Multiple sequence alignment - TraesCS7B01G499600

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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 TraesCS7B01G499600 chr7B 100.000 2561 0 0 1 2561 749590008 749592568 0 4730
1 TraesCS7B01G499600 chr5B 95.433 2562 115 2 1 2561 696644065 696641505 0 4082
2 TraesCS7B01G499600 chr5B 94.076 2566 146 4 1 2561 677692004 677689440 0 3892
3 TraesCS7B01G499600 chr2B 94.959 2559 127 2 1 2558 734404265 734406822 0 4010
4 TraesCS7B01G499600 chr2B 82.600 2569 429 17 1 2561 5815578 5813020 0 2252
5 TraesCS7B01G499600 chr2B 82.328 2569 433 19 1 2561 400776821 400774266 0 2209
6 TraesCS7B01G499600 chr6A 93.019 2564 175 4 1 2561 573468627 573466065 0 3740
7 TraesCS7B01G499600 chr6B 86.550 2565 335 9 1 2561 133370511 133367953 0 2817
8 TraesCS7B01G499600 chr3D 84.319 2570 390 10 1 2560 85071281 85073847 0 2501
9 TraesCS7B01G499600 chr3B 78.127 2039 424 21 528 2557 561509120 561511145 0 1275
10 TraesCS7B01G499600 chr3A 92.477 545 39 2 1 544 489601760 489602303 0 778


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 TraesCS7B01G499600 chr7B 749590008 749592568 2560 False 4730 4730 100.000 1 2561 1 chr7B.!!$F1 2560
1 TraesCS7B01G499600 chr5B 696641505 696644065 2560 True 4082 4082 95.433 1 2561 1 chr5B.!!$R2 2560
2 TraesCS7B01G499600 chr5B 677689440 677692004 2564 True 3892 3892 94.076 1 2561 1 chr5B.!!$R1 2560
3 TraesCS7B01G499600 chr2B 734404265 734406822 2557 False 4010 4010 94.959 1 2558 1 chr2B.!!$F1 2557
4 TraesCS7B01G499600 chr2B 5813020 5815578 2558 True 2252 2252 82.600 1 2561 1 chr2B.!!$R1 2560
5 TraesCS7B01G499600 chr2B 400774266 400776821 2555 True 2209 2209 82.328 1 2561 1 chr2B.!!$R2 2560
6 TraesCS7B01G499600 chr6A 573466065 573468627 2562 True 3740 3740 93.019 1 2561 1 chr6A.!!$R1 2560
7 TraesCS7B01G499600 chr6B 133367953 133370511 2558 True 2817 2817 86.550 1 2561 1 chr6B.!!$R1 2560
8 TraesCS7B01G499600 chr3D 85071281 85073847 2566 False 2501 2501 84.319 1 2560 1 chr3D.!!$F1 2559
9 TraesCS7B01G499600 chr3B 561509120 561511145 2025 False 1275 1275 78.127 528 2557 1 chr3B.!!$F1 2029
10 TraesCS7B01G499600 chr3A 489601760 489602303 543 False 778 778 92.477 1 544 1 chr3A.!!$F1 543

