Multiple sequence alignment - TraesCS7B01G048500

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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 TraesCS7B01G048500 chr7B 100.000 2255 0 0 1 2255 48448723 48450977 0 4165
1 TraesCS7B01G048500 chr7B 97.928 724 13 2 1 723 48430822 48430100 0 1253
2 TraesCS7B01G048500 chr7B 97.547 530 12 1 724 1252 580865002 580865531 0 905
3 TraesCS7B01G048500 chr7B 97.547 530 11 2 724 1252 708524015 708524543 0 905
4 TraesCS7B01G048500 chr7B 97.358 530 13 1 724 1252 593078946 593078417 0 900
5 TraesCS7B01G048500 chr3B 96.230 1008 38 0 1248 2255 678014400 678015407 0 1652
6 TraesCS7B01G048500 chr3B 96.131 1008 39 0 1248 2255 116900732 116901739 0 1646
7 TraesCS7B01G048500 chr3B 96.858 732 23 0 1 732 597245178 597245909 0 1225
8 TraesCS7B01G048500 chr3B 97.358 530 13 1 724 1252 761382948 761382419 0 900
9 TraesCS7B01G048500 chrUn 96.131 1008 39 0 1248 2255 304156919 304157926 0 1646
10 TraesCS7B01G048500 chrUn 96.131 1008 39 0 1248 2255 308092660 308091653 0 1646
11 TraesCS7B01G048500 chrUn 96.131 1008 39 0 1248 2255 309475025 309476032 0 1646
12 TraesCS7B01G048500 chrUn 96.032 1008 40 0 1248 2255 3675962 3676969 0 1640
13 TraesCS7B01G048500 chrUn 97.547 530 12 1 724 1252 297868352 297867823 0 905
14 TraesCS7B01G048500 chr2B 96.131 1008 39 0 1248 2255 143949227 143950234 0 1646
15 TraesCS7B01G048500 chr2B 97.517 725 17 1 1 724 487405937 487406661 0 1238
16 TraesCS7B01G048500 chr2B 97.510 723 18 0 2 724 13978743 13978021 0 1236
17 TraesCS7B01G048500 chr2B 96.990 731 20 2 1 731 26010051 26010779 0 1227
18 TraesCS7B01G048500 chr2B 98.491 530 7 1 724 1252 411507655 411508184 0 933
19 TraesCS7B01G048500 chr2B 98.302 530 9 0 724 1253 631112849 631112320 0 929
20 TraesCS7B01G048500 chr1B 96.131 1008 39 0 1248 2255 612201626 612202633 0 1646
21 TraesCS7B01G048500 chr1B 97.652 724 17 0 1 724 541258969 541259692 0 1243
22 TraesCS7B01G048500 chr4B 96.032 1008 40 0 1248 2255 237021946 237022953 0 1640
23 TraesCS7B01G048500 chr4A 97.649 723 17 0 1 723 726902809 726902087 0 1242
24 TraesCS7B01G048500 chr5B 97.510 723 18 0 1 723 677955448 677956170 0 1236
25 TraesCS7B01G048500 chr6B 97.507 722 18 0 2 723 132037725 132037004 0 1234
26 TraesCS7B01G048500 chr6B 97.547 530 12 1 724 1252 135854545 135854016 0 905
27 TraesCS7B01G048500 chr3A 97.358 530 13 1 724 1252 489209955 489210484 0 900


