Multiple sequence alignment - TraesCS6B01G189500

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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 TraesCS6B01G189500 chr6B 100.000 2939 0 0 1 2939 219217812 219214874 0.000000e+00 5428.0
1 TraesCS6B01G189500 chr6D 94.371 2789 115 27 180 2939 124145980 124143205 0.000000e+00 4242.0
2 TraesCS6B01G189500 chr6D 91.589 107 7 2 5 110 335364804 335364699 2.360000e-31 147.0
3 TraesCS6B01G189500 chr6D 89.796 98 9 1 13 110 111078995 111079091 1.110000e-24 124.0
4 TraesCS6B01G189500 chr6A 92.416 2057 108 24 180 2195 157025596 157027645 0.000000e+00 2891.0
5 TraesCS6B01G189500 chr6A 89.185 638 42 10 2306 2939 157027638 157028252 0.000000e+00 771.0
6 TraesCS6B01G189500 chr1D 84.286 140 22 0 1 140 126197581 126197442 1.420000e-28 137.0
7 TraesCS6B01G189500 chr1D 85.938 128 18 0 13 140 481460410 481460283 1.420000e-28 137.0
8 TraesCS6B01G189500 chr1D 100.000 33 0 0 2211 2243 39996962 39996930 8.790000e-06 62.1
9 TraesCS6B01G189500 chr7D 88.660 97 11 0 9 105 481829971 481830067 5.150000e-23 119.0
10 TraesCS6B01G189500 chr3D 89.247 93 10 0 6 98 133537600 133537692 1.850000e-22 117.0
11 TraesCS6B01G189500 chr3A 81.429 140 24 2 1 140 425288352 425288215 2.390000e-21 113.0
12 TraesCS6B01G189500 chr7B 83.193 119 18 1 22 140 106141122 106141238 1.110000e-19 108.0
13 TraesCS6B01G189500 chr5A 86.458 96 12 1 2210 2304 455462817 455462912 1.440000e-18 104.0
14 TraesCS6B01G189500 chr5A 96.970 33 1 0 2210 2242 646567093 646567061 4.090000e-04 56.5
15 TraesCS6B01G189500 chr3B 80.303 132 26 0 9 140 487515165 487515296 1.860000e-17 100.0
16 TraesCS6B01G189500 chr4A 89.796 49 4 1 2215 2263 87411184 87411137 8.790000e-06 62.1
17 TraesCS6B01G189500 chr5B 97.059 34 1 0 2210 2243 654901951 654901918 1.140000e-04 58.4


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 TraesCS6B01G189500 chr6B 219214874 219217812 2938 True 5428 5428 100.0000 1 2939 1 chr6B.!!$R1 2938
1 TraesCS6B01G189500 chr6D 124143205 124145980 2775 True 4242 4242 94.3710 180 2939 1 chr6D.!!$R1 2759
2 TraesCS6B01G189500 chr6A 157025596 157028252 2656 False 1831 2891 90.8005 180 2939 2 chr6A.!!$F1 2759

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
21 22 0.027194 CTGCGTCGATGCATTTCAGG 59.973 55.0 31.06 15.5 45.26 3.86 F
1326 1366 0.035458 CGTTCTGGAGCAAGAAGGGT 59.965 55.0 8.02 0.0 38.04 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1693 0.744414 CCACCGTGATCGCCATTTCT 60.744 55.0 0.00 0.0 35.54 2.52 R
2545 2590 1.107114 GGAGCATTCGAGGTCTGAGA 58.893 55.0 4.18 0.0 36.33 3.27 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
19 20 1.655484 ATCTGCGTCGATGCATTTCA 58.345 45.000 31.06 16.26 45.26 2.69
20 21 1.001624 TCTGCGTCGATGCATTTCAG 58.998 50.000 31.06 19.37 45.26 3.02
21 22 0.027194 CTGCGTCGATGCATTTCAGG 59.973 55.000 31.06 15.50 45.26 3.86
22 23 1.297893 GCGTCGATGCATTTCAGGC 60.298 57.895 24.45 1.50 34.15 4.85
23 24 1.980951 GCGTCGATGCATTTCAGGCA 61.981 55.000 24.45 0.00 46.66 4.75
24 25 0.247814 CGTCGATGCATTTCAGGCAC 60.248 55.000 0.00 0.00 45.23 5.01
25 26 0.804364 GTCGATGCATTTCAGGCACA 59.196 50.000 0.00 0.00 45.23 4.57
26 27 1.199789 GTCGATGCATTTCAGGCACAA 59.800 47.619 0.00 0.00 45.23 3.33
