Multiple sequence alignment - TraesCS1B01G463800

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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 TraesCS1B01G463800 chr1B 100.000 2480 0 0 1 2480 675725471 675727950 0.000000e+00 4580.0
1 TraesCS1B01G463800 chr1D 91.892 1221 40 25 524 1709 485420217 485421413 0.000000e+00 1652.0
2 TraesCS1B01G463800 chr1D 84.595 753 66 20 1772 2480 485421404 485422150 0.000000e+00 702.0
3 TraesCS1B01G463800 chr1D 84.498 329 42 4 1 328 485419769 485420089 1.430000e-82 316.0
4 TraesCS1B01G463800 chr1D 78.947 247 43 6 2081 2320 365282023 365281779 2.550000e-35 159.0
5 TraesCS1B01G463800 chr1A 94.832 774 23 8 945 1708 582642419 582643185 0.000000e+00 1192.0
6 TraesCS1B01G463800 chr1A 86.506 956 75 27 50 962 582641450 582642394 0.000000e+00 1002.0
7 TraesCS1B01G463800 chr1A 82.456 741 72 24 1772 2480 582643176 582643890 1.640000e-166 595.0
8 TraesCS1B01G463800 chr7D 79.286 280 45 7 2073 2345 136942786 136943059 1.510000e-42 183.0
9 TraesCS1B01G463800 chr7D 91.667 48 2 1 1727 1774 149735822 149735777 5.730000e-07 65.8
10 TraesCS1B01G463800 chr3D 78.929 280 51 5 2073 2345 291221800 291222078 1.510000e-42 183.0
11 TraesCS1B01G463800 chr3B 78.929 280 51 6 2073 2345 384306735 384307013 1.510000e-42 183.0
12 TraesCS1B01G463800 chr3B 97.297 37 1 0 2271 2307 578835043 578835079 2.060000e-06 63.9
13 TraesCS1B01G463800 chr6B 78.521 284 45 11 2073 2345 223262210 223261932 3.280000e-39 172.0
14 TraesCS1B01G463800 chr4B 80.992 121 20 3 178 297 417211905 417211787 2.630000e-15 93.5
15 TraesCS1B01G463800 chr2B 88.462 52 4 2 2425 2476 461541352 461541401 7.410000e-06 62.1


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 TraesCS1B01G463800 chr1B 675725471 675727950 2479 False 4580.000000 4580 100.000000 1 2480 1 chr1B.!!$F1 2479
1 TraesCS1B01G463800 chr1D 485419769 485422150 2381 False 890.000000 1652 86.995000 1 2480 3 chr1D.!!$F1 2479
2 TraesCS1B01G463800 chr1A 582641450 582643890 2440 False 929.666667 1192 87.931333 50 2480 3 chr1A.!!$F1 2430

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
936 984 0.111253 AACCTGGACTGCTTCTTGGG 59.889 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1932 0.039527 AAAGGAACAAATCGCACGCC 60.04 50.0 0.0 0.0 0.0 5.68 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
28 29 4.921644 TCACATATCTGCCATCCATGAT 57.078 40.909 0.00 0.00 0.00 2.45
40 41 5.419788 TGCCATCCATGATCATAATTAAGGC 59.580 40.000 20.36 20.36 36.50 4.35
41 42 5.163478 GCCATCCATGATCATAATTAAGGCC 60.163 44.000 8.15 0.00 0.00 5.19
46 47 7.805163 TCCATGATCATAATTAAGGCCGATAT 58.195 34.615 8.15 0.00 0.00 1.63
48 49 7.716560 CCATGATCATAATTAAGGCCGATATCA 59.283 37.037 8.15 0.26 0.00 2.15
60 61 0.673985 CGATATCACCCTCTTCGGCA 59.326 55.000 3.12 0.00 0.00 5.69
64 65 1.201429 ATCACCCTCTTCGGCAAGGT 61.201 55.000 0.00 0.00 0.00 3.50
92 93 4.922206 TGGGCTAGTTTGTGAGAATTCAT 58.078 39.130 8.44 0.00 35.39 2.57
96 97 5.163713 GGCTAGTTTGTGAGAATTCATGTCC 60.164 44.000 8.44 0.00 35.39 4.02
147 149 8.770438 ACAAATGTGTGTTTACAAAACTGAAT 57.230 26.923 4.35 0.00 38.82 2.57
151 153 7.074507 TGTGTGTTTACAAAACTGAATACGT 57.925 32.000 0.00 0.00 38.82 3.57
259 264 6.624352 AATCACATCCAAATTCATAGACCG 57.376 37.500 0.00 0.00 0.00 4.79
