Multiple sequence alignment - TraesCS3B01G436800

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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 TraesCS3B01G436800 chr3B 100.000 2354 0 0 1 2354 675150823 675153176 0.000000e+00 4348.0
1 TraesCS3B01G436800 chr3D 84.601 1078 77 28 839 1893 512666966 512665955 0.000000e+00 989.0
2 TraesCS3B01G436800 chr3D 89.852 473 25 6 1904 2354 512665975 512665504 9.370000e-164 586.0
3 TraesCS3B01G436800 chr3D 79.114 474 66 15 1904 2354 514998220 514997757 1.770000e-76 296.0
4 TraesCS3B01G436800 chr3D 93.714 175 11 0 517 691 512667358 512667184 1.790000e-66 263.0
5 TraesCS3B01G436800 chr3D 81.269 331 49 8 1931 2249 549526411 549526082 3.000000e-64 255.0
6 TraesCS3B01G436800 chr3D 78.738 428 54 19 1964 2354 462867267 462867694 3.880000e-63 252.0
7 TraesCS3B01G436800 chr3D 93.182 176 4 3 684 851 512667163 512666988 3.880000e-63 252.0
8 TraesCS3B01G436800 chr3D 77.754 463 64 21 1930 2354 114525419 114524958 5.020000e-62 248.0
9 TraesCS3B01G436800 chr3D 79.054 296 40 10 1904 2182 47337918 47338208 1.440000e-42 183.0
10 TraesCS3B01G436800 chr1B 99.029 515 5 0 3 517 613240315 613240829 0.000000e+00 924.0
11 TraesCS3B01G436800 chr1B 95.538 381 17 0 3 383 282308966 282308586 5.560000e-171 610.0
12 TraesCS3B01G436800 chr1B 76.991 452 63 18 1941 2354 262511049 262510601 1.100000e-53 220.0
13 TraesCS3B01G436800 chr1B 91.379 58 5 0 1829 1886 579966632 579966689 1.940000e-11 80.5
14 TraesCS3B01G436800 chr2B 97.087 515 15 0 3 517 698958083 698958597 0.000000e+00 869.0
15 TraesCS3B01G436800 chr2B 77.682 466 76 8 1912 2353 481120203 481120664 2.320000e-65 259.0
16 TraesCS3B01G436800 chr2B 76.559 465 66 19 1930 2354 399812065 399811604 5.100000e-52 215.0
17 TraesCS3B01G436800 chr2B 78.873 284 49 10 1930 2206 763524327 763524606 5.170000e-42 182.0
18 TraesCS3B01G436800 chr2B 84.884 172 24 2 1904 2074 425213724 425213554 3.110000e-39 172.0
19 TraesCS3B01G436800 chr4D 95.914 514 21 0 4 517 44915757 44916270 0.000000e+00 833.0
20 TraesCS3B01G436800 chr3A 85.521 815 51 19 935 1731 648241799 648241034 0.000000e+00 789.0
21 TraesCS3B01G436800 chr3A 90.680 515 46 2 4 517 628861775 628862288 0.000000e+00 684.0
22 TraesCS3B01G436800 chr3A 87.919 298 17 10 571 851 648242194 648241899 1.350000e-87 333.0
23 TraesCS3B01G436800 chr4A 93.191 514 35 0 4 517 562293356 562293869 0.000000e+00 756.0
24 TraesCS3B01G436800 chr4A 76.715 627 88 21 1651 2240 24941089 24941694 1.770000e-76 296.0
25 TraesCS3B01G436800 chr4A 77.505 489 58 21 1904 2354 503609107 503609581 1.810000e-61 246.0
26 TraesCS3B01G436800 chr4A 78.404 426 48 21 1967 2352 432542455 432542034 1.090000e-58 237.0
