Multiple sequence alignment - TraesCS5D01G199000

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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 TraesCS5D01G199000 chr5D 100.000 3770 0 0 1 3770 301993711 301997480 0.000000e+00 6962.0
1 TraesCS5D01G199000 chr5B 94.447 2125 68 27 888 2989 344943278 344945375 0.000000e+00 3225.0
2 TraesCS5D01G199000 chr5B 82.239 670 85 19 3111 3752 344945496 344946159 7.120000e-152 547.0
3 TraesCS5D01G199000 chr5B 86.245 458 48 9 431 886 344942717 344943161 2.040000e-132 483.0
4 TraesCS5D01G199000 chr5B 91.718 326 18 7 117 434 344942271 344942595 9.610000e-121 444.0
5 TraesCS5D01G199000 chr5A 92.937 2067 72 34 851 2889 395853430 395851410 0.000000e+00 2940.0
6 TraesCS5D01G199000 chr5A 86.551 632 71 11 2 622 395854150 395853522 0.000000e+00 684.0
7 TraesCS5D01G199000 chr5A 79.681 753 116 15 3045 3768 395851122 395850378 3.360000e-140 508.0
8 TraesCS5D01G199000 chr5A 92.254 142 5 3 2888 3027 395851247 395851110 2.970000e-46 196.0
9 TraesCS5D01G199000 chr3B 79.412 340 57 8 1647 1981 787655026 787654695 1.050000e-55 228.0
10 TraesCS5D01G199000 chr3D 79.331 329 56 12 1647 1969 589153985 589154307 1.760000e-53 220.0
11 TraesCS5D01G199000 chr3A 78.963 328 59 10 1647 1969 719195022 719194700 8.200000e-52 215.0
12 TraesCS5D01G199000 chr7B 100.000 28 0 0 3168 3195 228919307 228919334 7.000000e-03 52.8


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 TraesCS5D01G199000 chr5D 301993711 301997480 3769 False 6962.00 6962 100.00000 1 3770 1 chr5D.!!$F1 3769
1 TraesCS5D01G199000 chr5B 344942271 344946159 3888 False 1174.75 3225 88.66225 117 3752 4 chr5B.!!$F1 3635
2 TraesCS5D01G199000 chr5A 395850378 395854150 3772 True 1082.00 2940 87.85575 2 3768 4 chr5A.!!$R1 3766

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
842 980 0.107017 ATGTGTGTGGGCTCATAGGC 60.107 55.0 0.0 0.0 40.51 3.93 F
1093 1351 0.580104 CCGAACGGCATTACGGATTC 59.420 55.0 0.0 0.0 46.94 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2674 0.235144 GCGACTGATGATGATGCTGC 59.765 55.0 0.0 0.0 0.0 5.25 R
3014 3483 0.178944 TGAGGGGACGAAAGGAGTGA 60.179 55.0 0.0 0.0 0.0 3.41 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
25 26 5.045872 GCTCCTAAATCCAAATGCAACATC 58.954 41.667 0.00 0.00 0.00 3.06
38 39 2.095314 TGCAACATCATGTTAAGCCACG 60.095 45.455 1.72 0.00 38.77 4.94
39 40 2.095263 GCAACATCATGTTAAGCCACGT 60.095 45.455 1.72 0.00 38.77 4.49
41 42 1.999735 ACATCATGTTAAGCCACGTCG 59.000 47.619 0.00 0.00 0.00 5.12
44 45 2.485903 TCATGTTAAGCCACGTCGTTT 58.514 42.857 0.00 0.00 0.00 3.60
45 46 2.477375 TCATGTTAAGCCACGTCGTTTC 59.523 45.455 0.00 0.00 0.00 2.78
50 52 2.468532 AAGCCACGTCGTTTCAAAAG 57.531 45.000 0.00 0.00 0.00 2.27
106 108 2.149973 AGATCTTGGCAATTGGACCC 57.850 50.000 7.72 0.33 0.00 4.46
109 111 3.205056 AGATCTTGGCAATTGGACCCATA 59.795 43.478 7.72 0.00 0.00 2.74
110 112 3.464720 TCTTGGCAATTGGACCCATAA 57.535 42.857 7.72 0.00 0.00 1.90
