Multiple sequence alignment - TraesCS1D01G199400

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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 TraesCS1D01G199400 chr1D 100.000 2213 0 0 1 2213 282183568 282185780 0.000000e+00 4087.0
1 TraesCS1D01G199400 chr1B 92.203 1180 46 16 603 1756 383217917 383219076 0.000000e+00 1628.0
2 TraesCS1D01G199400 chr1A 88.713 1267 39 35 602 1824 354190338 354191544 0.000000e+00 1452.0
3 TraesCS1D01G199400 chr1A 83.084 467 51 16 123 577 539602067 539601617 1.230000e-107 399.0
4 TraesCS1D01G199400 chr1A 79.394 330 23 18 1919 2210 354191651 354191973 8.070000e-45 191.0
5 TraesCS1D01G199400 chr1A 92.453 53 3 1 2019 2071 509038325 509038376 8.470000e-10 75.0
6 TraesCS1D01G199400 chr1A 89.796 49 2 3 1897 1942 354191559 354191607 2.370000e-05 60.2
7 TraesCS1D01G199400 chr1A 100.000 31 0 0 1463 1493 354191233 354191263 8.530000e-05 58.4
8 TraesCS1D01G199400 chr3D 98.517 607 9 0 1 607 615103232 615103838 0.000000e+00 1072.0
9 TraesCS1D01G199400 chr2D 82.102 609 76 19 1 599 11251377 11250792 7.100000e-135 490.0
10 TraesCS1D01G199400 chr2B 82.869 467 52 16 123 577 231605471 231605921 5.730000e-106 394.0
11 TraesCS1D01G199400 chr7A 86.831 243 24 5 363 605 731116834 731117068 4.690000e-67 265.0
12 TraesCS1D01G199400 chr7A 86.831 243 24 5 363 605 731149006 731149240 4.690000e-67 265.0
13 TraesCS1D01G199400 chr7A 86.831 243 24 5 363 605 731177553 731177787 4.690000e-67 265.0
14 TraesCS1D01G199400 chr7A 86.831 243 24 5 363 605 731214848 731215082 4.690000e-67 265.0
15 TraesCS1D01G199400 chr7A 89.524 210 19 2 98 307 731177327 731177533 1.690000e-66 263.0
16 TraesCS1D01G199400 chr7A 86.420 243 25 5 363 605 731206288 731206522 2.180000e-65 259.0
17 TraesCS1D01G199400 chr7A 89.048 210 20 2 98 307 731148780 731148986 7.840000e-65 257.0
18 TraesCS1D01G199400 chr7A 89.048 210 20 2 98 307 731206062 731206268 7.840000e-65 257.0
19 TraesCS1D01G199400 chr7A 89.048 210 20 2 98 307 731214622 731214828 7.840000e-65 257.0
20 TraesCS1D01G199400 chr7A 88.571 210 21 2 98 307 731116608 731116814 3.650000e-63 252.0


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 TraesCS1D01G199400 chr1D 282183568 282185780 2212 False 4087.0 4087 100.00000 1 2213 1 chr1D.!!$F1 2212
1 TraesCS1D01G199400 chr1B 383217917 383219076 1159 False 1628.0 1628 92.20300 603 1756 1 chr1B.!!$F1 1153
2 TraesCS1D01G199400 chr1A 354190338 354191973 1635 False 440.4 1452 89.47575 602 2210 4 chr1A.!!$F2 1608
3 TraesCS1D01G199400 chr3D 615103232 615103838 606 False 1072.0 1072 98.51700 1 607 1 chr3D.!!$F1 606
4 TraesCS1D01G199400 chr2D 11250792 11251377 585 True 490.0 490 82.10200 1 599 1 chr2D.!!$R1 598

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
