Multiple sequence alignment - TraesCS7D01G259200

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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 TraesCS7D01G259200 chr7D 100.000 3919 0 0 1 3919 234806022 234802104 0.000000e+00 7238.0
1 TraesCS7D01G259200 chr7A 93.376 1887 76 12 1 1846 249593698 249591820 0.000000e+00 2747.0
2 TraesCS7D01G259200 chr7A 93.546 1503 54 13 1928 3396 249591822 249590329 0.000000e+00 2198.0
3 TraesCS7D01G259200 chr7A 94.465 542 27 3 3380 3919 249590082 249589542 0.000000e+00 832.0
4 TraesCS7D01G259200 chr7B 91.210 1570 72 19 1928 3445 210859912 210858357 0.000000e+00 2074.0
5 TraesCS7D01G259200 chr7B 90.684 1170 57 11 476 1609 210861256 210860103 0.000000e+00 1509.0
6 TraesCS7D01G259200 chr7B 96.552 406 14 0 1 406 210861686 210861281 0.000000e+00 673.0
7 TraesCS7D01G259200 chr7B 90.043 231 20 2 3507 3736 210858353 210858125 2.960000e-76 296.0
8 TraesCS7D01G259200 chr7B 96.364 110 4 0 3810 3919 210857899 210857790 8.650000e-42 182.0
9 TraesCS7D01G259200 chr7B 97.895 95 1 1 1836 1930 92400672 92400579 3.130000e-36 163.0
10 TraesCS7D01G259200 chr7B 94.340 106 5 1 3698 3802 210858089 210857984 1.130000e-35 161.0
11 TraesCS7D01G259200 chr7B 82.843 204 10 9 1640 1841 210860102 210859922 4.050000e-35 159.0
12 TraesCS7D01G259200 chr7B 100.000 39 0 0 3698 3736 210858126 210858088 5.430000e-09 73.1
13 TraesCS7D01G259200 chr2B 96.040 101 2 2 1831 1930 250686442 250686541 3.130000e-36 163.0
14 TraesCS7D01G259200 chr2B 97.872 94 2 0 1837 1930 303097359 303097266 3.130000e-36 163.0
15 TraesCS7D01G259200 chr2B 95.192 104 4 1 1827 1930 445897843 445897945 3.130000e-36 163.0
16 TraesCS7D01G259200 chr6B 94.286 105 2 3 1830 1930 291177537 291177641 1.460000e-34 158.0
17 TraesCS7D01G259200 chr5B 95.918 98 2 2 1833 1930 466369663 466369758 1.460000e-34 158.0
18 TraesCS7D01G259200 chr2A 98.837 86 1 0 1845 1930 71206602 71206687 1.890000e-33 154.0
19 TraesCS7D01G259200 chr2A 98.837 86 1 0 1845 1930 71259232 71259317 1.890000e-33 154.0
20 TraesCS7D01G259200 chr3A 91.892 111 5 4 1822 1930 38468505 38468613 6.780000e-33 152.0


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 TraesCS7D01G259200 chr7D 234802104 234806022 3918 True 7238.000000 7238 100.000000 1 3919 1 chr7D.!!$R1 3918
1 TraesCS7D01G259200 chr7A 249589542 249593698 4156 True 1925.666667 2747 93.795667 1 3919 3 chr7A.!!$R1 3918
2 TraesCS7D01G259200 chr7B 210857790 210861686 3896 True 640.887500 2074 92.754500 1 3919 8 chr7B.!!$R2 3918

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
165 166 0.977395 CTGATAGGATCCCCGTTCCC 59.023 60.000 8.55 0.0 37.58 3.97 F
424 425 1.198637 GTTGAGTGTTGAGGATGCTGC 59.801 52.381 0.00 0.0 0.00 5.25 F
1483 1538 1.115930 AGGATCTCGTAAGCCCGCAT 61.116 55.000 0.00 0.0 37.18 4.73 F
2405 2490 1.141449 GCAAACAAGCTGCCACACA 59.859 52.632 0.00 0.0 33.51 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1047 0.865769 GGCGAGAAAAGTCGAAGCAA 59.134 50.000 0.0 0.0 42.85 3.91 R
1915 1973 1.067071 CACAGTTACTCCCTCCGTTCC 60.067 57.143 0.0 0.0 0.00 3.62 R
2909 2994 0.040058 TCTCATGGCACCCAAATGCT 59.960 50.000 0.0 0.0 45.38 3.79 R
