Multiple sequence alignment - TraesCS3D01G454400

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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 TraesCS3D01G454400 chr3D 100.000 2774 0 0 1 2774 561010370 561013143 0.000000e+00 5123.0
1 TraesCS3D01G454400 chr3D 99.554 672 3 0 1 672 561032679 561033350 0.000000e+00 1225.0
2 TraesCS3D01G454400 chr3D 98.763 566 7 0 107 672 561048500 561049065 0.000000e+00 1007.0
3 TraesCS3D01G454400 chr2D 93.883 2109 93 18 667 2774 534496115 534498188 0.000000e+00 3147.0
4 TraesCS3D01G454400 chr2D 82.722 654 103 10 673 1324 471441316 471441961 8.620000e-160 573.0
5 TraesCS3D01G454400 chr2D 96.667 330 11 0 669 998 22427721 22427392 1.450000e-152 549.0
6 TraesCS3D01G454400 chr1D 93.308 2107 95 18 670 2774 78403023 78400961 0.000000e+00 3068.0
7 TraesCS3D01G454400 chr5B 85.016 1228 141 23 673 1876 522094336 522093128 0.000000e+00 1208.0
8 TraesCS3D01G454400 chr5B 80.444 900 127 32 1900 2774 522093133 522092258 2.330000e-180 641.0
9 TraesCS3D01G454400 chr5B 84.332 651 97 5 674 1324 42183114 42182469 1.400000e-177 632.0
10 TraesCS3D01G454400 chr5B 91.176 68 6 0 1 68 698046489 698046556 2.940000e-15 93.5
11 TraesCS3D01G454400 chr5B 94.231 52 3 0 106 157 534555600 534555549 2.290000e-11 80.5
12 TraesCS3D01G454400 chr2A 82.042 1381 160 48 1460 2774 718349641 718350999 0.000000e+00 1096.0
13 TraesCS3D01G454400 chr2A 85.696 797 93 10 673 1464 718340149 718340929 0.000000e+00 821.0
14 TraesCS3D01G454400 chr3A 90.784 510 38 4 172 672 719625408 719625917 0.000000e+00 673.0
15 TraesCS3D01G454400 chr3A 90.588 510 38 4 172 672 645618704 645619212 0.000000e+00 667.0
16 TraesCS3D01G454400 chr3A 94.083 169 10 0 1 169 645618505 645618673 9.860000e-65 257.0
17 TraesCS3D01G454400 chr3A 94.083 169 10 0 1 169 719625209 719625377 9.860000e-65 257.0
18 TraesCS3D01G454400 chr1A 84.202 652 98 5 673 1324 21631524 21632170 1.810000e-176 628.0
19 TraesCS3D01G454400 chr1A 83.920 653 100 5 672 1324 573957395 573956748 1.090000e-173 619.0
20 TraesCS3D01G454400 chr1A 84.980 253 33 5 402 650 295574473 295574222 4.590000e-63 252.0
21 TraesCS3D01G454400 chr4A 85.907 518 41 11 172 672 669173265 669172763 8.800000e-145 523.0
22 TraesCS3D01G454400 chr4A 92.537 201 14 1 172 371 715365381 715365181 1.260000e-73 287.0
23 TraesCS3D01G454400 chr4A 93.491 169 11 0 1 169 669173463 669173295 4.590000e-63 252.0
24 TraesCS3D01G454400 chr4A 93.491 169 11 0 1 169 715365580 715365412 4.590000e-63 252.0
25 TraesCS3D01G454400 chr4A 89.340 197 14 3 483 672 715365181 715364985 9.930000e-60 241.0
26 TraesCS3D01G454400 chrUn 89.873 237 22 2 172 407 70143704 70143939 1.250000e-78 303.0
27 TraesCS3D01G454400 chrUn 92.308 169 13 0 1 169 70143505 70143673 9.930000e-60 241.0
28 TraesCS3D01G454400 chr5D 84.064 251 37 3 402 650 50981436 50981685 3.570000e-59 239.0
29 TraesCS3D01G454400 chr6D 93.243 74 5 0 1 74 326983991 326984064 2.920000e-20 110.0
30 TraesCS3D01G454400 chr1B 92.000 75 5 1 1 74 610005207 610005133 1.360000e-18 104.0
