Multiple sequence alignment - TraesCS2D01G269100

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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 TraesCS2D01G269100 chr2D 100.000 3128 0 0 1 3128 330753289 330750162 0.000000e+00 5777.0
1 TraesCS2D01G269100 chr2A 92.605 2745 91 29 468 3128 437977332 437974616 0.000000e+00 3842.0
2 TraesCS2D01G269100 chr2A 94.737 399 3 1 13 393 437977731 437977333 3.450000e-169 604.0
3 TraesCS2D01G269100 chr2B 91.626 2687 78 59 12 2595 399355502 399352860 0.000000e+00 3579.0
4 TraesCS2D01G269100 chr2B 92.505 1014 30 13 2151 3128 399353296 399352293 0.000000e+00 1410.0
5 TraesCS2D01G269100 chr3D 84.722 216 30 2 2660 2874 615374340 615374553 2.440000e-51 213.0
6 TraesCS2D01G269100 chr1B 100.000 36 0 0 189 224 677125908 677125873 2.010000e-07 67.6


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 TraesCS2D01G269100 chr2D 330750162 330753289 3127 True 5777.0 5777 100.0000 1 3128 1 chr2D.!!$R1 3127
1 TraesCS2D01G269100 chr2A 437974616 437977731 3115 True 2223.0 3842 93.6710 13 3128 2 chr2A.!!$R1 3115
2 TraesCS2D01G269100 chr2B 399352293 399355502 3209 True 2494.5 3579 92.0655 12 3128 2 chr2B.!!$R1 3116

