Multiple sequence alignment - TraesCS3B01G363800

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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 TraesCS3B01G363800 chr3B 100.000 2797 0 0 1 2797 575754678 575751882 0.000000e+00 5166.0
1 TraesCS3B01G363800 chr5A 97.748 2798 62 1 1 2797 73031637 73034434 0.000000e+00 4817.0
2 TraesCS3B01G363800 chr7A 97.640 2797 62 3 1 2797 60106951 60104159 0.000000e+00 4796.0
3 TraesCS3B01G363800 chr1B 97.535 2799 67 1 1 2797 638749964 638747166 0.000000e+00 4785.0
4 TraesCS3B01G363800 chr2B 97.105 2798 80 1 1 2797 500714164 500716961 0.000000e+00 4717.0
5 TraesCS3B01G363800 chr2B 96.097 2793 107 2 4 2796 751970335 751967545 0.000000e+00 4553.0
6 TraesCS3B01G363800 chr2B 97.529 2347 55 3 452 2797 357761029 357758685 0.000000e+00 4010.0
7 TraesCS3B01G363800 chr2B 94.969 159 8 0 2366 2524 357527953 357527795 1.660000e-62 250.0
8 TraesCS3B01G363800 chr2B 97.500 40 1 0 2666 2705 159600378 159600417 5.000000e-08 69.4
9 TraesCS3B01G363800 chr6B 96.854 2797 87 1 1 2797 388367587 388364792 0.000000e+00 4676.0
10 TraesCS3B01G363800 chr6B 95.745 2797 110 5 1 2797 626863069 626865856 0.000000e+00 4497.0
11 TraesCS3B01G363800 chr6B 96.065 2287 89 1 1 2287 588839000 588841285 0.000000e+00 3723.0
12 TraesCS3B01G363800 chr2A 85.930 199 21 5 2487 2680 711551493 711551689 3.650000e-49 206.0


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 TraesCS3B01G363800 chr3B 575751882 575754678 2796 True 5166 5166 100.000 1 2797 1 chr3B.!!$R1 2796
1 TraesCS3B01G363800 chr5A 73031637 73034434 2797 False 4817 4817 97.748 1 2797 1 chr5A.!!$F1 2796
2 TraesCS3B01G363800 chr7A 60104159 60106951 2792 True 4796 4796 97.640 1 2797 1 chr7A.!!$R1 2796
3 TraesCS3B01G363800 chr1B 638747166 638749964 2798 True 4785 4785 97.535 1 2797 1 chr1B.!!$R1 2796
4 TraesCS3B01G363800 chr2B 500714164 500716961 2797 False 4717 4717 97.105 1 2797 1 chr2B.!!$F2 2796
5 TraesCS3B01G363800 chr2B 751967545 751970335 2790 True 4553 4553 96.097 4 2796 1 chr2B.!!$R3 2792
6 TraesCS3B01G363800 chr2B 357758685 357761029 2344 True 4010 4010 97.529 452 2797 1 chr2B.!!$R2 2345
7 TraesCS3B01G363800 chr6B 388364792 388367587 2795 True 4676 4676 96.854 1 2797 1 chr6B.!!$R1 2796
8 TraesCS3B01G363800 chr6B 626863069 626865856 2787 False 4497 4497 95.745 1 2797 1 chr6B.!!$F2 2796
9 TraesCS3B01G363800 chr6B 588839000 588841285 2285 False 3723 3723 96.065 1 2287 1 chr6B.!!$F1 2286

