Multiple sequence alignment - TraesCS7A01G382800

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 TraesCS7A01G382800 chr7A 100.000 3489 0 0 1 3489 557552815 557556303 0.000000e+00 6444
1 TraesCS7A01G382800 chr7D 96.753 3511 67 14 1 3489 491245696 491249181 0.000000e+00 5808
2 TraesCS7A01G382800 chr7B 95.880 3519 92 23 1 3489 519783435 519786930 0.000000e+00 5646
3 TraesCS7A01G382800 chr1A 82.828 198 31 2 6 202 373783070 373783265 1.290000e-39 174


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 TraesCS7A01G382800 chr7A 557552815 557556303 3488 False 6444 6444 100.000 1 3489 1 chr7A.!!$F1 3488
1 TraesCS7A01G382800 chr7D 491245696 491249181 3485 False 5808 5808 96.753 1 3489 1 chr7D.!!$F1 3488
2 TraesCS7A01G382800 chr7B 519783435 519786930 3495 False 5646 5646 95.880 1 3489 1 chr7B.!!$F1 3488

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
774 788 0.034960 TCTCCCCTCTCACTCACTCG 60.035 60.0 0.0 0.0 0.00 4.18 F
1048 1062 0.528901 CTCCGACACCGACAACAACA 60.529 55.0 0.0 0.0 38.22 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1751 2.259818 CTCGAGACAGCGGTGCTT 59.740 61.111 15.82 2.34 36.4 3.91 R
2493 2526 2.519013 GGTTTCTTCCTCTTGGCACAT 58.481 47.619 0.00 0.00 39.3 3.21 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
358 362 5.337089 CGCAGGTGTCCATTCATCTATCTAT 60.337 44.000 0.00 0.00 0.00 1.98
513 517 0.255890 CCCACCCAAATCATCCTCGT 59.744 55.000 0.00 0.00 0.00 4.18
525 529 0.039764 ATCCTCGTCACAGTCCAGGA 59.960 55.000 0.00 0.00 37.66 3.86
596 604 9.078990 CTCTACATAGTTAGAGAGAGAGAGAGA 57.921 40.741 1.55 0.00 41.65 3.10
598 606 7.067496 ACATAGTTAGAGAGAGAGAGAGAGG 57.933 44.000 0.00 0.00 0.00 3.69
599 607 6.043243 ACATAGTTAGAGAGAGAGAGAGAGGG 59.957 46.154 0.00 0.00 0.00 4.30
600 608 3.716872 AGTTAGAGAGAGAGAGAGAGGGG 59.283 52.174 0.00 0.00 0.00 4.79
702 710 4.279420 CACAGTGCATCTAGTAGGCTATGA 59.721 45.833 0.00 0.00 35.40 2.15
748 762 1.589716 GGTTGCTGGTGATGGTGCTC 61.590 60.000 0.00 0.00 0.00 4.26
774 788 0.034960 TCTCCCCTCTCACTCACTCG 60.035 60.000 0.00 0.00 0.00 4.18
1046 1060 1.068417 CCTCCGACACCGACAACAA 59.932 57.895 0.00 0.00 38.22 2.83
1047 1061 1.219522 CCTCCGACACCGACAACAAC 61.220 60.000 0.00 0.00 38.22 3.32
1048 1062 0.528901 CTCCGACACCGACAACAACA 60.529 55.000 0.00 0.00 38.22 3.33
1479 1505 2.413351 CGCGTCCACATCCTCGAT 59.587 61.111 0.00 0.00 0.00 3.59
1738 1764 4.335647 CCCCAAGCACCGCTGTCT 62.336 66.667 0.00 0.00 39.62 3.41
1878 1904 2.589442 GTGGTGACCGTTGCCGAA 60.589 61.111 0.00 0.00 35.63 4.30
2493 2526 4.409247 GGAGGAGGAGCTAGTTGGATTAAA 59.591 45.833 0.00 0.00 0.00 1.52
2614 2647 4.333926 AGATCGGAAAGCTTAGAAATGCAC 59.666 41.667 0.00 0.00 0.00 4.57
2616 2649 2.159627 CGGAAAGCTTAGAAATGCACGT 59.840 45.455 0.00 0.00 0.00 4.49
2715 2751 7.518188 TCCTCTTTCTAGGTTGTTCATTTCTT 58.482 34.615 0.00 0.00 37.91 2.52
2739 2775 4.377124 GCTTAGTTCGTGTTGGAGTAAAGC 60.377 45.833 0.00 0.00 0.00 3.51
