Multiple sequence alignment - TraesCS5D01G440200

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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 TraesCS5D01G440200 chr5D 100.000 2726 0 0 1 2726 493461322 493464047 0.000000e+00 5035.0
1 TraesCS5D01G440200 chr5D 85.000 180 24 3 167 345 529218336 529218159 2.160000e-41 180.0
2 TraesCS5D01G440200 chr5D 84.615 195 12 8 388 572 493454495 493454681 7.760000e-41 178.0
3 TraesCS5D01G440200 chr5B 92.506 1975 65 21 1 1935 609235589 609237520 0.000000e+00 2750.0
4 TraesCS5D01G440200 chr5B 97.170 106 3 0 2073 2178 609237776 609237881 2.160000e-41 180.0
5 TraesCS5D01G440200 chr5B 83.770 191 25 6 171 357 149590563 149590375 2.790000e-40 176.0
6 TraesCS5D01G440200 chr5B 82.927 82 9 4 74 153 537962949 537963027 4.870000e-08 69.4
7 TraesCS5D01G440200 chr5A 95.423 1158 41 5 781 1935 616621279 616622427 0.000000e+00 1834.0
8 TraesCS5D01G440200 chr5A 94.394 767 23 5 1 767 616620469 616621215 0.000000e+00 1160.0
9 TraesCS5D01G440200 chr5A 92.308 143 9 2 174 314 605798026 605797884 4.600000e-48 202.0
10 TraesCS5D01G440200 chr5A 86.932 176 20 3 168 342 688327041 688327214 7.700000e-46 195.0
11 TraesCS5D01G440200 chr5A 85.938 192 11 9 389 571 616612022 616612206 9.960000e-45 191.0
12 TraesCS5D01G440200 chr5A 90.226 133 13 0 2002 2134 616634128 616634260 1.000000e-39 174.0
13 TraesCS5D01G440200 chr5A 100.000 32 0 0 765 796 616621254 616621223 2.930000e-05 60.2
14 TraesCS5D01G440200 chrUn 98.047 512 7 2 2216 2726 206777715 206778224 0.000000e+00 887.0
15 TraesCS5D01G440200 chr4D 98.047 512 7 2 2216 2726 123314518 123315027 0.000000e+00 887.0
16 TraesCS5D01G440200 chr4D 97.656 512 9 2 2216 2726 123271129 123271638 0.000000e+00 876.0
17 TraesCS5D01G440200 chr3A 98.047 512 7 2 2216 2726 633127074 633127583 0.000000e+00 887.0
18 TraesCS5D01G440200 chr4B 97.852 512 8 2 2216 2726 209287505 209288014 0.000000e+00 881.0
19 TraesCS5D01G440200 chr6B 97.656 512 9 2 2216 2726 394452698 394453207 0.000000e+00 876.0
20 TraesCS5D01G440200 chr6B 86.286 175 17 5 173 343 112883212 112883041 1.670000e-42 183.0
21 TraesCS5D01G440200 chr7B 97.461 512 10 2 2216 2726 742961622 742961113 0.000000e+00 870.0
22 TraesCS5D01G440200 chr7A 97.461 512 10 2 2216 2726 120862079 120861570 0.000000e+00 870.0
23 TraesCS5D01G440200 chr2B 97.461 512 10 2 2216 2726 328777713 328778222 0.000000e+00 870.0
24 TraesCS5D01G440200 chr2B 94.444 36 2 0 127 162 753810809 753810844 3.790000e-04 56.5
25 TraesCS5D01G440200 chr2B 100.000 28 0 0 127 154 753782952 753782925 5.000000e-03 52.8
26 TraesCS5D01G440200 chr6A 86.047 172 22 2 168 337 408051091 408050920 1.670000e-42 183.0
27 TraesCS5D01G440200 chr6A 90.435 115 10 1 572 685 258130368 258130482 1.690000e-32 150.0
28 TraesCS5D01G440200 chr3D 85.465 172 23 2 173 343 128214171 128214001 7.760000e-41 178.0
29 TraesCS5D01G440200 chr3D 90.435 115 9 2 572 685 579384953 579385066 1.690000e-32 150.0
