Multiple sequence alignment - TraesCS6A01G255200

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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 TraesCS6A01G255200 chr6A 100.000 3684 0 0 1 3684 472951000 472947317 0.000000e+00 6804
1 TraesCS6A01G255200 chr6D 93.352 2858 113 37 519 3337 333349778 333346959 0.000000e+00 4154
2 TraesCS6A01G255200 chr6D 87.018 493 32 7 2 477 333351131 333350654 9.060000e-146 527
3 TraesCS6A01G255200 chr6D 92.982 285 7 5 3400 3684 333345986 333345715 1.590000e-108 403
4 TraesCS6A01G255200 chr6B 91.629 2879 146 40 522 3337 487132707 487135553 0.000000e+00 3893
5 TraesCS6A01G255200 chr6B 92.378 328 18 4 3363 3684 487135616 487135942 9.320000e-126 460
6 TraesCS6A01G255200 chr6B 88.163 245 17 1 197 429 487131579 487131823 7.790000e-72 281
7 TraesCS6A01G255200 chr2A 78.517 1564 265 51 1037 2565 656702438 656703965 0.000000e+00 961
8 TraesCS6A01G255200 chr2D 82.413 887 130 18 1698 2565 512923747 512924626 0.000000e+00 750
9 TraesCS6A01G255200 chr2D 77.387 597 118 15 1029 1618 512923093 512923679 4.560000e-89 339
10 TraesCS6A01G255200 chr2B 82.300 887 131 18 1698 2565 603426899 603427778 0.000000e+00 745
11 TraesCS6A01G255200 chr2B 85.220 318 43 4 1036 1351 603426256 603426571 1.280000e-84 324
12 TraesCS6A01G255200 chr4A 80.193 207 36 3 1 207 104268430 104268631 2.290000e-32 150


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 TraesCS6A01G255200 chr6A 472947317 472951000 3683 True 6804.000000 6804 100.000000 1 3684 1 chr6A.!!$R1 3683
1 TraesCS6A01G255200 chr6D 333345715 333351131 5416 True 1694.666667 4154 91.117333 2 3684 3 chr6D.!!$R1 3682
2 TraesCS6A01G255200 chr6B 487131579 487135942 4363 False 1544.666667 3893 90.723333 197 3684 3 chr6B.!!$F1 3487
3 TraesCS6A01G255200 chr2A 656702438 656703965 1527 False 961.000000 961 78.517000 1037 2565 1 chr2A.!!$F1 1528
4 TraesCS6A01G255200 chr2D 512923093 512924626 1533 False 544.500000 750 79.900000 1029 2565 2 chr2D.!!$F1 1536
5 TraesCS6A01G255200 chr2B 603426256 603427778 1522 False 534.500000 745 83.760000 1036 2565 2 chr2B.!!$F1 1529

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
664 2013 0.101399 CGGTCGTCTCCAATCTCCAG 59.899 60.0 0.0 0.0 0.0 3.86 F
740 2099 0.400594 ATATAAGCAAGTCCCCCGGC 59.599 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 4001 0.451135 CTTTCGTTTTCAGCTCGGCG 60.451 55.0 0.00 0.0 0.0 6.46 R
2694 4108 0.102481 TCCGGAGCGCTTTCATAGAC 59.898 55.0 13.26 0.0 0.0 2.59 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
46 47 1.275010 TGGCTAGCAACGTTCTGATCA 59.725 47.619 18.24 0.00 0.00 2.92
