Multiple sequence alignment - TraesCS5D01G158200

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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 TraesCS5D01G158200 chr5D 100.000 4718 0 0 1 4718 246295449 246300166 0.000000e+00 8713
1 TraesCS5D01G158200 chr5D 80.348 402 62 9 412 800 464536163 464535766 5.970000e-74 289
2 TraesCS5D01G158200 chr5B 94.840 4729 204 20 8 4718 280977517 280982223 0.000000e+00 7345
3 TraesCS5D01G158200 chr5A 96.041 3915 113 19 809 4718 330191361 330195238 0.000000e+00 6333
4 TraesCS5D01G158200 chr5A 84.897 629 64 15 427 1044 330169533 330170141 1.450000e-169 606
5 TraesCS5D01G158200 chr5A 86.387 382 51 1 413 794 330175403 330175783 2.630000e-112 416
6 TraesCS5D01G158200 chr5A 77.826 230 36 12 590 806 405001476 405001249 1.380000e-25 128
7 TraesCS5D01G158200 chr3D 73.333 420 95 11 410 816 378776661 378776246 6.370000e-29 139
8 TraesCS5D01G158200 chr3B 75.828 302 56 11 521 808 571019285 571019583 2.290000e-28 137
9 TraesCS5D01G158200 chr2A 78.166 229 37 10 590 806 743570479 743570252 2.960000e-27 134
10 TraesCS5D01G158200 chr4D 73.445 418 82 24 410 806 482769123 482769532 3.830000e-26 130
11 TraesCS5D01G158200 chr7A 75.465 269 52 11 553 809 189350574 189350840 8.290000e-23 119
12 TraesCS5D01G158200 chr4B 84.746 118 16 2 2219 2335 653520760 653520876 2.980000e-22 117


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 TraesCS5D01G158200 chr5D 246295449 246300166 4717 False 8713 8713 100.000 1 4718 1 chr5D.!!$F1 4717
1 TraesCS5D01G158200 chr5B 280977517 280982223 4706 False 7345 7345 94.840 8 4718 1 chr5B.!!$F1 4710
2 TraesCS5D01G158200 chr5A 330191361 330195238 3877 False 6333 6333 96.041 809 4718 1 chr5A.!!$F3 3909
3 TraesCS5D01G158200 chr5A 330169533 330170141 608 False 606 606 84.897 427 1044 1 chr5A.!!$F1 617

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
149 150 0.033228 GATCCCCTCTGATGCTCACG 59.967 60.000 0.00 0.00 0.00 4.35 F
713 715 0.040958 CGCTGCGGATTTATCCTTGC 60.041 55.000 15.40 4.77 44.93 4.01 F
1059 1077 0.377554 ACGATGAGGATGACGACGAC 59.622 55.000 0.00 0.00 0.00 4.34 F
1089 1107 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.00 41.06 3.73 F
