Multiple sequence alignment - TraesCS5B01G419100

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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 TraesCS5B01G419100 chr5B 100.000 5192 0 0 1 5192 594915943 594921134 0.000000e+00 9588
1 TraesCS5B01G419100 chr5A 94.162 3957 187 29 1 3940 605226455 605230384 0.000000e+00 5987
2 TraesCS5B01G419100 chr5A 88.874 764 39 19 3998 4719 605230385 605231144 0.000000e+00 898
3 TraesCS5B01G419100 chr5A 85.954 477 41 10 4718 5190 605231303 605231757 2.170000e-133 486
4 TraesCS5B01G419100 chr5D 94.888 3697 144 19 274 3946 483711190 483714865 0.000000e+00 5738
5 TraesCS5B01G419100 chr5D 91.440 1285 54 20 3945 5190 483714894 483716161 0.000000e+00 1712
6 TraesCS5B01G419100 chr5D 87.712 236 24 3 1 235 483710957 483711188 2.380000e-68 270


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 TraesCS5B01G419100 chr5B 594915943 594921134 5191 False 9588.000000 9588 100.000000 1 5192 1 chr5B.!!$F1 5191
1 TraesCS5B01G419100 chr5A 605226455 605231757 5302 False 2457.000000 5987 89.663333 1 5190 3 chr5A.!!$F1 5189
2 TraesCS5B01G419100 chr5D 483710957 483716161 5204 False 2573.333333 5738 91.346667 1 5190 3 chr5D.!!$F1 5189

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
970 999 0.036306 TTCTGCCTCGTTTTCCCTCC 59.964 55.000 0.00 0.0 0.00 4.30 F
1986 2015 0.320374 TTCAGAACGGGCTTGTCGAT 59.680 50.000 0.00 0.0 0.00 3.59 F
2343 2372 1.002315 GTGGGCATCAAACCAAATGCT 59.998 47.619 7.21 0.0 45.95 3.79 F
3622 3651 1.671328 TCGTTCAACCATTGCGTTTCA 59.329 42.857 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2373 0.253044 AACGTGCTAGCCACCATGAT 59.747 50.000 13.29 0.0 41.53 2.45 R
3518 3547 1.034838 GGTGGTGTTGTCTGGTTGCA 61.035 55.000 0.00 0.0 0.00 4.08 R
3902 3945 1.134640 GGTTTTGGTCGGCTTTGGTTT 60.135 47.619 0.00 0.0 0.00 3.27 R
4997 5273 1.134818 CATGCCATGCTGCTGTGAAAT 60.135 47.619 0.00 0.0 0.00 2.17 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 0.742990 GATCGGGAATTGCCACGACA 60.743 55.000 16.96 0.00 40.48 4.35
54 55 3.034635 AGTGTTTGGGTTTATGGTGCAA 58.965 40.909 0.00 0.00 0.00 4.08
99 100 5.423931 GGCCTTCCCATTTTCAACCTAATAA 59.576 40.000 0.00 0.00 0.00 1.40
103 104 8.197439 CCTTCCCATTTTCAACCTAATAACATC 58.803 37.037 0.00 0.00 0.00 3.06
104 105 7.654022 TCCCATTTTCAACCTAATAACATCC 57.346 36.000 0.00 0.00 0.00 3.51
123 124 5.049405 ACATCCAGAAACGAACTCACATTTC 60.049 40.000 0.00 0.00 0.00 2.17
134 135 6.406018 CGAACTCACATTTCGTTATCATGAG 58.594 40.000 0.09 0.00 40.77 2.90
135 136 6.253512 CGAACTCACATTTCGTTATCATGAGA 59.746 38.462 0.09 0.00 40.77 3.27
