Multiple sequence alignment - TraesCS2B01G216200

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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 TraesCS2B01G216200 chr2B 100.000 3314 0 0 1 3314 201771506 201768193 0.000000e+00 6120.0
1 TraesCS2B01G216200 chr2D 93.921 2599 52 33 1 2558 143759932 143757399 0.000000e+00 3827.0
2 TraesCS2B01G216200 chr2D 92.569 619 24 11 2541 3141 143757372 143756758 0.000000e+00 869.0
3 TraesCS2B01G216200 chr2A 91.115 2611 93 53 24 2558 157545324 157547871 0.000000e+00 3408.0
4 TraesCS2B01G216200 chr2A 91.193 704 31 14 2541 3226 157547895 157548585 0.000000e+00 928.0
5 TraesCS2B01G216200 chr4D 87.654 81 10 0 2074 2154 435650744 435650824 9.790000e-16 95.3
6 TraesCS2B01G216200 chr4D 93.333 45 2 1 3260 3303 496108058 496108014 7.680000e-07 65.8
7 TraesCS2B01G216200 chr4B 87.654 81 10 0 2074 2154 536919107 536919187 9.790000e-16 95.3
8 TraesCS2B01G216200 chr4B 85.246 61 6 3 3245 3303 35204477 35204418 3.570000e-05 60.2
9 TraesCS2B01G216200 chr4A 87.654 81 10 0 2074 2154 37032308 37032388 9.790000e-16 95.3
10 TraesCS2B01G216200 chr5D 91.379 58 5 0 3254 3311 544488213 544488270 2.740000e-11 80.5
11 TraesCS2B01G216200 chr5D 97.143 35 0 1 3260 3293 317721658 317721624 1.280000e-04 58.4
12 TraesCS2B01G216200 chr7A 89.655 58 6 0 3254 3311 77591416 77591473 1.280000e-09 75.0
13 TraesCS2B01G216200 chr7D 93.478 46 3 0 3254 3299 588666646 588666691 5.930000e-08 69.4
14 TraesCS2B01G216200 chr5B 89.091 55 6 0 3251 3305 712876421 712876367 5.930000e-08 69.4
15 TraesCS2B01G216200 chr1D 92.857 42 1 2 3260 3300 10044726 10044766 3.570000e-05 60.2
16 TraesCS2B01G216200 chr1D 87.273 55 4 3 3247 3300 490009938 490009990 3.570000e-05 60.2


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 TraesCS2B01G216200 chr2B 201768193 201771506 3313 True 6120 6120 100.000 1 3314 1 chr2B.!!$R1 3313
1 TraesCS2B01G216200 chr2D 143756758 143759932 3174 True 2348 3827 93.245 1 3141 2 chr2D.!!$R1 3140
2 TraesCS2B01G216200 chr2A 157545324 157548585 3261 False 2168 3408 91.154 24 3226 2 chr2A.!!$F1 3202

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
557 566 0.035881 CTGCTGCCTTCTTCTCCACA 59.964 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 2552 1.176527 ATTTCCGCATGTGTCTTGGG 58.823 50.0 5.38 0.0 0.0 4.12 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
20 21 3.458163 TGACCCCGAGATCACGCC 61.458 66.667 7.06 0.00 0.00 5.68
70 71 2.481568 CGTATATGCGTCCGGTTCTCTA 59.518 50.000 0.00 0.00 0.00 2.43
87 88 1.004799 TAAAAGCTACGGCGGCACA 60.005 52.632 13.24 0.00 44.37 4.57
179 183 2.344025 GGGACGACGCTTTTGAATACT 58.656 47.619 0.00 0.00 0.00 2.12
183 187 4.264849 GGACGACGCTTTTGAATACTACTC 59.735 45.833 0.00 0.00 0.00 2.59
184 188 4.801891 ACGACGCTTTTGAATACTACTCA 58.198 39.130 0.00 0.00 0.00 3.41
185 189 4.620184 ACGACGCTTTTGAATACTACTCAC 59.380 41.667 0.00 0.00 0.00 3.51
186 190 4.857588 CGACGCTTTTGAATACTACTCACT 59.142 41.667 0.00 0.00 0.00 3.41
229 233 3.991069 GCTAAGCGTGCCAATAATATCG 58.009 45.455 0.00 0.00 0.00 2.92
