Multiple sequence alignment - TraesCS3D01G148800

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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 TraesCS3D01G148800 chr3D 100.000 2288 0 0 1 2288 113913357 113911070 0.000000e+00 4226.0
1 TraesCS3D01G148800 chr3D 90.668 1736 118 27 1 1704 449746626 449748349 0.000000e+00 2268.0
2 TraesCS3D01G148800 chr3D 90.111 1264 82 19 477 1705 6288084 6289339 0.000000e+00 1602.0
3 TraesCS3D01G148800 chr7D 92.361 1728 108 11 1 1707 533932802 533934526 0.000000e+00 2438.0
4 TraesCS3D01G148800 chr7D 90.558 1737 126 19 1 1705 463975835 463974105 0.000000e+00 2265.0
5 TraesCS3D01G148800 chr7D 85.063 395 52 4 1896 2285 568770154 568770546 1.650000e-106 396.0
6 TraesCS3D01G148800 chr4D 91.889 1726 114 13 1 1706 414225593 414227312 0.000000e+00 2388.0
7 TraesCS3D01G148800 chr4D 90.893 1735 120 16 1 1706 493971114 493969389 0.000000e+00 2294.0
8 TraesCS3D01G148800 chr4D 90.867 1730 125 13 1 1705 116524562 116522841 0.000000e+00 2289.0
9 TraesCS3D01G148800 chr4D 90.214 1727 129 17 1 1700 48683933 48682220 0.000000e+00 2217.0
10 TraesCS3D01G148800 chr4D 91.064 996 46 8 734 1705 508925407 508926383 0.000000e+00 1306.0
11 TraesCS3D01G148800 chr3A 91.503 1730 120 11 1 1705 418765665 418763938 0.000000e+00 2355.0
12 TraesCS3D01G148800 chr3A 89.062 64 5 1 1759 1822 109328095 109328034 6.780000e-11 78.7
13 TraesCS3D01G148800 chr6D 91.339 1732 117 15 1 1705 450905954 450907679 0.000000e+00 2337.0
14 TraesCS3D01G148800 chr6D 91.065 1634 110 15 1 1610 305745359 305746980 0.000000e+00 2176.0
15 TraesCS3D01G148800 chr7B 90.699 1731 123 20 1 1705 679357632 679359350 0.000000e+00 2270.0
16 TraesCS3D01G148800 chr7B 86.002 893 98 21 836 1712 62888713 62889594 0.000000e+00 931.0
17 TraesCS3D01G148800 chr2D 89.863 1746 112 28 1 1707 591013971 591015690 0.000000e+00 2183.0
18 TraesCS3D01G148800 chr2D 84.096 415 59 5 1874 2281 359233887 359234301 5.920000e-106 394.0
19 TraesCS3D01G148800 chr3B 89.776 1741 125 20 1 1710 478550958 478549240 0.000000e+00 2180.0
20 TraesCS3D01G148800 chr3B 85.714 581 60 10 1724 2288 167048445 167049018 1.960000e-165 592.0
21 TraesCS3D01G148800 chr3B 83.924 423 59 7 1863 2278 726626759 726627179 1.650000e-106 396.0
22 TraesCS3D01G148800 chr1A 89.236 1728 146 17 1 1700 387995196 387996911 0.000000e+00 2124.0
23 TraesCS3D01G148800 chr1B 89.043 1734 151 22 1 1708 623938741 623937021 0.000000e+00 2113.0
