Multiple sequence alignment - TraesCS3D01G177800

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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 TraesCS3D01G177800 chr3D 100.000 2237 0 0 1 2237 159436235 159433999 0.000000e+00 4132.0
1 TraesCS3D01G177800 chr3D 87.565 193 11 6 236 417 67687678 67687868 6.260000e-51 211.0
2 TraesCS3D01G177800 chr3D 97.778 45 1 0 1432 1476 159434762 159434718 6.620000e-11 78.7
3 TraesCS3D01G177800 chr3D 97.778 45 1 0 1474 1518 159434804 159434760 6.620000e-11 78.7
4 TraesCS3D01G177800 chr3A 91.789 1498 88 15 6 1476 168831737 168833226 0.000000e+00 2052.0
5 TraesCS3D01G177800 chr3A 85.934 782 73 26 1471 2237 168833179 168833938 0.000000e+00 800.0
6 TraesCS3D01G177800 chr3A 83.406 229 18 12 195 417 79396380 79396594 6.300000e-46 195.0
7 TraesCS3D01G177800 chr3B 95.098 1020 44 4 461 1476 236152361 236151344 0.000000e+00 1602.0
8 TraesCS3D01G177800 chr3B 85.502 607 60 18 1474 2072 236151388 236150802 1.900000e-170 608.0
9 TraesCS3D01G177800 chr3B 87.719 171 14 4 2071 2237 236150544 236150377 2.270000e-45 193.0
10 TraesCS3D01G177800 chr3B 84.737 190 13 4 236 417 114152135 114151954 2.280000e-40 176.0
11 TraesCS3D01G177800 chr2B 78.395 162 30 5 3 161 77296640 77296481 1.410000e-17 100.0
12 TraesCS3D01G177800 chr5D 90.541 74 7 0 1 74 472567734 472567807 5.080000e-17 99.0
13 TraesCS3D01G177800 chr5D 87.097 62 7 1 110 171 416592612 416592672 3.990000e-08 69.4
14 TraesCS3D01G177800 chr7D 89.091 55 6 0 107 161 546194102 546194048 3.990000e-08 69.4


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 TraesCS3D01G177800 chr3D 159433999 159436235 2236 True 1429.8 4132 98.518667 1 2237 3 chr3D.!!$R1 2236
1 TraesCS3D01G177800 chr3A 168831737 168833938 2201 False 1426.0 2052 88.861500 6 2237 2 chr3A.!!$F2 2231
2 TraesCS3D01G177800 chr3B 236150377 236152361 1984 True 801.0 1602 89.439667 461 2237 3 chr3B.!!$R2 1776

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
28 29 0.035739 GCCCCCAACGTTTGTCTCTA 59.964 55.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1681 0.623723 GGGGCAACTTACCTCCATCA 59.376 55.0 0.0 0.0 0.0 3.07 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
27 28 1.228154 GCCCCCAACGTTTGTCTCT 60.228 57.895 0.00 0.00 0.00 3.10
28 29 0.035739 GCCCCCAACGTTTGTCTCTA 59.964 55.000 0.00 0.00 0.00 2.43
36 37 4.977963 CCAACGTTTGTCTCTAGTTTACGA 59.022 41.667 0.00 0.00 0.00 3.43
50 51 5.373981 AGTTTACGAGAGAAATCACGTCT 57.626 39.130 4.08 0.00 39.59 4.18
52 53 5.048921 AGTTTACGAGAGAAATCACGTCTGA 60.049 40.000 4.08 0.00 39.59 3.27
58 59 3.322254 AGAGAAATCACGTCTGAACCACT 59.678 43.478 0.00 0.00 0.00 4.00
66 67 0.319641 GTCTGAACCACTCCACGGAC 60.320 60.000 0.00 0.00 0.00 4.79
74 75 0.528924 CACTCCACGGACCGATACAA 59.471 55.000 23.38 0.00 0.00 2.41
77 78 0.968901 TCCACGGACCGATACAAGCT 60.969 55.000 23.38 0.00 0.00 3.74
78 79 0.108329 CCACGGACCGATACAAGCTT 60.108 55.000 23.38 0.00 0.00 3.74
