Multiple sequence alignment - TraesCS3A01G111200

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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 TraesCS3A01G111200 chr3A 100.000 2678 0 0 1 2678 78709239 78711916 0.000000e+00 4946.0
1 TraesCS3A01G111200 chr3A 78.027 223 34 12 2099 2308 12492909 12493129 2.800000e-25 126.0
2 TraesCS3A01G111200 chr3A 87.037 108 14 0 1448 1555 374446646 374446753 3.620000e-24 122.0
3 TraesCS3A01G111200 chr3A 89.744 78 6 2 2457 2532 640553472 640553549 6.100000e-17 99.0
4 TraesCS3A01G111200 chr3B 85.679 2430 165 87 260 2613 111942059 111944381 0.000000e+00 2390.0
5 TraesCS3A01G111200 chr3B 91.322 242 9 3 41 274 111941803 111942040 1.200000e-83 320.0
6 TraesCS3A01G111200 chr3B 84.000 175 25 3 2169 2340 2483041 2483215 5.930000e-37 165.0
7 TraesCS3A01G111200 chr3B 80.556 180 25 6 2170 2344 94878913 94878739 2.160000e-26 130.0
8 TraesCS3A01G111200 chr3B 96.970 33 1 0 2490 2522 661991357 661991389 3.720000e-04 56.5
9 TraesCS3A01G111200 chr3D 91.218 1617 73 29 383 1967 67350415 67351994 0.000000e+00 2135.0
10 TraesCS3A01G111200 chr3D 86.951 728 53 22 1977 2678 67352115 67352826 0.000000e+00 780.0
11 TraesCS3A01G111200 chr3D 85.372 376 20 16 38 384 67350011 67350380 9.120000e-95 357.0
12 TraesCS3A01G111200 chr3D 82.286 175 27 4 2170 2340 3002688 3002514 5.970000e-32 148.0
13 TraesCS3A01G111200 chr3D 87.037 108 14 0 1448 1555 286190173 286190280 3.620000e-24 122.0
14 TraesCS3A01G111200 chr3D 79.290 169 30 5 2356 2522 463181056 463180891 2.180000e-21 113.0
15 TraesCS3A01G111200 chr3D 91.139 79 3 4 2457 2532 500842805 500842728 1.310000e-18 104.0
16 TraesCS3A01G111200 chr1A 85.470 234 32 2 1343 1576 135182902 135182671 2.660000e-60 243.0
17 TraesCS3A01G111200 chr1A 78.804 184 26 13 2356 2532 586061910 586061733 7.840000e-21 111.0
18 TraesCS3A01G111200 chr2D 81.538 195 28 8 2340 2530 17823131 17822941 1.280000e-33 154.0
19 TraesCS3A01G111200 chrUn 82.759 174 27 3 2170 2340 32136624 32136451 4.620000e-33 152.0
20 TraesCS3A01G111200 chr4A 79.444 180 27 10 2360 2533 5403186 5403011 4.680000e-23 119.0
21 TraesCS3A01G111200 chr2B 78.173 197 33 8 2356 2549 715916551 715916362 1.680000e-22 117.0
22 TraesCS3A01G111200 chr7D 83.929 112 16 1 2210 2321 114857896 114857787 3.650000e-19 106.0
23 TraesCS3A01G111200 chr7D 84.507 71 9 2 2589 2658 177118543 177118474 4.780000e-08 69.4
24 TraesCS3A01G111200 chr6D 84.762 105 11 2 2540 2644 361169462 361169363 1.700000e-17 100.0


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 TraesCS3A01G111200 chr3A 78709239 78711916 2677 False 4946.000000 4946 100.0000 1 2678 1 chr3A.!!$F2 2677
