Multiple sequence alignment - TraesCS2B01G272100

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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 TraesCS2B01G272100 chr2B 100.000 2952 0 0 1 2952 373491054 373494005 0.000000e+00 5452
1 TraesCS2B01G272100 chr2B 74.848 330 55 18 2329 2634 67698983 67698658 1.110000e-24 124
2 TraesCS2B01G272100 chr2A 94.229 1265 41 10 949 2198 383608049 383609296 0.000000e+00 1903
3 TraesCS2B01G272100 chr2A 96.429 616 14 3 301 913 383607460 383608070 0.000000e+00 1009
4 TraesCS2B01G272100 chr2A 95.190 499 22 2 2456 2952 383609765 383610263 0.000000e+00 787
5 TraesCS2B01G272100 chr2A 96.246 293 8 3 1 290 383607076 383607368 7.400000e-131 477
6 TraesCS2B01G272100 chr2A 90.756 119 10 1 2283 2401 383609424 383609541 1.100000e-34 158
7 TraesCS2B01G272100 chr2A 92.661 109 8 0 2400 2508 383609657 383609765 1.100000e-34 158
8 TraesCS2B01G272100 chr2D 93.806 888 33 7 946 1824 304992312 304993186 0.000000e+00 1315
9 TraesCS2B01G272100 chr2D 96.480 625 14 4 301 923 304991715 304992333 0.000000e+00 1026
10 TraesCS2B01G272100 chr2D 97.638 381 7 2 1807 2185 304993207 304993587 0.000000e+00 652
11 TraesCS2B01G272100 chr2D 94.286 315 18 0 2638 2952 304993601 304993915 1.590000e-132 483
12 TraesCS2B01G272100 chr2D 91.786 280 13 5 1 280 304990504 304990773 5.970000e-102 381
13 TraesCS2B01G272100 chr5B 78.729 362 55 17 2219 2561 584110533 584110891 3.830000e-54 222
14 TraesCS2B01G272100 chr1D 74.324 296 57 15 2659 2950 480556810 480557090 1.120000e-19 108


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 TraesCS2B01G272100 chr2B 373491054 373494005 2951 False 5452.000000 5452 100.000000 1 2952 1 chr2B.!!$F1 2951
1 TraesCS2B01G272100 chr2A 383607076 383610263 3187 False 748.666667 1903 94.251833 1 2952 6 chr2A.!!$F1 2951
2 TraesCS2B01G272100 chr2D 304990504 304993915 3411 False 771.400000 1315 94.799200 1 2952 5 chr2D.!!$F1 2951

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
959 1886 0.478507 GAGAGAGGGAGAGGGAGAGG 59.521 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2826 4066 0.250338 GCTCCTCGAGTTGTGGGTTT 60.25 55.0 12.31 0.0 31.39 3.27 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
135 136 4.273969 CCAGTGGTTTCGTGTTAAGCTTAA 59.726 41.667 14.96 14.96 0.00 1.85
250 253 0.987294 TGAGGAGCCTTTTCTCAGGG 59.013 55.000 0.00 0.00 33.21 4.45
292 1118 7.768120 GCTGCTCCATTCTATTTAGTATGCTAT 59.232 37.037 0.00 0.00 31.97 2.97
626 1552 3.430218 GGCCTTCAAGTCATTCGATATCG 59.570 47.826 19.14 19.14 41.45 2.92
678 1604 4.696877 TCTGATCTGCATTGGTTTACACAG 59.303 41.667 0.00 0.00 0.00 3.66
765 1692 5.596836 TTTTTGGTTCATGAGTTGCTTCT 57.403 34.783 0.00 0.00 0.00 2.85
766 1693 5.596836 TTTTGGTTCATGAGTTGCTTCTT 57.403 34.783 0.00 0.00 0.00 2.52
767 1694 5.596836 TTTGGTTCATGAGTTGCTTCTTT 57.403 34.783 0.00 0.00 0.00 2.52
768 1695 4.836125 TGGTTCATGAGTTGCTTCTTTC 57.164 40.909 0.00 0.00 0.00 2.62
771 1698 4.225208 GTTCATGAGTTGCTTCTTTCAGC 58.775 43.478 0.00 0.00 40.55 4.26
906 1833 1.474879 GGAAAGAGACGGGTCAGAGAG 59.525 57.143 1.17 0.00 0.00 3.20
924 1851 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
