Multiple sequence alignment - TraesCS3D01G203500

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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 TraesCS3D01G203500 chr3D 100.000 3845 0 0 1 3845 253518977 253522821 0.000000e+00 7101
1 TraesCS3D01G203500 chr3A 97.330 3071 69 5 1 3061 336597330 336600397 0.000000e+00 5204
2 TraesCS3D01G203500 chr3A 94.030 536 19 8 3060 3583 336600796 336601330 0.000000e+00 800
3 TraesCS3D01G203500 chr3A 95.918 196 7 1 3650 3845 336604908 336605102 2.230000e-82 316
4 TraesCS3D01G203500 chr3B 97.060 2007 54 1 1055 3061 309421487 309419486 0.000000e+00 3374
5 TraesCS3D01G203500 chr3B 96.907 1067 20 4 1 1060 309616011 309614951 0.000000e+00 1775
6 TraesCS3D01G203500 chr3B 96.296 405 15 0 3224 3628 309419051 309418647 0.000000e+00 665
7 TraesCS3D01G203500 chr3B 95.192 208 9 1 3638 3845 309418349 309418143 1.030000e-85 327
8 TraesCS3D01G203500 chr3B 97.479 119 3 0 3060 3178 309419173 309419055 1.810000e-48 204


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 TraesCS3D01G203500 chr3D 253518977 253522821 3844 False 7101.000000 7101 100.000000 1 3845 1 chr3D.!!$F1 3844
1 TraesCS3D01G203500 chr3A 336597330 336605102 7772 False 2106.666667 5204 95.759333 1 3845 3 chr3A.!!$F1 3844
2 TraesCS3D01G203500 chr3B 309614951 309616011 1060 True 1775.000000 1775 96.907000 1 1060 1 chr3B.!!$R1 1059
3 TraesCS3D01G203500 chr3B 309418143 309421487 3344 True 1142.500000 3374 96.506750 1055 3845 4 chr3B.!!$R2 2790

