Multiple sequence alignment - TraesCS1B01G350400

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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 TraesCS1B01G350400 chr1B 100.000 2545 0 0 1 2545 581103657 581106201 0.000000e+00 4700
1 TraesCS1B01G350400 chr1B 82.447 188 30 1 1286 1473 581116822 581117006 7.290000e-36 161
2 TraesCS1B01G350400 chr1A 91.961 933 49 8 696 1610 527786264 527787188 0.000000e+00 1284
3 TraesCS1B01G350400 chr1A 90.491 936 62 8 696 1606 527757433 527758366 0.000000e+00 1210
4 TraesCS1B01G350400 chr1A 81.622 185 31 1 1289 1473 527885871 527886052 1.580000e-32 150
5 TraesCS1B01G350400 chr3A 98.711 698 8 1 1849 2545 126088586 126087889 0.000000e+00 1238
6 TraesCS1B01G350400 chr3B 93.211 707 34 10 1850 2545 15048295 15047592 0.000000e+00 1027
7 TraesCS1B01G350400 chr3B 92.469 717 39 9 1840 2545 733252962 733253674 0.000000e+00 1011
8 TraesCS1B01G350400 chr3B 90.895 648 56 2 40 686 676620613 676621258 0.000000e+00 867
9 TraesCS1B01G350400 chr4D 91.867 664 53 1 24 686 485527967 485528630 0.000000e+00 926
10 TraesCS1B01G350400 chr3D 92.085 657 51 1 31 686 148714129 148713473 0.000000e+00 924
11 TraesCS1B01G350400 chr3D 87.106 349 26 10 1849 2179 540885769 540885422 6.650000e-101 377
12 TraesCS1B01G350400 chr3D 86.084 309 26 9 1849 2142 607901316 607901010 1.470000e-82 316
13 TraesCS1B01G350400 chr3D 95.122 164 6 2 2382 2545 540884728 540884567 9.030000e-65 257
14 TraesCS1B01G350400 chr3D 95.122 164 6 2 2382 2545 607900520 607900359 9.030000e-65 257
15 TraesCS1B01G350400 chr3D 86.301 146 11 7 2045 2182 607901044 607900900 1.580000e-32 150
16 TraesCS1B01G350400 chr6D 91.793 658 41 3 30 686 296998881 296998236 0.000000e+00 904
17 TraesCS1B01G350400 chr2D 90.729 658 59 2 30 686 203073115 203072459 0.000000e+00 876
18 TraesCS1B01G350400 chr5A 90.563 657 59 3 30 683 148499052 148498396 0.000000e+00 867
19 TraesCS1B01G350400 chr5D 90.909 649 49 6 38 685 274527301 274526662 0.000000e+00 863
20 TraesCS1B01G350400 chr1D 93.401 591 26 8 696 1279 430310524 430311108 0.000000e+00 863
21 TraesCS1B01G350400 chr1D 86.742 445 43 12 1319 1748 430311108 430311551 4.920000e-132 481
22 TraesCS1B01G350400 chr1D 87.679 349 25 9 1849 2179 475239472 475239820 8.540000e-105 390
23 TraesCS1B01G350400 chr1D 83.511 188 28 1 1286 1473 430322222 430322406 3.370000e-39 172
24 TraesCS1B01G350400 chr2B 89.255 698 62 11 1849 2537 542350840 542351533 0.000000e+00 861
25 TraesCS1B01G350400 chr2B 90.226 665 54 7 30 686 707168278 707167617 0.000000e+00 857
26 TraesCS1B01G350400 chr2B 92.704 233 14 2 1851 2080 663917250 663917018 1.460000e-87 333
27 TraesCS1B01G350400 chr2B 81.862 419 49 15 2122 2537 663916749 663916355 6.790000e-86 327
