Multiple sequence alignment - TraesCS3D01G119600

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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 TraesCS3D01G119600 chr3D 100.000 6317 0 0 1 6317 75139258 75145574 0.000000e+00 11666
1 TraesCS3D01G119600 chr3A 94.606 5747 195 42 609 6317 88542485 88548154 0.000000e+00 8789
2 TraesCS3D01G119600 chr3A 83.103 580 70 17 26 590 180072619 180073185 2.630000e-138 503
3 TraesCS3D01G119600 chr3B 96.291 2966 86 12 2488 5450 120617077 120620021 0.000000e+00 4846
4 TraesCS3D01G119600 chr3B 91.005 1890 103 32 611 2486 120615076 120616912 0.000000e+00 2486
5 TraesCS3D01G119600 chr3B 91.206 887 54 13 5434 6317 120620188 120621053 0.000000e+00 1184
6 TraesCS3D01G119600 chr3B 92.746 386 28 0 164 549 424683386 424683001 5.530000e-155 558
7 TraesCS3D01G119600 chr3B 89.637 386 40 0 164 549 424697678 424697293 5.690000e-135 492
8 TraesCS3D01G119600 chr4D 96.916 616 13 4 1 610 50422154 50421539 0.000000e+00 1027
9 TraesCS3D01G119600 chr1D 97.199 607 15 2 1 605 404237646 404238252 0.000000e+00 1026
10 TraesCS3D01G119600 chr7D 96.817 597 18 1 1 596 10858087 10858683 0.000000e+00 996
11 TraesCS3D01G119600 chr2D 95.374 562 14 5 1 561 444758121 444757571 0.000000e+00 883
12 TraesCS3D01G119600 chr1A 88.021 576 45 6 27 596 142103218 142103775 0.000000e+00 660
13 TraesCS3D01G119600 chr5D 81.143 350 36 13 198 541 533118136 533117811 2.920000e-63 254


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 TraesCS3D01G119600 chr3D 75139258 75145574 6316 False 11666.000000 11666 100.000 1 6317 1 chr3D.!!$F1 6316
1 TraesCS3D01G119600 chr3A 88542485 88548154 5669 False 8789.000000 8789 94.606 609 6317 1 chr3A.!!$F1 5708
2 TraesCS3D01G119600 chr3A 180072619 180073185 566 False 503.000000 503 83.103 26 590 1 chr3A.!!$F2 564
3 TraesCS3D01G119600 chr3B 120615076 120621053 5977 False 2838.666667 4846 92.834 611 6317 3 chr3B.!!$F1 5706
4 TraesCS3D01G119600 chr4D 50421539 50422154 615 True 1027.000000 1027 96.916 1 610 1 chr4D.!!$R1 609
5 TraesCS3D01G119600 chr1D 404237646 404238252 606 False 1026.000000 1026 97.199 1 605 1 chr1D.!!$F1 604
6 TraesCS3D01G119600 chr7D 10858087 10858683 596 False 996.000000 996 96.817 1 596 1 chr7D.!!$F1 595
7 TraesCS3D01G119600 chr2D 444757571 444758121 550 True 883.000000 883 95.374 1 561 1 chr2D.!!$R1 560
8 TraesCS3D01G119600 chr1A 142103218 142103775 557 False 660.000000 660 88.021 27 596 1 chr1A.!!$F1 569

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
967 998 0.110486 ACCGCCATTTCCACTTGAGT 59.890 50.000 0.0 0.0 0.00 3.41 F
975 1006 1.827399 TTCCACTTGAGTCGGCCTCC 61.827 60.000 0.0 0.0 39.65 4.30 F
2527 2740 0.035317 TTGTCTTCGTGCTGCCTCAT 59.965 50.000 0.0 0.0 0.00 2.90 F
