Multiple sequence alignment - TraesCS6B01G409200

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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 TraesCS6B01G409200 chr6B 100.000 2273 0 0 1 2273 683422543 683420271 0.000000e+00 4198
1 TraesCS6B01G409200 chr4B 94.091 1303 74 2 1 1302 65529510 65528210 0.000000e+00 1977
2 TraesCS6B01G409200 chr4B 93.191 1307 79 6 1 1305 65145093 65143795 0.000000e+00 1912
3 TraesCS6B01G409200 chr4B 93.032 1306 83 4 1 1305 64820455 64819157 0.000000e+00 1901
4 TraesCS6B01G409200 chr3B 92.573 1306 96 1 1 1305 222250498 222249193 0.000000e+00 1873
5 TraesCS6B01G409200 chr1B 92.414 1305 97 1 1 1305 419276656 419275354 0.000000e+00 1860
6 TraesCS6B01G409200 chr1B 91.942 1303 103 2 1 1302 14989497 14988196 0.000000e+00 1823
7 TraesCS6B01G409200 chr1B 91.571 1305 108 2 1 1305 301294777 301296079 0.000000e+00 1799
8 TraesCS6B01G409200 chrUn 92.089 1302 103 0 1 1302 2466562 2465261 0.000000e+00 1834
9 TraesCS6B01G409200 chr3A 91.348 1306 112 1 1 1306 496599716 496598412 0.000000e+00 1784
10 TraesCS6B01G409200 chr6A 90.204 980 82 12 1303 2273 595705631 595704657 0.000000e+00 1266
11 TraesCS6B01G409200 chr6D 94.692 697 33 2 1539 2232 450291022 450290327 0.000000e+00 1079
12 TraesCS6B01G409200 chr6D 90.909 143 6 1 1303 1445 450291159 450291024 3.860000e-43 185


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 TraesCS6B01G409200 chr6B 683420271 683422543 2272 True 4198 4198 100.0000 1 2273 1 chr6B.!!$R1 2272
1 TraesCS6B01G409200 chr4B 65528210 65529510 1300 True 1977 1977 94.0910 1 1302 1 chr4B.!!$R3 1301
2 TraesCS6B01G409200 chr4B 65143795 65145093 1298 True 1912 1912 93.1910 1 1305 1 chr4B.!!$R2 1304
3 TraesCS6B01G409200 chr4B 64819157 64820455 1298 True 1901 1901 93.0320 1 1305 1 chr4B.!!$R1 1304
4 TraesCS6B01G409200 chr3B 222249193 222250498 1305 True 1873 1873 92.5730 1 1305 1 chr3B.!!$R1 1304
5 TraesCS6B01G409200 chr1B 419275354 419276656 1302 True 1860 1860 92.4140 1 1305 1 chr1B.!!$R2 1304
6 TraesCS6B01G409200 chr1B 14988196 14989497 1301 True 1823 1823 91.9420 1 1302 1 chr1B.!!$R1 1301
7 TraesCS6B01G409200 chr1B 301294777 301296079 1302 False 1799 1799 91.5710 1 1305 1 chr1B.!!$F1 1304
8 TraesCS6B01G409200 chrUn 2465261 2466562 1301 True 1834 1834 92.0890 1 1302 1 chrUn.!!$R1 1301
9 TraesCS6B01G409200 chr3A 496598412 496599716 1304 True 1784 1784 91.3480 1 1306 1 chr3A.!!$R1 1305
10 TraesCS6B01G409200 chr6A 595704657 595705631 974 True 1266 1266 90.2040 1303 2273 1 chr6A.!!$R1 970
11 TraesCS6B01G409200 chr6D 450290327 450291159 832 True 632 1079 92.8005 1303 2232 2 chr6D.!!$R1 929

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
