Multiple sequence alignment - TraesCS6D01G201000

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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 TraesCS6D01G201000 chr6D 100.000 2255 0 0 1 2255 283223913 283226167 0 4165
1 TraesCS6D01G201000 chr6D 99.046 629 6 0 1627 2255 124514521 124513893 0 1129
2 TraesCS6D01G201000 chr1D 98.000 1400 21 4 1 1396 141314952 141313556 0 2423
3 TraesCS6D01G201000 chr1B 97.857 1400 24 3 1 1396 668806978 668805581 0 2414
4 TraesCS6D01G201000 chr1B 97.643 1400 27 3 1 1396 672477344 672478741 0 2398
5 TraesCS6D01G201000 chr7B 97.786 1400 26 3 1 1396 644465626 644467024 0 2409
6 TraesCS6D01G201000 chr7B 99.046 629 6 0 1627 2255 716841549 716842177 0 1129
7 TraesCS6D01G201000 chr7B 98.887 629 7 0 1627 2255 716881790 716882418 0 1123
8 TraesCS6D01G201000 chr7A 97.714 1400 26 3 1 1396 60150104 60148707 0 2403
9 TraesCS6D01G201000 chr3A 97.714 1400 26 3 1 1396 633109437 633110834 0 2403
10 TraesCS6D01G201000 chr6B 97.500 1400 29 3 1 1396 306997807 306996410 0 2386
11 TraesCS6D01G201000 chr4B 97.429 1400 29 3 1 1396 209079334 209077938 0 2379
12 TraesCS6D01G201000 chr2B 97.357 1400 31 3 1 1396 391114653 391113256 0 2375
13 TraesCS6D01G201000 chr4A 99.205 629 5 0 1627 2255 67593775 67593147 0 1134
14 TraesCS6D01G201000 chrUn 99.046 629 6 0 1627 2255 453336030 453336658 0 1129
15 TraesCS6D01G201000 chrUn 98.887 629 7 0 1627 2255 332212003 332212631 0 1123
16 TraesCS6D01G201000 chr7D 99.046 629 6 0 1627 2255 203496996 203496368 0 1129
17 TraesCS6D01G201000 chr7D 98.887 629 7 0 1627 2255 381916975 381916347 0 1123
18 TraesCS6D01G201000 chr5A 98.887 629 7 0 1627 2255 19251858 19252486 0 1123


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 TraesCS6D01G201000 chr6D 283223913 283226167 2254 False 4165 4165 100.000 1 2255 1 chr6D.!!$F1 2254
1 TraesCS6D01G201000 chr6D 124513893 124514521 628 True 1129 1129 99.046 1627 2255 1 chr6D.!!$R1 628
2 TraesCS6D01G201000 chr1D 141313556 141314952 1396 True 2423 2423 98.000 1 1396 1 chr1D.!!$R1 1395
3 TraesCS6D01G201000 chr1B 668805581 668806978 1397 True 2414 2414 97.857 1 1396 1 chr1B.!!$R1 1395
4 TraesCS6D01G201000 chr1B 672477344 672478741 1397 False 2398 2398 97.643 1 1396 1 chr1B.!!$F1 1395
5 TraesCS6D01G201000 chr7B 644465626 644467024 1398 False 2409 2409 97.786 1 1396 1 chr7B.!!$F1 1395
6 TraesCS6D01G201000 chr7B 716841549 716842177 628 False 1129 1129 99.046 1627 2255 1 chr7B.!!$F2 628
