Multiple sequence alignment - TraesCS3B01G233600

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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 TraesCS3B01G233600 chr3B 100.000 2480 0 0 1 2480 361795828 361798307 0 4580
1 TraesCS3B01G233600 chr3B 98.234 1699 28 2 1 1699 389719857 389721553 0 2970
2 TraesCS3B01G233600 chr2B 98.185 2480 45 0 1 2480 728070273 728067794 0 4331
3 TraesCS3B01G233600 chr4D 97.904 2481 50 2 1 2480 393458505 393460984 0 4292
4 TraesCS3B01G233600 chr6B 97.661 2480 55 1 1 2480 587366782 587364306 0 4255
5 TraesCS3B01G233600 chr3D 97.661 2480 55 2 1 2480 359527469 359524993 0 4255
6 TraesCS3B01G233600 chr1D 97.500 2480 61 1 1 2480 251020561 251023039 0 4235
7 TraesCS3B01G233600 chr6A 95.058 2489 103 8 1 2480 583326532 583329009 0 3897
8 TraesCS3B01G233600 chr5D 97.864 1732 36 1 750 2480 565809433 565811164 0 2992
9 TraesCS3B01G233600 chr5D 96.793 1715 52 3 1 1713 557793950 557795663 0 2859
10 TraesCS3B01G233600 chr5D 97.300 963 25 1 1518 2480 557795523 557796484 0 1633
11 TraesCS3B01G233600 chr2D 96.618 1715 55 3 1 1713 621997765 621999478 0 2843
12 TraesCS3B01G233600 chr2D 97.819 963 21 0 1518 2480 621999338 622000300 0 1663


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 TraesCS3B01G233600 chr3B 361795828 361798307 2479 False 4580 4580 100.0000 1 2480 1 chr3B.!!$F1 2479
1 TraesCS3B01G233600 chr3B 389719857 389721553 1696 False 2970 2970 98.2340 1 1699 1 chr3B.!!$F2 1698
2 TraesCS3B01G233600 chr2B 728067794 728070273 2479 True 4331 4331 98.1850 1 2480 1 chr2B.!!$R1 2479
3 TraesCS3B01G233600 chr4D 393458505 393460984 2479 False 4292 4292 97.9040 1 2480 1 chr4D.!!$F1 2479
4 TraesCS3B01G233600 chr6B 587364306 587366782 2476 True 4255 4255 97.6610 1 2480 1 chr6B.!!$R1 2479
5 TraesCS3B01G233600 chr3D 359524993 359527469 2476 True 4255 4255 97.6610 1 2480 1 chr3D.!!$R1 2479
6 TraesCS3B01G233600 chr1D 251020561 251023039 2478 False 4235 4235 97.5000 1 2480 1 chr1D.!!$F1 2479
7 TraesCS3B01G233600 chr6A 583326532 583329009 2477 False 3897 3897 95.0580 1 2480 1 chr6A.!!$F1 2479
8 TraesCS3B01G233600 chr5D 565809433 565811164 1731 False 2992 2992 97.8640 750 2480 1 chr5D.!!$F1 1730
9 TraesCS3B01G233600 chr5D 557793950 557796484 2534 False 2246 2859 97.0465 1 2480 2 chr5D.!!$F2 2479
10 TraesCS3B01G233600 chr2D 621997765 622000300 2535 False 2253 2843 97.2185 1 2480 2 chr2D.!!$F1 2479

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
127 128 1.375098 GACCAGTCCTCGACGGTAGG 61.375 65.0 0.0 0.0 38.67 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2212 2.250939 CGCCCGAGTGCTTGAAACA 61.251 57.895 0.0 0.0 0.0 2.83 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
124 125 3.054503 CGACCAGTCCTCGACGGT 61.055 66.667 7.66 7.66 40.20 4.83
127 128 1.375098 GACCAGTCCTCGACGGTAGG 61.375 65.000 0.00 0.00 38.67 3.18
228 230 3.695606 GCCAGGAGTCAGCGTCCA 61.696 66.667 0.00 0.00 36.43 4.02
247 249 1.822990 CACCATGGATGCTGAAGCTTT 59.177 47.619 21.47 0.00 42.66 3.51
1264 1278 7.707624 AAAATCACAAAGATAGCTGAATCCA 57.292 32.000 0.00 0.00 35.39 3.41
1535 1549 9.478019 CTTACGTCATGTCATTTGAACTATTTC 57.522 33.333 0.00 0.00 0.00 2.17
1567 1691 7.936847 TGTATGTTGGAGTGAACTATTTTGTCT 59.063 33.333 0.00 0.00 0.00 3.41
1568 1692 6.861065 TGTTGGAGTGAACTATTTTGTCTC 57.139 37.500 0.00 0.00 0.00 3.36
2087 2212 6.603201 TGAGTCCAACAGAAGAGTTCAAAATT 59.397 34.615 0.00 0.00 0.00 1.82
2140 2265 6.581171 AGGAAATTTGATGAGGTTCTGAAC 57.419 37.500 12.05 12.05 0.00 3.18
2325 2450 9.965902 GGATAGTGTCAGATATATTGGGAAATT 57.034 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.371467 TGGGCAGAGAAATTGGAGGA 58.629 50.000 0.00 0.0 0.00 3.71
69 70 1.929860 CTCATCACTGGGGCCATGGT 61.930 60.000 14.67 0.0 0.00 3.55
124 125 3.072468 CAACGGACGGGGCTCCTA 61.072 66.667 0.00 0.0 0.00 2.94
194 196 2.032528 CTCGCAGGAAAGGGTGCA 59.967 61.111 0.00 0.0 39.83 4.57
228 230 1.822990 CAAAGCTTCAGCATCCATGGT 59.177 47.619 12.58 0.0 45.16 3.55
294 296 2.203596 ACGTCTCTTGGTCGGGGT 60.204 61.111 0.00 0.0 0.00 4.95
356 359 5.427378 TCATCTTCAACAGAACACAAGTGA 58.573 37.500 7.28 0.0 34.16 3.41
991 1003 2.009774 GTTGTCACTCATGGGATTCCG 58.990 52.381 0.00 0.0 35.24 4.30
1264 1278 5.562890 GCTTCATTGAAGTAAAAGAAGCGGT 60.563 40.000 23.66 0.0 43.78 5.68
1535 1549 8.964476 ATAGTTCACTCCAACATACATAAAGG 57.036 34.615 0.00 0.0 0.00 3.11
1567 1691 5.123820 GCAAATAGTTCAAGTGGCATACAGA 59.876 40.000 0.00 0.0 0.00 3.41
1568 1692 5.124457 AGCAAATAGTTCAAGTGGCATACAG 59.876 40.000 0.00 0.0 0.00 2.74
2087 2212 2.250939 CGCCCGAGTGCTTGAAACA 61.251 57.895 0.00 0.0 0.00 2.83
2140 2265 6.847956 TCTTTTGCCATTTTCATCAAACAG 57.152 33.333 0.00 0.0 0.00 3.16
2325 2450 2.574369 ACATTTTGAGTCGGTATCCCCA 59.426 45.455 0.00 0.0 0.00 4.96


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

AutoCloner maintained by Alex Coulton.