Multiple sequence alignment - TraesCS4A01G355700

Loading Multiple Alignment...

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 TraesCS4A01G355700 chr4A 100.000 3157 0 0 1 3157 629473797 629476953 0.000000e+00 5830
1 TraesCS4A01G355700 chr4A 95.238 84 4 0 1315 1398 629475030 629475113 1.980000e-27 134
2 TraesCS4A01G355700 chr4A 95.238 84 4 0 1234 1317 629475111 629475194 1.980000e-27 134
3 TraesCS4A01G355700 chr5B 91.715 1895 94 20 1315 3157 680605349 680603466 0.000000e+00 2571
4 TraesCS4A01G355700 chr5B 88.464 1361 77 31 3 1317 680606592 680605266 0.000000e+00 1570
5 TraesCS4A01G355700 chr5D 92.328 1160 50 8 2017 3157 539025733 539024594 0.000000e+00 1613
6 TraesCS4A01G355700 chr5D 96.247 746 23 2 1315 2058 539026470 539025728 0.000000e+00 1218
7 TraesCS4A01G355700 chr5D 89.904 624 38 11 715 1317 539027006 539026387 0.000000e+00 780


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 TraesCS4A01G355700 chr4A 629473797 629476953 3156 False 2032.666667 5830 96.825333 1 3157 3 chr4A.!!$F1 3156
1 TraesCS4A01G355700 chr5B 680603466 680606592 3126 True 2070.500000 2571 90.089500 3 3157 2 chr5B.!!$R1 3154
2 TraesCS4A01G355700 chr5D 539024594 539027006 2412 True 1203.666667 1613 92.826333 715 3157 3 chr5D.!!$R1 2442

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
438 473 0.036010 AGCGCTGTTAGGCAGTTCAT 60.036 50.0 10.39 0.0 46.64 2.57 F
549 589 0.257328 TCCAAACACAGGGCACAGAA 59.743 50.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1358 1.141053 GGTTGGACACAGAACTGAGGT 59.859 52.381 8.87 6.26 0.00 3.85 R
2494 2608 0.107214 AACATGGTATGCCTCCCACG 60.107 55.000 0.16 0.00 32.49 4.94 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
35 36 1.821216 ATATAAAATCCCCGCGCCAG 58.179 50.000 0.00 0.00 0.00 4.85
43 44 2.104331 CCCGCGCCAGTACTGTAG 59.896 66.667 21.18 14.91 0.00 2.74
86 87 0.671781 CTCTGCTCCGGTCAACCAAG 60.672 60.000 0.00 0.00 35.14 3.61
87 88 1.071471 CTGCTCCGGTCAACCAAGT 59.929 57.895 0.00 0.00 35.14 3.16
88 89 0.535102 CTGCTCCGGTCAACCAAGTT 60.535 55.000 0.00 0.00 35.14 2.66
89 90 0.534203 TGCTCCGGTCAACCAAGTTC 60.534 55.000 0.00 0.00 35.14 3.01
90 91 1.235281 GCTCCGGTCAACCAAGTTCC 61.235 60.000 0.00 0.00 35.14 3.62
184 197 0.237235 GCGACCAAGTTTCGATTGCA 59.763 50.000 1.17 0.00 38.85 4.08
191 204 1.156736 AGTTTCGATTGCAACGGGAG 58.843 50.000 17.28 2.79 0.00 4.30
192 205 1.153353 GTTTCGATTGCAACGGGAGA 58.847 50.000 17.28 4.80 0.00 3.71
193 206 1.136057 GTTTCGATTGCAACGGGAGAC 60.136 52.381 17.28 10.07 0.00 3.36
194 207 0.320374 TTCGATTGCAACGGGAGACT 59.680 50.000 17.28 0.00 0.00 3.24
195 208 0.389817 TCGATTGCAACGGGAGACTG 60.390 55.000 17.28 0.00 44.60 3.51
236 249 1.574702 GAGTTTCGGCCCTGTTTCCG 61.575 60.000 0.00 0.00 46.52 4.30
246 259 4.735132 TGTTTCCGGCTCGAGCGG 62.735 66.667 31.58 31.58 43.26 5.52
288 314 2.367567 TCTGGTTTTGGTTAGAGAGCGT 59.632 45.455 0.00 0.00 0.00 5.07
291 317 2.350484 GGTTTTGGTTAGAGAGCGTTGC 60.350 50.000 0.00 0.00 0.00 4.17
292 318 2.248280 TTTGGTTAGAGAGCGTTGCA 57.752 45.000 0.00 0.00 0.00 4.08
308 334 1.450312 GCAGAATCAGGTCGGGTGG 60.450 63.158 0.00 0.00 0.00 4.61
312 338 0.323629 GAATCAGGTCGGGTGGTTGA 59.676 55.000 0.00 0.00 0.00 3.18
313 339 0.991920 AATCAGGTCGGGTGGTTGAT 59.008 50.000 0.00 0.00 0.00 2.57
