Multiple sequence alignment - TraesCS3D01G414500

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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 TraesCS3D01G414500 chr3D 100.000 3240 0 0 1001 4240 526282743 526279504 0.000000e+00 5984.0
1 TraesCS3D01G414500 chr3D 100.000 628 0 0 1 628 526283743 526283116 0.000000e+00 1160.0
2 TraesCS3D01G414500 chr3A 97.781 3244 68 2 1001 4240 660516072 660512829 0.000000e+00 5589.0
3 TraesCS3D01G414500 chr3A 93.656 599 31 4 1 598 660519160 660518568 0.000000e+00 889.0
4 TraesCS3D01G414500 chr3A 94.595 37 2 0 4117 4153 42885305 42885341 1.650000e-04 58.4
5 TraesCS3D01G414500 chr3B 97.087 3227 82 5 1001 4223 695562233 695559015 0.000000e+00 5428.0
6 TraesCS3D01G414500 chr3B 94.412 340 19 0 1 340 695571856 695571517 1.350000e-144 523.0
7 TraesCS3D01G414500 chr3B 88.302 265 25 3 334 598 695563097 695562839 3.180000e-81 313.0
8 TraesCS3D01G414500 chr4B 96.889 225 5 1 3159 3381 283704753 283704977 4.000000e-100 375.0
9 TraesCS3D01G414500 chr4D 95.385 130 5 1 4111 4240 148416772 148416900 5.560000e-49 206.0
10 TraesCS3D01G414500 chr6B 99.029 103 1 0 4123 4225 442428609 442428507 7.240000e-43 185.0
11 TraesCS3D01G414500 chr7A 94.595 37 2 0 4117 4153 630991422 630991458 1.650000e-04 58.4
12 TraesCS3D01G414500 chr7A 94.595 37 2 0 4117 4153 655545628 655545664 1.650000e-04 58.4


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 TraesCS3D01G414500 chr3D 526279504 526283743 4239 True 3572.0 5984 100.0000 1 4240 2 chr3D.!!$R1 4239
1 TraesCS3D01G414500 chr3A 660512829 660519160 6331 True 3239.0 5589 95.7185 1 4240 2 chr3A.!!$R1 4239
2 TraesCS3D01G414500 chr3B 695559015 695563097 4082 True 2870.5 5428 92.6945 334 4223 2 chr3B.!!$R2 3889

