Multiple sequence alignment - TraesCS6A01G362200

Loading Multiple Alignment...

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 TraesCS6A01G362200 chr6A 100.000 2455 0 0 1 2455 592221612 592224066 0.000000e+00 4534.0
1 TraesCS6A01G362200 chr6B 91.119 2252 154 19 213 2455 672059705 672061919 0.000000e+00 3009.0
2 TraesCS6A01G362200 chr6D 91.729 2140 147 13 325 2455 445676254 445678372 0.000000e+00 2944.0
3 TraesCS6A01G362200 chr6D 90.598 117 11 0 213 329 445675979 445676095 3.270000e-34 156.0
4 TraesCS6A01G362200 chr6D 82.051 117 12 6 2166 2279 14158586 14158696 9.350000e-15 91.6
5 TraesCS6A01G362200 chr3D 82.301 113 15 3 2185 2295 299694791 299694682 2.600000e-15 93.5
6 TraesCS6A01G362200 chr3A 78.814 118 18 4 2185 2299 436415133 436415246 3.390000e-09 73.1


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 TraesCS6A01G362200 chr6A 592221612 592224066 2454 False 4534 4534 100.0000 1 2455 1 chr6A.!!$F1 2454
1 TraesCS6A01G362200 chr6B 672059705 672061919 2214 False 3009 3009 91.1190 213 2455 1 chr6B.!!$F1 2242
2 TraesCS6A01G362200 chr6D 445675979 445678372 2393 False 1550 2944 91.1635 213 2455 2 chr6D.!!$F2 2242

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
746 915 0.915904 CACAACACGCACAAAGCAAG 59.084 50.0 0.0 0.0 46.13 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2506 0.322816 CTGGTAGCAGCAATGGTGGT 60.323 55.0 20.77 20.77 43.99 4.16 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
35 36 9.739276 AAAAACCAGGAAAGAAAGAAAGAAAAT 57.261 25.926 0.00 0.00 0.00 1.82
36 37 8.948631 AAACCAGGAAAGAAAGAAAGAAAATC 57.051 30.769 0.00 0.00 0.00 2.17
37 38 6.739112 ACCAGGAAAGAAAGAAAGAAAATCG 58.261 36.000 0.00 0.00 0.00 3.34
38 39 6.546034 ACCAGGAAAGAAAGAAAGAAAATCGA 59.454 34.615 0.00 0.00 0.00 3.59
39 40 7.068226 ACCAGGAAAGAAAGAAAGAAAATCGAA 59.932 33.333 0.00 0.00 0.00 3.71
40 41 7.592903 CCAGGAAAGAAAGAAAGAAAATCGAAG 59.407 37.037 0.00 0.00 0.00 3.79
41 42 8.345565 CAGGAAAGAAAGAAAGAAAATCGAAGA 58.654 33.333 0.00 0.00 45.75 2.87
42 43 8.903820 AGGAAAGAAAGAAAGAAAATCGAAGAA 58.096 29.630 0.00 0.00 43.58 2.52
43 44 9.516314 GGAAAGAAAGAAAGAAAATCGAAGAAA 57.484 29.630 0.00 0.00 43.58 2.52
47 48 9.508567 AGAAAGAAAGAAAATCGAAGAAAACTG 57.491 29.630 0.00 0.00 43.58 3.16
48 49 9.503427 GAAAGAAAGAAAATCGAAGAAAACTGA 57.497 29.630 0.00 0.00 43.58 3.41
49 50 9.855021 AAAGAAAGAAAATCGAAGAAAACTGAA 57.145 25.926 0.00 0.00 43.58 3.02
50 51 9.508567 AAGAAAGAAAATCGAAGAAAACTGAAG 57.491 29.630 0.00 0.00 43.58 3.02
51 52 8.893727 AGAAAGAAAATCGAAGAAAACTGAAGA 58.106 29.630 0.00 0.00 43.58 2.87
52 53 9.503427 GAAAGAAAATCGAAGAAAACTGAAGAA 57.497 29.630 0.00 0.00 43.58 2.52
53 54 9.855021 AAAGAAAATCGAAGAAAACTGAAGAAA 57.145 25.926 0.00 0.00 43.58 2.52
54 55 8.842942 AGAAAATCGAAGAAAACTGAAGAAAC 57.157 30.769 0.00 0.00 43.58 2.78
55 56 8.678199 AGAAAATCGAAGAAAACTGAAGAAACT 58.322 29.630 0.00 0.00 43.58 2.66
56 57 9.931210 GAAAATCGAAGAAAACTGAAGAAACTA 57.069 29.630 0.00 0.00 43.58 2.24
58 59 9.937175 AAATCGAAGAAAACTGAAGAAACTAAG 57.063 29.630 0.00 0.00 43.58 2.18
59 60 8.888579 ATCGAAGAAAACTGAAGAAACTAAGA 57.111 30.769 0.00 0.00 43.58 2.10
60 61 8.712285 TCGAAGAAAACTGAAGAAACTAAGAA 57.288 30.769 0.00 0.00 0.00 2.52
