Multiple sequence alignment - TraesCS4B01G146600

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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 TraesCS4B01G146600 chr4B 100.000 3354 0 0 1 3354 209224814 209221461 0 6194
1 TraesCS4B01G146600 chr7A 98.480 3356 49 1 1 3354 60349348 60345993 0 5914
2 TraesCS4B01G146600 chr7B 98.420 3354 53 0 1 3354 742954450 742957803 0 5901
3 TraesCS4B01G146600 chr7B 98.361 3355 54 1 1 3354 716910713 716907359 0 5890
4 TraesCS4B01G146600 chr7B 98.301 3355 55 2 1 3354 716778896 716775543 0 5879
5 TraesCS4B01G146600 chr5A 98.420 3355 52 1 1 3354 16538870 16535516 0 5901
6 TraesCS4B01G146600 chr2B 98.153 3356 59 2 1 3354 391172732 391169378 0 5851
7 TraesCS4B01G146600 chr1B 98.151 3354 62 0 1 3354 583567260 583570613 0 5851
8 TraesCS4B01G146600 chr6B 97.436 3354 78 7 1 3354 388292747 388296092 0 5710
9 TraesCS4B01G146600 chr3B 97.379 3358 84 1 1 3354 39847344 39843987 0 5710


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 TraesCS4B01G146600 chr4B 209221461 209224814 3353 True 6194 6194 100.000 1 3354 1 chr4B.!!$R1 3353
1 TraesCS4B01G146600 chr7A 60345993 60349348 3355 True 5914 5914 98.480 1 3354 1 chr7A.!!$R1 3353
2 TraesCS4B01G146600 chr7B 742954450 742957803 3353 False 5901 5901 98.420 1 3354 1 chr7B.!!$F1 3353
3 TraesCS4B01G146600 chr7B 716907359 716910713 3354 True 5890 5890 98.361 1 3354 1 chr7B.!!$R2 3353
4 TraesCS4B01G146600 chr7B 716775543 716778896 3353 True 5879 5879 98.301 1 3354 1 chr7B.!!$R1 3353
5 TraesCS4B01G146600 chr5A 16535516 16538870 3354 True 5901 5901 98.420 1 3354 1 chr5A.!!$R1 3353
6 TraesCS4B01G146600 chr2B 391169378 391172732 3354 True 5851 5851 98.153 1 3354 1 chr2B.!!$R1 3353
7 TraesCS4B01G146600 chr1B 583567260 583570613 3353 False 5851 5851 98.151 1 3354 1 chr1B.!!$F1 3353
8 TraesCS4B01G146600 chr6B 388292747 388296092 3345 False 5710 5710 97.436 1 3354 1 chr6B.!!$F1 3353
9 TraesCS4B01G146600 chr3B 39843987 39847344 3357 True 5710 5710 97.379 1 3354 1 chr3B.!!$R1 3353

