Multiple sequence alignment - TraesCS6B01G252600

Loading Multiple Alignment...

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 TraesCS6B01G252600 chr6B 100.000 2288 0 0 1 2288 452621575 452619288 0.000000e+00 4226.0
1 TraesCS6B01G252600 chr6B 90.404 1709 139 14 19 1717 189103579 189105272 0.000000e+00 2224.0
2 TraesCS6B01G252600 chr6B 85.993 564 46 20 1724 2285 548638717 548638185 7.090000e-160 573.0
3 TraesCS6B01G252600 chr4B 91.297 1712 139 5 19 1724 551784730 551786437 0.000000e+00 2327.0
4 TraesCS6B01G252600 chr4B 90.888 1712 146 5 19 1724 551730122 551731829 0.000000e+00 2289.0
5 TraesCS6B01G252600 chr6D 91.074 1714 141 8 19 1727 450905977 450907683 0.000000e+00 2307.0
6 TraesCS6B01G252600 chr5B 91.063 1712 140 6 19 1725 641300585 641298882 0.000000e+00 2302.0
7 TraesCS6B01G252600 chr7B 90.760 1710 144 8 19 1724 150842129 150843828 0.000000e+00 2270.0
8 TraesCS6B01G252600 chr7D 90.485 1713 151 8 19 1724 463975812 463974105 0.000000e+00 2250.0
9 TraesCS6B01G252600 chr4D 90.368 1713 143 16 19 1725 414225616 414227312 0.000000e+00 2230.0
10 TraesCS6B01G252600 chr2B 90.300 1701 150 9 24 1717 459481001 459479309 0.000000e+00 2213.0
11 TraesCS6B01G252600 chr2A 86.819 349 38 5 1823 2170 675097404 675097745 1.280000e-102 383.0
12 TraesCS6B01G252600 chr3D 79.348 92 9 7 2013 2104 113460439 113460358 3.180000e-04 56.5


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 TraesCS6B01G252600 chr6B 452619288 452621575 2287 True 4226 4226 100.000 1 2288 1 chr6B.!!$R1 2287
1 TraesCS6B01G252600 chr6B 189103579 189105272 1693 False 2224 2224 90.404 19 1717 1 chr6B.!!$F1 1698
2 TraesCS6B01G252600 chr6B 548638185 548638717 532 True 573 573 85.993 1724 2285 1 chr6B.!!$R2 561
3 TraesCS6B01G252600 chr4B 551784730 551786437 1707 False 2327 2327 91.297 19 1724 1 chr4B.!!$F2 1705
4 TraesCS6B01G252600 chr4B 551730122 551731829 1707 False 2289 2289 90.888 19 1724 1 chr4B.!!$F1 1705
5 TraesCS6B01G252600 chr6D 450905977 450907683 1706 False 2307 2307 91.074 19 1727 1 chr6D.!!$F1 1708
6 TraesCS6B01G252600 chr5B 641298882 641300585 1703 True 2302 2302 91.063 19 1725 1 chr5B.!!$R1 1706
7 TraesCS6B01G252600 chr7B 150842129 150843828 1699 False 2270 2270 90.760 19 1724 1 chr7B.!!$F1 1705
8 TraesCS6B01G252600 chr7D 463974105 463975812 1707 True 2250 2250 90.485 19 1724 1 chr7D.!!$R1 1705
9 TraesCS6B01G252600 chr4D 414225616 414227312 1696 False 2230 2230 90.368 19 1725 1 chr4D.!!$F1 1706
10 TraesCS6B01G252600 chr2B 459479309 459481001 1692 True 2213 2213 90.300 24 1717 1 chr2B.!!$R1 1693

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