370 371 0.035439 GCTCCAGTCCCGAATTCCAA 60.035 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2191 0.031585 TGTCTCCACAAACTCGACCG 59.968 55.0 0.0 0.0 0.0 4.79 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
221 222 5.239306 TGCCGCTTCCATTTCTCATAATTAG 59.761 40.000 0.00 0.00 0.00 1.73
307 308 3.408634 AGCTAAATTGGTACGCAGTGTT 58.591 40.909 0.00 0.00 45.73 3.32
370 371 0.035439 GCTCCAGTCCCGAATTCCAA 60.035 55.000 0.00 0.00 0.00 3.53
408 409 1.617018 TTGATGGAGACGGGGAGCAG 61.617 60.000 0.00 0.00 0.00 4.24
530 531 2.440430 CGGAGGCCGGAGAAGAGA 60.440 66.667 5.05 0.00 44.15 3.10
639 640 1.378250 GCATCTGGGCTTGAGCTGT 60.378 57.895 0.00 0.00 41.70 4.40
666 668 1.895966 TGCTGTTTTTGTGCAGGCA 59.104 47.368 0.00 0.00 33.62 4.75
831 833 1.649321 TCCAGGTCAATGTCAGCTCT 58.351 50.000 0.00 0.00 0.00 4.09
840 842 3.195182 TCAATGTCAGCTCTGAGGAGAAG 59.805 47.826 6.83 0.00 41.86 2.85
841 843 1.554836 TGTCAGCTCTGAGGAGAAGG 58.445 55.000 6.83 0.00 41.86 3.46
842 844 1.076187 TGTCAGCTCTGAGGAGAAGGA 59.924 52.381 6.83 0.00 41.86 3.36
843 845 2.175202 GTCAGCTCTGAGGAGAAGGAA 58.825 52.381 6.83 0.00 41.86 3.36
844 846 2.166254 GTCAGCTCTGAGGAGAAGGAAG 59.834 54.545 6.83 0.00 41.86 3.46
845 847 2.042297 TCAGCTCTGAGGAGAAGGAAGA 59.958 50.000 6.83 0.00 41.86 2.87
933 941 2.778850 AGGAGAGTACTACACCGAGGAT 59.221 50.000 0.00 0.00 0.00 3.24
951 959 1.135333 GATGAGGACTGGGAAGACGAC 59.865 57.143 0.00 0.00 0.00 4.34
1305 1348 2.586425 CTCCCTGACACCAACACATTT 58.414 47.619 0.00 0.00 0.00 2.32
1381 1437 4.508662 CTGGTTCCAGTTATTCTGAGGAC 58.491 47.826 10.40 0.00 46.27 3.85
1382 1438 3.907474 TGGTTCCAGTTATTCTGAGGACA 59.093 43.478 0.00 0.00 46.27 4.02
1383 1439 4.536090 TGGTTCCAGTTATTCTGAGGACAT 59.464 41.667 0.00 0.00 46.27 3.06
1384 1440 4.878397 GGTTCCAGTTATTCTGAGGACATG 59.122 45.833 0.00 0.00 46.27 3.21
1385 1441 4.760530 TCCAGTTATTCTGAGGACATGG 57.239 45.455 0.00 0.00 46.27 3.66
1386 1442 4.104086 TCCAGTTATTCTGAGGACATGGT 58.896 43.478 0.00 0.00 46.27 3.55
1387 1443 4.080919 TCCAGTTATTCTGAGGACATGGTG 60.081 45.833 0.00 0.00 46.27 4.17
1388 1444 4.194640 CAGTTATTCTGAGGACATGGTGG 58.805 47.826 0.00 0.00 46.27 4.61
1389 1445 3.846588 AGTTATTCTGAGGACATGGTGGT 59.153 43.478 0.00 0.00 0.00 4.16
1390 1446 5.030147 AGTTATTCTGAGGACATGGTGGTA 58.970 41.667 0.00 0.00 0.00 3.25
1471 1538 4.634184 AATGCTCTCATTGTTCATGCTC 57.366 40.909 0.00 0.00 41.12 4.26
1472 1539 3.062122 TGCTCTCATTGTTCATGCTCA 57.938 42.857 0.00 0.00 32.13 4.26
1473 1540 3.617284 TGCTCTCATTGTTCATGCTCAT 58.383 40.909 0.00 0.00 32.13 2.90
1474 1541 4.014406 TGCTCTCATTGTTCATGCTCATT 58.986 39.130 0.00 0.00 32.13 2.57
1475 1542 4.095932 TGCTCTCATTGTTCATGCTCATTC 59.904 41.667 0.00 0.00 32.13 2.67
1476 1543 4.335874 GCTCTCATTGTTCATGCTCATTCT 59.664 41.667 0.00 0.00 32.13 2.40
1477 1544 5.730847 GCTCTCATTGTTCATGCTCATTCTG 60.731 44.000 0.00 0.00 32.13 3.02
1478 1545 5.250982 TCTCATTGTTCATGCTCATTCTGT 58.749 37.500 0.00 0.00 32.13 3.41
