Multiple sequence alignment - TraesCS5D01G298500

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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 TraesCS5D01G298500 chr5D 100.000 2495 0 0 1 2495 396170449 396167955 0.000000e+00 4608
1 TraesCS5D01G298500 chr7D 98.438 2496 35 3 1 2495 22665066 22667558 0.000000e+00 4390
2 TraesCS5D01G298500 chr7D 91.879 1059 78 4 1441 2495 4251036 4252090 0.000000e+00 1472
3 TraesCS5D01G298500 chr2A 93.012 1059 70 2 1441 2495 58556588 58555530 0.000000e+00 1543
4 TraesCS5D01G298500 chr1A 93.012 1059 70 2 1441 2495 298619875 298618817 0.000000e+00 1543
5 TraesCS5D01G298500 chr7B 92.750 1062 73 2 1438 2495 20885910 20886971 0.000000e+00 1531
6 TraesCS5D01G298500 chr3B 92.279 1062 78 2 1438 2495 754453165 754454226 0.000000e+00 1504
7 TraesCS5D01G298500 chr3D 91.604 1072 80 6 1428 2495 497963084 497964149 0.000000e+00 1472
8 TraesCS5D01G298500 chr3D 91.690 1059 80 4 1441 2495 49542380 49543434 0.000000e+00 1461
9 TraesCS5D01G298500 chr5A 91.272 1077 89 3 1423 2495 423038018 423036943 0.000000e+00 1463
10 TraesCS5D01G298500 chr6B 85.075 335 47 3 924 1257 493512189 493511857 3.070000e-89 339


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 TraesCS5D01G298500 chr5D 396167955 396170449 2494 True 4608 4608 100.000 1 2495 1 chr5D.!!$R1 2494
1 TraesCS5D01G298500 chr7D 22665066 22667558 2492 False 4390 4390 98.438 1 2495 1 chr7D.!!$F2 2494
2 TraesCS5D01G298500 chr7D 4251036 4252090 1054 False 1472 1472 91.879 1441 2495 1 chr7D.!!$F1 1054
3 TraesCS5D01G298500 chr2A 58555530 58556588 1058 True 1543 1543 93.012 1441 2495 1 chr2A.!!$R1 1054
4 TraesCS5D01G298500 chr1A 298618817 298619875 1058 True 1543 1543 93.012 1441 2495 1 chr1A.!!$R1 1054
5 TraesCS5D01G298500 chr7B 20885910 20886971 1061 False 1531 1531 92.750 1438 2495 1 chr7B.!!$F1 1057
6 TraesCS5D01G298500 chr3B 754453165 754454226 1061 False 1504 1504 92.279 1438 2495 1 chr3B.!!$F1 1057
7 TraesCS5D01G298500 chr3D 497963084 497964149 1065 False 1472 1472 91.604 1428 2495 1 chr3D.!!$F2 1067
8 TraesCS5D01G298500 chr3D 49542380 49543434 1054 False 1461 1461 91.690 1441 2495 1 chr3D.!!$F1 1054
9 TraesCS5D01G298500 chr5A 423036943 423038018 1075 True 1463 1463 91.272 1423 2495 1 chr5A.!!$R1 1072

