Multiple sequence alignment - TraesCS3D01G371600

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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 TraesCS3D01G371600 chr3D 100.000 4088 0 0 1 4088 484820439 484824526 0.000000e+00 7550
1 TraesCS3D01G371600 chr3B 92.948 3715 140 56 2 3684 647678179 647681803 0.000000e+00 5297
2 TraesCS3D01G371600 chr3B 85.149 303 21 8 3798 4088 647694737 647695027 5.170000e-74 289
3 TraesCS3D01G371600 chr3A 90.118 4169 210 80 2 4088 627862340 627866388 0.000000e+00 5230
4 TraesCS3D01G371600 chr1D 78.252 1007 157 41 1938 2905 367430161 367429178 1.270000e-164 590
5 TraesCS3D01G371600 chr1B 77.888 1004 164 41 1938 2905 491983648 491982667 4.580000e-159 571
6 TraesCS3D01G371600 chr1B 88.660 97 11 0 1531 1627 491983948 491983852 7.180000e-23 119
7 TraesCS3D01G371600 chr1A 77.854 1016 149 47 1938 2905 466928349 466927362 9.920000e-156 560
8 TraesCS3D01G371600 chr1A 85.455 110 15 1 1519 1627 466928725 466928616 3.340000e-21 113
9 TraesCS3D01G371600 chr2D 86.508 126 17 0 2590 2715 644095596 644095721 5.510000e-29 139
10 TraesCS3D01G371600 chr7D 84.444 135 20 1 2581 2715 412885774 412885641 9.220000e-27 132
11 TraesCS3D01G371600 chr7B 84.444 135 20 1 2581 2715 427302955 427302822 9.220000e-27 132
12 TraesCS3D01G371600 chr2B 84.921 126 19 0 2590 2715 792990348 792990223 1.190000e-25 128


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 TraesCS3D01G371600 chr3D 484820439 484824526 4087 False 7550.0 7550 100.0000 1 4088 1 chr3D.!!$F1 4087
1 TraesCS3D01G371600 chr3B 647678179 647681803 3624 False 5297.0 5297 92.9480 2 3684 1 chr3B.!!$F1 3682
2 TraesCS3D01G371600 chr3A 627862340 627866388 4048 False 5230.0 5230 90.1180 2 4088 1 chr3A.!!$F1 4086
3 TraesCS3D01G371600 chr1D 367429178 367430161 983 True 590.0 590 78.2520 1938 2905 1 chr1D.!!$R1 967
4 TraesCS3D01G371600 chr1B 491982667 491983948 1281 True 345.0 571 83.2740 1531 2905 2 chr1B.!!$R1 1374
5 TraesCS3D01G371600 chr1A 466927362 466928725 1363 True 336.5 560 81.6545 1519 2905 2 chr1A.!!$R1 1386

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
480 496 0.385390 GGCGGCAACTAATTGGGATG 59.615 55.000 3.07 0.0 36.23 3.51 F
1237 1253 0.251634 GGGCAAGTCTTCCTCCTGAG 59.748 60.000 0.00 0.0 0.00 3.35 F
1809 1903 1.000274 GCCTCGTTTCATGCAAACCTT 60.000 47.619 12.27 0.0 41.40 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2422 0.817654 TCAGCTCGTATGTCACCTGG 59.182 55.0 0.0 0.0 0.00 4.45 R
2907 3094 1.557443 GCTTCGGTCTTGGTGTCACG 61.557 60.0 0.0 0.0 0.00 4.35 R
