Multiple sequence alignment - TraesCS5B01G079000

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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 TraesCS5B01G079000 chr5B 100.000 2951 0 0 1 2951 96140473 96137523 0.000000e+00 5450
1 TraesCS5B01G079000 chr5D 96.383 2958 90 12 1 2951 90925829 90922882 0.000000e+00 4854
2 TraesCS5B01G079000 chr5D 90.132 152 15 0 1 152 441345040 441345191 6.450000e-47 198
3 TraesCS5B01G079000 chr5A 96.377 2953 84 14 1 2951 84389674 84386743 0.000000e+00 4839
4 TraesCS5B01G079000 chr4D 92.361 144 11 0 2 145 495615937 495616080 3.860000e-49 206
5 TraesCS5B01G079000 chr3B 91.391 151 10 1 2 152 20422490 20422343 1.390000e-48 204
6 TraesCS5B01G079000 chr7D 91.724 145 12 0 1 145 632120966 632120822 4.990000e-48 202
7 TraesCS5B01G079000 chr1D 91.724 145 12 0 1 145 463333296 463333440 4.990000e-48 202
8 TraesCS5B01G079000 chr3D 90.728 151 11 1 2 152 41272418 41272565 6.450000e-47 198
9 TraesCS5B01G079000 chr3D 90.132 152 14 1 1 152 577459128 577458978 2.320000e-46 196
10 TraesCS5B01G079000 chr7A 89.241 158 16 1 2 158 734077859 734077702 2.320000e-46 196


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 TraesCS5B01G079000 chr5B 96137523 96140473 2950 True 5450 5450 100.000 1 2951 1 chr5B.!!$R1 2950
1 TraesCS5B01G079000 chr5D 90922882 90925829 2947 True 4854 4854 96.383 1 2951 1 chr5D.!!$R1 2950
2 TraesCS5B01G079000 chr5A 84386743 84389674 2931 True 4839 4839 96.377 1 2951 1 chr5A.!!$R1 2950