286 291 3.002348 GCGAAAGTTACAAGCACTGAAGT 59.998 43.478 0.00 0.00 0.00 3.01
344 349 6.349033 GCCGGAGAAACATTGTTGTAGTAAAT 60.349 38.462 5.05 0.00 34.06 1.40
372 377 5.010922 TGAAAAGTTGTCGTACTAAGGCCTA 59.989 40.000 5.16 0.00 0.00 3.93
405 410 0.313043 ACGAGAACATCAACCGTCGT 59.687 50.000 0.00 0.00 35.90 4.34
406 411 1.269413 ACGAGAACATCAACCGTCGTT 60.269 47.619 0.00 0.00 37.36 3.85
425 430 3.996032 GTTGATGACGAGAATTGCTGAC 58.004 45.455 0.00 0.00 0.00 3.51
452 457 2.607187 GATCCAACCTGTAGACACACG 58.393 52.381 0.00 0.00 0.00 4.49
456 461 0.677842 AACCTGTAGACACACGGACC 59.322 55.000 0.00 0.00 31.31 4.46
506 511 0.613777 ACTAAGGCTCTTTGGACCCG 59.386 55.000 0.00 0.00 0.00 5.28
508 513 0.611714 TAAGGCTCTTTGGACCCGTC 59.388 55.000 0.00 0.00 0.00 4.79
564 569 1.709578 TAACATGCTGCCCCACAAAA 58.290 45.000 0.00 0.00 0.00 2.44
750 793 2.383368 TAAAAAGGCCATGCATGCAC 57.617 45.000 25.37 15.11 0.00 4.57
786 829 1.285578 GCTCGCTCTAGCTTTCCTTG 58.714 55.000 0.00 0.00 39.50 3.61
806 854 6.312918 TCCTTGACATGAATAAAAGCTACGTC 59.687 38.462 0.00 0.00 0.00 4.34
807 855 5.696260 TGACATGAATAAAAGCTACGTCG 57.304 39.130 0.00 0.00 0.00 5.12
808 856 5.165676 TGACATGAATAAAAGCTACGTCGT 58.834 37.500 2.21 2.21 0.00 4.34
932 980 1.490490 TCAACAACCTGGACTGCTTCT 59.510 47.619 0.00 0.00 0.00 2.85
934 982 1.972872 ACAACCTGGACTGCTTCTTG 58.027 50.000 0.00 0.00 0.00 3.02
935 983 1.242076 CAACCTGGACTGCTTCTTGG 58.758 55.000 0.00 0.00 0.00 3.61
936 984 0.111253 AACCTGGACTGCTTCTTGGG 59.889 55.000 0.00 0.00 0.00 4.12
938 986 2.032528 TGGACTGCTTCTTGGGCG 59.967 61.111 0.00 0.00 0.00 6.13
940 988 2.669569 GACTGCTTCTTGGGCGCA 60.670 61.111 10.83 0.00 0.00 6.09
941 989 2.970974 GACTGCTTCTTGGGCGCAC 61.971 63.158 10.83 6.04 0.00 5.34
942 990 4.093952 CTGCTTCTTGGGCGCACG 62.094 66.667 10.83 0.79 0.00 5.34
1287 1380 1.313812 ACGCCGAGAACGAAGAGGAT 61.314 55.000 0.00 0.00 42.66 3.24
1347 1440 3.423154 CAGCCGTTGGACTTCGCC 61.423 66.667 0.00 0.00 0.00 5.54
1483 1576 2.584608 CCACCGAGGTGTGATCCC 59.415 66.667 19.62 0.00 44.02 3.85
1485 1578 0.686441 CCACCGAGGTGTGATCCCTA 60.686 60.000 19.62 0.00 44.02 3.53
1486 1579 0.747255 CACCGAGGTGTGATCCCTAG 59.253 60.000 13.82 0.00 40.91 3.02
1537 1637 4.615452 GCTTCTTCTTCTTCTTCCGTCGTA 60.615 45.833 0.00 0.00 0.00 3.43
1567 1667 2.425592 CGGCCCGCCTGAATCATA 59.574 61.111 3.84 0.00 0.00 2.15
1568 1668 1.227823 CGGCCCGCCTGAATCATAA 60.228 57.895 3.84 0.00 0.00 1.90
1569 1669 1.230635 CGGCCCGCCTGAATCATAAG 61.231 60.000 3.84 0.00 0.00 1.73
1703 1808 7.611213 ACGATTCTTTCTCGTTCCAATATTT 57.389 32.000 0.00 0.00 46.49 1.40
1704 1809 8.040716 ACGATTCTTTCTCGTTCCAATATTTT 57.959 30.769 0.00 0.00 46.49 1.82
1705 1810 7.962918 ACGATTCTTTCTCGTTCCAATATTTTG 59.037 33.333 0.00 0.00 46.49 2.44
1706 1811 7.962918 CGATTCTTTCTCGTTCCAATATTTTGT 59.037 33.333 0.00 0.00 0.00 2.83
1707 1812 9.626045 GATTCTTTCTCGTTCCAATATTTTGTT 57.374 29.630 0.00 0.00 0.00 2.83
1708 1813 9.981114 ATTCTTTCTCGTTCCAATATTTTGTTT 57.019 25.926 0.00 0.00 0.00 2.83
1709 1814 9.810545 TTCTTTCTCGTTCCAATATTTTGTTTT 57.189 25.926 0.00 0.00 0.00 2.43
1710 1815 9.810545 TCTTTCTCGTTCCAATATTTTGTTTTT 57.189 25.926 0.00 0.00 0.00 1.94
1733 1838 6.648879 TTTTCCGAGAAAAACATCCAATCT 57.351 33.333 8.70 0.00 0.00 2.40
