Multiple sequence alignment - TraesCS3A01G267500

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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 TraesCS3A01G267500 chr3A 100.000 3152 0 0 1 3152 492738467 492735316 0.000000e+00 5821.0
1 TraesCS3A01G267500 chr3A 98.039 51 1 0 1 51 101441849 101441899 4.330000e-14 89.8
2 TraesCS3A01G267500 chr3A 98.039 51 1 0 1 51 333328266 333328316 4.330000e-14 89.8
3 TraesCS3A01G267500 chr3A 98.039 51 1 0 1 51 529744929 529744979 4.330000e-14 89.8
4 TraesCS3A01G267500 chr3D 93.166 3029 138 20 103 3105 371871590 371868605 0.000000e+00 4383.0
5 TraesCS3A01G267500 chr3B 92.577 3085 160 29 52 3105 482786231 482783185 0.000000e+00 4364.0
6 TraesCS3A01G267500 chr1B 78.579 929 173 19 1112 2030 638783744 638782832 9.740000e-165 590.0
7 TraesCS3A01G267500 chr1B 78.335 937 173 22 1109 2030 638821853 638820932 2.110000e-161 579.0
8 TraesCS3A01G267500 chr1D 77.908 937 177 22 1109 2030 463326368 463325447 9.880000e-155 556.0
9 TraesCS3A01G267500 chr1D 98.039 51 1 0 2 52 384739899 384739849 4.330000e-14 89.8
10 TraesCS3A01G267500 chr1A 77.801 937 178 22 1109 2030 555523073 555522152 4.590000e-153 551.0
11 TraesCS3A01G267500 chr1A 77.326 935 174 30 1112 2030 555484955 555484043 4.660000e-143 518.0
12 TraesCS3A01G267500 chr7A 98.039 51 1 0 1 51 123244956 123244906 4.330000e-14 89.8
13 TraesCS3A01G267500 chr5B 96.296 54 1 1 1 54 660212237 660212185 1.560000e-13 87.9
14 TraesCS3A01G267500 chr4D 96.226 53 2 0 1 53 494149274 494149222 1.560000e-13 87.9
15 TraesCS3A01G267500 chr2A 98.000 50 1 0 1 50 102328478 102328527 1.560000e-13 87.9
16 TraesCS3A01G267500 chr7B 93.103 58 4 0 1 58 732473915 732473858 5.600000e-13 86.1


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 TraesCS3A01G267500 chr3A 492735316 492738467 3151 True 5821 5821 100.000 1 3152 1 chr3A.!!$R1 3151
1 TraesCS3A01G267500 chr3D 371868605 371871590 2985 True 4383 4383 93.166 103 3105 1 chr3D.!!$R1 3002
2 TraesCS3A01G267500 chr3B 482783185 482786231 3046 True 4364 4364 92.577 52 3105 1 chr3B.!!$R1 3053
3 TraesCS3A01G267500 chr1B 638782832 638783744 912 True 590 590 78.579 1112 2030 1 chr1B.!!$R1 918
4 TraesCS3A01G267500 chr1B 638820932 638821853 921 True 579 579 78.335 1109 2030 1 chr1B.!!$R2 921
5 TraesCS3A01G267500 chr1D 463325447 463326368 921 True 556 556 77.908 1109 2030 1 chr1D.!!$R2 921
6 TraesCS3A01G267500 chr1A 555522152 555523073 921 True 551 551 77.801 1109 2030 1 chr1A.!!$R2 921
7 TraesCS3A01G267500 chr1A 555484043 555484955 912 True 518 518 77.326 1112 2030 1 chr1A.!!$R1 918


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
