Multiple sequence alignment - TraesCS5B01G374400

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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 TraesCS5B01G374400 chr5B 100.000 4431 0 0 1 4431 551674453 551678883 0.000000e+00 8183.0
1 TraesCS5B01G374400 chr5B 87.349 166 15 3 2339 2504 60810003 60810162 7.570000e-43 185.0
2 TraesCS5B01G374400 chr5D 93.476 2943 133 21 843 3754 451905276 451908190 0.000000e+00 4316.0
3 TraesCS5B01G374400 chr5D 85.272 808 58 26 1 792 451904497 451905259 0.000000e+00 776.0
4 TraesCS5B01G374400 chr5D 91.703 229 18 1 3897 4124 451908466 451908694 2.570000e-82 316.0
5 TraesCS5B01G374400 chr5D 91.912 136 11 0 4162 4297 451908758 451908893 1.630000e-44 191.0
6 TraesCS5B01G374400 chr5D 90.426 94 7 1 3803 3896 451908267 451908358 6.020000e-24 122.0
7 TraesCS5B01G374400 chr5A 90.013 3014 204 39 768 3754 570774159 570777102 0.000000e+00 3808.0
8 TraesCS5B01G374400 chr5A 86.829 410 37 11 3891 4299 570777463 570777856 4.070000e-120 442.0
9 TraesCS5B01G374400 chr5A 78.208 491 49 13 2339 2817 45927944 45927500 1.220000e-65 261.0
10 TraesCS5B01G374400 chr5A 79.394 165 22 8 214 375 640684080 640683925 6.060000e-19 106.0
11 TraesCS5B01G374400 chr5A 93.878 49 3 0 4337 4385 570777876 570777924 1.710000e-09 75.0
12 TraesCS5B01G374400 chr1A 81.503 519 51 14 2339 2835 82126721 82126226 6.950000e-103 385.0
13 TraesCS5B01G374400 chr1A 85.000 60 9 0 2548 2607 82126413 82126354 1.330000e-05 62.1
14 TraesCS5B01G374400 chr3B 83.047 407 41 8 2339 2742 758404327 758403946 1.180000e-90 344.0
15 TraesCS5B01G374400 chr3A 83.088 408 39 12 2339 2742 53327630 53327249 1.180000e-90 344.0


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 TraesCS5B01G374400 chr5B 551674453 551678883 4430 False 8183.000000 8183 100.0000 1 4431 1 chr5B.!!$F2 4430
1 TraesCS5B01G374400 chr5D 451904497 451908893 4396 False 1144.200000 4316 90.5578 1 4297 5 chr5D.!!$F1 4296
2 TraesCS5B01G374400 chr5A 570774159 570777924 3765 False 1441.666667 3808 90.2400 768 4385 3 chr5A.!!$F1 3617

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
781 796 0.114168 CCTCCCTCCCTCGATCTGAT 59.886 60.0 0.0 0.0 0.0 2.90 F
1700 1722 0.109342 CCAGCACCTTGTCTTGTCCT 59.891 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2140 0.694771 ACTCCTCCTGCAGCATGAAA 59.305 50.000 8.66 0.0 39.69 2.69 R
3606 3640 1.228245 GTGCAGGAAACAGGAGCCA 60.228 57.895 0.00 0.0 0.00 4.75 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
70 71 1.102978 CCCCCAAACACCGATGATTC 58.897 55.000 0.00 0.00 0.00 2.52
77 78 0.895530 ACACCGATGATTCGTGTCCT 59.104 50.000 0.00 0.00 43.97 3.85
78 79 1.275291 ACACCGATGATTCGTGTCCTT 59.725 47.619 0.00 0.00 43.97 3.36
80 81 1.200483 CCGATGATTCGTGTCCTTCG 58.800 55.000 0.00 0.00 43.97 3.79
81 82 1.469251 CCGATGATTCGTGTCCTTCGT 60.469 52.381 0.00 0.00 43.97 3.85
83 84 1.846782 GATGATTCGTGTCCTTCGTCG 59.153 52.381 0.00 0.00 0.00 5.12
84 85 0.594602 TGATTCGTGTCCTTCGTCGT 59.405 50.000 0.00 0.00 0.00 4.34
95 99 1.076332 CTTCGTCGTCCCCAAATGAC 58.924 55.000 0.00 0.00 32.82 3.06
102 106 2.907696 TCGTCCCCAAATGACTTTCCTA 59.092 45.455 0.00 0.00 0.00 2.94
105 109 4.814771 CGTCCCCAAATGACTTTCCTATAC 59.185 45.833 0.00 0.00 0.00 1.47
106 110 5.396436 CGTCCCCAAATGACTTTCCTATACT 60.396 44.000 0.00 0.00 0.00 2.12
141 154 3.038280 TGGATAACATGGTCCGACTCAT 58.962 45.455 0.00 0.00 37.32 2.90
160 173 9.651718 CGACTCATTTTTAATACTAGATTTGCC 57.348 33.333 0.00 0.00 0.00 4.52
202 215 7.945134 ACAATATGACATCTTTCCAAATAGCC 58.055 34.615 0.00 0.00 0.00 3.93
205 218 4.191544 TGACATCTTTCCAAATAGCCTCG 58.808 43.478 0.00 0.00 0.00 4.63
210 223 5.007385 TCTTTCCAAATAGCCTCGTCTAC 57.993 43.478 0.00 0.00 0.00 2.59
226 239 5.343249 TCGTCTACGGTAGGAATTTTTAGC 58.657 41.667 14.82 0.00 40.29 3.09
227 240 4.505556 CGTCTACGGTAGGAATTTTTAGCC 59.494 45.833 14.82 0.00 35.37 3.93
235 248 8.048514 ACGGTAGGAATTTTTAGCCTATGTTAA 58.951 33.333 0.00 0.00 36.72 2.01
283 298 6.131961 AGAAAAACAAGGCATATATGAGGCT 58.868 36.000 17.10 5.13 43.06 4.58
319 334 8.833493 GTTCTAGCTTGAACAAAGGTAAACTTA 58.167 33.333 28.63 0.00 45.71 2.24
320 335 8.967664 TCTAGCTTGAACAAAGGTAAACTTAA 57.032 30.769 0.00 0.00 45.71 1.85
321 336 8.833493 TCTAGCTTGAACAAAGGTAAACTTAAC 58.167 33.333 0.00 0.00 45.71 2.01
322 337 7.640597 AGCTTGAACAAAGGTAAACTTAACT 57.359 32.000 0.00 0.00 44.77 2.24
323 338 7.704271 AGCTTGAACAAAGGTAAACTTAACTC 58.296 34.615 0.00 0.00 44.77 3.01
465 480 2.375174 TCATAAAGGCTGGTGGTGTCTT 59.625 45.455 0.00 0.00 0.00 3.01
466 481 3.157087 CATAAAGGCTGGTGGTGTCTTT 58.843 45.455 0.00 0.00 0.00 2.52
467 482 2.159179 AAAGGCTGGTGGTGTCTTTT 57.841 45.000 0.00 0.00 0.00 2.27