53 54 2.661594 CAACGTTCTGATCACGAGACA 58.338 47.619 10.77 0.00 40.20 3.41
89 90 1.305046 TCACTCCCCGTCTCCTTCC 60.305 63.158 0.00 0.00 0.00 3.46
109 110 2.287368 CCAGTAAACGCTTGGTTTCACC 60.287 50.000 0.00 0.00 45.60 4.02
112 113 0.379316 AAACGCTTGGTTTCACCGAC 59.621 50.000 0.00 0.00 45.60 4.79
124 125 3.681835 ACCGACCAGAGCCGTCAC 61.682 66.667 0.00 0.00 0.00 3.67
125 126 4.436998 CCGACCAGAGCCGTCACC 62.437 72.222 0.00 0.00 0.00 4.02
139 140 1.178276 GTCACCGGAGATCTGTCAGT 58.822 55.000 9.46 0.00 0.00 3.41
150 151 1.937191 TCTGTCAGTACCATGCTCCA 58.063 50.000 0.00 0.00 0.00 3.86
181 182 1.446792 CCGCGACTGAGCAATCTGT 60.447 57.895 8.23 0.00 36.85 3.41
233 234 2.289820 GCCGGCGTCTATATATCGATCA 59.710 50.000 12.58 0.00 0.00 2.92
234 235 3.607310 GCCGGCGTCTATATATCGATCAG 60.607 52.174 12.58 0.00 0.00 2.90
361 377 4.326205 CGAATTTGTCGCACTACAGAATG 58.674 43.478 0.00 0.00 44.14 2.67
387 403 5.067805 GGATCAAATTGGCTAAGGACGAAAT 59.932 40.000 0.00 0.00 0.00 2.17
429 447 4.857588 ACTGACAAGTAACTAATCGAAGCG 59.142 41.667 0.00 0.00 33.79 4.68
431 449 4.082625 TGACAAGTAACTAATCGAAGCGGA 60.083 41.667 0.00 0.00 0.00 5.54
432 450 4.421948 ACAAGTAACTAATCGAAGCGGAG 58.578 43.478 0.00 0.00 0.00 4.63
446 464 1.521681 CGGAGCGGTCAGGAATTCC 60.522 63.158 17.31 17.31 0.00 3.01
456 474 1.766461 AGGAATTCCGGATCGCCCT 60.766 57.895 18.82 7.20 42.08 5.19
457 475 1.598130 GGAATTCCGGATCGCCCTG 60.598 63.158 9.17 0.00 0.00 4.45
460 478 2.666596 AATTCCGGATCGCCCTGAGC 62.667 60.000 4.15 0.00 38.52 4.26
481 499 1.764851 GGAGACGAGCAGATCAATCG 58.235 55.000 11.29 11.29 42.04 3.34
497 1814 1.226575 TCGTGATCGATCGTGTGGC 60.227 57.895 20.03 5.59 41.35 5.01
498 1815 2.568031 CGTGATCGATCGTGTGGCG 61.568 63.158 20.03 12.74 39.76 5.69
506 1823 3.018973 TCGTGTGGCGAGCAAAAC 58.981 55.556 0.00 0.00 45.68 2.43
507 1824 2.051345 CGTGTGGCGAGCAAAACC 60.051 61.111 0.00 0.00 44.77 3.27
514 1831 3.399770 CGAGCAAAACCGCGACGA 61.400 61.111 8.23 0.00 38.24 4.20
515 1832 2.170273 GAGCAAAACCGCGACGAC 59.830 61.111 8.23 0.00 36.85 4.34
516 1833 3.609422 GAGCAAAACCGCGACGACG 62.609 63.158 8.23 2.12 42.93 5.12
518 1835 2.166985 CAAAACCGCGACGACGAC 59.833 61.111 8.23 1.51 42.66 4.34
519 1836 3.389211 AAAACCGCGACGACGACG 61.389 61.111 15.13 15.13 42.66 5.12
521 1838 3.599792 AAACCGCGACGACGACGAT 62.600 57.895 22.94 4.95 42.66 3.73
542 1878 1.696832 GGAAACCGCACTCGATCTGC 61.697 60.000 5.35 5.35 38.10 4.26
550 1886 0.861866 CACTCGATCTGCACGTACCG 60.862 60.000 0.00 0.00 0.00 4.02
553 1889 3.617538 GATCTGCACGTACCGCGC 61.618 66.667 0.00 0.00 46.11 6.86
608 1957 1.877576 GCCCCTTTTCCTTTGCCGAG 61.878 60.000 0.00 0.00 0.00 4.63
664 2013 0.101399 CGGTCGTCTCCAATCTCCAG 59.899 60.000 0.00 0.00 0.00 3.86