7 TraesCS6D01G201000 chr7B 716881790 716882418 628 False 1123 1123 98.887 1627 2255 1 chr7B.!!$F3 628
8 TraesCS6D01G201000 chr7A 60148707 60150104 1397 True 2403 2403 97.714 1 1396 1 chr7A.!!$R1 1395
9 TraesCS6D01G201000 chr3A 633109437 633110834 1397 False 2403 2403 97.714 1 1396 1 chr3A.!!$F1 1395
10 TraesCS6D01G201000 chr6B 306996410 306997807 1397 True 2386 2386 97.500 1 1396 1 chr6B.!!$R1 1395
11 TraesCS6D01G201000 chr4B 209077938 209079334 1396 True 2379 2379 97.429 1 1396 1 chr4B.!!$R1 1395
12 TraesCS6D01G201000 chr2B 391113256 391114653 1397 True 2375 2375 97.357 1 1396 1 chr2B.!!$R1 1395
13 TraesCS6D01G201000 chr4A 67593147 67593775 628 True 1134 1134 99.205 1627 2255 1 chr4A.!!$R1 628
14 TraesCS6D01G201000 chrUn 453336030 453336658 628 False 1129 1129 99.046 1627 2255 1 chrUn.!!$F2 628
15 TraesCS6D01G201000 chrUn 332212003 332212631 628 False 1123 1123 98.887 1627 2255 1 chrUn.!!$F1 628
16 TraesCS6D01G201000 chr7D 203496368 203496996 628 True 1129 1129 99.046 1627 2255 1 chr7D.!!$R1 628
17 TraesCS6D01G201000 chr7D 381916347 381916975 628 True 1123 1123 98.887 1627 2255 1 chr7D.!!$R2 628
18 TraesCS6D01G201000 chr5A 19251858 19252486 628 False 1123 1123 98.887 1627 2255 1 chr5A.!!$F1 628

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
400 401 0.033228 CAGATCCGGTGAGCCAGATC 59.967 60.0 0.0 2.51 45.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1436 0.179004 CCACAGCTGGGTTACACCAA 60.179 55.0 19.93 0.0 41.02 3.67 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
229 230 9.168451 TGTCAATTGTAAAAAGTAGTTGAGTCA 57.832 29.630 5.13 0.00 0.00 3.41
399 400 1.406065 CCAGATCCGGTGAGCCAGAT 61.406 60.000 0.00 0.00 34.72 2.90
400 401 0.033228 CAGATCCGGTGAGCCAGATC 59.967 60.000 0.00 2.51 45.00 2.75
496 497 2.761208 CAAGGAGAGACTCGGTTATGGT 59.239 50.000 0.00 0.00 0.00 3.55
715 716 6.049149 TCGGGATCAGATCATTCAACTAAAC 58.951 40.000 12.66 0.00 0.00 2.01
818 819 7.075674 CAAAAACAGATTTGCAAGGAGTTTT 57.924 32.000 19.38 19.38 38.79 2.43
1005 1010 3.118408 TGCTGGTTATCGAGTTTATGGCT 60.118 43.478 0.00 0.00 0.00 4.75
1006 1011 3.877508 GCTGGTTATCGAGTTTATGGCTT 59.122 43.478 0.00 0.00 0.00 4.35
1053 1058 2.353269 TGGCGTCGGCATTTACTTATTG 59.647 45.455 18.58 0.00 42.47 1.90
1063 1068 6.261118 GGCATTTACTTATTGTGCTCTCTTG 58.739 40.000 0.00 0.00 36.15 3.02
1354 1361 0.925558 TTTCATATCCAGGGCAGGCA 59.074 50.000 0.00 0.00 0.00 4.75
