Multiple sequence alignment - TraesCS2D01G383900

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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 TraesCS2D01G383900 chr2D 100.000 2696 0 0 1 2696 488365446 488362751 0.000000e+00 4979.0
1 TraesCS2D01G383900 chr2D 96.488 1851 52 5 1 1841 488473508 488471661 0.000000e+00 3046.0
2 TraesCS2D01G383900 chr2D 78.261 184 37 3 93 274 488473201 488473019 6.100000e-22 115.0
3 TraesCS2D01G383900 chr2D 91.667 60 4 1 516 574 575354252 575354193 6.190000e-12 82.4
4 TraesCS2D01G383900 chr2A 93.231 916 37 7 963 1853 632929212 632928297 0.000000e+00 1325.0
5 TraesCS2D01G383900 chr2A 83.699 319 33 8 2394 2696 632927819 632927504 1.580000e-72 283.0
6 TraesCS2D01G383900 chr2A 93.103 145 7 2 827 968 632929392 632929248 2.720000e-50 209.0
7 TraesCS2D01G383900 chr2A 89.041 146 7 5 669 806 632929645 632929501 3.570000e-39 172.0
8 TraesCS2D01G383900 chr2B 90.525 971 47 20 4 968 572679794 572678863 0.000000e+00 1242.0
9 TraesCS2D01G383900 chr2B 93.513 817 37 2 969 1770 572678823 572678008 0.000000e+00 1201.0
10 TraesCS2D01G383900 chr2B 84.277 318 31 8 2394 2696 572677392 572677079 2.630000e-75 292.0
11 TraesCS2D01G383900 chr2B 100.000 30 0 0 919 948 572678976 572678947 3.750000e-04 56.5
12 TraesCS2D01G383900 chr6B 83.858 508 71 10 1129 1629 515022057 515022560 8.740000e-130 473.0
13 TraesCS2D01G383900 chr6D 82.584 534 69 18 1135 1647 311582634 311582104 1.470000e-122 449.0
14 TraesCS2D01G383900 chr6D 95.890 146 6 0 1368 1513 414098779 414098924 1.250000e-58 237.0
15 TraesCS2D01G383900 chr6D 91.379 58 3 2 517 574 155842310 155842255 8.000000e-11 78.7
16 TraesCS2D01G383900 chr6A 81.696 519 68 18 1135 1629 448351817 448351302 8.990000e-110 407.0
17 TraesCS2D01G383900 chr1B 96.000 250 10 0 1267 1516 378858372 378858123 8.990000e-110 407.0
18 TraesCS2D01G383900 chr7D 81.707 410 57 14 1135 1529 126880291 126879885 2.590000e-85 326.0
19 TraesCS2D01G383900 chr7D 81.034 116 13 4 308 418 585598748 585598859 1.720000e-12 84.2
20 TraesCS2D01G383900 chr5D 80.357 168 27 5 2 166 51021793 51021629 3.650000e-24 122.0
21 TraesCS2D01G383900 chr4A 76.961 204 40 5 1159 1357 503236421 503236220 2.840000e-20 110.0
22 TraesCS2D01G383900 chr4A 81.618 136 20 5 11 143 631672585 631672452 1.020000e-19 108.0
23 TraesCS2D01G383900 chr7B 84.158 101 12 3 41 138 526233371 526233470 7.950000e-16 95.3
24 TraesCS2D01G383900 chr7B 91.667 60 4 1 516 574 173865878 173865819 6.190000e-12 82.4
25 TraesCS2D01G383900 chr1A 85.417 96 8 5 29 121 551318713 551318621 7.950000e-16 95.3