505 520 5.896073 TTTTTAGGGGATTTTGAGGCAAA 57.104 34.783 0.00 0.00 0.00 3.68
506 521 6.446909 TTTTTAGGGGATTTTGAGGCAAAT 57.553 33.333 0.00 0.00 33.19 2.32
542 557 0.603065 AAAAGAACCATCGGGCTTGC 59.397 50.000 0.00 0.00 37.90 4.01
587 602 2.272230 TTTGACCCGTCACCAAGGCA 62.272 55.000 0.00 0.00 39.66 4.75
588 603 2.668550 GACCCGTCACCAAGGCAC 60.669 66.667 0.00 0.00 0.00 5.01
589 604 4.265056 ACCCGTCACCAAGGCACC 62.265 66.667 0.00 0.00 0.00 5.01
590 605 4.263572 CCCGTCACCAAGGCACCA 62.264 66.667 0.00 0.00 0.00 4.17
591 606 2.978010 CCGTCACCAAGGCACCAC 60.978 66.667 0.00 0.00 0.00 4.16
592 607 2.978010 CGTCACCAAGGCACCACC 60.978 66.667 0.00 0.00 39.61 4.61
593 608 2.194597 GTCACCAAGGCACCACCA 59.805 61.111 0.00 0.00 43.14 4.17
601 616 1.042559 AAGGCACCACCAACCAACAG 61.043 55.000 0.00 0.00 43.14 3.16
651 666 3.842923 CGTCAGGATCTGCCGCCT 61.843 66.667 0.00 0.00 43.43 5.52
705 720 3.805307 CTCTCAGCCGCTCGACGT 61.805 66.667 0.00 0.00 41.42 4.34
760 775 3.322466 CCGCAGGTCAACCTCCCT 61.322 66.667 0.00 0.00 46.65 4.20
761 776 2.750350 CGCAGGTCAACCTCCCTT 59.250 61.111 0.00 0.00 46.65 3.95
764 779 1.492993 GCAGGTCAACCTCCCTTCCT 61.493 60.000 0.00 0.00 46.65 3.36
781 796 0.114168 CCTCCCTCCCTCGATCTGAT 59.886 60.000 0.00 0.00 0.00 2.90
839 855 2.440796 CTGCGTGCCATCCCCATT 60.441 61.111 0.00 0.00 0.00 3.16
840 856 2.037049 TGCGTGCCATCCCCATTT 59.963 55.556 0.00 0.00 0.00 2.32
841 857 1.606885 CTGCGTGCCATCCCCATTTT 61.607 55.000 0.00 0.00 0.00 1.82
867 883 3.456105 GAACCGCCTACCATCCCCG 62.456 68.421 0.00 0.00 0.00 5.73
881 897 1.772979 CCCCGCCCCTAAACCCTAT 60.773 63.158 0.00 0.00 0.00 2.57
907 923 0.548031 TCCCCTCTTATTGCAGGCAG 59.452 55.000 0.00 0.00 0.00 4.85
924 940 1.144057 AGCAACCGGAATCTAGGCG 59.856 57.895 9.46 0.00 0.00 5.52
927 943 0.529992 CAACCGGAATCTAGGCGGAC 60.530 60.000 9.46 0.00 0.00 4.79
963 979 4.566070 CCACCGGAATTGGAAAACCTAGTA 60.566 45.833 9.46 0.00 36.02 1.82
965 981 4.287845 ACCGGAATTGGAAAACCTAGTAGT 59.712 41.667 9.46 0.00 0.00 2.73
966 982 4.874396 CCGGAATTGGAAAACCTAGTAGTC 59.126 45.833 0.00 0.00 0.00 2.59
967 983 4.874396 CGGAATTGGAAAACCTAGTAGTCC 59.126 45.833 0.00 0.00 0.00 3.85
1005 1021 1.080093 GAACTCACCGTCGATGGCA 60.080 57.895 23.85 9.59 0.00 4.92
1101 1117 1.758592 CGAGGTTGGTTCCCTTCCA 59.241 57.895 0.00 0.00 30.60 3.53
1110 1126 1.617322 GTTCCCTTCCAACCCTCAAC 58.383 55.000 0.00 0.00 0.00 3.18
1177 1194 1.666872 GTGGGGTCCGTTCGTCTTG 60.667 63.158 0.00 0.00 0.00 3.02
1185 1202 0.874175 CCGTTCGTCTTGTGTGCTCA 60.874 55.000 0.00 0.00 0.00 4.26
1301 1320 7.120285 CCAAATGTTCATCTATGTGAGTGTTCT 59.880 37.037 0.00 0.00 0.00 3.01
1302 1321 8.509690 CAAATGTTCATCTATGTGAGTGTTCTT 58.490 33.333 0.00 0.00 0.00 2.52
1313 1332 3.933332 GTGAGTGTTCTTATCTTTCCCCG 59.067 47.826 0.00 0.00 0.00 5.73
1387 1407 3.666797 CGCCGTTAAAAGTTTGGATTGTC 59.333 43.478 0.00 0.00 0.00 3.18
1407 1427 9.979578 GATTGTCTATCTGTATCTGAACTGAAT 57.020 33.333 0.00 0.00 32.08 2.57
1487 1507 3.670625 TGGCAACATAGTGGTACAGTTC 58.329 45.455 0.00 0.00 40.56 3.01
1516 1538 5.106908 GCAAGCTGGTTTCTACTTTCTAGTG 60.107 44.000 0.00 0.00 35.78 2.74
1556 1578 4.445385 GGCTGCACTGAACACTTAATTTTG 59.555 41.667 0.50 0.00 0.00 2.44
1584 1606 3.997021 AGTTTAACTGGCTGATCAACTCG 59.003 43.478 0.00 0.00 0.00 4.18
1645 1667 3.774766 AGATATGTGTGGTGCTAACTGGA 59.225 43.478 0.00 0.00 0.00 3.86
1648 1670 1.696884 TGTGTGGTGCTAACTGGATGA 59.303 47.619 0.00 0.00 0.00 2.92
1700 1722 0.109342 CCAGCACCTTGTCTTGTCCT 59.891 55.000 0.00 0.00 0.00 3.85
1760 1782 7.357532 GCAATTACTCACAAAAGTGTCATTTCG 60.358 37.037 0.00 0.00 35.07 3.46
1769 1791 7.111593 CACAAAAGTGTCATTTCGCTTTACTAC 59.888 37.037 5.83 0.00 44.07 2.73
1845 1874 8.764287 CATTTCAATGGTTAAAAAGAAGGTGAC 58.236 33.333 0.00 0.00 32.78 3.67
1950 1979 3.498397 CCATGTGCCTAACCACGATATTC 59.502 47.826 0.00 0.00 38.55 1.75
2001 2030 0.455410 TTTGCATATGCGGCTGAACC 59.545 50.000 22.21 0.00 45.83 3.62
2111 2140 7.106239 CCACTGTATTGAAGTGATACCTCTTT 58.894 38.462 5.17 0.00 46.55 2.52
2181 2210 5.444663 AATTTCTTGAGCAACACTTCCTC 57.555 39.130 0.00 0.00 0.00 3.71
2204 2233 3.492383 ACGATGCTGATAGATTTTGAGCG 59.508 43.478 0.00 0.00 32.05 5.03
2593 2622 6.061441 TGTTCTTTCTGGAAATCTAGCACAA 58.939 36.000 0.00 0.00 0.00 3.33
2598 2627 8.641541 TCTTTCTGGAAATCTAGCACAATTTTT 58.358 29.630 0.00 0.00 0.00 1.94
2734 2765 7.951530 ACCTTTTCTTGAATTATTGCTGTTG 57.048 32.000 0.00 0.00 0.00 3.33
2806 2837 3.311871 GCAGGACTAGCATTGAAGACATG 59.688 47.826 0.00 0.00 0.00 3.21
3006 3039 8.585881 TGACTAAGTAGCAGTTGAGTTCTTATT 58.414 33.333 0.00 0.00 0.00 1.40
3019 3052 5.586243 TGAGTTCTTATTACTCCATTGCTGC 59.414 40.000 0.00 0.00 41.02 5.25
