Multiple sequence alignment - TraesCS7D01G421500

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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 TraesCS7D01G421500 chr7D 100.000 3016 0 0 1 3016 540851725 540854740 0.000000e+00 5570
1 TraesCS7D01G421500 chr7A 92.707 3003 113 47 68 3016 623455097 623458047 0.000000e+00 4235
2 TraesCS7D01G421500 chr7B 92.510 2283 107 35 766 3016 584311476 584313726 0.000000e+00 3210
3 TraesCS7D01G421500 chr7B 89.633 762 23 17 1 746 584310783 584311504 0.000000e+00 918
4 TraesCS7D01G421500 chr1A 93.333 75 3 2 420 493 466043423 466043496 3.180000e-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 TraesCS7D01G421500 chr7D 540851725 540854740 3015 False 5570 5570 100.0000 1 3016 1 chr7D.!!$F1 3015
1 TraesCS7D01G421500 chr7A 623455097 623458047 2950 False 4235 4235 92.7070 68 3016 1 chr7A.!!$F1 2948
2 TraesCS7D01G421500 chr7B 584310783 584313726 2943 False 2064 3210 91.0715 1 3016 2 chr7B.!!$F1 3015


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
299 312 0.034198 CACATGGACCACACCACGTA 59.966 55.0 0.00 0.0 43.03 3.57 F
300 313 0.034337 ACATGGACCACACCACGTAC 59.966 55.0 0.00 0.0 43.03 3.67 F
473 502 0.798776 GAGTGGATCGCAAAGTGGTG 59.201 55.0 0.00 0.0 0.00 4.17 F
1269 1341 0.035725 CCAAGAGAGCAGGTGCATGA 60.036 55.0 4.48 0.0 45.16 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1218 0.396435 AGCACAAGTTGGATCGGTCA 59.604 50.000 7.96 0.0 0.0 4.02 R
1156 1228 1.226660 GCGCACAACAGCACAAGTT 60.227 52.632 0.30 0.0 0.0 2.66 R
1286 1358 3.264947 GTCTTGCATGATGTAGCTGTGA 58.735 45.455 5.49 0.0 0.0 3.58 R
2805 2896 0.469917 AGATGGGAATGGCACCTACG 59.530 55.000 0.00 0.0 0.0 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
19 20 2.409948 GGTGGGAGAGTTTGGAGATG 57.590 55.000 0.00 0.00 0.00 2.90
32 33 3.120468 TGGAGATGTGGAGAATCAGGA 57.880 47.619 0.00 0.00 36.25 3.86
37 38 1.279496 TGTGGAGAATCAGGAGTGGG 58.721 55.000 0.00 0.00 36.25 4.61
38 39 1.203300 TGTGGAGAATCAGGAGTGGGA 60.203 52.381 0.00 0.00 36.25 4.37
45 46 2.754012 ATCAGGAGTGGGAGAGAGAG 57.246 55.000 0.00 0.00 0.00 3.20
46 47 1.675007 TCAGGAGTGGGAGAGAGAGA 58.325 55.000 0.00 0.00 0.00 3.10
47 48 1.563879 TCAGGAGTGGGAGAGAGAGAG 59.436 57.143 0.00 0.00 0.00 3.20
48 49 0.926293 AGGAGTGGGAGAGAGAGAGG 59.074 60.000 0.00 0.00 0.00 3.69
49 50 0.106217 GGAGTGGGAGAGAGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
50 51 0.106217 GAGTGGGAGAGAGAGAGGGG 60.106 65.000 0.00 0.00 0.00 4.79
