Multiple sequence alignment - TraesCS5A01G281800

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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 TraesCS5A01G281800 chr5A 100.000 2423 0 0 1 2423 491161740 491164162 0.000000e+00 4475.0
1 TraesCS5A01G281800 chr5A 82.243 107 19 0 1172 1278 491093846 491093952 2.570000e-15 93.5
2 TraesCS5A01G281800 chr5D 91.877 554 41 3 938 1491 387989245 387989794 0.000000e+00 771.0
3 TraesCS5A01G281800 chr5D 91.033 513 17 9 1751 2263 387990804 387991287 0.000000e+00 665.0
4 TraesCS5A01G281800 chr5D 81.358 692 64 25 1734 2415 388025087 388025723 1.000000e-138 503.0
5 TraesCS5A01G281800 chr5D 90.493 284 13 6 531 814 387988686 387988955 1.770000e-96 363.0
6 TraesCS5A01G281800 chr5D 92.188 256 17 3 68 321 387982820 387983074 2.290000e-95 359.0
7 TraesCS5A01G281800 chr5D 88.953 172 11 2 2252 2423 387993878 387994041 3.160000e-49 206.0
8 TraesCS5A01G281800 chr5D 90.756 119 10 1 817 934 387989087 387989205 8.970000e-35 158.0
9 TraesCS5A01G281800 chr5D 82.243 107 19 0 1172 1278 387960856 387960962 2.570000e-15 93.5
10 TraesCS5A01G281800 chr5D 86.792 53 4 2 1683 1735 387990713 387990762 3.370000e-04 56.5
11 TraesCS5A01G281800 chr5B 90.827 556 46 4 937 1491 466616109 466616660 0.000000e+00 739.0
12 TraesCS5A01G281800 chr5B 86.402 706 51 21 1736 2423 466618780 466619458 0.000000e+00 730.0
13 TraesCS5A01G281800 chr5B 84.320 676 73 14 1747 2415 466633532 466634181 4.400000e-177 630.0
14 TraesCS5A01G281800 chr5B 90.437 481 36 3 1 477 466614850 466615324 2.050000e-175 625.0
15 TraesCS5A01G281800 chr5B 88.352 455 22 15 481 934 466615644 466616068 3.570000e-143 518.0
16 TraesCS5A01G281800 chr5B 79.327 416 55 14 1731 2122 466741752 466742160 1.850000e-66 263.0
17 TraesCS5A01G281800 chr5B 84.211 114 18 0 1172 1285 466525621 466525734 7.080000e-21 111.0
18 TraesCS5A01G281800 chr1D 87.234 94 12 0 1175 1268 10955130 10955037 9.160000e-20 108.0
19 TraesCS5A01G281800 chr6D 100.000 28 0 0 1173 1200 37449700 37449727 4.000000e-03 52.8
20 TraesCS5A01G281800 chr6B 100.000 28 0 0 1173 1200 87560144 87560171 4.000000e-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 TraesCS5A01G281800 chr5A 491161740 491164162 2422 False 4475.000000 4475 100.0000 1 2423 1 chr5A.!!$F2 2422
1 TraesCS5A01G281800 chr5D 388025087 388025723 636 False 503.000000 503 81.3580 1734 2415 1 chr5D.!!$F3 681
2 TraesCS5A01G281800 chr5D 387988686 387994041 5355 False 369.916667 771 89.9840 531 2423 6 chr5D.!!$F4 1892
3 TraesCS5A01G281800 chr5B 466614850 466619458 4608 False 653.000000 739 89.0045 1 2423 4 chr5B.!!$F4 2422
4 TraesCS5A01G281800 chr5B 466633532 466634181 649 False 630.000000 630 84.3200 1747 2415 1 chr5B.!!$F2 668

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