3254 3288 0.979187 AGGCCCGAATCGAACCCTTA 60.979 55.000 3.36 0.00 0.00 2.69
3351 3385 5.357314 GTGCTTTCTTCTTATTACCCTTCCC 59.643 44.000 0.00 0.00 0.00 3.97
3401 3435 3.650281 TGCAGCTGAAGGAATGGAATA 57.350 42.857 20.43 0.00 0.00 1.75
3446 3480 4.042187 ACCATTGAGCTTCTCTGGTTACTT 59.958 41.667 5.62 0.00 36.17 2.24
3495 3529 4.682778 AGCTTTGTGTGGTTGTAGAGTA 57.317 40.909 0.00 0.00 0.00 2.59
3498 3532 5.054477 GCTTTGTGTGGTTGTAGAGTAGAA 58.946 41.667 0.00 0.00 0.00 2.10
3501 3535 5.864418 TGTGTGGTTGTAGAGTAGAAGTT 57.136 39.130 0.00 0.00 0.00 2.66
3589 3623 1.597663 GTTGCAAGACGTAGCTGTTGT 59.402 47.619 0.00 0.00 0.00 3.32
3594 3628 3.486875 GCAAGACGTAGCTGTTGTGTTTT 60.487 43.478 0.00 0.00 0.00 2.43
3598 3632 3.753842 ACGTAGCTGTTGTGTTTTTGTG 58.246 40.909 0.00 0.00 0.00 3.33
3606 3640 5.557325 GCTGTTGTGTTTTTGTGTTTTCGTT 60.557 36.000 0.00 0.00 0.00 3.85
3608 3642 4.974103 TGTGTTTTTGTGTTTTCGTTGG 57.026 36.364 0.00 0.00 0.00 3.77
3640 3674 2.756760 CTGCACCCATAGTTGATGCTTT 59.243 45.455 0.00 0.00 37.20 3.51
3641 3675 2.492881 TGCACCCATAGTTGATGCTTTG 59.507 45.455 0.00 0.00 37.20 2.77
3642 3676 2.736400 GCACCCATAGTTGATGCTTTGC 60.736 50.000 0.00 0.00 33.79 3.68
3645 3679 3.834231 ACCCATAGTTGATGCTTTGCTTT 59.166 39.130 0.00 0.00 33.79 3.51
3646 3680 5.016173 ACCCATAGTTGATGCTTTGCTTTA 58.984 37.500 0.00 0.00 33.79 1.85
3647 3681 5.126061 ACCCATAGTTGATGCTTTGCTTTAG 59.874 40.000 0.00 0.00 33.79 1.85
3648 3682 5.126061 CCCATAGTTGATGCTTTGCTTTAGT 59.874 40.000 0.00 0.00 33.79 2.24
3649 3683 6.032094 CCATAGTTGATGCTTTGCTTTAGTG 58.968 40.000 0.00 0.00 33.79 2.74
3676 3725 3.077359 GTTCCATGTTCTCCCTTGACAG 58.923 50.000 0.00 0.00 0.00 3.51
3696 3746 5.227152 ACAGTTGTTTTTCAGTTTGGTGTC 58.773 37.500 0.00 0.00 0.00 3.67
3711 3761 4.111255 TGGTGTCCCAATTCTTCATGAA 57.889 40.909 8.12 8.12 37.98 2.57
3715 3765 6.043012 TGGTGTCCCAATTCTTCATGAAAAAT 59.957 34.615 9.88 5.31 37.98 1.82
3754 3805 4.343526 TGCATGTGTTCCCAAAATTACTGT 59.656 37.500 0.00 0.00 0.00 3.55
3755 3806 4.685628 GCATGTGTTCCCAAAATTACTGTG 59.314 41.667 0.00 0.00 0.00 3.66
3756 3807 4.314740 TGTGTTCCCAAAATTACTGTGC 57.685 40.909 0.00 0.00 0.00 4.57
3757 3808 3.068873 TGTGTTCCCAAAATTACTGTGCC 59.931 43.478 0.00 0.00 0.00 5.01
3761 3812 5.777732 TGTTCCCAAAATTACTGTGCCTATT 59.222 36.000 0.00 0.00 0.00 1.73
3764 3815 8.474831 GTTCCCAAAATTACTGTGCCTATTTAT 58.525 33.333 0.00 0.00 0.00 1.40
3765 3816 9.702253 TTCCCAAAATTACTGTGCCTATTTATA 57.298 29.630 0.00 0.00 0.00 0.98
3790 3951 8.877808 AAGGATTTTGAATCTGAAGTTGAAAC 57.122 30.769 1.21 0.00 0.00 2.78
3791 3952 8.010733 AGGATTTTGAATCTGAAGTTGAAACA 57.989 30.769 0.00 0.00 0.00 2.83
3792 3953 8.477256 AGGATTTTGAATCTGAAGTTGAAACAA 58.523 29.630 0.00 0.00 0.00 2.83
3793 3954 9.097257 GGATTTTGAATCTGAAGTTGAAACAAA 57.903 29.630 0.00 0.00 0.00 2.83
3810 3971 6.809689 TGAAACAAATATCAAGATTGCTGCAG 59.190 34.615 10.11 10.11 0.00 4.41
3954 4239 2.927553 GCTGTTAGCAACTGGGATTG 57.072 50.000 0.00 0.00 41.89 2.67
3992 4277 3.117512 GGATCTAATCATGGTGGGGTGTT 60.118 47.826 0.00 0.00 0.00 3.32
3996 4281 0.323725 ATCATGGTGGGGTGTTGAGC 60.324 55.000 0.00 0.00 0.00 4.26
4013 4298 2.515523 CCTGGAGGGAATGCAGCG 60.516 66.667 0.00 0.00 45.53 5.18
4016 4301 2.899339 GGAGGGAATGCAGCGAGC 60.899 66.667 0.00 0.00 45.96 5.03
4035 4320 1.517242 CAAGGTGACCAAGTGCTCTC 58.483 55.000 3.63 0.00 0.00 3.20
4038 4323 0.321122 GGTGACCAAGTGCTCTCCAG 60.321 60.000 0.00 0.00 0.00 3.86
4094 4381 1.153756 AAGCTGGGGTTCACCAAGG 59.846 57.895 0.00 0.00 41.06 3.61
4124 4411 2.291741 CAGGCAAAACCAGACTCTGTTC 59.708 50.000 5.32 0.00 43.14 3.18
4125 4412 2.173569 AGGCAAAACCAGACTCTGTTCT 59.826 45.455 5.32 0.00 43.14 3.01
4127 4414 3.206150 GCAAAACCAGACTCTGTTCTCA 58.794 45.455 5.32 0.00 0.00 3.27
4128 4415 3.249559 GCAAAACCAGACTCTGTTCTCAG 59.750 47.826 5.32 0.00 42.54 3.35
4130 4417 4.329462 AAACCAGACTCTGTTCTCAGTC 57.671 45.455 5.32 0.00 41.91 3.51
4132 4419 1.548269 CCAGACTCTGTTCTCAGTCCC 59.452 57.143 5.32 0.00 41.91 4.46
4133 4420 2.242926 CAGACTCTGTTCTCAGTCCCA 58.757 52.381 0.00 0.00 41.91 4.37
4134 4421 2.630098 CAGACTCTGTTCTCAGTCCCAA 59.370 50.000 0.00 0.00 41.91 4.12
4137 4424 4.349342 AGACTCTGTTCTCAGTCCCAAAAT 59.651 41.667 0.00 0.00 41.91 1.82
4138 4425 5.544176 AGACTCTGTTCTCAGTCCCAAAATA 59.456 40.000 0.00 0.00 41.91 1.40
4140 4427 6.234177 ACTCTGTTCTCAGTCCCAAAATAAG 58.766 40.000 0.00 0.00 41.91 1.73
4141 4428 6.183361 ACTCTGTTCTCAGTCCCAAAATAAGT 60.183 38.462 0.00 0.00 41.91 2.24
4142 4429 5.997746 TCTGTTCTCAGTCCCAAAATAAGTG 59.002 40.000 0.00 0.00 41.91 3.16
4143 4430 5.690865 TGTTCTCAGTCCCAAAATAAGTGT 58.309 37.500 0.00 0.00 0.00 3.55
4145 4432 4.566004 TCTCAGTCCCAAAATAAGTGTCG 58.434 43.478 0.00 0.00 0.00 4.35
