Multiple sequence alignment - TraesCS7B01G256200

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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 TraesCS7B01G256200 chr7B 100.000 2516 0 0 1 2516 475099969 475097454 0.000000e+00 4647
1 TraesCS7B01G256200 chr4B 96.628 2521 79 4 1 2516 664031650 664034169 0.000000e+00 4180
2 TraesCS7B01G256200 chr3B 96.508 2520 78 6 1 2516 40985977 40988490 0.000000e+00 4157
3 TraesCS7B01G256200 chr3B 95.597 159 7 0 2358 2516 28619781 28619623 3.210000e-64 255
4 TraesCS7B01G256200 chr3B 94.969 159 8 0 2358 2516 16120818 16120976 1.490000e-62 250
5 TraesCS7B01G256200 chr3B 93.711 159 10 0 2358 2516 112913324 112913166 3.230000e-59 239
6 TraesCS7B01G256200 chr5B 96.230 2520 90 3 1 2516 35444057 35441539 0.000000e+00 4122
7 TraesCS7B01G256200 chr5B 89.912 684 41 15 1815 2486 215733711 215734378 0.000000e+00 856
8 TraesCS7B01G256200 chr2B 95.873 2520 92 5 1 2516 649651758 649654269 0.000000e+00 4067
9 TraesCS7B01G256200 chr2B 94.361 2518 116 7 4 2516 757696507 757694011 0.000000e+00 3840
10 TraesCS7B01G256200 chr6A 94.306 2529 129 7 1 2516 79817747 79820273 0.000000e+00 3858
11 TraesCS7B01G256200 chr7D 94.678 2499 99 7 1 2486 16793651 16796128 0.000000e+00 3847
12 TraesCS7B01G256200 chr3A 94.148 2529 132 6 1 2516 22598050 22600575 0.000000e+00 3836
13 TraesCS7B01G256200 chr6B 93.997 2482 128 16 3 2469 425601957 425599482 0.000000e+00 3738
14 TraesCS7B01G256200 chr1B 93.772 2505 125 18 1 2486 14538219 14540711 0.000000e+00 3733
15 TraesCS7B01G256200 chr2A 91.853 2553 142 15 1 2516 601809139 601811662 0.000000e+00 3502
16 TraesCS7B01G256200 chr7A 92.072 2283 127 19 261 2514 7458962 7461219 0.000000e+00 3164


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 TraesCS7B01G256200 chr7B 475097454 475099969 2515 True 4647 4647 100.000 1 2516 1 chr7B.!!$R1 2515
1 TraesCS7B01G256200 chr4B 664031650 664034169 2519 False 4180 4180 96.628 1 2516 1 chr4B.!!$F1 2515
2 TraesCS7B01G256200 chr3B 40985977 40988490 2513 False 4157 4157 96.508 1 2516 1 chr3B.!!$F2 2515
3 TraesCS7B01G256200 chr5B 35441539 35444057 2518 True 4122 4122 96.230 1 2516 1 chr5B.!!$R1 2515
4 TraesCS7B01G256200 chr5B 215733711 215734378 667 False 856 856 89.912 1815 2486 1 chr5B.!!$F1 671
5 TraesCS7B01G256200 chr2B 649651758 649654269 2511 False 4067 4067 95.873 1 2516 1 chr2B.!!$F1 2515
6 TraesCS7B01G256200 chr2B 757694011 757696507 2496 True 3840 3840 94.361 4 2516 1 chr2B.!!$R1 2512
7 TraesCS7B01G256200 chr6A 79817747 79820273 2526 False 3858 3858 94.306 1 2516 1 chr6A.!!$F1 2515
8 TraesCS7B01G256200 chr7D 16793651 16796128 2477 False 3847 3847 94.678 1 2486 1 chr7D.!!$F1 2485
9 TraesCS7B01G256200 chr3A 22598050 22600575 2525 False 3836 3836 94.148 1 2516 1 chr3A.!!$F1 2515
10 TraesCS7B01G256200 chr6B 425599482 425601957 2475 True 3738 3738 93.997 3 2469 1 chr6B.!!$R1 2466
11 TraesCS7B01G256200 chr1B 14538219 14540711 2492 False 3733 3733 93.772 1 2486 1 chr1B.!!$F1 2485
12 TraesCS7B01G256200 chr2A 601809139 601811662 2523 False 3502 3502 91.853 1 2516 1 chr2A.!!$F1 2515
13 TraesCS7B01G256200 chr7A 7458962 7461219 2257 False 3164 3164 92.072 261 2514 1 chr7A.!!$F1 2253

