Multiple sequence alignment - TraesCS3B01G526200

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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 TraesCS3B01G526200 chr3B 100.000 4588 0 0 1 4588 768505294 768509881 0.000000e+00 8473.0
1 TraesCS3B01G526200 chr4A 99.085 4589 41 1 1 4588 481088393 481092981 0.000000e+00 8240.0
2 TraesCS3B01G526200 chr4A 88.343 2848 269 26 897 3723 90394584 90391779 0.000000e+00 3362.0
3 TraesCS3B01G526200 chr1A 98.692 4588 56 2 1 4588 146608815 146613398 0.000000e+00 8137.0
4 TraesCS3B01G526200 chr1A 98.915 3872 32 2 717 4588 482818549 482822410 0.000000e+00 6909.0
5 TraesCS3B01G526200 chr1A 84.717 2735 353 47 990 3693 555296116 555298816 0.000000e+00 2675.0
6 TraesCS3B01G526200 chr1A 98.615 722 10 0 1 722 482816841 482817562 0.000000e+00 1279.0
7 TraesCS3B01G526200 chr5D 97.457 4600 75 14 1 4588 550419957 550415388 0.000000e+00 7808.0
8 TraesCS3B01G526200 chr7D 97.196 4600 85 15 1 4588 4416617 4421184 0.000000e+00 7740.0
9 TraesCS3B01G526200 chr5A 97.856 4244 70 11 189 4431 612386600 612382377 0.000000e+00 7313.0
10 TraesCS3B01G526200 chr5A 97.297 37 1 0 3821 3857 612382912 612382876 3.830000e-06 63.9
11 TraesCS3B01G526200 chrUn 98.988 2766 26 2 1825 4588 62686915 62689680 0.000000e+00 4951.0
12 TraesCS3B01G526200 chrUn 99.074 1835 16 1 1 1834 62671811 62673645 0.000000e+00 3293.0
13 TraesCS3B01G526200 chr3D 89.032 2945 255 41 897 3797 41716731 41719651 0.000000e+00 3587.0
14 TraesCS3B01G526200 chr7A 88.943 2849 272 26 897 3723 727630581 727627754 0.000000e+00 3476.0
15 TraesCS3B01G526200 chr1D 88.428 2938 267 39 897 3797 69859692 69862593 0.000000e+00 3474.0
16 TraesCS3B01G526200 chr1D 96.238 1329 25 10 3260 4588 334045201 334043898 0.000000e+00 2154.0
17 TraesCS3B01G526200 chr1D 96.510 917 22 2 1 907 334046136 334045220 0.000000e+00 1507.0
18 TraesCS3B01G526200 chr6B 92.026 1091 39 18 3513 4588 279329654 279328597 0.000000e+00 1489.0
19 TraesCS3B01G526200 chr6B 95.216 878 30 3 1 868 279330534 279329659 0.000000e+00 1378.0
20 TraesCS3B01G526200 chr4D 81.169 154 21 5 4329 4475 40412377 40412225 2.900000e-22 117.0


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 TraesCS3B01G526200 chr3B 768505294 768509881 4587 False 8473.00 8473 100.0000 1 4588 1 chr3B.!!$F1 4587
1 TraesCS3B01G526200 chr4A 481088393 481092981 4588 False 8240.00 8240 99.0850 1 4588 1 chr4A.!!$F1 4587
2 TraesCS3B01G526200 chr4A 90391779 90394584 2805 True 3362.00 3362 88.3430 897 3723 1 chr4A.!!$R1 2826
3 TraesCS3B01G526200 chr1A 146608815 146613398 4583 False 8137.00 8137 98.6920 1 4588 1 chr1A.!!$F1 4587
4 TraesCS3B01G526200 chr1A 482816841 482822410 5569 False 4094.00 6909 98.7650 1 4588 2 chr1A.!!$F3 4587
5 TraesCS3B01G526200 chr1A 555296116 555298816 2700 False 2675.00 2675 84.7170 990 3693 1 chr1A.!!$F2 2703
6 TraesCS3B01G526200 chr5D 550415388 550419957 4569 True 7808.00 7808 97.4570 1 4588 1 chr5D.!!$R1 4587
7 TraesCS3B01G526200 chr7D 4416617 4421184 4567 False 7740.00 7740 97.1960 1 4588 1 chr7D.!!$F1 4587
8 TraesCS3B01G526200 chr5A 612382377 612386600 4223 True 3688.45 7313 97.5765 189 4431 2 chr5A.!!$R1 4242
9 TraesCS3B01G526200 chrUn 62686915 62689680 2765 False 4951.00 4951 98.9880 1825 4588 1 chrUn.!!$F2 2763
10 TraesCS3B01G526200 chrUn 62671811 62673645 1834 False 3293.00 3293 99.0740 1 1834 1 chrUn.!!$F1 1833
11 TraesCS3B01G526200 chr3D 41716731 41719651 2920 False 3587.00 3587 89.0320 897 3797 1 chr3D.!!$F1 2900
12 TraesCS3B01G526200 chr7A 727627754 727630581 2827 True 3476.00 3476 88.9430 897 3723 1 chr7A.!!$R1 2826
13 TraesCS3B01G526200 chr1D 69859692 69862593 2901 False 3474.00 3474 88.4280 897 3797 1 chr1D.!!$F1 2900
14 TraesCS3B01G526200 chr1D 334043898 334046136 2238 True 1830.50 2154 96.3740 1 4588 2 chr1D.!!$R1 4587
15 TraesCS3B01G526200 chr6B 279328597 279330534 1937 True 1433.50 1489 93.6210 1 4588 2 chr6B.!!$R1 4587

