Multiple sequence alignment - TraesCS6D01G187200

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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 TraesCS6D01G187200 chr6D 100.000 5239 0 0 1 5239 249996763 249991525 0.000000e+00 9675.0
1 TraesCS6D01G187200 chr6D 98.969 97 1 0 1897 1993 61144222 61144126 1.940000e-39 174.0
2 TraesCS6D01G187200 chr6D 91.358 81 6 1 1 80 44486222 44486142 5.550000e-20 110.0
3 TraesCS6D01G187200 chr6D 89.130 46 5 0 35 80 393943071 393943026 2.040000e-04 58.4
4 TraesCS6D01G187200 chr6A 97.721 2721 36 4 1992 4703 346572238 346574941 0.000000e+00 4658.0
5 TraesCS6D01G187200 chr6A 94.352 1735 39 23 213 1900 346570519 346572241 0.000000e+00 2606.0
6 TraesCS6D01G187200 chr6A 98.345 423 7 0 4667 5089 346574940 346575362 0.000000e+00 743.0
7 TraesCS6D01G187200 chr6A 97.714 175 4 0 2 176 346563020 346563194 8.530000e-78 302.0
8 TraesCS6D01G187200 chr6A 96.855 159 2 2 5084 5239 346575384 346575542 4.020000e-66 263.0
9 TraesCS6D01G187200 chr6A 91.304 46 4 0 35 80 540151962 540151917 4.380000e-06 63.9
10 TraesCS6D01G187200 chr6B 98.161 1142 11 3 2066 3202 338014600 338013464 0.000000e+00 1984.0
11 TraesCS6D01G187200 chr6B 96.104 1001 14 6 3207 4182 338013364 338012364 0.000000e+00 1609.0
12 TraesCS6D01G187200 chr6B 93.901 869 13 12 577 1409 338016013 338015149 0.000000e+00 1275.0
13 TraesCS6D01G187200 chr6B 94.923 453 19 2 4787 5239 337943299 337942851 0.000000e+00 706.0
14 TraesCS6D01G187200 chr6B 89.961 518 35 9 3 505 338016727 338016212 0.000000e+00 652.0
15 TraesCS6D01G187200 chr6B 92.340 470 15 5 4232 4699 338012361 338011911 0.000000e+00 649.0
16 TraesCS6D01G187200 chr6B 94.118 255 6 5 1651 1900 338014949 338014699 3.830000e-101 379.0
17 TraesCS6D01G187200 chr6B 80.311 193 11 10 1471 1651 338015159 338014982 2.560000e-23 121.0
18 TraesCS6D01G187200 chr2D 87.055 309 40 0 1208 1516 406950440 406950748 3.000000e-92 350.0
19 TraesCS6D01G187200 chr2D 93.694 111 5 2 1896 2005 107204179 107204070 1.170000e-36 165.0
20 TraesCS6D01G187200 chr2A 87.055 309 40 0 1208 1516 574971094 574971402 3.000000e-92 350.0
21 TraesCS6D01G187200 chr2B 86.731 309 41 0 1208 1516 482731107 482731415 1.400000e-90 344.0
22 TraesCS6D01G187200 chr7D 97.115 104 3 0 1892 1995 407261198 407261301 5.390000e-40 176.0
23 TraesCS6D01G187200 chr1A 97.980 99 2 0 1898 1996 12578142 12578044 6.980000e-39 172.0
24 TraesCS6D01G187200 chr1A 92.920 113 6 2 1894 2004 337013343 337013231 4.200000e-36 163.0
25 TraesCS6D01G187200 chr4D 97.959 98 2 0 1898 1995 54412657 54412560 2.510000e-38 171.0
26 TraesCS6D01G187200 chr3D 95.327 107 3 2 1899 2004 79601652 79601757 9.020000e-38 169.0
27 TraesCS6D01G187200 chr3D 94.495 109 4 2 1898 2006 462197511 462197405 3.250000e-37 167.0
28 TraesCS6D01G187200 chr7B 88.406 138 13 3 1868 2002 706811176 706811039 4.200000e-36 163.0


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 TraesCS6D01G187200 chr6D 249991525 249996763 5238 True 9675.000000 9675 100.00000 1 5239 1 chr6D.!!$R3 5238