4146 4433 4.039973 TCTCAGTCCCAAAATAAGTGTCGT 59.960 41.667 0.00 0.00 0.00 4.34
4147 4434 4.710324 TCAGTCCCAAAATAAGTGTCGTT 58.290 39.130 0.00 0.00 0.00 3.85
4148 4435 4.513692 TCAGTCCCAAAATAAGTGTCGTTG 59.486 41.667 0.00 0.00 0.00 4.10
4154 4470 4.274950 CCAAAATAAGTGTCGTTGACAGGT 59.725 41.667 0.00 0.00 43.57 4.00
4172 4488 1.594331 GTGTTCTCCTCGCCTTTTGT 58.406 50.000 0.00 0.00 0.00 2.83
4189 4505 5.402270 CCTTTTGTGTGCATAGTTAGTTTGC 59.598 40.000 0.00 0.00 36.91 3.68
4223 4539 7.875041 TCAGTCTCAAGTCTGAATTTTAGGAAG 59.125 37.037 4.77 0.00 37.30 3.46
4224 4540 7.659390 CAGTCTCAAGTCTGAATTTTAGGAAGT 59.341 37.037 0.00 0.00 33.96 3.01
4300 4616 6.903883 AATTCTCATTTTGCATGATGAAGC 57.096 33.333 12.04 0.00 32.33 3.86
4301 4617 4.023739 TCTCATTTTGCATGATGAAGCG 57.976 40.909 12.04 3.71 32.33 4.68
4302 4618 2.532235 TCATTTTGCATGATGAAGCGC 58.468 42.857 0.00 0.00 29.82 5.92
4303 4619 1.591158 CATTTTGCATGATGAAGCGCC 59.409 47.619 2.29 0.00 0.00 6.53
4304 4620 0.889994 TTTTGCATGATGAAGCGCCT 59.110 45.000 2.29 0.00 0.00 5.52
4306 4622 0.961857 TTGCATGATGAAGCGCCTGT 60.962 50.000 2.29 0.00 0.00 4.00
4307 4623 1.063649 GCATGATGAAGCGCCTGTG 59.936 57.895 2.29 0.00 0.00 3.66
4308 4624 1.063649 CATGATGAAGCGCCTGTGC 59.936 57.895 2.29 0.00 0.00 4.57
4310 4626 1.374343 ATGATGAAGCGCCTGTGCTG 61.374 55.000 2.29 0.00 46.60 4.41
4311 4627 3.392595 GATGAAGCGCCTGTGCTGC 62.393 63.158 2.29 4.72 46.60 5.25
4318 4634 3.123620 GCCTGTGCTGCCGAAGAG 61.124 66.667 0.00 0.00 33.53 2.85
4319 4635 2.435586 CCTGTGCTGCCGAAGAGG 60.436 66.667 0.00 0.00 44.97 3.69
4320 4636 2.345244 CTGTGCTGCCGAAGAGGT 59.655 61.111 0.00 0.00 43.70 3.85
4321 4637 1.739562 CTGTGCTGCCGAAGAGGTC 60.740 63.158 0.00 0.00 43.70 3.85
4354 4670 1.593196 CTTGGGCGAAAGTTGACTGA 58.407 50.000 0.00 0.00 0.00 3.41
4385 4701 9.126151 CTCACAGAAGGTAAGATCAAGATAGTA 57.874 37.037 0.00 0.00 0.00 1.82
4386 4702 8.904834 TCACAGAAGGTAAGATCAAGATAGTAC 58.095 37.037 0.00 0.00 0.00 2.73
4387 4703 8.908903 CACAGAAGGTAAGATCAAGATAGTACT 58.091 37.037 0.00 0.00 0.00 2.73
4388 4704 8.908903 ACAGAAGGTAAGATCAAGATAGTACTG 58.091 37.037 5.39 0.00 0.00 2.74
4389 4705 8.908903 CAGAAGGTAAGATCAAGATAGTACTGT 58.091 37.037 5.39 0.00 0.00 3.55
4390 4706 9.482175 AGAAGGTAAGATCAAGATAGTACTGTT 57.518 33.333 5.39 0.00 0.00 3.16
4392 4708 9.877178 AAGGTAAGATCAAGATAGTACTGTTTG 57.123 33.333 5.39 7.48 0.00 2.93
4393 4709 7.982354 AGGTAAGATCAAGATAGTACTGTTTGC 59.018 37.037 5.39 0.00 0.00 3.68
4394 4710 7.982354 GGTAAGATCAAGATAGTACTGTTTGCT 59.018 37.037 5.39 0.00 0.00 3.91
4396 4712 8.934507 AAGATCAAGATAGTACTGTTTGCTAC 57.065 34.615 5.39 3.21 0.00 3.58
4397 4713 8.299990 AGATCAAGATAGTACTGTTTGCTACT 57.700 34.615 5.39 5.06 0.00 2.57
4398 4714 8.194104 AGATCAAGATAGTACTGTTTGCTACTG 58.806 37.037 5.39 0.00 0.00 2.74
4399 4715 7.462571 TCAAGATAGTACTGTTTGCTACTGA 57.537 36.000 5.39 0.00 0.00 3.41
4400 4716 7.539436 TCAAGATAGTACTGTTTGCTACTGAG 58.461 38.462 5.39 0.00 0.00 3.35
4401 4717 7.176865 TCAAGATAGTACTGTTTGCTACTGAGT 59.823 37.037 5.39 0.00 0.00 3.41
4402 4718 7.469537 AGATAGTACTGTTTGCTACTGAGTT 57.530 36.000 5.39 0.00 0.00 3.01
4403 4719 7.897864 AGATAGTACTGTTTGCTACTGAGTTT 58.102 34.615 5.39 0.00 0.00 2.66
4404 4720 8.368668 AGATAGTACTGTTTGCTACTGAGTTTT 58.631 33.333 5.39 0.00 0.00 2.43
4405 4721 6.846325 AGTACTGTTTGCTACTGAGTTTTC 57.154 37.500 0.00 0.00 0.00 2.29
4406 4722 6.583562 AGTACTGTTTGCTACTGAGTTTTCT 58.416 36.000 0.00 0.00 0.00 2.52
4407 4723 7.048512 AGTACTGTTTGCTACTGAGTTTTCTT 58.951 34.615 0.00 0.00 0.00 2.52
4408 4724 6.124088 ACTGTTTGCTACTGAGTTTTCTTG 57.876 37.500 0.00 0.00 0.00 3.02
4409 4725 4.920376 TGTTTGCTACTGAGTTTTCTTGC 58.080 39.130 0.00 0.00 0.00 4.01
4410 4726 3.878086 TTGCTACTGAGTTTTCTTGCG 57.122 42.857 0.00 0.00 0.00 4.85
4411 4727 2.143122 TGCTACTGAGTTTTCTTGCGG 58.857 47.619 0.00 0.00 0.00 5.69
4412 4728 1.464997 GCTACTGAGTTTTCTTGCGGG 59.535 52.381 0.00 0.00 0.00 6.13
4413 4729 1.464997 CTACTGAGTTTTCTTGCGGGC 59.535 52.381 0.00 0.00 0.00 6.13
4414 4730 1.172812 ACTGAGTTTTCTTGCGGGCC 61.173 55.000 0.00 0.00 0.00 5.80
4415 4731 0.890996 CTGAGTTTTCTTGCGGGCCT 60.891 55.000 0.84 0.00 0.00 5.19
4416 4732 0.889186 TGAGTTTTCTTGCGGGCCTC 60.889 55.000 0.84 0.00 0.00 4.70
4417 4733 0.889186 GAGTTTTCTTGCGGGCCTCA 60.889 55.000 0.84 0.00 0.00 3.86
4418 4734 0.251341 AGTTTTCTTGCGGGCCTCAT 60.251 50.000 0.84 0.00 0.00 2.90
4419 4735 0.603065 GTTTTCTTGCGGGCCTCATT 59.397 50.000 0.84 0.00 0.00 2.57
4420 4736 1.816224 GTTTTCTTGCGGGCCTCATTA 59.184 47.619 0.84 0.00 0.00 1.90
4421 4737 2.427095 GTTTTCTTGCGGGCCTCATTAT 59.573 45.455 0.84 0.00 0.00 1.28
