Multiple sequence alignment - TraesCS2B01G451200

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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 TraesCS2B01G451200 chr2B 100.000 2234 0 0 1 2234 644525732 644523499 0.000000e+00 4126
1 TraesCS2B01G451200 chr4B 96.350 1370 48 2 1 1368 476356240 476357609 0.000000e+00 2252
2 TraesCS2B01G451200 chr4B 95.620 1370 56 4 1 1367 31659232 31657864 0.000000e+00 2194
3 TraesCS2B01G451200 chr4B 94.143 1366 78 2 1 1365 402974770 402973406 0.000000e+00 2078
4 TraesCS2B01G451200 chr3B 96.202 1369 46 6 1 1367 37965523 37966887 0.000000e+00 2235
5 TraesCS2B01G451200 chr3B 90.361 166 15 1 1726 1890 768858411 768858576 1.340000e-52 217
6 TraesCS2B01G451200 chr1B 96.129 1369 46 4 2 1366 570823411 570824776 0.000000e+00 2228
7 TraesCS2B01G451200 chr7B 95.401 1370 59 4 1 1367 427826516 427825148 0.000000e+00 2178
8 TraesCS2B01G451200 chr4A 95.332 1371 60 4 1 1368 3393398 3394767 0.000000e+00 2174
9 TraesCS2B01G451200 chr5D 95.385 1365 60 3 1 1363 116717329 116715966 0.000000e+00 2169
10 TraesCS2B01G451200 chr5D 90.303 165 15 1 1727 1890 249874928 249875092 4.830000e-52 215
11 TraesCS2B01G451200 chr5D 88.506 174 19 1 1727 1899 564973603 564973776 2.250000e-50 209
12 TraesCS2B01G451200 chr1A 95.255 1370 61 4 1 1367 57183105 57184473 0.000000e+00 2167
13 TraesCS2B01G451200 chr2D 93.239 355 15 6 1889 2234 540057628 540057274 4.250000e-142 514
14 TraesCS2B01G451200 chr2D 89.944 358 14 7 1367 1723 540057984 540057648 2.040000e-120 442
15 TraesCS2B01G451200 chr2D 89.474 171 17 1 1726 1895 51074641 51074811 4.830000e-52 215
16 TraesCS2B01G451200 chr7D 91.018 167 14 1 1727 1892 245316022 245316188 8.030000e-55 224
17 TraesCS2B01G451200 chr2A 85.845 219 22 3 1510 1723 683563464 683563250 8.030000e-55 224
18 TraesCS2B01G451200 chr2A 87.313 134 7 2 1889 2012 683563230 683563097 6.430000e-31 145
19 TraesCS2B01G451200 chr3D 89.714 175 17 1 1726 1899 218654634 218654460 2.890000e-54 222
20 TraesCS2B01G451200 chr3D 88.889 171 17 2 1722 1891 445811493 445811324 2.250000e-50 209
21 TraesCS2B01G451200 chr4D 90.000 170 15 2 1726 1894 404675283 404675451 3.740000e-53 219
22 TraesCS2B01G451200 chr1D 90.303 165 15 1 1727 1890 11354780 11354616 4.830000e-52 215


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 TraesCS2B01G451200 chr2B 644523499 644525732 2233 True 4126 4126 100.0000 1 2234 1 chr2B.!!$R1 2233
1 TraesCS2B01G451200 chr4B 476356240 476357609 1369 False 2252 2252 96.3500 1 1368 1 chr4B.!!$F1 1367
2 TraesCS2B01G451200 chr4B 31657864 31659232 1368 True 2194 2194 95.6200 1 1367 1 chr4B.!!$R1 1366
3 TraesCS2B01G451200 chr4B 402973406 402974770 1364 True 2078 2078 94.1430 1 1365 1 chr4B.!!$R2 1364
