Multiple sequence alignment - TraesCS6A01G025600

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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 TraesCS6A01G025600 chr6A 100.000 6790 0 0 1 6790 12700700 12693911 0.000000e+00 12539
1 TraesCS6A01G025600 chr6A 98.628 6632 71 16 169 6790 480630731 480637352 0.000000e+00 11725
2 TraesCS6A01G025600 chr6A 98.612 6629 80 11 169 6790 87934005 87940628 0.000000e+00 11721
3 TraesCS6A01G025600 chr6A 94.472 199 8 3 1 198 245331387 245331191 3.080000e-78 303
4 TraesCS6A01G025600 chr7A 99.049 6624 54 6 169 6790 624766227 624759611 0.000000e+00 11875
5 TraesCS6A01G025600 chr7A 98.568 6635 70 8 169 6790 634123266 634129888 0.000000e+00 11703
6 TraesCS6A01G025600 chr7A 97.038 4862 113 10 1942 6790 724100224 724105067 0.000000e+00 8152
7 TraesCS6A01G025600 chr1B 98.777 6625 62 11 169 6790 637607302 637613910 0.000000e+00 11767
8 TraesCS6A01G025600 chr7B 98.521 6627 85 11 169 6790 666533655 666527037 0.000000e+00 11683
9 TraesCS6A01G025600 chr7B 98.431 6630 81 16 169 6790 194120608 194127222 0.000000e+00 11646
10 TraesCS6A01G025600 chr6B 98.475 6622 69 11 169 6790 21371604 21365015 0.000000e+00 11640
11 TraesCS6A01G025600 chr6B 98.305 177 3 0 1 177 358138238 358138062 1.840000e-80 311
12 TraesCS6A01G025600 chr5A 98.592 5254 53 10 169 5418 396396016 396401252 0.000000e+00 9273
13 TraesCS6A01G025600 chr2B 98.289 4850 64 5 1942 6790 99560066 99564897 0.000000e+00 8479
14 TraesCS6A01G025600 chr2B 98.864 176 1 1 1 176 139986883 139987057 5.110000e-81 313
15 TraesCS6A01G025600 chr2A 95.222 4856 184 30 1942 6790 614229310 614224496 0.000000e+00 7638
16 TraesCS6A01G025600 chr4B 98.539 1780 15 7 169 1943 14718977 14717204 0.000000e+00 3133
17 TraesCS6A01G025600 chr4B 98.870 177 2 0 1 177 256247602 256247778 3.950000e-82 316
18 TraesCS6A01G025600 chr4B 98.315 178 2 1 1 177 263311373 263311550 1.840000e-80 311
19 TraesCS6A01G025600 chr4B 98.315 178 2 1 1 177 293029919 293029742 1.840000e-80 311
20 TraesCS6A01G025600 chr4B 95.876 194 4 3 1 192 509789668 509789477 1.840000e-80 311
21 TraesCS6A01G025600 chr4B 97.778 180 3 1 1 180 253379716 253379538 6.610000e-80 309
22 TraesCS6A01G025600 chrUn 98.315 178 2 1 1 177 253937048 253936871 1.840000e-80 311


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 TraesCS6A01G025600 chr6A 12693911 12700700 6789 True 12539 12539 100.000 1 6790 1 chr6A.!!$R1 6789
1 TraesCS6A01G025600 chr6A 480630731 480637352 6621 False 11725 11725 98.628 169 6790 1 chr6A.!!$F2 6621
2 TraesCS6A01G025600 chr6A 87934005 87940628 6623 False 11721 11721 98.612 169 6790 1 chr6A.!!$F1 6621
3 TraesCS6A01G025600 chr7A 624759611 624766227 6616 True 11875 11875 99.049 169 6790 1 chr7A.!!$R1 6621
4 TraesCS6A01G025600 chr7A 634123266 634129888 6622 False 11703 11703 98.568 169 6790 1 chr7A.!!$F1 6621
5 TraesCS6A01G025600 chr7A 724100224 724105067 4843 False 8152 8152 97.038 1942 6790 1 chr7A.!!$F2 4848
6 TraesCS6A01G025600 chr1B 637607302 637613910 6608 False 11767 11767 98.777 169 6790 1 chr1B.!!$F1 6621
