Multiple sequence alignment - TraesCS3D01G395200

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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 TraesCS3D01G395200 chr3D 100.000 3134 0 0 1 3134 510352042 510355175 0.000000e+00 5788
1 TraesCS3D01G395200 chr7D 90.428 2079 188 6 162 2238 505427982 505425913 0.000000e+00 2726
2 TraesCS3D01G395200 chr7D 90.274 1604 150 6 163 1763 613279223 613280823 0.000000e+00 2093
3 TraesCS3D01G395200 chr7D 89.508 1382 135 9 1759 3134 613282564 613283941 0.000000e+00 1740
4 TraesCS3D01G395200 chr7D 73.483 2176 500 55 1003 3134 626920134 626917992 0.000000e+00 750
5 TraesCS3D01G395200 chr7D 89.506 162 17 0 1 162 613278929 613279090 4.100000e-49 206
6 TraesCS3D01G395200 chr7D 88.272 162 17 1 1 162 505428273 505428114 3.190000e-45 193
7 TraesCS3D01G395200 chr6B 82.145 3002 476 47 156 3134 655900432 655897468 0.000000e+00 2519
8 TraesCS3D01G395200 chr6B 83.510 2080 309 25 1061 3131 119541632 119543686 0.000000e+00 1910
9 TraesCS3D01G395200 chr5B 82.199 2792 458 27 368 3134 556057840 556055063 0.000000e+00 2366
10 TraesCS3D01G395200 chr4B 83.669 2529 386 22 424 2941 535189875 535187363 0.000000e+00 2357
11 TraesCS3D01G395200 chr3A 84.330 2425 351 18 156 2572 485051291 485053694 0.000000e+00 2346
12 TraesCS3D01G395200 chr3A 85.988 521 68 4 2607 3126 485053696 485054212 1.270000e-153 553
13 TraesCS3D01G395200 chr7A 90.412 1554 136 12 1588 3134 162391590 162393137 0.000000e+00 2032
14 TraesCS3D01G395200 chr1B 83.191 1755 275 18 210 1954 492745566 492743822 0.000000e+00 1589
15 TraesCS3D01G395200 chr1B 84.936 1175 163 12 1967 3134 492714251 492713084 0.000000e+00 1177
16 TraesCS3D01G395200 chr3B 70.451 731 192 22 1007 1725 567273950 567274668 7.050000e-27 132


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 TraesCS3D01G395200 chr3D 510352042 510355175 3133 False 5788.000000 5788 100.000000 1 3134 1 chr3D.!!$F1 3133
1 TraesCS3D01G395200 chr7D 505425913 505428273 2360 True 1459.500000 2726 89.350000 1 2238 2 chr7D.!!$R2 2237
2 TraesCS3D01G395200 chr7D 613278929 613283941 5012 False 1346.333333 2093 89.762667 1 3134 3 chr7D.!!$F1 3133
3 TraesCS3D01G395200 chr7D 626917992 626920134 2142 True 750.000000 750 73.483000 1003 3134 1 chr7D.!!$R1 2131
4 TraesCS3D01G395200 chr6B 655897468 655900432 2964 True 2519.000000 2519 82.145000 156 3134 1 chr6B.!!$R1 2978
