Multiple sequence alignment - TraesCS3D01G326000

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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 TraesCS3D01G326000 chr3D 100.000 2222 0 0 1 2222 438471947 438469726 0.000000e+00 4104
1 TraesCS3D01G326000 chr3A 91.504 1636 107 18 1 1628 577067152 577065541 0.000000e+00 2222
2 TraesCS3D01G326000 chr3A 88.454 485 33 15 1744 2222 577065544 577065077 4.140000e-157 564
3 TraesCS3D01G326000 chr3B 89.145 1603 100 34 644 2222 574266878 574265326 0.000000e+00 1929
4 TraesCS3D01G326000 chr3B 93.659 615 28 6 1 614 574267479 574266875 0.000000e+00 909


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 TraesCS3D01G326000 chr3D 438469726 438471947 2221 True 4104 4104 100.000 1 2222 1 chr3D.!!$R1 2221
1 TraesCS3D01G326000 chr3A 577065077 577067152 2075 True 1393 2222 89.979 1 2222 2 chr3A.!!$R1 2221
2 TraesCS3D01G326000 chr3B 574265326 574267479 2153 True 1419 1929 91.402 1 2222 2 chr3B.!!$R1 2221

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
593 596 0.500178 CTAATCGACAGCGTGCATCG 59.5 55.0 11.03 11.03 43.12 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1859 0.100146 GTACCCGAACTCTACCTGCG 59.9 60.0 0.0 0.0 0.0 5.18 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
54 55 2.355837 GCGACGAAGAGCACCACA 60.356 61.111 0.00 0.00 35.25 4.17
194 195 2.559668 CAGGTTTCAGCAACACCATCAT 59.440 45.455 0.00 0.00 37.07 2.45
195 196 2.559668 AGGTTTCAGCAACACCATCATG 59.440 45.455 0.00 0.00 37.07 3.07
196 197 2.297033 GGTTTCAGCAACACCATCATGT 59.703 45.455 0.00 0.00 37.07 3.21
198 199 4.022416 GGTTTCAGCAACACCATCATGTAA 60.022 41.667 0.00 0.00 37.07 2.41
199 200 5.508825 GGTTTCAGCAACACCATCATGTAAA 60.509 40.000 0.00 0.00 37.07 2.01
200 201 5.781210 TTCAGCAACACCATCATGTAAAA 57.219 34.783 0.00 0.00 30.75 1.52
201 202 5.781210 TCAGCAACACCATCATGTAAAAA 57.219 34.783 0.00 0.00 30.75 1.94
202 203 5.527951 TCAGCAACACCATCATGTAAAAAC 58.472 37.500 0.00 0.00 30.75 2.43
203 204 4.382457 CAGCAACACCATCATGTAAAAACG 59.618 41.667 0.00 0.00 30.75 3.60
204 205 3.672867 GCAACACCATCATGTAAAAACGG 59.327 43.478 0.00 0.00 30.75 4.44
205 206 4.557695 GCAACACCATCATGTAAAAACGGA 60.558 41.667 0.00 0.00 30.75 4.69
206 207 5.524284 CAACACCATCATGTAAAAACGGAA 58.476 37.500 0.00 0.00 30.75 4.30
207 208 5.116069 ACACCATCATGTAAAAACGGAAC 57.884 39.130 0.00 0.00 0.00 3.62
208 209 4.022676 ACACCATCATGTAAAAACGGAACC 60.023 41.667 0.00 0.00 0.00 3.62