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 TraesCS7B01G048500 chr7B 48448723 48450977 2254 False 4165 4165 100.000 1 2255 1 chr7B.!!$F1 2254
1 TraesCS7B01G048500 chr7B 48430100 48430822 722 True 1253 1253 97.928 1 723 1 chr7B.!!$R1 722
2 TraesCS7B01G048500 chr7B 580865002 580865531 529 False 905 905 97.547 724 1252 1 chr7B.!!$F2 528
3 TraesCS7B01G048500 chr7B 708524015 708524543 528 False 905 905 97.547 724 1252 1 chr7B.!!$F3 528
4 TraesCS7B01G048500 chr7B 593078417 593078946 529 True 900 900 97.358 724 1252 1 chr7B.!!$R2 528
5 TraesCS7B01G048500 chr3B 678014400 678015407 1007 False 1652 1652 96.230 1248 2255 1 chr3B.!!$F3 1007
6 TraesCS7B01G048500 chr3B 116900732 116901739 1007 False 1646 1646 96.131 1248 2255 1 chr3B.!!$F1 1007
7 TraesCS7B01G048500 chr3B 597245178 597245909 731 False 1225 1225 96.858 1 732 1 chr3B.!!$F2 731
8 TraesCS7B01G048500 chr3B 761382419 761382948 529 True 900 900 97.358 724 1252 1 chr3B.!!$R1 528
9 TraesCS7B01G048500 chrUn 304156919 304157926 1007 False 1646 1646 96.131 1248 2255 1 chrUn.!!$F2 1007
10 TraesCS7B01G048500 chrUn 308091653 308092660 1007 True 1646 1646 96.131 1248 2255 1 chrUn.!!$R2 1007
11 TraesCS7B01G048500 chrUn 309475025 309476032 1007 False 1646 1646 96.131 1248 2255 1 chrUn.!!$F3 1007
12 TraesCS7B01G048500 chrUn 3675962 3676969 1007 False 1640 1640 96.032 1248 2255 1 chrUn.!!$F1 1007
13 TraesCS7B01G048500 chrUn 297867823 297868352 529 True 905 905 97.547 724 1252 1 chrUn.!!$R1 528
14 TraesCS7B01G048500 chr2B 143949227 143950234 1007 False 1646 1646 96.131 1248 2255 1 chr2B.!!$F2 1007
15 TraesCS7B01G048500 chr2B 487405937 487406661 724 False 1238 1238 97.517 1 724 1 chr2B.!!$F4 723
16 TraesCS7B01G048500 chr2B 13978021 13978743 722 True 1236 1236 97.510 2 724 1 chr2B.!!$R1 722
17 TraesCS7B01G048500 chr2B 26010051 26010779 728 False 1227 1227 96.990 1 731 1 chr2B.!!$F1 730
18 TraesCS7B01G048500 chr2B 411507655 411508184 529 False 933 933 98.491 724 1252 1 chr2B.!!$F3 528
19 TraesCS7B01G048500 chr2B 631112320 631112849 529 True 929 929 98.302 724 1253 1 chr2B.!!$R2 529
20 TraesCS7B01G048500 chr1B 612201626 612202633 1007 False 1646 1646 96.131 1248 2255 1 chr1B.!!$F2 1007
21 TraesCS7B01G048500 chr1B 541258969 541259692 723 False 1243 1243 97.652 1 724 1 chr1B.!!$F1 723
22 TraesCS7B01G048500 chr4B 237021946 237022953 1007 False 1640 1640 96.032 1248 2255 1 chr4B.!!$F1 1007
23 TraesCS7B01G048500 chr4A 726902087 726902809 722 True 1242 1242 97.649 1 723 1 chr4A.!!$R1 722
24 TraesCS7B01G048500 chr5B 677955448 677956170 722 False 1236 1236 97.510 1 723 1 chr5B.!!$F1 722
25 TraesCS7B01G048500 chr6B 132037004 132037725 721 True 1234 1234 97.507 2 723 1 chr6B.!!$R1 721
26 TraesCS7B01G048500 chr6B 135854016 135854545 529 True 905 905 97.547 724 1252 1 chr6B.!!$R2 528
27 TraesCS7B01G048500 chr3A 489209955 489210484 529 False 900 900 97.358 724 1252 1 chr3A.!!$F1 528

