Multiple sequence alignment - TraesCS5B01G363000

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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 TraesCS5B01G363000 chr5B 100.000 3684 0 0 1 3684 541960241 541963924 0 6804
1 TraesCS5B01G363000 chr5B 95.964 3692 132 13 1 3684 688572462 688576144 0 5976
2 TraesCS5B01G363000 chr5B 92.940 3697 215 20 1 3684 513861073 513864736 0 5339
3 TraesCS5B01G363000 chr5B 89.212 3717 318 45 1 3684 291232183 291235849 0 4566
4 TraesCS5B01G363000 chr1B 96.105 3697 127 9 1 3684 661025747 661029439 0 6013
5 TraesCS5B01G363000 chr1B 95.650 3701 131 16 1 3684 584639303 584635616 0 5915
6 TraesCS5B01G363000 chr6B 95.593 3699 134 14 1 3684 633817300 633820984 0 5901
7 TraesCS5B01G363000 chr6B 94.807 3697 146 19 1 3684 633493049 633496712 0 5722
8 TraesCS5B01G363000 chr3B 94.892 3700 157 12 1 3684 767572755 767576438 0 5757
9 TraesCS5B01G363000 chr3B 89.176 3714 323 41 5 3684 306803615 306807283 0 4558
10 TraesCS5B01G363000 chr3B 84.888 986 119 22 1 976 661696836 661695871 0 968
11 TraesCS5B01G363000 chr3B 89.364 771 73 9 1 764 709810864 709811632 0 961
12 TraesCS5B01G363000 chr3B 83.489 963 129 25 21 957 555264546 555263588 0 870
13 TraesCS5B01G363000 chr7B 94.834 3697 159 23 1 3684 142425304 142421627 0 5740
14 TraesCS5B01G363000 chr4B 95.840 3510 123 14 182 3684 95359623 95356130 0 5651


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 TraesCS5B01G363000 chr5B 541960241 541963924 3683 False 6804 6804 100.000 1 3684 1 chr5B.!!$F3 3683
1 TraesCS5B01G363000 chr5B 688572462 688576144 3682 False 5976 5976 95.964 1 3684 1 chr5B.!!$F4 3683
2 TraesCS5B01G363000 chr5B 513861073 513864736 3663 False 5339 5339 92.940 1 3684 1 chr5B.!!$F2 3683
3 TraesCS5B01G363000 chr5B 291232183 291235849 3666 False 4566 4566 89.212 1 3684 1 chr5B.!!$F1 3683
4 TraesCS5B01G363000 chr1B 661025747 661029439 3692 False 6013 6013 96.105 1 3684 1 chr1B.!!$F1 3683
5 TraesCS5B01G363000 chr1B 584635616 584639303 3687 True 5915 5915 95.650 1 3684 1 chr1B.!!$R1 3683
6 TraesCS5B01G363000 chr6B 633817300 633820984 3684 False 5901 5901 95.593 1 3684 1 chr6B.!!$F2 3683
7 TraesCS5B01G363000 chr6B 633493049 633496712 3663 False 5722 5722 94.807 1 3684 1 chr6B.!!$F1 3683
8 TraesCS5B01G363000 chr3B 767572755 767576438 3683 False 5757 5757 94.892 1 3684 1 chr3B.!!$F3 3683
9 TraesCS5B01G363000 chr3B 306803615 306807283 3668 False 4558 4558 89.176 5 3684 1 chr3B.!!$F1 3679
10 TraesCS5B01G363000 chr3B 661695871 661696836 965 True 968 968 84.888 1 976 1 chr3B.!!$R2 975
