Multiple sequence alignment - TraesCS7B01G328500

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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 TraesCS7B01G328500 chr7B 100.000 4301 0 0 1 4301 583478901 583474601 0.000000e+00 7943
1 TraesCS7B01G328500 chr7A 95.296 4188 150 18 1 4154 621586441 621582267 0.000000e+00 6599
2 TraesCS7B01G328500 chr7D 90.196 3774 238 58 1 3729 540234390 540238076 0.000000e+00 4798
3 TraesCS7B01G328500 chr4B 91.176 102 9 0 3313 3414 97390157 97390258 5.800000e-29 139
4 TraesCS7B01G328500 chr2D 91.176 102 8 1 3310 3411 636776251 636776351 2.090000e-28 137
5 TraesCS7B01G328500 chr2D 88.991 109 11 1 3312 3420 305909910 305909803 2.700000e-27 134
6 TraesCS7B01G328500 chr1D 91.089 101 9 0 3313 3413 490538213 490538113 2.090000e-28 137
7 TraesCS7B01G328500 chr6D 88.496 113 12 1 3302 3414 155253497 155253608 7.500000e-28 135
8 TraesCS7B01G328500 chr2A 88.991 109 11 1 3312 3420 384882142 384882035 2.700000e-27 134
9 TraesCS7B01G328500 chr1A 89.623 106 10 1 3310 3414 516778203 516778098 2.700000e-27 134
10 TraesCS7B01G328500 chr1B 87.611 113 12 2 3298 3410 659977927 659978037 3.490000e-26 130


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 TraesCS7B01G328500 chr7B 583474601 583478901 4300 True 7943 7943 100.000 1 4301 1 chr7B.!!$R1 4300
1 TraesCS7B01G328500 chr7A 621582267 621586441 4174 True 6599 6599 95.296 1 4154 1 chr7A.!!$R1 4153
2 TraesCS7B01G328500 chr7D 540234390 540238076 3686 False 4798 4798 90.196 1 3729 1 chr7D.!!$F1 3728

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
469 493 1.614996 TTGAAGCAGGAAATTCGGCA 58.385 45.0 10.14 0.0 0.00 5.69 F
1194 1230 1.087771 CGGGGTATTTGCGTGACTCC 61.088 60.0 0.00 0.0 0.00 3.85 F
1640 1676 0.953960 GACGGACCTCGCAATTTGGT 60.954 55.0 0.00 0.0 43.89 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1658 0.953960 GACCAAATTGCGAGGTCCGT 60.954 55.000 0.00 0.00 44.72 4.69 R
2201 2237 1.079438 GGGGAGCTATCCTCGGGAT 59.921 63.158 9.89 9.89 45.85 3.85 R
3455 3505 1.428912 AGTTGGAGGGCCTTGATTTGA 59.571 47.619 7.89 0.00 34.31 2.69 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
123 138 5.209977 TCGTTTCGATTCCAGATACATACG 58.790 41.667 0.00 0.00 0.00 3.06
128 143 6.812879 TCGATTCCAGATACATACGTACAT 57.187 37.500 0.00 0.00 0.00 2.29
129 144 7.910441 TCGATTCCAGATACATACGTACATA 57.090 36.000 0.00 0.00 0.00 2.29
130 145 7.745972 TCGATTCCAGATACATACGTACATAC 58.254 38.462 0.00 0.00 0.00 2.39
131 146 7.388500 TCGATTCCAGATACATACGTACATACA 59.612 37.037 0.00 0.00 0.00 2.29
147 162 7.864379 ACGTACATACACCTATTATGCAGTAAC 59.136 37.037 0.00 0.00 31.12 2.50
156 171 8.150945 CACCTATTATGCAGTAACCTGTAATCT 58.849 37.037 0.00 0.00 41.02 2.40
178 193 3.181455 TGTGTGTGTTTATGAGCTGAGGT 60.181 43.478 0.00 0.00 0.00 3.85
212 227 2.339728 TCTTAAATTTTGTGGGCGCG 57.660 45.000 0.00 0.00 0.00 6.86
218 233 3.888079 TTTTGTGGGCGCGCGATTG 62.888 57.895 37.18 4.39 0.00 2.67