51 52 1.075600 GTGGGAGAGAGAGAGGGGG 60.076 68.421 0.00 0.00 0.00 5.40
212 213 2.771943 TCCGGGCAATCTCTTAATGAGT 59.228 45.455 0.00 0.00 43.13 3.41
213 214 3.199946 TCCGGGCAATCTCTTAATGAGTT 59.800 43.478 0.00 0.00 43.13 3.01
214 215 3.947834 CCGGGCAATCTCTTAATGAGTTT 59.052 43.478 0.00 0.00 43.13 2.66
215 216 5.104693 TCCGGGCAATCTCTTAATGAGTTTA 60.105 40.000 0.00 0.00 43.13 2.01
267 280 2.865551 CACAAACAACATCAAACTGGCC 59.134 45.455 0.00 0.00 0.00 5.36
287 300 1.672854 GGACGGACGGATCACATGGA 61.673 60.000 0.00 0.00 0.00 3.41
288 301 0.527817 GACGGACGGATCACATGGAC 60.528 60.000 0.00 0.00 0.00 4.02
289 302 1.227263 CGGACGGATCACATGGACC 60.227 63.158 0.00 0.00 0.00 4.46
290 303 1.904771 GGACGGATCACATGGACCA 59.095 57.895 0.00 0.00 0.00 4.02
291 304 0.462047 GGACGGATCACATGGACCAC 60.462 60.000 0.00 0.00 0.00 4.16
292 305 0.249120 GACGGATCACATGGACCACA 59.751 55.000 0.00 0.00 0.00 4.17
293 306 0.036388 ACGGATCACATGGACCACAC 60.036 55.000 0.00 0.00 0.00 3.82
294 307 0.744414 CGGATCACATGGACCACACC 60.744 60.000 0.00 0.00 0.00 4.16
295 308 0.327924 GGATCACATGGACCACACCA 59.672 55.000 0.00 0.00 44.41 4.17
296 309 1.453155 GATCACATGGACCACACCAC 58.547 55.000 0.00 0.00 43.03 4.16
297 310 0.321564 ATCACATGGACCACACCACG 60.322 55.000 0.00 0.00 43.03 4.94
298 311 1.227823 CACATGGACCACACCACGT 60.228 57.895 0.00 0.00 43.03 4.49
299 312 0.034198 CACATGGACCACACCACGTA 59.966 55.000 0.00 0.00 43.03 3.57
300 313 0.034337 ACATGGACCACACCACGTAC 59.966 55.000 0.00 0.00 43.03 3.67
357 370 3.126858 TCGGTGTTCACATACGTACTACC 59.873 47.826 0.00 0.00 33.14 3.18
358 371 3.119884 CGGTGTTCACATACGTACTACCA 60.120 47.826 0.00 0.00 0.00 3.25
359 372 4.418392 GGTGTTCACATACGTACTACCAG 58.582 47.826 0.00 0.00 0.00 4.00
361 374 3.760151 TGTTCACATACGTACTACCAGCT 59.240 43.478 0.00 0.00 0.00 4.24
362 375 4.219070 TGTTCACATACGTACTACCAGCTT 59.781 41.667 0.00 0.00 0.00 3.74
363 376 5.166398 GTTCACATACGTACTACCAGCTTT 58.834 41.667 0.00 0.00 0.00 3.51
364 377 4.740268 TCACATACGTACTACCAGCTTTG 58.260 43.478 0.00 0.00 0.00 2.77
389 418 4.055227 GATGCCCCCGGGTTTGGA 62.055 66.667 21.85 9.33 37.65 3.53
405 434 5.221244 GGGTTTGGACATAGATTATTGGTGC 60.221 44.000 0.00 0.00 0.00 5.01
473 502 0.798776 GAGTGGATCGCAAAGTGGTG 59.201 55.000 0.00 0.00 0.00 4.17
575 604 4.067896 TGAGAATGAGTGCTCAACCTTTC 58.932 43.478 5.95 5.72 43.58 2.62
584 613 1.949525 GCTCAACCTTTCTGCAGACAA 59.050 47.619 18.03 12.84 0.00 3.18
