Multiple sequence alignment - TraesCS2B01G304800

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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 TraesCS2B01G304800 chr2B 100.000 3192 0 0 1 3192 434098631 434101822 0.000000e+00 5895
1 TraesCS2B01G304800 chr2A 96.577 3184 81 13 1 3169 493831562 493834732 0.000000e+00 5251
2 TraesCS2B01G304800 chr2D 96.625 2993 67 12 190 3166 365777569 365780543 0.000000e+00 4937
3 TraesCS2B01G304800 chr2D 95.349 86 4 0 1 86 365772644 365772729 1.540000e-28 137
4 TraesCS2B01G304800 chr2D 91.860 86 7 0 76 161 365777486 365777571 1.560000e-23 121


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 TraesCS2B01G304800 chr2B 434098631 434101822 3191 False 5895 5895 100.0000 1 3192 1 chr2B.!!$F1 3191
1 TraesCS2B01G304800 chr2A 493831562 493834732 3170 False 5251 5251 96.5770 1 3169 1 chr2A.!!$F1 3168
2 TraesCS2B01G304800 chr2D 365777486 365780543 3057 False 2529 4937 94.2425 76 3166 2 chr2D.!!$F2 3090

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
866 881 0.03213 CCGTATCACCACCTCATCGG 59.968 60.0 0.0 0.0 39.35 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2214 1.091771 CGCAAGCACCTTCGATCCAT 61.092 55.0 0.0 0.0 0.0 3.41 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
21 22 0.814410 TGTGCCTTTAACAACGGCGA 60.814 50.000 16.62 0.00 46.67 5.54
50 51 2.447887 GCACGTGGAGTCATGAGCG 61.448 63.158 18.88 0.00 36.92 5.03
64 65 2.654749 TGAGCGATGTTCTGGTGTAG 57.345 50.000 0.00 0.00 0.00 2.74
74 75 0.034380 TCTGGTGTAGCGAGTAGGCT 60.034 55.000 0.00 0.00 46.88 4.58
89 90 6.570692 CGAGTAGGCTTTGGAGTTTATCTTA 58.429 40.000 0.00 0.00 0.00 2.10
94 95 6.721318 AGGCTTTGGAGTTTATCTTATCACA 58.279 36.000 0.00 0.00 0.00 3.58
129 130 3.365472 AGCCAACCAAATATCTTGACCC 58.635 45.455 0.84 0.00 0.00 4.46
148 149 2.200052 GGAGTGGTACCCGAGAAGG 58.800 63.158 10.07 0.00 40.63 3.46
163 164 1.615392 AGAAGGCCAAATGTTGAGTGC 59.385 47.619 5.01 0.00 0.00 4.40
167 168 1.892474 GGCCAAATGTTGAGTGCCTTA 59.108 47.619 0.00 0.00 34.11 2.69
299 303 6.916440 TCTTACACACGTGTCACATAGTAAT 58.084 36.000 20.49 0.00 43.74 1.89
327 331 6.710295 TGGTATTATCTCCATTGAATGAACGG 59.290 38.462 6.76 0.00 0.00 4.44
329 333 3.931907 ATCTCCATTGAATGAACGGGA 57.068 42.857 6.76 0.00 0.00 5.14
473 484 8.568732 AAATTTAATGGCAATACCGAAATACG 57.431 30.769 0.00 0.00 43.94 3.06
578 589 7.446106 TCACTTCCCCTAGCTATCATTAAAA 57.554 36.000 0.00 0.00 0.00 1.52
866 881 0.032130 CCGTATCACCACCTCATCGG 59.968 60.000 0.00 0.00 39.35 4.18
1450 1465 5.409826 CGAAGTGCTTAAATTCAACTCCTCT 59.590 40.000 0.00 0.00 0.00 3.69
2334 2349 6.263168 TGGTGAACATTTCTTTCCTTCTTCTC 59.737 38.462 0.00 0.00 0.00 2.87
2723 2742 4.838665 AAATTTTGACTTTGTGTGTGCG 57.161 36.364 0.00 0.00 0.00 5.34
2735 2754 4.678509 TGTGTGTGCGGATTATTCTTTC 57.321 40.909 0.00 0.00 0.00 2.62
2750 2769 9.890352 GATTATTCTTTCATAACCTCTTGCATC 57.110 33.333 0.00 0.00 0.00 3.91
2780 2799 5.125100 TGTTCTTTCAATTTGCCAGCTAG 57.875 39.130 0.00 0.00 0.00 3.42
2808 2827 6.127563 TGACATATAGCTACGTCCTTGTCAAA 60.128 38.462 14.64 0.71 39.23 2.69
2994 3014 2.698855 AGTGCACATCCATGAGTACC 57.301 50.000 21.04 0.00 35.36 3.34
3023 3047 8.240883 ACTAATTACTAAGTTTGCTGAAGTCG 57.759 34.615 0.00 0.00 0.00 4.18
3096 3120 2.544267 GCGAGTAAACTACCATGCATCC 59.456 50.000 0.00 0.00 0.00 3.51
3155 3183 8.683615 TGACACGTACATATCTTCAGTTTCTAT 58.316 33.333 0.00 0.00 0.00 1.98
3157 3185 7.435488 ACACGTACATATCTTCAGTTTCTATGC 59.565 37.037 0.00 0.00 0.00 3.14