28 TraesCS1B01G350400 chr4A 90.122 658 64 1 30 686 69264543 69263886 0.000000e+00 854
29 TraesCS1B01G350400 chr7D 95.200 375 15 2 2174 2545 1141011 1141385 7.840000e-165 590
30 TraesCS1B01G350400 chr5B 82.446 507 56 19 1848 2334 489308054 489308547 1.820000e-111 412
31 TraesCS1B01G350400 chr7B 93.210 162 7 4 2386 2545 587919081 587919240 4.230000e-58 235


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 TraesCS1B01G350400 chr1B 581103657 581106201 2544 False 4700 4700 100.0000 1 2545 1 chr1B.!!$F1 2544
1 TraesCS1B01G350400 chr1A 527786264 527787188 924 False 1284 1284 91.9610 696 1610 1 chr1A.!!$F2 914
2 TraesCS1B01G350400 chr1A 527757433 527758366 933 False 1210 1210 90.4910 696 1606 1 chr1A.!!$F1 910
3 TraesCS1B01G350400 chr3A 126087889 126088586 697 True 1238 1238 98.7110 1849 2545 1 chr3A.!!$R1 696
4 TraesCS1B01G350400 chr3B 15047592 15048295 703 True 1027 1027 93.2110 1850 2545 1 chr3B.!!$R1 695
5 TraesCS1B01G350400 chr3B 733252962 733253674 712 False 1011 1011 92.4690 1840 2545 1 chr3B.!!$F2 705
6 TraesCS1B01G350400 chr3B 676620613 676621258 645 False 867 867 90.8950 40 686 1 chr3B.!!$F1 646
7 TraesCS1B01G350400 chr4D 485527967 485528630 663 False 926 926 91.8670 24 686 1 chr4D.!!$F1 662
8 TraesCS1B01G350400 chr3D 148713473 148714129 656 True 924 924 92.0850 31 686 1 chr3D.!!$R1 655
9 TraesCS1B01G350400 chr3D 540884567 540885769 1202 True 317 377 91.1140 1849 2545 2 chr3D.!!$R2 696
10 TraesCS1B01G350400 chr3D 607900359 607901316 957 True 241 316 89.1690 1849 2545 3 chr3D.!!$R3 696
11 TraesCS1B01G350400 chr6D 296998236 296998881 645 True 904 904 91.7930 30 686 1 chr6D.!!$R1 656
12 TraesCS1B01G350400 chr2D 203072459 203073115 656 True 876 876 90.7290 30 686 1 chr2D.!!$R1 656
13 TraesCS1B01G350400 chr5A 148498396 148499052 656 True 867 867 90.5630 30 683 1 chr5A.!!$R1 653
14 TraesCS1B01G350400 chr5D 274526662 274527301 639 True 863 863 90.9090 38 685 1 chr5D.!!$R1 647
15 TraesCS1B01G350400 chr1D 430310524 430311551 1027 False 672 863 90.0715 696 1748 2 chr1D.!!$F3 1052
16 TraesCS1B01G350400 chr2B 542350840 542351533 693 False 861 861 89.2550 1849 2537 1 chr2B.!!$F1 688
17 TraesCS1B01G350400 chr2B 707167617 707168278 661 True 857 857 90.2260 30 686 1 chr2B.!!$R1 656
18 TraesCS1B01G350400 chr2B 663916355 663917250 895 True 330 333 87.2830 1851 2537 2 chr2B.!!$R2 686
19 TraesCS1B01G350400 chr4A 69263886 69264543 657 True 854 854 90.1220 30 686 1 chr4A.!!$R1 656

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
686 696 0.102481 GATGCCATCGTCGTACCACT 59.898 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1876 0.03716 ACACCCCGCCGTTTCTAATT 59.963 50.0 0.0 0.0 0.0 1.4 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 3.059982 TCAGGTCCTGCGAAGTGG 58.940 61.111 14.64 0.00 0.00 4.00