115 117 2.168313 GGCAATTGGACCCATAAACAGG 59.832 50.000 7.72 0.00 0.00 4.00
178 180 9.264719 GGTGAAAAGATGTTTCTTCATGAAAAT 57.735 29.630 9.88 0.00 45.10 1.82
216 218 5.657470 TGTCTCTTCGTTGAAAGACATTG 57.343 39.130 14.67 0.00 42.26 2.82
217 219 4.511454 TGTCTCTTCGTTGAAAGACATTGG 59.489 41.667 14.67 0.00 42.26 3.16
218 220 4.511826 GTCTCTTCGTTGAAAGACATTGGT 59.488 41.667 12.65 0.00 38.39 3.67
219 221 4.511454 TCTCTTCGTTGAAAGACATTGGTG 59.489 41.667 0.00 0.00 32.03 4.17
220 222 4.447290 TCTTCGTTGAAAGACATTGGTGA 58.553 39.130 0.00 0.00 30.38 4.02
221 223 4.878971 TCTTCGTTGAAAGACATTGGTGAA 59.121 37.500 0.00 0.00 30.38 3.18
223 225 4.915704 TCGTTGAAAGACATTGGTGAAAC 58.084 39.130 0.00 0.00 0.00 2.78
224 226 3.723764 CGTTGAAAGACATTGGTGAAACG 59.276 43.478 0.00 0.00 38.12 3.60
227 236 5.107109 TGAAAGACATTGGTGAAACGATG 57.893 39.130 0.00 0.00 38.12 3.84
229 238 5.067153 TGAAAGACATTGGTGAAACGATGTT 59.933 36.000 2.76 0.00 42.02 2.71
508 646 7.976734 TCAACCCTGCCGTTTAAAAATATATTG 59.023 33.333 0.00 0.00 0.00 1.90
575 713 4.037446 TGCTACAAAAGTGTGGGCTTTAAG 59.963 41.667 0.00 0.00 38.82 1.85
585 723 6.745116 AGTGTGGGCTTTAAGAATAACAAAC 58.255 36.000 0.00 0.00 0.00 2.93
623 761 7.232118 AGCATAGCTCAAATGGTTAGTTTTT 57.768 32.000 0.00 0.00 30.62 1.94
656 794 2.338500 CAGCTCACCGGAGTTTAAGTC 58.662 52.381 9.46 0.00 43.37 3.01
660 798 3.429135 GCTCACCGGAGTTTAAGTCCTAG 60.429 52.174 9.46 9.96 43.37 3.02
734 872 2.467962 TCGTTCAGCGAGAGTCGAT 58.532 52.632 0.00 0.00 45.68 3.59
735 873 0.803117 TCGTTCAGCGAGAGTCGATT 59.197 50.000 0.00 0.00 45.68 3.34
736 874 2.004733 TCGTTCAGCGAGAGTCGATTA 58.995 47.619 0.00 0.00 45.68 1.75
737 875 2.102633 CGTTCAGCGAGAGTCGATTAC 58.897 52.381 0.00 0.00 43.74 1.89
738 876 2.102633 GTTCAGCGAGAGTCGATTACG 58.897 52.381 0.00 0.00 43.74 3.18
739 877 1.648504 TCAGCGAGAGTCGATTACGA 58.351 50.000 10.19 0.00 43.74 3.43
750 888 3.597377 TCGATTACGAGACGTATGTGG 57.403 47.619 4.92 0.48 41.97 4.17
751 889 2.938451 TCGATTACGAGACGTATGTGGT 59.062 45.455 4.92 0.00 41.97 4.16
752 890 3.033873 CGATTACGAGACGTATGTGGTG 58.966 50.000 4.92 0.00 41.97 4.17
753 891 3.242511 CGATTACGAGACGTATGTGGTGA 60.243 47.826 4.92 0.00 41.97 4.02
754 892 3.476295 TTACGAGACGTATGTGGTGAC 57.524 47.619 4.92 0.00 41.97 3.67
755 893 1.531423 ACGAGACGTATGTGGTGACT 58.469 50.000 0.00 0.00 38.73 3.41
756 894 1.884579 ACGAGACGTATGTGGTGACTT 59.115 47.619 0.00 0.00 38.73 3.01
764 902 3.807622 CGTATGTGGTGACTTGTGACTTT 59.192 43.478 0.00 0.00 0.00 2.66
785 923 9.683069 GACTTTGTCAATTTCAAGATATTGTGT 57.317 29.630 11.28 6.06 33.43 3.72
788 926 9.814899 TTTGTCAATTTCAAGATATTGTGTTGT 57.185 25.926 11.28 0.00 33.43 3.32
790 928 8.849168 TGTCAATTTCAAGATATTGTGTTGTCT 58.151 29.630 11.28 0.00 33.43 3.41
795 933 6.275494 TCAAGATATTGTGTTGTCTCGGTA 57.725 37.500 0.00 0.00 33.11 4.02
799 937 8.450964 CAAGATATTGTGTTGTCTCGGTATTTT 58.549 33.333 0.00 0.00 0.00 1.82
814 952 8.577296 TCTCGGTATTTTGAAGATACTCATAGG 58.423 37.037 5.94 0.00 32.02 2.57