237 241 4.445052 CGTGCCAATAATATCGTCGGTTAA 59.555 41.667 0.00 0.00 0.00 2.01
278 282 3.891977 TGTAGGAGTAGATTAGGCTGCTG 59.108 47.826 0.00 0.00 33.17 4.41
279 283 3.039252 AGGAGTAGATTAGGCTGCTGT 57.961 47.619 0.00 0.00 30.68 4.40
280 284 2.697751 AGGAGTAGATTAGGCTGCTGTG 59.302 50.000 0.00 0.00 30.68 3.66
281 285 2.478831 GAGTAGATTAGGCTGCTGTGC 58.521 52.381 0.00 0.00 30.68 4.57
282 286 2.102252 GAGTAGATTAGGCTGCTGTGCT 59.898 50.000 0.00 0.00 30.68 4.40
306 310 0.105709 TGTGGACTGTCTGTGGAGGA 60.106 55.000 7.85 0.00 0.00 3.71
314 318 1.080907 TCTGTGGAGGATGGCTGGA 59.919 57.895 0.00 0.00 0.00 3.86
321 325 2.203451 GGATGGCTGGATGGCTGG 60.203 66.667 0.00 0.00 42.34 4.85
322 326 2.760378 GGATGGCTGGATGGCTGGA 61.760 63.158 0.00 0.00 42.34 3.86
323 327 1.459369 GATGGCTGGATGGCTGGAT 59.541 57.895 0.00 0.00 42.34 3.41
324 328 0.894184 GATGGCTGGATGGCTGGATG 60.894 60.000 0.00 0.00 42.34 3.51
325 329 2.203451 GGCTGGATGGCTGGATGG 60.203 66.667 0.00 0.00 38.32 3.51
326 330 2.910994 GCTGGATGGCTGGATGGC 60.911 66.667 0.00 0.00 42.18 4.40
327 331 2.924640 CTGGATGGCTGGATGGCT 59.075 61.111 0.00 0.00 42.34 4.75
328 332 1.528542 CTGGATGGCTGGATGGCTG 60.529 63.158 0.00 0.00 42.34 4.85
376 380 1.084289 GCGCAGTTAGGTAAAGGGTG 58.916 55.000 0.30 0.00 0.00 4.61
377 381 1.609841 GCGCAGTTAGGTAAAGGGTGT 60.610 52.381 0.30 0.00 0.00 4.16
378 382 2.354003 GCGCAGTTAGGTAAAGGGTGTA 60.354 50.000 0.30 0.00 0.00 2.90
379 383 3.256558 CGCAGTTAGGTAAAGGGTGTAC 58.743 50.000 0.00 0.00 0.00 2.90
380 384 3.056322 CGCAGTTAGGTAAAGGGTGTACT 60.056 47.826 0.00 0.00 0.00 2.73
381 385 4.502016 GCAGTTAGGTAAAGGGTGTACTC 58.498 47.826 0.00 0.00 0.00 2.59
382 386 4.622457 GCAGTTAGGTAAAGGGTGTACTCC 60.622 50.000 5.35 5.35 0.00 3.85
545 554 4.648626 TCCAGTGGTGCTGCTGCC 62.649 66.667 13.47 4.00 43.71 4.85
555 564 1.002868 GCTGCTGCCTTCTTCTCCA 60.003 57.895 3.85 0.00 0.00 3.86
557 566 0.035881 CTGCTGCCTTCTTCTCCACA 59.964 55.000 0.00 0.00 0.00 4.17
569 578 0.894184 TCTCCACAGGGACAGACGAC 60.894 60.000 0.00 0.00 38.64 4.34
570 581 2.201436 CTCCACAGGGACAGACGACG 62.201 65.000 0.00 0.00 38.64 5.12
596 624 1.912043 AGGGTAAGCATGCTCTGAGTT 59.088 47.619 22.93 6.61 0.00 3.01
597 625 2.307098 AGGGTAAGCATGCTCTGAGTTT 59.693 45.455 22.93 5.78 0.00 2.66
687 724 2.414824 GGTCCTATGCATCGATCGACTC 60.415 54.545 22.06 15.20 0.00 3.36
692 729 0.751643 TGCATCGATCGACTCCTCCA 60.752 55.000 22.06 8.36 0.00 3.86
694 731 1.813178 GCATCGATCGACTCCTCCATA 59.187 52.381 22.06 0.00 0.00 2.74
698 735 1.068885 CGATCGACTCCTCCATAGCAC 60.069 57.143 10.26 0.00 0.00 4.40
700 737 1.299468 CGACTCCTCCATAGCACGC 60.299 63.158 0.00 0.00 0.00 5.34
701 738 1.068250 GACTCCTCCATAGCACGCC 59.932 63.158 0.00 0.00 0.00 5.68
703 740 1.068753 CTCCTCCATAGCACGCCAG 59.931 63.158 0.00 0.00 0.00 4.85
717 754 4.779475 CCAGTGTGGCGTTCTCTT 57.221 55.556 0.00 0.00 0.00 2.85
718 755 2.238353 CCAGTGTGGCGTTCTCTTG 58.762 57.895 0.00 0.00 0.00 3.02
719 756 0.532862 CCAGTGTGGCGTTCTCTTGT 60.533 55.000 0.00 0.00 0.00 3.16
