Multiple sequence alignment - TraesCS7B01G089400

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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 TraesCS7B01G089400 chr7B 100.000 4614 0 0 1 4614 104034024 104029411 0.000000e+00 8521
1 TraesCS7B01G089400 chr7B 91.053 190 17 0 1 190 104055317 104055128 1.650000e-64 257
2 TraesCS7B01G089400 chr7B 87.685 203 24 1 1 202 104047737 104047535 7.720000e-58 235
3 TraesCS7B01G089400 chr7B 94.203 69 4 0 118 186 104050440 104050372 6.310000e-19 106
4 TraesCS7B01G089400 chr7A 92.731 3398 178 40 1241 4613 138960122 138956769 0.000000e+00 4843
5 TraesCS7B01G089400 chr7A 84.211 608 33 19 651 1241 138960730 138960169 2.440000e-147 532
6 TraesCS7B01G089400 chr7A 81.496 254 43 4 285 535 618658602 618658350 6.050000e-49 206
7 TraesCS7B01G089400 chr7A 81.028 253 43 5 287 535 79196749 79196498 3.640000e-46 196
8 TraesCS7B01G089400 chr7D 93.707 2479 129 13 1775 4243 139053043 139050582 0.000000e+00 3688
9 TraesCS7B01G089400 chr7D 90.016 1252 84 23 1 1241 139054925 139053704 0.000000e+00 1581
10 TraesCS7B01G089400 chr7D 87.555 458 36 8 1328 1771 139053607 139053157 1.150000e-140 510
11 TraesCS7B01G089400 chr7D 89.119 193 17 2 1 189 139066131 139065939 2.150000e-58 237
12 TraesCS7B01G089400 chr2A 89.138 847 68 12 2243 3080 345885428 345884597 0.000000e+00 1033
13 TraesCS7B01G089400 chr2A 91.489 141 12 0 3180 3320 345884591 345884451 1.310000e-45 195
14 TraesCS7B01G089400 chr2A 93.694 111 6 1 2138 2247 345885676 345885566 1.030000e-36 165
15 TraesCS7B01G089400 chr5A 83.406 229 31 7 291 514 288672319 288672545 6.050000e-49 206
16 TraesCS7B01G089400 chr3B 82.684 231 36 4 288 514 384435070 384435300 7.830000e-48 202
17 TraesCS7B01G089400 chr6D 80.534 262 45 6 279 535 386057696 386057956 3.640000e-46 196
18 TraesCS7B01G089400 chr4B 82.051 234 36 6 292 521 493391145 493391376 1.310000e-45 195
19 TraesCS7B01G089400 chr4A 81.048 248 44 3 291 535 112854669 112854422 1.310000e-45 195
20 TraesCS7B01G089400 chr5D 80.800 250 44 4 290 535 309799952 309799703 4.710000e-45 193
21 TraesCS7B01G089400 chr1B 86.607 112 10 4 4262 4372 406351866 406351973 8.110000e-23 119
22 TraesCS7B01G089400 chr1B 89.130 92 9 1 4281 4372 446028541 446028451 3.770000e-21 113
23 TraesCS7B01G089400 chr3A 84.167 120 12 6 4263 4379 464022799 464022684 4.880000e-20 110


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 TraesCS7B01G089400 chr7B 104029411 104034024 4613 True 8521.000000 8521 100.000000 1 4614 1 chr7B.!!$R1 4613
1 TraesCS7B01G089400 chr7A 138956769 138960730 3961 True 2687.500000 4843 88.471000 651 4613 2 chr7A.!!$R3 3962
2 TraesCS7B01G089400 chr7D 139050582 139054925 4343 True 1926.333333 3688 90.426000 1 4243 3 chr7D.!!$R2 4242
3 TraesCS7B01G089400 chr2A 345884451 345885676 1225 True 464.333333 1033 91.440333 2138 3320 3 chr2A.!!$R1 1182

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
