Multiple sequence alignment - TraesCS3B01G060100

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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 TraesCS3B01G060100 chr3B 100.000 2934 0 0 1 2934 31814800 31811867 0.000000e+00 5419.0
1 TraesCS3B01G060100 chr3B 80.941 871 104 25 1 844 31851202 31850367 1.480000e-177 632.0
2 TraesCS3B01G060100 chr3B 90.575 435 40 1 493 926 32247427 32246993 2.540000e-160 575.0
3 TraesCS3B01G060100 chr3B 95.217 230 10 1 195 423 32247653 32247424 2.150000e-96 363.0
4 TraesCS3B01G060100 chr3B 100.000 28 0 0 559 586 685029129 685029156 5.000000e-03 52.8
5 TraesCS3B01G060100 chr3D 91.925 1486 94 14 926 2388 19886065 19884583 0.000000e+00 2056.0
6 TraesCS3B01G060100 chr3D 82.147 857 106 17 24 859 19898200 19897370 0.000000e+00 691.0
7 TraesCS3B01G060100 chr3D 77.737 548 109 12 985 1524 326549019 326548477 1.010000e-84 324.0
8 TraesCS3B01G060100 chr3D 100.000 28 0 0 2407 2434 604450447 604450474 5.000000e-03 52.8
9 TraesCS3B01G060100 chr3A 90.234 1024 95 4 927 1946 27551738 27550716 0.000000e+00 1332.0
10 TraesCS3B01G060100 chr3A 86.972 568 59 9 2380 2934 27547640 27547075 2.480000e-175 625.0
11 TraesCS3B01G060100 chr3A 77.111 533 115 7 985 1513 438615422 438615951 4.750000e-78 302.0
12 TraesCS3B01G060100 chrUn 81.056 871 103 25 1 844 343008339 343007504 3.190000e-179 638.0
13 TraesCS3B01G060100 chrUn 80.947 845 99 25 1 818 432942116 432942925 1.930000e-171 612.0
14 TraesCS3B01G060100 chr1D 94.444 36 2 0 551 586 477196486 477196521 4.080000e-04 56.5
15 TraesCS3B01G060100 chr4A 100.000 28 0 0 559 586 365586859 365586832 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 TraesCS3B01G060100 chr3B 31811867 31814800 2933 True 5419.0 5419 100.000 1 2934 1 chr3B.!!$R1 2933
1 TraesCS3B01G060100 chr3B 31850367 31851202 835 True 632.0 632 80.941 1 844 1 chr3B.!!$R2 843
2 TraesCS3B01G060100 chr3B 32246993 32247653 660 True 469.0 575 92.896 195 926 2 chr3B.!!$R3 731
3 TraesCS3B01G060100 chr3D 19884583 19886065 1482 True 2056.0 2056 91.925 926 2388 1 chr3D.!!$R1 1462
4 TraesCS3B01G060100 chr3D 19897370 19898200 830 True 691.0 691 82.147 24 859 1 chr3D.!!$R2 835
5 TraesCS3B01G060100 chr3D 326548477 326549019 542 True 324.0 324 77.737 985 1524 1 chr3D.!!$R3 539
6 TraesCS3B01G060100 chr3A 27547075 27551738 4663 True 978.5 1332 88.603 927 2934 2 chr3A.!!$R1 2007
7 TraesCS3B01G060100 chr3A 438615422 438615951 529 False 302.0 302 77.111 985 1513 1 chr3A.!!$F1 528
8 TraesCS3B01G060100 chrUn 343007504 343008339 835 True 638.0 638 81.056 1 844 1 chrUn.!!$R1 843
9 TraesCS3B01G060100 chrUn 432942116 432942925 809 False 612.0 612 80.947 1 818 1 chrUn.!!$F1 817

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