61 62 9.158233 TCGAAGAAAACTGAAGAAACTAAGAAA 57.842 29.630 0.00 0.00 0.00 2.52
62 63 9.937175 CGAAGAAAACTGAAGAAACTAAGAAAT 57.063 29.630 0.00 0.00 0.00 2.17
97 98 9.447157 ACCAATGAAAATCAAGAAAGAAACAAA 57.553 25.926 0.00 0.00 0.00 2.83
135 136 8.791327 AATGAAGAAAAAGAAAAGAAAAGCCA 57.209 26.923 0.00 0.00 0.00 4.75
136 137 7.832503 TGAAGAAAAAGAAAAGAAAAGCCAG 57.167 32.000 0.00 0.00 0.00 4.85
137 138 7.386059 TGAAGAAAAAGAAAAGAAAAGCCAGT 58.614 30.769 0.00 0.00 0.00 4.00
138 139 8.527810 TGAAGAAAAAGAAAAGAAAAGCCAGTA 58.472 29.630 0.00 0.00 0.00 2.74
139 140 9.366216 GAAGAAAAAGAAAAGAAAAGCCAGTAA 57.634 29.630 0.00 0.00 0.00 2.24
140 141 9.719355 AAGAAAAAGAAAAGAAAAGCCAGTAAA 57.281 25.926 0.00 0.00 0.00 2.01
141 142 9.719355 AGAAAAAGAAAAGAAAAGCCAGTAAAA 57.281 25.926 0.00 0.00 0.00 1.52
142 143 9.755064 GAAAAAGAAAAGAAAAGCCAGTAAAAC 57.245 29.630 0.00 0.00 0.00 2.43
143 144 7.843490 AAAGAAAAGAAAAGCCAGTAAAACC 57.157 32.000 0.00 0.00 0.00 3.27
144 145 6.538945 AGAAAAGAAAAGCCAGTAAAACCA 57.461 33.333 0.00 0.00 0.00 3.67
145 146 7.124573 AGAAAAGAAAAGCCAGTAAAACCAT 57.875 32.000 0.00 0.00 0.00 3.55
146 147 7.564793 AGAAAAGAAAAGCCAGTAAAACCATT 58.435 30.769 0.00 0.00 0.00 3.16
147 148 8.700973 AGAAAAGAAAAGCCAGTAAAACCATTA 58.299 29.630 0.00 0.00 0.00 1.90
148 149 9.320352 GAAAAGAAAAGCCAGTAAAACCATTAA 57.680 29.630 0.00 0.00 0.00 1.40
149 150 9.674068 AAAAGAAAAGCCAGTAAAACCATTAAA 57.326 25.926 0.00 0.00 0.00 1.52
150 151 8.887036 AAGAAAAGCCAGTAAAACCATTAAAG 57.113 30.769 0.00 0.00 0.00 1.85
151 152 8.245195 AGAAAAGCCAGTAAAACCATTAAAGA 57.755 30.769 0.00 0.00 0.00 2.52
152 153 8.700973 AGAAAAGCCAGTAAAACCATTAAAGAA 58.299 29.630 0.00 0.00 0.00 2.52
153 154 8.887036 AAAAGCCAGTAAAACCATTAAAGAAG 57.113 30.769 0.00 0.00 0.00 2.85
154 155 6.025749 AGCCAGTAAAACCATTAAAGAAGC 57.974 37.500 0.00 0.00 0.00 3.86
155 156 5.538433 AGCCAGTAAAACCATTAAAGAAGCA 59.462 36.000 0.00 0.00 0.00 3.91
156 157 6.041523 AGCCAGTAAAACCATTAAAGAAGCAA 59.958 34.615 0.00 0.00 0.00 3.91
157 158 6.704050 GCCAGTAAAACCATTAAAGAAGCAAA 59.296 34.615 0.00 0.00 0.00 3.68
158 159 7.095649 GCCAGTAAAACCATTAAAGAAGCAAAG 60.096 37.037 0.00 0.00 0.00 2.77
159 160 8.141268 CCAGTAAAACCATTAAAGAAGCAAAGA 58.859 33.333 0.00 0.00 0.00 2.52
160 161 9.528018 CAGTAAAACCATTAAAGAAGCAAAGAA 57.472 29.630 0.00 0.00 0.00 2.52
164 165 7.786178 AACCATTAAAGAAGCAAAGAAAACC 57.214 32.000 0.00 0.00 0.00 3.27
165 166 6.883744 ACCATTAAAGAAGCAAAGAAAACCA 58.116 32.000 0.00 0.00 0.00 3.67
166 167 7.508687 ACCATTAAAGAAGCAAAGAAAACCAT 58.491 30.769 0.00 0.00 0.00 3.55
167 168 7.992608 ACCATTAAAGAAGCAAAGAAAACCATT 59.007 29.630 0.00 0.00 0.00 3.16
168 169 8.284693 CCATTAAAGAAGCAAAGAAAACCATTG 58.715 33.333 0.00 0.00 0.00 2.82
169 170 9.044150 CATTAAAGAAGCAAAGAAAACCATTGA 57.956 29.630 0.00 0.00 0.00 2.57
170 171 9.612066 ATTAAAGAAGCAAAGAAAACCATTGAA 57.388 25.926 0.00 0.00 0.00 2.69
171 172 7.920160 AAAGAAGCAAAGAAAACCATTGAAA 57.080 28.000 0.00 0.00 0.00 2.69
172 173 7.543947 AAGAAGCAAAGAAAACCATTGAAAG 57.456 32.000 0.00 0.00 0.00 2.62
173 174 6.877236 AGAAGCAAAGAAAACCATTGAAAGA 58.123 32.000 0.00 0.00 0.00 2.52
174 175 7.330262 AGAAGCAAAGAAAACCATTGAAAGAA 58.670 30.769 0.00 0.00 0.00 2.52
175 176 7.989170 AGAAGCAAAGAAAACCATTGAAAGAAT 59.011 29.630 0.00 0.00 0.00 2.40