1479 1546 5.123344 TCTCATTGTTCATGCTCATTCTGTG 59.877 40.000 0.00 0.00 32.13 3.66
1480 1547 4.763279 TCATTGTTCATGCTCATTCTGTGT 59.237 37.500 0.00 0.00 32.13 3.72
1481 1548 5.939296 TCATTGTTCATGCTCATTCTGTGTA 59.061 36.000 0.00 0.00 32.13 2.90
1482 1549 6.600427 TCATTGTTCATGCTCATTCTGTGTAT 59.400 34.615 0.00 0.00 32.13 2.29
1483 1550 6.822667 TTGTTCATGCTCATTCTGTGTATT 57.177 33.333 0.00 0.00 0.00 1.89
1484 1551 6.426980 TGTTCATGCTCATTCTGTGTATTC 57.573 37.500 0.00 0.00 0.00 1.75
1485 1552 5.939296 TGTTCATGCTCATTCTGTGTATTCA 59.061 36.000 0.00 0.00 0.00 2.57
1486 1553 6.093082 TGTTCATGCTCATTCTGTGTATTCAG 59.907 38.462 0.00 0.00 36.85 3.02
1487 1554 5.737860 TCATGCTCATTCTGTGTATTCAGT 58.262 37.500 0.00 0.00 36.85 3.41
1488 1555 6.175471 TCATGCTCATTCTGTGTATTCAGTT 58.825 36.000 0.00 0.00 36.85 3.16
1489 1556 6.656270 TCATGCTCATTCTGTGTATTCAGTTT 59.344 34.615 0.00 0.00 36.85 2.66
1490 1557 6.882610 TGCTCATTCTGTGTATTCAGTTTT 57.117 33.333 0.00 0.00 36.85 2.43
1491 1558 6.902341 TGCTCATTCTGTGTATTCAGTTTTC 58.098 36.000 0.00 0.00 36.85 2.29
1542 1615 6.369890 TCAGTTTTCAGTTCATGCTCAGTATC 59.630 38.462 0.00 0.00 0.00 2.24
1601 1705 1.069022 CCAATACATACAGGCATGCGC 60.069 52.381 12.44 0.00 37.44 6.09
1687 1791 5.005203 TGAAAATGCAACATGACGTTTGTTC 59.995 36.000 13.10 9.75 35.18 3.18
1698 1802 4.930963 TGACGTTTGTTCATGCTCATTTT 58.069 34.783 0.00 0.00 0.00 1.82
1720 1824 3.181458 TGAGCTTTTCCGGTTACTGTTCT 60.181 43.478 0.00 0.00 0.00 3.01
1721 1825 3.400255 AGCTTTTCCGGTTACTGTTCTC 58.600 45.455 0.00 0.00 0.00 2.87
1722 1826 3.135994 GCTTTTCCGGTTACTGTTCTCA 58.864 45.455 0.00 0.00 0.00 3.27
1723 1827 3.562557 GCTTTTCCGGTTACTGTTCTCAA 59.437 43.478 0.00 0.00 0.00 3.02
1758 1863 1.228367 GCCTCGATCCCAATGGCAT 60.228 57.895 4.83 0.00 42.79 4.40
1759 1864 1.521450 GCCTCGATCCCAATGGCATG 61.521 60.000 0.00 0.00 42.79 4.06
1760 1865 0.179009 CCTCGATCCCAATGGCATGT 60.179 55.000 0.00 0.00 0.00 3.21
1761 1866 0.949397 CTCGATCCCAATGGCATGTG 59.051 55.000 0.00 1.66 0.00 3.21
1762 1867 0.255604 TCGATCCCAATGGCATGTGT 59.744 50.000 0.00 0.00 0.00 3.72
1763 1868 1.488393 TCGATCCCAATGGCATGTGTA 59.512 47.619 0.00 0.00 0.00 2.90
1812 1936 3.321111 AGAAGCAAGTGAAGTCCGAGTAA 59.679 43.478 0.00 0.00 0.00 2.24
1860 1984 8.575649 AAACTTCACCGAGGACATAAAAATAT 57.424 30.769 0.00 0.00 0.00 1.28
1861 1985 9.675464 AAACTTCACCGAGGACATAAAAATATA 57.325 29.630 0.00 0.00 0.00 0.86
1862 1986 8.658499 ACTTCACCGAGGACATAAAAATATAC 57.342 34.615 0.00 0.00 0.00 1.47
1863 1987 7.713942 ACTTCACCGAGGACATAAAAATATACC 59.286 37.037 0.00 0.00 0.00 2.73
1865 1989 7.439381 TCACCGAGGACATAAAAATATACCTC 58.561 38.462 0.00 0.00 38.99 3.85
1867 1991 6.328148 ACCGAGGACATAAAAATATACCTCCA 59.672 38.462 0.00 0.00 39.13 3.86
1868 1992 7.147444 ACCGAGGACATAAAAATATACCTCCAA 60.147 37.037 0.00 0.00 39.13 3.53
1869 1993 7.387948 CCGAGGACATAAAAATATACCTCCAAG 59.612 40.741 0.00 0.00 39.13 3.61
