Multiple sequence alignment - TraesCS3B01G195000

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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 TraesCS3B01G195000 chr3B 100.000 3413 0 0 1 3413 219344725 219341313 0.000000e+00 6303
1 TraesCS3B01G195000 chr3B 99.327 2824 18 1 1 2824 220634968 220632146 0.000000e+00 5108
2 TraesCS3B01G195000 chr3B 93.857 700 38 5 1 696 106068932 106068234 0.000000e+00 1050
3 TraesCS3B01G195000 chr3B 97.639 593 13 1 2821 3413 220629443 220628852 0.000000e+00 1016
4 TraesCS3B01G195000 chr3B 96.721 244 6 2 2582 2824 830784637 830784879 4.100000e-109 405
5 TraesCS3B01G195000 chr3B 96.311 244 8 1 2582 2824 827415354 827415111 1.910000e-107 399
6 TraesCS3B01G195000 chr2B 95.231 692 28 5 1 689 133681100 133681789 0.000000e+00 1090
7 TraesCS3B01G195000 chr2B 94.193 706 35 6 1 702 108191547 108192250 0.000000e+00 1072
8 TraesCS3B01G195000 chr2B 81.526 249 38 7 2582 2824 61349624 61349378 7.470000e-47 198
9 TraesCS3B01G195000 chrUn 94.835 697 30 6 1 694 70454684 70453991 0.000000e+00 1083
10 TraesCS3B01G195000 chrUn 93.096 478 27 2 2940 3413 63016587 63016112 0.000000e+00 695
11 TraesCS3B01G195000 chrUn 92.067 479 32 4 2938 3413 84786600 84787075 0.000000e+00 669
12 TraesCS3B01G195000 chrUn 86.475 244 32 1 2582 2824 47565912 47565669 2.020000e-67 267
13 TraesCS3B01G195000 chr7B 94.699 698 27 6 1 695 154539412 154540102 0.000000e+00 1075
14 TraesCS3B01G195000 chr7B 94.294 701 33 6 1 695 704642686 704641987 0.000000e+00 1066
15 TraesCS3B01G195000 chr7B 92.067 479 32 4 2938 3413 73290907 73291382 0.000000e+00 669
16 TraesCS3B01G195000 chr7B 96.327 245 7 2 2582 2824 5323591 5323835 5.310000e-108 401
17 TraesCS3B01G195000 chr5B 94.261 697 36 4 1 694 43189318 43190013 0.000000e+00 1062
18 TraesCS3B01G195000 chr4B 93.822 696 39 4 1 693 578306133 578306827 0.000000e+00 1044
19 TraesCS3B01G195000 chr7A 92.662 477 34 1 2935 3411 499580968 499581443 0.000000e+00 686
20 TraesCS3B01G195000 chr7A 92.373 472 36 0 2942 3413 44737474 44737003 0.000000e+00 673
21 TraesCS3B01G195000 chr5D 92.276 479 36 1 2936 3413 62150893 62151371 0.000000e+00 678
22 TraesCS3B01G195000 chr4D 92.276 479 33 2 2935 3413 489247498 489247972 0.000000e+00 676
23 TraesCS3B01G195000 chr1B 91.772 474 39 0 2940 3413 638064200 638063727 0.000000e+00 660
24 TraesCS3B01G195000 chr1A 95.082 244 10 2 2582 2824 555104249 555104007 1.920000e-102 383
25 TraesCS3B01G195000 chr6B 86.122 245 32 2 2582 2824 707825062 707824818 2.610000e-66 263
26 TraesCS3B01G195000 chr6B 80.894 246 42 5 2582 2824 700195736 700195493 4.500000e-44 189
27 TraesCS3B01G195000 chr3A 75.478 314 66 8 1351 1654 696619263 696619575 3.550000e-30 143


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 TraesCS3B01G195000 chr3B 219341313 219344725 3412 True 6303 6303 100.000 1 3413 1 chr3B.!!$R2 3412
1 TraesCS3B01G195000 chr3B 220628852 220634968 6116 True 3062 5108 98.483 1 3413 2 chr3B.!!$R4 3412
2 TraesCS3B01G195000 chr3B 106068234 106068932 698 True 1050 1050 93.857 1 696 1 chr3B.!!$R1 695
3 TraesCS3B01G195000 chr2B 133681100 133681789 689 False 1090 1090 95.231 1 689 1 chr2B.!!$F2 688
4 TraesCS3B01G195000 chr2B 108191547 108192250 703 False 1072 1072 94.193 1 702 1 chr2B.!!$F1 701
5 TraesCS3B01G195000 chrUn 70453991 70454684 693 True 1083 1083 94.835 1 694 1 chrUn.!!$R3 693
6 TraesCS3B01G195000 chr7B 154539412 154540102 690 False 1075 1075 94.699 1 695 1 chr7B.!!$F3 694
7 TraesCS3B01G195000 chr7B 704641987 704642686 699 True 1066 1066 94.294 1 695 1 chr7B.!!$R1 694
8 TraesCS3B01G195000 chr5B 43189318 43190013 695 False 1062 1062 94.261 1 694 1 chr5B.!!$F1 693
9 TraesCS3B01G195000 chr4B 578306133 578306827 694 False 1044 1044 93.822 1 693 1 chr4B.!!$F1 692