571 582 0.106015 TCATGGCGATGGAGAGGAGA 60.106 55.0 8.98 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1471 0.027586 GCACACTTCGACACAACCAC 59.972 55.0 0.0 0.0 0.0 4.16 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
22 23 3.711190 AGGAAAAACCAAGAACAATGGCT 59.289 39.130 0.00 0.00 41.89 4.75
35 36 5.771666 AGAACAATGGCTTTCATCTTCTTGA 59.228 36.000 0.00 0.00 32.88 3.02
76 77 2.730976 TCGTCGTCGTCGTCGTCT 60.731 61.111 18.44 0.00 45.27 4.18
90 91 1.006102 CGTCTGCGGAGTTGAGGTT 60.006 57.895 3.10 0.00 0.00 3.50
105 106 1.555075 GAGGTTGATCTGCCAGGTACA 59.445 52.381 8.45 0.00 0.00 2.90
218 219 0.965866 CCTCTCCCAGTACACTGCGA 60.966 60.000 3.75 0.38 42.47 5.10
268 269 5.510861 GCTCTTGTACTTGGACCACTTCTTA 60.511 44.000 0.00 0.00 0.00 2.10
279 283 6.245408 TGGACCACTTCTTATGTTTAGCATT 58.755 36.000 0.00 0.00 38.94 3.56
309 313 2.194056 CTGATTCATGGCCCGGCT 59.806 61.111 9.86 0.00 0.00 5.52
355 359 0.904865 TCGCTGGGTCAGGAATCACT 60.905 55.000 0.00 0.00 31.21 3.41
436 440 1.084370 CCATGGAGCCGAAGTTCGAC 61.084 60.000 26.37 15.56 43.74 4.20
460 464 2.015736 CCTCCATGGTGTTCTCGAAG 57.984 55.000 12.58 0.00 0.00 3.79
467 471 1.208535 TGGTGTTCTCGAAGTTGGTGT 59.791 47.619 0.00 0.00 0.00 4.16
544 555 2.032528 TTGGCGTTGGAGCTGGAG 59.967 61.111 0.00 0.00 37.29 3.86
545 556 4.704833 TGGCGTTGGAGCTGGAGC 62.705 66.667 0.00 0.00 42.49 4.70
571 582 0.106015 TCATGGCGATGGAGAGGAGA 60.106 55.000 8.98 0.00 0.00 3.71
590 601 6.201591 AGGAGAAAGGTTGATAGTGAGAGAT 58.798 40.000 0.00 0.00 0.00 2.75
610 621 1.437945 TGAGAGGGGGTGGGTAAGTAA 59.562 52.381 0.00 0.00 0.00 2.24
618 629 1.637035 GGTGGGTAAGTAATGGTGGGT 59.363 52.381 0.00 0.00 0.00 4.51
638 649 4.842380 GGGTAGGGTGAGTAAATATAGGCA 59.158 45.833 0.00 0.00 0.00 4.75
639 650 5.487845 GGGTAGGGTGAGTAAATATAGGCAT 59.512 44.000 0.00 0.00 0.00 4.40
670 683 3.007398 GGAGGAAGAGTGACAGTCATGTT 59.993 47.826 6.51 0.61 40.68 2.71
741 754 2.816087 ACTCCATGAATTGTGTGCAGAC 59.184 45.455 7.12 7.12 0.00 3.51
932 950 1.574428 GCCGCAACTACAACCACTG 59.426 57.895 0.00 0.00 0.00 3.66
959 977 1.204146 GAGGATGGCCCAACTCACTA 58.796 55.000 12.43 0.00 37.41 2.74
1063 1083 3.303395 GGAGTTCAAGCTCAAGAACAACG 60.303 47.826 21.38 0.00 44.94 4.10
1064 1084 3.531538 AGTTCAAGCTCAAGAACAACGA 58.468 40.909 21.38 0.00 44.94 3.85
1103 1123 2.456119 CGGTGGAGCTGATGAACGC 61.456 63.158 0.00 0.00 0.00 4.84
1108 1128 2.437359 AGCTGATGAACGCCAGGC 60.437 61.111 0.00 0.00 0.00 4.85
1142 1162 3.246112 TTGGGCCACCTACGCAGT 61.246 61.111 5.23 0.00 38.84 4.40
1162 1182 4.744137 CAGTCGTTCATCAGATCAAGATCC 59.256 45.833 6.45 0.00 38.58 3.36
1192 1212 2.030185 GTGACGTTCAAGCTCCTCACTA 60.030 50.000 0.00 0.00 0.00 2.74
1207 1227 0.966920 CACTACCGACACCCTCAAGT 59.033 55.000 0.00 0.00 0.00 3.16