816 954 7.289317 TCGGTATTTTGAAGATACTCATAGGGT 59.711 37.037 5.94 0.00 32.02 4.34
825 963 9.480861 TGAAGATACTCATAGGGTAAGGATATG 57.519 37.037 0.00 0.00 0.00 1.78
826 964 9.482175 GAAGATACTCATAGGGTAAGGATATGT 57.518 37.037 0.00 0.00 0.00 2.29
834 972 2.572290 GGTAAGGATATGTGTGTGGGC 58.428 52.381 0.00 0.00 0.00 5.36
841 979 3.557898 GGATATGTGTGTGGGCTCATAGG 60.558 52.174 0.00 0.00 31.25 2.57
842 980 0.107017 ATGTGTGTGGGCTCATAGGC 60.107 55.000 0.00 0.00 40.51 3.93
849 987 1.134491 GTGGGCTCATAGGCGTAAGTT 60.134 52.381 0.00 0.00 42.43 2.66
857 995 6.073927 GGCTCATAGGCGTAAGTTTATGTAAC 60.074 42.308 0.00 0.00 37.20 2.50
864 1002 7.732996 AGGCGTAAGTTTATGTAACCATCTAT 58.267 34.615 0.00 0.00 37.46 1.98
1093 1351 0.580104 CCGAACGGCATTACGGATTC 59.420 55.000 0.00 0.00 46.94 2.52
1095 1353 1.661617 CGAACGGCATTACGGATTCAA 59.338 47.619 0.00 0.00 38.39 2.69
1096 1354 2.285602 CGAACGGCATTACGGATTCAAG 60.286 50.000 0.00 0.00 38.39 3.02
1136 1401 1.002366 CCGTTGACTGTAGATGCTGC 58.998 55.000 0.00 0.00 0.00 5.25
1173 1445 2.970324 GTTTGTCGGGCACGCAGA 60.970 61.111 1.67 0.00 40.69 4.26
2134 2427 1.375523 CCAGGCTAACCACCACGAC 60.376 63.158 0.00 0.00 39.06 4.34
2381 2674 1.135915 ACGTGAAGCCAGAGATAGCAG 59.864 52.381 0.00 0.00 0.00 4.24
2382 2675 1.580815 GTGAAGCCAGAGATAGCAGC 58.419 55.000 0.00 0.00 0.00 5.25
2383 2676 1.134580 GTGAAGCCAGAGATAGCAGCA 60.135 52.381 0.00 0.00 0.00 4.41
2536 2829 1.812922 CATGGCAGCAGAGTCGTCC 60.813 63.158 0.00 0.00 0.00 4.79
2613 2911 1.117150 ATCCATGACCATGCAAAGGC 58.883 50.000 8.36 0.00 37.49 4.35
2674 2972 2.033424 GGCACAGTTTCTGTTCTTCACC 59.967 50.000 0.00 0.00 42.59 4.02
2911 3376 5.916661 TCTATGAAAGGAGTAGCTCGTTT 57.083 39.130 14.17 14.17 46.57 3.60
2912 3377 6.282199 TCTATGAAAGGAGTAGCTCGTTTT 57.718 37.500 15.05 7.35 44.82 2.43
3008 3477 6.815089 TGAACTTTTTCACAAAGGCACATAT 58.185 32.000 0.00 0.00 36.79 1.78
3014 3483 6.403866 TTTCACAAAGGCACATATCAAGTT 57.596 33.333 0.00 0.00 0.00 2.66
3015 3484 5.627499 TCACAAAGGCACATATCAAGTTC 57.373 39.130 0.00 0.00 0.00 3.01
3016 3485 5.069318 TCACAAAGGCACATATCAAGTTCA 58.931 37.500 0.00 0.00 0.00 3.18
3017 3486 5.048782 TCACAAAGGCACATATCAAGTTCAC 60.049 40.000 0.00 0.00 0.00 3.18
3018 3487 5.048504 CACAAAGGCACATATCAAGTTCACT 60.049 40.000 0.00 0.00 0.00 3.41
3019 3488 5.182001 ACAAAGGCACATATCAAGTTCACTC 59.818 40.000 0.00 0.00 0.00 3.51
3020 3489 3.878778 AGGCACATATCAAGTTCACTCC 58.121 45.455 0.00 0.00 0.00 3.85
3021 3490 3.521126 AGGCACATATCAAGTTCACTCCT 59.479 43.478 0.00 0.00 0.00 3.69
3022 3491 4.018960 AGGCACATATCAAGTTCACTCCTT 60.019 41.667 0.00 0.00 0.00 3.36
3023 3492 4.702131 GGCACATATCAAGTTCACTCCTTT 59.298 41.667 0.00 0.00 0.00 3.11
3024 3493 5.163713 GGCACATATCAAGTTCACTCCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
3025 3494 5.446473 GCACATATCAAGTTCACTCCTTTCG 60.446 44.000 0.00 0.00 0.00 3.46
3026 3495 5.639506 CACATATCAAGTTCACTCCTTTCGT 59.360 40.000 0.00 0.00 0.00 3.85
