Multiple sequence alignment - TraesCS5B01G390700

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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 TraesCS5B01G390700 chr5B 100.000 3501 0 0 1 3501 570098350 570094850 0 6466
1 TraesCS5B01G390700 chr5B 96.175 2719 98 4 789 3501 426073220 426075938 0 4440
2 TraesCS5B01G390700 chr7B 97.056 2717 76 2 789 3501 379738698 379741414 0 4571
3 TraesCS5B01G390700 chr7B 96.761 2717 84 3 789 3501 747731973 747729257 0 4527
4 TraesCS5B01G390700 chr7B 96.354 2715 89 6 789 3501 81910350 81913056 0 4457
5 TraesCS5B01G390700 chr3B 96.690 2719 81 6 789 3501 772609332 772612047 0 4514
6 TraesCS5B01G390700 chr3B 96.463 2714 94 2 789 3501 170820949 170818237 0 4479
7 TraesCS5B01G390700 chr3B 95.520 2723 112 5 789 3501 770031335 770034057 0 4344
8 TraesCS5B01G390700 chr4B 95.513 2719 115 5 789 3500 327349039 327351757 0 4338
9 TraesCS5B01G390700 chr6B 95.270 2727 117 9 783 3500 526744007 526746730 0 4311
10 TraesCS5B01G390700 chr2A 97.845 789 12 2 1 788 668900777 668899993 0 1358
11 TraesCS5B01G390700 chr2A 97.338 789 18 2 1 788 533054852 533054066 0 1338
12 TraesCS5B01G390700 chr3A 97.481 794 16 1 1 790 716903239 716904032 0 1352
13 TraesCS5B01G390700 chr3A 97.589 788 15 2 2 788 71589496 71588712 0 1347
14 TraesCS5B01G390700 chr1B 97.342 790 17 3 1 788 44312793 44313580 0 1339
15 TraesCS5B01G390700 chr7A 97.212 789 18 3 1 788 452743907 452744692 0 1332
16 TraesCS5B01G390700 chr5A 97.205 787 21 1 2 788 558931350 558932135 0 1330
17 TraesCS5B01G390700 chr5A 97.089 790 19 3 1 788 558938383 558939170 0 1328
18 TraesCS5B01G390700 chr1A 96.977 794 19 3 1 793 343341205 343341994 0 1328


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 TraesCS5B01G390700 chr5B 570094850 570098350 3500 True 6466 6466 100.000 1 3501 1 chr5B.!!$R1 3500
1 TraesCS5B01G390700 chr5B 426073220 426075938 2718 False 4440 4440 96.175 789 3501 1 chr5B.!!$F1 2712
2 TraesCS5B01G390700 chr7B 379738698 379741414 2716 False 4571 4571 97.056 789 3501 1 chr7B.!!$F2 2712
3 TraesCS5B01G390700 chr7B 747729257 747731973 2716 True 4527 4527 96.761 789 3501 1 chr7B.!!$R1 2712
4 TraesCS5B01G390700 chr7B 81910350 81913056 2706 False 4457 4457 96.354 789 3501 1 chr7B.!!$F1 2712
5 TraesCS5B01G390700 chr3B 772609332 772612047 2715 False 4514 4514 96.690 789 3501 1 chr3B.!!$F2 2712
6 TraesCS5B01G390700 chr3B 170818237 170820949 2712 True 4479 4479 96.463 789 3501 1 chr3B.!!$R1 2712
7 TraesCS5B01G390700 chr3B 770031335 770034057 2722 False 4344 4344 95.520 789 3501 1 chr3B.!!$F1 2712
8 TraesCS5B01G390700 chr4B 327349039 327351757 2718 False 4338 4338 95.513 789 3500 1 chr4B.!!$F1 2711
9 TraesCS5B01G390700 chr6B 526744007 526746730 2723 False 4311 4311 95.270 783 3500 1 chr6B.!!$F1 2717
10 TraesCS5B01G390700 chr2A 668899993 668900777 784 True 1358 1358 97.845 1 788 1 chr2A.!!$R2 787