314 340 1.874129 ATCAGGTCGGGTGGTTGATA 58.126 50.000 0.00 0.00 0.00 2.15
315 341 0.899720 TCAGGTCGGGTGGTTGATAC 59.100 55.000 0.00 0.00 0.00 2.24
316 342 0.902531 CAGGTCGGGTGGTTGATACT 59.097 55.000 0.00 0.00 0.00 2.12
317 343 1.278127 CAGGTCGGGTGGTTGATACTT 59.722 52.381 0.00 0.00 0.00 2.24
318 344 1.278127 AGGTCGGGTGGTTGATACTTG 59.722 52.381 0.00 0.00 0.00 3.16
389 421 1.886542 GATTATGAATCCCCCAACGGC 59.113 52.381 0.00 0.00 31.60 5.68
390 422 0.626382 TTATGAATCCCCCAACGGCA 59.374 50.000 0.00 0.00 0.00 5.69
391 423 0.182537 TATGAATCCCCCAACGGCAG 59.817 55.000 0.00 0.00 0.00 4.85
392 424 2.440247 GAATCCCCCAACGGCAGG 60.440 66.667 0.00 0.00 0.00 4.85
426 461 3.587797 TTAAGCTTACTGTAGCGCTGT 57.412 42.857 22.90 12.55 45.82 4.40
438 473 0.036010 AGCGCTGTTAGGCAGTTCAT 60.036 50.000 10.39 0.00 46.64 2.57
448 483 2.589540 CAGTTCATGCCCCGCCTA 59.410 61.111 0.00 0.00 0.00 3.93
456 491 1.136329 ATGCCCCGCCTAGATGGAAT 61.136 55.000 0.00 0.00 38.35 3.01
460 495 1.978580 CCCCGCCTAGATGGAATAACT 59.021 52.381 0.00 0.00 38.35 2.24
471 506 4.820716 AGATGGAATAACTGAGCATGCTTC 59.179 41.667 23.61 13.14 0.00 3.86
481 516 2.224378 TGAGCATGCTTCTAGGGCATAC 60.224 50.000 23.61 14.92 46.94 2.39
482 517 1.770658 AGCATGCTTCTAGGGCATACA 59.229 47.619 16.30 0.00 46.94 2.29
483 518 2.149578 GCATGCTTCTAGGGCATACAG 58.850 52.381 11.37 11.12 46.94 2.74
484 519 2.486191 GCATGCTTCTAGGGCATACAGT 60.486 50.000 11.37 1.40 46.94 3.55
485 520 2.988010 TGCTTCTAGGGCATACAGTG 57.012 50.000 7.11 0.00 34.56 3.66
486 521 2.187958 TGCTTCTAGGGCATACAGTGT 58.812 47.619 0.00 0.00 34.56 3.55
487 522 3.371034 TGCTTCTAGGGCATACAGTGTA 58.629 45.455 5.24 5.24 34.56 2.90
490 525 4.202264 GCTTCTAGGGCATACAGTGTATGT 60.202 45.833 33.25 21.59 46.45 2.29
495 530 5.950544 AGGGCATACAGTGTATGTTAAGA 57.049 39.130 33.25 3.03 39.96 2.10
546 581 1.411977 CATTTCCAAACACAGGGCACA 59.588 47.619 0.00 0.00 0.00 4.57
549 589 0.257328 TCCAAACACAGGGCACAGAA 59.743 50.000 0.00 0.00 0.00 3.02
564 604 3.008330 CACAGAAAGGAAGATCCAGCAG 58.992 50.000 0.00 0.00 39.61 4.24
568 608 4.335874 CAGAAAGGAAGATCCAGCAGAATG 59.664 45.833 0.00 0.00 39.61 2.67
596 637 8.916628 TTTTCCTTTATTTTGCAATTTAGCCT 57.083 26.923 0.00 0.00 0.00 4.58
603 644 1.685421 GCAATTTAGCCTGGGCCCA 60.685 57.895 26.67 26.67 43.17 5.36
630 671 1.135139 TCTCAGTACAGCGAATCTGCC 59.865 52.381 0.00 0.00 46.76 4.85
639 680 0.953727 GCGAATCTGCCATGCCATTA 59.046 50.000 0.00 0.00 0.00 1.90
649 691 3.451540 TGCCATGCCATTATGTTTGATGT 59.548 39.130 0.00 0.00 0.00 3.06
665 707 5.426689 TTGATGTCCAGCTTCTATTCTGT 57.573 39.130 0.00 0.00 0.00 3.41
708 750 0.947660 TTCTCTTCTGCTGTGCTGCG 60.948 55.000 0.00 0.00 35.36 5.18
812 856 0.609662 ACAAATTGCCATGGTCAGCC 59.390 50.000 14.67 0.00 0.00 4.85
867 927 3.121544 GCGGTACCTATGAAGCACTTAC 58.878 50.000 10.90 0.00 0.00 2.34
938 999 7.426929 TCTCTGTATTGCTCTTGTTCTTTTC 57.573 36.000 0.00 0.00 0.00 2.29
952 1013 4.334203 TGTTCTTTTCGCAAGCTCTAACAA 59.666 37.500 0.00 0.00 37.18 2.83
1071 1133 3.318839 CCACAACTGATGAAAGCCTCAAA 59.681 43.478 0.00 0.00 37.67 2.69
1172 1234 9.539825 TTTACAATTCAACAACTGCATATGTTT 57.460 25.926 12.97 3.15 37.66 2.83
1174 1236 6.073657 ACAATTCAACAACTGCATATGTTTGC 60.074 34.615 12.97 0.00 43.07 3.68