1251 1271 2.684001 TTGAGGTCGTCAACAAGTGT 57.316 45.000 3.85 0.00 40.45 3.55
1264 1284 0.813610 CAAGTGTGGGAAGCACGACA 60.814 55.000 0.00 0.00 41.36 4.35
1296 1317 4.020878 AAGGAGTAGGGCCGGGGT 62.021 66.667 2.18 0.00 0.00 4.95
1347 1368 8.637986 TCTGCTTTGAACTGTTTATGGTTTATT 58.362 29.630 0.00 0.00 0.00 1.40
1373 1397 7.387673 TCATTGAACTGTTATGAAGTGTGGTAG 59.612 37.037 4.02 0.00 0.00 3.18
1446 1471 4.259970 GCTCTGCTTATGATGTGTGTTACG 60.260 45.833 0.00 0.00 0.00 3.18
1455 1480 2.096220 TGTGTGTTACGTGGTTGTGT 57.904 45.000 0.00 0.00 0.00 3.72
1493 1518 2.303022 CCTCACCAACTAGCCAAAGAGA 59.697 50.000 0.00 0.00 0.00 3.10
1498 1523 5.248477 TCACCAACTAGCCAAAGAGATTACT 59.752 40.000 0.00 0.00 0.00 2.24
1571 1596 0.390124 CATGCAGGCAACCAAACACT 59.610 50.000 0.00 0.00 37.17 3.55
1636 1661 0.604578 CCAAACAACCTGCAGATGGG 59.395 55.000 17.39 0.66 0.00 4.00
1643 1668 0.630673 ACCTGCAGATGGGGCATTTA 59.369 50.000 17.39 0.00 41.06 1.40
1680 1705 3.686916 GTCAGGCTGACTTAAGAAGGT 57.313 47.619 34.49 0.00 43.73 3.50
1717 1742 3.007614 ACTGTAGCCTACGACAACCAAAT 59.992 43.478 0.00 0.00 30.54 2.32
1719 1744 5.105064 ACTGTAGCCTACGACAACCAAATAT 60.105 40.000 0.00 0.00 30.54 1.28
1739 1764 1.406065 GCCCTAGCATCTCAGGCTGA 61.406 60.000 17.68 17.68 42.62 4.26
1758 1783 4.459089 GGGAGCTCAGGCACGTCC 62.459 72.222 17.19 0.34 41.70 4.79
1769 1794 4.096003 CACGTCCGGGGCCTTCAT 62.096 66.667 0.84 0.00 0.00 2.57
1775 1801 2.135581 CCGGGGCCTTCATACCGTA 61.136 63.158 13.77 0.00 44.57 4.02
1792 1818 3.673956 TAATGGGCGCCGGTCACTG 62.674 63.158 22.54 0.00 0.00 3.66
1862 1888 2.270257 AACAGCGCCATGTGCATGT 61.270 52.632 2.29 0.00 42.00 3.21
1863 1889 0.959867 AACAGCGCCATGTGCATGTA 60.960 50.000 2.29 0.00 42.00 2.29
1864 1890 0.749091 ACAGCGCCATGTGCATGTAT 60.749 50.000 2.29 0.00 42.00 2.29
1865 1891 0.317519 CAGCGCCATGTGCATGTATG 60.318 55.000 2.29 0.00 42.00 2.39
1876 1902 3.794737 CATGTATGCTCCTGGTGCT 57.205 52.632 20.19 9.45 0.00 4.40
1877 1903 1.590932 CATGTATGCTCCTGGTGCTC 58.409 55.000 20.19 11.67 0.00 4.26
1878 1904 1.140452 CATGTATGCTCCTGGTGCTCT 59.860 52.381 20.19 10.94 0.00 4.09
1879 1905 0.826715 TGTATGCTCCTGGTGCTCTC 59.173 55.000 20.19 11.08 0.00 3.20
1880 1906 0.105778 GTATGCTCCTGGTGCTCTCC 59.894 60.000 20.19 3.96 0.00 3.71
1881 1907 1.050988 TATGCTCCTGGTGCTCTCCC 61.051 60.000 20.19 0.00 0.00 4.30
1882 1908 2.686835 GCTCCTGGTGCTCTCCCT 60.687 66.667 13.24 0.00 0.00 4.20
1883 1909 3.028921 GCTCCTGGTGCTCTCCCTG 62.029 68.421 13.24 0.00 0.00 4.45
1884 1910 2.284921 TCCTGGTGCTCTCCCTGG 60.285 66.667 0.00 0.00 41.22 4.45
1885 1911 2.284921 CCTGGTGCTCTCCCTGGA 60.285 66.667 0.00 0.00 42.15 3.86