3677 4058 0.673956 TCTCCGGTCGAGTCTGTGAG 60.674 60.000 0.0 0.0 39.84 3.51 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
163 164 1.718280 ACCTGATAGGATCCCCGTTC 58.282 55.000 8.55 0.94 37.67 3.95
165 166 0.977395 CTGATAGGATCCCCGTTCCC 59.023 60.000 8.55 0.00 37.58 3.97
191 192 8.049655 TCTCTCCAGATCATACAAAGATATCG 57.950 38.462 0.00 0.00 0.00 2.92
197 198 7.010275 CCAGATCATACAAAGATATCGCATCTG 59.990 40.741 0.00 6.66 35.38 2.90
325 326 7.986085 TTAGCTAGCATATTCCCATCTTTTC 57.014 36.000 18.83 0.00 0.00 2.29
424 425 1.198637 GTTGAGTGTTGAGGATGCTGC 59.801 52.381 0.00 0.00 0.00 5.25
502 511 4.444022 GCAATCAGACCTGTATCATCACCT 60.444 45.833 0.00 0.00 0.00 4.00
518 527 7.669089 TCATCACCTACATTGTTATCCTGTA 57.331 36.000 0.00 0.00 0.00 2.74
609 618 7.514784 TTTTCCATATGCATCCTGTTCTATG 57.485 36.000 0.19 0.00 0.00 2.23
635 644 1.518325 TGTATGTTCAACCCACTGCG 58.482 50.000 0.00 0.00 0.00 5.18
840 875 2.292016 TCACAACATGGCGATCGTTTTT 59.708 40.909 17.81 0.56 0.00 1.94
868 903 2.223249 CCGCGTGGACAAATTTGGATAG 60.223 50.000 21.74 10.09 37.49 2.08
869 904 2.418628 CGCGTGGACAAATTTGGATAGT 59.581 45.455 21.74 0.34 0.00 2.12
870 905 3.485216 CGCGTGGACAAATTTGGATAGTC 60.485 47.826 21.74 9.74 0.00 2.59
1001 1047 1.940242 AACGGGTTGGTTCCCCTTGT 61.940 55.000 0.00 0.00 44.32 3.16
1016 1062 2.618709 CCCTTGTTGCTTCGACTTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
1146 1193 3.371063 GTCCGACGACCTGCTCCA 61.371 66.667 0.00 0.00 32.40 3.86
1205 1252 2.541556 GTGATCCGGTAGCTGTTCTTC 58.458 52.381 0.00 0.00 0.00 2.87
1206 1253 1.480954 TGATCCGGTAGCTGTTCTTCC 59.519 52.381 0.00 0.00 0.00 3.46
1293 1348 4.779733 GGGAGGCAGTCGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
1429 1484 1.135333 GCCGAGTTCGAGATCCTCTTT 59.865 52.381 2.59 0.00 43.02 2.52
1483 1538 1.115930 AGGATCTCGTAAGCCCGCAT 61.116 55.000 0.00 0.00 37.18 4.73
1499 1554 1.745264 CATCCCTCTCGCCTTCTCC 59.255 63.158 0.00 0.00 0.00 3.71
1518 1573 1.154301 CCCCGTTGAACATTTCGCG 60.154 57.895 0.00 0.00 0.00 5.87
1519 1574 1.572447 CCCGTTGAACATTTCGCGT 59.428 52.632 5.77 0.00 0.00 6.01
1528 1583 3.427528 TGAACATTTCGCGTCTGACTAAC 59.572 43.478 5.77 0.00 0.00 2.34
1628 1686 2.360165 CCTGCCTTTATGGTGATTGAGC 59.640 50.000 0.00 0.00 38.35 4.26
1692 1750 3.891049 AGTAGCTAGCTTGGAATTTGGG 58.109 45.455 24.88 0.00 0.00 4.12
1698 1756 4.889995 GCTAGCTTGGAATTTGGGAAGTAT 59.110 41.667 7.70 0.00 0.00 2.12
1736 1794 4.382577 GGAATTTGGGCGGTGTTGAATAAT 60.383 41.667 0.00 0.00 0.00 1.28
1776 1834 1.271325 TGGTGTCCATGGTTACTGCTG 60.271 52.381 12.58 0.00 0.00 4.41
1830 1888 1.195115 TTAGGCTTGCTCGTCTGGAT 58.805 50.000 0.00 0.00 0.00 3.41
1852 1910 7.889073 TGGATACAGTCTATAATGTACTCCCTC 59.111 40.741 0.00 0.00 46.17 4.30
1853 1911 7.339976 GGATACAGTCTATAATGTACTCCCTCC 59.660 44.444 0.00 0.00 34.88 4.30
1854 1912 5.071370 ACAGTCTATAATGTACTCCCTCCG 58.929 45.833 0.00 0.00 0.00 4.63
1855 1913 5.071370 CAGTCTATAATGTACTCCCTCCGT 58.929 45.833 0.00 0.00 0.00 4.69
1856 1914 5.535406 CAGTCTATAATGTACTCCCTCCGTT 59.465 44.000 0.00 0.00 0.00 4.44
1857 1915 5.769162 AGTCTATAATGTACTCCCTCCGTTC 59.231 44.000 0.00 0.00 0.00 3.95
