Multiple sequence alignment - TraesCS5B01G181500

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 TraesCS5B01G181500 chr5B 100.000 2495 0 0 1 2495 331249115 331246621 0.000000e+00 4608.0
1 TraesCS5B01G181500 chr5A 92.777 1426 49 15 402 1784 382779038 382777624 0.000000e+00 2013.0
2 TraesCS5B01G181500 chr5A 91.624 585 35 10 1896 2467 382777627 382777044 0.000000e+00 797.0
3 TraesCS5B01G181500 chr5A 88.144 388 22 12 49 416 382779456 382779073 8.190000e-120 440.0
4 TraesCS5B01G181500 chr5D 93.978 1345 47 17 465 1784 290395483 290394148 0.000000e+00 2004.0
5 TraesCS5B01G181500 chr5D 90.630 619 37 12 1896 2495 290394151 290393535 0.000000e+00 802.0
6 TraesCS5B01G181500 chr5D 93.000 300 20 1 1 299 290395828 290395529 1.060000e-118 436.0
7 TraesCS5B01G181500 chr5D 97.143 35 1 0 227 261 506301845 506301879 2.680000e-05 60.2
8 TraesCS5B01G181500 chr5D 100.000 29 0 0 235 263 10777453 10777425 1.000000e-03 54.7
9 TraesCS5B01G181500 chr7D 90.690 580 41 9 944 1518 111114497 111115068 0.000000e+00 760.0
10 TraesCS5B01G181500 chr7D 83.570 493 68 8 500 990 111213971 111214452 1.360000e-122 449.0
11 TraesCS5B01G181500 chr7D 88.346 266 18 9 944 1203 111092047 111092305 8.670000e-80 307.0
12 TraesCS5B01G181500 chr7D 77.475 404 77 12 1070 1468 160487773 160488167 1.930000e-56 230.0
13 TraesCS5B01G181500 chr7D 85.567 194 18 6 475 660 111091665 111091856 7.040000e-46 195.0
14 TraesCS5B01G181500 chr7B 88.790 562 35 9 944 1503 70825102 70825637 0.000000e+00 664.0
15 TraesCS5B01G181500 chr7B 78.025 405 73 14 1070 1468 121053582 121053976 8.920000e-60 241.0
16 TraesCS5B01G181500 chr7B 77.778 405 74 14 1070 1468 121242622 121243016 4.150000e-58 235.0
17 TraesCS5B01G181500 chr7B 77.037 405 77 14 1070 1468 121320866 121321260 4.180000e-53 219.0
18 TraesCS5B01G181500 chr7B 92.647 136 10 0 1771 1906 506726663 506726798 1.960000e-46 196.0
19 TraesCS5B01G181500 chr7A 85.605 521 44 7 996 1514 116509279 116509770 3.680000e-143 518.0
20 TraesCS5B01G181500 chr2D 98.305 118 2 0 1782 1899 158283291 158283408 9.040000e-50 207.0
21 TraesCS5B01G181500 chr2D 94.203 138 5 3 1764 1899 381869604 381869740 9.040000e-50 207.0
22 TraesCS5B01G181500 chr2D 97.500 120 3 0 1780 1899 572692615 572692734 3.250000e-49 206.0
23 TraesCS5B01G181500 chr2D 92.143 140 7 4 1766 1902 424680352 424680490 7.040000e-46 195.0
24 TraesCS5B01G181500 chrUn 98.291 117 2 0 1783 1899 100620879 100620763 3.250000e-49 206.0
25 TraesCS5B01G181500 chrUn 94.488 127 7 0 1783 1909 455532624 455532498 1.960000e-46 196.0
26 TraesCS5B01G181500 chr3D 95.276 127 6 0 1783 1909 498226127 498226253 4.210000e-48 202.0
27 TraesCS5B01G181500 chr3D 94.444 126 6 1 1774 1899 587436609 587436485 2.530000e-45 193.0
28 TraesCS5B01G181500 chr6B 100.000 32 0 0 230 261 346710017 346709986 2.680000e-05 60.2
29 TraesCS5B01G181500 chr4A 89.583 48 3 2 215 261 430430237 430430283 2.680000e-05 60.2


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 TraesCS5B01G181500 chr5B 331246621 331249115 2494 True 4608.000000 4608 100.000000 1 2495 1 chr5B.!!$R1 2494
