Multiple sequence alignment - TraesCS7B01G250500

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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 TraesCS7B01G250500 chr7B 100.000 4905 0 0 1 4905 462534638 462539542 0.000000e+00 9058.0
1 TraesCS7B01G250500 chr7B 100.000 2522 0 0 5255 7776 462539892 462542413 0.000000e+00 4658.0
2 TraesCS7B01G250500 chr7B 75.849 265 64 0 5621 5885 693606688 693606424 1.360000e-27 135.0
3 TraesCS7B01G250500 chr7B 85.000 60 9 0 1540 1599 718823359 718823300 2.340000e-05 62.1
4 TraesCS7B01G250500 chr7D 97.018 4192 92 9 1 4177 446211527 446207354 0.000000e+00 7018.0
5 TraesCS7B01G250500 chr7D 97.084 1646 28 3 5364 6990 446206047 446204403 0.000000e+00 2756.0
6 TraesCS7B01G250500 chr7D 95.764 897 29 5 6883 7776 446204474 446203584 0.000000e+00 1437.0
7 TraesCS7B01G250500 chr7D 96.982 762 20 2 4145 4905 446207354 446206595 0.000000e+00 1277.0
8 TraesCS7B01G250500 chr7D 100.000 36 0 0 6955 6990 446204510 446204475 5.040000e-07 67.6
9 TraesCS7B01G250500 chr7A 91.787 3458 219 28 127 3554 496778739 496775317 0.000000e+00 4752.0
10 TraesCS7B01G250500 chr7A 91.578 1223 80 9 5604 6806 496773841 496772622 0.000000e+00 1666.0
11 TraesCS7B01G250500 chr7A 94.193 861 23 4 6919 7776 496772517 496771681 0.000000e+00 1288.0
12 TraesCS7B01G250500 chr7A 91.951 733 45 5 3625 4350 496775317 496774592 0.000000e+00 1014.0
13 TraesCS7B01G250500 chr7A 93.103 174 12 0 4732 4905 496774564 496774391 1.000000e-63 255.0
14 TraesCS7B01G250500 chr7A 94.521 146 8 0 5458 5603 496774031 496773886 7.850000e-55 226.0
15 TraesCS7B01G250500 chr7A 100.000 36 0 0 6955 6990 496772517 496772482 5.040000e-07 67.6
16 TraesCS7B01G250500 chr7A 85.000 60 9 0 1540 1599 73768648 73768589 2.340000e-05 62.1
17 TraesCS7B01G250500 chr7A 97.143 35 1 0 889 923 287905495 287905461 8.430000e-05 60.2
18 TraesCS7B01G250500 chr2A 83.217 286 45 3 5604 5888 522380050 522379767 7.740000e-65 259.0
19 TraesCS7B01G250500 chr1D 96.622 148 0 4 1 147 254396356 254396213 2.800000e-59 241.0
20 TraesCS7B01G250500 chrUn 99.242 132 1 0 1 132 216516849 216516718 1.010000e-58 239.0
21 TraesCS7B01G250500 chrUn 99.242 132 1 0 1 132 346594740 346594609 1.010000e-58 239.0
22 TraesCS7B01G250500 chrUn 99.242 132 1 0 1 132 436278402 436278271 1.010000e-58 239.0
23 TraesCS7B01G250500 chrUn 91.111 45 4 0 1540 1584 65763664 65763708 2.340000e-05 62.1
24 TraesCS7B01G250500 chr6D 99.242 132 1 0 1 132 14944721 14944590 1.010000e-58 239.0
25 TraesCS7B01G250500 chr6D 100.000 129 0 0 1 129 168256680 168256808 1.010000e-58 239.0
26 TraesCS7B01G250500 chr5D 100.000 129 0 0 1 129 6190694 6190822 1.010000e-58 239.0
