Multiple sequence alignment - TraesCS2D01G330500

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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 TraesCS2D01G330500 chr2D 100.000 2523 0 0 1 2523 423293515 423290993 0.000000e+00 4660.0
1 TraesCS2D01G330500 chr2D 85.022 681 56 22 970 1627 423347840 423347183 0.000000e+00 651.0
2 TraesCS2D01G330500 chr2D 84.821 448 39 11 2095 2522 423308780 423308342 8.340000e-115 424.0
3 TraesCS2D01G330500 chr2D 83.429 350 46 4 128 475 423311763 423311424 5.240000e-82 315.0
4 TraesCS2D01G330500 chr2D 89.879 247 13 4 734 972 423348128 423347886 8.770000e-80 307.0
5 TraesCS2D01G330500 chr2D 89.655 87 7 1 1900 1984 423345802 423345716 2.650000e-20 110.0
6 TraesCS2D01G330500 chr2D 73.944 284 36 23 646 920 423280775 423280521 2.080000e-11 80.5
7 TraesCS2D01G330500 chr2D 100.000 30 0 0 100 129 192313450 192313479 3.510000e-04 56.5
8 TraesCS2D01G330500 chr2A 89.506 991 57 12 1 968 565281873 565282839 0.000000e+00 1210.0
9 TraesCS2D01G330500 chr2A 87.500 912 50 26 969 1827 565282884 565283784 0.000000e+00 994.0
10 TraesCS2D01G330500 chr2A 84.526 685 66 22 970 1629 565234294 565234963 2.120000e-180 641.0
11 TraesCS2D01G330500 chr2A 86.323 563 52 15 975 1525 565324113 565324662 7.770000e-165 590.0
12 TraesCS2D01G330500 chr2A 84.710 569 62 16 973 1531 565288281 565288834 1.710000e-151 545.0
13 TraesCS2D01G330500 chr2A 82.222 675 67 27 976 1629 565256128 565256770 1.330000e-147 532.0
14 TraesCS2D01G330500 chr2A 82.615 650 57 24 1000 1611 565313417 565314048 8.000000e-145 523.0
15 TraesCS2D01G330500 chr2A 77.962 785 85 46 196 965 565269494 565270205 6.500000e-111 411.0
16 TraesCS2D01G330500 chr2A 83.784 444 43 11 2094 2521 565259191 565259621 6.540000e-106 394.0
17 TraesCS2D01G330500 chr2A 87.079 356 29 8 623 965 565233907 565234258 1.090000e-103 387.0
18 TraesCS2D01G330500 chr2A 85.141 249 24 5 2278 2522 565271712 565271951 2.510000e-60 243.0
19 TraesCS2D01G330500 chr2A 80.317 315 41 10 1970 2268 565314402 565314711 4.230000e-53 219.0
20 TraesCS2D01G330500 chr2A 86.935 199 18 5 2323 2519 565314707 565314899 1.520000e-52 217.0
21 TraesCS2D01G330500 chr2A 83.436 163 15 6 2054 2204 565271005 565271167 9.410000e-30 141.0
22 TraesCS2D01G330500 chr2A 88.350 103 10 2 2149 2251 565271261 565271361 3.410000e-24 122.0
23 TraesCS2D01G330500 chr2A 80.328 183 16 7 1667 1829 565235061 565235243 1.230000e-23 121.0
24 TraesCS2D01G330500 chr2A 89.286 56 4 2 2149 2204 565271163 565271216 4.500000e-08 69.4
25 TraesCS2D01G330500 chr2A 92.857 42 1 1 1900 1939 565235342 565235383 2.710000e-05 60.2
26 TraesCS2D01G330500 chr2A 100.000 30 0 0 100 129 205490674 205490645 3.510000e-04 56.5
27 TraesCS2D01G330500 chr2A 100.000 28 0 0 102 129 379154316 379154343 5.000000e-03 52.8
28 TraesCS2D01G330500 chr2B 82.493 1051 112 41 623 1629 496542775 496541753 0.000000e+00 856.0
29 TraesCS2D01G330500 chr2B 85.736 666 56 20 977 1626 496078783 496078141 0.000000e+00 667.0
