Multiple sequence alignment - TraesCS6D01G201100

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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 TraesCS6D01G201100 chr6D 100.000 2573 0 0 1 2573 283227177 283224605 0 4752
1 TraesCS6D01G201100 chr6D 98.359 1645 21 3 1 1639 124512877 124514521 0 2883
2 TraesCS6D01G201100 chr7D 98.237 1645 23 5 1 1639 203495352 203496996 0 2872
3 TraesCS6D01G201100 chr7D 98.237 1645 23 3 1 1639 381915331 381916975 0 2872
4 TraesCS6D01G201100 chr7D 98.232 1640 23 3 6 1639 381978404 381976765 0 2863
5 TraesCS6D01G201100 chr4A 97.994 1645 25 6 1 1639 67592133 67593775 0 2848
6 TraesCS6D01G201100 chr5A 97.756 1649 27 4 1 1639 19253506 19251858 0 2832
7 TraesCS6D01G201100 chr4D 97.753 1647 29 4 1 1639 123330821 123332467 0 2830
8 TraesCS6D01G201100 chr7B 97.574 1649 30 6 1 1639 716843197 716841549 0 2815
9 TraesCS6D01G201100 chr7B 97.574 1649 30 6 1 1639 716883438 716881790 0 2815
10 TraesCS6D01G201100 chr7B 97.458 708 13 3 1870 2573 644467024 644466318 0 1203
11 TraesCS6D01G201100 chr1B 97.458 708 12 3 1870 2573 668805581 668806286 0 1203
12 TraesCS6D01G201100 chr1B 97.458 708 12 3 1870 2573 672478741 672478036 0 1203
13 TraesCS6D01G201100 chr3A 97.316 708 13 3 1870 2573 633110834 633110129 0 1197
14 TraesCS6D01G201100 chr2B 97.316 708 12 4 1870 2573 799247551 799246847 0 1195
15 TraesCS6D01G201100 chr2B 97.034 708 15 3 1870 2573 391113256 391113961 0 1186
16 TraesCS6D01G201100 chr1D 97.316 708 12 4 1870 2573 141313556 141314260 0 1195
17 TraesCS6D01G201100 chrUn 97.175 708 14 3 1870 2573 225927833 225927128 0 1192
18 TraesCS6D01G201100 chr7A 97.034 708 15 3 1870 2573 60148707 60149412 0 1186


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 TraesCS6D01G201100 chr6D 283224605 283227177 2572 True 4752 4752 100.000 1 2573 1 chr6D.!!$R1 2572
1 TraesCS6D01G201100 chr6D 124512877 124514521 1644 False 2883 2883 98.359 1 1639 1 chr6D.!!$F1 1638
2 TraesCS6D01G201100 chr7D 203495352 203496996 1644 False 2872 2872 98.237 1 1639 1 chr7D.!!$F1 1638
3 TraesCS6D01G201100 chr7D 381915331 381916975 1644 False 2872 2872 98.237 1 1639 1 chr7D.!!$F2 1638
4 TraesCS6D01G201100 chr7D 381976765 381978404 1639 True 2863 2863 98.232 6 1639 1 chr7D.!!$R1 1633
5 TraesCS6D01G201100 chr4A 67592133 67593775 1642 False 2848 2848 97.994 1 1639 1 chr4A.!!$F1 1638
6 TraesCS6D01G201100 chr5A 19251858 19253506 1648 True 2832 2832 97.756 1 1639 1 chr5A.!!$R1 1638
