Multiple sequence alignment - TraesCS5B01G252600

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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 TraesCS5B01G252600 chr5B 100.000 2486 0 0 1 2486 435599199 435596714 0.000000e+00 4591
1 TraesCS5B01G252600 chr5D 88.410 1950 110 62 141 2031 367784958 367783066 0.000000e+00 2242
2 TraesCS5B01G252600 chr5D 88.069 461 27 14 2046 2484 367783100 367782646 2.830000e-144 521
3 TraesCS5B01G252600 chr5D 83.761 117 8 3 1 112 367785061 367784951 1.570000e-17 100
4 TraesCS5B01G252600 chr5A 86.859 2009 130 62 1 1939 469889738 469887794 0.000000e+00 2124
5 TraesCS5B01G252600 chr5A 88.112 429 31 10 2067 2484 469887709 469887290 2.220000e-135 492


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 TraesCS5B01G252600 chr5B 435596714 435599199 2485 True 4591.000000 4591 100.000000 1 2486 1 chr5B.!!$R1 2485
1 TraesCS5B01G252600 chr5D 367782646 367785061 2415 True 954.333333 2242 86.746667 1 2484 3 chr5D.!!$R1 2483
2 TraesCS5B01G252600 chr5A 469887290 469889738 2448 True 1308.000000 2124 87.485500 1 2484 2 chr5A.!!$R1 2483

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
458 477 0.10741 TTGATTTGGATCGGTCGGGG 60.107 55.0 0.0 0.0 34.91 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2190 0.035439 AAGTACCCGAATGGCACTGG 60.035 55.0 0.0 0.0 37.83 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.202703 GGCCGTAACTGCGTCGAT 60.203 61.111 0.00 0.00 0.00 3.59
70 82 2.317040 GTACCAGGAGATCGATTCCCA 58.683 52.381 17.64 4.45 35.20 4.37
71 83 2.109229 ACCAGGAGATCGATTCCCAT 57.891 50.000 17.64 6.22 35.20 4.00
72 84 1.974236 ACCAGGAGATCGATTCCCATC 59.026 52.381 17.64 5.42 35.20 3.51
73 85 1.277557 CCAGGAGATCGATTCCCATCC 59.722 57.143 17.64 12.21 35.20 3.51
74 86 1.277557 CAGGAGATCGATTCCCATCCC 59.722 57.143 17.64 5.64 35.20 3.85
97 109 2.509336 GGTGCACGGACTGATCGG 60.509 66.667 11.45 0.00 0.00 4.18
192 204 3.046870 ATCGGCGAGCTGATCCTC 58.953 61.111 17.22 0.00 37.48 3.71
193 205 2.569354 ATCGGCGAGCTGATCCTCC 61.569 63.158 17.22 0.00 37.48 4.30
194 206 2.992817 ATCGGCGAGCTGATCCTCCT 62.993 60.000 17.22 0.00 37.48 3.69
195 207 2.733945 GGCGAGCTGATCCTCCTC 59.266 66.667 0.00 0.00 0.00 3.71
196 208 2.733945 GCGAGCTGATCCTCCTCC 59.266 66.667 0.00 0.00 0.00 4.30
197 209 3.038280 CGAGCTGATCCTCCTCCG 58.962 66.667 0.00 0.00 0.00 4.63
198 210 2.560119 CGAGCTGATCCTCCTCCGG 61.560 68.421 0.00 0.00 0.00 5.14
199 211 2.123077 AGCTGATCCTCCTCCGGG 60.123 66.667 0.00 0.00 0.00 5.73
200 212 2.123251 GCTGATCCTCCTCCGGGA 60.123 66.667 0.00 0.00 39.70 5.14
201 213 1.535202 GCTGATCCTCCTCCGGGAT 60.535 63.158 0.00 0.00 45.23 3.85
202 214 1.124477 GCTGATCCTCCTCCGGGATT 61.124 60.000 0.00 0.00 42.91 3.01
236 251 6.514541 CGCAGAATCGGAAGGAAATACTACTA 60.515 42.308 0.00 0.00 0.00 1.82
237 252 7.379750 GCAGAATCGGAAGGAAATACTACTAT 58.620 38.462 0.00 0.00 0.00 2.12
285 301 4.351874 AATCCTCCGTCTTTTCAACTGA 57.648 40.909 0.00 0.00 0.00 3.41
286 302 3.830744 TCCTCCGTCTTTTCAACTGAA 57.169 42.857 0.00 0.00 0.00 3.02