5 TraesCS3D01G395200 chr6B 119541632 119543686 2054 False 1910.000000 1910 83.510000 1061 3131 1 chr6B.!!$F1 2070
6 TraesCS3D01G395200 chr5B 556055063 556057840 2777 True 2366.000000 2366 82.199000 368 3134 1 chr5B.!!$R1 2766
7 TraesCS3D01G395200 chr4B 535187363 535189875 2512 True 2357.000000 2357 83.669000 424 2941 1 chr4B.!!$R1 2517
8 TraesCS3D01G395200 chr3A 485051291 485054212 2921 False 1449.500000 2346 85.159000 156 3126 2 chr3A.!!$F1 2970
9 TraesCS3D01G395200 chr7A 162391590 162393137 1547 False 2032.000000 2032 90.412000 1588 3134 1 chr7A.!!$F1 1546
10 TraesCS3D01G395200 chr1B 492743822 492745566 1744 True 1589.000000 1589 83.191000 210 1954 1 chr1B.!!$R2 1744
11 TraesCS3D01G395200 chr1B 492713084 492714251 1167 True 1177.000000 1177 84.936000 1967 3134 1 chr1B.!!$R1 1167

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
760 902 0.108019 AAACGTTCCAGTGGGAGGAC 59.892 55.0 17.27 6.51 46.01 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 4255 2.024369 ACCCCATCTTCCCCATTGTTAC 60.024 50.0 0.0 0.0 0.0 2.5 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
66 67 9.980780 GAGATTCAGAAAAGTTAGTAGAAATGC 57.019 33.333 0.00 0.00 0.00 3.56
78 79 3.990469 AGTAGAAATGCTGACAACTCACG 59.010 43.478 0.00 0.00 0.00 4.35
105 106 3.814005 AATCAATTGCAAGGATGAGGC 57.186 42.857 14.91 0.00 0.00 4.70
111 112 1.221840 GCAAGGATGAGGCGGAGAA 59.778 57.895 0.00 0.00 0.00 2.87
118 119 5.825593 AGGATGAGGCGGAGAATAATAAA 57.174 39.130 0.00 0.00 0.00 1.40
154 155 7.013823 AGATGATTTAGATGGGTGGATAGTG 57.986 40.000 0.00 0.00 0.00 2.74
185 318 2.953284 AGAGGAATGGGCTGATGATG 57.047 50.000 0.00 0.00 0.00 3.07
196 329 3.609853 GGCTGATGATGTGGTTAGTTGA 58.390 45.455 0.00 0.00 0.00 3.18
222 355 2.223464 TTAAGGCCCACCCCAGATGC 62.223 60.000 0.00 0.00 36.11 3.91
241 374 1.271054 GCTGAAGAAAGCCTGGTGAGA 60.271 52.381 0.00 0.00 37.20 3.27
243 376 2.301296 CTGAAGAAAGCCTGGTGAGAGA 59.699 50.000 0.00 0.00 0.00 3.10
249 386 1.920835 GCCTGGTGAGAGAAGGGGT 60.921 63.158 0.00 0.00 0.00 4.95
255 392 1.276622 GTGAGAGAAGGGGTAAGGCA 58.723 55.000 0.00 0.00 0.00 4.75
330 467 1.888512 TGATTGCAAAGAAGAGGTGCC 59.111 47.619 1.71 0.00 37.48 5.01
364 503 0.674895 CACCGCCAGAAGAAGAAGGG 60.675 60.000 0.00 0.00 0.00 3.95
435 575 1.408822 GGGGGTACAGAGAATTGGCAG 60.409 57.143 0.00 0.00 0.00 4.85
454 594 4.406003 GGCAGTATAGGAAGAAGGAAGACA 59.594 45.833 0.00 0.00 0.00 3.41