18 19 1.533033 TCAGGTCCTGCGAAGTGGA 60.533 57.895 14.64 0.00 0.00 4.02
19 20 1.374758 CAGGTCCTGCGAAGTGGAC 60.375 63.158 5.79 3.77 46.51 4.02
21 22 2.432628 GTCCTGCGAAGTGGACGG 60.433 66.667 0.00 0.00 41.39 4.79
22 23 3.691342 TCCTGCGAAGTGGACGGG 61.691 66.667 0.00 0.00 0.00 5.28
23 24 4.003788 CCTGCGAAGTGGACGGGT 62.004 66.667 0.00 0.00 0.00 5.28
24 25 2.432628 CTGCGAAGTGGACGGGTC 60.433 66.667 0.00 0.00 0.00 4.46
25 26 4.351938 TGCGAAGTGGACGGGTCG 62.352 66.667 0.00 0.00 36.59 4.79
110 117 0.171455 CTCCTCGTCCTCTTGAACCG 59.829 60.000 0.00 0.00 0.00 4.44
383 392 3.280295 GTTCTCACTATCTCGAGTCCCA 58.720 50.000 13.13 0.00 0.00 4.37
540 549 2.334006 ACTCTGTTCATGAGGGGTCT 57.666 50.000 0.00 0.00 35.98 3.85
651 661 2.144078 TCGTTCACTGGGGCCTCAA 61.144 57.895 6.84 0.00 0.00 3.02
686 696 0.102481 GATGCCATCGTCGTACCACT 59.898 55.000 0.00 0.00 0.00 4.00
687 697 0.102481 ATGCCATCGTCGTACCACTC 59.898 55.000 0.00 0.00 0.00 3.51
688 698 1.585521 GCCATCGTCGTACCACTCG 60.586 63.158 0.00 0.00 0.00 4.18
689 699 1.063649 CCATCGTCGTACCACTCGG 59.936 63.158 0.00 0.00 38.77 4.63
690 700 1.063649 CATCGTCGTACCACTCGGG 59.936 63.158 0.00 0.00 44.81 5.14
691 701 2.768492 ATCGTCGTACCACTCGGGC 61.768 63.158 0.00 0.00 42.05 6.13
692 702 4.487412 CGTCGTACCACTCGGGCC 62.487 72.222 0.00 0.00 42.05 5.80
693 703 3.066814 GTCGTACCACTCGGGCCT 61.067 66.667 0.84 0.00 42.05 5.19
694 704 2.753043 TCGTACCACTCGGGCCTC 60.753 66.667 0.84 0.00 42.05 4.70
1063 1077 1.094073 CCCATGGCGCTTCTCAAGAG 61.094 60.000 6.09 0.00 0.00 2.85
1072 1086 1.271054 GCTTCTCAAGAGCAACCCAGA 60.271 52.381 0.00 0.00 0.00 3.86
1087 1101 1.402787 CCAGAGGTTTTGTGCTTGGT 58.597 50.000 0.00 0.00 0.00 3.67
1109 1123 1.869767 GCCCTTCTTGTGATATCTGCG 59.130 52.381 3.98 0.00 0.00 5.18
1142 1156 0.180406 GTGATGCATCCTACGGGGTT 59.820 55.000 23.67 0.00 36.25 4.11
1201 1216 3.931907 TTGCTCTATACAATGGCCTGT 57.068 42.857 3.32 3.03 0.00 4.00
1252 1267 5.163814 GCAAGTGATTGTGTTATGTCTCTCC 60.164 44.000 0.00 0.00 0.00 3.71
1398 1433 7.069208 TCAGTGTCAGATTTACTGCAGAGATAT 59.931 37.037 23.35 8.31 45.38 1.63
1414 1449 6.757010 GCAGAGATATCGGTTTTGTCTTAGAA 59.243 38.462 0.00 0.00 0.00 2.10
1504 1543 4.675114 GCGTGTGAATTCGTGAAAGAAAAT 59.325 37.500 0.04 0.00 33.43 1.82
1528 1567 7.834068 TCTTTTTCTGTATGAGAGATTTCGG 57.166 36.000 0.00 0.00 30.18 4.30
1574 1613 7.263496 TGTTTGATCTGTGTCTATCATCAGAG 58.737 38.462 0.00 0.00 37.49 3.35
1581 1620 7.286313 TCTGTGTCTATCATCAGAGTGACTAT 58.714 38.462 0.00 0.00 33.11 2.12
1589 1628 1.476891 TCAGAGTGACTATTCGGGTGC 59.523 52.381 0.00 0.00 0.00 5.01
1606 1645 2.646175 GCTCCCCGACAGTGCTACA 61.646 63.158 0.00 0.00 0.00 2.74
1607 1646 1.513158 CTCCCCGACAGTGCTACAG 59.487 63.158 0.00 0.00 0.00 2.74
1608 1647 2.125512 CCCCGACAGTGCTACAGC 60.126 66.667 0.00 0.00 42.50 4.40
