Multiple sequence alignment - TraesCS1B01G131100

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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 TraesCS1B01G131100 chr1B 100.000 3499 0 0 1 3499 163066963 163063465 0 6462
1 TraesCS1B01G131100 chr1B 96.203 3503 123 9 1 3499 256710706 256714202 0 5723
2 TraesCS1B01G131100 chr4B 95.978 3506 128 10 1 3499 310222159 310218660 0 5681
3 TraesCS1B01G131100 chr4B 95.805 3504 130 14 5 3499 407691758 407688263 0 5640
4 TraesCS1B01G131100 chr4B 95.307 3452 149 11 52 3499 335221428 335224870 0 5465
5 TraesCS1B01G131100 chr7B 95.698 3510 132 15 1 3499 202722426 202718925 0 5627
6 TraesCS1B01G131100 chr5B 95.668 3509 131 16 1 3499 299224937 299221440 0 5618
7 TraesCS1B01G131100 chr5B 95.491 3504 143 12 1 3499 104501012 104497519 0 5581
8 TraesCS1B01G131100 chr2B 95.184 3509 150 14 1 3499 300239857 300236358 0 5526
9 TraesCS1B01G131100 chr1A 94.702 3511 165 15 1 3499 70942062 70938561 0 5433


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 TraesCS1B01G131100 chr1B 163063465 163066963 3498 True 6462 6462 100.000 1 3499 1 chr1B.!!$R1 3498
1 TraesCS1B01G131100 chr1B 256710706 256714202 3496 False 5723 5723 96.203 1 3499 1 chr1B.!!$F1 3498
2 TraesCS1B01G131100 chr4B 310218660 310222159 3499 True 5681 5681 95.978 1 3499 1 chr4B.!!$R1 3498
3 TraesCS1B01G131100 chr4B 407688263 407691758 3495 True 5640 5640 95.805 5 3499 1 chr4B.!!$R2 3494
4 TraesCS1B01G131100 chr4B 335221428 335224870 3442 False 5465 5465 95.307 52 3499 1 chr4B.!!$F1 3447
5 TraesCS1B01G131100 chr7B 202718925 202722426 3501 True 5627 5627 95.698 1 3499 1 chr7B.!!$R1 3498
6 TraesCS1B01G131100 chr5B 299221440 299224937 3497 True 5618 5618 95.668 1 3499 1 chr5B.!!$R2 3498
7 TraesCS1B01G131100 chr5B 104497519 104501012 3493 True 5581 5581 95.491 1 3499 1 chr5B.!!$R1 3498
8 TraesCS1B01G131100 chr2B 300236358 300239857 3499 True 5526 5526 95.184 1 3499 1 chr2B.!!$R1 3498
9 TraesCS1B01G131100 chr1A 70938561 70942062 3501 True 5433 5433 94.702 1 3499 1 chr1A.!!$R1 3498