710 2069 1.089920 CATTGGAGTGCCTCGGAAAG 58.910 55.000 0.00 0.00 34.31 2.62
740 2099 0.400594 ATATAAGCAAGTCCCCCGGC 59.599 55.000 0.00 0.00 0.00 6.13
762 2121 3.059597 CGTCTCACAACATTCCAAGACAC 60.060 47.826 0.00 0.00 34.25 3.67
767 2126 1.806542 CAACATTCCAAGACACGGAGG 59.193 52.381 0.00 0.00 33.01 4.30
814 2173 1.443802 CTCGTTCCTTCCTTGGAAGC 58.556 55.000 20.71 9.02 45.62 3.86
830 2189 3.435186 GCTTGCGTTGCTCCCCTC 61.435 66.667 0.00 0.00 0.00 4.30
831 2190 2.747855 CTTGCGTTGCTCCCCTCC 60.748 66.667 0.00 0.00 0.00 4.30
832 2191 4.344865 TTGCGTTGCTCCCCTCCC 62.345 66.667 0.00 0.00 0.00 4.30
844 2203 2.444895 CCTCCCTTCTCCCTCCGG 60.445 72.222 0.00 0.00 0.00 5.14
866 2225 2.099263 TCCTGTCAGCTCGTAGCATAAC 59.901 50.000 9.09 5.09 45.56 1.89
918 2289 6.040616 AGCGGTCAACCTATATATACCATAGC 59.959 42.308 0.00 0.00 0.00 2.97
970 2341 2.592308 GCTTGCAGTAGGGAGGGG 59.408 66.667 0.00 0.00 0.00 4.79
1011 2382 2.507944 GTGATCATGGAGGCCGCT 59.492 61.111 6.40 0.00 0.00 5.52
1387 2758 1.722011 ACAAAACGGATCAGTAGCGG 58.278 50.000 0.00 0.00 0.00 5.52
1438 2809 5.252547 TGCATGTATTTACTCTTGGCTTGA 58.747 37.500 0.00 0.00 0.00 3.02
1590 2965 2.509336 CGAGCCGGTCATCACCAC 60.509 66.667 1.90 0.00 44.02 4.16
1606 2981 0.695347 CCACTGGCTCCCTCTTTCTT 59.305 55.000 0.00 0.00 0.00 2.52
1618 2993 4.461781 TCCCTCTTTCTTCTTGGTACGTAG 59.538 45.833 0.00 0.00 0.00 3.51
1620 2995 5.416952 CCCTCTTTCTTCTTGGTACGTAGTA 59.583 44.000 0.00 0.00 45.11 1.82
1643 3036 2.151881 TAAACCTTCGTGCGCACTTA 57.848 45.000 35.27 23.03 0.00 2.24
1652 3045 2.255172 TGCGCACTTACAAACCGGG 61.255 57.895 5.66 0.00 0.00 5.73
1693 3086 9.084164 GCCACACGTACTAATAATTATCTATGG 57.916 37.037 0.00 0.00 0.00 2.74
1694 3087 9.582431 CCACACGTACTAATAATTATCTATGGG 57.418 37.037 0.00 0.00 0.00 4.00
1833 3226 3.733960 CGTCGACGAGCTGGTGGA 61.734 66.667 33.35 7.95 43.02 4.02
1993 3386 3.760035 GAGGGCTGCGTCGAGGAA 61.760 66.667 9.75 0.00 0.00 3.36
2197 3611 1.079543 CTGCGTGGAGACCCTCAAG 60.080 63.158 0.00 0.00 31.08 3.02
2272 3686 4.626081 GTGTGCACGAGGCTGGGT 62.626 66.667 13.13 0.00 45.15 4.51
2584 3998 3.000041 CGATGATGACGACAAAAAGGGA 59.000 45.455 0.00 0.00 0.00 4.20
2587 4001 3.399330 TGATGACGACAAAAAGGGAGAC 58.601 45.455 0.00 0.00 0.00 3.36
2653 4067 2.417933 CGATGAGCCACCTGAAGAAAAG 59.582 50.000 0.00 0.00 0.00 2.27
2694 4108 0.982673 CAGGTTTAGAACGAGCGTCG 59.017 55.000 0.00 5.97 46.93 5.12
2737 4151 0.384669 CTGGACTTATCGGACCGGAC 59.615 60.000 15.25 0.00 0.00 4.79
2738 4152 1.358046 GGACTTATCGGACCGGACG 59.642 63.158 15.25 13.27 0.00 4.79
2739 4153 1.097547 GGACTTATCGGACCGGACGA 61.098 60.000 23.50 23.50 45.19 4.20