207 208 0.107993 CTTCATCCTCCTTGAGCGCA 60.108 55.0 11.47 0.0 0.0 6.09 F
2121 2179 0.179078 TTACAAGTGGCGACGTTGGT 60.179 50.0 4.64 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2188 0.458260 AAACGGTTTCAACTGCACCC 59.542 50.0 0.0 0.0 38.89 4.61 R
3105 3170 2.223805 CCTCTCAACCAACCAAACTTGC 60.224 50.0 0.0 0.0 0.00 4.01 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
34 35 8.818057 ACAAAAGATAGATGTACACTTATTCGC 58.182 33.333 0.00 0.00 0.00 4.70
35 36 7.624706 AAAGATAGATGTACACTTATTCGCG 57.375 36.000 0.00 0.00 0.00 5.87
36 37 5.700846 AGATAGATGTACACTTATTCGCGG 58.299 41.667 6.13 0.00 0.00 6.46
37 38 5.472478 AGATAGATGTACACTTATTCGCGGA 59.528 40.000 6.13 0.00 0.00 5.54
38 39 3.703420 AGATGTACACTTATTCGCGGAC 58.297 45.455 6.13 0.00 0.00 4.79
39 40 1.898938 TGTACACTTATTCGCGGACG 58.101 50.000 6.13 0.00 42.01 4.79
40 41 1.194495 GTACACTTATTCGCGGACGG 58.806 55.000 6.13 0.00 40.63 4.79
41 42 1.093972 TACACTTATTCGCGGACGGA 58.906 50.000 6.13 0.00 40.63 4.69
42 43 0.179145 ACACTTATTCGCGGACGGAG 60.179 55.000 6.13 0.00 40.63 4.63
43 44 0.870307 CACTTATTCGCGGACGGAGG 60.870 60.000 6.13 0.00 40.63 4.30
44 45 1.299926 CTTATTCGCGGACGGAGGG 60.300 63.158 6.13 0.00 40.63 4.30
45 46 1.731433 CTTATTCGCGGACGGAGGGA 61.731 60.000 6.13 0.00 40.63 4.20
46 47 1.731433 TTATTCGCGGACGGAGGGAG 61.731 60.000 6.13 0.00 40.63 4.30
47 48 2.898920 TATTCGCGGACGGAGGGAGT 62.899 60.000 6.13 0.00 40.63 3.85
48 49 2.898920 ATTCGCGGACGGAGGGAGTA 62.899 60.000 6.13 0.00 40.63 2.59
49 50 2.898920 TTCGCGGACGGAGGGAGTAT 62.899 60.000 6.13 0.00 40.63 2.12
50 51 1.598962 CGCGGACGGAGGGAGTATA 60.599 63.158 0.00 0.00 34.97 1.47
90 91 4.635765 CACCGGTGAAAAGTATGATGTGAT 59.364 41.667 31.31 0.00 0.00 3.06
115 116 1.946984 AGGGTTTGGTCAGGTATCGA 58.053 50.000 0.00 0.00 0.00 3.59
186 187 0.896923 GAAATCCAATGGCCAGCACA 59.103 50.000 13.05 0.00 0.00 4.57
206 207 0.813210 CCTTCATCCTCCTTGAGCGC 60.813 60.000 0.00 0.00 0.00 5.92
207 208 0.107993 CTTCATCCTCCTTGAGCGCA 60.108 55.000 11.47 0.00 0.00 6.09
212 213 0.391661 TCCTCCTTGAGCGCAATCAC 60.392 55.000 11.47 0.00 32.68 3.06
224 226 1.209621 GCAATCACCCCCTACACCTA 58.790 55.000 0.00 0.00 0.00 3.08
232 234 2.197465 CCCCCTACACCTAGCTTCTTT 58.803 52.381 0.00 0.00 0.00 2.52
273 275 2.055838 CATCTTTTCCGACGACGACAA 58.944 47.619 9.28 0.00 42.66 3.18
276 278 1.790623 CTTTTCCGACGACGACAACAT 59.209 47.619 9.28 0.00 42.66 2.71
314 317 1.953017 CTCTGGCGAGGTCCTATCG 59.047 63.158 0.00 0.00 43.00 2.92
416 419 7.476540 TTAGGTCTAAGCAATCACTTAGTGA 57.523 36.000 17.87 17.87 46.13 3.41
430 439 9.899226 AATCACTTAGTGAAAAAGATTACTTGC 57.101 29.630 19.42 0.00 45.96 4.01
