Multiple sequence alignment - TraesCS6D01G286400

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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 TraesCS6D01G286400 chr6D 100.000 4943 0 0 1 4943 394924004 394919062 0.000000e+00 9129
1 TraesCS6D01G286400 chr6A 92.185 5029 192 74 34 4941 541403838 541398890 0.000000e+00 6924
2 TraesCS6D01G286400 chr6B 93.657 2491 90 28 399 2863 591236014 591233566 0.000000e+00 3663
3 TraesCS6D01G286400 chr6B 91.509 1637 80 28 2850 4440 591233545 591231922 0.000000e+00 2198
4 TraesCS6D01G286400 chr6B 83.367 499 65 3 4445 4941 591231706 591231224 3.510000e-121 446
5 TraesCS6D01G286400 chr6B 91.589 321 9 3 33 339 591236786 591236470 1.270000e-115 427
6 TraesCS6D01G286400 chr7D 87.137 241 30 1 1250 1490 141188385 141188146 6.300000e-69 272
7 TraesCS6D01G286400 chr7A 87.137 241 30 1 1250 1490 143144982 143145221 6.300000e-69 272
8 TraesCS6D01G286400 chr7A 84.314 204 30 2 2919 3121 143146674 143146876 1.090000e-46 198
9 TraesCS6D01G286400 chr7B 86.777 242 29 3 1251 1491 106340131 106340370 2.930000e-67 267
10 TraesCS6D01G286400 chr7B 85.714 98 14 0 1377 1474 500254534 500254437 2.430000e-18 104


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 TraesCS6D01G286400 chr6D 394919062 394924004 4942 True 9129.0 9129 100.0000 1 4943 1 chr6D.!!$R1 4942
1 TraesCS6D01G286400 chr6A 541398890 541403838 4948 True 6924.0 6924 92.1850 34 4941 1 chr6A.!!$R1 4907
2 TraesCS6D01G286400 chr6B 591231224 591236786 5562 True 1683.5 3663 90.0305 33 4941 4 chr6B.!!$R1 4908
3 TraesCS6D01G286400 chr7A 143144982 143146876 1894 False 235.0 272 85.7255 1250 3121 2 chr7A.!!$F1 1871

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
912 1331 0.096108 GAGCAAGCGAGCAAAGCTAC 59.904 55.0 6.21 0.00 45.31 3.58 F
1588 2266 0.252375 AGCCACAAAAGCCATCCCAT 60.252 50.0 0.00 0.00 0.00 4.00 F
2707 3561 0.543749 ACTTAGGCAGGCCATGTCTC 59.456 55.0 13.63 0.21 41.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2867 0.036010 GGAGAAGCAGCCAAGCTACA 60.036 55.0 0.00 0.0 45.89 2.74 R
3202 4473 0.518636 CCACCTGCATGAACGAACAG 59.481 55.0 0.00 0.0 0.00 3.16 R
4583 6130 0.174162 GGCATTGCTCGGATTTGCTT 59.826 50.0 8.82 0.0 33.86 3.91 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
18 19 2.543578 TCGATCAAAGTGCACTGCC 58.456 52.632 22.49 7.10 0.00 4.85
19 20 0.250252 TCGATCAAAGTGCACTGCCA 60.250 50.000 22.49 7.26 0.00 4.92
20 21 0.806868 CGATCAAAGTGCACTGCCAT 59.193 50.000 22.49 12.17 0.00 4.40
21 22 1.200716 CGATCAAAGTGCACTGCCATT 59.799 47.619 22.49 8.03 0.00 3.16
22 23 2.730090 CGATCAAAGTGCACTGCCATTC 60.730 50.000 22.49 12.77 0.00 2.67
23 24 0.592637 TCAAAGTGCACTGCCATTCG 59.407 50.000 22.49 6.18 0.00 3.34
24 25 0.592637 CAAAGTGCACTGCCATTCGA 59.407 50.000 22.49 0.00 0.00 3.71
25 26 0.593128 AAAGTGCACTGCCATTCGAC 59.407 50.000 22.49 0.00 0.00 4.20