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
555 593 0.322456 TTGCTGGCGAGGTTATGCTT 60.322 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 2697 0.029567 TTTACCTTGCCGTTTGTGCG 59.97 50.0 0.0 0.0 0.0 5.34 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
316 335 2.034179 CGGTTCCTTGTTTGTTCTTCCC 59.966 50.000 0.00 0.00 0.00 3.97
381 413 1.893801 CGGGTTTCTAGACAGACAGGT 59.106 52.381 0.00 0.00 0.00 4.00
397 429 4.081586 AGACAGGTATTCTTCGGTTCTTCC 60.082 45.833 0.00 0.00 0.00 3.46
399 431 4.286291 ACAGGTATTCTTCGGTTCTTCCTT 59.714 41.667 0.00 0.00 0.00 3.36
400 432 5.221864 ACAGGTATTCTTCGGTTCTTCCTTT 60.222 40.000 0.00 0.00 0.00 3.11
401 433 5.351740 CAGGTATTCTTCGGTTCTTCCTTTC 59.648 44.000 0.00 0.00 0.00 2.62
555 593 0.322456 TTGCTGGCGAGGTTATGCTT 60.322 50.000 0.00 0.00 0.00 3.91
611 677 4.451774 CGGACGGAGGTTCTAGATTAGTAG 59.548 50.000 0.00 0.00 0.00 2.57
1088 1163 4.400961 GCCCTCCAGCAGCGAGTT 62.401 66.667 0.00 0.00 0.00 3.01
1785 1887 1.203050 CCTGTGGACCTGAAACCCATT 60.203 52.381 0.00 0.00 31.94 3.16
1937 2066 2.023673 GGTTGCCGATGAATTGGATCA 58.976 47.619 0.34 0.00 32.77 2.92
1944 2073 0.664761 ATGAATTGGATCAAGCGGCG 59.335 50.000 0.51 0.51 32.06 6.46
1956 2085 2.493907 AAGCGGCGGAGACAGAAGAC 62.494 60.000 9.78 0.00 27.25 3.01
1975 2104 0.229753 CGCTATAACGAAGGCAAGCG 59.770 55.000 0.00 0.00 45.48 4.68
2178 2311 1.825191 CCAATCCTGGGTGCATCCG 60.825 63.158 12.39 6.18 39.30 4.18
2218 2383 1.546029 CATGGTTCCTCGAGTGTCAGA 59.454 52.381 12.31 0.00 0.00 3.27
2219 2384 1.248486 TGGTTCCTCGAGTGTCAGAG 58.752 55.000 12.31 0.00 0.00 3.35
2540 2710 0.109272 TTTGAACGCACAAACGGCAA 60.109 45.000 3.97 0.00 35.29 4.52
2541 2711 0.524392 TTGAACGCACAAACGGCAAG 60.524 50.000 0.00 0.00 37.37 4.01
2542 2712 1.657181 GAACGCACAAACGGCAAGG 60.657 57.895 0.00 0.00 37.37 3.61
2543 2713 2.331019 GAACGCACAAACGGCAAGGT 62.331 55.000 0.00 0.00 37.37 3.50
2548 2718 1.601914 GCACAAACGGCAAGGTAAAGG 60.602 52.381 0.00 0.00 0.00 3.11
2549 2719 0.671796 ACAAACGGCAAGGTAAAGGC 59.328 50.000 0.00 0.00 0.00 4.35
2550 2720 0.038618 CAAACGGCAAGGTAAAGGCC 60.039 55.000 0.00 0.00 44.27 5.19
2553 2723 2.353573 GGCAAGGTAAAGGCCGGA 59.646 61.111 5.05 0.00 38.04 5.14
2555 2725 1.313091 GGCAAGGTAAAGGCCGGAAG 61.313 60.000 5.05 0.00 38.04 3.46
2579 2749 2.282827 GGGGGTATTTTGGCCACAC 58.717 57.895 3.88 0.44 0.00 3.82
2650 2845 3.314357 CGTCCGTGGTTCTGTATGATAGA 59.686 47.826 0.00 0.00 0.00 1.98
2728 2923 2.597510 GGTGGGGCAGTCCAACAC 60.598 66.667 0.00 0.00 43.75 3.32
2818 3013 4.242602 GGTGAGGCCCAAGCATAC 57.757 61.111 0.00 0.00 42.56 2.39
2909 3104 4.082949 TCGTGAAACACTACGTCTCATCAT 60.083 41.667 0.00 0.00 40.87 2.45
2923 3118 5.923114 CGTCTCATCATATTTCCTACCACAG 59.077 44.000 0.00 0.00 0.00 3.66
2924 3119 6.239036 CGTCTCATCATATTTCCTACCACAGA 60.239 42.308 0.00 0.00 0.00 3.41
2925 3120 7.151308 GTCTCATCATATTTCCTACCACAGAG 58.849 42.308 0.00 0.00 0.00 3.35
2926 3121 6.268617 TCTCATCATATTTCCTACCACAGAGG 59.731 42.308 0.00 0.00 45.67 3.69
3032 3238 2.969157 TGGCACACATTTTTGCACG 58.031 47.368 0.00 0.00 40.75 5.34
3098 3304 3.978723 CTCTGAGGACGCCTGCACG 62.979 68.421 2.98 0.00 31.76 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.040359 GGAAGGAGGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
1 2 4.089757 CGGAAGGAGGGGAGGGGA 62.090 72.222 0.00 0.00 0.00 4.81
2 3 4.416601 ACGGAAGGAGGGGAGGGG 62.417 72.222 0.00 0.00 0.00 4.79
3 4 3.083997 CACGGAAGGAGGGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