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
158 159 0.747852 TGTTACCAGTCGTGTCAGCA 59.252 50.0 0.00 0.0 0.0 4.41 F
529 531 0.758123 TGTCATGCGCCTCCATATCA 59.242 50.0 4.18 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 1116 0.035317 AGACATGCTTGCTCACCGAA 59.965 50.0 0.0 0.0 0.0 4.30 R
2263 2331 0.764890 TGGTTGCAAGTGTAGGCTCT 59.235 50.0 0.0 0.0 0.0 4.09 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
146 147 1.139256 TCAACGGACAAGCTGTTACCA 59.861 47.619 0.00 0.0 44.18 3.25
158 159 0.747852 TGTTACCAGTCGTGTCAGCA 59.252 50.000 0.00 0.0 0.00 4.41
228 229 2.044551 CCCTCAGGAAGGCAAGGC 60.045 66.667 0.00 0.0 44.71 4.35
432 434 7.428832 GGAGCTACTCAATAACTGGGATACCT 61.429 46.154 0.00 0.0 45.33 3.08
529 531 0.758123 TGTCATGCGCCTCCATATCA 59.242 50.000 4.18 0.0 0.00 2.15
608 610 1.506025 ATTGGCTGGGTTTGTTTGGT 58.494 45.000 0.00 0.0 0.00 3.67
1072 1076 5.300286 AGACAATTTGGAAGAAGACAAGGTG 59.700 40.000 0.78 0.0 0.00 4.00
1101 1105 2.639347 TGAGGAGAGCAATGAGGAAACA 59.361 45.455 0.00 0.0 0.00 2.83
1112 1116 5.426504 CAATGAGGAAACACTATCTCTGCT 58.573 41.667 0.00 0.0 0.00 4.24
1454 1458 6.992715 GCAGTAGGTTATCATACCTTCAACAT 59.007 38.462 0.00 0.0 46.39 2.71
1598 1607 2.297033 GTGTGTTCATGAATTGCAGGGT 59.703 45.455 12.12 0.0 0.00 4.34
1651 1660 3.836365 TGTTTCACTGAGTCATCCACA 57.164 42.857 0.00 0.0 0.00 4.17
1911 1924 1.482182 TCAGAACGATGAGGACATGGG 59.518 52.381 0.00 0.0 36.72 4.00
1938 1969 0.179936 GTCCATGAAGAGGAGCCAGG 59.820 60.000 0.00 0.0 35.42 4.45
2080 2147 0.036010 AAGGCAATGCTCGCACTAGT 60.036 50.000 4.82 0.0 0.00 2.57
2202 2270 7.212274 CCAAGAGGAATGCAAAAATATAAGGG 58.788 38.462 0.00 0.0 36.89 3.95
2285 2353 3.009033 AGAGCCTACACTTGCAACCATTA 59.991 43.478 0.00 0.0 0.00 1.90
2311 2379 2.564947 GAGAGGAAGGAAGAAGTGAGCA 59.435 50.000 0.00 0.0 0.00 4.26
2345 2414 2.093890 TGCATGAACTAGGTGGCATTG 58.906 47.619 0.00 0.0 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.831685 TTACCAATGCTGACACGACT 57.168 45.000 0.00 0.00 0.00 4.18
158 159 2.014128 CCGTTCTCGCCAATTACCAAT 58.986 47.619 0.00 0.00 35.54 3.16
332 333 6.614087 TGGTTAGTACATACCAAAGATAGGCT 59.386 38.462 14.61 0.00 41.30 4.58
432 434 1.335145 GCCGAACCCCAGCTATACTA 58.665 55.000 0.00 0.00 0.00 1.82
529 531 4.877251 AGCTGCAATCAAACAAACATGTTT 59.123 33.333 18.13 18.13 42.08 2.83
588 590 1.843206 ACCAAACAAACCCAGCCAATT 59.157 42.857 0.00 0.00 0.00 2.32
608 610 1.210234 CCACATCCACACAGATAGGCA 59.790 52.381 0.00 0.00 0.00 4.75
1072 1076 4.012374 TCATTGCTCTCCTCAATTGGAAC 58.988 43.478 5.42 0.00 35.43 3.62
1101 1105 1.407258 GCTCACCGAAGCAGAGATAGT 59.593 52.381 0.00 0.00 42.05 2.12
1112 1116 0.035317 AGACATGCTTGCTCACCGAA 59.965 50.000 0.00 0.00 0.00 4.30
1598 1607 3.636764 TGACACACAGAAGCAACTCTCTA 59.363 43.478 0.00 0.00 0.00 2.43
1651 1660 3.649981 CCTCTCAGATAATCCACCACCAT 59.350 47.826 0.00 0.00 0.00 3.55
1772 1785 3.070446 TGGAACCGCTTCTTGAACTTCTA 59.930 43.478 0.00 0.00 0.00 2.10
1869 1882 7.654923 TCTGAAGATAACGTCGTCTATTAGCTA 59.345 37.037 0.00 0.00 36.45 3.32
1911 1924 1.127343 CTCTTCATGGACCTCCTCCC 58.873 60.000 0.00 0.00 38.49 4.30
1938 1969 2.079925 GTGTTGGCTCCTCTTGATGTC 58.920 52.381 0.00 0.00 0.00 3.06
2202 2270 1.372087 CTCCTCCGCCTCATTGTTGC 61.372 60.000 0.00 0.00 0.00 4.17
2261 2329 1.160137 GTTGCAAGTGTAGGCTCTGG 58.840 55.000 0.00 0.00 0.00 3.86
2262 2330 1.160137 GGTTGCAAGTGTAGGCTCTG 58.840 55.000 0.00 0.00 0.00 3.35
2263 2331 0.764890 TGGTTGCAAGTGTAGGCTCT 59.235 50.000 0.00 0.00 0.00 4.09
2285 2353 5.090139 TCACTTCTTCCTTCCTCTCTTCAT 58.910 41.667 0.00 0.00 0.00 2.57
2311 2379 4.586001 AGTTCATGCAGTTCCAAACAAGAT 59.414 37.500 0.00 0.00 0.00 2.40
2345 2414 2.095853 CGACACCAAGTTCATGCATACC 59.904 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.