Multiple sequence alignment - TraesCS5B01G256400

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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 TraesCS5B01G256400 chr5B 100.000 1894 0 0 539 2432 439227114 439229007 0.000000e+00 3498
1 TraesCS5B01G256400 chr5B 100.000 78 0 0 1 78 439226576 439226653 7.010000e-31 145
2 TraesCS5B01G256400 chr5A 85.897 1957 161 64 545 2432 472341698 472343608 0.000000e+00 1978
3 TraesCS5B01G256400 chr5D 88.230 1113 48 30 544 1641 369869715 369870759 0.000000e+00 1253
4 TraesCS5B01G256400 chr5D 81.488 578 67 11 1878 2432 369870766 369871326 2.870000e-119 438
5 TraesCS5B01G256400 chr5D 85.530 387 54 2 1848 2234 505371560 505371944 1.050000e-108 403
6 TraesCS5B01G256400 chr1A 87.200 375 42 5 1861 2234 285980422 285980053 2.890000e-114 422
7 TraesCS5B01G256400 chr4D 86.269 386 53 0 1849 2234 417414955 417415340 1.040000e-113 420
8 TraesCS5B01G256400 chr2B 86.010 386 48 6 1852 2234 570064061 570063679 2.250000e-110 409
9 TraesCS5B01G256400 chr1D 85.455 385 51 4 1852 2234 431764198 431763817 1.750000e-106 396
10 TraesCS5B01G256400 chr6A 85.302 381 52 3 1852 2231 199805851 199806228 8.150000e-105 390
11 TraesCS5B01G256400 chr7D 84.536 388 58 2 1848 2234 621141912 621141526 1.360000e-102 383
12 TraesCS5B01G256400 chr6D 84.675 385 55 3 1852 2234 20135097 20134715 4.910000e-102 381


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 TraesCS5B01G256400 chr5B 439226576 439229007 2431 False 1821.5 3498 100.000 1 2432 2 chr5B.!!$F1 2431
1 TraesCS5B01G256400 chr5A 472341698 472343608 1910 False 1978.0 1978 85.897 545 2432 1 chr5A.!!$F1 1887
2 TraesCS5B01G256400 chr5D 369869715 369871326 1611 False 845.5 1253 84.859 544 2432 2 chr5D.!!$F2 1888

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
701 710 0.172803 GCCATCCACGTAACTCTCGT 59.827 55.0 0.0 0.0 42.33 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2101 0.033642 GTCCTATCGGGCCTTAGCAC 59.966 60.0 0.84 0.0 42.56 4.4 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
17 18 3.285215 GCCTCCATCTGCCGCATG 61.285 66.667 0.00 0.00 0.00 4.06
18 19 3.285215 CCTCCATCTGCCGCATGC 61.285 66.667 7.91 7.91 41.77 4.06
19 20 2.203167 CTCCATCTGCCGCATGCT 60.203 61.111 17.13 0.00 42.00 3.79
20 21 2.515290 TCCATCTGCCGCATGCTG 60.515 61.111 17.13 10.87 42.00 4.41
24 25 2.269883 TCTGCCGCATGCTGATGT 59.730 55.556 17.13 0.00 42.28 3.06
25 26 1.816679 TCTGCCGCATGCTGATGTC 60.817 57.895 17.13 0.00 42.28 3.06
26 27 3.164390 CTGCCGCATGCTGATGTCG 62.164 63.158 17.13 0.00 41.11 4.35
27 28 3.945434 GCCGCATGCTGATGTCGG 61.945 66.667 17.13 8.66 44.94 4.79
35 36 3.686622 GCTGATGTCGGCCTAATCA 57.313 52.632 0.00 6.44 42.27 2.57
36 37 2.175878 GCTGATGTCGGCCTAATCAT 57.824 50.000 0.00 0.00 42.27 2.45
37 38 2.072298 GCTGATGTCGGCCTAATCATC 58.928 52.381 0.00 9.88 42.27 2.92
38 39 2.332104 CTGATGTCGGCCTAATCATCG 58.668 52.381 0.00 3.26 39.33 3.84
39 40 1.686587 TGATGTCGGCCTAATCATCGT 59.313 47.619 0.00 0.00 39.33 3.73