4 TraesCS2B01G451200 chr3B 37965523 37966887 1364 False 2235 2235 96.2020 1 1367 1 chr3B.!!$F1 1366
5 TraesCS2B01G451200 chr1B 570823411 570824776 1365 False 2228 2228 96.1290 2 1366 1 chr1B.!!$F1 1364
6 TraesCS2B01G451200 chr7B 427825148 427826516 1368 True 2178 2178 95.4010 1 1367 1 chr7B.!!$R1 1366
7 TraesCS2B01G451200 chr4A 3393398 3394767 1369 False 2174 2174 95.3320 1 1368 1 chr4A.!!$F1 1367
8 TraesCS2B01G451200 chr5D 116715966 116717329 1363 True 2169 2169 95.3850 1 1363 1 chr5D.!!$R1 1362
9 TraesCS2B01G451200 chr1A 57183105 57184473 1368 False 2167 2167 95.2550 1 1367 1 chr1A.!!$F1 1366
10 TraesCS2B01G451200 chr2D 540057274 540057984 710 True 478 514 91.5915 1367 2234 2 chr2D.!!$R1 867

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
767 768 0.110486 AAGATTTGGGAGGCACACGT 59.89 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1890 0.035881 AGCCATGCATGATACTCCCG 59.964 55.0 28.31 9.48 0.0 5.14 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
106 107 1.605710 CCATCGCAAATCATCACCTCC 59.394 52.381 0.00 0.00 0.00 4.30
110 111 1.679944 CGCAAATCATCACCTCCCTGT 60.680 52.381 0.00 0.00 0.00 4.00
130 131 4.649705 TCCCGCTCCCCACTTGGA 62.650 66.667 0.00 0.00 37.39 3.53
157 158 4.774726 TCCAGAAGCTCAGTAAGATCACTT 59.225 41.667 0.00 0.00 39.81 3.16
329 330 3.118112 CCTTGGCTTATGTGGACTGATCT 60.118 47.826 0.00 0.00 0.00 2.75
408 409 0.833287 GGGCTTCTACCAGCATCTCA 59.167 55.000 0.00 0.00 42.10 3.27
454 455 2.028484 GGCACGACGACTGGACAA 59.972 61.111 0.00 0.00 0.00 3.18
578 579 1.302112 TTGCCCGTCTTTCATCGCA 60.302 52.632 0.00 0.00 0.00 5.10
767 768 0.110486 AAGATTTGGGAGGCACACGT 59.890 50.000 0.00 0.00 0.00 4.49
789 790 5.505654 CGTTGAGCCAACATGTAAGTTCTTT 60.506 40.000 15.40 0.00 43.70 2.52
1314 1321 6.347402 CGGAACACTCTTGTACATAAACCTTG 60.347 42.308 0.00 0.00 33.55 3.61
1340 1347 9.167311 GTTCTTCTTCTTATATGAAAAGGCAGA 57.833 33.333 15.29 4.97 0.00 4.26
1414 1422 0.248377 GGCTAGTGCGTACGTACCTG 60.248 60.000 29.08 22.57 40.82 4.00
1462 1470 8.145316 TGCCGTTTCATATAAATACTGGTAAC 57.855 34.615 0.00 0.00 0.00 2.50
1496 1504 6.754702 ATTAGCAGTACTACGAAGAACTGA 57.245 37.500 13.95 0.00 41.47 3.41
1509 1517 4.680537 ACTGAGGGCGGGAGTCGT 62.681 66.667 0.00 0.00 41.72 4.34
1510 1518 4.135153 CTGAGGGCGGGAGTCGTG 62.135 72.222 0.00 0.00 41.72 4.35
1511 1519 4.988716 TGAGGGCGGGAGTCGTGT 62.989 66.667 0.00 0.00 41.72 4.49
1537 1545 2.672961 TTAGCCAGTTGGAGACATCG 57.327 50.000 1.45 0.00 42.32 3.84
1550 1558 5.556915 TGGAGACATCGTTTTCTGGTATTT 58.443 37.500 0.00 0.00 33.40 1.40
1562 1570 7.253950 CGTTTTCTGGTATTTGGTCAAAACTTG 60.254 37.037 0.00 0.00 32.52 3.16
1570 1578 2.930950 TGGTCAAAACTTGTCCAGAGG 58.069 47.619 1.87 0.00 42.53 3.69
1571 1579 2.241176 TGGTCAAAACTTGTCCAGAGGT 59.759 45.455 1.87 0.00 42.53 3.85