1362 1369 0.773644 CCAGGGCAGGCATTAGGTAT 59.226 55.000 0.00 0.00 0.00 2.73
1423 1430 9.461312 AGAACCAATAAATTAGCATAGTCACAA 57.539 29.630 0.00 0.00 0.00 3.33
1425 1432 9.855021 AACCAATAAATTAGCATAGTCACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
1426 1433 9.243105 ACCAATAAATTAGCATAGTCACAAACT 57.757 29.630 0.00 0.00 42.33 2.66
1432 1439 7.849804 ATTAGCATAGTCACAAACTAGTTGG 57.150 36.000 9.34 8.92 43.64 3.77
1433 1440 5.228945 AGCATAGTCACAAACTAGTTGGT 57.771 39.130 10.02 10.02 43.64 3.67
1434 1441 4.997395 AGCATAGTCACAAACTAGTTGGTG 59.003 41.667 29.98 29.98 43.64 4.17
1435 1442 4.755123 GCATAGTCACAAACTAGTTGGTGT 59.245 41.667 32.58 21.69 43.64 4.16
1436 1443 5.929992 GCATAGTCACAAACTAGTTGGTGTA 59.070 40.000 32.58 22.83 43.64 2.90
1437 1444 6.425721 GCATAGTCACAAACTAGTTGGTGTAA 59.574 38.462 32.58 22.50 43.64 2.41
1438 1445 7.570691 GCATAGTCACAAACTAGTTGGTGTAAC 60.571 40.741 32.58 26.10 43.64 2.50
1460 1467 2.133553 CAGCTGTGGATATTCTCTGCG 58.866 52.381 5.25 2.39 0.00 5.18
1461 1468 2.034878 AGCTGTGGATATTCTCTGCGA 58.965 47.619 8.70 0.00 0.00 5.10
1462 1469 2.432146 AGCTGTGGATATTCTCTGCGAA 59.568 45.455 8.70 0.00 35.78 4.70
1463 1470 3.070734 AGCTGTGGATATTCTCTGCGAAT 59.929 43.478 8.70 0.00 44.35 3.34
1464 1471 4.281941 AGCTGTGGATATTCTCTGCGAATA 59.718 41.667 8.70 2.86 45.83 1.75
1522 1529 9.607988 TTGATTACATAAACTAGTGTACCATGG 57.392 33.333 11.19 11.19 31.05 3.66
1523 1530 8.764558 TGATTACATAAACTAGTGTACCATGGT 58.235 33.333 23.55 23.55 31.05 3.55
1524 1531 9.609346 GATTACATAAACTAGTGTACCATGGTT 57.391 33.333 25.38 7.46 31.05 3.67
1525 1532 8.780846 TTACATAAACTAGTGTACCATGGTTG 57.219 34.615 25.38 12.83 31.05 3.77
1526 1533 6.775708 ACATAAACTAGTGTACCATGGTTGT 58.224 36.000 25.38 13.53 0.00 3.32
1527 1534 6.877322 ACATAAACTAGTGTACCATGGTTGTC 59.123 38.462 25.38 14.37 0.00 3.18
1528 1535 4.967084 AACTAGTGTACCATGGTTGTCA 57.033 40.909 25.38 16.80 0.00 3.58
1529 1536 4.537135 ACTAGTGTACCATGGTTGTCAG 57.463 45.455 25.38 15.83 0.00 3.51
1530 1537 3.901844 ACTAGTGTACCATGGTTGTCAGT 59.098 43.478 25.38 22.13 0.00 3.41
1531 1538 5.081728 ACTAGTGTACCATGGTTGTCAGTA 58.918 41.667 25.38 22.07 0.00 2.74
1532 1539 4.967084 AGTGTACCATGGTTGTCAGTAA 57.033 40.909 25.38 0.00 0.00 2.24
1533 1540 5.499004 AGTGTACCATGGTTGTCAGTAAT 57.501 39.130 25.38 0.00 0.00 1.89
1534 1541 5.245531 AGTGTACCATGGTTGTCAGTAATG 58.754 41.667 25.38 0.00 0.00 1.90
1535 1542 4.394920 GTGTACCATGGTTGTCAGTAATGG 59.605 45.833 25.38 7.75 42.88 3.16