796 1117 0.241213 TACGCTCTCAGCTGTGTCAC 59.759 55.0 14.67 0.0 39.6 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 7858 0.112995 TGAAGAAGGGCCTGCACAAT 59.887 50.0 15.67 0.0 0.0 2.71 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
77 78 7.249147 CACTAAAGATGAAATGAAGAGGCAAG 58.751 38.462 0.00 0.00 0.00 4.01
79 80 7.833183 ACTAAAGATGAAATGAAGAGGCAAGAT 59.167 33.333 0.00 0.00 0.00 2.40
90 91 1.139853 GAGGCAAGATGGGTGGACTAG 59.860 57.143 0.00 0.00 0.00 2.57
91 92 0.464554 GGCAAGATGGGTGGACTAGC 60.465 60.000 0.00 0.00 0.00 3.42
100 101 1.442148 GTGGACTAGCCGGGATGAC 59.558 63.158 2.18 0.00 40.66 3.06
128 129 5.574891 AGTACAAGCACATCACAACAAAA 57.425 34.783 0.00 0.00 0.00 2.44
129 130 5.339990 AGTACAAGCACATCACAACAAAAC 58.660 37.500 0.00 0.00 0.00 2.43
130 131 3.520569 ACAAGCACATCACAACAAAACC 58.479 40.909 0.00 0.00 0.00 3.27
131 132 3.195396 ACAAGCACATCACAACAAAACCT 59.805 39.130 0.00 0.00 0.00 3.50
132 133 3.441496 AGCACATCACAACAAAACCTG 57.559 42.857 0.00 0.00 0.00 4.00
188 189 9.687210 ATGATGTGTATGAAATATGTTCAATGC 57.313 29.630 4.99 0.00 31.55 3.56
214 215 2.559231 GACGGCTTTGAACCCCAATTAA 59.441 45.455 0.00 0.00 34.23 1.40
300 301 5.709631 TGCTTGGCTGAGAAACAAACATATA 59.290 36.000 0.00 0.00 0.00 0.86
309 310 8.232913 TGAGAAACAAACATATATAAAGCCCC 57.767 34.615 0.00 0.00 0.00 5.80
321 322 1.543944 AAAGCCCCGGCATGAAAAGG 61.544 55.000 8.74 0.00 44.88 3.11
322 323 3.460868 GCCCCGGCATGAAAAGGG 61.461 66.667 0.00 1.07 43.41 3.95
364 365 1.649321 ATCACTGACCAGCCTTCTGA 58.351 50.000 0.00 0.00 42.95 3.27
372 373 1.273838 ACCAGCCTTCTGACCCATCTA 60.274 52.381 0.00 0.00 42.95 1.98
398 403 2.072298 GTCAACTCATCACACTGAGGC 58.928 52.381 6.10 0.00 45.67 4.70
406 411 2.029666 ACACTGAGGCACTGACGC 59.970 61.111 0.00 0.00 41.55 5.19
407 412 3.108289 CACTGAGGCACTGACGCG 61.108 66.667 3.53 3.53 41.55 6.01
408 413 4.363990 ACTGAGGCACTGACGCGG 62.364 66.667 12.47 0.00 41.55 6.46
449 454 4.835284 TGTAATCAGGCTGATTGGTGTA 57.165 40.909 39.67 24.14 45.77 2.90
464 469 1.204941 GGTGTAGTTCGGATCTGCAGT 59.795 52.381 14.67 0.42 0.00 4.40
479 484 3.855630 CAGTAGTGCTAGCCGCTAG 57.144 57.895 21.22 21.22 37.22 3.42
518 839 2.299326 ACCAGGAGAAAAGCTTGCAT 57.701 45.000 0.00 0.00 0.00 3.96
519 840 1.891150 ACCAGGAGAAAAGCTTGCATG 59.109 47.619 0.00 0.00 0.00 4.06
520 841 1.891150 CCAGGAGAAAAGCTTGCATGT 59.109 47.619 0.00 0.00 0.00 3.21
527 848 2.138596 AAAGCTTGCATGTTGGTTCG 57.861 45.000 0.00 0.00 0.00 3.95
566 887 1.678728 GCAACACCGGATCTTGGATGA 60.679 52.381 9.46 0.00 0.00 2.92
586 907 7.355778 GGATGAGATCCGTTGAATTTAATGAC 58.644 38.462 3.84 0.00 40.13 3.06
587 908 7.012327 GGATGAGATCCGTTGAATTTAATGACA 59.988 37.037 3.84 0.00 40.13 3.58
595 916 6.257849 CCGTTGAATTTAATGACAGCTAGCTA 59.742 38.462 18.86 1.73 0.00 3.32
598 919 6.291377 TGAATTTAATGACAGCTAGCTAGGG 58.709 40.000 18.86 8.06 0.00 3.53
603 924 0.387565 GACAGCTAGCTAGGGTGAGC 59.612 60.000 18.86 9.37 43.19 4.26
624 945 5.674933 GCTACTAGCTGTTTGTTTTGACT 57.325 39.130 0.00 0.00 38.45 3.41