431 440 8.445275 TCACTTAGTGAAAAAGATTACTTGCA 57.555 30.769 13.16 0.00 39.78 4.08
432 441 8.342634 TCACTTAGTGAAAAAGATTACTTGCAC 58.657 33.333 13.16 0.00 39.78 4.57
433 442 7.591426 CACTTAGTGAAAAAGATTACTTGCACC 59.409 37.037 6.50 0.00 35.79 5.01
434 443 7.284489 ACTTAGTGAAAAAGATTACTTGCACCA 59.716 33.333 0.00 0.00 35.79 4.17
435 444 6.076981 AGTGAAAAAGATTACTTGCACCAG 57.923 37.500 0.00 0.00 35.79 4.00
488 497 2.531326 GTTTGCCCCTTCCCCCTT 59.469 61.111 0.00 0.00 0.00 3.95
519 528 2.358737 CAACCCTCTGCCACGTCC 60.359 66.667 0.00 0.00 0.00 4.79
532 541 2.488355 CGTCCATGTAGGCGACGT 59.512 61.111 11.76 0.00 43.29 4.34
533 542 1.153901 CGTCCATGTAGGCGACGTT 60.154 57.895 11.76 0.00 43.29 3.99
535 544 1.447140 TCCATGTAGGCGACGTTGC 60.447 57.895 19.96 19.96 37.29 4.17
593 602 2.954611 CTCGCTGAGGACGACACA 59.045 61.111 0.00 0.00 35.35 3.72
727 758 8.732746 ATACTACTAGTTTGCATTAACAAGGG 57.267 34.615 0.00 0.00 0.00 3.95
840 871 3.568430 GCTTCCATTATTTTACTCCCCCG 59.432 47.826 0.00 0.00 0.00 5.73
854 885 1.116308 CCCCCGTCACAAAAAGGTTT 58.884 50.000 0.00 0.00 0.00 3.27
868 903 5.959618 AAAAGGTTTGTAAATCTCCTCCG 57.040 39.130 0.00 0.00 0.00 4.63
904 939 2.234300 TCGTAATCTCCCGCAAATCC 57.766 50.000 0.00 0.00 0.00 3.01
958 993 1.229984 CCCCTTTCCCTCCTCACCT 60.230 63.158 0.00 0.00 0.00 4.00
966 1001 1.992277 CCTCCTCACCTCACCCCAG 60.992 68.421 0.00 0.00 0.00 4.45
1317 1366 2.047750 TTGCTCATGGCGTGCGTA 60.048 55.556 0.65 0.00 45.43 4.42
2121 2179 0.179078 TTACAAGTGGCGACGTTGGT 60.179 50.000 4.64 0.00 0.00 3.67
2122 2180 0.876777 TACAAGTGGCGACGTTGGTG 60.877 55.000 4.64 3.27 0.00 4.17
2123 2181 1.885388 CAAGTGGCGACGTTGGTGA 60.885 57.895 4.64 0.00 0.00 4.02
2124 2182 1.594293 AAGTGGCGACGTTGGTGAG 60.594 57.895 4.64 0.00 0.00 3.51
2125 2183 2.989055 AAGTGGCGACGTTGGTGAGG 62.989 60.000 4.64 0.00 0.00 3.86
2126 2184 4.308458 TGGCGACGTTGGTGAGGG 62.308 66.667 4.64 0.00 0.00 4.30
2127 2185 3.998672 GGCGACGTTGGTGAGGGA 61.999 66.667 4.64 0.00 0.00 4.20
2128 2186 2.432628 GCGACGTTGGTGAGGGAG 60.433 66.667 4.64 0.00 0.00 4.30
2129 2187 2.261671 CGACGTTGGTGAGGGAGG 59.738 66.667 0.00 0.00 0.00 4.30
2130 2188 2.663196 GACGTTGGTGAGGGAGGG 59.337 66.667 0.00 0.00 0.00 4.30
2160 2218 5.469084 AGTTGAAACCGTTTGATCTAACCTC 59.531 40.000 13.34 6.75 0.00 3.85
2236 2294 9.702253 ATCTCAAAGGAAGTACATCTAGTCTAA 57.298 33.333 0.00 0.00 0.00 2.10
2256 2314 9.606631 AGTCTAATTGCACCTATTTCTAAGAAG 57.393 33.333 0.00 0.00 0.00 2.85
2379 2441 2.955660 GAGGTTGGTGATTGTGGTTTGA 59.044 45.455 0.00 0.00 0.00 2.69
2394 2456 3.196469 TGGTTTGATGGTTGCTTGTTTGA 59.804 39.130 0.00 0.00 0.00 2.69
2449 2511 5.314923 ACGAAATGGAAGGATGTTTGATG 57.685 39.130 0.00 0.00 0.00 3.07
