Multiple sequence alignment - TraesCS4D01G279700

Loading Multiple Alignment...

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 TraesCS4D01G279700 chr4D 100.000 2396 0 0 1 2396 450900098 450897703 0 4425
1 TraesCS4D01G279700 chr4D 97.247 2397 65 1 1 2396 123348179 123350575 0 4060
2 TraesCS4D01G279700 chr7B 97.540 2398 57 1 1 2396 742950681 742948284 0 4100
3 TraesCS4D01G279700 chr5A 97.540 2398 57 1 1 2396 16542611 16545008 0 4100
4 TraesCS4D01G279700 chr5A 97.331 2398 61 2 1 2396 420183760 420186156 0 4071
5 TraesCS4D01G279700 chr2A 97.541 2399 56 1 1 2396 755478605 755481003 0 4100
6 TraesCS4D01G279700 chr7A 97.498 2398 58 1 1 2396 60170710 60168313 0 4095
7 TraesCS4D01G279700 chr6A 97.162 2396 66 1 1 2394 155855356 155857751 0 4047
8 TraesCS4D01G279700 chr1B 97.123 2398 66 2 1 2396 583563491 583561095 0 4043
9 TraesCS4D01G279700 chr2D 97.081 2398 68 1 1 2396 200924354 200926751 0 4039


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 TraesCS4D01G279700 chr4D 450897703 450900098 2395 True 4425 4425 100.000 1 2396 1 chr4D.!!$R1 2395
1 TraesCS4D01G279700 chr4D 123348179 123350575 2396 False 4060 4060 97.247 1 2396 1 chr4D.!!$F1 2395
2 TraesCS4D01G279700 chr7B 742948284 742950681 2397 True 4100 4100 97.540 1 2396 1 chr7B.!!$R1 2395
3 TraesCS4D01G279700 chr5A 16542611 16545008 2397 False 4100 4100 97.540 1 2396 1 chr5A.!!$F1 2395
4 TraesCS4D01G279700 chr5A 420183760 420186156 2396 False 4071 4071 97.331 1 2396 1 chr5A.!!$F2 2395
5 TraesCS4D01G279700 chr2A 755478605 755481003 2398 False 4100 4100 97.541 1 2396 1 chr2A.!!$F1 2395
6 TraesCS4D01G279700 chr7A 60168313 60170710 2397 True 4095 4095 97.498 1 2396 1 chr7A.!!$R1 2395
7 TraesCS4D01G279700 chr6A 155855356 155857751 2395 False 4047 4047 97.162 1 2394 1 chr6A.!!$F1 2393
8 TraesCS4D01G279700 chr1B 583561095 583563491 2396 True 4043 4043 97.123 1 2396 1 chr1B.!!$R1 2395
9 TraesCS4D01G279700 chr2D 200924354 200926751 2397 False 4039 4039 97.081 1 2396 1 chr2D.!!$F1 2395