24 TraesCS3D01G148800 chr5D 88.818 1717 131 24 1 1700 460216223 460217895 0.000000e+00 2050.0
25 TraesCS3D01G148800 chr5D 89.950 1204 85 14 533 1705 369344087 369345285 0.000000e+00 1520.0
26 TraesCS3D01G148800 chr5D 83.964 449 63 7 1847 2287 506267767 506268214 2.720000e-114 422.0
27 TraesCS3D01G148800 chr5B 87.663 843 77 19 880 1705 565827973 565828805 0.000000e+00 955.0
28 TraesCS3D01G148800 chr7A 85.166 391 51 5 1903 2287 567677461 567677072 5.920000e-106 394.0
29 TraesCS3D01G148800 chr5A 83.645 428 53 15 1869 2287 575364052 575363633 9.910000e-104 387.0
30 TraesCS3D01G148800 chr2B 82.301 452 64 12 1847 2287 162882953 162882507 5.970000e-101 377.0
31 TraesCS3D01G148800 chr1D 82.301 452 64 12 1847 2286 217310110 217309663 5.970000e-101 377.0


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 TraesCS3D01G148800 chr3D 113911070 113913357 2287 True 4226 4226 100.000 1 2288 1 chr3D.!!$R1 2287
1 TraesCS3D01G148800 chr3D 449746626 449748349 1723 False 2268 2268 90.668 1 1704 1 chr3D.!!$F2 1703
2 TraesCS3D01G148800 chr3D 6288084 6289339 1255 False 1602 1602 90.111 477 1705 1 chr3D.!!$F1 1228
3 TraesCS3D01G148800 chr7D 533932802 533934526 1724 False 2438 2438 92.361 1 1707 1 chr7D.!!$F1 1706
4 TraesCS3D01G148800 chr7D 463974105 463975835 1730 True 2265 2265 90.558 1 1705 1 chr7D.!!$R1 1704
5 TraesCS3D01G148800 chr4D 414225593 414227312 1719 False 2388 2388 91.889 1 1706 1 chr4D.!!$F1 1705
6 TraesCS3D01G148800 chr4D 493969389 493971114 1725 True 2294 2294 90.893 1 1706 1 chr4D.!!$R3 1705
7 TraesCS3D01G148800 chr4D 116522841 116524562 1721 True 2289 2289 90.867 1 1705 1 chr4D.!!$R2 1704
8 TraesCS3D01G148800 chr4D 48682220 48683933 1713 True 2217 2217 90.214 1 1700 1 chr4D.!!$R1 1699
9 TraesCS3D01G148800 chr4D 508925407 508926383 976 False 1306 1306 91.064 734 1705 1 chr4D.!!$F2 971
10 TraesCS3D01G148800 chr3A 418763938 418765665 1727 True 2355 2355 91.503 1 1705 1 chr3A.!!$R2 1704
11 TraesCS3D01G148800 chr6D 450905954 450907679 1725 False 2337 2337 91.339 1 1705 1 chr6D.!!$F2 1704
12 TraesCS3D01G148800 chr6D 305745359 305746980 1621 False 2176 2176 91.065 1 1610 1 chr6D.!!$F1 1609
13 TraesCS3D01G148800 chr7B 679357632 679359350 1718 False 2270 2270 90.699 1 1705 1 chr7B.!!$F2 1704
14 TraesCS3D01G148800 chr7B 62888713 62889594 881 False 931 931 86.002 836 1712 1 chr7B.!!$F1 876
15 TraesCS3D01G148800 chr2D 591013971 591015690 1719 False 2183 2183 89.863 1 1707 1 chr2D.!!$F2 1706
