Multiple sequence alignment - TraesCS5D01G067200

Loading Multiple Alignment...

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 TraesCS5D01G067200 chr5D 100.000 2606 0 0 1 2606 62478126 62480731 0.000000e+00 4813.0
1 TraesCS5D01G067200 chr5D 91.386 743 52 7 911 1648 62510797 62511532 0.000000e+00 1007.0
2 TraesCS5D01G067200 chr5D 91.328 738 44 10 32 768 62509934 62510652 0.000000e+00 990.0
3 TraesCS5D01G067200 chr5D 89.666 329 34 0 1217 1545 62475555 62475227 1.120000e-113 420.0
4 TraesCS5D01G067200 chr5A 90.591 1573 108 22 90 1632 52356651 52358213 0.000000e+00 2049.0
5 TraesCS5D01G067200 chr5B 91.269 859 57 13 799 1650 68194980 68194133 0.000000e+00 1155.0
6 TraesCS5D01G067200 chr5B 94.118 748 35 4 12 750 68049962 68049215 0.000000e+00 1129.0
7 TraesCS5D01G067200 chr5B 88.939 895 69 16 917 1793 68048984 68048102 0.000000e+00 1077.0
8 TraesCS5D01G067200 chr5B 92.663 736 40 6 42 768 68195787 68195057 0.000000e+00 1048.0
9 TraesCS5D01G067200 chr5B 83.922 566 55 15 1541 2084 68167497 68168048 2.310000e-140 508.0
10 TraesCS5D01G067200 chr5B 84.146 492 43 15 1641 2113 68193522 68193047 6.620000e-121 444.0
11 TraesCS5D01G067200 chr5B 86.935 199 22 4 2130 2328 68047257 68047063 1.210000e-53 220.0
12 TraesCS5D01G067200 chr5B 84.177 158 11 12 2392 2539 68047075 68046922 9.720000e-30 141.0
13 TraesCS5D01G067200 chr6B 82.927 82 6 6 2345 2422 687504957 687505034 1.670000e-07 67.6
14 TraesCS5D01G067200 chr7B 92.500 40 3 0 2394 2433 391105902 391105863 1.010000e-04 58.4
15 TraesCS5D01G067200 chr7B 100.000 30 0 0 2393 2422 11552228 11552199 3.620000e-04 56.5
16 TraesCS5D01G067200 chr7B 100.000 28 0 0 2395 2422 449545514 449545541 5.000000e-03 52.8
17 TraesCS5D01G067200 chr6A 100.000 31 0 0 1842 1872 68613470 68613500 1.010000e-04 58.4
18 TraesCS5D01G067200 chr4D 97.059 34 0 1 2394 2427 546844 546812 3.620000e-04 56.5
19 TraesCS5D01G067200 chrUn 100.000 29 0 0 2394 2422 43402912 43402884 1.000000e-03 54.7
20 TraesCS5D01G067200 chr2A 100.000 29 0 0 2394 2422 611047153 611047125 1.000000e-03 54.7
21 TraesCS5D01G067200 chr3D 100.000 28 0 0 1858 1885 456595966 456595939 5.000000e-03 52.8
22 TraesCS5D01G067200 chr1A 90.244 41 3 1 2383 2422 494152048 494152008 5.000000e-03 52.8


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 TraesCS5D01G067200 chr5D 62478126 62480731 2605 False 4813.000000 4813 100.000000 1 2606 1 chr5D.!!$F1 2605
1 TraesCS5D01G067200 chr5D 62509934 62511532 1598 False 998.500000 1007 91.357000 32 1648 2 chr5D.!!$F2 1616
2 TraesCS5D01G067200 chr5A 52356651 52358213 1562 False 2049.000000 2049 90.591000 90 1632 1 chr5A.!!$F1 1542
3 TraesCS5D01G067200 chr5B 68193047 68195787 2740 True 882.333333 1155 89.359333 42 2113 3 chr5B.!!$R2 2071
4 TraesCS5D01G067200 chr5B 68046922 68049962 3040 True 641.750000 1129 88.542250 12 2539 4 chr5B.!!$R1 2527
5 TraesCS5D01G067200 chr5B 68167497 68168048 551 False 508.000000 508 83.922000 1541 2084 1 chr5B.!!$F1 543

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
697 706 0.039035 ATGGCCATGGGTACGTGTTT 59.961 50.0 20.04 0.0 31.5 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 3885 0.108709 TTCCCGACCGTTCGTAATGG 60.109 55.0 0.61 0.0 44.28 3.16 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