925 1852 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
926 1853 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
927 1854 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
928 1855 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
929 1856 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
930 1857 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
931 1858 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
932 1859 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
933 1860 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
934 1861 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
935 1862 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
936 1863 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
937 1864 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
938 1865 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
939 1866 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
940 1867 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
941 1868 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
942 1869 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
943 1870 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
944 1871 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
945 1872 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
946 1873 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
947 1874 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
948 1875 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
949 1876 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
950 1877 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
951 1878 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.00 0.00 0.00 3.71
952 1879 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
953 1880 2.370189 GAGAGAGAGAGAGAGGGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
954 1881 1.421646 GAGAGAGAGAGAGGGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
955 1882 1.010793 AGAGAGAGAGAGGGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
956 1883 1.421646 GAGAGAGAGAGGGAGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
957 1884 1.010793 AGAGAGAGAGGGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
958 1885 1.421646 GAGAGAGAGGGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
959 1886 0.478507 GAGAGAGGGAGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
960 1887 0.998945 AGAGAGGGAGAGGGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
961 1888 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
962 1889 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
963 1890 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
964 1891 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
965 1892 0.996762 GGGAGAGGGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
966 1893 0.478507 GGAGAGGGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
967 1894 1.518367 GAGAGGGAGAGGGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
1139 2067 3.616956 TGCTCTACCCTGTCATTTGAG 57.383 47.619 0.00 0.00 0.00 3.02
1153 2081 1.308047 TTTGAGCGCTGTTGTGTCAT 58.692 45.000 18.48 0.00 0.00 3.06