1572 1580 3.288092 GGTCAAAACTTGTCCAGAGGTT 58.712 45.455 0.00 0.00 38.50 3.50
1573 1581 3.699538 GGTCAAAACTTGTCCAGAGGTTT 59.300 43.478 0.00 0.00 38.50 3.27
1574 1582 4.202020 GGTCAAAACTTGTCCAGAGGTTTC 60.202 45.833 0.00 0.00 38.50 2.78
1575 1583 4.398044 GTCAAAACTTGTCCAGAGGTTTCA 59.602 41.667 0.00 0.00 31.95 2.69
1576 1584 4.640201 TCAAAACTTGTCCAGAGGTTTCAG 59.360 41.667 0.00 0.00 31.95 3.02
1577 1585 2.938956 ACTTGTCCAGAGGTTTCAGG 57.061 50.000 0.00 0.00 0.00 3.86
1578 1586 2.127708 ACTTGTCCAGAGGTTTCAGGT 58.872 47.619 0.00 0.00 32.15 4.00
1579 1587 2.158755 ACTTGTCCAGAGGTTTCAGGTG 60.159 50.000 0.00 0.00 32.15 4.00
1580 1588 1.801242 TGTCCAGAGGTTTCAGGTGA 58.199 50.000 0.00 0.00 32.15 4.02
1581 1589 1.416401 TGTCCAGAGGTTTCAGGTGAC 59.584 52.381 0.00 0.00 32.15 3.67
1582 1590 1.056660 TCCAGAGGTTTCAGGTGACC 58.943 55.000 0.00 0.00 36.15 4.02
1629 1637 3.515502 TCGACACCTCTTGGATCTGAAAT 59.484 43.478 0.00 0.00 37.04 2.17
1642 1650 6.899089 TGGATCTGAAATTAGTAAGCATGGA 58.101 36.000 0.00 0.00 0.00 3.41
1681 1689 2.548067 GGTGATGATCATCCCACGGTAC 60.548 54.545 28.61 18.85 37.02 3.34
1682 1690 2.065993 GATGATCATCCCACGGTACG 57.934 55.000 22.91 0.00 44.73 3.67
1683 1691 1.336887 GATGATCATCCCACGGTACGG 60.337 57.143 22.91 0.00 43.96 4.02
1684 1692 3.917400 GATGATCATCCCACGGTACGGT 61.917 54.545 22.91 0.00 43.96 4.83
1685 1693 4.617709 GATGATCATCCCACGGTACGGTA 61.618 52.174 22.91 0.00 43.96 4.02
1723 1731 5.464168 GCATTATCTTGTCTGCAGTTGTTT 58.536 37.500 14.67 0.00 34.77 2.83
1724 1732 5.344128 GCATTATCTTGTCTGCAGTTGTTTG 59.656 40.000 14.67 2.97 34.77 2.93
1725 1733 2.849880 TCTTGTCTGCAGTTGTTTGC 57.150 45.000 14.67 0.00 44.33 3.68
1726 1734 2.368439 TCTTGTCTGCAGTTGTTTGCT 58.632 42.857 14.67 0.00 44.38 3.91
1727 1735 3.540617 TCTTGTCTGCAGTTGTTTGCTA 58.459 40.909 14.67 0.00 44.38 3.49
1728 1736 3.312421 TCTTGTCTGCAGTTGTTTGCTAC 59.688 43.478 14.67 1.28 44.38 3.58
1730 1738 2.872245 TGTCTGCAGTTGTTTGCTACTC 59.128 45.455 14.67 0.00 44.38 2.59
1731 1739 2.224314 GTCTGCAGTTGTTTGCTACTCC 59.776 50.000 14.67 0.00 44.38 3.85
1734 1742 2.230660 GCAGTTGTTTGCTACTCCCTT 58.769 47.619 0.00 0.00 40.89 3.95
1735 1743 2.226674 GCAGTTGTTTGCTACTCCCTTC 59.773 50.000 0.00 0.00 40.89 3.46
1736 1744 2.480419 CAGTTGTTTGCTACTCCCTTCG 59.520 50.000 0.00 0.00 0.00 3.79
1740 1748 3.547746 TGTTTGCTACTCCCTTCGTTTT 58.452 40.909 0.00 0.00 0.00 2.43
1741 1749 3.949113 TGTTTGCTACTCCCTTCGTTTTT 59.051 39.130 0.00 0.00 0.00 1.94
1742 1750 5.124645 TGTTTGCTACTCCCTTCGTTTTTA 58.875 37.500 0.00 0.00 0.00 1.52
1743 1751 5.589452 TGTTTGCTACTCCCTTCGTTTTTAA 59.411 36.000 0.00 0.00 0.00 1.52
1744 1752 6.095160 TGTTTGCTACTCCCTTCGTTTTTAAA 59.905 34.615 0.00 0.00 0.00 1.52
1745 1753 6.887626 TTGCTACTCCCTTCGTTTTTAAAT 57.112 33.333 0.00 0.00 0.00 1.40