3133 3362 1.122849 GCGTGTGTGTGCTTTGATTG 58.877 50.000 0.0 0.0 0.00 2.67 F
3265 3494 1.771255 AGGACTCACTTGAACCTTGCT 59.229 47.619 0.0 0.0 30.49 3.91 F
3821 4051 2.675348 GTCTACTCAGCCAACAGAATGC 59.325 50.000 0.0 0.0 42.53 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 1986 0.179166 CATTGTGGCGTGGCACATAC 60.179 55.000 26.72 12.97 44.52 2.39 R
2782 2999 0.179234 GGGGCTTCAAGTAGAGGAGC 59.821 60.000 0.00 0.00 30.79 4.70 R
3821 4051 1.590238 CGATGCGTTTCTCCTTGCTAG 59.410 52.381 0.00 0.00 0.00 3.42 R
4806 5036 0.964700 CCTCAGAGAGTGACACTGCA 59.035 55.000 14.14 0.00 37.18 4.41 R
5022 5252 2.673368 CAACATCTCACCCTTCGCTAAC 59.327 50.000 0.00 0.00 0.00 2.34 R
5679 6092 0.030908 GTAGCGCTACTGGCCTACTG 59.969 60.000 34.70 0.00 39.43 2.74 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
71 74 4.373116 CTGCTACGCACCACCGGT 62.373 66.667 0.00 0.00 35.62 5.28
193 203 2.224523 ACTCATCTTTTTGCTGGGACGA 60.225 45.455 0.00 0.00 0.00 4.20
598 617 2.117156 GCGCAGATCAGTGCCCAAT 61.117 57.895 12.26 0.00 40.62 3.16
599 618 1.660560 GCGCAGATCAGTGCCCAATT 61.661 55.000 12.26 0.00 40.62 2.32
600 619 1.667236 CGCAGATCAGTGCCCAATTA 58.333 50.000 0.00 0.00 40.62 1.40
601 620 2.016318 CGCAGATCAGTGCCCAATTAA 58.984 47.619 0.00 0.00 40.62 1.40
605 624 5.422145 GCAGATCAGTGCCCAATTAAAAAT 58.578 37.500 0.00 0.00 37.49 1.82
606 625 6.572519 GCAGATCAGTGCCCAATTAAAAATA 58.427 36.000 0.00 0.00 37.49 1.40
607 626 6.476706 GCAGATCAGTGCCCAATTAAAAATAC 59.523 38.462 0.00 0.00 37.49 1.89
657 677 1.202405 CCTTCCAAACAGCACCAACAC 60.202 52.381 0.00 0.00 0.00 3.32
658 678 0.820871 TTCCAAACAGCACCAACACC 59.179 50.000 0.00 0.00 0.00 4.16
659 679 0.323816 TCCAAACAGCACCAACACCA 60.324 50.000 0.00 0.00 0.00 4.17
660 680 0.534412 CCAAACAGCACCAACACCAA 59.466 50.000 0.00 0.00 0.00 3.67
661 681 1.639280 CAAACAGCACCAACACCAAC 58.361 50.000 0.00 0.00 0.00 3.77
662 682 1.067283 CAAACAGCACCAACACCAACA 60.067 47.619 0.00 0.00 0.00 3.33
670 690 0.750182 CCAACACCAACAGAACCCGT 60.750 55.000 0.00 0.00 0.00 5.28
672 692 0.750182 AACACCAACAGAACCCGTGG 60.750 55.000 0.00 0.00 0.00 4.94
684 704 2.260869 CCCGTGGAAAGCACACAGG 61.261 63.158 0.00 0.00 38.74 4.00
693 713 2.281761 GCACACAGGTGGAGGGTG 60.282 66.667 4.24 0.00 45.38 4.61
694 714 2.431683 CACACAGGTGGAGGGTGG 59.568 66.667 4.24 0.00 41.45 4.61
695 715 2.854032 ACACAGGTGGAGGGTGGG 60.854 66.667 4.24 0.00 36.87 4.61
696 716 4.351054 CACAGGTGGAGGGTGGGC 62.351 72.222 0.00 0.00 0.00 5.36
697 717 4.599500 ACAGGTGGAGGGTGGGCT 62.599 66.667 0.00 0.00 0.00 5.19
810 835 1.503818 ATTCGTGCGCGTTGGAAACT 61.504 50.000 20.50 0.00 46.99 2.66
864 889 1.826385 AAGGAGATTGCCTTTGTCCG 58.174 50.000 0.00 0.00 45.85 4.79
934 965 1.613255 CCTAATCCACACCACCACCAC 60.613 57.143 0.00 0.00 0.00 4.16
