Multiple sequence alignment - TraesCS5A01G404700

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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 TraesCS5A01G404700 chr5A 100.000 2561 0 0 1 2561 596488232 596485672 0.000000e+00 4730.0
1 TraesCS5A01G404700 chr5A 100.000 28 0 0 2534 2561 217101443 217101416 5.000000e-03 52.8
2 TraesCS5A01G404700 chr5D 94.067 1736 75 9 470 2198 477297535 477295821 0.000000e+00 2610.0
3 TraesCS5A01G404700 chr5D 89.344 488 14 8 1 466 477298111 477297640 1.710000e-161 579.0
4 TraesCS5A01G404700 chr5B 93.480 1365 70 4 473 1833 584867833 584866484 0.000000e+00 2010.0
5 TraesCS5A01G404700 chr5B 94.385 374 9 4 1 365 584868592 584868222 4.780000e-157 564.0
6 TraesCS5A01G404700 chr5B 84.192 291 26 11 2186 2473 584861525 584861252 5.430000e-67 265.0
7 TraesCS5A01G404700 chr5B 93.827 162 10 0 2037 2198 584863746 584863585 7.080000e-61 244.0
8 TraesCS5A01G404700 chr5B 96.183 131 5 0 1875 2005 584865372 584865242 5.550000e-52 215.0
9 TraesCS5A01G404700 chr5B 97.980 99 2 0 2439 2537 584861252 584861154 3.390000e-39 172.0
10 TraesCS5A01G404700 chr3A 80.905 199 33 3 1361 1558 534478484 534478678 4.410000e-33 152.0
11 TraesCS5A01G404700 chr7D 91.667 96 7 1 2185 2279 582305610 582305515 5.750000e-27 132.0
12 TraesCS5A01G404700 chr7B 88.542 96 10 1 2185 2279 650133469 650133374 5.790000e-22 115.0
13 TraesCS5A01G404700 chr4B 100.000 28 0 0 2534 2561 635011305 635011278 5.000000e-03 52.8


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 TraesCS5A01G404700 chr5A 596485672 596488232 2560 True 4730.000000 4730 100.000000 1 2561 1 chr5A.!!$R2 2560
1 TraesCS5A01G404700 chr5D 477295821 477298111 2290 True 1594.500000 2610 91.705500 1 2198 2 chr5D.!!$R1 2197
2 TraesCS5A01G404700 chr5B 584861154 584868592 7438 True 578.333333 2010 93.341167 1 2537 6 chr5B.!!$R1 2536

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
92 98 1.860950 ACGATGCGCATAAACTAGCAG 59.139 47.619 25.4 8.55 43.20 4.24 F
1060 1380 0.037447 GGGAAAGAGCAGCTTCAGGT 59.963 55.000 0.0 0.00 35.24 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1520 0.251297 TCTTCCCGTCGTTGTCCCTA 60.251 55.0 0.0 0.0 0.00 3.53 R
2392 7337 0.178068 TAAGCCCAAGCGAGATGGTC 59.822 55.0 0.0 0.0 46.67 4.02 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
92 98 1.860950 ACGATGCGCATAAACTAGCAG 59.139 47.619 25.40 8.55 43.20 4.24
158 173 5.526111 CAGGTGGGTTATTTATCTACCAACG 59.474 44.000 0.00 0.00 40.51 4.10
159 174 5.426185 AGGTGGGTTATTTATCTACCAACGA 59.574 40.000 0.00 0.00 40.51 3.85
160 175 5.525012 GGTGGGTTATTTATCTACCAACGAC 59.475 44.000 0.00 0.00 36.85 4.34
