Multiple sequence alignment - TraesCS3D01G447700

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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 TraesCS3D01G447700 chr3D 100.000 2903 0 0 1 2903 556029498 556026596 0.000000e+00 5361.0
1 TraesCS3D01G447700 chr3A 90.105 1991 110 35 1 1945 692964164 692962215 0.000000e+00 2505.0
2 TraesCS3D01G447700 chr3A 90.618 469 40 3 2058 2526 692961969 692961505 1.140000e-173 619.0
3 TraesCS3D01G447700 chr3A 93.860 342 18 3 2552 2892 692961412 692961073 2.000000e-141 512.0
4 TraesCS3D01G447700 chr3A 77.600 125 24 4 69 191 569891074 569891196 4.010000e-09 73.1
5 TraesCS3D01G447700 chr3B 91.176 782 43 16 1 780 739030677 739029920 0.000000e+00 1038.0
6 TraesCS3D01G447700 chr3B 91.141 587 32 12 991 1576 739029712 739029145 0.000000e+00 778.0
7 TraesCS3D01G447700 chr3B 93.531 371 17 4 2156 2526 739027001 739026638 1.970000e-151 545.0
8 TraesCS3D01G447700 chr3B 90.796 402 28 3 1568 1969 739027652 739027260 1.980000e-146 529.0
9 TraesCS3D01G447700 chr3B 86.667 345 40 2 2553 2892 739026543 739026200 7.590000e-101 377.0
10 TraesCS3D01G447700 chr1B 83.654 312 51 0 1058 1369 296811244 296810933 7.870000e-76 294.0
11 TraesCS3D01G447700 chr1A 83.654 312 51 0 1058 1369 256985306 256984995 7.870000e-76 294.0
12 TraesCS3D01G447700 chr2B 79.456 331 50 9 1039 1369 775373683 775373371 4.870000e-53 219.0


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 TraesCS3D01G447700 chr3D 556026596 556029498 2902 True 5361.0 5361 100.000000 1 2903 1 chr3D.!!$R1 2902
1 TraesCS3D01G447700 chr3A 692961073 692964164 3091 True 1212.0 2505 91.527667 1 2892 3 chr3A.!!$R1 2891
2 TraesCS3D01G447700 chr3B 739026200 739030677 4477 True 653.4 1038 90.662200 1 2892 5 chr3B.!!$R1 2891

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
925 998 0.106719 CCACCACACTTGTCCACCTT 60.107 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 4064 0.677098 GGGTCGAAAGCCCTTCCTTC 60.677 60.0 2.32 0.0 42.07 3.46 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
138 139 4.789075 CTTGCGCTGGCCATGCAC 62.789 66.667 27.11 17.38 38.55 4.57
219 220 1.210234 TGCCCCATGTCACATCTACTG 59.790 52.381 0.00 0.00 0.00 2.74
263 267 5.514169 ACTACTGATCTGATCTTCCACTCA 58.486 41.667 17.82 0.00 0.00 3.41
268 272 4.880120 TGATCTGATCTTCCACTCAATTGC 59.120 41.667 17.82 0.00 0.00 3.56
270 274 4.259356 TCTGATCTTCCACTCAATTGCTG 58.741 43.478 0.00 0.00 0.00 4.41
271 275 4.008330 CTGATCTTCCACTCAATTGCTGT 58.992 43.478 0.00 0.00 0.00 4.40
280 284 3.066342 CACTCAATTGCTGTGATCCATCC 59.934 47.826 19.74 0.00 33.95 3.51
282 286 3.018856 TCAATTGCTGTGATCCATCCAC 58.981 45.455 0.00 0.00 35.23 4.02
290 294 0.389025 TGATCCATCCACACGATCGG 59.611 55.000 20.98 10.92 36.08 4.18
311 316 5.997746 TCGGTGACAATCTTTGAATCTTCTT 59.002 36.000 0.00 0.00 0.00 2.52
321 329 6.458210 TCTTTGAATCTTCTTTGCCATTTCC 58.542 36.000 0.00 0.00 0.00 3.13
346 354 1.776034 GATCATGGAGGAAACGGCGC 61.776 60.000 6.90 0.00 0.00 6.53
414 422 2.530661 TTTCTCCTGGGCCCCGAA 60.531 61.111 22.27 13.82 0.00 4.30
