Multiple sequence alignment - TraesCS3D01G091100

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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 TraesCS3D01G091100 chr3D 100.000 2620 0 0 1 2620 46196362 46198981 0.000000e+00 4839.0
1 TraesCS3D01G091100 chr3A 85.617 1474 102 50 54 1466 57811940 57813364 0.000000e+00 1447.0
2 TraesCS3D01G091100 chr3A 87.800 1000 76 20 1642 2620 57813501 57814475 0.000000e+00 1129.0
3 TraesCS3D01G091100 chr3A 90.909 66 6 0 1551 1616 57813437 57813502 3.590000e-14 89.8
4 TraesCS3D01G091100 chr3B 92.229 682 35 11 1946 2619 71803580 71802909 0.000000e+00 950.0
5 TraesCS3D01G091100 chr3B 91.071 616 38 9 2013 2620 72111320 72111926 0.000000e+00 817.0
6 TraesCS3D01G091100 chr3B 82.353 833 53 47 23 797 71805583 71804787 2.840000e-179 638.0
7 TraesCS3D01G091100 chr3B 85.443 474 36 11 984 1446 71804603 71804152 1.840000e-126 462.0
8 TraesCS3D01G091100 chr3B 96.465 198 6 1 2424 2620 71975763 71975960 2.510000e-85 326.0
9 TraesCS3D01G091100 chr3B 89.352 216 21 1 2404 2617 72092456 72092671 1.200000e-68 270.0
10 TraesCS3D01G091100 chr3B 93.793 145 9 0 2476 2620 71968139 71968283 4.390000e-53 219.0
11 TraesCS3D01G091100 chr3B 90.210 143 8 3 855 993 71804774 71804634 5.760000e-42 182.0
12 TraesCS3D01G091100 chr3B 79.710 276 29 13 2171 2436 71975231 71975489 9.640000e-40 174.0
13 TraesCS3D01G091100 chr3B 80.625 160 21 5 1663 1815 71803927 71803771 5.930000e-22 115.0
14 TraesCS3D01G091100 chr3B 94.231 52 3 0 1881 1932 71803683 71803632 2.160000e-11 80.5


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 TraesCS3D01G091100 chr3D 46196362 46198981 2619 False 4839.000000 4839 100.000000 1 2620 1 chr3D.!!$F1 2619
1 TraesCS3D01G091100 chr3A 57811940 57814475 2535 False 888.600000 1447 88.108667 54 2620 3 chr3A.!!$F1 2566
2 TraesCS3D01G091100 chr3B 72111320 72111926 606 False 817.000000 817 91.071000 2013 2620 1 chr3B.!!$F3 607
3 TraesCS3D01G091100 chr3B 71802909 71805583 2674 True 404.583333 950 87.515167 23 2619 6 chr3B.!!$R1 2596
4 TraesCS3D01G091100 chr3B 71975231 71975960 729 False 250.000000 326 88.087500 2171 2620 2 chr3B.!!$F4 449

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
844 930 0.179169 GTCGCCACTCTACTTCGACC 60.179 60.0 0.0 0.0 42.34 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1925 0.471617 ATGGCTGAGCAGTACCCATC 59.528 55.0 6.82 0.0 30.81 3.51 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
45 46 0.726118 GTGCTCGGCGAAAAAGCTTC 60.726 55.000 12.13 5.12 36.96 3.86
78 79 0.861837 GTGATGGAACCGATCGATGC 59.138 55.000 18.66 10.97 0.00 3.91
106 107 0.246635 CGATTCAACCGGAGTGTCCT 59.753 55.000 9.46 0.00 33.30 3.85
107 108 1.726853 GATTCAACCGGAGTGTCCTG 58.273 55.000 9.46 0.00 33.30 3.86
108 109 1.002087 GATTCAACCGGAGTGTCCTGT 59.998 52.381 9.46 0.00 35.39 4.00
109 110 0.391597 TTCAACCGGAGTGTCCTGTC 59.608 55.000 9.46 0.00 32.57 3.51