246 263 4.792513 AATGATTCAGAAGGCAGAGGAT 57.207 40.909 0.00 0.00 0.00 3.24
270 287 3.724508 TGGTTGTGCCTATTGTGTTTG 57.275 42.857 0.00 0.00 38.35 2.93
318 335 3.052036 CTGCCAACATTTCTTCGTTTGG 58.948 45.455 0.00 0.00 0.00 3.28
338 355 5.309323 TGGAAATCGATAGGCAGTTTTTG 57.691 39.130 0.00 0.00 0.00 2.44
339 356 4.764823 TGGAAATCGATAGGCAGTTTTTGT 59.235 37.500 0.00 0.00 0.00 2.83
389 413 4.399934 TGCAGTATGATGTTTGCACATGAT 59.600 37.500 0.00 0.00 44.22 2.45
406 430 7.038088 TGCACATGATATAGTTATCCATGACCT 60.038 37.037 0.00 0.00 34.45 3.85
467 491 3.641437 TGTTTGAAGCAGGAAATTCGG 57.359 42.857 0.00 0.00 0.00 4.30
469 493 1.614996 TTGAAGCAGGAAATTCGGCA 58.385 45.000 10.14 0.00 0.00 5.69
596 632 7.664731 CCAAGAGGCAGATAGAATAATGAACAT 59.335 37.037 0.00 0.00 0.00 2.71
876 912 8.670521 ATCATTACCTTCTTCCCATTTTCTTT 57.329 30.769 0.00 0.00 0.00 2.52
901 937 9.671279 TTCATGAACTGTATCATTTCTACATGT 57.329 29.630 3.38 2.69 37.96 3.21
920 956 6.910191 ACATGTGGATTTACATATTGGAGGA 58.090 36.000 0.00 0.00 39.17 3.71
1114 1150 6.183347 AGACCAAATCAGTTCCAGAATAAGG 58.817 40.000 0.00 0.00 0.00 2.69
1194 1230 1.087771 CGGGGTATTTGCGTGACTCC 61.088 60.000 0.00 0.00 0.00 3.85
1259 1295 5.702349 AAAGCTCCTGTCAGAAAGAATTG 57.298 39.130 0.00 0.00 0.00 2.32
1407 1443 1.622312 TGTGCTCAGCAGATTGAGTCT 59.378 47.619 0.00 0.00 45.07 3.24
1515 1551 6.092807 GGAGTTCTTCACATGTAGTTGATTCC 59.907 42.308 0.00 0.00 0.00 3.01
1622 1658 1.649321 ACTTCTGTCCATCAGCCTGA 58.351 50.000 0.00 0.00 43.32 3.86
1623 1659 1.277557 ACTTCTGTCCATCAGCCTGAC 59.722 52.381 0.00 0.00 43.32 3.51
1640 1676 0.953960 GACGGACCTCGCAATTTGGT 60.954 55.000 0.00 0.00 43.89 3.67
1818 1854 2.103373 TCTGATGGGGAGACTTCTTCG 58.897 52.381 0.00 0.00 0.00 3.79
1848 1884 1.888391 GCTTTAAGTGGGCAGCCTTCT 60.888 52.381 12.43 7.25 0.00 2.85
2201 2237 0.411452 AGGAGCAGAGGGAGTTCTCA 59.589 55.000 2.24 0.00 36.30 3.27
2721 2757 6.738114 ACCATGATATTGATTTTGCCGTAAG 58.262 36.000 0.00 0.00 0.00 2.34
2952 2989 4.329256 TGTCTCAGTCGAGTCGTGTATAAG 59.671 45.833 13.12 4.52 40.44 1.73
2954 2991 3.268330 TCAGTCGAGTCGTGTATAAGCT 58.732 45.455 13.12 0.00 0.00 3.74
3057 3094 4.644685 TGGGCCATTATTACTGCTTCTTTC 59.355 41.667 0.00 0.00 0.00 2.62
3174 3218 0.034896 TTGAGGACGAAGAGGTTGGC 59.965 55.000 0.00 0.00 0.00 4.52
3186 3230 1.200948 GAGGTTGGCAGAATGAAGTGC 59.799 52.381 0.00 0.00 39.69 4.40
3271 3315 2.038426 TGCAAAGCTTCAGCAGTACCTA 59.962 45.455 19.14 0.00 45.16 3.08
3404 3454 3.071892 AGACAGTTATTTTGGGACGGTGA 59.928 43.478 0.00 0.00 0.00 4.02
3521 3573 1.898574 CTCTTGCAAAGCCCCGTGT 60.899 57.895 0.00 0.00 45.70 4.49
3522 3574 1.856265 CTCTTGCAAAGCCCCGTGTC 61.856 60.000 0.00 0.00 45.70 3.67
3523 3575 1.898574 CTTGCAAAGCCCCGTGTCT 60.899 57.895 0.00 0.00 36.98 3.41
3524 3576 1.454847 TTGCAAAGCCCCGTGTCTT 60.455 52.632 0.00 0.00 0.00 3.01
3645 3711 5.064325 GGAAAATGGTGTACAATCTACGGAC 59.936 44.000 0.00 0.00 0.00 4.79
3659 3725 4.515361 TCTACGGACTACTGAAAGAGGAG 58.485 47.826 0.00 0.00 37.43 3.69