7 TraesCS6A01G025600 chr7B 666527037 666533655 6618 True 11683 11683 98.521 169 6790 1 chr7B.!!$R1 6621
8 TraesCS6A01G025600 chr7B 194120608 194127222 6614 False 11646 11646 98.431 169 6790 1 chr7B.!!$F1 6621
9 TraesCS6A01G025600 chr6B 21365015 21371604 6589 True 11640 11640 98.475 169 6790 1 chr6B.!!$R1 6621
10 TraesCS6A01G025600 chr5A 396396016 396401252 5236 False 9273 9273 98.592 169 5418 1 chr5A.!!$F1 5249
11 TraesCS6A01G025600 chr2B 99560066 99564897 4831 False 8479 8479 98.289 1942 6790 1 chr2B.!!$F1 4848
12 TraesCS6A01G025600 chr2A 614224496 614229310 4814 True 7638 7638 95.222 1942 6790 1 chr2A.!!$R1 4848
13 TraesCS6A01G025600 chr4B 14717204 14718977 1773 True 3133 3133 98.539 169 1943 1 chr4B.!!$R1 1774

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
75 76 0.392060 CGGTCCCGGGAAAAGGTAAG 60.392 60.000 28.84 6.57 35.56 2.34 F
1885 1922 0.385029 TGCACATTCAGTTGCACACC 59.615 50.000 0.00 0.00 32.11 4.16 F
1896 1933 1.723608 TTGCACACCGGCAGTCTTTG 61.724 55.000 0.00 0.00 45.88 2.77 F
2807 2847 1.561643 TTTGTTTGGGTCTGGTGCAA 58.438 45.000 0.00 0.00 0.00 4.08 F
4048 4098 2.268076 GCAAACTGGGGCATCACGT 61.268 57.895 0.00 0.00 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1934 2.028294 AGCTCATGAGGACAACTGACTG 60.028 50.000 23.89 0.0 0.0 3.51 R
2807 2847 4.022242 ACGAGCGCATCAAGGTATAGTATT 60.022 41.667 11.47 0.0 0.0 1.89 R
4048 4098 3.560068 GTCTCTTTCTTTTTGGAGCACGA 59.440 43.478 0.00 0.0 0.0 4.35 R
4456 4546 1.743958 TCGTCTTCTTCATCCTCGTCC 59.256 52.381 0.00 0.0 0.0 4.79 R
6187 6306 1.481363 GTAGGCTGTGGGGAGTTAGTC 59.519 57.143 0.00 0.0 0.0 2.59 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
23 24 6.530019 TCTTTATCATATGGATGCTAGCGA 57.470 37.500 10.77 0.00 36.72 4.93
24 25 6.333416 TCTTTATCATATGGATGCTAGCGAC 58.667 40.000 10.77 6.33 36.72 5.19
25 26 5.659440 TTATCATATGGATGCTAGCGACA 57.341 39.130 10.77 9.20 36.72 4.35
26 27 3.303881 TCATATGGATGCTAGCGACAC 57.696 47.619 10.77 0.81 32.62 3.67
27 28 2.893489 TCATATGGATGCTAGCGACACT 59.107 45.455 10.77 0.00 32.62 3.55
28 29 4.079253 TCATATGGATGCTAGCGACACTA 58.921 43.478 10.77 0.00 32.62 2.74
29 30 4.706962 TCATATGGATGCTAGCGACACTAT 59.293 41.667 10.77 7.20 32.62 2.12
30 31 3.584406 ATGGATGCTAGCGACACTATC 57.416 47.619 10.77 6.09 0.00 2.08
31 32 2.306847 TGGATGCTAGCGACACTATCA 58.693 47.619 10.77 0.00 31.82 2.15
32 33 2.893489 TGGATGCTAGCGACACTATCAT 59.107 45.455 10.77 0.00 39.77 2.45
33 34 4.079253 TGGATGCTAGCGACACTATCATA 58.921 43.478 10.77 0.00 37.73 2.15
34 35 4.706962 TGGATGCTAGCGACACTATCATAT 59.293 41.667 10.77 0.00 37.73 1.78
35 36 5.885912 TGGATGCTAGCGACACTATCATATA 59.114 40.000 10.77 0.00 37.73 0.86
36 37 6.183360 TGGATGCTAGCGACACTATCATATAC 60.183 42.308 10.77 0.00 37.73 1.47
37 38 5.217895 TGCTAGCGACACTATCATATACG 57.782 43.478 10.77 0.00 0.00 3.06
38 39 4.694037 TGCTAGCGACACTATCATATACGT 59.306 41.667 10.77 0.00 0.00 3.57
39 40 5.022653 GCTAGCGACACTATCATATACGTG 58.977 45.833 0.00 0.00 0.00 4.49
40 41 5.163884 GCTAGCGACACTATCATATACGTGA 60.164 44.000 0.00 0.00 0.00 4.35
41 42 5.284428 AGCGACACTATCATATACGTGAG 57.716 43.478 0.00 0.00 0.00 3.51
42 43 3.846896 GCGACACTATCATATACGTGAGC 59.153 47.826 0.00 0.00 0.00 4.26