3027 3496 5.869888 ACATATCAAGTTCACTCCTTTCGTC 59.130 40.000 0.00 0.00 0.00 4.20
3028 3497 3.107642 TCAAGTTCACTCCTTTCGTCC 57.892 47.619 0.00 0.00 0.00 4.79
3029 3498 2.143925 CAAGTTCACTCCTTTCGTCCC 58.856 52.381 0.00 0.00 0.00 4.46
3030 3499 0.685660 AGTTCACTCCTTTCGTCCCC 59.314 55.000 0.00 0.00 0.00 4.81
3031 3500 0.685660 GTTCACTCCTTTCGTCCCCT 59.314 55.000 0.00 0.00 0.00 4.79
3032 3501 0.974383 TTCACTCCTTTCGTCCCCTC 59.026 55.000 0.00 0.00 0.00 4.30
3033 3502 0.178944 TCACTCCTTTCGTCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
3034 3503 0.685097 CACTCCTTTCGTCCCCTCAA 59.315 55.000 0.00 0.00 0.00 3.02
3035 3504 1.071699 CACTCCTTTCGTCCCCTCAAA 59.928 52.381 0.00 0.00 0.00 2.69
3036 3505 1.772453 ACTCCTTTCGTCCCCTCAAAA 59.228 47.619 0.00 0.00 0.00 2.44
3037 3506 2.173996 ACTCCTTTCGTCCCCTCAAAAA 59.826 45.455 0.00 0.00 0.00 1.94
3083 3556 6.609237 TGAGCATGCATGTTTCTATCTAAC 57.391 37.500 26.79 7.27 0.00 2.34
3084 3557 5.234972 TGAGCATGCATGTTTCTATCTAACG 59.765 40.000 26.79 0.00 0.00 3.18
3141 3661 4.649218 AGTTTATTTTCATGCCGGCCTTAT 59.351 37.500 26.77 8.19 0.00 1.73
3143 3663 2.957491 TTTTCATGCCGGCCTTATTG 57.043 45.000 26.77 13.63 0.00 1.90
3144 3664 1.110442 TTTCATGCCGGCCTTATTGG 58.890 50.000 26.77 1.19 39.35 3.16
3150 3670 0.250338 GCCGGCCTTATTGGAGTAGG 60.250 60.000 18.11 0.00 38.35 3.18
3156 3676 2.688446 GCCTTATTGGAGTAGGTTTGCC 59.312 50.000 0.00 0.00 38.35 4.52
3163 3686 0.803117 GAGTAGGTTTGCCGGAAAGC 59.197 55.000 5.05 12.78 41.56 3.51
3175 3698 1.273327 CCGGAAAGCTGCCTGAATTTT 59.727 47.619 0.00 0.00 0.00 1.82
3198 3721 2.552585 TTCGGGTCAGTCGATTCGGC 62.553 60.000 1.60 1.60 36.49 5.54
3234 3757 0.535553 GACGGGGGCACAACAACTAA 60.536 55.000 0.00 0.00 0.00 2.24
3280 3810 2.423446 GTAGCGAGGCCCATGGAG 59.577 66.667 15.22 4.39 0.00 3.86
3281 3811 2.844362 TAGCGAGGCCCATGGAGG 60.844 66.667 15.22 0.00 37.03 4.30
3307 3837 0.398381 AGGCCTTGGCCAAGAACAAA 60.398 50.000 41.10 9.12 40.79 2.83
3308 3838 0.249868 GGCCTTGGCCAAGAACAAAC 60.250 55.000 41.10 23.18 40.79 2.93
3325 3855 3.528370 CTGTAGCCGGCGGTAGCT 61.528 66.667 28.82 20.38 44.37 3.32
3336 3880 2.565841 GGCGGTAGCTGAAATCTTGAT 58.434 47.619 0.00 0.00 44.37 2.57
3387 3933 1.335132 TTAGAGGGATGGACGTGGGC 61.335 60.000 0.00 0.00 0.00 5.36
3391 3937 4.077184 GGATGGACGTGGGCGACA 62.077 66.667 0.00 0.00 42.00 4.35
3408 3954 1.078214 CACCAGCACGATCATGGGT 60.078 57.895 7.82 0.00 38.48 4.51
3411 3957 1.078214 CAGCACGATCATGGGTGGT 60.078 57.895 10.10 10.10 44.90 4.16
3412 3958 0.177836 CAGCACGATCATGGGTGGTA 59.822 55.000 13.90 0.00 42.43 3.25
3453 4000 4.175337 GCTGGTATGGGAGCGCCA 62.175 66.667 9.31 0.00 35.15 5.69
3494 4041 2.740438 GCGGTTTGGCCATTGGTT 59.260 55.556 6.09 0.00 36.97 3.67
3503 4050 2.282816 CCATTGGTTCGTGGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
3532 4079 3.498661 GGAACCAGATGAACAAAGAGGGT 60.499 47.826 0.00 0.00 0.00 4.34
3534 4081 2.711009 ACCAGATGAACAAAGAGGGTGA 59.289 45.455 0.00 0.00 0.00 4.02
