Multiple sequence alignment - TraesCS7A01G085000

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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 TraesCS7A01G085000 chr7A 100.000 2549 0 0 1 2549 49207643 49210191 0 4708
1 TraesCS7A01G085000 chr7A 96.280 1989 54 6 564 2549 689996372 689994401 0 3245
2 TraesCS7A01G085000 chr7A 95.281 2013 54 10 567 2549 14473100 14471099 0 3153
3 TraesCS7A01G085000 chr7A 96.432 1149 36 3 567 1712 18189929 18191075 0 1890
4 TraesCS7A01G085000 chr5A 97.433 1987 43 4 565 2549 563443927 563445907 0 3380
5 TraesCS7A01G085000 chr5A 96.322 571 21 0 1 571 540853214 540853784 0 939
6 TraesCS7A01G085000 chr1A 97.031 1987 55 3 567 2549 50511105 50513091 0 3339
7 TraesCS7A01G085000 chr2A 96.974 1983 54 3 567 2549 771778418 771780394 0 3325
8 TraesCS7A01G085000 chr2A 96.477 1987 48 5 565 2549 775967965 775965999 0 3262
9 TraesCS7A01G085000 chr2A 94.761 1985 58 19 567 2549 744582028 744583968 0 3048
10 TraesCS7A01G085000 chr2A 96.516 1148 33 2 568 1712 764220190 764221333 0 1892
11 TraesCS7A01G085000 chr3A 96.633 1990 45 5 567 2549 683237674 683235700 0 3284
12 TraesCS7A01G085000 chr3A 96.864 1148 29 2 568 1712 719846459 719847602 0 1914
13 TraesCS7A01G085000 chr4A 95.978 1989 57 7 563 2549 29028997 29030964 0 3208
14 TraesCS7A01G085000 chr6A 95.567 1985 57 7 568 2549 203520912 203518956 0 3149
15 TraesCS7A01G085000 chr6B 98.249 571 10 0 1 571 648276452 648277022 0 1000
16 TraesCS7A01G085000 chr5B 98.249 571 10 0 1 571 347980531 347981101 0 1000
17 TraesCS7A01G085000 chr1D 97.898 571 12 0 1 571 462981152 462981722 0 989
18 TraesCS7A01G085000 chrUn 97.548 571 14 0 1 571 90489113 90488543 0 977
19 TraesCS7A01G085000 chr7D 97.548 571 14 0 1 571 195363581 195363011 0 977
20 TraesCS7A01G085000 chr7D 97.198 571 16 0 1 571 446939156 446938586 0 966
21 TraesCS7A01G085000 chr5D 97.548 571 14 0 1 571 552055718 552056288 0 977
22 TraesCS7A01G085000 chr3B 97.548 571 14 0 1 571 513676390 513675820 0 977


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 TraesCS7A01G085000 chr7A 49207643 49210191 2548 False 4708 4708 100.000 1 2549 1 chr7A.!!$F2 2548
1 TraesCS7A01G085000 chr7A 689994401 689996372 1971 True 3245 3245 96.280 564 2549 1 chr7A.!!$R2 1985
2 TraesCS7A01G085000 chr7A 14471099 14473100 2001 True 3153 3153 95.281 567 2549 1 chr7A.!!$R1 1982
3 TraesCS7A01G085000 chr7A 18189929 18191075 1146 False 1890 1890 96.432 567 1712 1 chr7A.!!$F1 1145
4 TraesCS7A01G085000 chr5A 563443927 563445907 1980 False 3380 3380 97.433 565 2549 1 chr5A.!!$F2 1984
5 TraesCS7A01G085000 chr5A 540853214 540853784 570 False 939 939 96.322 1 571 1 chr5A.!!$F1 570
6 TraesCS7A01G085000 chr1A 50511105 50513091 1986 False 3339 3339 97.031 567 2549 1 chr1A.!!$F1 1982
7 TraesCS7A01G085000 chr2A 771778418 771780394 1976 False 3325 3325 96.974 567 2549 1 chr2A.!!$F3 1982
8 TraesCS7A01G085000 chr2A 775965999 775967965 1966 True 3262 3262 96.477 565 2549 1 chr2A.!!$R1 1984
9 TraesCS7A01G085000 chr2A 744582028 744583968 1940 False 3048 3048 94.761 567 2549 1 chr2A.!!$F1 1982
10 TraesCS7A01G085000 chr2A 764220190 764221333 1143 False 1892 1892 96.516 568 1712 1 chr2A.!!$F2 1144
11 TraesCS7A01G085000 chr3A 683235700 683237674 1974 True 3284 3284 96.633 567 2549 1 chr3A.!!$R1 1982
12 TraesCS7A01G085000 chr3A 719846459 719847602 1143 False 1914 1914 96.864 568 1712 1 chr3A.!!$F1 1144
13 TraesCS7A01G085000 chr4A 29028997 29030964 1967 False 3208 3208 95.978 563 2549 1 chr4A.!!$F1 1986
14 TraesCS7A01G085000 chr6A 203518956 203520912 1956 True 3149 3149 95.567 568 2549 1 chr6A.!!$R1 1981
15 TraesCS7A01G085000 chr6B 648276452 648277022 570 False 1000 1000 98.249 1 571 1 chr6B.!!$F1 570
16 TraesCS7A01G085000 chr5B 347980531 347981101 570 False 1000 1000 98.249 1 571 1 chr5B.!!$F1 570
17 TraesCS7A01G085000 chr1D 462981152 462981722 570 False 989 989 97.898 1 571 1 chr1D.!!$F1 570
18 TraesCS7A01G085000 chrUn 90488543 90489113 570 True 977 977 97.548 1 571 1 chrUn.!!$R1 570
19 TraesCS7A01G085000 chr7D 195363011 195363581 570 True 977 977 97.548 1 571 1 chr7D.!!$R1 570
20 TraesCS7A01G085000 chr7D 446938586 446939156 570 True 966 966 97.198 1 571 1 chr7D.!!$R2 570
21 TraesCS7A01G085000 chr5D 552055718 552056288 570 False 977 977 97.548 1 571 1 chr5D.!!$F1 570
22 TraesCS7A01G085000 chr3B 513675820 513676390 570 True 977 977 97.548 1 571 1 chr3B.!!$R1 570