26 TraesCS2D01G383900 chr1A 85.882 85 8 4 51 133 549229817 549229899 1.330000e-13 87.9
27 TraesCS2D01G383900 chr1D 80.488 123 19 5 6 126 897641 897760 3.700000e-14 89.8
28 TraesCS2D01G383900 chr1D 93.103 58 3 1 518 574 338936269 338936212 1.720000e-12 84.2
29 TraesCS2D01G383900 chr1D 91.667 60 4 1 516 574 58573627 58573686 6.190000e-12 82.4
30 TraesCS2D01G383900 chr3D 93.103 58 3 1 517 573 355905415 355905472 1.720000e-12 84.2
31 TraesCS2D01G383900 chr5B 91.667 60 4 1 516 574 411034865 411034806 6.190000e-12 82.4


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 TraesCS2D01G383900 chr2D 488362751 488365446 2695 True 4979.000 4979 100.00000 1 2696 1 chr2D.!!$R1 2695
1 TraesCS2D01G383900 chr2D 488471661 488473508 1847 True 1580.500 3046 87.37450 1 1841 2 chr2D.!!$R3 1840
2 TraesCS2D01G383900 chr2A 632927504 632929645 2141 True 497.250 1325 89.76850 669 2696 4 chr2A.!!$R1 2027
3 TraesCS2D01G383900 chr2B 572677079 572679794 2715 True 697.875 1242 92.07875 4 2696 4 chr2B.!!$R1 2692
4 TraesCS2D01G383900 chr6B 515022057 515022560 503 False 473.000 473 83.85800 1129 1629 1 chr6B.!!$F1 500
5 TraesCS2D01G383900 chr6D 311582104 311582634 530 True 449.000 449 82.58400 1135 1647 1 chr6D.!!$R2 512
6 TraesCS2D01G383900 chr6A 448351302 448351817 515 True 407.000 407 81.69600 1135 1629 1 chr6A.!!$R1 494

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
767 778 0.890542 GGCATGCACTGAACCAGACA 60.891 55.0 21.36 0.0 35.18 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2248 0.227735 TCGTCGTTTCACTTTTCGCG 59.772 50.0 0.0 0.0 0.0 5.87 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
378 382 9.979578 TTATTTTCATATTAATGGATGTGTGCC 57.020 29.630 0.00 0.00 33.61 5.01
527 531 3.091545 CCCGTTTAGTAGTACTCCCACA 58.908 50.000 5.96 0.00 0.00 4.17
767 778 0.890542 GGCATGCACTGAACCAGACA 60.891 55.000 21.36 0.00 35.18 3.41
1635 1816 2.046892 GTCGCCATGGCTGTCACT 60.047 61.111 33.07 0.00 39.32 3.41
1656 1837 2.980233 GGCGTGCTCTGGCTGTTT 60.980 61.111 0.00 0.00 39.59 2.83
1690 1871 1.002142 ACATTCACGTCTCGTCGTTGA 60.002 47.619 0.00 0.00 42.27 3.18
1710 1891 4.641645 TGAAGTGGCCGTGCTGGG 62.642 66.667 0.00 0.00 38.63 4.45
1777 1958 3.969287 AGAGCTAGCTGTGTCAATTGA 57.031 42.857 24.99 3.38 0.00 2.57
1781 1962 5.128499 AGAGCTAGCTGTGTCAATTGATACT 59.872 40.000 28.52 15.80 37.13 2.12
1782 1963 5.738909 AGCTAGCTGTGTCAATTGATACTT 58.261 37.500 28.52 18.90 37.13 2.24
1783 1964 6.878317 AGCTAGCTGTGTCAATTGATACTTA 58.122 36.000 28.52 18.98 37.13 2.24
1784 1965 6.983307 AGCTAGCTGTGTCAATTGATACTTAG 59.017 38.462 28.52 24.96 37.13 2.18