4422 4738 3.569194 TTTCTTGCGGGCCTCATTATA 57.431 42.857 0.84 0.00 0.00 0.98
4423 4739 3.788227 TTCTTGCGGGCCTCATTATAT 57.212 42.857 0.84 0.00 0.00 0.86
4424 4740 3.788227 TCTTGCGGGCCTCATTATATT 57.212 42.857 0.84 0.00 0.00 1.28
4425 4741 3.674997 TCTTGCGGGCCTCATTATATTC 58.325 45.455 0.84 0.00 0.00 1.75
4426 4742 2.093306 TGCGGGCCTCATTATATTCG 57.907 50.000 0.84 0.00 0.00 3.34
4427 4743 1.346395 TGCGGGCCTCATTATATTCGT 59.654 47.619 0.84 0.00 0.00 3.85
4428 4744 2.000447 GCGGGCCTCATTATATTCGTC 59.000 52.381 0.84 0.00 0.00 4.20
4429 4745 2.259618 CGGGCCTCATTATATTCGTCG 58.740 52.381 0.84 0.00 0.00 5.12
4430 4746 2.094906 CGGGCCTCATTATATTCGTCGA 60.095 50.000 0.84 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.178921 TGGGGGTGCCAAATGCTAAA 60.179 50.000 0.00 0.00 42.00 1.85
40 41 1.461075 TTTGGGGGTGCCAAATGCT 60.461 52.632 0.00 0.00 42.00 3.79
41 42 1.302431 GTTTGGGGGTGCCAAATGC 60.302 57.895 0.00 0.00 39.00 3.56
42 43 0.250252 GTGTTTGGGGGTGCCAAATG 60.250 55.000 0.00 0.00 39.00 2.32
43 44 1.414866 GGTGTTTGGGGGTGCCAAAT 61.415 55.000 0.00 0.00 39.00 2.32
44 45 2.066999 GGTGTTTGGGGGTGCCAAA 61.067 57.895 0.00 0.00 35.21 3.28
45 46 2.444895 GGTGTTTGGGGGTGCCAA 60.445 61.111 0.00 0.00 0.00 4.52
46 47 4.904590 CGGTGTTTGGGGGTGCCA 62.905 66.667 0.00 0.00 0.00 4.92
47 48 3.879180 ATCGGTGTTTGGGGGTGCC 62.879 63.158 0.00 0.00 0.00 5.01
48 49 2.282887 ATCGGTGTTTGGGGGTGC 60.283 61.111 0.00 0.00 0.00 5.01
49 50 0.323360 ATCATCGGTGTTTGGGGGTG 60.323 55.000 0.00 0.00 0.00 4.61
50 51 0.407918 AATCATCGGTGTTTGGGGGT 59.592 50.000 0.00 0.00 0.00 4.95
51 52 1.102978 GAATCATCGGTGTTTGGGGG 58.897 55.000 0.00 0.00 0.00 5.40
70 71 2.126580 GGGACGACGAAGGACACG 60.127 66.667 0.00 0.00 0.00 4.49
77 78 0.682852 AGTCATTTGGGGACGACGAA 59.317 50.000 0.00 0.00 40.20 3.85
78 79 0.682852 AAGTCATTTGGGGACGACGA 59.317 50.000 0.00 0.00 40.20 4.20
80 81 1.810755 GGAAAGTCATTTGGGGACGAC 59.189 52.381 0.00 0.00 40.20 4.34
81 82 1.702957 AGGAAAGTCATTTGGGGACGA 59.297 47.619 0.00 0.00 40.20 4.20
83 84 5.823045 CAGTATAGGAAAGTCATTTGGGGAC 59.177 44.000 0.00 0.00 35.50 4.46
84 85 5.631481 GCAGTATAGGAAAGTCATTTGGGGA 60.631 44.000 0.00 0.00 0.00 4.81
95 99 5.543507 AGGACATGAGCAGTATAGGAAAG 57.456 43.478 0.00 0.00 0.00 2.62
165 178 9.601217 AAGATGTCATATTGTTACTAGTTCCAC 57.399 33.333 0.00 0.00 0.00 4.02
180 193 6.652481 CGAGGCTATTTGGAAAGATGTCATAT 59.348 38.462 0.00 0.00 0.00 1.78
181 194 5.991606 CGAGGCTATTTGGAAAGATGTCATA 59.008 40.000 0.00 0.00 0.00 2.15
183 196 4.191544 CGAGGCTATTTGGAAAGATGTCA 58.808 43.478 0.00 0.00 0.00 3.58
184 197 4.192317 ACGAGGCTATTTGGAAAGATGTC 58.808 43.478 0.00 0.00 0.00 3.06
185 198 4.080863 AGACGAGGCTATTTGGAAAGATGT 60.081 41.667 0.00 0.00 0.00 3.06
202 215 5.458126 GCTAAAAATTCCTACCGTAGACGAG 59.542 44.000 7.16 0.00 43.02 4.18
205 218 5.668471 AGGCTAAAAATTCCTACCGTAGAC 58.332 41.667 7.16 0.00 0.00 2.59
210 223 6.937436 AACATAGGCTAAAAATTCCTACCG 57.063 37.500 0.00 0.00 35.50 4.02
260 273 6.396829 AGCCTCATATATGCCTTGTTTTTC 57.603 37.500 7.92 0.00 0.00 2.29
283 298 6.061441 TGTTCAAGCTAGAACCAGAAATGAA 58.939 36.000 0.00 0.00 45.62 2.57
427 442 9.260002 GCCTTTATGATTTGTCTCAAAGAAAAA 57.740 29.630 1.67 0.00 36.02 1.94
428 443 8.641541 AGCCTTTATGATTTGTCTCAAAGAAAA 58.358 29.630 1.67 0.00 0.00 2.29
432 447 6.071728 ACCAGCCTTTATGATTTGTCTCAAAG 60.072 38.462 1.67 0.00 0.00 2.77
436 451 4.096984 CCACCAGCCTTTATGATTTGTCTC 59.903 45.833 0.00 0.00 0.00 3.36
449 464 2.159179 AAAAAGACACCACCAGCCTT 57.841 45.000 0.00 0.00 0.00 4.35
483 498 5.896073 TTTGCCTCAAAATCCCCTAAAAA 57.104 34.783 0.00 0.00 29.89 1.94
487 502 4.329638 TGATTTGCCTCAAAATCCCCTA 57.670 40.909 7.08 0.00 43.13 3.53
488 503 3.188880 TGATTTGCCTCAAAATCCCCT 57.811 42.857 7.08 0.00 43.13 4.79
489 504 4.499696 CGTATGATTTGCCTCAAAATCCCC 60.500 45.833 7.08 0.00 43.13 4.81
490 505 4.338118 TCGTATGATTTGCCTCAAAATCCC 59.662 41.667 7.08 0.00 43.13 3.85
491 506 5.499139 TCGTATGATTTGCCTCAAAATCC 57.501 39.130 7.08 0.00 43.13 3.01
492 507 5.514279 CCTCGTATGATTTGCCTCAAAATC 58.486 41.667 3.29 3.29 43.76 2.17
493 508 4.202050 GCCTCGTATGATTTGCCTCAAAAT 60.202 41.667 0.00 0.00 36.90 1.82
494 509 3.128589 GCCTCGTATGATTTGCCTCAAAA 59.871 43.478 0.00 0.00 36.90 2.44
495 510 2.682856 GCCTCGTATGATTTGCCTCAAA 59.317 45.455 0.00 0.00 37.75 2.69
496 511 2.288666 GCCTCGTATGATTTGCCTCAA 58.711 47.619 0.00 0.00 0.00 3.02
497 512 1.475034 GGCCTCGTATGATTTGCCTCA 60.475 52.381 0.00 0.00 35.99 3.86
498 513 1.230324 GGCCTCGTATGATTTGCCTC 58.770 55.000 0.00 0.00 35.99 4.70
499 514 0.179018 GGGCCTCGTATGATTTGCCT 60.179 55.000 0.84 0.00 38.89 4.75
500 515 1.507141 CGGGCCTCGTATGATTTGCC 61.507 60.000 0.84 10.38 38.16 4.52