3740 3999 0.324830 GGAGTAGGTCCCTGTCTGCT 60.325 60.0 0.0 0.0 39.88 4.24 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
22 23 1.107945 CTGGTTTCCGTGGGTTTTGT 58.892 50.000 0.00 0.00 0.00 2.83
45 46 1.134936 GGTTCTGTTTTTGTGCGGGTT 60.135 47.619 0.00 0.00 0.00 4.11
46 47 1.923864 GTTCTGTTTTTGTGCGGGTTG 59.076 47.619 0.00 0.00 0.00 3.77
47 48 1.178276 TCTGTTTTTGTGCGGGTTGT 58.822 45.000 0.00 0.00 0.00 3.32
48 49 1.135257 TCTGTTTTTGTGCGGGTTGTG 60.135 47.619 0.00 0.00 0.00 3.33
49 50 0.603569 TGTTTTTGTGCGGGTTGTGT 59.396 45.000 0.00 0.00 0.00 3.72
50 51 1.000955 TGTTTTTGTGCGGGTTGTGTT 59.999 42.857 0.00 0.00 0.00 3.32
51 52 1.656594 GTTTTTGTGCGGGTTGTGTTC 59.343 47.619 0.00 0.00 0.00 3.18
52 53 1.178276 TTTTGTGCGGGTTGTGTTCT 58.822 45.000 0.00 0.00 0.00 3.01
53 54 0.453793 TTTGTGCGGGTTGTGTTCTG 59.546 50.000 0.00 0.00 0.00 3.02
54 55 0.393132 TTGTGCGGGTTGTGTTCTGA 60.393 50.000 0.00 0.00 0.00 3.27
55 56 0.813610 TGTGCGGGTTGTGTTCTGAG 60.814 55.000 0.00 0.00 0.00 3.35
186 200 1.228657 GCGGAAGAGCGTGGACTTTT 61.229 55.000 0.00 0.00 0.00 2.27
426 442 1.134848 GTTTGGTTCTGCAAGGCACAA 60.135 47.619 0.00 0.00 33.79 3.33
480 496 0.385390 GGCGGCAACTAATTGGGATG 59.615 55.000 3.07 0.00 36.23 3.51
481 497 0.385390 GCGGCAACTAATTGGGATGG 59.615 55.000 0.00 0.00 36.23 3.51
482 498 1.762708 CGGCAACTAATTGGGATGGT 58.237 50.000 0.00 0.00 36.23 3.55
483 499 2.099405 CGGCAACTAATTGGGATGGTT 58.901 47.619 0.00 0.00 36.23 3.67
485 501 3.428862 CGGCAACTAATTGGGATGGTTTC 60.429 47.826 0.00 0.00 36.23 2.78
486 502 3.513515 GGCAACTAATTGGGATGGTTTCA 59.486 43.478 0.00 0.00 36.23 2.69
487 503 4.162131 GGCAACTAATTGGGATGGTTTCAT 59.838 41.667 0.00 0.00 36.23 2.57
488 504 5.338300 GGCAACTAATTGGGATGGTTTCATT 60.338 40.000 0.00 0.00 36.23 2.57
489 505 6.172630 GCAACTAATTGGGATGGTTTCATTT 58.827 36.000 0.00 0.00 36.23 2.32
490 506 6.313658 GCAACTAATTGGGATGGTTTCATTTC 59.686 38.462 0.00 0.00 36.23 2.17
491 507 7.385267 CAACTAATTGGGATGGTTTCATTTCA 58.615 34.615 0.00 0.00 30.82 2.69
492 508 7.738437 ACTAATTGGGATGGTTTCATTTCAT 57.262 32.000 0.00 0.00 32.98 2.57
493 509 7.785033 ACTAATTGGGATGGTTTCATTTCATC 58.215 34.615 0.00 0.00 37.23 2.92
494 510 6.879367 AATTGGGATGGTTTCATTTCATCT 57.121 33.333 0.00 0.00 37.85 2.90
495 511 6.879367 ATTGGGATGGTTTCATTTCATCTT 57.121 33.333 0.00 0.00 37.85 2.40
496 512 5.920193 TGGGATGGTTTCATTTCATCTTC 57.080 39.130 0.00 0.00 37.85 2.87
497 513 5.331906 TGGGATGGTTTCATTTCATCTTCA 58.668 37.500 0.00 0.00 37.85 3.02