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
43 44 0.320247 CCTTCAGCTCGCTTCAGTGT 60.320 55.0 0.00 0.00 0.0 3.55 F
642 646 0.393402 GTAGTTCGCCCCGGGATTTT 60.393 55.0 26.32 4.63 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1782 0.397941 TTACAGCAGCAGAGGCACTT 59.602 50.0 0.0 0.0 41.55 3.16 R
2517 2524 0.257905 TTGCGAGGGCTCCTAGTCTA 59.742 55.0 0.0 0.0 40.82 2.59 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
43 44 0.320247 CCTTCAGCTCGCTTCAGTGT 60.320 55.000 0.00 0.00 0.00 3.55
54 55 2.538449 CGCTTCAGTGTTTGTAGTCGTT 59.462 45.455 0.00 0.00 0.00 3.85
64 65 3.855689 TTGTAGTCGTTACTAGGTGGC 57.144 47.619 0.00 0.00 38.89 5.01
72 73 2.314246 GTTACTAGGTGGCCTACGGAT 58.686 52.381 3.32 0.00 34.61 4.18
445 448 1.721691 ACCAGGGATCAAAATTGGGGA 59.278 47.619 0.00 0.00 33.20 4.81
446 449 2.113414 ACCAGGGATCAAAATTGGGGAA 59.887 45.455 0.00 0.00 33.20 3.97
514 517 2.491621 CTCATCGGTGAGCTCGCA 59.508 61.111 27.48 9.68 44.86 5.10
529 532 2.473816 CTCGCATTTCGCTCTTGGATA 58.526 47.619 0.00 0.00 39.08 2.59
594 598 2.025699 CCGTCCTTCTTCCCCCAATTTA 60.026 50.000 0.00 0.00 0.00 1.40
642 646 0.393402 GTAGTTCGCCCCGGGATTTT 60.393 55.000 26.32 4.63 0.00 1.82
1552 1558 4.054671 CCAGAATTCTCAGCCTTCGATAC 58.945 47.826 4.57 0.00 0.00 2.24
1560 1566 3.829601 CTCAGCCTTCGATACCTTATCCT 59.170 47.826 0.00 0.00 31.43 3.24
1611 1617 1.749638 AGGTAGCGAGGACCTGTCG 60.750 63.158 0.00 0.00 45.90 4.35
1662 1668 5.391097 CGAAGGACTTAGCATATCCGTAGAG 60.391 48.000 0.00 0.00 37.60 2.43
1776 1782 2.169352 GAGGATGCCAGAAGCTAACAGA 59.831 50.000 0.00 0.00 44.23 3.41
1832 1838 2.086869 TGCCACTGCTTCAGATTTAGC 58.913 47.619 0.29 0.00 38.71 3.09
2265 2271 2.268076 CCAGGTTCCGTTGCTTGGG 61.268 63.158 0.00 0.00 0.00 4.12
2390 2396 0.178981 ACCATGCACTTGGAAGCAGT 60.179 50.000 13.35 0.00 44.94 4.40
2446 2453 2.237392 CCTTCCTCTTCGGAGTTTCCAT 59.763 50.000 0.00 0.00 44.28 3.41
2517 2524 4.708177 ACTAGCATTTGTTCTGACAGTGT 58.292 39.130 0.00 0.00 37.04 3.55
2582 2589 0.532573 TTGGATCTCACGGTGCTCTC 59.467 55.000 2.51 0.00 0.00 3.20
2668 2675 0.686441 ATGGGCTGCTACTCCACGTA 60.686 55.000 0.00 0.00 32.90 3.57
2724 2731 4.441695 CTCCGAGCTCGCCTGCAA 62.442 66.667 30.49 9.58 38.18 4.08
2828 2835 3.876309 TGTTTTGAGGGACTTAAGCCT 57.124 42.857 1.29 1.46 41.55 4.58
2829 2836 4.178956 TGTTTTGAGGGACTTAAGCCTT 57.821 40.909 1.29 1.22 41.55 4.35
2869 2876 6.875726 TCTTCAATCCCTGATATAATGCTTCG 59.124 38.462 0.00 0.00 32.78 3.79
2870 2877 6.114187 TCAATCCCTGATATAATGCTTCGT 57.886 37.500 0.00 0.00 0.00 3.85
2924 2932 1.244816 GTTCCCTTTGGTTCTTCCCG 58.755 55.000 0.00 0.00 34.77 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.224066 ACTACAAACACTGAAGCGAGCT 60.224 45.455 0.00 0.00 0.00 4.09
43 44 3.056607 GGCCACCTAGTAACGACTACAAA 60.057 47.826 0.00 0.00 37.10 2.83
97 98 3.386486 TCATGACAGTACAACGAACACC 58.614 45.455 0.00 0.00 0.00 4.16
153 154 8.026607 GCTCACCATAAGTGTTGCTTATAAAAA 58.973 33.333 0.00 0.00 45.77 1.94
154 155 7.175816 TGCTCACCATAAGTGTTGCTTATAAAA 59.824 33.333 12.03 0.00 45.77 1.52
155 156 6.657117 TGCTCACCATAAGTGTTGCTTATAAA 59.343 34.615 12.03 0.00 45.77 1.40
171 174 4.895668 AATTGTTTGGATTGCTCACCAT 57.104 36.364 0.00 0.00 36.02 3.55
219 222 3.312973 TCACACGTGCCGAAATAAAAACT 59.687 39.130 17.22 0.00 0.00 2.66
514 517 4.137543 GACCCAATATCCAAGAGCGAAAT 58.862 43.478 0.00 0.00 0.00 2.17
529 532 1.451387 GCCGAATCCACGACCCAAT 60.451 57.895 0.00 0.00 35.09 3.16
594 598 2.091665 AGATGCCAATTTCCCCGAGAAT 60.092 45.455 0.00 0.00 33.44 2.40
642 646 4.638421 ACCTCGAATTTCACAAACTTGACA 59.362 37.500 0.00 0.00 0.00 3.58
1443 1449 1.280133 CTGGCTTGATCAACCTCCTCA 59.720 52.381 20.58 7.57 0.00 3.86
1530 1536 2.680312 TCGAAGGCTGAGAATTCTGG 57.320 50.000 14.00 6.68 0.00 3.86
1552 1558 9.956640 ATTATAGCAAATCTCTGAAGGATAAGG 57.043 33.333 0.00 0.00 0.00 2.69
1611 1617 7.602517 TTTCAGCTTATTCTCAAGTAGCTTC 57.397 36.000 0.00 0.00 40.01 3.86
1644 1650 4.261656 GCACACTCTACGGATATGCTAAGT 60.262 45.833 0.00 0.00 0.00 2.24
1662 1668 1.731160 GAGTTCAGCAGATCAGCACAC 59.269 52.381 13.03 5.65 36.85 3.82
1776 1782 0.397941 TTACAGCAGCAGAGGCACTT 59.602 50.000 0.00 0.00 41.55 3.16
1832 1838 2.039084 AGTGAAGCTTGGTAGGAACAGG 59.961 50.000 2.10 0.00 0.00 4.00
2446 2453 4.873827 GTCGTGCCAAAATTCAGATACCTA 59.126 41.667 0.00 0.00 0.00 3.08
2492 2499 5.911280 CACTGTCAGAACAAATGCTAGTTTG 59.089 40.000 6.91 4.68 43.11 2.93
2517 2524 0.257905 TTGCGAGGGCTCCTAGTCTA 59.742 55.000 0.00 0.00 40.82 2.59
2668 2675 2.290960 GGTGGATAGAAGCCCAAACTGT 60.291 50.000 0.00 0.00 33.69 3.55
2723 2730 3.005554 CGAAGAGAGCCATCACACATTT 58.994 45.455 0.00 0.00 0.00 2.32
2724 2731 2.027745 ACGAAGAGAGCCATCACACATT 60.028 45.455 0.00 0.00 0.00 2.71
2828 2835 4.360405 GAGGCGGGAGGGGCAAAA 62.360 66.667 0.00 0.00 34.40 2.44
2869 2876 5.948992 AGGAGCAGAAAGAATACACAAAC 57.051 39.130 0.00 0.00 0.00 2.93
2870 2877 7.624549 AGATAGGAGCAGAAAGAATACACAAA 58.375 34.615 0.00 0.00 0.00 2.83
2924 2932 4.702131 AGGCCAGTTATTCAAACATCAGTC 59.298 41.667 5.01 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.