Multiple sequence alignment - TraesCS5D01G139000

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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 TraesCS5D01G139000 chr5D 100.000 5805 0 0 1 5805 221315878 221310074 0.000000e+00 10720.0
1 TraesCS5D01G139000 chr5D 79.461 594 89 20 5096 5668 218029609 218030190 1.960000e-104 390.0
2 TraesCS5D01G139000 chr5B 96.270 4450 115 18 668 5098 243920857 243916440 0.000000e+00 7251.0
3 TraesCS5D01G139000 chr5B 91.690 361 29 1 1 360 243921671 243921311 3.120000e-137 499.0
4 TraesCS5D01G139000 chr5A 97.134 2233 49 5 2871 5098 303284187 303281965 0.000000e+00 3755.0
5 TraesCS5D01G139000 chr5A 95.616 1688 34 15 1214 2871 303286153 303284476 0.000000e+00 2671.0
6 TraesCS5D01G139000 chr5A 90.801 587 52 2 1 587 303288339 303287755 0.000000e+00 784.0
7 TraesCS5D01G139000 chr5A 94.144 444 14 4 795 1227 303287343 303286901 0.000000e+00 665.0
8 TraesCS5D01G139000 chr5A 80.000 95 15 4 488 579 453190583 453190490 3.750000e-07 67.6
9 TraesCS5D01G139000 chr2D 88.131 733 53 12 5091 5805 442017771 442017055 0.000000e+00 841.0
10 TraesCS5D01G139000 chr2D 87.722 733 56 15 5094 5805 441033792 441033073 0.000000e+00 824.0
11 TraesCS5D01G139000 chr6D 87.741 726 58 7 5092 5803 342074364 342073656 0.000000e+00 819.0
12 TraesCS5D01G139000 chr6D 87.158 732 68 7 5093 5805 107953827 107954551 0.000000e+00 808.0
13 TraesCS5D01G139000 chr6D 85.811 740 47 20 5092 5805 4427622 4428329 0.000000e+00 732.0
14 TraesCS5D01G139000 chr6D 82.369 726 96 24 5093 5803 25284208 25284916 2.310000e-168 603.0
15 TraesCS5D01G139000 chr6D 81.613 620 84 18 5096 5693 347766664 347766053 2.430000e-133 486.0
16 TraesCS5D01G139000 chr6D 81.715 618 76 18 5096 5693 361486627 361486027 1.130000e-131 481.0
17 TraesCS5D01G139000 chr1D 86.538 728 71 15 5094 5804 414397286 414398003 0.000000e+00 776.0
18 TraesCS5D01G139000 chr1D 80.645 620 95 10 5094 5693 156011987 156011373 1.910000e-124 457.0
19 TraesCS5D01G139000 chr1D 80.831 626 79 23 5093 5693 204794988 204794379 2.470000e-123 453.0
20 TraesCS5D01G139000 chr3D 86.107 727 74 17 5100 5805 550395158 550394438 0.000000e+00 758.0
21 TraesCS5D01G139000 chr3D 83.959 586 54 20 5094 5651 378201823 378202396 5.150000e-145 525.0
22 TraesCS5D01G139000 chr3D 95.506 89 3 1 5092 5180 608194361 608194274 2.180000e-29 141.0
23 TraesCS5D01G139000 chr4D 87.864 618 64 8 5192 5805 20536233 20536843 0.000000e+00 715.0
24 TraesCS5D01G139000 chr4D 85.226 731 67 21 5093 5805 465157984 465158691 0.000000e+00 713.0


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 TraesCS5D01G139000 chr5D 221310074 221315878 5804 True 10720.00 10720 100.00000 1 5805 1 chr5D.!!$R1 5804