1154 2082 1.308047 TTGAGCGCTGTTGTGTCATT 58.692 45.000 18.48 0.00 0.00 2.57
1155 2083 1.308047 TGAGCGCTGTTGTGTCATTT 58.692 45.000 18.48 0.00 0.00 2.32
1156 2084 1.002576 TGAGCGCTGTTGTGTCATTTG 60.003 47.619 18.48 0.00 0.00 2.32
1157 2085 1.264020 GAGCGCTGTTGTGTCATTTGA 59.736 47.619 18.48 0.00 0.00 2.69
1158 2086 1.675483 AGCGCTGTTGTGTCATTTGAA 59.325 42.857 10.39 0.00 0.00 2.69
1159 2087 2.294233 AGCGCTGTTGTGTCATTTGAAT 59.706 40.909 10.39 0.00 0.00 2.57
1160 2088 2.658325 GCGCTGTTGTGTCATTTGAATC 59.342 45.455 0.00 0.00 0.00 2.52
1161 2089 3.852939 GCGCTGTTGTGTCATTTGAATCA 60.853 43.478 0.00 0.00 0.00 2.57
1162 2090 4.478699 CGCTGTTGTGTCATTTGAATCAT 58.521 39.130 0.00 0.00 0.00 2.45
1163 2091 4.322539 CGCTGTTGTGTCATTTGAATCATG 59.677 41.667 0.00 0.00 0.00 3.07
1164 2092 4.090930 GCTGTTGTGTCATTTGAATCATGC 59.909 41.667 0.00 0.00 0.00 4.06
1165 2093 5.197682 TGTTGTGTCATTTGAATCATGCA 57.802 34.783 0.00 0.00 0.00 3.96
1222 2163 2.600769 AAGGCCGAGTCGACCACT 60.601 61.111 20.56 3.60 38.45 4.00
1246 2187 1.075151 CCCTACCCTGTCTCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
1267 2208 2.427506 GAGGGAAACACGAGCTTCATT 58.572 47.619 0.00 0.00 0.00 2.57
1522 2463 4.017126 CCAAGAGGGACCCAAGTAAATTC 58.983 47.826 14.60 0.00 40.01 2.17
1525 2466 3.923425 AGAGGGACCCAAGTAAATTCCTT 59.077 43.478 14.60 0.00 0.00 3.36
1526 2467 4.357097 AGAGGGACCCAAGTAAATTCCTTT 59.643 41.667 14.60 0.00 0.00 3.11
1528 2469 5.084519 AGGGACCCAAGTAAATTCCTTTTC 58.915 41.667 14.60 0.00 0.00 2.29
1529 2470 4.222145 GGGACCCAAGTAAATTCCTTTTCC 59.778 45.833 5.33 0.00 0.00 3.13
1534 2479 7.867921 ACCCAAGTAAATTCCTTTTCCTTTTT 58.132 30.769 0.00 0.00 0.00 1.94
1564 2509 2.199208 TCTTCTGCTCCATTCCATCCA 58.801 47.619 0.00 0.00 0.00 3.41
1585 2530 2.375146 TCAGCGGATGTAGAGTGCTTA 58.625 47.619 0.00 0.00 32.66 3.09
1599 2544 6.215495 AGAGTGCTTACTCTTGATAAGTCC 57.785 41.667 4.21 0.00 43.98 3.85
1653 2598 2.769663 AGTTGTTCAGTGGTGTGACCTA 59.230 45.455 0.00 0.00 39.58 3.08
1755 2704 1.341976 ACCAAAGGCACTCCAGTTTGT 60.342 47.619 0.00 0.00 38.49 2.83
1783 2732 7.489113 ACACATGAATTTCACAAGAAACACTTC 59.511 33.333 0.00 0.00 45.79 3.01
1802 2751 6.133392 CACTTCCACACGTAATTTACTGTTG 58.867 40.000 5.11 5.03 0.00 3.33
1909 2897 0.376152 GGATGATCTGTGCTGCGTTG 59.624 55.000 0.00 0.00 0.00 4.10
1982 2970 1.306296 GGTGGCTGGGATGGCTTAA 59.694 57.895 0.00 0.00 0.00 1.85
2139 3130 6.624423 AGGTGATTGAATGCAAACTGAATAC 58.376 36.000 0.00 0.00 37.59 1.89
2229 3296 7.102847 AGTTAGATGCTTACTAGAAGGTGAC 57.897 40.000 0.00 0.00 0.00 3.67
2239 3308 2.591715 AAGGTGACGCGCTTTGCT 60.592 55.556 5.73 0.00 43.27 3.91
2246 3315 0.722799 GACGCGCTTTGCTGTTTCTC 60.723 55.000 5.73 0.00 43.27 2.87
2247 3316 1.789739 CGCGCTTTGCTGTTTCTCG 60.790 57.895 5.56 0.00 43.27 4.04
2256 3325 1.344438 TGCTGTTTCTCGGTCATGAGT 59.656 47.619 0.00 0.00 37.28 3.41
2257 3326 2.224281 TGCTGTTTCTCGGTCATGAGTT 60.224 45.455 0.00 0.00 37.28 3.01
2258 3327 3.006430 TGCTGTTTCTCGGTCATGAGTTA 59.994 43.478 0.00 0.00 37.28 2.24
2259 3328 3.994392 GCTGTTTCTCGGTCATGAGTTAA 59.006 43.478 0.00 0.00 37.28 2.01
2260 3329 4.092091 GCTGTTTCTCGGTCATGAGTTAAG 59.908 45.833 0.00 0.00 37.28 1.85