498 514 5.959594 TGGGATGGTTTCATTTCATCTTCAT 59.040 36.000 0.00 0.00 37.85 2.57
827 843 3.500343 AGTAATCCTGCCTTGTTTGCTT 58.500 40.909 0.00 0.00 0.00 3.91
882 898 2.789917 GGCTGCTTCAGTCATGCG 59.210 61.111 0.00 0.00 35.96 4.73
913 929 2.224090 GGTCTAATCTTTCCGAGGAGGC 60.224 54.545 0.00 0.00 40.77 4.70
932 948 2.264813 GCGCGGTAATCTACTTGTTCA 58.735 47.619 8.83 0.00 0.00 3.18
936 952 4.328983 CGCGGTAATCTACTTGTTCATTGT 59.671 41.667 0.00 0.00 0.00 2.71
937 953 5.163893 CGCGGTAATCTACTTGTTCATTGTT 60.164 40.000 0.00 0.00 0.00 2.83
938 954 6.248631 GCGGTAATCTACTTGTTCATTGTTC 58.751 40.000 0.00 0.00 0.00 3.18
939 955 6.092259 GCGGTAATCTACTTGTTCATTGTTCT 59.908 38.462 0.00 0.00 0.00 3.01
940 956 7.277098 GCGGTAATCTACTTGTTCATTGTTCTA 59.723 37.037 0.00 0.00 0.00 2.10
941 957 9.314321 CGGTAATCTACTTGTTCATTGTTCTAT 57.686 33.333 0.00 0.00 0.00 1.98
969 985 3.769739 TCAACTGGAGCAGCTAAAAGA 57.230 42.857 0.00 0.00 34.37 2.52
1005 1021 4.567971 TGTTTATTTCCAATTGCAGGCAG 58.432 39.130 0.00 0.00 0.00 4.85
1132 1148 2.225491 TGTGACAATCGCAAGCCTTTAC 59.775 45.455 0.00 0.00 33.43 2.01
1168 1184 1.077858 CAAGGGGAAGGCTCAGAGC 60.078 63.158 14.69 14.69 41.46 4.09
1172 1188 1.220477 GGGAAGGCTCAGAGCTCAC 59.780 63.158 21.99 10.18 41.99 3.51
1213 1229 3.870419 CAGCTCCTGTAATTCAAGAGAGC 59.130 47.826 15.49 15.49 40.74 4.09
1237 1253 0.251634 GGGCAAGTCTTCCTCCTGAG 59.748 60.000 0.00 0.00 0.00 3.35
1256 1272 5.483231 CCTGAGCTCCTCCAAGATATCATAA 59.517 44.000 12.15 0.00 0.00 1.90
1279 1295 1.006998 AGACTGGAGGCTGATGAGAGT 59.993 52.381 0.00 0.00 0.00 3.24
1628 1645 3.616219 TGTGCCTTACCAATGGTATGTC 58.384 45.455 13.55 6.20 38.05 3.06
1720 1814 8.731275 ATTATCTCACTGAGATATAGTCGAGG 57.269 38.462 23.66 0.00 46.70 4.63
1721 1815 5.554437 TCTCACTGAGATATAGTCGAGGT 57.446 43.478 4.50 0.00 33.35 3.85
1722 1816 5.543714 TCTCACTGAGATATAGTCGAGGTC 58.456 45.833 4.50 0.00 33.35 3.85
1723 1817 5.305902 TCTCACTGAGATATAGTCGAGGTCT 59.694 44.000 4.50 0.00 33.35 3.85
1724 1818 5.301555 TCACTGAGATATAGTCGAGGTCTG 58.698 45.833 0.00 0.00 0.00 3.51
1737 1831 2.028112 CGAGGTCTGGAGGATGAAAACA 60.028 50.000 0.00 0.00 0.00 2.83
1785 1879 5.053811 TGTTTGAGTGCTTTAATCGACTGA 58.946 37.500 0.00 0.00 0.00 3.41
1802 1896 1.329906 CTGATCTGCCTCGTTTCATGC 59.670 52.381 0.00 0.00 0.00 4.06
1809 1903 1.000274 GCCTCGTTTCATGCAAACCTT 60.000 47.619 12.27 0.00 41.40 3.50
1827 1921 4.342862 CCTTTCTGGTTCTGACTTCTGA 57.657 45.455 0.00 0.00 0.00 3.27
1895 1989 8.930846 ATTATCTCCTCCCACTTAATCAAATG 57.069 34.615 0.00 0.00 0.00 2.32
