Multiple sequence alignment - TraesCS7B01G139600

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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 TraesCS7B01G139600 chr7B 100.000 2607 0 0 1 2607 175997781 176000387 0 4815
1 TraesCS7B01G139600 chr7D 95.979 1691 41 8 939 2607 220979537 220977852 0 2721
2 TraesCS7B01G139600 chr7D 92.513 935 65 5 1 932 579548337 579547405 0 1334
3 TraesCS7B01G139600 chr7A 93.857 1693 55 16 932 2607 235469252 235467592 0 2505
4 TraesCS7B01G139600 chr5B 98.818 931 11 0 1 931 239430349 239431279 0 1659
5 TraesCS7B01G139600 chr6A 97.950 927 18 1 1 926 6900350 6899424 0 1605
6 TraesCS7B01G139600 chr6A 97.749 933 20 1 1 932 459870135 459869203 0 1605
7 TraesCS7B01G139600 chr2A 97.749 933 20 1 1 932 484296116 484295184 0 1605
8 TraesCS7B01G139600 chr3B 96.674 932 30 1 1 931 732887447 732888378 0 1548
9 TraesCS7B01G139600 chr3B 95.815 932 38 1 1 931 684082542 684083473 0 1504
10 TraesCS7B01G139600 chr1B 96.133 931 35 1 1 930 420751031 420750101 0 1519
11 TraesCS7B01G139600 chr2D 92.193 935 68 5 1 932 580270313 580269381 0 1317


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 TraesCS7B01G139600 chr7B 175997781 176000387 2606 False 4815 4815 100.000 1 2607 1 chr7B.!!$F1 2606
1 TraesCS7B01G139600 chr7D 220977852 220979537 1685 True 2721 2721 95.979 939 2607 1 chr7D.!!$R1 1668
2 TraesCS7B01G139600 chr7D 579547405 579548337 932 True 1334 1334 92.513 1 932 1 chr7D.!!$R2 931
3 TraesCS7B01G139600 chr7A 235467592 235469252 1660 True 2505 2505 93.857 932 2607 1 chr7A.!!$R1 1675
4 TraesCS7B01G139600 chr5B 239430349 239431279 930 False 1659 1659 98.818 1 931 1 chr5B.!!$F1 930
5 TraesCS7B01G139600 chr6A 6899424 6900350 926 True 1605 1605 97.950 1 926 1 chr6A.!!$R1 925
6 TraesCS7B01G139600 chr6A 459869203 459870135 932 True 1605 1605 97.749 1 932 1 chr6A.!!$R2 931
7 TraesCS7B01G139600 chr2A 484295184 484296116 932 True 1605 1605 97.749 1 932 1 chr2A.!!$R1 931
8 TraesCS7B01G139600 chr3B 732887447 732888378 931 False 1548 1548 96.674 1 931 1 chr3B.!!$F2 930
9 TraesCS7B01G139600 chr3B 684082542 684083473 931 False 1504 1504 95.815 1 931 1 chr3B.!!$F1 930
10 TraesCS7B01G139600 chr1B 420750101 420751031 930 True 1519 1519 96.133 1 930 1 chr1B.!!$R1 929
11 TraesCS7B01G139600 chr2D 580269381 580270313 932 True 1317 1317 92.193 1 932 1 chr2D.!!$R1 931

