Multiple sequence alignment - TraesCS2A01G288000

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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 TraesCS2A01G288000 chr2A 100.000 3186 0 0 1 3186 493831567 493834752 0.000000e+00 5884
1 TraesCS2A01G288000 chr2B 96.571 3179 81 13 1 3166 434098636 434101799 0.000000e+00 5241
2 TraesCS2A01G288000 chr2D 96.593 2994 62 16 185 3160 365777569 365780540 0.000000e+00 4927
3 TraesCS2A01G288000 chr2D 96.296 81 3 0 1 81 365772649 365772729 1.990000e-27 134


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 TraesCS2A01G288000 chr2A 493831567 493834752 3185 False 5884 5884 100.000 1 3186 1 chr2A.!!$F1 3185
1 TraesCS2A01G288000 chr2B 434098636 434101799 3163 False 5241 5241 96.571 1 3166 1 chr2B.!!$F1 3165
2 TraesCS2A01G288000 chr2D 365777569 365780540 2971 False 4927 4927 96.593 185 3160 1 chr2D.!!$F2 2975

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
69 70 1.180029 TCTGGTGTAACGAGTAGGCC 58.820 55.0 0.00 0.0 43.75 5.19 F
1660 1669 0.669318 CCAAGAAAGCGGCTCGTGTA 60.669 55.0 1.45 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1816 0.955428 GTTGCTGCAATCTGTCGGGA 60.955 55.0 19.11 0.0 0.00 5.14 R
3006 3029 2.175878 AGCGATGACTTCAGCAAACT 57.824 45.0 0.00 0.0 31.58 2.66 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
45 46 1.374631 GCACGTGGAGTCATGAGCA 60.375 57.895 18.88 0.00 43.07 4.26
59 60 4.455533 GTCATGAGCAATGTTCTGGTGTAA 59.544 41.667 0.00 0.00 37.56 2.41
69 70 1.180029 TCTGGTGTAACGAGTAGGCC 58.820 55.000 0.00 0.00 43.75 5.19
84 85 5.360649 AGTAGGCCTTGGAGTTTATCTTC 57.639 43.478 12.58 0.00 0.00 2.87
89 90 3.619038 GCCTTGGAGTTTATCTTCTCACG 59.381 47.826 0.00 0.00 32.93 4.35
124 125 4.322057 AGCCAACCAAATATCTTGACCT 57.678 40.909 0.84 0.00 0.00 3.85
142 143 1.486211 CTGGAGTGGTACCCGAGAAT 58.514 55.000 10.07 0.00 0.00 2.40
143 144 2.662866 CTGGAGTGGTACCCGAGAATA 58.337 52.381 10.07 0.00 0.00 1.75
158 159 4.935205 CCGAGAATACCAAATGTTGAGTGA 59.065 41.667 0.00 0.00 0.00 3.41
162 163 7.206981 AGAATACCAAATGTTGAGTGACTTG 57.793 36.000 0.00 0.00 0.00 3.16
336 337 4.090138 TGAATGAACGCGCAATGTTATT 57.910 36.364 5.73 4.93 0.00 1.40
857 866 2.109181 GGAGCAGCCGTATCACCC 59.891 66.667 0.00 0.00 0.00 4.61
1158 1167 6.375455 AGGAACAAGGTAATCAACAATAGCTG 59.625 38.462 0.00 0.00 30.76 4.24
1273 1282 1.686052 TCGCAGCCATTTGGAAACTTT 59.314 42.857 0.00 0.00 37.39 2.66
1359 1368 7.094118 TGGCGAGCTTAATTTAGTGGTAAAATT 60.094 33.333 0.00 0.00 39.31 1.82
1422 1431 0.838229 CGTGCACGAAGATACGCTAC 59.162 55.000 34.93 0.00 43.02 3.58
1660 1669 0.669318 CCAAGAAAGCGGCTCGTGTA 60.669 55.000 1.45 0.00 0.00 2.90
1969 1984 2.542907 CGCTGTCAACCTGCCGTTT 61.543 57.895 0.00 0.00 34.75 3.60
2053 2068 3.621225 CTCATCCGAGTGAGCCCA 58.379 61.111 4.45 0.00 39.19 5.36
2180 2195 6.071051 TGGGGAGCACAAAAATAATAAAGACC 60.071 38.462 0.00 0.00 0.00 3.85
2355 2370 8.887264 TCCCCAAATTTGTTTATCTAAAGCTA 57.113 30.769 16.73 0.00 0.00 3.32
2425 2442 5.763876 AATGGGTGACTCTTAACTAGCTT 57.236 39.130 0.00 0.00 0.00 3.74
2493 2512 4.767409 GGAGACCTTGTTCCTTGCTTAATT 59.233 41.667 0.00 0.00 0.00 1.40