695 724 4.153835 TGAAAAACTGCTTTTGTGCAAAGG 59.846 37.500 0.00 2.91 42.18 3.11
760 790 5.593095 ACGCCTCTTTTCTTACCTTTTTCTT 59.407 36.000 0.00 0.00 0.00 2.52
764 794 8.818057 GCCTCTTTTCTTACCTTTTTCTTTTTC 58.182 33.333 0.00 0.00 0.00 2.29
791 830 2.964740 TGAGAATCAGACGCCTCTTTG 58.035 47.619 0.00 0.00 42.56 2.77
961 1017 2.291043 ATCCACGACACACTCCCCC 61.291 63.158 0.00 0.00 0.00 5.40
1098 1170 1.893808 CAAGGTGCGCACTTCCACT 60.894 57.895 36.84 23.42 32.68 4.00
1100 1172 3.414700 GGTGCGCACTTCCACTCG 61.415 66.667 36.84 0.00 32.68 4.18
1101 1173 2.661866 GTGCGCACTTCCACTCGT 60.662 61.111 32.55 0.00 0.00 4.18
1102 1174 2.661537 TGCGCACTTCCACTCGTG 60.662 61.111 5.66 0.00 0.00 4.35
1119 1191 2.230266 TCGTGGCAGCCTTTTATTTTCC 59.770 45.455 14.15 0.00 0.00 3.13
1129 1201 6.709846 CAGCCTTTTATTTTCCAACCATTTCA 59.290 34.615 0.00 0.00 0.00 2.69
1132 1204 7.412891 GCCTTTTATTTTCCAACCATTTCATCG 60.413 37.037 0.00 0.00 0.00 3.84
1137 1209 1.633432 TCCAACCATTTCATCGTCCCT 59.367 47.619 0.00 0.00 0.00 4.20
1146 1218 1.376424 CATCGTCCCTTGCTGCACT 60.376 57.895 0.00 0.00 0.00 4.40
1156 1228 2.110757 TTGCTGCACTGACCGATCCA 62.111 55.000 0.00 0.00 0.00 3.41
1222 1294 2.343758 GTCTCAGCTTCGGCCACA 59.656 61.111 2.24 0.00 43.01 4.17
1226 1298 2.972505 CAGCTTCGGCCACACGTT 60.973 61.111 2.24 0.00 43.01 3.99
1249 1321 4.657824 AGACACCGAACCACCGCG 62.658 66.667 0.00 0.00 0.00 6.46
1266 1338 2.033141 GCCAAGAGAGCAGGTGCA 59.967 61.111 4.48 0.00 45.16 4.57
1267 1339 1.378250 GCCAAGAGAGCAGGTGCAT 60.378 57.895 4.48 0.00 45.16 3.96
1269 1341 0.035725 CCAAGAGAGCAGGTGCATGA 60.036 55.000 4.48 0.00 45.16 3.07
1270 1342 1.370609 CAAGAGAGCAGGTGCATGAG 58.629 55.000 4.48 0.00 45.16 2.90
1272 1344 2.125229 AGAGCAGGTGCATGAGCG 60.125 61.111 4.48 0.00 46.23 5.03
1275 1347 1.300971 GAGCAGGTGCATGAGCGAAA 61.301 55.000 4.48 0.00 46.23 3.46
1276 1348 0.890542 AGCAGGTGCATGAGCGAAAA 60.891 50.000 4.48 0.00 46.23 2.29
1277 1349 0.171903 GCAGGTGCATGAGCGAAAAT 59.828 50.000 0.00 0.00 46.23 1.82
1279 1351 2.159393 GCAGGTGCATGAGCGAAAATAA 60.159 45.455 0.00 0.00 46.23 1.40
1280 1352 3.688272 CAGGTGCATGAGCGAAAATAAG 58.312 45.455 0.00 0.00 46.23 1.73
1281 1353 3.374988 CAGGTGCATGAGCGAAAATAAGA 59.625 43.478 0.00 0.00 46.23 2.10
1282 1354 3.624861 AGGTGCATGAGCGAAAATAAGAG 59.375 43.478 0.00 0.00 46.23 2.85
1284 1356 4.094887 GGTGCATGAGCGAAAATAAGAGAA 59.905 41.667 0.00 0.00 46.23 2.87