1 TraesCS3A01G111200 chr3B 111941803 111944381 2578 False 1355.000000 2390 88.5005 41 2613 2 chr3B.!!$F3 2572
2 TraesCS3A01G111200 chr3D 67350011 67352826 2815 False 1090.666667 2135 87.8470 38 2678 3 chr3D.!!$F2 2640

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
580 697 0.109964 GCAGCCAATTAAACGACGCA 60.11 50.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2313 0.387367 GCTCGCTCGAACTCAACTCA 60.387 55.0 0.0 0.0 0.0 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
34 35 8.873830 TCTTAAAATCAGCTAAGAATTGAGTCG 58.126 33.333 0.00 0.00 32.50 4.18
35 36 8.771920 TTAAAATCAGCTAAGAATTGAGTCGA 57.228 30.769 0.00 0.00 0.00 4.20
36 37 6.900568 AAATCAGCTAAGAATTGAGTCGAG 57.099 37.500 0.00 0.00 0.00 4.04
37 38 5.843673 ATCAGCTAAGAATTGAGTCGAGA 57.156 39.130 0.00 0.00 0.00 4.04
38 39 4.987832 TCAGCTAAGAATTGAGTCGAGAC 58.012 43.478 0.00 0.00 0.00 3.36
39 40 4.702612 TCAGCTAAGAATTGAGTCGAGACT 59.297 41.667 5.31 5.31 45.84 3.24
82 83 2.107552 AGAGAGTAGGCTAGCTAGGTGG 59.892 54.545 22.10 2.14 0.00 4.61
163 164 2.729862 GATTCGATCGACCGGCCG 60.730 66.667 21.04 21.04 0.00 6.13
164 165 4.280494 ATTCGATCGACCGGCCGG 62.280 66.667 42.17 42.17 42.03 6.13
187 188 1.971167 TGCAATGGACTTGACCGCC 60.971 57.895 0.00 0.00 36.97 6.13
194 195 1.373748 GACTTGACCGCCAACGCTA 60.374 57.895 0.00 0.00 38.22 4.26
214 215 2.586648 ATTTGGACCCGAAAAGCTCT 57.413 45.000 0.00 0.00 0.00 4.09
276 318 0.438830 GCCGTTGTCTCGTTGTCATC 59.561 55.000 0.00 0.00 0.00 2.92
280 322 2.731451 CGTTGTCTCGTTGTCATCACAT 59.269 45.455 0.00 0.00 30.55 3.21
285 327 3.300853 GTCTCGTTGTCATCACATGTACG 59.699 47.826 8.41 8.41 34.55 3.67
286 328 3.057806 TCTCGTTGTCATCACATGTACGT 60.058 43.478 13.11 0.00 34.71 3.57
287 329 4.154556 TCTCGTTGTCATCACATGTACGTA 59.845 41.667 13.11 0.00 34.71 3.57
291 345 5.969435 CGTTGTCATCACATGTACGTAGTAT 59.031 40.000 0.00 0.00 37.63 2.12
311 369 9.698617 GTAGTATTATTTTCTTCAATTTCGCGT 57.301 29.630 5.77 0.00 0.00 6.01
475 587 5.629097 CGAGGAACGTACATAGATGGATAC 58.371 45.833 0.00 0.00 37.22 2.24
499 613 7.749808 ACATATACTTATCCTGTACGATCGTG 58.250 38.462 30.23 13.81 0.00 4.35
513 627 4.155733 CGTGGATGGCCGTGGCTA 62.156 66.667 0.00 4.86 41.60 3.93
575 689 2.769376 CGTACTGCAGCCAATTAAACG 58.231 47.619 15.27 7.27 0.00 3.60
580 697 0.109964 GCAGCCAATTAAACGACGCA 60.110 50.000 0.00 0.00 0.00 5.24
661 778 6.574465 GCCACATTTAAGTCTCCTCTTGACTA 60.574 42.308 0.00 0.00 43.16 2.59
662 779 7.038659 CCACATTTAAGTCTCCTCTTGACTAG 58.961 42.308 0.00 0.00 43.16 2.57