273 275 0.955178 TCTCGATGATCTCTTCGGGC 59.045 55.000 13.43 0.00 41.85 6.13
414 416 1.073722 CACTTTGCCCTGCCTCTCA 59.926 57.895 0.00 0.00 0.00 3.27
593 596 0.500178 CTAATCGACAGCGTGCATCG 59.500 55.000 11.03 11.03 43.12 3.84
595 598 4.794439 TCGACAGCGTGCATCGGG 62.794 66.667 15.50 0.00 40.26 5.14
641 644 2.289820 CGAGGAACAATGCATGGAGATG 59.710 50.000 8.45 0.23 0.00 2.90
703 706 2.282462 CAGGGGTGTCCTTGGTGC 60.282 66.667 0.00 0.00 45.47 5.01
858 861 1.069765 CCTGTGACTGACAACCGCT 59.930 57.895 0.00 0.00 32.80 5.52
1154 1162 1.135315 CGTGTACGTGTACGGGAGG 59.865 63.158 15.78 0.00 44.95 4.30
1266 1275 3.414700 CGAGCAGCAACGGTGGAC 61.415 66.667 0.90 0.00 0.00 4.02
1267 1276 2.031163 GAGCAGCAACGGTGGACT 59.969 61.111 0.90 0.00 0.00 3.85
1268 1277 2.281070 AGCAGCAACGGTGGACTG 60.281 61.111 0.90 2.73 0.00 3.51
1325 1334 2.202492 CCGTCCTTCGCGTCTCTG 60.202 66.667 5.77 0.00 38.35 3.35
1336 1345 4.838486 GTCTCTGCCCGCTCGACG 62.838 72.222 0.00 0.00 43.15 5.12
1420 1429 1.330655 ACTCCGGCCACTCTGGTATG 61.331 60.000 2.24 0.00 40.46 2.39
1432 1441 2.421424 CTCTGGTATGTTTGCTTCTGCC 59.579 50.000 0.00 0.00 38.71 4.85
1440 1449 0.039472 TTTGCTTCTGCCCCATGCTA 59.961 50.000 0.00 0.00 42.00 3.49
1465 1474 3.941573 TCTTGTGATAATGAGCTGCACA 58.058 40.909 1.49 1.49 37.66 4.57
1466 1475 3.937079 TCTTGTGATAATGAGCTGCACAG 59.063 43.478 5.89 0.00 40.16 3.66
1472 1481 1.747709 AATGAGCTGCACAGATCCAC 58.252 50.000 12.95 0.00 42.79 4.02
1473 1482 0.107312 ATGAGCTGCACAGATCCACC 60.107 55.000 12.95 0.00 42.79 4.61
1482 1491 0.749649 ACAGATCCACCGAGCAGATC 59.250 55.000 0.00 0.00 0.00 2.75
1579 1591 3.394836 GGGACAGAGGAGGCGCTT 61.395 66.667 7.64 0.00 0.00 4.68
1580 1592 2.058595 GGGACAGAGGAGGCGCTTA 61.059 63.158 7.64 0.00 0.00 3.09
1628 1747 0.321653 AAGCCACGGATGACAAGGTC 60.322 55.000 0.00 0.00 0.00 3.85
1629 1748 1.003839 GCCACGGATGACAAGGTCA 60.004 57.895 1.05 1.05 46.90 4.02
1630 1749 1.021390 GCCACGGATGACAAGGTCAG 61.021 60.000 5.25 0.00 46.04 3.51
1631 1750 1.021390 CCACGGATGACAAGGTCAGC 61.021 60.000 6.09 6.09 46.04 4.26
1636 1755 0.801251 GATGACAAGGTCAGCACAGC 59.199 55.000 9.51 0.00 46.52 4.40
1637 1756 0.109153 ATGACAAGGTCAGCACAGCA 59.891 50.000 5.25 0.00 46.04 4.41
1638 1757 0.109153 TGACAAGGTCAGCACAGCAT 59.891 50.000 0.00 0.00 37.67 3.79
1639 1758 0.520404 GACAAGGTCAGCACAGCATG 59.480 55.000 0.00 0.00 35.56 4.06
1652 1771 3.422303 GCATGCGTTGCGTCCTGA 61.422 61.111 0.00 0.00 42.54 3.86
