Multiple sequence alignment - TraesCS7A01G182400

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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 TraesCS7A01G182400 chr7A 100.000 4413 0 0 1 4413 137762703 137767115 0.000000e+00 8150.0
1 TraesCS7A01G182400 chr7B 93.864 2477 94 27 1966 4413 102228152 102230599 0.000000e+00 3679.0
2 TraesCS7A01G182400 chr7B 93.850 1496 62 14 496 1967 102226593 102228082 0.000000e+00 2226.0
3 TraesCS7A01G182400 chr7B 84.232 482 68 4 1 475 102225941 102226421 3.110000e-126 462.0
4 TraesCS7A01G182400 chr7D 93.151 2482 92 30 1980 4413 137556476 137558927 0.000000e+00 3570.0
5 TraesCS7A01G182400 chr7D 94.633 1472 50 15 509 1967 137554975 137556430 0.000000e+00 2254.0
6 TraesCS7A01G182400 chr7D 87.373 491 54 5 1 488 137554314 137554799 1.390000e-154 556.0
7 TraesCS7A01G182400 chr7D 85.000 80 10 1 1569 1648 589517788 589517865 3.660000e-11 80.5
8 TraesCS7A01G182400 chr7D 93.617 47 2 1 1603 1648 629074203 629074249 7.920000e-08 69.4
9 TraesCS7A01G182400 chr6B 91.304 161 12 1 978 1138 583612436 583612594 7.430000e-53 219.0
10 TraesCS7A01G182400 chr6D 91.195 159 12 1 978 1136 389971497 389971653 9.610000e-52 215.0
11 TraesCS7A01G182400 chr6A 90.683 161 13 1 978 1138 536251801 536251959 3.460000e-51 213.0
12 TraesCS7A01G182400 chr1B 85.000 80 10 1 1569 1648 534167871 534167794 3.660000e-11 80.5
13 TraesCS7A01G182400 chr3D 86.301 73 8 1 1576 1648 114316340 114316410 1.320000e-10 78.7
14 TraesCS7A01G182400 chr3D 84.932 73 9 1 1576 1648 49618127 49618197 6.120000e-09 73.1


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 TraesCS7A01G182400 chr7A 137762703 137767115 4412 False 8150.000000 8150 100.000000 1 4413 1 chr7A.!!$F1 4412
1 TraesCS7A01G182400 chr7B 102225941 102230599 4658 False 2122.333333 3679 90.648667 1 4413 3 chr7B.!!$F1 4412
2 TraesCS7A01G182400 chr7D 137554314 137558927 4613 False 2126.666667 3570 91.719000 1 4413 3 chr7D.!!$F3 4412

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
374 377 0.034863 AAGGGTGTGTCAAACCGTGT 60.035 50.000 8.17 0.0 38.70 4.49 F
1308 1502 1.003839 TGTGCAGATGGTTCGGTCC 60.004 57.895 0.00 0.0 0.00 4.46 F
1810 2010 0.817654 GGCAAATCTGGCTGGGTTAC 59.182 55.000 0.00 0.0 44.62 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1570 0.443869 CAGAAGAATCACGCAACCCG 59.556 55.000 0.00 0.00 44.21 5.28 R
2659 2948 1.292061 CTACTGGGACTCGAGACTCG 58.708 60.000 21.68 18.91 42.10 4.18 R