3535 4082 3.138283 ACCAGATGAACAAAGAGGGTGAA 59.862 43.478 0.00 0.00 0.00 3.18
3566 4113 2.922740 GGCCATCTATTGGACGGTTA 57.077 50.000 0.00 0.00 45.98 2.85
3576 4123 9.418045 CATCTATTGGACGGTTAAAAACAAATT 57.582 29.630 0.00 0.00 0.00 1.82
3577 4124 9.990360 ATCTATTGGACGGTTAAAAACAAATTT 57.010 25.926 0.00 0.00 0.00 1.82
3582 4129 7.545489 TGGACGGTTAAAAACAAATTTACTGT 58.455 30.769 0.22 0.22 0.00 3.55
3616 4163 0.681564 CAGTCGACTGACCCCTAGCT 60.682 60.000 36.73 0.00 46.74 3.32
3674 4221 3.069016 TGTTAACACGGGCGAGATGATAT 59.931 43.478 3.59 0.00 0.00 1.63
3697 4244 5.543714 TCGTGGCACTCTTTAAGTTTATCA 58.456 37.500 16.72 0.00 35.45 2.15
3754 4301 7.764901 GGCTATAGTAGGTTAGGCATAAACATC 59.235 40.741 9.11 0.99 39.91 3.06
3761 4308 7.716799 AGGTTAGGCATAAACATCATTTTCA 57.283 32.000 9.11 0.00 30.39 2.69
3768 4315 7.284034 AGGCATAAACATCATTTTCAGAGGTAG 59.716 37.037 0.00 0.00 28.84 3.18
3769 4316 7.283127 GGCATAAACATCATTTTCAGAGGTAGA 59.717 37.037 0.00 0.00 28.84 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.023673 TGCATTTGGATTTAGGAGCCG 58.976 47.619 0.00 0.00 0.00 5.52
10 11 5.813672 GCTTAACATGATGTTGCATTTGGAT 59.186 36.000 20.29 0.00 41.30 3.41
14 15 4.931002 GTGGCTTAACATGATGTTGCATTT 59.069 37.500 20.29 0.00 41.30 2.32
25 26 2.222213 TGAAACGACGTGGCTTAACATG 59.778 45.455 0.00 0.00 0.00 3.21
38 39 8.836959 AATTCTACAACTTCTTTTGAAACGAC 57.163 30.769 0.00 0.00 38.07 4.34
115 117 6.420008 GCATGTCTTTTCAATGAAGGATATGC 59.580 38.462 27.24 27.24 39.86 3.14
166 168 9.695526 CTTTTCACCAATGTATTTTCATGAAGA 57.304 29.630 8.41 4.49 0.00 2.87
178 180 6.368791 CGAAGAGACATCTTTTCACCAATGTA 59.631 38.462 11.47 0.00 45.98 2.29
214 216 5.766150 ATGAAGAAACATCGTTTCACCAA 57.234 34.783 18.81 5.06 32.90 3.67
216 218 8.568732 TTTTAATGAAGAAACATCGTTTCACC 57.431 30.769 18.81 11.44 32.90 4.02
217 219 9.445786 TCTTTTAATGAAGAAACATCGTTTCAC 57.554 29.630 18.81 13.26 32.95 3.18
218 220 9.445786 GTCTTTTAATGAAGAAACATCGTTTCA 57.554 29.630 18.81 2.91 37.40 2.69
219 221 9.445786 TGTCTTTTAATGAAGAAACATCGTTTC 57.554 29.630 10.85 10.85 37.40 2.78
220 222 9.965824 ATGTCTTTTAATGAAGAAACATCGTTT 57.034 25.926 0.00 0.00 37.40 3.60
221 223 9.965824 AATGTCTTTTAATGAAGAAACATCGTT 57.034 25.926 0.00 0.00 37.40 3.85
223 225 8.368126 GCAATGTCTTTTAATGAAGAAACATCG 58.632 33.333 0.00 0.00 37.40 3.84
224 226 9.415544 AGCAATGTCTTTTAATGAAGAAACATC 57.584 29.630 0.00 0.00 37.40 3.06
227 236 8.801715 TCAGCAATGTCTTTTAATGAAGAAAC 57.198 30.769 0.00 0.00 37.40 2.78
229 238 9.814899 TTTTCAGCAATGTCTTTTAATGAAGAA 57.185 25.926 0.00 0.00 37.40 2.52
263 272 2.735134 AGGAACGTGTCTTTATGCGAAC 59.265 45.455 0.00 0.00 0.00 3.95
531 669 9.490379 GTAGCAGGTATTGTTATATAGCAAGTT 57.510 33.333 15.88 4.82 32.31 2.66
575 713 6.370593 TCATCTCGCAACTTGTTTGTTATTC 58.629 36.000 0.00 0.00 37.54 1.75
585 723 2.033065 GCTATGCTCATCTCGCAACTTG 60.033 50.000 0.00 0.00 41.26 3.16
631 769 0.320697 AACTCCGGTGAGCTGGTTAC 59.679 55.000 11.17 0.00 42.74 2.50