27 28 2.093890 TCGATGCATTTCAGGCACAAT 58.906 42.857 0.00 0.00 45.23 2.71
28 29 2.492881 TCGATGCATTTCAGGCACAATT 59.507 40.909 0.00 0.00 45.23 2.32
29 30 3.056678 TCGATGCATTTCAGGCACAATTT 60.057 39.130 0.00 0.00 45.23 1.82
30 31 3.680937 CGATGCATTTCAGGCACAATTTT 59.319 39.130 0.00 0.00 45.23 1.82
31 32 4.434989 CGATGCATTTCAGGCACAATTTTG 60.435 41.667 0.00 0.00 45.23 2.44
32 33 3.139850 TGCATTTCAGGCACAATTTTGG 58.860 40.909 0.00 0.00 36.11 3.28
33 34 2.485038 GCATTTCAGGCACAATTTTGGG 59.515 45.455 0.00 0.00 33.81 4.12
43 44 3.075884 CACAATTTTGGGCTGGAAATGG 58.924 45.455 0.00 0.00 0.00 3.16
44 45 2.040145 ACAATTTTGGGCTGGAAATGGG 59.960 45.455 0.00 0.00 0.00 4.00
45 46 2.040145 CAATTTTGGGCTGGAAATGGGT 59.960 45.455 0.00 0.00 0.00 4.51
46 47 1.347062 TTTTGGGCTGGAAATGGGTC 58.653 50.000 0.00 0.00 0.00 4.46
47 48 0.544120 TTTGGGCTGGAAATGGGTCC 60.544 55.000 0.00 0.00 38.27 4.46
48 49 1.442886 TTGGGCTGGAAATGGGTCCT 61.443 55.000 0.00 0.00 38.62 3.85
49 50 1.076705 GGGCTGGAAATGGGTCCTC 60.077 63.158 0.00 0.00 38.62 3.71
50 51 1.452108 GGCTGGAAATGGGTCCTCG 60.452 63.158 0.00 0.00 38.62 4.63
51 52 2.115291 GCTGGAAATGGGTCCTCGC 61.115 63.158 0.00 0.00 38.62 5.03
52 53 1.815421 CTGGAAATGGGTCCTCGCG 60.815 63.158 0.00 0.00 38.62 5.87
53 54 2.513897 GGAAATGGGTCCTCGCGG 60.514 66.667 6.13 0.00 34.56 6.46
54 55 2.582436 GAAATGGGTCCTCGCGGA 59.418 61.111 6.13 0.00 36.83 5.54
73 74 3.098555 GCGATGCGGACGGATTTT 58.901 55.556 0.00 0.00 0.00 1.82
74 75 1.297598 GCGATGCGGACGGATTTTG 60.298 57.895 0.00 0.00 0.00 2.44
75 76 1.351707 CGATGCGGACGGATTTTGG 59.648 57.895 0.00 0.00 0.00 3.28
76 77 1.727467 GATGCGGACGGATTTTGGG 59.273 57.895 0.00 0.00 0.00 4.12
77 78 0.746563 GATGCGGACGGATTTTGGGA 60.747 55.000 0.00 0.00 0.00 4.37
78 79 0.322997 ATGCGGACGGATTTTGGGAA 60.323 50.000 0.00 0.00 0.00 3.97
79 80 0.322997 TGCGGACGGATTTTGGGAAT 60.323 50.000 0.00 0.00 0.00 3.01
80 81 0.100503 GCGGACGGATTTTGGGAATG 59.899 55.000 0.00 0.00 0.00 2.67
81 82 0.738389 CGGACGGATTTTGGGAATGG 59.262 55.000 0.00 0.00 0.00 3.16
82 83 1.111277 GGACGGATTTTGGGAATGGG 58.889 55.000 0.00 0.00 0.00 4.00
83 84 1.618616 GGACGGATTTTGGGAATGGGT 60.619 52.381 0.00 0.00 0.00 4.51
84 85 1.749063 GACGGATTTTGGGAATGGGTC 59.251 52.381 0.00 0.00 0.00 4.46
85 86 0.738389 CGGATTTTGGGAATGGGTCG 59.262 55.000 0.00 0.00 0.00 4.79
86 87 1.111277 GGATTTTGGGAATGGGTCGG 58.889 55.000 0.00 0.00 0.00 4.79
87 88 0.459899 GATTTTGGGAATGGGTCGGC 59.540 55.000 0.00 0.00 0.00 5.54
88 89 1.319614 ATTTTGGGAATGGGTCGGCG 61.320 55.000 0.00 0.00 0.00 6.46
93 94 4.160635 GAATGGGTCGGCGCGTTG 62.161 66.667 16.87 0.00 36.98 4.10
106 107 4.273257 CGTTGGGCCGGCGTTTTT 62.273 61.111 22.54 0.00 0.00 1.94
107 108 2.660224 GTTGGGCCGGCGTTTTTG 60.660 61.111 22.54 0.00 0.00 2.44
108 109 3.148279 TTGGGCCGGCGTTTTTGT 61.148 55.556 22.54 0.00 0.00 2.83
109 110 3.140225 TTGGGCCGGCGTTTTTGTC 62.140 57.895 22.54 2.98 0.00 3.18
110 111 3.597728 GGGCCGGCGTTTTTGTCA 61.598 61.111 22.54 0.00 0.00 3.58
111 112 2.413765 GGCCGGCGTTTTTGTCAA 59.586 55.556 22.54 0.00 0.00 3.18
112 113 1.006688 GGCCGGCGTTTTTGTCAAT 60.007 52.632 22.54 0.00 0.00 2.57
113 114 0.241481 GGCCGGCGTTTTTGTCAATA 59.759 50.000 22.54 0.00 0.00 1.90