27 TraesCS3B01G436800 chr5D 95.433 416 18 1 4 419 565331499 565331913 0.000000e+00 662.0
28 TraesCS3B01G436800 chr7A 85.214 514 76 0 4 517 43476806 43477319 1.600000e-146 529.0
29 TraesCS3B01G436800 chr7A 76.763 482 73 23 1911 2354 250980247 250980727 1.410000e-57 233.0
30 TraesCS3B01G436800 chr5A 80.943 509 91 6 4 509 367707980 367707475 4.710000e-107 398.0
31 TraesCS3B01G436800 chr6B 82.368 397 46 6 1972 2352 583050138 583049750 8.110000e-85 324.0
32 TraesCS3B01G436800 chr7B 78.913 460 58 19 1925 2354 527855463 527855013 2.300000e-70 276.0
33 TraesCS3B01G436800 chrUn 78.233 464 57 23 1931 2354 20702529 20702070 8.350000e-65 257.0
34 TraesCS3B01G436800 chr6D 77.459 488 68 18 1904 2352 421988416 421987932 1.080000e-63 254.0
35 TraesCS3B01G436800 chr7D 77.479 484 64 19 1904 2352 139300654 139300181 5.020000e-62 248.0
36 TraesCS3B01G436800 chr7D 77.066 484 67 19 1909 2352 367392501 367392022 3.020000e-59 239.0
37 TraesCS3B01G436800 chr5B 77.160 486 64 19 1909 2351 87141897 87141416 3.020000e-59 239.0
38 TraesCS3B01G436800 chr2D 92.500 40 3 0 1615 1654 564093448 564093409 9.090000e-05 58.4


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 TraesCS3B01G436800 chr3B 675150823 675153176 2353 False 4348.0 4348 100.00000 1 2354 1 chr3B.!!$F1 2353
1 TraesCS3B01G436800 chr3D 512665504 512667358 1854 True 522.5 989 90.33725 517 2354 4 chr3D.!!$R4 1837
2 TraesCS3B01G436800 chr1B 613240315 613240829 514 False 924.0 924 99.02900 3 517 1 chr1B.!!$F2 514
3 TraesCS3B01G436800 chr2B 698958083 698958597 514 False 869.0 869 97.08700 3 517 1 chr2B.!!$F2 514
4 TraesCS3B01G436800 chr4D 44915757 44916270 513 False 833.0 833 95.91400 4 517 1 chr4D.!!$F1 513
5 TraesCS3B01G436800 chr3A 628861775 628862288 513 False 684.0 684 90.68000 4 517 1 chr3A.!!$F1 513
6 TraesCS3B01G436800 chr3A 648241034 648242194 1160 True 561.0 789 86.72000 571 1731 2 chr3A.!!$R1 1160
7 TraesCS3B01G436800 chr4A 562293356 562293869 513 False 756.0 756 93.19100 4 517 1 chr4A.!!$F3 513
8 TraesCS3B01G436800 chr4A 24941089 24941694 605 False 296.0 296 76.71500 1651 2240 1 chr4A.!!$F1 589
9 TraesCS3B01G436800 chr7A 43476806 43477319 513 False 529.0 529 85.21400 4 517 1 chr7A.!!$F1 513
10 TraesCS3B01G436800 chr5A 367707475 367707980 505 True 398.0 398 80.94300 4 509 1 chr5A.!!$R1 505

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
954 1055 0.038166 TGGTCCATCAGTTGCCTTCC 59.962 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2222 1.097232 ACAACATGACCATGGATGCG 58.903 50.0 21.47 9.96 42.91 4.73 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
205 206 5.791336 TCAGCGAATAGTAGGTGATTCAT 57.209 39.130 0.97 0.00 39.56 2.57
442 443 3.245586 ACCAGATTAGCATTGAACCCCAA 60.246 43.478 0.00 0.00 39.41 4.12