673 994 2.317371 TTCTGACTCTCAAGCCTCCT 57.683 50.000 0.00 0.00 0.00 3.69
763 1084 6.372659 TCCACTGACAAAGCAATAAGAATCTC 59.627 38.462 0.00 0.00 0.00 2.75
766 1087 6.373774 ACTGACAAAGCAATAAGAATCTCAGG 59.626 38.462 0.00 0.00 0.00 3.86
767 1088 5.124457 TGACAAAGCAATAAGAATCTCAGGC 59.876 40.000 0.00 0.00 0.00 4.85
768 1089 5.259632 ACAAAGCAATAAGAATCTCAGGCT 58.740 37.500 0.00 0.00 0.00 4.58
769 1090 6.418101 ACAAAGCAATAAGAATCTCAGGCTA 58.582 36.000 0.00 0.00 0.00 3.93
770 1091 6.317391 ACAAAGCAATAAGAATCTCAGGCTAC 59.683 38.462 0.00 0.00 0.00 3.58
771 1092 4.626042 AGCAATAAGAATCTCAGGCTACG 58.374 43.478 0.00 0.00 0.00 3.51
772 1093 3.743396 GCAATAAGAATCTCAGGCTACGG 59.257 47.826 0.00 0.00 0.00 4.02
773 1094 3.669251 ATAAGAATCTCAGGCTACGGC 57.331 47.619 0.00 0.00 37.82 5.68
796 1117 0.241213 TACGCTCTCAGCTGTGTCAC 59.759 55.000 14.67 0.00 39.60 3.67
808 1129 1.476891 CTGTGTCACCGCCACTATACT 59.523 52.381 0.00 0.00 33.92 2.12
852 1302 1.086696 AATGGTGATGCGTGCACTAC 58.913 50.000 16.19 7.56 36.53 2.73
875 1325 4.396166 CCTACCATTAACTTTGGTCAGCTG 59.604 45.833 7.63 7.63 44.15 4.24
878 1328 3.573967 CCATTAACTTTGGTCAGCTGGTT 59.426 43.478 15.13 11.17 0.00 3.67
890 1341 3.011818 TCAGCTGGTTAACGACTCGATA 58.988 45.455 15.13 0.00 0.00 2.92
920 1371 5.964758 ACAGCTTGAATGTTGACTGAAAAA 58.035 33.333 0.00 0.00 0.00 1.94
1005 1494 1.212616 GGCATCGATCACACAGCTAC 58.787 55.000 0.00 0.00 0.00 3.58
1040 1529 1.207811 GCATTGACTTGGGATTTGGGG 59.792 52.381 0.00 0.00 0.00 4.96
1204 1694 2.768344 CGGAGGTGGTGGGGCTAT 60.768 66.667 0.00 0.00 0.00 2.97
1252 1742 2.905996 AAGGACAAGCCCGATGCCA 61.906 57.895 0.00 0.00 42.71 4.92
1297 1787 1.536072 CGATGGTCACCATGGACTACG 60.536 57.143 16.24 6.49 45.26 3.51
1304 1794 0.264955 ACCATGGACTACGATCCCCT 59.735 55.000 21.47 0.00 38.06 4.79
1326 1816 1.298413 CGTCCGCATCTTCGTCGAT 60.298 57.895 0.00 0.00 0.00 3.59
1360 1850 2.363975 CCCCACACCGGCTAGCTAA 61.364 63.158 15.72 0.00 0.00 3.09
1385 1875 2.557924 TGGTACCTACACGGTTACACAG 59.442 50.000 14.36 0.00 46.37 3.66
1392 1882 7.453729 ACCTACACGGTTACACAGAAGTGAC 62.454 48.000 2.22 0.00 46.37 3.67
1408 1898 7.038302 ACAGAAGTGACTATTAATGTCAAGGGA 60.038 37.037 16.96 0.00 44.63 4.20
1491 1981 5.039333 GTGCTAGCTCCTTAATTTGCATTG 58.961 41.667 17.23 0.00 0.00 2.82
1492 1982 4.706476 TGCTAGCTCCTTAATTTGCATTGT 59.294 37.500 17.23 0.00 0.00 2.71
1498 2665 5.928264 GCTCCTTAATTTGCATTGTCACTTT 59.072 36.000 0.00 0.00 0.00 2.66
1501 2668 8.177119 TCCTTAATTTGCATTGTCACTTTAGT 57.823 30.769 0.00 0.00 0.00 2.24
1507 2674 4.041049 TGCATTGTCACTTTAGTTTTGCG 58.959 39.130 0.00 0.00 0.00 4.85
1508 2675 3.121362 GCATTGTCACTTTAGTTTTGCGC 60.121 43.478 0.00 0.00 0.00 6.09
1512 2679 1.877443 TCACTTTAGTTTTGCGCCTCC 59.123 47.619 4.18 0.00 0.00 4.30
1516 2683 2.094762 TTAGTTTTGCGCCTCCTCTC 57.905 50.000 4.18 0.00 0.00 3.20
1519 2686 0.884704 GTTTTGCGCCTCCTCTCACA 60.885 55.000 4.18 0.00 0.00 3.58
