Multiple sequence alignment - TraesCS2D01G230100

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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 TraesCS2D01G230100 chr2D 100.000 3530 0 0 1 3530 200924305 200927834 0.000000e+00 6519
1 TraesCS2D01G230100 chr1D 97.793 3534 73 4 1 3530 185745753 185742221 0.000000e+00 6089
2 TraesCS2D01G230100 chr1D 96.015 1330 25 5 2205 3530 185797629 185796324 0.000000e+00 2137
3 TraesCS2D01G230100 chr7B 98.452 3229 50 0 1 3229 742950730 742947502 0.000000e+00 5686
4 TraesCS2D01G230100 chr7B 98.019 3230 62 2 1 3229 716782615 716785843 0.000000e+00 5609
5 TraesCS2D01G230100 chr2A 98.421 3230 50 1 1 3229 755478556 755481785 0.000000e+00 5681
6 TraesCS2D01G230100 chr7A 98.359 3229 53 0 1 3229 60170759 60167531 0.000000e+00 5670
7 TraesCS2D01G230100 chr7A 87.500 104 8 3 3242 3341 60262649 60262751 8.010000e-22 115
8 TraesCS2D01G230100 chr5A 98.204 3229 57 1 1 3229 420183711 420186938 0.000000e+00 5640
9 TraesCS2D01G230100 chr5A 98.463 3187 49 0 43 3229 16542604 16545790 0.000000e+00 5614
10 TraesCS2D01G230100 chr5A 90.654 107 6 2 3233 3335 162145443 162145337 4.750000e-29 139
11 TraesCS2D01G230100 chr4D 98.142 3230 58 2 1 3229 123348130 123351358 0.000000e+00 5631
12 TraesCS2D01G230100 chr6A 97.832 3229 70 0 1 3229 155855307 155858535 0.000000e+00 5576
13 TraesCS2D01G230100 chrUn 95.175 974 19 5 2561 3530 422736166 422735217 0.000000e+00 1513
14 TraesCS2D01G230100 chrUn 90.805 87 4 2 3259 3341 86444841 86444927 2.880000e-21 113
15 TraesCS2D01G230100 chrUn 90.805 87 4 2 3259 3341 206782010 206782096 2.880000e-21 113
16 TraesCS2D01G230100 chr4A 88.785 107 8 2 3233 3335 350191142 350191036 1.030000e-25 128
17 TraesCS2D01G230100 chr3B 88.119 101 7 3 3233 3329 575857967 575857868 8.010000e-22 115


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 TraesCS2D01G230100 chr2D 200924305 200927834 3529 False 6519 6519 100.000 1 3530 1 chr2D.!!$F1 3529
1 TraesCS2D01G230100 chr1D 185742221 185745753 3532 True 6089 6089 97.793 1 3530 1 chr1D.!!$R1 3529
2 TraesCS2D01G230100 chr1D 185796324 185797629 1305 True 2137 2137 96.015 2205 3530 1 chr1D.!!$R2 1325
3 TraesCS2D01G230100 chr7B 742947502 742950730 3228 True 5686 5686 98.452 1 3229 1 chr7B.!!$R1 3228
4 TraesCS2D01G230100 chr7B 716782615 716785843 3228 False 5609 5609 98.019 1 3229 1 chr7B.!!$F1 3228
5 TraesCS2D01G230100 chr2A 755478556 755481785 3229 False 5681 5681 98.421 1 3229 1 chr2A.!!$F1 3228
6 TraesCS2D01G230100 chr7A 60167531 60170759 3228 True 5670 5670 98.359 1 3229 1 chr7A.!!$R1 3228
7 TraesCS2D01G230100 chr5A 420183711 420186938 3227 False 5640 5640 98.204 1 3229 1 chr5A.!!$F2 3228
8 TraesCS2D01G230100 chr5A 16542604 16545790 3186 False 5614 5614 98.463 43 3229 1 chr5A.!!$F1 3186
9 TraesCS2D01G230100 chr4D 123348130 123351358 3228 False 5631 5631 98.142 1 3229 1 chr4D.!!$F1 3228
10 TraesCS2D01G230100 chr6A 155855307 155858535 3228 False 5576 5576 97.832 1 3229 1 chr6A.!!$F1 3228
11 TraesCS2D01G230100 chrUn 422735217 422736166 949 True 1513 1513 95.175 2561 3530 1 chrUn.!!$R1 969