47 49 0.251073 GGCCCAAGAGTAGCCGTAAA 59.749 55.0 0.00 0.0 36.84 2.01 F
927 957 0.601841 TTCCCTTGTCGTTCCTTCGC 60.602 55.0 0.00 0.0 0.00 4.70 F
2306 2660 0.183014 CTGCAGGAATGATGGGCTCT 59.817 55.0 5.57 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1589 0.404040 CCCACACCACCACCAGTAAT 59.596 55.000 0.00 0.0 0.00 1.89 R
2673 3031 1.338105 TGAGATGTTGGCGAGAACAGG 60.338 52.381 5.97 0.0 39.18 4.00 R
3620 3982 0.614697 TGCATCCTTCGTCTCCTGGA 60.615 55.000 0.00 0.0 0.00 3.86 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
26 28 5.939764 AAGAACATGCTCATACTAGGTCA 57.060 39.130 0.00 0.00 0.00 4.02
47 49 0.251073 GGCCCAAGAGTAGCCGTAAA 59.749 55.000 0.00 0.00 36.84 2.01
64 66 6.811665 AGCCGTAAAATTTTATTTTCTCTGCC 59.188 34.615 13.54 0.00 0.00 4.85
65 67 6.035650 GCCGTAAAATTTTATTTTCTCTGCCC 59.964 38.462 13.54 0.00 0.00 5.36
66 68 6.252655 CCGTAAAATTTTATTTTCTCTGCCCG 59.747 38.462 13.54 7.77 0.00 6.13
76 78 1.227764 CTCTGCCCGCATATGCACT 60.228 57.895 26.52 0.00 42.21 4.40
93 95 2.606308 GCACTTGGATGCTTTCACACAG 60.606 50.000 0.00 0.00 42.62 3.66
140 142 4.098960 TGGTGAATATCTCCACGGTAGAAC 59.901 45.833 0.00 0.00 35.34 3.01
188 190 6.150641 TGCATAATATAGTACTCACTCCGTCC 59.849 42.308 0.00 0.00 36.14 4.79
189 191 6.675002 GCATAATATAGTACTCACTCCGTCCG 60.675 46.154 0.00 0.00 36.14 4.79
190 192 2.706339 ATAGTACTCACTCCGTCCGT 57.294 50.000 0.00 0.00 36.14 4.69
205 207 4.218200 TCCGTCCGTAAATACTTGTCAGAA 59.782 41.667 0.00 0.00 0.00 3.02
210 212 8.649841 CGTCCGTAAATACTTGTCAGAAAAATA 58.350 33.333 0.00 0.00 0.00 1.40
250 252 7.773489 TCCATTTCATTGACAAGTATTTCCA 57.227 32.000 0.00 0.00 0.00 3.53
251 253 8.187913 TCCATTTCATTGACAAGTATTTCCAA 57.812 30.769 0.00 0.00 0.00 3.53
304 306 4.081807 ACATGTTAGTACTCCCTCCGTTTC 60.082 45.833 0.00 0.00 0.00 2.78
317 319 2.745281 CTCCGTTTCTTTTTATCCCGCA 59.255 45.455 0.00 0.00 0.00 5.69
338 340 7.819415 CCCGCATATAAGATTTATCTGAAGTCA 59.181 37.037 0.00 0.00 37.19 3.41
516 518 3.809832 AGTTTGACCTCAGACAAATCGTG 59.190 43.478 0.00 0.00 39.29 4.35
529 531 8.517056 TCAGACAAATCGTGTATACAGAGTAAA 58.483 33.333 5.62 0.00 41.96 2.01
555 557 4.935808 AGAAATGGACCGAATACAGAACAC 59.064 41.667 0.00 0.00 0.00 3.32
564 566 7.171630 ACCGAATACAGAACACTATCTCTTT 57.828 36.000 0.00 0.00 0.00 2.52
565 567 7.612677 ACCGAATACAGAACACTATCTCTTTT 58.387 34.615 0.00 0.00 0.00 2.27
611 613 9.594478 CTTCTAACTCTAGAAAGGAAAGGATTC 57.406 37.037 0.00 0.00 42.35 2.52
626 628 7.067494 AGGAAAGGATTCAAATCGTATTTCCAG 59.933 37.037 26.70 0.00 44.75 3.86
631 633 8.028938 AGGATTCAAATCGTATTTCCAGTTTTG 58.971 33.333 0.00 0.00 36.27 2.44
635 637 7.936584 TCAAATCGTATTTCCAGTTTTGAAGT 58.063 30.769 0.00 0.00 33.40 3.01
705 707 2.726760 TCAACACACAACAAAAACGTGC 59.273 40.909 0.00 0.00 33.89 5.34
710 712 4.140247 CACACAACAAAAACGTGCAAAAG 58.860 39.130 0.00 0.00 33.89 2.27
727 731 2.185004 AAGACACCGTTTCCAGGATG 57.815 50.000 0.00 0.00 0.00 3.51
741 745 1.023513 AGGATGTTGCTGCTTCTCGC 61.024 55.000 0.00 0.00 39.77 5.03
