Multiple sequence alignment - TraesCS6B01G232200

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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 TraesCS6B01G232200 chr6B 100.000 2298 0 0 1 2298 388040484 388038187 0 4244
1 TraesCS6B01G232200 chr5A 97.007 2305 61 6 1 2298 238859715 238862018 0 3868
2 TraesCS6B01G232200 chr5A 96.788 2304 64 9 1 2298 238829763 238827464 0 3836
3 TraesCS6B01G232200 chr1A 96.353 2303 77 7 1 2298 334091121 334093421 0 3781
4 TraesCS6B01G232200 chr5B 97.602 2085 45 5 1 2082 130613165 130615247 0 3568
5 TraesCS6B01G232200 chr5B 97.266 2085 52 5 1 2082 130608141 130610223 0 3530
6 TraesCS6B01G232200 chrUn 97.511 2089 47 5 1 2085 261514802 261512715 0 3565
7 TraesCS6B01G232200 chrUn 97.506 2085 47 5 1 2082 45099056 45101138 0 3557
8 TraesCS6B01G232200 chrUn 97.537 406 9 1 1894 2298 396261046 396261451 0 693
9 TraesCS6B01G232200 chrUn 97.297 407 9 1 1894 2298 209406993 209407399 0 689
10 TraesCS6B01G232200 chr2D 97.318 2088 49 5 1 2082 644701524 644703610 0 3539
11 TraesCS6B01G232200 chr2D 97.291 406 10 1 1894 2298 17994448 17994043 0 688
12 TraesCS6B01G232200 chr3A 97.270 2088 53 4 1 2085 66032050 66029964 0 3537
13 TraesCS6B01G232200 chr4D 98.030 406 7 1 1894 2298 241377397 241377802 0 704
14 TraesCS6B01G232200 chr7D 97.537 406 9 1 1894 2298 579000902 579000497 0 693
15 TraesCS6B01G232200 chr1D 97.291 406 10 1 1894 2298 212438990 212438585 0 688


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 TraesCS6B01G232200 chr6B 388038187 388040484 2297 True 4244 4244 100.000 1 2298 1 chr6B.!!$R1 2297
1 TraesCS6B01G232200 chr5A 238859715 238862018 2303 False 3868 3868 97.007 1 2298 1 chr5A.!!$F1 2297
2 TraesCS6B01G232200 chr5A 238827464 238829763 2299 True 3836 3836 96.788 1 2298 1 chr5A.!!$R1 2297
3 TraesCS6B01G232200 chr1A 334091121 334093421 2300 False 3781 3781 96.353 1 2298 1 chr1A.!!$F1 2297
4 TraesCS6B01G232200 chr5B 130608141 130615247 7106 False 3549 3568 97.434 1 2082 2 chr5B.!!$F1 2081
5 TraesCS6B01G232200 chrUn 261512715 261514802 2087 True 3565 3565 97.511 1 2085 1 chrUn.!!$R1 2084
6 TraesCS6B01G232200 chrUn 45099056 45101138 2082 False 3557 3557 97.506 1 2082 1 chrUn.!!$F1 2081
7 TraesCS6B01G232200 chr2D 644701524 644703610 2086 False 3539 3539 97.318 1 2082 1 chr2D.!!$F1 2081
8 TraesCS6B01G232200 chr3A 66029964 66032050 2086 True 3537 3537 97.270 1 2085 1 chr3A.!!$R1 2084