1858 1916 5.048154 GTCTATAATGTACTCCCTCCGTTCC 60.048 48.000 0.00 0.00 0.00 3.62
1859 1917 1.946984 AATGTACTCCCTCCGTTCCA 58.053 50.000 0.00 0.00 0.00 3.53
1860 1918 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
1861 1919 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
1862 1920 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
1863 1921 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
1864 1922 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
1865 1923 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1866 1924 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1867 1925 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1868 1926 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1869 1927 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1870 1928 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1871 1929 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1872 1930 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1873 1931 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1874 1932 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1875 1933 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1876 1934 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1877 1935 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1878 1936 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1879 1937 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1880 1938 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1881 1939 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1882 1940 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1883 1941 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1916 1974 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1917 1975 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1918 1976 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1919 1977 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1920 1978 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1921 1979 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1922 1980 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1923 1981 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1924 1982 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1925 1983 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1926 1984 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1990 2061 7.785028 AGGTAGAGATGTATCAGTGGTAAATCA 59.215 37.037 14.78 0.00 0.00 2.57
1991 2062 8.589338 GGTAGAGATGTATCAGTGGTAAATCAT 58.411 37.037 14.78 6.48 0.00 2.45
2182 2253 2.695585 CTGGCCTTAGAGGGTAGGAAT 58.304 52.381 3.32 0.00 35.37 3.01
2183 2254 2.635427 CTGGCCTTAGAGGGTAGGAATC 59.365 54.545 3.32 0.00 35.37 2.52
2184 2255 2.022428 TGGCCTTAGAGGGTAGGAATCA 60.022 50.000 3.32 0.00 35.37 2.57
2185 2256 3.252351 GGCCTTAGAGGGTAGGAATCAT 58.748 50.000 0.00 0.00 35.37 2.45
2186 2257 4.140543 TGGCCTTAGAGGGTAGGAATCATA 60.141 45.833 3.32 0.00 35.37 2.15
2250 2335 7.981789 TGTACATTCTGTAGAGGCTCATTTAAG 59.018 37.037 18.26 6.81 32.84 1.85