90 91 2.561478 ACAAGCTTACGTTGGATGGT 57.439 45.000 0.00 0.00 0.00 3.55
102 103 0.953471 TGGATGGTTTTCGCTGTCCG 60.953 55.000 0.00 0.00 38.61 4.79
124 125 1.072505 AGCGTGGTCCAAACGGATT 59.927 52.632 0.00 0.00 41.31 3.01
125 126 0.322322 AGCGTGGTCCAAACGGATTA 59.678 50.000 0.00 0.00 41.31 1.75
135 137 3.845398 TCCAAACGGATTAGGGAGGTTTA 59.155 43.478 0.00 0.00 30.35 2.01
138 140 4.498894 AACGGATTAGGGAGGTTTAAGG 57.501 45.455 0.00 0.00 0.00 2.69
142 144 3.181457 GGATTAGGGAGGTTTAAGGGTCG 60.181 52.174 0.00 0.00 0.00 4.79
144 146 1.077930 GGGAGGTTTAAGGGTCGGC 60.078 63.158 0.00 0.00 0.00 5.54
149 151 0.603439 GGTTTAAGGGTCGGCGTTGA 60.603 55.000 6.85 0.00 0.00 3.18
165 167 3.195661 CGTTGAAGATGCCCTAAGTACC 58.804 50.000 0.00 0.00 0.00 3.34
173 175 3.553828 TGCCCTAAGTACCATGCTTAC 57.446 47.619 0.00 0.00 0.00 2.34
177 179 5.309543 TGCCCTAAGTACCATGCTTACATAT 59.690 40.000 5.73 0.00 33.67 1.78
214 220 6.841119 CAATCTTATGTTCGTGATTGTTCCA 58.159 36.000 0.00 0.00 40.20 3.53
293 300 4.940654 AGCTGCTTTTGGTTTCTATCTCTC 59.059 41.667 0.00 0.00 0.00 3.20
296 303 4.690748 TGCTTTTGGTTTCTATCTCTCACG 59.309 41.667 0.00 0.00 0.00 4.35
301 308 7.795482 TTTGGTTTCTATCTCTCACGAAAAA 57.205 32.000 0.00 0.00 0.00 1.94
434 446 5.053145 AGTCTAATGAACGGATGAAGATGC 58.947 41.667 0.00 0.00 0.00 3.91
459 471 6.038825 CACGATCTACTGTATGAGGTTTCTCT 59.961 42.308 0.00 0.00 40.58 3.10
467 479 2.623418 TGAGGTTTCTCTAGGGCAGA 57.377 50.000 0.00 0.00 40.58 4.26
493 505 4.015872 ACAACAGGTACGTCCAATGAAT 57.984 40.909 0.00 0.00 39.02 2.57
514 526 2.223502 TGGATGAAGACGCACGATCTAC 60.224 50.000 0.00 0.00 0.00 2.59
535 551 2.611518 GAGCTAGTGCACTGTACCAAG 58.388 52.381 29.57 17.82 42.74 3.61
609 627 6.572519 GCCAAAACCATATGCAGAATAAAGA 58.427 36.000 0.00 0.00 0.00 2.52
629 647 4.319177 AGAAGAATCTGCACACAAGGTAC 58.681 43.478 0.00 0.00 33.59 3.34
664 682 4.457466 TCTTCCTTTTCGCACCTAAAAGT 58.543 39.130 0.00 0.00 40.67 2.66
720 738 2.680339 GGGTGAAGAGAATTAGCAGTGC 59.320 50.000 7.13 7.13 0.00 4.40
815 843 7.598118 ACATATCATAAGCTTTCTGTGATCGAG 59.402 37.037 3.20 6.45 33.37 4.04
831 859 3.584406 TCGAGCAGAAGAGGAAAAGAG 57.416 47.619 0.00 0.00 0.00 2.85
935 967 4.153411 GGCTCACTATATGTACCTGAGGT 58.847 47.826 10.00 10.00 40.16 3.85
969 1001 6.150976 TGTTGCTACCATCATTCCAAAGTAAG 59.849 38.462 0.00 0.00 0.00 2.34
1039 1071 2.020131 CTGCAAGCCATCATCCGTC 58.980 57.895 0.00 0.00 0.00 4.79
1321 1353 3.869912 GCTCTGCCTTCCAATGTAGTTCA 60.870 47.826 0.00 0.00 0.00 3.18
1343 1375 5.251468 TCATGCCTACATTGCCTAGGATAAT 59.749 40.000 14.75 9.41 33.65 1.28
1386 1418 3.387374 TGTTGGTTGATTTCTTGCATGGT 59.613 39.130 0.00 0.00 0.00 3.55
1455 1487 7.661536 AAACTCTATCTGTATACAGGAAGCA 57.338 36.000 28.33 12.50 43.91 3.91
1456 1488 7.661536 AACTCTATCTGTATACAGGAAGCAA 57.338 36.000 28.33 11.83 43.91 3.91
1457 1489 7.283625 ACTCTATCTGTATACAGGAAGCAAG 57.716 40.000 28.33 20.38 43.91 4.01
1458 1490 6.090483 TCTATCTGTATACAGGAAGCAAGC 57.910 41.667 28.33 0.00 43.91 4.01
