Multiple sequence alignment - TraesCS7B01G034100

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 TraesCS7B01G034100 chr7B 100.000 3232 0 0 1 3232 33772009 33768778 0 5969
1 TraesCS7B01G034100 chr7B 97.690 2814 61 3 422 3232 449123724 449126536 0 4833
2 TraesCS7B01G034100 chr7B 91.348 3005 190 43 262 3227 654664522 654667495 0 4045
3 TraesCS7B01G034100 chr7B 98.381 556 9 0 1 556 33755935 33755380 0 977
4 TraesCS7B01G034100 chr2B 97.713 3236 69 3 1 3232 749453086 749456320 0 5561
5 TraesCS7B01G034100 chr2B 96.473 2835 93 6 402 3232 684312025 684309194 0 4674
6 TraesCS7B01G034100 chr2B 96.151 2832 74 17 402 3230 637510076 637507277 0 4593
7 TraesCS7B01G034100 chr2B 88.391 3170 298 50 105 3227 337499658 337502804 0 3751
8 TraesCS7B01G034100 chr2B 88.981 1207 101 22 2051 3232 762707492 762708691 0 1463
9 TraesCS7B01G034100 chr2B 85.231 1212 126 37 2051 3232 405162993 405164181 0 1197
10 TraesCS7B01G034100 chr4B 95.306 2876 96 27 392 3232 363771531 363774402 0 4527
11 TraesCS7B01G034100 chr4B 90.719 3157 243 37 93 3227 349260746 349263874 0 4161
12 TraesCS7B01G034100 chr5B 91.067 3000 207 37 262 3227 337439150 337436178 0 3999


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 TraesCS7B01G034100 chr7B 33768778 33772009 3231 True 5969 5969 100.000 1 3232 1 chr7B.!!$R2 3231
1 TraesCS7B01G034100 chr7B 449123724 449126536 2812 False 4833 4833 97.690 422 3232 1 chr7B.!!$F1 2810
2 TraesCS7B01G034100 chr7B 654664522 654667495 2973 False 4045 4045 91.348 262 3227 1 chr7B.!!$F2 2965
3 TraesCS7B01G034100 chr7B 33755380 33755935 555 True 977 977 98.381 1 556 1 chr7B.!!$R1 555
4 TraesCS7B01G034100 chr2B 749453086 749456320 3234 False 5561 5561 97.713 1 3232 1 chr2B.!!$F3 3231
5 TraesCS7B01G034100 chr2B 684309194 684312025 2831 True 4674 4674 96.473 402 3232 1 chr2B.!!$R2 2830
6 TraesCS7B01G034100 chr2B 637507277 637510076 2799 True 4593 4593 96.151 402 3230 1 chr2B.!!$R1 2828
7 TraesCS7B01G034100 chr2B 337499658 337502804 3146 False 3751 3751 88.391 105 3227 1 chr2B.!!$F1 3122
8 TraesCS7B01G034100 chr2B 762707492 762708691 1199 False 1463 1463 88.981 2051 3232 1 chr2B.!!$F4 1181
9 TraesCS7B01G034100 chr2B 405162993 405164181 1188 False 1197 1197 85.231 2051 3232 1 chr2B.!!$F2 1181
10 TraesCS7B01G034100 chr4B 363771531 363774402 2871 False 4527 4527 95.306 392 3232 1 chr4B.!!$F2 2840
11 TraesCS7B01G034100 chr4B 349260746 349263874 3128 False 4161 4161 90.719 93 3227 1 chr4B.!!$F1 3134
12 TraesCS7B01G034100 chr5B 337436178 337439150 2972 True 3999 3999 91.067 262 3227 1 chr5B.!!$R1 2965