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
587 589 3.501062 GCACTATGACATCATGATGGTGG 59.499 47.826 33.31 23.25 42.91 4.61 F
1162 3470 0.392595 CTCCTGCCCCCGTTTACTTC 60.393 60.000 0.00 0.00 0.00 3.01 F
1974 4286 0.673333 TGGGACTGCACATGCTTACG 60.673 55.000 5.31 0.00 42.66 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 4444 0.901580 CCTCACCAGCATGCCCTTTT 60.902 55.000 15.66 0.0 31.97 2.27 R
2558 4870 2.497138 CCATGAAGCTGAACACACAGA 58.503 47.619 0.00 0.0 39.94 3.41 R
3683 5998 1.822990 CAGATGCCAATCAAGCCAACT 59.177 47.619 0.00 0.0 35.03 3.16 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
31 32 3.804786 GGGCTACAAAGAGACCTAGTC 57.195 52.381 0.00 0.00 42.05 2.59
91 92 8.854614 AAGGTATGCAAATTATACTCCATCTC 57.145 34.615 0.00 0.00 32.81 2.75
92 93 7.398024 AGGTATGCAAATTATACTCCATCTCC 58.602 38.462 0.00 0.00 32.81 3.71
97 98 7.345691 TGCAAATTATACTCCATCTCCTTTGA 58.654 34.615 0.00 0.00 0.00 2.69
139 140 8.292448 TGTCTCTAAGATTTGCTTTTGATGAAC 58.708 33.333 0.00 0.00 38.05 3.18
143 144 8.177663 TCTAAGATTTGCTTTTGATGAACGATC 58.822 33.333 0.00 0.00 38.05 3.69
166 167 9.921637 GATCAGTCTATGGTTTTCCTAGATAAG 57.078 37.037 0.00 0.00 41.38 1.73
281 282 9.933723 AAATTCTGGATCAAAGATAAAGTTTGG 57.066 29.630 0.00 0.00 35.88 3.28
313 314 4.425577 CACCTTATGCTTCTGGACAAAC 57.574 45.455 0.00 0.00 0.00 2.93
340 341 8.883731 GGTGTATATATGAACATAAGACCATGC 58.116 37.037 0.00 0.00 0.00 4.06
362 363 5.714333 TGCTGGTAATGGTTGATGTTAACAT 59.286 36.000 20.93 20.93 39.70 2.71
363 364 6.887002 TGCTGGTAATGGTTGATGTTAACATA 59.113 34.615 20.83 5.78 36.57 2.29
364 365 7.394641 TGCTGGTAATGGTTGATGTTAACATAA 59.605 33.333 20.83 11.48 36.57 1.90
365 366 7.915397 GCTGGTAATGGTTGATGTTAACATAAG 59.085 37.037 20.83 0.00 36.57 1.73
410 411 6.916360 TGAGATTTAATTTTCAGGCAACCT 57.084 33.333 0.00 0.00 37.17 3.50
416 417 9.087424 GATTTAATTTTCAGGCAACCTATGAAC 57.913 33.333 0.00 0.00 32.91 3.18
420 421 6.418057 TTTTCAGGCAACCTATGAACAAAT 57.582 33.333 0.00 0.00 32.91 2.32
426 427 7.831690 TCAGGCAACCTATGAACAAATAATACA 59.168 33.333 0.00 0.00 29.64 2.29
526 528 9.442047 AAAACCACTAAAATCACATCTAGAGAG 57.558 33.333 0.00 0.00 0.00 3.20
547 549 9.312904 AGAGAGAACCCATGAAAATTAAAATCA 57.687 29.630 0.00 0.00 0.00 2.57
587 589 3.501062 GCACTATGACATCATGATGGTGG 59.499 47.826 33.31 23.25 42.91 4.61
1133 3441 2.539263 AAGCTCTTCGTCGCCGGTAC 62.539 60.000 1.90 0.41 33.95 3.34
1140 3448 3.376078 GTCGCCGGTACCACTCCA 61.376 66.667 13.54 0.00 0.00 3.86
1149 3457 1.612442 TACCACTCCACCCTCCTGC 60.612 63.158 0.00 0.00 0.00 4.85
1162 3470 0.392595 CTCCTGCCCCCGTTTACTTC 60.393 60.000 0.00 0.00 0.00 3.01
1363 3672 1.192534 GCAATATAACCTCTCGCGTGC 59.807 52.381 5.77 0.00 0.00 5.34
1605 3917 2.285083 CAAACTCGTTCACCTTGGTCA 58.715 47.619 0.00 0.00 0.00 4.02
1619 3931 2.507992 GTCAGTGCATCGCTCGCT 60.508 61.111 0.00 0.00 0.00 4.93
1974 4286 0.673333 TGGGACTGCACATGCTTACG 60.673 55.000 5.31 0.00 42.66 3.18
2037 4349 3.028130 TCGATACTGGGCATGTACTTGA 58.972 45.455 12.65 0.00 0.00 3.02
2044 4356 3.561143 TGGGCATGTACTTGAGTTTTGT 58.439 40.909 12.65 0.00 0.00 2.83
2048 4360 5.154222 GGCATGTACTTGAGTTTTGTTAGC 58.846 41.667 12.65 0.00 0.00 3.09
2079 4391 5.171339 TGGAAGAGAGATTTTCAGGAAGG 57.829 43.478 0.00 0.00 0.00 3.46
2132 4444 4.996793 TGATGATGGGTTTCCTTCTTGAA 58.003 39.130 0.00 0.00 37.89 2.69
2150 4462 0.971386 AAAAAGGGCATGCTGGTGAG 59.029 50.000 18.92 0.00 0.00 3.51
2192 4504 7.439655 GTCAAGATGAGGTCAAATGGTATAGTC 59.560 40.741 0.00 0.00 0.00 2.59
2558 4870 7.629222 GCCTGTTATGTGATTGCTAAGTTTGAT 60.629 37.037 0.00 0.00 0.00 2.57
3268 5580 2.353357 TCCATGATCCATCACAAGGC 57.647 50.000 0.00 0.00 40.03 4.35
