Multiple sequence alignment - TraesCS3D01G318200

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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 TraesCS3D01G318200 chr3D 100.000 6653 0 0 1 6653 432035915 432029263 0.000000e+00 12286.0
1 TraesCS3D01G318200 chr3D 94.545 55 3 0 1 55 80569553 80569499 1.190000e-12 86.1
2 TraesCS3D01G318200 chr3B 93.463 3702 116 30 69 3692 564253849 564250196 0.000000e+00 5398.0
3 TraesCS3D01G318200 chr3B 96.607 2977 61 12 3691 6653 564249936 564246986 0.000000e+00 4902.0
4 TraesCS3D01G318200 chr3A 96.294 3076 66 18 3592 6653 569426427 569423386 0.000000e+00 5005.0
5 TraesCS3D01G318200 chr3A 94.581 3137 106 20 469 3595 569429631 569426549 0.000000e+00 4793.0
6 TraesCS3D01G318200 chr3A 94.719 303 12 2 81 383 569429983 569429685 1.010000e-127 468.0
7 TraesCS3D01G318200 chr7D 94.545 55 3 0 1 55 169917065 169917119 1.190000e-12 86.1
8 TraesCS3D01G318200 chr6D 96.154 52 2 0 1 52 150779817 150779868 1.190000e-12 86.1
9 TraesCS3D01G318200 chr6D 94.545 55 3 0 1 55 335344094 335344148 1.190000e-12 86.1
10 TraesCS3D01G318200 chr5A 94.545 55 3 0 1 55 611336031 611335977 1.190000e-12 86.1
11 TraesCS3D01G318200 chr2B 94.545 55 3 0 1 55 50625703 50625649 1.190000e-12 86.1
12 TraesCS3D01G318200 chr2A 94.545 55 3 0 1 55 650607111 650607165 1.190000e-12 86.1
13 TraesCS3D01G318200 chr1B 94.545 55 3 0 1 55 532066477 532066423 1.190000e-12 86.1
14 TraesCS3D01G318200 chr5B 92.857 56 4 0 1 56 10401797 10401852 1.540000e-11 82.4


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 TraesCS3D01G318200 chr3D 432029263 432035915 6652 True 12286 12286 100.000 1 6653 1 chr3D.!!$R2 6652
1 TraesCS3D01G318200 chr3B 564246986 564253849 6863 True 5150 5398 95.035 69 6653 2 chr3B.!!$R1 6584
2 TraesCS3D01G318200 chr3A 569423386 569429983 6597 True 3422 5005 95.198 81 6653 3 chr3A.!!$R1 6572

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
505 562 0.031111 AATCGATCCCACCTCCAGGA 60.031 55.000 0.00 0.00 38.94 3.86 F
927 999 0.807667 CTCCGTTTCGCATCTGAGGG 60.808 60.000 0.00 0.00 0.00 4.30 F
993 1065 2.576832 CCTGGTTGGGCTTGGCTTG 61.577 63.158 0.00 0.00 0.00 4.01 F
1359 1431 2.911819 AATGGTAACCGATGCAAACG 57.088 45.000 9.21 9.21 0.00 3.60 F
1670 1759 3.136443 TCTGGTTGCAATTATCCGGATCT 59.864 43.478 23.08 6.95 31.39 2.75 F
2523 2616 3.426292 GCTTTTATTCGCTGAAGGACCAC 60.426 47.826 0.00 0.00 0.00 4.16 F
3422 3516 4.168883 GGCTGTCTATATTCTAACCCCCT 58.831 47.826 0.00 0.00 0.00 4.79 F