2740 4154 0.307146 GACTTATCGGACCGGACGAG 59.693 60.000 24.79 16.52 44.24 4.18
2741 4155 0.393537 ACTTATCGGACCGGACGAGT 60.394 55.000 24.79 17.02 44.24 4.18
2742 4156 1.134401 ACTTATCGGACCGGACGAGTA 60.134 52.381 24.79 16.33 44.24 2.59
2743 4157 1.942657 CTTATCGGACCGGACGAGTAA 59.057 52.381 24.79 20.37 44.24 2.24
2744 4158 1.299541 TATCGGACCGGACGAGTAAC 58.700 55.000 24.79 0.00 44.24 2.50
2857 4279 1.263484 GCGGACAGAAGATGATGCATG 59.737 52.381 2.46 0.00 0.00 4.06
2891 4314 1.060122 CGGCGTTCAGGTCGAATAAAC 59.940 52.381 0.00 0.00 37.14 2.01
3035 4460 5.477291 TGAAAAGACAGTAGCTGCTAGTAGT 59.523 40.000 16.18 15.46 34.37 2.73
3086 4511 3.788766 CGACGGAAAAGGCGGCTG 61.789 66.667 14.21 1.10 39.34 4.85
3087 4512 2.358247 GACGGAAAAGGCGGCTGA 60.358 61.111 14.21 0.00 0.00 4.26
3088 4513 2.358737 ACGGAAAAGGCGGCTGAG 60.359 61.111 14.21 5.05 0.00 3.35
3089 4514 3.804193 CGGAAAAGGCGGCTGAGC 61.804 66.667 14.21 4.30 0.00 4.26
3090 4515 2.672996 GGAAAAGGCGGCTGAGCA 60.673 61.111 14.21 0.00 39.27 4.26
3093 4534 2.463675 GAAAAGGCGGCTGAGCACAC 62.464 60.000 14.21 0.00 39.27 3.82
3098 4539 3.414700 CGGCTGAGCACACGAACC 61.415 66.667 6.82 0.00 0.00 3.62
3108 4549 2.281761 CACGAACCTTGCAGGGCT 60.282 61.111 16.02 1.44 40.58 5.19
3114 4555 2.439156 CCTTGCAGGGCTGGCTAC 60.439 66.667 0.13 0.00 0.00 3.58
3115 4556 2.439156 CTTGCAGGGCTGGCTACC 60.439 66.667 0.00 0.00 0.00 3.18
3128 4569 4.447180 GGCTGGCTACCCTAAAATAATCCA 60.447 45.833 0.00 0.00 0.00 3.41
3129 4570 5.325239 GCTGGCTACCCTAAAATAATCCAT 58.675 41.667 0.00 0.00 0.00 3.41
3130 4571 5.416013 GCTGGCTACCCTAAAATAATCCATC 59.584 44.000 0.00 0.00 0.00 3.51
3131 4572 5.887754 TGGCTACCCTAAAATAATCCATCC 58.112 41.667 0.00 0.00 0.00 3.51
3132 4573 5.615261 TGGCTACCCTAAAATAATCCATCCT 59.385 40.000 0.00 0.00 0.00 3.24
3134 4575 7.464265 TGGCTACCCTAAAATAATCCATCCTAT 59.536 37.037 0.00 0.00 0.00 2.57
3139 4580 9.629649 ACCCTAAAATAATCCATCCTATAGACA 57.370 33.333 0.00 0.00 0.00 3.41
3184 4636 2.213499 CCTAGTCGATGCCATGTTTCC 58.787 52.381 0.00 0.00 0.00 3.13
3200 4652 1.538047 TTCCATTTCTCTGGTGCAGC 58.462 50.000 9.47 9.47 37.57 5.25
3236 4688 2.107141 GCGGCGCACTAGAGGATT 59.893 61.111 29.21 0.00 0.00 3.01
3243 4695 3.748863 CACTAGAGGATTGTGCGCT 57.251 52.632 9.73 0.00 0.00 5.92
3244 4696 1.565305 CACTAGAGGATTGTGCGCTC 58.435 55.000 9.73 5.51 0.00 5.03
3364 4838 2.507102 CGTTGAGCTCGATGGCGT 60.507 61.111 14.63 0.00 38.98 5.68
3366 4840 0.595053 CGTTGAGCTCGATGGCGTAT 60.595 55.000 14.63 0.00 38.98 3.06
3518 5887 2.874701 ACGCCTCATGCATATCTGAAAC 59.125 45.455 0.00 0.00 41.33 2.78
3543 5924 2.105128 CGGACCGCTGGATCACTC 59.895 66.667 0.00 0.00 0.00 3.51