1653 1772 2.965147 GCATGCGTTGCGTCCTGAA 61.965 57.895 0.00 0.00 42.54 3.02
1654 1773 1.573932 CATGCGTTGCGTCCTGAAA 59.426 52.632 0.00 0.00 0.00 2.69
1655 1774 0.453282 CATGCGTTGCGTCCTGAAAG 60.453 55.000 0.00 0.00 0.00 2.62
1656 1775 2.127232 GCGTTGCGTCCTGAAAGC 60.127 61.111 0.00 0.00 0.00 3.51
1657 1776 2.607892 GCGTTGCGTCCTGAAAGCT 61.608 57.895 0.00 0.00 0.00 3.74
1658 1777 1.205064 CGTTGCGTCCTGAAAGCTG 59.795 57.895 0.00 0.00 0.00 4.24
1659 1778 1.221466 CGTTGCGTCCTGAAAGCTGA 61.221 55.000 0.00 0.00 0.00 4.26
1660 1779 0.944386 GTTGCGTCCTGAAAGCTGAA 59.056 50.000 0.00 0.00 0.00 3.02
1661 1780 1.333619 GTTGCGTCCTGAAAGCTGAAA 59.666 47.619 0.00 0.00 0.00 2.69
1662 1781 1.896220 TGCGTCCTGAAAGCTGAAAT 58.104 45.000 0.00 0.00 0.00 2.17
1663 1782 1.806542 TGCGTCCTGAAAGCTGAAATC 59.193 47.619 0.00 0.00 0.00 2.17
1664 1783 1.201965 GCGTCCTGAAAGCTGAAATCG 60.202 52.381 0.00 0.00 0.00 3.34
1665 1784 2.069273 CGTCCTGAAAGCTGAAATCGT 58.931 47.619 0.00 0.00 0.00 3.73
1666 1785 2.092838 CGTCCTGAAAGCTGAAATCGTC 59.907 50.000 0.00 0.00 0.00 4.20
1667 1786 3.067106 GTCCTGAAAGCTGAAATCGTCA 58.933 45.455 0.00 0.00 34.17 4.35
1679 1798 3.336566 TCGTCAGCGACTCGTTCA 58.663 55.556 0.00 0.00 42.81 3.18
1680 1799 1.206831 TCGTCAGCGACTCGTTCAG 59.793 57.895 0.00 0.00 42.81 3.02
1681 1800 1.082038 CGTCAGCGACTCGTTCAGT 60.082 57.895 0.00 0.00 41.33 3.41
1689 1808 3.867723 ACTCGTTCAGTCTTCCACG 57.132 52.632 0.00 0.00 0.00 4.94
1690 1809 0.318784 ACTCGTTCAGTCTTCCACGC 60.319 55.000 0.00 0.00 32.59 5.34
1691 1810 1.006571 TCGTTCAGTCTTCCACGCC 60.007 57.895 0.00 0.00 32.59 5.68
1692 1811 2.372690 CGTTCAGTCTTCCACGCCG 61.373 63.158 0.00 0.00 0.00 6.46
1693 1812 2.357034 TTCAGTCTTCCACGCCGC 60.357 61.111 0.00 0.00 0.00 6.53
1694 1813 4.717629 TCAGTCTTCCACGCCGCG 62.718 66.667 12.14 12.14 0.00 6.46
1696 1815 4.719369 AGTCTTCCACGCCGCGTC 62.719 66.667 17.16 3.45 38.32 5.19
1707 1826 4.867599 CCGCGTCGGGAGCTAACC 62.868 72.222 11.36 0.00 44.15 2.85
1708 1827 4.124351 CGCGTCGGGAGCTAACCA 62.124 66.667 2.62 0.00 0.00 3.67
1709 1828 2.202756 GCGTCGGGAGCTAACCAG 60.203 66.667 7.62 0.00 0.00 4.00
1710 1829 2.494918 CGTCGGGAGCTAACCAGG 59.505 66.667 7.62 0.00 0.00 4.45
1711 1830 2.187163 GTCGGGAGCTAACCAGGC 59.813 66.667 7.62 0.00 0.00 4.85
1712 1831 2.284331 TCGGGAGCTAACCAGGCA 60.284 61.111 7.62 0.00 0.00 4.75
1713 1832 1.916273 TCGGGAGCTAACCAGGCAA 60.916 57.895 7.62 0.00 0.00 4.52
