Multiple sequence alignment - TraesCS5B01G227900

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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 TraesCS5B01G227900 chr5B 100.000 2931 0 0 1 2931 404192196 404189266 0.000000e+00 5413
1 TraesCS5B01G227900 chr5A 93.156 1651 62 29 572 2195 444945616 444943990 0.000000e+00 2375
2 TraesCS5B01G227900 chr5A 89.069 741 56 15 2202 2931 444944055 444943329 0.000000e+00 896
3 TraesCS5B01G227900 chr5A 86.104 367 36 4 71 422 444946114 444945748 5.930000e-102 381
4 TraesCS5B01G227900 chr5D 91.044 1753 111 26 1 1731 346635769 346637497 0.000000e+00 2326
5 TraesCS5B01G227900 chr5D 90.393 1197 72 12 1743 2931 346637569 346638730 0.000000e+00 1533
6 TraesCS5B01G227900 chr2A 78.771 179 34 4 3 179 659704558 659704734 1.850000e-22 117


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 TraesCS5B01G227900 chr5B 404189266 404192196 2930 True 5413.000000 5413 100.0000 1 2931 1 chr5B.!!$R1 2930
1 TraesCS5B01G227900 chr5A 444943329 444946114 2785 True 1217.333333 2375 89.4430 71 2931 3 chr5A.!!$R1 2860
2 TraesCS5B01G227900 chr5D 346635769 346638730 2961 False 1929.500000 2326 90.7185 1 2931 2 chr5D.!!$F1 2930

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
272 274 0.319900 CTATCCGTTGGCAGGATCGG 60.320 60.0 11.22 12.46 44.68 4.18 F
1212 1279 0.108585 AGGCCACACGAAACATCACT 59.891 50.0 5.01 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1347 0.034337 GTCACCCGCCAAACTACAGA 59.966 55.0 0.0 0.0 0.0 3.41 R
2451 2583 0.035820 TTACCCGTCCTGTCATTGGC 60.036 55.0 0.0 0.0 0.0 4.52 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
49 50 0.749454 GAGAACCCTAGCCCGTCGTA 60.749 60.000 0.00 0.00 0.00 3.43
74 75 4.457496 CGATGGTGGTGGCGCTCT 62.457 66.667 7.64 0.00 0.00 4.09
132 133 4.030216 TCAGGTATCATCTGGTTACAGCA 58.970 43.478 0.00 0.00 44.54 4.41
192 193 2.303175 CTTCTTCGGTTTTGGGTGGAA 58.697 47.619 0.00 0.00 0.00 3.53
199 200 3.093057 CGGTTTTGGGTGGAATGGATTA 58.907 45.455 0.00 0.00 0.00 1.75
221 222 7.496346 TTAGTTGGTCTCCTCTCATTTACAT 57.504 36.000 0.00 0.00 0.00 2.29
242 243 1.472878 GTATCCTCGCAGTCACAGTCA 59.527 52.381 0.00 0.00 0.00 3.41
272 274 0.319900 CTATCCGTTGGCAGGATCGG 60.320 60.000 11.22 12.46 44.68 4.18
280 282 0.982852 TGGCAGGATCGGAACTCCAT 60.983 55.000 0.79 0.00 35.08 3.41
318 330 3.717707 ACATGCGCTTACGATATCTTGT 58.282 40.909 9.73 0.00 43.93 3.16
328 340 2.671396 ACGATATCTTGTTGTGTTCGGC 59.329 45.455 0.34 0.00 0.00 5.54
330 342 2.157834 TATCTTGTTGTGTTCGGCGT 57.842 45.000 6.85 0.00 0.00 5.68
340 352 3.902086 TTCGGCGTGTCGGTGTCA 61.902 61.111 6.85 0.00 0.00 3.58
341 353 3.215597 TTCGGCGTGTCGGTGTCAT 62.216 57.895 6.85 0.00 0.00 3.06
348 360 0.586319 GTGTCGGTGTCATGTGGTTG 59.414 55.000 0.00 0.00 0.00 3.77
372 389 1.142965 GGCAGTGCGGTTTTGGTTT 59.857 52.632 9.45 0.00 0.00 3.27
419 436 4.396166 AGTGTGGCGATTCCTATTTTCTTG 59.604 41.667 0.00 0.00 35.26 3.02
422 439 5.095490 GTGGCGATTCCTATTTTCTTGTTG 58.905 41.667 0.00 0.00 35.26 3.33
