Multiple sequence alignment - TraesCS2B01G327100

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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 TraesCS2B01G327100 chr2B 100.000 2474 0 0 1 2474 468456057 468453584 0.000000e+00 4569.0
1 TraesCS2B01G327100 chr2B 93.157 833 55 1 15 845 673672564 673673396 0.000000e+00 1221.0
2 TraesCS2B01G327100 chr2B 83.951 162 24 2 2085 2245 677870855 677870695 1.180000e-33 154.0
3 TraesCS2B01G327100 chr2D 91.911 989 58 10 880 1858 395320736 395319760 0.000000e+00 1363.0
4 TraesCS2B01G327100 chr2D 84.393 173 26 1 2073 2245 569088864 569089035 4.230000e-38 169.0
5 TraesCS2B01G327100 chr4B 93.868 848 51 1 1 847 406672520 406671673 0.000000e+00 1277.0
6 TraesCS2B01G327100 chr4B 92.773 844 59 2 1 844 44676762 44677603 0.000000e+00 1219.0
7 TraesCS2B01G327100 chr3B 93.868 848 50 2 1 848 20412060 20412905 0.000000e+00 1277.0
8 TraesCS2B01G327100 chr3B 74.550 444 92 19 1645 2077 415662786 415662353 9.090000e-40 174.0
9 TraesCS2B01G327100 chr3B 83.616 177 23 6 2076 2250 112836709 112836537 7.080000e-36 161.0
10 TraesCS2B01G327100 chr6B 93.560 854 46 5 1 849 413958859 413959708 0.000000e+00 1264.0
11 TraesCS2B01G327100 chr6B 84.302 172 24 3 2076 2245 200305224 200305054 5.470000e-37 165.0
12 TraesCS2B01G327100 chr7B 92.815 849 54 4 1 844 678970061 678970907 0.000000e+00 1223.0
13 TraesCS2B01G327100 chr7B 82.286 175 28 3 2073 2245 14218148 14218321 5.510000e-32 148.0
14 TraesCS2B01G327100 chr5B 92.891 844 57 3 4 846 29385050 29384209 0.000000e+00 1223.0
15 TraesCS2B01G327100 chr7A 92.580 849 61 2 1 848 24471477 24472324 0.000000e+00 1218.0
16 TraesCS2B01G327100 chr7A 85.276 163 22 1 2083 2243 588751316 588751478 1.520000e-37 167.0
17 TraesCS2B01G327100 chr1D 92.663 845 60 2 1 844 492466766 492465923 0.000000e+00 1216.0
18 TraesCS2B01G327100 chr1D 76.201 437 93 9 1645 2077 452590018 452589589 1.150000e-53 220.0
19 TraesCS2B01G327100 chr2A 97.458 708 17 1 844 1550 533546753 533546046 0.000000e+00 1206.0
20 TraesCS2B01G327100 chr2A 85.982 906 91 18 1576 2474 533546057 533545181 0.000000e+00 937.0
21 TraesCS2B01G327100 chr2A 82.286 175 28 3 2073 2245 738969204 738969377 5.510000e-32 148.0
22 TraesCS2B01G327100 chr7D 77.117 437 90 8 1645 2077 403744530 403744100 6.830000e-61 244.0
23 TraesCS2B01G327100 chr6D 83.523 176 24 5 2073 2245 109274308 109274135 2.550000e-35 159.0