750 758 3.963374 AGTACATCTGAGCTAGCCATCAA 59.037 43.478 12.13 1.71 0.00 2.57
760 768 0.829990 TAGCCATCAACTCATCGCCA 59.170 50.000 0.00 0.00 0.00 5.69
776 784 1.741770 CCAGTACAGGCTGCCGTTC 60.742 63.158 15.89 14.24 35.28 3.95
829 901 5.810587 TCTCGCTGTCATAAGTAAACAATCC 59.189 40.000 0.00 0.00 0.00 3.01
833 905 6.742718 CGCTGTCATAAGTAAACAATCCAAAG 59.257 38.462 0.00 0.00 0.00 2.77
834 906 7.573096 CGCTGTCATAAGTAAACAATCCAAAGT 60.573 37.037 0.00 0.00 0.00 2.66
835 907 7.538678 GCTGTCATAAGTAAACAATCCAAAGTG 59.461 37.037 0.00 0.00 0.00 3.16
864 936 0.254462 TTCAGCACAACCACCACTCA 59.746 50.000 0.00 0.00 0.00 3.41
865 937 0.179048 TCAGCACAACCACCACTCAG 60.179 55.000 0.00 0.00 0.00 3.35
884 957 7.137426 CACTCAGAAAAAGTGGAGAAATTGAG 58.863 38.462 0.00 0.00 40.36 3.02
922 995 1.140252 ACTACCACCACACTTGTCCAC 59.860 52.381 0.00 0.00 0.00 4.02
923 996 0.470766 TACCACCACACTTGTCCACC 59.529 55.000 0.00 0.00 0.00 4.61
924 997 1.279025 ACCACCACACTTGTCCACCT 61.279 55.000 0.00 0.00 0.00 4.00
925 998 0.106719 CCACCACACTTGTCCACCTT 60.107 55.000 0.00 0.00 0.00 3.50
926 999 1.024271 CACCACACTTGTCCACCTTG 58.976 55.000 0.00 0.00 0.00 3.61
927 1000 0.623723 ACCACACTTGTCCACCTTGT 59.376 50.000 0.00 0.00 0.00 3.16
928 1001 1.024271 CCACACTTGTCCACCTTGTG 58.976 55.000 0.00 0.00 37.83 3.33
929 1002 1.681780 CCACACTTGTCCACCTTGTGT 60.682 52.381 0.00 0.00 41.75 3.72
930 1003 1.670811 CACACTTGTCCACCTTGTGTC 59.329 52.381 0.00 0.00 39.46 3.67
931 1004 0.937304 CACTTGTCCACCTTGTGTCG 59.063 55.000 0.00 0.00 0.00 4.35
932 1005 0.814010 ACTTGTCCACCTTGTGTCGC 60.814 55.000 0.00 0.00 0.00 5.19
933 1006 0.813610 CTTGTCCACCTTGTGTCGCA 60.814 55.000 0.00 0.00 0.00 5.10
934 1007 0.393132 TTGTCCACCTTGTGTCGCAA 60.393 50.000 0.00 0.00 35.50 4.85
935 1008 0.179032 TGTCCACCTTGTGTCGCAAT 60.179 50.000 0.00 0.00 36.36 3.56
936 1009 0.517316 GTCCACCTTGTGTCGCAATC 59.483 55.000 0.00 0.00 36.36 2.67
937 1010 0.605319 TCCACCTTGTGTCGCAATCC 60.605 55.000 0.00 0.00 36.36 3.01
938 1011 0.888736 CCACCTTGTGTCGCAATCCA 60.889 55.000 0.00 0.00 36.36 3.41
939 1012 0.518636 CACCTTGTGTCGCAATCCAG 59.481 55.000 0.00 0.00 36.36 3.86
940 1013 1.237285 ACCTTGTGTCGCAATCCAGC 61.237 55.000 0.00 0.00 36.36 4.85
941 1014 1.503542 CTTGTGTCGCAATCCAGCC 59.496 57.895 0.00 0.00 36.36 4.85
942 1015 1.926511 CTTGTGTCGCAATCCAGCCC 61.927 60.000 0.00 0.00 36.36 5.19
943 1016 2.359850 GTGTCGCAATCCAGCCCA 60.360 61.111 0.00 0.00 0.00 5.36
960 1033 0.331278 CCAGGGGATTTGTACCAGCA 59.669 55.000 0.00 0.00 0.00 4.41
1011 1084 2.125106 AAACCGATGGAGAGCGCC 60.125 61.111 2.29 0.00 0.00 6.53
1192 1265 3.003763 AGGAGGTGGGCTCGTTCC 61.004 66.667 0.00 0.00 0.00 3.62
1426 1501 1.685765 CCTCTCGATCCACACCCCA 60.686 63.158 0.00 0.00 0.00 4.96
1427 1502 1.517832 CTCTCGATCCACACCCCAC 59.482 63.158 0.00 0.00 0.00 4.61
1428 1503 2.184322 CTCGATCCACACCCCACG 59.816 66.667 0.00 0.00 0.00 4.94
1455 1531 3.562141 CACCATGAACGAACCTAACACAA 59.438 43.478 0.00 0.00 0.00 3.33
1456 1532 3.562557 ACCATGAACGAACCTAACACAAC 59.437 43.478 0.00 0.00 0.00 3.32