31 32 4.230455 CTCCCAGAATCCTTCTACTCCAT 58.770 47.826 0.00 0.00 38.11 3.41
37 38 4.896482 AGAATCCTTCTACTCCATAAGCGT 59.104 41.667 0.00 0.00 38.49 5.07
595 598 0.250770 AAAACCAAGAGGGCGAGGAC 60.251 55.000 0.00 0.00 42.05 3.85
638 641 1.734465 CAGTTGTCGAAGAAGCCATCC 59.266 52.381 0.00 0.00 39.69 3.51
694 703 0.756294 TCTATGGCCATGGGTACGTG 59.244 55.000 29.04 7.79 0.00 4.49
697 706 0.039035 ATGGCCATGGGTACGTGTTT 59.961 50.000 20.04 0.00 31.50 2.83
768 813 3.807209 GCTTGGAGGCGGTGATGTATATT 60.807 47.826 0.00 0.00 0.00 1.28
769 814 3.401033 TGGAGGCGGTGATGTATATTG 57.599 47.619 0.00 0.00 0.00 1.90
771 816 2.076863 GAGGCGGTGATGTATATTGCC 58.923 52.381 0.00 0.00 41.27 4.52
772 817 1.165270 GGCGGTGATGTATATTGCCC 58.835 55.000 0.00 0.00 35.01 5.36
791 846 3.028850 CCCTAATTGGTCTCCGTGTAGA 58.971 50.000 0.00 0.00 0.00 2.59
792 847 3.068307 CCCTAATTGGTCTCCGTGTAGAG 59.932 52.174 0.00 0.00 35.04 2.43
793 848 3.952323 CCTAATTGGTCTCCGTGTAGAGA 59.048 47.826 0.00 0.00 40.62 3.10
794 849 4.036971 CCTAATTGGTCTCCGTGTAGAGAG 59.963 50.000 0.00 0.00 43.47 3.20
795 850 2.873094 TTGGTCTCCGTGTAGAGAGA 57.127 50.000 0.00 0.00 43.47 3.10
829 922 2.996631 AGCATTAGAAACTGCCTCTGG 58.003 47.619 0.00 0.00 39.22 3.86
833 931 4.521146 CATTAGAAACTGCCTCTGGACAT 58.479 43.478 0.00 0.00 0.00 3.06
835 933 1.280421 AGAAACTGCCTCTGGACATCC 59.720 52.381 0.00 0.00 0.00 3.51
876 974 2.513897 CGGCCCGATTCCAACTCC 60.514 66.667 0.00 0.00 0.00 3.85
878 976 1.303282 GGCCCGATTCCAACTCCTT 59.697 57.895 0.00 0.00 0.00 3.36
879 977 0.544697 GGCCCGATTCCAACTCCTTA 59.455 55.000 0.00 0.00 0.00 2.69
881 980 2.370849 GGCCCGATTCCAACTCCTTATA 59.629 50.000 0.00 0.00 0.00 0.98
955 1086 3.001365 CACGTCGCTTAATTAACCTCGAC 60.001 47.826 21.14 21.14 41.72 4.20
956 1087 3.813073 GTCGCTTAATTAACCTCGACG 57.187 47.619 18.66 0.00 37.24 5.12
957 1088 3.429085 GTCGCTTAATTAACCTCGACGA 58.571 45.455 18.66 0.00 37.24 4.20
974 1105 1.653341 CGAGATCGATCGTCGTCTTG 58.347 55.000 25.78 15.62 41.35 3.02
975 1106 1.258197 CGAGATCGATCGTCGTCTTGA 59.742 52.381 25.78 0.00 41.35 3.02
977 1108 3.605002 CGAGATCGATCGTCGTCTTGATT 60.605 47.826 25.78 6.99 41.35 2.57
1093 1230 2.027625 GCCGTCACCCTTGTTCTCG 61.028 63.158 0.00 0.00 0.00 4.04
1285 1422 0.386352 GAACGTCACGATCACGGTGA 60.386 55.000 14.01 14.01 37.29 4.02
1367 1504 3.344215 CATGGAGATGAGCGCCGC 61.344 66.667 2.29 0.00 39.67 6.53
1431 1568 2.654079 CCTGGACTCGGAGCTGCTT 61.654 63.158 2.53 0.00 0.00 3.91
1465 1602 1.819229 CTGGATGTGGAGACGAGGG 59.181 63.158 0.00 0.00 0.00 4.30
1506 1644 1.202927 CCTCTCTTTTGGGAGTGCCAA 60.203 52.381 12.77 12.77 45.47 4.52
1713 2477 7.944729 AAAGTAGCATACATTTCCATGACTT 57.055 32.000 0.00 0.00 46.26 3.01
1736 2500 5.463286 TGTACGTCGATTCTGTGTAATTGT 58.537 37.500 0.00 0.00 0.00 2.71
1744 2508 8.709646 GTCGATTCTGTGTAATTGTAAAGTTCT 58.290 33.333 0.00 0.00 0.00 3.01
1829 2593 2.795470 GCTAATAACCTCCGCTTCGAAG 59.205 50.000 21.02 21.02 0.00 3.79
1835 2599 1.617357 ACCTCCGCTTCGAAGTACTTT 59.383 47.619 25.24 4.48 0.00 2.66
1840 2604 2.414559 CCGCTTCGAAGTACTTTCCGTA 60.415 50.000 25.24 2.93 31.82 4.02
1874 2638 8.833231 TCAAATTTGTTTGAACTAAAACCACA 57.167 26.923 17.47 0.00 38.93 4.17
1886 2650 8.740906 TGAACTAAAACCACAACAAGTATTTCA 58.259 29.630 0.00 0.00 0.00 2.69
1887 2651 9.575783 GAACTAAAACCACAACAAGTATTTCAA 57.424 29.630 0.00 0.00 0.00 2.69