26 27 0.534877 AAGTGCACTGCCATTCGACA 60.535 50.000 22.49 0.00 0.00 4.35
27 28 0.952497 AGTGCACTGCCATTCGACAG 60.952 55.000 20.97 0.00 39.86 3.51
28 29 2.327343 TGCACTGCCATTCGACAGC 61.327 57.895 0.00 0.00 37.42 4.40
29 30 2.780643 CACTGCCATTCGACAGCG 59.219 61.111 0.96 0.00 37.42 5.18
30 31 2.029288 CACTGCCATTCGACAGCGT 61.029 57.895 0.96 0.00 37.42 5.07
31 32 1.738099 ACTGCCATTCGACAGCGTC 60.738 57.895 0.96 0.00 37.42 5.19
154 169 2.061028 CGAGCCCTGCATTTGAAAAAC 58.939 47.619 0.00 0.00 0.00 2.43
239 254 2.222027 CCTCCGGCCAATGATAAACTC 58.778 52.381 2.24 0.00 0.00 3.01
244 259 1.409661 GGCCAATGATAAACTCCCGGT 60.410 52.381 0.00 0.00 0.00 5.28
259 274 3.066198 GGTACGGCTGTCCTGGTT 58.934 61.111 0.00 0.00 0.00 3.67
260 275 2.279842 GGTACGGCTGTCCTGGTTA 58.720 57.895 0.00 0.00 0.00 2.85
270 285 1.892474 TGTCCTGGTTATTGGCTTTGC 59.108 47.619 0.00 0.00 0.00 3.68
341 356 3.128349 GTCAACCTAAACACAAGCTCGA 58.872 45.455 0.00 0.00 0.00 4.04
407 818 4.043812 CCCTGAAATATCCATCCATCACCT 59.956 45.833 0.00 0.00 0.00 4.00
413 829 7.666804 TGAAATATCCATCCATCACCTACAATG 59.333 37.037 0.00 0.00 0.00 2.82
428 844 5.480422 ACCTACAATGGAATTTGTTTCTCCC 59.520 40.000 0.00 0.00 40.25 4.30
669 1086 6.350612 GGGATTTGGTTTATTTCGTCCAATGA 60.351 38.462 0.00 0.00 39.27 2.57
674 1091 5.124776 TGGTTTATTTCGTCCAATGACCATC 59.875 40.000 0.00 0.00 38.32 3.51
683 1100 0.096976 CAATGACCATCCGACAACGC 59.903 55.000 0.00 0.00 38.29 4.84
731 1148 3.335579 ACTAATGGAGAAAACACGGAGC 58.664 45.455 0.00 0.00 0.00 4.70
752 1169 0.319383 CGGGAGATTGATCGGAGCTG 60.319 60.000 0.00 0.00 0.00 4.24
767 1184 2.561885 CTGAGCAGCAGCACAAGC 59.438 61.111 3.17 0.00 45.49 4.01
822 1239 0.390472 GGTGAGTGTGGACTGCTAGC 60.390 60.000 8.10 8.10 30.16 3.42
877 1296 1.982958 CCAGCCCTATAAATACCCCGT 59.017 52.381 0.00 0.00 0.00 5.28
905 1324 1.968017 CCCAAAGAGCAAGCGAGCA 60.968 57.895 6.21 0.00 36.85 4.26
912 1331 0.096108 GAGCAAGCGAGCAAAGCTAC 59.904 55.000 6.21 0.00 45.31 3.58
924 1343 3.691609 AGCAAAGCTACTTCATGTAAGCC 59.308 43.478 0.00 0.00 36.99 4.35
1032 1451 3.003763 AGGTCGAACTCCAGGGCC 61.004 66.667 0.00 0.00 0.00 5.80
1158 1577 0.687354 TCCTCAAGAAGGTGAGCCAC 59.313 55.000 0.00 0.00 46.32 5.01
1240 1664 0.719465 ATGAATGACGCGAACGGTTC 59.281 50.000 15.93 10.83 46.04 3.62
1403 1827 0.603065 TCATGATCTATGCCGTCGGG 59.397 55.000 14.38 0.00 36.70 5.14
1588 2266 0.252375 AGCCACAAAAGCCATCCCAT 60.252 50.000 0.00 0.00 0.00 4.00
1702 2382 1.067565 TCTCGACTGGATGACACAAGC 60.068 52.381 0.00 0.00 0.00 4.01
1734 2414 5.760484 AAACCCATGGATTGCTTTGTTAT 57.240 34.783 15.22 0.00 0.00 1.89
1786 2466 3.242518 GTTAAAGAAATGTTCAGCGCCC 58.757 45.455 2.29 0.00 0.00 6.13
1791 2471 2.945668 AGAAATGTTCAGCGCCCTTATC 59.054 45.455 2.29 0.00 0.00 1.75
1885 2569 7.870445 TGATTTGTTTAGTCATGGCTAAAAACC 59.130 33.333 29.09 19.16 41.04 3.27