176 177 9.260002 GAAGCAAAGAAAACCATTGAAAGAATA 57.740 29.630 0.00 0.00 0.00 1.75
177 178 9.612066 AAGCAAAGAAAACCATTGAAAGAATAA 57.388 25.926 0.00 0.00 0.00 1.40
178 179 9.612066 AGCAAAGAAAACCATTGAAAGAATAAA 57.388 25.926 0.00 0.00 0.00 1.40
179 180 9.868389 GCAAAGAAAACCATTGAAAGAATAAAG 57.132 29.630 0.00 0.00 0.00 1.85
220 221 4.028993 AGAAAACCATTAAAGAGGCCGA 57.971 40.909 0.00 0.00 0.00 5.54
244 245 1.674651 GGGAGGAAAACCCACGCTC 60.675 63.158 0.00 0.00 46.05 5.03
259 260 2.892425 CTCGCATCGGGGAACTGC 60.892 66.667 0.00 0.00 35.34 4.40
283 284 1.172175 GCTCTTTCTTTGCCCAGAGG 58.828 55.000 0.00 0.00 34.46 3.69
340 504 2.206750 TGCAAGTACAACGTTGGAGTC 58.793 47.619 30.34 15.40 0.00 3.36
341 505 2.206750 GCAAGTACAACGTTGGAGTCA 58.793 47.619 30.34 8.71 0.00 3.41
349 513 3.442273 ACAACGTTGGAGTCATGTTGTTT 59.558 39.130 30.34 2.88 43.74 2.83
360 524 6.404734 GGAGTCATGTTGTTTTCTGACACTTT 60.405 38.462 4.56 0.00 40.32 2.66
489 656 2.425143 CCTCTGGCAGGCTAAATTGA 57.575 50.000 15.73 0.00 34.56 2.57
527 696 4.408821 TGGGCTCGCGGCTTGATT 62.409 61.111 17.07 0.00 41.46 2.57
604 773 1.909302 AGTGTATCACCAGGGTGGAAG 59.091 52.381 17.88 0.00 45.43 3.46
666 835 2.191128 AGACGAGCAGAGCCAAAATT 57.809 45.000 0.00 0.00 0.00 1.82
690 859 1.822613 CATGCTACTGGCTGGCAGG 60.823 63.158 31.07 17.56 42.39 4.85
692 861 3.402681 GCTACTGGCTGGCAGGGA 61.403 66.667 31.07 19.12 38.06 4.20
705 874 2.092323 GGCAGGGAATTTAAGAGCGTT 58.908 47.619 0.00 0.00 0.00 4.84
735 904 2.159761 ACAACGAACAACTCACAACACG 60.160 45.455 0.00 0.00 0.00 4.49
746 915 0.915904 CACAACACGCACAAAGCAAG 59.084 50.000 0.00 0.00 46.13 4.01
768 937 1.771854 TCTCTCTCGCTGTCTATCCCT 59.228 52.381 0.00 0.00 0.00 4.20
778 947 3.006003 GCTGTCTATCCCTTGTAGCTACC 59.994 52.174 21.01 4.03 0.00 3.18
789 958 1.089920 GTAGCTACCGACTCGAACCA 58.910 55.000 13.20 0.00 0.00 3.67
794 963 2.019249 CTACCGACTCGAACCACCATA 58.981 52.381 0.00 0.00 0.00 2.74
897 1069 1.042229 TTTGCAGCTTCACAGGCAAT 58.958 45.000 7.61 0.00 44.70 3.56
898 1070 1.908344 TTGCAGCTTCACAGGCAATA 58.092 45.000 3.00 0.00 40.94 1.90
952 1124 4.522114 CAATTTCCCCTCTCTTTCCTCTC 58.478 47.826 0.00 0.00 0.00 3.20
998 1170 1.751924 CAACTCTTCCCCTCTAGACGG 59.248 57.143 0.98 0.98 0.00 4.79
1010 1182 2.490115 CTCTAGACGGCATGATCTACCC 59.510 54.545 0.00 0.00 0.00 3.69
1013 1185 0.464036 GACGGCATGATCTACCCACA 59.536 55.000 0.00 0.00 0.00 4.17
1038 1210 3.149196 AGCCACATGTTTTCTCGTCATT 58.851 40.909 0.00 0.00 0.00 2.57
1045 1217 1.136057 GTTTTCTCGTCATTGCCGTCC 60.136 52.381 0.00 0.00 0.00 4.79
1048 1220 1.215382 CTCGTCATTGCCGTCCTCA 59.785 57.895 0.00 0.00 0.00 3.86
1062 1234 0.478942 TCCTCATCCTCCTCCTACCG 59.521 60.000 0.00 0.00 0.00 4.02
1069 1241 0.757188 CCTCCTCCTACCGCTGATGT 60.757 60.000 0.00 0.00 0.00 3.06
1079 1251 2.672098 ACCGCTGATGTCTTCCTATCT 58.328 47.619 0.00 0.00 0.00 1.98
1083 1255 4.172505 CGCTGATGTCTTCCTATCTATGC 58.827 47.826 0.00 0.00 0.00 3.14
1084 1256 4.321527 CGCTGATGTCTTCCTATCTATGCA 60.322 45.833 0.00 0.00 0.00 3.96
1109 1281 2.669229 CGCACATGACCCACTGCA 60.669 61.111 0.00 0.00 0.00 4.41
1139 1311 6.731292 TCCAGGTATATCTATATGCGCAAT 57.269 37.500 17.11 12.19 0.00 3.56
1195 1367 8.632679 GGATTTGTTGTTCATATGTATGGATGT 58.367 33.333 1.90 0.00 34.50 3.06