1457 1533 3.562141 CCATGAACGAACCTAACACAACA 59.438 43.478 0.00 0.00 0.00 3.33
1608 3190 0.826715 GACTGTATCAGCTCAGCCCA 59.173 55.000 0.00 0.00 34.37 5.36
1609 3191 0.829333 ACTGTATCAGCTCAGCCCAG 59.171 55.000 0.00 0.00 34.37 4.45
1692 3274 1.264749 TGATGAACGGGGAGGAGGTG 61.265 60.000 0.00 0.00 0.00 4.00
1735 3317 4.746951 TGAGCCGCGTGTACGTCG 62.747 66.667 4.92 9.67 42.22 5.12
1866 3448 2.123632 AAGCCCAGGGAGCTCTCA 59.876 61.111 17.82 0.00 40.49 3.27
1869 3451 1.765657 GCCCAGGGAGCTCTCAGAT 60.766 63.158 17.82 0.00 0.00 2.90
1899 3481 3.068165 TGGAGATAGCCGACAAGTACATG 59.932 47.826 0.00 0.00 0.00 3.21
1904 3486 3.120321 AGCCGACAAGTACATGTGAAA 57.880 42.857 8.74 0.00 32.57 2.69
1905 3487 3.674997 AGCCGACAAGTACATGTGAAAT 58.325 40.909 8.74 0.00 32.57 2.17
1906 3488 4.072131 AGCCGACAAGTACATGTGAAATT 58.928 39.130 8.74 0.00 32.57 1.82
1907 3489 4.154195 AGCCGACAAGTACATGTGAAATTC 59.846 41.667 8.74 0.00 32.57 2.17
1908 3490 4.154195 GCCGACAAGTACATGTGAAATTCT 59.846 41.667 8.74 0.00 32.57 2.40
1909 3491 5.621422 CCGACAAGTACATGTGAAATTCTG 58.379 41.667 8.74 0.00 32.57 3.02
1910 3492 5.408299 CCGACAAGTACATGTGAAATTCTGA 59.592 40.000 8.74 0.00 32.57 3.27
1911 3493 6.073276 CCGACAAGTACATGTGAAATTCTGAA 60.073 38.462 8.74 0.00 32.57 3.02
1912 3494 7.361201 CCGACAAGTACATGTGAAATTCTGAAT 60.361 37.037 8.74 0.00 32.57 2.57
1960 3549 8.743085 TGAATTCTGAATAATTCCTTGAGAGG 57.257 34.615 7.05 0.00 42.63 3.69
1972 3561 2.961741 CCTTGAGAGGAATCGAGATGGA 59.038 50.000 0.00 0.00 46.74 3.41
1976 3565 3.244009 TGAGAGGAATCGAGATGGATTGC 60.244 47.826 1.68 1.68 42.87 3.56
1979 3568 3.892918 GGAATCGAGATGGATTGCTTG 57.107 47.619 0.00 0.00 40.38 4.01
1980 3569 2.551459 GGAATCGAGATGGATTGCTTGG 59.449 50.000 0.00 0.00 40.38 3.61
1982 3571 0.911769 TCGAGATGGATTGCTTGGGT 59.088 50.000 0.00 0.00 0.00 4.51
1984 3573 1.407299 CGAGATGGATTGCTTGGGTCA 60.407 52.381 0.00 0.00 0.00 4.02
1985 3574 2.726821 GAGATGGATTGCTTGGGTCAA 58.273 47.619 0.00 0.00 0.00 3.18
1986 3575 3.091545 GAGATGGATTGCTTGGGTCAAA 58.908 45.455 0.00 0.00 0.00 2.69
1989 3578 4.533311 AGATGGATTGCTTGGGTCAAAATT 59.467 37.500 0.00 0.00 0.00 1.82
2026 3764 6.513806 TGGATGTCACAAAGAACATTATGG 57.486 37.500 0.00 0.00 0.00 2.74
2034 3772 8.564574 GTCACAAAGAACATTATGGTACAGAAA 58.435 33.333 0.00 0.00 44.93 2.52
2035 3773 9.295825 TCACAAAGAACATTATGGTACAGAAAT 57.704 29.630 0.00 0.00 44.93 2.17
2049 3787 6.819649 TGGTACAGAAATATTTACCACTTCCG 59.180 38.462 14.06 0.00 39.25 4.30
2050 3788 5.813080 ACAGAAATATTTACCACTTCCGC 57.187 39.130 0.00 0.00 0.00 5.54
2051 3789 5.497474 ACAGAAATATTTACCACTTCCGCT 58.503 37.500 0.00 0.00 0.00 5.52
2052 3790 5.944007 ACAGAAATATTTACCACTTCCGCTT 59.056 36.000 0.00 0.00 0.00 4.68
2053 3791 6.093633 ACAGAAATATTTACCACTTCCGCTTC 59.906 38.462 0.00 0.00 0.00 3.86
2072 3810 7.906010 TCCGCTTCAACATTTATTTATGTTACG 59.094 33.333 0.00 0.00 44.64 3.18
2097 3835 1.617357 ACTCCTCGGCTAAACGAAACT 59.383 47.619 0.00 0.00 42.98 2.66
2103 3841 4.171005 CTCGGCTAAACGAAACTATGACA 58.829 43.478 0.00 0.00 42.98 3.58
2105 3843 5.172934 TCGGCTAAACGAAACTATGACATT 58.827 37.500 0.00 0.00 40.34 2.71