1 TraesCS5B01G181500 chr5A 382777044 382779456 2412 True 1083.333333 2013 90.848333 49 2467 3 chr5A.!!$R1 2418
2 TraesCS5B01G181500 chr5D 290393535 290395828 2293 True 1080.666667 2004 92.536000 1 2495 3 chr5D.!!$R2 2494
3 TraesCS5B01G181500 chr7D 111114497 111115068 571 False 760.000000 760 90.690000 944 1518 1 chr7D.!!$F1 574
4 TraesCS5B01G181500 chr7D 111091665 111092305 640 False 251.000000 307 86.956500 475 1203 2 chr7D.!!$F4 728
5 TraesCS5B01G181500 chr7B 70825102 70825637 535 False 664.000000 664 88.790000 944 1503 1 chr7B.!!$F1 559

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
160 167 0.555769 AAGGACTTTGGGCCTGTCAA 59.444 50.0 20.21 0.0 34.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1929 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 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
25 26 3.244582 TGCCACCTCACTTCTACCTAAA 58.755 45.455 0.00 0.00 0.00 1.85
83 84 5.222151 TGGGGTATTTGGTGTGTCAGAAATA 60.222 40.000 0.00 0.00 0.00 1.40
136 143 5.853572 TTGAGGGTTGGAAGTATTACCTT 57.146 39.130 0.00 0.00 0.00 3.50
160 167 0.555769 AAGGACTTTGGGCCTGTCAA 59.444 50.000 20.21 0.00 34.00 3.18
168 175 1.067295 TGGGCCTGTCAAATCAGAGT 58.933 50.000 4.53 0.00 37.61 3.24
188 196 7.068839 TCAGAGTTAAACAGAAGAAGACAGAGT 59.931 37.037 0.00 0.00 0.00 3.24
209 217 8.463930 AGAGTAGATCTGTCTTTGGATAGAAG 57.536 38.462 5.18 0.00 41.69 2.85
210 218 7.505585 AGAGTAGATCTGTCTTTGGATAGAAGG 59.494 40.741 5.18 0.00 41.69 3.46
268 276 6.041979 AGAGCTGGTATTGGTTGATTTGTTTT 59.958 34.615 0.00 0.00 0.00 2.43
291 299 8.600449 TTTCTTTGCCCTTGTATTTGTAAATG 57.400 30.769 0.27 0.00 0.00 2.32
319 327 2.571216 CCGGTCGGTCACAAGGTCT 61.571 63.158 0.55 0.00 0.00 3.85
320 328 1.246056 CCGGTCGGTCACAAGGTCTA 61.246 60.000 0.55 0.00 0.00 2.59
322 330 1.000060 CGGTCGGTCACAAGGTCTAAA 60.000 52.381 0.00 0.00 0.00 1.85
370 382 0.968405 GCCTGAATTTTGTCCCTGCA 59.032 50.000 0.00 0.00 0.00 4.41
626 702 0.842635 ATGCTCCTCCTGGAACCATC 59.157 55.000 0.00 0.00 42.66 3.51
650 726 1.274596 CGTTACATACGTGAGCCACC 58.725 55.000 0.00 0.00 45.14 4.61
796 878 2.293122 TGTTCGTGGAATTCTTTGCCAG 59.707 45.455 5.23 0.00 31.18 4.85
976 1063 2.571653 TGCAGGCACATAGTAGAAACCT 59.428 45.455 0.00 0.00 0.00 3.50
995 1089 2.038033 CCTTTTAGACACCGAACCAGGA 59.962 50.000 0.00 0.00 34.73 3.86
1252 1346 0.106967 GGAGAACATCTTCTGGGGGC 60.107 60.000 0.00 0.00 36.82 5.80
1318 1412 2.818432 GTGGACGAGAAGAAGGACTACA 59.182 50.000 0.00 0.00 0.00 2.74
1498 1592 4.575885 TGGACAGAAACCATACTAACTGC 58.424 43.478 0.00 0.00 32.03 4.40
1585 1714 4.686554 GGATTCATGCACGTTCCTATCTAC 59.313 45.833 0.00 0.00 0.00 2.59
1586 1715 5.509840 GGATTCATGCACGTTCCTATCTACT 60.510 44.000 0.00 0.00 0.00 2.57
1587 1716 4.307443 TCATGCACGTTCCTATCTACTG 57.693 45.455 0.00 0.00 0.00 2.74
1606 1735 3.462579 ACTGTAACTAGCTAGAGGGGCTA 59.537 47.826 27.45 5.72 40.74 3.93
1607 1736 4.106663 ACTGTAACTAGCTAGAGGGGCTAT 59.893 45.833 27.45 0.00 40.79 2.97