459 488 0.242825 TTGGGACTGCTTACTCGTCG 59.757 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 3116 0.038526 CGTCCAAGCGTTACCAGTCT 60.039 55.0 0.0 0.0 0.0 3.24 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
44 45 1.003233 GGGTGGCCACTGAGAGAAC 60.003 63.158 33.91 15.35 0.00 3.01
52 53 2.355108 GCCACTGAGAGAACTTATGCCA 60.355 50.000 0.00 0.00 0.00 4.92
82 83 6.990798 TGTGTCAATTGAAATATTCTTGCCA 58.009 32.000 10.35 0.00 0.00 4.92
86 87 7.177216 TGTCAATTGAAATATTCTTGCCACTCT 59.823 33.333 10.35 0.00 0.00 3.24
133 134 0.609131 CAAGCCAGTCCATTCCGGTT 60.609 55.000 0.00 0.00 35.57 4.44
138 139 0.248289 CAGTCCATTCCGGTTACCGT 59.752 55.000 22.78 0.68 46.80 4.83
166 167 3.052642 AGGTGCCCAATGGTATGATCTTT 60.053 43.478 0.00 0.00 0.00 2.52
178 179 7.181569 TGGTATGATCTTTATGTCAGTCACA 57.818 36.000 0.00 0.00 40.18 3.58
190 191 1.227853 AGTCACAAACTCGTGCCCC 60.228 57.895 0.00 0.00 36.80 5.80
209 237 5.070001 GCCCCTGTGAATAGCAATACAATA 58.930 41.667 0.00 0.00 0.00 1.90
241 269 1.892209 CAACTTTAACTCGCCCTGGT 58.108 50.000 0.00 0.00 0.00 4.00
265 293 1.354101 TGAGTGGGTTGGTACCGATT 58.646 50.000 4.77 0.00 46.04 3.34
423 452 1.140161 CATGGCCATTGCAGTTCCG 59.860 57.895 17.92 0.00 40.13 4.30
442 471 0.248458 GCAGTTGTGGTCGTGGTTTG 60.248 55.000 0.00 0.00 0.00 2.93
452 481 0.759959 TCGTGGTTTGGGACTGCTTA 59.240 50.000 0.00 0.00 0.00 3.09
455 484 2.152016 GTGGTTTGGGACTGCTTACTC 58.848 52.381 0.00 0.00 0.00 2.59
459 488 0.242825 TTGGGACTGCTTACTCGTCG 59.757 55.000 0.00 0.00 0.00 5.12
467 496 1.198408 TGCTTACTCGTCGAACATCGT 59.802 47.619 0.00 0.00 41.35 3.73
468 497 1.578023 GCTTACTCGTCGAACATCGTG 59.422 52.381 0.00 0.00 41.35 4.35
469 498 2.174764 CTTACTCGTCGAACATCGTGG 58.825 52.381 0.00 0.00 41.35 4.94
486 515 1.875813 GGTGATGCTGACGAGCTCG 60.876 63.158 33.45 33.45 46.39 5.03
587 620 3.773649 GAAGCATAAGCCGCGCGTG 62.774 63.158 29.95 20.60 43.56 5.34
650 683 2.202623 GCGCCCTCGACACTACAG 60.203 66.667 0.00 0.00 38.10 2.74
684 717 1.531423 AGTTGGAATCTGTGCAGCTG 58.469 50.000 10.11 10.11 37.73 4.24
696 729 2.656646 CAGCTGGCAGACGTGGTA 59.343 61.111 20.86 0.00 0.00 3.25
700 733 3.989698 CTGGCAGACGTGGTAGCGG 62.990 68.421 9.42 0.00 35.98 5.52
738 771 3.793144 CGGGCTCAAGAGTTGCGC 61.793 66.667 0.00 0.00 40.50 6.09
741 774 2.359230 GCTCAAGAGTTGCGCCCT 60.359 61.111 4.18 0.00 35.44 5.19
857 890 0.878416 GTGGCCGCTGTATCAAAACA 59.122 50.000 9.68 0.00 0.00 2.83
859 892 2.094752 GTGGCCGCTGTATCAAAACAAT 60.095 45.455 9.68 0.00 0.00 2.71
888 922 8.511465 AAAATAGCATGCTATAAAATTCAGCG 57.489 30.769 34.51 0.00 38.20 5.18
891 925 4.576053 AGCATGCTATAAAATTCAGCGTCA 59.424 37.500 21.21 0.00 38.15 4.35
898 932 1.156736 AAATTCAGCGTCACCCTTCG 58.843 50.000 0.00 0.00 0.00 3.79
905 939 3.383026 CGTCACCCTTCGCAAAATG 57.617 52.632 0.00 0.00 0.00 2.32