1870 1994 7.095187 CGAGGACATAAAAATATACCTCCAAGC 60.095 40.741 0.00 0.00 39.13 4.01
1871 1995 7.582719 AGGACATAAAAATATACCTCCAAGCA 58.417 34.615 0.00 0.00 0.00 3.91
1872 1996 7.502561 AGGACATAAAAATATACCTCCAAGCAC 59.497 37.037 0.00 0.00 0.00 4.40
1873 1997 7.284489 GGACATAAAAATATACCTCCAAGCACA 59.716 37.037 0.00 0.00 0.00 4.57
1874 1998 8.588290 ACATAAAAATATACCTCCAAGCACAA 57.412 30.769 0.00 0.00 0.00 3.33
1875 1999 9.200817 ACATAAAAATATACCTCCAAGCACAAT 57.799 29.630 0.00 0.00 0.00 2.71
1878 2002 8.823220 AAAAATATACCTCCAAGCACAATAGT 57.177 30.769 0.00 0.00 0.00 2.12
1879 2003 8.823220 AAAATATACCTCCAAGCACAATAGTT 57.177 30.769 0.00 0.00 0.00 2.24
1880 2004 8.451908 AAATATACCTCCAAGCACAATAGTTC 57.548 34.615 0.00 0.00 0.00 3.01
1881 2005 2.699954 ACCTCCAAGCACAATAGTTCG 58.300 47.619 0.00 0.00 0.00 3.95
1882 2006 2.301870 ACCTCCAAGCACAATAGTTCGA 59.698 45.455 0.00 0.00 0.00 3.71
1883 2007 2.932614 CCTCCAAGCACAATAGTTCGAG 59.067 50.000 0.00 0.00 0.00 4.04
1884 2008 3.368427 CCTCCAAGCACAATAGTTCGAGA 60.368 47.826 0.00 0.00 0.00 4.04
1885 2009 4.245660 CTCCAAGCACAATAGTTCGAGAA 58.754 43.478 0.00 0.00 0.00 2.87
1886 2010 4.832248 TCCAAGCACAATAGTTCGAGAAT 58.168 39.130 0.00 0.00 0.00 2.40
1887 2011 5.972935 TCCAAGCACAATAGTTCGAGAATA 58.027 37.500 0.00 0.00 0.00 1.75
1888 2012 6.403049 TCCAAGCACAATAGTTCGAGAATAA 58.597 36.000 0.00 0.00 0.00 1.40
1889 2013 6.312918 TCCAAGCACAATAGTTCGAGAATAAC 59.687 38.462 0.00 0.00 0.00 1.89
1890 2014 6.456988 CCAAGCACAATAGTTCGAGAATAACC 60.457 42.308 0.00 0.00 0.00 2.85
1891 2015 5.116882 AGCACAATAGTTCGAGAATAACCC 58.883 41.667 0.00 0.00 0.00 4.11
1892 2016 5.104900 AGCACAATAGTTCGAGAATAACCCT 60.105 40.000 0.00 0.00 0.00 4.34
1893 2017 6.097839 AGCACAATAGTTCGAGAATAACCCTA 59.902 38.462 0.00 0.00 0.00 3.53
1894 2018 6.929606 GCACAATAGTTCGAGAATAACCCTAT 59.070 38.462 0.00 0.00 0.00 2.57
1895 2019 7.116519 GCACAATAGTTCGAGAATAACCCTATC 59.883 40.741 0.00 0.00 0.00 2.08
1896 2020 8.141909 CACAATAGTTCGAGAATAACCCTATCA 58.858 37.037 0.00 0.00 0.00 2.15
1897 2021 8.701895 ACAATAGTTCGAGAATAACCCTATCAA 58.298 33.333 0.00 0.00 0.00 2.57
1898 2022 9.542462 CAATAGTTCGAGAATAACCCTATCAAA 57.458 33.333 0.00 0.00 0.00 2.69
1933 2057 3.013921 TCCAGAAAATTATGGACCACGC 58.986 45.455 5.43 0.00 43.15 5.34
1934 2058 3.016736 CCAGAAAATTATGGACCACGCT 58.983 45.455 0.00 0.00 42.03 5.07
1942 2066 8.840833 AAAATTATGGACCACGCTTTATTTTT 57.159 26.923 0.00 0.00 0.00 1.94
1943 2067 9.930693 AAAATTATGGACCACGCTTTATTTTTA 57.069 25.926 0.00 0.00 0.00 1.52
1964 2156 8.760980 TTTTATGAAAATAGTCCCCGATCAAT 57.239 30.769 0.00 0.00 0.00 2.57
1966 2158 9.854668 TTTATGAAAATAGTCCCCGATCAATAA 57.145 29.630 0.00 0.00 0.00 1.40
1967 2159 9.854668 TTATGAAAATAGTCCCCGATCAATAAA 57.145 29.630 0.00 0.00 0.00 1.40
1971 2163 2.919228 AGTCCCCGATCAATAAAGCAC 58.081 47.619 0.00 0.00 0.00 4.40
