Multiple sequence alignment - TraesCS2D01G408100

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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 TraesCS2D01G408100 chr2D 100.000 2498 0 0 1 2498 523027514 523030011 0.000000e+00 4614
1 TraesCS2D01G408100 chr2D 77.491 271 61 0 981 1251 220670835 220671105 1.990000e-36 163
2 TraesCS2D01G408100 chr2A 93.620 1489 55 18 540 2008 668242310 668243778 0.000000e+00 2187
3 TraesCS2D01G408100 chr2A 91.107 551 35 7 1 551 668241737 668242273 0.000000e+00 734
4 TraesCS2D01G408100 chr2A 87.117 163 12 8 2284 2440 711470672 711470513 2.550000e-40 176
5 TraesCS2D01G408100 chr2B 89.115 1718 97 37 323 2008 616933969 616935628 0.000000e+00 2054
6 TraesCS2D01G408100 chr2B 91.385 325 16 7 1 324 616933576 616933889 3.820000e-118 435
7 TraesCS2D01G408100 chr2B 76.534 277 61 4 981 1255 290519726 290520000 5.570000e-32 148
8 TraesCS2D01G408100 chr5B 86.992 369 46 2 2073 2440 6930901 6930534 4.970000e-112 414
9 TraesCS2D01G408100 chr5B 81.934 393 45 7 2051 2440 695897191 695896822 2.410000e-80 309
10 TraesCS2D01G408100 chr7A 83.415 410 48 11 2050 2440 165924095 165924503 1.830000e-96 363
11 TraesCS2D01G408100 chr4B 81.796 412 50 8 2053 2440 462771279 462770869 3.100000e-84 322
12 TraesCS2D01G408100 chr4B 81.564 179 29 4 1075 1251 475811240 475811416 7.200000e-31 145
13 TraesCS2D01G408100 chr6B 85.616 292 37 4 2053 2342 647175953 647176241 4.040000e-78 302
14 TraesCS2D01G408100 chr6B 83.333 276 44 2 977 1251 502484423 502484149 1.150000e-63 254
15 TraesCS2D01G408100 chr3B 87.597 258 29 3 2087 2342 32757357 32757613 1.880000e-76 296
16 TraesCS2D01G408100 chr7B 88.571 245 25 3 2051 2294 750145442 750145684 6.760000e-76 294
17 TraesCS2D01G408100 chr7D 89.270 233 23 2 2052 2283 3567169 3566938 8.740000e-75 291
18 TraesCS2D01G408100 chr7D 89.441 161 17 0 2338 2498 62142225 62142385 1.170000e-48 204
19 TraesCS2D01G408100 chr7D 78.916 332 37 16 2199 2498 62399678 62400008 7.050000e-46 195
20 TraesCS2D01G408100 chr1D 79.254 429 62 15 2085 2498 217974131 217973715 8.800000e-70 274
21 TraesCS2D01G408100 chr6D 80.163 368 57 15 2060 2419 466512192 466511833 6.850000e-66 261
22 TraesCS2D01G408100 chr6D 82.909 275 47 0 977 1251 320228156 320228430 5.340000e-62 248
23 TraesCS2D01G408100 chr6A 82.182 275 49 0 977 1251 457685918 457686192 1.150000e-58 237
24 TraesCS2D01G408100 chr1B 87.143 140 17 1 2355 2494 311673794 311673656 9.250000e-35 158
25 TraesCS2D01G408100 chr1B 82.993 147 24 1 2345 2490 497309435 497309289 5.610000e-27 132
26 TraesCS2D01G408100 chr5D 89.916 119 10 2 2325 2442 27849165 27849048 4.300000e-33 152
27 TraesCS2D01G408100 chr4A 81.319 182 30 4 1072 1251 68689364 68689543 7.200000e-31 145
28 TraesCS2D01G408100 chr4D 81.006 179 30 4 1075 1251 387441775 387441951 3.350000e-29 139


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 TraesCS2D01G408100 chr2D 523027514 523030011 2497 False 4614.0 4614 100.0000 1 2498 1 chr2D.!!$F2 2497
1 TraesCS2D01G408100 chr2A 668241737 668243778 2041 False 1460.5 2187 92.3635 1 2008 2 chr2A.!!$F1 2007
2 TraesCS2D01G408100 chr2B 616933576 616935628 2052 False 1244.5 2054 90.2500 1 2008 2 chr2B.!!$F2 2007