907 941 0.388520 GTCACCCTTCGCAAAATGCC 60.389 55.000 0.00 0.00 41.12 4.40
910 944 1.476085 CACCCTTCGCAAAATGCCATA 59.524 47.619 0.00 0.00 41.12 2.74
911 945 1.476488 ACCCTTCGCAAAATGCCATAC 59.524 47.619 0.00 0.00 41.12 2.39
998 1032 6.402118 CGTGTTTATTCAATAGACTGTGTGGG 60.402 42.308 0.16 0.00 0.00 4.61
1053 1087 6.263754 AGAAATTGGGGGAAATGACTACAAT 58.736 36.000 0.00 0.00 0.00 2.71
1182 1216 4.627467 GCTCCTTATGCTATCATTACCACG 59.373 45.833 0.00 0.00 34.22 4.94
1183 1217 4.566004 TCCTTATGCTATCATTACCACGC 58.434 43.478 0.00 0.00 34.22 5.34
1381 1421 2.693591 GGATTATGAGTCAGACACGGGA 59.306 50.000 2.66 0.00 0.00 5.14
1513 1554 4.940483 ACTATGGAGCTGCTATGGAGATA 58.060 43.478 6.82 0.00 0.00 1.98
1530 1571 7.465900 TGGAGATATTTGTTTCCCCTTATCT 57.534 36.000 0.00 0.00 0.00 1.98
1631 1674 2.417719 GTATGCTAATCCCGGCTCTTG 58.582 52.381 0.00 0.00 0.00 3.02
1638 1681 0.618458 ATCCCGGCTCTTGTTTGCTA 59.382 50.000 0.00 0.00 0.00 3.49
1647 1690 4.876107 GGCTCTTGTTTGCTATAACTGCTA 59.124 41.667 0.00 0.00 0.00 3.49
1705 1748 2.916934 TGTAGAAGGGCCTTATGGTGTT 59.083 45.455 23.23 0.00 35.27 3.32
1709 1752 2.514458 AGGGCCTTATGGTGTTTCAG 57.486 50.000 0.00 0.00 35.27 3.02
1806 1849 3.313012 TCCCACAGAAACGTCATACAG 57.687 47.619 0.00 0.00 0.00 2.74
1834 1877 1.403323 GCTGATGGTTTGCTAAGAGGC 59.597 52.381 0.00 0.00 0.00 4.70
1843 1886 0.837272 TGCTAAGAGGCCCATACACC 59.163 55.000 0.00 0.00 0.00 4.16
1906 1949 3.760673 GAGCTTGTCTCGTCTGCG 58.239 61.111 0.00 0.00 39.92 5.18
1977 2984 7.391148 ACGATTAATGTATGAAAACTTGCCT 57.609 32.000 0.00 0.00 0.00 4.75
2005 3013 7.003482 TGATAAACATATTTGGCATGGCTAGA 58.997 34.615 21.08 6.29 0.00 2.43
2017 3025 1.496060 TGGCTAGATGTCGTTCCCAT 58.504 50.000 0.00 0.00 0.00 4.00
2021 3029 4.836175 TGGCTAGATGTCGTTCCCATATAA 59.164 41.667 0.00 0.00 0.00 0.98
2048 3056 1.328680 GATATCTAATGCCGGCATGCG 59.671 52.381 41.00 31.72 36.68 4.73
2065 3077 2.009051 TGCGTGCCAAATGATCTGTAG 58.991 47.619 0.00 0.00 0.00 2.74
2071 3083 5.580691 CGTGCCAAATGATCTGTAGTTAAGA 59.419 40.000 0.00 0.00 0.00 2.10
2078 3090 9.302345 CAAATGATCTGTAGTTAAGATACACGT 57.698 33.333 0.00 0.00 34.50 4.49
2099 3111 5.221521 ACGTGTATCAATATCTGCACCTCAT 60.222 40.000 0.00 0.00 0.00 2.90
2100 3112 5.347093 CGTGTATCAATATCTGCACCTCATC 59.653 44.000 0.00 0.00 0.00 2.92
2104 3116 5.619132 TCAATATCTGCACCTCATCTTCA 57.381 39.130 0.00 0.00 0.00 3.02
2106 3118 5.364735 TCAATATCTGCACCTCATCTTCAGA 59.635 40.000 0.00 0.00 38.05 3.27
2114 3126 4.499183 CACCTCATCTTCAGACTGGTAAC 58.501 47.826 1.81 0.00 0.00 2.50
2117 3129 2.826128 TCATCTTCAGACTGGTAACGCT 59.174 45.455 1.81 0.00 42.51 5.07
2123 3135 0.038526 AGACTGGTAACGCTTGGACG 60.039 55.000 0.00 0.00 42.51 4.79
2129 3141 1.337821 GTAACGCTTGGACGACTCTG 58.662 55.000 0.00 0.00 36.70 3.35