2261 3330 5.209818 TGTTTCTCGGTCATGAGTTAAGT 57.790 39.130 0.00 0.00 37.28 2.24
2262 3331 5.227908 TGTTTCTCGGTCATGAGTTAAGTC 58.772 41.667 0.00 3.15 37.28 3.01
2263 3332 5.010719 TGTTTCTCGGTCATGAGTTAAGTCT 59.989 40.000 11.52 0.00 37.28 3.24
2264 3333 5.723672 TTCTCGGTCATGAGTTAAGTCTT 57.276 39.130 11.52 2.50 37.28 3.01
2265 3334 5.723672 TCTCGGTCATGAGTTAAGTCTTT 57.276 39.130 11.52 0.00 37.28 2.52
2266 3335 6.097915 TCTCGGTCATGAGTTAAGTCTTTT 57.902 37.500 11.52 0.00 37.28 2.27
2267 3336 6.522054 TCTCGGTCATGAGTTAAGTCTTTTT 58.478 36.000 11.52 0.00 37.28 1.94
2314 3383 8.637986 AGTTGAGCATTTTTACATAGAAAACCA 58.362 29.630 0.00 0.00 0.00 3.67
2316 3385 8.810652 TGAGCATTTTTACATAGAAAACCAAC 57.189 30.769 0.00 0.00 0.00 3.77
2320 3389 8.211838 GCATTTTTACATAGAAAACCAACGAAC 58.788 33.333 0.00 0.00 0.00 3.95
2342 3411 2.680841 CAAACCAAACTGAGTTGACCGA 59.319 45.455 0.00 0.00 0.00 4.69
2350 3419 4.392921 ACTGAGTTGACCGATATTCCTG 57.607 45.455 0.00 0.00 0.00 3.86
2352 3421 4.223032 ACTGAGTTGACCGATATTCCTGTT 59.777 41.667 0.00 0.00 0.00 3.16
2364 3433 9.847224 ACCGATATTCCTGTTTATTCAGTTTAT 57.153 29.630 0.00 0.00 34.02 1.40
2407 3593 3.850273 CCGTAGCTAGTCGTTTAGTGTTG 59.150 47.826 0.00 0.00 0.00 3.33
2411 3597 2.289257 GCTAGTCGTTTAGTGTTGGGGT 60.289 50.000 0.00 0.00 0.00 4.95
2418 3604 3.816523 CGTTTAGTGTTGGGGTGTATTGT 59.183 43.478 0.00 0.00 0.00 2.71
2426 3612 2.144730 TGGGGTGTATTGTCGTTTTCG 58.855 47.619 0.00 0.00 45.64 3.46
2450 3636 4.560739 TCCTACATGATCCCAACTGATCT 58.439 43.478 0.00 0.00 41.42 2.75
2508 3746 1.355720 ACTTCCCTACTTTGCTGGCAT 59.644 47.619 0.00 0.00 0.00 4.40
2576 3815 6.690194 ATTCACTCATACATTTGCCTCTTC 57.310 37.500 0.00 0.00 0.00 2.87
2582 3821 5.674525 TCATACATTTGCCTCTTCGAATCT 58.325 37.500 0.00 0.00 0.00 2.40
2593 3832 4.381398 CCTCTTCGAATCTCTCTTTCTGCA 60.381 45.833 0.00 0.00 0.00 4.41
2603 3842 4.687948 TCTCTCTTTCTGCACTGATTTTCG 59.312 41.667 0.00 0.00 0.00 3.46
2736 3976 4.747108 GCATAGCTACAACGATTGTCAGAT 59.253 41.667 0.00 5.53 44.12 2.90
2763 4003 2.166459 CTCACGTTGGCTTGGATCTCTA 59.834 50.000 0.00 0.00 0.00 2.43
2826 4066 2.338620 CGTCGGTCTTCCACTGCA 59.661 61.111 0.00 0.00 0.00 4.41
2835 4075 1.110442 CTTCCACTGCAAACCCACAA 58.890 50.000 0.00 0.00 0.00 3.33
2869 4109 0.458716 CGAGGAAGACGGAGAAAGCC 60.459 60.000 0.00 0.00 0.00 4.35
2902 4142 1.728971 CTTGACGCAGAACTAGCAAGG 59.271 52.381 0.00 0.00 31.60 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 0.893727 GCCACATCCGGGAAACTTGT 60.894 55.000 0.00 0.00 0.00 3.16
167 168 4.006319 AGTAGCTGGCAAGAACTCAATTC 58.994 43.478 0.00 0.00 37.62 2.17
379 1305 2.789409 AAGGGAAGAACCTCCATTCG 57.211 50.000 0.00 0.00 40.87 3.34
485 1411 0.473694 TCTCTCAAGGGGCCAAGTGA 60.474 55.000 4.39 4.24 0.00 3.41
678 1604 1.849976 GCAGAGAGGCTTGTGTGTGC 61.850 60.000 0.00 0.00 0.00 4.57
764 1691 2.159824 TCACTACTCGAGTCGCTGAAAG 59.840 50.000 23.89 14.38 35.64 2.62
765 1692 2.148768 TCACTACTCGAGTCGCTGAAA 58.851 47.619 23.89 0.88 35.64 2.69
766 1693 1.804601 TCACTACTCGAGTCGCTGAA 58.195 50.000 23.89 1.72 35.64 3.02
767 1694 1.463831 GTTCACTACTCGAGTCGCTGA 59.536 52.381 23.89 17.25 35.64 4.26
