Multiple sequence alignment - TraesCS6B01G277300

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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 TraesCS6B01G277300 chr6B 100.000 2540 0 0 1 2540 501555805 501553266 0.000000e+00 4691.0
1 TraesCS6B01G277300 chr6B 91.787 414 32 2 1739 2150 19441828 19441415 2.190000e-160 575.0
2 TraesCS6B01G277300 chr6B 91.148 418 33 3 1739 2152 136907285 136907702 4.740000e-157 564.0
3 TraesCS6B01G277300 chr6B 91.220 410 32 2 1739 2144 340156165 340156574 2.860000e-154 555.0
4 TraesCS6B01G277300 chr6A 93.857 1758 70 18 1 1747 459506676 459508406 0.000000e+00 2614.0
5 TraesCS6B01G277300 chr6A 96.855 318 10 0 2223 2540 459508606 459508923 1.340000e-147 532.0
6 TraesCS6B01G277300 chr6A 86.283 226 29 2 553 777 601961146 601961370 7.020000e-61 244.0
7 TraesCS6B01G277300 chr6D 95.489 931 30 5 795 1724 321988085 321989004 0.000000e+00 1476.0
8 TraesCS6B01G277300 chr6D 92.020 802 37 6 1 799 321987212 321987989 0.000000e+00 1101.0
9 TraesCS6B01G277300 chr6D 89.623 318 11 2 2223 2540 321989650 321989945 3.960000e-103 385.0
10 TraesCS6B01G277300 chr6D 85.654 237 32 2 536 771 440639496 440639731 5.430000e-62 248.0
11 TraesCS6B01G277300 chr6D 92.157 51 3 1 2174 2223 236052605 236052655 1.260000e-08 71.3
12 TraesCS6B01G277300 chr2B 91.827 416 31 3 1739 2152 324662209 324662623 6.090000e-161 577.0
13 TraesCS6B01G277300 chr4B 91.607 417 32 2 1739 2152 286229432 286229848 7.880000e-160 573.0
14 TraesCS6B01G277300 chr4B 90.385 52 4 1 2174 2224 403958903 403958852 1.630000e-07 67.6
15 TraesCS6B01G277300 chr4B 91.111 45 4 0 2180 2224 439793297 439793253 7.590000e-06 62.1
16 TraesCS6B01G277300 chr5B 91.084 415 36 1 1739 2152 102440119 102439705 6.140000e-156 560.0
17 TraesCS6B01G277300 chr5B 88.679 53 4 1 2172 2224 143731917 143731967 2.110000e-06 63.9
18 TraesCS6B01G277300 chr4D 90.261 421 35 6 1736 2151 173996521 173996940 1.720000e-151 545.0
19 TraesCS6B01G277300 chr4D 84.109 258 38 3 533 789 315080261 315080516 1.950000e-61 246.0
20 TraesCS6B01G277300 chr7B 90.261 421 33 6 1742 2159 222698179 222697764 6.180000e-151 544.0
21 TraesCS6B01G277300 chr3B 90.385 416 37 3 1739 2152 501660415 501660001 6.180000e-151 544.0
22 TraesCS6B01G277300 chr3B 95.556 45 2 0 2180 2224 776203822 776203778 3.510000e-09 73.1
23 TraesCS6B01G277300 chr2D 84.252 254 36 4 535 788 645896774 645896525 7.020000e-61 244.0
24 TraesCS6B01G277300 chr2D 84.127 252 38 2 535 786 620601550 620601799 2.520000e-60 243.0
25 TraesCS6B01G277300 chr4A 83.529 255 38 4 536 789 160254826 160254575 4.220000e-58 235.0
26 TraesCS6B01G277300 chr1B 82.946 258 41 3 533 788 645529255 645529511 1.970000e-56 230.0
27 TraesCS6B01G277300 chr2A 95.918 49 2 0 2176 2224 724733646 724733598 2.090000e-11 80.5
28 TraesCS6B01G277300 chr3D 91.837 49 3 1 2177 2224 157440574 157440622 1.630000e-07 67.6
29 TraesCS6B01G277300 chr3D 91.837 49 3 1 2177 2224 499895652 499895700 1.630000e-07 67.6
30 TraesCS6B01G277300 chr1A 93.333 45 3 0 2180 2224 561070551 561070507 1.630000e-07 67.6


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 TraesCS6B01G277300 chr6B 501553266 501555805 2539 True 4691.000000 4691 100.000000 1 2540 1 chr6B.!!$R2 2539
1 TraesCS6B01G277300 chr6A 459506676 459508923 2247 False 1573.000000 2614 95.356000 1 2540 2 chr6A.!!$F2 2539
2 TraesCS6B01G277300 chr6D 321987212 321989945 2733 False 987.333333 1476 92.377333 1 2540 3 chr6D.!!$F3 2539

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