481 621 6.272558 AGGAGATGGGTTTAGAAACTACAACT 59.727 38.462 5.20 8.37 38.89 3.16
519 659 2.399600 ATTGGGGGCAAGGCTTTGGA 62.400 55.000 10.89 0.00 34.79 3.53
571 711 3.181471 CCAGCAAGATCAGAAGTATCCGT 60.181 47.826 0.00 0.00 0.00 4.69
724 866 3.667960 GCGTTTACTCTCAGCATTGTTGG 60.668 47.826 0.40 0.00 0.00 3.77
741 883 1.440618 TGGCCCAACTTACTCAAGGA 58.559 50.000 0.00 0.00 35.97 3.36
748 890 4.024302 CCCAACTTACTCAAGGAAACGTTC 60.024 45.833 0.00 0.00 35.97 3.95
760 902 0.108019 AAACGTTCCAGTGGGAGGAC 59.892 55.000 17.27 6.51 46.01 3.85
836 978 2.235898 AGATGGTCAGAGGAGAAAGCAC 59.764 50.000 0.00 0.00 0.00 4.40
858 1000 1.774254 TGTCTGCAAGGAGAGGGAAAA 59.226 47.619 0.00 0.00 0.00 2.29
929 1071 0.767375 GCATGGAAGGAGGATAGCCA 59.233 55.000 0.00 0.00 36.29 4.75
943 1085 3.967987 GGATAGCCAAAGGGAGAGAGTTA 59.032 47.826 0.00 0.00 35.59 2.24
947 1089 2.169561 GCCAAAGGGAGAGAGTTAGGAG 59.830 54.545 0.00 0.00 35.59 3.69
954 1096 2.583143 GAGAGAGTTAGGAGGAGGAGC 58.417 57.143 0.00 0.00 0.00 4.70
983 1125 5.363101 TGAAAGATGGTAGCAAGATAGCTG 58.637 41.667 0.00 0.00 46.11 4.24
993 1138 1.926426 AAGATAGCTGTGGGGGTGCC 61.926 60.000 0.00 0.00 0.00 5.01
1084 1229 3.450457 TGCAGTGTGTGGAAAAAGGAATT 59.550 39.130 0.00 0.00 0.00 2.17
1131 1276 3.769300 TGAAGCAGATGAAGCTAGTACCA 59.231 43.478 0.00 0.00 42.53 3.25
1226 1371 0.400381 AATCCCAATCCAATGGCCCC 60.400 55.000 0.00 0.00 39.26 5.80
1276 1421 2.262423 AACTCAACTGCTGGAAGGAC 57.738 50.000 0.00 0.00 0.00 3.85
1352 1497 4.461781 CAGTGCCTTTTTGATGAGATTCCT 59.538 41.667 0.00 0.00 0.00 3.36
1353 1498 4.461781 AGTGCCTTTTTGATGAGATTCCTG 59.538 41.667 0.00 0.00 0.00 3.86
1440 1585 7.631377 GCAGTGATAAACATAAAGAAATGGGCT 60.631 37.037 0.00 0.00 0.00 5.19
1466 1611 2.887152 ACTCACAAGCAGTTGGGAAATC 59.113 45.455 0.00 0.00 45.72 2.17
1478 1624 3.126001 TGGGAAATCACACACTGTCTC 57.874 47.619 0.00 0.00 0.00 3.36
1538 1685 4.431416 TCTTTGGTATGTGTGAAGTGGT 57.569 40.909 0.00 0.00 0.00 4.16
1712 1862 1.680249 GGAGAAGGTGGTTGAGATGGC 60.680 57.143 0.00 0.00 0.00 4.40
1777 3672 3.071874 TGGATTGTGTGGGAGATGAAC 57.928 47.619 0.00 0.00 0.00 3.18
1794 3689 9.057089 GGAGATGAACTTAGAAAGAGACAAAAA 57.943 33.333 0.00 0.00 0.00 1.94
1844 3745 8.317679 CAATAGAGAGGCTATTAACTTAGGCAT 58.682 37.037 11.09 1.29 45.71 4.40
1854 3755 7.657761 GCTATTAACTTAGGCATCTTGAGCTTA 59.342 37.037 0.00 0.00 0.00 3.09
1916 3819 3.593442 TTTGACCCAACAGGAACAGAT 57.407 42.857 0.00 0.00 39.89 2.90