768 1695 1.465387 AGTTCACTACTCGAGTCGCTG 59.535 52.381 23.89 15.20 35.64 5.18
771 1698 3.808116 TTCAGTTCACTACTCGAGTCG 57.192 47.619 23.89 18.96 35.64 4.18
906 1833 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
924 1851 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
925 1852 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
926 1853 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
927 1854 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
928 1855 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
929 1856 3.051803 TCTCCCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
930 1857 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
931 1858 3.312890 CTCTCCCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
932 1859 2.370189 CCTCTCCCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
933 1860 2.412591 CCTCTCCCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
934 1861 1.421646 CCCTCTCCCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
935 1862 1.010793 TCCCTCTCCCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
936 1863 1.421646 CTCCCTCTCCCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
937 1864 1.010793 TCTCCCTCTCCCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
938 1865 1.421646 CTCTCCCTCTCCCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
939 1866 1.522900 CTCTCCCTCTCCCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
940 1867 0.478507 CCTCTCCCTCTCCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
941 1868 0.998945 CCCTCTCCCTCTCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
942 1869 0.996762 TCCCTCTCCCTCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
943 1870 0.998945 CTCCCTCTCCCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
944 1871 0.996762 TCTCCCTCTCCCTCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
945 1872 0.998945 CTCTCCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
946 1873 0.996762 TCTCTCCCTCTCCCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
947 1874 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
948 1875 1.421646 CTCTCTCTCCCTCTCCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
949 1876 1.522900 CTCTCTCTCCCTCTCCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
950 1877 0.478507 CCTCTCTCTCCCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
951 1878 0.998945 CCCTCTCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
952 1879 1.541672 CCCTCTCTCTCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
953 1880 1.293683 ACCCCTCTCTCTCCCTCTCC 61.294 65.000 0.00 0.00 0.00 3.71
954 1881 0.106217 CACCCCTCTCTCTCCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
955 1882 0.853586 ACACCCCTCTCTCTCCCTCT 60.854 60.000 0.00 0.00 0.00 3.69
956 1883 0.396556 GACACCCCTCTCTCTCCCTC 60.397 65.000 0.00 0.00 0.00 4.30
957 1884 0.853586 AGACACCCCTCTCTCTCCCT 60.854 60.000 0.00 0.00 0.00 4.20
958 1885 0.041982 AAGACACCCCTCTCTCTCCC 59.958 60.000 0.00 0.00 0.00 4.30
959 1886 1.945580 AAAGACACCCCTCTCTCTCC 58.054 55.000 0.00 0.00 0.00 3.71
960 1887 2.900546 TCAAAAGACACCCCTCTCTCTC 59.099 50.000 0.00 0.00 0.00 3.20
961 1888 2.903135 CTCAAAAGACACCCCTCTCTCT 59.097 50.000 0.00 0.00 0.00 3.10