720 757 1.299541 CAGTGTGGCGTTCTCTTGTT 58.700 50.000 0.00 0.00 0.00 2.83
721 758 1.003545 CAGTGTGGCGTTCTCTTGTTG 60.004 52.381 0.00 0.00 0.00 3.33
722 759 0.307760 GTGTGGCGTTCTCTTGTTGG 59.692 55.000 0.00 0.00 0.00 3.77
723 760 0.179234 TGTGGCGTTCTCTTGTTGGA 59.821 50.000 0.00 0.00 0.00 3.53
724 761 1.202758 TGTGGCGTTCTCTTGTTGGAT 60.203 47.619 0.00 0.00 0.00 3.41
725 762 1.880027 GTGGCGTTCTCTTGTTGGATT 59.120 47.619 0.00 0.00 0.00 3.01
726 763 2.293399 GTGGCGTTCTCTTGTTGGATTT 59.707 45.455 0.00 0.00 0.00 2.17
727 764 2.552315 TGGCGTTCTCTTGTTGGATTTC 59.448 45.455 0.00 0.00 0.00 2.17
732 769 5.733373 GCGTTCTCTTGTTGGATTTCTGTTT 60.733 40.000 0.00 0.00 0.00 2.83
771 813 4.335315 CCAGTTGCTGTTTGAGTAGTTGAA 59.665 41.667 0.00 0.00 0.00 2.69
773 815 6.138761 CAGTTGCTGTTTGAGTAGTTGAATC 58.861 40.000 0.00 0.00 0.00 2.52
927 985 6.457663 CCGAAATTAACGCCAATCTTGTATGA 60.458 38.462 0.00 0.00 0.00 2.15
945 1006 8.964420 TTGTATGAATTTCGTTTGATTCCTTC 57.036 30.769 0.00 0.00 32.57 3.46
948 1009 9.065871 GTATGAATTTCGTTTGATTCCTTCTTG 57.934 33.333 0.00 0.00 32.57 3.02
949 1010 7.038154 TGAATTTCGTTTGATTCCTTCTTGT 57.962 32.000 0.00 0.00 32.57 3.16
1013 1074 0.249955 TTCATCATGGAGTCGCAGCA 59.750 50.000 0.00 0.00 0.00 4.41
1014 1075 0.179092 TCATCATGGAGTCGCAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
1015 1076 0.179092 CATCATGGAGTCGCAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1539 1609 3.210528 GCCGATCCCGACGAGTCT 61.211 66.667 0.00 0.00 38.22 3.24
1547 1617 1.296755 CCCGACGAGTCTGAGAACGA 61.297 60.000 15.03 0.00 0.00 3.85
1905 1987 0.807667 CAGGAAACGCCCTCTCATCG 60.808 60.000 0.00 0.00 37.37 3.84
1928 2010 1.223211 GCCAGAAGGAGAAGGCCTC 59.777 63.158 5.23 0.00 41.25 4.70
1929 2011 1.519719 CCAGAAGGAGAAGGCCTCG 59.480 63.158 5.23 0.00 42.89 4.63
1930 2012 1.519719 CAGAAGGAGAAGGCCTCGG 59.480 63.158 5.23 0.00 42.89 4.63
1931 2013 0.972983 CAGAAGGAGAAGGCCTCGGA 60.973 60.000 5.23 0.00 42.89 4.55
1932 2014 0.252284 AGAAGGAGAAGGCCTCGGAA 60.252 55.000 5.23 0.00 42.89 4.30
1933 2015 0.176910 GAAGGAGAAGGCCTCGGAAG 59.823 60.000 5.23 0.00 42.89 3.46
1934 2016 1.904990 AAGGAGAAGGCCTCGGAAGC 61.905 60.000 5.23 0.00 42.89 3.86
1935 2017 2.202810 GAGAAGGCCTCGGAAGCG 60.203 66.667 5.23 0.00 31.32 4.68
1936 2018 3.724914 GAGAAGGCCTCGGAAGCGG 62.725 68.421 5.23 0.00 39.52 5.52
2015 2097 1.080230 CCAGCACCGTGTCTGAGAG 60.080 63.158 18.74 4.76 32.26 3.20
2443 2544 5.181690 TGCTGTTGTTTTACTTAGGCTTG 57.818 39.130 0.00 0.00 0.00 4.01
2451 2552 5.938125 TGTTTTACTTAGGCTTGGTCAGATC 59.062 40.000 0.00 0.00 0.00 2.75
2524 2626 4.621991 TCGCTACTCTAATGAGAAATGCC 58.378 43.478 0.00 0.00 42.73 4.40
2547 2649 5.065731 CCTGGCTTCTTTTGCTTGAGTATAG 59.934 44.000 0.00 0.00 0.00 1.31
2558 2660 8.429493 TTTGCTTGAGTATAGACATCTGAATG 57.571 34.615 0.00 0.00 38.93 2.67
2560 2662 6.982724 TGCTTGAGTATAGACATCTGAATGTG 59.017 38.462 0.00 0.00 46.20 3.21
2563 2718 9.761504 CTTGAGTATAGACATCTGAATGTGATT 57.238 33.333 0.00 0.00 46.20 2.57