1536 1543 3.085952 ACCATGGTTGTCAGTAATGGG 57.914 47.619 13.00 0.00 41.76 4.00
1537 1544 2.378547 ACCATGGTTGTCAGTAATGGGT 59.621 45.455 13.00 0.00 41.76 4.51
1538 1545 3.181423 ACCATGGTTGTCAGTAATGGGTT 60.181 43.478 13.00 0.00 41.76 4.11
1539 1546 3.831911 CCATGGTTGTCAGTAATGGGTTT 59.168 43.478 2.57 0.00 35.22 3.27
1540 1547 4.321899 CCATGGTTGTCAGTAATGGGTTTG 60.322 45.833 2.57 0.00 35.22 2.93
1541 1548 4.171878 TGGTTGTCAGTAATGGGTTTGA 57.828 40.909 0.00 0.00 0.00 2.69
1542 1549 4.735369 TGGTTGTCAGTAATGGGTTTGAT 58.265 39.130 0.00 0.00 0.00 2.57
1543 1550 4.522405 TGGTTGTCAGTAATGGGTTTGATG 59.478 41.667 0.00 0.00 0.00 3.07
1544 1551 4.082245 GGTTGTCAGTAATGGGTTTGATGG 60.082 45.833 0.00 0.00 0.00 3.51
1545 1552 4.649267 TGTCAGTAATGGGTTTGATGGA 57.351 40.909 0.00 0.00 0.00 3.41
1546 1553 5.191727 TGTCAGTAATGGGTTTGATGGAT 57.808 39.130 0.00 0.00 0.00 3.41
1547 1554 6.320434 TGTCAGTAATGGGTTTGATGGATA 57.680 37.500 0.00 0.00 0.00 2.59
1548 1555 6.726379 TGTCAGTAATGGGTTTGATGGATAA 58.274 36.000 0.00 0.00 0.00 1.75
1549 1556 7.353525 TGTCAGTAATGGGTTTGATGGATAAT 58.646 34.615 0.00 0.00 0.00 1.28
1550 1557 8.498575 TGTCAGTAATGGGTTTGATGGATAATA 58.501 33.333 0.00 0.00 0.00 0.98
1551 1558 9.520515 GTCAGTAATGGGTTTGATGGATAATAT 57.479 33.333 0.00 0.00 0.00 1.28
1552 1559 9.739276 TCAGTAATGGGTTTGATGGATAATATC 57.261 33.333 0.00 0.00 0.00 1.63
1553 1560 9.519191 CAGTAATGGGTTTGATGGATAATATCA 57.481 33.333 2.41 0.00 33.00 2.15
1581 1588 8.459911 AACACAATAAATTACAGGTATAGCCC 57.540 34.615 0.00 0.00 38.26 5.19
1582 1589 7.812306 ACACAATAAATTACAGGTATAGCCCT 58.188 34.615 0.00 0.00 38.26 5.19
1583 1590 8.940982 ACACAATAAATTACAGGTATAGCCCTA 58.059 33.333 0.00 0.00 38.26 3.53
1584 1591 9.787435 CACAATAAATTACAGGTATAGCCCTAA 57.213 33.333 0.00 0.00 38.26 2.69
1593 1600 7.317722 ACAGGTATAGCCCTAAAATAGAAGG 57.682 40.000 0.00 0.00 38.26 3.46
1594 1601 6.850231 ACAGGTATAGCCCTAAAATAGAAGGT 59.150 38.462 0.00 0.00 38.26 3.50
1595 1602 8.014859 ACAGGTATAGCCCTAAAATAGAAGGTA 58.985 37.037 0.00 0.00 38.26 3.08
1596 1603 9.047947 CAGGTATAGCCCTAAAATAGAAGGTAT 57.952 37.037 0.00 0.00 38.26 2.73
1597 1604 9.631056 AGGTATAGCCCTAAAATAGAAGGTATT 57.369 33.333 0.00 0.00 38.26 1.89
1598 1605 9.668497 GGTATAGCCCTAAAATAGAAGGTATTG 57.332 37.037 0.00 0.00 30.57 1.90
1603 1610 9.404848 AGCCCTAAAATAGAAGGTATTGTTTAC 57.595 33.333 0.00 0.00 0.00 2.01
1604 1611 9.404848 GCCCTAAAATAGAAGGTATTGTTTACT 57.595 33.333 0.00 0.00 0.00 2.24
