Multiple sequence alignment - TraesCS7B01G009600

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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 TraesCS7B01G009600 chr7B 100.000 2371 0 0 1 2371 6004351 6001981 0.000000e+00 4379
1 TraesCS7B01G009600 chr7B 83.093 1455 162 48 949 2347 6082911 6081485 0.000000e+00 1247
2 TraesCS7B01G009600 chr7B 91.209 455 30 4 280 726 6083495 6083043 5.600000e-171 610
3 TraesCS7B01G009600 chr7B 89.399 283 25 2 1 278 6085331 6085049 3.750000e-93 351
4 TraesCS7B01G009600 chr7D 95.572 1671 59 8 1 1669 64451767 64450110 0.000000e+00 2662
5 TraesCS7B01G009600 chr7D 89.403 1406 113 20 40 1435 64534548 64533169 0.000000e+00 1738
6 TraesCS7B01G009600 chr7D 83.345 1417 128 41 965 2322 64497329 64495962 0.000000e+00 1210
7 TraesCS7B01G009600 chr7D 89.175 582 53 4 1 575 64506604 64506026 0.000000e+00 717
8 TraesCS7B01G009600 chr7D 85.994 664 28 23 1768 2371 64449791 64449133 0.000000e+00 651
9 TraesCS7B01G009600 chr7D 89.331 478 44 7 975 1448 64493590 64493116 5.640000e-166 593
10 TraesCS7B01G009600 chr7D 89.802 353 22 7 621 969 64506018 64505676 7.780000e-120 440
11 TraesCS7B01G009600 chr7D 80.705 596 70 20 1504 2072 64533029 64532452 2.820000e-114 422
12 TraesCS7B01G009600 chr7D 89.494 257 21 5 2070 2322 64530920 64530666 1.060000e-83 320
13 TraesCS7B01G009600 chr7A 86.372 2084 184 44 321 2322 68774575 68772510 0.000000e+00 2183
14 TraesCS7B01G009600 chr7A 91.837 1274 57 15 1130 2371 68239792 68238534 0.000000e+00 1733
15 TraesCS7B01G009600 chr7A 82.415 1433 150 51 939 2322 68344579 68343200 0.000000e+00 1157
16 TraesCS7B01G009600 chr7A 90.743 821 50 8 1 816 68240596 68239797 0.000000e+00 1072
17 TraesCS7B01G009600 chr7A 85.584 874 66 30 1449 2279 68768685 68767829 0.000000e+00 861
18 TraesCS7B01G009600 chr7A 90.586 478 39 6 975 1448 68770452 68769977 1.550000e-176 628
19 TraesCS7B01G009600 chr7A 89.627 482 41 3 1 477 68348524 68348047 2.610000e-169 604
20 TraesCS7B01G009600 chr7A 89.244 344 19 6 506 849 68344991 68344666 4.710000e-112 414
21 TraesCS7B01G009600 chr7A 88.462 286 27 2 40 324 68774935 68774655 8.120000e-90 340
22 TraesCS7B01G009600 chr5D 79.596 892 117 40 428 1293 2285962 2286814 1.580000e-161 579
23 TraesCS7B01G009600 chrUn 78.511 940 122 42 426 1321 300170073 300170976 5.760000e-151 544
24 TraesCS7B01G009600 chr5B 79.752 242 44 4 2085 2322 3864795 3864555 1.130000e-38 171
25 TraesCS7B01G009600 chr5A 83.333 156 18 5 61 214 1291505 1291654 1.140000e-28 137
26 TraesCS7B01G009600 chr5A 88.889 99 9 2 807 905 1293927 1294023 1.150000e-23 121


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 TraesCS7B01G009600 chr7B 6001981 6004351 2370 True 4379.000000 4379 100.000000 1 2371 1 chr7B.!!$R1 2370
1 TraesCS7B01G009600 chr7B 6081485 6085331 3846 True 736.000000 1247 87.900333 1 2347 3 chr7B.!!$R2 2346
2 TraesCS7B01G009600 chr7D 64449133 64451767 2634 True 1656.500000 2662 90.783000 1 2371 2 chr7D.!!$R1 2370
3 TraesCS7B01G009600 chr7D 64493116 64497329 4213 True 901.500000 1210 86.338000 965 2322 2 chr7D.!!$R2 1357
4 TraesCS7B01G009600 chr7D 64530666 64534548 3882 True 826.666667 1738 86.534000 40 2322 3 chr7D.!!$R4 2282
5 TraesCS7B01G009600 chr7D 64505676 64506604 928 True 578.500000 717 89.488500 1 969 2 chr7D.!!$R3 968
6 TraesCS7B01G009600 chr7A 68238534 68240596 2062 True 1402.500000 1733 91.290000 1 2371 2 chr7A.!!$R1 2370
7 TraesCS7B01G009600 chr7A 68767829 68774935 7106 True 1003.000000 2183 87.751000 40 2322 4 chr7A.!!$R3 2282
8 TraesCS7B01G009600 chr7A 68343200 68348524 5324 True 725.000000 1157 87.095333 1 2322 3 chr7A.!!$R2 2321
9 TraesCS7B01G009600 chr5D 2285962 2286814 852 False 579.000000 579 79.596000 428 1293 1 chr5D.!!$F1 865
10 TraesCS7B01G009600 chrUn 300170073 300170976 903 False 544.000000 544 78.511000 426 1321 1 chrUn.!!$F1 895