935 966 0.402504 TAATCCACACCACCACCACC 59.597 55.000 0.00 0.00 0.00 4.61
936 967 1.650242 AATCCACACCACCACCACCA 61.650 55.000 0.00 0.00 0.00 4.17
937 968 2.351924 ATCCACACCACCACCACCAC 62.352 60.000 0.00 0.00 0.00 4.16
938 969 2.518349 CACACCACCACCACCACC 60.518 66.667 0.00 0.00 0.00 4.61
939 970 3.018193 ACACCACCACCACCACCA 61.018 61.111 0.00 0.00 0.00 4.17
940 971 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
941 972 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
942 973 4.947147 CCACCACCACCACCACCG 62.947 72.222 0.00 0.00 0.00 4.94
964 995 1.586028 CCACCGCCATTTCCACTTG 59.414 57.895 0.00 0.00 0.00 3.16
965 996 0.893270 CCACCGCCATTTCCACTTGA 60.893 55.000 0.00 0.00 0.00 3.02
966 997 0.523072 CACCGCCATTTCCACTTGAG 59.477 55.000 0.00 0.00 0.00 3.02
967 998 0.110486 ACCGCCATTTCCACTTGAGT 59.890 50.000 0.00 0.00 0.00 3.41
975 1006 1.827399 TTCCACTTGAGTCGGCCTCC 61.827 60.000 0.00 0.00 39.65 4.30
991 1022 4.351054 CCGCCTTTGCCTCTGGGT 62.351 66.667 0.00 0.00 34.45 4.51
1023 1054 2.188161 GTACCTCCTCCTCTCGCCG 61.188 68.421 0.00 0.00 0.00 6.46
1322 1353 3.961477 TGTCAATTCCGTCTTGTGTTG 57.039 42.857 0.00 0.00 0.00 3.33
1329 1360 5.718649 ATTCCGTCTTGTGTTGATATTCG 57.281 39.130 0.00 0.00 0.00 3.34
1331 1362 5.313520 TCCGTCTTGTGTTGATATTCGTA 57.686 39.130 0.00 0.00 0.00 3.43
1359 1394 3.165875 AGCACTAAAGCCTAGTCTGTCA 58.834 45.455 0.00 0.00 34.23 3.58
1365 1400 5.952947 ACTAAAGCCTAGTCTGTCAGTGTAT 59.047 40.000 0.00 0.00 0.00 2.29
1370 1405 5.952947 AGCCTAGTCTGTCAGTGTATTACTT 59.047 40.000 0.00 0.00 37.60 2.24
1406 1441 6.564709 GGTTTTACCCTCAATTCGTTACTT 57.435 37.500 0.00 0.00 30.04 2.24
1473 1508 8.260114 CCAAAAACCTTCTATGGAATTGCTAAT 58.740 33.333 0.00 0.00 32.82 1.73
1474 1509 9.657419 CAAAAACCTTCTATGGAATTGCTAATT 57.343 29.630 0.00 0.00 0.00 1.40
1528 1563 6.723298 AGACTCTCACCTAAACATATCAGG 57.277 41.667 0.00 0.00 35.45 3.86
1666 1709 5.633830 AAAAACACCATATGCAGAGAGTG 57.366 39.130 10.93 10.93 0.00 3.51
1772 1815 5.051816 ACTGTGGATCTTTGTTGCATTTTG 58.948 37.500 0.00 0.00 0.00 2.44
1821 1866 9.226606 CGAGGCCCATTAGTTTATAAATATTGA 57.773 33.333 0.00 0.00 0.00 2.57
1894 1943 7.678947 ACTTCTACAAAAAGATGGTGATGAG 57.321 36.000 0.00 0.00 0.00 2.90
1895 1944 7.227156 ACTTCTACAAAAAGATGGTGATGAGT 58.773 34.615 0.00 0.00 0.00 3.41
1896 1945 7.389053 ACTTCTACAAAAAGATGGTGATGAGTC 59.611 37.037 0.00 0.00 0.00 3.36
1899 1948 6.263516 ACAAAAAGATGGTGATGAGTCATG 57.736 37.500 11.20 0.00 36.60 3.07
1900 1949 6.005823 ACAAAAAGATGGTGATGAGTCATGA 58.994 36.000 11.20 0.00 36.60 3.07
1936 1986 6.481643 TCCTCAAACTAAATCTTACCCTTGG 58.518 40.000 0.00 0.00 0.00 3.61
2041 2091 9.035607 CATAAATCCTGTACTTAGTGCAGTTAG 57.964 37.037 24.45 12.62 43.02 2.34