962 1889 2.635427 ACTCAAAAGACACCCCTCTCTC 59.365 50.000 0.00 0.00 0.00 3.20
963 1890 2.695585 ACTCAAAAGACACCCCTCTCT 58.304 47.619 0.00 0.00 0.00 3.10
964 1891 3.493767 AACTCAAAAGACACCCCTCTC 57.506 47.619 0.00 0.00 0.00 3.20
965 1892 3.974642 ACTAACTCAAAAGACACCCCTCT 59.025 43.478 0.00 0.00 0.00 3.69
966 1893 4.353383 ACTAACTCAAAAGACACCCCTC 57.647 45.455 0.00 0.00 0.00 4.30
967 1894 4.790718 AACTAACTCAAAAGACACCCCT 57.209 40.909 0.00 0.00 0.00 4.79
1139 2067 2.118228 TTCAAATGACACAACAGCGC 57.882 45.000 0.00 0.00 0.00 5.92
1153 2081 4.850347 TCACACACATGCATGATTCAAA 57.150 36.364 32.75 11.05 0.00 2.69
1154 2082 4.459685 TGATCACACACATGCATGATTCAA 59.540 37.500 32.75 13.29 31.96 2.69
1155 2083 4.011023 TGATCACACACATGCATGATTCA 58.989 39.130 32.75 18.41 31.96 2.57
1156 2084 4.095932 ACTGATCACACACATGCATGATTC 59.904 41.667 32.75 16.40 31.96 2.52
1157 2085 4.014406 ACTGATCACACACATGCATGATT 58.986 39.130 32.75 15.68 31.96 2.57
1158 2086 3.377172 CACTGATCACACACATGCATGAT 59.623 43.478 32.75 15.69 34.50 2.45
1159 2087 2.745281 CACTGATCACACACATGCATGA 59.255 45.455 32.75 11.01 0.00 3.07
1160 2088 2.486592 ACACTGATCACACACATGCATG 59.513 45.455 25.09 25.09 0.00 4.06
1161 2089 2.486592 CACACTGATCACACACATGCAT 59.513 45.455 0.00 0.00 0.00 3.96
1162 2090 1.874872 CACACTGATCACACACATGCA 59.125 47.619 0.00 0.00 0.00 3.96
1163 2091 1.400629 GCACACTGATCACACACATGC 60.401 52.381 0.00 0.00 0.00 4.06
1164 2092 1.136169 CGCACACTGATCACACACATG 60.136 52.381 0.00 0.00 0.00 3.21
1165 2093 1.150827 CGCACACTGATCACACACAT 58.849 50.000 0.00 0.00 0.00 3.21
1222 2163 0.185416 GAGACAGGGTAGGGATCGGA 59.815 60.000 0.00 0.00 0.00 4.55
1246 2187 0.319555 TGAAGCTCGTGTTTCCCTCG 60.320 55.000 10.86 0.00 33.31 4.63
1267 2208 2.818841 CACCAGGTGACACCGTCA 59.181 61.111 15.35 0.00 44.90 4.35
1384 2325 0.611618 TGTTGGGCTGGTAGCAATGG 60.612 55.000 2.99 0.00 44.75 3.16
1408 2349 2.047274 TAGGAGGCGTGCAACAGC 60.047 61.111 0.00 0.00 35.74 4.40
1534 2479 8.219868 TGGAATGGAGCAGAAGATATATTTCAA 58.780 33.333 9.07 0.00 0.00 2.69
1564 2509 1.407936 AGCACTCTACATCCGCTGAT 58.592 50.000 0.00 0.00 0.00 2.90
1581 2526 4.113354 CCACGGACTTATCAAGAGTAAGC 58.887 47.826 0.00 0.00 33.47 3.09
1585 2530 2.093973 CAGCCACGGACTTATCAAGAGT 60.094 50.000 0.00 0.00 0.00 3.24
1599 2544 6.545504 AATAAAATATGTAGCTCAGCCACG 57.454 37.500 0.00 0.00 0.00 4.94
1633 2578 2.038387 AGGTCACACCACTGAACAAC 57.962 50.000 0.00 0.00 41.95 3.32
1653 2598 5.171339 ACCTATCAAGACAGACAGCAAAT 57.829 39.130 0.00 0.00 0.00 2.32
1755 2704 8.465999 AGTGTTTCTTGTGAAATTCATGTGTTA 58.534 29.630 0.00 0.00 43.14 2.41
1783 2732 9.834628 AATAATTCAACAGTAAATTACGTGTGG 57.165 29.630 0.00 6.46 31.95 4.17
1814 2763 8.759641 CAGCAGAAGCACTTAATATTACTACTG 58.240 37.037 0.00 0.00 45.49 2.74
2139 3130 3.496309 TGGCAGTGGGCACTTCCTG 62.496 63.158 0.00 0.00 43.72 3.86
2200 3267 9.649316 ACCTTCTAGTAAGCATCTAACTTATCT 57.351 33.333 0.00 0.00 32.53 1.98
2221 3288 2.127232 GCAAAGCGCGTCACCTTC 60.127 61.111 8.43 0.00 0.00 3.46
2239 3308 5.010719 AGACTTAACTCATGACCGAGAAACA 59.989 40.000 0.00 0.00 36.47 2.83
2264 3333 8.945193 ACTCTATCTGTAATAGCCCCATAAAAA 58.055 33.333 0.00 0.00 0.00 1.94