2386 2404 1.556373 CCCACTCCACTGATGGCTCA 61.556 60.000 0.00 0.00 46.80 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1047 0.589229 CCTCATCGTCGTCGTAGTGC 60.589 60.000 1.33 0.0 38.33 4.40 R
2522 2540 1.052124 TGGAACTGGAGGACAACCGT 61.052 55.000 0.00 0.0 41.83 4.83 R
2660 2678 2.206900 TCTGGGGCAAGACCTCCA 59.793 61.111 0.00 0.0 38.71 3.86 R
2789 2807 2.555325 CTGATTTTGTCAAGCAGGAGCA 59.445 45.455 0.00 0.0 37.24 4.26 R
4107 4139 1.803334 TACACGGCAAGATGACCAAC 58.197 50.000 0.00 0.0 0.00 3.77 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
30 31 1.633945 GGGTTTCCTTCCTCTTAGGCA 59.366 52.381 0.00 0.00 34.61 4.75
36 37 1.672881 CCTTCCTCTTAGGCAATTGCG 59.327 52.381 23.48 10.33 43.26 4.85
46 47 0.315382 GGCAATTGCGATCGTCTTCG 60.315 55.000 23.48 4.37 43.26 3.79
59 60 1.538512 CGTCTTCGAGTCCAACCTACA 59.461 52.381 0.00 0.00 39.71 2.74
62 63 3.056749 GTCTTCGAGTCCAACCTACATGT 60.057 47.826 2.69 2.69 0.00 3.21
79 80 3.691342 TGTTCGGCCTGAGGTCCG 61.691 66.667 22.69 22.69 41.33 4.79
102 103 2.269241 CCCCTCGTCCTTCTTGGC 59.731 66.667 0.00 0.00 35.26 4.52
106 107 2.920912 TCGTCCTTCTTGGCCGGT 60.921 61.111 1.90 0.00 37.84 5.28
112 113 2.203938 TTCTTGGCCGGTCCTCCT 60.204 61.111 2.12 0.00 35.26 3.69
128 129 2.202932 CTGACCTCCGCCGAATGG 60.203 66.667 0.00 0.00 38.77 3.16
140 141 0.683973 CCGAATGGAGATCCCCTCTG 59.316 60.000 0.00 0.00 41.66 3.35
149 150 0.033228 GATCCCCTCTGATGCTCACG 59.967 60.000 0.00 0.00 0.00 4.35
153 154 2.182791 CTCTGATGCTCACGCCGT 59.817 61.111 0.00 0.00 34.43 5.68
261 263 2.290260 TGTTGTGGTGGATGAGGATGAC 60.290 50.000 0.00 0.00 0.00 3.06
263 265 0.181350 GTGGTGGATGAGGATGACCC 59.819 60.000 0.00 0.00 36.73 4.46
272 274 2.675583 TGAGGATGACCCAGAGATCAG 58.324 52.381 0.00 0.00 37.41 2.90
273 275 1.344114 GAGGATGACCCAGAGATCAGC 59.656 57.143 0.00 0.00 37.41 4.26
277 279 2.364972 TGACCCAGAGATCAGCGATA 57.635 50.000 0.00 0.00 0.00 2.92
279 281 2.235016 GACCCAGAGATCAGCGATAGT 58.765 52.381 0.00 0.00 39.35 2.12
280 282 1.959985 ACCCAGAGATCAGCGATAGTG 59.040 52.381 0.00 0.00 39.35 2.74
283 285 3.181471 CCCAGAGATCAGCGATAGTGTTT 60.181 47.826 0.00 0.00 39.35 2.83
284 286 3.801050 CCAGAGATCAGCGATAGTGTTTG 59.199 47.826 0.00 0.00 39.35 2.93
320 322 4.967036 GCTAGGGCTCATACTCAGAAAAT 58.033 43.478 0.00 0.00 35.22 1.82
324 326 5.679601 AGGGCTCATACTCAGAAAATCTTC 58.320 41.667 0.00 0.00 0.00 2.87