1909 2673 6.551975 TCAAAACCGAGGGAGTATATCACATA 59.448 38.462 0.00 0.00 31.63 2.29
1929 2693 8.638873 TCACATATAAATTCTAGACCGTGTGAT 58.361 33.333 12.44 0.00 37.78 3.06
1931 2695 8.638873 ACATATAAATTCTAGACCGTGTGATGA 58.361 33.333 0.00 0.00 0.00 2.92
1940 2704 3.498397 AGACCGTGTGATGAAATGTTCAC 59.502 43.478 0.00 0.00 43.48 3.18
1953 2717 7.215696 TGAAATGTTCACGTTCATGTTTTTC 57.784 32.000 0.00 0.00 34.08 2.29
2082 2865 0.461548 CTTGCAGACTCGGCCTATCA 59.538 55.000 0.00 0.00 0.00 2.15
2093 2876 1.674221 CGGCCTATCATTGCTAGCTCC 60.674 57.143 17.23 2.52 0.00 4.70
2099 2882 5.279708 GCCTATCATTGCTAGCTCCTTCTTA 60.280 44.000 17.23 0.00 0.00 2.10
2116 2899 7.978925 TCCTTCTTAGGATTTTTCTCAAGAGT 58.021 34.615 0.00 0.00 45.82 3.24
2118 2901 9.726438 CCTTCTTAGGATTTTTCTCAAGAGTTA 57.274 33.333 0.00 0.00 45.05 2.24
2167 3474 3.552604 AAATCGTTCATTGGTTGACCG 57.447 42.857 0.00 0.00 41.20 4.79
2169 3476 1.956297 TCGTTCATTGGTTGACCGTT 58.044 45.000 0.00 0.00 40.72 4.44
2176 3483 1.384525 TTGGTTGACCGTTTGACCTG 58.615 50.000 0.00 0.00 39.43 4.00
2179 3486 1.658994 GTTGACCGTTTGACCTGTGA 58.341 50.000 0.00 0.00 0.00 3.58
2246 3553 5.940192 ATGCAGAAAAGTTCACGAATACA 57.060 34.783 0.00 0.00 0.00 2.29
2249 3556 6.198687 TGCAGAAAAGTTCACGAATACAAAG 58.801 36.000 0.00 0.00 0.00 2.77
2284 3591 7.887709 CACATTTGAAAATTTCTTCGCGAATAC 59.112 33.333 23.67 2.70 0.00 1.89
2290 3597 8.476142 TGAAAATTTCTTCGCGAATACAAAAAG 58.524 29.630 23.67 8.00 0.00 2.27
2297 3604 3.187637 TCGCGAATACAAAAAGGTTCAGG 59.812 43.478 6.20 0.00 0.00 3.86
2298 3605 3.187637 CGCGAATACAAAAAGGTTCAGGA 59.812 43.478 0.00 0.00 0.00 3.86
2304 3611 7.116233 CGAATACAAAAAGGTTCAGGAATTTGG 59.884 37.037 9.39 0.00 33.31 3.28
2313 3620 6.997655 AGGTTCAGGAATTTGGAAAAAGATC 58.002 36.000 0.00 0.00 0.00 2.75
2315 3622 7.071071 AGGTTCAGGAATTTGGAAAAAGATCAA 59.929 33.333 0.00 0.00 0.00 2.57
2316 3623 7.714813 GGTTCAGGAATTTGGAAAAAGATCAAA 59.285 33.333 0.00 0.00 35.30 2.69
2317 3624 9.108284 GTTCAGGAATTTGGAAAAAGATCAAAA 57.892 29.630 0.00 0.00 34.63 2.44
2319 3626 9.850198 TCAGGAATTTGGAAAAAGATCAAAATT 57.150 25.926 2.81 2.81 42.76 1.82
2338 3645 9.059485 TCAAAATTTTGAAAAAGAATGTTTGCG 57.941 25.926 27.22 0.00 43.62 4.85
2339 3646 9.059485 CAAAATTTTGAAAAAGAATGTTTGCGA 57.941 25.926 23.72 0.00 40.55 5.10
2340 3647 9.617975 AAAATTTTGAAAAAGAATGTTTGCGAA 57.382 22.222 1.75 0.00 0.00 4.70
2341 3648 8.599876 AATTTTGAAAAAGAATGTTTGCGAAC 57.400 26.923 10.09 10.09 36.29 3.95
2351 3658 2.662700 TGTTTGCGAACACAAAAACGT 58.337 38.095 15.77 0.00 40.71 3.99
2352 3659 3.818387 TGTTTGCGAACACAAAAACGTA 58.182 36.364 15.77 0.00 40.71 3.57
2353 3660 4.413087 TGTTTGCGAACACAAAAACGTAT 58.587 34.783 15.77 0.00 40.71 3.06
2354 3661 5.566623 TGTTTGCGAACACAAAAACGTATA 58.433 33.333 15.77 0.00 40.71 1.47
2355 3662 5.677612 TGTTTGCGAACACAAAAACGTATAG 59.322 36.000 15.77 0.00 40.71 1.31
2356 3663 4.392619 TGCGAACACAAAAACGTATAGG 57.607 40.909 0.00 0.00 0.00 2.57
2357 3664 4.056740 TGCGAACACAAAAACGTATAGGA 58.943 39.130 0.00 0.00 0.00 2.94
2358 3665 4.510711 TGCGAACACAAAAACGTATAGGAA 59.489 37.500 0.00 0.00 0.00 3.36
2359 3666 5.179742 TGCGAACACAAAAACGTATAGGAAT 59.820 36.000 0.00 0.00 0.00 3.01
2360 3667 6.081693 GCGAACACAAAAACGTATAGGAATT 58.918 36.000 0.00 0.00 0.00 2.17
2361 3668 6.579666 GCGAACACAAAAACGTATAGGAATTT 59.420 34.615 0.00 0.00 0.00 1.82