1886 1912 1.920325 CCTGGTGCTCTCCCTGGAA 60.920 63.158 0.00 0.00 42.15 3.53
1887 1913 1.492133 CCTGGTGCTCTCCCTGGAAA 61.492 60.000 0.00 0.00 42.15 3.13
1888 1914 0.035630 CTGGTGCTCTCCCTGGAAAG 60.036 60.000 0.00 0.00 0.00 2.62
1889 1915 1.301293 GGTGCTCTCCCTGGAAAGG 59.699 63.158 0.00 0.00 0.00 3.11
1890 1916 1.201429 GGTGCTCTCCCTGGAAAGGA 61.201 60.000 0.00 0.00 0.00 3.36
1891 1917 0.035915 GTGCTCTCCCTGGAAAGGAC 60.036 60.000 0.00 0.00 0.00 3.85
1892 1918 0.473694 TGCTCTCCCTGGAAAGGACA 60.474 55.000 0.00 0.00 0.00 4.02
1893 1919 0.915364 GCTCTCCCTGGAAAGGACAT 59.085 55.000 0.00 0.00 0.00 3.06
1894 1920 2.119495 GCTCTCCCTGGAAAGGACATA 58.881 52.381 0.00 0.00 0.00 2.29
1895 1921 2.103941 GCTCTCCCTGGAAAGGACATAG 59.896 54.545 0.00 0.00 0.00 2.23
1896 1922 3.647636 CTCTCCCTGGAAAGGACATAGA 58.352 50.000 0.00 0.00 0.00 1.98
1897 1923 3.375699 TCTCCCTGGAAAGGACATAGAC 58.624 50.000 0.00 0.00 0.00 2.59
1898 1924 2.101582 CTCCCTGGAAAGGACATAGACG 59.898 54.545 0.00 0.00 0.00 4.18
1899 1925 2.108168 CCCTGGAAAGGACATAGACGA 58.892 52.381 0.00 0.00 0.00 4.20
1900 1926 2.159085 CCCTGGAAAGGACATAGACGAC 60.159 54.545 0.00 0.00 0.00 4.34
1901 1927 2.496070 CCTGGAAAGGACATAGACGACA 59.504 50.000 0.00 0.00 0.00 4.35
1902 1928 3.429547 CCTGGAAAGGACATAGACGACAG 60.430 52.174 0.00 0.00 0.00 3.51
1903 1929 3.427573 TGGAAAGGACATAGACGACAGA 58.572 45.455 0.00 0.00 0.00 3.41
1904 1930 3.444034 TGGAAAGGACATAGACGACAGAG 59.556 47.826 0.00 0.00 0.00 3.35
1905 1931 3.440228 GAAAGGACATAGACGACAGAGC 58.560 50.000 0.00 0.00 0.00 4.09
1906 1932 2.428544 AGGACATAGACGACAGAGCT 57.571 50.000 0.00 0.00 0.00 4.09
1907 1933 2.020720 AGGACATAGACGACAGAGCTG 58.979 52.381 0.00 0.00 0.00 4.24
1998 2025 2.758009 ACAACATGGATGCAAAGCAAC 58.242 42.857 0.00 0.00 43.62 4.17
2019 2046 0.739462 TCGGTGCCTTGCAGTATTCG 60.739 55.000 0.00 0.00 40.08 3.34
2023 2050 0.245266 TGCCTTGCAGTATTCGTCGA 59.755 50.000 0.00 0.00 33.32 4.20
2042 2069 4.065088 TCGAGGCATGGATATTAAGCAAC 58.935 43.478 0.00 0.00 0.00 4.17
2056 2083 3.368046 GCAACAAGCTCGTGTTAGC 57.632 52.632 3.51 6.69 39.73 3.09
2064 2091 1.956620 GCTCGTGTTAGCCAGTTCGC 61.957 60.000 0.00 0.00 36.45 4.70
2070 2097 1.301401 TTAGCCAGTTCGCTGCGTT 60.301 52.632 22.48 6.30 43.67 4.84
2092 2119 1.345741 CCTAGATCCATGCCGATGTGT 59.654 52.381 0.00 0.00 0.00 3.72
2110 2137 6.238293 CGATGTGTTCTAGTAGTATCCGTTCA 60.238 42.308 0.00 0.00 0.00 3.18
2114 2141 7.076983 GTGTTCTAGTAGTATCCGTTCATAGC 58.923 42.308 0.00 0.00 0.00 2.97
2127 2154 4.026804 CCGTTCATAGCGCTAGTTAAGTTG 60.027 45.833 23.37 13.89 0.00 3.16
2130 2157 5.531122 TCATAGCGCTAGTTAAGTTGGAT 57.469 39.130 23.37 0.00 0.00 3.41
2133 2160 2.500098 AGCGCTAGTTAAGTTGGATCCA 59.500 45.455 8.99 11.44 0.00 3.41