2265 3334 8.506196 ACTCTATCTGTAATAGCCCCATAAAA 57.494 34.615 0.00 0.00 0.00 1.52
2266 3335 8.375506 CAACTCTATCTGTAATAGCCCCATAAA 58.624 37.037 0.00 0.00 0.00 1.40
2267 3336 7.733047 TCAACTCTATCTGTAATAGCCCCATAA 59.267 37.037 0.00 0.00 0.00 1.90
2268 3337 7.246027 TCAACTCTATCTGTAATAGCCCCATA 58.754 38.462 0.00 0.00 0.00 2.74
2269 3338 6.084738 TCAACTCTATCTGTAATAGCCCCAT 58.915 40.000 0.00 0.00 0.00 4.00
2270 3339 5.464069 TCAACTCTATCTGTAATAGCCCCA 58.536 41.667 0.00 0.00 0.00 4.96
2271 3340 5.567823 GCTCAACTCTATCTGTAATAGCCCC 60.568 48.000 0.00 0.00 0.00 5.80
2272 3341 5.011125 TGCTCAACTCTATCTGTAATAGCCC 59.989 44.000 0.00 0.00 0.00 5.19
2273 3342 6.090483 TGCTCAACTCTATCTGTAATAGCC 57.910 41.667 0.00 0.00 0.00 3.93
2274 3343 8.600449 AAATGCTCAACTCTATCTGTAATAGC 57.400 34.615 0.00 0.00 0.00 2.97
2278 3347 9.719355 TGTAAAAATGCTCAACTCTATCTGTAA 57.281 29.630 0.00 0.00 0.00 2.41
2279 3348 9.890629 ATGTAAAAATGCTCAACTCTATCTGTA 57.109 29.630 0.00 0.00 0.00 2.74
2280 3349 8.798859 ATGTAAAAATGCTCAACTCTATCTGT 57.201 30.769 0.00 0.00 0.00 3.41
2314 3383 3.086282 ACTCAGTTTGGTTTGGTTCGTT 58.914 40.909 0.00 0.00 0.00 3.85
2316 3385 3.127895 TCAACTCAGTTTGGTTTGGTTCG 59.872 43.478 0.00 0.00 0.00 3.95
2320 3389 2.223479 CGGTCAACTCAGTTTGGTTTGG 60.223 50.000 0.00 0.00 0.00 3.28
2364 3433 3.878699 GGAAACACCGAACTAAAGACCAA 59.121 43.478 0.00 0.00 0.00 3.67
2387 3456 4.171754 CCCAACACTAAACGACTAGCTAC 58.828 47.826 0.00 0.00 0.00 3.58
2396 3465 3.816523 ACAATACACCCCAACACTAAACG 59.183 43.478 0.00 0.00 0.00 3.60
2407 3593 2.415776 TCGAAAACGACAATACACCCC 58.584 47.619 0.00 0.00 0.00 4.95
2411 3597 5.712004 TGTAGGATCGAAAACGACAATACA 58.288 37.500 0.00 0.00 0.00 2.29
2418 3604 4.500887 GGGATCATGTAGGATCGAAAACGA 60.501 45.833 0.00 0.00 43.69 3.85
2426 3612 4.963318 TCAGTTGGGATCATGTAGGATC 57.037 45.455 0.00 0.00 42.36 3.36
2436 3622 3.198635 TGGTCTGAAGATCAGTTGGGATC 59.801 47.826 7.21 0.00 44.58 3.36
2450 3636 5.364778 CCATTTCGGTGTATATGGTCTGAA 58.635 41.667 0.00 0.00 34.23 3.02
2454 3640 2.812011 GGCCATTTCGGTGTATATGGTC 59.188 50.000 0.00 0.00 39.75 4.02
2508 3746 3.281158 CACATTGGATCATGCCTACACA 58.719 45.455 0.00 0.00 0.00 3.72
2576 3815 3.842820 TCAGTGCAGAAAGAGAGATTCG 58.157 45.455 0.00 0.00 32.04 3.34
2582 3821 4.380531 ACGAAAATCAGTGCAGAAAGAGA 58.619 39.130 0.00 0.00 0.00 3.10
2593 3832 4.887655 AGTTCTTTTGGGACGAAAATCAGT 59.112 37.500 0.00 0.00 0.00 3.41
2603 3842 4.657013 AGAGATTGGAGTTCTTTTGGGAC 58.343 43.478 0.00 0.00 0.00 4.46
2652 3892 7.941238 CCAACAAGGTTGAGAGATTGGATATAT 59.059 37.037 10.48 0.00 37.85 0.86
2763 4003 1.929836 GAAACAGAATGATCGAGCGCT 59.070 47.619 11.27 11.27 39.69 5.92
2826 4066 0.250338 GCTCCTCGAGTTGTGGGTTT 60.250 55.000 12.31 0.00 31.39 3.27
2835 4075 1.747367 CTCGTCAGGCTCCTCGAGT 60.747 63.158 12.31 0.00 42.83 4.18
2869 4109 2.126850 TCAAGCAGTCGAGTCGCG 60.127 61.111 7.92 0.00 42.69 5.87
2871 4111 3.742353 CGTCAAGCAGTCGAGTCG 58.258 61.111 6.09 6.09 0.00 4.18
2895 4135 2.260434 GGCGACGACACCTTGCTA 59.740 61.111 0.00 0.00 0.00 3.49
2902 4142 4.131088 GAGAGGGGGCGACGACAC 62.131 72.222 1.63 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.