Multiple sequence alignment - TraesCS1D01G061400

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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 TraesCS1D01G061400 chr1D 100.000 3380 0 0 418 3797 41596199 41599578 0.000000e+00 6242
1 TraesCS1D01G061400 chr1D 100.000 66 0 0 1 66 41595782 41595847 5.150000e-24 122
2 TraesCS1D01G061400 chr1B 94.897 2175 90 7 966 3119 61667135 61669309 0.000000e+00 3382
3 TraesCS1D01G061400 chr1B 90.250 400 33 4 3121 3518 61669345 61669740 5.620000e-143 518
4 TraesCS1D01G061400 chr1B 90.254 236 17 5 3567 3797 61669831 61670065 1.710000e-78 303
5 TraesCS1D01G061400 chr1B 85.930 199 19 4 635 824 61666845 61667043 1.790000e-48 204
6 TraesCS1D01G061400 chr1B 91.667 120 5 3 427 541 61640740 61640859 1.090000e-35 161
7 TraesCS1D01G061400 chr1A 95.817 2032 64 6 995 3005 41712103 41714134 0.000000e+00 3262
8 TraesCS1D01G061400 chr1A 93.625 502 26 2 419 915 41711600 41712100 0.000000e+00 745


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 TraesCS1D01G061400 chr1D 41595782 41599578 3796 False 3182.00 6242 100.00000 1 3797 2 chr1D.!!$F1 3796
1 TraesCS1D01G061400 chr1B 61666845 61670065 3220 False 1101.75 3382 90.33275 635 3797 4 chr1B.!!$F2 3162
2 TraesCS1D01G061400 chr1A 41711600 41714134 2534 False 2003.50 3262 94.72100 419 3005 2 chr1A.!!$F1 2586

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
63 64 0.105658 AAGTAGGAGGGCGCAGGATA 60.106 55.0 10.83 0.00 0.00 2.59 F
545 551 0.465705 CACATGGGCCTCATCTACGT 59.534 55.0 4.53 0.00 32.92 3.57 F
2268 2352 0.031585 TTCTTACTGCGCTGTGTCGT 59.968 50.0 27.70 4.92 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1063 0.538118 TCGCTAACGTAATTGGGCCT 59.462 50.0 4.53 0.0 41.18 5.19 R
2289 2373 2.238245 GTTGATGAAGCAGCTCAACG 57.762 50.0 8.93 0.0 39.34 4.10 R
3215 3337 0.319405 GCAGCAGATGGGCAAACTTT 59.681 50.0 0.00 0.0 35.83 2.66 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
17 18 3.691342 TGAGGGTTGGCGACGGAG 61.691 66.667 0.00 0.00 0.00 4.63
21 22 4.373116 GGTTGGCGACGGAGCAGA 62.373 66.667 6.70 0.00 39.27 4.26
22 23 2.811317 GTTGGCGACGGAGCAGAG 60.811 66.667 6.70 0.00 39.27 3.35
23 24 4.069232 TTGGCGACGGAGCAGAGG 62.069 66.667 6.70 0.00 39.27 3.69
51 52 4.124351 CGTCGCCGGCAAGTAGGA 62.124 66.667 28.98 11.71 0.00 2.94
52 53 2.202756 GTCGCCGGCAAGTAGGAG 60.203 66.667 28.98 7.38 0.00 3.69
53 54 3.458163 TCGCCGGCAAGTAGGAGG 61.458 66.667 28.98 6.54 0.00 4.30
54 55 4.530857 CGCCGGCAAGTAGGAGGG 62.531 72.222 28.98 0.98 0.00 4.30
55 56 4.858680 GCCGGCAAGTAGGAGGGC 62.859 72.222 24.80 0.00 0.00 5.19
58 59 4.096003 GGCAAGTAGGAGGGCGCA 62.096 66.667 10.83 0.00 0.00 6.09
59 60 2.512515 GCAAGTAGGAGGGCGCAG 60.513 66.667 10.83 0.00 0.00 5.18
60 61 2.187946 CAAGTAGGAGGGCGCAGG 59.812 66.667 10.83 0.00 0.00 4.85
61 62 2.038975 AAGTAGGAGGGCGCAGGA 59.961 61.111 10.83 0.00 0.00 3.86
62 63 1.383248 AAGTAGGAGGGCGCAGGAT 60.383 57.895 10.83 0.00 0.00 3.24
63 64 0.105658 AAGTAGGAGGGCGCAGGATA 60.106 55.000 10.83 0.00 0.00 2.59
64 65 0.828343 AGTAGGAGGGCGCAGGATAC 60.828 60.000 10.83 5.32 0.00 2.24
