Multiple sequence alignment - TraesCS7B01G241000

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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 TraesCS7B01G241000 chr7B 100.000 2354 0 0 1 2354 448640874 448638521 0 4348
1 TraesCS7B01G241000 chr7A 91.126 2141 154 22 1 2131 501920445 501922559 0 2868
2 TraesCS7B01G241000 chr7D 95.438 1096 36 7 685 1768 431121048 431119955 0 1735
3 TraesCS7B01G241000 chr7D 94.898 588 27 3 1765 2351 431080033 431079448 0 917
4 TraesCS7B01G241000 chr7D 89.675 707 46 13 1 687 431151494 431150795 0 876


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 TraesCS7B01G241000 chr7B 448638521 448640874 2353 True 4348 4348 100.000 1 2354 1 chr7B.!!$R1 2353
1 TraesCS7B01G241000 chr7A 501920445 501922559 2114 False 2868 2868 91.126 1 2131 1 chr7A.!!$F1 2130
2 TraesCS7B01G241000 chr7D 431119955 431121048 1093 True 1735 1735 95.438 685 1768 1 chr7D.!!$R2 1083
3 TraesCS7B01G241000 chr7D 431079448 431080033 585 True 917 917 94.898 1765 2351 1 chr7D.!!$R1 586
4 TraesCS7B01G241000 chr7D 431150795 431151494 699 True 876 876 89.675 1 687 1 chr7D.!!$R3 686

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
325 343 1.240641 TACAACAAGCATGTGCCCGG 61.241 55.0 0.0 0.0 40.46 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2122 0.744874 CTAGCTAAGCACCGGCAGTA 59.255 55.0 0.0 0.0 44.61 2.74 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
59 61 2.070783 GCTACAACGACGATTGGGAAA 58.929 47.619 0.00 0.0 33.63 3.13
77 79 4.556233 GGAAACTACAAGGGAACATTTGC 58.444 43.478 0.00 0.0 0.00 3.68
131 133 3.474570 GAGGGGCGAGGTGCTGAT 61.475 66.667 0.00 0.0 45.43 2.90
132 134 3.746949 GAGGGGCGAGGTGCTGATG 62.747 68.421 0.00 0.0 45.43 3.07
188 190 1.440938 CGAGGGGCGTTTTGTTGTGA 61.441 55.000 0.00 0.0 34.64 3.58
197 199 3.669557 GCGTTTTGTTGTGACTCTGTGTT 60.670 43.478 0.00 0.0 0.00 3.32
198 200 3.845775 CGTTTTGTTGTGACTCTGTGTTG 59.154 43.478 0.00 0.0 0.00 3.33
226 228 3.671716 TCCTAATCTATCTCGCGCACTA 58.328 45.455 8.75 0.0 0.00 2.74
229 231 1.898902 ATCTATCTCGCGCACTACCT 58.101 50.000 8.75 0.0 0.00 3.08
325 343 1.240641 TACAACAAGCATGTGCCCGG 61.241 55.000 0.00 0.0 40.46 5.73
341 359 2.668632 GGCATGAACCCTGACCGA 59.331 61.111 0.00 0.0 0.00 4.69
442 463 2.568623 TTGCTCCCTTCTGAACTTCC 57.431 50.000 0.00 0.0 0.00 3.46
492 513 8.912787 TGAAAACACAAAAATGTACGTTGTAT 57.087 26.923 0.00 0.0 33.80 2.29