524 525 1.089920 GTTTGATCGCACCATGCTCT 58.910 50.000 0.00 0.00 42.25 4.09
533 534 1.450848 ACCATGCTCTCCACATGCG 60.451 57.895 0.00 0.00 42.89 4.73
669 670 2.361104 GCTTGCATGGGAACGGGA 60.361 61.111 1.34 0.00 0.00 5.14
826 874 2.765807 CACCAGCTCGATCCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
848 896 1.134280 TCTATTGCTTGCAGCCTCCTC 60.134 52.381 5.82 0.00 41.51 3.71
850 898 1.860944 ATTGCTTGCAGCCTCCTCCT 61.861 55.000 5.82 0.00 41.51 3.69
853 901 1.077858 CTTGCAGCCTCCTCCTTCC 60.078 63.158 0.00 0.00 0.00 3.46
857 905 2.042435 AGCCTCCTCCTTCCTCCG 60.042 66.667 0.00 0.00 0.00 4.63
858 906 2.364448 GCCTCCTCCTTCCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
859 907 2.428085 GCCTCCTCCTTCCTCCGTC 61.428 68.421 0.00 0.00 0.00 4.79
861 909 1.000486 CTCCTCCTTCCTCCGTCCA 60.000 63.158 0.00 0.00 0.00 4.02
862 910 1.000486 TCCTCCTTCCTCCGTCCAG 60.000 63.158 0.00 0.00 0.00 3.86
863 911 2.060980 CCTCCTTCCTCCGTCCAGG 61.061 68.421 0.00 0.00 42.97 4.45
865 913 3.787001 CCTTCCTCCGTCCAGGCC 61.787 72.222 0.00 0.00 40.77 5.19
866 914 4.148825 CTTCCTCCGTCCAGGCCG 62.149 72.222 0.00 0.00 40.77 6.13
880 971 4.493747 GCCGCGGCTACGAGTTCT 62.494 66.667 41.71 0.00 44.60 3.01
908 999 2.646175 CCGGCCGGAGAGTTTCTCA 61.646 63.158 41.82 0.00 45.12 3.27
911 1002 0.827368 GGCCGGAGAGTTTCTCATCT 59.173 55.000 5.05 0.00 45.12 2.90
915 1006 3.798548 GCCGGAGAGTTTCTCATCTCATC 60.799 52.174 5.05 0.00 45.12 2.92
922 1013 7.255451 GGAGAGTTTCTCATCTCATCGTCTAAT 60.255 40.741 8.23 0.00 45.12 1.73
924 1015 6.434596 AGTTTCTCATCTCATCGTCTAATCG 58.565 40.000 0.00 0.00 0.00 3.34
931 1022 2.801111 CTCATCGTCTAATCGTCGGAGA 59.199 50.000 0.00 0.00 0.00 3.71
932 1023 2.801111 TCATCGTCTAATCGTCGGAGAG 59.199 50.000 0.00 0.00 36.95 3.20
941 1032 1.674651 CGTCGGAGAGAGTGGTCCA 60.675 63.158 0.00 0.00 36.95 4.02
949 1050 1.277557 AGAGAGTGGTCCATCAGTTGC 59.722 52.381 0.00 0.00 0.00 4.17
950 1051 0.326264 AGAGTGGTCCATCAGTTGCC 59.674 55.000 0.00 0.00 0.00 4.52
951 1052 0.326264 GAGTGGTCCATCAGTTGCCT 59.674 55.000 0.00 0.00 0.00 4.75
952 1053 0.773644 AGTGGTCCATCAGTTGCCTT 59.226 50.000 0.00 0.00 0.00 4.35
953 1054 1.168714 GTGGTCCATCAGTTGCCTTC 58.831 55.000 0.00 0.00 0.00 3.46
954 1055 0.038166 TGGTCCATCAGTTGCCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
955 1056 0.681243 GGTCCATCAGTTGCCTTCCC 60.681 60.000 0.00 0.00 0.00 3.97
956 1057 1.026718 GTCCATCAGTTGCCTTCCCG 61.027 60.000 0.00 0.00 0.00 5.14
957 1058 2.409870 CCATCAGTTGCCTTCCCGC 61.410 63.158 0.00 0.00 0.00 6.13
965 1066 2.125106 GCCTTCCCGCGTCTGAAT 60.125 61.111 4.92 0.00 0.00 2.57
975 1076 2.247637 CGCGTCTGAATTTCTCGTACA 58.752 47.619 0.00 0.00 0.00 2.90
985 1086 3.328382 TTTCTCGTACAATCCCTGTGG 57.672 47.619 0.00 0.00 39.20 4.17