4 5 3.787001 GCACGGAAGGAGGGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
5 6 2.685380 AGCACGGAAGGAGGGGAG 60.685 66.667 0.00 0.00 0.00 4.30
6 7 3.003173 CAGCACGGAAGGAGGGGA 61.003 66.667 0.00 0.00 0.00 4.81
7 8 4.785453 GCAGCACGGAAGGAGGGG 62.785 72.222 0.00 0.00 0.00 4.79
316 335 1.594293 ACGGACAGCAACGACCAAG 60.594 57.895 0.00 0.00 0.00 3.61
381 413 5.492855 TGGAAAGGAAGAACCGAAGAATA 57.507 39.130 0.00 0.00 44.74 1.75
397 429 1.039233 ATTCCCTGCGGCATGGAAAG 61.039 55.000 33.31 10.27 40.43 2.62
399 431 0.257328 TTATTCCCTGCGGCATGGAA 59.743 50.000 32.31 32.31 41.07 3.53
400 432 0.478072 ATTATTCCCTGCGGCATGGA 59.522 50.000 21.07 21.07 0.00 3.41
401 433 1.000060 CAATTATTCCCTGCGGCATGG 60.000 52.381 17.09 17.09 0.00 3.66
508 546 7.176515 TGCAAGGAAGCTATCAAACAAGAAATA 59.823 33.333 0.00 0.00 34.99 1.40
569 607 2.094545 CCGTACCAGCTACCTTTAACGT 60.095 50.000 0.00 0.00 0.00 3.99
571 609 3.515630 GTCCGTACCAGCTACCTTTAAC 58.484 50.000 0.00 0.00 0.00 2.01
576 614 1.751927 CCGTCCGTACCAGCTACCT 60.752 63.158 0.00 0.00 0.00 3.08
579 617 1.452651 CCTCCGTCCGTACCAGCTA 60.453 63.158 0.00 0.00 0.00 3.32
748 818 5.106475 ACGACAAAAATAAGCTTATCGCCAA 60.106 36.000 19.11 0.00 40.39 4.52
1508 1610 2.538141 CCACCTCTCAAAGCCCCCA 61.538 63.158 0.00 0.00 0.00 4.96
1613 1715 2.846532 CACCCCTTGGCCTTGAGT 59.153 61.111 3.32 0.00 33.59 3.41
1785 1887 0.537143 AAGCGGAAACAGCCATGTCA 60.537 50.000 0.00 0.00 39.29 3.58
1937 2066 2.262915 CTTCTGTCTCCGCCGCTT 59.737 61.111 0.00 0.00 0.00 4.68
1944 2073 3.311871 TCGTTATAGCGTCTTCTGTCTCC 59.688 47.826 8.89 0.00 0.00 3.71
1956 2085 0.229753 CGCTTGCCTTCGTTATAGCG 59.770 55.000 2.12 2.12 44.18 4.26
2068 2197 1.002857 AAGGCCTTCACCCTGCTATT 58.997 50.000 13.78 0.00 31.73 1.73
2070 2199 1.685224 CAAGGCCTTCACCCTGCTA 59.315 57.895 17.29 0.00 31.73 3.49
2145 2278 2.805099 GGATTGGTCGATCAGCAGAATC 59.195 50.000 0.00 0.00 32.85 2.52
2146 2279 2.437281 AGGATTGGTCGATCAGCAGAAT 59.563 45.455 0.00 0.00 32.85 2.40
2178 2311 4.841443 TGATCACAGCATATTCAATGCC 57.159 40.909 6.36 0.00 45.59 4.40
2218 2383 5.646360 CCAAGGAAACCATCGTATAAACACT 59.354 40.000 0.00 0.00 0.00 3.55
2219 2384 5.413523 ACCAAGGAAACCATCGTATAAACAC 59.586 40.000 0.00 0.00 0.00 3.32
2527 2697 0.029567 TTTACCTTGCCGTTTGTGCG 59.970 50.000 0.00 0.00 0.00 5.34
2540 2710 2.306384 CCCCTTCCGGCCTTTACCT 61.306 63.158 0.00 0.00 0.00 3.08
2541 2711 2.266816 CTCCCCTTCCGGCCTTTACC 62.267 65.000 0.00 0.00 0.00 2.85
2542 2712 1.223763 CTCCCCTTCCGGCCTTTAC 59.776 63.158 0.00 0.00 0.00 2.01
2543 2713 1.999002 CCTCCCCTTCCGGCCTTTA 60.999 63.158 0.00 0.00 0.00 1.85
2579 2749 3.750652 GCTCTCTGGTCCTTTCTTTTGAG 59.249 47.826 0.00 0.00 0.00 3.02
2650 2845 3.745799 TGACTCTCTTGTCGTTCTCTCT 58.254 45.455 0.00 0.00 39.64 3.10
2728 2923 1.126488 TTGAGGCTCCAGCTGGATAG 58.874 55.000 35.11 24.89 44.46 2.08
2818 3013 2.224523 TGGTTCTGTAGCCCTGAACTTG 60.225 50.000 17.45 0.00 45.95 3.16
2909 3104 2.124411 GGCCCTCTGTGGTAGGAAATA 58.876 52.381 0.00 0.00 36.08 1.40
2923 3118 2.436824 GCCTCTCAAACGGCCCTC 60.437 66.667 0.00 0.00 40.43 4.30
2924 3119 2.606587 ATGCCTCTCAAACGGCCCT 61.607 57.895 0.00 0.00 45.71 5.19
2925 3120 2.044946 ATGCCTCTCAAACGGCCC 60.045 61.111 0.00 0.00 45.71 5.80
2926 3121 2.409870 CCATGCCTCTCAAACGGCC 61.410 63.158 0.00 0.00 45.71 6.13
3032 3238 5.233988 AGCATTACTCTAGCGAAATCATCC 58.766 41.667 0.00 0.00 0.00 3.51
3098 3304 4.920340 CGATCAATACTGATACTGACTGCC 59.080 45.833 0.00 0.00 42.60 4.85


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

AutoCloner maintained by Alex Coulton.