2830 2874 3.253188 TGTTGCTATTGCTTCTGTTCACC 59.747 43.478 0.00 0.00 40.48 4.02
2881 2925 4.082081 TGTGTGATCTTGCAAAATGGATCC 60.082 41.667 18.52 4.20 35.18 3.36
2882 2926 4.082081 GTGTGATCTTGCAAAATGGATCCA 60.082 41.667 18.88 18.88 35.18 3.41
2883 2927 4.712829 TGTGATCTTGCAAAATGGATCCAT 59.287 37.500 22.15 22.15 38.46 3.41
2884 2928 5.047847 GTGATCTTGCAAAATGGATCCATG 58.952 41.667 27.97 18.02 36.68 3.66
3358 3405 6.676990 TCTGTGTCTCATGCTCCATATATT 57.323 37.500 0.00 0.00 0.00 1.28
3359 3406 6.461640 TCTGTGTCTCATGCTCCATATATTG 58.538 40.000 0.00 0.00 0.00 1.90
3375 3422 8.710239 TCCATATATTGTGGTAAGCTGTCTTTA 58.290 33.333 0.00 0.00 37.96 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 139 7.708998 AGCTTTTGACGGTTTAAAAGTTATCA 58.291 30.769 21.73 0.00 42.79 2.15
358 362 1.134699 CAGTGGCAGCTTTAGATCGGA 60.135 52.381 0.00 0.00 0.00 4.55
403 407 6.258287 CAGAGCTTAGCTTCTACGACTAGTTA 59.742 42.308 8.58 0.00 39.88 2.24
513 517 4.838423 TGTCTTTTATCTCCTGGACTGTGA 59.162 41.667 0.00 0.00 0.00 3.58
525 529 2.039879 AGGGTGGCGTTGTCTTTTATCT 59.960 45.455 0.00 0.00 0.00 1.98
596 604 0.787084 TCTCTCTCCTCACAACCCCT 59.213 55.000 0.00 0.00 0.00 4.79
598 606 2.614229 GCTTTCTCTCTCCTCACAACCC 60.614 54.545 0.00 0.00 0.00 4.11
599 607 2.037772 TGCTTTCTCTCTCCTCACAACC 59.962 50.000 0.00 0.00 0.00 3.77
600 608 3.244044 ACTGCTTTCTCTCTCCTCACAAC 60.244 47.826 0.00 0.00 0.00 3.32
702 710 6.696148 GCTACGCTACTACAAATAATGTCAGT 59.304 38.462 0.00 0.00 42.70 3.41
1046 1060 3.276846 GGTCGGCGTTGCTGTTGT 61.277 61.111 6.85 0.00 36.18 3.32
1047 1061 2.954753 GAGGTCGGCGTTGCTGTTG 61.955 63.158 6.85 0.00 36.18 3.33
1048 1062 2.665185 GAGGTCGGCGTTGCTGTT 60.665 61.111 6.85 0.00 36.18 3.16
1209 1235 1.832167 GAGGAGGATCTCGGCAGCT 60.832 63.158 0.00 0.00 33.73 4.24
1725 1751 2.259818 CTCGAGACAGCGGTGCTT 59.740 61.111 15.82 2.34 36.40 3.91
1872 1898 4.082523 CTCGCCTCCCTTTCGGCA 62.083 66.667 0.00 0.00 46.62 5.69
2262 2288 3.282745 CTACTGCCACGCCGACACT 62.283 63.158 0.00 0.00 0.00 3.55
2493 2526 2.519013 GGTTTCTTCCTCTTGGCACAT 58.481 47.619 0.00 0.00 39.30 3.21
2614 2647 2.733552 CTCTAATCCAATGCGATCCACG 59.266 50.000 0.00 0.00 45.66 4.94
2616 2649 2.705658 ACCTCTAATCCAATGCGATCCA 59.294 45.455 0.00 0.00 0.00 3.41
2715 2751 2.902705 ACTCCAACACGAACTAAGCA 57.097 45.000 0.00 0.00 0.00 3.91
2739 2775 7.229506 GGTCCAACAATCATAATCTCCCTAAAG 59.770 40.741 0.00 0.00 0.00 1.85
2795 2839 5.724769 GCAATAGCAACAAATCCGCAAAATC 60.725 40.000 0.00 0.00 41.58 2.17
2830 2874 9.773328 CTCACTTAAATAACATGGTAATGTGTG 57.227 33.333 0.00 1.64 46.58 3.82
3144 3188 8.941977 GTGATCATTACTACCACATAAACAACA 58.058 33.333 0.00 0.00 0.00 3.33
3358 3405 4.262894 CCTTCCTAAAGACAGCTTACCACA 60.263 45.833 0.00 0.00 34.14 4.17
3359 3406 4.254492 CCTTCCTAAAGACAGCTTACCAC 58.746 47.826 0.00 0.00 34.14 4.16
3375 3422 0.178970 GGATCATGCCATGCCTTCCT 60.179 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.