136 137 7.201435 CGAACTCACATTTCGTTATCATGAGAA 60.201 37.037 0.09 0.00 40.77 2.87
137 138 7.531280 ACTCACATTTCGTTATCATGAGAAG 57.469 36.000 2.29 0.00 36.45 2.85
141 142 9.087424 TCACATTTCGTTATCATGAGAAGTAAG 57.913 33.333 2.29 0.00 0.00 2.34
176 178 4.155644 TGCATCTCACATTGCGAAACATAA 59.844 37.500 0.00 0.00 41.80 1.90
189 191 5.866633 TGCGAAACATAAAAACCATTCCATC 59.133 36.000 0.00 0.00 0.00 3.51
191 193 6.183360 GCGAAACATAAAAACCATTCCATCAC 60.183 38.462 0.00 0.00 0.00 3.06
200 202 1.600957 CCATTCCATCACGCAGTCATC 59.399 52.381 0.00 0.00 41.61 2.92
209 211 1.133253 CGCAGTCATCGTTGCAAGG 59.867 57.895 12.91 12.91 40.28 3.61
213 215 1.462283 CAGTCATCGTTGCAAGGACAG 59.538 52.381 23.02 17.93 0.00 3.51
283 285 7.503566 TCATCAAAACTCTCTTCAAGTTCCAAT 59.496 33.333 0.00 0.00 35.96 3.16
325 327 2.447443 TGGACGACAGCATCTCTAAGT 58.553 47.619 0.00 0.00 0.00 2.24
345 347 3.880490 AGTGGCAAAACATCGAACACTTA 59.120 39.130 0.00 0.00 34.36 2.24
394 396 0.736325 ACACGCACGCTTCATCTACC 60.736 55.000 0.00 0.00 0.00 3.18
405 407 4.396166 CGCTTCATCTACCAGAAAAACCAT 59.604 41.667 0.00 0.00 0.00 3.55
423 425 2.289002 CCATTGCACGAATAGAAGGAGC 59.711 50.000 0.00 0.00 0.00 4.70
445 461 1.972872 ATTTCATTGCTCCCGGCTAG 58.027 50.000 0.00 0.00 42.39 3.42
487 504 0.112606 TCCTTCTCACGGACAGGAGT 59.887 55.000 0.00 0.00 32.01 3.85
489 506 1.746220 CCTTCTCACGGACAGGAGTAG 59.254 57.143 0.00 0.00 32.93 2.57
498 515 6.161381 TCACGGACAGGAGTAGTTTTAATTC 58.839 40.000 0.00 0.00 0.00 2.17
500 517 7.177216 TCACGGACAGGAGTAGTTTTAATTCTA 59.823 37.037 0.00 0.00 0.00 2.10
502 519 8.033626 ACGGACAGGAGTAGTTTTAATTCTAAG 58.966 37.037 0.00 0.00 0.00 2.18
517 534 1.003839 TAAGGCAGCGGGTTCTGTG 60.004 57.895 0.00 0.00 36.49 3.66
776 799 2.422591 GTGAACCCCACGAACGGA 59.577 61.111 0.00 0.00 35.86 4.69
777 800 1.957695 GTGAACCCCACGAACGGAC 60.958 63.158 0.00 0.00 35.86 4.79
778 801 2.735857 GAACCCCACGAACGGACG 60.736 66.667 0.00 2.26 39.31 4.79
779 802 4.303993 AACCCCACGAACGGACGG 62.304 66.667 8.20 0.00 37.61 4.79
861 885 1.136984 CAGGAGCGTACGGTGAGAC 59.863 63.158 26.54 10.09 0.00 3.36
862 886 1.303074 AGGAGCGTACGGTGAGACA 60.303 57.895 26.54 0.00 0.00 3.41
863 887 1.154073 GGAGCGTACGGTGAGACAC 60.154 63.158 26.54 8.91 0.00 3.67
900 924 3.250280 AGCGCGAGATAGAACGATAGAAA 59.750 43.478 12.10 0.00 41.38 2.52
964 993 3.123050 GCACAATTTTCTGCCTCGTTTT 58.877 40.909 0.00 0.00 0.00 2.43
967 996 3.243737 ACAATTTTCTGCCTCGTTTTCCC 60.244 43.478 0.00 0.00 0.00 3.97
968 997 2.358322 TTTTCTGCCTCGTTTTCCCT 57.642 45.000 0.00 0.00 0.00 4.20
970 999 0.036306 TTCTGCCTCGTTTTCCCTCC 59.964 55.000 0.00 0.00 0.00 4.30
972 1001 0.391793 CTGCCTCGTTTTCCCTCCTC 60.392 60.000 0.00 0.00 0.00 3.71