3544 5925 2.105128 GGACCGCTGGATCACTCG 59.895 66.667 0.00 0.00 0.00 4.18
3545 5926 2.105128 GACCGCTGGATCACTCGG 59.895 66.667 14.54 14.54 46.61 4.63
3547 5928 2.579201 CCGCTGGATCACTCGGTT 59.421 61.111 9.67 0.00 37.33 4.44
3548 5929 1.811266 CCGCTGGATCACTCGGTTG 60.811 63.158 9.67 0.00 37.33 3.77
3549 5930 1.811266 CGCTGGATCACTCGGTTGG 60.811 63.158 0.00 0.00 0.00 3.77
3558 5939 3.643159 TCACTCGGTTGGATATCATCG 57.357 47.619 4.83 0.00 0.00 3.84
3561 5942 2.296471 ACTCGGTTGGATATCATCGTCC 59.704 50.000 4.83 0.00 35.02 4.79
3633 6014 3.270027 TGGAAACAGCGTTATCTCCATG 58.730 45.455 8.36 0.00 35.01 3.66
3662 6043 4.633126 CCGTGGCTGAATAATATCTCATGG 59.367 45.833 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.002982 TCAAAATTGCTGCTATGTCTCGT 58.997 39.130 0.00 0.00 0.00 4.18
53 54 5.105997 GGAGTGAGTTCAAAATTGCTGCTAT 60.106 40.000 0.00 0.00 0.00 2.97
124 125 1.763968 TGGTACTGACAGATCTCCGG 58.236 55.000 10.08 0.00 0.00 5.14
125 126 2.544694 GCATGGTACTGACAGATCTCCG 60.545 54.545 10.08 0.00 0.00 4.63
163 164 1.416813 GACAGATTGCTCAGTCGCGG 61.417 60.000 6.13 0.00 29.65 6.46
181 182 0.625849 GGCCCCTTTCATCCTTGAGA 59.374 55.000 0.00 0.00 32.27 3.27
233 234 1.741770 GGCACAAACTCGATCGCCT 60.742 57.895 11.09 0.00 36.58 5.52
234 235 2.750888 GGGCACAAACTCGATCGCC 61.751 63.158 11.09 2.57 38.85 5.54
301 314 2.843077 CTGCTGCGTAATTGTCAGTTG 58.157 47.619 0.00 0.00 0.00 3.16
351 367 5.591877 GCCAATTTGATCCTCATTCTGTAGT 59.408 40.000 0.00 0.00 0.00 2.73
359 375 5.136105 GTCCTTAGCCAATTTGATCCTCAT 58.864 41.667 0.00 0.00 0.00 2.90
361 377 3.561725 CGTCCTTAGCCAATTTGATCCTC 59.438 47.826 0.00 0.00 0.00 3.71
368 384 4.220602 AGCAATTTCGTCCTTAGCCAATTT 59.779 37.500 0.00 0.00 0.00 1.82
387 403 3.634702 TACCGCGTCGCATCAGCAA 62.635 57.895 18.75 0.00 42.27 3.91
429 447 1.521681 CGGAATTCCTGACCGCTCC 60.522 63.158 22.05 0.00 40.19 4.70
431 449 1.338136 ATCCGGAATTCCTGACCGCT 61.338 55.000 19.57 2.59 44.45 5.52
432 450 0.880718 GATCCGGAATTCCTGACCGC 60.881 60.000 19.57 9.47 44.45 5.68
433 451 0.597637 CGATCCGGAATTCCTGACCG 60.598 60.000 17.07 17.07 45.24 4.79
434 452 0.880718 GCGATCCGGAATTCCTGACC 60.881 60.000 19.57 10.34 32.00 4.02
435 453 0.880718 GGCGATCCGGAATTCCTGAC 60.881 60.000 19.57 12.71 32.00 3.51
436 454 1.445942 GGCGATCCGGAATTCCTGA 59.554 57.895 22.05 20.72 33.75 3.86
456 474 3.443925 CTGCTCGTCTCCGGCTCA 61.444 66.667 0.00 0.00 33.31 4.26
457 475 2.400896 GATCTGCTCGTCTCCGGCTC 62.401 65.000 0.00 0.00 33.31 4.70
460 478 0.387202 ATTGATCTGCTCGTCTCCGG 59.613 55.000 0.00 0.00 33.95 5.14
462 480 1.066303 ACGATTGATCTGCTCGTCTCC 59.934 52.381 10.59 0.00 41.42 3.71
480 498 3.299585 GCCACACGATCGATCACG 58.700 61.111 24.34 16.35 41.26 4.35