1734 1839 7.753309 TTTTCCGAGAAAAACATCCAATCTA 57.247 32.000 8.70 0.00 0.00 1.98
1735 1840 7.938140 TTTCCGAGAAAAACATCCAATCTAT 57.062 32.000 0.00 0.00 0.00 1.98
1736 1841 7.938140 TTCCGAGAAAAACATCCAATCTATT 57.062 32.000 0.00 0.00 0.00 1.73
1737 1842 7.553881 TCCGAGAAAAACATCCAATCTATTC 57.446 36.000 0.00 0.00 0.00 1.75
1738 1843 6.257849 TCCGAGAAAAACATCCAATCTATTCG 59.742 38.462 0.00 0.00 0.00 3.34
1739 1844 5.904080 CGAGAAAAACATCCAATCTATTCGC 59.096 40.000 0.00 0.00 0.00 4.70
1740 1845 6.238211 CGAGAAAAACATCCAATCTATTCGCT 60.238 38.462 0.00 0.00 0.00 4.93
1741 1846 7.396540 AGAAAAACATCCAATCTATTCGCTT 57.603 32.000 0.00 0.00 0.00 4.68
1742 1847 7.475840 AGAAAAACATCCAATCTATTCGCTTC 58.524 34.615 0.00 0.00 0.00 3.86
1743 1848 6.757897 AAAACATCCAATCTATTCGCTTCA 57.242 33.333 0.00 0.00 0.00 3.02
1744 1849 5.998454 AACATCCAATCTATTCGCTTCAG 57.002 39.130 0.00 0.00 0.00 3.02
1745 1850 5.028549 ACATCCAATCTATTCGCTTCAGT 57.971 39.130 0.00 0.00 0.00 3.41
1746 1851 5.053145 ACATCCAATCTATTCGCTTCAGTC 58.947 41.667 0.00 0.00 0.00 3.51
1747 1852 4.736126 TCCAATCTATTCGCTTCAGTCA 57.264 40.909 0.00 0.00 0.00 3.41
1748 1853 5.282055 TCCAATCTATTCGCTTCAGTCAT 57.718 39.130 0.00 0.00 0.00 3.06
1749 1854 5.052481 TCCAATCTATTCGCTTCAGTCATG 58.948 41.667 0.00 0.00 0.00 3.07
1750 1855 4.212847 CCAATCTATTCGCTTCAGTCATGG 59.787 45.833 0.00 0.00 0.00 3.66
1751 1856 2.826428 TCTATTCGCTTCAGTCATGGC 58.174 47.619 0.00 0.00 0.00 4.40
1752 1857 2.168313 TCTATTCGCTTCAGTCATGGCA 59.832 45.455 0.00 0.00 0.00 4.92
1753 1858 1.376543 ATTCGCTTCAGTCATGGCAG 58.623 50.000 0.00 0.00 0.00 4.85
1754 1859 0.035317 TTCGCTTCAGTCATGGCAGT 59.965 50.000 0.00 0.00 0.00 4.40
1755 1860 0.894835 TCGCTTCAGTCATGGCAGTA 59.105 50.000 0.00 0.00 0.00 2.74
1756 1861 1.002366 CGCTTCAGTCATGGCAGTAC 58.998 55.000 0.00 0.00 0.00 2.73
1757 1862 1.672737 CGCTTCAGTCATGGCAGTACA 60.673 52.381 0.00 0.00 0.00 2.90
1758 1863 2.426522 GCTTCAGTCATGGCAGTACAA 58.573 47.619 0.00 0.00 0.00 2.41
1759 1864 3.012518 GCTTCAGTCATGGCAGTACAAT 58.987 45.455 0.00 0.00 0.00 2.71
1760 1865 3.181503 GCTTCAGTCATGGCAGTACAATG 60.182 47.826 0.00 0.00 0.00 2.82
1761 1866 3.979101 TCAGTCATGGCAGTACAATGA 57.021 42.857 0.00 0.00 0.00 2.57
1762 1867 4.284829 TCAGTCATGGCAGTACAATGAA 57.715 40.909 0.00 0.00 0.00 2.57
1763 1868 4.002982 TCAGTCATGGCAGTACAATGAAC 58.997 43.478 0.00 0.00 0.00 3.18
1764 1869 3.752747 CAGTCATGGCAGTACAATGAACA 59.247 43.478 0.00 0.00 0.00 3.18
1765 1870 3.753272 AGTCATGGCAGTACAATGAACAC 59.247 43.478 0.00 0.00 0.00 3.32
1766 1871 3.753272 GTCATGGCAGTACAATGAACACT 59.247 43.478 0.00 0.00 0.00 3.55
1767 1872 4.935205 GTCATGGCAGTACAATGAACACTA 59.065 41.667 0.00 0.00 0.00 2.74
1768 1873 5.063944 GTCATGGCAGTACAATGAACACTAG 59.936 44.000 0.00 0.00 0.00 2.57
1769 1874 4.882842 TGGCAGTACAATGAACACTAGA 57.117 40.909 0.00 0.00 0.00 2.43
1770 1875 4.820897 TGGCAGTACAATGAACACTAGAG 58.179 43.478 0.00 0.00 0.00 2.43
1771 1876 4.526650 TGGCAGTACAATGAACACTAGAGA 59.473 41.667 0.00 0.00 0.00 3.10
1772 1877 5.187772 TGGCAGTACAATGAACACTAGAGAT 59.812 40.000 0.00 0.00 0.00 2.75
1786 1891 6.163476 ACACTAGAGATATTTTGTTGACGCA 58.837 36.000 0.00 0.00 0.00 5.24
1823 1932 2.386661 AATGAGTACCAGAAGCACCG 57.613 50.000 0.00 0.00 0.00 4.94