287 303 4.145365 TCCTCCGTCTTTTCAACTGAAA 57.855 40.909 0.69 0.69 41.77 2.69
288 304 4.714632 TCCTCCGTCTTTTCAACTGAAAT 58.285 39.130 5.75 0.00 42.83 2.17
289 305 4.515191 TCCTCCGTCTTTTCAACTGAAATG 59.485 41.667 5.75 8.37 42.83 2.32
290 306 4.515191 CCTCCGTCTTTTCAACTGAAATGA 59.485 41.667 13.75 13.75 42.83 2.57
294 310 4.223320 TCTTTTCAACTGAAATGACCGC 57.777 40.909 13.75 0.00 42.83 5.68
295 311 3.004315 TCTTTTCAACTGAAATGACCGCC 59.996 43.478 13.75 0.00 42.83 6.13
296 312 0.871722 TTCAACTGAAATGACCGCCG 59.128 50.000 0.00 0.00 0.00 6.46
297 313 1.154225 CAACTGAAATGACCGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
298 314 1.599518 AACTGAAATGACCGCCGCA 60.600 52.632 0.00 0.00 0.00 5.69
299 315 1.577328 AACTGAAATGACCGCCGCAG 61.577 55.000 0.00 0.00 0.00 5.18
300 316 1.741401 CTGAAATGACCGCCGCAGA 60.741 57.895 0.00 0.00 0.00 4.26
301 317 1.298157 CTGAAATGACCGCCGCAGAA 61.298 55.000 0.00 0.00 0.00 3.02
302 318 0.886938 TGAAATGACCGCCGCAGAAA 60.887 50.000 0.00 0.00 0.00 2.52
303 319 0.179189 GAAATGACCGCCGCAGAAAG 60.179 55.000 0.00 0.00 0.00 2.62
304 320 0.605319 AAATGACCGCCGCAGAAAGA 60.605 50.000 0.00 0.00 0.00 2.52
305 321 0.605319 AATGACCGCCGCAGAAAGAA 60.605 50.000 0.00 0.00 0.00 2.52
306 322 0.605319 ATGACCGCCGCAGAAAGAAA 60.605 50.000 0.00 0.00 0.00 2.52
307 323 0.816018 TGACCGCCGCAGAAAGAAAA 60.816 50.000 0.00 0.00 0.00 2.29
308 324 0.385598 GACCGCCGCAGAAAGAAAAC 60.386 55.000 0.00 0.00 0.00 2.43
309 325 0.818040 ACCGCCGCAGAAAGAAAACT 60.818 50.000 0.00 0.00 0.00 2.66
310 326 0.385974 CCGCCGCAGAAAGAAAACTG 60.386 55.000 0.00 0.00 37.22 3.16
334 350 5.490139 AATGAGGTTGCGATAATGTCTTG 57.510 39.130 0.00 0.00 0.00 3.02
358 374 3.335534 AAGCACGTCACGGTTCGC 61.336 61.111 0.35 0.00 0.00 4.70
362 378 2.202770 ACGTCACGGTTCGCAACA 60.203 55.556 0.35 0.00 0.00 3.33
373 389 2.440501 GTTCGCAACAGATAAATGGCG 58.559 47.619 0.00 0.00 45.24 5.69
376 392 0.385390 GCAACAGATAAATGGCGGGG 59.615 55.000 0.00 0.00 0.00 5.73
395 411 0.598680 GATCGTGCTGAGCCGCTTAT 60.599 55.000 0.23 0.00 0.00 1.73
404 420 1.206523 GAGCCGCTTATGTTCGGTAC 58.793 55.000 0.00 0.00 46.79 3.34
432 451 2.426522 TGAATTCCCTTTCGCACTCAG 58.573 47.619 2.27 0.00 0.00 3.35
437 456 0.954452 CCCTTTCGCACTCAGCTTTT 59.046 50.000 0.00 0.00 42.61 2.27
438 457 1.338020 CCCTTTCGCACTCAGCTTTTT 59.662 47.619 0.00 0.00 42.61 1.94
457 476 1.745232 TTTGATTTGGATCGGTCGGG 58.255 50.000 0.00 0.00 34.91 5.14
458 477 0.107410 TTGATTTGGATCGGTCGGGG 60.107 55.000 0.00 0.00 34.91 5.73
459 478 1.892391 GATTTGGATCGGTCGGGGC 60.892 63.158 0.00 0.00 0.00 5.80
460 479 3.415650 ATTTGGATCGGTCGGGGCC 62.416 63.158 0.00 0.00 0.00 5.80
550 582 4.261447 CGGTCACTCGATATTGTACCATCA 60.261 45.833 0.00 0.00 0.00 3.07
551 583 5.564848 CGGTCACTCGATATTGTACCATCAT 60.565 44.000 0.00 0.00 0.00 2.45
552 584 5.864474 GGTCACTCGATATTGTACCATCATC 59.136 44.000 0.00 0.00 0.00 2.92
562 601 1.134521 GTACCATCATCTCCGGTGCAA 60.135 52.381 0.00 0.00 35.68 4.08
650 695 0.675208 ACGCATTATTGGACGCCACA 60.675 50.000 0.00 0.00 30.78 4.17
741 795 2.029964 GCGCGGGGAATTATCGGA 59.970 61.111 8.83 0.00 0.00 4.55