497 1814 3.399770 TCGTCGCGGTTTTGCTCG 61.400 61.111 6.13 0.00 0.00 5.03
498 1815 2.170273 GTCGTCGCGGTTTTGCTC 59.830 61.111 6.13 0.00 0.00 4.26
499 1816 3.698463 CGTCGTCGCGGTTTTGCT 61.698 61.111 6.13 0.00 0.00 3.91
500 1817 3.694394 TCGTCGTCGCGGTTTTGC 61.694 61.111 6.13 0.00 36.96 3.68
501 1818 2.166985 GTCGTCGTCGCGGTTTTG 59.833 61.111 6.13 0.00 36.96 2.44
502 1819 3.389211 CGTCGTCGTCGCGGTTTT 61.389 61.111 6.13 0.00 36.96 2.43
503 1820 3.599792 ATCGTCGTCGTCGCGGTTT 62.600 57.895 6.13 3.15 37.27 3.27
504 1821 4.093952 ATCGTCGTCGTCGCGGTT 62.094 61.111 6.13 4.97 37.27 4.44
505 1822 4.806481 CATCGTCGTCGTCGCGGT 62.806 66.667 6.13 8.41 37.27 5.68
510 1827 1.074872 GGTTTCCCATCGTCGTCGTC 61.075 60.000 1.33 0.00 38.33 4.20
511 1828 1.080298 GGTTTCCCATCGTCGTCGT 60.080 57.895 1.33 0.00 38.33 4.34
513 1830 2.450345 GCGGTTTCCCATCGTCGTC 61.450 63.158 0.00 0.00 0.00 4.20
514 1831 2.433664 GCGGTTTCCCATCGTCGT 60.434 61.111 0.00 0.00 0.00 4.34
515 1832 2.433491 TGCGGTTTCCCATCGTCG 60.433 61.111 0.00 0.00 0.00 5.12
516 1833 1.359459 GAGTGCGGTTTCCCATCGTC 61.359 60.000 0.00 0.00 0.00 4.20
518 1835 2.452813 CGAGTGCGGTTTCCCATCG 61.453 63.158 0.00 0.00 0.00 3.84
519 1836 0.462047 ATCGAGTGCGGTTTCCCATC 60.462 55.000 0.00 0.00 38.28 3.51
521 1838 1.079405 GATCGAGTGCGGTTTCCCA 60.079 57.895 0.00 0.00 38.28 4.37
523 1840 1.696832 GCAGATCGAGTGCGGTTTCC 61.697 60.000 6.78 0.00 38.28 3.13
550 1886 1.453745 TGGATGGAAATGGAGGCGC 60.454 57.895 0.00 0.00 0.00 6.53
552 1888 0.756815 GGGTGGATGGAAATGGAGGC 60.757 60.000 0.00 0.00 0.00 4.70
553 1889 0.929244 AGGGTGGATGGAAATGGAGG 59.071 55.000 0.00 0.00 0.00 4.30
589 1925 1.877576 CTCGGCAAAGGAAAAGGGGC 61.878 60.000 0.00 0.00 0.00 5.80
644 1993 1.320344 TGGAGATTGGAGACGACCGG 61.320 60.000 0.00 0.00 0.00 5.28
664 2013 2.973082 GTGGGGCATTTGTCAGGC 59.027 61.111 0.00 0.00 0.00 4.85
710 2069 4.884247 ACTTGCTTATATAGGGACGAAGC 58.116 43.478 0.00 0.00 42.27 3.86
740 2099 3.059597 GTGTCTTGGAATGTTGTGAGACG 60.060 47.826 0.00 0.00 37.04 4.18
762 2121 4.891727 CCGGGCGAATGACCTCCG 62.892 72.222 0.00 0.00 43.41 4.63
844 2203 0.457851 ATGCTACGAGCTGACAGGAC 59.542 55.000 4.26 0.00 42.97 3.85
866 2225 3.325870 TGCGTCACTTATTCTGTTGGAG 58.674 45.455 0.00 0.00 0.00 3.86
970 2341 1.446966 GAAGCAGGTCCAGACGAGC 60.447 63.158 0.00 5.30 39.41 5.03
1294 2665 0.106569 GTCATGATGGCCCACATGGA 60.107 55.000 27.34 17.01 42.53 3.41
1387 2758 3.242673 GCATGCTGAAGATACAGTTGCTC 60.243 47.826 11.37 0.00 41.32 4.26
1390 2761 4.598062 CATGCATGCTGAAGATACAGTTG 58.402 43.478 20.33 0.00 39.73 3.16
1413 2784 5.762825 AGCCAAGAGTAAATACATGCATG 57.237 39.130 25.09 25.09 0.00 4.06