2581 2736 6.003326 TGTGATTTGCAATCTTCTTAGGTCA 58.997 36.000 0.00 0.00 0.00 4.02
2620 2775 9.320295 ACCAAAATTTACAGGAATTTCATAGGA 57.680 29.630 10.26 0.00 38.04 2.94
2630 2785 7.827236 ACAGGAATTTCATAGGAACGTATCAAA 59.173 33.333 0.00 0.00 31.35 2.69
2638 2793 2.230508 AGGAACGTATCAAACAGAGCGA 59.769 45.455 0.00 0.00 34.21 4.93
2755 2910 2.623889 CTCAAGGGTTAGGACGATCGAT 59.376 50.000 24.34 9.73 0.00 3.59
2765 2920 2.026169 AGGACGATCGATAGGGATGCTA 60.026 50.000 24.34 0.00 0.00 3.49
2789 2944 3.056821 TCTTGTCGGGAAGATGTGTGTAG 60.057 47.826 0.00 0.00 0.00 2.74
2818 2974 0.034767 CTGATGGCTGTGGATGTGGT 60.035 55.000 0.00 0.00 0.00 4.16
2829 2985 3.146066 GTGGATGTGGTAAGTTGAAGCA 58.854 45.455 0.00 0.00 0.00 3.91
2872 3028 5.622180 CCATCATCATGTCATCTCTTTCCT 58.378 41.667 0.00 0.00 0.00 3.36
2983 3139 1.586154 CCATGGACCTCGCCAACAAC 61.586 60.000 5.56 0.00 42.16 3.32
2989 3145 1.034838 ACCTCGCCAACAACTTTGCA 61.035 50.000 0.00 0.00 0.00 4.08
3003 3159 1.610522 CTTTGCAGTGCCTAGTTTGCT 59.389 47.619 13.72 0.00 37.45 3.91
3116 3276 9.710818 AAGTATGAGTAAGTTACAATAGGGAGA 57.289 33.333 15.28 0.00 0.00 3.71
3144 3310 4.853007 AGAAGAAGGAGACAATCATTGGG 58.147 43.478 1.58 0.00 30.53 4.12
3155 3321 3.517500 ACAATCATTGGGCCGGTTAAAAT 59.482 39.130 1.90 0.00 34.12 1.82
3211 3377 6.478344 GCCATAACAAGACTAGAAGTGATCTG 59.522 42.308 0.00 0.00 39.30 2.90
3226 3392 5.999044 AGTGATCTGTTATCCAAGCTTGAT 58.001 37.500 28.05 19.44 0.00 2.57
3227 3393 6.421485 AGTGATCTGTTATCCAAGCTTGATT 58.579 36.000 28.05 16.03 0.00 2.57
3228 3394 6.318144 AGTGATCTGTTATCCAAGCTTGATTG 59.682 38.462 28.05 11.35 0.00 2.67
3229 3395 4.970662 TCTGTTATCCAAGCTTGATTGC 57.029 40.909 28.05 13.28 0.00 3.56
3230 3396 4.334552 TCTGTTATCCAAGCTTGATTGCA 58.665 39.130 28.05 16.70 34.99 4.08
3231 3397 4.951715 TCTGTTATCCAAGCTTGATTGCAT 59.048 37.500 28.05 12.71 34.99 3.96
3232 3398 5.066893 TCTGTTATCCAAGCTTGATTGCATC 59.933 40.000 28.05 11.49 34.99 3.91
3233 3399 4.098349 TGTTATCCAAGCTTGATTGCATCC 59.902 41.667 28.05 7.96 34.99 3.51
3234 3400 2.219080 TCCAAGCTTGATTGCATCCA 57.781 45.000 28.05 0.00 34.99 3.41
3235 3401 1.820519 TCCAAGCTTGATTGCATCCAC 59.179 47.619 28.05 0.00 34.99 4.02
3236 3402 1.546923 CCAAGCTTGATTGCATCCACA 59.453 47.619 28.05 0.00 34.99 4.17
3237 3403 2.602878 CAAGCTTGATTGCATCCACAC 58.397 47.619 22.31 0.00 34.99 3.82
3238 3404 1.913778 AGCTTGATTGCATCCACACA 58.086 45.000 0.00 0.00 34.99 3.72
3239 3405 1.542915 AGCTTGATTGCATCCACACAC 59.457 47.619 0.00 0.00 34.99 3.82
3240 3406 1.542915 GCTTGATTGCATCCACACACT 59.457 47.619 0.00 0.00 0.00 3.55
3241 3407 2.415090 GCTTGATTGCATCCACACACTC 60.415 50.000 0.00 0.00 0.00 3.51
3242 3408 1.825090 TGATTGCATCCACACACTCC 58.175 50.000 0.00 0.00 0.00 3.85
3243 3409 0.729116 GATTGCATCCACACACTCCG 59.271 55.000 0.00 0.00 0.00 4.63
3244 3410 0.677731 ATTGCATCCACACACTCCGG 60.678 55.000 0.00 0.00 0.00 5.14
3245 3411 3.127533 GCATCCACACACTCCGGC 61.128 66.667 0.00 0.00 0.00 6.13
3246 3412 2.347114 CATCCACACACTCCGGCA 59.653 61.111 0.00 0.00 0.00 5.69