2063 2113 8.507249 GTTAGTTGTCATGAGAATGCTTAAACT 58.493 33.333 8.72 1.98 0.00 2.66
2335 2385 3.726557 TGCTTGATGGTCAGAATTCCT 57.273 42.857 0.65 0.00 0.00 3.36
2407 2457 2.821969 GACTTCCGTAGTAACCCTGTCA 59.178 50.000 0.00 0.00 37.17 3.58
2515 2728 7.896811 AGGTTATTTTGAATTCCCTTGTCTTC 58.103 34.615 2.27 0.00 0.00 2.87
2524 2737 1.302033 CCTTGTCTTCGTGCTGCCT 60.302 57.895 0.00 0.00 0.00 4.75
2525 2738 1.294659 CCTTGTCTTCGTGCTGCCTC 61.295 60.000 0.00 0.00 0.00 4.70
2526 2739 0.601046 CTTGTCTTCGTGCTGCCTCA 60.601 55.000 0.00 0.00 0.00 3.86
2527 2740 0.035317 TTGTCTTCGTGCTGCCTCAT 59.965 50.000 0.00 0.00 0.00 2.90
2782 2999 1.216710 GGCGGGACTCAGTCAGAAG 59.783 63.158 7.24 0.00 33.68 2.85
2916 3133 3.019564 AGTTCTTGCTGGATTGTATGGC 58.980 45.455 0.00 0.00 0.00 4.40
2935 3152 1.734465 GCACATCTCGACAGGAAAAGG 59.266 52.381 0.00 0.00 0.00 3.11
3052 3269 1.477740 GGCCAAGATCCTAAGGAAGGC 60.478 57.143 0.00 0.00 46.10 4.35
3133 3362 1.122849 GCGTGTGTGTGCTTTGATTG 58.877 50.000 0.00 0.00 0.00 2.67
3158 3387 2.164624 GGCGTGGGCATGTGTTTTATAA 59.835 45.455 0.00 0.00 42.47 0.98
3189 3418 3.411446 CACTCTCAAATTAGGGTGTGCA 58.589 45.455 0.68 0.00 42.10 4.57
3207 3436 5.760253 GTGTGCAGGAGCTTACATATATTGT 59.240 40.000 0.00 0.00 42.74 2.71
3255 3484 5.485708 AGGCTTGAAAGTATAGGACTCACTT 59.514 40.000 0.00 0.00 37.44 3.16
3265 3494 1.771255 AGGACTCACTTGAACCTTGCT 59.229 47.619 0.00 0.00 30.49 3.91
3287 3516 7.796054 TGCTAGCTTGAATACTCTTATTTCCT 58.204 34.615 17.23 0.00 0.00 3.36
3331 3560 7.865706 AACATGTCTTAAGTTGACTCACTTT 57.134 32.000 0.00 0.00 38.07 2.66
3472 3702 4.415881 TGCTACTTTGTTCAGTTGGAGA 57.584 40.909 0.00 0.00 0.00 3.71
3698 3928 4.503991 GGAGCTCAAGGATGAAATACGGAT 60.504 45.833 17.19 0.00 34.49 4.18
3702 3932 6.652481 AGCTCAAGGATGAAATACGGATATTG 59.348 38.462 0.00 0.00 34.49 1.90
3821 4051 2.675348 GTCTACTCAGCCAACAGAATGC 59.325 50.000 0.00 0.00 42.53 3.56
4006 4236 7.366513 TGATCTTGCTTCTAAGATATCGTCAG 58.633 38.462 0.00 0.00 45.00 3.51
4017 4247 8.346300 TCTAAGATATCGTCAGTTGATTCACTC 58.654 37.037 0.00 0.00 0.00 3.51
4125 4355 4.029520 AGGCTTCTTCTGAGATAAGAGCA 58.970 43.478 8.70 0.00 34.59 4.26
4202 4432 6.006759 AGAAAAGCTCTCTGTTGCATTAAC 57.993 37.500 0.00 0.00 39.80 2.01
4546 4776 7.554118 CAGCTAAAGAGATGATTCAAAAGGGTA 59.446 37.037 0.00 0.00 41.90 3.69
4806 5036 4.023450 TCACTAAACGAGATGAACACGAGT 60.023 41.667 0.00 0.00 36.51 4.18
5488 5901 3.074412 CCTTTCCTGTAATTCACGTGCT 58.926 45.455 11.67 0.00 0.00 4.40
5489 5902 3.120199 CCTTTCCTGTAATTCACGTGCTG 60.120 47.826 11.67 0.25 0.00 4.41
5490 5903 1.438651 TCCTGTAATTCACGTGCTGC 58.561 50.000 11.67 1.97 0.00 5.25
5509 5922 4.470462 CTGCGAGTTTTGAGAATTTGAGG 58.530 43.478 0.00 0.00 0.00 3.86
5533 5946 7.726738 AGGGTTTACATGTGTACAGGTTAATTT 59.273 33.333 9.11 0.00 41.46 1.82