3580 3874 1.074248 CCCCCGCTGTAACCAAACT 59.926 57.895 0.00 0.00 0.00 2.66 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
58 59 4.116328 CTCGAGCGGCGGTCTTCA 62.116 66.667 32.55 17.48 41.33 3.02
91 92 1.135315 CGATGGCAATGTTGGTGAAGG 60.135 52.381 0.00 0.00 0.00 3.46
94 95 1.523154 GGCAATGTTGGTGAAGGCGA 61.523 55.000 0.00 0.00 0.00 5.54
145 146 2.519541 ATCGCTAGCTCGGCCTGA 60.520 61.111 13.93 0.52 0.00 3.86
152 153 2.235016 CTAGCTCGGCCTGACTAGATT 58.765 52.381 14.45 0.00 33.64 2.40
218 219 3.243873 GCATGACATCAGACCCGAATCTA 60.244 47.826 0.00 0.00 0.00 1.98
229 230 8.014070 TCAGACCCGAATCTATTATACAACAA 57.986 34.615 0.00 0.00 0.00 2.83
259 261 8.372459 GGGTGTTATTTTCCAGGTTTTCTTTAT 58.628 33.333 0.00 0.00 0.00 1.40
286 289 3.564053 TCAGTTTTGGTTTAGGACGGT 57.436 42.857 0.00 0.00 0.00 4.83
311 314 2.423803 GCCCGGGGTAGGAATAATGTTT 60.424 50.000 25.28 0.00 0.00 2.83
329 332 4.340617 TGTTTTTCCCATCCTATCACCAC 58.659 43.478 0.00 0.00 0.00 4.16
331 334 5.251932 TGTTTTTCCCATCCTATCACCACTA 59.748 40.000 0.00 0.00 0.00 2.74
366 369 2.425592 CTGGCGAAGGGTGTGTCA 59.574 61.111 0.00 0.00 0.00 3.58
368 371 0.817634 CTGGCGAAGGGTGTGTCAAA 60.818 55.000 0.00 0.00 0.00 2.69
374 377 0.034863 AAGGGTGTGTCAAACCGTGT 60.035 50.000 8.17 0.00 38.70 4.49
377 380 1.375551 GGTGTGTCAAACCGTGTCTT 58.624 50.000 0.00 0.00 0.00 3.01
379 382 2.477189 GGTGTGTCAAACCGTGTCTTTG 60.477 50.000 0.00 0.00 0.00 2.77
380 383 2.417239 GTGTGTCAAACCGTGTCTTTGA 59.583 45.455 0.00 0.00 35.68 2.69
384 387 2.875933 GTCAAACCGTGTCTTTGATGGA 59.124 45.455 0.00 0.00 39.28 3.41
389 392 4.021102 ACCGTGTCTTTGATGGATCTTT 57.979 40.909 0.00 0.00 0.00 2.52
408 411 8.688747 GATCTTTCAGGATCCAATCAGTTTAT 57.311 34.615 15.82 0.00 36.91 1.40
410 413 6.319658 TCTTTCAGGATCCAATCAGTTTATGC 59.680 38.462 15.82 0.00 0.00 3.14
416 419 5.824624 GGATCCAATCAGTTTATGCTTCTGA 59.175 40.000 6.95 0.00 41.43 3.27
417 420 6.489361 GGATCCAATCAGTTTATGCTTCTGAT 59.511 38.462 6.95 0.00 46.54 2.90
422 425 7.201884 CCAATCAGTTTATGCTTCTGATGGATT 60.202 37.037 9.49 0.00 44.70 3.01
426 429 7.558807 TCAGTTTATGCTTCTGATGGATTCATT 59.441 33.333 3.04 0.00 34.00 2.57
435 438 8.131100 GCTTCTGATGGATTCATTTAAATTCGA 58.869 33.333 0.00 0.00 32.72 3.71
440 443 6.503589 TGGATTCATTTAAATTCGAACGGT 57.496 33.333 0.00 0.00 0.00 4.83
442 445 7.371936 TGGATTCATTTAAATTCGAACGGTTT 58.628 30.769 0.00 0.00 0.00 3.27
443 446 7.868415 TGGATTCATTTAAATTCGAACGGTTTT 59.132 29.630 0.00 0.00 0.00 2.43