663 780 6.533367 CACATTTAAGTCTCCTCTTGACTAGC 59.467 42.308 0.00 0.00 43.16 3.42
664 781 5.662674 TTTAAGTCTCCTCTTGACTAGCC 57.337 43.478 0.00 0.00 43.16 3.93
667 784 1.754226 GTCTCCTCTTGACTAGCCAGG 59.246 57.143 0.00 0.00 0.00 4.45
846 963 4.834892 CACCGTACGTACCCGCCG 62.835 72.222 19.67 7.79 37.70 6.46
992 1124 3.755404 CGTAGCTCGTCTGTGCAC 58.245 61.111 10.75 10.75 37.07 4.57
1005 1137 2.113562 TGCACTGCACTCATGGCA 59.886 55.556 0.00 0.00 39.32 4.92
1024 1159 1.810030 GCTTCGCTGGGACTTACCG 60.810 63.158 0.00 0.00 40.11 4.02
1032 1167 1.146263 GGGACTTACCGGCCATGAG 59.854 63.158 0.00 0.00 40.11 2.90
1033 1168 1.335132 GGGACTTACCGGCCATGAGA 61.335 60.000 0.00 0.00 40.11 3.27
1036 1171 0.907704 ACTTACCGGCCATGAGACCA 60.908 55.000 0.00 0.00 0.00 4.02
1042 1177 1.147153 GGCCATGAGACCAGCTACC 59.853 63.158 0.00 0.00 0.00 3.18
1097 1232 3.682292 AAGCCGGTGATCCCTTCGC 62.682 63.158 1.90 0.00 0.00 4.70
1146 1281 3.358076 CTTCCCGGAGCTCGTGGAC 62.358 68.421 21.69 1.27 37.73 4.02
1172 1307 2.829458 GCCCTCCGACTACTCGCT 60.829 66.667 0.00 0.00 38.70 4.93
1220 1355 1.533129 CGAGGCGATGAACATGTACGA 60.533 52.381 0.00 0.00 0.00 3.43
1227 1362 0.885879 TGAACATGTACGAGCGGAGT 59.114 50.000 0.00 0.00 0.00 3.85
1251 1386 1.682323 GTCTTCCCTATGACGACCTCC 59.318 57.143 0.00 0.00 36.51 4.30
1329 1464 2.357517 GGGATCGGTGCTATGGCG 60.358 66.667 0.00 0.00 42.25 5.69
1381 1516 4.083862 GGTCGGAGGTGGAGGTGC 62.084 72.222 0.00 0.00 0.00 5.01
1383 1518 1.681327 GTCGGAGGTGGAGGTGCTA 60.681 63.158 0.00 0.00 0.00 3.49
1695 1840 3.951037 ACTGAACTGAGCTACTGATCGAT 59.049 43.478 0.00 0.00 0.00 3.59
1709 1854 3.451526 TGATCGATCAGTACGAGTACGT 58.548 45.455 23.99 0.00 42.81 3.57
1710 1855 4.610945 TGATCGATCAGTACGAGTACGTA 58.389 43.478 23.99 0.00 44.08 3.57
1721 1866 3.048942 CGAGTACGTAGCTGTGGTTAG 57.951 52.381 0.00 0.00 34.56 2.34
1795 1940 1.075482 CCTTGATGGTGGTGTGCCT 59.925 57.895 0.00 0.00 35.27 4.75
1796 1941 1.246056 CCTTGATGGTGGTGTGCCTG 61.246 60.000 0.00 0.00 35.27 4.85
1797 1942 1.870055 CTTGATGGTGGTGTGCCTGC 61.870 60.000 0.00 0.00 35.27 4.85
1798 1943 3.064324 GATGGTGGTGTGCCTGCC 61.064 66.667 0.00 0.00 35.27 4.85
1827 1973 0.458889 TAATTCGGTCGCTTCCACGG 60.459 55.000 0.00 0.00 0.00 4.94
1840 1986 4.403137 CACGGCCATTGTGCACGG 62.403 66.667 13.13 8.69 31.88 4.94
1967 2115 1.838077 AGTTGGTAGGCTCCACATACC 59.162 52.381 5.34 0.00 39.57 2.73
1968 2116 1.557832 GTTGGTAGGCTCCACATACCA 59.442 52.381 5.20 5.20 45.53 3.25
1969 2117 1.200519 TGGTAGGCTCCACATACCAC 58.799 55.000 5.20 0.00 43.06 4.16
1970 2118 1.200519 GGTAGGCTCCACATACCACA 58.799 55.000 0.00 0.00 39.05 4.17