24 TraesCS2B01G327100 chr1B 92.308 39 0 3 2413 2451 542689367 542689402 4.000000e-03 52.8


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 TraesCS2B01G327100 chr2B 468453584 468456057 2473 True 4569.0 4569 100.000 1 2474 1 chr2B.!!$R1 2473
1 TraesCS2B01G327100 chr2B 673672564 673673396 832 False 1221.0 1221 93.157 15 845 1 chr2B.!!$F1 830
2 TraesCS2B01G327100 chr2D 395319760 395320736 976 True 1363.0 1363 91.911 880 1858 1 chr2D.!!$R1 978
3 TraesCS2B01G327100 chr4B 406671673 406672520 847 True 1277.0 1277 93.868 1 847 1 chr4B.!!$R1 846
4 TraesCS2B01G327100 chr4B 44676762 44677603 841 False 1219.0 1219 92.773 1 844 1 chr4B.!!$F1 843
5 TraesCS2B01G327100 chr3B 20412060 20412905 845 False 1277.0 1277 93.868 1 848 1 chr3B.!!$F1 847
6 TraesCS2B01G327100 chr6B 413958859 413959708 849 False 1264.0 1264 93.560 1 849 1 chr6B.!!$F1 848
7 TraesCS2B01G327100 chr7B 678970061 678970907 846 False 1223.0 1223 92.815 1 844 1 chr7B.!!$F2 843
8 TraesCS2B01G327100 chr5B 29384209 29385050 841 True 1223.0 1223 92.891 4 846 1 chr5B.!!$R1 842
9 TraesCS2B01G327100 chr7A 24471477 24472324 847 False 1218.0 1218 92.580 1 848 1 chr7A.!!$F1 847
10 TraesCS2B01G327100 chr1D 492465923 492466766 843 True 1216.0 1216 92.663 1 844 1 chr1D.!!$R2 843
11 TraesCS2B01G327100 chr2A 533545181 533546753 1572 True 1071.5 1206 91.720 844 2474 2 chr2A.!!$R1 1630

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
172 173 0.690762 GGGTGGAACTACTTCTGCCA 59.309 55.0 0.0 0.0 36.74 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1882 0.179032 TCACCACAACAGCCACGAAT 60.179 50.0 0.0 0.0 0.0 3.34 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
172 173 0.690762 GGGTGGAACTACTTCTGCCA 59.309 55.000 0.00 0.00 36.74 4.92
180 181 2.172483 CTACTTCTGCCACCGCCACT 62.172 60.000 0.00 0.00 0.00 4.00
257 258 3.418047 TCAGATCTACAACCACGACTCA 58.582 45.455 0.00 0.00 0.00 3.41
276 277 2.170397 TCATCGGTGATGTGCAGGTATT 59.830 45.455 0.00 0.00 40.55 1.89
285 286 1.875262 TGCAGGTATTGTTGCAGCG 59.125 52.632 0.00 0.00 44.72 5.18
330 331 4.036498 TCGAGCAGGCTATGTAGTTAAGTC 59.964 45.833 0.00 0.00 0.00 3.01
350 351 4.900054 AGTCAAGTAAGGTGTTAGTGGAGT 59.100 41.667 0.00 0.00 0.00 3.85
501 506 4.580167 AGTAGTTTGCTGTCATTTGCTTGA 59.420 37.500 0.00 0.00 0.00 3.02
551 556 5.818857 ACATTGCTTGCTTTGTTTGATCTTT 59.181 32.000 0.00 0.00 0.00 2.52
557 562 6.036408 GCTTGCTTTGTTTGATCTTTCTGTTT 59.964 34.615 0.00 0.00 0.00 2.83
