Multiple sequence alignment - TraesCS6D01G165600

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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 TraesCS6D01G165600 chr6D 100.000 3109 0 0 1 3109 144879634 144876526 0.000000e+00 5742.0
1 TraesCS6D01G165600 chr6D 82.388 335 49 7 2709 3037 467186405 467186075 1.830000e-72 283.0
2 TraesCS6D01G165600 chr6D 93.617 47 3 0 3061 3107 59338093 59338139 1.550000e-08 71.3
3 TraesCS6D01G165600 chr6B 97.036 1822 27 3 528 2331 259087901 259086089 0.000000e+00 3040.0
4 TraesCS6D01G165600 chr6B 91.017 846 42 20 2295 3109 259085709 259084867 0.000000e+00 1110.0
5 TraesCS6D01G165600 chr6A 94.568 1841 67 13 528 2351 201089579 201087755 0.000000e+00 2815.0
6 TraesCS6D01G165600 chr6A 89.313 131 11 3 2945 3072 408021665 408021535 8.920000e-36 161.0
7 TraesCS6D01G165600 chr6A 100.000 29 0 0 2919 2947 408021710 408021682 2.000000e-03 54.7
8 TraesCS6D01G165600 chr7D 97.148 526 13 1 1 524 322918332 322917807 0.000000e+00 887.0
9 TraesCS6D01G165600 chr7D 96.388 526 16 2 1 524 601717056 601717580 0.000000e+00 863.0
10 TraesCS6D01G165600 chr1D 96.970 528 14 1 1 526 71356837 71356310 0.000000e+00 885.0
11 TraesCS6D01G165600 chr1D 96.591 528 16 1 1 526 433786334 433785807 0.000000e+00 874.0
12 TraesCS6D01G165600 chr2D 96.768 526 16 1 1 526 606976631 606976107 0.000000e+00 876.0
13 TraesCS6D01G165600 chr2D 95.833 528 20 1 1 526 28406670 28407197 0.000000e+00 852.0
14 TraesCS6D01G165600 chr2D 87.719 171 17 3 2943 3109 411960538 411960368 2.450000e-46 196.0
15 TraesCS6D01G165600 chr4D 96.212 528 18 1 1 526 504433361 504433888 0.000000e+00 863.0
16 TraesCS6D01G165600 chr3B 95.455 528 22 1 1 526 166554200 166554727 0.000000e+00 841.0
17 TraesCS6D01G165600 chr3B 84.375 288 25 3 2842 3109 782357018 782357305 6.610000e-67 265.0
18 TraesCS6D01G165600 chr2B 95.455 528 22 1 1 526 385909283 385909810 0.000000e+00 841.0
19 TraesCS6D01G165600 chr4A 80.499 682 79 30 2431 3072 584421056 584420389 1.010000e-129 473.0
20 TraesCS6D01G165600 chr5A 80.117 684 81 30 2430 3071 470762544 470763214 2.830000e-125 459.0
21 TraesCS6D01G165600 chr5A 88.000 50 4 2 3061 3109 456624944 456624896 1.200000e-04 58.4
22 TraesCS6D01G165600 chrUn 80.452 619 82 25 2520 3109 250906685 250907293 1.320000e-118 436.0
23 TraesCS6D01G165600 chrUn 80.247 567 75 23 2520 3059 283169004 283168448 2.910000e-105 392.0
24 TraesCS6D01G165600 chr1A 79.559 680 85 26 2433 3072 577989671 577989006 1.320000e-118 436.0
25 TraesCS6D01G165600 chr4B 88.000 50 4 2 3061 3109 663072836 663072884 1.200000e-04 58.4


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 TraesCS6D01G165600 chr6D 144876526 144879634 3108 True 5742 5742 100.0000 1 3109 1 chr6D.!!$R1 3108
1 TraesCS6D01G165600 chr6B 259084867 259087901 3034 True 2075 3040 94.0265 528 3109 2 chr6B.!!$R1 2581
2 TraesCS6D01G165600 chr6A 201087755 201089579 1824 True 2815 2815 94.5680 528 2351 1 chr6A.!!$R1 1823