40 41 2.288213 TGATGTCGGCCTAATCATCGTC 60.288 50.000 0.00 0.00 39.33 4.20
41 42 0.387929 TGTCGGCCTAATCATCGTCC 59.612 55.000 0.00 0.00 0.00 4.79
42 43 0.319641 GTCGGCCTAATCATCGTCCC 60.320 60.000 0.00 0.00 0.00 4.46
43 44 1.004918 CGGCCTAATCATCGTCCCC 60.005 63.158 0.00 0.00 0.00 4.81
44 45 1.375326 GGCCTAATCATCGTCCCCC 59.625 63.158 0.00 0.00 0.00 5.40
45 46 1.415672 GGCCTAATCATCGTCCCCCA 61.416 60.000 0.00 0.00 0.00 4.96
46 47 0.250338 GCCTAATCATCGTCCCCCAC 60.250 60.000 0.00 0.00 0.00 4.61
47 48 0.396811 CCTAATCATCGTCCCCCACC 59.603 60.000 0.00 0.00 0.00 4.61
48 49 1.128200 CTAATCATCGTCCCCCACCA 58.872 55.000 0.00 0.00 0.00 4.17
49 50 0.834612 TAATCATCGTCCCCCACCAC 59.165 55.000 0.00 0.00 0.00 4.16
50 51 1.921869 AATCATCGTCCCCCACCACC 61.922 60.000 0.00 0.00 0.00 4.61
51 52 4.109675 CATCGTCCCCCACCACCC 62.110 72.222 0.00 0.00 0.00 4.61
592 595 6.036735 CCTTGAGATTAGGAAACGCGAAATTA 59.963 38.462 15.93 0.00 34.56 1.40
646 650 4.729918 CCCTGCACAGCCACCTCC 62.730 72.222 0.00 0.00 0.00 4.30
648 652 2.433446 CTGCACAGCCACCTCCTT 59.567 61.111 0.00 0.00 0.00 3.36
701 710 0.172803 GCCATCCACGTAACTCTCGT 59.827 55.000 0.00 0.00 42.33 4.18
707 716 2.183555 CGTAACTCTCGTGGGGCC 59.816 66.667 0.00 0.00 0.00 5.80
738 753 1.566563 GTCACAGTGCTGACTTGCG 59.433 57.895 14.72 0.00 38.05 4.85
742 757 2.281070 AGTGCTGACTTGCGGTGG 60.281 61.111 0.00 0.00 35.36 4.61
754 769 0.541998 TGCGGTGGGAAGAGAAGAGA 60.542 55.000 0.00 0.00 0.00 3.10
760 776 4.574892 GGTGGGAAGAGAAGAGAAGAAAG 58.425 47.826 0.00 0.00 0.00 2.62
774 790 6.547402 AGAGAAGAAAGAAAAGGTATGGCTT 58.453 36.000 0.00 0.00 0.00 4.35
781 797 8.773216 AGAAAGAAAAGGTATGGCTTAGATACT 58.227 33.333 0.00 0.00 0.00 2.12
823 839 2.669229 CACGCCATGAGCACACCA 60.669 61.111 0.00 0.00 44.04 4.17
912 928 1.272807 CCCCCTATATACCCACACCG 58.727 60.000 0.00 0.00 0.00 4.94
940 956 4.584327 CGTAGTACGTAGCGCCTG 57.416 61.111 14.62 0.00 36.74 4.85
976 992 1.890041 CCGCACGTTGGTCCTTGAA 60.890 57.895 0.00 0.00 0.00 2.69
991 1013 0.546122 TTGAACACCCACACAGCTCT 59.454 50.000 0.00 0.00 0.00 4.09
997 1028 0.616111 ACCCACACAGCTCTAGAGGG 60.616 60.000 21.23 14.71 40.66 4.30
1410 1444 0.107214 CCACCACCAGCAACGGATAT 60.107 55.000 0.00 0.00 0.00 1.63
1425 1459 2.172717 CGGATATGACCCACCCTTCTTT 59.827 50.000 0.00 0.00 0.00 2.52
1435 1478 0.035056 ACCCTTCTTTGGCTGATCCG 60.035 55.000 0.00 0.00 37.80 4.18
1446 1489 0.249657 GCTGATCCGTCCCATGTCTC 60.250 60.000 0.00 0.00 0.00 3.36
1447 1490 0.390860 CTGATCCGTCCCATGTCTCC 59.609 60.000 0.00 0.00 0.00 3.71
1456 1499 2.593978 CATGTCTCCCCTGCCTGG 59.406 66.667 0.00 0.00 0.00 4.45
1511 1554 6.092122 TCTGCCGTGTTTTCATTAGTTCTATG 59.908 38.462 0.00 0.00 0.00 2.23
1529 1572 5.528870 TCTATGTTATACGCTGATGGTGTG 58.471 41.667 0.00 0.00 39.23 3.82
1540 1583 4.129380 GCTGATGGTGTGCTATCATGTTA 58.871 43.478 0.00 0.00 40.90 2.41
1544 1587 6.280643 TGATGGTGTGCTATCATGTTAGTAC 58.719 40.000 19.45 19.45 37.62 2.73
1545 1588 5.669164 TGGTGTGCTATCATGTTAGTACA 57.331 39.130 23.04 23.04 40.87 2.90