16 TraesCS3D01G148800 chr3B 478549240 478550958 1718 True 2180 2180 89.776 1 1710 1 chr3B.!!$R1 1709
17 TraesCS3D01G148800 chr3B 167048445 167049018 573 False 592 592 85.714 1724 2288 1 chr3B.!!$F1 564
18 TraesCS3D01G148800 chr1A 387995196 387996911 1715 False 2124 2124 89.236 1 1700 1 chr1A.!!$F1 1699
19 TraesCS3D01G148800 chr1B 623937021 623938741 1720 True 2113 2113 89.043 1 1708 1 chr1B.!!$R1 1707
20 TraesCS3D01G148800 chr5D 460216223 460217895 1672 False 2050 2050 88.818 1 1700 1 chr5D.!!$F2 1699
21 TraesCS3D01G148800 chr5D 369344087 369345285 1198 False 1520 1520 89.950 533 1705 1 chr5D.!!$F1 1172
22 TraesCS3D01G148800 chr5B 565827973 565828805 832 False 955 955 87.663 880 1705 1 chr5B.!!$F1 825

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
237 250 0.456221 CACGACGGTCATTAGGAGCT 59.544 55.0 9.1 0.0 41.89 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2000 0.036732 GGGAGGCCGAATGCATATGA 59.963 55.0 6.97 0.0 43.89 2.15 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
149 162 1.597797 ATTGGCATCTGCACCGGTTG 61.598 55.000 2.97 0.27 44.36 3.77
153 166 1.237285 GCATCTGCACCGGTTGTTCT 61.237 55.000 2.97 0.00 41.59 3.01
237 250 0.456221 CACGACGGTCATTAGGAGCT 59.544 55.000 9.10 0.00 41.89 4.09
358 372 0.911769 TTCGCTGGGTCAGGAATCAT 59.088 50.000 0.00 0.00 31.21 2.45
387 402 3.052082 CTTGTGCAGTGGCCCTCG 61.052 66.667 0.00 0.00 40.13 4.63
503 519 2.294078 CCACCCGAGGAAGAAGGCT 61.294 63.158 0.00 0.00 0.00 4.58
544 561 3.056328 GGGTTGGCGTTGGAGCTC 61.056 66.667 4.71 4.71 37.29 4.09
613 631 1.945317 AGAGAGGGGGTGGGTAAGTAT 59.055 52.381 0.00 0.00 0.00 2.12
620 638 1.917568 GGGTGGGTAAGTATTGGTGGA 59.082 52.381 0.00 0.00 0.00 4.02
657 678 2.786495 GCGCGATGGAGAGGAGGAA 61.786 63.158 12.10 0.00 0.00 3.36
1026 1071 2.301346 CTGGACTTCACCAAGCACTTT 58.699 47.619 0.00 0.00 39.59 2.66
1296 1358 1.616628 CAAGGACTAGGGCTGGGGT 60.617 63.158 0.00 0.00 0.00 4.95
1325 1387 8.358582 TCCTTCCTAAGTACTTTCGAGTTTAT 57.641 34.615 14.49 0.00 0.00 1.40
1326 1388 8.465201 TCCTTCCTAAGTACTTTCGAGTTTATC 58.535 37.037 14.49 0.00 0.00 1.75
1467 1597 2.331166 TGGTAACCTCACCAACTAGCA 58.669 47.619 0.00 0.00 45.65 3.49
1554 1685 1.227234 GCAGGCAACCAAACACCAC 60.227 57.895 0.00 0.00 37.17 4.16
1610 1743 1.405391 GCAGGCAACCAAACAACTTGT 60.405 47.619 0.00 0.00 32.65 3.16
1712 1845 4.342092 GCAACCAAACATGCCCTATTCTAT 59.658 41.667 0.00 0.00 36.56 1.98
1713 1846 5.163416 GCAACCAAACATGCCCTATTCTATT 60.163 40.000 0.00 0.00 36.56 1.73