2366 2451 6.166279 TGCTTTTGTGGTTGTTTTGTATGAA 58.834 32.000 0.00 0.00 0.00 2.57
2379 2464 7.213678 TGTTTTGTATGAACCCTGATTTTTCC 58.786 34.615 0.00 0.00 0.00 3.13
2405 2490 1.141449 GCAAACAAGCTGCCACACA 59.859 52.632 0.00 0.00 33.51 3.72
2449 2534 7.180229 TGAAGTCACCTATATTTCTTCTCCACA 59.820 37.037 0.00 0.00 34.37 4.17
2509 2594 3.616956 TGATCTCTGAGCGATTTGGTT 57.383 42.857 0.00 0.00 0.00 3.67
2585 2670 1.153349 GGTCTGGACGATTGGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
2758 2843 6.232581 ACTGAAGTTATTGATAGCTCTGCT 57.767 37.500 0.00 0.00 43.41 4.24
2793 2878 8.704668 ACATGGTGTGTGACTATCAGATAAATA 58.295 33.333 0.00 0.00 40.28 1.40
2848 2933 6.876257 GGATCATGGTTATTAGATTTCGCTCT 59.124 38.462 0.00 0.00 0.00 4.09
2909 2994 8.759481 TTTTGGTCATATATAAGGTGCATTGA 57.241 30.769 0.00 0.00 0.00 2.57
2925 3010 0.609151 TTGAGCATTTGGGTGCCATG 59.391 50.000 0.00 0.00 46.19 3.66
2934 3019 0.325933 TGGGTGCCATGAGACTTCAG 59.674 55.000 0.00 0.00 36.61 3.02
2935 3020 0.326264 GGGTGCCATGAGACTTCAGT 59.674 55.000 0.00 0.00 36.61 3.41
2936 3021 1.677217 GGGTGCCATGAGACTTCAGTC 60.677 57.143 0.00 0.00 45.08 3.51
3039 3156 7.686434 AGGCCACTTAATAATACGGATAATGT 58.314 34.615 5.01 0.00 0.00 2.71
3107 3224 7.519008 CGTTCAGAGTGTTTCTTAAAATGAGCT 60.519 37.037 0.00 0.00 32.41 4.09
3127 3244 3.594134 CTCAGTGGCTGTTAGAGAAAGG 58.406 50.000 0.00 0.00 32.61 3.11
3153 3270 6.887626 ATGTTTGATGTGATATAGCATGCA 57.112 33.333 21.98 6.36 0.00 3.96
3288 3405 2.032924 CAGTTTTCTGGGGAAACACGTC 59.967 50.000 4.55 0.00 43.61 4.34
3330 3447 5.923733 TTGGTGTCTAATTTTTGTGTGGT 57.076 34.783 0.00 0.00 0.00 4.16
3332 3449 5.655488 TGGTGTCTAATTTTTGTGTGGTTG 58.345 37.500 0.00 0.00 0.00 3.77
3333 3450 4.506288 GGTGTCTAATTTTTGTGTGGTTGC 59.494 41.667 0.00 0.00 0.00 4.17
3471 3851 7.302524 GTCAACTCTAGTAACTCACTGAGAAG 58.697 42.308 13.25 2.77 38.24 2.85
3478 3858 1.428869 ACTCACTGAGAAGCCTTGGT 58.571 50.000 13.25 0.00 33.32 3.67
3518 3898 3.814625 TGACCATGTCTTGTTTAGCACA 58.185 40.909 0.00 0.00 33.15 4.57
3532 3912 1.413118 AGCACACCCCTTTTCCTTTG 58.587 50.000 0.00 0.00 0.00 2.77
3580 3960 9.896263 ATGTCAAATTTTCATTTTTAATGCCAC 57.104 25.926 0.00 0.00 29.41 5.01
3611 3991 5.350914 GTGTCAGTTTGATCTCCTCTCAATG 59.649 44.000 0.00 0.00 32.94 2.82
3644 4024 1.737838 TGCCGAAGTGATGGATTGTC 58.262 50.000 0.00 0.00 0.00 3.18
3677 4058 1.742761 ATAGCCCATACGATGCATGC 58.257 50.000 11.82 11.82 0.00 4.06
3736 4154 7.227314 TGAAGGATGTAAAGGATCATGATTTCG 59.773 37.037 10.14 0.00 0.00 3.46
3742 4197 6.763135 TGTAAAGGATCATGATTTCGAGAAGG 59.237 38.462 10.14 0.00 0.00 3.46
3770 4225 4.098349 TGGACTATTGATTGCCAGCATTTC 59.902 41.667 0.00 0.00 0.00 2.17
3792 4248 3.666902 CGTTGGGACGTCAAAATCATGTC 60.667 47.826 18.91 0.00 44.08 3.06
3905 4438 7.035004 TGTAATGATAACATTGGAAGCTTTGC 58.965 34.615 8.38 0.00 44.97 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 4.898265 TCTTTGTATGATCTGGAGAGAGGG 59.102 45.833 0.00 0.00 0.00 4.30
165 166 8.183536 CGATATCTTTGTATGATCTGGAGAGAG 58.816 40.741 0.34 0.00 0.00 3.20
191 192 2.960819 ACTGACTAAACCGACAGATGC 58.039 47.619 0.00 0.00 34.88 3.91