1549 1592 6.524101 TGTGCTATCATGTTAGTACACTGA 57.476 37.500 23.04 7.73 39.09 3.41
1550 1593 7.112452 TGTGCTATCATGTTAGTACACTGAT 57.888 36.000 23.04 0.00 39.09 2.90
1551 1594 6.980397 TGTGCTATCATGTTAGTACACTGATG 59.020 38.462 23.04 0.00 39.09 3.07
1552 1595 6.422100 GTGCTATCATGTTAGTACACTGATGG 59.578 42.308 20.66 0.00 37.03 3.51
1553 1596 6.323739 TGCTATCATGTTAGTACACTGATGGA 59.676 38.462 11.53 0.00 37.03 3.41
1569 1612 4.033009 TGATGGAGTATGTGAGATGGTGT 58.967 43.478 0.00 0.00 0.00 4.16
1571 1614 5.069119 TGATGGAGTATGTGAGATGGTGTAC 59.931 44.000 0.00 0.00 0.00 2.90
1572 1615 4.610333 TGGAGTATGTGAGATGGTGTACT 58.390 43.478 0.00 0.00 0.00 2.73
1575 1618 6.490381 TGGAGTATGTGAGATGGTGTACTATC 59.510 42.308 0.61 0.61 34.50 2.08
1576 1619 6.490381 GGAGTATGTGAGATGGTGTACTATCA 59.510 42.308 10.39 0.00 36.45 2.15
1577 1620 7.177568 GGAGTATGTGAGATGGTGTACTATCAT 59.822 40.741 10.39 0.00 36.45 2.45
1578 1621 7.890515 AGTATGTGAGATGGTGTACTATCATG 58.109 38.462 10.39 0.00 36.45 3.07
1579 1622 6.737720 ATGTGAGATGGTGTACTATCATGT 57.262 37.500 10.39 0.00 36.45 3.21
1580 1623 6.544928 TGTGAGATGGTGTACTATCATGTT 57.455 37.500 10.39 0.00 36.45 2.71
1581 1624 7.654022 TGTGAGATGGTGTACTATCATGTTA 57.346 36.000 10.39 0.00 36.45 2.41
1582 1625 7.716612 TGTGAGATGGTGTACTATCATGTTAG 58.283 38.462 10.39 8.92 36.45 2.34
1619 1662 0.724453 GCAACCGCGTGTGTGTATTG 60.724 55.000 4.92 0.00 0.00 1.90
1620 1663 0.862490 CAACCGCGTGTGTGTATTGA 59.138 50.000 4.92 0.00 0.00 2.57
1621 1664 1.463056 CAACCGCGTGTGTGTATTGAT 59.537 47.619 4.92 0.00 0.00 2.57
1622 1665 1.075542 ACCGCGTGTGTGTATTGATG 58.924 50.000 4.92 0.00 0.00 3.07
1624 1667 1.933181 CCGCGTGTGTGTATTGATGAT 59.067 47.619 4.92 0.00 0.00 2.45
1635 1678 5.066764 TGTGTATTGATGATTGCCACATGAG 59.933 40.000 0.00 0.00 0.00 2.90
1658 1701 6.894682 AGTGATTTTATCTCTCTCTTTCCCC 58.105 40.000 0.00 0.00 0.00 4.81
1659 1702 6.445139 AGTGATTTTATCTCTCTCTTTCCCCA 59.555 38.462 0.00 0.00 0.00 4.96
1660 1703 7.128573 AGTGATTTTATCTCTCTCTTTCCCCAT 59.871 37.037 0.00 0.00 0.00 4.00
1661 1704 8.432805 GTGATTTTATCTCTCTCTTTCCCCATA 58.567 37.037 0.00 0.00 0.00 2.74
1662 1705 8.654997 TGATTTTATCTCTCTCTTTCCCCATAG 58.345 37.037 0.00 0.00 0.00 2.23
1663 1706 7.380423 TTTTATCTCTCTCTTTCCCCATAGG 57.620 40.000 0.00 0.00 0.00 2.57
1677 1720 4.559862 CCCATAGGGCCATAGTAGAAAG 57.440 50.000 6.18 0.00 35.35 2.62
1689 1732 8.446599 GCCATAGTAGAAAGGCAATTTTACTA 57.553 34.615 12.56 12.56 46.26 1.82
1703 1746 6.622896 GCAATTTTACTATGCACGGGATATCC 60.623 42.308 13.87 13.87 39.81 2.59
1718 1761 5.513233 GGGATATCCTGTGCATAAATCCAT 58.487 41.667 21.18 0.00 34.39 3.41
1723 1766 2.549754 CCTGTGCATAAATCCATCGTCC 59.450 50.000 0.00 0.00 0.00 4.79
1725 1768 2.159028 TGTGCATAAATCCATCGTCCGA 60.159 45.455 0.00 0.00 0.00 4.55
1736 1779 1.298859 ATCGTCCGAGGTTGCTTTGC 61.299 55.000 0.00 0.00 0.00 3.68
1741 1784 1.425428 CGAGGTTGCTTTGCGATCC 59.575 57.895 0.00 0.00 0.00 3.36
1749 1792 2.006772 CTTTGCGATCCGTGCTACC 58.993 57.895 0.00 0.00 0.00 3.18
1753 1796 0.036765 TGCGATCCGTGCTACCTTTT 60.037 50.000 0.00 0.00 0.00 2.27
