Multiple sequence alignment - TraesCS6A01G323500

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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 TraesCS6A01G323500 chr6A 100.000 2138 0 0 445 2582 556909614 556911751 0.000000e+00 3949.0
1 TraesCS6A01G323500 chr6A 100.000 69 0 0 1 69 556909170 556909238 7.500000e-26 128.0
2 TraesCS6A01G323500 chr6B 93.755 1361 63 10 445 1785 619860731 619862089 0.000000e+00 2023.0
3 TraesCS6A01G323500 chr6B 85.092 436 55 6 2042 2475 619862112 619862539 1.100000e-118 436.0
4 TraesCS6A01G323500 chr6B 100.000 29 0 0 2522 2550 619862712 619862740 1.000000e-03 54.7
5 TraesCS6A01G323500 chr6D 91.137 1275 57 14 568 1813 411925103 411926350 0.000000e+00 1677.0
6 TraesCS6A01G323500 chr6D 89.914 347 32 3 2042 2386 411926594 411926939 6.560000e-121 444.0
7 TraesCS6A01G323500 chr6D 87.500 216 16 5 2368 2582 411927044 411927249 3.320000e-59 239.0
8 TraesCS6A01G323500 chr6D 91.139 79 6 1 492 570 411923918 411923995 3.510000e-19 106.0
9 TraesCS6A01G323500 chr6D 100.000 28 0 0 1836 1863 470768182 470768155 5.000000e-03 52.8
10 TraesCS6A01G323500 chr7B 82.927 164 23 3 1883 2043 517101281 517101120 2.680000e-30 143.0
11 TraesCS6A01G323500 chr1B 84.252 127 13 6 1913 2034 4889326 4889450 1.620000e-22 117.0
12 TraesCS6A01G323500 chr2D 81.818 143 18 6 1897 2033 390365384 390365524 2.100000e-21 113.0
13 TraesCS6A01G323500 chr7D 89.286 56 6 0 1988 2043 588621188 588621133 1.280000e-08 71.3
14 TraesCS6A01G323500 chr7A 90.476 42 4 0 2002 2043 578994254 578994295 3.590000e-04 56.5
15 TraesCS6A01G323500 chr2B 92.308 39 3 0 2005 2043 708985432 708985394 3.590000e-04 56.5
16 TraesCS6A01G323500 chr5D 100.000 29 0 0 1836 1864 104604933 104604905 1.000000e-03 54.7
17 TraesCS6A01G323500 chrUn 100.000 28 0 0 1838 1865 441690315 441690342 5.000000e-03 52.8
18 TraesCS6A01G323500 chr5B 100.000 28 0 0 1836 1863 694151154 694151181 5.000000e-03 52.8


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 TraesCS6A01G323500 chr6A 556909170 556911751 2581 False 2038.5 3949 100.0000 1 2582 2 chr6A.!!$F1 2581
1 TraesCS6A01G323500 chr6B 619860731 619862740 2009 False 837.9 2023 92.9490 445 2550 3 chr6B.!!$F1 2105
2 TraesCS6A01G323500 chr6D 411923918 411927249 3331 False 616.5 1677 89.9225 492 2582 4 chr6D.!!$F1 2090

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
62 63 0.250513 CCCGAAGAAGGAGACCAAGG 59.749 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3145 1.416401 ACATAGGCGAATCCGTTGGAT 59.584 47.619 0.0 0.0 45.46 3.41 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
39 40 3.827898 CCTCCGAGCTCCACCGAC 61.828 72.222 8.47 0.00 0.00 4.79
40 41 4.180946 CTCCGAGCTCCACCGACG 62.181 72.222 8.47 0.00 0.00 5.12
41 42 4.710167 TCCGAGCTCCACCGACGA 62.710 66.667 8.47 0.00 0.00 4.20