2179 4318 3.495434 TTAGGTCTTTCTTTGGCGGAA 57.505 42.857 0.00 0.00 0.00 4.30
2182 4321 3.230976 AGGTCTTTCTTTGGCGGAAATT 58.769 40.909 0.00 0.00 33.12 1.82
2184 4323 3.317150 GTCTTTCTTTGGCGGAAATTGG 58.683 45.455 0.00 0.00 33.12 3.16
2200 4503 6.338146 GGAAATTGGCTTTGTTATTCTACCC 58.662 40.000 0.00 0.00 0.00 3.69
2240 4543 6.154021 ACAACCAACGAACATATACTAGGACT 59.846 38.462 0.00 0.00 0.00 3.85
2297 4795 2.662791 GCATGTAGACACACTTTGCACG 60.663 50.000 0.00 0.00 37.54 5.34
2354 4862 2.284190 GCTCATGTGCTTTCTAGGACC 58.716 52.381 12.42 0.00 41.62 4.46
2362 4870 2.884639 TGCTTTCTAGGACCTTTTGCAC 59.115 45.455 0.00 0.00 0.00 4.57
2364 4872 3.317993 GCTTTCTAGGACCTTTTGCACAA 59.682 43.478 0.00 0.00 0.00 3.33
2400 5097 0.609131 ATCGGTTTGTGCCCTTGGAG 60.609 55.000 0.00 0.00 0.00 3.86
2410 5108 1.843851 TGCCCTTGGAGTATAGTTGGG 59.156 52.381 0.00 0.00 36.41 4.12
2441 5139 1.522668 GCAGTTGCATGTAGTGGTCA 58.477 50.000 0.00 0.00 41.59 4.02
2451 5149 2.226330 TGTAGTGGTCAACATGCAACC 58.774 47.619 0.00 0.00 0.00 3.77
2472 5170 1.965219 CGTCGACAACTCCCCTTCT 59.035 57.895 17.16 0.00 0.00 2.85
2484 5182 0.914417 CCCCTTCTGGCCCTAGTTGA 60.914 60.000 0.00 0.00 0.00 3.18
2485 5183 1.216990 CCCTTCTGGCCCTAGTTGAT 58.783 55.000 0.00 0.00 0.00 2.57
2501 5208 5.070770 AGTTGATGTCACTTTTGTTGCAA 57.929 34.783 0.00 0.00 0.00 4.08
2504 5211 7.264221 AGTTGATGTCACTTTTGTTGCAATTA 58.736 30.769 0.59 0.00 0.00 1.40
2518 5225 6.726230 TGTTGCAATTAAGTTACAACGCTTA 58.274 32.000 0.59 0.00 43.84 3.09
2519 5226 7.364200 TGTTGCAATTAAGTTACAACGCTTAT 58.636 30.769 0.59 0.00 43.84 1.73
2537 5244 4.932200 GCTTATAGTTGCATGCCTAGTAGG 59.068 45.833 16.68 12.27 38.80 3.18
2555 5262 1.360393 GGCCATCAATACCCCTCCCA 61.360 60.000 0.00 0.00 0.00 4.37
2562 5269 4.745013 TACCCCTCCCAACCCCGG 62.745 72.222 0.00 0.00 0.00 5.73
2576 5283 1.590259 CCCGGTTGCCGTTGTTTTG 60.590 57.895 0.00 0.00 46.80 2.44
2579 5286 0.456995 CGGTTGCCGTTGTTTTGTGT 60.457 50.000 0.00 0.00 42.73 3.72
2612 5319 7.606456 AGTTACACTTGGGTTACAATGTGATAG 59.394 37.037 0.00 0.00 38.95 2.08
2618 5325 8.713971 ACTTGGGTTACAATGTGATAGATATGA 58.286 33.333 0.00 0.00 38.65 2.15
2643 5351 0.529833 CACACTTGTGGGTGTTTGCA 59.470 50.000 5.72 0.00 46.71 4.08
2647 5355 3.181480 ACACTTGTGGGTGTTTGCATAAC 60.181 43.478 5.72 0.00 46.71 1.89
2670 5378 7.698836 ACAAAAACATAAGCACACTGAAATC 57.301 32.000 0.00 0.00 0.00 2.17
2675 5383 1.308047 AAGCACACTGAAATCGCACA 58.692 45.000 0.00 0.00 0.00 4.57
2701 5409 5.038683 TGTATTCGTCGTATGAACATGGAC 58.961 41.667 0.00 4.64 0.00 4.02
2708 5416 6.254804 TCGTCGTATGAACATGGACAAAATAG 59.745 38.462 15.46 4.58 0.00 1.73
2781 5489 9.700831 AGGTGAAATAAGAAAATAAGGCATACT 57.299 29.630 0.00 0.00 0.00 2.12
2782 5490 9.736023 GGTGAAATAAGAAAATAAGGCATACTG 57.264 33.333 0.00 0.00 0.00 2.74