987 1088 0.462047 CTCGTACAATCCCTGTGGCC 60.462 60.000 0.00 0.00 39.20 5.36
988 1089 0.907704 TCGTACAATCCCTGTGGCCT 60.908 55.000 3.32 0.00 39.20 5.19
989 1090 0.744414 CGTACAATCCCTGTGGCCTG 60.744 60.000 3.32 0.00 39.20 4.85
990 1091 0.328258 GTACAATCCCTGTGGCCTGT 59.672 55.000 3.32 0.00 39.20 4.00
991 1092 0.327924 TACAATCCCTGTGGCCTGTG 59.672 55.000 3.32 0.00 39.20 3.66
992 1093 2.036256 AATCCCTGTGGCCTGTGC 59.964 61.111 3.32 0.00 0.00 4.57
1021 1122 4.116585 AGAGGAGAGCGGCGAGGA 62.117 66.667 12.98 0.00 0.00 3.71
1023 1124 4.116585 AGGAGAGCGGCGAGGAGA 62.117 66.667 12.98 0.00 0.00 3.71
1025 1126 2.411290 GAGAGCGGCGAGGAGAAG 59.589 66.667 12.98 0.00 0.00 2.85
1037 1138 3.706373 GAGAAGCTCCGCCCACCA 61.706 66.667 0.00 0.00 0.00 4.17
1038 1139 3.959991 GAGAAGCTCCGCCCACCAC 62.960 68.421 0.00 0.00 0.00 4.16
1083 1184 3.368571 GTGGGGCAGAAGCAGCAC 61.369 66.667 0.00 0.00 44.61 4.40
1086 1187 3.060615 GGGCAGAAGCAGCACCAG 61.061 66.667 0.00 0.00 44.61 4.00
1087 1188 3.745803 GGCAGAAGCAGCACCAGC 61.746 66.667 0.00 0.00 44.61 4.85
1088 1189 2.981909 GCAGAAGCAGCACCAGCA 60.982 61.111 0.00 0.00 45.49 4.41
1089 1190 2.979197 GCAGAAGCAGCACCAGCAG 61.979 63.158 0.00 0.00 45.49 4.24
1090 1191 1.302271 CAGAAGCAGCACCAGCAGA 60.302 57.895 0.00 0.00 45.49 4.26
1091 1192 1.302351 AGAAGCAGCACCAGCAGAC 60.302 57.895 0.00 0.00 45.49 3.51
1096 1197 3.619767 AGCACCAGCAGACGCAGA 61.620 61.111 0.00 0.00 45.49 4.26
1392 1499 1.306642 CCGTGTCGGTCAGAGCTAGT 61.307 60.000 0.00 0.00 42.73 2.57
1540 1657 7.709269 TCTCACGGTATTTATGCTTATCAAC 57.291 36.000 0.00 0.00 0.00 3.18
1541 1658 7.497595 TCTCACGGTATTTATGCTTATCAACT 58.502 34.615 0.00 0.00 0.00 3.16
1542 1659 7.438160 TCTCACGGTATTTATGCTTATCAACTG 59.562 37.037 0.00 0.00 0.00 3.16
1543 1660 7.269316 TCACGGTATTTATGCTTATCAACTGA 58.731 34.615 0.00 0.00 0.00 3.41
1544 1661 7.766738 TCACGGTATTTATGCTTATCAACTGAA 59.233 33.333 0.00 0.00 0.00 3.02
1545 1662 8.394877 CACGGTATTTATGCTTATCAACTGAAA 58.605 33.333 0.00 0.00 0.00 2.69
1546 1663 8.952278 ACGGTATTTATGCTTATCAACTGAAAA 58.048 29.630 0.00 0.00 0.00 2.29
1547 1664 9.438291 CGGTATTTATGCTTATCAACTGAAAAG 57.562 33.333 0.00 0.00 0.00 2.27
1554 1671 6.970484 TGCTTATCAACTGAAAAGAACTTCC 58.030 36.000 0.00 0.00 0.00 3.46
1555 1672 6.545666 TGCTTATCAACTGAAAAGAACTTCCA 59.454 34.615 0.00 0.00 0.00 3.53
1556 1673 7.080724 GCTTATCAACTGAAAAGAACTTCCAG 58.919 38.462 12.08 12.08 32.83 3.86
1557 1674 7.510549 TTATCAACTGAAAAGAACTTCCAGG 57.489 36.000 15.61 0.00 31.68 4.45
1558 1675 5.110814 TCAACTGAAAAGAACTTCCAGGA 57.889 39.130 15.61 0.00 31.68 3.86
1559 1676 5.505780 TCAACTGAAAAGAACTTCCAGGAA 58.494 37.500 0.71 0.71 31.68 3.36
1602 1719 7.886191 TCGTTGAAACAAGAAAGAAAATACG 57.114 32.000 0.00 0.00 0.00 3.06