325 327 4.509600 GGGCTCATACTCAGAAAATCTTCG 59.490 45.833 0.00 0.00 36.61 3.79
350 352 5.751028 GCCAATCTGTGTTCTATAGAGACAC 59.249 44.000 25.45 25.45 35.76 3.67
379 381 2.432444 CTTGGAATCCGGTGCAAAGTA 58.568 47.619 0.00 0.00 0.00 2.24
391 393 2.096980 GTGCAAAGTATAAGGTTCCGCC 59.903 50.000 0.00 0.00 37.58 6.13
396 398 1.761198 AGTATAAGGTTCCGCCCTGTC 59.239 52.381 0.00 0.00 38.26 3.51
406 408 2.348888 CGCCCTGTCGGACCTAACT 61.349 63.158 5.55 0.00 0.00 2.24
435 437 7.624360 TGCAACTTATCGAGTTATTTTCCAT 57.376 32.000 0.00 0.00 46.75 3.41
447 449 6.560711 AGTTATTTTCCATTGTAACGATGCC 58.439 36.000 0.00 0.00 33.46 4.40
455 457 3.410631 TTGTAACGATGCCTTGGAAGA 57.589 42.857 0.00 0.00 0.00 2.87
469 471 4.462133 CTTGGAAGAGGAGATTCATGCAT 58.538 43.478 0.00 0.00 0.00 3.96
514 516 6.072175 GGCTATCCAACATACAACACTTTCAA 60.072 38.462 0.00 0.00 0.00 2.69
528 530 7.068103 ACAACACTTTCAATTATGGTTCAGTCA 59.932 33.333 0.00 0.00 0.00 3.41
538 540 9.605275 CAATTATGGTTCAGTCAGATTCTTCTA 57.395 33.333 0.00 0.00 0.00 2.10
581 583 1.068610 CAATGCATTGGTTCGTTCGGT 60.069 47.619 28.34 0.00 34.22 4.69
637 639 7.724061 AGTTGATGTGTAATAGGGAGTTTTGTT 59.276 33.333 0.00 0.00 0.00 2.83
658 660 4.866508 TCACAGAAGATTCACCGTAGTT 57.133 40.909 0.00 0.00 0.00 2.24
672 674 4.733887 CACCGTAGTTAGAATAGAGTTGCG 59.266 45.833 0.00 0.00 0.00 4.85
676 678 6.207213 CGTAGTTAGAATAGAGTTGCGGATT 58.793 40.000 0.00 0.00 0.00 3.01
698 700 4.049393 GGCCAACTATAGCCGCTG 57.951 61.111 2.16 0.00 39.87 5.18
709 711 0.320421 TAGCCGCTGCGGATTTATCC 60.320 55.000 42.12 23.10 45.97 2.59
710 712 2.044806 AGCCGCTGCGGATTTATCCT 62.045 55.000 42.12 24.93 45.97 3.24
713 715 0.040958 CGCTGCGGATTTATCCTTGC 60.041 55.000 15.40 4.77 44.93 4.01
722 724 3.694566 GGATTTATCCTTGCTGTCGGTTT 59.305 43.478 1.40 0.00 43.73 3.27
794 796 4.090819 GCAATAAAACTCCCTTTACCCCA 58.909 43.478 0.00 0.00 0.00 4.96
795 797 4.081862 GCAATAAAACTCCCTTTACCCCAC 60.082 45.833 0.00 0.00 0.00 4.61
796 798 5.081032 CAATAAAACTCCCTTTACCCCACA 58.919 41.667 0.00 0.00 0.00 4.17
797 799 3.691698 AAAACTCCCTTTACCCCACAA 57.308 42.857 0.00 0.00 0.00 3.33
798 800 3.691698 AAACTCCCTTTACCCCACAAA 57.308 42.857 0.00 0.00 0.00 2.83
799 801 3.691698 AACTCCCTTTACCCCACAAAA 57.308 42.857 0.00 0.00 0.00 2.44
800 802 3.238788 ACTCCCTTTACCCCACAAAAG 57.761 47.619 0.00 0.00 33.41 2.27