429 483 2.562298 CCTATTTTCTTGTTGGGCTGCA 59.438 45.455 0.50 0.00 0.00 4.41
473 527 2.290960 ACTGGCTTGTATGGGGTTCTTC 60.291 50.000 0.00 0.00 0.00 2.87
490 544 2.434336 TCTTCCCATCACCTTGTATCGG 59.566 50.000 0.00 0.00 0.00 4.18
494 548 2.093181 CCCATCACCTTGTATCGGTTCA 60.093 50.000 0.00 0.00 30.82 3.18
516 570 5.125739 TCAACCGTTTGTATTTTGTTCAGGT 59.874 36.000 0.00 0.00 34.02 4.00
517 571 5.585820 ACCGTTTGTATTTTGTTCAGGTT 57.414 34.783 0.00 0.00 0.00 3.50
520 574 5.685511 CCGTTTGTATTTTGTTCAGGTTCAG 59.314 40.000 0.00 0.00 0.00 3.02
521 575 5.685511 CGTTTGTATTTTGTTCAGGTTCAGG 59.314 40.000 0.00 0.00 0.00 3.86
522 576 6.459024 CGTTTGTATTTTGTTCAGGTTCAGGA 60.459 38.462 0.00 0.00 0.00 3.86
523 577 7.433680 GTTTGTATTTTGTTCAGGTTCAGGAT 58.566 34.615 0.00 0.00 0.00 3.24
524 578 6.817765 TGTATTTTGTTCAGGTTCAGGATC 57.182 37.500 0.00 0.00 0.00 3.36
525 579 6.542821 TGTATTTTGTTCAGGTTCAGGATCT 58.457 36.000 0.00 0.00 0.00 2.75
526 580 5.972107 ATTTTGTTCAGGTTCAGGATCTG 57.028 39.130 0.00 0.00 0.00 2.90
535 589 4.039004 CAGGTTCAGGATCTGGTCTCATAG 59.961 50.000 0.00 0.00 31.51 2.23
588 642 4.360951 TTTCCCTATTTCGTGTGGAAGT 57.639 40.909 0.00 0.00 36.52 3.01
600 654 3.119637 CGTGTGGAAGTGGTTGAAAGTTT 60.120 43.478 0.00 0.00 0.00 2.66
699 753 0.806884 TCAACCGAACGTGCGTTTCT 60.807 50.000 16.18 0.00 38.60 2.52
847 901 3.513225 GCAGTGGCGCCAACATAT 58.487 55.556 34.66 12.33 0.00 1.78
983 1039 2.601666 ACTCACTCTCCTGCCGCA 60.602 61.111 0.00 0.00 0.00 5.69
1187 1254 2.772691 CCTACCTCGACGGCAGGTC 61.773 68.421 14.64 0.00 43.68 3.85
1188 1255 2.034532 TACCTCGACGGCAGGTCA 59.965 61.111 14.64 1.59 46.42 4.02
1189 1256 1.994507 CTACCTCGACGGCAGGTCAG 61.995 65.000 14.64 8.22 46.42 3.51
1190 1257 4.803426 CCTCGACGGCAGGTCAGC 62.803 72.222 7.75 0.00 46.42 4.26
1191 1258 4.056125 CTCGACGGCAGGTCAGCA 62.056 66.667 7.75 0.00 46.42 4.41
1192 1259 4.357947 TCGACGGCAGGTCAGCAC 62.358 66.667 7.75 0.00 46.42 4.40
1193 1260 4.662961 CGACGGCAGGTCAGCACA 62.663 66.667 7.75 0.00 46.42 4.57
1194 1261 2.740055 GACGGCAGGTCAGCACAG 60.740 66.667 2.57 0.00 45.36 3.66
1195 1262 4.320456 ACGGCAGGTCAGCACAGG 62.320 66.667 0.00 0.00 35.83 4.00
1198 1265 4.648626 GCAGGTCAGCACAGGCCA 62.649 66.667 5.01 0.00 42.56 5.36
1199 1266 2.670934 CAGGTCAGCACAGGCCAC 60.671 66.667 5.01 0.00 42.56 5.01
1202 1269 3.349006 GTCAGCACAGGCCACACG 61.349 66.667 5.01 0.00 42.56 4.49
1204 1271 2.591429 CAGCACAGGCCACACGAA 60.591 61.111 5.01 0.00 42.56 3.85
1206 1273 2.186826 AGCACAGGCCACACGAAAC 61.187 57.895 5.01 0.00 42.56 2.78
1207 1274 2.477176 GCACAGGCCACACGAAACA 61.477 57.895 5.01 0.00 0.00 2.83
1208 1275 1.795170 GCACAGGCCACACGAAACAT 61.795 55.000 5.01 0.00 0.00 2.71
1211 1278 0.238289 CAGGCCACACGAAACATCAC 59.762 55.000 5.01 0.00 0.00 3.06
1212 1279 0.108585 AGGCCACACGAAACATCACT 59.891 50.000 5.01 0.00 0.00 3.41
1213 1280 0.517316 GGCCACACGAAACATCACTC 59.483 55.000 0.00 0.00 0.00 3.51
1214 1281 0.517316 GCCACACGAAACATCACTCC 59.483 55.000 0.00 0.00 0.00 3.85