3708 3774 1.349026 CTGCCCACCAGAGAAAGAAGA 59.651 52.381 0.00 0.00 44.64 2.87
3709 3775 1.774254 TGCCCACCAGAGAAAGAAGAA 59.226 47.619 0.00 0.00 0.00 2.52
3710 3776 2.224621 TGCCCACCAGAGAAAGAAGAAG 60.225 50.000 0.00 0.00 0.00 2.85
3731 3797 9.588096 AAGAAGCTCCTAGGAAAAGAATAAAAA 57.412 29.630 13.77 0.00 0.00 1.94
3737 3803 7.410991 TCCTAGGAAAAGAATAAAAAGAGGGG 58.589 38.462 9.71 0.00 0.00 4.79
3741 3807 5.012664 GGAAAAGAATAAAAAGAGGGGGCAA 59.987 40.000 0.00 0.00 0.00 4.52
3747 3813 3.986996 AAAAAGAGGGGGCAAATGATG 57.013 42.857 0.00 0.00 0.00 3.07
3751 3817 2.041612 GGGGGCAAATGATGGGCT 60.042 61.111 0.00 0.00 0.00 5.19
3760 3826 2.235402 CAAATGATGGGCTCCAGCTTTT 59.765 45.455 13.73 13.73 44.22 2.27
3761 3827 1.481871 ATGATGGGCTCCAGCTTTTG 58.518 50.000 10.24 0.00 41.01 2.44
3762 3828 0.112995 TGATGGGCTCCAGCTTTTGT 59.887 50.000 10.24 0.00 41.01 2.83
3763 3829 0.529378 GATGGGCTCCAGCTTTTGTG 59.471 55.000 0.00 0.00 36.92 3.33
3795 3861 2.236146 TCCCATCATTACTCGTGCTGTT 59.764 45.455 0.00 0.00 0.00 3.16
3810 3881 3.121944 GTGCTGTTCTGTGTCATAACTCG 59.878 47.826 0.00 0.00 0.00 4.18
3862 3933 1.549203 GTGATCATGGTGGCCAACTT 58.451 50.000 24.13 13.85 36.95 2.66
3904 3976 2.213499 CATAGTTGGTCAAGATCCGCC 58.787 52.381 0.00 0.00 0.00 6.13
3910 3982 0.322546 GGTCAAGATCCGCCCTTTGT 60.323 55.000 0.00 0.00 0.00 2.83
3919 3991 1.008995 CGCCCTTTGTGTTCAACGG 60.009 57.895 0.00 0.00 41.00 4.44
3925 3997 2.538132 CCTTTGTGTTCAACGGTCGAAC 60.538 50.000 5.02 5.02 42.52 3.95
3970 4043 7.065204 GCTTGTTCTTCTCCTAATTAACCTCTG 59.935 40.741 0.00 0.00 0.00 3.35
3989 4062 0.375106 GAAAGTCATGGCAGCGCTAC 59.625 55.000 10.99 3.45 0.00 3.58
3991 4064 0.824109 AAGTCATGGCAGCGCTACTA 59.176 50.000 10.99 1.42 0.00 1.82
4027 4100 6.418057 TGTTTGCCAAAAATATTCTGAGGT 57.582 33.333 0.00 0.00 0.00 3.85
4074 4147 0.109532 TGATTCGTTGTTGGGCCTCA 59.890 50.000 4.53 0.87 0.00 3.86
4105 4178 2.843730 TGGGCTTCCTACTTCTAATGCA 59.156 45.455 0.00 0.00 0.00 3.96
4145 4218 2.032550 GCATCAGTGAACGGAATGATGG 59.967 50.000 17.69 5.83 45.85 3.51
4146 4219 1.737838 TCAGTGAACGGAATGATGGC 58.262 50.000 0.00 0.00 0.00 4.40
4163 4236 2.050895 CGGAGCGCCTATGTCTCG 60.051 66.667 2.29 0.00 0.00 4.04
4167 4240 4.110493 GCGCCTATGTCTCGCTTT 57.890 55.556 0.00 0.00 44.79 3.51
4168 4241 1.927931 GCGCCTATGTCTCGCTTTC 59.072 57.895 0.00 0.00 44.79 2.62
4169 4242 0.806102 GCGCCTATGTCTCGCTTTCA 60.806 55.000 0.00 0.00 44.79 2.69
4170 4243 1.203928 CGCCTATGTCTCGCTTTCAG 58.796 55.000 0.00 0.00 0.00 3.02
4171 4244 0.933796 GCCTATGTCTCGCTTTCAGC 59.066 55.000 0.00 0.00 38.02 4.26
4182 4255 1.714794 GCTTTCAGCGAGTAGAAGCA 58.285 50.000 0.00 0.00 35.48 3.91
4183 4256 2.275318 GCTTTCAGCGAGTAGAAGCAT 58.725 47.619 0.00 0.00 35.48 3.79
4184 4257 2.030213 GCTTTCAGCGAGTAGAAGCATG 59.970 50.000 0.00 0.00 35.48 4.06
4185 4258 1.645034 TTCAGCGAGTAGAAGCATGC 58.355 50.000 10.51 10.51 35.48 4.06
