Multiple sequence alignment - TraesCS4A01G043100

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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 TraesCS4A01G043100 chr4A 100.000 2441 0 0 1 2441 36313073 36315513 0 4508
1 TraesCS4A01G043100 chr4D 91.175 2459 109 44 1 2441 434821554 434823922 0 3240
2 TraesCS4A01G043100 chr4B 86.806 2486 164 86 1 2441 534720906 534723272 0 2623


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 TraesCS4A01G043100 chr4A 36313073 36315513 2440 False 4508 4508 100.000 1 2441 1 chr4A.!!$F1 2440
1 TraesCS4A01G043100 chr4D 434821554 434823922 2368 False 3240 3240 91.175 1 2441 1 chr4D.!!$F1 2440
2 TraesCS4A01G043100 chr4B 534720906 534723272 2366 False 2623 2623 86.806 1 2441 1 chr4B.!!$F1 2440

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
166 167 0.031857 CGAGCATGCAACCAAACCAA 59.968 50.0 21.98 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2195 0.599558 TGCCATGCTTCAAGTTGAGC 59.4 50.0 15.97 15.97 0.0 4.26 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
24 25 7.121974 CATAACATAACCTTGGTGATCGATC 57.878 40.000 18.72 18.72 0.00 3.69
25 26 4.753516 ACATAACCTTGGTGATCGATCA 57.246 40.909 23.99 23.99 0.00 2.92
82 83 3.576356 GTCCGCGTCCATGGCATG 61.576 66.667 20.56 20.56 0.00 4.06
147 148 3.235369 GGGGGAGAGCCACTGATC 58.765 66.667 0.00 0.00 37.87 2.92
148 149 2.801631 GGGGGAGAGCCACTGATCG 61.802 68.421 0.00 0.00 37.87 3.69
149 150 1.758514 GGGGAGAGCCACTGATCGA 60.759 63.158 0.00 0.00 33.55 3.59
162 163 1.469703 CTGATCGAGCATGCAACCAAA 59.530 47.619 21.98 0.00 0.00 3.28
165 166 0.821301 TCGAGCATGCAACCAAACCA 60.821 50.000 21.98 0.00 0.00 3.67
166 167 0.031857 CGAGCATGCAACCAAACCAA 59.968 50.000 21.98 0.00 0.00 3.67
169 170 0.884259 GCATGCAACCAAACCAACCC 60.884 55.000 14.21 0.00 0.00 4.11
170 171 0.758123 CATGCAACCAAACCAACCCT 59.242 50.000 0.00 0.00 0.00 4.34
171 172 1.047801 ATGCAACCAAACCAACCCTC 58.952 50.000 0.00 0.00 0.00 4.30
172 173 1.362355 GCAACCAAACCAACCCTCG 59.638 57.895 0.00 0.00 0.00 4.63
173 174 2.037871 CAACCAAACCAACCCTCGG 58.962 57.895 0.00 0.00 0.00 4.63
174 175 0.466555 CAACCAAACCAACCCTCGGA 60.467 55.000 0.00 0.00 0.00 4.55
176 177 0.481128 ACCAAACCAACCCTCGGAAT 59.519 50.000 0.00 0.00 0.00 3.01
177 178 1.133294 ACCAAACCAACCCTCGGAATT 60.133 47.619 0.00 0.00 0.00 2.17
179 180 3.158676 CCAAACCAACCCTCGGAATTAA 58.841 45.455 0.00 0.00 0.00 1.40
182 183 5.227152 CAAACCAACCCTCGGAATTAAAAG 58.773 41.667 0.00 0.00 0.00 2.27
183 184 4.108501 ACCAACCCTCGGAATTAAAAGT 57.891 40.909 0.00 0.00 0.00 2.66
187 188 6.550481 ACCAACCCTCGGAATTAAAAGTAAAA 59.450 34.615 0.00 0.00 0.00 1.52
190 191 7.683437 ACCCTCGGAATTAAAAGTAAAAGAG 57.317 36.000 0.00 0.00 0.00 2.85
193 194 8.451748 CCCTCGGAATTAAAAGTAAAAGAGAAG 58.548 37.037 0.00 0.00 0.00 2.85