1215 1282 1.156736 CCACACGAAACATCACTCCC 58.843 55.000 0.00 0.00 0.00 4.30
1216 1283 0.790207 CACACGAAACATCACTCCCG 59.210 55.000 0.00 0.00 0.00 5.14
1217 1284 0.391597 ACACGAAACATCACTCCCGT 59.608 50.000 0.00 0.00 0.00 5.28
1219 1286 0.677288 ACGAAACATCACTCCCGTCA 59.323 50.000 0.00 0.00 0.00 4.35
1221 1288 1.660607 CGAAACATCACTCCCGTCATG 59.339 52.381 0.00 0.00 0.00 3.07
1222 1289 1.398390 GAAACATCACTCCCGTCATGC 59.602 52.381 0.00 0.00 0.00 4.06
1223 1290 0.740868 AACATCACTCCCGTCATGCG 60.741 55.000 3.02 3.02 40.95 4.73
1224 1291 2.202932 ATCACTCCCGTCATGCGC 60.203 61.111 0.00 0.00 39.71 6.09
1225 1292 3.017771 ATCACTCCCGTCATGCGCA 62.018 57.895 14.96 14.96 39.71 6.09
1226 1293 2.315781 ATCACTCCCGTCATGCGCAT 62.316 55.000 19.28 19.28 39.71 4.73
1227 1294 2.512286 ACTCCCGTCATGCGCATG 60.512 61.111 38.48 38.48 39.71 4.06
1228 1295 3.945434 CTCCCGTCATGCGCATGC 61.945 66.667 39.11 31.42 38.65 4.06
1238 1305 2.803670 GCGCATGCAGCTGTGTTG 60.804 61.111 19.57 11.48 42.61 3.33
1244 1311 3.573569 TGCAGCTGTGTTGCATTTC 57.426 47.368 16.64 0.00 44.16 2.17
1246 1313 1.001048 TGCAGCTGTGTTGCATTTCTC 60.001 47.619 16.64 0.00 44.16 2.87
1249 1316 3.669023 GCAGCTGTGTTGCATTTCTCTAC 60.669 47.826 16.64 0.00 39.50 2.59
1251 1318 2.736721 GCTGTGTTGCATTTCTCTACGA 59.263 45.455 0.00 0.00 0.00 3.43
1252 1319 3.423645 GCTGTGTTGCATTTCTCTACGAC 60.424 47.826 0.00 0.00 0.00 4.34
1253 1320 3.064207 TGTGTTGCATTTCTCTACGACC 58.936 45.455 0.00 0.00 0.00 4.79
1254 1321 2.092211 GTGTTGCATTTCTCTACGACCG 59.908 50.000 0.00 0.00 0.00 4.79
1256 1323 1.990799 TGCATTTCTCTACGACCGTG 58.009 50.000 5.20 0.00 0.00 4.94
1259 1326 2.479049 GCATTTCTCTACGACCGTGCTA 60.479 50.000 5.20 0.00 0.00 3.49
1260 1327 3.766151 CATTTCTCTACGACCGTGCTAA 58.234 45.455 5.20 0.00 0.00 3.09
1262 1329 3.416119 TTCTCTACGACCGTGCTAATG 57.584 47.619 5.20 0.00 0.00 1.90
1264 1331 1.674441 CTCTACGACCGTGCTAATGGA 59.326 52.381 5.20 0.00 36.21 3.41
1267 1334 0.821517 ACGACCGTGCTAATGGATGA 59.178 50.000 0.00 0.00 36.21 2.92
1268 1335 1.412710 ACGACCGTGCTAATGGATGAT 59.587 47.619 0.00 0.00 36.21 2.45
1269 1336 2.626266 ACGACCGTGCTAATGGATGATA 59.374 45.455 0.00 0.00 36.21 2.15
1270 1337 2.987149 CGACCGTGCTAATGGATGATAC 59.013 50.000 0.00 0.00 36.21 2.24
1272 1339 2.364324 ACCGTGCTAATGGATGATACGT 59.636 45.455 0.00 0.00 36.21 3.57
1273 1340 3.570975 ACCGTGCTAATGGATGATACGTA 59.429 43.478 0.00 0.00 36.21 3.57
1274 1341 4.038282 ACCGTGCTAATGGATGATACGTAA 59.962 41.667 0.00 0.00 36.21 3.18
1275 1342 4.384846 CCGTGCTAATGGATGATACGTAAC 59.615 45.833 0.00 0.00 33.87 2.50
1277 1344 5.117135 CGTGCTAATGGATGATACGTAACTG 59.883 44.000 0.00 0.00 0.00 3.16
1279 1346 5.221441 TGCTAATGGATGATACGTAACTGCT 60.221 40.000 0.00 0.00 0.00 4.24
1280 1347 5.696724 GCTAATGGATGATACGTAACTGCTT 59.303 40.000 0.00 0.00 0.00 3.91
1281 1348 6.128795 GCTAATGGATGATACGTAACTGCTTC 60.129 42.308 0.00 0.00 0.00 3.86
1282 1349 5.537300 ATGGATGATACGTAACTGCTTCT 57.463 39.130 0.00 0.00 0.00 2.85