1199 1371 6.883756 TGTTGTTCATATGTATGGATGTGTGT 59.116 34.615 1.90 0.00 34.50 3.72
1203 1375 6.923928 TCATATGTATGGATGTGTGTGTTG 57.076 37.500 1.90 0.00 34.50 3.33
1279 1452 1.831286 GGCTGCATCATGAAGGGGG 60.831 63.158 0.00 0.00 0.00 5.40
1299 1472 0.863956 AAAGGTGTTTGGGATGGGGA 59.136 50.000 0.00 0.00 0.00 4.81
1346 1519 1.195115 CGATGAAGAACCCTCCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
1349 1522 0.104672 TGAAGAACCCTCCCTCACCA 60.105 55.000 0.00 0.00 0.00 4.17
1418 1591 5.475220 ACCACCATCGTTGATCAATAAACAA 59.525 36.000 12.12 0.00 0.00 2.83
1459 1632 2.368439 GAGCATGCCATGGTGACTTTA 58.632 47.619 15.09 0.00 41.77 1.85
1472 1645 2.808543 GTGACTTTAGTGCACCTCCTTG 59.191 50.000 14.63 1.92 0.00 3.61
1475 1648 2.706190 ACTTTAGTGCACCTCCTTGTCT 59.294 45.455 14.63 0.00 0.00 3.41
1476 1649 2.839486 TTAGTGCACCTCCTTGTCTG 57.161 50.000 14.63 0.00 0.00 3.51
1477 1650 1.717032 TAGTGCACCTCCTTGTCTGT 58.283 50.000 14.63 0.00 0.00 3.41
1478 1651 0.839946 AGTGCACCTCCTTGTCTGTT 59.160 50.000 14.63 0.00 0.00 3.16
1479 1652 0.947244 GTGCACCTCCTTGTCTGTTG 59.053 55.000 5.22 0.00 0.00 3.33
1480 1653 0.546122 TGCACCTCCTTGTCTGTTGT 59.454 50.000 0.00 0.00 0.00 3.32
1481 1654 1.064758 TGCACCTCCTTGTCTGTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
1482 1655 1.334869 GCACCTCCTTGTCTGTTGTTG 59.665 52.381 0.00 0.00 0.00 3.33
1483 1656 2.643551 CACCTCCTTGTCTGTTGTTGT 58.356 47.619 0.00 0.00 0.00 3.32
1484 1657 3.016736 CACCTCCTTGTCTGTTGTTGTT 58.983 45.455 0.00 0.00 0.00 2.83
1485 1658 3.016736 ACCTCCTTGTCTGTTGTTGTTG 58.983 45.455 0.00 0.00 0.00 3.33
1486 1659 3.016736 CCTCCTTGTCTGTTGTTGTTGT 58.983 45.455 0.00 0.00 0.00 3.32
1604 1778 3.754965 TGGACTTTTGAGAGAATGGTGG 58.245 45.455 0.00 0.00 0.00 4.61
1652 1826 5.057149 GTCAAGTGGTCTCAAGCTTAAGAA 58.943 41.667 6.67 0.00 0.00 2.52
1661 1837 4.220821 TCTCAAGCTTAAGAACTGGTCGAT 59.779 41.667 6.67 0.00 0.00 3.59
1794 1970 4.808558 CACACACCCCAATGAACTATTTG 58.191 43.478 0.00 0.00 0.00 2.32
1834 2010 3.145286 GGCCTCTAAGCAAATCCAGATC 58.855 50.000 0.00 0.00 0.00 2.75
1842 2018 2.357009 AGCAAATCCAGATCATTCGTGC 59.643 45.455 0.00 0.00 0.00 5.34
1913 2089 2.511218 AGATTGGCCATACATGTGACCT 59.489 45.455 6.09 0.00 0.00 3.85
1917 2093 3.648739 TGGCCATACATGTGACCTACTA 58.351 45.455 9.11 0.00 0.00 1.82
1918 2094 4.231273 TGGCCATACATGTGACCTACTAT 58.769 43.478 9.11 0.00 0.00 2.12
1928 2104 6.717540 ACATGTGACCTACTATGGATCTCTAC 59.282 42.308 0.00 0.00 0.00 2.59
1934 2110 5.163012 ACCTACTATGGATCTCTACGGGAAA 60.163 44.000 0.00 0.00 0.00 3.13
1940 2116 3.384789 TGGATCTCTACGGGAAAGTCATG 59.615 47.826 0.00 0.00 0.00 3.07
1972 2149 1.264749 TAGAGCGATGTGTGGGCCTT 61.265 55.000 4.53 0.00 0.00 4.35
2118 2296 8.997960 CACGGCAATTTATTTCAATTTTTATGC 58.002 29.630 0.00 0.00 0.00 3.14
2154 2332 1.811965 TCGTCCAAACATGCATTCCAG 59.188 47.619 0.00 0.00 0.00 3.86
2214 2392 3.583806 CATAATTTGTGCCAAAAGGCGA 58.416 40.909 1.66 0.00 37.77 5.54
2221 2400 1.067635 GTGCCAAAAGGCGATGTGAAT 60.068 47.619 1.66 0.00 37.77 2.57
2317 2496 4.664677 GTCAGCGGCGACACCACT 62.665 66.667 12.98 0.00 39.03 4.00
2392 2571 6.549364 TCGCCATGATTAAACTCCCAATATTT 59.451 34.615 0.00 0.00 0.00 1.40
