Multiple sequence alignment - TraesCS4B01G146200

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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 TraesCS4B01G146200 chr4B 100.000 2471 0 0 1 2471 209111348 209113818 0.000000e+00 4564
1 TraesCS4B01G146200 chr3A 97.746 2484 43 7 1 2471 495099948 495097465 0.000000e+00 4265
2 TraesCS4B01G146200 chr2B 97.544 2484 48 7 1 2471 449214522 449212039 0.000000e+00 4237
3 TraesCS4B01G146200 chr2B 97.345 2486 45 9 1 2471 234536346 234533867 0.000000e+00 4205
4 TraesCS4B01G146200 chr1B 97.544 2484 48 8 1 2471 619190520 619188037 0.000000e+00 4237
5 TraesCS4B01G146200 chr3B 97.422 2483 52 8 1 2471 6005955 6003473 0.000000e+00 4220
6 TraesCS4B01G146200 chr1A 97.142 2484 58 8 1 2471 278526004 278528487 0.000000e+00 4181
7 TraesCS4B01G146200 chr6A 97.506 2446 46 7 41 2471 84404696 84402251 0.000000e+00 4165
8 TraesCS4B01G146200 chr6D 96.940 2484 62 9 1 2471 458923550 458921068 0.000000e+00 4154
9 TraesCS4B01G146200 chr7A 96.622 2487 67 10 1 2471 563517286 563514801 0.000000e+00 4111
10 TraesCS4B01G146200 chr3D 96.459 2485 72 9 1 2471 501833569 501831087 0.000000e+00 4087
11 TraesCS4B01G146200 chr6B 96.548 1999 57 5 1 1988 625617902 625615905 0.000000e+00 3299
12 TraesCS4B01G146200 chrUn 97.575 1732 29 5 1 1719 352979907 352978176 0.000000e+00 2953
13 TraesCS4B01G146200 chrUn 97.244 1560 31 6 1 1548 217912479 217914038 0.000000e+00 2632
14 TraesCS4B01G146200 chr4D 97.207 752 10 4 1 741 123444168 123443417 0.000000e+00 1262
15 TraesCS4B01G146200 chr7D 100.000 86 0 0 1 86 606916636 606916721 2.540000e-35 159


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 TraesCS4B01G146200 chr4B 209111348 209113818 2470 False 4564 4564 100.000 1 2471 1 chr4B.!!$F1 2470
1 TraesCS4B01G146200 chr3A 495097465 495099948 2483 True 4265 4265 97.746 1 2471 1 chr3A.!!$R1 2470
2 TraesCS4B01G146200 chr2B 449212039 449214522 2483 True 4237 4237 97.544 1 2471 1 chr2B.!!$R2 2470
3 TraesCS4B01G146200 chr2B 234533867 234536346 2479 True 4205 4205 97.345 1 2471 1 chr2B.!!$R1 2470
4 TraesCS4B01G146200 chr1B 619188037 619190520 2483 True 4237 4237 97.544 1 2471 1 chr1B.!!$R1 2470
5 TraesCS4B01G146200 chr3B 6003473 6005955 2482 True 4220 4220 97.422 1 2471 1 chr3B.!!$R1 2470
6 TraesCS4B01G146200 chr1A 278526004 278528487 2483 False 4181 4181 97.142 1 2471 1 chr1A.!!$F1 2470
7 TraesCS4B01G146200 chr6A 84402251 84404696 2445 True 4165 4165 97.506 41 2471 1 chr6A.!!$R1 2430
8 TraesCS4B01G146200 chr6D 458921068 458923550 2482 True 4154 4154 96.940 1 2471 1 chr6D.!!$R1 2470
9 TraesCS4B01G146200 chr7A 563514801 563517286 2485 True 4111 4111 96.622 1 2471 1 chr7A.!!$R1 2470
10 TraesCS4B01G146200 chr3D 501831087 501833569 2482 True 4087 4087 96.459 1 2471 1 chr3D.!!$R1 2470
11 TraesCS4B01G146200 chr6B 625615905 625617902 1997 True 3299 3299 96.548 1 1988 1 chr6B.!!$R1 1987
12 TraesCS4B01G146200 chrUn 352978176 352979907 1731 True 2953 2953 97.575 1 1719 1 chrUn.!!$R1 1718
13 TraesCS4B01G146200 chrUn 217912479 217914038 1559 False 2632 2632 97.244 1 1548 1 chrUn.!!$F1 1547
14 TraesCS4B01G146200 chr4D 123443417 123444168 751 True 1262 1262 97.207 1 741 1 chr4D.!!$R1 740