1746 1754 7.982761 TTGCTACTCCCTTCGTTTTTAAATA 57.017 32.000 0.00 0.00 0.00 1.40
1747 1755 8.570068 TTGCTACTCCCTTCGTTTTTAAATAT 57.430 30.769 0.00 0.00 0.00 1.28
1748 1756 8.570068 TGCTACTCCCTTCGTTTTTAAATATT 57.430 30.769 0.00 0.00 0.00 1.28
1749 1757 9.016438 TGCTACTCCCTTCGTTTTTAAATATTT 57.984 29.630 5.89 5.89 0.00 1.40
1750 1758 9.285770 GCTACTCCCTTCGTTTTTAAATATTTG 57.714 33.333 11.05 0.00 0.00 2.32
1785 1793 9.988350 GAGATTTCAACAAATGATTACATACGT 57.012 29.630 0.00 0.00 38.03 3.57
1788 1796 9.716507 ATTTCAACAAATGATTACATACGTAGC 57.283 29.630 0.08 0.00 38.03 3.58
1789 1797 7.835634 TCAACAAATGATTACATACGTAGCA 57.164 32.000 0.08 0.00 35.50 3.49
1790 1798 8.257830 TCAACAAATGATTACATACGTAGCAA 57.742 30.769 0.08 0.00 35.50 3.91
1791 1799 8.722394 TCAACAAATGATTACATACGTAGCAAA 58.278 29.630 0.08 0.00 35.50 3.68
1792 1800 9.335891 CAACAAATGATTACATACGTAGCAAAA 57.664 29.630 0.08 0.00 35.50 2.44
1794 1802 9.502145 ACAAATGATTACATACGTAGCAAAATG 57.498 29.630 0.08 0.00 35.50 2.32
1795 1803 9.715123 CAAATGATTACATACGTAGCAAAATGA 57.285 29.630 0.08 0.00 35.50 2.57
1798 1806 9.882996 ATGATTACATACGTAGCAAAATGAATG 57.117 29.630 0.08 0.00 34.71 2.67
1799 1807 9.103861 TGATTACATACGTAGCAAAATGAATGA 57.896 29.630 0.08 0.00 0.00 2.57
1800 1808 9.929722 GATTACATACGTAGCAAAATGAATGAA 57.070 29.630 0.08 0.00 0.00 2.57
1807 1815 8.447787 ACGTAGCAAAATGAATGAATTTACAC 57.552 30.769 0.00 0.00 0.00 2.90
1808 1816 8.296713 ACGTAGCAAAATGAATGAATTTACACT 58.703 29.630 0.00 0.00 0.00 3.55
1809 1817 8.788813 CGTAGCAAAATGAATGAATTTACACTC 58.211 33.333 0.00 0.00 0.00 3.51
1810 1818 9.846248 GTAGCAAAATGAATGAATTTACACTCT 57.154 29.630 0.00 0.00 0.00 3.24
1850 1858 8.675705 ACATCCGTATGTGATAATTCATTTGA 57.324 30.769 0.00 0.00 44.79 2.69
1851 1859 9.119418 ACATCCGTATGTGATAATTCATTTGAA 57.881 29.630 0.00 0.00 44.79 2.69
1852 1860 9.949174 CATCCGTATGTGATAATTCATTTGAAA 57.051 29.630 0.00 0.00 37.61 2.69
1883 1891 7.790861 AAAAGACAAATATTTAGAAACGGCG 57.209 32.000 4.80 4.80 0.00 6.46
1884 1892 5.479716 AGACAAATATTTAGAAACGGCGG 57.520 39.130 13.24 0.00 0.00 6.13
1885 1893 4.334481 AGACAAATATTTAGAAACGGCGGG 59.666 41.667 13.24 0.00 0.00 6.13
1886 1894 4.263435 ACAAATATTTAGAAACGGCGGGA 58.737 39.130 13.24 0.00 0.00 5.14
1887 1895 4.334481 ACAAATATTTAGAAACGGCGGGAG 59.666 41.667 13.24 0.00 0.00 4.30
1952 1960 5.279106 GCCACCGGTTAATTAGGAAGTTTTT 60.279 40.000 2.97 0.00 0.00 1.94
1961 1969 8.978539 GTTAATTAGGAAGTTTTTCAAGGCTTG 58.021 33.333 21.17 21.17 34.90 4.01
1993 2001 6.346096 ACAGTGACTTAAGTTAAAGCTGTGA 58.654 36.000 16.50 0.00 34.02 3.58
2049 2058 4.866508 TCAGTCAACTCAACCGAATACT 57.133 40.909 0.00 0.00 0.00 2.12
2074 2083 6.764308 AACTGAACATTATTGCATAGTGCT 57.236 33.333 3.41 0.00 45.31 4.40