1632 1685 0.108138 AATGGCTGTGGAGTAGTCGC 60.108 55.000 0.00 0.00 0.00 5.19
1633 1686 0.972983 ATGGCTGTGGAGTAGTCGCT 60.973 55.000 0.00 0.00 0.00 4.93
1638 1691 2.298610 CTGTGGAGTAGTCGCTATCCA 58.701 52.381 10.73 10.73 39.50 3.41
1641 1694 4.072839 TGTGGAGTAGTCGCTATCCATAG 58.927 47.826 14.51 0.00 43.42 2.23
1653 1706 8.351461 AGTCGCTATCCATAGAAAAACTAGTAC 58.649 37.037 0.00 0.00 34.35 2.73
1661 1714 8.114102 TCCATAGAAAAACTAGTACTCTCTCCA 58.886 37.037 0.00 0.00 34.35 3.86
1668 1721 4.993028 ACTAGTACTCTCTCCATCCCATC 58.007 47.826 0.00 0.00 0.00 3.51
1698 1751 8.707796 AAGAGTTCTTATATTATGAGACGGGA 57.292 34.615 0.00 0.00 33.79 5.14
1699 1752 8.343168 AGAGTTCTTATATTATGAGACGGGAG 57.657 38.462 0.00 0.00 0.00 4.30
1701 1754 7.239438 AGTTCTTATATTATGAGACGGGAGGA 58.761 38.462 0.00 0.00 0.00 3.71
1702 1755 7.728981 AGTTCTTATATTATGAGACGGGAGGAA 59.271 37.037 0.00 0.00 0.00 3.36
1718 1773 6.040616 ACGGGAGGAATACTACATAGAGTTTG 59.959 42.308 0.00 0.00 0.00 2.93
1719 1774 6.224584 GGGAGGAATACTACATAGAGTTTGC 58.775 44.000 0.00 0.00 0.00 3.68
1722 1777 7.386299 GGAGGAATACTACATAGAGTTTGCATG 59.614 40.741 0.00 0.00 0.00 4.06
1723 1778 8.023021 AGGAATACTACATAGAGTTTGCATGA 57.977 34.615 0.00 0.00 0.00 3.07
1743 1798 9.104965 TGCATGAAACTTACACATAGGTAATAC 57.895 33.333 0.00 0.00 33.13 1.89
1751 1806 9.745880 ACTTACACATAGGTAATACGATTTCTG 57.254 33.333 0.00 0.00 33.13 3.02
1752 1807 9.961265 CTTACACATAGGTAATACGATTTCTGA 57.039 33.333 0.00 0.00 33.13 3.27
1755 1810 9.909644 ACACATAGGTAATACGATTTCTGATAC 57.090 33.333 0.00 0.00 0.00 2.24
1758 1813 9.790389 CATAGGTAATACGATTTCTGATACTCC 57.210 37.037 0.00 0.00 0.00 3.85
1759 1814 9.756571 ATAGGTAATACGATTTCTGATACTCCT 57.243 33.333 0.00 0.00 0.00 3.69
1761 1816 9.012161 AGGTAATACGATTTCTGATACTCCTAC 57.988 37.037 0.00 0.00 0.00 3.18
1762 1817 8.790718 GGTAATACGATTTCTGATACTCCTACA 58.209 37.037 0.00 0.00 0.00 2.74
1767 1822 8.234136 ACGATTTCTGATACTCCTACAATACA 57.766 34.615 0.00 0.00 0.00 2.29
1768 1823 8.136165 ACGATTTCTGATACTCCTACAATACAC 58.864 37.037 0.00 0.00 0.00 2.90
1769 1824 8.353684 CGATTTCTGATACTCCTACAATACACT 58.646 37.037 0.00 0.00 0.00 3.55
1796 1851 4.219033 GTGATTGACACTTTTTAGGTGCG 58.781 43.478 0.00 0.00 45.13 5.34
1797 1852 4.024387 GTGATTGACACTTTTTAGGTGCGA 60.024 41.667 0.00 0.00 45.13 5.10
1798 1853 4.759693 TGATTGACACTTTTTAGGTGCGAT 59.240 37.500 0.00 0.00 38.14 4.58
1799 1854 4.742438 TTGACACTTTTTAGGTGCGATC 57.258 40.909 0.00 0.00 38.14 3.69
1800 1855 3.734463 TGACACTTTTTAGGTGCGATCA 58.266 40.909 0.00 0.00 38.14 2.92
1801 1856 3.745975 TGACACTTTTTAGGTGCGATCAG 59.254 43.478 0.00 0.00 38.14 2.90
1802 1857 3.074412 ACACTTTTTAGGTGCGATCAGG 58.926 45.455 0.00 0.00 38.14 3.86
1803 1858 2.084546 ACTTTTTAGGTGCGATCAGGC 58.915 47.619 0.00 0.00 0.00 4.85