1714 1847 6.507023 CAACCAAACATGCCCTATTCTATTC 58.493 40.000 0.00 0.00 0.00 1.75
1715 1848 6.018433 ACCAAACATGCCCTATTCTATTCT 57.982 37.500 0.00 0.00 0.00 2.40
1716 1849 5.829924 ACCAAACATGCCCTATTCTATTCTG 59.170 40.000 0.00 0.00 0.00 3.02
1717 1850 5.278660 CCAAACATGCCCTATTCTATTCTGC 60.279 44.000 0.00 0.00 0.00 4.26
1718 1851 4.989875 ACATGCCCTATTCTATTCTGCT 57.010 40.909 0.00 0.00 0.00 4.24
1719 1852 4.904241 ACATGCCCTATTCTATTCTGCTC 58.096 43.478 0.00 0.00 0.00 4.26
1720 1853 4.596643 ACATGCCCTATTCTATTCTGCTCT 59.403 41.667 0.00 0.00 0.00 4.09
1721 1854 5.782331 ACATGCCCTATTCTATTCTGCTCTA 59.218 40.000 0.00 0.00 0.00 2.43
1722 1855 6.443206 ACATGCCCTATTCTATTCTGCTCTAT 59.557 38.462 0.00 0.00 0.00 1.98
1729 1862 7.882271 CCTATTCTATTCTGCTCTATTGCCTTT 59.118 37.037 0.00 0.00 0.00 3.11
1732 1865 2.315925 TCTGCTCTATTGCCTTTCCG 57.684 50.000 0.00 0.00 0.00 4.30
1752 1885 3.012722 GGAACACCGGGGGATCCA 61.013 66.667 19.86 0.00 34.36 3.41
1756 1889 1.933307 AACACCGGGGGATCCATTCC 61.933 60.000 15.23 10.78 44.62 3.01
1764 1897 0.035458 GGGATCCATTCCTAGCACCG 59.965 60.000 15.23 0.00 44.75 4.94
1799 1932 2.023673 ACTCCTCTCAATCAGCTCTCG 58.976 52.381 0.00 0.00 0.00 4.04
1802 1935 1.747924 CCTCTCAATCAGCTCTCGTGA 59.252 52.381 0.00 0.00 0.00 4.35
1808 1941 1.102154 ATCAGCTCTCGTGAGTCCTG 58.898 55.000 15.37 14.02 42.13 3.86
1811 1944 0.540830 AGCTCTCGTGAGTCCTGGTT 60.541 55.000 15.37 0.00 42.13 3.67
1812 1945 0.389166 GCTCTCGTGAGTCCTGGTTG 60.389 60.000 15.37 0.00 42.13 3.77
1837 1970 2.344521 AAAAACTTGCCCGCGGACAC 62.345 55.000 30.73 16.57 0.00 3.67
1838 1971 4.555709 AACTTGCCCGCGGACACA 62.556 61.111 30.73 19.27 0.00 3.72
1839 1972 4.988598 ACTTGCCCGCGGACACAG 62.989 66.667 30.73 22.26 0.00 3.66
1840 1973 4.988598 CTTGCCCGCGGACACAGT 62.989 66.667 30.73 0.00 0.00 3.55
1841 1974 4.555709 TTGCCCGCGGACACAGTT 62.556 61.111 30.73 0.00 0.00 3.16
1861 2000 0.527565 GCAGGCCATTCAACGATGTT 59.472 50.000 5.01 0.00 0.00 2.71
1863 2002 1.811965 CAGGCCATTCAACGATGTTCA 59.188 47.619 5.01 0.00 0.00 3.18
1882 2021 0.326264 ATATGCATTCGGCCTCCCTC 59.674 55.000 3.54 0.00 43.89 4.30
1889 2031 2.302587 TTCGGCCTCCCTCAATTTTT 57.697 45.000 0.00 0.00 0.00 1.94
1893 2035 2.159240 CGGCCTCCCTCAATTTTTAAGC 60.159 50.000 0.00 0.00 0.00 3.09
1896 2038 3.440127 CCTCCCTCAATTTTTAAGCCCA 58.560 45.455 0.00 0.00 0.00 5.36
1897 2039 3.195610 CCTCCCTCAATTTTTAAGCCCAC 59.804 47.826 0.00 0.00 0.00 4.61
1917 2059 5.106948 CCCACATGATCAAATAGTCGCATAC 60.107 44.000 0.00 0.00 0.00 2.39