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
311 314 1.918293 TGACTTGCGATGGAGGGGT 60.918 57.895 0.00 0.0 0.00 4.95 F
1080 1097 1.405821 CCGGCTAAGTCAGTACTCAGG 59.594 57.143 0.00 0.0 33.75 3.86 F
1223 1240 2.594131 CCATGGGCAGATGATGAACAT 58.406 47.619 2.85 0.0 42.47 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2145 0.392461 CCAGTCATGGGGTTGTACGG 60.392 60.0 0.0 0.0 43.54 4.02 R
2347 2364 1.478631 TGTCTGCTCTCGATCATGGT 58.521 50.0 0.0 0.0 0.00 3.55 R
3131 5854 0.377203 CGAACCGAAAATAGCCCTGC 59.623 55.0 0.0 0.0 0.00 4.85 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
27 28 5.238583 ACTTACACTCCCTTTCAATCGAAG 58.761 41.667 0.00 0.00 31.28 3.79
311 314 1.918293 TGACTTGCGATGGAGGGGT 60.918 57.895 0.00 0.00 0.00 4.95
606 623 5.703730 TTAGGTCGAAAATACCCTTGGAT 57.296 39.130 0.00 0.00 37.77 3.41
938 955 5.764192 TGCCCACGGGTAATATATAAAACAC 59.236 40.000 3.54 0.00 37.65 3.32
1080 1097 1.405821 CCGGCTAAGTCAGTACTCAGG 59.594 57.143 0.00 0.00 33.75 3.86
1223 1240 2.594131 CCATGGGCAGATGATGAACAT 58.406 47.619 2.85 0.00 42.47 2.71
2128 2145 4.443063 GCACAACCGGTTTCAAACTATTTC 59.557 41.667 19.55 0.00 0.00 2.17
2567 2584 1.756375 GCTGCGTCCATACTTGAGCG 61.756 60.000 0.00 0.00 0.00 5.03
2995 5718 2.222217 CCGTCGGAGCGAATTCGAC 61.222 63.158 31.01 21.44 46.52 4.20
3096 5819 9.853177 ATATTTCGAACTGATTAGATTTTCCCT 57.147 29.630 0.00 0.00 0.00 4.20
3182 5905 3.528532 CGTTCGCTAGGGTTTATTCCTT 58.471 45.455 6.70 0.00 35.92 3.36
3260 5983 0.033109 CCTTCCTCCACCCCAATTCC 60.033 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.260253 GGTTTCAGAAAGTTGTGACGAGAC 60.260 45.833 0.00 0.00 29.43 3.36
311 314 0.325671 CTGCTCCTACTTCCCCCTCA 60.326 60.000 0.00 0.00 0.00 3.86
606 623 5.144100 TGAGAATAACTGGGCCTTTTTGAA 58.856 37.500 4.53 0.00 0.00 2.69
860 877 4.142227 ACACCATGTAAGAGTCCGTGATAC 60.142 45.833 0.00 0.00 0.00 2.24
876 893 6.500684 AGTACTAATTGAAAGCACACCATG 57.499 37.500 0.00 0.00 0.00 3.66
938 955 4.153475 TCGCCGATGTTTTCTTTCTTTAGG 59.847 41.667 0.00 0.00 0.00 2.69
1223 1240 1.891919 GCTTTGTCTGGCGACCACA 60.892 57.895 6.94 0.00 39.47 4.17
2128 2145 0.392461 CCAGTCATGGGGTTGTACGG 60.392 60.000 0.00 0.00 43.54 4.02
2347 2364 1.478631 TGTCTGCTCTCGATCATGGT 58.521 50.000 0.00 0.00 0.00 3.55
2567 2584 5.221891 TCATGTAGTAACGTCGTAGGAAC 57.778 43.478 0.00 0.00 0.00 3.62
3009 5732 2.652172 CACGTGACATCAGCGTATATCG 59.348 50.000 10.90 0.00 43.12 2.92
3011 5734 3.710326 ACACGTGACATCAGCGTATAT 57.290 42.857 25.01 0.00 34.24 0.86
3012 5735 4.823790 ATACACGTGACATCAGCGTATA 57.176 40.909 25.01 0.00 34.24 1.47
3096 5819 5.576128 AGAATACCCTCGAAATTTTTGGGA 58.424 37.500 22.61 7.17 40.23 4.37
3121 5844 2.256117 ATAGCCCTGCAATTCGTACC 57.744 50.000 0.00 0.00 0.00 3.34
3131 5854 0.377203 CGAACCGAAAATAGCCCTGC 59.623 55.000 0.00 0.00 0.00 4.85
3182 5905 2.466523 TTAAAACCCTAGCGGCGGCA 62.467 55.000 19.21 3.77 43.41 5.69
3277 6000 2.610374 TCGTGTTCTTCGTTGAAAAGGG 59.390 45.455 0.00 0.00 31.46 3.95
3327 6050 1.656652 GCTTAATCTTCGCTGGCAGA 58.343 50.000 20.86 0.00 0.00 4.26
3329 6052 1.705337 GCGCTTAATCTTCGCTGGCA 61.705 55.000 0.00 0.00 44.79 4.92


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

AutoCloner maintained by Alex Coulton.