1639 1780 3.755965 TGCCGTAACAAGCATGTATTG 57.244 42.857 10.21 10.21 39.40 1.90
1781 1928 6.640092 GGTACTCTACAAGACTACAACACAAC 59.360 42.308 0.00 0.00 0.00 3.32
1782 1929 6.466885 ACTCTACAAGACTACAACACAACT 57.533 37.500 0.00 0.00 0.00 3.16
1783 1930 7.578310 ACTCTACAAGACTACAACACAACTA 57.422 36.000 0.00 0.00 0.00 2.24
1784 1931 7.424001 ACTCTACAAGACTACAACACAACTAC 58.576 38.462 0.00 0.00 0.00 2.73
1785 1932 7.284944 ACTCTACAAGACTACAACACAACTACT 59.715 37.037 0.00 0.00 0.00 2.57
1786 1933 7.646314 TCTACAAGACTACAACACAACTACTC 58.354 38.462 0.00 0.00 0.00 2.59
1787 1934 5.598769 ACAAGACTACAACACAACTACTCC 58.401 41.667 0.00 0.00 0.00 3.85
1788 1935 4.868314 AGACTACAACACAACTACTCCC 57.132 45.455 0.00 0.00 0.00 4.30
1789 1936 4.481072 AGACTACAACACAACTACTCCCT 58.519 43.478 0.00 0.00 0.00 4.20
1790 1937 4.523558 AGACTACAACACAACTACTCCCTC 59.476 45.833 0.00 0.00 0.00 4.30
1791 1938 3.577415 ACTACAACACAACTACTCCCTCC 59.423 47.826 0.00 0.00 0.00 4.30
1792 1939 1.343465 ACAACACAACTACTCCCTCCG 59.657 52.381 0.00 0.00 0.00 4.63
1793 1940 1.343465 CAACACAACTACTCCCTCCGT 59.657 52.381 0.00 0.00 0.00 4.69
1794 1941 1.254954 ACACAACTACTCCCTCCGTC 58.745 55.000 0.00 0.00 0.00 4.79
1795 1942 0.531200 CACAACTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
1796 1943 0.964358 ACAACTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
1797 1944 1.379576 AACTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1798 1945 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1799 1946 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1800 1947 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
1801 1948 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1802 1949 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1803 1950 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1804 1951 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1805 1952 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1806 1953 2.034124 CCCTCCGTCCGGAAATACTTA 58.966 52.381 5.23 0.00 44.66 2.24
1807 1954 2.631545 CCCTCCGTCCGGAAATACTTAT 59.368 50.000 5.23 0.00 44.66 1.73
1808 1955 3.070590 CCCTCCGTCCGGAAATACTTATT 59.929 47.826 5.23 0.00 44.66 1.40
1809 1956 4.056050 CCTCCGTCCGGAAATACTTATTG 58.944 47.826 5.23 0.00 44.66 1.90
1810 1957 4.202182 CCTCCGTCCGGAAATACTTATTGA 60.202 45.833 5.23 0.00 44.66 2.57
1811 1958 5.341872 TCCGTCCGGAAATACTTATTGAA 57.658 39.130 5.23 0.00 42.05 2.69
1812 1959 5.353938 TCCGTCCGGAAATACTTATTGAAG 58.646 41.667 5.23 0.00 42.05 3.02
1813 1960 4.510340 CCGTCCGGAAATACTTATTGAAGG 59.490 45.833 5.23 0.00 35.57 3.46
1814 1961 5.353938 CGTCCGGAAATACTTATTGAAGGA 58.646 41.667 5.23 0.00 36.95 3.36
1815 1962 5.813672 CGTCCGGAAATACTTATTGAAGGAA 59.186 40.000 5.23 0.00 36.95 3.36
1816 1963 6.482308 CGTCCGGAAATACTTATTGAAGGAAT 59.518 38.462 5.23 0.00 36.95 3.01
1817 1964 7.518370 CGTCCGGAAATACTTATTGAAGGAATG 60.518 40.741 5.23 0.00 36.95 2.67
1818 1965 6.770785 TCCGGAAATACTTATTGAAGGAATGG 59.229 38.462 0.00 0.00 36.95 3.16