1900 2011 6.151144 TGAATGAGACAACTTCGATCTACTCA 59.849 38.462 0.00 0.00 37.50 3.41
1904 2015 5.885881 AGACAACTTCGATCTACTCATGTC 58.114 41.667 0.00 0.00 35.95 3.06
1913 2024 8.777865 TTCGATCTACTCATGTCAAAATCTTT 57.222 30.769 0.00 0.00 0.00 2.52
1920 2031 6.339730 ACTCATGTCAAAATCTTTTTGTGCA 58.660 32.000 11.30 11.51 0.00 4.57
1954 2065 2.080693 TCGGTTGGATCATCCGTTTTG 58.919 47.619 17.41 0.00 44.23 2.44
1959 2070 4.698304 GGTTGGATCATCCGTTTTGTTCTA 59.302 41.667 0.00 0.00 40.17 2.10
1967 2104 4.261578 TCCGTTTTGTTCTAGGTGTAGG 57.738 45.455 0.00 0.00 0.00 3.18
1972 2109 5.332808 CGTTTTGTTCTAGGTGTAGGTTTCG 60.333 44.000 0.00 0.00 0.00 3.46
1982 2119 1.332375 TGTAGGTTTCGCTTGTGTTGC 59.668 47.619 0.00 0.00 0.00 4.17
2002 2139 3.068024 TGCTCATTCAAGTTCAACCAACC 59.932 43.478 0.00 0.00 35.28 3.77
2051 2188 5.680619 TCCAACTTCAAGAACACACTACAT 58.319 37.500 0.00 0.00 0.00 2.29
2057 2194 1.148310 AGAACACACTACATGCACGC 58.852 50.000 0.00 0.00 0.00 5.34
2100 2238 0.033796 ACACTGCCCCTTGGATGATG 60.034 55.000 0.00 0.00 0.00 3.07
2113 2257 2.039348 TGGATGATGCACCATCGATGAT 59.961 45.455 26.86 6.74 43.14 2.45
2114 2258 3.079578 GGATGATGCACCATCGATGATT 58.920 45.455 26.86 10.24 43.14 2.57
2115 2259 3.119955 GGATGATGCACCATCGATGATTG 60.120 47.826 26.86 21.64 43.14 2.67
2116 2260 3.196939 TGATGCACCATCGATGATTGA 57.803 42.857 26.86 12.48 43.14 2.57
2117 2261 3.135994 TGATGCACCATCGATGATTGAG 58.864 45.455 26.86 11.73 43.14 3.02
2118 2262 2.985957 TGCACCATCGATGATTGAGA 57.014 45.000 26.86 10.18 0.00 3.27
2127 2271 4.192429 TCGATGATTGAGAGACTTTGCA 57.808 40.909 0.00 0.00 0.00 4.08
2162 2306 1.598130 GCGCATCGGATTAGGGCTT 60.598 57.895 0.30 0.00 38.09 4.35
2163 2307 0.320421 GCGCATCGGATTAGGGCTTA 60.320 55.000 0.30 0.00 38.09 3.09
2202 2349 3.561313 GGAACCAAGAGTGAATGGCCTAA 60.561 47.826 3.32 0.00 40.51 2.69
2235 2382 3.508793 CCTTTTGCTCTGTGTCATGGATT 59.491 43.478 0.00 0.00 0.00 3.01
2236 2383 4.021719 CCTTTTGCTCTGTGTCATGGATTT 60.022 41.667 0.00 0.00 0.00 2.17
2283 2433 2.432628 CACAACTCGTCCTCCCGC 60.433 66.667 0.00 0.00 0.00 6.13
2286 2436 0.968901 ACAACTCGTCCTCCCGCATA 60.969 55.000 0.00 0.00 0.00 3.14
2310 2460 4.426704 TGAAGCTTTCTACTCTACCCCTT 58.573 43.478 0.00 0.00 0.00 3.95
2317 2467 5.656213 TTCTACTCTACCCCTTTTCTTCG 57.344 43.478 0.00 0.00 0.00 3.79
2322 2472 3.446968 TCTACCCCTTTTCTTCGGATCA 58.553 45.455 0.00 0.00 0.00 2.92
2324 2474 2.791655 ACCCCTTTTCTTCGGATCAAC 58.208 47.619 0.00 0.00 0.00 3.18
2345 2495 7.898918 TCAACAACAAATTCATCCAGATCATT 58.101 30.769 0.00 0.00 0.00 2.57
2348 2498 7.673180 ACAACAAATTCATCCAGATCATTGTT 58.327 30.769 0.00 0.00 37.23 2.83
2355 2505 1.075212 TCCAGATCATTGTTGCCACCA 59.925 47.619 0.00 0.00 0.00 4.17
2356 2506 2.104967 CCAGATCATTGTTGCCACCAT 58.895 47.619 0.00 0.00 0.00 3.55
2364 2514 1.067295 TGTTGCCACCATTCTCCTCT 58.933 50.000 0.00 0.00 0.00 3.69
2371 2521 0.539051 ACCATTCTCCTCTTGCTCCG 59.461 55.000 0.00 0.00 0.00 4.63
2379 2529 0.035458 CCTCTTGCTCCGGTTGTCTT 59.965 55.000 0.00 0.00 0.00 3.01
2397 2547 3.939592 GTCTTGTAACCCAATCCTACTGC 59.060 47.826 0.00 0.00 31.20 4.40
2404 2559 1.656652 CCAATCCTACTGCTTCCACG 58.343 55.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.419788 GCCTTAATTATGATCATGGATGGCA 59.580 40.000 18.72 0.00 34.82 4.92
