Multiple sequence alignment - TraesCS4A01G278100

Loading Multiple Alignment...

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 TraesCS4A01G278100 chr4A 100.000 2864 0 0 1 2864 585645903 585648766 0.000000e+00 5289
1 TraesCS4A01G278100 chr4A 88.235 102 9 2 2701 2801 37298227 37298326 5.010000e-23 119
2 TraesCS4A01G278100 chr5A 99.289 984 7 0 1881 2864 693648337 693647354 0.000000e+00 1779
3 TraesCS4A01G278100 chr5A 97.563 985 21 1 1 985 463088871 463089852 0.000000e+00 1683
4 TraesCS4A01G278100 chr5A 96.154 988 34 2 1 984 670281282 670282269 0.000000e+00 1611
5 TraesCS4A01G278100 chr5A 96.244 985 29 2 1 984 580479575 580480552 0.000000e+00 1607
6 TraesCS4A01G278100 chr7A 97.157 985 27 1 1 984 519119256 519120240 0.000000e+00 1663
7 TraesCS4A01G278100 chr7A 96.878 993 29 2 1 992 149848935 149849926 0.000000e+00 1661
8 TraesCS4A01G278100 chr7A 96.569 991 29 1 1 986 712156715 712155725 0.000000e+00 1637
9 TraesCS4A01G278100 chr1A 96.850 984 29 2 1 983 545723123 545722141 0.000000e+00 1644
10 TraesCS4A01G278100 chr1A 96.165 991 31 3 1 984 365628766 365629756 0.000000e+00 1613
11 TraesCS4A01G278100 chr3A 96.162 990 31 3 1 984 674760823 674759835 0.000000e+00 1611
12 TraesCS4A01G278100 chr2A 95.098 918 24 3 984 1883 195773458 195774372 0.000000e+00 1426
13 TraesCS4A01G278100 chr4D 93.435 914 43 2 984 1880 15243801 15244714 0.000000e+00 1339
14 TraesCS4A01G278100 chr4B 93.958 480 29 0 984 1463 25559186 25559665 0.000000e+00 726
15 TraesCS4A01G278100 chr4B 92.483 439 15 6 1460 1883 25571127 25571562 1.890000e-171 612
16 TraesCS4A01G278100 chr3D 81.794 747 103 21 1881 2606 374274117 374273383 1.900000e-166 595
17 TraesCS4A01G278100 chr3D 90.385 104 8 2 2701 2803 374273179 374273077 4.980000e-28 135
18 TraesCS4A01G278100 chr1D 81.067 750 103 28 1881 2606 161033086 161033820 1.930000e-156 562
19 TraesCS4A01G278100 chr1D 88.571 105 9 2 2701 2803 161034025 161034128 1.080000e-24 124
20 TraesCS4A01G278100 chr2B 86.667 165 15 2 2321 2478 653278760 653278924 2.930000e-40 176
21 TraesCS4A01G278100 chr7D 88.462 104 10 2 2701 2803 616926517 616926619 1.080000e-24 124


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 TraesCS4A01G278100 chr4A 585645903 585648766 2863 False 5289 5289 100.0000 1 2864 1 chr4A.!!$F2 2863
1 TraesCS4A01G278100 chr5A 693647354 693648337 983 True 1779 1779 99.2890 1881 2864 1 chr5A.!!$R1 983
2 TraesCS4A01G278100 chr5A 463088871 463089852 981 False 1683 1683 97.5630 1 985 1 chr5A.!!$F1 984
3 TraesCS4A01G278100 chr5A 670281282 670282269 987 False 1611 1611 96.1540 1 984 1 chr5A.!!$F3 983
4 TraesCS4A01G278100 chr5A 580479575 580480552 977 False 1607 1607 96.2440 1 984 1 chr5A.!!$F2 983
5 TraesCS4A01G278100 chr7A 519119256 519120240 984 False 1663 1663 97.1570 1 984 1 chr7A.!!$F2 983
6 TraesCS4A01G278100 chr7A 149848935 149849926 991 False 1661 1661 96.8780 1 992 1 chr7A.!!$F1 991
7 TraesCS4A01G278100 chr7A 712155725 712156715 990 True 1637 1637 96.5690 1 986 1 chr7A.!!$R1 985
8 TraesCS4A01G278100 chr1A 545722141 545723123 982 True 1644 1644 96.8500 1 983 1 chr1A.!!$R1 982
9 TraesCS4A01G278100 chr1A 365628766 365629756 990 False 1613 1613 96.1650 1 984 1 chr1A.!!$F1 983
10 TraesCS4A01G278100 chr3A 674759835 674760823 988 True 1611 1611 96.1620 1 984 1 chr3A.!!$R1 983
11 TraesCS4A01G278100 chr2A 195773458 195774372 914 False 1426 1426 95.0980 984 1883 1 chr2A.!!$F1 899
12 TraesCS4A01G278100 chr4D 15243801 15244714 913 False 1339 1339 93.4350 984 1880 1 chr4D.!!$F1 896
13 TraesCS4A01G278100 chr3D 374273077 374274117 1040 True 365 595 86.0895 1881 2803 2 chr3D.!!$R1 922
14 TraesCS4A01G278100 chr1D 161033086 161034128 1042 False 343 562 84.8190 1881 2803 2 chr1D.!!$F1 922