110 111 1.004918 CAACCGGAGTGTCCTGTCC 60.005 63.158 9.46 0.00 32.57 4.02
119 120 2.038557 GAGTGTCCTGTCCCTTAAAGCA 59.961 50.000 0.00 0.00 0.00 3.91
124 125 1.272147 CCTGTCCCTTAAAGCAGCCTT 60.272 52.381 0.00 0.00 0.00 4.35
125 126 2.087646 CTGTCCCTTAAAGCAGCCTTC 58.912 52.381 0.00 0.00 0.00 3.46
126 127 1.271926 TGTCCCTTAAAGCAGCCTTCC 60.272 52.381 0.00 0.00 0.00 3.46
127 128 1.004862 GTCCCTTAAAGCAGCCTTCCT 59.995 52.381 0.00 0.00 0.00 3.36
128 129 1.282157 TCCCTTAAAGCAGCCTTCCTC 59.718 52.381 0.00 0.00 0.00 3.71
129 130 1.373570 CCTTAAAGCAGCCTTCCTCG 58.626 55.000 0.00 0.00 0.00 4.63
130 131 0.729690 CTTAAAGCAGCCTTCCTCGC 59.270 55.000 0.00 0.00 0.00 5.03
131 132 0.676782 TTAAAGCAGCCTTCCTCGCC 60.677 55.000 0.00 0.00 0.00 5.54
132 133 1.553690 TAAAGCAGCCTTCCTCGCCT 61.554 55.000 0.00 0.00 0.00 5.52
139 146 2.103934 CTTCCTCGCCTCTGCTCG 59.896 66.667 0.00 0.00 34.43 5.03
146 153 3.800863 GCCTCTGCTCGTCGTCGA 61.801 66.667 4.42 4.42 44.12 4.20
160 167 1.278637 GTCGACGCAACCAACCAAG 59.721 57.895 0.00 0.00 0.00 3.61
161 168 1.144276 TCGACGCAACCAACCAAGA 59.856 52.632 0.00 0.00 0.00 3.02
162 169 0.878523 TCGACGCAACCAACCAAGAG 60.879 55.000 0.00 0.00 0.00 2.85
163 170 1.157870 CGACGCAACCAACCAAGAGT 61.158 55.000 0.00 0.00 0.00 3.24
173 180 1.734388 AACCAAGAGTTGCCAACCGC 61.734 55.000 3.45 0.00 37.29 5.68
297 306 1.302832 CCTTCTTCTGCCGTGCCTT 60.303 57.895 0.00 0.00 0.00 4.35
298 307 0.890996 CCTTCTTCTGCCGTGCCTTT 60.891 55.000 0.00 0.00 0.00 3.11
299 308 0.239347 CTTCTTCTGCCGTGCCTTTG 59.761 55.000 0.00 0.00 0.00 2.77
300 309 1.795170 TTCTTCTGCCGTGCCTTTGC 61.795 55.000 0.00 0.00 38.26 3.68
342 355 2.673523 GGCTGCAGTGATCACCCT 59.326 61.111 22.21 1.56 0.00 4.34
423 470 2.993264 GGGTTGGTCCGAGGTCGA 60.993 66.667 0.00 0.00 43.02 4.20
426 473 3.744719 TTGGTCCGAGGTCGAGCG 61.745 66.667 9.28 2.00 43.02 5.03
573 635 1.000385 CTGATTGCGCCTTTTTGTCCA 60.000 47.619 4.18 0.00 0.00 4.02
576 643 2.729491 GCGCCTTTTTGTCCACGC 60.729 61.111 0.00 0.00 39.49 5.34
706 788 4.090819 CCATCATTGCCCATGGATCATTA 58.909 43.478 15.22 0.00 42.11 1.90
710 792 0.537143 TGCCCATGGATCATTACGCC 60.537 55.000 15.22 0.00 0.00 5.68
742 824 2.288273 CCCAAGCTAGCCATACTCGTAC 60.288 54.545 12.13 0.00 0.00 3.67
743 825 2.288273 CCAAGCTAGCCATACTCGTACC 60.288 54.545 12.13 0.00 0.00 3.34
744 826 1.236628 AGCTAGCCATACTCGTACCG 58.763 55.000 12.13 0.00 0.00 4.02
745 827 0.950116 GCTAGCCATACTCGTACCGT 59.050 55.000 2.29 0.00 0.00 4.83
770 852 2.031314 TACACGCCACGCCATTGT 59.969 55.556 0.00 0.00 0.00 2.71
822 908 4.803426 CAGCTCCAGGGACGACGC 62.803 72.222 0.00 0.00 0.00 5.19
844 930 0.179169 GTCGCCACTCTACTTCGACC 60.179 60.000 0.00 0.00 42.34 4.79
845 931 0.322277 TCGCCACTCTACTTCGACCT 60.322 55.000 0.00 0.00 0.00 3.85
918 1008 1.749634 ACCACCGTTATCTCCTCTTCG 59.250 52.381 0.00 0.00 0.00 3.79
1188 1320 2.126031 GTCAAGACGTCGGAGGGC 60.126 66.667 10.46 0.00 0.00 5.19
1360 1498 1.398739 TCGACGATGTTCTCTGCTCTC 59.601 52.381 0.00 0.00 0.00 3.20
