Multiple sequence alignment - TraesCS2A01G133000

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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 TraesCS2A01G133000 chr2A 100.000 3479 0 0 1 3479 80123332 80126810 0 6425
1 TraesCS2A01G133000 chr2A 97.057 3500 80 10 1 3479 685100614 685097117 0 5871
2 TraesCS2A01G133000 chr2A 96.744 3501 88 13 1 3479 284803618 284807114 0 5810
3 TraesCS2A01G133000 chr2A 96.599 3499 90 10 1 3479 572966213 572962724 0 5775
4 TraesCS2A01G133000 chr2A 96.314 3500 105 9 1 3479 716650468 716646972 0 5727
5 TraesCS2A01G133000 chr6A 97.142 3499 74 10 1 3479 158979762 158976270 0 5884
6 TraesCS2A01G133000 chr1A 97.057 3500 77 12 1 3479 70942062 70938568 0 5869
7 TraesCS2A01G133000 chr5A 96.716 3502 90 9 1 3479 34939662 34936163 0 5806
8 TraesCS2A01G133000 chr5A 96.715 3501 90 12 1 3479 465657820 465661317 0 5805
9 TraesCS2A01G133000 chr5A 96.456 3499 100 10 1 3479 541980602 541984096 0 5753
10 TraesCS2A01G133000 chr5A 96.230 1565 38 11 1 1545 141905803 141907366 0 2543
11 TraesCS2A01G133000 chr7A 96.374 3502 98 16 1 3479 245432352 245428857 0 5736
12 TraesCS2A01G133000 chr3A 96.058 3501 114 14 1 3479 554831141 554834639 0 5679


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 TraesCS2A01G133000 chr2A 80123332 80126810 3478 False 6425 6425 100.000 1 3479 1 chr2A.!!$F1 3478
1 TraesCS2A01G133000 chr2A 685097117 685100614 3497 True 5871 5871 97.057 1 3479 1 chr2A.!!$R2 3478
2 TraesCS2A01G133000 chr2A 284803618 284807114 3496 False 5810 5810 96.744 1 3479 1 chr2A.!!$F2 3478
3 TraesCS2A01G133000 chr2A 572962724 572966213 3489 True 5775 5775 96.599 1 3479 1 chr2A.!!$R1 3478
4 TraesCS2A01G133000 chr2A 716646972 716650468 3496 True 5727 5727 96.314 1 3479 1 chr2A.!!$R3 3478
5 TraesCS2A01G133000 chr6A 158976270 158979762 3492 True 5884 5884 97.142 1 3479 1 chr6A.!!$R1 3478
6 TraesCS2A01G133000 chr1A 70938568 70942062 3494 True 5869 5869 97.057 1 3479 1 chr1A.!!$R1 3478
7 TraesCS2A01G133000 chr5A 34936163 34939662 3499 True 5806 5806 96.716 1 3479 1 chr5A.!!$R1 3478
8 TraesCS2A01G133000 chr5A 465657820 465661317 3497 False 5805 5805 96.715 1 3479 1 chr5A.!!$F2 3478
9 TraesCS2A01G133000 chr5A 541980602 541984096 3494 False 5753 5753 96.456 1 3479 1 chr5A.!!$F3 3478
10 TraesCS2A01G133000 chr5A 141905803 141907366 1563 False 2543 2543 96.230 1 1545 1 chr5A.!!$F1 1544
11 TraesCS2A01G133000 chr7A 245428857 245432352 3495 True 5736 5736 96.374 1 3479 1 chr7A.!!$R1 3478
12 TraesCS2A01G133000 chr3A 554831141 554834639 3498 False 5679 5679 96.058 1 3479 1 chr3A.!!$F1 3478