1975 2234 3.115390 AGGCTCCACATACCACAATACT 58.885 45.455 0.00 0.00 0.00 2.12
1987 2246 4.957296 ACCACAATACTAATCCGTCCATC 58.043 43.478 0.00 0.00 0.00 3.51
2035 2309 7.483307 TGTAGTTCTACGAAGTTTTGTACTGT 58.517 34.615 0.00 0.00 37.78 3.55
2039 2313 9.538508 AGTTCTACGAAGTTTTGTACTGTAAAT 57.461 29.630 0.00 0.00 37.78 1.40
2058 2332 0.387367 TGAGTTGAGTTCGAGCGAGC 60.387 55.000 0.00 0.00 0.00 5.03
2083 2364 2.894126 ACTAGCTATGCTCGGCACTAAT 59.106 45.455 0.00 0.00 43.04 1.73
2096 2377 3.381949 GGCACTAATATTCGAGCGACTT 58.618 45.455 0.00 0.00 0.00 3.01
2102 2383 6.034577 CACTAATATTCGAGCGACTTCAAACA 59.965 38.462 0.00 0.00 0.00 2.83
2132 2413 5.810095 AGCTCAAGGTCAAGCTATAAAAGT 58.190 37.500 0.00 0.00 46.73 2.66
2133 2414 5.645497 AGCTCAAGGTCAAGCTATAAAAGTG 59.355 40.000 0.00 0.00 46.73 3.16
2135 2416 4.700213 TCAAGGTCAAGCTATAAAAGTGGC 59.300 41.667 0.00 0.00 0.00 5.01
2152 2440 1.322442 GGCCCAGCTTGTAATGATCC 58.678 55.000 0.00 0.00 0.00 3.36
2158 2446 4.019174 CCAGCTTGTAATGATCCCAAGTT 58.981 43.478 11.02 4.96 38.24 2.66
2244 2537 5.734720 AGATAGGACACAACACAACATAGG 58.265 41.667 0.00 0.00 0.00 2.57
2414 2708 1.000938 CTGCTCTCAAACCTTGGCAAC 60.001 52.381 0.00 0.00 0.00 4.17
2448 2742 3.902218 AGCTAACACATTGGCCATGTAT 58.098 40.909 6.09 8.36 45.06 2.29
2456 2750 4.340097 CACATTGGCCATGTATCATCTTGT 59.660 41.667 6.09 0.00 45.06 3.16
2457 2751 4.957954 ACATTGGCCATGTATCATCTTGTT 59.042 37.500 6.09 0.00 45.00 2.83
2458 2752 4.987408 TTGGCCATGTATCATCTTGTTG 57.013 40.909 6.09 0.00 0.00 3.33
2459 2753 3.966979 TGGCCATGTATCATCTTGTTGT 58.033 40.909 0.00 0.00 0.00 3.32
2536 2830 9.814899 AAATGAAGAAAATCATACACAAACACA 57.185 25.926 0.00 0.00 39.08 3.72
2538 2832 8.627487 TGAAGAAAATCATACACAAACACAAC 57.373 30.769 0.00 0.00 0.00 3.32
2539 2833 8.246871 TGAAGAAAATCATACACAAACACAACA 58.753 29.630 0.00 0.00 0.00 3.33
2540 2834 9.248291 GAAGAAAATCATACACAAACACAACAT 57.752 29.630 0.00 0.00 0.00 2.71
2575 2869 4.831155 CCTCCGTCCCATATTAGTTGTAGA 59.169 45.833 0.00 0.00 0.00 2.59
2584 2878 8.944138 TCCCATATTAGTTGTAGATGAAATGGA 58.056 33.333 0.00 0.00 33.54 3.41
2585 2879 9.745018 CCCATATTAGTTGTAGATGAAATGGAT 57.255 33.333 0.00 0.00 33.54 3.41
2622 2916 5.673514 TGCATTTCAGTGCTAGATACATCA 58.326 37.500 0.00 0.00 45.27 3.07
2630 2924 8.703604 TCAGTGCTAGATACATCAGTTTAAAC 57.296 34.615 10.47 10.47 0.00 2.01
2632 2926 7.488150 CAGTGCTAGATACATCAGTTTAAACGA 59.512 37.037 12.54 12.72 0.00 3.85
2636 2930 8.108782 GCTAGATACATCAGTTTAAACGACAAC 58.891 37.037 12.54 2.20 0.00 3.32
2651 2945 5.097742 ACGACAACTGATATGGAATGGAA 57.902 39.130 0.00 0.00 0.00 3.53