565 586 9.778741 CCTTTAACTAGGCTATCATGTATGAAA 57.221 33.333 0.00 0.0 40.69 2.69
662 685 7.813331 TGAGAGTAGGTGTCCTATAACAGTAT 58.187 38.462 0.00 0.0 38.48 2.12
1010 1033 2.324541 CCCCAAAACCATGAGAACCAA 58.675 47.619 0.00 0.0 0.00 3.67
1158 1181 2.910319 AGTATTGGAGCACACCCAACTA 59.090 45.455 0.00 0.0 45.40 2.24
1197 1225 0.668535 GGTTTGTGAAGGTGGTGAGC 59.331 55.000 0.00 0.0 0.00 4.26
1236 1264 4.634443 GTGAATGGTGTAAACTATCGGCTT 59.366 41.667 0.00 0.0 0.00 4.35
1254 1282 2.159282 GCTTGTCATTGATGCCTTGAGG 60.159 50.000 0.00 0.0 38.53 3.86
1354 1382 2.627699 TCTTTCACCCCTGCAAATTGAC 59.372 45.455 0.00 0.0 0.00 3.18
1355 1383 0.958091 TTCACCCCTGCAAATTGACG 59.042 50.000 0.00 0.0 0.00 4.35
1431 1459 8.868522 AGAAATGTCAAGGAATTGATGTTCTA 57.131 30.769 9.88 0.0 31.95 2.10
1470 1504 7.838884 TGAAATTATTCATCATTGGCAACTCA 58.161 30.769 0.00 0.0 40.59 3.41
1473 1507 6.778834 TTATTCATCATTGGCAACTCACAT 57.221 33.333 0.00 0.0 37.61 3.21
1482 1516 2.550606 TGGCAACTCACATCGTTTTACC 59.449 45.455 0.00 0.0 37.61 2.85
1760 1795 6.061022 TGTCTTGGTGTTGGTATATGTGAT 57.939 37.500 0.00 0.0 0.00 3.06
2132 2168 6.515696 GCCAATCTGGACTGCTATTTTTATCC 60.516 42.308 0.00 0.0 40.96 2.59
2133 2169 6.547141 CCAATCTGGACTGCTATTTTTATCCA 59.453 38.462 0.00 0.0 40.96 3.41
2135 2171 6.313519 TCTGGACTGCTATTTTTATCCACT 57.686 37.500 0.00 0.0 32.83 4.00
2137 2173 5.815581 TGGACTGCTATTTTTATCCACTGT 58.184 37.500 0.00 0.0 31.30 3.55
2141 2177 8.182227 GGACTGCTATTTTTATCCACTGTAAAC 58.818 37.037 0.00 0.0 0.00 2.01
2176 2212 2.763627 ATTTTTGCACGAAGGGCGGC 62.764 55.000 0.00 0.0 46.49 6.53
2214 2250 2.288152 GCAACCCCCACGCATTATATTG 60.288 50.000 0.00 0.0 0.00 1.90
2234 2270 0.255890 GGGCGGCCCATGTATGATAT 59.744 55.000 32.90 0.0 44.65 1.63
2272 2308 6.350906 TCTGGAAGTTTTAGAAAGGTTTCGA 58.649 36.000 0.00 0.0 37.48 3.71
2335 2371 3.056465 AGTTTGTGGCGGTTTTCTTTCAA 60.056 39.130 0.00 0.0 0.00 2.69
2339 2375 3.695060 TGTGGCGGTTTTCTTTCAAGTTA 59.305 39.130 0.00 0.0 0.00 2.24
2345 2381 8.794553 TGGCGGTTTTCTTTCAAGTTATTATTA 58.205 29.630 0.00 0.0 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 2.558359 GCAGCAAATGTTCCCTTGTAGT 59.442 45.455 0.00 0.00 0.00 2.73
77 79 2.507102 CGCCGTCACTGGTAGCAG 60.507 66.667 20.16 20.16 0.00 4.24
180 182 2.161410 GCACAACACAGAGTCACAACAA 59.839 45.455 0.00 0.00 0.00 2.83
182 184 2.009774 AGCACAACACAGAGTCACAAC 58.990 47.619 0.00 0.00 0.00 3.32