1 TraesCS5D01G139000 chr5D 218029609 218030190 581 False 390.00 390 79.46100 5096 5668 1 chr5D.!!$F1 572
2 TraesCS5D01G139000 chr5B 243916440 243921671 5231 True 3875.00 7251 93.98000 1 5098 2 chr5B.!!$R1 5097
3 TraesCS5D01G139000 chr5A 303281965 303288339 6374 True 1968.75 3755 94.42375 1 5098 4 chr5A.!!$R2 5097
4 TraesCS5D01G139000 chr2D 442017055 442017771 716 True 841.00 841 88.13100 5091 5805 1 chr2D.!!$R2 714
5 TraesCS5D01G139000 chr2D 441033073 441033792 719 True 824.00 824 87.72200 5094 5805 1 chr2D.!!$R1 711
6 TraesCS5D01G139000 chr6D 342073656 342074364 708 True 819.00 819 87.74100 5092 5803 1 chr6D.!!$R1 711
7 TraesCS5D01G139000 chr6D 107953827 107954551 724 False 808.00 808 87.15800 5093 5805 1 chr6D.!!$F3 712
8 TraesCS5D01G139000 chr6D 4427622 4428329 707 False 732.00 732 85.81100 5092 5805 1 chr6D.!!$F1 713
9 TraesCS5D01G139000 chr6D 25284208 25284916 708 False 603.00 603 82.36900 5093 5803 1 chr6D.!!$F2 710
10 TraesCS5D01G139000 chr6D 347766053 347766664 611 True 486.00 486 81.61300 5096 5693 1 chr6D.!!$R2 597
11 TraesCS5D01G139000 chr6D 361486027 361486627 600 True 481.00 481 81.71500 5096 5693 1 chr6D.!!$R3 597
12 TraesCS5D01G139000 chr1D 414397286 414398003 717 False 776.00 776 86.53800 5094 5804 1 chr1D.!!$F1 710
13 TraesCS5D01G139000 chr1D 156011373 156011987 614 True 457.00 457 80.64500 5094 5693 1 chr1D.!!$R1 599
14 TraesCS5D01G139000 chr1D 204794379 204794988 609 True 453.00 453 80.83100 5093 5693 1 chr1D.!!$R2 600
15 TraesCS5D01G139000 chr3D 550394438 550395158 720 True 758.00 758 86.10700 5100 5805 1 chr3D.!!$R1 705
16 TraesCS5D01G139000 chr3D 378201823 378202396 573 False 525.00 525 83.95900 5094 5651 1 chr3D.!!$F1 557
17 TraesCS5D01G139000 chr4D 20536233 20536843 610 False 715.00 715 87.86400 5192 5805 1 chr4D.!!$F1 613
18 TraesCS5D01G139000 chr4D 465157984 465158691 707 False 713.00 713 85.22600 5093 5805 1 chr4D.!!$F2 712

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
313 315 0.037232 CCTCGGTCTGTGGAAAGGAC 60.037 60.000 0.00 0.0 32.77 3.85 F
676 918 0.104304 AGACAAGCGGACGTTGACTT 59.896 50.000 11.78 0.0 0.00 3.01 F
683 925 0.179250 CGGACGTTGACTTGCATTCG 60.179 55.000 0.00 0.0 0.00 3.34 F
856 1374 0.246635 ATCGTTGACCGGACCTGAAG 59.753 55.000 9.46 0.0 37.11 3.02 F
1960 3286 3.071602 TGCAACCTGCTCTAGTCTTTCTT 59.928 43.478 0.00 0.0 45.31 2.52 F
2691 4017 3.688185 AGTTTGTCTCTGCTGCATACATG 59.312 43.478 1.31 0.0 0.00 3.21 F