64 66 2.158959 GCGTACGTACAGCAGCCAG 61.159 63.158 26.39 11.5 0.00 4.85 F
65 67 2.158959 CGTACGTACAGCAGCCAGC 61.159 63.158 24.50 0.0 46.19 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1096 1206 0.376152 GCTTCGCATGAGGTGATGTG 59.624 55.0 0.00 0.0 35.59 3.21 R
1552 1663 0.593618 GCTCTCATCCGTGATCGCTA 59.406 55.0 4.48 0.0 32.98 4.26 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
36 38 3.875727 TGTCAACGGTCCGATTAACAAAA 59.124 39.130 20.51 0.00 0.00 2.44
64 66 2.158959 GCGTACGTACAGCAGCCAG 61.159 63.158 26.39 11.50 0.00 4.85
65 67 2.158959 CGTACGTACAGCAGCCAGC 61.159 63.158 24.50 0.00 46.19 4.85
145 150 7.037438 GGTCACATCGAAGGTATAAACTGTAA 58.963 38.462 0.00 0.00 0.00 2.41
217 225 3.195610 TGGTACTAGAACAGTGGCAGATG 59.804 47.826 0.00 0.00 38.24 2.90
405 413 2.349155 CGCTCTTCGTTTGTTTACCACC 60.349 50.000 0.00 0.00 0.00 4.61
408 416 4.554134 GCTCTTCGTTTGTTTACCACCTTC 60.554 45.833 0.00 0.00 0.00 3.46
550 558 9.995003 TTGAATTACAATACTGCCTTCATTTTT 57.005 25.926 0.00 0.00 33.18 1.94
561 569 6.493458 ACTGCCTTCATTTTTATACACAAGGT 59.507 34.615 0.00 0.00 32.92 3.50
569 577 7.442969 TCATTTTTATACACAAGGTCACTTCGT 59.557 33.333 0.00 0.00 33.81 3.85
753 762 5.193679 AGACATACAAATAAGAAGTGGCCC 58.806 41.667 0.00 0.00 0.00 5.80
761 770 7.179269 ACAAATAAGAAGTGGCCCTGTATAAA 58.821 34.615 0.00 0.00 0.00 1.40
766 775 3.646736 AGTGGCCCTGTATAAAGGAAC 57.353 47.619 10.90 5.99 40.02 3.62
771 780 2.612672 GCCCTGTATAAAGGAACGAAGC 59.387 50.000 10.90 0.20 40.02 3.86
834 943 4.398044 CCAAATACGCCTTGTGTATTCCTT 59.602 41.667 12.03 0.00 44.89 3.36
890 999 3.000684 CCCCCTTTTCTAGCTTGTACC 57.999 52.381 0.00 0.00 0.00 3.34
891 1000 2.307686 CCCCCTTTTCTAGCTTGTACCA 59.692 50.000 0.00 0.00 0.00 3.25
892 1001 3.344515 CCCCTTTTCTAGCTTGTACCAC 58.655 50.000 0.00 0.00 0.00 4.16
893 1002 3.009143 CCCCTTTTCTAGCTTGTACCACT 59.991 47.826 0.00 0.00 0.00 4.00
894 1003 4.224370 CCCCTTTTCTAGCTTGTACCACTA 59.776 45.833 0.00 0.00 0.00 2.74
895 1004 5.176592 CCCTTTTCTAGCTTGTACCACTAC 58.823 45.833 0.00 0.00 0.00 2.73
1096 1206 3.576550 AGTGTTCTTCCTCTTCACTCTCC 59.423 47.826 0.00 0.00 34.87 3.71
1127 1237 3.179481 CGAAGCTCGTCGTCTCCT 58.821 61.111 0.00 0.00 36.26 3.69
1173 1283 2.094286 CAGCAAGTCTTCCTCGTCATCT 60.094 50.000 0.00 0.00 0.00 2.90
1186 1296 2.300152 TCGTCATCTCAGGTTTGCTTCT 59.700 45.455 0.00 0.00 0.00 2.85
1224 1334 6.767080 TCGGTTAAACATCATAATGTCAACG 58.233 36.000 0.00 0.00 45.48 4.10
1225 1335 6.590677 TCGGTTAAACATCATAATGTCAACGA 59.409 34.615 0.00 0.00 45.48 3.85
1474 1585 1.300971 GCTTCCTCATCGCAAGCACA 61.301 55.000 0.00 0.00 41.87 4.57
1549 1660 9.908152 CTCCGTATCACAACTGAACATATATAA 57.092 33.333 0.00 0.00 0.00 0.98
1658 1773 5.425577 TTGAATCTCACTAGCTAGCTACG 57.574 43.478 20.67 17.54 0.00 3.51
1724 1840 7.867403 AGTTATTTTCTGCAATTTTGACGACAT 59.133 29.630 0.00 0.00 0.00 3.06
1725 1841 9.123709 GTTATTTTCTGCAATTTTGACGACATA 57.876 29.630 0.00 0.00 0.00 2.29
1726 1842 9.853555 TTATTTTCTGCAATTTTGACGACATAT 57.146 25.926 0.00 0.00 0.00 1.78
1738 1854 3.747529 TGACGACATATATAGTTCGCCGA 59.252 43.478 13.19 0.00 0.00 5.54
1739 1855 4.393990 TGACGACATATATAGTTCGCCGAT 59.606 41.667 13.19 0.00 0.00 4.18
1740 1856 5.581874 TGACGACATATATAGTTCGCCGATA 59.418 40.000 13.19 0.00 0.00 2.92
1779 1895 7.854166 ATAGAGAGAGAAAATGCATCCTACT 57.146 36.000 0.00 0.00 0.00 2.57
1780 1896 8.948401 ATAGAGAGAGAAAATGCATCCTACTA 57.052 34.615 0.00 2.02 0.00 1.82
1781 1897 7.049799 AGAGAGAGAAAATGCATCCTACTAC 57.950 40.000 0.00 0.00 0.00 2.73