454 465 3.739167 CGGTTTTCGTGGGCTTCA 58.261 55.556 0.00 0.00 0.00 3.02
455 466 2.026522 CGGTTTTCGTGGGCTTCAA 58.973 52.632 0.00 0.00 0.00 2.69
463 474 1.346395 TCGTGGGCTTCAACTACATGT 59.654 47.619 2.69 2.69 0.00 3.21
490 502 5.560966 AACGACATTTCTCTCTCTCTCTC 57.439 43.478 0.00 0.00 0.00 3.20
491 503 4.843728 ACGACATTTCTCTCTCTCTCTCT 58.156 43.478 0.00 0.00 0.00 3.10
492 504 4.876107 ACGACATTTCTCTCTCTCTCTCTC 59.124 45.833 0.00 0.00 0.00 3.20
493 505 5.118990 CGACATTTCTCTCTCTCTCTCTCT 58.881 45.833 0.00 0.00 0.00 3.10
547 717 1.535896 GGTCTCAGCCCTTTTCGAAAC 59.464 52.381 10.79 0.00 0.00 2.78
552 722 3.776340 TCAGCCCTTTTCGAAACAAAAC 58.224 40.909 10.79 0.00 0.00 2.43
556 726 4.998033 AGCCCTTTTCGAAACAAAACAAAA 59.002 33.333 10.79 0.00 0.00 2.44
623 795 1.790755 GACACACACAATAGTCGCCA 58.209 50.000 0.00 0.00 0.00 5.69
689 863 7.062371 CAGCTCGAGGATAAATATAGTTTTCCG 59.938 40.741 15.58 6.33 0.00 4.30
691 865 5.860182 TCGAGGATAAATATAGTTTTCCGCG 59.140 40.000 28.54 28.54 39.85 6.46
732 906 1.383248 CGAGGAATCCCACTCCCCT 60.383 63.158 0.00 0.00 32.95 4.79
752 927 3.203040 CCTCTTCTCTCTCTCCCTCTCTT 59.797 52.174 0.00 0.00 0.00 2.85
931 1111 2.770048 CCTGAATCCCTCCGCCCT 60.770 66.667 0.00 0.00 0.00 5.19
1162 1346 3.369388 GACCTCCCTCCCCCTCCT 61.369 72.222 0.00 0.00 0.00 3.69
1308 1502 1.003839 TGTGCAGATGGTTCGGTCC 60.004 57.895 0.00 0.00 0.00 4.46
1371 1565 3.254166 ACACAGTGATTTGATCAGGTTGC 59.746 43.478 7.81 0.00 40.53 4.17
1376 1570 1.064654 GATTTGATCAGGTTGCTCCGC 59.935 52.381 0.00 0.00 41.99 5.54
1405 1599 3.365364 CGTGATTCTTCTGTTCTTTGGCC 60.365 47.826 0.00 0.00 0.00 5.36
1474 1668 1.041447 TCTCCTTGCCCGTAGTAGCC 61.041 60.000 0.00 0.00 0.00 3.93
1481 1675 0.819582 GCCCGTAGTAGCCAACACTA 59.180 55.000 0.00 0.00 0.00 2.74
1482 1676 1.470458 GCCCGTAGTAGCCAACACTAC 60.470 57.143 3.15 3.15 43.20 2.73
1541 1737 9.730420 TCTACAAGTTCTTGCATTTTCTTAAAC 57.270 29.630 11.79 0.00 0.00 2.01
1553 1749 2.743636 TCTTAAACGGGCAGACAGAG 57.256 50.000 0.00 0.00 0.00 3.35
1686 1886 3.181434 ACCATTTGAGGAGGCTGTTTGTA 60.181 43.478 0.00 0.00 0.00 2.41
1755 1955 3.007398 GTGGTCCAGTCTCAGTTCTGAAT 59.993 47.826 0.00 0.00 34.02 2.57
1810 2010 0.817654 GGCAAATCTGGCTGGGTTAC 59.182 55.000 0.00 0.00 44.62 2.50
1835 2035 5.638234 GCTCGTAACTGTAAATTTGGAGAGT 59.362 40.000 0.00 0.00 0.00 3.24
1847 2047 7.770801 AAATTTGGAGAGTGTTTTTAAGCAC 57.229 32.000 1.73 1.73 39.99 4.40
1858 2058 3.746045 TTTTAAGCACGAGTCTGGACT 57.254 42.857 2.62 2.62 45.84 3.85