1283 1350 4.682787 TGGATGATACGTAACTGCTTCTG 58.317 43.478 0.00 0.00 0.00 3.02
1284 1351 4.159693 TGGATGATACGTAACTGCTTCTGT 59.840 41.667 0.00 0.00 0.00 3.41
1287 1354 5.892160 TGATACGTAACTGCTTCTGTAGT 57.108 39.130 0.00 0.00 40.83 2.73
1305 1372 1.151679 TTTGGCGGGTGACAATGGA 59.848 52.632 0.00 0.00 44.30 3.41
1734 1807 1.004560 TCCTCTGCTTGCTTCACCG 60.005 57.895 0.00 0.00 0.00 4.94
1760 1886 2.528041 ATTTCTAATCGGACGGCTCC 57.472 50.000 0.00 0.00 0.00 4.70
1849 1980 3.345808 CAGCACAACGTGACCGGG 61.346 66.667 6.32 0.00 38.78 5.73
1855 1986 3.633116 AACGTGACCGGGAAGGGG 61.633 66.667 6.32 0.00 46.96 4.79
2071 2203 0.310854 GCTCCGGTGGTGAAACTTTG 59.689 55.000 0.00 0.00 36.74 2.77
2138 2270 6.544197 TGTAATATCACCCATGCGTGTTATTT 59.456 34.615 22.57 12.62 38.58 1.40
2184 2316 5.847670 AGTTTGAAGCATTAGTCTCGAAC 57.152 39.130 0.00 0.00 0.00 3.95
2217 2349 9.179909 TGATATCACCCGTGTTATTTTAAACAT 57.820 29.630 0.00 0.00 41.18 2.71
2244 2376 7.698130 GGCAAAATATAGTTTGAAGCACTAGTG 59.302 37.037 25.42 18.93 40.29 2.74
2262 2394 1.662629 GTGCTGAACTCGATGTGATGG 59.337 52.381 0.00 0.00 0.00 3.51
2266 2398 3.429547 GCTGAACTCGATGTGATGGTAGT 60.430 47.826 0.00 0.00 0.00 2.73
2267 2399 4.202020 GCTGAACTCGATGTGATGGTAGTA 60.202 45.833 0.00 0.00 0.00 1.82
2268 2400 5.678871 GCTGAACTCGATGTGATGGTAGTAA 60.679 44.000 0.00 0.00 0.00 2.24
2269 2401 6.465439 TGAACTCGATGTGATGGTAGTAAT 57.535 37.500 0.00 0.00 0.00 1.89
2306 2438 6.601613 AGAGCATAATTTCATAAAACACCGGA 59.398 34.615 9.46 0.00 0.00 5.14
2347 2479 6.361748 CAGCGGAATCAAAGAAGAAGAAAAAG 59.638 38.462 0.00 0.00 0.00 2.27
2348 2480 6.263168 AGCGGAATCAAAGAAGAAGAAAAAGA 59.737 34.615 0.00 0.00 0.00 2.52
2349 2481 6.918022 GCGGAATCAAAGAAGAAGAAAAAGAA 59.082 34.615 0.00 0.00 0.00 2.52
2350 2482 7.435192 GCGGAATCAAAGAAGAAGAAAAAGAAA 59.565 33.333 0.00 0.00 0.00 2.52
2351 2483 9.301153 CGGAATCAAAGAAGAAGAAAAAGAAAA 57.699 29.630 0.00 0.00 0.00 2.29
2387 2519 7.936950 ATCAAGTCACAGATATACAACATCG 57.063 36.000 0.00 0.00 0.00 3.84
2400 2532 8.958119 ATATACAACATCGGTCACAAAACTAT 57.042 30.769 0.00 0.00 0.00 2.12
2412 2544 6.286941 GTCACAAAACTATAACTTCGTCGTG 58.713 40.000 0.00 0.00 0.00 4.35
2424 2556 0.320334 TCGTCGTGTGGAATGTGCAT 60.320 50.000 0.00 0.00 0.00 3.96
2426 2558 0.095245 GTCGTGTGGAATGTGCATCG 59.905 55.000 0.00 0.00 0.00 3.84
2451 2583 4.697352 CACAAGATTAGTGTCCTTCAAGGG 59.303 45.833 2.75 0.00 35.59 3.95
2452 2584 3.636153 AGATTAGTGTCCTTCAAGGGC 57.364 47.619 0.00 0.00 41.40 5.19
2456 2588 0.779997 AGTGTCCTTCAAGGGCCAAT 59.220 50.000 5.32 0.00 39.91 3.16
2458 2590 0.776810 TGTCCTTCAAGGGCCAATGA 59.223 50.000 5.32 7.18 39.91 2.57
2459 2591 1.177401 GTCCTTCAAGGGCCAATGAC 58.823 55.000 6.18 0.25 32.63 3.06
2460 2592 0.776810 TCCTTCAAGGGCCAATGACA 59.223 50.000 6.18 0.78 35.59 3.58
2461 2593 1.180029 CCTTCAAGGGCCAATGACAG 58.820 55.000 6.18 9.74 0.00 3.51
2463 2595 0.776810 TTCAAGGGCCAATGACAGGA 59.223 50.000 6.18 0.00 0.00 3.86