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
974 1122 0.498095 GTGTTGTTTGCGTGATTGCG 59.502 50.0 0.0 0.0 37.81 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2392 0.106894 GCCGGAGAAACCCTAGATGG 59.893 60.0 5.05 0.0 34.64 3.51 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
114 115 0.600057 AAGCAAAGCAACCTAGCAGC 59.400 50.000 0.00 0.00 36.85 5.25
125 126 1.299014 CTAGCAGCGGCGAGAAGAG 60.299 63.158 12.98 0.00 44.53 2.85
127 128 2.490217 GCAGCGGCGAGAAGAGTA 59.510 61.111 12.98 0.00 0.00 2.59
300 301 7.168972 GCAATGAGAATGTATCTGTCTACACTC 59.831 40.741 0.00 0.00 38.96 3.51
338 420 9.224267 AGATGTCATATAATTTGAAATCTCCGG 57.776 33.333 5.73 0.00 42.09 5.14
340 422 8.746052 TGTCATATAATTTGAAATCTCCGGTT 57.254 30.769 0.00 0.00 0.00 4.44
343 425 9.184523 TCATATAATTTGAAATCTCCGGTTGTT 57.815 29.630 0.00 0.00 0.00 2.83
356 438 2.069273 CGGTTGTTCATCAGTCCTCAC 58.931 52.381 0.00 0.00 0.00 3.51
361 443 3.154710 TGTTCATCAGTCCTCACTACGT 58.845 45.455 0.00 0.00 0.00 3.57
382 464 7.266922 ACGTTATGGTTACACAGAATTTGTT 57.733 32.000 0.00 0.00 38.16 2.83
390 472 9.733556 TGGTTACACAGAATTTGTTATATGACT 57.266 29.630 0.00 0.00 38.16 3.41
396 478 9.669353 CACAGAATTTGTTATATGACTTATGGC 57.331 33.333 0.00 0.00 38.16 4.40
397 479 8.850156 ACAGAATTTGTTATATGACTTATGGCC 58.150 33.333 0.00 0.00 36.31 5.36
621 767 3.257561 CATGGCTCTCGCGAACGG 61.258 66.667 11.33 4.17 40.63 4.44
622 768 3.449227 ATGGCTCTCGCGAACGGA 61.449 61.111 11.33 2.88 40.63 4.69
623 769 3.701604 ATGGCTCTCGCGAACGGAC 62.702 63.158 11.33 5.86 40.63 4.79
668 814 1.539124 AACCGCCCCTCTTCTTCCT 60.539 57.895 0.00 0.00 0.00 3.36
669 815 1.554583 AACCGCCCCTCTTCTTCCTC 61.555 60.000 0.00 0.00 0.00 3.71
670 816 2.736826 CCGCCCCTCTTCTTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
689 835 2.102161 CCTAAAACGGCGGCATGC 59.898 61.111 13.24 9.90 45.38 4.06
947 1095 6.182627 TGATTGTTGATAATGAGGTGCTCTT 58.817 36.000 0.00 0.00 0.00 2.85
955 1103 1.679139 TGAGGTGCTCTTGTTGTTGG 58.321 50.000 0.00 0.00 0.00 3.77
965 1113 3.321497 TCTTGTTGTTGGTGTTGTTTGC 58.679 40.909 0.00 0.00 0.00 3.68
974 1122 0.498095 GTGTTGTTTGCGTGATTGCG 59.502 50.000 0.00 0.00 37.81 4.85
1250 1398 5.163364 GCAAGATCTTCTTCATCTCCTGGTA 60.163 44.000 4.57 0.00 33.78 3.25
1251 1399 6.279882 CAAGATCTTCTTCATCTCCTGGTAC 58.720 44.000 4.57 0.00 33.78 3.34
1252 1400 4.582656 AGATCTTCTTCATCTCCTGGTACG 59.417 45.833 0.00 0.00 0.00 3.67
1253 1401 3.698289 TCTTCTTCATCTCCTGGTACGT 58.302 45.455 0.00 0.00 0.00 3.57
1254 1402 3.444034 TCTTCTTCATCTCCTGGTACGTG 59.556 47.826 0.00 0.00 0.00 4.49
1292 1440 0.325602 TGCATGCATGGTCTCTCACA 59.674 50.000 27.34 11.60 0.00 3.58
1295 1443 0.742281 ATGCATGGTCTCTCACACGC 60.742 55.000 0.00 0.00 0.00 5.34
1330 1498 0.320771 GAACGATCTGTGCCTGTGGT 60.321 55.000 0.00 0.00 0.00 4.16
1331 1499 0.603707 AACGATCTGTGCCTGTGGTG 60.604 55.000 0.00 0.00 0.00 4.17
1650 1822 6.926272 CCTCCTTGTAAACTAGACATAGATGC 59.074 42.308 0.00 0.00 32.93 3.91
1742 1917 3.368843 AGGTGCGTACTACGTAAATTTGC 59.631 43.478 10.23 0.00 44.73 3.68
1812 1988 7.323656 CACTTATCCACGAAAAGACAAACATTC 59.676 37.037 0.00 0.00 0.00 2.67
1847 2023 1.139853 CCTGGTCTCCTTATGTGCTCC 59.860 57.143 0.00 0.00 0.00 4.70