1754 1797 0.651031 GCGATCCGTGCTACCTTTTC 59.349 55.000 0.00 0.00 0.00 2.29
1755 1798 1.739371 GCGATCCGTGCTACCTTTTCT 60.739 52.381 0.00 0.00 0.00 2.52
1760 1803 5.121142 CGATCCGTGCTACCTTTTCTTTTTA 59.879 40.000 0.00 0.00 0.00 1.52
1761 1804 5.678132 TCCGTGCTACCTTTTCTTTTTAC 57.322 39.130 0.00 0.00 0.00 2.01
1762 1805 5.370679 TCCGTGCTACCTTTTCTTTTTACT 58.629 37.500 0.00 0.00 0.00 2.24
1763 1806 5.237779 TCCGTGCTACCTTTTCTTTTTACTG 59.762 40.000 0.00 0.00 0.00 2.74
1767 1810 7.165318 CGTGCTACCTTTTCTTTTTACTGTTTC 59.835 37.037 0.00 0.00 0.00 2.78
1768 1811 7.434307 GTGCTACCTTTTCTTTTTACTGTTTCC 59.566 37.037 0.00 0.00 0.00 3.13
1770 1813 5.898174 ACCTTTTCTTTTTACTGTTTCCGG 58.102 37.500 0.00 0.00 0.00 5.14
1772 1815 6.153170 ACCTTTTCTTTTTACTGTTTCCGGAA 59.847 34.615 14.35 14.35 0.00 4.30
1773 1816 7.147794 ACCTTTTCTTTTTACTGTTTCCGGAAT 60.148 33.333 19.62 5.36 0.00 3.01
1774 1817 7.709182 CCTTTTCTTTTTACTGTTTCCGGAATT 59.291 33.333 19.62 5.56 0.00 2.17
1845 1888 6.201234 TCGAACACAACATTTGAAACGAGATA 59.799 34.615 0.00 0.00 0.00 1.98
1846 1889 6.848800 CGAACACAACATTTGAAACGAGATAA 59.151 34.615 0.00 0.00 0.00 1.75
1847 1890 7.149351 CGAACACAACATTTGAAACGAGATAAC 60.149 37.037 0.00 0.00 0.00 1.89
1848 1891 7.259290 ACACAACATTTGAAACGAGATAACT 57.741 32.000 0.00 0.00 0.00 2.24
1849 1892 7.703328 ACACAACATTTGAAACGAGATAACTT 58.297 30.769 0.00 0.00 0.00 2.66
1850 1893 7.855904 ACACAACATTTGAAACGAGATAACTTC 59.144 33.333 0.00 0.00 0.00 3.01
1906 1949 5.984233 TCTATCATGGCAATACAACGAAC 57.016 39.130 0.00 0.00 0.00 3.95
1908 1951 3.822594 TCATGGCAATACAACGAACAC 57.177 42.857 0.00 0.00 0.00 3.32
1924 1967 9.240159 ACAACGAACACCAGAAATAATAAAAAC 57.760 29.630 0.00 0.00 0.00 2.43
1941 1984 3.627395 AAACTACATCCAGATCCGCAA 57.373 42.857 0.00 0.00 0.00 4.85
1942 1985 2.898729 ACTACATCCAGATCCGCAAG 57.101 50.000 0.00 0.00 0.00 4.01
1968 2011 3.315470 CCTAGCGATGACTACAAGCACTA 59.685 47.826 0.00 0.00 36.63 2.74
2006 2051 1.605058 CCGTCGTCATTGGTCCTCCT 61.605 60.000 0.00 0.00 34.23 3.69
2010 2055 0.246635 CGTCATTGGTCCTCCTTCGT 59.753 55.000 0.00 0.00 34.23 3.85
2013 2058 0.530744 CATTGGTCCTCCTTCGTCGA 59.469 55.000 0.00 0.00 34.23 4.20
2025 2070 1.457303 CTTCGTCGAAGCCAGACAAAG 59.543 52.381 21.19 0.00 38.46 2.77
2038 2083 5.011738 AGCCAGACAAAGCTTACTGTAGTAA 59.988 40.000 19.45 4.57 35.22 2.24
2056 2101 5.968387 AGTAAACAGTCAGAAAGTCGTTG 57.032 39.130 0.00 0.00 0.00 4.10
2068 2113 2.047655 TCGTTGTGCTAAGGCCCG 60.048 61.111 0.00 0.00 37.74 6.13
2091 2136 1.064758 AGGACCAGCACAACAGAACAA 60.065 47.619 0.00 0.00 0.00 2.83
2098 2143 1.135517 GCACAACAGAACAACAACCGT 60.136 47.619 0.00 0.00 0.00 4.83
2100 2145 2.160615 CACAACAGAACAACAACCGTCA 59.839 45.455 0.00 0.00 0.00 4.35
2109 2154 1.070175 CAACAACCGTCACCGATGAAC 60.070 52.381 0.00 0.00 36.31 3.18
2151 2196 4.647424 TCCAACCTGAAAACACATGAAC 57.353 40.909 0.00 0.00 0.00 3.18
2162 2207 3.637998 ACACATGAACGTAGACGAACT 57.362 42.857 9.41 0.00 43.02 3.01
2163 2208 4.754372 ACACATGAACGTAGACGAACTA 57.246 40.909 9.41 0.00 43.02 2.24
