Multiple sequence alignment - TraesCS7A01G190400

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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 TraesCS7A01G190400 chr7A 100.000 2846 0 0 1 2846 148374327 148377172 0 5256
1 TraesCS7A01G190400 chr7A 94.965 2264 109 4 585 2846 252463521 252461261 0 3544
2 TraesCS7A01G190400 chr7A 94.920 2264 113 2 585 2846 479458841 479461104 0 3542
3 TraesCS7A01G190400 chr7A 94.653 2263 118 3 585 2846 553405416 553403156 0 3506
4 TraesCS7A01G190400 chr3A 95.232 2265 104 4 585 2846 210043747 210041484 0 3581
5 TraesCS7A01G190400 chr4A 94.876 2264 114 2 585 2846 539731930 539729667 0 3537
6 TraesCS7A01G190400 chr4A 94.655 2264 119 2 585 2846 491126405 491124142 0 3509
7 TraesCS7A01G190400 chr6A 94.879 2265 110 5 585 2846 542213533 542211272 0 3535
8 TraesCS7A01G190400 chr6A 99.317 586 4 0 1 586 98935816 98936401 0 1061
9 TraesCS7A01G190400 chr5A 94.830 2263 115 2 585 2846 12388302 12386041 0 3530
10 TraesCS7A01G190400 chr1A 94.786 2263 117 1 585 2846 530710903 530713165 0 3524
11 TraesCS7A01G190400 chr1B 99.317 586 4 0 1 586 206398326 206398911 0 1061
12 TraesCS7A01G190400 chrUn 98.978 587 5 1 1 586 382258323 382257737 0 1050
13 TraesCS7A01G190400 chr6B 98.974 585 6 0 1 585 262286790 262287374 0 1048
14 TraesCS7A01G190400 chr6B 98.807 587 7 0 1 587 504037595 504037009 0 1046
15 TraesCS7A01G190400 chr5B 98.805 586 7 0 1 586 673346443 673345858 0 1044
16 TraesCS7A01G190400 chr5B 98.480 592 8 1 1 591 673337135 673336544 0 1042
17 TraesCS7A01G190400 chr2B 98.805 586 7 0 1 586 178734142 178734727 0 1044
18 TraesCS7A01G190400 chr2B 98.805 586 7 0 1 586 281918866 281918281 0 1044


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 TraesCS7A01G190400 chr7A 148374327 148377172 2845 False 5256 5256 100.000 1 2846 1 chr7A.!!$F1 2845
1 TraesCS7A01G190400 chr7A 252461261 252463521 2260 True 3544 3544 94.965 585 2846 1 chr7A.!!$R1 2261
2 TraesCS7A01G190400 chr7A 479458841 479461104 2263 False 3542 3542 94.920 585 2846 1 chr7A.!!$F2 2261
3 TraesCS7A01G190400 chr7A 553403156 553405416 2260 True 3506 3506 94.653 585 2846 1 chr7A.!!$R2 2261
4 TraesCS7A01G190400 chr3A 210041484 210043747 2263 True 3581 3581 95.232 585 2846 1 chr3A.!!$R1 2261
5 TraesCS7A01G190400 chr4A 539729667 539731930 2263 True 3537 3537 94.876 585 2846 1 chr4A.!!$R2 2261
6 TraesCS7A01G190400 chr4A 491124142 491126405 2263 True 3509 3509 94.655 585 2846 1 chr4A.!!$R1 2261
7 TraesCS7A01G190400 chr6A 542211272 542213533 2261 True 3535 3535 94.879 585 2846 1 chr6A.!!$R1 2261
8 TraesCS7A01G190400 chr6A 98935816 98936401 585 False 1061 1061 99.317 1 586 1 chr6A.!!$F1 585
9 TraesCS7A01G190400 chr5A 12386041 12388302 2261 True 3530 3530 94.830 585 2846 1 chr5A.!!$R1 2261
10 TraesCS7A01G190400 chr1A 530710903 530713165 2262 False 3524 3524 94.786 585 2846 1 chr1A.!!$F1 2261
11 TraesCS7A01G190400 chr1B 206398326 206398911 585 False 1061 1061 99.317 1 586 1 chr1B.!!$F1 585
12 TraesCS7A01G190400 chrUn 382257737 382258323 586 True 1050 1050 98.978 1 586 1 chrUn.!!$R1 585
13 TraesCS7A01G190400 chr6B 262286790 262287374 584 False 1048 1048 98.974 1 585 1 chr6B.!!$F1 584
14 TraesCS7A01G190400 chr6B 504037009 504037595 586 True 1046 1046 98.807 1 587 1 chr6B.!!$R1 586
15 TraesCS7A01G190400 chr5B 673345858 673346443 585 True 1044 1044 98.805 1 586 1 chr5B.!!$R2 585
16 TraesCS7A01G190400 chr5B 673336544 673337135 591 True 1042 1042 98.480 1 591 1 chr5B.!!$R1 590
17 TraesCS7A01G190400 chr2B 178734142 178734727 585 False 1044 1044 98.805 1 586 1 chr2B.!!$F1 585
18 TraesCS7A01G190400 chr2B 281918281 281918866 585 True 1044 1044 98.805 1 586 1 chr2B.!!$R1 585