54 55 1.00408 ACTCGCAGCAAGCATCACT 60.004 52.632 0.0 0.0 46.13 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1461 0.037303 CTCCAAGGCTGGCAAGAAGA 59.963 55.0 3.38 0.0 43.17 2.87 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
38 39 1.068741 GACTCCACTGTTTCGTCCACT 59.931 52.381 0.00 0.00 0.00 4.00
47 48 1.221466 TTTCGTCCACTCGCAGCAAG 61.221 55.000 0.00 0.00 0.00 4.01
54 55 1.004080 ACTCGCAGCAAGCATCACT 60.004 52.632 0.00 0.00 46.13 3.41
60 61 1.269936 GCAGCAAGCATCACTTTGGTT 60.270 47.619 0.00 0.00 44.79 3.67
252 253 4.987419 CGAGCTCTAGTGACTCGC 57.013 61.111 12.85 0.00 45.67 5.03
299 300 1.406887 GCAGGCTACCGGATCTTCAAA 60.407 52.381 9.46 0.00 0.00 2.69
320 321 3.185246 AGATAAACAGCGGATGTGGAG 57.815 47.619 0.00 0.00 43.00 3.86
591 592 2.159517 GGCCGAAGACATCATTTGTGAC 60.160 50.000 0.00 0.00 39.18 3.67
645 647 1.737793 GTTTCGGTCATGTGGTCCATC 59.262 52.381 0.00 0.00 0.00 3.51
657 659 1.323271 GGTCCATCTGGCACTCGAGA 61.323 60.000 21.68 0.00 34.44 4.04
662 664 2.416747 CATCTGGCACTCGAGAAACAA 58.583 47.619 21.68 0.00 0.00 2.83
670 672 4.497340 GGCACTCGAGAAACAAATTGACAA 60.497 41.667 21.68 0.00 0.00 3.18
702 704 2.656651 CTCGATCCGGCAAGCTCG 60.657 66.667 0.00 0.00 0.00 5.03
729 731 1.813859 CACTCGGGAGGCGTTATCA 59.186 57.895 0.00 0.00 0.00 2.15
810 812 2.990479 GAGGGCCTCGTCACCATT 59.010 61.111 19.53 0.00 0.00 3.16
882 884 1.267574 TTGCCCGATCCTCTTGCTCT 61.268 55.000 0.00 0.00 0.00 4.09
1000 1002 4.710865 TGAGGGGTTATACACACGTCATTA 59.289 41.667 7.94 0.00 46.55 1.90
1095 1097 6.376581 CCATTCTGTTAGAAATTGGAGAGCTT 59.623 38.462 5.63 0.00 36.80 3.74
1099 1101 7.907389 TCTGTTAGAAATTGGAGAGCTTTCTA 58.093 34.615 4.01 1.16 39.34 2.10
1163 1167 3.877508 GCTAACGGTCCTGCTCATATTTT 59.122 43.478 0.00 0.00 0.00 1.82
1173 1177 5.595542 TCCTGCTCATATTTTTGCTAAGCAT 59.404 36.000 0.00 0.00 38.76 3.79
1206 1210 0.034896 ACGTGACCGAAAGCTGGATT 59.965 50.000 0.00 0.00 37.88 3.01
1233 1237 0.179051 CTCCCAGCTTCCTGATCAGC 60.179 60.000 17.76 6.89 41.77 4.26
1321 1325 0.744281 AAAGTGGTTTTGCGGGACAG 59.256 50.000 0.00 0.00 0.00 3.51
1347 1351 7.933577 GTGATATGTGGGATTTGTTAGAGATGA 59.066 37.037 0.00 0.00 0.00 2.92
1403 1407 6.037098 CCTCACTATGGAGTAGAGTTTTTCG 58.963 44.000 0.00 0.00 33.32 3.46
1409 1413 7.813627 ACTATGGAGTAGAGTTTTTCGTTCTTC 59.186 37.037 0.00 0.00 32.65 2.87
1446 1450 2.436646 CATGTCACCGTGGAGGGC 60.437 66.667 0.00 0.00 46.96 5.19
1447 1451 2.607750 ATGTCACCGTGGAGGGCT 60.608 61.111 0.00 0.00 46.96 5.19
1448 1452 2.660064 ATGTCACCGTGGAGGGCTC 61.660 63.158 0.00 0.00 46.96 4.70
1449 1453 2.997897 GTCACCGTGGAGGGCTCT 60.998 66.667 0.00 0.00 46.96 4.09
1450 1454 1.681327 GTCACCGTGGAGGGCTCTA 60.681 63.158 0.00 0.00 46.96 2.43