1252 1315 4.301072 TGCCTGCTACTGGACTATTTTT 57.699 40.909 0.00 0.00 0.00 1.94
1307 1370 7.180051 AGAGATCAATCTTTACCTCAGTTCTGT 59.820 37.037 0.00 0.00 37.25 3.41
1308 1371 7.102346 AGATCAATCTTTACCTCAGTTCTGTG 58.898 38.462 0.00 0.00 31.97 3.66
1309 1372 6.174720 TCAATCTTTACCTCAGTTCTGTGT 57.825 37.500 0.00 2.29 0.00 3.72
1310 1373 6.223852 TCAATCTTTACCTCAGTTCTGTGTC 58.776 40.000 0.00 0.00 0.00 3.67
1311 1374 4.602340 TCTTTACCTCAGTTCTGTGTCC 57.398 45.455 0.00 0.00 0.00 4.02
1312 1375 3.964688 TCTTTACCTCAGTTCTGTGTCCA 59.035 43.478 0.00 0.00 0.00 4.02
1313 1376 4.407621 TCTTTACCTCAGTTCTGTGTCCAA 59.592 41.667 0.00 0.00 0.00 3.53
1314 1377 2.622064 ACCTCAGTTCTGTGTCCAAC 57.378 50.000 0.00 0.00 0.00 3.77
1315 1378 1.141053 ACCTCAGTTCTGTGTCCAACC 59.859 52.381 0.00 0.00 0.00 3.77
1316 1379 1.417890 CCTCAGTTCTGTGTCCAACCT 59.582 52.381 0.00 0.00 0.00 3.50
1317 1380 2.487934 CTCAGTTCTGTGTCCAACCTG 58.512 52.381 0.00 0.00 0.00 4.00
1318 1381 0.947244 CAGTTCTGTGTCCAACCTGC 59.053 55.000 0.00 0.00 0.00 4.85
1319 1382 0.839946 AGTTCTGTGTCCAACCTGCT 59.160 50.000 0.00 0.00 0.00 4.24
1320 1383 2.047061 AGTTCTGTGTCCAACCTGCTA 58.953 47.619 0.00 0.00 0.00 3.49
1321 1384 2.143925 GTTCTGTGTCCAACCTGCTAC 58.856 52.381 0.00 0.00 0.00 3.58
1322 1385 1.717032 TCTGTGTCCAACCTGCTACT 58.283 50.000 0.00 0.00 0.00 2.57
1323 1386 1.344438 TCTGTGTCCAACCTGCTACTG 59.656 52.381 0.00 0.00 0.00 2.74
1324 1387 0.396435 TGTGTCCAACCTGCTACTGG 59.604 55.000 0.00 0.00 0.00 4.00
1325 1388 0.685097 GTGTCCAACCTGCTACTGGA 59.315 55.000 0.00 0.00 36.89 3.86
1327 1390 3.475932 TCCAACCTGCTACTGGACT 57.524 52.632 0.00 0.00 34.26 3.85
1328 1391 1.267121 TCCAACCTGCTACTGGACTC 58.733 55.000 0.00 0.00 34.26 3.36
1329 1392 1.203187 TCCAACCTGCTACTGGACTCT 60.203 52.381 0.00 0.00 34.26 3.24
1330 1393 1.625818 CCAACCTGCTACTGGACTCTT 59.374 52.381 0.00 0.00 31.38 2.85
1331 1394 2.039084 CCAACCTGCTACTGGACTCTTT 59.961 50.000 0.00 0.00 31.38 2.52
1332 1395 3.496870 CCAACCTGCTACTGGACTCTTTT 60.497 47.826 0.00 0.00 31.38 2.27
1333 1396 3.686916 ACCTGCTACTGGACTCTTTTC 57.313 47.619 0.00 0.00 0.00 2.29
1334 1397 2.028930 ACCTGCTACTGGACTCTTTTCG 60.029 50.000 0.00 0.00 0.00 3.46
1335 1398 2.028930 CCTGCTACTGGACTCTTTTCGT 60.029 50.000 0.00 0.00 0.00 3.85
1336 1399 3.246619 CTGCTACTGGACTCTTTTCGTC 58.753 50.000 0.00 0.00 0.00 4.20
1337 1400 2.626266 TGCTACTGGACTCTTTTCGTCA 59.374 45.455 0.00 0.00 33.11 4.35
1338 1401 2.987821 GCTACTGGACTCTTTTCGTCAC 59.012 50.000 0.00 0.00 33.11 3.67
1339 1402 3.305471 GCTACTGGACTCTTTTCGTCACT 60.305 47.826 0.00 0.00 33.11 3.41
1340 1403 4.082895 GCTACTGGACTCTTTTCGTCACTA 60.083 45.833 0.00 0.00 33.11 2.74
1341 1404 4.506886 ACTGGACTCTTTTCGTCACTAG 57.493 45.455 0.00 0.00 33.11 2.57
1342 1405 3.890147 ACTGGACTCTTTTCGTCACTAGT 59.110 43.478 0.00 0.00 33.11 2.57
1343 1406 4.341520 ACTGGACTCTTTTCGTCACTAGTT 59.658 41.667 0.00 0.00 33.11 2.24
1344 1407 5.533903 ACTGGACTCTTTTCGTCACTAGTTA 59.466 40.000 0.00 0.00 33.11 2.24
1345 1408 6.208994 ACTGGACTCTTTTCGTCACTAGTTAT 59.791 38.462 0.00 0.00 33.11 1.89
1346 1409 6.989659 TGGACTCTTTTCGTCACTAGTTATT 58.010 36.000 0.00 0.00 33.11 1.40
1347 1410 7.439381 TGGACTCTTTTCGTCACTAGTTATTT 58.561 34.615 0.00 0.00 33.11 1.40
1348 1411 8.579006 TGGACTCTTTTCGTCACTAGTTATTTA 58.421 33.333 0.00 0.00 33.11 1.40