770 774 9.612620 GGATCAAAGTGGATAAAATATTTAGCG 57.387 33.333 0.01 0.00 0.00 4.26
771 775 9.118236 GATCAAAGTGGATAAAATATTTAGCGC 57.882 33.333 0.00 0.00 0.00 5.92
772 776 7.990917 TCAAAGTGGATAAAATATTTAGCGCA 58.009 30.769 11.47 0.00 0.00 6.09
773 777 8.128582 TCAAAGTGGATAAAATATTTAGCGCAG 58.871 33.333 11.47 0.00 0.00 5.18
794 798 1.337387 CAAGGGGCGAAACGGTAAAAA 59.663 47.619 0.00 0.00 0.00 1.94
799 803 1.875514 GGCGAAACGGTAAAAACTCCT 59.124 47.619 0.00 0.00 0.00 3.69
888 918 4.767255 CGAGGCCACCAGCTCCAC 62.767 72.222 5.01 0.00 43.05 4.02
889 919 4.416738 GAGGCCACCAGCTCCACC 62.417 72.222 5.01 0.00 43.05 4.61
891 921 4.729918 GGCCACCAGCTCCACCAG 62.730 72.222 0.00 0.00 43.05 4.00
927 957 0.601841 TTCCCTTGTCGTTCCTTCGC 60.602 55.000 0.00 0.00 0.00 4.70
966 998 1.684734 CCACGGCCACCTACTACCT 60.685 63.158 2.24 0.00 0.00 3.08
1219 1255 3.584406 AGACATCGAGAGGTTTGTCTG 57.416 47.619 14.58 0.00 45.22 3.51
1222 1258 2.628178 ACATCGAGAGGTTTGTCTGTCA 59.372 45.455 0.00 0.00 0.00 3.58
1253 1336 2.035237 TTGCTCGACTTTGGGGACGT 62.035 55.000 0.00 0.00 0.00 4.34
1254 1337 2.027625 GCTCGACTTTGGGGACGTG 61.028 63.158 0.00 0.00 0.00 4.49
1294 1377 0.744414 TTCTGCCTGCCTGTAATCGC 60.744 55.000 0.00 0.00 0.00 4.58
1296 1379 2.511600 GCCTGCCTGTAATCGCGT 60.512 61.111 5.77 0.00 0.00 6.01
1299 1382 2.813179 CTGCCTGTAATCGCGTGGC 61.813 63.158 5.77 11.89 43.49 5.01
1370 1453 2.357323 GGTTGGTGGCAAAATTTGTTGG 59.643 45.455 7.60 0.00 0.00 3.77
1422 1512 2.350964 CGATTTGGGGTAAACGTGGTTG 60.351 50.000 0.00 0.00 0.00 3.77
1499 1589 3.555586 GGTTTTGCTTGGTCGAGTAGGTA 60.556 47.826 0.00 0.00 0.00 3.08
1515 1605 2.627933 AGGTATTACTGGTGGTGGTGT 58.372 47.619 0.00 0.00 0.00 4.16
1519 1609 0.989212 TTACTGGTGGTGGTGTGGGT 60.989 55.000 0.00 0.00 0.00 4.51
1521 1611 2.692741 TGGTGGTGGTGTGGGTCA 60.693 61.111 0.00 0.00 0.00 4.02
1524 1614 1.529796 GTGGTGGTGTGGGTCAGAA 59.470 57.895 0.00 0.00 0.00 3.02
1527 1617 1.172812 GGTGGTGTGGGTCAGAAAGC 61.173 60.000 0.00 0.00 0.00 3.51
1530 1620 0.668535 GGTGTGGGTCAGAAAGCAAC 59.331 55.000 0.00 0.00 0.00 4.17
1531 1621 1.680338 GTGTGGGTCAGAAAGCAACT 58.320 50.000 0.00 0.00 30.12 3.16
1533 1623 2.808543 GTGTGGGTCAGAAAGCAACTAG 59.191 50.000 0.00 0.00 30.12 2.57
1534 1624 2.438021 TGTGGGTCAGAAAGCAACTAGT 59.562 45.455 0.00 0.00 30.12 2.57
1536 1626 4.246458 GTGGGTCAGAAAGCAACTAGTAG 58.754 47.826 0.00 0.00 0.00 2.57
1543 1633 8.035984 GGTCAGAAAGCAACTAGTAGTATTCTT 58.964 37.037 2.50 4.76 0.00 2.52
1554 1644 8.934507 ACTAGTAGTATTCTTTTGTCTGATGC 57.065 34.615 0.00 0.00 0.00 3.91
1555 1645 8.754080 ACTAGTAGTATTCTTTTGTCTGATGCT 58.246 33.333 0.00 0.00 0.00 3.79
1598 1688 6.013379 TGCATCCTAACTGGTGGAATTTAAA 58.987 36.000 0.00 0.00 35.81 1.52
1612 1702 8.581578 GGTGGAATTTAAATTGTGTCCTAGAAA 58.418 33.333 17.98 0.00 0.00 2.52
1640 1730 6.877611 AACTGATGGAGTTTAAATCAACGT 57.122 33.333 0.00 0.00 42.70 3.99