1 TraesCS6D01G187200 chr6A 346570519 346575542 5023 False 2067.500000 4658 96.81825 213 5239 4 chr6A.!!$F2 5026
2 TraesCS6D01G187200 chr6B 338011911 338016727 4816 True 952.714286 1984 92.12800 3 4699 7 chr6B.!!$R2 4696

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
449 468 0.595567 GCATATGGGTTGCGTGCATG 60.596 55.0 4.56 0.09 35.93 4.06 F
543 725 1.514003 ACACACGTGACAACACACAA 58.486 45.0 25.01 0.00 46.20 3.33 F
1734 2092 0.252558 TCAACAGTACCCTCCCTCCC 60.253 60.0 0.00 0.00 0.00 4.30 F
2144 2547 0.035317 TTGCTCACCAATCGCTGTCT 59.965 50.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1770 0.250234 TGAAGAAGAGATGGGTGGCG 59.750 55.000 0.00 0.00 0.00 5.69 R
1736 2094 0.940833 TGGCACACACATTACACACG 59.059 50.000 0.00 0.00 0.00 4.49 R
3409 3925 0.107017 TAGCTCAATTCCTGCAGCCC 60.107 55.000 8.66 0.00 32.01 5.19 R
4395 4928 3.805971 AGGCTATACGTCAATTAAACGGC 59.194 43.478 14.72 9.16 44.21 5.68 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
26 27 4.163427 TCTCTCTCCTCCAACTCAACAAT 58.837 43.478 0.00 0.00 0.00 2.71
94 95 0.605319 TTGCTCTTACCACCTTGCCG 60.605 55.000 0.00 0.00 0.00 5.69
95 96 1.295423 GCTCTTACCACCTTGCCGA 59.705 57.895 0.00 0.00 0.00 5.54
146 147 8.129840 CCAAGAGAAGATGATGCTTTATTTCTG 58.870 37.037 0.00 0.00 0.00 3.02
211 221 3.495377 TGTTTAGTCGAAATGTTGGTCGG 59.505 43.478 0.00 0.00 37.84 4.79
268 278 6.793505 AGTTACCCAAATAGAGACTACCAG 57.206 41.667 0.00 0.00 0.00 4.00
297 307 1.302285 AGGCAAGCATGTCTCCCAG 59.698 57.895 0.00 0.00 36.59 4.45
324 335 5.870978 GCATGCTACCAAACAAAATCTCAAT 59.129 36.000 11.37 0.00 0.00 2.57
325 336 7.035004 GCATGCTACCAAACAAAATCTCAATA 58.965 34.615 11.37 0.00 0.00 1.90
410 425 1.677217 GGTTGCATGGGAGAGTGAGAC 60.677 57.143 0.00 0.00 0.00 3.36
413 428 1.226802 CATGGGAGAGTGAGACGCG 60.227 63.158 3.53 3.53 0.00 6.01
449 468 0.595567 GCATATGGGTTGCGTGCATG 60.596 55.000 4.56 0.09 35.93 4.06
465 485 3.996363 GTGCATGGAGAAAACAATTTCCC 59.004 43.478 0.00 1.16 44.96 3.97
466 486 3.903090 TGCATGGAGAAAACAATTTCCCT 59.097 39.130 0.00 0.00 44.96 4.20
485 505 2.882137 CCTTCGGTGTTTGGTTACATGT 59.118 45.455 2.69 2.69 0.00 3.21
493 513 5.105957 GGTGTTTGGTTACATGTATGCATCA 60.106 40.000 0.19 1.39 31.99 3.07
505 525 4.139038 TGTATGCATCATGATTGGGAGTG 58.861 43.478 5.16 0.00 0.00 3.51
507 527 2.927028 TGCATCATGATTGGGAGTGAG 58.073 47.619 5.16 0.00 0.00 3.51
508 528 2.228059 GCATCATGATTGGGAGTGAGG 58.772 52.381 5.16 0.00 0.00 3.86
509 529 2.860009 CATCATGATTGGGAGTGAGGG 58.140 52.381 5.16 0.00 0.00 4.30
510 530 1.971149 TCATGATTGGGAGTGAGGGT 58.029 50.000 0.00 0.00 0.00 4.34
543 725 1.514003 ACACACGTGACAACACACAA 58.486 45.000 25.01 0.00 46.20 3.33
544 726 2.080693 ACACACGTGACAACACACAAT 58.919 42.857 25.01 0.00 46.20 2.71
1228 1453 2.847234 TGTGGTTCAGGCGGGACT 60.847 61.111 0.00 0.00 0.00 3.85
1516 1813 2.022934 ACCTCTACGGTTCGATTCCTC 58.977 52.381 5.78 0.00 46.37 3.71
1517 1814 1.337387 CCTCTACGGTTCGATTCCTCC 59.663 57.143 5.78 0.00 0.00 4.30
1518 1815 2.299521 CTCTACGGTTCGATTCCTCCT 58.700 52.381 5.78 0.00 0.00 3.69