1285 1357 5.391950 GGTGCATGAGCGAAAATAAGAGAAA 60.392 40.000 0.00 0.00 46.23 2.52
1286 1358 6.261118 GTGCATGAGCGAAAATAAGAGAAAT 58.739 36.000 0.00 0.00 46.23 2.17
1289 1361 6.413235 GCATGAGCGAAAATAAGAGAAATCAC 59.587 38.462 0.00 0.00 0.00 3.06
1290 1362 7.466805 CATGAGCGAAAATAAGAGAAATCACA 58.533 34.615 0.00 0.00 0.00 3.58
1291 1363 7.065216 TGAGCGAAAATAAGAGAAATCACAG 57.935 36.000 0.00 0.00 0.00 3.66
1292 1364 5.873732 AGCGAAAATAAGAGAAATCACAGC 58.126 37.500 0.00 0.00 0.00 4.40
1293 1365 5.645497 AGCGAAAATAAGAGAAATCACAGCT 59.355 36.000 0.00 0.00 0.00 4.24
1294 1366 6.818644 AGCGAAAATAAGAGAAATCACAGCTA 59.181 34.615 0.00 0.00 0.00 3.32
1295 1367 6.902417 GCGAAAATAAGAGAAATCACAGCTAC 59.098 38.462 0.00 0.00 0.00 3.58
1296 1368 7.413000 GCGAAAATAAGAGAAATCACAGCTACA 60.413 37.037 0.00 0.00 0.00 2.74
1297 1369 8.607459 CGAAAATAAGAGAAATCACAGCTACAT 58.393 33.333 0.00 0.00 0.00 2.29
1298 1370 9.928236 GAAAATAAGAGAAATCACAGCTACATC 57.072 33.333 0.00 0.00 0.00 3.06
1299 1371 9.453572 AAAATAAGAGAAATCACAGCTACATCA 57.546 29.630 0.00 0.00 0.00 3.07
1300 1372 9.624373 AAATAAGAGAAATCACAGCTACATCAT 57.376 29.630 0.00 0.00 0.00 2.45
1301 1373 6.922247 AAGAGAAATCACAGCTACATCATG 57.078 37.500 0.00 0.00 0.00 3.07
1302 1374 4.815308 AGAGAAATCACAGCTACATCATGC 59.185 41.667 0.00 0.00 0.00 4.06
1303 1375 4.520179 AGAAATCACAGCTACATCATGCA 58.480 39.130 0.00 0.00 0.00 3.96
1304 1376 4.945543 AGAAATCACAGCTACATCATGCAA 59.054 37.500 0.00 0.00 0.00 4.08
1305 1377 4.895224 AATCACAGCTACATCATGCAAG 57.105 40.909 0.00 0.00 0.00 4.01
1306 1378 3.615224 TCACAGCTACATCATGCAAGA 57.385 42.857 0.00 0.00 0.00 3.02
1307 1379 3.264947 TCACAGCTACATCATGCAAGAC 58.735 45.455 0.00 0.00 0.00 3.01
1308 1380 3.004862 CACAGCTACATCATGCAAGACA 58.995 45.455 0.00 0.00 0.00 3.41
1311 1383 3.688185 CAGCTACATCATGCAAGACAAGT 59.312 43.478 0.00 0.00 0.00 3.16
1317 1389 7.225538 GCTACATCATGCAAGACAAGTATAGTT 59.774 37.037 0.00 0.00 0.00 2.24
1321 1393 8.671921 CATCATGCAAGACAAGTATAGTTCTTT 58.328 33.333 0.00 0.00 0.00 2.52
1323 1395 7.334421 TCATGCAAGACAAGTATAGTTCTTTCC 59.666 37.037 0.00 0.00 0.00 3.13
1336 1408 9.315525 GTATAGTTCTTTCCAGAATTGTAGGAC 57.684 37.037 0.00 0.00 41.26 3.85
1338 1410 6.234177 AGTTCTTTCCAGAATTGTAGGACTG 58.766 40.000 0.00 0.00 41.26 3.51
1340 1412 6.433847 TCTTTCCAGAATTGTAGGACTGAA 57.566 37.500 0.00 0.00 32.90 3.02
1345 1417 5.013079 TCCAGAATTGTAGGACTGAACATGT 59.987 40.000 0.00 0.00 32.90 3.21