161 176 6.343703 GTGGGTTATTTATCTACCAACGACT 58.656 40.000 0.00 0.00 33.51 4.18
162 177 6.257193 GTGGGTTATTTATCTACCAACGACTG 59.743 42.308 0.00 0.00 33.51 3.51
163 178 6.154877 TGGGTTATTTATCTACCAACGACTGA 59.845 38.462 0.00 0.00 33.51 3.41
235 257 4.202461 TGACTTGCACAATTCCTAACTCCT 60.202 41.667 0.00 0.00 0.00 3.69
277 299 2.401766 GGCACATGGAGGTTCAGCG 61.402 63.158 0.00 0.00 0.00 5.18
381 588 9.260002 GAAATCTCAGTATCCATCTTCTTCTTC 57.740 37.037 0.00 0.00 0.00 2.87
382 589 8.551682 AATCTCAGTATCCATCTTCTTCTTCT 57.448 34.615 0.00 0.00 0.00 2.85
383 590 7.969690 TCTCAGTATCCATCTTCTTCTTCTT 57.030 36.000 0.00 0.00 0.00 2.52
384 591 8.372877 TCTCAGTATCCATCTTCTTCTTCTTT 57.627 34.615 0.00 0.00 0.00 2.52
385 592 8.820831 TCTCAGTATCCATCTTCTTCTTCTTTT 58.179 33.333 0.00 0.00 0.00 2.27
386 593 9.447157 CTCAGTATCCATCTTCTTCTTCTTTTT 57.553 33.333 0.00 0.00 0.00 1.94
434 641 5.535783 TGACATTTGAAGAAAGCCAGATCAA 59.464 36.000 0.00 0.00 0.00 2.57
438 645 6.906157 TTTGAAGAAAGCCAGATCAAGAAT 57.094 33.333 0.00 0.00 32.21 2.40
441 648 5.646793 TGAAGAAAGCCAGATCAAGAATCAG 59.353 40.000 0.00 0.00 36.79 2.90
442 649 3.946558 AGAAAGCCAGATCAAGAATCAGC 59.053 43.478 0.00 0.00 36.79 4.26
444 651 3.579534 AGCCAGATCAAGAATCAGCAT 57.420 42.857 0.00 0.00 38.01 3.79
462 669 5.049828 CAGCATTGTGATCGGTTGATACTA 58.950 41.667 0.00 0.00 34.09 1.82
463 670 5.698089 CAGCATTGTGATCGGTTGATACTAT 59.302 40.000 0.00 0.00 34.09 2.12
464 671 5.928839 AGCATTGTGATCGGTTGATACTATC 59.071 40.000 0.00 0.00 34.09 2.08
465 672 5.696270 GCATTGTGATCGGTTGATACTATCA 59.304 40.000 0.00 0.00 34.09 2.15
466 673 6.346919 GCATTGTGATCGGTTGATACTATCAC 60.347 42.308 0.00 0.00 42.06 3.06
468 675 5.831997 TGTGATCGGTTGATACTATCACTG 58.168 41.667 13.17 1.01 42.13 3.66
485 800 5.055265 TCACTGAACCCATAAGTTTCCAA 57.945 39.130 0.00 0.00 0.00 3.53
491 806 7.893302 ACTGAACCCATAAGTTTCCAATATTCA 59.107 33.333 0.00 0.00 0.00 2.57
507 822 5.695851 ATATTCAAAATCTGCATCGTCCC 57.304 39.130 0.00 0.00 0.00 4.46
534 849 6.094325 ACCTCGTGAAAGAAGAGATACTACTG 59.906 42.308 0.00 0.00 32.22 2.74
536 851 7.280428 CCTCGTGAAAGAAGAGATACTACTGTA 59.720 40.741 0.00 0.00 32.22 2.74
756 1075 2.625790 GGGGAGTAGCTGACAGTATCTG 59.374 54.545 3.99 0.00 37.52 2.90
789 1108 2.213499 CAGTTGCCAACGAACTTCTCT 58.787 47.619 1.20 0.00 36.23 3.10
864 1183 2.360191 TTGGCATCCCAAGCTCCC 59.640 61.111 0.00 0.00 46.01 4.30
920 1240 3.084039 CCTTTCTTCCACAGCTGCATTA 58.916 45.455 15.27 0.00 0.00 1.90
921 1241 3.128242 CCTTTCTTCCACAGCTGCATTAG 59.872 47.826 15.27 6.89 0.00 1.73
