Multiple sequence alignment - TraesCS7A01G489100

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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 TraesCS7A01G489100 chr7A 100.000 3137 0 0 1 3137 679361216 679364352 0.000000e+00 5794.0
1 TraesCS7A01G489100 chr7A 99.441 2147 8 4 995 3137 679377865 679380011 0.000000e+00 3895.0
2 TraesCS7A01G489100 chr7A 95.258 2151 67 17 995 3137 679389333 679391456 0.000000e+00 3374.0
3 TraesCS7A01G489100 chr7A 92.308 1339 90 7 996 2329 679525692 679527022 0.000000e+00 1890.0
4 TraesCS7A01G489100 chr7A 99.686 956 3 0 1 956 679375863 679376818 0.000000e+00 1749.0
5 TraesCS7A01G489100 chr7A 99.372 956 6 0 1 956 679387331 679388286 0.000000e+00 1733.0
6 TraesCS7A01G489100 chr7A 88.725 1153 113 10 995 2140 679594573 679593431 0.000000e+00 1393.0
7 TraesCS7A01G489100 chr7A 79.913 458 62 13 2543 2990 679527084 679527521 3.040000e-80 309.0
8 TraesCS7A01G489100 chr7A 81.879 149 24 3 107 255 517518589 517518444 4.250000e-24 122.0
9 TraesCS7A01G489100 chr7A 100.000 30 0 0 956 985 679362136 679362165 4.370000e-04 56.5
10 TraesCS7A01G489100 chr7A 100.000 30 0 0 921 950 679362171 679362200 4.370000e-04 56.5
11 TraesCS7A01G489100 chr7A 100.000 30 0 0 956 985 679376783 679376812 4.370000e-04 56.5
12 TraesCS7A01G489100 chr7A 100.000 30 0 0 956 985 679388251 679388280 4.370000e-04 56.5
13 TraesCS7A01G489100 chr7B 92.532 1339 96 3 995 2329 658880473 658881811 0.000000e+00 1916.0
14 TraesCS7A01G489100 chr7B 85.912 433 42 7 2543 2967 658624099 658624520 7.980000e-121 444.0
15 TraesCS7A01G489100 chr7B 85.912 433 42 7 2543 2967 658749264 658749685 7.980000e-121 444.0
16 TraesCS7A01G489100 chr7B 82.915 199 21 8 2366 2553 97758783 97758979 1.940000e-37 167.0
17 TraesCS7A01G489100 chr7B 85.235 149 19 2 107 255 503376093 503376238 1.950000e-32 150.0
18 TraesCS7A01G489100 chr7B 89.011 91 9 1 3037 3126 747370722 747370632 9.200000e-21 111.0
19 TraesCS7A01G489100 chr7B 91.304 46 2 2 514 558 733670948 733670904 9.390000e-06 62.1
20 TraesCS7A01G489100 chr7B 91.304 46 2 2 514 558 741954930 741954886 9.390000e-06 62.1
21 TraesCS7A01G489100 chr7D 92.399 1355 72 8 995 2329 587554881 587556224 0.000000e+00 1903.0
22 TraesCS7A01G489100 chr7D 92.282 1218 91 1 995 2209 587728250 587727033 0.000000e+00 1725.0
23 TraesCS7A01G489100 chr7D 83.461 1173 167 18 995 2153 587302266 587303425 0.000000e+00 1066.0
24 TraesCS7A01G489100 chr7D 83.461 393 41 12 2543 2924 587726890 587726511 8.330000e-91 344.0
25 TraesCS7A01G489100 chr7D 86.926 283 37 0 1858 2140 587761865 587761583 5.050000e-83 318.0
26 TraesCS7A01G489100 chr7D 85.235 149 19 2 107 255 478220721 478220866 1.950000e-32 150.0
27 TraesCS7A01G489100 chr7D 98.780 82 1 0 2248 2329 587727033 587726952 2.520000e-31 147.0
28 TraesCS7A01G489100 chr7D 78.788 198 35 6 649 843 485823272 485823465 3.280000e-25 126.0
29 TraesCS7A01G489100 chr7D 95.946 74 3 0 2959 3032 587726514 587726441 1.530000e-23 121.0
30 TraesCS7A01G489100 chr7D 88.776 98 10 1 3030 3126 556128077 556128174 5.500000e-23 119.0
31 TraesCS7A01G489100 chr7D 91.026 78 7 0 876 953 587729357 587729280 4.280000e-19 106.0
32 TraesCS7A01G489100 chrUn 100.000 938 0 0 995 1932 361995734 361994797 0.000000e+00 1733.0
