Multiple sequence alignment - TraesCS6D01G044300

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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 TraesCS6D01G044300 chr6D 100.000 2033 0 0 481 2513 18937846 18935814 0.000000e+00 3755
1 TraesCS6D01G044300 chr6D 88.760 863 63 19 741 1579 18940479 18941331 0.000000e+00 1026
2 TraesCS6D01G044300 chr6D 100.000 79 0 0 1 79 18938326 18938248 2.010000e-31 147
3 TraesCS6D01G044300 chr6A 90.856 1892 104 26 495 2358 19162610 19160760 0.000000e+00 2471
4 TraesCS6D01G044300 chr6A 91.630 681 42 6 922 1590 19167404 19168081 0.000000e+00 928
5 TraesCS6D01G044300 chr6A 82.905 895 112 25 759 1628 19175091 19174213 0.000000e+00 767
6 TraesCS6D01G044300 chr6A 90.854 164 8 5 2350 2513 19160721 19160565 1.960000e-51 213
7 TraesCS6D01G044300 chr6B 89.925 1727 134 17 481 2183 32998735 32997025 0.000000e+00 2189
8 TraesCS6D01G044300 chr6B 91.741 787 42 13 758 1531 33011345 33012121 0.000000e+00 1072
9 TraesCS6D01G044300 chr6B 85.779 879 88 25 759 1605 33042589 33041716 0.000000e+00 896
10 TraesCS6D01G044300 chr7D 94.412 340 19 0 1173 1512 108085665 108086004 7.960000e-145 523
11 TraesCS6D01G044300 chr7B 94.412 340 19 0 1173 1512 67808249 67808588 7.960000e-145 523


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 TraesCS6D01G044300 chr6D 18935814 18938326 2512 True 1951 3755 100.000 1 2513 2 chr6D.!!$R1 2512
1 TraesCS6D01G044300 chr6D 18940479 18941331 852 False 1026 1026 88.760 741 1579 1 chr6D.!!$F1 838
2 TraesCS6D01G044300 chr6A 19160565 19162610 2045 True 1342 2471 90.855 495 2513 2 chr6A.!!$R2 2018
3 TraesCS6D01G044300 chr6A 19167404 19168081 677 False 928 928 91.630 922 1590 1 chr6A.!!$F1 668
4 TraesCS6D01G044300 chr6A 19174213 19175091 878 True 767 767 82.905 759 1628 1 chr6A.!!$R1 869
5 TraesCS6D01G044300 chr6B 32997025 32998735 1710 True 2189 2189 89.925 481 2183 1 chr6B.!!$R1 1702
6 TraesCS6D01G044300 chr6B 33011345 33012121 776 False 1072 1072 91.741 758 1531 1 chr6B.!!$F1 773
7 TraesCS6D01G044300 chr6B 33041716 33042589 873 True 896 896 85.779 759 1605 1 chr6B.!!$R2 846

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
76 77 0.178992 CCGGATGCCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.0 3.10 F
78 79 1.202806 CGGATGCCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.0 3.10 F
1127 1225 1.078918 CCTGTTCCGATCTGCTGCA 60.079 57.895 0.88 0.88 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1150 0.042731 ATCGGAACAGGGGAGGAAGA 59.957 55.0 0.0 0.0 0.0 2.87 R