1785 1966 6.758886 GCTAGCTGTGTCAATTGATACTTAGT 59.241 38.462 28.52 16.49 37.13 2.24
1786 1967 7.043059 GCTAGCTGTGTCAATTGATACTTAGTC 60.043 40.741 28.52 19.13 37.13 2.59
1787 1968 5.807520 AGCTGTGTCAATTGATACTTAGTCG 59.192 40.000 28.52 14.70 37.13 4.18
1788 1969 5.577164 GCTGTGTCAATTGATACTTAGTCGT 59.423 40.000 28.52 0.00 37.13 4.34
1789 1970 6.237595 GCTGTGTCAATTGATACTTAGTCGTC 60.238 42.308 28.52 7.02 37.13 4.20
1790 1971 6.920817 TGTGTCAATTGATACTTAGTCGTCT 58.079 36.000 28.52 0.00 37.13 4.18
1791 1972 8.047413 TGTGTCAATTGATACTTAGTCGTCTA 57.953 34.615 28.52 8.29 37.13 2.59
1793 1974 7.966753 GTGTCAATTGATACTTAGTCGTCTACA 59.033 37.037 23.58 5.00 33.99 2.74
1794 1975 8.683615 TGTCAATTGATACTTAGTCGTCTACAT 58.316 33.333 12.12 0.00 0.00 2.29
1795 1976 9.517609 GTCAATTGATACTTAGTCGTCTACATT 57.482 33.333 12.12 0.00 0.00 2.71
1857 2083 3.937814 TCAATCGTTGTGTAATGGCTCT 58.062 40.909 0.00 0.00 0.00 4.09
1858 2084 3.684305 TCAATCGTTGTGTAATGGCTCTG 59.316 43.478 0.00 0.00 0.00 3.35
1878 2104 0.965439 GTTGGTGGCAATGTAAGGCA 59.035 50.000 0.00 0.00 39.41 4.75
1899 2130 8.622948 AGGCAAGGCTAATGAAAATACTATAC 57.377 34.615 0.00 0.00 0.00 1.47
1900 2131 8.217799 AGGCAAGGCTAATGAAAATACTATACA 58.782 33.333 0.00 0.00 0.00 2.29
1901 2132 9.014297 GGCAAGGCTAATGAAAATACTATACAT 57.986 33.333 0.00 0.00 0.00 2.29
1905 2136 9.799106 AGGCTAATGAAAATACTATACATGCTT 57.201 29.630 0.00 0.00 0.00 3.91
1917 2148 7.264373 ACTATACATGCTTTTTACCATCTGC 57.736 36.000 0.00 0.00 0.00 4.26
1920 2151 3.184541 CATGCTTTTTACCATCTGCTGC 58.815 45.455 0.00 0.00 0.00 5.25
1921 2152 2.237643 TGCTTTTTACCATCTGCTGCA 58.762 42.857 0.88 0.88 0.00 4.41
1924 2155 2.945447 TTTTACCATCTGCTGCATGC 57.055 45.000 11.82 11.82 43.25 4.06
1925 2156 1.105457 TTTACCATCTGCTGCATGCC 58.895 50.000 16.68 0.28 42.00 4.40
1926 2157 0.256752 TTACCATCTGCTGCATGCCT 59.743 50.000 16.68 0.00 42.00 4.75
1927 2158 1.130777 TACCATCTGCTGCATGCCTA 58.869 50.000 16.68 0.00 42.00 3.93
1928 2159 0.477204 ACCATCTGCTGCATGCCTAT 59.523 50.000 16.68 0.00 42.00 2.57
1929 2160 1.701292 ACCATCTGCTGCATGCCTATA 59.299 47.619 16.68 0.00 42.00 1.31
1930 2161 2.290134 ACCATCTGCTGCATGCCTATAG 60.290 50.000 16.68 6.83 42.00 1.31
1932 2163 2.538512 TCTGCTGCATGCCTATAGTG 57.461 50.000 16.68 3.72 42.00 2.74
1933 2164 1.764723 TCTGCTGCATGCCTATAGTGT 59.235 47.619 16.68 0.00 42.00 3.55
1935 2166 2.547211 CTGCTGCATGCCTATAGTGTTC 59.453 50.000 16.68 0.00 42.00 3.18
1938 2169 3.743396 GCTGCATGCCTATAGTGTTCTAC 59.257 47.826 16.68 0.00 35.15 2.59
1939 2170 4.310769 CTGCATGCCTATAGTGTTCTACC 58.689 47.826 16.68 0.00 0.00 3.18