880 894 7.539022 GCAACTTGTTAGAAAAAGAGATAAGGC 59.461 37.037 0.00 0.00 0.00 4.35
881 895 8.567948 CAACTTGTTAGAAAAAGAGATAAGGCA 58.432 33.333 0.00 0.00 0.00 4.75
882 896 8.691661 ACTTGTTAGAAAAAGAGATAAGGCAA 57.308 30.769 0.00 0.00 0.00 4.52
883 897 9.131791 ACTTGTTAGAAAAAGAGATAAGGCAAA 57.868 29.630 0.00 0.00 0.00 3.68
884 898 9.965824 CTTGTTAGAAAAAGAGATAAGGCAAAA 57.034 29.630 0.00 0.00 0.00 2.44
1029 1047 1.153168 CGCATCCAAGTACCCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
1059 1077 0.377554 ACGATGAGGATGACGACGAC 59.622 55.000 0.00 0.00 0.00 4.34
1089 1107 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.00 41.06 3.73
1426 1444 2.046988 TCGACGTCACCGAGGCTA 60.047 61.111 17.16 0.00 37.88 3.93
1488 1506 3.139029 GGTCCACACCGATCTCAAC 57.861 57.895 0.00 0.00 31.06 3.18
1547 1565 6.172966 GCACGATTGCTTGATTTATTAACG 57.827 37.500 0.00 0.00 46.17 3.18
1560 1578 8.428186 TGATTTATTAACGTCAGACCAATACC 57.572 34.615 0.00 0.00 0.00 2.73
1635 1653 7.624549 TCAGCTAAAACATTAGAGAATGGAGT 58.375 34.615 2.96 0.00 45.83 3.85
1676 1694 7.669722 TGTATTTAGCTTCTTTTCTCCCACAAT 59.330 33.333 0.00 0.00 0.00 2.71
1679 1697 4.670765 AGCTTCTTTTCTCCCACAATGAT 58.329 39.130 0.00 0.00 0.00 2.45
1685 1703 9.618890 CTTCTTTTCTCCCACAATGATTAGATA 57.381 33.333 0.00 0.00 0.00 1.98
1698 1716 8.854117 ACAATGATTAGATAATGCTTTCCCTTC 58.146 33.333 0.00 0.00 0.00 3.46
1702 1720 8.375506 TGATTAGATAATGCTTTCCCTTCGTAT 58.624 33.333 0.00 0.00 0.00 3.06
1731 1749 6.014669 AGCCTTTATCTAGAAGGTATCTGCAG 60.015 42.308 7.63 7.63 44.44 4.41
1734 1752 7.201956 CCTTTATCTAGAAGGTATCTGCAGTGT 60.202 40.741 14.67 6.61 39.30 3.55
1737 1755 5.265191 TCTAGAAGGTATCTGCAGTGTCTT 58.735 41.667 14.67 12.84 39.30 3.01
1762 1780 5.397899 GGGTGATGGATAGGAATGAGACAAA 60.398 44.000 0.00 0.00 0.00 2.83
1778 1796 5.469760 TGAGACAAATTGAGGTGTATGTGTG 59.530 40.000 0.00 0.00 0.00 3.82
1852 1870 7.519032 TGGGAAAACGAGAAATTGTTCTTAT 57.481 32.000 0.00 0.00 44.42 1.73
1854 1872 8.079809 TGGGAAAACGAGAAATTGTTCTTATTC 58.920 33.333 0.00 0.00 44.42 1.75
1948 1966 9.313118 AGTTTTGCTAACATTTCCTAGTTTTTG 57.687 29.630 5.33 0.00 0.00 2.44
1949 1967 7.707774 TTTGCTAACATTTCCTAGTTTTTGC 57.292 32.000 0.00 0.00 0.00 3.68
1997 2015 4.657814 TGATTTCCTGTTCTAGCCCTTT 57.342 40.909 0.00 0.00 0.00 3.11
