Multiple sequence alignment - TraesCS3B01G301300

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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 TraesCS3B01G301300 chr3B 100.000 2543 0 0 1 2543 483359962 483357420 0.000000e+00 4697
1 TraesCS3B01G301300 chr3B 94.615 130 6 1 1583 1711 39818925 39819054 1.540000e-47 200
2 TraesCS3B01G301300 chr3B 98.276 58 1 0 1 58 518278529 518278586 4.480000e-18 102
3 TraesCS3B01G301300 chr3B 98.276 58 1 0 1 58 518661052 518661109 4.480000e-18 102
4 TraesCS3B01G301300 chr6B 97.278 2241 51 5 1 2238 394542380 394540147 0.000000e+00 3792
5 TraesCS3B01G301300 chr6B 93.350 391 25 1 1213 1602 625639000 625638610 6.100000e-161 577
6 TraesCS3B01G301300 chr7B 97.232 2240 52 4 1 2238 716817911 716815680 0.000000e+00 3784
7 TraesCS3B01G301300 chr7B 98.701 308 4 0 2236 2543 716815654 716815347 4.780000e-152 547
8 TraesCS3B01G301300 chr7A 97.381 1718 38 3 1 1716 60341193 60342905 0.000000e+00 2916
9 TraesCS3B01G301300 chr7A 98.440 705 9 1 1536 2238 60343028 60343732 0.000000e+00 1240
10 TraesCS3B01G301300 chr7A 93.913 230 3 3 674 903 60290578 60290796 1.130000e-88 337
11 TraesCS3B01G301300 chr7A 84.825 257 17 9 610 857 60262502 60262745 3.270000e-59 239
12 TraesCS3B01G301300 chr1B 98.004 1403 23 2 837 2238 339013703 339015101 0.000000e+00 2431
13 TraesCS3B01G301300 chr1B 97.862 1403 27 2 837 2238 338938004 338939404 0.000000e+00 2422
14 TraesCS3B01G301300 chr5B 97.309 1375 29 4 1 1373 127841056 127839688 0.000000e+00 2327
15 TraesCS3B01G301300 chr5B 97.205 823 20 2 1416 2238 127839690 127838871 0.000000e+00 1389
16 TraesCS3B01G301300 chr5B 98.628 729 9 1 1 728 533047224 533046496 0.000000e+00 1290
17 TraesCS3B01G301300 chr5B 96.067 356 8 2 703 1057 22039066 22038716 2.190000e-160 575
18 TraesCS3B01G301300 chr5B 98.701 308 4 0 2236 2543 127838845 127838538 4.780000e-152 547
19 TraesCS3B01G301300 chr4D 99.071 538 4 1 1701 2238 123671394 123671930 0.000000e+00 965
20 TraesCS3B01G301300 chr4D 99.026 308 3 0 2236 2543 123671956 123672263 1.030000e-153 553
21 TraesCS3B01G301300 chr7D 98.885 538 5 1 1701 2238 203566795 203566259 0.000000e+00 959
22 TraesCS3B01G301300 chr7D 98.699 538 4 1 1701 2238 382036839 382037373 0.000000e+00 952
23 TraesCS3B01G301300 chr7D 98.701 308 4 0 2236 2543 382037399 382037706 4.780000e-152 547
24 TraesCS3B01G301300 chr7D 98.701 308 4 0 2236 2543 579007963 579007656 4.780000e-152 547
25 TraesCS3B01G301300 chrUn 99.026 308 3 0 2236 2543 267898377 267898070 1.030000e-153 553
26 TraesCS3B01G301300 chrUn 98.701 308 4 0 2236 2543 351637626 351637933 4.780000e-152 547
27 TraesCS3B01G301300 chrUn 94.348 230 2 3 674 903 403078581 403078363 2.420000e-90 342
28 TraesCS3B01G301300 chrUn 98.276 58 1 0 1 58 5019133 5019190 4.480000e-18 102
29 TraesCS3B01G301300 chr1A 99.026 308 3 0 2236 2543 278509848 278510155 1.030000e-153 553
30 TraesCS3B01G301300 chr3D 98.701 308 4 0 2236 2543 154777524 154777217 4.780000e-152 547
31 TraesCS3B01G301300 chr3D 95.420 131 4 2 1583 1711 478075366 478075236 9.220000e-50 207
32 TraesCS3B01G301300 chr3A 97.720 307 2 1 536 842 272052898 272052597 8.060000e-145 523
33 TraesCS3B01G301300 chr3A 95.000 140 7 0 1207 1346 83376975 83377114 1.180000e-53 220
34 TraesCS3B01G301300 chr2B 93.913 230 3 4 674 903 112852481 112852699 1.130000e-88 337
35 TraesCS3B01G301300 chr4B 96.875 64 2 0 333 396 605806166 605806103 9.620000e-20 108


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 TraesCS3B01G301300 chr3B 483357420 483359962 2542 True 4697.0 4697 100.000000 1 2543 1 chr3B.!!$R1 2542
1 TraesCS3B01G301300 chr6B 394540147 394542380 2233 True 3792.0 3792 97.278000 1 2238 1 chr6B.!!$R1 2237
2 TraesCS3B01G301300 chr7B 716815347 716817911 2564 True 2165.5 3784 97.966500 1 2543 2 chr7B.!!$R1 2542
3 TraesCS3B01G301300 chr7A 60341193 60343732 2539 False 2078.0 2916 97.910500 1 2238 2 chr7A.!!$F3 2237
4 TraesCS3B01G301300 chr1B 339013703 339015101 1398 False 2431.0 2431 98.004000 837 2238 1 chr1B.!!$F2 1401
5 TraesCS3B01G301300 chr1B 338938004 338939404 1400 False 2422.0 2422 97.862000 837 2238 1 chr1B.!!$F1 1401
6 TraesCS3B01G301300 chr5B 127838538 127841056 2518 True 1421.0 2327 97.738333 1 2543 3 chr5B.!!$R3 2542
7 TraesCS3B01G301300 chr5B 533046496 533047224 728 True 1290.0 1290 98.628000 1 728 1 chr5B.!!$R2 727
8 TraesCS3B01G301300 chr4D 123671394 123672263 869 False 759.0 965 99.048500 1701 2543 2 chr4D.!!$F1 842
9 TraesCS3B01G301300 chr7D 203566259 203566795 536 True 959.0 959 98.885000 1701 2238 1 chr7D.!!$R1 537
10 TraesCS3B01G301300 chr7D 382036839 382037706 867 False 749.5 952 98.700000 1701 2543 2 chr7D.!!$F1 842

