Multiple sequence alignment - TraesCS2D01G294900

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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 TraesCS2D01G294900 chr2D 100.000 1510 0 0 989 2498 377122097 377123606 0.000000e+00 2789
1 TraesCS2D01G294900 chr2D 100.000 555 0 0 1 555 377121109 377121663 0.000000e+00 1026
2 TraesCS2D01G294900 chr2D 88.793 232 15 1 2278 2498 131043850 131044081 8.800000e-70 274
3 TraesCS2D01G294900 chr2D 87.931 232 17 1 2278 2498 131003309 131003540 1.910000e-66 263
4 TraesCS2D01G294900 chr2D 87.931 232 14 5 2278 2498 316712908 316712680 6.850000e-66 261
5 TraesCS2D01G294900 chr2D 84.454 238 27 8 2049 2282 587269021 587269252 2.500000e-55 226
6 TraesCS2D01G294900 chr2D 76.696 339 53 17 1080 1414 160211464 160211148 5.530000e-37 165
7 TraesCS2D01G294900 chr2A 89.652 1237 90 23 989 2193 511076308 511077538 0.000000e+00 1541
8 TraesCS2D01G294900 chr2A 88.702 593 16 11 1 555 511075641 511076220 0.000000e+00 676
9 TraesCS2D01G294900 chr2A 90.086 232 11 2 2278 2498 511077682 511077912 8.740000e-75 291
10 TraesCS2D01G294900 chr2A 83.682 239 33 6 2047 2282 738394525 738394760 1.160000e-53 220
11 TraesCS2D01G294900 chr2A 76.106 339 55 16 1080 1414 171609456 171609772 1.200000e-33 154
12 TraesCS2D01G294900 chr2B 92.451 1020 41 22 989 1978 448694978 448695991 0.000000e+00 1424
13 TraesCS2D01G294900 chr2B 95.495 555 10 3 1 555 448694350 448694889 0.000000e+00 872
14 TraesCS2D01G294900 chr2B 77.286 339 51 16 1080 1414 216965367 216965051 2.550000e-40 176
15 TraesCS2D01G294900 chr7B 88.362 232 16 4 2278 2498 4808380 4808611 4.100000e-68 268
16 TraesCS2D01G294900 chr3D 87.124 233 27 3 2051 2282 579373614 579373844 6.850000e-66 261
17 TraesCS2D01G294900 chr3D 84.681 235 28 7 2049 2282 106334208 106334435 6.950000e-56 228
18 TraesCS2D01G294900 chr5A 87.124 233 18 2 2278 2498 697247091 697247323 1.150000e-63 254
19 TraesCS2D01G294900 chr6B 86.667 225 26 3 2278 2498 400355523 400355299 1.920000e-61 246
20 TraesCS2D01G294900 chr6B 84.914 232 20 3 2278 2498 179372802 179373029 1.160000e-53 220
21 TraesCS2D01G294900 chr6B 87.179 195 20 3 2089 2282 476020805 476020995 1.500000e-52 217
22 TraesCS2D01G294900 chr5D 86.076 237 24 5 2047 2282 81261678 81261906 1.920000e-61 246
23 TraesCS2D01G294900 chr3A 86.878 221 24 2 2278 2498 609377281 609377496 2.480000e-60 243
24 TraesCS2D01G294900 chr1B 86.522 230 20 4 2278 2496 520239821 520239592 2.480000e-60 243