1819 1966 6.770785 CCGGAAATACTTATTGAAGGAATGGA 59.229 38.462 0.00 0.00 36.95 3.41
1820 1967 7.448469 CCGGAAATACTTATTGAAGGAATGGAT 59.552 37.037 0.00 0.00 36.95 3.41
1821 1968 8.292448 CGGAAATACTTATTGAAGGAATGGATG 58.708 37.037 0.00 0.00 36.95 3.51
1822 1969 9.136323 GGAAATACTTATTGAAGGAATGGATGT 57.864 33.333 0.00 0.00 36.95 3.06
1831 1978 6.332735 TGAAGGAATGGATGTATCTAGACG 57.667 41.667 0.00 0.00 0.00 4.18
1832 1979 5.833667 TGAAGGAATGGATGTATCTAGACGT 59.166 40.000 0.00 0.00 0.00 4.34
1833 1980 7.002276 TGAAGGAATGGATGTATCTAGACGTA 58.998 38.462 0.00 0.00 0.00 3.57
1834 1981 7.670140 TGAAGGAATGGATGTATCTAGACGTAT 59.330 37.037 0.00 0.00 0.00 3.06
1835 1982 8.423906 AAGGAATGGATGTATCTAGACGTATT 57.576 34.615 0.00 0.00 0.00 1.89
1836 1983 8.423906 AGGAATGGATGTATCTAGACGTATTT 57.576 34.615 0.00 0.00 0.00 1.40
1837 1984 8.871125 AGGAATGGATGTATCTAGACGTATTTT 58.129 33.333 0.00 0.00 0.00 1.82
1864 2011 9.851686 AGTTCTAGATACATCCATTTTTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
1871 2018 9.415544 GATACATCCATTTTTATGCATTTCTCC 57.584 33.333 3.54 0.00 0.00 3.71
1872 2019 6.275335 ACATCCATTTTTATGCATTTCTCCG 58.725 36.000 3.54 0.00 0.00 4.63
1873 2020 6.096705 ACATCCATTTTTATGCATTTCTCCGA 59.903 34.615 3.54 0.00 0.00 4.55
1874 2021 5.890334 TCCATTTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
1875 2022 5.417266 TCCATTTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
1876 2023 6.071672 TCCATTTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
1877 2024 6.254157 CCATTTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
1878 2025 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
1879 2026 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
1880 2027 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
1881 2028 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
1882 2029 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
1883 2030 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
1884 2031 4.394920 TGCATTTCTCCGACAAGTATTTCC 59.605 41.667 0.00 0.00 0.00 3.13
1885 2032 4.494199 GCATTTCTCCGACAAGTATTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
1886 2033 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
1887 2034 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
1888 2035 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
1889 2036 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
1890 2037 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1891 2038 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1892 2039 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1893 2040 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1894 2041 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1895 2042 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1942 2089 6.480763 TGAAAAATCCAAGCAGAGTACCATA 58.519 36.000 0.00 0.00 0.00 2.74
1949 2096 6.953101 TCCAAGCAGAGTACCATATGTTTAA 58.047 36.000 1.24 0.00 0.00 1.52
2152 2310 0.976073 TCGAGCGGGGATTCTCCTTT 60.976 55.000 0.04 0.00 36.57 3.11