1451 1455 1.043673 GTCACCGTGGAGGGCTCTAT 61.044 60.000 0.00 0.00 46.96 1.98
1452 1456 0.755698 TCACCGTGGAGGGCTCTATC 60.756 60.000 0.00 0.00 46.96 2.08
1453 1457 1.828660 ACCGTGGAGGGCTCTATCG 60.829 63.158 0.00 0.00 46.96 2.92
1454 1458 1.828660 CCGTGGAGGGCTCTATCGT 60.829 63.158 0.00 0.00 35.97 3.73
1455 1459 1.655329 CGTGGAGGGCTCTATCGTC 59.345 63.158 0.00 0.00 0.00 4.20
1456 1460 1.655329 GTGGAGGGCTCTATCGTCG 59.345 63.158 0.00 0.00 0.00 5.12
1457 1461 1.102222 GTGGAGGGCTCTATCGTCGT 61.102 60.000 0.00 0.00 0.00 4.34
1458 1462 0.818445 TGGAGGGCTCTATCGTCGTC 60.818 60.000 0.00 0.00 0.00 4.20
1459 1463 0.535553 GGAGGGCTCTATCGTCGTCT 60.536 60.000 0.00 0.00 0.00 4.18
1460 1464 1.310904 GAGGGCTCTATCGTCGTCTT 58.689 55.000 0.00 0.00 0.00 3.01
1461 1465 1.264826 GAGGGCTCTATCGTCGTCTTC 59.735 57.143 0.00 0.00 0.00 2.87
1462 1466 1.134037 AGGGCTCTATCGTCGTCTTCT 60.134 52.381 0.00 0.00 0.00 2.85
1463 1467 1.677052 GGGCTCTATCGTCGTCTTCTT 59.323 52.381 0.00 0.00 0.00 2.52
1464 1468 2.541999 GGGCTCTATCGTCGTCTTCTTG 60.542 54.545 0.00 0.00 0.00 3.02
1465 1469 2.113289 GCTCTATCGTCGTCTTCTTGC 58.887 52.381 0.00 0.00 0.00 4.01
1466 1470 2.722071 CTCTATCGTCGTCTTCTTGCC 58.278 52.381 0.00 0.00 0.00 4.52
1467 1471 2.089201 TCTATCGTCGTCTTCTTGCCA 58.911 47.619 0.00 0.00 0.00 4.92
1468 1472 2.097629 TCTATCGTCGTCTTCTTGCCAG 59.902 50.000 0.00 0.00 0.00 4.85
1469 1473 0.737715 ATCGTCGTCTTCTTGCCAGC 60.738 55.000 0.00 0.00 0.00 4.85
1470 1474 2.383527 CGTCGTCTTCTTGCCAGCC 61.384 63.158 0.00 0.00 0.00 4.85
1471 1475 1.004440 GTCGTCTTCTTGCCAGCCT 60.004 57.895 0.00 0.00 0.00 4.58
1472 1476 0.603975 GTCGTCTTCTTGCCAGCCTT 60.604 55.000 0.00 0.00 0.00 4.35
1473 1477 0.603707 TCGTCTTCTTGCCAGCCTTG 60.604 55.000 0.00 0.00 0.00 3.61
1486 1490 4.730487 CCTTGGAGGGCTTCACTG 57.270 61.111 0.00 0.00 0.00 3.66
1487 1491 1.676967 CCTTGGAGGGCTTCACTGC 60.677 63.158 0.00 0.00 0.00 4.40
1488 1492 1.377994 CTTGGAGGGCTTCACTGCT 59.622 57.895 0.00 0.00 0.00 4.24
1489 1493 0.251077 CTTGGAGGGCTTCACTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
1490 1494 0.538057 TTGGAGGGCTTCACTGCTTG 60.538 55.000 0.00 0.00 0.00 4.01
1491 1495 1.676967 GGAGGGCTTCACTGCTTGG 60.677 63.158 0.00 0.00 0.00 3.61
1492 1496 1.676967 GAGGGCTTCACTGCTTGGG 60.677 63.158 0.00 0.00 0.00 4.12
1493 1497 2.116125 GGGCTTCACTGCTTGGGT 59.884 61.111 0.00 0.00 0.00 4.51
1494 1498 1.973812 GGGCTTCACTGCTTGGGTC 60.974 63.158 0.00 0.00 0.00 4.46
1495 1499 1.073897 GGCTTCACTGCTTGGGTCT 59.926 57.895 0.00 0.00 0.00 3.85
1496 1500 1.239968 GGCTTCACTGCTTGGGTCTG 61.240 60.000 0.00 0.00 0.00 3.51
1497 1501 1.239968 GCTTCACTGCTTGGGTCTGG 61.240 60.000 0.00 0.00 0.00 3.86