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
189 190 0.108567 GACCTTCCTCGAGTTGCCTC 60.109 60.0 12.31 0.0 0.00 4.70 F
555 556 0.260230 TCAAAAGTTGGAGCACCCCA 59.740 50.0 0.00 0.0 34.81 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1213 0.679505 CTGGTTCCTCGGTGTCTGAA 59.320 55.000 0.0 0.0 0.0 3.02 R
2231 2372 2.826488 AGTCTTGCCATCTGTCCTAGT 58.174 47.619 0.0 0.0 0.0 2.57 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
55 56 6.830912 TGCCATGTAGTTTATGAGCTAGAAT 58.169 36.000 0.00 0.0 0.00 2.40
189 190 0.108567 GACCTTCCTCGAGTTGCCTC 60.109 60.000 12.31 0.0 0.00 4.70
228 229 6.071616 GGCATTTTTGTCTATGTAACCCTGAA 60.072 38.462 0.00 0.0 0.00 3.02
555 556 0.260230 TCAAAAGTTGGAGCACCCCA 59.740 50.000 0.00 0.0 34.81 4.96
643 644 4.455533 AGATGCGAATTGTGCTCAGTTTTA 59.544 37.500 0.00 0.0 0.00 1.52
693 694 1.289380 GAACTCTGCCGTCTCCGTT 59.711 57.895 0.00 0.0 0.00 4.44
745 746 1.300697 GACCAGGCGACAGAAACGT 60.301 57.895 0.00 0.0 0.00 3.99
789 807 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.0 34.18 4.12
812 830 0.897863 AGAGCCGTTGAGCAGAGAGT 60.898 55.000 0.00 0.0 34.23 3.24
816 849 0.730834 CCGTTGAGCAGAGAGTCGTG 60.731 60.000 0.00 0.0 0.00 4.35
954 1058 3.458163 CGGCGGTGGGAAGCTAGA 61.458 66.667 0.00 0.0 0.00 2.43
992 1096 0.827368 GTTGAGATCCCTTCGGCTCT 59.173 55.000 0.00 0.0 37.33 4.09
1078 1182 1.957562 CCTGTCTTCGTCTGTCCGT 59.042 57.895 0.00 0.0 0.00 4.69
1109 1213 0.958876 GGCGTTGATCGGAGGGTTTT 60.959 55.000 0.00 0.0 40.26 2.43
1170 1274 3.545703 CAGCGAGAATGGGGTAAGAATT 58.454 45.455 0.00 0.0 0.00 2.17
1397 1501 3.318875 CGAAGCACGCACTGACAA 58.681 55.556 0.00 0.0 34.51 3.18
1539 1644 7.382110 TGGTTGTAATGTTGAAAATGTATGGG 58.618 34.615 0.00 0.0 0.00 4.00
1963 2102 3.574614 CGGAGCCAAACAATTAAGGTTG 58.425 45.455 0.00 0.0 35.25 3.77
2160 2301 4.885413 TGAAGGATGGAAAATGCACAAAG 58.115 39.130 0.00 0.0 0.00 2.77
2231 2372 0.324552 TAGGGCTACGCTGGTAACCA 60.325 55.000 0.00 0.0 36.73 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.888716 TGCTTTTATCGATTACTAAATGCTCAA 58.111 29.630 20.69 7.00 38.14 3.02
189 190 6.924111 ACAAAAATGCCTCCTATTTACACAG 58.076 36.000 0.00 0.00 0.00 3.66
228 229 1.884579 CTCATGCTTGGTTCTGTGCTT 59.115 47.619 0.00 0.00 0.00 3.91
555 556 6.557633 AGGATAATTAACCCTATCCGTTCAGT 59.442 38.462 8.09 0.00 45.65 3.41
745 746 4.520874 TGCAACGGTCTGAATAAAATTGGA 59.479 37.500 0.00 0.00 0.00 3.53
789 807 1.181741 TCTGCTCAACGGCTCTCTGT 61.182 55.000 0.00 0.00 0.00 3.41
816 849 2.094762 CTTATATAGCACACCCGCCC 57.905 55.000 0.00 0.00 0.00 6.13
992 1096 1.942776 TGAGGAAGACATGGAGCTCA 58.057 50.000 17.19 1.87 0.00 4.26
1109 1213 0.679505 CTGGTTCCTCGGTGTCTGAA 59.320 55.000 0.00 0.00 0.00 3.02
1539 1644 6.661304 AATTCCTCCATAATTCATGCCTTC 57.339 37.500 0.00 0.00 32.84 3.46
2144 2285 5.470777 CACCAATTCTTTGTGCATTTTCCAT 59.529 36.000 0.00 0.00 0.00 3.41
2160 2301 3.451894 CCCCAGCCGCACCAATTC 61.452 66.667 0.00 0.00 0.00 2.17
2200 2341 3.078837 CGTAGCCCTAAACACCACAAAT 58.921 45.455 0.00 0.00 0.00 2.32
2231 2372 2.826488 AGTCTTGCCATCTGTCCTAGT 58.174 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.