7 TraesCS6D01G201100 chr4D 123330821 123332467 1646 False 2830 2830 97.753 1 1639 1 chr4D.!!$F1 1638
8 TraesCS6D01G201100 chr7B 716841549 716843197 1648 True 2815 2815 97.574 1 1639 1 chr7B.!!$R2 1638
9 TraesCS6D01G201100 chr7B 716881790 716883438 1648 True 2815 2815 97.574 1 1639 1 chr7B.!!$R3 1638
10 TraesCS6D01G201100 chr7B 644466318 644467024 706 True 1203 1203 97.458 1870 2573 1 chr7B.!!$R1 703
11 TraesCS6D01G201100 chr1B 668805581 668806286 705 False 1203 1203 97.458 1870 2573 1 chr1B.!!$F1 703
12 TraesCS6D01G201100 chr1B 672478036 672478741 705 True 1203 1203 97.458 1870 2573 1 chr1B.!!$R1 703
13 TraesCS6D01G201100 chr3A 633110129 633110834 705 True 1197 1197 97.316 1870 2573 1 chr3A.!!$R1 703
14 TraesCS6D01G201100 chr2B 799246847 799247551 704 True 1195 1195 97.316 1870 2573 1 chr2B.!!$R1 703
15 TraesCS6D01G201100 chr2B 391113256 391113961 705 False 1186 1186 97.034 1870 2573 1 chr2B.!!$F1 703
16 TraesCS6D01G201100 chr1D 141313556 141314260 704 False 1195 1195 97.316 1870 2573 1 chr1D.!!$F1 703
17 TraesCS6D01G201100 chrUn 225927128 225927833 705 True 1192 1192 97.175 1870 2573 1 chrUn.!!$R1 703
18 TraesCS6D01G201100 chr7A 60148707 60149412 705 False 1186 1186 97.034 1870 2573 1 chr7A.!!$F1 703

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
889 900 1.610102 CCAGTCTTCCACTTCTGCCTG 60.61 57.143 0.0 0.0 30.26 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1915 0.773644 CCAGGGCAGGCATTAGGTAT 59.226 55.0 0.0 0.0 0.0 2.73 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
500 507 8.703604 TTTTTCGTTTTGTCAATATCCAACAA 57.296 26.923 0.00 0.00 0.00 2.83
789 796 3.392616 ACCAAGCATCCTGGGTTCTATAG 59.607 47.826 0.00 0.00 43.16 1.31
811 818 3.525537 CCGATTCAACACTAGAGCATGT 58.474 45.455 0.00 0.00 0.00 3.21
877 888 5.760743 GGATCTTTATTGGTAGCCAGTCTTC 59.239 44.000 0.00 0.00 33.81 2.87
889 900 1.610102 CCAGTCTTCCACTTCTGCCTG 60.610 57.143 0.00 0.00 30.26 4.85
937 948 1.677820 CCAACCTAACCGGCGATTTCT 60.678 52.381 9.30 0.00 35.61 2.52
1278 1289 3.462982 TCGTGTACAAACAAGTGCAGAT 58.537 40.909 0.00 0.00 37.36 2.90
1379 1390 5.573219 TGGTGTTTCTTCCATCAATCATCT 58.427 37.500 0.00 0.00 0.00 2.90
1639 1652 8.975295 AGGAAATGCTATTTGCTTCTTAAGAAT 58.025 29.630 18.02 5.98 43.37 2.40
1645 1658 9.407380 TGCTATTTGCTTCTTAAGAATATTCCA 57.593 29.630 18.02 8.09 43.37 3.53
1646 1659 9.670719 GCTATTTGCTTCTTAAGAATATTCCAC 57.329 33.333 18.02 2.41 38.95 4.02