1782 1898 6.041523 AGAGAGAGAAAATGCATCCTACTACC 59.958 42.308 0.00 0.00 0.00 3.18
1784 1900 4.058817 GAGAAAATGCATCCTACTACCGG 58.941 47.826 0.00 0.00 0.00 5.28
1785 1901 2.930826 AAATGCATCCTACTACCGGG 57.069 50.000 6.32 0.00 0.00 5.73
1786 1902 1.802553 AATGCATCCTACTACCGGGT 58.197 50.000 6.32 4.46 0.00 5.28
1787 1903 1.048601 ATGCATCCTACTACCGGGTG 58.951 55.000 10.66 0.00 35.71 4.61
1788 1904 0.324923 TGCATCCTACTACCGGGTGT 60.325 55.000 10.66 6.62 35.06 4.16
1789 1905 1.063792 TGCATCCTACTACCGGGTGTA 60.064 52.381 10.66 7.54 35.06 2.90
1811 1927 8.004087 TGTAGTTACACCCACTTCTCATATAC 57.996 38.462 0.00 0.00 0.00 1.47
1812 1928 7.837689 TGTAGTTACACCCACTTCTCATATACT 59.162 37.037 0.00 0.00 0.00 2.12
1813 1929 9.347240 GTAGTTACACCCACTTCTCATATACTA 57.653 37.037 0.00 0.00 0.00 1.82
1814 1930 8.235359 AGTTACACCCACTTCTCATATACTAC 57.765 38.462 0.00 0.00 0.00 2.73
1815 1931 7.287235 AGTTACACCCACTTCTCATATACTACC 59.713 40.741 0.00 0.00 0.00 3.18
1818 1934 6.098409 ACACCCACTTCTCATATACTACCTTG 59.902 42.308 0.00 0.00 0.00 3.61
1819 1935 6.098409 CACCCACTTCTCATATACTACCTTGT 59.902 42.308 0.00 0.00 0.00 3.16
1820 1936 6.098409 ACCCACTTCTCATATACTACCTTGTG 59.902 42.308 0.00 0.00 0.00 3.33
1823 1939 7.287005 CCACTTCTCATATACTACCTTGTGGTA 59.713 40.741 0.00 0.00 46.43 3.25
1839 1955 9.933240 ACCTTGTGGTAGTATATACTCTACTTT 57.067 33.333 18.68 0.00 46.43 2.66
1922 2038 5.557891 AATTGCAAGTGAGCTCATAGTTC 57.442 39.130 21.47 6.41 34.99 3.01
1924 2040 5.405935 TTGCAAGTGAGCTCATAGTTCTA 57.594 39.130 21.47 3.14 34.99 2.10
1930 2046 9.868277 GCAAGTGAGCTCATAGTTCTATTATAT 57.132 33.333 21.47 0.00 0.00 0.86
1967 2103 8.826710 CATACATATTTGTACACGAAATGGAGT 58.173 33.333 0.00 0.00 41.02 3.85
1975 2111 3.407698 ACACGAAATGGAGTATGCACAA 58.592 40.909 0.00 0.00 41.42 3.33
1977 2113 4.277174 ACACGAAATGGAGTATGCACAAAA 59.723 37.500 0.00 0.00 41.42 2.44
1981 2520 7.166307 CACGAAATGGAGTATGCACAAAATATG 59.834 37.037 0.00 0.00 41.42 1.78
1982 2521 6.638063 CGAAATGGAGTATGCACAAAATATGG 59.362 38.462 0.00 0.00 41.42 2.74
1983 2522 7.422465 AAATGGAGTATGCACAAAATATGGT 57.578 32.000 0.00 0.00 41.42 3.55
1984 2523 8.532186 AAATGGAGTATGCACAAAATATGGTA 57.468 30.769 0.00 0.00 41.42 3.25
1985 2524 6.935741 TGGAGTATGCACAAAATATGGTAC 57.064 37.500 0.00 0.00 0.00 3.34
1986 2525 7.059788 ATGGAGTATGCACAAAATATGGTACA 58.940 34.615 0.00 0.00 41.42 2.90
1987 2526 7.725397 ATGGAGTATGCACAAAATATGGTACAT 59.275 33.333 0.00 0.00 42.48 2.29
2058 2597 9.775854 ACTACATATTACGTGTACATACTCTCT 57.224 33.333 0.00 0.00 0.00 3.10
2100 2639 9.878599 ACTTAGAACGTATGAAACAAAAATGAG 57.121 29.630 0.00 0.00 0.00 2.90
2103 2642 8.154649 AGAACGTATGAAACAAAAATGAGAGT 57.845 30.769 0.00 0.00 0.00 3.24
2104 2643 9.268268 AGAACGTATGAAACAAAAATGAGAGTA 57.732 29.630 0.00 0.00 0.00 2.59
2105 2644 9.872757 GAACGTATGAAACAAAAATGAGAGTAA 57.127 29.630 0.00 0.00 0.00 2.24
2106 2645 9.659830 AACGTATGAAACAAAAATGAGAGTAAC 57.340 29.630 0.00 0.00 0.00 2.50
2107 2646 9.052759 ACGTATGAAACAAAAATGAGAGTAACT 57.947 29.630 0.00 0.00 0.00 2.24
2112 2651 8.617809 TGAAACAAAAATGAGAGTAACTACACC 58.382 33.333 0.00 0.00 0.00 4.16
2113 2652 7.506328 AACAAAAATGAGAGTAACTACACCC 57.494 36.000 0.00 0.00 0.00 4.61
2114 2653 5.699458 ACAAAAATGAGAGTAACTACACCCG 59.301 40.000 0.00 0.00 0.00 5.28
2115 2654 5.733620 AAAATGAGAGTAACTACACCCGA 57.266 39.130 0.00 0.00 0.00 5.14
2116 2655 5.934402 AAATGAGAGTAACTACACCCGAT 57.066 39.130 0.00 0.00 0.00 4.18
2117 2656 5.934402 AATGAGAGTAACTACACCCGATT 57.066 39.130 0.00 0.00 0.00 3.34
