Multiple sequence alignment - TraesCS6B01G100300

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 TraesCS6B01G100300 chr6B 100.000 4952 0 0 1 4952 78452112 78457063 0.000000e+00 9145
1 TraesCS6B01G100300 chr6B 93.234 2276 121 19 2430 4693 79717635 79715381 0.000000e+00 3319
2 TraesCS6B01G100300 chr6B 93.532 1979 113 8 463 2435 79720540 79718571 0.000000e+00 2931
3 TraesCS6B01G100300 chr6B 86.791 1499 136 36 1947 3431 59872734 59874184 0.000000e+00 1615
4 TraesCS6B01G100300 chr6B 84.026 1371 166 32 512 1868 59870796 59872127 0.000000e+00 1269
5 TraesCS6B01G100300 chr6B 88.222 433 31 7 10 429 79721706 79721281 2.660000e-137 499
6 TraesCS6B01G100300 chr6B 80.702 171 24 6 4714 4883 59931424 59931586 1.870000e-24 124
7 TraesCS6B01G100300 chr6A 96.931 3878 108 8 463 4336 45652304 45656174 0.000000e+00 6492
8 TraesCS6B01G100300 chr6A 88.725 2031 176 23 2070 4091 33020586 33022572 0.000000e+00 2433
9 TraesCS6B01G100300 chr6A 90.636 1634 117 15 2892 4518 46489691 46488087 0.000000e+00 2137
10 TraesCS6B01G100300 chr6A 86.828 1154 137 8 792 1941 33019358 33020500 0.000000e+00 1275
11 TraesCS6B01G100300 chr6A 82.343 1195 196 5 2774 3953 13807758 13806564 0.000000e+00 1024
12 TraesCS6B01G100300 chr6A 82.688 439 55 14 1 429 45651192 45651619 2.180000e-98 370
13 TraesCS6B01G100300 chr6A 89.691 291 23 3 4406 4693 45656175 45656461 1.010000e-96 364
14 TraesCS6B01G100300 chr6A 87.097 248 23 2 4714 4952 46301383 46301136 6.320000e-69 272
15 TraesCS6B01G100300 chr6A 82.584 178 22 6 4718 4894 33024399 33024568 1.110000e-31 148
16 TraesCS6B01G100300 chrUn 92.514 2124 113 20 2596 4693 27716266 27718369 0.000000e+00 3000
17 TraesCS6B01G100300 chrUn 92.699 1849 117 11 773 2610 27714335 27716176 0.000000e+00 2651
18 TraesCS6B01G100300 chrUn 89.504 343 27 6 91 429 27710441 27710778 4.580000e-115 425
19 TraesCS6B01G100300 chrUn 85.597 243 19 10 463 695 27713932 27714168 1.780000e-59 241
20 TraesCS6B01G100300 chr6D 85.038 2787 316 67 792 3538 29376892 29374167 0.000000e+00 2743
21 TraesCS6B01G100300 chr6D 83.540 565 60 12 3527 4091 29371007 29370476 9.570000e-137 497
22 TraesCS6B01G100300 chr2B 88.722 133 13 1 2 134 794591413 794591283 1.430000e-35 161
23 TraesCS6B01G100300 chr5D 72.591 467 109 19 3098 3556 362886461 362886006 8.650000e-28 135


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 TraesCS6B01G100300 chr6B 78452112 78457063 4951 False 9145.000000 9145 100.000000 1 4952 1 chr6B.!!$F2 4951
1 TraesCS6B01G100300 chr6B 79715381 79721706 6325 True 2249.666667 3319 91.662667 10 4693 3 chr6B.!!$R1 4683
