Multiple sequence alignment - TraesCS3B01G512600

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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 TraesCS3B01G512600 chr3B 100.000 3463 0 0 1 3463 756129934 756126472 0.000000e+00 6396.0
1 TraesCS3B01G512600 chr3B 97.280 919 24 1 2545 3463 154226874 154225957 0.000000e+00 1557.0
2 TraesCS3B01G512600 chrUn 97.407 1697 42 2 1767 3463 255359103 255360797 0.000000e+00 2889.0
3 TraesCS3B01G512600 chrUn 97.991 1394 25 3 1152 2543 40897049 40895657 0.000000e+00 2416.0
4 TraesCS3B01G512600 chrUn 97.489 916 21 2 2549 3463 116818755 116817841 0.000000e+00 1563.0
5 TraesCS3B01G512600 chrUn 96.345 684 6 1 1 665 255357828 255358511 0.000000e+00 1107.0
6 TraesCS3B01G512600 chrUn 97.697 608 13 1 824 1431 255358506 255359112 0.000000e+00 1044.0
7 TraesCS3B01G512600 chrUn 91.418 268 18 4 886 1150 41053994 41053729 2.540000e-96 363.0
8 TraesCS3B01G512600 chr5A 97.407 1697 42 2 1767 3463 42269981 42268287 0.000000e+00 2889.0
9 TraesCS3B01G512600 chr5A 96.345 684 6 1 1 665 42271256 42270573 0.000000e+00 1107.0
10 TraesCS3B01G512600 chr5A 97.697 608 13 1 824 1431 42270578 42269972 0.000000e+00 1044.0
11 TraesCS3B01G512600 chr3D 91.532 1677 105 15 897 2544 569555057 569556725 0.000000e+00 2276.0
12 TraesCS3B01G512600 chr3D 100.000 39 0 0 854 892 569554972 569555010 4.790000e-09 73.1
13 TraesCS3B01G512600 chr3D 100.000 28 0 0 886 913 569555014 569555041 6.000000e-03 52.8
14 TraesCS3B01G512600 chr3A 90.361 1577 102 24 985 2517 700580535 700582105 0.000000e+00 2025.0
15 TraesCS3B01G512600 chr2B 97.814 915 18 2 2549 3463 628457157 628456245 0.000000e+00 1578.0
16 TraesCS3B01G512600 chr2B 97.377 915 23 1 2549 3463 482628129 482627216 0.000000e+00 1555.0
17 TraesCS3B01G512600 chr2B 87.356 87 10 1 764 850 741737155 741737070 7.910000e-17 99.0
18 TraesCS3B01G512600 chr7B 97.705 915 20 1 2549 3463 729321367 729320454 0.000000e+00 1572.0
19 TraesCS3B01G512600 chr7B 97.286 921 22 3 2545 3463 647427709 647428628 0.000000e+00 1559.0
20 TraesCS3B01G512600 chr7B 97.280 919 22 3 2543 3460 372050305 372051221 0.000000e+00 1555.0
21 TraesCS3B01G512600 chr1B 89.912 684 66 3 1856 2538 320105746 320105065 0.000000e+00 878.0
22 TraesCS3B01G512600 chr1B 83.629 788 88 14 889 1654 320106996 320106228 0.000000e+00 702.0
23 TraesCS3B01G512600 chr1B 83.525 261 30 4 889 1143 321040282 321040029 7.470000e-57 231.0
24 TraesCS3B01G512600 chr4B 81.776 867 117 27 1 856 664240822 664239986 0.000000e+00 688.0
25 TraesCS3B01G512600 chr4B 81.243 869 118 33 1 856 664216175 664215339 0.000000e+00 660.0