943 1263 3.368843 GCAATTTAGCATTGGACAAGTGC 59.631 43.478 9.77 9.77 39.10 4.40
1015 1335 1.301322 TTCATGGCGAACGTGAGCA 60.301 52.632 15.82 4.52 45.35 4.26
1060 1380 0.037447 GGGAAAGAGCAGCTTCAGGT 59.963 55.000 0.00 0.00 35.24 4.00
1066 1386 2.359230 GCAGCTTCAGGTTCGGCT 60.359 61.111 0.00 0.00 35.23 5.52
1080 1400 2.980233 GGCTTGCCGCTGTTCTGT 60.980 61.111 0.00 0.00 39.13 3.41
1200 1520 2.114616 AGGATCTTCCAGCACTTCGAT 58.885 47.619 0.00 0.00 39.61 3.59
1230 1550 3.541713 GGGAAGATCTCCGGCGCT 61.542 66.667 7.64 0.00 46.51 5.92
1295 1615 2.484203 GTCCTCGTCGTCGGAAGG 59.516 66.667 1.55 2.89 37.69 3.46
1296 1616 3.437795 TCCTCGTCGTCGGAAGGC 61.438 66.667 1.55 0.00 37.69 4.35
1320 1640 4.116328 CTGCTCGACTTCGCCGGA 62.116 66.667 5.05 0.00 39.60 5.14
1613 1933 4.020573 CCAGTGGTGGTTGTTCATACTCTA 60.021 45.833 0.00 0.00 39.30 2.43
1703 2023 5.120830 GTCTCACAAGTGACACCATTGTATC 59.879 44.000 11.59 2.31 37.99 2.24
1717 2037 8.213679 ACACCATTGTATCAATGAAGCTATACT 58.786 33.333 19.74 0.00 32.60 2.12
1834 2156 9.617523 AAAATGAGAAGTTCCATGAACAAAAAT 57.382 25.926 9.42 0.00 44.11 1.82
1880 3286 7.096551 CACCGTTTGAAATTTTAGATGGGAAT 58.903 34.615 14.07 0.00 0.00 3.01
1918 3324 2.765135 TCTTCTCATCTGGAAGGCTGAG 59.235 50.000 0.00 0.00 42.06 3.35
2015 3421 6.428159 TGAAGCAAGATTCAGTTACTTTCTCC 59.572 38.462 0.00 0.00 34.31 3.71
2031 3455 4.301072 TTCTCCCCCAAATCTTACACAG 57.699 45.455 0.00 0.00 0.00 3.66
2120 4990 7.658261 CCGTAATATGTCTGTTGATCCTCTAA 58.342 38.462 0.00 0.00 0.00 2.10
2134 5004 5.536538 TGATCCTCTAACAGATAGCGTCAAT 59.463 40.000 0.00 0.00 0.00 2.57
2138 5008 8.631480 TCCTCTAACAGATAGCGTCAATATAA 57.369 34.615 0.00 0.00 0.00 0.98
2209 5079 9.563898 TTACTAGTATGTATATACGTGCAATGC 57.436 33.333 20.89 0.00 43.17 3.56
2216 7159 6.508777 TGTATATACGTGCAATGCTGTCTTA 58.491 36.000 6.82 2.20 0.00 2.10
2224 7167 5.509272 CGTGCAATGCTGTCTTAAATTACAG 59.491 40.000 6.82 2.29 44.79 2.74
2229 7172 6.992063 ATGCTGTCTTAAATTACAGAGTGG 57.008 37.500 9.75 0.00 44.79 4.00
2234 7177 8.780249 GCTGTCTTAAATTACAGAGTGGTTTTA 58.220 33.333 9.75 0.00 44.79 1.52
2236 7179 9.841295 TGTCTTAAATTACAGAGTGGTTTTAGT 57.159 29.630 0.00 0.00 0.00 2.24
2246 7191 8.514330 ACAGAGTGGTTTTAGTTACAAAATCA 57.486 30.769 3.23 3.23 36.42 2.57
2383 7328 7.363031 AGTGGTATTCTACTCTCTCCCATTAA 58.637 38.462 0.00 0.00 29.39 1.40
2388 7333 9.364653 GTATTCTACTCTCTCCCATTAACCTAA 57.635 37.037 0.00 0.00 0.00 2.69
2392 7337 4.717280 ACTCTCTCCCATTAACCTAACCAG 59.283 45.833 0.00 0.00 0.00 4.00
2401 7346 4.730949 TTAACCTAACCAGACCATCTCG 57.269 45.455 0.00 0.00 0.00 4.04
2408 7353 1.817099 CAGACCATCTCGCTTGGGC 60.817 63.158 3.65 0.20 43.13 5.36