2362 3669 7.408921 GCGAACACAAAAACGTATAGGAATTTG 60.409 37.037 17.71 17.71 34.75 2.32
2363 3670 7.799447 CGAACACAAAAACGTATAGGAATTTGA 59.201 33.333 22.28 0.00 33.30 2.69
2364 3671 9.453325 GAACACAAAAACGTATAGGAATTTGAA 57.547 29.630 22.28 0.00 33.30 2.69
2365 3672 9.804758 AACACAAAAACGTATAGGAATTTGAAA 57.195 25.926 22.28 0.00 33.30 2.69
2366 3673 9.804758 ACACAAAAACGTATAGGAATTTGAAAA 57.195 25.926 22.28 0.00 33.30 2.29
2435 3742 9.534565 TGAATTTGGAAAACGATTGTGAATAAA 57.465 25.926 0.00 0.00 0.00 1.40
2479 3793 9.863845 AAATCTAGACAAAAACCGAAAGAAAAA 57.136 25.926 0.00 0.00 0.00 1.94
2542 3856 4.939052 CGGGAGGCTTCTAGAAAATAGA 57.061 45.455 6.63 0.00 0.00 1.98
2543 3857 5.277857 CGGGAGGCTTCTAGAAAATAGAA 57.722 43.478 6.63 0.00 33.10 2.10
2544 3858 5.051153 CGGGAGGCTTCTAGAAAATAGAAC 58.949 45.833 6.63 0.00 31.09 3.01
2545 3859 5.369833 GGGAGGCTTCTAGAAAATAGAACC 58.630 45.833 6.63 4.34 31.09 3.62
2546 3860 5.131308 GGGAGGCTTCTAGAAAATAGAACCT 59.869 44.000 6.63 13.71 37.56 3.50
2547 3861 6.285224 GGAGGCTTCTAGAAAATAGAACCTC 58.715 44.000 22.14 22.14 42.70 3.85
2548 3862 5.908341 AGGCTTCTAGAAAATAGAACCTCG 58.092 41.667 6.63 0.00 33.73 4.63
2549 3863 5.657302 AGGCTTCTAGAAAATAGAACCTCGA 59.343 40.000 6.63 0.00 33.73 4.04
2550 3864 6.154706 AGGCTTCTAGAAAATAGAACCTCGAA 59.845 38.462 6.63 0.00 33.73 3.71
2551 3865 6.256104 GGCTTCTAGAAAATAGAACCTCGAAC 59.744 42.308 6.63 0.00 31.09 3.95
2552 3866 6.020520 GCTTCTAGAAAATAGAACCTCGAACG 60.021 42.308 6.63 0.00 31.09 3.95
2553 3867 6.748333 TCTAGAAAATAGAACCTCGAACGA 57.252 37.500 0.00 0.00 0.00 3.85
2554 3868 6.549952 TCTAGAAAATAGAACCTCGAACGAC 58.450 40.000 0.00 0.00 0.00 4.34
2555 3869 5.388408 AGAAAATAGAACCTCGAACGACT 57.612 39.130 0.00 0.00 0.00 4.18
2556 3870 5.400703 AGAAAATAGAACCTCGAACGACTC 58.599 41.667 0.00 0.00 0.00 3.36
2557 3871 5.183522 AGAAAATAGAACCTCGAACGACTCT 59.816 40.000 0.00 0.00 0.00 3.24
2558 3872 5.388408 AAATAGAACCTCGAACGACTCTT 57.612 39.130 0.00 0.00 0.00 2.85
2559 3873 6.506500 AAATAGAACCTCGAACGACTCTTA 57.493 37.500 0.00 0.00 0.00 2.10
2560 3874 5.738118 ATAGAACCTCGAACGACTCTTAG 57.262 43.478 0.00 0.00 0.00 2.18
2561 3875 3.672808 AGAACCTCGAACGACTCTTAGA 58.327 45.455 0.00 0.00 0.00 2.10
2562 3876 4.263435 AGAACCTCGAACGACTCTTAGAT 58.737 43.478 0.00 0.00 0.00 1.98
2563 3877 4.095185 AGAACCTCGAACGACTCTTAGATG 59.905 45.833 0.00 0.00 0.00 2.90
2564 3878 2.683867 ACCTCGAACGACTCTTAGATGG 59.316 50.000 0.00 0.00 0.00 3.51
2565 3879 2.033550 CCTCGAACGACTCTTAGATGGG 59.966 54.545 0.00 0.00 0.00 4.00
2566 3880 1.404391 TCGAACGACTCTTAGATGGGC 59.596 52.381 0.00 0.00 0.00 5.36
2567 3881 1.536284 CGAACGACTCTTAGATGGGCC 60.536 57.143 0.00 0.00 0.00 5.80
2568 3882 0.460311 AACGACTCTTAGATGGGCCG 59.540 55.000 0.00 0.00 0.00 6.13
2569 3883 1.364171 CGACTCTTAGATGGGCCGG 59.636 63.158 0.00 0.00 0.00 6.13
2570 3884 1.069935 GACTCTTAGATGGGCCGGC 59.930 63.158 21.18 21.18 0.00 6.13
2571 3885 2.384653 GACTCTTAGATGGGCCGGCC 62.385 65.000 38.57 38.57 0.00 6.13
2581 3895 3.206957 GGCCGGCCCATTACGAAC 61.207 66.667 36.64 5.01 0.00 3.95
2582 3896 3.569690 GCCGGCCCATTACGAACG 61.570 66.667 18.11 0.00 0.00 3.95
2583 3897 2.893404 CCGGCCCATTACGAACGG 60.893 66.667 0.00 0.00 35.01 4.44
2584 3898 2.125431 CGGCCCATTACGAACGGT 60.125 61.111 0.00 0.00 0.00 4.83
2585 3899 2.169146 CGGCCCATTACGAACGGTC 61.169 63.158 0.00 0.00 0.00 4.79