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
643 644 0.399806 ATTGAGAGGGGGAGAGGAGC 60.400 60.000 0.0 0.0 0.0 4.70 F
1024 1040 1.152652 ATCGTCCTCATCGGCCTCT 60.153 57.895 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1685 0.036388 GGGATGAACAAGTCGAGGCA 60.036 55.000 0.0 0.0 0.0 4.75 R
2282 2325 2.092646 CGGGGAAGAGAGAGAGAGAGAA 60.093 54.545 0.0 0.0 0.0 2.87 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
411 412 5.981174 TCCATAAACTAAACTAGGGTTCCG 58.019 41.667 0.00 0.0 34.14 4.30
643 644 0.399806 ATTGAGAGGGGGAGAGGAGC 60.400 60.000 0.00 0.0 0.00 4.70
799 815 2.771639 CGGAGGCGCTGCACTACTA 61.772 63.158 7.64 0.0 0.00 1.82
868 884 1.509463 CTAGGCGTTGCACCGTAGA 59.491 57.895 5.30 0.0 0.00 2.59
927 943 5.105756 GGCCAGTGCTGTGAAATAGTTTTAT 60.106 40.000 0.00 0.0 37.74 1.40
932 948 4.142491 TGCTGTGAAATAGTTTTATGGGCG 60.142 41.667 0.00 0.0 0.00 6.13
1024 1040 1.152652 ATCGTCCTCATCGGCCTCT 60.153 57.895 0.00 0.0 0.00 3.69
1040 1056 3.536917 CTCATGGGGCGCGGTCTA 61.537 66.667 8.83 0.0 0.00 2.59
1358 1374 3.652869 TCCAACTCCTTGACAAGAATCCT 59.347 43.478 16.99 0.0 0.00 3.24
1572 1603 3.083997 AGGATGTCTGGGGCCGTC 61.084 66.667 0.00 0.0 0.00 4.79
1573 1604 3.399181 GGATGTCTGGGGCCGTCA 61.399 66.667 0.00 0.0 0.00 4.35
1654 1685 0.962489 CCGAGATAAGATCACCGGCT 59.038 55.000 0.00 0.0 39.54 5.52
2282 2325 0.178990 GCCCCAGTTGGTTGTTCTCT 60.179 55.000 0.00 0.0 0.00 3.10
2645 2694 5.536538 TGTAATGCTTCATGTGTTTGGGTTA 59.463 36.000 0.00 0.0 0.00 2.85
2835 3029 9.492973 GTGTAAGGTTAGGTTCAAGTGTTATTA 57.507 33.333 0.00 0.0 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
411 412 4.394610 ACAACCCTTGTTTGTTTGATTTGC 59.605 37.500 0.00 0.00 42.22 3.68
848 864 3.652539 TACGGTGCAACGCCTAGCC 62.653 63.158 26.87 0.00 38.12 3.93
1024 1040 3.845259 GTAGACCGCGCCCCATGA 61.845 66.667 0.00 0.00 0.00 3.07
1062 1078 3.066190 GCTTGCATGGCCTCAGCA 61.066 61.111 12.29 12.29 42.56 4.41
1206 1222 0.245539 GGTCGGATCCGTTGAGAACA 59.754 55.000 32.15 9.00 40.74 3.18
1654 1685 0.036388 GGGATGAACAAGTCGAGGCA 60.036 55.000 0.00 0.00 0.00 4.75
2282 2325 2.092646 CGGGGAAGAGAGAGAGAGAGAA 60.093 54.545 0.00 0.00 0.00 2.87
2645 2694 3.584848 ACTCCCACTAGAGCAAAATCACT 59.415 43.478 0.00 0.00 37.39 3.41
2835 3029 5.410355 AAAATGCTGCCAAATACATGACT 57.590 34.783 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.