1857 2033 3.119352 CCTTATGTGCTCCTTCCAAAAGC 60.119 47.826 0.00 0.00 36.56 3.51
1864 2040 0.540365 TCCTTCCAAAAGCAGCCCTG 60.540 55.000 0.00 0.00 0.00 4.45
1915 2091 5.567552 GCATTTGTCTTCTGCTAGTGATTC 58.432 41.667 0.00 0.00 33.15 2.52
1916 2092 5.353678 GCATTTGTCTTCTGCTAGTGATTCT 59.646 40.000 0.00 0.00 33.15 2.40
1917 2093 6.128063 GCATTTGTCTTCTGCTAGTGATTCTT 60.128 38.462 0.00 0.00 33.15 2.52
2002 2182 2.130193 AGGGCATCTCCAAAGCAGATA 58.870 47.619 0.00 0.00 36.21 1.98
2008 2188 5.238214 GGCATCTCCAAAGCAGATACTTAAG 59.762 44.000 0.00 0.00 34.01 1.85
2009 2189 6.051717 GCATCTCCAAAGCAGATACTTAAGA 58.948 40.000 10.09 0.00 0.00 2.10
2010 2190 6.018343 GCATCTCCAAAGCAGATACTTAAGAC 60.018 42.308 10.09 0.41 0.00 3.01
2011 2191 6.605471 TCTCCAAAGCAGATACTTAAGACA 57.395 37.500 10.09 0.00 0.00 3.41
2012 2192 7.187824 TCTCCAAAGCAGATACTTAAGACAT 57.812 36.000 10.09 1.63 0.00 3.06
2013 2193 7.044181 TCTCCAAAGCAGATACTTAAGACATG 58.956 38.462 10.09 3.67 0.00 3.21
2014 2194 6.946340 TCCAAAGCAGATACTTAAGACATGA 58.054 36.000 10.09 0.00 0.00 3.07
2015 2195 7.394016 TCCAAAGCAGATACTTAAGACATGAA 58.606 34.615 10.09 0.00 0.00 2.57
2016 2196 8.049117 TCCAAAGCAGATACTTAAGACATGAAT 58.951 33.333 10.09 0.00 0.00 2.57
2017 2197 9.330063 CCAAAGCAGATACTTAAGACATGAATA 57.670 33.333 10.09 0.00 0.00 1.75
2045 2225 9.787532 TTTGCAAGTAATTAAATACAGCAGATC 57.212 29.630 15.72 0.00 38.98 2.75
2046 2226 7.930217 TGCAAGTAATTAAATACAGCAGATCC 58.070 34.615 13.56 0.00 35.54 3.36
2047 2227 7.072030 GCAAGTAATTAAATACAGCAGATCCG 58.928 38.462 11.18 0.00 32.62 4.18
2048 2228 7.576236 CAAGTAATTAAATACAGCAGATCCGG 58.424 38.462 0.00 0.00 0.00 5.14
2049 2229 5.701290 AGTAATTAAATACAGCAGATCCGGC 59.299 40.000 0.00 0.00 0.00 6.13
2050 2230 2.543777 TAAATACAGCAGATCCGGCC 57.456 50.000 0.00 0.00 0.00 6.13
2051 2231 0.179018 AAATACAGCAGATCCGGCCC 60.179 55.000 0.00 0.00 0.00 5.80
2052 2232 2.056906 AATACAGCAGATCCGGCCCC 62.057 60.000 0.00 0.00 0.00 5.80
2053 2233 2.972589 ATACAGCAGATCCGGCCCCT 62.973 60.000 0.00 0.00 0.00 4.79
2054 2234 4.247380 CAGCAGATCCGGCCCCTC 62.247 72.222 0.00 0.00 0.00 4.30
2055 2235 4.488911 AGCAGATCCGGCCCCTCT 62.489 66.667 0.00 0.00 0.00 3.69
2056 2236 3.934962 GCAGATCCGGCCCCTCTC 61.935 72.222 0.00 0.00 0.00 3.20
2057 2237 3.610669 CAGATCCGGCCCCTCTCG 61.611 72.222 0.00 0.00 0.00 4.04
2058 2238 3.822035 AGATCCGGCCCCTCTCGA 61.822 66.667 0.00 0.00 0.00 4.04
2059 2239 3.607661 GATCCGGCCCCTCTCGAC 61.608 72.222 0.00 0.00 0.00 4.20
2065 2245 4.131088 GCCCCTCTCGACCGTGAC 62.131 72.222 0.00 0.00 0.00 3.67
2066 2246 3.450115 CCCCTCTCGACCGTGACC 61.450 72.222 0.00 0.00 0.00 4.02
2067 2247 3.812019 CCCTCTCGACCGTGACCG 61.812 72.222 0.00 0.00 0.00 4.79
2068 2248 4.477975 CCTCTCGACCGTGACCGC 62.478 72.222 0.00 0.00 0.00 5.68
2069 2249 4.813526 CTCTCGACCGTGACCGCG 62.814 72.222 0.00 0.00 0.00 6.46
2111 2291 3.412408 GCCTCCCCTCTTCCCCAC 61.412 72.222 0.00 0.00 0.00 4.61
2112 2292 3.083997 CCTCCCCTCTTCCCCACG 61.084 72.222 0.00 0.00 0.00 4.94
2113 2293 2.038975 CTCCCCTCTTCCCCACGA 59.961 66.667 0.00 0.00 0.00 4.35
2114 2294 2.038975 TCCCCTCTTCCCCACGAG 59.961 66.667 0.00 0.00 0.00 4.18
2115 2295 3.787001 CCCCTCTTCCCCACGAGC 61.787 72.222 0.00 0.00 0.00 5.03