870 925 1.985460 TATAAATGCGCCCACCCCGT 61.985 55.000 4.18 0.00 0.00 5.28
906 965 0.916086 GTATCCATCCCACCACACCA 59.084 55.000 0.00 0.00 0.00 4.17
907 966 1.134098 GTATCCATCCCACCACACCAG 60.134 57.143 0.00 0.00 0.00 4.00
912 971 4.202574 CCCACCACACCAGCACCA 62.203 66.667 0.00 0.00 0.00 4.17
928 994 4.056125 CACAGCCGCTCAGACCGA 62.056 66.667 0.00 0.00 0.00 4.69
929 995 3.303135 ACAGCCGCTCAGACCGAA 61.303 61.111 0.00 0.00 0.00 4.30
1494 1581 1.656652 CCTGGATTTAGGCACGAGTG 58.343 55.000 0.00 0.00 0.00 3.51
1495 1582 1.207089 CCTGGATTTAGGCACGAGTGA 59.793 52.381 7.50 0.00 0.00 3.41
1608 1695 6.087456 AGGAATTTAGATGGATCCTAGCAGA 58.913 40.000 14.23 0.00 38.71 4.26
1609 1696 6.213195 AGGAATTTAGATGGATCCTAGCAGAG 59.787 42.308 14.23 0.00 38.71 3.35
1612 1699 0.612744 GATGGATCCTAGCAGAGGGC 59.387 60.000 14.23 0.00 46.70 5.19
1742 1837 3.254166 AGCGCTTTGTGTGATGAGAAATT 59.746 39.130 2.64 0.00 0.00 1.82
1754 1849 3.134574 TGAGAAATTTGTGTACGGCCT 57.865 42.857 0.00 0.00 0.00 5.19
1818 1918 0.182537 TGTTGTGAACACCAGAGGGG 59.817 55.000 2.46 0.00 44.81 4.79
1820 1920 2.034221 GTGAACACCAGAGGGGCC 59.966 66.667 0.00 0.00 42.05 5.80
1821 1921 2.121963 TGAACACCAGAGGGGCCT 60.122 61.111 0.84 0.00 42.05 5.19
1822 1922 2.224159 TGAACACCAGAGGGGCCTC 61.224 63.158 0.84 0.00 42.05 4.70
1970 2089 6.599638 GGTAGCTGATCTTAACAAGAAACCAT 59.400 38.462 0.00 0.00 41.63 3.55
1974 2093 5.698832 TGATCTTAACAAGAAACCATTGCG 58.301 37.500 0.00 0.00 41.63 4.85
1997 2117 6.255215 CGAATCGTTGCAGGTGTTTATTAAT 58.745 36.000 0.00 0.00 0.00 1.40
1998 2118 7.403421 CGAATCGTTGCAGGTGTTTATTAATA 58.597 34.615 0.00 0.00 0.00 0.98
1999 2119 7.906010 CGAATCGTTGCAGGTGTTTATTAATAA 59.094 33.333 3.71 3.71 0.00 1.40
2000 2120 9.562583 GAATCGTTGCAGGTGTTTATTAATAAA 57.437 29.630 15.19 15.19 0.00 1.40
2001 2121 9.567848 AATCGTTGCAGGTGTTTATTAATAAAG 57.432 29.630 18.76 9.53 33.31 1.85
2031 2158 3.454812 AGAAACCAGTGCTATTCGGGTAT 59.545 43.478 0.00 0.00 33.44 2.73
2033 2160 3.926058 ACCAGTGCTATTCGGGTATTT 57.074 42.857 0.00 0.00 32.15 1.40
2034 2161 4.230745 ACCAGTGCTATTCGGGTATTTT 57.769 40.909 0.00 0.00 32.15 1.82
2035 2162 3.945285 ACCAGTGCTATTCGGGTATTTTG 59.055 43.478 0.00 0.00 32.15 2.44
2036 2163 3.945285 CCAGTGCTATTCGGGTATTTTGT 59.055 43.478 0.00 0.00 0.00 2.83
2037 2164 5.120399 CCAGTGCTATTCGGGTATTTTGTA 58.880 41.667 0.00 0.00 0.00 2.41
2038 2165 5.007332 CCAGTGCTATTCGGGTATTTTGTAC 59.993 44.000 0.00 0.00 0.00 2.90
2039 2166 5.007332 CAGTGCTATTCGGGTATTTTGTACC 59.993 44.000 0.00 0.00 36.88 3.34
2043 2170 5.587443 GCTATTCGGGTATTTTGTACCTGTT 59.413 40.000 11.66 5.25 42.96 3.16
2044 2171 5.890424 ATTCGGGTATTTTGTACCTGTTG 57.110 39.130 11.66 0.00 42.96 3.33
2045 2172 4.354893 TCGGGTATTTTGTACCTGTTGT 57.645 40.909 11.66 0.00 42.96 3.32
2046 2173 4.716794 TCGGGTATTTTGTACCTGTTGTT 58.283 39.130 11.66 0.00 42.96 2.83
2047 2174 5.862845 TCGGGTATTTTGTACCTGTTGTTA 58.137 37.500 11.66 0.00 42.96 2.41
2048 2175 6.294473 TCGGGTATTTTGTACCTGTTGTTAA 58.706 36.000 11.66 0.00 42.96 2.01
2049 2176 6.769822 TCGGGTATTTTGTACCTGTTGTTAAA 59.230 34.615 11.66 0.00 42.96 1.52