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
235 238 0.806884 TCCACACCACAACGAACGAC 60.807 55.000 0.14 0.0 0.0 4.34 F
527 534 1.352622 ACAACTCCCTGGGCACTGAA 61.353 55.000 8.22 0.0 0.0 3.02 F
916 928 1.487976 TCCATCTCTGCCTCATTCACC 59.512 52.381 0.00 0.0 0.0 4.02 F
2317 2337 3.618351 AGAAGAAGATGAACATGGCAGG 58.382 45.455 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1139 1152 0.037326 GGTGCAGACGATCTCCAACA 60.037 55.000 0.00 0.00 0.0 3.33 R
2349 2369 1.269883 TGCGTACGTGATGAGGTTGTT 60.270 47.619 17.90 0.00 0.0 2.83 R
2428 2448 6.197168 TCCTGCTCTTTTGAAATATCCCAAT 58.803 36.000 0.00 0.00 0.0 3.16 R
3313 3354 5.403897 TGTGATTTTTCTCTTGTGTCGAC 57.596 39.130 9.11 9.11 0.0 4.20 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
235 238 0.806884 TCCACACCACAACGAACGAC 60.807 55.000 0.14 0.00 0.00 4.34
347 354 1.954362 GATCAGTCAGGCCACTCGCT 61.954 60.000 5.01 0.00 37.74 4.93
440 447 9.463443 AAACATAAGTGCACTAAAAATGAGAAC 57.537 29.630 22.01 0.00 0.00 3.01
517 524 3.018423 AGTTTTGAGCAACAACTCCCT 57.982 42.857 0.00 0.00 38.29 4.20
527 534 1.352622 ACAACTCCCTGGGCACTGAA 61.353 55.000 8.22 0.00 0.00 3.02
678 685 1.880027 GAGACGTGCAAGTGGGATTTT 59.120 47.619 10.87 0.00 0.00 1.82
755 764 2.633967 TGTCTTGGGCGGTTAGTTCTTA 59.366 45.455 0.00 0.00 0.00 2.10
807 817 2.945984 CCACGACGCACTGCAAAT 59.054 55.556 1.11 0.00 0.00 2.32
829 840 1.520666 GACCCCCATGACCACTACG 59.479 63.158 0.00 0.00 0.00 3.51
861 872 1.671054 CGAACCGCCTCCAACACAT 60.671 57.895 0.00 0.00 0.00 3.21
916 928 1.487976 TCCATCTCTGCCTCATTCACC 59.512 52.381 0.00 0.00 0.00 4.02
988 1001 4.335647 CCCAAGCCCACAGTCGCT 62.336 66.667 0.00 0.00 36.74 4.93
1107 1120 4.890088 AGAAGCACGAGTACACCAAAATA 58.110 39.130 0.00 0.00 0.00 1.40
1141 1154 3.805928 TCCACGGCAAGGAGATGT 58.194 55.556 0.00 0.00 0.00 3.06
1218 1231 3.750373 GATGAAGGGCGGCGGCTTA 62.750 63.158 32.30 12.22 39.81 3.09
1372 1385 8.426489 GGTAACCCATACTACTGTTCATTCATA 58.574 37.037 0.00 0.00 34.74 2.15
2311 2331 5.507637 AGGCATGAAGAAGAAGATGAACAT 58.492 37.500 0.00 0.00 0.00 2.71
2317 2337 3.618351 AGAAGAAGATGAACATGGCAGG 58.382 45.455 0.00 0.00 0.00 4.85
2428 2448 4.126437 ACAATCAACAACATCGTGACAGA 58.874 39.130 0.00 0.00 0.00 3.41
2711 2732 5.595952 AGCTTCCTATTTTGTTGATCCATCC 59.404 40.000 0.00 0.00 0.00 3.51
2770 2791 0.179111 GCCACGCAGCACTAGTCATA 60.179 55.000 0.00 0.00 0.00 2.15
3028 3066 2.961062 ACTGCATCAGGAAAAGCAAAGT 59.039 40.909 0.00 0.00 36.44 2.66
3033 3071 5.010922 TGCATCAGGAAAAGCAAAGTAACAT 59.989 36.000 0.00 0.00 33.48 2.71
3047 3085 9.426837 AGCAAAGTAACATTAGTACGTATTTCA 57.573 29.630 0.00 0.00 0.00 2.69
3273 3313 4.162509 GCCTAGAGAAGAACCACAACCTAT 59.837 45.833 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 238 7.201911 GGGGTTTGAGATTATTTTATGACCAGG 60.202 40.741 0.00 0.00 0.00 4.45
347 354 6.272318 GTTTGAAATTTGATGTCACAGTGGA 58.728 36.000 0.00 0.00 0.00 4.02
608 615 4.018490 TGTTTAGGTGACGTATGGCTCTA 58.982 43.478 0.00 0.00 0.00 2.43
678 685 4.921515 GTCAAGTTGTACTTACGATCTGCA 59.078 41.667 2.11 0.00 36.03 4.41
728 737 1.408969 AACCGCCCAAGACAAATGTT 58.591 45.000 0.00 0.00 0.00 2.71
729 738 2.159382 CTAACCGCCCAAGACAAATGT 58.841 47.619 0.00 0.00 0.00 2.71
742 751 1.338389 TGGCCTGTAAGAACTAACCGC 60.338 52.381 3.32 0.00 34.07 5.68
861 872 2.432456 GCAGTGCATCGACGGTGA 60.432 61.111 13.40 0.00 0.00 4.02
916 928 1.959085 AAGCAGCAATGGTGGTTCG 59.041 52.632 21.95 0.00 46.33 3.95
988 1001 4.161295 CGCCATCGCCTTCCTCCA 62.161 66.667 0.00 0.00 0.00 3.86
1025 1038 0.904649 TGAAGTCTCGCCATGGTGAT 59.095 50.000 27.68 13.61 33.90 3.06
1082 1095 0.240411 GGTGTACTCGTGCTTCTCGT 59.760 55.000 0.00 0.00 0.00 4.18
1139 1152 0.037326 GGTGCAGACGATCTCCAACA 60.037 55.000 0.00 0.00 0.00 3.33
1141 1154 0.247460 CTGGTGCAGACGATCTCCAA 59.753 55.000 0.00 0.00 32.44 3.53
1293 1306 0.603569 AGAGTTCCTCGACGCACAAT 59.396 50.000 0.00 0.00 35.36 2.71
1372 1385 8.413309 TTTAGTGACTAGTACTGGTACAACAT 57.587 34.615 12.36 5.23 38.70 2.71
1731 1744 8.367911 CCTATACCAGTGCTTGATACATCTTTA 58.632 37.037 0.00 0.00 0.00 1.85
1801 1814 5.426689 ACCAGAGTCAATGATACATGTGT 57.573 39.130 9.11 0.10 0.00 3.72
2311 2331 2.126596 CACAGTTTGTGGCCTGCCA 61.127 57.895 6.80 6.80 44.27 4.92
2349 2369 1.269883 TGCGTACGTGATGAGGTTGTT 60.270 47.619 17.90 0.00 0.00 2.83
2428 2448 6.197168 TCCTGCTCTTTTGAAATATCCCAAT 58.803 36.000 0.00 0.00 0.00 3.16
2711 2732 7.321745 ACTTCAACCTACTTCAACTTCAAAG 57.678 36.000 0.00 0.00 0.00 2.77
3033 3071 9.112725 TGCTAGTGACTATGAAATACGTACTAA 57.887 33.333 0.00 0.00 0.00 2.24
3047 3085 4.522405 CAGTCCTAGCATGCTAGTGACTAT 59.478 45.833 41.23 31.33 44.96 2.12
3088 3127 5.407084 TGTAGAATGAACATACCGTGTGTTG 59.593 40.000 17.31 0.00 41.14 3.33
3313 3354 5.403897 TGTGATTTTTCTCTTGTGTCGAC 57.596 39.130 9.11 9.11 0.00 4.20
3320 3361 8.375465 GTTGTGTTTCTTGTGATTTTTCTCTTG 58.625 33.333 0.00 0.00 0.00 3.02
3389 3431 9.495754 GATTTCAATTGTGCTAGTACTTTGATC 57.504 33.333 21.19 15.99 0.00 2.92


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

AutoCloner maintained by Alex Coulton.