1604 1721 6.560166 GTTGAAACAAGAAAGAAAATACGCG 58.440 36.000 3.53 3.53 0.00 6.01
1605 1722 5.812652 TGAAACAAGAAAGAAAATACGCGT 58.187 33.333 19.17 19.17 0.00 6.01
1606 1723 5.679355 TGAAACAAGAAAGAAAATACGCGTG 59.321 36.000 24.59 2.00 0.00 5.34
1607 1724 4.806342 ACAAGAAAGAAAATACGCGTGT 57.194 36.364 24.59 13.76 0.00 4.49
1608 1725 4.769215 ACAAGAAAGAAAATACGCGTGTC 58.231 39.130 24.59 13.58 0.00 3.67
1609 1726 4.148891 CAAGAAAGAAAATACGCGTGTCC 58.851 43.478 24.59 8.41 0.00 4.02
1610 1727 3.395639 AGAAAGAAAATACGCGTGTCCA 58.604 40.909 24.59 0.62 0.00 4.02
1611 1728 3.810941 AGAAAGAAAATACGCGTGTCCAA 59.189 39.130 24.59 0.13 0.00 3.53
1612 1729 4.454504 AGAAAGAAAATACGCGTGTCCAAT 59.545 37.500 24.59 3.27 0.00 3.16
1617 1734 7.173863 AGAAAATACGCGTGTCCAATAATAG 57.826 36.000 24.59 0.00 0.00 1.73
1668 1785 1.671054 CAAACCGGACACCGCATCT 60.671 57.895 9.46 0.00 46.86 2.90
1704 1822 4.395959 GACCAGTCCATAAACACGGATA 57.604 45.455 0.00 0.00 0.00 2.59
1740 1858 5.092554 TCCAAAACTAGCCGAATACATCA 57.907 39.130 0.00 0.00 0.00 3.07
1741 1859 5.492895 TCCAAAACTAGCCGAATACATCAA 58.507 37.500 0.00 0.00 0.00 2.57
1745 1863 3.039011 ACTAGCCGAATACATCAACCCT 58.961 45.455 0.00 0.00 0.00 4.34
1749 1867 3.117888 AGCCGAATACATCAACCCTCAAT 60.118 43.478 0.00 0.00 0.00 2.57
1791 1911 4.083581 GCATCTGCACGTTCAAAATAGT 57.916 40.909 0.00 0.00 41.59 2.12
1792 1912 4.475944 GCATCTGCACGTTCAAAATAGTT 58.524 39.130 0.00 0.00 41.59 2.24
1793 1913 4.554973 GCATCTGCACGTTCAAAATAGTTC 59.445 41.667 0.00 0.00 41.59 3.01
1799 1919 7.766738 TCTGCACGTTCAAAATAGTTCCATATA 59.233 33.333 0.00 0.00 0.00 0.86
1800 1920 8.445275 TGCACGTTCAAAATAGTTCCATATAT 57.555 30.769 0.00 0.00 0.00 0.86
1801 1921 8.556194 TGCACGTTCAAAATAGTTCCATATATC 58.444 33.333 0.00 0.00 0.00 1.63
1802 1922 8.774586 GCACGTTCAAAATAGTTCCATATATCT 58.225 33.333 0.00 0.00 0.00 1.98
1852 1972 4.916983 TGTTCAAATGCAGCAGTAGTTT 57.083 36.364 0.00 0.00 0.00 2.66
1888 2008 7.490962 TTACACTTCAACAATGTTGTCCTAG 57.509 36.000 23.41 17.76 41.31 3.02
1890 2010 5.885912 ACACTTCAACAATGTTGTCCTAGTT 59.114 36.000 23.41 11.44 41.31 2.24
1891 2011 7.051623 ACACTTCAACAATGTTGTCCTAGTTA 58.948 34.615 23.41 1.17 41.31 2.24
1894 2014 8.962679 ACTTCAACAATGTTGTCCTAGTTAAAA 58.037 29.630 23.41 7.51 41.31 1.52
1895 2015 9.796120 CTTCAACAATGTTGTCCTAGTTAAAAA 57.204 29.630 23.41 7.06 41.31 1.94
1932 2072 2.243602 TGTCCTTGTTAACCGTCCAC 57.756 50.000 2.48 0.00 0.00 4.02
1933 2073 1.142474 GTCCTTGTTAACCGTCCACG 58.858 55.000 2.48 0.00 39.44 4.94
1979 2119 5.521372 TCAGTTATTCATGAGTTGCTCGATG 59.479 40.000 0.00 0.00 32.35 3.84
2035 2175 5.652014 TCAAATGTAGCCGGATTTTGATCTT 59.348 36.000 12.74 0.00 32.88 2.40
2082 2222 2.678336 CTCAAATTCAAGACCTACGGCC 59.322 50.000 0.00 0.00 0.00 6.13
