Multiple sequence alignment - TraesCS3B01G469800

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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 TraesCS3B01G469800 chr3B 100.000 2498 0 0 1 2498 717182108 717179611 0 4614
1 TraesCS3B01G469800 chr3B 98.564 905 13 0 673 1577 201526993 201526089 0 1600
2 TraesCS3B01G469800 chr3B 95.761 920 33 4 1581 2497 643217777 643216861 0 1478
3 TraesCS3B01G469800 chr5D 98.674 905 12 0 673 1577 503218187 503217283 0 1605
4 TraesCS3B01G469800 chrUn 98.564 905 13 0 673 1577 216518633 216519537 0 1600
5 TraesCS3B01G469800 chrUn 98.564 905 13 0 673 1577 216521733 216520829 0 1600
6 TraesCS3B01G469800 chrUn 98.343 905 14 1 673 1577 93409662 93410565 0 1587
7 TraesCS3B01G469800 chrUn 98.126 907 15 1 673 1577 216522021 216522927 0 1580
8 TraesCS3B01G469800 chrUn 95.542 673 29 1 1 672 5642756 5643428 0 1075
9 TraesCS3B01G469800 chr6D 98.564 905 13 0 673 1577 168251795 168252699 0 1600
10 TraesCS3B01G469800 chr6D 98.564 905 13 0 673 1577 168254895 168253991 0 1600
11 TraesCS3B01G469800 chr3D 98.453 905 14 0 673 1577 589279573 589280477 0 1594
12 TraesCS3B01G469800 chr7B 96.192 919 32 2 1581 2497 151802041 151801124 0 1500
13 TraesCS3B01G469800 chr7B 95.892 925 30 6 1581 2497 503352238 503351314 0 1491
14 TraesCS3B01G469800 chr2B 95.582 928 31 5 1580 2497 539608118 539607191 0 1478
15 TraesCS3B01G469800 chr2B 95.562 676 24 4 1 672 444656385 444655712 0 1077
16 TraesCS3B01G469800 chr2B 95.542 673 28 2 1 672 210883122 210883793 0 1075
17 TraesCS3B01G469800 chr1B 95.756 919 36 2 1582 2497 615080676 615079758 0 1478
18 TraesCS3B01G469800 chr1B 95.582 928 30 4 1581 2497 129943694 129942767 0 1476
19 TraesCS3B01G469800 chr5B 95.676 925 29 7 1581 2494 213572666 213573590 0 1476
20 TraesCS3B01G469800 chr5B 95.647 919 38 1 1581 2497 448339816 448338898 0 1474
21 TraesCS3B01G469800 chr5B 96.285 673 23 2 1 672 497427917 497428588 0 1103
22 TraesCS3B01G469800 chr5B 95.542 673 28 2 1 672 497436081 497436752 0 1075
23 TraesCS3B01G469800 chr4B 95.652 920 37 2 1581 2497 372861057 372861976 0 1474
24 TraesCS3B01G469800 chr4B 95.407 675 27 3 1 672 404814212 404814885 0 1072
25 TraesCS3B01G469800 chr6B 95.876 679 19 4 1 672 436853197 436852521 0 1090
26 TraesCS3B01G469800 chr6B 95.549 674 25 5 1 672 333923282 333922612 0 1074
27 TraesCS3B01G469800 chr6B 95.542 673 26 4 1 670 436869636 436868965 0 1074


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 TraesCS3B01G469800 chr3B 717179611 717182108 2497 True 4614 4614 100.000 1 2498 1 chr3B.!!$R3 2497
1 TraesCS3B01G469800 chr3B 201526089 201526993 904 True 1600 1600 98.564 673 1577 1 chr3B.!!$R1 904
2 TraesCS3B01G469800 chr3B 643216861 643217777 916 True 1478 1478 95.761 1581 2497 1 chr3B.!!$R2 916