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
708 712 0.179194 GAGAGCGTAGTCGAAAGCGT 60.179 55.0 0.0 0.0 39.71 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 1952 0.471191 TAGGCCGATACGTCTCCAGA 59.529 55.0 0.0 0.0 0.0 3.86 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
34 35 0.749649 CTCTAGTTCCGGCAGATGCT 59.250 55.000 4.59 0.00 41.70 3.79
81 82 8.657712 GGAAGTAGTGGGTTATTGGAAGTATAT 58.342 37.037 0.00 0.00 0.00 0.86
152 153 2.517875 GGATGCGGCATCTGGCTT 60.518 61.111 34.29 6.31 44.01 4.35
313 314 1.341852 GGGCTATCCGAAAGAGGAGAC 59.658 57.143 0.00 0.00 44.55 3.36
333 334 8.160106 AGGAGACCAATAATTCCACTATCAATC 58.840 37.037 0.00 0.00 32.02 2.67
487 488 0.824109 TCGGAATCATTCTCACGGCT 59.176 50.000 0.00 0.00 0.00 5.52
496 497 1.541310 TTCTCACGGCTACCCCACAG 61.541 60.000 0.00 0.00 0.00 3.66
530 531 1.942657 CCGCCAATCGATCATCACTTT 59.057 47.619 0.00 0.00 41.67 2.66
541 542 9.778993 AATCGATCATCACTTTCATACAAAAAG 57.221 29.630 0.00 0.00 39.20 2.27
542 543 7.243487 TCGATCATCACTTTCATACAAAAAGC 58.757 34.615 0.00 0.00 37.26 3.51
695 699 1.855360 GCTGATTCCTTAACGAGAGCG 59.145 52.381 0.00 0.00 44.79 5.03
708 712 0.179194 GAGAGCGTAGTCGAAAGCGT 60.179 55.000 0.00 0.00 39.71 5.07
870 874 7.758980 CGGTTCACCAAATGATAATTCAAATCA 59.241 33.333 0.00 0.00 37.11 2.57
929 933 6.514048 GCGGATTTCTCCCTTCAAAATATCAG 60.514 42.308 0.00 0.00 38.45 2.90
965 969 7.235079 TGTTAAAGTATGGAATTCTCACCCAA 58.765 34.615 5.23 0.00 33.15 4.12
1049 1053 0.318275 GATGAGATCGGTCGAGTGGC 60.318 60.000 0.00 0.00 0.00 5.01
1128 1132 1.976474 GGTGGAATTTGCCAGCGGA 60.976 57.895 0.00 0.00 45.32 5.54
1279 1283 1.206132 CCATGTTAGGCCGTGTAGTCA 59.794 52.381 0.00 0.00 0.00 3.41
1393 1397 0.036732 ATCTGTGCACGAACCCATGT 59.963 50.000 13.13 0.00 0.00 3.21
1430 1434 3.681874 GCAGTGGATAACCTGGTTCCTAC 60.682 52.174 16.75 16.03 37.04 3.18
1549 1553 1.271597 GGGGCACAAATGAGAGTGAGT 60.272 52.381 0.00 0.00 37.97 3.41
1590 1594 1.069227 GCGATTGGACAAAAACGCTCT 60.069 47.619 19.05 0.00 37.90 4.09
1689 1693 1.948145 GATCCTGCTCCTCTGCAATTG 59.052 52.381 0.00 0.00 42.83 2.32
2033 2037 6.545666 TGTTTGGAAACAGAGCTCTTTTATCA 59.454 34.615 15.27 12.79 43.45 2.15
2034 2038 7.231317 TGTTTGGAAACAGAGCTCTTTTATCAT 59.769 33.333 15.27 0.00 43.45 2.45
2139 2143 4.023536 TGCGGTAGTTCAAAACTGGAATTC 60.024 41.667 0.00 0.00 42.84 2.17
2307 2311 5.047872 TGTTGTGATTTATGCTGCTGTCAAT 60.048 36.000 0.00 0.00 0.00 2.57
2313 2317 2.133281 ATGCTGCTGTCAATGGCTTA 57.867 45.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.115467 CATCTGCCGGAACTAGAGGT 58.885 55.000 5.05 0.00 0.00 3.85
81 82 6.430925 CCTTGGTGACACTTGAGAAATAATCA 59.569 38.462 5.39 0.00 42.67 2.57
113 114 4.163458 CCACAGGCCTATTTAGTAAGTGGA 59.837 45.833 22.48 0.00 45.05 4.02
152 153 3.286353 TCCCATTGCTTTCATCGCATAA 58.714 40.909 0.00 0.00 37.22 1.90
313 314 7.006509 ACCCAGATTGATAGTGGAATTATTGG 58.993 38.462 0.00 0.00 32.60 3.16
333 334 4.861196 TCTAGATATAGCAGCCTACCCAG 58.139 47.826 0.00 0.00 0.00 4.45
397 398 3.131933 AGTGCCTAGCTGAGTGATAACAG 59.868 47.826 0.00 0.00 37.22 3.16
399 400 3.810310 AGTGCCTAGCTGAGTGATAAC 57.190 47.619 0.00 0.00 0.00 1.89
404 405 3.319137 TTGTAAGTGCCTAGCTGAGTG 57.681 47.619 0.00 0.00 0.00 3.51
530 531 4.227197 TGGAAAAGGGGCTTTTTGTATGA 58.773 39.130 0.00 0.00 42.72 2.15
562 566 2.107950 TGAGCAACTGTATTTCCCCG 57.892 50.000 0.00 0.00 0.00 5.73
634 638 1.424493 GCGAGAATTGCTACGCTGCT 61.424 55.000 0.00 0.00 44.02 4.24
695 699 5.346822 TCTTTTTATGGACGCTTTCGACTAC 59.653 40.000 0.00 0.00 39.41 2.73
708 712 8.231837 CCGAAAACGATTTACTCTTTTTATGGA 58.768 33.333 0.00 0.00 35.96 3.41
965 969 1.664965 GTCGTGAGTTCCGCAGCTT 60.665 57.895 0.00 0.00 0.00 3.74
1049 1053 2.928334 CAATCCCATCTCCAACTGAGG 58.072 52.381 0.00 0.00 41.76 3.86
1195 1199 9.883142 CTTGACAAGATCTCCTTCTTTAATAGT 57.117 33.333 9.76 0.00 33.69 2.12
1275 1279 0.320697 GTACTCCCAAGGCGTTGACT 59.679 55.000 20.29 2.49 35.46 3.41
1279 1283 1.875488 ATAGGTACTCCCAAGGCGTT 58.125 50.000 0.00 0.00 41.75 4.84
1510 1514 4.707105 CCCCTTGAGTTCATTTGCTTTTT 58.293 39.130 0.00 0.00 0.00 1.94
1549 1553 5.872070 TCGCAACATAGACACAATACAATGA 59.128 36.000 0.00 0.00 0.00 2.57
1590 1594 6.892658 ATTTGAACTAATTGTGCCACAGTA 57.107 33.333 0.00 0.00 0.00 2.74
1689 1693 1.228675 CCCTGAATATGGGGCCAGC 60.229 63.158 4.39 0.00 40.97 4.85
1948 1952 0.471191 TAGGCCGATACGTCTCCAGA 59.529 55.000 0.00 0.00 0.00 3.86
2033 2037 6.827727 ACGTTAATAGCTGGTCTAATTCCAT 58.172 36.000 0.00 0.00 34.26 3.41
2034 2038 6.229936 ACGTTAATAGCTGGTCTAATTCCA 57.770 37.500 0.00 0.00 0.00 3.53
2307 2311 2.221169 GGCATTCGATCACATAAGCCA 58.779 47.619 0.00 0.00 40.50 4.75
2313 2317 3.132824 TGTCTAGTGGCATTCGATCACAT 59.867 43.478 0.00 0.00 34.17 3.21


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

AutoCloner maintained by Alex Coulton.