33 TraesCS7A01G489100 chrUn 99.787 938 2 0 995 1932 361872494 361871557 0.000000e+00 1722.0
34 TraesCS7A01G489100 chrUn 99.331 897 6 0 1 897 356065091 356064195 0.000000e+00 1624.0
35 TraesCS7A01G489100 chrUn 99.331 897 6 0 1 897 419941037 419940141 0.000000e+00 1624.0
36 TraesCS7A01G489100 chrUn 91.045 67 6 0 6 72 96940992 96941058 1.200000e-14 91.6
37 TraesCS7A01G489100 chrUn 91.304 46 2 2 514 558 344285220 344285176 9.390000e-06 62.1
38 TraesCS7A01G489100 chr3B 92.568 148 10 1 304 450 733415030 733415177 8.810000e-51 211.0
39 TraesCS7A01G489100 chr3B 91.304 92 6 1 467 556 733415163 733415254 1.180000e-24 124.0
40 TraesCS7A01G489100 chr3B 90.110 91 8 1 3037 3126 548846935 548846845 1.980000e-22 117.0
41 TraesCS7A01G489100 chr5D 87.283 173 19 3 2378 2548 344470177 344470348 8.880000e-46 195.0
42 TraesCS7A01G489100 chr5D 86.538 104 13 1 3030 3132 386674021 386674124 2.560000e-21 113.0
43 TraesCS7A01G489100 chr5B 86.550 171 20 3 2378 2546 372169435 372169266 5.340000e-43 185.0
44 TraesCS7A01G489100 chr5B 77.778 180 27 9 664 843 674427167 674427001 7.160000e-17 99.0
45 TraesCS7A01G489100 chr5B 90.278 72 7 0 1 72 467383146 467383217 9.260000e-16 95.3
46 TraesCS7A01G489100 chr2B 85.380 171 19 3 2378 2542 717099166 717098996 4.160000e-39 172.0
47 TraesCS7A01G489100 chr4A 84.066 182 21 4 2378 2553 555189623 555189802 5.380000e-38 169.0
48 TraesCS7A01G489100 chr6A 82.383 193 27 6 2366 2553 429600630 429600820 9.000000e-36 161.0
49 TraesCS7A01G489100 chr2A 82.383 193 27 6 2366 2553 369580700 369580890 9.000000e-36 161.0
50 TraesCS7A01G489100 chr2A 83.871 124 18 2 720 843 459548709 459548830 1.980000e-22 117.0
51 TraesCS7A01G489100 chr2A 88.889 72 8 0 1 72 766446282 766446211 4.310000e-14 89.8
52 TraesCS7A01G489100 chr2D 89.000 100 9 2 3037 3135 641579060 641578962 4.250000e-24 122.0
53 TraesCS7A01G489100 chr1A 88.776 98 10 1 3031 3127 255757800 255757897 5.500000e-23 119.0
54 TraesCS7A01G489100 chr1B 87.379 103 11 2 741 843 687298074 687298174 1.980000e-22 117.0
55 TraesCS7A01G489100 chr1B 85.484 62 5 4 500 559 588218282 588218223 9.390000e-06 62.1
56 TraesCS7A01G489100 chr4B 87.129 101 12 1 3028 3127 265515904 265516004 2.560000e-21 113.0
57 TraesCS7A01G489100 chr6D 82.787 122 19 2 718 839 27322099 27322218 1.190000e-19 108.0
58 TraesCS7A01G489100 chr3A 88.889 72 8 0 1 72 705930128 705930057 4.310000e-14 89.8
59 TraesCS7A01G489100 chr3A 89.552 67 7 0 6 72 74675135 74675201 5.570000e-13 86.1


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 TraesCS7A01G489100 chr7A 679361216 679364352 3136 False 1969.000000 5794 100.0000 1 3137 3 chr7A.!!$F1 3136
1 TraesCS7A01G489100 chr7A 679375863 679380011 4148 False 1900.166667 3895 99.7090 1 3137 3 chr7A.!!$F2 3136
2 TraesCS7A01G489100 chr7A 679387331 679391456 4125 False 1721.166667 3374 98.2100 1 3137 3 chr7A.!!$F3 3136
3 TraesCS7A01G489100 chr7A 679593431 679594573 1142 True 1393.000000 1393 88.7250 995 2140 1 chr7A.!!$R2 1145
4 TraesCS7A01G489100 chr7A 679525692 679527521 1829 False 1099.500000 1890 86.1105 996 2990 2 chr7A.!!$F4 1994
5 TraesCS7A01G489100 chr7B 658880473 658881811 1338 False 1916.000000 1916 92.5320 995 2329 1 chr7B.!!$F5 1334