1498 1502 1.228245 TTCACTGCTTGGGTCTGGC 60.228 57.895 0.00 0.00 0.00 4.85
1499 1503 1.708993 TTCACTGCTTGGGTCTGGCT 61.709 55.000 0.00 0.00 0.00 4.75
1500 1504 1.673665 CACTGCTTGGGTCTGGCTC 60.674 63.158 0.00 0.00 0.00 4.70
1501 1505 2.045536 CTGCTTGGGTCTGGCTCC 60.046 66.667 0.00 0.00 0.00 4.70
1502 1506 3.635268 CTGCTTGGGTCTGGCTCCC 62.635 68.421 6.14 6.14 44.81 4.30
1503 1507 4.432741 GCTTGGGTCTGGCTCCCC 62.433 72.222 9.65 5.38 44.00 4.81
1504 1508 2.612115 CTTGGGTCTGGCTCCCCT 60.612 66.667 9.65 0.00 44.00 4.79
1505 1509 2.610859 TTGGGTCTGGCTCCCCTC 60.611 66.667 9.65 0.00 44.00 4.30
1506 1510 3.194025 TTGGGTCTGGCTCCCCTCT 62.194 63.158 9.65 0.00 44.00 3.69
1507 1511 2.766229 GGGTCTGGCTCCCCTCTC 60.766 72.222 2.42 0.00 39.08 3.20
1508 1512 2.766229 GGTCTGGCTCCCCTCTCC 60.766 72.222 0.00 0.00 0.00 3.71
1509 1513 3.151022 GTCTGGCTCCCCTCTCCG 61.151 72.222 0.00 0.00 0.00 4.63
1510 1514 4.465446 TCTGGCTCCCCTCTCCGG 62.465 72.222 0.00 0.00 0.00 5.14
1515 1519 2.201490 CTCCCCTCTCCGGCCATA 59.799 66.667 2.24 0.00 0.00 2.74
1516 1520 1.910772 CTCCCCTCTCCGGCCATAG 60.911 68.421 2.24 0.00 0.00 2.23
1517 1521 2.122813 CCCCTCTCCGGCCATAGT 60.123 66.667 2.24 0.00 0.00 2.12
1518 1522 2.210711 CCCCTCTCCGGCCATAGTC 61.211 68.421 2.24 0.00 0.00 2.59
1519 1523 1.457643 CCCTCTCCGGCCATAGTCA 60.458 63.158 2.24 0.00 0.00 3.41
1520 1524 1.467678 CCCTCTCCGGCCATAGTCAG 61.468 65.000 2.24 0.00 0.00 3.51
1521 1525 0.468214 CCTCTCCGGCCATAGTCAGA 60.468 60.000 2.24 0.00 0.00 3.27
1522 1526 1.626686 CTCTCCGGCCATAGTCAGAT 58.373 55.000 2.24 0.00 0.00 2.90
1523 1527 1.271934 CTCTCCGGCCATAGTCAGATG 59.728 57.143 2.24 0.00 0.00 2.90
1525 1529 1.121407 TCCGGCCATAGTCAGATGGG 61.121 60.000 2.24 0.00 45.73 4.00
1526 1530 1.372683 CGGCCATAGTCAGATGGGG 59.627 63.158 2.24 0.00 45.73 4.96
1527 1531 1.410850 CGGCCATAGTCAGATGGGGT 61.411 60.000 2.24 0.00 45.73 4.95
1528 1532 0.109342 GGCCATAGTCAGATGGGGTG 59.891 60.000 0.00 0.00 45.73 4.61
1529 1533 0.109342 GCCATAGTCAGATGGGGTGG 59.891 60.000 4.67 0.00 45.73 4.61
1530 1534 1.806496 CCATAGTCAGATGGGGTGGA 58.194 55.000 0.00 0.00 42.46 4.02
1531 1535 1.696336 CCATAGTCAGATGGGGTGGAG 59.304 57.143 0.00 0.00 42.46 3.86
1532 1536 2.682594 CATAGTCAGATGGGGTGGAGA 58.317 52.381 0.00 0.00 0.00 3.71
1533 1537 2.940514 TAGTCAGATGGGGTGGAGAA 57.059 50.000 0.00 0.00 0.00 2.87
1534 1538 1.577736 AGTCAGATGGGGTGGAGAAG 58.422 55.000 0.00 0.00 0.00 2.85
1535 1539 0.543749 GTCAGATGGGGTGGAGAAGG 59.456 60.000 0.00 0.00 0.00 3.46
1536 1540 0.417437 TCAGATGGGGTGGAGAAGGA 59.583 55.000 0.00 0.00 0.00 3.36
1537 1541 0.835941 CAGATGGGGTGGAGAAGGAG 59.164 60.000 0.00 0.00 0.00 3.69