3348 5662 9.118300 AGTCTCAAGCTATTGGAATCTATTTTG 57.882 33.333 0.00 0.00 37.02 2.44
3497 5812 5.256474 CCATTGGGTCTTAAGTCTTGTGAT 58.744 41.667 1.63 0.00 0.00 3.06
3683 5998 6.134754 GGAGTCCCAATCTTACTAACCTCTA 58.865 44.000 0.00 0.00 0.00 2.43
3900 6215 6.569179 TTACTTTTGAGTAAGATGGTTGGC 57.431 37.500 0.00 0.00 31.45 4.52
4136 6451 3.485877 GGTGTTCATGAATCTAGTTGCGC 60.486 47.826 12.12 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.249073 CTCCTCAACCGCCATAGTCG 60.249 60.000 0.00 0.00 0.00 4.18
91 92 6.913170 ACATATGCGCCTTATATTTCAAAGG 58.087 36.000 4.18 0.00 44.32 3.11
92 93 7.810658 AGACATATGCGCCTTATATTTCAAAG 58.189 34.615 4.18 0.00 0.00 2.77
97 98 8.531982 TCTTAGAGACATATGCGCCTTATATTT 58.468 33.333 4.18 0.00 0.00 1.40
106 107 4.450419 AGCAAATCTTAGAGACATATGCGC 59.550 41.667 0.00 0.00 36.45 6.09
139 140 6.392625 TCTAGGAAAACCATAGACTGATCG 57.607 41.667 0.00 0.00 0.00 3.69
143 144 9.892130 AAACTTATCTAGGAAAACCATAGACTG 57.108 33.333 0.00 0.00 0.00 3.51
166 167 7.813645 AGAAGTATTTTTCGGTGGTATCAAAC 58.186 34.615 0.00 0.00 32.33 2.93
260 261 7.543520 GCTTTCCAAACTTTATCTTTGATCCAG 59.456 37.037 0.00 0.00 31.32 3.86
304 305 6.759356 TGTTCATATATACACCGTTTGTCCAG 59.241 38.462 0.00 0.00 39.91 3.86
313 314 9.087424 CATGGTCTTATGTTCATATATACACCG 57.913 37.037 0.00 0.00 0.00 4.94
340 341 8.956426 ACTTATGTTAACATCAACCATTACCAG 58.044 33.333 24.00 3.85 37.76 4.00
420 421 9.892130 AGGTTTGGTTTCAAAATTTGTGTATTA 57.108 25.926 5.56 0.00 43.56 0.98
426 427 6.061022 AGGAGGTTTGGTTTCAAAATTTGT 57.939 33.333 5.56 0.00 43.56 2.83
435 436 2.095372 CGCGAATAGGAGGTTTGGTTTC 59.905 50.000 0.00 0.00 0.00 2.78
516 518 9.618890 TTAATTTTCATGGGTTCTCTCTAGATG 57.381 33.333 0.00 0.00 0.00 2.90
548 550 9.314321 GTCATAGTGCTTACTAATGCTCTTTTA 57.686 33.333 0.00 0.00 35.19 1.52
566 568 4.514066 CACCACCATCATGATGTCATAGTG 59.486 45.833 29.23 26.30 37.11 2.74
571 573 1.282738 AGCACCACCATCATGATGTCA 59.717 47.619 29.23 0.00 37.11 3.58
587 589 5.068067 TGGGTTTAAGAACAGGTTTTAGCAC 59.932 40.000 0.00 0.00 37.51 4.40
1133 3441 3.721706 GGCAGGAGGGTGGAGTGG 61.722 72.222 0.00 0.00 0.00 4.00
1140 3448 3.876255 TAAACGGGGGCAGGAGGGT 62.876 63.158 0.00 0.00 0.00 4.34
1149 3457 0.034767 GGGGAAGAAGTAAACGGGGG 60.035 60.000 0.00 0.00 0.00 5.40
1162 3470 2.031097 GCCAGGGAATGATTGGGGAAG 61.031 57.143 0.00 0.00 32.53 3.46
1974 4286 2.128771 TCAAGCCCCATCTTAACTGC 57.871 50.000 0.00 0.00 0.00 4.40
1976 4288 4.026052 CCAAATCAAGCCCCATCTTAACT 58.974 43.478 0.00 0.00 0.00 2.24
1979 4291 4.217510 CATCCAAATCAAGCCCCATCTTA 58.782 43.478 0.00 0.00 0.00 2.10
2037 4349 5.385198 TCCAATCTCAAGGCTAACAAAACT 58.615 37.500 0.00 0.00 0.00 2.66
2044 4356 5.026121 TCTCTCTTCCAATCTCAAGGCTAA 58.974 41.667 0.00 0.00 0.00 3.09
2048 4360 6.883217 TGAAAATCTCTCTTCCAATCTCAAGG 59.117 38.462 0.00 0.00 0.00 3.61
2132 4444 0.901580 CCTCACCAGCATGCCCTTTT 60.902 55.000 15.66 0.00 31.97 2.27
2192 4504 3.582998 ACCATTGATACCATGTCAGGG 57.417 47.619 0.92 0.92 0.00 4.45
2282 4594 3.243468 GCTCTCTACTAAACCCACGGATC 60.243 52.174 0.00 0.00 0.00 3.36
2558 4870 2.497138 CCATGAAGCTGAACACACAGA 58.503 47.619 0.00 0.00 39.94 3.41
3296 5608 5.760253 GTGGTCCTTGTGTGATATATCCTTG 59.240 44.000 10.25 0.00 0.00 3.61
3348 5662 9.824534 CAAAGTAAAATTCAAACATTAATGCCC 57.175 29.630 15.48 0.00 0.00 5.36
3357 5671 9.442047 ACCATTTGACAAAGTAAAATTCAAACA 57.558 25.926 6.77 0.00 38.60 2.83
3614 5929 6.957020 TCCAACCCATATGTAAAGGAAAATGT 59.043 34.615 1.24 0.00 0.00 2.71
3683 5998 1.822990 CAGATGCCAATCAAGCCAACT 59.177 47.619 0.00 0.00 35.03 3.16
3900 6215 9.229784 GTTCATGAATTACATAATGAAGTGCAG 57.770 33.333 12.12 0.00 39.14 4.41


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

AutoCloner maintained by Alex Coulton.