1459 1491 4.760530 ATCTGTATACAGGAAGCAAGCA 57.239 40.909 28.33 9.81 43.91 3.91
1460 1492 3.861840 TCTGTATACAGGAAGCAAGCAC 58.138 45.455 28.33 0.00 43.91 4.40
1461 1493 3.515502 TCTGTATACAGGAAGCAAGCACT 59.484 43.478 28.33 0.00 43.91 4.40
1462 1494 4.020218 TCTGTATACAGGAAGCAAGCACTT 60.020 41.667 28.33 0.00 43.91 3.16
1463 1495 4.002982 TGTATACAGGAAGCAAGCACTTG 58.997 43.478 0.08 6.01 43.14 3.16
1464 1496 2.638480 TACAGGAAGCAAGCACTTGT 57.362 45.000 11.77 10.41 42.31 3.16
1465 1497 1.767759 ACAGGAAGCAAGCACTTGTT 58.232 45.000 11.77 3.09 42.31 2.83
1466 1498 2.930950 ACAGGAAGCAAGCACTTGTTA 58.069 42.857 11.77 0.00 42.31 2.41
1467 1499 3.490348 ACAGGAAGCAAGCACTTGTTAT 58.510 40.909 11.77 0.00 42.31 1.89
1468 1500 3.891366 ACAGGAAGCAAGCACTTGTTATT 59.109 39.130 11.77 5.11 42.31 1.40
1469 1501 4.232221 CAGGAAGCAAGCACTTGTTATTG 58.768 43.478 11.77 2.70 42.31 1.90
1470 1502 4.022935 CAGGAAGCAAGCACTTGTTATTGA 60.023 41.667 11.77 0.00 42.31 2.57
1471 1503 4.768968 AGGAAGCAAGCACTTGTTATTGAT 59.231 37.500 11.77 0.00 42.31 2.57
1472 1504 4.860907 GGAAGCAAGCACTTGTTATTGATG 59.139 41.667 11.77 0.00 42.31 3.07
1473 1505 5.335897 GGAAGCAAGCACTTGTTATTGATGA 60.336 40.000 11.77 0.00 42.31 2.92
1474 1506 5.710513 AGCAAGCACTTGTTATTGATGAA 57.289 34.783 11.77 0.00 42.31 2.57
1475 1507 6.088016 AGCAAGCACTTGTTATTGATGAAA 57.912 33.333 11.77 0.00 42.31 2.69
1476 1508 5.922544 AGCAAGCACTTGTTATTGATGAAAC 59.077 36.000 11.77 0.00 42.31 2.78
1477 1509 5.922544 GCAAGCACTTGTTATTGATGAAACT 59.077 36.000 11.77 0.00 42.31 2.66
1478 1510 6.088616 GCAAGCACTTGTTATTGATGAAACTC 59.911 38.462 11.77 0.00 42.31 3.01
1479 1511 7.365741 CAAGCACTTGTTATTGATGAAACTCT 58.634 34.615 2.12 0.00 35.92 3.24
1480 1512 8.506437 CAAGCACTTGTTATTGATGAAACTCTA 58.494 33.333 2.12 0.00 35.92 2.43
1481 1513 8.798859 AGCACTTGTTATTGATGAAACTCTAT 57.201 30.769 0.00 0.00 0.00 1.98
1482 1514 8.887717 AGCACTTGTTATTGATGAAACTCTATC 58.112 33.333 0.00 0.00 0.00 2.08
1483 1515 8.887717 GCACTTGTTATTGATGAAACTCTATCT 58.112 33.333 0.00 0.00 0.00 1.98
1485 1517 9.950496 ACTTGTTATTGATGAAACTCTATCTGT 57.050 29.630 0.00 0.00 0.00 3.41
1493 1525 8.996651 TGATGAAACTCTATCTGTATACAGGA 57.003 34.615 28.33 18.21 43.91 3.86
1494 1526 9.421399 TGATGAAACTCTATCTGTATACAGGAA 57.579 33.333 28.33 17.31 43.91 3.36
1495 1527 9.906660 GATGAAACTCTATCTGTATACAGGAAG 57.093 37.037 28.33 23.97 43.91 3.46
1509 1541 2.618709 ACAGGAAGCAAGCACTTGTTAC 59.381 45.455 11.77 6.15 42.31 2.50
1512 1544 2.878406 GGAAGCAAGCACTTGTTACTGA 59.122 45.455 11.77 0.00 42.31 3.41
1561 1593 3.391296 ACCGGTCAAATATACAGCATCCT 59.609 43.478 0.00 0.00 0.00 3.24
1564 1596 5.639506 CCGGTCAAATATACAGCATCCTAAG 59.360 44.000 0.00 0.00 0.00 2.18
1581 1613 7.466996 GCATCCTAAGTGATCAACATTTCAGAG 60.467 40.741 0.00 0.00 31.22 3.35
1588 1620 5.879223 GTGATCAACATTTCAGAGAGGTGAT 59.121 40.000 0.00 0.00 0.00 3.06
1589 1621 5.878669 TGATCAACATTTCAGAGAGGTGATG 59.121 40.000 0.00 0.00 0.00 3.07
1591 1623 5.868454 TCAACATTTCAGAGAGGTGATGAA 58.132 37.500 0.00 0.00 0.00 2.57