1983 2175 7.307632 CGATCAATAAAGCACAAAGATCCCTAG 60.308 40.741 0.00 0.00 0.00 3.02
1999 2191 9.620259 AAGATCCCTAGAAGTATCAAAAATCAC 57.380 33.333 0.00 0.00 0.00 3.06
2010 2202 4.203950 TCAAAAATCACGGTCGAGTTTG 57.796 40.909 0.00 8.65 33.78 2.93
2015 2207 0.031585 TCACGGTCGAGTTTGTGGAG 59.968 55.000 0.00 0.00 33.25 3.86
2016 2208 0.031585 CACGGTCGAGTTTGTGGAGA 59.968 55.000 0.00 0.00 0.00 3.71
2017 2209 0.031721 ACGGTCGAGTTTGTGGAGAC 59.968 55.000 0.00 0.00 0.00 3.36
2018 2210 0.031585 CGGTCGAGTTTGTGGAGACA 59.968 55.000 0.00 0.00 38.70 3.41
2020 2212 2.135933 GGTCGAGTTTGTGGAGACAAG 58.864 52.381 0.00 0.00 46.06 3.16
2021 2213 1.527311 GTCGAGTTTGTGGAGACAAGC 59.473 52.381 0.00 0.00 46.06 4.01
2022 2214 1.138069 TCGAGTTTGTGGAGACAAGCA 59.862 47.619 0.00 0.00 43.70 3.91
2023 2215 1.261619 CGAGTTTGTGGAGACAAGCAC 59.738 52.381 0.00 0.00 43.70 4.40
2024 2216 2.565841 GAGTTTGTGGAGACAAGCACT 58.434 47.619 0.00 0.00 43.70 4.40
2025 2217 2.545946 GAGTTTGTGGAGACAAGCACTC 59.454 50.000 0.00 0.00 43.70 3.51
2033 2235 2.431601 ACAAGCACTCGAGCGAGC 60.432 61.111 18.80 14.44 45.54 5.03
2067 2269 1.133041 TCATCATCGTCCCTCCCTCAT 60.133 52.381 0.00 0.00 0.00 2.90
2071 2273 0.263172 ATCGTCCCTCCCTCATCTGT 59.737 55.000 0.00 0.00 0.00 3.41
2073 2275 0.684479 CGTCCCTCCCTCATCTGTGA 60.684 60.000 0.00 0.00 0.00 3.58
2074 2276 1.799933 GTCCCTCCCTCATCTGTGAT 58.200 55.000 0.00 0.00 32.98 3.06
2075 2277 2.122768 GTCCCTCCCTCATCTGTGATT 58.877 52.381 0.00 0.00 32.98 2.57
2076 2278 2.121948 TCCCTCCCTCATCTGTGATTG 58.878 52.381 0.00 0.00 32.98 2.67
2077 2279 1.842562 CCCTCCCTCATCTGTGATTGT 59.157 52.381 0.00 0.00 32.98 2.71
2078 2280 3.041211 CCCTCCCTCATCTGTGATTGTA 58.959 50.000 0.00 0.00 32.98 2.41
2082 2352 3.513912 TCCCTCATCTGTGATTGTACGTT 59.486 43.478 0.00 0.00 32.98 3.99
2099 2369 1.523758 GTTCGCATGTCCAACTCCTT 58.476 50.000 0.00 0.00 0.00 3.36
2210 2482 8.794335 ACTTTCCTTATCTTTCCAACTCATAC 57.206 34.615 0.00 0.00 0.00 2.39
2211 2483 8.606830 ACTTTCCTTATCTTTCCAACTCATACT 58.393 33.333 0.00 0.00 0.00 2.12
2212 2484 9.103861 CTTTCCTTATCTTTCCAACTCATACTC 57.896 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.465512 GCACGAATGGCAGCACCG 62.466 66.667 0.00 0.00 43.94 4.94
33 34 4.217210 CCCACACCACCCTGCCAA 62.217 66.667 0.00 0.00 0.00 4.52
157 158 2.046023 CCTCTGCAATGGCGACCA 60.046 61.111 1.01 1.01 45.35 4.02
158 159 2.825836 CCCTCTGCAATGGCGACC 60.826 66.667 0.00 0.00 45.35 4.79
307 308 3.513680 ACGAACACTACTCACACAACA 57.486 42.857 0.00 0.00 0.00 3.33
370 371 7.888021 TCCATCAACACCAACAAATTAGATACT 59.112 33.333 0.00 0.00 0.00 2.12
666 668 2.123726 GGCGGGGGATCAGCAATT 60.124 61.111 0.00 0.00 38.33 2.32
751 753 2.249557 CTGCTGCTCACGTGGAATGC 62.250 60.000 17.00 15.30 0.00 3.56
831 833 2.003830 TCCTCCTCTTCCTTCTCCTCA 58.996 52.381 0.00 0.00 0.00 3.86
840 842 1.036707 CACCGATCTCCTCCTCTTCC 58.963 60.000 0.00 0.00 0.00 3.46