2142 2169 5.480422 AGTTAAGTTGGATCCAATTTGGGAC 59.520 40.000 33.80 27.84 40.44 4.46
2173 2200 8.622948 TCTTCTTTCATAAAAGGAGGAAGAAC 57.377 34.615 0.00 0.00 45.01 3.01
2175 2202 7.745620 TCTTTCATAAAAGGAGGAAGAACAC 57.254 36.000 0.00 0.00 41.88 3.32
2186 2213 4.567159 GGAGGAAGAACACGAATATGACAC 59.433 45.833 0.00 0.00 0.00 3.67
2205 2232 1.098050 CGTAGGCCCACGTAGTAAGT 58.902 55.000 16.09 0.00 41.61 2.24
2206 2233 2.288666 CGTAGGCCCACGTAGTAAGTA 58.711 52.381 16.09 0.00 41.61 2.24
2210 2237 3.434309 AGGCCCACGTAGTAAGTAAGAA 58.566 45.455 0.00 0.00 41.61 2.52
2229 2256 0.762418 AAAGTGTGTGATCCCGGTCA 59.238 50.000 0.00 0.00 0.00 4.02
2265 2292 0.375106 GTGCGGCAAACAGATCTAGC 59.625 55.000 3.23 0.00 0.00 3.42
2266 2293 0.036483 TGCGGCAAACAGATCTAGCA 60.036 50.000 0.00 0.00 0.00 3.49
2285 2312 4.346730 AGCATTGAAATTGACTGGGATCA 58.653 39.130 0.00 0.00 0.00 2.92
2286 2313 4.773674 AGCATTGAAATTGACTGGGATCAA 59.226 37.500 0.00 0.00 42.62 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.711190 AGCCATTGTTCTTGGTTTTTCCT 59.289 39.130 0.00 0.00 36.57 3.36
1 2 4.071961 AGCCATTGTTCTTGGTTTTTCC 57.928 40.909 0.00 0.00 36.57 3.13
2 3 5.584251 TGAAAGCCATTGTTCTTGGTTTTTC 59.416 36.000 6.09 9.26 44.53 2.29
3 4 5.495640 TGAAAGCCATTGTTCTTGGTTTTT 58.504 33.333 6.09 1.40 44.53 1.94
4 5 5.096443 TGAAAGCCATTGTTCTTGGTTTT 57.904 34.783 4.51 4.51 46.36 2.43
5 6 4.751767 TGAAAGCCATTGTTCTTGGTTT 57.248 36.364 0.00 0.00 39.08 3.27
6 7 4.590222 AGATGAAAGCCATTGTTCTTGGTT 59.410 37.500 0.00 0.00 36.57 3.67
7 8 4.154942 AGATGAAAGCCATTGTTCTTGGT 58.845 39.130 0.00 0.00 36.57 3.67
8 9 4.796038 AGATGAAAGCCATTGTTCTTGG 57.204 40.909 0.00 0.00 35.17 3.61
9 10 6.022163 AGAAGATGAAAGCCATTGTTCTTG 57.978 37.500 0.00 0.00 36.35 3.02
10 11 6.266103 TCAAGAAGATGAAAGCCATTGTTCTT 59.734 34.615 0.00 0.00 42.92 2.52
11 12 5.771666 TCAAGAAGATGAAAGCCATTGTTCT 59.228 36.000 0.00 0.00 39.01 3.01
12 13 6.017400 TCAAGAAGATGAAAGCCATTGTTC 57.983 37.500 0.00 0.00 35.17 3.18
13 14 6.209986 TGATCAAGAAGATGAAAGCCATTGTT 59.790 34.615 0.00 0.00 37.00 2.83
14 15 5.713389 TGATCAAGAAGATGAAAGCCATTGT 59.287 36.000 0.00 0.00 37.00 2.71
15 16 6.203808 TGATCAAGAAGATGAAAGCCATTG 57.796 37.500 0.00 0.00 37.00 2.82
16 17 6.605995 TGATGATCAAGAAGATGAAAGCCATT 59.394 34.615 0.00 0.00 37.00 3.16
17 18 6.039493 GTGATGATCAAGAAGATGAAAGCCAT 59.961 38.462 0.00 0.00 37.00 4.40
22 23 5.352293 CACGGTGATGATCAAGAAGATGAAA 59.648 40.000 0.74 0.00 37.00 2.69
35 36 4.856801 GCCCCGCACGGTGATGAT 62.857 66.667 13.29 0.00 0.00 2.45
76 77 0.976641 AGATCAACCTCAACTCCGCA 59.023 50.000 0.00 0.00 0.00 5.69
90 91 0.249120 CCGTTGTACCTGGCAGATCA 59.751 55.000 17.94 9.00 0.00 2.92