2501 2520 8.087750 CCTTGTTCCTTGCTTAATTGTTTATCA 58.912 33.333 0.00 0.00 0.00 2.15
2556 2575 9.606631 AAGTCTTAGATGAAAGTACATCCATTC 57.393 33.333 0.00 0.00 45.20 2.67
2643 2662 8.397148 ACTTTAGGAACATTGTTTGCAAAATTG 58.603 29.630 14.67 13.62 38.21 2.32
2654 2673 8.939201 TTGTTTGCAAAATTGAACTCATAGAA 57.061 26.923 14.67 0.00 0.00 2.10
2792 2811 8.616942 CAGCTAATATGACATATAGCTACGTCT 58.383 37.037 23.98 10.59 38.65 4.18
2877 2896 7.416154 ACATGCATCATTTTTCAAACTCAAG 57.584 32.000 0.00 0.00 0.00 3.02
3003 3026 9.962783 CCATGAGTACTGGTACTAATTACTAAC 57.037 37.037 12.61 0.00 45.63 2.34
3004 3027 9.962783 CATGAGTACTGGTACTAATTACTAACC 57.037 37.037 12.61 0.00 45.63 2.85
3005 3028 9.705103 ATGAGTACTGGTACTAATTACTAACCA 57.295 33.333 12.61 8.02 45.63 3.67
3006 3029 9.532494 TGAGTACTGGTACTAATTACTAACCAA 57.468 33.333 12.61 0.00 45.63 3.67
3152 3179 6.163476 ACACGTGCATATCTTCAGTTTCTAA 58.837 36.000 17.22 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.436646 CATGACTCCACGTGCCCC 60.437 66.667 10.91 0.00 0.00 5.80
45 46 4.817517 CCTACTCGTTACACCAGAACATT 58.182 43.478 0.00 0.00 0.00 2.71
59 60 1.349067 AAACTCCAAGGCCTACTCGT 58.651 50.000 5.16 0.00 0.00 4.18
69 70 5.073311 TCCGTGAGAAGATAAACTCCAAG 57.927 43.478 0.00 0.00 32.84 3.61
89 90 6.959639 TTGGTTGGCTTATATTCTCATTCC 57.040 37.500 0.00 0.00 0.00 3.01
101 102 5.652014 CAGGTCAAGATATTTGGTTGGCTTA 59.348 40.000 0.00 0.00 0.00 3.09
142 143 3.568007 GCCAAGTCACTCAACATTTGGTA 59.432 43.478 3.36 0.00 37.85 3.25
143 144 2.362077 GCCAAGTCACTCAACATTTGGT 59.638 45.455 3.36 0.00 37.85 3.67
158 159 4.002906 TGAACTAATCTCAACGCCAAGT 57.997 40.909 0.00 0.00 0.00 3.16
162 163 5.348986 TCTGTATGAACTAATCTCAACGCC 58.651 41.667 0.00 0.00 0.00 5.68
703 712 3.804193 CCTGCCGCCGCTTCTTTC 61.804 66.667 0.00 0.00 35.36 2.62
1041 1050 1.003233 GGGTAGTAGGCTTGTTGCTGT 59.997 52.381 0.00 0.00 42.39 4.40
1273 1282 3.033368 TCGACGTGTTTGGATGATTCA 57.967 42.857 0.00 0.00 0.00 2.57
1315 1324 5.541845 TCGCCACATATTAGGATGAAGAAG 58.458 41.667 0.00 0.00 0.00 2.85
1359 1368 5.717178 ACTTCTCTCCAGAGTTTATACAGCA 59.283 40.000 3.50 0.00 42.60 4.41
1660 1669 1.675641 GTCAAAGGTGCCGAGCCAT 60.676 57.895 0.00 0.00 0.00 4.40
1807 1816 0.955428 GTTGCTGCAATCTGTCGGGA 60.955 55.000 19.11 0.00 0.00 5.14
2180 2195 1.001924 CGATCCACTGATCTCTCACGG 60.002 57.143 0.00 0.00 44.40 4.94
2273 2288 3.586470 ATTGACCAACACTTACCCACA 57.414 42.857 0.00 0.00 0.00 4.17
2398 2415 4.172807 AGTTAAGAGTCACCCATTACCCA 58.827 43.478 0.00 0.00 0.00 4.51
2556 2575 7.280205 GTCTACAATCCAAAGGTATTGGTACTG 59.720 40.741 7.07 5.96 40.40 2.74
2699 2718 3.976793 AATCAGCACACACAAAGTCAG 57.023 42.857 0.00 0.00 0.00 3.51
2792 2811 9.733556 ATGGTTGATATAGTTACACTTGACAAA 57.266 29.630 0.00 0.00 0.00 2.83
3003 3026 2.666619 GCGATGACTTCAGCAAACTTGG 60.667 50.000 0.00 0.00 31.58 3.61
3004 3027 2.225019 AGCGATGACTTCAGCAAACTTG 59.775 45.455 0.00 0.00 31.58 3.16
3005 3028 2.498167 AGCGATGACTTCAGCAAACTT 58.502 42.857 0.00 0.00 31.58 2.66
3006 3029 2.175878 AGCGATGACTTCAGCAAACT 57.824 45.000 0.00 0.00 31.58 2.66


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

AutoCloner maintained by Alex Coulton.