672 677 3.151554 TGAAGTTTGCATCTGCTCACAT 58.848 40.909 3.53 0.00 42.66 3.21
715 722 0.850784 AAACAGCAGGGGGTAAGTGT 59.149 50.000 0.00 0.00 0.00 3.55
849 856 3.380637 TGCAACTAAACACGCCCTAAAAA 59.619 39.130 0.00 0.00 0.00 1.94
900 907 1.187567 CCTTCCCAAACCAAGCCCAG 61.188 60.000 0.00 0.00 0.00 4.45
905 912 0.967380 CCAAACCAAGCCCAGCTAGG 60.967 60.000 0.00 0.00 38.25 3.02
920 927 1.962402 GCTAGGACAGAGCTCCCTTGA 60.962 57.143 18.31 2.57 36.96 3.02
948 955 1.065491 CACTTTCCCATCCATCCGTCA 60.065 52.381 0.00 0.00 0.00 4.35
1083 1092 0.704664 TCCTCACTAGCTCCACCTCA 59.295 55.000 0.00 0.00 0.00 3.86
1139 1148 3.155167 GGATCGGTTCGGCCTCCT 61.155 66.667 0.00 0.00 34.25 3.69
1504 1516 4.703897 ACTAGAGCAGTTAGTTTGTTGCA 58.296 39.130 0.00 0.00 38.97 4.08
1562 1578 2.398588 TGACGCTGGAGGAAGGAATAT 58.601 47.619 0.00 0.00 0.00 1.28
1563 1579 2.365617 TGACGCTGGAGGAAGGAATATC 59.634 50.000 0.00 0.00 0.00 1.63
1581 1597 8.019669 AGGAATATCGAATACGTGTGTGTATAC 58.980 37.037 0.00 0.00 40.69 1.47
1615 1631 8.728337 ACATCCACACATTATATGAGCATATC 57.272 34.615 6.27 0.00 35.71 1.63
1671 1687 0.106569 TTCATGGCTGGCAGGTATGG 60.107 55.000 17.64 0.00 0.00 2.74
1686 1702 1.066430 GTATGGTTTGCTCCTCCGACA 60.066 52.381 0.00 0.00 0.00 4.35
1744 1760 1.003355 CGTGTCTGGGATGTTGCCT 60.003 57.895 0.00 0.00 0.00 4.75
1749 1765 0.482446 TCTGGGATGTTGCCTTGGTT 59.518 50.000 0.00 0.00 0.00 3.67
1780 1797 9.536558 TCGTTTAACGTAATGATTTCATCTTTG 57.463 29.630 17.16 0.00 43.14 2.77
1792 1809 3.272574 TCATCTTTGGTGAGCCATCTC 57.727 47.619 0.00 0.00 45.56 2.75
1793 1810 1.938577 CATCTTTGGTGAGCCATCTCG 59.061 52.381 0.00 0.00 45.56 4.04
1842 1859 3.255379 GCCGCGTCAAGATCGGAC 61.255 66.667 4.92 9.68 45.53 4.79
1855 1872 0.183971 ATCGGACGAGGAGGTGATCT 59.816 55.000 0.00 0.00 0.00 2.75
1858 1875 1.746171 CGGACGAGGAGGTGATCTGTA 60.746 57.143 0.00 0.00 0.00 2.74
1861 1878 3.194968 GGACGAGGAGGTGATCTGTAAAA 59.805 47.826 0.00 0.00 0.00 1.52
1862 1879 4.322499 GGACGAGGAGGTGATCTGTAAAAA 60.322 45.833 0.00 0.00 0.00 1.94
1894 1915 1.003839 TTGTGGTGATGTCGGAGGC 60.004 57.895 0.00 0.00 0.00 4.70
1905 1926 3.991051 CGGAGGCAGGTGACACGT 61.991 66.667 0.00 0.00 0.00 4.49
1911 1932 3.022287 CAGGTGACACGTGTTGGC 58.978 61.111 24.26 15.12 0.00 4.52
1912 1933 2.587753 AGGTGACACGTGTTGGCG 60.588 61.111 24.26 0.00 34.92 5.69
1913 1934 2.893404 GGTGACACGTGTTGGCGT 60.893 61.111 24.26 0.00 46.88 5.68