2790 5498 6.825721 AGAAAATAAGGCATACTGGAGACAAG 59.174 38.462 0.00 0.00 42.06 3.16
2793 5501 0.811616 GGCATACTGGAGACAAGCCG 60.812 60.000 0.00 0.00 42.06 5.52
2811 5519 0.527817 CGGCAACACGGATCTACTCC 60.528 60.000 0.00 0.00 41.07 3.85
2816 5524 3.670625 CAACACGGATCTACTCCCAAAA 58.329 45.455 0.00 0.00 41.49 2.44
2818 5526 4.569719 ACACGGATCTACTCCCAAAATT 57.430 40.909 0.00 0.00 41.49 1.82
2827 5535 7.201705 GGATCTACTCCCAAAATTTTCTAACGG 60.202 40.741 0.00 0.00 38.19 4.44
2839 5547 8.913487 AAATTTTCTAACGGTAAAAGAGAGGA 57.087 30.769 0.00 0.00 0.00 3.71
2845 5553 7.376615 TCTAACGGTAAAAGAGAGGAGAAAAG 58.623 38.462 0.00 0.00 0.00 2.27
2847 5555 3.685272 CGGTAAAAGAGAGGAGAAAAGGC 59.315 47.826 0.00 0.00 0.00 4.35
2851 5559 0.178861 AGAGAGGAGAAAAGGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
2852 5560 0.034960 GAGAGGAGAAAAGGCCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
2853 5561 0.772124 AGAGGAGAAAAGGCCCCACA 60.772 55.000 0.00 0.00 0.00 4.17
2854 5562 0.332972 GAGGAGAAAAGGCCCCACAT 59.667 55.000 0.00 0.00 0.00 3.21
2923 5632 5.784023 TCATGGGGATACAACTTAGGTCTA 58.216 41.667 0.00 0.00 39.74 2.59
2927 5636 6.449956 TGGGGATACAACTTAGGTCTAGAAT 58.550 40.000 0.00 0.00 39.74 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.756172 CAGTGGCCACCCAACAACA 60.756 57.895 32.29 0.00 44.33 3.33
44 45 5.762825 ATTGACACAGCTAATGGCATAAG 57.237 39.130 6.53 0.00 44.79 1.73
82 83 6.836527 ACAGTCCAATGCTAGTAGATTAGAGT 59.163 38.462 0.00 0.00 0.00 3.24
86 87 6.791867 ACACAGTCCAATGCTAGTAGATTA 57.208 37.500 0.00 0.00 0.00 1.75
166 167 3.057019 GCACGAGTTTGTGACTGACATA 58.943 45.455 3.68 0.00 42.55 2.29
178 179 0.110486 ATTCACAGGGGCACGAGTTT 59.890 50.000 0.00 0.00 0.00 2.66
190 191 5.466728 AGGCGTATTGTATTGCTATTCACAG 59.533 40.000 0.00 0.00 0.00 3.66
241 269 2.657143 GGTACCAACCCACTCAAACAA 58.343 47.619 7.15 0.00 40.21 2.83
423 452 0.248458 CAAACCACGACCACAACTGC 60.248 55.000 0.00 0.00 0.00 4.40
442 471 0.524862 TTCGACGAGTAAGCAGTCCC 59.475 55.000 0.00 0.00 0.00 4.46
452 481 0.386858 CACCACGATGTTCGACGAGT 60.387 55.000 3.62 0.00 43.74 4.18
455 484 0.640262 CATCACCACGATGTTCGACG 59.360 55.000 3.62 0.00 45.61 5.12
476 505 2.355132 GAGGAATTACTCGAGCTCGTCA 59.645 50.000 33.33 16.31 40.80 4.35
486 515 2.094894 TCACGTCGTCGAGGAATTACTC 59.905 50.000 20.87 7.71 40.62 2.59
587 620 1.554392 CACTCAGAGTCTGCATACGC 58.446 55.000 15.72 0.00 39.24 4.42
588 621 1.554392 GCACTCAGAGTCTGCATACG 58.446 55.000 15.72 3.26 0.00 3.06
589 622 1.480137 AGGCACTCAGAGTCTGCATAC 59.520 52.381 15.72 5.04 0.00 2.39
590 623 1.857965 AGGCACTCAGAGTCTGCATA 58.142 50.000 15.72 0.00 0.00 3.14
591 624 0.982704 AAGGCACTCAGAGTCTGCAT 59.017 50.000 15.72 5.07 38.49 3.96
594 627 1.337635 GGTCAAGGCACTCAGAGTCTG 60.338 57.143 14.36 14.36 38.49 3.51