1248 1346 0.831307 GGTACTTGCGGATCTCCCTT 59.169 55.0 0.0 0.0 0.0 3.95 R
2301 2428 0.255033 GCTTGTTACCCCCTCCGAAT 59.745 55.0 0.0 0.0 0.0 3.34 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
27 28 9.926158 AGCATTTCAAAATTCACATACATAACA 57.074 25.926 0.00 0.00 0.00 2.41
41 42 7.959718 CATACATAACATGTGTGCTCTTTTC 57.040 36.000 0.00 0.00 43.64 2.29
42 43 7.755591 CATACATAACATGTGTGCTCTTTTCT 58.244 34.615 0.00 0.00 43.64 2.52
43 44 6.005583 ACATAACATGTGTGCTCTTTTCTG 57.994 37.500 0.00 0.00 43.01 3.02
44 45 5.532406 ACATAACATGTGTGCTCTTTTCTGT 59.468 36.000 0.00 0.00 43.01 3.41
45 46 4.558538 AACATGTGTGCTCTTTTCTGTC 57.441 40.909 0.00 0.00 0.00 3.51
46 47 3.813443 ACATGTGTGCTCTTTTCTGTCT 58.187 40.909 0.00 0.00 0.00 3.41
47 48 3.812053 ACATGTGTGCTCTTTTCTGTCTC 59.188 43.478 0.00 0.00 0.00 3.36
48 49 3.541996 TGTGTGCTCTTTTCTGTCTCA 57.458 42.857 0.00 0.00 0.00 3.27
49 50 3.872696 TGTGTGCTCTTTTCTGTCTCAA 58.127 40.909 0.00 0.00 0.00 3.02
50 51 3.623060 TGTGTGCTCTTTTCTGTCTCAAC 59.377 43.478 0.00 0.00 0.00 3.18
51 52 3.873952 GTGTGCTCTTTTCTGTCTCAACT 59.126 43.478 0.00 0.00 0.00 3.16
52 53 4.333926 GTGTGCTCTTTTCTGTCTCAACTT 59.666 41.667 0.00 0.00 0.00 2.66
53 54 4.943705 TGTGCTCTTTTCTGTCTCAACTTT 59.056 37.500 0.00 0.00 0.00 2.66
54 55 5.065218 TGTGCTCTTTTCTGTCTCAACTTTC 59.935 40.000 0.00 0.00 0.00 2.62
55 56 5.295540 GTGCTCTTTTCTGTCTCAACTTTCT 59.704 40.000 0.00 0.00 0.00 2.52
56 57 5.882557 TGCTCTTTTCTGTCTCAACTTTCTT 59.117 36.000 0.00 0.00 0.00 2.52
57 58 6.037610 TGCTCTTTTCTGTCTCAACTTTCTTC 59.962 38.462 0.00 0.00 0.00 2.87
58 59 6.512578 GCTCTTTTCTGTCTCAACTTTCTTCC 60.513 42.308 0.00 0.00 0.00 3.46
59 60 5.523916 TCTTTTCTGTCTCAACTTTCTTCCG 59.476 40.000 0.00 0.00 0.00 4.30
60 61 3.386768 TCTGTCTCAACTTTCTTCCGG 57.613 47.619 0.00 0.00 0.00 5.14
61 62 2.963101 TCTGTCTCAACTTTCTTCCGGA 59.037 45.455 0.00 0.00 0.00 5.14
62 63 3.578716 TCTGTCTCAACTTTCTTCCGGAT 59.421 43.478 4.15 0.00 0.00 4.18
63 64 3.664107 TGTCTCAACTTTCTTCCGGATG 58.336 45.455 4.15 8.29 0.00 3.51
64 65 2.416893 GTCTCAACTTTCTTCCGGATGC 59.583 50.000 4.15 0.00 0.00 3.91
65 66 1.740025 CTCAACTTTCTTCCGGATGCC 59.260 52.381 4.15 0.00 0.00 4.40
66 67 1.351017 TCAACTTTCTTCCGGATGCCT 59.649 47.619 4.15 0.00 0.00 4.75
67 68 1.740025 CAACTTTCTTCCGGATGCCTC 59.260 52.381 4.15 0.00 0.00 4.70
68 69 1.280457 ACTTTCTTCCGGATGCCTCT 58.720 50.000 4.15 0.00 0.00 3.69
69 70 1.208293 ACTTTCTTCCGGATGCCTCTC 59.792 52.381 4.15 0.00 0.00 3.20
70 71 1.484240 CTTTCTTCCGGATGCCTCTCT 59.516 52.381 4.15 0.00 0.00 3.10