1648 1661 8.593945 ATTTGCTTCTTAAGAATATTCCACCA 57.406 30.769 18.02 3.86 33.01 4.17
1649 1662 7.391148 TTGCTTCTTAAGAATATTCCACCAC 57.609 36.000 18.02 0.30 33.01 4.16
1650 1663 5.885912 TGCTTCTTAAGAATATTCCACCACC 59.114 40.000 18.02 0.00 33.01 4.61
1651 1664 5.007724 GCTTCTTAAGAATATTCCACCACCG 59.992 44.000 18.02 3.52 33.01 4.94
1652 1665 5.943349 TCTTAAGAATATTCCACCACCGA 57.057 39.130 11.92 0.00 0.00 4.69
1653 1666 5.667466 TCTTAAGAATATTCCACCACCGAC 58.333 41.667 11.92 0.00 0.00 4.79
1654 1667 3.992943 AAGAATATTCCACCACCGACA 57.007 42.857 11.92 0.00 0.00 4.35
1655 1668 3.543680 AGAATATTCCACCACCGACAG 57.456 47.619 11.92 0.00 0.00 3.51
1656 1669 3.104512 AGAATATTCCACCACCGACAGA 58.895 45.455 11.92 0.00 0.00 3.41
1657 1670 3.711704 AGAATATTCCACCACCGACAGAT 59.288 43.478 11.92 0.00 0.00 2.90
1658 1671 3.753294 ATATTCCACCACCGACAGATC 57.247 47.619 0.00 0.00 0.00 2.75
1675 1688 7.452630 GACAGATCGAGTAAACAATACCTTC 57.547 40.000 0.00 0.00 0.00 3.46
1676 1689 7.171630 ACAGATCGAGTAAACAATACCTTCT 57.828 36.000 0.00 0.00 0.00 2.85
1677 1690 8.289939 ACAGATCGAGTAAACAATACCTTCTA 57.710 34.615 0.00 0.00 0.00 2.10
1678 1691 8.915036 ACAGATCGAGTAAACAATACCTTCTAT 58.085 33.333 0.00 0.00 0.00 1.98
1679 1692 9.751542 CAGATCGAGTAAACAATACCTTCTATT 57.248 33.333 0.00 0.00 0.00 1.73
1686 1699 9.404848 AGTAAACAATACCTTCTATTTTAGGGC 57.595 33.333 0.00 0.00 35.79 5.19
1687 1700 9.404848 GTAAACAATACCTTCTATTTTAGGGCT 57.595 33.333 0.00 0.00 35.79 5.19
1692 1705 9.668497 CAATACCTTCTATTTTAGGGCTATACC 57.332 37.037 0.00 0.00 35.79 2.73
1693 1706 9.631056 AATACCTTCTATTTTAGGGCTATACCT 57.369 33.333 0.00 0.00 44.75 3.08
1694 1707 7.317722 ACCTTCTATTTTAGGGCTATACCTG 57.682 40.000 0.00 0.00 42.02 4.00
1695 1708 6.850231 ACCTTCTATTTTAGGGCTATACCTGT 59.150 38.462 0.00 0.00 42.02 4.00
1696 1709 8.014859 ACCTTCTATTTTAGGGCTATACCTGTA 58.985 37.037 0.00 0.00 42.02 2.74
1697 1710 8.877195 CCTTCTATTTTAGGGCTATACCTGTAA 58.123 37.037 0.00 0.00 42.02 2.41
1706 1719 9.787435 TTAGGGCTATACCTGTAATTTATTGTG 57.213 33.333 0.00 0.00 42.02 3.33
1707 1720 7.812306 AGGGCTATACCTGTAATTTATTGTGT 58.188 34.615 0.00 0.00 40.04 3.72
1708 1721 8.279361 AGGGCTATACCTGTAATTTATTGTGTT 58.721 33.333 0.00 0.00 40.04 3.32
1709 1722 8.909923 GGGCTATACCTGTAATTTATTGTGTTT 58.090 33.333 0.00 0.00 39.10 2.83
1729 1742 9.868277 TGTGTTTTTGATATTATCCATCAAACC 57.132 29.630 9.39 5.34 46.65 3.27
1730 1743 9.313118 GTGTTTTTGATATTATCCATCAAACCC 57.687 33.333 9.39 5.07 46.65 4.11