2118 2657 4.713824 TGAGAGTAACTACACCCGATTG 57.286 45.455 0.00 0.00 0.00 2.67
2119 2658 4.084287 TGAGAGTAACTACACCCGATTGT 58.916 43.478 0.00 0.00 0.00 2.71
2120 2659 5.255687 TGAGAGTAACTACACCCGATTGTA 58.744 41.667 0.00 0.00 0.00 2.41
2128 2667 5.560966 CTACACCCGATTGTAGCAAAAAT 57.439 39.130 9.59 0.00 41.88 1.82
2129 2668 4.864704 ACACCCGATTGTAGCAAAAATT 57.135 36.364 0.00 0.00 0.00 1.82
2130 2669 5.208463 ACACCCGATTGTAGCAAAAATTT 57.792 34.783 0.00 0.00 0.00 1.82
2131 2670 4.987912 ACACCCGATTGTAGCAAAAATTTG 59.012 37.500 1.52 1.52 41.03 2.32
2132 2671 4.987912 CACCCGATTGTAGCAAAAATTTGT 59.012 37.500 7.64 0.00 40.24 2.83
2133 2672 5.465056 CACCCGATTGTAGCAAAAATTTGTT 59.535 36.000 7.64 4.34 40.24 2.83
2134 2673 6.642950 CACCCGATTGTAGCAAAAATTTGTTA 59.357 34.615 7.64 3.41 40.24 2.41
2135 2674 7.330700 CACCCGATTGTAGCAAAAATTTGTTAT 59.669 33.333 7.64 0.00 40.24 1.89
2136 2675 8.524487 ACCCGATTGTAGCAAAAATTTGTTATA 58.476 29.630 7.64 2.12 40.24 0.98
2137 2676 9.528018 CCCGATTGTAGCAAAAATTTGTTATAT 57.472 29.630 7.64 4.57 40.24 0.86
2173 2712 2.055299 GGGACGGAGGAAGTGTTCA 58.945 57.895 0.00 0.00 0.00 3.18
2174 2713 0.613777 GGGACGGAGGAAGTGTTCAT 59.386 55.000 0.00 0.00 0.00 2.57
2175 2714 1.829222 GGGACGGAGGAAGTGTTCATA 59.171 52.381 0.00 0.00 0.00 2.15
2176 2715 2.434702 GGGACGGAGGAAGTGTTCATAT 59.565 50.000 0.00 0.00 0.00 1.78
2177 2716 3.640029 GGGACGGAGGAAGTGTTCATATA 59.360 47.826 0.00 0.00 0.00 0.86
2178 2717 4.501058 GGGACGGAGGAAGTGTTCATATAC 60.501 50.000 0.00 0.00 0.00 1.47
2179 2718 4.098960 GGACGGAGGAAGTGTTCATATACA 59.901 45.833 0.00 0.00 0.00 2.29
2180 2719 5.007385 ACGGAGGAAGTGTTCATATACAC 57.993 43.478 1.15 1.15 46.86 2.90
2189 2728 5.007385 GTGTTCATATACACTTCCTCCGT 57.993 43.478 2.11 0.00 43.92 4.69
2190 2729 5.041940 GTGTTCATATACACTTCCTCCGTC 58.958 45.833 2.11 0.00 43.92 4.79
2191 2730 4.098960 TGTTCATATACACTTCCTCCGTCC 59.901 45.833 0.00 0.00 0.00 4.79
2192 2731 4.180377 TCATATACACTTCCTCCGTCCT 57.820 45.455 0.00 0.00 0.00 3.85
2193 2732 3.889538 TCATATACACTTCCTCCGTCCTG 59.110 47.826 0.00 0.00 0.00 3.86
2194 2733 2.233305 ATACACTTCCTCCGTCCTGT 57.767 50.000 0.00 0.00 0.00 4.00
2195 2734 2.885135 TACACTTCCTCCGTCCTGTA 57.115 50.000 0.00 0.00 0.00 2.74
2196 2735 2.005370 ACACTTCCTCCGTCCTGTAA 57.995 50.000 0.00 0.00 0.00 2.41
2197 2736 2.537143 ACACTTCCTCCGTCCTGTAAT 58.463 47.619 0.00 0.00 0.00 1.89
2198 2737 3.705051 ACACTTCCTCCGTCCTGTAATA 58.295 45.455 0.00 0.00 0.00 0.98
2199 2738 4.287552 ACACTTCCTCCGTCCTGTAATAT 58.712 43.478 0.00 0.00 0.00 1.28
2200 2739 5.452255 ACACTTCCTCCGTCCTGTAATATA 58.548 41.667 0.00 0.00 0.00 0.86
2201 2740 5.895534 ACACTTCCTCCGTCCTGTAATATAA 59.104 40.000 0.00 0.00 0.00 0.98
2202 2741 6.040616 ACACTTCCTCCGTCCTGTAATATAAG 59.959 42.308 0.00 0.00 0.00 1.73
2203 2742 6.264744 CACTTCCTCCGTCCTGTAATATAAGA 59.735 42.308 0.00 0.00 0.00 2.10
2204 2743 6.837568 ACTTCCTCCGTCCTGTAATATAAGAA 59.162 38.462 0.00 0.00 0.00 2.52
2205 2744 7.509659 ACTTCCTCCGTCCTGTAATATAAGAAT 59.490 37.037 0.00 0.00 0.00 2.40
2206 2745 7.228314 TCCTCCGTCCTGTAATATAAGAATG 57.772 40.000 0.00 0.00 0.00 2.67
2207 2746 6.781014 TCCTCCGTCCTGTAATATAAGAATGT 59.219 38.462 0.00 0.00 0.00 2.71
2208 2747 7.289317 TCCTCCGTCCTGTAATATAAGAATGTT 59.711 37.037 0.00 0.00 0.00 2.71
2209 2748 7.931948 CCTCCGTCCTGTAATATAAGAATGTTT 59.068 37.037 0.00 0.00 0.00 2.83
2210 2749 9.326413 CTCCGTCCTGTAATATAAGAATGTTTT 57.674 33.333 0.00 0.00 0.00 2.43
