Multiple sequence alignment - TraesCS2B01G102600

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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 TraesCS2B01G102600 chr2B 100.000 2924 0 0 1 2924 63584153 63587076 0.000000e+00 5400
1 TraesCS2B01G102600 chr2B 98.393 2924 46 1 1 2924 563765234 563768156 0.000000e+00 5138
2 TraesCS2B01G102600 chr2B 98.291 2925 49 1 1 2924 106932289 106935213 0.000000e+00 5123
3 TraesCS2B01G102600 chr2B 98.222 2924 51 1 1 2924 257723647 257720725 0.000000e+00 5110
4 TraesCS2B01G102600 chr2B 98.120 2925 54 1 1 2924 327771513 327768589 0.000000e+00 5096
5 TraesCS2B01G102600 chr2B 98.013 2868 57 0 57 2924 297490474 297493341 0.000000e+00 4981
6 TraesCS2B01G102600 chr2B 96.384 1134 40 1 1791 2924 6977359 6976227 0.000000e+00 1866
7 TraesCS2B01G102600 chr2B 93.229 384 22 3 1 381 34398111 34398493 1.970000e-156 562
8 TraesCS2B01G102600 chr1B 98.290 2924 50 0 1 2924 26649580 26652503 0.000000e+00 5123
9 TraesCS2B01G102600 chr3B 98.256 2924 51 0 1 2924 717600181 717597258 0.000000e+00 5118
10 TraesCS2B01G102600 chr5B 98.222 2925 51 1 1 2924 36453480 36450556 0.000000e+00 5112
11 TraesCS2B01G102600 chr3A 90.099 2424 152 32 561 2924 604792355 604794750 0.000000e+00 3066
12 TraesCS2B01G102600 chr3A 94.118 187 11 0 383 569 604765480 604765666 4.770000e-73 285


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 TraesCS2B01G102600 chr2B 63584153 63587076 2923 False 5400 5400 100.000 1 2924 1 chr2B.!!$F2 2923
1 TraesCS2B01G102600 chr2B 563765234 563768156 2922 False 5138 5138 98.393 1 2924 1 chr2B.!!$F5 2923
2 TraesCS2B01G102600 chr2B 106932289 106935213 2924 False 5123 5123 98.291 1 2924 1 chr2B.!!$F3 2923
3 TraesCS2B01G102600 chr2B 257720725 257723647 2922 True 5110 5110 98.222 1 2924 1 chr2B.!!$R2 2923
4 TraesCS2B01G102600 chr2B 327768589 327771513 2924 True 5096 5096 98.120 1 2924 1 chr2B.!!$R3 2923
5 TraesCS2B01G102600 chr2B 297490474 297493341 2867 False 4981 4981 98.013 57 2924 1 chr2B.!!$F4 2867
6 TraesCS2B01G102600 chr2B 6976227 6977359 1132 True 1866 1866 96.384 1791 2924 1 chr2B.!!$R1 1133
7 TraesCS2B01G102600 chr1B 26649580 26652503 2923 False 5123 5123 98.290 1 2924 1 chr1B.!!$F1 2923
8 TraesCS2B01G102600 chr3B 717597258 717600181 2923 True 5118 5118 98.256 1 2924 1 chr3B.!!$R1 2923
9 TraesCS2B01G102600 chr5B 36450556 36453480 2924 True 5112 5112 98.222 1 2924 1 chr5B.!!$R1 2923
10 TraesCS2B01G102600 chr3A 604792355 604794750 2395 False 3066 3066 90.099 561 2924 1 chr3A.!!$F2 2363