1914 1935 2.624264 GTGACACGTGTTGGCGTC 59.376 61.111 24.26 9.32 43.83 5.19
1915 1936 2.168503 GTGACACGTGTTGGCGTCA 61.169 57.895 24.26 12.09 43.83 4.35
1916 1937 1.448013 TGACACGTGTTGGCGTCAA 60.448 52.632 24.26 0.00 43.83 3.18
1917 1938 1.275657 GACACGTGTTGGCGTCAAG 59.724 57.895 24.26 0.00 43.83 3.02
1918 1939 2.052237 CACGTGTTGGCGTCAAGC 60.052 61.111 0.75 0.00 43.83 4.01
1996 2017 3.867857 TGTGCAAAGACTAGTGTTGTGA 58.132 40.909 5.96 0.00 0.00 3.58
2019 2040 5.560966 TGTCTTTTCAGTTTTGTCAGACC 57.439 39.130 0.00 0.00 30.96 3.85
2021 2042 4.094442 GTCTTTTCAGTTTTGTCAGACCGT 59.906 41.667 0.00 0.00 0.00 4.83
2028 2049 4.272504 CAGTTTTGTCAGACCGTTGTGTAT 59.727 41.667 0.00 0.00 0.00 2.29
2112 2134 3.105283 GGTTAGGTGGACAGTGGTATCT 58.895 50.000 0.00 0.00 0.00 1.98
2116 2138 2.180276 GGTGGACAGTGGTATCTCAGT 58.820 52.381 0.00 0.00 0.00 3.41
2117 2139 2.166664 GGTGGACAGTGGTATCTCAGTC 59.833 54.545 0.00 0.00 0.00 3.51
2118 2140 2.166664 GTGGACAGTGGTATCTCAGTCC 59.833 54.545 11.56 11.56 40.90 3.85
2119 2141 2.225267 TGGACAGTGGTATCTCAGTCCA 60.225 50.000 15.91 15.91 44.82 4.02
2120 2142 4.380488 TGGACAGTGGTATCTCAGTCCAC 61.380 52.174 15.91 3.60 43.35 4.02
2128 2150 1.747444 ATCTCAGTCCACCAGGGTTT 58.253 50.000 0.00 0.00 38.11 3.27
2133 2155 4.010349 CTCAGTCCACCAGGGTTTAAATC 58.990 47.826 0.00 0.00 38.11 2.17
2135 2157 2.042569 AGTCCACCAGGGTTTAAATCCC 59.957 50.000 14.12 14.40 44.90 3.85
2146 2168 3.632145 GGTTTAAATCCCGATGCTCACAT 59.368 43.478 0.00 0.00 39.98 3.21
2156 2178 2.743664 CGATGCTCACATTTGTTCCTGA 59.256 45.455 0.00 0.00 36.35 3.86
2165 2187 8.992073 GCTCACATTTGTTCCTGAATTTATTTT 58.008 29.630 0.00 0.00 0.00 1.82
2181 2203 8.702163 AATTTATTTTAGGATTTCCAGCGTTG 57.298 30.769 0.00 0.00 38.89 4.10
2185 2207 0.326264 AGGATTTCCAGCGTTGCTCT 59.674 50.000 0.00 0.00 36.40 4.09
2194 2216 0.886490 AGCGTTGCTCTTTCAGTGGG 60.886 55.000 0.00 0.00 30.62 4.61
2196 2218 1.151668 CGTTGCTCTTTCAGTGGGAG 58.848 55.000 0.00 0.00 0.00 4.30
2197 2219 1.528129 GTTGCTCTTTCAGTGGGAGG 58.472 55.000 9.48 0.00 0.00 4.30
2201 2223 1.066502 GCTCTTTCAGTGGGAGGAGAC 60.067 57.143 9.62 0.69 32.47 3.36
2205 2227 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
2220 2242 2.163010 GACGTTCCCATCAACTACGAGA 59.837 50.000 0.00 0.00 36.21 4.04
2228 2250 4.568359 CCCATCAACTACGAGATGTCTTTG 59.432 45.833 0.00 0.00 39.92 2.77
2229 2251 4.568359 CCATCAACTACGAGATGTCTTTGG 59.432 45.833 0.00 0.00 39.92 3.28