1714 1833 1.224592 CGGGAGCTAACCAGGCAAT 59.775 57.895 7.62 0.00 0.00 3.56
1715 1834 0.394352 CGGGAGCTAACCAGGCAATT 60.394 55.000 7.62 0.00 0.00 2.32
1716 1835 1.393603 GGGAGCTAACCAGGCAATTC 58.606 55.000 2.14 0.00 0.00 2.17
1717 1836 1.017387 GGAGCTAACCAGGCAATTCG 58.983 55.000 0.00 0.00 0.00 3.34
1718 1837 0.378610 GAGCTAACCAGGCAATTCGC 59.621 55.000 0.00 0.00 41.28 4.70
1852 1971 3.009584 AGGTGACCCTCTTCTTGATTTCC 59.990 47.826 0.00 0.00 35.62 3.13
1862 1984 6.209391 CCTCTTCTTGATTTCCCTAGCAAAAA 59.791 38.462 0.00 0.00 0.00 1.94
1865 1987 5.144100 TCTTGATTTCCCTAGCAAAAACCA 58.856 37.500 0.00 0.00 0.00 3.67
1897 2019 2.478539 GGTTTGCCATCGATGAAGAAGC 60.479 50.000 26.86 19.85 34.09 3.86
1898 2020 2.408271 TTGCCATCGATGAAGAAGCT 57.592 45.000 26.86 0.00 0.00 3.74
1900 2022 1.065926 TGCCATCGATGAAGAAGCTGT 60.066 47.619 26.86 0.00 0.00 4.40
1901 2023 1.596727 GCCATCGATGAAGAAGCTGTC 59.403 52.381 26.86 0.73 0.00 3.51
1902 2024 2.741228 GCCATCGATGAAGAAGCTGTCT 60.741 50.000 26.86 0.00 38.69 3.41
1903 2025 2.864946 CCATCGATGAAGAAGCTGTCTG 59.135 50.000 26.86 1.02 36.40 3.51
1911 2040 5.403897 TGAAGAAGCTGTCTGTTTTTACG 57.596 39.130 0.00 0.00 36.40 3.18
1919 2048 4.508861 GCTGTCTGTTTTTACGTGAACCTA 59.491 41.667 0.00 0.00 0.00 3.08
1923 2052 6.203338 TGTCTGTTTTTACGTGAACCTAATCC 59.797 38.462 0.00 0.00 0.00 3.01
1924 2053 6.426025 GTCTGTTTTTACGTGAACCTAATCCT 59.574 38.462 0.00 0.00 0.00 3.24
1925 2054 6.425721 TCTGTTTTTACGTGAACCTAATCCTG 59.574 38.462 0.00 0.00 0.00 3.86
1926 2055 6.289834 TGTTTTTACGTGAACCTAATCCTGA 58.710 36.000 0.00 0.00 0.00 3.86
1927 2056 6.938030 TGTTTTTACGTGAACCTAATCCTGAT 59.062 34.615 0.00 0.00 0.00 2.90
1928 2057 7.118680 TGTTTTTACGTGAACCTAATCCTGATC 59.881 37.037 0.00 0.00 0.00 2.92
1929 2058 5.925506 TTACGTGAACCTAATCCTGATCA 57.074 39.130 0.00 0.00 0.00 2.92
1930 2059 4.124851 ACGTGAACCTAATCCTGATCAC 57.875 45.455 0.00 0.00 35.13 3.06
1934 2063 5.175859 GTGAACCTAATCCTGATCACGAAA 58.824 41.667 0.00 0.00 0.00 3.46
1937 2066 3.123804 CCTAATCCTGATCACGAAACCG 58.876 50.000 0.00 0.00 0.00 4.44
1949 2078 1.070275 GAAACCGTTCCCTGACCGT 59.930 57.895 0.00 0.00 0.00 4.83
2135 2264 2.814336 GGTGAGCTAGTGACCCTTTTTG 59.186 50.000 0.00 0.00 0.00 2.44
2137 2266 1.813178 GAGCTAGTGACCCTTTTTGCC 59.187 52.381 0.00 0.00 0.00 4.52
2138 2267 1.144913 AGCTAGTGACCCTTTTTGCCA 59.855 47.619 0.00 0.00 0.00 4.92
2140 2269 2.863809 CTAGTGACCCTTTTTGCCACT 58.136 47.619 0.00 0.00 40.66 4.00