30 TraesCS2D01G330500 chr2B 86.894 557 41 17 989 1525 496355511 496354967 1.670000e-166 595.0
31 TraesCS2D01G330500 chr2B 86.715 557 42 17 989 1525 496353354 496352810 7.770000e-165 590.0
32 TraesCS2D01G330500 chr2B 83.756 671 55 29 989 1629 496351197 496350551 1.010000e-163 586.0
33 TraesCS2D01G330500 chr2B 83.016 683 53 29 974 1629 496512602 496511956 6.090000e-156 560.0
34 TraesCS2D01G330500 chr2B 84.790 572 50 22 973 1531 496087926 496087379 7.940000e-150 540.0
35 TraesCS2D01G330500 chr2B 83.048 643 52 24 974 1595 496118340 496117734 4.780000e-147 531.0
36 TraesCS2D01G330500 chr2B 85.545 505 45 14 1068 1564 496359753 496359269 1.040000e-138 503.0
37 TraesCS2D01G330500 chr2B 84.753 446 42 10 2094 2522 496117120 496116684 8.340000e-115 424.0
38 TraesCS2D01G330500 chr2B 78.869 672 64 34 326 965 496351881 496351256 1.420000e-102 383.0
39 TraesCS2D01G330500 chr2B 78.869 672 64 34 326 965 496354038 496353413 1.420000e-102 383.0
40 TraesCS2D01G330500 chr2B 78.869 672 64 34 326 965 496356195 496355570 1.420000e-102 383.0
41 TraesCS2D01G330500 chr2B 84.750 400 41 11 2094 2477 496494748 496494353 1.420000e-102 383.0
42 TraesCS2D01G330500 chr2B 86.719 256 21 9 2270 2522 496329438 496329193 3.200000e-69 272.0
43 TraesCS2D01G330500 chr2B 77.515 507 59 28 334 836 496513208 496512753 1.160000e-63 254.0
44 TraesCS2D01G330500 chr2B 88.095 126 8 3 2150 2268 496077698 496077573 2.620000e-30 143.0
45 TraesCS2D01G330500 chr2B 89.320 103 7 3 1527 1627 496176298 496176198 2.630000e-25 126.0
46 TraesCS2D01G330500 chr2B 77.489 231 30 17 1752 1973 496330033 496329816 4.410000e-23 119.0
47 TraesCS2D01G330500 chr2B 91.139 79 7 0 1751 1829 496117613 496117535 9.540000e-20 108.0
48 TraesCS2D01G330500 chr2B 88.608 79 9 0 1751 1829 496511511 496511433 2.070000e-16 97.1
49 TraesCS2D01G330500 chr7D 96.774 62 2 0 735 796 51234758 51234819 1.230000e-18 104.0
50 TraesCS2D01G330500 chr7D 100.000 29 0 0 102 130 18888876 18888904 1.000000e-03 54.7
51 TraesCS2D01G330500 chr7A 84.000 100 9 3 31 129 172323945 172324038 3.460000e-14 89.8
52 TraesCS2D01G330500 chr3A 77.982 109 19 3 21 129 673906205 673906308 2.100000e-06 63.9
53 TraesCS2D01G330500 chr3D 96.875 32 1 0 98 129 538406549 538406580 1.000000e-03 54.7


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 TraesCS2D01G330500 chr2D 423290993 423293515 2522 True 4660.000000 4660 100.000000 1 2523 1 chr2D.!!$R2 2522
1 TraesCS2D01G330500 chr2D 423308342 423311763 3421 True 369.500000 424 84.125000 128 2522 2 chr2D.!!$R3 2394
2 TraesCS2D01G330500 chr2D 423345716 423348128 2412 True 356.000000 651 88.185333 734 1984 3 chr2D.!!$R4 1250
3 TraesCS2D01G330500 chr2A 565281873 565283784 1911 False 1102.000000 1210 88.503000 1 1827 2 chr2A.!!$F7 1826
4 TraesCS2D01G330500 chr2A 565324113 565324662 549 False 590.000000 590 86.323000 975 1525 1 chr2A.!!$F3 550
5 TraesCS2D01G330500 chr2A 565288281 565288834 553 False 545.000000 545 84.710000 973 1531 1 chr2A.!!$F2 558