2 TraesCS6B01G100300 chr6B 59870796 59874184 3388 False 1442.000000 1615 85.408500 512 3431 2 chr6B.!!$F3 2919
3 TraesCS6B01G100300 chr6A 45651192 45656461 5269 False 2408.666667 6492 89.770000 1 4693 3 chr6A.!!$F2 4692
4 TraesCS6B01G100300 chr6A 46488087 46489691 1604 True 2137.000000 2137 90.636000 2892 4518 1 chr6A.!!$R3 1626
5 TraesCS6B01G100300 chr6A 33019358 33024568 5210 False 1285.333333 2433 86.045667 792 4894 3 chr6A.!!$F1 4102
6 TraesCS6B01G100300 chr6A 13806564 13807758 1194 True 1024.000000 1024 82.343000 2774 3953 1 chr6A.!!$R1 1179
7 TraesCS6B01G100300 chrUn 27710441 27718369 7928 False 1579.250000 3000 90.078500 91 4693 4 chrUn.!!$F1 4602
8 TraesCS6B01G100300 chr6D 29370476 29376892 6416 True 1620.000000 2743 84.289000 792 4091 2 chr6D.!!$R1 3299

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
390 419 0.104934 AATCCTCCTCCGCCATACCT 60.105 55.000 0.00 0.0 0.00 3.08 F
391 420 0.543174 ATCCTCCTCCGCCATACCTC 60.543 60.000 0.00 0.0 0.00 3.85 F
1086 4356 1.586028 CCCCGGATGCAAAACACAG 59.414 57.895 0.73 0.0 0.00 3.66 F
2297 6172 0.661187 GTCTGCAACATGCCACAACG 60.661 55.000 0.00 0.0 44.23 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 5768 1.347707 TCAAAATCGGGACAGACAGCT 59.652 47.619 0.00 0.0 0.00 4.24 R
2252 6127 5.991606 TCGGGCATATACTTGAATTCTTCTG 59.008 40.000 7.05 0.0 0.00 3.02 R
2846 7807 3.988379 TGACATTCGCAAGCTTTCTTT 57.012 38.095 0.00 0.0 37.18 2.52 R
4191 12349 0.762418 TTTCACACCCAGTCGTCCAT 59.238 50.000 0.00 0.0 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
54 55 2.725008 CCCGGCGAGCAAAACAAA 59.275 55.556 9.30 0.00 0.00 2.83
83 88 0.955919 GGAGTTTGGCCAAGTCTCCG 60.956 60.000 34.76 0.00 35.40 4.63
95 100 2.171341 AGTCTCCGTTCTGAAAAGGC 57.829 50.000 7.95 1.45 34.37 4.35
101 106 2.076863 CCGTTCTGAAAAGGCCAGTAG 58.923 52.381 5.01 0.00 33.57 2.57
114 119 1.102978 CCAGTAGAAAAATGGCCCGG 58.897 55.000 0.00 0.00 0.00 5.73
115 120 1.615919 CCAGTAGAAAAATGGCCCGGT 60.616 52.381 0.00 0.00 0.00 5.28
123 128 0.973632 AAATGGCCCGGTTCCTTTTC 59.026 50.000 14.30 0.00 0.00 2.29
135 140 3.901222 GGTTCCTTTTCCTTTGGATGGAA 59.099 43.478 10.13 10.13 41.33 3.53
139 144 2.621556 TTTCCTTTGGATGGAAGGGG 57.378 50.000 3.30 0.00 43.48 4.79
238 243 3.793144 CGCTCCGCTTCAGTTGGC 61.793 66.667 0.00 0.00 0.00 4.52
241 246 2.032528 TCCGCTTCAGTTGGCCAG 59.967 61.111 5.11 0.00 0.00 4.85
284 297 4.096681 CCTCCATATCCCAGCTACATACA 58.903 47.826 0.00 0.00 0.00 2.29
382 411 3.056749 CCCGACTAATAAATCCTCCTCCG 60.057 52.174 0.00 0.00 0.00 4.63