1376 1514 2.037901 CTCTCCTCTGCTATTGCCTCA 58.962 52.381 0.00 0.00 38.71 3.86
1379 1517 1.483827 TCCTCTGCTATTGCCTCAGTG 59.516 52.381 0.00 0.00 38.71 3.66
1403 1547 5.466728 GGCAGCTTCTTCGTATGATTGATTA 59.533 40.000 0.00 0.00 0.00 1.75
1406 1550 7.562412 CAGCTTCTTCGTATGATTGATTACAG 58.438 38.462 0.00 0.00 0.00 2.74
1412 1562 6.262193 TCGTATGATTGATTACAGGCGATA 57.738 37.500 0.00 0.00 0.00 2.92
1462 1617 9.635632 GTACTATATACGTATCGATTCTTCAGC 57.364 37.037 12.24 0.00 0.00 4.26
1466 1621 2.860735 ACGTATCGATTCTTCAGCTTGC 59.139 45.455 1.71 0.00 0.00 4.01
1467 1622 2.860136 CGTATCGATTCTTCAGCTTGCA 59.140 45.455 1.71 0.00 0.00 4.08
1470 1625 2.703416 TCGATTCTTCAGCTTGCATGT 58.297 42.857 1.14 0.00 0.00 3.21
1471 1626 3.076621 TCGATTCTTCAGCTTGCATGTT 58.923 40.909 1.14 0.00 0.00 2.71
1473 1628 3.850273 CGATTCTTCAGCTTGCATGTTTC 59.150 43.478 1.14 0.00 0.00 2.78
1474 1629 3.648339 TTCTTCAGCTTGCATGTTTCC 57.352 42.857 1.14 0.00 0.00 3.13
1476 1631 0.597568 TTCAGCTTGCATGTTTCCCG 59.402 50.000 1.14 0.00 0.00 5.14
1477 1632 0.537143 TCAGCTTGCATGTTTCCCGT 60.537 50.000 1.14 0.00 0.00 5.28
1478 1633 1.164411 CAGCTTGCATGTTTCCCGTA 58.836 50.000 1.14 0.00 0.00 4.02
1479 1634 1.135689 CAGCTTGCATGTTTCCCGTAC 60.136 52.381 1.14 0.00 0.00 3.67
1480 1635 0.878416 GCTTGCATGTTTCCCGTACA 59.122 50.000 1.14 0.00 0.00 2.90
1481 1636 1.472480 GCTTGCATGTTTCCCGTACAT 59.528 47.619 1.14 0.00 36.70 2.29
1482 1637 2.680841 GCTTGCATGTTTCCCGTACATA 59.319 45.455 1.14 0.00 34.59 2.29
1483 1638 3.486875 GCTTGCATGTTTCCCGTACATAC 60.487 47.826 1.14 0.00 34.59 2.39
1484 1639 2.634600 TGCATGTTTCCCGTACATACC 58.365 47.619 0.00 0.00 34.59 2.73
1486 1641 1.595794 CATGTTTCCCGTACATACCGC 59.404 52.381 0.00 0.00 34.59 5.68
1490 1645 0.607112 TTCCCGTACATACCGCACAA 59.393 50.000 0.00 0.00 0.00 3.33
1493 1648 1.395608 CCCGTACATACCGCACAAAAG 59.604 52.381 0.00 0.00 0.00 2.27
1497 1652 3.430895 CGTACATACCGCACAAAAGACTT 59.569 43.478 0.00 0.00 0.00 3.01
1517 1672 6.585695 ACTTATCGTCTGTTAAGTTCAGGA 57.414 37.500 0.00 0.00 37.33 3.86
1518 1673 6.622549 ACTTATCGTCTGTTAAGTTCAGGAG 58.377 40.000 0.00 0.00 37.33 3.69
1519 1674 6.433404 ACTTATCGTCTGTTAAGTTCAGGAGA 59.567 38.462 0.00 0.00 37.33 3.71
1521 1676 3.255149 TCGTCTGTTAAGTTCAGGAGACC 59.745 47.826 0.00 0.00 34.15 3.85
1522 1677 3.576648 GTCTGTTAAGTTCAGGAGACCG 58.423 50.000 0.00 0.00 34.15 4.79
1523 1678 3.005578 GTCTGTTAAGTTCAGGAGACCGT 59.994 47.826 0.00 0.00 34.15 4.83
1524 1679 4.217118 GTCTGTTAAGTTCAGGAGACCGTA 59.783 45.833 0.00 0.00 34.15 4.02
1539 1710 2.036958 CCGTATTGGTGCCTGAATGA 57.963 50.000 0.00 0.00 0.00 2.57
1546 1718 3.940209 TGGTGCCTGAATGAATTGTTC 57.060 42.857 0.00 0.00 0.00 3.18
1554 1755 4.020839 CCTGAATGAATTGTTCCTGCCTTT 60.021 41.667 0.00 0.00 0.00 3.11
1555 1756 4.885413 TGAATGAATTGTTCCTGCCTTTG 58.115 39.130 0.00 0.00 0.00 2.77
1572 1780 0.944386 TTGTTCGCAACTCTGAAGCC 59.056 50.000 1.68 0.00 31.15 4.35