1419 2790 4.570772 GCGATCAAGCCAAGAGTAAATACA 59.429 41.667 0.00 0.00 0.00 2.29
1423 2794 3.002791 CAGCGATCAAGCCAAGAGTAAA 58.997 45.455 0.00 0.00 38.01 2.01
1438 2809 5.182950 TCCATACACAAACAAAATCAGCGAT 59.817 36.000 0.00 0.00 0.00 4.58
1590 2965 2.617532 CCAAGAAGAAAGAGGGAGCCAG 60.618 54.545 0.00 0.00 0.00 4.85
1606 2981 8.807948 AAGGTTTATAGTACTACGTACCAAGA 57.192 34.615 21.82 0.00 39.58 3.02
1618 2993 3.000376 GTGCGCACGAAGGTTTATAGTAC 60.000 47.826 26.77 0.00 0.00 2.73
1619 2994 3.119388 AGTGCGCACGAAGGTTTATAGTA 60.119 43.478 32.94 0.00 36.20 1.82
1620 2995 1.997606 GTGCGCACGAAGGTTTATAGT 59.002 47.619 26.77 0.00 0.00 2.12
1643 3036 2.667199 GTAGCGTGCCCGGTTTGT 60.667 61.111 0.00 0.00 43.33 2.83
1652 3045 1.671054 TGGCAGAAAGGTAGCGTGC 60.671 57.895 3.84 3.84 0.00 5.34
1993 3386 0.824182 CCTCCTCCTCGCCGAAGTAT 60.824 60.000 0.00 0.00 0.00 2.12
2430 3844 3.893763 CGATCAGCGACGCCTCCT 61.894 66.667 17.79 0.00 44.57 3.69
2584 3998 2.022129 CGTTTTCAGCTCGGCGTCT 61.022 57.895 6.85 2.32 0.00 4.18
2587 4001 0.451135 CTTTCGTTTTCAGCTCGGCG 60.451 55.000 0.00 0.00 0.00 6.46
2653 4067 4.112634 GCTCAGAAGGTTTGGTTGTTTTC 58.887 43.478 0.00 0.00 0.00 2.29
2694 4108 0.102481 TCCGGAGCGCTTTCATAGAC 59.898 55.000 13.26 0.00 0.00 2.59
2695 4109 0.385751 CTCCGGAGCGCTTTCATAGA 59.614 55.000 20.67 2.25 0.00 1.98
2696 4110 1.218230 GCTCCGGAGCGCTTTCATAG 61.218 60.000 38.78 7.67 45.29 2.23
2737 4151 5.614923 ATCTGATCATACTCGGTTACTCG 57.385 43.478 0.00 0.00 0.00 4.18
2738 4152 9.182933 GTTAAATCTGATCATACTCGGTTACTC 57.817 37.037 0.00 0.00 0.00 2.59
2739 4153 8.142551 GGTTAAATCTGATCATACTCGGTTACT 58.857 37.037 0.00 0.00 0.00 2.24
2740 4154 8.142551 AGGTTAAATCTGATCATACTCGGTTAC 58.857 37.037 0.00 0.00 0.00 2.50
2741 4155 8.141909 CAGGTTAAATCTGATCATACTCGGTTA 58.858 37.037 0.00 0.00 34.36 2.85
2742 4156 6.986817 CAGGTTAAATCTGATCATACTCGGTT 59.013 38.462 0.00 0.00 34.36 4.44
2743 4157 6.323996 TCAGGTTAAATCTGATCATACTCGGT 59.676 38.462 0.00 0.00 36.46 4.69
2744 4158 6.642950 GTCAGGTTAAATCTGATCATACTCGG 59.357 42.308 11.44 0.00 42.36 4.63
2857 4279 2.517450 CGCCGCGGATCAGAAGTTC 61.517 63.158 33.48 5.54 0.00 3.01
2891 4314 0.792640 GCGATGATCATAAGCCGGTG 59.207 55.000 19.44 0.00 0.00 4.94
2924 4347 2.420022 GCACAGGTACAACATGATGGAC 59.580 50.000 9.79 9.79 33.56 4.02
3016 4441 4.121317 CGTACTACTAGCAGCTACTGTCT 58.879 47.826 0.00 0.00 33.43 3.41
3021 4446 3.496507 GGGTACGTACTACTAGCAGCTAC 59.503 52.174 24.07 3.72 0.00 3.58
3085 4510 1.153269 TGCAAGGTTCGTGTGCTCA 60.153 52.632 0.00 0.00 39.09 4.26
3086 4511 1.571460 CTGCAAGGTTCGTGTGCTC 59.429 57.895 0.00 0.00 39.09 4.26
