10
4084 4692 4.192317 CAGAGCCCATAAGTACTTTCCAC 58.808 47.826 14.49 0.57 0.00 4.02
4136 4744 2.029828 GGTACATCGCTATCTGACCCAG 60.030 54.545 0.00 0.00 0.00 4.45
4167 4775 1.464997 CTTTCTTCCCTTTCTTCGGCG 59.535 52.381 0.00 0.00 0.00 6.46
4205 4813 0.732880 ACCTCATGTCGTTTCTCGCG 60.733 55.000 0.00 0.00 39.67 5.87
4207 4815 2.947852 AGAACCTCATGTCGTTTCTCG 58.052 47.619 0.00 0.00 41.41 4.04
4209 4817 3.665190 GGAAGAACCTCATGTCGTTTCT 58.335 45.455 0.00 0.00 35.41 2.52
4230 4838 4.022329 GGATCAAAACTGTAAACCCACCAG 60.022 45.833 0.00 0.00 0.00 4.00
4235 4843 3.509967 CCCTGGATCAAAACTGTAAACCC 59.490 47.826 0.00 0.00 0.00 4.11
4244 4852 7.001073 AGAATAGAATAGCCCTGGATCAAAAC 58.999 38.462 0.00 0.00 0.00 2.43
4250 4858 5.165652 TCCAAGAATAGAATAGCCCTGGAT 58.834 41.667 0.00 0.00 0.00 3.41
4283 4891 1.127567 AGGTCTGCAGGTAAGTGGCA 61.128 55.000 15.13 0.00 35.96 4.92
4306 4914 1.338769 GCCTACTGTTTCCGTCATGGT 60.339 52.381 0.00 0.00 39.52 3.55
4307 4915 1.338674 TGCCTACTGTTTCCGTCATGG 60.339 52.381 0.00 0.00 40.09 3.66
4314 4922 5.644644 CATGAATTTCTGCCTACTGTTTCC 58.355 41.667 0.00 0.00 0.00 3.13
4411 5020 4.520492 AGGAGGCAATTGAAACTACACAAG 59.480 41.667 10.34 0.00 0.00 3.16
4431 5041 3.901844 ACACAGAGTAAGCTAACCAAGGA 59.098 43.478 0.00 0.00 0.00 3.36
4442 5052 7.878477 TCATTAAACGGTTACACAGAGTAAG 57.122 36.000 0.00 0.00 43.06 2.34
4453 5063 8.826710 CATCTTTCTAGCATCATTAAACGGTTA 58.173 33.333 0.00 0.00 0.00 2.85
4519 5129 4.278310 ACAAACAAAGGAGGCTAAAGTGT 58.722 39.130 0.00 0.00 0.00 3.55
4520 5130 4.918810 ACAAACAAAGGAGGCTAAAGTG 57.081 40.909 0.00 0.00 0.00 3.16
4521 5131 4.953579 TCAACAAACAAAGGAGGCTAAAGT 59.046 37.500 0.00 0.00 0.00 2.66
4522 5132 5.514274 TCAACAAACAAAGGAGGCTAAAG 57.486 39.130 0.00 0.00 0.00 1.85
4523 5133 5.596361 TCATCAACAAACAAAGGAGGCTAAA 59.404 36.000 0.00 0.00 0.00 1.85
4524 5134 5.136828 TCATCAACAAACAAAGGAGGCTAA 58.863 37.500 0.00 0.00 0.00 3.09
4525 5135 4.724399 TCATCAACAAACAAAGGAGGCTA 58.276 39.130 0.00 0.00 0.00 3.93
4527 5137 3.305608 CCTCATCAACAAACAAAGGAGGC 60.306 47.826 0.00 0.00 34.84 4.70
4528 5138 3.891366 ACCTCATCAACAAACAAAGGAGG 59.109 43.478 0.00 0.00 44.78 4.30
4533 5143 5.788450 ACACAAACCTCATCAACAAACAAA 58.212 33.333 0.00 0.00 0.00 2.83
4534 5144 5.398603 ACACAAACCTCATCAACAAACAA 57.601 34.783 0.00 0.00 0.00 2.83
4535 5145 4.142271 GGACACAAACCTCATCAACAAACA 60.142 41.667 0.00 0.00 0.00 2.83
4536 5146 4.142271 TGGACACAAACCTCATCAACAAAC 60.142 41.667 0.00 0.00 0.00 2.93
4541 5151 2.174639 AGGTGGACACAAACCTCATCAA 59.825 45.455 4.69 0.00 43.52 2.57
4548 5158 1.156736 CGATGAGGTGGACACAAACC 58.843 55.000 4.69 0.00 36.66 3.27
4549 5159 1.156736 CCGATGAGGTGGACACAAAC 58.843 55.000 4.69 0.00 34.51 2.93
4550 5160 0.605319 GCCGATGAGGTGGACACAAA 60.605 55.000 4.69 0.00 43.70 2.83
4551 5161 1.003839 GCCGATGAGGTGGACACAA 60.004 57.895 4.69 0.00 43.70 3.33
4552 5162 1.913262 AGCCGATGAGGTGGACACA 60.913 57.895 4.69 0.00 43.70 3.72
4553 5163 1.448540 CAGCCGATGAGGTGGACAC 60.449 63.158 0.00 0.00 43.70 3.67
4554 5164 2.981302 CAGCCGATGAGGTGGACA 59.019 61.111 0.00 0.00 43.70 4.02
4555 5165 2.512515 GCAGCCGATGAGGTGGAC 60.513 66.667 0.00 0.00 43.70 4.02