388 417 3.983044 ATAAATCCTCCTCCGCCATAC 57.017 47.619 0.00 0.00 0.00 2.39
390 419 0.104934 AATCCTCCTCCGCCATACCT 60.105 55.000 0.00 0.00 0.00 3.08
391 420 0.543174 ATCCTCCTCCGCCATACCTC 60.543 60.000 0.00 0.00 0.00 3.85
392 421 2.210711 CCTCCTCCGCCATACCTCC 61.211 68.421 0.00 0.00 0.00 4.30
405 434 3.289836 CATACCTCCATTGTCAATGCCA 58.710 45.455 18.52 7.48 37.57 4.92
433 3556 5.911752 ACAATTGAGCACACTCTAGGATAG 58.088 41.667 13.59 0.00 43.85 2.08
446 3569 2.559381 AGGATAGGCCACACTCTTCT 57.441 50.000 5.01 0.00 40.02 2.85
563 3722 6.827586 ACAACCAAAAACTTACAACTCAGA 57.172 33.333 0.00 0.00 0.00 3.27
638 3808 5.975693 ATCCAAAGGCGAGAAACAATTTA 57.024 34.783 0.00 0.00 0.00 1.40
805 4067 7.999679 AGCAGCTTGATATTTACAAAGCATTA 58.000 30.769 8.75 0.00 0.00 1.90
1086 4356 1.586028 CCCCGGATGCAAAACACAG 59.414 57.895 0.73 0.00 0.00 3.66
1243 4513 1.871418 TCTAAGCATCTCAGTGCCCT 58.129 50.000 0.00 0.00 46.19 5.19
1495 4765 2.610374 GCACTGACAAACGGTTCTTGTA 59.390 45.455 0.00 0.00 37.14 2.41
1674 4944 6.485648 ACTTCATAACCACTACAAGGTTCAAC 59.514 38.462 0.18 0.00 45.98 3.18
1941 5711 5.580691 TGTGCAATCGTTTTATGAGGAGTAG 59.419 40.000 0.00 0.00 0.00 2.57
1957 5760 8.530804 TGAGGAGTAGTAGTTAAGGGAAATAC 57.469 38.462 0.00 0.00 38.59 1.89
2252 6127 3.128068 TGCTGCAGATGTCAATGAATGTC 59.872 43.478 20.43 0.00 0.00 3.06
2297 6172 0.661187 GTCTGCAACATGCCACAACG 60.661 55.000 0.00 0.00 44.23 4.10
2342 6217 4.431416 TGTTCTCCAGGCAGAAAGTTTA 57.569 40.909 3.64 0.00 34.11 2.01
2452 7304 3.343941 ACAATGGCCAACAGTACGTAT 57.656 42.857 10.96 0.00 0.00 3.06
2846 7807 8.710835 TTCTGCATACGTGTAATATTTGAGAA 57.289 30.769 0.00 0.00 0.00 2.87
2921 7882 9.798994 GATGCTATTGTTTGAGAAGATGAAATT 57.201 29.630 0.00 0.00 0.00 1.82
3256 8223 3.745975 TCTTATTCACGGCAAGAACAGTG 59.254 43.478 0.00 0.00 36.06 3.66
3297 8264 5.802956 CAGTTCTCTTCTAAGGATCGTCAAC 59.197 44.000 0.00 0.00 0.00 3.18
3411 8378 4.666512 AGAATTACATGGCAAAGGTGTCT 58.333 39.130 0.00 0.00 0.00 3.41
3597 11735 2.421619 GAGGAGCCACTGAAACTTGAG 58.578 52.381 0.00 0.00 0.00 3.02
3928 12084 5.857471 TGAAAGAATGCCCATAAATCCAG 57.143 39.130 0.00 0.00 0.00 3.86
4124 12280 3.426615 TGGTACAAAATGGGGACACATC 58.573 45.455 0.00 0.00 38.76 3.06
4161 12317 3.812609 TGAACTTGTGCGAGCTTTCATAA 59.187 39.130 0.00 0.00 0.00 1.90
4191 12349 7.822161 TCCAAAATCACTCAAAGAAGATCAA 57.178 32.000 0.00 0.00 0.00 2.57
4218 12376 3.253188 CGACTGGGTGTGAAAATGTGATT 59.747 43.478 0.00 0.00 0.00 2.57
4246 12404 9.243105 AGTTTGGTATTGAAACTGTGCTATTAT 57.757 29.630 0.00 0.00 41.16 1.28
4282 12440 6.620877 ACTTTTCCTTTTTCAGGGAAGTTT 57.379 33.333 0.00 0.00 41.78 2.66