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
322 324 0.321564 TCGGTCGGTCCTAGAAACGA 60.322 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 6633 0.389391 ACCTGGAGAACGTGTGACAG 59.611 55.0 0.0 0.0 0.0 3.51 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
152 154 1.205460 ACCTTAGCATGGGGGACGTT 61.205 55.000 0.00 0.00 0.00 3.99
167 169 3.344515 GGACGTTCTAATCCTTTTGCCT 58.655 45.455 0.00 0.00 31.75 4.75
196 198 1.143373 CGGCTAATCGTACGCAGCAA 61.143 55.000 26.47 7.25 35.69 3.91
231 233 2.633860 CTGGTTCAGGAAGGCACAC 58.366 57.895 0.00 0.00 0.00 3.82
256 258 6.080648 AGTCCGAACGCTATTATGAATGTA 57.919 37.500 0.00 0.00 0.00 2.29
302 304 2.674033 GTGCATGCAGGTGAGGCA 60.674 61.111 23.41 0.00 46.66 4.75
322 324 0.321564 TCGGTCGGTCCTAGAAACGA 60.322 55.000 0.00 0.00 0.00 3.85
347 349 2.033550 CAGCTAGCGAGGAGTTAACGAT 59.966 50.000 9.55 0.00 0.00 3.73
406 410 1.567649 TCGCCTATAGGGATATCGGGT 59.432 52.381 20.58 0.00 37.23 5.28
416 5443 0.541863 GATATCGGGTGGGGCATAGG 59.458 60.000 0.00 0.00 0.00 2.57
497 5524 1.064758 TCCCGCCAATTCTATTGCACT 60.065 47.619 0.00 0.00 0.00 4.40
572 5599 2.355818 GGAAAGAAAGGGCGGTAGATGT 60.356 50.000 0.00 0.00 0.00 3.06
586 5613 4.196971 GGTAGATGTTAATGCGAAAGGGT 58.803 43.478 0.00 0.00 0.00 4.34
623 5650 7.094592 GCTTGATAGTAAAGCCAAAGAAAGACT 60.095 37.037 0.00 0.00 43.45 3.24
1198 6226 2.814336 GTCTGAATTTTCCACGGAAGCT 59.186 45.455 0.00 0.00 35.38 3.74
1338 6366 5.173664 ACGTAGTTGTAATTCTAGGGCAAC 58.826 41.667 0.00 0.00 37.78 4.17
1366 6394 2.136026 CTTTCCCCATAGCCCTAAGGT 58.864 52.381 0.00 0.00 34.57 3.50
1409 6437 4.379603 CGCGAAAGATAAGATACGGGAGAT 60.380 45.833 0.00 0.00 36.20 2.75
1411 6439 4.859798 CGAAAGATAAGATACGGGAGATGC 59.140 45.833 0.00 0.00 0.00 3.91
1454 6482 1.280998 ACCCTTGGTCTAATTCCACGG 59.719 52.381 1.28 1.28 41.96 4.94
1570 6598 2.105993 GGGGCCCGATACTTCAACTAAT 59.894 50.000 17.79 0.00 0.00 1.73
1605 6633 0.106419 TTCACCAAACCCTGACCCAC 60.106 55.000 0.00 0.00 0.00 4.61
1660 6688 0.324460 CCCAACTACCGACTCCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
1676 6704 2.483013 CCTCCTGGAATTGCGTTATCGA 60.483 50.000 0.00 0.00 35.64 3.59
1801 6829 4.857679 ACTCGGTCATAGGAACTTAGACT 58.142 43.478 0.00 0.00 41.75 3.24
1816 6844 1.226603 GACTACCTACGCGCTGGTG 60.227 63.158 26.99 19.89 37.74 4.17
1834 6862 2.140717 GTGAACGAAAACCACCTCGAT 58.859 47.619 0.00 0.00 38.43 3.59
1845 6873 1.605753 CACCTCGATCGGATCTACCA 58.394 55.000 16.41 0.00 38.90 3.25
1859 6887 1.975680 TCTACCAAACGAAGAAGGCCT 59.024 47.619 0.00 0.00 0.00 5.19
1862 6890 1.298859 CCAAACGAAGAAGGCCTCCG 61.299 60.000 5.23 10.53 0.00 4.63
1880 6908 3.255725 TCCGCGTCGAAAGAATTAACAT 58.744 40.909 4.92 0.00 45.01 2.71