2116 3854 4.346734 ACTATGACATTCGCAAGCAAAG 57.653 40.909 0.00 0.00 37.18 2.77
2127 3865 3.562141 TCGCAAGCAAAGTTACAAGCTAA 59.438 39.130 0.00 0.00 36.07 3.09
2134 3872 7.559590 AGCAAAGTTACAAGCTAATGGATAG 57.440 36.000 0.00 0.00 35.19 2.08
2137 3875 8.458843 GCAAAGTTACAAGCTAATGGATAGAAA 58.541 33.333 0.00 0.00 33.04 2.52
2138 3876 9.774742 CAAAGTTACAAGCTAATGGATAGAAAC 57.225 33.333 0.00 0.00 33.04 2.78
2140 3878 8.950208 AGTTACAAGCTAATGGATAGAAACTC 57.050 34.615 0.00 0.00 33.04 3.01
2186 3924 7.093354 ACTGTGTGTGTATCTACAAGATCAAG 58.907 38.462 0.00 0.00 38.04 3.02
2248 3986 1.897802 TCTTCCTTAACCGACCTCCAC 59.102 52.381 0.00 0.00 0.00 4.02
2326 4064 4.101790 GCCACATTGTGCCGTCGG 62.102 66.667 11.41 6.99 31.34 4.79
2329 4067 1.497278 CACATTGTGCCGTCGGAAG 59.503 57.895 17.49 0.00 0.00 3.46
2344 4082 0.677098 GGAAGGAAGGGCTTTCGACC 60.677 60.000 3.09 3.28 39.31 4.79
2497 4235 0.609957 TAGGACCGCCGAAAGACTCA 60.610 55.000 0.00 0.00 39.96 3.41
2513 4251 2.746362 GACTCAATCCTGTTCCAAGCAG 59.254 50.000 0.00 0.00 0.00 4.24
2515 4253 3.152341 CTCAATCCTGTTCCAAGCAGTT 58.848 45.455 0.00 0.00 32.41 3.16
2519 4257 2.297701 TCCTGTTCCAAGCAGTTCAAC 58.702 47.619 0.00 0.00 32.41 3.18
2520 4258 2.023673 CCTGTTCCAAGCAGTTCAACA 58.976 47.619 0.00 0.00 32.41 3.33
2521 4259 2.426738 CCTGTTCCAAGCAGTTCAACAA 59.573 45.455 0.00 0.00 32.41 2.83
2523 4261 4.044336 TGTTCCAAGCAGTTCAACAATG 57.956 40.909 0.00 0.00 0.00 2.82
2532 4270 4.479619 GCAGTTCAACAATGCTTTAGAGG 58.520 43.478 0.00 0.00 37.00 3.69
2534 4272 5.105997 GCAGTTCAACAATGCTTTAGAGGAT 60.106 40.000 0.00 0.00 37.00 3.24
2581 4384 4.238514 CAGGAACTCAAGTGTACTAGCAC 58.761 47.826 0.00 0.00 34.60 4.40
2599 4406 3.383185 AGCACTAGGAAGATCTCTTTCGG 59.617 47.826 0.00 0.00 36.57 4.30
2601 4408 4.677584 CACTAGGAAGATCTCTTTCGGTG 58.322 47.826 0.00 10.60 36.57 4.94
2613 4420 2.500098 TCTTTCGGTGGGATAGAAGTGG 59.500 50.000 0.00 0.00 30.96 4.00
2676 4483 5.621555 GCATACTTACGAGAAGTCTTGTGGA 60.622 44.000 10.90 0.34 40.63 4.02
2682 4489 2.405172 GAGAAGTCTTGTGGAACGGTC 58.595 52.381 0.00 0.00 42.39 4.79
2685 4492 0.031721 AGTCTTGTGGAACGGTCGAC 59.968 55.000 8.88 8.88 42.39 4.20
2693 4500 1.001520 TGGAACGGTCGACACAATGAT 59.998 47.619 18.91 0.00 0.00 2.45
2694 4501 2.231721 TGGAACGGTCGACACAATGATA 59.768 45.455 18.91 0.00 0.00 2.15
2754 4561 3.936203 GCCACCGGTCCACTGACA 61.936 66.667 2.59 0.00 43.65 3.58
2811 4618 1.404843 GCGGAGGGTCTAGTGATCTT 58.595 55.000 0.00 0.00 0.00 2.40
2892 4699 4.442612 GCTGGATAGATGAACTCTGCAGAA 60.443 45.833 18.85 2.60 41.26 3.02
2893 4700 5.273674 TGGATAGATGAACTCTGCAGAAG 57.726 43.478 18.85 13.95 35.28 2.85
2894 4701 4.958581 TGGATAGATGAACTCTGCAGAAGA 59.041 41.667 18.85 1.94 35.28 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.120718 AGGACCACCTTCTCGCCT 59.879 61.111 0.00 0.00 45.36 5.52
136 137 2.738521 CTTGTCCGGGTGAGCGTG 60.739 66.667 0.00 0.00 0.00 5.34
138 139 4.003788 ACCTTGTCCGGGTGAGCG 62.004 66.667 0.00 0.00 35.51 5.03
219 220 4.687215 TCAGCCAGTGCCTGCGAC 62.687 66.667 0.00 0.00 38.69 5.19