1634 1666 1.749033 CGGAGGATAGCCACCTTCC 59.251 63.158 11.90 2.41 42.25 3.46
1649 1681 4.974438 TCCGGGGGAGGTTGCAGT 62.974 66.667 0.00 0.00 0.00 4.40
1719 1751 7.451255 TCCCTGTGAATTGTGACAGAAATAAAT 59.549 33.333 9.45 0.00 41.90 1.40
1728 1760 7.905604 TGTGACAGAAATAAATGTAGTCAGG 57.094 36.000 0.00 0.00 35.48 3.86
1729 1761 6.371548 TGTGACAGAAATAAATGTAGTCAGGC 59.628 38.462 0.00 0.00 35.48 4.85
1730 1762 5.880332 TGACAGAAATAAATGTAGTCAGGCC 59.120 40.000 0.00 0.00 31.63 5.19
1731 1763 5.815581 ACAGAAATAAATGTAGTCAGGCCA 58.184 37.500 5.01 0.00 0.00 5.36
1732 1764 5.882557 ACAGAAATAAATGTAGTCAGGCCAG 59.117 40.000 5.01 0.00 0.00 4.85
1733 1765 5.882557 CAGAAATAAATGTAGTCAGGCCAGT 59.117 40.000 5.01 0.00 0.00 4.00
1734 1766 7.047891 CAGAAATAAATGTAGTCAGGCCAGTA 58.952 38.462 5.01 0.00 0.00 2.74
1735 1767 7.225538 CAGAAATAAATGTAGTCAGGCCAGTAG 59.774 40.741 5.01 0.00 0.00 2.57
1736 1768 2.990066 AATGTAGTCAGGCCAGTAGC 57.010 50.000 5.01 0.00 42.60 3.58
1737 1769 2.166907 ATGTAGTCAGGCCAGTAGCT 57.833 50.000 5.01 0.00 43.05 3.32
1786 1818 1.300620 CAACGGCGAGTCCAACAGA 60.301 57.895 16.62 0.00 34.01 3.41
1824 1856 2.514803 GAGCCTGCCCTAGAAAACAAA 58.485 47.619 0.00 0.00 0.00 2.83
1825 1857 2.890945 GAGCCTGCCCTAGAAAACAAAA 59.109 45.455 0.00 0.00 0.00 2.44
1826 1858 3.304829 AGCCTGCCCTAGAAAACAAAAA 58.695 40.909 0.00 0.00 0.00 1.94
1850 1884 9.592196 AAAATATTACTATAGTACTCCGGGTGA 57.408 33.333 12.25 0.00 0.00 4.02
1854 1888 2.154567 ATAGTACTCCGGGTGAAGCA 57.845 50.000 0.00 0.00 0.00 3.91
1855 1889 1.471119 TAGTACTCCGGGTGAAGCAG 58.529 55.000 0.00 0.00 0.00 4.24
1856 1890 1.448013 GTACTCCGGGTGAAGCAGC 60.448 63.158 0.00 0.00 0.00 5.25
1862 1896 3.727387 GGGTGAAGCAGCCCTAGA 58.273 61.111 4.36 0.00 45.22 2.43
1863 1897 1.991230 GGGTGAAGCAGCCCTAGAA 59.009 57.895 4.36 0.00 45.22 2.10
1865 1899 1.271926 GGGTGAAGCAGCCCTAGAAAA 60.272 52.381 4.36 0.00 45.22 2.29
1866 1900 2.514803 GGTGAAGCAGCCCTAGAAAAA 58.485 47.619 0.00 0.00 0.00 1.94
1903 1937 4.566488 GCCCATTCACCATATAGAAGAGGG 60.566 50.000 14.39 14.39 41.92 4.30
1954 1993 0.737804 TTCACACGCACAAGCACAAT 59.262 45.000 0.00 0.00 42.27 2.71
1957 1996 2.017783 CACGCACAAGCACAATGCC 61.018 57.895 0.00 0.00 46.52 4.40
1958 1997 2.431260 CGCACAAGCACAATGCCC 60.431 61.111 0.00 0.00 46.52 5.36
1960 1999 2.259204 CACAAGCACAATGCCCCG 59.741 61.111 0.00 0.00 46.52 5.73
1962 2001 3.376078 CAAGCACAATGCCCCGCT 61.376 61.111 0.00 0.00 46.52 5.52
1965 2004 2.749839 GCACAATGCCCCGCTACA 60.750 61.111 0.00 0.00 37.42 2.74
1979 2019 0.393537 GCTACACAGCCAGAAGCCAT 60.394 55.000 0.00 0.00 45.47 4.40
2041 2081 9.265901 TCTAATTCTCAGATTACATTGCTAAGC 57.734 33.333 0.00 0.00 0.00 3.09
2051 2091 6.737254 TTACATTGCTAAGCCAGTAAACTC 57.263 37.500 0.00 0.00 32.19 3.01
2053 2093 6.049955 ACATTGCTAAGCCAGTAAACTCTA 57.950 37.500 0.00 0.00 32.19 2.43
2059 2099 6.037726 GCTAAGCCAGTAAACTCTAAGTCTC 58.962 44.000 0.00 0.00 0.00 3.36
2112 2411 1.327303 AAAATTTGCTCGCAGTCCCA 58.673 45.000 0.00 0.00 0.00 4.37