2050 2177 6.857451 CGGGTATTTTGTACCTGTTGTTAAAC 59.143 38.462 5.15 0.00 38.76 2.01
2051 2178 7.147312 GGGTATTTTGTACCTGTTGTTAAACC 58.853 38.462 4.42 0.00 37.71 3.27
2052 2179 7.201893 GGGTATTTTGTACCTGTTGTTAAACCA 60.202 37.037 4.42 0.00 37.71 3.67
2053 2180 7.863877 GGTATTTTGTACCTGTTGTTAAACCAG 59.136 37.037 0.00 0.00 35.25 4.00
2054 2181 7.648039 ATTTTGTACCTGTTGTTAAACCAGA 57.352 32.000 0.00 0.00 35.25 3.86
2055 2182 7.648039 TTTTGTACCTGTTGTTAAACCAGAT 57.352 32.000 0.00 0.00 35.25 2.90
2056 2183 6.627395 TTGTACCTGTTGTTAAACCAGATG 57.373 37.500 0.00 0.00 35.25 2.90
2057 2184 5.931294 TGTACCTGTTGTTAAACCAGATGA 58.069 37.500 0.00 0.00 35.25 2.92
2058 2185 6.358178 TGTACCTGTTGTTAAACCAGATGAA 58.642 36.000 0.00 0.00 35.25 2.57
2059 2186 6.485313 TGTACCTGTTGTTAAACCAGATGAAG 59.515 38.462 0.00 0.00 35.25 3.02
2060 2187 5.690865 ACCTGTTGTTAAACCAGATGAAGA 58.309 37.500 0.00 0.00 35.25 2.87
2061 2188 6.126409 ACCTGTTGTTAAACCAGATGAAGAA 58.874 36.000 0.00 0.00 35.25 2.52
2062 2189 6.605594 ACCTGTTGTTAAACCAGATGAAGAAA 59.394 34.615 0.00 0.00 35.25 2.52
2063 2190 6.918022 CCTGTTGTTAAACCAGATGAAGAAAC 59.082 38.462 0.00 0.00 35.25 2.78
2064 2191 6.801575 TGTTGTTAAACCAGATGAAGAAACC 58.198 36.000 0.00 0.00 35.25 3.27
2065 2192 6.378564 TGTTGTTAAACCAGATGAAGAAACCA 59.621 34.615 0.00 0.00 35.25 3.67
2066 2193 6.633500 TGTTAAACCAGATGAAGAAACCAG 57.367 37.500 0.00 0.00 0.00 4.00
2067 2194 6.126409 TGTTAAACCAGATGAAGAAACCAGT 58.874 36.000 0.00 0.00 0.00 4.00
2068 2195 6.039270 TGTTAAACCAGATGAAGAAACCAGTG 59.961 38.462 0.00 0.00 0.00 3.66
2069 2196 2.508526 ACCAGATGAAGAAACCAGTGC 58.491 47.619 0.00 0.00 0.00 4.40
2070 2197 1.815003 CCAGATGAAGAAACCAGTGCC 59.185 52.381 0.00 0.00 0.00 5.01
2071 2198 2.507484 CAGATGAAGAAACCAGTGCCA 58.493 47.619 0.00 0.00 0.00 4.92
2072 2199 3.087031 CAGATGAAGAAACCAGTGCCAT 58.913 45.455 0.00 0.00 0.00 4.40
2073 2200 3.508793 CAGATGAAGAAACCAGTGCCATT 59.491 43.478 0.00 0.00 0.00 3.16
2074 2201 3.760684 AGATGAAGAAACCAGTGCCATTC 59.239 43.478 0.00 0.00 0.00 2.67
2075 2202 1.879380 TGAAGAAACCAGTGCCATTCG 59.121 47.619 0.00 0.00 0.00 3.34
2076 2203 1.200020 GAAGAAACCAGTGCCATTCGG 59.800 52.381 0.00 0.00 0.00 4.30
2077 2204 0.609131 AGAAACCAGTGCCATTCGGG 60.609 55.000 0.00 0.00 40.85 5.14
2118 2252 7.411486 TTGTTAAACCAGATCAAGAAACCAA 57.589 32.000 0.00 0.00 0.00 3.67
2121 2255 8.573035 TGTTAAACCAGATCAAGAAACCAATAC 58.427 33.333 0.00 0.00 0.00 1.89
2122 2256 8.793592 GTTAAACCAGATCAAGAAACCAATACT 58.206 33.333 0.00 0.00 0.00 2.12
2158 2293 9.959749 TTTACAAAGTGTTCATTAAACCAGATC 57.040 29.630 0.00 0.00 37.03 2.75
2162 2297 6.824305 AGTGTTCATTAAACCAGATCAAGG 57.176 37.500 0.00 0.00 37.03 3.61
2171 2310 2.057922 ACCAGATCAAGGAACCACTGT 58.942 47.619 10.82 0.00 0.00 3.55
2182 2321 3.584848 AGGAACCACTGTAGCAATCTCTT 59.415 43.478 0.00 0.00 0.00 2.85
2184 2323 3.618690 ACCACTGTAGCAATCTCTTCC 57.381 47.619 0.00 0.00 0.00 3.46
2197 2340 6.316390 AGCAATCTCTTCCGGTGTTTATTAAG 59.684 38.462 0.00 0.00 0.00 1.85