43 44 4.404324 CGACACTATCATATACGTGAGCC 58.596 47.826 0.00 0.00 0.00 4.70
44 45 4.083484 CGACACTATCATATACGTGAGCCA 60.083 45.833 0.00 0.00 0.00 4.75
45 46 5.562113 CGACACTATCATATACGTGAGCCAA 60.562 44.000 0.00 0.00 0.00 4.52
46 47 6.156748 ACACTATCATATACGTGAGCCAAA 57.843 37.500 0.00 0.00 0.00 3.28
47 48 6.578944 ACACTATCATATACGTGAGCCAAAA 58.421 36.000 0.00 0.00 0.00 2.44
48 49 6.701841 ACACTATCATATACGTGAGCCAAAAG 59.298 38.462 0.00 0.00 0.00 2.27
49 50 6.146184 CACTATCATATACGTGAGCCAAAAGG 59.854 42.308 0.00 0.00 0.00 3.11
50 51 3.202906 TCATATACGTGAGCCAAAAGGC 58.797 45.455 0.00 0.00 0.00 4.35
51 52 1.647346 TATACGTGAGCCAAAAGGCG 58.353 50.000 0.00 0.00 40.23 5.52
52 53 1.644786 ATACGTGAGCCAAAAGGCGC 61.645 55.000 0.00 0.00 40.23 6.53
53 54 2.997952 TACGTGAGCCAAAAGGCGCA 62.998 55.000 10.83 8.86 41.90 6.09
54 55 2.727544 GTGAGCCAAAAGGCGCAA 59.272 55.556 14.31 0.00 45.17 4.85
55 56 1.067250 GTGAGCCAAAAGGCGCAAA 59.933 52.632 14.31 0.00 45.17 3.68
56 57 1.067250 TGAGCCAAAAGGCGCAAAC 59.933 52.632 10.83 0.00 41.28 2.93
57 58 2.016165 GAGCCAAAAGGCGCAAACG 61.016 57.895 10.83 0.00 44.07 3.60
58 59 3.035503 GCCAAAAGGCGCAAACGG 61.036 61.111 10.83 3.45 40.57 4.44
59 60 2.415426 CCAAAAGGCGCAAACGGT 59.585 55.556 10.83 0.00 40.57 4.83
60 61 1.660264 CCAAAAGGCGCAAACGGTC 60.660 57.895 10.83 0.00 40.57 4.79
61 62 1.660264 CAAAAGGCGCAAACGGTCC 60.660 57.895 10.83 0.00 40.57 4.46
62 63 2.852180 AAAAGGCGCAAACGGTCCC 61.852 57.895 10.83 0.00 40.57 4.46
67 68 4.992511 CGCAAACGGTCCCGGGAA 62.993 66.667 28.84 6.65 44.69 3.97
68 69 2.595172 GCAAACGGTCCCGGGAAA 60.595 61.111 28.84 0.00 44.69 3.13
69 70 2.194889 GCAAACGGTCCCGGGAAAA 61.195 57.895 28.84 0.00 44.69 2.29
70 71 1.953772 CAAACGGTCCCGGGAAAAG 59.046 57.895 28.84 21.49 44.69 2.27
71 72 1.228337 AAACGGTCCCGGGAAAAGG 60.228 57.895 28.84 16.97 44.69 3.11
72 73 1.998444 AAACGGTCCCGGGAAAAGGT 61.998 55.000 28.84 17.68 44.69 3.50
73 74 1.126948 AACGGTCCCGGGAAAAGGTA 61.127 55.000 28.84 0.00 44.69 3.08
74 75 1.126948 ACGGTCCCGGGAAAAGGTAA 61.127 55.000 28.84 0.00 44.69 2.85
75 76 0.392060 CGGTCCCGGGAAAAGGTAAG 60.392 60.000 28.84 6.57 35.56 2.34
76 77 0.986527 GGTCCCGGGAAAAGGTAAGA 59.013 55.000 28.84 0.00 0.00 2.10
77 78 1.339438 GGTCCCGGGAAAAGGTAAGAC 60.339 57.143 28.84 9.16 0.00 3.01
78 79 0.609662 TCCCGGGAAAAGGTAAGACG 59.390 55.000 24.50 0.00 0.00 4.18
79 80 0.609662 CCCGGGAAAAGGTAAGACGA 59.390 55.000 18.48 0.00 0.00 4.20
80 81 1.673923 CCCGGGAAAAGGTAAGACGAC 60.674 57.143 18.48 0.00 0.00 4.34
81 82 1.001181 CCGGGAAAAGGTAAGACGACA 59.999 52.381 0.00 0.00 0.00 4.35
82 83 2.064014 CGGGAAAAGGTAAGACGACAC 58.936 52.381 0.00 0.00 0.00 3.67
83 84 2.420642 GGGAAAAGGTAAGACGACACC 58.579 52.381 0.00 0.00 34.86 4.16
84 85 2.420642 GGAAAAGGTAAGACGACACCC 58.579 52.381 0.00 0.00 35.25 4.61
85 86 2.064014 GAAAAGGTAAGACGACACCCG 58.936 52.381 0.00 0.00 45.44 5.28
106 107 2.585247 GGATACCGTGCGTGAGGC 60.585 66.667 0.00 0.00 43.96 4.70
107 108 2.585247 GATACCGTGCGTGAGGCC 60.585 66.667 0.00 0.00 42.61 5.19
108 109 4.508128 ATACCGTGCGTGAGGCCG 62.508 66.667 0.00 0.00 42.61 6.13