31 TraesCS3D01G454400 chr7B 94.231 52 3 0 106 157 266592854 266592803 2.290000e-11 80.5


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 TraesCS3D01G454400 chr3D 561010370 561013143 2773 False 5123.0 5123 100.000000 1 2774 1 chr3D.!!$F1 2773
1 TraesCS3D01G454400 chr3D 561032679 561033350 671 False 1225.0 1225 99.554000 1 672 1 chr3D.!!$F2 671
2 TraesCS3D01G454400 chr3D 561048500 561049065 565 False 1007.0 1007 98.763000 107 672 1 chr3D.!!$F3 565
3 TraesCS3D01G454400 chr2D 534496115 534498188 2073 False 3147.0 3147 93.883000 667 2774 1 chr2D.!!$F2 2107
4 TraesCS3D01G454400 chr2D 471441316 471441961 645 False 573.0 573 82.722000 673 1324 1 chr2D.!!$F1 651
5 TraesCS3D01G454400 chr1D 78400961 78403023 2062 True 3068.0 3068 93.308000 670 2774 1 chr1D.!!$R1 2104
6 TraesCS3D01G454400 chr5B 522092258 522094336 2078 True 924.5 1208 82.730000 673 2774 2 chr5B.!!$R3 2101
7 TraesCS3D01G454400 chr5B 42182469 42183114 645 True 632.0 632 84.332000 674 1324 1 chr5B.!!$R1 650
8 TraesCS3D01G454400 chr2A 718349641 718350999 1358 False 1096.0 1096 82.042000 1460 2774 1 chr2A.!!$F2 1314
9 TraesCS3D01G454400 chr2A 718340149 718340929 780 False 821.0 821 85.696000 673 1464 1 chr2A.!!$F1 791
10 TraesCS3D01G454400 chr3A 719625209 719625917 708 False 465.0 673 92.433500 1 672 2 chr3A.!!$F2 671
11 TraesCS3D01G454400 chr3A 645618505 645619212 707 False 462.0 667 92.335500 1 672 2 chr3A.!!$F1 671
12 TraesCS3D01G454400 chr1A 21631524 21632170 646 False 628.0 628 84.202000 673 1324 1 chr1A.!!$F1 651
13 TraesCS3D01G454400 chr1A 573956748 573957395 647 True 619.0 619 83.920000 672 1324 1 chr1A.!!$R2 652
14 TraesCS3D01G454400 chr4A 669172763 669173463 700 True 387.5 523 89.699000 1 672 2 chr4A.!!$R1 671
15 TraesCS3D01G454400 chr4A 715364985 715365580 595 True 260.0 287 91.789333 1 672 3 chr4A.!!$R2 671

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
794 842 0.687354 TTTCTCTGGAGTGGAGCACC 59.313 55.000 0.0 0.0 34.49 5.01 F
932 981 1.340017 GCCACTTTATCTGAGCCACCA 60.340 52.381 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1814 1.001974 ACTGCAGCCATAAGAACGACA 59.998 47.619 15.27 0.0 0.0 4.35 R
1876 2037 1.271656 CTAAACCTGGGTCGTCGTCTT 59.728 52.381 0.00 0.0 0.0 3.01 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
68 69 6.903534 TCCCTTAGTCTTCAGTTATCATTCCT 59.096 38.462 0.00 0.00 0.00 3.36
794 842 0.687354 TTTCTCTGGAGTGGAGCACC 59.313 55.000 0.00 0.00 34.49 5.01
932 981 1.340017 GCCACTTTATCTGAGCCACCA 60.340 52.381 0.00 0.00 0.00 4.17
957 1006 2.040178 CCGTATGGGCTAACTTCTCCT 58.960 52.381 0.00 0.00 0.00 3.69
1068 1120 3.560882 CCCTCCAACATCTCTTTTGCTCT 60.561 47.826 0.00 0.00 0.00 4.09
1130 1182 4.262121 CGCTTCATCTTCATCATCTCTCCT 60.262 45.833 0.00 0.00 0.00 3.69
1245 1297 3.313526 GGCATCGATTCTACAAGTGCATT 59.686 43.478 0.00 0.00 33.05 3.56
1281 1334 3.747099 ACTTTTTGATCCGATCTTGCG 57.253 42.857 9.78 0.00 0.00 4.85
1485 1538 4.531351 CCACCCGGGTTTGGATTT 57.469 55.556 27.83 0.00 34.46 2.17