1731 1744 9.040259 TGTTTTTGATATTATCCATCAAACCCA 57.960 29.630 9.39 7.06 46.65 4.51
1737 1750 9.519191 TGATATTATCCATCAAACCCATTACTG 57.481 33.333 1.27 0.00 29.55 2.74
1738 1751 9.739276 GATATTATCCATCAAACCCATTACTGA 57.261 33.333 0.00 0.00 0.00 3.41
1739 1752 7.823745 ATTATCCATCAAACCCATTACTGAC 57.176 36.000 0.00 0.00 0.00 3.51
1740 1753 4.649267 TCCATCAAACCCATTACTGACA 57.351 40.909 0.00 0.00 0.00 3.58
1741 1754 4.991776 TCCATCAAACCCATTACTGACAA 58.008 39.130 0.00 0.00 0.00 3.18
1742 1755 4.764823 TCCATCAAACCCATTACTGACAAC 59.235 41.667 0.00 0.00 0.00 3.32
1743 1756 4.082245 CCATCAAACCCATTACTGACAACC 60.082 45.833 0.00 0.00 0.00 3.77
1744 1757 4.171878 TCAAACCCATTACTGACAACCA 57.828 40.909 0.00 0.00 0.00 3.67
1745 1758 4.735369 TCAAACCCATTACTGACAACCAT 58.265 39.130 0.00 0.00 0.00 3.55
1746 1759 4.522405 TCAAACCCATTACTGACAACCATG 59.478 41.667 0.00 0.00 0.00 3.66
1747 1760 3.085952 ACCCATTACTGACAACCATGG 57.914 47.619 11.19 11.19 35.13 3.66
1748 1761 2.378547 ACCCATTACTGACAACCATGGT 59.621 45.455 13.00 13.00 33.73 3.55
1749 1762 3.589735 ACCCATTACTGACAACCATGGTA 59.410 43.478 20.12 0.40 33.73 3.25
1750 1763 3.945285 CCCATTACTGACAACCATGGTAC 59.055 47.826 20.12 13.27 33.73 3.34
1822 1835 2.515926 TCGCAGAGAATATCCACAGC 57.484 50.000 0.00 0.00 0.00 4.40
1823 1836 2.034878 TCGCAGAGAATATCCACAGCT 58.965 47.619 0.00 0.00 0.00 4.24
1824 1837 2.133553 CGCAGAGAATATCCACAGCTG 58.866 52.381 13.48 13.48 0.00 4.24
1825 1838 2.492012 GCAGAGAATATCCACAGCTGG 58.508 52.381 19.93 6.95 39.23 4.85
1826 1839 2.809665 GCAGAGAATATCCACAGCTGGG 60.810 54.545 19.93 15.23 38.25 4.45
1827 1840 2.437281 CAGAGAATATCCACAGCTGGGT 59.563 50.000 19.93 0.61 38.25 4.51
1828 1841 3.118112 CAGAGAATATCCACAGCTGGGTT 60.118 47.826 19.93 13.32 38.25 4.11
1829 1842 4.101585 CAGAGAATATCCACAGCTGGGTTA 59.898 45.833 19.93 14.95 38.25 2.85
1830 1843 4.101741 AGAGAATATCCACAGCTGGGTTAC 59.898 45.833 19.93 2.56 38.25 2.50
1831 1844 3.780294 AGAATATCCACAGCTGGGTTACA 59.220 43.478 19.93 0.00 38.25 2.41
1832 1845 3.560636 ATATCCACAGCTGGGTTACAC 57.439 47.619 19.93 0.00 38.25 2.90
1833 1846 0.328258 ATCCACAGCTGGGTTACACC 59.672 55.000 19.93 0.00 38.25 4.16
1834 1847 1.057275 TCCACAGCTGGGTTACACCA 61.057 55.000 19.93 0.00 41.02 4.17
1835 1848 0.179004 CCACAGCTGGGTTACACCAA 60.179 55.000 19.93 0.00 41.02 3.67
1836 1849 0.951558 CACAGCTGGGTTACACCAAC 59.048 55.000 19.93 0.00 41.02 3.77
1837 1850 0.843984 ACAGCTGGGTTACACCAACT 59.156 50.000 19.93 0.00 41.02 3.16