650 683 2.367567 TCCAACTTCTACTGTGGACCAC 59.632 50.000 18.28 18.28 34.56 4.16
659 692 4.573900 CTGCACAGATTCCAACTTCTACT 58.426 43.478 0.00 0.00 0.00 2.57
661 694 3.008375 AGCTGCACAGATTCCAACTTCTA 59.992 43.478 1.02 0.00 0.00 2.10
664 697 1.884579 CAGCTGCACAGATTCCAACTT 59.115 47.619 0.00 0.00 0.00 2.66
684 717 4.065281 ACCGCTACCACGTCTGCC 62.065 66.667 0.00 0.00 0.00 4.85
696 729 2.044946 GCTCCCATTTCCACCGCT 60.045 61.111 0.00 0.00 0.00 5.52
700 733 2.700773 GCACCGCTCCCATTTCCAC 61.701 63.158 0.00 0.00 0.00 4.02
727 760 1.743252 GGAGAGGGCGCAACTCTTG 60.743 63.158 27.52 0.00 44.89 3.02
738 771 1.776662 TCCACATAACGAGGAGAGGG 58.223 55.000 0.00 0.00 29.93 4.30
762 795 2.738521 GCACCATCGTCACACGCT 60.739 61.111 0.00 0.00 42.21 5.07
871 905 4.275936 GGGTGACGCTGAATTTTATAGCAT 59.724 41.667 0.00 0.00 37.29 3.79
880 914 2.840974 CGAAGGGTGACGCTGAATT 58.159 52.632 1.94 0.00 0.00 2.17
881 915 4.598257 CGAAGGGTGACGCTGAAT 57.402 55.556 1.94 0.00 0.00 2.57
888 922 0.388520 GGCATTTTGCGAAGGGTGAC 60.389 55.000 0.00 0.00 46.21 3.67
891 925 1.476488 GTATGGCATTTTGCGAAGGGT 59.524 47.619 4.78 0.00 46.21 4.34
898 932 5.399301 CGCTATAACTTGTATGGCATTTTGC 59.601 40.000 4.78 0.00 44.08 3.68
900 934 6.494842 CACGCTATAACTTGTATGGCATTTT 58.505 36.000 4.78 0.00 31.94 1.82
905 939 2.869801 TGCACGCTATAACTTGTATGGC 59.130 45.455 0.00 0.00 0.00 4.40
907 941 7.409697 AGAAAATGCACGCTATAACTTGTATG 58.590 34.615 0.00 0.00 0.00 2.39
910 944 5.880054 AGAAAATGCACGCTATAACTTGT 57.120 34.783 0.00 0.00 0.00 3.16
911 945 8.841444 ATTTAGAAAATGCACGCTATAACTTG 57.159 30.769 0.00 0.00 0.00 3.16
956 990 5.779806 AACACGTTACTCTATCAATGTGC 57.220 39.130 6.58 0.00 42.71 4.57
967 1001 9.136952 ACAGTCTATTGAATAAACACGTTACTC 57.863 33.333 0.00 0.00 0.00 2.59
998 1032 7.063074 CCAAGAAAAGAGATTTGTTCATCATGC 59.937 37.037 0.00 0.00 32.60 4.06
1137 1171 4.032786 GCAACAAACAACAAATGACTCACC 59.967 41.667 0.00 0.00 0.00 4.02
1182 1216 6.862209 TGTAATTGGGATTTGACATAACAGC 58.138 36.000 0.00 0.00 0.00 4.40
1183 1217 8.279970 TCTGTAATTGGGATTTGACATAACAG 57.720 34.615 0.00 0.00 0.00 3.16
1267 1307 0.811281 GAGTTTTGGCTCCCAATCCG 59.189 55.000 0.00 0.00 43.55 4.18
1513 1554 5.843969 ACCAAACAGATAAGGGGAAACAAAT 59.156 36.000 0.00 0.00 0.00 2.32
1530 1571 6.934645 CCATAAAGTTCTAGACTCACCAAACA 59.065 38.462 0.00 0.00 37.72 2.83
1569 1610 1.691196 TTTCTTGACCTGCCAAGTGG 58.309 50.000 0.00 0.00 42.95 4.00
1575 1616 4.279420 AGAGAATGTTTTTCTTGACCTGCC 59.721 41.667 0.00 0.00 0.00 4.85
1611 1654 2.224305 ACAAGAGCCGGGATTAGCATAC 60.224 50.000 2.18 0.00 0.00 2.39
1631 1674 8.622948 ATCCCTAAATAGCAGTTATAGCAAAC 57.377 34.615 0.00 0.00 0.00 2.93
1638 1681 6.017192 TCCTCGATCCCTAAATAGCAGTTAT 58.983 40.000 0.00 0.00 0.00 1.89
1823 1866 1.211949 GGTGTATGGGCCTCTTAGCAA 59.788 52.381 4.53 0.00 0.00 3.91