2416 7361 2.024176 TCTCGCTTGGGCTTAATGTC 57.976 50.000 0.00 0.00 36.09 3.06
2428 7373 3.456280 GCTTAATGTCTCCTCTGCTCAG 58.544 50.000 0.00 0.00 0.00 3.35
2502 7481 0.104304 ATGGGACGCGATGGTTCTAC 59.896 55.000 15.93 0.00 0.00 2.59
2537 7516 6.299141 AGACATCCATGTTTTACTGTTCACT 58.701 36.000 0.00 0.00 41.95 3.41
2538 7517 7.450074 AGACATCCATGTTTTACTGTTCACTA 58.550 34.615 0.00 0.00 41.95 2.74
2539 7518 7.604164 AGACATCCATGTTTTACTGTTCACTAG 59.396 37.037 0.00 0.00 41.95 2.57
2540 7519 7.450074 ACATCCATGTTTTACTGTTCACTAGA 58.550 34.615 0.00 0.00 37.90 2.43
2541 7520 7.936847 ACATCCATGTTTTACTGTTCACTAGAA 59.063 33.333 0.00 0.00 37.90 2.10
2552 7531 2.579207 TCACTAGAACATGTAGGCGC 57.421 50.000 0.00 0.00 0.00 6.53
2553 7532 1.200483 CACTAGAACATGTAGGCGCG 58.800 55.000 0.00 0.00 0.00 6.86
2554 7533 0.527817 ACTAGAACATGTAGGCGCGC 60.528 55.000 25.94 25.94 0.00 6.86
2555 7534 1.540607 CTAGAACATGTAGGCGCGCG 61.541 60.000 28.44 28.44 0.00 6.86
2556 7535 2.274232 TAGAACATGTAGGCGCGCGT 62.274 55.000 32.35 30.14 0.00 6.01
2557 7536 2.736682 GAACATGTAGGCGCGCGTT 61.737 57.895 32.36 24.25 0.00 4.84
2558 7537 2.879942 GAACATGTAGGCGCGCGTTG 62.880 60.000 32.36 24.87 0.00 4.10
2559 7538 4.868900 CATGTAGGCGCGCGTTGC 62.869 66.667 32.36 23.42 41.47 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 4.021102 AGATTGTCAGGTACCAACTTGG 57.979 45.455 15.94 6.24 45.02 3.61
92 98 4.054671 CGCATCCACTAGAAGAATCTTCC 58.945 47.826 18.46 2.29 37.10 3.46
158 173 2.558378 TGCTGCTGCTTATCATCAGTC 58.442 47.619 17.00 0.00 40.19 3.51
159 174 2.704464 TGCTGCTGCTTATCATCAGT 57.296 45.000 17.00 0.00 40.19 3.41
160 175 3.403968 AGATGCTGCTGCTTATCATCAG 58.596 45.455 17.00 2.21 40.81 2.90
161 176 3.487120 AGATGCTGCTGCTTATCATCA 57.513 42.857 17.00 0.00 40.48 3.07
162 177 4.389382 CACTAGATGCTGCTGCTTATCATC 59.611 45.833 17.00 10.41 40.48 2.92
163 178 4.316645 CACTAGATGCTGCTGCTTATCAT 58.683 43.478 17.00 0.96 40.48 2.45
235 257 0.473755 ATGGATGCCATCAACCGCTA 59.526 50.000 7.06 0.00 40.74 4.26
277 299 2.898705 TGGTTCAACAACAATGCAACC 58.101 42.857 0.00 0.00 33.70 3.77
413 620 6.263516 TCTTGATCTGGCTTTCTTCAAATG 57.736 37.500 0.00 0.00 0.00 2.32
434 641 3.272574 ACCGATCACAATGCTGATTCT 57.727 42.857 0.00 0.00 30.62 2.40
438 645 2.470983 TCAACCGATCACAATGCTGA 57.529 45.000 0.00 0.00 0.00 4.26
441 648 5.696270 TGATAGTATCAACCGATCACAATGC 59.304 40.000 10.50 0.00 36.11 3.56
442 649 6.925718 AGTGATAGTATCAACCGATCACAATG 59.074 38.462 14.44 0.00 44.46 2.82
444 651 6.096282 TCAGTGATAGTATCAACCGATCACAA 59.904 38.462 14.44 1.59 44.46 3.33
462 669 5.255397 TGGAAACTTATGGGTTCAGTGAT 57.745 39.130 0.00 0.00 43.06 3.06