6 TraesCS2D01G330500 chr2A 565256128 565259621 3493 False 463.000000 532 83.003000 976 2521 2 chr2A.!!$F5 1545
7 TraesCS2D01G330500 chr2A 565313417 565314899 1482 False 319.666667 523 83.289000 1000 2519 3 chr2A.!!$F8 1519
8 TraesCS2D01G330500 chr2A 565233907 565235383 1476 False 302.300000 641 86.197500 623 1939 4 chr2A.!!$F4 1316
9 TraesCS2D01G330500 chr2B 496541753 496542775 1022 True 856.000000 856 82.493000 623 1629 1 chr2B.!!$R4 1006
10 TraesCS2D01G330500 chr2B 496087379 496087926 547 True 540.000000 540 84.790000 973 1531 1 chr2B.!!$R1 558
11 TraesCS2D01G330500 chr2B 496350551 496359753 9202 True 489.000000 595 82.788143 326 1629 7 chr2B.!!$R8 1303
12 TraesCS2D01G330500 chr2B 496077573 496078783 1210 True 405.000000 667 86.915500 977 2268 2 chr2B.!!$R5 1291
13 TraesCS2D01G330500 chr2B 496116684 496118340 1656 True 354.333333 531 86.313333 974 2522 3 chr2B.!!$R6 1548
14 TraesCS2D01G330500 chr2B 496511433 496513208 1775 True 303.700000 560 83.046333 334 1829 3 chr2B.!!$R9 1495

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
145 149 0.465705 CTCGTGCATGTGGGGTCTAT 59.534 55.0 5.68 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 14562 0.032615 AAAACCAGGCCCAACACTGA 60.033 50.0 0.0 0.0 36.86 3.41 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
62 63 6.094325 TGCCCACTACTTAATTAAATCAACGG 59.906 38.462 0.00 0.00 0.00 4.44
65 66 7.407337 CCACTACTTAATTAAATCAACGGCTC 58.593 38.462 0.00 0.00 0.00 4.70
67 68 7.009815 CACTACTTAATTAAATCAACGGCTCGA 59.990 37.037 0.00 0.00 0.00 4.04
68 69 6.730960 ACTTAATTAAATCAACGGCTCGAA 57.269 33.333 0.00 0.00 0.00 3.71
145 149 0.465705 CTCGTGCATGTGGGGTCTAT 59.534 55.000 5.68 0.00 0.00 1.98
164 168 2.526304 TACAGGTAGCAATGCCGATC 57.474 50.000 0.00 0.00 0.00 3.69
170 174 1.873591 GTAGCAATGCCGATCGGAAAT 59.126 47.619 37.64 25.24 37.50 2.17
371 3608 4.511617 TTGTGTGCAGTTGTGAAAAAGA 57.488 36.364 0.00 0.00 0.00 2.52
373 3610 5.826601 TGTGTGCAGTTGTGAAAAAGATA 57.173 34.783 0.00 0.00 0.00 1.98
444 3681 9.361315 CAAAATTATTGTTGATTGAGCTGATCA 57.639 29.630 0.00 0.00 35.62 2.92
475 3712 0.884704 TCGGTTGAACTTGAGCTGCC 60.885 55.000 0.00 0.00 0.00 4.85
709 6121 2.286418 GCGTTTACATGCATGGCTACTC 60.286 50.000 29.41 14.73 34.70 2.59
710 6122 2.935849 CGTTTACATGCATGGCTACTCA 59.064 45.455 29.41 4.45 0.00 3.41
712 6124 3.912496 TTACATGCATGGCTACTCACT 57.088 42.857 29.41 8.64 0.00 3.41
713 6125 2.034104 ACATGCATGGCTACTCACTG 57.966 50.000 29.41 2.68 0.00 3.66
716 6128 1.560505 TGCATGGCTACTCACTGAGA 58.439 50.000 13.25 0.00 33.32 3.27
868 6295 3.952675 GCCCACTGTGTGCGTGTG 61.953 66.667 7.08 0.00 31.34 3.82
872 6299 1.337354 CCCACTGTGTGCGTGTGTATA 60.337 52.381 7.08 0.00 31.34 1.47
873 6300 2.616960 CCACTGTGTGCGTGTGTATAT 58.383 47.619 7.08 0.00 31.34 0.86
917 6348 1.838112 TCACCAAATCATCACAGGCC 58.162 50.000 0.00 0.00 0.00 5.19
921 6352 2.022195 CCAAATCATCACAGGCCAGAG 58.978 52.381 5.01 0.00 0.00 3.35
965 6396 5.995282 CGATCAATAGCTACCCAAACCAATA 59.005 40.000 0.00 0.00 0.00 1.90