3621 3840 0.038618 GGGCGTTGGATGACAAAACC 60.039 55.000 0.00 0.00 41.58 3.27 F
3961 4441 2.024414 GATGGTCCAAATGGTGCCTAC 58.976 52.381 0.00 0.13 36.34 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1674 0.462581 TGATTCCACATCTGCGGCTC 60.463 55.000 0.00 0.00 0.00 4.70 R
2238 2331 1.176527 CGGCTTGTTCAACATCCCAT 58.823 50.000 0.00 0.00 0.00 4.00 R
2852 2945 1.414550 GGAACTATGGGAGACAGGCTC 59.585 57.143 0.00 0.00 43.17 4.70 R
3258 3351 1.112950 TGTTACCCACAGTCACGTCA 58.887 50.000 0.00 0.00 0.00 4.35 R
3324 3418 1.369091 CGGCATCTACACAGGGTTGC 61.369 60.000 0.00 0.00 0.00 4.17 R
3572 3666 2.238646 ACTATCTTTGATTCCCACGCCA 59.761 45.455 0.00 0.00 0.00 5.69 R
4873 5356 1.069204 TGTGTCTGCAGTTCACTCTCC 59.931 52.381 29.15 14.45 33.82 3.71 R
4903 5386 3.739519 CGGATCTTGACCAGACTGGAATC 60.740 52.174 28.56 16.10 40.96 2.52 R
5951 6438 2.552315 CACCCTAAAACGACACAGCAAT 59.448 45.455 0.00 0.00 0.00 3.56 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
21 22 3.531538 CATAGAAATAGGGTGTGCGTGT 58.468 45.455 0.00 0.00 0.00 4.49
22 23 1.808411 AGAAATAGGGTGTGCGTGTG 58.192 50.000 0.00 0.00 0.00 3.82
23 24 1.071699 AGAAATAGGGTGTGCGTGTGT 59.928 47.619 0.00 0.00 0.00 3.72
24 25 1.196808 GAAATAGGGTGTGCGTGTGTG 59.803 52.381 0.00 0.00 0.00 3.82
25 26 1.234615 AATAGGGTGTGCGTGTGTGC 61.235 55.000 0.00 0.00 0.00 4.57
26 27 2.390306 ATAGGGTGTGCGTGTGTGCA 62.390 55.000 0.00 0.00 43.95 4.57
35 36 2.013400 TGCGTGTGTGCATTTATAGGG 58.987 47.619 0.00 0.00 40.62 3.53
36 37 1.333619 GCGTGTGTGCATTTATAGGGG 59.666 52.381 0.00 0.00 34.15 4.79
37 38 2.639065 CGTGTGTGCATTTATAGGGGT 58.361 47.619 0.00 0.00 0.00 4.95
38 39 2.354510 CGTGTGTGCATTTATAGGGGTG 59.645 50.000 0.00 0.00 0.00 4.61
39 40 3.616219 GTGTGTGCATTTATAGGGGTGA 58.384 45.455 0.00 0.00 0.00 4.02
40 41 3.627577 GTGTGTGCATTTATAGGGGTGAG 59.372 47.826 0.00 0.00 0.00 3.51
41 42 3.265737 TGTGTGCATTTATAGGGGTGAGT 59.734 43.478 0.00 0.00 0.00 3.41
42 43 3.627577 GTGTGCATTTATAGGGGTGAGTG 59.372 47.826 0.00 0.00 0.00 3.51
43 44 3.265737 TGTGCATTTATAGGGGTGAGTGT 59.734 43.478 0.00 0.00 0.00 3.55
44 45 4.471747 TGTGCATTTATAGGGGTGAGTGTA 59.528 41.667 0.00 0.00 0.00 2.90
45 46 5.131977 TGTGCATTTATAGGGGTGAGTGTAT 59.868 40.000 0.00 0.00 0.00 2.29
46 47 5.470098 GTGCATTTATAGGGGTGAGTGTATG 59.530 44.000 0.00 0.00 0.00 2.39
47 48 4.455877 GCATTTATAGGGGTGAGTGTATGC 59.544 45.833 0.00 0.00 0.00 3.14
48 49 4.330944 TTTATAGGGGTGAGTGTATGCG 57.669 45.455 0.00 0.00 0.00 4.73
