Multiple sequence alignment - TraesCS4A01G111000

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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 TraesCS4A01G111000 chr4A 100.000 4205 0 0 1 4205 136232412 136236616 0.000000e+00 7766
1 TraesCS4A01G111000 chr4A 92.593 135 10 0 4037 4171 136235970 136236104 1.190000e-45 195
2 TraesCS4A01G111000 chr4A 92.593 135 10 0 3559 3693 136236448 136236582 1.190000e-45 195
3 TraesCS4A01G111000 chr4B 96.880 4231 100 13 1 4205 416167134 416162910 0.000000e+00 7053
4 TraesCS4A01G111000 chr4B 91.045 134 12 0 4038 4171 416163566 416163433 9.290000e-42 182
5 TraesCS4A01G111000 chr4D 96.848 4220 111 12 1 4205 337074711 337070499 0.000000e+00 7036
6 TraesCS4A01G111000 chr4D 91.852 135 11 0 4037 4171 337071145 337071011 5.550000e-44 189


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 TraesCS4A01G111000 chr4A 136232412 136236616 4204 False 2718.666667 7766 95.0620 1 4205 3 chr4A.!!$F1 4204
1 TraesCS4A01G111000 chr4B 416162910 416167134 4224 True 3617.500000 7053 93.9625 1 4205 2 chr4B.!!$R1 4204
2 TraesCS4A01G111000 chr4D 337070499 337074711 4212 True 3612.500000 7036 94.3500 1 4205 2 chr4D.!!$R1 4204