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
343 344 0.467384 CTCTCCGGTGCATCAGGAAT 59.533 55.0 10.94 0.0 39.71 3.01 F
795 796 1.326951 GCTCTCCCTCCTCACTCCAC 61.327 65.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1169 0.544357 AGGTACTGGTGCTACTGCCA 60.544 55.000 0.0 0.0 37.18 4.92 R
2311 2330 1.134580 ACATGGCTTCCTCTGTCATCG 60.135 52.381 0.0 0.0 0.00 3.84 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
314 315 2.429058 CCTCAGTGTGGTGCAGCT 59.571 61.111 18.08 0.00 0.00 4.24
325 326 3.573229 TGCAGCTGAGTTGGGCCT 61.573 61.111 20.43 0.00 0.00 5.19
343 344 0.467384 CTCTCCGGTGCATCAGGAAT 59.533 55.000 10.94 0.00 39.71 3.01
553 554 5.923733 TGTGGTGTTGGTTCAATTTAGTT 57.076 34.783 0.00 0.00 0.00 2.24
795 796 1.326951 GCTCTCCCTCCTCACTCCAC 61.327 65.000 0.00 0.00 0.00 4.02
1047 1048 8.202811 TGAATTGAATTGATTGGTTCAGTTTCA 58.797 29.630 0.00 0.00 35.36 2.69
1063 1064 8.956426 GTTCAGTTTCATATATTCTTCACCCAA 58.044 33.333 0.00 0.00 0.00 4.12
1168 1169 7.874016 TCATGCTTACAAGATTTTTCTTTGCAT 59.126 29.630 0.00 0.00 33.97 3.96
1215 1216 1.838073 TTGGGAACGGAAGGGAGCTC 61.838 60.000 4.71 4.71 0.00 4.09
1284 1285 1.152483 ACCTTGGGCATGCTTGTGT 60.152 52.632 18.92 6.14 0.00 3.72
1285 1286 0.760189 ACCTTGGGCATGCTTGTGTT 60.760 50.000 18.92 0.00 0.00 3.32
1414 1415 0.999406 CCATCCGTCTGCAGTTAACG 59.001 55.000 14.67 16.04 36.22 3.18
1593 1594 7.307751 GCATGAGTTTTACTACTGCTAACACAA 60.308 37.037 0.00 0.00 34.64 3.33
1683 1685 9.419297 GTAATATTTCACCTTCGTATGCATAGA 57.581 33.333 6.67 4.31 0.00 1.98
1998 2000 4.175962 TGGTTCCCTTTATTCTCTCCTGT 58.824 43.478 0.00 0.00 0.00 4.00
2211 2213 7.030165 TCATTTTAACTTGCTCGACAACAAAA 58.970 30.769 0.00 0.00 33.68 2.44
2311 2330 9.552114 CTCATTCTTTTCTGATTCATGTAACAC 57.448 33.333 0.00 0.00 0.00 3.32
2407 2427 4.929211 TGTTGTTCATCTGACTATGGTTCG 59.071 41.667 0.00 0.00 0.00 3.95
2420 2440 0.251653 TGGTTCGAGCCCTGACTACT 60.252 55.000 16.38 0.00 0.00 2.57
2479 2516 1.000993 AGTCCAGCGAGTCCAGGAT 59.999 57.895 0.00 0.00 31.91 3.24
2887 2950 9.829507 AAAAACACAAATAGGATGAATTGTTGA 57.170 25.926 0.00 0.00 33.97 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
314 315 3.003173 CCGGAGAGGCCCAACTCA 61.003 66.667 19.15 0.00 39.97 3.41
325 326 0.911769 AATTCCTGATGCACCGGAGA 59.088 50.000 9.46 0.00 33.64 3.71
1047 1048 9.170890 TGATAGAAGGTTGGGTGAAGAATATAT 57.829 33.333 0.00 0.00 0.00 0.86
1063 1064 8.091449 GCACTAGTTATAAGCATGATAGAAGGT 58.909 37.037 0.00 0.00 0.00 3.50
1168 1169 0.544357 AGGTACTGGTGCTACTGCCA 60.544 55.000 0.00 0.00 37.18 4.92
1215 1216 2.364324 CCCCAGATTCAATGCATGGAAG 59.636 50.000 20.85 8.37 32.55 3.46
1414 1415 1.895131 ACATCAATGGGGCACAACTTC 59.105 47.619 0.00 0.00 0.00 3.01
1593 1594 6.765403 TGTGTTGGCAGTAGTAAATACTCTT 58.235 36.000 0.00 0.00 43.13 2.85
1683 1685 7.489113 GTCATGCAGAATTCAAACCGAATAAAT 59.511 33.333 8.44 0.00 43.83 1.40
1998 2000 5.756347 ACACGCATACTAAACTTCACAAAGA 59.244 36.000 0.00 0.00 36.30 2.52
2197 2199 2.543445 CCATGCTTTTTGTTGTCGAGCA 60.543 45.455 0.00 0.00 46.11 4.26
2211 2213 4.494091 ACATTCAGCTAGTACCATGCTT 57.506 40.909 2.64 0.00 34.51 3.91
2311 2330 1.134580 ACATGGCTTCCTCTGTCATCG 60.135 52.381 0.00 0.00 0.00 3.84
2407 2427 3.686916 AAACTTCAGTAGTCAGGGCTC 57.313 47.619 0.00 0.00 35.54 4.70
2420 2440 5.975693 ACTTCAACAGGACAAAAACTTCA 57.024 34.783 0.00 0.00 0.00 3.02
2876 2939 1.098050 GGCCGAGCTCAACAATTCAT 58.902 50.000 15.40 0.00 0.00 2.57
2887 2950 0.618458 TTTTCTACATGGGCCGAGCT 59.382 50.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.