Multiple sequence alignment - TraesCS6D01G145100

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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 TraesCS6D01G145100 chr6D 100.000 3965 0 0 1 3965 115541924 115545888 0.000000e+00 7323
1 TraesCS6D01G145100 chr6B 96.382 2128 64 7 1 2118 204919739 204921863 0.000000e+00 3491
2 TraesCS6D01G145100 chr6B 94.657 1853 56 12 2146 3965 204921860 204923702 0.000000e+00 2833
3 TraesCS6D01G145100 chr6A 96.777 1955 56 7 1 1949 143961494 143963447 0.000000e+00 3254
4 TraesCS6D01G145100 chr6A 95.193 1581 43 7 1947 3494 143963529 143965109 0.000000e+00 2468
5 TraesCS6D01G145100 chr6A 95.444 439 13 2 3528 3965 143965106 143965538 0.000000e+00 693
6 TraesCS6D01G145100 chr7A 82.690 907 141 12 1036 1930 678580701 678581603 0.000000e+00 791
7 TraesCS6D01G145100 chr7A 83.149 362 61 0 2609 2970 678581655 678582016 8.210000e-87 331
8 TraesCS6D01G145100 chr7D 82.470 907 143 13 1036 1930 587070265 587071167 0.000000e+00 780
9 TraesCS6D01G145100 chr7D 83.621 348 57 0 2623 2970 587071234 587071581 1.060000e-85 327
10 TraesCS6D01G145100 chr7B 81.477 907 152 11 1036 1930 657932969 657933871 0.000000e+00 730
11 TraesCS6D01G145100 chr7B 82.873 362 62 0 2609 2970 657933923 657934284 3.820000e-85 326


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 TraesCS6D01G145100 chr6D 115541924 115545888 3964 False 7323.000000 7323 100.000000 1 3965 1 chr6D.!!$F1 3964
1 TraesCS6D01G145100 chr6B 204919739 204923702 3963 False 3162.000000 3491 95.519500 1 3965 2 chr6B.!!$F1 3964
2 TraesCS6D01G145100 chr6A 143961494 143965538 4044 False 2138.333333 3254 95.804667 1 3965 3 chr6A.!!$F1 3964
3 TraesCS6D01G145100 chr7A 678580701 678582016 1315 False 561.000000 791 82.919500 1036 2970 2 chr7A.!!$F1 1934
4 TraesCS6D01G145100 chr7D 587070265 587071581 1316 False 553.500000 780 83.045500 1036 2970 2 chr7D.!!$F1 1934
5 TraesCS6D01G145100 chr7B 657932969 657934284 1315 False 528.000000 730 82.175000 1036 2970 2 chr7B.!!$F1 1934