3 TraesCS6D01G165600 chr7D 322917807 322918332 525 True 887 887 97.1480 1 524 1 chr7D.!!$R1 523
4 TraesCS6D01G165600 chr7D 601717056 601717580 524 False 863 863 96.3880 1 524 1 chr7D.!!$F1 523
5 TraesCS6D01G165600 chr1D 71356310 71356837 527 True 885 885 96.9700 1 526 1 chr1D.!!$R1 525
6 TraesCS6D01G165600 chr1D 433785807 433786334 527 True 874 874 96.5910 1 526 1 chr1D.!!$R2 525
7 TraesCS6D01G165600 chr2D 606976107 606976631 524 True 876 876 96.7680 1 526 1 chr2D.!!$R2 525
8 TraesCS6D01G165600 chr2D 28406670 28407197 527 False 852 852 95.8330 1 526 1 chr2D.!!$F1 525
9 TraesCS6D01G165600 chr4D 504433361 504433888 527 False 863 863 96.2120 1 526 1 chr4D.!!$F1 525
10 TraesCS6D01G165600 chr3B 166554200 166554727 527 False 841 841 95.4550 1 526 1 chr3B.!!$F1 525
11 TraesCS6D01G165600 chr2B 385909283 385909810 527 False 841 841 95.4550 1 526 1 chr2B.!!$F1 525
12 TraesCS6D01G165600 chr4A 584420389 584421056 667 True 473 473 80.4990 2431 3072 1 chr4A.!!$R1 641
13 TraesCS6D01G165600 chr5A 470762544 470763214 670 False 459 459 80.1170 2430 3071 1 chr5A.!!$F1 641
14 TraesCS6D01G165600 chrUn 250906685 250907293 608 False 436 436 80.4520 2520 3109 1 chrUn.!!$F1 589
15 TraesCS6D01G165600 chrUn 283168448 283169004 556 True 392 392 80.2470 2520 3059 1 chrUn.!!$R1 539
16 TraesCS6D01G165600 chr1A 577989006 577989671 665 True 436 436 79.5590 2433 3072 1 chr1A.!!$R1 639

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
87 88 0.678048 AGGATTTTGAGCGTGGGAGC 60.678 55.0 0.0 0.0 37.41 4.70 F
857 875 0.882042 AACAACTCAGCTCAGCCACG 60.882 55.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1382 2.440430 CCGGCTTCCTCCTCTCGA 60.440 66.667 0.00 0.00 0.00 4.04 R
2635 3098 0.163788 CTCACCGTAGCAGCAAAACG 59.836 55.000 7.72 7.72 36.42 3.60 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
87 88 0.678048 AGGATTTTGAGCGTGGGAGC 60.678 55.000 0.00 0.00 37.41 4.70
117 118 0.901827 TTCAATCTGTAGGCGCTCCA 59.098 50.000 7.64 0.15 33.74 3.86
526 529 3.027170 GCGTGTGGTTGAGATGGCG 62.027 63.158 0.00 0.00 0.00 5.69
857 875 0.882042 AACAACTCAGCTCAGCCACG 60.882 55.000 0.00 0.00 0.00 4.94
862 880 4.767255 CAGCTCAGCCACGACCCC 62.767 72.222 0.00 0.00 0.00 4.95
868 886 3.256960 AGCCACGACCCCCACAAT 61.257 61.111 0.00 0.00 0.00 2.71
947 965 6.304683 GGATTGTTATCGGTTCTTTTCGTTTG 59.695 38.462 0.00 0.00 0.00 2.93
948 966 5.987777 TGTTATCGGTTCTTTTCGTTTGA 57.012 34.783 0.00 0.00 0.00 2.69
1379 1397 1.251527 TGTGTCGAGAGGAGGAAGCC 61.252 60.000 0.00 0.00 0.00 4.35
1539 1557 2.029964 GGAAGGGTGTTCGTCGCA 59.970 61.111 0.00 0.00 0.00 5.10
2228 2256 7.665559 AGGAAAAATCTACAAGACTGCAACATA 59.334 33.333 0.00 0.00 0.00 2.29
2272 2300 1.969064 CCGTGGGATCGGTTGCAAA 60.969 57.895 0.00 0.00 44.77 3.68
2513 2959 2.181777 GCTCTCCATCGTGCGTCA 59.818 61.111 0.00 0.00 0.00 4.35
2540 2997 5.324832 TCACTCTTCCTTCCAATCCTTTT 57.675 39.130 0.00 0.00 0.00 2.27