2009 2027 1.832167 GCCCTTTGTGTGGAAGCCA 60.832 57.895 0.00 0.00 0.00 4.75
2225 2243 3.415212 CCCTTCAAATCTCTTGCAGACA 58.585 45.455 0.00 0.00 32.26 3.41
2361 2379 5.513267 GGAGCCTTAATACCGAGAATTGGAT 60.513 44.000 0.00 0.00 45.05 3.41
2386 2404 1.556373 CCCACTCCACTGATGGCTCA 61.556 60.000 0.00 0.00 46.80 4.26
2503 2521 4.815308 CCTTGCTTACAATCTCTCATGGAG 59.185 45.833 5.18 5.18 43.12 3.86
2522 2540 4.473196 TGGAGAACTATAATTGACCCAGCA 59.527 41.667 0.00 0.00 0.00 4.41
2660 2678 7.338800 TGCTTTTCTTTCATCTTCTCAAGTT 57.661 32.000 0.00 0.00 0.00 2.66
2790 2808 8.436046 TTTTTGTCCATCCTTTTCAATCTTTG 57.564 30.769 0.00 0.00 0.00 2.77
2854 2872 9.413048 GGAATAGTCTCCATCGTTATTTTCTAG 57.587 37.037 0.00 0.00 35.36 2.43
2855 2873 9.968870 GAATAGTCTCCATCGTTATTTTCTAGT 57.031 33.333 0.00 0.00 0.00 2.57
2858 2876 8.522542 AGTCTCCATCGTTATTTTCTAGTACT 57.477 34.615 0.00 0.00 0.00 2.73
2859 2877 9.624373 AGTCTCCATCGTTATTTTCTAGTACTA 57.376 33.333 1.89 1.89 0.00 1.82
2956 2975 9.683069 AGAAGTAGCAAAAACATACATTTTCAG 57.317 29.630 0.00 0.00 31.35 3.02
2970 2989 9.016623 CATACATTTTCAGTTGTCATTAGCATG 57.983 33.333 0.00 0.00 0.00 4.06
3099 3118 2.104967 CATTGGCCACAGGATCAACAT 58.895 47.619 3.88 0.00 0.00 2.71
3145 3164 2.479560 GCTTTTACTTGGGCGGCAATAG 60.480 50.000 12.47 7.00 0.00 1.73
3668 3689 3.243704 TGCCACATCCTAAAACAGTTTGC 60.244 43.478 0.00 0.00 0.00 3.68
4107 4139 8.530311 AGGCAGAAATAGACATCTACTATGATG 58.470 37.037 0.00 0.00 46.61 3.07
4544 4577 5.822204 TCAGTCTACCTCTTCTAAGCTTCT 58.178 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.596338 AAGGAAACCCCAACCGCG 60.596 61.111 0.00 0.00 37.41 6.46
3 4 2.273179 GGAAGGAAACCCCAACCGC 61.273 63.158 0.00 0.00 37.41 5.68
4 5 0.608308 GAGGAAGGAAACCCCAACCG 60.608 60.000 0.00 0.00 37.43 4.44
5 6 0.778083 AGAGGAAGGAAACCCCAACC 59.222 55.000 0.00 0.00 37.41 3.77
6 7 2.677542 AAGAGGAAGGAAACCCCAAC 57.322 50.000 0.00 0.00 37.41 3.77
9 10 1.064611 GCCTAAGAGGAAGGAAACCCC 60.065 57.143 0.00 0.00 37.67 4.95
46 47 2.993899 CGAACACATGTAGGTTGGACTC 59.006 50.000 6.31 0.00 0.00 3.36
59 60 1.296715 GACCTCAGGCCGAACACAT 59.703 57.895 0.00 0.00 0.00 3.21
62 63 3.691342 CGGACCTCAGGCCGAACA 61.691 66.667 18.74 0.00 42.08 3.18
95 96 2.203938 AGGAGGACCGGCCAAGAA 60.204 61.111 15.92 0.00 41.83 2.52
112 113 2.682136 TCCATTCGGCGGAGGTCA 60.682 61.111 7.21 0.00 0.00 4.02