2211 2750 9.675464 TCCGTCCTGTAATATAAGAATGTTTTT 57.325 29.630 0.00 0.00 0.00 1.94
2212 2751 9.716507 CCGTCCTGTAATATAAGAATGTTTTTG 57.283 33.333 0.00 0.00 0.00 2.44
2345 2884 1.292223 GTGGCTCTAACGGAGTGCA 59.708 57.895 13.44 0.00 45.00 4.57
2351 2890 2.017782 CTCTAACGGAGTGCAGCTAGA 58.982 52.381 0.00 0.00 45.00 2.43
2530 3069 2.016318 GCATGGATCGGTCAATGTTCA 58.984 47.619 14.55 0.00 37.96 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 2.357396 TGTGCTGGCTGCTGTACG 60.357 61.111 17.45 0.00 43.37 3.67
64 66 4.269363 GCTTGATGATTAATTTGCCTGTGC 59.731 41.667 0.00 0.00 38.26 4.57
65 67 5.412640 TGCTTGATGATTAATTTGCCTGTG 58.587 37.500 0.00 0.00 0.00 3.66
66 68 5.664294 TGCTTGATGATTAATTTGCCTGT 57.336 34.783 0.00 0.00 0.00 4.00
67 69 5.870433 TGTTGCTTGATGATTAATTTGCCTG 59.130 36.000 0.00 0.00 0.00 4.85
68 70 6.040209 TGTTGCTTGATGATTAATTTGCCT 57.960 33.333 0.00 0.00 0.00 4.75
203 211 0.607489 AGTGCCATCTGCCACTGTTC 60.607 55.000 0.00 0.00 40.16 3.18
217 225 2.159448 TGCAATTATTACGTGCAGTGCC 60.159 45.455 13.72 2.92 43.09 5.01
405 413 1.805945 GCACCTGCCGTACGAGAAG 60.806 63.158 18.76 10.66 34.31 2.85
408 416 2.507102 CAGCACCTGCCGTACGAG 60.507 66.667 18.76 6.94 43.38 4.18
534 542 8.686334 CCTTGTGTATAAAAATGAAGGCAGTAT 58.314 33.333 0.00 0.00 0.00 2.12
547 555 7.556733 AAACGAAGTGACCTTGTGTATAAAA 57.443 32.000 0.00 0.00 45.00 1.52
753 762 4.421948 ACTCGCTTCGTTCCTTTATACAG 58.578 43.478 0.00 0.00 0.00 2.74
761 770 4.715527 AATTAGTACTCGCTTCGTTCCT 57.284 40.909 0.00 0.00 0.00 3.36
766 775 7.230466 ACCAAAATAATTAGTACTCGCTTCG 57.770 36.000 0.00 0.00 0.00 3.79
820 929 5.355596 TGTTTTTGCAAGGAATACACAAGG 58.644 37.500 0.00 0.00 0.00 3.61
834 943 8.399425 TCTTTACGTAAGATTTCTGTTTTTGCA 58.601 29.630 8.23 0.00 37.96 4.08
890 999 1.325476 GGGGGAGGTACGTGGTAGTG 61.325 65.000 0.00 0.00 0.00 2.74
891 1000 1.000866 GGGGGAGGTACGTGGTAGT 59.999 63.158 0.00 0.00 0.00 2.73
892 1001 0.398098 ATGGGGGAGGTACGTGGTAG 60.398 60.000 0.00 0.00 0.00 3.18
893 1002 0.932955 TATGGGGGAGGTACGTGGTA 59.067 55.000 0.00 0.00 0.00 3.25
894 1003 0.266753 ATATGGGGGAGGTACGTGGT 59.733 55.000 0.00 0.00 0.00 4.16
895 1004 0.974383 GATATGGGGGAGGTACGTGG 59.026 60.000 0.00 0.00 0.00 4.94
1096 1206 0.376152 GCTTCGCATGAGGTGATGTG 59.624 55.000 0.00 0.00 35.59 3.21
1127 1237 2.177394 TAAGTGCTTGCCATTGACGA 57.823 45.000 0.00 0.00 0.00 4.20
1173 1283 1.064003 TAGGGCAGAAGCAAACCTGA 58.936 50.000 0.00 0.00 44.61 3.86
1186 1296 2.279935 AACCGAATTGTGTTAGGGCA 57.720 45.000 0.00 0.00 0.00 5.36
1217 1327 6.912203 TGTTAGAACAAAATCTCGTTGACA 57.088 33.333 0.00 0.00 35.67 3.58
1224 1334 6.272822 AGGGCAATGTTAGAACAAAATCTC 57.727 37.500 0.00 0.00 43.03 2.75
1225 1335 5.185828 GGAGGGCAATGTTAGAACAAAATCT 59.814 40.000 0.00 0.00 43.03 2.40
1474 1585 3.725797 AGGTGAATTCCCTGATCATCCAT 59.274 43.478 12.98 0.00 0.00 3.41
1549 1660 3.066064 GCTCTCATCCGTGATCGCTATAT 59.934 47.826 4.48 0.00 32.98 0.86
1550 1661 2.420372 GCTCTCATCCGTGATCGCTATA 59.580 50.000 4.48 0.00 32.98 1.31
1551 1662 1.201181 GCTCTCATCCGTGATCGCTAT 59.799 52.381 4.48 0.00 32.98 2.97
1552 1663 0.593618 GCTCTCATCCGTGATCGCTA 59.406 55.000 4.48 0.00 32.98 4.26
1553 1664 1.361993 GCTCTCATCCGTGATCGCT 59.638 57.895 4.48 0.00 32.98 4.93
1554 1665 1.663074 GGCTCTCATCCGTGATCGC 60.663 63.158 0.00 0.00 32.98 4.58
1658 1773 2.857152 CAGATACGACTTGAAGCTGCTC 59.143 50.000 1.00 0.00 0.00 4.26
1756 1872 7.231722 GGTAGTAGGATGCATTTTCTCTCTCTA 59.768 40.741 0.00 0.00 0.00 2.43
1757 1873 6.041523 GGTAGTAGGATGCATTTTCTCTCTCT 59.958 42.308 0.00 0.78 0.00 3.10