2230 2252 4.866508 TCAACTACGAGATGTCTTTGGT 57.133 40.909 0.00 0.00 0.00 3.67
2233 2255 4.175787 ACTACGAGATGTCTTTGGTGAC 57.824 45.455 0.00 0.00 37.47 3.67
2234 2256 3.827302 ACTACGAGATGTCTTTGGTGACT 59.173 43.478 0.00 0.00 37.79 3.41
2235 2257 3.753294 ACGAGATGTCTTTGGTGACTT 57.247 42.857 0.00 0.00 37.79 3.01
2236 2258 3.654414 ACGAGATGTCTTTGGTGACTTC 58.346 45.455 0.00 0.00 39.75 3.01
2237 2259 2.663602 CGAGATGTCTTTGGTGACTTCG 59.336 50.000 0.00 0.00 42.37 3.79
2238 2260 3.654414 GAGATGTCTTTGGTGACTTCGT 58.346 45.455 0.00 0.00 42.37 3.85
2239 2261 3.654414 AGATGTCTTTGGTGACTTCGTC 58.346 45.455 0.00 0.00 42.37 4.20
2240 2262 2.971660 TGTCTTTGGTGACTTCGTCA 57.028 45.000 0.00 0.00 40.50 4.35
2241 2263 3.254470 TGTCTTTGGTGACTTCGTCAA 57.746 42.857 0.00 0.00 44.49 3.18
2244 2266 4.058817 GTCTTTGGTGACTTCGTCAATCT 58.941 43.478 0.00 0.00 44.49 2.40
2252 2274 4.926238 GTGACTTCGTCAATCTGTCAATCT 59.074 41.667 0.00 0.00 44.49 2.40
2259 2281 5.406477 TCGTCAATCTGTCAATCTCAAGTTG 59.594 40.000 0.00 0.00 0.00 3.16
2273 2295 9.125906 CAATCTCAAGTTGAAATGAAATGAGAC 57.874 33.333 7.06 0.00 43.03 3.36
2283 2305 9.699410 TTGAAATGAAATGAGACCCATATAACT 57.301 29.630 0.00 0.00 34.45 2.24
2315 2337 7.478322 AGAATACATACTTTCATGCAAAGCAG 58.522 34.615 13.98 8.88 45.00 4.24
2332 2354 4.273148 AGCAGGTACTACTTTTGACTGG 57.727 45.455 0.00 0.00 36.02 4.00
2338 2360 4.753610 GGTACTACTTTTGACTGGTGTTCC 59.246 45.833 0.00 0.00 0.00 3.62
2339 2361 3.816994 ACTACTTTTGACTGGTGTTCCC 58.183 45.455 0.00 0.00 0.00 3.97
2344 2366 3.502123 TTTGACTGGTGTTCCCCTTAG 57.498 47.619 0.00 0.00 0.00 2.18
2362 2384 5.504853 CCTTAGGAAGAGCAAGGAAGAAAT 58.495 41.667 0.00 0.00 41.18 2.17
2363 2385 5.948758 CCTTAGGAAGAGCAAGGAAGAAATT 59.051 40.000 0.00 0.00 41.18 1.82
2364 2386 6.435591 CCTTAGGAAGAGCAAGGAAGAAATTT 59.564 38.462 0.00 0.00 41.18 1.82
2405 2427 3.379445 CCACACCCTAGCCGACGT 61.379 66.667 0.00 0.00 0.00 4.34
2431 2453 2.736826 CCCTCTTCCTTCCCCTCGC 61.737 68.421 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.119484 TTGTTGGCCGAGAACCCGAT 62.119 55.000 0.00 0.00 0.00 4.18
78 79 2.626780 GCTTGTTGGCCGAGAACCC 61.627 63.158 0.00 0.00 0.00 4.11
81 82 2.668212 CCGCTTGTTGGCCGAGAA 60.668 61.111 1.97 1.97 0.00 2.87
172 173 4.760047 GGACGATGCAGTGGCGGT 62.760 66.667 0.00 0.00 45.35 5.68
257 258 2.092968 ACAATACCTGCACATCACCGAT 60.093 45.455 0.00 0.00 0.00 4.18