325 326 6.985059 GGTTTTACCCTACAGAGTAAGCATAG 59.015 42.308 0.00 0.00 30.04 2.23
424 425 1.002366 CAGAATCTTGGTCTTCGCCG 58.998 55.000 0.00 0.00 0.00 6.46
495 504 7.041780 GCTTACAGGATAACAATGTAGGTGATG 60.042 40.741 0.00 0.00 31.30 3.07
502 511 5.601583 TCGGCTTACAGGATAACAATGTA 57.398 39.130 0.00 0.00 0.00 2.29
518 527 2.380081 CCGTTCGCTTATTCGGCTT 58.620 52.632 0.00 0.00 36.68 4.35
609 618 3.190535 GTGGGTTGAACATACATCACCAC 59.809 47.826 0.00 0.00 0.00 4.16
783 796 3.815401 GCTCTTCTAGTCCAGTGCAAAAA 59.185 43.478 0.00 0.00 31.24 1.94
840 875 1.950828 TTTGTCCACGCGGTTCTAAA 58.049 45.000 12.47 3.43 0.00 1.85
953 992 1.396301 CAGCTCAGCGAGTCCAAATTC 59.604 52.381 0.00 0.00 31.39 2.17
1001 1047 0.865769 GGCGAGAAAAGTCGAAGCAA 59.134 50.000 0.00 0.00 42.85 3.91
1016 1062 2.071844 GATCTTGGATCGGACGGCGA 62.072 60.000 16.62 0.00 0.00 5.54
1090 1136 2.579738 GAGAGGGTGGGTTCGAGC 59.420 66.667 0.00 0.00 0.00 5.03
1092 1138 2.678934 CGGAGAGGGTGGGTTCGA 60.679 66.667 0.00 0.00 0.00 3.71
1205 1252 2.675242 TATGGCTGGGTGAACGGGG 61.675 63.158 0.00 0.00 0.00 5.73
1206 1253 1.451387 GTATGGCTGGGTGAACGGG 60.451 63.158 0.00 0.00 0.00 5.28
1429 1484 1.478510 GCGATGAGGAAGAAGAGGACA 59.521 52.381 0.00 0.00 0.00 4.02
1483 1538 2.042843 GGGAGAAGGCGAGAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
1499 1554 1.211709 GCGAAATGTTCAACGGGGG 59.788 57.895 0.00 0.00 0.00 5.40
1518 1573 2.806608 TTGACCCGTGTTAGTCAGAC 57.193 50.000 0.00 0.00 43.48 3.51
1519 1574 3.823281 TTTTGACCCGTGTTAGTCAGA 57.177 42.857 0.00 0.00 43.48 3.27
1528 1583 1.335872 GCACCAGAATTTTGACCCGTG 60.336 52.381 0.00 0.00 0.00 4.94
1692 1750 3.686726 CCAAGCCACAGACAGAATACTTC 59.313 47.826 0.00 0.00 0.00 3.01
1698 1756 2.957402 ATTCCAAGCCACAGACAGAA 57.043 45.000 0.00 0.00 0.00 3.02
1736 1794 3.069586 CCAATGCCTACATTCGACCTCTA 59.930 47.826 0.00 0.00 44.83 2.43
1776 1834 3.778954 ATAGCATAGTTGGAGGCTTCC 57.221 47.619 8.18 8.18 44.31 3.46
1830 1888 6.183361 ACGGAGGGAGTACATTATAGACTGTA 60.183 42.308 0.00 0.00 0.00 2.74
1834 1892 5.048154 GGAACGGAGGGAGTACATTATAGAC 60.048 48.000 0.00 0.00 0.00 2.59
1835 1893 5.075493 GGAACGGAGGGAGTACATTATAGA 58.925 45.833 0.00 0.00 0.00 1.98
1836 1894 4.831155 TGGAACGGAGGGAGTACATTATAG 59.169 45.833 0.00 0.00 0.00 1.31
1838 1896 3.649843 TGGAACGGAGGGAGTACATTAT 58.350 45.455 0.00 0.00 0.00 1.28
1841 1899 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
1842 1900 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
1843 1901 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1845 1903 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1846 1904 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1847 1905 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1848 1906 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1849 1907 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1850 1908 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1852 1910 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1853 1911 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1854 1912 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1855 1913 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1856 