4556 5166 1.841302 AAAGCAGCCGATGAGGTGGA 61.841 55.000 0.00 0.00 43.70 4.02
4557 5167 1.372087 GAAAGCAGCCGATGAGGTGG 61.372 60.000 0.00 0.00 43.70 4.61
4584 5357 6.292757 GGATGACGATTGAATCTCATCAGTTG 60.293 42.308 28.23 8.66 41.03 3.16
4585 5358 5.757320 GGATGACGATTGAATCTCATCAGTT 59.243 40.000 28.23 10.73 41.03 3.16
4586 5359 5.295950 GGATGACGATTGAATCTCATCAGT 58.704 41.667 28.23 12.52 41.03 3.41
4587 5360 4.689812 GGGATGACGATTGAATCTCATCAG 59.310 45.833 28.23 10.21 41.03 2.90
4600 5373 5.770162 AGAAAGAAAAACTTGGGATGACGAT 59.230 36.000 0.00 0.00 38.98 3.73
4651 5460 5.247337 ACAAGTTGGGTTGGAGAAAGAAAAA 59.753 36.000 7.96 0.00 0.00 1.94
4667 5476 0.974383 ACGGAGGGAGTACAAGTTGG 59.026 55.000 7.96 0.00 0.00 3.77
4674 5483 8.854117 TCTTATATTTTAGAACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
4677 5486 7.953752 AGTCTTATATTTTAGAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
4678 5487 7.909485 AGTCTTATATTTTAGAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
4695 5504 8.813951 CCCTCCGTTCCTAAATATAAGTCTTAT 58.186 37.037 9.98 9.98 0.00 1.73
4696 5505 8.006564 TCCCTCCGTTCCTAAATATAAGTCTTA 58.993 37.037 0.00 0.00 0.00 2.10
4697 5506 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4698 5507 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4699 5508 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4700 5509 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4701 5510 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4702 5511 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
4703 5512 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
4704 5513 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4705 5514 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4706 5515 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4707 5516 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4708 5517 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
4709 5518 4.662179 TCTTATCTACTCCCTCCGTTCCTA 59.338 45.833 0.00 0.00 0.00 2.94
4710 5519 3.462579 TCTTATCTACTCCCTCCGTTCCT 59.537 47.826 0.00 0.00 0.00 3.36
4711 5520 3.830121 TCTTATCTACTCCCTCCGTTCC 58.170 50.000 0.00 0.00 0.00 3.62
4712 5521 5.774630 CAATCTTATCTACTCCCTCCGTTC 58.225 45.833 0.00 0.00 0.00 3.95
4713 5522 4.039366 GCAATCTTATCTACTCCCTCCGTT 59.961 45.833 0.00 0.00 0.00 4.44
4714 5523 3.574826 GCAATCTTATCTACTCCCTCCGT 59.425 47.826 0.00 0.00 0.00 4.69
4715 5524 3.574396 TGCAATCTTATCTACTCCCTCCG 59.426 47.826 0.00 0.00 0.00 4.63
4716 5525 5.247110 TCATGCAATCTTATCTACTCCCTCC 59.753 44.000 0.00 0.00 0.00 4.30
4717 5526 6.352016 TCATGCAATCTTATCTACTCCCTC 57.648 41.667 0.00 0.00 0.00 4.30
4718 5527 6.709281 CATCATGCAATCTTATCTACTCCCT 58.291 40.000 0.00 0.00 0.00 4.20
4719 5528 5.353678 GCATCATGCAATCTTATCTACTCCC 59.646 44.000 4.20 0.00 44.26 4.30
4720 5529 6.419980 GCATCATGCAATCTTATCTACTCC 57.580 41.667 4.20 0.00 44.26 3.85
4764 5573 0.945265 TACGTCGGGCCAAAAACGAG 60.945 55.000 20.56 9.67 37.30 4.18
4771 5580 1.406539 GAGTTAGATACGTCGGGCCAA 59.593 52.381 4.39 0.00 0.00 4.52
4773 5582 1.316651 AGAGTTAGATACGTCGGGCC 58.683 55.000 0.00 0.00 0.00 5.80