330 331 6.342338 AGTACTCCACTAACACCTTACTTG 57.658 41.667 0.00 0.00 34.98 3.16
350 351 3.007074 TCTCGCCACACACCATAAAAGTA 59.993 43.478 0.00 0.00 0.00 2.24
501 506 8.770438 AATGACAACAAACTTAACACAACAAT 57.230 26.923 0.00 0.00 0.00 2.71
551 556 2.230992 ACAACAGCAACAGCAAAACAGA 59.769 40.909 0.00 0.00 0.00 3.41
557 562 0.179132 CAGCACAACAGCAACAGCAA 60.179 50.000 0.00 0.00 36.85 3.91
619 624 3.238441 TGCAAACAACGTTTGTGTTCTC 58.762 40.909 18.02 0.00 44.59 2.87
672 677 1.312371 GCCCGCATTTGTGCTTAGGA 61.312 55.000 0.00 0.00 0.00 2.94
884 891 1.431195 TAGCTGGGCTTGGTTTGGGA 61.431 55.000 0.00 0.00 40.44 4.37
900 907 0.463620 CAAGGGAGCTCTGTCCTAGC 59.536 60.000 14.64 0.00 40.40 3.42
905 912 1.216710 CGGTCAAGGGAGCTCTGTC 59.783 63.158 14.64 1.94 39.38 3.51
920 927 2.764637 GATGGGAAAGTGCCACCGGT 62.765 60.000 0.00 0.00 41.95 5.28
948 955 2.357952 GGGCGTTTGTTGTTTCTCTCTT 59.642 45.455 0.00 0.00 0.00 2.85
1615 1631 7.850982 GCGTGAAAGTATATATTTGACCAACAG 59.149 37.037 0.00 0.00 0.00 3.16
1671 1687 2.100605 AAGATGTCGGAGGAGCAAAC 57.899 50.000 0.00 0.00 0.00 2.93
1686 1702 0.460311 CTTCCCCGCACGACTAAGAT 59.540 55.000 0.00 0.00 0.00 2.40
1744 1760 7.637229 TCATTACGTTAAACGAATCAAACCAA 58.363 30.769 0.00 0.00 46.05 3.67
1780 1797 1.144936 CCCTTCGAGATGGCTCACC 59.855 63.158 0.00 0.00 41.36 4.02
1792 1809 2.255252 CAACTTTGCGGCCCTTCG 59.745 61.111 0.00 0.00 0.00 3.79
1793 1810 2.049156 GCAACTTTGCGGCCCTTC 60.049 61.111 0.00 0.00 45.11 3.46
1861 1878 2.167487 ACCACAACAGCCACGAATTTTT 59.833 40.909 0.00 0.00 0.00 1.94
1862 1879 1.754226 ACCACAACAGCCACGAATTTT 59.246 42.857 0.00 0.00 0.00 1.82
1864 1881 0.667993 CACCACAACAGCCACGAATT 59.332 50.000 0.00 0.00 0.00 2.17
1865 1882 0.179032 TCACCACAACAGCCACGAAT 60.179 50.000 0.00 0.00 0.00 3.34
1872 1893 0.602638 TCCGACATCACCACAACAGC 60.603 55.000 0.00 0.00 0.00 4.40
1876 1897 1.003839 GCCTCCGACATCACCACAA 60.004 57.895 0.00 0.00 0.00 3.33
1894 1915 2.881266 CGCCAACACGTGTCACCTG 61.881 63.158 23.61 16.15 0.00 4.00
1912 1933 1.129437 GAAACCATCTCTGCGCTTGAC 59.871 52.381 9.73 0.00 0.00 3.18
1913 1934 1.002430 AGAAACCATCTCTGCGCTTGA 59.998 47.619 9.73 6.21 30.46 3.02
1914 1935 1.446907 AGAAACCATCTCTGCGCTTG 58.553 50.000 9.73 1.08 30.46 4.01
1915 1936 2.079925 GAAGAAACCATCTCTGCGCTT 58.920 47.619 9.73 0.00 37.42 4.68
1916 1937 1.277557 AGAAGAAACCATCTCTGCGCT 59.722 47.619 9.73 0.00 37.42 5.92