1928 2070 7.862873 TCAAATAGTCGCATACATAGAGTTCAG 59.137 37.037 0.00 0.00 0.00 3.02
1930 2072 5.176407 AGTCGCATACATAGAGTTCAGAC 57.824 43.478 0.00 0.00 0.00 3.51
1935 2077 5.583495 GCATACATAGAGTTCAGACGTTCT 58.417 41.667 0.00 0.00 0.00 3.01
1950 2092 2.621998 ACGTTCTACTAGCCGCATACAT 59.378 45.455 0.00 0.00 0.00 2.29
1958 2100 2.991434 AGCCGCATACATAGAGTACG 57.009 50.000 0.00 0.00 35.05 3.67
1959 2101 1.540267 AGCCGCATACATAGAGTACGG 59.460 52.381 0.00 0.00 42.27 4.02
1960 2102 1.538512 GCCGCATACATAGAGTACGGA 59.461 52.381 2.23 0.00 42.07 4.69
1961 2103 2.163815 GCCGCATACATAGAGTACGGAT 59.836 50.000 2.23 0.00 42.07 4.18
1962 2104 3.759418 CCGCATACATAGAGTACGGATG 58.241 50.000 0.00 3.90 42.07 3.51
1973 2115 9.962783 ACATAGAGTACGGATGTTTAAATAGTC 57.037 33.333 4.96 0.00 29.46 2.59
2046 2188 2.585330 TGTTTTCCCCTTTAACCGTCC 58.415 47.619 0.00 0.00 0.00 4.79
2047 2189 1.536766 GTTTTCCCCTTTAACCGTCCG 59.463 52.381 0.00 0.00 0.00 4.79
2053 2195 1.137479 CCCTTTAACCGTCCGCTGATA 59.863 52.381 0.00 0.00 0.00 2.15
2066 2211 3.319405 TCCGCTGATACTCAAGATCTTCC 59.681 47.826 4.57 0.00 0.00 3.46
2068 2213 4.202202 CCGCTGATACTCAAGATCTTCCTT 60.202 45.833 4.57 0.00 0.00 3.36
2085 2230 1.738350 CCTTCAGCTGCTCATGAGTTG 59.262 52.381 23.38 16.59 0.00 3.16
2108 2253 1.847999 CGATGCCGAATTTGTTGATGC 59.152 47.619 0.00 0.00 38.22 3.91
2137 2282 1.247567 AACTCTTCAAATGTGGCCGG 58.752 50.000 0.00 0.00 0.00 6.13
2139 2284 1.004745 ACTCTTCAAATGTGGCCGGAT 59.995 47.619 5.05 0.00 0.00 4.18
2149 2294 1.612146 TGGCCGGATTCTGGTCTGA 60.612 57.895 16.88 0.00 30.50 3.27
2160 2305 6.183360 CGGATTCTGGTCTGAAAGTTTGATAC 60.183 42.308 0.00 0.00 33.76 2.24
2170 2315 6.535150 TCTGAAAGTTTGATACGATCATCCAC 59.465 38.462 0.00 0.00 35.37 4.02
2176 2321 4.649088 TGATACGATCATCCACGTTCTT 57.351 40.909 0.00 0.00 42.61 2.52
2193 2338 6.965500 CACGTTCTTAAATTCTAGAGCTACGA 59.035 38.462 14.37 0.00 0.00 3.43
2196 2341 7.484007 CGTTCTTAAATTCTAGAGCTACGACAA 59.516 37.037 0.00 0.00 0.00 3.18
2215 2360 3.310954 ACAACATCCTACCCTCATCCTCT 60.311 47.826 0.00 0.00 0.00 3.69
2216 2361 4.078571 ACAACATCCTACCCTCATCCTCTA 60.079 45.833 0.00 0.00 0.00 2.43
2217 2362 4.120946 ACATCCTACCCTCATCCTCTAC 57.879 50.000 0.00 0.00 0.00 2.59
2220 2365 2.106166 TCCTACCCTCATCCTCTACGAC 59.894 54.545 0.00 0.00 0.00 4.34
2227 2372 3.133003 CCTCATCCTCTACGACCATGTTT 59.867 47.826 0.00 0.00 0.00 2.83
2232 2377 2.066262 CTCTACGACCATGTTTTGCGT 58.934 47.619 0.00 0.00 38.81 5.24