1965 3868 3.058160 GCGGACATGGCAGCAGTT 61.058 61.111 19.57 0.00 0.00 3.16
1985 3888 6.349611 GCAGTTATGAAGAGGATGCAAGAAAA 60.350 38.462 0.00 0.00 32.58 2.29
2016 3919 5.482175 AGAGAAAGCTAGACAGAAAGCCTTA 59.518 40.000 0.00 0.00 39.64 2.69
2021 3924 4.775253 AGCTAGACAGAAAGCCTTAAGAGT 59.225 41.667 3.36 0.00 39.64 3.24
2133 4036 6.329496 GTGTGTGGAAAAAGTTGAAAGATGA 58.671 36.000 0.00 0.00 0.00 2.92
2137 4040 7.922811 GTGTGGAAAAAGTTGAAAGATGAGAAT 59.077 33.333 0.00 0.00 0.00 2.40
2166 4069 8.797438 AGAGAAAAGGAAATAGAAAACATCACC 58.203 33.333 0.00 0.00 0.00 4.02
2196 4099 4.006247 ACTGGAGAAGATGGAAGAGGAT 57.994 45.455 0.00 0.00 0.00 3.24
2276 4207 3.902881 ATCAGTGGACTCCTTTGCTAG 57.097 47.619 0.00 0.00 0.00 3.42
2289 4220 0.909623 TTGCTAGTAGGTTGGGCCTC 59.090 55.000 4.53 0.00 46.96 4.70
2302 4233 3.987594 GGCCTCAACCCTGAAGATT 57.012 52.632 0.00 0.00 0.00 2.40
2324 4255 2.836981 AGAAGGAAGGAGATGACACTGG 59.163 50.000 0.00 0.00 0.00 4.00
2351 4282 0.256177 GGGGAAGATGGGGTGAGAAC 59.744 60.000 0.00 0.00 0.00 3.01
2367 4298 4.931601 GTGAGAACATGCAACAGACTCATA 59.068 41.667 13.79 0.00 35.82 2.15
2440 4373 9.213799 GGCAAAAACAATTATGGTAAGATTCAA 57.786 29.630 0.00 0.00 0.00 2.69
2450 4383 6.927294 ATGGTAAGATTCAAAACTCCGATC 57.073 37.500 0.00 0.00 0.00 3.69
2602 4575 7.701539 TGCTCATATTAAGCAAAAAGAGGAA 57.298 32.000 7.01 0.00 46.29 3.36
2603 4576 7.538575 TGCTCATATTAAGCAAAAAGAGGAAC 58.461 34.615 7.01 0.00 46.29 3.62
2604 4577 6.975197 GCTCATATTAAGCAAAAAGAGGAACC 59.025 38.462 2.60 0.00 39.61 3.62
2605 4578 7.362920 GCTCATATTAAGCAAAAAGAGGAACCA 60.363 37.037 2.60 0.00 39.61 3.67
2606 4579 8.415950 TCATATTAAGCAAAAAGAGGAACCAA 57.584 30.769 0.00 0.00 0.00 3.67
2607 4580 8.303876 TCATATTAAGCAAAAAGAGGAACCAAC 58.696 33.333 0.00 0.00 0.00 3.77
2608 4581 5.923733 TTAAGCAAAAAGAGGAACCAACA 57.076 34.783 0.00 0.00 0.00 3.33
2609 4582 4.391405 AAGCAAAAAGAGGAACCAACAG 57.609 40.909 0.00 0.00 0.00 3.16
2610 4583 3.365472 AGCAAAAAGAGGAACCAACAGT 58.635 40.909 0.00 0.00 0.00 3.55
2611 4584 3.131046 AGCAAAAAGAGGAACCAACAGTG 59.869 43.478 0.00 0.00 0.00 3.66
2612 4585 3.447742 CAAAAAGAGGAACCAACAGTGC 58.552 45.455 0.00 0.00 0.00 4.40
2613 4586 2.435372 AAAGAGGAACCAACAGTGCA 57.565 45.000 0.00 0.00 0.00 4.57
2614 4587 2.435372 AAGAGGAACCAACAGTGCAA 57.565 45.000 0.00 0.00 0.00 4.08
2615 4588 2.435372 AGAGGAACCAACAGTGCAAA 57.565 45.000 0.00 0.00 0.00 3.68
2616 4589 2.733956 AGAGGAACCAACAGTGCAAAA 58.266 42.857 0.00 0.00 0.00 2.44