3184 3212 4.914177 TTTAACAAATACTCCCTCCCGT 57.086 40.909 0.00 0.00 0.00 5.28
3185 3213 4.476628 TTAACAAATACTCCCTCCCGTC 57.523 45.455 0.00 0.00 0.00 4.79
3186 3214 2.249309 ACAAATACTCCCTCCCGTCT 57.751 50.000 0.00 0.00 0.00 4.18
3187 3215 1.831736 ACAAATACTCCCTCCCGTCTG 59.168 52.381 0.00 0.00 0.00 3.51
3188 3216 2.108168 CAAATACTCCCTCCCGTCTGA 58.892 52.381 0.00 0.00 0.00 3.27
3189 3217 2.500098 CAAATACTCCCTCCCGTCTGAA 59.500 50.000 0.00 0.00 0.00 3.02
3190 3218 2.544844 ATACTCCCTCCCGTCTGAAA 57.455 50.000 0.00 0.00 0.00 2.69
3191 3219 2.314071 TACTCCCTCCCGTCTGAAAA 57.686 50.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.892819 CTCATGACTCCACGTGCCCT 61.893 60.000 10.91 0.00 0.00 5.19
50 51 2.656560 ACTCGCTACACCAGAACATC 57.343 50.000 0.00 0.00 0.00 3.06
64 65 1.809684 AAACTCCAAAGCCTACTCGC 58.190 50.000 0.00 0.00 0.00 5.03
74 75 9.958180 TCATTCTGTGATAAGATAAACTCCAAA 57.042 29.630 0.00 0.00 0.00 3.28
89 90 6.244552 TGGCTTCTATTCTCATTCTGTGAT 57.755 37.500 0.00 0.00 35.97 3.06
94 95 5.441718 TGGTTGGCTTCTATTCTCATTCT 57.558 39.130 0.00 0.00 0.00 2.40
148 149 2.672195 GCTAAGGCACTCAACATTTGGC 60.672 50.000 0.00 0.00 38.49 4.52
163 164 6.978659 TGTATGAACTAATCTCAACGCTAAGG 59.021 38.462 0.00 0.00 0.00 2.69
167 168 6.208988 TCTGTATGAACTAATCTCAACGCT 57.791 37.500 0.00 0.00 0.00 5.07
399 404 4.761739 TCAGCATTTTGGAGTCTAACAAGG 59.238 41.667 0.00 0.00 0.00 3.61
473 484 1.497722 GCTGAGCACTTTGTACGGC 59.502 57.895 0.00 0.00 0.00 5.68
578 589 0.109504 GACGAGCTCTTCTGAACGCT 60.110 55.000 12.85 8.65 35.03 5.07
1450 1465 3.904800 TCGTGCAGGATTGAATAAGGA 57.095 42.857 4.68 0.00 0.00 3.36
2009 2024 3.617538 GTCGAGTATGTGCGGCGC 61.618 66.667 27.44 27.44 0.00 6.53
2080 2095 2.375766 CGTTGTGCCTGAGCTCGAC 61.376 63.158 9.64 3.75 41.51 4.20
2199 2214 1.091771 CGCAAGCACCTTCGATCCAT 61.092 55.000 0.00 0.00 0.00 3.41
2334 2349 8.260114 AGCTTTAGATAAACAAATTTGGGGATG 58.740 33.333 21.74 0.00 0.00 3.51
2404 2419 1.153229 GAGTCACCCATTACCCGCC 60.153 63.158 0.00 0.00 0.00 6.13
2462 2479 4.957327 AGGTCTCCCTCTGTTCTATGTTAC 59.043 45.833 0.00 0.00 35.62 2.50
2495 2513 8.617761 AGAAGAGAAACGATAAACGATTAGAC 57.382 34.615 0.00 0.00 45.77 2.59
2497 2515 8.844441 AGAGAAGAGAAACGATAAACGATTAG 57.156 34.615 0.00 0.00 45.77 1.73
2723 2742 8.225603 TGCAAGAGGTTATGAAAGAATAATCC 57.774 34.615 0.00 0.00 0.00 3.01
2750 2769 5.368374 GCAAATTGAAAGAACAAATGCTCG 58.632 37.500 0.00 0.00 40.30 5.03
2780 2799 6.910995 ACAAGGACGTAGCTATATGTCATAC 58.089 40.000 19.16 7.67 45.90 2.39
2808 2827 8.922931 TGAATGCATGGTTGATATAGTTACAT 57.077 30.769 0.00 0.00 0.00 2.29
2918 2938 8.291032 AGATTATATTCTCGTTACGGTTCTCTG 58.709 37.037 4.53 0.00 0.00 3.35
2994 3014 8.470040 TTCAGCAAACTTAGTAATTAGTACCG 57.530 34.615 0.00 0.00 32.58 4.02
3023 3047 2.742053 TCTGGTGATTAAAGCAAGCGAC 59.258 45.455 0.00 0.00 0.00 5.19
3096 3120 9.369904 TGTTCGTATCATTATCACCATCATATG 57.630 33.333 0.00 0.00 0.00 1.78
3115 3143 1.693467 GTGTCAGACGCATGTTCGTA 58.307 50.000 9.36 0.00 43.42 3.43
3137 3165 8.798859 AAACTGCATAGAAACTGAAGATATGT 57.201 30.769 0.00 0.00 0.00 2.29
3169 3197 2.544844 TCAGACGGGAGGGAGTATTT 57.455 50.000 0.00 0.00 0.00 1.40
3170 3198 2.544844 TTCAGACGGGAGGGAGTATT 57.455 50.000 0.00 0.00 0.00 1.89
3171 3199 2.544844 TTTCAGACGGGAGGGAGTAT 57.455 50.000 0.00 0.00 0.00 2.12
3172 3200 2.314071 TTTTCAGACGGGAGGGAGTA 57.686 50.000 0.00 0.00 0.00 2.59
3173 3201 3.159141 TTTTCAGACGGGAGGGAGT 57.841 52.632 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.