65 66 1.901948 TAGGAGGGCGCAGGATACG 60.902 63.158 10.83 0.00 46.39 3.06
497 503 5.044558 AGAGAAACTGTCGTTGAAGAACTC 58.955 41.667 0.00 0.00 32.65 3.01
509 515 3.857909 GAACTCGTCGTTCTGGGC 58.142 61.111 11.33 0.00 46.74 5.36
510 516 1.289380 GAACTCGTCGTTCTGGGCT 59.711 57.895 11.33 0.00 46.74 5.19
514 520 4.680237 CGTCGTTCTGGGCTGCCA 62.680 66.667 22.05 5.83 0.00 4.92
545 551 0.465705 CACATGGGCCTCATCTACGT 59.534 55.000 4.53 0.00 32.92 3.57
589 595 2.158449 CCAGCATTGTTCAGTCTCGTTC 59.842 50.000 0.00 0.00 0.00 3.95
592 598 2.221055 GCATTGTTCAGTCTCGTTCGTT 59.779 45.455 0.00 0.00 0.00 3.85
616 622 3.181491 CCCTTTTTCGAAGCAAGTCAACA 60.181 43.478 14.68 0.00 0.00 3.33
684 690 7.385752 ACGAAGATACCGTTCATTCAAGTTTTA 59.614 33.333 0.00 0.00 36.83 1.52
685 691 8.388103 CGAAGATACCGTTCATTCAAGTTTTAT 58.612 33.333 0.00 0.00 0.00 1.40
725 731 5.550290 TGCCTCAAATTCATTTTCCCTTTC 58.450 37.500 0.00 0.00 0.00 2.62
745 754 9.846248 CCCTTTCAATTACTCTTCTTTTGTATG 57.154 33.333 0.00 0.00 0.00 2.39
859 919 4.470334 TTTGGGCAGCCTTTGATATTTC 57.530 40.909 12.43 0.00 0.00 2.17
905 965 7.404671 TTCTTTTTGGGTATATCCTTTGCTC 57.595 36.000 3.09 0.00 36.25 4.26
906 966 6.731467 TCTTTTTGGGTATATCCTTTGCTCT 58.269 36.000 3.09 0.00 36.25 4.09
907 967 6.828785 TCTTTTTGGGTATATCCTTTGCTCTC 59.171 38.462 3.09 0.00 36.25 3.20
934 994 8.893563 TTTTTGAGACATTGGGTATATCCTTT 57.106 30.769 3.09 0.00 36.25 3.11
935 995 7.880160 TTTGAGACATTGGGTATATCCTTTG 57.120 36.000 3.09 3.59 36.25 2.77
936 996 5.376625 TGAGACATTGGGTATATCCTTTGC 58.623 41.667 3.09 0.00 36.25 3.68
937 997 5.132648 TGAGACATTGGGTATATCCTTTGCT 59.867 40.000 3.09 3.24 36.25 3.91
938 998 6.328934 TGAGACATTGGGTATATCCTTTGCTA 59.671 38.462 3.09 0.00 36.25 3.49
939 999 7.147391 TGAGACATTGGGTATATCCTTTGCTAA 60.147 37.037 3.09 0.00 36.25 3.09
940 1000 7.582719 AGACATTGGGTATATCCTTTGCTAAA 58.417 34.615 3.09 0.00 36.25 1.85
941 1001 7.721399 AGACATTGGGTATATCCTTTGCTAAAG 59.279 37.037 3.09 0.00 38.24 1.85
942 1002 6.265422 ACATTGGGTATATCCTTTGCTAAAGC 59.735 38.462 3.09 0.00 37.18 3.51
943 1003 5.646692 TGGGTATATCCTTTGCTAAAGCT 57.353 39.130 3.09 0.00 37.18 3.74
944 1004 6.013554 TGGGTATATCCTTTGCTAAAGCTT 57.986 37.500 3.09 0.00 37.18 3.74
945 1005 6.431722 TGGGTATATCCTTTGCTAAAGCTTT 58.568 36.000 17.30 17.30 37.18 3.51
946 1006 6.895204 TGGGTATATCCTTTGCTAAAGCTTTT 59.105 34.615 18.47 1.58 37.18 2.27
947 1007 7.398904 TGGGTATATCCTTTGCTAAAGCTTTTT 59.601 33.333 18.47 0.00 37.18 1.94
974 1034 6.699575 TTTAGGATCATCCTTTGCTAAAGC 57.300 37.500 12.79 0.00 46.91 3.51
977 1037 5.619220 AGGATCATCCTTTGCTAAAGCTAG 58.381 41.667 0.00 1.18 46.91 3.42
978 1038 5.367937 AGGATCATCCTTTGCTAAAGCTAGA 59.632 40.000 0.00 0.00 46.91 2.43
982 1042 4.060038 TCCTTTGCTAAAGCTAGATCCG 57.940 45.455 3.26 0.00 42.66 4.18
1133 1202 4.564116 CCTTATCGTCGCCGCGGT 62.564 66.667 28.70 8.14 0.00 5.68
1230 1299 0.327576 CATACCCTTCCCTCCCCACT 60.328 60.000 0.00 0.00 0.00 4.00
1239 1308 1.303317 CCTCCCCACTCCCAAAACG 60.303 63.158 0.00 0.00 0.00 3.60