42 43 4.180946 CCGAGCTCCACCGACGAG 62.181 72.222 8.47 0.00 0.00 4.18
49 50 4.796231 CCACCGACGAGCCCGAAG 62.796 72.222 0.00 0.00 39.50 3.79
50 51 3.744719 CACCGACGAGCCCGAAGA 61.745 66.667 0.00 0.00 39.50 2.87
51 52 2.987547 ACCGACGAGCCCGAAGAA 60.988 61.111 0.00 0.00 39.50 2.52
52 53 2.202623 CCGACGAGCCCGAAGAAG 60.203 66.667 0.00 0.00 39.50 2.85
53 54 2.202623 CGACGAGCCCGAAGAAGG 60.203 66.667 0.00 0.00 39.50 3.46
54 55 2.697761 CGACGAGCCCGAAGAAGGA 61.698 63.158 0.00 0.00 39.50 3.36
55 56 1.139947 GACGAGCCCGAAGAAGGAG 59.860 63.158 0.00 0.00 39.50 3.69
56 57 1.304217 ACGAGCCCGAAGAAGGAGA 60.304 57.895 0.00 0.00 39.50 3.71
57 58 1.139947 CGAGCCCGAAGAAGGAGAC 59.860 63.158 0.00 0.00 38.22 3.36
58 59 1.518302 GAGCCCGAAGAAGGAGACC 59.482 63.158 0.00 0.00 0.00 3.85
59 60 1.229209 AGCCCGAAGAAGGAGACCA 60.229 57.895 0.00 0.00 0.00 4.02
60 61 0.836400 AGCCCGAAGAAGGAGACCAA 60.836 55.000 0.00 0.00 0.00 3.67
61 62 0.391793 GCCCGAAGAAGGAGACCAAG 60.392 60.000 0.00 0.00 0.00 3.61
62 63 0.250513 CCCGAAGAAGGAGACCAAGG 59.749 60.000 0.00 0.00 0.00 3.61
63 64 0.391793 CCGAAGAAGGAGACCAAGGC 60.392 60.000 0.00 0.00 0.00 4.35
64 65 0.737715 CGAAGAAGGAGACCAAGGCG 60.738 60.000 0.00 0.00 0.00 5.52
65 66 0.391793 GAAGAAGGAGACCAAGGCGG 60.392 60.000 0.00 0.00 42.50 6.13
66 67 2.436824 GAAGGAGACCAAGGCGGC 60.437 66.667 0.00 0.00 39.03 6.53
67 68 3.978571 GAAGGAGACCAAGGCGGCC 62.979 68.421 12.11 12.11 39.03 6.13
480 482 4.403113 TCACATACACAATAAGCTACGGGA 59.597 41.667 0.00 0.00 0.00 5.14
485 487 2.943033 CACAATAAGCTACGGGAAAGGG 59.057 50.000 0.00 0.00 0.00 3.95
487 489 3.203716 CAATAAGCTACGGGAAAGGGTC 58.796 50.000 0.00 0.00 0.00 4.46
526 528 8.685427 TCTTTGATGAGTCATTTTCTTTGTCAA 58.315 29.630 7.16 1.59 33.56 3.18
548 550 1.180029 GTGCTTCTGGGTGCATGAAT 58.820 50.000 0.00 0.00 41.45 2.57
727 1841 5.047377 GCTTTGAAATTTCCACTATCCCACA 60.047 40.000 15.48 0.00 0.00 4.17
734 1848 8.837099 AAATTTCCACTATCCCACATAATTCA 57.163 30.769 0.00 0.00 0.00 2.57
735 1849 9.438163 AAATTTCCACTATCCCACATAATTCAT 57.562 29.630 0.00 0.00 0.00 2.57
771 1885 7.336176 TCCTACAATCACTAGTATAGCATACGG 59.664 40.741 0.00 0.00 44.39 4.02
819 1956 4.545823 TTCGAAATGACACTTGTGGTTC 57.454 40.909 0.00 3.12 0.00 3.62
1032 2179 3.322466 CTCCCTTCCCGTGCCACT 61.322 66.667 0.00 0.00 0.00 4.00
1158 2305 4.595538 ACGACGTCGGCAGCCAAA 62.596 61.111 37.89 0.00 44.95 3.28
1254 2401 1.869774 TGAGGCGTGATATGATGTGC 58.130 50.000 0.00 0.00 0.00 4.57
1489 2636 2.434185 GGAACGCGCTGTCCATGA 60.434 61.111 18.44 0.00 0.00 3.07
1505 2652 1.838073 ATGACCAGGGGTTCGTCCAC 61.838 60.000 0.00 0.00 40.64 4.02
1739 2894 6.464222 TCTTTTCCTGTCATTTCTGTATCGT 58.536 36.000 0.00 0.00 0.00 3.73
1768 2923 8.830580 CCTGTGAATATAGTCACCATACTTTTG 58.169 37.037 25.79 8.37 46.13 2.44
1788 2943 7.435784 ACTTTTGTTTTTCTTACAACGTTGTGT 59.564 29.630 37.43 21.13 42.31 3.72