1611 1618 9.751542 AATAGAAGGTATTGTTTACTCGATCTG 57.248 33.333 0.00 0.00 0.00 2.90
1612 1619 7.171630 AGAAGGTATTGTTTACTCGATCTGT 57.828 36.000 0.00 0.00 0.00 3.41
1613 1620 7.259161 AGAAGGTATTGTTTACTCGATCTGTC 58.741 38.462 0.00 0.00 0.00 3.51
1622 1629 3.284336 CGATCTGTCGGTGGTGGA 58.716 61.111 0.00 0.00 44.00 4.02
1623 1630 1.589630 CGATCTGTCGGTGGTGGAA 59.410 57.895 0.00 0.00 44.00 3.53
1624 1631 0.175760 CGATCTGTCGGTGGTGGAAT 59.824 55.000 0.00 0.00 44.00 3.01
1625 1632 1.407618 CGATCTGTCGGTGGTGGAATA 59.592 52.381 0.00 0.00 44.00 1.75
1798 1805 5.127845 ACACGTTTCTCTGGATCATCATAGT 59.872 40.000 0.00 0.00 0.00 2.12
1873 1880 9.658799 CCTCGAAACCATAATCTGTTGATATAT 57.341 33.333 0.00 0.00 31.70 0.86
1885 1892 6.764379 TCTGTTGATATATGGCGTAAATCCA 58.236 36.000 0.00 0.00 38.09 3.41
1986 1993 4.400251 ACCGGAGATATTCGTGTTACTTCA 59.600 41.667 9.46 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.566879 AGATAGATAGGTCCACAAGTTGAGATT 59.433 37.037 10.54 2.22 0.00 2.40
14 15 7.072562 AGATAGATAGGTCCACAAGTTGAGAT 58.927 38.462 10.54 0.00 0.00 2.75
23 24 7.979786 AAAGAAGAAGATAGATAGGTCCACA 57.020 36.000 0.00 0.00 0.00 4.17
229 230 1.808945 CTTTTTGCTCCTGCGAGACAT 59.191 47.619 0.00 0.00 43.34 3.06
399 400 6.647334 TTGTATGTCCATTTTTGCTTGAGA 57.353 33.333 0.00 0.00 0.00 3.27
400 401 7.092079 TGATTGTATGTCCATTTTTGCTTGAG 58.908 34.615 0.00 0.00 0.00 3.02
496 497 2.698803 TGAAGCAAGCTCTTTATCGCA 58.301 42.857 0.00 0.00 0.00 5.10
715 716 3.470888 CCTACCCGGCCTGACAGG 61.471 72.222 17.83 17.83 38.80 4.00
818 819 2.039746 TCCGAATGAGAAAGCCTTTGGA 59.960 45.455 0.00 0.00 0.00 3.53
847 849 9.136323 GGAGAAGGGAAATATACATGAAATTGT 57.864 33.333 0.00 0.00 0.00 2.71
856 858 7.690301 GCAGAGAATGGAGAAGGGAAATATACA 60.690 40.741 0.00 0.00 0.00 2.29
1005 1010 0.878416 CTTTTTGGATGGTCGGCGAA 59.122 50.000 12.92 0.00 0.00 4.70
1006 1011 0.250553 ACTTTTTGGATGGTCGGCGA 60.251 50.000 4.99 4.99 0.00 5.54
1053 1058 4.434520 GGACCACTATTACAAGAGAGCAC 58.565 47.826 0.00 0.00 0.00 4.40
1063 1068 6.243216 TGAATACCAAGGGACCACTATTAC 57.757 41.667 0.00 0.00 0.00 1.89
1214 1220 0.894835 AGCGGCCCAAAAATGGTAAG 59.105 50.000 0.00 0.00 0.00 2.34
1397 1404 9.461312 TTGTGACTATGCTAATTTATTGGTTCT 57.539 29.630 0.00 0.00 0.00 3.01
1399 1406 9.855021 GTTTGTGACTATGCTAATTTATTGGTT 57.145 29.630 0.00 0.00 0.00 3.67
1400 1407 9.243105 AGTTTGTGACTATGCTAATTTATTGGT 57.757 29.630 0.00 0.00 36.65 3.67