30 TraesCS5D01G440200 chr4A 91.964 112 7 2 572 683 723714452 723714343 3.630000e-34 156.0
31 TraesCS5D01G440200 chr1A 90.678 118 10 1 569 685 209335002 209335119 3.630000e-34 156.0
32 TraesCS5D01G440200 chr1A 76.271 118 21 5 44 156 592923214 592923329 3.790000e-04 56.5
33 TraesCS5D01G440200 chr3B 88.525 122 12 2 566 685 534863823 534863944 2.190000e-31 147.0
34 TraesCS5D01G440200 chr2A 87.903 124 13 2 563 685 12944127 12944249 7.870000e-31 145.0
35 TraesCS5D01G440200 chr2A 88.430 121 13 1 566 685 221734738 221734618 7.870000e-31 145.0


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 TraesCS5D01G440200 chr5D 493461322 493464047 2725 False 5035 5035 100.0000 1 2726 1 chr5D.!!$F2 2725
1 TraesCS5D01G440200 chr5B 609235589 609237881 2292 False 1465 2750 94.8380 1 2178 2 chr5B.!!$F2 2177
2 TraesCS5D01G440200 chr5A 616620469 616622427 1958 False 1497 1834 94.9085 1 1935 2 chr5A.!!$F4 1934
3 TraesCS5D01G440200 chrUn 206777715 206778224 509 False 887 887 98.0470 2216 2726 1 chrUn.!!$F1 510
4 TraesCS5D01G440200 chr4D 123314518 123315027 509 False 887 887 98.0470 2216 2726 1 chr4D.!!$F2 510
5 TraesCS5D01G440200 chr4D 123271129 123271638 509 False 876 876 97.6560 2216 2726 1 chr4D.!!$F1 510
6 TraesCS5D01G440200 chr3A 633127074 633127583 509 False 887 887 98.0470 2216 2726 1 chr3A.!!$F1 510
7 TraesCS5D01G440200 chr4B 209287505 209288014 509 False 881 881 97.8520 2216 2726 1 chr4B.!!$F1 510
8 TraesCS5D01G440200 chr6B 394452698 394453207 509 False 876 876 97.6560 2216 2726 1 chr6B.!!$F1 510
9 TraesCS5D01G440200 chr7B 742961113 742961622 509 True 870 870 97.4610 2216 2726 1 chr7B.!!$R1 510
10 TraesCS5D01G440200 chr7A 120861570 120862079 509 True 870 870 97.4610 2216 2726 1 chr7A.!!$R1 510
11 TraesCS5D01G440200 chr2B 328777713 328778222 509 False 870 870 97.4610 2216 2726 1 chr2B.!!$F1 510

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
124 125 1.739562 CAGAGCCCGAGTGCTTCAC 60.74 63.158 0.0 0.0 42.95 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2310 0.24912 ATCGATGCCAAACACCTCGA 59.751 50.0 0.0 0.0 42.3 4.04 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
72 73 6.479331 GGCAACTTTATTTTTCGGGTTTGTAA 59.521 34.615 0.00 0.00 0.00 2.41
124 125 1.739562 CAGAGCCCGAGTGCTTCAC 60.740 63.158 0.00 0.00 42.95 3.18
431 436 6.113411 GCAAACTTCCTATGGCTTAGACTTA 58.887 40.000 8.87 0.00 0.00 2.24
432 437 6.598064 GCAAACTTCCTATGGCTTAGACTTAA 59.402 38.462 8.87 0.00 0.00 1.85
473 478 6.948309 GCATAGGAAAGGGTGGACAATATATT 59.052 38.462 0.00 0.00 0.00 1.28
474 479 8.107095 GCATAGGAAAGGGTGGACAATATATTA 58.893 37.037 0.00 0.00 0.00 0.98
475 480 9.672673 CATAGGAAAGGGTGGACAATATATTAG 57.327 37.037 0.00 0.00 0.00 1.73
476 481 7.091533 AGGAAAGGGTGGACAATATATTAGG 57.908 40.000 0.00 0.00 0.00 2.69
477 482 6.855061 AGGAAAGGGTGGACAATATATTAGGA 59.145 38.462 0.00 0.00 0.00 2.94