1519 1816 3.474600 CTCTACGGTTCGATTCCTCCTA 58.525 50.000 5.78 0.00 0.00 2.94
1614 1915 8.432805 ACTTGGTTAAGATTTCTTCTCTTCTCA 58.567 33.333 0.00 0.00 37.36 3.27
1734 2092 0.252558 TCAACAGTACCCTCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
1735 2093 0.252742 CAACAGTACCCTCCCTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
1736 2094 0.042881 AACAGTACCCTCCCTCCCTC 59.957 60.000 0.00 0.00 0.00 4.30
1737 2095 1.455959 CAGTACCCTCCCTCCCTCG 60.456 68.421 0.00 0.00 0.00 4.63
1743 2101 1.000019 CCTCCCTCCCTCGTGTGTA 60.000 63.158 0.00 0.00 0.00 2.90
1851 2212 2.026822 AGCATCAAACACTACTCCCTGG 60.027 50.000 0.00 0.00 0.00 4.45
1900 2261 3.834231 TCTTGTACCCACCAACCTAGTAC 59.166 47.826 0.00 0.00 35.08 2.73
1902 2263 3.434309 TGTACCCACCAACCTAGTACTC 58.566 50.000 0.00 0.00 35.45 2.59
1903 2264 1.948391 ACCCACCAACCTAGTACTCC 58.052 55.000 0.00 0.00 0.00 3.85
1904 2265 1.201424 CCCACCAACCTAGTACTCCC 58.799 60.000 0.00 0.00 0.00 4.30
1905 2266 1.273666 CCCACCAACCTAGTACTCCCT 60.274 57.143 0.00 0.00 0.00 4.20
1906 2267 2.108970 CCACCAACCTAGTACTCCCTC 58.891 57.143 0.00 0.00 0.00 4.30
1907 2268 2.108970 CACCAACCTAGTACTCCCTCC 58.891 57.143 0.00 0.00 0.00 4.30
1908 2269 1.341778 ACCAACCTAGTACTCCCTCCG 60.342 57.143 0.00 0.00 0.00 4.63
1909 2270 1.341778 CCAACCTAGTACTCCCTCCGT 60.342 57.143 0.00 0.00 0.00 4.69
1910 2271 2.454538 CAACCTAGTACTCCCTCCGTT 58.545 52.381 0.00 0.00 0.00 4.44
1911 2272 2.830321 CAACCTAGTACTCCCTCCGTTT 59.170 50.000 0.00 0.00 0.00 3.60
1912 2273 2.732763 ACCTAGTACTCCCTCCGTTTC 58.267 52.381 0.00 0.00 0.00 2.78
1913 2274 2.042162 ACCTAGTACTCCCTCCGTTTCA 59.958 50.000 0.00 0.00 0.00 2.69
1914 2275 3.094572 CCTAGTACTCCCTCCGTTTCAA 58.905 50.000 0.00 0.00 0.00 2.69
1915 2276 3.512724 CCTAGTACTCCCTCCGTTTCAAA 59.487 47.826 0.00 0.00 0.00 2.69
1916 2277 4.020839 CCTAGTACTCCCTCCGTTTCAAAA 60.021 45.833 0.00 0.00 0.00 2.44
1917 2278 4.635699 AGTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
1918 2279 5.750352 AGTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
1919 2280 5.731591 AGTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
1920 2281 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1921 2282 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1922 2283 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1923 2284 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1924 2285 6.001449 TCCCTCCGTTTCAAAATAGATGAT 57.999 37.500 0.00 0.00 0.00 2.45
1925 2286 6.055588 TCCCTCCGTTTCAAAATAGATGATC 58.944 40.000 0.00 0.00 0.00 2.92
1926 2287 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
1927 2288 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
1928 2289 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
1929 2290 7.083875 TCCGTTTCAAAATAGATGATCCAAC 57.916 36.000 0.00 0.00 0.00 3.77
1930 2291 6.884295 TCCGTTTCAAAATAGATGATCCAACT 59.116 34.615 0.00 0.00 0.00 3.16
1931 2292 7.393234 TCCGTTTCAAAATAGATGATCCAACTT 59.607 33.333 0.00 0.00 0.00 2.66