25 TraesCS2D01G294900 chr1D 89.840 187 14 4 2097 2282 338374588 338374406 4.150000e-58 235
26 TraesCS2D01G294900 chrUn 85.776 232 20 3 2278 2498 323479709 323479480 1.490000e-57 233
27 TraesCS2D01G294900 chrUn 85.776 232 20 3 2278 2498 323486101 323485872 1.490000e-57 233
28 TraesCS2D01G294900 chrUn 85.345 232 21 3 2278 2498 252875135 252875364 6.950000e-56 228
29 TraesCS2D01G294900 chr1A 89.418 189 13 5 2096 2282 437235031 437235214 5.370000e-57 231
30 TraesCS2D01G294900 chr4B 85.345 232 23 6 2278 2498 117040702 117040471 1.930000e-56 230
31 TraesCS2D01G294900 chr6D 88.770 187 15 4 2097 2282 362695243 362695062 8.990000e-55 224
32 TraesCS2D01G294900 chr6D 84.889 225 24 6 2278 2498 354539500 354539282 4.180000e-53 219
33 TraesCS2D01G294900 chr6A 96.923 65 2 0 2434 2498 600723962 600724026 2.630000e-20 110


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 TraesCS2D01G294900 chr2D 377121109 377123606 2497 False 1907.5 2789 100.000 1 2498 2 chr2D.!!$F4 2497
1 TraesCS2D01G294900 chr2A 511075641 511077912 2271 False 836.0 1541 89.480 1 2498 3 chr2A.!!$F3 2497
2 TraesCS2D01G294900 chr2B 448694350 448695991 1641 False 1148.0 1424 93.973 1 1978 2 chr2B.!!$F1 1977

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
392 430 0.663153 GAGCAAACGACAAGCAACCT 59.337 50.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2296 0.10104 GCTGCATGCGGCTATTTGAA 59.899 50.0 38.27 5.55 44.39 2.69 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
392 430 0.663153 GAGCAAACGACAAGCAACCT 59.337 50.000 0.00 0.00 0.00 3.50
397 435 1.213094 AACGACAAGCAACCTCGACG 61.213 55.000 0.00 0.00 0.00 5.12
398 436 2.853914 GACAAGCAACCTCGACGC 59.146 61.111 0.00 0.00 0.00 5.19
399 437 1.664965 GACAAGCAACCTCGACGCT 60.665 57.895 0.00 0.00 37.68 5.07
400 438 1.891060 GACAAGCAACCTCGACGCTG 61.891 60.000 0.00 0.00 35.79 5.18
401 439 3.044305 AAGCAACCTCGACGCTGC 61.044 61.111 2.08 2.08 35.79 5.25
524 562 7.236847 TCTCCTGATTTTAGTAAGTTTCCTCCA 59.763 37.037 0.00 0.00 0.00 3.86
1507 1545 3.198853 GTCCAAGCCTTAGTCAGATTCCT 59.801 47.826 0.00 0.00 0.00 3.36
1583 1621 4.081142 CAGATCCAATGTGTACTGGTACCA 60.081 45.833 15.39 15.39 35.26 3.25
1665 1714 1.045407 TATACAGGGCCTAACCAGCG 58.955 55.000 5.28 0.00 42.05 5.18
1670 1719 2.125106 GGCCTAACCAGCGACCAG 60.125 66.667 0.00 0.00 38.86 4.00
1740 1789 1.829222 TCCGTGTTTAGACTCCATCCC 59.171 52.381 0.00 0.00 0.00 3.85
1777 1826 8.672823 ACCGATAAACTCTTCAAACTAAACTT 57.327 30.769 0.00 0.00 0.00 2.66