2455 2517 4.933134 TGGAAGGATGTTTGATGATGGAA 58.067 39.130 0.00 0.00 0.00 3.53
2513 2578 6.293004 TCTTCACAAAATGTTGGTTCCTTT 57.707 33.333 0.00 0.00 39.22 3.11
2514 2579 7.411486 TCTTCACAAAATGTTGGTTCCTTTA 57.589 32.000 0.00 0.00 39.22 1.85
2532 2597 4.282195 CCTTTAGAGCCTAATCGGTGATCT 59.718 45.833 0.00 0.00 34.25 2.75
2533 2598 5.221541 CCTTTAGAGCCTAATCGGTGATCTT 60.222 44.000 0.00 0.00 34.25 2.40
2537 2602 5.141182 AGAGCCTAATCGGTGATCTTCTAA 58.859 41.667 0.00 0.00 34.25 2.10
2559 2624 8.625651 TCTAACAGAAGAGAGAAATATTCCTCG 58.374 37.037 0.00 0.00 34.34 4.63
2563 2628 4.599047 AGAGAGAAATATTCCTCGGCTG 57.401 45.455 0.00 0.00 34.34 4.85
2578 2643 0.610232 GGCTGGACTGCTCCAAATGT 60.610 55.000 0.00 0.00 46.63 2.71
2597 2662 4.727507 TGTTGCCTTGTTTTGTGTACAT 57.272 36.364 0.00 0.00 0.00 2.29
2615 2680 6.465781 GTGTACATGCGTCAACAATTTATCTG 59.534 38.462 0.00 0.00 0.00 2.90
2666 2731 4.539870 CTTGTGTCATTGTGGAATGTGAC 58.460 43.478 0.00 0.00 40.09 3.67
2795 2860 6.874134 TGTTTTGTAATGTAGCCTCTTCTCTC 59.126 38.462 0.00 0.00 0.00 3.20
2797 2862 3.632604 TGTAATGTAGCCTCTTCTCTCGG 59.367 47.826 0.00 0.00 0.00 4.63
2802 2867 1.216710 GCCTCTTCTCTCGGTGTGG 59.783 63.158 0.00 0.00 0.00 4.17
2818 2883 4.278170 CGGTGTGGTATAAATCATGGCAAT 59.722 41.667 0.00 0.00 0.00 3.56
2828 2893 9.964303 GTATAAATCATGGCAATTGAATACACA 57.036 29.630 10.34 0.00 0.00 3.72
2892 2957 8.411318 ACAATTCAACAAAGCTTGAAGTTTAG 57.589 30.769 0.00 0.00 42.13 1.85
2978 3043 6.451393 TGCATGGTGGTTTTATTCTGTTTAC 58.549 36.000 0.00 0.00 0.00 2.01
3037 3102 5.627367 TGTGCGCACAAAAATAATAGTTCAC 59.373 36.000 39.13 7.92 38.56 3.18
3057 3122 9.388506 AGTTCACTTCCTTAAGTATGAATCATG 57.611 33.333 5.91 0.00 44.28 3.07
3058 3123 8.616076 GTTCACTTCCTTAAGTATGAATCATGG 58.384 37.037 5.91 0.00 44.28 3.66
3079 3144 6.620877 TGGTTGTTTACTCTCAGATATGGT 57.379 37.500 0.00 0.00 0.00 3.55
3084 3149 6.330278 TGTTTACTCTCAGATATGGTGTTCG 58.670 40.000 0.00 0.00 0.00 3.95
3114 3179 8.585471 ATGATATTATAGGGATGCAAGTTTGG 57.415 34.615 0.00 0.00 0.00 3.28
3115 3180 7.526041 TGATATTATAGGGATGCAAGTTTGGT 58.474 34.615 0.00 0.00 0.00 3.67
3116 3181 8.004215 TGATATTATAGGGATGCAAGTTTGGTT 58.996 33.333 0.00 0.00 0.00 3.67
3117 3182 5.913137 TTATAGGGATGCAAGTTTGGTTG 57.087 39.130 0.00 0.00 0.00 3.77
3118 3183 1.341080 AGGGATGCAAGTTTGGTTGG 58.659 50.000 0.00 0.00 0.00 3.77
3119 3184 1.047801 GGGATGCAAGTTTGGTTGGT 58.952 50.000 0.00 0.00 0.00 3.67
3120 3185 1.416030 GGGATGCAAGTTTGGTTGGTT 59.584 47.619 0.00 0.00 0.00 3.67
3121 3186 2.482864 GGATGCAAGTTTGGTTGGTTG 58.517 47.619 0.00 0.00 0.00 3.77
3122 3187 2.102252 GGATGCAAGTTTGGTTGGTTGA 59.898 45.455 0.00 0.00 0.00 3.18