2256 2340 7.526142 TGTCTCATACAACACTCTTCTTACT 57.474 36.000 0.00 0.00 34.29 2.24
2268 2352 0.031585 TTCTTACTGCGCTGTGTCGT 59.968 50.000 27.70 4.92 0.00 4.34
2282 2366 3.246112 TCGTGGTGGGGAGGTTGG 61.246 66.667 0.00 0.00 0.00 3.77
2322 2406 3.754965 TCATCAACTCAAGGACAAAGGG 58.245 45.455 0.00 0.00 0.00 3.95
2496 2580 2.423892 TCGGGAAGACAGAATCGAAGAG 59.576 50.000 0.00 0.00 43.63 2.85
2628 2712 7.096023 GCTATCGATCTGTTTACTTACATGGTG 60.096 40.741 0.00 0.00 0.00 4.17
2655 2739 2.303163 GCTGCATGCCAAATGAATCA 57.697 45.000 16.68 0.00 35.15 2.57
2874 2958 6.543465 CCAGGAATATGTTCTTGTGCATCTTA 59.457 38.462 12.28 0.00 39.16 2.10
2880 2964 1.742761 TCTTGTGCATCTTAGGCAGC 58.257 50.000 0.00 0.00 42.85 5.25
3016 3104 6.931840 ACAAACTTGTACAGGATTCTTCTCTC 59.068 38.462 12.54 0.00 40.16 3.20
3052 3140 6.810500 ACTCAATAGGGAGCTATCCTATCTT 58.189 40.000 21.59 10.46 44.38 2.40
3055 3143 7.019388 TCAATAGGGAGCTATCCTATCTTGTT 58.981 38.462 21.59 9.38 44.38 2.83
3072 3160 5.667466 TCTTGTTTCCGTAGAACTGTTCTT 58.333 37.500 26.33 11.97 41.14 2.52
3081 3169 5.634020 CCGTAGAACTGTTCTTACTGGAAAG 59.366 44.000 26.33 10.06 41.14 2.62
3119 3207 9.017509 TCTTAGATTACACGGACTAAAGAAAGA 57.982 33.333 0.00 0.00 0.00 2.52
3150 3272 5.641209 GCTTTCTCAGCTGAGTTCTCAATAA 59.359 40.000 36.32 21.36 46.27 1.40
3195 3317 9.866655 TGTTTATGCTATTTTCCCAGATAATCT 57.133 29.630 0.00 0.00 0.00 2.40
3201 3323 9.561069 TGCTATTTTCCCAGATAATCTTAAGAC 57.439 33.333 7.48 0.00 0.00 3.01
3202 3324 9.561069 GCTATTTTCCCAGATAATCTTAAGACA 57.439 33.333 7.48 0.00 0.00 3.41
3204 3326 8.753497 ATTTTCCCAGATAATCTTAAGACACC 57.247 34.615 7.48 0.00 0.00 4.16
3225 3347 7.214381 ACACCTAAATTTTCTAAAGTTTGCCC 58.786 34.615 0.00 0.00 31.54 5.36
3234 3356 0.319405 AAAGTTTGCCCATCTGCTGC 59.681 50.000 0.00 0.00 0.00 5.25
3246 3368 3.181462 CCATCTGCTGCAACTATCCACTA 60.181 47.826 3.02 0.00 0.00 2.74
3249 3371 2.611292 CTGCTGCAACTATCCACTAAGC 59.389 50.000 3.02 0.00 0.00 3.09
3251 3373 3.274288 GCTGCAACTATCCACTAAGCTT 58.726 45.455 3.48 3.48 0.00 3.74
3263 3385 4.830046 TCCACTAAGCTTTTTGGTTATGCA 59.170 37.500 20.11 0.00 37.89 3.96
3273 3395 9.203421 AGCTTTTTGGTTATGCAAAGTTTATAC 57.797 29.630 0.00 0.00 0.00 1.47
3332 3454 4.184629 CACCTGCATTTACTACTCTGGTC 58.815 47.826 0.00 0.00 0.00 4.02
3333 3455 3.119101 ACCTGCATTTACTACTCTGGTCG 60.119 47.826 0.00 0.00 0.00 4.79
3337 3459 4.703575 TGCATTTACTACTCTGGTCGTAGT 59.296 41.667 7.82 7.82 46.63 2.73
3406 3528 2.694628 AGAAACTTCAGTTGGCATTGCA 59.305 40.909 11.39 0.00 38.44 4.08
3416 3538 3.057315 AGTTGGCATTGCACTGTTCATAC 60.057 43.478 11.39 6.42 0.00 2.39
3438 3560 2.296752 TGTTGGATCCATGCAGTTTGTG 59.703 45.455 17.06 0.00 0.00 3.33
3463 3585 4.599047 TCCCAGTTTGCATAAAAAGGTG 57.401 40.909 0.00 0.00 0.00 4.00
3468 3590 6.147656 CCCAGTTTGCATAAAAAGGTGATTTC 59.852 38.462 0.00 0.00 0.00 2.17
3469 3591 6.705381 CCAGTTTGCATAAAAAGGTGATTTCA 59.295 34.615 0.00 0.00 0.00 2.69
3473 3595 9.423061 GTTTGCATAAAAAGGTGATTTCATAGT 57.577 29.630 0.00 0.00 0.00 2.12
3490 3612 1.154225 GTTGACGAAGCATTGGCCG 60.154 57.895 0.00 0.00 42.56 6.13