26 TraesCS3B01G512600 chr4B 87.246 541 59 8 1 538 664239012 664238479 2.960000e-170 608.0
27 TraesCS3B01G512600 chr4B 79.793 871 109 32 1 856 664214364 664213546 3.880000e-159 571.0
28 TraesCS3B01G512600 chr4B 85.393 89 8 4 764 850 364039503 364039588 1.710000e-13 87.9
29 TraesCS3B01G512600 chr5B 84.259 540 74 9 10 546 712142985 712142454 1.840000e-142 516.0
30 TraesCS3B01G512600 chr5B 94.074 270 14 2 587 855 664498589 664498321 3.220000e-110 409.0
31 TraesCS3B01G512600 chr5B 91.200 125 7 3 1 125 664498729 664498609 2.140000e-37 167.0
32 TraesCS3B01G512600 chr5D 84.946 93 13 1 764 856 563204347 563204256 3.680000e-15 93.5
33 TraesCS3B01G512600 chr6D 87.342 79 9 1 775 853 340436430 340436353 4.760000e-14 89.8
34 TraesCS3B01G512600 chr4D 84.615 91 13 1 764 854 483466700 483466789 4.760000e-14 89.8


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 TraesCS3B01G512600 chr3B 756126472 756129934 3462 True 6396.000000 6396 100.000000 1 3463 1 chr3B.!!$R2 3462
1 TraesCS3B01G512600 chr3B 154225957 154226874 917 True 1557.000000 1557 97.280000 2545 3463 1 chr3B.!!$R1 918
2 TraesCS3B01G512600 chrUn 40895657 40897049 1392 True 2416.000000 2416 97.991000 1152 2543 1 chrUn.!!$R1 1391
3 TraesCS3B01G512600 chrUn 255357828 255360797 2969 False 1680.000000 2889 97.149667 1 3463 3 chrUn.!!$F1 3462
4 TraesCS3B01G512600 chrUn 116817841 116818755 914 True 1563.000000 1563 97.489000 2549 3463 1 chrUn.!!$R3 914
5 TraesCS3B01G512600 chr5A 42268287 42271256 2969 True 1680.000000 2889 97.149667 1 3463 3 chr5A.!!$R1 3462
6 TraesCS3B01G512600 chr3D 569554972 569556725 1753 False 800.633333 2276 97.177333 854 2544 3 chr3D.!!$F1 1690
7 TraesCS3B01G512600 chr3A 700580535 700582105 1570 False 2025.000000 2025 90.361000 985 2517 1 chr3A.!!$F1 1532
8 TraesCS3B01G512600 chr2B 628456245 628457157 912 True 1578.000000 1578 97.814000 2549 3463 1 chr2B.!!$R2 914
9 TraesCS3B01G512600 chr2B 482627216 482628129 913 True 1555.000000 1555 97.377000 2549 3463 1 chr2B.!!$R1 914
10 TraesCS3B01G512600 chr7B 729320454 729321367 913 True 1572.000000 1572 97.705000 2549 3463 1 chr7B.!!$R1 914
11 TraesCS3B01G512600 chr7B 647427709 647428628 919 False 1559.000000 1559 97.286000 2545 3463 1 chr7B.!!$F2 918
12 TraesCS3B01G512600 chr7B 372050305 372051221 916 False 1555.000000 1555 97.280000 2543 3460 1 chr7B.!!$F1 917
13 TraesCS3B01G512600 chr1B 320105065 320106996 1931 True 790.000000 878 86.770500 889 2538 2 chr1B.!!$R2 1649
14 TraesCS3B01G512600 chr4B 664238479 664240822 2343 True 648.000000 688 84.511000 1 856 2 chr4B.!!$R2 855
15 TraesCS3B01G512600 chr4B 664213546 664216175 2629 True 615.500000 660 80.518000 1 856 2 chr4B.!!$R1 855