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
615 617 1.136891 CTATCATGAGTGCGGTGGTCA 59.863 52.381 0.09 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2246 1.137825 CGCTGTTCGAGAGGTCTCC 59.862 63.158 1.32 0.0 41.67 3.71 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
442 444 1.792006 GGTTGGATCGTGAAGACGTT 58.208 50.000 0.00 0.00 46.20 3.99
514 516 2.816087 GGTACGTAGACAACACTCTCCA 59.184 50.000 0.00 0.00 0.00 3.86
615 617 1.136891 CTATCATGAGTGCGGTGGTCA 59.863 52.381 0.09 0.00 0.00 4.02
761 763 1.597663 CGGTGTTCGTGAAGAAAAGCT 59.402 47.619 0.00 0.00 41.27 3.74
790 792 7.443302 AGAGGATCAAATGATAACTCAGGAA 57.557 36.000 20.54 0.00 39.30 3.36
1410 1413 2.026262 ACTGGATGCCGTGGAGTTTTAT 60.026 45.455 0.00 0.00 0.00 1.40
1567 1570 3.517901 CCTTATAATCCGGATGTGGCCTA 59.482 47.826 19.95 5.65 0.00 3.93
1668 1671 2.107750 ATCTGCATCGAGGGTGCG 59.892 61.111 0.00 0.00 45.37 5.34
1695 1698 1.404583 GCTTTTACCCGAGCGAAGGTA 60.405 52.381 0.00 0.00 39.88 3.08
1938 1946 2.551912 CCTTCTGTGCGGCCGTTTT 61.552 57.895 28.70 0.00 0.00 2.43
1939 1947 1.358759 CTTCTGTGCGGCCGTTTTT 59.641 52.632 28.70 0.00 0.00 1.94
2092 2101 4.757149 AGGCAATCGGACTATAATGCTTTC 59.243 41.667 0.00 0.00 27.39 2.62
2160 2169 1.289244 CCCCTGGTATTTGGAGGGCT 61.289 60.000 0.00 0.00 44.74 5.19
2188 2197 2.457366 GGCGCTATACATGCCTAAGT 57.543 50.000 7.64 0.00 45.40 2.24
2237 2246 4.515567 AGCGGAAAAAGTCTTTAAGGACTG 59.484 41.667 19.78 8.27 44.67 3.51
2293 2302 6.430925 CCTTATCATGACAGTCAGTTTTTGGA 59.569 38.462 9.64 0.00 0.00 3.53
2475 2486 0.539986 ATAAGTTCGGGGTGTCGCAT 59.460 50.000 0.00 0.00 0.00 4.73
2750 2762 5.276678 GCTACGCATAAATAGTGAAAAGCGA 60.277 40.000 10.54 0.00 46.01 4.93
2781 2793 7.130099 TCAATTATTACTAGAGACCACCTGGA 58.870 38.462 0.00 0.00 38.94 3.86
2803 2815 2.007608 GTTCCCGTGTTCATCTTAGCC 58.992 52.381 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
442 444 3.434641 CACAACGTAGAGGAAGTAGTCGA 59.565 47.826 0.00 0.00 0.00 4.20
514 516 2.385013 TGTGATGCATAGCAACGAGT 57.615 45.000 0.00 0.00 43.62 4.18