232 233 6.633500 AGATCAGATCAGTAGTAGTTCAGC 57.367 41.667 13.14 0.00 0.00 4.26
263 267 2.756760 GTGTGGATGGATCACAGCAATT 59.243 45.455 0.00 0.00 44.52 2.32
268 272 2.477825 GATCGTGTGGATGGATCACAG 58.522 52.381 0.00 0.00 44.52 3.66
270 274 1.491670 CGATCGTGTGGATGGATCAC 58.508 55.000 7.03 0.00 37.10 3.06
271 275 0.389025 CCGATCGTGTGGATGGATCA 59.611 55.000 15.09 0.00 37.10 2.92
280 284 1.996292 AGATTGTCACCGATCGTGTG 58.004 50.000 22.83 22.83 43.51 3.82
282 286 2.993220 TCAAAGATTGTCACCGATCGTG 59.007 45.455 15.09 12.28 44.50 4.35
290 294 6.364435 GGCAAAGAAGATTCAAAGATTGTCAC 59.636 38.462 0.00 0.00 0.00 3.67
311 316 3.454719 TGATCTGGAAGGAAATGGCAA 57.545 42.857 0.00 0.00 0.00 4.52
696 704 3.219928 ATGAGGATCGCGGCGAGT 61.220 61.111 29.64 16.96 39.91 4.18
750 758 1.517832 GCCTGTACTGGCGATGAGT 59.482 57.895 25.62 0.00 43.74 3.41
760 768 2.261671 CGAACGGCAGCCTGTACT 59.738 61.111 10.54 0.00 0.00 2.73
818 862 8.962679 TGAAAAGTACACTTTGGATTGTTTACT 58.037 29.630 8.06 0.00 44.69 2.24
829 901 6.264832 TGTGCTGAATGAAAAGTACACTTTG 58.735 36.000 8.06 0.00 44.69 2.77
833 905 4.976116 GGTTGTGCTGAATGAAAAGTACAC 59.024 41.667 0.00 0.00 38.51 2.90
834 906 4.642437 TGGTTGTGCTGAATGAAAAGTACA 59.358 37.500 0.00 0.00 37.26 2.90
835 907 4.976116 GTGGTTGTGCTGAATGAAAAGTAC 59.024 41.667 0.00 0.00 0.00 2.73
846 918 0.179048 CTGAGTGGTGGTTGTGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
864 936 6.129179 TCACCTCAATTTCTCCACTTTTTCT 58.871 36.000 0.00 0.00 0.00 2.52
865 937 6.391227 TCACCTCAATTTCTCCACTTTTTC 57.609 37.500 0.00 0.00 0.00 2.29
881 954 0.458370 CACGCGACATGATCACCTCA 60.458 55.000 15.93 0.00 38.53 3.86
884 957 1.153647 TCCACGCGACATGATCACC 60.154 57.895 15.93 0.00 0.00 4.02
910 983 1.670811 GACACAAGGTGGACAAGTGTG 59.329 52.381 0.00 0.00 42.86 3.82
911 984 1.742411 CGACACAAGGTGGACAAGTGT 60.742 52.381 0.00 0.00 45.21 3.55
922 995 1.503542 GCTGGATTGCGACACAAGG 59.496 57.895 0.00 0.00 42.87 3.61
923 996 1.503542 GGCTGGATTGCGACACAAG 59.496 57.895 0.00 0.00 42.87 3.16
924 997 1.971167 GGGCTGGATTGCGACACAA 60.971 57.895 0.00 0.00 44.01 3.33
925 998 2.359850 GGGCTGGATTGCGACACA 60.360 61.111 0.00 0.00 0.00 3.72
926 999 2.359850 TGGGCTGGATTGCGACAC 60.360 61.111 0.00 0.00 0.00 3.67
927 1000 2.046023 CTGGGCTGGATTGCGACA 60.046 61.111 0.00 0.00 0.00 4.35
928 1001 2.825836 CCTGGGCTGGATTGCGAC 60.826 66.667 0.00 0.00 0.00 5.19
929 1002 4.113815 CCCTGGGCTGGATTGCGA 62.114 66.667 0.00 0.00 0.00 5.10
931 1004 2.594365 AATCCCCTGGGCTGGATTGC 62.594 60.000 7.39 0.00 46.89 3.56
932 1005 1.622499 AATCCCCTGGGCTGGATTG 59.378 57.895 7.39 0.00 46.89 2.67
933 1006 4.211794 AATCCCCTGGGCTGGATT 57.788 55.556 7.39 8.52 44.59 3.01
934 1007 1.224003 ACAAATCCCCTGGGCTGGAT 61.224 55.000 7.39 1.79 43.23 3.41
935 1008 0.551377 TACAAATCCCCTGGGCTGGA 60.551 55.000 7.39 0.00 34.68 3.86
936 1009 0.395724 GTACAAATCCCCTGGGCTGG 60.396 60.000 7.39 0.00 34.68 4.85
937 1010 0.395724 GGTACAAATCCCCTGGGCTG 60.396 60.000 7.39 4.06 34.68 4.85
938 1011 0.849094 TGGTACAAATCCCCTGGGCT 60.849 55.000 7.39 0.00 31.92 5.19