1520 2687 0.884704 TTTTGCGCCTCCTCTCACAC 60.885 55.000 4.18 0.00 0.00 3.82
1522 2689 2.038814 TTGCGCCTCCTCTCACACAA 62.039 55.000 4.18 0.00 0.00 3.33
1523 2690 1.739562 GCGCCTCCTCTCACACAAG 60.740 63.158 0.00 0.00 0.00 3.16
1524 2691 1.079543 CGCCTCCTCTCACACAAGG 60.080 63.158 0.00 0.00 0.00 3.61
1525 2692 1.536073 CGCCTCCTCTCACACAAGGA 61.536 60.000 0.00 0.00 39.38 3.36
1526 2693 0.687354 GCCTCCTCTCACACAAGGAA 59.313 55.000 0.00 0.00 41.09 3.36
1527 2694 1.338579 GCCTCCTCTCACACAAGGAAG 60.339 57.143 0.00 0.00 41.09 3.46
1528 2695 2.251818 CCTCCTCTCACACAAGGAAGA 58.748 52.381 0.00 0.00 41.09 2.87
1530 2697 3.262915 CCTCCTCTCACACAAGGAAGATT 59.737 47.826 0.00 0.00 41.09 2.40
1533 4297 4.103153 TCCTCTCACACAAGGAAGATTTGT 59.897 41.667 0.00 0.00 38.74 2.83
1536 4300 5.684704 TCTCACACAAGGAAGATTTGTCTT 58.315 37.500 0.00 0.00 36.67 3.01
1537 4301 5.528690 TCTCACACAAGGAAGATTTGTCTTG 59.471 40.000 0.00 0.00 41.46 3.02
1548 4312 9.014297 AGGAAGATTTGTCTTGTTAATTAGTGG 57.986 33.333 0.00 0.00 0.00 4.00
1554 4318 9.758651 ATTTGTCTTGTTAATTAGTGGAAAACC 57.241 29.630 0.00 0.00 0.00 3.27
1560 4324 1.734163 ATTAGTGGAAAACCGAGCGG 58.266 50.000 7.48 7.48 42.03 5.52
1566 4330 0.664224 GGAAAACCGAGCGGAAACAA 59.336 50.000 16.83 0.00 38.96 2.83
1567 4331 1.065851 GGAAAACCGAGCGGAAACAAA 59.934 47.619 16.83 0.00 38.96 2.83
1600 4364 8.914011 AGAACAAGAAACAATTATTATAGGCCC 58.086 33.333 0.00 0.00 0.00 5.80
1601 4365 7.272037 ACAAGAAACAATTATTATAGGCCCG 57.728 36.000 0.00 0.00 0.00 6.13
1602 4366 7.057894 ACAAGAAACAATTATTATAGGCCCGA 58.942 34.615 0.00 0.00 0.00 5.14
1603 4367 7.012989 ACAAGAAACAATTATTATAGGCCCGAC 59.987 37.037 0.00 0.00 0.00 4.79
1604 4368 5.699458 AGAAACAATTATTATAGGCCCGACG 59.301 40.000 0.00 0.00 0.00 5.12
1605 4369 3.332034 ACAATTATTATAGGCCCGACGC 58.668 45.455 0.00 0.00 0.00 5.19
1606 4370 2.288961 ATTATTATAGGCCCGACGCG 57.711 50.000 3.53 3.53 38.94 6.01
1608 4372 2.216750 TATTATAGGCCCGACGCGGC 62.217 60.000 12.47 6.41 46.86 6.53
1625 4389 0.523072 GGCGACGCCCGTAGAATATA 59.477 55.000 28.74 0.00 44.06 0.86
1628 4392 3.248266 GCGACGCCCGTAGAATATATTT 58.752 45.455 9.14 0.00 41.15 1.40
1677 4477 1.094785 CAAACCAGCACTATTCCCCG 58.905 55.000 0.00 0.00 0.00 5.73
1678 4478 0.034477 AAACCAGCACTATTCCCCGG 60.034 55.000 0.00 0.00 0.00 5.73
1680 4480 2.588877 CAGCACTATTCCCCGGCG 60.589 66.667 0.00 0.00 0.00 6.46
1698 4498 4.221422 GCGGCGCCCTCAGATGTA 62.221 66.667 23.58 0.00 0.00 2.29
1705 4517 2.746472 GCGCCCTCAGATGTAAAATCCT 60.746 50.000 0.00 0.00 0.00 3.24
1706 4518 3.134458 CGCCCTCAGATGTAAAATCCTC 58.866 50.000 0.00 0.00 0.00 3.71
1778 4616 1.525077 CGACCTCTCCTCTCCTCCG 60.525 68.421 0.00 0.00 0.00 4.63
1783 4621 3.522731 CTCCTCTCCTCCGTGGCG 61.523 72.222 0.00 0.00 35.26 5.69
1855 4693 1.906824 TCGTGTTTCCTCGGAGGCT 60.907 57.895 19.48 0.00 34.61 4.58
1870 4708 1.538666 GGCTACATGGGGCCAAGAT 59.461 57.895 21.21 0.00 46.84 2.40
2036 4877 2.164624 GGCTCTATGTACAGGGCTATCG 59.835 54.545 6.90 0.00 42.05 2.92