973 1002 1.448013 GCCTCGTTTTCCCTCCTCG 60.448 63.158 0.00 0.00 0.00 4.63
975 1004 1.448013 CTCGTTTTCCCTCCTCGCC 60.448 63.158 0.00 0.00 0.00 5.54
976 1005 1.889530 CTCGTTTTCCCTCCTCGCCT 61.890 60.000 0.00 0.00 0.00 5.52
977 1006 1.448013 CGTTTTCCCTCCTCGCCTC 60.448 63.158 0.00 0.00 0.00 4.70
978 1007 1.448013 GTTTTCCCTCCTCGCCTCG 60.448 63.158 0.00 0.00 0.00 4.63
1263 1292 3.755628 ATGTACGTCCTGGCGCGT 61.756 61.111 8.43 17.28 44.02 6.01
1411 1440 1.380302 GTCAAGATGTGGGCCCACT 59.620 57.895 45.89 34.07 46.30 4.00
1416 1445 4.082523 ATGTGGGCCCACTCGTCG 62.083 66.667 45.89 0.00 46.30 5.12
1791 1820 1.220477 GGAGGCTGACTTGCTCTCC 59.780 63.158 0.00 0.00 40.45 3.71
1803 1832 2.435586 CTCTCCGGGTTGCAGCTG 60.436 66.667 10.11 10.11 0.00 4.24
1836 1865 2.483188 GGTGAAGTATGGGTTAGAGCCG 60.483 54.545 0.00 0.00 38.98 5.52
1887 1916 1.921982 TGTATGCCAAATGCCAGTGT 58.078 45.000 0.00 0.00 40.16 3.55
1986 2015 0.320374 TTCAGAACGGGCTTGTCGAT 59.680 50.000 0.00 0.00 0.00 3.59
1993 2022 1.723870 GGGCTTGTCGATGATGCAC 59.276 57.895 0.00 0.00 0.00 4.57
2010 2039 4.011966 TGCACTGAGATTGTTCTGTGAT 57.988 40.909 14.54 0.00 44.83 3.06
2248 2277 2.033299 GCCATCGATGTGGTTATTGGTG 59.967 50.000 23.27 5.22 41.47 4.17
2310 2339 2.030363 AGCGGCAATGAAAATGTTTCGA 60.030 40.909 1.45 0.00 0.00 3.71
2343 2372 1.002315 GTGGGCATCAAACCAAATGCT 59.998 47.619 7.21 0.00 45.95 3.79
2344 2373 2.233431 GTGGGCATCAAACCAAATGCTA 59.767 45.455 7.21 0.00 45.95 3.49
2352 2381 5.327616 TCAAACCAAATGCTATCATGGTG 57.672 39.130 0.00 0.00 31.57 4.17
2461 2490 3.910627 AGGAAGGTGTTATGTGGAGAGTT 59.089 43.478 0.00 0.00 0.00 3.01
2837 2866 5.632347 GTGTTTTTGAATTCATGCCTGAGAG 59.368 40.000 9.40 0.00 31.68 3.20
2898 2927 2.097825 GCTCATGGCCTTGTTGAAGAT 58.902 47.619 17.54 0.00 34.27 2.40
3054 3083 3.070018 GGAATATCAGATTGCACCTCGG 58.930 50.000 0.00 0.00 0.00 4.63
3501 3530 2.435410 GGTTACGTTCCCAGGCCG 60.435 66.667 0.00 0.00 0.00 6.13
3518 3547 3.844211 AGGCCGGACATATGTTATACCAT 59.156 43.478 11.69 0.00 0.00 3.55
3563 3592 4.142227 GGTTCAGCAATGATTTCTCTGCAT 60.142 41.667 0.00 0.00 37.26 3.96
3603 3632 6.024552 TGCATTTTCATAGTTCAAACCCTC 57.975 37.500 0.00 0.00 0.00 4.30
3622 3651 1.671328 TCGTTCAACCATTGCGTTTCA 59.329 42.857 0.00 0.00 0.00 2.69
3682 3712 8.472007 AAAATGAACTATTTGGACAAGGTACA 57.528 30.769 0.00 0.00 38.93 2.90
3696 3726 4.755123 ACAAGGTACAACTGTATTGCTGAC 59.245 41.667 0.00 0.00 32.54 3.51
3717 3747 5.191727 ACCCATCCATGTCAAACTTCATA 57.808 39.130 0.00 0.00 0.00 2.15
3812 3848 8.958175 TTAATTTTAACATAGTTCGCAGGTTG 57.042 30.769 0.00 0.00 0.00 3.77