841 843 1.770294 ACACCGATCTCCTCCTCTTC 58.230 55.000 0.00 0.00 0.00 2.87
842 844 1.827969 CAACACCGATCTCCTCCTCTT 59.172 52.381 0.00 0.00 0.00 2.85
843 845 1.006043 TCAACACCGATCTCCTCCTCT 59.994 52.381 0.00 0.00 0.00 3.69
844 846 1.135333 GTCAACACCGATCTCCTCCTC 59.865 57.143 0.00 0.00 0.00 3.71
845 847 1.187087 GTCAACACCGATCTCCTCCT 58.813 55.000 0.00 0.00 0.00 3.69
933 941 1.241990 CGTCGTCTTCCCAGTCCTCA 61.242 60.000 0.00 0.00 0.00 3.86
1016 1024 2.909662 CCAACCTTCTTCTTCTCCTCCT 59.090 50.000 0.00 0.00 0.00 3.69
1045 1053 2.825836 GTGCCTGCCCTCGAATGG 60.826 66.667 0.00 0.00 0.00 3.16
1047 1055 2.045926 GTGTGCCTGCCCTCGAAT 60.046 61.111 0.00 0.00 0.00 3.34
1305 1348 6.418057 AAGATAGCATGTCCAAACCAAAAA 57.582 33.333 0.00 0.00 0.00 1.94
1381 1437 5.560760 GCAATAACATCGATGTACCACCATG 60.561 44.000 30.16 20.65 40.80 3.66
1382 1438 4.515191 GCAATAACATCGATGTACCACCAT 59.485 41.667 30.16 15.69 40.80 3.55
1383 1439 3.874543 GCAATAACATCGATGTACCACCA 59.125 43.478 30.16 12.28 40.80 4.17
1384 1440 4.024893 CAGCAATAACATCGATGTACCACC 60.025 45.833 30.16 18.11 40.80 4.61
1385 1441 4.024893 CCAGCAATAACATCGATGTACCAC 60.025 45.833 30.16 18.24 40.80 4.16
1386 1442 4.126437 CCAGCAATAACATCGATGTACCA 58.874 43.478 30.16 18.60 40.80 3.25
1387 1443 4.127171 ACCAGCAATAACATCGATGTACC 58.873 43.478 30.16 16.19 40.80 3.34
1388 1444 5.293324 TGAACCAGCAATAACATCGATGTAC 59.707 40.000 30.16 16.95 40.80 2.90
1389 1445 5.423886 TGAACCAGCAATAACATCGATGTA 58.576 37.500 30.16 18.36 40.80 2.29
1390 1446 4.260985 TGAACCAGCAATAACATCGATGT 58.739 39.130 25.18 25.18 44.20 3.06
1464 1531 5.737860 ACTGAATACACAGAATGAGCATGA 58.262 37.500 0.00 0.00 39.69 3.07
1465 1532 6.432607 AACTGAATACACAGAATGAGCATG 57.567 37.500 0.00 0.00 39.69 4.06
1466 1533 7.175467 TGAAAACTGAATACACAGAATGAGCAT 59.825 33.333 0.00 0.00 39.69 3.79
1467 1534 6.486320 TGAAAACTGAATACACAGAATGAGCA 59.514 34.615 0.00 0.00 39.69 4.26
1468 1535 6.902341 TGAAAACTGAATACACAGAATGAGC 58.098 36.000 0.00 0.00 39.69 4.26
1469 1536 8.092521 ACTGAAAACTGAATACACAGAATGAG 57.907 34.615 0.00 0.00 39.69 2.90
1470 1537 8.450578 AACTGAAAACTGAATACACAGAATGA 57.549 30.769 0.00 0.00 39.69 2.57
1471 1538 8.344831 TGAACTGAAAACTGAATACACAGAATG 58.655 33.333 0.00 0.00 46.00 2.67
1472 1539 8.450578 TGAACTGAAAACTGAATACACAGAAT 57.549 30.769 0.00 0.00 40.63 2.40
1473 1540 7.857734 TGAACTGAAAACTGAATACACAGAA 57.142 32.000 0.00 0.00 40.63 3.02
1474 1541 7.520453 GCATGAACTGAAAACTGAATACACAGA 60.520 37.037 0.00 0.00 40.63 3.41
1475 1542 6.580041 GCATGAACTGAAAACTGAATACACAG 59.420 38.462 0.00 0.00 42.78 3.66
1476 1543 6.262944 AGCATGAACTGAAAACTGAATACACA 59.737 34.615 0.00 0.00 0.00 3.72
1477 1544 6.672147 AGCATGAACTGAAAACTGAATACAC 58.328 36.000 0.00 0.00 0.00 2.90
1478 1545 6.486320 TGAGCATGAACTGAAAACTGAATACA 59.514 34.615 0.00 0.00 0.00 2.29