966 6397 6.147821 CGATCAATAGCTACCCAAACCAATAG 59.852 42.308 0.00 0.00 0.00 1.73
967 6398 5.130350 TCAATAGCTACCCAAACCAATAGC 58.870 41.667 0.00 0.00 40.32 2.97
1052 6635 7.506261 TCTTCTCCTAGTTTCTGTGTACTTCTT 59.494 37.037 0.00 0.00 0.00 2.52
1053 6636 7.598759 TCTCCTAGTTTCTGTGTACTTCTTT 57.401 36.000 0.00 0.00 0.00 2.52
1131 7043 1.414181 TGATCCATCGCTTTCCTCCTC 59.586 52.381 0.00 0.00 0.00 3.71
1336 10146 4.008933 AAGAAGCTCGGCCACGCT 62.009 61.111 9.82 9.82 40.69 5.07
1450 10264 2.713967 GCCGTACTTCTACCCGCCA 61.714 63.158 0.00 0.00 0.00 5.69
1599 10471 8.308931 TCATTGAAGGAAATGAAAAAGATGAGG 58.691 33.333 0.00 0.00 42.22 3.86
1669 10832 7.446625 GCCATGGTTATATGAATCTCAGTTCTT 59.553 37.037 14.67 0.00 0.00 2.52
1670 10833 8.781196 CCATGGTTATATGAATCTCAGTTCTTG 58.219 37.037 2.57 0.00 0.00 3.02
1671 10834 8.781196 CATGGTTATATGAATCTCAGTTCTTGG 58.219 37.037 0.00 0.00 0.00 3.61
1673 10836 7.770433 TGGTTATATGAATCTCAGTTCTTGGTG 59.230 37.037 0.00 0.00 0.00 4.17
1681 12807 3.134458 CTCAGTTCTTGGTGAAGGTGAC 58.866 50.000 0.00 0.00 35.01 3.67
1729 12866 4.427394 GCCATGTGCCGACTAGAG 57.573 61.111 0.00 0.00 0.00 2.43
1743 12911 2.950309 GACTAGAGGGACAGCACGATAA 59.050 50.000 0.00 0.00 0.00 1.75
1745 12913 2.674796 AGAGGGACAGCACGATAAAC 57.325 50.000 0.00 0.00 0.00 2.01
1747 12915 0.739813 AGGGACAGCACGATAAACGC 60.740 55.000 0.00 0.00 46.94 4.84
1748 12916 1.702491 GGGACAGCACGATAAACGCC 61.702 60.000 0.00 0.00 46.94 5.68
1770 12952 1.676006 CGTCACCTGCAAGAAAAGGTT 59.324 47.619 0.00 0.00 44.63 3.50
1812 12994 1.302511 AGCCCCACATTGTGACGAC 60.303 57.895 18.33 4.89 35.23 4.34
1815 12997 0.034756 CCCCACATTGTGACGACTGA 59.965 55.000 18.33 0.00 35.23 3.41
1829 13019 8.391075 TGTGACGACTGACATCTAATCATATA 57.609 34.615 0.00 0.00 0.00 0.86
1830 13020 8.507249 TGTGACGACTGACATCTAATCATATAG 58.493 37.037 0.00 0.00 0.00 1.31
1831 13021 7.483375 GTGACGACTGACATCTAATCATATAGC 59.517 40.741 0.00 0.00 0.00 2.97
1832 13022 7.391833 TGACGACTGACATCTAATCATATAGCT 59.608 37.037 0.00 0.00 0.00 3.32
1833 13023 7.534282 ACGACTGACATCTAATCATATAGCTG 58.466 38.462 0.00 0.00 0.00 4.24
1834 13024 7.391833 ACGACTGACATCTAATCATATAGCTGA 59.608 37.037 0.00 0.00 0.00 4.26
1835 13025 8.239998 CGACTGACATCTAATCATATAGCTGAA 58.760 37.037 0.00 0.00 0.00 3.02
1849 13039 5.808366 ATAGCTGAATAAGATCGGGTGAA 57.192 39.130 0.00 0.00 37.05 3.18
1870 13060 7.119997 GTGAAAATTCGAGTCGATCCATTTAG 58.880 38.462 17.34 0.00 35.23 1.85
1885 13121 7.816513 CGATCCATTTAGCTGAATAAGATCTGA 59.183 37.037 25.16 0.00 31.86 3.27
1895 13131 7.980662 AGCTGAATAAGATCTGAATATGATCGG 59.019 37.037 0.00 0.00 43.52 4.18
1898 14420 8.037166 TGAATAAGATCTGAATATGATCGGGTG 58.963 37.037 0.00 0.00 43.52 4.61
1932 14485 4.827692 TCTGAATAAACATAGCACCGTGT 58.172 39.130 0.00 0.00 0.00 4.49
2009 14562 1.149101 TTGAGTGGCCCTCTTCCTTT 58.851 50.000 18.49 0.00 41.11 3.11
2011 14564 0.693049 GAGTGGCCCTCTTCCTTTCA 59.307 55.000 12.53 0.00 37.22 2.69
2012 14565 0.695347 AGTGGCCCTCTTCCTTTCAG 59.305 55.000 0.00 0.00 0.00 3.02