16 TraesCS3B01G512600 chr5B 712142454 712142985 531 True 516.000000 516 84.259000 10 546 1 chr5B.!!$R1 536

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
719 2536 0.036306 GGAGGAAGGGAAAGAACGCA 59.964 55.0 0.00 0.0 0.0 5.24 F
1972 4239 0.106819 ATGGGCTGCCTGATTGAGAC 60.107 55.0 19.68 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 4446 1.805254 GCATCCGCACATTGAAGCT 59.195 52.632 0.0 0.0 38.36 3.74 R
3249 5535 0.724549 TCGCGAACGATGAATTTGGG 59.275 50.000 6.2 0.0 45.12 4.12 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
120 121 2.556622 CCGGCAAAAGTTTGGTACTGAT 59.443 45.455 5.95 0.00 37.12 2.90
529 2321 1.373748 TGGCGACAAAGGCTACGTC 60.374 57.895 0.00 6.23 37.44 4.34
533 2325 0.736325 CGACAAAGGCTACGTCTGGG 60.736 60.000 12.70 0.00 0.00 4.45
710 2527 2.683933 GGCGTGAGGAGGAAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
714 2531 1.267121 CGTGAGGAGGAAGGGAAAGA 58.733 55.000 0.00 0.00 0.00 2.52
715 2532 1.623811 CGTGAGGAGGAAGGGAAAGAA 59.376 52.381 0.00 0.00 0.00 2.52
719 2536 0.036306 GGAGGAAGGGAAAGAACGCA 59.964 55.000 0.00 0.00 0.00 5.24
720 2537 1.544759 GGAGGAAGGGAAAGAACGCAA 60.545 52.381 0.00 0.00 0.00 4.85
726 2543 0.875059 GGGAAAGAACGCAAGGTGAG 59.125 55.000 0.00 0.00 37.50 3.51
727 2544 0.238553 GGAAAGAACGCAAGGTGAGC 59.761 55.000 0.00 0.00 37.50 4.26
728 2545 1.230324 GAAAGAACGCAAGGTGAGCT 58.770 50.000 0.00 0.00 37.50 4.09
729 2546 0.947244 AAAGAACGCAAGGTGAGCTG 59.053 50.000 0.00 0.00 37.50 4.24
730 2547 0.886490 AAGAACGCAAGGTGAGCTGG 60.886 55.000 0.00 0.00 37.50 4.85
731 2548 2.970974 GAACGCAAGGTGAGCTGGC 61.971 63.158 0.00 0.00 37.50 4.85
734 2551 4.666253 GCAAGGTGAGCTGGCCCA 62.666 66.667 0.00 0.00 0.00 5.36
735 2552 2.360852 CAAGGTGAGCTGGCCCAG 60.361 66.667 6.32 6.32 34.12 4.45
753 2570 1.200020 CAGCTGGGTGAATCGTTTTCC 59.800 52.381 5.57 0.00 0.00 3.13
765 2582 2.853705 TCGTTTTCCTTTCGGTCCAAT 58.146 42.857 0.00 0.00 0.00 3.16
766 2583 2.809696 TCGTTTTCCTTTCGGTCCAATC 59.190 45.455 0.00 0.00 0.00 2.67
767 2584 2.812011 CGTTTTCCTTTCGGTCCAATCT 59.188 45.455 0.00 0.00 0.00 2.40
768 2585 3.998341 CGTTTTCCTTTCGGTCCAATCTA 59.002 43.478 0.00 0.00 0.00 1.98
770 2587 5.616204 CGTTTTCCTTTCGGTCCAATCTAAC 60.616 44.000 0.00 0.00 0.00 2.34
771 2588 3.241067 TCCTTTCGGTCCAATCTAACG 57.759 47.619 0.00 0.00 0.00 3.18
779 2597 0.457166 TCCAATCTAACGGACGCACG 60.457 55.000 0.00 0.00 40.31 5.34
1059 2931 1.726853 GACCATCCGAGTTTGACTGG 58.273 55.000 0.00 0.00 0.00 4.00
1410 3304 3.752339 CTTTTCCCCAGCTGCGCC 61.752 66.667 8.66 0.00 0.00 6.53
1972 4239 0.106819 ATGGGCTGCCTGATTGAGAC 60.107 55.000 19.68 0.00 0.00 3.36