3191 4809 2.110011 AGAGGTAATGGCAAACACCCTT 59.890 45.455 10.78 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 3052 0.865769 AGTTCAGTACGCGCAAAAGG 59.134 50.000 5.73 0.0 0.00 3.11 R
1939 3265 3.326836 AGAAAGACTAGAGCAGGTTGC 57.673 47.619 0.00 0.0 45.46 4.17 R
2352 3678 6.058183 CCTTTACAGAAGCAGCCTACATATT 58.942 40.000 0.00 0.0 0.00 1.28 R
2691 4017 7.199766 TGCACCGGATTGAAATTATAAATGAC 58.800 34.615 9.46 0.0 0.00 3.06 R
3191 4809 1.229820 AGTGGTGATGGGGCAGGTA 60.230 57.895 0.00 0.0 0.00 3.08 R
4013 5631 0.755327 GGGAACACAAAGCAGTGGGT 60.755 55.000 8.50 0.0 43.72 4.51 R
4963 6584 1.059584 TCCTCCAGTCCAAAGTGCCA 61.060 55.000 0.00 0.0 0.00 4.92 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
51 52 4.351938 TGGAGGTCGCGTTCACGG 62.352 66.667 5.77 0.00 40.23 4.94
125 126 3.067742 CCCTATCAACGATAACGAGTGGT 59.932 47.826 0.00 0.00 42.66 4.16
166 168 0.838122 CTAGGGGCTGGGGTATCCTG 60.838 65.000 0.00 0.00 37.51 3.86
172 174 1.823295 CTGGGGTATCCTGTCCACG 59.177 63.158 0.00 0.00 36.20 4.94
203 205 8.716674 TCTTAGGGTCTTCTTCACTTTTACTA 57.283 34.615 0.00 0.00 0.00 1.82
277 279 3.438087 CGTCATGCTTTGTGAATCCTTCT 59.562 43.478 0.00 0.00 0.00 2.85
284 286 4.683320 GCTTTGTGAATCCTTCTTTTGCTC 59.317 41.667 0.00 0.00 0.00 4.26
292 294 0.890996 CTTCTTTTGCTCCCAGCCGT 60.891 55.000 0.00 0.00 41.51 5.68
308 310 2.260247 CGTACCTCGGTCTGTGGAA 58.740 57.895 6.77 0.00 35.17 3.53
313 315 0.037232 CCTCGGTCTGTGGAAAGGAC 60.037 60.000 0.00 0.00 32.77 3.85
315 317 1.070134 CTCGGTCTGTGGAAAGGACAA 59.930 52.381 0.00 0.00 0.00 3.18
360 362 1.744368 AGCATCAGAGCCGCACTTG 60.744 57.895 0.00 0.00 34.23 3.16
407 409 1.657751 GCACCTCCTTTCAATCCGGC 61.658 60.000 0.00 0.00 0.00 6.13
411 413 1.982073 CTCCTTTCAATCCGGCGCAC 61.982 60.000 10.83 0.00 0.00 5.34
412 414 2.485122 CTTTCAATCCGGCGCACC 59.515 61.111 10.83 0.00 0.00 5.01
506 747 0.955428 GTTGCTCTGGCCGACATCAA 60.955 55.000 0.00 0.00 37.74 2.57
522 763 3.264947 CATCAATGTCATGGAGTCACGT 58.735 45.455 0.00 0.00 0.00 4.49
524 765 4.736126 TCAATGTCATGGAGTCACGTAT 57.264 40.909 0.00 0.00 0.00 3.06
535 776 2.594654 GAGTCACGTATGCTCTGAAACG 59.405 50.000 0.00 0.00 40.99 3.60
536 777 1.654105 GTCACGTATGCTCTGAAACGG 59.346 52.381 0.00 0.00 39.57 4.44
610 852 1.062275 TGGATGGGGATTTCAATGGGG 60.062 52.381 0.00 0.00 0.00 4.96
615 857 0.682855 GGGATTTCAATGGGGCGTGA 60.683 55.000 0.00 0.00 0.00 4.35
620 862 0.742990 TTCAATGGGGCGTGACGATC 60.743 55.000 10.10 0.00 0.00 3.69
644 886 1.128507 CGCATACGTGTGACTTGCATT 59.871 47.619 17.22 0.00 38.10 3.56
645 887 2.412716 CGCATACGTGTGACTTGCATTT 60.413 45.455 17.22 0.00 38.10 2.32
647 889 3.491356 CATACGTGTGACTTGCATTTGG 58.509 45.455 6.42 0.00 0.00 3.28
