Multiple sequence alignment - TraesCS7D01G080100

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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 TraesCS7D01G080100 chr7D 100.000 2452 0 0 1 2452 47254203 47251752 0.000000e+00 4529
1 TraesCS7D01G080100 chr4B 93.370 1463 58 10 1 1438 284635172 284633724 0.000000e+00 2128
2 TraesCS7D01G080100 chr4B 91.431 1027 61 9 1437 2452 284633029 284632019 0.000000e+00 1384
3 TraesCS7D01G080100 chrUn 97.801 1228 19 6 1 1228 373517724 373516505 0.000000e+00 2111
4 TraesCS7D01G080100 chrUn 97.189 676 17 1 1779 2452 347400959 347401634 0.000000e+00 1142
5 TraesCS7D01G080100 chrUn 95.833 216 9 0 1436 1651 480295185 480295400 1.400000e-92 350
6 TraesCS7D01G080100 chrUn 97.674 172 4 0 1606 1777 480295401 480295572 1.840000e-76 296
7 TraesCS7D01G080100 chr5A 82.177 735 100 18 157 862 62191629 62190897 9.700000e-169 603
8 TraesCS7D01G080100 chr1A 80.029 701 108 11 1767 2452 388487353 388488036 7.880000e-135 490
9 TraesCS7D01G080100 chr3A 83.412 422 49 14 159 561 369489354 369488935 2.980000e-99 372
10 TraesCS7D01G080100 chr3A 89.434 265 24 4 2188 2450 369488886 369488624 5.050000e-87 331


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 TraesCS7D01G080100 chr7D 47251752 47254203 2451 True 4529.0 4529 100.0000 1 2452 1 chr7D.!!$R1 2451
1 TraesCS7D01G080100 chr4B 284632019 284635172 3153 True 1756.0 2128 92.4005 1 2452 2 chr4B.!!$R1 2451
2 TraesCS7D01G080100 chrUn 373516505 373517724 1219 True 2111.0 2111 97.8010 1 1228 1 chrUn.!!$R1 1227
3 TraesCS7D01G080100 chrUn 347400959 347401634 675 False 1142.0 1142 97.1890 1779 2452 1 chrUn.!!$F1 673
4 TraesCS7D01G080100 chr5A 62190897 62191629 732 True 603.0 603 82.1770 157 862 1 chr5A.!!$R1 705
5 TraesCS7D01G080100 chr1A 388487353 388488036 683 False 490.0 490 80.0290 1767 2452 1 chr1A.!!$F1 685
6 TraesCS7D01G080100 chr3A 369488624 369489354 730 True 351.5 372 86.4230 159 2450 2 chr3A.!!$R1 2291

