Multiple sequence alignment - TraesCS4B01G201400

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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 TraesCS4B01G201400 chr4B 100.000 2564 0 0 1 2564 431427785 431425222 0 4735
1 TraesCS4B01G201400 chr1B 95.175 2570 106 14 1 2564 54018236 54020793 0 4043
2 TraesCS4B01G201400 chr2B 94.905 2571 110 10 1 2564 485103563 485106119 0 4002
3 TraesCS4B01G201400 chr2A 94.637 2573 122 13 1 2564 297037254 297039819 0 3973
4 TraesCS4B01G201400 chr2A 91.540 1182 92 5 1 1178 521562256 521561079 0 1622
5 TraesCS4B01G201400 chr2A 90.641 1186 95 12 1 1175 507049695 507050875 0 1561
6 TraesCS4B01G201400 chr1A 94.604 2576 119 11 1 2564 162628032 162630599 0 3969
7 TraesCS4B01G201400 chr1A 94.561 2574 121 14 1 2564 342136627 342134063 0 3960
8 TraesCS4B01G201400 chr1A 93.820 2573 119 21 1 2564 151026577 151024036 0 3834
9 TraesCS4B01G201400 chr6A 94.408 2575 125 15 1 2564 475089142 475091708 0 3940
10 TraesCS4B01G201400 chr6A 94.175 2575 130 15 1 2564 363465263 363467828 0 3906
11 TraesCS4B01G201400 chr3A 94.650 1944 94 10 628 2564 672058348 672060288 0 3005


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 TraesCS4B01G201400 chr4B 431425222 431427785 2563 True 4735 4735 100.000 1 2564 1 chr4B.!!$R1 2563
1 TraesCS4B01G201400 chr1B 54018236 54020793 2557 False 4043 4043 95.175 1 2564 1 chr1B.!!$F1 2563
2 TraesCS4B01G201400 chr2B 485103563 485106119 2556 False 4002 4002 94.905 1 2564 1 chr2B.!!$F1 2563
3 TraesCS4B01G201400 chr2A 297037254 297039819 2565 False 3973 3973 94.637 1 2564 1 chr2A.!!$F1 2563
4 TraesCS4B01G201400 chr2A 521561079 521562256 1177 True 1622 1622 91.540 1 1178 1 chr2A.!!$R1 1177
5 TraesCS4B01G201400 chr2A 507049695 507050875 1180 False 1561 1561 90.641 1 1175 1 chr2A.!!$F2 1174
6 TraesCS4B01G201400 chr1A 162628032 162630599 2567 False 3969 3969 94.604 1 2564 1 chr1A.!!$F1 2563
7 TraesCS4B01G201400 chr1A 342134063 342136627 2564 True 3960 3960 94.561 1 2564 1 chr1A.!!$R2 2563
8 TraesCS4B01G201400 chr1A 151024036 151026577 2541 True 3834 3834 93.820 1 2564 1 chr1A.!!$R1 2563
9 TraesCS4B01G201400 chr6A 475089142 475091708 2566 False 3940 3940 94.408 1 2564 1 chr6A.!!$F2 2563
10 TraesCS4B01G201400 chr6A 363465263 363467828 2565 False 3906 3906 94.175 1 2564 1 chr6A.!!$F1 2563
11 TraesCS4B01G201400 chr3A 672058348 672060288 1940 False 3005 3005 94.650 628 2564 1 chr3A.!!$F1 1936