4299 12457 6.161381 GGAAGTTTACTGATTTACTCGGTCA 58.839 40.000 0.00 0.00 42.69 4.02
4403 12561 2.264005 TGCCGCCGTTATATTCCATT 57.736 45.000 0.00 0.00 0.00 3.16
4404 12562 2.577700 TGCCGCCGTTATATTCCATTT 58.422 42.857 0.00 0.00 0.00 2.32
4468 13390 4.345859 TTTCGCCGTTATATTCCAGGAT 57.654 40.909 0.00 0.00 0.00 3.24
4476 13398 6.258727 GCCGTTATATTCCAGGATATGATGTG 59.741 42.308 0.00 0.00 0.00 3.21
4491 13416 7.016268 GGATATGATGTGTTCTAGGTCCCTAAA 59.984 40.741 0.00 0.00 0.00 1.85
4593 13537 3.926058 AAGTCTAACACACACACCCTT 57.074 42.857 0.00 0.00 0.00 3.95
4603 13547 1.476085 CACACACCCTTGCTTGTTTGA 59.524 47.619 0.00 0.00 0.00 2.69
4619 13577 0.902984 TTGACGAGGCAGGGAGCTTA 60.903 55.000 0.00 0.00 44.79 3.09
4669 13627 1.405526 CGGCCGGGGATATATCTTGTG 60.406 57.143 20.10 1.49 0.00 3.33
4684 13642 3.732212 TCTTGTGATAAGGATGATGCCG 58.268 45.455 0.00 0.00 0.00 5.69
4690 13648 1.496060 TAAGGATGATGCCGTGTCCT 58.504 50.000 0.00 0.00 42.73 3.85
4691 13649 0.107508 AAGGATGATGCCGTGTCCTG 60.108 55.000 0.00 0.00 40.10 3.86
4694 13668 1.344438 GGATGATGCCGTGTCCTGATA 59.656 52.381 0.00 0.00 0.00 2.15
4698 13672 3.496331 TGATGCCGTGTCCTGATAGATA 58.504 45.455 0.00 0.00 0.00 1.98
4720 13694 9.829507 AGATATCCTGATGAACAAAAGAAGTAG 57.170 33.333 0.00 0.00 0.00 2.57
4723 14376 7.730364 TCCTGATGAACAAAAGAAGTAGAAC 57.270 36.000 0.00 0.00 0.00 3.01
4735 14388 9.878599 CAAAAGAAGTAGAACGATGTAACAAAT 57.121 29.630 0.00 0.00 0.00 2.32
4746 14399 8.502161 AACGATGTAACAAATTAAAGTTGAGC 57.498 30.769 8.74 0.00 0.00 4.26
4799 14452 2.311841 ACGGAATTGGAAGAAGGGGAAT 59.688 45.455 0.00 0.00 0.00 3.01
4801 14454 3.624707 CGGAATTGGAAGAAGGGGAATGA 60.625 47.826 0.00 0.00 0.00 2.57
4802 14455 4.550669 GGAATTGGAAGAAGGGGAATGAT 58.449 43.478 0.00 0.00 0.00 2.45
4804 14457 5.772169 GGAATTGGAAGAAGGGGAATGATAG 59.228 44.000 0.00 0.00 0.00 2.08
4805 14458 6.410853 GGAATTGGAAGAAGGGGAATGATAGA 60.411 42.308 0.00 0.00 0.00 1.98
4806 14459 5.373812 TTGGAAGAAGGGGAATGATAGAC 57.626 43.478 0.00 0.00 0.00 2.59
4807 14460 3.716872 TGGAAGAAGGGGAATGATAGACC 59.283 47.826 0.00 0.00 0.00 3.85
4809 14462 2.330216 AGAAGGGGAATGATAGACCGG 58.670 52.381 0.00 0.00 0.00 5.28
4810 14463 2.090719 AGAAGGGGAATGATAGACCGGA 60.091 50.000 9.46 0.00 0.00 5.14
4811 14464 2.723530 AGGGGAATGATAGACCGGAT 57.276 50.000 9.46 0.00 0.00 4.18
4812 14465 2.260822 AGGGGAATGATAGACCGGATG 58.739 52.381 9.46 0.00 0.00 3.51
4813 14466 2.158158 AGGGGAATGATAGACCGGATGA 60.158 50.000 9.46 0.00 0.00 2.92
4814 14467 2.028020 GGGGAATGATAGACCGGATGAC 60.028 54.545 9.46 0.00 0.00 3.06