1823 3153 2.080286 ACGAGAGTGAAATCCAACGG 57.920 50.000 0.00 0.00 46.97 4.44
1847 3177 2.175069 TCGCCTATGTTCTACTCCCTCT 59.825 50.000 0.00 0.00 0.00 3.69
1850 3180 3.707102 GCCTATGTTCTACTCCCTCTGTT 59.293 47.826 0.00 0.00 0.00 3.16
1851 3181 4.162509 GCCTATGTTCTACTCCCTCTGTTT 59.837 45.833 0.00 0.00 0.00 2.83
1858 3188 7.741785 TGTTCTACTCCCTCTGTTTCAAAATA 58.258 34.615 0.00 0.00 0.00 1.40
1859 3189 8.383175 TGTTCTACTCCCTCTGTTTCAAAATAT 58.617 33.333 0.00 0.00 0.00 1.28
1864 3194 8.794335 ACTCCCTCTGTTTCAAAATATAAGAC 57.206 34.615 0.00 0.00 0.00 3.01
1908 3238 9.853177 ATTACTCCCTCTATTTCCAAATACAAG 57.147 33.333 0.00 0.00 0.00 3.16
1909 3239 7.510675 ACTCCCTCTATTTCCAAATACAAGA 57.489 36.000 0.00 0.00 0.00 3.02
1910 3240 7.339482 ACTCCCTCTATTTCCAAATACAAGAC 58.661 38.462 0.00 0.00 0.00 3.01
1911 3241 6.659824 TCCCTCTATTTCCAAATACAAGACC 58.340 40.000 0.00 0.00 0.00 3.85
1912 3242 6.447084 TCCCTCTATTTCCAAATACAAGACCT 59.553 38.462 0.00 0.00 0.00 3.85
1913 3243 7.036863 TCCCTCTATTTCCAAATACAAGACCTT 60.037 37.037 0.00 0.00 0.00 3.50
1914 3244 7.615757 CCCTCTATTTCCAAATACAAGACCTTT 59.384 37.037 0.00 0.00 0.00 3.11
1915 3245 9.025041 CCTCTATTTCCAAATACAAGACCTTTT 57.975 33.333 0.00 0.00 0.00 2.27
1919 3249 8.950007 ATTTCCAAATACAAGACCTTTTAGGA 57.050 30.769 0.00 0.00 37.67 2.94
1920 3250 8.950007 TTTCCAAATACAAGACCTTTTAGGAT 57.050 30.769 0.00 0.00 37.67 3.24
1921 3251 8.950007 TTCCAAATACAAGACCTTTTAGGATT 57.050 30.769 0.00 0.00 37.67 3.01
1922 3252 8.575649 TCCAAATACAAGACCTTTTAGGATTC 57.424 34.615 0.00 0.00 37.67 2.52
1923 3253 7.614192 TCCAAATACAAGACCTTTTAGGATTCC 59.386 37.037 0.00 0.00 37.67 3.01
1924 3254 7.396055 CCAAATACAAGACCTTTTAGGATTCCA 59.604 37.037 5.29 0.00 37.67 3.53
1925 3255 7.939784 AATACAAGACCTTTTAGGATTCCAC 57.060 36.000 5.29 0.00 37.67 4.02
1926 3256 5.319043 ACAAGACCTTTTAGGATTCCACA 57.681 39.130 5.29 0.00 37.67 4.17
1927 3257 5.701224 ACAAGACCTTTTAGGATTCCACAA 58.299 37.500 5.29 0.00 37.67 3.33
1928 3258 6.314917 ACAAGACCTTTTAGGATTCCACAAT 58.685 36.000 5.29 0.00 37.67 2.71
1929 3259 7.466804 ACAAGACCTTTTAGGATTCCACAATA 58.533 34.615 5.29 0.00 37.67 1.90
1930 3260 7.611855 ACAAGACCTTTTAGGATTCCACAATAG 59.388 37.037 5.29 3.53 37.67 1.73
1931 3261 7.510675 AGACCTTTTAGGATTCCACAATAGA 57.489 36.000 5.29 0.00 37.67 1.98
1932 3262 7.339482 AGACCTTTTAGGATTCCACAATAGAC 58.661 38.462 5.29 2.51 37.67 2.59
1933 3263 7.182930 AGACCTTTTAGGATTCCACAATAGACT 59.817 37.037 5.29 4.31 37.67 3.24
1934 3264 8.388656 ACCTTTTAGGATTCCACAATAGACTA 57.611 34.615 5.29 0.00 37.67 2.59
1935 3265 9.004231 ACCTTTTAGGATTCCACAATAGACTAT 57.996 33.333 5.29 0.00 37.67 2.12
1940 3270 9.892444 TTAGGATTCCACAATAGACTATAAGGA 57.108 33.333 5.29 1.39 0.00 3.36
1941 3271 8.429237 AGGATTCCACAATAGACTATAAGGAG 57.571 38.462 5.29 0.00 0.00 3.69