2115 2415 0.957395 ATTTGCTCGCAGTCCCACAG 60.957 55.000 0.00 0.00 0.00 3.66
2164 2466 7.711339 ACAAAAATGAAGAGAAAGAGTACGAGT 59.289 33.333 0.00 0.00 0.00 4.18
2170 2472 5.899120 AGAGAAAGAGTACGAGTATGCAA 57.101 39.130 0.00 0.00 0.00 4.08
2176 2478 9.431887 AGAAAGAGTACGAGTATGCAATTTTTA 57.568 29.630 0.00 0.00 0.00 1.52
2177 2479 9.474249 GAAAGAGTACGAGTATGCAATTTTTAC 57.526 33.333 0.00 0.00 0.00 2.01
2178 2480 8.542497 AAGAGTACGAGTATGCAATTTTTACA 57.458 30.769 0.00 0.00 0.00 2.41
2179 2481 8.542497 AGAGTACGAGTATGCAATTTTTACAA 57.458 30.769 0.00 0.00 0.00 2.41
2180 2482 8.656849 AGAGTACGAGTATGCAATTTTTACAAG 58.343 33.333 0.00 0.00 0.00 3.16
2181 2483 7.748847 AGTACGAGTATGCAATTTTTACAAGG 58.251 34.615 0.00 0.00 0.00 3.61
2182 2484 5.399013 ACGAGTATGCAATTTTTACAAGGC 58.601 37.500 0.00 0.00 0.00 4.35
2201 2503 2.162408 GGCCACAAGCAGTTCAGTTATC 59.838 50.000 0.00 0.00 46.50 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.200092 GTTGGGGGCTTTGTGGGA 59.800 61.111 0.00 0.00 0.00 4.37
1 2 3.302344 CGTTGGGGGCTTTGTGGG 61.302 66.667 0.00 0.00 0.00 4.61
2 3 1.681486 AAACGTTGGGGGCTTTGTGG 61.681 55.000 0.00 0.00 0.00 4.17
3 4 0.529555 CAAACGTTGGGGGCTTTGTG 60.530 55.000 0.00 0.00 0.00 3.33
4 5 0.973496 ACAAACGTTGGGGGCTTTGT 60.973 50.000 7.76 0.00 33.07 2.83
10 11 1.346722 ACTAGAGACAAACGTTGGGGG 59.653 52.381 7.76 0.00 34.12 5.40
15 16 6.017605 TCTCTCGTAAACTAGAGACAAACGTT 60.018 38.462 9.59 0.00 42.52 3.99
36 37 3.322254 AGTGGTTCAGACGTGATTTCTCT 59.678 43.478 0.00 0.00 30.85 3.10
45 46 1.362717 CGTGGAGTGGTTCAGACGT 59.637 57.895 0.00 0.00 31.88 4.34
50 51 2.863346 CGGTCCGTGGAGTGGTTCA 61.863 63.158 2.08 0.00 0.00 3.18
52 53 0.612732 TATCGGTCCGTGGAGTGGTT 60.613 55.000 11.88 0.00 0.00 3.67
58 59 0.968901 AGCTTGTATCGGTCCGTGGA 60.969 55.000 11.88 0.00 0.00 4.02
66 67 2.883574 TCCAACGTAAGCTTGTATCGG 58.116 47.619 9.86 4.47 45.62 4.18
74 75 2.482721 CGAAAACCATCCAACGTAAGCT 59.517 45.455 0.00 0.00 45.62 3.74
77 78 2.224549 CAGCGAAAACCATCCAACGTAA 59.775 45.455 0.00 0.00 0.00 3.18
78 79 1.801771 CAGCGAAAACCATCCAACGTA 59.198 47.619 0.00 0.00 0.00 3.57
117 118 3.201487 CCCTTAAACCTCCCTAATCCGTT 59.799 47.826 0.00 0.00 0.00 4.44
124 125 1.870064 CCGACCCTTAAACCTCCCTA 58.130 55.000 0.00 0.00 0.00 3.53
125 126 1.559965 GCCGACCCTTAAACCTCCCT 61.560 60.000 0.00 0.00 0.00 4.20
135 137 0.673644 CATCTTCAACGCCGACCCTT 60.674 55.000 0.00 0.00 0.00 3.95
138 140 2.750888 GGCATCTTCAACGCCGACC 61.751 63.158 0.00 0.00 35.79 4.79
142 144 1.017387 CTTAGGGCATCTTCAACGCC 58.983 55.000 0.00 0.00 45.47 5.68
144 146 3.195661 GGTACTTAGGGCATCTTCAACG 58.804 50.000 0.00 0.00 0.00 4.10
149 151 2.780010 AGCATGGTACTTAGGGCATCTT 59.220 45.455 0.00 0.00 0.00 2.40
156 158 9.244292 TCTCTATATGTAAGCATGGTACTTAGG 57.756 37.037 0.00 0.00 36.58 2.69
205 211 3.740115 ACACACAGTACCTGGAACAATC 58.260 45.455 0.00 0.00 38.70 2.67
210 216 5.104859 TCAAAACTACACACAGTACCTGGAA 60.105 40.000 0.00 0.00 35.51 3.53
