Multiple sequence alignment - TraesCS7A01G058900

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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 TraesCS7A01G058900 chr7A 100.000 2993 0 0 1 2993 28455188 28458180 0.000000e+00 5528
1 TraesCS7A01G058900 chr7D 97.896 2995 54 3 1 2993 28036368 28039355 0.000000e+00 5173
2 TraesCS7A01G058900 chr4A 95.769 2647 87 11 1 2640 701758482 701761110 0.000000e+00 4244
3 TraesCS7A01G058900 chr4A 90.000 290 21 4 2710 2993 701761116 701761403 4.710000e-98 368
4 TraesCS7A01G058900 chr3D 78.687 990 184 22 963 1945 4958018 4957049 4.210000e-178 634
5 TraesCS7A01G058900 chr3D 82.982 570 91 6 963 1528 9634699 9635266 7.400000e-141 510
6 TraesCS7A01G058900 chrUn 77.800 982 193 19 963 1938 35296487 35297449 1.550000e-162 582
7 TraesCS7A01G058900 chrUn 79.002 862 156 19 963 1818 284401434 284400592 1.560000e-157 566
8 TraesCS7A01G058900 chrUn 79.002 862 156 19 963 1818 284407968 284407126 1.560000e-157 566
9 TraesCS7A01G058900 chrUn 79.002 862 156 19 963 1818 302991593 302990751 1.560000e-157 566
10 TraesCS7A01G058900 chrUn 78.886 862 157 19 963 1818 257885879 257885037 7.250000e-156 560
11 TraesCS7A01G058900 chr1A 77.230 953 195 16 583 1526 402229745 402230684 3.390000e-149 538


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 TraesCS7A01G058900 chr7A 28455188 28458180 2992 False 5528 5528 100.0000 1 2993 1 chr7A.!!$F1 2992
1 TraesCS7A01G058900 chr7D 28036368 28039355 2987 False 5173 5173 97.8960 1 2993 1 chr7D.!!$F1 2992
2 TraesCS7A01G058900 chr4A 701758482 701761403 2921 False 2306 4244 92.8845 1 2993 2 chr4A.!!$F1 2992
3 TraesCS7A01G058900 chr3D 4957049 4958018 969 True 634 634 78.6870 963 1945 1 chr3D.!!$R1 982
4 TraesCS7A01G058900 chr3D 9634699 9635266 567 False 510 510 82.9820 963 1528 1 chr3D.!!$F1 565
5 TraesCS7A01G058900 chrUn 35296487 35297449 962 False 582 582 77.8000 963 1938 1 chrUn.!!$F1 975
6 TraesCS7A01G058900 chrUn 284400592 284401434 842 True 566 566 79.0020 963 1818 1 chrUn.!!$R2 855
7 TraesCS7A01G058900 chrUn 284407126 284407968 842 True 566 566 79.0020 963 1818 1 chrUn.!!$R3 855
8 TraesCS7A01G058900 chrUn 302990751 302991593 842 True 566 566 79.0020 963 1818 1 chrUn.!!$R4 855
9 TraesCS7A01G058900 chrUn 257885037 257885879 842 True 560 560 78.8860 963 1818 1 chrUn.!!$R1 855
10 TraesCS7A01G058900 chr1A 402229745 402230684 939 False 538 538 77.2300 583 1526 1 chr1A.!!$F1 943