1671 1761 8.782533 AAATCTTGTTGTCGAATTTGTTCTAC 57.217 30.769 0.00 0.00 0.00 2.59
1682 1777 0.524862 TTGTTCTACGACGAGGAGGC 59.475 55.000 0.00 0.00 0.00 4.70
1684 1779 0.739561 GTTCTACGACGAGGAGGCAT 59.260 55.000 0.00 0.00 0.00 4.40
1771 1866 5.548406 AGGCGTATAAGTTTTGTCTGAAGT 58.452 37.500 0.00 0.00 0.00 3.01
1816 2021 7.763985 GGCCAAGTTTATTTAGCACACATTTAT 59.236 33.333 0.00 0.00 0.00 1.40
1956 2165 1.006571 GCGGTTTCCTGACGAGACA 60.007 57.895 0.00 0.00 0.00 3.41
2129 2339 2.560105 GCTTCTGGGCATCTTTTTGACT 59.440 45.455 0.00 0.00 0.00 3.41
2187 2397 2.890311 TCAGTTTGAATTGAATGGGCGT 59.110 40.909 0.00 0.00 0.00 5.68
2306 2660 0.183014 CTGCAGGAATGATGGGCTCT 59.817 55.000 5.57 0.00 0.00 4.09
2468 2823 5.726793 AGACAGTGAGGTAAATATTCCCTGT 59.273 40.000 10.53 7.14 33.65 4.00
2557 2914 6.480524 TGGACTAACGATTTCTGTGATTTG 57.519 37.500 0.00 0.00 0.00 2.32
2586 2944 3.877508 ACTTGTTTTGCAGAGTAGTGTCC 59.122 43.478 0.00 0.00 0.00 4.02
2646 3004 0.906066 TGGAGGCGGTGCTGTTATTA 59.094 50.000 0.00 0.00 0.00 0.98
2699 3057 1.462283 CTCGCCAACATCTCACTTGTG 59.538 52.381 0.00 0.00 0.00 3.33
2738 3096 9.838339 ATCACGTTTTCTCCTTTAGATGAATAT 57.162 29.630 0.00 0.00 33.05 1.28
2772 3130 7.036220 TGATCTCTGTCGATTTTTCTTACTCC 58.964 38.462 0.00 0.00 0.00 3.85
3058 3420 2.807967 TCTCAAGTCGTTTGCATCTTGG 59.192 45.455 12.50 6.98 38.13 3.61
3286 3648 1.664321 GCCTCTCCCGAGCGAAGTTA 61.664 60.000 0.00 0.00 35.90 2.24
3296 3658 3.067106 CGAGCGAAGTTATAATGCCCAT 58.933 45.455 0.00 0.00 0.00 4.00
3317 3679 7.556844 CCCATACAGAGAATAACACAACTAGT 58.443 38.462 0.00 0.00 0.00 2.57
3318 3680 8.692710 CCCATACAGAGAATAACACAACTAGTA 58.307 37.037 0.00 0.00 0.00 1.82
3427 3789 3.809905 ACTTCTCAAGTCAACTGTTCCC 58.190 45.455 0.00 0.00 37.02 3.97
3464 3826 7.725818 TTGCAAAGAATTATTCATGTGCAAA 57.274 28.000 25.82 16.42 43.48 3.68
3507 3869 1.382629 CACCCACCCCCTCGAAAAT 59.617 57.895 0.00 0.00 0.00 1.82
3513 3875 3.383505 CCCACCCCCTCGAAAATAATTTC 59.616 47.826 0.00 0.00 41.27 2.17
3569 3931 7.038373 AGGCCCTGCAAAAGATTAAGAATTTTA 60.038 33.333 0.00 0.00 0.00 1.52
3620 3982 6.037830 CCCATTCGACGACTTATAAATTGGTT 59.962 38.462 0.00 0.00 0.00 3.67
3633 3995 2.770164 ATTGGTTCCAGGAGACGAAG 57.230 50.000 0.00 0.00 0.00 3.79
3814 4176 6.017852 GCTAATGTTAAGAGCTCCATGGTTAC 60.018 42.308 12.58 2.32 33.28 2.50
4019 4381 7.868415 AGCGAAGTATCACTATAGGTTCATTTC 59.132 37.037 4.43 1.29 0.00 2.17
4068 4430 3.055167 TGACCATGACCACAGTCCAATAG 60.055 47.826 0.00 0.00 42.81 1.73
4080 4442 5.882557 CACAGTCCAATAGCCAAGAAATACT 59.117 40.000 0.00 0.00 0.00 2.12
4120 4485 6.670695 AAGAAAAGACATGCAGGGTTAAAT 57.329 33.333 2.31 0.00 0.00 1.40
4129 4494 9.420118 AGACATGCAGGGTTAAATTTATGATAA 57.580 29.630 2.31 0.00 0.00 1.75
4199 4565 2.949451 TTTCCAGCGCAAGTTTTTGA 57.051 40.000 11.47 0.00 36.36 2.69
4243 4609 9.483489 TTGTGAGATGTATAAAGGAGGTACTAA 57.517 33.333 0.00 0.00 41.55 2.24
4312 4678 7.807687 TTATAAGACGTTTTAGACAGCTGAC 57.192 36.000 23.35 15.44 0.00 3.51