1349 1412 8.858186 GGACTCTTTTCGTCACTAGTTATTTAC 58.142 37.037 0.00 0.00 33.11 2.01
1350 1413 9.623350 GACTCTTTTCGTCACTAGTTATTTACT 57.377 33.333 0.00 0.00 41.04 2.24
1351 1414 9.978044 ACTCTTTTCGTCACTAGTTATTTACTT 57.022 29.630 0.00 0.00 38.33 2.24
1380 1443 9.823647 TTTGTCTCATAGATCAATCTTTACCTC 57.176 33.333 0.00 0.00 38.32 3.85
1381 1444 8.539117 TGTCTCATAGATCAATCTTTACCTCA 57.461 34.615 0.00 0.00 38.32 3.86
1382 1445 8.637099 TGTCTCATAGATCAATCTTTACCTCAG 58.363 37.037 0.00 0.00 38.32 3.35
1383 1446 8.637986 GTCTCATAGATCAATCTTTACCTCAGT 58.362 37.037 0.00 0.00 38.32 3.41
1384 1447 9.206690 TCTCATAGATCAATCTTTACCTCAGTT 57.793 33.333 0.00 0.00 38.32 3.16
1385 1448 9.474920 CTCATAGATCAATCTTTACCTCAGTTC 57.525 37.037 0.00 0.00 38.32 3.01
1386 1449 9.206690 TCATAGATCAATCTTTACCTCAGTTCT 57.793 33.333 0.00 0.00 38.32 3.01
1387 1450 9.258826 CATAGATCAATCTTTACCTCAGTTCTG 57.741 37.037 0.00 0.00 38.32 3.02
1394 1457 4.039245 TCTTTACCTCAGTTCTGTGTCCAG 59.961 45.833 0.00 0.00 40.25 3.86
1548 1612 3.057946 GGTTGACTGAGTGATGCCTTTTC 60.058 47.826 0.00 0.00 0.00 2.29
1561 1627 2.426738 TGCCTTTTCACCTTCACAACTG 59.573 45.455 0.00 0.00 0.00 3.16
1886 1952 4.183858 CGTGGTGGTGGTGGTGGT 62.184 66.667 0.00 0.00 0.00 4.16
1887 1953 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
1888 1954 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
1937 2003 0.247736 ACTTTGCTAGAGAGTGCCCG 59.752 55.000 0.00 0.00 0.00 6.13
2012 2078 1.183549 GTGGTAGATCTGACCGTGGT 58.816 55.000 5.18 0.00 40.09 4.16
2015 2081 0.179108 GTAGATCTGACCGTGGTGGC 60.179 60.000 5.18 0.00 43.94 5.01
2111 2213 2.417516 CGTAGCCGAGATGGTGGG 59.582 66.667 0.00 0.00 41.21 4.61
2114 2216 1.043673 GTAGCCGAGATGGTGGGAGT 61.044 60.000 0.00 0.00 41.21 3.85
2162 2264 1.064240 TCAGGTCCGTACTGATAGCCA 60.064 52.381 0.00 0.00 39.87 4.75
2163 2265 1.754803 CAGGTCCGTACTGATAGCCAA 59.245 52.381 0.00 0.00 38.20 4.52
2232 2334 4.698201 TCATGAGGTGTGTTTCCTTGTA 57.302 40.909 0.00 0.00 35.20 2.41
2234 2336 5.630121 TCATGAGGTGTGTTTCCTTGTATT 58.370 37.500 0.00 0.00 35.20 1.89
2242 2344 6.695713 GGTGTGTTTCCTTGTATTTGAAACTC 59.304 38.462 13.50 10.98 45.02 3.01
2265 2367 9.322773 ACTCTGTGATCATGTATTTGAACTATG 57.677 33.333 0.00 0.00 0.00 2.23
2269 2371 9.617523 TGTGATCATGTATTTGAACTATGATGT 57.382 29.630 0.00 0.00 38.28 3.06
2323 2425 5.986135 CAGACCATATTACTGACCTGCTTAC 59.014 44.000 0.00 0.00 34.07 2.34
2324 2426 5.070580 AGACCATATTACTGACCTGCTTACC 59.929 44.000 0.00 0.00 0.00 2.85
2328 2431 6.772716 CCATATTACTGACCTGCTTACCATTT 59.227 38.462 0.00 0.00 0.00 2.32
2336 2439 2.424956 CCTGCTTACCATTTCTTCCTGC 59.575 50.000 0.00 0.00 0.00 4.85
2349 2452 3.849911 TCTTCCTGCTTAATGTGAGTCG 58.150 45.455 0.00 0.00 0.00 4.18
2477 2591 3.695556 CCATCATGTTGGTTGTGCTCATA 59.304 43.478 13.81 0.00 31.74 2.15
2480 2594 1.518325 TGTTGGTTGTGCTCATACGG 58.482 50.000 0.00 0.00 0.00 4.02
2547 2668 1.375523 CCGGGAAGGAAACGGTCAG 60.376 63.158 0.00 0.00 45.00 3.51
2566 2687 5.985530 GGTCAGCTAAACTTTGCTTGAAAAT 59.014 36.000 0.00 0.00 37.15 1.82
2652 2773 7.752686 GGTAATCTCTTTCAATGCTCTGTTTTC 59.247 37.037 0.00 0.00 0.00 2.29
2664 2785 4.816385 TGCTCTGTTTTCGAGATTGAGTTT 59.184 37.500 0.00 0.00 0.00 2.66