1804 1859 1.401905 CTTTTTAGGTGCGATCAGGCC 59.598 52.381 0.00 0.00 0.00 5.19
1805 1860 0.326595 TTTTAGGTGCGATCAGGCCA 59.673 50.000 5.01 0.00 0.00 5.36
1806 1861 0.546122 TTTAGGTGCGATCAGGCCAT 59.454 50.000 5.01 0.00 0.00 4.40
1807 1862 0.179048 TTAGGTGCGATCAGGCCATG 60.179 55.000 5.01 0.00 0.00 3.66
1808 1863 1.337384 TAGGTGCGATCAGGCCATGT 61.337 55.000 5.01 0.00 0.00 3.21
1809 1864 1.750399 GGTGCGATCAGGCCATGTT 60.750 57.895 5.01 0.00 0.00 2.71
1810 1865 1.315257 GGTGCGATCAGGCCATGTTT 61.315 55.000 5.01 0.00 0.00 2.83
1811 1866 0.527565 GTGCGATCAGGCCATGTTTT 59.472 50.000 5.01 0.00 0.00 2.43
1812 1867 1.067635 GTGCGATCAGGCCATGTTTTT 60.068 47.619 5.01 0.00 0.00 1.94
1836 1891 1.856597 CGTAGAATTAGAAACGGCGGG 59.143 52.381 13.24 0.00 0.00 6.13
1837 1892 2.207590 GTAGAATTAGAAACGGCGGGG 58.792 52.381 13.24 0.00 0.00 5.73
1838 1893 0.616891 AGAATTAGAAACGGCGGGGT 59.383 50.000 13.24 0.00 0.00 4.95
1839 1894 0.730840 GAATTAGAAACGGCGGGGTG 59.269 55.000 13.24 0.00 0.00 4.61
1840 1895 0.037160 AATTAGAAACGGCGGGGTGT 59.963 50.000 13.24 0.00 0.00 4.16
1841 1896 0.037160 ATTAGAAACGGCGGGGTGTT 59.963 50.000 13.24 0.00 0.00 3.32
1842 1897 0.683973 TTAGAAACGGCGGGGTGTTA 59.316 50.000 13.24 0.00 0.00 2.41
1843 1898 0.247185 TAGAAACGGCGGGGTGTTAG 59.753 55.000 13.24 0.00 0.00 2.34
1844 1899 1.004679 GAAACGGCGGGGTGTTAGA 60.005 57.895 13.24 0.00 0.00 2.10
1845 1900 0.392060 GAAACGGCGGGGTGTTAGAT 60.392 55.000 13.24 0.00 0.00 1.98
1846 1901 0.037160 AAACGGCGGGGTGTTAGATT 59.963 50.000 13.24 0.00 0.00 2.40
1847 1902 0.675522 AACGGCGGGGTGTTAGATTG 60.676 55.000 13.24 0.00 0.00 2.67
1902 1957 1.504900 GTTCGGCGAAATGAACCCC 59.495 57.895 25.48 5.32 38.79 4.95
1920 1975 0.322187 CCCAAGTCGAAATCCCGGTT 60.322 55.000 0.00 0.00 0.00 4.44
2225 2897 1.058404 GACAAGACCTACGTTGCGTC 58.942 55.000 0.00 1.74 41.54 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.060866 GTCCACTTCGCAGGACCT 58.939 61.111 0.00 0.00 46.79 3.85
6 7 3.934391 GACCCGTCCACTTCGCAGG 62.934 68.421 0.00 0.00 0.00 4.85
7 8 2.432628 GACCCGTCCACTTCGCAG 60.433 66.667 0.00 0.00 0.00 5.18
8 9 4.351938 CGACCCGTCCACTTCGCA 62.352 66.667 0.00 0.00 0.00 5.10
20 21 0.883370 AAAGAAGAACACGGCGACCC 60.883 55.000 16.62 0.00 0.00 4.46
21 22 0.942252 AAAAGAAGAACACGGCGACC 59.058 50.000 16.62 0.00 0.00 4.79
22 23 1.920272 GCAAAAGAAGAACACGGCGAC 60.920 52.381 16.62 1.68 0.00 5.19
23 24 0.306533 GCAAAAGAAGAACACGGCGA 59.693 50.000 16.62 0.00 0.00 5.54
24 25 0.307760 AGCAAAAGAAGAACACGGCG 59.692 50.000 4.80 4.80 0.00 6.46
25 26 1.335051 GGAGCAAAAGAAGAACACGGC 60.335 52.381 0.00 0.00 0.00 5.68
26 27 1.266989 GGGAGCAAAAGAAGAACACGG 59.733 52.381 0.00 0.00 0.00 4.94
27 28 2.222027 AGGGAGCAAAAGAAGAACACG 58.778 47.619 0.00 0.00 0.00 4.49
28 29 3.481453 AGAGGGAGCAAAAGAAGAACAC 58.519 45.455 0.00 0.00 0.00 3.32