939 1012 0.395724 CTGGTACAAATCCCCTGGGC 60.396 60.000 7.39 0.00 38.70 5.36
940 1013 0.395724 GCTGGTACAAATCCCCTGGG 60.396 60.000 5.50 5.50 38.70 4.45
941 1014 0.331278 TGCTGGTACAAATCCCCTGG 59.669 55.000 0.00 0.00 38.70 4.45
942 1015 2.094675 CTTGCTGGTACAAATCCCCTG 58.905 52.381 0.00 0.00 38.70 4.45
943 1016 1.992557 TCTTGCTGGTACAAATCCCCT 59.007 47.619 0.00 0.00 38.70 4.79
960 1033 1.079750 GTCCGCCGAGCTCTTTCTT 60.080 57.895 12.85 0.00 0.00 2.52
986 1059 0.107654 CTCCATCGGTTTGTCCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
990 1063 1.084370 CGCTCTCCATCGGTTTGTCC 61.084 60.000 0.00 0.00 0.00 4.02
992 1065 1.741770 GCGCTCTCCATCGGTTTGT 60.742 57.895 0.00 0.00 0.00 2.83
993 1066 2.464459 GGCGCTCTCCATCGGTTTG 61.464 63.158 7.64 0.00 0.00 2.93
1038 1111 4.657824 ACGAGCACGAACCGGTGG 62.658 66.667 8.52 6.02 42.66 4.61
1192 1265 4.514577 CGGCCGGCTGTACTCCTG 62.515 72.222 27.83 0.00 0.00 3.86
1406 1481 1.686110 GGGTGTGGATCGAGAGGGT 60.686 63.158 0.00 0.00 0.00 4.34
1426 1501 4.715523 CGTTCATGGTGGGGGCGT 62.716 66.667 0.00 0.00 0.00 5.68
1427 1502 3.910914 TTCGTTCATGGTGGGGGCG 62.911 63.158 0.00 0.00 0.00 6.13
1428 1503 2.034999 TTCGTTCATGGTGGGGGC 59.965 61.111 0.00 0.00 0.00 5.80
1455 1531 3.306166 GCGCAAACTGTAATATCGAGTGT 59.694 43.478 0.30 0.00 0.00 3.55
1456 1532 3.305897 TGCGCAAACTGTAATATCGAGTG 59.694 43.478 8.16 0.00 0.00 3.51
1457 1533 3.517602 TGCGCAAACTGTAATATCGAGT 58.482 40.909 8.16 0.00 0.00 4.18
1538 1619 4.986645 TCTTGCAAGCGCGCTCCA 62.987 61.111 36.57 29.64 42.97 3.86
1590 3172 0.829333 CTGGGCTGAGCTGATACAGT 59.171 55.000 3.72 0.00 36.62 3.55
1609 3191 4.803426 CAGCGTCAGGTCCTCCGC 62.803 72.222 20.04 20.04 46.07 5.54
1673 3255 1.080354 ACCTCCTCCCCGTTCATCA 59.920 57.895 0.00 0.00 0.00 3.07
1692 3274 3.138798 TACCTCTCCGCCGTGAGC 61.139 66.667 0.00 0.00 38.52 4.26
1764 3346 4.514577 ATCCGCCGCTGGAACTCG 62.515 66.667 7.82 0.00 42.46 4.18
1899 3481 6.919662 TGAAGTTTGCTGATTCAGAATTTCAC 59.080 34.615 17.87 2.37 32.44 3.18
1904 3486 7.176165 TGAAGATGAAGTTTGCTGATTCAGAAT 59.824 33.333 17.87 0.00 36.47 2.40
1905 3487 6.487668 TGAAGATGAAGTTTGCTGATTCAGAA 59.512 34.615 17.87 3.67 36.47 3.02
1906 3488 5.999600 TGAAGATGAAGTTTGCTGATTCAGA 59.000 36.000 17.87 0.08 36.47 3.27
1907 3489 6.072618 ACTGAAGATGAAGTTTGCTGATTCAG 60.073 38.462 9.40 9.40 36.47 3.02
1908 3490 5.766670 ACTGAAGATGAAGTTTGCTGATTCA 59.233 36.000 0.00 0.00 37.36 2.57
1909 3491 6.251655 ACTGAAGATGAAGTTTGCTGATTC 57.748 37.500 0.00 0.00 0.00 2.52
1910 3492 6.645790 AACTGAAGATGAAGTTTGCTGATT 57.354 33.333 0.00 0.00 32.75 2.57
1911 3493 7.609146 TCATAACTGAAGATGAAGTTTGCTGAT 59.391 33.333 0.00 0.00 37.74 2.90
1912 3494 6.936335 TCATAACTGAAGATGAAGTTTGCTGA 59.064 34.615 0.00 0.00 37.74 4.26
1952 3541 4.870123 ATCCATCTCGATTCCTCTCAAG 57.130 45.455 0.00 0.00 0.00 3.02
1954 3543 3.244009 GCAATCCATCTCGATTCCTCTCA 60.244 47.826 0.00 0.00 29.85 3.27
1956 3545 2.971330 AGCAATCCATCTCGATTCCTCT 59.029 45.455 0.00 0.00 29.85 3.69
1957 3546 3.399440 AGCAATCCATCTCGATTCCTC 57.601 47.619 0.00 0.00 29.85 3.71