1406 1413 8.730680 CCAACTAGTTTGTGACTATGCTAATTT 58.269 33.333 5.07 0.00 40.01 1.82
1407 1414 7.883311 ACCAACTAGTTTGTGACTATGCTAATT 59.117 33.333 11.31 0.00 40.01 1.40
1408 1415 7.334421 CACCAACTAGTTTGTGACTATGCTAAT 59.666 37.037 27.55 0.00 40.01 1.73
1409 1416 6.649141 CACCAACTAGTTTGTGACTATGCTAA 59.351 38.462 27.55 0.00 40.01 3.09
1410 1417 6.163476 CACCAACTAGTTTGTGACTATGCTA 58.837 40.000 27.55 0.00 40.01 3.49
1411 1418 4.997395 CACCAACTAGTTTGTGACTATGCT 59.003 41.667 27.55 0.00 40.01 3.79
1412 1419 4.755123 ACACCAACTAGTTTGTGACTATGC 59.245 41.667 34.30 0.00 40.01 3.14
1413 1420 7.095355 GGTTACACCAACTAGTTTGTGACTATG 60.095 40.741 34.30 15.73 37.96 2.23
1414 1421 6.932960 GGTTACACCAACTAGTTTGTGACTAT 59.067 38.462 34.30 20.37 37.96 2.12
1415 1422 6.282930 GGTTACACCAACTAGTTTGTGACTA 58.717 40.000 34.30 20.38 38.15 2.59
1416 1423 5.121105 GGTTACACCAACTAGTTTGTGACT 58.879 41.667 34.30 21.20 38.15 3.41
1417 1424 4.274214 GGGTTACACCAACTAGTTTGTGAC 59.726 45.833 34.30 26.68 41.02 3.67
1418 1425 4.080469 TGGGTTACACCAACTAGTTTGTGA 60.080 41.667 34.30 19.53 41.02 3.58
1419 1426 4.200874 TGGGTTACACCAACTAGTTTGTG 58.799 43.478 28.93 28.93 41.02 3.33
1420 1427 4.457466 CTGGGTTACACCAACTAGTTTGT 58.543 43.478 15.40 15.40 41.02 2.83
1421 1428 3.252458 GCTGGGTTACACCAACTAGTTTG 59.748 47.826 5.07 5.14 41.02 2.93
1422 1429 3.137728 AGCTGGGTTACACCAACTAGTTT 59.862 43.478 5.07 0.00 41.02 2.66
1423 1430 2.709397 AGCTGGGTTACACCAACTAGTT 59.291 45.455 1.12 1.12 41.02 2.24
1424 1431 2.038557 CAGCTGGGTTACACCAACTAGT 59.961 50.000 5.57 0.00 41.02 2.57
1425 1432 2.038557 ACAGCTGGGTTACACCAACTAG 59.961 50.000 19.93 0.00 41.02 2.57
1426 1433 2.051692 ACAGCTGGGTTACACCAACTA 58.948 47.619 19.93 0.00 41.02 2.24
1427 1434 0.843984 ACAGCTGGGTTACACCAACT 59.156 50.000 19.93 0.00 41.02 3.16
1428 1435 0.951558 CACAGCTGGGTTACACCAAC 59.048 55.000 19.93 0.00 41.02 3.77
1429 1436 0.179004 CCACAGCTGGGTTACACCAA 60.179 55.000 19.93 0.00 41.02 3.67
1430 1437 1.057275 TCCACAGCTGGGTTACACCA 61.057 55.000 19.93 0.00 41.02 4.17
1431 1438 0.328258 ATCCACAGCTGGGTTACACC 59.672 55.000 19.93 0.00 38.25 4.16
1432 1439 3.560636 ATATCCACAGCTGGGTTACAC 57.439 47.619 19.93 0.00 38.25 2.90
1433 1440 3.780294 AGAATATCCACAGCTGGGTTACA 59.220 43.478 19.93 0.00 38.25 2.41
1434 1441 4.101741 AGAGAATATCCACAGCTGGGTTAC 59.898 45.833 19.93 2.56 38.25 2.50
1435 1442 4.101585 CAGAGAATATCCACAGCTGGGTTA 59.898 45.833 19.93 14.95 38.25 2.85