3247 3413 1.078214 CATCCACACACTCCGGCAT 60.078 57.895 0.00 0.00 0.00 4.40
3248 3414 1.091771 CATCCACACACTCCGGCATC 61.092 60.000 0.00 0.00 0.00 3.91
3249 3415 1.267574 ATCCACACACTCCGGCATCT 61.268 55.000 0.00 0.00 0.00 2.90
3250 3416 1.448540 CCACACACTCCGGCATCTC 60.449 63.158 0.00 0.00 0.00 2.75
3251 3417 1.807165 CACACACTCCGGCATCTCG 60.807 63.158 0.00 0.00 0.00 4.04
3252 3418 2.276116 ACACACTCCGGCATCTCGT 61.276 57.895 0.00 0.00 0.00 4.18
3253 3419 1.517257 CACACTCCGGCATCTCGTC 60.517 63.158 0.00 0.00 0.00 4.20
3254 3420 2.105128 CACTCCGGCATCTCGTCC 59.895 66.667 0.00 0.00 0.00 4.79
3255 3421 3.148279 ACTCCGGCATCTCGTCCC 61.148 66.667 0.00 0.00 0.00 4.46
3256 3422 3.917760 CTCCGGCATCTCGTCCCC 61.918 72.222 0.00 0.00 0.00 4.81
3259 3425 3.550431 CGGCATCTCGTCCCCCAT 61.550 66.667 0.00 0.00 0.00 4.00
3260 3426 2.111878 GGCATCTCGTCCCCCATG 59.888 66.667 0.00 0.00 0.00 3.66
3261 3427 2.746375 GGCATCTCGTCCCCCATGT 61.746 63.158 0.00 0.00 0.00 3.21
3262 3428 1.227674 GCATCTCGTCCCCCATGTC 60.228 63.158 0.00 0.00 0.00 3.06
3263 3429 1.068083 CATCTCGTCCCCCATGTCG 59.932 63.158 0.00 0.00 0.00 4.35
3264 3430 2.797278 ATCTCGTCCCCCATGTCGC 61.797 63.158 0.00 0.00 0.00 5.19
3265 3431 4.530857 CTCGTCCCCCATGTCGCC 62.531 72.222 0.00 0.00 0.00 5.54
3268 3434 4.796495 GTCCCCCATGTCGCCCAC 62.796 72.222 0.00 0.00 0.00 4.61
3301 3467 3.733960 GGCGAAACCCAAGCCGTC 61.734 66.667 0.00 0.00 41.53 4.79
3302 3468 4.084888 GCGAAACCCAAGCCGTCG 62.085 66.667 0.00 0.00 34.89 5.12
3303 3469 3.419759 CGAAACCCAAGCCGTCGG 61.420 66.667 6.99 6.99 0.00 4.79
3308 3474 4.760047 CCCAAGCCGTCGGGTGAG 62.760 72.222 18.22 12.66 37.70 3.51
3310 3476 4.379243 CAAGCCGTCGGGTGAGCT 62.379 66.667 18.22 1.39 37.10 4.09
3311 3477 2.678934 AAGCCGTCGGGTGAGCTA 60.679 61.111 18.22 0.00 34.49 3.32
3312 3478 3.003113 AAGCCGTCGGGTGAGCTAC 62.003 63.158 18.22 0.00 34.49 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.458163 GGCGTGATCTCGGGGTCA 61.458 66.667 17.94 0.00 0.00 4.02
6 7 4.873129 CACGGCGTGATCTCGGGG 62.873 72.222 34.85 3.69 35.23 5.73
70 71 2.281208 TGTGCCGCCGTAGCTTTT 60.281 55.556 0.00 0.00 36.60 2.27
87 88 1.734163 CCGGAGGCGTAGAAAATTGT 58.266 50.000 0.00 0.00 46.14 2.71
179 183 7.941919 AGATTATTCAGATTACGCAGTGAGTA 58.058 34.615 2.23 2.23 45.73 2.59
183 187 7.359598 GCCTTAGATTATTCAGATTACGCAGTG 60.360 40.741 0.00 0.00 45.73 3.66
185 189 6.870965 AGCCTTAGATTATTCAGATTACGCAG 59.129 38.462 0.00 0.00 0.00 5.18
186 190 6.759272 AGCCTTAGATTATTCAGATTACGCA 58.241 36.000 0.00 0.00 0.00 5.24
229 233 7.078228 GCAGGATGATTGATAATTTAACCGAC 58.922 38.462 0.00 0.00 39.69 4.79
237 241 6.044754 TCCTACAGGCAGGATGATTGATAATT 59.955 38.462 0.00 0.00 39.89 1.40
278 282 1.502163 GACAGTCCACAGCACAGCAC 61.502 60.000 0.00 0.00 0.00 4.40
279 283 1.227645 GACAGTCCACAGCACAGCA 60.228 57.895 0.00 0.00 0.00 4.41
280 284 1.070445 AGACAGTCCACAGCACAGC 59.930 57.895 0.00 0.00 0.00 4.40
281 285 0.105593 ACAGACAGTCCACAGCACAG 59.894 55.000 0.00 0.00 0.00 3.66
282 286 0.179076 CACAGACAGTCCACAGCACA 60.179 55.000 0.00 0.00 0.00 4.57