2251 2396 3.370672 GCGTGATCACACAACATGTCATA 59.629 43.478 24.93 0.00 46.20 2.15
2253 2398 5.315982 CGTGATCACACAACATGTCATAAC 58.684 41.667 24.93 0.00 46.20 1.89
2257 2403 3.153130 CACACAACATGTCATAACCCCA 58.847 45.455 0.00 0.00 40.64 4.96
2258 2404 3.571828 CACACAACATGTCATAACCCCAA 59.428 43.478 0.00 0.00 40.64 4.12
2267 2413 3.244770 TGTCATAACCCCAACAAGGTCTC 60.245 47.826 0.00 0.00 36.27 3.36
2268 2414 3.009143 GTCATAACCCCAACAAGGTCTCT 59.991 47.826 0.00 0.00 36.27 3.10
2281 2427 3.641434 AGGTCTCTGAATCCCATTGTG 57.359 47.619 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 202 1.496060 ACTGGGAGACGGCAATCATA 58.504 50.000 0.00 0.00 0.00 2.15
237 250 4.897076 TGGTCCAAGTACAAGAACTACTGA 59.103 41.667 0.00 0.00 0.00 3.41
295 308 0.251698 TTGCTGGGCCATGAATCACA 60.252 50.000 6.72 0.00 0.00 3.58
296 309 0.896923 TTTGCTGGGCCATGAATCAC 59.103 50.000 6.72 0.00 0.00 3.06
358 372 0.389025 TGCACAAGAGCTGAAGACGA 59.611 50.000 0.00 0.00 34.99 4.20
387 402 1.669779 GGAATCTGATGCAGTGCTCAC 59.330 52.381 17.60 8.12 32.61 3.51
503 519 1.284785 CCTTGGGGTATTTGCTGGAGA 59.715 52.381 0.00 0.00 0.00 3.71
550 567 1.664017 CTCCATCGCCATGAGCTCG 60.664 63.158 9.64 0.00 40.39 5.03
613 631 1.809133 TTACTCACCCTGTCCACCAA 58.191 50.000 0.00 0.00 0.00 3.67
620 638 3.244112 GCGCCTATATTTACTCACCCTGT 60.244 47.826 0.00 0.00 0.00 4.00
679 704 5.118990 TGGCTTATTGAAGAGCATGTAGTC 58.881 41.667 5.83 0.00 40.63 2.59
784 809 0.459489 GCTTGCCCTTGTTGTCAACA 59.541 50.000 14.48 14.48 40.21 3.33
849 886 1.740664 GGCGTCTTCGGTTCTTCCC 60.741 63.158 0.00 0.00 37.56 3.97
928 972 2.682594 CCATCCTCCTCATGGTAGTGA 58.317 52.381 0.00 0.00 36.74 3.41
1055 1100 1.598130 GAGCAGCCGGTGTTGTTCT 60.598 57.895 1.90 0.00 31.70 3.01
1140 1185 2.315925 TCTTGATCTGATGAACGGCC 57.684 50.000 0.00 0.00 0.00 6.13
1296 1358 5.819991 TCGAAAGTACTTAGGAAGGAGGTA 58.180 41.667 8.92 0.00 0.00 3.08
1325 1387 4.446385 CGATAGTTCAAACAGTTCAACGGA 59.554 41.667 0.00 0.00 0.00 4.69
1326 1388 4.698276 CGATAGTTCAAACAGTTCAACGG 58.302 43.478 0.00 0.00 0.00 4.44
1467 1597 3.551846 CTGGTGTGTGGTAACCTCTTTT 58.448 45.455 0.00 0.00 37.36 2.27
1554 1685 1.836391 TGGGGAGAACCACACTGTG 59.164 57.895 6.19 6.19 45.65 3.66
1610 1743 2.646930 CAGCCTCAAATGCACCATCTA 58.353 47.619 0.00 0.00 0.00 1.98
1644 1777 3.471680 CATAGCCTTCTCAACTTAGCCC 58.528 50.000 0.00 0.00 0.00 5.19
1712 1845 2.632377 CGGAAAGGCAATAGAGCAGAA 58.368 47.619 0.00 0.00 35.83 3.02
1713 1846 1.134401 CCGGAAAGGCAATAGAGCAGA 60.134 52.381 0.00 0.00 35.83 4.26
