Multiple sequence alignment - TraesCS7B01G047800

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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 TraesCS7B01G047800 chr7B 100.000 2351 0 0 1 2351 47218556 47220906 0 4342
1 TraesCS7B01G047800 chr7B 96.414 2370 55 4 7 2351 716796726 716794362 0 3879
2 TraesCS7B01G047800 chr7B 96.370 2369 55 4 7 2351 742936595 742938956 0 3869
3 TraesCS7B01G047800 chr7B 96.916 2270 42 2 105 2351 698127721 698125457 0 3779
4 TraesCS7B01G047800 chr7A 96.581 2369 52 3 7 2351 60097085 60094722 0 3899
5 TraesCS7B01G047800 chr6B 96.581 2369 52 3 7 2351 128890870 128888507 0 3899
6 TraesCS7B01G047800 chr5B 96.414 2370 54 5 7 2351 713094878 713097241 0 3877
7 TraesCS7B01G047800 chr5B 96.243 2369 59 8 7 2351 713113849 713111487 0 3855
8 TraesCS7B01G047800 chr1B 96.243 2369 59 4 7 2351 583549423 583551785 0 3855
9 TraesCS7B01G047800 chr1B 95.742 2372 69 6 7 2351 49816957 49819323 0 3792
10 TraesCS7B01G047800 chrUn 96.833 2305 48 3 71 2351 257943290 257945593 0 3829
11 TraesCS7B01G047800 chrUn 96.573 2305 49 4 71 2351 233526090 233523792 0 3792
12 TraesCS7B01G047800 chrUn 95.469 618 5 1 1757 2351 369795034 369795651 0 965
13 TraesCS7B01G047800 chr2D 96.354 2304 61 1 71 2351 637309527 637307224 0 3768
14 TraesCS7B01G047800 chr6D 95.794 2306 71 4 71 2351 283186590 283188894 0 3698
15 TraesCS7B01G047800 chr3B 93.766 1139 48 1 1236 2351 797561013 797559875 0 1688


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 TraesCS7B01G047800 chr7B 47218556 47220906 2350 False 4342 4342 100.000 1 2351 1 chr7B.!!$F1 2350
1 TraesCS7B01G047800 chr7B 716794362 716796726 2364 True 3879 3879 96.414 7 2351 1 chr7B.!!$R2 2344
2 TraesCS7B01G047800 chr7B 742936595 742938956 2361 False 3869 3869 96.370 7 2351 1 chr7B.!!$F2 2344
3 TraesCS7B01G047800 chr7B 698125457 698127721 2264 True 3779 3779 96.916 105 2351 1 chr7B.!!$R1 2246
4 TraesCS7B01G047800 chr7A 60094722 60097085 2363 True 3899 3899 96.581 7 2351 1 chr7A.!!$R1 2344
5 TraesCS7B01G047800 chr6B 128888507 128890870 2363 True 3899 3899 96.581 7 2351 1 chr6B.!!$R1 2344
6 TraesCS7B01G047800 chr5B 713094878 713097241 2363 False 3877 3877 96.414 7 2351 1 chr5B.!!$F1 2344
7 TraesCS7B01G047800 chr5B 713111487 713113849 2362 True 3855 3855 96.243 7 2351 1 chr5B.!!$R1 2344
8 TraesCS7B01G047800 chr1B 583549423 583551785 2362 False 3855 3855 96.243 7 2351 1 chr1B.!!$F2 2344
9 TraesCS7B01G047800 chr1B 49816957 49819323 2366 False 3792 3792 95.742 7 2351 1 chr1B.!!$F1 2344
10 TraesCS7B01G047800 chrUn 257943290 257945593 2303 False 3829 3829 96.833 71 2351 1 chrUn.!!$F1 2280
11 TraesCS7B01G047800 chrUn 233523792 233526090 2298 True 3792 3792 96.573 71 2351 1 chrUn.!!$R1 2280
12 TraesCS7B01G047800 chrUn 369795034 369795651 617 False 965 965 95.469 1757 2351 1 chrUn.!!$F2 594
13 TraesCS7B01G047800 chr2D 637307224 637309527 2303 True 3768 3768 96.354 71 2351 1 chr2D.!!$R1 2280
14 TraesCS7B01G047800 chr6D 283186590 283188894 2304 False 3698 3698 95.794 71 2351 1 chr6D.!!$F1 2280
15 TraesCS7B01G047800 chr3B 797559875 797561013 1138 True 1688 1688 93.766 1236 2351 1 chr3B.!!$R1 1115