2617 4590 3.096092 AGAGGAACCAACAGTGCAAAAA 58.904 40.909 0.00 0.00 0.00 1.94
2618 4591 3.131046 AGAGGAACCAACAGTGCAAAAAG 59.869 43.478 0.00 0.00 0.00 2.27
2619 4592 3.096092 AGGAACCAACAGTGCAAAAAGA 58.904 40.909 0.00 0.00 0.00 2.52
2790 4764 2.091541 ACCAGTGTGAAACCAACTGTG 58.908 47.619 0.00 0.00 39.75 3.66
2797 4776 7.255451 CCAGTGTGAAACCAACTGTGTATATTT 60.255 37.037 0.00 0.00 39.75 1.40
2823 4803 5.546499 GGGGAAAAAGGGTAGAAAAGGAAAT 59.454 40.000 0.00 0.00 0.00 2.17
2824 4804 6.043938 GGGGAAAAAGGGTAGAAAAGGAAATT 59.956 38.462 0.00 0.00 0.00 1.82
2825 4805 7.236019 GGGGAAAAAGGGTAGAAAAGGAAATTA 59.764 37.037 0.00 0.00 0.00 1.40
2881 4863 3.954258 GGATTGGGTCCCACATTAAGAAG 59.046 47.826 11.24 0.00 41.50 2.85
2884 4866 4.946160 TGGGTCCCACATTAAGAAGAAT 57.054 40.909 6.47 0.00 0.00 2.40
2958 4946 7.428020 CAAGAGACCATCAAAAATGAGTTCAA 58.572 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.715657 TCTCTCATTCTTTCTATCTCTTCTGC 58.284 38.462 0.00 0.00 0.00 4.26
54 55 5.633601 CGTGAGTTGTCAGCATTTCTACTAA 59.366 40.000 0.00 0.00 31.53 2.24
66 67 2.823196 TTTTGCACGTGAGTTGTCAG 57.177 45.000 22.23 0.00 46.40 3.51
154 155 7.038048 CAGCCCATTCCTCTAAAATTTCTTTC 58.962 38.462 0.00 0.00 0.00 2.62
185 318 1.897560 AAGCCTGCTCAACTAACCAC 58.102 50.000 0.00 0.00 0.00 4.16
213 346 1.101331 GCTTTCTTCAGCATCTGGGG 58.899 55.000 0.00 0.00 39.83 4.96
222 355 2.301296 TCTCTCACCAGGCTTTCTTCAG 59.699 50.000 0.00 0.00 0.00 3.02
241 374 0.834687 TCGTGTGCCTTACCCCTTCT 60.835 55.000 0.00 0.00 0.00 2.85
243 376 1.677552 CTCGTGTGCCTTACCCCTT 59.322 57.895 0.00 0.00 0.00 3.95
255 392 0.691078 ATATCCACAGGGCCTCGTGT 60.691 55.000 24.69 12.02 42.00 4.49
344 481 1.301677 CCTTCTTCTTCTGGCGGTGC 61.302 60.000 0.00 0.00 0.00 5.01
364 503 0.034089 CCCCAAACCTGTCCATCTCC 60.034 60.000 0.00 0.00 0.00 3.71
422 562 6.166984 TCTTCCTATACTGCCAATTCTCTG 57.833 41.667 0.00 0.00 0.00 3.35
435 575 6.130569 TCCTCTGTCTTCCTTCTTCCTATAC 58.869 44.000 0.00 0.00 0.00 1.47
454 594 6.023603 TGTAGTTTCTAAACCCATCTCCTCT 58.976 40.000 2.02 0.00 39.71 3.69
481 621 0.556258 TCCTTCCTGGCCTCTCGATA 59.444 55.000 3.32 0.00 35.26 2.92
519 659 2.263741 CCCTTGCGAGCTGCTGTTT 61.264 57.895 7.01 0.00 46.63 2.83
571 711 2.927007 TCCTCAACTCCTCCTTCTCCTA 59.073 50.000 0.00 0.00 0.00 2.94
586 726 5.477607 TTATCTTTGTCCGTCTTCCTCAA 57.522 39.130 0.00 0.00 0.00 3.02
708 850 0.610232 GGGCCAACAATGCTGAGAGT 60.610 55.000 4.39 0.00 0.00 3.24