2088 4929 2.659826 GCGATCGTAGCGAGAGTAAGTC 60.660 54.545 17.81 0.00 39.91 3.01
2089 4930 2.408738 CGATCGTAGCGAGAGTAAGTCG 60.409 54.545 7.03 0.00 39.91 4.18
2106 4950 7.306953 AGTAAGTCGTCAATACTTGTCTCTTC 58.693 38.462 0.00 0.00 37.71 2.87
2132 4978 9.884465 CTGTCTTTTCTTATTCTTTACTGGTTG 57.116 33.333 0.00 0.00 0.00 3.77
2133 4979 8.349983 TGTCTTTTCTTATTCTTTACTGGTTGC 58.650 33.333 0.00 0.00 0.00 4.17
2134 4980 8.568794 GTCTTTTCTTATTCTTTACTGGTTGCT 58.431 33.333 0.00 0.00 0.00 3.91
2135 4981 8.567948 TCTTTTCTTATTCTTTACTGGTTGCTG 58.432 33.333 0.00 0.00 0.00 4.41
2136 4982 7.817418 TTTCTTATTCTTTACTGGTTGCTGT 57.183 32.000 0.00 0.00 0.00 4.40
2137 4983 7.817418 TTCTTATTCTTTACTGGTTGCTGTT 57.183 32.000 0.00 0.00 0.00 3.16
2138 4984 8.911918 TTCTTATTCTTTACTGGTTGCTGTTA 57.088 30.769 0.00 0.00 0.00 2.41
2306 7770 0.478072 ACCCTCATTGTCTTGCACCA 59.522 50.000 0.00 0.00 0.00 4.17
2335 7799 4.136796 TCAGTTAACTGCAATGCAAGTCT 58.863 39.130 27.49 1.09 43.46 3.24
2394 7858 3.133721 CCACCCACAAAACCTGAATTCAA 59.866 43.478 9.88 0.00 0.00 2.69
2415 7879 0.112995 TGTGCAGGCCCTTCTTCAAT 59.887 50.000 0.00 0.00 0.00 2.57
2419 7883 1.101331 CAGGCCCTTCTTCAATCTGC 58.899 55.000 0.00 0.00 0.00 4.26
2420 7884 0.393537 AGGCCCTTCTTCAATCTGCG 60.394 55.000 0.00 0.00 0.00 5.18
2421 7885 1.431036 GCCCTTCTTCAATCTGCGC 59.569 57.895 0.00 0.00 0.00 6.09
2422 7886 1.308069 GCCCTTCTTCAATCTGCGCA 61.308 55.000 10.98 10.98 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.621532 TTTCATCTTTAGTGCTGTACATCTTT 57.378 30.769 0.00 0.00 0.00 2.52
48 49 6.373774 CCTCTTCATTTCATCTTTAGTGCTGT 59.626 38.462 0.00 0.00 0.00 4.40
49 50 6.677431 GCCTCTTCATTTCATCTTTAGTGCTG 60.677 42.308 0.00 0.00 0.00 4.41
50 51 5.356470 GCCTCTTCATTTCATCTTTAGTGCT 59.644 40.000 0.00 0.00 0.00 4.40
51 52 5.124457 TGCCTCTTCATTTCATCTTTAGTGC 59.876 40.000 0.00 0.00 0.00 4.40
52 53 6.748333 TGCCTCTTCATTTCATCTTTAGTG 57.252 37.500 0.00 0.00 0.00 2.74
61 62 3.245371 ACCCATCTTGCCTCTTCATTTCA 60.245 43.478 0.00 0.00 0.00 2.69
77 78 2.808206 CCCGGCTAGTCCACCCATC 61.808 68.421 0.00 0.00 34.01 3.51
79 80 3.326385 ATCCCGGCTAGTCCACCCA 62.326 63.158 0.00 0.00 34.01 4.51
90 91 4.530710 TGTACTATATTGTCATCCCGGC 57.469 45.455 0.00 0.00 0.00 6.13
91 92 4.929808 GCTTGTACTATATTGTCATCCCGG 59.070 45.833 0.00 0.00 0.00 5.73
100 101 7.973601 TGTTGTGATGTGCTTGTACTATATTG 58.026 34.615 0.00 0.00 0.00 1.90
165 166 8.468399 TGTGCATTGAACATATTTCATACACAT 58.532 29.630 16.18 3.65 34.23 3.21
166 167 7.824672 TGTGCATTGAACATATTTCATACACA 58.175 30.769 16.18 16.18 35.48 3.72
188 189 0.240945 GGGTTCAAAGCCGTCATGTG 59.759 55.000 0.00 0.00 36.76 3.21
214 215 4.463539 TCCATATTGCACACTTTGAGCATT 59.536 37.500 0.00 0.00 43.07 3.56
257 258 5.989551 AGCAAATGATTTGACCAAAACAC 57.010 34.783 21.14 0.71 43.26 3.32
264 265 2.997986 CAGCCAAGCAAATGATTTGACC 59.002 45.455 21.14 4.88 43.26 4.02