6 TraesCS7A01G489100 chr7D 587554881 587556224 1343 False 1903.000000 1903 92.3990 995 2329 1 chr7D.!!$F5 1334
7 TraesCS7A01G489100 chr7D 587302266 587303425 1159 False 1066.000000 1066 83.4610 995 2153 1 chr7D.!!$F4 1158
8 TraesCS7A01G489100 chr7D 587726441 587729357 2916 True 488.600000 1725 92.2990 876 3032 5 chr7D.!!$R2 2156
9 TraesCS7A01G489100 chrUn 361994797 361995734 937 True 1733.000000 1733 100.0000 995 1932 1 chrUn.!!$R4 937
10 TraesCS7A01G489100 chrUn 361871557 361872494 937 True 1722.000000 1722 99.7870 995 1932 1 chrUn.!!$R3 937
11 TraesCS7A01G489100 chrUn 356064195 356065091 896 True 1624.000000 1624 99.3310 1 897 1 chrUn.!!$R2 896
12 TraesCS7A01G489100 chrUn 419940141 419941037 896 True 1624.000000 1624 99.3310 1 897 1 chrUn.!!$R5 896

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
968 973 1.078848 GGGTAGCCACACAGCTGAG 60.079 63.158 23.35 16.23 44.67 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 3875 4.60564 ATTTTGTCCATGTGAAGGGTTG 57.394 40.909 0.0 0.0 0.0 3.77 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
645 646 1.332028 CGAAGCGAACAACAGACACAC 60.332 52.381 0.00 0.00 0.00 3.82
956 961 3.541713 CCGAGAGCCCAGGGTAGC 61.542 72.222 7.55 0.00 0.00 3.58
958 963 2.365635 GAGAGCCCAGGGTAGCCA 60.366 66.667 14.62 0.00 0.00 4.75
962 967 3.646715 GCCCAGGGTAGCCACACA 61.647 66.667 14.62 0.00 0.00 3.72
963 968 2.671070 CCCAGGGTAGCCACACAG 59.329 66.667 14.62 0.00 0.00 3.66
964 969 2.045926 CCAGGGTAGCCACACAGC 60.046 66.667 14.62 0.00 0.00 4.40
966 971 1.376424 CAGGGTAGCCACACAGCTG 60.376 63.158 13.48 13.48 44.67 4.24
967 972 1.536418 AGGGTAGCCACACAGCTGA 60.536 57.895 23.35 0.00 44.67 4.26
968 973 1.078848 GGGTAGCCACACAGCTGAG 60.079 63.158 23.35 16.23 44.67 3.35
969 974 1.743252 GGTAGCCACACAGCTGAGC 60.743 63.158 23.35 16.76 44.67 4.26
980 1077 2.112198 AGCTGAGCTCGACCGAGAG 61.112 63.158 21.91 11.87 44.53 3.20
986 1083 4.180946 CTCGACCGAGAGCCCACG 62.181 72.222 13.64 0.00 44.53 4.94
993 1090 4.314440 GAGAGCCCACGCCACACA 62.314 66.667 0.00 0.00 34.57 3.72
2265 3318 2.676471 GGGCCAAACCATCAGCGT 60.676 61.111 4.39 0.00 42.05 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
645 646 3.791245 CTTCGAGAGGAGGAAAGAATGG 58.209 50.000 0.00 0.00 31.14 3.16
956 961 1.735920 GTCGAGCTCAGCTGTGTGG 60.736 63.158 2.14 5.19 39.88 4.17
958 963 2.653702 GGTCGAGCTCAGCTGTGT 59.346 61.111 2.14 2.10 39.88 3.72
962 967 2.045829 TCTCGGTCGAGCTCAGCT 60.046 61.111 15.40 0.00 43.88 4.24
963 968 2.407210 CTCTCGGTCGAGCTCAGC 59.593 66.667 15.40 9.62 41.71 4.26
969 974 4.180946 CGTGGGCTCTCGGTCGAG 62.181 72.222 13.56 13.56 43.21 4.04
981 1078 3.596066 CTCCTCTGTGTGGCGTGGG 62.596 68.421 0.00 0.00 0.00 4.61
983 1080 0.738762 CATCTCCTCTGTGTGGCGTG 60.739 60.000 0.00 0.00 0.00 5.34
985 1082 1.812922 GCATCTCCTCTGTGTGGCG 60.813 63.158 0.00 0.00 0.00 5.69
986 1083 0.461693 GAGCATCTCCTCTGTGTGGC 60.462 60.000 0.00 0.00 0.00 5.01
988 1085 3.756739 GGAGCATCTCCTCTGTGTG 57.243 57.895 5.65 0.00 46.41 3.82
2265 3318 4.976224 TGCAAGTCGAAGCACTATAGTA 57.024 40.909 4.74 0.00 35.51 1.82
2764 3875 4.605640 ATTTTGTCCATGTGAAGGGTTG 57.394 40.909 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.