Multiple sequence alignment - TraesCS6A01G100100

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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 TraesCS6A01G100100 chr6A 100.000 3439 0 0 1 3439 67493890 67497328 0.000000e+00 6351
1 TraesCS6A01G100100 chr6A 97.101 276 7 1 1 276 158983604 158983330 6.720000e-127 464
2 TraesCS6A01G100100 chr3A 96.722 3173 93 9 271 3439 662010138 662006973 0.000000e+00 5273
3 TraesCS6A01G100100 chr3A 97.101 276 8 0 1 276 417393485 417393760 1.870000e-127 466
4 TraesCS6A01G100100 chr3A 97.101 276 8 0 1 276 554827281 554827556 1.870000e-127 466
5 TraesCS6A01G100100 chr3A 97.101 276 8 0 1 276 662010568 662010293 1.870000e-127 466
6 TraesCS6A01G100100 chr5A 96.565 3173 95 11 271 3439 465654386 465657548 0.000000e+00 5243
7 TraesCS6A01G100100 chr5A 96.505 3176 93 15 271 3439 141902367 141905531 0.000000e+00 5234
8 TraesCS6A01G100100 chr5A 97.464 276 7 0 1 276 141901936 141902211 4.020000e-129 472
9 TraesCS6A01G100100 chr5A 97.101 276 8 0 1 276 541976742 541977017 1.870000e-127 466
10 TraesCS6A01G100100 chr2A 96.566 3174 94 13 271 3439 384174619 384171456 0.000000e+00 5243
11 TraesCS6A01G100100 chr2A 96.537 3176 95 11 271 3439 685104052 685100885 0.000000e+00 5241
12 TraesCS6A01G100100 chr2A 96.507 3178 89 14 271 3439 572969648 572966484 0.000000e+00 5234
13 TraesCS6A01G100100 chr2A 96.471 3174 100 12 271 3439 284800180 284803346 0.000000e+00 5230
14 TraesCS6A01G100100 chr2A 96.440 3174 95 11 271 3439 80119902 80123062 0.000000e+00 5219
15 TraesCS6A01G100100 chr2A 97.464 276 7 0 1 276 685104482 685104207 4.020000e-129 472
16 TraesCS6A01G100100 chr2A 97.464 276 6 1 1 276 80119472 80119746 1.440000e-128 470
17 TraesCS6A01G100100 chr2A 96.739 276 9 0 1 276 572970079 572969804 8.700000e-126 460
18 TraesCS6A01G100100 chr7B 95.223 3182 128 20 271 3439 300041802 300044972 0.000000e+00 5012


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 TraesCS6A01G100100 chr6A 67493890 67497328 3438 False 6351.0 6351 100.0000 1 3439 1 chr6A.!!$F1 3438
1 TraesCS6A01G100100 chr3A 662006973 662010568 3595 True 2869.5 5273 96.9115 1 3439 2 chr3A.!!$R1 3438
2 TraesCS6A01G100100 chr5A 465654386 465657548 3162 False 5243.0 5243 96.5650 271 3439 1 chr5A.!!$F1 3168
3 TraesCS6A01G100100 chr5A 141901936 141905531 3595 False 2853.0 5234 96.9845 1 3439 2 chr5A.!!$F3 3438
4 TraesCS6A01G100100 chr2A 384171456 384174619 3163 True 5243.0 5243 96.5660 271 3439 1 chr2A.!!$R1 3168
5 TraesCS6A01G100100 chr2A 284800180 284803346 3166 False 5230.0 5230 96.4710 271 3439 1 chr2A.!!$F1 3168
6 TraesCS6A01G100100 chr2A 685100885 685104482 3597 True 2856.5 5241 97.0005 1 3439 2 chr2A.!!$R3 3438
7 TraesCS6A01G100100 chr2A 572966484 572970079 3595 True 2847.0 5234 96.6230 1 3439 2 chr2A.!!$R2 3438
8 TraesCS6A01G100100 chr2A 80119472 80123062 3590 False 2844.5 5219 96.9520 1 3439 2 chr2A.!!$F2 3438
9 TraesCS6A01G100100 chr7B 300041802 300044972 3170 False 5012.0 5012 95.2230 271 3439 1 chr7B.!!$F1 3168