306 310 1.153061 CATCCAGCCATCCAGCCAT 59.847 57.895 0.00 0.00 0.00 4.40
314 318 0.178998 CTTAGCAGCCATCCAGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
325 329 0.244721 CCTTGTTTGGCCTTAGCAGC 59.755 55.000 3.32 0.00 42.56 5.25
326 330 0.244721 GCCTTGTTTGGCCTTAGCAG 59.755 55.000 3.32 0.00 46.82 4.24
327 331 2.350738 GCCTTGTTTGGCCTTAGCA 58.649 52.632 3.32 0.00 46.82 3.49
376 380 4.502016 CCTTTCTTTTCTACGGGGAGTAC 58.498 47.826 0.00 0.00 0.00 2.73
377 381 3.055602 GCCTTTCTTTTCTACGGGGAGTA 60.056 47.826 0.00 0.00 0.00 2.59
378 382 2.290134 GCCTTTCTTTTCTACGGGGAGT 60.290 50.000 0.00 0.00 0.00 3.85
379 383 2.290071 TGCCTTTCTTTTCTACGGGGAG 60.290 50.000 0.00 0.00 0.00 4.30
380 384 1.700739 TGCCTTTCTTTTCTACGGGGA 59.299 47.619 0.00 0.00 0.00 4.81
381 385 2.084546 CTGCCTTTCTTTTCTACGGGG 58.915 52.381 0.00 0.00 0.00 5.73
382 386 3.003480 CTCTGCCTTTCTTTTCTACGGG 58.997 50.000 0.00 0.00 0.00 5.28
383 387 3.003480 CCTCTGCCTTTCTTTTCTACGG 58.997 50.000 0.00 0.00 0.00 4.02
384 388 3.003480 CCCTCTGCCTTTCTTTTCTACG 58.997 50.000 0.00 0.00 0.00 3.51
545 554 2.028567 GTCTGTCCCTGTGGAGAAGAAG 60.029 54.545 0.00 0.00 42.85 2.85
555 564 2.910479 TGCGTCGTCTGTCCCTGT 60.910 61.111 0.00 0.00 0.00 4.00
557 566 4.039357 CGTGCGTCGTCTGTCCCT 62.039 66.667 0.00 0.00 34.52 4.20
569 578 2.819595 ATGCTTACCCTGCGTGCG 60.820 61.111 0.00 0.00 0.00 5.34
570 581 2.793946 CATGCTTACCCTGCGTGC 59.206 61.111 0.00 0.00 39.99 5.34
614 642 4.527816 TCAAATCCCATGGAAAACAAGGAG 59.472 41.667 15.22 0.00 40.39 3.69
667 695 2.414824 GGAGTCGATCGATGCATAGGAC 60.415 54.545 22.50 5.36 0.00 3.85
668 696 1.813178 GGAGTCGATCGATGCATAGGA 59.187 52.381 22.50 0.00 0.00 2.94
687 724 1.522355 CACTGGCGTGCTATGGAGG 60.522 63.158 0.00 0.00 33.82 4.30
700 737 0.532862 ACAAGAGAACGCCACACTGG 60.533 55.000 0.00 0.00 41.55 4.00
701 738 1.003545 CAACAAGAGAACGCCACACTG 60.004 52.381 0.00 0.00 0.00 3.66
703 740 0.307760 CCAACAAGAGAACGCCACAC 59.692 55.000 0.00 0.00 0.00 3.82
705 742 1.523758 ATCCAACAAGAGAACGCCAC 58.476 50.000 0.00 0.00 0.00 5.01
706 743 2.270352 AATCCAACAAGAGAACGCCA 57.730 45.000 0.00 0.00 0.00 5.69
707 744 2.814336 AGAAATCCAACAAGAGAACGCC 59.186 45.455 0.00 0.00 0.00 5.68
708 745 3.251004 ACAGAAATCCAACAAGAGAACGC 59.749 43.478 0.00 0.00 0.00 4.84
709 746 5.424121 AACAGAAATCCAACAAGAGAACG 57.576 39.130 0.00 0.00 0.00 3.95
710 747 7.228706 TCCTAAACAGAAATCCAACAAGAGAAC 59.771 37.037 0.00 0.00 0.00 3.01
711 748 7.287061 TCCTAAACAGAAATCCAACAAGAGAA 58.713 34.615 0.00 0.00 0.00 2.87
712 749 6.837312 TCCTAAACAGAAATCCAACAAGAGA 58.163 36.000 0.00 0.00 0.00 3.10
713 750 6.712547 ACTCCTAAACAGAAATCCAACAAGAG 59.287 38.462 0.00 0.00 0.00 2.85
714 751 6.601332 ACTCCTAAACAGAAATCCAACAAGA 58.399 36.000 0.00 0.00 0.00 3.02
715 752 6.884280 ACTCCTAAACAGAAATCCAACAAG 57.116 37.500 0.00 0.00 0.00 3.16
716 753 7.060421 AGAACTCCTAAACAGAAATCCAACAA 58.940 34.615 0.00 0.00 0.00 2.83
717 754 6.601332 AGAACTCCTAAACAGAAATCCAACA 58.399 36.000 0.00 0.00 0.00 3.33
718 755 7.511959 AAGAACTCCTAAACAGAAATCCAAC 57.488 36.000 0.00 0.00 0.00 3.77