2836 2957 0.645496 TAGCCATTGGAGGTCCCCTA 59.355 55.000 6.95 0.00 31.76 3.53
2887 3008 4.283403 TGCCTTTGCCGCTGTTGC 62.283 61.111 0.00 0.00 36.33 4.17
2897 3018 2.429739 GCTGTTGCTCGGCTTTGC 60.430 61.111 6.14 0.00 44.39 3.68
2922 3043 0.472471 GGTCACTGGAGTTTGTCCCA 59.528 55.000 0.00 0.00 46.31 4.37
2996 3117 1.771073 TTCGTTGAGCTGTGCCGTTG 61.771 55.000 0.00 0.00 0.00 4.10
3050 3171 2.798804 CGAGAGATGCGCATCAGAG 58.201 57.895 42.35 28.75 40.22 3.35
3063 3184 2.801679 GCATCAGAGTAATGCTGAGCTC 59.198 50.000 6.82 6.82 44.75 4.09
3064 3185 3.493002 GCATCAGAGTAATGCTGAGCTCT 60.493 47.826 16.19 0.00 44.75 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.069208 GGGGATTTTATATACCTCCCGTAGTAG 59.931 44.444 13.56 0.00 45.51 2.57
3 4 6.897413 GGGGATTTTATATACCTCCCGTAGTA 59.103 42.308 13.56 0.00 45.51 1.82
4 5 5.723405 GGGGATTTTATATACCTCCCGTAGT 59.277 44.000 13.56 0.00 45.51 2.73
5 6 6.231258 GGGGATTTTATATACCTCCCGTAG 57.769 45.833 13.56 0.00 45.51 3.51
8 9 4.133013 CGGGGATTTTATATACCTCCCG 57.867 50.000 13.56 12.46 45.51 5.14
10 11 3.528532 CGCGGGGATTTTATATACCTCC 58.471 50.000 0.00 0.00 0.00 4.30
11 12 2.934553 GCGCGGGGATTTTATATACCTC 59.065 50.000 8.83 0.00 0.00 3.85
12 13 2.355412 GGCGCGGGGATTTTATATACCT 60.355 50.000 8.83 0.00 0.00 3.08
13 14 2.011947 GGCGCGGGGATTTTATATACC 58.988 52.381 8.83 0.00 0.00 2.73
14 15 2.676342 CTGGCGCGGGGATTTTATATAC 59.324 50.000 8.83 0.00 0.00 1.47
35 36 0.376502 GAGACCGCGTCCTACAGTAC 59.623 60.000 4.92 0.00 32.18 2.73
43 44 3.519930 GGAGGAGAGACCGCGTCC 61.520 72.222 4.92 4.74 44.74 4.79
64 65 0.460987 GGTTGACCGGAGCAGAGATG 60.461 60.000 9.46 0.00 0.00 2.90
86 87 1.838073 TTGGGAAGCGGAGGAGGAAC 61.838 60.000 0.00 0.00 0.00 3.62
87 88 1.537889 TTGGGAAGCGGAGGAGGAA 60.538 57.895 0.00 0.00 0.00 3.36
88 89 1.990060 CTTGGGAAGCGGAGGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
89 90 2.586792 CTTGGGAAGCGGAGGAGG 59.413 66.667 0.00 0.00 0.00 4.30
90 91 2.124942 GCTTGGGAAGCGGAGGAG 60.125 66.667 0.00 0.00 45.74 3.69
164 177 0.517316 GCAATCGAAACTTGGTCGCT 59.483 50.000 0.00 0.00 38.39 4.93
253 266 2.671177 CCAGACGCCTGAGCAAACG 61.671 63.158 0.00 0.00 43.02 3.60
264 277 2.737252 CTCTCTAACCAAAACCAGACGC 59.263 50.000 0.00 0.00 0.00 5.19
288 314 0.321564 CACCCGACCTGATTCTGCAA 60.322 55.000 0.00 0.00 0.00 4.08
291 317 0.324943 AACCACCCGACCTGATTCTG 59.675 55.000 0.00 0.00 0.00 3.02
292 318 0.324943 CAACCACCCGACCTGATTCT 59.675 55.000 0.00 0.00 0.00 2.40
308 334 5.848406 AGTAGCAGGCTATCAAGTATCAAC 58.152 41.667 4.06 0.00 0.00 3.18
312 338 3.508012 CGGAGTAGCAGGCTATCAAGTAT 59.492 47.826 4.06 0.00 0.00 2.12
313 339 2.885266 CGGAGTAGCAGGCTATCAAGTA 59.115 50.000 4.06 0.00 0.00 2.24
314 340 1.683917 CGGAGTAGCAGGCTATCAAGT 59.316 52.381 4.06 0.00 0.00 3.16
315 341 1.957177 TCGGAGTAGCAGGCTATCAAG 59.043 52.381 4.06 0.00 0.00 3.02
316 342 2.067365 TCGGAGTAGCAGGCTATCAA 57.933 50.000 4.06 0.00 0.00 2.57
317 343 1.889170 CATCGGAGTAGCAGGCTATCA 59.111 52.381 4.06 0.00 0.00 2.15
318 344 1.403514 GCATCGGAGTAGCAGGCTATC 60.404 57.143 4.06 3.77 0.00 2.08
347 379 1.002868 GAGGCAGAAGGAGCAGCAA 60.003 57.895 0.00 0.00 0.00 3.91
388 420 4.261363 GCTTAAATCTTAGATGTGCCCTGC 60.261 45.833 0.00 0.00 0.00 4.85
389 421 5.128919 AGCTTAAATCTTAGATGTGCCCTG 58.871 41.667 0.00 0.00 0.00 4.45