28 29 5.487488 AGGGTGATATCGGCCTTAATTATGA 59.513 40.000 0.00 0.00 0.00 2.15
41 42 0.673985 TGCCGAAGAGGGTGATATCG 59.326 55.000 0.00 0.00 41.48 2.92
46 47 1.415672 AACCTTGCCGAAGAGGGTGA 61.416 55.000 0.00 0.00 41.48 4.02
48 49 1.073199 CAACCTTGCCGAAGAGGGT 59.927 57.895 0.00 0.00 41.48 4.34
60 61 3.165071 CAAACTAGCCCATTCCAACCTT 58.835 45.455 0.00 0.00 0.00 3.50
64 65 3.073798 TCTCACAAACTAGCCCATTCCAA 59.926 43.478 0.00 0.00 0.00 3.53
92 93 8.934023 AGTTTAATCTTAACTCCAATTGGACA 57.066 30.769 23.63 8.72 39.78 4.02
169 174 6.697395 TGAATAGATCTGAAGTTCGTTTCCA 58.303 36.000 5.18 0.00 0.00 3.53
206 211 7.502561 AGTTACTTCTGGCATTCTTTGTACTTT 59.497 33.333 0.00 0.00 0.00 2.66
207 212 6.998673 AGTTACTTCTGGCATTCTTTGTACTT 59.001 34.615 0.00 0.00 0.00 2.24
219 224 7.094377 GGATGTGATTTTTAGTTACTTCTGGCA 60.094 37.037 0.00 0.00 0.00 4.92
259 264 2.073816 TGCTTGTAACTTTCGCTAGGC 58.926 47.619 0.00 0.00 0.00 3.93
268 273 3.561725 GCTCACTTCAGTGCTTGTAACTT 59.438 43.478 1.74 0.00 45.25 2.66
269 274 3.134458 GCTCACTTCAGTGCTTGTAACT 58.866 45.455 1.74 0.00 45.25 2.24
270 275 2.224314 GGCTCACTTCAGTGCTTGTAAC 59.776 50.000 1.74 0.00 45.25 2.50
271 276 2.494059 GGCTCACTTCAGTGCTTGTAA 58.506 47.619 1.74 0.00 45.25 2.41
304 309 3.838271 GGCTCCGCTCGATGGTGA 61.838 66.667 9.38 0.00 0.00 4.02
320 325 6.548441 TTTACTACAACAATGTTTCTCCGG 57.452 37.500 0.00 0.00 41.05 5.14
344 349 7.095102 GGCCTTAGTACGACAACTTTTCAATTA 60.095 37.037 0.00 0.00 0.00 1.40
359 364 4.147321 TGGTCCTATTAGGCCTTAGTACG 58.853 47.826 12.58 0.00 34.61 3.67
362 367 2.973406 GCTGGTCCTATTAGGCCTTAGT 59.027 50.000 12.58 0.00 34.61 2.24
363 368 2.303311 GGCTGGTCCTATTAGGCCTTAG 59.697 54.545 12.58 7.67 34.61 2.18
372 377 0.325296 TCTCGTGGGCTGGTCCTATT 60.325 55.000 0.00 0.00 34.39 1.73
384 389 1.068474 GACGGTTGATGTTCTCGTGG 58.932 55.000 0.00 0.00 34.06 4.94
405 410 3.002791 GGTCAGCAATTCTCGTCATCAA 58.997 45.455 0.00 0.00 0.00 2.57
406 411 2.621338 GGTCAGCAATTCTCGTCATCA 58.379 47.619 0.00 0.00 0.00 3.07
412 417 1.002366 CCTTCGGTCAGCAATTCTCG 58.998 55.000 0.00 0.00 0.00 4.04
425 430 1.139058 CTACAGGTTGGATCCCTTCGG 59.861 57.143 9.90 1.75 0.00 4.30
431 436 2.674177 CGTGTGTCTACAGGTTGGATCC 60.674 54.545 4.20 4.20 37.52 3.36
452 457 1.525077 TGCTCGTTTGTGTGGGTCC 60.525 57.895 0.00 0.00 0.00 4.46
456 461 2.631428 CCGTGCTCGTTTGTGTGG 59.369 61.111 7.47 0.00 35.01 4.17
494 499 1.067495 GTGAGAGACGGGTCCAAAGAG 60.067 57.143 0.00 0.00 0.00 2.85
500 505 0.450983 CGTTAGTGAGAGACGGGTCC 59.549 60.000 0.00 0.00 33.45 4.46
506 511 3.579335 AGAAAGCCGTTAGTGAGAGAC 57.421 47.619 0.00 0.00 0.00 3.36
508 513 5.444122 CAAAAAGAAAGCCGTTAGTGAGAG 58.556 41.667 0.00 0.00 0.00 3.20
564 569 2.959516 TCGCTCGATGTTTCACTGATT 58.040 42.857 0.00 0.00 0.00 2.57
713 725 7.757173 GCCTTTTTATCTGTCCTTCATCTTTTC 59.243 37.037 0.00 0.00 0.00 2.29
714 726 7.310052 GGCCTTTTTATCTGTCCTTCATCTTTT 60.310 37.037 0.00 0.00 0.00 2.27
715 727 6.153510 GGCCTTTTTATCTGTCCTTCATCTTT 59.846 38.462 0.00 0.00 0.00 2.52
716 728 5.654209 GGCCTTTTTATCTGTCCTTCATCTT 59.346 40.000 0.00 0.00 0.00 2.40
721 733 4.440663 GCATGGCCTTTTTATCTGTCCTTC 60.441 45.833 3.32 0.00 0.00 3.46
750 793 2.125832 CGGCTTTGGCTTGCATGG 60.126 61.111 1.34 0.00 38.73 3.66
786 829 5.697848 ACGACGTAGCTTTTATTCATGTC 57.302 39.130 0.00 0.00 0.00 3.06