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
692 724 2.861462 TTTCCTTGTTGTTGCTTCGG 57.139 45.0 0.0 0.0 0.0 4.30 F
1191 1224 2.165437 GAGATCCTCAGCTTCGTTCAGT 59.835 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2236 0.614979 GCTCTGAGTCCACCAGGGTA 60.615 60.0 6.53 0.0 34.68 3.69 R
2884 2923 1.368374 TTACTGCCCAAGCTAACCCT 58.632 50.0 0.00 0.0 40.80 4.34 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
692 724 2.861462 TTTCCTTGTTGTTGCTTCGG 57.139 45.000 0.00 0.0 0.00 4.30
894 927 6.389906 GCAGAAAATTTTGAGCTAAAGCCTA 58.610 36.000 8.47 0.0 43.38 3.93
1191 1224 2.165437 GAGATCCTCAGCTTCGTTCAGT 59.835 50.000 0.00 0.0 0.00 3.41
1229 1262 5.735285 TGTATGATGCTTGGGAGAGATAG 57.265 43.478 0.00 0.0 0.00 2.08
1476 1510 4.499696 GCTTGCAACAAATCACTACACCTT 60.500 41.667 0.00 0.0 0.00 3.50
1516 1550 4.846940 ACAAAACCCTGAACCTCTATCTCT 59.153 41.667 0.00 0.0 0.00 3.10
1767 1801 3.378911 TCGATGATGTTAGCCGCATTA 57.621 42.857 0.00 0.0 0.00 1.90
1792 1826 2.533266 TCAACACTTGAGCCTGAGAC 57.467 50.000 0.00 0.0 34.08 3.36
1830 1864 3.843619 TGAGTATGGTGAGGTGGATTCAA 59.156 43.478 0.00 0.0 0.00 2.69
1868 1902 7.335422 CCAAGCTCTACTATTTCACTTGTTGAT 59.665 37.037 0.00 0.0 32.84 2.57
2045 2079 7.592938 TGTTGTTGATACATGTTCCTGATTTC 58.407 34.615 2.30 0.0 33.44 2.17
2093 2127 6.839454 AGGGTACTCTATCGATGACTTAGAA 58.161 40.000 8.54 0.0 0.00 2.10
2202 2236 1.348064 TCGAGGTGACATTCCTTGGT 58.652 50.000 0.60 0.0 37.15 3.67
2884 2923 2.571212 GGATCGGTGGCATGTGAAATA 58.429 47.619 0.00 0.0 0.00 1.40
3175 3266 1.846007 TTAGGAACCATTTGGCGCAT 58.154 45.000 10.83 0.0 39.32 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
577 602 2.991434 ACATAATCGCTCGACGCTAT 57.009 45.000 0.00 0.0 43.23 2.97
742 775 7.753630 ACCTGCAAATAGATCAGATTTCCTAT 58.246 34.615 0.00 0.0 0.00 2.57
894 927 6.127479 TGTTGTTGAACCAAAGCAATAAGACT 60.127 34.615 0.00 0.0 0.00 3.24
1191 1224 0.966179 TACAAGCTCTCGCCTTCACA 59.034 50.000 0.00 0.0 36.60 3.58
1229 1262 4.819088 GGACATCTCCTGAATAAAGCCTTC 59.181 45.833 0.00 0.0 33.07 3.46
1476 1510 5.010213 GGTTTTGTGTAAGAATTGGTGGCTA 59.990 40.000 0.00 0.0 0.00 3.93
1516 1550 2.291465 GCAAGCTCAATCTTGTCACACA 59.709 45.455 5.55 0.0 43.92 3.72
1792 1826 1.066573 ACTCAACCATGAAGCTCTCCG 60.067 52.381 0.00 0.0 34.49 4.63
1868 1902 4.261578 AGAAATTTCAACCGGACTCGTA 57.738 40.909 19.99 0.0 33.95 3.43
2093 2127 2.636893 ACAAGTGACAGAGAGAATGCCT 59.363 45.455 0.00 0.0 0.00 4.75
2202 2236 0.614979 GCTCTGAGTCCACCAGGGTA 60.615 60.000 6.53 0.0 34.68 3.69
2884 2923 1.368374 TTACTGCCCAAGCTAACCCT 58.632 50.000 0.00 0.0 40.80 4.34
3175 3266 9.300681 AGAGGATCAACAAGTTTAAATGATGAA 57.699 29.630 6.07 0.0 37.82 2.57


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

AutoCloner maintained by Alex Coulton.