2464 2596 0.038166 TCAAGGGCCAATGACAGGAC 59.962 55.000 6.18 0.00 0.00 3.85
2465 2597 1.002134 AAGGGCCAATGACAGGACG 60.002 57.895 6.18 0.00 33.83 4.79
2467 2599 2.438434 GGCCAATGACAGGACGGG 60.438 66.667 0.00 0.00 0.00 5.28
2468 2600 2.351276 GCCAATGACAGGACGGGT 59.649 61.111 0.00 0.00 0.00 5.28
2472 2604 2.944094 GCCAATGACAGGACGGGTAAAT 60.944 50.000 0.00 0.00 0.00 1.40
2475 2607 4.944930 CCAATGACAGGACGGGTAAATTTA 59.055 41.667 0.00 0.00 0.00 1.40
2477 2609 4.210724 TGACAGGACGGGTAAATTTAGG 57.789 45.455 0.00 0.00 0.00 2.69
2479 2611 4.041938 TGACAGGACGGGTAAATTTAGGTT 59.958 41.667 0.00 0.00 0.00 3.50
2481 2613 6.125589 ACAGGACGGGTAAATTTAGGTTAA 57.874 37.500 0.00 0.00 0.00 2.01
2484 2616 7.670979 ACAGGACGGGTAAATTTAGGTTAAAAT 59.329 33.333 0.00 0.00 0.00 1.82
2540 2672 8.567948 TGATTCAACTGGAAATTCAGAACTAAC 58.432 33.333 1.40 0.00 39.39 2.34
2561 2695 8.213679 ACTAACATATGTATCCACATGAGCTTT 58.786 33.333 9.21 0.00 45.17 3.51
2572 2706 6.721318 TCCACATGAGCTTTTCCTAATTAGT 58.279 36.000 11.50 0.00 0.00 2.24
2604 2738 7.100458 AGTAACTCAGCACATTTCTTTTGTT 57.900 32.000 0.00 0.00 0.00 2.83
2622 2757 1.134946 GTTGGTGCACTGCAGAAACTT 59.865 47.619 23.35 0.00 40.08 2.66
2665 2800 2.092212 ACAATCTGGGGCAGGATAAGTG 60.092 50.000 0.00 0.00 31.51 3.16
2902 3037 3.521560 AGAAATCTCGCGAATACAGCAA 58.478 40.909 11.33 0.00 34.19 3.91
2906 3041 2.954316 TCTCGCGAATACAGCAAAAGA 58.046 42.857 11.33 0.00 34.19 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 3.853104 CCAAGAGGGTAATGACGCA 57.147 52.632 0.00 0.00 40.92 5.24
132 133 3.737172 GCATGAAGGCGCCAACGT 61.737 61.111 31.54 19.89 42.83 3.99
192 193 4.624913 TGAGAGGAGACCAACTAATCCAT 58.375 43.478 0.00 0.00 34.08 3.41
199 200 5.249393 ACATGTAAATGAGAGGAGACCAACT 59.751 40.000 0.00 0.00 0.00 3.16
221 222 1.472878 GACTGTGACTGCGAGGATACA 59.527 52.381 0.00 0.00 41.41 2.29
242 243 1.681793 CAACGGATAGTGAGGACCGAT 59.318 52.381 11.27 0.00 46.94 4.18
280 282 4.043100 TCCTCTCGCTCCGGACCA 62.043 66.667 0.00 0.00 0.00 4.02
318 330 2.962786 CCGACACGCCGAACACAA 60.963 61.111 0.00 0.00 0.00 3.33
328 340 0.878523 AACCACATGACACCGACACG 60.879 55.000 0.00 0.00 0.00 4.49
330 342 1.163420 GCAACCACATGACACCGACA 61.163 55.000 0.00 0.00 0.00 4.35
357 374 1.679153 CTACCAAACCAAAACCGCACT 59.321 47.619 0.00 0.00 0.00 4.40
362 379 4.722220 ACCTAGACTACCAAACCAAAACC 58.278 43.478 0.00 0.00 0.00 3.27
372 389 0.622136 TGAGGCGACCTAGACTACCA 59.378 55.000 0.00 0.00 31.76 3.25
419 436 2.521708 ACCAACCTGCAGCCCAAC 60.522 61.111 8.66 0.00 0.00 3.77
429 483 2.671070 CGAGGATGCCACCAACCT 59.329 61.111 0.00 0.00 45.87 3.50
473 527 2.093181 TGAACCGATACAAGGTGATGGG 60.093 50.000 0.00 0.00 41.95 4.00
490 544 6.020201 CCTGAACAAAATACAAACGGTTGAAC 60.020 38.462 22.35 0.96 38.20 3.18
494 548 5.585820 ACCTGAACAAAATACAAACGGTT 57.414 34.783 0.00 0.00 0.00 4.44
504 558 4.768968 CCAGATCCTGAACCTGAACAAAAT 59.231 41.667 0.00 0.00 32.44 1.82
516 570 4.542906 TCCTATGAGACCAGATCCTGAA 57.457 45.455 0.00 0.00 32.44 3.02