1942 3272 7.038658 AGGATTCCACAATAGACTATAAGGAGC 60.039 40.741 5.29 1.39 0.00 4.70
1943 3273 7.038658 GGATTCCACAATAGACTATAAGGAGCT 60.039 40.741 0.00 0.00 0.00 4.09
1944 3274 8.958060 ATTCCACAATAGACTATAAGGAGCTA 57.042 34.615 0.00 0.00 0.00 3.32
1945 3275 8.777578 TTCCACAATAGACTATAAGGAGCTAA 57.222 34.615 0.00 0.00 0.00 3.09
1946 3276 8.777578 TCCACAATAGACTATAAGGAGCTAAA 57.222 34.615 0.00 0.00 0.00 1.85
1947 3277 9.381038 TCCACAATAGACTATAAGGAGCTAAAT 57.619 33.333 0.00 0.00 0.00 1.40
1948 3278 9.429359 CCACAATAGACTATAAGGAGCTAAATG 57.571 37.037 0.00 0.00 0.00 2.32
1953 3283 9.815306 ATAGACTATAAGGAGCTAAATGAGTGA 57.185 33.333 0.00 0.00 0.00 3.41
1954 3284 8.540507 AGACTATAAGGAGCTAAATGAGTGAA 57.459 34.615 0.00 0.00 0.00 3.18
1955 3285 9.153479 AGACTATAAGGAGCTAAATGAGTGAAT 57.847 33.333 0.00 0.00 0.00 2.57
1960 3290 9.862371 ATAAGGAGCTAAATGAGTGAATATACG 57.138 33.333 0.00 0.00 0.00 3.06
1961 3291 6.159988 AGGAGCTAAATGAGTGAATATACGC 58.840 40.000 0.00 0.00 0.00 4.42
1962 3292 6.015010 AGGAGCTAAATGAGTGAATATACGCT 60.015 38.462 0.00 0.00 0.00 5.07
1963 3293 6.309251 GGAGCTAAATGAGTGAATATACGCTC 59.691 42.308 0.00 0.00 44.55 5.03
1964 3294 6.987386 AGCTAAATGAGTGAATATACGCTCT 58.013 36.000 0.00 0.00 44.58 4.09
1965 3295 8.112016 AGCTAAATGAGTGAATATACGCTCTA 57.888 34.615 0.00 0.00 44.58 2.43
1966 3296 8.577296 AGCTAAATGAGTGAATATACGCTCTAA 58.423 33.333 0.00 0.00 44.58 2.10
1967 3297 8.640291 GCTAAATGAGTGAATATACGCTCTAAC 58.360 37.037 0.00 0.00 44.58 2.34
1968 3298 9.678941 CTAAATGAGTGAATATACGCTCTAACA 57.321 33.333 0.00 0.00 44.58 2.41
1972 3302 9.794685 ATGAGTGAATATACGCTCTAACATATG 57.205 33.333 0.00 0.00 44.58 1.78
1973 3303 8.793592 TGAGTGAATATACGCTCTAACATATGT 58.206 33.333 1.41 1.41 44.58 2.29
1974 3304 9.279904 GAGTGAATATACGCTCTAACATATGTC 57.720 37.037 9.23 0.00 42.10 3.06
1975 3305 9.015367 AGTGAATATACGCTCTAACATATGTCT 57.985 33.333 9.23 2.50 0.00 3.41
2057 3387 7.921214 ACGGATGTAGTATTTGACAATCTGTAG 59.079 37.037 0.00 0.00 34.76 2.74
2058 3388 8.135529 CGGATGTAGTATTTGACAATCTGTAGA 58.864 37.037 0.00 0.00 0.00 2.59
2080 3410 6.334202 AGAATGAACCGATTCTAACACTCTC 58.666 40.000 0.00 0.00 40.27 3.20
2137 3467 2.373169 TCAGTTTCTGTTCTCTGCCCAT 59.627 45.455 0.00 0.00 32.61 4.00
2142 3472 1.555075 TCTGTTCTCTGCCCATACACC 59.445 52.381 0.00 0.00 0.00 4.16
2151 3481 3.118038 TCTGCCCATACACCAAGGTATTC 60.118 47.826 0.00 0.00 31.75 1.75
2188 3518 5.243060 TCAGTTTCGACAGAATCAGTTAGGA 59.757 40.000 0.00 0.00 36.09 2.94
2219 3549 1.165907 TGGCAAAGCTGGTTCGACAG 61.166 55.000 0.00 0.00 41.41 3.51
2230 3560 2.028839 TGGTTCGACAGAATCCGCTTTA 60.029 45.455 0.00 0.00 36.67 1.85
2249 3579 1.301165 GCGTTGAAGTACACCGGGT 60.301 57.895 6.32 3.22 35.04 5.28
2266 3596 1.626654 GGTCGTGCGTCAGTCCAATG 61.627 60.000 0.00 0.00 0.00 2.82
2299 3630 2.094675 CCCGAATCAGATTTTGGCTGT 58.905 47.619 9.05 0.00 34.98 4.40