1860 2060 1.617322 TAAGCACGAGTCTGGACTGT 58.383 50.000 8.06 4.38 42.66 3.55
1895 2095 7.392113 CACATGGGAAGTACCAAAATACTAACA 59.608 37.037 0.00 0.00 45.13 2.41
1898 2098 6.178324 GGGAAGTACCAAAATACTAACAGCT 58.822 40.000 0.00 0.00 41.20 4.24
1976 2247 7.860373 TCAAACAAGAAACACTAATTTGGATCG 59.140 33.333 0.00 0.00 35.79 3.69
1981 2252 2.919228 ACACTAATTTGGATCGGAGGC 58.081 47.619 0.00 0.00 0.00 4.70
2111 2382 7.933577 CCTGCACAGATTAATAATAGGAACTGA 59.066 37.037 0.00 0.00 41.52 3.41
2357 2644 4.104776 CGCAAAATGGTCCATAACATGTC 58.895 43.478 4.33 0.00 0.00 3.06
2400 2687 6.897966 AGGAGAGTTTACCTTGTGATGAGATA 59.102 38.462 0.00 0.00 31.95 1.98
2499 2786 7.551035 AATTCTCTGAATACTGCTGTTGATC 57.449 36.000 0.09 0.00 0.00 2.92
2560 2848 5.499139 TCTGTGTTAAGAGTGCCTTTTTG 57.501 39.130 0.00 0.00 36.34 2.44
2659 2948 6.739112 ACTTGAGAATAACAAAACTCTTGCC 58.261 36.000 0.00 0.00 0.00 4.52
2804 3093 8.778358 GTCCCATCTCTTTATATGTTTGATGAC 58.222 37.037 0.00 0.00 33.74 3.06
2892 3186 2.526304 TGTCTGTCCGAAGAAGTTGG 57.474 50.000 0.00 0.00 0.00 3.77
2961 3255 5.853936 AGACTTAAGAGTGCACACATTGTA 58.146 37.500 21.04 1.51 35.88 2.41
2962 3256 5.696724 AGACTTAAGAGTGCACACATTGTAC 59.303 40.000 21.04 4.84 40.97 2.90
3037 3331 5.116882 GCCTCGTTTAGTTGATCCATTACT 58.883 41.667 0.00 0.00 0.00 2.24
3052 3346 3.801050 CCATTACTCGATGCTCAGTTCTG 59.199 47.826 0.00 0.00 0.00 3.02
3174 3468 0.671781 ATTGCGGCCGCTATCTGATC 60.672 55.000 45.79 18.70 42.51 2.92
3273 3567 4.293415 GCATATTGCACTCCAGCATTTAC 58.707 43.478 0.00 0.00 45.19 2.01
3310 3604 2.534757 GCTTTAGCATCGTAGTTCCGTC 59.465 50.000 0.00 0.00 41.59 4.79
3361 3655 7.039082 CCACCATCCTTTTTCTTTCCAGATAAA 60.039 37.037 0.00 0.00 31.45 1.40
3614 3909 2.240510 GGGGGCCTTCCATACATCA 58.759 57.895 0.84 0.00 37.22 3.07
3615 3910 0.779997 GGGGGCCTTCCATACATCAT 59.220 55.000 0.84 0.00 37.22 2.45
3718 4013 3.146847 GTCGGAAATGAGGTTCCACTTT 58.853 45.455 4.93 0.00 46.45 2.66
3789 4087 2.128729 TTTTTCCCCCAAGTTGCCG 58.871 52.632 0.00 0.00 0.00 5.69
3803 4101 6.037172 CCCAAGTTGCCGCTACATATTATATC 59.963 42.308 7.70 0.00 0.00 1.63
3852 4150 3.971305 TCTGTCCAGAAGTGTAAAGGGAA 59.029 43.478 0.00 0.00 33.91 3.97
3857 4155 6.012858 TGTCCAGAAGTGTAAAGGGAATATGT 60.013 38.462 0.00 0.00 0.00 2.29
4080 4385 3.991051 CAGGGTGGCTGACGACGT 61.991 66.667 0.00 0.00 0.00 4.34
4113 4418 5.606348 AACATGGCCAGTTTTCTTGTTAA 57.394 34.783 13.05 0.00 30.50 2.01
4143 4448 8.370182 GGCTATCCATTTTTAATGGTCATGAAT 58.630 33.333 15.89 6.01 40.06 2.57