3825 3861 4.075682 TCGCAGGTTGGTCAAAAATATCA 58.924 39.130 0.00 0.00 0.00 2.15
3878 3914 1.742510 GCACCCAAATGCATGCCAC 60.743 57.895 16.68 0.00 45.39 5.01
3889 3932 3.862877 TGCATGCCACTGTATTAGGAT 57.137 42.857 16.68 0.00 0.00 3.24
3891 3934 4.535781 TGCATGCCACTGTATTAGGATTT 58.464 39.130 16.68 0.00 0.00 2.17
3978 4051 8.478775 TGTATATAATGCCTCTCTGTTACTGT 57.521 34.615 0.00 0.00 0.00 3.55
4130 4203 5.428253 TCCATGCAGTTAGTTCTATTGTCC 58.572 41.667 0.00 0.00 0.00 4.02
4237 4322 8.884124 TTCTGATGGTGATAAAAGGAGAATTT 57.116 30.769 0.00 0.00 0.00 1.82
4371 4457 1.062587 ACGCTCAATTCGTAATGCAGC 59.937 47.619 0.00 0.00 38.52 5.25
4383 4469 1.696063 AATGCAGCAAGAACACAGGT 58.304 45.000 0.00 0.00 0.00 4.00
4404 4490 5.703592 AGGTCCCTTTTGTTTTGTTTGTTTC 59.296 36.000 0.00 0.00 0.00 2.78
4411 4497 5.931441 TTGTTTTGTTTGTTTCCTGGTTG 57.069 34.783 0.00 0.00 0.00 3.77
4496 4582 9.598517 TTCTCCTTTTTGTTTAACTACGAGTTA 57.401 29.630 0.00 0.00 39.51 2.24
4555 4668 2.093181 TGGCCATGTATCACCTGTACAC 60.093 50.000 0.00 0.00 35.11 2.90
4566 4679 1.738099 CTGTACACAGGCGCTGTCC 60.738 63.158 7.64 0.00 43.43 4.02
4616 4729 3.094572 AGGGTCAAAATCTCAATGCTGG 58.905 45.455 0.00 0.00 0.00 4.85
4622 4735 4.766373 TCAAAATCTCAATGCTGGCAGTTA 59.234 37.500 17.16 6.20 0.00 2.24
4695 4809 6.293955 CGTCTTGAACCTGGACAACATTATTT 60.294 38.462 0.00 0.00 0.00 1.40
4751 5025 9.679661 ATTGGTGTAATTTCTTGGAAAGTTTTT 57.320 25.926 0.00 0.00 46.34 1.94
4778 5052 8.002984 TCCGGTGAAAAGAAAATCTAAAAGTT 57.997 30.769 0.00 0.00 0.00 2.66
4813 5087 9.950496 ATGGATAAATCTAAGCTATTGGTGTAG 57.050 33.333 0.00 0.00 0.00 2.74
4820 5094 6.582636 TCTAAGCTATTGGTGTAGATTGTGG 58.417 40.000 0.00 0.00 32.94 4.17
4821 5095 4.844349 AGCTATTGGTGTAGATTGTGGT 57.156 40.909 0.00 0.00 0.00 4.16
4822 5096 5.950544 AGCTATTGGTGTAGATTGTGGTA 57.049 39.130 0.00 0.00 0.00 3.25
4860 5135 5.850557 TGTCCAGTGACATGAACAAAAAT 57.149 34.783 0.00 0.00 46.40 1.82
4863 5138 7.776107 TGTCCAGTGACATGAACAAAAATAAA 58.224 30.769 0.00 0.00 46.40 1.40
4864 5139 8.420222 TGTCCAGTGACATGAACAAAAATAAAT 58.580 29.630 0.00 0.00 46.40 1.40
4865 5140 9.906660 GTCCAGTGACATGAACAAAAATAAATA 57.093 29.630 0.00 0.00 41.37 1.40
4894 5169 0.040958 CTGTTGGTTCTGAGTTGCGC 60.041 55.000 0.00 0.00 0.00 6.09
4899 5174 1.279840 GTTCTGAGTTGCGCGCTTT 59.720 52.632 33.29 17.44 0.00 3.51
4914 5189 1.606668 CGCTTTTGCCCTCTACACAAA 59.393 47.619 0.00 0.00 43.93 2.83
4915 5190 2.034053 CGCTTTTGCCCTCTACACAAAA 59.966 45.455 0.00 0.00 43.93 2.44
4960 5236 4.069869 CAGGTTGACAGGCCTGTG 57.930 61.111 42.40 22.94 45.05 3.66
4961 5237 1.451504 CAGGTTGACAGGCCTGTGA 59.548 57.895 42.40 32.80 45.05 3.58