120 121 1.124477 AGAGGGGATCTCCATTCGGC 61.124 60.000 15.83 0.00 43.44 5.54
124 125 1.704070 GCATCAGAGGGGATCTCCATT 59.296 52.381 15.83 0.00 43.44 3.16
128 129 1.714541 TGAGCATCAGAGGGGATCTC 58.285 55.000 0.00 0.00 42.56 2.75
173 175 0.673644 AAGATTCACCTTGGCGGTCG 60.674 55.000 0.00 0.00 44.93 4.79
243 245 0.911769 GGTCATCCTCATCCACCACA 59.088 55.000 0.00 0.00 0.00 4.17
244 246 0.181350 GGGTCATCCTCATCCACCAC 59.819 60.000 0.00 0.00 0.00 4.16
261 263 1.959985 ACACTATCGCTGATCTCTGGG 59.040 52.381 0.00 0.00 0.00 4.45
263 265 3.801050 CCAAACACTATCGCTGATCTCTG 59.199 47.826 0.00 0.00 0.00 3.35
272 274 1.135689 CCAAGCACCAAACACTATCGC 60.136 52.381 0.00 0.00 0.00 4.58
273 275 1.135689 GCCAAGCACCAAACACTATCG 60.136 52.381 0.00 0.00 0.00 2.92
277 279 0.106519 AGAGCCAAGCACCAAACACT 60.107 50.000 0.00 0.00 0.00 3.55
279 281 1.896220 CTAGAGCCAAGCACCAAACA 58.104 50.000 0.00 0.00 0.00 2.83
280 282 0.523519 GCTAGAGCCAAGCACCAAAC 59.476 55.000 0.00 0.00 39.83 2.93
283 285 0.826715 CTAGCTAGAGCCAAGCACCA 59.173 55.000 16.15 0.00 42.62 4.17
284 286 0.105778 CCTAGCTAGAGCCAAGCACC 59.894 60.000 22.70 0.00 42.62 5.01
305 307 4.509600 GGCCGAAGATTTTCTGAGTATGAG 59.490 45.833 0.00 0.00 0.00 2.90
320 322 1.347707 AGAACACAGATTGGCCGAAGA 59.652 47.619 0.00 0.00 0.00 2.87
324 326 4.038042 TCTCTATAGAACACAGATTGGCCG 59.962 45.833 3.57 0.00 0.00 6.13
325 327 5.163405 TGTCTCTATAGAACACAGATTGGCC 60.163 44.000 3.57 0.00 32.16 5.36
350 352 1.884926 GGATTCCAAGCCGCTCTCG 60.885 63.158 0.00 0.00 0.00 4.04
379 381 1.520666 CGACAGGGCGGAACCTTAT 59.479 57.895 0.00 0.00 39.34 1.73
391 393 3.621715 GCAAATAAGTTAGGTCCGACAGG 59.378 47.826 0.00 0.00 39.46 4.00
396 398 5.622770 AAGTTGCAAATAAGTTAGGTCCG 57.377 39.130 0.00 0.00 0.00 4.79
435 437 3.334691 CTCTTCCAAGGCATCGTTACAA 58.665 45.455 0.00 0.00 0.00 2.41
447 449 3.882444 TGCATGAATCTCCTCTTCCAAG 58.118 45.455 0.00 0.00 0.00 3.61
480 482 1.922447 TGTTGGATAGCCAGGACCATT 59.078 47.619 0.00 0.00 46.91 3.16
484 486 3.838244 TGTATGTTGGATAGCCAGGAC 57.162 47.619 0.00 0.00 46.91 3.85
485 487 3.521531 TGTTGTATGTTGGATAGCCAGGA 59.478 43.478 0.00 0.00 46.91 3.86
528 530 8.757877 AGAACTGATAGTGCTTTAGAAGAATCT 58.242 33.333 0.00 0.00 26.37 2.40
538 540 8.621532 TTGTTTGATAGAACTGATAGTGCTTT 57.378 30.769 0.00 0.00 35.26 3.51