4168 4473 3.005472 GGAAAAGGTTGAAAGTGGGTAGC 59.995 47.826 0.00 0.00 0.00 3.58
4169 4474 3.306472 AAAGGTTGAAAGTGGGTAGCA 57.694 42.857 0.00 0.00 0.00 3.49
4170 4475 2.568623 AGGTTGAAAGTGGGTAGCAG 57.431 50.000 0.00 0.00 0.00 4.24
4171 4476 1.073923 AGGTTGAAAGTGGGTAGCAGG 59.926 52.381 0.00 0.00 0.00 4.85
4172 4477 1.202891 GGTTGAAAGTGGGTAGCAGGT 60.203 52.381 0.00 0.00 0.00 4.00
4173 4478 2.039348 GGTTGAAAGTGGGTAGCAGGTA 59.961 50.000 0.00 0.00 0.00 3.08
4205 4517 2.480845 AGTCTTCAACCACTACGCAAC 58.519 47.619 0.00 0.00 0.00 4.17
4271 4592 0.036388 TCAGTCCATGGAAGTTCGGC 60.036 55.000 18.20 1.52 0.00 5.54
4301 4628 6.657888 CATTTGGTTAAGACAAAATGCAACC 58.342 36.000 8.75 0.00 45.38 3.77
4311 4638 4.886579 ACAAAATGCAACCTCCAAAGATC 58.113 39.130 0.00 0.00 0.00 2.75
4341 4668 3.242867 AGGAACTGGAACTGACATCTCA 58.757 45.455 0.00 0.00 37.18 3.27
4356 4692 1.852633 TCTCATCGCTCCTCCAAAGA 58.147 50.000 0.00 0.00 0.00 2.52
4370 4706 7.201741 GCTCCTCCAAAGAACCTATACAAAATC 60.202 40.741 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.134367 CCATCTCCTTCGCAGTCGTAA 59.866 52.381 0.00 0.00 36.96 3.18
78 79 1.234615 CCGTCGCCTTCACCAACATT 61.235 55.000 0.00 0.00 0.00 2.71
91 92 3.499737 CCATCCAACAGCCGTCGC 61.500 66.667 0.00 0.00 0.00 5.19
94 95 2.351276 GGTCCATCCAACAGCCGT 59.649 61.111 0.00 0.00 35.97 5.68
145 146 4.083565 GCCCTCTTCTCCGATAATCTAGT 58.916 47.826 0.00 0.00 0.00 2.57
152 153 1.133167 TCCATGCCCTCTTCTCCGATA 60.133 52.381 0.00 0.00 0.00 2.92
199 200 6.918067 ATAATAGATTCGGGTCTGATGTCA 57.082 37.500 1.43 0.00 0.00 3.58
229 230 4.675063 ACCTGGAAAATAACACCCATCT 57.325 40.909 0.00 0.00 0.00 2.90
259 261 6.373216 CGTCCTAAACCAAAACTGAATATCCA 59.627 38.462 0.00 0.00 0.00 3.41
286 289 0.620990 TATTCCTACCCCGGGCAACA 60.621 55.000 17.73 0.00 39.74 3.33
294 297 5.274015 TGGGAAAAACATTATTCCTACCCC 58.726 41.667 0.00 0.00 43.75 4.95
311 314 4.975147 ACATAGTGGTGATAGGATGGGAAA 59.025 41.667 0.00 0.00 0.00 3.13
329 332 2.012673 GCAGAAAGCAGACCCACATAG 58.987 52.381 0.00 0.00 44.79 2.23
331 334 2.952714 GCAGAAAGCAGACCCACAT 58.047 52.632 0.00 0.00 44.79 3.21
366 369 4.021102 AGATCCATCAAAGACACGGTTT 57.979 40.909 0.00 0.00 0.00 3.27
368 371 3.703001 AAGATCCATCAAAGACACGGT 57.297 42.857 0.00 0.00 0.00 4.83
384 387 7.014038 GCATAAACTGATTGGATCCTGAAAGAT 59.986 37.037 14.23 0.00 34.07 2.40
389 392 5.378230 AGCATAAACTGATTGGATCCTGA 57.622 39.130 14.23 1.70 0.00 3.86