11 TraesCS5B01G390700 chr2A 533054066 533054852 786 True 1338 1338 97.338 1 788 1 chr2A.!!$R1 787
12 TraesCS5B01G390700 chr3A 716903239 716904032 793 False 1352 1352 97.481 1 790 1 chr3A.!!$F1 789
13 TraesCS5B01G390700 chr3A 71588712 71589496 784 True 1347 1347 97.589 2 788 1 chr3A.!!$R1 786
14 TraesCS5B01G390700 chr1B 44312793 44313580 787 False 1339 1339 97.342 1 788 1 chr1B.!!$F1 787
15 TraesCS5B01G390700 chr7A 452743907 452744692 785 False 1332 1332 97.212 1 788 1 chr7A.!!$F1 787
16 TraesCS5B01G390700 chr5A 558931350 558932135 785 False 1330 1330 97.205 2 788 1 chr5A.!!$F1 786
17 TraesCS5B01G390700 chr5A 558938383 558939170 787 False 1328 1328 97.089 1 788 1 chr5A.!!$F2 787
18 TraesCS5B01G390700 chr1A 343341205 343341994 789 False 1328 1328 96.977 1 793 1 chr1A.!!$F1 792

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
661 673 0.035056 CCATCCCCTTGAACGCTTCT 60.035 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 2634 0.036483 CCAAATTTTTGAGGCCCCCG 60.036 55.0 0.0 0.0 40.55 5.73 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
661 673 0.035056 CCATCCCCTTGAACGCTTCT 60.035 55.000 0.00 0.00 0.00 2.85
669 681 1.221466 TTGAACGCTTCTGCACTCGG 61.221 55.000 0.00 0.00 39.64 4.63
671 683 0.388134 GAACGCTTCTGCACTCGGTA 60.388 55.000 0.00 0.00 39.64 4.02
961 981 3.516615 GTCTGTTCCTACATCAGCAGAC 58.483 50.000 6.72 6.72 43.54 3.51
1050 1070 0.175989 GACGGAGAAAAGAGGGCGAT 59.824 55.000 0.00 0.00 0.00 4.58
1264 1288 8.282592 CGTCTGACTCTGTTGATTGAAAAATTA 58.717 33.333 6.21 0.00 0.00 1.40
1275 1299 6.244999 TGATTGAAAAATTAACCGACGATCG 58.755 36.000 14.88 14.88 40.07 3.69
1436 1460 3.009033 ACTTCCGTTGAATGAGGAATCCA 59.991 43.478 0.61 0.00 42.43 3.41
1485 1509 3.378339 GACATATCAAAGTCCCGTACGG 58.622 50.000 27.68 27.68 0.00 4.02
1590 1614 2.515523 GCTGCAGGCCATGACGAT 60.516 61.111 17.12 0.00 34.27 3.73
1594 1618 2.191513 GCAGGCCATGACGATGCAT 61.192 57.895 5.01 0.00 36.88 3.96
1727 1751 9.634021 ATCCATCCTTTCTACTTTATTTTCCTC 57.366 33.333 0.00 0.00 0.00 3.71
1751 1775 0.247460 CTTCTGGCTCCGATGTCACA 59.753 55.000 0.00 0.00 0.00 3.58
1890 1918 7.817418 ACATGAACTGGTGTAAGTTTATTGT 57.183 32.000 0.00 0.00 40.48 2.71
2019 2048 3.548668 CACAGTTTTATTCATGCATGGCG 59.451 43.478 25.97 1.04 0.00 5.69
2153 2188 2.751259 CAACTGCCAGCACACTATGATT 59.249 45.455 0.00 0.00 0.00 2.57
2352 2389 2.840102 CTCTGGGGTAGGAGGCCG 60.840 72.222 0.00 0.00 0.00 6.13
2375 2412 1.153353 GCCTACGCACAAGTTTGCTA 58.847 50.000 7.94 0.00 40.62 3.49
2381 2418 4.147219 ACGCACAAGTTTGCTATTTCTC 57.853 40.909 7.94 0.00 40.62 2.87
2444 2481 4.796110 AGGGCAACTGATACCACATATT 57.204 40.909 0.00 0.00 0.00 1.28
2597 2634 4.669318 TGCTATAGACTACAGCGTGTTTC 58.331 43.478 8.19 0.00 38.15 2.78
2816 2857 1.173043 GTTTGCATCCGGAATGACCA 58.827 50.000 9.01 0.00 37.59 4.02
2875 2916 2.125391 GCCTCTGACAGCGATGCA 60.125 61.111 0.00 0.00 0.00 3.96
2955 2996 1.404449 CGGCCGGTATGACTACAACAA 60.404 52.381 20.10 0.00 0.00 2.83