2414 2593 2.168521 CCTTGCCTTCTCGTCCATCTTA 59.831 50.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.739276 ATTTTCTTTCTTTCTTTCCTGGTTTTT 57.261 25.926 0.00 0.00 0.00 1.94
10 11 9.383519 GATTTTCTTTCTTTCTTTCCTGGTTTT 57.616 29.630 0.00 0.00 0.00 2.43
11 12 7.706607 CGATTTTCTTTCTTTCTTTCCTGGTTT 59.293 33.333 0.00 0.00 0.00 3.27
12 13 7.068226 TCGATTTTCTTTCTTTCTTTCCTGGTT 59.932 33.333 0.00 0.00 0.00 3.67
13 14 6.546034 TCGATTTTCTTTCTTTCTTTCCTGGT 59.454 34.615 0.00 0.00 0.00 4.00
14 15 6.970484 TCGATTTTCTTTCTTTCTTTCCTGG 58.030 36.000 0.00 0.00 0.00 4.45
15 16 8.345565 TCTTCGATTTTCTTTCTTTCTTTCCTG 58.654 33.333 0.00 0.00 0.00 3.86
16 17 8.451908 TCTTCGATTTTCTTTCTTTCTTTCCT 57.548 30.769 0.00 0.00 0.00 3.36
17 18 9.516314 TTTCTTCGATTTTCTTTCTTTCTTTCC 57.484 29.630 0.00 0.00 0.00 3.13
21 22 9.508567 CAGTTTTCTTCGATTTTCTTTCTTTCT 57.491 29.630 0.00 0.00 0.00 2.52
22 23 9.503427 TCAGTTTTCTTCGATTTTCTTTCTTTC 57.497 29.630 0.00 0.00 0.00 2.62
23 24 9.855021 TTCAGTTTTCTTCGATTTTCTTTCTTT 57.145 25.926 0.00 0.00 0.00 2.52
24 25 9.508567 CTTCAGTTTTCTTCGATTTTCTTTCTT 57.491 29.630 0.00 0.00 0.00 2.52
25 26 8.893727 TCTTCAGTTTTCTTCGATTTTCTTTCT 58.106 29.630 0.00 0.00 0.00 2.52
26 27 9.503427 TTCTTCAGTTTTCTTCGATTTTCTTTC 57.497 29.630 0.00 0.00 0.00 2.62
27 28 9.855021 TTTCTTCAGTTTTCTTCGATTTTCTTT 57.145 25.926 0.00 0.00 0.00 2.52
28 29 9.290483 GTTTCTTCAGTTTTCTTCGATTTTCTT 57.710 29.630 0.00 0.00 0.00 2.52
29 30 8.678199 AGTTTCTTCAGTTTTCTTCGATTTTCT 58.322 29.630 0.00 0.00 0.00 2.52
30 31 8.842942 AGTTTCTTCAGTTTTCTTCGATTTTC 57.157 30.769 0.00 0.00 0.00 2.29
32 33 9.937175 CTTAGTTTCTTCAGTTTTCTTCGATTT 57.063 29.630 0.00 0.00 0.00 2.17
33 34 9.326413 TCTTAGTTTCTTCAGTTTTCTTCGATT 57.674 29.630 0.00 0.00 0.00 3.34
34 35 8.888579 TCTTAGTTTCTTCAGTTTTCTTCGAT 57.111 30.769 0.00 0.00 0.00 3.59
35 36 8.712285 TTCTTAGTTTCTTCAGTTTTCTTCGA 57.288 30.769 0.00 0.00 0.00 3.71
36 37 9.937175 ATTTCTTAGTTTCTTCAGTTTTCTTCG 57.063 29.630 0.00 0.00 0.00 3.79
71 72 9.447157 TTTGTTTCTTTCTTGATTTTCATTGGT 57.553 25.926 0.00 0.00 0.00 3.67
109 110 9.230122 TGGCTTTTCTTTTCTTTTTCTTCATTT 57.770 25.926 0.00 0.00 0.00 2.32
110 111 8.791327 TGGCTTTTCTTTTCTTTTTCTTCATT 57.209 26.923 0.00 0.00 0.00 2.57
111 112 8.043113 ACTGGCTTTTCTTTTCTTTTTCTTCAT 58.957 29.630 0.00 0.00 0.00 2.57
112 113 7.386059 ACTGGCTTTTCTTTTCTTTTTCTTCA 58.614 30.769 0.00 0.00 0.00 3.02
113 114 7.834068 ACTGGCTTTTCTTTTCTTTTTCTTC 57.166 32.000 0.00 0.00 0.00 2.87
114 115 9.719355 TTTACTGGCTTTTCTTTTCTTTTTCTT 57.281 25.926 0.00 0.00 0.00 2.52
115 116 9.719355 TTTTACTGGCTTTTCTTTTCTTTTTCT 57.281 25.926 0.00 0.00 0.00 2.52
116 117 9.755064 GTTTTACTGGCTTTTCTTTTCTTTTTC 57.245 29.630 0.00 0.00 0.00 2.29
117 118 8.726988 GGTTTTACTGGCTTTTCTTTTCTTTTT 58.273 29.630 0.00 0.00 0.00 1.94
118 119 7.880713 TGGTTTTACTGGCTTTTCTTTTCTTTT 59.119 29.630 0.00 0.00 0.00 2.27
119 120 7.390823 TGGTTTTACTGGCTTTTCTTTTCTTT 58.609 30.769 0.00 0.00 0.00 2.52
120 121 6.941857 TGGTTTTACTGGCTTTTCTTTTCTT 58.058 32.000 0.00 0.00 0.00 2.52
121 122 6.538945 TGGTTTTACTGGCTTTTCTTTTCT 57.461 33.333 0.00 0.00 0.00 2.52
122 123 7.786178 AATGGTTTTACTGGCTTTTCTTTTC 57.214 32.000 0.00 0.00 0.00 2.29
123 124 9.674068 TTTAATGGTTTTACTGGCTTTTCTTTT 57.326 25.926 0.00 0.00 0.00 2.27
124 125 9.325198 CTTTAATGGTTTTACTGGCTTTTCTTT 57.675 29.630 0.00 0.00 0.00 2.52