2014 14567 0.401738 TGGCCCTCTTCCTTTCAGTG 59.598 55.000 0.00 0.00 0.00 3.66
2015 14568 0.402121 GGCCCTCTTCCTTTCAGTGT 59.598 55.000 0.00 0.00 0.00 3.55
2016 14569 1.202940 GGCCCTCTTCCTTTCAGTGTT 60.203 52.381 0.00 0.00 0.00 3.32
2017 14570 1.882623 GCCCTCTTCCTTTCAGTGTTG 59.117 52.381 0.00 0.00 0.00 3.33
2042 14606 4.152580 GCCTGGTTTTCTTCGTCTTCTTAG 59.847 45.833 0.00 0.00 0.00 2.18
2043 14607 4.691216 CCTGGTTTTCTTCGTCTTCTTAGG 59.309 45.833 0.00 0.00 0.00 2.69
2063 14654 0.469144 TGGCCTGGTTTTCTTGGTCC 60.469 55.000 3.32 0.00 0.00 4.46
2077 14675 5.916661 TCTTGGTCCTACTACATCAGTTC 57.083 43.478 0.00 0.00 38.80 3.01
2080 14679 3.693085 TGGTCCTACTACATCAGTTCGTC 59.307 47.826 0.00 0.00 38.80 4.20
2082 14681 3.620374 GTCCTACTACATCAGTTCGTCGA 59.380 47.826 0.00 0.00 38.80 4.20
2085 14684 4.807834 CCTACTACATCAGTTCGTCGAGTA 59.192 45.833 0.00 0.00 38.80 2.59
2086 14685 4.596801 ACTACATCAGTTCGTCGAGTAC 57.403 45.455 0.00 0.00 31.59 2.73
2101 14705 1.860326 GAGTACGAGTAGGACGAGAGC 59.140 57.143 0.00 0.00 39.19 4.09
2146 14750 8.091449 ACCAGAAGTTTGTGACAATAACAAAAA 58.909 29.630 0.00 0.00 46.11 1.94
2226 14830 0.251922 ATTGGCCACCAACTGCAGAT 60.252 50.000 23.35 5.41 46.95 2.90
2229 14837 1.843206 TGGCCACCAACTGCAGATATA 59.157 47.619 23.35 0.00 0.00 0.86
2232 14840 3.433598 GGCCACCAACTGCAGATATAGAA 60.434 47.826 23.35 0.00 0.00 2.10
2254 14862 3.420397 GGCAACGAGACTGGTCTAC 57.580 57.895 3.03 0.00 40.61 2.59
2268 14892 1.969208 GGTCTACCGGGGATTTAGGAG 59.031 57.143 6.32 0.00 0.00 3.69
2274 14898 3.508426 ACCGGGGATTTAGGAGTAGATC 58.492 50.000 6.32 0.00 0.00 2.75
2291 14915 6.508777 AGTAGATCGTTAGAATTCTCTTGGC 58.491 40.000 12.24 0.00 32.70 4.52
2294 14918 4.537135 TCGTTAGAATTCTCTTGGCACT 57.463 40.909 12.24 0.00 32.70 4.40
2296 14920 4.929808 TCGTTAGAATTCTCTTGGCACTTC 59.070 41.667 12.24 0.00 32.70 3.01
2310 14934 2.423538 GGCACTTCTGCACCGATATTTT 59.576 45.455 0.00 0.00 46.28 1.82
2312 14936 4.095782 GGCACTTCTGCACCGATATTTTTA 59.904 41.667 0.00 0.00 46.28 1.52
2313 14937 5.392595 GGCACTTCTGCACCGATATTTTTAA 60.393 40.000 0.00 0.00 46.28 1.52
2314 14938 5.739161 GCACTTCTGCACCGATATTTTTAAG 59.261 40.000 0.00 0.00 43.62 1.85
2315 14939 6.258160 CACTTCTGCACCGATATTTTTAAGG 58.742 40.000 0.00 0.00 0.00 2.69
2409 15036 2.301870 TCCAAATACGACCAGAGCAACT 59.698 45.455 0.00 0.00 0.00 3.16
2434 15061 1.202758 CCACAACACAACTAGGAGCCA 60.203 52.381 0.00 0.00 0.00 4.75
2476 15105 5.004821 CAGTAATTAGAGTGCTACGCAGTTG 59.995 44.000 0.00 0.00 42.74 3.16
2477 15106 2.363788 TTAGAGTGCTACGCAGTTGG 57.636 50.000 0.00 0.00 42.74 3.77
2478 15107 1.541379 TAGAGTGCTACGCAGTTGGA 58.459 50.000 0.00 0.00 42.74 3.53
2479 15108 0.244994 AGAGTGCTACGCAGTTGGAG 59.755 55.000 0.00 0.00 42.74 3.86
2480 15109 0.038159 GAGTGCTACGCAGTTGGAGT 60.038 55.000 0.00 0.00 42.74 3.85
2481 15110 0.393077 AGTGCTACGCAGTTGGAGTT 59.607 50.000 0.00 0.00 37.78 3.01
2522 15151 5.352284 ACAGCAGAAATAGAACTACATCCG 58.648 41.667 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 110 1.204704 GCAGTTTTAACATGGCCCCTC 59.795 52.381 0.00 0.00 0.00 4.30
