Multiple sequence alignment - TraesCS2D01G519900

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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 TraesCS2D01G519900 chr2D 100.000 2668 0 0 1 2668 609434210 609436877 0.000000e+00 4927
1 TraesCS2D01G519900 chr2D 90.110 91 2 5 331 416 272795807 272795895 7.810000e-21 111
2 TraesCS2D01G519900 chr2A 97.603 2670 53 7 1 2668 742132850 742135510 0.000000e+00 4566
3 TraesCS2D01G519900 chr2A 90.110 91 2 5 331 416 726910964 726911052 7.810000e-21 111
4 TraesCS2D01G519900 chr2B 96.682 1296 30 2 1385 2668 743730360 743731654 0.000000e+00 2143
5 TraesCS2D01G519900 chr2B 94.766 1089 28 5 264 1351 743729302 743730362 0.000000e+00 1668
6 TraesCS2D01G519900 chr2B 96.903 226 7 0 1 226 743729079 743729304 1.940000e-101 379
7 TraesCS2D01G519900 chr6A 91.111 90 2 4 331 416 445904256 445904343 1.680000e-22 117
8 TraesCS2D01G519900 chr5D 90.000 90 3 5 331 416 329122020 329122107 7.810000e-21 111
9 TraesCS2D01G519900 chr3B 90.110 91 2 5 331 416 201525096 201525008 7.810000e-21 111
10 TraesCS2D01G519900 chrUn 89.130 92 2 4 331 416 23290066 23290155 1.010000e-19 108
11 TraesCS2D01G519900 chrUn 89.130 92 2 4 331 416 93411545 93411634 1.010000e-19 108


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 TraesCS2D01G519900 chr2D 609434210 609436877 2667 False 4927.000000 4927 100.000 1 2668 1 chr2D.!!$F2 2667
1 TraesCS2D01G519900 chr2A 742132850 742135510 2660 False 4566.000000 4566 97.603 1 2668 1 chr2A.!!$F2 2667
2 TraesCS2D01G519900 chr2B 743729079 743731654 2575 False 1396.666667 2143 96.117 1 2668 3 chr2B.!!$F1 2667