125 126 8.700973 TCTTTAATGGTTTTACTGGCTTTTCTT 58.299 29.630 0.00 0.00 0.00 2.52
126 127 8.245195 TCTTTAATGGTTTTACTGGCTTTTCT 57.755 30.769 0.00 0.00 0.00 2.52
127 128 8.880878 TTCTTTAATGGTTTTACTGGCTTTTC 57.119 30.769 0.00 0.00 0.00 2.29
128 129 7.441157 GCTTCTTTAATGGTTTTACTGGCTTTT 59.559 33.333 0.00 0.00 0.00 2.27
129 130 6.929049 GCTTCTTTAATGGTTTTACTGGCTTT 59.071 34.615 0.00 0.00 0.00 3.51
130 131 6.041523 TGCTTCTTTAATGGTTTTACTGGCTT 59.958 34.615 0.00 0.00 0.00 4.35
131 132 5.538433 TGCTTCTTTAATGGTTTTACTGGCT 59.462 36.000 0.00 0.00 0.00 4.75
132 133 5.778862 TGCTTCTTTAATGGTTTTACTGGC 58.221 37.500 0.00 0.00 0.00 4.85
133 134 8.141268 TCTTTGCTTCTTTAATGGTTTTACTGG 58.859 33.333 0.00 0.00 0.00 4.00
134 135 9.528018 TTCTTTGCTTCTTTAATGGTTTTACTG 57.472 29.630 0.00 0.00 0.00 2.74
138 139 8.673711 GGTTTTCTTTGCTTCTTTAATGGTTTT 58.326 29.630 0.00 0.00 0.00 2.43
139 140 7.826744 TGGTTTTCTTTGCTTCTTTAATGGTTT 59.173 29.630 0.00 0.00 0.00 3.27
140 141 7.334858 TGGTTTTCTTTGCTTCTTTAATGGTT 58.665 30.769 0.00 0.00 0.00 3.67
141 142 6.883744 TGGTTTTCTTTGCTTCTTTAATGGT 58.116 32.000 0.00 0.00 0.00 3.55
142 143 7.967890 ATGGTTTTCTTTGCTTCTTTAATGG 57.032 32.000 0.00 0.00 0.00 3.16
143 144 9.044150 TCAATGGTTTTCTTTGCTTCTTTAATG 57.956 29.630 0.00 0.00 32.48 1.90
144 145 9.612066 TTCAATGGTTTTCTTTGCTTCTTTAAT 57.388 25.926 0.00 0.00 32.48 1.40
145 146 9.442047 TTTCAATGGTTTTCTTTGCTTCTTTAA 57.558 25.926 0.00 0.00 32.48 1.52
146 147 9.097257 CTTTCAATGGTTTTCTTTGCTTCTTTA 57.903 29.630 0.00 0.00 32.48 1.85
147 148 7.823799 TCTTTCAATGGTTTTCTTTGCTTCTTT 59.176 29.630 0.00 0.00 32.48 2.52
148 149 7.330262 TCTTTCAATGGTTTTCTTTGCTTCTT 58.670 30.769 0.00 0.00 32.48 2.52
149 150 6.877236 TCTTTCAATGGTTTTCTTTGCTTCT 58.123 32.000 0.00 0.00 32.48 2.85
150 151 7.538303 TTCTTTCAATGGTTTTCTTTGCTTC 57.462 32.000 0.00 0.00 32.48 3.86
151 152 9.612066 TTATTCTTTCAATGGTTTTCTTTGCTT 57.388 25.926 0.00 0.00 32.48 3.91
152 153 9.612066 TTTATTCTTTCAATGGTTTTCTTTGCT 57.388 25.926 0.00 0.00 32.48 3.91
153 154 9.868389 CTTTATTCTTTCAATGGTTTTCTTTGC 57.132 29.630 0.00 0.00 32.48 3.68
191 192 9.929180 GCCTCTTTAATGGTTTTCTTTATTCTT 57.071 29.630 0.00 0.00 0.00 2.52
192 193 8.531982 GGCCTCTTTAATGGTTTTCTTTATTCT 58.468 33.333 0.00 0.00 0.00 2.40
193 194 7.488150 CGGCCTCTTTAATGGTTTTCTTTATTC 59.512 37.037 0.00 0.00 0.00 1.75
194 195 7.177744 TCGGCCTCTTTAATGGTTTTCTTTATT 59.822 33.333 0.00 0.00 0.00 1.40
195 196 6.661805 TCGGCCTCTTTAATGGTTTTCTTTAT 59.338 34.615 0.00 0.00 0.00 1.40
196 197 6.005198 TCGGCCTCTTTAATGGTTTTCTTTA 58.995 36.000 0.00 0.00 0.00 1.85
197 198 4.830600 TCGGCCTCTTTAATGGTTTTCTTT 59.169 37.500 0.00 0.00 0.00 2.52
198 199 4.403734 TCGGCCTCTTTAATGGTTTTCTT 58.596 39.130 0.00 0.00 0.00 2.52
199 200 4.028993 TCGGCCTCTTTAATGGTTTTCT 57.971 40.909 0.00 0.00 0.00 2.52
200 201 4.457949 TCTTCGGCCTCTTTAATGGTTTTC 59.542 41.667 0.00 0.00 0.00 2.29
201 202 4.403734 TCTTCGGCCTCTTTAATGGTTTT 58.596 39.130 0.00 0.00 0.00 2.43
202 203 4.028993 TCTTCGGCCTCTTTAATGGTTT 57.971 40.909 0.00 0.00 0.00 3.27
203 204 3.713826 TCTTCGGCCTCTTTAATGGTT 57.286 42.857 0.00 0.00 0.00 3.67
204 205 3.610911 CTTCTTCGGCCTCTTTAATGGT 58.389 45.455 0.00 0.00 0.00 3.55