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
145 147 0.259065 AGAGCCGGACACTATCCTGA 59.741 55.0 5.05 0.0 46.69 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1923 0.456221 GGAGCAAGCTCGTAGCACTA 59.544 55.0 15.2 0.0 45.56 2.74 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
51 53 2.030371 TGGTAGTGGTGTGACGTTACA 58.970 47.619 9.37 9.37 0.00 2.41
145 147 0.259065 AGAGCCGGACACTATCCTGA 59.741 55.000 5.05 0.00 46.69 3.86
423 425 8.908903 GGATATGTAGATCTCCTACCATTGTAG 58.091 40.741 0.00 0.00 45.60 2.74
452 454 0.396695 TGTAACCCTAGCCCTCTCCG 60.397 60.000 0.00 0.00 0.00 4.63
467 469 4.220163 CCCTCTCCGGTGTCTATATAAACC 59.780 50.000 0.00 0.68 0.00 3.27
548 550 1.480954 GCCTCCTTGATCTCGTGGTAA 59.519 52.381 0.00 0.00 0.00 2.85
703 706 1.232216 GACCCCCTACCCGAGATCA 59.768 63.158 0.00 0.00 0.00 2.92
806 810 9.066892 TCACATTTACTCAAATCTTGCTAGTTT 57.933 29.630 0.00 0.00 31.82 2.66
1234 1532 1.795768 TGATCGTGCACTTCCAACTC 58.204 50.000 16.19 1.75 0.00 3.01
1243 1541 2.418197 GCACTTCCAACTCACGCCTATA 60.418 50.000 0.00 0.00 0.00 1.31
1253 1551 3.707611 ACTCACGCCTATAACCAACCATA 59.292 43.478 0.00 0.00 0.00 2.74
1328 1626 1.270785 TGCTTTCTTGATCTCGGTGCA 60.271 47.619 0.00 0.00 0.00 4.57
1334 1632 2.153547 TTGATCTCGGTGCACTGCGA 62.154 55.000 20.00 20.00 0.00 5.10
1416 1714 3.503800 AGAAGGGAACACTTTACCACC 57.496 47.619 0.00 0.00 38.39 4.61
1421 1719 4.755437 AGGGAACACTTTACCACCTAGTA 58.245 43.478 0.00 0.00 38.39 1.82
1425 1723 7.458806 AGGGAACACTTTACCACCTAGTAAATA 59.541 37.037 0.00 0.00 38.39 1.40
1647 1945 2.161486 GCTACGAGCTTGCTCCACG 61.161 63.158 15.87 8.55 38.45 4.94
1648 1946 1.213013 CTACGAGCTTGCTCCACGT 59.787 57.895 15.87 13.45 40.23 4.49
1673 1971 0.176219 TGGAAGCGGGTAACATACGG 59.824 55.000 0.00 0.00 39.74 4.02
1676 1974 0.179092 AAGCGGGTAACATACGGAGC 60.179 55.000 0.00 0.00 39.74 4.70
1705 2003 4.565652 GCTTGTCCCAGTCCTTTATCTTCA 60.566 45.833 0.00 0.00 0.00 3.02
1950 2248 5.423610 GCATAAGCTAGAGATCCTTATCCCA 59.576 44.000 0.00 0.00 37.91 4.37
2004 2302 2.741878 TACCCCAAGCTCTCACCCGT 62.742 60.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 0.796312 CTGCTGACGTATTTTGCGGT 59.204 50.000 0.00 0.00 0.00 5.68
104 106 7.209471 TCTGCAAAAATAAATTCCACGTACT 57.791 32.000 0.00 0.00 0.00 2.73
222 224 1.734465 GAACCAGGCTTCAATGACGAG 59.266 52.381 0.00 0.00 0.00 4.18
423 425 1.134560 CTAGGGTTACACAGAGTCGGC 59.865 57.143 0.00 0.00 0.00 5.54
452 454 4.020485 AGCCATCCGGTTTATATAGACACC 60.020 45.833 0.00 2.59 33.28 4.16
467 469 2.632996 TCCTATGGACTAAAGCCATCCG 59.367 50.000 0.00 0.00 44.70 4.18
548 550 5.620206 TGATGTGTGTTACAAGAGTGGATT 58.380 37.500 0.00 0.00 43.77 3.01
788 791 4.082125 CCCCAAACTAGCAAGATTTGAGT 58.918 43.478 4.74 0.00 35.73 3.41
1234 1532 5.060506 TGATTATGGTTGGTTATAGGCGTG 58.939 41.667 0.00 0.00 0.00 5.34
1243 1541 3.096092 ACGGCAATGATTATGGTTGGTT 58.904 40.909 0.00 0.00 0.00 3.67
1328 1626 5.675575 GCATTCATTCTTTCTCATTCGCAGT 60.676 40.000 0.00 0.00 0.00 4.40
1334 1632 6.261118 GCTAACGCATTCATTCTTTCTCATT 58.739 36.000 0.00 0.00 35.78 2.57
1416 1714 4.809426 CCTGCTGTTCCGGTTATTTACTAG 59.191 45.833 0.00 0.00 0.00 2.57
1421 1719 1.353022 TCCCTGCTGTTCCGGTTATTT 59.647 47.619 0.00 0.00 0.00 1.40
1425 1723 2.113243 GAGTCCCTGCTGTTCCGGTT 62.113 60.000 0.00 0.00 0.00 4.44
1453 1751 2.094494 AGTACAACAGAGATGTCAGGCG 60.094 50.000 0.00 0.00 32.27 5.52
1532 1830 1.069090 GTTGAGATATGCCCGCCGA 59.931 57.895 0.00 0.00 0.00 5.54
1572 1870 5.346822 ACTTGCTTTTGATAACTACGTACGG 59.653 40.000 21.06 5.00 0.00 4.02
1625 1923 0.456221 GGAGCAAGCTCGTAGCACTA 59.544 55.000 15.20 0.00 45.56 2.74
1647 1945 1.736126 GTTACCCGCTTCCAGCTTTAC 59.264 52.381 0.00 0.00 39.60 2.01
1648 1946 1.348366 TGTTACCCGCTTCCAGCTTTA 59.652 47.619 0.00 0.00 39.60 1.85
1676 1974 1.064906 AGGACTGGGACAAGCATCATG 60.065 52.381 0.00 0.00 38.70 3.07
1950 2248 0.606401 CCTCAACCCGATGTGCTTGT 60.606 55.000 0.00 0.00 0.00 3.16
1979 2277 1.229082 AGAGCTTGGGGTACACCGA 60.229 57.895 10.24 6.83 41.60 4.69


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

AutoCloner maintained by Alex Coulton.