5563 5976 6.243900 ACTGTCAACATGATGGAGAATTCTT 58.756 36.000 9.87 0.00 0.00 2.52
5564 5977 6.718454 ACTGTCAACATGATGGAGAATTCTTT 59.282 34.615 9.87 0.00 0.00 2.52
5594 6007 8.771920 TGTAGTTACACTGAATTGTTCATAGG 57.228 34.615 0.00 0.00 39.30 2.57
5597 6010 8.773404 AGTTACACTGAATTGTTCATAGGTAC 57.227 34.615 0.00 0.00 39.30 3.34
5621 6034 8.202745 ACTATCTGCTTGTTTTATCTACTTGC 57.797 34.615 0.00 0.00 0.00 4.01
5680 6093 7.293402 GCAGTATTGCTTATTTTCAATTGCA 57.707 32.000 2.45 0.00 46.95 4.08
5681 6094 7.396419 GCAGTATTGCTTATTTTCAATTGCAG 58.604 34.615 2.45 0.00 46.95 4.41
5682 6095 7.063780 GCAGTATTGCTTATTTTCAATTGCAGT 59.936 33.333 2.45 0.00 46.95 4.40
5683 6096 9.571810 CAGTATTGCTTATTTTCAATTGCAGTA 57.428 29.630 0.00 0.00 34.95 2.74
5684 6097 9.793252 AGTATTGCTTATTTTCAATTGCAGTAG 57.207 29.630 0.00 0.00 34.95 2.57
5685 6098 9.023967 GTATTGCTTATTTTCAATTGCAGTAGG 57.976 33.333 0.00 0.00 34.95 3.18
5686 6099 5.410067 TGCTTATTTTCAATTGCAGTAGGC 58.590 37.500 0.00 4.22 45.13 3.93
5694 6107 0.179073 ATTGCAGTAGGCCAGTAGCG 60.179 55.000 5.01 0.00 45.17 4.26
5716 6129 4.991056 CGCTACCTATACTTTGTGCATCAT 59.009 41.667 0.00 0.00 0.00 2.45
5717 6130 5.107337 CGCTACCTATACTTTGTGCATCATG 60.107 44.000 0.00 0.00 0.00 3.07
5748 6161 0.896940 AACCCACATGCTCCTGCTTG 60.897 55.000 0.00 0.00 46.02 4.01
5755 6168 0.917533 ATGCTCCTGCTTGATCACCT 59.082 50.000 0.00 0.00 40.48 4.00
5758 6171 1.743091 GCTCCTGCTTGATCACCTCAG 60.743 57.143 0.00 3.01 34.68 3.35
5760 6173 1.980765 TCCTGCTTGATCACCTCAGTT 59.019 47.619 13.69 0.00 34.68 3.16
5823 6236 0.253044 GGATCCAGTGGTTGCTGCTA 59.747 55.000 9.54 0.00 35.28 3.49
5827 6240 0.537143 CCAGTGGTTGCTGCTACCAA 60.537 55.000 31.85 16.76 46.62 3.67
5873 6286 9.626045 GTGTATAAAACTTGCAGAGCTTTATTT 57.374 29.630 15.79 3.62 37.63 1.40
6100 6516 2.200373 AAAATGTCTCCCCCGTTCAG 57.800 50.000 0.00 0.00 0.00 3.02
6106 6522 0.903454 TCTCCCCCGTTCAGTTCTCC 60.903 60.000 0.00 0.00 0.00 3.71
6107 6523 1.900545 CTCCCCCGTTCAGTTCTCCC 61.901 65.000 0.00 0.00 0.00 4.30
6108 6524 1.918800 CCCCCGTTCAGTTCTCCCT 60.919 63.158 0.00 0.00 0.00 4.20
6248 6666 6.486320 TCTCAATCTAACATGAAACTGCAACA 59.514 34.615 0.00 0.00 0.00 3.33
6260 6678 7.697352 TGAAACTGCAACACATTTTCTTATG 57.303 32.000 9.10 0.00 44.25 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 74 3.347216 GGTCATAGCTTTTTCTCTGCCA 58.653 45.455 0.00 0.00 0.00 4.92
142 145 0.250338 GTCCCAGCAAGAAACTCGGT 60.250 55.000 0.00 0.00 0.00 4.69
193 203 1.005630 GTCTCTGGTGCAGCTTCGT 60.006 57.895 18.08 0.00 0.00 3.85
303 314 3.083349 CCACCCTCTCGCCATCCA 61.083 66.667 0.00 0.00 0.00 3.41
577 596 4.819761 GGCACTGATCTGCGCCGA 62.820 66.667 14.84 3.73 38.12 5.54
598 617 3.083293 GTGGTCGGCAGGGTATTTTTAA 58.917 45.455 0.00 0.00 0.00 1.52