2454 4735 3.513912 AGTCTATTGGTCAACCATCGTCA 59.486 43.478 2.03 0.00 46.97 4.35
2538 4819 7.669089 TTTGAAGTTTTTGATCTTTACCCCT 57.331 32.000 0.00 0.00 0.00 4.79
2610 4892 6.039047 GGTGTCACATAGGTTCTCGAACTATA 59.961 42.308 5.12 4.34 40.94 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 4.865761 GCGGCACCATCGTCGCTA 62.866 66.667 2.22 0.00 44.10 4.26
529 2321 2.821378 TGATTGCAACATGACTTCCCAG 59.179 45.455 0.00 0.00 0.00 4.45
533 2325 2.165030 CCCCTGATTGCAACATGACTTC 59.835 50.000 0.00 0.00 0.00 3.01
665 2476 1.131303 AAATCCACGGACCAGTCCCA 61.131 55.000 11.22 0.00 46.96 4.37
668 2479 2.232941 TGACTAAATCCACGGACCAGTC 59.767 50.000 13.09 13.09 33.67 3.51
672 2483 1.997606 CGTTGACTAAATCCACGGACC 59.002 52.381 0.00 0.00 41.57 4.46
676 2487 0.725117 GCCCGTTGACTAAATCCACG 59.275 55.000 0.00 0.00 44.14 4.94
694 2505 0.391793 CTTTCCCTTCCTCCTCACGC 60.392 60.000 0.00 0.00 0.00 5.34
710 2527 0.947244 CAGCTCACCTTGCGTTCTTT 59.053 50.000 0.00 0.00 35.28 2.52
714 2531 2.980233 GCCAGCTCACCTTGCGTT 60.980 61.111 0.00 0.00 35.28 4.84
732 2549 1.200020 GAAAACGATTCACCCAGCTGG 59.800 52.381 26.87 26.87 41.37 4.85
733 2550 1.200020 GGAAAACGATTCACCCAGCTG 59.800 52.381 6.78 6.78 0.00 4.24
734 2551 1.073923 AGGAAAACGATTCACCCAGCT 59.926 47.619 0.00 0.00 0.00 4.24
735 2552 1.534729 AGGAAAACGATTCACCCAGC 58.465 50.000 0.00 0.00 0.00 4.85
736 2553 3.364964 CGAAAGGAAAACGATTCACCCAG 60.365 47.826 0.00 0.00 0.00 4.45
737 2554 2.550606 CGAAAGGAAAACGATTCACCCA 59.449 45.455 0.00 0.00 0.00 4.51
753 2570 3.241067 TCCGTTAGATTGGACCGAAAG 57.759 47.619 0.00 0.00 0.00 2.62
765 2582 3.332493 GAGCCGTGCGTCCGTTAGA 62.332 63.158 0.00 0.00 0.00 2.10
766 2583 2.879462 GAGCCGTGCGTCCGTTAG 60.879 66.667 0.00 0.00 0.00 2.34
767 2584 3.672447 TGAGCCGTGCGTCCGTTA 61.672 61.111 0.00 0.00 0.00 3.18
779 2597 3.741476 ACCCGTACGACGTGAGCC 61.741 66.667 18.76 0.00 40.58 4.70
787 2605 3.829044 CGCATCCCACCCGTACGA 61.829 66.667 18.76 0.00 0.00 3.43
941 2802 3.327757 CCGGATTGGGGATTGAATAGAGA 59.672 47.826 0.00 0.00 0.00 3.10
1004 2876 3.178539 GGCTACCTTCTGTTGCGC 58.821 61.111 0.00 0.00 45.20 6.09
1059 2931 1.153628 CCCCTCGTCGGTGAACATC 60.154 63.158 0.00 0.00 0.00 3.06
1972 4239 6.537355 TCCTTGCCCTTGATCTTTATATCAG 58.463 40.000 0.00 0.00 37.20 2.90
2172 4446 1.805254 GCATCCGCACATTGAAGCT 59.195 52.632 0.00 0.00 38.36 3.74
2610 4892 5.484715 TCGAGGACCTAAATGACGATTTTT 58.515 37.500 0.00 0.00 33.63 1.94
3249 5535 0.724549 TCGCGAACGATGAATTTGGG 59.275 50.000 6.20 0.00 45.12 4.12


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

AutoCloner maintained by Alex Coulton.