2594 3908 2.125673 CGAACGGTCGGGAAGCAT 60.126 61.111 16.82 0.00 43.81 3.79
2595 3909 2.452813 CGAACGGTCGGGAAGCATG 61.453 63.158 16.82 0.00 43.81 4.06
2596 3910 2.046314 AACGGTCGGGAAGCATGG 60.046 61.111 0.00 0.00 0.00 3.66
2597 3911 2.798148 GAACGGTCGGGAAGCATGGT 62.798 60.000 0.00 0.00 0.00 3.55
2598 3912 2.046314 CGGTCGGGAAGCATGGTT 60.046 61.111 10.50 10.50 0.00 3.67
2599 3913 2.398554 CGGTCGGGAAGCATGGTTG 61.399 63.158 16.18 0.60 0.00 3.77
2600 3914 2.046285 GGTCGGGAAGCATGGTTGG 61.046 63.158 16.18 4.31 0.00 3.77
2601 3915 1.002624 GTCGGGAAGCATGGTTGGA 60.003 57.895 16.18 6.70 0.00 3.53
2602 3916 0.608035 GTCGGGAAGCATGGTTGGAA 60.608 55.000 16.18 0.00 0.00 3.53
2603 3917 0.322456 TCGGGAAGCATGGTTGGAAG 60.322 55.000 16.18 3.94 0.00 3.46
2604 3918 1.315257 CGGGAAGCATGGTTGGAAGG 61.315 60.000 16.18 0.00 0.00 3.46
2605 3919 0.251787 GGGAAGCATGGTTGGAAGGT 60.252 55.000 16.18 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.078426 ATTCTGGGAGCGTTTCGGG 60.078 57.895 0.00 0.00 0.00 5.14
1 2 1.090052 GGATTCTGGGAGCGTTTCGG 61.090 60.000 0.00 0.00 0.00 4.30
2 3 0.108138 AGGATTCTGGGAGCGTTTCG 60.108 55.000 0.00 0.00 0.00 3.46
31 32 3.629398 GCCTAGGAGTACACTTACGCTTA 59.371 47.826 14.75 0.00 32.93 3.09
37 38 5.884792 GTGAGTTAGCCTAGGAGTACACTTA 59.115 44.000 14.75 0.34 0.00 2.24
388 390 1.731433 TGCTGGGGCGACGATAGTAC 61.731 60.000 0.00 0.00 45.87 2.73
511 514 4.826183 GGAGGATCAAATTCTCCATGGAAG 59.174 45.833 17.00 10.18 44.72 3.46
595 598 0.721718 GATTCTCGCCTTGTTCACCG 59.278 55.000 0.00 0.00 0.00 4.94
638 641 1.738099 CACTTTGAGGGGCGACTCG 60.738 63.158 0.00 0.00 40.39 4.18
694 703 0.721718 CAGATTGGCCTCGTCGAAAC 59.278 55.000 3.32 0.00 0.00 2.78
697 706 0.320374 AAACAGATTGGCCTCGTCGA 59.680 50.000 3.32 0.00 0.00 4.20
728 737 6.745116 TCCAAGCTACGCGCATATATATATT 58.255 36.000 5.73 0.00 42.61 1.28
730 739 5.278315 CCTCCAAGCTACGCGCATATATATA 60.278 44.000 5.73 0.00 42.61 0.86
731 740 4.499865 CCTCCAAGCTACGCGCATATATAT 60.500 45.833 5.73 0.00 42.61 0.86
732 741 3.181490 CCTCCAAGCTACGCGCATATATA 60.181 47.826 5.73 0.00 42.61 0.86
742 787 2.298158 ATCACCGCCTCCAAGCTACG 62.298 60.000 0.00 0.00 0.00 3.51
771 816 3.952323 TCTCTACACGGAGACCAATTAGG 59.048 47.826 0.00 0.00 37.43 2.69
772 817 4.882427 TCTCTCTACACGGAGACCAATTAG 59.118 45.833 0.00 0.00 37.43 1.73
791 846 0.814457 CTTACGGCTGCTCTGTCTCT 59.186 55.000 0.00 0.00 35.51 3.10
792 847 0.804156 GCTTACGGCTGCTCTGTCTC 60.804 60.000 0.00 0.00 38.06 3.36
793 848 1.216710 GCTTACGGCTGCTCTGTCT 59.783 57.895 0.00 0.00 38.06 3.41
794 849 0.460987 ATGCTTACGGCTGCTCTGTC 60.461 55.000 0.00 0.00 42.39 3.51
795 850 0.036010 AATGCTTACGGCTGCTCTGT 60.036 50.000 0.00 0.00 42.39 3.41
796 851 1.863454 CTAATGCTTACGGCTGCTCTG 59.137 52.381 0.00 0.00 42.39 3.35
816 909 1.743996 GGATGTCCAGAGGCAGTTTC 58.256 55.000 0.00 0.00 35.64 2.78
829 922 4.799678 ACACGATGAATATCTCGGATGTC 58.200 43.478 0.00 0.00 39.16 3.06
833 931 2.225727 CGGACACGATGAATATCTCGGA 59.774 50.000 0.00 0.00 44.60 4.55
835 933 1.979469 GCGGACACGATGAATATCTCG 59.021 52.381 0.00 0.00 44.60 4.04
876 974 4.692625 GTGTGCCAGCCAGATACATATAAG 59.307 45.833 0.00 0.00 0.00 1.73
878 976 3.007940 GGTGTGCCAGCCAGATACATATA 59.992 47.826 0.00 0.00 34.09 0.86
879 977 2.224621 GGTGTGCCAGCCAGATACATAT 60.225 50.000 0.00 0.00 34.09 1.78