3502 3624 0.981183 ATTGGCCGTTGGTCAGAGTA 59.019 50.000 0.00 0.00 39.05 2.59
3529 3653 9.908747 AGAGTAGATATTACTTGTGTACTCACT 57.091 33.333 10.29 0.00 44.14 3.41
3531 3655 9.908747 AGTAGATATTACTTGTGTACTCACTCT 57.091 33.333 0.00 0.00 44.14 3.24
3532 3656 9.938670 GTAGATATTACTTGTGTACTCACTCTG 57.061 37.037 0.00 0.00 44.14 3.35
3534 3658 8.679100 AGATATTACTTGTGTACTCACTCTGTC 58.321 37.037 0.00 0.00 44.14 3.51
3535 3659 5.449107 TTACTTGTGTACTCACTCTGTCC 57.551 43.478 0.00 0.00 44.14 4.02
3537 3661 3.319405 ACTTGTGTACTCACTCTGTCCAG 59.681 47.826 0.00 0.00 44.14 3.86
3538 3662 3.223674 TGTGTACTCACTCTGTCCAGA 57.776 47.619 0.00 0.00 44.14 3.86
3540 3664 4.152647 TGTGTACTCACTCTGTCCAGAAT 58.847 43.478 0.00 0.00 44.14 2.40
3541 3665 4.588951 TGTGTACTCACTCTGTCCAGAATT 59.411 41.667 0.00 0.00 44.14 2.17
3543 3667 6.094061 GTGTACTCACTCTGTCCAGAATTAC 58.906 44.000 0.00 0.00 40.98 1.89
3546 3670 5.788450 ACTCACTCTGTCCAGAATTACTTG 58.212 41.667 0.00 0.00 36.94 3.16
3547 3671 5.540337 ACTCACTCTGTCCAGAATTACTTGA 59.460 40.000 0.00 0.00 36.94 3.02
3548 3672 5.784177 TCACTCTGTCCAGAATTACTTGAC 58.216 41.667 0.00 0.00 40.36 3.18
3549 3673 4.623167 CACTCTGTCCAGAATTACTTGACG 59.377 45.833 0.00 0.00 42.08 4.35
3551 3675 3.258372 TCTGTCCAGAATTACTTGACGCT 59.742 43.478 0.00 0.00 42.08 5.07
3552 3676 3.997021 CTGTCCAGAATTACTTGACGCTT 59.003 43.478 0.00 0.00 42.08 4.68
3553 3677 5.047590 TCTGTCCAGAATTACTTGACGCTTA 60.048 40.000 0.00 0.00 42.08 3.09
3555 3679 5.992829 TGTCCAGAATTACTTGACGCTTAAA 59.007 36.000 0.00 0.00 42.08 1.52
3556 3680 6.073440 TGTCCAGAATTACTTGACGCTTAAAC 60.073 38.462 0.00 0.00 42.08 2.01
3557 3681 5.992829 TCCAGAATTACTTGACGCTTAAACA 59.007 36.000 0.00 0.00 0.00 2.83
3558 3682 6.147164 TCCAGAATTACTTGACGCTTAAACAG 59.853 38.462 0.00 0.00 0.00 3.16
3560 3684 7.148407 CCAGAATTACTTGACGCTTAAACAGAT 60.148 37.037 0.00 0.00 0.00 2.90
3561 3685 7.689812 CAGAATTACTTGACGCTTAAACAGATG 59.310 37.037 0.00 0.00 0.00 2.90
3562 3686 7.387948 AGAATTACTTGACGCTTAAACAGATGT 59.612 33.333 0.00 0.00 0.00 3.06
3565 3689 8.542497 TTACTTGACGCTTAAACAGATGTATT 57.458 30.769 0.00 0.00 0.00 1.89
3568 3692 8.656849 ACTTGACGCTTAAACAGATGTATTTAG 58.343 33.333 0.00 0.00 0.00 1.85
3570 3694 8.181487 TGACGCTTAAACAGATGTATTTAGAC 57.819 34.615 0.00 0.00 0.00 2.59
3571 3695 8.033038 TGACGCTTAAACAGATGTATTTAGACT 58.967 33.333 0.00 0.00 0.00 3.24
3572 3696 8.773404 ACGCTTAAACAGATGTATTTAGACTT 57.227 30.769 0.00 0.00 0.00 3.01
3573 3697 8.656849 ACGCTTAAACAGATGTATTTAGACTTG 58.343 33.333 0.00 0.00 0.00 3.16
3574 3698 8.656849 CGCTTAAACAGATGTATTTAGACTTGT 58.343 33.333 0.00 0.00 0.00 3.16
3575 3699 9.760660 GCTTAAACAGATGTATTTAGACTTGTG 57.239 33.333 0.00 0.00 0.00 3.33
3645 3813 4.617959 TGAGTCCGAGTTCTGTAAACTTG 58.382 43.478 0.00 0.00 0.00 3.16
3686 3854 0.109597 CGAAGCATGACTTTGCCCAC 60.110 55.000 0.00 0.00 43.83 4.61
3694 3862 1.202758 TGACTTTGCCCACACTGTAGG 60.203 52.381 0.00 0.00 0.00 3.18
3709 3877 4.333649 CACTGTAGGCACAACTATGATTGG 59.666 45.833 0.00 0.00 33.22 3.16