1436 1443 3.118112 CAGAGAATATCCACAGCTGGGTT 60.118 47.826 19.93 13.32 38.25 4.11
1437 1444 2.437281 CAGAGAATATCCACAGCTGGGT 59.563 50.000 19.93 0.61 38.25 4.51
1438 1445 2.809665 GCAGAGAATATCCACAGCTGGG 60.810 54.545 19.93 15.23 38.25 4.45
1439 1446 2.492012 GCAGAGAATATCCACAGCTGG 58.508 52.381 19.93 6.95 39.23 4.85
1440 1447 2.133553 CGCAGAGAATATCCACAGCTG 58.866 52.381 13.48 13.48 0.00 4.24
1441 1448 2.034878 TCGCAGAGAATATCCACAGCT 58.965 47.619 0.00 0.00 0.00 4.24
1442 1449 2.515926 TCGCAGAGAATATCCACAGC 57.484 50.000 0.00 0.00 0.00 4.40
1514 1521 3.945285 CCCATTACTGACAACCATGGTAC 59.055 47.826 20.12 13.27 33.73 3.34
1515 1522 3.589735 ACCCATTACTGACAACCATGGTA 59.410 43.478 20.12 0.40 33.73 3.25
1516 1523 2.378547 ACCCATTACTGACAACCATGGT 59.621 45.455 13.00 13.00 33.73 3.55
1517 1524 3.085952 ACCCATTACTGACAACCATGG 57.914 47.619 11.19 11.19 35.13 3.66
1518 1525 4.522405 TCAAACCCATTACTGACAACCATG 59.478 41.667 0.00 0.00 0.00 3.66
1519 1526 4.735369 TCAAACCCATTACTGACAACCAT 58.265 39.130 0.00 0.00 0.00 3.55
1520 1527 4.171878 TCAAACCCATTACTGACAACCA 57.828 40.909 0.00 0.00 0.00 3.67
1521 1528 4.082245 CCATCAAACCCATTACTGACAACC 60.082 45.833 0.00 0.00 0.00 3.77
1522 1529 4.764823 TCCATCAAACCCATTACTGACAAC 59.235 41.667 0.00 0.00 0.00 3.32
1523 1530 4.991776 TCCATCAAACCCATTACTGACAA 58.008 39.130 0.00 0.00 0.00 3.18
1524 1531 4.649267 TCCATCAAACCCATTACTGACA 57.351 40.909 0.00 0.00 0.00 3.58
1525 1532 7.823745 ATTATCCATCAAACCCATTACTGAC 57.176 36.000 0.00 0.00 0.00 3.51
1526 1533 9.739276 GATATTATCCATCAAACCCATTACTGA 57.261 33.333 0.00 0.00 0.00 3.41
1527 1534 9.519191 TGATATTATCCATCAAACCCATTACTG 57.481 33.333 1.27 0.00 29.55 2.74
1533 1540 9.040259 TGTTTTTGATATTATCCATCAAACCCA 57.960 29.630 9.39 7.06 46.65 4.51
1534 1541 9.313118 GTGTTTTTGATATTATCCATCAAACCC 57.687 33.333 9.39 5.07 46.65 4.11
1535 1542 9.868277 TGTGTTTTTGATATTATCCATCAAACC 57.132 29.630 9.39 5.34 46.65 3.27
1555 1562 8.909923 GGGCTATACCTGTAATTTATTGTGTTT 58.090 33.333 0.00 0.00 39.10 2.83
1556 1563 8.279361 AGGGCTATACCTGTAATTTATTGTGTT 58.721 33.333 0.00 0.00 40.04 3.32
1557 1564 7.812306 AGGGCTATACCTGTAATTTATTGTGT 58.188 34.615 0.00 0.00 40.04 3.72
1558 1565 9.787435 TTAGGGCTATACCTGTAATTTATTGTG 57.213 33.333 0.00 0.00 42.02 3.33
1567 1574 8.877195 CCTTCTATTTTAGGGCTATACCTGTAA 58.123 37.037 0.00 0.00 42.02 2.41
1568 1575 8.014859 ACCTTCTATTTTAGGGCTATACCTGTA 58.985 37.037 0.00 0.00 42.02 2.74