2090 2245 3.161450 ACCTACGGCCGCATCCAT 61.161 61.111 28.58 7.06 0.00 3.41
2165 2320 3.525199 AGATCCCATTGTTTAGCAGGTCT 59.475 43.478 0.00 0.00 0.00 3.85
2190 2345 2.361789 ACAACTGCAAAACGTACCTGT 58.638 42.857 0.00 0.00 0.00 4.00
2217 2372 2.369860 TCCAACTGCACTCTCAACATCT 59.630 45.455 0.00 0.00 0.00 2.90
2232 2387 2.633488 ACATCTTTTCTAGCCGCTTCC 58.367 47.619 0.00 0.00 0.00 3.46
2248 2425 2.297033 GCTTCCTGCTTTGACCAATTGA 59.703 45.455 7.12 0.00 38.95 2.57
2279 2456 3.327757 TGGTCTTGACAAAGGTAGCTCAT 59.672 43.478 0.00 0.00 33.90 2.90
2295 2472 7.947332 AGGTAGCTCATGAAGAATAGATACTGA 59.053 37.037 0.00 0.00 32.75 3.41
2299 2476 8.649591 AGCTCATGAAGAATAGATACTGACAAT 58.350 33.333 0.00 0.00 0.00 2.71
2322 2499 6.101650 TCAGATAGTAGCCCATGTTGTATG 57.898 41.667 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 3.584406 AGTGAACTTCAGATCACCATGGA 59.416 43.478 21.47 0.00 45.40 3.41
306 307 1.163309 AGGGGTGTCCAATCTCCCA 59.837 57.895 0.00 0.00 41.38 4.37
442 443 3.840666 TCTGGAAGCCATACTCTTGAAGT 59.159 43.478 0.00 0.00 42.33 3.01
524 525 2.347114 CCAGTGGACGCATGTGGA 59.653 61.111 11.65 0.00 0.00 4.02
669 670 5.486526 CTCCCTACCTCGTATAGTCGTATT 58.513 45.833 0.00 0.00 0.00 1.89
774 815 7.557719 ACGGCTTTATTAGTACTAGTGTAGGAA 59.442 37.037 5.39 0.00 0.00 3.36
848 896 3.787001 GGCCTGGACGGAGGAAGG 61.787 72.222 0.00 0.00 34.69 3.46
863 911 3.984200 AAGAACTCGTAGCCGCGGC 62.984 63.158 42.34 42.34 42.33 6.53
865 913 1.872679 GGAAGAACTCGTAGCCGCG 60.873 63.158 0.00 0.00 0.00 6.46
866 914 1.872679 CGGAAGAACTCGTAGCCGC 60.873 63.158 0.00 0.00 31.80 6.53
867 915 0.522915 GTCGGAAGAACTCGTAGCCG 60.523 60.000 0.00 0.00 45.01 5.52
868 916 0.810016 AGTCGGAAGAACTCGTAGCC 59.190 55.000 0.00 0.00 45.01 3.93
869 917 1.467713 CCAGTCGGAAGAACTCGTAGC 60.468 57.143 0.00 0.00 45.01 3.58
870 918 1.467713 GCCAGTCGGAAGAACTCGTAG 60.468 57.143 0.00 0.00 45.01 3.51
903 994 5.333416 CGACGATTAGACGATGAGATGAGAA 60.333 44.000 0.00 0.00 40.26 2.87
908 999 3.400255 TCCGACGATTAGACGATGAGAT 58.600 45.455 0.00 0.00 40.26 2.75
911 1002 2.801111 CTCTCCGACGATTAGACGATGA 59.199 50.000 0.00 0.00 40.26 2.92
915 1006 2.033577 CACTCTCTCCGACGATTAGACG 60.034 54.545 0.00 0.00 37.73 4.18
922 1013 1.376942 GGACCACTCTCTCCGACGA 60.377 63.158 0.00 0.00 0.00 4.20
924 1015 0.741915 GATGGACCACTCTCTCCGAC 59.258 60.000 0.00 0.00 0.00 4.79
931 1022 0.326264 GGCAACTGATGGACCACTCT 59.674 55.000 0.00 0.00 0.00 3.24
932 1023 2.859992 GGCAACTGATGGACCACTC 58.140 57.895 0.00 0.00 0.00 3.51
949 1050 0.727398 GAAATTCAGACGCGGGAAGG 59.273 55.000 12.47 0.00 0.00 3.46
950 1051 1.661112 GAGAAATTCAGACGCGGGAAG 59.339 52.381 12.47 0.00 0.00 3.46
951 1052 1.722011 GAGAAATTCAGACGCGGGAA 58.278 50.000 12.47 11.90 0.00 3.97