463 670 4.715534 TGGAAACTTATGGGTTCAGTGA 57.284 40.909 0.00 0.00 43.06 3.41
464 671 5.982890 ATTGGAAACTTATGGGTTCAGTG 57.017 39.130 0.00 0.00 43.06 3.66
465 672 7.893302 TGAATATTGGAAACTTATGGGTTCAGT 59.107 33.333 0.00 0.00 43.06 3.41
466 673 8.292444 TGAATATTGGAAACTTATGGGTTCAG 57.708 34.615 0.00 0.00 43.06 3.02
468 675 9.936759 TTTTGAATATTGGAAACTTATGGGTTC 57.063 29.630 0.00 0.00 40.70 3.62
485 800 5.132502 TGGGACGATGCAGATTTTGAATAT 58.867 37.500 0.00 0.00 0.00 1.28
491 806 1.818674 GGTTGGGACGATGCAGATTTT 59.181 47.619 0.00 0.00 0.00 1.82
507 822 5.715070 AGTATCTCTTCTTTCACGAGGTTG 58.285 41.667 0.00 0.00 0.00 3.77
534 849 1.398390 CAGGGAAAGCGCAAGTGATAC 59.602 52.381 11.47 0.00 41.68 2.24
536 851 0.036732 TCAGGGAAAGCGCAAGTGAT 59.963 50.000 11.47 0.00 41.68 3.06
545 860 0.875059 CGGAAACTGTCAGGGAAAGC 59.125 55.000 4.53 0.00 0.00 3.51
756 1075 1.743252 CAACTGCCTCGCCTTCCTC 60.743 63.158 0.00 0.00 0.00 3.71
789 1108 0.533085 TGCGTTTGACCGGTCATGAA 60.533 50.000 36.52 25.82 39.64 2.57
864 1183 2.158957 TCCTTTTATAGGTGCTCGGCTG 60.159 50.000 0.00 0.00 45.03 4.85
873 1192 3.181439 GCCATGAGCCTCCTTTTATAGGT 60.181 47.826 0.00 0.00 39.49 3.08
891 1210 3.624777 CTGTGGAAGAAAGGTATGCCAT 58.375 45.455 1.54 0.00 37.19 4.40
892 1211 2.879756 GCTGTGGAAGAAAGGTATGCCA 60.880 50.000 1.54 0.00 37.19 4.92
920 1240 4.813027 CACTTGTCCAATGCTAAATTGCT 58.187 39.130 0.00 0.00 0.00 3.91
921 1241 3.368843 GCACTTGTCCAATGCTAAATTGC 59.631 43.478 0.00 0.00 36.40 3.56
922 1242 4.386652 GTGCACTTGTCCAATGCTAAATTG 59.613 41.667 10.32 0.00 40.13 2.32
923 1243 4.281688 AGTGCACTTGTCCAATGCTAAATT 59.718 37.500 15.25 0.00 40.13 1.82
924 1244 3.828451 AGTGCACTTGTCCAATGCTAAAT 59.172 39.130 15.25 0.00 40.13 1.40
925 1245 3.221771 AGTGCACTTGTCCAATGCTAAA 58.778 40.909 15.25 0.00 40.13 1.85
926 1246 2.862541 AGTGCACTTGTCCAATGCTAA 58.137 42.857 15.25 0.00 40.13 3.09
927 1247 2.566833 AGTGCACTTGTCCAATGCTA 57.433 45.000 15.25 2.09 40.13 3.49
928 1248 1.610522 GAAGTGCACTTGTCCAATGCT 59.389 47.619 35.67 8.58 40.13 3.79
1015 1335 2.187946 CTTGGCCGGCTTCGAGAT 59.812 61.111 28.56 0.00 35.61 2.75
1044 1364 1.517242 CGAACCTGAAGCTGCTCTTT 58.483 50.000 1.00 0.00 34.56 2.52
1066 1386 3.286751 GCCACAGAACAGCGGCAA 61.287 61.111 1.45 0.00 44.25 4.52
1075 1395 2.741092 GTCAGACCGGCCACAGAA 59.259 61.111 0.00 0.00 0.00 3.02
1114 1434 4.517703 CGAGGACGACCGAGCGAC 62.518 72.222 10.13 0.00 42.66 5.19
1115 1435 4.747529 TCGAGGACGACCGAGCGA 62.748 66.667 13.14 13.14 43.81 4.93
1128 1448 2.766400 GGACGACCTCCTGCTCGAG 61.766 68.421 8.45 8.45 35.89 4.04