3123 3188 2.957491 TGCAAGTTTGGTTGGTTGAG 57.043 45.000 0.00 0.00 0.00 3.02
3124 3189 2.451490 TGCAAGTTTGGTTGGTTGAGA 58.549 42.857 0.00 0.00 0.00 3.27
3125 3190 2.426738 TGCAAGTTTGGTTGGTTGAGAG 59.573 45.455 0.00 0.00 0.00 3.20
3126 3191 2.223805 GCAAGTTTGGTTGGTTGAGAGG 60.224 50.000 0.00 0.00 0.00 3.69
3127 3192 3.287222 CAAGTTTGGTTGGTTGAGAGGA 58.713 45.455 0.00 0.00 0.00 3.71
3128 3193 3.214696 AGTTTGGTTGGTTGAGAGGAG 57.785 47.619 0.00 0.00 0.00 3.69
3129 3194 2.509964 AGTTTGGTTGGTTGAGAGGAGT 59.490 45.455 0.00 0.00 0.00 3.85
3130 3195 3.714798 AGTTTGGTTGGTTGAGAGGAGTA 59.285 43.478 0.00 0.00 0.00 2.59
3131 3196 4.165372 AGTTTGGTTGGTTGAGAGGAGTAA 59.835 41.667 0.00 0.00 0.00 2.24
3132 3197 4.993705 TTGGTTGGTTGAGAGGAGTAAT 57.006 40.909 0.00 0.00 0.00 1.89
3133 3198 4.553330 TGGTTGGTTGAGAGGAGTAATC 57.447 45.455 0.00 0.00 0.00 1.75
3134 3199 3.907474 TGGTTGGTTGAGAGGAGTAATCA 59.093 43.478 0.00 0.00 0.00 2.57
3135 3200 4.020218 TGGTTGGTTGAGAGGAGTAATCAG 60.020 45.833 0.00 0.00 0.00 2.90
3136 3201 3.895232 TGGTTGAGAGGAGTAATCAGC 57.105 47.619 0.00 0.00 0.00 4.26
3137 3202 3.173151 TGGTTGAGAGGAGTAATCAGCA 58.827 45.455 0.00 0.00 0.00 4.41
3138 3203 3.776969 TGGTTGAGAGGAGTAATCAGCAT 59.223 43.478 0.00 0.00 0.00 3.79
3139 3204 4.125703 GGTTGAGAGGAGTAATCAGCATG 58.874 47.826 0.00 0.00 37.54 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.818057 GCGAATAAGTGTACATCTATCTTTTGT 58.182 33.333 0.00 0.00 0.00 2.83
9 10 7.998767 CGCGAATAAGTGTACATCTATCTTTTG 59.001 37.037 0.00 0.00 0.00 2.44
10 11 7.169308 CCGCGAATAAGTGTACATCTATCTTTT 59.831 37.037 8.23 0.00 0.00 2.27
11 12 6.641314 CCGCGAATAAGTGTACATCTATCTTT 59.359 38.462 8.23 0.00 0.00 2.52
12 13 6.016527 TCCGCGAATAAGTGTACATCTATCTT 60.017 38.462 8.23 0.00 0.00 2.40
13 14 5.472478 TCCGCGAATAAGTGTACATCTATCT 59.528 40.000 8.23 0.00 0.00 1.98
14 15 5.568296 GTCCGCGAATAAGTGTACATCTATC 59.432 44.000 8.23 0.00 0.00 2.08
15 16 5.458891 GTCCGCGAATAAGTGTACATCTAT 58.541 41.667 8.23 0.00 0.00 1.98
16 17 4.553351 CGTCCGCGAATAAGTGTACATCTA 60.553 45.833 8.23 0.00 41.33 1.98
17 18 3.703420 GTCCGCGAATAAGTGTACATCT 58.297 45.455 8.23 0.00 0.00 2.90
18 19 2.466571 CGTCCGCGAATAAGTGTACATC 59.533 50.000 8.23 0.00 41.33 3.06
19 20 2.456989 CGTCCGCGAATAAGTGTACAT 58.543 47.619 8.23 0.00 41.33 2.29
20 21 1.467883 CCGTCCGCGAATAAGTGTACA 60.468 52.381 8.23 0.00 41.33 2.90
21 22 1.194495 CCGTCCGCGAATAAGTGTAC 58.806 55.000 8.23 0.00 41.33 2.90
22 23 1.064505 CTCCGTCCGCGAATAAGTGTA 59.935 52.381 8.23 0.00 41.33 2.90
23 24 0.179145 CTCCGTCCGCGAATAAGTGT 60.179 55.000 8.23 0.00 41.33 3.55
24 25 0.870307 CCTCCGTCCGCGAATAAGTG 60.870 60.000 8.23 0.00 41.33 3.16