881 980 0.107017 GGTGTGCCAGCCAGATACAT 60.107 55.000 0.00 0.00 34.09 2.29
955 1086 1.258197 TCAAGACGACGATCGATCTCG 59.742 52.381 29.23 29.23 43.74 4.04
956 1087 3.529634 ATCAAGACGACGATCGATCTC 57.470 47.619 24.34 16.62 43.74 2.75
957 1088 3.622828 CAATCAAGACGACGATCGATCT 58.377 45.455 24.34 17.53 43.74 2.75
1022 1159 2.506217 TCATCGTCGGCGCTTCAC 60.506 61.111 3.52 0.02 38.14 3.18
1023 1160 2.202610 CTCATCGTCGGCGCTTCA 60.203 61.111 3.52 0.00 38.14 3.02
1093 1230 1.084289 GAATACCACCCGCAGACAAC 58.916 55.000 0.00 0.00 0.00 3.32
1255 1392 2.435059 GACGTTCTCCCTGCAGGC 60.435 66.667 28.39 12.29 34.51 4.85
1386 1523 0.247736 GCAGGTCATCGGTGAGAACT 59.752 55.000 0.00 0.00 34.36 3.01
1596 1734 3.173599 CAAAACAGATGCCTAATGCGTG 58.826 45.455 0.00 0.00 45.60 5.34
1610 1749 5.429957 AAACAAGAGCTAGAGCAAAACAG 57.570 39.130 4.01 0.00 45.16 3.16
1705 2469 3.547868 CAGAATCGACGTACAAGTCATGG 59.452 47.826 0.00 0.00 40.98 3.66
1713 2477 5.463286 ACAATTACACAGAATCGACGTACA 58.537 37.500 0.00 0.00 0.00 2.90
1744 2508 8.508883 TGCTACTTTAAGAACTTTTAACACCA 57.491 30.769 0.00 0.00 0.00 4.17
1756 2520 8.443160 CGAGTCATGAAAATGCTACTTTAAGAA 58.557 33.333 0.00 0.00 0.00 2.52
1874 2638 5.134661 TCCCTCGGTTTTGAAATACTTGTT 58.865 37.500 0.00 0.00 0.00 2.83
1886 2650 5.888982 ATGTGATATACTCCCTCGGTTTT 57.111 39.130 0.00 0.00 0.00 2.43
1887 2651 8.660295 TTATATGTGATATACTCCCTCGGTTT 57.340 34.615 0.00 0.00 0.00 3.27
1909 2673 8.830580 CATTTCATCACACGGTCTAGAATTTAT 58.169 33.333 0.00 0.00 0.00 1.40
1929 2693 6.021074 CGAAAAACATGAACGTGAACATTTCA 60.021 34.615 0.00 0.00 37.33 2.69
1931 2695 6.030849 TCGAAAAACATGAACGTGAACATTT 58.969 32.000 0.00 0.00 0.00 2.32
1940 2704 2.574322 CAGGCTCGAAAAACATGAACG 58.426 47.619 0.00 0.00 0.00 3.95
1993 2757 2.867109 CCTGAGGGGCGAATCATTAT 57.133 50.000 0.00 0.00 0.00 1.28
2043 2826 1.658409 GGCTGAACAAAGCGTGTGC 60.658 57.895 0.00 0.00 44.52 4.57
2058 2841 4.749310 CCGAGTCTGCAAGCGGCT 62.749 66.667 0.00 0.00 45.15 5.52
2167 3474 2.293399 GGTCATTGGTCACAGGTCAAAC 59.707 50.000 0.00 0.00 0.00 2.93
2169 3476 1.542328 CGGTCATTGGTCACAGGTCAA 60.542 52.381 0.00 0.00 0.00 3.18
2176 3483 1.588674 TGTCAACGGTCATTGGTCAC 58.411 50.000 0.00 0.00 0.00 3.67
2179 3486 5.975693 ATAAAATGTCAACGGTCATTGGT 57.024 34.783 0.00 0.00 33.90 3.67
2220 3527 7.704472 TGTATTCGTGAACTTTTCTGCATTTTT 59.296 29.630 0.00 0.00 0.00 1.94
2222 3529 6.734137 TGTATTCGTGAACTTTTCTGCATTT 58.266 32.000 0.00 0.00 0.00 2.32
2226 3533 6.427150 TCTTTGTATTCGTGAACTTTTCTGC 58.573 36.000 0.00 0.00 0.00 4.26
2273 3580 4.778904 TGAACCTTTTTGTATTCGCGAAG 58.221 39.130 27.20 12.17 0.00 3.79
2284 3591 7.622893 TTTTCCAAATTCCTGAACCTTTTTG 57.377 32.000 0.00 0.00 0.00 2.44
2290 3597 6.758254 TGATCTTTTTCCAAATTCCTGAACC 58.242 36.000 0.00 0.00 0.00 3.62
2313 3620 9.059485 TCGCAAACATTCTTTTTCAAAATTTTG 57.941 25.926 22.40 22.40 39.48 2.44
2315 3622 9.060547 GTTCGCAAACATTCTTTTTCAAAATTT 57.939 25.926 0.00 0.00 35.36 1.82
2316 3623 8.233190 TGTTCGCAAACATTCTTTTTCAAAATT 58.767 25.926 0.00 0.00 40.45 1.82
2317 3624 7.691877 GTGTTCGCAAACATTCTTTTTCAAAAT 59.308 29.630 0.00 0.00 46.58 1.82
2319 3626 6.146184 TGTGTTCGCAAACATTCTTTTTCAAA 59.854 30.769 0.00 0.00 46.58 2.69
2320 3627 5.635280 TGTGTTCGCAAACATTCTTTTTCAA 59.365 32.000 0.00 0.00 46.58 2.69