599 618 2.040012 TGTGGTCGGCAGGGTATTTTTA 59.960 45.455 0.00 0.00 0.00 1.52
600 619 1.202952 TGTGGTCGGCAGGGTATTTTT 60.203 47.619 0.00 0.00 0.00 1.94
601 620 0.402504 TGTGGTCGGCAGGGTATTTT 59.597 50.000 0.00 0.00 0.00 1.82
605 624 1.697082 TTTGTGTGGTCGGCAGGGTA 61.697 55.000 0.00 0.00 0.00 3.69
606 625 2.559922 TTTTGTGTGGTCGGCAGGGT 62.560 55.000 0.00 0.00 0.00 4.34
607 626 1.826054 TTTTGTGTGGTCGGCAGGG 60.826 57.895 0.00 0.00 0.00 4.45
657 677 0.951558 CTTTCCACGGGTTCTGTTGG 59.048 55.000 0.00 0.00 0.00 3.77
658 678 0.310854 GCTTTCCACGGGTTCTGTTG 59.689 55.000 0.00 0.00 0.00 3.33
659 679 0.106918 TGCTTTCCACGGGTTCTGTT 60.107 50.000 0.00 0.00 0.00 3.16
660 680 0.818040 GTGCTTTCCACGGGTTCTGT 60.818 55.000 0.00 0.00 34.22 3.41
661 681 1.949257 GTGCTTTCCACGGGTTCTG 59.051 57.895 0.00 0.00 34.22 3.02
662 682 4.475527 GTGCTTTCCACGGGTTCT 57.524 55.556 0.00 0.00 34.22 3.01
670 690 0.179020 CTCCACCTGTGTGCTTTCCA 60.179 55.000 0.00 0.00 41.35 3.53
672 692 0.890996 CCCTCCACCTGTGTGCTTTC 60.891 60.000 0.00 0.00 41.35 2.62
695 715 4.754667 GTCGGTTCGGTGGGGAGC 62.755 72.222 0.00 0.00 0.00 4.70
696 716 2.874664 TTGTCGGTTCGGTGGGGAG 61.875 63.158 0.00 0.00 0.00 4.30
697 717 2.843411 TTGTCGGTTCGGTGGGGA 60.843 61.111 0.00 0.00 0.00 4.81
699 719 2.667199 GGTTGTCGGTTCGGTGGG 60.667 66.667 0.00 0.00 0.00 4.61
774 799 2.159653 CGAATCTTGGCGAGGTTTTCTG 60.160 50.000 0.86 0.00 0.00 3.02
832 857 3.253838 TCCTTTGGGTGACGGGGG 61.254 66.667 0.00 0.00 0.00 5.40
864 889 1.600916 GTGGGTGGGTCTCAACTGC 60.601 63.158 0.00 0.00 32.53 4.40
975 1006 3.058160 CACCCAGAGGCAAAGGCG 61.058 66.667 0.00 0.00 42.47 5.52
991 1022 4.460683 GTACCCCATCGCGCCACA 62.461 66.667 0.00 0.00 0.00 4.17
1329 1360 9.984190 AGACTAGGCTTTAGTGCTTTAATATAC 57.016 33.333 0.00 0.00 0.00 1.47
1331 1362 8.487028 ACAGACTAGGCTTTAGTGCTTTAATAT 58.513 33.333 0.00 0.00 0.00 1.28
1359 1394 6.649557 CCCTTTTCGTCAGAAAGTAATACACT 59.350 38.462 0.00 0.00 45.86 3.55
1365 1400 6.762702 AAAACCCTTTTCGTCAGAAAGTAA 57.237 33.333 0.00 0.00 45.86 2.24
1406 1441 2.357075 TGTACTGCAAACGTTGGTGAA 58.643 42.857 0.00 0.00 0.00 3.18
1437 1472 8.852135 CCATAGAAGGTTTTTGGTTTTACAGTA 58.148 33.333 0.00 0.00 0.00 2.74
1474 1509 4.698780 CAGGCTGACATTCAATCTCTTTGA 59.301 41.667 9.42 0.00 42.62 2.69
1614 1649 6.475402 GGTTGCATATGGTGTTATTTAGTTGC 59.525 38.462 4.56 0.00 0.00 4.17
1666 1709 5.163913 GCATCTCTACAACACAAGACATGTC 60.164 44.000 18.47 18.47 41.46 3.06
1821 1866 6.741240 GCCCAAACTCAATTTGTAGTTCCAAT 60.741 38.462 11.86 0.00 45.45 3.16
1824 1869 4.280929 AGCCCAAACTCAATTTGTAGTTCC 59.719 41.667 11.86 5.16 45.45 3.62
1867 1916 8.154203 TCATCACCATCTTTTTGTAGAAGTACA 58.846 33.333 0.00 0.00 37.38 2.90