1779 1828 8.228464 CCGATAAACTCTTCAAACTAAACTTCC 58.772 37.037 0.00 0.00 0.00 3.46
1780 1829 7.950496 CGATAAACTCTTCAAACTAAACTTCCG 59.050 37.037 0.00 0.00 0.00 4.30
1781 1830 8.897872 ATAAACTCTTCAAACTAAACTTCCGA 57.102 30.769 0.00 0.00 0.00 4.55
1782 1831 7.803279 AAACTCTTCAAACTAAACTTCCGAT 57.197 32.000 0.00 0.00 0.00 4.18
1783 1832 6.787085 ACTCTTCAAACTAAACTTCCGATG 57.213 37.500 0.00 0.00 0.00 3.84
1785 1834 5.305585 TCTTCAAACTAAACTTCCGATGCT 58.694 37.500 0.00 0.00 0.00 3.79
1786 1835 5.408604 TCTTCAAACTAAACTTCCGATGCTC 59.591 40.000 0.00 0.00 0.00 4.26
1788 1837 4.451096 TCAAACTAAACTTCCGATGCTCAC 59.549 41.667 0.00 0.00 0.00 3.51
1789 1838 3.678056 ACTAAACTTCCGATGCTCACA 57.322 42.857 0.00 0.00 0.00 3.58
1790 1839 4.207891 ACTAAACTTCCGATGCTCACAT 57.792 40.909 0.00 0.00 39.98 3.21
1791 1840 5.339008 ACTAAACTTCCGATGCTCACATA 57.661 39.130 0.00 0.00 36.35 2.29
1792 1841 5.109903 ACTAAACTTCCGATGCTCACATAC 58.890 41.667 0.00 0.00 36.35 2.39
1793 1842 3.895232 AACTTCCGATGCTCACATACT 57.105 42.857 0.00 0.00 36.35 2.12
1794 1843 3.895232 ACTTCCGATGCTCACATACTT 57.105 42.857 0.00 0.00 36.35 2.24
1796 1845 5.339008 ACTTCCGATGCTCACATACTTTA 57.661 39.130 0.00 0.00 36.35 1.85
1816 1873 8.110860 ACTTTAGTTTTCATTATGTCCACCAG 57.889 34.615 0.00 0.00 0.00 4.00
1824 1881 3.769189 TTATGTCCACCAGGTAGGAGA 57.231 47.619 10.22 9.82 41.22 3.71
2027 2105 5.635549 AAAATTAACTCACGCAAAGCAAC 57.364 34.783 0.00 0.00 0.00 4.17
2028 2106 4.568152 AATTAACTCACGCAAAGCAACT 57.432 36.364 0.00 0.00 0.00 3.16
2029 2107 3.602390 TTAACTCACGCAAAGCAACTC 57.398 42.857 0.00 0.00 0.00 3.01
2030 2108 1.668419 AACTCACGCAAAGCAACTCT 58.332 45.000 0.00 0.00 0.00 3.24
2031 2109 0.940126 ACTCACGCAAAGCAACTCTG 59.060 50.000 0.00 0.00 0.00 3.35
2055 2144 0.116143 TTGGGCAAGGTTAGGGCATT 59.884 50.000 0.00 0.00 0.00 3.56
2062 2151 1.834188 AGGTTAGGGCATTTCCAACG 58.166 50.000 0.00 0.00 36.21 4.10
2081 2170 2.347697 GGTGACCCGCAAATTTTCTC 57.652 50.000 0.00 0.00 0.00 2.87
2083 2172 1.611491 GTGACCCGCAAATTTTCTCCA 59.389 47.619 0.00 0.00 0.00 3.86
2088 2177 2.533266 CCGCAAATTTTCTCCAGCATC 58.467 47.619 0.00 0.00 0.00 3.91
2093 2182 3.356529 AATTTTCTCCAGCATCCGTCT 57.643 42.857 0.00 0.00 0.00 4.18
2094 2183 2.099141 TTTTCTCCAGCATCCGTCTG 57.901 50.000 0.00 0.00 0.00 3.51
2106 2196 3.036084 CGTCTGTGGACACGGTGC 61.036 66.667 8.30 0.93 42.21 5.01
2108 2198 4.293648 TCTGTGGACACGGTGCGG 62.294 66.667 8.30 0.00 38.77 5.69
2114 2204 3.771160 GACACGGTGCGGGAGGAT 61.771 66.667 8.30 0.00 32.98 3.24