25 26 1.436336 CCTCCGTCCGCGAATAAGT 59.564 57.895 8.23 0.00 41.33 2.24
26 27 1.299926 CCCTCCGTCCGCGAATAAG 60.300 63.158 8.23 0.00 41.33 1.73
27 28 1.731433 CTCCCTCCGTCCGCGAATAA 61.731 60.000 8.23 0.00 41.33 1.40
28 29 2.124193 TCCCTCCGTCCGCGAATA 60.124 61.111 8.23 0.00 41.33 1.75
29 30 2.898920 TACTCCCTCCGTCCGCGAAT 62.899 60.000 8.23 0.00 41.33 3.34
30 31 2.898920 ATACTCCCTCCGTCCGCGAA 62.899 60.000 8.23 0.00 41.33 4.70
31 32 2.043604 TATACTCCCTCCGTCCGCGA 62.044 60.000 8.23 0.00 41.33 5.87
32 33 1.168407 TTATACTCCCTCCGTCCGCG 61.168 60.000 0.00 0.00 37.95 6.46
33 34 1.035139 TTTATACTCCCTCCGTCCGC 58.965 55.000 0.00 0.00 0.00 5.54
34 35 3.806625 TTTTTATACTCCCTCCGTCCG 57.193 47.619 0.00 0.00 0.00 4.79
60 61 1.876497 CTTTTCACCGGTGGCATGGG 61.876 60.000 33.40 15.22 0.00 4.00
90 91 7.011994 TCGATACCTGACCAAACCCTATATAA 58.988 38.462 0.00 0.00 0.00 0.98
115 116 4.734398 TTTGAAATTTATGCCAGGCGAT 57.266 36.364 7.03 4.29 0.00 4.58
176 177 1.303561 GATGAAGGTGTGCTGGCCA 60.304 57.895 4.71 4.71 0.00 5.36
180 181 0.617413 AGGAGGATGAAGGTGTGCTG 59.383 55.000 0.00 0.00 0.00 4.41
181 182 1.004044 CAAGGAGGATGAAGGTGTGCT 59.996 52.381 0.00 0.00 0.00 4.40
186 187 0.539051 CGCTCAAGGAGGATGAAGGT 59.461 55.000 0.00 0.00 0.00 3.50
206 207 1.141053 GCTAGGTGTAGGGGGTGATTG 59.859 57.143 0.00 0.00 0.00 2.67
207 208 1.009675 AGCTAGGTGTAGGGGGTGATT 59.990 52.381 0.00 0.00 0.00 2.57
212 213 1.880941 AAGAAGCTAGGTGTAGGGGG 58.119 55.000 0.00 0.00 0.00 5.40
251 253 0.734942 TCGTCGTCGGAAAAGATGCC 60.735 55.000 1.55 0.00 37.69 4.40
252 254 0.365859 GTCGTCGTCGGAAAAGATGC 59.634 55.000 1.55 0.00 37.69 3.91
253 255 1.693467 TGTCGTCGTCGGAAAAGATG 58.307 50.000 1.55 0.00 37.69 2.90
254 256 2.056577 GTTGTCGTCGTCGGAAAAGAT 58.943 47.619 1.55 0.00 37.69 2.40
352 355 3.127895 GTCGCTATGATTCGGATAGAGCT 59.872 47.826 0.00 0.00 0.00 4.09
393 396 7.476540 TTCACTAAGTGATTGCTTAGACCTA 57.523 36.000 16.70 0.75 46.55 3.08
416 419 5.067283 ACGAACTGGTGCAAGTAATCTTTTT 59.933 36.000 0.00 0.00 0.00 1.94
430 439 3.875134 ACTTAGACCAAAACGAACTGGTG 59.125 43.478 10.94 1.46 46.12 4.17
432 441 5.494632 AAACTTAGACCAAAACGAACTGG 57.505 39.130 0.00 0.00 38.77 4.00
433 442 7.473027 TCTAAACTTAGACCAAAACGAACTG 57.527 36.000 0.00 0.00 34.99 3.16
434 443 7.767659 AGTTCTAAACTTAGACCAAAACGAACT 59.232 33.333 0.00 0.00 39.04 3.01
435 444 7.913423 AGTTCTAAACTTAGACCAAAACGAAC 58.087 34.615 0.00 0.00 39.04 3.95
446 455 8.800332 ACCGTTGAAGATAGTTCTAAACTTAGA 58.200 33.333 0.00 0.00 42.81 2.10
488 497 1.423794 GGGTTGACAGGTTCAGGGGA 61.424 60.000 0.00 0.00 34.94 4.81
519 528 1.803922 TCGCAACGTCGCCTACATG 60.804 57.895 0.00 0.00 0.00 3.21
581 590 3.258123 TCAGATCAATTGTGTCGTCCTCA 59.742 43.478 5.13 0.00 0.00 3.86