4186 4259 0.526310 TCAGCGAGTAGAAGCATGCG 60.526 55.000 13.01 0.00 35.48 4.73
4187 4260 1.227089 AGCGAGTAGAAGCATGCGG 60.227 57.895 13.01 0.00 35.48 5.69
4188 4261 2.240500 GCGAGTAGAAGCATGCGGG 61.241 63.158 13.01 0.00 0.00 6.13
4189 4262 2.240500 CGAGTAGAAGCATGCGGGC 61.241 63.158 13.01 5.69 0.00 6.13
4190 4263 1.153369 GAGTAGAAGCATGCGGGCA 60.153 57.895 13.01 0.00 35.83 5.36
4191 4264 0.533755 GAGTAGAAGCATGCGGGCAT 60.534 55.000 13.01 0.00 37.08 4.40
4192 4265 0.758734 AGTAGAAGCATGCGGGCATA 59.241 50.000 13.01 0.00 34.91 3.14
4193 4266 1.151668 GTAGAAGCATGCGGGCATAG 58.848 55.000 13.01 2.70 34.91 2.23
4194 4267 1.047801 TAGAAGCATGCGGGCATAGA 58.952 50.000 13.01 0.00 34.91 1.98
4195 4268 0.399454 AGAAGCATGCGGGCATAGAT 59.601 50.000 13.01 0.00 34.91 1.98
4196 4269 0.801251 GAAGCATGCGGGCATAGATC 59.199 55.000 13.01 1.48 34.91 2.75
4197 4270 0.952497 AAGCATGCGGGCATAGATCG 60.952 55.000 13.01 0.00 34.91 3.69
4198 4271 1.669115 GCATGCGGGCATAGATCGT 60.669 57.895 0.00 0.00 34.91 3.73
4199 4272 1.230635 GCATGCGGGCATAGATCGTT 61.231 55.000 0.00 0.00 34.91 3.85
4200 4273 0.514255 CATGCGGGCATAGATCGTTG 59.486 55.000 5.74 0.00 34.91 4.10
4201 4274 0.603707 ATGCGGGCATAGATCGTTGG 60.604 55.000 3.96 0.00 34.49 3.77
4202 4275 1.961277 GCGGGCATAGATCGTTGGG 60.961 63.158 0.00 0.00 0.00 4.12
4203 4276 1.961277 CGGGCATAGATCGTTGGGC 60.961 63.158 0.00 0.00 0.00 5.36
4204 4277 1.451936 GGGCATAGATCGTTGGGCT 59.548 57.895 0.00 0.00 0.00 5.19
4205 4278 0.886490 GGGCATAGATCGTTGGGCTG 60.886 60.000 0.00 0.00 0.00 4.85
4206 4279 0.106708 GGCATAGATCGTTGGGCTGA 59.893 55.000 0.00 0.00 0.00 4.26
4207 4280 1.475034 GGCATAGATCGTTGGGCTGAA 60.475 52.381 0.00 0.00 0.00 3.02
4208 4281 1.869767 GCATAGATCGTTGGGCTGAAG 59.130 52.381 0.98 0.00 0.00 3.02
4209 4282 1.869767 CATAGATCGTTGGGCTGAAGC 59.130 52.381 0.00 0.00 41.14 3.86
4210 4283 0.901827 TAGATCGTTGGGCTGAAGCA 59.098 50.000 4.43 0.00 44.36 3.91
4211 4284 0.254178 AGATCGTTGGGCTGAAGCAT 59.746 50.000 4.43 0.00 44.36 3.79
4212 4285 0.379669 GATCGTTGGGCTGAAGCATG 59.620 55.000 4.43 0.00 44.36 4.06
4213 4286 1.660560 ATCGTTGGGCTGAAGCATGC 61.661 55.000 10.51 10.51 44.36 4.06
4214 4287 2.180017 GTTGGGCTGAAGCATGCG 59.820 61.111 13.01 0.00 44.36 4.73
4215 4288 3.063704 TTGGGCTGAAGCATGCGG 61.064 61.111 13.01 5.39 44.36 5.69
4219 4292 3.524606 GCTGAAGCATGCGGGCAT 61.525 61.111 13.01 0.00 41.59 4.40
4220 4293 2.188829 GCTGAAGCATGCGGGCATA 61.189 57.895 13.01 0.00 41.59 3.14
4221 4294 1.521450 GCTGAAGCATGCGGGCATAT 61.521 55.000 13.01 0.00 41.59 1.78
4222 4295 0.520404 CTGAAGCATGCGGGCATATC 59.480 55.000 13.01 6.15 34.91 1.63
4223 4296 1.229975 TGAAGCATGCGGGCATATCG 61.230 55.000 13.01 0.00 34.91 2.92
4224 4297 1.915614 GAAGCATGCGGGCATATCGG 61.916 60.000 13.01 0.00 34.91 4.18
4225 4298 4.107051 GCATGCGGGCATATCGGC 62.107 66.667 0.00 1.97 34.91 5.54
4233 4306 4.606071 GCATATCGGCCAGCCTAG 57.394 61.111 2.24 0.00 0.00 3.02
4234 4307 1.674057 GCATATCGGCCAGCCTAGT 59.326 57.895 2.24 0.00 0.00 2.57