2652 2946 4.876107 ACGACAACTGATATGGAATGGAAC 59.124 41.667 0.00 0.00 0.00 3.62
2660 2954 6.931281 ACTGATATGGAATGGAACGAGTAATG 59.069 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.873830 CGACTCAATTCTTAGCTGATTTTAAGA 58.126 33.333 0.00 0.00 34.89 2.10
9 10 8.873830 TCGACTCAATTCTTAGCTGATTTTAAG 58.126 33.333 0.00 0.00 0.00 1.85
10 11 8.771920 TCGACTCAATTCTTAGCTGATTTTAA 57.228 30.769 0.00 0.00 0.00 1.52
11 12 8.251026 TCTCGACTCAATTCTTAGCTGATTTTA 58.749 33.333 0.00 0.00 0.00 1.52
12 13 7.064016 GTCTCGACTCAATTCTTAGCTGATTTT 59.936 37.037 0.00 0.00 0.00 1.82
13 14 6.533367 GTCTCGACTCAATTCTTAGCTGATTT 59.467 38.462 0.00 0.00 0.00 2.17
14 15 6.039616 GTCTCGACTCAATTCTTAGCTGATT 58.960 40.000 0.00 0.00 0.00 2.57
15 16 5.359576 AGTCTCGACTCAATTCTTAGCTGAT 59.640 40.000 0.00 0.00 36.92 2.90
16 17 4.702612 AGTCTCGACTCAATTCTTAGCTGA 59.297 41.667 0.00 0.00 36.92 4.26
17 18 4.992688 AGTCTCGACTCAATTCTTAGCTG 58.007 43.478 0.00 0.00 36.92 4.24
18 19 6.238897 CCATAGTCTCGACTCAATTCTTAGCT 60.239 42.308 2.32 0.00 42.54 3.32
19 20 5.918011 CCATAGTCTCGACTCAATTCTTAGC 59.082 44.000 2.32 0.00 42.54 3.09
20 21 5.918011 GCCATAGTCTCGACTCAATTCTTAG 59.082 44.000 2.32 0.00 42.54 2.18
21 22 5.594725 AGCCATAGTCTCGACTCAATTCTTA 59.405 40.000 2.32 0.00 42.54 2.10
22 23 4.404073 AGCCATAGTCTCGACTCAATTCTT 59.596 41.667 2.32 0.00 42.54 2.52
23 24 3.957497 AGCCATAGTCTCGACTCAATTCT 59.043 43.478 2.32 0.00 42.54 2.40
24 25 4.314740 AGCCATAGTCTCGACTCAATTC 57.685 45.455 2.32 0.00 42.54 2.17
25 26 4.890581 AGTAGCCATAGTCTCGACTCAATT 59.109 41.667 2.32 0.00 42.54 2.32
26 27 4.465886 AGTAGCCATAGTCTCGACTCAAT 58.534 43.478 2.32 0.00 42.54 2.57
27 28 3.878103 GAGTAGCCATAGTCTCGACTCAA 59.122 47.826 2.32 0.00 42.54 3.02
28 29 3.118371 TGAGTAGCCATAGTCTCGACTCA 60.118 47.826 2.32 0.00 42.54 3.41
29 30 3.468770 TGAGTAGCCATAGTCTCGACTC 58.531 50.000 2.32 0.00 42.54 3.36
30 31 3.562343 TGAGTAGCCATAGTCTCGACT 57.438 47.619 4.81 4.81 45.02 4.18
31 32 4.839668 ATTGAGTAGCCATAGTCTCGAC 57.160 45.455 0.00 0.00 33.21 4.20
32 33 4.499865 GCAATTGAGTAGCCATAGTCTCGA 60.500 45.833 10.34 0.00 33.21 4.04
33 34 3.738282 GCAATTGAGTAGCCATAGTCTCG 59.262 47.826 10.34 0.00 33.21 4.04
34 35 4.749099 CAGCAATTGAGTAGCCATAGTCTC 59.251 45.833 10.34 0.00 33.21 3.36
35 36 4.444022 CCAGCAATTGAGTAGCCATAGTCT 60.444 45.833 10.34 0.00 33.21 3.24
36 37 3.812053 CCAGCAATTGAGTAGCCATAGTC 59.188 47.826 10.34 0.00 32.72 2.59
37 38 3.813443 CCAGCAATTGAGTAGCCATAGT 58.187 45.455 10.34 0.00 0.00 2.12
38 39 2.551459 GCCAGCAATTGAGTAGCCATAG 59.449 50.000 10.34 0.00 0.00 2.23
39 40 2.173356 AGCCAGCAATTGAGTAGCCATA 59.827 45.455 10.34 0.00 0.00 2.74