1569 1576 6.850231 ACCTTCTATTTTAGGGCTATACCTGT 59.150 38.462 0.00 0.00 42.02 4.00
1570 1577 7.317722 ACCTTCTATTTTAGGGCTATACCTG 57.682 40.000 0.00 0.00 42.02 4.00
1571 1578 9.631056 AATACCTTCTATTTTAGGGCTATACCT 57.369 33.333 0.00 0.00 44.75 3.08
1572 1579 9.668497 CAATACCTTCTATTTTAGGGCTATACC 57.332 37.037 0.00 0.00 35.79 2.73
1577 1584 9.404848 GTAAACAATACCTTCTATTTTAGGGCT 57.595 33.333 0.00 0.00 35.79 5.19
1578 1585 9.404848 AGTAAACAATACCTTCTATTTTAGGGC 57.595 33.333 0.00 0.00 35.79 5.19
1585 1592 9.751542 CAGATCGAGTAAACAATACCTTCTATT 57.248 33.333 0.00 0.00 0.00 1.73
1586 1593 8.915036 ACAGATCGAGTAAACAATACCTTCTAT 58.085 33.333 0.00 0.00 0.00 1.98
1587 1594 8.289939 ACAGATCGAGTAAACAATACCTTCTA 57.710 34.615 0.00 0.00 0.00 2.10
1588 1595 7.171630 ACAGATCGAGTAAACAATACCTTCT 57.828 36.000 0.00 0.00 0.00 2.85
1589 1596 7.452630 GACAGATCGAGTAAACAATACCTTC 57.547 40.000 0.00 0.00 0.00 3.46
1606 1613 3.753294 ATATTCCACCACCGACAGATC 57.247 47.619 0.00 0.00 0.00 2.75
1607 1614 3.711704 AGAATATTCCACCACCGACAGAT 59.288 43.478 11.92 0.00 0.00 2.90
1608 1615 3.104512 AGAATATTCCACCACCGACAGA 58.895 45.455 11.92 0.00 0.00 3.41
1609 1616 3.543680 AGAATATTCCACCACCGACAG 57.456 47.619 11.92 0.00 0.00 3.51
1610 1617 3.992943 AAGAATATTCCACCACCGACA 57.007 42.857 11.92 0.00 0.00 4.35
1611 1618 5.667466 TCTTAAGAATATTCCACCACCGAC 58.333 41.667 11.92 0.00 0.00 4.79
1612 1619 5.943349 TCTTAAGAATATTCCACCACCGA 57.057 39.130 11.92 0.00 0.00 4.69
1613 1620 5.007724 GCTTCTTAAGAATATTCCACCACCG 59.992 44.000 18.02 3.52 33.01 4.94
1614 1621 5.885912 TGCTTCTTAAGAATATTCCACCACC 59.114 40.000 18.02 0.00 33.01 4.61
1615 1622 7.391148 TTGCTTCTTAAGAATATTCCACCAC 57.609 36.000 18.02 0.30 33.01 4.16
1616 1623 8.593945 ATTTGCTTCTTAAGAATATTCCACCA 57.406 30.769 18.02 3.86 33.01 4.17
1618 1625 9.670719 GCTATTTGCTTCTTAAGAATATTCCAC 57.329 33.333 18.02 2.41 38.95 4.02
1619 1626 9.407380 TGCTATTTGCTTCTTAAGAATATTCCA 57.593 29.630 18.02 8.09 43.37 3.53
1625 1632 8.975295 AGGAAATGCTATTTGCTTCTTAAGAAT 58.025 29.630 18.02 5.98 43.37 2.40
1798 1805 5.269189 TCTGAGTGGATATGTGGAAGTACA 58.731 41.667 0.00 0.00 34.63 2.90
1873 1880 4.149511 TCAATCATCTGGATTTACGCCA 57.850 40.909 0.00 0.00 43.76 5.69
1885 1892 5.573219 TGGTGTTTCTTCCATCAATCATCT 58.427 37.500 0.00 0.00 0.00 2.90
1986 1993 3.462982 TCGTGTACAAACAAGTGCAGAT 58.537 40.909 0.00 0.00 37.36 2.90


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

AutoCloner maintained by Alex Coulton.