2321 3628 5.164233 TGTGTTCGCAAACATTCTTTTTCA 58.836 33.333 0.00 0.00 46.58 2.69
2322 3629 5.694674 TGTGTTCGCAAACATTCTTTTTC 57.305 34.783 0.00 0.00 46.58 2.29
2323 3630 6.473397 TTTGTGTTCGCAAACATTCTTTTT 57.527 29.167 7.33 0.00 46.58 1.94
2324 3631 6.473397 TTTTGTGTTCGCAAACATTCTTTT 57.527 29.167 10.42 0.00 46.58 2.27
2325 3632 6.303370 GTTTTTGTGTTCGCAAACATTCTTT 58.697 32.000 10.42 0.00 46.58 2.52
2326 3633 5.443955 CGTTTTTGTGTTCGCAAACATTCTT 60.444 36.000 10.42 0.00 46.58 2.52
2327 3634 4.031201 CGTTTTTGTGTTCGCAAACATTCT 59.969 37.500 10.42 0.00 46.58 2.40
2328 3635 4.201542 ACGTTTTTGTGTTCGCAAACATTC 60.202 37.500 10.42 0.00 46.58 2.67
2329 3636 3.675698 ACGTTTTTGTGTTCGCAAACATT 59.324 34.783 10.42 0.00 46.58 2.71
2330 3637 3.246619 ACGTTTTTGTGTTCGCAAACAT 58.753 36.364 10.42 0.00 46.58 2.71
2331 3638 2.662700 ACGTTTTTGTGTTCGCAAACA 58.337 38.095 10.42 2.87 43.06 2.83
2332 3639 5.114423 CCTATACGTTTTTGTGTTCGCAAAC 59.886 40.000 10.42 1.95 37.98 2.93
2333 3640 5.007430 TCCTATACGTTTTTGTGTTCGCAAA 59.993 36.000 7.33 7.33 36.67 3.68
2334 3641 4.510711 TCCTATACGTTTTTGTGTTCGCAA 59.489 37.500 0.00 0.00 0.00 4.85
2335 3642 4.056740 TCCTATACGTTTTTGTGTTCGCA 58.943 39.130 0.00 0.00 0.00 5.10
2336 3643 4.650545 TCCTATACGTTTTTGTGTTCGC 57.349 40.909 0.00 0.00 0.00 4.70
2337 3644 7.799447 TCAAATTCCTATACGTTTTTGTGTTCG 59.201 33.333 0.00 0.00 0.00 3.95
2338 3645 9.453325 TTCAAATTCCTATACGTTTTTGTGTTC 57.547 29.630 0.00 0.00 0.00 3.18
2339 3646 9.804758 TTTCAAATTCCTATACGTTTTTGTGTT 57.195 25.926 0.00 0.00 0.00 3.32
2340 3647 9.804758 TTTTCAAATTCCTATACGTTTTTGTGT 57.195 25.926 0.00 0.00 0.00 3.72
2392 3699 9.835389 TCCAAATTCATGAACTTTTCTCAAATT 57.165 25.926 11.07 0.00 0.00 1.82
2393 3700 9.835389 TTCCAAATTCATGAACTTTTCTCAAAT 57.165 25.926 11.07 0.00 0.00 2.32
2394 3701 9.664332 TTTCCAAATTCATGAACTTTTCTCAAA 57.336 25.926 11.07 4.62 0.00 2.69
2395 3702 9.664332 TTTTCCAAATTCATGAACTTTTCTCAA 57.336 25.926 11.07 0.00 0.00 3.02
2396 3703 9.097257 GTTTTCCAAATTCATGAACTTTTCTCA 57.903 29.630 11.07 0.00 0.00 3.27
2397 3704 8.268738 CGTTTTCCAAATTCATGAACTTTTCTC 58.731 33.333 11.07 0.00 0.00 2.87
2398 3705 7.978975 TCGTTTTCCAAATTCATGAACTTTTCT 59.021 29.630 11.07 0.00 0.00 2.52
2399 3706 8.125728 TCGTTTTCCAAATTCATGAACTTTTC 57.874 30.769 11.07 0.00 0.00 2.29
2403 3710 7.169645 CACAATCGTTTTCCAAATTCATGAACT 59.830 33.333 11.07 0.00 0.00 3.01
2479 3793 6.621316 ACCGGTTTTTCTTTTTGTTTTGTT 57.379 29.167 0.00 0.00 0.00 2.83
2480 3794 6.431278 CAACCGGTTTTTCTTTTTGTTTTGT 58.569 32.000 19.55 0.00 0.00 2.83
2481 3795 5.853810 CCAACCGGTTTTTCTTTTTGTTTTG 59.146 36.000 19.55 0.32 0.00 2.44
2482 3796 5.048643 CCCAACCGGTTTTTCTTTTTGTTTT 60.049 36.000 19.55 0.00 0.00 2.43
2483 3797 4.456222 CCCAACCGGTTTTTCTTTTTGTTT 59.544 37.500 19.55 0.00 0.00 2.83
2484 3798 4.004314 CCCAACCGGTTTTTCTTTTTGTT 58.996 39.130 19.55 0.00 0.00 2.83
2485 3799 3.261137 TCCCAACCGGTTTTTCTTTTTGT 59.739 39.130 19.55 0.00 0.00 2.83
2486 3800 3.863041 TCCCAACCGGTTTTTCTTTTTG 58.137 40.909 19.55 3.26 0.00 2.44
2490 3804 1.411246 GCTTCCCAACCGGTTTTTCTT 59.589 47.619 19.55 0.00 0.00 2.52
2496 3810 0.822121 GTGAAGCTTCCCAACCGGTT 60.822 55.000 23.42 15.86 0.00 4.44
2528 3842 7.218583 GTCGTTCGAGGTTCTATTTTCTAGAAG 59.781 40.741 5.12 0.00 34.59 2.85
2529 3843 7.025963 GTCGTTCGAGGTTCTATTTTCTAGAA 58.974 38.462 0.00 0.00 0.00 2.10