1364 1437 7.325660 ACATGTGTTGATTGATTGATACCTC 57.674 36.000 0.00 0.00 0.00 3.85
1666 1739 1.153939 CGTCGAGAAGGTCAGCCAG 60.154 63.158 0.00 0.00 37.19 4.85
1732 1806 3.745458 CACTTGTCTCTTTTCTGAGCCTC 59.255 47.826 0.00 0.00 34.29 4.70
1742 1816 8.160106 TCTCTTTTCTGAGCCTCTAAATTTCTT 58.840 33.333 0.00 0.00 34.29 2.52
1754 1828 7.553044 GCCTCTAAATTTCTTTTACAGCCTAGA 59.447 37.037 0.00 0.00 0.00 2.43
1755 1829 8.884726 CCTCTAAATTTCTTTTACAGCCTAGAC 58.115 37.037 0.00 0.00 0.00 2.59
1967 2042 4.789095 ACGTGTAGCTGTAACACAAAAG 57.211 40.909 16.41 4.70 46.05 2.27
2033 2118 5.292834 AGAGTAGAAACATGTGCATCAATCG 59.707 40.000 0.00 0.00 0.00 3.34
2092 2177 7.732025 TCCATGTCAGTACTTCAGTCTTTTAA 58.268 34.615 0.00 0.00 0.00 1.52
2182 2273 3.929610 GGGAGAGAAGAAAACTCATGTCG 59.070 47.826 0.00 0.00 36.91 4.35
2185 2276 3.067106 GAGAAGAAAACTCATGTCGCCA 58.933 45.455 0.00 0.00 34.87 5.69
2186 2277 3.679389 AGAAGAAAACTCATGTCGCCAT 58.321 40.909 0.00 0.00 0.00 4.40
2187 2278 4.074970 AGAAGAAAACTCATGTCGCCATT 58.925 39.130 0.00 0.00 0.00 3.16
2805 2896 1.244019 AAACCCTGAATGCACGCTCC 61.244 55.000 0.00 0.00 0.00 4.70
2883 2974 3.011818 CACATCTCTGCAGCATAAACCA 58.988 45.455 9.47 0.00 0.00 3.67
2901 2992 3.751518 ACCAGTAACCAGAACATCCAAC 58.248 45.455 0.00 0.00 0.00 3.77
2913 3004 1.311859 CATCCAACGCATGCCTATGT 58.688 50.000 13.15 0.33 36.65 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.484240 CTCCCACTCCTGATTCTCCAC 59.516 57.143 0.00 0.00 0.00 4.02
32 33 1.589399 CCCCCTCTCTCTCTCCCACT 61.589 65.000 0.00 0.00 0.00 4.00
51 52 2.861974 TGTCCTCCCCAAACCCCC 60.862 66.667 0.00 0.00 0.00 5.40
58 59 1.638589 CCTTATTTGGTGTCCTCCCCA 59.361 52.381 0.00 0.00 0.00 4.96
60 61 2.684038 GCTCCTTATTTGGTGTCCTCCC 60.684 54.545 0.00 0.00 0.00 4.30
267 280 1.588932 CATGTGATCCGTCCGTCCG 60.589 63.158 0.00 0.00 0.00 4.79
287 300 1.144496 GTGGTGTACGTGGTGTGGT 59.856 57.895 0.00 0.00 0.00 4.16
288 301 1.144276 TGTGGTGTACGTGGTGTGG 59.856 57.895 0.00 0.00 0.00 4.17
289 302 1.155424 GGTGTGGTGTACGTGGTGTG 61.155 60.000 0.00 0.00 0.00 3.82
290 303 1.144496 GGTGTGGTGTACGTGGTGT 59.856 57.895 0.00 0.00 0.00 4.16
291 304 1.144276 TGGTGTGGTGTACGTGGTG 59.856 57.895 0.00 0.00 0.00 4.17
292 305 1.144496 GTGGTGTGGTGTACGTGGT 59.856 57.895 0.00 0.00 0.00 4.16
293 306 1.595929 GGTGGTGTGGTGTACGTGG 60.596 63.158 0.00 0.00 0.00 4.94
294 307 1.144276 TGGTGGTGTGGTGTACGTG 59.856 57.895 0.00 0.00 0.00 4.49
295 308 1.144496 GTGGTGGTGTGGTGTACGT 59.856 57.895 0.00 0.00 0.00 3.57