398 401 7.558807 TGAATCCATCAGAAGCATAAACTGATT 59.441 33.333 0.00 0.00 45.27 2.57
402 405 7.893124 AATGAATCCATCAGAAGCATAAACT 57.107 32.000 0.00 0.00 42.53 2.66
408 411 7.916977 CGAATTTAAATGAATCCATCAGAAGCA 59.083 33.333 0.39 0.00 42.53 3.91
416 419 7.095695 ACCGTTCGAATTTAAATGAATCCAT 57.904 32.000 0.00 0.00 33.66 3.41
417 420 6.503589 ACCGTTCGAATTTAAATGAATCCA 57.496 33.333 0.00 0.00 0.00 3.41
422 425 6.898451 CGAAAACCGTTCGAATTTAAATGA 57.102 33.333 0.00 0.00 43.97 2.57
440 443 2.920524 TGTAGTTGAAGCCCACGAAAA 58.079 42.857 0.00 0.00 0.00 2.29
442 445 2.224426 ACATGTAGTTGAAGCCCACGAA 60.224 45.455 0.00 0.00 0.00 3.85
443 446 1.346395 ACATGTAGTTGAAGCCCACGA 59.654 47.619 0.00 0.00 0.00 4.35
449 452 4.927425 TCGTTAAGGACATGTAGTTGAAGC 59.073 41.667 0.00 0.00 0.00 3.86
463 474 5.946972 AGAGAGAGAGAAATGTCGTTAAGGA 59.053 40.000 0.00 0.00 0.00 3.36
475 486 7.829211 CCTTAAAGAGAGAGAGAGAGAGAGAAA 59.171 40.741 0.00 0.00 0.00 2.52
476 487 7.338710 CCTTAAAGAGAGAGAGAGAGAGAGAA 58.661 42.308 0.00 0.00 0.00 2.87
478 489 6.058183 CCCTTAAAGAGAGAGAGAGAGAGAG 58.942 48.000 0.00 0.00 0.00 3.20
480 491 5.590259 CACCCTTAAAGAGAGAGAGAGAGAG 59.410 48.000 0.00 0.00 0.00 3.20
482 493 5.125417 CACACCCTTAAAGAGAGAGAGAGAG 59.875 48.000 0.00 0.00 0.00 3.20
490 502 7.201530 CGCTTATAAACACACCCTTAAAGAGAG 60.202 40.741 0.00 0.00 0.00 3.20
491 503 6.592607 CGCTTATAAACACACCCTTAAAGAGA 59.407 38.462 0.00 0.00 0.00 3.10
492 504 6.674760 GCGCTTATAAACACACCCTTAAAGAG 60.675 42.308 0.00 0.00 0.00 2.85
493 505 5.122711 GCGCTTATAAACACACCCTTAAAGA 59.877 40.000 0.00 0.00 0.00 2.52
598 768 2.404215 ACTATTGTGTGTGTCGACAGC 58.596 47.619 20.73 15.38 30.74 4.40
623 795 2.985456 GCCTACCTGCTGCTGAGT 59.015 61.111 8.20 6.94 0.00 3.41
689 863 4.944372 CGCAGATACGTCCCCCGC 62.944 72.222 0.00 0.00 41.42 6.13
691 865 0.108041 TTTTCGCAGATACGTCCCCC 60.108 55.000 0.00 0.00 35.04 5.40
732 906 3.202151 GGAAGAGAGGGAGAGAGAGAAGA 59.798 52.174 0.00 0.00 0.00 2.87
752 927 2.392816 CGAGGGTAGGGAGGGAGGA 61.393 68.421 0.00 0.00 0.00 3.71
945 1125 4.988598 ACAACCGGCGGCTCAGTG 62.989 66.667 28.71 18.11 0.00 3.66
955 1135 1.883021 GCAAGATCCCAACAACCGG 59.117 57.895 0.00 0.00 0.00 5.28
1041 1225 2.126071 ATGTCCGTGCCGTCGAAG 60.126 61.111 0.00 0.00 0.00 3.79
1162 1346 7.970061 GTGTATATATATGTACGCGGAGGAAAA 59.030 37.037 12.47 0.00 0.00 2.29
1308 1502 2.746359 GGATGGCTCCCAGATCCG 59.254 66.667 0.00 0.00 36.75 4.18
1376 1570 0.443869 CAGAAGAATCACGCAACCCG 59.556 55.000 0.00 0.00 44.21 5.28