202 203 6.765355 AAAGTAAAAGAGAAGGAAGGGAGA 57.235 37.500 0.00 0.00 0.00 3.71
223 224 2.299297 ACGTCAAGGGTTAGAGGACAAG 59.701 50.000 0.00 0.00 0.00 3.16
365 366 2.752030 TCCAATCACCAAACCAAACCA 58.248 42.857 0.00 0.00 0.00 3.67
370 371 2.257207 TCACCAAACCAAACCAAACCA 58.743 42.857 0.00 0.00 0.00 3.67
375 393 3.412386 CAAACCAAACCAAACCAAACCA 58.588 40.909 0.00 0.00 0.00 3.67
376 394 3.790089 AACCAAACCAAACCAAACCAA 57.210 38.095 0.00 0.00 0.00 3.67
377 395 3.790089 ACCAAACCAAACCAAACCAAA 57.210 38.095 0.00 0.00 0.00 3.28
378 396 3.413327 ACCAAACCAAACCAAACCAAAC 58.587 40.909 0.00 0.00 0.00 2.93
379 397 2.750166 CCAAACCAAACCAAACCAAACC 59.250 45.455 0.00 0.00 0.00 3.27
380 398 2.750166 CAAACCAAACCAAACCAAACCC 59.250 45.455 0.00 0.00 0.00 4.11
381 399 1.657804 ACCAAACCAAACCAAACCCA 58.342 45.000 0.00 0.00 0.00 4.51
382 400 1.985895 ACCAAACCAAACCAAACCCAA 59.014 42.857 0.00 0.00 0.00 4.12
383 401 2.290387 ACCAAACCAAACCAAACCCAAC 60.290 45.455 0.00 0.00 0.00 3.77
384 402 2.360844 CAAACCAAACCAAACCCAACC 58.639 47.619 0.00 0.00 0.00 3.77
385 403 0.913205 AACCAAACCAAACCCAACCC 59.087 50.000 0.00 0.00 0.00 4.11
386 404 0.983905 ACCAAACCAAACCCAACCCC 60.984 55.000 0.00 0.00 0.00 4.95
387 405 1.701031 CCAAACCAAACCCAACCCCC 61.701 60.000 0.00 0.00 0.00 5.40
388 406 0.692756 CAAACCAAACCCAACCCCCT 60.693 55.000 0.00 0.00 0.00 4.79
389 407 0.942721 AAACCAAACCCAACCCCCTA 59.057 50.000 0.00 0.00 0.00 3.53
390 408 0.189080 AACCAAACCCAACCCCCTAC 59.811 55.000 0.00 0.00 0.00 3.18
391 409 1.077805 CCAAACCCAACCCCCTACC 59.922 63.158 0.00 0.00 0.00 3.18
392 410 1.731324 CCAAACCCAACCCCCTACCA 61.731 60.000 0.00 0.00 0.00 3.25
393 411 0.541063 CAAACCCAACCCCCTACCAC 60.541 60.000 0.00 0.00 0.00 4.16
396 414 2.761160 CCAACCCCCTACCACACC 59.239 66.667 0.00 0.00 0.00 4.16
407 425 1.001633 CTACCACACCACCACTACACC 59.998 57.143 0.00 0.00 0.00 4.16
519 541 4.426313 CTTTCCACCCCTCGCCCC 62.426 72.222 0.00 0.00 0.00 5.80
543 565 0.626382 CCCTTCCCTTTCTTCCTCCC 59.374 60.000 0.00 0.00 0.00 4.30
550 572 0.690762 CTTTCTTCCTCCCCGAACCA 59.309 55.000 0.00 0.00 0.00 3.67
559 581 0.611714 TCCCCGAACCACTTTAGCTC 59.388 55.000 0.00 0.00 0.00 4.09
631 653 1.201954 CGGAAACACATGCGATCACTG 60.202 52.381 0.00 0.00 36.09 3.66
633 655 2.413239 GGAAACACATGCGATCACTGTG 60.413 50.000 14.44 14.44 44.51 3.66
657 679 0.247655 CCCAAACGAACGCATCATCG 60.248 55.000 0.00 0.00 44.33 3.84
658 680 0.718904 CCAAACGAACGCATCATCGA 59.281 50.000 1.84 0.00 41.43 3.59
659 681 1.327460 CCAAACGAACGCATCATCGAT 59.673 47.619 1.84 0.00 41.43 3.59
660 682 2.597505 CCAAACGAACGCATCATCGATC 60.598 50.000 0.00 0.00 41.43 3.69
672 694 3.650070 TCATCGATCATGAGTAGCCAC 57.350 47.619 0.09 0.00 36.51 5.01
678 700 2.159179 TCATGAGTAGCCACTAGCCA 57.841 50.000 0.00 0.00 45.47 4.75