1834 1877 1.570857 TTGGAGGCTGGGTGTATGGG 61.571 60.000 0.00 0.00 0.00 4.00
1843 1886 2.353610 GGTGGCAATTGGAGGCTGG 61.354 63.158 7.72 0.00 0.00 4.85
1906 1949 8.738645 ACAAATCATAGAGAACCTTGTATTCC 57.261 34.615 0.00 0.00 30.44 3.01
1952 2959 7.826690 AGGCAAGTTTTCATACATTAATCGTT 58.173 30.769 0.00 0.00 0.00 3.85
1977 2984 8.192743 AGCCATGCCAAATATGTTTATCATTA 57.807 30.769 0.00 0.00 37.91 1.90
1983 2990 6.777091 ACATCTAGCCATGCCAAATATGTTTA 59.223 34.615 0.00 0.00 0.00 2.01
1990 2997 2.224606 CGACATCTAGCCATGCCAAAT 58.775 47.619 0.00 0.00 0.00 2.32
2005 3013 6.826668 TCACTTGATTATATGGGAACGACAT 58.173 36.000 0.00 0.00 0.00 3.06
2017 3025 7.710907 GCCGGCATTAGATATCACTTGATTATA 59.289 37.037 24.80 0.00 36.05 0.98
2021 3029 4.256920 GCCGGCATTAGATATCACTTGAT 58.743 43.478 24.80 0.00 38.51 2.57
2048 3056 6.985188 TCTTAACTACAGATCATTTGGCAC 57.015 37.500 0.00 0.00 0.00 5.01
2056 3068 7.387119 ACACGTGTATCTTAACTACAGATCA 57.613 36.000 21.98 0.00 32.94 2.92
2071 3083 5.926542 GGTGCAGATATTGATACACGTGTAT 59.073 40.000 35.10 35.10 43.38 2.29
2078 3090 6.676990 AGATGAGGTGCAGATATTGATACA 57.323 37.500 0.00 0.00 0.00 2.29
2091 3103 1.277557 ACCAGTCTGAAGATGAGGTGC 59.722 52.381 0.00 0.00 0.00 5.01
2099 3111 2.288825 CCAAGCGTTACCAGTCTGAAGA 60.289 50.000 0.00 0.00 0.00 2.87
2100 3112 2.069273 CCAAGCGTTACCAGTCTGAAG 58.931 52.381 0.00 0.00 0.00 3.02
2104 3116 0.038526 CGTCCAAGCGTTACCAGTCT 60.039 55.000 0.00 0.00 0.00 3.24
2106 3118 0.319297 GTCGTCCAAGCGTTACCAGT 60.319 55.000 0.00 0.00 0.00 4.00
2114 3126 1.135257 AGATTCAGAGTCGTCCAAGCG 60.135 52.381 0.00 0.00 0.00 4.68
2117 3129 4.336889 ACAAAGATTCAGAGTCGTCCAA 57.663 40.909 0.00 0.00 0.00 3.53
2159 4107 3.495434 TTCCGCCAAAGAAAGACCTAA 57.505 42.857 0.00 0.00 0.00 2.69
2160 4108 3.495434 TTTCCGCCAAAGAAAGACCTA 57.505 42.857 0.00 0.00 0.00 3.08
2162 4110 3.317150 CAATTTCCGCCAAAGAAAGACC 58.683 45.455 0.00 0.00 36.71 3.85
2175 4314 6.033966 GGTAGAATAACAAAGCCAATTTCCG 58.966 40.000 0.00 0.00 0.00 4.30
2179 4318 7.454694 AGAAAGGGTAGAATAACAAAGCCAATT 59.545 33.333 0.00 0.00 31.85 2.32
2182 4321 5.887754 AGAAAGGGTAGAATAACAAAGCCA 58.112 37.500 0.00 0.00 31.85 4.75
2184 4323 6.208797 ACCAAGAAAGGGTAGAATAACAAAGC 59.791 38.462 0.00 0.00 36.72 3.51
2275 4773 2.290367 GTGCAAAGTGTGTCTACATGCA 59.710 45.455 4.63 4.63 40.75 3.96
2279 4777 2.588027 TCGTGCAAAGTGTGTCTACA 57.412 45.000 0.00 0.00 0.00 2.74
2297 4795 2.276430 GCGCGCGTGGTGTTATTC 60.276 61.111 32.35 6.30 0.00 1.75
2354 4862 3.190118 TGCCTTTGGTTTTTGTGCAAAAG 59.810 39.130 9.59 0.00 40.83 2.27
2362 4870 4.083908 CCGATTGATTGCCTTTGGTTTTTG 60.084 41.667 0.00 0.00 0.00 2.44
2364 4872 3.070878 ACCGATTGATTGCCTTTGGTTTT 59.929 39.130 0.00 0.00 0.00 2.43