1894 1943 9.685828 GTTTGAGGAGTTATCTATAGTCATGAC 57.314 37.037 18.47 18.47 0.00 3.06
1895 1944 9.647918 AGTTTGAGGAGTTATCTATAGTCATGA 57.352 33.333 0.00 0.00 0.00 3.07
1936 1986 0.179166 CATTGTGGCGTGGCACATAC 60.179 55.000 26.72 12.97 44.52 2.39
1954 2004 7.013846 CCTTTCACAAAACCTAGACATAAACCA 59.986 37.037 0.00 0.00 0.00 3.67
1998 2048 1.167851 ATGCCATGTCCAAACTGACG 58.832 50.000 0.00 0.00 38.11 4.35
2041 2091 7.362662 TCAAGTTTAAGCATTCTCATGACAAC 58.637 34.615 0.00 0.00 31.07 3.32
2407 2457 4.497516 AGGAATGCATCATAGTAGACCCT 58.502 43.478 0.00 0.00 0.00 4.34
2441 2491 9.216117 GCACACTAGTAAATATTTATACCAGGG 57.784 37.037 11.00 4.54 0.00 4.45
2515 2728 0.376152 GATGACAATGAGGCAGCACG 59.624 55.000 0.00 0.00 42.70 5.34
2525 2738 2.161012 GCACTCCAGTGTGATGACAATG 59.839 50.000 5.73 5.73 45.73 2.82
2782 2999 0.179234 GGGGCTTCAAGTAGAGGAGC 59.821 60.000 0.00 0.00 30.79 4.70
2916 3133 3.257393 CTCCTTTTCCTGTCGAGATGTG 58.743 50.000 0.00 0.00 0.00 3.21
2924 3141 0.322906 CAGGGCCTCCTTTTCCTGTC 60.323 60.000 0.95 0.00 42.67 3.51
2935 3152 1.817099 CGACAGATTGCAGGGCCTC 60.817 63.158 0.95 0.00 0.00 4.70
3052 3269 7.147312 TGCTATTTGTGTCCATTTCTCTTTTG 58.853 34.615 0.00 0.00 0.00 2.44
3188 3417 9.935241 AATCAGTACAATATATGTAAGCTCCTG 57.065 33.333 0.00 0.00 45.81 3.86
3255 3484 5.046304 AGAGTATTCAAGCTAGCAAGGTTCA 60.046 40.000 18.83 0.00 41.45 3.18
3265 3494 9.209048 TGGTAGGAAATAAGAGTATTCAAGCTA 57.791 33.333 0.00 0.00 0.00 3.32
3287 3516 4.288366 TGTTTCCCTGAGAACATCATGGTA 59.712 41.667 0.00 0.00 42.63 3.25
3331 3560 7.543947 CATTCATATGCAAGTTACACTCTCA 57.456 36.000 0.00 0.00 0.00 3.27
3472 3702 4.020039 TGCCTCATTTTCAGCCAATTTGAT 60.020 37.500 0.00 0.00 0.00 2.57
3702 3932 6.459923 CCCAGCTTTATCAATACTACTCTCC 58.540 44.000 0.00 0.00 0.00 3.71
3821 4051 1.590238 CGATGCGTTTCTCCTTGCTAG 59.410 52.381 0.00 0.00 0.00 3.42
4006 4236 6.258727 TGAAGTTTCTCACTGAGTGAATCAAC 59.741 38.462 16.94 17.08 42.26 3.18
4017 4247 8.316640 AGCTTAATACTTGAAGTTTCTCACTG 57.683 34.615 1.97 0.00 35.12 3.66
4125 4355 4.957296 ACAGTAGTTCAGAATCGTGGTTT 58.043 39.130 0.00 0.00 0.00 3.27
4546 4776 4.595350 AGAGGTAGCTTCAAGTTCTTCCTT 59.405 41.667 0.00 0.00 29.44 3.36
4716 4946 7.543172 GCTTGAGAATCTGCATTCAATTGTTTA 59.457 33.333 5.13 0.00 41.03 2.01
4806 5036 0.964700 CCTCAGAGAGTGACACTGCA 59.035 55.000 14.14 0.00 37.18 4.41
5022 5252 2.673368 CAACATCTCACCCTTCGCTAAC 59.327 50.000 0.00 0.00 0.00 2.34
5392 5622 3.365064 CGACGCTACAGGATGGTAGTATG 60.365 52.174 0.00 0.00 43.62 2.39
5488 5901 3.253188 CCCTCAAATTCTCAAAACTCGCA 59.747 43.478 0.00 0.00 0.00 5.10
5489 5902 3.253432 ACCCTCAAATTCTCAAAACTCGC 59.747 43.478 0.00 0.00 0.00 5.03
5490 5903 5.438761 AACCCTCAAATTCTCAAAACTCG 57.561 39.130 0.00 0.00 0.00 4.18