183 185 2.009051 CAGCACAACACAGAGTCACAA 58.991 47.619 0.00 0.00 0.00 3.33
184 186 1.655484 CAGCACAACACAGAGTCACA 58.345 50.000 0.00 0.00 0.00 3.58
188 190 0.533755 GGAGCAGCACAACACAGAGT 60.534 55.000 0.00 0.00 0.00 3.24
197 199 3.254411 CGAGATAGATTAGGAGCAGCACA 59.746 47.826 0.00 0.00 0.00 4.57
198 200 3.832276 CGAGATAGATTAGGAGCAGCAC 58.168 50.000 0.00 0.00 0.00 4.40
226 228 3.533907 TCATTCCCTCTCTTCCTCTAGGT 59.466 47.826 0.00 0.00 36.34 3.08
229 231 4.487804 CCATCATTCCCTCTCTTCCTCTA 58.512 47.826 0.00 0.00 0.00 2.43
325 343 1.154205 CGATCGGTCAGGGTTCATGC 61.154 60.000 7.38 0.00 0.00 4.06
341 359 0.249398 AAAGCTACTTGTCGGGCGAT 59.751 50.000 0.00 0.00 0.00 4.58
492 513 6.885952 TGACCGAAAACAATAGGAATTTCA 57.114 33.333 0.00 0.00 32.64 2.69
565 586 7.844493 ATGATAAAATGCTGATTACCCACAT 57.156 32.000 0.00 0.00 0.00 3.21
853 876 0.909623 TAGCAGTAGGGGGCAAGAAC 59.090 55.000 0.00 0.00 0.00 3.01
912 935 1.618487 TGCAATGGTTGTGCTGATGA 58.382 45.000 0.00 0.00 42.69 2.92
1010 1033 1.142688 AATGGCCACAAGGAGGAGGT 61.143 55.000 8.16 0.00 36.89 3.85
1158 1181 3.031873 AGCCCATCATTGCCCCCT 61.032 61.111 0.00 0.00 0.00 4.79
1197 1225 2.169789 CACAATCTGCTCCTCGCCG 61.170 63.158 0.00 0.00 38.05 6.46
1254 1282 2.279502 TACCGTGTGAGCCATCGAGC 62.280 60.000 0.00 0.00 0.00 5.03
1355 1383 6.091441 GTCTAAATATCATCAGATCGGCAACC 59.909 42.308 0.00 0.00 35.67 3.77
1557 1591 5.097742 TGTGAAGGGACCATGTAATGTAG 57.902 43.478 0.00 0.00 44.81 2.74
1567 1601 1.547675 GCCATCTTTGTGAAGGGACCA 60.548 52.381 0.00 0.00 34.33 4.02
1568 1602 1.177401 GCCATCTTTGTGAAGGGACC 58.823 55.000 0.00 0.00 34.33 4.46
1760 1795 4.876679 TGACAAAACAACGAGGATACACAA 59.123 37.500 0.00 0.00 41.41 3.33
2086 2122 0.744874 CTAGCTAAGCACCGGCAGTA 59.255 55.000 0.00 0.00 44.61 2.74
2146 2182 8.552034 CCCTTCGTGCAAAAATAAAAATAACAA 58.448 29.630 0.00 0.00 0.00 2.83
2196 2232 1.203001 CCCAATATAATGCGTGGGGGT 60.203 52.381 0.00 0.00 46.04 4.95
2202 2238 1.241315 GCCGCCCCAATATAATGCGT 61.241 55.000 0.00 0.00 43.44 5.24
2234 2270 5.815233 ACTTCCAGAATCAGAAGAGACAA 57.185 39.130 16.56 0.00 41.69 3.18
2295 2331 9.647797 CCACAAACTTTTCTAAAACTAAAAGGT 57.352 29.630 11.09 2.98 42.83 3.50
2310 2346 3.603158 AGAAAACCGCCACAAACTTTT 57.397 38.095 0.00 0.00 0.00 2.27
2320 2356 9.797556 ATAATAATAACTTGAAAGAAAACCGCC 57.202 29.630 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.