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
897 909 1.843206 GGCTTGGAGGGAGATCTTTCT 59.157 52.381 0.0 0.0 33.88 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2300 5.411361 CCTCATTAGACCGTAGATCTCTCTG 59.589 48.0 0.0 0.0 32.66 3.35 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
87 88 6.520021 TGATACCATCATTCCAATCTTCCT 57.480 37.500 0.00 0.00 33.59 3.36
89 90 8.044574 TGATACCATCATTCCAATCTTCCTTA 57.955 34.615 0.00 0.00 33.59 2.69
90 91 7.939039 TGATACCATCATTCCAATCTTCCTTAC 59.061 37.037 0.00 0.00 33.59 2.34
91 92 5.126067 ACCATCATTCCAATCTTCCTTACG 58.874 41.667 0.00 0.00 0.00 3.18
92 93 5.126067 CCATCATTCCAATCTTCCTTACGT 58.874 41.667 0.00 0.00 0.00 3.57
93 94 6.126883 ACCATCATTCCAATCTTCCTTACGTA 60.127 38.462 0.00 0.00 0.00 3.57
95 96 7.282224 CCATCATTCCAATCTTCCTTACGTAAA 59.718 37.037 9.68 0.00 0.00 2.01
385 397 5.125900 CAGTAATGAATCATCAACAAGGGCA 59.874 40.000 0.00 0.00 39.49 5.36
528 540 7.174599 ACCATGAGACAAAAGATCTTCTTTCTG 59.825 37.037 8.78 4.46 45.19 3.02
622 634 4.442375 TGTCCGTGTCAACAAACAATTT 57.558 36.364 0.00 0.00 0.00 1.82
762 774 3.042108 AGGATTTCCGATCCTAGCGGC 62.042 57.143 5.79 0.00 46.11 6.53
821 833 7.210873 AGTAAACAGAATTCCATACTCGATCC 58.789 38.462 0.65 0.00 0.00 3.36
859 871 3.410631 TTCTGTGGAAAGCCGTATTCA 57.589 42.857 0.00 0.00 36.79 2.57
897 909 1.843206 GGCTTGGAGGGAGATCTTTCT 59.157 52.381 0.00 0.00 33.88 2.52
989 1005 6.465439 AAAGAAAACGGATTCTTGAACCTT 57.535 33.333 15.61 0.48 46.25 3.50
1007 1023 2.290367 CCTTTTTCACGCTCATGTCACA 59.710 45.455 0.00 0.00 0.00 3.58
1151 1170 3.040147 TCGAGCCGTGAAAAAGATTCT 57.960 42.857 0.00 0.00 0.00 2.40
1179 1198 9.185192 CAAAAGACAGAAACAAATCCACTATTC 57.815 33.333 0.00 0.00 0.00 1.75
1338 1357 0.251341 AAGCATCCCAAAAGCGTCCT 60.251 50.000 0.00 0.00 0.00 3.85
1422 1441 1.067915 GCCATACGCAAAAAGGAAGCA 60.068 47.619 0.00 0.00 37.47 3.91
1481 1500 6.364706 GCACATTTTCGTTAATCCATGAACAA 59.635 34.615 0.00 0.00 0.00 2.83
1796 1816 6.433716 TGATCTGGCATGTACAGAATGAAAAA 59.566 34.615 20.81 2.38 46.89 1.94
1923 1943 7.555965 TCTTATTCTTCTGATCGATTCAACCA 58.444 34.615 0.00 0.00 32.78 3.67
2151 2171 8.800370 TGAATGTACAGAAATGGCTATAACAA 57.200 30.769 0.33 0.00 0.00 2.83
2280 2300 6.500336 TCCTACCTATTGTCTGGATATACCC 58.500 44.000 0.00 0.00 38.00 3.69
2353 2373 2.570135 GGCAAGCTCTTCTATTCTGGG 58.430 52.381 0.00 0.00 0.00 4.45
2417 2440 5.947228 TCGAGCTTCAAGAAATTGTGAAT 57.053 34.783 0.00 0.00 33.45 2.57
2465 2488 3.102204 CTCCCAAGGAATTTCCATTGCT 58.898 45.455 17.57 0.00 42.60 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 8.316946 ACCTTAGCTACTTAATTTCCTTTACGT 58.683 33.333 0.00 0.00 0.00 3.57
90 91 8.713737 ACCTTAGCTACTTAATTTCCTTTACG 57.286 34.615 0.00 0.00 0.00 3.18
91 92 9.887629 AGACCTTAGCTACTTAATTTCCTTTAC 57.112 33.333 0.00 0.00 0.00 2.01
95 96 8.697292 CACTAGACCTTAGCTACTTAATTTCCT 58.303 37.037 0.00 0.00 0.00 3.36
367 379 4.346730 AGAATGCCCTTGTTGATGATTCA 58.653 39.130 0.00 0.00 0.00 2.57
385 397 7.868415 GGATAAGAATCTACAACGCACTAGAAT 59.132 37.037 0.00 0.00 32.29 2.40
528 540 4.927422 AGAGTTCCGAATCGAATCTCTTC 58.073 43.478 3.36 0.00 31.75 2.87
622 634 6.764085 TGTTCTGAAAAAGTCGAGGTATTTCA 59.236 34.615 12.32 12.32 37.59 2.69
762 774 3.939592 GAGTATCCGTTTCCCTCCTTTTG 59.060 47.826 0.00 0.00 0.00 2.44
821 833 7.621285 TCCACAGAATTCTATAGGGATCTATGG 59.379 40.741 7.86 15.23 36.87 2.74
989 1005 2.157474 CGATGTGACATGAGCGTGAAAA 59.843 45.455 1.23 0.00 0.00 2.29
1151 1170 7.639113 AGTGGATTTGTTTCTGTCTTTTGTA 57.361 32.000 0.00 0.00 0.00 2.41
1318 1337 0.603065 GGACGCTTTTGGGATGCTTT 59.397 50.000 0.00 0.00 36.14 3.51
1338 1357 5.913137 ATTTGAAAGCCATATTTCGACCA 57.087 34.783 0.00 0.00 41.21 4.02
1422 1441 2.507058 TGCCTCTGCCATTCTATGAGTT 59.493 45.455 0.00 0.00 36.33 3.01
1481 1500 9.935241 GATCCATGTGTCTACATACATAGATTT 57.065 33.333 0.00 0.00 45.53 2.17
1902 1922 5.583854 CAGTGGTTGAATCGATCAGAAGAAT 59.416 40.000 0.00 0.00 39.77 2.40
1923 1943 6.784031 ACCAAGGTCTATCTTTTTGATCAGT 58.216 36.000 0.00 0.00 36.65 3.41
2280 2300 5.411361 CCTCATTAGACCGTAGATCTCTCTG 59.589 48.000 0.00 0.00 32.66 3.35
2353 2373 5.471456 CCATATAGCCAAGAGAAACCATGAC 59.529 44.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.