1593 1691 0.320771 GTTGGCCTTGAGAGCTCGAA 60.321 55.000 8.37 4.56 0.00 3.71
1680 1778 9.826574 TTTTATAGGCTGAGTAATACACGAAAT 57.173 29.630 0.00 0.00 0.00 2.17
1703 1801 2.202690 CAGGATTACGACGCCGCA 60.203 61.111 0.00 0.00 39.95 5.69
1748 1846 4.193865 CCATACATTGTCTGCTGATCACA 58.806 43.478 0.00 0.00 0.00 3.58
1749 1847 4.820173 CCATACATTGTCTGCTGATCACAT 59.180 41.667 0.00 0.00 0.00 3.21
1756 1854 3.111838 GTCTGCTGATCACATACACGAG 58.888 50.000 0.00 0.00 0.00 4.18
1772 1870 0.796491 CGAGTCGAGAGAGCACTTGC 60.796 60.000 6.73 0.00 43.49 4.01
1796 1897 6.128007 GCTTAATTACCATATGTAAGGCGCAT 60.128 38.462 10.83 0.00 42.50 4.73
1811 1912 1.746760 CGCATAATCGCTTTTCTGGC 58.253 50.000 0.00 0.00 0.00 4.85
1863 1964 5.870433 CCACGTACACAAGTTATATTGACCA 59.130 40.000 0.00 0.00 34.20 4.02
1905 2006 0.679002 ACACATGGGCTGACAGATGC 60.679 55.000 6.65 0.00 0.00 3.91
1918 2019 2.194212 AGATGCGATCGGCCTACGT 61.194 57.895 18.30 0.13 44.69 3.57
1937 2038 2.417379 CGTTGTCAGAATCGGACCTGAT 60.417 50.000 10.80 0.00 40.95 2.90
1952 2053 5.624159 GGACCTGATCATCATCATAAACCA 58.376 41.667 0.00 0.00 38.42 3.67
2050 2151 1.480954 GGTGCTTATCCAAGACCGAGA 59.519 52.381 0.00 0.00 33.20 4.04
2195 2296 1.774894 TTGAAGACCGGTTCAGGGGG 61.775 60.000 9.42 0.00 37.72 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.239082 CAAAGTGATGCTTGCTGCGA 59.761 50.000 0.00 0.00 46.63 5.10
47 48 2.527442 GTCGCTAACCAAAGTGATGC 57.473 50.000 0.00 0.00 38.23 3.91
60 61 0.172578 CCGTGTCAATCAGGTCGCTA 59.827 55.000 0.00 0.00 0.00 4.26
69 70 1.798813 GTCCAGTTGTCCGTGTCAATC 59.201 52.381 0.00 0.00 0.00 2.67
114 115 1.630148 CGTCCGGAGTGATGAAGTTC 58.370 55.000 3.06 0.00 0.00 3.01
206 207 3.366273 CGACTTAACGGTGTAGTTGCCTA 60.366 47.826 0.00 0.00 35.70 3.93
299 300 3.055094 ACTCCACATCCGCTGTTTATCTT 60.055 43.478 0.00 0.00 35.29 2.40
309 310 1.153549 GAGGTCACTCCACATCCGC 60.154 63.158 0.00 0.00 37.79 5.54
320 321 5.712152 AACATTCAATTTCCAGAGGTCAC 57.288 39.130 0.00 0.00 0.00 3.67
591 592 0.249489 CCCTGGAAGTAAGGCGATCG 60.249 60.000 11.69 11.69 33.07 3.69
645 647 3.250762 TCAATTTGTTTCTCGAGTGCCAG 59.749 43.478 13.13 0.00 0.00 4.85
657 659 6.232581 TCCTCACCATTTGTCAATTTGTTT 57.767 33.333 0.00 0.00 0.00 2.83
662 664 4.159135 GCTGATCCTCACCATTTGTCAATT 59.841 41.667 0.00 0.00 0.00 2.32
670 672 1.489481 TCGAGCTGATCCTCACCATT 58.511 50.000 0.00 0.00 0.00 3.16
729 731 2.357517 CGCGGCACCTCAAGAAGT 60.358 61.111 0.00 0.00 0.00 3.01
799 801 2.357327 TCGGTGTTAATGGTGACGAG 57.643 50.000 0.00 0.00 0.00 4.18
827 829 4.065088 TCCTTTGTCATCTTCTCGTTTGG 58.935 43.478 0.00 0.00 0.00 3.28
882 884 3.420893 CTTACTCCATGCACCCAGAAAA 58.579 45.455 0.00 0.00 0.00 2.29