1758 1874 6.220201 GGTAGTAGGATGCATTTTCTCTCTC 58.780 44.000 0.00 0.00 0.00 3.20
1759 1875 5.221342 CGGTAGTAGGATGCATTTTCTCTCT 60.221 44.000 0.00 4.98 0.00 3.10
1760 1876 4.985409 CGGTAGTAGGATGCATTTTCTCTC 59.015 45.833 0.00 0.00 0.00 3.20
1761 1877 4.202264 CCGGTAGTAGGATGCATTTTCTCT 60.202 45.833 0.00 0.00 0.00 3.10
1764 1880 3.139077 CCCGGTAGTAGGATGCATTTTC 58.861 50.000 0.00 0.00 0.00 2.29
1767 1883 1.416401 CACCCGGTAGTAGGATGCATT 59.584 52.381 0.00 0.00 0.00 3.56
1768 1884 1.048601 CACCCGGTAGTAGGATGCAT 58.951 55.000 0.00 0.00 0.00 3.96
1770 1886 1.612463 CTACACCCGGTAGTAGGATGC 59.388 57.143 18.15 0.00 43.73 3.91
1786 1902 7.837689 AGTATATGAGAAGTGGGTGTAACTACA 59.162 37.037 0.00 0.00 36.74 2.74
1787 1903 8.235359 AGTATATGAGAAGTGGGTGTAACTAC 57.765 38.462 0.00 0.00 36.74 2.73
1788 1904 9.347240 GTAGTATATGAGAAGTGGGTGTAACTA 57.653 37.037 0.00 0.00 36.74 2.24
1789 1905 7.287235 GGTAGTATATGAGAAGTGGGTGTAACT 59.713 40.741 0.00 0.00 36.74 2.24
1790 1906 7.287235 AGGTAGTATATGAGAAGTGGGTGTAAC 59.713 40.741 0.00 0.00 0.00 2.50
1791 1907 7.359849 AGGTAGTATATGAGAAGTGGGTGTAA 58.640 38.462 0.00 0.00 0.00 2.41
1793 1909 5.778542 AGGTAGTATATGAGAAGTGGGTGT 58.221 41.667 0.00 0.00 0.00 4.16
1794 1910 6.098409 ACAAGGTAGTATATGAGAAGTGGGTG 59.902 42.308 0.00 0.00 0.00 4.61
1795 1911 6.098409 CACAAGGTAGTATATGAGAAGTGGGT 59.902 42.308 0.00 0.00 0.00 4.51
1796 1912 6.463049 CCACAAGGTAGTATATGAGAAGTGGG 60.463 46.154 0.00 0.00 38.30 4.61
1797 1913 6.516718 CCACAAGGTAGTATATGAGAAGTGG 58.483 44.000 0.00 0.00 36.13 4.00
1897 2013 6.336842 ACTATGAGCTCACTTGCAATTTTT 57.663 33.333 20.97 0.33 34.99 1.94
1898 2014 5.972107 ACTATGAGCTCACTTGCAATTTT 57.028 34.783 20.97 0.92 34.99 1.82
1899 2015 5.709164 AGAACTATGAGCTCACTTGCAATTT 59.291 36.000 20.97 1.76 34.99 1.82
1900 2016 5.251764 AGAACTATGAGCTCACTTGCAATT 58.748 37.500 20.97 6.72 34.99 2.32
1901 2017 4.841422 AGAACTATGAGCTCACTTGCAAT 58.159 39.130 20.97 3.44 34.99 3.56
1902 2018 4.277515 AGAACTATGAGCTCACTTGCAA 57.722 40.909 20.97 0.00 34.99 4.08
1903 2019 3.969287 AGAACTATGAGCTCACTTGCA 57.031 42.857 20.97 0.00 34.99 4.08
1904 2020 9.868277 ATATAATAGAACTATGAGCTCACTTGC 57.132 33.333 20.97 7.91 0.00 4.01
1942 2058 8.958119 ACTCCATTTCGTGTACAAATATGTAT 57.042 30.769 0.00 0.00 43.60 2.29
1944 2060 8.826710 CATACTCCATTTCGTGTACAAATATGT 58.173 33.333 0.00 0.00 43.74 2.29
1945 2061 7.798516 GCATACTCCATTTCGTGTACAAATATG 59.201 37.037 0.00 0.35 0.00 1.78
1947 2063 6.819146 TGCATACTCCATTTCGTGTACAAATA 59.181 34.615 0.00 0.00 0.00 1.40
1948 2064 5.645929 TGCATACTCCATTTCGTGTACAAAT 59.354 36.000 0.00 0.00 0.00 2.32
1949 2065 4.998033 TGCATACTCCATTTCGTGTACAAA 59.002 37.500 0.00 0.00 0.00 2.83
1951 2067 3.930229 GTGCATACTCCATTTCGTGTACA 59.070 43.478 0.00 0.00 0.00 2.90
1952 2068 3.930229 TGTGCATACTCCATTTCGTGTAC 59.070 43.478 0.00 0.00 0.00 2.90
1957 2073 6.638063 CCATATTTTGTGCATACTCCATTTCG 59.362 38.462 0.00 0.00 0.00 3.46
1958 2074 7.491682 ACCATATTTTGTGCATACTCCATTTC 58.508 34.615 0.00 0.00 0.00 2.17
1959 2075 7.422465 ACCATATTTTGTGCATACTCCATTT 57.578 32.000 0.00 0.00 0.00 2.32
1960 2076 7.559533 TGTACCATATTTTGTGCATACTCCATT 59.440 33.333 0.00 0.00 0.00 3.16
1961 2077 7.059788 TGTACCATATTTTGTGCATACTCCAT 58.940 34.615 0.00 0.00 0.00 3.41
1963 2079 6.935741 TGTACCATATTTTGTGCATACTCC 57.064 37.500 0.00 0.00 0.00 3.85
1967 2103 9.496873 GGTAGTATGTACCATATTTTGTGCATA 57.503 33.333 0.00 0.00 38.49 3.14
2032 2571 9.775854 AGAGAGTATGTACACGTAATATGTAGT 57.224 33.333 0.00 0.00 33.26 2.73