3105 3146 1.593265 GCAACAAGGGCAAGGATGG 59.407 57.895 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
319 331 3.424105 GAGATGGGCAAGGGGGCT 61.424 66.667 0.00 0.00 42.84 5.19
332 344 7.156965 TCACCCCTCTATATATAGGAGGAGAT 58.843 42.308 25.04 14.67 34.58 2.75
550 562 0.459078 TCAACACACGTACGGGACAA 59.541 50.000 27.01 1.43 0.00 3.18
669 681 8.548721 GTTTGCATCTACATACCACTTGTATAC 58.451 37.037 0.00 0.00 38.10 1.47
671 683 7.338710 AGTTTGCATCTACATACCACTTGTAT 58.661 34.615 0.00 0.00 40.91 2.29
760 772 5.221541 TGGGGAACGTTGCAGAAAATTAAAT 60.222 36.000 21.74 0.00 0.00 1.40
961 981 1.953138 GATGATCGCCACGAGCCAG 60.953 63.158 2.56 0.00 41.81 4.85
1050 1070 2.835764 GGGTGTGTGGATAGTTACCTCA 59.164 50.000 0.00 0.00 0.00 3.86
1264 1288 1.217244 CCCCTTTCGATCGTCGGTT 59.783 57.895 15.94 0.00 40.88 4.44
1275 1299 1.228552 TCAGCAGCAACCCCCTTTC 60.229 57.895 0.00 0.00 0.00 2.62
1426 1450 2.306805 AGTGCAGAACATGGATTCCTCA 59.693 45.455 3.95 0.00 0.00 3.86
1485 1509 4.873746 TCCTCGATCTCATTATTGACCC 57.126 45.455 0.00 0.00 0.00 4.46
1520 1544 3.888930 GACTCCAATCCAGGAAACAAACA 59.111 43.478 0.00 0.00 37.20 2.83
1590 1614 5.011586 TCATCTTGAAAACATCTCCATGCA 58.988 37.500 0.00 0.00 32.57 3.96
1594 1618 5.319453 AGCTTCATCTTGAAAACATCTCCA 58.681 37.500 0.00 0.00 35.73 3.86
1727 1751 1.134280 ACATCGGAGCCAGAAGATTGG 60.134 52.381 0.00 0.00 41.35 3.16
1751 1775 4.637534 CACTGGCAGTCATTAGCTTAACAT 59.362 41.667 19.13 0.00 0.00 2.71
1801 1828 1.596727 GCAAAAAGTTTGCCGCATCAA 59.403 42.857 13.49 0.00 39.38 2.57
1890 1918 3.616956 AAGCATCATGGAGAAAGTCGA 57.383 42.857 0.00 0.00 0.00 4.20
2019 2048 2.808543 GCCATCTTGTTATGATCGGGTC 59.191 50.000 0.00 0.00 0.00 4.46
2139 2174 3.754955 CAGTTGCAATCATAGTGTGCTG 58.245 45.455 0.59 0.00 39.09 4.41
2141 2176 2.523015 GCAGTTGCAATCATAGTGTGC 58.477 47.619 0.59 0.00 41.59 4.57
2146 2181 1.746787 TGCTGGCAGTTGCAATCATAG 59.253 47.619 17.16 0.00 44.36 2.23
2153 2188 0.250858 ATAGTGTGCTGGCAGTTGCA 60.251 50.000 17.16 6.03 44.36 4.08
2375 2412 3.282021 CGTTGATGGTCCATGGAGAAAT 58.718 45.455 16.81 9.13 0.00 2.17
2381 2418 0.677731 ACAGCGTTGATGGTCCATGG 60.678 55.000 9.76 4.97 0.00 3.66
2444 2481 7.706100 AACAAAAACTAACCTGTAGTTTCCA 57.294 32.000 10.93 0.00 44.27 3.53
2597 2634 0.036483 CCAAATTTTTGAGGCCCCCG 60.036 55.000 0.00 0.00 40.55 5.73
2816 2857 1.302832 CCAACTTCCCGAGCAAGCT 60.303 57.895 0.00 0.00 0.00 3.74
2875 2916 0.179045 AAGTGAACTGCCTCGCAACT 60.179 50.000 0.00 0.00 38.41 3.16
2935 2976 0.173935 TGTTGTAGTCATACCGGCCG 59.826 55.000 21.04 21.04 0.00 6.13
2955 2996 0.329596 GTCACTGGGCTCTTGGGAAT 59.670 55.000 0.00 0.00 0.00 3.01
3043 3084 0.173481 CATCGTCATCCGTGTCCTGT 59.827 55.000 0.00 0.00 37.94 4.00
3344 3391 0.387565 GACAACAAACCCATTGCCGT 59.612 50.000 0.00 0.00 43.13 5.68
3463 3510 1.330521 GTTCAAGCGAGCAGAAACACA 59.669 47.619 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.