1932 2293 8.028938 CCGTTTCAAAATAGATGATCCAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
1933 2294 8.853345 CGTTTCAAAATAGATGATCCAACTTTG 58.147 33.333 0.00 0.00 0.00 2.77
1934 2295 9.696917 GTTTCAAAATAGATGATCCAACTTTGT 57.303 29.630 0.00 0.00 0.00 2.83
1937 2298 9.739276 TCAAAATAGATGATCCAACTTTGTACT 57.261 29.630 0.00 0.00 0.00 2.73
1968 2329 7.797038 AGTACAAAGTTAGTACAAAGTTGGG 57.203 36.000 6.30 0.00 43.24 4.12
1969 2330 7.341030 AGTACAAAGTTAGTACAAAGTTGGGT 58.659 34.615 6.30 0.00 43.24 4.51
1970 2331 6.688637 ACAAAGTTAGTACAAAGTTGGGTC 57.311 37.500 0.00 0.00 0.00 4.46
1971 2332 6.181908 ACAAAGTTAGTACAAAGTTGGGTCA 58.818 36.000 0.00 0.00 0.00 4.02
1972 2333 6.831868 ACAAAGTTAGTACAAAGTTGGGTCAT 59.168 34.615 0.00 0.00 0.00 3.06
1973 2334 7.012989 ACAAAGTTAGTACAAAGTTGGGTCATC 59.987 37.037 0.00 0.00 0.00 2.92
1974 2335 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
1975 2336 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
1976 2337 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
1977 2338 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
1978 2339 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
1979 2340 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1980 2341 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1981 2342 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1982 2343 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1983 2344 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1984 2345 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1985 2346 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1986 2347 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1987 2348 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1988 2349 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1989 2350 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1990 2351 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2142 2545 0.534877 TGTTGCTCACCAATCGCTGT 60.535 50.000 0.00 0.00 35.55 4.40
2143 2546 0.166814 GTTGCTCACCAATCGCTGTC 59.833 55.000 0.00 0.00 35.55 3.51
2144 2547 0.035317 TTGCTCACCAATCGCTGTCT 59.965 50.000 0.00 0.00 0.00 3.41
2145 2548 0.671472 TGCTCACCAATCGCTGTCTG 60.671 55.000 0.00 0.00 0.00 3.51
2146 2549 1.975363 GCTCACCAATCGCTGTCTGC 61.975 60.000 0.00 0.00 38.57 4.26
2460 2871 9.080097 AGGAACAATCACTACTGACCTATATAC 57.920 37.037 0.00 0.00 0.00 1.47
2800 3213 1.294780 CTGCAGCCTCTTCCTTCGT 59.705 57.895 0.00 0.00 0.00 3.85
3409 3925 4.363990 ACCCGAGTCTGTGCTGCG 62.364 66.667 0.00 0.00 0.00 5.18
3820 4342 2.158696 GGATGGAAGTCAGGGATGAAGG 60.159 54.545 0.00 0.00 0.00 3.46
3823 4345 1.630878 GGAAGTCAGGGATGAAGGTGT 59.369 52.381 0.00 0.00 0.00 4.16
4395 4928 7.477144 TGTACATTATATTGCCTTCTGTTCG 57.523 36.000 0.00 0.00 0.00 3.95
4398 4931 1.299541 ATATTGCCTTCTGTTCGCCG 58.700 50.000 0.00 0.00 0.00 6.46
4399 4932 0.036765 TATTGCCTTCTGTTCGCCGT 60.037 50.000 0.00 0.00 0.00 5.68
4400 4933 0.889186 ATTGCCTTCTGTTCGCCGTT 60.889 50.000 0.00 0.00 0.00 4.44
4401 4934 1.098712 TTGCCTTCTGTTCGCCGTTT 61.099 50.000 0.00 0.00 0.00 3.60