4962 5238 0.179020 CAGGTTGACAGGCCTGTGAA 60.179 55.000 42.40 36.39 45.05 3.18
4963 5239 0.550914 AGGTTGACAGGCCTGTGAAA 59.449 50.000 42.40 30.48 45.05 2.69
4964 5240 1.064017 AGGTTGACAGGCCTGTGAAAA 60.064 47.619 42.40 28.04 45.05 2.29
4965 5241 1.067060 GGTTGACAGGCCTGTGAAAAC 59.933 52.381 42.40 34.84 45.05 2.43
4966 5242 2.024414 GTTGACAGGCCTGTGAAAACT 58.976 47.619 42.40 17.02 45.05 2.66
4989 5265 4.024387 TGAAAACCATAAGAACACGTGAGC 60.024 41.667 25.01 13.33 0.00 4.26
4991 5267 2.960819 ACCATAAGAACACGTGAGCTC 58.039 47.619 25.01 15.00 0.00 4.09
4997 5273 1.134521 AGAACACGTGAGCTCCAACAA 60.135 47.619 25.01 0.00 0.00 2.83
5010 5286 2.030371 TCCAACAATTTCACAGCAGCA 58.970 42.857 0.00 0.00 0.00 4.41
5084 5360 0.032130 GCGTGACCTGTTGAGTCAGA 59.968 55.000 0.00 0.00 44.57 3.27
5106 5382 7.704047 TCAGACGATCATTTTAACTGATCTGAG 59.296 37.037 18.54 9.26 44.42 3.35
5150 5426 4.106029 ACTGCTATGTGTACACCTTACG 57.894 45.455 22.91 9.62 0.00 3.18
5168 5444 6.812160 ACCTTACGAACAAGTCTTGTATCATC 59.188 38.462 18.45 11.16 44.59 2.92
5190 5466 4.829808 CGAATTGATCGCCATATATGCTG 58.170 43.478 7.24 1.94 45.89 4.41
5191 5467 4.260497 CGAATTGATCGCCATATATGCTGG 60.260 45.833 7.24 0.00 45.89 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.830648 AATTCCCGATCCTCGCTTGA 59.169 50.000 0.00 0.00 38.82 3.02
21 22 1.078072 AAACACTGGTGTCGTGGCA 60.078 52.632 6.84 0.00 44.13 4.92
30 31 2.962421 CACCATAAACCCAAACACTGGT 59.038 45.455 0.00 0.00 44.76 4.00
54 55 2.158914 CCAAGCTGCAAACTTTCCCTTT 60.159 45.455 1.02 0.00 0.00 3.11
99 100 3.469008 TGTGAGTTCGTTTCTGGATGT 57.531 42.857 0.00 0.00 0.00 3.06
103 104 3.799035 CGAAATGTGAGTTCGTTTCTGG 58.201 45.455 0.00 0.00 42.23 3.86
123 124 9.077674 GGCATATACTTACTTCTCATGATAACG 57.922 37.037 0.00 0.00 0.00 3.18
129 130 8.019669 GCAATTGGCATATACTTACTTCTCATG 58.980 37.037 7.72 0.00 43.97 3.07
130 131 8.103948 GCAATTGGCATATACTTACTTCTCAT 57.896 34.615 7.72 0.00 43.97 2.90
131 132 7.496529 GCAATTGGCATATACTTACTTCTCA 57.503 36.000 7.72 0.00 43.97 3.27
176 178 2.228822 GACTGCGTGATGGAATGGTTTT 59.771 45.455 0.00 0.00 0.00 2.43
189 191 0.451628 CTTGCAACGATGACTGCGTG 60.452 55.000 0.00 0.00 41.75 5.34
191 193 1.133253 CCTTGCAACGATGACTGCG 59.867 57.895 0.00 0.00 41.63 5.18
200 202 3.853671 GCATAATTTCTGTCCTTGCAACG 59.146 43.478 0.00 0.00 0.00 4.10
209 211 3.372206 ACGCTCACTGCATAATTTCTGTC 59.628 43.478 0.00 0.00 43.06 3.51
213 215 4.340894 TTCACGCTCACTGCATAATTTC 57.659 40.909 0.00 0.00 43.06 2.17
283 285 8.527810 GTCCAAAGGTTGAAATGGTTAATATGA 58.472 33.333 0.00 0.00 34.50 2.15
325 327 4.902443 TTAAGTGTTCGATGTTTTGCCA 57.098 36.364 0.00 0.00 0.00 4.92