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
874 881 1.335506 CGAGGAGCCGAAGATTCTAGC 60.336 57.143 0.0 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1763 2.379907 AGGAAGGAGGCATTGGAAAGAA 59.62 45.455 0.0 0.0 0.0 2.52 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
37 38 4.747316 GCGGGTGGTGGTATGGATAATTTA 60.747 45.833 0.00 0.00 0.00 1.40
83 84 4.141018 ACCCTAATACCCCATTGGATCAAC 60.141 45.833 3.62 0.00 38.00 3.18
170 171 3.459232 TGTATATGCTGCTCACTGTCC 57.541 47.619 0.00 0.00 0.00 4.02
271 275 6.200286 TGGTCGAGCTTATTTATGATTTCGTC 59.800 38.462 16.64 0.00 0.00 4.20
676 683 4.454678 TGCTTGGACTATGCTATTTCTGG 58.545 43.478 0.00 0.00 0.00 3.86
756 763 2.798499 CGGTCTGGAATTAGGTGTAGCG 60.798 54.545 0.00 0.00 0.00 4.26
874 881 1.335506 CGAGGAGCCGAAGATTCTAGC 60.336 57.143 0.00 0.00 0.00 3.42
913 920 2.300433 TGCAGCACTGAACATTGTTCT 58.700 42.857 25.49 8.05 0.00 3.01
1131 1139 6.575244 TTAGGTATCAGTGGGAACATGAAT 57.425 37.500 0.00 0.00 46.14 2.57
1233 1241 0.250513 GGGGAGAACGAGCAGACATT 59.749 55.000 0.00 0.00 0.00 2.71
1247 1255 7.064134 ACGAGCAGACATTGAACGATTAATTTA 59.936 33.333 0.00 0.00 33.46 1.40
1294 1302 3.584406 TCATCAAGATGGATCGCCCTTAT 59.416 43.478 9.96 0.00 39.24 1.73
1385 1393 4.606961 GAAAGAACAAGCAACGGATTTCA 58.393 39.130 0.00 0.00 0.00 2.69
1448 1456 4.494484 TGGTACTTGTCTGATCAATCACG 58.506 43.478 0.00 0.00 32.50 4.35
1513 1521 6.147581 ACCGCTTACTAATCACGTATACATG 58.852 40.000 3.32 0.00 0.00 3.21
1584 1593 0.753867 TTTGCCCGCCTATCGTATCA 59.246 50.000 0.00 0.00 36.19 2.15
1684 1693 3.756933 TGTAGTAGTCGGCCTTTGTTT 57.243 42.857 0.00 0.00 0.00 2.83
1691 1700 1.877443 GTCGGCCTTTGTTTAGCTTCA 59.123 47.619 0.00 0.00 0.00 3.02
1784 1793 2.437359 CTCCTTCCTTGCCGCCAG 60.437 66.667 0.00 0.00 0.00 4.85
1976 1985 5.557576 TCTTTTCGGATGATGAGGATGAT 57.442 39.130 0.00 0.00 0.00 2.45
2100 2109 3.459969 GGGTCAGGAGGGAAAAGATATGT 59.540 47.826 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.321298 CCACCCGCCCGAATATTAGG 60.321 60.000 7.59 7.59 0.00 2.69
3 4 0.395312 ACCACCCGCCCGAATATTAG 59.605 55.000 0.00 0.00 0.00 1.73
4 5 0.107081 CACCACCCGCCCGAATATTA 59.893 55.000 0.00 0.00 0.00 0.98
5 6 1.153046 CACCACCCGCCCGAATATT 60.153 57.895 0.00 0.00 0.00 1.28
83 84 8.130671 AGATCAATTATTGGGATAATGGCAAG 57.869 34.615 5.02 0.00 38.23 4.01
197 201 6.322931 ACTTTCCACCTCCCTTTTTCATAAT 58.677 36.000 0.00 0.00 0.00 1.28
201 205 3.053245 TGACTTTCCACCTCCCTTTTTCA 60.053 43.478 0.00 0.00 0.00 2.69
271 275 2.841215 TGTTCGTTTACCAGGTTCAGG 58.159 47.619 0.00 0.00 0.00 3.86
461 465 3.435327 TGTCTTTGAAATCCAACGATCGG 59.565 43.478 20.98 1.81 35.81 4.18
756 763 6.697455 TCGTAGAAACATGAGCTTGTGATATC 59.303 38.462 0.00 0.00 0.00 1.63
908 915 5.428253 GCAATATCTTGAGTACCCAGAACA 58.572 41.667 0.00 0.00 34.04 3.18
913 920 4.481368 AACGCAATATCTTGAGTACCCA 57.519 40.909 0.80 0.00 43.46 4.51
1247 1255 8.833231 ACGAATTCCACGATAATGAGAAATAT 57.167 30.769 0.00 0.00 34.70 1.28
1294 1302 1.271379 AGTATGAGTTCGTTGACCGCA 59.729 47.619 0.00 0.00 36.19 5.69
1385 1393 2.014068 GCTTTAGCAAGGGATGAGCGT 61.014 52.381 0.00 0.00 41.59 5.07
1417 1425 3.135712 TCAGACAAGTACCAAGGAGCAAA 59.864 43.478 0.00 0.00 0.00 3.68
1513 1521 0.619543 TGGTGAAGGGGGCCTACTAC 60.620 60.000 0.84 0.00 31.13 2.73
1754 1763 2.379907 AGGAAGGAGGCATTGGAAAGAA 59.620 45.455 0.00 0.00 0.00 2.52
1784 1793 4.854784 TCTCCATCTCGCGTGCGC 62.855 66.667 9.79 0.00 39.59 6.09
1792 1801 3.817709 AGCTTGCTTACTCTCCATCTC 57.182 47.619 0.00 0.00 0.00 2.75
1976 1985 4.974645 AATTATGTTAGGATCGGCTGGA 57.025 40.909 0.00 0.00 0.00 3.86
2100 2109 3.751175 CGCTTGGGACTGATAGAAAACAA 59.249 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.