2200 2344 5.553123 TCTCTTCCGGTGTTTATTAAGCAA 58.447 37.500 0.00 0.00 0.00 3.91
2213 2357 9.823647 TGTTTATTAAGCAAATCAAGAAACCAA 57.176 25.926 0.00 0.00 27.94 3.67
2278 2426 4.798882 TCAAGAAACCACCACCACTATTT 58.201 39.130 0.00 0.00 0.00 1.40
2311 2459 1.454847 AGGCTCCAAACAAACGGCA 60.455 52.632 0.00 0.00 0.00 5.69
2319 2467 2.403259 CAAACAAACGGCAAGGGAATC 58.597 47.619 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.038329 CACTACGTCCCCTCCCCA 59.962 66.667 0.00 0.00 0.00 4.96
70 82 1.748879 CCGTGCACCGAATTGGGAT 60.749 57.895 14.12 0.00 44.64 3.85
71 83 2.359354 CCGTGCACCGAATTGGGA 60.359 61.111 14.12 0.00 44.64 4.37
72 84 2.359354 TCCGTGCACCGAATTGGG 60.359 61.111 12.15 4.73 44.64 4.12
73 85 1.671054 AGTCCGTGCACCGAATTGG 60.671 57.895 12.15 5.50 46.41 3.16
74 86 0.948623 TCAGTCCGTGCACCGAATTG 60.949 55.000 12.15 12.02 39.56 2.32
198 210 2.341846 TTCTGCGGGAATGGTAATCC 57.658 50.000 0.00 0.00 36.16 3.01
199 211 2.480419 CGATTCTGCGGGAATGGTAATC 59.520 50.000 9.04 1.07 43.90 1.75
200 212 2.494059 CGATTCTGCGGGAATGGTAAT 58.506 47.619 9.04 0.00 43.90 1.89
201 213 1.948104 CGATTCTGCGGGAATGGTAA 58.052 50.000 9.04 0.00 43.90 2.85
202 214 3.678921 CGATTCTGCGGGAATGGTA 57.321 52.632 9.04 0.00 43.90 3.25
236 251 4.575885 TCCGAATCTTTTCTCGTGGAAAT 58.424 39.130 7.02 0.00 42.63 2.17
237 252 3.997762 TCCGAATCTTTTCTCGTGGAAA 58.002 40.909 3.12 3.12 41.58 3.13
243 258 6.743172 GGATTTTTCTTCCGAATCTTTTCTCG 59.257 38.462 0.00 0.00 31.96 4.04
244 259 7.821652 AGGATTTTTCTTCCGAATCTTTTCTC 58.178 34.615 0.00 0.00 38.36 2.87
285 301 0.605319 TCTTTCTGCGGCGGTCATTT 60.605 50.000 9.78 0.00 0.00 2.32
286 302 0.605319 TTCTTTCTGCGGCGGTCATT 60.605 50.000 9.78 0.00 0.00 2.57
287 303 0.605319 TTTCTTTCTGCGGCGGTCAT 60.605 50.000 9.78 0.00 0.00 3.06
288 304 0.816018 TTTTCTTTCTGCGGCGGTCA 60.816 50.000 9.78 0.00 0.00 4.02
289 305 0.385598 GTTTTCTTTCTGCGGCGGTC 60.386 55.000 9.78 0.00 0.00 4.79
290 306 0.818040 AGTTTTCTTTCTGCGGCGGT 60.818 50.000 9.78 0.00 0.00 5.68
291 307 0.385974 CAGTTTTCTTTCTGCGGCGG 60.386 55.000 9.78 1.35 0.00 6.13
292 308 0.586319 TCAGTTTTCTTTCTGCGGCG 59.414 50.000 0.51 0.51 0.00 6.46
293 309 2.774439 TTCAGTTTTCTTTCTGCGGC 57.226 45.000 0.00 0.00 0.00 6.53
294 310 4.858935 TCATTTCAGTTTTCTTTCTGCGG 58.141 39.130 0.00 0.00 0.00 5.69
295 311 4.913924 CCTCATTTCAGTTTTCTTTCTGCG 59.086 41.667 0.00 0.00 0.00 5.18
296 312 5.836347 ACCTCATTTCAGTTTTCTTTCTGC 58.164 37.500 0.00 0.00 0.00 4.26
297 313 6.199719 GCAACCTCATTTCAGTTTTCTTTCTG 59.800 38.462 0.00 0.00 0.00 3.02
298 314 6.276091 GCAACCTCATTTCAGTTTTCTTTCT 58.724 36.000 0.00 0.00 0.00 2.52
299 315 5.173854 CGCAACCTCATTTCAGTTTTCTTTC 59.826 40.000 0.00 0.00 0.00 2.62
300 316 5.043248 CGCAACCTCATTTCAGTTTTCTTT 58.957 37.500 0.00 0.00 0.00 2.52
301 317 4.338118 TCGCAACCTCATTTCAGTTTTCTT 59.662 37.500 0.00 0.00 0.00 2.52
302 318 3.882888 TCGCAACCTCATTTCAGTTTTCT 59.117 39.130 0.00 0.00 0.00 2.52
303 319 4.223320 TCGCAACCTCATTTCAGTTTTC 57.777 40.909 0.00 0.00 0.00 2.29
304 320 4.853924 ATCGCAACCTCATTTCAGTTTT 57.146 36.364 0.00 0.00 0.00 2.43