1925 2609 2.566833 TTCAGGGTGTTGTCATGGAG 57.433 50.000 0.00 0.00 0.00 3.86
2068 2756 2.155155 GGTATATGCTCGCGTAACTTGC 59.845 50.000 5.77 3.13 0.00 4.01
2074 2762 1.674611 CTCGCGTAACTTGCTGTCCG 61.675 60.000 5.77 0.00 0.00 4.79
2090 2778 2.874751 CGAACCAACCAATCGGGC 59.125 61.111 0.00 0.00 42.05 6.13
2095 2783 0.623723 ACCAACCAATCGGGCAGTAT 59.376 50.000 0.00 0.00 42.05 2.12
2165 2853 3.073062 ACAATGAGTAGCCACTTGGAGTT 59.927 43.478 0.00 0.00 34.21 3.01
2166 2854 4.286032 ACAATGAGTAGCCACTTGGAGTTA 59.714 41.667 0.00 0.00 34.21 2.24
2167 2855 4.744795 ATGAGTAGCCACTTGGAGTTAG 57.255 45.455 0.00 0.00 34.21 2.34
2168 2856 3.507411 TGAGTAGCCACTTGGAGTTAGT 58.493 45.455 0.00 0.00 34.21 2.24
2169 2857 4.669700 TGAGTAGCCACTTGGAGTTAGTA 58.330 43.478 0.00 0.00 34.21 1.82
2170 2858 4.705507 TGAGTAGCCACTTGGAGTTAGTAG 59.294 45.833 0.00 0.00 34.21 2.57
2171 2859 3.447944 AGTAGCCACTTGGAGTTAGTAGC 59.552 47.826 0.00 0.00 37.39 3.58
2172 2860 1.555533 AGCCACTTGGAGTTAGTAGCC 59.444 52.381 0.00 0.00 37.39 3.93
2173 2861 1.278127 GCCACTTGGAGTTAGTAGCCA 59.722 52.381 0.00 0.00 37.39 4.75
2174 2862 2.935676 GCCACTTGGAGTTAGTAGCCAC 60.936 54.545 0.00 0.00 37.39 5.01
2175 2863 2.567615 CCACTTGGAGTTAGTAGCCACT 59.432 50.000 0.00 0.00 36.65 4.00
2176 2864 3.008049 CCACTTGGAGTTAGTAGCCACTT 59.992 47.826 0.00 0.00 35.03 3.16
2177 2865 3.997021 CACTTGGAGTTAGTAGCCACTTG 59.003 47.826 0.00 0.00 36.14 3.16
2178 2866 3.646637 ACTTGGAGTTAGTAGCCACTTGT 59.353 43.478 0.00 0.00 36.14 3.16
2179 2867 4.102681 ACTTGGAGTTAGTAGCCACTTGTT 59.897 41.667 0.00 0.00 36.14 2.83
2180 2868 4.002906 TGGAGTTAGTAGCCACTTGTTG 57.997 45.455 0.00 0.00 36.14 3.33
2181 2869 3.389983 TGGAGTTAGTAGCCACTTGTTGT 59.610 43.478 0.00 0.00 36.14 3.32
2187 2875 3.403038 AGTAGCCACTTGTTGTAGCTTG 58.597 45.455 0.00 0.00 40.62 4.01
2300 2988 5.091261 ACTATTAGGCAGGCTATATGTGC 57.909 43.478 4.19 0.00 36.42 4.57
2631 3485 1.423845 CGGCCTTTACATGTGTCGC 59.576 57.895 9.11 4.58 0.00 5.19
2707 3561 0.543749 ACTTAGGCAGGCCATGTCTC 59.456 55.000 13.63 0.21 41.00 3.36
2752 3643 1.067295 AGGTGCTGTGAGATTTGGGA 58.933 50.000 0.00 0.00 0.00 4.37
2794 3685 2.429907 GATCTGCCGGAGATCGCG 60.430 66.667 20.76 0.00 46.10 5.87
3189 4460 7.065085 ACCTCTGTAAAATCATTGATTCTGACG 59.935 37.037 12.15 6.62 30.29 4.35
3195 4466 7.858052 AAAATCATTGATTCTGACGTTGTTC 57.142 32.000 12.15 0.00 30.29 3.18
3201 4472 4.703897 TGATTCTGACGTTGTTCTTTCCT 58.296 39.130 0.00 0.00 0.00 3.36
3202 4473 4.750098 TGATTCTGACGTTGTTCTTTCCTC 59.250 41.667 0.00 0.00 0.00 3.71
3295 4568 7.755591 TCTTCGCAGGGTAAATATATACTACG 58.244 38.462 0.00 0.00 0.00 3.51
3339 4618 2.109181 CCCTTGCCGGCTAGTAGC 59.891 66.667 31.32 14.09 41.46 3.58
3367 4646 5.979288 AGAAATCACTACTTGGACTACGT 57.021 39.130 0.00 0.00 0.00 3.57