1838 1851 2.051692 ACAGCTGGGTTACACCAACTA 58.948 47.619 19.93 0.00 41.02 2.24
1839 1852 2.038557 ACAGCTGGGTTACACCAACTAG 59.961 50.000 19.93 0.00 41.02 2.57
1840 1853 2.038557 CAGCTGGGTTACACCAACTAGT 59.961 50.000 5.57 0.00 41.02 2.57
1841 1854 2.709397 AGCTGGGTTACACCAACTAGTT 59.291 45.455 1.12 1.12 41.02 2.24
1842 1855 3.137728 AGCTGGGTTACACCAACTAGTTT 59.862 43.478 5.07 0.00 41.02 2.66
1843 1856 3.252458 GCTGGGTTACACCAACTAGTTTG 59.748 47.826 5.07 5.14 41.02 2.93
1844 1857 4.457466 CTGGGTTACACCAACTAGTTTGT 58.543 43.478 15.40 15.40 41.02 2.83
1845 1858 4.200874 TGGGTTACACCAACTAGTTTGTG 58.799 43.478 28.93 28.93 41.02 3.33
1846 1859 4.080469 TGGGTTACACCAACTAGTTTGTGA 60.080 41.667 34.30 19.53 41.02 3.58
1847 1860 4.274214 GGGTTACACCAACTAGTTTGTGAC 59.726 45.833 34.30 26.68 41.02 3.67
1848 1861 5.121105 GGTTACACCAACTAGTTTGTGACT 58.879 41.667 34.30 21.20 38.15 3.41
1849 1862 6.282930 GGTTACACCAACTAGTTTGTGACTA 58.717 40.000 34.30 20.38 38.15 2.59
1850 1863 6.932960 GGTTACACCAACTAGTTTGTGACTAT 59.067 38.462 34.30 20.37 37.96 2.12
1851 1864 7.095355 GGTTACACCAACTAGTTTGTGACTATG 60.095 40.741 34.30 15.73 37.96 2.23
1852 1865 4.755123 ACACCAACTAGTTTGTGACTATGC 59.245 41.667 34.30 0.00 40.01 3.14
1853 1866 4.997395 CACCAACTAGTTTGTGACTATGCT 59.003 41.667 27.55 0.00 40.01 3.79
1854 1867 6.163476 CACCAACTAGTTTGTGACTATGCTA 58.837 40.000 27.55 0.00 40.01 3.49
1855 1868 6.649141 CACCAACTAGTTTGTGACTATGCTAA 59.351 38.462 27.55 0.00 40.01 3.09
1856 1869 7.334421 CACCAACTAGTTTGTGACTATGCTAAT 59.666 37.037 27.55 0.00 40.01 1.73
1857 1870 7.883311 ACCAACTAGTTTGTGACTATGCTAATT 59.117 33.333 11.31 0.00 40.01 1.40
1858 1871 8.730680 CCAACTAGTTTGTGACTATGCTAATTT 58.269 33.333 5.07 0.00 40.01 1.82
1864 1877 9.243105 AGTTTGTGACTATGCTAATTTATTGGT 57.757 29.630 0.00 0.00 36.65 3.67
1865 1878 9.855021 GTTTGTGACTATGCTAATTTATTGGTT 57.145 29.630 0.00 0.00 0.00 3.67
1867 1880 9.461312 TTGTGACTATGCTAATTTATTGGTTCT 57.539 29.630 0.00 0.00 0.00 3.01
2201 2215 6.243216 TGAATACCAAGGGACCACTATTAC 57.757 41.667 0.00 0.00 0.00 1.89
2211 2225 4.434520 GGACCACTATTACAAGAGAGCAC 58.565 47.826 0.00 0.00 0.00 4.40
2258 2272 0.250553 ACTTTTTGGATGGTCGGCGA 60.251 50.000 4.99 4.99 0.00 5.54
2259 2273 0.878416 CTTTTTGGATGGTCGGCGAA 59.122 50.000 12.92 0.00 0.00 4.70
2408 2425 7.690301 GCAGAGAATGGAGAAGGGAAATATACA 60.690 40.741 0.00 0.00 0.00 2.29
2446 2463 2.039746 TCCGAATGAGAAAGCCTTTGGA 59.960 45.455 0.00 0.00 0.00 3.53