727 749 5.782893 AGAGGACAGACAATCTATGCTAC 57.217 43.478 0.00 0.00 0.00 3.58
755 777 1.237163 CCATGCCTCCTCCCTCCTA 59.763 63.158 0.00 0.00 0.00 2.94
777 807 6.952358 CCTACATACATATATATACCCCGGCT 59.048 42.308 0.00 0.00 0.00 5.52
778 808 6.912951 ACATACATATATATACCCCGGCTC 57.087 41.667 0.00 0.00 0.00 4.70
800 830 1.997874 CCCTCCAACCTCCCCTCAG 60.998 68.421 0.00 0.00 0.00 3.35
821 851 1.452110 CAGTGATCGGTCCATTTGCA 58.548 50.000 0.00 0.00 0.00 4.08
829 859 1.176527 GGTCCATTTGCAGCTTGCTA 58.823 50.000 9.12 0.00 45.31 3.49
849 879 0.107945 GCTAGCTCCAACCAGACCAG 60.108 60.000 7.70 0.00 0.00 4.00
900 930 0.032678 CTCGCATACCCACCTAGCTG 59.967 60.000 0.00 0.00 0.00 4.24
901 931 1.069765 CGCATACCCACCTAGCTGG 59.930 63.158 0.00 0.00 42.93 4.85
902 932 1.227973 GCATACCCACCTAGCTGGC 60.228 63.158 0.00 0.00 40.22 4.85
903 933 1.700042 GCATACCCACCTAGCTGGCT 61.700 60.000 0.00 0.00 40.22 4.75
904 934 0.394565 CATACCCACCTAGCTGGCTC 59.605 60.000 0.00 0.00 40.22 4.70
980 1014 3.188965 GAGCCAGCTACTCGTCGT 58.811 61.111 0.00 0.00 0.00 4.34
996 1030 2.186076 GTCGTAAGCAAGTCCATCTCG 58.814 52.381 0.00 0.00 37.18 4.04
1026 1060 4.809496 CAGGGGCGCAATGAGGCT 62.809 66.667 10.83 0.00 0.00 4.58
1050 1084 1.194280 CGTCGATCATCCACACGTCG 61.194 60.000 0.00 0.00 0.00 5.12
1113 1147 3.483869 AAGGAGATGCGGGAGGGC 61.484 66.667 0.00 0.00 0.00 5.19
1443 1480 5.509840 GGACACCTCGCTTCATCTGTAATAT 60.510 44.000 0.00 0.00 0.00 1.28
1444 1481 5.533482 ACACCTCGCTTCATCTGTAATATC 58.467 41.667 0.00 0.00 0.00 1.63
1445 1482 4.618912 CACCTCGCTTCATCTGTAATATCG 59.381 45.833 0.00 0.00 0.00 2.92
1562 1603 5.718130 TGCAGTACCACTAGTTATTACCTGT 59.282 40.000 0.00 0.00 0.00 4.00
1563 1604 6.211986 TGCAGTACCACTAGTTATTACCTGTT 59.788 38.462 0.00 0.00 0.00 3.16
1564 1605 6.534079 GCAGTACCACTAGTTATTACCTGTTG 59.466 42.308 0.00 0.00 0.00 3.33
1606 1647 1.920835 GGTCTCCCAGTCCCAGCTT 60.921 63.158 0.00 0.00 0.00 3.74
1615 1656 0.977395 AGTCCCAGCTTAGTCACACC 59.023 55.000 0.00 0.00 0.00 4.16
1633 1674 6.874134 GTCACACCACTTTACATATCTGAACT 59.126 38.462 0.00 0.00 0.00 3.01
1634 1675 6.873605 TCACACCACTTTACATATCTGAACTG 59.126 38.462 0.00 0.00 0.00 3.16
1635 1676 6.873605 CACACCACTTTACATATCTGAACTGA 59.126 38.462 0.00 0.00 0.00 3.41
1636 1677 7.387673 CACACCACTTTACATATCTGAACTGAA 59.612 37.037 0.00 0.00 0.00 3.02
1637 1678 7.387948 ACACCACTTTACATATCTGAACTGAAC 59.612 37.037 0.00 0.00 0.00 3.18
1670 1711 3.120546 CGCGCATATGCTTGCTTACTTAT 60.121 43.478 24.56 0.00 40.54 1.73
1731 1772 2.539274 GCATCTCTCAGAATGCGACTTC 59.461 50.000 6.19 0.00 34.76 3.01
1738 1782 4.081697 TCTCAGAATGCGACTTCCAATACA 60.082 41.667 0.00 0.00 34.76 2.29
1739 1783 4.769688 TCAGAATGCGACTTCCAATACAT 58.230 39.130 0.00 0.00 34.76 2.29
1740 1784 5.912892 TCAGAATGCGACTTCCAATACATA 58.087 37.500 0.00 0.00 34.76 2.29