116 117 2.664851 CGTGAGGCCGCAAAGTGA 60.665 61.111 12.05 0.00 0.00 3.41
117 118 2.034879 CGTGAGGCCGCAAAGTGAT 61.035 57.895 12.05 0.00 0.00 3.06
118 119 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.00 0.00 2.15
119 120 1.668419 GTGAGGCCGCAAAGTGATAT 58.332 50.000 12.05 0.00 0.00 1.63
120 121 1.331756 GTGAGGCCGCAAAGTGATATG 59.668 52.381 12.05 0.00 0.00 1.78
121 122 1.209261 TGAGGCCGCAAAGTGATATGA 59.791 47.619 6.75 0.00 0.00 2.15
122 123 2.288666 GAGGCCGCAAAGTGATATGAA 58.711 47.619 0.00 0.00 0.00 2.57
123 124 2.289002 GAGGCCGCAAAGTGATATGAAG 59.711 50.000 0.00 0.00 0.00 3.02
124 125 2.017049 GGCCGCAAAGTGATATGAAGT 58.983 47.619 0.00 0.00 0.00 3.01
125 126 2.223340 GGCCGCAAAGTGATATGAAGTG 60.223 50.000 0.00 0.00 0.00 3.16
126 127 2.420022 GCCGCAAAGTGATATGAAGTGT 59.580 45.455 0.00 0.00 0.00 3.55
127 128 3.119849 GCCGCAAAGTGATATGAAGTGTT 60.120 43.478 0.00 0.00 0.00 3.32
128 129 4.094294 GCCGCAAAGTGATATGAAGTGTTA 59.906 41.667 0.00 0.00 0.00 2.41
129 130 5.560148 CCGCAAAGTGATATGAAGTGTTAC 58.440 41.667 0.00 0.00 0.00 2.50
130 131 5.447279 CCGCAAAGTGATATGAAGTGTTACC 60.447 44.000 0.00 0.00 0.00 2.85
131 132 5.121611 CGCAAAGTGATATGAAGTGTTACCA 59.878 40.000 0.00 0.00 0.00 3.25
132 133 6.546395 GCAAAGTGATATGAAGTGTTACCAG 58.454 40.000 0.00 0.00 0.00 4.00
133 134 6.546395 CAAAGTGATATGAAGTGTTACCAGC 58.454 40.000 0.00 0.00 0.00 4.85
134 135 5.683876 AGTGATATGAAGTGTTACCAGCT 57.316 39.130 0.00 0.00 0.00 4.24
135 136 6.791867 AGTGATATGAAGTGTTACCAGCTA 57.208 37.500 0.00 0.00 0.00 3.32
136 137 6.810911 AGTGATATGAAGTGTTACCAGCTAG 58.189 40.000 0.00 0.00 0.00 3.42
137 138 6.607600 AGTGATATGAAGTGTTACCAGCTAGA 59.392 38.462 0.00 0.00 0.00 2.43
138 139 7.288852 AGTGATATGAAGTGTTACCAGCTAGAT 59.711 37.037 0.00 0.00 0.00 1.98
139 140 7.596995 GTGATATGAAGTGTTACCAGCTAGATC 59.403 40.741 0.00 0.00 0.00 2.75
140 141 4.371855 TGAAGTGTTACCAGCTAGATCG 57.628 45.455 0.00 0.00 0.00 3.69
141 142 4.014406 TGAAGTGTTACCAGCTAGATCGA 58.986 43.478 0.00 0.00 0.00 3.59
142 143 4.645136 TGAAGTGTTACCAGCTAGATCGAT 59.355 41.667 0.00 0.00 0.00 3.59
143 144 4.576216 AGTGTTACCAGCTAGATCGATG 57.424 45.455 0.54 0.00 0.00 3.84
144 145 3.954904 AGTGTTACCAGCTAGATCGATGT 59.045 43.478 0.54 0.00 0.00 3.06
145 146 4.045104 GTGTTACCAGCTAGATCGATGTG 58.955 47.826 0.54 0.00 0.00 3.21
146 147 3.951680 TGTTACCAGCTAGATCGATGTGA 59.048 43.478 0.54 0.00 0.00 3.58
147 148 4.202020 TGTTACCAGCTAGATCGATGTGAC 60.202 45.833 0.54 0.01 0.00 3.67
148 149 2.379005 ACCAGCTAGATCGATGTGACA 58.621 47.619 0.54 0.00 0.00 3.58
149 150 2.961741 ACCAGCTAGATCGATGTGACAT 59.038 45.455 0.54 0.00 0.00 3.06
150 151 3.005261 ACCAGCTAGATCGATGTGACATC 59.995 47.826 15.36 15.36 0.00 3.06
151 152 3.232771 CAGCTAGATCGATGTGACATCG 58.767 50.000 34.77 34.77 42.38 3.84
162 163 2.806237 GACATCGAGTCGGGGTCC 59.194 66.667 20.03 8.02 37.53 4.46
163 164 1.753463 GACATCGAGTCGGGGTCCT 60.753 63.158 20.03 0.00 37.53 3.85
164 165 2.005960 GACATCGAGTCGGGGTCCTG 62.006 65.000 20.03 9.27 37.53 3.86
165 166 1.753078 CATCGAGTCGGGGTCCTGA 60.753 63.158 13.54 0.00 0.00 3.86
991 1008 3.546002 TTTGTTGTATTTCCTTCCGCG 57.454 42.857 0.00 0.00 0.00 6.46