1479 1546 6.902341 TGAGCATGAACTGAAAACTGAATAC 58.098 36.000 0.00 0.00 0.00 1.89
1480 1547 7.692460 ATGAGCATGAACTGAAAACTGAATA 57.308 32.000 0.00 0.00 0.00 1.75
1481 1548 6.585695 ATGAGCATGAACTGAAAACTGAAT 57.414 33.333 0.00 0.00 0.00 2.57
1482 1549 6.263842 AGAATGAGCATGAACTGAAAACTGAA 59.736 34.615 0.00 0.00 0.00 3.02
1483 1550 5.766670 AGAATGAGCATGAACTGAAAACTGA 59.233 36.000 0.00 0.00 0.00 3.41
1484 1551 5.856986 CAGAATGAGCATGAACTGAAAACTG 59.143 40.000 0.00 0.00 39.69 3.16
1485 1552 5.533903 ACAGAATGAGCATGAACTGAAAACT 59.466 36.000 0.00 0.00 39.69 2.66
1486 1553 5.628193 CACAGAATGAGCATGAACTGAAAAC 59.372 40.000 0.00 0.00 39.69 2.43
1487 1554 5.300034 ACACAGAATGAGCATGAACTGAAAA 59.700 36.000 0.00 0.00 39.69 2.29
1488 1555 4.823442 ACACAGAATGAGCATGAACTGAAA 59.177 37.500 0.00 0.00 39.69 2.69
1489 1556 4.214758 CACACAGAATGAGCATGAACTGAA 59.785 41.667 0.00 0.00 39.69 3.02
1490 1557 3.749609 CACACAGAATGAGCATGAACTGA 59.250 43.478 0.00 0.00 39.69 3.41
1491 1558 3.749609 TCACACAGAATGAGCATGAACTG 59.250 43.478 0.00 0.00 39.69 3.16
1568 1672 7.763528 CCTGTATGTATTGGATCTTAGCTGATC 59.236 40.741 0.00 0.23 41.39 2.92
1601 1705 6.165577 CCCAAAGAATTACCAACAGAATTGG 58.834 40.000 4.11 4.11 44.91 3.16
1698 1802 2.922740 ACAGTAACCGGAAAAGCTCA 57.077 45.000 9.46 0.00 0.00 4.26
1708 1812 4.124238 TCCAAACTTGAGAACAGTAACCG 58.876 43.478 0.00 0.00 0.00 4.44
1720 1824 3.069443 GGCAGTCCATTTTCCAAACTTGA 59.931 43.478 0.00 0.00 0.00 3.02
1721 1825 3.070015 AGGCAGTCCATTTTCCAAACTTG 59.930 43.478 0.00 0.00 33.74 3.16
1722 1826 3.308401 AGGCAGTCCATTTTCCAAACTT 58.692 40.909 0.00 0.00 33.74 2.66
1723 1827 2.893489 GAGGCAGTCCATTTTCCAAACT 59.107 45.455 0.00 0.00 33.74 2.66
1758 1863 7.751768 TTCATGTCCACAATTTGTATACACA 57.248 32.000 4.68 0.00 30.37 3.72
1759 1864 9.469807 TTTTTCATGTCCACAATTTGTATACAC 57.530 29.630 4.68 5.70 30.37 2.90
1830 1954 3.881220 TGTCCTCGGTGAAGTTTTTCTT 58.119 40.909 0.00 0.00 39.32 2.52
1831 1955 3.553828 TGTCCTCGGTGAAGTTTTTCT 57.446 42.857 0.00 0.00 34.31 2.52
1832 1956 5.934935 TTATGTCCTCGGTGAAGTTTTTC 57.065 39.130 0.00 0.00 0.00 2.29
1833 1957 6.702716 TTTTATGTCCTCGGTGAAGTTTTT 57.297 33.333 0.00 0.00 0.00 1.94
1834 1958 6.702716 TTTTTATGTCCTCGGTGAAGTTTT 57.297 33.333 0.00 0.00 0.00 2.43
1835 1959 6.894339 ATTTTTATGTCCTCGGTGAAGTTT 57.106 33.333 0.00 0.00 0.00 2.66
1836 1960 9.106070 GTATATTTTTATGTCCTCGGTGAAGTT 57.894 33.333 0.00 0.00 0.00 2.66
1837 1961 7.713942 GGTATATTTTTATGTCCTCGGTGAAGT 59.286 37.037 0.00 0.00 0.00 3.01
1838 1962 7.931948 AGGTATATTTTTATGTCCTCGGTGAAG 59.068 37.037 0.00 0.00 0.00 3.02
1839 1963 7.798071 AGGTATATTTTTATGTCCTCGGTGAA 58.202 34.615 0.00 0.00 0.00 3.18
1840 1964 7.369551 AGGTATATTTTTATGTCCTCGGTGA 57.630 36.000 0.00 0.00 0.00 4.02
1843 1967 6.765403 TGGAGGTATATTTTTATGTCCTCGG 58.235 40.000 0.00 0.00 40.30 4.63
1860 1984 3.512329 TCGAACTATTGTGCTTGGAGGTA 59.488 43.478 0.00 0.00 0.00 3.08