4313 4679 4.323553 AAGACGTTTTAGACAGCTGACT 57.676 40.909 23.35 22.53 0.00 3.41
4314 4680 3.903360 AGACGTTTTAGACAGCTGACTC 58.097 45.455 23.35 8.66 0.00 3.36
4320 4686 5.293560 GTTTTAGACAGCTGACTCTGAACT 58.706 41.667 23.35 8.36 37.51 3.01
4321 4687 6.448006 GTTTTAGACAGCTGACTCTGAACTA 58.552 40.000 23.35 0.00 37.51 2.24
4328 4694 4.394300 CAGCTGACTCTGAACTATTTTGGG 59.606 45.833 8.42 0.00 36.19 4.12
4342 4708 0.817634 TTTGGGCACTGTCTGAACGG 60.818 55.000 0.00 0.00 37.81 4.44
4362 4728 8.702438 TGAACGGTCTAAAACGTCTTATAAAAG 58.298 33.333 0.33 0.00 43.31 2.27
4407 4775 4.154195 CCCTCCTGTTTGTCTTTTCATACG 59.846 45.833 0.00 0.00 0.00 3.06
4408 4776 4.154195 CCTCCTGTTTGTCTTTTCATACGG 59.846 45.833 0.00 0.00 0.00 4.02
4419 4787 8.270080 TGTCTTTTCATACGGCATACAAATAA 57.730 30.769 0.00 0.00 0.00 1.40
4421 4789 8.609176 GTCTTTTCATACGGCATACAAATAAGA 58.391 33.333 0.00 0.00 0.00 2.10
4422 4790 8.609176 TCTTTTCATACGGCATACAAATAAGAC 58.391 33.333 0.00 0.00 0.00 3.01
4423 4791 6.854496 TTCATACGGCATACAAATAAGACC 57.146 37.500 0.00 0.00 0.00 3.85
4424 4792 6.169557 TCATACGGCATACAAATAAGACCT 57.830 37.500 0.00 0.00 0.00 3.85
4425 4793 6.220930 TCATACGGCATACAAATAAGACCTC 58.779 40.000 0.00 0.00 0.00 3.85
4426 4794 4.755266 ACGGCATACAAATAAGACCTCT 57.245 40.909 0.00 0.00 0.00 3.69
4429 4797 5.944007 ACGGCATACAAATAAGACCTCTTTT 59.056 36.000 0.00 0.00 37.40 2.27
4431 4799 7.608761 ACGGCATACAAATAAGACCTCTTTTAA 59.391 33.333 0.00 0.00 37.40 1.52
4465 4833 3.485463 AGTTTTCCCACTCATTCGACA 57.515 42.857 0.00 0.00 0.00 4.35
4474 4842 3.119743 CCACTCATTCGACAATGTGCATT 60.120 43.478 0.00 0.00 40.47 3.56
4477 4845 3.244156 TCATTCGACAATGTGCATTTGC 58.756 40.909 11.11 0.00 40.47 3.68
4518 4886 6.681729 TTAGTAACTTGGAACCAGTGAGAT 57.318 37.500 0.00 0.00 0.00 2.75
4528 4896 3.045601 ACCAGTGAGATTTTGACCTCG 57.954 47.619 0.00 0.00 32.30 4.63
4554 4922 6.811665 TCATCTCGGTACTTTAAGTGTTGATG 59.188 38.462 8.00 12.75 0.00 3.07
4613 4986 2.350498 GCAATGCTGCCACATGAATTTC 59.650 45.455 0.00 0.00 43.26 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.744867 GCCATGACCTAGTATGAGCATGTT 60.745 45.833 0.00 0.00 33.22 2.71
26 28 0.689745 TACGGCTACTCTTGGGCCAT 60.690 55.000 7.26 0.00 45.50 4.40
47 49 4.799564 TGCGGGCAGAGAAAATAAAATT 57.200 36.364 0.00 0.00 0.00 1.82
64 66 0.039798 GCATCCAAGTGCATATGCGG 60.040 55.000 22.21 16.69 44.43 5.69
65 67 3.467043 GCATCCAAGTGCATATGCG 57.533 52.632 22.21 8.12 44.43 4.73
76 78 1.689984 TGCTGTGTGAAAGCATCCAA 58.310 45.000 0.00 0.00 45.50 3.53
93 95 2.200170 GAAACCCACGCCAGATGTGC 62.200 60.000 0.00 0.00 36.01 4.57
95 97 0.889186 GTGAAACCCACGCCAGATGT 60.889 55.000 0.00 0.00 35.86 3.06
96 98 1.875963 GTGAAACCCACGCCAGATG 59.124 57.895 0.00 0.00 35.86 2.90
122 124 3.294214 ACCGTTCTACCGTGGAGATATT 58.706 45.455 0.00 0.00 0.00 1.28
127 129 0.453390 GGTACCGTTCTACCGTGGAG 59.547 60.000 0.00 0.00 0.00 3.86
228 230 9.258826 TGTTTGGAAATACTTGTCAATGAAATG 57.741 29.630 0.00 0.00 0.00 2.32