478 483 7.017651 AGGAAAGGGTGGACAATATATTAGGAG 59.982 40.741 0.00 0.00 0.00 3.69
594 599 6.180472 TGGGAAATTTTTGTTTTTGCCACTA 58.820 32.000 4.76 0.00 44.99 2.74
612 617 7.814642 TGCCACTATAATTTTTGCCAATTTTG 58.185 30.769 0.00 0.00 0.00 2.44
1170 1234 1.336125 CCCGGAGACTGGTACGTAATC 59.664 57.143 0.73 0.00 0.00 1.75
1186 1250 3.550233 CGTAATCCACCACGATCGAGATT 60.550 47.826 24.34 20.29 40.56 2.40
1198 1262 6.642540 CCACGATCGAGATTAATCAATTCTCA 59.357 38.462 24.34 0.00 0.00 3.27
1210 1274 0.741221 AATTCTCACGCTCCTTCGCC 60.741 55.000 0.00 0.00 0.00 5.54
1269 1333 2.034558 CCTCCATGCTTTTGTGTTTCGT 59.965 45.455 0.00 0.00 0.00 3.85
1303 1367 2.611800 ATGAGGTGAGGGCCAGCA 60.612 61.111 6.18 0.00 45.30 4.41
1431 1495 2.708865 CCGACGATGTACGCCGTA 59.291 61.111 11.48 0.00 45.47 4.02
1548 1612 1.599047 CATGACGGTGAAGGAGGCT 59.401 57.895 0.00 0.00 0.00 4.58
1560 1624 4.129737 GAGGCTGTGGCGCTCGTA 62.130 66.667 7.64 0.00 39.81 3.43
1712 1776 3.118738 AGTCAGGGAACGCCTATTGTAAG 60.119 47.826 0.00 0.00 0.00 2.34
1714 1778 1.557832 AGGGAACGCCTATTGTAAGCA 59.442 47.619 0.00 0.00 0.00 3.91
1736 1800 8.644318 AGCACGAATAATTAAAGTAGTGGTAG 57.356 34.615 10.60 0.00 37.32 3.18
1737 1801 8.255905 AGCACGAATAATTAAAGTAGTGGTAGT 58.744 33.333 10.60 0.00 37.32 2.73
1738 1802 9.520204 GCACGAATAATTAAAGTAGTGGTAGTA 57.480 33.333 0.00 0.00 0.00 1.82
1748 1812 9.874205 TTAAAGTAGTGGTAGTATATTTTGCGT 57.126 29.630 0.00 0.00 0.00 5.24
1853 1919 0.179210 CGCCACGTTTATCAAACCCG 60.179 55.000 0.00 0.00 38.14 5.28
1918 1984 1.757699 AGGAATCACTAGCTCCGGTTC 59.242 52.381 0.00 0.00 34.22 3.62
1948 2014 4.157120 GGTGCCCGTGCGGTCTAT 62.157 66.667 9.90 0.00 41.78 1.98
1949 2015 2.788640 GGTGCCCGTGCGGTCTATA 61.789 63.158 9.90 0.00 41.78 1.31
1951 2017 2.355956 GCCCGTGCGGTCTATAGC 60.356 66.667 9.90 0.94 0.00 2.97
1957 2023 1.454295 TGCGGTCTATAGCGGTGGA 60.454 57.895 0.00 0.00 46.48 4.02
1958 2024 1.038681 TGCGGTCTATAGCGGTGGAA 61.039 55.000 0.00 0.00 46.48 3.53
1959 2025 0.103572 GCGGTCTATAGCGGTGGAAA 59.896 55.000 0.00 0.00 46.48 3.13
1961 2027 2.805657 GCGGTCTATAGCGGTGGAAATT 60.806 50.000 0.00 0.00 46.48 1.82
1962 2028 2.800544 CGGTCTATAGCGGTGGAAATTG 59.199 50.000 0.00 0.00 42.79 2.32
1963 2029 3.740141 CGGTCTATAGCGGTGGAAATTGT 60.740 47.826 0.00 0.00 42.79 2.71
1964 2030 3.808174 GGTCTATAGCGGTGGAAATTGTC 59.192 47.826 0.00 0.00 0.00 3.18
1966 2032 4.508124 GTCTATAGCGGTGGAAATTGTCTG 59.492 45.833 0.00 0.00 0.00 3.51
1967 2033 2.851263 TAGCGGTGGAAATTGTCTGT 57.149 45.000 0.00 0.00 0.00 3.41
1968 2034 1.981256 AGCGGTGGAAATTGTCTGTT 58.019 45.000 0.00 0.00 0.00 3.16
1969 2035 1.608590 AGCGGTGGAAATTGTCTGTTG 59.391 47.619 0.00 0.00 0.00 3.33
1970 2036 1.335872 GCGGTGGAAATTGTCTGTTGG 60.336 52.381 0.00 0.00 0.00 3.77
1971 2037 1.335872 CGGTGGAAATTGTCTGTTGGC 60.336 52.381 0.00 0.00 0.00 4.52
1978 2208 2.038387 ATTGTCTGTTGGCCGATACC 57.962 50.000 0.00 0.00 0.00 2.73
1991 2221 0.389391 CGATACCTCTTGGCCGACAT 59.611 55.000 0.00 0.00 36.63 3.06