2164 2209 5.306532 ACACATGAACGTAGACGAACTAT 57.693 39.130 9.41 0.00 43.02 2.12
2168 2213 5.123502 ACATGAACGTAGACGAACTATGACT 59.876 40.000 9.41 6.64 43.02 3.41
2183 2228 6.019779 ACTATGACTAGATCCGAGCAAATC 57.980 41.667 0.00 0.00 0.00 2.17
2186 2231 3.181475 TGACTAGATCCGAGCAAATCCAC 60.181 47.826 0.00 0.00 0.00 4.02
2200 2245 4.081406 CAAATCCACCAAGAACAGATCCA 58.919 43.478 0.00 0.00 0.00 3.41
2203 2248 1.073763 CCACCAAGAACAGATCCACCA 59.926 52.381 0.00 0.00 0.00 4.17
2218 2263 0.319728 CACCAGAGACACACCTCCAG 59.680 60.000 0.00 0.00 33.76 3.86
2234 2279 2.101415 CTCCAGACGCTCACCAATGATA 59.899 50.000 0.00 0.00 33.22 2.15
2263 2339 5.946942 AGAGAAGCCAATCTCAACATCTA 57.053 39.130 12.64 0.00 46.73 1.98
2389 2469 5.293079 ACGATTACTAACCAGACGTAGACTC 59.707 44.000 0.00 0.00 0.00 3.36
2415 2496 4.682787 TGCCAACTGAATCAGTACTATCG 58.317 43.478 17.04 2.19 44.62 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.285215 CATGCGGCAGATGGAGGC 61.285 66.667 9.25 0.00 0.00 4.70
1 2 3.285215 GCATGCGGCAGATGGAGG 61.285 66.667 9.25 0.00 43.97 4.30
3 4 2.333701 ATCAGCATGCGGCAGATGGA 62.334 55.000 13.45 4.27 45.79 3.41
4 5 1.897137 ATCAGCATGCGGCAGATGG 60.897 57.895 13.45 0.00 45.79 3.51
5 6 3.745912 ATCAGCATGCGGCAGATG 58.254 55.556 13.45 9.81 45.79 2.90
10 11 3.945434 CCGACATCAGCATGCGGC 61.945 66.667 13.45 0.00 40.44 6.53
11 12 3.945434 GCCGACATCAGCATGCGG 61.945 66.667 13.01 12.49 45.23 5.69
12 13 2.976692 TAGGCCGACATCAGCATGCG 62.977 60.000 13.01 7.64 34.76 4.73
13 14 0.815213 TTAGGCCGACATCAGCATGC 60.815 55.000 10.51 10.51 34.76 4.06
14 15 1.802960 GATTAGGCCGACATCAGCATG 59.197 52.381 0.00 0.00 35.92 4.06
15 16 1.417517 TGATTAGGCCGACATCAGCAT 59.582 47.619 9.72 0.00 0.00 3.79
16 17 0.829990 TGATTAGGCCGACATCAGCA 59.170 50.000 9.72 0.00 0.00 4.41
17 18 2.072298 GATGATTAGGCCGACATCAGC 58.928 52.381 20.71 17.01 38.92 4.26
18 19 2.288457 ACGATGATTAGGCCGACATCAG 60.288 50.000 23.17 19.23 38.99 2.90
19 20 1.686587 ACGATGATTAGGCCGACATCA 59.313 47.619 23.17 19.51 38.99 3.07
20 21 2.329379 GACGATGATTAGGCCGACATC 58.671 52.381 17.80 17.80 36.70 3.06
21 22 1.000955 GGACGATGATTAGGCCGACAT 59.999 52.381 0.00 1.62 0.00 3.06
22 23 0.387929 GGACGATGATTAGGCCGACA 59.612 55.000 0.00 0.00 0.00 4.35
23 24 0.319641 GGGACGATGATTAGGCCGAC 60.320 60.000 0.00 0.00 36.05 4.79
24 25 1.469335 GGGGACGATGATTAGGCCGA 61.469 60.000 0.00 0.00 36.05 5.54
25 26 1.004918 GGGGACGATGATTAGGCCG 60.005 63.158 0.00 0.00 36.05 6.13
26 27 1.375326 GGGGGACGATGATTAGGCC 59.625 63.158 0.00 0.00 33.88 5.19
27 28 0.250338 GTGGGGGACGATGATTAGGC 60.250 60.000 0.00 0.00 0.00 3.93
28 29 0.396811 GGTGGGGGACGATGATTAGG 59.603 60.000 0.00 0.00 0.00 2.69
29 30 1.128200 TGGTGGGGGACGATGATTAG 58.872 55.000 0.00 0.00 0.00 1.73
30 31 0.834612 GTGGTGGGGGACGATGATTA 59.165 55.000 0.00 0.00 0.00 1.75
31 32 1.607612 GTGGTGGGGGACGATGATT 59.392 57.895 0.00 0.00 0.00 2.57
32 33 2.375345 GGTGGTGGGGGACGATGAT 61.375 63.158 0.00 0.00 0.00 2.45
33 34 3.006728 GGTGGTGGGGGACGATGA 61.007 66.667 0.00 0.00 0.00 2.92