1714 1847 1.134401 TCCGGAAAGGCAATAGAGCAG 60.134 52.381 0.00 0.00 40.77 4.24
1715 1848 0.908910 TCCGGAAAGGCAATAGAGCA 59.091 50.000 0.00 0.00 40.77 4.26
1716 1849 1.587547 CTCCGGAAAGGCAATAGAGC 58.412 55.000 5.23 0.00 40.77 4.09
1717 1850 1.762957 TCCTCCGGAAAGGCAATAGAG 59.237 52.381 5.23 0.00 40.77 2.43
1718 1851 1.874129 TCCTCCGGAAAGGCAATAGA 58.126 50.000 5.23 0.00 40.77 1.98
1719 1852 2.289565 GTTCCTCCGGAAAGGCAATAG 58.710 52.381 5.23 0.00 43.86 1.73
1720 1853 1.631388 TGTTCCTCCGGAAAGGCAATA 59.369 47.619 5.23 0.00 43.86 1.90
1721 1854 0.404040 TGTTCCTCCGGAAAGGCAAT 59.596 50.000 5.23 0.00 43.86 3.56
1722 1855 0.536460 GTGTTCCTCCGGAAAGGCAA 60.536 55.000 5.23 0.00 43.86 4.52
1732 1865 2.691252 ATCCCCCGGTGTTCCTCC 60.691 66.667 0.00 0.00 0.00 4.30
1756 1889 2.865343 ATAACTCGTTCCGGTGCTAG 57.135 50.000 0.00 0.00 0.00 3.42
1764 1897 6.628185 TGAGAGGAGTAAAATAACTCGTTCC 58.372 40.000 1.29 0.00 45.69 3.62
1774 1907 6.558488 AGAGCTGATTGAGAGGAGTAAAAT 57.442 37.500 0.00 0.00 0.00 1.82
1821 1954 4.555709 TGTGTCCGCGGGCAAGTT 62.556 61.111 37.31 0.00 0.00 2.66
1830 1963 4.030452 GCCTGCAACTGTGTCCGC 62.030 66.667 0.00 0.00 0.00 5.54
1837 1970 0.387622 CGTTGAATGGCCTGCAACTG 60.388 55.000 23.61 16.82 39.66 3.16
1838 1971 0.537143 TCGTTGAATGGCCTGCAACT 60.537 50.000 23.61 0.00 39.66 3.16
1839 1972 0.527565 ATCGTTGAATGGCCTGCAAC 59.472 50.000 19.40 19.40 38.73 4.17
1840 1973 0.527113 CATCGTTGAATGGCCTGCAA 59.473 50.000 3.32 2.55 0.00 4.08
1841 1974 0.608856 ACATCGTTGAATGGCCTGCA 60.609 50.000 3.32 0.00 0.00 4.41
1861 2000 0.036732 GGGAGGCCGAATGCATATGA 59.963 55.000 6.97 0.00 43.89 2.15
1863 2002 0.326264 GAGGGAGGCCGAATGCATAT 59.674 55.000 0.00 0.00 43.89 1.78
1882 2021 7.670009 TTTGATCATGTGGGCTTAAAAATTG 57.330 32.000 0.00 0.00 0.00 2.32
1889 2031 5.056480 CGACTATTTGATCATGTGGGCTTA 58.944 41.667 0.00 0.00 0.00 3.09
1893 2035 3.205338 TGCGACTATTTGATCATGTGGG 58.795 45.455 0.00 0.00 0.00 4.61
1896 2038 8.306761 TCTATGTATGCGACTATTTGATCATGT 58.693 33.333 0.00 0.00 0.00 3.21
1897 2039 8.693542 TCTATGTATGCGACTATTTGATCATG 57.306 34.615 0.00 0.00 0.00 3.07
1917 2059 6.423862 GCTAGTAGAACGTCTGAACTCTATG 58.576 44.000 0.00 0.00 0.00 2.23
1928 2070 2.032550 TGTATGCGGCTAGTAGAACGTC 59.967 50.000 13.78 8.46 0.00 4.34
1930 2072 2.768833 TGTATGCGGCTAGTAGAACG 57.231 50.000 0.00 5.86 0.00 3.95
1935 2077 4.628766 CGTACTCTATGTATGCGGCTAGTA 59.371 45.833 0.00 0.00 32.20 1.82