2066 2161 9.700831 ATTGGAAAGCTGAGGTAATTAATACTT 57.299 29.630 0.00 0.00 34.74 2.24
2068 2163 9.609346 TGGAAAGCTGAGGTAATTAATACTTAC 57.391 33.333 0.00 0.00 34.74 2.34
2289 2422 1.664151 GCCGTCAGTTACAACATAGCC 59.336 52.381 0.00 0.00 0.00 3.93
2370 2503 2.822399 CACTCCATACCGGCCTCC 59.178 66.667 0.00 0.00 33.14 4.30
2596 2753 3.378399 GAGGGCGAGGTCAAGGAGC 62.378 68.421 0.00 0.00 0.00 4.70
2907 3094 4.156008 ACGAAACTGGCCTGTGAATAATTC 59.844 41.667 16.89 13.24 0.00 2.17
2922 3110 1.508632 AATTCGTGACACCAAGACCG 58.491 50.000 0.00 0.00 30.70 4.79
3007 3199 5.347907 CCTTAGGTTGTTGTAGATCGTGTTC 59.652 44.000 0.00 0.00 0.00 3.18
3060 3252 2.542020 TGTGCTTGCTGCTGTAGTAA 57.458 45.000 0.00 0.00 43.37 2.24
3062 3254 3.411446 TGTGCTTGCTGCTGTAGTAATT 58.589 40.909 0.00 0.00 43.37 1.40
3063 3255 3.820467 TGTGCTTGCTGCTGTAGTAATTT 59.180 39.130 0.00 0.00 43.37 1.82
3068 3261 5.371115 TTGCTGCTGTAGTAATTTGAACC 57.629 39.130 0.00 0.00 0.00 3.62
3132 3325 2.029470 GCCCTCTCTCTTCCATGATACG 60.029 54.545 0.00 0.00 0.00 3.06
3144 3337 1.940883 ATGATACGACGTGCACCCGT 61.941 55.000 27.25 27.25 45.18 5.28
3170 3369 1.056125 AGGCATCCACCGATCCATCA 61.056 55.000 0.00 0.00 33.69 3.07
3293 3520 2.026945 AAACAAAAGCTGGCGTGGGG 62.027 55.000 0.00 0.00 0.00 4.96
3491 3723 0.385390 GGGTTAATCATTGCCTGCGG 59.615 55.000 0.00 0.00 0.00 5.69
3550 3782 2.355009 CAAAACAGTGCCTGCCGC 60.355 61.111 2.50 0.00 34.37 6.53
3593 3825 1.524621 GCATCGTCTCACATGGGGG 60.525 63.158 0.00 0.00 0.00 5.40
3636 3878 0.179023 TTGAGTGAGTGTGCATGCCA 60.179 50.000 16.68 10.08 0.00 4.92
3684 3926 4.082026 GGGTTTCTTTCATCAATCAGTGGG 60.082 45.833 0.00 0.00 0.00 4.61
3685 3927 4.082026 GGTTTCTTTCATCAATCAGTGGGG 60.082 45.833 0.00 0.00 0.00 4.96
3690 3945 0.549950 CATCAATCAGTGGGGGAGCT 59.450 55.000 0.00 0.00 0.00 4.09
3691 3946 0.842635 ATCAATCAGTGGGGGAGCTC 59.157 55.000 4.71 4.71 0.00 4.09
3693 3948 1.613630 AATCAGTGGGGGAGCTCGT 60.614 57.895 7.83 0.00 0.00 4.18
3730 3989 1.993301 AGGGGAAAAGATCGAAAGGGT 59.007 47.619 0.00 0.00 0.00 4.34
3732 3991 2.092323 GGGAAAAGATCGAAAGGGTGG 58.908 52.381 0.00 0.00 0.00 4.61
3733 3992 2.290705 GGGAAAAGATCGAAAGGGTGGA 60.291 50.000 0.00 0.00 0.00 4.02
3734 3993 3.418047 GGAAAAGATCGAAAGGGTGGAA 58.582 45.455 0.00 0.00 0.00 3.53
3736 3995 2.789409 AAGATCGAAAGGGTGGAAGG 57.211 50.000 0.00 0.00 0.00 3.46
3737 3996 0.912486 AGATCGAAAGGGTGGAAGGG 59.088 55.000 0.00 0.00 0.00 3.95
3738 3997 0.748367 GATCGAAAGGGTGGAAGGGC 60.748 60.000 0.00 0.00 0.00 5.19