1611 1819 4.735369 TCATTTCCTACAAGGAGCCAAAA 58.265 39.130 0.00 0.00 46.73 2.44
1616 1824 3.826157 TCCTACAAGGAGCCAAAATGTTG 59.174 43.478 0.00 0.00 40.06 3.33
1617 1825 2.531522 ACAAGGAGCCAAAATGTTGC 57.468 45.000 0.00 0.00 33.01 4.17
1619 1827 1.070445 CAAGGAGCCAAAATGTTGCCA 59.930 47.619 0.00 0.00 33.01 4.92
1620 1828 1.422531 AGGAGCCAAAATGTTGCCAA 58.577 45.000 0.00 0.00 33.01 4.52
1648 1856 9.442047 AAATAACCAGAACTCTGTATTCTCTTG 57.558 33.333 6.01 0.00 42.27 3.02
1679 1888 1.354040 AGAAGTGCTCATTTCTCGCG 58.646 50.000 0.00 0.00 32.86 5.87
1685 1894 2.028165 GTGCTCATTTCTCGCGACTAAC 59.972 50.000 3.71 0.00 0.00 2.34
1692 1904 2.927437 CTCGCGACTAACCGAGTTC 58.073 57.895 3.71 0.00 44.25 3.01
1693 1905 0.856490 CTCGCGACTAACCGAGTTCG 60.856 60.000 3.71 0.00 44.25 3.95
1694 1906 1.133253 CGCGACTAACCGAGTTCGA 59.867 57.895 0.00 0.00 39.06 3.71
1713 1925 3.057019 CGATCTCCTCTCTACTCTCACG 58.943 54.545 0.00 0.00 0.00 4.35
1719 1931 2.422235 CCTCTCTACTCTCACGATGGGT 60.422 54.545 0.00 0.00 0.00 4.51
1762 1984 1.600013 GCATTGTCACACCACACGTTA 59.400 47.619 0.00 0.00 0.00 3.18
1764 1986 3.666902 GCATTGTCACACCACACGTTATC 60.667 47.826 0.00 0.00 0.00 1.75
1782 2004 3.559238 ATCGTGTGCAAGGAACAAATC 57.441 42.857 0.00 0.00 0.00 2.17
1786 2008 4.050553 CGTGTGCAAGGAACAAATCAATT 58.949 39.130 0.00 0.00 0.00 2.32
1792 2014 6.202570 GTGCAAGGAACAAATCAATTGCTTTA 59.797 34.615 6.93 0.00 45.43 1.85
1818 2040 4.507710 TCTCTTCATAAAATGAGCACGCT 58.492 39.130 0.00 0.00 40.94 5.07
1826 2048 4.882671 AAAATGAGCACGCTACCATAAG 57.117 40.909 0.00 0.00 0.00 1.73
1835 2057 4.235360 CACGCTACCATAAGCCTGTATAC 58.765 47.826 0.00 0.00 39.43 1.47
1836 2058 3.057736 ACGCTACCATAAGCCTGTATACG 60.058 47.826 0.00 0.00 39.43 3.06
1847 2103 9.647797 CATAAGCCTGTATACGATTACCATAAA 57.352 33.333 0.00 0.00 0.00 1.40
1863 2119 8.795842 TTACCATAAACAATTTCACGATACCT 57.204 30.769 0.00 0.00 0.00 3.08
1866 2122 7.392113 ACCATAAACAATTTCACGATACCTCAA 59.608 33.333 0.00 0.00 0.00 3.02
1878 2134 8.095937 TCACGATACCTCAATAGTAGTACATG 57.904 38.462 2.52 0.00 0.00 3.21
1898 2154 5.812642 ACATGCTAGGAACAAACTAATCGAG 59.187 40.000 0.00 0.00 0.00 4.04
1899 2155 4.181578 TGCTAGGAACAAACTAATCGAGC 58.818 43.478 0.00 0.00 0.00 5.03
1932 2189 0.393944 CACACTGGCCATGATCAGCT 60.394 55.000 5.51 0.00 34.57 4.24
1933 2190 0.393944 ACACTGGCCATGATCAGCTG 60.394 55.000 5.51 7.63 34.57 4.24
1934 2191 0.107361 CACTGGCCATGATCAGCTGA 60.107 55.000 20.79 20.79 34.57 4.26
1944 2234 2.759191 TGATCAGCTGAGTGACACAAC 58.241 47.619 22.96 2.19 0.00 3.32
1949 2239 3.132111 TCAGCTGAGTGACACAACAGTTA 59.868 43.478 23.61 12.99 33.57 2.24
1950 2240 3.492383 CAGCTGAGTGACACAACAGTTAG 59.508 47.826 23.61 14.89 33.57 2.34
1951 2241 3.133003 AGCTGAGTGACACAACAGTTAGT 59.867 43.478 23.61 11.07 32.05 2.24
1952 2242 3.491267 GCTGAGTGACACAACAGTTAGTC 59.509 47.826 23.61 9.93 32.05 2.59
1986 2287 2.245159 TCTGCTGTTGTCTCTTGTGG 57.755 50.000 0.00 0.00 0.00 4.17