3466 4746 0.964358 CAGCCAAGGGAAGAGCCAAG 60.964 60.000 0.00 0.00 38.95 3.61
3468 4748 1.680314 CCAAGGGAAGAGCCAAGCC 60.680 63.158 0.00 0.00 38.95 4.35
3944 5233 0.541863 GACCACATCCCCGTCTGATT 59.458 55.000 0.00 0.00 0.00 2.57
3946 5235 0.530650 CCACATCCCCGTCTGATTCG 60.531 60.000 0.00 0.00 0.00 3.34
3994 5308 4.819630 CCTTGGTAGTTGTTATGTGTGTGT 59.180 41.667 0.00 0.00 0.00 3.72
3996 5310 3.562141 TGGTAGTTGTTATGTGTGTGTGC 59.438 43.478 0.00 0.00 0.00 4.57
3998 5312 2.285083 AGTTGTTATGTGTGTGTGCGT 58.715 42.857 0.00 0.00 0.00 5.24
4013 5327 1.864711 GTGCGTGTGTGTCACTTGTAT 59.135 47.619 4.27 0.00 44.16 2.29
4074 5389 0.179202 TGCGCGCATGTGTATGTTTC 60.179 50.000 33.09 0.00 36.65 2.78
4318 5637 2.889522 TGGAGGGGCTCTACCTTTAT 57.110 50.000 0.00 0.00 38.79 1.40
4319 5638 4.289837 TTGGAGGGGCTCTACCTTTATA 57.710 45.455 0.00 0.00 38.79 0.98
4320 5639 4.289837 TGGAGGGGCTCTACCTTTATAA 57.710 45.455 0.00 0.00 38.79 0.98
4322 5641 5.232347 TGGAGGGGCTCTACCTTTATAATT 58.768 41.667 0.00 0.00 38.79 1.40
4323 5642 5.674958 TGGAGGGGCTCTACCTTTATAATTT 59.325 40.000 0.00 0.00 38.79 1.82
4324 5643 6.161526 TGGAGGGGCTCTACCTTTATAATTTT 59.838 38.462 0.00 0.00 38.79 1.82
4349 5668 9.513906 TTGAGTTTGAACCATGAAGTATGATTA 57.486 29.630 0.00 0.00 39.21 1.75
4370 5689 9.978044 TGATTATGATTCATCTTCAGACTACTG 57.022 33.333 1.55 0.00 44.66 2.74
4371 5690 9.421806 GATTATGATTCATCTTCAGACTACTGG 57.578 37.037 1.55 0.00 43.60 4.00
4372 5691 6.805016 ATGATTCATCTTCAGACTACTGGT 57.195 37.500 0.00 0.00 43.60 4.00
4375 5694 8.134202 TGATTCATCTTCAGACTACTGGTTAA 57.866 34.615 0.00 0.00 43.60 2.01
4376 5695 8.762645 TGATTCATCTTCAGACTACTGGTTAAT 58.237 33.333 0.00 0.00 43.60 1.40
4377 5696 9.255304 GATTCATCTTCAGACTACTGGTTAATC 57.745 37.037 0.00 0.00 43.60 1.75
4406 5739 1.955080 ACTATCGTTAAGGAGGCGGAG 59.045 52.381 3.98 0.00 0.00 4.63
4407 5740 2.228059 CTATCGTTAAGGAGGCGGAGA 58.772 52.381 3.98 0.00 0.00 3.71
4492 6039 3.439857 AGGTTCTTCAATAGCAAGGCA 57.560 42.857 0.00 0.00 0.00 4.75
4519 6066 1.153549 GAGAAGGGCGATCAAGCGT 60.154 57.895 0.00 0.00 38.18 5.07
4542 6089 0.810031 CATCGTCGGATCCAACCACC 60.810 60.000 13.41 0.00 0.00 4.61
4554 6101 3.379452 TCCAACCACCAAAGGTCAAATT 58.621 40.909 0.00 0.00 42.25 1.82
4555 6102 3.777522 TCCAACCACCAAAGGTCAAATTT 59.222 39.130 0.00 0.00 42.25 1.82
4566 6113 5.545063 AAGGTCAAATTTCGGGTTTTCAT 57.455 34.783 0.00 0.00 0.00 2.57
4569 6116 4.021456 GGTCAAATTTCGGGTTTTCATCCT 60.021 41.667 0.00 0.00 0.00 3.24
4583 6130 8.491958 GGGTTTTCATCCTAAAGATAAGGACTA 58.508 37.037 0.00 0.00 45.78 2.59
4620 6167 2.367567 TGCCTTCCATAAGATACCGACC 59.632 50.000 0.00 0.00 34.37 4.79
4632 6179 1.416243 TACCGACCCAAGAACACTGT 58.584 50.000 0.00 0.00 0.00 3.55
4638 6185 2.554032 GACCCAAGAACACTGTCATTGG 59.446 50.000 14.47 14.47 40.10 3.16
4691 6239 4.680537 ACCCCGGTGCTCGAGACT 62.681 66.667 18.75 0.00 42.43 3.24