2116 2296 4.148825 CCCTCTTCCCCACGAGCG 62.149 72.222 0.00 0.00 0.00 5.03
2117 2297 3.382832 CCTCTTCCCCACGAGCGT 61.383 66.667 0.00 0.00 0.00 5.07
2118 2298 2.657237 CTCTTCCCCACGAGCGTT 59.343 61.111 0.00 0.00 0.00 4.84
2119 2299 1.446272 CTCTTCCCCACGAGCGTTC 60.446 63.158 0.00 0.00 0.00 3.95
2120 2300 2.434359 CTTCCCCACGAGCGTTCC 60.434 66.667 0.00 0.00 0.00 3.62
2121 2301 3.952628 CTTCCCCACGAGCGTTCCC 62.953 68.421 0.00 0.00 0.00 3.97
2125 2305 4.323477 CCACGAGCGTTCCCCCAA 62.323 66.667 0.00 0.00 0.00 4.12
2126 2306 2.046314 CACGAGCGTTCCCCCAAT 60.046 61.111 0.00 0.00 0.00 3.16
2127 2307 2.106683 CACGAGCGTTCCCCCAATC 61.107 63.158 0.00 0.00 0.00 2.67
2128 2308 2.291043 ACGAGCGTTCCCCCAATCT 61.291 57.895 0.00 0.00 0.00 2.40
2129 2309 1.521681 CGAGCGTTCCCCCAATCTC 60.522 63.158 0.00 0.00 0.00 2.75
2130 2310 1.908483 GAGCGTTCCCCCAATCTCT 59.092 57.895 0.00 0.00 0.00 3.10
2131 2311 0.253327 GAGCGTTCCCCCAATCTCTT 59.747 55.000 0.00 0.00 0.00 2.85
2132 2312 0.253327 AGCGTTCCCCCAATCTCTTC 59.747 55.000 0.00 0.00 0.00 2.87
2133 2313 0.748367 GCGTTCCCCCAATCTCTTCC 60.748 60.000 0.00 0.00 0.00 3.46
2134 2314 0.618458 CGTTCCCCCAATCTCTTCCA 59.382 55.000 0.00 0.00 0.00 3.53
2135 2315 1.679032 CGTTCCCCCAATCTCTTCCAC 60.679 57.143 0.00 0.00 0.00 4.02
2136 2316 0.999712 TTCCCCCAATCTCTTCCACC 59.000 55.000 0.00 0.00 0.00 4.61
2137 2317 0.121197 TCCCCCAATCTCTTCCACCT 59.879 55.000 0.00 0.00 0.00 4.00
2138 2318 0.548510 CCCCCAATCTCTTCCACCTC 59.451 60.000 0.00 0.00 0.00 3.85
2139 2319 0.548510 CCCCAATCTCTTCCACCTCC 59.451 60.000 0.00 0.00 0.00 4.30
2140 2320 0.548510 CCCAATCTCTTCCACCTCCC 59.451 60.000 0.00 0.00 0.00 4.30
2141 2321 1.589414 CCAATCTCTTCCACCTCCCT 58.411 55.000 0.00 0.00 0.00 4.20
2142 2322 1.211457 CCAATCTCTTCCACCTCCCTG 59.789 57.143 0.00 0.00 0.00 4.45
2143 2323 0.915364 AATCTCTTCCACCTCCCTGC 59.085 55.000 0.00 0.00 0.00 4.85
2144 2324 0.985490 ATCTCTTCCACCTCCCTGCC 60.985 60.000 0.00 0.00 0.00 4.85
2145 2325 3.003173 TCTTCCACCTCCCTGCCG 61.003 66.667 0.00 0.00 0.00 5.69
2146 2326 4.785453 CTTCCACCTCCCTGCCGC 62.785 72.222 0.00 0.00 0.00 6.53
2216 2396 4.522975 CCCCGGCCCTTTCCCATC 62.523 72.222 0.00 0.00 0.00 3.51
2217 2397 3.420482 CCCGGCCCTTTCCCATCT 61.420 66.667 0.00 0.00 0.00 2.90
2218 2398 2.076184 CCCGGCCCTTTCCCATCTA 61.076 63.158 0.00 0.00 0.00 1.98
2219 2399 1.451936 CCGGCCCTTTCCCATCTAG 59.548 63.158 0.00 0.00 0.00 2.43
2220 2400 1.451936 CGGCCCTTTCCCATCTAGG 59.548 63.158 0.00 0.00 37.03 3.02
2231 2411 0.106894 CCATCTAGGGTTTCTCCGGC 59.893 60.000 0.00 0.00 37.00 6.13
2232 2412 0.249489 CATCTAGGGTTTCTCCGGCG 60.249 60.000 0.00 0.00 37.00 6.46
2233 2413 2.029307 ATCTAGGGTTTCTCCGGCGC 62.029 60.000 0.00 0.00 37.00 6.53
2234 2414 4.137872 TAGGGTTTCTCCGGCGCG 62.138 66.667 0.00 0.00 37.00 6.86
2238 2418 3.774702 GTTTCTCCGGCGCGTGAC 61.775 66.667 8.43 0.00 0.00 3.67
2263 2443 3.691342 CTCCGGGCGGTGTCTTCA 61.691 66.667 0.00 0.00 36.47 3.02
2264 2444 3.649277 CTCCGGGCGGTGTCTTCAG 62.649 68.421 0.00 0.00 36.47 3.02
2265 2445 4.760047 CCGGGCGGTGTCTTCAGG 62.760 72.222 0.00 0.00 0.00 3.86
2271 2451 4.373116 GGTGTCTTCAGGCGGCGA 62.373 66.667 12.98 0.76 0.00 5.54