305 321 5.957842 TTATCGCAACCTCATTTCAGTTT 57.042 34.783 0.00 0.00 0.00 2.66
306 322 5.415701 ACATTATCGCAACCTCATTTCAGTT 59.584 36.000 0.00 0.00 0.00 3.16
307 323 4.943705 ACATTATCGCAACCTCATTTCAGT 59.056 37.500 0.00 0.00 0.00 3.41
308 324 5.295292 AGACATTATCGCAACCTCATTTCAG 59.705 40.000 0.00 0.00 0.00 3.02
309 325 5.185454 AGACATTATCGCAACCTCATTTCA 58.815 37.500 0.00 0.00 0.00 2.69
310 326 5.741388 AGACATTATCGCAACCTCATTTC 57.259 39.130 0.00 0.00 0.00 2.17
334 350 1.548973 CCGTGACGTGCTTGACTCAC 61.549 60.000 3.64 0.00 33.14 3.51
358 374 2.051334 TCCCCGCCATTTATCTGTTG 57.949 50.000 0.00 0.00 0.00 3.33
362 378 1.056660 ACGATCCCCGCCATTTATCT 58.943 50.000 0.00 0.00 43.32 1.98
373 389 4.899239 CGGCTCAGCACGATCCCC 62.899 72.222 0.00 0.00 0.00 4.81
376 392 0.598680 ATAAGCGGCTCAGCACGATC 60.599 55.000 11.22 0.00 40.15 3.69
395 411 2.027897 AACGCAGCGTACCGAACA 59.972 55.556 23.30 0.00 39.99 3.18
404 420 0.240945 AAAGGGAATTCAACGCAGCG 59.759 50.000 14.82 14.82 0.00 5.18
405 421 1.729149 CGAAAGGGAATTCAACGCAGC 60.729 52.381 7.93 0.00 0.00 5.25
406 422 1.729149 GCGAAAGGGAATTCAACGCAG 60.729 52.381 20.07 6.13 43.18 5.18
407 423 0.239879 GCGAAAGGGAATTCAACGCA 59.760 50.000 20.07 0.00 43.18 5.24
410 426 2.552315 TGAGTGCGAAAGGGAATTCAAC 59.448 45.455 7.93 0.00 0.00 3.18
437 456 2.088423 CCCGACCGATCCAAATCAAAA 58.912 47.619 0.00 0.00 31.76 2.44
438 457 1.680555 CCCCGACCGATCCAAATCAAA 60.681 52.381 0.00 0.00 31.76 2.69
439 458 0.107410 CCCCGACCGATCCAAATCAA 60.107 55.000 0.00 0.00 31.76 2.57
459 478 2.046023 TGATTGGCTGGCTGACGG 60.046 61.111 2.00 0.00 0.00 4.79
460 479 2.758089 GCTGATTGGCTGGCTGACG 61.758 63.158 2.00 0.00 0.00 4.35
461 480 0.964358 AAGCTGATTGGCTGGCTGAC 60.964 55.000 2.00 0.00 42.24 3.51
462 481 0.679002 GAAGCTGATTGGCTGGCTGA 60.679 55.000 2.00 0.00 42.24 4.26
463 482 1.807886 GAAGCTGATTGGCTGGCTG 59.192 57.895 2.00 0.00 42.24 4.85
464 483 1.748122 CGAAGCTGATTGGCTGGCT 60.748 57.895 2.00 0.00 42.24 4.75
465 484 2.796651 CGAAGCTGATTGGCTGGC 59.203 61.111 0.00 0.00 42.24 4.85
497 516 1.418264 TCACGGGACAGTGGAAAATCA 59.582 47.619 2.91 0.00 42.10 2.57
562 601 3.967734 GACGCATTTGTACGTGCAT 57.032 47.368 7.30 2.90 43.71 3.96
650 695 2.032071 CCCGCTCTGGTTCGGTTT 59.968 61.111 0.00 0.00 43.87 3.27
870 925 0.854039 TACAGTGAGGGAGGGGGAGA 60.854 60.000 0.00 0.00 0.00 3.71
906 965 4.694233 CTGAGCGGCTGTGGTGCT 62.694 66.667 7.50 0.00 42.73 4.40
907 966 4.687215 TCTGAGCGGCTGTGGTGC 62.687 66.667 7.50 0.00 0.00 5.01
912 971 3.303135 TTCGGTCTGAGCGGCTGT 61.303 61.111 26.42 0.00 39.89 4.40
928 994 1.074951 CCTTCTTTCAGGGGCGGTT 59.925 57.895 0.00 0.00 0.00 4.44
929 995 2.757077 CCTTCTTTCAGGGGCGGT 59.243 61.111 0.00 0.00 0.00 5.68
937 1003 1.782044 GCAATTTGCGCCTTCTTTCA 58.218 45.000 4.18 0.00 31.71 2.69
1487 1574 1.982223 CTTCTCTTCGCTTCACTCGTG 59.018 52.381 0.00 0.00 0.00 4.35
1491 1578 3.823873 TCTTCTCTTCTCTTCGCTTCACT 59.176 43.478 0.00 0.00 0.00 3.41
1492 1579 4.083003 TCTCTTCTCTTCTCTTCGCTTCAC 60.083 45.833 0.00 0.00 0.00 3.18
1493 1580 4.075682 TCTCTTCTCTTCTCTTCGCTTCA 58.924 43.478 0.00 0.00 0.00 3.02