1958 3547 3.474600 CAAGCAATCCATCTCGATTCCT 58.525 45.455 0.00 0.00 29.85 3.36
1959 3548 2.551459 CCAAGCAATCCATCTCGATTCC 59.449 50.000 0.00 0.00 29.85 3.01
1960 3549 2.551459 CCCAAGCAATCCATCTCGATTC 59.449 50.000 0.00 0.00 29.85 2.52
1962 3551 1.492176 ACCCAAGCAATCCATCTCGAT 59.508 47.619 0.00 0.00 0.00 3.59
1963 3552 0.911769 ACCCAAGCAATCCATCTCGA 59.088 50.000 0.00 0.00 0.00 4.04
1964 3553 1.303309 GACCCAAGCAATCCATCTCG 58.697 55.000 0.00 0.00 0.00 4.04
1965 3554 2.425143 TGACCCAAGCAATCCATCTC 57.575 50.000 0.00 0.00 0.00 2.75
1966 3555 2.905415 TTGACCCAAGCAATCCATCT 57.095 45.000 0.00 0.00 0.00 2.90
1967 3556 3.959535 TTTTGACCCAAGCAATCCATC 57.040 42.857 0.00 0.00 0.00 3.51
1968 3557 4.286549 TGAATTTTGACCCAAGCAATCCAT 59.713 37.500 0.00 0.00 0.00 3.41
1969 3558 3.645212 TGAATTTTGACCCAAGCAATCCA 59.355 39.130 0.00 0.00 0.00 3.41
1970 3559 4.270245 TGAATTTTGACCCAAGCAATCC 57.730 40.909 0.00 0.00 0.00 3.01
1972 3561 5.683681 AGTTTGAATTTTGACCCAAGCAAT 58.316 33.333 0.00 0.00 0.00 3.56
1976 3565 6.476706 GTCTGAAGTTTGAATTTTGACCCAAG 59.523 38.462 0.00 0.00 0.00 3.61
1979 3568 5.901552 TGTCTGAAGTTTGAATTTTGACCC 58.098 37.500 0.00 0.00 0.00 4.46
1980 3569 6.421801 CCATGTCTGAAGTTTGAATTTTGACC 59.578 38.462 0.00 0.00 0.00 4.02
1982 3571 7.345422 TCCATGTCTGAAGTTTGAATTTTGA 57.655 32.000 0.00 0.00 0.00 2.69
1984 3573 7.729116 ACATCCATGTCTGAAGTTTGAATTTT 58.271 30.769 0.00 0.00 35.87 1.82
1985 3574 7.294017 ACATCCATGTCTGAAGTTTGAATTT 57.706 32.000 0.00 0.00 35.87 1.82
1986 3575 6.906157 ACATCCATGTCTGAAGTTTGAATT 57.094 33.333 0.00 0.00 35.87 2.17
2022 3760 9.841295 GGAAGTGGTAAATATTTCTGTACCATA 57.159 33.333 18.90 0.50 45.75 2.74
2026 3764 6.537660 AGCGGAAGTGGTAAATATTTCTGTAC 59.462 38.462 3.39 0.00 0.00 2.90
2031 3769 6.431198 TGAAGCGGAAGTGGTAAATATTTC 57.569 37.500 3.39 0.00 0.00 2.17
2034 3772 5.250200 TGTTGAAGCGGAAGTGGTAAATAT 58.750 37.500 0.00 0.00 0.00 1.28
2035 3773 4.643463 TGTTGAAGCGGAAGTGGTAAATA 58.357 39.130 0.00 0.00 0.00 1.40
2036 3774 3.482436 TGTTGAAGCGGAAGTGGTAAAT 58.518 40.909 0.00 0.00 0.00 1.40
2037 3775 2.920524 TGTTGAAGCGGAAGTGGTAAA 58.079 42.857 0.00 0.00 0.00 2.01
2038 3776 2.623878 TGTTGAAGCGGAAGTGGTAA 57.376 45.000 0.00 0.00 0.00 2.85
2039 3777 2.851263 ATGTTGAAGCGGAAGTGGTA 57.149 45.000 0.00 0.00 0.00 3.25
2040 3778 1.981256 AATGTTGAAGCGGAAGTGGT 58.019 45.000 0.00 0.00 0.00 4.16
2041 3779 4.701956 ATAAATGTTGAAGCGGAAGTGG 57.298 40.909 0.00 0.00 0.00 4.00
2042 3780 7.754924 ACATAAATAAATGTTGAAGCGGAAGTG 59.245 33.333 0.00 0.00 36.71 3.16
2043 3781 7.826690 ACATAAATAAATGTTGAAGCGGAAGT 58.173 30.769 0.00 0.00 36.71 3.01
2044 3782 8.687824 AACATAAATAAATGTTGAAGCGGAAG 57.312 30.769 1.63 0.00 45.90 3.46
2045 3783 9.562583 GTAACATAAATAAATGTTGAAGCGGAA 57.437 29.630 11.45 0.00 46.77 4.30
2046 3784 7.906010 CGTAACATAAATAAATGTTGAAGCGGA 59.094 33.333 11.45 0.00 46.77 5.54
2047 3785 7.694784 ACGTAACATAAATAAATGTTGAAGCGG 59.305 33.333 11.45 0.00 46.77 5.52
2048 3786 8.595781 ACGTAACATAAATAAATGTTGAAGCG 57.404 30.769 11.45 11.74 46.77 4.68