637 639 4.866508 AACTACGGTGAATCTTCTGTGA 57.133 40.909 0.00 0.00 0.00 3.58
658 660 5.116180 CAACCAATCCGCAACTCTATTCTA 58.884 41.667 0.00 0.00 0.00 2.10
701 703 4.394920 TGAAACCGACAGCAAGGATAAATC 59.605 41.667 0.00 0.00 0.00 2.17
722 724 5.009631 CCACAAATCCTCAATACAAGGTGA 58.990 41.667 0.00 0.00 35.29 4.02
751 753 7.416154 TTGCATTGTAGTAGTGTTACAGTTC 57.584 36.000 0.00 0.00 33.00 3.01
794 796 9.744468 GTATTCTGGTGTATGTTTTTCTTTTGT 57.256 29.630 0.00 0.00 0.00 2.83
795 797 9.743057 TGTATTCTGGTGTATGTTTTTCTTTTG 57.257 29.630 0.00 0.00 0.00 2.44
892 910 3.559069 ACATGGATTGATTCGCATTCCT 58.441 40.909 0.00 0.00 43.99 3.36
980 998 0.496382 TGGAGGAAGGGAGGGAGAAA 59.504 55.000 0.00 0.00 0.00 2.52
991 1009 0.967380 GTGGTGGCCATTGGAGGAAG 60.967 60.000 9.72 0.00 35.28 3.46
1029 1047 0.589229 CCTCATCGTCGTCGTAGTGC 60.589 60.000 1.33 0.00 38.33 4.40
1455 1473 2.027625 GACCTCCGTGTTGGCGAAG 61.028 63.158 0.00 0.00 37.80 3.79
1488 1506 5.673337 TCAACAGAAGGAAGACATTTTCG 57.327 39.130 0.00 0.00 0.00 3.46
1533 1551 9.916397 GTATTGGTCTGACGTTAATAAATCAAG 57.084 33.333 1.07 0.00 0.00 3.02
1547 1565 2.973694 TAAGGCGGTATTGGTCTGAC 57.026 50.000 0.00 0.00 0.00 3.51
1560 1578 4.573201 TCGTCCCTAAATTGAATTAAGGCG 59.427 41.667 0.00 2.13 0.00 5.52
1667 1685 7.756395 AAGCATTATCTAATCATTGTGGGAG 57.244 36.000 0.00 0.00 0.00 4.30
1669 1687 7.373493 GGAAAGCATTATCTAATCATTGTGGG 58.627 38.462 0.00 0.00 0.00 4.61
1676 1694 6.591935 ACGAAGGGAAAGCATTATCTAATCA 58.408 36.000 0.00 0.00 0.00 2.57
1679 1697 7.990886 ACAATACGAAGGGAAAGCATTATCTAA 59.009 33.333 0.00 0.00 0.00 2.10
1685 1703 4.335594 GCTACAATACGAAGGGAAAGCATT 59.664 41.667 0.00 0.00 0.00 3.56
1698 1716 7.659186 ACCTTCTAGATAAAGGCTACAATACG 58.341 38.462 8.62 0.00 46.03 3.06
1702 1720 8.861086 CAGATACCTTCTAGATAAAGGCTACAA 58.139 37.037 8.62 0.00 46.03 2.41
1726 1744 1.162698 CATCACCCAAGACACTGCAG 58.837 55.000 13.48 13.48 0.00 4.41
1731 1749 2.771943 TCCTATCCATCACCCAAGACAC 59.228 50.000 0.00 0.00 0.00 3.67
1734 1752 4.306391 TCATTCCTATCCATCACCCAAGA 58.694 43.478 0.00 0.00 0.00 3.02
1737 1755 3.648067 GTCTCATTCCTATCCATCACCCA 59.352 47.826 0.00 0.00 0.00 4.51
1762 1780 5.316167 ACACATTCACACATACACCTCAAT 58.684 37.500 0.00 0.00 0.00 2.57
1778 1796 8.663911 TCCATTCTTTTGAAACAAAACACATTC 58.336 29.630 5.70 0.00 42.31 2.67