390 422 5.379706 AGCTTAAATCTTAGATGTGCCCT 57.620 39.130 0.00 0.00 0.00 5.19
391 423 6.768381 AGTAAGCTTAAATCTTAGATGTGCCC 59.232 38.462 7.99 0.00 0.00 5.36
392 424 7.281100 ACAGTAAGCTTAAATCTTAGATGTGCC 59.719 37.037 7.99 0.00 31.43 5.01
438 473 0.472925 TATTCCATCTAGGCGGGGCA 60.473 55.000 0.00 0.00 37.29 5.36
444 479 4.342862 TGCTCAGTTATTCCATCTAGGC 57.657 45.455 0.00 0.00 37.29 3.93
448 483 4.434545 AGCATGCTCAGTTATTCCATCT 57.565 40.909 16.30 0.00 0.00 2.90
456 491 2.158900 GCCCTAGAAGCATGCTCAGTTA 60.159 50.000 22.93 10.05 0.00 2.24
460 495 2.299975 TGCCCTAGAAGCATGCTCA 58.700 52.632 22.93 9.94 34.69 4.26
471 506 7.050970 TCTTAACATACACTGTATGCCCTAG 57.949 40.000 23.65 16.71 36.98 3.02
495 530 8.924511 TGCAGAAGGCTATAGCTTAATAATTT 57.075 30.769 23.53 0.00 45.15 1.82
506 541 7.650903 GGAAATGAATTTTGCAGAAGGCTATAG 59.349 37.037 0.00 0.00 45.15 1.31
507 542 7.123997 TGGAAATGAATTTTGCAGAAGGCTATA 59.876 33.333 0.00 0.00 40.29 1.31
508 543 6.070653 TGGAAATGAATTTTGCAGAAGGCTAT 60.071 34.615 0.00 0.00 40.29 2.97
509 544 5.245751 TGGAAATGAATTTTGCAGAAGGCTA 59.754 36.000 0.00 0.00 40.29 3.93
510 545 4.040706 TGGAAATGAATTTTGCAGAAGGCT 59.959 37.500 0.00 0.00 40.29 4.58
546 581 4.525024 CATTCTGCTGGATCTTCCTTTCT 58.475 43.478 0.00 0.00 37.46 2.52
549 589 2.686118 GCCATTCTGCTGGATCTTCCTT 60.686 50.000 0.00 0.00 38.69 3.36
564 604 6.799926 TGCAAAATAAAGGAAAAGCCATTC 57.200 33.333 0.00 0.00 40.02 2.67
568 608 7.750458 GCTAAATTGCAAAATAAAGGAAAAGCC 59.250 33.333 1.71 0.00 0.00 4.35
603 644 1.680522 CGCTGTACTGAGATGCCCCT 61.681 60.000 3.61 0.00 0.00 4.79
616 657 0.815213 GGCATGGCAGATTCGCTGTA 60.815 55.000 15.47 0.00 46.62 2.74
630 671 5.265350 TGGACATCAAACATAATGGCATG 57.735 39.130 0.00 0.00 32.21 4.06
639 680 6.318144 CAGAATAGAAGCTGGACATCAAACAT 59.682 38.462 0.00 0.00 0.00 2.71
649 691 4.225942 ACATTGGACAGAATAGAAGCTGGA 59.774 41.667 0.00 0.00 36.47 3.86
665 707 2.026729 TGGAACGCCTATGAACATTGGA 60.027 45.455 16.69 0.00 36.06 3.53
708 750 1.813513 TTACAGGAAGCAGAAGCAGC 58.186 50.000 0.00 0.00 45.49 5.25
820 875 2.840651 AGTTGGTACATCTTAGCCAGCT 59.159 45.455 0.00 0.00 39.30 4.24
837 892 3.857052 TCATAGGTACCGCAAAGAGTTG 58.143 45.455 6.18 0.00 37.83 3.16
867 927 2.678336 GTTCATTCAACCTCCTAAGCGG 59.322 50.000 0.00 0.00 0.00 5.52
914 975 6.146184 CGAAAAGAACAAGAGCAATACAGAGA 59.854 38.462 0.00 0.00 0.00 3.10
915 976 6.302615 CGAAAAGAACAAGAGCAATACAGAG 58.697 40.000 0.00 0.00 0.00 3.35
938 999 5.122396 AGGTAAGAAATTGTTAGAGCTTGCG 59.878 40.000 0.00 0.00 0.00 4.85
952 1013 3.456380 ACACATGGGCAGGTAAGAAAT 57.544 42.857 0.00 0.00 0.00 2.17
979 1040 3.670625 TCACTGGGAGGATAAACAAACG 58.329 45.455 0.00 0.00 0.00 3.60
981 1042 4.599041 CCATCACTGGGAGGATAAACAAA 58.401 43.478 0.00 0.00 39.04 2.83
1071 1133 3.947196 TGCCGTATTTTGAGAATGCATCT 59.053 39.130 0.00 0.00 42.61 2.90
1118 1180 5.651139 AGAATCAATGACCAAGAGATTGTGG 59.349 40.000 0.00 0.00 41.00 4.17
1172 1234 4.515191 GCGTAGGATCAGGAAAATAATGCA 59.485 41.667 0.00 0.00 0.00 3.96
1174 1236 5.991606 TGAGCGTAGGATCAGGAAAATAATG 59.008 40.000 0.00 0.00 32.73 1.90
1295 1358 1.141053 GGTTGGACACAGAACTGAGGT 59.859 52.381 8.87 6.26 0.00 3.85
1307 1370 3.157518 TCCAGTAGCAGGTTGGACA 57.842 52.632 0.00 0.00 36.13 4.02