267 268 4.182693 TCTCAGCCAAGCAAATGATTTG 57.817 40.909 13.32 13.32 43.44 2.32
300 301 1.756538 CTTTTCATGCCGGGGCTTTAT 59.243 47.619 11.55 0.00 42.51 1.40
309 310 3.591196 TCAATTTCCCTTTTCATGCCG 57.409 42.857 0.00 0.00 0.00 5.69
364 365 8.589338 GTGATGAGTTGACTATAATAGATGGGT 58.411 37.037 0.00 0.00 0.00 4.51
372 373 7.495901 CCTCAGTGTGATGAGTTGACTATAAT 58.504 38.462 3.29 0.00 44.35 1.28
398 403 2.010817 GCTTTTTGCCGCGTCAGTG 61.011 57.895 4.92 0.00 35.15 3.66
406 411 0.238289 ATCACTGACGCTTTTTGCCG 59.762 50.000 0.00 0.00 38.78 5.69
407 412 1.266718 TCATCACTGACGCTTTTTGCC 59.733 47.619 0.00 0.00 38.78 4.52
408 413 2.686558 TCATCACTGACGCTTTTTGC 57.313 45.000 0.00 0.00 38.57 3.68
419 424 4.700700 TCAGCCTGATTACATCATCACTG 58.299 43.478 0.00 0.00 38.85 3.66
435 440 1.066143 CCGAACTACACCAATCAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
439 444 3.678806 GCAGATCCGAACTACACCAATCA 60.679 47.826 0.00 0.00 0.00 2.57
443 448 1.204704 CTGCAGATCCGAACTACACCA 59.795 52.381 8.42 0.00 0.00 4.17
449 454 1.134965 GCACTACTGCAGATCCGAACT 60.135 52.381 23.35 0.00 43.62 3.01
477 482 3.449918 TCATCCTCCACAACCACATCTA 58.550 45.455 0.00 0.00 0.00 1.98
479 484 2.749621 GTTCATCCTCCACAACCACATC 59.250 50.000 0.00 0.00 0.00 3.06
518 839 1.153329 ACGTCAAGCCGAACCAACA 60.153 52.632 0.00 0.00 0.00 3.33
519 840 1.155424 TGACGTCAAGCCGAACCAAC 61.155 55.000 17.62 0.00 0.00 3.77
520 841 0.878523 CTGACGTCAAGCCGAACCAA 60.879 55.000 20.49 0.00 0.00 3.67
527 848 1.363744 CCAAGATCTGACGTCAAGCC 58.636 55.000 20.49 10.77 0.00 4.35
566 887 5.882557 AGCTGTCATTAAATTCAACGGATCT 59.117 36.000 0.00 0.00 0.00 2.75
580 901 3.891977 CTCACCCTAGCTAGCTGTCATTA 59.108 47.826 27.68 4.87 0.00 1.90
603 924 9.599322 CAAATAGTCAAAACAAACAGCTAGTAG 57.401 33.333 0.00 0.00 0.00 2.57
604 925 9.116067 ACAAATAGTCAAAACAAACAGCTAGTA 57.884 29.630 0.00 0.00 0.00 1.82
605 926 7.996385 ACAAATAGTCAAAACAAACAGCTAGT 58.004 30.769 0.00 0.00 0.00 2.57
673 994 5.180117 GCTGCAGTTCAGAAGATTTGACTTA 59.820 40.000 16.64 0.00 45.72 2.24
808 1129 8.934023 TGACCAGATCGCCATGTATATATATA 57.066 34.615 0.00 0.00 0.00 0.86
875 1325 1.107720 CGCGTATCGAGTCGTTAACC 58.892 55.000 13.12 2.61 41.67 2.85
878 1328 0.809636 TCCCGCGTATCGAGTCGTTA 60.810 55.000 13.12 5.78 41.67 3.18
890 1341 2.034879 CATTCAAGCTGTCCCGCGT 61.035 57.895 4.92 0.00 34.40 6.01
920 1371 8.552034 GCGAATGCTAGTAGAAAGTCAAAATAT 58.448 33.333 0.00 0.00 38.39 1.28
958 1447 7.805083 ACATCACTCCTGCTATTTATAGGAT 57.195 36.000 0.00 0.00 39.71 3.24
959 1448 7.618019 AACATCACTCCTGCTATTTATAGGA 57.382 36.000 0.00 0.00 38.25 2.94
971 1460 1.747355 GATGCCCAAACATCACTCCTG 59.253 52.381 0.00 0.00 44.81 3.86
974 1463 1.737838 TCGATGCCCAAACATCACTC 58.262 50.000 5.46 0.00 45.56 3.51
1252 1742 1.214589 CGGGGAGAACGACGATGTT 59.785 57.895 0.00 0.00 34.02 2.71
1345 1835 4.110493 GCTTAGCTAGCCGGTGTG 57.890 61.111 12.13 0.00 44.48 3.82
1365 1855 8.920986 CACTTCTGTGTAACCGTGTAGGTACC 62.921 50.000 2.73 2.73 45.08 3.34