1917 1938 1.396301 CAGAAGAAACCATCTCTGCGC 59.604 52.381 0.00 0.00 37.42 6.09
1918 1939 2.693069 ACAGAAGAAACCATCTCTGCG 58.307 47.619 0.00 0.00 37.42 5.18
1920 1941 6.624352 TCAAAACAGAAGAAACCATCTCTG 57.376 37.500 0.00 0.00 37.42 3.35
1921 1942 7.286316 ACAATCAAAACAGAAGAAACCATCTCT 59.714 33.333 0.00 0.00 37.42 3.10
1922 1943 7.428826 ACAATCAAAACAGAAGAAACCATCTC 58.571 34.615 0.00 0.00 37.42 2.75
1923 1944 7.352079 ACAATCAAAACAGAAGAAACCATCT 57.648 32.000 0.00 0.00 41.32 2.90
1924 1945 9.696917 ATTACAATCAAAACAGAAGAAACCATC 57.303 29.630 0.00 0.00 0.00 3.51
1926 1947 9.883142 AAATTACAATCAAAACAGAAGAAACCA 57.117 25.926 0.00 0.00 0.00 3.67
1953 1974 4.400529 AAGGAACACCAACCATGAAAAC 57.599 40.909 0.00 0.00 0.00 2.43
1954 1975 4.223923 ACAAAGGAACACCAACCATGAAAA 59.776 37.500 0.00 0.00 0.00 2.29
1959 1980 1.412343 GCACAAAGGAACACCAACCAT 59.588 47.619 0.00 0.00 0.00 3.55
1993 2014 6.688813 GTCTGACAAAACTGAAAAGACATCAC 59.311 38.462 2.24 0.00 34.19 3.06
1996 2017 5.220854 CGGTCTGACAAAACTGAAAAGACAT 60.221 40.000 10.38 0.00 35.40 3.06
2019 2040 6.706055 ATAGTTCAAGTCACATACACAACG 57.294 37.500 0.00 0.00 0.00 4.10
2021 2042 7.931407 AGACAATAGTTCAAGTCACATACACAA 59.069 33.333 0.00 0.00 33.56 3.33
2028 2049 9.725019 ATCATAAAGACAATAGTTCAAGTCACA 57.275 29.630 0.00 0.00 33.56 3.58
2078 2099 4.141274 TCCACCTAACCATCCAACCATATG 60.141 45.833 0.00 0.00 0.00 1.78
2079 2100 4.051478 TCCACCTAACCATCCAACCATAT 58.949 43.478 0.00 0.00 0.00 1.78
2081 2102 2.025321 GTCCACCTAACCATCCAACCAT 60.025 50.000 0.00 0.00 0.00 3.55
2112 2134 3.245122 GGATTTAAACCCTGGTGGACTGA 60.245 47.826 0.00 0.00 38.00 3.41
2116 2138 1.004979 CGGGATTTAAACCCTGGTGGA 59.995 52.381 18.10 0.00 44.72 4.02
2117 2139 1.004979 TCGGGATTTAAACCCTGGTGG 59.995 52.381 7.63 0.79 44.72 4.61
2118 2140 2.500392 TCGGGATTTAAACCCTGGTG 57.500 50.000 7.63 1.10 44.72 4.17
2119 2141 2.948600 GCATCGGGATTTAAACCCTGGT 60.949 50.000 7.63 0.00 44.72 4.00
2120 2142 1.681264 GCATCGGGATTTAAACCCTGG 59.319 52.381 7.63 5.97 44.72 4.45
2121 2143 2.618709 GAGCATCGGGATTTAAACCCTG 59.381 50.000 18.10 11.68 44.72 4.45
2128 2150 4.269183 ACAAATGTGAGCATCGGGATTTA 58.731 39.130 0.00 0.00 38.61 1.40
2133 2155 1.133025 GGAACAAATGTGAGCATCGGG 59.867 52.381 0.00 0.00 38.61 5.14
2135 2157 2.743664 TCAGGAACAAATGTGAGCATCG 59.256 45.455 0.00 0.00 38.61 3.84
2156 2178 7.277760 GCAACGCTGGAAATCCTAAAATAAATT 59.722 33.333 0.44 0.00 36.82 1.82