1309 1372 1.203187 AGAGTCCAGTAGCAGGTTGGA 60.203 52.381 0.00 0.00 38.62 3.53
1310 1373 1.270907 AGAGTCCAGTAGCAGGTTGG 58.729 55.000 0.00 0.00 0.00 3.77
1311 1374 3.409026 AAAGAGTCCAGTAGCAGGTTG 57.591 47.619 0.00 0.00 0.00 3.77
1312 1375 3.555168 CGAAAAGAGTCCAGTAGCAGGTT 60.555 47.826 0.00 0.00 0.00 3.50
1313 1376 2.028930 CGAAAAGAGTCCAGTAGCAGGT 60.029 50.000 0.00 0.00 0.00 4.00
1314 1377 2.028930 ACGAAAAGAGTCCAGTAGCAGG 60.029 50.000 0.00 0.00 0.00 4.85
1315 1378 3.246619 GACGAAAAGAGTCCAGTAGCAG 58.753 50.000 0.00 0.00 32.78 4.24
1316 1379 2.626266 TGACGAAAAGAGTCCAGTAGCA 59.374 45.455 0.00 0.00 37.80 3.49
1317 1380 2.987821 GTGACGAAAAGAGTCCAGTAGC 59.012 50.000 0.00 0.00 37.80 3.58
1318 1381 4.506886 AGTGACGAAAAGAGTCCAGTAG 57.493 45.455 0.00 0.00 37.80 2.57
1319 1382 5.068636 ACTAGTGACGAAAAGAGTCCAGTA 58.931 41.667 0.00 0.00 37.80 2.74
1320 1383 3.890147 ACTAGTGACGAAAAGAGTCCAGT 59.110 43.478 0.00 0.00 37.80 4.00
1321 1384 4.506886 ACTAGTGACGAAAAGAGTCCAG 57.493 45.455 0.00 0.00 37.80 3.86
1322 1385 4.931661 AACTAGTGACGAAAAGAGTCCA 57.068 40.909 0.00 0.00 37.80 4.02
1323 1386 7.886405 AAATAACTAGTGACGAAAAGAGTCC 57.114 36.000 0.00 0.00 37.80 3.85
1324 1387 9.623350 AGTAAATAACTAGTGACGAAAAGAGTC 57.377 33.333 0.00 0.00 36.36 3.36
1325 1388 9.978044 AAGTAAATAACTAGTGACGAAAAGAGT 57.022 29.630 0.00 0.00 37.50 3.24
1354 1417 9.823647 GAGGTAAAGATTGATCTATGAGACAAA 57.176 33.333 0.00 0.00 35.76 2.83
1355 1418 8.981659 TGAGGTAAAGATTGATCTATGAGACAA 58.018 33.333 0.00 0.00 35.76 3.18
1356 1419 8.539117 TGAGGTAAAGATTGATCTATGAGACA 57.461 34.615 0.00 0.00 35.76 3.41
1357 1420 8.637986 ACTGAGGTAAAGATTGATCTATGAGAC 58.362 37.037 0.00 0.00 35.76 3.36
1358 1421 8.774546 ACTGAGGTAAAGATTGATCTATGAGA 57.225 34.615 0.00 0.00 35.76 3.27
1359 1422 9.474920 GAACTGAGGTAAAGATTGATCTATGAG 57.525 37.037 0.00 0.00 35.76 2.90
1360 1423 9.206690 AGAACTGAGGTAAAGATTGATCTATGA 57.793 33.333 0.00 0.00 35.76 2.15
1361 1424 9.258826 CAGAACTGAGGTAAAGATTGATCTATG 57.741 37.037 0.00 0.00 35.76 2.23
1362 1425 8.986991 ACAGAACTGAGGTAAAGATTGATCTAT 58.013 33.333 8.87 0.00 35.76 1.98
1363 1426 8.253810 CACAGAACTGAGGTAAAGATTGATCTA 58.746 37.037 8.87 0.00 35.76 1.98
1364 1427 7.102346 CACAGAACTGAGGTAAAGATTGATCT 58.898 38.462 8.87 0.00 39.22 2.75
1365 1428 6.876257 ACACAGAACTGAGGTAAAGATTGATC 59.124 38.462 8.87 0.00 0.00 2.92
1366 1429 6.773638 ACACAGAACTGAGGTAAAGATTGAT 58.226 36.000 8.87 0.00 0.00 2.57
1367 1430 6.174720 ACACAGAACTGAGGTAAAGATTGA 57.825 37.500 8.87 0.00 0.00 2.57
1368 1431 5.409826 GGACACAGAACTGAGGTAAAGATTG 59.590 44.000 8.87 0.00 0.00 2.67
1369 1432 5.071788 TGGACACAGAACTGAGGTAAAGATT 59.928 40.000 8.87 0.00 0.00 2.40
1370 1433 4.593206 TGGACACAGAACTGAGGTAAAGAT 59.407 41.667 8.87 0.00 0.00 2.40
1371 1434 3.964688 TGGACACAGAACTGAGGTAAAGA 59.035 43.478 8.87 0.00 0.00 2.52
1372 1435 4.336889 TGGACACAGAACTGAGGTAAAG 57.663 45.455 8.87 0.00 0.00 1.85
1386 1449 3.719268 ATTGTATCAAGGCTGGACACA 57.281 42.857 0.00 0.00 0.00 3.72
1387 1450 5.023533 TCTATTGTATCAAGGCTGGACAC 57.976 43.478 0.00 0.00 0.00 3.67
1394 1457 6.425417 GTCCTAAAGCTCTATTGTATCAAGGC 59.575 42.308 0.00 0.00 0.00 4.35
1506 1569 9.816354 GTCAACCAATATAAAGCCAATATTTGT 57.184 29.630 0.00 0.00 30.54 2.83
1548 1612 2.364632 TGTGGAACAGTTGTGAAGGTG 58.635 47.619 0.00 0.00 45.67 4.00