2234 2392 7.749126 GGCAAAGATACCGCAATACAAATATAC 59.251 37.037 0.00 0.00 0.00 1.47
2264 2424 2.645838 TTGCCCTCCTAGATGAATGC 57.354 50.000 0.00 0.00 0.00 3.56
2311 2471 6.423182 CCCATCTTTGAGGATTACCAAGTAA 58.577 40.000 0.00 0.00 38.94 2.24
2312 2472 7.062957 CCCATCTTTGAGGATTACCAAGTAAT 58.937 38.462 0.00 0.00 40.82 1.89
2390 2550 2.096496 GCAGAAAGAATCACATCCACCG 59.904 50.000 0.00 0.00 0.00 4.94
2397 2557 0.107508 ATCACATCCACCGGCTCAAG 60.108 55.000 0.00 0.00 0.00 3.02
2408 2568 1.593196 CGGCTCAAGGAGAAACAACA 58.407 50.000 0.00 0.00 0.00 3.33
2409 2569 2.154462 CGGCTCAAGGAGAAACAACAT 58.846 47.619 0.00 0.00 0.00 2.71
2416 2577 5.875224 TCAAGGAGAAACAACATGTGGATA 58.125 37.500 7.39 0.00 0.00 2.59
2469 2636 0.843309 TTTGAGAGTGCCTTGGGACA 59.157 50.000 13.55 0.00 0.00 4.02
2483 2650 2.368011 GGACAGGTCCACCTAGGCC 61.368 68.421 9.30 1.20 46.65 5.19
2484 2651 2.683933 ACAGGTCCACCTAGGCCG 60.684 66.667 9.30 0.00 46.65 6.13
2486 2653 1.762460 CAGGTCCACCTAGGCCGAT 60.762 63.158 9.30 0.00 46.65 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.461182 AAGCATAATATCTAGAGCGAAGTCT 57.539 36.000 0.00 0.00 0.00 3.24
102 109 7.127339 ACTTCCAACCCTCAATATGTACTACAT 59.873 37.037 6.90 6.90 42.35 2.29
136 143 2.445525 ACAGGCCCAAAGTCCTTCTTTA 59.554 45.455 0.00 0.00 43.57 1.85
160 167 8.424918 TCTGTCTTCTTCTGTTTAACTCTGATT 58.575 33.333 0.00 0.00 0.00 2.57
168 175 9.303116 AGATCTACTCTGTCTTCTTCTGTTTAA 57.697 33.333 0.00 0.00 31.12 1.52
188 196 6.683537 TCCCTTCTATCCAAAGACAGATCTA 58.316 40.000 0.00 0.00 33.57 1.98
268 276 7.296628 ACATTTACAAATACAAGGGCAAAGA 57.703 32.000 0.00 0.00 0.00 2.52
301 309 1.246056 TAGACCTTGTGACCGACCGG 61.246 60.000 6.94 6.94 42.03 5.28
322 330 7.039714 AGTGGAGGCGAAGAGATTTTTATTTTT 60.040 33.333 0.00 0.00 0.00 1.94
327 339 4.553330 AGTGGAGGCGAAGAGATTTTTA 57.447 40.909 0.00 0.00 0.00 1.52
333 345 0.747255 GCATAGTGGAGGCGAAGAGA 59.253 55.000 0.00 0.00 0.00 3.10
335 347 0.687757 AGGCATAGTGGAGGCGAAGA 60.688 55.000 0.00 0.00 34.98 2.87
370 382 1.888215 CAACTGTGCCTGAGTCATGT 58.112 50.000 0.00 0.00 0.00 3.21
498 565 5.398711 CGTACGCATTACTGGATTCTTCTAC 59.601 44.000 0.52 0.00 0.00 2.59
796 878 5.170748 CCATGGCAAGGAATTTTCTAACAC 58.829 41.667 1.66 0.00 0.00 3.32
874 956 2.715763 TAGCTTGGGTATAGAGGGGG 57.284 55.000 0.00 0.00 0.00 5.40
976 1063 3.135167 ACTTCCTGGTTCGGTGTCTAAAA 59.865 43.478 0.00 0.00 0.00 1.52
995 1089 1.679032 GCTTGGGCGTCTCCATTACTT 60.679 52.381 0.00 0.00 36.58 2.24
1473 1567 5.995282 CAGTTAGTATGGTTTCTGTCCAACA 59.005 40.000 0.00 0.00 38.52 3.33
1585 1714 2.952116 AGCCCCTCTAGCTAGTTACAG 58.048 52.381 20.10 10.08 39.29 2.74
1586 1715 4.743705 ATAGCCCCTCTAGCTAGTTACA 57.256 45.455 20.10 0.05 45.52 2.41
1587 1716 8.820153 TTATTATAGCCCCTCTAGCTAGTTAC 57.180 38.462 20.10 7.17 45.52 2.50
1606 1735 7.147983 TGCTTGTTACGGCATTCCTTTTATTAT 60.148 33.333 0.00 0.00 33.23 1.28
1607 1736 6.151312 TGCTTGTTACGGCATTCCTTTTATTA 59.849 34.615 0.00 0.00 33.23 0.98
1666 1807 5.067413 TGTTTCAAGGTACCGTAAAAATGCA 59.933 36.000 6.18 0.00 0.00 3.96