1745 1789 8.939929 AGAATGCGACTTCCAATACATATAATG 58.060 33.333 0.00 0.00 0.00 1.90
1747 1791 8.621532 ATGCGACTTCCAATACATATAATGTT 57.378 30.769 0.00 0.00 41.63 2.71
1799 1845 2.681848 GCCAGACAAGATCATGACCTTG 59.318 50.000 25.61 25.61 43.84 3.61
1800 1846 3.276857 CCAGACAAGATCATGACCTTGG 58.723 50.000 29.41 12.41 42.86 3.61
1802 1848 4.330250 CAGACAAGATCATGACCTTGGTT 58.670 43.478 29.41 16.44 42.86 3.67
1806 1852 6.825721 AGACAAGATCATGACCTTGGTTAATC 59.174 38.462 29.41 18.71 42.86 1.75
1818 1864 7.232534 TGACCTTGGTTAATCATAAAAAGCACT 59.767 33.333 0.00 0.00 30.96 4.40
1819 1865 7.602753 ACCTTGGTTAATCATAAAAAGCACTC 58.397 34.615 0.00 0.00 30.96 3.51
1938 1995 6.235231 ACTTACATATACACTTGGTCAGGG 57.765 41.667 0.00 0.00 0.00 4.45
1941 1998 5.975988 ACATATACACTTGGTCAGGGAAT 57.024 39.130 0.00 0.00 0.00 3.01
1942 1999 8.555896 TTACATATACACTTGGTCAGGGAATA 57.444 34.615 0.00 0.00 0.00 1.75
1943 2000 7.446106 ACATATACACTTGGTCAGGGAATAA 57.554 36.000 0.00 0.00 0.00 1.40
1944 2001 7.867921 ACATATACACTTGGTCAGGGAATAAA 58.132 34.615 0.00 0.00 0.00 1.40
1945 2002 8.333235 ACATATACACTTGGTCAGGGAATAAAA 58.667 33.333 0.00 0.00 0.00 1.52
1946 2003 8.840321 CATATACACTTGGTCAGGGAATAAAAG 58.160 37.037 0.00 0.00 0.00 2.27
1947 2004 5.319043 ACACTTGGTCAGGGAATAAAAGA 57.681 39.130 0.00 0.00 0.00 2.52
1948 2005 5.701224 ACACTTGGTCAGGGAATAAAAGAA 58.299 37.500 0.00 0.00 0.00 2.52
1949 2006 5.535030 ACACTTGGTCAGGGAATAAAAGAAC 59.465 40.000 0.00 0.00 0.00 3.01
1998 2069 3.182967 GAGCATACGCATATACTCCTGC 58.817 50.000 0.00 0.00 42.27 4.85
2084 2163 8.269424 GTCGCATCGGATATTATATTTAGCTTG 58.731 37.037 0.00 0.00 0.00 4.01
2116 2195 0.247655 GTTCACACACGCACACACTG 60.248 55.000 0.00 0.00 0.00 3.66
2129 2208 1.672881 ACACACTGCTCAACTTGAAGC 59.327 47.619 0.00 0.48 0.00 3.86
2228 2314 0.259065 ATAGTGGCTCCTCGGTCAGA 59.741 55.000 0.00 0.00 0.00 3.27
2230 2316 0.832135 AGTGGCTCCTCGGTCAGAAA 60.832 55.000 0.00 0.00 0.00 2.52
2232 2318 1.079057 GGCTCCTCGGTCAGAAACC 60.079 63.158 0.00 0.00 45.45 3.27
2262 2348 2.792290 CGGACAGCGCGTGATCAAG 61.792 63.158 8.43 4.06 0.00 3.02
2275 2361 3.665675 ATCAAGGCGGACGGACAGC 62.666 63.158 0.00 0.00 38.89 4.40
2276 2362 4.680237 CAAGGCGGACGGACAGCA 62.680 66.667 5.02 0.00 41.24 4.41
2305 2391 2.503331 CAGGGTATTCAATATGGCGCA 58.497 47.619 10.83 0.00 0.00 6.09
2354 2440 1.271446 CGAGCCGACATCGCATAGTG 61.271 60.000 0.00 0.00 38.18 2.74
2376 2464 8.340618 AGTGTTTGAATTGAATACATACTGCT 57.659 30.769 0.00 0.00 0.00 4.24
2377 2465 8.239314 AGTGTTTGAATTGAATACATACTGCTG 58.761 33.333 0.00 0.00 0.00 4.41
2378 2466 7.485913 GTGTTTGAATTGAATACATACTGCTGG 59.514 37.037 0.00 0.00 0.00 4.85
2379 2467 7.176515 TGTTTGAATTGAATACATACTGCTGGT 59.823 33.333 0.00 0.00 0.00 4.00