806 854 1.484356 GCCAGCTACCAATACGTACG 58.516 55.000 15.01 15.01 0.00 3.67
807 855 1.484356 CGCCAGCTACCAATACGTAC 58.516 55.000 0.00 0.00 0.00 3.67
808 856 0.249155 GCGCCAGCTACCAATACGTA 60.249 55.000 0.00 0.00 41.01 3.57
932 980 3.620419 ATGTGATCCGTGCGCCCAA 62.620 57.895 4.18 0.00 0.00 4.12
934 982 3.272334 GATGTGATCCGTGCGCCC 61.272 66.667 4.18 0.00 0.00 6.13
935 983 2.202932 AGATGTGATCCGTGCGCC 60.203 61.111 4.18 0.00 0.00 6.53
936 984 2.240500 GGAGATGTGATCCGTGCGC 61.241 63.158 0.00 0.00 0.00 6.09
938 986 0.461548 TCTGGAGATGTGATCCGTGC 59.538 55.000 0.00 0.00 39.91 5.34
940 988 1.115467 GGTCTGGAGATGTGATCCGT 58.885 55.000 0.00 0.00 39.91 4.69
941 989 1.114627 TGGTCTGGAGATGTGATCCG 58.885 55.000 0.00 0.00 39.91 4.18
942 990 1.139853 GGTGGTCTGGAGATGTGATCC 59.860 57.143 0.00 0.00 37.35 3.36
1006 1096 3.195002 CGTGTACCCGCCATGCAG 61.195 66.667 0.00 0.00 0.00 4.41
1326 1419 1.675641 GAAGTCCAACGGCTGGCAT 60.676 57.895 1.08 0.00 45.98 4.40
1347 1440 3.214123 TCGTAGTGGATCGCCCCG 61.214 66.667 0.00 0.00 0.00 5.73
1483 1576 1.762522 ATGCAGCCCCGTCCATCTAG 61.763 60.000 0.00 0.00 0.00 2.43
1485 1578 3.092511 ATGCAGCCCCGTCCATCT 61.093 61.111 0.00 0.00 0.00 2.90
1486 1579 2.903855 CATGCAGCCCCGTCCATC 60.904 66.667 0.00 0.00 0.00 3.51
1507 1604 4.122143 AGAAGAAGAAGAAGCAGATCGG 57.878 45.455 0.00 0.00 0.00 4.18
1559 1659 8.196103 CACACATCTCTCTCTTCTTATGATTCA 58.804 37.037 0.00 0.00 0.00 2.57
1567 1667 2.094286 CGCCACACATCTCTCTCTTCTT 60.094 50.000 0.00 0.00 0.00 2.52
1568 1668 1.476085 CGCCACACATCTCTCTCTTCT 59.524 52.381 0.00 0.00 0.00 2.85
1569 1669 1.474478 TCGCCACACATCTCTCTCTTC 59.526 52.381 0.00 0.00 0.00 2.87
1659 1764 7.609760 ATCGTTCTACTCATTATGTGCAAAA 57.390 32.000 0.00 0.00 0.00 2.44
1709 1814 7.049799 AGATTGGATGTTTTTCTCGGAAAAA 57.950 32.000 15.90 15.90 30.95 1.94
1710 1815 6.648879 AGATTGGATGTTTTTCTCGGAAAA 57.351 33.333 7.46 7.46 0.00 2.29
1711 1816 7.938140 ATAGATTGGATGTTTTTCTCGGAAA 57.062 32.000 0.00 0.00 0.00 3.13
1712 1817 7.201609 CGAATAGATTGGATGTTTTTCTCGGAA 60.202 37.037 0.00 0.00 0.00 4.30
1713 1818 6.257849 CGAATAGATTGGATGTTTTTCTCGGA 59.742 38.462 0.00 0.00 0.00 4.55
1714 1819 6.422223 CGAATAGATTGGATGTTTTTCTCGG 58.578 40.000 0.00 0.00 0.00 4.63
1715 1820 5.904080 GCGAATAGATTGGATGTTTTTCTCG 59.096 40.000 0.00 0.00 0.00 4.04
1716 1821 7.020914 AGCGAATAGATTGGATGTTTTTCTC 57.979 36.000 0.00 0.00 0.00 2.87
1717 1822 7.121168 TGAAGCGAATAGATTGGATGTTTTTCT 59.879 33.333 0.00 0.00 0.00 2.52
1718 1823 7.250569 TGAAGCGAATAGATTGGATGTTTTTC 58.749 34.615 0.00 0.00 0.00 2.29
1719 1824 7.094205 ACTGAAGCGAATAGATTGGATGTTTTT 60.094 33.333 0.00 0.00 0.00 1.94
1720 1825 6.375455 ACTGAAGCGAATAGATTGGATGTTTT 59.625 34.615 0.00 0.00 0.00 2.43
1721 1826 5.882557 ACTGAAGCGAATAGATTGGATGTTT 59.117 36.000 0.00 0.00 0.00 2.83
1722 1827 5.431765 ACTGAAGCGAATAGATTGGATGTT 58.568 37.500 0.00 0.00 0.00 2.71
1723 1828 5.028549 ACTGAAGCGAATAGATTGGATGT 57.971 39.130 0.00 0.00 0.00 3.06
1724 1829 5.052481 TGACTGAAGCGAATAGATTGGATG 58.948 41.667 0.00 0.00 0.00 3.51
1725 1830 5.282055 TGACTGAAGCGAATAGATTGGAT 57.718 39.130 0.00 0.00 0.00 3.41
1726 1831 4.736126 TGACTGAAGCGAATAGATTGGA 57.264 40.909 0.00 0.00 0.00 3.53