110 117 3.127352 CTGCCTCGTCGTCTAGGGC 62.127 68.421 2.63 0.00 42.73 5.19
383 392 3.553096 CGGATGCGCTAAGTTCTATCCTT 60.553 47.826 9.73 0.00 33.58 3.36
515 524 5.091552 ACCCCTCATGAACAGAGTAGTAAA 58.908 41.667 0.00 0.00 0.00 2.01
520 529 3.099905 CAGACCCCTCATGAACAGAGTA 58.900 50.000 0.00 0.00 0.00 2.59
540 549 4.563140 AAAGGCGGATTTAAGGAGTACA 57.437 40.909 0.00 0.00 0.00 2.90
637 647 4.020617 CGCTTGAGGCCCCAGTGA 62.021 66.667 0.00 0.00 37.74 3.41
686 696 2.504175 AGTATTTTAGCTTGAGGCCCGA 59.496 45.455 0.00 0.00 43.05 5.14
687 697 2.919228 AGTATTTTAGCTTGAGGCCCG 58.081 47.619 0.00 0.00 43.05 6.13
688 698 6.769134 TTTTAGTATTTTAGCTTGAGGCCC 57.231 37.500 0.00 0.00 43.05 5.80
689 699 8.466798 TCATTTTTAGTATTTTAGCTTGAGGCC 58.533 33.333 0.00 0.00 43.05 5.19
690 700 9.290483 GTCATTTTTAGTATTTTAGCTTGAGGC 57.710 33.333 0.00 0.00 42.19 4.70
691 701 9.490663 CGTCATTTTTAGTATTTTAGCTTGAGG 57.509 33.333 0.00 0.00 0.00 3.86
692 702 9.000018 GCGTCATTTTTAGTATTTTAGCTTGAG 58.000 33.333 0.00 0.00 0.00 3.02
693 703 8.508062 TGCGTCATTTTTAGTATTTTAGCTTGA 58.492 29.630 0.00 0.00 0.00 3.02
694 704 8.667987 TGCGTCATTTTTAGTATTTTAGCTTG 57.332 30.769 0.00 0.00 0.00 4.01
729 739 0.690762 AGACTAACCACCAATGCCGT 59.309 50.000 0.00 0.00 0.00 5.68
992 1004 4.107622 CGTTGTACTTCCGGTCGATTTAT 58.892 43.478 0.00 0.00 0.00 1.40
1072 1086 1.685355 GGCCACCAAGCACAAAACCT 61.685 55.000 0.00 0.00 0.00 3.50
1087 1101 2.421952 GCAGATATCACAAGAAGGGCCA 60.422 50.000 6.18 0.00 0.00 5.36
1109 1123 5.180868 GGATGCATCACATGATAAGAAGGTC 59.819 44.000 27.25 0.69 39.84 3.85
1194 1209 2.865079 TCGGAAAAATGTTACAGGCCA 58.135 42.857 5.01 0.00 0.00 5.36
1201 1216 9.703892 ATTTGTTTGATCATCGGAAAAATGTTA 57.296 25.926 0.00 0.00 0.00 2.41
1398 1433 4.641094 TGCCTTTTTCTAAGACAAAACCGA 59.359 37.500 0.00 0.00 0.00 4.69
1504 1543 7.611770 TCCGAAATCTCTCATACAGAAAAAGA 58.388 34.615 0.00 0.00 0.00 2.52
1559 1598 7.075121 CGAATAGTCACTCTGATGATAGACAC 58.925 42.308 0.00 0.00 32.09 3.67
1574 1613 3.364277 GGAGCACCCGAATAGTCAC 57.636 57.895 0.00 0.00 0.00 3.67
1589 1628 1.513158 CTGTAGCACTGTCGGGGAG 59.487 63.158 0.00 0.00 0.00 4.30
1606 1645 1.272313 ACTCCACAGCCATTGATTGCT 60.272 47.619 0.00 0.00 38.67 3.91
1607 1646 1.180029 ACTCCACAGCCATTGATTGC 58.820 50.000 0.00 0.00 0.00 3.56
1608 1647 3.614092 ACTACTCCACAGCCATTGATTG 58.386 45.455 0.00 0.00 0.00 2.67
1609 1648 3.679917 CGACTACTCCACAGCCATTGATT 60.680 47.826 0.00 0.00 0.00 2.57
1610 1649 2.159043 CGACTACTCCACAGCCATTGAT 60.159 50.000 0.00 0.00 0.00 2.57
1611 1650 1.204704 CGACTACTCCACAGCCATTGA 59.795 52.381 0.00 0.00 0.00 2.57
1615 1654 0.323087 TAGCGACTACTCCACAGCCA 60.323 55.000 0.00 0.00 0.00 4.75
1616 1655 1.001158 GATAGCGACTACTCCACAGCC 60.001 57.143 0.00 0.00 0.00 4.85
1617 1656 1.001158 GGATAGCGACTACTCCACAGC 60.001 57.143 0.00 0.00 0.00 4.40