2133 2223 2.895372 CCATCCAACCGTAGCCGC 60.895 66.667 0.00 0.00 0.00 6.53
2142 2232 1.733041 CCGTAGCCGCATACATCCG 60.733 63.158 0.00 0.00 0.00 4.18
2148 2238 1.868997 CCGCATACATCCGGCATTC 59.131 57.895 0.00 0.00 37.85 2.67
2151 2241 1.160137 GCATACATCCGGCATTCCTC 58.840 55.000 0.00 0.00 0.00 3.71
2153 2243 2.877300 GCATACATCCGGCATTCCTCAT 60.877 50.000 0.00 0.00 0.00 2.90
2156 2246 3.795688 ACATCCGGCATTCCTCATATT 57.204 42.857 0.00 0.00 0.00 1.28
2157 2247 4.104383 ACATCCGGCATTCCTCATATTT 57.896 40.909 0.00 0.00 0.00 1.40
2158 2248 4.473444 ACATCCGGCATTCCTCATATTTT 58.527 39.130 0.00 0.00 0.00 1.82
2159 2249 4.895297 ACATCCGGCATTCCTCATATTTTT 59.105 37.500 0.00 0.00 0.00 1.94
2160 2250 5.010012 ACATCCGGCATTCCTCATATTTTTC 59.990 40.000 0.00 0.00 0.00 2.29
2161 2251 4.792068 TCCGGCATTCCTCATATTTTTCT 58.208 39.130 0.00 0.00 0.00 2.52
2163 2253 6.361433 TCCGGCATTCCTCATATTTTTCTTA 58.639 36.000 0.00 0.00 0.00 2.10
2169 2259 9.521503 GCATTCCTCATATTTTTCTTAAAGTCC 57.478 33.333 0.00 0.00 0.00 3.85
2172 2262 6.882140 TCCTCATATTTTTCTTAAAGTCCGCA 59.118 34.615 0.00 0.00 0.00 5.69
2173 2263 6.967199 CCTCATATTTTTCTTAAAGTCCGCAC 59.033 38.462 0.00 0.00 0.00 5.34
2174 2264 6.539324 TCATATTTTTCTTAAAGTCCGCACG 58.461 36.000 0.00 0.00 0.00 5.34
2175 2265 6.369340 TCATATTTTTCTTAAAGTCCGCACGA 59.631 34.615 0.00 0.00 0.00 4.35
2176 2266 5.622770 ATTTTTCTTAAAGTCCGCACGAT 57.377 34.783 0.00 0.00 0.00 3.73
2177 2267 4.657075 TTTTCTTAAAGTCCGCACGATC 57.343 40.909 0.00 0.00 0.00 3.69
2178 2268 3.306917 TTCTTAAAGTCCGCACGATCA 57.693 42.857 0.00 0.00 0.00 2.92
2179 2269 3.306917 TCTTAAAGTCCGCACGATCAA 57.693 42.857 0.00 0.00 0.00 2.57
2180 2270 3.655486 TCTTAAAGTCCGCACGATCAAA 58.345 40.909 0.00 0.00 0.00 2.69
2181 2271 4.250464 TCTTAAAGTCCGCACGATCAAAT 58.750 39.130 0.00 0.00 0.00 2.32
2182 2272 5.412640 TCTTAAAGTCCGCACGATCAAATA 58.587 37.500 0.00 0.00 0.00 1.40
2183 2273 5.518847 TCTTAAAGTCCGCACGATCAAATAG 59.481 40.000 0.00 0.00 0.00 1.73
2184 2274 1.571919 AGTCCGCACGATCAAATAGC 58.428 50.000 0.00 0.00 0.00 2.97
2185 2275 0.582005 GTCCGCACGATCAAATAGCC 59.418 55.000 0.00 0.00 0.00 3.93
2186 2276 0.874175 TCCGCACGATCAAATAGCCG 60.874 55.000 0.00 0.00 0.00 5.52
2187 2277 1.083401 CGCACGATCAAATAGCCGC 60.083 57.895 0.00 0.00 0.00 6.53
2188 2278 1.761244 CGCACGATCAAATAGCCGCA 61.761 55.000 0.00 0.00 0.00 5.69
2189 2279 0.588252 GCACGATCAAATAGCCGCAT 59.412 50.000 0.00 0.00 0.00 4.73