1494 1581 4.394920 TCTCTCTTCTCTTCTCTTCGCTTC 59.605 45.833 0.00 0.00 0.00 3.86
1495 1582 4.331968 TCTCTCTTCTCTTCTCTTCGCTT 58.668 43.478 0.00 0.00 0.00 4.68
1711 1805 0.668096 CACAAAGCGCTACACCCGTA 60.668 55.000 12.05 0.00 0.00 4.02
1800 1900 1.172812 GCCCCTCTGGTGTTCACAAC 61.173 60.000 5.32 0.00 36.04 3.32
1803 1903 2.034221 GGCCCCTCTGGTGTTCAC 59.966 66.667 0.00 0.00 36.04 3.18
1818 1918 0.036022 AGAGGCAAGAACACAGAGGC 59.964 55.000 0.00 0.00 0.00 4.70
1820 1920 2.149578 CCAAGAGGCAAGAACACAGAG 58.850 52.381 0.00 0.00 0.00 3.35
1821 1921 1.768275 TCCAAGAGGCAAGAACACAGA 59.232 47.619 0.00 0.00 33.74 3.41
1822 1922 2.260844 TCCAAGAGGCAAGAACACAG 57.739 50.000 0.00 0.00 33.74 3.66
1823 1923 2.507484 CATCCAAGAGGCAAGAACACA 58.493 47.619 0.00 0.00 33.74 3.72
1912 2014 2.144730 TGGTAATACAACGGTGTGCAC 58.855 47.619 18.38 10.75 38.82 4.57
1954 2056 5.759506 TTCGCAATGGTTTCTTGTTAAGA 57.240 34.783 0.00 0.00 35.26 2.10
1956 2058 5.150683 CGATTCGCAATGGTTTCTTGTTAA 58.849 37.500 0.00 0.00 0.00 2.01
1957 2059 4.214545 ACGATTCGCAATGGTTTCTTGTTA 59.785 37.500 5.86 0.00 0.00 2.41
1958 2060 3.004315 ACGATTCGCAATGGTTTCTTGTT 59.996 39.130 5.86 0.00 0.00 2.83
1959 2061 2.552315 ACGATTCGCAATGGTTTCTTGT 59.448 40.909 5.86 0.00 0.00 3.16
1970 2089 1.163420 ACACCTGCAACGATTCGCAA 61.163 50.000 5.86 0.00 37.76 4.85
1974 2093 9.562583 TTTATTAATAAACACCTGCAACGATTC 57.437 29.630 15.19 0.00 0.00 2.52
1997 2117 4.216257 GCACTGGTTTCTTGATCTGCTTTA 59.784 41.667 0.00 0.00 0.00 1.85
1998 2118 3.005155 GCACTGGTTTCTTGATCTGCTTT 59.995 43.478 0.00 0.00 0.00 3.51
1999 2119 2.555757 GCACTGGTTTCTTGATCTGCTT 59.444 45.455 0.00 0.00 0.00 3.91
2000 2120 2.157738 GCACTGGTTTCTTGATCTGCT 58.842 47.619 0.00 0.00 0.00 4.24
2001 2121 2.157738 AGCACTGGTTTCTTGATCTGC 58.842 47.619 0.00 0.00 0.00 4.26
2031 2158 7.339721 TCATCTGGTTTAACAACAGGTACAAAA 59.660 33.333 0.00 0.00 34.15 2.44
2033 2160 6.358178 TCATCTGGTTTAACAACAGGTACAA 58.642 36.000 0.00 0.00 34.15 2.41
2034 2161 5.931294 TCATCTGGTTTAACAACAGGTACA 58.069 37.500 0.00 0.00 34.15 2.90
2035 2162 6.708949 TCTTCATCTGGTTTAACAACAGGTAC 59.291 38.462 0.00 0.00 34.15 3.34
2036 2163 6.833041 TCTTCATCTGGTTTAACAACAGGTA 58.167 36.000 0.00 0.00 34.15 3.08
2037 2164 5.690865 TCTTCATCTGGTTTAACAACAGGT 58.309 37.500 0.00 0.00 34.15 4.00
2038 2165 6.633500 TTCTTCATCTGGTTTAACAACAGG 57.367 37.500 0.00 0.00 34.15 4.00
2039 2166 6.918022 GGTTTCTTCATCTGGTTTAACAACAG 59.082 38.462 0.00 0.00 34.15 3.16
2043 2170 6.039270 CACTGGTTTCTTCATCTGGTTTAACA 59.961 38.462 0.00 0.00 0.00 2.41
2044 2171 6.438763 CACTGGTTTCTTCATCTGGTTTAAC 58.561 40.000 0.00 0.00 0.00 2.01
2045 2172 5.009610 GCACTGGTTTCTTCATCTGGTTTAA 59.990 40.000 0.00 0.00 0.00 1.52
2046 2173 4.518970 GCACTGGTTTCTTCATCTGGTTTA 59.481 41.667 0.00 0.00 0.00 2.01
2047 2174 3.319122 GCACTGGTTTCTTCATCTGGTTT 59.681 43.478 0.00 0.00 0.00 3.27
2048 2175 2.887152 GCACTGGTTTCTTCATCTGGTT 59.113 45.455 0.00 0.00 0.00 3.67
2049 2176 2.508526 GCACTGGTTTCTTCATCTGGT 58.491 47.619 0.00 0.00 0.00 4.00