296 309 1.595929 GGTGGTGGTGTGGTGTACG 60.596 63.158 0.00 0.00 0.00 3.67
297 310 1.228033 GGGTGGTGGTGTGGTGTAC 60.228 63.158 0.00 0.00 0.00 2.90
298 311 2.453812 GGGGTGGTGGTGTGGTGTA 61.454 63.158 0.00 0.00 0.00 2.90
299 312 3.816090 GGGGTGGTGGTGTGGTGT 61.816 66.667 0.00 0.00 0.00 4.16
300 313 4.947147 CGGGGTGGTGGTGTGGTG 62.947 72.222 0.00 0.00 0.00 4.17
357 370 0.529378 GCATCCAAGGACCAAAGCTG 59.471 55.000 0.00 0.00 0.00 4.24
358 371 0.613012 GGCATCCAAGGACCAAAGCT 60.613 55.000 0.00 0.00 0.00 3.74
359 372 1.607801 GGGCATCCAAGGACCAAAGC 61.608 60.000 0.00 0.00 0.00 3.51
361 374 1.078347 GGGGCATCCAAGGACCAAA 59.922 57.895 0.00 0.00 35.00 3.28
362 375 2.770130 GGGGCATCCAAGGACCAA 59.230 61.111 0.00 0.00 35.00 3.67
363 376 3.346734 GGGGGCATCCAAGGACCA 61.347 66.667 0.00 0.00 37.22 4.02
364 377 4.506255 CGGGGGCATCCAAGGACC 62.506 72.222 0.00 0.00 37.22 4.46
473 502 0.532862 CATATCACCACGCCCTGGAC 60.533 60.000 0.00 0.00 43.95 4.02
768 798 3.685139 AGAGGCGTCTGATTCTCAAAA 57.315 42.857 8.40 0.00 0.00 2.44
777 816 0.966179 TACTGCAAAGAGGCGTCTGA 59.034 50.000 10.16 0.00 36.28 3.27
791 830 2.413837 TCGAACTGAAAAGCCTACTGC 58.586 47.619 0.00 0.00 41.71 4.40
834 874 1.148273 GCCTAATGTGGCCCATCGA 59.852 57.895 0.00 0.00 46.82 3.59
1007 1067 1.368969 CGGAGATTCGGCGAGTACG 60.369 63.158 10.46 7.98 42.93 3.67
1008 1068 1.008767 CCGGAGATTCGGCGAGTAC 60.009 63.158 10.46 5.83 43.71 2.73
1063 1135 3.497932 GCCGAGAGCTGCTGCAAG 61.498 66.667 18.42 5.61 42.74 4.01
1098 1170 2.230266 GGAAAATAAAAGGCTGCCACGA 59.770 45.455 22.65 3.08 0.00 4.35
1100 1172 3.676291 TGGAAAATAAAAGGCTGCCAC 57.324 42.857 22.65 0.00 0.00 5.01
1101 1173 3.244387 GGTTGGAAAATAAAAGGCTGCCA 60.244 43.478 22.65 0.00 0.00 4.92
1102 1174 3.244387 TGGTTGGAAAATAAAAGGCTGCC 60.244 43.478 11.65 11.65 0.00 4.85
1110 1182 7.093992 GGACGATGAAATGGTTGGAAAATAAA 58.906 34.615 0.00 0.00 34.53 1.40
1119 1191 2.415893 GCAAGGGACGATGAAATGGTTG 60.416 50.000 0.00 0.00 34.53 3.77
1129 1201 1.376424 CAGTGCAGCAAGGGACGAT 60.376 57.895 0.00 0.00 33.93 3.73
1132 1204 1.968540 GGTCAGTGCAGCAAGGGAC 60.969 63.158 0.00 5.20 0.00 4.46
1137 1209 1.375908 GGATCGGTCAGTGCAGCAA 60.376 57.895 0.00 0.00 0.00 3.91
1146 1218 0.396435 AGCACAAGTTGGATCGGTCA 59.604 50.000 7.96 0.00 0.00 4.02
1156 1228 1.226660 GCGCACAACAGCACAAGTT 60.227 52.632 0.30 0.00 0.00 2.66
1222 1294 2.916502 TTCGGTGTCTGCAGCAACGT 62.917 55.000 32.42 0.00 45.99 3.99