2020 2321 5.240183 ACGGAATGAAAGCCAATGATATCAG 59.760 40.000 11.78 0.00 0.00 2.90
2021 2322 5.467705 GGAATGAAAGCCAATGATATCAGC 58.532 41.667 11.78 9.27 0.00 4.26
2102 2403 3.126831 GGTGTCTTAGAATCAGCCATCG 58.873 50.000 0.00 0.00 0.00 3.84
2103 2404 3.430929 GGTGTCTTAGAATCAGCCATCGT 60.431 47.826 0.00 0.00 0.00 3.73
2104 2405 3.799420 GTGTCTTAGAATCAGCCATCGTC 59.201 47.826 0.00 0.00 0.00 4.20
2105 2406 3.046390 GTCTTAGAATCAGCCATCGTCG 58.954 50.000 0.00 0.00 0.00 5.12
2234 2537 1.929169 ACTGATGAATGACACGCATCG 59.071 47.619 12.25 10.13 40.89 3.84
2315 2624 3.057526 CACATTACAGAGTGACACGAGGA 60.058 47.826 0.00 0.00 37.97 3.71
2316 2625 3.572682 ACATTACAGAGTGACACGAGGAA 59.427 43.478 0.00 0.00 0.00 3.36
2317 2626 3.917329 TTACAGAGTGACACGAGGAAG 57.083 47.619 0.00 0.00 0.00 3.46
2318 2627 1.982660 ACAGAGTGACACGAGGAAGA 58.017 50.000 0.00 0.00 0.00 2.87
2319 2628 2.307768 ACAGAGTGACACGAGGAAGAA 58.692 47.619 0.00 0.00 0.00 2.52
2371 2688 0.929615 CAAAACAAGCCAAACCGCTG 59.070 50.000 0.00 0.00 39.64 5.18
2399 2723 0.742281 CTGATCTGTGGAAGCACGGG 60.742 60.000 0.00 0.00 32.55 5.28
2447 3060 3.117663 GGTGAAACTATGGATGGGGCTAA 60.118 47.826 0.00 0.00 36.74 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.787001 CACCCTCCCTTCGGGCTC 61.787 72.222 0.00 0.00 46.04 4.70
15 16 4.148825 CGAGCACCCTCCCTTCGG 62.149 72.222 0.00 0.00 34.49 4.30
16 17 4.148825 CCGAGCACCCTCCCTTCG 62.149 72.222 0.00 0.00 34.49 3.79
17 18 4.475135 GCCGAGCACCCTCCCTTC 62.475 72.222 0.00 0.00 34.49 3.46
21 22 3.894547 TTTTCGCCGAGCACCCTCC 62.895 63.158 0.00 0.00 34.49 4.30
22 23 1.912371 CTTTTTCGCCGAGCACCCTC 61.912 60.000 0.00 0.00 34.66 4.30
23 24 1.966451 CTTTTTCGCCGAGCACCCT 60.966 57.895 0.00 0.00 0.00 4.34
24 25 2.561373 CTTTTTCGCCGAGCACCC 59.439 61.111 0.00 0.00 0.00 4.61
25 26 2.126850 GCTTTTTCGCCGAGCACC 60.127 61.111 0.00 0.00 36.45 5.01
26 27 0.726118 GAAGCTTTTTCGCCGAGCAC 60.726 55.000 0.00 0.00 38.85 4.40
27 28 1.574428 GAAGCTTTTTCGCCGAGCA 59.426 52.632 0.00 0.00 38.85 4.26
28 29 1.509995 CGAAGCTTTTTCGCCGAGC 60.510 57.895 0.00 0.00 35.05 5.03
29 30 1.132640 CCGAAGCTTTTTCGCCGAG 59.867 57.895 0.00 0.00 40.30 4.63
30 31 1.289109 CTCCGAAGCTTTTTCGCCGA 61.289 55.000 0.00 0.00 40.30 5.54
31 32 1.132640 CTCCGAAGCTTTTTCGCCG 59.867 57.895 0.00 0.00 40.30 6.46
36 37 3.070302 ACTGTCTCTCTCCGAAGCTTTTT 59.930 43.478 0.00 0.00 0.00 1.94
45 46 1.133982 CCATCACACTGTCTCTCTCCG 59.866 57.143 0.00 0.00 0.00 4.63
96 97 1.263356 TTAAGGGACAGGACACTCCG 58.737 55.000 0.00 0.00 42.75 4.63
106 107 1.271926 GGAAGGCTGCTTTAAGGGACA 60.272 52.381 0.00 0.00 0.00 4.02
107 108 1.004862 AGGAAGGCTGCTTTAAGGGAC 59.995 52.381 0.00 0.00 0.00 4.46
108 109 1.282157 GAGGAAGGCTGCTTTAAGGGA 59.718 52.381 0.00 0.00 0.00 4.20
109 110 1.756430 GAGGAAGGCTGCTTTAAGGG 58.244 55.000 0.00 0.00 0.00 3.95
110 111 1.373570 CGAGGAAGGCTGCTTTAAGG 58.626 55.000 0.00 0.00 0.00 2.69
129 130 3.800863 TCGACGACGAGCAGAGGC 61.801 66.667 5.75 0.00 43.81 4.70