724 866 2.225727 CGTTTCCTTGAGTAAGTTGGGC 59.774 50.000 0.00 0.00 31.80 5.36
741 883 0.108019 GTCCTCCCACTGGAACGTTT 59.892 55.000 0.46 0.00 41.17 3.60
748 890 0.902531 ACATTACGTCCTCCCACTGG 59.097 55.000 0.00 0.00 0.00 4.00
760 902 4.385447 CCCACTTTGCAAATTGACATTACG 59.615 41.667 25.99 10.68 0.00 3.18
852 994 3.005791 CCCATTGTTGTCTCTGTTTTCCC 59.994 47.826 0.00 0.00 0.00 3.97
858 1000 1.774254 TGACCCCATTGTTGTCTCTGT 59.226 47.619 4.93 0.00 0.00 3.41
929 1071 3.310288 CCTCCTCCTAACTCTCTCCCTTT 60.310 52.174 0.00 0.00 0.00 3.11
943 1085 1.661463 TCATTTGTGCTCCTCCTCCT 58.339 50.000 0.00 0.00 0.00 3.69
947 1089 3.129988 CCATCTTTCATTTGTGCTCCTCC 59.870 47.826 0.00 0.00 0.00 4.30
954 1096 6.258230 TCTTGCTACCATCTTTCATTTGTG 57.742 37.500 0.00 0.00 0.00 3.33
983 1125 3.224007 ATCCTGTTGGCACCCCCAC 62.224 63.158 0.00 0.00 45.34 4.61
1084 1229 2.833943 AGGTGCAGTCATCTGTGATGTA 59.166 45.455 7.33 0.00 43.05 2.29
1131 1276 4.822685 TGCAGCATATCCCACAAATTTT 57.177 36.364 0.00 0.00 0.00 1.82
1185 1330 8.314021 GGATTTTCAAGTTCCACATTATCCTTT 58.686 33.333 0.00 0.00 0.00 3.11
1226 1371 3.328382 TCCCAGATTTAACAGTCACCG 57.672 47.619 0.00 0.00 0.00 4.94
1352 1497 1.271543 CCATCAGTCTGCCCTTGTTCA 60.272 52.381 0.00 0.00 0.00 3.18
1353 1498 1.003580 TCCATCAGTCTGCCCTTGTTC 59.996 52.381 0.00 0.00 0.00 3.18
1440 1585 2.426738 CCCAACTGCTTGTGAGTCAAAA 59.573 45.455 0.00 0.00 35.48 2.44
1466 1611 2.795175 AGTAACCGAGACAGTGTGTG 57.205 50.000 0.00 0.00 0.00 3.82
1478 1624 4.007659 AGGCACCTTATCAAAAGTAACCG 58.992 43.478 0.00 0.00 0.00 4.44
1538 1685 1.131638 CACTGGCCCTAAGGATGCTA 58.868 55.000 0.00 0.00 33.47 3.49
1638 1788 8.807118 AGATCTCTGTCAGTTATTTCAGTGTAA 58.193 33.333 0.00 0.00 0.00 2.41
1712 1862 7.864108 TGTCTTTTATGATCACCATACCAAG 57.136 36.000 0.00 0.00 37.46 3.61
1794 3689 5.531287 GGTATCTCCTGAGTTGTTTGTGTTT 59.469 40.000 0.00 0.00 0.00 2.83
1795 3690 5.063880 GGTATCTCCTGAGTTGTTTGTGTT 58.936 41.667 0.00 0.00 0.00 3.32
1796 3691 4.102524 TGGTATCTCCTGAGTTGTTTGTGT 59.897 41.667 0.00 0.00 37.07 3.72
1797 3692 4.641396 TGGTATCTCCTGAGTTGTTTGTG 58.359 43.478 0.00 0.00 37.07 3.33
1798 3693 4.974645 TGGTATCTCCTGAGTTGTTTGT 57.025 40.909 0.00 0.00 37.07 2.83
1799 3694 7.331026 TCTATTGGTATCTCCTGAGTTGTTTG 58.669 38.462 0.00 0.00 37.07 2.93
1844 3745 5.764686 TCTTCAAATTGCACTAAGCTCAAGA 59.235 36.000 3.19 0.00 45.94 3.02