952 1053 0.457853 CGAGAAATTCAGACGCGGGA 60.458 55.000 12.47 1.43 0.00 5.14
953 1054 0.736325 ACGAGAAATTCAGACGCGGG 60.736 55.000 12.47 0.00 0.00 6.13
954 1055 1.582502 GTACGAGAAATTCAGACGCGG 59.417 52.381 12.47 0.00 0.00 6.46
955 1056 2.247637 TGTACGAGAAATTCAGACGCG 58.752 47.619 3.53 3.53 0.00 6.01
956 1057 4.259850 GGATTGTACGAGAAATTCAGACGC 60.260 45.833 0.00 0.00 0.00 5.19
957 1058 4.267928 GGGATTGTACGAGAAATTCAGACG 59.732 45.833 0.00 1.05 0.00 4.18
965 1066 2.614481 GCCACAGGGATTGTACGAGAAA 60.614 50.000 0.00 0.00 38.16 2.52
975 1076 2.036256 GCACAGGCCACAGGGATT 59.964 61.111 5.01 0.00 35.59 3.01
985 1086 0.253044 TCCATCTTGTAGGCACAGGC 59.747 55.000 0.00 0.00 35.67 4.85
987 1088 2.158986 CCTCTCCATCTTGTAGGCACAG 60.159 54.545 0.00 0.00 35.67 3.66
988 1089 1.833630 CCTCTCCATCTTGTAGGCACA 59.166 52.381 0.00 0.00 0.00 4.57
989 1090 2.102252 CTCCTCTCCATCTTGTAGGCAC 59.898 54.545 0.00 0.00 0.00 5.01
990 1091 2.023984 TCTCCTCTCCATCTTGTAGGCA 60.024 50.000 0.00 0.00 0.00 4.75
991 1092 2.627699 CTCTCCTCTCCATCTTGTAGGC 59.372 54.545 0.00 0.00 0.00 3.93
992 1093 2.627699 GCTCTCCTCTCCATCTTGTAGG 59.372 54.545 0.00 0.00 0.00 3.18
993 1094 2.293122 CGCTCTCCTCTCCATCTTGTAG 59.707 54.545 0.00 0.00 0.00 2.74
994 1095 2.302260 CGCTCTCCTCTCCATCTTGTA 58.698 52.381 0.00 0.00 0.00 2.41
995 1096 1.110442 CGCTCTCCTCTCCATCTTGT 58.890 55.000 0.00 0.00 0.00 3.16
996 1097 0.388659 CCGCTCTCCTCTCCATCTTG 59.611 60.000 0.00 0.00 0.00 3.02
997 1098 1.398958 GCCGCTCTCCTCTCCATCTT 61.399 60.000 0.00 0.00 0.00 2.40
998 1099 1.832167 GCCGCTCTCCTCTCCATCT 60.832 63.158 0.00 0.00 0.00 2.90
1031 1132 3.443045 GCATTCGGCTGTGGTGGG 61.443 66.667 0.00 0.00 40.25 4.61
1032 1133 2.672651 TGCATTCGGCTGTGGTGG 60.673 61.111 0.00 0.00 45.15 4.61
1037 1138 2.117156 GGCATCTGCATTCGGCTGT 61.117 57.895 4.33 0.00 45.15 4.40
1038 1139 2.719979 GGCATCTGCATTCGGCTG 59.280 61.111 4.33 0.00 45.15 4.85
1041 1142 3.957535 GGCGGCATCTGCATTCGG 61.958 66.667 3.07 0.00 44.36 4.30
1114 1215 0.244994 GTTCTCTGGCAGCTCTTCGA 59.755 55.000 10.34 0.00 0.00 3.71
1392 1499 6.436218 TGTACTACAGGCTAGATCTGAAACAA 59.564 38.462 16.97 0.00 36.22 2.83
1553 1670 5.448654 TGATTTATGGATTCCACTTCCTGG 58.551 41.667 7.76 0.00 42.29 4.45
1554 1671 7.521099 CGAATGATTTATGGATTCCACTTCCTG 60.521 40.741 7.76 0.00 35.80 3.86
1555 1672 6.488006 CGAATGATTTATGGATTCCACTTCCT 59.512 38.462 7.76 0.00 35.80 3.36
1556 1673 6.263168 ACGAATGATTTATGGATTCCACTTCC 59.737 38.462 7.76 0.00 35.80 3.46
1557 1674 7.264373 ACGAATGATTTATGGATTCCACTTC 57.736 36.000 7.76 3.59 35.80 3.01
1558 1675 7.339212 TCAACGAATGATTTATGGATTCCACTT 59.661 33.333 7.76 0.00 31.69 3.16
1559 1676 6.828273 TCAACGAATGATTTATGGATTCCACT 59.172 34.615 7.76 0.36 31.69 4.00