2190 2280 1.661178 GCACGATCAAATAGCCGCATG 60.661 52.381 0.00 0.00 0.00 4.06
2191 2281 0.588252 ACGATCAAATAGCCGCATGC 59.412 50.000 7.91 7.91 41.71 4.06
2192 2282 0.587768 CGATCAAATAGCCGCATGCA 59.412 50.000 19.57 0.00 44.83 3.96
2193 2283 1.002576 CGATCAAATAGCCGCATGCAA 60.003 47.619 19.57 0.00 44.83 4.08
2194 2284 2.541383 CGATCAAATAGCCGCATGCAAA 60.541 45.455 19.57 0.00 44.83 3.68
2195 2285 2.565210 TCAAATAGCCGCATGCAAAG 57.435 45.000 19.57 6.76 44.83 2.77
2196 2286 1.134753 TCAAATAGCCGCATGCAAAGG 59.865 47.619 19.57 12.18 44.83 3.11
2197 2287 0.461135 AAATAGCCGCATGCAAAGGG 59.539 50.000 19.57 11.79 44.83 3.95
2198 2288 0.684153 AATAGCCGCATGCAAAGGGT 60.684 50.000 19.57 18.17 44.83 4.34
2199 2289 0.182537 ATAGCCGCATGCAAAGGGTA 59.817 50.000 19.57 19.71 44.83 3.69
2200 2290 0.746563 TAGCCGCATGCAAAGGGTAC 60.747 55.000 19.57 0.00 44.83 3.34
2201 2291 2.339556 GCCGCATGCAAAGGGTACA 61.340 57.895 19.57 0.00 40.77 2.90
2202 2292 1.872197 GCCGCATGCAAAGGGTACAA 61.872 55.000 19.57 0.00 40.77 2.41
2206 2296 1.000717 GCATGCAAAGGGTACAAACGT 60.001 47.619 14.21 0.00 0.00 3.99
2215 2305 5.366829 AAGGGTACAAACGTTCAAATAGC 57.633 39.130 0.00 1.74 0.00 2.97
2240 2330 5.345741 CGCATGCAGCACTAGTTTAAATTTT 59.654 36.000 19.57 0.00 46.13 1.82
2291 2472 2.229792 TGTTGTCTCCTCAAATGTGGC 58.770 47.619 0.00 0.00 0.00 5.01
2303 2484 2.134789 AATGTGGCTGGATTCTGGTC 57.865 50.000 0.00 0.00 0.00 4.02
2306 2487 2.190578 GGCTGGATTCTGGTCCGG 59.809 66.667 0.00 0.00 45.70 5.14
2312 2493 2.500098 CTGGATTCTGGTCCGGAAGTTA 59.500 50.000 18.10 6.27 45.79 2.24
2352 2533 3.002791 CTCAAATTCTAGAGTTGCCGCA 58.997 45.455 0.66 0.00 0.00 5.69
2363 2544 2.612567 TTGCCGCAACATCGTCACC 61.613 57.895 0.38 0.00 0.00 4.02
2382 2563 1.067985 CCCTCATCCTCGACGATCATG 60.068 57.143 0.00 3.94 0.00 3.07
2478 2670 1.670967 GGCTTGCAGAACTCCAAATGC 60.671 52.381 0.00 0.00 39.14 3.56
2490 2682 1.134401 TCCAAATGCCCTCTCGACATC 60.134 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
378 416 1.213094 CGTCGAGGTTGCTTGTCGTT 61.213 55.000 0.00 0.00 35.22 3.85
426 464 1.135046 CTCGTGACTGCACTGAACAG 58.865 55.000 0.00 0.00 42.93 3.16
429 467 0.317854 CGTCTCGTGACTGCACTGAA 60.318 55.000 15.02 0.00 42.93 3.02
524 562 0.889994 TATAACGTGACCAGTGGCGT 59.110 50.000 9.78 8.40 39.37 5.68
1483 1521 0.246635 TCTGACTAAGGCTTGGACGC 59.753 55.000 18.10 6.75 0.00 5.19
1507 1545 6.263842 AGAAGATCACAGAAGCAATTTTCACA 59.736 34.615 0.00 0.00 0.00 3.58
1583 1621 6.088541 TGTGGAGTAGGAGTAGGATTTAGT 57.911 41.667 0.00 0.00 0.00 2.24