3739 3998 2.536997 ATCGAAAGGGTGGAAGGGCG 62.537 60.000 0.00 0.00 0.00 6.13
3740 3999 2.754375 GAAAGGGTGGAAGGGCGA 59.246 61.111 0.00 0.00 0.00 5.54
3741 4000 1.377333 GAAAGGGTGGAAGGGCGAG 60.377 63.158 0.00 0.00 0.00 5.03
3742 4001 3.569200 AAAGGGTGGAAGGGCGAGC 62.569 63.158 0.00 0.00 0.00 5.03
3744 4003 4.785453 GGGTGGAAGGGCGAGCAG 62.785 72.222 0.00 0.00 0.00 4.24
3788 4047 1.591158 GTGTGTCGCTGTTTCTTCGAA 59.409 47.619 0.00 0.00 33.81 3.71
3800 4059 0.103390 TCTTCGAACTGGAACGCACA 59.897 50.000 0.00 0.00 0.00 4.57
3895 4165 1.001641 AAGAGGGATGTGCTGGTGC 60.002 57.895 0.00 0.00 40.20 5.01
3965 4238 4.421479 ACAGGAGAAGCGACGGCG 62.421 66.667 6.12 6.12 46.35 6.46
3966 4239 4.116328 CAGGAGAAGCGACGGCGA 62.116 66.667 18.90 0.00 46.35 5.54
3967 4240 4.117661 AGGAGAAGCGACGGCGAC 62.118 66.667 18.90 5.74 46.35 5.19
4059 4332 0.322456 GCTGATGTGGGTACTTGGCA 60.322 55.000 0.00 0.00 0.00 4.92
4063 4336 0.038166 ATGTGGGTACTTGGCACCAG 59.962 55.000 0.00 0.00 37.84 4.00
4065 4338 0.179001 GTGGGTACTTGGCACCAGTT 60.179 55.000 0.00 0.00 37.84 3.16
4070 4343 1.396996 GTACTTGGCACCAGTTATGCG 59.603 52.381 0.00 0.00 44.37 4.73
4077 4350 2.343101 GCACCAGTTATGCGTTCAGTA 58.657 47.619 0.00 0.00 32.45 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.457851 CGCACAAAAACAGAACCCCA 59.542 50.000 0.00 0.00 0.00 4.96
45 46 1.206132 ACGGAACACACTCAGAACACA 59.794 47.619 0.00 0.00 0.00 3.72
46 47 1.593006 CACGGAACACACTCAGAACAC 59.407 52.381 0.00 0.00 0.00 3.32
47 48 1.478916 TCACGGAACACACTCAGAACA 59.521 47.619 0.00 0.00 0.00 3.18
48 49 2.128035 CTCACGGAACACACTCAGAAC 58.872 52.381 0.00 0.00 0.00 3.01
49 50 1.754803 ACTCACGGAACACACTCAGAA 59.245 47.619 0.00 0.00 0.00 3.02
50 51 1.067060 CACTCACGGAACACACTCAGA 59.933 52.381 0.00 0.00 0.00 3.27
51 52 1.491670 CACTCACGGAACACACTCAG 58.508 55.000 0.00 0.00 0.00 3.35
52 53 0.104120 CCACTCACGGAACACACTCA 59.896 55.000 0.00 0.00 0.00 3.41
53 54 1.222115 GCCACTCACGGAACACACTC 61.222 60.000 0.00 0.00 0.00 3.51
54 55 1.227556 GCCACTCACGGAACACACT 60.228 57.895 0.00 0.00 0.00 3.55
55 56 2.594962 CGCCACTCACGGAACACAC 61.595 63.158 0.00 0.00 0.00 3.82
171 185 1.172812 GCCCAAAAGTCCACGCTCTT 61.173 55.000 0.00 0.00 0.00 2.85
172 186 1.600916 GCCCAAAAGTCCACGCTCT 60.601 57.895 0.00 0.00 0.00 4.09
480 496 7.874528 ACCAAGAAATGAAGATGAAATGAAACC 59.125 33.333 0.00 0.00 0.00 3.27
481 497 8.706035 CACCAAGAAATGAAGATGAAATGAAAC 58.294 33.333 0.00 0.00 0.00 2.78
482 498 7.385752 GCACCAAGAAATGAAGATGAAATGAAA 59.614 33.333 0.00 0.00 0.00 2.69
