Multiple sequence alignment - TraesCS1B01G031300

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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 TraesCS1B01G031300 chr1B 100.000 4331 0 0 1 4331 15364358 15360028 0.000 7998.0
1 TraesCS1B01G031300 chr1B 98.285 4316 61 3 25 4331 40549232 40553543 0.000 7548.0
2 TraesCS1B01G031300 chr6A 98.679 4316 43 4 25 4331 116294582 116290272 0.000 7642.0
3 TraesCS1B01G031300 chr6A 98.309 4317 61 3 24 4331 479920804 479925117 0.000 7557.0
4 TraesCS1B01G031300 chr6A 97.962 4319 76 4 25 4331 295085854 295090172 0.000 7478.0
5 TraesCS1B01G031300 chr6A 98.278 3543 52 2 25 3558 114364544 114368086 0.000 6196.0
6 TraesCS1B01G031300 chr6A 98.399 2061 25 1 2279 4331 398836050 398838110 0.000 3616.0
7 TraesCS1B01G031300 chr2A 98.610 4316 47 3 25 4331 8431580 8435891 0.000 7625.0
8 TraesCS1B01G031300 chr7A 98.379 4318 58 4 25 4331 600045047 600040731 0.000 7576.0
9 TraesCS1B01G031300 chr5A 98.262 4316 65 3 25 4331 118892991 118888677 0.000 7546.0
10 TraesCS1B01G031300 chr4B 98.263 4317 64 3 24 4331 5205170 5209484 0.000 7546.0
11 TraesCS1B01G031300 chr6B 98.239 4316 65 3 25 4331 389198 384885 0.000 7539.0
12 TraesCS1B01G031300 chr6B 100.000 29 0 0 2 30 76264542 76264514 0.002 54.7
13 TraesCS1B01G031300 chr7B 98.194 4320 63 5 24 4331 293640645 293644961 0.000 7531.0
14 TraesCS1B01G031300 chr7B 98.101 4317 72 3 24 4331 716509665 716513980 0.000 7509.0
15 TraesCS1B01G031300 chr1A 94.094 4318 244 7 23 4331 112988321 112984006 0.000 6551.0
16 TraesCS1B01G031300 chr4A 89.967 1495 141 9 2844 4331 270450603 270449111 0.000 1921.0
17 TraesCS1B01G031300 chrUn 94.630 987 49 2 3345 4331 82816130 82815148 0.000 1526.0
18 TraesCS1B01G031300 chr7D 100.000 29 0 0 2 30 566924864 566924836 0.002 54.7
19 TraesCS1B01G031300 chr3B 100.000 29 0 0 2 30 769849837 769849809 0.002 54.7
20 TraesCS1B01G031300 chr2D 100.000 29 0 0 2 30 638541944 638541972 0.002 54.7


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 TraesCS1B01G031300 chr1B 15360028 15364358 4330 True 7998 7998 100.000 1 4331 1 chr1B.!!$R1 4330
1 TraesCS1B01G031300 chr1B 40549232 40553543 4311 False 7548 7548 98.285 25 4331 1 chr1B.!!$F1 4306
2 TraesCS1B01G031300 chr6A 116290272 116294582 4310 True 7642 7642 98.679 25 4331 1 chr6A.!!$R1 4306
3 TraesCS1B01G031300 chr6A 479920804 479925117 4313 False 7557 7557 98.309 24 4331 1 chr6A.!!$F4 4307
4 TraesCS1B01G031300 chr6A 295085854 295090172 4318 False 7478 7478 97.962 25 4331 1 chr6A.!!$F2 4306
5 TraesCS1B01G031300 chr6A 114364544 114368086 3542 False 6196 6196 98.278 25 3558 1 chr6A.!!$F1 3533
6 TraesCS1B01G031300 chr6A 398836050 398838110 2060 False 3616 3616 98.399 2279 4331 1 chr6A.!!$F3 2052
7 TraesCS1B01G031300 chr2A 8431580 8435891 4311 False 7625 7625 98.610 25 4331 1 chr2A.!!$F1 4306
8 TraesCS1B01G031300 chr7A 600040731 600045047 4316 True 7576 7576 98.379 25 4331 1 chr7A.!!$R1 4306
9 TraesCS1B01G031300 chr5A 118888677 118892991 4314 True 7546 7546 98.262 25 4331 1 chr5A.!!$R1 4306
10 TraesCS1B01G031300 chr4B 5205170 5209484 4314 False 7546 7546 98.263 24 4331 1 chr4B.!!$F1 4307
11 TraesCS1B01G031300 chr6B 384885 389198 4313 True 7539 7539 98.239 25 4331 1 chr6B.!!$R1 4306
12 TraesCS1B01G031300 chr7B 293640645 293644961 4316 False 7531 7531 98.194 24 4331 1 chr7B.!!$F1 4307
13 TraesCS1B01G031300 chr7B 716509665 716513980 4315 False 7509 7509 98.101 24 4331 1 chr7B.!!$F2 4307
14 TraesCS1B01G031300 chr1A 112984006 112988321 4315 True 6551 6551 94.094 23 4331 1 chr1A.!!$R1 4308
15 TraesCS1B01G031300 chr4A 270449111 270450603 1492 True 1921 1921 89.967 2844 4331 1 chr4A.!!$R1 1487
16 TraesCS1B01G031300 chrUn 82815148 82816130 982 True 1526 1526 94.630 3345 4331 1 chrUn.!!$R1 986