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
208 209 4.816925 GGTGAGGAATAGGATTGTTACAGC 59.183 45.833 0.00 0.00 0.00 4.40 F
1257 1265 4.597004 ACAATGATGATGTGAAGGAAGCT 58.403 39.130 0.00 0.00 0.00 3.74 F
1442 1450 0.983378 CCACCTCCCCTACCTTCCAG 60.983 65.000 0.00 0.00 0.00 3.86 F
2475 2485 1.349259 CTTTGAAGCGCATGCAAGCC 61.349 55.000 19.57 4.36 46.23 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1274 1.806542 CTGTAACATGCCGAGCTGTTT 59.193 47.619 0.0 2.53 36.92 2.83 R
2271 2281 3.130734 AGTTCCCCATCTAGCCACTTA 57.869 47.619 0.0 0.00 0.00 2.24 R
2613 2623 4.530553 TCCTTGTATCTTCCACTTGCACTA 59.469 41.667 0.0 0.00 0.00 2.74 R
3936 3957 1.102978 GGATTGTGGGAAATGTCGGG 58.897 55.000 0.0 0.00 0.00 5.14 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
208 209 4.816925 GGTGAGGAATAGGATTGTTACAGC 59.183 45.833 0.00 0.00 0.00 4.40
279 280 7.551035 AGATAAACACATTCAGATCTGCTTC 57.449 36.000 18.36 1.14 0.00 3.86
280 281 6.541641 AGATAAACACATTCAGATCTGCTTCC 59.458 38.462 18.36 0.00 0.00 3.46
412 413 5.057149 TCTGAGTTCCTTTTACACAGCTTC 58.943 41.667 0.00 0.00 35.18 3.86
470 472 7.170658 TGTCACAACTTCACAAAAAGGAAAAAG 59.829 33.333 0.00 0.00 0.00 2.27
471 473 6.147000 TCACAACTTCACAAAAAGGAAAAAGC 59.853 34.615 0.00 0.00 0.00 3.51
486 489 5.366477 AGGAAAAAGCCCAATCAGAAGAAAA 59.634 36.000 0.00 0.00 0.00 2.29
1257 1265 4.597004 ACAATGATGATGTGAAGGAAGCT 58.403 39.130 0.00 0.00 0.00 3.74
1266 1274 5.840693 TGATGTGAAGGAAGCTATGGATCTA 59.159 40.000 0.00 0.00 0.00 1.98
1314 1322 3.008049 AGCAATTTTCTAGGACACCGTCT 59.992 43.478 0.00 0.00 32.47 4.18
1442 1450 0.983378 CCACCTCCCCTACCTTCCAG 60.983 65.000 0.00 0.00 0.00 3.86
1802 1810 2.206750 TGACAGTTACCAGTTCGTTGC 58.793 47.619 0.00 0.00 0.00 4.17
1968 1976 2.477189 GCATCAAAAAGCAATGCCATGC 60.477 45.455 0.00 3.08 46.78 4.06
2143 2153 8.720562 CATTAATTTCCTCACCAATCCAAAAAC 58.279 33.333 0.00 0.00 0.00 2.43
2271 2281 3.214328 AGCCGATGTTGAAGAGTTTGTT 58.786 40.909 0.00 0.00 0.00 2.83
2475 2485 1.349259 CTTTGAAGCGCATGCAAGCC 61.349 55.000 19.57 4.36 46.23 4.35
2524 2534 4.946772 TGCATGCATTTAGTAAGGCTGTTA 59.053 37.500 18.46 0.00 41.44 2.41
2850 2867 7.172703 CCCACTACCCTTTTAGCTATAAATTCG 59.827 40.741 0.00 0.00 31.07 3.34
3467 3484 4.871933 AAAATTTCATTCGAGGCTGGTT 57.128 36.364 0.00 0.00 0.00 3.67
3706 3724 7.308435 GCTGTAAATGCTCAAAAACTAGATGT 58.692 34.615 0.00 0.00 0.00 3.06
3723 3741 5.021033 AGATGTCTGCTCCAAGTATTCAG 57.979 43.478 0.00 0.00 0.00 3.02
3859 3880 2.117941 GAGGGTGTTCAAGTGCACGC 62.118 60.000 12.01 0.00 45.17 5.34
3873 3894 1.002576 TGCACGCTGAATCAACAACAG 60.003 47.619 0.00 0.00 35.14 3.16
3896 3917 4.389374 CCTCTACTTCTCAGGAGCTCTAG 58.611 52.174 14.64 9.12 29.53 2.43
3936 3957 2.420058 ACCACCTAAGCACCATAAGC 57.580 50.000 0.00 0.00 0.00 3.09
4103 4133 5.065914 AGATTCACAACTGTTAGTGCACAT 58.934 37.500 21.04 6.83 35.76 3.21
4146 4176 4.843220 AGAATTTGTCTGAGGTTTGCTG 57.157 40.909 0.00 0.00 34.29 4.41
4184 4214 6.972901 GCTGTAAATGCTTCCCATTAAGTAAC 59.027 38.462 0.00 0.00 43.22 2.50
4198 4228 6.878389 CCATTAAGTAACAATTGCCAAACCAT 59.122 34.615 5.05 0.00 0.00 3.55