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
468 469 0.037975 GCTCCCGACCGAAACTAACA 60.038 55.000 0.00 0.0 0.0 2.41 F
991 992 1.741145 GTTTACATACAACCGGGGCAG 59.259 52.381 6.32 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1468 0.183971 TGCTCGTTTTTCCTTCCCCA 59.816 50.000 0.00 0.0 0.00 4.96 R
2769 2777 1.609841 GGGAATCGAACCCGTGTCTTT 60.610 52.381 13.87 0.0 37.85 2.52 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
36 37 6.249951 AGATGAGACTTTACTACTGTGGAGT 58.750 40.000 0.00 0.00 36.07 3.85
135 136 0.586319 TTGCTCGCGGCTAAATATGC 59.414 50.000 18.14 5.43 42.39 3.14
154 155 2.877786 TGCATTGAGACGAAAGCTTTCA 59.122 40.909 32.52 15.66 37.01 2.69
277 278 2.119484 ATTTTCACGGGTCGCCCTCA 62.119 55.000 12.26 0.00 42.67 3.86
349 350 3.679917 GCATCTCGAGGTTCTTTGATGGA 60.680 47.826 13.56 0.00 33.89 3.41
372 373 7.039882 GGACATAAAGAAATCGTCTTGGTAGA 58.960 38.462 0.00 0.00 46.36 2.59
468 469 0.037975 GCTCCCGACCGAAACTAACA 60.038 55.000 0.00 0.00 0.00 2.41
573 574 6.489361 CCAGACATAGACTACGTAAAGGGTAT 59.511 42.308 0.00 0.00 0.00 2.73
622 623 4.915085 CGCGTGAACAAAATCCAAAGTAAT 59.085 37.500 0.00 0.00 0.00 1.89
735 736 3.515502 CCCACCATTGAAGTCAGAGTCTA 59.484 47.826 0.00 0.00 0.00 2.59
991 992 1.741145 GTTTACATACAACCGGGGCAG 59.259 52.381 6.32 0.00 0.00 4.85
1006 1007 2.952310 GGGGCAGAGTGGTTTATGATTC 59.048 50.000 0.00 0.00 0.00 2.52
1325 1328 6.126863 TGGGCTTCTTCTCATTCTTCTTTA 57.873 37.500 0.00 0.00 0.00 1.85
1465 1468 2.232452 GGGCTCATCATGCTATACTCGT 59.768 50.000 0.00 0.00 0.00 4.18
1769 1773 4.701171 GTGGTTCGGTTATTCCCATTTGTA 59.299 41.667 0.00 0.00 0.00 2.41
1857 1861 4.341235 TCGAAGACAAAGAGAACTTCTCCA 59.659 41.667 14.19 0.00 44.42 3.86
2052 2056 4.690748 CACATTACTTTCTCTTCCGAAGCA 59.309 41.667 3.00 0.00 0.00 3.91
2161 2165 9.534565 GACAGCATAACAATAACATTCTCTCTA 57.465 33.333 0.00 0.00 0.00 2.43
2288 2292 7.554476 GGGTTCTTAATTCTAGCATGAAAGTCT 59.446 37.037 0.00 0.00 0.00 3.24
2299 2303 3.127721 GCATGAAAGTCTAAGTTGGAGGC 59.872 47.826 0.00 0.00 0.00 4.70
2359 2363 7.567250 TGACATAACATTCCTATGGTTCCTCTA 59.433 37.037 0.00 0.00 36.01 2.43
2475 2479 0.979665 CCCTCCTTGAGTCAGCAAGA 59.020 55.000 5.74 0.00 46.31 3.02
2476 2480 1.558756 CCCTCCTTGAGTCAGCAAGAT 59.441 52.381 5.74 0.00 46.31 2.40
2613 2621 5.134202 TGAGTTACGAGAATGAAGAAGCA 57.866 39.130 0.00 0.00 0.00 3.91
2630 2638 2.350522 AGCATAGCACACCTTTTCTCG 58.649 47.619 0.00 0.00 0.00 4.04
2744 2752 1.358152 TTGGTCCCTTTCGTCCAGAT 58.642 50.000 0.00 0.00 0.00 2.90