1655 1704 1.135083 CACTACTGGTCGCTGGTTAGG 60.135 57.143 0.00 0.00 0.00 2.69
1665 1714 4.792189 CGTAAAACGAGATCACTACTGGTC 59.208 45.833 0.00 0.00 46.05 4.02
1740 1789 5.185056 AGAGTTTATCGGTTTGGGAATTTGG 59.815 40.000 0.00 0.00 0.00 3.28
1777 1826 5.339008 AACTAAAGTATGTGAGCATCGGA 57.661 39.130 0.00 0.00 38.61 4.55
1779 1828 7.060600 TGAAAACTAAAGTATGTGAGCATCG 57.939 36.000 0.00 0.00 38.61 3.84
1789 1838 9.747898 TGGTGGACATAATGAAAACTAAAGTAT 57.252 29.630 0.00 0.00 0.00 2.12
1790 1839 9.226606 CTGGTGGACATAATGAAAACTAAAGTA 57.773 33.333 0.00 0.00 0.00 2.24
1791 1840 7.176690 CCTGGTGGACATAATGAAAACTAAAGT 59.823 37.037 0.00 0.00 34.57 2.66
1792 1841 7.176690 ACCTGGTGGACATAATGAAAACTAAAG 59.823 37.037 0.00 0.00 37.04 1.85
1793 1842 7.007723 ACCTGGTGGACATAATGAAAACTAAA 58.992 34.615 0.00 0.00 37.04 1.85
1794 1843 6.548321 ACCTGGTGGACATAATGAAAACTAA 58.452 36.000 0.00 0.00 37.04 2.24
1796 1845 4.998051 ACCTGGTGGACATAATGAAAACT 58.002 39.130 0.00 0.00 37.04 2.66
1814 1871 2.159170 CGGAAGCTCTTTCTCCTACCTG 60.159 54.545 0.10 0.00 36.03 4.00
1816 1873 2.100989 TCGGAAGCTCTTTCTCCTACC 58.899 52.381 0.10 0.00 36.03 3.18
2009 2087 3.002246 CAGAGTTGCTTTGCGTGAGTTAA 59.998 43.478 0.00 0.00 0.00 2.01
2010 2088 2.543848 CAGAGTTGCTTTGCGTGAGTTA 59.456 45.455 0.00 0.00 0.00 2.24
2011 2089 1.331756 CAGAGTTGCTTTGCGTGAGTT 59.668 47.619 0.00 0.00 0.00 3.01
2012 2090 0.940126 CAGAGTTGCTTTGCGTGAGT 59.060 50.000 0.00 0.00 0.00 3.41
2013 2091 0.385223 GCAGAGTTGCTTTGCGTGAG 60.385 55.000 0.00 0.00 46.95 3.51
2014 2092 1.648720 GCAGAGTTGCTTTGCGTGA 59.351 52.632 0.00 0.00 46.95 4.35
2015 2093 4.216963 GCAGAGTTGCTTTGCGTG 57.783 55.556 0.00 0.00 46.95 5.34
2025 2103 2.291800 ACCTTGCCCAATATGCAGAGTT 60.292 45.455 0.00 0.00 40.35 3.01
2027 2105 2.062971 ACCTTGCCCAATATGCAGAG 57.937 50.000 0.00 0.00 40.35 3.35
2028 2106 2.530460 AACCTTGCCCAATATGCAGA 57.470 45.000 0.00 0.00 40.35 4.26
2029 2107 2.624838 CCTAACCTTGCCCAATATGCAG 59.375 50.000 0.00 0.00 40.35 4.41
2030 2108 2.665165 CCTAACCTTGCCCAATATGCA 58.335 47.619 0.00 0.00 36.84 3.96
2031 2109 1.963515 CCCTAACCTTGCCCAATATGC 59.036 52.381 0.00 0.00 0.00 3.14
2032 2110 1.963515 GCCCTAACCTTGCCCAATATG 59.036 52.381 0.00 0.00 0.00 1.78
2062 2151 1.067846 GGAGAAAATTTGCGGGTCACC 60.068 52.381 0.00 0.00 0.00 4.02
2075 2164 1.347707 ACAGACGGATGCTGGAGAAAA 59.652 47.619 0.00 0.00 37.69 2.29
2080 2169 1.609210 TCCACAGACGGATGCTGGA 60.609 57.895 0.00 8.37 37.69 3.86