1887 3789 2.426738 CTGTTGGGTCAAAAGAACTGCA 59.573 45.455 0.00 0.00 30.76 4.41
1900 3802 2.224867 CCTTGATCTGTTCCTGTTGGGT 60.225 50.000 0.00 0.00 36.25 4.51
1916 3819 2.894731 TCCTTGCTTCTCTCTCCTTGA 58.105 47.619 0.00 0.00 0.00 3.02
1950 3853 2.042686 TCATAACTGCTGCCATGTCC 57.957 50.000 0.00 0.00 0.00 4.02
1954 3857 2.507058 TCCTCTTCATAACTGCTGCCAT 59.493 45.455 0.00 0.00 0.00 4.40
1965 3868 7.830697 TCTTCATTTTCTTGCATCCTCTTCATA 59.169 33.333 0.00 0.00 0.00 2.15
1985 3888 6.849085 TCTGTCTAGCTTTCTCTTCTTCAT 57.151 37.500 0.00 0.00 0.00 2.57
2016 3919 5.896073 TTCTTTTCTCCTCTTGGACTCTT 57.104 39.130 0.00 0.00 37.46 2.85
2021 3924 5.310594 TCTCCAATTCTTTTCTCCTCTTGGA 59.689 40.000 0.00 0.00 38.58 3.53
2105 4008 6.605594 TCTTTCAACTTTTTCCACACACCTAT 59.394 34.615 0.00 0.00 0.00 2.57
2108 4011 5.066968 TCTTTCAACTTTTTCCACACACC 57.933 39.130 0.00 0.00 0.00 4.16
2166 4069 3.681897 CCATCTTCTCCAGTTCAGTTTCG 59.318 47.826 0.00 0.00 0.00 3.46
2289 4220 5.045578 TCCTTCCTTCTAATCTTCAGGGTTG 60.046 44.000 0.00 0.00 0.00 3.77
2302 4233 4.026744 CCAGTGTCATCTCCTTCCTTCTA 58.973 47.826 0.00 0.00 0.00 2.10
2324 4255 2.024369 ACCCCATCTTCCCCATTGTTAC 60.024 50.000 0.00 0.00 0.00 2.50
2351 4282 7.543947 TGTTTATCTATGAGTCTGTTGCATG 57.456 36.000 0.00 0.00 0.00 4.06
2367 4298 8.324306 TCCTCAATCTTCACATCTTGTTTATCT 58.676 33.333 0.00 0.00 0.00 1.98
2440 4373 2.092375 GGAATTCCCCTGATCGGAGTTT 60.092 50.000 14.03 0.00 30.15 2.66
2446 4379 3.567478 AAAGAGGAATTCCCCTGATCG 57.433 47.619 21.22 0.00 36.49 3.69
2450 4383 6.010219 TGAAAAGTAAAGAGGAATTCCCCTG 58.990 40.000 21.22 0.00 36.49 4.45
2580 4552 8.055279 TGGTTCCTCTTTTTGCTTAATATGAG 57.945 34.615 0.00 0.00 0.00 2.90
2581 4553 8.303876 GTTGGTTCCTCTTTTTGCTTAATATGA 58.696 33.333 0.00 0.00 0.00 2.15
2582 4554 8.087750 TGTTGGTTCCTCTTTTTGCTTAATATG 58.912 33.333 0.00 0.00 0.00 1.78
2583 4555 8.189119 TGTTGGTTCCTCTTTTTGCTTAATAT 57.811 30.769 0.00 0.00 0.00 1.28
2584 4556 7.286775 ACTGTTGGTTCCTCTTTTTGCTTAATA 59.713 33.333 0.00 0.00 0.00 0.98
2585 4557 6.098266 ACTGTTGGTTCCTCTTTTTGCTTAAT 59.902 34.615 0.00 0.00 0.00 1.40
2586 4558 5.420739 ACTGTTGGTTCCTCTTTTTGCTTAA 59.579 36.000 0.00 0.00 0.00 1.85
2587 4559 4.953579 ACTGTTGGTTCCTCTTTTTGCTTA 59.046 37.500 0.00 0.00 0.00 3.09
2588 4560 3.769300 ACTGTTGGTTCCTCTTTTTGCTT 59.231 39.130 0.00 0.00 0.00 3.91
2589 4561 3.131046 CACTGTTGGTTCCTCTTTTTGCT 59.869 43.478 0.00 0.00 0.00 3.91