4200 4230 9.598517 CATTAAGTAACAATTGCCAAACCATAT 57.401 29.630 5.05 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 209 1.902508 TCCTTGGAACTGTAGCTCCTG 59.097 52.381 0.00 0.00 31.72 3.86
280 281 0.251519 AGCTGAGCAAAAGAAGGGGG 60.252 55.000 7.39 0.00 0.00 5.40
412 413 4.456911 TGAATACAAGCTTTCTTCTGCCTG 59.543 41.667 0.00 0.00 0.00 4.85
470 472 3.243839 TGCTTGTTTTCTTCTGATTGGGC 60.244 43.478 0.00 0.00 0.00 5.36
471 473 4.589216 TGCTTGTTTTCTTCTGATTGGG 57.411 40.909 0.00 0.00 0.00 4.12
486 489 5.733620 ATGTCATTTTCCTTCATGCTTGT 57.266 34.783 0.00 0.00 0.00 3.16
515 518 8.432805 AGGTTTTTGATCACTCTTCTTTCTCTA 58.567 33.333 0.00 0.00 0.00 2.43
952 957 6.669631 TCTCTCTGTATGGTGGTACTGATTA 58.330 40.000 0.00 0.00 33.78 1.75
1158 1166 5.007136 CGGCTTCTTCCACATTATCTTTCTC 59.993 44.000 0.00 0.00 0.00 2.87
1257 1265 2.698274 TGCCGAGCTGTTTAGATCCATA 59.302 45.455 0.00 0.00 35.96 2.74
1266 1274 1.806542 CTGTAACATGCCGAGCTGTTT 59.193 47.619 0.00 2.53 36.92 2.83
1314 1322 2.886523 CCTTGGTGCTCTTGATTTCACA 59.113 45.455 0.00 0.00 0.00 3.58
1442 1450 3.055094 TCCCTTGGTGCTCTTCAGTAATC 60.055 47.826 0.00 0.00 0.00 1.75
1669 1677 4.702131 AGGAATTGGCAGCTAAGTAAACAG 59.298 41.667 0.00 0.00 0.00 3.16
1942 1950 4.632251 TGGCATTGCTTTTTGATGCATAAG 59.368 37.500 8.82 0.15 46.01 1.73
1968 1976 3.366724 TGTCGCATGCTCTTAAACTAACG 59.633 43.478 17.13 0.00 0.00 3.18
2112 2122 8.501904 TGGATTGGTGAGGAAATTAATGATCTA 58.498 33.333 0.00 0.00 0.00 1.98
2119 2129 7.796054 TGTTTTTGGATTGGTGAGGAAATTAA 58.204 30.769 0.00 0.00 0.00 1.40
2143 2153 6.071447 TGTTGGAACACAATCATAAGGGAATG 60.071 38.462 0.00 0.00 41.95 2.67
2271 2281 3.130734 AGTTCCCCATCTAGCCACTTA 57.869 47.619 0.00 0.00 0.00 2.24
2475 2485 5.366460 TCGTCTACTCACTTATCCTGTAGG 58.634 45.833 0.00 0.00 33.51 3.18
2524 2534 9.248291 GTCATATTGTTGAAAGTTTGACAATGT 57.752 29.630 23.96 18.86 41.37 2.71
2613 2623 4.530553 TCCTTGTATCTTCCACTTGCACTA 59.469 41.667 0.00 0.00 0.00 2.74
2747 2763 7.321271 CGAGTTTGTAAAATGCACTTAACTCTG 59.679 37.037 15.41 8.30 36.81 3.35
2749 2765 7.130269 ACGAGTTTGTAAAATGCACTTAACTC 58.870 34.615 9.99 9.99 36.28 3.01
2965 2982 6.866010 TCCTCATCATTTACAAATGGATCG 57.134 37.500 13.30 2.47 44.51 3.69
3251 3268 5.124776 CCTCGGCAAAACTTAATTATGTCCA 59.875 40.000 4.61 0.00 0.00 4.02
3410 3427 9.893305 CCAAAAGGTGTACTTAAATTAAGAGTG 57.107 33.333 18.55 0.00 38.85 3.51
3457 3474 6.674066 TGTTTTCTTTTATTAACCAGCCTCG 58.326 36.000 0.00 0.00 0.00 4.63
3467 3484 7.289084 AGGGTTGGCTCTTGTTTTCTTTTATTA 59.711 33.333 0.00 0.00 0.00 0.98
3525 3542 5.902613 TGCCATTTCCAGATTCTTACTTG 57.097 39.130 0.00 0.00 0.00 3.16
3706 3724 3.196469 CAGGTCTGAATACTTGGAGCAGA 59.804 47.826 0.00 0.00 33.58 4.26
3859 3880 4.573900 AGTAGAGGCTGTTGTTGATTCAG 58.426 43.478 0.00 0.00 0.00 3.02
3873 3894 1.681264 GAGCTCCTGAGAAGTAGAGGC 59.319 57.143 0.87 0.00 0.00 4.70
3896 3917 7.753580 GGTGGTATTTTTATTGCTACAGACAAC 59.246 37.037 0.00 0.00 0.00 3.32
3936 3957 1.102978 GGATTGTGGGAAATGTCGGG 58.897 55.000 0.00 0.00 0.00 5.14
3963 3984 6.097129 GTCCTCTGTATAATAGGGCTATCCAC 59.903 46.154 0.00 0.00 38.24 4.02
4146 4176 4.328169 GCATTTACAGCCAATTTGCTCTTC 59.672 41.667 0.05 0.00 40.32 2.87


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

AutoCloner maintained by Alex Coulton.