2769 2777 4.271696 AGGACATCGTCTTTTCATGTCA 57.728 40.909 12.13 0.00 45.61 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.325109 GGCATCTTACTTAGTTTCCCCCTT 60.325 45.833 0.00 0.00 0.00 3.95
135 136 6.998258 AATTTGAAAGCTTTCGTCTCAATG 57.002 33.333 29.03 0.00 40.01 2.82
154 155 4.763279 ACGGAAGATCGGGTTACAAAATTT 59.237 37.500 0.00 0.00 0.00 1.82
277 278 3.251004 GTGAAAGAACTCAACTGCGGAAT 59.749 43.478 0.00 0.00 0.00 3.01
349 350 8.718734 GTTTCTACCAAGACGATTTCTTTATGT 58.281 33.333 0.00 0.00 42.37 2.29
372 373 5.941555 TTGTTCTATTGGTTTGGTGGTTT 57.058 34.783 0.00 0.00 0.00 3.27
581 582 2.416027 CGCGGTGATCTTCTCTCTTTCA 60.416 50.000 0.00 0.00 0.00 2.69
622 623 0.252057 TCCCTCGGGAGTGACATTCA 60.252 55.000 0.00 0.00 39.76 2.57
735 736 7.444299 TCCGTATTAGTAAGAAAAACACACCT 58.556 34.615 0.00 0.00 0.00 4.00
796 797 3.069289 GGGTTCTACCAACGAAACGAAT 58.931 45.455 0.00 0.00 41.02 3.34
991 992 7.226325 CCTCTGAGATTGAATCATAAACCACTC 59.774 40.741 8.03 0.00 0.00 3.51
1006 1007 7.747155 AATGATAAGAATGCCTCTGAGATTG 57.253 36.000 6.17 0.00 33.37 2.67
1174 1175 0.916086 AGAACATCCCGCCACCATAA 59.084 50.000 0.00 0.00 0.00 1.90
1465 1468 0.183971 TGCTCGTTTTTCCTTCCCCA 59.816 50.000 0.00 0.00 0.00 4.96
1769 1773 4.510303 ACCTCCCCACCAATAGATAGAT 57.490 45.455 0.00 0.00 0.00 1.98
1857 1861 7.016153 TCCAAACACAATATCTTGAGTACCT 57.984 36.000 0.00 0.00 35.48 3.08
2052 2056 5.255687 TCCATACTGAACTCAAATGTGCAT 58.744 37.500 0.00 0.00 0.00 3.96
2161 2165 8.394877 GTCTCGATCAATACATCTCGAATCTAT 58.605 37.037 0.00 0.00 39.39 1.98
2288 2292 4.728772 CCCAATATCATGCCTCCAACTTA 58.271 43.478 0.00 0.00 0.00 2.24
2299 2303 5.128205 TCACTTCTCAAGCCCAATATCATG 58.872 41.667 0.00 0.00 0.00 3.07
2402 2406 8.265764 AGGAAGAAACAACCATAGTAACTATCC 58.734 37.037 0.00 0.00 0.00 2.59
2463 2467 3.428180 GCTCGAGTTATCTTGCTGACTCA 60.428 47.826 15.13 0.00 38.69 3.41
2475 2479 3.778618 GAGGGTAAAACGCTCGAGTTAT 58.221 45.455 15.13 0.00 45.91 1.89
2476 2480 3.221964 GAGGGTAAAACGCTCGAGTTA 57.778 47.619 15.13 1.54 45.91 2.24
2613 2621 2.472695 TGCGAGAAAAGGTGTGCTAT 57.527 45.000 0.00 0.00 0.00 2.97
2630 2638 8.437742 CACTTATTGAATGGAAACTTGAATTGC 58.562 33.333 0.00 0.00 0.00 3.56
2744 2752 5.547465 ACATGAAAAGACGATGTCCTAACA 58.453 37.500 0.00 0.00 40.38 2.41
2769 2777 1.609841 GGGAATCGAACCCGTGTCTTT 60.610 52.381 13.87 0.00 37.85 2.52


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

AutoCloner maintained by Alex Coulton.