214 220 5.010314 TCGATCAAAACTACACACAGTACCT 59.990 40.000 0.00 0.00 0.00 3.08
222 228 4.152223 CACATGCTCGATCAAAACTACACA 59.848 41.667 0.00 0.00 0.00 3.72
223 229 4.388773 TCACATGCTCGATCAAAACTACAC 59.611 41.667 0.00 0.00 0.00 2.90
224 230 4.565022 TCACATGCTCGATCAAAACTACA 58.435 39.130 0.00 0.00 0.00 2.74
232 238 4.654091 TTCAGTATCACATGCTCGATCA 57.346 40.909 0.00 0.00 0.00 2.92
410 422 5.176590 GCATCTTCATCCGTTCATTAGACTC 59.823 44.000 0.00 0.00 0.00 3.36
414 426 4.318333 CGTGCATCTTCATCCGTTCATTAG 60.318 45.833 0.00 0.00 0.00 1.73
434 446 6.038825 AGAGAAACCTCATACAGTAGATCGTG 59.961 42.308 0.00 0.00 33.16 4.35
459 471 1.486310 CCTGTTGTATGCTCTGCCCTA 59.514 52.381 0.00 0.00 0.00 3.53
467 479 1.897133 TGGACGTACCTGTTGTATGCT 59.103 47.619 0.00 0.00 39.63 3.79
493 505 0.817654 AGATCGTGCGTCTTCATCCA 59.182 50.000 0.00 0.00 0.00 3.41
514 526 0.526211 TGGTACAGTGCACTAGCTCG 59.474 55.000 21.20 9.46 42.74 5.03
535 551 1.153353 TTCTTCGTCCGTTGATTGGC 58.847 50.000 0.00 0.00 0.00 4.52
609 627 3.067106 CGTACCTTGTGTGCAGATTCTT 58.933 45.455 0.00 0.00 0.00 2.52
664 682 7.825331 TTGGTCATCTAACATTTTGGTTACA 57.175 32.000 0.00 0.00 32.29 2.41
720 738 6.804783 GGTTGGTACTGATATTTTGGAAAACG 59.195 38.462 0.00 0.00 0.00 3.60
815 843 4.014569 AGGAACTCTTTTCCTCTTCTGC 57.985 45.455 0.00 0.00 45.32 4.26
831 859 1.343465 TCTGTTTCGTGAGGGAGGAAC 59.657 52.381 0.00 0.00 0.00 3.62
969 1001 4.719106 AGGACTGCTGCTGGCTGC 62.719 66.667 12.30 15.66 42.51 5.25
1053 1085 2.915659 TCCCTTGTGCCGAGACGT 60.916 61.111 0.00 0.00 0.00 4.34
1152 1184 2.549992 CCACCGTTCTTCTTCCACATCA 60.550 50.000 0.00 0.00 0.00 3.07
1321 1353 5.014544 ACATTATCCTAGGCAATGTAGGCAT 59.985 40.000 27.24 11.59 40.24 4.40
1343 1375 7.490725 CCAACATTTGTTCAGACACAAAATACA 59.509 33.333 12.17 0.00 46.95 2.29
1408 1440 6.544928 TTATTGGCAGTGAGATAGTTCTGA 57.455 37.500 0.00 0.00 30.30 3.27
1454 1486 7.365741 AGAGTTTCATCAATAACAAGTGCTTG 58.634 34.615 10.09 10.09 45.58 4.01
1455 1487 7.516198 AGAGTTTCATCAATAACAAGTGCTT 57.484 32.000 0.00 0.00 0.00 3.91
1456 1488 8.798859 ATAGAGTTTCATCAATAACAAGTGCT 57.201 30.769 0.00 0.00 0.00 4.40
1457 1489 8.887717 AGATAGAGTTTCATCAATAACAAGTGC 58.112 33.333 0.00 0.00 0.00 4.40
1459 1491 9.950496 ACAGATAGAGTTTCATCAATAACAAGT 57.050 29.630 0.00 0.00 0.00 3.16
1467 1499 9.421399 TCCTGTATACAGATAGAGTTTCATCAA 57.579 33.333 30.41 0.00 46.59 2.57
1468 1500 8.996651 TCCTGTATACAGATAGAGTTTCATCA 57.003 34.615 30.41 0.00 46.59 3.07
1469 1501 9.906660 CTTCCTGTATACAGATAGAGTTTCATC 57.093 37.037 30.41 0.00 46.59 2.92
1470 1502 8.364142 GCTTCCTGTATACAGATAGAGTTTCAT 58.636 37.037 30.41 0.00 46.59 2.57
1471 1503 7.342026 TGCTTCCTGTATACAGATAGAGTTTCA 59.658 37.037 30.41 16.42 46.59 2.69
1472 1504 7.717568 TGCTTCCTGTATACAGATAGAGTTTC 58.282 38.462 30.41 14.58 46.59 2.78
1473 1505 7.661536 TGCTTCCTGTATACAGATAGAGTTT 57.338 36.000 30.41 0.00 46.59 2.66
1474 1506 7.661536 TTGCTTCCTGTATACAGATAGAGTT 57.338 36.000 30.41 0.00 46.59 3.01