114 115 1.613270 GCCGGCGTTTTTGTCAATAG 58.387 50.000 12.58 0.00 0.00 1.73
115 116 1.613270 CCGGCGTTTTTGTCAATAGC 58.387 50.000 6.01 0.00 0.00 2.97
116 117 1.246970 CGGCGTTTTTGTCAATAGCG 58.753 50.000 0.00 7.68 0.00 4.26
117 118 1.136197 CGGCGTTTTTGTCAATAGCGA 60.136 47.619 14.53 0.00 0.00 4.93
118 119 2.475519 CGGCGTTTTTGTCAATAGCGAT 60.476 45.455 14.53 0.00 0.00 4.58
119 120 3.098636 GGCGTTTTTGTCAATAGCGATC 58.901 45.455 14.53 4.18 0.00 3.69
120 121 3.098636 GCGTTTTTGTCAATAGCGATCC 58.901 45.455 14.53 0.00 0.00 3.36
121 122 3.425625 GCGTTTTTGTCAATAGCGATCCA 60.426 43.478 14.53 0.00 0.00 3.41
122 123 4.717991 CGTTTTTGTCAATAGCGATCCAA 58.282 39.130 6.44 0.00 0.00 3.53
123 124 5.150683 CGTTTTTGTCAATAGCGATCCAAA 58.849 37.500 6.44 0.00 0.00 3.28
124 125 5.799936 CGTTTTTGTCAATAGCGATCCAAAT 59.200 36.000 6.44 0.00 0.00 2.32
125 126 6.237279 CGTTTTTGTCAATAGCGATCCAAATG 60.237 38.462 6.44 0.00 0.00 2.32
126 127 4.898829 TTGTCAATAGCGATCCAAATGG 57.101 40.909 0.00 0.00 0.00 3.16
135 136 4.277239 TCCAAATGGACGTGAGCG 57.723 55.556 0.00 0.00 39.78 5.03
136 137 1.375396 TCCAAATGGACGTGAGCGG 60.375 57.895 0.00 0.00 43.45 5.52
137 138 1.375396 CCAAATGGACGTGAGCGGA 60.375 57.895 0.00 0.00 43.45 5.54
138 139 1.635663 CCAAATGGACGTGAGCGGAC 61.636 60.000 0.00 0.00 43.45 4.79
139 140 1.736645 AAATGGACGTGAGCGGACG 60.737 57.895 8.75 8.75 45.09 4.79
174 175 4.177673 GGTGGGCCGGTGTTTTTA 57.822 55.556 1.90 0.00 0.00 1.52
175 176 2.661054 GGTGGGCCGGTGTTTTTAT 58.339 52.632 1.90 0.00 0.00 1.40
176 177 0.528924 GGTGGGCCGGTGTTTTTATC 59.471 55.000 1.90 0.00 0.00 1.75
177 178 1.249407 GTGGGCCGGTGTTTTTATCA 58.751 50.000 1.90 0.00 0.00 2.15
178 179 1.614413 GTGGGCCGGTGTTTTTATCAA 59.386 47.619 1.90 0.00 0.00 2.57
206 207 5.455392 CCATGAAGATACGATTTTGGCATC 58.545 41.667 0.00 0.00 0.00 3.91
218 219 5.613360 CGATTTTGGCATCATCTATCACGAC 60.613 44.000 0.00 0.00 0.00 4.34
237 238 3.364465 CGACGCCAAACAATCACATACAA 60.364 43.478 0.00 0.00 0.00 2.41
242 243 6.072175 ACGCCAAACAATCACATACAATACTT 60.072 34.615 0.00 0.00 0.00 2.24
265 266 7.872483 ACTTTATGTTTTCTGTTTATTGCAGGG 59.128 33.333 0.00 0.00 34.89 4.45
266 267 7.531857 TTATGTTTTCTGTTTATTGCAGGGA 57.468 32.000 0.00 0.00 34.89 4.20
289 296 4.053469 ACACTATGTTTTGTTGTTGGCC 57.947 40.909 0.00 0.00 0.00 5.36
323 330 3.326747 AGAAGATTGTTCCCGTTTCGAG 58.673 45.455 0.00 0.00 0.00 4.04
326 333 3.064931 AGATTGTTCCCGTTTCGAGAAC 58.935 45.455 9.01 9.01 40.23 3.01
462 472 3.429085 CTGTTCTATTTTCATGGCGCAC 58.571 45.455 10.83 0.00 0.00 5.34
464 474 2.418368 TCTATTTTCATGGCGCACCT 57.582 45.000 10.83 0.00 36.63 4.00
485 500 0.323360 GTGCATACCACCACCACCAT 60.323 55.000 0.00 0.00 38.55 3.55
591 606 1.679032 CGTCAACCCCCTTTCTCCATC 60.679 57.143 0.00 0.00 0.00 3.51
621 638 2.037121 CCAAGCCGGAGTTTCCATTTTT 59.963 45.455 5.05 0.00 35.91 1.94
626 643 2.161609 CCGGAGTTTCCATTTTTCCTCG 59.838 50.000 0.00 0.00 35.91 4.63
673 699 4.678499 TGCACGCATCCGACTGCA 62.678 61.111 9.37 0.00 41.99 4.41
683 709 2.252260 CGACTGCAAACGCCAAGG 59.748 61.111 0.00 0.00 0.00 3.61
692 718 2.974935 AAACGCCAAGGCACGTACGA 62.975 55.000 24.41 0.00 42.68 3.43
699 725 2.412325 CCAAGGCACGTACGAACATTTC 60.412 50.000 24.41 4.05 0.00 2.17