1366 1856 6.070568 CACTTCTGTGTAACCGTGTAGGTAC 61.071 48.000 0.00 0.00 45.08 3.34
1378 1868 9.990360 TTGACATTAATAGTCACTTCTGTGTAA 57.010 29.630 15.73 1.45 44.95 2.41
1385 1875 7.103641 TGTCCCTTGACATTAATAGTCACTTC 58.896 38.462 15.73 8.88 46.40 3.01
1408 1898 9.533831 GGGGTATATGAAATTATTCTTCCATGT 57.466 33.333 0.00 0.00 36.48 3.21
1491 1981 2.350484 GGAGGCGCAAAACTAAAGTGAC 60.350 50.000 10.83 0.00 0.00 3.67
1492 1982 1.877443 GGAGGCGCAAAACTAAAGTGA 59.123 47.619 10.83 0.00 0.00 3.41
1498 2665 0.973632 TGAGAGGAGGCGCAAAACTA 59.026 50.000 10.83 0.00 0.00 2.24
1501 2668 0.884704 GTGTGAGAGGAGGCGCAAAA 60.885 55.000 10.83 0.00 0.00 2.44
1505 2672 1.739562 CTTGTGTGAGAGGAGGCGC 60.740 63.158 0.00 0.00 0.00 6.53
1507 2674 0.687354 TTCCTTGTGTGAGAGGAGGC 59.313 55.000 0.00 0.00 42.67 4.70
1508 2675 2.251818 TCTTCCTTGTGTGAGAGGAGG 58.748 52.381 0.00 0.00 42.67 4.30
1512 2679 5.303971 AGACAAATCTTCCTTGTGTGAGAG 58.696 41.667 0.00 0.00 37.14 3.20
1516 2683 5.505173 ACAAGACAAATCTTCCTTGTGTG 57.495 39.130 0.00 0.00 43.69 3.82
1522 2689 9.014297 CCACTAATTAACAAGACAAATCTTCCT 57.986 33.333 0.00 0.00 43.69 3.36
1523 2690 9.010029 TCCACTAATTAACAAGACAAATCTTCC 57.990 33.333 0.00 0.00 43.69 3.46
1528 2695 9.758651 GGTTTTCCACTAATTAACAAGACAAAT 57.241 29.630 0.00 0.00 40.31 2.32
1530 2697 7.282675 TCGGTTTTCCACTAATTAACAAGACAA 59.717 33.333 0.00 0.00 40.70 3.18
1533 4297 6.072893 GCTCGGTTTTCCACTAATTAACAAGA 60.073 38.462 0.00 0.00 40.70 3.02
1536 4300 4.152759 CGCTCGGTTTTCCACTAATTAACA 59.847 41.667 0.00 0.00 40.70 2.41
1537 4301 4.436451 CCGCTCGGTTTTCCACTAATTAAC 60.436 45.833 0.00 0.00 40.70 2.01
1547 4311 0.664224 TTGTTTCCGCTCGGTTTTCC 59.336 50.000 8.28 0.00 36.47 3.13
1548 4312 2.478547 TTTGTTTCCGCTCGGTTTTC 57.521 45.000 8.28 0.00 36.47 2.29
1576 4340 7.558444 TCGGGCCTATAATAATTGTTTCTTGTT 59.442 33.333 0.84 0.00 0.00 2.83
1577 4341 7.012989 GTCGGGCCTATAATAATTGTTTCTTGT 59.987 37.037 0.84 0.00 0.00 3.16
1578 4342 7.360361 GTCGGGCCTATAATAATTGTTTCTTG 58.640 38.462 0.84 0.00 0.00 3.02
1579 4343 6.204108 CGTCGGGCCTATAATAATTGTTTCTT 59.796 38.462 0.84 0.00 0.00 2.52
1580 4344 5.699458 CGTCGGGCCTATAATAATTGTTTCT 59.301 40.000 0.84 0.00 0.00 2.52
1581 4345 5.616204 GCGTCGGGCCTATAATAATTGTTTC 60.616 44.000 0.84 0.00 34.80 2.78
1582 4346 4.214758 GCGTCGGGCCTATAATAATTGTTT 59.785 41.667 0.84 0.00 34.80 2.83
1583 4347 3.749609 GCGTCGGGCCTATAATAATTGTT 59.250 43.478 0.84 0.00 34.80 2.83
1584 4348 3.332034 GCGTCGGGCCTATAATAATTGT 58.668 45.455 0.84 0.00 34.80 2.71
1585 4349 2.347452 CGCGTCGGGCCTATAATAATTG 59.653 50.000 0.84 0.00 38.94 2.32
1586 4350 2.613691 CGCGTCGGGCCTATAATAATT 58.386 47.619 0.84 0.00 38.94 1.40
1587 4351 1.134907 CCGCGTCGGGCCTATAATAAT 60.135 52.381 4.92 0.00 44.15 1.28
1588 4352 0.244450 CCGCGTCGGGCCTATAATAA 59.756 55.000 4.92 0.00 44.15 1.40
1589 4353 1.885157 CCGCGTCGGGCCTATAATA 59.115 57.895 4.92 0.00 44.15 0.98