2272 2452 3.112709 GTGTCTTCAGGCGGCGAC 61.113 66.667 12.98 8.50 0.00 5.19
2363 2543 4.227134 CCGCCCGACCCAGATCTG 62.227 72.222 16.24 16.24 0.00 2.90
2372 2552 4.672251 CCAGATCTGGGCCCTTTG 57.328 61.111 31.14 13.48 46.81 2.77
2373 2553 1.076485 CCAGATCTGGGCCCTTTGG 60.076 63.158 31.14 18.29 46.81 3.28
2374 2554 2.578586 CCAGATCTGGGCCCTTTGGG 62.579 65.000 31.14 13.16 46.81 4.12
2383 2563 3.768374 CCCTTTGGGCCCCATCTA 58.232 61.111 22.27 0.00 35.35 1.98
2384 2564 1.538666 CCCTTTGGGCCCCATCTAG 59.461 63.158 22.27 8.99 35.35 2.43
2385 2565 1.538666 CCTTTGGGCCCCATCTAGG 59.461 63.158 22.27 14.44 31.53 3.02
2394 2574 3.142393 CCATCTAGGCTGGGACGG 58.858 66.667 0.00 0.00 38.10 4.79
2395 2575 2.511452 CCATCTAGGCTGGGACGGG 61.511 68.421 0.00 0.00 33.56 5.28
2403 2583 4.394712 CTGGGACGGGCTGGTGAC 62.395 72.222 0.00 0.00 0.00 3.67
2441 2621 4.087892 CCTCAGGAGGCGGTGGTG 62.088 72.222 1.73 0.00 42.44 4.17
2442 2622 4.087892 CTCAGGAGGCGGTGGTGG 62.088 72.222 0.00 0.00 0.00 4.61
2443 2623 4.954118 TCAGGAGGCGGTGGTGGT 62.954 66.667 0.00 0.00 0.00 4.16
2444 2624 4.704833 CAGGAGGCGGTGGTGGTG 62.705 72.222 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 4.619160 GCTGCTAGGTTGCTTTGCTTTAAT 60.619 41.667 0.00 0.00 0.00 1.40
92 93 3.305335 GCTGCTAGGTTGCTTTGCTTTAA 60.305 43.478 0.00 0.00 0.00 1.52
93 94 2.228822 GCTGCTAGGTTGCTTTGCTTTA 59.771 45.455 0.00 0.00 0.00 1.85
114 115 1.226717 GCTGGTACTCTTCTCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
125 126 4.134563 TCCTTTTGACTTTGAGCTGGTAC 58.865 43.478 0.00 0.00 0.00 3.34
127 128 3.297134 TCCTTTTGACTTTGAGCTGGT 57.703 42.857 0.00 0.00 0.00 4.00
300 301 7.728847 TTATATGACATCTTTCCAACATCGG 57.271 36.000 0.00 0.00 0.00 4.18
333 415 1.276421 AGGACTGATGAACAACCGGAG 59.724 52.381 9.46 1.96 32.92 4.63
336 418 2.069273 GTGAGGACTGATGAACAACCG 58.931 52.381 0.00 0.00 32.92 4.44
338 420 3.921021 CGTAGTGAGGACTGATGAACAAC 59.079 47.826 0.00 0.00 33.21 3.32
340 422 3.154710 ACGTAGTGAGGACTGATGAACA 58.845 45.455 0.00 0.00 42.51 3.18
343 425 4.338400 CCATAACGTAGTGAGGACTGATGA 59.662 45.833 0.00 0.00 45.00 2.92
356 438 8.025243 ACAAATTCTGTGTAACCATAACGTAG 57.975 34.615 0.00 0.00 36.69 3.51
382 464 4.474651 CCCCATGAGGCCATAAGTCATATA 59.525 45.833 5.01 0.00 29.64 0.86
387 469 0.846693 ACCCCATGAGGCCATAAGTC 59.153 55.000 5.01 0.00 0.00 3.01
389 471 1.496429 AGAACCCCATGAGGCCATAAG 59.504 52.381 5.01 0.00 0.00 1.73
390 472 1.607225 AGAACCCCATGAGGCCATAA 58.393 50.000 5.01 0.00 0.00 1.90
391 473 2.054799 GTAGAACCCCATGAGGCCATA 58.945 52.381 5.01 0.00 0.00 2.74
392 474 0.846693 GTAGAACCCCATGAGGCCAT 59.153 55.000 5.01 0.00 0.00 4.40
393 475 1.622607 CGTAGAACCCCATGAGGCCA 61.623 60.000 5.01 0.00 0.00 5.36
394 476 1.146263 CGTAGAACCCCATGAGGCC 59.854 63.158 0.00 0.00 0.00 5.19
395 477 0.105039 CTCGTAGAACCCCATGAGGC 59.895 60.000 0.00 0.00 34.09 4.70
396 478 0.105039 GCTCGTAGAACCCCATGAGG 59.895 60.000 0.00 0.00 34.09 3.86
397 479 0.249073 CGCTCGTAGAACCCCATGAG 60.249 60.000 0.00 0.00 34.09 2.90
433 515 1.219646 CAAACCAACAATGCAGCCAC 58.780 50.000 0.00 0.00 0.00 5.01
440 522 4.554586 CGAATCGATGACAAACCAACAATG 59.445 41.667 0.00 0.00 0.00 2.82
504 586 8.785946 AGCACAGCAGCATTTTTATTTTATTTT 58.214 25.926 0.00 0.00 36.85 1.82