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
829 1006 0.105224 CCCACGACCACTACACACAA 59.895 55.0 0.0 0.0 0.0 3.33 F
831 1008 0.859232 CACGACCACTACACACAAGC 59.141 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2235 0.667184 GCTGAAACCGGCAAATGTGG 60.667 55.0 0.00 0.0 36.01 4.17 R
2813 3002 1.019673 TAGTAGCGCTTACGGACTGG 58.980 55.0 18.68 0.0 40.57 4.00 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
274 437 8.367911 ACTTATCCTCATATATCTGACGCAAAA 58.632 33.333 0.00 0.00 0.00 2.44
291 454 3.609853 CAAAACTATGCCTGCTCCTACA 58.390 45.455 0.00 0.00 0.00 2.74
532 701 0.109873 CACCAGTCCGAGTACGACAC 60.110 60.000 0.00 0.00 42.66 3.67
580 749 1.066752 ACGCTGACACGTGCAAGTA 59.933 52.632 17.22 0.00 46.28 2.24
694 863 5.414789 TTTGCAGGTCATAAGTACAGCTA 57.585 39.130 0.00 0.00 0.00 3.32
695 864 4.386867 TGCAGGTCATAAGTACAGCTAC 57.613 45.455 0.00 0.00 0.00 3.58
706 875 4.705337 AGTACAGCTACACAAGACTAGC 57.295 45.455 0.00 0.00 36.40 3.42
753 922 3.244112 ACTTGGACGGTTAGTTCTTCCAG 60.244 47.826 0.00 0.00 0.00 3.86
829 1006 0.105224 CCCACGACCACTACACACAA 59.895 55.000 0.00 0.00 0.00 3.33
831 1008 0.859232 CACGACCACTACACACAAGC 59.141 55.000 0.00 0.00 0.00 4.01
911 1088 2.498078 GTCTTCCATCTCTCCCTCGTTT 59.502 50.000 0.00 0.00 0.00 3.60
1079 1256 1.131883 CCTCGTCGACATTAACGTCCT 59.868 52.381 17.16 0.00 39.78 3.85
1387 1564 4.991789 TGCCCTGCATATGGTTTATCTA 57.008 40.909 4.56 0.00 31.71 1.98
1542 1721 8.090788 ACCTGATACACTGGATTACTATTTGT 57.909 34.615 0.00 0.00 40.23 2.83
2050 2235 1.665161 GCTGCAGCATGACAAGTTGTC 60.665 52.381 33.36 25.99 43.30 3.18
2085 2270 2.998772 TCAGCATTGAAAGCGACAAAC 58.001 42.857 0.00 0.00 37.01 2.93
2187 2372 3.586892 GGAAAAGAGTACGACTCCTTGG 58.413 50.000 10.24 0.00 46.18 3.61
2813 3002 9.946165 ACTACAATAAAAAGTACAAAGAAGCAC 57.054 29.630 0.00 0.00 0.00 4.40
2892 3081 8.446273 CAAGTACCATAGTTCTGAAAATGACAG 58.554 37.037 12.96 0.00 36.80 3.51
2916 3106 7.118825 CAGCAGAAGACACTTGAGAATAATCAA 59.881 37.037 0.00 0.00 34.02 2.57
2984 3177 4.419522 ACACTCACACAAAACTGACAAC 57.580 40.909 0.00 0.00 0.00 3.32
3002 3195 7.011828 TGACAACAGCTAGAACAAAAAGTAC 57.988 36.000 0.00 0.00 0.00 2.73
3111 3304 3.948473 TGCTAGATACTTGAACTCGAGCT 59.052 43.478 13.61 0.00 38.15 4.09
3139 3332 2.673833 GAATCCCTAGTAATCCGCACG 58.326 52.381 0.00 0.00 0.00 5.34
3145 3338 0.170784 TAGTAATCCGCACGACGCAA 59.829 50.000 0.00 0.00 42.60 4.85
3191 3388 3.513438 GAGAGAGAGCGAGCGCCA 61.513 66.667 11.66 0.00 43.17 5.69
