Multiple sequence alignment - TraesCS1B01G300200

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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 TraesCS1B01G300200 chr1B 100.000 2549 0 0 1 2549 520844687 520842139 0 4708
1 TraesCS1B01G300200 chr1B 96.229 1989 66 7 569 2549 581717561 581715574 0 3249
2 TraesCS1B01G300200 chr1B 96.825 567 18 0 2 568 47234286 47234852 0 948
3 TraesCS1B01G300200 chr1B 96.473 567 20 0 2 568 159834869 159834303 0 937
4 TraesCS1B01G300200 chr1B 96.479 568 19 1 2 568 397865705 397865138 0 937
5 TraesCS1B01G300200 chr1B 96.460 565 20 0 4 568 190856479 190855915 0 933
6 TraesCS1B01G300200 chr4A 96.171 1985 72 4 568 2549 705529253 705527270 0 3241
7 TraesCS1B01G300200 chr7B 96.123 1986 71 6 569 2549 720989190 720987206 0 3236
8 TraesCS1B01G300200 chr7B 95.643 1997 75 10 562 2549 677862797 677860804 0 3195
9 TraesCS1B01G300200 chr7B 96.473 567 18 1 2 568 448392656 448393220 0 935
10 TraesCS1B01G300200 chr7B 96.296 567 21 0 2 568 264568671 264569237 0 931
11 TraesCS1B01G300200 chr2B 95.970 1985 73 6 569 2549 458657423 458659404 0 3216
12 TraesCS1B01G300200 chr2B 95.919 1985 75 5 569 2549 692955897 692957879 0 3212
13 TraesCS1B01G300200 chr2B 95.630 1991 75 9 569 2549 492636665 492638653 0 3184
14 TraesCS1B01G300200 chr5B 95.768 1985 78 5 569 2548 497276165 497278148 0 3195
15 TraesCS1B01G300200 chr5B 96.296 567 21 0 2 568 453345987 453346553 0 931
16 TraesCS1B01G300200 chr4B 95.718 1985 72 8 569 2549 17791851 17789876 0 3182
17 TraesCS1B01G300200 chr4D 97.002 567 17 0 2 568 73513390 73513956 0 953
18 TraesCS1B01G300200 chr6B 96.649 567 19 0 2 568 140871798 140872364 0 942


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 TraesCS1B01G300200 chr1B 520842139 520844687 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R4 2548
1 TraesCS1B01G300200 chr1B 581715574 581717561 1987 True 3249 3249 96.229 569 2549 1 chr1B.!!$R5 1980
2 TraesCS1B01G300200 chr1B 47234286 47234852 566 False 948 948 96.825 2 568 1 chr1B.!!$F1 566
3 TraesCS1B01G300200 chr1B 159834303 159834869 566 True 937 937 96.473 2 568 1 chr1B.!!$R1 566
4 TraesCS1B01G300200 chr1B 397865138 397865705 567 True 937 937 96.479 2 568 1 chr1B.!!$R3 566
5 TraesCS1B01G300200 chr1B 190855915 190856479 564 True 933 933 96.460 4 568 1 chr1B.!!$R2 564
6 TraesCS1B01G300200 chr4A 705527270 705529253 1983 True 3241 3241 96.171 568 2549 1 chr4A.!!$R1 1981
7 TraesCS1B01G300200 chr7B 720987206 720989190 1984 True 3236 3236 96.123 569 2549 1 chr7B.!!$R2 1980
8 TraesCS1B01G300200 chr7B 677860804 677862797 1993 True 3195 3195 95.643 562 2549 1 chr7B.!!$R1 1987
9 TraesCS1B01G300200 chr7B 448392656 448393220 564 False 935 935 96.473 2 568 1 chr7B.!!$F2 566
10 TraesCS1B01G300200 chr7B 264568671 264569237 566 False 931 931 96.296 2 568 1 chr7B.!!$F1 566
11 TraesCS1B01G300200 chr2B 458657423 458659404 1981 False 3216 3216 95.970 569 2549 1 chr2B.!!$F1 1980
12 TraesCS1B01G300200 chr2B 692955897 692957879 1982 False 3212 3212 95.919 569 2549 1 chr2B.!!$F3 1980
13 TraesCS1B01G300200 chr2B 492636665 492638653 1988 False 3184 3184 95.630 569 2549 1 chr2B.!!$F2 1980
14 TraesCS1B01G300200 chr5B 497276165 497278148 1983 False 3195 3195 95.768 569 2548 1 chr5B.!!$F2 1979
15 TraesCS1B01G300200 chr5B 453345987 453346553 566 False 931 931 96.296 2 568 1 chr5B.!!$F1 566
16 TraesCS1B01G300200 chr4B 17789876 17791851 1975 True 3182 3182 95.718 569 2549 1 chr4B.!!$R1 1980
17 TraesCS1B01G300200 chr4D 73513390 73513956 566 False 953 953 97.002 2 568 1 chr4D.!!$F1 566
18 TraesCS1B01G300200 chr6B 140871798 140872364 566 False 942 942 96.649 2 568 1 chr6B.!!$F1 566