4693 6241 3.062466 CCCGGTGCTCGAGACTGA 61.062 66.667 18.75 0.00 42.43 3.41
4738 6286 3.325870 TCGAAGTCATCATGTGTTGTCC 58.674 45.455 0.00 0.00 0.00 4.02
4759 6307 2.513897 CCACTTTCCGCGATCCCC 60.514 66.667 8.23 0.00 0.00 4.81
4780 6328 2.165641 CTCAACTACATGGTAGGCACGA 59.834 50.000 8.16 0.00 0.00 4.35
4818 6366 0.403271 AGCAAGTGAAGACCATGCCT 59.597 50.000 0.00 0.00 36.52 4.75
4850 6398 0.748005 AGTCAAGCCGCAACAAGTGT 60.748 50.000 0.00 0.00 0.00 3.55
4871 6419 2.094675 CAGTTGCCACCTATTTGGGAG 58.905 52.381 0.00 0.00 38.38 4.30
4938 6487 5.528043 TGACAAACCATATTTGCTGTTGT 57.472 34.783 0.00 0.00 32.93 3.32
4941 6490 5.055812 ACAAACCATATTTGCTGTTGTTGG 58.944 37.500 0.00 0.00 32.93 3.77
4942 6491 3.959535 ACCATATTTGCTGTTGTTGGG 57.040 42.857 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250252 TGGCAGTGCACTTTGATCGA 60.250 50.000 18.94 0.00 0.00 3.59
1 2 0.806868 ATGGCAGTGCACTTTGATCG 59.193 50.000 18.94 5.88 0.00 3.69
2 3 2.730090 CGAATGGCAGTGCACTTTGATC 60.730 50.000 18.94 11.06 0.00 2.92
3 4 1.200716 CGAATGGCAGTGCACTTTGAT 59.799 47.619 18.94 6.01 0.00 2.57
4 5 0.592637 CGAATGGCAGTGCACTTTGA 59.407 50.000 18.94 3.52 0.00 2.69
5 6 0.592637 TCGAATGGCAGTGCACTTTG 59.407 50.000 18.94 9.41 0.00 2.77
6 7 0.593128 GTCGAATGGCAGTGCACTTT 59.407 50.000 18.94 9.18 0.00 2.66
7 8 0.534877 TGTCGAATGGCAGTGCACTT 60.535 50.000 18.94 9.33 0.00 3.16
8 9 0.952497 CTGTCGAATGGCAGTGCACT 60.952 55.000 15.25 15.25 0.00 4.40
9 10 1.499056 CTGTCGAATGGCAGTGCAC 59.501 57.895 18.61 9.40 0.00 4.57
10 11 2.327343 GCTGTCGAATGGCAGTGCA 61.327 57.895 18.61 3.40 35.33 4.57
11 12 2.482374 GCTGTCGAATGGCAGTGC 59.518 61.111 6.55 6.55 35.33 4.40
12 13 1.959899 GACGCTGTCGAATGGCAGTG 61.960 60.000 11.50 11.50 45.56 3.66
13 14 1.738099 GACGCTGTCGAATGGCAGT 60.738 57.895 0.00 0.00 39.41 4.40
14 15 1.737735 TGACGCTGTCGAATGGCAG 60.738 57.895 0.00 0.00 39.41 4.85
15 16 2.027073 GTGACGCTGTCGAATGGCA 61.027 57.895 0.00 0.00 39.41 4.92
16 17 1.959899 CTGTGACGCTGTCGAATGGC 61.960 60.000 0.00 0.00 39.41 4.40
17 18 1.959899 GCTGTGACGCTGTCGAATGG 61.960 60.000 0.00 0.00 39.41 3.16
18 19 1.417592 GCTGTGACGCTGTCGAATG 59.582 57.895 0.00 0.00 39.41 2.67
19 20 2.088763 CGCTGTGACGCTGTCGAAT 61.089 57.895 0.00 0.00 39.41 3.34
20 21 2.729491 CGCTGTGACGCTGTCGAA 60.729 61.111 0.00 0.00 39.41 3.71
21 22 4.700365 CCGCTGTGACGCTGTCGA 62.700 66.667 9.85 0.00 39.41 4.20
23 24 3.406361 CACCGCTGTGACGCTGTC 61.406 66.667 1.41 2.32 45.76 3.51
24 25 3.911698 TCACCGCTGTGACGCTGT 61.912 61.111 6.89 0.00 46.40 4.40
31 32 4.969196 ACTGCCGTCACCGCTGTG 62.969 66.667 1.20 1.20 44.18 3.66
51 52 4.202131 GGGGTTATCTTAACCACTCTCTCG 60.202 50.000 16.13 0.00 40.53 4.04
135 150 3.110447 TGTTTTTCAAATGCAGGGCTC 57.890 42.857 0.00 0.00 0.00 4.70
137 152 2.743664 GGATGTTTTTCAAATGCAGGGC 59.256 45.455 0.00 0.00 0.00 5.19