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
349 352 0.035152 ATCAATCAGGCCACTCGCAA 60.035 50.000 5.01 0.0 40.31 4.85 F
963 968 1.077140 TGCACACAAACCTCCAGCA 60.077 52.632 0.00 0.0 0.00 4.41 F
1343 1351 0.372679 CACATCGCAGCAGTCACATC 59.627 55.000 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1196 1.402896 CGCCCTTCATCCTGAGCCTA 61.403 60.000 0.0 0.0 0.00 3.93 R
2446 2476 2.249309 CGCGAAGTTGCAGTGGTG 59.751 61.111 0.0 0.0 34.15 4.17 R
2917 2951 2.367567 TGTCCTCGGCTGAAACTTAGTT 59.632 45.455 0.0 0.0 0.00 2.24 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
349 352 0.035152 ATCAATCAGGCCACTCGCAA 60.035 50.000 5.01 0.00 40.31 4.85
364 367 2.481568 CTCGCAACACTGTGACATCAAT 59.518 45.455 15.86 0.00 37.15 2.57
595 598 9.522804 GAAAAACAATACTTAAACATCCACACA 57.477 29.630 0.00 0.00 0.00 3.72
963 968 1.077140 TGCACACAAACCTCCAGCA 60.077 52.632 0.00 0.00 0.00 4.41
1191 1196 0.753479 AGGCCGACGAGATGATGAGT 60.753 55.000 0.00 0.00 0.00 3.41
1342 1350 1.022982 CCACATCGCAGCAGTCACAT 61.023 55.000 0.00 0.00 0.00 3.21
1343 1351 0.372679 CACATCGCAGCAGTCACATC 59.627 55.000 0.00 0.00 0.00 3.06
1435 1462 8.693120 TGAACTACTATAGTCTATGAAGTGGG 57.307 38.462 9.12 0.97 38.26 4.61
1436 1463 7.230913 TGAACTACTATAGTCTATGAAGTGGGC 59.769 40.741 9.12 1.38 38.26 5.36
1582 1610 9.107177 CTGAACTTGATGAACTAGCATAGATTT 57.893 33.333 0.00 0.00 42.77 2.17
1782 1810 7.428826 AGAAAACTAAACTTGAATCAAGCAGG 58.571 34.615 21.69 12.16 44.43 4.85
1842 1870 2.961741 TGGTGAAGCATTTGGTAAAGCA 59.038 40.909 0.00 0.00 0.00 3.91
2101 2131 5.183140 CGGGAGGAGAAATTGTACACATTTT 59.817 40.000 13.58 7.18 33.65 1.82
2231 2261 6.888632 ACTAGAAAATACTACGACTCCTTGGA 59.111 38.462 0.00 0.00 0.00 3.53
2397 2427 4.836825 AGTCATGGAAGACAATCGACAAT 58.163 39.130 0.00 0.00 40.98 2.71
2446 2476 2.066999 CAGGAGGCTGACCCCTACC 61.067 68.421 0.00 0.00 36.40 3.18
2472 2502 0.796312 GCAACTTCGCGGATGAAGAA 59.204 50.000 6.13 0.00 46.64 2.52
2516 2546 4.901197 TGTTGAACCAGCTACCTTATGA 57.099 40.909 0.00 0.00 0.00 2.15
2616 2646 4.282195 TGTGTCAGGGTTTGAACAAGTTTT 59.718 37.500 0.00 0.00 37.61 2.43
2665 2695 4.783242 CTTATGTCGTCCAACAAGTTTGG 58.217 43.478 0.00 0.00 40.87 3.28
2944 2978 1.522668 TTCAGCCGAGGACAACATTG 58.477 50.000 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
323 326 0.627451 TGGCCTGATTGATCCTGCTT 59.373 50.000 3.32 0.0 0.00 3.91
349 352 6.042143 GGTTTGAAAATTGATGTCACAGTGT 58.958 36.000 0.00 0.0 0.00 3.55
364 367 3.902881 AACAGTGCATGGGTTTGAAAA 57.097 38.095 0.00 0.0 0.00 2.29
595 598 6.173339 ACGTATGGATCTGTGATGTTTTTCT 58.827 36.000 0.00 0.0 0.00 2.52
792 795 2.174969 TCGCCGTTTGCACTTCGTT 61.175 52.632 0.00 0.0 41.33 3.85
963 968 1.130054 TGTGGGCTTTGGAGAGAGCT 61.130 55.000 0.00 0.0 38.89 4.09
1018 1023 2.108514 CGGCATGATGACGCTTGGT 61.109 57.895 8.12 0.0 44.33 3.67
1191 1196 1.402896 CGCCCTTCATCCTGAGCCTA 61.403 60.000 0.00 0.0 0.00 3.93
1342 1350 4.888917 TGGTACAACAGATGAATGAACGA 58.111 39.130 0.00 0.0 31.92 3.85
1343 1351 4.690748 ACTGGTACAACAGATGAATGAACG 59.309 41.667 0.24 0.0 40.97 3.95
1435 1462 6.542852 ACTTGATAAACATGTAATCGTGTGC 58.457 36.000 0.00 0.0 42.20 4.57
1718 1746 5.459505 AGACCTATACCAGTGCTTGATACT 58.540 41.667 0.00 0.0 0.00 2.12
1782 1810 4.348863 ACCAGAGTCAATGATAGATGCC 57.651 45.455 0.00 0.0 0.00 4.40
2101 2131 2.364970 CACCTCCAATGCTGAAACCAAA 59.635 45.455 0.00 0.0 0.00 3.28
2208 2238 6.183360 CGTCCAAGGAGTCGTAGTATTTTCTA 60.183 42.308 0.00 0.0 0.00 2.10
2248 2278 3.071602 CCTTCGTAGAATGGGTGGATGAT 59.928 47.826 0.00 0.0 45.90 2.45
2397 2427 5.129650 TGAAATATCCCAACCTGTCACGATA 59.870 40.000 0.00 0.0 0.00 2.92
2446 2476 2.249309 CGCGAAGTTGCAGTGGTG 59.751 61.111 0.00 0.0 34.15 4.17
2472 2502 4.595762 AACAAATGCAGACTTTCATGCT 57.404 36.364 0.00 0.0 42.98 3.79
2516 2546 6.296026 ACAACAATACTAAGGACACACACAT 58.704 36.000 0.00 0.0 0.00 3.21
2616 2646 7.818997 AACGATGTACTTGATAGACATAGGA 57.181 36.000 0.00 0.0 33.99 2.94
2665 2695 7.283127 TGATGGATGAACAAAATAGGAAGCTAC 59.717 37.037 0.00 0.0 0.00 3.58
2917 2951 2.367567 TGTCCTCGGCTGAAACTTAGTT 59.632 45.455 0.00 0.0 0.00 2.24
3302 3337 9.487790 TGTTTCTTGTGATTTTTCTCTTTTGTT 57.512 25.926 0.00 0.0 0.00 2.83


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

AutoCloner maintained by Alex Coulton.