Multiple sequence alignment - TraesCS1D01G100500

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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 TraesCS1D01G100500 chr1D 100.000 3430 0 0 1 3430 88013088 88009659 0.000000e+00 6335
1 TraesCS1D01G100500 chr1D 96.330 3433 117 7 1 3430 296768536 296771962 0.000000e+00 5633
2 TraesCS1D01G100500 chr5D 96.538 3437 108 10 1 3430 108670111 108666679 0.000000e+00 5677
3 TraesCS1D01G100500 chr2D 96.271 3433 123 5 1 3430 259247794 259244364 0.000000e+00 5626
4 TraesCS1D01G100500 chr2D 88.546 227 6 9 23 229 259248011 259247785 1.220000e-64 257
5 TraesCS1D01G100500 chr7D 96.190 3438 122 8 1 3430 243734966 243731530 0.000000e+00 5614
6 TraesCS1D01G100500 chr4D 96.102 3438 122 12 1 3430 426270113 426266680 0.000000e+00 5596
7 TraesCS1D01G100500 chr3D 96.154 3432 120 7 1 3428 353281227 353284650 0.000000e+00 5596
8 TraesCS1D01G100500 chr1A 94.003 3235 179 13 205 3430 277154040 277150812 0.000000e+00 4885
9 TraesCS1D01G100500 chr1A 93.578 3239 191 14 205 3430 366070931 366074165 0.000000e+00 4813
10 TraesCS1D01G100500 chr1A 94.444 144 6 2 1 142 419944876 419945019 1.600000e-53 220
11 TraesCS1D01G100500 chr2A 93.430 3242 193 18 205 3430 367432668 367429431 0.000000e+00 4789
12 TraesCS1D01G100500 chr7A 81.541 2660 331 84 23 2579 384857073 384854471 0.000000e+00 2045
13 TraesCS1D01G100500 chr7A 92.450 1245 88 6 1 1242 458671407 458670166 0.000000e+00 1773
14 TraesCS1D01G100500 chr5A 83.453 278 19 16 24 276 686267858 686267583 2.060000e-57 233
15 TraesCS1D01G100500 chr5A 95.035 141 5 2 4 142 368433205 368433065 1.600000e-53 220
16 TraesCS1D01G100500 chr3A 95.105 143 6 1 1 142 240525609 240525467 1.240000e-54 224


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 TraesCS1D01G100500 chr1D 88009659 88013088 3429 True 6335.0 6335 100.0000 1 3430 1 chr1D.!!$R1 3429
1 TraesCS1D01G100500 chr1D 296768536 296771962 3426 False 5633.0 5633 96.3300 1 3430 1 chr1D.!!$F1 3429
2 TraesCS1D01G100500 chr5D 108666679 108670111 3432 True 5677.0 5677 96.5380 1 3430 1 chr5D.!!$R1 3429
3 TraesCS1D01G100500 chr2D 259244364 259248011 3647 True 2941.5 5626 92.4085 1 3430 2 chr2D.!!$R1 3429
4 TraesCS1D01G100500 chr7D 243731530 243734966 3436 True 5614.0 5614 96.1900 1 3430 1 chr7D.!!$R1 3429
5 TraesCS1D01G100500 chr4D 426266680 426270113 3433 True 5596.0 5596 96.1020 1 3430 1 chr4D.!!$R1 3429
6 TraesCS1D01G100500 chr3D 353281227 353284650 3423 False 5596.0 5596 96.1540 1 3428 1 chr3D.!!$F1 3427
7 TraesCS1D01G100500 chr1A 277150812 277154040 3228 True 4885.0 4885 94.0030 205 3430 1 chr1A.!!$R1 3225
8 TraesCS1D01G100500 chr1A 366070931 366074165 3234 False 4813.0 4813 93.5780 205 3430 1 chr1A.!!$F1 3225
9 TraesCS1D01G100500 chr2A 367429431 367432668 3237 True 4789.0 4789 93.4300 205 3430 1 chr2A.!!$R1 3225
