Multiple sequence alignment - TraesCS7B01G457700

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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 TraesCS7B01G457700 chr7B 100.000 2594 0 0 1 2594 716838603 716836010 0 4791
1 TraesCS7B01G457700 chr7B 98.749 1839 19 1 756 2594 716878059 716876225 0 3265
2 TraesCS7B01G457700 chr7B 99.075 757 6 1 1 757 742989382 742990137 0 1358
3 TraesCS7B01G457700 chr5A 98.753 1844 14 3 756 2594 19248121 19246282 0 3269
4 TraesCS7B01G457700 chr5A 99.208 758 5 1 1 757 19248908 19248151 0 1365
5 TraesCS7B01G457700 chr7D 98.699 1845 15 4 756 2594 381973045 381971204 0 3265
6 TraesCS7B01G457700 chr7D 98.590 1844 17 3 756 2594 381924723 381926562 0 3253
7 TraesCS7B01G457700 chr7D 98.536 1844 18 3 756 2594 382050801 382052640 0 3247
8 TraesCS7B01G457700 chr7D 98.373 1844 21 3 756 2594 203500721 203502560 0 3230
9 TraesCS7B01G457700 chr7D 99.339 757 5 0 1 757 203499935 203500691 0 1371
10 TraesCS7B01G457700 chr7D 99.207 757 6 0 1 757 381973831 381973075 0 1365
11 TraesCS7B01G457700 chr7D 99.075 757 7 0 1 757 381923937 381924693 0 1360
12 TraesCS7B01G457700 chr1A 98.532 1839 23 1 756 2594 498690505 498688671 0 3243
13 TraesCS7B01G457700 chr1A 98.943 757 8 0 1 757 498691291 498690535 0 1354
14 TraesCS7B01G457700 chrUn 98.477 1839 24 1 756 2594 186207699 186205865 0 3238
15 TraesCS7B01G457700 chr7A 98.423 1839 25 1 756 2594 60280035 60281869 0 3232
16 TraesCS7B01G457700 chr7A 99.075 757 7 0 1 757 60279249 60280005 0 1360
17 TraesCS7B01G457700 chr6D 99.339 757 5 0 1 757 124517458 124518214 0 1371
18 TraesCS7B01G457700 chr4D 99.075 757 7 0 1 757 123549862 123550618 0 1360


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 TraesCS7B01G457700 chr7B 716836010 716838603 2593 True 4791.0 4791 100.0000 1 2594 1 chr7B.!!$R1 2593
1 TraesCS7B01G457700 chr7B 716876225 716878059 1834 True 3265.0 3265 98.7490 756 2594 1 chr7B.!!$R2 1838
2 TraesCS7B01G457700 chr7B 742989382 742990137 755 False 1358.0 1358 99.0750 1 757 1 chr7B.!!$F1 756
3 TraesCS7B01G457700 chr5A 19246282 19248908 2626 True 2317.0 3269 98.9805 1 2594 2 chr5A.!!$R1 2593
4 TraesCS7B01G457700 chr7D 382050801 382052640 1839 False 3247.0 3247 98.5360 756 2594 1 chr7D.!!$F1 1838
5 TraesCS7B01G457700 chr7D 381971204 381973831 2627 True 2315.0 3265 98.9530 1 2594 2 chr7D.!!$R1 2593
6 TraesCS7B01G457700 chr7D 381923937 381926562 2625 False 2306.5 3253 98.8325 1 2594 2 chr7D.!!$F3 2593
7 TraesCS7B01G457700 chr7D 203499935 203502560 2625 False 2300.5 3230 98.8560 1 2594 2 chr7D.!!$F2 2593
8 TraesCS7B01G457700 chr1A 498688671 498691291 2620 True 2298.5 3243 98.7375 1 2594 2 chr1A.!!$R1 2593
9 TraesCS7B01G457700 chrUn 186205865 186207699 1834 True 3238.0 3238 98.4770 756 2594 1 chrUn.!!$R1 1838
10 TraesCS7B01G457700 chr7A 60279249 60281869 2620 False 2296.0 3232 98.7490 1 2594 2 chr7A.!!$F1 2593
11 TraesCS7B01G457700 chr6D 124517458 124518214 756 False 1371.0 1371 99.3390 1 757 1 chr6D.!!$F1 756
12 TraesCS7B01G457700 chr4D 123549862 123550618 756 False 1360.0 1360 99.0750 1 757 1 chr4D.!!$F1 756