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
555 556 0.378257 CGTTCAATGGCTCAATCCCG 59.622 55.0 0.0 0.0 0.0 5.14 F
556 557 0.740737 GTTCAATGGCTCAATCCCGG 59.259 55.0 0.0 0.0 0.0 5.73 F
557 558 1.037030 TTCAATGGCTCAATCCCGGC 61.037 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 1430 1.321474 CCAAAGTCTGCCACATGTGT 58.679 50.000 23.79 1.62 0.00 3.72 R
1477 1484 1.445716 GGCATGCTGGCAGAGATCAC 61.446 60.000 20.86 0.00 43.14 3.06 R
2317 2334 2.448961 TCCCCTTTTCTTTGTCCATCCA 59.551 45.455 0.00 0.00 0.00 3.41 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
282 283 0.958382 TACCAACCAGCATCGGCAAC 60.958 55.000 0.00 0.00 44.61 4.17
322 323 6.723298 ACATTGACTTGTCCAATAACCAAA 57.277 33.333 0.00 0.00 33.35 3.28
443 444 6.183360 GCTGATGGTCTAATACAAATCGATCG 60.183 42.308 9.36 9.36 0.00 3.69
541 542 6.367695 CCTAAATATGTCACACAACTCGTTCA 59.632 38.462 0.00 0.00 0.00 3.18
555 556 0.378257 CGTTCAATGGCTCAATCCCG 59.622 55.000 0.00 0.00 0.00 5.14
556 557 0.740737 GTTCAATGGCTCAATCCCGG 59.259 55.000 0.00 0.00 0.00 5.73
557 558 1.037030 TTCAATGGCTCAATCCCGGC 61.037 55.000 0.00 0.00 0.00 6.13
558 559 2.123726 AATGGCTCAATCCCGGCC 60.124 61.111 0.00 0.00 45.45 6.13
559 560 3.738745 AATGGCTCAATCCCGGCCC 62.739 63.158 0.00 0.00 44.71 5.80
611 612 4.384647 GCAACATTAGACCTCTCCTCCAAT 60.385 45.833 0.00 0.00 0.00 3.16
625 626 2.880890 CCTCCAATAATCTTTCCGGCAG 59.119 50.000 0.00 0.00 0.00 4.85
706 707 3.456277 AGGCTAGAAGGACAAATACCAGG 59.544 47.826 0.00 0.00 0.00 4.45
835 837 2.951642 GCAGTAGGCATTTGCTGGAATA 59.048 45.455 2.12 0.00 43.97 1.75
935 937 4.081406 AGCAAGATGTTGTTAATGCCTCA 58.919 39.130 4.33 0.00 35.92 3.86
946 948 1.762522 AATGCCTCAGCCGATCCGAT 61.763 55.000 0.00 0.00 38.69 4.18
960 962 5.062308 GCCGATCCGATTGATTCTGTAATAC 59.938 44.000 0.00 0.00 32.41 1.89
1000 1002 6.604396 TCCTACCATGAGTTAGTTCGTATCAA 59.396 38.462 0.00 0.00 0.00 2.57
1287 1294 4.040755 ACTACCCTCAAGGCTCAACATAT 58.959 43.478 0.00 0.00 40.58 1.78
1423 1430 1.067915 TGTTCGATGAGCACATGACGA 60.068 47.619 0.00 2.50 36.82 4.20
1477 1484 1.566211 ACTCTGGGATGACACCTCTG 58.434 55.000 0.00 0.00 0.00 3.35
1550 1557 7.104290 ACTTGTCTAGACCTTGTAATTAAGCC 58.896 38.462 20.11 0.00 0.00 4.35
2317 2334 9.594478 AAACCACGAAAGAACAGAAAAATAATT 57.406 25.926 0.00 0.00 0.00 1.40
2452 2470 4.543692 CGTCAATAGTAACGACATAGGGG 58.456 47.826 0.00 0.00 41.29 4.79
2699 2717 5.171476 ACACGAATCCTAATCTCAACACAG 58.829 41.667 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.223187 CGGTTAACTTGTTGCGACCT 58.777 50.000 5.42 0.00 0.00 3.85
148 149 3.306088 CGAGAGAGGTTAAGAAGCACCAA 60.306 47.826 0.00 0.00 35.25 3.67
282 283 6.319658 AGTCAATGTATTCCAACATGCTAAGG 59.680 38.462 0.00 0.00 39.98 2.69
322 323 6.407202 AGCTTGTCGGTATCTTTGAACTTAT 58.593 36.000 0.00 0.00 0.00 1.73
366 367 8.782339 AATTTTGGAAAAGAAATAGCTGGATG 57.218 30.769 0.00 0.00 0.00 3.51
443 444 6.581171 AGAAGTTGGAAGAAATGTCCATTC 57.419 37.500 0.00 0.00 44.62 2.67
541 542 2.123726 GGCCGGGATTGAGCCATT 60.124 61.111 2.18 0.00 46.34 3.16
555 556 1.228552 TTTGAAGCTGGTCTGGGCC 60.229 57.895 0.00 0.00 0.00 5.80
556 557 1.246737 CCTTTGAAGCTGGTCTGGGC 61.247 60.000 0.00 0.00 0.00 5.36
557 558 0.111253 ACCTTTGAAGCTGGTCTGGG 59.889 55.000 0.00 0.00 0.00 4.45
558 559 1.986882 AACCTTTGAAGCTGGTCTGG 58.013 50.000 0.00 0.00 32.98 3.86
559 560 3.253432 GGTTAACCTTTGAAGCTGGTCTG 59.747 47.826 17.83 0.00 32.98 3.51
611 612 3.053991 TGGGAATTCTGCCGGAAAGATTA 60.054 43.478 5.05 0.00 37.49 1.75
706 707 1.617322 GGTTGAGAAAACACCTCCCC 58.383 55.000 0.00 0.00 0.00 4.81
915 917 4.418392 GCTGAGGCATTAACAACATCTTG 58.582 43.478 0.00 0.00 38.54 3.02
916 918 3.445096 GGCTGAGGCATTAACAACATCTT 59.555 43.478 0.00 0.00 40.87 2.40
935 937 1.414181 ACAGAATCAATCGGATCGGCT 59.586 47.619 0.00 0.00 34.28 5.52
946 948 5.670485 ACTGATGGCGTATTACAGAATCAA 58.330 37.500 0.00 0.00 33.53 2.57
960 962 3.357166 GTAGGAGACTAACTGATGGCG 57.643 52.381 0.00 0.00 46.54 5.69
1287 1294 0.112412 GCCTCTCAAGGAACCCCAAA 59.888 55.000 0.00 0.00 46.67 3.28
1423 1430 1.321474 CCAAAGTCTGCCACATGTGT 58.679 50.000 23.79 1.62 0.00 3.72
1462 1469 1.833630 GATCACAGAGGTGTCATCCCA 59.166 52.381 0.00 0.00 45.45 4.37
1477 1484 1.445716 GGCATGCTGGCAGAGATCAC 61.446 60.000 20.86 0.00 43.14 3.06
1550 1557 4.201724 GCTTAACAACAATAGACCGAGCAG 60.202 45.833 0.00 0.00 0.00 4.24
2317 2334 2.448961 TCCCCTTTTCTTTGTCCATCCA 59.551 45.455 0.00 0.00 0.00 3.41
2333 2351 4.724279 TTTCTAGTGAGCTTTTTCCCCT 57.276 40.909 0.00 0.00 0.00 4.79
2334 2352 5.984695 ATTTTCTAGTGAGCTTTTTCCCC 57.015 39.130 0.00 0.00 0.00 4.81
2676 2694 5.047306 TCTGTGTTGAGATTAGGATTCGTGT 60.047 40.000 0.00 0.00 0.00 4.49
2699 2717 6.016860 TGCATGCATGTTATGAACTTAGGATC 60.017 38.462 26.79 5.42 0.00 3.36


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

AutoCloner maintained by Alex Coulton.