2350 3681 3.769739 TCAGCCTTCTCAAAGCTGTAA 57.230 42.857 10.68 0.00 37.63 2.41
2395 3850 2.093181 CACCCCCTAACATTGACGATGA 60.093 50.000 9.78 0.00 39.15 2.92
2402 3857 5.815222 CCCTAACATTGACGATGACATTGTA 59.185 40.000 8.36 0.00 39.15 2.41
2573 4164 4.465632 TTCTAAAGTGCAGCGGATAGAA 57.534 40.909 0.00 5.94 0.00 2.10
2575 4166 3.699538 TCTAAAGTGCAGCGGATAGAAGA 59.300 43.478 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.827898 GTCGGTGGAGCTCGGAGG 61.828 72.222 7.83 0.00 0.00 4.30
23 24 4.180946 CGTCGGTGGAGCTCGGAG 62.181 72.222 7.83 0.00 0.00 4.63
24 25 4.710167 TCGTCGGTGGAGCTCGGA 62.710 66.667 7.83 0.00 0.00 4.55
25 26 4.180946 CTCGTCGGTGGAGCTCGG 62.181 72.222 7.83 0.00 0.00 4.63
32 33 4.796231 CTTCGGGCTCGTCGGTGG 62.796 72.222 5.57 0.00 37.69 4.61
33 34 3.277211 TTCTTCGGGCTCGTCGGTG 62.277 63.158 5.57 0.00 37.69 4.94
34 35 2.987547 TTCTTCGGGCTCGTCGGT 60.988 61.111 5.57 0.00 37.69 4.69
35 36 2.202623 CTTCTTCGGGCTCGTCGG 60.203 66.667 5.57 0.00 37.69 4.79
36 37 2.202623 CCTTCTTCGGGCTCGTCG 60.203 66.667 5.57 0.00 37.69 5.12
37 38 1.139947 CTCCTTCTTCGGGCTCGTC 59.860 63.158 5.57 0.00 37.69 4.20
38 39 1.304217 TCTCCTTCTTCGGGCTCGT 60.304 57.895 5.57 0.00 37.69 4.18
39 40 1.139947 GTCTCCTTCTTCGGGCTCG 59.860 63.158 0.00 0.00 37.82 5.03
40 41 1.258445 TGGTCTCCTTCTTCGGGCTC 61.258 60.000 0.00 0.00 0.00 4.70
41 42 0.836400 TTGGTCTCCTTCTTCGGGCT 60.836 55.000 0.00 0.00 0.00 5.19
42 43 0.391793 CTTGGTCTCCTTCTTCGGGC 60.392 60.000 0.00 0.00 0.00 6.13
43 44 0.250513 CCTTGGTCTCCTTCTTCGGG 59.749 60.000 0.00 0.00 0.00 5.14
44 45 0.391793 GCCTTGGTCTCCTTCTTCGG 60.392 60.000 0.00 0.00 0.00 4.30
45 46 0.737715 CGCCTTGGTCTCCTTCTTCG 60.738 60.000 0.00 0.00 0.00 3.79
46 47 0.391793 CCGCCTTGGTCTCCTTCTTC 60.392 60.000 0.00 0.00 0.00 2.87
47 48 1.679898 CCGCCTTGGTCTCCTTCTT 59.320 57.895 0.00 0.00 0.00 2.52
48 49 2.960688 GCCGCCTTGGTCTCCTTCT 61.961 63.158 0.00 0.00 41.21 2.85
49 50 2.436824 GCCGCCTTGGTCTCCTTC 60.437 66.667 0.00 0.00 41.21 3.46
50 51 4.035102 GGCCGCCTTGGTCTCCTT 62.035 66.667 0.71 0.00 40.15 3.36
444 445 5.192927 TGTGTATGTGAATTGAAGATCCCC 58.807 41.667 0.00 0.00 0.00 4.81
445 446 6.757897 TTGTGTATGTGAATTGAAGATCCC 57.242 37.500 0.00 0.00 0.00 3.85
446 447 9.941664 CTTATTGTGTATGTGAATTGAAGATCC 57.058 33.333 0.00 0.00 0.00 3.36
447 448 9.443283 GCTTATTGTGTATGTGAATTGAAGATC 57.557 33.333 0.00 0.00 0.00 2.75
448 449 9.182214 AGCTTATTGTGTATGTGAATTGAAGAT 57.818 29.630 0.00 0.00 0.00 2.40
455 456 5.758296 CCCGTAGCTTATTGTGTATGTGAAT 59.242 40.000 0.00 0.00 0.00 2.57
458 459 4.689071 TCCCGTAGCTTATTGTGTATGTG 58.311 43.478 0.00 0.00 0.00 3.21
459 460 5.347620 TTCCCGTAGCTTATTGTGTATGT 57.652 39.130 0.00 0.00 0.00 2.29
480 482 0.464916 AAGCGAACGTTGGACCCTTT 60.465 50.000 14.98 0.00 0.00 3.11