501 516 0.531974 TCGGGCCTCGTATGATTTGC 60.532 55.000 0.84 0.00 40.32 3.68
502 517 1.217882 GTCGGGCCTCGTATGATTTG 58.782 55.000 0.84 0.00 40.32 2.32
503 518 0.106149 GGTCGGGCCTCGTATGATTT 59.894 55.000 0.84 0.00 40.32 2.17
504 519 1.046472 TGGTCGGGCCTCGTATGATT 61.046 55.000 0.84 0.00 40.32 2.57
505 520 1.046472 TTGGTCGGGCCTCGTATGAT 61.046 55.000 0.84 0.00 40.32 2.45
506 521 1.259142 TTTGGTCGGGCCTCGTATGA 61.259 55.000 0.84 0.00 40.32 2.15
542 557 3.233578 CCGATGTTCCGACACAAAATTG 58.766 45.455 0.00 0.00 38.91 2.32
587 602 2.123468 GGGCTGTTGGTTGGTGGT 60.123 61.111 0.00 0.00 0.00 4.16
588 603 3.294493 CGGGCTGTTGGTTGGTGG 61.294 66.667 0.00 0.00 0.00 4.61
589 604 3.977244 GCGGGCTGTTGGTTGGTG 61.977 66.667 0.00 0.00 0.00 4.17
636 651 2.364186 TGAGGCGGCAGATCCTGA 60.364 61.111 13.08 0.00 32.44 3.86
651 666 4.314440 GAGCAGGGCACGGTGTGA 62.314 66.667 10.24 0.00 35.23 3.58
758 773 0.830023 GATCGAGGGAGGGAGGAAGG 60.830 65.000 0.00 0.00 0.00 3.46
759 774 0.187361 AGATCGAGGGAGGGAGGAAG 59.813 60.000 0.00 0.00 0.00 3.46
760 775 0.105964 CAGATCGAGGGAGGGAGGAA 60.106 60.000 0.00 0.00 0.00 3.36
761 776 0.994050 TCAGATCGAGGGAGGGAGGA 60.994 60.000 0.00 0.00 0.00 3.71
764 779 3.612795 TTTATCAGATCGAGGGAGGGA 57.387 47.619 0.00 0.00 0.00 4.20
826 842 1.153588 CGCAAAATGGGGATGGCAC 60.154 57.895 0.00 0.00 0.00 5.01
827 843 3.296851 CGCAAAATGGGGATGGCA 58.703 55.556 0.00 0.00 0.00 4.92
835 851 1.079888 GGTTCTGCCCGCAAAATGG 60.080 57.895 0.00 0.00 0.00 3.16
836 852 1.444212 CGGTTCTGCCCGCAAAATG 60.444 57.895 0.00 0.00 41.78 2.32
837 853 2.961768 CGGTTCTGCCCGCAAAAT 59.038 55.556 0.00 0.00 41.78 1.82
867 883 5.262009 GGATAATTGATAGGGTTTAGGGGC 58.738 45.833 0.00 0.00 0.00 5.80
868 884 5.281558 GGGGATAATTGATAGGGTTTAGGGG 60.282 48.000 0.00 0.00 0.00 4.79
881 897 5.634118 CCTGCAATAAGAGGGGATAATTGA 58.366 41.667 0.00 0.00 30.77 2.57
907 923 1.887707 CCGCCTAGATTCCGGTTGC 60.888 63.158 0.00 0.00 37.36 4.17
910 926 2.132352 GGTCCGCCTAGATTCCGGT 61.132 63.158 0.00 0.00 42.48 5.28
911 927 2.735237 GGTCCGCCTAGATTCCGG 59.265 66.667 0.00 0.00 43.21 5.14
950 966 2.181975 CCGGGACTACTAGGTTTTCCA 58.818 52.381 0.00 0.00 43.73 3.53
1063 1079 1.516423 GGGAGAAGGCCGTGAGTAC 59.484 63.158 0.00 0.00 0.00 2.73
1101 1117 4.675029 CCGGCGTCGTTGAGGGTT 62.675 66.667 9.28 0.00 33.95 4.11
1120 1136 2.224314 AGCTTTTTCACTAGTCAAGCGC 59.776 45.455 0.00 0.00 43.82 5.92
1121 1137 4.458708 GAAGCTTTTTCACTAGTCAAGCG 58.541 43.478 0.00 0.00 43.82 4.68
1122 1138 4.458708 CGAAGCTTTTTCACTAGTCAAGC 58.541 43.478 0.00 13.95 40.20 4.01
1123 1139 4.083802 CCCGAAGCTTTTTCACTAGTCAAG 60.084 45.833 0.00 0.00 0.00 3.02
1124 1140 3.813166 CCCGAAGCTTTTTCACTAGTCAA 59.187 43.478 0.00 0.00 0.00 3.18
1125 1141 3.399330 CCCGAAGCTTTTTCACTAGTCA 58.601 45.455 0.00 0.00 0.00 3.41
1126 1142 2.159824 GCCCGAAGCTTTTTCACTAGTC 59.840 50.000 0.00 0.00 38.99 2.59
1127 1143 2.152016 GCCCGAAGCTTTTTCACTAGT 58.848 47.619 0.00 0.00 38.99 2.57
1155 1171 2.091102 GACGAACGGACCCCACTCAA 62.091 60.000 0.00 0.00 0.00 3.02
1164 1180 0.874607 AGCACACAAGACGAACGGAC 60.875 55.000 0.00 0.00 0.00 4.79
1177 1194 4.634883 AGTCAATTCATCTCATGAGCACAC 59.365 41.667 18.36 5.72 40.94 3.82
1185 1202 7.984050 AGAATAACACGAGTCAATTCATCTCAT 59.016 33.333 17.22 0.93 34.73 2.90
1268 1287 6.599244 CACATAGATGAACATTTGGTACAGGT 59.401 38.462 0.00 0.00 42.39 4.00
1301 1320 2.640826 ACTGTGAACCGGGGAAAGATAA 59.359 45.455 6.32 0.00 0.00 1.75
1302 1321 2.262637 ACTGTGAACCGGGGAAAGATA 58.737 47.619 6.32 0.00 0.00 1.98
1313 1332 6.166982 AGAGATTTAGCAGTAACTGTGAACC 58.833 40.000 0.00 0.00 33.43 3.62
1407 1427 9.847224 AAAGGAAAACAGATCAGAAGTTAAGTA 57.153 29.630 0.00 0.00 0.00 2.24
1450 1470 1.469703 TGCCATGCAAAGACTTGATCG 59.530 47.619 0.00 0.00 34.76 3.69
1487 1507 0.874390 TAGAAACCAGCTTGCGCAAG 59.126 50.000 39.20 39.20 41.24 4.01
1516 1538 5.232838 GTGCAGCCTTAAATATTTGCATCAC 59.767 40.000 11.05 12.27 42.64 3.06
1556 1578 3.045601 TCAGCCAGTTAAACTCTGCTC 57.954 47.619 0.00 0.00 32.78 4.26
1611 1633 5.983720 ACCACACATATCTAGAAATGTACGC 59.016 40.000 0.00 0.00 34.61 4.42
1615 1637 5.994250 AGCACCACACATATCTAGAAATGT 58.006 37.500 0.00 0.00 36.78 2.71
1645 1667 9.676861 TTTCTGAAGATAAGATTGTGTCATCAT 57.323 29.630 0.00 0.00 0.00 2.45
1648 1670 8.853077 TGTTTCTGAAGATAAGATTGTGTCAT 57.147 30.769 0.00 0.00 0.00 3.06
1708 1730 9.607285 CACAGTTTACAAGTAATACAATTCCAC 57.393 33.333 0.00 0.00 0.00 4.02
1760 1782 1.702491 CCCAAGGCGCGTAGTAAAGC 61.702 60.000 8.43 0.00 0.00 3.51
1845 1874 5.859114 CCTGCACTATACAGTTATTAGCTCG 59.141 44.000 0.00 0.00 33.09 5.03
2083 2112 4.332819 GGTATCACTTCAATACAGTGGCAC 59.667 45.833 10.29 10.29 41.83 5.01