4402 4935 0.249953 TGCCTTCTGTTCGCCGTTTA 60.250 50.000 0.00 0.00 0.00 2.01
4403 4936 0.869730 GCCTTCTGTTCGCCGTTTAA 59.130 50.000 0.00 0.00 0.00 1.52
4404 4937 1.467342 GCCTTCTGTTCGCCGTTTAAT 59.533 47.619 0.00 0.00 0.00 1.40
4405 4938 2.095415 GCCTTCTGTTCGCCGTTTAATT 60.095 45.455 0.00 0.00 0.00 1.40
4406 4939 3.488489 CCTTCTGTTCGCCGTTTAATTG 58.512 45.455 0.00 0.00 0.00 2.32
4407 4940 3.187637 CCTTCTGTTCGCCGTTTAATTGA 59.812 43.478 0.00 0.00 0.00 2.57
4408 4941 3.799137 TCTGTTCGCCGTTTAATTGAC 57.201 42.857 0.00 0.00 0.00 3.18
4409 4942 2.156117 TCTGTTCGCCGTTTAATTGACG 59.844 45.455 8.65 8.65 40.05 4.35
4603 5138 0.968405 GGTTCTTGCCATCTTTGCCA 59.032 50.000 0.00 0.00 0.00 4.92
4715 5285 7.273815 CGAACAAGCCAAAAGTAAGTTAAAACA 59.726 33.333 0.00 0.00 0.00 2.83
4798 5368 5.643379 TCTTCATGGCCTTACAATCAAAC 57.357 39.130 3.32 0.00 0.00 2.93
4799 5369 4.462483 TCTTCATGGCCTTACAATCAAACC 59.538 41.667 3.32 0.00 0.00 3.27
4839 5409 5.659525 TGGGAGCTGCTACAAAATAGTACTA 59.340 40.000 14.92 4.77 0.00 1.82
5003 5573 2.079925 GACAAGCAACTCATCTGGTCC 58.920 52.381 0.00 0.00 29.13 4.46
5077 5647 2.936498 CCCTACGTTGCCAGAATACAAG 59.064 50.000 0.00 0.00 0.00 3.16
5174 5774 9.979578 AAACAATCACAACAGCTCAAAATATAA 57.020 25.926 0.00 0.00 0.00 0.98
5180 5780 8.817100 TCACAACAGCTCAAAATATAATACTCG 58.183 33.333 0.00 0.00 0.00 4.18
5191 5791 7.745620 AAATATAATACTCGGAAAGGCTTGG 57.254 36.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.881019 TGAGTTGGAGGAGAGAGAAAAG 57.119 45.455 0.00 0.00 0.00 2.27
4 5 3.244887 TGTTGAGTTGGAGGAGAGAGA 57.755 47.619 0.00 0.00 0.00 3.10
5 6 4.550076 ATTGTTGAGTTGGAGGAGAGAG 57.450 45.455 0.00 0.00 0.00 3.20
6 7 6.627087 ATTATTGTTGAGTTGGAGGAGAGA 57.373 37.500 0.00 0.00 0.00 3.10
7 8 7.331026 TGTATTATTGTTGAGTTGGAGGAGAG 58.669 38.462 0.00 0.00 0.00 3.20
111 112 6.609533 CATCATCTTCTCTTGGTTTTCACAG 58.390 40.000 0.00 0.00 0.00 3.66
186 187 6.128499 CCGACCAACATTTCGACTAAACATAA 60.128 38.462 0.00 0.00 37.43 1.90
204 214 1.240256 GCCAATACAACACCGACCAA 58.760 50.000 0.00 0.00 0.00 3.67
211 221 5.447624 AGTTTTAGGTGCCAATACAACAC 57.552 39.130 0.00 0.00 0.00 3.32
227 237 6.071616 GGGTAACTTGCATCAATGGAGTTTTA 60.072 38.462 3.23 0.00 0.00 1.52
268 278 1.527034 TGCTTGCCTCAGATTGTGTC 58.473 50.000 0.00 0.00 0.00 3.67
297 307 5.413499 AGATTTTGTTTGGTAGCATGCATC 58.587 37.500 21.98 11.91 0.00 3.91
324 335 6.818142 CCTTGTATGTGTTGAGACATGTCATA 59.182 38.462 27.02 12.80 37.16 2.15
325 336 5.645067 CCTTGTATGTGTTGAGACATGTCAT 59.355 40.000 27.02 13.02 37.16 3.06
410 425 1.070175 CAGGGAACTAAACAACACGCG 60.070 52.381 3.53 3.53 40.21 6.01
413 428 5.393027 CCATATGCAGGGAACTAAACAACAC 60.393 44.000 0.00 0.00 40.21 3.32
465 485 5.627172 CATACATGTAACCAAACACCGAAG 58.373 41.667 10.14 0.00 30.75 3.79
466 486 4.083217 GCATACATGTAACCAAACACCGAA 60.083 41.667 10.14 0.00 30.75 4.30
485 505 4.506095 CCTCACTCCCAATCATGATGCATA 60.506 45.833 9.46 0.00 0.00 3.14
493 513 2.774234 CTGTACCCTCACTCCCAATCAT 59.226 50.000 0.00 0.00 0.00 2.45