3733 3901 3.373001 CCCATAGAAAGAAATGCAGGGGA 60.373 47.826 0.00 0.00 33.64 4.81
3734 3902 4.280819 CCATAGAAAGAAATGCAGGGGAA 58.719 43.478 0.00 0.00 0.00 3.97
3735 3903 4.098501 CCATAGAAAGAAATGCAGGGGAAC 59.901 45.833 0.00 0.00 0.00 3.62
3736 3904 3.243359 AGAAAGAAATGCAGGGGAACA 57.757 42.857 0.00 0.00 0.00 3.18
3737 3905 3.782992 AGAAAGAAATGCAGGGGAACAT 58.217 40.909 0.00 0.00 0.00 2.71
3741 3909 4.980339 AGAAATGCAGGGGAACATTTTT 57.020 36.364 0.00 0.00 44.36 1.94
3742 3910 6.432403 AAGAAATGCAGGGGAACATTTTTA 57.568 33.333 0.00 0.00 44.36 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.691342 CTCCGTCGCCAACCCTCA 61.691 66.667 0.00 0.00 0.00 3.86
4 5 4.373116 TCTGCTCCGTCGCCAACC 62.373 66.667 0.00 0.00 0.00 3.77
5 6 2.811317 CTCTGCTCCGTCGCCAAC 60.811 66.667 0.00 0.00 0.00 3.77
6 7 4.069232 CCTCTGCTCCGTCGCCAA 62.069 66.667 0.00 0.00 0.00 4.52
35 36 2.202756 CTCCTACTTGCCGGCGAC 60.203 66.667 23.90 0.00 0.00 5.19
36 37 3.458163 CCTCCTACTTGCCGGCGA 61.458 66.667 23.90 20.69 0.00 5.54
37 38 4.530857 CCCTCCTACTTGCCGGCG 62.531 72.222 23.90 11.34 0.00 6.46
38 39 4.858680 GCCCTCCTACTTGCCGGC 62.859 72.222 22.73 22.73 0.00 6.13
39 40 4.530857 CGCCCTCCTACTTGCCGG 62.531 72.222 0.00 0.00 0.00 6.13
41 42 4.096003 TGCGCCCTCCTACTTGCC 62.096 66.667 4.18 0.00 0.00 4.52
42 43 2.512515 CTGCGCCCTCCTACTTGC 60.513 66.667 4.18 0.00 0.00 4.01
43 44 1.690219 ATCCTGCGCCCTCCTACTTG 61.690 60.000 4.18 0.00 0.00 3.16
44 45 0.105658 TATCCTGCGCCCTCCTACTT 60.106 55.000 4.18 0.00 0.00 2.24
45 46 0.828343 GTATCCTGCGCCCTCCTACT 60.828 60.000 4.18 0.00 0.00 2.57
46 47 1.666580 GTATCCTGCGCCCTCCTAC 59.333 63.158 4.18 0.00 0.00 3.18
47 48 1.901948 CGTATCCTGCGCCCTCCTA 60.902 63.158 4.18 0.00 0.00 2.94
48 49 3.227276 CGTATCCTGCGCCCTCCT 61.227 66.667 4.18 0.00 0.00 3.69
417 418 3.490890 GGCTTCGCCTCATGTGAC 58.509 61.111 0.00 0.00 46.69 3.67
433 434 4.415150 ATCTGCGGTGGCCAGTGG 62.415 66.667 5.11 4.20 38.85 4.00
437 438 4.783621 GCTCATCTGCGGTGGCCA 62.784 66.667 0.00 0.00 38.85 5.36
465 466 2.070028 GACAGTTTCTCTTTCCTCGCC 58.930 52.381 0.00 0.00 0.00 5.54
497 503 4.680237 TGGCAGCCCAGAACGACG 62.680 66.667 9.64 0.00 35.79 5.12
514 520 1.378514 CCATGTGTAAAGGCGGCCT 60.379 57.895 17.69 17.69 33.87 5.19
519 525 0.323360 TGAGGCCCATGTGTAAAGGC 60.323 55.000 0.00 0.15 44.99 4.35
545 551 1.523154 GAAATGTCGGTTGGGCTGCA 61.523 55.000 0.50 0.00 0.00 4.41
589 595 0.030101 TGCTTCGAAAAAGGGCAACG 59.970 50.000 6.56 0.00 37.60 4.10
592 598 1.336755 GACTTGCTTCGAAAAAGGGCA 59.663 47.619 19.14 13.23 0.00 5.36
616 622 3.435275 TGAGCAGTATGGAGTGAAGTCT 58.565 45.455 0.00 0.00 35.86 3.24
684 690 2.908916 GCATGCTAAATGTGCCCAAAT 58.091 42.857 11.37 0.00 32.88 2.32
685 691 2.383368 GCATGCTAAATGTGCCCAAA 57.617 45.000 11.37 0.00 32.88 3.28
736 742 3.851403 CCCGTGCGAAATTCATACAAAAG 59.149 43.478 0.00 0.00 0.00 2.27
745 754 0.879090 AAGTTCCCCGTGCGAAATTC 59.121 50.000 0.00 0.00 0.00 2.17
859 919 1.620323 AGGCTGCCCTTTGCTTAAAAG 59.380 47.619 16.57 0.00 44.27 2.27
875 935 6.503041 AGGATATACCCAAAAAGAAAAGGCT 58.497 36.000 0.00 0.00 40.05 4.58