1200 1520 0.251297 TCTTCCCGTCGTTGTCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
1292 1612 3.771160 CGAGCAGGTACCCGCCTT 61.771 66.667 16.70 0.00 36.58 4.35
1295 1615 2.885774 GAAGTCGAGCAGGTACCCGC 62.886 65.000 12.49 12.49 0.00 6.13
1296 1616 1.139095 GAAGTCGAGCAGGTACCCG 59.861 63.158 8.74 4.99 0.00 5.28
1320 1640 1.522355 CTCCATCAGCGCCACGAAT 60.522 57.895 2.29 0.00 0.00 3.34
1474 1794 4.457496 CATGGCCTCGCAGTCGGT 62.457 66.667 3.32 0.00 36.13 4.69
1613 1933 1.688772 GGCTCATCTGGATGCAATGT 58.311 50.000 5.77 0.00 38.65 2.71
1657 1977 4.889409 ACACCAAACAACACAAGATGAGAT 59.111 37.500 0.00 0.00 0.00 2.75
1751 2071 4.697514 TCTGGAGAAAACACAGTCTTCTG 58.302 43.478 0.00 0.00 46.18 3.02
1787 2109 3.350219 TCACTCCCTTACAGCCATTTC 57.650 47.619 0.00 0.00 0.00 2.17
1880 3286 0.331954 AGACCAGACCTCTTCGGCTA 59.668 55.000 0.00 0.00 35.61 3.93
1918 3324 7.413109 GCTTCCTGCTAAGTCAGTGTTATTAAC 60.413 40.741 0.00 0.00 38.95 2.01
1959 3365 2.378038 TGCCTGGGATTCTGTAAATGC 58.622 47.619 0.00 0.00 0.00 3.56
2005 3411 6.183361 TGTGTAAGATTTGGGGGAGAAAGTAA 60.183 38.462 0.00 0.00 0.00 2.24
2015 3421 5.496556 TGTGATACTGTGTAAGATTTGGGG 58.503 41.667 0.00 0.00 0.00 4.96
2049 4919 9.089601 TGAATGATTGTGATGCAATTGTAAATC 57.910 29.630 7.40 9.10 46.90 2.17
2077 4947 1.986378 CGGCTCACGTGTAGAAAGAAG 59.014 52.381 16.51 3.76 37.93 2.85
2120 4990 6.323266 GGTCGATTATATTGACGCTATCTGT 58.677 40.000 0.00 0.00 43.28 3.41
2134 5004 3.056821 CAGAAGGCATCGGGTCGATTATA 60.057 47.826 0.00 0.00 44.59 0.98
2198 5068 5.621197 AATTTAAGACAGCATTGCACGTA 57.379 34.783 11.91 2.29 0.00 3.57
2199 5069 4.503741 AATTTAAGACAGCATTGCACGT 57.496 36.364 11.91 7.43 0.00 4.49
2200 5070 5.389778 TGTAATTTAAGACAGCATTGCACG 58.610 37.500 11.91 3.94 0.00 5.34
2201 5071 6.611381 TCTGTAATTTAAGACAGCATTGCAC 58.389 36.000 11.91 2.07 42.35 4.57
2202 5072 6.430925 ACTCTGTAATTTAAGACAGCATTGCA 59.569 34.615 11.91 0.00 42.35 4.08
2204 5074 7.094634 ACCACTCTGTAATTTAAGACAGCATTG 60.095 37.037 8.60 6.22 42.35 2.82
2207 5077 5.865085 ACCACTCTGTAATTTAAGACAGCA 58.135 37.500 8.60 0.77 42.35 4.41
2208 5078 6.803154 AACCACTCTGTAATTTAAGACAGC 57.197 37.500 8.60 0.00 42.35 4.40
2224 7167 9.575783 TTTGTGATTTTGTAACTAAAACCACTC 57.424 29.630 9.19 0.00 42.14 3.51
2246 7191 9.926158 TTTCTGCATTTGTATAATGACATTTGT 57.074 25.926 5.89 0.00 0.00 2.83
2301 7246 9.053840 CGATTGTGTACTACTCCTCTATAAAGA 57.946 37.037 0.00 0.00 0.00 2.52
2302 7247 7.804129 GCGATTGTGTACTACTCCTCTATAAAG 59.196 40.741 0.00 0.00 0.00 1.85
2303 7248 7.283807 TGCGATTGTGTACTACTCCTCTATAAA 59.716 37.037 0.00 0.00 0.00 1.40