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
846 848 0.615331 GAGACCATTGAGCAGGACCA 59.385 55.0 0.00 0.0 0.0 4.02 F
1279 1281 2.417379 GGAGATCTTGTCAAGCGCACTA 60.417 50.0 11.47 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1882 1.063417 CATCCCTTGGGAAAGCCTCAT 60.063 52.381 12.93 0.0 0.0 2.90 R
3278 3281 0.171455 AGACTGATCTTGACGTCGGC 59.829 55.000 11.62 0.0 0.0 5.54 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
307 308 3.871594 CGGTAGATTCCATTCAACTGGTC 59.128 47.826 0.00 0.00 37.57 4.02
320 321 1.672356 CTGGTCGGTCAAGCCCTTG 60.672 63.158 1.62 1.62 41.71 3.61
478 479 3.003480 CAGCTAGGCACTTACAAACCTC 58.997 50.000 0.00 0.00 41.75 3.85
485 486 6.819397 AGGCACTTACAAACCTCTTTATTC 57.181 37.500 0.00 0.00 27.25 1.75
540 541 0.620556 AATCATTCTCACGGCCACCT 59.379 50.000 2.24 0.00 0.00 4.00
807 809 3.078836 GGTACGCTGGCCCCTACA 61.079 66.667 0.00 0.00 0.00 2.74
846 848 0.615331 GAGACCATTGAGCAGGACCA 59.385 55.000 0.00 0.00 0.00 4.02
987 989 7.819500 TCTCCCTTCAAAATATCATCCATCTT 58.180 34.615 0.00 0.00 0.00 2.40
1014 1016 8.698973 TTTGTTAAAGTATGGAATTCTCACCA 57.301 30.769 5.23 0.00 40.57 4.17
1279 1281 2.417379 GGAGATCTTGTCAAGCGCACTA 60.417 50.000 11.47 0.00 0.00 2.74
1351 1353 2.961062 GACGCCTTGGGAGTACCTATTA 59.039 50.000 0.00 0.00 35.49 0.98
2120 2122 4.053295 GCTATTAACGTTGGCTTATCCGA 58.947 43.478 11.99 0.00 37.80 4.55
2128 2130 1.141019 GGCTTATCCGACAGTCGCA 59.859 57.895 18.02 2.36 38.82 5.10
2219 2221 2.668212 CGAAGTGGCCGCCTTTGA 60.668 61.111 14.07 0.00 0.00 2.69
2299 2301 3.550842 GCTTACAGAAGTGCCCAAACAAG 60.551 47.826 0.00 0.00 34.90 3.16
2566 2568 1.538419 GCCCCTTACTCGCAGATGTAC 60.538 57.143 0.00 0.00 33.89 2.90
2674 2676 2.143122 CGTAAACCAAGCTGCTGAGAA 58.857 47.619 1.35 0.00 0.00 2.87
2876 2878 6.481976 TGTATCAAATTAGTGGTCCGCATAAG 59.518 38.462 4.97 0.00 0.00 1.73
3022 3025 3.053693 AGGTGCTAAATCAATAGGTGCCA 60.054 43.478 0.00 0.00 0.00 4.92
3219 3222 4.754322 TGATCTCATTCGTTTTCCGATCA 58.246 39.130 0.00 0.00 46.75 2.92
3229 3232 5.933790 TCGTTTTCCGATCACATAAAAAGG 58.066 37.500 0.00 0.00 41.60 3.11
3230 3233 5.701750 TCGTTTTCCGATCACATAAAAAGGA 59.298 36.000 0.00 0.00 41.60 3.36
3494 3501 6.887626 TTTTTGTTCCCTTGTATGGTACTC 57.112 37.500 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