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
476 481 2.573869 CGAGTGCACCGGATGTCT 59.426 61.111 14.63 6.07 0.0 3.41 F
1233 1248 0.463204 CCTCGCAGTGATCCATGACT 59.537 55.000 0.00 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1563 0.254178 AAGATGTACCCTGCCTGCAG 59.746 55.000 12.17 12.17 43.26 4.41 R
2404 2438 1.072505 GAGGACTTTCCAACGGCCA 59.927 57.895 2.24 0.00 39.61 5.36 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
476 481 2.573869 CGAGTGCACCGGATGTCT 59.426 61.111 14.63 6.07 0.00 3.41
567 572 6.364701 TGTTTTGGCTCTATAGGTTGCATAT 58.635 36.000 0.00 0.00 0.00 1.78
989 994 3.071206 GGTGAGGCGAGGCTGAGA 61.071 66.667 3.24 0.00 0.00 3.27
1098 1113 4.373116 GGGTCGCTGTCTCGGCAA 62.373 66.667 1.60 0.00 35.49 4.52
1233 1248 0.463204 CCTCGCAGTGATCCATGACT 59.537 55.000 0.00 0.00 0.00 3.41
1241 1256 4.039004 GCAGTGATCCATGACTATCTGACT 59.961 45.833 0.00 0.00 0.00 3.41
1244 1259 5.476599 AGTGATCCATGACTATCTGACTAGC 59.523 44.000 0.00 0.00 0.00 3.42
1246 1261 6.015519 GTGATCCATGACTATCTGACTAGCTT 60.016 42.308 0.00 0.00 0.00 3.74
1261 1276 4.192317 ACTAGCTTAAGTTATGCACCTGC 58.808 43.478 19.55 0.00 42.50 4.85
1529 1563 1.228154 AACCGGAGTCCCTTGTTGC 60.228 57.895 9.46 0.00 0.00 4.17
1549 1583 1.486310 CTGCAGGCAGGGTACATCTTA 59.514 52.381 13.39 0.00 40.17 2.10
1652 1686 3.559238 GATCGAGCTGGAGATCTTCTC 57.441 52.381 4.31 4.24 42.66 2.87
1776 1810 3.976306 GCATTTTGTTTTTGCTCCATTGC 59.024 39.130 0.00 0.00 33.61 3.56
1802 1836 7.307396 CCAATGAATGTTATAGTAGCTTGGTCG 60.307 40.741 0.00 0.00 0.00 4.79
2019 2053 2.759355 CATGGGGTAGAGGTTGGAGTA 58.241 52.381 0.00 0.00 0.00 2.59
2029 2063 3.198853 AGAGGTTGGAGTAGAGGAAATGC 59.801 47.826 0.00 0.00 0.00 3.56
2217 2251 4.645535 CCCTGTCTTTCATCTTTCTGTGA 58.354 43.478 0.00 0.00 0.00 3.58
2509 2543 6.068010 ACTTGATTAGGGTGTGAAATTGACA 58.932 36.000 0.00 0.00 0.00 3.58
2515 2549 3.642848 AGGGTGTGAAATTGACATTGCTT 59.357 39.130 0.00 0.00 0.00 3.91
2571 2605 7.118680 GGTTCTACACAGAAATTATTCAACGGA 59.881 37.037 0.00 0.00 42.41 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
379 384 0.108019 GAACCAAACCACTCGGAGGT 59.892 55.000 10.23 0.00 42.34 3.85
567 572 4.730949 AAATCGTCTTAATCCGAGGTCA 57.269 40.909 3.49 0.00 36.41 4.02
937 942 2.773993 TAAAATCGCGAGGGAAAGGT 57.226 45.000 16.66 0.00 0.00 3.50
989 994 2.165998 GCACAGCCATTCTCTTCCTTT 58.834 47.619 0.00 0.00 0.00 3.11
1082 1088 3.112709 GTTGCCGAGACAGCGACC 61.113 66.667 0.00 0.00 38.48 4.79
1233 1248 7.287927 AGGTGCATAACTTAAGCTAGTCAGATA 59.712 37.037 1.29 0.00 0.00 1.98
1241 1256 4.442706 GAGCAGGTGCATAACTTAAGCTA 58.557 43.478 1.29 0.00 45.16 3.32
1244 1259 3.873952 GAGGAGCAGGTGCATAACTTAAG 59.126 47.826 4.48 0.00 45.16 1.85
1246 1261 2.170607 GGAGGAGCAGGTGCATAACTTA 59.829 50.000 4.48 0.00 45.16 2.24
1261 1276 4.633565 GTGAGAATTGTTAGCTTGGAGGAG 59.366 45.833 0.00 0.00 0.00 3.69
1505 1521 4.754667 GGGACTCCGGTTGGTCGC 62.755 72.222 19.01 19.01 38.01 5.19
1529 1563 0.254178 AAGATGTACCCTGCCTGCAG 59.746 55.000 12.17 12.17 43.26 4.41
1537 1571 3.928754 TCTCTGGCATAAGATGTACCCT 58.071 45.455 0.00 0.00 0.00 4.34
1549 1583 0.987081 AGACCCTGCATCTCTGGCAT 60.987 55.000 0.00 0.00 41.06 4.40
1652 1686 3.549299 AGAAGAAGCAGCAAAACGATG 57.451 42.857 0.00 0.00 0.00 3.84
1776 1810 7.307396 CGACCAAGCTACTATAACATTCATTGG 60.307 40.741 0.00 0.00 39.43 3.16
1802 1836 6.710744 TGGTAATCAGAGAAGTTTTTCCTGAC 59.289 38.462 0.00 0.00 40.33 3.51
1948 1982 1.743996 GCCCTGATGTTTGAGAGACC 58.256 55.000 0.00 0.00 0.00 3.85
2019 2053 1.625818 ACCAGTTCTCGCATTTCCTCT 59.374 47.619 0.00 0.00 0.00 3.69
2029 2063 2.492088 TCTCACCATACACCAGTTCTCG 59.508 50.000 0.00 0.00 0.00 4.04
2322 2356 2.159382 CGTTGCCTTTTCCATGGTACT 58.841 47.619 12.58 0.00 0.00 2.73
2404 2438 1.072505 GAGGACTTTCCAACGGCCA 59.927 57.895 2.24 0.00 39.61 5.36
2515 2549 1.808411 CCTCCAAACGCTAAGCAAGA 58.192 50.000 0.00 0.00 0.00 3.02
2571 2605 6.207810 TGACCAAATTCCGCAAGTAAGTATTT 59.792 34.615 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.