2441 5139 3.722295 CGACGCCGGTTGCATGTT 61.722 61.111 1.90 0.00 41.33 2.71
2459 5157 2.539081 GGGCCAGAAGGGGAGTTGT 61.539 63.158 4.39 0.00 37.04 3.32
2472 5170 1.656587 AGTGACATCAACTAGGGCCA 58.343 50.000 6.18 0.00 0.00 5.36
2484 5182 9.030301 GTAACTTAATTGCAACAAAAGTGACAT 57.970 29.630 21.88 11.91 33.48 3.06
2485 5183 8.029522 TGTAACTTAATTGCAACAAAAGTGACA 58.970 29.630 23.89 23.89 38.58 3.58
2501 5208 8.259049 TGCAACTATAAGCGTTGTAACTTAAT 57.741 30.769 0.00 0.00 42.73 1.40
2504 5211 6.542852 CATGCAACTATAAGCGTTGTAACTT 58.457 36.000 0.00 0.00 42.73 2.66
2529 5236 2.572104 GGGGTATTGATGGCCTACTAGG 59.428 54.545 3.32 0.00 38.80 3.02
2537 5244 0.555769 TTGGGAGGGGTATTGATGGC 59.444 55.000 0.00 0.00 0.00 4.40
2540 5247 1.231963 GGGTTGGGAGGGGTATTGAT 58.768 55.000 0.00 0.00 0.00 2.57
2562 5269 1.273688 GGACACAAAACAACGGCAAC 58.726 50.000 0.00 0.00 0.00 4.17
2566 5273 1.202348 TGCATGGACACAAAACAACGG 60.202 47.619 0.00 0.00 0.00 4.44
2567 5274 2.118683 CTGCATGGACACAAAACAACG 58.881 47.619 0.00 0.00 0.00 4.10
2570 5277 3.696548 TGTAACTGCATGGACACAAAACA 59.303 39.130 0.00 0.00 0.00 2.83
2643 5351 9.762933 ATTTCAGTGTGCTTATGTTTTTGTTAT 57.237 25.926 0.00 0.00 0.00 1.89
2647 5355 6.614162 GCGATTTCAGTGTGCTTATGTTTTTG 60.614 38.462 0.00 0.00 0.00 2.44
2653 5361 3.120234 TGTGCGATTTCAGTGTGCTTATG 60.120 43.478 0.00 0.00 0.00 1.90
2658 5366 0.588252 AGTGTGCGATTTCAGTGTGC 59.412 50.000 0.00 0.00 0.00 4.57
2670 5378 1.057636 ACGACGAATACAAGTGTGCG 58.942 50.000 0.00 0.00 0.00 5.34
2675 5383 5.518847 CCATGTTCATACGACGAATACAAGT 59.481 40.000 0.00 0.00 0.00 3.16
2761 5469 9.343539 GTCTCCAGTATGCCTTATTTTCTTATT 57.656 33.333 0.00 0.00 31.97 1.40
2774 5482 0.811616 CGGCTTGTCTCCAGTATGCC 60.812 60.000 0.00 0.00 35.94 4.40
2775 5483 0.811616 CCGGCTTGTCTCCAGTATGC 60.812 60.000 0.00 0.00 31.97 3.14
2780 5488 2.032528 TTGCCGGCTTGTCTCCAG 59.967 61.111 29.70 0.00 0.00 3.86
2781 5489 2.281484 GTTGCCGGCTTGTCTCCA 60.281 61.111 29.70 0.07 0.00 3.86
2782 5490 2.281484 TGTTGCCGGCTTGTCTCC 60.281 61.111 29.70 7.72 0.00 3.71
2793 5501 3.364277 GGAGTAGATCCGTGTTGCC 57.636 57.895 0.00 0.00 38.67 4.52
2807 5515 7.585579 TTTACCGTTAGAAAATTTTGGGAGT 57.414 32.000 8.47 1.23 0.00 3.85
2811 5519 9.394477 CTCTCTTTTACCGTTAGAAAATTTTGG 57.606 33.333 8.47 5.44 0.00 3.28
2816 5524 7.904205 TCTCCTCTCTTTTACCGTTAGAAAAT 58.096 34.615 0.00 0.00 0.00 1.82
2818 5526 6.906157 TCTCCTCTCTTTTACCGTTAGAAA 57.094 37.500 0.00 0.00 0.00 2.52
2827 5535 4.011023 GGGCCTTTTCTCCTCTCTTTTAC 58.989 47.826 0.84 0.00 0.00 2.01
2880 5589 8.739039 CCCATGAAGTTGTTACTTGATCAATAA 58.261 33.333 8.96 7.31 44.51 1.40
2895 5604 5.590259 CCTAAGTTGTATCCCCATGAAGTTG 59.410 44.000 0.00 0.00 0.00 3.16
2898 5607 5.131142 AGACCTAAGTTGTATCCCCATGAAG 59.869 44.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.