Multiple sequence alignment - TraesCS4D01G189500

Loading Multiple Alignment...

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 TraesCS4D01G189500 chr4D 100.000 3356 0 0 1 3356 329132553 329135908 0.000000e+00 6198.0
1 TraesCS4D01G189500 chr4A 93.518 3363 95 45 81 3356 140984433 140981107 0.000000e+00 4889.0
2 TraesCS4D01G189500 chr4B 90.764 3205 157 58 236 3356 408974960 408978109 0.000000e+00 4150.0
3 TraesCS4D01G189500 chr4B 88.950 181 15 3 75 254 408974103 408974279 5.640000e-53 219.0
4 TraesCS4D01G189500 chr4B 91.379 58 2 2 1 55 180671201 180671144 3.590000e-10 76.8
5 TraesCS4D01G189500 chr1B 95.661 2028 58 16 335 2352 135827746 135825739 0.000000e+00 3230.0
6 TraesCS4D01G189500 chr1B 88.166 769 54 17 2611 3356 135819487 135818733 0.000000e+00 881.0
7 TraesCS4D01G189500 chr1B 92.941 255 16 2 81 334 135828060 135827807 1.470000e-98 370.0
8 TraesCS4D01G189500 chr1B 96.396 222 6 1 2350 2569 135825578 135825357 6.840000e-97 364.0
9 TraesCS4D01G189500 chr1B 100.000 45 0 0 1 45 314566594 314566638 2.150000e-12 84.2
10 TraesCS4D01G189500 chr1A 93.284 670 24 2 2687 3356 586341737 586342385 0.000000e+00 968.0
11 TraesCS4D01G189500 chr1A 86.257 684 43 13 2677 3356 587486338 587486974 0.000000e+00 695.0
12 TraesCS4D01G189500 chr5A 86.676 683 40 13 2677 3356 637292723 637292089 0.000000e+00 710.0
13 TraesCS4D01G189500 chr3A 86.423 685 42 17 2677 3356 55174354 55173716 0.000000e+00 702.0
14 TraesCS4D01G189500 chr7A 86.257 684 40 15 2677 3356 168660419 168659786 0.000000e+00 693.0
15 TraesCS4D01G189500 chr7A 97.872 47 1 0 1 47 20400164 20400118 7.720000e-12 82.4
16 TraesCS4D01G189500 chr6A 85.044 682 47 18 2677 3356 265618508 265617880 0.000000e+00 643.0
17 TraesCS4D01G189500 chr2D 93.917 411 7 3 1 393 407120141 407119731 3.700000e-169 604.0
18 TraesCS4D01G189500 chr2D 91.071 56 3 2 1 55 430723750 430723696 1.290000e-09 75.0
19 TraesCS4D01G189500 chr2D 92.453 53 2 2 1 52 439417418 439417469 1.290000e-09 75.0
20 TraesCS4D01G189500 chr5D 82.297 209 17 10 2475 2664 69952041 69952248 2.680000e-36 163.0
21 TraesCS4D01G189500 chr5D 100.000 31 0 0 1095 1125 218261284 218261254 1.300000e-04 58.4
22 TraesCS4D01G189500 chr7B 92.857 56 2 1 1 54 600579096 600579151 2.780000e-11 80.5
23 TraesCS4D01G189500 chr2B 95.745 47 2 0 1 47 652619007 652619053 3.590000e-10 76.8
24 TraesCS4D01G189500 chr5B 89.831 59 4 2 1 59 221844447 221844503 1.290000e-09 75.0


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 TraesCS4D01G189500 chr4D 329132553 329135908 3355 False 6198.000000 6198 100.000000 1 3356 1 chr4D.!!$F1 3355
1 TraesCS4D01G189500 chr4A 140981107 140984433 3326 True 4889.000000 4889 93.518000 81 3356 1 chr4A.!!$R1 3275
2 TraesCS4D01G189500 chr4B 408974103 408978109 4006 False 2184.500000 4150 89.857000 75 3356 2 chr4B.!!$F1 3281
3 TraesCS4D01G189500 chr1B 135825357 135828060 2703 True 1321.333333 3230 94.999333 81 2569 3 chr1B.!!$R2 2488
4 TraesCS4D01G189500 chr1B 135818733 135819487 754 True 881.000000 881 88.166000 2611 3356 1 chr1B.!!$R1 745
5 TraesCS4D01G189500 chr1A 586341737 586342385 648 False 968.000000 968 93.284000 2687 3356 1 chr1A.!!$F1 669
6 TraesCS4D01G189500 chr1A 587486338 587486974 636 False 695.000000 695 86.257000 2677 3356 1 chr1A.!!$F2 679
7 TraesCS4D01G189500 chr5A 637292089 637292723 634 True 710.000000 710 86.676000 2677 3356 1 chr5A.!!$R1 679
8 TraesCS4D01G189500 chr3A 55173716 55174354 638 True 702.000000 702 86.423000 2677 3356 1 chr3A.!!$R1 679
9 TraesCS4D01G189500 chr7A 168659786 168660419 633 True 693.000000 693 86.257000 2677 3356 1 chr7A.!!$R2 679
10 TraesCS4D01G189500 chr6A 265617880 265618508 628 True 643.000000 643 85.044000 2677 3356 1 chr6A.!!$R1 679


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
410 1179 0.099259 CGCACCCATACGAGTACGAA 59.901 55.0 0.0 0.0 42.66 3.85 F
433 1202 0.252789 TTAACCCCTGACCCATCCGA 60.253 55.0 0.0 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2818 1.221566 CACCATGGCCGACTGATCA 59.778 57.895 13.04 0.0 0.00 2.92 R
2641 3712 4.436523 GTGAAATGTACACTTGCGACAAAC 59.563 41.667 0.00 0.0 35.66 2.93 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)



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

AutoCloner maintained by Alex Coulton.