2074 2613 9.878599 CTCATTTTTGTTTCATACGTTCTAAGT 57.121 29.630 0.00 0.00 0.00 2.24
2077 2616 9.268268 ACTCTCATTTTTGTTTCATACGTTCTA 57.732 29.630 0.00 0.00 0.00 2.10
2078 2617 8.154649 ACTCTCATTTTTGTTTCATACGTTCT 57.845 30.769 0.00 0.00 0.00 3.01
2079 2618 9.872757 TTACTCTCATTTTTGTTTCATACGTTC 57.127 29.630 0.00 0.00 0.00 3.95
2080 2619 9.659830 GTTACTCTCATTTTTGTTTCATACGTT 57.340 29.630 0.00 0.00 0.00 3.99
2081 2620 9.052759 AGTTACTCTCATTTTTGTTTCATACGT 57.947 29.630 0.00 0.00 0.00 3.57
2086 2625 8.617809 GGTGTAGTTACTCTCATTTTTGTTTCA 58.382 33.333 0.00 0.00 0.00 2.69
2087 2626 8.074370 GGGTGTAGTTACTCTCATTTTTGTTTC 58.926 37.037 0.00 0.00 0.00 2.78
2088 2627 7.255001 CGGGTGTAGTTACTCTCATTTTTGTTT 60.255 37.037 0.00 0.00 0.00 2.83
2089 2628 6.204108 CGGGTGTAGTTACTCTCATTTTTGTT 59.796 38.462 0.00 0.00 0.00 2.83
2090 2629 5.699458 CGGGTGTAGTTACTCTCATTTTTGT 59.301 40.000 0.00 0.00 0.00 2.83
2091 2630 5.929992 TCGGGTGTAGTTACTCTCATTTTTG 59.070 40.000 0.00 0.00 0.00 2.44
2092 2631 6.105397 TCGGGTGTAGTTACTCTCATTTTT 57.895 37.500 0.00 0.00 0.00 1.94
2093 2632 5.733620 TCGGGTGTAGTTACTCTCATTTT 57.266 39.130 0.00 0.00 0.00 1.82
2094 2633 5.934402 ATCGGGTGTAGTTACTCTCATTT 57.066 39.130 0.00 0.00 0.00 2.32
2095 2634 5.187186 ACAATCGGGTGTAGTTACTCTCATT 59.813 40.000 0.00 0.00 0.00 2.57
2096 2635 4.710375 ACAATCGGGTGTAGTTACTCTCAT 59.290 41.667 0.00 0.00 0.00 2.90
2097 2636 4.084287 ACAATCGGGTGTAGTTACTCTCA 58.916 43.478 0.00 0.00 0.00 3.27
2098 2637 4.715527 ACAATCGGGTGTAGTTACTCTC 57.284 45.455 0.00 0.00 0.00 3.20
2099 2638 5.831702 CTACAATCGGGTGTAGTTACTCT 57.168 43.478 14.67 0.00 43.99 3.24
2107 2646 5.968528 AATTTTTGCTACAATCGGGTGTA 57.031 34.783 0.23 0.23 32.75 2.90
2108 2647 4.864704 AATTTTTGCTACAATCGGGTGT 57.135 36.364 0.00 0.00 35.43 4.16
2109 2648 4.987912 ACAAATTTTTGCTACAATCGGGTG 59.012 37.500 3.00 0.00 41.79 4.61
2110 2649 5.208463 ACAAATTTTTGCTACAATCGGGT 57.792 34.783 3.00 0.00 41.79 5.28
2111 2650 7.826260 ATAACAAATTTTTGCTACAATCGGG 57.174 32.000 3.00 0.00 41.79 5.14
2141 2680 9.730705 CTTCCTCCGTCCCGTAATATATATATA 57.269 37.037 5.66 4.92 0.00 0.86
2142 2681 8.223330 ACTTCCTCCGTCCCGTAATATATATAT 58.777 37.037 0.00 0.00 0.00 0.86
2143 2682 7.500227 CACTTCCTCCGTCCCGTAATATATATA 59.500 40.741 0.00 0.00 0.00 0.86
2144 2683 6.320672 CACTTCCTCCGTCCCGTAATATATAT 59.679 42.308 0.00 0.00 0.00 0.86
2145 2684 5.649395 CACTTCCTCCGTCCCGTAATATATA 59.351 44.000 0.00 0.00 0.00 0.86
2146 2685 4.461781 CACTTCCTCCGTCCCGTAATATAT 59.538 45.833 0.00 0.00 0.00 0.86
2147 2686 3.822735 CACTTCCTCCGTCCCGTAATATA 59.177 47.826 0.00 0.00 0.00 0.86
2148 2687 2.626743 CACTTCCTCCGTCCCGTAATAT 59.373 50.000 0.00 0.00 0.00 1.28
2149 2688 2.026641 CACTTCCTCCGTCCCGTAATA 58.973 52.381 0.00 0.00 0.00 0.98
2150 2689 0.822164 CACTTCCTCCGTCCCGTAAT 59.178 55.000 0.00 0.00 0.00 1.89
2151 2690 0.540365 ACACTTCCTCCGTCCCGTAA 60.540 55.000 0.00 0.00 0.00 3.18
2152 2691 0.540365 AACACTTCCTCCGTCCCGTA 60.540 55.000 0.00 0.00 0.00 4.02
2153 2692 1.813728 GAACACTTCCTCCGTCCCGT 61.814 60.000 0.00 0.00 0.00 5.28
2154 2693 1.080025 GAACACTTCCTCCGTCCCG 60.080 63.158 0.00 0.00 0.00 5.14
2155 2694 0.613777 ATGAACACTTCCTCCGTCCC 59.386 55.000 0.00 0.00 0.00 4.46
2156 2695 3.821421 ATATGAACACTTCCTCCGTCC 57.179 47.619 0.00 0.00 0.00 4.79
2157 2696 5.041940 GTGTATATGAACACTTCCTCCGTC 58.958 45.833 2.11 0.00 45.12 4.79
2158 2697 5.007385 GTGTATATGAACACTTCCTCCGT 57.993 43.478 2.11 0.00 45.12 4.69
2168 2707 4.098960 GGACGGAGGAAGTGTATATGAACA 59.901 45.833 0.00 0.00 0.00 3.18