345 347 1.002315 GGGGCAATGTCACTGCATTTT 59.998 47.619 8.74 0.00 41.78 1.82
394 396 5.698832 TCTATTCGTGCAATGGTTTTTCTG 58.301 37.500 0.00 0.00 0.00 3.02
405 407 2.760634 TGCTCCTTCTATTCGTGCAA 57.239 45.000 0.00 0.00 0.00 4.08
423 425 1.643880 GCCGGGAGCAATGAAATTTG 58.356 50.000 2.18 0.00 42.97 2.32
436 452 2.044252 AGCTCGAACTAGCCGGGA 60.044 61.111 2.18 0.00 43.86 5.14
445 461 1.068472 TCGTCTTTCCAGAGCTCGAAC 60.068 52.381 8.37 0.00 0.00 3.95
487 504 4.879545 CCCGCTGCCTTAGAATTAAAACTA 59.120 41.667 0.00 0.00 0.00 2.24
489 506 3.442625 ACCCGCTGCCTTAGAATTAAAAC 59.557 43.478 0.00 0.00 0.00 2.43
498 515 1.021390 CACAGAACCCGCTGCCTTAG 61.021 60.000 0.00 0.00 39.51 2.18
500 517 2.281761 CACAGAACCCGCTGCCTT 60.282 61.111 0.00 0.00 39.51 4.35
502 519 3.357079 CACACAGAACCCGCTGCC 61.357 66.667 0.00 0.00 39.51 4.85
517 534 3.563808 TGTAAGTCACCAATTGAGCACAC 59.436 43.478 7.12 0.00 33.71 3.82
594 611 2.224137 CGAAGATTAGCATGAGCCTCCA 60.224 50.000 0.00 0.00 43.56 3.86
710 733 4.697756 TTGCCGTTGCCCTCCTCG 62.698 66.667 0.00 0.00 36.33 4.63
856 880 0.753848 TCCCTCGTGTGTGTGTCTCA 60.754 55.000 0.00 0.00 0.00 3.27
861 885 0.388649 GCTAGTCCCTCGTGTGTGTG 60.389 60.000 0.00 0.00 0.00 3.82
862 886 1.863662 CGCTAGTCCCTCGTGTGTGT 61.864 60.000 0.00 0.00 0.00 3.72
863 887 1.154016 CGCTAGTCCCTCGTGTGTG 60.154 63.158 0.00 0.00 0.00 3.82
900 924 1.153289 GCTCACGTGCCATCCATCT 60.153 57.895 11.67 0.00 0.00 2.90
929 953 7.271223 CAGAAAATTGTGCTATGGACTTTAACG 59.729 37.037 0.00 0.00 0.00 3.18
933 957 5.473039 GCAGAAAATTGTGCTATGGACTTT 58.527 37.500 7.92 0.00 43.38 2.66
970 999 4.244802 GAGACGAGGCGAGGCGAG 62.245 72.222 0.00 0.00 0.00 5.03
1224 1253 3.781770 GATGAGCCGCGTCTGGAGG 62.782 68.421 4.92 0.00 38.87 4.30
1527 1556 1.136147 GACGTACATGTCGCGGTCT 59.864 57.895 21.38 6.04 0.00 3.85
1689 1718 4.021925 GCTCCGAACAGCCCCACT 62.022 66.667 0.00 0.00 32.76 4.00
1887 1916 1.031571 GCCTCCACGCATCATCCAAA 61.032 55.000 0.00 0.00 0.00 3.28
1986 2015 3.749609 CACAGAACAATCTCAGTGCATCA 59.250 43.478 0.00 0.00 32.03 3.07
1993 2022 6.047231 TCTGCATATCACAGAACAATCTCAG 58.953 40.000 3.03 0.00 41.10 3.35
2010 2039 3.753272 GCTGAAGACCACTTTTCTGCATA 59.247 43.478 10.04 0.00 43.48 3.14
2019 2048 2.373169 TGAATCAGGCTGAAGACCACTT 59.627 45.455 22.84 9.22 39.24 3.16
2227 2256 2.033299 CACCAATAACCACATCGATGGC 59.967 50.000 28.09 0.00 44.33 4.40
2248 2277 2.325583 TAACCCGAGATCATTGTGCC 57.674 50.000 0.00 0.00 0.00 5.01
2296 2325 6.884295 TCCAAGAGGTATCGAAACATTTTCAT 59.116 34.615 0.00 0.00 35.89 2.57
2310 2339 1.668826 TGCCCACTTCCAAGAGGTAT 58.331 50.000 2.58 0.00 35.31 2.73