5509 5922 9.752961 AAAAATTAACCTGTACACATGTAAACC 57.247 29.630 0.00 0.00 31.52 3.27
5533 5946 5.827267 TCTCCATCATGTTGACAGTTCAAAA 59.173 36.000 5.30 0.00 43.52 2.44
5541 5954 7.528996 AAAAGAATTCTCCATCATGTTGACA 57.471 32.000 8.78 0.00 0.00 3.58
5545 5958 9.471702 ACAGATAAAAGAATTCTCCATCATGTT 57.528 29.630 8.78 0.00 0.00 2.71
5597 6010 8.430801 AGCAAGTAGATAAAACAAGCAGATAG 57.569 34.615 0.00 0.00 0.00 2.08
5602 6015 8.792830 ATTCTAGCAAGTAGATAAAACAAGCA 57.207 30.769 0.00 0.00 37.62 3.91
5621 6034 9.932699 CAGTGAATAGCAGAAAATTGATTCTAG 57.067 33.333 0.00 0.00 37.56 2.43
5632 6045 8.040727 TGCTAGATTAACAGTGAATAGCAGAAA 58.959 33.333 4.48 0.00 33.75 2.52
5633 6046 7.555965 TGCTAGATTAACAGTGAATAGCAGAA 58.444 34.615 4.48 0.00 33.75 3.02
5676 6089 1.218047 CGCTACTGGCCTACTGCAA 59.782 57.895 3.32 0.00 43.89 4.08
5679 6092 0.030908 GTAGCGCTACTGGCCTACTG 59.969 60.000 34.70 0.00 39.43 2.74
5680 6093 1.108132 GGTAGCGCTACTGGCCTACT 61.108 60.000 38.27 5.05 40.83 2.57
5681 6094 1.108132 AGGTAGCGCTACTGGCCTAC 61.108 60.000 38.27 23.80 40.58 3.18
5682 6095 0.475475 TAGGTAGCGCTACTGGCCTA 59.525 55.000 38.27 29.57 36.72 3.93
5683 6096 0.178958 ATAGGTAGCGCTACTGGCCT 60.179 55.000 38.27 30.50 38.28 5.19
5684 6097 1.201880 GTATAGGTAGCGCTACTGGCC 59.798 57.143 38.27 26.10 37.74 5.36
5685 6098 2.161030 AGTATAGGTAGCGCTACTGGC 58.839 52.381 38.27 25.71 36.36 4.85
5686 6099 4.037684 ACAAAGTATAGGTAGCGCTACTGG 59.962 45.833 38.27 21.64 36.36 4.00
5694 6107 5.760253 ACATGATGCACAAAGTATAGGTAGC 59.240 40.000 0.00 0.00 0.00 3.58
5716 6129 2.719739 TGTGGGTTAACCGAAAACACA 58.280 42.857 22.31 22.31 44.64 3.72
5717 6130 3.634283 CATGTGGGTTAACCGAAAACAC 58.366 45.455 18.39 18.57 44.64 3.32
5748 6161 5.239306 TGAAAATGTGTGAACTGAGGTGATC 59.761 40.000 0.00 0.00 0.00 2.92
5755 6168 6.349528 CCAGCATATGAAAATGTGTGAACTGA 60.350 38.462 6.97 0.00 0.00 3.41
5758 6171 5.953183 TCCAGCATATGAAAATGTGTGAAC 58.047 37.500 6.97 0.00 0.00 3.18
5760 6173 4.641541 CCTCCAGCATATGAAAATGTGTGA 59.358 41.667 6.97 0.00 0.00 3.58
5811 6224 1.067635 CCAATTGGTAGCAGCAACCAC 60.068 52.381 16.90 0.00 46.56 4.16
5827 6240 4.904853 ACACCATGTTTCCCTTAAACCAAT 59.095 37.500 0.00 0.00 45.83 3.16
5966 6380 4.870123 TGTCCATGAAAAAGATGTTGGG 57.130 40.909 0.00 0.00 0.00 4.12
6082 6498 1.064825 ACTGAACGGGGGAGACATTT 58.935 50.000 0.00 0.00 0.00 2.32
6093 6509 1.406069 CCATGAGGGAGAACTGAACGG 60.406 57.143 0.00 0.00 40.01 4.44
6106 6522 1.066573 GTGAGGTGTGTCTCCATGAGG 60.067 57.143 0.00 0.00 33.04 3.86
6107 6523 1.066573 GGTGAGGTGTGTCTCCATGAG 60.067 57.143 0.00 0.00 33.04 2.90
6108 6524 0.976641 GGTGAGGTGTGTCTCCATGA 59.023 55.000 0.00 0.00 33.04 3.07
6260 6678 6.265422 ACTTAAGCCCATAATATTTGCCACTC 59.735 38.462 1.29 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.