2549 2566 3.470888 CCTACCCGGCCTGACAGG 61.471 72.222 17.83 17.83 38.80 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.727824 AGAATCAGTTAAGGATGTTGTTCG 57.272 37.500 0.00 0.00 0.00 3.95
455 456 8.076178 CGAAAAAGACTTCTAATGTTGTTGGAT 58.924 33.333 0.00 0.00 0.00 3.41
456 457 7.066525 ACGAAAAAGACTTCTAATGTTGTTGGA 59.933 33.333 0.00 0.00 0.00 3.53
457 458 7.193595 ACGAAAAAGACTTCTAATGTTGTTGG 58.806 34.615 0.00 0.00 0.00 3.77
458 459 8.614994 AACGAAAAAGACTTCTAATGTTGTTG 57.385 30.769 0.00 0.00 0.00 3.33
460 461 9.072294 CAAAACGAAAAAGACTTCTAATGTTGT 57.928 29.630 0.00 0.00 0.00 3.32
500 507 4.637534 TCTGGAACGATTACTACGCTAAGT 59.362 41.667 0.00 0.00 0.00 2.24
731 738 0.249489 CTAAACCATCGCTCGGGGAG 60.249 60.000 7.65 0.00 0.00 4.30
789 796 2.010145 TGCTCTAGTGTTGAATCGGC 57.990 50.000 0.00 0.00 0.00 5.54
811 818 4.673968 AGTTATGTATCCAGGATCGGCTA 58.326 43.478 4.75 0.00 0.00 3.93
877 888 0.321122 GAGTGGACAGGCAGAAGTGG 60.321 60.000 0.00 0.00 0.00 4.00
889 900 0.329596 AGAAAGGCATGGGAGTGGAC 59.670 55.000 0.00 0.00 0.00 4.02
923 934 2.289195 ACTTGTCAGAAATCGCCGGTTA 60.289 45.455 1.90 0.00 0.00 2.85
937 948 4.310769 GCTCTAAGCAGAAAGACTTGTCA 58.689 43.478 3.49 0.00 41.89 3.58
1278 1289 4.400251 ACCGGAGATATTCGTGTTACTTCA 59.600 41.667 9.46 0.00 0.00 3.02
1379 1390 6.764379 TCTGTTGATATATGGCGTAAATCCA 58.236 36.000 0.00 0.00 38.09 3.41
1639 1652 1.407618 CGATCTGTCGGTGGTGGAATA 59.592 52.381 0.00 0.00 44.00 1.75
1640 1653 0.175760 CGATCTGTCGGTGGTGGAAT 59.824 55.000 0.00 0.00 44.00 3.01
1641 1654 1.589630 CGATCTGTCGGTGGTGGAA 59.410 57.895 0.00 0.00 44.00 3.53
1642 1655 3.284336 CGATCTGTCGGTGGTGGA 58.716 61.111 0.00 0.00 44.00 4.02
1651 1664 7.259161 AGAAGGTATTGTTTACTCGATCTGTC 58.741 38.462 0.00 0.00 0.00 3.51
1652 1665 7.171630 AGAAGGTATTGTTTACTCGATCTGT 57.828 36.000 0.00 0.00 0.00 3.41
1653 1666 9.751542 AATAGAAGGTATTGTTTACTCGATCTG 57.248 33.333 0.00 0.00 0.00 2.90
1660 1673 9.404848 GCCCTAAAATAGAAGGTATTGTTTACT 57.595 33.333 0.00 0.00 0.00 2.24
1661 1674 9.404848 AGCCCTAAAATAGAAGGTATTGTTTAC 57.595 33.333 0.00 0.00 0.00 2.01
1666 1679 9.668497 GGTATAGCCCTAAAATAGAAGGTATTG 57.332 37.037 0.00 0.00 30.57 1.90
1667 1680 9.631056 AGGTATAGCCCTAAAATAGAAGGTATT 57.369 33.333 0.00 0.00 38.26 1.89
1668 1681 9.047947 CAGGTATAGCCCTAAAATAGAAGGTAT 57.952 37.037 0.00 0.00 38.26 2.73
1669 1682 8.014859 ACAGGTATAGCCCTAAAATAGAAGGTA 58.985 37.037 0.00 0.00 38.26 3.08
1670 1683 6.850231 ACAGGTATAGCCCTAAAATAGAAGGT 59.150 38.462 0.00 0.00 38.26 3.50