2304 7249 6.769341 TGCGATTGTGTACTACTCCTCTATAA 59.231 38.462 0.00 0.00 0.00 0.98
2305 7250 6.204301 GTGCGATTGTGTACTACTCCTCTATA 59.796 42.308 0.00 0.00 0.00 1.31
2306 7251 5.008811 GTGCGATTGTGTACTACTCCTCTAT 59.991 44.000 0.00 0.00 0.00 1.98
2307 7252 4.334759 GTGCGATTGTGTACTACTCCTCTA 59.665 45.833 0.00 0.00 0.00 2.43
2308 7253 3.128938 GTGCGATTGTGTACTACTCCTCT 59.871 47.826 0.00 0.00 0.00 3.69
2309 7254 3.128938 AGTGCGATTGTGTACTACTCCTC 59.871 47.826 0.00 0.00 32.75 3.71
2310 7255 3.090037 AGTGCGATTGTGTACTACTCCT 58.910 45.455 0.00 0.00 32.75 3.69
2311 7256 3.119602 TCAGTGCGATTGTGTACTACTCC 60.120 47.826 0.00 0.00 32.75 3.85
2312 7257 4.092771 TCAGTGCGATTGTGTACTACTC 57.907 45.455 0.00 0.00 32.75 2.59
2313 7258 4.424626 CATCAGTGCGATTGTGTACTACT 58.575 43.478 0.00 0.00 32.75 2.57
2314 7259 3.551890 CCATCAGTGCGATTGTGTACTAC 59.448 47.826 0.00 0.00 32.75 2.73
2322 7267 1.129251 GTGTCACCATCAGTGCGATTG 59.871 52.381 0.00 0.00 46.81 2.67
2325 7270 0.321346 ATGTGTCACCATCAGTGCGA 59.679 50.000 0.00 0.00 46.81 5.10
2352 7297 9.536510 GGGAGAGAGTAGAATACCACTTTATAT 57.463 37.037 0.00 0.00 44.47 0.86
2354 7299 7.363031 TGGGAGAGAGTAGAATACCACTTTAT 58.637 38.462 0.00 0.00 44.47 1.40
2360 7305 6.553852 GGTTAATGGGAGAGAGTAGAATACCA 59.446 42.308 0.00 0.00 44.47 3.25
2361 7306 6.783482 AGGTTAATGGGAGAGAGTAGAATACC 59.217 42.308 0.00 0.00 44.47 2.73
2367 7312 5.897824 TGGTTAGGTTAATGGGAGAGAGTAG 59.102 44.000 0.00 0.00 0.00 2.57
2376 7321 4.166144 AGATGGTCTGGTTAGGTTAATGGG 59.834 45.833 0.00 0.00 0.00 4.00
2383 7328 0.824759 GCGAGATGGTCTGGTTAGGT 59.175 55.000 0.00 0.00 0.00 3.08
2388 7333 1.599047 CCAAGCGAGATGGTCTGGT 59.401 57.895 0.00 0.00 33.08 4.00
2392 7337 0.178068 TAAGCCCAAGCGAGATGGTC 59.822 55.000 0.00 0.00 46.67 4.02
2401 7346 2.092699 AGAGGAGACATTAAGCCCAAGC 60.093 50.000 0.00 0.00 40.32 4.01
2408 7353 3.740764 GCCTGAGCAGAGGAGACATTAAG 60.741 52.174 5.23 0.00 39.53 1.85
2416 7361 2.181445 TTGCAGCCTGAGCAGAGGAG 62.181 60.000 0.00 0.00 43.75 3.69
2428 7373 3.766691 CTGGGCCATGTTGCAGCC 61.767 66.667 6.72 5.37 46.37 4.85
2537 7516 1.587876 CGCGCGCCTACATGTTCTA 60.588 57.895 27.72 0.00 0.00 2.10
2538 7517 2.885644 CGCGCGCCTACATGTTCT 60.886 61.111 27.72 0.00 0.00 3.01
2539 7518 2.736682 AACGCGCGCCTACATGTTC 61.737 57.895 32.58 0.00 0.00 3.18
2540 7519 2.740826 AACGCGCGCCTACATGTT 60.741 55.556 32.58 19.36 0.00 2.71
2541 7520 3.487202 CAACGCGCGCCTACATGT 61.487 61.111 32.58 13.86 0.00 3.21
2542 7521 4.868900 GCAACGCGCGCCTACATG 62.869 66.667 32.58 19.25 0.00 3.21


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

AutoCloner maintained by Alex Coulton.