505 587 8.231837 CAGCACAGCAGCATTTTTATTTTATTT 58.768 29.630 0.00 0.00 36.85 1.40
506 588 7.388500 ACAGCACAGCAGCATTTTTATTTTATT 59.612 29.630 0.00 0.00 36.85 1.40
507 589 6.875195 ACAGCACAGCAGCATTTTTATTTTAT 59.125 30.769 0.00 0.00 36.85 1.40
513 595 2.350676 CGACAGCACAGCAGCATTTTTA 60.351 45.455 0.00 0.00 36.85 1.52
670 816 1.721487 CATGCCGCCGTTTTAGGAG 59.279 57.895 0.00 0.00 0.00 3.69
690 836 1.830847 ATCGCATGCATGGTGCCAT 60.831 52.632 27.34 6.94 44.23 4.40
691 837 2.440613 ATCGCATGCATGGTGCCA 60.441 55.556 27.34 4.55 44.23 4.92
692 838 2.027024 CATCGCATGCATGGTGCC 59.973 61.111 27.34 10.17 44.23 5.01
889 1035 5.913751 GGATCGAATCGAACCATCGTCGT 62.914 52.174 23.99 0.00 45.83 4.34
947 1095 1.000163 ACGCAAACAACACCAACAACA 60.000 42.857 0.00 0.00 0.00 3.33
955 1103 0.498095 CGCAATCACGCAAACAACAC 59.502 50.000 0.00 0.00 0.00 3.32
974 1122 3.093278 CCGAGTTCGCCTTGCATC 58.907 61.111 0.00 0.00 38.18 3.91
1250 1398 1.541310 ATGGATGGGTCACGTCACGT 61.541 55.000 0.00 0.00 42.36 4.49
1251 1399 0.806102 GATGGATGGGTCACGTCACG 60.806 60.000 0.00 0.00 36.81 4.35
1252 1400 0.462047 GGATGGATGGGTCACGTCAC 60.462 60.000 0.00 0.00 36.81 3.67
1253 1401 0.907230 TGGATGGATGGGTCACGTCA 60.907 55.000 0.00 0.00 36.81 4.35
1254 1402 0.469917 ATGGATGGATGGGTCACGTC 59.530 55.000 0.00 0.00 0.00 4.34
1295 1443 2.600420 TCGTTCACTAGCTACGTACTCG 59.400 50.000 5.92 6.45 43.34 4.18
1299 1447 4.033702 CACAGATCGTTCACTAGCTACGTA 59.966 45.833 5.92 0.00 36.70 3.57
1303 1451 2.099263 GGCACAGATCGTTCACTAGCTA 59.901 50.000 0.00 0.00 0.00 3.32
1389 1558 0.397941 TGAACCTGTCCTTGGAGCTG 59.602 55.000 0.00 0.00 0.00 4.24
1650 1822 2.414824 CGGGAAAGACAACGAGAGAGAG 60.415 54.545 0.00 0.00 0.00 3.20
1742 1917 1.897398 GCTTACACAACGAGCACGGG 61.897 60.000 8.74 2.10 44.46 5.28
1793 1969 4.202010 ACCAGAATGTTTGTCTTTTCGTGG 60.202 41.667 0.00 0.00 0.00 4.94
1812 1988 0.670162 CCAGGAGCAAAACACACCAG 59.330 55.000 0.00 0.00 0.00 4.00
1847 2023 1.203994 CATCAGGGCTGCTTTTGGAAG 59.796 52.381 0.00 0.00 35.92 3.46
1864 2040 5.886960 AACTTTTGGATAGTGTGAGCATC 57.113 39.130 0.00 0.00 0.00 3.91
1980 2160 0.815734 CTGCTTTGGAGATGCCCTTG 59.184 55.000 0.00 0.00 34.97 3.61
2019 2199 9.787532 GATCTGCTGTATTTAATTACTTGCAAA 57.212 29.630 19.08 12.72 34.50 3.68
2020 2200 8.405531 GGATCTGCTGTATTTAATTACTTGCAA 58.594 33.333 19.08 0.00 34.50 4.08
2021 2201 7.254761 CGGATCTGCTGTATTTAATTACTTGCA 60.255 37.037 18.28 18.28 34.11 4.08
2022 2202 7.072030 CGGATCTGCTGTATTTAATTACTTGC 58.928 38.462 8.54 11.56 0.00 4.01
2023 2203 7.576236 CCGGATCTGCTGTATTTAATTACTTG 58.424 38.462 0.00 3.98 0.00 3.16
2024 2204 6.204882 GCCGGATCTGCTGTATTTAATTACTT 59.795 38.462 5.05 0.00 0.00 2.24
2025 2205 5.701290 GCCGGATCTGCTGTATTTAATTACT 59.299 40.000 5.05 0.00 0.00 2.24
2026 2206 5.106673 GGCCGGATCTGCTGTATTTAATTAC 60.107 44.000 5.05 1.36 0.00 1.89
2027 2207 5.001232 GGCCGGATCTGCTGTATTTAATTA 58.999 41.667 5.05 0.00 0.00 1.40
2028 2208 3.821033 GGCCGGATCTGCTGTATTTAATT 59.179 43.478 5.05 0.00 0.00 1.40
2029 2209 3.412386 GGCCGGATCTGCTGTATTTAAT 58.588 45.455 5.05 0.00 0.00 1.40
2030 2210 2.486548 GGGCCGGATCTGCTGTATTTAA 60.487 50.000 5.05 0.00 0.00 1.52
