Multiple sequence alignment - TraesCS3A01G290600

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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 TraesCS3A01G290600 chr3A 100.000 2736 0 0 1 2736 519408036 519405301 0 5053
1 TraesCS3A01G290600 chr3A 92.743 2742 173 8 1 2736 489938533 489935812 0 3938
2 TraesCS3A01G290600 chr3A 87.450 2749 309 28 10 2733 171435826 171438563 0 3133
3 TraesCS3A01G290600 chr3A 86.403 2758 343 22 2 2733 182404210 182406961 0 2987
4 TraesCS3A01G290600 chr2A 92.597 2742 184 10 9 2736 588107556 588110292 0 3921
5 TraesCS3A01G290600 chr2A 87.055 2696 322 18 1 2674 370047367 370050057 0 3020
6 TraesCS3A01G290600 chr2A 85.927 2757 352 27 1 2736 264093284 264090543 0 2909
7 TraesCS3A01G290600 chr2A 85.964 2750 331 28 10 2736 651148293 651151010 0 2889
8 TraesCS3A01G290600 chr2A 81.772 2754 431 46 8 2733 160234984 160232274 0 2239
9 TraesCS3A01G290600 chr2A 80.956 1465 243 22 1 1440 457413743 457415196 0 1127
10 TraesCS3A01G290600 chr7A 88.466 2757 279 30 7 2736 94527849 94530593 0 3293
11 TraesCS3A01G290600 chr7A 88.808 2609 269 12 10 2601 726821100 726823702 0 3179
12 TraesCS3A01G290600 chr7A 86.270 2753 347 22 2 2733 658249007 658251749 0 2961
13 TraesCS3A01G290600 chr5A 88.848 2690 276 14 2 2674 336429178 336431860 0 3284
14 TraesCS3A01G290600 chr5A 86.981 2696 325 19 1 2674 350641588 350644279 0 3011


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 TraesCS3A01G290600 chr3A 519405301 519408036 2735 True 5053 5053 100.000 1 2736 1 chr3A.!!$R2 2735
1 TraesCS3A01G290600 chr3A 489935812 489938533 2721 True 3938 3938 92.743 1 2736 1 chr3A.!!$R1 2735
2 TraesCS3A01G290600 chr3A 171435826 171438563 2737 False 3133 3133 87.450 10 2733 1 chr3A.!!$F1 2723
3 TraesCS3A01G290600 chr3A 182404210 182406961 2751 False 2987 2987 86.403 2 2733 1 chr3A.!!$F2 2731
4 TraesCS3A01G290600 chr2A 588107556 588110292 2736 False 3921 3921 92.597 9 2736 1 chr2A.!!$F3 2727
5 TraesCS3A01G290600 chr2A 370047367 370050057 2690 False 3020 3020 87.055 1 2674 1 chr2A.!!$F1 2673
6 TraesCS3A01G290600 chr2A 264090543 264093284 2741 True 2909 2909 85.927 1 2736 1 chr2A.!!$R2 2735
7 TraesCS3A01G290600 chr2A 651148293 651151010 2717 False 2889 2889 85.964 10 2736 1 chr2A.!!$F4 2726
8 TraesCS3A01G290600 chr2A 160232274 160234984 2710 True 2239 2239 81.772 8 2733 1 chr2A.!!$R1 2725
9 TraesCS3A01G290600 chr2A 457413743 457415196 1453 False 1127 1127 80.956 1 1440 1 chr2A.!!$F2 1439
10 TraesCS3A01G290600 chr7A 94527849 94530593 2744 False 3293 3293 88.466 7 2736 1 chr7A.!!$F1 2729
11 TraesCS3A01G290600 chr7A 726821100 726823702 2602 False 3179 3179 88.808 10 2601 1 chr7A.!!$F3 2591
12 TraesCS3A01G290600 chr7A 658249007 658251749 2742 False 2961 2961 86.270 2 2733 1 chr7A.!!$F2 2731
13 TraesCS3A01G290600 chr5A 336429178 336431860 2682 False 3284 3284 88.848 2 2674 1 chr5A.!!$F1 2672
14 TraesCS3A01G290600 chr5A 350641588 350644279 2691 False 3011 3011 86.981 1 2674 1 chr5A.!!$F2 2673