1475 1507 6.239176 GCTTGCTTCCTGTATACAGATAGAGT 60.239 42.308 30.41 0.00 46.59 3.24
1476 1508 6.155827 GCTTGCTTCCTGTATACAGATAGAG 58.844 44.000 30.41 21.25 46.59 2.43
1477 1509 5.598417 TGCTTGCTTCCTGTATACAGATAGA 59.402 40.000 30.41 17.93 46.59 1.98
1478 1510 5.694006 GTGCTTGCTTCCTGTATACAGATAG 59.306 44.000 30.41 24.87 46.59 2.08
1479 1511 5.363868 AGTGCTTGCTTCCTGTATACAGATA 59.636 40.000 30.41 16.98 46.59 1.98
1480 1512 4.163078 AGTGCTTGCTTCCTGTATACAGAT 59.837 41.667 30.41 0.00 46.59 2.90
1481 1513 3.515502 AGTGCTTGCTTCCTGTATACAGA 59.484 43.478 30.41 15.68 46.59 3.41
1482 1514 3.866651 AGTGCTTGCTTCCTGTATACAG 58.133 45.455 23.58 23.58 43.40 2.74
1483 1515 3.981071 AGTGCTTGCTTCCTGTATACA 57.019 42.857 5.25 5.25 0.00 2.29
1484 1516 4.003648 ACAAGTGCTTGCTTCCTGTATAC 58.996 43.478 11.43 0.00 44.03 1.47
1485 1517 4.286297 ACAAGTGCTTGCTTCCTGTATA 57.714 40.909 11.43 0.00 44.03 1.47
1486 1518 3.146104 ACAAGTGCTTGCTTCCTGTAT 57.854 42.857 11.43 0.00 44.03 2.29
1487 1519 2.638480 ACAAGTGCTTGCTTCCTGTA 57.362 45.000 11.43 0.00 44.03 2.74
1488 1520 1.767759 AACAAGTGCTTGCTTCCTGT 58.232 45.000 11.43 0.00 44.03 4.00
1489 1521 2.880890 AGTAACAAGTGCTTGCTTCCTG 59.119 45.455 11.43 0.00 44.03 3.86
1490 1522 2.880890 CAGTAACAAGTGCTTGCTTCCT 59.119 45.455 11.43 1.15 44.03 3.36
1491 1523 2.878406 TCAGTAACAAGTGCTTGCTTCC 59.122 45.455 11.43 0.00 44.03 3.46
1492 1524 4.214119 TCATCAGTAACAAGTGCTTGCTTC 59.786 41.667 11.43 0.00 44.03 3.86
1493 1525 4.136796 TCATCAGTAACAAGTGCTTGCTT 58.863 39.130 11.43 7.98 44.03 3.91
1494 1526 3.743521 TCATCAGTAACAAGTGCTTGCT 58.256 40.909 11.43 2.73 44.03 3.91
1495 1527 4.488126 TTCATCAGTAACAAGTGCTTGC 57.512 40.909 11.43 0.00 44.03 4.01
1509 1541 7.916977 TGAAGTGTGTGAAAGAAATTTCATCAG 59.083 33.333 19.99 0.00 42.20 2.90
1531 1563 7.011950 TGCTGTATATTTGACCGGTTATTGAAG 59.988 37.037 9.42 2.71 0.00 3.02
1538 1570 4.134563 GGATGCTGTATATTTGACCGGTT 58.865 43.478 9.42 0.00 0.00 4.44
1539 1571 3.391296 AGGATGCTGTATATTTGACCGGT 59.609 43.478 6.92 6.92 0.00 5.28
1561 1593 6.875726 CACCTCTCTGAAATGTTGATCACTTA 59.124 38.462 0.00 0.00 0.00 2.24
1564 1596 5.240891 TCACCTCTCTGAAATGTTGATCAC 58.759 41.667 0.00 0.00 0.00 3.06
1581 1613 2.025887 ACTGGGGTTGATTCATCACCTC 60.026 50.000 15.39 8.65 36.36 3.85
1588 1620 1.052617 TGTCGACTGGGGTTGATTCA 58.947 50.000 17.92 0.00 38.06 2.57
1589 1621 2.178912 TTGTCGACTGGGGTTGATTC 57.821 50.000 17.92 0.00 38.06 2.52
1591 1623 2.504367 CTTTTGTCGACTGGGGTTGAT 58.496 47.619 17.92 0.00 38.06 2.57
1634 1666 2.971598 ATCACTGCAACCTCCCCCG 61.972 63.158 0.00 0.00 0.00 5.73
1649 1681 0.623723 GGGGCAACTTACCTCCATCA 59.376 55.000 0.00 0.00 0.00 3.07
1719 1751 1.825474 GAAGCTACTGGCCTGACTACA 59.175 52.381 17.64 0.00 43.05 2.74
1724 1756 2.618816 CCATTTGAAGCTACTGGCCTGA 60.619 50.000 17.64 0.00 43.05 3.86
1725 1757 1.747355 CCATTTGAAGCTACTGGCCTG 59.253 52.381 8.29 8.29 43.05 4.85
1726 1758 1.635487 TCCATTTGAAGCTACTGGCCT 59.365 47.619 3.32 0.00 43.05 5.19