632 770 1.053424 AAACTCCGGTGAGCTGGTTA 58.947 50.000 11.17 0.00 42.74 2.85
640 778 3.760684 GTCTAGGACTTAAACTCCGGTGA 59.239 47.826 11.17 0.00 32.45 4.02
656 794 8.899427 ATGTGAACATCAATATCAAGTCTAGG 57.101 34.615 0.00 0.00 28.78 3.02
666 804 9.818270 AATCCAGGATAATGTGAACATCAATAT 57.182 29.630 1.02 0.00 35.10 1.28
667 805 9.645128 AAATCCAGGATAATGTGAACATCAATA 57.355 29.630 1.02 0.00 35.10 1.90
683 821 9.844257 CTAGAAAGTCTGAAATAAATCCAGGAT 57.156 33.333 0.00 0.00 0.00 3.24
726 864 4.025896 CACATACGTCTCGTAATCGACTCT 60.026 45.833 6.12 0.00 45.39 3.24
730 868 2.938451 ACCACATACGTCTCGTAATCGA 59.062 45.455 6.12 0.00 45.39 3.59
731 869 3.033873 CACCACATACGTCTCGTAATCG 58.966 50.000 6.12 1.79 45.39 3.34
734 872 3.076621 AGTCACCACATACGTCTCGTAA 58.923 45.455 6.12 0.00 45.39 3.18
735 873 2.703416 AGTCACCACATACGTCTCGTA 58.297 47.619 0.00 4.56 46.28 3.43
736 874 1.531423 AGTCACCACATACGTCTCGT 58.469 50.000 0.00 0.00 44.35 4.18
737 875 2.251040 CAAGTCACCACATACGTCTCG 58.749 52.381 0.00 0.00 0.00 4.04
738 876 2.987149 CACAAGTCACCACATACGTCTC 59.013 50.000 0.00 0.00 0.00 3.36
739 877 2.626266 TCACAAGTCACCACATACGTCT 59.374 45.455 0.00 0.00 0.00 4.18
741 879 2.364324 AGTCACAAGTCACCACATACGT 59.636 45.455 0.00 0.00 0.00 3.57
742 880 3.026630 AGTCACAAGTCACCACATACG 57.973 47.619 0.00 0.00 0.00 3.06
743 881 4.574828 ACAAAGTCACAAGTCACCACATAC 59.425 41.667 0.00 0.00 0.00 2.39
744 882 4.776349 ACAAAGTCACAAGTCACCACATA 58.224 39.130 0.00 0.00 0.00 2.29
746 884 3.006940 GACAAAGTCACAAGTCACCACA 58.993 45.455 0.00 0.00 32.09 4.17
747 885 3.006940 TGACAAAGTCACAAGTCACCAC 58.993 45.455 0.00 0.00 37.67 4.16
748 886 3.342377 TGACAAAGTCACAAGTCACCA 57.658 42.857 0.00 0.00 37.67 4.17
749 887 4.900635 ATTGACAAAGTCACAAGTCACC 57.099 40.909 0.00 0.00 42.60 4.02
750 888 6.321717 TGAAATTGACAAAGTCACAAGTCAC 58.678 36.000 0.00 0.00 42.60 3.67
751 889 6.507958 TGAAATTGACAAAGTCACAAGTCA 57.492 33.333 0.00 0.00 42.60 3.41
752 890 7.250569 TCTTGAAATTGACAAAGTCACAAGTC 58.749 34.615 19.03 8.91 42.60 3.01
753 891 7.156876 TCTTGAAATTGACAAAGTCACAAGT 57.843 32.000 19.03 0.00 42.60 3.16
754 892 9.903682 ATATCTTGAAATTGACAAAGTCACAAG 57.096 29.630 16.04 16.04 42.60 3.16
756 894 9.681692 CAATATCTTGAAATTGACAAAGTCACA 57.318 29.630 0.00 0.00 37.10 3.58
764 902 8.849168 AGACAACACAATATCTTGAAATTGACA 58.151 29.630 0.00 0.00 36.73 3.58
785 923 7.608153 TGAGTATCTTCAAAATACCGAGACAA 58.392 34.615 0.00 0.00 34.92 3.18
788 926 8.577296 CCTATGAGTATCTTCAAAATACCGAGA 58.423 37.037 0.00 0.00 34.92 4.04
790 928 7.289317 ACCCTATGAGTATCTTCAAAATACCGA 59.711 37.037 0.00 0.00 34.92 4.69
795 933 9.225682 TCCTTACCCTATGAGTATCTTCAAAAT 57.774 33.333 0.00 0.00 34.92 1.82
799 937 9.480861 CATATCCTTACCCTATGAGTATCTTCA 57.519 37.037 0.00 0.00 34.92 3.02
814 952 2.172717 AGCCCACACACATATCCTTACC 59.827 50.000 0.00 0.00 0.00 2.85
816 954 3.111484 TGAGCCCACACACATATCCTTA 58.889 45.455 0.00 0.00 0.00 2.69
825 963 1.815421 CGCCTATGAGCCCACACAC 60.815 63.158 0.00 0.00 0.00 3.82