1830 1867 4.211374 ACACTAGAACTTTTTGTAGCTGCG 59.789 41.667 0.00 0.00 32.83 5.18
1885 1922 0.385029 TGCACATTCAGTTGCACACC 59.615 50.000 0.00 0.00 32.11 4.16
1896 1933 1.723608 TTGCACACCGGCAGTCTTTG 61.724 55.000 0.00 0.00 45.88 2.77
1932 1969 5.220931 CCTCATGAGCTTTATTAGTTGCACC 60.221 44.000 17.76 0.00 0.00 5.01
2227 2264 2.097825 GCGGACCTCACTAAGTTCCTA 58.902 52.381 0.00 0.00 0.00 2.94
2285 2322 3.348938 CCAGGAAGGGGAAGGATCT 57.651 57.895 0.00 0.00 0.00 2.75
2807 2847 1.561643 TTTGTTTGGGTCTGGTGCAA 58.438 45.000 0.00 0.00 0.00 4.08
4048 4098 2.268076 GCAAACTGGGGCATCACGT 61.268 57.895 0.00 0.00 0.00 4.49
4372 4462 2.284995 GGTGAGGCCAGAGAGGGT 60.285 66.667 5.01 0.00 38.09 4.34
4456 4546 1.138661 GATGGCAGTGAGAGGGAAGAG 59.861 57.143 0.00 0.00 0.00 2.85
4633 4738 2.273370 CGAGCAGCAGCAATTCATTT 57.727 45.000 3.17 0.00 45.49 2.32
4808 4913 1.016130 CGTGCCAGATTTCAGCGACT 61.016 55.000 0.00 0.00 0.00 4.18
4863 4968 5.809001 TGACAAGAGCCTGTTCTTATCAAT 58.191 37.500 2.74 0.00 37.59 2.57
5451 5558 2.306847 GGTCACAGTCAAAACCACCAT 58.693 47.619 0.00 0.00 0.00 3.55
5903 6022 3.851458 ATGAAGGATGTGATGCTGCTA 57.149 42.857 0.00 0.00 0.00 3.49
5999 6118 0.601311 AGAACTTGGCACGAGCAGTC 60.601 55.000 7.26 0.00 44.61 3.51
6637 6763 1.065410 TTGAGGGAGGCCTTTCACCA 61.065 55.000 6.77 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.071391 TGTCGCTAGCATCCATATGATAAAGA 60.071 38.462 16.45 0.00 33.75 2.52
1 2 6.035435 GTGTCGCTAGCATCCATATGATAAAG 59.965 42.308 16.45 0.00 33.75 1.85
2 3 5.869344 GTGTCGCTAGCATCCATATGATAAA 59.131 40.000 16.45 0.00 33.75 1.40
3 4 5.185828 AGTGTCGCTAGCATCCATATGATAA 59.814 40.000 16.45 0.00 33.75 1.75
4 5 4.706962 AGTGTCGCTAGCATCCATATGATA 59.293 41.667 16.45 0.00 34.84 2.15
5 6 3.513119 AGTGTCGCTAGCATCCATATGAT 59.487 43.478 16.45 0.00 34.84 2.45
6 7 2.893489 AGTGTCGCTAGCATCCATATGA 59.107 45.455 16.45 0.00 34.84 2.15
7 8 3.309961 AGTGTCGCTAGCATCCATATG 57.690 47.619 16.45 0.00 36.09 1.78
8 9 4.706962 TGATAGTGTCGCTAGCATCCATAT 59.293 41.667 16.45 6.97 40.72 1.78
9 10 4.079253 TGATAGTGTCGCTAGCATCCATA 58.921 43.478 16.45 1.98 40.72 2.74
10 11 2.893489 TGATAGTGTCGCTAGCATCCAT 59.107 45.455 16.45 0.00 40.72 3.41
11 12 2.306847 TGATAGTGTCGCTAGCATCCA 58.693 47.619 16.45 4.65 40.72 3.41
16 17 5.022653 CACGTATATGATAGTGTCGCTAGC 58.977 45.833 4.06 4.06 36.67 3.42
17 18 6.404712 TCACGTATATGATAGTGTCGCTAG 57.595 41.667 0.00 0.00 36.16 3.42
18 19 5.163884 GCTCACGTATATGATAGTGTCGCTA 60.164 44.000 0.00 0.00 36.16 4.26
19 20 4.378563 GCTCACGTATATGATAGTGTCGCT 60.379 45.833 0.00 0.00 36.16 4.93
20 21 3.846896 GCTCACGTATATGATAGTGTCGC 59.153 47.826 0.00 0.00 36.16 5.19
21 22 4.083484 TGGCTCACGTATATGATAGTGTCG 60.083 45.833 0.00 0.00 36.16 4.35
22 23 5.372547 TGGCTCACGTATATGATAGTGTC 57.627 43.478 0.00 0.00 36.16 3.67
23 24 5.784578 TTGGCTCACGTATATGATAGTGT 57.215 39.130 0.00 0.00 36.16 3.55
24 25 6.146184 CCTTTTGGCTCACGTATATGATAGTG 59.854 42.308 0.00 0.00 36.06 2.74
25 26 6.223852 CCTTTTGGCTCACGTATATGATAGT 58.776 40.000 0.00 0.00 0.00 2.12
26 27 6.712241 CCTTTTGGCTCACGTATATGATAG 57.288 41.667 0.00 0.00 0.00 2.08