10 TraesCS1D01G100500 chr7A 384854471 384857073 2602 True 2045.0 2045 81.5410 23 2579 1 chr7A.!!$R1 2556
11 TraesCS1D01G100500 chr7A 458670166 458671407 1241 True 1773.0 1773 92.4500 1 1242 1 chr7A.!!$R2 1241

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
810 1100 0.817634 CCACAAGGGACAGCAAACGA 60.818 55.0 0.0 0.0 40.01 3.85 F
1035 1329 0.674581 CTGCCAAGCGTCATCAAGGA 60.675 55.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2719 0.180406 TAGAATTTCGCAGCCTCCCC 59.820 55.0 0.0 0.0 0.00 4.81 R
2932 3272 1.075542 TAATCTGCAAGCGACCAACG 58.924 50.0 0.0 0.0 45.66 4.10 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
551 826 5.453866 AGTACCACAGTAGAGGAGTACAT 57.546 43.478 0.00 0.00 34.03 2.29
554 829 5.453866 ACCACAGTAGAGGAGTACATACT 57.546 43.478 0.00 0.00 39.71 2.12
657 935 1.305219 AAATGCCGTCATCACCACCG 61.305 55.000 0.00 0.00 31.27 4.94
692 970 4.781934 AGTGGGATTTAGCAGGTCATAAC 58.218 43.478 0.00 0.00 0.00 1.89
713 991 5.793030 ACTACAGCTTGACAAGACTAGTT 57.207 39.130 19.51 6.22 0.00 2.24
802 1092 2.203280 CGGTTGCCACAAGGGACA 60.203 61.111 0.00 0.00 40.01 4.02
810 1100 0.817634 CCACAAGGGACAGCAAACGA 60.818 55.000 0.00 0.00 40.01 3.85
839 1131 3.319198 CACTACACCCACGCCCCT 61.319 66.667 0.00 0.00 0.00 4.79
876 1169 2.444700 AAATCCCCGTCGACGCACTT 62.445 55.000 31.73 17.88 38.18 3.16
983 1277 1.423584 TCTCTCTCACAAGCCCACAA 58.576 50.000 0.00 0.00 0.00 3.33
1035 1329 0.674581 CTGCCAAGCGTCATCAAGGA 60.675 55.000 0.00 0.00 0.00 3.36
1116 1410 3.709653 AGTACACCAAAACACTCAGAGGA 59.290 43.478 1.53 0.00 0.00 3.71
1442 1738 7.038302 TCAGACTTGTTTCCCAACTAGATGTAT 60.038 37.037 0.00 0.00 37.81 2.29
2299 2633 0.742281 CTGCCAGACAACCTCATCGG 60.742 60.000 0.00 0.00 39.35 4.18
2343 2677 1.359848 CACGTACAAGTCATGGAGCC 58.640 55.000 0.00 0.00 0.00 4.70
2359 2693 2.560542 GGAGCCTGATCGACTACATCAT 59.439 50.000 0.00 0.00 29.78 2.45
2385 2719 3.243704 TGGTTCGGAATTTGCAAAAGAGG 60.244 43.478 17.19 6.64 0.00 3.69
2523 2857 7.284489 TCAAATTAGTAGTTTGCTCTTGTTGGT 59.716 33.333 12.08 0.00 36.69 3.67
2565 2899 2.602933 CGTGCTTGTCATGGTTGAACAG 60.603 50.000 0.00 0.00 32.48 3.16
2709 3044 7.416438 GGCTGCTCTAAAGTACTAGTTATGACA 60.416 40.741 0.00 0.00 0.00 3.58
2726 3061 7.497579 AGTTATGACACAACTAATCACACAACA 59.502 33.333 0.00 0.00 34.50 3.33
2792 3127 1.195448 CGTTCAGACCAATCAGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
2932 3272 3.070018 AGAAGCATCAGCACACACTTAC 58.930 45.455 0.00 0.00 45.49 2.34
3025 3365 8.773404 ATAAAAAGTACATAGAAGCGTCAGTT 57.227 30.769 1.61 0.00 0.00 3.16
3173 3517 8.496751 GGAGTCAAGTACTAGATTCAAACAAAC 58.503 37.037 0.00 0.00 39.07 2.93
3174 3518 8.958119 AGTCAAGTACTAGATTCAAACAAACA 57.042 30.769 0.00 0.00 36.36 2.83
3175 3519 9.391006 AGTCAAGTACTAGATTCAAACAAACAA 57.609 29.630 0.00 0.00 36.36 2.83
3324 3674 3.209097 GAGAGAGAGCGAGCGCCT 61.209 66.667 11.66 8.31 43.17 5.52