615 617 0.472471 TTGGCGGACTGAACCTTCTT 59.528 50.000 0.00 0.00 0.00 2.52
761 763 9.993454 CTGAGTTATCATTTGATCCTCTATTCA 57.007 33.333 15.51 5.43 35.44 2.57
1084 1087 3.736740 GCTTCTTGCTTTTCCCGTTCAAA 60.737 43.478 0.00 0.00 38.95 2.69
1153 1156 1.544691 GTCAAGCTCCAAGGACTCGTA 59.455 52.381 0.00 0.00 0.00 3.43
1360 1363 0.371645 GGAAGATCTGCAAACGCTCG 59.628 55.000 2.29 0.00 0.00 5.03
1410 1413 4.465446 CTCCCCTCCTCAGCCCGA 62.465 72.222 0.00 0.00 0.00 5.14
1541 1544 3.244911 CCACATCCGGATTATAAGGCCTT 60.245 47.826 24.18 24.18 0.00 4.35
1542 1545 2.305927 CCACATCCGGATTATAAGGCCT 59.694 50.000 16.19 0.00 0.00 5.19
1552 1555 2.872388 CGCTAGGCCACATCCGGAT 61.872 63.158 12.38 12.38 0.00 4.18
1668 1671 3.810896 CGGGTAAAAGCCCTGCGC 61.811 66.667 0.00 0.00 46.47 6.09
1681 1684 1.605738 AGTGTACCTTCGCTCGGGT 60.606 57.895 0.00 0.00 39.40 5.28
1686 1689 2.663196 GCCCAGTGTACCTTCGCT 59.337 61.111 0.00 0.00 0.00 4.93
1695 1698 3.241530 TCCAGCTTCGCCCAGTGT 61.242 61.111 0.00 0.00 0.00 3.55
1887 1891 1.355971 TAAGAAAGCGTCGCATGGAC 58.644 50.000 21.09 5.94 42.48 4.02
1888 1892 2.087501 TTAAGAAAGCGTCGCATGGA 57.912 45.000 21.09 0.00 0.00 3.41
1938 1946 4.985538 ACTGGCCAACTCTCAGATTTTAA 58.014 39.130 7.01 0.00 33.19 1.52
1939 1947 4.579869 GACTGGCCAACTCTCAGATTTTA 58.420 43.478 7.01 0.00 33.19 1.52
2092 2101 5.359576 ACTTCTATGGCTAAGTGAGAGTGAG 59.640 44.000 0.00 0.00 34.70 3.51
2160 2169 2.719531 TGTATAGCGCCCCAAATTCA 57.280 45.000 2.29 0.00 0.00 2.57
2237 2246 1.137825 CGCTGTTCGAGAGGTCTCC 59.862 63.158 1.32 0.00 41.67 3.71
2293 2302 4.100808 GGATGAGCACCTCAGTAGAGAAAT 59.899 45.833 1.20 0.00 44.08 2.17
2562 2573 9.823647 CTCTTATATGTCCACTTACAACAATCT 57.176 33.333 0.00 0.00 32.02 2.40
2569 2580 9.475620 TCTCTTTCTCTTATATGTCCACTTACA 57.524 33.333 0.00 0.00 0.00 2.41
2655 2667 5.860716 GCACTACTTGTACTAAGTACGCTTT 59.139 40.000 16.98 0.00 41.41 3.51
2803 2815 1.455383 AACAACCAAGGCGGCAAGAG 61.455 55.000 13.08 0.00 39.03 2.85


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

AutoCloner maintained by Alex Coulton.