2005 2235 2.819115 CCGACATCATCCTCAAGTCTG 58.181 52.381 0.00 0.00 0.00 3.51
2011 2241 3.685139 TCATCCTCAAGTCTGGTTGTC 57.315 47.619 0.00 0.00 0.00 3.18
2012 2242 2.303022 TCATCCTCAAGTCTGGTTGTCC 59.697 50.000 0.00 0.00 0.00 4.02
2013 2243 1.801242 TCCTCAAGTCTGGTTGTCCA 58.199 50.000 0.00 0.00 42.05 4.02
2014 2244 1.416401 TCCTCAAGTCTGGTTGTCCAC 59.584 52.381 0.00 0.00 39.03 4.02
2022 2252 4.519610 GGTTGTCCACCTGCCAAT 57.480 55.556 0.00 0.00 43.29 3.16
2023 2253 2.267045 GGTTGTCCACCTGCCAATC 58.733 57.895 0.00 0.00 43.29 2.67
2024 2254 0.251341 GGTTGTCCACCTGCCAATCT 60.251 55.000 0.00 0.00 43.29 2.40
2025 2255 1.168714 GTTGTCCACCTGCCAATCTC 58.831 55.000 0.00 0.00 0.00 2.75
2026 2256 0.038166 TTGTCCACCTGCCAATCTCC 59.962 55.000 0.00 0.00 0.00 3.71
2027 2257 0.842030 TGTCCACCTGCCAATCTCCT 60.842 55.000 0.00 0.00 0.00 3.69
2028 2258 1.204146 GTCCACCTGCCAATCTCCTA 58.796 55.000 0.00 0.00 0.00 2.94
2029 2259 1.139853 GTCCACCTGCCAATCTCCTAG 59.860 57.143 0.00 0.00 0.00 3.02
2030 2260 0.471617 CCACCTGCCAATCTCCTAGG 59.528 60.000 0.82 0.82 34.70 3.02
2034 2264 2.505982 GCCAATCTCCTAGGCGCA 59.494 61.111 10.83 0.00 38.86 6.09
2035 2265 1.153168 GCCAATCTCCTAGGCGCAA 60.153 57.895 10.83 0.00 38.86 4.85
2036 2266 1.440145 GCCAATCTCCTAGGCGCAAC 61.440 60.000 10.83 0.00 38.86 4.17
2037 2267 1.154205 CCAATCTCCTAGGCGCAACG 61.154 60.000 10.83 0.00 0.00 4.10
2038 2268 1.144057 AATCTCCTAGGCGCAACGG 59.856 57.895 10.83 5.65 0.00 4.44
2039 2269 1.614241 AATCTCCTAGGCGCAACGGT 61.614 55.000 10.83 0.00 0.00 4.83
2040 2270 2.298158 ATCTCCTAGGCGCAACGGTG 62.298 60.000 10.83 0.00 0.00 4.94
2041 2271 4.077184 TCCTAGGCGCAACGGTGG 62.077 66.667 10.83 2.03 0.00 4.61
2042 2272 4.077184 CCTAGGCGCAACGGTGGA 62.077 66.667 10.83 0.00 0.00 4.02
2043 2273 2.509336 CTAGGCGCAACGGTGGAG 60.509 66.667 10.83 0.00 0.00 3.86
2044 2274 4.077184 TAGGCGCAACGGTGGAGG 62.077 66.667 10.83 0.00 0.00 4.30
2056 2286 4.704103 TGGAGGGCCAGCGAGTCT 62.704 66.667 6.18 0.00 39.92 3.24
2057 2287 2.442272 GGAGGGCCAGCGAGTCTA 60.442 66.667 6.18 0.00 0.00 2.59
2058 2288 2.494530 GGAGGGCCAGCGAGTCTAG 61.495 68.421 6.18 0.00 0.00 2.43
2059 2289 1.755008 GAGGGCCAGCGAGTCTAGT 60.755 63.158 6.18 0.00 0.00 2.57
2060 2290 1.730451 GAGGGCCAGCGAGTCTAGTC 61.730 65.000 6.18 0.00 0.00 2.59
2061 2291 1.755008 GGGCCAGCGAGTCTAGTCT 60.755 63.158 4.39 0.00 0.00 3.24
2062 2292 0.465824 GGGCCAGCGAGTCTAGTCTA 60.466 60.000 4.39 0.00 0.00 2.59
2063 2293 1.611519 GGCCAGCGAGTCTAGTCTAT 58.388 55.000 0.00 0.00 0.00 1.98
2064 2294 2.552591 GGGCCAGCGAGTCTAGTCTATA 60.553 54.545 4.39 0.00 0.00 1.31
2065 2295 2.745281 GGCCAGCGAGTCTAGTCTATAG 59.255 54.545 0.00 0.00 0.00 1.31
2066 2296 3.404899 GCCAGCGAGTCTAGTCTATAGT 58.595 50.000 0.00 0.00 0.00 2.12
2067 2297 3.816523 GCCAGCGAGTCTAGTCTATAGTT 59.183 47.826 0.00 0.00 0.00 2.24
2068 2298 4.276431 GCCAGCGAGTCTAGTCTATAGTTT 59.724 45.833 0.00 0.00 0.00 2.66