138 142 3.557264 GGCATTGCTACCTGTATAGACCC 60.557 52.174 8.82 0.00 0.00 4.46
145 149 1.269569 CGATCGGCATTGCTACCTGTA 60.270 52.381 7.38 0.00 0.00 2.74
353 3590 4.887071 ACCTATCTTTTTCACAACTGCACA 59.113 37.500 0.00 0.00 0.00 4.57
371 3608 0.246635 GCTCACACGGTCACACCTAT 59.753 55.000 0.00 0.00 35.66 2.57
373 3610 2.421739 GCTCACACGGTCACACCT 59.578 61.111 0.00 0.00 35.66 4.00
475 3712 3.429543 CAGCATGAAACGGGACAAAAATG 59.570 43.478 0.00 0.00 39.69 2.32
560 3811 3.225069 ATTGGCCACTTTGCACGCC 62.225 57.895 3.88 0.00 41.99 5.68
565 3816 0.961019 TCACTGATTGGCCACTTTGC 59.039 50.000 3.88 0.00 0.00 3.68
709 6121 6.199908 CAGTGAGTAAACAACTTCTCTCAGTG 59.800 42.308 11.53 11.53 39.87 3.66
710 6122 6.096987 TCAGTGAGTAAACAACTTCTCTCAGT 59.903 38.462 0.00 0.00 39.07 3.41
712 6124 6.321435 TCTCAGTGAGTAAACAACTTCTCTCA 59.679 38.462 19.53 0.00 39.07 3.27
713 6125 6.740110 TCTCAGTGAGTAAACAACTTCTCTC 58.260 40.000 19.53 0.00 39.07 3.20
716 6128 6.716934 TCTCTCAGTGAGTAAACAACTTCT 57.283 37.500 19.53 0.00 43.13 2.85
717 6129 5.404066 GCTCTCTCAGTGAGTAAACAACTTC 59.596 44.000 19.53 0.00 43.13 3.01
718 6130 5.069781 AGCTCTCTCAGTGAGTAAACAACTT 59.930 40.000 19.53 0.00 43.13 2.66
859 6286 2.465855 CGCCTTATATACACACGCACA 58.534 47.619 0.00 0.00 0.00 4.57
868 6295 0.739813 CGCCTGCCCGCCTTATATAC 60.740 60.000 0.00 0.00 0.00 1.47
965 6396 3.070302 GGTTGTAAGATGCCTAGCTAGCT 59.930 47.826 23.12 23.12 0.00 3.32
966 6397 3.394719 GGTTGTAAGATGCCTAGCTAGC 58.605 50.000 15.74 6.62 0.00 3.42
967 6398 3.388024 TGGGTTGTAAGATGCCTAGCTAG 59.612 47.826 14.20 14.20 0.00 3.42
968 6399 3.380393 TGGGTTGTAAGATGCCTAGCTA 58.620 45.455 0.00 0.00 0.00 3.32
1052 6635 7.369803 TGCTCAAAATTAACAAAGCAACAAA 57.630 28.000 0.00 0.00 36.86 2.83
1053 6636 6.974932 TGCTCAAAATTAACAAAGCAACAA 57.025 29.167 0.00 0.00 36.86 2.83
1131 7043 3.374220 TCTTTTGCTGCAACATCAAGG 57.626 42.857 15.72 0.46 0.00 3.61
1222 7801 2.315794 CCCCATGGATGTCACCCCA 61.316 63.158 15.22 0.00 36.79 4.96
1254 7866 3.086600 CCTCCAGCTGGTCCCTCC 61.087 72.222 31.58 0.00 36.34 4.30
1336 10146 4.043310 ACTTCCTCCACCTTGATGATTTGA 59.957 41.667 0.00 0.00 0.00 2.69
1450 10264 0.691413 GCTGGGGGTAGTAGGAGCTT 60.691 60.000 0.00 0.00 0.00 3.74
1595 10467 7.778853 ACTCGTAAATAGATAGAGTTTCCCTCA 59.221 37.037 0.00 0.00 43.12 3.86
1669 10832 3.755112 TTATGAACGTCACCTTCACCA 57.245 42.857 0.00 0.00 30.46 4.17
1670 10833 4.062991 AGTTTATGAACGTCACCTTCACC 58.937 43.478 0.00 0.00 40.75 4.02
1671 10834 5.693104 TGTAGTTTATGAACGTCACCTTCAC 59.307 40.000 0.00 0.00 40.75 3.18
1673 10836 6.367969 ACATGTAGTTTATGAACGTCACCTTC 59.632 38.462 0.00 0.00 40.75 3.46
1681 12807 6.083630 CCAAACCACATGTAGTTTATGAACG 58.916 40.000 19.74 8.41 40.75 3.95
1727 12864 1.278238 CGTTTATCGTGCTGTCCCTC 58.722 55.000 0.00 0.00 34.52 4.30
1729 12866 1.702491 GGCGTTTATCGTGCTGTCCC 61.702 60.000 0.00 0.00 42.13 4.46
1743 12911 4.539083 TGCAGGTGACGTGGCGTT 62.539 61.111 7.43 0.00 41.37 4.84
1745 12913 3.716006 CTTGCAGGTGACGTGGCG 61.716 66.667 7.43 0.00 0.00 5.69