42 43 1.660264 GACCGTTTGCGCCTTTTGG 60.660 57.895 4.18 2.72 44.18 3.28
43 44 1.660264 GGACCGTTTGCGCCTTTTG 60.660 57.895 4.18 0.00 36.67 2.44
44 45 2.725641 GGACCGTTTGCGCCTTTT 59.274 55.556 4.18 0.00 36.67 2.27
45 46 3.292159 GGGACCGTTTGCGCCTTT 61.292 61.111 4.18 0.00 36.67 3.11
50 51 4.992511 TTCCCGGGACCGTTTGCG 62.993 66.667 26.87 0.00 37.81 4.85
51 52 2.137425 CTTTTCCCGGGACCGTTTGC 62.137 60.000 26.87 0.00 37.81 3.68
52 53 1.520600 CCTTTTCCCGGGACCGTTTG 61.521 60.000 26.87 10.30 37.81 2.93
53 54 1.228337 CCTTTTCCCGGGACCGTTT 60.228 57.895 26.87 0.00 37.81 3.60
54 55 1.126948 TACCTTTTCCCGGGACCGTT 61.127 55.000 26.87 9.48 37.81 4.44
55 56 1.126948 TTACCTTTTCCCGGGACCGT 61.127 55.000 26.87 18.60 37.81 4.83
56 57 0.392060 CTTACCTTTTCCCGGGACCG 60.392 60.000 26.87 14.42 39.44 4.79
57 58 0.986527 TCTTACCTTTTCCCGGGACC 59.013 55.000 26.87 0.00 0.00 4.46
58 59 1.673923 CGTCTTACCTTTTCCCGGGAC 60.674 57.143 26.87 7.18 0.00 4.46
59 60 0.609662 CGTCTTACCTTTTCCCGGGA 59.390 55.000 22.63 22.63 0.00 5.14
60 61 0.609662 TCGTCTTACCTTTTCCCGGG 59.390 55.000 16.85 16.85 0.00 5.73
61 62 1.001181 TGTCGTCTTACCTTTTCCCGG 59.999 52.381 0.00 0.00 0.00 5.73
62 63 2.064014 GTGTCGTCTTACCTTTTCCCG 58.936 52.381 0.00 0.00 0.00 5.14
63 64 2.420642 GGTGTCGTCTTACCTTTTCCC 58.579 52.381 0.00 0.00 34.11 3.97
64 65 2.420642 GGGTGTCGTCTTACCTTTTCC 58.579 52.381 0.00 0.00 37.15 3.13
65 66 2.064014 CGGGTGTCGTCTTACCTTTTC 58.936 52.381 0.00 0.00 37.15 2.29
66 67 2.159327 CGGGTGTCGTCTTACCTTTT 57.841 50.000 0.00 0.00 37.15 2.27
67 68 3.900446 CGGGTGTCGTCTTACCTTT 57.100 52.632 0.00 0.00 37.15 3.11
77 78 2.497770 GTATCCCCACGGGTGTCG 59.502 66.667 0.41 0.00 44.74 4.35
78 79 2.905681 GGTATCCCCACGGGTGTC 59.094 66.667 0.41 0.00 44.74 3.67
79 80 3.078836 CGGTATCCCCACGGGTGT 61.079 66.667 0.41 0.00 44.74 4.16
80 81 3.078836 ACGGTATCCCCACGGGTG 61.079 66.667 0.41 0.00 44.74 4.61
81 82 3.078836 CACGGTATCCCCACGGGT 61.079 66.667 0.41 0.00 44.74 5.28
82 83 4.540735 GCACGGTATCCCCACGGG 62.541 72.222 0.00 0.00 46.11 5.28
83 84 4.884257 CGCACGGTATCCCCACGG 62.884 72.222 0.00 0.00 0.00 4.94
84 85 4.137872 ACGCACGGTATCCCCACG 62.138 66.667 0.00 0.00 0.00 4.94
85 86 2.510691 CACGCACGGTATCCCCAC 60.511 66.667 0.00 0.00 0.00 4.61
86 87 2.680707 TCACGCACGGTATCCCCA 60.681 61.111 0.00 0.00 0.00 4.96
87 88 2.106332 CTCACGCACGGTATCCCC 59.894 66.667 0.00 0.00 0.00 4.81
88 89 2.106332 CCTCACGCACGGTATCCC 59.894 66.667 0.00 0.00 0.00 3.85
89 90 2.585247 GCCTCACGCACGGTATCC 60.585 66.667 0.00 0.00 37.47 2.59
90 91 2.585247 GGCCTCACGCACGGTATC 60.585 66.667 0.00 0.00 40.31 2.24
91 92 4.508128 CGGCCTCACGCACGGTAT 62.508 66.667 0.00 0.00 40.31 2.73
99 100 0.739462 TATCACTTTGCGGCCTCACG 60.739 55.000 0.00 0.00 0.00 4.35
100 101 1.331756 CATATCACTTTGCGGCCTCAC 59.668 52.381 0.00 0.00 0.00 3.51
101 102 1.209261 TCATATCACTTTGCGGCCTCA 59.791 47.619 0.00 0.00 0.00 3.86
102 103 1.953559 TCATATCACTTTGCGGCCTC 58.046 50.000 0.00 0.00 0.00 4.70
103 104 2.292267 CTTCATATCACTTTGCGGCCT 58.708 47.619 0.00 0.00 0.00 5.19
104 105 2.017049 ACTTCATATCACTTTGCGGCC 58.983 47.619 0.00 0.00 0.00 6.13