1941 2172 4.039245 TGCATGCCTATAGTGTTCTACCTC 59.961 45.833 16.68 0.00 0.00 3.85
1943 2174 5.777802 CATGCCTATAGTGTTCTACCTCTG 58.222 45.833 0.00 0.00 0.00 3.35
1944 2175 5.125367 TGCCTATAGTGTTCTACCTCTGA 57.875 43.478 0.00 0.00 0.00 3.27
1945 2176 5.516044 TGCCTATAGTGTTCTACCTCTGAA 58.484 41.667 0.00 0.00 0.00 3.02
1946 2177 5.955959 TGCCTATAGTGTTCTACCTCTGAAA 59.044 40.000 0.00 0.00 0.00 2.69
1947 2178 6.096987 TGCCTATAGTGTTCTACCTCTGAAAG 59.903 42.308 0.00 0.00 0.00 2.62
1981 2212 0.605589 GGGGTTCCACCTCTGAAACG 60.606 60.000 0.00 0.00 35.29 3.60
1982 2213 0.108019 GGGTTCCACCTCTGAAACGT 59.892 55.000 0.00 0.00 38.64 3.99
1983 2214 1.476291 GGGTTCCACCTCTGAAACGTT 60.476 52.381 0.00 0.00 38.64 3.99
1984 2215 2.294979 GGTTCCACCTCTGAAACGTTT 58.705 47.619 14.57 14.57 34.73 3.60
1985 2216 2.289820 GGTTCCACCTCTGAAACGTTTC 59.710 50.000 29.72 29.72 34.73 2.78
2017 2248 1.466950 TGGGATCGATTGCAACGAAAC 59.533 47.619 21.77 18.31 42.80 2.78
2027 2258 0.492737 GCAACGAAACGCGAAAAGTG 59.507 50.000 15.93 4.51 44.57 3.16
2033 2264 2.696255 GAAACGCGAAAAGTGAAACGA 58.304 42.857 15.93 0.00 45.86 3.85
2060 2322 3.565482 TGCGTTTCAGCAGAAGAAAGAAT 59.435 39.130 0.00 0.00 42.92 2.40
2061 2323 4.754618 TGCGTTTCAGCAGAAGAAAGAATA 59.245 37.500 0.00 0.00 42.92 1.75
2084 2346 1.070038 GAAAAACGTATCCGCGACCA 58.930 50.000 8.23 0.00 37.70 4.02
2089 2351 1.949133 CGTATCCGCGACCATGGTG 60.949 63.158 25.52 15.67 0.00 4.17
2102 2364 2.723273 CCATGGTGGTTCTACCTTTCC 58.277 52.381 2.57 0.00 41.43 3.13
2103 2365 2.356135 CATGGTGGTTCTACCTTTCCG 58.644 52.381 6.87 0.00 41.43 4.30
2104 2366 1.426751 TGGTGGTTCTACCTTTCCGT 58.573 50.000 6.87 0.00 41.43 4.69
2105 2367 2.607499 TGGTGGTTCTACCTTTCCGTA 58.393 47.619 6.87 0.00 41.43 4.02
2106 2368 2.564062 TGGTGGTTCTACCTTTCCGTAG 59.436 50.000 6.87 0.00 41.43 3.51
2107 2369 2.827921 GGTGGTTCTACCTTTCCGTAGA 59.172 50.000 0.00 0.00 42.31 2.59
2111 2373 3.498927 TTCTACCTTTCCGTAGAAGCG 57.501 47.619 7.02 0.00 45.83 4.68
2112 2374 2.440409 TCTACCTTTCCGTAGAAGCGT 58.560 47.619 0.00 0.00 41.34 5.07
2113 2375 2.421424 TCTACCTTTCCGTAGAAGCGTC 59.579 50.000 0.00 0.00 41.34 5.19
2114 2376 1.254954 ACCTTTCCGTAGAAGCGTCT 58.745 50.000 7.47 7.47 37.95 4.18
2115 2377 2.440409 ACCTTTCCGTAGAAGCGTCTA 58.560 47.619 5.17 5.17 35.12 2.59
2116 2378 2.821969 ACCTTTCCGTAGAAGCGTCTAA 59.178 45.455 11.11 0.00 38.11 2.10
2117 2379 3.256631 ACCTTTCCGTAGAAGCGTCTAAA 59.743 43.478 11.11 3.34 38.11 1.85
2118 2380 4.240096 CCTTTCCGTAGAAGCGTCTAAAA 58.760 43.478 11.11 7.70 38.11 1.52