826 964 0.973496 TACGCCTATGAGCCCACACA 60.973 55.000 0.00 0.00 0.00 3.72
834 972 6.982141 TGGTTACATAAACTTACGCCTATGAG 59.018 38.462 0.00 0.00 38.23 2.90
841 979 7.592533 TCGATAGATGGTTACATAAACTTACGC 59.407 37.037 0.00 0.00 42.67 4.42
976 1232 2.490991 GTTAGGGTGTCGCTCAGTTTT 58.509 47.619 0.00 0.00 0.00 2.43
985 1243 1.445582 GAGTGCCGTTAGGGTGTCG 60.446 63.158 0.00 0.00 38.44 4.35
1093 1351 4.034510 GCCATTTCGATCCAGAAGTACTTG 59.965 45.833 14.14 0.00 0.00 3.16
1095 1353 3.432326 GGCCATTTCGATCCAGAAGTACT 60.432 47.826 0.00 0.00 0.00 2.73
1096 1354 2.872858 GGCCATTTCGATCCAGAAGTAC 59.127 50.000 0.00 0.00 0.00 2.73
1152 1424 2.660552 CGTGCCCGACAAACTCGT 60.661 61.111 0.00 0.00 41.18 4.18
1173 1445 4.664677 GTCGTGTGCCTCCTGCGT 62.665 66.667 0.00 0.00 45.60 5.24
1183 1455 0.790207 CGAGTGGAATTGGTCGTGTG 59.210 55.000 0.00 0.00 0.00 3.82
1184 1456 0.320421 CCGAGTGGAATTGGTCGTGT 60.320 55.000 0.00 0.00 37.49 4.49
1251 1528 5.010213 AGTTGGACACAGAAGAGAAGACTAC 59.990 44.000 0.00 0.00 0.00 2.73
1252 1529 5.141182 AGTTGGACACAGAAGAGAAGACTA 58.859 41.667 0.00 0.00 0.00 2.59
1253 1530 3.964031 AGTTGGACACAGAAGAGAAGACT 59.036 43.478 0.00 0.00 0.00 3.24
1254 1531 4.329462 AGTTGGACACAGAAGAGAAGAC 57.671 45.455 0.00 0.00 0.00 3.01
1552 1842 3.723348 GCGGAGGTGTTTGCGGTC 61.723 66.667 0.00 0.00 32.14 4.79
2134 2427 2.677199 CCGACCAGATAATGATCGTGG 58.323 52.381 6.89 6.89 37.15 4.94
2176 2469 3.259425 CTGGTGCTTCTGCGGTTGC 62.259 63.158 0.00 0.00 43.34 4.17
2177 2470 2.949106 CTGGTGCTTCTGCGGTTG 59.051 61.111 0.00 0.00 43.34 3.77
2178 2471 2.980233 GCTGGTGCTTCTGCGGTT 60.980 61.111 0.00 0.00 43.34 4.44
2381 2674 0.235144 GCGACTGATGATGATGCTGC 59.765 55.000 0.00 0.00 0.00 5.25
2382 2675 0.866427 GGCGACTGATGATGATGCTG 59.134 55.000 0.00 0.00 0.00 4.41
2383 2676 0.599466 CGGCGACTGATGATGATGCT 60.599 55.000 0.00 0.00 0.00 3.79
2564 2857 5.627182 ATCTACATGCATCAGAAGGAAGT 57.373 39.130 10.73 0.00 0.00 3.01
2674 2972 5.799827 TTTCTTAACCCTGTTGAAATGGG 57.200 39.130 2.68 2.68 46.07 4.00
2811 3111 2.799126 TTCCTCGCATAACCAATGGT 57.201 45.000 0.00 0.00 37.65 3.55
2901 3366 5.662211 TTTTGTAGTCCAAAACGAGCTAC 57.338 39.130 0.00 0.00 45.68 3.58
2911 3376 7.160049 TGACACGGTATATTTTTGTAGTCCAA 58.840 34.615 0.00 0.00 0.00 3.53
2912 3377 6.699366 TGACACGGTATATTTTTGTAGTCCA 58.301 36.000 0.00 0.00 0.00 4.02
3000 3469 3.878778 AGGAGTGAACTTGATATGTGCC 58.121 45.455 0.00 0.00 0.00 5.01
3008 3477 2.224209 GGGACGAAAGGAGTGAACTTGA 60.224 50.000 0.00 0.00 0.00 3.02
3014 3483 0.178944 TGAGGGGACGAAAGGAGTGA 60.179 55.000 0.00 0.00 0.00 3.41
3015 3484 0.685097 TTGAGGGGACGAAAGGAGTG 59.315 55.000 0.00 0.00 0.00 3.51
3016 3485 1.430992 TTTGAGGGGACGAAAGGAGT 58.569 50.000 0.00 0.00 0.00 3.85
3017 3486 2.561478 TTTTGAGGGGACGAAAGGAG 57.439 50.000 0.00 0.00 0.00 3.69
3058 3527 7.519488 CGTTAGATAGAAACATGCATGCTCATT 60.519 37.037 26.53 15.71 0.00 2.57
3083 3556 3.739300 ACAAGTATTCGAAAGTGTGTCCG 59.261 43.478 0.00 0.00 0.00 4.79