2343 2372 1.119684 ACGTGCTAGCCACCATGATA 58.880 50.000 13.29 0.00 41.53 2.15
2344 2373 0.253044 AACGTGCTAGCCACCATGAT 59.747 50.000 13.29 0.00 41.53 2.45
2461 2490 6.934048 TTTCGCATACATGTCCATTAATGA 57.066 33.333 17.23 0.00 0.00 2.57
2490 2519 8.268878 AGATATAATGGCTAAGGTCAAGTCTT 57.731 34.615 0.00 0.00 0.00 3.01
2745 2774 1.136141 GCACTCTCAGCAAACACATCG 60.136 52.381 0.00 0.00 0.00 3.84
2837 2866 9.778741 TTATACTATTCCATGACACTTCATTCC 57.221 33.333 0.00 0.00 40.79 3.01
2898 2927 2.610374 GCGGCATAATAAACTCACCGAA 59.390 45.455 2.23 0.00 41.61 4.30
3054 3083 1.604604 TGCAAGCTAAGTGTTCCACC 58.395 50.000 0.00 0.00 34.49 4.61
3249 3278 8.297470 ACATGAGCACATAATAACCTGAATTT 57.703 30.769 0.00 0.00 35.09 1.82
3387 3416 3.661944 TGCAACAAATAAATGGCTGGTG 58.338 40.909 0.00 0.00 0.00 4.17
3501 3530 5.767665 TGGTTGCATGGTATAACATATGTCC 59.232 40.000 9.23 6.59 0.00 4.02
3518 3547 1.034838 GGTGGTGTTGTCTGGTTGCA 61.035 55.000 0.00 0.00 0.00 4.08
3603 3632 2.112475 TGAAACGCAATGGTTGAACG 57.888 45.000 0.00 0.00 0.00 3.95
3682 3712 2.308570 TGGATGGGTCAGCAATACAGTT 59.691 45.455 0.00 0.00 0.00 3.16
3696 3726 5.887598 TCTTATGAAGTTTGACATGGATGGG 59.112 40.000 0.00 0.00 0.00 4.00
3717 3747 3.843027 ACTGATCCTGATTCCTGTGTCTT 59.157 43.478 0.00 0.00 0.00 3.01
3785 3816 9.620660 AACCTGCGAACTATGTTAAAATTAAAG 57.379 29.630 0.00 0.00 0.00 1.85
3786 3817 9.400638 CAACCTGCGAACTATGTTAAAATTAAA 57.599 29.630 0.00 0.00 0.00 1.52
3787 3818 8.024285 CCAACCTGCGAACTATGTTAAAATTAA 58.976 33.333 0.00 0.00 0.00 1.40
3788 3819 7.175293 ACCAACCTGCGAACTATGTTAAAATTA 59.825 33.333 0.00 0.00 0.00 1.40
3789 3820 6.015772 ACCAACCTGCGAACTATGTTAAAATT 60.016 34.615 0.00 0.00 0.00 1.82
3790 3821 5.475564 ACCAACCTGCGAACTATGTTAAAAT 59.524 36.000 0.00 0.00 0.00 1.82
3791 3822 4.822896 ACCAACCTGCGAACTATGTTAAAA 59.177 37.500 0.00 0.00 0.00 1.52
3804 3840 4.433186 TGATATTTTTGACCAACCTGCG 57.567 40.909 0.00 0.00 0.00 5.18
3845 3881 2.151202 GGGTGCATGTTCGAGAAGAAA 58.849 47.619 0.00 0.00 41.10 2.52
3889 3932 5.808030 CGGCTTTGGTTTTTAGTTCTTCAAA 59.192 36.000 0.00 0.00 0.00 2.69
3891 3934 4.641094 TCGGCTTTGGTTTTTAGTTCTTCA 59.359 37.500 0.00 0.00 0.00 3.02
3902 3945 1.134640 GGTTTTGGTCGGCTTTGGTTT 60.135 47.619 0.00 0.00 0.00 3.27
3978 4051 2.173356 CAATCCCTTGCCAGGAGATACA 59.827 50.000 5.14 0.00 44.19 2.29
4237 4322 9.838975 CTCTATGCAACAATTTGTACAATAACA 57.161 29.630 9.56 2.22 34.90 2.41
4273 4358 4.794278 TGGAACGTACTGCATTAGAAGA 57.206 40.909 0.00 0.00 0.00 2.87
4371 4457 3.023832 ACAAAAGGGACCTGTGTTCTTG 58.976 45.455 0.00 0.00 0.00 3.02
4383 4469 5.703130 CAGGAAACAAACAAAACAAAAGGGA 59.297 36.000 0.00 0.00 0.00 4.20