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
544 559 0.525668 CGTGTATCTCGCCGCTTTCT 60.526 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1987 0.036388 GGATTCTGTCGCCAGTTCCA 60.036 55.0 11.53 0.0 39.64 3.53 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
173 178 2.184020 CTCGAACCACTGCCATGGGA 62.184 60.000 15.13 10.50 44.81 4.37
433 447 1.351076 TCTCCTTGCCACTCATGTCA 58.649 50.000 0.00 0.00 0.00 3.58
544 559 0.525668 CGTGTATCTCGCCGCTTTCT 60.526 55.000 0.00 0.00 0.00 2.52
571 586 2.650322 TGTGTGAAAACTTCCTGGGTC 58.350 47.619 0.00 0.00 0.00 4.46
575 590 1.487142 TGAAAACTTCCTGGGTCGTCA 59.513 47.619 0.00 0.00 0.00 4.35
685 700 1.607801 CCAGATGTGCGGAGGTCTCA 61.608 60.000 0.14 0.00 0.00 3.27
742 757 3.314307 TGATCCTTCCCGAGTCAGTAT 57.686 47.619 0.00 0.00 0.00 2.12
896 911 0.601558 GTGAAGGTACTGGTCGAGCA 59.398 55.000 17.59 17.59 40.86 4.26
1014 1029 3.254903 CGATGTGGATGTACTCGGGAATA 59.745 47.826 0.00 0.00 0.00 1.75
1146 1163 0.984109 CATTCGACCATTTGCGCAAC 59.016 50.000 24.99 10.16 0.00 4.17
1269 1290 9.948964 CAGGATCTTGTTGATATGTATTCCATA 57.051 33.333 0.00 0.00 40.27 2.74
1375 1402 1.898459 GAGCGACGACTCGAGTGACA 61.898 60.000 25.58 0.00 43.06 3.58
1436 1463 1.399744 AAGCACACTCACGACCCAGA 61.400 55.000 0.00 0.00 0.00 3.86
1447 1474 3.249189 ACCCAGAAAGCGCTCCCA 61.249 61.111 12.06 0.00 0.00 4.37
1735 1767 0.544697 GGACTTCCTCCCGCCAATAA 59.455 55.000 0.00 0.00 31.83 1.40
1858 1890 2.034053 GGGTCGACTGATTTGTTTGCAA 59.966 45.455 16.46 0.00 0.00 4.08
1937 1969 0.322546 AGGAGCAAAAAGGTAGCGGG 60.323 55.000 0.00 0.00 0.00 6.13
1955 1987 0.035630 GGTGGCAAGACATCTCAGCT 60.036 55.000 0.00 0.00 0.00 4.24
2139 2171 1.375326 GCCGTCTGTCCCCTTCTTT 59.625 57.895 0.00 0.00 0.00 2.52
2141 2173 0.396811 CCGTCTGTCCCCTTCTTTGT 59.603 55.000 0.00 0.00 0.00 2.83
2316 2348 4.212004 TGCTTTTCGACTGATCTTGTTCTG 59.788 41.667 0.00 0.00 0.00 3.02
2568 2606 0.601558 CTTTCTTCCACTCGACCCGA 59.398 55.000 0.00 0.00 0.00 5.14
2569 2607 1.000506 CTTTCTTCCACTCGACCCGAA 59.999 52.381 0.00 0.00 34.74 4.30
2612 2656 2.034066 CAGTGGGGGCACGTCAAT 59.966 61.111 0.00 0.00 0.00 2.57
2693 2742 7.873739 GCTGAATAGCTATTCTCTTCTTCTC 57.126 40.000 34.91 15.26 46.57 2.87
2694 2743 7.661040 GCTGAATAGCTATTCTCTTCTTCTCT 58.339 38.462 34.91 6.71 46.57 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 167 1.005215 CTTCTCCTTTCCCATGGCAGT 59.995 52.381 6.09 0.00 0.00 4.40
173 178 1.004918 CGCCACCGTCTTCTCCTTT 60.005 57.895 0.00 0.00 0.00 3.11
232 237 3.781307 CGAAGATCCACCCCGGCA 61.781 66.667 0.00 0.00 33.14 5.69
544 559 4.097741 CAGGAAGTTTTCACACATGGACAA 59.902 41.667 0.00 0.00 0.00 3.18
571 586 1.597027 GACCCCAGTGTGGTTGACG 60.597 63.158 0.00 0.00 35.85 4.35
575 590 0.765510 GAAGAGACCCCAGTGTGGTT 59.234 55.000 0.00 0.00 35.85 3.67
685 700 4.383989 GCTCTTGTTCCTCATCTGGATTCT 60.384 45.833 0.00 0.00 35.83 2.40
742 757 3.948719 GGTCGACTGCCAACCCCA 61.949 66.667 16.46 0.00 0.00 4.96
896 911 2.571216 CGGACGAGTTGGACCACCT 61.571 63.158 0.00 0.00 37.04 4.00
1146 1163 1.051812 AGAATCATACCTGCTCCGGG 58.948 55.000 0.00 0.00 35.68 5.73
1269 1290 0.108019 GTTCCTGTTCTCCGTTGGGT 59.892 55.000 0.00 0.00 33.83 4.51
1375 1402 1.596895 GGCGAGTCGACTTCCTCCTT 61.597 60.000 21.08 0.00 0.00 3.36
1436 1463 2.282462 CCAGGTTGGGAGCGCTTT 60.282 61.111 13.26 0.00 32.67 3.51
1471 1498 1.355066 CGAGGGCGCTTTGAAGACTC 61.355 60.000 7.64 1.98 0.00 3.36
1599 1626 2.938838 ACGGTCACTTTGATTTTGGGA 58.061 42.857 0.00 0.00 0.00 4.37
1735 1767 4.330250 CATCTTCCATGTCCTTGTCTTGT 58.670 43.478 0.00 0.00 0.00 3.16
1858 1890 1.193462 TCGATAACGTTGGGTGGGGT 61.193 55.000 11.99 0.00 40.69 4.95
1937 1969 1.085091 CAGCTGAGATGTCTTGCCAC 58.915 55.000 8.42 0.00 0.00 5.01
1955 1987 0.036388 GGATTCTGTCGCCAGTTCCA 60.036 55.000 11.53 0.00 39.64 3.53
2139 2171 2.101415 CTCCGGAACATGATAGCTGACA 59.899 50.000 5.23 0.00 0.00 3.58
2141 2173 2.666317 TCTCCGGAACATGATAGCTGA 58.334 47.619 5.23 0.00 0.00 4.26
2518 2553 0.178903 AAGTACTCAGACCCCAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
2568 2606 4.003788 CCACTCGGCCGGTCTGTT 62.004 66.667 27.83 0.00 0.00 3.16
2703 2760 1.289380 GTCTGCCCGAGTCGAGTTT 59.711 57.895 15.64 0.00 0.00 2.66
2704 2761 2.637383 GGTCTGCCCGAGTCGAGTT 61.637 63.158 15.64 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.