517 571 4.756203 ATCCTATGAGACCAGATCCTGA 57.244 45.455 0.00 0.00 32.44 3.86
568 622 3.558321 CCACTTCCACACGAAATAGGGAA 60.558 47.826 0.00 0.00 36.31 3.97
569 623 2.027561 CCACTTCCACACGAAATAGGGA 60.028 50.000 0.00 0.00 0.00 4.20
574 628 2.925724 TCAACCACTTCCACACGAAAT 58.074 42.857 0.00 0.00 0.00 2.17
588 642 6.096695 GTCTGTTTGCTTAAACTTTCAACCA 58.903 36.000 4.76 0.00 33.95 3.67
600 654 1.600023 CGGGTTGGTCTGTTTGCTTA 58.400 50.000 0.00 0.00 0.00 3.09
681 735 0.382636 GAGAAACGCACGTTCGGTTG 60.383 55.000 17.10 0.00 39.76 3.77
713 767 1.821216 TGCGGAATCAAAAGGAGGAC 58.179 50.000 0.00 0.00 0.00 3.85
782 836 3.126831 CGTTTGGAGACTGGATAGATGC 58.873 50.000 0.00 0.00 0.00 3.91
964 1020 2.125753 CGGCAGGAGAGTGAGTGC 60.126 66.667 0.00 0.00 35.07 4.40
966 1022 2.601666 TGCGGCAGGAGAGTGAGT 60.602 61.111 0.00 0.00 0.00 3.41
983 1039 0.458543 CATCTTGACTACGGCGCACT 60.459 55.000 10.83 0.00 0.00 4.40
994 1050 1.068472 ACTGACCGACGACATCTTGAC 60.068 52.381 0.00 0.00 0.00 3.18
995 1051 1.068541 CACTGACCGACGACATCTTGA 60.069 52.381 0.00 0.00 0.00 3.02
1187 1254 2.186160 TTTCGTGTGGCCTGTGCTG 61.186 57.895 3.32 0.00 37.74 4.41
1188 1255 2.186826 GTTTCGTGTGGCCTGTGCT 61.187 57.895 3.32 0.00 37.74 4.40
1189 1256 1.795170 ATGTTTCGTGTGGCCTGTGC 61.795 55.000 3.32 0.00 0.00 4.57
1190 1257 0.238289 GATGTTTCGTGTGGCCTGTG 59.762 55.000 3.32 0.00 0.00 3.66
1191 1258 0.179032 TGATGTTTCGTGTGGCCTGT 60.179 50.000 3.32 0.00 0.00 4.00
1192 1259 0.238289 GTGATGTTTCGTGTGGCCTG 59.762 55.000 3.32 0.00 0.00 4.85
1193 1260 0.108585 AGTGATGTTTCGTGTGGCCT 59.891 50.000 3.32 0.00 0.00 5.19
1194 1261 0.517316 GAGTGATGTTTCGTGTGGCC 59.483 55.000 0.00 0.00 0.00 5.36
1195 1262 0.517316 GGAGTGATGTTTCGTGTGGC 59.483 55.000 0.00 0.00 0.00 5.01
1197 1264 0.790207 CGGGAGTGATGTTTCGTGTG 59.210 55.000 0.00 0.00 0.00 3.82
1198 1265 0.391597 ACGGGAGTGATGTTTCGTGT 59.608 50.000 0.00 0.00 44.82 4.49
1199 1266 3.210857 ACGGGAGTGATGTTTCGTG 57.789 52.632 0.00 0.00 44.82 4.35
1211 1278 3.945434 GCATGCGCATGACGGGAG 61.945 66.667 45.47 23.51 43.93 4.30
1212 1279 4.774503 TGCATGCGCATGACGGGA 62.775 61.111 45.47 23.36 45.36 5.14
1222 1289 3.545707 TGCAACACAGCTGCATGCG 62.546 57.895 24.83 9.16 44.67 4.73
1223 1290 2.337170 TGCAACACAGCTGCATGC 59.663 55.556 24.24 24.24 44.67 4.06
1227 1294 1.268899 AGAGAAATGCAACACAGCTGC 59.731 47.619 15.27 0.00 40.35 5.25
1228 1295 3.424039 CGTAGAGAAATGCAACACAGCTG 60.424 47.826 13.48 13.48 34.99 4.24
1230 1297 2.736721 TCGTAGAGAAATGCAACACAGC 59.263 45.455 0.00 0.00 0.00 4.40
1231 1298 3.123621 GGTCGTAGAGAAATGCAACACAG 59.876 47.826 0.00 0.00 36.95 3.66
1233 1300 2.092211 CGGTCGTAGAGAAATGCAACAC 59.908 50.000 0.00 0.00 36.95 3.32
1234 1301 2.288579 ACGGTCGTAGAGAAATGCAACA 60.289 45.455 0.00 0.00 36.95 3.33
1235 1302 2.092211 CACGGTCGTAGAGAAATGCAAC 59.908 50.000 0.00 0.00 36.95 4.17
1236 1303 2.333926 CACGGTCGTAGAGAAATGCAA 58.666 47.619 0.00 0.00 36.95 4.08
1237 1304 1.990799 CACGGTCGTAGAGAAATGCA 58.009 50.000 0.00 0.00 36.95 3.96