648 890 1.388547 ACGTGTGACTTGCATTTGGT 58.611 45.000 0.00 0.00 0.00 3.67
649 891 1.748493 ACGTGTGACTTGCATTTGGTT 59.252 42.857 0.00 0.00 0.00 3.67
650 892 2.165437 ACGTGTGACTTGCATTTGGTTT 59.835 40.909 0.00 0.00 0.00 3.27
651 893 3.378742 ACGTGTGACTTGCATTTGGTTTA 59.621 39.130 0.00 0.00 0.00 2.01
652 894 4.037446 ACGTGTGACTTGCATTTGGTTTAT 59.963 37.500 0.00 0.00 0.00 1.40
653 895 4.382457 CGTGTGACTTGCATTTGGTTTATG 59.618 41.667 0.00 0.00 0.00 1.90
654 896 4.685628 GTGTGACTTGCATTTGGTTTATGG 59.314 41.667 0.00 0.00 0.00 2.74
655 897 4.343526 TGTGACTTGCATTTGGTTTATGGT 59.656 37.500 0.00 0.00 0.00 3.55
656 898 4.923281 GTGACTTGCATTTGGTTTATGGTC 59.077 41.667 0.00 0.00 0.00 4.02
657 899 4.586421 TGACTTGCATTTGGTTTATGGTCA 59.414 37.500 0.00 0.00 0.00 4.02
658 900 5.138125 ACTTGCATTTGGTTTATGGTCAG 57.862 39.130 0.00 0.00 0.00 3.51
659 901 4.832266 ACTTGCATTTGGTTTATGGTCAGA 59.168 37.500 0.00 0.00 0.00 3.27
660 902 4.782019 TGCATTTGGTTTATGGTCAGAC 57.218 40.909 0.00 0.00 0.00 3.51
661 903 4.148079 TGCATTTGGTTTATGGTCAGACA 58.852 39.130 2.17 0.00 0.00 3.41
662 904 4.586421 TGCATTTGGTTTATGGTCAGACAA 59.414 37.500 2.17 0.00 0.00 3.18
663 905 5.163513 GCATTTGGTTTATGGTCAGACAAG 58.836 41.667 2.17 0.00 0.00 3.16
664 906 4.846779 TTTGGTTTATGGTCAGACAAGC 57.153 40.909 2.17 0.00 0.00 4.01
665 907 2.422597 TGGTTTATGGTCAGACAAGCG 58.577 47.619 2.17 0.00 0.00 4.68
666 908 1.737793 GGTTTATGGTCAGACAAGCGG 59.262 52.381 2.17 0.00 0.00 5.52
667 909 2.614481 GGTTTATGGTCAGACAAGCGGA 60.614 50.000 2.17 0.00 0.00 5.54
668 910 2.380084 TTATGGTCAGACAAGCGGAC 57.620 50.000 2.17 0.00 40.44 4.79
669 911 0.172578 TATGGTCAGACAAGCGGACG 59.827 55.000 2.17 0.00 41.84 4.79
670 912 1.816863 ATGGTCAGACAAGCGGACGT 61.817 55.000 2.17 0.00 41.84 4.34
671 913 1.300697 GGTCAGACAAGCGGACGTT 60.301 57.895 2.17 0.00 41.84 3.99
672 914 1.557443 GGTCAGACAAGCGGACGTTG 61.557 60.000 2.17 0.16 41.84 4.10
673 915 0.596600 GTCAGACAAGCGGACGTTGA 60.597 55.000 11.78 0.00 32.20 3.18
674 916 0.596600 TCAGACAAGCGGACGTTGAC 60.597 55.000 11.78 7.36 0.00 3.18
675 917 0.597637 CAGACAAGCGGACGTTGACT 60.598 55.000 11.78 8.95 31.36 3.41
676 918 0.104304 AGACAAGCGGACGTTGACTT 59.896 50.000 11.78 0.00 0.00 3.01
677 919 0.232303 GACAAGCGGACGTTGACTTG 59.768 55.000 18.25 18.25 43.99 3.16
678 920 1.082756 CAAGCGGACGTTGACTTGC 60.083 57.895 10.98 0.80 33.77 4.01
679 921 1.522806 AAGCGGACGTTGACTTGCA 60.523 52.632 0.00 0.00 0.00 4.08
680 922 0.884704 AAGCGGACGTTGACTTGCAT 60.885 50.000 0.00 0.00 0.00 3.96
681 923 0.884704 AGCGGACGTTGACTTGCATT 60.885 50.000 0.00 0.00 0.00 3.56
682 924 0.452784 GCGGACGTTGACTTGCATTC 60.453 55.000 0.00 0.00 0.00 2.67