2119 2381 4.687483 CCTTTCCGTAGAAGCGTCTAAAAA 59.313 41.667 11.11 10.72 38.11 1.94
2143 2405 1.002684 CTTTCCGTAGATCCCTCGTCG 60.003 57.143 0.00 0.00 0.00 5.12
2144 2406 0.107508 TTCCGTAGATCCCTCGTCGT 60.108 55.000 0.00 0.00 0.00 4.34
2163 2425 5.444218 CGTCGTTTTCTGTAACTGCCTATTC 60.444 44.000 0.00 0.00 0.00 1.75
2169 2431 5.675684 TCTGTAACTGCCTATTCATGTGA 57.324 39.130 0.00 0.00 0.00 3.58
2172 2434 3.610040 AACTGCCTATTCATGTGACGA 57.390 42.857 0.00 0.00 0.00 4.20
2194 2456 2.520982 ACGCTAGCCGCCCTGATA 60.521 61.111 9.66 0.00 41.76 2.15
2199 2461 1.537202 GCTAGCCGCCCTGATATTTTG 59.463 52.381 2.29 0.00 0.00 2.44
2200 2462 2.851195 CTAGCCGCCCTGATATTTTGT 58.149 47.619 0.00 0.00 0.00 2.83
2201 2463 2.143876 AGCCGCCCTGATATTTTGTT 57.856 45.000 0.00 0.00 0.00 2.83
2236 2536 1.750193 CTAGCCGCCCTGATTTTCAA 58.250 50.000 0.00 0.00 0.00 2.69
2279 2579 4.406456 TCTTTCATCTTGGGCTGCTTTAA 58.594 39.130 0.00 0.00 0.00 1.52
2298 2598 6.200475 GCTTTAAGCCCAATTAGTACGTCTAG 59.800 42.308 5.52 0.00 34.48 2.43
2302 2602 4.954826 AGCCCAATTAGTACGTCTAGTTCT 59.045 41.667 0.00 0.00 34.72 3.01
2303 2603 6.125029 AGCCCAATTAGTACGTCTAGTTCTA 58.875 40.000 0.00 0.00 32.55 2.10
2325 2629 1.033746 ACCGGCATTCATGAGCAAGG 61.034 55.000 0.00 14.80 36.55 3.61
2341 2645 5.470098 TGAGCAAGGATAACTGAACAAGAAC 59.530 40.000 0.00 0.00 0.00 3.01
2342 2646 4.762251 AGCAAGGATAACTGAACAAGAACC 59.238 41.667 0.00 0.00 0.00 3.62
2343 2647 4.082733 GCAAGGATAACTGAACAAGAACCC 60.083 45.833 0.00 0.00 0.00 4.11
2344 2648 4.302559 AGGATAACTGAACAAGAACCCC 57.697 45.455 0.00 0.00 0.00 4.95
2345 2649 3.916989 AGGATAACTGAACAAGAACCCCT 59.083 43.478 0.00 0.00 0.00 4.79
2346 2650 5.098663 AGGATAACTGAACAAGAACCCCTA 58.901 41.667 0.00 0.00 0.00 3.53
2347 2651 5.550403 AGGATAACTGAACAAGAACCCCTAA 59.450 40.000 0.00 0.00 0.00 2.69
2381 2685 5.253330 AGTGAACAAGAAACACTTCCTTCA 58.747 37.500 0.00 0.00 41.21 3.02
2382 2686 5.888161 AGTGAACAAGAAACACTTCCTTCAT 59.112 36.000 0.00 0.00 41.21 2.57
2383 2687 5.973565 GTGAACAAGAAACACTTCCTTCATG 59.026 40.000 0.00 0.00 36.03 3.07
2384 2688 5.652014 TGAACAAGAAACACTTCCTTCATGT 59.348 36.000 0.00 0.00 35.59 3.21
2385 2689 6.152661 TGAACAAGAAACACTTCCTTCATGTT 59.847 34.615 5.42 5.42 42.79 2.71
2386 2690 7.338196 TGAACAAGAAACACTTCCTTCATGTTA 59.662 33.333 5.66 0.00 41.18 2.41
2387 2691 7.027778 ACAAGAAACACTTCCTTCATGTTAC 57.972 36.000 0.00 0.00 35.54 2.50
2388 2692 6.828785 ACAAGAAACACTTCCTTCATGTTACT 59.171 34.615 0.00 0.00 35.54 2.24
2389 2693 7.990886 ACAAGAAACACTTCCTTCATGTTACTA 59.009 33.333 0.00 0.00 35.54 1.82
2390 2694 8.836413 CAAGAAACACTTCCTTCATGTTACTAA 58.164 33.333 0.00 0.00 35.54 2.24
