Multiple sequence alignment - TraesCS7A01G029200

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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 TraesCS7A01G029200 chr7A 100.000 2615 0 0 1 2615 11928984 11931598 0.000000e+00 4830.0
1 TraesCS7A01G029200 chr7A 99.237 2620 15 2 1 2615 11882000 11884619 0.000000e+00 4723.0
2 TraesCS7A01G029200 chr7A 96.735 2358 49 10 1 2330 11801976 11804333 0.000000e+00 3903.0
3 TraesCS7A01G029200 chr7A 96.061 1371 19 12 1 1336 11828478 11829848 0.000000e+00 2200.0
4 TraesCS7A01G029200 chr7A 97.973 296 5 1 2321 2615 11804926 11805221 1.790000e-141 512.0
5 TraesCS7A01G029200 chr7A 97.297 296 7 1 2321 2615 11838277 11838572 3.890000e-138 501.0
6 TraesCS7A01G029200 chr7A 97.297 296 7 1 2321 2615 11938129 11938424 3.890000e-138 501.0
7 TraesCS7A01G029200 chr7A 97.270 293 7 1 2324 2615 554291605 554291313 1.810000e-136 496.0
8 TraesCS7A01G029200 chrUn 96.061 1371 19 12 1 1336 341054313 341052943 0.000000e+00 2200.0
9 TraesCS7A01G029200 chrUn 96.396 999 29 3 1338 2330 349443138 349442141 0.000000e+00 1639.0
10 TraesCS7A01G029200 chrUn 97.952 293 5 1 2324 2615 349441545 349441253 8.350000e-140 507.0
11 TraesCS7A01G029200 chr4A 92.520 762 50 3 850 1611 725838036 725837282 0.000000e+00 1085.0
12 TraesCS7A01G029200 chr4A 92.982 285 18 2 531 814 725838319 725838036 5.210000e-112 414.0
13 TraesCS7A01G029200 chr4A 88.623 334 22 9 104 424 725838719 725838389 2.440000e-105 392.0
14 TraesCS7A01G029200 chr4A 95.200 125 4 2 1 124 45489283 45489160 2.050000e-46 196.0
15 TraesCS7A01G029200 chr1D 92.938 354 24 1 1607 1960 289723772 289724124 4.990000e-142 514.0
16 TraesCS7A01G029200 chr1D 92.157 357 23 5 1607 1960 246668310 246668664 1.400000e-137 499.0
17 TraesCS7A01G029200 chr1D 92.351 353 24 3 1610 1960 298085394 298085745 1.400000e-137 499.0
18 TraesCS7A01G029200 chr1D 100.000 108 0 0 1 108 342177580 342177473 1.590000e-47 200.0
19 TraesCS7A01G029200 chr5D 92.135 356 24 4 1607 1960 297633584 297633937 1.400000e-137 499.0
20 TraesCS7A01G029200 chr5D 90.816 98 9 0 435 532 526139274 526139177 5.870000e-27 132.0
21 TraesCS7A01G029200 chr7D 92.308 351 25 2 1611 1960 165171344 165171693 5.030000e-137 497.0
22 TraesCS7A01G029200 chr2D 92.135 356 23 3 1611 1963 198455382 198455029 5.030000e-137 497.0
23 TraesCS7A01G029200 chr2D 89.565 345 33 2 1988 2330 201839765 201839422 4.000000e-118 435.0
24 TraesCS7A01G029200 chr1A 97.595 291 6 1 2326 2615 11017929 11018219 5.030000e-137 497.0
25 TraesCS7A01G029200 chr1A 99.074 108 1 0 1 108 266772989 266773096 7.380000e-46 195.0
26 TraesCS7A01G029200 chr6A 96.959 296 8 1 2321 2615 30020819 30021114 1.810000e-136 496.0
27 TraesCS7A01G029200 chr2A 96.959 296 8 1 2321 2615 777941596 777941891 1.810000e-136 496.0
28 TraesCS7A01G029200 chr5A 89.518 353 33 2 1982 2330 510073803 510074155 6.640000e-121 444.0
29 TraesCS7A01G029200 chr1B 89.565 345 33 2 1988 2330 259048928 259048585 4.000000e-118 435.0
30 TraesCS7A01G029200 chr3D 89.049 347 34 3 1988 2331 276170725 276170380 6.690000e-116 427.0
31 TraesCS7A01G029200 chr7B 88.986 345 36 1 1988 2330 446932684 446933028 2.410000e-115 425.0
32 TraesCS7A01G029200 chr4B 88.986 345 36 1 1988 2330 360014929 360015273 2.410000e-115 425.0
33 TraesCS7A01G029200 chr4B 100.000 108 0 0 1 108 540457874 540457767 1.590000e-47 200.0
34 TraesCS7A01G029200 chr4B 92.784 97 7 0 436 532 664775714 664775618 9.760000e-30 141.0
35 TraesCS7A01G029200 chr6D 100.000 108 0 0 1 108 451746397 451746290 1.590000e-47 200.0
36 TraesCS7A01G029200 chr3B 93.000 100 7 0 433 532 327059389 327059290 2.100000e-31 147.0
37 TraesCS7A01G029200 chr4D 94.505 91 5 0 436 526 31822000 31822090 9.760000e-30 141.0
38 TraesCS7A01G029200 chr4D 92.000 100 8 0 436 535 360449785 360449686 9.760000e-30 141.0
39 TraesCS7A01G029200 chr6B 100.000 37 0 0 531 567 681466863 681466899 4.670000e-08 69.4
40 TraesCS7A01G029200 chr3A 95.349 43 2 0 531 573 47157079 47157121 4.670000e-08 69.4