2072 3810 3.578688 TCGTTTAGCCGAGGAGTAAAAC 58.421 45.455 0.00 0.00 32.18 2.43
2076 3814 2.821969 AGTTTCGTTTAGCCGAGGAGTA 59.178 45.455 0.00 0.00 38.23 2.59
2097 3835 4.764679 AACTTTGCTTGCGAATGTCATA 57.235 36.364 0.00 0.00 0.00 2.15
2103 3841 3.004734 AGCTTGTAACTTTGCTTGCGAAT 59.995 39.130 0.00 0.00 30.96 3.34
2105 3843 1.946768 AGCTTGTAACTTTGCTTGCGA 59.053 42.857 0.00 0.00 30.96 5.10
2107 3845 4.622740 CCATTAGCTTGTAACTTTGCTTGC 59.377 41.667 0.00 0.00 37.02 4.01
2109 3847 6.840780 ATCCATTAGCTTGTAACTTTGCTT 57.159 33.333 0.00 0.00 37.02 3.91
2116 3854 7.226918 GGGAGTTTCTATCCATTAGCTTGTAAC 59.773 40.741 0.00 0.00 38.70 2.50
2127 3865 3.459969 GACCCTTGGGAGTTTCTATCCAT 59.540 47.826 13.39 0.00 38.70 3.41
2134 3872 1.354368 TCCATGACCCTTGGGAGTTTC 59.646 52.381 13.39 0.00 34.85 2.78
2137 3875 2.127708 GTATCCATGACCCTTGGGAGT 58.872 52.381 13.39 0.00 34.85 3.85
2138 3876 2.126882 TGTATCCATGACCCTTGGGAG 58.873 52.381 13.39 0.00 34.85 4.30
2140 3878 3.380471 TTTGTATCCATGACCCTTGGG 57.620 47.619 3.77 3.77 34.85 4.12
2186 3924 2.402305 CTTCAGCCTAGTGATCGATGC 58.598 52.381 0.54 0.00 0.00 3.91
2326 4064 0.677098 GGGTCGAAAGCCCTTCCTTC 60.677 60.000 2.32 0.00 42.07 3.46
2329 4067 2.436115 CGGGTCGAAAGCCCTTCC 60.436 66.667 7.90 0.00 42.82 3.46
2344 4082 5.517322 AATACTACAAGCTAGAGTTCCGG 57.483 43.478 0.00 0.00 0.00 5.14
2497 4235 3.228188 TGAACTGCTTGGAACAGGATT 57.772 42.857 0.00 0.00 42.39 3.01
2513 4251 7.334421 TCAGTATCCTCTAAAGCATTGTTGAAC 59.666 37.037 0.00 0.00 0.00 3.18
2515 4253 6.946340 TCAGTATCCTCTAAAGCATTGTTGA 58.054 36.000 0.00 0.00 0.00 3.18
2545 4283 4.946772 TGAGTTCCTGTGTGAAAATTGACA 59.053 37.500 0.00 0.00 0.00 3.58
2546 4284 5.499139 TGAGTTCCTGTGTGAAAATTGAC 57.501 39.130 0.00 0.00 0.00 3.18
2550 4353 4.949856 ACACTTGAGTTCCTGTGTGAAAAT 59.050 37.500 0.00 0.00 41.37 1.82
2551 4354 4.331968 ACACTTGAGTTCCTGTGTGAAAA 58.668 39.130 0.00 0.00 41.37 2.29
2581 4384 3.068873 CCCACCGAAAGAGATCTTCCTAG 59.931 52.174 0.00 0.00 34.61 3.02
2587 4390 4.186077 TCTATCCCACCGAAAGAGATCT 57.814 45.455 0.00 0.00 0.00 2.75
2591 4394 3.430929 CCACTTCTATCCCACCGAAAGAG 60.431 52.174 0.00 0.00 0.00 2.85
2599 4406 4.141711 TGAGTATTGCCACTTCTATCCCAC 60.142 45.833 0.00 0.00 0.00 4.61
2601 4408 4.689612 TGAGTATTGCCACTTCTATCCC 57.310 45.455 0.00 0.00 0.00 3.85
2613 4420 8.677300 TCAGTTCCTAAATGAAATGAGTATTGC 58.323 33.333 0.35 0.00 42.45 3.56
2653 4460 5.950883 TCCACAAGACTTCTCGTAAGTATG 58.049 41.667 6.01 9.95 39.48 2.39
2676 4483 3.057104 TCAGTATCATTGTGTCGACCGTT 60.057 43.478 14.12 0.00 0.00 4.44
2682 4489 5.501413 GCTCAATGTCAGTATCATTGTGTCG 60.501 44.000 15.09 6.91 46.76 4.35
2685 4492 5.007430 GGAGCTCAATGTCAGTATCATTGTG 59.993 44.000 17.19 13.98 46.76 3.33
2693 4500 0.824109 CGGGGAGCTCAATGTCAGTA 59.176 55.000 17.19 0.00 0.00 2.74
2694 4501 1.194781 ACGGGGAGCTCAATGTCAGT 61.195 55.000 17.19 2.38 0.00 3.41
2754 4561 1.133761 TCTCCATCTCGACCTCGGAAT 60.134 52.381 0.00 0.00 40.29 3.01
2835 4642 6.304624 TGGAGACCAGACGATACTATACAAT 58.695 40.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.