1746 12914 1.444119 TTTCTTGCAGGTGACGTGGC 61.444 55.000 7.43 0.60 0.00 5.01
1747 12915 1.002468 CTTTTCTTGCAGGTGACGTGG 60.002 52.381 7.43 0.00 0.00 4.94
1748 12916 1.002468 CCTTTTCTTGCAGGTGACGTG 60.002 52.381 0.00 0.12 0.00 4.49
1770 12952 1.202639 GGCATCATGGTATGACGTCCA 60.203 52.381 14.12 4.37 43.01 4.02
1829 13019 4.487714 TTTCACCCGATCTTATTCAGCT 57.512 40.909 0.00 0.00 0.00 4.24
1830 13020 5.757850 ATTTTCACCCGATCTTATTCAGC 57.242 39.130 0.00 0.00 0.00 4.26
1831 13021 6.257849 TCGAATTTTCACCCGATCTTATTCAG 59.742 38.462 0.00 0.00 0.00 3.02
1832 13022 6.110033 TCGAATTTTCACCCGATCTTATTCA 58.890 36.000 0.00 0.00 0.00 2.57
1833 13023 6.258068 ACTCGAATTTTCACCCGATCTTATTC 59.742 38.462 0.00 0.00 0.00 1.75
1834 13024 6.113411 ACTCGAATTTTCACCCGATCTTATT 58.887 36.000 0.00 0.00 0.00 1.40
1835 13025 5.671493 ACTCGAATTTTCACCCGATCTTAT 58.329 37.500 0.00 0.00 0.00 1.73
1836 13026 5.080969 ACTCGAATTTTCACCCGATCTTA 57.919 39.130 0.00 0.00 0.00 2.10
1837 13027 3.933332 GACTCGAATTTTCACCCGATCTT 59.067 43.478 0.00 0.00 0.00 2.40
1838 13028 3.522553 GACTCGAATTTTCACCCGATCT 58.477 45.455 0.00 0.00 0.00 2.75
1849 13039 5.235186 CAGCTAAATGGATCGACTCGAATTT 59.765 40.000 5.00 9.52 39.99 1.82
1870 13060 7.224362 CCCGATCATATTCAGATCTTATTCAGC 59.776 40.741 0.00 0.00 39.73 4.26
1885 13121 8.924511 ATATTTTGAGAACACCCGATCATATT 57.075 30.769 0.00 0.00 0.00 1.28
1887 13123 7.657354 CAGATATTTTGAGAACACCCGATCATA 59.343 37.037 0.00 0.00 0.00 2.15
1889 13125 5.817296 CAGATATTTTGAGAACACCCGATCA 59.183 40.000 0.00 0.00 0.00 2.92
1890 13126 6.049149 TCAGATATTTTGAGAACACCCGATC 58.951 40.000 0.00 0.00 0.00 3.69
1891 13127 5.989477 TCAGATATTTTGAGAACACCCGAT 58.011 37.500 0.00 0.00 0.00 4.18
1892 13128 5.414789 TCAGATATTTTGAGAACACCCGA 57.585 39.130 0.00 0.00 0.00 5.14
1893 13129 6.683974 ATTCAGATATTTTGAGAACACCCG 57.316 37.500 0.00 0.00 0.00 5.28
1932 14485 5.497464 TTTGACAGTGGAGATGACCATTA 57.503 39.130 0.00 0.00 42.17 1.90
1939 14492 4.155462 CCTGATGTTTTGACAGTGGAGATG 59.845 45.833 0.00 0.00 0.00 2.90
1940 14493 4.042062 TCCTGATGTTTTGACAGTGGAGAT 59.958 41.667 0.00 0.00 0.00 2.75
2009 14562 0.032615 AAAACCAGGCCCAACACTGA 60.033 50.000 0.00 0.00 36.86 3.41
2011 14564 0.261696 AGAAAACCAGGCCCAACACT 59.738 50.000 0.00 0.00 0.00 3.55
2012 14565 1.068588 GAAGAAAACCAGGCCCAACAC 59.931 52.381 0.00 0.00 0.00 3.32
2014 14567 0.313987 CGAAGAAAACCAGGCCCAAC 59.686 55.000 0.00 0.00 0.00 3.77
2015 14568 0.106419 ACGAAGAAAACCAGGCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
2016 14569 0.536460 GACGAAGAAAACCAGGCCCA 60.536 55.000 0.00 0.00 0.00 5.36
2017 14570 0.250770 AGACGAAGAAAACCAGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
2042 14606 0.759060 ACCAAGAAAACCAGGCCACC 60.759 55.000 5.01 0.00 0.00 4.61
2043 14607 0.673985 GACCAAGAAAACCAGGCCAC 59.326 55.000 5.01 0.00 0.00 5.01
2063 14654 4.861389 ACTCGACGAACTGATGTAGTAG 57.139 45.455 0.00 0.00 39.18 2.57
2080 14679 2.118683 CTCTCGTCCTACTCGTACTCG 58.881 57.143 0.00 0.00 38.55 4.18