234 236 7.451255 TCCATCTGTTTGGAAATACTTGTCAAT 59.549 33.333 0.00 0.00 42.82 2.57
235 237 6.775142 TCCATCTGTTTGGAAATACTTGTCAA 59.225 34.615 0.00 0.00 42.82 3.18
248 250 5.365021 AGAATCCTACTCCATCTGTTTGG 57.635 43.478 0.00 0.00 38.18 3.28
249 251 7.533426 CAAAAGAATCCTACTCCATCTGTTTG 58.467 38.462 0.00 0.00 0.00 2.93
250 252 6.151817 GCAAAAGAATCCTACTCCATCTGTTT 59.848 38.462 0.00 0.00 0.00 2.83
251 253 5.649831 GCAAAAGAATCCTACTCCATCTGTT 59.350 40.000 0.00 0.00 0.00 3.16
469 471 9.743057 CTTCATAATGTTTGACCAACTTTACAA 57.257 29.630 1.35 0.00 37.65 2.41
488 490 7.095229 CGATTTGTCTGAGGTCAAACTTCATAA 60.095 37.037 6.05 0.00 33.62 1.90
529 531 6.488683 TGTTCTGTATTCGGTCCATTTCTTTT 59.511 34.615 0.00 0.00 0.00 2.27
538 540 5.299782 AGAGATAGTGTTCTGTATTCGGTCC 59.700 44.000 0.00 0.00 0.00 4.46
606 608 8.026607 TCAAAACTGGAAATACGATTTGAATCC 58.973 33.333 0.00 0.00 33.74 3.01
611 613 8.574196 AACTTCAAAACTGGAAATACGATTTG 57.426 30.769 0.00 0.00 0.00 2.32
679 681 2.937469 TTTGTTGTGTGTTGAGGCTG 57.063 45.000 0.00 0.00 0.00 4.85
705 707 2.294074 TCCTGGAAACGGTGTCTTTTG 58.706 47.619 0.00 0.00 33.66 2.44
710 712 1.535462 CAACATCCTGGAAACGGTGTC 59.465 52.381 0.00 0.00 33.66 3.67
770 774 4.404654 CGTTTCGCCCCTTGCTGC 62.405 66.667 0.00 0.00 38.05 5.25
771 775 3.737172 CCGTTTCGCCCCTTGCTG 61.737 66.667 0.00 0.00 38.05 4.41
772 776 2.400269 TTACCGTTTCGCCCCTTGCT 62.400 55.000 0.00 0.00 38.05 3.91
773 777 1.517210 TTTACCGTTTCGCCCCTTGC 61.517 55.000 0.00 0.00 0.00 4.01
774 778 0.953003 TTTTACCGTTTCGCCCCTTG 59.047 50.000 0.00 0.00 0.00 3.61
775 779 1.337703 GTTTTTACCGTTTCGCCCCTT 59.662 47.619 0.00 0.00 0.00 3.95
776 780 0.953727 GTTTTTACCGTTTCGCCCCT 59.046 50.000 0.00 0.00 0.00 4.79
777 781 0.953727 AGTTTTTACCGTTTCGCCCC 59.046 50.000 0.00 0.00 0.00 5.80
799 803 4.051167 TAGGAGGGGTGCGACCGA 62.051 66.667 0.00 0.00 39.83 4.69
851 870 1.467920 CGGTCCCGGTCTTAAGTAGT 58.532 55.000 0.00 0.00 35.56 2.73
980 1012 3.721706 GTGCTGCTGCTACCCCCT 61.722 66.667 17.00 0.00 40.48 4.79
1219 1255 6.039616 AGTCGAGCAATAGAAAGAATCTGAC 58.960 40.000 0.00 0.00 39.30 3.51
1222 1258 6.314896 CCAAAGTCGAGCAATAGAAAGAATCT 59.685 38.462 0.00 0.00 42.48 2.40
1254 1337 2.808206 ATAGTAGCACCGGCCCAGC 61.808 63.158 0.00 0.00 42.56 4.85
1263 1346 2.805099 GCAGGCAGAATCATAGTAGCAC 59.195 50.000 0.00 0.00 0.00 4.40
1269 1352 2.634815 ACAGGCAGGCAGAATCATAG 57.365 50.000 0.00 0.00 0.00 2.23
1294 1377 1.674441 TCTCAGTATTACGAGGCCACG 59.326 52.381 21.59 21.59 39.31 4.94
1296 1379 1.674441 CGTCTCAGTATTACGAGGCCA 59.326 52.381 5.01 0.00 38.89 5.36
1299 1382 2.548904 CTCCCGTCTCAGTATTACGAGG 59.451 54.545 12.51 0.00 38.89 4.63
1345 1428 2.617774 CAAATTTTGCCACCAACCCTTG 59.382 45.455 0.00 0.00 0.00 3.61
1422 1512 0.724785 GCTTTGTTTAGTCCACGCGC 60.725 55.000 5.73 0.00 0.00 6.86
1430 1520 7.425606 CCTGAAACTACATTGCTTTGTTTAGT 58.574 34.615 0.00 0.00 32.01 2.24
1499 1589 0.404040 CCCACACCACCACCAGTAAT 59.596 55.000 0.00 0.00 0.00 1.89