3084 3557 6.774354 TTACAAGTATTCGAAAGTGTGTCC 57.226 37.500 0.00 0.00 0.00 4.02
3141 3661 0.766131 TTCCGGCAAACCTACTCCAA 59.234 50.000 0.00 0.00 0.00 3.53
3143 3663 1.450025 CTTTCCGGCAAACCTACTCC 58.550 55.000 0.00 0.00 0.00 3.85
3144 3664 0.803117 GCTTTCCGGCAAACCTACTC 59.197 55.000 0.00 0.00 0.00 2.59
3150 3670 2.049156 GGCAGCTTTCCGGCAAAC 60.049 61.111 0.00 0.00 36.27 2.93
3156 3676 2.030007 TCAAAATTCAGGCAGCTTTCCG 60.030 45.455 0.00 0.00 0.00 4.30
3163 3686 3.056607 ACCCGAATTCAAAATTCAGGCAG 60.057 43.478 12.48 6.41 30.61 4.85
3175 3698 2.734175 CGAATCGACTGACCCGAATTCA 60.734 50.000 6.22 0.00 39.62 2.57
3198 3721 2.029288 TCGCTTGCTTGCTTCTCCG 61.029 57.895 0.00 0.00 0.00 4.63
3222 3745 1.081442 GGCGGCTTAGTTGTTGTGC 60.081 57.895 0.00 0.00 0.00 4.57
3223 3746 1.803334 TAGGCGGCTTAGTTGTTGTG 58.197 50.000 19.76 0.00 0.00 3.33
3224 3747 2.423577 CTTAGGCGGCTTAGTTGTTGT 58.576 47.619 19.76 0.00 0.00 3.32
3225 3748 1.737793 CCTTAGGCGGCTTAGTTGTTG 59.262 52.381 19.76 0.00 0.00 3.33
3226 3749 1.949079 GCCTTAGGCGGCTTAGTTGTT 60.949 52.381 19.76 0.00 46.63 2.83
3227 3750 0.392595 GCCTTAGGCGGCTTAGTTGT 60.393 55.000 19.76 0.00 46.63 3.32
3294 3824 1.953686 GCTACAGTTTGTTCTTGGCCA 59.046 47.619 0.00 0.00 0.00 5.36
3307 3837 3.834799 GCTACCGCCGGCTACAGT 61.835 66.667 26.68 18.16 0.00 3.55
3308 3838 3.528370 AGCTACCGCCGGCTACAG 61.528 66.667 26.68 18.33 37.00 2.74
3336 3880 2.938798 ACCCCCGGCCTTGAATCA 60.939 61.111 0.00 0.00 0.00 2.57
3387 3933 1.423721 CCATGATCGTGCTGGTGTCG 61.424 60.000 9.58 0.00 0.00 4.35
3391 3937 1.078214 CACCCATGATCGTGCTGGT 60.078 57.895 9.58 9.48 0.00 4.00
3400 3946 1.511613 CCCTCACTACCACCCATGAT 58.488 55.000 0.00 0.00 0.00 2.45
3408 3954 1.987855 CGCCTTCCCCTCACTACCA 60.988 63.158 0.00 0.00 0.00 3.25
3411 3957 2.365105 CCCGCCTTCCCCTCACTA 60.365 66.667 0.00 0.00 0.00 2.74
3483 4030 2.282816 CCCACGAACCAATGGCCA 60.283 61.111 8.56 8.56 34.37 5.36
3489 4036 1.076632 AAACTGCCCCACGAACCAA 60.077 52.632 0.00 0.00 0.00 3.67
3494 4041 4.278513 CCCCAAACTGCCCCACGA 62.279 66.667 0.00 0.00 0.00 4.35
3503 4050 2.176798 TGTTCATCTGGTTCCCCAAACT 59.823 45.455 0.00 0.00 41.27 2.66
3515 4062 4.217118 CCTTTCACCCTCTTTGTTCATCTG 59.783 45.833 0.00 0.00 0.00 2.90
3532 4079 2.746279 TGGCCTTCTTCAACCTTTCA 57.254 45.000 3.32 0.00 0.00 2.69
3534 4081 3.532641 AGATGGCCTTCTTCAACCTTT 57.467 42.857 15.26 0.00 0.00 3.11
3535 4082 4.870021 ATAGATGGCCTTCTTCAACCTT 57.130 40.909 24.84 2.51 0.00 3.50
3559 4106 9.292846 AGAACAGTAAATTTGTTTTTAACCGTC 57.707 29.630 0.00 0.00 38.78 4.79
3577 4124 9.537192 TCGACTGAAAAGAAAATTAGAACAGTA 57.463 29.630 0.00 0.00 36.45 2.74
3649 4196 2.172851 TCTCGCCCGTGTTAACAAAT 57.827 45.000 10.51 0.00 0.00 2.32
3674 4221 5.543714 TGATAAACTTAAAGAGTGCCACGA 58.456 37.500 0.00 0.00 39.00 4.35
3697 4244 9.881529 GTTTTGTACAATCAAATTCATTTGCAT 57.118 25.926 9.56 0.93 45.06 3.96
3725 4272 7.808279 TTATGCCTAACCTACTATAGCCATT 57.192 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.