747 773 1.302366 CCTTATCGCTCTTGCATGCA 58.698 50.000 18.46 18.46 39.64 3.96
756 782 1.337071 CTCTTGCATGCAGCCCATAAG 59.663 52.381 21.50 13.47 44.83 1.73
770 796 3.338249 CCCATAAGAATCAATCGCCGAT 58.662 45.455 0.00 0.00 0.00 4.18
775 801 6.142798 CCATAAGAATCAATCGCCGATTTTTG 59.857 38.462 10.09 0.65 33.26 2.44
776 802 4.032703 AGAATCAATCGCCGATTTTTGG 57.967 40.909 10.09 0.00 33.26 3.28
798 829 5.187687 GGTATTTCGTTGTCCCCTTGATTA 58.812 41.667 0.00 0.00 0.00 1.75
803 834 7.948034 TTTCGTTGTCCCCTTGATTATTATT 57.052 32.000 0.00 0.00 0.00 1.40
804 835 9.635404 ATTTCGTTGTCCCCTTGATTATTATTA 57.365 29.630 0.00 0.00 0.00 0.98
835 866 9.672086 TCTTTGTTTATAATTTGGTCTTTGACG 57.328 29.630 0.00 0.00 32.65 4.35
836 867 9.672086 CTTTGTTTATAATTTGGTCTTTGACGA 57.328 29.630 0.00 0.00 32.65 4.20
889 922 4.801516 GGAGCTTACTTCTTCTTGATCGAC 59.198 45.833 0.00 0.00 0.00 4.20
957 990 1.681538 TCCTCTTGTCCTAGCTAGCG 58.318 55.000 15.74 8.89 0.00 4.26
1092 1129 2.458610 CGACGACTCGATCACGGGA 61.459 63.158 5.20 0.00 43.41 5.14
1227 1264 1.734655 ACCAGTCCTTCACCATCACT 58.265 50.000 0.00 0.00 0.00 3.41
1326 1366 0.035458 CGTTCTGGAGCAAGAAGGGT 59.965 55.000 8.02 0.00 38.04 4.34
1726 1766 3.501040 TGGAAGTTCCGGGGCAACC 62.501 63.158 17.13 0.95 46.67 3.77
1878 1918 2.683933 GGGTTGGAGAGCGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
1890 1930 3.090532 GGGAGAGGCATTCCCGGT 61.091 66.667 10.14 0.00 44.58 5.28
1982 2022 2.706890 ACTTTCATGTACGGGCGAAAT 58.293 42.857 0.00 0.00 0.00 2.17
2137 2179 8.712285 TCATTTACTTCTAATTACAGGTTCGG 57.288 34.615 0.00 0.00 0.00 4.30
2138 2180 6.973229 TTTACTTCTAATTACAGGTTCGGC 57.027 37.500 0.00 0.00 0.00 5.54
2140 2182 4.901868 ACTTCTAATTACAGGTTCGGCAA 58.098 39.130 0.00 0.00 0.00 4.52
2142 2184 5.944007 ACTTCTAATTACAGGTTCGGCAAAT 59.056 36.000 0.00 0.00 0.00 2.32
2188 2230 5.838531 AACACCAAAAGGACGTGATTTAA 57.161 34.783 0.00 0.00 0.00 1.52
2196 2238 7.008266 CCAAAAGGACGTGATTTAAAATGATCG 59.992 37.037 0.00 0.00 0.00 3.69
2208 2250 3.525268 AAATGATCGGGAATGTTTGGC 57.475 42.857 0.00 0.00 0.00 4.52
2220 2262 5.530543 GGGAATGTTTGGCAAAGAAAATTGA 59.469 36.000 13.94 0.00 31.84 2.57
2228 2270 4.168760 GGCAAAGAAAATTGACATCCTCG 58.831 43.478 0.00 0.00 38.25 4.63
2229 2271 3.609807 GCAAAGAAAATTGACATCCTCGC 59.390 43.478 0.00 0.00 31.84 5.03
2230 2272 4.797471 CAAAGAAAATTGACATCCTCGCA 58.203 39.130 0.00 0.00 31.84 5.10
2234 2276 4.278170 AGAAAATTGACATCCTCGCAACAA 59.722 37.500 0.00 0.00 0.00 2.83
2253 2295 5.088680 ACAACATAATTTGCCATCTTGGG 57.911 39.130 0.00 0.00 38.19 4.12
2272 2314 2.894763 GCATTCCATTTGCCATGCTA 57.105 45.000 0.00 0.00 39.20 3.49
2297 2339 6.973229 AAAATTTGGCATTTGATCTGTAGC 57.027 33.333 0.00 0.00 0.00 3.58
2305 2347 5.394443 GGCATTTGATCTGTAGCAAAATCCA 60.394 40.000 0.00 0.00 43.64 3.41
2466 2511 5.401531 AGTCTTATTCTAGAACGCCAACA 57.598 39.130 7.48 0.00 0.00 3.33
2495 2540 7.148722 GCAACTAAATATCTAGTTCGCATCTCC 60.149 40.741 13.76 0.00 39.57 3.71
2545 2590 8.560903 ACCATTTCCTCCAAAAGTATAGAGATT 58.439 33.333 0.00 0.00 0.00 2.40
2610 2655 8.358582 AGAAAGAAATAAGGATTGCAATGTCT 57.641 30.769 18.59 11.19 0.00 3.41
2611 2656 8.248945 AGAAAGAAATAAGGATTGCAATGTCTG 58.751 33.333 18.59 0.00 0.00 3.51