2075 2084 7.864108 AACTGAACATTATTGCATAGTGCTA 57.136 32.000 3.41 0.00 45.31 3.49
2076 2085 7.251704 ACTGAACATTATTGCATAGTGCTAC 57.748 36.000 3.41 0.00 45.31 3.58
2077 2086 6.018751 ACTGAACATTATTGCATAGTGCTACG 60.019 38.462 3.41 0.00 45.31 3.51
2078 2087 6.045955 TGAACATTATTGCATAGTGCTACGA 58.954 36.000 3.41 0.00 45.31 3.43
2079 2088 5.907197 ACATTATTGCATAGTGCTACGAC 57.093 39.130 3.41 0.00 45.31 4.34
2080 2089 4.444388 ACATTATTGCATAGTGCTACGACG 59.556 41.667 3.41 0.00 45.31 5.12
2081 2090 2.579207 ATTGCATAGTGCTACGACGT 57.421 45.000 5.52 5.52 45.31 4.34
2082 2091 3.703286 ATTGCATAGTGCTACGACGTA 57.297 42.857 7.60 7.60 45.31 3.57
2083 2092 3.703286 TTGCATAGTGCTACGACGTAT 57.297 42.857 8.39 0.00 45.31 3.06
2084 2093 2.994849 TGCATAGTGCTACGACGTATG 58.005 47.619 8.39 5.03 45.31 2.39
2085 2094 2.614983 TGCATAGTGCTACGACGTATGA 59.385 45.455 8.39 0.00 45.31 2.15
2096 2113 1.656652 GACGTATGATGCCACAAGCT 58.343 50.000 0.00 0.00 44.23 3.74
2128 2145 3.813166 CCGAAATATGCGGTCCATAGTTT 59.187 43.478 8.67 0.00 42.78 2.66
2148 2165 1.134521 TCGTACACCCATTCCTCATGC 60.135 52.381 0.00 0.00 0.00 4.06
2153 2170 0.179009 ACCCATTCCTCATGCCATCG 60.179 55.000 0.00 0.00 0.00 3.84
2162 2179 2.033801 CCTCATGCCATCGAAATCAACC 59.966 50.000 0.00 0.00 0.00 3.77
2172 2189 2.882137 TCGAAATCAACCAACTCCAACC 59.118 45.455 0.00 0.00 0.00 3.77
2185 2202 2.575279 ACTCCAACCATGAGCTCATCTT 59.425 45.455 26.44 16.85 33.61 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.918957 CCAGATTCTTCCCCTTCCAGT 59.081 52.381 0.00 0.00 0.00 4.00
130 131 5.188555 TGATCTTACTGAGCTTCTGGATTGT 59.811 40.000 0.00 0.00 31.32 2.71
157 158 2.039746 CCCCACACCAGATGAAGTTACA 59.960 50.000 0.00 0.00 0.00 2.41
329 330 2.282816 CCACCCATTGGCGGTCAA 60.283 61.111 0.00 0.00 39.07 3.18
408 409 2.773661 GGATTTTCTCCCATTGCCCAAT 59.226 45.455 0.00 0.00 38.19 3.16
578 579 0.912486 GAACTCCTGCAGGTGGGTAT 59.088 55.000 32.32 18.52 36.34 2.73
767 768 5.735922 GCAAAGAACTTACATGTTGGCTCAA 60.736 40.000 2.30 0.00 0.00 3.02
776 777 2.821969 AGCCAGGCAAAGAACTTACATG 59.178 45.455 15.80 0.00 0.00 3.21
789 790 3.888460 TGGAGCACAAGCCAGGCA 61.888 61.111 15.80 0.00 43.56 4.75
886 887 2.362503 ATGAGTGGCCGTCTCCGA 60.363 61.111 20.23 7.51 35.63 4.55
982 983 4.636435 CGAAGGGGGCAACGTGGT 62.636 66.667 0.00 0.00 37.60 4.16
1314 1321 9.167311 TCTGCCTTTTCATATAAGAAGAAGAAC 57.833 33.333 11.11 6.51 0.00 3.01
1340 1347 3.394836 GAGGAACCGGCAGGAGCT 61.395 66.667 10.86 0.00 41.02 4.09
1397 1404 1.089920 ACCAGGTACGTACGCACTAG 58.910 55.000 16.72 9.29 0.00 2.57
1424 1432 8.939201 ATATGAAACGGCAATCTATGATAGAG 57.061 34.615 8.30 0.00 38.38 2.43
1462 1470 9.297586 TCGTAGTACTGCTAATTTACTCAATTG 57.702 33.333 5.39 0.00 35.71 2.32
1474 1482 5.123502 CCTCAGTTCTTCGTAGTACTGCTAA 59.876 44.000 19.46 1.33 44.74 3.09