3 TraesCS3B01G469800 chr5D 503217283 503218187 904 True 1605 1605 98.674 673 1577 1 chr5D.!!$R1 904
4 TraesCS3B01G469800 chrUn 216520829 216521733 904 True 1600 1600 98.564 673 1577 1 chrUn.!!$R1 904
5 TraesCS3B01G469800 chrUn 216518633 216522927 4294 False 1590 1600 98.345 673 1577 2 chrUn.!!$F3 904
6 TraesCS3B01G469800 chrUn 93409662 93410565 903 False 1587 1587 98.343 673 1577 1 chrUn.!!$F2 904
7 TraesCS3B01G469800 chrUn 5642756 5643428 672 False 1075 1075 95.542 1 672 1 chrUn.!!$F1 671
8 TraesCS3B01G469800 chr6D 168251795 168252699 904 False 1600 1600 98.564 673 1577 1 chr6D.!!$F1 904
9 TraesCS3B01G469800 chr6D 168253991 168254895 904 True 1600 1600 98.564 673 1577 1 chr6D.!!$R1 904
10 TraesCS3B01G469800 chr3D 589279573 589280477 904 False 1594 1594 98.453 673 1577 1 chr3D.!!$F1 904
11 TraesCS3B01G469800 chr7B 151801124 151802041 917 True 1500 1500 96.192 1581 2497 1 chr7B.!!$R1 916
12 TraesCS3B01G469800 chr7B 503351314 503352238 924 True 1491 1491 95.892 1581 2497 1 chr7B.!!$R2 916
13 TraesCS3B01G469800 chr2B 539607191 539608118 927 True 1478 1478 95.582 1580 2497 1 chr2B.!!$R2 917
14 TraesCS3B01G469800 chr2B 444655712 444656385 673 True 1077 1077 95.562 1 672 1 chr2B.!!$R1 671
15 TraesCS3B01G469800 chr2B 210883122 210883793 671 False 1075 1075 95.542 1 672 1 chr2B.!!$F1 671
16 TraesCS3B01G469800 chr1B 615079758 615080676 918 True 1478 1478 95.756 1582 2497 1 chr1B.!!$R2 915
17 TraesCS3B01G469800 chr1B 129942767 129943694 927 True 1476 1476 95.582 1581 2497 1 chr1B.!!$R1 916
18 TraesCS3B01G469800 chr5B 213572666 213573590 924 False 1476 1476 95.676 1581 2494 1 chr5B.!!$F1 913
19 TraesCS3B01G469800 chr5B 448338898 448339816 918 True 1474 1474 95.647 1581 2497 1 chr5B.!!$R1 916
20 TraesCS3B01G469800 chr5B 497427917 497428588 671 False 1103 1103 96.285 1 672 1 chr5B.!!$F2 671
21 TraesCS3B01G469800 chr5B 497436081 497436752 671 False 1075 1075 95.542 1 672 1 chr5B.!!$F3 671
22 TraesCS3B01G469800 chr4B 372861057 372861976 919 False 1474 1474 95.652 1581 2497 1 chr4B.!!$F1 916
23 TraesCS3B01G469800 chr4B 404814212 404814885 673 False 1072 1072 95.407 1 672 1 chr4B.!!$F2 671
24 TraesCS3B01G469800 chr6B 436852521 436853197 676 True 1090 1090 95.876 1 672 1 chr6B.!!$R2 671
25 TraesCS3B01G469800 chr6B 333922612 333923282 670 True 1074 1074 95.549 1 672 1 chr6B.!!$R1 671
26 TraesCS3B01G469800 chr6B 436868965 436869636 671 True 1074 1074 95.542 1 670 1 chr6B.!!$R3 669

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
275 288 1.048601 CCGCCAAGCCCTAATCTCTA 58.951 55.0 0.0 0.0 0.0 2.43 F
366 379 2.620115 CCATCCTCCATCACCAATTTCG 59.380 50.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1132 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.0 0.0 44.23 4.00 R
