Multiple sequence alignment - TraesCS1A01G160400

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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 TraesCS1A01G160400 chr1A 100.000 2110 0 0 551 2660 287690564 287688455 0.000000e+00 3897
1 TraesCS1A01G160400 chr1A 100.000 175 0 0 1 175 287691114 287690940 9.180000e-85 324
2 TraesCS1A01G160400 chr1B 97.158 2111 49 4 552 2660 317583323 317585424 0.000000e+00 3555
3 TraesCS1A01G160400 chr1D 97.667 2057 42 3 604 2660 222019746 222017696 0.000000e+00 3528
4 TraesCS1A01G160400 chr1D 93.064 173 9 2 3 175 222020533 222020364 1.580000e-62 250


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 TraesCS1A01G160400 chr1A 287688455 287691114 2659 True 2110.5 3897 100.0000 1 2660 2 chr1A.!!$R1 2659
1 TraesCS1A01G160400 chr1B 317583323 317585424 2101 False 3555.0 3555 97.1580 552 2660 1 chr1B.!!$F1 2108
2 TraesCS1A01G160400 chr1D 222017696 222020533 2837 True 1889.0 3528 95.3655 3 2660 2 chr1D.!!$R1 2657

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
849 1266 2.41129 CTCCTCTCCGCGCTTCTC 59.589 66.667 5.56 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2601 3020 1.202818 ACAGGCTGGAGGTTTGTCTTC 60.203 52.381 20.34 0.0 0.0 2.87 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
20 21 2.709213 TGTGATTCATGCACGGAATGA 58.291 42.857 17.47 8.67 39.07 2.57
62 63 7.545615 GTCAAAACATCTGAAATTCATAACCCC 59.454 37.037 0.00 0.00 0.00 4.95
63 64 7.234371 TCAAAACATCTGAAATTCATAACCCCA 59.766 33.333 0.00 0.00 0.00 4.96
70 71 3.737559 AATTCATAACCCCACTGCTCA 57.262 42.857 0.00 0.00 0.00 4.26
849 1266 2.411290 CTCCTCTCCGCGCTTCTC 59.589 66.667 5.56 0.00 0.00 2.87
996 1413 3.446570 GCCCGCAAGCTGCTCAAT 61.447 61.111 1.00 0.00 42.25 2.57
1140 1557 0.694771 ATGAGAACAAGCTGGAGCCA 59.305 50.000 0.00 0.00 43.38 4.75
1143 1560 1.268079 GAGAACAAGCTGGAGCCAAAC 59.732 52.381 0.00 0.00 43.38 2.93
1416 1833 4.023963 GTCCTGCTGTTTAAGAGTTTGGTC 60.024 45.833 0.00 0.00 0.00 4.02
1521 1938 1.609841 GGTTTAGTCGAGGGGTTGGTG 60.610 57.143 0.00 0.00 0.00 4.17
1841 2258 4.039730 TCTCTATAAGGCAGAATGGTCAGC 59.960 45.833 0.00 0.00 35.86 4.26
1867 2284 7.428826 GCCATTTCATAATCCCTTTTCTGTAG 58.571 38.462 0.00 0.00 0.00 2.74
1937 2354 4.469657 ACATTTGTTGAAGTGCTAAGGGA 58.530 39.130 0.00 0.00 0.00 4.20
1983 2401 5.721876 TCACTGTAACCGTTTGTTTAGTG 57.278 39.130 12.22 12.22 44.22 2.74
2040 2458 0.514691 GCCTCAGTTGTTCTGCTTCG 59.485 55.000 0.00 0.00 43.32 3.79
2356 2775 3.735746 GCCATGTAAAGCTTGTTTGTGAC 59.264 43.478 0.00 0.00 0.00 3.67
2365 2784 4.469657 AGCTTGTTTGTGACCTTTCCATA 58.530 39.130 0.00 0.00 0.00 2.74
2424 2843 1.940613 GTTAATGCCCCGAACTAGCAG 59.059 52.381 0.00 0.00 40.40 4.24
2536 2955 4.526650 TCCAGCACATAGAAGACTGTGTTA 59.473 41.667 4.78 0.00 43.93 2.41
2601 3020 5.947228 TTGAGTTTATCTGGCTCAAGTTG 57.053 39.130 0.00 0.00 42.24 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.709213 TCATTCCGTGCATGAATCACA 58.291 42.857 7.72 0.00 34.27 3.58
1 2 3.763097 TTCATTCCGTGCATGAATCAC 57.237 42.857 7.72 0.00 36.03 3.06
7 8 0.801872 TCCGTTTCATTCCGTGCATG 59.198 50.000 0.00 0.00 0.00 4.06
12 13 1.636988 GACGATCCGTTTCATTCCGT 58.363 50.000 0.00 0.00 41.37 4.69
15 16 0.300789 GCCGACGATCCGTTTCATTC 59.699 55.000 0.00 0.00 41.37 2.67
20 21 1.445582 GACAGCCGACGATCCGTTT 60.446 57.895 0.00 0.00 41.37 3.60
62 63 5.621228 GTCGTTGTTTTAAATCTGAGCAGTG 59.379 40.000 0.00 0.00 0.00 3.66
63 64 5.558273 CGTCGTTGTTTTAAATCTGAGCAGT 60.558 40.000 0.00 0.00 0.00 4.40
70 71 8.029642 AGATTGATCGTCGTTGTTTTAAATCT 57.970 30.769 0.00 0.00 0.00 2.40
624 1041 1.682684 GGCGAGGGAGAAGAGGTCA 60.683 63.158 0.00 0.00 0.00 4.02
996 1413 6.723298 TTAAACTTCTTCTTGGCCATTTCA 57.277 33.333 6.09 0.00 0.00 2.69
1416 1833 2.977914 TCATCAAGCCTTTCCTTCTCG 58.022 47.619 0.00 0.00 0.00 4.04
1521 1938 1.613630 TGCAGACCTCCCTCCCTTC 60.614 63.158 0.00 0.00 0.00 3.46
1841 2258 5.163519 ACAGAAAAGGGATTATGAAATGGCG 60.164 40.000 0.00 0.00 0.00 5.69
1867 2284 4.460731 AGGCAACAAAATAGAAGAAGCTCC 59.539 41.667 0.00 0.00 41.41 4.70
2075 2493 4.754618 TGTACAAGTGCATGACCAAACTAG 59.245 41.667 0.00 0.00 0.00 2.57
2083 2501 5.605564 TGTACAATGTACAAGTGCATGAC 57.394 39.130 22.36 6.61 36.07 3.06
2331 2750 2.704725 AACAAGCTTTACATGGCACG 57.295 45.000 0.00 0.00 0.00 5.34
2424 2843 2.165030 CCAGGCATCACATTTGAAGGAC 59.835 50.000 0.00 0.00 34.61 3.85
2536 2955 3.264193 TGAACTATGGGAATGTGAGCAGT 59.736 43.478 0.00 0.00 0.00 4.40
2601 3020 1.202818 ACAGGCTGGAGGTTTGTCTTC 60.203 52.381 20.34 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.