2031 2211 1.071699 GGGCCGGATCTGCTGTATTTA 59.928 52.381 5.05 0.00 0.00 1.40
2032 2212 0.179018 GGGCCGGATCTGCTGTATTT 60.179 55.000 5.05 0.00 0.00 1.40
2033 2213 1.451936 GGGCCGGATCTGCTGTATT 59.548 57.895 5.05 0.00 0.00 1.89
2034 2214 2.520536 GGGGCCGGATCTGCTGTAT 61.521 63.158 5.05 0.00 0.00 2.29
2035 2215 3.161450 GGGGCCGGATCTGCTGTA 61.161 66.667 5.05 0.00 0.00 2.74
2037 2217 4.247380 GAGGGGCCGGATCTGCTG 62.247 72.222 5.05 0.00 0.00 4.41
2038 2218 4.488911 AGAGGGGCCGGATCTGCT 62.489 66.667 5.05 0.00 0.00 4.24
2039 2219 3.934962 GAGAGGGGCCGGATCTGC 61.935 72.222 5.05 0.00 0.00 4.26
2040 2220 3.610669 CGAGAGGGGCCGGATCTG 61.611 72.222 5.05 0.00 0.00 2.90
2041 2221 3.822035 TCGAGAGGGGCCGGATCT 61.822 66.667 5.05 1.36 0.00 2.75
2042 2222 3.607661 GTCGAGAGGGGCCGGATC 61.608 72.222 5.05 0.00 0.00 3.36
2048 2228 4.131088 GTCACGGTCGAGAGGGGC 62.131 72.222 0.00 0.00 0.00 5.80
2049 2229 3.450115 GGTCACGGTCGAGAGGGG 61.450 72.222 0.00 0.00 0.00 4.79
2050 2230 3.812019 CGGTCACGGTCGAGAGGG 61.812 72.222 0.00 0.00 36.18 4.30
2051 2231 4.477975 GCGGTCACGGTCGAGAGG 62.478 72.222 0.00 0.00 41.36 3.69
2052 2232 4.813526 CGCGGTCACGGTCGAGAG 62.814 72.222 0.00 0.00 41.36 3.20
2094 2274 3.412408 GTGGGGAAGAGGGGAGGC 61.412 72.222 0.00 0.00 0.00 4.70
2095 2275 3.083997 CGTGGGGAAGAGGGGAGG 61.084 72.222 0.00 0.00 0.00 4.30
2096 2276 2.038975 TCGTGGGGAAGAGGGGAG 59.961 66.667 0.00 0.00 0.00 4.30
2097 2277 2.038975 CTCGTGGGGAAGAGGGGA 59.961 66.667 0.00 0.00 0.00 4.81
2098 2278 3.787001 GCTCGTGGGGAAGAGGGG 61.787 72.222 0.00 0.00 35.19 4.79
2099 2279 4.148825 CGCTCGTGGGGAAGAGGG 62.149 72.222 0.00 0.00 40.21 4.30
2100 2280 2.837371 GAACGCTCGTGGGGAAGAGG 62.837 65.000 6.49 0.00 35.19 3.69
2101 2281 1.446272 GAACGCTCGTGGGGAAGAG 60.446 63.158 6.49 0.00 37.54 2.85
2102 2282 2.654877 GAACGCTCGTGGGGAAGA 59.345 61.111 6.49 0.00 0.00 2.87
2103 2283 2.434359 GGAACGCTCGTGGGGAAG 60.434 66.667 6.49 0.00 0.00 3.46
2104 2284 4.011517 GGGAACGCTCGTGGGGAA 62.012 66.667 6.49 0.00 0.00 3.97
2108 2288 3.622060 ATTGGGGGAACGCTCGTGG 62.622 63.158 0.00 0.00 45.02 4.94
2109 2289 2.046314 ATTGGGGGAACGCTCGTG 60.046 61.111 0.00 0.00 45.02 4.35
2110 2290 2.240162 GAGATTGGGGGAACGCTCGT 62.240 60.000 0.00 0.00 45.02 4.18
2111 2291 1.521681 GAGATTGGGGGAACGCTCG 60.522 63.158 0.00 0.00 45.02 5.03
2112 2292 0.253327 AAGAGATTGGGGGAACGCTC 59.747 55.000 0.00 0.00 45.02 5.03
2113 2293 0.253327 GAAGAGATTGGGGGAACGCT 59.747 55.000 0.00 0.00 45.02 5.07
2114 2294 0.748367 GGAAGAGATTGGGGGAACGC 60.748 60.000 0.00 0.00 44.99 4.84
2115 2295 0.618458 TGGAAGAGATTGGGGGAACG 59.382 55.000 0.00 0.00 0.00 3.95
2116 2296 1.341089 GGTGGAAGAGATTGGGGGAAC 60.341 57.143 0.00 0.00 0.00 3.62
2117 2297 0.999712 GGTGGAAGAGATTGGGGGAA 59.000 55.000 0.00 0.00 0.00 3.97
2118 2298 0.121197 AGGTGGAAGAGATTGGGGGA 59.879 55.000 0.00 0.00 0.00 4.81
2119 2299 0.548510 GAGGTGGAAGAGATTGGGGG 59.451 60.000 0.00 0.00 0.00 5.40
2120 2300 0.548510 GGAGGTGGAAGAGATTGGGG 59.451 60.000 0.00 0.00 0.00 4.96
2121 2301 0.548510 GGGAGGTGGAAGAGATTGGG 59.451 60.000 0.00 0.00 0.00 4.12
2122 2302 1.211457 CAGGGAGGTGGAAGAGATTGG 59.789 57.143 0.00 0.00 0.00 3.16
2123 2303 1.407989 GCAGGGAGGTGGAAGAGATTG 60.408 57.143 0.00 0.00 0.00 2.67