913 973 5.132648 AGCAAAGGATATACCCAATGTCTCA 59.867 40.000 0.00 0.00 40.05 3.27
914 974 5.625150 AGCAAAGGATATACCCAATGTCTC 58.375 41.667 0.00 0.00 40.05 3.36
915 975 5.653255 AGCAAAGGATATACCCAATGTCT 57.347 39.130 0.00 0.00 40.05 3.41
916 976 7.522236 GCTTTAGCAAAGGATATACCCAATGTC 60.522 40.741 9.63 0.00 41.59 3.06
917 977 6.265422 GCTTTAGCAAAGGATATACCCAATGT 59.735 38.462 9.63 0.00 41.59 2.71
918 978 6.491403 AGCTTTAGCAAAGGATATACCCAATG 59.509 38.462 4.33 0.00 45.16 2.82
919 979 6.614657 AGCTTTAGCAAAGGATATACCCAAT 58.385 36.000 4.33 0.00 45.16 3.16
920 980 6.013554 AGCTTTAGCAAAGGATATACCCAA 57.986 37.500 4.33 0.00 45.16 4.12
921 981 5.646692 AGCTTTAGCAAAGGATATACCCA 57.353 39.130 4.33 0.00 45.16 4.51
922 982 6.961360 AAAGCTTTAGCAAAGGATATACCC 57.039 37.500 10.72 0.00 45.16 3.69
948 1008 7.067494 GCTTTAGCAAAGGATGATCCTAAAAGA 59.933 37.037 15.54 0.00 43.28 2.52
949 1009 7.067981 AGCTTTAGCAAAGGATGATCCTAAAAG 59.932 37.037 15.54 17.69 45.17 2.27
950 1010 6.891908 AGCTTTAGCAAAGGATGATCCTAAAA 59.108 34.615 15.54 9.41 45.17 1.52
951 1011 6.426587 AGCTTTAGCAAAGGATGATCCTAAA 58.573 36.000 15.54 10.01 45.17 1.85
952 1012 6.006275 AGCTTTAGCAAAGGATGATCCTAA 57.994 37.500 15.54 1.65 45.17 2.69
953 1013 5.636903 AGCTTTAGCAAAGGATGATCCTA 57.363 39.130 15.54 0.00 45.17 2.94
954 1014 4.516652 AGCTTTAGCAAAGGATGATCCT 57.483 40.909 8.51 8.51 46.89 3.24
955 1015 5.615289 TCTAGCTTTAGCAAAGGATGATCC 58.385 41.667 2.46 2.46 45.16 3.36
956 1016 6.371271 GGATCTAGCTTTAGCAAAGGATGATC 59.629 42.308 4.33 0.00 45.16 2.92
957 1017 6.237154 GGATCTAGCTTTAGCAAAGGATGAT 58.763 40.000 4.33 0.00 45.16 2.45
958 1018 5.615289 GGATCTAGCTTTAGCAAAGGATGA 58.385 41.667 4.33 0.00 45.16 2.92
959 1019 4.450419 CGGATCTAGCTTTAGCAAAGGATG 59.550 45.833 4.33 0.00 45.16 3.51
960 1020 4.636249 CGGATCTAGCTTTAGCAAAGGAT 58.364 43.478 4.33 2.24 45.16 3.24
961 1021 3.741388 GCGGATCTAGCTTTAGCAAAGGA 60.741 47.826 4.33 0.00 45.16 3.36
962 1022 2.545946 GCGGATCTAGCTTTAGCAAAGG 59.454 50.000 4.33 0.00 45.16 3.11
963 1023 3.198068 TGCGGATCTAGCTTTAGCAAAG 58.802 45.455 13.23 1.52 45.16 2.77
964 1024 3.260475 TGCGGATCTAGCTTTAGCAAA 57.740 42.857 13.23 0.00 45.16 3.68
1003 1063 0.538118 TCGCTAACGTAATTGGGCCT 59.462 50.000 4.53 0.00 41.18 5.19
1004 1064 1.371595 TTCGCTAACGTAATTGGGCC 58.628 50.000 0.00 0.00 41.18 5.80
1860 1944 2.621998 CAAGAACTCCATGGCATCATCC 59.378 50.000 6.96 0.00 0.00 3.51
2127 2211 5.873164 GTGAAGTATCGGGTTGTAACTCAAT 59.127 40.000 0.00 0.00 38.38 2.57
2232 2316 7.371159 CAGTAAGAAGAGTGTTGTATGAGACA 58.629 38.462 0.00 0.00 35.78 3.41
2268 2352 3.897122 GCACCAACCTCCCCACCA 61.897 66.667 0.00 0.00 0.00 4.17
2289 2373 2.238245 GTTGATGAAGCAGCTCAACG 57.762 50.000 8.93 0.00 39.34 4.10
2322 2406 2.359900 CTAATCAAGACAGGGGTGCAC 58.640 52.381 8.80 8.80 0.00 4.57
2496 2580 4.923281 ACTTTACAAAATGCTTTGATCGCC 59.077 37.500 5.51 0.00 44.03 5.54
2589 2673 1.130561 TCGATAGCACTGTGTGTCTCG 59.869 52.381 9.86 12.34 35.75 4.04
2592 2676 3.111838 CAGATCGATAGCACTGTGTGTC 58.888 50.000 9.86 4.67 35.75 3.67