1950 2092 7.134815 GCGACTATTTAAACATCCGTACTCTA 58.865 38.462 0.00 0.00 0.00 2.43
1958 2100 5.168526 TGCATGCGACTATTTAAACATCC 57.831 39.130 14.09 0.00 0.00 3.51
1959 2101 8.070171 AGTATTGCATGCGACTATTTAAACATC 58.930 33.333 10.57 0.00 0.00 3.06
1960 2102 7.930217 AGTATTGCATGCGACTATTTAAACAT 58.070 30.769 10.57 0.00 0.00 2.71
1961 2103 7.315247 AGTATTGCATGCGACTATTTAAACA 57.685 32.000 10.57 0.00 0.00 2.83
1962 2104 9.878599 ATTAGTATTGCATGCGACTATTTAAAC 57.121 29.630 20.95 7.29 0.00 2.01
2012 2154 4.284746 GGGGAAAACAATGTTGGGATGTAA 59.715 41.667 0.00 0.00 0.00 2.41
2019 2161 5.060506 GGTTAAAGGGGAAAACAATGTTGG 58.939 41.667 0.00 0.00 0.00 3.77
2031 2173 1.914764 AGCGGACGGTTAAAGGGGA 60.915 57.895 0.00 0.00 0.00 4.81
2032 2174 1.743995 CAGCGGACGGTTAAAGGGG 60.744 63.158 0.00 0.00 0.00 4.79
2053 2195 3.619487 GCAGCTGAAGGAAGATCTTGAGT 60.619 47.826 20.43 0.00 31.96 3.41
2066 2211 1.738350 CCAACTCATGAGCAGCTGAAG 59.262 52.381 22.83 6.51 0.00 3.02
2068 2213 0.689055 ACCAACTCATGAGCAGCTGA 59.311 50.000 22.83 0.00 0.00 4.26
2085 2230 1.466950 TCAACAAATTCGGCATCGACC 59.533 47.619 0.00 0.00 45.92 4.79
2137 2282 6.590292 TCGTATCAAACTTTCAGACCAGAATC 59.410 38.462 0.00 0.00 0.00 2.52
2139 2284 5.849510 TCGTATCAAACTTTCAGACCAGAA 58.150 37.500 0.00 0.00 0.00 3.02
2149 2294 5.175859 ACGTGGATGATCGTATCAAACTTT 58.824 37.500 0.00 0.00 43.50 2.66
2160 2305 6.589830 AGAATTTAAGAACGTGGATGATCG 57.410 37.500 0.00 0.00 0.00 3.69
2170 2315 6.965500 TGTCGTAGCTCTAGAATTTAAGAACG 59.035 38.462 0.00 0.00 0.00 3.95
2176 2321 7.068348 AGGATGTTGTCGTAGCTCTAGAATTTA 59.932 37.037 0.00 0.00 0.00 1.40
2193 2338 3.041946 GAGGATGAGGGTAGGATGTTGT 58.958 50.000 0.00 0.00 0.00 3.32
2196 2341 3.498841 CGTAGAGGATGAGGGTAGGATGT 60.499 52.174 0.00 0.00 0.00 3.06
2215 2360 1.867166 TCACGCAAAACATGGTCGTA 58.133 45.000 0.00 0.00 0.00 3.43
2216 2361 1.196808 GATCACGCAAAACATGGTCGT 59.803 47.619 0.00 0.00 0.00 4.34
2217 2362 1.196581 TGATCACGCAAAACATGGTCG 59.803 47.619 0.00 0.00 0.00 4.79
2220 2365 2.318578 GTGTGATCACGCAAAACATGG 58.681 47.619 29.82 0.00 41.22 3.66
2232 2377 4.699735 GGGTTATGACATGTTGTGTGATCA 59.300 41.667 0.00 0.00 42.36 2.92
2251 2396 1.518367 TCAGAGACCTTGTTGGGGTT 58.482 50.000 0.00 0.00 41.11 4.11
2253 2398 2.619074 GGATTCAGAGACCTTGTTGGGG 60.619 54.545 0.00 0.00 41.11 4.96
2257 2403 4.202609 ACAATGGGATTCAGAGACCTTGTT 60.203 41.667 0.00 0.00 0.00 2.83
2258 2404 3.331889 ACAATGGGATTCAGAGACCTTGT 59.668 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.