163 164 2.676471 AAGTCCATTGCACCGGCC 60.676 61.111 0.00 0.00 40.13 6.13
164 165 1.971167 TCAAGTCCATTGCACCGGC 60.971 57.895 0.00 0.00 38.89 6.13
165 166 1.586154 GGTCAAGTCCATTGCACCGG 61.586 60.000 0.00 0.00 38.89 5.28
166 167 1.875963 GGTCAAGTCCATTGCACCG 59.124 57.895 0.00 0.00 38.89 4.94
172 173 1.234615 CGTTGGCGGTCAAGTCCATT 61.235 55.000 0.00 0.00 35.80 3.16
187 188 1.444836 TCGGGTCCAAATTAGCGTTG 58.555 50.000 0.00 0.00 0.00 4.10
194 195 2.876581 AGAGCTTTTCGGGTCCAAATT 58.123 42.857 0.00 0.00 34.64 1.82
214 215 2.380064 ACACCCAAAATCCAGCTGAA 57.620 45.000 17.39 0.00 0.00 3.02
285 327 9.698617 ACGCGAAATTGAAGAAAATAATACTAC 57.301 29.630 15.93 0.00 0.00 2.73
291 345 8.661257 TCAGATACGCGAAATTGAAGAAAATAA 58.339 29.630 15.93 0.00 0.00 1.40
298 352 3.302740 GGCTCAGATACGCGAAATTGAAG 60.303 47.826 15.93 2.76 0.00 3.02
301 355 1.261619 GGGCTCAGATACGCGAAATTG 59.738 52.381 15.93 6.08 0.00 2.32
302 356 1.583054 GGGCTCAGATACGCGAAATT 58.417 50.000 15.93 0.00 0.00 1.82
303 357 0.597637 CGGGCTCAGATACGCGAAAT 60.598 55.000 15.93 5.62 44.04 2.17
311 369 4.521639 ACGTATAAACATCGGGCTCAGATA 59.478 41.667 0.00 0.00 0.00 1.98
353 416 1.520342 GAGACATCGGTGCTCTGGC 60.520 63.158 11.39 0.00 39.26 4.85
475 587 7.065443 TCCACGATCGTACAGGATAAGTATATG 59.935 40.741 22.26 1.85 0.00 1.78
499 613 2.980233 GCATAGCCACGGCCATCC 60.980 66.667 2.24 0.00 43.17 3.51
727 844 0.383124 GCGTGCGCTTTCGGATTATC 60.383 55.000 9.73 0.00 38.56 1.75
846 963 0.248377 GCTTCATGGATGCTTCACGC 60.248 55.000 1.64 0.00 39.77 5.34
847 964 1.329906 GAGCTTCATGGATGCTTCACG 59.670 52.381 7.86 0.00 41.89 4.35
848 965 1.329906 CGAGCTTCATGGATGCTTCAC 59.670 52.381 7.86 0.00 41.89 3.18
883 1000 2.736144 TGGCCCGCGATTTATACTAG 57.264 50.000 8.23 0.00 0.00 2.57
1014 1146 1.146263 CTCATGGCCGGTAAGTCCC 59.854 63.158 1.90 0.00 0.00 4.46
1024 1159 1.147153 GGTAGCTGGTCTCATGGCC 59.853 63.158 0.00 0.00 0.00 5.36
1156 1291 3.111939 CAGCGAGTAGTCGGAGGG 58.888 66.667 20.94 0.00 46.91 4.30
1204 1339 0.227234 CGCTCGTACATGTTCATCGC 59.773 55.000 2.30 0.64 0.00 4.58
1220 1355 2.637383 GGGAAGACGACACTCCGCT 61.637 63.158 0.00 0.00 0.00 5.52
1381 1516 2.042831 ACCGGAACCCGTCGTCTAG 61.043 63.158 9.46 0.00 46.80 2.43
1383 1518 3.677648 CACCGGAACCCGTCGTCT 61.678 66.667 9.46 0.00 46.80 4.18
1608 1746 3.322466 CTCCAGGTCCAAGCGGGT 61.322 66.667 0.00 0.00 38.11 5.28
1650 1788 4.779733 TCCGAGGAGTGAGCCCCC 62.780 72.222 0.00 0.00 0.00 5.40
1651 1789 3.151022 CTCCGAGGAGTGAGCCCC 61.151 72.222 10.88 0.00 37.47 5.80
1703 1848 4.861102 AAACTAACCACAGCTACGTACT 57.139 40.909 0.00 0.00 0.00 2.73