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
774 776 0.107214 TCCTCCACCCATGATTTCGC 60.107 55.0 0.0 0.0 0.0 4.70 F
1120 1128 0.322322 TTGGTTATTCGTCAGCCCGT 59.678 50.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2311 2319 0.404040 AATCCCTTGTCGGCTTTCCA 59.596 50.000 0.0 0.0 0.0 3.53 R
2817 2825 4.655963 TGACGTTCCTGGTACTAGTAGTT 58.344 43.478 8.4 0.0 0.0 2.24 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
128 129 1.279271 ACAGGGCTAAGTCGAAGCATT 59.721 47.619 9.64 0.00 41.93 3.56
774 776 0.107214 TCCTCCACCCATGATTTCGC 60.107 55.000 0.00 0.00 0.00 4.70
853 861 6.894682 AGAAAAGAAGTGTTCTCTTTCTCCT 58.105 36.000 14.45 4.28 39.77 3.69
1120 1128 0.322322 TTGGTTATTCGTCAGCCCGT 59.678 50.000 0.00 0.00 0.00 5.28
1137 1145 3.702330 CCCGTCTTTCACTTGGAAAAAC 58.298 45.455 0.00 0.00 44.52 2.43
1492 1500 3.878086 TCAAGCATGAGTTCGTTCAAC 57.122 42.857 0.00 0.00 34.86 3.18
1540 1548 5.392380 GGGCTGTTTAGTCAACAATCATGAG 60.392 44.000 0.09 0.00 45.11 2.90
1625 1633 4.079253 GGAAAAGCATTTACCCTGAGTCA 58.921 43.478 0.00 0.00 37.28 3.41
1634 1642 2.254152 ACCCTGAGTCAGCTATTCCA 57.746 50.000 15.10 0.00 0.00 3.53
1641 1649 5.396101 CCTGAGTCAGCTATTCCAGATTCAA 60.396 44.000 15.10 0.00 0.00 2.69
1725 1733 4.625607 AGCAAGGACAAGTAGCTAGTTT 57.374 40.909 11.24 3.73 33.06 2.66
1788 1796 5.426833 AGAGCATTATCTACAACCCTGAAGT 59.573 40.000 0.00 0.00 0.00 3.01
1910 1918 0.968901 AATGTCGACCTACCGCTCCA 60.969 55.000 14.12 0.00 0.00 3.86
2029 2037 9.660180 TTATTGTTGTGTGCATATTAGTCACTA 57.340 29.630 0.00 0.00 0.00 2.74
2311 2319 3.315191 CCTCGGCCAAACGAATATTTCAT 59.685 43.478 2.24 0.00 42.98 2.57
2767 2775 6.018994 GGGATACGTATTTACAGACTGCAAAG 60.019 42.308 9.92 0.00 37.60 2.77
2817 2825 7.255346 CCATGCATGCAAATCTTAGTTCTATGA 60.255 37.037 26.68 0.00 0.00 2.15
2961 2969 4.701956 ATTGACAAAGCGTCCTATTTGG 57.298 40.909 0.00 0.00 44.71 3.28
3014 3022 2.498167 GAATTGCTATCATCTGCGGGT 58.502 47.619 0.00 0.00 0.00 5.28
3048 3056 5.913137 TTGAATTTATCCGCCTTTGATGT 57.087 34.783 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 5.047235 GCTCACTACTAAAGAAGGTTCTGGA 60.047 44.000 0.00 0.0 37.65 3.86
189 190 4.219725 GGAAAGTTTTGGCAGGCATTACTA 59.780 41.667 10.71 0.0 0.00 1.82
367 368 9.113838 GCTCACTTCCTTGAGAATATAAAATCA 57.886 33.333 4.29 0.0 45.19 2.57
372 373 6.156949 AGTGGCTCACTTCCTTGAGAATATAA 59.843 38.462 4.29 0.0 42.59 0.98
559 561 6.141685 GCGTTGTCATTTTCACGAGTTTTTAT 59.858 34.615 0.00 0.0 0.00 1.40
774 776 6.494893 TCGTCTAATTTGTCAATGGGAAAG 57.505 37.500 0.00 0.0 0.00 2.62
853 861 0.859232 GCGAGACTGTTCTTTTCGCA 59.141 50.000 11.70 0.0 40.55 5.10
1097 1105 1.339727 GGCTGACGAATAACCAACCCT 60.340 52.381 0.00 0.0 0.00 4.34
1120 1128 5.505780 TCTCCTGTTTTTCCAAGTGAAAGA 58.494 37.500 0.00 0.0 43.57 2.52
1137 1145 3.252974 AGCGTGGAACTAAATCTCCTG 57.747 47.619 0.00 0.0 32.51 3.86
1302 1310 6.864421 ACCCTATTCTTTCTTTCCTTCCTTT 58.136 36.000 0.00 0.0 0.00 3.11
1492 1500 1.815421 CTGATTCCCCTTGCCGACG 60.815 63.158 0.00 0.0 0.00 5.12
1625 1633 7.093596 CCTTTCCTTTTTGAATCTGGAATAGCT 60.094 37.037 0.00 0.0 36.78 3.32
1634 1642 6.211384 CCCACATACCTTTCCTTTTTGAATCT 59.789 38.462 0.00 0.0 0.00 2.40
1641 1649 5.073965 TGTCTACCCACATACCTTTCCTTTT 59.926 40.000 0.00 0.0 0.00 2.27
1788 1796 9.507329 ACTGCTAGATTTCTTTTTCATAGTTCA 57.493 29.630 0.00 0.0 0.00 3.18
1910 1918 1.720781 AAGCAAGGTTCAAAGCCCAT 58.279 45.000 0.00 0.0 0.00 4.00
2256 2264 6.641474 AGCTGTTCCTATTTCAACTAGGTAC 58.359 40.000 4.20 4.2 37.24 3.34
2311 2319 0.404040 AATCCCTTGTCGGCTTTCCA 59.596 50.000 0.00 0.0 0.00 3.53
2620 2628 5.123936 GGAGCTTTATTAGTTGTAGGTGGG 58.876 45.833 0.00 0.0 0.00 4.61
2767 2775 6.485648 GGTGGGTAACAACATTGTATCTATCC 59.514 42.308 0.00 0.0 41.31 2.59
2817 2825 4.655963 TGACGTTCCTGGTACTAGTAGTT 58.344 43.478 8.40 0.0 0.00 2.24
3014 3022 5.476599 CGGATAAATTCAATAATGAGGGCCA 59.523 40.000 6.18 0.0 36.78 5.36
3048 3056 9.146984 CTCGTAAGTCAATAGTGAATTTGGTTA 57.853 33.333 11.33 0.0 38.91 2.85


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

AutoCloner maintained by Alex Coulton.