71 72 1.115467 TTCTTCCGGATGCCTCTCTC 58.885 55.000 4.15 0.00 0.00 3.20
72 73 0.260230 TCTTCCGGATGCCTCTCTCT 59.740 55.000 4.15 0.00 0.00 3.10
73 74 0.673437 CTTCCGGATGCCTCTCTCTC 59.327 60.000 4.15 0.00 0.00 3.20
74 75 0.260230 TTCCGGATGCCTCTCTCTCT 59.740 55.000 4.15 0.00 0.00 3.10
75 76 0.179004 TCCGGATGCCTCTCTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
76 77 0.178992 CCGGATGCCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
77 78 1.238439 CGGATGCCTCTCTCTCTCTC 58.762 60.000 0.00 0.00 0.00 3.20
78 79 1.202806 CGGATGCCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
516 517 1.475403 TCCTCTTGCCTTCTCCGTAG 58.525 55.000 0.00 0.00 0.00 3.51
545 546 2.823154 TGCGGCTAAACCTATTTGCTTT 59.177 40.909 0.00 0.00 35.61 3.51
554 555 3.227614 ACCTATTTGCTTTGGTTTCCGT 58.772 40.909 0.00 0.00 0.00 4.69
556 557 3.254657 CCTATTTGCTTTGGTTTCCGTCA 59.745 43.478 0.00 0.00 0.00 4.35
557 558 4.082245 CCTATTTGCTTTGGTTTCCGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
624 627 2.752354 CAACTCCATCCATGCGGTTTAA 59.248 45.455 0.00 0.00 0.00 1.52
638 641 5.347342 TGCGGTTTAAATCATGCTTATTGG 58.653 37.500 0.00 0.00 0.00 3.16
675 680 3.731652 TTTTGTCTCACCCATTGCAAG 57.268 42.857 4.94 0.00 0.00 4.01
686 691 1.469595 CCATTGCAAGGCACGGTTATG 60.470 52.381 5.36 0.00 38.71 1.90
701 707 3.059868 CGGTTATGTATTTGCTAGTGCCG 60.060 47.826 0.00 0.00 38.71 5.69
703 709 4.755123 GGTTATGTATTTGCTAGTGCCGAT 59.245 41.667 0.00 0.00 38.71 4.18
705 711 6.425721 GGTTATGTATTTGCTAGTGCCGATAA 59.574 38.462 0.00 0.00 38.71 1.75
706 712 7.119262 GGTTATGTATTTGCTAGTGCCGATAAT 59.881 37.037 0.00 0.00 38.71 1.28
708 714 9.884636 TTATGTATTTGCTAGTGCCGATAATAT 57.115 29.630 0.00 0.00 38.71 1.28
874 887 1.228154 GGTCACAGGAAACCGCCTT 60.228 57.895 0.00 0.00 35.66 4.35
1100 1150 3.775654 CGCCGCCTCCCTTCTCTT 61.776 66.667 0.00 0.00 0.00 2.85
1127 1225 1.078918 CCTGTTCCGATCTGCTGCA 60.079 57.895 0.88 0.88 0.00 4.41
1284 1382 0.820871 ACCAGAAGAGCACGGATCTC 59.179 55.000 0.00 0.00 0.00 2.75
1575 1681 9.401058 AGCTATGTATTAGTTGATTTGCTTCTT 57.599 29.630 0.00 0.00 0.00 2.52
1709 1820 6.588756 GCTTACTATTTTGGTTTGCCCTAAAC 59.411 38.462 0.00 0.00 46.30 2.01
1731 1842 5.451908 ACGTGAAACAAATGCTGTATTGAG 58.548 37.500 0.00 0.00 37.23 3.02
1796 1908 3.055530 TCTGCTCTTTGATCCTCTTGTCC 60.056 47.826 0.00 0.00 0.00 4.02
1810 1922 4.534897 CCTCTTGTCCTTTCCCCTACTTTA 59.465 45.833 0.00 0.00 0.00 1.85
1834 1946 0.807496 GCAACCTGTGATTCTCCTGC 59.193 55.000 0.00 0.00 0.00 4.85