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
164 165 1.133262 CAAATCCAGGCCATCCATCCT 60.133 52.381 5.01 0.00 33.74 3.24 F
1155 1175 1.687123 ACTGACAACTACAACCTCGCT 59.313 47.619 0.00 0.00 0.00 4.93 F
1263 1283 1.026718 ATGCTCCAACCGCAAGCTAC 61.027 55.000 0.00 0.00 41.26 3.58 F
2157 2263 4.466827 TGGATGCTCTGATTGTATGCAAT 58.533 39.130 8.93 8.93 46.99 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1283 0.532862 AGACACTGTTGCCAACCGAG 60.533 55.000 4.90 0.00 0.00 4.63 R
1995 2099 4.116961 CAGGATTTGGCATGTGCAAATAG 58.883 43.478 7.36 2.74 44.36 1.73 R
2114 2219 5.020132 CCAGGTACATTGTGGGGAAAAATA 58.980 41.667 0.00 0.00 0.00 1.40 R
3878 4017 0.899720 CCCTGACAAGCCATTTGCAT 59.100 50.000 0.00 0.00 44.83 3.96 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
46 47 1.847890 CGGACGGACGCACCAAATTT 61.848 55.000 8.67 0.00 38.90 1.82
61 62 4.722700 TTTGGGCGGGAGAGCAGC 62.723 66.667 0.00 0.00 39.27 5.25
67 68 3.121030 CGGGAGAGCAGCCAAACG 61.121 66.667 0.00 0.00 0.00 3.60
164 165 1.133262 CAAATCCAGGCCATCCATCCT 60.133 52.381 5.01 0.00 33.74 3.24
524 530 3.508840 CCTCACGCCCAATTCGGC 61.509 66.667 3.64 3.64 46.13 5.54
687 693 1.705186 CTGGGAAGGGTCTGGAGAAAA 59.295 52.381 0.00 0.00 0.00 2.29
913 924 5.059161 CAGCTTGCTATAATTGCAGGTCTA 58.941 41.667 0.00 0.00 41.71 2.59
952 963 3.067320 GGGCATTTCTTAGTTGAGGATGC 59.933 47.826 0.00 0.00 36.99 3.91
1155 1175 1.687123 ACTGACAACTACAACCTCGCT 59.313 47.619 0.00 0.00 0.00 4.93
1263 1283 1.026718 ATGCTCCAACCGCAAGCTAC 61.027 55.000 0.00 0.00 41.26 3.58
2157 2263 4.466827 TGGATGCTCTGATTGTATGCAAT 58.533 39.130 8.93 8.93 46.99 3.56
2273 2400 4.994852 TGAAACGATTGAAGGTTGGACTAG 59.005 41.667 0.00 0.00 0.00 2.57
2320 2447 7.490657 AGTCTATTATACCACAGTTCCAACA 57.509 36.000 0.00 0.00 0.00 3.33
2349 2476 2.036958 TACAAAGCATGGTCCATCGG 57.963 50.000 0.00 0.00 0.00 4.18
2922 3061 0.739462 TGAGCCATGTCCGTAAAGCG 60.739 55.000 0.00 0.00 40.95 4.68
3282 3421 2.925724 TGATTTCTGTGGTGTCGGTTT 58.074 42.857 0.00 0.00 0.00 3.27
3311 3450 7.601130 TGGACACTATATTGCGGTTCATAATAC 59.399 37.037 0.00 0.00 0.00 1.89
3390 3529 4.422073 TCACTGTCACTTGATCCAAAGT 57.578 40.909 0.00 0.00 41.08 2.66
3602 3741 1.732259 CTAACGCGAGCTGTTTGGATT 59.268 47.619 15.93 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.961522 TCGACAAAACGATCAAAGCC 57.038 45.000 0.00 0.00 37.37 4.35
192 193 5.247862 CCCCTTTGCTGCAAAAATAGAAAT 58.752 37.500 25.93 0.00 32.75 2.17
687 693 7.686859 GCCCTTCAACCTAGAAAACAAGAAAAT 60.687 37.037 0.00 0.00 0.00 1.82
790 801 8.352201 CAACCAAGAACATTCTCAGTAAATGAA 58.648 33.333 3.06 0.00 37.52 2.57
799 810 9.219603 CTTATCTTACAACCAAGAACATTCTCA 57.780 33.333 0.00 0.00 38.03 3.27
802 813 6.961554 CGCTTATCTTACAACCAAGAACATTC 59.038 38.462 0.00 0.00 38.03 2.67
913 924 0.903454 CCCTCTTCCGTACACCCACT 60.903 60.000 0.00 0.00 0.00 4.00
1155 1175 1.298340 CATGGTAACGGAGCCACCA 59.702 57.895 0.31 0.31 46.42 4.17
1263 1283 0.532862 AGACACTGTTGCCAACCGAG 60.533 55.000 4.90 0.00 0.00 4.63
1509 1529 5.060693 CGATTGTGCTCTCTCGATATCATTG 59.939 44.000 3.12 0.00 33.07 2.82
1782 1802 3.675348 TTATCCGACTTCAGGTCCCTA 57.325 47.619 0.00 0.00 41.64 3.53
1995 2099 4.116961 CAGGATTTGGCATGTGCAAATAG 58.883 43.478 7.36 2.74 44.36 1.73
2114 2219 5.020132 CCAGGTACATTGTGGGGAAAAATA 58.980 41.667 0.00 0.00 0.00 1.40
2157 2263 7.016153 ACAGTTTGAGTTATATGAGAACCCA 57.984 36.000 0.00 0.00 0.00 4.51
2273 2400 8.139521 ACTTGCTTCGTTAATAGTTATAAGGC 57.860 34.615 0.00 0.00 0.00 4.35
2349 2476 8.937634 ACTCTGCAATATTTCAATTTGGATTC 57.062 30.769 0.00 0.00 0.00 2.52
2582 2717 9.778741 CCAACCACTACATCAATTATATACACT 57.221 33.333 0.00 0.00 0.00 3.55
3282 3421 2.394632 ACCGCAATATAGTGTCCAGGA 58.605 47.619 1.67 0.00 0.00 3.86
3390 3529 6.883756 TGAAGTGTCACCATGATTAGCATAAA 59.116 34.615 0.00 0.00 34.82 1.40
3562 3701 4.955811 AGGACACACAAGATGTAGAACA 57.044 40.909 0.00 0.00 40.64 3.18
3602 3741 2.172505 TCCTGTCTCCTCAAAGCAAACA 59.827 45.455 0.00 0.00 0.00 2.83
3661 3800 4.715896 GTGCACACACATACATCAAAGAG 58.284 43.478 13.17 0.00 46.61 2.85
3702 3841 8.911918 TTGCCCACATATTAAATTATACGAGT 57.088 30.769 0.00 0.00 0.00 4.18
3703 3842 8.999431 ACTTGCCCACATATTAAATTATACGAG 58.001 33.333 0.00 0.00 0.00 4.18
3704 3843 8.911918 ACTTGCCCACATATTAAATTATACGA 57.088 30.769 0.00 0.00 0.00 3.43
3705 3844 8.779303 TGACTTGCCCACATATTAAATTATACG 58.221 33.333 0.00 0.00 0.00 3.06
3717 3856 4.286032 AGTCTACTTTGACTTGCCCACATA 59.714 41.667 0.00 0.00 44.01 2.29
3718 3857 3.073062 AGTCTACTTTGACTTGCCCACAT 59.927 43.478 0.00 0.00 44.01 3.21
3734 3873 3.843999 CAGGCAGAAGAGAACAGTCTAC 58.156 50.000 0.00 0.00 32.80 2.59
3851 3990 1.754803 TCTCCATTACTGATTCGCGGT 59.245 47.619 6.13 0.00 39.97 5.68
3878 4017 0.899720 CCCTGACAAGCCATTTGCAT 59.100 50.000 0.00 0.00 44.83 3.96


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

AutoCloner maintained by Alex Coulton.