1618 1657 2.298610 TGGATAGCGACTACTCCACAG 58.701 52.381 0.00 0.00 32.92 3.66
1619 1658 2.430248 TGGATAGCGACTACTCCACA 57.570 50.000 0.00 0.00 32.92 4.17
1638 1691 9.138596 GGATGGAGAGAGTACTAGTTTTTCTAT 57.861 37.037 0.00 0.00 0.00 1.98
1641 1694 6.154706 TGGGATGGAGAGAGTACTAGTTTTTC 59.845 42.308 0.00 0.00 0.00 2.29
1653 1706 6.896860 ACTCTTATATGATGGGATGGAGAGAG 59.103 42.308 0.00 0.00 33.96 3.20
1688 1741 4.180377 TGTAGTATTCCTCCCGTCTCAT 57.820 45.455 0.00 0.00 0.00 2.90
1698 1751 8.023021 TCATGCAAACTCTATGTAGTATTCCT 57.977 34.615 0.00 0.00 0.00 3.36
1699 1752 8.662781 TTCATGCAAACTCTATGTAGTATTCC 57.337 34.615 0.00 0.00 0.00 3.01
1718 1773 8.273557 CGTATTACCTATGTGTAAGTTTCATGC 58.726 37.037 0.00 0.00 34.41 4.06
1719 1774 9.524106 TCGTATTACCTATGTGTAAGTTTCATG 57.476 33.333 0.00 0.00 34.41 3.07
1743 1798 8.353684 AGTGTATTGTAGGAGTATCAGAAATCG 58.646 37.037 0.00 0.00 36.25 3.34
1774 1829 4.024387 TCGCACCTAAAAAGTGTCAATCAC 60.024 41.667 0.00 0.00 46.46 3.06
1775 1830 4.130857 TCGCACCTAAAAAGTGTCAATCA 58.869 39.130 0.00 0.00 37.56 2.57
1776 1831 4.742438 TCGCACCTAAAAAGTGTCAATC 57.258 40.909 0.00 0.00 37.56 2.67
1777 1832 4.759693 TGATCGCACCTAAAAAGTGTCAAT 59.240 37.500 0.00 0.00 37.56 2.57
1778 1833 4.130857 TGATCGCACCTAAAAAGTGTCAA 58.869 39.130 0.00 0.00 37.56 3.18
1779 1834 3.734463 TGATCGCACCTAAAAAGTGTCA 58.266 40.909 0.00 0.00 37.56 3.58
1780 1835 3.125316 CCTGATCGCACCTAAAAAGTGTC 59.875 47.826 0.00 0.00 37.56 3.67
1781 1836 3.074412 CCTGATCGCACCTAAAAAGTGT 58.926 45.455 0.00 0.00 37.56 3.55
1782 1837 2.159517 GCCTGATCGCACCTAAAAAGTG 60.160 50.000 0.00 0.00 38.30 3.16
1783 1838 2.084546 GCCTGATCGCACCTAAAAAGT 58.915 47.619 0.00 0.00 0.00 2.66
1784 1839 1.401905 GGCCTGATCGCACCTAAAAAG 59.598 52.381 0.00 0.00 0.00 2.27
1785 1840 1.271652 TGGCCTGATCGCACCTAAAAA 60.272 47.619 3.32 0.00 0.00 1.94
1786 1841 0.326595 TGGCCTGATCGCACCTAAAA 59.673 50.000 3.32 0.00 0.00 1.52
1787 1842 0.546122 ATGGCCTGATCGCACCTAAA 59.454 50.000 3.32 0.00 0.00 1.85
1788 1843 0.179048 CATGGCCTGATCGCACCTAA 60.179 55.000 3.32 0.00 0.00 2.69
1789 1844 1.337384 ACATGGCCTGATCGCACCTA 61.337 55.000 3.32 0.00 0.00 3.08
1790 1845 2.191375 CATGGCCTGATCGCACCT 59.809 61.111 3.32 0.00 0.00 4.00
1791 1846 1.315257 AAACATGGCCTGATCGCACC 61.315 55.000 3.32 0.00 0.00 5.01
1792 1847 0.527565 AAAACATGGCCTGATCGCAC 59.472 50.000 3.32 0.00 0.00 5.34
1793 1848 1.255882 AAAAACATGGCCTGATCGCA 58.744 45.000 3.32 0.00 0.00 5.10
1809 1864 5.691815 CCGTTTCTAATTCTACGGCAAAAA 58.308 37.500 0.00 0.00 45.75 1.94
1810 1865 5.285798 CCGTTTCTAATTCTACGGCAAAA 57.714 39.130 0.00 0.00 45.75 2.44
1811 1866 4.932268 CCGTTTCTAATTCTACGGCAAA 57.068 40.909 0.00 0.00 45.75 3.68
1816 1871 1.856597 CCCGCCGTTTCTAATTCTACG 59.143 52.381 0.00 0.00 0.00 3.51