1842 1954 2.642311 TGTGATTCTCCTGCCTTTGGTA 59.358 45.455 0.00 0.00 0.00 3.25
1886 2012 5.067954 GTGGATTAACTGGGTTGTAGTTGT 58.932 41.667 0.00 0.00 38.70 3.32
1970 2096 4.169461 TCCCTACTACTAATAGGTGTGGCT 59.831 45.833 0.00 0.00 38.03 4.75
1983 2109 1.210155 GTGGCTGACGATGGTTTGC 59.790 57.895 0.00 0.00 0.00 3.68
1985 2111 1.236616 TGGCTGACGATGGTTTGCTG 61.237 55.000 0.00 0.00 0.00 4.41
2000 2126 2.949106 CTGGAACACGCCTGCAAG 59.051 61.111 0.00 0.00 0.00 4.01
2008 2134 3.197790 CGCCTGCAAGATGACGGG 61.198 66.667 0.00 0.00 34.07 5.28
2011 2137 2.401766 CCTGCAAGATGACGGGTGC 61.402 63.158 0.00 0.00 34.07 5.01
2019 2145 3.418684 AGATGACGGGTGCTAAGTTTT 57.581 42.857 0.00 0.00 0.00 2.43
2023 2149 2.875933 TGACGGGTGCTAAGTTTTGAAG 59.124 45.455 0.00 0.00 0.00 3.02
2036 2162 4.125703 AGTTTTGAAGAGTGACTGCTCTG 58.874 43.478 0.00 0.00 44.34 3.35
2068 2194 3.259123 AGGAATTGCTTTGGCCTTGTAAG 59.741 43.478 3.32 3.73 37.74 2.34
2071 2197 1.234821 TGCTTTGGCCTTGTAAGACG 58.765 50.000 3.32 0.00 37.74 4.18
2140 2267 8.621532 TTTACTGTTCATCTGAATGCTAACTT 57.378 30.769 0.00 0.00 36.33 2.66
2188 2315 9.778741 AGATTGTTGAGAACAGTATAAGTTTGA 57.221 29.630 0.00 0.00 43.27 2.69
2189 2316 9.813080 GATTGTTGAGAACAGTATAAGTTTGAC 57.187 33.333 0.00 0.00 43.27 3.18
2190 2317 8.958119 TTGTTGAGAACAGTATAAGTTTGACT 57.042 30.769 0.00 0.00 43.27 3.41
2191 2318 8.365399 TGTTGAGAACAGTATAAGTTTGACTG 57.635 34.615 12.84 12.84 44.98 3.51
2192 2319 8.201464 TGTTGAGAACAGTATAAGTTTGACTGA 58.799 33.333 18.68 0.00 42.65 3.41
2248 2375 8.614469 TTACACATATTATCATTCGCAATGGA 57.386 30.769 8.40 0.00 39.38 3.41
2249 2376 6.902341 ACACATATTATCATTCGCAATGGAC 58.098 36.000 8.40 0.00 39.38 4.02
2254 2381 9.247126 CATATTATCATTCGCAATGGACAAAAA 57.753 29.630 8.40 0.00 39.38 1.94
2257 2384 4.297510 TCATTCGCAATGGACAAAAAGTG 58.702 39.130 8.40 0.00 39.38 3.16
2275 2402 8.725148 CAAAAAGTGAATCAGCTCAATACTAGT 58.275 33.333 0.00 0.00 0.00 2.57
2276 2403 9.944376 AAAAAGTGAATCAGCTCAATACTAGTA 57.056 29.630 4.77 4.77 0.00 1.82
2330 2457 2.033448 TAACAAGCACCCCCAGCG 59.967 61.111 0.00 0.00 37.01 5.18
2334 2461 4.431131 AAGCACCCCCAGCGGATG 62.431 66.667 0.00 0.00 37.01 3.51
2434 2608 7.559486 AGTTAATCTGACAGTTGATAGATGCA 58.441 34.615 1.59 0.00 30.77 3.96
2438 2612 6.170846 TCTGACAGTTGATAGATGCATGAT 57.829 37.500 2.46 0.00 0.00 2.45
2479 2653 3.713858 TTGTGCTGTTTCATGGAGTTG 57.286 42.857 0.00 0.00 0.00 3.16
2491 2665 8.828644 TGTTTCATGGAGTTGAATTCAATTTTG 58.171 29.630 23.05 16.44 38.24 2.44
2492 2666 8.829612 GTTTCATGGAGTTGAATTCAATTTTGT 58.170 29.630 23.05 8.08 38.24 2.83