4235 4308 0.035458 GCATATCGGCCAGCCTAGTT 59.965 55.000 2.24 0.00 0.00 2.24
4236 4309 1.941668 GCATATCGGCCAGCCTAGTTC 60.942 57.143 2.24 0.00 0.00 3.01
4237 4310 0.603569 ATATCGGCCAGCCTAGTTCG 59.396 55.000 2.24 0.00 0.00 3.95
4238 4311 2.083835 TATCGGCCAGCCTAGTTCGC 62.084 60.000 2.24 0.00 0.00 4.70
4241 4314 4.452733 GCCAGCCTAGTTCGCGGT 62.453 66.667 6.13 0.00 0.00 5.68
4242 4315 3.072486 GCCAGCCTAGTTCGCGGTA 62.072 63.158 6.13 0.00 0.00 4.02
4243 4316 1.065928 CCAGCCTAGTTCGCGGTAG 59.934 63.158 6.13 5.16 0.00 3.18
4244 4317 1.381928 CCAGCCTAGTTCGCGGTAGA 61.382 60.000 6.13 0.00 0.00 2.59
4245 4318 0.454600 CAGCCTAGTTCGCGGTAGAA 59.545 55.000 6.13 0.00 0.00 2.10
4260 4333 4.117685 CGGTAGAACACTGCCTTATTACC 58.882 47.826 0.00 0.00 34.92 2.85
4261 4334 4.142004 CGGTAGAACACTGCCTTATTACCT 60.142 45.833 0.00 0.00 34.92 3.08
4262 4335 5.626116 CGGTAGAACACTGCCTTATTACCTT 60.626 44.000 0.00 0.00 34.92 3.50
4263 4336 6.178324 GGTAGAACACTGCCTTATTACCTTT 58.822 40.000 0.00 0.00 34.39 3.11
4264 4337 6.657966 GGTAGAACACTGCCTTATTACCTTTT 59.342 38.462 0.00 0.00 34.39 2.27
4265 4338 7.176165 GGTAGAACACTGCCTTATTACCTTTTT 59.824 37.037 0.00 0.00 34.39 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.348250 CCAAATGATCGACACGCCG 59.652 57.895 0.00 0.00 0.00 6.46
123 138 8.365647 AGGTTACTGCATAATAGGTGTATGTAC 58.634 37.037 0.00 0.00 32.51 2.90
147 162 6.402550 GCTCATAAACACACACAGATTACAGG 60.403 42.308 0.00 0.00 0.00 4.00
156 171 3.181455 ACCTCAGCTCATAAACACACACA 60.181 43.478 0.00 0.00 0.00 3.72
178 193 3.795755 TTAAGAATCCCTCCCCTCAGA 57.204 47.619 0.00 0.00 0.00 3.27
218 233 4.433615 TGCCTTCTGAATCATTACGAGAC 58.566 43.478 0.00 0.00 0.00 3.36
246 263 4.093472 ACACAATAGGCACAACCAAGTA 57.907 40.909 0.00 0.00 43.14 2.24
270 287 6.091123 ACTCAATCGCGTAAAGAATAACAC 57.909 37.500 5.77 0.00 0.00 3.32
318 335 6.149633 ACAACAAAAACTGCCTATCGATTTC 58.850 36.000 1.71 0.00 0.00 2.17
368 392 8.996271 ACTATATCATGTGCAAACATCATACTG 58.004 33.333 0.00 0.00 0.00 2.74
369 393 9.565090 AACTATATCATGTGCAAACATCATACT 57.435 29.630 0.00 0.00 0.00 2.12
406 430 7.945664 ACCACCCAGACAATATAAAAACACTTA 59.054 33.333 0.00 0.00 0.00 2.24
467 491 7.065085 ACAGTTTAGATTGTGATACAGTGATGC 59.935 37.037 0.00 0.00 0.00 3.91
704 740 0.390209 GGCGCTACAAGTTAACCGGA 60.390 55.000 9.46 0.00 0.00 5.14
755 791 5.312079 AGGAAGCCATATTCAGCTATGTTC 58.688 41.667 0.00 0.00 38.74 3.18
763 799 3.881688 CACTCCAAGGAAGCCATATTCAG 59.118 47.826 0.00 0.00 0.00 3.02
876 912 9.101655 CACATGTAGAAATGATACAGTTCATGA 57.898 33.333 12.91 0.00 40.31 3.07
901 937 7.888514 AGGTATCCTCCAATATGTAAATCCA 57.111 36.000 0.00 0.00 0.00 3.41
920 956 3.821033 GCCACAAACAGTCAGAAAGGTAT 59.179 43.478 0.00 0.00 0.00 2.73
1114 1150 1.109323 AGCTTTGTGGTGTTCCCTGC 61.109 55.000 0.00 0.00 0.00 4.85
1194 1230 7.555554 ACAGACTTGGATCCTGATGAATTAAAG 59.444 37.037 14.23 6.46 0.00 1.85
1259 1295 1.058903 CGCCTTAGCTTTTCGTCGC 59.941 57.895 0.00 0.00 36.60 5.19