505 525 6.749118 CGTGTGTAGTTTATTACTGTACCCTC 59.251 42.308 0.00 0.00 37.73 4.30
507 527 6.308766 CACGTGTGTAGTTTATTACTGTACCC 59.691 42.308 7.58 0.00 37.73 3.69
508 528 7.061094 GTCACGTGTGTAGTTTATTACTGTACC 59.939 40.741 16.51 0.00 37.73 3.34
509 529 7.591057 TGTCACGTGTGTAGTTTATTACTGTAC 59.409 37.037 16.51 0.00 37.73 2.90
510 530 7.647228 TGTCACGTGTGTAGTTTATTACTGTA 58.353 34.615 16.51 0.00 37.73 2.74
543 725 6.483974 TGGTACGTGTCTTGTTCATGTAAAAT 59.516 34.615 0.00 0.00 38.47 1.82
544 726 5.816258 TGGTACGTGTCTTGTTCATGTAAAA 59.184 36.000 0.00 0.00 38.47 1.52
638 825 4.927267 ATCCCATAATATTCGCCTCCAA 57.073 40.909 0.00 0.00 0.00 3.53
1228 1453 2.970324 GTTGTCCTCCACGCGCAA 60.970 61.111 5.73 0.00 0.00 4.85
1470 1767 4.473520 AAGAGATGGGTGGCGCCG 62.474 66.667 23.90 0.00 38.44 6.46
1471 1768 2.514824 GAAGAGATGGGTGGCGCC 60.515 66.667 22.73 22.73 0.00 6.53
1472 1769 1.078143 AAGAAGAGATGGGTGGCGC 60.078 57.895 0.00 0.00 0.00 6.53
1473 1770 0.250234 TGAAGAAGAGATGGGTGGCG 59.750 55.000 0.00 0.00 0.00 5.69
1474 1771 2.087646 GTTGAAGAAGAGATGGGTGGC 58.912 52.381 0.00 0.00 0.00 5.01
1475 1772 2.040278 TGGTTGAAGAAGAGATGGGTGG 59.960 50.000 0.00 0.00 0.00 4.61
1516 1813 4.037446 GCAAGAGTGAGAGATGTAGGTAGG 59.963 50.000 0.00 0.00 0.00 3.18
1517 1814 4.887071 AGCAAGAGTGAGAGATGTAGGTAG 59.113 45.833 0.00 0.00 0.00 3.18
1518 1815 4.861196 AGCAAGAGTGAGAGATGTAGGTA 58.139 43.478 0.00 0.00 0.00 3.08
1519 1816 3.707316 AGCAAGAGTGAGAGATGTAGGT 58.293 45.455 0.00 0.00 0.00 3.08
1635 1951 6.502158 TGGATCTAGTTCCTTTCTCCTTTTCT 59.498 38.462 18.59 0.00 36.68 2.52
1636 1952 6.596106 GTGGATCTAGTTCCTTTCTCCTTTTC 59.404 42.308 18.59 0.00 36.68 2.29
1637 1953 6.273495 AGTGGATCTAGTTCCTTTCTCCTTTT 59.727 38.462 18.59 0.00 36.68 2.27
1638 1954 5.788014 AGTGGATCTAGTTCCTTTCTCCTTT 59.212 40.000 18.59 0.00 36.68 3.11
1639 1955 5.346270 AGTGGATCTAGTTCCTTTCTCCTT 58.654 41.667 18.59 0.00 36.68 3.36
1640 1956 4.954089 AGTGGATCTAGTTCCTTTCTCCT 58.046 43.478 18.59 4.81 36.68 3.69
1641 1957 4.202070 CGAGTGGATCTAGTTCCTTTCTCC 60.202 50.000 18.59 9.01 36.68 3.71
1734 2092 1.194547 GGCACACACATTACACACGAG 59.805 52.381 0.00 0.00 0.00 4.18
1735 2093 1.222300 GGCACACACATTACACACGA 58.778 50.000 0.00 0.00 0.00 4.35
1736 2094 0.940833 TGGCACACACATTACACACG 59.059 50.000 0.00 0.00 0.00 4.49
1737 2095 3.004210 TGATTGGCACACACATTACACAC 59.996 43.478 0.00 0.00 39.29 3.82
1743 2101 4.811969 ATGATTGATTGGCACACACATT 57.188 36.364 0.00 0.00 39.29 2.71
1851 2212 6.877611 TTTGGGAATTAAAGACTGAGTGTC 57.122 37.500 0.00 0.00 45.67 3.67
1900 2261 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
1902 2263 5.239525 GGATCATCTATTTTGAAACGGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
1903 2264 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
1904 2265 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
1905 2266 6.884295 AGTTGGATCATCTATTTTGAAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
1906 2267 7.088589 AGTTGGATCATCTATTTTGAAACGG 57.911 36.000 0.00 0.00 0.00 4.44
1907 2268 8.853345 CAAAGTTGGATCATCTATTTTGAAACG 58.147 33.333 0.00 0.00 0.00 3.60