2380 2468 6.682423 TGAATTGAATACATACTGCTGGTG 57.318 37.500 0.00 0.00 0.00 4.17
2381 2469 6.413892 TGAATTGAATACATACTGCTGGTGA 58.586 36.000 5.49 0.00 0.00 4.02
2382 2470 7.056006 TGAATTGAATACATACTGCTGGTGAT 58.944 34.615 5.49 0.00 0.00 3.06
2383 2471 7.557358 TGAATTGAATACATACTGCTGGTGATT 59.443 33.333 5.49 2.31 0.00 2.57
2389 2477 3.054139 ACATACTGCTGGTGATTGGTGAT 60.054 43.478 5.49 0.00 0.00 3.06
2400 2488 3.084039 TGATTGGTGATGAAAGACCAGC 58.916 45.455 0.00 0.00 43.17 4.85
2401 2489 1.909700 TTGGTGATGAAAGACCAGCC 58.090 50.000 0.00 0.00 43.17 4.85
2417 2505 1.211709 GCCGTTTGAATCAACCGGG 59.788 57.895 28.34 15.58 46.75 5.73
2422 2510 2.033550 CGTTTGAATCAACCGGGAACAA 59.966 45.455 6.32 3.25 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.243365 TTGTTTCATGCCATGGACGC 59.757 50.000 18.40 0.00 0.00 5.19
78 79 2.352503 ATCGTTGCCTTGTTTCATGC 57.647 45.000 0.00 0.00 0.00 4.06
82 83 5.118510 CCAATGTTTATCGTTGCCTTGTTTC 59.881 40.000 0.00 0.00 40.56 2.78
131 132 1.743321 CTCGATCAGTGGCTCTCCCC 61.743 65.000 0.00 0.00 0.00 4.81
135 136 0.104487 CATGCTCGATCAGTGGCTCT 59.896 55.000 0.00 0.00 0.00 4.09
136 137 1.497223 GCATGCTCGATCAGTGGCTC 61.497 60.000 11.37 0.00 0.00 4.70
137 138 1.523258 GCATGCTCGATCAGTGGCT 60.523 57.895 11.37 0.00 0.00 4.75
138 139 1.371337 TTGCATGCTCGATCAGTGGC 61.371 55.000 20.33 0.00 0.00 5.01
139 140 0.376152 GTTGCATGCTCGATCAGTGG 59.624 55.000 20.33 0.00 0.00 4.00
140 141 0.376152 GGTTGCATGCTCGATCAGTG 59.624 55.000 20.33 0.00 0.00 3.66
141 142 0.036105 TGGTTGCATGCTCGATCAGT 60.036 50.000 20.33 0.00 0.00 3.41
142 143 1.089112 TTGGTTGCATGCTCGATCAG 58.911 50.000 20.33 0.00 0.00 2.90
143 144 1.199789 GTTTGGTTGCATGCTCGATCA 59.800 47.619 20.33 8.62 0.00 2.92
144 145 1.468054 GGTTTGGTTGCATGCTCGATC 60.468 52.381 20.33 5.94 0.00 3.69
145 146 0.527565 GGTTTGGTTGCATGCTCGAT 59.472 50.000 20.33 0.00 0.00 3.59
146 147 0.821301 TGGTTTGGTTGCATGCTCGA 60.821 50.000 20.33 6.65 0.00 4.04
147 148 0.031857 TTGGTTTGGTTGCATGCTCG 59.968 50.000 20.33 0.00 0.00 5.03
148 149 1.501169 GTTGGTTTGGTTGCATGCTC 58.499 50.000 20.33 11.78 0.00 4.26
149 150 0.106521 GGTTGGTTTGGTTGCATGCT 59.893 50.000 20.33 0.00 0.00 3.79
162 163 4.108501 ACTTTTAATTCCGAGGGTTGGT 57.891 40.909 0.00 0.00 0.00 3.67
165 166 7.940688 TCTCTTTTACTTTTAATTCCGAGGGTT 59.059 33.333 0.00 0.00 0.00 4.11
166 167 7.455891 TCTCTTTTACTTTTAATTCCGAGGGT 58.544 34.615 0.00 0.00 0.00 4.34
169 170 9.216117 TCCTTCTCTTTTACTTTTAATTCCGAG 57.784 33.333 0.00 0.00 0.00 4.63
170 171 9.563748 TTCCTTCTCTTTTACTTTTAATTCCGA 57.436 29.630 0.00 0.00 0.00 4.55
171 172 9.827411 CTTCCTTCTCTTTTACTTTTAATTCCG 57.173 33.333 0.00 0.00 0.00 4.30
174 175 9.877222 TCCCTTCCTTCTCTTTTACTTTTAATT 57.123 29.630 0.00 0.00 0.00 1.40
176 177 8.720537 TCTCCCTTCCTTCTCTTTTACTTTTAA 58.279 33.333 0.00 0.00 0.00 1.52