2082 14681 1.206610 TGCTCTCGTCCTACTCGTACT 59.793 52.381 0.00 0.00 0.00 2.73
2085 14684 0.249676 TCTGCTCTCGTCCTACTCGT 59.750 55.000 0.00 0.00 0.00 4.18
2086 14685 0.934496 CTCTGCTCTCGTCCTACTCG 59.066 60.000 0.00 0.00 0.00 4.18
2088 14687 3.272581 GTTACTCTGCTCTCGTCCTACT 58.727 50.000 0.00 0.00 0.00 2.57
2089 14688 2.355444 GGTTACTCTGCTCTCGTCCTAC 59.645 54.545 0.00 0.00 0.00 3.18
2090 14689 2.026542 TGGTTACTCTGCTCTCGTCCTA 60.027 50.000 0.00 0.00 0.00 2.94
2091 14690 1.271982 TGGTTACTCTGCTCTCGTCCT 60.272 52.381 0.00 0.00 0.00 3.85
2101 14705 2.808543 GGTCAGCAGTTTGGTTACTCTG 59.191 50.000 0.00 0.00 0.00 3.35
2146 14750 6.379133 ACAATCTGATGCCAACAATCTTGTAT 59.621 34.615 0.00 0.00 41.31 2.29
2154 14758 2.557924 GTGGACAATCTGATGCCAACAA 59.442 45.455 8.23 0.00 31.44 2.83
2226 14830 2.751259 AGTCTCGTTGCCGTGTTCTATA 59.249 45.455 0.00 0.00 35.01 1.31
2229 14837 0.597637 CAGTCTCGTTGCCGTGTTCT 60.598 55.000 0.00 0.00 35.01 3.01
2232 14840 2.029073 CCAGTCTCGTTGCCGTGT 59.971 61.111 0.00 0.00 35.01 4.49
2242 14850 0.106116 ATCCCCGGTAGACCAGTCTC 60.106 60.000 3.00 0.00 40.93 3.36
2254 14862 2.492484 CGATCTACTCCTAAATCCCCGG 59.508 54.545 0.00 0.00 0.00 5.73
2268 14892 6.199342 GTGCCAAGAGAATTCTAACGATCTAC 59.801 42.308 8.25 0.00 31.96 2.59
2274 14898 4.932200 AGAAGTGCCAAGAGAATTCTAACG 59.068 41.667 8.25 0.00 31.96 3.18
2291 14915 6.128007 ACCTTAAAAATATCGGTGCAGAAGTG 60.128 38.462 0.00 0.00 0.00 3.16
2294 14918 6.827586 AACCTTAAAAATATCGGTGCAGAA 57.172 33.333 0.00 0.00 0.00 3.02
2296 14920 5.288472 GCAAACCTTAAAAATATCGGTGCAG 59.712 40.000 0.00 0.00 0.00 4.41
2310 14934 7.385267 AGCAAACATTCATATGCAAACCTTAA 58.615 30.769 0.00 0.00 41.18 1.85
2312 14936 5.797051 AGCAAACATTCATATGCAAACCTT 58.203 33.333 0.00 0.00 41.18 3.50
2313 14937 5.186409 AGAGCAAACATTCATATGCAAACCT 59.814 36.000 0.00 0.00 41.18 3.50
2314 14938 5.290158 CAGAGCAAACATTCATATGCAAACC 59.710 40.000 0.00 0.00 41.18 3.27
2315 14939 5.865552 ACAGAGCAAACATTCATATGCAAAC 59.134 36.000 0.00 0.00 41.18 2.93
2378 15005 6.488683 TCTGGTCGTATTTGGATTTCAAACTT 59.511 34.615 0.00 0.00 46.72 2.66
2383 15010 3.938963 GCTCTGGTCGTATTTGGATTTCA 59.061 43.478 0.00 0.00 0.00 2.69
2397 15024 3.674997 TGTGGAATTAGTTGCTCTGGTC 58.325 45.455 0.00 0.00 0.00 4.02
2409 15036 5.001232 GCTCCTAGTTGTGTTGTGGAATTA 58.999 41.667 0.00 0.00 0.00 1.40
2434 15061 2.146342 CTGTGCGGTCTGTCATTTTCT 58.854 47.619 0.00 0.00 0.00 2.52
2476 15105 5.886960 AAATGTGAATGTAGAGCAACTCC 57.113 39.130 0.00 0.00 0.00 3.85
2477 15106 7.364522 TGTAAATGTGAATGTAGAGCAACTC 57.635 36.000 0.00 0.00 0.00 3.01
2478 15107 6.128172 GCTGTAAATGTGAATGTAGAGCAACT 60.128 38.462 1.31 0.00 34.08 3.16
2479 15108 6.024049 GCTGTAAATGTGAATGTAGAGCAAC 58.976 40.000 1.31 0.00 34.08 4.17
2480 15109 5.704978 TGCTGTAAATGTGAATGTAGAGCAA 59.295 36.000 5.52 0.00 39.19 3.91
2481 15110 5.244755 TGCTGTAAATGTGAATGTAGAGCA 58.755 37.500 4.16 4.16 39.65 4.26


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

AutoCloner maintained by Alex Coulton.