485 487 2.031191 TCAAAGAAAGCGAACGTTGGAC 59.969 45.455 14.98 5.62 0.00 4.02
487 489 2.748461 TCAAAGAAAGCGAACGTTGG 57.252 45.000 5.00 5.50 0.00 3.77
526 528 3.196207 ATGCACCCAGAAGCACCGT 62.196 57.895 0.00 0.00 44.49 4.83
628 1740 8.633075 AGTGAAGTGACATATTTTTGTTTGTG 57.367 30.769 0.00 0.00 0.00 3.33
734 1848 9.686683 ACTAGTGATTGTAGGATTGCTTAAAAT 57.313 29.630 0.00 0.00 0.00 1.82
771 1885 2.755952 ATAGGGGGTGCTTGGAATTC 57.244 50.000 0.00 0.00 0.00 2.17
819 1956 9.880157 ACAAATTATGAGAAAATGGAGGATTTG 57.120 29.630 0.00 0.00 34.30 2.32
871 2010 3.339061 TCGTATTGCAACGCGAGAT 57.661 47.368 15.93 1.22 42.56 2.75
878 2017 5.501715 CATGTGTTATCCTCGTATTGCAAC 58.498 41.667 0.00 0.00 0.00 4.17
954 2101 1.528309 GTGGGAGTGTGGGTTGTGG 60.528 63.158 0.00 0.00 0.00 4.17
1254 2401 4.883354 GGGAAGGCCAGCATCCGG 62.883 72.222 5.01 0.00 33.90 5.14
1441 2588 3.256960 GAGCTCCCACCCCACCAA 61.257 66.667 0.87 0.00 0.00 3.67
1489 2636 3.622826 CGTGGACGAACCCCTGGT 61.623 66.667 0.00 0.00 43.02 4.00
1505 2652 1.686052 CCTCCTCATCTTCCTCTTCCG 59.314 57.143 0.00 0.00 0.00 4.30
1739 2894 7.298374 AGTATGGTGACTATATTCACAGGAGA 58.702 38.462 20.87 3.43 46.68 3.71
1768 2923 5.284424 GTGGACACAACGTTGTAAGAAAAAC 59.716 40.000 31.86 19.01 39.91 2.43
1815 3145 1.416401 ACATAGGCGAATCCGTTGGAT 59.584 47.619 0.00 0.00 45.46 3.41
1821 3151 3.566523 GAGTAGAACATAGGCGAATCCG 58.433 50.000 0.00 0.00 40.77 4.18
1823 3153 3.574826 AGGGAGTAGAACATAGGCGAATC 59.425 47.826 0.00 0.00 0.00 2.52
1829 3159 5.422331 TGAAACAGAGGGAGTAGAACATAGG 59.578 44.000 0.00 0.00 0.00 2.57
1830 3160 6.531503 TGAAACAGAGGGAGTAGAACATAG 57.468 41.667 0.00 0.00 0.00 2.23
1883 3213 9.053472 TCTTGTATTTGGAAATAGAGGGAGTAA 57.947 33.333 0.00 0.00 31.94 2.24
1884 3214 8.483758 GTCTTGTATTTGGAAATAGAGGGAGTA 58.516 37.037 0.00 0.00 31.94 2.59
1885 3215 7.339482 GTCTTGTATTTGGAAATAGAGGGAGT 58.661 38.462 0.00 0.00 31.94 3.85
1886 3216 6.768381 GGTCTTGTATTTGGAAATAGAGGGAG 59.232 42.308 0.00 0.00 31.94 4.30
1887 3217 6.447084 AGGTCTTGTATTTGGAAATAGAGGGA 59.553 38.462 0.00 0.00 31.94 4.20
1888 3218 6.663734 AGGTCTTGTATTTGGAAATAGAGGG 58.336 40.000 0.00 0.00 31.94 4.30
1889 3219 8.581253 AAAGGTCTTGTATTTGGAAATAGAGG 57.419 34.615 0.00 0.00 31.94 3.69
1894 3224 8.950007 TCCTAAAAGGTCTTGTATTTGGAAAT 57.050 30.769 0.00 0.00 36.53 2.17
1895 3225 8.950007 ATCCTAAAAGGTCTTGTATTTGGAAA 57.050 30.769 0.00 0.00 36.53 3.13
1896 3226 8.950007 AATCCTAAAAGGTCTTGTATTTGGAA 57.050 30.769 0.00 0.00 36.53 3.53
1897 3227 7.614192 GGAATCCTAAAAGGTCTTGTATTTGGA 59.386 37.037 0.00 0.00 36.53 3.53
1898 3228 7.396055 TGGAATCCTAAAAGGTCTTGTATTTGG 59.604 37.037 0.00 0.00 36.53 3.28
1899 3229 8.244113 GTGGAATCCTAAAAGGTCTTGTATTTG 58.756 37.037 0.00 0.00 36.53 2.32
1900 3230 7.947890 TGTGGAATCCTAAAAGGTCTTGTATTT 59.052 33.333 0.00 0.00 36.53 1.40
1901 3231 7.466804 TGTGGAATCCTAAAAGGTCTTGTATT 58.533 34.615 0.00 0.00 36.53 1.89