1407 1443 5.591472 GGTTGATGTGGATGATGAATCTTCA 59.409 40.000 1.23 1.23 42.14 3.02
1515 1551 1.290203 ATGCAGTATTTCTCGCCACG 58.710 50.000 0.00 0.00 0.00 4.94
1622 1658 0.953960 GACCAAATTGCGAGGTCCGT 60.954 55.000 0.00 0.00 44.72 4.69
1623 1659 1.794222 GACCAAATTGCGAGGTCCG 59.206 57.895 0.00 0.00 44.72 4.79
1640 1676 6.014413 ACCATTTGATGATTTCACACCAATGA 60.014 34.615 11.39 0.00 32.84 2.57
1818 1854 2.437413 CCACTTAAAGCCCTTGGTCTC 58.563 52.381 0.00 0.00 0.00 3.36
1848 1884 2.910319 ACCAGTACTGCCAGGATACAAA 59.090 45.455 17.86 0.00 41.41 2.83
2034 2070 2.434359 GCCCCCGAAACAGTCTCG 60.434 66.667 0.00 0.00 36.06 4.04
2201 2237 1.079438 GGGGAGCTATCCTCGGGAT 59.921 63.158 9.89 9.89 45.85 3.85
2362 2398 4.927425 CAGCTCATAAAAAGCATTGCACTT 59.073 37.500 11.91 0.65 42.35 3.16
2369 2405 4.785301 TCCTAGCAGCTCATAAAAAGCAT 58.215 39.130 0.00 0.00 42.35 3.79
2380 2416 2.232452 TGTCAAGACTTCCTAGCAGCTC 59.768 50.000 0.00 0.00 0.00 4.09
2721 2757 7.530863 AGAAAAGAACGGCTCTAATCAAATTC 58.469 34.615 0.00 0.00 32.46 2.17
3057 3094 4.041049 TGCACAAACAATAGTTTCTTGCG 58.959 39.130 14.50 0.00 46.80 4.85
3174 3218 2.004733 TGATGCTCGCACTTCATTCTG 58.995 47.619 0.00 0.00 0.00 3.02
3186 3230 1.929169 CACACATGGTACTGATGCTCG 59.071 52.381 0.00 0.00 0.00 5.03
3271 3315 4.695231 CTTGTCCGCGTCCGACGT 62.695 66.667 21.37 0.00 44.73 4.34
3374 3424 7.360101 CGTCCCAAAATAACTGTCTCTACTTTG 60.360 40.741 0.00 0.00 0.00 2.77
3393 3443 2.885135 TACTACTCTCACCGTCCCAA 57.115 50.000 0.00 0.00 0.00 4.12
3404 3454 8.204836 GGTTTCATGGTATGTTCATACTACTCT 58.795 37.037 18.37 0.66 0.00 3.24
3455 3505 1.428912 AGTTGGAGGGCCTTGATTTGA 59.571 47.619 7.89 0.00 34.31 2.69
3500 3552 2.042831 CGGGGCTTTGCAAGAGAGG 61.043 63.158 0.00 0.00 0.00 3.69
3600 3663 2.939103 CAGTCCCAAGGATGATCGTTTC 59.061 50.000 0.00 0.00 32.73 2.78
3645 3711 5.713792 TCACACTTCTCCTCTTTCAGTAG 57.286 43.478 0.00 0.00 0.00 2.57
3659 3725 6.974622 CCATAAATTTACAGCCATCACACTTC 59.025 38.462 0.00 0.00 0.00 3.01
3708 3774 9.237187 CTCTTTTTATTCTTTTCCTAGGAGCTT 57.763 33.333 12.26 0.00 0.00 3.74
3709 3775 7.831690 CCTCTTTTTATTCTTTTCCTAGGAGCT 59.168 37.037 12.26 0.00 0.00 4.09
3710 3776 7.067615 CCCTCTTTTTATTCTTTTCCTAGGAGC 59.932 40.741 12.26 0.00 0.00 4.70
3731 3797 1.622499 CCCATCATTTGCCCCCTCT 59.378 57.895 0.00 0.00 0.00 3.69
3737 3803 2.024590 GCTGGAGCCCATCATTTGCC 62.025 60.000 0.00 0.00 30.82 4.52
3741 3807 1.829222 CAAAAGCTGGAGCCCATCATT 59.171 47.619 0.00 0.00 43.38 2.57
3747 3813 0.538287 AGACACAAAAGCTGGAGCCC 60.538 55.000 0.00 0.00 43.38 5.19
3751 3817 1.141657 AGAGCAGACACAAAAGCTGGA 59.858 47.619 0.00 0.00 37.48 3.86
3760 3826 1.552337 GATGGGAGAAGAGCAGACACA 59.448 52.381 0.00 0.00 0.00 3.72
3761 3827 1.552337 TGATGGGAGAAGAGCAGACAC 59.448 52.381 0.00 0.00 0.00 3.67
3762 3828 1.942776 TGATGGGAGAAGAGCAGACA 58.057 50.000 0.00 0.00 0.00 3.41
3763 3829 3.557228 AATGATGGGAGAAGAGCAGAC 57.443 47.619 0.00 0.00 0.00 3.51