683 925 0.179250 CGGACGTTGACTTGCATTCG 60.179 55.000 0.00 0.00 0.00 3.34
725 967 1.676529 CGTGTCCATAGACCGATGAGT 59.323 52.381 0.00 0.00 42.81 3.41
856 1374 0.246635 ATCGTTGACCGGACCTGAAG 59.753 55.000 9.46 0.00 37.11 3.02
885 1414 3.128068 GCCGAATTAAACACCCCTACTTG 59.872 47.826 0.00 0.00 0.00 3.16
1162 1691 6.206634 TCTCCGTCATGTTAAGCTTTCAATTT 59.793 34.615 3.20 0.00 0.00 1.82
1329 2647 5.163814 GCTGGAGCAGTGAAGTTAATTAGTG 60.164 44.000 0.00 0.00 41.59 2.74
1330 2648 5.865085 TGGAGCAGTGAAGTTAATTAGTGT 58.135 37.500 0.00 0.00 0.00 3.55
1364 2682 3.815401 ACACACTGCAGGTTAATGTTCTC 59.185 43.478 19.93 0.00 0.00 2.87
1408 2726 6.143758 TGCGCAAAAGAAGTTGAAATGTAATC 59.856 34.615 8.16 0.00 0.00 1.75
1726 3052 6.208402 TGATGAGATAACAGTAGAGGATGCTC 59.792 42.308 6.03 6.03 0.00 4.26
1887 3213 5.912955 GTGCTTTGGTAAGTATGACACAAAC 59.087 40.000 0.00 0.00 33.74 2.93
1904 3230 6.560711 ACACAAACATTTGAGTCTTGGTTAC 58.439 36.000 11.24 0.00 37.40 2.50
1945 3271 4.165950 TGATGGTACCAATCTATGCAACCT 59.834 41.667 20.76 0.00 34.83 3.50
1960 3286 3.071602 TGCAACCTGCTCTAGTCTTTCTT 59.928 43.478 0.00 0.00 45.31 2.52
2280 3606 4.615588 TGCCCCTTTTGTTTATCCTTTG 57.384 40.909 0.00 0.00 0.00 2.77
2352 3678 6.389830 TTCAGCTTTGCTCTTTTGTTATGA 57.610 33.333 0.00 0.00 36.40 2.15
2691 4017 3.688185 AGTTTGTCTCTGCTGCATACATG 59.312 43.478 1.31 0.00 0.00 3.21
2801 4127 6.946583 AGGTTGATTTTAAGAGGGAAGGTTAC 59.053 38.462 0.00 0.00 0.00 2.50
3191 4809 2.110011 AGAGGTAATGGCAAACACCCTT 59.890 45.455 10.78 0.00 0.00 3.95
3320 4938 7.885297 AGACTGAGATGTCTGAATAGCTTATC 58.115 38.462 3.65 0.00 44.64 1.75
3367 4985 8.621286 TCAGACACTGGATTTTTCTAAGAAAAC 58.379 33.333 0.00 0.00 30.46 2.43
3866 5484 6.951971 AGTTTGGATCTCTGTATAGCTTTGT 58.048 36.000 0.00 0.00 0.00 2.83
3867 5485 6.820656 AGTTTGGATCTCTGTATAGCTTTGTG 59.179 38.462 0.00 0.00 0.00 3.33
4288 5909 9.778993 CAGTCTGTGATGGTATTTTAGAATTTG 57.221 33.333 0.00 0.00 0.00 2.32
4318 5939 2.229543 TGGCTGAGCTGCTTATGTTTTG 59.770 45.455 2.53 0.00 0.00 2.44
4453 6074 6.473778 CGACCAGTTACTGTTTAGATGATCTG 59.526 42.308 11.68 0.00 0.00 2.90
4779 6400 1.338769 ACTGGTCCGTTATCTTGCCAC 60.339 52.381 0.00 0.00 0.00 5.01
4790 6411 0.948623 TCTTGCCACGATGTTCACGG 60.949 55.000 0.00 0.00 34.93 4.94
4825 6446 2.159226 GGATGGTCGTTGTGAGTCTAGG 60.159 54.545 0.00 0.00 0.00 3.02
4963 6584 3.964031 TGTTTTGGTATGGAGTTTTGCCT 59.036 39.130 0.00 0.00 0.00 4.75
4982 6603 1.059584 TGGCACTTTGGACTGGAGGA 61.060 55.000 0.00 0.00 0.00 3.71
5000 6621 4.223032 GGAGGAGATGGTCTCTTTGTGTTA 59.777 45.833 6.89 0.00 42.95 2.41
5047 6671 4.153117 CAGTTTCAGAATGTCCTTCCTTCG 59.847 45.833 0.00 0.00 37.40 3.79