1914 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1857 1915 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1890 1948 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1891 1949 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1892 1950 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1893 1951 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1894 1952 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1895 1953 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1896 1954 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1897 1955 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1898 1956 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1899 1957 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1900 1958 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1901 1959 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1902 1960 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1903 1961 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1904 1962 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1905 1963 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1906 1964 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1907 1965 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1908 1966 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1909 1967 4.533311 AGTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
1910 1968 3.329814 AGTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
1911 1969 2.707257 AGTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
1912 1970 2.038033 CAGTTACTCCCTCCGTTCCAAA 59.962 50.000 0.00 0.00 0.00 3.28
1913 1971 1.621814 CAGTTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
1914 1972 1.263356 CAGTTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
1915 1973 1.067071 CACAGTTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
1916 1974 1.891150 TCACAGTTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
1917 1975 2.005370 TCACAGTTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
1918 1976 2.005370 TTCACAGTTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
1919 1977 2.761208 AGATTCACAGTTACTCCCTCCG 59.239 50.000 0.00 0.00 0.00 4.63
1920 1978 4.828072 AAGATTCACAGTTACTCCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
1921 1979 7.387643 ACTAAAAGATTCACAGTTACTCCCTC 58.612 38.462 0.00 0.00 0.00 4.30
1922 1980 7.016268 TGACTAAAAGATTCACAGTTACTCCCT 59.984 37.037 0.00 0.00 0.00 4.20
1923 1981 7.159372 TGACTAAAAGATTCACAGTTACTCCC 58.841 38.462 0.00 0.00 0.00 4.30
1924 1982 8.088981 TCTGACTAAAAGATTCACAGTTACTCC 58.911 37.037 0.00 0.00 0.00 3.85
1925 1983 9.646427 ATCTGACTAAAAGATTCACAGTTACTC 57.354 33.333 0.00 0.00 29.94 2.59
1926 1984 9.646427 GATCTGACTAAAAGATTCACAGTTACT 57.354 33.333 0.00 0.00 34.50 2.24
1990 2061 4.019321 ACACTTGTTCCACTACAGGCATAT 60.019 41.667 0.00 0.00 0.00 1.78
1991 2062 3.326588 ACACTTGTTCCACTACAGGCATA 59.673 43.478 0.00 0.00 0.00 3.14
2206 2291 3.671008 ACATACCGCAACACAGTAAGA 57.329 42.857 0.00 0.00 0.00 2.10