1704 1849 6.808212 TCATAAAACTAACCACAGCTACGTAC 59.192 38.462 0.00 0.00 0.00 3.67
1705 1850 6.923012 TCATAAAACTAACCACAGCTACGTA 58.077 36.000 0.00 0.00 0.00 3.57
1706 1851 5.786311 TCATAAAACTAACCACAGCTACGT 58.214 37.500 0.00 0.00 0.00 3.57
1707 1852 6.291637 CGATCATAAAACTAACCACAGCTACG 60.292 42.308 0.00 0.00 0.00 3.51
1709 1854 6.869695 TCGATCATAAAACTAACCACAGCTA 58.130 36.000 0.00 0.00 0.00 3.32
1710 1855 5.730550 TCGATCATAAAACTAACCACAGCT 58.269 37.500 0.00 0.00 0.00 4.24
1711 1856 6.604735 ATCGATCATAAAACTAACCACAGC 57.395 37.500 0.00 0.00 0.00 4.40
1713 1858 7.223193 CCGTAATCGATCATAAAACTAACCACA 59.777 37.037 0.00 0.00 39.71 4.17
1714 1859 7.223387 ACCGTAATCGATCATAAAACTAACCAC 59.777 37.037 0.00 0.00 39.71 4.16
1716 1861 7.704789 ACCGTAATCGATCATAAAACTAACC 57.295 36.000 0.00 0.00 39.71 2.85
1718 1863 8.929827 TGAACCGTAATCGATCATAAAACTAA 57.070 30.769 0.00 0.00 39.71 2.24
1720 1865 7.262772 TCTGAACCGTAATCGATCATAAAACT 58.737 34.615 0.00 0.00 39.71 2.66
1721 1866 7.459394 TCTGAACCGTAATCGATCATAAAAC 57.541 36.000 0.00 0.00 39.71 2.43
1827 1973 2.081425 TTTCCACCGTGCACAATGGC 62.081 55.000 25.04 0.00 38.72 4.40
1840 1986 2.785105 CGTCGATCGGCGTTTCCAC 61.785 63.158 32.27 11.33 41.80 4.02
1928 2074 2.568062 ACTTGCCAATGAATGATTGCCA 59.432 40.909 0.00 0.00 40.32 4.92
1967 2115 5.215252 AGGATGGACGGATTAGTATTGTG 57.785 43.478 0.00 0.00 0.00 3.33
1968 2116 5.888982 AAGGATGGACGGATTAGTATTGT 57.111 39.130 0.00 0.00 0.00 2.71
1969 2117 6.288294 TGAAAGGATGGACGGATTAGTATTG 58.712 40.000 0.00 0.00 0.00 1.90
1970 2118 6.326583 TCTGAAAGGATGGACGGATTAGTATT 59.673 38.462 0.00 0.00 0.00 1.89
1975 2234 4.040461 GGATCTGAAAGGATGGACGGATTA 59.960 45.833 0.00 0.00 0.00 1.75
2015 2274 9.531942 TCATTTACAGTACAAAACTTCGTAGAA 57.468 29.630 0.00 0.00 45.90 2.10
2018 2277 8.876275 ACTCATTTACAGTACAAAACTTCGTA 57.124 30.769 0.00 0.00 35.76 3.43
2023 2282 8.732746 ACTCAACTCATTTACAGTACAAAACT 57.267 30.769 0.00 0.00 39.81 2.66
2024 2283 9.434559 GAACTCAACTCATTTACAGTACAAAAC 57.565 33.333 0.00 0.00 0.00 2.43
2028 2287 6.741109 TCGAACTCAACTCATTTACAGTACA 58.259 36.000 0.00 0.00 0.00 2.90
2029 2288 6.183359 GCTCGAACTCAACTCATTTACAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
2030 2289 5.862323 GCTCGAACTCAACTCATTTACAGTA 59.138 40.000 0.00 0.00 0.00 2.74
2035 2309 4.166523 CTCGCTCGAACTCAACTCATTTA 58.833 43.478 0.00 0.00 0.00 1.40
2039 2313 0.387367 GCTCGCTCGAACTCAACTCA 60.387 55.000 0.00 0.00 0.00 3.41
2058 2332 1.067669 TGCCGAGCATAGCTAGTTCAG 59.932 52.381 0.00 0.00 39.88 3.02
2070 2351 3.013276 CTCGAATATTAGTGCCGAGCA 57.987 47.619 9.67 0.00 39.88 4.26