957 959 3.447229 TCAGACATGCGAAGATAACTCCA 59.553 43.478 0.00 0.00 0.00 3.86
1000 1002 1.347050 CTCCGAGCAATCCATCTCCAT 59.653 52.381 0.00 0.00 0.00 3.41
1173 1177 1.020437 TCACGTCAATTGTGCAAGCA 58.980 45.000 5.13 0.00 37.26 3.91
1206 1210 2.303022 CAGGAAGCTGGGAGTACTTTCA 59.697 50.000 0.00 0.00 0.00 2.69
1321 1325 7.933577 TCATCTCTAACAAATCCCACATATCAC 59.066 37.037 0.00 0.00 0.00 3.06
1347 1351 4.039973 TCCTGAAGTTTGACGGTGTTAGAT 59.960 41.667 0.00 0.00 0.00 1.98
1403 1407 6.759356 GGAAAGAGTCCTTGCTATAGAAGAAC 59.241 42.308 3.21 0.00 43.98 3.01
1409 1413 5.163258 ACATGGGAAAGAGTCCTTGCTATAG 60.163 44.000 0.00 0.00 46.92 1.31
1430 1434 2.607750 AGCCCTCCACGGTGACAT 60.608 61.111 10.28 0.00 0.00 3.06
1445 1449 2.113289 GCAAGAAGACGACGATAGAGC 58.887 52.381 0.00 0.00 41.38 4.09
1446 1450 2.097629 TGGCAAGAAGACGACGATAGAG 59.902 50.000 0.00 0.00 41.38 2.43
1447 1451 2.089201 TGGCAAGAAGACGACGATAGA 58.911 47.619 0.00 0.00 41.38 1.98
1448 1452 2.455032 CTGGCAAGAAGACGACGATAG 58.545 52.381 0.00 0.00 46.19 2.08
1449 1453 1.469251 GCTGGCAAGAAGACGACGATA 60.469 52.381 0.00 0.00 0.00 2.92
1450 1454 0.737715 GCTGGCAAGAAGACGACGAT 60.738 55.000 0.00 0.00 0.00 3.73
1451 1455 1.372997 GCTGGCAAGAAGACGACGA 60.373 57.895 0.00 0.00 0.00 4.20
1452 1456 2.383527 GGCTGGCAAGAAGACGACG 61.384 63.158 0.00 0.00 0.00 5.12
1453 1457 0.603975 AAGGCTGGCAAGAAGACGAC 60.604 55.000 3.38 0.00 0.00 4.34
1454 1458 0.603707 CAAGGCTGGCAAGAAGACGA 60.604 55.000 3.38 0.00 0.00 4.20
1455 1459 1.580845 CCAAGGCTGGCAAGAAGACG 61.581 60.000 3.38 0.00 35.39 4.18
1456 1460 0.250901 TCCAAGGCTGGCAAGAAGAC 60.251 55.000 3.38 0.00 43.17 3.01
1457 1461 0.037303 CTCCAAGGCTGGCAAGAAGA 59.963 55.000 3.38 0.00 43.17 2.87
1458 1462 0.964358 CCTCCAAGGCTGGCAAGAAG 60.964 60.000 3.38 0.00 43.17 2.85
1459 1463 1.075482 CCTCCAAGGCTGGCAAGAA 59.925 57.895 3.38 0.00 43.17 2.52
1460 1464 2.759114 CCTCCAAGGCTGGCAAGA 59.241 61.111 3.38 0.00 43.17 3.02
1461 1465 2.362120 CCCTCCAAGGCTGGCAAG 60.362 66.667 3.38 0.00 43.17 4.01
1469 1473 1.676967 GCAGTGAAGCCCTCCAAGG 60.677 63.158 0.00 0.00 34.30 3.61
1470 1474 0.251077 AAGCAGTGAAGCCCTCCAAG 60.251 55.000 0.00 0.00 34.23 3.61
1471 1475 0.538057 CAAGCAGTGAAGCCCTCCAA 60.538 55.000 0.00 0.00 34.23 3.53
1472 1476 1.073722 CAAGCAGTGAAGCCCTCCA 59.926 57.895 0.00 0.00 34.23 3.86
1473 1477 1.676967 CCAAGCAGTGAAGCCCTCC 60.677 63.158 0.00 0.00 34.23 4.30
1474 1478 1.676967 CCCAAGCAGTGAAGCCCTC 60.677 63.158 0.00 0.00 34.23 4.30
1475 1479 2.417558 GACCCAAGCAGTGAAGCCCT 62.418 60.000 0.00 0.00 34.23 5.19
1476 1480 1.973812 GACCCAAGCAGTGAAGCCC 60.974 63.158 0.00 0.00 34.23 5.19
1477 1481 1.073897 AGACCCAAGCAGTGAAGCC 59.926 57.895 0.00 0.00 34.23 4.35