583 592 3.961480 TCAGATCAATTGTGTCGTCCT 57.039 42.857 5.13 0.00 0.00 3.85
727 758 8.154649 ACACAAATTCGAATATATGTCCTTCC 57.845 34.615 11.83 0.00 0.00 3.46
854 885 2.457598 AGAGTGCGGAGGAGATTTACA 58.542 47.619 0.00 0.00 0.00 2.41
895 930 1.133792 AGATAAGTGGGGGATTTGCGG 60.134 52.381 0.00 0.00 0.00 5.69
904 939 5.855045 AGTATTTAAGCGAGATAAGTGGGG 58.145 41.667 0.00 0.00 0.00 4.96
966 1001 3.741476 CTTGACTTGGCGCTGGGC 61.741 66.667 7.64 8.35 42.51 5.36
975 1015 3.249091 CGAGTGAGATGGACTTGACTTG 58.751 50.000 0.00 0.00 0.00 3.16
1086 1126 2.925170 AACAGCAGCCTCCTCCGT 60.925 61.111 0.00 0.00 0.00 4.69
1317 1366 1.524002 CATGAGCACCCCGATGACT 59.476 57.895 0.00 0.00 0.00 3.41
1983 2032 1.072015 GAGAATCCCCAGATGCAGAGG 59.928 57.143 0.00 0.00 29.07 3.69
2121 2179 3.810687 AACTGCACCCCCTCCCTCA 62.811 63.158 0.00 0.00 0.00 3.86
2122 2180 2.936032 AACTGCACCCCCTCCCTC 60.936 66.667 0.00 0.00 0.00 4.30
2123 2181 3.260100 CAACTGCACCCCCTCCCT 61.260 66.667 0.00 0.00 0.00 4.20
2124 2182 2.366153 TTTCAACTGCACCCCCTCCC 62.366 60.000 0.00 0.00 0.00 4.30
2125 2183 1.152830 TTTCAACTGCACCCCCTCC 59.847 57.895 0.00 0.00 0.00 4.30
2126 2184 1.179174 GGTTTCAACTGCACCCCCTC 61.179 60.000 0.00 0.00 0.00 4.30
2127 2185 1.152546 GGTTTCAACTGCACCCCCT 60.153 57.895 0.00 0.00 0.00 4.79
2128 2186 2.561037 CGGTTTCAACTGCACCCCC 61.561 63.158 0.00 0.00 0.00 5.40
2129 2187 1.388837 AACGGTTTCAACTGCACCCC 61.389 55.000 0.00 0.00 38.89 4.95
2130 2188 0.458260 AAACGGTTTCAACTGCACCC 59.542 50.000 0.00 0.00 38.89 4.61
2160 2218 9.080915 GGATGCTAAAGCTCTAAAAATGAAAAG 57.919 33.333 3.26 0.00 42.66 2.27
2179 2237 1.148273 GCCCATGTTCCGGATGCTA 59.852 57.895 4.15 0.00 0.00 3.49
2379 2441 4.486125 AACCTTTCAAACAAGCAACCAT 57.514 36.364 0.00 0.00 0.00 3.55
2449 2511 5.413833 CCATCACATAAGGTAGCATTCCATC 59.586 44.000 0.00 0.00 0.00 3.51
2455 2517 6.247229 TGTTACCATCACATAAGGTAGCAT 57.753 37.500 0.00 0.00 41.95 3.79
2513 2578 4.730966 AGAAGATCACCGATTAGGCTCTA 58.269 43.478 0.00 0.00 46.52 2.43
2514 2579 3.571590 AGAAGATCACCGATTAGGCTCT 58.428 45.455 0.00 0.00 46.52 4.09
2533 2598 8.625651 CGAGGAATATTTCTCTCTTCTGTTAGA 58.374 37.037 19.48 0.00 0.00 2.10
2537 2602 5.452636 GCCGAGGAATATTTCTCTCTTCTGT 60.453 44.000 19.48 0.00 0.00 3.41
2563 2628 0.244721 GGCAACATTTGGAGCAGTCC 59.755 55.000 0.00 0.00 44.24 3.85
2578 2643 3.452474 GCATGTACACAAAACAAGGCAA 58.548 40.909 0.00 0.00 33.75 4.52
2597 2662 2.816672 TGCCAGATAAATTGTTGACGCA 59.183 40.909 0.00 0.00 0.00 5.24
2648 2713 2.150390 CGGTCACATTCCACAATGACA 58.850 47.619 5.66 0.00 41.97 3.58
2795 2860 3.210227 TGCCATGATTTATACCACACCG 58.790 45.455 0.00 0.00 0.00 4.94