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
634 678 0.3199 CCGCTGGATGGATAAGACGG 60.32 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2969 0.614697 TCAAGCAGACAGGGATCGGA 60.615 55.0 0.0 0.0 0.0 4.55 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
155 156 9.500785 AAAAAGTCAAAGAAAGAAAACATTCCA 57.499 25.926 0.00 0.00 0.00 3.53
423 441 2.096442 CGCCCGTTAACGTCCTTCC 61.096 63.158 25.15 6.92 37.74 3.46
634 678 0.319900 CCGCTGGATGGATAAGACGG 60.320 60.000 0.00 0.00 0.00 4.79
972 1018 5.956642 AGAAGCAACGAAACTTGGTAAAAA 58.043 33.333 0.00 0.00 31.60 1.94
1139 1185 2.831333 AGACATTCTCTATTGCTGCGG 58.169 47.619 0.00 0.00 0.00 5.69
1174 1220 8.125448 CCAATTTCGAATTCCTCTTAATCAGAC 58.875 37.037 0.00 0.00 0.00 3.51
1239 1285 0.679640 TATGCAGGGCAAGGAAACCG 60.680 55.000 0.00 0.00 43.62 4.44
1305 1351 4.675190 ACAAAACGATTGAGATCTGCTG 57.325 40.909 0.00 0.00 0.00 4.41
1317 1363 6.120507 TGAGATCTGCTGTAGAGATAGCTA 57.879 41.667 0.00 0.00 40.33 3.32
1419 1466 2.449464 CAGCTGACCCAATGGATTCAA 58.551 47.619 8.42 0.00 34.81 2.69
1448 2191 5.069251 TCCGGACATGGTGTTGTTTTATTTT 59.931 36.000 0.00 0.00 0.00 1.82
1504 2247 5.065988 TGACAGTGAAGGCAGTTAAAAGAAC 59.934 40.000 0.00 0.00 0.00 3.01
1529 2272 5.069119 ACGAGAAGTGAATGCTACATCCATA 59.931 40.000 0.00 0.00 0.00 2.74
1535 2278 5.414765 AGTGAATGCTACATCCATATGCATG 59.585 40.000 10.16 5.01 42.57 4.06
1568 2311 1.284657 CTGCTATGACCACTTGAGCG 58.715 55.000 0.00 0.00 35.88 5.03
1681 2424 1.174783 TACAGAGTTGTCGGCTCCTC 58.825 55.000 0.00 0.00 38.76 3.71
1724 2467 6.139169 GCAAAGTCGCTTAACATAAATGATCG 59.861 38.462 0.00 0.00 0.00 3.69
1750 2493 1.134670 GGAAGGACAGACTGAATCCCG 60.135 57.143 10.08 0.00 32.47 5.14
1793 2536 2.542020 TCTCGTGCCATGACAGAAAA 57.458 45.000 0.00 0.00 0.00 2.29
1837 2580 7.730358 AGCACTTGAAGTGATCTTCGTCGAA 62.730 44.000 27.97 7.57 41.62 3.71
1853 2596 3.665190 GTCGAAGGTGGTGAAGAGATTT 58.335 45.455 0.00 0.00 0.00 2.17
1875 2618 2.133553 CAATAGCGACATGAGCTCCAG 58.866 52.381 20.10 6.09 44.79 3.86
2214 2969 1.055040 ACAACAGAAGCAGCCTCTCT 58.945 50.000 0.00 0.00 0.00 3.10
2299 3055 5.652014 ACATCCATACTGGGTTTTACATGTG 59.348 40.000 9.11 0.00 38.32 3.21
2342 3099 0.037790 ACTCGCCTGCTTTCTCAGAC 60.038 55.000 0.00 0.00 36.19 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
415 433 0.323908 AGAGACAGGGAGGAAGGACG 60.324 60.000 0.00 0.00 0.00 4.79
423 441 3.131933 ACATGATTCGAAGAGACAGGGAG 59.868 47.826 3.35 0.00 38.43 4.30
657 701 6.414079 CGATATGTAAATCGCTGCATATTCC 58.586 40.000 0.00 0.00 41.93 3.01
972 1018 5.534407 ACAGTTGGTTCGAAAACAACTTTT 58.466 33.333 31.08 22.97 35.98 2.27
973 1019 5.128992 ACAGTTGGTTCGAAAACAACTTT 57.871 34.783 31.08 25.99 35.98 2.66
974 1020 4.776795 ACAGTTGGTTCGAAAACAACTT 57.223 36.364 31.08 23.23 35.98 2.66
975 1021 4.481463 CAACAGTTGGTTCGAAAACAACT 58.519 39.130 29.34 29.34 37.72 3.16
1019 1065 5.579511 GCGTTGTAAAACTCATAAGCCTCTA 59.420 40.000 0.00 0.00 0.00 2.43
1174 1220 7.591426 GCTTAGCAAGGAAATATATTTTGTCGG 59.409 37.037 11.92 3.56 0.00 4.79
1239 1285 3.983044 AGGTTCAGGAGGTAACACATC 57.017 47.619 0.00 0.00 41.41 3.06
1317 1363 7.887495 AGAGCACTTCCTTTTATTCTTCTCAAT 59.113 33.333 0.00 0.00 0.00 2.57
1419 1466 0.472471 AACACCATGTCCGGAGTGTT 59.528 50.000 25.96 25.96 45.90 3.32
1504 2247 3.553511 GGATGTAGCATTCACTTCTCGTG 59.446 47.826 0.00 0.00 45.18 4.35
1529 2272 1.402968 GTCGCTTTGTGATCCATGCAT 59.597 47.619 0.00 0.00 0.00 3.96
1546 2289 2.534298 CTCAAGTGGTCATAGCAGTCG 58.466 52.381 0.00 0.00 0.00 4.18
1559 2302 1.633852 GCCTTCTGCTCGCTCAAGTG 61.634 60.000 0.00 0.00 36.87 3.16
1609 2352 1.102222 GGTCCATCTAGCCTCGTCGT 61.102 60.000 0.00 0.00 0.00 4.34
1681 2424 4.668576 TTGCTTCTTGCTTATGAAGACG 57.331 40.909 6.88 0.00 41.38 4.18
1724 2467 6.052360 GGATTCAGTCTGTCCTTCCTATTTC 58.948 44.000 0.00 0.00 0.00 2.17
1750 2493 2.287915 CGTTTCCGGATCACCATGAATC 59.712 50.000 4.15 0.00 35.59 2.52
1793 2536 1.550524 TCATTCAACGGCTAGTGCTCT 59.449 47.619 0.00 0.00 39.59 4.09
1837 2580 4.664688 ATTGGAAATCTCTTCACCACCT 57.335 40.909 0.00 0.00 0.00 4.00
1853 2596 1.069204 GGAGCTCATGTCGCTATTGGA 59.931 52.381 17.19 0.00 37.96 3.53
2214 2969 0.614697 TCAAGCAGACAGGGATCGGA 60.615 55.000 0.00 0.00 0.00 4.55
2299 3055 4.784550 GTGCGTAAATGTATTTCACGTTCC 59.215 41.667 14.54 5.65 35.22 3.62
2342 3099 2.787473 TGCATCTAGGTTCACTTGGG 57.213 50.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.