5086 6710 0.834687 ACCGGGAAGGCAGAGTGTTA 60.835 55.000 6.32 0.00 46.52 2.41
5310 6994 8.249327 TGTTCGGCGTTTACATAAGTTATTAA 57.751 30.769 6.85 0.00 0.00 1.40
5311 6995 8.715998 TGTTCGGCGTTTACATAAGTTATTAAA 58.284 29.630 6.85 0.63 0.00 1.52
5312 6996 9.540431 GTTCGGCGTTTACATAAGTTATTAAAA 57.460 29.630 6.85 0.00 0.00 1.52
5450 7145 3.002583 TGCCTGGCGTCTCCATGA 61.003 61.111 14.98 0.00 45.50 3.07
5726 7441 1.014564 CCGACTCCGTCTTTGGCTTC 61.015 60.000 0.00 0.00 0.00 3.86
5728 7443 1.673033 CGACTCCGTCTTTGGCTTCAT 60.673 52.381 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.351938 CCGTGAACGCGACCTCCA 62.352 66.667 15.93 0.00 38.18 3.86
51 52 2.266055 CGAGTTGAGCCCAGACCC 59.734 66.667 0.00 0.00 0.00 4.46
166 168 3.154589 CCTAAGAAAGGGCGTGGAC 57.845 57.895 0.00 0.00 42.32 4.02
203 205 4.701765 CGAAAGATGATGGAGTTGGAGAT 58.298 43.478 0.00 0.00 0.00 2.75
277 279 1.302993 GGTACGGCTGGGAGCAAAA 60.303 57.895 0.00 0.00 44.75 2.44
292 294 1.203087 TCCTTTCCACAGACCGAGGTA 60.203 52.381 0.00 0.00 0.00 3.08
308 310 5.190528 ACACCACATCTCATATCTTGTCCTT 59.809 40.000 0.00 0.00 0.00 3.36
313 315 4.573607 CACCACACCACATCTCATATCTTG 59.426 45.833 0.00 0.00 0.00 3.02
315 317 3.432749 GCACCACACCACATCTCATATCT 60.433 47.826 0.00 0.00 0.00 1.98
345 347 2.555199 GTATTCAAGTGCGGCTCTGAT 58.445 47.619 5.20 3.72 0.00 2.90
360 362 2.516225 GCCTGCCCGTGGGTATTC 60.516 66.667 6.82 0.00 37.65 1.75
407 409 2.490217 CCTACTCCGACTGGTGCG 59.510 66.667 0.00 0.00 36.30 5.34
439 441 1.650153 CACTTCAATGCAATTTCGGCG 59.350 47.619 0.00 0.00 31.22 6.46
506 747 2.432146 AGCATACGTGACTCCATGACAT 59.568 45.455 0.00 0.00 33.58 3.06
511 752 2.379005 TCAGAGCATACGTGACTCCAT 58.621 47.619 0.00 0.00 32.44 3.41
514 755 2.594654 CGTTTCAGAGCATACGTGACTC 59.405 50.000 0.00 1.92 0.00 3.36
522 763 2.346803 GTCAAGCCGTTTCAGAGCATA 58.653 47.619 0.00 0.00 0.00 3.14
524 765 0.884704 GGTCAAGCCGTTTCAGAGCA 60.885 55.000 0.00 0.00 0.00 4.26
535 776 2.031682 GCATATTCATGTCGGTCAAGCC 60.032 50.000 0.00 0.00 34.40 4.35
536 777 2.348872 CGCATATTCATGTCGGTCAAGC 60.349 50.000 0.00 0.00 34.40 4.01
546 787 3.460114 CGGTTGCCGCATATTCATG 57.540 52.632 0.00 0.00 41.17 3.07
615 857 1.588932 CACGTATGCGCCTGATCGT 60.589 57.895 4.18 6.16 42.83 3.73
620 862 1.014044 AAGTCACACGTATGCGCCTG 61.014 55.000 4.18 0.00 42.83 4.85
644 886 2.811431 CGCTTGTCTGACCATAAACCAA 59.189 45.455 5.17 0.00 0.00 3.67
645 887 2.422597 CGCTTGTCTGACCATAAACCA 58.577 47.619 5.17 0.00 0.00 3.67
647 889 2.415512 GTCCGCTTGTCTGACCATAAAC 59.584 50.000 5.17 0.00 0.00 2.01
648 890 2.695359 GTCCGCTTGTCTGACCATAAA 58.305 47.619 5.17 0.00 0.00 1.40