2083 2364 5.444087 CGATTTGTTTGAAGTCGCTCGAATA 60.444 40.000 0.00 0.00 0.00 1.75
2096 2377 3.882888 ACCTTGAGCTTCGATTTGTTTGA 59.117 39.130 0.00 0.00 0.00 2.69
2102 2383 2.485814 GCTTGACCTTGAGCTTCGATTT 59.514 45.455 0.00 0.00 36.01 2.17
2131 2412 1.678101 GATCATTACAAGCTGGGCCAC 59.322 52.381 0.00 0.00 0.00 5.01
2132 2413 1.410083 GGATCATTACAAGCTGGGCCA 60.410 52.381 5.85 5.85 0.00 5.36
2133 2414 1.322442 GGATCATTACAAGCTGGGCC 58.678 55.000 0.00 0.00 0.00 5.80
2135 2416 2.734755 TGGGATCATTACAAGCTGGG 57.265 50.000 0.00 0.00 0.00 4.45
2152 2440 7.114388 GCCGAAACTAGTTTAAAATCAACTTGG 59.886 37.037 20.58 9.27 35.95 3.61
2215 2508 5.055642 TGTGTTGTGTCCTATCTAGTTCG 57.944 43.478 0.00 0.00 0.00 3.95
2216 2509 6.220930 TGTTGTGTTGTGTCCTATCTAGTTC 58.779 40.000 0.00 0.00 0.00 3.01
2309 2602 9.224267 CCAGTCTTCAATTGAGAGAGAATAAAA 57.776 33.333 8.41 0.00 0.00 1.52
2325 2618 8.357290 TGCTATTAAGTAGTACCAGTCTTCAA 57.643 34.615 0.00 0.00 32.72 2.69
2414 2708 8.131100 CCAATGTGTTAGCTATCCTGTTATTTG 58.869 37.037 0.00 0.00 0.00 2.32
2448 2742 6.267471 AGAAAATTTAGGCCACAACAAGATGA 59.733 34.615 5.01 0.00 0.00 2.92
2456 2750 3.258123 GCTGGAGAAAATTTAGGCCACAA 59.742 43.478 5.01 0.00 0.00 3.33
2457 2751 2.825532 GCTGGAGAAAATTTAGGCCACA 59.174 45.455 5.01 0.00 0.00 4.17
2458 2752 3.092301 AGCTGGAGAAAATTTAGGCCAC 58.908 45.455 5.01 0.00 0.00 5.01
2459 2753 3.456380 AGCTGGAGAAAATTTAGGCCA 57.544 42.857 5.01 0.00 0.00 5.36
2532 2826 6.518369 CGGAGGGTGTATCATATATGTTGTGT 60.518 42.308 12.42 0.00 0.00 3.72
2533 2827 5.869344 CGGAGGGTGTATCATATATGTTGTG 59.131 44.000 12.42 0.00 0.00 3.33
2534 2828 5.542635 ACGGAGGGTGTATCATATATGTTGT 59.457 40.000 12.42 3.49 0.00 3.32
2535 2829 6.037786 ACGGAGGGTGTATCATATATGTTG 57.962 41.667 12.42 0.00 0.00 3.33
2536 2830 5.187186 GGACGGAGGGTGTATCATATATGTT 59.813 44.000 12.42 7.04 0.00 2.71
2538 2832 4.099573 GGGACGGAGGGTGTATCATATATG 59.900 50.000 6.36 6.36 0.00 1.78
2539 2833 4.264668 TGGGACGGAGGGTGTATCATATAT 60.265 45.833 0.00 0.00 0.00 0.86
2540 2834 3.076333 TGGGACGGAGGGTGTATCATATA 59.924 47.826 0.00 0.00 0.00 0.86
2541 2835 2.158219 TGGGACGGAGGGTGTATCATAT 60.158 50.000 0.00 0.00 0.00 1.78
2622 2916 7.972832 TTCCATATCAGTTGTCGTTTAAACT 57.027 32.000 16.01 0.00 37.09 2.66
2630 2924 4.025730 CGTTCCATTCCATATCAGTTGTCG 60.026 45.833 0.00 0.00 0.00 4.35
2632 2926 5.097742 TCGTTCCATTCCATATCAGTTGT 57.902 39.130 0.00 0.00 0.00 3.32
2636 2930 7.154656 TCATTACTCGTTCCATTCCATATCAG 58.845 38.462 0.00 0.00 0.00 2.90
2638 2932 7.962964 TTCATTACTCGTTCCATTCCATATC 57.037 36.000 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.