2141 2270 1.692411 AGTGACCCTTTTTGCCACTC 58.308 50.000 0.00 0.00 33.27 3.51
2142 2271 1.215423 AGTGACCCTTTTTGCCACTCT 59.785 47.619 0.00 0.00 33.27 3.24
2143 2272 1.609072 GTGACCCTTTTTGCCACTCTC 59.391 52.381 0.00 0.00 0.00 3.20
2144 2273 1.494721 TGACCCTTTTTGCCACTCTCT 59.505 47.619 0.00 0.00 0.00 3.10
2147 2276 0.600057 CCTTTTTGCCACTCTCTGCC 59.400 55.000 0.00 0.00 0.00 4.85
2148 2277 1.613836 CTTTTTGCCACTCTCTGCCT 58.386 50.000 0.00 0.00 0.00 4.75
2150 2279 0.473755 TTTTGCCACTCTCTGCCTGA 59.526 50.000 0.00 0.00 0.00 3.86
2151 2280 0.035881 TTTGCCACTCTCTGCCTGAG 59.964 55.000 0.00 0.00 43.96 3.35
2152 2281 1.834856 TTGCCACTCTCTGCCTGAGG 61.835 60.000 0.00 0.00 42.86 3.86
2163 2292 2.029073 CCTGAGGCACACGACGTT 59.971 61.111 0.00 0.00 0.00 3.99
2164 2293 2.022129 CCTGAGGCACACGACGTTC 61.022 63.158 0.00 0.00 0.00 3.95
2167 2296 0.874175 TGAGGCACACGACGTTCAAG 60.874 55.000 0.00 0.00 0.00 3.02
2175 2313 1.517276 CACGACGTTCAAGTGTGAGTC 59.483 52.381 0.00 0.00 34.49 3.36
2183 2321 1.067060 TCAAGTGTGAGTCGTGACTGG 59.933 52.381 7.35 0.00 42.66 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.402474 TGATGCAGTACTACAGCTATGTGT 59.598 41.667 12.36 0.00 40.79 3.72
194 195 4.139859 TCAGTCAGGTTCCGTTTTTACA 57.860 40.909 0.00 0.00 0.00 2.41
195 196 6.790285 TTATCAGTCAGGTTCCGTTTTTAC 57.210 37.500 0.00 0.00 0.00 2.01
196 197 6.993902 AGTTTATCAGTCAGGTTCCGTTTTTA 59.006 34.615 0.00 0.00 0.00 1.52
198 199 5.374071 AGTTTATCAGTCAGGTTCCGTTTT 58.626 37.500 0.00 0.00 0.00 2.43
199 200 4.969484 AGTTTATCAGTCAGGTTCCGTTT 58.031 39.130 0.00 0.00 0.00 3.60
200 201 4.618920 AGTTTATCAGTCAGGTTCCGTT 57.381 40.909 0.00 0.00 0.00 4.44
201 202 4.618920 AAGTTTATCAGTCAGGTTCCGT 57.381 40.909 0.00 0.00 0.00 4.69
202 203 5.475719 TGTAAGTTTATCAGTCAGGTTCCG 58.524 41.667 0.00 0.00 0.00 4.30
203 204 6.969828 CTGTAAGTTTATCAGTCAGGTTCC 57.030 41.667 0.00 0.00 0.00 3.62
267 269 1.228124 CAACACCTTGGAGCCCGAA 60.228 57.895 0.00 0.00 0.00 4.30
273 275 2.113139 ACCGGCAACACCTTGGAG 59.887 61.111 0.00 0.00 35.61 3.86
359 361 1.296392 CTCATCCGCCTGACCAACA 59.704 57.895 0.00 0.00 0.00 3.33
414 416 2.092914 GGTGGAGGTGAAATTCGAGGAT 60.093 50.000 0.00 0.00 0.00 3.24
474 476 0.036164 TGCGAGTGGCCAACATACTT 59.964 50.000 7.24 0.00 42.61 2.24
593 596 3.134081 TGCTAGTACCTATCTTGCAACCC 59.866 47.826 0.00 0.00 39.66 4.11
595 598 4.120589 GGTGCTAGTACCTATCTTGCAAC 58.879 47.826 21.62 3.21 42.72 4.17