154 169 0.533755 GGAGCCGGATCAACTGGATG 60.534 60.000 23.22 0.00 44.43 3.51
244 259 1.208535 CCAATAACCAGGACAGCCGTA 59.791 52.381 0.00 0.00 39.96 4.02
270 285 4.827087 AGCGCAGGCGTGATGAGG 62.827 66.667 11.47 0.00 46.35 3.86
285 300 1.811679 GCCCTAGAAGACACGCAGC 60.812 63.158 0.00 0.00 0.00 5.25
377 426 1.776667 TGGATATTTCAGGGGAGGCAG 59.223 52.381 0.00 0.00 0.00 4.85
378 427 1.905839 TGGATATTTCAGGGGAGGCA 58.094 50.000 0.00 0.00 0.00 4.75
379 428 2.291217 GGATGGATATTTCAGGGGAGGC 60.291 54.545 0.00 0.00 0.00 4.70
386 435 6.772605 TGTAGGTGATGGATGGATATTTCAG 58.227 40.000 0.00 0.00 0.00 3.02
407 818 5.317808 TCGGGAGAAACAAATTCCATTGTA 58.682 37.500 0.00 0.00 42.49 2.41
413 829 2.159382 TGCTCGGGAGAAACAAATTCC 58.841 47.619 0.00 0.00 38.94 3.01
420 836 0.611714 TAGGGTTGCTCGGGAGAAAC 59.388 55.000 10.53 10.53 44.51 2.78
428 844 3.596214 TCTTTTAAGCTAGGGTTGCTCG 58.404 45.455 0.00 0.00 40.22 5.03
594 1011 2.032924 GCATAAACGTGTTAGGGCCATC 59.967 50.000 6.18 0.00 0.00 3.51
669 1086 2.025418 GAACGCGTTGTCGGATGGT 61.025 57.895 31.89 0.00 37.56 3.55
674 1091 4.117372 GCTCGAACGCGTTGTCGG 62.117 66.667 31.89 20.49 38.98 4.79
683 1100 6.133392 TCTTGTTTTTAAATCTGCTCGAACG 58.867 36.000 0.00 0.00 0.00 3.95
719 1136 4.084888 CCCGCGCTCCGTGTTTTC 62.085 66.667 5.56 0.00 35.46 2.29
731 1148 1.372251 CTCCGATCAATCTCCCGCG 60.372 63.158 0.00 0.00 0.00 6.46
752 1169 3.745803 GGGCTTGTGCTGCTGCTC 61.746 66.667 17.00 13.53 40.48 4.26
766 1183 3.161450 TCGGATAGGCACTGGGGC 61.161 66.667 0.00 0.00 41.52 5.80
767 1184 2.063979 TGTCGGATAGGCACTGGGG 61.064 63.158 0.00 0.00 41.52 4.96
845 1263 0.476611 AGGGCTGGAGAGGAAACCTT 60.477 55.000 0.00 0.00 31.76 3.50
877 1296 2.269023 TGCTCTTTGGGGAGATGAGAA 58.731 47.619 0.00 0.00 35.52 2.87
905 1324 4.226168 AGGAGGCTTACATGAAGTAGCTTT 59.774 41.667 0.00 0.00 37.49 3.51
912 1331 3.037549 AGAGGAGGAGGCTTACATGAAG 58.962 50.000 0.00 0.00 38.30 3.02
924 1343 2.534042 TTGTAGGTGGAGAGGAGGAG 57.466 55.000 0.00 0.00 0.00 3.69
1216 1636 0.858961 GTTCGCGTCATTCATGCAGC 60.859 55.000 5.77 0.00 36.74 5.25
1236 1660 0.247736 ACCTGCAGATCGACAGAACC 59.752 55.000 17.39 0.00 35.90 3.62
1240 1664 0.738762 CACCACCTGCAGATCGACAG 60.739 60.000 17.39 10.18 0.00 3.51
1588 2266 8.554528 CGAGAGGATTAACGTGATTACTAGTAA 58.445 37.037 17.41 17.41 0.00 2.24
1702 2382 0.038343 CCATGGGTTTTCTTGTGCGG 60.038 55.000 2.85 0.00 0.00 5.69
1734 2414 1.134818 CCTGAGCATTGTACGTAGCCA 60.135 52.381 0.00 0.00 0.00 4.75
1786 2466 6.595326 TGAAGCAACTGTGGTAATCTGATAAG 59.405 38.462 0.00 0.00 34.25 1.73
1791 2471 4.067896 ACTGAAGCAACTGTGGTAATCTG 58.932 43.478 0.00 0.00 34.25 2.90
1885 2569 5.521010 TGAAAAGTACGTGTGAGTTAACTGG 59.479 40.000 14.14 0.00 0.00 4.00
1925 2609 4.601019 CGATTGAATTTGGCAGTATCACC 58.399 43.478 0.00 0.00 0.00 4.02
2068 2756 0.796312 CGATTGGTTGGTTCGGACAG 59.204 55.000 0.00 0.00 0.00 3.51