1478 1482 1.239968 CCAGACCCAAGCAGTGAAGC 61.240 60.000 0.00 0.00 0.00 3.86
1479 1483 1.239968 GCCAGACCCAAGCAGTGAAG 61.240 60.000 0.00 0.00 0.00 3.02
1480 1484 1.228245 GCCAGACCCAAGCAGTGAA 60.228 57.895 0.00 0.00 0.00 3.18
1481 1485 2.116983 GAGCCAGACCCAAGCAGTGA 62.117 60.000 0.00 0.00 0.00 3.41
1482 1486 1.673665 GAGCCAGACCCAAGCAGTG 60.674 63.158 0.00 0.00 0.00 3.66
1483 1487 2.753029 GAGCCAGACCCAAGCAGT 59.247 61.111 0.00 0.00 0.00 4.40
1484 1488 2.045536 GGAGCCAGACCCAAGCAG 60.046 66.667 0.00 0.00 0.00 4.24
1485 1489 3.650950 GGGAGCCAGACCCAAGCA 61.651 66.667 0.00 0.00 46.05 3.91
1491 1495 2.766229 GGAGAGGGGAGCCAGACC 60.766 72.222 0.00 0.00 0.00 3.85
1492 1496 3.151022 CGGAGAGGGGAGCCAGAC 61.151 72.222 0.00 0.00 0.00 3.51
1493 1497 4.465446 CCGGAGAGGGGAGCCAGA 62.465 72.222 0.00 0.00 35.97 3.86
1498 1502 1.910772 CTATGGCCGGAGAGGGGAG 60.911 68.421 5.05 0.00 41.48 4.30
1499 1503 2.201490 CTATGGCCGGAGAGGGGA 59.799 66.667 5.05 0.00 41.48 4.81
1500 1504 2.122813 ACTATGGCCGGAGAGGGG 60.123 66.667 5.05 0.00 41.48 4.79
1501 1505 1.457643 TGACTATGGCCGGAGAGGG 60.458 63.158 5.05 0.00 41.48 4.30
1502 1506 0.468214 TCTGACTATGGCCGGAGAGG 60.468 60.000 5.05 0.00 44.97 3.69
1503 1507 1.271934 CATCTGACTATGGCCGGAGAG 59.728 57.143 5.05 0.00 0.00 3.20
1504 1508 1.332195 CATCTGACTATGGCCGGAGA 58.668 55.000 5.05 0.00 0.00 3.71
1505 1509 0.319728 CCATCTGACTATGGCCGGAG 59.680 60.000 5.05 0.00 40.07 4.63
1506 1510 1.121407 CCCATCTGACTATGGCCGGA 61.121 60.000 5.05 0.00 44.40 5.14
1507 1511 1.372683 CCCATCTGACTATGGCCGG 59.627 63.158 0.00 0.00 44.40 6.13
1508 1512 1.372683 CCCCATCTGACTATGGCCG 59.627 63.158 0.00 0.00 44.40 6.13
1509 1513 0.109342 CACCCCATCTGACTATGGCC 59.891 60.000 0.00 0.00 44.40 5.36
1510 1514 0.109342 CCACCCCATCTGACTATGGC 59.891 60.000 0.00 0.00 44.40 4.40
1511 1515 1.696336 CTCCACCCCATCTGACTATGG 59.304 57.143 0.00 0.00 45.20 2.74
1512 1516 2.682594 TCTCCACCCCATCTGACTATG 58.317 52.381 0.00 0.00 0.00 2.23
1513 1517 3.312890 CTTCTCCACCCCATCTGACTAT 58.687 50.000 0.00 0.00 0.00 2.12
1514 1518 2.626950 CCTTCTCCACCCCATCTGACTA 60.627 54.545 0.00 0.00 0.00 2.59
1515 1519 1.577736 CTTCTCCACCCCATCTGACT 58.422 55.000 0.00 0.00 0.00 3.41
1516 1520 0.543749 CCTTCTCCACCCCATCTGAC 59.456 60.000 0.00 0.00 0.00 3.51
1517 1521 0.417437 TCCTTCTCCACCCCATCTGA 59.583 55.000 0.00 0.00 0.00 3.27
1518 1522 0.835941 CTCCTTCTCCACCCCATCTG 59.164 60.000 0.00 0.00 0.00 2.90
1519 1523 0.985490 GCTCCTTCTCCACCCCATCT 60.985 60.000 0.00 0.00 0.00 2.90
1520 1524 1.529309 GCTCCTTCTCCACCCCATC 59.471 63.158 0.00 0.00 0.00 3.51
1521 1525 2.370445 CGCTCCTTCTCCACCCCAT 61.370 63.158 0.00 0.00 0.00 4.00