1226 1298 2.280797 GGTTCGGTGTCTGCAGCA 60.281 61.111 9.47 7.85 42.79 4.41
1249 1321 1.378250 ATGCACCTGCTCTCTTGGC 60.378 57.895 0.00 0.00 42.66 4.52
1266 1338 7.615582 TGTGATTTCTCTTATTTTCGCTCAT 57.384 32.000 0.00 0.00 0.00 2.90
1267 1339 6.402550 GCTGTGATTTCTCTTATTTTCGCTCA 60.403 38.462 0.00 0.00 0.00 4.26
1269 1341 5.645497 AGCTGTGATTTCTCTTATTTTCGCT 59.355 36.000 0.00 0.00 0.00 4.93
1270 1342 5.873732 AGCTGTGATTTCTCTTATTTTCGC 58.126 37.500 0.00 0.00 0.00 4.70
1272 1344 9.928236 GATGTAGCTGTGATTTCTCTTATTTTC 57.072 33.333 0.00 0.00 0.00 2.29
1275 1347 9.053840 CATGATGTAGCTGTGATTTCTCTTATT 57.946 33.333 0.00 0.00 0.00 1.40
1276 1348 7.172875 GCATGATGTAGCTGTGATTTCTCTTAT 59.827 37.037 0.00 0.00 0.00 1.73
1277 1349 6.481313 GCATGATGTAGCTGTGATTTCTCTTA 59.519 38.462 0.00 0.00 0.00 2.10
1279 1351 4.815308 GCATGATGTAGCTGTGATTTCTCT 59.185 41.667 0.00 0.00 0.00 3.10
1280 1352 4.573607 TGCATGATGTAGCTGTGATTTCTC 59.426 41.667 0.00 0.00 0.00 2.87
1281 1353 4.520179 TGCATGATGTAGCTGTGATTTCT 58.480 39.130 0.00 0.00 0.00 2.52
1282 1354 4.888038 TGCATGATGTAGCTGTGATTTC 57.112 40.909 0.00 0.00 0.00 2.17
1284 1356 4.334759 GTCTTGCATGATGTAGCTGTGATT 59.665 41.667 5.49 0.00 0.00 2.57
1285 1357 3.875727 GTCTTGCATGATGTAGCTGTGAT 59.124 43.478 5.49 0.00 0.00 3.06
1286 1358 3.264947 GTCTTGCATGATGTAGCTGTGA 58.735 45.455 5.49 0.00 0.00 3.58
1289 1361 3.688185 ACTTGTCTTGCATGATGTAGCTG 59.312 43.478 5.49 0.00 0.00 4.24
1290 1362 3.947868 ACTTGTCTTGCATGATGTAGCT 58.052 40.909 5.49 0.00 0.00 3.32
1291 1363 5.998454 ATACTTGTCTTGCATGATGTAGC 57.002 39.130 5.49 0.00 0.00 3.58
1292 1364 8.654230 AACTATACTTGTCTTGCATGATGTAG 57.346 34.615 5.49 4.75 0.00 2.74
1293 1365 8.478066 AGAACTATACTTGTCTTGCATGATGTA 58.522 33.333 5.49 9.68 0.00 2.29
1294 1366 7.334090 AGAACTATACTTGTCTTGCATGATGT 58.666 34.615 5.49 7.99 0.00 3.06
1295 1367 7.783090 AGAACTATACTTGTCTTGCATGATG 57.217 36.000 5.49 2.74 0.00 3.07
1296 1368 8.798859 AAAGAACTATACTTGTCTTGCATGAT 57.201 30.769 5.49 0.00 0.00 2.45
1297 1369 7.334421 GGAAAGAACTATACTTGTCTTGCATGA 59.666 37.037 0.00 0.00 0.00 3.07
1298 1370 7.119699 TGGAAAGAACTATACTTGTCTTGCATG 59.880 37.037 0.00 0.00 0.00 4.06
1299 1371 7.168219 TGGAAAGAACTATACTTGTCTTGCAT 58.832 34.615 0.00 0.00 0.00 3.96
1300 1372 6.530120 TGGAAAGAACTATACTTGTCTTGCA 58.470 36.000 0.00 0.00 0.00 4.08
1301 1373 6.874134 TCTGGAAAGAACTATACTTGTCTTGC 59.126 38.462 0.00 0.00 0.00 4.01