1561 1627 3.687698 ACGGCAAAGTGTATATGTGGAAC 59.312 43.478 0.00 0.00 37.35 3.62
1783 1849 3.127548 GTCACCGTTACGATCTCTACCAA 59.872 47.826 6.24 0.00 0.00 3.67
1886 1952 1.228245 GCACTTGAAGCAGTCCCCA 60.228 57.895 0.00 0.00 0.00 4.96
1887 1953 2.328099 CGCACTTGAAGCAGTCCCC 61.328 63.158 0.00 0.00 0.00 4.81
1888 1954 2.328099 CCGCACTTGAAGCAGTCCC 61.328 63.158 0.00 0.00 0.00 4.46
1937 2003 4.530857 CTCCCGCCGTCACCATCC 62.531 72.222 0.00 0.00 0.00 3.51
2012 2078 4.351938 CGGTCAGAACGGTCGCCA 62.352 66.667 0.00 0.00 0.00 5.69
2015 2081 2.430244 CCACGGTCAGAACGGTCG 60.430 66.667 13.63 0.00 36.88 4.79
2111 2213 2.682494 TAGCGGTCACCCCCACTC 60.682 66.667 0.00 0.00 0.00 3.51
2114 2216 3.000819 CTGTAGCGGTCACCCCCA 61.001 66.667 0.00 0.00 0.00 4.96
2126 2228 2.231478 ACCTGATCGGTCACAACTGTAG 59.769 50.000 0.00 0.00 44.93 2.74
2150 2252 6.398234 TCTCAAGATCTTGGCTATCAGTAC 57.602 41.667 30.33 0.00 40.78 2.73
2158 2260 3.072184 ACACACTTCTCAAGATCTTGGCT 59.928 43.478 30.33 9.75 40.78 4.75
2162 2264 6.429385 GGATGAAACACACTTCTCAAGATCTT 59.571 38.462 0.88 0.88 0.00 2.40
2163 2265 5.936956 GGATGAAACACACTTCTCAAGATCT 59.063 40.000 0.00 0.00 0.00 2.75
2232 2334 9.850628 CAAATACATGATCACAGAGTTTCAAAT 57.149 29.630 0.00 0.00 0.00 2.32
2234 2336 8.620116 TCAAATACATGATCACAGAGTTTCAA 57.380 30.769 0.00 0.00 0.00 2.69
2265 2367 3.581755 TGCTTACTCACGGTACAACATC 58.418 45.455 0.00 0.00 0.00 3.06
2269 2371 3.119245 GGATCTGCTTACTCACGGTACAA 60.119 47.826 0.00 0.00 0.00 2.41
2323 2425 5.416952 ACTCACATTAAGCAGGAAGAAATGG 59.583 40.000 0.00 0.00 32.97 3.16
2324 2426 6.506500 ACTCACATTAAGCAGGAAGAAATG 57.493 37.500 0.00 0.00 34.48 2.32
2328 2431 3.849911 CGACTCACATTAAGCAGGAAGA 58.150 45.455 0.00 0.00 0.00 2.87
2336 2439 3.933155 GTCCATGCGACTCACATTAAG 57.067 47.619 6.98 0.00 38.57 1.85
2349 2452 3.152341 AGCATTATGGCTAAGTCCATGC 58.848 45.455 5.60 2.67 45.84 4.06
2375 2481 1.607178 CAAACATGCAGGGCCCAGA 60.607 57.895 27.56 7.30 0.00 3.86
2385 2491 2.179589 CAGCGTATCAAGCAAACATGC 58.820 47.619 0.00 0.00 37.01 4.06
2463 2577 0.687920 TCCCGTATGAGCACAACCAA 59.312 50.000 0.00 0.00 0.00 3.67
2494 2608 0.107214 AACATGGTATGCCTCCCACG 60.107 55.000 0.16 0.00 32.49 4.94
2545 2666 7.908230 TGAAATTTTCAAGCAAAGTTTAGCTG 58.092 30.769 9.36 7.66 41.70 4.24
2547 2668 7.737311 CGATGAAATTTTCAAGCAAAGTTTAGC 59.263 33.333 15.34 0.00 43.95 3.09
2566 2687 2.298729 CCCCCTTTTTCTTGCGATGAAA 59.701 45.455 0.00 0.00 0.00 2.69
2581 2702 1.566231 GATGATTGTCACCTCCCCCTT 59.434 52.381 0.00 0.00 0.00 3.95
2887 3008 0.741221 GACCAGGTAGCAAAGCCGAG 60.741 60.000 0.00 0.00 0.00 4.63
2897 3018 2.368875 ACAAACTCCAGTGACCAGGTAG 59.631 50.000 0.00 0.00 0.00 3.18
2922 3043 1.003718 GTAGCAAGGCCGACCAACT 60.004 57.895 0.00 0.00 39.06 3.16
2996 3117 2.735663 CAATGATGCATCTCTAGCGACC 59.264 50.000 26.32 0.00 33.85 4.79
3050 3171 1.297664 CAGGCAGAGCTCAGCATTAC 58.702 55.000 29.30 14.05 0.00 1.89
3063 3184 2.686915 CCAAAGAAGAATAGCCAGGCAG 59.313 50.000 15.80 0.00 0.00 4.85
3064 3185 2.726821 CCAAAGAAGAATAGCCAGGCA 58.273 47.619 15.80 0.00 0.00 4.75
3065 3186 1.406898 GCCAAAGAAGAATAGCCAGGC 59.593 52.381 1.84 1.84 0.00 4.85


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

AutoCloner maintained by Alex Coulton.