719 756 9.807921 ATAAAGAACTCCTAAACAGAAATCCAA 57.192 29.630 0.00 0.00 0.00 3.53
720 757 9.449719 GATAAAGAACTCCTAAACAGAAATCCA 57.550 33.333 0.00 0.00 0.00 3.41
721 758 9.674068 AGATAAAGAACTCCTAAACAGAAATCC 57.326 33.333 0.00 0.00 0.00 3.01
723 760 9.674068 GGAGATAAAGAACTCCTAAACAGAAAT 57.326 33.333 0.00 0.00 46.28 2.17
771 813 2.267006 CACACCAGCCAGCTCGAT 59.733 61.111 0.00 0.00 0.00 3.59
773 815 4.994471 TGCACACCAGCCAGCTCG 62.994 66.667 0.00 0.00 0.00 5.03
927 985 8.197439 AGAAACAAGAAGGAATCAAACGAAATT 58.803 29.630 0.00 0.00 0.00 1.82
945 1006 2.604462 GCAACTGCAACCAAGAAACAAG 59.396 45.455 0.00 0.00 41.59 3.16
948 1009 1.199624 CGCAACTGCAACCAAGAAAC 58.800 50.000 2.12 0.00 42.21 2.78
949 1010 0.102120 CCGCAACTGCAACCAAGAAA 59.898 50.000 2.12 0.00 42.21 2.52
1013 1074 1.224039 GCCTCCATCTGCTGCTTCT 59.776 57.895 0.00 0.00 0.00 2.85
1014 1075 2.178890 CGCCTCCATCTGCTGCTTC 61.179 63.158 0.00 0.00 0.00 3.86
1015 1076 2.124819 CGCCTCCATCTGCTGCTT 60.125 61.111 0.00 0.00 0.00 3.91
1281 1351 4.521062 ATCCAGACCTCGCAGCGC 62.521 66.667 10.87 0.00 0.00 5.92
1539 1609 4.717629 CCAGCGCCGTCGTTCTCA 62.718 66.667 2.29 0.00 38.14 3.27
1905 1987 3.689002 CTTCTCCTTCTGGCCCGCC 62.689 68.421 0.00 0.00 0.00 6.13
1908 1990 2.273776 GCCTTCTCCTTCTGGCCC 59.726 66.667 0.00 0.00 39.49 5.80
2443 2544 2.636830 CATGTGTCTTGGGATCTGACC 58.363 52.381 0.00 0.00 0.00 4.02
2451 2552 1.176527 ATTTCCGCATGTGTCTTGGG 58.823 50.000 5.38 0.00 0.00 4.12
2524 2626 5.877012 TCTATACTCAAGCAAAAGAAGCCAG 59.123 40.000 0.00 0.00 0.00 4.85
2547 2649 6.561614 AGATTGCAAATCACATTCAGATGTC 58.438 36.000 1.71 0.00 44.55 3.06
2558 2660 6.317857 GTGACCTAAGAAGATTGCAAATCAC 58.682 40.000 1.71 1.77 0.00 3.06
2559 2661 5.122239 CGTGACCTAAGAAGATTGCAAATCA 59.878 40.000 1.71 0.00 0.00 2.57
2560 2662 5.563842 CGTGACCTAAGAAGATTGCAAATC 58.436 41.667 1.71 2.47 0.00 2.17
2563 2718 2.742053 GCGTGACCTAAGAAGATTGCAA 59.258 45.455 0.00 0.00 0.00 4.08
2581 2736 0.171455 TTTTGGTGCGTTTCAAGCGT 59.829 45.000 0.00 0.00 37.44 5.07
2620 2775 1.983605 CGTCGCTCTGTTTGATACGTT 59.016 47.619 0.00 0.00 0.00 3.99
2622 2777 1.317611 CACGTCGCTCTGTTTGATACG 59.682 52.381 0.00 0.00 33.96 3.06
2630 2785 1.576920 CTGTCTCACGTCGCTCTGT 59.423 57.895 0.00 0.00 0.00 3.41
2638 2793 0.747255 ACTCTGTTGCTGTCTCACGT 59.253 50.000 0.00 0.00 0.00 4.49
2755 2910 2.632996 CCCGACAAGATTAGCATCCCTA 59.367 50.000 0.00 0.00 0.00 3.53
2765 2920 3.244561 ACACACATCTTCCCGACAAGATT 60.245 43.478 6.18 0.00 40.52 2.40
2818 2974 3.071479 GTTCCCGATGTGCTTCAACTTA 58.929 45.455 0.00 0.00 0.00 2.24
2829 2985 1.338769 GCTACACAAGGTTCCCGATGT 60.339 52.381 0.00 0.00 0.00 3.06
2872 3028 6.243900 AGAAGAAGATGAGCTGGATTGAAAA 58.756 36.000 0.00 0.00 0.00 2.29
2983 3139 1.610522 AGCAAACTAGGCACTGCAAAG 59.389 47.619 2.82 1.96 41.52 2.77
2989 3145 3.944476 CCTCAGCAAACTAGGCACT 57.056 52.632 0.00 0.00 46.37 4.40
3003 3159 5.302568 ACAGATTTGATGTTTTCTTGCCTCA 59.697 36.000 0.00 0.00 0.00 3.86