2625 2670 5.246656 TGCAATGTCTGGAATTTGATCCTTT 59.753 36.000 0.00 0.00 40.35 3.11
2828 2873 6.016024 CCTCAAATTTCTCCAACTTGACATCA 60.016 38.462 0.00 0.00 0.00 3.07
2834 2879 6.817765 TTCTCCAACTTGACATCAAATACC 57.182 37.500 0.00 0.00 35.15 2.73
2870 2915 0.392706 TCTCTTCAGACTTTGCGGCA 59.607 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.596260 CTGAAATGCATCGACGCAGAT 59.404 47.619 13.19 2.48 46.99 2.90
1 2 1.001624 CTGAAATGCATCGACGCAGA 58.998 50.000 13.19 0.00 46.99 4.26
2 3 0.027194 CCTGAAATGCATCGACGCAG 59.973 55.000 13.19 0.00 46.99 5.18
4 5 1.297893 GCCTGAAATGCATCGACGC 60.298 57.895 0.00 0.00 0.00 5.19
5 6 0.247814 GTGCCTGAAATGCATCGACG 60.248 55.000 0.00 0.00 40.30 5.12
6 7 0.804364 TGTGCCTGAAATGCATCGAC 59.196 50.000 0.00 0.00 40.30 4.20
7 8 1.532523 TTGTGCCTGAAATGCATCGA 58.467 45.000 0.00 0.00 40.30 3.59
8 9 2.572191 ATTGTGCCTGAAATGCATCG 57.428 45.000 0.00 0.00 40.30 3.84
9 10 4.142773 CCAAAATTGTGCCTGAAATGCATC 60.143 41.667 0.00 0.00 40.30 3.91
10 11 3.754323 CCAAAATTGTGCCTGAAATGCAT 59.246 39.130 0.00 0.00 40.30 3.96
11 12 3.139850 CCAAAATTGTGCCTGAAATGCA 58.860 40.909 0.00 0.00 34.21 3.96
12 13 2.485038 CCCAAAATTGTGCCTGAAATGC 59.515 45.455 0.00 0.00 0.00 3.56
13 14 2.485038 GCCCAAAATTGTGCCTGAAATG 59.515 45.455 0.00 0.00 0.00 2.32
14 15 2.372837 AGCCCAAAATTGTGCCTGAAAT 59.627 40.909 0.00 0.00 31.60 2.17
15 16 1.767681 AGCCCAAAATTGTGCCTGAAA 59.232 42.857 0.00 0.00 31.60 2.69
16 17 1.070445 CAGCCCAAAATTGTGCCTGAA 59.930 47.619 8.18 0.00 31.60 3.02
17 18 0.680618 CAGCCCAAAATTGTGCCTGA 59.319 50.000 8.18 0.00 31.60 3.86
18 19 0.320946 CCAGCCCAAAATTGTGCCTG 60.321 55.000 7.28 7.28 31.60 4.85
19 20 0.471591 TCCAGCCCAAAATTGTGCCT 60.472 50.000 0.00 0.00 31.60 4.75
20 21 0.396060 TTCCAGCCCAAAATTGTGCC 59.604 50.000 0.00 0.00 31.60 5.01
21 22 2.252976 TTTCCAGCCCAAAATTGTGC 57.747 45.000 0.00 0.00 0.00 4.57
22 23 3.075884 CCATTTCCAGCCCAAAATTGTG 58.924 45.455 0.00 0.00 0.00 3.33
23 24 2.040145 CCCATTTCCAGCCCAAAATTGT 59.960 45.455 0.00 0.00 0.00 2.71
24 25 2.040145 ACCCATTTCCAGCCCAAAATTG 59.960 45.455 0.00 0.00 0.00 2.32
25 26 2.305635 GACCCATTTCCAGCCCAAAATT 59.694 45.455 0.00 0.00 0.00 1.82
26 27 1.908619 GACCCATTTCCAGCCCAAAAT 59.091 47.619 0.00 0.00 0.00 1.82
27 28 1.347062 GACCCATTTCCAGCCCAAAA 58.653 50.000 0.00 0.00 0.00 2.44
28 29 0.544120 GGACCCATTTCCAGCCCAAA 60.544 55.000 0.00 0.00 35.49 3.28
29 30 1.078347 GGACCCATTTCCAGCCCAA 59.922 57.895 0.00 0.00 35.49 4.12
30 31 1.856873 AGGACCCATTTCCAGCCCA 60.857 57.895 0.00 0.00 38.25 5.36
31 32 1.076705 GAGGACCCATTTCCAGCCC 60.077 63.158 0.00 0.00 38.25 5.19
32 33 1.452108 CGAGGACCCATTTCCAGCC 60.452 63.158 0.00 0.00 38.25 4.85
33 34 2.115291 GCGAGGACCCATTTCCAGC 61.115 63.158 0.00 0.00 38.25 4.85
34 35 1.815421 CGCGAGGACCCATTTCCAG 60.815 63.158 0.00 0.00 38.25 3.86
35 36 2.267642 CGCGAGGACCCATTTCCA 59.732 61.111 0.00 0.00 38.25 3.53
56 57 1.297598 CAAAATCCGTCCGCATCGC 60.298 57.895 0.00 0.00 0.00 4.58
57 58 1.351707 CCAAAATCCGTCCGCATCG 59.648 57.895 0.00 0.00 0.00 3.84
58 59 0.746563 TCCCAAAATCCGTCCGCATC 60.747 55.000 0.00 0.00 0.00 3.91
59 60 0.322997 TTCCCAAAATCCGTCCGCAT 60.323 50.000 0.00 0.00 0.00 4.73
60 61 0.322997 ATTCCCAAAATCCGTCCGCA 60.323 50.000 0.00 0.00 0.00 5.69