2124 2304 0.915364 GCAGGGAGGTGGAAGAGATT 59.085 55.000 0.00 0.00 0.00 2.40
2125 2305 0.985490 GGCAGGGAGGTGGAAGAGAT 60.985 60.000 0.00 0.00 0.00 2.75
2126 2306 1.613630 GGCAGGGAGGTGGAAGAGA 60.614 63.158 0.00 0.00 0.00 3.10
2127 2307 2.993853 GGCAGGGAGGTGGAAGAG 59.006 66.667 0.00 0.00 0.00 2.85
2128 2308 3.003173 CGGCAGGGAGGTGGAAGA 61.003 66.667 0.00 0.00 0.00 2.87
2129 2309 4.785453 GCGGCAGGGAGGTGGAAG 62.785 72.222 0.00 0.00 0.00 3.46
2199 2379 4.522975 GATGGGAAAGGGCCGGGG 62.523 72.222 2.18 0.00 0.00 5.73
2200 2380 2.056906 CTAGATGGGAAAGGGCCGGG 62.057 65.000 2.18 0.00 0.00 5.73
2201 2381 1.451936 CTAGATGGGAAAGGGCCGG 59.548 63.158 0.00 0.00 0.00 6.13
2202 2382 1.451936 CCTAGATGGGAAAGGGCCG 59.548 63.158 0.00 0.00 0.00 6.13
2212 2392 0.106894 GCCGGAGAAACCCTAGATGG 59.893 60.000 5.05 0.00 34.64 3.51
2213 2393 0.249489 CGCCGGAGAAACCCTAGATG 60.249 60.000 5.05 0.00 34.64 2.90
2214 2394 2.029307 GCGCCGGAGAAACCCTAGAT 62.029 60.000 10.31 0.00 34.64 1.98
2215 2395 2.718073 GCGCCGGAGAAACCCTAGA 61.718 63.158 10.31 0.00 34.64 2.43
2216 2396 2.202892 GCGCCGGAGAAACCCTAG 60.203 66.667 10.31 0.00 34.64 3.02
2217 2397 4.137872 CGCGCCGGAGAAACCCTA 62.138 66.667 10.31 0.00 34.64 3.53
2221 2401 3.774702 GTCACGCGCCGGAGAAAC 61.775 66.667 10.31 0.00 0.00 2.78
2246 2426 3.649277 CTGAAGACACCGCCCGGAG 62.649 68.421 14.44 8.24 38.96 4.63
2247 2427 3.691342 CTGAAGACACCGCCCGGA 61.691 66.667 14.44 0.00 38.96 5.14
2248 2428 4.760047 CCTGAAGACACCGCCCGG 62.760 72.222 4.96 4.96 42.03 5.73
2254 2434 4.373116 TCGCCGCCTGAAGACACC 62.373 66.667 0.00 0.00 0.00 4.16
2255 2435 3.112709 GTCGCCGCCTGAAGACAC 61.113 66.667 0.00 0.00 34.09 3.67
2256 2436 4.717629 CGTCGCCGCCTGAAGACA 62.718 66.667 0.00 0.00 33.56 3.41
2346 2526 4.227134 CAGATCTGGGTCGGGCGG 62.227 72.222 15.38 0.00 0.00 6.13
2347 2527 4.227134 CCAGATCTGGGTCGGGCG 62.227 72.222 31.14 5.44 46.81 6.13
2355 2535 2.578586 CCCAAAGGGCCCAGATCTGG 62.579 65.000 31.69 31.69 41.54 3.86
2356 2536 1.076485 CCCAAAGGGCCCAGATCTG 60.076 63.158 27.56 16.24 35.35 2.90
2357 2537 3.431658 CCCAAAGGGCCCAGATCT 58.568 61.111 27.56 0.00 35.35 2.75
2367 2547 1.538666 CCTAGATGGGGCCCAAAGG 59.461 63.158 32.57 29.62 36.95 3.11
2368 2548 1.152673 GCCTAGATGGGGCCCAAAG 60.153 63.158 32.57 25.18 43.49 2.77
2369 2549 3.015383 GCCTAGATGGGGCCCAAA 58.985 61.111 32.57 17.25 43.49 3.28
2377 2557 2.511452 CCCGTCCCAGCCTAGATGG 61.511 68.421 6.91 6.91 39.04 3.51
2378 2558 3.142393 CCCGTCCCAGCCTAGATG 58.858 66.667 0.00 0.00 0.00 2.90
2379 2559 2.844839 GCCCGTCCCAGCCTAGAT 60.845 66.667 0.00 0.00 0.00 1.98
2380 2560 4.075793 AGCCCGTCCCAGCCTAGA 62.076 66.667 0.00 0.00 0.00 2.43
2381 2561 3.854669 CAGCCCGTCCCAGCCTAG 61.855 72.222 0.00 0.00 0.00 3.02
2386 2566 4.394712 GTCACCAGCCCGTCCCAG 62.395 72.222 0.00 0.00 0.00 4.45
2388 2568 4.394712 CTGTCACCAGCCCGTCCC 62.395 72.222 0.00 0.00 0.00 4.46
2389 2569 4.394712 CCTGTCACCAGCCCGTCC 62.395 72.222 0.00 0.00 37.38 4.79
2425 2605 4.087892 CCACCACCGCCTCCTGAG 62.088 72.222 0.00 0.00 0.00 3.35
2426 2606 4.954118 ACCACCACCGCCTCCTGA 62.954 66.667 0.00 0.00 0.00 3.86
2427 2607 4.704833 CACCACCACCGCCTCCTG 62.705 72.222 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.