Multiple sequence alignment - TraesCS2A01G121500

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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 TraesCS2A01G121500 chr2A 100.000 4622 0 0 1 4622 71214835 71210214 0.000000e+00 8536
1 TraesCS2A01G121500 chr2A 98.334 4623 52 11 1 4622 71162053 71157455 0.000000e+00 8087
2 TraesCS2A01G121500 chr2A 96.343 3281 91 10 1105 4366 71315305 71312035 0.000000e+00 5367
3 TraesCS2A01G121500 chr2A 94.300 2456 79 16 3 2436 71120751 71118335 0.000000e+00 3703
4 TraesCS2A01G121500 chr2A 99.931 1442 0 1 1372 2812 71265189 71263748 0.000000e+00 2656
5 TraesCS2A01G121500 chr2A 94.623 1618 67 5 2426 4042 71115899 71114301 0.000000e+00 2488
6 TraesCS2A01G121500 chr2A 95.507 1046 41 5 3 1045 71316363 71315321 0.000000e+00 1666
7 TraesCS2A01G121500 chr2A 99.553 895 4 0 3728 4622 71263737 71262843 0.000000e+00 1631
8 TraesCS2A01G121500 chr2A 84.825 257 29 4 4049 4305 71346996 71346750 2.760000e-62 250
9 TraesCS2A01G121500 chrUn 99.747 4347 11 0 1 4347 289663201 289658855 0.000000e+00 7967
10 TraesCS2A01G121500 chrUn 93.259 3412 163 22 3 3364 235541335 235544729 0.000000e+00 4964
11 TraesCS2A01G121500 chrUn 93.259 3412 163 22 3 3364 256966704 256963310 0.000000e+00 4964
12 TraesCS2A01G121500 chrUn 93.259 3412 163 22 3 3364 271157749 271154355 0.000000e+00 4964
13 TraesCS2A01G121500 chrUn 100.000 1689 0 0 582 2270 379030677 379032365 0.000000e+00 3120
14 TraesCS2A01G121500 chrUn 96.109 257 7 2 4366 4622 76192483 76192736 2.570000e-112 416
15 TraesCS2A01G121500 chr2D 93.335 3961 167 18 158 4042 72657080 72653141 0.000000e+00 5762
16 TraesCS2A01G121500 chr2D 93.593 3871 167 16 158 3969 72376582 72372734 0.000000e+00 5699
17 TraesCS2A01G121500 chr2D 86.786 280 27 3 4049 4327 72439013 72438743 2.090000e-78 303
18 TraesCS2A01G121500 chr2D 86.170 282 29 3 4049 4329 72698897 72698625 3.500000e-76 296
19 TraesCS2A01G121500 chr2B 93.338 2657 139 15 3 2627 109093679 109091029 0.000000e+00 3892
20 TraesCS2A01G121500 chr2B 93.071 2641 140 20 3 2609 109873079 109870448 0.000000e+00 3823
21 TraesCS2A01G121500 chr2B 92.744 2660 129 24 3 2609 109184704 109182056 0.000000e+00 3784
22 TraesCS2A01G121500 chr2B 93.488 1597 88 9 2047 3638 109360136 109358551 0.000000e+00 2359
23 TraesCS2A01G121500 chr2B 93.777 1382 70 3 2662 4042 109870452 109869086 0.000000e+00 2061
24 TraesCS2A01G121500 chr2B 93.777 1382 69 7 2662 4042 109182060 109180695 0.000000e+00 2060
25 TraesCS2A01G121500 chr2B 94.617 1226 58 2 2818 4042 109085403 109084185 0.000000e+00 1892
26 TraesCS2A01G121500 chr2B 84.698 281 33 3 4049 4329 109095201 109094931 5.890000e-69 272
27 TraesCS2A01G121500 chr2B 84.698 281 33 3 4049 4329 109874604 109874334 5.890000e-69 272
28 TraesCS2A01G121500 chr2B 84.397 282 33 4 4049 4329 109193670 109193399 2.740000e-67 267
29 TraesCS2A01G121500 chr2B 85.283 265 29 4 4066 4329 109933134 109932879 9.860000e-67 265
30 TraesCS2A01G121500 chr2B 90.090 111 3 1 4049 4159 109975128 109975026 2.240000e-28 137
31 TraesCS2A01G121500 chr1A 96.887 257 5 2 4366 4622 548306792 548307045 1.190000e-115 427
32 TraesCS2A01G121500 chr4A 97.211 251 5 1 4367 4617 642673532 642673284 1.540000e-114 424
33 TraesCS2A01G121500 chr1B 96.109 257 7 2 4366 4622 489539000 489538747 2.570000e-112 416
34 TraesCS2A01G121500 chr5D 95.703 256 9 1 4367 4622 223510296 223510043 1.200000e-110 411
35 TraesCS2A01G121500 chr4B 95.703 256 9 1 4367 4622 117779875 117780128 1.200000e-110 411
36 TraesCS2A01G121500 chr6D 95.703 256 7 3 4367 4622 7743256 7743507 4.300000e-110 409