197 198 0.614979 GCAGTGTACTGGGAGAGGGA 60.615 60.000 13.41 0.00 43.94 4.20
218 219 0.104304 GATCCTAATGACCGCCGTGT 59.896 55.000 0.00 0.00 0.00 4.49
268 269 4.307432 CCGTCTCCGATAATGCTAAACAT 58.693 43.478 0.00 0.00 37.01 2.71
279 283 0.959553 GAATCAGGCCGTCTCCGATA 59.040 55.000 0.00 0.00 35.63 2.92
306 310 1.221414 GGCAGTCGACATCATTAGCC 58.779 55.000 19.50 14.15 0.00 3.93
355 359 1.139654 ACTGCACAAGAGCTGAAGACA 59.860 47.619 0.00 0.00 37.23 3.41
488 493 3.002371 CTGGAGGGCCTTCTTCCC 58.998 66.667 14.33 7.37 44.25 3.97
544 555 2.110627 ATCGCCATGAGCTCCAGC 59.889 61.111 12.15 10.35 40.39 4.85
545 556 1.597302 CCATCGCCATGAGCTCCAG 60.597 63.158 12.15 3.17 40.39 3.86
546 557 2.036428 CTCCATCGCCATGAGCTCCA 62.036 60.000 12.15 0.00 40.39 3.86
547 558 1.301558 CTCCATCGCCATGAGCTCC 60.302 63.158 12.15 0.00 40.39 4.70
548 559 0.319727 CTCTCCATCGCCATGAGCTC 60.320 60.000 6.82 6.82 40.39 4.09
549 560 1.747145 CTCTCCATCGCCATGAGCT 59.253 57.895 0.00 0.00 40.39 4.09
571 582 6.098124 CCTCTCATCTCTCACTATCAACCTTT 59.902 42.308 0.00 0.00 0.00 3.11
590 601 1.095130 TACTTACCCACCCCCTCTCA 58.905 55.000 0.00 0.00 0.00 3.27
610 621 2.653543 TTACTCACCCTACCCACCAT 57.346 50.000 0.00 0.00 0.00 3.55
618 629 7.092891 CCATCATGCCTATATTTACTCACCCTA 60.093 40.741 0.00 0.00 0.00 3.53
638 649 3.052262 TCACTCTTCCTCCTCTCCATCAT 60.052 47.826 0.00 0.00 0.00 2.45
639 650 2.313041 TCACTCTTCCTCCTCTCCATCA 59.687 50.000 0.00 0.00 0.00 3.07
741 754 1.270199 CCATCTCATTGCTCTCCTCGG 60.270 57.143 0.00 0.00 0.00 4.63
879 894 3.068064 TCCTCCATGCGCTCGTCA 61.068 61.111 9.73 0.00 0.00 4.35
1055 1074 1.664965 GAGCAGCCGTCGTTGTTCT 60.665 57.895 0.00 0.00 29.57 3.01
1063 1083 2.125350 CTTCCAGGAGCAGCCGTC 60.125 66.667 0.00 0.00 43.43 4.79
1064 1084 3.710722 CCTTCCAGGAGCAGCCGT 61.711 66.667 0.00 0.00 43.43 5.68
1090 1110 2.467826 GCCTGGCGTTCATCAGCTC 61.468 63.158 1.35 0.00 0.00 4.09
1142 1162 3.796844 GCGGATCTTGATCTGATGAACGA 60.797 47.826 20.09 0.00 0.00 3.85
1162 1182 1.390123 CTTGAACGTCACCATGTAGCG 59.610 52.381 0.00 0.00 0.00 4.26
1192 1212 1.002087 GATGAACTTGAGGGTGTCGGT 59.998 52.381 0.00 0.00 0.00 4.69
1251 1271 1.896660 GGCTTTGTCGTGCTTCCCA 60.897 57.895 0.00 0.00 0.00 4.37
1296 1317 9.282569 GACTCGATAGTAATTAGAAAGGAGGTA 57.717 37.037 0.00 0.00 35.56 3.08
1347 1368 6.061441 ACCACACTTCATAACAGTTCAATGA 58.939 36.000 0.00 0.00 0.00 2.57
1446 1471 0.027586 GCACACTTCGACACAACCAC 59.972 55.000 0.00 0.00 0.00 4.16
1455 1480 1.000506 GAGGTTACCAGCACACTTCGA 59.999 52.381 3.51 0.00 0.00 3.71
1493 1518 2.482721 GCAACGCCTTGTGTGTAGTAAT 59.517 45.455 0.00 0.00 36.45 1.89
1498 1523 1.801771 GTATGCAACGCCTTGTGTGTA 59.198 47.619 0.00 0.00 36.45 2.90