1727 1759 2.128771 TCCATTTGAAGCTACTGGCC 57.871 50.000 0.00 0.00 43.05 5.36
1728 1760 3.772060 CTTCCATTTGAAGCTACTGGC 57.228 47.619 0.00 0.00 43.79 4.85
1737 1769 6.248433 ACCTCTTTATGAGCTTCCATTTGAA 58.752 36.000 0.00 0.00 41.35 2.69
1786 1818 1.377725 CGAGCCTGTTGAAGCCCAT 60.378 57.895 0.00 0.00 0.00 4.00
1804 1836 2.200373 TTGTTTTCTAGGGCAGGCTC 57.800 50.000 0.00 0.00 0.00 4.70
1824 1856 9.592196 TCACCCGGAGTACTATAGTAATATTTT 57.408 33.333 14.20 0.00 31.52 1.82
1825 1857 9.592196 TTCACCCGGAGTACTATAGTAATATTT 57.408 33.333 14.20 0.00 31.52 1.40
1826 1858 9.240734 CTTCACCCGGAGTACTATAGTAATATT 57.759 37.037 14.20 1.27 31.52 1.28
1827 1859 7.338957 GCTTCACCCGGAGTACTATAGTAATAT 59.661 40.741 14.20 3.94 31.52 1.28
1865 1899 8.160106 TGGTGAATGGGCTTTTGTAATATTTTT 58.840 29.630 0.00 0.00 0.00 1.94
1866 1900 7.684529 TGGTGAATGGGCTTTTGTAATATTTT 58.315 30.769 0.00 0.00 0.00 1.82
1867 1901 7.251321 TGGTGAATGGGCTTTTGTAATATTT 57.749 32.000 0.00 0.00 0.00 1.40
1868 1902 6.865834 TGGTGAATGGGCTTTTGTAATATT 57.134 33.333 0.00 0.00 0.00 1.28
1871 1905 8.004215 TCTATATGGTGAATGGGCTTTTGTAAT 58.996 33.333 0.00 0.00 0.00 1.89
1873 1907 6.905736 TCTATATGGTGAATGGGCTTTTGTA 58.094 36.000 0.00 0.00 0.00 2.41
1874 1908 5.765510 TCTATATGGTGAATGGGCTTTTGT 58.234 37.500 0.00 0.00 0.00 2.83
1875 1909 6.547141 TCTTCTATATGGTGAATGGGCTTTTG 59.453 38.462 0.00 0.00 0.00 2.44
1903 1937 2.489329 TGGCTAACTGCTGCATTCTTTC 59.511 45.455 1.31 0.00 42.39 2.62
1962 2001 0.677731 GCATGGCTTCTGGCTGTGTA 60.678 55.000 0.00 0.00 41.46 2.90
1965 2004 2.362120 GGCATGGCTTCTGGCTGT 60.362 61.111 12.86 0.00 41.46 4.40
1979 2019 2.662596 CTTGTACCTCCAGCGGCA 59.337 61.111 1.45 0.00 0.00 5.69
1991 2031 5.416326 ACAAATAAATACTTGGCGGCTTGTA 59.584 36.000 11.43 13.29 0.00 2.41
2026 2066 7.281100 AGAGTTTACTGGCTTAGCAATGTAATC 59.719 37.037 6.53 10.29 0.00 1.75
2032 2072 6.712276 ACTTAGAGTTTACTGGCTTAGCAAT 58.288 36.000 6.53 0.00 0.00 3.56
2094 2393 0.598065 GTGGGACTGCGAGCAAATTT 59.402 50.000 0.00 0.00 0.00 1.82
2101 2400 1.572085 CTTTGCTGTGGGACTGCGAG 61.572 60.000 0.00 0.00 44.63 5.03
2112 2411 5.643379 TCTGAACAAGTTTTCTTTGCTGT 57.357 34.783 0.00 0.00 38.17 4.40
2115 2415 8.406172 TGTAAATCTGAACAAGTTTTCTTTGC 57.594 30.769 0.00 0.00 38.17 3.68
2164 2466 5.474578 TGTGGCCTTGTAAAAATTGCATA 57.525 34.783 3.32 0.00 0.00 3.14
2170 2472 3.387699 ACTGCTTGTGGCCTTGTAAAAAT 59.612 39.130 3.32 0.00 40.92 1.82
2176 2478 0.395586 TGAACTGCTTGTGGCCTTGT 60.396 50.000 3.32 0.00 40.92 3.16
2177 2479 0.313043 CTGAACTGCTTGTGGCCTTG 59.687 55.000 3.32 0.00 40.92 3.61
2178 2480 0.106519 ACTGAACTGCTTGTGGCCTT 60.107 50.000 3.32 0.00 40.92 4.35
2179 2481 0.106519 AACTGAACTGCTTGTGGCCT 60.107 50.000 3.32 0.00 40.92 5.19
2180 2482 1.604604 TAACTGAACTGCTTGTGGCC 58.395 50.000 0.00 0.00 40.92 5.36
2181 2483 2.162408 GGATAACTGAACTGCTTGTGGC 59.838 50.000 0.00 0.00 42.22 5.01
2182 2484 2.749621 GGGATAACTGAACTGCTTGTGG 59.250 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.