2797 2862 6.804677 TCAATTGCCATGATTTATACCACAC 58.195 36.000 0.00 0.00 0.00 3.82
2802 2867 9.964303 TGTGTATTCAATTGCCATGATTTATAC 57.036 29.630 0.00 0.00 0.00 1.47
2876 2941 5.400485 GCATGTCACTAAACTTCAAGCTTTG 59.600 40.000 0.00 0.00 0.00 2.77
2892 2957 4.519540 ACCTTATGGTTTTGCATGTCAC 57.480 40.909 0.00 0.00 46.05 3.67
2937 3002 7.262772 CACCATGCATCAGTTTTCTATTGATT 58.737 34.615 0.00 0.00 29.48 2.57
3037 3102 8.511604 ACAACCATGATTCATACTTAAGGAAG 57.488 34.615 7.53 0.00 38.76 3.46
3057 3122 6.407202 ACACCATATCTGAGAGTAAACAACC 58.593 40.000 0.00 0.00 0.00 3.77
3058 3123 7.201444 CGAACACCATATCTGAGAGTAAACAAC 60.201 40.741 0.00 0.00 0.00 3.32
3105 3170 2.223805 CCTCTCAACCAACCAAACTTGC 60.224 50.000 0.00 0.00 0.00 4.01
3106 3171 3.287222 TCCTCTCAACCAACCAAACTTG 58.713 45.455 0.00 0.00 0.00 3.16
3107 3172 3.053619 ACTCCTCTCAACCAACCAAACTT 60.054 43.478 0.00 0.00 0.00 2.66
3108 3173 2.509964 ACTCCTCTCAACCAACCAAACT 59.490 45.455 0.00 0.00 0.00 2.66
3109 3174 2.932261 ACTCCTCTCAACCAACCAAAC 58.068 47.619 0.00 0.00 0.00 2.93
3110 3175 4.781775 TTACTCCTCTCAACCAACCAAA 57.218 40.909 0.00 0.00 0.00 3.28
3111 3176 4.349636 TGATTACTCCTCTCAACCAACCAA 59.650 41.667 0.00 0.00 0.00 3.67
3112 3177 3.907474 TGATTACTCCTCTCAACCAACCA 59.093 43.478 0.00 0.00 0.00 3.67
3113 3178 4.508662 CTGATTACTCCTCTCAACCAACC 58.491 47.826 0.00 0.00 0.00 3.77
3114 3179 3.935828 GCTGATTACTCCTCTCAACCAAC 59.064 47.826 0.00 0.00 0.00 3.77
3115 3180 3.582647 TGCTGATTACTCCTCTCAACCAA 59.417 43.478 0.00 0.00 0.00 3.67
3116 3181 3.173151 TGCTGATTACTCCTCTCAACCA 58.827 45.455 0.00 0.00 0.00 3.67
3117 3182 3.895232 TGCTGATTACTCCTCTCAACC 57.105 47.619 0.00 0.00 0.00 3.77
3118 3183 5.016051 TCATGCTGATTACTCCTCTCAAC 57.984 43.478 0.00 0.00 0.00 3.18
3119 3184 4.958581 TCTCATGCTGATTACTCCTCTCAA 59.041 41.667 0.00 0.00 0.00 3.02
3120 3185 4.540715 TCTCATGCTGATTACTCCTCTCA 58.459 43.478 0.00 0.00 0.00 3.27
3121 3186 5.528043 TTCTCATGCTGATTACTCCTCTC 57.472 43.478 0.00 0.00 0.00 3.20
3122 3187 5.601729 TCATTCTCATGCTGATTACTCCTCT 59.398 40.000 0.00 0.00 0.00 3.69
3123 3188 5.851720 TCATTCTCATGCTGATTACTCCTC 58.148 41.667 0.00 0.00 0.00 3.71
3124 3189 5.221682 CCTCATTCTCATGCTGATTACTCCT 60.222 44.000 0.00 0.00 0.00 3.69
3125 3190 4.996122 CCTCATTCTCATGCTGATTACTCC 59.004 45.833 0.00 0.00 0.00 3.85
3126 3191 5.609423 ACCTCATTCTCATGCTGATTACTC 58.391 41.667 0.00 0.00 0.00 2.59
3127 3192 5.627182 ACCTCATTCTCATGCTGATTACT 57.373 39.130 0.00 0.00 0.00 2.24
3128 3193 6.297694 GAACCTCATTCTCATGCTGATTAC 57.702 41.667 0.00 0.00 34.15 1.89



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

AutoCloner maintained by Alex Coulton.