1752 1899 6.016527 TGTTGTAGTCTTGTAGAGTACCAGTG 60.017 42.308 15.49 0.00 45.91 3.66
1781 1928 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
1782 1929 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1783 1930 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1784 1931 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1785 1932 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1786 1933 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1787 1934 4.056050 CAATAAGTATTTCCGGACGGAGG 58.944 47.826 13.64 0.00 46.06 4.30
1788 1935 4.940463 TCAATAAGTATTTCCGGACGGAG 58.060 43.478 13.64 0.00 46.06 4.63
1789 1936 5.341872 TTCAATAAGTATTTCCGGACGGA 57.658 39.130 1.83 9.76 43.52 4.69
1790 1937 4.510340 CCTTCAATAAGTATTTCCGGACGG 59.490 45.833 1.83 3.96 0.00 4.79
1791 1938 5.353938 TCCTTCAATAAGTATTTCCGGACG 58.646 41.667 1.83 0.00 0.00 4.79
1792 1939 7.255139 CCATTCCTTCAATAAGTATTTCCGGAC 60.255 40.741 1.83 0.00 0.00 4.79
1793 1940 6.770785 CCATTCCTTCAATAAGTATTTCCGGA 59.229 38.462 0.00 0.00 0.00 5.14
1794 1941 6.770785 TCCATTCCTTCAATAAGTATTTCCGG 59.229 38.462 0.00 0.00 0.00 5.14
1795 1942 7.801716 TCCATTCCTTCAATAAGTATTTCCG 57.198 36.000 0.00 0.00 0.00 4.30
1796 1943 9.136323 ACATCCATTCCTTCAATAAGTATTTCC 57.864 33.333 0.00 0.00 0.00 3.13
1805 1952 8.523658 CGTCTAGATACATCCATTCCTTCAATA 58.476 37.037 0.00 0.00 0.00 1.90
1806 1953 7.015682 ACGTCTAGATACATCCATTCCTTCAAT 59.984 37.037 0.00 0.00 0.00 2.57
1807 1954 6.323996 ACGTCTAGATACATCCATTCCTTCAA 59.676 38.462 0.00 0.00 0.00 2.69
1808 1955 5.833667 ACGTCTAGATACATCCATTCCTTCA 59.166 40.000 0.00 0.00 0.00 3.02
1809 1956 6.334102 ACGTCTAGATACATCCATTCCTTC 57.666 41.667 0.00 0.00 0.00 3.46
1810 1957 8.423906 AATACGTCTAGATACATCCATTCCTT 57.576 34.615 0.00 0.00 0.00 3.36
1811 1958 8.423906 AAATACGTCTAGATACATCCATTCCT 57.576 34.615 0.00 0.00 0.00 3.36
1838 1985 9.851686 TGCATAAAAATGGATGTATCTAGAACT 57.148 29.630 0.00 0.00 0.00 3.01
1845 1992 9.415544 GGAGAAATGCATAAAAATGGATGTATC 57.584 33.333 0.00 0.00 32.82 2.24
1846 1993 8.084073 CGGAGAAATGCATAAAAATGGATGTAT 58.916 33.333 0.00 0.00 32.82 2.29
1847 1994 7.284261 TCGGAGAAATGCATAAAAATGGATGTA 59.716 33.333 0.00 0.00 32.82 2.29
1848 1995 6.096705 TCGGAGAAATGCATAAAAATGGATGT 59.903 34.615 0.00 0.00 32.82 3.06
1849 1996 6.418819 GTCGGAGAAATGCATAAAAATGGATG 59.581 38.462 0.00 0.00 39.69 3.51
1850 1997 6.096705 TGTCGGAGAAATGCATAAAAATGGAT 59.903 34.615 0.00 0.00 39.69 3.41
1851 1998 5.417266 TGTCGGAGAAATGCATAAAAATGGA 59.583 36.000 0.00 0.00 39.69 3.41
1852 1999 5.649557 TGTCGGAGAAATGCATAAAAATGG 58.350 37.500 0.00 0.00 39.69 3.16
1853 2000 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
1854 2001 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
1855 2002 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
1856 2003 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
1857 2004 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
1858 2005 7.201696 GGAAATACTTGTCGGAGAAATGCATAA 60.202 37.037 0.00 0.00 39.69 1.90