3795 3861 4.857037 CACGAATTCGAGTTATGACACAGA 59.143 41.667 33.05 0.00 43.02 3.41
3810 3881 0.169009 GGCTGAACTGGCACGAATTC 59.831 55.000 0.00 0.00 0.00 2.17
3904 3976 1.292061 TCGACCGTTGAACACAAAGG 58.708 50.000 11.88 11.88 44.47 3.11
3910 3982 1.155424 GCTGGTTCGACCGTTGAACA 61.155 55.000 26.14 14.93 45.86 3.18
3919 3991 3.377485 TGACATAGAGTAGCTGGTTCGAC 59.623 47.826 0.00 0.00 0.00 4.20
3925 3997 2.692557 AGCACTGACATAGAGTAGCTGG 59.307 50.000 0.00 0.00 31.13 4.85
3970 4043 0.375106 GTAGCGCTGCCATGACTTTC 59.625 55.000 22.90 0.00 0.00 2.62
4074 4147 3.840078 AGTAGGAAGCCCAAATTTTGCAT 59.160 39.130 11.03 0.48 33.88 3.96
4105 4178 2.158769 TGCAAATGATCTATGTCGGGCT 60.159 45.455 0.00 0.00 0.00 5.19
4146 4219 2.050895 CGAGACATAGGCGCTCCG 60.051 66.667 7.64 0.00 37.47 4.63
4164 4237 2.030213 GCATGCTTCTACTCGCTGAAAG 59.970 50.000 11.37 0.00 0.00 2.62
4165 4238 2.002586 GCATGCTTCTACTCGCTGAAA 58.997 47.619 11.37 0.00 0.00 2.69
4166 4239 1.645034 GCATGCTTCTACTCGCTGAA 58.355 50.000 11.37 0.00 0.00 3.02
4167 4240 0.526310 CGCATGCTTCTACTCGCTGA 60.526 55.000 17.13 0.00 0.00 4.26
4168 4241 1.485838 CCGCATGCTTCTACTCGCTG 61.486 60.000 17.13 0.00 0.00 5.18
4169 4242 1.227089 CCGCATGCTTCTACTCGCT 60.227 57.895 17.13 0.00 0.00 4.93
4170 4243 2.240500 CCCGCATGCTTCTACTCGC 61.241 63.158 17.13 0.00 0.00 5.03
4171 4244 2.240500 GCCCGCATGCTTCTACTCG 61.241 63.158 17.13 0.00 0.00 4.18
4172 4245 0.533755 ATGCCCGCATGCTTCTACTC 60.534 55.000 17.13 0.00 35.03 2.59
4173 4246 0.758734 TATGCCCGCATGCTTCTACT 59.241 50.000 17.13 0.00 37.82 2.57
4174 4247 1.151668 CTATGCCCGCATGCTTCTAC 58.848 55.000 17.13 1.12 37.82 2.59
4175 4248 1.047801 TCTATGCCCGCATGCTTCTA 58.952 50.000 17.13 0.00 37.82 2.10
4176 4249 0.399454 ATCTATGCCCGCATGCTTCT 59.601 50.000 17.13 0.00 37.82 2.85
4177 4250 0.801251 GATCTATGCCCGCATGCTTC 59.199 55.000 17.13 4.96 37.82 3.86
4178 4251 0.952497 CGATCTATGCCCGCATGCTT 60.952 55.000 17.13 0.00 37.82 3.91
4179 4252 1.375140 CGATCTATGCCCGCATGCT 60.375 57.895 17.13 0.00 37.82 3.79
4180 4253 1.230635 AACGATCTATGCCCGCATGC 61.231 55.000 7.91 7.91 37.82 4.06
4181 4254 0.514255 CAACGATCTATGCCCGCATG 59.486 55.000 12.42 3.07 37.82 4.06
4182 4255 0.603707 CCAACGATCTATGCCCGCAT 60.604 55.000 7.43 7.43 40.19 4.73
4183 4256 1.227527 CCAACGATCTATGCCCGCA 60.228 57.895 0.00 0.00 0.00 5.69
4184 4257 1.961277 CCCAACGATCTATGCCCGC 60.961 63.158 0.00 0.00 0.00 6.13
4185 4258 1.961277 GCCCAACGATCTATGCCCG 60.961 63.158 0.00 0.00 0.00 6.13
4186 4259 0.886490 CAGCCCAACGATCTATGCCC 60.886 60.000 0.00 0.00 0.00 5.36
4187 4260 0.106708 TCAGCCCAACGATCTATGCC 59.893 55.000 0.00 0.00 0.00 4.40
4188 4261 1.869767 CTTCAGCCCAACGATCTATGC 59.130 52.381 0.00 0.00 0.00 3.14
4189 4262 1.869767 GCTTCAGCCCAACGATCTATG 59.130 52.381 0.00 0.00 34.31 2.23
4190 4263 1.486310 TGCTTCAGCCCAACGATCTAT 59.514 47.619 0.00 0.00 41.18 1.98
4191 4264 0.901827 TGCTTCAGCCCAACGATCTA 59.098 50.000 0.00 0.00 41.18 1.98