3087 4512 3.736483 CTGCAAGGTTCGTGTGCT 58.264 55.556 0.00 0.00 39.09 4.40
3098 4539 2.439156 GGTAGCCAGCCCTGCAAG 60.439 66.667 0.00 0.00 0.00 4.01
3108 4549 5.615261 AGGATGGATTATTTTAGGGTAGCCA 59.385 40.000 14.62 0.00 0.00 4.75
3120 4561 6.156949 ACCGCATGTCTATAGGATGGATTATT 59.843 38.462 12.13 0.00 0.00 1.40
3121 4562 5.663106 ACCGCATGTCTATAGGATGGATTAT 59.337 40.000 12.13 0.00 0.00 1.28
3122 4563 5.023452 ACCGCATGTCTATAGGATGGATTA 58.977 41.667 12.13 0.00 0.00 1.75
3128 4569 3.501349 AGTGACCGCATGTCTATAGGAT 58.499 45.455 0.00 0.00 44.75 3.24
3129 4570 2.885266 GAGTGACCGCATGTCTATAGGA 59.115 50.000 0.00 0.00 44.75 2.94
3130 4571 2.887783 AGAGTGACCGCATGTCTATAGG 59.112 50.000 0.00 0.00 44.75 2.57
3131 4572 3.057876 GGAGAGTGACCGCATGTCTATAG 60.058 52.174 5.13 0.00 44.75 1.31
3132 4573 2.885266 GGAGAGTGACCGCATGTCTATA 59.115 50.000 5.13 0.00 44.75 1.31
3134 4575 1.103803 GGAGAGTGACCGCATGTCTA 58.896 55.000 5.13 0.00 44.75 2.59
3136 4577 1.517257 CGGAGAGTGACCGCATGTC 60.517 63.158 0.00 0.00 43.74 3.06
3137 4578 2.573869 CGGAGAGTGACCGCATGT 59.426 61.111 0.00 0.00 43.74 3.21
3184 4636 0.809385 CAGGCTGCACCAGAGAAATG 59.191 55.000 0.00 0.00 43.14 2.32
3200 4652 0.179181 CGCTGCTGTAATGCAACAGG 60.179 55.000 17.95 5.75 45.75 4.00
3348 4822 1.132588 GATACGCCATCGAGCTCAAC 58.867 55.000 15.40 0.00 39.41 3.18
3364 4838 1.452953 CCTCGGCAGCAGGTACGATA 61.453 60.000 0.00 0.00 34.60 2.92
3366 4840 3.449227 CCTCGGCAGCAGGTACGA 61.449 66.667 0.00 0.00 0.00 3.43
3369 4843 1.327690 CCTAACCTCGGCAGCAGGTA 61.328 60.000 4.86 0.00 44.03 3.08
3456 5823 1.074926 TCCTCTCCCATCTCCCAGC 60.075 63.158 0.00 0.00 0.00 4.85
3501 5870 6.140786 CCATTTCGTTTCAGATATGCATGAG 58.859 40.000 10.16 0.00 31.25 2.90
3537 5918 3.574396 ACGATGATATCCAACCGAGTGAT 59.426 43.478 0.00 0.00 0.00 3.06
3538 5919 2.956333 ACGATGATATCCAACCGAGTGA 59.044 45.455 0.00 0.00 0.00 3.41
3539 5920 3.309388 GACGATGATATCCAACCGAGTG 58.691 50.000 0.00 0.00 0.00 3.51
3540 5921 2.296471 GGACGATGATATCCAACCGAGT 59.704 50.000 0.00 0.00 34.87 4.18
3541 5922 2.558795 AGGACGATGATATCCAACCGAG 59.441 50.000 0.00 0.00 37.47 4.63
3542 5923 2.557056 GAGGACGATGATATCCAACCGA 59.443 50.000 0.00 0.00 37.47 4.69
3543 5924 2.668556 CGAGGACGATGATATCCAACCG 60.669 54.545 0.00 1.38 42.66 4.44
3544 5925 2.557056 TCGAGGACGATGATATCCAACC 59.443 50.000 0.00 0.00 43.81 3.77
3545 5926 3.917329 TCGAGGACGATGATATCCAAC 57.083 47.619 0.00 0.00 43.81 3.77
3558 5939 1.299014 CATCGCTCAGCTCGAGGAC 60.299 63.158 15.58 0.00 42.55 3.85
3561 5942 2.657944 GCCATCGCTCAGCTCGAG 60.658 66.667 8.45 8.45 45.37 4.04


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

AutoCloner maintained by Alex Coulton.