139 146 2.542896 GTTGGTTGCGTCGACGAC 59.457 61.111 39.74 28.35 43.02 4.34
146 153 3.184736 AACTCTTGGTTGGTTGCGT 57.815 47.368 0.00 0.00 36.70 5.24
160 167 3.365265 CCCAGCGGTTGGCAACTC 61.365 66.667 27.77 19.58 46.32 3.01
299 308 3.112709 GACAGTCCGGCGACAAGC 61.113 66.667 9.30 0.00 41.87 4.01
300 309 2.805353 CGACAGTCCGGCGACAAG 60.805 66.667 9.30 4.60 41.87 3.16
342 355 2.743538 GCATGCACGCTCAGGTCA 60.744 61.111 14.21 0.00 0.00 4.02
376 397 1.552792 GATCTCCGATGAATCCTCCCC 59.447 57.143 0.00 0.00 0.00 4.81
380 401 2.166829 CTCCGATCTCCGATGAATCCT 58.833 52.381 0.00 0.00 41.76 3.24
385 432 0.106149 TCGTCTCCGATCTCCGATGA 59.894 55.000 0.00 0.00 41.76 2.92
386 433 0.236187 GTCGTCTCCGATCTCCGATG 59.764 60.000 0.00 0.00 46.30 3.84
408 455 2.126031 GCTCGACCTCGGACCAAC 60.126 66.667 0.00 0.00 40.29 3.77
573 635 3.735029 GACACGAGACGGGAGCGT 61.735 66.667 0.00 0.00 39.04 5.07
576 643 1.067846 TGATTTGACACGAGACGGGAG 60.068 52.381 0.00 0.00 32.98 4.30
587 654 0.389817 CGAGCGACCCTGATTTGACA 60.390 55.000 0.00 0.00 0.00 3.58
742 824 0.671796 TGGCGTGTAGGATGATACGG 59.328 55.000 0.00 0.00 37.06 4.02
743 825 1.767289 GTGGCGTGTAGGATGATACG 58.233 55.000 0.00 0.00 39.37 3.06
744 826 1.767289 CGTGGCGTGTAGGATGATAC 58.233 55.000 0.00 0.00 0.00 2.24
745 827 0.031585 GCGTGGCGTGTAGGATGATA 59.968 55.000 0.00 0.00 0.00 2.15
801 887 4.154347 CGTCCCTGGAGCTGGAGC 62.154 72.222 0.00 0.00 42.49 4.70
803 889 2.680352 GTCGTCCCTGGAGCTGGA 60.680 66.667 0.00 0.00 0.00 3.86
804 890 4.135153 CGTCGTCCCTGGAGCTGG 62.135 72.222 0.00 0.00 0.00 4.85
822 908 1.139095 GAAGTAGAGTGGCGACCGG 59.861 63.158 0.00 0.00 0.00 5.28
844 930 3.597728 GGCGGCGGTAGGAGAGAG 61.598 72.222 9.78 0.00 0.00 3.20
845 931 4.124943 AGGCGGCGGTAGGAGAGA 62.125 66.667 9.78 0.00 0.00 3.10
918 1008 2.766229 GACAGGGGAGGAGGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
1081 1210 4.047059 GACGACGTGGCCGAGGAA 62.047 66.667 4.58 0.00 37.88 3.36
1161 1293 3.470567 GTCTTGACGTGCGCCGAG 61.471 66.667 22.10 8.56 40.70 4.63
1172 1304 3.744719 CGCCCTCCGACGTCTTGA 61.745 66.667 14.70 9.11 40.02 3.02
1319 1451 1.217001 TTCATACATGCATCGGCGAC 58.783 50.000 13.76 0.00 45.35 5.19
1360 1498 1.474677 CCACTGAGGCAATAGCAGAGG 60.475 57.143 0.00 0.00 44.61 3.69
1376 1514 1.550524 TCATACGAAGAAGCTGCCACT 59.449 47.619 0.00 0.00 0.00 4.00
1379 1517 3.198068 TCAATCATACGAAGAAGCTGCC 58.802 45.455 0.00 0.00 0.00 4.85
1381 1519 7.307042 CCTGTAATCAATCATACGAAGAAGCTG 60.307 40.741 0.00 0.00 0.00 4.24
1451 1606 3.482722 AACATGCAAGCTGAAGAATCG 57.517 42.857 0.00 0.00 0.00 3.34
1452 1607 4.171754 GGAAACATGCAAGCTGAAGAATC 58.828 43.478 0.00 0.00 0.00 2.52
1462 1617 3.064820 GGTATGTACGGGAAACATGCAAG 59.935 47.826 0.00 0.00 40.46 4.01
1466 1621 1.595794 GCGGTATGTACGGGAAACATG 59.404 52.381 0.00 0.00 38.05 3.21
1467 1622 1.207570 TGCGGTATGTACGGGAAACAT 59.792 47.619 0.00 0.00 40.57 2.71
1470 1625 0.607112 TGTGCGGTATGTACGGGAAA 59.393 50.000 0.00 0.00 35.72 3.13