27 TraesCS7B01G250500 chr4D 100.000 129 0 0 1 129 19930328 19930456 1.010000e-58 239.0
28 TraesCS7B01G250500 chr3B 76.604 265 62 0 5621 5885 547328606 547328870 6.290000e-31 147.0
29 TraesCS7B01G250500 chr3B 75.735 272 66 0 5614 5885 381486272 381486001 3.780000e-28 137.0
30 TraesCS7B01G250500 chr3B 75.089 281 69 1 5605 5885 643846350 643846629 6.330000e-26 130.0
31 TraesCS7B01G250500 chr4B 75.735 272 66 0 5614 5885 338490548 338490277 3.780000e-28 137.0
32 TraesCS7B01G250500 chr4B 91.111 45 4 0 1540 1584 520274322 520274366 2.340000e-05 62.1
33 TraesCS7B01G250500 chr1A 74.733 281 71 0 5605 5885 82082256 82082536 8.190000e-25 126.0
34 TraesCS7B01G250500 chr1A 91.111 45 4 0 1540 1584 9151179 9151223 2.340000e-05 62.1
35 TraesCS7B01G250500 chr1A 91.111 45 4 0 1540 1584 50938665 50938709 2.340000e-05 62.1
36 TraesCS7B01G250500 chr6A 85.075 67 9 1 2177 2242 524804818 524804752 5.040000e-07 67.6
37 TraesCS7B01G250500 chr6A 85.000 60 9 0 1540 1599 598878926 598878867 2.340000e-05 62.1
38 TraesCS7B01G250500 chr3D 89.796 49 5 0 3792 3840 614285781 614285733 6.510000e-06 63.9


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 TraesCS7B01G250500 chr7B 462534638 462542413 7775 False 6858.000000 9058 100.000000 1 7776 2 chr7B.!!$F1 7775
1 TraesCS7B01G250500 chr7D 446203584 446211527 7943 True 2511.120000 7018 97.369600 1 7776 5 chr7D.!!$R1 7775
2 TraesCS7B01G250500 chr7A 496771681 496778739 7058 True 1324.085714 4752 93.876143 127 7776 7 chr7A.!!$R3 7649

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
720 722 1.108727 TGCCAGTCCAGCAAAACAGG 61.109 55.0 0.00 0.0 37.28 4.00 F
1359 1364 0.603707 CGCTGTCTTCCTCCTTGCAA 60.604 55.0 0.00 0.0 0.00 4.08 F
2025 2030 0.817654 TGAGGATGAAGATCGCGTGT 59.182 50.0 5.77 0.0 0.00 4.49 F
2396 2401 0.931005 CTATCGCCGCTTGTTCCTTC 59.069 55.0 0.00 0.0 0.00 3.46 F
3341 3370 0.036164 CTGGAACATCCGTGGGTTCA 59.964 55.0 10.98 0.0 43.96 3.18 F
3744 3775 0.248012 TTTGATTCGCTCCCGTGCTA 59.752 50.0 0.00 0.0 35.54 3.49 F
4359 4429 0.623324 TAGGGGTGGGATGAAGTGGG 60.623 60.0 0.00 0.0 0.00 4.61 F
5307 5378 0.033228 CCCCTATCGCTGCTTCTCTG 59.967 60.0 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1601 0.036732 GCACCCCACTGTCTTCATCA 59.963 55.000 0.00 0.00 0.00 3.07 R
3254 3283 0.036388 CCTCACCGTGCCAGTACAAT 60.036 55.000 0.00 0.00 0.00 2.71 R
3341 3370 1.066143 CGTCTTCCTACCAACATGGCT 60.066 52.381 0.00 0.00 42.67 4.75 R
4359 4429 1.094785 TTTGCATCGCCCTTAAGAGC 58.905 50.000 3.36 0.35 0.00 4.09 R
5275 5346 0.179018 ATAGGGGATTGCCTTGTCGC 60.179 55.000 0.00 0.00 0.00 5.19 R
5278 5349 0.179018 GCGATAGGGGATTGCCTTGT 60.179 55.000 0.00 0.00 38.86 3.16 R
5553 5735 0.461961 GGTGGAGATTGGGAGACTCG 59.538 60.000 0.00 0.00 0.00 4.18 R