1302 1374 8.833231 TTCTGGAAAGAACTATACTTGTCTTG 57.167 34.615 0.00 0.00 0.00 3.02
1304 1376 9.442047 CAATTCTGGAAAGAACTATACTTGTCT 57.558 33.333 0.00 0.00 0.00 3.41
1305 1377 9.220767 ACAATTCTGGAAAGAACTATACTTGTC 57.779 33.333 0.00 0.00 0.00 3.18
1308 1380 9.892130 CCTACAATTCTGGAAAGAACTATACTT 57.108 33.333 0.00 0.00 0.00 2.24
1311 1383 9.268282 AGTCCTACAATTCTGGAAAGAACTATA 57.732 33.333 0.00 0.00 0.00 1.31
1317 1389 6.183361 TGTTCAGTCCTACAATTCTGGAAAGA 60.183 38.462 0.00 0.00 0.00 2.52
1321 1393 5.013079 ACATGTTCAGTCCTACAATTCTGGA 59.987 40.000 0.00 0.00 0.00 3.86
1323 1395 5.702670 ACACATGTTCAGTCCTACAATTCTG 59.297 40.000 0.00 0.00 0.00 3.02
1336 1408 7.699391 GGTATCAATCAATCAACACATGTTCAG 59.301 37.037 0.00 0.00 35.83 3.02
1338 1410 7.765307 AGGTATCAATCAATCAACACATGTTC 58.235 34.615 0.00 0.00 35.83 3.18
1340 1412 6.885918 TGAGGTATCAATCAATCAACACATGT 59.114 34.615 0.00 0.00 30.61 3.21
1345 1417 5.887598 CCCTTGAGGTATCAATCAATCAACA 59.112 40.000 0.00 0.00 44.32 3.33
1462 1535 4.193334 TCGATCTCGTGCAGGGCG 62.193 66.667 6.56 6.12 40.80 6.13
1732 1806 9.220767 ACTGTCTAGGCTGTAAAAGAAATTTAG 57.779 33.333 4.90 0.00 34.21 1.85
1742 1816 6.659745 TGAACTAACTGTCTAGGCTGTAAA 57.340 37.500 7.34 0.00 0.00 2.01
1754 1828 8.491331 AAATGCATTTTTGTTGAACTAACTGT 57.509 26.923 18.99 0.00 40.05 3.55
1755 1829 9.771915 AAAAATGCATTTTTGTTGAACTAACTG 57.228 25.926 36.98 0.00 45.31 3.16
1967 2042 4.938080 TCGATGGTATTTTCTCTCTCAGC 58.062 43.478 0.00 0.00 0.00 4.26
2033 2118 6.199719 CACAAAGCTGAATTTTGTCTTCCTTC 59.800 38.462 0.00 0.00 44.50 3.46
2132 2223 7.250569 CCACATAATTCTTGTACATGACAACC 58.749 38.462 10.76 0.00 43.30 3.77
2138 2229 5.221106 CCCAGCCACATAATTCTTGTACATG 60.221 44.000 0.00 0.00 0.00 3.21
2222 2313 5.184096 TGTTGTCACTGTTGTAACAATGGTT 59.816 36.000 6.39 0.00 36.83 3.67
2416 2507 4.147449 GCCCCAAGCCGCCAATTC 62.147 66.667 0.00 0.00 34.35 2.17
2631 2722 9.337396 GGTCCCTTTTGAAAAGAAACATATTTT 57.663 29.630 18.59 0.00 0.00 1.82
2712 2803 2.675889 GCAAATGATGAAGGCAACCCAG 60.676 50.000 0.00 0.00 37.17 4.45
2805 2896 0.469917 AGATGGGAATGGCACCTACG 59.530 55.000 0.00 0.00 0.00 3.51
2883 2974 2.224426 TGCGTTGGATGTTCTGGTTACT 60.224 45.455 0.00 0.00 0.00 2.24
2901 2992 0.937304 GTGTACCACATAGGCATGCG 59.063 55.000 12.44 0.00 43.14 4.73
2913 3004 1.646912 TCGGGAAAGGATGTGTACCA 58.353 50.000 0.00 0.00 0.00 3.25



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

AutoCloner maintained by Alex Coulton.