1859 2006 6.260050 GGAAATACTTGTCGGAGAAATGCATA 59.740 38.462 0.00 0.00 39.69 3.14
1860 2007 5.066505 GGAAATACTTGTCGGAGAAATGCAT 59.933 40.000 0.00 0.00 39.69 3.96
1861 2008 4.394920 GGAAATACTTGTCGGAGAAATGCA 59.605 41.667 0.00 0.00 39.69 3.96
1862 2009 4.494199 CGGAAATACTTGTCGGAGAAATGC 60.494 45.833 0.00 0.00 39.69 3.56
1863 2010 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
1864 2011 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
1865 2012 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
1866 2013 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
1867 2014 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
1868 2015 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
1869 2016 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
1870 2017 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
1871 2018 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1872 2019 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1873 2020 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1874 2021 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1875 2022 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1876 2023 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1877 2024 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1878 2025 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1879 2026 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1880 2027 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
1881 2028 0.251742 TTTACTCCCTCCGTCCGGAA 60.252 55.000 5.23 0.00 44.66 4.30
1882 2029 0.032813 ATTTACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
1883 2030 1.612463 CTATTTACTCCCTCCGTCCGG 59.388 57.143 0.00 0.00 0.00 5.14
1884 2031 1.612463 CCTATTTACTCCCTCCGTCCG 59.388 57.143 0.00 0.00 0.00 4.79
1885 2032 2.892215 CTCCTATTTACTCCCTCCGTCC 59.108 54.545 0.00 0.00 0.00 4.79
1886 2033 3.564264 ACTCCTATTTACTCCCTCCGTC 58.436 50.000 0.00 0.00 0.00 4.79
1887 2034 3.684408 ACTCCTATTTACTCCCTCCGT 57.316 47.619 0.00 0.00 0.00 4.69
1888 2035 9.287373 GATATATACTCCTATTTACTCCCTCCG 57.713 40.741 0.00 0.00 0.00 4.63
1891 2038 9.939424 GGTGATATATACTCCTATTTACTCCCT 57.061 37.037 0.00 0.00 0.00 4.20
1892 2039 9.939424 AGGTGATATATACTCCTATTTACTCCC 57.061 37.037 0.00 0.00 30.86 4.30
2126 2284 0.969894 AATCCCCGCTCGATTAGAGG 59.030 55.000 0.00 0.00 46.91 3.69
2152 2310 4.639135 AGTTCATGATCGATCGAGTTCA 57.361 40.909 23.84 21.91 0.00 3.18
2234 2392 3.372440 AGGAGGGCAATTTAGTCCTTG 57.628 47.619 0.00 0.00 45.46 3.61
2264 2424 8.040132 TGGGCAAAATTACCAATGAAATCTAAG 58.960 33.333 0.00 0.00 0.00 2.18
2379 2539 1.296392 CTTGAGCCGGTGGATGTGA 59.704 57.895 1.90 0.00 0.00 3.58
2390 2550 2.887152 ACATGTTGTTTCTCCTTGAGCC 59.113 45.455 0.00 0.00 0.00 4.70
2397 2557 4.759693 TGTGTATCCACATGTTGTTTCTCC 59.240 41.667 0.00 0.00 46.45 3.71
2416 2577 3.679980 CGATTTCCTCGTTGATCTTGTGT 59.320 43.478 0.00 0.00 42.56 3.72


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

AutoCloner maintained by Alex Coulton.