4815 14468 2.352814 GGGAATGATAGACCGGATGACG 60.353 54.545 9.46 0.00 43.80 4.35
4816 14469 2.296471 GGAATGATAGACCGGATGACGT 59.704 50.000 9.46 0.00 42.24 4.34
4817 14470 3.566523 GAATGATAGACCGGATGACGTC 58.433 50.000 9.46 9.11 42.24 4.34
4818 14471 0.942252 TGATAGACCGGATGACGTCG 59.058 55.000 9.46 0.00 42.24 5.12
4853 14506 4.760220 GGGCAGGGAGGGAAGGGA 62.760 72.222 0.00 0.00 0.00 4.20
4855 14508 2.285743 GCAGGGAGGGAAGGGAGT 60.286 66.667 0.00 0.00 0.00 3.85
4864 14517 2.754658 GAAGGGAGTCCGCCGAGA 60.755 66.667 2.26 0.00 38.33 4.04
4904 14557 4.181010 CTCCGGCCCACCCATCTG 62.181 72.222 0.00 0.00 0.00 2.90
4917 14570 4.827087 ATCTGCGTGCGCCTGGAG 62.827 66.667 14.16 8.19 41.09 3.86
4920 14573 4.617520 TGCGTGCGCCTGGAGAAA 62.618 61.111 14.16 0.00 41.09 2.52
4921 14574 3.793144 GCGTGCGCCTGGAGAAAG 61.793 66.667 4.18 0.00 34.56 2.62
4922 14575 3.121030 CGTGCGCCTGGAGAAAGG 61.121 66.667 4.18 0.00 40.63 3.11
4928 14581 4.547859 CCTGGAGAAAGGCATCGG 57.452 61.111 0.00 0.00 0.00 4.18
4929 14582 1.821332 CCTGGAGAAAGGCATCGGC 60.821 63.158 0.00 0.00 40.13 5.54
4930 14583 2.125147 TGGAGAAAGGCATCGGCG 60.125 61.111 0.00 0.00 42.47 6.46
4931 14584 2.125106 GGAGAAAGGCATCGGCGT 60.125 61.111 6.85 0.00 42.47 5.68
4933 14586 1.425428 GAGAAAGGCATCGGCGTTG 59.575 57.895 13.36 13.36 46.56 4.10
4934 14587 1.298859 GAGAAAGGCATCGGCGTTGT 61.299 55.000 18.14 0.00 46.56 3.32
4935 14588 0.036765 AGAAAGGCATCGGCGTTGTA 60.037 50.000 18.14 0.00 46.56 2.41
4936 14589 0.373716 GAAAGGCATCGGCGTTGTAG 59.626 55.000 18.14 1.72 46.56 2.74
4937 14590 1.024579 AAAGGCATCGGCGTTGTAGG 61.025 55.000 18.14 0.00 46.56 3.18
4938 14591 3.573491 GGCATCGGCGTTGTAGGC 61.573 66.667 18.14 7.10 42.47 3.93
4939 14592 2.817834 GCATCGGCGTTGTAGGCA 60.818 61.111 18.14 0.00 36.37 4.75
4940 14593 2.813179 GCATCGGCGTTGTAGGCAG 61.813 63.158 18.14 0.00 36.37 4.85
4941 14594 2.173669 CATCGGCGTTGTAGGCAGG 61.174 63.158 6.85 0.00 36.37 4.85
4942 14595 4.752879 TCGGCGTTGTAGGCAGGC 62.753 66.667 6.85 0.00 36.37 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.896122 TCCATTCGCTAGTTTGTTTTGC 58.104 40.909 0.00 0.00 0.00 3.68
54 55 1.679032 GGCCAAACTCCATTCGCTAGT 60.679 52.381 0.00 0.00 0.00 2.57
83 88 5.767816 TTTTCTACTGGCCTTTTCAGAAC 57.232 39.130 3.32 0.00 36.22 3.01
95 100 1.102978 CCGGGCCATTTTTCTACTGG 58.897 55.000 4.39 0.00 0.00 4.00
101 106 0.973632 AAGGAACCGGGCCATTTTTC 59.026 50.000 16.76 4.45 0.00 2.29
113 118 3.506398 TCCATCCAAAGGAAAAGGAACC 58.494 45.455 3.65 0.00 34.34 3.62
114 119 4.021104 CCTTCCATCCAAAGGAAAAGGAAC 60.021 45.833 14.97 0.00 45.15 3.62