1554 1607 4.113815 CCCCAGATCCAGGCGCAA 62.114 66.667 10.83 0.00 0.00 4.85
1655 1765 4.400961 AGCTGACGCTGGAAGGCC 62.401 66.667 0.00 0.00 46.86 5.19
1656 1766 4.400961 GCTGACGCTGGAAGGCCT 62.401 66.667 0.00 0.00 34.31 5.19
1657 1767 2.435586 CTGACGCTGGAAGGCCTG 60.436 66.667 5.69 0.00 36.29 4.85
1704 1814 0.607489 CACAAGGCCTAGCTGCAGTT 60.607 55.000 16.64 12.62 0.00 3.16
1706 1816 0.607489 CAAGGCCTAGCTGCAGTTGT 60.607 55.000 16.64 2.99 0.00 3.32
1775 1885 8.512138 GTTGATGGTTGTGTTAGCTAAGTAATT 58.488 33.333 6.38 0.00 0.00 1.40
1779 1889 6.999272 TGGTTGTGTTAGCTAAGTAATTTCCA 59.001 34.615 6.38 7.40 0.00 3.53
1812 1944 5.646692 AGGGCACTCCTTTATTAATAGCA 57.353 39.130 0.00 0.00 45.47 3.49
1876 2037 4.655186 TCCCTTTACCGCTAAGCCTATTTA 59.345 41.667 0.00 0.00 0.00 1.40
1895 2056 1.331214 AAGACGACGACCCAGGTTTA 58.669 50.000 0.00 0.00 0.00 2.01
1947 2108 9.765795 ACTATGTAATGCTTTATCAGACCTTAC 57.234 33.333 0.00 0.00 0.00 2.34
1958 2120 2.758979 TCAGACCTTACTTAAGCTCCCG 59.241 50.000 1.29 0.00 32.02 5.14
2211 2377 0.319083 TTCGTTATGCCACACGTCCT 59.681 50.000 0.00 0.00 37.66 3.85
2288 2455 3.312697 GGGCAGAACCGTCATTTCTATTC 59.687 47.826 0.00 0.00 40.62 1.75
2330 2497 2.434331 CGGTTCCACCCACACCAT 59.566 61.111 0.00 0.00 33.75 3.55
2509 2680 8.988064 TCTACAGCTCTTTTGTATCTAGTTTG 57.012 34.615 0.00 0.00 31.17 2.93
2590 2781 4.277174 CAGGATGATAGTAGTTCGCAGTCT 59.723 45.833 0.00 0.00 39.69 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
853 901 2.096013 GCACAGATAAGAAAACGAGCCC 59.904 50.000 0.00 0.00 0.00 5.19
957 1006 1.512522 CGTGTTGACGCCGTCGATA 60.513 57.895 10.88 4.99 39.10 2.92
996 1045 2.274948 GATGGGCTGTGAGCATGGGA 62.275 60.000 0.00 0.00 44.75 4.37
1068 1120 0.114560 GGACGGAGGAGGATATGGGA 59.885 60.000 0.00 0.00 0.00 4.37
1245 1297 6.380995 TCAAAAAGTACTTACATCGTAGCGA 58.619 36.000 8.92 0.00 41.13 4.93
1704 1814 1.001974 ACTGCAGCCATAAGAACGACA 59.998 47.619 15.27 0.00 0.00 4.35
1706 1816 1.275010 TCACTGCAGCCATAAGAACGA 59.725 47.619 15.27 0.00 0.00 3.85
1775 1885 4.827789 AGTGCCCTAGAATACCTATGGAA 58.172 43.478 0.00 0.00 35.79 3.53
1779 1889 4.768807 AGGAGTGCCCTAGAATACCTAT 57.231 45.455 0.00 0.00 45.48 2.57
1876 2037 1.271656 CTAAACCTGGGTCGTCGTCTT 59.728 52.381 0.00 0.00 0.00 3.01
1895 2056 2.029020 TGTCGAATAGCACAACAGCTCT 60.029 45.455 0.00 0.00 45.26 4.09
1964 2127 7.716799 ACAATCTGAACCCAGCAAAATAATA 57.283 32.000 0.00 0.00 40.20 0.98
2211 2377 3.909662 GGGGAGACGCGTGTACTA 58.090 61.111 20.70 0.00 0.00 1.82
2288 2455 4.122776 GGATAGGGATATAATGCGTGCTG 58.877 47.826 0.00 0.00 0.00 4.41
2330 2497 3.718434 AGAAATGGGCAGGATATGAGTGA 59.282 43.478 0.00 0.00 0.00 3.41
2485 2653 8.988064 TCAAACTAGATACAAAAGAGCTGTAG 57.012 34.615 0.00 0.00 32.96 2.74
2487 2655 9.593134 CTATCAAACTAGATACAAAAGAGCTGT 57.407 33.333 0.00 0.00 0.00 4.40
2488 2656 9.809096 TCTATCAAACTAGATACAAAAGAGCTG 57.191 33.333 0.00 0.00 0.00 4.24
2509 2680 6.291648 TCAGATCCAGGCATACAATCTATC 57.708 41.667 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.