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
465 466 0.65416 AATCGCATCGCACTCACATG 59.346 50.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2502 2.033675 TGAGTGACGTTACGAGCAGAAA 59.966 45.455 13.03 0.0 0.0 2.52 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
58 59 5.426504 AGTATGCTCTTGTCCATCTTCTTG 58.573 41.667 0.00 0.00 0.00 3.02
153 154 1.276421 TGCTTCAGGTCCTCTAGCAAC 59.724 52.381 18.04 0.00 38.76 4.17
465 466 0.654160 AATCGCATCGCACTCACATG 59.346 50.000 0.00 0.00 0.00 3.21
546 548 2.682155 AACTCCTCGATTCAGCTTCC 57.318 50.000 0.00 0.00 0.00 3.46
728 731 3.807309 TGGGACCTCCAGTGTATGT 57.193 52.632 0.00 0.00 41.46 2.29
887 890 6.183360 CCTGGAGATGAGATTTCTTTCTACGA 60.183 42.308 0.00 0.00 0.00 3.43
1290 1294 6.363088 GCACTCTTCTCAAGAATATCGATCTG 59.637 42.308 0.00 0.00 37.02 2.90
1958 2271 6.311690 TGCTTTTGAACATTCATGTGCATATG 59.688 34.615 16.69 16.69 45.34 1.78
1977 2290 7.488792 TGCATATGTTTTCATTAGATGTGCAAC 59.511 33.333 4.29 0.00 41.25 4.17
2001 2314 5.808030 CCGAAATCAGTAGGAGAGAAACTTC 59.192 44.000 0.00 0.00 0.00 3.01
2189 2502 1.337823 CCGGATTCAACTTGTCGAGGT 60.338 52.381 0.00 0.00 0.00 3.85
2321 2662 6.627087 TTCACTTCCATCTCTTGATACCTT 57.373 37.500 0.00 0.00 0.00 3.50
2514 2855 5.560724 TCTCTTCCCTGTAGAAAACCAATG 58.439 41.667 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 0.729116 GGATGTCGCATTGTCTGTGG 59.271 55.000 0.00 0.0 35.98 4.17
284 285 6.436847 CCTCTCTATTAGCTCCATCATTGAGA 59.563 42.308 0.00 0.0 31.26 3.27
366 367 3.394606 AGGGAGTGTGGTCTGTAAAATGT 59.605 43.478 0.00 0.0 0.00 2.71
465 466 5.354234 TCTTTCTCTATGCGTTTTTGATCCC 59.646 40.000 0.00 0.0 0.00 3.85
728 731 3.328382 AATGCTAGTTGCCTCGTAACA 57.672 42.857 0.00 0.0 42.00 2.41
750 753 8.237949 TCTTTCACGAACTTTAATGACAAAACA 58.762 29.630 0.00 0.0 0.00 2.83
751 754 8.609478 TCTTTCACGAACTTTAATGACAAAAC 57.391 30.769 0.00 0.0 0.00 2.43
752 755 9.796120 ATTCTTTCACGAACTTTAATGACAAAA 57.204 25.926 0.00 0.0 0.00 2.44
753 756 9.232082 CATTCTTTCACGAACTTTAATGACAAA 57.768 29.630 0.00 0.0 0.00 2.83
754 757 8.402472 ACATTCTTTCACGAACTTTAATGACAA 58.598 29.630 0.00 0.0 0.00 3.18
887 890 9.829507 CAAAGTCACTCTTCTATCCTTCATATT 57.170 33.333 0.00 0.0 35.02 1.28
972 976 6.521527 AAGGAGAACCATAGCCAGAATATT 57.478 37.500 0.00 0.0 38.94 1.28
980 984 9.569122 TTAACATTATTAAGGAGAACCATAGCC 57.431 33.333 0.00 0.0 38.94 3.93
1290 1294 2.737252 GTGATGGTTCTGGAACGAGTTC 59.263 50.000 7.40 7.4 42.02 3.01
1527 1531 3.570550 CCAGTAACTATCCTTCTCCCTCG 59.429 52.174 0.00 0.0 0.00 4.63
1958 2271 5.041951 TCGGTTGCACATCTAATGAAAAC 57.958 39.130 0.00 0.0 0.00 2.43
1977 2290 5.331876 AGTTTCTCTCCTACTGATTTCGG 57.668 43.478 0.00 0.0 0.00 4.30
2189 2502 2.033675 TGAGTGACGTTACGAGCAGAAA 59.966 45.455 13.03 0.0 0.00 2.52
2321 2662 5.810074 GCAGTGGTAAGAAAAGCAAGAAAAA 59.190 36.000 0.00 0.0 0.00 1.94
2514 2855 5.561679 AGTGAAAATAAGGAGGGACTTGTC 58.438 41.667 0.00 0.0 41.55 3.18


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

AutoCloner maintained by Alex Coulton.