483 499 6.869913 GCACCAAGAAATGAAGATGAAATGAA 59.130 34.615 0.00 0.00 0.00 2.57
485 501 6.395629 AGCACCAAGAAATGAAGATGAAATG 58.604 36.000 0.00 0.00 0.00 2.32
486 502 6.600882 AGCACCAAGAAATGAAGATGAAAT 57.399 33.333 0.00 0.00 0.00 2.17
487 503 6.348458 CGTAGCACCAAGAAATGAAGATGAAA 60.348 38.462 0.00 0.00 0.00 2.69
488 504 5.122239 CGTAGCACCAAGAAATGAAGATGAA 59.878 40.000 0.00 0.00 0.00 2.57
489 505 4.631377 CGTAGCACCAAGAAATGAAGATGA 59.369 41.667 0.00 0.00 0.00 2.92
490 506 4.393062 ACGTAGCACCAAGAAATGAAGATG 59.607 41.667 0.00 0.00 0.00 2.90
491 507 4.579869 ACGTAGCACCAAGAAATGAAGAT 58.420 39.130 0.00 0.00 0.00 2.40
492 508 4.002906 ACGTAGCACCAAGAAATGAAGA 57.997 40.909 0.00 0.00 0.00 2.87
493 509 4.378459 GGAACGTAGCACCAAGAAATGAAG 60.378 45.833 0.00 0.00 0.00 3.02
494 510 3.500680 GGAACGTAGCACCAAGAAATGAA 59.499 43.478 0.00 0.00 0.00 2.57
495 511 3.071479 GGAACGTAGCACCAAGAAATGA 58.929 45.455 0.00 0.00 0.00 2.57
496 512 2.161609 GGGAACGTAGCACCAAGAAATG 59.838 50.000 0.00 0.00 0.00 2.32
497 513 2.433436 GGGAACGTAGCACCAAGAAAT 58.567 47.619 0.00 0.00 0.00 2.17
498 514 1.543871 GGGGAACGTAGCACCAAGAAA 60.544 52.381 4.84 0.00 0.00 2.52
882 898 2.317530 AGATTAGACCGCCAGAAAGC 57.682 50.000 0.00 0.00 0.00 3.51
913 929 4.328983 ACAATGAACAAGTAGATTACCGCG 59.671 41.667 0.00 0.00 0.00 6.46
932 948 9.775854 CTCCAGTTGATAGAATCATAGAACAAT 57.224 33.333 0.00 0.00 39.39 2.71
936 952 7.365497 TGCTCCAGTTGATAGAATCATAGAA 57.635 36.000 0.00 0.00 39.39 2.10
937 953 6.518032 GCTGCTCCAGTTGATAGAATCATAGA 60.518 42.308 0.00 0.00 33.84 1.98
938 954 5.638657 GCTGCTCCAGTTGATAGAATCATAG 59.361 44.000 0.00 0.00 33.84 2.23
939 955 5.306419 AGCTGCTCCAGTTGATAGAATCATA 59.694 40.000 0.00 0.00 33.84 2.15
940 956 4.102838 AGCTGCTCCAGTTGATAGAATCAT 59.897 41.667 0.00 0.00 33.84 2.45
941 957 3.453717 AGCTGCTCCAGTTGATAGAATCA 59.546 43.478 0.00 0.00 33.51 2.57
942 958 4.070630 AGCTGCTCCAGTTGATAGAATC 57.929 45.455 0.00 0.00 33.43 2.52
943 959 5.620738 TTAGCTGCTCCAGTTGATAGAAT 57.379 39.130 4.91 0.00 33.43 2.40
951 967 4.401925 ACAATCTTTTAGCTGCTCCAGTT 58.598 39.130 4.91 0.00 33.43 3.16
969 985 8.024145 TGGAAATAAACAAGGTTACCAACAAT 57.976 30.769 3.51 0.00 0.00 2.71
1132 1148 1.375523 GTGGTGCCCAGTAAGACCG 60.376 63.158 0.00 0.00 32.34 4.79
1213 1229 2.359975 GGAAGACTTGCCCACCGG 60.360 66.667 0.00 0.00 0.00 5.28
1237 1253 5.719085 TCTCCTTATGATATCTTGGAGGAGC 59.281 44.000 27.34 0.00 45.27 4.70
1256 1272 0.337773 TCATCAGCCTCCAGTCTCCT 59.662 55.000 0.00 0.00 0.00 3.69
1526 1543 1.118965 TCGAGGACCAGGCTGTCAAA 61.119 55.000 14.43 0.00 36.97 2.69