2050 2177 1.815003 GGCACTGGTTTCTTCATCTGG 59.185 52.381 0.00 0.00 0.00 3.86
2051 2178 2.507484 TGGCACTGGTTTCTTCATCTG 58.493 47.619 0.00 0.00 0.00 2.90
2052 2179 2.957402 TGGCACTGGTTTCTTCATCT 57.043 45.000 0.00 0.00 0.00 2.90
2053 2180 3.426695 CGAATGGCACTGGTTTCTTCATC 60.427 47.826 0.00 0.00 0.00 2.92
2054 2181 2.489329 CGAATGGCACTGGTTTCTTCAT 59.511 45.455 0.00 0.00 0.00 2.57
2055 2182 1.879380 CGAATGGCACTGGTTTCTTCA 59.121 47.619 0.00 0.00 0.00 3.02
2056 2183 1.200020 CCGAATGGCACTGGTTTCTTC 59.800 52.381 0.00 0.00 0.00 2.87
2057 2184 1.247567 CCGAATGGCACTGGTTTCTT 58.752 50.000 0.00 0.00 0.00 2.52
2058 2185 0.609131 CCCGAATGGCACTGGTTTCT 60.609 55.000 0.00 0.00 0.00 2.52
2059 2186 0.893727 ACCCGAATGGCACTGGTTTC 60.894 55.000 0.00 0.00 37.83 2.78
2060 2187 0.402504 TACCCGAATGGCACTGGTTT 59.597 50.000 4.67 0.00 37.83 3.27
2061 2188 0.322187 GTACCCGAATGGCACTGGTT 60.322 55.000 4.67 0.00 37.83 3.67
2062 2189 1.198759 AGTACCCGAATGGCACTGGT 61.199 55.000 0.00 0.00 37.83 4.00
2063 2190 0.035439 AAGTACCCGAATGGCACTGG 60.035 55.000 0.00 0.00 37.83 4.00
2064 2191 1.468520 CAAAGTACCCGAATGGCACTG 59.531 52.381 0.00 0.00 37.83 3.66
2065 2192 1.073284 ACAAAGTACCCGAATGGCACT 59.927 47.619 0.00 0.00 37.83 4.40
2066 2193 1.530323 ACAAAGTACCCGAATGGCAC 58.470 50.000 0.00 0.00 37.83 5.01
2067 2194 2.303600 ACTACAAAGTACCCGAATGGCA 59.696 45.455 0.00 0.00 37.83 4.92
2068 2195 2.981898 ACTACAAAGTACCCGAATGGC 58.018 47.619 0.00 0.00 37.83 4.40
2069 2196 4.117685 GCTACTACAAAGTACCCGAATGG 58.882 47.826 0.00 0.00 37.15 3.16
2070 2197 3.795101 CGCTACTACAAAGTACCCGAATG 59.205 47.826 0.00 0.00 37.15 2.67
2071 2198 3.445096 ACGCTACTACAAAGTACCCGAAT 59.555 43.478 0.00 0.00 37.15 3.34
2072 2199 2.819608 ACGCTACTACAAAGTACCCGAA 59.180 45.455 0.00 0.00 37.15 4.30
2073 2200 2.436417 ACGCTACTACAAAGTACCCGA 58.564 47.619 0.00 0.00 37.15 5.14
2074 2201 2.927553 ACGCTACTACAAAGTACCCG 57.072 50.000 0.00 0.00 37.15 5.28
2075 2202 4.309933 ACAAACGCTACTACAAAGTACCC 58.690 43.478 0.00 0.00 37.15 3.69
2076 2203 5.912360 AACAAACGCTACTACAAAGTACC 57.088 39.130 0.00 0.00 37.15 3.34
2077 2204 7.793888 GGTTTAACAAACGCTACTACAAAGTAC 59.206 37.037 0.00 0.00 42.29 2.73
2121 2255 9.965824 ATGAACACTTTGTAAAAATTGGTAGAG 57.034 29.630 1.29 0.00 0.00 2.43
2158 2293 3.679389 AGATTGCTACAGTGGTTCCTTG 58.321 45.455 0.00 0.00 0.00 3.61
2162 2297 3.935828 GGAAGAGATTGCTACAGTGGTTC 59.064 47.826 0.00 0.00 0.00 3.62
2171 2310 3.695830 AAACACCGGAAGAGATTGCTA 57.304 42.857 9.46 0.00 0.00 3.49
2182 2321 6.431543 TCTTGATTTGCTTAATAAACACCGGA 59.568 34.615 9.46 0.00 0.00 5.14
2184 2323 8.424731 GTTTCTTGATTTGCTTAATAAACACCG 58.575 33.333 0.00 0.00 0.00 4.94
2197 2340 7.432252 CCGAATAGTATTGGTTTCTTGATTTGC 59.568 37.037 0.00 0.00 0.00 3.68
2200 2344 7.116736 ACCCGAATAGTATTGGTTTCTTGATT 58.883 34.615 0.00 0.00 0.00 2.57
2213 2357 7.224522 ACGCTAGAAATTACCCGAATAGTAT 57.775 36.000 0.00 0.00 0.00 2.12
2311 2459 4.162040 CTGATTAGTGCAGGATTCCCTT 57.838 45.455 0.00 0.00 42.02 3.95


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

AutoCloner maintained by Alex Coulton.