1727 1832 4.212847 CCATGACTGAAGCGAATAGATTGG 59.787 45.833 0.00 0.00 0.00 3.16
1728 1833 4.319333 GCCATGACTGAAGCGAATAGATTG 60.319 45.833 0.00 0.00 0.00 2.67
1729 1834 3.812053 GCCATGACTGAAGCGAATAGATT 59.188 43.478 0.00 0.00 0.00 2.40
1730 1835 3.181462 TGCCATGACTGAAGCGAATAGAT 60.181 43.478 0.00 0.00 0.00 1.98
1731 1836 2.168313 TGCCATGACTGAAGCGAATAGA 59.832 45.455 0.00 0.00 0.00 1.98
1732 1837 2.543012 CTGCCATGACTGAAGCGAATAG 59.457 50.000 0.00 0.00 0.00 1.73
1733 1838 2.093500 ACTGCCATGACTGAAGCGAATA 60.093 45.455 0.00 0.00 0.00 1.75
1734 1839 1.339438 ACTGCCATGACTGAAGCGAAT 60.339 47.619 0.00 0.00 0.00 3.34
1735 1840 0.035317 ACTGCCATGACTGAAGCGAA 59.965 50.000 0.00 0.00 0.00 4.70
1736 1841 0.894835 TACTGCCATGACTGAAGCGA 59.105 50.000 0.00 0.00 0.00 4.93
1737 1842 1.002366 GTACTGCCATGACTGAAGCG 58.998 55.000 0.00 0.00 0.00 4.68
1738 1843 2.099141 TGTACTGCCATGACTGAAGC 57.901 50.000 0.00 0.00 0.00 3.86
1739 1844 4.256110 TCATTGTACTGCCATGACTGAAG 58.744 43.478 0.00 0.00 0.00 3.02
1740 1845 4.284829 TCATTGTACTGCCATGACTGAA 57.715 40.909 0.00 0.00 0.00 3.02
1741 1846 3.979101 TCATTGTACTGCCATGACTGA 57.021 42.857 0.00 0.00 0.00 3.41
1742 1847 3.752747 TGTTCATTGTACTGCCATGACTG 59.247 43.478 0.00 0.00 0.00 3.51
1743 1848 3.753272 GTGTTCATTGTACTGCCATGACT 59.247 43.478 0.00 0.00 0.00 3.41
1744 1849 3.753272 AGTGTTCATTGTACTGCCATGAC 59.247 43.478 0.00 0.00 0.00 3.06
1745 1850 4.019792 AGTGTTCATTGTACTGCCATGA 57.980 40.909 0.00 0.00 0.00 3.07
1746 1851 5.178061 TCTAGTGTTCATTGTACTGCCATG 58.822 41.667 0.00 0.00 0.00 3.66
1747 1852 5.187772 TCTCTAGTGTTCATTGTACTGCCAT 59.812 40.000 0.00 0.00 0.00 4.40
1748 1853 4.526650 TCTCTAGTGTTCATTGTACTGCCA 59.473 41.667 0.00 0.00 0.00 4.92
1749 1854 5.073311 TCTCTAGTGTTCATTGTACTGCC 57.927 43.478 0.00 0.00 0.00 4.85
1750 1855 8.879342 AATATCTCTAGTGTTCATTGTACTGC 57.121 34.615 0.00 0.00 0.00 4.40
1758 1863 8.873830 CGTCAACAAAATATCTCTAGTGTTCAT 58.126 33.333 0.00 0.00 0.00 2.57
1759 1864 7.148639 GCGTCAACAAAATATCTCTAGTGTTCA 60.149 37.037 0.00 0.00 0.00 3.18
1760 1865 7.148639 TGCGTCAACAAAATATCTCTAGTGTTC 60.149 37.037 0.00 0.00 0.00 3.18
1761 1866 6.649141 TGCGTCAACAAAATATCTCTAGTGTT 59.351 34.615 0.00 0.00 0.00 3.32
1762 1867 6.163476 TGCGTCAACAAAATATCTCTAGTGT 58.837 36.000 0.00 0.00 0.00 3.55
1763 1868 6.647212 TGCGTCAACAAAATATCTCTAGTG 57.353 37.500 0.00 0.00 0.00 2.74
1764 1869 7.849804 ATTGCGTCAACAAAATATCTCTAGT 57.150 32.000 0.00 0.00 32.27 2.57
1765 1870 8.177663 ACAATTGCGTCAACAAAATATCTCTAG 58.822 33.333 5.05 0.00 32.27 2.43
1766 1871 8.039603 ACAATTGCGTCAACAAAATATCTCTA 57.960 30.769 5.05 0.00 32.27 2.43
1767 1872 6.913170 ACAATTGCGTCAACAAAATATCTCT 58.087 32.000 5.05 0.00 32.27 3.10
1768 1873 7.566858 AACAATTGCGTCAACAAAATATCTC 57.433 32.000 5.05 0.00 32.27 2.75
1769 1874 7.116233 GGAAACAATTGCGTCAACAAAATATCT 59.884 33.333 5.05 0.00 32.27 1.98
1770 1875 7.226772 GGAAACAATTGCGTCAACAAAATATC 58.773 34.615 5.05 0.00 32.27 1.63
1771 1876 6.128956 CGGAAACAATTGCGTCAACAAAATAT 60.129 34.615 5.05 0.00 44.25 1.28
1772 1877 5.174035 CGGAAACAATTGCGTCAACAAAATA 59.826 36.000 5.05 0.00 44.25 1.40
1786 1891 5.891551 ACTCATTATAAGCCCGGAAACAATT 59.108 36.000 0.73 0.00 0.00 2.32
1823 1932 0.039527 AAAGGAACAAATCGCACGCC 60.040 50.000 0.00 0.00 0.00 5.68