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 TraesCS7A01G029200 chr7A 11928984 11931598 2614 False 4830.000000 4830 100.000 1 2615 1 chr7A.!!$F4 2614
1 TraesCS7A01G029200 chr7A 11882000 11884619 2619 False 4723.000000 4723 99.237 1 2615 1 chr7A.!!$F3 2614
2 TraesCS7A01G029200 chr7A 11801976 11805221 3245 False 2207.500000 3903 97.354 1 2615 2 chr7A.!!$F6 2614
3 TraesCS7A01G029200 chr7A 11828478 11829848 1370 False 2200.000000 2200 96.061 1 1336 1 chr7A.!!$F1 1335
4 TraesCS7A01G029200 chrUn 341052943 341054313 1370 True 2200.000000 2200 96.061 1 1336 1 chrUn.!!$R1 1335
5 TraesCS7A01G029200 chrUn 349441253 349443138 1885 True 1073.000000 1639 97.174 1338 2615 2 chrUn.!!$R2 1277
6 TraesCS7A01G029200 chr4A 725837282 725838719 1437 True 630.333333 1085 91.375 104 1611 3 chr4A.!!$R2 1507

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
967 1041 1.539929 CCATTCATCGTCTCCCTCAGC 60.54 57.143 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2228 5.221541 GCCACTGCTCTACTAGGATAAACAT 60.222 44.0 0.0 0.0 33.53 2.71 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
967 1041 1.539929 CCATTCATCGTCTCCCTCAGC 60.540 57.143 0.00 0.00 0.00 4.26
1815 1893 4.499696 CCTTGCAAAGTTTCGTTCCATTCT 60.500 41.667 0.00 0.00 44.25 2.40
2064 2142 2.169832 ACATTGAGCTAGCACAACGT 57.830 45.000 26.61 22.64 30.10 3.99
2282 2362 5.247337 TGTGGAAATGTCATGTGTACTAGGA 59.753 40.000 0.00 0.00 0.00 2.94
2442 3124 4.582656 AGTATGCCTCTACTTGACTAGCTG 59.417 45.833 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
899 973 0.902531 ATGGGTTGAGGTGGAGTACG 59.097 55.000 0.00 0.0 0.00 3.67
1785 1863 5.966636 ACGAAACTTTGCAAGGATTTTTC 57.033 34.783 16.36 13.1 0.00 2.29
2150 2228 5.221541 GCCACTGCTCTACTAGGATAAACAT 60.222 44.000 0.00 0.0 33.53 2.71
2310 2390 8.098912 TCATGATATAAGGACATGATTCCACAG 58.901 37.037 0.00 0.0 43.17 3.66
2442 3124 7.035612 GGAAACATAACCATCTTTGATCAACC 58.964 38.462 7.89 0.0 0.00 3.77


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

AutoCloner maintained by Alex Coulton.