1522 1526 3.003173 CGCTCCTTCTCCACCCCA 61.003 66.667 0.00 0.00 0.00 4.96
1523 1527 3.787001 CCGCTCCTTCTCCACCCC 61.787 72.222 0.00 0.00 0.00 4.95
1524 1528 3.787001 CCCGCTCCTTCTCCACCC 61.787 72.222 0.00 0.00 0.00 4.61
1525 1529 4.475135 GCCCGCTCCTTCTCCACC 62.475 72.222 0.00 0.00 0.00 4.61
1526 1530 3.672295 CTGCCCGCTCCTTCTCCAC 62.672 68.421 0.00 0.00 0.00 4.02
1527 1531 3.393970 CTGCCCGCTCCTTCTCCA 61.394 66.667 0.00 0.00 0.00 3.86
1528 1532 3.077556 TCTGCCCGCTCCTTCTCC 61.078 66.667 0.00 0.00 0.00 3.71
1529 1533 1.398958 ATCTCTGCCCGCTCCTTCTC 61.399 60.000 0.00 0.00 0.00 2.87
1530 1534 0.980231 AATCTCTGCCCGCTCCTTCT 60.980 55.000 0.00 0.00 0.00 2.85
1531 1535 0.107459 AAATCTCTGCCCGCTCCTTC 60.107 55.000 0.00 0.00 0.00 3.46
1532 1536 0.329596 AAAATCTCTGCCCGCTCCTT 59.670 50.000 0.00 0.00 0.00 3.36
1533 1537 0.393537 CAAAATCTCTGCCCGCTCCT 60.394 55.000 0.00 0.00 0.00 3.69
1534 1538 1.997928 GCAAAATCTCTGCCCGCTCC 61.998 60.000 0.00 0.00 33.51 4.70
1535 1539 1.431036 GCAAAATCTCTGCCCGCTC 59.569 57.895 0.00 0.00 33.51 5.03
1536 1540 2.401766 CGCAAAATCTCTGCCCGCT 61.402 57.895 0.00 0.00 36.40 5.52
1537 1541 2.100991 CGCAAAATCTCTGCCCGC 59.899 61.111 0.00 0.00 36.40 6.13
1579 1677 3.192422 TCTTCTTCTTCGAGCTCTCAAGG 59.808 47.826 12.85 2.77 0.00 3.61
1593 1691 3.759618 CCTACCAGTCTTCGTCTTCTTCT 59.240 47.826 0.00 0.00 0.00 2.85
1664 1762 5.474825 TGCAGTCATTTCGTGTATTACTCA 58.525 37.500 0.00 0.00 0.00 3.41
1680 1778 0.457853 GCGTCGTAATCCTGCAGTCA 60.458 55.000 13.81 0.00 0.00 3.41
1703 1801 7.369434 TGGGAAAATGGAGGAATTATTACCAT 58.631 34.615 0.00 0.00 42.17 3.55
1748 1846 1.666700 GTGCTCTCTCGACTCGTGTAT 59.333 52.381 0.00 0.00 0.00 2.29
1749 1847 1.077123 GTGCTCTCTCGACTCGTGTA 58.923 55.000 0.00 0.00 0.00 2.90
1772 1870 6.795098 TGCGCCTTACATATGGTAATTAAG 57.205 37.500 4.18 5.50 41.00 1.85
1796 1897 2.415168 CGTCTTGCCAGAAAAGCGATTA 59.585 45.455 0.00 0.00 0.00 1.75
1811 1912 2.216046 CCCCATCATCATCACGTCTTG 58.784 52.381 0.00 0.00 0.00 3.02
1863 1964 2.158475 TGGAAGGTGCCTTTGTCTCAAT 60.158 45.455 4.83 0.00 36.26 2.57
1905 2006 0.866061 CTGACAACGTAGGCCGATCG 60.866 60.000 8.51 8.51 40.70 3.69
1918 2019 2.831526 TGATCAGGTCCGATTCTGACAA 59.168 45.455 9.95 0.00 42.00 3.18
1937 2038 2.287644 CGCGCTTGGTTTATGATGATGA 59.712 45.455 5.56 0.00 0.00 2.92
1952 2053 2.171725 GCGAAGTATTCCCGCGCTT 61.172 57.895 5.56 0.00 43.81 4.68
2004 2105 0.601057 TCTCCGTGCTGATCGAAACA 59.399 50.000 0.00 0.00 0.00 2.83
2050 2151 2.257207 TCCGAGGAACTTCAAGACCAT 58.743 47.619 0.00 0.00 41.55 3.55
2101 2202 3.407443 GTTCAACGAACCCTTCCCA 57.593 52.632 0.00 0.00 36.65 4.37
2195 2296 4.202090 CCCTATCCAAGACACCGTAAGTAC 60.202 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.