1831 1849 8.630840 GCTGAATAAGAACAATTTCTCGTTTTC 58.369 33.333 0.00 0.00 41.56 2.29
1852 1870 2.886523 CACAGTCCATTCCTTTGCTGAA 59.113 45.455 0.00 0.00 0.00 3.02
1854 1872 2.507484 TCACAGTCCATTCCTTTGCTG 58.493 47.619 0.00 0.00 0.00 4.41
1948 1966 5.897377 AGGAACCTATAATTTGTGTGTGC 57.103 39.130 0.00 0.00 0.00 4.57
1997 2015 3.495331 ACATAAACATGGCTTCCACACA 58.505 40.909 0.00 0.00 35.80 3.72
2009 2027 5.299279 GCCATGGCTGTACTAACATAAACAT 59.701 40.000 29.98 0.00 38.26 2.71
2225 2243 4.298103 ACCTTCAACTGAGCATGATCTT 57.702 40.909 12.92 0.00 0.00 2.40
2361 2379 3.912496 CATCAGTGGAGTGGGTATTGA 57.088 47.619 0.00 0.00 0.00 2.57
2386 2404 4.837860 AGTCCTCAGAGAGAAATGACACTT 59.162 41.667 0.00 0.00 0.00 3.16
2503 2521 3.560068 CCGTGCTGGGTCAATTATAGTTC 59.440 47.826 0.00 0.00 0.00 3.01
2522 2540 1.052124 TGGAACTGGAGGACAACCGT 61.052 55.000 0.00 0.00 41.83 4.83
2660 2678 2.206900 TCTGGGGCAAGACCTCCA 59.793 61.111 0.00 0.00 38.71 3.86
2774 2792 4.081807 GCAGGAGCAAAGATTGAAAAGGAT 60.082 41.667 0.00 0.00 41.58 3.24
2789 2807 2.555325 CTGATTTTGTCAAGCAGGAGCA 59.445 45.455 0.00 0.00 37.24 4.26
2790 2808 2.670509 GCTGATTTTGTCAAGCAGGAGC 60.671 50.000 11.65 0.00 36.14 4.70
2891 2909 8.948631 TGAATAGGTTCAGTTGCTAAAGATAG 57.051 34.615 0.00 0.00 39.36 2.08
2970 2989 9.736023 CTAATGCAGGGTGAATAAAAATTAGTC 57.264 33.333 0.00 0.00 0.00 2.59
2974 2993 7.732222 TCCTAATGCAGGGTGAATAAAAATT 57.268 32.000 0.00 0.00 45.58 1.82
3099 3118 4.540715 TCTGGAAGTGATGAGATAGAGCA 58.459 43.478 0.00 0.00 33.76 4.26
3145 3164 0.040067 CAAGCGGCAAACAAGAGACC 60.040 55.000 1.45 0.00 0.00 3.85
3173 3192 4.265073 ACTTGAAGCCCAATAGTGATGAC 58.735 43.478 0.00 0.00 33.68 3.06
3632 3653 1.977854 TGTGGCAGTAGTTCATCTGGT 59.022 47.619 0.00 0.00 32.94 4.00
3668 3689 2.544685 CTGTCTTCGCCCTGTCATTAG 58.455 52.381 0.00 0.00 0.00 1.73
3809 3833 6.429385 CAGTTTGTGAATTTCTAGAGAGGCTT 59.571 38.462 0.00 0.00 0.00 4.35
4107 4139 1.803334 TACACGGCAAGATGACCAAC 58.197 50.000 0.00 0.00 0.00 3.77
4506 4539 7.562135 AGGTAGACTGAAACAGAAACTGTAAA 58.438 34.615 4.84 0.00 44.62 2.01
4544 4577 5.472148 CAGGCTGATATTGCAAAGAAACAA 58.528 37.500 9.42 0.00 0.00 2.83
4638 4671 6.712095 TCCTAGCTGCAATAATAGTCCATTTG 59.288 38.462 1.02 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.