2493 2667 8.961294 TTCATGGAGTTGAATTCAATTTTGTT 57.039 26.923 23.05 5.59 38.24 2.83
2496 2670 9.480053 CATGGAGTTGAATTCAATTTTGTTAGT 57.520 29.630 23.05 1.94 38.24 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.926158 TGTTATGTATGTGAATTTTGAAATGCT 57.074 25.926 0.00 0.00 0.00 3.79
16 17 7.391554 AGAAAAGAGCACACATGTTATGTATGT 59.608 33.333 0.00 0.00 42.70 2.29
17 18 7.695201 CAGAAAAGAGCACACATGTTATGTATG 59.305 37.037 0.00 0.00 42.70 2.39
18 19 7.391554 ACAGAAAAGAGCACACATGTTATGTAT 59.608 33.333 0.00 0.00 42.70 2.29
19 20 6.710295 ACAGAAAAGAGCACACATGTTATGTA 59.290 34.615 0.00 0.00 42.70 2.29
20 21 5.532406 ACAGAAAAGAGCACACATGTTATGT 59.468 36.000 0.00 0.00 46.22 2.29
21 22 6.005583 ACAGAAAAGAGCACACATGTTATG 57.994 37.500 0.00 0.00 0.00 1.90
22 23 6.000219 AGACAGAAAAGAGCACACATGTTAT 59.000 36.000 0.00 0.00 0.00 1.89
23 24 5.368145 AGACAGAAAAGAGCACACATGTTA 58.632 37.500 0.00 0.00 0.00 2.41
24 25 4.202441 AGACAGAAAAGAGCACACATGTT 58.798 39.130 0.00 0.00 0.00 2.71
25 26 3.812053 GAGACAGAAAAGAGCACACATGT 59.188 43.478 0.00 0.00 0.00 3.21
26 27 3.811497 TGAGACAGAAAAGAGCACACATG 59.189 43.478 0.00 0.00 0.00 3.21
27 28 4.077300 TGAGACAGAAAAGAGCACACAT 57.923 40.909 0.00 0.00 0.00 3.21
28 29 3.541996 TGAGACAGAAAAGAGCACACA 57.458 42.857 0.00 0.00 0.00 3.72
29 30 3.873952 AGTTGAGACAGAAAAGAGCACAC 59.126 43.478 0.00 0.00 0.00 3.82
30 31 4.142609 AGTTGAGACAGAAAAGAGCACA 57.857 40.909 0.00 0.00 0.00 4.57
31 32 5.295540 AGAAAGTTGAGACAGAAAAGAGCAC 59.704 40.000 0.00 0.00 0.00 4.40
32 33 5.431765 AGAAAGTTGAGACAGAAAAGAGCA 58.568 37.500 0.00 0.00 0.00 4.26
33 34 6.370433 AAGAAAGTTGAGACAGAAAAGAGC 57.630 37.500 0.00 0.00 0.00 4.09
34 35 6.292596 CGGAAGAAAGTTGAGACAGAAAAGAG 60.293 42.308 0.00 0.00 0.00 2.85
35 36 5.523916 CGGAAGAAAGTTGAGACAGAAAAGA 59.476 40.000 0.00 0.00 0.00 2.52
36 37 5.277538 CCGGAAGAAAGTTGAGACAGAAAAG 60.278 44.000 0.00 0.00 0.00 2.27
37 38 4.574828 CCGGAAGAAAGTTGAGACAGAAAA 59.425 41.667 0.00 0.00 0.00 2.29
38 39 4.127171 CCGGAAGAAAGTTGAGACAGAAA 58.873 43.478 0.00 0.00 0.00 2.52
39 40 3.386726 TCCGGAAGAAAGTTGAGACAGAA 59.613 43.478 0.00 0.00 0.00 3.02
40 41 2.963101 TCCGGAAGAAAGTTGAGACAGA 59.037 45.455 0.00 0.00 0.00 3.41
41 42 3.386768 TCCGGAAGAAAGTTGAGACAG 57.613 47.619 0.00 0.00 0.00 3.51
42 43 3.664107 CATCCGGAAGAAAGTTGAGACA 58.336 45.455 9.01 0.00 0.00 3.41
43 44 2.416893 GCATCCGGAAGAAAGTTGAGAC 59.583 50.000 9.01 0.00 0.00 3.36
44 45 2.615493 GGCATCCGGAAGAAAGTTGAGA 60.615 50.000 9.01 0.00 0.00 3.27