2391 2695 8.974060 AGAAACACTTCCTTCATGTTACTAAA 57.026 30.769 0.00 0.00 35.54 1.85
2392 2696 9.403583 AGAAACACTTCCTTCATGTTACTAAAA 57.596 29.630 0.00 0.00 35.54 1.52
2422 2726 9.640974 CACTTCTTTCATAAAATGTTTTGCAAG 57.359 29.630 0.00 0.00 0.00 4.01
2444 2748 9.423061 GCAAGAAAATAAAAACATGTGATACCT 57.577 29.630 0.00 0.00 0.00 3.08
2465 2771 4.486090 CTGCACTGACACTTTAGATACGT 58.514 43.478 0.00 0.00 0.00 3.57
2472 2778 7.753580 CACTGACACTTTAGATACGTGATACAA 59.246 37.037 0.00 0.00 33.13 2.41
2487 2793 3.437395 TGATACAACACCACATTTACGCC 59.563 43.478 0.00 0.00 0.00 5.68
2492 2798 4.521256 ACAACACCACATTTACGCCTTTAT 59.479 37.500 0.00 0.00 0.00 1.40
2497 2803 6.093082 ACACCACATTTACGCCTTTATAGAAC 59.907 38.462 0.00 0.00 0.00 3.01
2555 2862 1.070786 GGAACGAGCACAACCCTCA 59.929 57.895 0.00 0.00 0.00 3.86
2581 2888 2.010817 CACAACAAAGCTTCGCCGC 61.011 57.895 0.00 0.00 0.00 6.53
2597 2904 1.691196 CCGCCCCACATCATTGTATT 58.309 50.000 0.00 0.00 33.76 1.89
2626 2933 1.606224 GCAATGAAGCCACAAACTGGG 60.606 52.381 0.00 0.00 41.02 4.45
2632 2939 2.086610 AGCCACAAACTGGGAATTGT 57.913 45.000 0.00 0.00 41.02 2.71
2663 2982 3.474798 TCTCATGTTGGGAGAGTAGGT 57.525 47.619 0.00 0.00 36.52 3.08
2665 2984 3.515502 TCTCATGTTGGGAGAGTAGGTTG 59.484 47.826 0.00 0.00 36.52 3.77
2691 3011 3.884895 TCTATTGTCACGCATTTGGGAT 58.115 40.909 1.25 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 156 1.806542 GTCGTGGTTTCACATGCAGAT 59.193 47.619 0.00 0.00 43.79 2.90
324 328 7.374272 TGAAAATCAAGCACCGAATCAATTTA 58.626 30.769 0.00 0.00 0.00 1.40
378 382 2.097466 GCGGTTGGTACATCATCCTTTG 59.903 50.000 0.00 0.00 39.30 2.77
563 567 8.889717 TCAAGGAATCAATTCGGTTTAGATTAC 58.110 33.333 0.00 0.00 37.67 1.89
767 778 3.463574 CGTATCTCGCTCGCTGATT 57.536 52.632 3.84 0.00 0.00 2.57
1635 1816 3.691342 AGCCAGAGCACGCCGTAA 61.691 61.111 0.00 0.00 43.56 3.18
1690 1871 3.560251 AGCACGGCCACTTCACCT 61.560 61.111 2.24 0.00 0.00 4.00
1710 1891 2.912025 CACCCACCACCTGCCAAC 60.912 66.667 0.00 0.00 0.00 3.77
1781 1962 6.314400 GCCATTAACCAAATGTAGACGACTAA 59.686 38.462 0.00 0.00 43.03 2.24
1782 1963 5.813672 GCCATTAACCAAATGTAGACGACTA 59.186 40.000 0.00 0.00 43.03 2.59
1783 1964 4.634443 GCCATTAACCAAATGTAGACGACT 59.366 41.667 0.00 0.00 43.03 4.18
1784 1965 4.634443 AGCCATTAACCAAATGTAGACGAC 59.366 41.667 0.00 0.00 43.03 4.34
1785 1966 4.839121 AGCCATTAACCAAATGTAGACGA 58.161 39.130 0.00 0.00 43.03 4.20
1786 1967 5.007332 GGTAGCCATTAACCAAATGTAGACG 59.993 44.000 0.00 0.00 43.03 4.18
1787 1968 5.298527 GGGTAGCCATTAACCAAATGTAGAC 59.701 44.000 5.96 0.00 43.03 2.59