2081 2170 1.448540 GTCCACAGACGGATGCTGG 60.449 63.158 0.00 0.00 37.41 4.85
2083 2172 1.293498 GTGTCCACAGACGGATGCT 59.707 57.895 0.00 0.00 46.74 3.79
2114 2204 2.270850 GGCTACGGTTGGATGGCA 59.729 61.111 0.00 0.00 0.00 4.92
2116 2206 2.895372 GCGGCTACGGTTGGATGG 60.895 66.667 0.00 0.00 41.36 3.51
2133 2223 2.549064 TGAGGAATGCCGGATGTATG 57.451 50.000 5.05 0.00 39.96 2.39
2142 2232 9.521503 GACTTTAAGAAAAATATGAGGAATGCC 57.478 33.333 0.00 0.00 0.00 4.40
2144 2234 9.722056 CGGACTTTAAGAAAAATATGAGGAATG 57.278 33.333 0.00 0.00 0.00 2.67
2145 2235 8.406297 GCGGACTTTAAGAAAAATATGAGGAAT 58.594 33.333 0.00 0.00 0.00 3.01
2148 2238 6.967199 GTGCGGACTTTAAGAAAAATATGAGG 59.033 38.462 0.00 0.00 0.00 3.86
2151 2241 6.539324 TCGTGCGGACTTTAAGAAAAATATG 58.461 36.000 5.27 0.00 0.00 1.78
2153 2243 6.369340 TGATCGTGCGGACTTTAAGAAAAATA 59.631 34.615 5.27 0.00 0.00 1.40
2156 2246 4.059511 TGATCGTGCGGACTTTAAGAAAA 58.940 39.130 5.27 0.00 0.00 2.29
2157 2247 3.655486 TGATCGTGCGGACTTTAAGAAA 58.345 40.909 5.27 0.00 0.00 2.52
2158 2248 3.306917 TGATCGTGCGGACTTTAAGAA 57.693 42.857 5.27 0.00 0.00 2.52
2159 2249 3.306917 TTGATCGTGCGGACTTTAAGA 57.693 42.857 5.27 0.00 0.00 2.10
2160 2250 4.600012 ATTTGATCGTGCGGACTTTAAG 57.400 40.909 5.27 0.00 0.00 1.85
2161 2251 4.033587 GCTATTTGATCGTGCGGACTTTAA 59.966 41.667 5.27 0.00 0.00 1.52
2163 2253 2.351726 GCTATTTGATCGTGCGGACTTT 59.648 45.455 5.27 0.00 0.00 2.66
2169 2259 1.083401 GCGGCTATTTGATCGTGCG 60.083 57.895 0.00 0.00 0.00 5.34
2172 2262 0.588252 GCATGCGGCTATTTGATCGT 59.412 50.000 0.00 0.00 40.25 3.73
2173 2263 0.587768 TGCATGCGGCTATTTGATCG 59.412 50.000 14.09 0.00 45.15 3.69
2174 2264 2.780065 TTGCATGCGGCTATTTGATC 57.220 45.000 14.09 0.00 45.15 2.92
2175 2265 2.223876 CCTTTGCATGCGGCTATTTGAT 60.224 45.455 14.09 0.00 45.15 2.57
2176 2266 1.134753 CCTTTGCATGCGGCTATTTGA 59.865 47.619 14.09 0.00 45.15 2.69
2177 2267 1.563111 CCTTTGCATGCGGCTATTTG 58.437 50.000 14.09 0.00 45.15 2.32
2178 2268 0.461135 CCCTTTGCATGCGGCTATTT 59.539 50.000 14.09 0.00 45.15 1.40
2179 2269 0.684153 ACCCTTTGCATGCGGCTATT 60.684 50.000 14.09 0.00 45.15 1.73
2180 2270 0.182537 TACCCTTTGCATGCGGCTAT 59.817 50.000 14.09 0.00 45.15 2.97
2181 2271 0.746563 GTACCCTTTGCATGCGGCTA 60.747 55.000 14.09 0.00 45.15 3.93
2182 2272 2.046285 GTACCCTTTGCATGCGGCT 61.046 57.895 14.09 0.00 45.15 5.52
2183 2273 1.872197 TTGTACCCTTTGCATGCGGC 61.872 55.000 14.09 0.00 45.13 6.53
2184 2274 0.600557 TTTGTACCCTTTGCATGCGG 59.399 50.000 14.09 10.56 0.00 5.69