617 620 1.811965 TCCATGCATTGTTCCTCGTTG 59.188 47.619 0.00 0.00 0.00 4.10
621 624 2.621998 CCATCTCCATGCATTGTTCCTC 59.378 50.000 0.00 0.00 0.00 3.71
641 644 4.268884 CGATTCTTGCTGTACTTTCTAGCC 59.731 45.833 0.00 0.00 36.64 3.93
703 706 1.532868 CTTCGTGTTCTTCAAGGCCAG 59.467 52.381 5.01 0.00 0.00 4.85
1266 1275 1.645034 CATGGTTGCCGAGTAGTCAG 58.355 55.000 0.00 0.00 0.00 3.51
1267 1276 0.249120 CCATGGTTGCCGAGTAGTCA 59.751 55.000 2.57 0.00 0.00 3.41
1268 1277 1.090052 GCCATGGTTGCCGAGTAGTC 61.090 60.000 14.67 0.00 0.00 2.59
1372 1381 1.961277 CGTCTTGCCAAAGCGGAGT 60.961 57.895 0.00 0.00 44.31 3.85
1398 1407 3.699894 CAGAGTGGCCGGAGTGCT 61.700 66.667 5.05 0.00 0.00 4.40
1420 1429 1.079612 GCATGGGGCAGAAGCAAAC 60.080 57.895 0.00 0.00 44.61 2.93
1432 1441 7.944061 TCATTATCACAAGAAAATAGCATGGG 58.056 34.615 0.00 0.00 0.00 4.00
1440 1449 6.071784 TGTGCAGCTCATTATCACAAGAAAAT 60.072 34.615 0.00 0.00 35.08 1.82
1465 1474 2.037053 CGATCTGCTCGGTGGATCT 58.963 57.895 0.00 0.00 43.82 2.75
1466 1475 4.643733 CGATCTGCTCGGTGGATC 57.356 61.111 0.00 0.00 43.82 3.36
1472 1481 4.092821 TTGTTAACAAATCGATCTGCTCGG 59.907 41.667 18.54 0.00 39.25 4.63
1473 1482 5.203358 TTGTTAACAAATCGATCTGCTCG 57.797 39.130 18.54 0.00 39.73 5.03
1497 1506 7.523709 GCCTTTTGGAGAACATAACAAGATCAA 60.524 37.037 0.00 0.00 44.07 2.57
1565 1577 2.896443 GCTAAGCGCCTCCTCTGT 59.104 61.111 2.29 0.00 0.00 3.41
1636 1755 0.453282 CTTTCAGGACGCAACGCATG 60.453 55.000 0.00 0.00 0.00 4.06
1637 1756 1.868997 CTTTCAGGACGCAACGCAT 59.131 52.632 0.00 0.00 0.00 4.73
1638 1757 2.892334 GCTTTCAGGACGCAACGCA 61.892 57.895 0.00 0.00 0.00 5.24
1639 1758 2.127232 GCTTTCAGGACGCAACGC 60.127 61.111 0.00 0.00 0.00 4.84
1640 1759 1.205064 CAGCTTTCAGGACGCAACG 59.795 57.895 0.00 0.00 0.00 4.10
1641 1760 0.944386 TTCAGCTTTCAGGACGCAAC 59.056 50.000 0.00 0.00 0.00 4.17
1642 1761 1.674359 TTTCAGCTTTCAGGACGCAA 58.326 45.000 0.00 0.00 0.00 4.85
1643 1762 1.806542 GATTTCAGCTTTCAGGACGCA 59.193 47.619 0.00 0.00 0.00 5.24
1644 1763 1.201965 CGATTTCAGCTTTCAGGACGC 60.202 52.381 0.00 0.00 0.00 5.19
1645 1764 2.069273 ACGATTTCAGCTTTCAGGACG 58.931 47.619 0.00 0.00 0.00 4.79
1646 1765 3.067106 TGACGATTTCAGCTTTCAGGAC 58.933 45.455 0.00 0.00 0.00 3.85
1647 1766 3.329386 CTGACGATTTCAGCTTTCAGGA 58.671 45.455 0.00 0.00 45.51 3.86
1648 1767 3.736530 CTGACGATTTCAGCTTTCAGG 57.263 47.619 0.00 0.00 45.51 3.86