2089 2118 9.219603 TGAAAAAGAGGTATCACTTCAATACAG 57.780 33.333 0.00 0.00 32.35 2.74
2111 2140 0.694771 ACTCCTCCTGCAGCATGAAA 59.305 50.000 8.66 0.00 39.69 2.69
2139 2168 7.544566 AGAAATTACTTCTATTTCGTCGCAGAA 59.455 33.333 0.00 0.00 42.90 3.02
2181 2210 4.607778 CGCTCAAAATCTATCAGCATCGTG 60.608 45.833 0.00 0.00 0.00 4.35
2204 2233 3.658757 TTATGTTGAGCCCAAAAGTGC 57.341 42.857 0.00 0.00 33.49 4.40
2452 2481 7.816031 CGTGTGGTCCTATTTCTTAAAAGAGTA 59.184 37.037 0.00 0.00 36.22 2.59
2453 2482 6.649557 CGTGTGGTCCTATTTCTTAAAAGAGT 59.350 38.462 0.00 0.00 36.22 3.24
2593 2622 8.539544 TCTGGAGAAAGGAAAAACAAGAAAAAT 58.460 29.630 0.00 0.00 0.00 1.82
2598 2627 5.755849 ACTCTGGAGAAAGGAAAAACAAGA 58.244 37.500 4.49 0.00 0.00 3.02
2747 2778 7.715249 GCTGTCATCCCAAGTAAACTATATTGA 59.285 37.037 0.00 0.00 0.00 2.57
2806 2837 9.454859 TTCTTCTCCTTTGATATCCTTTCTTTC 57.545 33.333 0.00 0.00 0.00 2.62
3006 3039 1.533625 GTGTTGGCAGCAATGGAGTA 58.466 50.000 5.34 0.00 0.00 2.59
3019 3052 4.491234 TTGCAACTAAATACCGTGTTGG 57.509 40.909 0.00 0.00 46.41 3.77
3265 3299 7.396540 ACATCTCTTGTGTCATTAAAATCCC 57.603 36.000 0.00 0.00 37.11 3.85
3272 3306 4.864806 GCGAGAACATCTCTTGTGTCATTA 59.135 41.667 5.88 0.00 41.26 1.90
3294 3328 4.453177 AGACCTAAAGTAAGACCTTCGC 57.547 45.455 0.00 0.00 0.00 4.70
3351 3385 5.126061 AGTCCCAGGAAATCGAATGAAAATG 59.874 40.000 0.00 0.00 0.00 2.32
3401 3435 1.373812 TGCAGCTCTGACATGCAGT 59.626 52.632 14.21 0.00 44.56 4.40
3495 3529 3.306641 GCATGACTCCTGACTCAACTTCT 60.307 47.826 0.00 0.00 0.00 2.85
3498 3532 2.233431 GAGCATGACTCCTGACTCAACT 59.767 50.000 0.00 0.00 39.75 3.16
3546 3580 5.050091 ACTCAGAAACAAAATCACGCTACAG 60.050 40.000 0.00 0.00 0.00 2.74
3589 3623 3.654414 AGCCAACGAAAACACAAAAACA 58.346 36.364 0.00 0.00 0.00 2.83
3594 3628 1.403679 CAGGAGCCAACGAAAACACAA 59.596 47.619 0.00 0.00 0.00 3.33
3598 3632 2.543031 GGAAACAGGAGCCAACGAAAAC 60.543 50.000 0.00 0.00 0.00 2.43
3606 3640 1.228245 GTGCAGGAAACAGGAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
3608 3642 1.973812 GGGTGCAGGAAACAGGAGC 60.974 63.158 0.00 0.00 34.98 4.70
3640 3674 1.771854 TGGAACCAGGACACTAAAGCA 59.228 47.619 0.00 0.00 0.00 3.91
3641 3675 2.561478 TGGAACCAGGACACTAAAGC 57.439 50.000 0.00 0.00 0.00 3.51
3642 3676 4.021102 ACATGGAACCAGGACACTAAAG 57.979 45.455 12.42 0.00 0.00 1.85
3645 3679 3.248024 AGAACATGGAACCAGGACACTA 58.752 45.455 12.42 0.00 0.00 2.74
3646 3680 2.039084 GAGAACATGGAACCAGGACACT 59.961 50.000 12.42 7.75 0.00 3.55
3647 3681 2.427506 GAGAACATGGAACCAGGACAC 58.572 52.381 12.42 3.54 0.00 3.67
3648 3682 1.351017 GGAGAACATGGAACCAGGACA 59.649 52.381 12.42 0.00 0.00 4.02
3649 3683 1.340114 GGGAGAACATGGAACCAGGAC 60.340 57.143 12.42 6.04 0.00 3.85
3676 3725 3.930229 GGGACACCAAACTGAAAAACAAC 59.070 43.478 0.00 0.00 36.50 3.32
3696 3746 4.637091 GGGCATTTTTCATGAAGAATTGGG 59.363 41.667 18.80 10.94 35.83 4.12
3701 3751 5.804944 TCTTGGGCATTTTTCATGAAGAA 57.195 34.783 13.25 13.25 0.00 2.52
3764 3815 9.965824 GTTTCAACTTCAGATTCAAAATCCTTA 57.034 29.630 0.00 0.00 0.00 2.69
3765 3816 8.477256 TGTTTCAACTTCAGATTCAAAATCCTT 58.523 29.630 0.00 0.00 0.00 3.36
3810 3971 2.486472 ATGGCTATGCTATGGAGTGC 57.514 50.000 0.00 0.00 0.00 4.40
3937 4222 5.279406 CCAATTTCAATCCCAGTTGCTAACA 60.279 40.000 0.00 0.00 0.00 2.41
3954 4239 4.890158 AGATCCCAAACCAACCAATTTC 57.110 40.909 0.00 0.00 0.00 2.17
3992 4277 1.918467 CTGCATTCCCTCCAGGCTCA 61.918 60.000 0.00 0.00 34.51 4.26
3996 4281 2.515523 CGCTGCATTCCCTCCAGG 60.516 66.667 0.00 0.00 0.00 4.45
4013 4298 0.536006 AGCACTTGGTCACCTTGCTC 60.536 55.000 11.29 0.00 39.32 4.26
4016 4301 1.517242 GAGAGCACTTGGTCACCTTG 58.483 55.000 10.86 0.00 44.42 3.61
4017 4302 0.398318 GGAGAGCACTTGGTCACCTT 59.602 55.000 15.22 0.00 45.57 3.50
4038 4323 1.462670 CGTCTCCAAAGAAGCTGCTTC 59.537 52.381 30.02 30.02 40.45 3.86
4111 4398 2.243810 GGACTGAGAACAGAGTCTGGT 58.756 52.381 23.79 18.55 46.03 4.00
4124 4411 4.315803 ACGACACTTATTTTGGGACTGAG 58.684 43.478 0.00 0.00 0.00 3.35
4125 4412 4.345859 ACGACACTTATTTTGGGACTGA 57.654 40.909 0.00 0.00 0.00 3.41
4127 4414 4.514066 GTCAACGACACTTATTTTGGGACT 59.486 41.667 0.00 0.00 32.09 3.85
4128 4415 4.273969 TGTCAACGACACTTATTTTGGGAC 59.726 41.667 0.00 0.00 37.67 4.46
4130 4417 4.320202 CCTGTCAACGACACTTATTTTGGG 60.320 45.833 0.00 0.00 37.67 4.12
4132 4419 5.204833 CACCTGTCAACGACACTTATTTTG 58.795 41.667 0.00 0.00 37.67 2.44
4133 4420 4.879545 ACACCTGTCAACGACACTTATTTT 59.120 37.500 0.00 0.00 37.67 1.82
4134 4421 4.448210 ACACCTGTCAACGACACTTATTT 58.552 39.130 0.00 0.00 37.67 1.40
4137 4424 3.131577 AGAACACCTGTCAACGACACTTA 59.868 43.478 0.00 0.00 37.67 2.24
4138 4425 2.093658 AGAACACCTGTCAACGACACTT 60.094 45.455 0.00 0.00 37.67 3.16