1990 7018 5.070981 TCCGCCTATCTTTCTGATCTCATTT 59.929 40.000 0.00 0.00 36.65 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.002544 GCTGGGCGATAATAGCTCCTT 59.997 52.381 0.00 0.00 33.29 3.36
152 154 2.038387 GCGGAGGCAAAAGGATTAGA 57.962 50.000 0.00 0.00 39.62 2.10
167 169 3.750373 GATTAGCCGGCCTTGCGGA 62.750 63.158 26.15 1.16 0.00 5.54
231 233 3.263602 TCATAATAGCGTTCGGACTCG 57.736 47.619 0.00 0.00 37.82 4.18
256 258 0.792640 CGTAGTGTAGTGTCGGTCGT 59.207 55.000 0.00 0.00 0.00 4.34
302 304 0.737219 CGTTTCTAGGACCGACCGAT 59.263 55.000 0.00 0.00 44.74 4.18
322 324 3.522731 CTCCTCGCTAGCTGCCGT 61.523 66.667 13.93 0.00 38.78 5.68
347 349 2.486636 CTAGGTTGCAGCACGTCCGA 62.487 60.000 2.05 0.00 0.00 4.55
406 410 2.852449 AGAAGAATTGTCCTATGCCCCA 59.148 45.455 0.00 0.00 0.00 4.96
416 5443 3.009584 ACCCTCCTCCAAGAAGAATTGTC 59.990 47.826 0.00 0.00 0.00 3.18
497 5524 0.250124 ATGTTCGACTTCGGTTGCCA 60.250 50.000 0.00 0.00 40.29 4.92
572 5599 2.176140 CGGCACCCTTTCGCATTAA 58.824 52.632 0.00 0.00 0.00 1.40
623 5650 3.650942 ACAGTTGTATCTTGTCTTGGGGA 59.349 43.478 0.00 0.00 0.00 4.81
687 5714 2.772191 TGGGCGCCACTATCCCAT 60.772 61.111 30.85 0.00 44.62 4.00
988 6016 6.817765 ATCGAAACACATTGAAATGGTACT 57.182 33.333 7.87 0.00 40.70 2.73
1095 6123 6.778834 ACATGGCAATTAAATCATGAGTCA 57.221 33.333 0.09 0.00 39.27 3.41
1198 6226 7.416664 GCACCTAAGATCAAATATTTTGAGCCA 60.417 37.037 12.98 3.31 35.61 4.75
1338 6366 1.543429 GCTATGGGGAAAGTGGATCGG 60.543 57.143 0.00 0.00 0.00 4.18
1366 6394 1.400846 GCGTAGGAGATCGAGACACAA 59.599 52.381 0.00 0.00 0.00 3.33
1409 6437 0.399376 ACCCATACCATAGGACCGCA 60.399 55.000 0.00 0.00 0.00 5.69
1411 6439 2.011122 AGACCCATACCATAGGACCG 57.989 55.000 0.00 0.00 0.00 4.79
1570 6598 1.070786 GAACCAACAGGTCGCTCCA 59.929 57.895 0.00 0.00 39.02 3.86
1605 6633 0.389391 ACCTGGAGAACGTGTGACAG 59.611 55.000 0.00 0.00 0.00 3.51
1660 6688 1.668751 GGCTTCGATAACGCAATTCCA 59.331 47.619 0.00 0.00 39.58 3.53
1676 6704 1.147153 GCTATTCCTGGCTCGGCTT 59.853 57.895 0.00 0.00 0.00 4.35
1801 6829 1.213537 GTTCACCAGCGCGTAGGTA 59.786 57.895 21.20 7.27 36.07 3.08
1816 6844 1.389106 CGATCGAGGTGGTTTTCGTTC 59.611 52.381 10.26 0.00 37.99 3.95
1834 6862 3.119245 CCTTCTTCGTTTGGTAGATCCGA 60.119 47.826 0.00 0.00 39.52 4.55
1845 6873 1.671379 GCGGAGGCCTTCTTCGTTT 60.671 57.895 6.77 0.00 45.99 3.60
1859 6887 2.674954 TGTTAATTCTTTCGACGCGGA 58.325 42.857 12.47 0.00 0.00 5.54
1862 6890 3.098636 GGCATGTTAATTCTTTCGACGC 58.901 45.455 0.00 0.00 0.00 5.19
1990 7018 6.431278 TGACTTTTTATGCGATCGAAAAACA 58.569 32.000 21.57 13.97 30.89 2.83
1996 7024 5.348164 TCTCATGACTTTTTATGCGATCGA 58.652 37.500 21.57 4.34 0.00 3.59


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

AutoCloner maintained by Alex Coulton.