4192 4265 0.254178 ATGCTTCAGCCCAACGATCT 59.746 50.000 0.00 0.00 41.18 2.75
4193 4266 0.379669 CATGCTTCAGCCCAACGATC 59.620 55.000 0.00 0.00 41.18 3.69
4194 4267 1.660560 GCATGCTTCAGCCCAACGAT 61.661 55.000 11.37 0.00 41.18 3.73
4195 4268 2.334946 GCATGCTTCAGCCCAACGA 61.335 57.895 11.37 0.00 41.18 3.85
4196 4269 2.180017 GCATGCTTCAGCCCAACG 59.820 61.111 11.37 0.00 41.18 4.10
4197 4270 2.180017 CGCATGCTTCAGCCCAAC 59.820 61.111 17.13 0.00 41.18 3.77
4198 4271 3.063704 CCGCATGCTTCAGCCCAA 61.064 61.111 17.13 0.00 41.18 4.12
4202 4275 1.521450 ATATGCCCGCATGCTTCAGC 61.521 55.000 17.13 13.02 37.82 4.26
4203 4276 0.520404 GATATGCCCGCATGCTTCAG 59.480 55.000 17.13 0.00 37.82 3.02
4204 4277 1.229975 CGATATGCCCGCATGCTTCA 61.230 55.000 17.13 10.76 37.82 3.02
4205 4278 1.499056 CGATATGCCCGCATGCTTC 59.501 57.895 17.13 4.96 37.82 3.86
4206 4279 1.968017 CCGATATGCCCGCATGCTT 60.968 57.895 17.13 0.00 37.82 3.91
4207 4280 2.359107 CCGATATGCCCGCATGCT 60.359 61.111 17.13 0.00 37.82 3.79
4208 4281 4.107051 GCCGATATGCCCGCATGC 62.107 66.667 7.91 7.91 37.82 4.06
4209 4282 3.434319 GGCCGATATGCCCGCATG 61.434 66.667 12.42 0.00 46.11 4.06
4216 4289 0.035458 AACTAGGCTGGCCGATATGC 59.965 55.000 5.93 0.00 41.95 3.14
4217 4290 1.670087 CGAACTAGGCTGGCCGATATG 60.670 57.143 5.93 0.00 41.95 1.78
4218 4291 0.603569 CGAACTAGGCTGGCCGATAT 59.396 55.000 5.93 0.00 41.95 1.63
4219 4292 2.038690 CGAACTAGGCTGGCCGATA 58.961 57.895 5.93 0.00 41.95 2.92
4220 4293 2.815308 CGAACTAGGCTGGCCGAT 59.185 61.111 5.93 0.00 41.95 4.18
4221 4294 4.143333 GCGAACTAGGCTGGCCGA 62.143 66.667 15.27 0.00 41.95 5.54
4224 4297 2.955751 CTACCGCGAACTAGGCTGGC 62.956 65.000 8.23 0.00 0.00 4.85
4225 4298 1.065928 CTACCGCGAACTAGGCTGG 59.934 63.158 8.23 0.00 0.00 4.85
4226 4299 0.454600 TTCTACCGCGAACTAGGCTG 59.545 55.000 8.23 0.00 0.00 4.85
4227 4300 0.455005 GTTCTACCGCGAACTAGGCT 59.545 55.000 8.23 0.00 40.03 4.58
4228 4301 0.171903 TGTTCTACCGCGAACTAGGC 59.828 55.000 8.23 1.54 42.82 3.93
4229 4302 1.471684 AGTGTTCTACCGCGAACTAGG 59.528 52.381 8.23 0.00 42.82 3.02
4230 4303 2.516923 CAGTGTTCTACCGCGAACTAG 58.483 52.381 8.23 3.19 42.82 2.57
4231 4304 1.401931 GCAGTGTTCTACCGCGAACTA 60.402 52.381 8.23 0.00 42.82 2.24
4232 4305 0.666577 GCAGTGTTCTACCGCGAACT 60.667 55.000 8.23 0.00 42.82 3.01
4233 4306 1.623973 GGCAGTGTTCTACCGCGAAC 61.624 60.000 8.23 4.24 42.73 3.95
4234 4307 1.373748 GGCAGTGTTCTACCGCGAA 60.374 57.895 8.23 0.00 33.39 4.70
4235 4308 1.812686 AAGGCAGTGTTCTACCGCGA 61.813 55.000 8.23 0.00 33.39 5.87
4236 4309 0.108992 TAAGGCAGTGTTCTACCGCG 60.109 55.000 0.00 0.00 33.39 6.46
4237 4310 2.311124 ATAAGGCAGTGTTCTACCGC 57.689 50.000 0.00 0.00 32.58 5.68
4238 4311 4.117685 GGTAATAAGGCAGTGTTCTACCG 58.882 47.826 0.00 0.00 32.58 4.02
4239 4312 5.354842 AGGTAATAAGGCAGTGTTCTACC 57.645 43.478 0.00 0.00 0.00 3.18
4240 4313 7.683437 AAAAGGTAATAAGGCAGTGTTCTAC 57.317 36.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.