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 TraesCS2A01G121500 chr2A 71210214 71214835 4621 True 8536.0 8536 100.000000 1 4622 1 chr2A.!!$R2 4621
1 TraesCS2A01G121500 chr2A 71157455 71162053 4598 True 8087.0 8087 98.334000 1 4622 1 chr2A.!!$R1 4621
2 TraesCS2A01G121500 chr2A 71312035 71316363 4328 True 3516.5 5367 95.925000 3 4366 2 chr2A.!!$R6 4363
3 TraesCS2A01G121500 chr2A 71114301 71120751 6450 True 3095.5 3703 94.461500 3 4042 2 chr2A.!!$R4 4039
4 TraesCS2A01G121500 chr2A 71262843 71265189 2346 True 2143.5 2656 99.742000 1372 4622 2 chr2A.!!$R5 3250
5 TraesCS2A01G121500 chrUn 289658855 289663201 4346 True 7967.0 7967 99.747000 1 4347 1 chrUn.!!$R3 4346
6 TraesCS2A01G121500 chrUn 235541335 235544729 3394 False 4964.0 4964 93.259000 3 3364 1 chrUn.!!$F2 3361
7 TraesCS2A01G121500 chrUn 256963310 256966704 3394 True 4964.0 4964 93.259000 3 3364 1 chrUn.!!$R1 3361
8 TraesCS2A01G121500 chrUn 271154355 271157749 3394 True 4964.0 4964 93.259000 3 3364 1 chrUn.!!$R2 3361
9 TraesCS2A01G121500 chrUn 379030677 379032365 1688 False 3120.0 3120 100.000000 582 2270 1 chrUn.!!$F3 1688
10 TraesCS2A01G121500 chr2D 72653141 72657080 3939 True 5762.0 5762 93.335000 158 4042 1 chr2D.!!$R3 3884
11 TraesCS2A01G121500 chr2D 72372734 72376582 3848 True 5699.0 5699 93.593000 158 3969 1 chr2D.!!$R1 3811
12 TraesCS2A01G121500 chr2B 109180695 109184704 4009 True 2922.0 3784 93.260500 3 4042 2 chr2B.!!$R7 4039
13 TraesCS2A01G121500 chr2B 109358551 109360136 1585 True 2359.0 2359 93.488000 2047 3638 1 chr2B.!!$R3 1591
14 TraesCS2A01G121500 chr2B 109091029 109095201 4172 True 2082.0 3892 89.018000 3 4329 2 chr2B.!!$R6 4326
15 TraesCS2A01G121500 chr2B 109869086 109874604 5518 True 2052.0 3823 90.515333 3 4329 3 chr2B.!!$R8 4326
16 TraesCS2A01G121500 chr2B 109084185 109085403 1218 True 1892.0 1892 94.617000 2818 4042 1 chr2B.!!$R1 1224

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
2909 7011 1.774217 AAGACCCTGTCCCTTGGCA 60.774 57.895 0.0 0.0 32.18 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4347 8459 1.355005 CGCCATCACACACGTTATCA 58.645 50.0 0.0 0.0 0.0 2.15 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
2909 7011 1.774217 AAGACCCTGTCCCTTGGCA 60.774 57.895 0.0 0.0 32.18 4.92
4347 8459 1.202927 CCTGTTGGGTCCACTTGTCAT 60.203 52.381 0.0 0.0 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
580 2106 2.203538 CCACCTTGCAGCTTGGGT 60.204 61.111 8.71 4.39 0.00 4.51
2812 6914 6.389830 TTGCACATAAAATGAGTGTTCAGT 57.610 33.333 0.00 0.00 36.61 3.41
2909 7011 2.094675 GTCTGCAGCCATACACCATTT 58.905 47.619 9.47 0.00 0.00 2.32
4347 8459 1.355005 CGCCATCACACACGTTATCA 58.645 50.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.