105 106 2.420022 ACACTTCATATCACTTTGCGGC 59.580 45.455 0.00 0.00 0.00 6.53
106 107 4.685169 AACACTTCATATCACTTTGCGG 57.315 40.909 0.00 0.00 0.00 5.69
107 108 5.121611 TGGTAACACTTCATATCACTTTGCG 59.878 40.000 0.00 0.00 46.17 4.85
108 109 6.494893 TGGTAACACTTCATATCACTTTGC 57.505 37.500 0.00 0.00 46.17 3.68
109 110 6.372659 AGCTGGTAACACTTCATATCACTTTG 59.627 38.462 0.00 0.00 46.17 2.77
110 111 6.476378 AGCTGGTAACACTTCATATCACTTT 58.524 36.000 0.00 0.00 46.17 2.66
111 112 6.054860 AGCTGGTAACACTTCATATCACTT 57.945 37.500 0.00 0.00 46.17 3.16
112 113 5.683876 AGCTGGTAACACTTCATATCACT 57.316 39.130 0.00 0.00 46.17 3.41
113 114 6.806751 TCTAGCTGGTAACACTTCATATCAC 58.193 40.000 0.00 0.00 46.17 3.06
114 115 7.522236 CGATCTAGCTGGTAACACTTCATATCA 60.522 40.741 0.00 0.00 46.17 2.15
115 116 6.804295 CGATCTAGCTGGTAACACTTCATATC 59.196 42.308 0.00 0.00 46.17 1.63
116 117 6.490381 TCGATCTAGCTGGTAACACTTCATAT 59.510 38.462 0.00 0.00 46.17 1.78
117 118 5.826208 TCGATCTAGCTGGTAACACTTCATA 59.174 40.000 0.00 0.00 46.17 2.15
118 119 4.645136 TCGATCTAGCTGGTAACACTTCAT 59.355 41.667 0.00 0.00 46.17 2.57
119 120 4.014406 TCGATCTAGCTGGTAACACTTCA 58.986 43.478 0.00 0.00 46.17 3.02
120 121 4.634184 TCGATCTAGCTGGTAACACTTC 57.366 45.455 0.00 0.00 46.17 3.01
121 122 4.402793 ACATCGATCTAGCTGGTAACACTT 59.597 41.667 0.00 0.00 46.17 3.16
122 123 3.954904 ACATCGATCTAGCTGGTAACACT 59.045 43.478 0.00 0.00 46.17 3.55
123 124 4.045104 CACATCGATCTAGCTGGTAACAC 58.955 47.826 0.00 0.00 46.17 3.32
125 126 4.202020 TGTCACATCGATCTAGCTGGTAAC 60.202 45.833 0.00 0.00 0.00 2.50
126 127 3.951680 TGTCACATCGATCTAGCTGGTAA 59.048 43.478 0.00 0.00 0.00 2.85
127 128 3.551846 TGTCACATCGATCTAGCTGGTA 58.448 45.455 0.00 0.00 0.00 3.25
128 129 2.379005 TGTCACATCGATCTAGCTGGT 58.621 47.619 0.00 0.00 0.00 4.00
129 130 3.573598 GATGTCACATCGATCTAGCTGG 58.426 50.000 0.93 0.00 0.00 4.85
130 131 3.058639 TCGATGTCACATCGATCTAGCTG 60.059 47.826 33.92 7.87 44.42 4.24
131 132 3.142174 TCGATGTCACATCGATCTAGCT 58.858 45.455 33.92 0.00 44.42 3.32
132 133 3.544356 TCGATGTCACATCGATCTAGC 57.456 47.619 33.92 0.00 44.42 3.42
138 139 0.377203 CCGACTCGATGTCACATCGA 59.623 55.000 34.63 34.63 46.69 3.59
139 140 0.592500 CCCGACTCGATGTCACATCG 60.593 60.000 30.60 30.60 45.60 3.84
140 141 0.249073 CCCCGACTCGATGTCACATC 60.249 60.000 7.83 7.83 45.60 3.06
141 142 0.970937 ACCCCGACTCGATGTCACAT 60.971 55.000 13.14 0.00 45.60 3.21
142 143 1.592400 GACCCCGACTCGATGTCACA 61.592 60.000 13.14 0.00 45.60 3.58
143 144 1.139095 GACCCCGACTCGATGTCAC 59.861 63.158 13.14 0.00 45.60 3.67
144 145 2.050350 GGACCCCGACTCGATGTCA 61.050 63.158 16.91 0.00 45.60 3.58
145 146 1.753463 AGGACCCCGACTCGATGTC 60.753 63.158 0.00 5.96 42.06 3.06
146 147 2.052690 CAGGACCCCGACTCGATGT 61.053 63.158 0.00 0.00 0.00 3.06
147 148 1.753078 TCAGGACCCCGACTCGATG 60.753 63.158 0.00 0.00 0.00 3.84
148 149 1.753463 GTCAGGACCCCGACTCGAT 60.753 63.158 0.00 0.00 0.00 3.59
149 150 2.360852 GTCAGGACCCCGACTCGA 60.361 66.667 0.00 0.00 0.00 4.04
150 151 2.675423 TGTCAGGACCCCGACTCG 60.675 66.667 11.80 0.00 31.80 4.18
151 152 3.007973 GCTGTCAGGACCCCGACTC 62.008 68.421 11.80 2.37 31.80 3.36