1471 1626 0.607112 TTGTGCGGTATGTACGGGAA 59.393 50.000 0.00 0.00 35.72 3.97
1473 1628 1.395608 CTTTTGTGCGGTATGTACGGG 59.604 52.381 0.00 0.00 35.72 5.28
1474 1629 2.093152 GTCTTTTGTGCGGTATGTACGG 59.907 50.000 0.00 0.00 35.72 4.02
1476 1631 6.507456 CGATAAGTCTTTTGTGCGGTATGTAC 60.507 42.308 0.00 0.00 0.00 2.90
1477 1632 5.517411 CGATAAGTCTTTTGTGCGGTATGTA 59.483 40.000 0.00 0.00 0.00 2.29
1478 1633 4.328983 CGATAAGTCTTTTGTGCGGTATGT 59.671 41.667 0.00 0.00 0.00 2.29
1479 1634 4.328983 ACGATAAGTCTTTTGTGCGGTATG 59.671 41.667 0.00 0.00 0.00 2.39
1480 1635 4.501071 ACGATAAGTCTTTTGTGCGGTAT 58.499 39.130 0.00 0.00 0.00 2.73
1481 1636 3.916761 ACGATAAGTCTTTTGTGCGGTA 58.083 40.909 0.00 0.00 0.00 4.02
1482 1637 2.735134 GACGATAAGTCTTTTGTGCGGT 59.265 45.455 0.00 0.00 46.13 5.68
1483 1638 3.369835 GACGATAAGTCTTTTGTGCGG 57.630 47.619 0.00 0.00 46.13 5.69
1497 1652 5.125097 GGTCTCCTGAACTTAACAGACGATA 59.875 44.000 0.00 0.00 37.54 2.92
1507 1662 4.730949 CCAATACGGTCTCCTGAACTTA 57.269 45.455 0.00 0.00 0.00 2.24
1521 1676 4.142403 ACAATTCATTCAGGCACCAATACG 60.142 41.667 0.00 0.00 0.00 3.06
1522 1677 5.329035 ACAATTCATTCAGGCACCAATAC 57.671 39.130 0.00 0.00 0.00 1.89
1523 1678 5.105392 GGAACAATTCATTCAGGCACCAATA 60.105 40.000 2.28 0.00 0.00 1.90
1524 1679 4.322953 GGAACAATTCATTCAGGCACCAAT 60.323 41.667 2.28 0.00 0.00 3.16
1539 1710 2.545742 GCGAACAAAGGCAGGAACAATT 60.546 45.455 0.00 0.00 0.00 2.32
1546 1718 0.040067 GAGTTGCGAACAAAGGCAGG 60.040 55.000 0.00 0.00 40.75 4.85
1554 1755 1.221466 CGGCTTCAGAGTTGCGAACA 61.221 55.000 0.00 0.00 0.00 3.18
1555 1756 1.222115 ACGGCTTCAGAGTTGCGAAC 61.222 55.000 0.00 0.00 0.00 3.95
1572 1780 5.795441 GGAAATGAGAAGGAAATTTTCGACG 59.205 40.000 3.17 0.00 0.00 5.12
1631 1839 8.594881 TTGAAGAACAAGAGAATACAGAGTTC 57.405 34.615 0.00 0.00 35.40 3.01
1633 1841 7.987458 TGTTTGAAGAACAAGAGAATACAGAGT 59.013 33.333 0.00 0.00 39.77 3.24
1646 1854 5.182950 TGAGCACTTCTTGTTTGAAGAACAA 59.817 36.000 10.68 4.50 44.40 2.83
1648 1856 5.235305 TGAGCACTTCTTGTTTGAAGAAC 57.765 39.130 10.68 3.16 44.40 3.01
1679 1888 2.944349 AGGAGATCGAACTCGGTTAGTC 59.056 50.000 15.53 1.35 37.50 2.59
1685 1894 1.961793 AGAGAGGAGATCGAACTCGG 58.038 55.000 15.53 0.00 40.29 4.63
1691 1903 3.243602 CGTGAGAGTAGAGAGGAGATCGA 60.244 52.174 0.00 0.00 0.00 3.59
1692 1904 3.057019 CGTGAGAGTAGAGAGGAGATCG 58.943 54.545 0.00 0.00 0.00 3.69
1693 1905 4.330944 TCGTGAGAGTAGAGAGGAGATC 57.669 50.000 0.00 0.00 34.84 2.75
1713 1925 0.471617 ATGGCTGAGCAGTACCCATC 59.528 55.000 6.82 0.00 30.81 3.51
1719 1931 1.069204 GGAATCGATGGCTGAGCAGTA 59.931 52.381 6.82 0.00 0.00 2.74
1762 1984 2.884012 TGATTTGTTCCTTGCACACGAT 59.116 40.909 0.00 0.00 0.00 3.73
1764 1986 2.772568 TGATTTGTTCCTTGCACACG 57.227 45.000 0.00 0.00 0.00 4.49
1792 2014 6.621596 GCGTGCTCATTTTATGAAGAGAAACT 60.622 38.462 0.00 0.00 39.11 2.66
1818 2040 6.720748 TGGTAATCGTATACAGGCTTATGGTA 59.279 38.462 3.32 0.00 0.00 3.25