1908 2269 9.696917 ACAAAGTTGGATCATCTATTTTGAAAC 57.303 29.630 12.56 0.00 0.00 2.78
1911 2272 9.739276 AGTACAAAGTTGGATCATCTATTTTGA 57.261 29.630 12.56 0.00 0.00 2.69
1942 2303 9.328845 CCCAACTTTGTACTAACTTTGTACTAA 57.671 33.333 12.73 10.75 40.44 2.24
1943 2304 8.485392 ACCCAACTTTGTACTAACTTTGTACTA 58.515 33.333 12.73 4.86 40.44 1.82
1944 2305 7.341030 ACCCAACTTTGTACTAACTTTGTACT 58.659 34.615 12.73 0.00 40.44 2.73
1945 2306 7.280652 TGACCCAACTTTGTACTAACTTTGTAC 59.719 37.037 6.58 6.58 40.27 2.90
1946 2307 7.337167 TGACCCAACTTTGTACTAACTTTGTA 58.663 34.615 0.00 0.00 0.00 2.41
1947 2308 6.181908 TGACCCAACTTTGTACTAACTTTGT 58.818 36.000 0.00 0.00 0.00 2.83
1948 2309 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
1949 2310 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
1950 2311 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
1951 2312 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
1952 2313 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
1953 2314 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1954 2315 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1955 2316 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1956 2317 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1957 2318 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1958 2319 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1959 2320 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1960 2321 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1961 2322 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1962 2323 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1963 2324 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1964 2325 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1965 2326 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1966 2327 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1967 2328 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1968 2329 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1969 2330 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1970 2331 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1971 2332 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1972 2333 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1973 2334 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1974 2335 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1975 2336 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1976 2337 4.376225 AAATACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
1977 2338 5.703730 ATAAATACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
1978 2339 5.703730 AATAAATACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
1979 2340 5.901276 AGTAATAAATACTCCCTCCGTTCCA 59.099 40.000 0.00 0.00 41.04 3.53
1980 2341 6.416631 AGTAATAAATACTCCCTCCGTTCC 57.583 41.667 0.00 0.00 41.04 3.62
1981 2342 8.175925 AGTAGTAATAAATACTCCCTCCGTTC 57.824 38.462 0.00 0.00 43.87 3.95