177 178 8.155510 GTCTCCCTTCCTTCTCTTTTACTTTTA 58.844 37.037 0.00 0.00 0.00 1.52
179 180 6.535540 GTCTCCCTTCCTTCTCTTTTACTTT 58.464 40.000 0.00 0.00 0.00 2.66
182 183 4.021280 ACGTCTCCCTTCCTTCTCTTTTAC 60.021 45.833 0.00 0.00 0.00 2.01
183 184 4.158015 ACGTCTCCCTTCCTTCTCTTTTA 58.842 43.478 0.00 0.00 0.00 1.52
187 188 1.075698 TGACGTCTCCCTTCCTTCTCT 59.924 52.381 17.92 0.00 0.00 3.10
190 191 1.066787 CCTTGACGTCTCCCTTCCTTC 60.067 57.143 17.92 0.00 0.00 3.46
193 194 1.192803 ACCCTTGACGTCTCCCTTCC 61.193 60.000 17.92 0.00 0.00 3.46
198 199 1.477295 CCTCTAACCCTTGACGTCTCC 59.523 57.143 17.92 0.00 0.00 3.71
202 203 2.005370 TGTCCTCTAACCCTTGACGT 57.995 50.000 0.00 0.00 0.00 4.34
223 224 2.622064 ATAGGATTTCGTGGTGCTCC 57.378 50.000 0.00 0.00 0.00 4.70
365 366 1.282447 GGGTTGGGTTTGGTTTGGTTT 59.718 47.619 0.00 0.00 0.00 3.27
370 371 0.942721 TAGGGGGTTGGGTTTGGTTT 59.057 50.000 0.00 0.00 0.00 3.27
375 393 1.000041 TGTGGTAGGGGGTTGGGTTT 61.000 55.000 0.00 0.00 0.00 3.27
376 394 1.387636 TGTGGTAGGGGGTTGGGTT 60.388 57.895 0.00 0.00 0.00 4.11
377 395 2.158130 GTGTGGTAGGGGGTTGGGT 61.158 63.158 0.00 0.00 0.00 4.51
378 396 2.761160 GTGTGGTAGGGGGTTGGG 59.239 66.667 0.00 0.00 0.00 4.12
379 397 2.157452 TGGTGTGGTAGGGGGTTGG 61.157 63.158 0.00 0.00 0.00 3.77
380 398 1.074248 GTGGTGTGGTAGGGGGTTG 59.926 63.158 0.00 0.00 0.00 3.77
381 399 2.158130 GGTGGTGTGGTAGGGGGTT 61.158 63.158 0.00 0.00 0.00 4.11
382 400 2.530916 GGTGGTGTGGTAGGGGGT 60.531 66.667 0.00 0.00 0.00 4.95
383 401 2.530661 TGGTGGTGTGGTAGGGGG 60.531 66.667 0.00 0.00 0.00 5.40
384 402 0.545787 TAGTGGTGGTGTGGTAGGGG 60.546 60.000 0.00 0.00 0.00 4.79
385 403 0.611714 GTAGTGGTGGTGTGGTAGGG 59.388 60.000 0.00 0.00 0.00 3.53
386 404 1.001633 GTGTAGTGGTGGTGTGGTAGG 59.998 57.143 0.00 0.00 0.00 3.18
387 405 1.001633 GGTGTAGTGGTGGTGTGGTAG 59.998 57.143 0.00 0.00 0.00 3.18
388 406 1.050204 GGTGTAGTGGTGGTGTGGTA 58.950 55.000 0.00 0.00 0.00 3.25
389 407 0.983905 TGGTGTAGTGGTGGTGTGGT 60.984 55.000 0.00 0.00 0.00 4.16
390 408 0.250295 CTGGTGTAGTGGTGGTGTGG 60.250 60.000 0.00 0.00 0.00 4.17
391 409 0.884704 GCTGGTGTAGTGGTGGTGTG 60.885 60.000 0.00 0.00 0.00 3.82
392 410 1.450211 GCTGGTGTAGTGGTGGTGT 59.550 57.895 0.00 0.00 0.00 4.16
393 411 1.667830 CGCTGGTGTAGTGGTGGTG 60.668 63.158 0.00 0.00 33.19 4.17
396 414 0.458543 CTAGCGCTGGTGTAGTGGTG 60.459 60.000 22.90 0.00 46.32 4.17
438 460 1.914798 TGGACATGGACATGGACATGA 59.085 47.619 27.93 11.33 45.55 3.07
519 541 2.239907 AGGAAGAAAGGGAAGGGAATCG 59.760 50.000 0.00 0.00 0.00 3.34
543 565 1.359459 GGCGAGCTAAAGTGGTTCGG 61.359 60.000 0.00 0.00 37.75 4.30
550 572 1.160137 CTTTGCTGGCGAGCTAAAGT 58.840 50.000 21.84 0.00 46.39 2.66
559 581 3.726517 CCGTCCACTTTGCTGGCG 61.727 66.667 0.00 0.00 33.34 5.69