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
229 230 1.343069 ATCTCCCCGATTACTCCAGC 58.657 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1713 1.470098 CTTCCCCAAGCATCTTGTTCG 59.53 52.381 5.92 0.0 0.0 3.95 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
130 131 2.666098 GGAGAGGGGTTTGGCGCTA 61.666 63.158 7.64 0.00 0.00 4.26
169 170 5.298276 TGTTCTTGTTTGTTAGGGTGATCAC 59.702 40.000 17.91 17.91 0.00 3.06
229 230 1.343069 ATCTCCCCGATTACTCCAGC 58.657 55.000 0.00 0.00 0.00 4.85
300 301 1.401530 CATGTGTTGAAGCTTGCACG 58.598 50.000 2.10 0.00 34.86 5.34
344 345 3.386768 TCCTTCCTTTTGACTGACGAG 57.613 47.619 0.00 0.00 0.00 4.18
374 375 5.791974 CGATTGCACTTACTCATTGAAACAG 59.208 40.000 0.00 0.00 0.00 3.16
397 398 4.919754 GGCCGACCATTATTAGTACTAACG 59.080 45.833 17.45 13.56 35.26 3.18
445 446 4.727734 GCTGTTCAGTTAATGTGCATACCG 60.728 45.833 0.00 0.00 0.00 4.02
476 477 8.795842 ATGGTGTTATCCTTATACGTTTGAAA 57.204 30.769 0.00 0.00 0.00 2.69
661 662 8.190122 TGTGATCATCATAATTAAACAACTGGC 58.810 33.333 0.00 0.00 0.00 4.85
672 673 1.741770 CAACTGGCCTGCCGACTAC 60.742 63.158 9.95 0.00 39.42 2.73
728 729 5.284079 CCATTAATTAGCTGCACCACAATC 58.716 41.667 1.02 0.00 0.00 2.67
777 778 7.043391 GCTGGAACTAAACAACTTTTGCTAAAG 60.043 37.037 17.45 17.45 45.08 1.85
779 780 7.093684 TGGAACTAAACAACTTTTGCTAAAGGT 60.094 33.333 21.83 14.70 44.10 3.50
816 817 6.202516 GGTTGCATACCTTTAGCATTAACA 57.797 37.500 9.89 0.00 44.10 2.41
835 836 3.790126 ACAGGACCTGGGCATTTTAAAT 58.210 40.909 25.34 0.00 35.51 1.40
940 941 4.641541 TGTGATGGTTTGATTGCATAGAGG 59.358 41.667 0.00 0.00 0.00 3.69
1257 1258 8.552083 TGGTTATTATGGATGATGAAGAATCG 57.448 34.615 0.00 0.00 38.22 3.34
1339 1340 2.553028 CCAAAAGAGCCTAGTGCCAAGA 60.553 50.000 0.21 0.00 42.71 3.02
1360 1361 4.957327 AGACTAGTGATTGGGAGGTAGAAC 59.043 45.833 0.00 0.00 0.00 3.01
1392 1393 3.888930 GACAATGGGGAGAAGAACAACAA 59.111 43.478 0.00 0.00 0.00 2.83
1492 1493 2.034879 CGTGCGTTTCATCAGCCCT 61.035 57.895 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.504175 CCAAACCCCTCTCCGATCTTAA 59.496 50.000 0.00 0.00 0.00 1.85
130 131 5.449553 ACAAGAACAAAGGATCTCAAACCT 58.550 37.500 0.00 0.00 38.23 3.50
229 230 4.127040 ACGAGCAGAGCGCCTCAG 62.127 66.667 2.29 2.96 44.04 3.35
300 301 4.806571 CATCATTGCACTGCAGGC 57.193 55.556 19.93 18.37 40.61 4.85
374 375 4.919754 CGTTAGTACTAATAATGGTCGGCC 59.080 45.833 18.03 0.00 0.00 6.13
445 446 5.344128 CGTATAAGGATAACACCATACGCAC 59.656 44.000 0.00 0.00 36.38 5.34
661 662 1.320344 TGGCTACTGTAGTCGGCAGG 61.320 60.000 14.15 0.00 40.41 4.85
692 693 8.577296 CAGCTAATTAATGGCTACTACACTCTA 58.423 37.037 13.52 0.00 34.71 2.43
699 700 5.163248 TGGTGCAGCTAATTAATGGCTACTA 60.163 40.000 18.08 7.03 34.71 1.82
777 778 2.423538 GCAACCTGGAATACACATGACC 59.576 50.000 0.00 0.00 0.00 4.02
779 780 3.431673 TGCAACCTGGAATACACATGA 57.568 42.857 0.00 0.00 0.00 3.07
816 817 5.841267 AAAATTTAAAATGCCCAGGTCCT 57.159 34.783 0.00 0.00 0.00 3.85
940 941 8.113062 GCGATCTGCACATATATAAGATTGAAC 58.887 37.037 10.81 0.00 45.45 3.18
1257 1258 4.039124 ACACATTTGACCATTTGAAGGACC 59.961 41.667 0.00 0.00 0.00 4.46
1339 1340 4.684724 TGTTCTACCTCCCAATCACTAGT 58.315 43.478 0.00 0.00 0.00 2.57
1360 1361 1.639635 CCCCATTGTCCCTCTCCCTG 61.640 65.000 0.00 0.00 0.00 4.45
1392 1393 6.882610 TTCTGCTGATCTACACATTGTTTT 57.117 33.333 0.00 0.00 0.00 2.43
1459 1460 1.572085 GCACGTGCATCTTCAGCTGT 61.572 55.000 34.52 0.00 41.59 4.40
1492 1493 7.648039 TCTTCCTAAAAACTGGCAACTTTTA 57.352 32.000 11.02 11.02 37.61 1.52
1709 1713 1.470098 CTTCCCCAAGCATCTTGTTCG 59.530 52.381 5.92 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.