2541 2998 5.705400 TCACTCTTCCTTCCAATCCTTTTT 58.295 37.500 0.00 0.00 0.00 1.94
2542 2999 5.770162 TCACTCTTCCTTCCAATCCTTTTTC 59.230 40.000 0.00 0.00 0.00 2.29
2594 3057 1.804748 CGTAGCAACCACTCCTTTTCC 59.195 52.381 0.00 0.00 0.00 3.13
2660 3127 4.735132 TGCTACGGTGAGCCACGC 62.735 66.667 4.09 0.00 42.11 5.34
2706 3173 1.293498 GAGAAGTTGCGAGGCAGGA 59.707 57.895 0.00 0.00 40.61 3.86
2787 3256 1.446792 CGACAGCGAGGTGATGCTT 60.447 57.895 9.41 0.00 40.03 3.91
2857 3326 3.313526 CAGCGGCATATAAAGCTTCAACT 59.686 43.478 0.00 0.00 37.94 3.16
2871 3340 0.529773 TCAACTGAGACACCGTGCAC 60.530 55.000 6.82 6.82 0.00 4.57
2889 3358 2.742053 GCACTGGAAAAGCTACAATCGA 59.258 45.455 0.00 0.00 0.00 3.59
2903 3372 7.661968 AGCTACAATCGATCATAAGAAAGCTA 58.338 34.615 0.00 0.00 33.91 3.32
2947 3418 7.595130 GCTACAATCGTTCTGGAAAAAGATTTT 59.405 33.333 0.00 0.00 35.89 1.82
2948 3419 7.930513 ACAATCGTTCTGGAAAAAGATTTTC 57.069 32.000 6.96 6.96 35.89 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.304282 GCCTGCATTTCTCCCCTCA 59.696 57.895 0.00 0.00 0.00 3.86
87 88 3.238108 ACAGATTGAAGGTAGTGCTCG 57.762 47.619 0.00 0.00 0.00 5.03
93 94 2.101582 AGCGCCTACAGATTGAAGGTAG 59.898 50.000 2.29 0.00 35.42 3.18
836 854 1.678101 GTGGCTGAGCTGAGTTGTTTT 59.322 47.619 3.72 0.00 0.00 2.43
857 875 0.251341 AGCAGTGAATTGTGGGGGTC 60.251 55.000 0.00 0.00 0.00 4.46
862 880 3.005554 AGAATCGAGCAGTGAATTGTGG 58.994 45.455 0.00 0.00 0.00 4.17
863 881 4.256140 GAGAATCGAGCAGTGAATTGTG 57.744 45.455 0.00 0.00 0.00 3.33
947 965 4.954092 AATTCGCTCACTCCTTCAAATC 57.046 40.909 0.00 0.00 0.00 2.17
948 966 5.355350 CCTTAATTCGCTCACTCCTTCAAAT 59.645 40.000 0.00 0.00 0.00 2.32
1364 1382 2.440430 CCGGCTTCCTCCTCTCGA 60.440 66.667 0.00 0.00 0.00 4.04
1395 1413 2.657237 CACGTCTCAGGGTCCCAC 59.343 66.667 11.55 0.00 0.00 4.61
2134 2162 9.520204 AACTTTCAGATTTAATTGACAACTGTG 57.480 29.630 0.00 0.00 0.00 3.66
2228 2256 3.192844 CGCGTGGGGTATCATCTAAGTAT 59.807 47.826 0.00 0.00 0.00 2.12
2379 2825 2.618709 GTGTGGGAAAAGTTCACCTCAG 59.381 50.000 0.00 0.00 29.93 3.35
2513 2959 0.976641 TGGAAGGAAGAGTGATGCGT 59.023 50.000 0.00 0.00 0.00 5.24
2540 2997 7.615757 GGGGGAGAAGAAGATAATGAAAAAGAA 59.384 37.037 0.00 0.00 0.00 2.52
2541 2998 7.119387 GGGGGAGAAGAAGATAATGAAAAAGA 58.881 38.462 0.00 0.00 0.00 2.52
2542 2999 7.340122 GGGGGAGAAGAAGATAATGAAAAAG 57.660 40.000 0.00 0.00 0.00 2.27
2635 3098 0.163788 CTCACCGTAGCAGCAAAACG 59.836 55.000 7.72 7.72 36.42 3.60
2660 3127 1.388065 ATGTCTTCTCTCGCCCTCGG 61.388 60.000 0.00 0.00 36.13 4.63
2706 3173 4.093291 CGGGCCTCTTGCAGCTCT 62.093 66.667 0.84 0.00 43.89 4.09
2769 3238 1.446792 AAGCATCACCTCGCTGTCG 60.447 57.895 0.00 0.00 38.82 4.35
2857 3326 1.681486 TTCCAGTGCACGGTGTCTCA 61.681 55.000 21.61 0.00 0.00 3.27
2871 3340 5.998454 ATGATCGATTGTAGCTTTTCCAG 57.002 39.130 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.