34 35 4.109675 GGGTGGTGGGGGACGATG 62.110 72.222 0.00 0.00 0.00 3.84
665 670 4.601794 CCAACTGGCCAGCACCCA 62.602 66.667 33.06 0.00 0.00 4.51
690 699 2.183555 GGCCCCACGAGAGTTACG 59.816 66.667 0.00 0.00 46.40 3.18
707 716 1.821241 CTGTGACGTGTCGCTTGTGG 61.821 60.000 14.02 0.00 40.54 4.17
738 753 4.284746 TCTTTCTTCTCTTCTCTTCCCACC 59.715 45.833 0.00 0.00 0.00 4.61
742 757 6.995686 ACCTTTTCTTTCTTCTCTTCTCTTCC 59.004 38.462 0.00 0.00 0.00 3.46
754 769 9.397280 GTATCTAAGCCATACCTTTTCTTTCTT 57.603 33.333 0.00 0.00 0.00 2.52
774 790 4.838986 GGAGGGTGCTGGATAAAGTATCTA 59.161 45.833 0.00 0.00 35.52 1.98
781 797 2.358090 CCATTGGAGGGTGCTGGATAAA 60.358 50.000 0.00 0.00 0.00 1.40
823 839 2.687566 AGGGGAGCGGGATTTCGT 60.688 61.111 0.00 0.00 0.00 3.85
912 928 0.785979 CGTACTACGTGGTGTTTGGC 59.214 55.000 15.58 0.00 36.74 4.52
976 992 1.261480 CTCTAGAGCTGTGTGGGTGT 58.739 55.000 6.86 0.00 0.00 4.16
1410 1444 1.152830 GCCAAAGAAGGGTGGGTCA 59.847 57.895 0.00 0.00 35.28 4.02
1425 1459 1.971505 GACATGGGACGGATCAGCCA 61.972 60.000 0.00 0.00 35.94 4.75
1435 1478 2.592308 GCAGGGGAGACATGGGAC 59.408 66.667 0.00 0.00 0.00 4.46
1511 1554 2.550978 AGCACACCATCAGCGTATAAC 58.449 47.619 0.00 0.00 0.00 1.89
1529 1572 6.749139 TCCATCAGTGTACTAACATGATAGC 58.251 40.000 9.75 0.00 38.08 2.97
1540 1583 5.510430 TCTCACATACTCCATCAGTGTACT 58.490 41.667 0.00 0.00 36.43 2.73
1544 1587 4.100653 ACCATCTCACATACTCCATCAGTG 59.899 45.833 0.00 0.00 36.43 3.66
1545 1588 4.100653 CACCATCTCACATACTCCATCAGT 59.899 45.833 0.00 0.00 39.41 3.41
1546 1589 4.100653 ACACCATCTCACATACTCCATCAG 59.899 45.833 0.00 0.00 0.00 2.90
1547 1590 4.033009 ACACCATCTCACATACTCCATCA 58.967 43.478 0.00 0.00 0.00 3.07
1548 1591 4.679373 ACACCATCTCACATACTCCATC 57.321 45.455 0.00 0.00 0.00 3.51
1549 1592 5.211973 AGTACACCATCTCACATACTCCAT 58.788 41.667 0.00 0.00 0.00 3.41
1550 1593 4.610333 AGTACACCATCTCACATACTCCA 58.390 43.478 0.00 0.00 0.00 3.86
1551 1594 6.490381 TGATAGTACACCATCTCACATACTCC 59.510 42.308 0.00 0.00 0.00 3.85
1552 1595 7.511959 TGATAGTACACCATCTCACATACTC 57.488 40.000 0.00 0.00 0.00 2.59
1553 1596 7.507277 ACATGATAGTACACCATCTCACATACT 59.493 37.037 0.00 0.00 0.00 2.12
1575 1618 7.010552 GCACTACTTGTCCAGATTACTAACATG 59.989 40.741 0.00 0.00 0.00 3.21
1576 1619 7.042335 GCACTACTTGTCCAGATTACTAACAT 58.958 38.462 0.00 0.00 0.00 2.71
1577 1620 6.014925 TGCACTACTTGTCCAGATTACTAACA 60.015 38.462 0.00 0.00 0.00 2.41
1578 1621 6.395629 TGCACTACTTGTCCAGATTACTAAC 58.604 40.000 0.00 0.00 0.00 2.34
1579 1622 6.599356 TGCACTACTTGTCCAGATTACTAA 57.401 37.500 0.00 0.00 0.00 2.24
1580 1623 6.395629 GTTGCACTACTTGTCCAGATTACTA 58.604 40.000 0.00 0.00 0.00 1.82
1581 1624 5.238583 GTTGCACTACTTGTCCAGATTACT 58.761 41.667 0.00 0.00 0.00 2.24
1582 1625 4.392138 GGTTGCACTACTTGTCCAGATTAC 59.608 45.833 0.00 0.00 0.00 1.89
1619 1662 4.913335 AATCACTCATGTGGCAATCATC 57.087 40.909 0.00 0.00 43.94 2.92
1620 1663 5.670792 AAAATCACTCATGTGGCAATCAT 57.329 34.783 0.00 0.00 43.94 2.45