1817 1872 2.207590 CCCCGCCGTTTCTAATTCTAC 58.792 52.381 0.00 0.00 0.00 2.59
1818 1873 1.832998 ACCCCGCCGTTTCTAATTCTA 59.167 47.619 0.00 0.00 0.00 2.10
1819 1874 0.616891 ACCCCGCCGTTTCTAATTCT 59.383 50.000 0.00 0.00 0.00 2.40
1820 1875 0.730840 CACCCCGCCGTTTCTAATTC 59.269 55.000 0.00 0.00 0.00 2.17
1821 1876 0.037160 ACACCCCGCCGTTTCTAATT 59.963 50.000 0.00 0.00 0.00 1.40
1822 1877 0.037160 AACACCCCGCCGTTTCTAAT 59.963 50.000 0.00 0.00 0.00 1.73
1823 1878 0.683973 TAACACCCCGCCGTTTCTAA 59.316 50.000 0.00 0.00 0.00 2.10
1824 1879 0.247185 CTAACACCCCGCCGTTTCTA 59.753 55.000 0.00 0.00 0.00 2.10
1825 1880 1.004200 CTAACACCCCGCCGTTTCT 60.004 57.895 0.00 0.00 0.00 2.52
1826 1881 0.392060 ATCTAACACCCCGCCGTTTC 60.392 55.000 0.00 0.00 0.00 2.78
1827 1882 0.037160 AATCTAACACCCCGCCGTTT 59.963 50.000 0.00 0.00 0.00 3.60
1828 1883 0.675522 CAATCTAACACCCCGCCGTT 60.676 55.000 0.00 0.00 0.00 4.44
1829 1884 1.078708 CAATCTAACACCCCGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
1830 1885 1.817941 CCAATCTAACACCCCGCCG 60.818 63.158 0.00 0.00 0.00 6.46
1831 1886 1.453197 CCCAATCTAACACCCCGCC 60.453 63.158 0.00 0.00 0.00 6.13
1832 1887 1.453197 CCCCAATCTAACACCCCGC 60.453 63.158 0.00 0.00 0.00 6.13
1833 1888 0.621609 TTCCCCAATCTAACACCCCG 59.378 55.000 0.00 0.00 0.00 5.73
1834 1889 2.911552 TTTCCCCAATCTAACACCCC 57.088 50.000 0.00 0.00 0.00 4.95
1835 1890 4.157246 ACTTTTTCCCCAATCTAACACCC 58.843 43.478 0.00 0.00 0.00 4.61
1836 1891 4.219944 GGACTTTTTCCCCAATCTAACACC 59.780 45.833 0.00 0.00 38.70 4.16
1837 1892 4.830600 TGGACTTTTTCCCCAATCTAACAC 59.169 41.667 0.00 0.00 45.17 3.32
1838 1893 5.068215 TGGACTTTTTCCCCAATCTAACA 57.932 39.130 0.00 0.00 45.17 2.41
1839 1894 6.605471 AATGGACTTTTTCCCCAATCTAAC 57.395 37.500 0.00 0.00 45.17 2.34
1840 1895 7.625498 AAAATGGACTTTTTCCCCAATCTAA 57.375 32.000 0.00 0.00 45.17 2.10
1841 1896 8.728596 TTAAAATGGACTTTTTCCCCAATCTA 57.271 30.769 0.00 0.00 45.17 1.98
1842 1897 7.625498 TTAAAATGGACTTTTTCCCCAATCT 57.375 32.000 0.00 0.00 45.17 2.40
1843 1898 7.174253 GGTTTAAAATGGACTTTTTCCCCAATC 59.826 37.037 0.00 0.00 45.17 2.67
1844 1899 7.001674 GGTTTAAAATGGACTTTTTCCCCAAT 58.998 34.615 0.00 0.00 45.17 3.16
1845 1900 6.358178 GGTTTAAAATGGACTTTTTCCCCAA 58.642 36.000 0.00 0.00 45.17 4.12
1846 1901 5.163184 GGGTTTAAAATGGACTTTTTCCCCA 60.163 40.000 14.24 0.00 45.17 4.96
1847 1902 5.072600 AGGGTTTAAAATGGACTTTTTCCCC 59.927 40.000 11.67 12.20 45.17 4.81
1902 1957 0.802494 CAACCGGGATTTCGACTTGG 59.198 55.000 6.32 0.00 0.00 3.61
1920 1975 1.943968 GCATAGTTCAGGGTGCGAACA 60.944 52.381 0.00 0.00 44.22 3.18
2080 2147 2.033675 GTGTTCCACCGTTCGGAATTTT 59.966 45.455 18.28 0.00 44.18 1.82


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

AutoCloner maintained by Alex Coulton.