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
817 819 0.531532 ATTCGCATTGGCTCTCCTCG 60.532 55.0 0.0 0.0 38.1 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 2511 4.283467 TCATGAAATCCCCATAGTCCTACG 59.717 45.833 0.0 0.0 0.0 3.51 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
42 43 4.900635 AAGGAAGTGTTAACAACTGCAG 57.099 40.909 13.48 13.48 0.00 4.41
86 87 7.039993 GGAGTAAGAAAAAGGAGGCAAATAACA 60.040 37.037 0.00 0.00 0.00 2.41
134 135 9.525826 AGTTCAGGATTTGTCAAAAGATCTAAT 57.474 29.630 1.31 0.00 0.00 1.73
234 235 3.876341 TCGGTTACAAACAGAAACAGGT 58.124 40.909 0.00 0.00 32.68 4.00
376 377 6.058183 CCATCTAAGATTTCGATTCCCAGTT 58.942 40.000 0.00 0.00 0.00 3.16
691 693 9.455847 CTTCTGTTCTTGTTTCTCATAAAAAGG 57.544 33.333 0.00 0.00 0.00 3.11
817 819 0.531532 ATTCGCATTGGCTCTCCTCG 60.532 55.000 0.00 0.00 38.10 4.63
824 826 3.743396 GCATTGGCTCTCCTCGTAATAAG 59.257 47.826 0.00 0.00 36.96 1.73
848 850 2.087646 GTCCATGCTTTTCCTCTCCAC 58.912 52.381 0.00 0.00 0.00 4.02
873 875 6.976349 CCGTAAAGAATAACCCCTAAAAATGC 59.024 38.462 0.00 0.00 0.00 3.56
935 937 4.518970 AGGCAAACGCATTACCATATAAGG 59.481 41.667 0.00 0.00 0.00 2.69
1048 1050 1.118356 CATCCTCCCCTTCCTCCTCG 61.118 65.000 0.00 0.00 0.00 4.63
1085 1087 2.203877 TACTGGTTCCCCTGCCGT 60.204 61.111 0.00 0.00 33.14 5.68
1372 1374 2.455032 CTAGCTCTGACGTACATGTGC 58.545 52.381 9.11 6.17 0.00 4.57
1373 1375 0.603065 AGCTCTGACGTACATGTGCA 59.397 50.000 14.55 3.90 0.00 4.57
1417 1419 4.486090 GATGAATCATGGATTGCATGCTC 58.514 43.478 20.33 8.93 31.89 4.26
1451 1453 0.184211 ATGCATGCAGGTATGAGGCA 59.816 50.000 26.69 0.00 42.43 4.75
1538 1540 2.591753 GTATCTGCAGGCCAGGCA 59.408 61.111 19.46 19.46 42.05 4.75
1585 1587 0.758734 CAGGACTCACCAGAACACCA 59.241 55.000 0.00 0.00 42.04 4.17
1712 1714 6.467677 GTGGTATATGACTGCCATATTGTCT 58.532 40.000 1.76 0.00 43.97 3.41
1719 1721 6.839124 TGACTGCCATATTGTCTTTTGAAT 57.161 33.333 0.00 0.00 0.00 2.57
1973 1988 2.052891 CAACATCGTGCACCAACAATG 58.947 47.619 12.15 9.79 0.00 2.82
2080 2095 4.696479 AATCCGCTCTCCATAGAACATT 57.304 40.909 0.00 0.00 0.00 2.71
2434 2449 0.595095 GCAAAGAGCCCAGTGACAAG 59.405 55.000 0.00 0.00 37.23 3.16
2496 2511 3.557595 CGTTAGGCATCTGATCCTCAAAC 59.442 47.826 10.60 9.93 34.02 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.613801 TCTTACTCCTATCCTATCAAGATGCTC 59.386 40.741 0.00 0.00 0.00 4.26
52 53 7.016760 GCCTCCTTTTTCTTACTCCTATCCTAT 59.983 40.741 0.00 0.00 0.00 2.57
73 74 4.332828 ACAAGTAGGTGTTATTTGCCTCC 58.667 43.478 0.00 0.00 33.56 4.30
234 235 5.809001 AGGAAACTTCATGCTGATACTTGA 58.191 37.500 0.00 0.00 37.44 3.02
261 262 5.930135 AGTTGTCTTGTGGAGAAAGTGTAT 58.070 37.500 0.00 0.00 35.79 2.29
480 481 0.031043 GTGTGTGCTGCATGCTCAAA 59.969 50.000 20.33 9.20 45.14 2.69
487 488 0.887836 CTCACCAGTGTGTGCTGCAT 60.888 55.000 5.27 0.00 43.26 3.96
673 675 9.463443 CTGGTTAACCTTTTTATGAGAAACAAG 57.537 33.333 24.78 4.43 36.82 3.16
691 693 6.442513 AGATAGCATTTTCAGCTGGTTAAC 57.557 37.500 15.13 0.00 43.33 2.01
817 819 5.299531 GGAAAAGCATGGACCTCCTTATTAC 59.700 44.000 0.00 0.00 36.82 1.89
824 826 1.283321 AGAGGAAAAGCATGGACCTCC 59.717 52.381 0.00 0.00 45.53 4.30
848 850 6.976349 GCATTTTTAGGGGTTATTCTTTACGG 59.024 38.462 0.00 0.00 0.00 4.02
873 875 2.430080 GAAAGTGCCTGCGTCGTGTG 62.430 60.000 0.00 0.00 0.00 3.82
935 937 2.045926 ACGCCATGCAAGGTCCTC 60.046 61.111 10.15 0.00 0.00 3.71
1048 1050 2.704342 GATTGGGGCAATGCGATGGC 62.704 60.000 0.00 6.56 44.56 4.40
1305 1307 2.257371 CATTGTTGCAGCTGCGCT 59.743 55.556 32.11 12.76 45.83 5.92
1372 1374 4.444056 CGTTAAAGTTGCCTTTGGTGATTG 59.556 41.667 0.00 0.00 41.03 2.67
1373 1375 4.339814 TCGTTAAAGTTGCCTTTGGTGATT 59.660 37.500 0.00 0.00 41.03 2.57
1417 1419 8.033626 ACCTGCATGCATATATATGATCGATAG 58.966 37.037 22.97 13.76 35.75 2.08
1538 1540 3.567308 TGGCACAGCTTCACCTCT 58.433 55.556 0.00 0.00 0.00 3.69
1585 1587 2.110627 GCGCCATGAGGATGCTCT 59.889 61.111 15.82 0.00 36.89 4.09
1712 1714 5.565509 TCACTAGCCACCATGTATTCAAAA 58.434 37.500 0.00 0.00 0.00 2.44
1719 1721 9.860650 ATAAATTAATTCACTAGCCACCATGTA 57.139 29.630 0.10 0.00 0.00 2.29
2496 2511 4.283467 TCATGAAATCCCCATAGTCCTACG 59.717 45.833 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.