3123 3284 3.379688 GCCCAATGATTGTCTCCTTCTTC 59.620 47.826 4.27 0.00 0.00 2.87
3124 3285 3.359950 GCCCAATGATTGTCTCCTTCTT 58.640 45.455 4.27 0.00 0.00 2.52
3130 3291 0.394352 ACCGGCCCAATGATTGTCTC 60.394 55.000 0.00 0.00 0.00 3.36
3132 3293 1.757682 TAACCGGCCCAATGATTGTC 58.242 50.000 0.00 0.00 0.00 3.18
3155 3321 5.772393 TCCTAGAGCTGGAATTGGTTAAA 57.228 39.130 0.00 0.00 0.00 1.52
3184 3350 7.561722 AGATCACTTCTAGTCTTGTTATGGCTA 59.438 37.037 0.00 0.00 30.96 3.93
3198 3364 6.815089 AGCTTGGATAACAGATCACTTCTAG 58.185 40.000 0.00 0.00 31.77 2.43
3201 3367 5.877012 TCAAGCTTGGATAACAGATCACTTC 59.123 40.000 25.73 0.00 0.00 3.01
3203 3369 5.426689 TCAAGCTTGGATAACAGATCACT 57.573 39.130 25.73 0.00 0.00 3.41
3226 3392 1.302431 CCGGAGTGTGTGGATGCAA 60.302 57.895 0.00 0.00 0.00 4.08
3227 3393 2.347114 CCGGAGTGTGTGGATGCA 59.653 61.111 0.00 0.00 0.00 3.96
3228 3394 3.127533 GCCGGAGTGTGTGGATGC 61.128 66.667 5.05 0.00 0.00 3.91
3229 3395 1.078214 ATGCCGGAGTGTGTGGATG 60.078 57.895 5.05 0.00 0.00 3.51
3230 3396 1.221840 GATGCCGGAGTGTGTGGAT 59.778 57.895 5.05 0.00 0.00 3.41
3231 3397 1.888436 GAGATGCCGGAGTGTGTGGA 61.888 60.000 5.05 0.00 0.00 4.02
3232 3398 1.448540 GAGATGCCGGAGTGTGTGG 60.449 63.158 5.05 0.00 0.00 4.17
3233 3399 1.807165 CGAGATGCCGGAGTGTGTG 60.807 63.158 5.05 0.00 0.00 3.82
3234 3400 2.214181 GACGAGATGCCGGAGTGTGT 62.214 60.000 5.05 0.00 0.00 3.72
3235 3401 1.517257 GACGAGATGCCGGAGTGTG 60.517 63.158 5.05 0.00 0.00 3.82
3236 3402 2.711922 GGACGAGATGCCGGAGTGT 61.712 63.158 5.05 0.00 0.00 3.55
3237 3403 2.105128 GGACGAGATGCCGGAGTG 59.895 66.667 5.05 0.00 0.00 3.51
3238 3404 3.148279 GGGACGAGATGCCGGAGT 61.148 66.667 5.05 0.00 0.00 3.85
3239 3405 3.917760 GGGGACGAGATGCCGGAG 61.918 72.222 5.05 0.00 40.60 4.63
3242 3408 3.550431 ATGGGGGACGAGATGCCG 61.550 66.667 0.00 0.00 40.60 5.69
3243 3409 2.111878 CATGGGGGACGAGATGCC 59.888 66.667 0.00 0.00 38.35 4.40
3244 3410 1.227674 GACATGGGGGACGAGATGC 60.228 63.158 0.00 0.00 0.00 3.91
3245 3411 1.068083 CGACATGGGGGACGAGATG 59.932 63.158 0.00 0.00 0.00 2.90
3246 3412 2.797278 GCGACATGGGGGACGAGAT 61.797 63.158 0.00 0.00 0.00 2.75
3247 3413 3.458163 GCGACATGGGGGACGAGA 61.458 66.667 0.00 0.00 0.00 4.04
3248 3414 4.530857 GGCGACATGGGGGACGAG 62.531 72.222 0.00 0.00 0.00 4.18
3251 3417 4.796495 GTGGGCGACATGGGGGAC 62.796 72.222 0.00 0.00 0.00 4.46
3284 3450 3.733960 GACGGCTTGGGTTTCGCC 61.734 66.667 0.00 0.00 40.40 5.54
3285 3451 4.084888 CGACGGCTTGGGTTTCGC 62.085 66.667 0.00 0.00 0.00 4.70
3286 3452 3.419759 CCGACGGCTTGGGTTTCG 61.420 66.667 0.00 0.00 0.00 3.46
3287 3453 3.053896 CCCGACGGCTTGGGTTTC 61.054 66.667 8.86 0.00 40.76 2.78
3293 3459 3.001902 TAGCTCACCCGACGGCTTG 62.002 63.158 8.86 7.91 36.40 4.01
3294 3460 2.678934 TAGCTCACCCGACGGCTT 60.679 61.111 8.86 0.00 36.40 4.35
3295 3461 3.450115 GTAGCTCACCCGACGGCT 61.450 66.667 8.86 4.45 38.62 5.52
3296 3462 4.509737 GGTAGCTCACCCGACGGC 62.510 72.222 8.86 0.00 42.07 5.68


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

AutoCloner maintained by Alex Coulton.