4496 4582 9.227777 GTGGAAAAGTACAGTGTTAGGAATTAT 57.772 33.333 0.00 0.00 0.00 1.28
4555 4668 2.584418 CTGATCGGACAGCGCCTG 60.584 66.667 2.29 4.31 37.52 4.85
4562 4675 8.902540 ATTATATAAACTTTGCTGATCGGACA 57.097 30.769 5.48 0.00 0.00 4.02
4604 4717 4.340381 GGAATTAACTGCCAGCATTGAGAT 59.660 41.667 0.00 0.00 0.00 2.75
4616 4729 3.821033 ACACAGTCCAAGGAATTAACTGC 59.179 43.478 5.17 0.00 40.74 4.40
4622 4735 5.765182 CAGAACTTACACAGTCCAAGGAATT 59.235 40.000 0.00 0.00 32.94 2.17
4695 4809 5.574891 AGAACATTATGGCGCACAAATAA 57.425 34.783 10.83 8.07 0.00 1.40
4751 5025 8.471609 ACTTTTAGATTTTCTTTTCACCGGAAA 58.528 29.630 9.46 0.00 41.13 3.13
4752 5026 8.002984 ACTTTTAGATTTTCTTTTCACCGGAA 57.997 30.769 9.46 0.00 0.00 4.30
4863 5138 7.671398 ACTCAGAACCAACAGAATTGGATTTAT 59.329 33.333 12.55 0.00 42.06 1.40
4864 5139 7.004086 ACTCAGAACCAACAGAATTGGATTTA 58.996 34.615 12.55 0.00 42.06 1.40
4865 5140 5.835280 ACTCAGAACCAACAGAATTGGATTT 59.165 36.000 12.55 0.00 42.06 2.17
4866 5141 5.388654 ACTCAGAACCAACAGAATTGGATT 58.611 37.500 12.55 3.46 42.06 3.01
4867 5142 4.990526 ACTCAGAACCAACAGAATTGGAT 58.009 39.130 12.55 0.09 42.06 3.41
4868 5143 4.437682 ACTCAGAACCAACAGAATTGGA 57.562 40.909 12.55 0.00 42.06 3.53
4869 5144 4.794003 GCAACTCAGAACCAACAGAATTGG 60.794 45.833 4.11 4.11 44.91 3.16
4870 5145 4.293415 GCAACTCAGAACCAACAGAATTG 58.707 43.478 0.00 0.00 0.00 2.32
4894 5169 1.234821 TTGTGTAGAGGGCAAAAGCG 58.765 50.000 0.00 0.00 0.00 4.68
4960 5236 6.970613 ACGTGTTCTTATGGTTTTCAGTTTTC 59.029 34.615 0.00 0.00 0.00 2.29
4961 5237 6.750039 CACGTGTTCTTATGGTTTTCAGTTTT 59.250 34.615 7.58 0.00 0.00 2.43
4962 5238 6.094325 TCACGTGTTCTTATGGTTTTCAGTTT 59.906 34.615 16.51 0.00 0.00 2.66
4963 5239 5.587043 TCACGTGTTCTTATGGTTTTCAGTT 59.413 36.000 16.51 0.00 0.00 3.16
4964 5240 5.120399 TCACGTGTTCTTATGGTTTTCAGT 58.880 37.500 16.51 0.00 0.00 3.41
4965 5241 5.666969 TCACGTGTTCTTATGGTTTTCAG 57.333 39.130 16.51 0.00 0.00 3.02
4966 5242 4.024387 GCTCACGTGTTCTTATGGTTTTCA 60.024 41.667 16.51 0.00 0.00 2.69
4989 5265 2.034939 TGCTGCTGTGAAATTGTTGGAG 59.965 45.455 0.00 0.00 0.00 3.86
4991 5267 2.512485 TGCTGCTGTGAAATTGTTGG 57.488 45.000 0.00 0.00 0.00 3.77
4997 5273 1.134818 CATGCCATGCTGCTGTGAAAT 60.135 47.619 0.00 0.00 0.00 2.17
5010 5286 5.864418 ATCTTGTTTCATAAGCATGCCAT 57.136 34.783 15.66 6.44 31.73 4.40
5106 5382 7.226128 CAGTAGGGAGAAACGATAAAATTACCC 59.774 40.741 0.00 0.00 0.00 3.69
5150 5426 7.963981 TCAATTCGATGATACAAGACTTGTTC 58.036 34.615 25.10 20.11 42.22 3.18


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

AutoCloner maintained by Alex Coulton.