1621 1664 6.604396 AGATAAAATCACTCATGTGGCAATCA 59.396 34.615 0.00 0.00 43.94 2.57
1622 1665 7.013083 AGAGATAAAATCACTCATGTGGCAATC 59.987 37.037 0.00 0.00 43.94 2.67
1624 1667 6.182627 AGAGATAAAATCACTCATGTGGCAA 58.817 36.000 0.00 0.00 43.94 4.52
1635 1678 6.653989 TGGGGAAAGAGAGAGATAAAATCAC 58.346 40.000 0.00 0.00 0.00 3.06
1658 1701 3.327757 TGCCTTTCTACTATGGCCCTATG 59.672 47.826 0.00 0.00 44.32 2.23
1659 1702 3.598264 TGCCTTTCTACTATGGCCCTAT 58.402 45.455 0.00 0.00 44.32 2.57
1660 1703 3.054779 TGCCTTTCTACTATGGCCCTA 57.945 47.619 0.00 0.00 44.32 3.53
1661 1704 1.893315 TGCCTTTCTACTATGGCCCT 58.107 50.000 0.00 0.00 44.32 5.19
1662 1705 2.729028 TTGCCTTTCTACTATGGCCC 57.271 50.000 0.00 0.00 44.32 5.80
1663 1706 5.598416 AAAATTGCCTTTCTACTATGGCC 57.402 39.130 0.00 0.00 44.32 5.36
1664 1707 7.334844 AGTAAAATTGCCTTTCTACTATGGC 57.665 36.000 0.00 0.00 45.10 4.40
1666 1709 9.884465 GCATAGTAAAATTGCCTTTCTACTATG 57.116 33.333 23.08 23.08 42.96 2.23
1677 1720 2.685897 TCCCGTGCATAGTAAAATTGCC 59.314 45.455 0.00 0.00 35.51 4.52
1687 1730 2.964740 CACAGGATATCCCGTGCATAG 58.035 52.381 22.21 2.09 40.87 2.23
1703 1746 2.221749 CGGACGATGGATTTATGCACAG 59.778 50.000 0.00 0.00 0.00 3.66
1709 1752 3.728845 CAACCTCGGACGATGGATTTAT 58.271 45.455 14.18 0.00 0.00 1.40
1712 1755 0.462047 GCAACCTCGGACGATGGATT 60.462 55.000 14.18 5.37 0.00 3.01
1718 1761 1.959226 GCAAAGCAACCTCGGACGA 60.959 57.895 0.00 0.00 0.00 4.20
1723 1766 1.425428 GGATCGCAAAGCAACCTCG 59.575 57.895 0.00 0.00 0.00 4.63
1725 1768 1.302511 ACGGATCGCAAAGCAACCT 60.303 52.632 0.00 0.00 0.00 3.50
1736 1779 2.295253 AGAAAAGGTAGCACGGATCG 57.705 50.000 0.00 0.00 0.00 3.69
1741 1784 6.056428 ACAGTAAAAAGAAAAGGTAGCACG 57.944 37.500 0.00 0.00 0.00 5.34
1749 1792 8.642908 AATTCCGGAAACAGTAAAAAGAAAAG 57.357 30.769 23.08 0.00 0.00 2.27
1753 1796 7.067737 AGACAAATTCCGGAAACAGTAAAAAGA 59.932 33.333 23.08 0.00 0.00 2.52
1754 1797 7.200455 AGACAAATTCCGGAAACAGTAAAAAG 58.800 34.615 23.08 4.93 0.00 2.27
1755 1798 7.102847 AGACAAATTCCGGAAACAGTAAAAA 57.897 32.000 23.08 0.00 0.00 1.94
1760 1803 3.243401 GCAAGACAAATTCCGGAAACAGT 60.243 43.478 23.08 18.74 0.00 3.55
1761 1804 3.004734 AGCAAGACAAATTCCGGAAACAG 59.995 43.478 23.08 15.58 0.00 3.16
1762 1805 2.955660 AGCAAGACAAATTCCGGAAACA 59.044 40.909 23.08 0.00 0.00 2.83
1763 1806 3.643159 AGCAAGACAAATTCCGGAAAC 57.357 42.857 23.08 10.35 0.00 2.78
1767 1810 3.641437 TTGAAGCAAGACAAATTCCGG 57.359 42.857 0.00 0.00 0.00 5.14
1815 1858 7.858382 TCGTTTCAAATGTTGTGTTCGATTTAT 59.142 29.630 0.00 0.00 0.00 1.40
1816 1859 7.187480 TCGTTTCAAATGTTGTGTTCGATTTA 58.813 30.769 0.00 0.00 0.00 1.40
1821 1864 4.583426 TCTCGTTTCAAATGTTGTGTTCG 58.417 39.130 0.00 0.00 0.00 3.95
1825 1868 8.070171 AGAAGTTATCTCGTTTCAAATGTTGTG 58.930 33.333 0.00 0.00 30.46 3.33
1827 1870 9.450807 AAAGAAGTTATCTCGTTTCAAATGTTG 57.549 29.630 0.00 0.00 37.42 3.33
1857 1900 9.346725 AGATGAATAAATTGAAAGTTTTCTCGC 57.653 29.630 6.21 0.00 38.02 5.03
1886 1929 4.334203 GGTGTTCGTTGTATTGCCATGATA 59.666 41.667 0.00 0.00 0.00 2.15