1590 4354 2.654877 CCGCGTCGGGCCTATAAT 59.345 61.111 4.92 0.00 44.15 1.28
1607 4371 2.556534 ATATATTCTACGGGCGTCGC 57.443 50.000 9.22 9.22 43.89 5.19
1608 4372 5.834239 AAAAATATATTCTACGGGCGTCG 57.166 39.130 0.00 0.00 45.88 5.12
1651 4426 2.736144 TAGTGCTGGTTTGGACGTAG 57.264 50.000 0.00 0.00 33.42 3.51
1652 4427 3.592059 GAATAGTGCTGGTTTGGACGTA 58.408 45.455 0.00 0.00 33.42 3.57
1656 4456 1.005450 GGGGAATAGTGCTGGTTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
1661 4461 3.043999 GCCGGGGAATAGTGCTGGT 62.044 63.158 2.18 0.00 0.00 4.00
1662 4462 2.203209 GCCGGGGAATAGTGCTGG 60.203 66.667 2.18 0.00 0.00 4.85
1683 4483 1.604278 GATTTTACATCTGAGGGCGCC 59.396 52.381 21.18 21.18 0.00 6.53
1686 4486 4.133078 CAGAGGATTTTACATCTGAGGGC 58.867 47.826 0.00 0.00 46.98 5.19
1687 4487 4.133078 GCAGAGGATTTTACATCTGAGGG 58.867 47.826 13.15 0.00 46.98 4.30
1690 4490 5.188555 ACAGAGCAGAGGATTTTACATCTGA 59.811 40.000 13.15 0.00 46.98 3.27
1692 4492 5.690464 ACAGAGCAGAGGATTTTACATCT 57.310 39.130 0.00 0.00 0.00 2.90
1693 4493 6.112058 AGAACAGAGCAGAGGATTTTACATC 58.888 40.000 0.00 0.00 0.00 3.06
1694 4494 6.059787 AGAACAGAGCAGAGGATTTTACAT 57.940 37.500 0.00 0.00 0.00 2.29
1696 4496 5.517054 CGTAGAACAGAGCAGAGGATTTTAC 59.483 44.000 0.00 0.00 0.00 2.01
1697 4497 5.185249 ACGTAGAACAGAGCAGAGGATTTTA 59.815 40.000 0.00 0.00 0.00 1.52
1698 4498 4.021016 ACGTAGAACAGAGCAGAGGATTTT 60.021 41.667 0.00 0.00 0.00 1.82
1705 4517 1.174783 GGGACGTAGAACAGAGCAGA 58.825 55.000 0.00 0.00 0.00 4.26
1706 4518 0.173708 GGGGACGTAGAACAGAGCAG 59.826 60.000 0.00 0.00 0.00 4.24
1855 4693 1.294041 TCACATCTTGGCCCCATGTA 58.706 50.000 0.00 0.00 0.00 2.29
1870 4708 0.320683 CGCTGTCATGGAGGTTCACA 60.321 55.000 0.00 0.00 0.00 3.58
2036 4877 1.913262 CCCTTTTCCAGCCCCAACC 60.913 63.158 0.00 0.00 0.00 3.77
2106 4950 9.884465 CAACCAGTAAAGAATAAGAAAAGACAG 57.116 33.333 0.00 0.00 0.00 3.51
2132 4978 8.480643 AGTTCATATCTGTAACAACTAACAGC 57.519 34.615 0.00 0.00 42.31 4.40
2255 7706 7.223971 GGAAGTTCGCACACAGATATAACATTA 59.776 37.037 0.00 0.00 0.00 1.90
2260 7711 5.339008 AGGAAGTTCGCACACAGATATAA 57.661 39.130 0.00 0.00 0.00 0.98
2306 7770 5.183713 TGCATTGCAGTTAACTGAAAGCTAT 59.816 36.000 34.43 19.66 44.21 2.97
2356 7820 3.585289 TGGGTGGAAGTGCTAACTAATGA 59.415 43.478 0.00 0.00 34.77 2.57
2357 7821 3.689649 GTGGGTGGAAGTGCTAACTAATG 59.310 47.826 0.00 0.00 34.77 1.90
2358 7822 3.329520 TGTGGGTGGAAGTGCTAACTAAT 59.670 43.478 0.00 0.00 34.77 1.73
2359 7823 2.706723 TGTGGGTGGAAGTGCTAACTAA 59.293 45.455 0.00 0.00 34.77 2.24
2360 7824 2.331166 TGTGGGTGGAAGTGCTAACTA 58.669 47.619 0.00 0.00 34.77 2.24
2361 7825 1.136828 TGTGGGTGGAAGTGCTAACT 58.863 50.000 0.00 0.00 38.71 2.24
2362 7826 1.975660 TTGTGGGTGGAAGTGCTAAC 58.024 50.000 0.00 0.00 0.00 2.34
2394 7858 0.112995 TGAAGAAGGGCCTGCACAAT 59.887 50.000 15.67 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.