49 50 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
50 51 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
51 52 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
52 53 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
53 54 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
54 55 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
55 56 0.638746 GTGAGTGTATGCGCGTGTAC 59.361 55.000 13.61 11.02 0.00 2.90
56 57 0.524414 TGAGTGTATGCGCGTGTACT 59.476 50.000 13.61 15.77 0.00 2.73
57 58 0.914551 GAGTGTATGCGCGTGTACTG 59.085 55.000 20.68 0.00 0.00 2.74
58 59 0.242825 AGTGTATGCGCGTGTACTGT 59.757 50.000 13.61 7.74 0.00 3.55
59 60 0.365523 GTGTATGCGCGTGTACTGTG 59.634 55.000 13.61 0.00 0.00 3.66
60 61 0.038983 TGTATGCGCGTGTACTGTGT 60.039 50.000 13.61 0.00 0.00 3.72
61 62 1.065358 GTATGCGCGTGTACTGTGTT 58.935 50.000 13.61 0.00 0.00 3.32
62 63 2.252747 GTATGCGCGTGTACTGTGTTA 58.747 47.619 13.61 0.00 0.00 2.41
63 64 1.785768 ATGCGCGTGTACTGTGTTAA 58.214 45.000 8.43 0.00 0.00 2.01
64 65 1.568606 TGCGCGTGTACTGTGTTAAA 58.431 45.000 8.43 0.00 0.00 1.52
65 66 1.931841 TGCGCGTGTACTGTGTTAAAA 59.068 42.857 8.43 0.00 0.00 1.52
66 67 2.350804 TGCGCGTGTACTGTGTTAAAAA 59.649 40.909 8.43 0.00 0.00 1.94
150 151 1.944676 CTAGCGCGGTGAATCGACC 60.945 63.158 23.02 0.00 0.00 4.79
215 236 0.894184 AGGACCACACGACACGAGAT 60.894 55.000 0.00 0.00 0.00 2.75
229 250 2.293122 CACGAGATAGAGAGCTGGGAAG 59.707 54.545 0.00 0.00 0.00 3.46
274 295 1.435105 GAACGTAGTCGGGTAGGCC 59.565 63.158 0.00 0.00 45.00 5.19
300 321 1.586422 TCGATCCCCGTTACTACTCG 58.414 55.000 0.00 0.00 39.75 4.18
386 412 2.151202 CGAAGCCAAGCAAAACTAGGA 58.849 47.619 0.00 0.00 0.00 2.94
408 434 4.697756 CCAACCGGCTTCGCTCCA 62.698 66.667 0.00 0.00 0.00 3.86
422 448 6.371548 GGCTTCGCTCCACATCATTATTATTA 59.628 38.462 0.00 0.00 0.00 0.98
423 449 7.066284 GGCTTCGCTCCACATCATTATTATTAT 59.934 37.037 0.00 0.00 0.00 1.28
424 450 8.454106 GCTTCGCTCCACATCATTATTATTATT 58.546 33.333 0.00 0.00 0.00 1.40
471 528 2.288152 GGAAGCAGCAACCGATTTTTCA 60.288 45.455 0.00 0.00 0.00 2.69
505 562 0.031111 AATCGATCCCACCTCCAGGA 60.031 55.000 0.00 0.00 38.94 3.86
710 777 3.131478 CGCCGATTCCCCCAACAC 61.131 66.667 0.00 0.00 0.00 3.32
711 778 3.131478 GCCGATTCCCCCAACACG 61.131 66.667 0.00 0.00 0.00 4.49
715 782 2.359478 ATTCCCCCAACACGCGAC 60.359 61.111 15.93 0.00 0.00 5.19
721 788 4.351938 CCAACACGCGACCTCCGA 62.352 66.667 15.93 0.00 41.76 4.55
722 789 2.805353 CAACACGCGACCTCCGAG 60.805 66.667 15.93 0.00 43.81 4.63