2074 2762 0.893727 ACTGCCCGATTGGTTGGTTC 60.894 55.000 0.00 0.00 36.04 3.62
2095 2783 9.913310 TTGGTGTATAAATACCATCATGAAAGA 57.087 29.630 0.00 0.00 45.27 2.52
2171 2859 1.267806 CAGCCAAGCTACAACAAGTGG 59.732 52.381 0.00 0.00 36.40 4.00
2172 2860 1.335324 GCAGCCAAGCTACAACAAGTG 60.335 52.381 0.00 0.00 36.40 3.16
2173 2861 0.954452 GCAGCCAAGCTACAACAAGT 59.046 50.000 0.00 0.00 36.40 3.16
2174 2862 1.242076 AGCAGCCAAGCTACAACAAG 58.758 50.000 0.00 0.00 44.50 3.16
2175 2863 1.608590 GAAGCAGCCAAGCTACAACAA 59.391 47.619 0.00 0.00 45.89 2.83
2176 2864 1.202806 AGAAGCAGCCAAGCTACAACA 60.203 47.619 0.00 0.00 45.89 3.33
2177 2865 1.466558 GAGAAGCAGCCAAGCTACAAC 59.533 52.381 0.00 0.00 45.89 3.32
2178 2866 1.611673 GGAGAAGCAGCCAAGCTACAA 60.612 52.381 0.00 0.00 45.89 2.41
2179 2867 0.036010 GGAGAAGCAGCCAAGCTACA 60.036 55.000 0.00 0.00 45.89 2.74
2180 2868 0.251634 AGGAGAAGCAGCCAAGCTAC 59.748 55.000 0.00 0.00 45.89 3.58
2181 2869 0.539051 GAGGAGAAGCAGCCAAGCTA 59.461 55.000 0.00 0.00 45.89 3.32
2187 2875 2.817396 GTGCGAGGAGAAGCAGCC 60.817 66.667 0.00 0.00 44.70 4.85
2273 2961 4.810191 ATAGCCTGCCTAATAGTACTGC 57.190 45.455 5.39 0.00 0.00 4.40
2300 2988 0.040870 CCTCGATCGATCACACCTCG 60.041 60.000 24.40 10.89 37.47 4.63
2503 3357 3.964875 GGTTGGTGCGGCACAGTG 61.965 66.667 31.74 0.00 35.86 3.66
2610 3464 1.977594 GACACATGTAAAGGCCGGCG 61.978 60.000 22.54 6.21 0.00 6.46
2611 3465 1.800681 GACACATGTAAAGGCCGGC 59.199 57.895 21.18 21.18 0.00 6.13
2612 3466 1.977594 GCGACACATGTAAAGGCCGG 61.978 60.000 0.00 0.00 0.00 6.13
2631 3485 4.154347 GGAGAGCTCCTGTGGCCG 62.154 72.222 10.93 0.00 46.16 6.13
2691 3545 0.618680 ACAGAGACATGGCCTGCCTA 60.619 55.000 14.80 0.00 36.94 3.93
2707 3561 4.335647 AACCTGCGAGCCCCACAG 62.336 66.667 0.00 0.00 0.00 3.66
2752 3643 7.801280 CGGACCTCGAATATATGGCACATGT 62.801 48.000 0.00 0.00 42.85 3.21
2837 3856 1.000938 GCAGCTAGCATGGTAATTGGC 60.001 52.381 18.83 5.97 44.79 4.52
3189 4460 4.331717 TGAACGAACAGAGGAAAGAACAAC 59.668 41.667 0.00 0.00 0.00 3.32
3195 4466 2.807967 TGCATGAACGAACAGAGGAAAG 59.192 45.455 0.00 0.00 0.00 2.62
3201 4472 1.511850 CACCTGCATGAACGAACAGA 58.488 50.000 0.00 0.00 31.67 3.41
3202 4473 0.518636 CCACCTGCATGAACGAACAG 59.481 55.000 0.00 0.00 0.00 3.16
3339 4618 9.141400 GTAGTCCAAGTAGTGATTTCTTAACTG 57.859 37.037 0.00 0.00 0.00 3.16
3367 4646 8.076781 GCGTGAGTGAGAATGAATTAGATACTA 58.923 37.037 0.00 0.00 0.00 1.82
3471 4751 1.202533 AGAATGTTATCAGCGACCCCG 60.203 52.381 0.00 0.00 39.16 5.73
3472 4752 2.622064 AGAATGTTATCAGCGACCCC 57.378 50.000 0.00 0.00 0.00 4.95
3473 4753 5.992217 AGATTAAGAATGTTATCAGCGACCC 59.008 40.000 0.00 0.00 0.00 4.46
3474 4754 7.348201 CAAGATTAAGAATGTTATCAGCGACC 58.652 38.462 0.00 0.00 0.00 4.79
3644 4933 4.802039 GTCGCGTCTCAGTTTTATTCCATA 59.198 41.667 5.77 0.00 0.00 2.74