1902 3232 7.027874 TGTGGAATCCTAAAAGGTCTTGTAT 57.972 36.000 0.00 0.00 36.53 2.29
1903 3233 6.442541 TGTGGAATCCTAAAAGGTCTTGTA 57.557 37.500 0.00 0.00 36.53 2.41
1904 3234 5.319043 TGTGGAATCCTAAAAGGTCTTGT 57.681 39.130 0.00 0.00 36.53 3.16
1905 3235 6.840780 ATTGTGGAATCCTAAAAGGTCTTG 57.159 37.500 0.00 0.00 36.53 3.02
1906 3236 7.829706 GTCTATTGTGGAATCCTAAAAGGTCTT 59.170 37.037 0.00 0.00 36.53 3.01
1907 3237 7.182930 AGTCTATTGTGGAATCCTAAAAGGTCT 59.817 37.037 0.00 0.00 36.53 3.85
1908 3238 7.339482 AGTCTATTGTGGAATCCTAAAAGGTC 58.661 38.462 0.00 0.00 36.53 3.85
1909 3239 7.272144 AGTCTATTGTGGAATCCTAAAAGGT 57.728 36.000 0.00 0.00 36.53 3.50
1914 3244 9.892444 TCCTTATAGTCTATTGTGGAATCCTAA 57.108 33.333 0.00 0.00 0.00 2.69
1915 3245 9.535170 CTCCTTATAGTCTATTGTGGAATCCTA 57.465 37.037 0.00 0.00 0.00 2.94
1916 3246 7.038658 GCTCCTTATAGTCTATTGTGGAATCCT 60.039 40.741 0.00 0.00 0.00 3.24
1917 3247 7.038658 AGCTCCTTATAGTCTATTGTGGAATCC 60.039 40.741 0.00 0.00 0.00 3.01
1918 3248 7.902087 AGCTCCTTATAGTCTATTGTGGAATC 58.098 38.462 0.00 0.51 0.00 2.52
1919 3249 7.863901 AGCTCCTTATAGTCTATTGTGGAAT 57.136 36.000 0.00 0.00 0.00 3.01
1920 3250 8.777578 TTAGCTCCTTATAGTCTATTGTGGAA 57.222 34.615 0.00 0.00 0.00 3.53
1921 3251 8.777578 TTTAGCTCCTTATAGTCTATTGTGGA 57.222 34.615 0.00 3.45 0.00 4.02
1922 3252 9.429359 CATTTAGCTCCTTATAGTCTATTGTGG 57.571 37.037 0.00 0.00 0.00 4.17
1927 3257 9.815306 TCACTCATTTAGCTCCTTATAGTCTAT 57.185 33.333 0.00 0.00 0.00 1.98
1928 3258 9.642343 TTCACTCATTTAGCTCCTTATAGTCTA 57.358 33.333 0.00 0.00 0.00 2.59
1929 3259 8.540507 TTCACTCATTTAGCTCCTTATAGTCT 57.459 34.615 0.00 0.00 0.00 3.24
1934 3264 9.862371 CGTATATTCACTCATTTAGCTCCTTAT 57.138 33.333 0.00 0.00 0.00 1.73
1935 3265 7.813148 GCGTATATTCACTCATTTAGCTCCTTA 59.187 37.037 0.00 0.00 0.00 2.69
1936 3266 6.647067 GCGTATATTCACTCATTTAGCTCCTT 59.353 38.462 0.00 0.00 0.00 3.36
1937 3267 6.015010 AGCGTATATTCACTCATTTAGCTCCT 60.015 38.462 0.00 0.00 0.00 3.69
1938 3268 6.159988 AGCGTATATTCACTCATTTAGCTCC 58.840 40.000 0.00 0.00 0.00 4.70
1939 3269 7.087639 AGAGCGTATATTCACTCATTTAGCTC 58.912 38.462 0.00 0.00 44.35 4.09
1940 3270 6.987386 AGAGCGTATATTCACTCATTTAGCT 58.013 36.000 0.00 0.00 0.00 3.32
1941 3271 8.640291 GTTAGAGCGTATATTCACTCATTTAGC 58.360 37.037 0.97 0.00 0.00 3.09
1942 3272 9.678941 TGTTAGAGCGTATATTCACTCATTTAG 57.321 33.333 0.97 0.00 0.00 1.85
1946 3276 9.794685 CATATGTTAGAGCGTATATTCACTCAT 57.205 33.333 0.00 0.00 0.00 2.90
1947 3277 8.793592 ACATATGTTAGAGCGTATATTCACTCA 58.206 33.333 1.41 0.00 0.00 3.41
1948 3278 9.279904 GACATATGTTAGAGCGTATATTCACTC 57.720 37.037 10.30 0.00 0.00 3.51
1949 3279 9.015367 AGACATATGTTAGAGCGTATATTCACT 57.985 33.333 10.30 0.00 0.00 3.41
2023 3353 9.661563 TGTCAAATACTACATCCGTTTCTAAAT 57.338 29.630 0.00 0.00 0.00 1.40