4774 5583 2.098770 ACAAGAGTTAGATACGTCGGGC 59.901 50.000 0.00 0.00 0.00 6.13
4775 5584 4.367386 AACAAGAGTTAGATACGTCGGG 57.633 45.455 0.00 0.00 35.85 5.14
4796 5634 4.820775 AGGGATTGGTTAGAGATGCTCTA 58.179 43.478 0.22 0.22 41.50 2.43
4820 5658 9.706846 GTCAAAATGAGGAATTGAAAGTTTTTG 57.293 29.630 0.00 0.00 35.07 2.44
4823 5661 9.101655 CTTGTCAAAATGAGGAATTGAAAGTTT 57.898 29.630 0.00 0.00 35.07 2.66
4825 5663 7.785033 ACTTGTCAAAATGAGGAATTGAAAGT 58.215 30.769 0.00 0.00 35.07 2.66
4826 5664 8.652810 AACTTGTCAAAATGAGGAATTGAAAG 57.347 30.769 0.00 0.00 35.07 2.62
4829 5667 8.141268 GGTTAACTTGTCAAAATGAGGAATTGA 58.859 33.333 5.42 0.00 0.00 2.57
4830 5668 7.925483 TGGTTAACTTGTCAAAATGAGGAATTG 59.075 33.333 5.42 0.00 0.00 2.32
4846 5684 6.231211 AGATCAACTAGGTGTGGTTAACTTG 58.769 40.000 7.85 0.00 0.00 3.16
4847 5685 6.270231 AGAGATCAACTAGGTGTGGTTAACTT 59.730 38.462 7.85 0.00 0.00 2.66
4864 5702 7.447594 ACTCCTTTAACGGTTTAAGAGATCAA 58.552 34.615 18.31 0.00 29.85 2.57
4914 5837 1.268352 CAGATAGGTCGAGTAGCTGCC 59.732 57.143 6.98 0.00 37.13 4.85
4916 5839 3.002862 GTGACAGATAGGTCGAGTAGCTG 59.997 52.174 15.24 15.24 40.72 4.24
4929 5852 1.191535 CCGGGAAGTGGTGACAGATA 58.808 55.000 0.00 0.00 44.46 1.98
4933 5856 4.308458 CGCCGGGAAGTGGTGACA 62.308 66.667 2.18 0.00 39.39 3.58
4958 5881 1.717791 AATCATGCGCATCGGTGGTG 61.718 55.000 22.51 9.50 0.00 4.17
4959 5882 1.031571 AAATCATGCGCATCGGTGGT 61.032 50.000 22.51 3.79 0.00 4.16
4961 5884 0.377905 TGAAATCATGCGCATCGGTG 59.622 50.000 22.51 11.63 0.00 4.94
4962 5885 0.659427 CTGAAATCATGCGCATCGGT 59.341 50.000 22.51 9.91 0.00 4.69
4965 5888 0.659417 CGGCTGAAATCATGCGCATC 60.659 55.000 22.51 10.81 0.00 3.91
4966 5889 1.357690 CGGCTGAAATCATGCGCAT 59.642 52.632 19.28 19.28 0.00 4.73
4967 5890 2.763273 CCGGCTGAAATCATGCGCA 61.763 57.895 14.96 14.96 0.00 6.09
4968 5891 1.992233 TTCCGGCTGAAATCATGCGC 61.992 55.000 0.00 0.00 0.00 6.09
4969 5892 0.664761 ATTCCGGCTGAAATCATGCG 59.335 50.000 0.00 0.00 36.33 4.73
4971 5894 2.300433 TCCATTCCGGCTGAAATCATG 58.700 47.619 0.00 0.00 36.33 3.07
4972 5895 2.689983 GTTCCATTCCGGCTGAAATCAT 59.310 45.455 0.00 0.00 36.33 2.45
4973 5896 2.091541 GTTCCATTCCGGCTGAAATCA 58.908 47.619 0.00 0.00 36.33 2.57
4974 5897 1.405463 GGTTCCATTCCGGCTGAAATC 59.595 52.381 0.00 0.00 36.33 2.17
4975 5898 1.474330 GGTTCCATTCCGGCTGAAAT 58.526 50.000 0.00 0.00 36.33 2.17
4976 5899 0.958382 CGGTTCCATTCCGGCTGAAA 60.958 55.000 0.00 0.00 43.68 2.69
4977 5900 1.376683 CGGTTCCATTCCGGCTGAA 60.377 57.895 0.00 0.00 43.68 3.02
4978 5901 2.267642 CGGTTCCATTCCGGCTGA 59.732 61.111 0.00 0.00 43.68 4.26
4979 5902 3.508840 GCGGTTCCATTCCGGCTG 61.509 66.667 0.00 0.00 46.90 4.85
4980 5903 3.561120 TTGCGGTTCCATTCCGGCT 62.561 57.895 0.00 0.00 46.90 5.52
4981 5904 3.051392 CTTGCGGTTCCATTCCGGC 62.051 63.158 0.00 0.25 46.90 6.13
4982 5905 0.748005 ATCTTGCGGTTCCATTCCGG 60.748 55.000 0.00 0.00 46.90 5.14
5020 5943 1.597663 GCGATAGGTTGGTCAATTCCG 59.402 52.381 0.00 0.00 0.00 4.30
5073 5996 2.690778 GGCGGCTCGAAGCATGTTT 61.691 57.895 0.00 0.00 44.75 2.83


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

AutoCloner maintained by Alex Coulton.