3948 5237 3.269381 ACACACTGGGAAATGGATATGGT 59.731 43.478 0.00 0.00 0.00 3.55
3950 5239 3.885297 GGACACACTGGGAAATGGATATG 59.115 47.826 0.00 0.00 0.00 1.78
3951 5240 3.788142 AGGACACACTGGGAAATGGATAT 59.212 43.478 0.00 0.00 0.00 1.63
3952 5241 3.189606 AGGACACACTGGGAAATGGATA 58.810 45.455 0.00 0.00 0.00 2.59
3953 5242 1.995542 AGGACACACTGGGAAATGGAT 59.004 47.619 0.00 0.00 0.00 3.41
3954 5243 1.444933 AGGACACACTGGGAAATGGA 58.555 50.000 0.00 0.00 0.00 3.41
3957 5246 1.499007 ACCAAGGACACACTGGGAAAT 59.501 47.619 0.00 0.00 34.98 2.17
3958 5247 0.923358 ACCAAGGACACACTGGGAAA 59.077 50.000 0.00 0.00 34.98 3.13
3959 5248 1.697432 CTACCAAGGACACACTGGGAA 59.303 52.381 0.00 0.00 34.98 3.97
3998 5312 4.126437 CCACTGAATACAAGTGACACACA 58.874 43.478 8.59 0.00 36.74 3.72
4013 5327 0.542333 TCGACCAACCAACCACTGAA 59.458 50.000 0.00 0.00 0.00 3.02
4319 5638 9.480053 CATACTTCATGGTTCAAACTCAAAATT 57.520 29.630 0.00 0.00 0.00 1.82
4320 5639 8.859090 TCATACTTCATGGTTCAAACTCAAAAT 58.141 29.630 0.00 0.00 35.16 1.82
4322 5641 7.815840 TCATACTTCATGGTTCAAACTCAAA 57.184 32.000 0.00 0.00 35.16 2.69
4323 5642 8.408043 AATCATACTTCATGGTTCAAACTCAA 57.592 30.769 0.00 0.00 32.12 3.02
4324 5643 9.685276 ATAATCATACTTCATGGTTCAAACTCA 57.315 29.630 0.00 0.00 38.88 3.41
4349 5668 6.805016 ACCAGTAGTCTGAAGATGAATCAT 57.195 37.500 0.00 0.00 43.76 2.45
4492 6039 1.781786 TCGCCCTTCTCTTGCTAGAT 58.218 50.000 0.00 0.00 0.00 1.98
4506 6053 0.882042 ATGATGACGCTTGATCGCCC 60.882 55.000 0.00 0.00 0.00 6.13
4519 6066 1.068588 GGTTGGATCCGACGATGATGA 59.931 52.381 23.36 0.00 0.00 2.92
4542 6089 5.112686 TGAAAACCCGAAATTTGACCTTTG 58.887 37.500 0.00 0.00 0.00 2.77
4554 6101 6.826741 CCTTATCTTTAGGATGAAAACCCGAA 59.173 38.462 0.00 0.00 35.98 4.30
4555 6102 6.157297 TCCTTATCTTTAGGATGAAAACCCGA 59.843 38.462 0.00 0.00 36.88 5.14
4566 6113 8.211629 GGATTTGCTTAGTCCTTATCTTTAGGA 58.788 37.037 0.00 0.00 39.46 2.94
4569 6116 7.788026 TCGGATTTGCTTAGTCCTTATCTTTA 58.212 34.615 0.00 0.00 0.00 1.85
4583 6130 0.174162 GGCATTGCTCGGATTTGCTT 59.826 50.000 8.82 0.00 33.86 3.91
4620 6167 1.955778 TGCCAATGACAGTGTTCTTGG 59.044 47.619 23.59 23.59 39.47 3.61
4638 6185 7.991460 AGGTCTAACTTAATTGGTTATACCTGC 59.009 37.037 24.86 11.25 45.92 4.85
4691 6239 3.452990 TGGTGGTGTTTCTTGAGTACTCA 59.547 43.478 21.74 21.74 37.91 3.41
4693 6241 4.497291 TTGGTGGTGTTTCTTGAGTACT 57.503 40.909 0.00 0.00 0.00 2.73
4738 6286 2.046314 ATCGCGGAAAGTGGTGGG 60.046 61.111 6.13 0.00 0.00 4.61
4759 6307 2.165641 TCGTGCCTACCATGTAGTTGAG 59.834 50.000 0.00 0.00 0.00 3.02
4780 6328 3.441222 TGCTTCGCATCTCACATCAAAAT 59.559 39.130 0.00 0.00 31.71 1.82
4850 6398 1.707989 TCCCAAATAGGTGGCAACTGA 59.292 47.619 17.03 0.00 37.34 3.41


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

AutoCloner maintained by Alex Coulton.