2531 3845 6.553524 AGTCGTTCGAGGTTCTATTTTCTAG 58.446 40.000 0.00 0.00 0.00 2.43
2532 3846 6.373774 AGAGTCGTTCGAGGTTCTATTTTCTA 59.626 38.462 0.00 0.00 0.00 2.10
2533 3847 5.183522 AGAGTCGTTCGAGGTTCTATTTTCT 59.816 40.000 0.00 0.00 0.00 2.52
2536 3850 5.388408 AAGAGTCGTTCGAGGTTCTATTT 57.612 39.130 0.00 0.00 0.00 1.40
2539 3853 4.825422 TCTAAGAGTCGTTCGAGGTTCTA 58.175 43.478 0.00 0.00 0.00 2.10
2541 3855 4.344448 CATCTAAGAGTCGTTCGAGGTTC 58.656 47.826 0.00 0.00 0.00 3.62
2542 3856 3.128938 CCATCTAAGAGTCGTTCGAGGTT 59.871 47.826 0.00 0.00 0.00 3.50
2543 3857 2.683867 CCATCTAAGAGTCGTTCGAGGT 59.316 50.000 0.00 0.00 0.00 3.85
2544 3858 2.033550 CCCATCTAAGAGTCGTTCGAGG 59.966 54.545 0.00 0.00 0.00 4.63
2545 3859 2.541999 GCCCATCTAAGAGTCGTTCGAG 60.542 54.545 0.00 0.00 0.00 4.04
2546 3860 1.404391 GCCCATCTAAGAGTCGTTCGA 59.596 52.381 0.00 0.00 0.00 3.71
2547 3861 1.536284 GGCCCATCTAAGAGTCGTTCG 60.536 57.143 0.00 0.00 0.00 3.95
2548 3862 1.536284 CGGCCCATCTAAGAGTCGTTC 60.536 57.143 0.00 0.00 0.00 3.95
2549 3863 0.460311 CGGCCCATCTAAGAGTCGTT 59.540 55.000 0.00 0.00 0.00 3.85
2550 3864 1.392710 CCGGCCCATCTAAGAGTCGT 61.393 60.000 0.00 0.00 0.00 4.34
2551 3865 1.364171 CCGGCCCATCTAAGAGTCG 59.636 63.158 0.00 0.00 0.00 4.18
2552 3866 1.069935 GCCGGCCCATCTAAGAGTC 59.930 63.158 18.11 0.00 0.00 3.36
2553 3867 2.444256 GGCCGGCCCATCTAAGAGT 61.444 63.158 36.64 0.00 0.00 3.24
2554 3868 2.427753 GGCCGGCCCATCTAAGAG 59.572 66.667 36.64 0.00 0.00 2.85
2564 3878 3.206957 GTTCGTAATGGGCCGGCC 61.207 66.667 38.57 38.57 0.00 6.13
2565 3879 3.569690 CGTTCGTAATGGGCCGGC 61.570 66.667 21.18 21.18 0.00 6.13
2566 3880 2.893404 CCGTTCGTAATGGGCCGG 60.893 66.667 0.00 0.00 33.75 6.13
2567 3881 2.125431 ACCGTTCGTAATGGGCCG 60.125 61.111 0.00 0.00 42.07 6.13
2568 3882 2.169146 CGACCGTTCGTAATGGGCC 61.169 63.158 0.00 0.00 43.08 5.80
2569 3883 2.169146 CCGACCGTTCGTAATGGGC 61.169 63.158 0.61 6.31 44.28 5.36
2570 3884 1.519898 CCCGACCGTTCGTAATGGG 60.520 63.158 0.61 0.00 44.28 4.00
2571 3885 0.108709 TTCCCGACCGTTCGTAATGG 60.109 55.000 0.61 0.00 44.28 3.16
2572 3886 1.274596 CTTCCCGACCGTTCGTAATG 58.725 55.000 0.61 0.00 44.28 1.90
2573 3887 0.459063 GCTTCCCGACCGTTCGTAAT 60.459 55.000 0.61 0.00 44.28 1.89
2574 3888 1.080569 GCTTCCCGACCGTTCGTAA 60.081 57.895 0.61 0.00 44.28 3.18
2575 3889 1.597797 ATGCTTCCCGACCGTTCGTA 61.598 55.000 0.61 0.00 44.28 3.43
2576 3890 2.939261 ATGCTTCCCGACCGTTCGT 61.939 57.895 0.61 0.00 44.28 3.85
2577 3891 2.125673 ATGCTTCCCGACCGTTCG 60.126 61.111 0.00 0.00 45.44 3.95
2578 3892 2.106683 CCATGCTTCCCGACCGTTC 61.107 63.158 0.00 0.00 0.00 3.95
2579 3893 2.046314 CCATGCTTCCCGACCGTT 60.046 61.111 0.00 0.00 0.00 4.44
2580 3894 2.890766 AACCATGCTTCCCGACCGT 61.891 57.895 0.00 0.00 0.00 4.83
2581 3895 2.046314 AACCATGCTTCCCGACCG 60.046 61.111 0.00 0.00 0.00 4.79
2582 3896 2.046285 CCAACCATGCTTCCCGACC 61.046 63.158 0.00 0.00 0.00 4.79
2583 3897 0.608035 TTCCAACCATGCTTCCCGAC 60.608 55.000 0.00 0.00 0.00 4.79
2584 3898 0.322456 CTTCCAACCATGCTTCCCGA 60.322 55.000 0.00 0.00 0.00 5.14
2585 3899 1.315257 CCTTCCAACCATGCTTCCCG 61.315 60.000 0.00 0.00 0.00 5.14
2586 3900 0.251787 ACCTTCCAACCATGCTTCCC 60.252 55.000 0.00 0.00 0.00 3.97
2587 3901 3.363787 ACCTTCCAACCATGCTTCC 57.636 52.632 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.