2655 2739 7.806180 AGCCTTCAATCAATATAGTGTAGGTT 58.194 34.615 0.00 0.00 35.28 3.50
2874 2958 3.199508 ACAATGAAGTATCTCTGCTGCCT 59.800 43.478 0.00 0.00 0.00 4.75
2980 3068 6.358118 TGTACAAGTTTGTAGCAAGTTGAG 57.642 37.500 7.16 0.00 43.67 3.02
3040 3128 6.328641 TCTACGGAAACAAGATAGGATAGC 57.671 41.667 0.00 0.00 0.00 2.97
3052 3140 5.981315 CAGTAAGAACAGTTCTACGGAAACA 59.019 40.000 16.46 0.00 39.61 2.83
3055 3143 4.828939 TCCAGTAAGAACAGTTCTACGGAA 59.171 41.667 16.46 0.00 39.61 4.30
3081 3169 9.590088 CCGTGTAATCTAAGAAAACAAAACTAC 57.410 33.333 0.00 0.00 0.00 2.73
3106 3194 6.934048 AAGCAGCATATCTTTCTTTAGTCC 57.066 37.500 0.00 0.00 0.00 3.85
3133 3255 7.172190 TCTCAGTTTTTATTGAGAACTCAGCTG 59.828 37.037 7.63 7.63 44.92 4.24
3144 3266 9.695526 CATTGGATTTGTCTCAGTTTTTATTGA 57.304 29.630 0.00 0.00 0.00 2.57
3150 3272 9.480053 CATAAACATTGGATTTGTCTCAGTTTT 57.520 29.630 0.00 0.00 0.00 2.43
3183 3305 8.618240 TTTAGGTGTCTTAAGATTATCTGGGA 57.382 34.615 8.75 0.00 0.00 4.37
3184 3306 9.853177 AATTTAGGTGTCTTAAGATTATCTGGG 57.147 33.333 8.75 0.00 0.00 4.45
3198 3320 8.141909 GGCAAACTTTAGAAAATTTAGGTGTCT 58.858 33.333 0.00 0.00 0.00 3.41
3199 3321 7.384115 GGGCAAACTTTAGAAAATTTAGGTGTC 59.616 37.037 0.00 0.00 0.00 3.67
3200 3322 7.147637 TGGGCAAACTTTAGAAAATTTAGGTGT 60.148 33.333 0.00 0.00 0.00 4.16
3201 3323 7.213678 TGGGCAAACTTTAGAAAATTTAGGTG 58.786 34.615 0.00 0.00 0.00 4.00
3202 3324 7.368198 TGGGCAAACTTTAGAAAATTTAGGT 57.632 32.000 0.00 0.00 0.00 3.08
3203 3325 8.314021 AGATGGGCAAACTTTAGAAAATTTAGG 58.686 33.333 0.00 0.00 0.00 2.69
3204 3326 9.143631 CAGATGGGCAAACTTTAGAAAATTTAG 57.856 33.333 0.00 0.00 0.00 1.85
3215 3337 0.319405 GCAGCAGATGGGCAAACTTT 59.681 50.000 0.00 0.00 35.83 2.66
3225 3347 2.915349 AGTGGATAGTTGCAGCAGATG 58.085 47.619 2.55 0.00 0.00 2.90
3234 3356 6.575162 ACCAAAAAGCTTAGTGGATAGTTG 57.425 37.500 27.04 9.72 35.04 3.16
3246 3368 8.675705 ATAAACTTTGCATAACCAAAAAGCTT 57.324 26.923 0.00 0.00 34.59 3.74
3324 3446 1.819288 CATCACCACTACGACCAGAGT 59.181 52.381 0.00 0.00 0.00 3.24
3325 3447 1.819288 ACATCACCACTACGACCAGAG 59.181 52.381 0.00 0.00 0.00 3.35
3326 3448 1.919240 ACATCACCACTACGACCAGA 58.081 50.000 0.00 0.00 0.00 3.86
3332 3454 9.692749 AATATATAACTGAACATCACCACTACG 57.307 33.333 0.00 0.00 0.00 3.51
3363 3485 4.751767 AATGTTTTGCTGGAAACTTGGA 57.248 36.364 0.00 0.00 39.62 3.53
3365 3487 7.492344 AGTTTCTAATGTTTTGCTGGAAACTTG 59.508 33.333 10.94 0.00 44.62 3.16
3367 3489 7.112452 AGTTTCTAATGTTTTGCTGGAAACT 57.888 32.000 10.94 10.94 43.25 2.66
3406 3528 4.908601 TGGATCCAACAGTATGAACAGT 57.091 40.909 13.46 0.00 39.69 3.55
3416 3538 2.559668 ACAAACTGCATGGATCCAACAG 59.440 45.455 31.81 31.81 38.97 3.16
3438 3560 4.452114 CCTTTTTATGCAAACTGGGAAAGC 59.548 41.667 0.00 0.00 0.00 3.51
3463 3585 5.967674 CCAATGCTTCGTCAACTATGAAATC 59.032 40.000 0.00 0.00 37.30 2.17
3468 3590 2.223340 GGCCAATGCTTCGTCAACTATG 60.223 50.000 0.00 0.00 37.74 2.23
3469 3591 2.017049 GGCCAATGCTTCGTCAACTAT 58.983 47.619 0.00 0.00 37.74 2.12
3473 3595 1.169661 AACGGCCAATGCTTCGTCAA 61.170 50.000 2.24 0.00 34.89 3.18