624 646 0.889994 TTTGGGCATGCACAGTGATC 59.110 50.000 23.95 0.00 0.00 2.92
631 653 1.729131 CGTTCGTTTGGGCATGCAC 60.729 57.895 21.36 18.25 0.00 4.57
633 655 2.804931 GCGTTCGTTTGGGCATGC 60.805 61.111 9.90 9.90 0.00 4.06
637 659 0.523335 GATGATGCGTTCGTTTGGGC 60.523 55.000 0.00 0.00 0.00 5.36
657 679 2.630098 TGGCTAGTGGCTACTCATGATC 59.370 50.000 5.78 0.00 41.46 2.92
658 680 2.366916 GTGGCTAGTGGCTACTCATGAT 59.633 50.000 5.78 0.00 46.77 2.45
659 681 1.757118 GTGGCTAGTGGCTACTCATGA 59.243 52.381 5.78 0.00 46.77 3.07
660 682 2.231215 GTGGCTAGTGGCTACTCATG 57.769 55.000 5.78 0.00 46.77 3.07
678 700 5.358442 CACTAATACTCTCACACTGGCTAGT 59.642 44.000 0.00 0.00 37.75 2.57
745 767 9.756571 GGTATATATATGTATGTAGGAGGGAGG 57.243 40.741 5.44 0.00 0.00 4.30
746 768 9.756571 GGGTATATATATGTATGTAGGAGGGAG 57.243 40.741 5.44 0.00 0.00 4.30
748 770 7.614583 CGGGGTATATATATGTATGTAGGAGGG 59.385 44.444 5.44 0.00 0.00 4.30
755 777 5.475909 CGAGCCGGGGTATATATATGTATGT 59.524 44.000 2.18 0.00 0.00 2.29
800 830 0.734889 CAAATGGACCGATCACTGGC 59.265 55.000 0.00 0.00 0.00 4.85
829 859 0.545309 TGGTCTGGTTGGAGCTAGCT 60.545 55.000 19.45 19.45 35.11 3.32
900 930 1.035932 TGTAGTGGGTAGAGCGAGCC 61.036 60.000 0.00 0.00 37.51 4.70
901 931 0.815734 TTGTAGTGGGTAGAGCGAGC 59.184 55.000 0.00 0.00 0.00 5.03
902 932 2.093106 ACTTGTAGTGGGTAGAGCGAG 58.907 52.381 0.00 0.00 0.00 5.03
903 933 1.816835 CACTTGTAGTGGGTAGAGCGA 59.183 52.381 0.00 0.00 42.35 4.93
904 934 1.816835 TCACTTGTAGTGGGTAGAGCG 59.183 52.381 6.96 0.00 45.94 5.03
964 998 0.733729 CTTACGACGAGTAGCTGGCT 59.266 55.000 0.00 0.00 36.56 4.75
996 1030 2.203126 CCCTGCCTTCTCATCGGC 60.203 66.667 0.00 0.00 46.46 5.54
1026 1060 0.973496 TGTGGATGATCGACGGGGAA 60.973 55.000 3.19 0.00 0.00 3.97
1050 1084 1.124477 CCTGGAGGAGGGCTATGGAC 61.124 65.000 0.00 0.00 38.36 4.02
1395 1432 2.832733 GTCTACATCACCCCTATAGCCC 59.167 54.545 0.00 0.00 0.00 5.19
1562 1603 6.948886 TCAAATTATAGTAACCCAACAGGCAA 59.051 34.615 0.00 0.00 40.58 4.52
1563 1604 6.486056 TCAAATTATAGTAACCCAACAGGCA 58.514 36.000 0.00 0.00 40.58 4.75
1564 1605 6.039382 CCTCAAATTATAGTAACCCAACAGGC 59.961 42.308 0.00 0.00 40.58 4.85
1606 1647 7.712204 TCAGATATGTAAAGTGGTGTGACTA 57.288 36.000 0.00 0.00 0.00 2.59
1615 1656 8.553459 AAGGTTCAGTTCAGATATGTAAAGTG 57.447 34.615 0.00 0.00 0.00 3.16
1637 1678 1.439353 ATATGCGCGCACCTTGAAGG 61.439 55.000 39.05 10.24 42.49 3.46
1670 1711 7.526041 ACCATCCTAATAATGGACATGCTAAA 58.474 34.615 9.04 0.00 45.51 1.85
1740 1784 9.321562 ACGTGTATTCCGATAAAGAAACATTAT 57.678 29.630 0.00 0.00 0.00 1.28
1745 1789 8.123445 ACATACGTGTATTCCGATAAAGAAAC 57.877 34.615 0.00 0.00 36.63 2.78
1799 1845 8.863049 CAACATGAGTGCTTTTTATGATTAACC 58.137 33.333 0.00 0.00 0.00 2.85
1800 1846 9.624697 TCAACATGAGTGCTTTTTATGATTAAC 57.375 29.630 0.00 0.00 0.00 2.01