61 62 0.100503 CATTCCCAAAATCCGTCCGC 59.899 55.000 0.00 0.00 0.00 5.54
62 63 0.738389 CCATTCCCAAAATCCGTCCG 59.262 55.000 0.00 0.00 0.00 4.79
63 64 1.111277 CCCATTCCCAAAATCCGTCC 58.889 55.000 0.00 0.00 0.00 4.79
64 65 1.749063 GACCCATTCCCAAAATCCGTC 59.251 52.381 0.00 0.00 0.00 4.79
65 66 1.847328 GACCCATTCCCAAAATCCGT 58.153 50.000 0.00 0.00 0.00 4.69
66 67 0.738389 CGACCCATTCCCAAAATCCG 59.262 55.000 0.00 0.00 0.00 4.18
67 68 1.111277 CCGACCCATTCCCAAAATCC 58.889 55.000 0.00 0.00 0.00 3.01
68 69 0.459899 GCCGACCCATTCCCAAAATC 59.540 55.000 0.00 0.00 0.00 2.17
69 70 1.319614 CGCCGACCCATTCCCAAAAT 61.320 55.000 0.00 0.00 0.00 1.82
70 71 1.974343 CGCCGACCCATTCCCAAAA 60.974 57.895 0.00 0.00 0.00 2.44
71 72 2.360600 CGCCGACCCATTCCCAAA 60.361 61.111 0.00 0.00 0.00 3.28
76 77 4.160635 CAACGCGCCGACCCATTC 62.161 66.667 5.73 0.00 0.00 2.67
89 90 4.273257 AAAAACGCCGGCCCAACG 62.273 61.111 23.46 9.08 0.00 4.10
90 91 2.660224 CAAAAACGCCGGCCCAAC 60.660 61.111 23.46 0.00 0.00 3.77
91 92 3.140225 GACAAAAACGCCGGCCCAA 62.140 57.895 23.46 0.00 0.00 4.12
92 93 3.597728 GACAAAAACGCCGGCCCA 61.598 61.111 23.46 0.00 0.00 5.36
93 94 2.428960 ATTGACAAAAACGCCGGCCC 62.429 55.000 23.46 0.00 0.00 5.80
94 95 0.241481 TATTGACAAAAACGCCGGCC 59.759 50.000 23.46 4.19 0.00 6.13
95 96 1.613270 CTATTGACAAAAACGCCGGC 58.387 50.000 19.07 19.07 0.00 6.13
96 97 1.613270 GCTATTGACAAAAACGCCGG 58.387 50.000 0.00 0.00 0.00 6.13
97 98 1.136197 TCGCTATTGACAAAAACGCCG 60.136 47.619 0.00 0.00 0.00 6.46
98 99 2.604969 TCGCTATTGACAAAAACGCC 57.395 45.000 0.00 0.00 0.00 5.68
99 100 3.098636 GGATCGCTATTGACAAAAACGC 58.901 45.455 0.00 0.00 0.00 4.84
100 101 4.335082 TGGATCGCTATTGACAAAAACG 57.665 40.909 0.00 0.00 0.00 3.60
101 102 6.034898 CCATTTGGATCGCTATTGACAAAAAC 59.965 38.462 0.00 0.00 37.39 2.43
102 103 6.071672 TCCATTTGGATCGCTATTGACAAAAA 60.072 34.615 0.00 0.00 39.78 1.94
103 104 5.417266 TCCATTTGGATCGCTATTGACAAAA 59.583 36.000 0.00 0.00 39.78 2.44
104 105 4.946772 TCCATTTGGATCGCTATTGACAAA 59.053 37.500 0.00 0.00 39.78 2.83
105 106 4.522114 TCCATTTGGATCGCTATTGACAA 58.478 39.130 0.00 0.00 39.78 3.18
106 107 4.149511 TCCATTTGGATCGCTATTGACA 57.850 40.909 0.00 0.00 39.78 3.58
118 119 1.375396 CCGCTCACGTCCATTTGGA 60.375 57.895 0.00 0.00 38.03 3.53
119 120 1.375396 TCCGCTCACGTCCATTTGG 60.375 57.895 0.00 0.00 37.70 3.28
120 121 1.787847 GTCCGCTCACGTCCATTTG 59.212 57.895 0.00 0.00 37.70 2.32
121 122 1.736645 CGTCCGCTCACGTCCATTT 60.737 57.895 0.00 0.00 37.70 2.32
122 123 2.126071 CGTCCGCTCACGTCCATT 60.126 61.111 0.00 0.00 37.70 3.16
157 158 0.528924 GATAAAAACACCGGCCCACC 59.471 55.000 0.00 0.00 0.00 4.61
158 159 1.249407 TGATAAAAACACCGGCCCAC 58.751 50.000 0.00 0.00 0.00 4.61
159 160 1.996798 TTGATAAAAACACCGGCCCA 58.003 45.000 0.00 0.00 0.00 5.36
160 161 4.426416 GTTATTGATAAAAACACCGGCCC 58.574 43.478 0.00 0.00 0.00 5.80
161 162 4.426416 GGTTATTGATAAAAACACCGGCC 58.574 43.478 0.00 0.00 0.00 6.13
162 163 4.082136 TGGGTTATTGATAAAAACACCGGC 60.082 41.667 0.00 0.00 0.00 6.13
163 164 5.646577 TGGGTTATTGATAAAAACACCGG 57.353 39.130 0.00 0.00 0.00 5.28
164 165 6.857956 TCATGGGTTATTGATAAAAACACCG 58.142 36.000 0.00 0.00 0.00 4.94