2185 2275 1.696988 GTTTGTACCCTTTGCATGCG 58.303 50.000 14.09 0.00 0.00 4.73
2186 2276 1.000717 ACGTTTGTACCCTTTGCATGC 60.001 47.619 11.82 11.82 0.00 4.06
2187 2277 3.243234 TGAACGTTTGTACCCTTTGCATG 60.243 43.478 0.46 0.00 0.00 4.06
2188 2278 2.952978 TGAACGTTTGTACCCTTTGCAT 59.047 40.909 0.46 0.00 0.00 3.96
2189 2279 2.366533 TGAACGTTTGTACCCTTTGCA 58.633 42.857 0.46 0.00 0.00 4.08
2190 2280 3.423996 TTGAACGTTTGTACCCTTTGC 57.576 42.857 0.46 0.00 0.00 3.68
2191 2281 5.627780 GCTATTTGAACGTTTGTACCCTTTG 59.372 40.000 0.46 0.00 0.00 2.77
2192 2282 5.278610 GGCTATTTGAACGTTTGTACCCTTT 60.279 40.000 0.46 0.00 0.00 3.11
2193 2283 4.216902 GGCTATTTGAACGTTTGTACCCTT 59.783 41.667 0.46 0.00 0.00 3.95
2194 2284 3.754850 GGCTATTTGAACGTTTGTACCCT 59.245 43.478 0.46 0.00 0.00 4.34
2195 2285 3.425227 CGGCTATTTGAACGTTTGTACCC 60.425 47.826 0.46 0.00 0.00 3.69
2196 2286 3.739494 CGGCTATTTGAACGTTTGTACC 58.261 45.455 0.46 0.00 0.00 3.34
2197 2287 3.158268 GCGGCTATTTGAACGTTTGTAC 58.842 45.455 0.46 0.00 0.00 2.90
2198 2288 2.806818 TGCGGCTATTTGAACGTTTGTA 59.193 40.909 0.46 0.00 0.00 2.41
2199 2289 1.604755 TGCGGCTATTTGAACGTTTGT 59.395 42.857 0.46 0.00 0.00 2.83
2200 2290 2.323939 TGCGGCTATTTGAACGTTTG 57.676 45.000 0.46 0.00 0.00 2.93
2201 2291 2.862512 CATGCGGCTATTTGAACGTTT 58.137 42.857 0.46 0.00 0.00 3.60
2202 2292 1.467374 GCATGCGGCTATTTGAACGTT 60.467 47.619 0.00 0.00 40.25 3.99
2206 2296 0.101040 GCTGCATGCGGCTATTTGAA 59.899 50.000 38.27 5.55 44.39 2.69
2215 2305 1.368641 TAAACTAGTGCTGCATGCGG 58.631 50.000 22.66 22.66 46.63 5.69
2263 2353 3.855255 TGAGGAGACAACAATGTTGGA 57.145 42.857 27.15 2.49 40.74 3.53
2275 2365 1.003580 TCCAGCCACATTTGAGGAGAC 59.996 52.381 0.00 0.00 0.00 3.36
2291 2472 0.905357 ACTTCCGGACCAGAATCCAG 59.095 55.000 1.83 0.00 38.87 3.86
2303 2484 3.258622 GGGTGATCCTATCTAACTTCCGG 59.741 52.174 0.00 0.00 0.00 5.14
2306 2487 6.426646 ACATGGGTGATCCTATCTAACTTC 57.573 41.667 0.00 0.00 32.46 3.01
2312 2493 4.560739 TGAGAACATGGGTGATCCTATCT 58.439 43.478 0.00 0.00 32.46 1.98
2352 2533 1.482593 GAGGATGAGGGTGACGATGTT 59.517 52.381 0.00 0.00 0.00 2.71
2363 2544 1.611006 ACATGATCGTCGAGGATGAGG 59.389 52.381 24.24 19.71 30.72 3.86
2382 2563 5.258685 CATGTTGTTTGATCATGCACAAC 57.741 39.130 25.26 25.26 46.12 3.32
2426 2607 1.304630 TTCGTGGACCTGGATCCGA 60.305 57.895 7.39 0.00 42.24 4.55
2465 2657 1.065854 CGAGAGGGCATTTGGAGTTCT 60.066 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.