11 TraesCS5B01G363000 chr3B 709810864 709811632 768 False 961 961 89.364 1 764 1 chr3B.!!$F2 763
12 TraesCS5B01G363000 chr3B 555263588 555264546 958 True 870 870 83.489 21 957 1 chr3B.!!$R1 936
13 TraesCS5B01G363000 chr7B 142421627 142425304 3677 True 5740 5740 94.834 1 3684 1 chr7B.!!$R1 3683
14 TraesCS5B01G363000 chr4B 95356130 95359623 3493 True 5651 5651 95.840 182 3684 1 chr4B.!!$R1 3502

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
976 1041 1.414158 GGTATCTGCCAGGACAGCTA 58.586 55.0 6.12 0.0 37.59 3.32 F
1226 1291 0.326264 GCTCCATCTCCTGTTGGTGT 59.674 55.0 0.00 0.0 35.22 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2709 0.598562 AGATACCGTATCTGCAGGCG 59.401 55.0 18.47 15.46 43.59 5.52 R
2793 2883 1.531423 CTCCTTCATGTGCTTGCTGT 58.469 50.0 0.00 0.00 0.00 4.40 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
58 60 2.288579 TGGTTGACGAGCAGTTACGAAT 60.289 45.455 0.00 0.00 0.00 3.34
136 141 2.813726 CGGTGACACCCCTTCCACA 61.814 63.158 19.11 0.00 33.75 4.17
150 155 2.398754 TCCACAAGGTCTTCTCCTCA 57.601 50.000 0.00 0.00 36.74 3.86
460 484 2.858745 ACTGCCATCTTTTACCGTTGT 58.141 42.857 0.00 0.00 0.00 3.32
769 826 2.958818 AGCATATCAGTAAGGACCCGA 58.041 47.619 0.00 0.00 0.00 5.14
772 829 3.258372 GCATATCAGTAAGGACCCGATCA 59.742 47.826 0.00 0.00 0.00 2.92
796 853 3.880490 ACGCCTACATTCAAAGTTGTCAA 59.120 39.130 0.00 0.00 0.00 3.18
976 1041 1.414158 GGTATCTGCCAGGACAGCTA 58.586 55.000 6.12 0.00 37.59 3.32
1213 1278 1.303888 CCTGGCACAACAGCTCCAT 60.304 57.895 0.00 0.00 38.70 3.41
1226 1291 0.326264 GCTCCATCTCCTGTTGGTGT 59.674 55.000 0.00 0.00 35.22 4.16
1240 1305 5.127194 CCTGTTGGTGTAGATACTGCTAAGA 59.873 44.000 0.00 0.00 0.00 2.10
1242 1307 5.479027 TGTTGGTGTAGATACTGCTAAGACA 59.521 40.000 0.00 0.00 0.00 3.41
1359 1424 2.496470 AGACGAGTCTGGTTATGTTCCC 59.504 50.000 4.78 0.00 38.75 3.97
1590 1655 5.444663 ACAAGAAGATTGTCAAGAAAGCC 57.555 39.130 0.00 0.00 0.00 4.35
1618 1683 1.324740 TACCGCTGATAACACGCCCT 61.325 55.000 0.00 0.00 0.00 5.19
1653 1718 1.478510 CCCGATCATTCTATAGCGGCT 59.521 52.381 7.98 7.98 37.57 5.52
1894 1959 0.944386 GAAGGCTGTCAAGTTCGCAA 59.056 50.000 0.00 0.00 0.00 4.85
2306 2391 4.331108 TGTAGTTGCTGTGATATGGCAAA 58.669 39.130 0.00 0.00 45.49 3.68
2619 2709 1.551883 AGGGCAATCAAGTTCCAATGC 59.448 47.619 0.00 0.00 0.00 3.56
2744 2834 3.685550 CGAATTCAGGGCCACTAAGGAAT 60.686 47.826 6.18 2.58 41.22 3.01
2785 2875 1.035923 TCAAGCGGTTTGGAAATGCA 58.964 45.000 0.00 0.00 37.39 3.96
2793 2883 1.135094 TTTGGAAATGCAAGGGCCAA 58.865 45.000 6.18 8.92 40.13 4.52
2904 3005 4.707105 TCGTACTTCCTATACACGATCCA 58.293 43.478 0.00 0.00 36.77 3.41