165 166 8.527810 TCTTCATGGGTTATTGATAAAAACACC 58.472 33.333 0.00 0.00 0.00 4.16
170 171 9.839817 TCGTATCTTCATGGGTTATTGATAAAA 57.160 29.630 0.00 0.00 0.00 1.52
174 175 8.924511 AAATCGTATCTTCATGGGTTATTGAT 57.075 30.769 0.00 0.00 0.00 2.57
175 176 8.620416 CAAAATCGTATCTTCATGGGTTATTGA 58.380 33.333 0.00 0.00 0.00 2.57
176 177 7.862372 CCAAAATCGTATCTTCATGGGTTATTG 59.138 37.037 0.00 0.00 0.00 1.90
177 178 7.470009 GCCAAAATCGTATCTTCATGGGTTATT 60.470 37.037 0.00 0.00 0.00 1.40
178 179 6.016276 GCCAAAATCGTATCTTCATGGGTTAT 60.016 38.462 0.00 0.00 0.00 1.89
206 207 2.267426 TGTTTGGCGTCGTGATAGATG 58.733 47.619 0.00 0.00 0.00 2.90
218 219 5.879237 AGTATTGTATGTGATTGTTTGGCG 58.121 37.500 0.00 0.00 0.00 5.69
242 243 7.531857 TCCCTGCAATAAACAGAAAACATAA 57.468 32.000 0.00 0.00 37.32 1.90
289 296 4.008330 ACAATCTTCTTCTGCACCATGAG 58.992 43.478 0.00 0.00 0.00 2.90
326 333 5.939883 TGGTATGGAGTTGAACAATCTTCTG 59.060 40.000 0.00 0.00 0.00 3.02
462 472 0.908910 TGGTGGTGGTATGCACTAGG 59.091 55.000 0.00 0.00 0.00 3.02
464 474 0.616371 GGTGGTGGTGGTATGCACTA 59.384 55.000 0.00 0.00 0.00 2.74
485 500 5.123227 GTTGTCAGCTGGGCACTATTTATA 58.877 41.667 15.13 0.00 0.00 0.98
621 638 1.204704 AGAACATCAATCGTGCGAGGA 59.795 47.619 0.00 1.20 0.00 3.71
626 643 2.280183 GTCTCGAGAACATCAATCGTGC 59.720 50.000 18.55 0.00 37.69 5.34
673 699 2.600475 CGTACGTGCCTTGGCGTTT 61.600 57.895 7.22 0.00 41.77 3.60
683 709 3.466836 GAACAGAAATGTTCGTACGTGC 58.533 45.455 16.05 9.79 38.75 5.34
692 718 5.799936 CGAACAACACAAGAACAGAAATGTT 59.200 36.000 0.00 0.00 34.29 2.71
699 725 5.615581 CGTAAATCGAACAACACAAGAACAG 59.384 40.000 0.00 0.00 42.86 3.16
732 758 2.478890 GGCTGCATGCAAGAGCGAT 61.479 57.895 22.88 0.00 46.23 4.58
747 773 2.508526 GGCGATTGATTCTTATGGGCT 58.491 47.619 0.00 0.00 0.00 5.19
756 782 3.769536 ACCAAAAATCGGCGATTGATTC 58.230 40.909 33.07 0.00 35.07 2.52
770 796 4.216708 AGGGGACAACGAAATACCAAAAA 58.783 39.130 0.00 0.00 0.00 1.94
775 801 3.062122 TCAAGGGGACAACGAAATACC 57.938 47.619 0.00 0.00 0.00 2.73
776 802 6.937436 ATAATCAAGGGGACAACGAAATAC 57.063 37.500 0.00 0.00 0.00 1.89
810 841 9.672086 TCGTCAAAGACCAAATTATAAACAAAG 57.328 29.630 0.00 0.00 0.00 2.77
812 843 9.834628 GATCGTCAAAGACCAAATTATAAACAA 57.165 29.630 0.00 0.00 0.00 2.83
816 847 8.128582 GCATGATCGTCAAAGACCAAATTATAA 58.871 33.333 0.00 0.00 0.00 0.98
818 849 6.095300 TGCATGATCGTCAAAGACCAAATTAT 59.905 34.615 0.00 0.00 0.00 1.28
827 858 1.372582 GGCTGCATGATCGTCAAAGA 58.627 50.000 0.50 0.00 0.00 2.52
828 859 0.379669 GGGCTGCATGATCGTCAAAG 59.620 55.000 0.50 0.00 0.00 2.77
830 861 0.107066 ATGGGCTGCATGATCGTCAA 60.107 50.000 0.50 0.00 0.00 3.18
831 862 0.816421 CATGGGCTGCATGATCGTCA 60.816 55.000 0.50 0.00 32.09 4.35
832 863 0.533531 TCATGGGCTGCATGATCGTC 60.534 55.000 0.50 0.00 34.50 4.20
835 866 0.533531 TCGTCATGGGCTGCATGATC 60.534 55.000 9.22 3.98 40.62 2.92
836 867 0.109913 ATCGTCATGGGCTGCATGAT 59.890 50.000 9.22 0.00 40.62 2.45
837 868 0.533531 GATCGTCATGGGCTGCATGA 60.534 55.000 0.50 0.00 36.79 3.07
871 904 3.508762 GCGGTCGATCAAGAAGAAGTAA 58.491 45.455 0.00 0.00 0.00 2.24
873 906 1.404315 GGCGGTCGATCAAGAAGAAGT 60.404 52.381 0.00 0.00 0.00 3.01
889 922 3.951655 GCGTCAACAGCAATGGCGG 62.952 63.158 11.42 0.00 45.46 6.13