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
155 156 1.611977 TCCTGAAGTTCTCGCGAAGAA 59.388 47.619 11.33 13.22 41.81 2.52 F
562 564 7.200778 TGAGATGTCGATTTGTTTTTCATCA 57.799 32.000 8.87 0.00 34.55 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1360 1.730501 ATGGCGAATGCATCTATCGG 58.269 50.0 18.19 3.7 45.35 4.18 R
2408 2445 0.396811 AGACCCAAGTGTGGTGTAGC 59.603 55.0 0.00 0.0 44.30 3.58 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
155 156 1.611977 TCCTGAAGTTCTCGCGAAGAA 59.388 47.619 11.33 13.22 41.81 2.52
562 564 7.200778 TGAGATGTCGATTTGTTTTTCATCA 57.799 32.000 8.87 0.00 34.55 3.07
576 578 7.846066 TGTTTTTCATCAAAAAGGAAGAAGGA 58.154 30.769 0.00 0.00 41.23 3.36
1713 1749 3.130516 GGTCGAGTCTGATACATCAACCA 59.869 47.826 0.00 0.00 36.18 3.67
1871 1907 4.047059 GGAACGACACGAGCCGGA 62.047 66.667 5.05 0.00 0.00 5.14
1945 1981 2.230130 TCTCATTTGGGGCGGAAAAT 57.770 45.000 0.00 0.00 0.00 1.82
2202 2238 3.385433 TGGGGCTGATTGCAAAAGATATG 59.615 43.478 14.83 0.00 45.15 1.78
2401 2438 1.272554 CGGGAAGGGGCCTAGAAGTT 61.273 60.000 0.84 0.00 0.00 2.66
2408 2445 1.763545 GGGGCCTAGAAGTTCCTACTG 59.236 57.143 0.84 0.00 34.01 2.74
2454 2496 2.921834 TACAGAGCTTACCCCTGTCT 57.078 50.000 8.18 0.00 41.01 3.41
2537 2579 3.799420 GCTAACAGAGCCTGACTTATTCG 59.201 47.826 8.91 0.00 46.41 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 1.855599 AGGGGGAGCTGCATCTTATTT 59.144 47.619 7.79 0.00 0.00 1.40
290 291 1.008538 GGTGCTTTCCTGTGTTGCG 60.009 57.895 0.00 0.00 0.00 4.85
562 564 2.224793 CCCCTCGTCCTTCTTCCTTTTT 60.225 50.000 0.00 0.00 0.00 1.94
576 578 1.383248 AAGGCTGCTATCCCCTCGT 60.383 57.895 0.00 0.00 0.00 4.18
1324 1360 1.730501 ATGGCGAATGCATCTATCGG 58.269 50.000 18.19 3.70 45.35 4.18
1640 1676 3.496884 GTGTTGCAACTGATTCGGTAAGA 59.503 43.478 28.61 2.21 0.00 2.10
1713 1749 4.395625 TCGTACAAGGATATGGAGTCGAT 58.604 43.478 0.00 0.00 0.00 3.59
1871 1907 2.253403 GAAAGGAATCGAGGCCCGGT 62.253 60.000 12.77 3.78 39.14 5.28
2202 2238 9.598517 GATGGATGGATCTATCTTTCTATTCAC 57.401 37.037 17.50 0.00 40.41 3.18
2401 2438 2.299013 CAAGTGTGGTGTAGCAGTAGGA 59.701 50.000 0.00 0.00 0.00 2.94
2408 2445 0.396811 AGACCCAAGTGTGGTGTAGC 59.603 55.000 0.00 0.00 44.30 3.58
2424 2466 5.811100 GGGTAAGCTCTGTAAATGTGTAGAC 59.189 44.000 0.00 0.00 0.00 2.59
2454 2496 1.270094 CCAACGTTCTGCCAGACACTA 60.270 52.381 0.00 0.00 0.00 2.74
2521 2563 1.123928 CCCCGAATAAGTCAGGCTCT 58.876 55.000 0.00 0.00 0.00 4.09
2537 2579 1.950748 TAGGCTCCACTCTCTCCCCC 61.951 65.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.