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
686 697 3.173599 CAATGTGAAGTTGCGGCAATAG 58.826 45.455 19.53 0.0 0.00 1.73 F
974 1978 9.715121 ACAAAATGACTCATCTTGCATTATTTT 57.285 25.926 5.17 0.0 26.00 1.82 F
2496 3529 9.295825 TGGATGAACAACTACTCATGTTTTTAT 57.704 29.630 0.00 0.0 39.73 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 2799 3.625764 TGTGCTACTGTTTTCTTCGCTTT 59.374 39.130 0.0 0.0 0.0 3.51 R
2818 3855 2.159338 CCTGATTTTCGCCTCAATGTGG 60.159 50.000 0.0 0.0 0.0 4.17 R
3712 4767 2.599677 AGCCGTAAATAGAGAGAGGGG 58.400 52.381 0.0 0.0 0.0 4.79 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
686 697 3.173599 CAATGTGAAGTTGCGGCAATAG 58.826 45.455 19.53 0.00 0.00 1.73
974 1978 9.715121 ACAAAATGACTCATCTTGCATTATTTT 57.285 25.926 5.17 0.00 26.00 1.82
2182 3215 9.658799 GATATCAATAGTGTATATTGTGCAGGT 57.341 33.333 0.00 0.00 36.56 4.00
2496 3529 9.295825 TGGATGAACAACTACTCATGTTTTTAT 57.704 29.630 0.00 0.00 39.73 1.40
2818 3855 0.539986 TAGGAGCAATTGACGGGACC 59.460 55.000 10.34 2.62 0.00 4.46
2982 4023 4.384647 GGATCAAGCTGTTCTAAGATGGGT 60.385 45.833 0.00 0.00 0.00 4.51
3364 4407 8.495148 CCAAGTTAAAATTGTTATGGCTTGTTC 58.505 33.333 0.00 0.00 31.73 3.18
3712 4767 7.768807 TTATAGGCTTATGAACTCTCTCTCC 57.231 40.000 0.00 0.00 0.00 3.71
3924 5001 3.278574 ACAGCTTTCAGTGCTACAAACA 58.721 40.909 0.00 0.00 38.92 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.937379 ATCCAGCCTGTGCGATCTGC 62.937 60.000 3.07 3.07 44.33 4.26
686 697 2.211468 CTGGGCTAGGTTTCCCCACC 62.211 65.000 1.18 0.00 43.67 4.61
1541 2552 4.641541 AGATTTGCTTGTACATGCAGCATA 59.358 37.500 28.58 20.24 41.50 3.14
1787 2799 3.625764 TGTGCTACTGTTTTCTTCGCTTT 59.374 39.130 0.00 0.00 0.00 3.51
2182 3215 4.635765 GCACATCCAAGCTGTTCATAGTTA 59.364 41.667 0.00 0.00 0.00 2.24
2818 3855 2.159338 CCTGATTTTCGCCTCAATGTGG 60.159 50.000 0.00 0.00 0.00 4.17
2982 4023 2.784682 ACCAAACCCCCACTAGTAACAA 59.215 45.455 0.00 0.00 0.00 2.83
3364 4407 5.439721 TCCTTATGAAGTTGTGGATGATGG 58.560 41.667 0.00 0.00 0.00 3.51
3712 4767 2.599677 AGCCGTAAATAGAGAGAGGGG 58.400 52.381 0.00 0.00 0.00 4.79
4154 5231 9.429359 TGATTTTTCTTTTTGCAAACTCTGTAA 57.571 25.926 12.39 1.26 0.00 2.41


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

AutoCloner maintained by Alex Coulton.