1092 1129 2.355481 GACGACGACGCCACCTTT 60.355 61.111 7.30 0.00 43.96 3.11
1272 1312 1.302033 CACCTTGAGGCTGAGCGTT 60.302 57.895 0.00 0.00 39.32 4.84
1326 1366 2.490115 GTCGAGGAAGAAGCTCTTGAGA 59.510 50.000 1.30 0.00 36.73 3.27
1595 1635 1.344438 TGTCGTGATCTTTCCTGCTGT 59.656 47.619 0.00 0.00 0.00 4.40
1653 1693 0.744414 CCACCGTGATCGCCATTTCT 60.744 55.000 0.00 0.00 35.54 2.52
1878 1918 3.728373 GGGTCACCGGGAATGCCT 61.728 66.667 6.32 0.00 0.00 4.75
1890 1930 2.897207 CTGTAATCCGCCGGGTCA 59.103 61.111 1.90 0.00 33.83 4.02
1982 2022 8.988934 GCTATCAGTTTCATATAAACGAATCCA 58.011 33.333 0.00 0.00 35.42 3.41
2029 2070 5.512060 GCATATCCTCATTCAGCCTAGTGAA 60.512 44.000 0.00 0.00 40.68 3.18
2138 2180 5.588568 TGAAACGGCTTGCAATTTATTTG 57.411 34.783 0.00 0.00 38.43 2.32
2140 2182 6.426328 TGATTTGAAACGGCTTGCAATTTATT 59.574 30.769 0.00 0.00 0.00 1.40
2142 2184 5.292765 TGATTTGAAACGGCTTGCAATTTA 58.707 33.333 0.00 0.00 0.00 1.40
2153 2195 5.220567 CCTTTTGGTGTTTGATTTGAAACGG 60.221 40.000 0.00 0.00 38.46 4.44
2188 2230 2.830923 TGCCAAACATTCCCGATCATTT 59.169 40.909 0.00 0.00 0.00 2.32
2196 2238 5.530543 TCAATTTTCTTTGCCAAACATTCCC 59.469 36.000 0.00 0.00 0.00 3.97
2208 2250 4.797471 TGCGAGGATGTCAATTTTCTTTG 58.203 39.130 0.00 0.00 0.00 2.77
2220 2262 5.401550 CAAATTATGTTGTTGCGAGGATGT 58.598 37.500 0.00 0.00 0.00 3.06
2228 2270 5.163834 CCAAGATGGCAAATTATGTTGTTGC 60.164 40.000 0.00 0.00 45.48 4.17
2229 2271 5.352016 CCCAAGATGGCAAATTATGTTGTTG 59.648 40.000 0.00 0.00 35.79 3.33
2230 2272 5.490159 CCCAAGATGGCAAATTATGTTGTT 58.510 37.500 0.00 0.00 35.79 2.83
2253 2295 2.894763 TAGCATGGCAAATGGAATGC 57.105 45.000 0.00 0.00 44.56 3.56
2279 2321 5.465532 TTTTGCTACAGATCAAATGCCAA 57.534 34.783 0.00 0.00 32.92 4.52
2284 2326 9.158233 CATTTTGGATTTTGCTACAGATCAAAT 57.842 29.630 0.00 0.00 32.92 2.32
2287 2329 7.465353 TCATTTTGGATTTTGCTACAGATCA 57.535 32.000 0.00 0.00 0.00 2.92
2368 2410 2.221055 GTGAAAGAAATGTCGACGCTGT 59.779 45.455 11.62 0.46 0.00 4.40
2369 2411 2.411547 GGTGAAAGAAATGTCGACGCTG 60.412 50.000 11.62 0.00 0.00 5.18
2370 2412 1.798813 GGTGAAAGAAATGTCGACGCT 59.201 47.619 11.62 2.67 0.00 5.07
2371 2413 1.136057 GGGTGAAAGAAATGTCGACGC 60.136 52.381 11.62 0.15 0.00 5.19
2372 2414 2.139917 TGGGTGAAAGAAATGTCGACG 58.860 47.619 11.62 0.00 0.00 5.12
2373 2415 3.139077 ACTGGGTGAAAGAAATGTCGAC 58.861 45.455 9.11 9.11 0.00 4.20
2374 2416 3.485463 ACTGGGTGAAAGAAATGTCGA 57.515 42.857 0.00 0.00 0.00 4.20
2375 2417 3.058224 GGAACTGGGTGAAAGAAATGTCG 60.058 47.826 0.00 0.00 0.00 4.35
2466 2511 9.360093 GATGCGAACTAGATATTTAGTTGCTAT 57.640 33.333 20.19 16.88 42.38 2.97
2495 2540 3.463944 ACTTGTGACAGGTAACGAAAGG 58.536 45.455 0.00 0.00 46.39 3.11
2545 2590 1.107114 GGAGCATTCGAGGTCTGAGA 58.893 55.000 4.18 0.00 36.33 3.27
2610 2655 6.603201 GTGATGGAGTAAAGGATCAAATTCCA 59.397 38.462 0.00 0.32 38.32 3.53
2611 2656 6.603201 TGTGATGGAGTAAAGGATCAAATTCC 59.397 38.462 0.00 0.00 35.90 3.01
2625 2670 1.696884 TGGTGTTGCTGTGATGGAGTA 59.303 47.619 0.00 0.00 0.00 2.59
2828 2873 6.551227 AGAAAAAGGCTGAGAAGTTGGTATTT 59.449 34.615 0.00 0.00 0.00 1.40
2834 2879 5.297776 TGAAGAGAAAAAGGCTGAGAAGTTG 59.702 40.000 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.