723 790 4.719369 AACACGCGACCTCCGAGC 62.719 66.667 15.93 0.00 41.91 5.03
927 999 0.807667 CTCCGTTTCGCATCTGAGGG 60.808 60.000 0.00 0.00 0.00 4.30
946 1018 3.775654 GAGGAGGAGCGGTGGTGG 61.776 72.222 0.00 0.00 0.00 4.61
947 1019 4.640690 AGGAGGAGCGGTGGTGGT 62.641 66.667 0.00 0.00 0.00 4.16
948 1020 4.394712 GGAGGAGCGGTGGTGGTG 62.395 72.222 0.00 0.00 0.00 4.17
993 1065 2.576832 CCTGGTTGGGCTTGGCTTG 61.577 63.158 0.00 0.00 0.00 4.01
1359 1431 2.911819 AATGGTAACCGATGCAAACG 57.088 45.000 9.21 9.21 0.00 3.60
1535 1607 6.657117 TGTACTTGCTCTTTTGGCATGTTATA 59.343 34.615 11.27 0.00 42.59 0.98
1536 1608 6.780457 ACTTGCTCTTTTGGCATGTTATAT 57.220 33.333 0.00 0.00 42.59 0.86
1585 1674 3.610242 GCAAAGTGTCTGATGAGTAGACG 59.390 47.826 0.00 0.00 45.82 4.18
1664 1753 5.643379 TTGAGTTCTGGTTGCAATTATCC 57.357 39.130 0.59 0.00 0.00 2.59
1670 1759 3.136443 TCTGGTTGCAATTATCCGGATCT 59.864 43.478 23.08 6.95 31.39 2.75
1688 1777 3.874383 TCTGAAATGTTCCTGTTGGGA 57.126 42.857 0.00 0.00 43.41 4.37
1870 1963 6.490721 TCTTGTAAAAAGGGCTAATCGGAAAA 59.509 34.615 0.00 0.00 0.00 2.29
2135 2228 6.932356 AAATGTGCTAATACATGTCCTCTG 57.068 37.500 0.00 0.00 40.24 3.35
2238 2331 4.443457 GCATACAGATCAGGCTTCCAAGTA 60.443 45.833 0.00 0.00 0.00 2.24
2523 2616 3.426292 GCTTTTATTCGCTGAAGGACCAC 60.426 47.826 0.00 0.00 0.00 4.16
2742 2835 6.667558 ATACACTTCTTACCAGCCCTATAC 57.332 41.667 0.00 0.00 0.00 1.47
3092 3185 6.427853 GGCATACTATTGACAGTGAATATGCA 59.572 38.462 16.25 0.00 38.02 3.96
3258 3351 4.876580 AGACCGTTAGGGACCTAATAACT 58.123 43.478 13.51 8.52 43.47 2.24
3370 3464 6.629128 CAAAACTCATGGTTGTGGCATATTA 58.371 36.000 8.57 0.00 38.99 0.98
3408 3502 8.023021 AGACAACATAATAGAATGGCTGTCTA 57.977 34.615 16.08 1.11 44.21 2.59
3409 3503 8.654997 AGACAACATAATAGAATGGCTGTCTAT 58.345 33.333 16.08 5.12 44.21 1.98
3422 3516 4.168883 GGCTGTCTATATTCTAACCCCCT 58.831 47.826 0.00 0.00 0.00 4.79
3572 3666 0.786435 AATCCCTCCTGCCTTTGGTT 59.214 50.000 0.00 0.00 0.00 3.67
3621 3840 0.038618 GGGCGTTGGATGACAAAACC 60.039 55.000 0.00 0.00 41.58 3.27
3898 4378 3.508744 ATTCATGGCCGAAACATCAAC 57.491 42.857 0.00 0.00 0.00 3.18
3956 4436 3.689347 TCAGAAGATGGTCCAAATGGTG 58.311 45.455 0.00 0.00 36.34 4.17
3961 4441 2.024414 GATGGTCCAAATGGTGCCTAC 58.976 52.381 0.00 0.13 36.34 3.18
4300 4780 2.948979 TCATTGGTCTCAAAACGCAAGT 59.051 40.909 0.00 0.00 44.04 3.16
4386 4866 9.444600 TGTTGTTAGTAGAATAAGAAATGGGAC 57.555 33.333 0.00 0.00 0.00 4.46