1924 1967 1.506493 GCTTGCGGATCTGGATGTAG 58.494 55.000 3.14 0.00 0.00 2.74
1941 1984 1.033574 GTAGTCATCGCTAGGTGGCT 58.966 55.000 0.00 0.00 34.20 4.75
1942 1985 0.744874 TGTAGTCATCGCTAGGTGGC 59.255 55.000 0.00 0.00 0.00 5.01
1954 1997 3.498397 GCTTGCTTTAGTGCTTGTAGTCA 59.502 43.478 0.00 0.00 0.00 3.41
1989 2032 1.736032 CGAAGGAGGACCAATGACGAC 60.736 57.143 0.00 0.00 38.94 4.34
1995 2038 1.204941 CTTCGACGAAGGAGGACCAAT 59.795 52.381 26.43 0.00 36.16 3.16
1999 2042 1.153804 GGCTTCGACGAAGGAGGAC 60.154 63.158 32.41 18.46 39.76 3.85
2000 2043 1.595993 CTGGCTTCGACGAAGGAGGA 61.596 60.000 32.41 2.14 39.76 3.71
2006 2051 1.497991 CTTTGTCTGGCTTCGACGAA 58.502 50.000 10.34 10.34 34.51 3.85
2010 2055 2.037251 AGTAAGCTTTGTCTGGCTTCGA 59.963 45.455 3.20 0.00 45.88 3.71
2038 2083 2.351726 GCACAACGACTTTCTGACTGTT 59.648 45.455 0.00 0.00 0.00 3.16
2044 2089 2.096218 GCCTTAGCACAACGACTTTCTG 60.096 50.000 0.00 0.00 39.53 3.02
2045 2090 2.143925 GCCTTAGCACAACGACTTTCT 58.856 47.619 0.00 0.00 39.53 2.52
2056 2101 0.033642 GTCCTATCGGGCCTTAGCAC 59.966 60.000 0.84 0.00 42.56 4.40
2068 2113 3.003480 GTTCTGTTGTGCTGGTCCTATC 58.997 50.000 0.00 0.00 0.00 2.08
2073 2118 1.742831 TGTTGTTCTGTTGTGCTGGTC 59.257 47.619 0.00 0.00 0.00 4.02
2080 2125 2.160813 GTGACGGTTGTTGTTCTGTTGT 59.839 45.455 0.00 0.00 0.00 3.32
2083 2128 1.375551 GGTGACGGTTGTTGTTCTGT 58.624 50.000 0.00 0.00 0.00 3.41
2098 2143 0.885879 ACGCTACTGTTCATCGGTGA 59.114 50.000 0.00 0.00 36.91 4.02
2100 2145 2.362736 TCTACGCTACTGTTCATCGGT 58.637 47.619 0.00 0.00 39.26 4.69
2109 2154 3.965292 TCCTTTCGATCTACGCTACTG 57.035 47.619 0.00 0.00 42.26 2.74
2138 2183 4.959631 TCGTCTACGTTCATGTGTTTTC 57.040 40.909 0.00 0.00 40.80 2.29
2151 2196 5.164070 CGGATCTAGTCATAGTTCGTCTACG 60.164 48.000 0.00 0.00 41.45 3.51
2162 2207 4.832823 TGGATTTGCTCGGATCTAGTCATA 59.167 41.667 0.00 0.00 0.00 2.15
2163 2208 3.643320 TGGATTTGCTCGGATCTAGTCAT 59.357 43.478 0.00 0.00 0.00 3.06
2164 2209 3.031013 TGGATTTGCTCGGATCTAGTCA 58.969 45.455 0.00 0.00 0.00 3.41
2168 2213 2.115427 TGGTGGATTTGCTCGGATCTA 58.885 47.619 0.00 0.00 0.00 1.98
2183 2228 1.073763 TGGTGGATCTGTTCTTGGTGG 59.926 52.381 0.00 0.00 0.00 4.61
2186 2231 2.568956 TCTCTGGTGGATCTGTTCTTGG 59.431 50.000 0.00 0.00 0.00 3.61
2200 2245 0.188587 TCTGGAGGTGTGTCTCTGGT 59.811 55.000 0.00 0.00 34.39 4.00
2203 2248 1.528292 GCGTCTGGAGGTGTGTCTCT 61.528 60.000 0.00 0.00 34.39 3.10
2218 2263 1.588404 CGTGTATCATTGGTGAGCGTC 59.412 52.381 0.00 0.00 37.87 5.19
2234 2279 2.166664 GAGATTGGCTTCTCTACCGTGT 59.833 50.000 9.79 0.00 39.27 4.49
2292 2368 1.061411 CCATTGCGACGCATGTCAG 59.939 57.895 25.09 11.40 45.80 3.51
2319 2397 0.385390 AGGGTGCTTGCGAACAAAAG 59.615 50.000 0.00 0.00 34.74 2.27
2366 2446 5.523188 AGAGTCTACGTCTGGTTAGTAATCG 59.477 44.000 0.00 0.00 0.00 3.34
2389 2469 1.531423 ACTGATTCAGTTGGCAGCAG 58.469 50.000 13.61 0.00 42.59 4.24


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

AutoCloner maintained by Alex Coulton.