1486 1494 2.125512 CCCGCCCTCAGTTCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
1496 1504 4.003788 CAACACGACTCCCGCCCT 62.004 66.667 0.00 0.00 43.32 5.19
1509 1517 5.009610 GTCTCCAACTGGCTAAATTTCAACA 59.990 40.000 0.00 0.00 34.44 3.33
1510 1518 5.009610 TGTCTCCAACTGGCTAAATTTCAAC 59.990 40.000 0.00 0.00 34.44 3.18
1511 1519 5.136828 TGTCTCCAACTGGCTAAATTTCAA 58.863 37.500 0.00 0.00 34.44 2.69
1537 1545 7.547722 ACAAGTTTTGACCAAATACCAGAAAAC 59.452 33.333 0.00 0.00 33.85 2.43
1562 1570 1.270893 GGTCACCTGAAACCTCTGGAC 60.271 57.143 5.19 0.00 41.99 4.02
1570 1578 1.541588 GCTTCCATGGTCACCTGAAAC 59.458 52.381 12.58 0.00 0.00 2.78
1571 1579 1.547675 GGCTTCCATGGTCACCTGAAA 60.548 52.381 12.58 0.00 0.00 2.69
1572 1580 0.038166 GGCTTCCATGGTCACCTGAA 59.962 55.000 12.58 0.00 0.00 3.02
1573 1581 1.133181 TGGCTTCCATGGTCACCTGA 61.133 55.000 12.58 0.00 0.00 3.86
1574 1582 0.251297 TTGGCTTCCATGGTCACCTG 60.251 55.000 12.58 0.00 31.53 4.00
1575 1583 0.482446 TTTGGCTTCCATGGTCACCT 59.518 50.000 12.58 0.00 31.53 4.00
1576 1584 0.890683 CTTTGGCTTCCATGGTCACC 59.109 55.000 12.58 11.83 31.53 4.02
1577 1585 0.244721 GCTTTGGCTTCCATGGTCAC 59.755 55.000 12.58 1.72 31.53 3.67
1578 1586 0.899717 GGCTTTGGCTTCCATGGTCA 60.900 55.000 12.58 3.80 38.73 4.02
1579 1587 0.899717 TGGCTTTGGCTTCCATGGTC 60.900 55.000 12.58 2.22 38.73 4.02
1580 1588 0.471591 TTGGCTTTGGCTTCCATGGT 60.472 50.000 12.58 0.00 38.73 3.55
1581 1589 0.906775 ATTGGCTTTGGCTTCCATGG 59.093 50.000 4.97 4.97 38.73 3.66
1582 1590 3.493699 CCATATTGGCTTTGGCTTCCATG 60.494 47.826 0.00 0.00 38.73 3.66
1642 1650 7.058525 TCATCACCTGCTCAATTAATCATTCT 58.941 34.615 0.00 0.00 0.00 2.40
1681 1689 1.136057 GCGCTTTCTGGAAAACTACCG 60.136 52.381 0.00 0.00 0.00 4.02
1682 1690 1.877443 TGCGCTTTCTGGAAAACTACC 59.123 47.619 9.73 0.00 0.00 3.18
1683 1691 3.831715 ATGCGCTTTCTGGAAAACTAC 57.168 42.857 9.73 0.00 0.00 2.73
1684 1692 5.880332 AGATAATGCGCTTTCTGGAAAACTA 59.120 36.000 12.27 0.00 0.00 2.24
1685 1693 4.702131 AGATAATGCGCTTTCTGGAAAACT 59.298 37.500 12.27 0.00 0.00 2.66
1690 1698 3.609853 ACAAGATAATGCGCTTTCTGGA 58.390 40.909 12.27 0.00 0.00 3.86
1697 1705 1.938577 CTGCAGACAAGATAATGCGCT 59.061 47.619 8.42 0.00 41.58 5.92
1723 1731 8.570068 AATATTTAAAAACGAAGGGAGTAGCA 57.430 30.769 0.00 0.00 0.00 3.49
1724 1732 9.285770 CAAATATTTAAAAACGAAGGGAGTAGC 57.714 33.333 0.00 0.00 0.00 3.58
1759 1767 9.988350 ACGTATGTAATCATTTGTTGAAATCTC 57.012 29.630 0.00 0.00 38.03 2.75
1762 1770 9.716507 GCTACGTATGTAATCATTTGTTGAAAT 57.283 29.630 0.00 0.00 38.03 2.17
1763 1771 8.722394 TGCTACGTATGTAATCATTTGTTGAAA 58.278 29.630 0.00 0.00 38.03 2.69
1764 1772 8.257830 TGCTACGTATGTAATCATTTGTTGAA 57.742 30.769 0.00 0.00 38.03 2.69