2590 4562 3.447742 CACTGTTGGTTCCTCTTTTTGC 58.552 45.455 0.00 0.00 0.00 3.68
2600 4573 4.241681 TGTTCTTTTTGCACTGTTGGTTC 58.758 39.130 0.00 0.00 0.00 3.62
2601 4574 4.264460 TGTTCTTTTTGCACTGTTGGTT 57.736 36.364 0.00 0.00 0.00 3.67
2602 4575 3.951775 TGTTCTTTTTGCACTGTTGGT 57.048 38.095 0.00 0.00 0.00 3.67
2603 4576 6.042143 AGTAATGTTCTTTTTGCACTGTTGG 58.958 36.000 0.00 0.00 0.00 3.77
2604 4577 6.751425 TGAGTAATGTTCTTTTTGCACTGTTG 59.249 34.615 0.00 0.00 0.00 3.33
2605 4578 6.862209 TGAGTAATGTTCTTTTTGCACTGTT 58.138 32.000 0.00 0.00 0.00 3.16
2606 4579 6.449635 TGAGTAATGTTCTTTTTGCACTGT 57.550 33.333 0.00 0.00 0.00 3.55
2607 4580 7.648908 TCAATGAGTAATGTTCTTTTTGCACTG 59.351 33.333 0.00 0.00 0.00 3.66
2608 4581 7.649306 GTCAATGAGTAATGTTCTTTTTGCACT 59.351 33.333 0.00 0.00 0.00 4.40
2609 4582 7.434897 TGTCAATGAGTAATGTTCTTTTTGCAC 59.565 33.333 0.00 0.00 0.00 4.57
2610 4583 7.434897 GTGTCAATGAGTAATGTTCTTTTTGCA 59.565 33.333 0.00 0.00 0.00 4.08
2611 4584 7.649306 AGTGTCAATGAGTAATGTTCTTTTTGC 59.351 33.333 0.00 0.00 0.00 3.68
2612 4585 8.961092 CAGTGTCAATGAGTAATGTTCTTTTTG 58.039 33.333 0.00 0.00 0.00 2.44
2613 4586 8.137437 CCAGTGTCAATGAGTAATGTTCTTTTT 58.863 33.333 0.89 0.00 0.00 1.94
2614 4587 7.502226 TCCAGTGTCAATGAGTAATGTTCTTTT 59.498 33.333 0.89 0.00 0.00 2.27
2615 4588 6.998074 TCCAGTGTCAATGAGTAATGTTCTTT 59.002 34.615 0.89 0.00 0.00 2.52
2616 4589 6.533730 TCCAGTGTCAATGAGTAATGTTCTT 58.466 36.000 0.89 0.00 0.00 2.52
2617 4590 6.014242 TCTCCAGTGTCAATGAGTAATGTTCT 60.014 38.462 0.89 0.00 0.00 3.01
2618 4591 6.091441 GTCTCCAGTGTCAATGAGTAATGTTC 59.909 42.308 0.89 0.00 0.00 3.18
2619 4592 5.934625 GTCTCCAGTGTCAATGAGTAATGTT 59.065 40.000 0.89 0.00 0.00 2.71
2790 4764 6.675565 TCTACCCTTTTTCCCCCAAATATAC 58.324 40.000 0.00 0.00 0.00 1.47
2797 4776 3.438816 CCTTTTCTACCCTTTTTCCCCCA 60.439 47.826 0.00 0.00 0.00 4.96
2904 4889 9.211485 GACCAATGAAATCAATTTTTGTCTCAT 57.789 29.630 0.00 0.00 0.00 2.90
2910 4897 7.192148 TGCAGACCAATGAAATCAATTTTTG 57.808 32.000 0.00 0.00 0.00 2.44
2958 4946 7.678194 CACGAATTGTGTAGTTCATTTTTGT 57.322 32.000 0.00 0.00 43.88 2.83
2978 4967 0.540365 AAGTTCCTACCCCGACACGA 60.540 55.000 0.00 0.00 0.00 4.35
2979 4968 0.319405 AAAGTTCCTACCCCGACACG 59.681 55.000 0.00 0.00 0.00 4.49
2984 4973 2.568509 TCCAACTAAAGTTCCTACCCCG 59.431 50.000 0.00 0.00 35.83 5.73


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

AutoCloner maintained by Alex Coulton.