2069 2299 5.221087 GCCAGCGAGTCTAGTCTATAGTTTT 60.221 44.000 0.00 0.00 0.00 2.43
2070 2300 6.202937 CCAGCGAGTCTAGTCTATAGTTTTG 58.797 44.000 0.00 0.00 0.00 2.44
2071 2301 6.202937 CAGCGAGTCTAGTCTATAGTTTTGG 58.797 44.000 0.00 0.00 0.00 3.28
2080 2310 3.676646 GTCTATAGTTTTGGTCGCGTGTT 59.323 43.478 5.77 0.00 0.00 3.32
2099 2329 0.249120 TCGAGGTGTTTGGCATCGAT 59.751 50.000 4.65 0.00 34.76 3.59
2181 2411 4.675404 GTGGAGGAGTCACGGTTG 57.325 61.111 0.00 0.00 0.00 3.77
2182 2412 2.046938 GTGGAGGAGTCACGGTTGA 58.953 57.895 0.00 0.00 0.00 3.18
2183 2413 0.391597 GTGGAGGAGTCACGGTTGAA 59.608 55.000 0.00 0.00 31.90 2.69
2184 2414 0.679505 TGGAGGAGTCACGGTTGAAG 59.320 55.000 0.00 0.00 31.90 3.02
2185 2415 0.670854 GGAGGAGTCACGGTTGAAGC 60.671 60.000 0.00 0.00 31.90 3.86
2186 2416 0.033504 GAGGAGTCACGGTTGAAGCA 59.966 55.000 0.00 0.00 31.90 3.91
2187 2417 0.468226 AGGAGTCACGGTTGAAGCAA 59.532 50.000 0.00 0.00 31.90 3.91
2188 2418 1.134220 AGGAGTCACGGTTGAAGCAAA 60.134 47.619 0.00 0.00 31.90 3.68
2189 2419 1.002792 GGAGTCACGGTTGAAGCAAAC 60.003 52.381 0.00 0.00 31.90 2.93
2190 2420 1.002792 GAGTCACGGTTGAAGCAAACC 60.003 52.381 6.03 6.03 45.24 3.27
2197 2427 2.492019 GTTGAAGCAAACCACAGGTC 57.508 50.000 0.00 0.00 33.12 3.85
2198 2428 1.748493 GTTGAAGCAAACCACAGGTCA 59.252 47.619 0.00 0.00 33.12 4.02
2199 2429 2.136298 TGAAGCAAACCACAGGTCAA 57.864 45.000 0.00 0.00 33.12 3.18
2200 2430 2.665165 TGAAGCAAACCACAGGTCAAT 58.335 42.857 0.00 0.00 33.12 2.57
2201 2431 3.030291 TGAAGCAAACCACAGGTCAATT 58.970 40.909 0.00 0.00 33.12 2.32
2202 2432 3.450457 TGAAGCAAACCACAGGTCAATTT 59.550 39.130 0.00 0.00 33.12 1.82
2203 2433 4.081198 TGAAGCAAACCACAGGTCAATTTT 60.081 37.500 0.00 0.00 33.12 1.82
2204 2434 4.486125 AGCAAACCACAGGTCAATTTTT 57.514 36.364 0.00 0.00 33.12 1.94
2581 2812 1.334960 CGAGTGCACACAAATCAACCC 60.335 52.381 21.04 0.00 0.00 4.11
2582 2813 1.956477 GAGTGCACACAAATCAACCCT 59.044 47.619 21.04 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 8.267620 TCATTTTGCTCCGTATATAATCCATG 57.732 34.615 0.00 0.00 0.00 3.66
473 478 5.818678 TCTTGCAAAAGAACCTACTCCTA 57.181 39.130 0.00 0.00 0.00 2.94
474 479 4.706842 TCTTGCAAAAGAACCTACTCCT 57.293 40.909 0.00 0.00 0.00 3.69
475 480 6.879458 TCTTATCTTGCAAAAGAACCTACTCC 59.121 38.462 9.16 0.00 31.77 3.85
476 481 7.387948 TGTCTTATCTTGCAAAAGAACCTACTC 59.612 37.037 12.47 1.71 31.41 2.59
477 482 7.224297 TGTCTTATCTTGCAAAAGAACCTACT 58.776 34.615 12.47 0.00 31.41 2.57
478 483 7.435068 TGTCTTATCTTGCAAAAGAACCTAC 57.565 36.000 12.47 3.35 31.41 3.18
598 603 6.317140 TGTGACATAAGCAAAATTGGCAAAAA 59.683 30.769 3.01 0.00 0.00 1.94
1170 1234 3.977427 TGATTAATCTCGATCGTGGTGG 58.023 45.455 15.94 2.14 0.00 4.61
1186 1250 4.112634 CGAAGGAGCGTGAGAATTGATTA 58.887 43.478 0.00 0.00 0.00 1.75
1198 1262 2.992114 ACTCAGGCGAAGGAGCGT 60.992 61.111 0.00 0.00 38.18 5.07
1210 1274 4.620609 CACAAAGACTGATCGAAGACTCAG 59.379 45.833 11.33 11.33 42.51 3.35