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
117 118 0.668535 GTGGTGTTTTCAGGCACTCC 59.331 55.0 0.0 0.0 34.6 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 10803 3.584733 AAGAACAAACTGAGGGAGCTT 57.415 42.857 0.0 0.0 0.0 3.74 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
117 118 0.668535 GTGGTGTTTTCAGGCACTCC 59.331 55.000 0.00 0.0 34.60 3.85
142 143 7.193595 CGTTGTTCTATTTCTGTCCAAACTTT 58.806 34.615 0.00 0.0 0.00 2.66
161 166 7.506328 AACTTTTGTCCTTATCACTTGGTAC 57.494 36.000 0.00 0.0 0.00 3.34
279 285 3.086600 GCTAGGGGCAGCTCTGGT 61.087 66.667 0.00 0.0 41.35 4.00
326 1968 5.640357 CACCGCAAGTTAAGGTATTACTTCA 59.360 40.000 1.62 0.0 36.34 3.02
327 1969 6.315393 CACCGCAAGTTAAGGTATTACTTCAT 59.685 38.462 1.62 0.0 36.34 2.57
761 5462 1.812235 TCGATCAGCATGCACTTTGT 58.188 45.000 21.98 0.0 34.76 2.83
824 5526 6.125029 AGTTGCATATTTGGATGAGTAGCTT 58.875 36.000 0.00 0.0 0.00 3.74
954 5723 8.632679 AGATAGATAGCTAGCAGATGATTAAGC 58.367 37.037 18.83 0.0 35.49 3.09
1192 5969 3.140073 AATCCACCGCCACCACCAA 62.140 57.895 0.00 0.0 0.00 3.67
1256 9764 4.162131 TCTGCACAAGATCACCATTAGCTA 59.838 41.667 0.00 0.0 0.00 3.32
1460 10002 8.985315 TCTAATGATGTTATGCTCCTTTGAAT 57.015 30.769 0.00 0.0 0.00 2.57
1706 10315 2.143231 AGTTTTGGGAAGGGGGAGTA 57.857 50.000 0.00 0.0 0.00 2.59
1925 10779 2.564947 ACTGGAGAAGAGCTTACACTGG 59.435 50.000 0.00 0.0 0.00 4.00
1934 10788 8.719645 AGAAGAGCTTACACTGGATATTAGAT 57.280 34.615 0.00 0.0 0.00 1.98
1935 10789 8.584157 AGAAGAGCTTACACTGGATATTAGATG 58.416 37.037 0.00 0.0 0.00 2.90
1949 10803 9.601810 TGGATATTAGATGAAAGAAGGTAGCTA 57.398 33.333 0.00 0.0 0.00 3.32
2146 12536 3.002862 TCACTCGTGTGTGCAATTTTACC 59.997 43.478 16.49 0.0 44.14 2.85
2253 12680 6.185114 AGGGATACATCTTTCATCAAGAGG 57.815 41.667 0.00 0.0 45.11 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 6.300354 AGTTTGGACAGAAATAGAACAACG 57.700 37.500 0.00 0.00 0.00 4.10
142 143 7.913789 ACTTATGTACCAAGTGATAAGGACAA 58.086 34.615 8.69 0.00 34.96 3.18
161 166 7.065683 GCCCCAAAATTAATTTCCACACTTATG 59.934 37.037 13.68 5.41 0.00 1.90
279 285 4.158394 GGATTTGTTTGCTGAGATTAGGCA 59.842 41.667 0.00 0.00 0.00 4.75
954 5723 7.715265 ATTAAGCACTATATTCACTCAACCG 57.285 36.000 0.00 0.00 0.00 4.44
988 5757 2.971330 CCCTCACCATGATAGCTCTTCT 59.029 50.000 0.00 0.00 0.00 2.85
1244 9751 8.034313 AGACTGGATTTAATAGCTAATGGTGA 57.966 34.615 0.00 0.00 0.00 4.02
1256 9764 6.600822 CCATGACTTGTGAGACTGGATTTAAT 59.399 38.462 0.00 0.00 0.00 1.40
1517 10116 9.436957 GGTGTAGTGCTAAAAGTATATGCATAT 57.563 33.333 22.31 22.31 36.04 1.78
1695 10304 6.183361 TGCTATAATTTCCTTACTCCCCCTTC 60.183 42.308 0.00 0.00 0.00 3.46
1706 10315 7.173907 CCGATGATGTTCTGCTATAATTTCCTT 59.826 37.037 0.00 0.00 0.00 3.36
1850 10681 7.841729 ACTCCTAAGTTTGATAATCTCTCCTCA 59.158 37.037 0.00 0.00 28.74 3.86
1934 10788 4.473477 GGAGCTTAGCTACCTTCTTTCA 57.527 45.455 6.75 0.00 39.88 2.69
1949 10803 3.584733 AAGAACAAACTGAGGGAGCTT 57.415 42.857 0.00 0.00 0.00 3.74
2056 10912 6.644347 TGGCAAAACTTTGTTCCTAAAATGA 58.356 32.000 4.23 0.00 40.24 2.57
2146 12536 8.488651 AACTTTACACGATAATGGGAAACTAG 57.511 34.615 0.00 0.00 0.00 2.57
2253 12680 4.417426 TTTCCCCGGAGAGTCAAATATC 57.583 45.455 0.73 0.00 0.00 1.63
2259 12686 2.093128 GCTTTATTTCCCCGGAGAGTCA 60.093 50.000 0.73 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.