1238 1305 0.645868 GCACGGTCGTAGAGAAATGC 59.354 55.000 0.00 0.00 36.95 3.56
1242 1309 2.098607 CCATTAGCACGGTCGTAGAGAA 59.901 50.000 0.00 0.00 36.95 2.87
1243 1310 1.674441 CCATTAGCACGGTCGTAGAGA 59.326 52.381 0.00 0.00 36.95 3.10
1244 1311 1.674441 TCCATTAGCACGGTCGTAGAG 59.326 52.381 0.00 0.00 36.95 2.43
1246 1313 2.034179 TCATCCATTAGCACGGTCGTAG 59.966 50.000 0.00 0.00 0.00 3.51
1249 1316 2.154854 ATCATCCATTAGCACGGTCG 57.845 50.000 0.00 0.00 0.00 4.79
1251 1318 2.364324 ACGTATCATCCATTAGCACGGT 59.636 45.455 0.00 0.00 32.52 4.83
1252 1319 3.026630 ACGTATCATCCATTAGCACGG 57.973 47.619 0.00 0.00 32.52 4.94
1253 1320 5.117135 CAGTTACGTATCATCCATTAGCACG 59.883 44.000 6.43 0.00 0.00 5.34
1254 1321 5.107453 GCAGTTACGTATCATCCATTAGCAC 60.107 44.000 6.43 0.00 0.00 4.40
1256 1323 5.230942 AGCAGTTACGTATCATCCATTAGC 58.769 41.667 6.43 0.00 0.00 3.09
1259 1326 5.755375 CAGAAGCAGTTACGTATCATCCATT 59.245 40.000 6.43 0.00 0.00 3.16
1260 1327 5.163405 ACAGAAGCAGTTACGTATCATCCAT 60.163 40.000 6.43 0.00 0.00 3.41
1262 1329 4.683832 ACAGAAGCAGTTACGTATCATCC 58.316 43.478 6.43 0.00 0.00 3.51
1264 1331 6.452494 ACTACAGAAGCAGTTACGTATCAT 57.548 37.500 6.43 0.00 0.00 2.45
1267 1334 5.867716 CCAAACTACAGAAGCAGTTACGTAT 59.132 40.000 0.00 0.00 33.92 3.06
1268 1335 5.224888 CCAAACTACAGAAGCAGTTACGTA 58.775 41.667 0.00 0.00 33.92 3.57
1269 1336 4.056050 CCAAACTACAGAAGCAGTTACGT 58.944 43.478 0.00 0.00 33.92 3.57
1270 1337 3.120649 GCCAAACTACAGAAGCAGTTACG 60.121 47.826 0.00 0.00 33.92 3.18
1272 1339 3.064207 CGCCAAACTACAGAAGCAGTTA 58.936 45.455 0.00 0.00 33.92 2.24
1273 1340 1.873591 CGCCAAACTACAGAAGCAGTT 59.126 47.619 0.00 0.00 36.56 3.16
1274 1341 1.512926 CGCCAAACTACAGAAGCAGT 58.487 50.000 0.00 0.00 0.00 4.40
1275 1342 0.798776 CCGCCAAACTACAGAAGCAG 59.201 55.000 0.00 0.00 0.00 4.24
1277 1344 0.605589 ACCCGCCAAACTACAGAAGC 60.606 55.000 0.00 0.00 0.00 3.86
1279 1346 0.759959 TCACCCGCCAAACTACAGAA 59.240 50.000 0.00 0.00 0.00 3.02
1280 1347 0.034337 GTCACCCGCCAAACTACAGA 59.966 55.000 0.00 0.00 0.00 3.41
1281 1348 0.250124 TGTCACCCGCCAAACTACAG 60.250 55.000 0.00 0.00 0.00 2.74
1282 1349 0.180642 TTGTCACCCGCCAAACTACA 59.819 50.000 0.00 0.00 0.00 2.74
1283 1350 1.199097 CATTGTCACCCGCCAAACTAC 59.801 52.381 0.00 0.00 0.00 2.73
1284 1351 1.529226 CATTGTCACCCGCCAAACTA 58.471 50.000 0.00 0.00 0.00 2.24
1287 1354 0.251564 ATCCATTGTCACCCGCCAAA 60.252 50.000 0.00 0.00 0.00 3.28
1707 1774 0.809241 CAAGCAGAGGAGCGATGGAC 60.809 60.000 0.00 0.00 40.15 4.02
1713 1780 1.375140 TGAAGCAAGCAGAGGAGCG 60.375 57.895 0.00 0.00 40.15 5.03
1715 1782 1.018226 CGGTGAAGCAAGCAGAGGAG 61.018 60.000 0.00 0.00 0.00 3.69
1716 1783 1.004560 CGGTGAAGCAAGCAGAGGA 60.005 57.895 0.00 0.00 0.00 3.71
1734 1807 4.317628 GCCGTCCGATTAGAAATTAACGAC 60.318 45.833 0.00 0.00 0.00 4.34
1849 1980 1.740664 GTTCTCGAACGGCCCCTTC 60.741 63.158 0.00 0.00 0.00 3.46
1855 1986 2.357034 TGCAGGTTCTCGAACGGC 60.357 61.111 14.31 14.31 42.02 5.68