7161 7471 1.153369 CATCAAGGTCGGCGTCCAT 60.153 57.895 24.24 10.64 0.00 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
39 40 9.860898 AAAGCACCTTTTCATTCTTTCATATAC 57.139 29.630 0.00 0.00 28.27 1.47
85 87 8.738645 AGACAATGTTCCATACTAAAGGATTC 57.261 34.615 0.00 0.00 33.10 2.52
185 187 6.243900 CAAAAGCATATCCCTAGACCATCAT 58.756 40.000 0.00 0.00 0.00 2.45
425 427 2.368548 TGCTAAGTGACAAGCTTCCAGA 59.631 45.455 10.59 0.00 39.53 3.86
442 444 1.952296 CAGATTCCAGTAGCCAATGCC 59.048 52.381 0.00 0.00 38.69 4.40
720 722 1.108727 TGCCAGTCCAGCAAAACAGG 61.109 55.000 0.00 0.00 37.28 4.00
819 821 1.758440 GACTGTCAGCCCACTGGTCA 61.758 60.000 2.24 0.00 44.59 4.02
1008 1013 1.599518 GGTGGTCGCCATGTGTTCA 60.600 57.895 1.90 0.00 35.28 3.18
1010 1015 1.147153 TGGTCGCCATGTGTTCACA 59.853 52.632 8.09 8.09 0.00 3.58
1208 1213 1.194781 AAGAAGGAGGAGCGAAGGCA 61.195 55.000 0.00 0.00 43.41 4.75
1230 1235 1.427592 GGACTCAAGATCTGCAGCGC 61.428 60.000 9.47 0.00 0.00 5.92
1255 1260 1.397672 TAAGCAGCACCAGTTTTGCA 58.602 45.000 0.00 0.00 42.83 4.08
1281 1286 0.748367 GGGTTGGAGATCCTTTCGCC 60.748 60.000 0.00 0.00 44.11 5.54
1355 1360 2.177594 CTGGCGCTGTCTTCCTCCTT 62.178 60.000 7.64 0.00 0.00 3.36
1359 1364 0.603707 CGCTGTCTTCCTCCTTGCAA 60.604 55.000 0.00 0.00 0.00 4.08
1439 1444 3.814268 CCGCATTGGGCACTTCCG 61.814 66.667 0.00 0.00 45.17 4.30
1448 1453 2.970324 GCACTTCCGGTCGCAACA 60.970 61.111 0.00 0.00 0.00 3.33
1505 1510 1.559219 TGGGCATGCTTCTGCTTACTA 59.441 47.619 18.92 0.00 41.95 1.82
1548 1553 2.530460 TGCTTCAAACTATGGGCCAT 57.470 45.000 24.69 24.69 0.00 4.40
1596 1601 3.594134 CTTGCAGTTCGAGGAAGAAGAT 58.406 45.455 0.00 0.00 36.66 2.40
1838 1843 6.009589 ACAACAATATCACAACAAGGATCCA 58.990 36.000 15.82 0.00 0.00 3.41
2025 2030 0.817654 TGAGGATGAAGATCGCGTGT 59.182 50.000 5.77 0.00 0.00 4.49
2117 2122 2.044650 GGAGCTCAAGCCCATGCA 60.045 61.111 17.19 0.00 43.38 3.96
2251 2256 1.228154 AAGTTGGGCGACAAGGGAC 60.228 57.895 0.00 0.00 40.38 4.46
2396 2401 0.931005 CTATCGCCGCTTGTTCCTTC 59.069 55.000 0.00 0.00 0.00 3.46
2871 2891 2.047655 CGTTCCAAGGCGGCTACA 60.048 61.111 13.71 0.00 33.14 2.74
2872 2892 1.669760 CGTTCCAAGGCGGCTACAA 60.670 57.895 13.71 2.10 33.14 2.41
3009 3038 8.320617 AGATATTCCATTCTAGATGCTTTCTCC 58.679 37.037 0.00 0.00 35.79 3.71
3024 3053 3.548745 TTCTCCGATGATCACATGCTT 57.451 42.857 0.00 0.00 36.82 3.91
3214 3243 2.042639 GCCCACTGCCCATGGAAT 60.043 61.111 15.22 0.00 39.87 3.01
3215 3244 1.686800 GCCCACTGCCCATGGAATT 60.687 57.895 15.22 0.00 39.87 2.17
3229 3258 1.218844 GGAATTAGGGGTGGTGGCTA 58.781 55.000 0.00 0.00 0.00 3.93
3233 3262 2.127685 TTAGGGGTGGTGGCTAGGGT 62.128 60.000 0.00 0.00 0.00 4.34