1671 1684 7.317722 ACAGGTATAGCCCTAAAATAGAAGG 57.682 40.000 0.00 0.00 38.26 3.46
1680 1693 9.787435 CACAATAAATTACAGGTATAGCCCTAA 57.213 33.333 0.00 0.00 38.26 2.69
1681 1694 8.940982 ACACAATAAATTACAGGTATAGCCCTA 58.059 33.333 0.00 0.00 38.26 3.53
1682 1695 7.812306 ACACAATAAATTACAGGTATAGCCCT 58.188 34.615 0.00 0.00 38.26 5.19
1683 1696 8.459911 AACACAATAAATTACAGGTATAGCCC 57.540 34.615 0.00 0.00 38.26 5.19
1711 1724 9.519191 CAGTAATGGGTTTGATGGATAATATCA 57.481 33.333 2.41 0.00 33.00 2.15
1712 1725 9.739276 TCAGTAATGGGTTTGATGGATAATATC 57.261 33.333 0.00 0.00 0.00 1.63
1713 1726 9.520515 GTCAGTAATGGGTTTGATGGATAATAT 57.479 33.333 0.00 0.00 0.00 1.28
1714 1727 8.498575 TGTCAGTAATGGGTTTGATGGATAATA 58.501 33.333 0.00 0.00 0.00 0.98
1715 1728 7.353525 TGTCAGTAATGGGTTTGATGGATAAT 58.646 34.615 0.00 0.00 0.00 1.28
1716 1729 6.726379 TGTCAGTAATGGGTTTGATGGATAA 58.274 36.000 0.00 0.00 0.00 1.75
1717 1730 6.320434 TGTCAGTAATGGGTTTGATGGATA 57.680 37.500 0.00 0.00 0.00 2.59
1718 1731 5.191727 TGTCAGTAATGGGTTTGATGGAT 57.808 39.130 0.00 0.00 0.00 3.41
1719 1732 4.649267 TGTCAGTAATGGGTTTGATGGA 57.351 40.909 0.00 0.00 0.00 3.41
1720 1733 4.082245 GGTTGTCAGTAATGGGTTTGATGG 60.082 45.833 0.00 0.00 0.00 3.51
1721 1734 4.522405 TGGTTGTCAGTAATGGGTTTGATG 59.478 41.667 0.00 0.00 0.00 3.07
1722 1735 4.735369 TGGTTGTCAGTAATGGGTTTGAT 58.265 39.130 0.00 0.00 0.00 2.57
1723 1736 4.171878 TGGTTGTCAGTAATGGGTTTGA 57.828 40.909 0.00 0.00 0.00 2.69
1724 1737 4.321899 CCATGGTTGTCAGTAATGGGTTTG 60.322 45.833 2.57 0.00 35.22 2.93
1725 1738 3.831911 CCATGGTTGTCAGTAATGGGTTT 59.168 43.478 2.57 0.00 35.22 3.27
1726 1739 3.181423 ACCATGGTTGTCAGTAATGGGTT 60.181 43.478 13.00 0.00 41.76 4.11
1727 1740 2.378547 ACCATGGTTGTCAGTAATGGGT 59.621 45.455 13.00 0.00 41.76 4.51
1728 1741 3.085952 ACCATGGTTGTCAGTAATGGG 57.914 47.619 13.00 0.00 41.76 4.00
1729 1742 4.394920 GTGTACCATGGTTGTCAGTAATGG 59.605 45.833 25.38 7.75 42.88 3.16
1730 1743 5.245531 AGTGTACCATGGTTGTCAGTAATG 58.754 41.667 25.38 0.00 0.00 1.90
1731 1744 5.499004 AGTGTACCATGGTTGTCAGTAAT 57.501 39.130 25.38 0.00 0.00 1.89
1732 1745 4.967084 AGTGTACCATGGTTGTCAGTAA 57.033 40.909 25.38 0.00 0.00 2.24
1733 1746 5.081728 ACTAGTGTACCATGGTTGTCAGTA 58.918 41.667 25.38 22.07 0.00 2.74
1734 1747 3.901844 ACTAGTGTACCATGGTTGTCAGT 59.098 43.478 25.38 22.13 0.00 3.41
1735 1748 4.537135 ACTAGTGTACCATGGTTGTCAG 57.463 45.455 25.38 15.83 0.00 3.51
1736 1749 4.967084 AACTAGTGTACCATGGTTGTCA 57.033 40.909 25.38 16.80 0.00 3.58