1405 1599 1.336148 TGGACGCGTGTTACCTAACTG 60.336 52.381 20.70 0.00 37.12 3.16
1462 1656 0.819582 TAGTGTTGGCTACTACGGGC 59.180 55.000 0.01 0.00 0.00 6.13
1481 1675 2.826128 TCTATTCTCTGCCTGTCAACGT 59.174 45.455 0.00 0.00 0.00 3.99
1482 1676 3.510388 TCTATTCTCTGCCTGTCAACG 57.490 47.619 0.00 0.00 0.00 4.10
1541 1737 1.043816 ATATGTCCTCTGTCTGCCCG 58.956 55.000 0.00 0.00 0.00 6.13
1553 1749 4.142491 TGTCATCACCGCAAAAATATGTCC 60.142 41.667 0.00 0.00 0.00 4.02
1686 1886 3.010584 ACACCAACAGGATAAGAAGGCAT 59.989 43.478 0.00 0.00 0.00 4.40
1810 2010 4.624024 TCTCCAAATTTACAGTTACGAGCG 59.376 41.667 0.00 0.00 0.00 5.03
1820 2020 8.470805 TGCTTAAAAACACTCTCCAAATTTACA 58.529 29.630 0.00 0.00 0.00 2.41
1835 2035 3.558418 GTCCAGACTCGTGCTTAAAAACA 59.442 43.478 0.00 0.00 0.00 2.83
1847 2047 3.489398 GCCTACATTACAGTCCAGACTCG 60.489 52.174 0.00 0.00 40.20 4.18
1858 2058 3.265737 ACTTCCCATGTGCCTACATTACA 59.734 43.478 0.00 0.00 45.01 2.41
1860 2060 4.141574 GGTACTTCCCATGTGCCTACATTA 60.142 45.833 0.00 0.00 45.01 1.90
1895 2095 0.539051 ACTAATCTGCCGCTTCAGCT 59.461 50.000 0.00 0.00 39.32 4.24
1898 2098 4.400529 TCATAACTAATCTGCCGCTTCA 57.599 40.909 0.00 0.00 0.00 3.02
1952 2152 7.013846 TCCGATCCAAATTAGTGTTTCTTGTTT 59.986 33.333 0.00 0.00 0.00 2.83
1976 2247 1.731720 CAGAAACAGCTACTGCCTCC 58.268 55.000 0.00 0.00 40.80 4.30
1981 2252 5.152097 CAATTTCTGCAGAAACAGCTACTG 58.848 41.667 37.28 22.33 45.55 2.74
2111 2382 1.617018 TTCACCCATGCGAGCTAGCT 61.617 55.000 19.45 19.45 38.13 3.32
2357 2644 1.938577 CCTTCTGAAGCATGGTCATCG 59.061 52.381 11.93 0.00 0.00 3.84
2400 2687 3.070015 CCCTGGAAGTGCAAACTCAAAAT 59.930 43.478 0.00 0.00 0.00 1.82
2423 2710 3.732212 CCCTGAAAAGAAAAGGGCAAAG 58.268 45.455 0.00 0.00 44.17 2.77
2465 2752 7.574592 GCAGTATTCAGAGAATTTGAAGCACTT 60.575 37.037 0.00 0.00 37.91 3.16
2499 2786 8.180267 CCATAAAGCTTCTACAAGACTGAAATG 58.820 37.037 0.00 0.00 0.00 2.32
2553 2841 7.117523 TGTCTGTCAAAAACATTGTCAAAAAGG 59.882 33.333 0.00 0.00 37.23 3.11
2560 2848 6.806249 TGTCTTTGTCTGTCAAAAACATTGTC 59.194 34.615 3.06 0.00 40.60 3.18
2659 2948 1.292061 CTACTGGGACTCGAGACTCG 58.708 60.000 21.68 18.91 42.10 4.18
2804 3093 4.202245 TCGGATCTTAAACCAAGTGAGG 57.798 45.455 0.00 0.00 35.58 3.86
2892 3186 2.027837 AGAATGGCAAAAAGGTGGATGC 60.028 45.455 0.00 0.00 38.06 3.91
3037 3331 1.403382 GCTGACAGAACTGAGCATCGA 60.403 52.381 6.65 0.00 38.61 3.59
3110 3404 5.521735 AGTCATCTAATCGCATTCTGACAAC 59.478 40.000 0.00 0.00 35.22 3.32