3050 3153 0.904865 TGGGTGATCTTGCCGAGTCT 60.905 55.000 0.00 0.00 0.00 3.24
3203 3306 3.138283 ACTTCCACCACAAAATCCTGAGA 59.862 43.478 0.00 0.00 0.00 3.27
3494 3604 3.692593 ACCCATAACCAAACATTCTACGC 59.307 43.478 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 43 4.548494 TGTTTATTCGTAACTGCTCGTCA 58.452 39.130 0.00 0.00 0.00 4.35
136 141 2.683867 CGTCGTATGAGGAGAAGACCTT 59.316 50.000 0.00 0.00 40.73 3.50
150 155 0.109597 GGTGTTGGTCGTCGTCGTAT 60.110 55.000 1.33 0.00 38.33 3.06
403 423 6.942576 ACAGTAAGAGTTGTCATTTGGCTTAT 59.057 34.615 0.00 0.00 0.00 1.73
415 435 5.247564 TGCCATTAGGTACAGTAAGAGTTGT 59.752 40.000 0.00 0.00 37.19 3.32
769 826 5.009610 ACAACTTTGAATGTAGGCGTTTGAT 59.990 36.000 0.00 0.00 0.00 2.57
772 829 4.336993 TGACAACTTTGAATGTAGGCGTTT 59.663 37.500 0.00 0.00 0.00 3.60
796 853 0.038744 CATCTGAGTTGCCCCCTGTT 59.961 55.000 0.00 0.00 0.00 3.16
915 980 1.675714 CGGATGCCTGTTGTTCTAGCA 60.676 52.381 0.00 0.00 37.94 3.49
976 1041 7.938140 TTGCTAGTAGAGTTGGCAATATTTT 57.062 32.000 1.92 0.00 37.87 1.82
1213 1278 3.447586 GCAGTATCTACACCAACAGGAGA 59.552 47.826 0.00 0.00 0.00 3.71
1226 1291 7.027760 CGAAACAGTTGTCTTAGCAGTATCTA 58.972 38.462 0.00 0.00 0.00 1.98
1240 1305 0.311790 CCAGCATGCGAAACAGTTGT 59.688 50.000 13.01 0.00 31.97 3.32
1242 1307 0.593128 GACCAGCATGCGAAACAGTT 59.407 50.000 13.01 0.00 31.97 3.16
1359 1424 3.041940 GGGAACAGTGTGGACGCG 61.042 66.667 3.53 3.53 0.00 6.01
1484 1549 0.251386 TTCCAATGCGGGTAAAGGCA 60.251 50.000 0.00 0.00 44.29 4.75
1608 1673 4.715523 GCAGGGCAGGGCGTGTTA 62.716 66.667 15.40 0.00 0.00 2.41
1618 1683 2.051518 CGGGCTTATTTGCAGGGCA 61.052 57.895 0.00 0.00 36.47 5.36
1653 1718 8.722480 AAAGATCGACAAACATATCTGAATCA 57.278 30.769 0.00 0.00 0.00 2.57
1858 1923 1.198094 TTCCTGCCCTCGACCATTGA 61.198 55.000 0.00 0.00 0.00 2.57
1894 1959 1.165270 GTACCTTGCACAATCGGCTT 58.835 50.000 0.00 0.00 0.00 4.35
2246 2331 1.734707 GCTGCACTTGCCATGTGATTC 60.735 52.381 14.30 0.00 41.18 2.52
2306 2391 7.837689 TGTAGTTACCATCTAGTTGGACTGTAT 59.162 37.037 23.87 5.42 39.25 2.29
2619 2709 0.598562 AGATACCGTATCTGCAGGCG 59.401 55.000 18.47 15.46 43.59 5.52
2744 2834 3.072211 CGATATCGTACAGCTGGGTCTA 58.928 50.000 19.93 3.30 34.11 2.59
2785 2875 2.123338 TGCTTGCTGTTGGCCCTT 60.123 55.556 0.00 0.00 40.92 3.95
2793 2883 1.531423 CTCCTTCATGTGCTTGCTGT 58.469 50.000 0.00 0.00 0.00 4.40
3050 3153 2.054232 TTTTACCGTTTGGCCTCACA 57.946 45.000 3.32 0.00 39.70 3.58
3203 3306 4.111916 CACCGTGTTGAGCAAAATTCTTT 58.888 39.130 0.00 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.