1577 1590 2.225382 TCACCGAGAAGTATCCCACA 57.775 50.000 0.0 0.0 0.00 4.17 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
49 50 1.534729 ATCCACGGAGGCACTTTTTC 58.465 50.000 0.00 0.00 41.55 2.29
79 80 4.773323 AAGAATTTCTGGGCGAAAGAAG 57.227 40.909 0.00 0.00 44.29 2.85
275 288 1.048601 CCGCCAAGCCCTAATCTCTA 58.951 55.000 0.00 0.00 0.00 2.43
366 379 2.620115 CCATCCTCCATCACCAATTTCG 59.380 50.000 0.00 0.00 0.00 3.46
627 640 7.890515 TGATCCTATCTTGCAAGTCTATAGTG 58.109 38.462 25.19 16.66 0.00 2.74
829 842 9.416794 GTCATTCGATCTGAATACTACATGAAT 57.583 33.333 0.00 0.00 45.59 2.57
1070 1083 5.941948 AAAGAAGAATGTACTTCAACCGG 57.058 39.130 0.00 0.00 45.83 5.28
1118 1131 5.607119 AACATAGAAATCACACGTGGAAC 57.393 39.130 21.57 9.90 0.00 3.62
1119 1132 4.637276 ACATAGAAATCACACGTGGAACA 58.363 39.130 21.57 0.07 35.74 3.18
1232 1245 5.005740 GGTCCGTTTAGTATCCCAAAACTT 58.994 41.667 0.00 0.00 32.25 2.66
1299 1312 0.539986 GTTTGGGTAGAGCCGGATCA 59.460 55.000 23.83 5.01 38.44 2.92
1381 1394 2.287194 ATGGGGGAGGTGAAGGGG 60.287 66.667 0.00 0.00 0.00 4.79
1684 1702 6.858792 AAAGGAGGCCTTAATATCCCTTAA 57.141 37.500 17.50 0.00 43.92 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.925161 TTCGCCCAGAAATTCTTATTAATTTG 57.075 30.769 0.00 0.00 38.77 2.32
79 80 4.043100 GTGGGCCCCCTGGTGTAC 62.043 72.222 22.27 3.64 36.94 2.90
170 183 1.056660 TGGAGTTGGAGTTGAGGTCC 58.943 55.000 0.00 0.00 34.31 4.46
219 232 4.918810 AAACGCAATGAAACTTTCTCCT 57.081 36.364 3.22 0.00 0.00 3.69
275 288 0.327867 TCCAGATCAGCCCTCCCAAT 60.328 55.000 0.00 0.00 0.00 3.16
627 640 7.375834 TGTCGGATCATAACACATAATAGGTC 58.624 38.462 0.00 0.00 0.00 3.85
819 832 8.432013 TCATCTGGCTTATGTTATTCATGTAGT 58.568 33.333 0.00 0.00 37.91 2.73
829 842 4.439057 GTTCCGTCATCTGGCTTATGTTA 58.561 43.478 0.00 0.00 0.00 2.41
1058 1071 1.208776 AGGGCATACCGGTTGAAGTAC 59.791 52.381 15.04 0.00 46.96 2.73
1118 1131 2.843701 CTCTAGCTAATTGCCCACCTG 58.156 52.381 0.00 0.00 44.23 4.00
1119 1132 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
1232 1245 2.364324 ACTTGTCCGACTGTTGCTAAGA 59.636 45.455 0.00 0.00 0.00 2.10
1299 1312 2.551032 GCGTTTACCTAGCCAACACTTT 59.449 45.455 0.00 0.00 0.00 2.66
1371 1384 3.827752 GGAGCTTCCCCTTCACCT 58.172 61.111 0.00 0.00 0.00 4.00
1577 1590 2.225382 TCACCGAGAAGTATCCCACA 57.775 50.000 0.00 0.00 0.00 4.17
1684 1702 3.103091 GCGGGGTCCTAGCGGAAAT 62.103 63.158 0.00 0.00 42.08 2.17
2093 4163 7.877097 CCAAATTTATTGATTTGACACAAGGGA 59.123 33.333 10.89 0.00 45.47 4.20
2206 4467 4.159321 CCAAGTGACTCAGAGAATAGAGCA 59.841 45.833 3.79 0.00 35.28 4.26
2240 4501 6.951256 TCAAGTTCTTCATAGTGATCAACG 57.049 37.500 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.