1788 1969 5.044772 TGGGTAGCCATTAACCAAATGTAGA 60.045 40.000 10.27 0.00 46.28 2.59
1789 1970 5.197451 TGGGTAGCCATTAACCAAATGTAG 58.803 41.667 10.27 0.00 46.28 2.74
1790 1971 5.194473 TGGGTAGCCATTAACCAAATGTA 57.806 39.130 10.27 0.00 46.28 2.29
1791 1972 4.054359 TGGGTAGCCATTAACCAAATGT 57.946 40.909 10.27 0.00 46.28 2.71
1843 2040 2.158534 ACCAACCAGAGCCATTACACAA 60.159 45.455 0.00 0.00 0.00 3.33
1857 2083 1.626686 CCTTACATTGCCACCAACCA 58.373 50.000 0.00 0.00 32.95 3.67
1858 2084 0.246360 GCCTTACATTGCCACCAACC 59.754 55.000 0.00 0.00 32.95 3.77
1878 2104 9.799106 AGCATGTATAGTATTTTCATTAGCCTT 57.201 29.630 0.00 0.00 0.00 4.35
1898 2129 3.367703 GCAGCAGATGGTAAAAAGCATGT 60.368 43.478 0.00 0.00 0.00 3.21
1899 2130 3.184541 GCAGCAGATGGTAAAAAGCATG 58.815 45.455 0.00 0.00 0.00 4.06
1900 2131 2.827322 TGCAGCAGATGGTAAAAAGCAT 59.173 40.909 0.00 0.00 0.00 3.79
1901 2132 2.237643 TGCAGCAGATGGTAAAAAGCA 58.762 42.857 0.00 0.00 0.00 3.91
1905 2136 2.945447 GCATGCAGCAGATGGTAAAA 57.055 45.000 14.21 0.00 44.79 1.52
1916 2147 2.843701 AGAACACTATAGGCATGCAGC 58.156 47.619 21.36 2.42 44.65 5.25
1917 2148 4.039730 AGGTAGAACACTATAGGCATGCAG 59.960 45.833 21.36 10.72 0.00 4.41
1920 2151 5.536538 TCAGAGGTAGAACACTATAGGCATG 59.463 44.000 4.43 0.00 0.00 4.06
1921 2152 5.706447 TCAGAGGTAGAACACTATAGGCAT 58.294 41.667 4.43 0.00 0.00 4.40
1924 2155 7.045126 CCTTTCAGAGGTAGAACACTATAGG 57.955 44.000 4.43 0.00 40.95 2.57
1964 2195 2.289820 GAAACGTTTCAGAGGTGGAACC 59.710 50.000 30.99 4.16 46.80 3.62
1981 2212 2.164338 TCCCATTTTACGGGCTGAAAC 58.836 47.619 0.00 0.00 44.11 2.78
1982 2213 2.588464 TCCCATTTTACGGGCTGAAA 57.412 45.000 0.00 0.00 44.11 2.69
1983 2214 2.650322 GATCCCATTTTACGGGCTGAA 58.350 47.619 0.00 0.00 44.11 3.02
1984 2215 1.474320 CGATCCCATTTTACGGGCTGA 60.474 52.381 0.00 0.00 44.11 4.26
1985 2216 0.944386 CGATCCCATTTTACGGGCTG 59.056 55.000 0.00 0.00 44.11 4.85
1990 2221 3.961477 TGCAATCGATCCCATTTTACG 57.039 42.857 0.00 0.00 0.00 3.18
2017 2248 0.227735 TCGTCGTTTCACTTTTCGCG 59.772 50.000 0.00 0.00 0.00 5.87
2020 2251 2.645647 CGCAATCGTCGTTTCACTTTTC 59.354 45.455 0.00 0.00 0.00 2.29
2084 2346 1.982958 ACGGAAAGGTAGAACCACCAT 59.017 47.619 0.00 0.00 41.95 3.55
2097 2359 5.834239 TTTTTAGACGCTTCTACGGAAAG 57.166 39.130 0.00 0.00 33.81 2.62
2118 2380 4.251268 CGAGGGATCTACGGAAAGTTTTT 58.749 43.478 0.00 0.00 0.00 1.94
2119 2381 3.260128 ACGAGGGATCTACGGAAAGTTTT 59.740 43.478 0.00 0.00 0.00 2.43
2120 2382 2.830321 ACGAGGGATCTACGGAAAGTTT 59.170 45.455 0.00 0.00 0.00 2.66