115 120 4.159557 CCTTCCATCCAAAGGAAAAGGAA 58.840 43.478 14.97 14.30 45.15 3.36
123 128 2.621556 TTTCCCCTTCCATCCAAAGG 57.378 50.000 0.00 0.00 42.52 3.11
135 140 2.289257 CGTCCGTAACTCTTTTTCCCCT 60.289 50.000 0.00 0.00 0.00 4.79
139 144 2.477754 CACCCGTCCGTAACTCTTTTTC 59.522 50.000 0.00 0.00 0.00 2.29
241 246 1.810030 GGCACGACGATCCAGTTCC 60.810 63.158 0.00 0.00 0.00 3.62
257 262 1.846712 GCTGGGATATGGAGGGAGGC 61.847 65.000 0.00 0.00 0.00 4.70
284 297 8.217131 AGTAATTTCGAACAAAAAGTACCTGT 57.783 30.769 0.00 0.00 37.70 4.00
365 391 4.559862 ATGGCGGAGGAGGATTTATTAG 57.440 45.455 0.00 0.00 0.00 1.73
366 392 4.224370 GGTATGGCGGAGGAGGATTTATTA 59.776 45.833 0.00 0.00 0.00 0.98
367 393 3.009143 GGTATGGCGGAGGAGGATTTATT 59.991 47.826 0.00 0.00 0.00 1.40
368 394 2.572104 GGTATGGCGGAGGAGGATTTAT 59.428 50.000 0.00 0.00 0.00 1.40
369 395 1.975680 GGTATGGCGGAGGAGGATTTA 59.024 52.381 0.00 0.00 0.00 1.40
382 411 2.035066 GCATTGACAATGGAGGTATGGC 59.965 50.000 25.64 7.74 39.31 4.40
388 417 2.449464 TCTTGGCATTGACAATGGAGG 58.551 47.619 25.64 4.79 39.31 4.30
390 419 3.640498 TGTTTCTTGGCATTGACAATGGA 59.360 39.130 25.64 13.73 39.31 3.41
391 420 3.992643 TGTTTCTTGGCATTGACAATGG 58.007 40.909 25.64 11.85 39.31 3.16
392 421 6.203145 TCAATTGTTTCTTGGCATTGACAATG 59.797 34.615 21.56 21.56 37.66 2.82
405 434 5.471456 CCTAGAGTGTGCTCAATTGTTTCTT 59.529 40.000 5.13 0.00 44.00 2.52
433 3556 2.191128 ACATTGAGAAGAGTGTGGCC 57.809 50.000 0.00 0.00 0.00 5.36
446 3569 3.582647 TCCAGGCTGAGAACTAACATTGA 59.417 43.478 17.94 0.00 0.00 2.57
563 3722 5.219633 GTGCAAATATGAAGACCGTGTTTT 58.780 37.500 0.00 0.00 0.00 2.43
597 3766 3.426695 GGATTTCTGGCACTGAATTCACG 60.427 47.826 3.38 3.82 45.27 4.35
638 3808 7.173735 TGCATGTCTAGATTCGAATTATGCAAT 59.826 33.333 24.64 11.88 43.47 3.56
805 4067 9.895138 ATTTTAGCATGGCTGAAGAATTTTAAT 57.105 25.926 0.07 0.00 40.10 1.40
979 4249 5.049405 CCATGTTACTTGTCTGAAACTGGAC 60.049 44.000 0.00 0.00 0.00 4.02
1042 4312 1.067669 CTGCGCTGATGTAGAGGCTAA 59.932 52.381 9.73 0.00 0.00 3.09
1674 4944 1.371758 CCGCCCATCGTCAGTATCG 60.372 63.158 0.00 0.00 36.19 2.92
1941 5711 9.486497 GCTAGTAATGGTATTTCCCTTAACTAC 57.514 37.037 0.00 0.00 34.77 2.73
1957 5760 2.223829 CGGGACAGACAGCTAGTAATGG 60.224 54.545 0.00 0.00 0.00 3.16
1965 5768 1.347707 TCAAAATCGGGACAGACAGCT 59.652 47.619 0.00 0.00 0.00 4.24
2252 6127 5.991606 TCGGGCATATACTTGAATTCTTCTG 59.008 40.000 7.05 0.00 0.00 3.02
2297 6172 8.322091 ACATGAACAATAATACCCTCCTATAGC 58.678 37.037 0.00 0.00 0.00 2.97
2342 6217 8.875168 TGGGTTACAAGATTTTGTTTCCATTAT 58.125 29.630 6.97 0.00 45.01 1.28