4519 4999 3.631145 TCAGATGACAGTTTGCTTTGC 57.369 42.857 0.00 0.00 0.00 3.68
4807 5290 5.773680 CCGGAAAGGAACTAGTATCTATCCA 59.226 44.000 12.10 0.00 45.00 3.41
4952 5435 7.128331 GGTACTTCTTTTTACCTGTTTTCGTC 58.872 38.462 0.00 0.00 35.72 4.20
4973 5456 6.711194 TCGTCCAATACCACATTTGTCTTTTA 59.289 34.615 0.00 0.00 0.00 1.52
5114 5597 7.327032 GGAAATCGAAATTGAAAAAGTCCAGAG 59.673 37.037 0.00 0.00 0.00 3.35
5208 5691 4.997395 CAGACAAGGTTTGCTCTAAGCTTA 59.003 41.667 5.94 5.94 42.23 3.09
5225 5708 2.288395 GCTTACATTTGTGCTTGGTGCT 60.288 45.455 0.00 0.00 43.37 4.40
5330 5813 6.658391 TGATGATGGTGTGTTGATGTTATTCA 59.342 34.615 0.00 0.00 0.00 2.57
5699 6183 1.000052 GAGCTACTCCCGGACTTATGC 60.000 57.143 0.73 0.00 0.00 3.14
5804 6288 3.257375 AGTGTGTTGCATTGCATCTGAAT 59.743 39.130 12.95 0.00 38.76 2.57
5815 6299 7.143340 GCATTGCATCTGAATAATTGAGCTTA 58.857 34.615 3.15 0.00 0.00 3.09
5816 6300 7.650504 GCATTGCATCTGAATAATTGAGCTTAA 59.349 33.333 3.15 0.00 0.00 1.85
5892 6379 4.749598 TGCACTAATAATATGTGGTGCTCG 59.250 41.667 17.74 0.00 46.61 5.03
5903 6390 1.734465 GTGGTGCTCGATCTCCAAAAG 59.266 52.381 11.33 0.00 32.18 2.27
5904 6391 1.347707 TGGTGCTCGATCTCCAAAAGT 59.652 47.619 7.56 0.00 0.00 2.66
5905 6392 2.565391 TGGTGCTCGATCTCCAAAAGTA 59.435 45.455 7.56 0.00 0.00 2.24
5906 6393 3.007506 TGGTGCTCGATCTCCAAAAGTAA 59.992 43.478 7.56 0.00 0.00 2.24
5907 6394 4.000988 GGTGCTCGATCTCCAAAAGTAAA 58.999 43.478 2.59 0.00 0.00 2.01
5908 6395 4.454504 GGTGCTCGATCTCCAAAAGTAAAA 59.545 41.667 2.59 0.00 0.00 1.52
5951 6438 9.845740 AAAGTGGTGCTCAACATATATTGTATA 57.154 29.630 0.00 0.00 37.68 1.47
6364 6858 0.322008 TGCATATGTGTCGGTGGCAA 60.322 50.000 4.29 0.00 0.00 4.52
6381 6875 5.363005 GGTGGCAACTACTAGAGATTTCCTA 59.637 44.000 0.00 0.00 37.61 2.94
6489 6983 4.879598 AACGATTAGTTCCTGACGAAGTT 58.120 39.130 0.00 0.00 39.42 2.66
6504 6998 5.812665 ACGAAGTTTAAGTTGCTACGTAC 57.187 39.130 0.00 0.00 37.78 3.67
6505 6999 5.280945 ACGAAGTTTAAGTTGCTACGTACA 58.719 37.500 0.00 0.00 37.78 2.90
6506 7000 5.400485 ACGAAGTTTAAGTTGCTACGTACAG 59.600 40.000 0.00 0.00 37.78 2.74
6507 7001 5.400485 CGAAGTTTAAGTTGCTACGTACAGT 59.600 40.000 0.00 0.00 0.00 3.55
6508 7002 6.578545 CGAAGTTTAAGTTGCTACGTACAGTA 59.421 38.462 0.00 0.00 0.00 2.74
6606 7100 1.975680 AGGCCGAAAGAGTTCTGGTTA 59.024 47.619 0.00 0.00 32.97 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.309682 CACACGCACACCCTATTTCTATG 59.690 47.826 0.00 0.00 0.00 2.23
1 2 3.055385 ACACACGCACACCCTATTTCTAT 60.055 43.478 0.00 0.00 0.00 1.98