1737 1750 6.877322 ACATAAACTAGTGTACCATGGTTGTC 59.123 38.462 25.38 14.37 0.00 3.18
1738 1751 6.775708 ACATAAACTAGTGTACCATGGTTGT 58.224 36.000 25.38 13.53 0.00 3.32
1739 1752 8.780846 TTACATAAACTAGTGTACCATGGTTG 57.219 34.615 25.38 12.83 31.05 3.77
1740 1753 9.609346 GATTACATAAACTAGTGTACCATGGTT 57.391 33.333 25.38 7.46 31.05 3.67
1741 1754 8.764558 TGATTACATAAACTAGTGTACCATGGT 58.235 33.333 23.55 23.55 31.05 3.55
1742 1755 9.607988 TTGATTACATAAACTAGTGTACCATGG 57.392 33.333 11.19 11.19 31.05 3.66
1800 1813 4.281941 AGCTGTGGATATTCTCTGCGAATA 59.718 41.667 8.70 2.86 45.83 1.75
1801 1814 3.070734 AGCTGTGGATATTCTCTGCGAAT 59.929 43.478 8.70 0.00 44.35 3.34
1802 1815 2.432146 AGCTGTGGATATTCTCTGCGAA 59.568 45.455 8.70 0.00 35.78 4.70
1803 1816 2.034878 AGCTGTGGATATTCTCTGCGA 58.965 47.619 8.70 0.00 0.00 5.10
1804 1817 2.133553 CAGCTGTGGATATTCTCTGCG 58.866 52.381 5.25 2.39 0.00 5.18
1826 1839 7.570691 GCATAGTCACAAACTAGTTGGTGTAAC 60.571 40.741 32.58 26.10 43.64 2.50
1827 1840 6.425721 GCATAGTCACAAACTAGTTGGTGTAA 59.574 38.462 32.58 22.50 43.64 2.41
1828 1841 5.929992 GCATAGTCACAAACTAGTTGGTGTA 59.070 40.000 32.58 22.83 43.64 2.90
1829 1842 4.755123 GCATAGTCACAAACTAGTTGGTGT 59.245 41.667 32.58 21.69 43.64 4.16
1830 1843 4.997395 AGCATAGTCACAAACTAGTTGGTG 59.003 41.667 29.98 29.98 43.64 4.17
1831 1844 5.228945 AGCATAGTCACAAACTAGTTGGT 57.771 39.130 10.02 10.02 43.64 3.67
1832 1845 7.849804 ATTAGCATAGTCACAAACTAGTTGG 57.150 36.000 9.34 8.92 43.64 3.77
1838 1851 9.243105 ACCAATAAATTAGCATAGTCACAAACT 57.757 29.630 0.00 0.00 42.33 2.66
1839 1852 9.855021 AACCAATAAATTAGCATAGTCACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
1841 1854 9.461312 AGAACCAATAAATTAGCATAGTCACAA 57.539 29.630 0.00 0.00 0.00 3.33
1902 1915 0.773644 CCAGGGCAGGCATTAGGTAT 59.226 55.000 0.00 0.00 0.00 2.73
1910 1923 0.925558 TTTCATATCCAGGGCAGGCA 59.074 50.000 0.00 0.00 0.00 4.75
2201 2215 6.261118 GGCATTTACTTATTGTGCTCTCTTG 58.739 40.000 0.00 0.00 36.15 3.02
2211 2225 2.353269 TGGCGTCGGCATTTACTTATTG 59.647 45.455 18.58 0.00 42.47 1.90
2258 2272 3.877508 GCTGGTTATCGAGTTTATGGCTT 59.122 43.478 0.00 0.00 0.00 4.35
2259 2273 3.118408 TGCTGGTTATCGAGTTTATGGCT 60.118 43.478 0.00 0.00 0.00 4.75
2446 2463 7.075674 CAAAAACAGATTTGCAAGGAGTTTT 57.924 32.000 19.38 19.38 38.79 2.43
2549 2566 6.292389 CGGGATCAGATCATTCAACTAAAC 57.708 41.667 12.66 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.