2121 2383 2.426381 GACGAGGGATCTACGGAAAGTT 59.574 50.000 0.00 0.00 0.00 2.66
2122 2384 2.022934 GACGAGGGATCTACGGAAAGT 58.977 52.381 0.00 0.00 0.00 2.66
2143 2405 7.023575 CACATGAATAGGCAGTTACAGAAAAC 58.976 38.462 0.00 0.00 0.00 2.43
2144 2406 6.939730 TCACATGAATAGGCAGTTACAGAAAA 59.060 34.615 0.00 0.00 0.00 2.29
2169 2431 4.415332 CGGCTAGCGTGTGGTCGT 62.415 66.667 9.00 0.00 0.00 4.34
2255 2555 1.632409 AGCAGCCCAAGATGAAAGAGA 59.368 47.619 0.00 0.00 0.00 3.10
2279 2579 4.954826 AGAACTAGACGTACTAATTGGGCT 59.045 41.667 0.00 0.00 0.00 5.19
2298 2598 4.662145 CTCATGAATGCCGGTTTTAGAAC 58.338 43.478 1.90 0.00 34.96 3.01
2302 2602 2.441410 TGCTCATGAATGCCGGTTTTA 58.559 42.857 1.90 0.00 0.00 1.52
2303 2603 1.255882 TGCTCATGAATGCCGGTTTT 58.744 45.000 1.90 0.00 0.00 2.43
2325 2629 7.754851 TTTTAGGGGTTCTTGTTCAGTTATC 57.245 36.000 0.00 0.00 0.00 1.75
2359 2663 5.560966 TGAAGGAAGTGTTTCTTGTTCAC 57.439 39.130 0.00 0.00 36.40 3.18
2366 2670 8.974060 TTTAGTAACATGAAGGAAGTGTTTCT 57.026 30.769 0.00 0.00 37.30 2.52
2393 2697 9.986833 GCAAAACATTTTATGAAAGAAGTGTTT 57.013 25.926 6.59 6.59 39.42 2.83
2394 2698 9.160496 TGCAAAACATTTTATGAAAGAAGTGTT 57.840 25.926 0.00 0.00 0.00 3.32
2395 2699 8.715191 TGCAAAACATTTTATGAAAGAAGTGT 57.285 26.923 0.00 0.00 0.00 3.55
2396 2700 9.640974 CTTGCAAAACATTTTATGAAAGAAGTG 57.359 29.630 0.00 0.00 0.00 3.16
2397 2701 9.598517 TCTTGCAAAACATTTTATGAAAGAAGT 57.401 25.926 0.00 0.00 0.00 3.01
2418 2722 9.423061 AGGTATCACATGTTTTTATTTTCTTGC 57.577 29.630 0.00 0.00 0.00 4.01
2422 2726 8.647226 GTGCAGGTATCACATGTTTTTATTTTC 58.353 33.333 0.00 0.00 31.66 2.29
2444 2748 4.022676 TCACGTATCTAAAGTGTCAGTGCA 60.023 41.667 0.00 0.00 37.20 4.57
2465 2771 3.437395 GGCGTAAATGTGGTGTTGTATCA 59.563 43.478 0.00 0.00 0.00 2.15
2472 2778 5.736813 TCTATAAAGGCGTAAATGTGGTGT 58.263 37.500 0.00 0.00 0.00 4.16
2528 2835 0.674895 GTGCTCGTTCCAGATTGCCT 60.675 55.000 0.00 0.00 0.00 4.75
2555 2862 3.003689 CGAAGCTTTGTTGTGGAAGACAT 59.996 43.478 0.00 0.00 33.40 3.06
2581 2888 6.514870 CGGATACAAAATACAATGATGTGGGG 60.515 42.308 0.00 0.00 40.84 4.96
2589 2896 7.306167 GCTTCATTGCGGATACAAAATACAATG 60.306 37.037 0.00 0.00 42.52 2.82
2597 2904 2.163412 GTGGCTTCATTGCGGATACAAA 59.837 45.455 0.00 0.00 32.27 2.83
2626 2933 4.789012 TGAGATTGCCCAAAGACAATTC 57.211 40.909 0.00 0.00 36.65 2.17
2632 2939 2.827322 CCAACATGAGATTGCCCAAAGA 59.173 45.455 0.00 0.00 0.00 2.52
2663 2982 6.403092 CCAAATGCGTGACAATAGATACACAA 60.403 38.462 0.00 0.00 33.56 3.33
2665 2984 5.501715 CCAAATGCGTGACAATAGATACAC 58.498 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.