1303 1367 1.446792 CGCTGTGGATCTTGCTCGT 60.447 57.895 0.00 0.00 0.00 4.18
1501 1565 0.535335 TAGTGGTTCTCCATCACCGC 59.465 55.000 0.00 0.00 46.20 5.68
1548 1612 2.566529 CTGTCTACGAGCGCCACA 59.433 61.111 2.29 0.00 0.00 4.17
1560 1624 0.617413 CCTCCTTGATGCACCTGTCT 59.383 55.000 0.00 0.00 0.00 3.41
1712 1776 8.416485 ACTACCACTACTTTAATTATTCGTGC 57.584 34.615 0.00 0.00 0.00 5.34
1780 1844 9.965824 CATGTATATGAACCCCACTTAAATTTC 57.034 33.333 0.00 0.00 36.36 2.17
1839 1905 1.396996 CCAGAGCGGGTTTGATAAACG 59.603 52.381 0.00 0.00 42.29 3.60
1853 1919 1.067354 CCAAAACAATGCCTCCAGAGC 60.067 52.381 0.00 0.00 0.00 4.09
1898 1964 1.757699 GAACCGGAGCTAGTGATTCCT 59.242 52.381 9.46 0.00 0.00 3.36
1899 1965 1.536284 CGAACCGGAGCTAGTGATTCC 60.536 57.143 9.46 0.00 0.00 3.01
1900 1966 1.134560 ACGAACCGGAGCTAGTGATTC 59.865 52.381 9.46 0.00 0.00 2.52
1901 1967 1.134560 GACGAACCGGAGCTAGTGATT 59.865 52.381 9.46 0.00 0.00 2.57
1902 1968 0.739561 GACGAACCGGAGCTAGTGAT 59.260 55.000 9.46 0.00 0.00 3.06
1903 1969 1.642037 CGACGAACCGGAGCTAGTGA 61.642 60.000 9.46 0.00 0.00 3.41
1935 2001 2.050351 CGCTATAGACCGCACGGG 60.050 66.667 14.51 0.00 43.62 5.28
1937 2003 1.657487 CACCGCTATAGACCGCACG 60.657 63.158 3.21 0.00 0.00 5.34
1939 2005 1.038681 TTCCACCGCTATAGACCGCA 61.039 55.000 3.21 0.00 0.00 5.69
1941 2007 2.800544 CAATTTCCACCGCTATAGACCG 59.199 50.000 3.21 0.00 0.00 4.79
1942 2008 3.805207 ACAATTTCCACCGCTATAGACC 58.195 45.455 3.21 0.00 0.00 3.85
1944 2010 4.161565 ACAGACAATTTCCACCGCTATAGA 59.838 41.667 3.21 0.00 0.00 1.98
1945 2011 4.442706 ACAGACAATTTCCACCGCTATAG 58.557 43.478 0.00 0.00 0.00 1.31
1946 2012 4.481368 ACAGACAATTTCCACCGCTATA 57.519 40.909 0.00 0.00 0.00 1.31
1947 2013 3.350219 ACAGACAATTTCCACCGCTAT 57.650 42.857 0.00 0.00 0.00 2.97
1948 2014 2.811431 CAACAGACAATTTCCACCGCTA 59.189 45.455 0.00 0.00 0.00 4.26
1949 2015 1.608590 CAACAGACAATTTCCACCGCT 59.391 47.619 0.00 0.00 0.00 5.52
1951 2017 1.335872 GCCAACAGACAATTTCCACCG 60.336 52.381 0.00 0.00 0.00 4.94
1952 2018 1.000843 GGCCAACAGACAATTTCCACC 59.999 52.381 0.00 0.00 0.00 4.61
1957 2023 2.752903 GGTATCGGCCAACAGACAATTT 59.247 45.455 2.24 0.00 0.00 1.82
1958 2024 2.026262 AGGTATCGGCCAACAGACAATT 60.026 45.455 2.24 0.00 0.00 2.32
1959 2025 1.559682 AGGTATCGGCCAACAGACAAT 59.440 47.619 2.24 0.00 0.00 2.71
1961 2027 0.535335 GAGGTATCGGCCAACAGACA 59.465 55.000 2.24 0.00 0.00 3.41
1962 2028 0.824759 AGAGGTATCGGCCAACAGAC 59.175 55.000 2.24 0.00 0.00 3.51
1963 2029 1.207089 CAAGAGGTATCGGCCAACAGA 59.793 52.381 2.24 0.00 0.00 3.41
1964 2030 1.656652 CAAGAGGTATCGGCCAACAG 58.343 55.000 2.24 0.00 0.00 3.16
1966 2032 1.095807 GCCAAGAGGTATCGGCCAAC 61.096 60.000 2.24 0.00 38.67 3.77
1967 2033 1.223487 GCCAAGAGGTATCGGCCAA 59.777 57.895 2.24 0.00 38.67 4.52
1968 2034 2.908015 GCCAAGAGGTATCGGCCA 59.092 61.111 2.24 0.00 38.67 5.36
1970 2036 2.280186 CGGCCAAGAGGTATCGGC 60.280 66.667 2.24 0.00 44.10 5.54