1663 1782 1.060726 GACTGAACGAGTCGCTGACG 61.061 60.000 13.59 0.07 41.91 4.35
1664 1783 2.714530 GACTGAACGAGTCGCTGAC 58.285 57.895 13.59 2.26 41.91 3.51
1671 1790 0.318784 GCGTGGAAGACTGAACGAGT 60.319 55.000 8.53 0.00 38.27 4.18
1672 1791 1.009389 GGCGTGGAAGACTGAACGAG 61.009 60.000 8.53 0.00 38.27 4.18
1673 1792 1.006571 GGCGTGGAAGACTGAACGA 60.007 57.895 8.53 0.00 38.27 3.85
1674 1793 2.372690 CGGCGTGGAAGACTGAACG 61.373 63.158 0.00 0.00 39.00 3.95
1675 1794 2.668280 GCGGCGTGGAAGACTGAAC 61.668 63.158 9.37 0.00 0.00 3.18
1676 1795 2.357034 GCGGCGTGGAAGACTGAA 60.357 61.111 9.37 0.00 0.00 3.02
1677 1796 4.717629 CGCGGCGTGGAAGACTGA 62.718 66.667 15.36 0.00 0.00 3.41
1679 1798 4.719369 GACGCGGCGTGGAAGACT 62.719 66.667 34.44 4.92 41.37 3.24
1691 1810 4.124351 TGGTTAGCTCCCGACGCG 62.124 66.667 3.53 3.53 0.00 6.01
1692 1811 2.202756 CTGGTTAGCTCCCGACGC 60.203 66.667 0.00 0.00 0.00 5.19
1693 1812 2.494918 CCTGGTTAGCTCCCGACG 59.505 66.667 0.00 0.00 0.00 5.12
1694 1813 2.180159 TTGCCTGGTTAGCTCCCGAC 62.180 60.000 0.00 0.00 0.00 4.79
1695 1814 1.271840 ATTGCCTGGTTAGCTCCCGA 61.272 55.000 0.00 0.00 0.00 5.14
1696 1815 0.394352 AATTGCCTGGTTAGCTCCCG 60.394 55.000 0.00 0.00 0.00 5.14
1697 1816 1.393603 GAATTGCCTGGTTAGCTCCC 58.606 55.000 0.00 0.00 0.00 4.30
1698 1817 1.017387 CGAATTGCCTGGTTAGCTCC 58.983 55.000 0.00 0.00 0.00 4.70
1699 1818 0.378610 GCGAATTGCCTGGTTAGCTC 59.621 55.000 0.00 0.00 37.76 4.09
1700 1819 2.482326 GCGAATTGCCTGGTTAGCT 58.518 52.632 0.00 0.00 37.76 3.32
1735 1854 1.347320 CGAACTCTACCTGCGGAAAC 58.653 55.000 0.00 0.00 0.00 2.78
1736 1855 0.245539 CCGAACTCTACCTGCGGAAA 59.754 55.000 0.00 0.00 44.43 3.13
1737 1856 1.601419 CCCGAACTCTACCTGCGGAA 61.601 60.000 0.00 0.00 44.43 4.30
1738 1857 2.050350 CCCGAACTCTACCTGCGGA 61.050 63.158 0.00 0.00 44.43 5.54
1739 1858 1.033746 TACCCGAACTCTACCTGCGG 61.034 60.000 0.00 0.00 41.53 5.69
1740 1859 0.100146 GTACCCGAACTCTACCTGCG 59.900 60.000 0.00 0.00 0.00 5.18
1741 1860 1.404748 GAGTACCCGAACTCTACCTGC 59.595 57.143 5.58 0.00 42.21 4.85
1742 1861 1.669779 CGAGTACCCGAACTCTACCTG 59.330 57.143 0.00 0.00 43.11 4.00
1743 1862 1.556911 TCGAGTACCCGAACTCTACCT 59.443 52.381 0.00 0.00 43.11 3.08
1744 1863 1.939255 CTCGAGTACCCGAACTCTACC 59.061 57.143 3.62 0.00 43.11 3.18
1745 1864 1.939255 CCTCGAGTACCCGAACTCTAC 59.061 57.143 12.31 0.00 43.11 2.59
1746 1865 1.833630 TCCTCGAGTACCCGAACTCTA 59.166 52.381 12.31 0.69 43.11 2.43