649 891 1.403647 CGTCCGCTTGTCTGACCATAA 60.404 52.381 5.17 0.00 0.00 1.90
650 892 0.172578 CGTCCGCTTGTCTGACCATA 59.827 55.000 5.17 0.00 0.00 2.74
651 893 1.079819 CGTCCGCTTGTCTGACCAT 60.080 57.895 5.17 0.00 0.00 3.55
652 894 2.023414 AACGTCCGCTTGTCTGACCA 62.023 55.000 5.17 0.00 0.00 4.02
653 895 1.300697 AACGTCCGCTTGTCTGACC 60.301 57.895 5.17 0.00 0.00 4.02
654 896 0.596600 TCAACGTCCGCTTGTCTGAC 60.597 55.000 0.00 0.00 0.00 3.51
655 897 0.596600 GTCAACGTCCGCTTGTCTGA 60.597 55.000 0.00 0.00 0.00 3.27
656 898 0.597637 AGTCAACGTCCGCTTGTCTG 60.598 55.000 0.00 0.00 0.00 3.51
657 899 0.104304 AAGTCAACGTCCGCTTGTCT 59.896 50.000 0.00 0.00 0.00 3.41
658 900 0.232303 CAAGTCAACGTCCGCTTGTC 59.768 55.000 14.06 0.00 35.09 3.18
659 901 1.772063 GCAAGTCAACGTCCGCTTGT 61.772 55.000 19.72 0.00 40.09 3.16
660 902 1.082756 GCAAGTCAACGTCCGCTTG 60.083 57.895 16.55 16.55 40.68 4.01
661 903 0.884704 ATGCAAGTCAACGTCCGCTT 60.885 50.000 0.00 0.00 0.00 4.68
662 904 0.884704 AATGCAAGTCAACGTCCGCT 60.885 50.000 0.00 0.00 0.00 5.52
663 905 0.452784 GAATGCAAGTCAACGTCCGC 60.453 55.000 0.00 0.00 0.00 5.54
664 906 0.179250 CGAATGCAAGTCAACGTCCG 60.179 55.000 0.00 0.00 0.00 4.79
665 907 0.165944 CCGAATGCAAGTCAACGTCC 59.834 55.000 0.00 0.00 0.00 4.79
666 908 0.865769 ACCGAATGCAAGTCAACGTC 59.134 50.000 0.00 0.00 0.00 4.34
667 909 1.305201 AACCGAATGCAAGTCAACGT 58.695 45.000 0.00 0.00 0.00 3.99
668 910 2.043411 CAAACCGAATGCAAGTCAACG 58.957 47.619 0.00 0.00 0.00 4.10
669 911 2.788786 CACAAACCGAATGCAAGTCAAC 59.211 45.455 0.00 0.00 0.00 3.18
670 912 2.223688 CCACAAACCGAATGCAAGTCAA 60.224 45.455 0.00 0.00 0.00 3.18
671 913 1.336440 CCACAAACCGAATGCAAGTCA 59.664 47.619 0.00 0.00 0.00 3.41
672 914 1.336755 ACCACAAACCGAATGCAAGTC 59.663 47.619 0.00 0.00 0.00 3.01
673 915 1.336755 GACCACAAACCGAATGCAAGT 59.663 47.619 0.00 0.00 0.00 3.16
674 916 1.336440 TGACCACAAACCGAATGCAAG 59.664 47.619 0.00 0.00 0.00 4.01
675 917 1.336440 CTGACCACAAACCGAATGCAA 59.664 47.619 0.00 0.00 0.00 4.08
676 918 0.950836 CTGACCACAAACCGAATGCA 59.049 50.000 0.00 0.00 0.00 3.96
677 919 1.069227 GTCTGACCACAAACCGAATGC 60.069 52.381 0.00 0.00 0.00 3.56
678 920 2.217750 TGTCTGACCACAAACCGAATG 58.782 47.619 5.17 0.00 0.00 2.67
679 921 2.631160 TGTCTGACCACAAACCGAAT 57.369 45.000 5.17 0.00 0.00 3.34
680 922 2.285083 CTTGTCTGACCACAAACCGAA 58.715 47.619 5.17 0.00 35.83 4.30
681 923 1.948104 CTTGTCTGACCACAAACCGA 58.052 50.000 5.17 0.00 35.83 4.69
682 924 0.307760 GCTTGTCTGACCACAAACCG 59.692 55.000 5.17 0.00 35.83 4.44
683 925 0.307760 CGCTTGTCTGACCACAAACC 59.692 55.000 5.17 0.00 35.83 3.27