1602 1719 7.149973 TGGTCTTATACTATTATTGGACACGC 58.850 38.462 0.00 0.00 0.00 5.34
1612 1729 9.627123 AGCTTGCAAAATGGTCTTATACTATTA 57.373 29.630 0.00 0.00 38.24 0.98
1617 1734 7.707104 ACATAGCTTGCAAAATGGTCTTATAC 58.293 34.615 16.24 0.00 0.00 1.47
1668 1785 0.178973 TGGTCCCTTCTCTGTCGACA 60.179 55.000 18.88 18.88 0.00 4.35
1693 1811 1.069513 CGGCTCCCATATCCGTGTTTA 59.930 52.381 0.00 0.00 38.47 2.01
1694 1812 0.179056 CGGCTCCCATATCCGTGTTT 60.179 55.000 0.00 0.00 38.47 2.83
1695 1813 1.445942 CGGCTCCCATATCCGTGTT 59.554 57.895 0.00 0.00 38.47 3.32
1770 1890 4.083581 ACTATTTTGAACGTGCAGATGC 57.916 40.909 0.00 0.00 42.50 3.91
1775 1895 6.751514 ATATGGAACTATTTTGAACGTGCA 57.248 33.333 0.00 0.00 0.00 4.57
1894 2014 5.704978 AGGACAACATTGCTTGTTTGTTTTT 59.295 32.000 3.28 0.00 46.51 1.94
1895 2015 5.244755 AGGACAACATTGCTTGTTTGTTTT 58.755 33.333 3.28 0.00 46.51 2.43
1896 2016 4.831107 AGGACAACATTGCTTGTTTGTTT 58.169 34.783 3.28 0.00 46.51 2.83
1897 2017 4.470334 AGGACAACATTGCTTGTTTGTT 57.530 36.364 3.28 0.00 46.51 2.83
1898 2018 4.183101 CAAGGACAACATTGCTTGTTTGT 58.817 39.130 3.28 5.72 46.51 2.83
1904 2024 4.499019 CGGTTAACAAGGACAACATTGCTT 60.499 41.667 8.10 0.00 40.78 3.91
1905 2025 3.004315 CGGTTAACAAGGACAACATTGCT 59.996 43.478 8.10 0.00 40.78 3.91
1907 2027 4.533222 GACGGTTAACAAGGACAACATTG 58.467 43.478 8.10 0.00 42.45 2.82
1909 2029 3.143728 GGACGGTTAACAAGGACAACAT 58.856 45.455 8.10 0.00 0.00 2.71
1932 2072 5.327616 AGATAGATCTGATTGAGCATCCG 57.672 43.478 5.18 0.00 35.42 4.18
1933 2073 6.699366 TGAAGATAGATCTGATTGAGCATCC 58.301 40.000 5.18 0.00 37.19 3.51
1979 2119 6.942886 TTGAAATACATCAACAAATTCGGC 57.057 33.333 0.00 0.00 34.50 5.54
2019 2159 3.690460 ACTTCAAGATCAAAATCCGGCT 58.310 40.909 0.00 0.00 31.78 5.52
2035 2175 6.903516 ACATGGATGATCCTATTGAACTTCA 58.096 36.000 13.44 0.00 37.46 3.02
2082 2222 1.097232 ACAACATGACCATGGATGCG 58.903 50.000 21.47 9.96 42.91 4.73
2143 2298 3.525199 AGACCTGCTAAACAATGGGATCT 59.475 43.478 0.00 0.00 0.00 2.75
2165 2320 5.800941 CAGGTACGTTTTGCAGTTGTTTTTA 59.199 36.000 0.00 0.00 0.00 1.52
2190 2345 3.230976 TGAGAGTGCAGTTGGAGTTCTA 58.769 45.455 0.00 0.00 0.00 2.10
2217 2372 2.854522 GCAGGAAGCGGCTAGAAAA 58.145 52.632 1.35 0.00 0.00 2.29
2232 2387 3.817084 TCTGACTCAATTGGTCAAAGCAG 59.183 43.478 22.08 14.94 42.15 4.24
2248 2425 4.262808 CCTTTGTCAAGACCATCTCTGACT 60.263 45.833 15.63 0.00 36.45 3.41
2295 2472 5.104360 ACAACATGGGCTACTATCTGATTGT 60.104 40.000 9.55 9.55 0.00 2.71
2299 2476 5.511373 GCATACAACATGGGCTACTATCTGA 60.511 44.000 0.00 0.00 0.00 3.27
2322 2499 3.251729 CACTATACTGTCAATGGGCATGC 59.748 47.826 9.90 9.90 0.00 4.06


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

AutoCloner maintained by Alex Coulton.