152 153 2.997897 GCTGTCAGGACCCCGACT 60.998 66.667 11.80 0.00 31.80 4.18
153 154 2.185310 ATTGCTGTCAGGACCCCGAC 62.185 60.000 1.14 4.95 0.00 4.79
154 155 1.918293 ATTGCTGTCAGGACCCCGA 60.918 57.895 1.14 0.00 0.00 5.14
155 156 1.746615 CATTGCTGTCAGGACCCCG 60.747 63.158 1.14 0.00 0.00 5.73
156 157 2.048603 GCATTGCTGTCAGGACCCC 61.049 63.158 0.16 0.00 0.00 4.95
157 158 0.682209 ATGCATTGCTGTCAGGACCC 60.682 55.000 10.49 0.00 0.00 4.46
158 159 1.135199 CAATGCATTGCTGTCAGGACC 60.135 52.381 25.50 0.00 0.00 4.46
159 160 1.135199 CCAATGCATTGCTGTCAGGAC 60.135 52.381 30.15 0.00 36.48 3.85
160 161 1.179152 CCAATGCATTGCTGTCAGGA 58.821 50.000 30.15 0.00 36.48 3.86
161 162 0.459585 GCCAATGCATTGCTGTCAGG 60.460 55.000 30.15 17.67 36.48 3.86
162 163 0.530744 AGCCAATGCATTGCTGTCAG 59.469 50.000 30.15 17.89 41.13 3.51
163 164 0.245266 CAGCCAATGCATTGCTGTCA 59.755 50.000 32.92 0.00 41.13 3.58
164 165 0.528924 TCAGCCAATGCATTGCTGTC 59.471 50.000 35.79 24.54 40.03 3.51
165 166 1.191535 ATCAGCCAATGCATTGCTGT 58.808 45.000 35.79 27.74 40.03 4.40
166 167 2.309528 AATCAGCCAATGCATTGCTG 57.690 45.000 34.17 34.17 40.24 4.41
167 168 2.737359 CGAAATCAGCCAATGCATTGCT 60.737 45.455 30.15 25.89 41.13 3.91
991 1008 6.014584 CCTCCTATTATAACCATTTTTGCCCC 60.015 42.308 0.00 0.00 0.00 5.80
1896 1933 2.344950 CTCATGAGGACAACTGACTGC 58.655 52.381 15.38 0.00 0.00 4.40
1897 1934 2.028294 AGCTCATGAGGACAACTGACTG 60.028 50.000 23.89 0.00 0.00 3.51
1898 1935 2.255406 AGCTCATGAGGACAACTGACT 58.745 47.619 23.89 6.38 0.00 3.41
1899 1936 2.758736 AGCTCATGAGGACAACTGAC 57.241 50.000 23.89 4.09 0.00 3.51
1900 1937 3.777106 AAAGCTCATGAGGACAACTGA 57.223 42.857 23.89 0.00 0.00 3.41
1932 1969 9.961265 AAAACTAGCAATCATCATGATGTATTG 57.039 29.630 31.22 31.22 37.15 1.90
2195 2232 1.961277 GGTCCGCTGGAAGTGTGTG 60.961 63.158 0.00 0.00 44.74 3.82
2227 2264 1.536418 TGGCTGGTAGGACTGCACT 60.536 57.895 0.00 0.00 37.08 4.40
2285 2322 0.389025 ACACTGTCAGCATCGACACA 59.611 50.000 0.00 0.00 40.94 3.72
2711 2749 4.103153 ACAGAAAGAACAGGAACAGATGGA 59.897 41.667 0.00 0.00 0.00 3.41
2807 2847 4.022242 ACGAGCGCATCAAGGTATAGTATT 60.022 41.667 11.47 0.00 0.00 1.89
4048 4098 3.560068 GTCTCTTTCTTTTTGGAGCACGA 59.440 43.478 0.00 0.00 0.00 4.35
4372 4462 3.961414 GCCCCTTTGTCCCCGTCA 61.961 66.667 0.00 0.00 0.00 4.35
4456 4546 1.743958 TCGTCTTCTTCATCCTCGTCC 59.256 52.381 0.00 0.00 0.00 4.79
4633 4738 3.017442 CTGTAGTGTGCTCCTGCTACTA 58.983 50.000 0.00 0.00 37.98 1.82
4863 4968 7.980662 TGTCAATTTGATTCTTTTCAGCTTCAA 59.019 29.630 1.78 0.00 0.00 2.69
5369 5476 6.061022 TGTAATTGGCATCTTTCCAGTCTA 57.939 37.500 0.00 0.00 34.66 2.59
5451 5558 1.553690 GGTGCCTTCCTGACCAGCTA 61.554 60.000 0.00 0.00 0.00 3.32
5903 6022 2.167075 GAGCTATTGCCTTGCCAACATT 59.833 45.455 0.00 0.00 40.80 2.71
5944 6063 1.598701 GGGTGTGGCAATTCTCTGGC 61.599 60.000 0.00 0.00 42.07 4.85
6187 6306 1.481363 GTAGGCTGTGGGGAGTTAGTC 59.519 57.143 0.00 0.00 0.00 2.59
6375 6497 7.286316 ACCTAATTATCTCAGGGCTGATTTTTG 59.714 37.037 0.00 0.00 39.13 2.44


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

AutoCloner maintained by Alex Coulton.