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
418 422 0.535102 CACTGACGCAGGGAAAAGGT 60.535 55.000 10.80 0.0 36.97 3.50 F
1232 1239 1.079543 CCAAGTCTGACCAGAGGCG 60.080 63.158 3.76 0.0 38.27 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 1515 0.744281 TCTATCAATCGCTGCGTCCA 59.256 50.0 22.48 2.7 0.0 4.02 R
2256 2268 3.580731 CAGACTTTCCGTTCTTCCTCTC 58.419 50.0 0.00 0.0 0.0 3.20 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
77 78 1.951602 GAGTTTGCGGGTTTGTAGGTT 59.048 47.619 0.00 0.00 0.00 3.50
159 160 1.970917 CTGATTGCGCCGGAGTTCAC 61.971 60.000 5.05 0.00 0.00 3.18
234 238 1.529713 CGGGAGGAGGAGGTAGAGC 60.530 68.421 0.00 0.00 0.00 4.09
254 258 1.439644 GGTTTTGCGGCAGGAACAA 59.560 52.632 23.51 6.76 0.00 2.83
309 313 6.413892 AGTTAAGTAGTTCGGCTAGTAGTCT 58.586 40.000 0.00 0.00 33.21 3.24
331 335 7.614583 AGTCTCTTGAAATCAAATGATGTCCAT 59.385 33.333 10.36 0.00 37.87 3.41
387 391 0.698818 TTTGAGGAGAAGGGGAAGGC 59.301 55.000 0.00 0.00 0.00 4.35
418 422 0.535102 CACTGACGCAGGGAAAAGGT 60.535 55.000 10.80 0.00 36.97 3.50
653 658 3.808618 GCACTCCTGGATGTTCAGAAGTT 60.809 47.826 0.00 0.00 29.72 2.66
841 846 7.367285 TCATGGTGTAACTGCAAACTTTATTC 58.633 34.615 0.00 0.00 36.74 1.75
848 853 9.891828 TGTAACTGCAAACTTTATTCATGTAAG 57.108 29.630 0.00 0.00 0.00 2.34
1173 1179 3.875727 CAGTATGCAACTCAAGATGGAGG 59.124 47.826 0.00 0.00 39.27 4.30
1227 1234 3.499918 GTGAAATGACCAAGTCTGACCAG 59.500 47.826 3.76 0.00 33.15 4.00
1232 1239 1.079543 CCAAGTCTGACCAGAGGCG 60.080 63.158 3.76 0.00 38.27 5.52
1393 1400 4.821260 GCCTTGGACCATTCAAACAAAAAT 59.179 37.500 0.00 0.00 0.00 1.82
1508 1515 2.121948 TCTGAGAACATGGCCAGCTAT 58.878 47.619 13.05 0.00 0.00 2.97
1618 1625 2.086869 GAGCTAATTGGCTGAAGCACA 58.913 47.619 22.13 0.00 43.20 4.57
1878 1889 2.680352 ACGGAGGAGGATGTGCGT 60.680 61.111 0.00 0.00 35.75 5.24
2012 2023 6.533367 GTGTTAGAGGCTATCAACTCAAGAAG 59.467 42.308 0.00 0.00 36.20 2.85
2167 2178 1.066143 GGCTCAAGTTGATTCTCCCGA 60.066 52.381 5.91 0.00 0.00 5.14
2267 2279 4.150804 GTCAACACAATCGAGAGGAAGAAC 59.849 45.833 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.042297 TCCCATGTTCCTTTGCCACATA 59.958 45.455 0.00 0.00 29.78 2.29
159 160 1.478288 GCCCAATCTGATCCTCCCTTG 60.478 57.143 0.00 0.00 0.00 3.61
234 238 3.291383 TTCCTGCCGCAAAACCCG 61.291 61.111 0.00 0.00 0.00 5.28
254 258 1.005215 CTTCCTTGGTCTGCTGGGATT 59.995 52.381 0.00 0.00 0.00 3.01
263 267 5.222213 ACTCATCATTTTCCTTCCTTGGTCT 60.222 40.000 0.00 0.00 0.00 3.85
309 313 7.252708 CGAATGGACATCATTTGATTTCAAGA 58.747 34.615 8.51 0.00 45.73 3.02
331 335 0.859232 GAGCACTCGAAGTTTGCGAA 59.141 50.000 0.00 0.00 40.32 4.70
387 391 1.690283 CGTCAGTGCCAGCTGATTCG 61.690 60.000 17.39 6.19 45.81 3.34
418 422 0.551396 TCGCCTCTACTCCATCCTCA 59.449 55.000 0.00 0.00 0.00 3.86
681 686 2.035832 TGCGTCAGACAGATGAGTTTCA 59.964 45.455 0.41 0.00 35.12 2.69
841 846 6.470278 TCCTTCCATCATCTATGCTTACATG 58.530 40.000 0.00 0.00 37.04 3.21
848 853 4.070716 CCACTTCCTTCCATCATCTATGC 58.929 47.826 0.00 0.00 33.92 3.14
1173 1179 2.019984 CCTGCATTAGGGAAGAGTTGC 58.980 52.381 0.00 0.00 43.33 4.17
1227 1234 3.197434 GTGTTAATCACCAAACGCCTC 57.803 47.619 0.00 0.00 40.84 4.70
1279 1286 6.314120 TCCCCTCAAATCTCTTCATTGAAAA 58.686 36.000 0.01 0.00 33.08 2.29
1280 1287 5.891198 TCCCCTCAAATCTCTTCATTGAAA 58.109 37.500 0.01 0.00 33.08 2.69
1393 1400 6.324770 TGCAGATCATTATGGACTGAGTCTAA 59.675 38.462 12.92 4.73 32.47 2.10
1496 1503 2.256591 GCGTCCATAGCTGGCCATG 61.257 63.158 5.51 0.16 42.80 3.66
1498 1505 3.390183 CTGCGTCCATAGCTGGCCA 62.390 63.158 4.71 4.71 42.80 5.36
1508 1515 0.744281 TCTATCAATCGCTGCGTCCA 59.256 50.000 22.48 2.70 0.00 4.02
1559 1566 3.382278 TCAATCTCTTCCTGCTCCATCT 58.618 45.455 0.00 0.00 0.00 2.90
2137 2148 3.609853 TCAACTTGAGCCGATTAGCAAT 58.390 40.909 0.00 0.00 34.23 3.56
2167 2178 5.240623 CGCTCTGAGTAGGACTAATGATCTT 59.759 44.000 6.53 0.00 0.00 2.40
2256 2268 3.580731 CAGACTTTCCGTTCTTCCTCTC 58.419 50.000 0.00 0.00 0.00 3.20
2267 2279 5.661458 ACTACACATAATCCAGACTTTCCG 58.339 41.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.