3253 3282 2.234908 GTTGCTGCTCTTTCCTCTCCTA 59.765 50.000 0.00 0.00 0.00 2.94
3254 3283 2.540383 TGCTGCTCTTTCCTCTCCTAA 58.460 47.619 0.00 0.00 0.00 2.69
3255 3284 3.110705 TGCTGCTCTTTCCTCTCCTAAT 58.889 45.455 0.00 0.00 0.00 1.73
3277 3306 4.624364 CTGGCACGGTGAGGCACA 62.624 66.667 13.29 1.43 36.56 4.57
3341 3370 0.036164 CTGGAACATCCGTGGGTTCA 59.964 55.000 10.98 0.00 43.96 3.18
3482 3511 3.139077 CCTCTAGAACGCTTTGTTTGGT 58.861 45.455 0.00 0.00 42.09 3.67
3518 3547 2.493278 GGCTGCTTCTTGGCTTTAATCA 59.507 45.455 0.00 0.00 0.00 2.57
3634 3665 2.270850 GTATGGGCCGGCAGACAA 59.729 61.111 30.85 4.36 0.00 3.18
3744 3775 0.248012 TTTGATTCGCTCCCGTGCTA 59.752 50.000 0.00 0.00 35.54 3.49
4359 4429 0.623324 TAGGGGTGGGATGAAGTGGG 60.623 60.000 0.00 0.00 0.00 4.61
4410 4480 3.275617 TTCATGCCTACGCTAATGGTT 57.724 42.857 0.00 0.00 35.36 3.67
4653 4724 1.078709 GCGCTCTGTGCAATGAAGTA 58.921 50.000 0.00 0.00 43.06 2.24
4665 4736 2.926200 CAATGAAGTAGGACACTGCTCG 59.074 50.000 0.00 0.00 38.84 5.03
4688 4759 0.967380 CCCTGATGGTTGGCCTGTTC 60.967 60.000 3.32 0.00 35.27 3.18
4729 4800 1.340795 CCTGCTCTGAAGGGCATCTTT 60.341 52.381 5.11 0.00 37.83 2.52
4730 4801 2.444421 CTGCTCTGAAGGGCATCTTTT 58.556 47.619 5.11 0.00 37.83 2.27
4757 4828 2.455032 TCCATTTTCAACGTGTTTGCG 58.545 42.857 0.00 0.00 34.88 4.85
4791 4862 0.825410 TATCCCGCGCCTCAACTTTA 59.175 50.000 0.00 0.00 0.00 1.85
5272 5343 1.377333 CTTCCGGAACAAGAGGGGC 60.377 63.158 14.35 0.00 0.00 5.80
5273 5344 1.842381 CTTCCGGAACAAGAGGGGCT 61.842 60.000 14.35 0.00 0.00 5.19
5274 5345 1.423794 TTCCGGAACAAGAGGGGCTT 61.424 55.000 14.35 0.00 37.29 4.35
5307 5378 0.033228 CCCCTATCGCTGCTTCTCTG 59.967 60.000 0.00 0.00 0.00 3.35
5333 5404 4.572985 TTTGTTGTGGATGCTCTTTCTG 57.427 40.909 0.00 0.00 0.00 3.02
5340 5411 3.944015 GTGGATGCTCTTTCTGCTATGTT 59.056 43.478 0.00 0.00 0.00 2.71
5341 5412 4.397417 GTGGATGCTCTTTCTGCTATGTTT 59.603 41.667 0.00 0.00 0.00 2.83
5342 5413 4.397103 TGGATGCTCTTTCTGCTATGTTTG 59.603 41.667 0.00 0.00 0.00 2.93
5343 5414 4.637534 GGATGCTCTTTCTGCTATGTTTGA 59.362 41.667 0.00 0.00 0.00 2.69
5344 5415 5.448360 GGATGCTCTTTCTGCTATGTTTGAC 60.448 44.000 0.00 0.00 0.00 3.18
5345 5416 4.388485 TGCTCTTTCTGCTATGTTTGACA 58.612 39.130 0.00 0.00 0.00 3.58
5346 5417 5.005740 TGCTCTTTCTGCTATGTTTGACAT 58.994 37.500 0.00 0.00 42.35 3.06
5358 5429 2.946564 GTTTGACATGGCCAAACTAGC 58.053 47.619 25.64 0.00 45.80 3.42
5359 5430 2.284754 TTGACATGGCCAAACTAGCA 57.715 45.000 10.96 0.00 0.00 3.49
5360 5431 2.284754 TGACATGGCCAAACTAGCAA 57.715 45.000 10.96 0.00 0.00 3.91
5361 5432 1.885887 TGACATGGCCAAACTAGCAAC 59.114 47.619 10.96 0.00 0.00 4.17
5362 5433 2.162681 GACATGGCCAAACTAGCAACT 58.837 47.619 10.96 0.00 0.00 3.16