205 206 2.945668 CCTTCTTCGGCCTCTTTAATGG 59.054 50.000 0.00 0.00 0.00 3.16
206 207 2.945668 CCCTTCTTCGGCCTCTTTAATG 59.054 50.000 0.00 0.00 0.00 1.90
207 208 2.092375 CCCCTTCTTCGGCCTCTTTAAT 60.092 50.000 0.00 0.00 0.00 1.40
208 209 1.280998 CCCCTTCTTCGGCCTCTTTAA 59.719 52.381 0.00 0.00 0.00 1.52
209 210 0.909623 CCCCTTCTTCGGCCTCTTTA 59.090 55.000 0.00 0.00 0.00 1.85
210 211 0.840722 TCCCCTTCTTCGGCCTCTTT 60.841 55.000 0.00 0.00 0.00 2.52
211 212 1.229529 TCCCCTTCTTCGGCCTCTT 60.230 57.895 0.00 0.00 0.00 2.85
220 221 1.147191 GTGGGTTTTCCTCCCCTTCTT 59.853 52.381 0.00 0.00 44.00 2.52
242 243 2.892425 GCAGTTCCCCGATGCGAG 60.892 66.667 0.00 0.00 0.00 5.03
251 252 2.470938 AAAGAGCTCCCGCAGTTCCC 62.471 60.000 10.93 0.00 39.10 3.97
259 260 1.308783 GGGCAAAGAAAGAGCTCCCG 61.309 60.000 10.93 0.00 0.00 5.14
283 284 3.059120 GGTTTGGAGTCGTTCAAGTTAGC 60.059 47.826 0.00 0.00 0.00 3.09
340 504 7.167968 CCATACAAAGTGTCAGAAAACAACATG 59.832 37.037 0.00 0.00 0.00 3.21
341 505 7.068103 TCCATACAAAGTGTCAGAAAACAACAT 59.932 33.333 0.00 0.00 0.00 2.71
349 513 8.463930 AAAATCTTCCATACAAAGTGTCAGAA 57.536 30.769 0.00 0.00 0.00 3.02
378 543 6.374613 GGGTGACTAAAAATAGAGAAACTGGG 59.625 42.308 0.00 0.00 0.00 4.45
380 545 7.168905 AGGGGTGACTAAAAATAGAGAAACTG 58.831 38.462 0.00 0.00 0.00 3.16
489 656 4.700213 CCACGATTAGGTCAGACCAAAATT 59.300 41.667 22.31 2.82 41.95 1.82
527 696 3.610791 CTCTCACGCGGCGAAGTGA 62.611 63.158 30.94 27.63 44.11 3.41
604 773 2.222819 GCTAGATGTACGTTGCTTGCAC 60.223 50.000 0.00 0.00 0.00 4.57
642 811 3.847709 GCTCTGCTCGTCTTGCGC 61.848 66.667 0.00 0.00 41.07 6.09
690 859 5.989777 TCCTATAGCAACGCTCTTAAATTCC 59.010 40.000 0.00 0.00 40.44 3.01
692 861 6.346096 TGTCCTATAGCAACGCTCTTAAATT 58.654 36.000 0.00 0.00 40.44 1.82
705 874 4.021807 TGAGTTGTTCGTTGTCCTATAGCA 60.022 41.667 0.00 0.00 0.00 3.49
735 904 1.464219 GAGAGAGAGCTTGCTTTGTGC 59.536 52.381 0.00 0.00 43.25 4.57
746 915 1.535462 GGATAGACAGCGAGAGAGAGC 59.465 57.143 0.00 0.00 0.00 4.09
768 937 1.470098 GGTTCGAGTCGGTAGCTACAA 59.530 52.381 24.75 9.97 0.00 2.41
778 947 6.418956 CAAATAAATATGGTGGTTCGAGTCG 58.581 40.000 6.09 6.09 0.00 4.18
794 963 8.426881 AAAACTTGCACGTAAACCAAATAAAT 57.573 26.923 0.00 0.00 0.00 1.40
834 1006 1.855451 GGGGGAAAGGGTTGGGAGA 60.855 63.158 0.00 0.00 0.00 3.71
898 1070 8.535335 ACAATGATCAGAGTAGTTAACACATCT 58.465 33.333 8.61 4.64 0.00 2.90
952 1124 1.000731 GATGAGAGATCTGGAAGGCGG 59.999 57.143 0.00 0.00 0.00 6.13
998 1170 2.547642 GCTCTCTGTGGGTAGATCATGC 60.548 54.545 0.00 0.00 0.00 4.06
1010 1182 3.144506 AGAAAACATGTGGCTCTCTGTG 58.855 45.455 0.00 0.00 0.00 3.66
1013 1185 2.037772 ACGAGAAAACATGTGGCTCTCT 59.962 45.455 20.97 10.90 32.13 3.10
1038 1210 1.758514 GAGGAGGATGAGGACGGCA 60.759 63.158 0.00 0.00 0.00 5.69
1045 1217 0.178975 AGCGGTAGGAGGAGGATGAG 60.179 60.000 0.00 0.00 0.00 2.90
1048 1220 0.485099 ATCAGCGGTAGGAGGAGGAT 59.515 55.000 0.00 0.00 0.00 3.24
1062 1234 5.144692 TGCATAGATAGGAAGACATCAGC 57.855 43.478 0.00 0.00 0.00 4.26
1069 1241 2.234661 CGGCCATGCATAGATAGGAAGA 59.765 50.000 2.24 0.00 0.00 2.87
1109 1281 7.309683 CGCATATAGATATACCTGGAGCATGAT 60.310 40.741 0.00 0.00 0.00 2.45
1162 1334 8.137745 ACATATGAACAACAAATCCAGGATTT 57.862 30.769 20.35 20.35 42.14 2.17