1965 2096 4.219725 ACCCCAAAATAACAATTCAGACCG 59.780 41.667 0.00 0.00 0.00 4.79
2071 2203 1.133025 CATGGGCGAATCCACAAGAAC 59.867 52.381 0.00 0.00 39.97 3.01
2097 2229 8.148351 GTGATATTACAAGTACAGCCTCCATTA 58.852 37.037 0.00 0.00 0.00 1.90
2098 2230 6.992715 GTGATATTACAAGTACAGCCTCCATT 59.007 38.462 0.00 0.00 0.00 3.16
2138 2270 9.509956 ACTAGTAGTATGTTTTGCCATGTTTAA 57.490 29.630 0.00 0.00 0.00 1.52
2217 2349 6.588719 AGTGCTTCAAACTATATTTTGCCA 57.411 33.333 9.98 5.44 36.56 4.92
2244 2376 2.015736 ACCATCACATCGAGTTCAGC 57.984 50.000 0.00 0.00 0.00 4.26
2280 2412 6.912591 CCGGTGTTTTATGAAATTATGCTCTC 59.087 38.462 0.00 0.00 0.00 3.20
2282 2414 6.691388 GTCCGGTGTTTTATGAAATTATGCTC 59.309 38.462 0.00 0.00 0.00 4.26
2287 2419 5.163834 GCGAGTCCGGTGTTTTATGAAATTA 60.164 40.000 0.00 0.00 36.06 1.40
2290 2422 2.481185 GCGAGTCCGGTGTTTTATGAAA 59.519 45.455 0.00 0.00 36.06 2.69
2297 2429 0.670546 CATCTGCGAGTCCGGTGTTT 60.671 55.000 0.00 0.00 36.06 2.83
2306 2438 2.285827 GCTGTTCTACATCTGCGAGT 57.714 50.000 0.00 0.00 0.00 4.18
2347 2479 7.987458 TGTGACTTGATATACTGGATCCTTTTC 59.013 37.037 14.23 2.42 0.00 2.29
2348 2480 7.861629 TGTGACTTGATATACTGGATCCTTTT 58.138 34.615 14.23 0.00 0.00 2.27
2349 2481 7.345653 TCTGTGACTTGATATACTGGATCCTTT 59.654 37.037 14.23 1.84 0.00 3.11
2350 2482 6.841229 TCTGTGACTTGATATACTGGATCCTT 59.159 38.462 14.23 2.24 0.00 3.36
2351 2483 6.377080 TCTGTGACTTGATATACTGGATCCT 58.623 40.000 14.23 0.00 0.00 3.24
2412 2544 3.589579 TGCCGATGCACATTCCAC 58.410 55.556 0.00 0.00 44.23 4.02
2424 2556 1.899814 AGGACACTAATCTTGTGCCGA 59.100 47.619 0.00 0.00 38.86 5.54
2426 2558 3.674997 TGAAGGACACTAATCTTGTGCC 58.325 45.455 0.00 0.00 38.86 5.01
2439 2571 0.776810 TCATTGGCCCTTGAAGGACA 59.223 50.000 13.97 8.65 45.91 4.02
2451 2583 0.035820 TTACCCGTCCTGTCATTGGC 60.036 55.000 0.00 0.00 0.00 4.52
2452 2584 2.483014 TTTACCCGTCCTGTCATTGG 57.517 50.000 0.00 0.00 0.00 3.16
2456 2588 3.583966 ACCTAAATTTACCCGTCCTGTCA 59.416 43.478 0.00 0.00 0.00 3.58
2458 2590 4.645863 AACCTAAATTTACCCGTCCTGT 57.354 40.909 0.00 0.00 0.00 4.00
2459 2591 7.451501 TTTTAACCTAAATTTACCCGTCCTG 57.548 36.000 0.00 0.00 0.00 3.86
2460 2592 8.654485 AATTTTAACCTAAATTTACCCGTCCT 57.346 30.769 0.00 0.00 34.86 3.85
2481 2613 8.061304 TGCCTCTTCCAATAGGATCTTAAATTT 58.939 33.333 0.00 0.00 45.26 1.82
2484 2616 6.575244 TGCCTCTTCCAATAGGATCTTAAA 57.425 37.500 0.00 0.00 45.26 1.52
2561 2695 7.848128 AGTTACTTGCAGCTACTAATTAGGAA 58.152 34.615 16.73 3.81 0.00 3.36
2604 2738 0.740149 CAAGTTTCTGCAGTGCACCA 59.260 50.000 15.37 4.23 33.79 4.17
2622 2757 0.323360 GTGCCAAGGGTAGATTGCCA 60.323 55.000 0.00 0.00 0.00 4.92
2665 2800 3.551250 GGAAGCCGAAGCAGTCTATCTAC 60.551 52.174 0.00 0.00 43.56 2.59
2902 3037 4.278419 GCACTGGTAAATCCTGTTGTCTTT 59.722 41.667 0.00 0.00 44.20 2.52
2906 3041 3.222173 TGCACTGGTAAATCCTGTTGT 57.778 42.857 0.00 0.00 44.20 3.32


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

AutoCloner maintained by Alex Coulton.