5417 5577 1.070601 CCGGATCAGCATACCATCACA 59.929 52.381 0.00 0.00 0.00 3.58
5553 5735 4.225042 AGGCAATTTTCCCATTTCTTACCC 59.775 41.667 0.00 0.00 0.00 3.69
5555 5737 4.081917 GCAATTTTCCCATTTCTTACCCGA 60.082 41.667 0.00 0.00 0.00 5.14
5780 6006 6.133698 GCGTAAGTATCACATGGTCAAGTGA 61.134 44.000 10.74 10.74 44.09 3.41
5781 6007 7.394880 GCGTAAGTATCACATGGTCAAGTGAT 61.395 42.308 20.56 20.56 46.75 3.06
5901 6127 0.250858 AAATGCTTTGGGGCTTTGGC 60.251 50.000 0.00 0.00 37.82 4.52
5922 6148 3.192633 GCCGGATCTTCTTAAAGCCAAAA 59.807 43.478 5.05 0.00 32.18 2.44
6180 6406 0.966875 ATTGCCTTTCGCCATGAGCA 60.967 50.000 0.00 0.00 44.04 4.26
6382 6608 2.683362 GCCAGAATTCCCCTTAAAGTCG 59.317 50.000 0.65 0.00 0.00 4.18
6420 6646 3.711814 TTCCGCAATCGCCTCCCA 61.712 61.111 0.00 0.00 33.11 4.37
6588 6819 0.449388 CCTGCTTCTTGTGCCGATTC 59.551 55.000 0.00 0.00 0.00 2.52
6812 7058 0.804933 GGCTAAGCTCCGTTGTACCG 60.805 60.000 0.00 0.00 0.00 4.02
6891 7165 3.778075 TGGCCCTGTAAGCTGACTATTTA 59.222 43.478 0.00 0.00 0.00 1.40
6914 7188 6.976934 ATATCTGGTTGTGTGAACCTTTTT 57.023 33.333 5.25 0.00 40.88 1.94
6944 7254 6.597562 ACTATTTCTACCTGGTTGTGTGAAA 58.402 36.000 3.84 8.96 31.60 2.69
6953 7263 3.827625 TGGTTGTGTGAAACTTTTCGTG 58.172 40.909 0.00 0.00 40.01 4.35
6999 7309 3.183793 ACCTTTTCGTACCGTCTGTTT 57.816 42.857 0.00 0.00 0.00 2.83
7015 7325 4.093556 GTCTGTTTTATGTACTCTGCCTGC 59.906 45.833 0.00 0.00 0.00 4.85
7048 7358 6.900299 GCTTCGTTCTACATACTGTATTTTGC 59.100 38.462 0.00 0.00 31.66 3.68
7161 7471 5.399991 TGAAGTAGGTACCAGAGGAAGAAA 58.600 41.667 15.94 0.00 0.00 2.52
7275 7585 3.825160 GAGCCAGCCACGGAACACA 62.825 63.158 0.00 0.00 0.00 3.72
7530 7840 2.284331 TAGCTCAGGCACGGGGAA 60.284 61.111 0.00 0.00 41.70 3.97
7690 8000 0.898326 GTGGATTGGTGGGTTGGGAC 60.898 60.000 0.00 0.00 0.00 4.46
7691 8001 1.071314 TGGATTGGTGGGTTGGGACT 61.071 55.000 0.00 0.00 0.00 3.85
7692 8002 0.114364 GGATTGGTGGGTTGGGACTT 59.886 55.000 0.00 0.00 0.00 3.01
7693 8003 1.256812 GATTGGTGGGTTGGGACTTG 58.743 55.000 0.00 0.00 0.00 3.16
7696 8006 2.466186 GGTGGGTTGGGACTTGGGA 61.466 63.158 0.00 0.00 0.00 4.37
7697 8007 1.074951 GTGGGTTGGGACTTGGGAG 59.925 63.158 0.00 0.00 0.00 4.30
7698 8008 1.073319 TGGGTTGGGACTTGGGAGA 60.073 57.895 0.00 0.00 0.00 3.71
7699 8009 1.379146 GGGTTGGGACTTGGGAGAC 59.621 63.158 0.00 0.00 0.00 3.36
7700 8010 1.003718 GGTTGGGACTTGGGAGACG 60.004 63.158 0.00 0.00 0.00 4.18
7701 8011 1.003718 GTTGGGACTTGGGAGACGG 60.004 63.158 0.00 0.00 0.00 4.79
7702 8012 1.152204 TTGGGACTTGGGAGACGGA 60.152 57.895 0.00 0.00 0.00 4.69
7743 8053 0.179936 GGGCAGATGAGAACAGAGGG 59.820 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.548251 TGTCTTTTCCAAGTAAAAACCCCTAG 59.452 38.462 0.00 0.00 0.00 3.02