2 3 2.300723 ACACACGCACACCCTATTTCTA 59.699 45.455 0.00 0.00 0.00 2.10
4 5 1.196808 CACACACGCACACCCTATTTC 59.803 52.381 0.00 0.00 0.00 2.17
5 6 1.234821 CACACACGCACACCCTATTT 58.765 50.000 0.00 0.00 0.00 1.40
6 7 1.234615 GCACACACGCACACCCTATT 61.235 55.000 0.00 0.00 0.00 1.73
9 10 3.772853 ATGCACACACGCACACCCT 62.773 57.895 0.00 0.00 46.56 4.34
10 11 2.348605 AAATGCACACACGCACACCC 62.349 55.000 0.00 0.00 46.56 4.61
11 12 0.309302 TAAATGCACACACGCACACC 59.691 50.000 0.00 0.00 46.56 4.16
12 13 2.330231 ATAAATGCACACACGCACAC 57.670 45.000 0.00 0.00 46.56 3.82
13 14 2.418280 CCTATAAATGCACACACGCACA 59.582 45.455 0.00 0.00 46.56 4.57
14 15 2.223249 CCCTATAAATGCACACACGCAC 60.223 50.000 0.00 0.00 46.56 5.34
16 17 1.333619 CCCCTATAAATGCACACACGC 59.666 52.381 0.00 0.00 0.00 5.34
17 18 2.354510 CACCCCTATAAATGCACACACG 59.645 50.000 0.00 0.00 0.00 4.49
18 19 3.616219 TCACCCCTATAAATGCACACAC 58.384 45.455 0.00 0.00 0.00 3.82
19 20 3.265737 ACTCACCCCTATAAATGCACACA 59.734 43.478 0.00 0.00 0.00 3.72
20 21 3.627577 CACTCACCCCTATAAATGCACAC 59.372 47.826 0.00 0.00 0.00 3.82
21 22 3.265737 ACACTCACCCCTATAAATGCACA 59.734 43.478 0.00 0.00 0.00 4.57
22 23 3.886123 ACACTCACCCCTATAAATGCAC 58.114 45.455 0.00 0.00 0.00 4.57
23 24 5.620206 CATACACTCACCCCTATAAATGCA 58.380 41.667 0.00 0.00 0.00 3.96
24 25 4.455877 GCATACACTCACCCCTATAAATGC 59.544 45.833 0.00 0.00 0.00 3.56
25 26 4.690748 CGCATACACTCACCCCTATAAATG 59.309 45.833 0.00 0.00 0.00 2.32
26 27 4.802918 GCGCATACACTCACCCCTATAAAT 60.803 45.833 0.30 0.00 0.00 1.40
27 28 3.493699 GCGCATACACTCACCCCTATAAA 60.494 47.826 0.30 0.00 0.00 1.40
28 29 2.036733 GCGCATACACTCACCCCTATAA 59.963 50.000 0.30 0.00 0.00 0.98
29 30 1.616865 GCGCATACACTCACCCCTATA 59.383 52.381 0.30 0.00 0.00 1.31
30 31 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
31 32 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
32 33 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
33 34 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
34 35 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
35 36 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
36 37 0.638746 GTACACGCGCATACACTCAC 59.361 55.000 5.73 0.00 0.00 3.51
37 38 0.524414 AGTACACGCGCATACACTCA 59.476 50.000 19.11 0.00 0.00 3.41
38 39 0.914551 CAGTACACGCGCATACACTC 59.085 55.000 19.11 0.00 0.00 3.51
39 40 0.242825 ACAGTACACGCGCATACACT 59.757 50.000 19.11 1.58 0.00 3.55
40 41 0.365523 CACAGTACACGCGCATACAC 59.634 55.000 19.11 0.00 0.00 2.90