1900 2011 7.043565 AGAACTGCACAAAAAGATTTTGACAT 58.956 30.769 19.24 6.08 33.83 3.06
1904 2015 8.016801 ACAAAAGAACTGCACAAAAAGATTTTG 58.983 29.630 12.63 12.63 38.93 2.44
1913 2024 4.797868 CGATCAACAAAAGAACTGCACAAA 59.202 37.500 0.00 0.00 0.00 2.83
1917 2028 2.948979 ACCGATCAACAAAAGAACTGCA 59.051 40.909 0.00 0.00 0.00 4.41
1920 2031 4.204012 TCCAACCGATCAACAAAAGAACT 58.796 39.130 0.00 0.00 0.00 3.01
1954 2065 3.589495 AGCGAAACCTACACCTAGAAC 57.411 47.619 0.00 0.00 0.00 3.01
1959 2070 1.140252 ACACAAGCGAAACCTACACCT 59.860 47.619 0.00 0.00 0.00 4.00
1967 2104 2.405892 ATGAGCAACACAAGCGAAAC 57.594 45.000 0.00 0.00 37.01 2.78
1972 2109 3.360249 ACTTGAATGAGCAACACAAGC 57.640 42.857 0.00 0.00 40.72 4.01
1982 2119 4.916983 TGGTTGGTTGAACTTGAATGAG 57.083 40.909 0.00 0.00 34.66 2.90
2002 2139 2.079158 AGAACTTCACCGTCATGCATG 58.921 47.619 21.07 21.07 0.00 4.06
2051 2188 2.322212 TTTTTAGCCTTCGCGTGCA 58.678 47.368 17.33 0.00 41.18 4.57
2074 2211 1.906574 CCAAGGGGCAGTGTCTAAGTA 59.093 52.381 0.00 0.00 0.00 2.24
2079 2217 0.842030 TCATCCAAGGGGCAGTGTCT 60.842 55.000 0.00 0.00 0.00 3.41
2100 2238 2.799412 GTCTCTCAATCATCGATGGTGC 59.201 50.000 24.61 7.07 0.00 5.01
2113 2257 1.581934 CGTGGTGCAAAGTCTCTCAA 58.418 50.000 0.00 0.00 0.00 3.02
2114 2258 0.249868 CCGTGGTGCAAAGTCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
2115 2259 0.249911 ACCGTGGTGCAAAGTCTCTC 60.250 55.000 0.00 0.00 0.00 3.20
2116 2260 0.180406 AACCGTGGTGCAAAGTCTCT 59.820 50.000 0.00 0.00 0.00 3.10
2117 2261 0.307760 CAACCGTGGTGCAAAGTCTC 59.692 55.000 0.00 0.00 0.00 3.36
2118 2262 1.724582 GCAACCGTGGTGCAAAGTCT 61.725 55.000 8.77 0.00 0.00 3.24
2127 2271 2.047274 CTCATCCGCAACCGTGGT 60.047 61.111 0.00 0.00 43.79 4.16
2148 2292 2.104281 ACGCTTTAAGCCCTAATCCGAT 59.896 45.455 11.64 0.00 38.18 4.18
2162 2306 4.498345 GGTTCCATGAACACAAACGCTTTA 60.498 41.667 9.01 0.00 43.54 1.85
2163 2307 3.443976 GTTCCATGAACACAAACGCTTT 58.556 40.909 0.00 0.00 41.62 3.51
2202 2349 2.435437 AGAGCAAAAGGGCACAACATTT 59.565 40.909 0.00 0.00 35.83 2.32
2283 2433 6.931840 GGGGTAGAGTAGAAAGCTTCAATATG 59.068 42.308 0.00 0.00 0.00 1.78
2286 2436 5.033522 AGGGGTAGAGTAGAAAGCTTCAAT 58.966 41.667 0.00 0.00 0.00 2.57
2310 2460 6.800543 TGAATTTGTTGTTGATCCGAAGAAA 58.199 32.000 0.00 0.00 0.00 2.52
2317 2467 6.271488 TCTGGATGAATTTGTTGTTGATCC 57.729 37.500 0.00 0.00 39.08 3.36
2322 2472 7.673180 ACAATGATCTGGATGAATTTGTTGTT 58.327 30.769 0.00 0.00 0.00 2.83
2324 2474 7.412563 GCAACAATGATCTGGATGAATTTGTTG 60.413 37.037 16.93 16.93 44.50 3.33
2348 2498 0.322816 GCAAGAGGAGAATGGTGGCA 60.323 55.000 0.00 0.00 0.00 4.92
2355 2505 1.065854 CAACCGGAGCAAGAGGAGAAT 60.066 52.381 9.46 0.00 0.00 2.40
2356 2506 0.321671 CAACCGGAGCAAGAGGAGAA 59.678 55.000 9.46 0.00 0.00 2.87
2364 2514 2.215196 GTTACAAGACAACCGGAGCAA 58.785 47.619 9.46 0.00 0.00 3.91
2371 2521 3.763057 AGGATTGGGTTACAAGACAACC 58.237 45.455 0.00 0.00 43.48 3.77
2379 2529 3.054655 GGAAGCAGTAGGATTGGGTTACA 60.055 47.826 0.00 0.00 0.00 2.41
2432 2587 2.027460 CCAACAAGGCACGCAACC 59.973 61.111 0.00 0.00 0.00 3.77
2443 2598 3.516300 AGTCCGATACATACACCCAACAA 59.484 43.478 0.00 0.00 0.00 2.83
2446 2601 2.432874 CCAGTCCGATACATACACCCAA 59.567 50.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.