335 337 8.797266 AATTTGGATTTTTCGTTCTGTTCTAC 57.203 30.769 0.00 0.00 0.00 2.59
425 427 2.025863 GCTGGCATTGGCTACTGGAAT 61.026 52.381 11.84 0.00 40.87 3.01
442 444 1.475280 CACCACTGGGAAATGATGCTG 59.525 52.381 0.00 0.00 38.05 4.41
1010 1015 4.595538 TTGTGCGCCGGTCTTCGT 62.596 61.111 4.18 0.00 37.11 3.85
1026 1031 3.249189 TCCAGAGGCCGCTTGGTT 61.249 61.111 6.13 0.00 34.16 3.67
1208 1213 1.202510 GCTGCAGATCTTGAGTCCGAT 60.203 52.381 20.43 0.00 0.00 4.18
1214 1219 0.374063 CTTGCGCTGCAGATCTTGAG 59.626 55.000 20.43 2.88 40.61 3.02
1230 1235 2.119801 ACTGGTGCTGCTTATCCTTG 57.880 50.000 0.00 0.02 0.00 3.61
1255 1260 1.299976 GATCTCCAACCCGGTTGCT 59.700 57.895 22.97 8.38 41.62 3.91
1281 1286 3.244976 CGGCTTATGCTTTGGTTTCTTG 58.755 45.455 0.13 0.00 39.59 3.02
1439 1444 0.307760 CTTGAACTGGTGTTGCGACC 59.692 55.000 0.45 0.00 36.39 4.79
1448 1453 1.302033 CAGAGCGGCTTGAACTGGT 60.302 57.895 2.97 0.00 0.00 4.00
1596 1601 0.036732 GCACCCCACTGTCTTCATCA 59.963 55.000 0.00 0.00 0.00 3.07
1814 1819 6.009589 TGGATCCTTGTTGTGATATTGTTGT 58.990 36.000 14.23 0.00 0.00 3.32
1838 1843 0.396811 CTCCTCCCAAACCAACTCGT 59.603 55.000 0.00 0.00 0.00 4.18
2025 2030 2.517414 AGCTTGGCTGGAGCACAA 59.483 55.556 0.20 2.23 42.56 3.33
2117 2122 2.444256 GGCGGGCCTCCACTCTTAT 61.444 63.158 7.92 0.00 0.00 1.73
2251 2256 0.107703 TTAGAAGCACCGCCATCCTG 60.108 55.000 0.00 0.00 0.00 3.86
2547 2558 0.396811 GCAGGTTGACAGTGGTAGGT 59.603 55.000 0.00 0.00 0.00 3.08
2712 2732 2.524887 ACCGGACGGGGAGTTTCA 60.525 61.111 9.46 0.00 41.60 2.69
3009 3038 1.671979 ACCCAAGCATGTGATCATCG 58.328 50.000 0.00 0.00 31.15 3.84
3024 3053 2.636893 CCCACAATCATCCAAAAACCCA 59.363 45.455 0.00 0.00 0.00 4.51
3214 3243 1.307517 CCCTAGCCACCACCCCTAA 60.308 63.158 0.00 0.00 0.00 2.69
3215 3244 2.127685 AACCCTAGCCACCACCCCTA 62.128 60.000 0.00 0.00 0.00 3.53
3229 3258 0.037447 GAGGAAAGAGCAGCAACCCT 59.963 55.000 0.00 0.00 0.00 4.34
3233 3262 1.356124 AGGAGAGGAAAGAGCAGCAA 58.644 50.000 0.00 0.00 0.00 3.91
3253 3282 1.610624 CCTCACCGTGCCAGTACAATT 60.611 52.381 0.00 0.00 0.00 2.32
3254 3283 0.036388 CCTCACCGTGCCAGTACAAT 60.036 55.000 0.00 0.00 0.00 2.71
3255 3284 1.369692 CCTCACCGTGCCAGTACAA 59.630 57.895 0.00 0.00 0.00 2.41
3275 3304 8.716674 ATATGATTTCTAAGATTTGGCCATGT 57.283 30.769 6.09 0.00 0.00 3.21
3341 3370 1.066143 CGTCTTCCTACCAACATGGCT 60.066 52.381 0.00 0.00 42.67 4.75
3439 3468 4.223032 GGGTCACTGGAGAGAAAATAGTGA 59.777 45.833 0.00 0.00 43.74 3.41
3482 3511 4.648626 GCCCACCAGAGTGCAGCA 62.649 66.667 0.00 0.00 43.09 4.41
3518 3547 2.010145 AACTACGTCGCAGCAATCAT 57.990 45.000 0.00 0.00 0.00 2.45