45 46 1.740025 GGCATCCGGAAGAAAGTTGAG 59.260 52.381 9.01 0.00 0.00 3.02
46 47 1.351017 AGGCATCCGGAAGAAAGTTGA 59.649 47.619 9.01 0.00 0.00 3.18
47 48 1.740025 GAGGCATCCGGAAGAAAGTTG 59.260 52.381 9.01 0.31 0.00 3.16
48 49 1.630878 AGAGGCATCCGGAAGAAAGTT 59.369 47.619 9.01 0.00 0.00 2.66
49 50 1.208293 GAGAGGCATCCGGAAGAAAGT 59.792 52.381 9.01 0.00 0.00 2.66
50 51 1.484240 AGAGAGGCATCCGGAAGAAAG 59.516 52.381 9.01 0.00 0.00 2.62
51 52 1.482593 GAGAGAGGCATCCGGAAGAAA 59.517 52.381 9.01 0.00 0.00 2.52
52 53 1.115467 GAGAGAGGCATCCGGAAGAA 58.885 55.000 9.01 0.00 0.00 2.52
53 54 0.260230 AGAGAGAGGCATCCGGAAGA 59.740 55.000 9.01 0.00 0.00 2.87
54 55 0.673437 GAGAGAGAGGCATCCGGAAG 59.327 60.000 9.01 4.82 0.00 3.46
55 56 0.260230 AGAGAGAGAGGCATCCGGAA 59.740 55.000 9.01 0.00 0.00 4.30
56 57 0.179004 GAGAGAGAGAGGCATCCGGA 60.179 60.000 6.61 6.61 0.00 5.14
57 58 0.178992 AGAGAGAGAGAGGCATCCGG 60.179 60.000 0.00 0.00 0.00 5.14
58 59 1.202806 AGAGAGAGAGAGAGGCATCCG 60.203 57.143 0.00 0.00 0.00 4.18
59 60 2.664402 AGAGAGAGAGAGAGGCATCC 57.336 55.000 0.00 0.00 0.00 3.51
483 484 1.799933 AGAGGATCCGCCAGAGAATT 58.200 50.000 12.40 0.00 40.02 2.17
545 546 0.536233 CCACACCATGACGGAAACCA 60.536 55.000 0.00 0.00 38.63 3.67
556 557 2.685366 CATCCAGGGCCACACCAT 59.315 61.111 6.18 0.00 42.05 3.55
557 558 4.365111 GCATCCAGGGCCACACCA 62.365 66.667 6.18 0.00 42.05 4.17
576 577 1.448540 CAGTTGGAGAAGCCGCGAT 60.449 57.895 8.23 0.00 40.66 4.58
624 627 6.266103 CAGTTCATACCCCAATAAGCATGATT 59.734 38.462 0.17 0.17 0.00 2.57
659 662 0.895100 TGCCTTGCAATGGGTGAGAC 60.895 55.000 14.32 1.04 34.76 3.36
675 680 3.875134 ACTAGCAAATACATAACCGTGCC 59.125 43.478 0.00 0.00 32.38 5.01
686 691 6.456988 GGCATATTATCGGCACTAGCAAATAC 60.457 42.308 0.00 0.00 44.61 1.89
821 830 3.792736 TTTCGGGATGGCCTCGGG 61.793 66.667 3.32 0.00 0.00 5.14
874 887 2.833227 CTGGGGAAACGTGGACCA 59.167 61.111 0.00 0.00 0.00 4.02
1100 1150 0.042731 ATCGGAACAGGGGAGGAAGA 59.957 55.000 0.00 0.00 0.00 2.87
1127 1225 2.159282 ACCGTCGATAATCAGCGAAACT 60.159 45.455 0.00 0.00 45.40 2.66
1248 1346 0.831307 GGTACTTGCGGATCTCCCTT 59.169 55.000 0.00 0.00 0.00 3.95
1284 1382 3.207669 GGCAGCTTGCGGATGAGG 61.208 66.667 0.00 0.00 46.21 3.86
1575 1681 1.335597 CGAGTGACACGGCTAAGAACA 60.336 52.381 0.00 0.00 0.00 3.18
1677 1786 6.381801 CAAACCAAAATAGTAAGCACCAGAG 58.618 40.000 0.00 0.00 0.00 3.35
1709 1820 4.321745 GCTCAATACAGCATTTGTTTCACG 59.678 41.667 0.00 0.00 41.29 4.35
1731 1842 9.994432 ATTGCTAAGAATAAATAGCGATAATGC 57.006 29.630 5.87 0.00 43.95 3.56