1765 1773 7.835634 TGCTACGTATGTAATCATTTGTTGA 57.164 32.000 0.00 0.00 39.12 3.18
1766 1774 8.888332 TTTGCTACGTATGTAATCATTTGTTG 57.112 30.769 0.00 0.00 35.70 3.33
1768 1776 9.502145 CATTTTGCTACGTATGTAATCATTTGT 57.498 29.630 0.00 0.00 35.70 2.83
1769 1777 9.715123 TCATTTTGCTACGTATGTAATCATTTG 57.285 29.630 0.00 0.00 35.70 2.32
1772 1780 9.882996 CATTCATTTTGCTACGTATGTAATCAT 57.117 29.630 0.00 0.00 38.00 2.45
1773 1781 9.103861 TCATTCATTTTGCTACGTATGTAATCA 57.896 29.630 0.00 0.00 0.00 2.57
1774 1782 9.929722 TTCATTCATTTTGCTACGTATGTAATC 57.070 29.630 0.00 0.00 0.00 1.75
1781 1789 9.549509 GTGTAAATTCATTCATTTTGCTACGTA 57.450 29.630 0.00 0.00 0.00 3.57
1782 1790 8.296713 AGTGTAAATTCATTCATTTTGCTACGT 58.703 29.630 0.00 0.00 0.00 3.57
1783 1791 8.673626 AGTGTAAATTCATTCATTTTGCTACG 57.326 30.769 0.00 0.00 0.00 3.51
1784 1792 9.846248 AGAGTGTAAATTCATTCATTTTGCTAC 57.154 29.630 0.00 0.00 0.00 3.58
1824 1832 9.119418 TCAAATGAATTATCACATACGGATGTT 57.881 29.630 11.57 0.00 44.18 2.71
1826 1834 9.949174 TTTCAAATGAATTATCACATACGGATG 57.051 29.630 5.94 5.94 38.69 3.51
1857 1865 9.332301 CGCCGTTTCTAAATATTTGTCTTTTTA 57.668 29.630 11.05 0.00 0.00 1.52
1858 1866 7.327518 CCGCCGTTTCTAAATATTTGTCTTTTT 59.672 33.333 11.05 0.00 0.00 1.94
1859 1867 6.804783 CCGCCGTTTCTAAATATTTGTCTTTT 59.195 34.615 11.05 0.00 0.00 2.27
1860 1868 6.319399 CCGCCGTTTCTAAATATTTGTCTTT 58.681 36.000 11.05 0.00 0.00 2.52
1861 1869 5.163693 CCCGCCGTTTCTAAATATTTGTCTT 60.164 40.000 11.05 0.00 0.00 3.01
1862 1870 4.334481 CCCGCCGTTTCTAAATATTTGTCT 59.666 41.667 11.05 0.00 0.00 3.41
1863 1871 4.333372 TCCCGCCGTTTCTAAATATTTGTC 59.667 41.667 11.05 0.00 0.00 3.18
1864 1872 4.263435 TCCCGCCGTTTCTAAATATTTGT 58.737 39.130 11.05 0.00 0.00 2.83
1865 1873 4.334481 ACTCCCGCCGTTTCTAAATATTTG 59.666 41.667 11.05 1.65 0.00 2.32
1866 1874 4.520179 ACTCCCGCCGTTTCTAAATATTT 58.480 39.130 5.89 5.89 0.00 1.40
1867 1875 4.146745 ACTCCCGCCGTTTCTAAATATT 57.853 40.909 0.00 0.00 0.00 1.28
1868 1876 3.832615 ACTCCCGCCGTTTCTAAATAT 57.167 42.857 0.00 0.00 0.00 1.28
1869 1877 4.341806 TGATACTCCCGCCGTTTCTAAATA 59.658 41.667 0.00 0.00 0.00 1.40
1870 1878 3.133362 TGATACTCCCGCCGTTTCTAAAT 59.867 43.478 0.00 0.00 0.00 1.40
1871 1879 2.496871 TGATACTCCCGCCGTTTCTAAA 59.503 45.455 0.00 0.00 0.00 1.85
1872 1880 2.101783 TGATACTCCCGCCGTTTCTAA 58.898 47.619 0.00 0.00 0.00 2.10
1873 1881 1.766494 TGATACTCCCGCCGTTTCTA 58.234 50.000 0.00 0.00 0.00 2.10
1874 1882 1.120530 ATGATACTCCCGCCGTTTCT 58.879 50.000 0.00 0.00 0.00 2.52
1875 1883 1.217882 CATGATACTCCCGCCGTTTC 58.782 55.000 0.00 0.00 0.00 2.78
1876 1884 0.814010 GCATGATACTCCCGCCGTTT 60.814 55.000 0.00 0.00 0.00 3.60
1877 1885 1.227556 GCATGATACTCCCGCCGTT 60.228 57.895 0.00 0.00 0.00 4.44