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
458 459 1.275291 TGTCCTAGAAGTCCAAAGCCG 59.725 52.381 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1817 1.127567 TACCTTGGCTGAGGCACTGT 61.128 55.0 8.71 11.38 41.55 3.55 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
184 185 2.367567 TGGAGTTCTTGTAGCTTCGGTT 59.632 45.455 0.00 0.00 0.00 4.44
259 260 3.873883 CGGCTGCTTGCAGCTAGC 61.874 66.667 35.89 23.44 46.69 3.42
306 307 3.090532 AAGATCGGGCCACCCTCC 61.091 66.667 4.39 0.00 42.67 4.30
344 345 1.821088 GGGTTCCCACCTATCATCCT 58.179 55.000 2.59 0.00 43.65 3.24
458 459 1.275291 TGTCCTAGAAGTCCAAAGCCG 59.725 52.381 0.00 0.00 0.00 5.52
477 480 3.748568 GCCGCACCAAAAATAAATCCAAA 59.251 39.130 0.00 0.00 0.00 3.28
588 600 4.159321 TCAGATTTGGTTGTTGTGCTTTGA 59.841 37.500 0.00 0.00 0.00 2.69
616 638 7.686438 AAAAGAGAAACAAAGTGGCAAAAAT 57.314 28.000 0.00 0.00 0.00 1.82
739 781 4.236935 AGCTTGTGTGTTGTGTTTTTCAG 58.763 39.130 0.00 0.00 0.00 3.02
789 832 7.234371 TCCATCCACATATTTTTCTTGGTTTGA 59.766 33.333 0.00 0.00 0.00 2.69
833 876 2.399580 CCCTTTTTGTTTACCCCACCA 58.600 47.619 0.00 0.00 0.00 4.17
1156 1200 1.762957 CAGGTGGTGATAGGGTTCGAT 59.237 52.381 0.00 0.00 0.00 3.59
1207 1251 2.787473 AGTTGGCGATGAGAATTCCA 57.213 45.000 0.65 0.28 0.00 3.53
1243 1287 3.474600 GATGGTGACTTGGAGGATGATG 58.525 50.000 0.00 0.00 0.00 3.07
1248 1292 4.521146 GTGACTTGGAGGATGATGACAAT 58.479 43.478 0.00 0.00 0.00 2.71
1262 1306 1.299541 GACAATAGCCATGGTGGACG 58.700 55.000 14.67 2.29 40.96 4.79
1368 1412 2.116238 GGGCACTACTATGACCCTCAA 58.884 52.381 0.00 0.00 42.70 3.02
1402 1446 5.351948 TCGTGGTCATGGAGATGATTTTA 57.648 39.130 0.00 0.00 40.78 1.52
1448 1492 1.676635 GTGCTGCTGAAGATGGGCA 60.677 57.895 0.00 0.00 34.66 5.36
1835 1879 4.525912 ACAAAGAGATGGAATTGTTGCC 57.474 40.909 0.00 0.00 0.00 4.52
1987 2031 2.932234 CGCACGGAGAGGAAGGTGT 61.932 63.158 0.00 0.00 33.09 4.16
2007 2051 2.509336 CGGAGTGGTCATGGACGC 60.509 66.667 0.00 0.00 32.65 5.19
2160 2205 3.682718 CGGCTCCTAGGAATGTTGACAAT 60.683 47.826 13.77 0.00 0.00 2.71
2177 2222 2.146342 CAATCGTGCTCCTTCTGTTGT 58.854 47.619 0.00 0.00 0.00 3.32
2273 2318 5.357878 GGCATGGTCACATTTCTTCTGAATA 59.642 40.000 0.00 0.00 34.35 1.75
2276 2321 7.201758 GCATGGTCACATTTCTTCTGAATATCA 60.202 37.037 0.00 0.00 34.35 2.15
2417 2462 0.107017 CAGGCCGACATGGGAGATTT 60.107 55.000 0.00 0.00 38.63 2.17
2474 2520 1.356124 AGAGAAGAGAAAGGGCAGCA 58.644 50.000 0.00 0.00 0.00 4.41
2557 2604 0.249573 GGCAGCTGCAACAACATTGT 60.250 50.000 37.63 0.00 44.36 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 185 1.678598 CCGTACGTTGGGGATGGCTA 61.679 60.000 15.21 0.00 0.00 3.93
228 229 1.874320 GCAGCCGGGATAACTAGCTTC 60.874 57.143 2.18 0.00 0.00 3.86
259 260 3.093057 AGGATCGAATCGGAAGGGATAG 58.907 50.000 1.76 0.00 0.00 2.08
344 345 2.290450 TGTCAATGAAGGCTCTGATGCA 60.290 45.455 0.00 0.00 34.04 3.96
458 459 6.262049 ACAAGGTTTGGATTTATTTTTGGTGC 59.738 34.615 0.00 0.00 34.12 5.01
602 615 8.084073 TCTCTCTTTGATATTTTTGCCACTTTG 58.916 33.333 0.00 0.00 0.00 2.77
666 702 7.836842 ACTTTTGGATCTTACACAACACTTTT 58.163 30.769 0.00 0.00 0.00 2.27
789 832 4.986659 GCTTGTGCTGAAATGAAGTTGATT 59.013 37.500 0.00 0.00 36.03 2.57
798 841 0.971386 AAGGGGCTTGTGCTGAAATG 59.029 50.000 0.00 0.00 39.59 2.32
833 876 1.681264 CTTCGGTTTTTGGTGGAGCTT 59.319 47.619 0.00 0.00 0.00 3.74
1156 1200 3.133362 GGATCAATAGGGTGTTGTCGGTA 59.867 47.826 0.00 0.00 0.00 4.02
1243 1287 1.299541 CGTCCACCATGGCTATTGTC 58.700 55.000 13.04 0.00 37.47 3.18
1248 1292 1.295101 CACACGTCCACCATGGCTA 59.705 57.895 13.04 0.00 37.47 3.93
1262 1306 3.720193 CACGAGCAGCAGCCACAC 61.720 66.667 0.00 0.00 43.56 3.82
1335 1379 2.927856 TGCCCACGAGGACCATGT 60.928 61.111 0.00 0.00 38.24 3.21
1497 1541 1.217916 TTCCTGTGAACTTGGGGACA 58.782 50.000 0.00 0.00 39.83 4.02
1685 1729 1.270550 CTTCCCAAGTGTCAATGTGGC 59.729 52.381 0.00 0.00 0.00 5.01
1773 1817 1.127567 TACCTTGGCTGAGGCACTGT 61.128 55.000 8.71 11.38 41.55 3.55
1835 1879 1.255342 CATGAATACGAGCACGAACCG 59.745 52.381 11.40 0.00 42.66 4.44
1987 2031 1.663379 CGTCCATGACCACTCCGCTA 61.663 60.000 0.00 0.00 0.00 4.26
2007 2051 2.341257 GTGGTGCGGCTATGAGATATG 58.659 52.381 0.00 0.00 0.00 1.78
2160 2205 1.581934 CAACAACAGAAGGAGCACGA 58.418 50.000 0.00 0.00 0.00 4.35
2177 2222 4.018779 CCATGGGGTTAGAAGTACTTCCAA 60.019 45.833 28.05 20.16 40.33 3.53
2417 2462 1.292061 CACACGACGGGAAACAAAGA 58.708 50.000 2.90 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.