41 42 0.038983 ACACAGTACACGCGCATACA 60.039 50.000 19.11 0.00 0.00 2.29
42 43 1.065358 AACACAGTACACGCGCATAC 58.935 50.000 5.73 9.35 0.00 2.39
43 44 2.633199 TAACACAGTACACGCGCATA 57.367 45.000 5.73 0.00 0.00 3.14
44 45 1.785768 TTAACACAGTACACGCGCAT 58.214 45.000 5.73 0.00 0.00 4.73
45 46 1.568606 TTTAACACAGTACACGCGCA 58.431 45.000 5.73 0.00 0.00 6.09
46 47 2.649140 TTTTAACACAGTACACGCGC 57.351 45.000 5.73 0.00 0.00 6.86
64 65 9.092876 TCTTCGTTTGAAAAAGTATGCATTTTT 57.907 25.926 3.54 6.74 41.32 1.94
65 66 8.641499 TCTTCGTTTGAAAAAGTATGCATTTT 57.359 26.923 3.54 0.00 32.66 1.82
66 67 8.641499 TTCTTCGTTTGAAAAAGTATGCATTT 57.359 26.923 3.54 0.00 32.66 2.32
67 68 8.641499 TTTCTTCGTTTGAAAAAGTATGCATT 57.359 26.923 3.54 0.00 32.66 3.56
85 86 6.904011 GTCATGAGTATGCATCTTTTTCTTCG 59.096 38.462 0.19 0.00 34.21 3.79
86 87 7.755591 TGTCATGAGTATGCATCTTTTTCTTC 58.244 34.615 0.19 0.00 34.21 2.87
88 89 7.065563 GTCTGTCATGAGTATGCATCTTTTTCT 59.934 37.037 0.19 0.00 34.21 2.52
89 90 7.185453 GTCTGTCATGAGTATGCATCTTTTTC 58.815 38.462 0.19 0.00 34.21 2.29
215 236 1.681538 CTACGCTTCCCAGCTCTCTA 58.318 55.000 0.00 0.00 44.85 2.43
274 295 4.785511 AGTAACGGGGATCGATTATCTG 57.214 45.455 0.00 0.17 42.43 2.90
300 321 0.107800 GGAAGGGAGCCGAGGTTAAC 60.108 60.000 0.00 0.00 0.00 2.01
424 450 4.687018 TGAGTTTTCGAATCGAATCGGAAA 59.313 37.500 22.30 22.30 45.43 3.13
706 773 4.719369 GCTCGGAGGTCGCGTGTT 62.719 66.667 5.77 0.00 39.05 3.32
720 787 4.521062 AGCGACATGGCCGAGCTC 62.521 66.667 2.73 2.73 31.94 4.09
721 788 4.521062 GAGCGACATGGCCGAGCT 62.521 66.667 12.90 6.55 41.29 4.09
722 789 4.819761 TGAGCGACATGGCCGAGC 62.820 66.667 12.90 1.40 0.00 5.03
723 790 2.887568 GTGAGCGACATGGCCGAG 60.888 66.667 12.90 0.00 0.00 4.63
724 791 4.451150 GGTGAGCGACATGGCCGA 62.451 66.667 12.90 0.00 0.00 5.54
858 928 3.793144 GAACGCTCGCTTGGCCTG 61.793 66.667 3.32 0.00 0.00 4.85
927 999 2.363147 ACCACCGCTCCTCCTCTC 60.363 66.667 0.00 0.00 0.00 3.20
993 1065 3.508840 CCGTTCCGCATCAAGCCC 61.509 66.667 0.00 0.00 41.38 5.19
1516 1588 6.528537 ACAATATAACATGCCAAAAGAGCA 57.471 33.333 0.00 0.00 45.94 4.26
1585 1674 0.462581 TGATTCCACATCTGCGGCTC 60.463 55.000 0.00 0.00 0.00 4.70
1664 1753 3.127548 CCAACAGGAACATTTCAGATCCG 59.872 47.826 0.00 0.00 35.77 4.18
1688 1777 3.850454 TCAGAGTGTCCTGACCTGT 57.150 52.632 0.00 0.00 38.18 4.00
1870 1963 6.403866 TTCAAGGTTAATGACACAGCAAAT 57.596 33.333 0.00 0.00 0.00 2.32
2135 2228 5.221048 GCCCATTGTACCTGTAAATCACATC 60.221 44.000 0.00 0.00 36.29 3.06