2169 2708 4.341520 AGGACGGAGGAAGTGTATATGAAC 59.658 45.833 0.00 0.00 0.00 3.18
2170 2709 4.341235 CAGGACGGAGGAAGTGTATATGAA 59.659 45.833 0.00 0.00 0.00 2.57
2171 2710 3.889538 CAGGACGGAGGAAGTGTATATGA 59.110 47.826 0.00 0.00 0.00 2.15
2172 2711 3.637229 ACAGGACGGAGGAAGTGTATATG 59.363 47.826 0.00 0.00 0.00 1.78
2173 2712 3.912248 ACAGGACGGAGGAAGTGTATAT 58.088 45.455 0.00 0.00 0.00 0.86
2174 2713 3.377253 ACAGGACGGAGGAAGTGTATA 57.623 47.619 0.00 0.00 0.00 1.47
2175 2714 2.233305 ACAGGACGGAGGAAGTGTAT 57.767 50.000 0.00 0.00 0.00 2.29
2176 2715 2.885135 TACAGGACGGAGGAAGTGTA 57.115 50.000 0.00 0.00 0.00 2.90
2177 2716 2.005370 TTACAGGACGGAGGAAGTGT 57.995 50.000 0.00 0.00 0.00 3.55
2178 2717 4.939052 ATATTACAGGACGGAGGAAGTG 57.061 45.455 0.00 0.00 0.00 3.16
2179 2718 6.371278 TCTTATATTACAGGACGGAGGAAGT 58.629 40.000 0.00 0.00 0.00 3.01
2180 2719 6.896021 TCTTATATTACAGGACGGAGGAAG 57.104 41.667 0.00 0.00 0.00 3.46
2181 2720 7.289317 ACATTCTTATATTACAGGACGGAGGAA 59.711 37.037 0.00 0.00 0.00 3.36
2182 2721 6.781014 ACATTCTTATATTACAGGACGGAGGA 59.219 38.462 0.00 0.00 0.00 3.71
2183 2722 6.994221 ACATTCTTATATTACAGGACGGAGG 58.006 40.000 0.00 0.00 0.00 4.30
2184 2723 8.888579 AAACATTCTTATATTACAGGACGGAG 57.111 34.615 0.00 0.00 0.00 4.63
2185 2724 9.675464 AAAAACATTCTTATATTACAGGACGGA 57.325 29.630 0.00 0.00 0.00 4.69
2186 2725 9.716507 CAAAAACATTCTTATATTACAGGACGG 57.283 33.333 0.00 0.00 0.00 4.79
2200 2739 9.561069 AGATAGTGTAGTGTCAAAAACATTCTT 57.439 29.630 0.00 0.00 40.80 2.52
2201 2740 9.209175 GAGATAGTGTAGTGTCAAAAACATTCT 57.791 33.333 0.00 0.00 40.80 2.40
2202 2741 8.988934 TGAGATAGTGTAGTGTCAAAAACATTC 58.011 33.333 0.00 0.00 40.80 2.67
2203 2742 8.902540 TGAGATAGTGTAGTGTCAAAAACATT 57.097 30.769 0.00 0.00 40.80 2.71
2205 2744 9.419297 GTATGAGATAGTGTAGTGTCAAAAACA 57.581 33.333 0.00 0.00 34.78 2.83
2206 2745 9.419297 TGTATGAGATAGTGTAGTGTCAAAAAC 57.581 33.333 0.00 0.00 0.00 2.43
2208 2747 9.586435 CATGTATGAGATAGTGTAGTGTCAAAA 57.414 33.333 0.00 0.00 0.00 2.44
2209 2748 7.706607 GCATGTATGAGATAGTGTAGTGTCAAA 59.293 37.037 0.00 0.00 0.00 2.69
2210 2749 7.203218 GCATGTATGAGATAGTGTAGTGTCAA 58.797 38.462 0.00 0.00 0.00 3.18
2211 2750 6.239036 GGCATGTATGAGATAGTGTAGTGTCA 60.239 42.308 0.00 0.00 0.00 3.58
2212 2751 6.153067 GGCATGTATGAGATAGTGTAGTGTC 58.847 44.000 0.00 0.00 0.00 3.67
2213 2752 5.278512 CGGCATGTATGAGATAGTGTAGTGT 60.279 44.000 0.00 0.00 0.00 3.55
2214 2753 5.157067 CGGCATGTATGAGATAGTGTAGTG 58.843 45.833 0.00 0.00 0.00 2.74
2215 2754 4.218635 CCGGCATGTATGAGATAGTGTAGT 59.781 45.833 0.00 0.00 0.00 2.73
2216 2755 4.218635 ACCGGCATGTATGAGATAGTGTAG 59.781 45.833 0.00 0.00 0.00 2.74
2217 2756 4.022329 CACCGGCATGTATGAGATAGTGTA 60.022 45.833 0.00 0.00 0.00 2.90
2218 2757 2.965831 ACCGGCATGTATGAGATAGTGT 59.034 45.455 0.00 0.00 0.00 3.55
2219 2758 3.320626 CACCGGCATGTATGAGATAGTG 58.679 50.000 0.00 0.00 0.00 2.74
2220 2759 2.289072 GCACCGGCATGTATGAGATAGT 60.289 50.000 0.00 0.00 40.72 2.12
2221 2760 2.341257 GCACCGGCATGTATGAGATAG 58.659 52.381 0.00 0.00 40.72 2.08
2342 2881 2.031870 TCGCCTTAGATTCTAGCTGCA 58.968 47.619 1.02 0.00 0.00 4.41
2345 2884 2.362717 GTGGTCGCCTTAGATTCTAGCT 59.637 50.000 0.00 0.00 0.00 3.32
2351 2890 0.108329 CACGGTGGTCGCCTTAGATT 60.108 55.000 0.00 0.00 43.89 2.40
2462 3001 3.587061 TCAATCAAAGAGGTAAGCCCTGA 59.413 43.478 0.00 0.00 46.51 3.86


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

AutoCloner maintained by Alex Coulton.