1971 2037 1.067582 GTCGGCCAAGAGGTATCGG 59.932 63.158 2.24 0.00 37.19 4.18
1978 2208 0.467384 AGGATGATGTCGGCCAAGAG 59.533 55.000 2.24 0.00 0.00 2.85
1991 2221 2.303022 GGACAACCAGACTTGAGGATGA 59.697 50.000 0.00 0.00 35.97 2.92
2011 2241 0.471617 CCTAGGAGATTGGCAGGTGG 59.528 60.000 1.05 0.00 0.00 4.61
2017 2247 1.153168 TTGCGCCTAGGAGATTGGC 60.153 57.895 17.75 7.47 45.33 4.52
2018 2248 1.154205 CGTTGCGCCTAGGAGATTGG 61.154 60.000 17.75 0.00 0.00 3.16
2019 2249 1.154205 CCGTTGCGCCTAGGAGATTG 61.154 60.000 17.75 2.27 0.00 2.67
2020 2250 1.144057 CCGTTGCGCCTAGGAGATT 59.856 57.895 17.75 0.00 0.00 2.40
2021 2251 2.058595 ACCGTTGCGCCTAGGAGAT 61.059 57.895 17.75 0.00 0.00 2.75
2022 2252 2.678934 ACCGTTGCGCCTAGGAGA 60.679 61.111 17.75 0.00 0.00 3.71
2023 2253 2.509336 CACCGTTGCGCCTAGGAG 60.509 66.667 14.75 11.38 0.00 3.69
2024 2254 4.077184 CCACCGTTGCGCCTAGGA 62.077 66.667 14.75 0.00 0.00 2.94
2025 2255 4.077184 TCCACCGTTGCGCCTAGG 62.077 66.667 4.18 3.67 0.00 3.02
2026 2256 2.509336 CTCCACCGTTGCGCCTAG 60.509 66.667 4.18 0.00 0.00 3.02
2027 2257 4.077184 CCTCCACCGTTGCGCCTA 62.077 66.667 4.18 0.00 0.00 3.93
2038 2268 4.459089 GACTCGCTGGCCCTCCAC 62.459 72.222 0.00 0.00 37.47 4.02
2039 2269 3.296842 TAGACTCGCTGGCCCTCCA 62.297 63.158 0.00 0.00 40.85 3.86
2040 2270 2.442272 TAGACTCGCTGGCCCTCC 60.442 66.667 0.00 0.00 0.00 4.30
2041 2271 1.730451 GACTAGACTCGCTGGCCCTC 61.730 65.000 0.00 0.00 0.00 4.30
2042 2272 1.755008 GACTAGACTCGCTGGCCCT 60.755 63.158 0.00 0.00 0.00 5.19
2043 2273 0.465824 TAGACTAGACTCGCTGGCCC 60.466 60.000 0.00 0.00 0.00 5.80
2044 2274 1.611519 ATAGACTAGACTCGCTGGCC 58.388 55.000 0.00 0.00 0.00 5.36
2045 2275 3.404899 ACTATAGACTAGACTCGCTGGC 58.595 50.000 6.78 0.00 0.00 4.85
2046 2276 6.202937 CAAAACTATAGACTAGACTCGCTGG 58.797 44.000 6.78 0.00 0.00 4.85
2047 2277 6.183360 ACCAAAACTATAGACTAGACTCGCTG 60.183 42.308 6.78 0.00 0.00 5.18
2048 2278 5.887035 ACCAAAACTATAGACTAGACTCGCT 59.113 40.000 6.78 0.00 0.00 4.93
2049 2279 6.134040 ACCAAAACTATAGACTAGACTCGC 57.866 41.667 6.78 0.00 0.00 5.03
2050 2280 6.420588 CGACCAAAACTATAGACTAGACTCG 58.579 44.000 6.78 1.02 0.00 4.18
2051 2281 6.200808 GCGACCAAAACTATAGACTAGACTC 58.799 44.000 6.78 0.00 0.00 3.36
2052 2282 5.220815 CGCGACCAAAACTATAGACTAGACT 60.221 44.000 6.78 0.00 0.00 3.24
2053 2283 4.968788 CGCGACCAAAACTATAGACTAGAC 59.031 45.833 6.78 0.00 0.00 2.59
2054 2284 4.637534 ACGCGACCAAAACTATAGACTAGA 59.362 41.667 15.93 0.00 0.00 2.43
2055 2285 4.733887 CACGCGACCAAAACTATAGACTAG 59.266 45.833 15.93 0.00 0.00 2.57
2056 2286 4.156556 ACACGCGACCAAAACTATAGACTA 59.843 41.667 15.93 0.00 0.00 2.59
2057 2287 3.057033 ACACGCGACCAAAACTATAGACT 60.057 43.478 15.93 0.00 0.00 3.24
2058 2288 3.248266 ACACGCGACCAAAACTATAGAC 58.752 45.455 15.93 0.00 0.00 2.59
2059 2289 3.581024 ACACGCGACCAAAACTATAGA 57.419 42.857 15.93 0.00 0.00 1.98
2060 2290 3.241552 CGAACACGCGACCAAAACTATAG 60.242 47.826 15.93 0.00 0.00 1.31