1515 1605 3.901844 ACTACTAGTTGCTTTCTGACCCA 59.098 43.478 0.00 0.00 0.00 4.51
1519 1609 9.998106 AAAAGAATACTACTAGTTGCTTTCTGA 57.002 29.630 17.04 0.00 0.00 3.27
1521 1611 9.780186 ACAAAAGAATACTACTAGTTGCTTTCT 57.220 29.630 0.00 8.43 0.00 2.52
1524 1614 9.209175 CAGACAAAAGAATACTACTAGTTGCTT 57.791 33.333 0.00 0.00 0.00 3.91
1530 1620 9.029243 CAGCATCAGACAAAAGAATACTACTAG 57.971 37.037 0.00 0.00 0.00 2.57
1531 1621 8.749354 TCAGCATCAGACAAAAGAATACTACTA 58.251 33.333 0.00 0.00 0.00 1.82
1533 1623 7.834068 TCAGCATCAGACAAAAGAATACTAC 57.166 36.000 0.00 0.00 0.00 2.73
1534 1624 8.043113 ACATCAGCATCAGACAAAAGAATACTA 58.957 33.333 0.00 0.00 0.00 1.82
1536 1626 7.081526 ACATCAGCATCAGACAAAAGAATAC 57.918 36.000 0.00 0.00 0.00 1.89
1543 1633 4.080413 TCCCATACATCAGCATCAGACAAA 60.080 41.667 0.00 0.00 0.00 2.83
1553 1643 5.474532 TGCAAGAATATTCCCATACATCAGC 59.525 40.000 11.92 1.58 0.00 4.26
1554 1644 7.148120 GGATGCAAGAATATTCCCATACATCAG 60.148 40.741 22.52 3.54 33.55 2.90
1555 1645 6.660521 GGATGCAAGAATATTCCCATACATCA 59.339 38.462 22.52 9.91 33.55 3.07
1640 1730 5.794687 ATTCGACAACAAGATTTATCGCA 57.205 34.783 0.00 0.00 0.00 5.10
1671 1761 1.405821 ACTTCTAATGCCTCCTCGTCG 59.594 52.381 0.00 0.00 0.00 5.12
1674 1764 3.526931 TTCACTTCTAATGCCTCCTCG 57.473 47.619 0.00 0.00 0.00 4.63
1710 1805 1.271656 GGAGCGGTACACTGTTGTAGT 59.728 52.381 0.00 0.00 38.95 2.73
1791 1996 8.702163 ATAAATGTGTGCTAAATAAACTTGGC 57.298 30.769 0.00 0.00 33.68 4.52
1803 2008 9.642327 TCTAAAACGAAGTATAAATGTGTGCTA 57.358 29.630 0.00 0.00 45.00 3.49
1816 2021 8.500773 CAACTTAGCCAAATCTAAAACGAAGTA 58.499 33.333 0.00 0.00 45.00 2.24
1912 2121 6.238731 CCAAGAGAAAATATTAAGATGCGGCA 60.239 38.462 4.58 4.58 0.00 5.69
1956 2165 5.237344 GTCAGTTTGACTAATCAGCTTGTGT 59.763 40.000 2.08 0.00 43.73 3.72
2129 2339 8.415950 TTTCCTCTGAAAGGCAATACAATTTA 57.584 30.769 0.00 0.00 45.78 1.40
2306 2660 2.429930 CCCACCGTGCTCTTTCCA 59.570 61.111 0.00 0.00 0.00 3.53
2504 2860 9.968743 GTCTTTCCATTCTAATTACTACAAACG 57.031 33.333 0.00 0.00 0.00 3.60
2557 2914 5.485662 ACTCTGCAAAACAAGTAGTTCAC 57.514 39.130 0.00 0.00 40.26 3.18
2586 2944 6.091034 CGATGCATTGAGGATAAATCTCTCAG 59.909 42.308 8.37 3.93 36.33 3.35
2673 3031 1.338105 TGAGATGTTGGCGAGAACAGG 60.338 52.381 5.97 0.00 39.18 4.00
2764 3122 8.001300 TCTTCATATATCTCCTGGGAGTAAGA 57.999 38.462 15.30 10.83 42.49 2.10
2772 3130 7.016072 ACAGACCTTTCTTCATATATCTCCTGG 59.984 40.741 0.00 0.00 0.00 4.45
2987 3345 5.666969 TTGGTGTCTCATTTAGTGTTTCG 57.333 39.130 0.00 0.00 0.00 3.46
3058 3420 5.527582 AGAAAGACAGATGTGTACAACCAAC 59.472 40.000 0.00 0.00 36.88 3.77
3286 3648 7.517320 TGTGTTATTCTCTGTATGGGCATTAT 58.483 34.615 0.00 0.00 0.00 1.28
3427 3789 6.695292 ATTCTTTGCAAAAATAGAAGCACG 57.305 33.333 13.84 0.00 36.62 5.34
3464 3826 2.158769 TGGAGAAAGCGTGATATGCCAT 60.159 45.455 0.00 0.00 0.00 4.40
3507 3869 6.449041 AGGTAAGTTACATCAGGGGGAAATTA 59.551 38.462 14.81 0.00 0.00 1.40