3160 3454 1.342819 ACAAGAGATCAGATAGCGGCC 59.657 52.381 0.00 0.00 0.00 6.13
3174 3468 9.927668 ACAATAAAATGGTTCCATTTACAAGAG 57.072 29.630 24.21 16.14 43.32 2.85
3310 3604 7.487189 GGCACATTAAGATCAGAAACAAATCAG 59.513 37.037 0.00 0.00 0.00 2.90
3361 3655 1.938585 TGGGAGAATTCGAGAGGTGT 58.061 50.000 0.00 0.00 0.00 4.16
3580 3874 1.074248 CCCCCGCTGTAACCAAACT 59.926 57.895 0.00 0.00 0.00 2.66
3600 3895 6.093219 CAGCTTACATATGATGTATGGAAGGC 59.907 42.308 17.31 11.54 44.51 4.35
3614 3909 5.221561 TGCATACCCGTTACAGCTTACATAT 60.222 40.000 0.00 0.00 0.00 1.78
3615 3910 4.099727 TGCATACCCGTTACAGCTTACATA 59.900 41.667 0.00 0.00 0.00 2.29
3744 4039 6.918022 TCTCGACAAATACTATACGACGAGTA 59.082 38.462 0.00 0.00 42.96 2.59
3745 4040 5.750547 TCTCGACAAATACTATACGACGAGT 59.249 40.000 0.00 0.00 42.96 4.18
3746 4041 6.207864 TCTCGACAAATACTATACGACGAG 57.792 41.667 0.00 0.00 43.50 4.18
3747 4042 6.775939 ATCTCGACAAATACTATACGACGA 57.224 37.500 0.00 0.00 0.00 4.20
3748 4043 7.833284 AAATCTCGACAAATACTATACGACG 57.167 36.000 0.00 0.00 0.00 5.12
3852 4150 3.873910 CCTTCCGTCAGTCCAAACATAT 58.126 45.455 0.00 0.00 0.00 1.78
3857 4155 0.250295 CTGCCTTCCGTCAGTCCAAA 60.250 55.000 0.00 0.00 0.00 3.28
4080 4385 2.107031 CTGGCCATGTTATCATCCCTGA 59.893 50.000 5.51 0.00 35.41 3.86
4113 4418 6.549364 TGACCATTAAAAATGGATAGCCGAAT 59.451 34.615 22.29 0.00 41.64 3.34
4143 4448 4.874199 ACCCACTTTCAACCTTTTCCTAA 58.126 39.130 0.00 0.00 0.00 2.69
4199 4511 4.643387 GGGCCTCCAGTGTTGCGT 62.643 66.667 0.84 0.00 0.00 5.24
4205 4517 4.087892 CCAGACGGGCCTCCAGTG 62.088 72.222 0.84 0.00 0.00 3.66
4223 4535 4.576879 AGTGGTTAGGAAATTCCTTCGAC 58.423 43.478 20.79 18.44 46.91 4.20
4242 4554 6.118170 ACTTCCATGGACTGAATATTGAGTG 58.882 40.000 15.91 0.00 0.00 3.51
4243 4555 6.319048 ACTTCCATGGACTGAATATTGAGT 57.681 37.500 15.91 7.33 0.00 3.41
4271 4592 7.358352 GCATTTTGTCTTAACCAAATGAGTTCG 60.358 37.037 15.32 0.00 44.99 3.95
4301 4628 8.025445 CAGTTCCTTGTTTATTGATCTTTGGAG 58.975 37.037 0.00 0.00 0.00 3.86
4311 4638 6.039270 TGTCAGTTCCAGTTCCTTGTTTATTG 59.961 38.462 0.00 0.00 0.00 1.90
4341 4668 1.280457 AGGTTCTTTGGAGGAGCGAT 58.720 50.000 0.00 0.00 33.96 4.58
4356 4692 9.308000 TGAACATTTCTGGATTTTGTATAGGTT 57.692 29.630 0.00 0.00 0.00 3.50
4370 4706 7.741027 AGCTGTCATATATGAACATTTCTGG 57.259 36.000 16.97 6.38 38.75 3.86


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

AutoCloner maintained by Alex Coulton.