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
613 614 0.617535 TCCCCGATGGCTTTCTGAGA 60.618 55.000 0.0 0.0 0.0 3.27 F
1341 1362 2.286523 CCACTCTCACCCGCTTCCT 61.287 63.158 0.0 0.0 0.0 3.36 F
2151 2172 0.477597 TGGAGATGGTGGGGAAAGGT 60.478 55.000 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1851 0.600255 CGTCTGGCTCGAAACCTTGT 60.600 55.000 5.78 0.0 0.00 3.16 R
2567 2588 1.063942 TCTCATTCGGCTGGAGACCTA 60.064 52.381 0.00 0.0 33.01 3.08 R
3634 7370 0.949105 CGCGACAGTTGCCTAACCTT 60.949 55.000 0.00 0.0 37.52 3.50 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
174 175 2.775890 ACATCTCCACACAGAAAGCAG 58.224 47.619 0.00 0.00 0.00 4.24
201 202 0.904865 ATCCAGTCTGTCGCCCTTGA 60.905 55.000 0.00 0.00 0.00 3.02
547 548 0.737367 TGAGCCTCGATGTTGCTTCG 60.737 55.000 0.00 0.00 34.99 3.79
613 614 0.617535 TCCCCGATGGCTTTCTGAGA 60.618 55.000 0.00 0.00 0.00 3.27
947 954 5.261216 TCTCCCTCTCTCTCTCTCTTTTTC 58.739 45.833 0.00 0.00 0.00 2.29
1053 1068 4.160252 GGGCCAACATGTCATACAAAGAAT 59.840 41.667 4.39 0.00 0.00 2.40
1099 1114 3.376918 GTCCAAGCCAAGGCCAGC 61.377 66.667 5.01 4.62 43.17 4.85
1341 1362 2.286523 CCACTCTCACCCGCTTCCT 61.287 63.158 0.00 0.00 0.00 3.36
1439 1460 2.750350 CACCACCCGCTCCTTCTT 59.250 61.111 0.00 0.00 0.00 2.52
1830 1851 3.370104 CTTCTTAGAGGAGCTGGAGGAA 58.630 50.000 0.00 0.00 0.00 3.36
1977 1998 6.890268 ACTTAGTGTCACATACTGTCCTGATA 59.110 38.462 5.62 0.00 0.00 2.15
2038 2059 2.161855 GCATGTTTGACAGGATGGTGA 58.838 47.619 0.00 0.00 43.62 4.02
2151 2172 0.477597 TGGAGATGGTGGGGAAAGGT 60.478 55.000 0.00 0.00 0.00 3.50
2234 2255 2.424601 TGCTCACTTGCTTGAATATGGC 59.575 45.455 0.00 0.00 0.00 4.40
2280 2301 3.104512 TGTCATCCCGTTGGAGAGTTAT 58.895 45.455 0.00 0.00 46.08 1.89
2332 2353 2.993008 GTCCTCATGCTGCCAGGA 59.007 61.111 7.74 7.74 33.68 3.86
2567 2588 5.128919 GGTTATGGCAGAGATGATTGAGTT 58.871 41.667 0.00 0.00 0.00 3.01
2664 2685 4.439837 GCAGAATTGATCCTGAAGGCTTTC 60.440 45.833 0.00 0.77 34.44 2.62
2738 2759 3.739519 GCTTACTGTATGACCAGGAGCAG 60.740 52.174 0.00 0.00 41.48 4.24
2754 2775 0.801251 GCAGCACAGAGTCATTGGAC 59.199 55.000 0.00 0.00 44.66 4.02
2799 2820 1.067060 GGTTTTGTCCCAAGCAGTGAC 59.933 52.381 0.00 0.00 0.00 3.67
3170 3608 6.676950 CATGGCTGACAAATTACTGTAAACA 58.323 36.000 4.11 0.80 0.00 2.83
3178 3616 5.596772 ACAAATTACTGTAAACACCCTGCTT 59.403 36.000 4.11 0.00 0.00 3.91
3222 3660 9.454859 AATATTGCTTGAATATTAGCCCTAGAC 57.545 33.333 7.58 0.00 42.90 2.59
3317 3757 4.826733 TGCACTGTTTGGTAAATCTCATGT 59.173 37.500 0.00 0.00 0.00 3.21
3378 3818 5.418840 ACAATAGCATTTGTGAAAGGGTAGG 59.581 40.000 3.75 0.00 38.33 3.18
3449 3889 1.953559 TGTAATCTTCCTCATGCGGC 58.046 50.000 0.00 0.00 0.00 6.53
3601 7337 5.605069 TGGTAGGCCTGAAATATGCTAGTTA 59.395 40.000 17.99 0.00 35.27 2.24
3633 7369 4.564782 ATCTCTCTGAACCTCATTTGCA 57.435 40.909 0.00 0.00 0.00 4.08
3634 7370 4.356405 TCTCTCTGAACCTCATTTGCAA 57.644 40.909 0.00 0.00 0.00 4.08
3635 7371 4.717877 TCTCTCTGAACCTCATTTGCAAA 58.282 39.130 15.44 15.44 0.00 3.68
3709 7733 2.763448 CCCTTTTTGGTTCAGTGTTGGA 59.237 45.455 0.00 0.00 0.00 3.53
3720 7744 0.944311 AGTGTTGGAGCACTAACGCG 60.944 55.000 15.83 3.53 46.68 6.01
3745 7769 5.858381 TCAAATCCTCTATCTACCACATGC 58.142 41.667 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 2.202987 CAGACTGGATGAGGCGGC 60.203 66.667 0.00 0.00 33.15 6.53
201 202 5.250774 ACTGGTTGATTATACAGGGTCTGTT 59.749 40.000 5.86 0.00 42.59 3.16
1053 1068 1.870055 CGAAACCCTCCGACTCCGAA 61.870 60.000 0.00 0.00 38.22 4.30
1341 1362 1.107538 CGATGAGGAAGCGGAGGGTA 61.108 60.000 0.00 0.00 0.00 3.69
1433 1454 3.181967 CGAGCGCGTGGAAGAAGG 61.182 66.667 8.43 0.00 0.00 3.46
1830 1851 0.600255 CGTCTGGCTCGAAACCTTGT 60.600 55.000 5.78 0.00 0.00 3.16
1977 1998 2.980233 GCTTTGCACAGCCCGTCT 60.980 61.111 14.04 0.00 33.21 4.18
2151 2172 1.402259 GCGAATCCTTCAGACGAGAGA 59.598 52.381 0.00 0.00 0.00 3.10
2234 2255 3.875134 ACCATATTTCCTTAAAGGCGACG 59.125 43.478 0.00 0.00 34.61 5.12
2280 2301 4.930405 CACAATGCACCAATCAAGCAATTA 59.070 37.500 0.00 0.00 42.15 1.40
2332 2353 5.338708 CCTCTATCATCCACTGGAACAAACT 60.339 44.000 0.66 0.00 38.70 2.66
2567 2588 1.063942 TCTCATTCGGCTGGAGACCTA 60.064 52.381 0.00 0.00 33.01 3.08
2664 2685 3.193157 CAGACCTGCAAATCAAGAACG 57.807 47.619 0.00 0.00 0.00 3.95
2754 2775 2.507484 TCCAACATCCTGTTCTGCAAG 58.493 47.619 0.00 0.00 38.77 4.01
2799 2820 5.007039 CCCATAAACAAGAGATCGACATGTG 59.993 44.000 1.15 0.00 0.00 3.21
2893 2914 5.359576 GCAATTATGTAGACCACCCATTGAA 59.640 40.000 0.00 0.00 0.00 2.69
3027 3049 9.189723 CTCACATCACTTACATACAGTATCATG 57.810 37.037 0.00 0.00 31.53 3.07
3040 3062 3.264947 TCAGCATGCTCACATCACTTAC 58.735 45.455 19.68 0.00 32.87 2.34
3095 3523 2.868839 GCAGTTTGCCAAACATGCATCT 60.869 45.455 25.85 5.38 43.79 2.90
3170 3608 5.688766 GCTCTCTAATTCCATAAAGCAGGGT 60.689 44.000 0.00 0.00 0.00 4.34
3210 3648 1.619332 GCCGCTTAGTCTAGGGCTAAT 59.381 52.381 10.03 0.00 40.59 1.73
3222 3660 1.299541 AAATCATGTCCGCCGCTTAG 58.700 50.000 0.00 0.00 0.00 2.18
3331 3771 1.542915 ACCATGCATGTGAACTCTTGC 59.457 47.619 24.58 7.46 38.43 4.01
3378 3818 5.059161 TCTCAATGCTAACCATACTGCATC 58.941 41.667 0.00 0.00 44.15 3.91
3601 7337 4.445448 GGTTCAGAGAGATACATGGCCATT 60.445 45.833 17.92 10.51 0.00 3.16
3633 7369 1.235724 GCGACAGTTGCCTAACCTTT 58.764 50.000 0.51 0.00 37.52 3.11
3634 7370 0.949105 CGCGACAGTTGCCTAACCTT 60.949 55.000 0.00 0.00 37.52 3.50
3635 7371 1.374252 CGCGACAGTTGCCTAACCT 60.374 57.895 0.00 0.00 37.52 3.50
3720 7744 5.537300 TGTGGTAGATAGAGGATTTGAGC 57.463 43.478 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.