1526 1551 2.107378 TGGACAAACTCAAGGCATGGTA 59.893 45.455 0.00 0.00 0.00 3.25
1571 1596 0.902531 GGGCTGAACTACACTGCCTA 59.097 55.000 13.54 0.00 46.52 3.93
1636 1661 2.976589 ACAAATGCAGCCTTAAATGCC 58.023 42.857 0.00 0.00 41.85 4.40
1643 1668 4.202441 CCTGACTATACAAATGCAGCCTT 58.798 43.478 0.00 0.00 0.00 4.35
1670 1695 6.624423 AGTTGCATTGCATAACCTTCTTAAG 58.376 36.000 12.95 0.00 38.76 1.85
1680 1705 4.335315 GGCTACAGTAGTTGCATTGCATAA 59.665 41.667 12.95 0.00 46.27 1.90
1733 1758 2.071262 CCTGAGCTCCCATCAGCCT 61.071 63.158 12.15 0.00 42.36 4.58
1739 1764 3.005539 ACGTGCCTGAGCTCCCAT 61.006 61.111 12.15 0.00 40.80 4.00
1758 1783 0.395312 ATTACGGTATGAAGGCCCCG 59.605 55.000 13.53 13.53 45.72 5.73
1769 1794 4.224274 CCGGCGCCCATTACGGTA 62.224 66.667 23.46 0.00 41.34 4.02
1787 1813 1.598962 GTGCTTGAGCTGCCAGTGA 60.599 57.895 4.44 0.00 42.66 3.41
1792 1818 2.037136 ATGACGTGCTTGAGCTGCC 61.037 57.895 0.00 0.00 42.66 4.85
1862 1888 1.050988 GGGAGAGCACCAGGAGCATA 61.051 60.000 11.90 0.00 0.00 3.14
1863 1889 2.373707 GGGAGAGCACCAGGAGCAT 61.374 63.158 11.90 0.00 0.00 3.79
1864 1890 3.005539 GGGAGAGCACCAGGAGCA 61.006 66.667 11.90 0.00 0.00 4.26
1865 1891 2.686835 AGGGAGAGCACCAGGAGC 60.687 66.667 0.00 0.00 0.00 4.70
1866 1892 2.365586 CCAGGGAGAGCACCAGGAG 61.366 68.421 0.00 0.00 0.00 3.69
1867 1893 2.284921 CCAGGGAGAGCACCAGGA 60.285 66.667 0.00 0.00 0.00 3.86
1868 1894 1.492133 TTTCCAGGGAGAGCACCAGG 61.492 60.000 0.00 0.00 0.00 4.45
1870 1896 1.492133 CCTTTCCAGGGAGAGCACCA 61.492 60.000 0.43 0.00 36.36 4.17
1872 1898 0.035915 GTCCTTTCCAGGGAGAGCAC 60.036 60.000 0.43 0.00 41.25 4.40
1873 1899 0.473694 TGTCCTTTCCAGGGAGAGCA 60.474 55.000 0.43 0.00 41.25 4.26
1874 1900 0.915364 ATGTCCTTTCCAGGGAGAGC 59.085 55.000 0.43 0.00 41.25 4.09
1876 1902 3.375699 GTCTATGTCCTTTCCAGGGAGA 58.624 50.000 0.00 0.00 41.25 3.71
1877 1903 2.101582 CGTCTATGTCCTTTCCAGGGAG 59.898 54.545 0.00 0.00 41.25 4.30
1878 1904 2.108168 CGTCTATGTCCTTTCCAGGGA 58.892 52.381 0.00 0.00 41.25 4.20
1879 1905 2.108168 TCGTCTATGTCCTTTCCAGGG 58.892 52.381 0.00 0.00 41.25 4.45
1880 1906 2.496070 TGTCGTCTATGTCCTTTCCAGG 59.504 50.000 0.00 0.00 42.50 4.45
1881 1907 3.444034 TCTGTCGTCTATGTCCTTTCCAG 59.556 47.826 0.00 0.00 0.00 3.86
1882 1908 3.427573 TCTGTCGTCTATGTCCTTTCCA 58.572 45.455 0.00 0.00 0.00 3.53
1883 1909 3.735514 GCTCTGTCGTCTATGTCCTTTCC 60.736 52.174 0.00 0.00 0.00 3.13
1884 1910 3.129638 AGCTCTGTCGTCTATGTCCTTTC 59.870 47.826 0.00 0.00 0.00 2.62
1885 1911 3.093057 AGCTCTGTCGTCTATGTCCTTT 58.907 45.455 0.00 0.00 0.00 3.11
1886 1912 2.425312 CAGCTCTGTCGTCTATGTCCTT 59.575 50.000 0.00 0.00 0.00 3.36