3329 3679 1.587613 GAGAGCGAGCGCCTTGTAG 60.588 63.158 11.66 0.00 43.17 2.74
3348 3698 3.719173 AGAAGCGCTCAGGTAAGTATC 57.281 47.619 12.06 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
458 730 8.239314 AGACTATGTGTGATGCTAATGTTTTTG 58.761 33.333 0.00 0.00 0.00 2.44
551 826 3.054434 CAGGGTTGGTGATGATGGAAGTA 60.054 47.826 0.00 0.00 0.00 2.24
554 829 1.991813 TCAGGGTTGGTGATGATGGAA 59.008 47.619 0.00 0.00 0.00 3.53
657 935 2.320587 CCCACTTGCACGTCTCAGC 61.321 63.158 0.00 0.00 0.00 4.26
692 970 6.804295 CACTAACTAGTCTTGTCAAGCTGTAG 59.196 42.308 7.78 10.01 33.46 2.74
713 991 6.644592 GTCAAATGGTTTTTATTGCTGCACTA 59.355 34.615 0.00 0.00 0.00 2.74
802 1092 2.280592 GTGGGGTCGTCGTTTGCT 60.281 61.111 0.00 0.00 0.00 3.91
810 1100 3.688159 GTAGTGGCGTGGGGTCGT 61.688 66.667 0.00 0.00 0.00 4.34
839 1131 3.998672 GTGGGAGGCGGTTCGTCA 61.999 66.667 0.00 0.00 32.13 4.35
1017 1311 0.674581 CTCCTTGATGACGCTTGGCA 60.675 55.000 0.00 0.00 0.00 4.92
1035 1329 2.995872 GCTCTTGTCCGACGGCTCT 61.996 63.158 9.66 0.00 0.00 4.09
1116 1410 1.302033 CTTGCCGTGGAGCTCAACT 60.302 57.895 19.09 0.00 0.00 3.16
1293 1587 0.174389 AGAGCTCATCGACGCACAAT 59.826 50.000 17.77 0.00 0.00 2.71
1305 1599 0.321671 GGTACACCAAGCAGAGCTCA 59.678 55.000 17.77 0.00 38.25 4.26
1354 1648 2.789409 ACAGGGCAAATGAGTAGGAC 57.211 50.000 0.00 0.00 0.00 3.85
1442 1738 5.010933 TCCACTTTTCACAAACCACACTAA 58.989 37.500 0.00 0.00 0.00 2.24
2299 2633 3.571741 GCATCTACTCCTGCGTACC 57.428 57.895 0.00 0.00 0.00 3.34
2343 2677 6.507958 ACCATCTATGATGTAGTCGATCAG 57.492 41.667 6.78 0.00 33.38 2.90
2359 2693 5.475220 TCTTTTGCAAATTCCGAACCATCTA 59.525 36.000 13.65 0.00 0.00 1.98
2385 2719 0.180406 TAGAATTTCGCAGCCTCCCC 59.820 55.000 0.00 0.00 0.00 4.81
2523 2857 6.183360 GCACGACATAATCATACTGGTTCAAA 60.183 38.462 0.00 0.00 0.00 2.69
2565 2899 9.988350 CATTGTACTTGATGACATAAGTAAACC 57.012 33.333 14.06 7.41 40.07 3.27
2709 3044 6.096141 TGGAACAATGTTGTGTGATTAGTTGT 59.904 34.615 2.20 0.00 41.31 3.32
2776 3111 2.880268 TCAAAGTGTGCTGATTGGTCTG 59.120 45.455 0.00 0.00 0.00 3.51
2780 3115 3.635331 CAACTCAAAGTGTGCTGATTGG 58.365 45.455 0.00 0.00 0.00 3.16
2850 3185 5.525012 GCAGCTACATATGAATGAGAACACA 59.475 40.000 10.38 0.00 36.54 3.72
2932 3272 1.075542 TAATCTGCAAGCGACCAACG 58.924 50.000 0.00 0.00 45.66 4.10
3019 3359 2.259505 AGTAGCGCTTACGAACTGAC 57.740 50.000 18.68 3.69 43.93 3.51
3025 3365 3.566742 TCCATTCATAGTAGCGCTTACGA 59.433 43.478 18.68 8.74 43.93 3.43
3218 3564 4.157840 TCGAGTTCAAGTATCTAGCAGCAA 59.842 41.667 0.00 0.00 0.00 3.91
3219 3565 3.694566 TCGAGTTCAAGTATCTAGCAGCA 59.305 43.478 0.00 0.00 0.00 4.41
3324 3674 2.561419 ACTTACCTGAGCGCTTCTACAA 59.439 45.455 13.26 2.80 0.00 2.41
3329 3679 2.100916 TGGATACTTACCTGAGCGCTTC 59.899 50.000 13.26 5.55 37.61 3.86
3348 3698 0.244994 CACTGGTCGAACTCCTCTGG 59.755 60.000 0.33 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.