2250 2335 9.362539 TCGAATAAGTAGTCATAACAAGGAAAC 57.637 33.333 0.00 0.00 0.00 2.78
2366 2451 3.412386 CAGAGAACGGAAAAATCAGGGT 58.588 45.455 0.00 0.00 0.00 4.34
2379 2464 1.923316 GCAGCTTGTTTGCAGAGAACG 60.923 52.381 0.00 0.00 41.17 3.95
2405 2490 5.570320 ACTTCACTATGCCCACTTAACATT 58.430 37.500 0.00 0.00 0.00 2.71
2449 2534 8.892723 TGATATAAATGAAGAAAACGTCATGCT 58.107 29.630 0.00 0.00 34.70 3.79
2492 2577 5.084818 TCATAAACCAAATCGCTCAGAGA 57.915 39.130 0.00 0.00 0.00 3.10
2509 2594 8.177119 ACCAAAGAAAGTACTGCATTTCATAA 57.823 30.769 11.89 0.00 37.78 1.90
2585 2670 3.985279 TGTTCTCAACAAGATTACCGTCG 59.015 43.478 0.00 0.00 38.72 5.12
2758 2843 5.189928 AGTCACACACCATGTTTCTACAAA 58.810 37.500 0.00 0.00 40.64 2.83
2848 2933 7.120579 CCACTTGTGGAAACAATATAACAGCTA 59.879 37.037 14.15 0.00 46.06 3.32
2909 2994 0.040058 TCTCATGGCACCCAAATGCT 59.960 50.000 0.00 0.00 45.38 3.79
2925 3010 9.944663 CAGATAACTAATAGTGACTGAAGTCTC 57.055 37.037 11.55 8.04 44.99 3.36
3030 3147 6.148948 ACAACAACATTTGTCACATTATCCG 58.851 36.000 0.00 0.00 44.59 4.18
3039 3156 5.574891 AAGCTGTACAACAACATTTGTCA 57.425 34.783 0.00 0.00 44.59 3.58
3107 3224 2.303022 CCCTTTCTCTAACAGCCACTGA 59.697 50.000 0.78 0.00 35.18 3.41
3127 3244 6.805271 GCATGCTATATCACATCAAACATTCC 59.195 38.462 11.37 0.00 0.00 3.01
3153 3270 9.607988 AATTGATATGTGCATGTCAAATTGAAT 57.392 25.926 21.84 7.54 46.74 2.57
3198 3315 7.377398 GATATCGATCAATGGATATCCCAGAG 58.623 42.308 19.34 6.76 43.41 3.35
3285 3402 4.516092 AACTTCGTTTCACAAGAAGACG 57.484 40.909 10.84 0.00 42.75 4.18
3288 3405 5.861787 ACCAAAAACTTCGTTTCACAAGAAG 59.138 36.000 3.24 3.24 44.86 2.85
3312 3429 4.355437 CGCAACCACACAAAAATTAGACA 58.645 39.130 0.00 0.00 0.00 3.41
3330 3447 2.401583 AACAGATGATACTGCCGCAA 57.598 45.000 0.00 0.00 41.06 4.85
3332 3449 2.555199 AGAAACAGATGATACTGCCGC 58.445 47.619 0.00 0.00 41.06 6.53
3333 3450 5.188327 TCTAGAAACAGATGATACTGCCG 57.812 43.478 0.00 0.00 41.06 5.69
3427 3807 1.623811 ACCAGCAACCTAGTACCACAG 59.376 52.381 0.00 0.00 0.00 3.66
3439 3819 9.554162 AGTGAGTTACTAGAGTTGACCAGCAAC 62.554 44.444 0.00 0.00 46.49 4.17
3457 3837 2.972713 ACCAAGGCTTCTCAGTGAGTTA 59.027 45.455 19.53 8.52 0.00 2.24
3471 3851 1.067142 TGTATGAGTGTCGACCAAGGC 60.067 52.381 14.12 0.00 0.00 4.35
3478 3858 3.987868 GTCAGCTTTTGTATGAGTGTCGA 59.012 43.478 0.00 0.00 0.00 4.20
3518 3898 3.328535 ACATGACAAAGGAAAAGGGGT 57.671 42.857 0.00 0.00 0.00 4.95
3532 3912 6.016276 ACATTCCACTTCCAAAGTAACATGAC 60.016 38.462 0.00 0.00 40.46 3.06
3580 3960 4.084328 GGAGATCAAACTGACACAGAAACG 60.084 45.833 5.76 0.00 35.18 3.60
3611 3991 1.388547 TCGGCATTAGGGCAAATCAC 58.611 50.000 0.00 0.00 43.60 3.06
3677 4058 0.673956 TCTCCGGTCGAGTCTGTGAG 60.674 60.000 0.00 0.00 39.84 3.51
3736 4154 6.258947 GCAATCAATAGTCCAGTTACCTTCTC 59.741 42.308 0.00 0.00 0.00 2.87
3742 4197 4.035675 GCTGGCAATCAATAGTCCAGTTAC 59.964 45.833 8.19 0.00 44.53 2.50
3753 4208 3.255725 CAACGAAATGCTGGCAATCAAT 58.744 40.909 0.00 0.00 0.00 2.57
3792 4248 6.363088 ACGAACAACAAACATCTATGCATTTG 59.637 34.615 3.54 5.52 37.91 2.32


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

AutoCloner maintained by Alex Coulton.