1628 1645 4.274459 GCTAGTACAAATGAGGGAAGCATG 59.726 45.833 0.00 0.00 0.00 4.06
1715 1809 2.231716 TTTCATCCTCCAGACCTCGA 57.768 50.000 0.00 0.00 0.00 4.04
1717 1811 3.703001 TGTTTTCATCCTCCAGACCTC 57.297 47.619 0.00 0.00 0.00 3.85
1718 1812 5.501156 GTTATGTTTTCATCCTCCAGACCT 58.499 41.667 0.00 0.00 41.25 3.85
1719 1813 4.640647 GGTTATGTTTTCATCCTCCAGACC 59.359 45.833 0.00 0.00 41.25 3.85
1720 1814 5.253330 TGGTTATGTTTTCATCCTCCAGAC 58.747 41.667 0.00 0.00 41.25 3.51
1721 1815 5.014123 ACTGGTTATGTTTTCATCCTCCAGA 59.986 40.000 20.69 0.00 44.74 3.86
1722 1816 5.256474 ACTGGTTATGTTTTCATCCTCCAG 58.744 41.667 16.34 16.34 45.81 3.86
1723 1817 5.014123 AGACTGGTTATGTTTTCATCCTCCA 59.986 40.000 0.00 0.00 41.25 3.86
1724 1818 5.501156 AGACTGGTTATGTTTTCATCCTCC 58.499 41.667 0.00 0.00 41.25 4.30
1760 1854 6.204688 TCAGTCGATTAAAGCACTCAAACATT 59.795 34.615 0.00 0.00 0.00 2.71
1779 1873 1.272781 GAAACGAGGCAGATCAGTCG 58.727 55.000 0.00 0.00 38.40 4.18
1785 1879 1.825090 TTGCATGAAACGAGGCAGAT 58.175 45.000 0.00 0.00 37.59 2.90
1809 1903 4.753516 TGTTCAGAAGTCAGAACCAGAA 57.246 40.909 12.39 0.00 40.34 3.02
1819 1913 5.712152 AACATTTCCCATGTTCAGAAGTC 57.288 39.130 0.00 0.00 37.69 3.01
1824 1918 6.282930 ACAGAAAAACATTTCCCATGTTCAG 58.717 36.000 0.81 0.00 40.94 3.02
1827 1921 7.961351 TCATACAGAAAAACATTTCCCATGTT 58.039 30.769 0.00 0.00 43.35 2.71
1895 1989 5.750067 TGCTCAAAAGAAAAAGATTCAGCAC 59.250 36.000 0.00 0.00 0.00 4.40
2289 2422 0.817654 TCAGCTCGTATGTCACCTGG 59.182 55.000 0.00 0.00 0.00 4.45
2907 3094 1.557443 GCTTCGGTCTTGGTGTCACG 61.557 60.000 0.00 0.00 0.00 4.35
2922 3110 2.159774 CCTTCTTCTTCGCTTTCGCTTC 60.160 50.000 0.00 0.00 35.26 3.86
2972 3163 2.124695 CCTAAGGAACCAGGGCGC 60.125 66.667 0.00 0.00 0.00 6.53
3060 3252 5.013568 TGTATGATACGTCCGGTTCAAAT 57.986 39.130 0.00 0.00 0.00 2.32
3062 3254 4.098196 TCATGTATGATACGTCCGGTTCAA 59.902 41.667 0.00 0.00 0.00 2.69
3063 3255 3.633065 TCATGTATGATACGTCCGGTTCA 59.367 43.478 0.00 0.00 0.00 3.18
3068 3261 4.506288 TGCTTTTCATGTATGATACGTCCG 59.494 41.667 0.00 0.00 36.56 4.79
3144 3337 4.408821 GGTGGATGCCTGCGTGGA 62.409 66.667 0.00 0.00 38.35 4.02
3170 3369 3.181473 GCATGTTACATTGCACCATGGAT 60.181 43.478 21.47 0.00 38.72 3.41
3366 3594 1.227497 CATGCCGAGCCTTCCTCTC 60.227 63.158 0.00 0.00 38.49 3.20
3367 3595 2.739996 CCATGCCGAGCCTTCCTCT 61.740 63.158 0.00 0.00 38.49 3.69
3432 3664 4.742201 CTCAGGCGTGGTCACCGG 62.742 72.222 6.56 0.00 0.00 5.28