1982 2343 9.294614 CTAGTAGTAATAAATACTCCCTCCGTT 57.705 37.037 0.00 0.00 43.87 4.44
1983 2344 8.443979 ACTAGTAGTAATAAATACTCCCTCCGT 58.556 37.037 0.00 0.00 43.87 4.69
1984 2345 8.860780 ACTAGTAGTAATAAATACTCCCTCCG 57.139 38.462 0.00 0.00 43.87 4.63
1985 2346 9.241919 GGACTAGTAGTAATAAATACTCCCTCC 57.758 40.741 1.88 0.00 43.87 4.30
1986 2347 8.945057 CGGACTAGTAGTAATAAATACTCCCTC 58.055 40.741 1.88 0.00 43.87 4.30
1987 2348 7.887495 CCGGACTAGTAGTAATAAATACTCCCT 59.113 40.741 1.88 0.00 43.87 4.20
1988 2349 7.667635 ACCGGACTAGTAGTAATAAATACTCCC 59.332 40.741 9.46 0.00 43.87 4.30
1989 2350 8.628630 ACCGGACTAGTAGTAATAAATACTCC 57.371 38.462 9.46 0.00 43.87 3.85
2142 2545 2.265109 GCAGCAGAGCAGAGCAGA 59.735 61.111 0.00 0.00 0.00 4.26
2143 2546 2.820479 GGCAGCAGAGCAGAGCAG 60.820 66.667 0.00 0.00 35.83 4.24
2144 2547 4.405671 GGGCAGCAGAGCAGAGCA 62.406 66.667 0.00 0.00 35.83 4.26
2460 2871 4.272504 ACAAGTCACCTGTCGTTATTGTTG 59.727 41.667 0.00 0.00 0.00 3.33
2797 3210 4.812476 CGCAGGCCGATGGAACGA 62.812 66.667 0.00 0.00 40.02 3.85
2800 3213 3.074369 TCTCGCAGGCCGATGGAA 61.074 61.111 0.00 0.00 46.31 3.53
3409 3925 0.107017 TAGCTCAATTCCTGCAGCCC 60.107 55.000 8.66 0.00 32.01 5.19
4395 4928 3.805971 AGGCTATACGTCAATTAAACGGC 59.194 43.478 14.72 9.16 44.21 5.68
4398 4931 6.673154 ACCAAGGCTATACGTCAATTAAAC 57.327 37.500 0.00 0.00 0.00 2.01
4399 4932 7.041644 GCATACCAAGGCTATACGTCAATTAAA 60.042 37.037 0.00 0.00 0.00 1.52
4400 4933 6.425721 GCATACCAAGGCTATACGTCAATTAA 59.574 38.462 0.00 0.00 0.00 1.40
4401 4934 5.929992 GCATACCAAGGCTATACGTCAATTA 59.070 40.000 0.00 0.00 0.00 1.40
4402 4935 4.755123 GCATACCAAGGCTATACGTCAATT 59.245 41.667 0.00 0.00 0.00 2.32
4403 4936 4.202315 TGCATACCAAGGCTATACGTCAAT 60.202 41.667 0.00 0.00 32.35 2.57
4404 4937 3.133183 TGCATACCAAGGCTATACGTCAA 59.867 43.478 0.00 0.00 32.35 3.18
4405 4938 2.696187 TGCATACCAAGGCTATACGTCA 59.304 45.455 0.00 0.00 32.35 4.35
4406 4939 3.318017 CTGCATACCAAGGCTATACGTC 58.682 50.000 0.00 0.00 32.35 4.34
4407 4940 2.037251 CCTGCATACCAAGGCTATACGT 59.963 50.000 0.00 0.00 32.35 3.57
4408 4941 2.299013 TCCTGCATACCAAGGCTATACG 59.701 50.000 0.00 0.00 32.35 3.06
4409 4942 4.040461 TCTTCCTGCATACCAAGGCTATAC 59.960 45.833 0.00 0.00 32.35 1.47
4530 5063 3.326836 TCTGATAAACGGTGCACATCA 57.673 42.857 20.43 16.67 0.00 3.07
4577 5112 2.242043 AGATGGCAAGAACCAAAGGTG 58.758 47.619 0.00 0.00 44.65 4.00
4603 5138 3.073062 AGCTATGTGGTGACTTCTTGGTT 59.927 43.478 0.00 0.00 0.00 3.67
4715 5285 0.746659 GGTGAGGCTTGTGCAGTTTT 59.253 50.000 0.00 0.00 41.91 2.43
4798 5368 0.248289 CCAGTTACACCACTACCCGG 59.752 60.000 0.00 0.00 0.00 5.73
4799 5369 0.248289 CCCAGTTACACCACTACCCG 59.752 60.000 0.00 0.00 0.00 5.28
4862 5432 7.581213 TCTGTCCACTTGTGTTAATTTTGAT 57.419 32.000 0.00 0.00 0.00 2.57
5077 5647 4.819630 TGTAACAGAACACCACAATCCTTC 59.180 41.667 0.00 0.00 0.00 3.46
5174 5774 0.107165 GGCCAAGCCTTTCCGAGTAT 60.107 55.000 0.00 0.00 46.69 2.12
5191 5791 1.533625 TGAGCTATTGTTGTGTGGGC 58.466 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.