1878 1886 1.758440 ATGCATGATACTCCCGCCGT 61.758 55.000 0.00 0.00 0.00 5.68
1879 1887 1.004560 ATGCATGATACTCCCGCCG 60.005 57.895 0.00 0.00 0.00 6.46
1880 1888 0.957395 CCATGCATGATACTCCCGCC 60.957 60.000 28.31 0.00 0.00 6.13
1881 1889 1.580845 GCCATGCATGATACTCCCGC 61.581 60.000 28.31 15.59 0.00 6.13
1882 1890 0.035881 AGCCATGCATGATACTCCCG 59.964 55.000 28.31 9.48 0.00 5.14
1883 1891 2.157738 GAAGCCATGCATGATACTCCC 58.842 52.381 28.31 12.72 0.00 4.30
1884 1892 2.157738 GGAAGCCATGCATGATACTCC 58.842 52.381 28.31 21.07 0.00 3.85
1885 1893 2.812591 CAGGAAGCCATGCATGATACTC 59.187 50.000 28.31 16.69 0.00 2.59
1886 1894 2.488528 CCAGGAAGCCATGCATGATACT 60.489 50.000 28.31 18.05 0.00 2.12
1887 1895 1.884579 CCAGGAAGCCATGCATGATAC 59.115 52.381 28.31 16.11 0.00 2.24
1952 1960 1.376466 GTGCCTCCTCAAGCCTTGA 59.624 57.895 7.00 7.00 38.17 3.02
1961 1969 2.300437 ACTTAAGTCACTGTGCCTCCTC 59.700 50.000 1.12 0.00 0.00 3.71
1993 2001 3.714144 AGCCTAGTCATAGTGTCAAGGT 58.286 45.455 0.00 0.00 0.00 3.50
2041 2050 8.394877 TGCAATAATGTTCAGTTTAGTATTCGG 58.605 33.333 0.00 0.00 0.00 4.30
2072 2081 1.129326 GTGGCATCATACGTCGTAGC 58.871 55.000 11.31 8.36 0.00 3.58
2074 2083 2.804647 CTTGTGGCATCATACGTCGTA 58.195 47.619 7.69 7.69 0.00 3.43
2075 2084 1.640428 CTTGTGGCATCATACGTCGT 58.360 50.000 2.21 2.21 0.00 4.34
2076 2085 0.301687 GCTTGTGGCATCATACGTCG 59.698 55.000 0.00 0.00 41.35 5.12
2077 2086 1.656652 AGCTTGTGGCATCATACGTC 58.343 50.000 0.00 0.00 44.79 4.34
2078 2087 2.113860 AAGCTTGTGGCATCATACGT 57.886 45.000 0.00 0.00 44.79 3.57
2079 2088 4.273235 TCATTAAGCTTGTGGCATCATACG 59.727 41.667 9.86 0.00 44.79 3.06
2080 2089 5.756195 TCATTAAGCTTGTGGCATCATAC 57.244 39.130 9.86 0.00 44.79 2.39
2081 2090 6.736519 GCAATCATTAAGCTTGTGGCATCATA 60.737 38.462 9.86 0.00 44.79 2.15
2082 2091 5.597806 CAATCATTAAGCTTGTGGCATCAT 58.402 37.500 9.86 0.00 44.79 2.45
2083 2092 4.678574 GCAATCATTAAGCTTGTGGCATCA 60.679 41.667 9.86 0.00 44.79 3.07
2084 2093 3.800506 GCAATCATTAAGCTTGTGGCATC 59.199 43.478 9.86 0.00 44.79 3.91
2085 2094 3.431207 GGCAATCATTAAGCTTGTGGCAT 60.431 43.478 9.86 0.00 44.79 4.40
2096 2113 4.793071 CCGCATATTTCGGCAATCATTAA 58.207 39.130 0.74 0.00 40.46 1.40
2122 2139 4.468510 TGAGGAATGGGTGTACGAAACTAT 59.531 41.667 0.00 0.00 0.00 2.12
2128 2145 1.134521 GCATGAGGAATGGGTGTACGA 60.135 52.381 0.00 0.00 36.71 3.43
2148 2165 3.081061 TGGAGTTGGTTGATTTCGATGG 58.919 45.455 0.00 0.00 0.00 3.51
2153 2170 4.280677 TCATGGTTGGAGTTGGTTGATTTC 59.719 41.667 0.00 0.00 0.00 2.17
2162 2179 2.189594 TGAGCTCATGGTTGGAGTTG 57.810 50.000 13.74 0.00 34.83 3.16
2172 2189 4.331992 CACCTGTTACAAGATGAGCTCATG 59.668 45.833 33.33 22.52 36.57 3.07
2185 2202 2.486548 GCAGAAACCTCCACCTGTTACA 60.487 50.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.