3634 3665 8.403306 TTCTCCCAAGAAATCCACAGAATGGT 62.403 42.308 0.00 0.00 42.87 3.55
3744 3775 7.960738 CCAATAGATGTCGTCGTTATTTTTGTT 59.039 33.333 0.00 0.00 0.00 2.83
3998 4036 4.943705 TCAAAGAAGAATCTAGCCGCAAAT 59.056 37.500 0.00 0.00 33.77 2.32
4147 4185 4.047059 CCCAGCCTTGCAGCAACG 62.047 66.667 2.83 1.22 34.23 4.10
4290 4360 7.254286 GCGAACAATGGACAACACTAAATTTTT 60.254 33.333 0.00 0.00 0.00 1.94
4359 4429 1.094785 TTTGCATCGCCCTTAAGAGC 58.905 50.000 3.36 0.35 0.00 4.09
4688 4759 2.893637 CCAGAACCTACAGAACATCGG 58.106 52.381 0.00 0.00 0.00 4.18
4750 4821 2.035704 TCTACGGTTCCTAACGCAAACA 59.964 45.455 0.00 0.00 0.00 2.83
4757 4828 3.366781 GCGGGATATCTACGGTTCCTAAC 60.367 52.174 17.57 0.00 0.00 2.34
4791 4862 2.632996 TCGGGATTGGCGAGAGAATAAT 59.367 45.455 0.00 0.00 0.00 1.28
5254 5325 1.377333 GCCCCTCTTGTTCCGGAAG 60.377 63.158 19.50 6.16 0.00 3.46
5255 5326 1.423794 AAGCCCCTCTTGTTCCGGAA 61.424 55.000 14.35 14.35 32.79 4.30
5256 5327 1.846124 AAGCCCCTCTTGTTCCGGA 60.846 57.895 0.00 0.00 32.79 5.14
5257 5328 1.675641 CAAGCCCCTCTTGTTCCGG 60.676 63.158 0.00 0.00 45.48 5.14
5258 5329 3.987404 CAAGCCCCTCTTGTTCCG 58.013 61.111 0.00 0.00 45.48 4.30
5264 5335 1.302832 CTTGTCGCAAGCCCCTCTT 60.303 57.895 6.65 0.00 34.78 2.85
5265 5336 2.348998 CTTGTCGCAAGCCCCTCT 59.651 61.111 6.65 0.00 37.18 3.69
5266 5337 2.747855 CCTTGTCGCAAGCCCCTC 60.748 66.667 12.35 0.00 37.18 4.30
5269 5340 3.294493 TTGCCTTGTCGCAAGCCC 61.294 61.111 12.35 7.43 43.65 5.19
5274 5345 1.558167 TAGGGGATTGCCTTGTCGCA 61.558 55.000 0.00 0.00 36.85 5.10
5275 5346 0.179018 ATAGGGGATTGCCTTGTCGC 60.179 55.000 0.00 0.00 0.00 5.19
5276 5347 1.873903 CGATAGGGGATTGCCTTGTCG 60.874 57.143 10.53 10.53 0.00 4.35
5277 5348 1.884235 CGATAGGGGATTGCCTTGTC 58.116 55.000 0.00 0.00 0.00 3.18
5278 5349 0.179018 GCGATAGGGGATTGCCTTGT 60.179 55.000 0.00 0.00 38.86 3.16
5285 5356 1.346068 GAGAAGCAGCGATAGGGGATT 59.654 52.381 0.00 0.00 0.00 3.01
5307 5378 5.438761 AAGAGCATCCACAACAAAACTAC 57.561 39.130 0.00 0.00 33.66 2.73
5333 5404 3.591196 TTTGGCCATGTCAAACATAGC 57.409 42.857 6.09 2.44 41.46 2.97
5340 5411 2.284754 TGCTAGTTTGGCCATGTCAA 57.715 45.000 6.09 0.00 0.00 3.18
5341 5412 1.885887 GTTGCTAGTTTGGCCATGTCA 59.114 47.619 6.09 0.00 0.00 3.58
5342 5413 2.095059 CAGTTGCTAGTTTGGCCATGTC 60.095 50.000 6.09 0.00 0.00 3.06
5343 5414 1.888512 CAGTTGCTAGTTTGGCCATGT 59.111 47.619 6.09 0.00 0.00 3.21
5344 5415 1.403249 GCAGTTGCTAGTTTGGCCATG 60.403 52.381 6.09 0.00 38.21 3.66
5345 5416 0.890683 GCAGTTGCTAGTTTGGCCAT 59.109 50.000 6.09 0.00 38.21 4.40
5346 5417 0.467106 TGCAGTTGCTAGTTTGGCCA 60.467 50.000 0.00 0.00 42.66 5.36
5417 5577 2.301346 AGCAGCAGCAACTTAACAGTT 58.699 42.857 3.17 0.00 44.72 3.16