2846 7807 3.988379 TGACATTCGCAAGCTTTCTTT 57.012 38.095 0.00 0.00 37.18 2.52
2921 7882 7.038302 ACACTGTAAATGAAAGTCCCTGATCTA 60.038 37.037 0.00 0.00 0.00 1.98
3256 8223 1.339151 ACTGAAAGGGAGATGCGGTTC 60.339 52.381 0.00 0.00 39.30 3.62
3411 8378 6.434028 GTGCTATTATAGATGCCCCAAAATCA 59.566 38.462 3.04 0.00 0.00 2.57
3597 11735 2.808206 CCGGCATACCTCAGGACCC 61.808 68.421 0.00 0.00 0.00 4.46
3835 11973 3.750371 AGCTATCTGTCTCAGTATCGCT 58.250 45.455 0.00 0.00 32.61 4.93
4100 12256 2.495669 GTGTCCCCATTTTGTACCATGG 59.504 50.000 11.19 11.19 39.92 3.66
4124 12280 5.003804 ACAAGTTCAAATAGGTAGCACTGG 58.996 41.667 0.00 0.00 0.00 4.00
4133 12289 2.744202 AGCTCGCACAAGTTCAAATAGG 59.256 45.455 0.00 0.00 0.00 2.57
4135 12291 4.274705 TGAAAGCTCGCACAAGTTCAAATA 59.725 37.500 0.00 0.00 0.00 1.40
4161 12317 8.531146 TCTTCTTTGAGTGATTTTGGAAACTTT 58.469 29.630 0.00 0.00 0.00 2.66
4191 12349 0.762418 TTTCACACCCAGTCGTCCAT 59.238 50.000 0.00 0.00 0.00 3.41
4218 12376 4.887071 AGCACAGTTTCAATACCAAACTCA 59.113 37.500 0.00 0.00 41.25 3.41
4282 12440 4.142026 CCCACATGACCGAGTAAATCAGTA 60.142 45.833 0.00 0.00 0.00 2.74
4299 12457 2.937689 AGTGAGCCCAGCCCACAT 60.938 61.111 4.03 0.00 33.53 3.21
4360 12518 0.827925 AAGTGCAGAGACCCTGACGA 60.828 55.000 0.00 0.00 45.78 4.20
4468 13390 6.901300 AGTTTAGGGACCTAGAACACATCATA 59.099 38.462 17.58 0.00 0.00 2.15
4476 13398 6.822170 CCAAATGTAGTTTAGGGACCTAGAAC 59.178 42.308 11.91 11.91 0.00 3.01
4491 13416 8.630054 TTATGTGTTTAGAAGCCAAATGTAGT 57.370 30.769 0.00 0.00 0.00 2.73
4593 13537 1.165907 CCTGCCTCGTCAAACAAGCA 61.166 55.000 0.00 0.00 0.00 3.91
4603 13547 0.912486 AAATAAGCTCCCTGCCTCGT 59.088 50.000 0.00 0.00 44.23 4.18
4619 13577 1.094785 GGCAGTATGGTGACGCAAAT 58.905 50.000 0.00 0.00 35.86 2.32
4646 13604 3.087906 ATATATCCCCGGCCGGCC 61.088 66.667 39.46 36.69 0.00 6.13
4647 13605 1.623542 AAGATATATCCCCGGCCGGC 61.624 60.000 39.46 21.18 0.00 6.13
4648 13606 0.178068 CAAGATATATCCCCGGCCGG 59.822 60.000 37.99 37.99 0.00 6.13
4662 13620 4.202398 ACGGCATCATCCTTATCACAAGAT 60.202 41.667 0.00 0.00 38.29 2.40
4669 13627 2.037772 AGGACACGGCATCATCCTTATC 59.962 50.000 0.00 0.00 38.47 1.75
4684 13642 7.039434 TGTTCATCAGGATATCTATCAGGACAC 60.039 40.741 2.05 0.00 34.40 3.67
4694 13668 9.829507 CTACTTCTTTTGTTCATCAGGATATCT 57.170 33.333 2.05 0.00 0.00 1.98
4698 13672 7.118390 CGTTCTACTTCTTTTGTTCATCAGGAT 59.882 37.037 0.00 0.00 0.00 3.24
4719 13693 9.878599 CTCAACTTTAATTTGTTACATCGTTCT 57.121 29.630 0.00 0.00 0.00 3.01
4720 13694 8.627428 GCTCAACTTTAATTTGTTACATCGTTC 58.373 33.333 0.00 0.00 0.00 3.95