1887 1913 2.020720 CAGCTCTGTCGTCTATGTCCT 58.979 52.381 0.00 0.00 0.00 3.85
1888 1914 1.066303 CCAGCTCTGTCGTCTATGTCC 59.934 57.143 0.00 0.00 0.00 4.02
1889 1915 1.535015 GCCAGCTCTGTCGTCTATGTC 60.535 57.143 0.00 0.00 0.00 3.06
1890 1916 0.457851 GCCAGCTCTGTCGTCTATGT 59.542 55.000 0.00 0.00 0.00 2.29
1891 1917 0.593518 CGCCAGCTCTGTCGTCTATG 60.594 60.000 0.00 0.00 0.00 2.23
1892 1918 1.730487 CGCCAGCTCTGTCGTCTAT 59.270 57.895 0.00 0.00 0.00 1.98
1893 1919 3.052620 GCGCCAGCTCTGTCGTCTA 62.053 63.158 0.00 0.00 41.01 2.59
1894 1920 4.427661 GCGCCAGCTCTGTCGTCT 62.428 66.667 0.00 0.00 41.01 4.18
1910 1936 3.749064 TCCGTGAGACCGCTGAGC 61.749 66.667 0.00 0.00 0.00 4.26
1946 1972 4.888325 CCATCTCCCGCCTCCCCT 62.888 72.222 0.00 0.00 0.00 4.79
1956 1983 1.066587 CTCGTTCTCCGCCATCTCC 59.933 63.158 0.00 0.00 36.19 3.71
1972 1999 3.921119 TTGCATCCATGTTGTTGTCTC 57.079 42.857 0.00 0.00 0.00 3.36
1978 2005 2.548493 GGTTGCTTTGCATCCATGTTGT 60.548 45.455 13.01 0.00 44.92 3.32
1998 2025 0.392998 AATACTGCAAGGCACCGAGG 60.393 55.000 0.00 0.00 39.30 4.63
1999 2026 1.009829 GAATACTGCAAGGCACCGAG 58.990 55.000 0.00 0.00 39.30 4.63
2019 2046 3.664107 TGCTTAATATCCATGCCTCGAC 58.336 45.455 0.00 0.00 0.00 4.20
2023 2050 4.038402 GCTTGTTGCTTAATATCCATGCCT 59.962 41.667 0.00 0.00 38.95 4.75
2042 2069 1.461127 GAACTGGCTAACACGAGCTTG 59.539 52.381 0.00 0.00 42.43 4.01
2056 2083 2.501223 TAGGGAACGCAGCGAACTGG 62.501 60.000 24.65 0.00 44.63 4.00
2064 2091 1.875576 GCATGGATCTAGGGAACGCAG 60.876 57.143 0.00 0.00 0.00 5.18
2070 2097 1.269958 CATCGGCATGGATCTAGGGA 58.730 55.000 0.00 0.00 0.00 4.20
2092 2119 5.106791 GCGCTATGAACGGATACTACTAGAA 60.107 44.000 0.00 0.00 0.00 2.10
2110 2137 4.344102 TGGATCCAACTTAACTAGCGCTAT 59.656 41.667 19.19 6.69 0.00 2.97
2114 2141 6.258160 CAAATTGGATCCAACTTAACTAGCG 58.742 40.000 29.32 7.38 38.88 4.26
2127 2154 5.019470 AGAAGAAAGTCCCAAATTGGATCC 58.981 41.667 14.62 4.20 40.96 3.36
2130 2157 5.705400 AGAAGAAGAAAGTCCCAAATTGGA 58.295 37.500 14.62 0.00 40.96 3.53
2133 2160 7.660030 TGAAAGAAGAAGAAAGTCCCAAATT 57.340 32.000 0.00 0.00 0.00 1.82
2142 2169 9.289782 TCCTCCTTTTATGAAAGAAGAAGAAAG 57.710 33.333 11.34 0.00 44.03 2.62
2173 2200 2.124903 GGCCTACGTGTCATATTCGTG 58.875 52.381 0.00 0.00 38.27 4.35
2175 2202 1.067974 TGGGCCTACGTGTCATATTCG 59.932 52.381 4.53 0.00 0.00 3.34
2205 2232 3.071892 ACCGGGATCACACACTTTTCTTA 59.928 43.478 6.32 0.00 0.00 2.10
2206 2233 2.158667 ACCGGGATCACACACTTTTCTT 60.159 45.455 6.32 0.00 0.00 2.52
2210 2237 0.762418 TGACCGGGATCACACACTTT 59.238 50.000 6.32 0.00 0.00 2.66
2229 2256 2.437413 GCACCGGAAAAAGAAGATCCT 58.563 47.619 9.46 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.