3513 3875 2.844348 ACAGGTAAGTTACATCAGGGGG 59.156 50.000 14.81 0.00 0.00 5.40
3569 3931 1.688772 GCCATGGAATGCTCAGTGAT 58.311 50.000 18.40 0.00 44.97 3.06
3620 3982 0.614697 TGCATCCTTCGTCTCCTGGA 60.615 55.000 0.00 0.00 0.00 3.86
3767 4129 6.769512 AGCTCCATCCGCTATTCTTTTATTA 58.230 36.000 0.00 0.00 35.63 0.98
3814 4176 7.007725 GTGAAAAATGTAAGTGCAATGATCTCG 59.992 37.037 0.00 0.00 0.00 4.04
3872 4234 2.289274 TGAACACCAATGTACTGTTGCG 59.711 45.455 2.48 1.55 38.45 4.85
3874 4236 5.163663 ACAACTGAACACCAATGTACTGTTG 60.164 40.000 0.00 0.00 42.03 3.33
4019 4381 6.453943 ACTATTGATTCCTGTCATGATCTCG 58.546 40.000 0.00 0.00 0.00 4.04
4093 4458 3.960102 ACCCTGCATGTCTTTTCTTTTCA 59.040 39.130 0.00 0.00 0.00 2.69
4153 4519 4.145807 CTCTCACACGGTTCCTATAGGAT 58.854 47.826 22.30 4.47 44.98 3.24
4250 4616 9.378551 GAAGGAGTGTCAAATTATATACACACA 57.621 33.333 7.15 0.00 43.65 3.72
4255 4621 8.522178 CTCGGAAGGAGTGTCAAATTATATAC 57.478 38.462 0.00 0.00 38.02 1.47
4296 4662 3.902150 TCAGAGTCAGCTGTCTAAAACG 58.098 45.455 13.61 1.63 37.20 3.60
4298 4664 5.537300 AGTTCAGAGTCAGCTGTCTAAAA 57.463 39.130 13.61 5.88 37.20 1.52
4300 4666 6.842437 AATAGTTCAGAGTCAGCTGTCTAA 57.158 37.500 13.61 2.19 37.20 2.10
4309 4675 4.072131 GTGCCCAAAATAGTTCAGAGTCA 58.928 43.478 0.00 0.00 0.00 3.41
4312 4678 4.074970 ACAGTGCCCAAAATAGTTCAGAG 58.925 43.478 0.00 0.00 0.00 3.35
4313 4679 4.072131 GACAGTGCCCAAAATAGTTCAGA 58.928 43.478 0.00 0.00 0.00 3.27
4314 4680 4.074970 AGACAGTGCCCAAAATAGTTCAG 58.925 43.478 0.00 0.00 0.00 3.02
4320 4686 2.811431 CGTTCAGACAGTGCCCAAAATA 59.189 45.455 0.00 0.00 0.00 1.40
4321 4687 1.608590 CGTTCAGACAGTGCCCAAAAT 59.391 47.619 0.00 0.00 0.00 1.82
4328 4694 2.433868 TTAGACCGTTCAGACAGTGC 57.566 50.000 0.00 0.00 0.00 4.40
4362 4728 8.850007 AGGGACTTAAAATACTCTCTTTTCAC 57.150 34.615 0.00 0.00 27.25 3.18
4367 4733 6.731448 ACAGGAGGGACTTAAAATACTCTCTT 59.269 38.462 0.00 0.00 41.55 2.85
4407 4775 8.957466 ACTTAAAAGAGGTCTTATTTGTATGCC 58.043 33.333 0.00 0.00 34.61 4.40
4408 4776 9.989869 GACTTAAAAGAGGTCTTATTTGTATGC 57.010 33.333 0.00 0.00 34.61 3.14
4436 4804 7.651704 CGAATGAGTGGGAAAACTACAATTTTT 59.348 33.333 0.00 0.00 31.90 1.94
4450 4818 2.698803 CACATTGTCGAATGAGTGGGA 58.301 47.619 4.12 0.00 41.49 4.37
4453 4821 3.752412 ATGCACATTGTCGAATGAGTG 57.248 42.857 4.12 4.78 41.49 3.51
4454 4822 4.478699 CAAATGCACATTGTCGAATGAGT 58.521 39.130 4.12 0.00 41.49 3.41
4455 4823 3.302434 GCAAATGCACATTGTCGAATGAG 59.698 43.478 13.77 0.00 41.96 2.90
4456 4824 3.244156 GCAAATGCACATTGTCGAATGA 58.756 40.909 13.77 0.00 41.96 2.57
4496 4864 6.681729 AATCTCACTGGTTCCAAGTTACTA 57.318 37.500 0.00 0.00 0.00 1.82
4504 4872 3.138283 AGGTCAAAATCTCACTGGTTCCA 59.862 43.478 0.00 0.00 0.00 3.53
4518 4886 1.616865 ACCGAGATGACGAGGTCAAAA 59.383 47.619 2.20 0.00 45.96 2.44
4528 4896 6.154445 TCAACACTTAAAGTACCGAGATGAC 58.846 40.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.