320 321 6.048509 CCCATTTTGAATAAGTGTTATGGGC 58.951 40.000 0.00 0.0 43.06 5.36
478 479 5.243730 ACCCATGTGGAACTTGTGAATAAAG 59.756 40.000 0.00 0.0 40.09 1.85
485 486 1.881973 CAGACCCATGTGGAACTTGTG 59.118 52.381 0.00 0.0 40.09 3.33
540 541 4.373116 GAAGCCGCTCCCGTGTGA 62.373 66.667 0.00 0.0 0.00 3.58
807 809 1.202769 TACCTTGCTTACCGCCCCTT 61.203 55.000 0.00 0.0 38.05 3.95
834 836 1.371183 CCTTCGTGGTCCTGCTCAA 59.629 57.895 0.00 0.0 0.00 3.02
835 837 2.583441 CCCTTCGTGGTCCTGCTCA 61.583 63.158 0.00 0.0 0.00 4.26
1014 1016 1.373497 CGTGAGTTCCGCAGCTCTT 60.373 57.895 0.00 0.0 33.22 2.85
1279 1281 4.712476 GCAGGAACATCCACAATAGATCT 58.288 43.478 0.00 0.0 39.61 2.75
1351 1353 2.739943 GCTTAGAGCCCCTTTTCCATT 58.260 47.619 0.00 0.0 34.48 3.16
1411 1413 7.240674 TCATGCACAGATTTACGTTCAATAAC 58.759 34.615 0.00 0.0 0.00 1.89
1486 1488 5.803461 CGATTATAAGTTCTCGTTGACCACA 59.197 40.000 0.00 0.0 0.00 4.17
1720 1722 2.054232 AATTGCAGAGGAGCAGGATG 57.946 50.000 0.00 0.0 46.54 3.51
1880 1882 1.063417 CATCCCTTGGGAAAGCCTCAT 60.063 52.381 12.93 0.0 0.00 2.90
1894 1896 6.546034 CGGGAATGTAAATAGAAAACATCCCT 59.454 38.462 14.56 0.0 38.03 4.20
2120 2122 2.573869 CAGACCCGATGCGACTGT 59.426 61.111 0.00 0.0 0.00 3.55
2217 2219 4.081406 CAAGGTCTGACCCAAATTGATCA 58.919 43.478 22.81 0.0 39.75 2.92
2219 2221 4.387026 TCAAGGTCTGACCCAAATTGAT 57.613 40.909 22.81 0.0 39.75 2.57
2299 2301 4.782019 TTGGAAGTGGTTCATATTGTGC 57.218 40.909 0.00 0.0 33.93 4.57
2566 2568 3.957474 GCGAGAAAAGCCTTCTTCG 57.043 52.632 0.51 6.8 0.00 3.79
2589 2591 4.231890 TCCAAAATAGCCTATTGGGGTTCT 59.768 41.667 12.84 0.0 44.41 3.01
2674 2676 1.281925 CCCTTGTGGCTGGGGTAGAT 61.282 60.000 0.00 0.0 39.76 1.98
2876 2878 7.041848 GCACCTCCATAATTTTCAAATATTGGC 60.042 37.037 7.89 0.0 33.71 4.52
2997 3000 4.640201 GCACCTATTGATTTAGCACCTTCA 59.360 41.667 0.00 0.0 0.00 3.02
3022 3025 3.376546 GCTAAAGCAATTGTAGCAGCTCT 59.623 43.478 17.28 0.0 40.02 4.09
3142 3145 2.037136 CGGTGAGAGCAAAGCCCAG 61.037 63.158 0.00 0.0 0.00 4.45
3219 3222 8.161699 ACGTAACTTCACATTCCTTTTTATGT 57.838 30.769 0.00 0.0 35.45 2.29
3278 3281 0.171455 AGACTGATCTTGACGTCGGC 59.829 55.000 11.62 0.0 0.00 5.54
3423 3428 2.338500 AGATCTTCCAAGTTCGCGTTC 58.662 47.619 5.77 0.0 31.60 3.95


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

AutoCloner maintained by Alex Coulton.