725 967 2.680339 TGCAAATAATCCAACGCGATGA 59.320 40.909 18.77 8.66 0.00 2.92
856 1374 3.991773 GGGTGTTTAATTCGGCTTTTTCC 59.008 43.478 0.00 0.00 0.00 3.13
885 1414 2.370281 TCCTCGACTTGCAATCTGTC 57.630 50.000 0.00 3.19 0.00 3.51
1162 1691 3.579709 CAAGAGAAAAGTGCTCTCGCTA 58.420 45.455 0.00 0.00 43.47 4.26
1174 1703 3.555139 CGCACCAAATTTGCAAGAGAAAA 59.445 39.130 12.92 0.00 40.20 2.29
1290 2582 2.483877 CTCCAGCAACATACAAAGCGAA 59.516 45.455 0.00 0.00 0.00 4.70
1364 2682 3.282885 GCACTGATTAAAGAAGGGGAGG 58.717 50.000 0.00 0.00 0.00 4.30
1433 2759 1.401552 GCCTTCACATAGCGCAATCAA 59.598 47.619 11.47 0.00 0.00 2.57
1587 2913 7.594015 CAGATTTGCATATTTTGTAGCATCTCC 59.406 37.037 0.00 0.00 36.80 3.71
1726 3052 0.865769 AGTTCAGTACGCGCAAAAGG 59.134 50.000 5.73 0.00 0.00 3.11
1887 3213 3.739300 ACGACGTAACCAAGACTCAAATG 59.261 43.478 0.00 0.00 0.00 2.32
1904 3230 5.520288 ACCATCATTCTAGAAATCAACGACG 59.480 40.000 9.71 0.00 0.00 5.12
1939 3265 3.326836 AGAAAGACTAGAGCAGGTTGC 57.673 47.619 0.00 0.00 45.46 4.17
2352 3678 6.058183 CCTTTACAGAAGCAGCCTACATATT 58.942 40.000 0.00 0.00 0.00 1.28
2691 4017 7.199766 TGCACCGGATTGAAATTATAAATGAC 58.800 34.615 9.46 0.00 0.00 3.06
3191 4809 1.229820 AGTGGTGATGGGGCAGGTA 60.230 57.895 0.00 0.00 0.00 3.08
3320 4938 9.626045 GTCTGAGAAAGGGTAATTAAAATTGTG 57.374 33.333 0.00 0.00 0.00 3.33
3367 4985 3.364889 CATGTTGCCATGCTTATGAGG 57.635 47.619 0.00 0.00 41.88 3.86
3912 5530 7.489160 TGTTCTCGCATATCACAAGTATAGTT 58.511 34.615 0.00 0.00 0.00 2.24
4013 5631 0.755327 GGGAACACAAAGCAGTGGGT 60.755 55.000 8.50 0.00 43.72 4.51
4017 5636 1.340991 ACACAGGGAACACAAAGCAGT 60.341 47.619 0.00 0.00 0.00 4.40
4216 5837 6.948309 GCATTCTACCCTTATTTGGTCCATAT 59.052 38.462 0.00 0.00 37.31 1.78
4288 5909 2.751806 AGCAGCTCAGCCAAACTATTTC 59.248 45.455 0.00 0.00 34.23 2.17
4453 6074 8.850156 ACCTGGAAAATAGTATTATGCAATGAC 58.150 33.333 0.00 0.00 0.00 3.06
4779 6400 1.086696 ATTCTTGCCCGTGAACATCG 58.913 50.000 0.00 0.00 0.00 3.84
4790 6411 3.471680 GACCATCCTAGTCATTCTTGCC 58.528 50.000 0.00 0.00 34.27 4.52
4825 6446 1.805869 AGCACTTGCATCAGAGTCAC 58.194 50.000 3.62 0.00 45.16 3.67
4963 6584 1.059584 TCCTCCAGTCCAAAGTGCCA 61.060 55.000 0.00 0.00 0.00 4.92
4982 6603 8.762645 TCTTCATATAACACAAAGAGACCATCT 58.237 33.333 0.00 0.00 41.27 2.90
5000 6621 6.660521 TGAAACTGCAGTTCCAATCTTCATAT 59.339 34.615 31.20 11.73 37.25 1.78
5047 6671 4.330074 CGGTGAATCACTGTTATCCAAGTC 59.670 45.833 13.79 0.00 36.14 3.01
5086 6710 1.135960 GGAGATGCTCTTAGGCCCTT 58.864 55.000 0.00 0.00 0.00 3.95
5201 6838 2.118313 AATAAAAACCCGCGCCTAGT 57.882 45.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.