2226 2319 2.208872 ACATCCCATACTTGGAAGCCT 58.791 47.619 0.00 0.00 46.92 4.58
2238 2331 1.176527 CGGCTTGTTCAACATCCCAT 58.823 50.000 0.00 0.00 0.00 4.00
2523 2616 7.304735 TGAACTTCATTGAATGAACATAACCG 58.695 34.615 16.04 7.80 43.84 4.44
2742 2835 4.438744 GCCATAACCAGAAATCGGTGAAAG 60.439 45.833 0.00 0.00 36.67 2.62
2852 2945 1.414550 GGAACTATGGGAGACAGGCTC 59.585 57.143 0.00 0.00 43.17 4.70
3258 3351 1.112950 TGTTACCCACAGTCACGTCA 58.887 50.000 0.00 0.00 0.00 4.35
3324 3418 1.369091 CGGCATCTACACAGGGTTGC 61.369 60.000 0.00 0.00 0.00 4.17
3408 3502 8.981659 CAAAATCTTTTCAGGGGGTTAGAATAT 58.018 33.333 0.00 0.00 0.00 1.28
3409 3503 7.953493 ACAAAATCTTTTCAGGGGGTTAGAATA 59.047 33.333 0.00 0.00 0.00 1.75
3572 3666 2.238646 ACTATCTTTGATTCCCACGCCA 59.761 45.455 0.00 0.00 0.00 5.69
3621 3840 4.253685 TCAACTTAATCGAAGAGGGCAAG 58.746 43.478 0.00 0.00 43.63 4.01
3898 4378 3.543494 CAGAAGGCATAATGCGAAAAACG 59.457 43.478 0.00 0.00 46.21 3.60
3956 4436 6.144724 TGCAATTTAAACAAATGAACGTAGGC 59.855 34.615 0.00 0.00 0.00 3.93
3961 4441 7.793427 CCTCTTTGCAATTTAAACAAATGAACG 59.207 33.333 0.00 0.00 33.19 3.95
4300 4780 2.834549 CTGACTAAGGCTCAAAGAGGGA 59.165 50.000 0.00 0.00 0.00 4.20
4386 4866 3.214328 ACAGCACCCTTCAACAAGTTAG 58.786 45.455 0.00 0.00 0.00 2.34
4549 5029 7.785028 AGAACATACTGTATGATACTCCCAGAA 59.215 37.037 29.17 0.00 39.45 3.02
4784 5267 6.896021 TGGATAGATACTAGTTCCTTTCCG 57.104 41.667 19.08 0.00 31.97 4.30
4807 5290 1.561076 TCAGTAGCAGCACCATTGGAT 59.439 47.619 10.37 0.00 0.00 3.41
4873 5356 1.069204 TGTGTCTGCAGTTCACTCTCC 59.931 52.381 29.15 14.45 33.82 3.71
4903 5386 3.739519 CGGATCTTGACCAGACTGGAATC 60.740 52.174 28.56 16.10 40.96 2.52
4952 5435 9.487790 AAACATAAAAGACAAATGTGGTATTGG 57.512 29.630 0.00 0.00 34.20 3.16
5114 5597 8.956426 TCTTTGACCTTGATTCCACATTATAAC 58.044 33.333 0.00 0.00 0.00 1.89
5699 6183 4.508124 GCTTACCTTTGATATCGTCACTGG 59.492 45.833 0.00 0.00 36.32 4.00
5815 6299 9.649167 GAATTGAGAAGATCCAAAACATCATTT 57.351 29.630 0.00 0.00 0.00 2.32
5816 6300 9.032624 AGAATTGAGAAGATCCAAAACATCATT 57.967 29.630 0.00 0.00 0.00 2.57
5929 6416 8.729756 GCAATATACAATATATGTTGAGCACCA 58.270 33.333 17.96 0.00 43.63 4.17
5951 6438 2.552315 CACCCTAAAACGACACAGCAAT 59.448 45.455 0.00 0.00 0.00 3.56
6364 6858 9.349713 CAGAACTGATAGGAAATCTCTAGTAGT 57.650 37.037 0.00 0.00 0.00 2.73
6606 7100 2.833943 GCCAAAAATCCTCACTCCCAAT 59.166 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.