5553 5735 0.461961 GGTGGAGATTGGGAGACTCG 59.538 60.000 0.00 0.00 0.00 4.18
5555 5737 2.044793 TTGGTGGAGATTGGGAGACT 57.955 50.000 0.00 0.00 0.00 3.24
5901 6127 5.385509 TTTTTGGCTTTAAGAAGATCCGG 57.614 39.130 0.00 0.00 34.71 5.14
5922 6148 7.496747 TCGAAAAAGAATCTGTTGGGAATTTT 58.503 30.769 0.00 0.00 0.00 1.82
5924 6150 6.265422 ACTCGAAAAAGAATCTGTTGGGAATT 59.735 34.615 0.00 0.00 0.00 2.17
5925 6151 5.770162 ACTCGAAAAAGAATCTGTTGGGAAT 59.230 36.000 0.00 0.00 0.00 3.01
5985 6211 1.337118 CCCAAGGCAAAAGCCACTTA 58.663 50.000 9.42 0.00 0.00 2.24
6180 6406 3.461773 CACGCTCGATGGGGGAGT 61.462 66.667 0.00 0.00 33.34 3.85
6382 6608 6.512415 CGGAACATTTGCCATAAGAAGATCTC 60.512 42.308 0.00 0.00 0.00 2.75
6420 6646 1.906333 GGCAATGTTGACCGGGGTT 60.906 57.895 6.32 0.00 0.00 4.11
6588 6819 5.006649 TGCACATAAGATAAGCAAGTAAGCG 59.993 40.000 0.00 0.00 40.15 4.68
6790 7036 2.629051 GTACAACGGAGCTTAGCCATT 58.371 47.619 0.00 0.00 0.00 3.16
6891 7165 6.323739 ACAAAAAGGTTCACACAACCAGATAT 59.676 34.615 6.30 0.00 42.69 1.63
6914 7188 7.038587 ACACAACCAGGTAGAAATAGTCATACA 60.039 37.037 0.00 0.00 0.00 2.29
6944 7254 7.545965 CCAGATAGAAATAGTCACACGAAAAGT 59.454 37.037 0.00 0.00 0.00 2.66
6953 7263 7.097192 TCACACAACCAGATAGAAATAGTCAC 58.903 38.462 0.00 0.00 0.00 3.67
6999 7309 2.567169 ACACAGCAGGCAGAGTACATAA 59.433 45.455 0.00 0.00 0.00 1.90
7015 7325 1.270094 TGTAGAACGAAGCCCACACAG 60.270 52.381 0.00 0.00 0.00 3.66
7048 7358 8.875803 CATTTAAGACACATTGGGATTGATTTG 58.124 33.333 0.00 0.00 0.00 2.32
7117 7427 2.190578 CCACTTCCCCTCGCCATC 59.809 66.667 0.00 0.00 0.00 3.51
7161 7471 1.153369 CATCAAGGTCGGCGTCCAT 60.153 57.895 24.24 10.64 0.00 3.41
7326 7636 1.897802 GACTACAACGAGGGGAAGGAA 59.102 52.381 0.00 0.00 0.00 3.36
7461 7771 4.451150 TTCGCGCCGATGGAGCTT 62.451 61.111 0.00 0.00 46.11 3.74
7690 8000 2.060980 CCTCCCTCCGTCTCCCAAG 61.061 68.421 0.00 0.00 0.00 3.61
7691 8001 2.038975 CCTCCCTCCGTCTCCCAA 59.961 66.667 0.00 0.00 0.00 4.12
7692 8002 4.075793 CCCTCCCTCCGTCTCCCA 62.076 72.222 0.00 0.00 0.00 4.37
7693 8003 3.742248 CTCCCTCCCTCCGTCTCCC 62.742 73.684 0.00 0.00 0.00 4.30
7696 8006 3.756783 CCCTCCCTCCCTCCGTCT 61.757 72.222 0.00 0.00 0.00 4.18
7697 8007 4.862823 CCCCTCCCTCCCTCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
7699 8009 4.548513 CTCCCCTCCCTCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
7700 8010 4.179599 CCTCCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
7701 8011 4.179599 CCCTCCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
7743 8053 0.729690 GAACATCTCGCAAGCTTCCC 59.270 55.000 0.00 0.00 37.18 3.97


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

AutoCloner maintained by Alex Coulton.