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
733 737 1.571773 GCCCTTACAGGTGGGACCAT 61.572 60.0 1.75 0.0 46.15 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 2409 0.040781 CTAACCAAAACCACGTGGCG 60.041 55.0 34.26 19.27 38.58 5.69 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
123 126 7.104043 TCAATGGAAATTCTCATAGCTTTGG 57.896 36.000 4.23 0.0 0.00 3.28
186 189 6.808829 AGTTTCAAAGAATCAACATCAAGCA 58.191 32.000 0.00 0.0 0.00 3.91
203 206 7.172532 ACATCAAGCAAAAGTCTATCAACGTTA 59.827 33.333 0.00 0.0 0.00 3.18
708 712 3.564225 GTCTCCGTCAGGTCAATGTTTTT 59.436 43.478 0.00 0.0 39.05 1.94
733 737 1.571773 GCCCTTACAGGTGGGACCAT 61.572 60.000 1.75 0.0 46.15 3.55
758 762 2.418609 GCAGAGGCGGCCAATTTTATTT 60.419 45.455 23.09 0.0 0.00 1.40
836 844 3.463944 GTTGCGGGTGTGCTATATTAGT 58.536 45.455 0.00 0.0 35.36 2.24
866 874 4.953868 CGGTGACCACGGCGACAA 62.954 66.667 16.62 0.0 0.00 3.18
874 882 2.108157 ACGGCGACAAAGAGCACA 59.892 55.556 16.62 0.0 34.54 4.57
981 989 2.125512 GCGGCGGTGTTGAGATCT 60.126 61.111 9.78 0.0 0.00 2.75
1008 1016 1.110442 CTCCGAGCTCCATGTCTTCT 58.890 55.000 8.47 0.0 0.00 2.85
1522 1530 5.815740 GGTATGGTAATCACACTGGTTGTAG 59.184 44.000 0.00 0.0 35.67 2.74
1867 1876 2.165998 GGAAAATGTGCCTCAGCTCTT 58.834 47.619 0.00 0.0 40.80 2.85
2175 2192 2.363297 GGGACTCGAACCCAAGACT 58.637 57.895 18.78 0.0 46.05 3.24
2489 2508 8.891671 AAATTTGCATGTTAGTTCATGACTTT 57.108 26.923 10.28 0.0 45.41 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.142578 TGCTTTGTAAAAGCGTGTTCTTCA 60.143 37.500 17.27 0.00 45.80 3.02
123 126 6.817641 CCTAAGCATGATATCAATGAGTCTCC 59.182 42.308 9.99 0.00 0.00 3.71
186 189 6.694447 TGGCTAGTAACGTTGATAGACTTTT 58.306 36.000 21.26 0.00 0.00 2.27
203 206 6.434028 TGCTTAAAGTTGATGATTTGGCTAGT 59.566 34.615 0.00 0.00 0.00 2.57
282 285 6.349300 TGCCCTCTGATTTTGAGAATAGTAC 58.651 40.000 0.00 0.00 33.68 2.73
362 366 6.997942 AATCCTAGACCATTCCCTAGTAAC 57.002 41.667 0.00 0.00 32.54 2.50
640 644 1.745489 GCACGGACTAGGGGCAAAG 60.745 63.158 0.00 0.00 0.00 2.77
791 795 3.562141 GCTCTATGCTCAACGACTCTCTA 59.438 47.826 0.00 0.00 38.95 2.43
909 917 0.254178 CACAGCTAGCTTCCCACCAT 59.746 55.000 16.46 0.00 0.00 3.55
944 952 1.142748 CCCTCCACAGCTAGCTTCG 59.857 63.158 16.46 7.60 0.00 3.79
971 979 0.888619 AGCCGAACGAGATCTCAACA 59.111 50.000 22.31 0.00 0.00 3.33
1058 1066 0.534412 CGGACAGATGAAGACAGGCT 59.466 55.000 0.00 0.00 0.00 4.58
1388 1396 3.897239 ACAGCTAGCTCTCTATCAGTGT 58.103 45.455 16.15 3.48 0.00 3.55
1522 1530 5.537188 TGCCTTTCCATACATTTTCAACAC 58.463 37.500 0.00 0.00 0.00 3.32
1814 1823 7.747155 TTGGTCTTTGATTTAAATCACGGTA 57.253 32.000 26.69 12.35 44.54 4.02
1867 1876 4.528987 TGGCACTAGGTGTAAACATCTACA 59.471 41.667 0.00 0.00 38.47 2.74
2175 2192 2.125773 AAACACCACAAACCCACGTA 57.874 45.000 0.00 0.00 0.00 3.57
2390 2409 0.040781 CTAACCAAAACCACGTGGCG 60.041 55.000 34.26 19.27 38.58 5.69
2496 2519 4.711846 GGTGAGAAGCCCTCCATTTTATTT 59.288 41.667 1.79 0.00 41.25 1.40


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

AutoCloner maintained by Alex Coulton.