2165 2187 1.555075 AGAGCAACGCTGGAAATCCTA 59.445 47.619 0.44 0.00 39.88 2.94
2181 2203 1.066502 GTCTCCTCCCACTGAAAGAGC 60.067 57.143 0.00 0.00 37.43 4.09
2185 2207 1.343465 GAACGTCTCCTCCCACTGAAA 59.657 52.381 0.00 0.00 0.00 2.69
2194 2216 1.550976 AGTTGATGGGAACGTCTCCTC 59.449 52.381 13.94 7.51 46.90 3.71
2196 2218 2.734492 CGTAGTTGATGGGAACGTCTCC 60.734 54.545 7.90 7.90 46.90 3.71
2197 2219 2.163010 TCGTAGTTGATGGGAACGTCTC 59.837 50.000 0.00 0.00 46.90 3.36
2201 2223 2.933495 TCTCGTAGTTGATGGGAACG 57.067 50.000 0.00 0.00 34.99 3.95
2205 2227 4.392921 AAGACATCTCGTAGTTGATGGG 57.607 45.455 7.69 0.00 41.09 4.00
2233 2255 5.636965 ACTTGAGATTGACAGATTGACGAAG 59.363 40.000 0.00 0.00 0.00 3.79
2234 2256 5.541845 ACTTGAGATTGACAGATTGACGAA 58.458 37.500 0.00 0.00 0.00 3.85
2235 2257 5.139435 ACTTGAGATTGACAGATTGACGA 57.861 39.130 0.00 0.00 0.00 4.20
2236 2258 5.406477 TCAACTTGAGATTGACAGATTGACG 59.594 40.000 0.00 0.00 31.11 4.35
2237 2259 6.791887 TCAACTTGAGATTGACAGATTGAC 57.208 37.500 0.00 0.00 31.11 3.18
2238 2260 7.806409 TTTCAACTTGAGATTGACAGATTGA 57.194 32.000 0.00 0.00 35.82 2.57
2239 2261 8.294577 TCATTTCAACTTGAGATTGACAGATTG 58.705 33.333 0.00 0.00 35.82 2.67
2240 2262 8.400184 TCATTTCAACTTGAGATTGACAGATT 57.600 30.769 0.00 0.00 35.82 2.40
2241 2263 7.991084 TCATTTCAACTTGAGATTGACAGAT 57.009 32.000 0.00 0.00 35.82 2.90
2244 2266 8.631797 TCATTTCATTTCAACTTGAGATTGACA 58.368 29.630 0.00 0.00 35.82 3.58
2252 2274 5.832595 TGGGTCTCATTTCATTTCAACTTGA 59.167 36.000 0.00 0.00 0.00 3.02
2296 2318 4.445452 ACCTGCTTTGCATGAAAGTATG 57.555 40.909 14.83 11.42 42.85 2.39
2300 2322 4.697352 AGTAGTACCTGCTTTGCATGAAAG 59.303 41.667 0.00 5.14 43.63 2.62
2306 2328 4.274950 GTCAAAAGTAGTACCTGCTTTGCA 59.725 41.667 7.87 0.00 43.46 4.08
2307 2329 4.515567 AGTCAAAAGTAGTACCTGCTTTGC 59.484 41.667 7.87 3.36 43.46 3.68
2315 2337 4.753610 GGAACACCAGTCAAAAGTAGTACC 59.246 45.833 0.00 0.00 0.00 3.34
2338 2360 2.840651 TCTTCCTTGCTCTTCCTAAGGG 59.159 50.000 0.00 0.00 41.01 3.95
2339 2361 4.559862 TTCTTCCTTGCTCTTCCTAAGG 57.440 45.455 0.00 0.00 41.81 2.69
2363 2385 1.477295 ACGCGGGTGAAAAAGGAAAAA 59.523 42.857 12.47 0.00 0.00 1.94
2364 2386 1.065851 GACGCGGGTGAAAAAGGAAAA 59.934 47.619 10.96 0.00 0.00 2.29
2371 2393 3.039588 GAGCGACGCGGGTGAAAA 61.040 61.111 15.18 0.00 0.00 2.29
2405 2427 2.188817 GGAAGGAAGAGGGCTAGTTGA 58.811 52.381 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.