1747 1866 0.617413 TCCTCGAGTACCCGAACTCT 59.383 55.000 12.31 0.00 43.11 3.24
1838 1957 6.824305 TTTTGCTAGGGAAATCAAGAAGAG 57.176 37.500 0.00 0.00 0.00 2.85
1841 1960 5.600484 TGGTTTTTGCTAGGGAAATCAAGAA 59.400 36.000 0.00 0.00 0.00 2.52
1846 1965 3.258123 TGCTGGTTTTTGCTAGGGAAATC 59.742 43.478 0.00 0.00 0.00 2.17
1852 1971 0.109597 CGCTGCTGGTTTTTGCTAGG 60.110 55.000 0.00 0.00 0.00 3.02
1877 1999 2.421424 AGCTTCTTCATCGATGGCAAAC 59.579 45.455 24.61 10.48 0.00 2.93
1897 2019 6.592798 TTAGGTTCACGTAAAAACAGACAG 57.407 37.500 9.12 0.00 0.00 3.51
1898 2020 6.203338 GGATTAGGTTCACGTAAAAACAGACA 59.797 38.462 9.12 0.00 31.18 3.41
1900 2022 6.425721 CAGGATTAGGTTCACGTAAAAACAGA 59.574 38.462 9.12 0.00 31.18 3.41
1901 2023 6.425721 TCAGGATTAGGTTCACGTAAAAACAG 59.574 38.462 9.12 0.00 31.18 3.16
1902 2024 6.289834 TCAGGATTAGGTTCACGTAAAAACA 58.710 36.000 9.12 0.00 31.18 2.83
1903 2025 6.790285 TCAGGATTAGGTTCACGTAAAAAC 57.210 37.500 0.00 0.00 31.18 2.43
1911 2040 4.386867 TCGTGATCAGGATTAGGTTCAC 57.613 45.455 13.94 0.00 0.00 3.18
1930 2059 2.025418 CGGTCAGGGAACGGTTTCG 61.025 63.158 0.00 0.00 39.28 3.46
1931 2060 3.961729 CGGTCAGGGAACGGTTTC 58.038 61.111 0.00 0.00 39.28 2.78
1937 2066 4.980805 TGCGCACGGTCAGGGAAC 62.981 66.667 5.66 0.00 0.00 3.62
2147 2276 0.874175 TTGAACGTCGTGTGCCTCAG 60.874 55.000 0.00 0.00 0.00 3.35
2148 2277 0.874175 CTTGAACGTCGTGTGCCTCA 60.874 55.000 0.00 0.00 0.00 3.86
2150 2279 1.143183 ACTTGAACGTCGTGTGCCT 59.857 52.632 0.00 0.00 0.00 4.75
2151 2280 1.275657 CACTTGAACGTCGTGTGCC 59.724 57.895 0.00 0.00 0.00 5.01
2152 2281 2.003672 ACACTTGAACGTCGTGTGC 58.996 52.632 12.08 0.77 40.11 4.57
2156 2285 1.836383 GACTCACACTTGAACGTCGT 58.164 50.000 0.00 0.00 0.00 4.34
2157 2286 0.770590 CGACTCACACTTGAACGTCG 59.229 55.000 0.00 0.00 41.34 5.12
2158 2287 1.517276 CACGACTCACACTTGAACGTC 59.483 52.381 0.00 0.00 40.47 4.34
2160 2289 1.517276 GTCACGACTCACACTTGAACG 59.483 52.381 0.00 0.00 37.51 3.95
2162 2291 2.481276 CCAGTCACGACTCACACTTGAA 60.481 50.000 0.00 0.00 40.20 2.69
2163 2292 1.067060 CCAGTCACGACTCACACTTGA 59.933 52.381 0.00 0.00 40.20 3.02
2164 2293 1.491670 CCAGTCACGACTCACACTTG 58.508 55.000 0.00 0.00 40.20 3.16
2167 2296 0.597637 CACCCAGTCACGACTCACAC 60.598 60.000 0.00 0.00 40.20 3.82
2183 2321 3.649073 GAAAACAGTTAATGGTGGCACC 58.351 45.455 29.75 29.75 39.22 5.01


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

AutoCloner maintained by Alex Coulton.