1826 2048 7.718272 TTGTTTATGGTAATCGTATACAGGC 57.282 36.000 3.32 0.00 32.91 4.85
1835 2057 9.365311 GTATCGTGAAATTGTTTATGGTAATCG 57.635 33.333 0.00 0.00 0.00 3.34
1836 2058 9.659830 GGTATCGTGAAATTGTTTATGGTAATC 57.340 33.333 0.00 0.00 0.00 1.75
1847 2103 8.475639 ACTACTATTGAGGTATCGTGAAATTGT 58.524 33.333 0.00 0.00 0.00 2.71
1853 2109 7.308408 GCATGTACTACTATTGAGGTATCGTGA 60.308 40.741 0.00 0.00 0.00 4.35
1863 2119 7.891498 TGTTCCTAGCATGTACTACTATTGA 57.109 36.000 0.00 0.00 0.00 2.57
1866 2122 8.307582 AGTTTGTTCCTAGCATGTACTACTAT 57.692 34.615 0.00 0.00 0.00 2.12
1878 2134 4.268884 CAGCTCGATTAGTTTGTTCCTAGC 59.731 45.833 0.00 0.00 0.00 3.42
1898 2154 4.437930 GCCAGTGTGATCTTGATTTACAGC 60.438 45.833 0.00 0.00 0.00 4.40
1899 2155 4.095483 GGCCAGTGTGATCTTGATTTACAG 59.905 45.833 0.00 0.00 0.00 2.74
1932 2189 6.096423 ACTTAGACTAACTGTTGTGTCACTCA 59.904 38.462 21.56 3.24 32.41 3.41
1933 2190 6.418226 CACTTAGACTAACTGTTGTGTCACTC 59.582 42.308 21.56 0.00 32.41 3.51
1934 2191 6.127423 ACACTTAGACTAACTGTTGTGTCACT 60.127 38.462 21.56 10.83 34.97 3.41
1944 2234 7.171678 CAGAAAGGGAAACACTTAGACTAACTG 59.828 40.741 0.00 0.00 0.00 3.16
1949 2239 4.103311 AGCAGAAAGGGAAACACTTAGACT 59.897 41.667 0.00 0.00 0.00 3.24
1950 2240 4.214332 CAGCAGAAAGGGAAACACTTAGAC 59.786 45.833 0.00 0.00 0.00 2.59
1951 2241 4.141482 ACAGCAGAAAGGGAAACACTTAGA 60.141 41.667 0.00 0.00 0.00 2.10
1952 2242 4.137543 ACAGCAGAAAGGGAAACACTTAG 58.862 43.478 0.00 0.00 0.00 2.18
1986 2287 4.467735 GCTTTCATTCCGTTTCTTCTCAC 58.532 43.478 0.00 0.00 0.00 3.51
2020 2321 1.000145 GTCTTCGGATGTTTCCTCGC 59.000 55.000 0.00 0.00 40.17 5.03
2021 2322 1.641577 GGTCTTCGGATGTTTCCTCG 58.358 55.000 0.00 0.00 40.17 4.63
2105 2406 2.359975 CACTTTCGGCAGGGGGTC 60.360 66.667 0.00 0.00 0.00 4.46
2191 2492 2.349886 GAGGCTGCAGAATTAGTGTTCG 59.650 50.000 20.43 0.00 33.36 3.95
2234 2537 3.454375 TGCCGATCGAAGAGAATAAACC 58.546 45.455 18.66 0.00 43.63 3.27
2287 2596 4.386049 GTGTCACTCTGTAATGTGTACTGC 59.614 45.833 0.00 0.00 35.82 4.40
2288 2597 4.617223 CGTGTCACTCTGTAATGTGTACTG 59.383 45.833 0.65 0.00 35.82 2.74
2289 2598 4.517832 TCGTGTCACTCTGTAATGTGTACT 59.482 41.667 0.65 0.00 35.82 2.73
2290 2599 4.790878 TCGTGTCACTCTGTAATGTGTAC 58.209 43.478 0.65 0.00 35.82 2.90
2291 2600 4.082949 CCTCGTGTCACTCTGTAATGTGTA 60.083 45.833 0.65 0.00 35.82 2.90
2315 2624 4.084011 AGCTCAGCTCTGTTCTTTTCTT 57.916 40.909 0.00 0.00 30.62 2.52
2316 2625 3.767902 AGCTCAGCTCTGTTCTTTTCT 57.232 42.857 0.00 0.00 30.62 2.52
2360 2677 4.043200 GGACAGCAGCGGTTTGGC 62.043 66.667 0.00 0.00 0.00 4.52
2371 2688 2.103373 TCCACAGATCAGTAGGACAGC 58.897 52.381 0.00 0.00 0.00 4.40
2399 2723 5.599242 ACCTACTAGGAGAGGTATTTTCAGC 59.401 44.000 2.52 0.00 44.51 4.26
2471 3084 1.211969 CAGGATCACCGTCGTCGTT 59.788 57.895 0.71 0.00 41.83 3.85


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

AutoCloner maintained by Alex Coulton.