2024 3354 9.491675 TTGTCAAATACTACATCCGTTTCTAAA 57.508 29.630 0.00 0.00 0.00 1.85
2025 3355 9.661563 ATTGTCAAATACTACATCCGTTTCTAA 57.338 29.630 0.00 0.00 0.00 2.10
2026 3356 9.309516 GATTGTCAAATACTACATCCGTTTCTA 57.690 33.333 0.00 0.00 0.00 2.10
2027 3357 8.041323 AGATTGTCAAATACTACATCCGTTTCT 58.959 33.333 0.00 0.00 0.00 2.52
2028 3358 8.116753 CAGATTGTCAAATACTACATCCGTTTC 58.883 37.037 0.00 0.00 0.00 2.78
2029 3359 7.606456 ACAGATTGTCAAATACTACATCCGTTT 59.394 33.333 0.00 0.00 0.00 3.60
2030 3360 7.103641 ACAGATTGTCAAATACTACATCCGTT 58.896 34.615 0.00 0.00 0.00 4.44
2031 3361 6.640518 ACAGATTGTCAAATACTACATCCGT 58.359 36.000 0.00 0.00 0.00 4.69
2032 3362 8.135529 TCTACAGATTGTCAAATACTACATCCG 58.864 37.037 0.00 0.00 0.00 4.18
2033 3363 9.817809 TTCTACAGATTGTCAAATACTACATCC 57.182 33.333 0.00 0.00 0.00 3.51
2039 3369 9.167311 GGTTCATTCTACAGATTGTCAAATACT 57.833 33.333 0.00 0.00 0.00 2.12
2040 3370 8.116753 CGGTTCATTCTACAGATTGTCAAATAC 58.883 37.037 0.00 0.00 0.00 1.89
2057 3387 5.520649 GGAGAGTGTTAGAATCGGTTCATTC 59.479 44.000 11.72 0.00 36.79 2.67
2058 3388 5.187967 AGGAGAGTGTTAGAATCGGTTCATT 59.812 40.000 11.72 0.00 36.79 2.57
2080 3410 9.558648 GAAATGGCTGCAATTTAAATTTTAAGG 57.441 29.630 14.69 1.22 0.00 2.69
2137 3467 5.536916 CCCAAACAAAGAATACCTTGGTGTA 59.463 40.000 2.03 0.00 38.06 2.90
2142 3472 4.871933 AGCCCAAACAAAGAATACCTTG 57.128 40.909 0.00 0.00 34.79 3.61
2151 3481 3.115554 CGAAACTGAAGCCCAAACAAAG 58.884 45.455 0.00 0.00 0.00 2.77
2188 3518 1.869342 GCTTTGCCAACACAGCGAATT 60.869 47.619 0.00 0.00 39.62 2.17
2249 3579 0.666274 GACATTGGACTGACGCACGA 60.666 55.000 0.00 0.00 0.00 4.35
2266 3596 4.876107 TCTGATTCGGGCTATTTTTCAGAC 59.124 41.667 0.00 0.00 34.72 3.51
2314 3645 4.936891 AGGCTGAATCTGAAACAAACAAC 58.063 39.130 0.00 0.00 0.00 3.32
2395 3850 7.611770 TGCTACAGAGTAGTTTGATACAATGT 58.388 34.615 6.11 0.00 33.67 2.71
2509 4100 5.681337 TGATCTGTGTATTCACGCAAAAA 57.319 34.783 0.00 0.00 44.27 1.94
2510 4101 5.411053 TCATGATCTGTGTATTCACGCAAAA 59.589 36.000 0.00 0.00 44.27 2.44
2511 4102 4.934602 TCATGATCTGTGTATTCACGCAAA 59.065 37.500 0.00 0.00 44.27 3.68
2512 4103 4.502962 TCATGATCTGTGTATTCACGCAA 58.497 39.130 0.00 0.00 44.27 4.85
2513 4104 4.122143 TCATGATCTGTGTATTCACGCA 57.878 40.909 0.00 0.00 46.49 5.24
2514 4105 5.663795 ATTCATGATCTGTGTATTCACGC 57.336 39.130 0.00 0.00 46.49 5.34
2515 4106 7.687445 TCAAATTCATGATCTGTGTATTCACG 58.313 34.615 0.00 0.00 46.49 4.35
2516 4107 9.447040 CATCAAATTCATGATCTGTGTATTCAC 57.553 33.333 0.00 0.00 40.05 3.18
2517 4108 9.181061 ACATCAAATTCATGATCTGTGTATTCA 57.819 29.630 0.00 0.00 37.96 2.57
2519 4110 9.797556 CAACATCAAATTCATGATCTGTGTATT 57.202 29.630 0.00 0.00 37.96 1.89
2560 4151 0.461548 CACCTCTTCTATCCGCTGCA 59.538 55.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.