4723 14376 8.417176 GTTGCTCAACTTTAATTTGTTACATCG 58.583 33.333 5.56 0.00 38.25 3.84
4735 14388 6.426937 GTCATACTCAGGTTGCTCAACTTTAA 59.573 38.462 11.91 0.00 40.94 1.52
4738 14391 4.319177 GTCATACTCAGGTTGCTCAACTT 58.681 43.478 11.91 2.32 40.94 2.66
4743 14396 1.927895 CGGTCATACTCAGGTTGCTC 58.072 55.000 0.00 0.00 0.00 4.26
4746 14399 1.645034 CTGCGGTCATACTCAGGTTG 58.355 55.000 0.00 0.00 0.00 3.77
4786 14439 3.244249 CGGTCTATCATTCCCCTTCTTCC 60.244 52.174 0.00 0.00 0.00 3.46
4790 14443 2.326428 TCCGGTCTATCATTCCCCTTC 58.674 52.381 0.00 0.00 0.00 3.46
4799 14452 0.942252 CGACGTCATCCGGTCTATCA 59.058 55.000 17.16 0.00 42.24 2.15
4801 14454 1.793134 GCCGACGTCATCCGGTCTAT 61.793 60.000 17.16 0.00 46.84 1.98
4802 14455 2.475466 GCCGACGTCATCCGGTCTA 61.475 63.158 17.16 0.00 46.84 2.59
4809 14462 3.255379 GAAGCCGCCGACGTCATC 61.255 66.667 17.16 5.16 37.70 2.92
4810 14463 4.814294 GGAAGCCGCCGACGTCAT 62.814 66.667 17.16 0.00 37.70 3.06
4835 14488 4.767892 CCCTTCCCTCCCTGCCCT 62.768 72.222 0.00 0.00 0.00 5.19
4837 14490 3.093172 CTCCCTTCCCTCCCTGCC 61.093 72.222 0.00 0.00 0.00 4.85
4900 14553 4.827087 CTCCAGGCGCACGCAGAT 62.827 66.667 17.69 0.00 44.11 2.90
4903 14556 4.617520 TTTCTCCAGGCGCACGCA 62.618 61.111 17.69 0.00 44.11 5.24
4904 14557 3.793144 CTTTCTCCAGGCGCACGC 61.793 66.667 10.83 6.46 41.06 5.34
4905 14558 3.121030 CCTTTCTCCAGGCGCACG 61.121 66.667 10.83 0.00 0.00 5.34
4911 14564 1.821332 GCCGATGCCTTTCTCCAGG 60.821 63.158 0.00 0.00 36.95 4.45
4912 14565 2.176273 CGCCGATGCCTTTCTCCAG 61.176 63.158 0.00 0.00 0.00 3.86
4913 14566 2.125147 CGCCGATGCCTTTCTCCA 60.125 61.111 0.00 0.00 0.00 3.86
4914 14567 1.745489 AACGCCGATGCCTTTCTCC 60.745 57.895 0.00 0.00 0.00 3.71
4915 14568 1.298859 ACAACGCCGATGCCTTTCTC 61.299 55.000 0.00 0.00 0.00 2.87
4916 14569 0.036765 TACAACGCCGATGCCTTTCT 60.037 50.000 0.00 0.00 0.00 2.52
4917 14570 0.373716 CTACAACGCCGATGCCTTTC 59.626 55.000 0.00 0.00 0.00 2.62
4918 14571 1.024579 CCTACAACGCCGATGCCTTT 61.025 55.000 0.00 0.00 0.00 3.11
4919 14572 1.449601 CCTACAACGCCGATGCCTT 60.450 57.895 0.00 0.00 0.00 4.35
4920 14573 2.186903 CCTACAACGCCGATGCCT 59.813 61.111 0.00 0.00 0.00 4.75
4921 14574 3.573491 GCCTACAACGCCGATGCC 61.573 66.667 0.00 0.00 0.00 4.40
4922 14575 2.813179 CTGCCTACAACGCCGATGC 61.813 63.158 0.00 0.00 0.00 3.91
4923 14576 2.173669 CCTGCCTACAACGCCGATG 61.174 63.158 0.00 0.00 0.00 3.84
4924 14577 2.186903 CCTGCCTACAACGCCGAT 59.813 61.111 0.00 0.00 0.00 4.18
4925 14578 4.752879 GCCTGCCTACAACGCCGA 62.753 66.667 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.