4140 4427 1.859080 GAGAACACCTGTCAACGACAC 59.141 52.381 0.00 0.00 37.67 3.67
4141 4428 1.202486 GGAGAACACCTGTCAACGACA 60.202 52.381 0.00 0.00 40.50 4.35
4142 4429 1.068741 AGGAGAACACCTGTCAACGAC 59.931 52.381 0.00 0.00 39.01 4.34
4143 4430 1.340248 GAGGAGAACACCTGTCAACGA 59.660 52.381 0.00 0.00 40.73 3.85
4145 4432 1.784525 CGAGGAGAACACCTGTCAAC 58.215 55.000 0.00 0.00 40.73 3.18
4146 4433 0.033504 GCGAGGAGAACACCTGTCAA 59.966 55.000 0.00 0.00 40.73 3.18
4147 4434 1.666011 GCGAGGAGAACACCTGTCA 59.334 57.895 0.00 0.00 40.73 3.58
4148 4435 1.079750 GGCGAGGAGAACACCTGTC 60.080 63.158 0.00 0.00 40.73 3.51
4154 4470 1.134220 ACACAAAAGGCGAGGAGAACA 60.134 47.619 0.00 0.00 0.00 3.18
4172 4488 4.893608 TCTGAGCAAACTAACTATGCACA 58.106 39.130 0.00 0.00 42.45 4.57
4223 4539 6.318900 CCACTCCATCTTACAGGGAAATTAAC 59.681 42.308 0.00 0.00 0.00 2.01
4224 4540 6.423182 CCACTCCATCTTACAGGGAAATTAA 58.577 40.000 0.00 0.00 0.00 1.40
4301 4617 3.123620 CTCTTCGGCAGCACAGGC 61.124 66.667 0.00 0.00 41.61 4.85
4302 4618 2.435586 CCTCTTCGGCAGCACAGG 60.436 66.667 0.00 0.00 0.00 4.00
4303 4619 1.739562 GACCTCTTCGGCAGCACAG 60.740 63.158 0.00 0.00 35.61 3.66
4304 4620 2.343758 GACCTCTTCGGCAGCACA 59.656 61.111 0.00 0.00 35.61 4.57
4327 4643 4.697756 TTCGCCCAAGCCGAGGTG 62.698 66.667 0.00 0.00 34.57 4.00
4328 4644 3.901797 CTTTCGCCCAAGCCGAGGT 62.902 63.158 0.00 0.00 34.57 3.85
4329 4645 3.127533 CTTTCGCCCAAGCCGAGG 61.128 66.667 0.00 0.00 34.57 4.63
4330 4646 1.966451 AACTTTCGCCCAAGCCGAG 60.966 57.895 0.00 0.00 34.57 4.63
4331 4647 2.112297 AACTTTCGCCCAAGCCGA 59.888 55.556 0.00 0.00 34.57 5.54
4332 4648 2.255252 CAACTTTCGCCCAAGCCG 59.745 61.111 0.00 0.00 34.57 5.52
4333 4649 1.172812 AGTCAACTTTCGCCCAAGCC 61.173 55.000 0.00 0.00 34.57 4.35
4334 4650 0.040067 CAGTCAACTTTCGCCCAAGC 60.040 55.000 0.00 0.00 0.00 4.01
4335 4651 1.593196 TCAGTCAACTTTCGCCCAAG 58.407 50.000 0.00 0.00 0.00 3.61
4336 4652 2.270352 ATCAGTCAACTTTCGCCCAA 57.730 45.000 0.00 0.00 0.00 4.12
4337 4653 2.151202 GAATCAGTCAACTTTCGCCCA 58.849 47.619 0.00 0.00 0.00 5.36
4338 4654 2.095718 GTGAATCAGTCAACTTTCGCCC 60.096 50.000 0.00 0.00 38.23 6.13
4339 4655 2.808543 AGTGAATCAGTCAACTTTCGCC 59.191 45.455 5.09 0.00 38.23 5.54
4340 4656 3.494626 TGAGTGAATCAGTCAACTTTCGC 59.505 43.478 17.57 0.00 40.33 4.70
4341 4657 4.507756 TGTGAGTGAATCAGTCAACTTTCG 59.492 41.667 20.99 0.00 44.06 3.46
4342 4658 5.755375 TCTGTGAGTGAATCAGTCAACTTTC 59.245 40.000 20.99 9.91 44.06 2.62
4354 4670 6.611613 TGATCTTACCTTCTGTGAGTGAAT 57.388 37.500 0.00 0.00 32.58 2.57
4385 4701 5.449177 GCAAGAAAACTCAGTAGCAAACAGT 60.449 40.000 0.00 0.00 0.00 3.55
4386 4702 4.972440 GCAAGAAAACTCAGTAGCAAACAG 59.028 41.667 0.00 0.00 0.00 3.16
4387 4703 4.495679 CGCAAGAAAACTCAGTAGCAAACA 60.496 41.667 0.00 0.00 43.02 2.83
4388 4704 3.968724 CGCAAGAAAACTCAGTAGCAAAC 59.031 43.478 0.00 0.00 43.02 2.93
4389 4705 3.003275 CCGCAAGAAAACTCAGTAGCAAA 59.997 43.478 0.00 0.00 43.02 3.68
4390 4706 2.548057 CCGCAAGAAAACTCAGTAGCAA 59.452 45.455 0.00 0.00 43.02 3.91
4391 4707 2.143122 CCGCAAGAAAACTCAGTAGCA 58.857 47.619 0.00 0.00 43.02 3.49
4392 4708 1.464997 CCCGCAAGAAAACTCAGTAGC 59.535 52.381 0.00 0.00 43.02 3.58
4393 4709 1.464997 GCCCGCAAGAAAACTCAGTAG 59.535 52.381 0.00 0.00 43.02 2.57
4394 4710 1.519408 GCCCGCAAGAAAACTCAGTA 58.481 50.000 0.00 0.00 43.02 2.74
4395 4711 1.172812 GGCCCGCAAGAAAACTCAGT 61.173 55.000 0.00 0.00 43.02 3.41
4396 4712 0.890996 AGGCCCGCAAGAAAACTCAG 60.891 55.000 0.00 0.00 43.02 3.35
4397 4713 0.889186 GAGGCCCGCAAGAAAACTCA 60.889 55.000 0.00 0.00 43.02 3.41
4398 4714 0.889186 TGAGGCCCGCAAGAAAACTC 60.889 55.000 0.00 0.00 43.02 3.01
4399 4715 0.251341 ATGAGGCCCGCAAGAAAACT 60.251 50.000 0.00 0.00 43.02 2.66
4400 4716 0.603065 AATGAGGCCCGCAAGAAAAC 59.397 50.000 0.00 0.00 43.02 2.43
4401 4717 2.208132 TAATGAGGCCCGCAAGAAAA 57.792 45.000 0.00 0.00 43.02 2.29
4402 4718 2.435372 ATAATGAGGCCCGCAAGAAA 57.565 45.000 0.00 0.00 43.02 2.52
4403 4719 3.788227 ATATAATGAGGCCCGCAAGAA 57.212 42.857 0.00 0.00 43.02 2.52
4404 4720 3.674997 GAATATAATGAGGCCCGCAAGA 58.325 45.455 0.00 0.00 43.02 3.02
4405 4721 2.416547 CGAATATAATGAGGCCCGCAAG 59.583 50.000 0.00 0.00 0.00 4.01
4406 4722 2.224426 ACGAATATAATGAGGCCCGCAA 60.224 45.455 0.00 0.00 0.00 4.85
4407 4723 1.346395 ACGAATATAATGAGGCCCGCA 59.654 47.619 0.00 0.00 0.00 5.69
4408 4724 2.000447 GACGAATATAATGAGGCCCGC 59.000 52.381 0.00 0.00 0.00 6.13
4409 4725 2.094906 TCGACGAATATAATGAGGCCCG 60.095 50.000 0.00 0.00 0.00 6.13
4410 4726 3.587797 TCGACGAATATAATGAGGCCC 57.412 47.619 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.