1195 1367 9.883142 TCATCATAGTAATTACATCAACACACA 57.117 29.630 17.65 0.00 0.00 3.72
1199 1371 9.783081 AGCATCATCATAGTAATTACATCAACA 57.217 29.630 17.65 0.00 0.00 3.33
1279 1452 1.203125 TCCCCATCCCAAACACCTTTC 60.203 52.381 0.00 0.00 0.00 2.62
1346 1519 0.256464 TGTTTTCGTTGGGGACTGGT 59.744 50.000 0.00 0.00 0.00 4.00
1349 1522 1.616159 CCATGTTTTCGTTGGGGACT 58.384 50.000 0.00 0.00 0.00 3.85
1391 1564 0.690192 TGATCAACGATGGTGGTGGT 59.310 50.000 0.00 0.00 0.00 4.16
1418 1591 0.042131 TATCCCGGACCTCCAACACT 59.958 55.000 0.73 0.00 35.14 3.55
1459 1632 0.839946 AACAGACAAGGAGGTGCACT 59.160 50.000 17.98 2.27 0.00 4.40
1472 1645 4.742659 ACAACAACAACAACAACAACAGAC 59.257 37.500 0.00 0.00 0.00 3.51
1475 1648 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1476 1649 5.193936 CACAACAACAACAACAACAACAAC 58.806 37.500 0.00 0.00 0.00 3.32
1477 1650 4.870426 ACACAACAACAACAACAACAACAA 59.130 33.333 0.00 0.00 0.00 2.83
1478 1651 4.433615 ACACAACAACAACAACAACAACA 58.566 34.783 0.00 0.00 0.00 3.33
1479 1652 5.396750 AACACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1480 1653 6.040247 TGTAACACAACAACAACAACAACAA 58.960 32.000 0.00 0.00 0.00 2.83
1481 1654 5.588240 TGTAACACAACAACAACAACAACA 58.412 33.333 0.00 0.00 0.00 3.33
1482 1655 6.418226 TCTTGTAACACAACAACAACAACAAC 59.582 34.615 0.00 0.00 35.56 3.32
1483 1656 6.504398 TCTTGTAACACAACAACAACAACAA 58.496 32.000 0.00 0.00 35.56 2.83
1484 1657 6.073327 TCTTGTAACACAACAACAACAACA 57.927 33.333 0.00 0.00 35.56 3.33
1485 1658 6.994868 TTCTTGTAACACAACAACAACAAC 57.005 33.333 0.00 0.00 35.56 3.32
1486 1659 9.862371 ATTATTCTTGTAACACAACAACAACAA 57.138 25.926 0.00 0.00 35.56 2.83
1516 1689 6.153340 AGCATGCCAACTTATTTCACAATAGT 59.847 34.615 15.66 0.00 0.00 2.12
1652 1826 6.710597 TTTATTAGTAGCTCATCGACCAGT 57.289 37.500 0.00 0.00 0.00 4.00
1794 1970 4.345547 AGGCCTAAGATAGCTAAACTGGAC 59.654 45.833 1.29 1.80 0.00 4.02
1834 2010 6.428385 AGAATTAAGGAAGAAGCACGAATG 57.572 37.500 0.00 0.00 0.00 2.67
1873 2049 6.994496 CCAATCTCCTCTTCAGTTAATGCATA 59.006 38.462 0.00 0.00 0.00 3.14
1879 2055 3.587061 TGGCCAATCTCCTCTTCAGTTAA 59.413 43.478 0.61 0.00 0.00 2.01
1913 2089 5.950023 ACTTTCCCGTAGAGATCCATAGTA 58.050 41.667 0.00 0.00 0.00 1.82
1917 2093 3.643237 TGACTTTCCCGTAGAGATCCAT 58.357 45.455 0.00 0.00 0.00 3.41
1918 2094 3.095912 TGACTTTCCCGTAGAGATCCA 57.904 47.619 0.00 0.00 0.00 3.41
1928 2104 4.638421 TGCCTAATAAACATGACTTTCCCG 59.362 41.667 0.00 0.00 0.00 5.14
1934 2110 6.425114 CGCTCTATTGCCTAATAAACATGACT 59.575 38.462 0.00 0.00 0.00 3.41
1940 2116 6.202954 ACACATCGCTCTATTGCCTAATAAAC 59.797 38.462 0.00 0.00 0.00 2.01
2118 2296 4.250464 TGGACGACAATGCCTTAACTAAG 58.750 43.478 0.00 0.00 0.00 2.18
2154 2332 3.635373 TGATAGATCCGTCCAAGGTACAC 59.365 47.826 0.00 0.00 0.00 2.90
2252 2431 4.188937 AGTATGATGGCATTTGGTCCAT 57.811 40.909 0.00 1.73 45.17 3.41
2272 2451 1.576421 GCGTGAAGCCCTTGTGAAG 59.424 57.895 0.00 0.00 40.81 3.02
2310 2489 1.689813 TGGTGACGACAATAGTGGTGT 59.310 47.619 0.00 0.00 36.79 4.16
2317 2496 2.080693 GCAATGGTGGTGACGACAATA 58.919 47.619 0.00 0.00 0.00 1.90
2327 2506 0.322816 CTGGTAGCAGCAATGGTGGT 60.323 55.000 20.77 20.77 43.99 4.16
2392 2571 0.537188 GATGGACGAGAAGGCAAGGA 59.463 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.