1861 1985 2.301870 TCGAACTATTGTGCTTGGAGGT 59.698 45.455 0.00 0.00 0.00 3.85
1862 1986 2.932614 CTCGAACTATTGTGCTTGGAGG 59.067 50.000 0.00 0.00 0.00 4.30
1863 1987 3.849911 TCTCGAACTATTGTGCTTGGAG 58.150 45.455 0.00 0.00 0.00 3.86
1865 1989 6.456988 GGTTATTCTCGAACTATTGTGCTTGG 60.457 42.308 0.00 0.00 0.00 3.61
1867 1991 5.585047 GGGTTATTCTCGAACTATTGTGCTT 59.415 40.000 0.00 0.00 0.00 3.91
1868 1992 5.104900 AGGGTTATTCTCGAACTATTGTGCT 60.105 40.000 0.00 0.00 0.00 4.40
1869 1993 5.116882 AGGGTTATTCTCGAACTATTGTGC 58.883 41.667 0.00 0.00 0.00 4.57
1870 1994 8.141909 TGATAGGGTTATTCTCGAACTATTGTG 58.858 37.037 0.00 0.00 0.00 3.33
1871 1995 8.246430 TGATAGGGTTATTCTCGAACTATTGT 57.754 34.615 0.00 0.00 0.00 2.71
1872 1996 9.542462 TTTGATAGGGTTATTCTCGAACTATTG 57.458 33.333 0.00 0.00 0.00 1.90
1903 2027 9.354673 GGTCCATAATTTTCTGGATATTCTCAA 57.645 33.333 7.19 0.00 43.20 3.02
1904 2028 8.501904 TGGTCCATAATTTTCTGGATATTCTCA 58.498 33.333 7.19 0.00 43.20 3.27
1942 2066 9.502091 CTTTATTGATCGGGGACTATTTTCATA 57.498 33.333 0.00 0.00 0.00 2.15
1943 2067 7.040409 GCTTTATTGATCGGGGACTATTTTCAT 60.040 37.037 0.00 0.00 0.00 2.57
1964 2156 6.374417 ACTTCTAGGGATCTTTGTGCTTTA 57.626 37.500 0.00 0.00 0.00 1.85
1966 2158 4.917906 ACTTCTAGGGATCTTTGTGCTT 57.082 40.909 0.00 0.00 0.00 3.91
1967 2159 5.663106 TGATACTTCTAGGGATCTTTGTGCT 59.337 40.000 0.00 0.00 0.00 4.40
1983 2175 5.347907 ACTCGACCGTGATTTTTGATACTTC 59.652 40.000 0.00 0.00 0.00 3.01
1999 2191 0.031585 TGTCTCCACAAACTCGACCG 59.968 55.000 0.00 0.00 0.00 4.79
2010 2202 1.011451 GCTCGAGTGCTTGTCTCCAC 61.011 60.000 15.13 0.00 0.00 4.02
2015 2207 2.440569 GCTCGCTCGAGTGCTTGTC 61.441 63.158 21.17 4.36 43.70 3.18
2016 2208 2.431601 GCTCGCTCGAGTGCTTGT 60.432 61.111 21.17 0.00 43.70 3.16
2017 2209 3.184683 GGCTCGCTCGAGTGCTTG 61.185 66.667 21.17 13.77 43.70 4.01
2018 2210 4.785512 CGGCTCGCTCGAGTGCTT 62.786 66.667 21.17 0.00 43.70 3.91
2037 2239 3.330853 GATGATGACGACGCGCCC 61.331 66.667 5.73 0.00 0.00 6.13
2067 2269 2.425578 TGCGAACGTACAATCACAGA 57.574 45.000 0.00 0.00 0.00 3.41
2071 2273 1.996898 GGACATGCGAACGTACAATCA 59.003 47.619 0.00 0.00 0.00 2.57
2073 2275 2.087501 TGGACATGCGAACGTACAAT 57.912 45.000 0.00 0.00 0.00 2.71
2074 2276 1.527736 GTTGGACATGCGAACGTACAA 59.472 47.619 0.00 0.00 33.53 2.41
2075 2277 1.141645 GTTGGACATGCGAACGTACA 58.858 50.000 0.00 0.00 0.00 2.90
2076 2278 1.389106 GAGTTGGACATGCGAACGTAC 59.611 52.381 0.00 0.00 39.82 3.67
2077 2279 1.670674 GGAGTTGGACATGCGAACGTA 60.671 52.381 0.00 0.00 39.82 3.57
2078 2280 0.949105 GGAGTTGGACATGCGAACGT 60.949 55.000 0.00 0.00 39.82 3.99
2082 2352 0.976641 AGAAGGAGTTGGACATGCGA 59.023 50.000 0.00 0.00 0.00 5.10
2099 2369 0.928505 AATGCATGACATGGGGGAGA 59.071 50.000 17.03 0.00 39.60 3.71


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

AutoCloner maintained by Alex Coulton.