3262 3459 2.280628 GCTGCGCTTATAAACAGGTCT 58.719 47.619 9.73 0.00 0.00 3.85
3358 3555 0.393808 GCTATCTGGGCCGGAAAACA 60.394 55.000 21.02 4.19 0.00 2.83
3435 3632 2.002018 AACCAGAGGGCGGGACAAAA 62.002 55.000 0.00 0.00 37.90 2.44
3436 3633 1.675641 CCAGAGGGCGGGACAAAAG 60.676 63.158 0.00 0.00 0.00 2.27
3438 3635 0.250727 CAGAGGGCGGGACAAAAGAA 60.251 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 1.893137 TGCCTTGTACTGACGACTGAT 59.107 47.619 0.00 0.0 0.00 2.90
164 165 1.290009 GCTTCAGCGGGCACAAATT 59.710 52.632 0.00 0.0 0.00 1.82
255 256 7.412346 GGCATAGTTTTGCGTCAGATATATGAG 60.412 40.741 0.00 0.0 43.71 2.90
257 258 6.369890 AGGCATAGTTTTGCGTCAGATATATG 59.630 38.462 0.00 0.0 43.71 1.78
274 437 2.432510 GACTTGTAGGAGCAGGCATAGT 59.567 50.000 0.00 0.0 0.00 2.12
291 454 4.453480 TGGTCTTTCTGAATTGGGACTT 57.547 40.909 0.00 0.0 0.00 3.01
580 749 6.095432 CTGTACTTATCAGCTGCTTATCCT 57.905 41.667 9.47 0.0 0.00 3.24
694 863 3.118408 TGTTGAACTGGCTAGTCTTGTGT 60.118 43.478 2.06 0.0 35.69 3.72
695 864 3.466836 TGTTGAACTGGCTAGTCTTGTG 58.533 45.455 2.06 0.0 35.69 3.33
706 875 8.813282 GTTAAATGGTTTTTACTGTTGAACTGG 58.187 33.333 7.13 0.0 0.00 4.00
777 946 3.367051 CTTCGTCATGGCAACCGCG 62.367 63.158 0.00 0.0 39.92 6.46
804 973 3.512154 TAGTGGTCGTGGGGGTCGT 62.512 63.158 0.00 0.0 0.00 4.34
911 1088 1.459455 CGGCAATGGTGGTTTGTGGA 61.459 55.000 0.00 0.0 0.00 4.02
1079 1256 2.036571 TAGTCACGCTTCTCGCCGA 61.037 57.895 0.00 0.0 43.23 5.54
1092 1269 1.324383 TGAGCGTTCTGGTGTAGTCA 58.676 50.000 0.00 0.0 0.00 3.41
1420 1597 3.821033 ACATCTAGTTGGGAAACAAGTGC 59.179 43.478 5.80 0.0 42.57 4.40
2050 2235 0.667184 GCTGAAACCGGCAAATGTGG 60.667 55.000 0.00 0.0 36.01 4.17
2085 2270 1.151668 CCGGACAACTTCAGCTTCTG 58.848 55.000 0.00 0.0 0.00 3.02
2118 2303 4.384940 TGAATGTCGATGAACTTGTTGGA 58.615 39.130 0.00 0.0 0.00 3.53
2628 2816 5.794687 TGGATTAACAACATACGAAGCTG 57.205 39.130 0.00 0.0 0.00 4.24
2813 3002 1.019673 TAGTAGCGCTTACGGACTGG 58.980 55.000 18.68 0.0 40.57 4.00
2892 3081 6.974932 TGATTATTCTCAAGTGTCTTCTGC 57.025 37.500 0.00 0.0 0.00 4.26
2984 3177 5.179555 GGACTGGTACTTTTTGTTCTAGCTG 59.820 44.000 0.00 0.0 29.93 4.24
2986 3179 5.061179 TGGACTGGTACTTTTTGTTCTAGC 58.939 41.667 0.00 0.0 29.93 3.42
3139 3332 2.804090 GTCGACGGGTCTTGCGTC 60.804 66.667 0.00 0.0 0.00 5.19
3262 3459 2.058595 GCTAGTCGAGGGGGCTTCA 61.059 63.158 0.00 0.0 0.00 3.02


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

AutoCloner maintained by Alex Coulton.