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
646 649 2.256117 ACCTTTGCGCTCTAGTTGTT 57.744 45.0 9.73 0.0 0.0 2.83 F
1388 1391 0.321122 CCAGAAGAGGGTGAGTGTGC 60.321 60.0 0.00 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2375 2.844122 TCATCATCATCGTCGTCGTT 57.156 45.0 1.33 0.0 38.33 3.85 R
3378 3384 0.970937 CAGTCGACCCTAGCCTTGGA 60.971 60.0 13.01 0.0 0.00 3.53 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
205 206 8.960591 GGATTATGAATGTATGGATTACAAGGG 58.039 37.037 0.00 0.00 43.84 3.95
206 207 9.520515 GATTATGAATGTATGGATTACAAGGGT 57.479 33.333 0.00 0.00 43.84 4.34
646 649 2.256117 ACCTTTGCGCTCTAGTTGTT 57.744 45.000 9.73 0.00 0.00 2.83
1066 1069 1.360852 TCTCCCTCTGCTCTCTTCCTT 59.639 52.381 0.00 0.00 0.00 3.36
1388 1391 0.321122 CCAGAAGAGGGTGAGTGTGC 60.321 60.000 0.00 0.00 0.00 4.57
2232 2235 1.144936 GCGACTGCTAGGCCTTCAT 59.855 57.895 12.58 0.08 38.39 2.57
2372 2375 1.459348 TCGGATGCTGCAGGGGATA 60.459 57.895 17.12 0.00 0.00 2.59
2406 2412 5.374071 TGATGATGATGAAGGTGATGAAGG 58.626 41.667 0.00 0.00 0.00 3.46
3937 3960 5.242171 TGCTTGTTTCAACATCTGATCATGT 59.758 36.000 0.00 0.00 38.95 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.080705 CGACAGTGAAGACGGGGAC 60.081 63.158 0.00 0.00 0.00 4.46
11 12 1.529948 ACGACAGTGAAGACGGGGA 60.530 57.895 0.00 0.00 0.00 4.81
12 13 3.048602 ACGACAGTGAAGACGGGG 58.951 61.111 0.00 0.00 0.00 5.73
71 72 2.091055 TCTCCATAGCTAGGACCTTGCT 60.091 50.000 29.31 29.31 43.90 3.91
205 206 0.890996 CACAGGCAGAAGGGTTGGAC 60.891 60.000 0.00 0.00 0.00 4.02
206 207 1.455849 CACAGGCAGAAGGGTTGGA 59.544 57.895 0.00 0.00 0.00 3.53
646 649 3.401033 TTCTTTGATCCAGAACAGCGA 57.599 42.857 1.18 0.00 0.00 4.93
1066 1069 4.383861 CAGGCACGCTGAGCAGGA 62.384 66.667 4.88 0.00 0.00 3.86
1133 1136 2.970639 CCGCCGTCTTCTCCTTGA 59.029 61.111 0.00 0.00 0.00 3.02
1178 1181 1.113517 CCCCTTCGCCTTCTCCGATA 61.114 60.000 0.00 0.00 34.35 2.92
1388 1391 2.513204 CATGAGTGGCCAGGAGCG 60.513 66.667 5.11 0.00 45.17 5.03
2372 2375 2.844122 TCATCATCATCGTCGTCGTT 57.156 45.000 1.33 0.00 38.33 3.85
2800 2806 1.522668 CACCTGGATTCGAAGTTGCA 58.477 50.000 3.35 0.00 0.00 4.08
2978 2984 1.875813 GCTGACGCATCCTGAGACG 60.876 63.158 0.00 0.00 35.78 4.18
3378 3384 0.970937 CAGTCGACCCTAGCCTTGGA 60.971 60.000 13.01 0.00 0.00 3.53
3604 3626 2.192175 CGTGCCCCCACTAATCCC 59.808 66.667 0.00 0.00 39.86 3.85
3852 3875 1.002544 CAGTCTCCTCCTTCGCCTTTT 59.997 52.381 0.00 0.00 0.00 2.27
3937 3960 4.425180 TTACCTTACCTGCAAGACACAA 57.575 40.909 0.00 0.00 34.07 3.33


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

AutoCloner maintained by Alex Coulton.