1796 1908 4.028993 TGCAAGGTAAAGTAGGGGAAAG 57.971 45.455 0.00 0.00 0.00 2.62
1810 1922 2.508526 GAGAATCACAGGTTGCAAGGT 58.491 47.619 0.00 0.00 33.17 3.50
1834 1946 3.552684 CCACAGCAACATTGTACCAAAGG 60.553 47.826 0.00 0.00 0.00 3.11
1842 1954 1.741525 GGCACCACAGCAACATTGT 59.258 52.632 0.00 0.00 35.83 2.71
1912 2038 3.766691 GGAAGGCCCGCGACAGTA 61.767 66.667 8.23 0.00 0.00 2.74
1948 2074 4.281182 CAGCCACACCTATTAGTAGTAGGG 59.719 50.000 19.75 12.40 42.47 3.53
1970 2096 1.234821 GTTCCAGCAAACCATCGTCA 58.765 50.000 0.00 0.00 0.00 4.35
1983 2109 0.957395 ATCTTGCAGGCGTGTTCCAG 60.957 55.000 8.40 0.00 0.00 3.86
1985 2111 0.955428 TCATCTTGCAGGCGTGTTCC 60.955 55.000 8.40 0.00 0.00 3.62
2000 2126 3.071479 TCAAAACTTAGCACCCGTCATC 58.929 45.455 0.00 0.00 0.00 2.92
2008 2134 5.742446 CAGTCACTCTTCAAAACTTAGCAC 58.258 41.667 0.00 0.00 0.00 4.40
2011 2137 5.988561 AGAGCAGTCACTCTTCAAAACTTAG 59.011 40.000 0.00 0.00 44.76 2.18
2019 2145 3.005897 GGTAACAGAGCAGTCACTCTTCA 59.994 47.826 0.00 0.00 44.76 3.02
2036 2162 6.299023 CCAAAGCAATTCCTTTTTGGTAAC 57.701 37.500 6.67 0.00 42.78 2.50
2097 2224 9.733556 AACAGTAAATATGTACACCAATCAAGA 57.266 29.630 5.84 0.00 0.00 3.02
2104 2231 8.536175 TCAGATGAACAGTAAATATGTACACCA 58.464 33.333 5.84 0.00 0.00 4.17
2186 2313 9.958180 TTTATGATCCAAACTCTAAATCAGTCA 57.042 29.630 0.00 0.00 30.51 3.41
2188 2315 9.739276 TGTTTATGATCCAAACTCTAAATCAGT 57.261 29.630 16.55 0.00 36.92 3.41
2219 2346 8.726650 TTGCGAATGATAATATGTGTAATTGC 57.273 30.769 0.00 0.00 0.00 3.56
2233 2360 6.072230 TCACTTTTTGTCCATTGCGAATGATA 60.072 34.615 9.56 0.00 41.46 2.15
2240 2367 4.297510 TGATTCACTTTTTGTCCATTGCG 58.702 39.130 0.00 0.00 0.00 4.85
2248 2375 7.516198 AGTATTGAGCTGATTCACTTTTTGT 57.484 32.000 0.00 0.00 0.00 2.83
2249 2376 8.725148 ACTAGTATTGAGCTGATTCACTTTTTG 58.275 33.333 0.00 0.00 0.00 2.44
2301 2428 0.255033 GCTTGTTACCCCCTCCGAAT 59.745 55.000 0.00 0.00 0.00 3.34
2334 2461 6.717084 ACATAAATTCTAATTAGCAGGGGAGC 59.283 38.462 7.67 0.00 0.00 4.70
2374 2548 6.268617 TCGTCCATTTCTCAATCTCCTCATAT 59.731 38.462 0.00 0.00 0.00 1.78
2424 2598 8.863872 AATGAAAGATCATCATGCATCTATCA 57.136 30.769 13.00 0.00 45.60 2.15
2425 2599 9.561270 CAAATGAAAGATCATCATGCATCTATC 57.439 33.333 13.00 0.00 45.60 2.08
2430 2604 8.002984 TGTACAAATGAAAGATCATCATGCAT 57.997 30.769 13.00 0.00 45.60 3.96
2438 2612 8.763356 GCACAAAATTGTACAAATGAAAGATCA 58.237 29.630 13.23 0.00 39.91 2.92


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

AutoCloner maintained by Alex Coulton.