1818 1864 8.303156 CCCATGTGTAAATTTTACTCAACATGA 58.697 33.333 29.91 12.36 34.83 3.07
1819 1865 8.303156 TCCCATGTGTAAATTTTACTCAACATG 58.697 33.333 25.92 25.92 0.00 3.21
1941 1998 9.052759 GTGTCTCTGTTAGGATTTGTTCTTTTA 57.947 33.333 0.00 0.00 0.00 1.52
1942 1999 7.775561 AGTGTCTCTGTTAGGATTTGTTCTTTT 59.224 33.333 0.00 0.00 0.00 2.27
1943 2000 7.283329 AGTGTCTCTGTTAGGATTTGTTCTTT 58.717 34.615 0.00 0.00 0.00 2.52
1944 2001 6.831976 AGTGTCTCTGTTAGGATTTGTTCTT 58.168 36.000 0.00 0.00 0.00 2.52
1945 2002 6.426646 AGTGTCTCTGTTAGGATTTGTTCT 57.573 37.500 0.00 0.00 0.00 3.01
1946 2003 7.116519 GTGTAGTGTCTCTGTTAGGATTTGTTC 59.883 40.741 0.00 0.00 0.00 3.18
1947 2004 6.929606 GTGTAGTGTCTCTGTTAGGATTTGTT 59.070 38.462 0.00 0.00 0.00 2.83
1948 2005 6.041637 TGTGTAGTGTCTCTGTTAGGATTTGT 59.958 38.462 0.00 0.00 0.00 2.83
1949 2006 6.455647 TGTGTAGTGTCTCTGTTAGGATTTG 58.544 40.000 0.00 0.00 0.00 2.32
1998 2069 7.563888 TCATCTTTTATTTCCTCTCTGCATG 57.436 36.000 0.00 0.00 0.00 4.06
2116 2195 0.599558 TGCCATGCTTCAAGTTGAGC 59.400 50.000 15.97 15.97 0.00 4.26
2129 2208 2.154462 ACGTTTCTTCTCCTTGCCATG 58.846 47.619 0.00 0.00 0.00 3.66
2212 2298 0.670854 GTTTCTGACCGAGGAGCCAC 60.671 60.000 0.00 0.00 0.00 5.01
2228 2314 0.682852 TCCGTGATCCACTTCGGTTT 59.317 50.000 0.00 0.00 42.95 3.27
2230 2316 1.183030 TGTCCGTGATCCACTTCGGT 61.183 55.000 0.00 0.00 42.95 4.69
2232 2318 1.078759 GCTGTCCGTGATCCACTTCG 61.079 60.000 0.00 0.00 31.34 3.79
2262 2348 4.373116 TTCTGCTGTCCGTCCGCC 62.373 66.667 0.00 0.00 0.00 6.13
2275 2361 1.281867 TGAATACCCTGGCCAGTTCTG 59.718 52.381 30.63 17.87 0.00 3.02
2276 2362 1.668826 TGAATACCCTGGCCAGTTCT 58.331 50.000 30.63 14.83 0.00 3.01
2305 2391 1.628340 TGATGAGATCACGGTTTGGGT 59.372 47.619 0.00 0.00 33.59 4.51
2354 2440 7.485913 CACCAGCAGTATGTATTCAATTCAAAC 59.514 37.037 0.00 0.00 39.31 2.93
2373 2461 2.583024 TTCATCACCAATCACCAGCA 57.417 45.000 0.00 0.00 0.00 4.41
2375 2463 3.441572 GGTCTTTCATCACCAATCACCAG 59.558 47.826 0.00 0.00 32.33 4.00
2376 2464 3.181435 TGGTCTTTCATCACCAATCACCA 60.181 43.478 0.00 0.00 39.85 4.17
2377 2465 3.420893 TGGTCTTTCATCACCAATCACC 58.579 45.455 0.00 0.00 39.85 4.02
2378 2466 3.119708 GCTGGTCTTTCATCACCAATCAC 60.120 47.826 0.00 0.00 42.28 3.06
2379 2467 3.084039 GCTGGTCTTTCATCACCAATCA 58.916 45.455 0.00 0.00 42.28 2.57
2380 2468 2.424956 GGCTGGTCTTTCATCACCAATC 59.575 50.000 0.00 0.00 42.28 2.67
2381 2469 2.450476 GGCTGGTCTTTCATCACCAAT 58.550 47.619 0.00 0.00 42.28 3.16
2382 2470 1.881925 CGGCTGGTCTTTCATCACCAA 60.882 52.381 0.00 0.00 42.28 3.67
2383 2471 0.321564 CGGCTGGTCTTTCATCACCA 60.322 55.000 0.00 0.00 40.56 4.17
2389 2477 2.045561 TTCAAACGGCTGGTCTTTCA 57.954 45.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.