2061 2291 2.662637 CGAACACGCGACCAAAACTATA 59.337 45.455 15.93 0.00 0.00 1.31
2062 2292 1.458064 CGAACACGCGACCAAAACTAT 59.542 47.619 15.93 0.00 0.00 2.12
2063 2293 0.854062 CGAACACGCGACCAAAACTA 59.146 50.000 15.93 0.00 0.00 2.24
2064 2294 0.806884 TCGAACACGCGACCAAAACT 60.807 50.000 15.93 0.00 35.01 2.66
2065 2295 0.382636 CTCGAACACGCGACCAAAAC 60.383 55.000 15.93 0.00 36.17 2.43
2066 2296 1.492319 CCTCGAACACGCGACCAAAA 61.492 55.000 15.93 0.00 36.17 2.44
2067 2297 1.952133 CCTCGAACACGCGACCAAA 60.952 57.895 15.93 0.00 36.17 3.28
2068 2298 2.355363 CCTCGAACACGCGACCAA 60.355 61.111 15.93 0.00 36.17 3.67
2069 2299 3.598715 ACCTCGAACACGCGACCA 61.599 61.111 15.93 0.00 36.17 4.02
2070 2300 3.103911 CACCTCGAACACGCGACC 61.104 66.667 15.93 0.00 36.17 4.79
2071 2301 1.485032 AAACACCTCGAACACGCGAC 61.485 55.000 15.93 0.00 36.17 5.19
2080 2310 0.249120 ATCGATGCCAAACACCTCGA 59.751 50.000 0.00 0.00 42.30 4.04
2170 2400 1.002792 GGTTTGCTTCAACCGTGACTC 60.003 52.381 0.00 0.00 31.90 3.36
2178 2408 1.748493 TGACCTGTGGTTTGCTTCAAC 59.252 47.619 0.00 0.00 35.25 3.18
2179 2409 2.136298 TGACCTGTGGTTTGCTTCAA 57.864 45.000 0.00 0.00 35.25 2.69
2180 2410 2.136298 TTGACCTGTGGTTTGCTTCA 57.864 45.000 0.00 0.00 35.25 3.02
2181 2411 3.733443 AATTGACCTGTGGTTTGCTTC 57.267 42.857 0.00 0.00 35.25 3.86
2182 2412 4.486125 AAAATTGACCTGTGGTTTGCTT 57.514 36.364 0.00 0.00 35.25 3.91
2183 2413 4.486125 AAAAATTGACCTGTGGTTTGCT 57.514 36.364 0.00 0.00 35.25 3.91
2202 2432 4.836825 TCAACTCCAAATGTTGCCAAAAA 58.163 34.783 0.00 0.00 43.00 1.94
2203 2433 4.161189 TCTCAACTCCAAATGTTGCCAAAA 59.839 37.500 0.00 0.00 43.00 2.44
2204 2434 3.703556 TCTCAACTCCAAATGTTGCCAAA 59.296 39.130 0.00 0.00 43.00 3.28
2205 2435 3.068024 GTCTCAACTCCAAATGTTGCCAA 59.932 43.478 0.00 0.00 43.00 4.52
2206 2436 2.622942 GTCTCAACTCCAAATGTTGCCA 59.377 45.455 0.00 0.00 43.00 4.92
2207 2437 2.887152 AGTCTCAACTCCAAATGTTGCC 59.113 45.455 0.00 0.00 43.00 4.52
2208 2438 4.574599 AAGTCTCAACTCCAAATGTTGC 57.425 40.909 0.00 0.00 43.00 4.17
2209 2439 6.382869 AGAAAGTCTCAACTCCAAATGTTG 57.617 37.500 0.00 0.00 44.21 3.33
2210 2440 8.697507 ATAAGAAAGTCTCAACTCCAAATGTT 57.302 30.769 0.00 0.00 33.48 2.71
2211 2441 7.391833 GGATAAGAAAGTCTCAACTCCAAATGT 59.608 37.037 0.00 0.00 33.48 2.71
2212 2442 7.148171 GGGATAAGAAAGTCTCAACTCCAAATG 60.148 40.741 0.00 0.00 33.48 2.32
2213 2443 6.887002 GGGATAAGAAAGTCTCAACTCCAAAT 59.113 38.462 0.00 0.00 33.48 2.32
2214 2444 6.044404 AGGGATAAGAAAGTCTCAACTCCAAA 59.956 38.462 0.00 0.00 33.48 3.28
2349 2579 8.860517 TGGAGAAGCCACCATAGAATATATAT 57.139 34.615 0.00 0.00 43.33 0.86
2581 2812 7.768120 ACTTTTGACATAGCAGAATCCTTCTAG 59.232 37.037 0.00 0.00 38.11 2.43
2582 2813 7.550551 CACTTTTGACATAGCAGAATCCTTCTA 59.449 37.037 0.00 0.00 38.11 2.10
2618 2849 4.717991 CATCTTGGCGTTAAACAATTCGA 58.282 39.130 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.