3448 3680 2.219458 CTTGCATAGCATAGCACAGCT 58.781 47.619 0.00 0.00 41.05 4.24
3491 3723 2.202892 GAAGGGGCGTCGACATCC 60.203 66.667 17.16 15.22 0.00 3.51
3573 3805 1.884464 CCCATGTGAGACGATGCCG 60.884 63.158 0.00 0.00 42.50 5.69
3636 3878 5.760484 ACCCAATTAAAAGATGTTGGCAT 57.240 34.783 0.00 0.00 39.76 4.40
3684 3926 2.896443 CCTCCTCAACGAGCTCCC 59.104 66.667 8.47 0.00 0.00 4.30
3685 3927 2.185608 GCCTCCTCAACGAGCTCC 59.814 66.667 8.47 0.00 0.00 4.70
3690 3945 1.860641 TTATCCTGCCTCCTCAACGA 58.139 50.000 0.00 0.00 0.00 3.85
3691 3946 2.555199 CTTTATCCTGCCTCCTCAACG 58.445 52.381 0.00 0.00 0.00 4.10
3693 3948 1.846439 CCCTTTATCCTGCCTCCTCAA 59.154 52.381 0.00 0.00 0.00 3.02
3730 3989 2.922503 TGTCTGCTCGCCCTTCCA 60.923 61.111 0.00 0.00 0.00 3.53
3732 3991 2.125350 CCTGTCTGCTCGCCCTTC 60.125 66.667 0.00 0.00 0.00 3.46
3733 3992 3.710722 CCCTGTCTGCTCGCCCTT 61.711 66.667 0.00 0.00 0.00 3.95
3734 3993 4.704103 TCCCTGTCTGCTCGCCCT 62.704 66.667 0.00 0.00 0.00 5.19
3736 3995 4.459089 GGTCCCTGTCTGCTCGCC 62.459 72.222 0.00 0.00 0.00 5.54
3737 3996 2.052690 TAGGTCCCTGTCTGCTCGC 61.053 63.158 0.00 0.00 0.00 5.03
3738 3997 0.681564 AGTAGGTCCCTGTCTGCTCG 60.682 60.000 0.00 0.00 0.00 5.03
3739 3998 1.107945 GAGTAGGTCCCTGTCTGCTC 58.892 60.000 0.00 0.00 36.06 4.26
3740 3999 0.324830 GGAGTAGGTCCCTGTCTGCT 60.325 60.000 0.00 0.00 39.88 4.24
3741 4000 1.668101 CGGAGTAGGTCCCTGTCTGC 61.668 65.000 0.00 0.00 43.47 4.26
3742 4001 1.038130 CCGGAGTAGGTCCCTGTCTG 61.038 65.000 0.00 0.00 43.47 3.51
3743 4002 1.306970 CCGGAGTAGGTCCCTGTCT 59.693 63.158 0.00 0.00 43.47 3.41
3744 4003 2.424733 GCCGGAGTAGGTCCCTGTC 61.425 68.421 5.05 0.00 43.47 3.51
3788 4047 1.591594 CGTCTGTGTGCGTTCCAGT 60.592 57.895 0.00 0.00 0.00 4.00
3876 4143 1.310933 GCACCAGCACATCCCTCTTG 61.311 60.000 0.00 0.00 41.58 3.02
3877 4144 1.001641 GCACCAGCACATCCCTCTT 60.002 57.895 0.00 0.00 41.58 2.85
3878 4145 2.673523 GCACCAGCACATCCCTCT 59.326 61.111 0.00 0.00 41.58 3.69
3880 4147 4.415150 CGGCACCAGCACATCCCT 62.415 66.667 0.00 0.00 44.61 4.20
3910 4180 0.581053 TTCCAAACGTACGCGAAACC 59.419 50.000 15.93 0.00 42.00 3.27
4024 4297 2.715046 TCAGCCATTCTCGAAAGCAAT 58.285 42.857 7.49 0.00 0.00 3.56
4059 4332 3.863424 CGATTACTGAACGCATAACTGGT 59.137 43.478 0.00 0.00 0.00 4.00
4063 4336 4.673761 TCGATCGATTACTGAACGCATAAC 59.326 41.667 15.15 0.00 32.49 1.89
4065 4338 4.477302 TCGATCGATTACTGAACGCATA 57.523 40.909 15.15 0.00 32.49 3.14


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

AutoCloner maintained by Alex Coulton.