3519 3643 4.792521 ATTCTGGACAGAGTGAGTACAC 57.207 45.455 1.92 0.00 46.24 2.90
3520 3644 6.010850 AGTAATTCTGGACAGAGTGAGTACA 58.989 40.000 10.72 0.00 38.88 2.90
3521 3645 6.518208 AGTAATTCTGGACAGAGTGAGTAC 57.482 41.667 1.92 2.73 38.88 2.73
3522 3646 6.719829 TCAAGTAATTCTGGACAGAGTGAGTA 59.280 38.462 1.92 0.00 38.88 2.59
3523 3647 5.540337 TCAAGTAATTCTGGACAGAGTGAGT 59.460 40.000 1.92 0.00 38.88 3.41
3524 3648 5.866633 GTCAAGTAATTCTGGACAGAGTGAG 59.133 44.000 1.92 0.00 44.33 3.51
3526 3650 4.623167 CGTCAAGTAATTCTGGACAGAGTG 59.377 45.833 1.92 0.00 44.98 3.51
3527 3651 4.810790 CGTCAAGTAATTCTGGACAGAGT 58.189 43.478 1.92 0.00 44.98 3.24
3528 3652 3.614616 GCGTCAAGTAATTCTGGACAGAG 59.385 47.826 1.92 0.00 44.98 3.35
3529 3653 3.258372 AGCGTCAAGTAATTCTGGACAGA 59.742 43.478 0.00 0.00 44.98 3.41
3530 3654 3.589988 AGCGTCAAGTAATTCTGGACAG 58.410 45.455 10.92 0.00 44.98 3.51
3531 3655 3.678056 AGCGTCAAGTAATTCTGGACA 57.322 42.857 10.92 0.00 44.98 4.02
3532 3656 6.073440 TGTTTAAGCGTCAAGTAATTCTGGAC 60.073 38.462 3.57 3.57 42.18 4.02
3534 3658 6.147164 TCTGTTTAAGCGTCAAGTAATTCTGG 59.853 38.462 0.00 0.00 0.00 3.86
3535 3659 7.117241 TCTGTTTAAGCGTCAAGTAATTCTG 57.883 36.000 0.00 0.00 0.00 3.02
3537 3661 7.519002 ACATCTGTTTAAGCGTCAAGTAATTC 58.481 34.615 0.00 0.00 0.00 2.17
3538 3662 7.435068 ACATCTGTTTAAGCGTCAAGTAATT 57.565 32.000 0.00 0.00 0.00 1.40
3540 3664 8.542497 AATACATCTGTTTAAGCGTCAAGTAA 57.458 30.769 0.00 0.00 0.00 2.24
3541 3665 8.542497 AAATACATCTGTTTAAGCGTCAAGTA 57.458 30.769 0.00 0.00 0.00 2.24
3543 3667 8.869897 TCTAAATACATCTGTTTAAGCGTCAAG 58.130 33.333 0.00 0.00 0.00 3.02
3546 3670 8.408743 AGTCTAAATACATCTGTTTAAGCGTC 57.591 34.615 0.00 0.00 0.00 5.19
3547 3671 8.656849 CAAGTCTAAATACATCTGTTTAAGCGT 58.343 33.333 0.00 0.00 0.00 5.07
3548 3672 8.656849 ACAAGTCTAAATACATCTGTTTAAGCG 58.343 33.333 0.00 0.00 0.00 4.68
3549 3673 9.760660 CACAAGTCTAAATACATCTGTTTAAGC 57.239 33.333 0.00 0.00 0.00 3.09
3553 3677 9.778741 TCTTCACAAGTCTAAATACATCTGTTT 57.221 29.630 0.00 0.00 0.00 2.83
3555 3679 9.429359 CTTCTTCACAAGTCTAAATACATCTGT 57.571 33.333 0.00 0.00 0.00 3.41
3556 3680 9.429359 ACTTCTTCACAAGTCTAAATACATCTG 57.571 33.333 0.00 0.00 30.25 2.90
3568 3692 9.865484 GTACTATTGAAAACTTCTTCACAAGTC 57.135 33.333 4.06 0.00 35.45 3.01
3620 3787 5.855045 AGTTTACAGAACTCGGACTCAAAT 58.145 37.500 0.00 0.00 0.00 2.32
3645 3813 2.066262 TGAAATTCTGTCGGAACTCGC 58.934 47.619 0.00 0.00 36.70 5.03
3686 3854 4.333649 CCAATCATAGTTGTGCCTACAGTG 59.666 45.833 0.00 0.00 38.23 3.66
3694 3862 2.722094 TGGGACCAATCATAGTTGTGC 58.278 47.619 0.00 0.00 0.00 4.57
3709 3877 3.633986 CCCTGCATTTCTTTCTATGGGAC 59.366 47.826 0.00 0.00 34.34 4.46
3750 3918 4.363999 CCAGCACTTAGTAGGATCTTTCG 58.636 47.826 0.00 0.00 0.00 3.46
3761 3929 2.959465 AGAAAAGGCCAGCACTTAGT 57.041 45.000 5.01 0.00 0.00 2.24
3762 3930 6.349300 TCTATAAGAAAAGGCCAGCACTTAG 58.651 40.000 5.01 1.34 0.00 2.18


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

AutoCloner maintained by Alex Coulton.