Multiple sequence alignment - TraesCS5D01G112900

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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 TraesCS5D01G112900 chr5D 100.000 3854 0 0 1 3854 129479706 129475853 0.000000e+00 7118.0
1 TraesCS5D01G112900 chr5A 95.724 3859 125 16 3 3854 144709396 144705571 0.000000e+00 6176.0
2 TraesCS5D01G112900 chr5B 97.273 2934 58 8 935 3854 141575069 141572144 0.000000e+00 4955.0
3 TraesCS5D01G112900 chr5B 90.084 958 65 16 1 950 141578398 141577463 0.000000e+00 1216.0
4 TraesCS5D01G112900 chr1A 80.840 381 66 7 1463 1839 52237608 52237231 3.770000e-75 292.0
5 TraesCS5D01G112900 chr1B 80.851 376 66 6 1467 1839 83640134 83639762 1.350000e-74 291.0
6 TraesCS5D01G112900 chr1D 80.577 381 67 7 1463 1839 52576433 52576056 1.750000e-73 287.0
7 TraesCS5D01G112900 chr7D 80.114 176 32 3 91 265 100860214 100860387 1.120000e-25 128.0
8 TraesCS5D01G112900 chr2D 100.000 32 0 0 198 229 391431 391462 4.160000e-05 60.2
9 TraesCS5D01G112900 chr4B 97.059 34 1 0 197 230 3750084 3750117 1.500000e-04 58.4
10 TraesCS5D01G112900 chr3D 75.424 118 25 3 53 166 609501084 609500967 2.000000e-03 54.7


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 TraesCS5D01G112900 chr5D 129475853 129479706 3853 True 7118.0 7118 100.0000 1 3854 1 chr5D.!!$R1 3853
1 TraesCS5D01G112900 chr5A 144705571 144709396 3825 True 6176.0 6176 95.7240 3 3854 1 chr5A.!!$R1 3851
2 TraesCS5D01G112900 chr5B 141572144 141578398 6254 True 3085.5 4955 93.6785 1 3854 2 chr5B.!!$R1 3853

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
730 740 0.179156 TCGCCGGTAAAAGCTACTCG 60.179 55.0 1.90 0.00 0.00 4.18 F
1923 4342 0.253113 TGGGGATGGGACTGTCATCA 60.253 55.0 10.38 7.75 41.89 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 4951 1.004560 CTTGAGACGGCCAAGCTCA 60.005 57.895 13.44 13.44 35.23 4.26 R
3289 5722 1.067283 AGTCGAGTCATGGAGCAACAG 60.067 52.381 0.00 0.00 0.00 3.16 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
119 120 5.728471 TGGATCTTGAGAGATGAACACTTC 58.272 41.667 0.00 0.00 42.66 3.01
132 133 5.097742 TGAACACTTCTGAAGACCTTTCA 57.902 39.130 23.36 18.96 0.00 2.69
141 142 4.103153 TCTGAAGACCTTTCAATGACCACT 59.897 41.667 0.00 0.00 0.00 4.00
170 171 1.560611 AGAGTAGTAGGAGGTCGCTGT 59.439 52.381 0.00 0.00 0.00 4.40
188 189 4.710423 CTGTAGCACAGTCTGTAGTCAT 57.290 45.455 4.85 0.00 41.19 3.06
335 336 7.653767 TTTTCTCCGATTCTCTAACAGTTTC 57.346 36.000 0.00 0.00 0.00 2.78
337 338 7.698506 TTCTCCGATTCTCTAACAGTTTCTA 57.301 36.000 0.00 0.00 0.00 2.10
467 472 3.422862 CGTTAATGCAAAAATTGGCGGTG 60.423 43.478 0.00 0.00 0.00 4.94
472 478 3.995199 TGCAAAAATTGGCGGTGAAATA 58.005 36.364 0.00 0.00 0.00 1.40
501 507 3.118629 TGGAATCTTGCTTGCGTAGATCT 60.119 43.478 0.00 0.00 0.00 2.75
542 551 8.593492 ATTTTTGACCAATCTAAAGAAAGCAC 57.407 30.769 0.00 0.00 32.33 4.40
544 553 3.188460 TGACCAATCTAAAGAAAGCACGC 59.812 43.478 0.00 0.00 0.00 5.34
589 599 7.275920 TCTAAGATAAAGAAGGAGAATGTGCC 58.724 38.462 0.00 0.00 0.00 5.01
594 604 5.876651 AAAGAAGGAGAATGTGCCTTTTT 57.123 34.783 0.00 0.00 44.23 1.94
704 714 3.430929 CCTCCTCCACTCAAAATCCTACG 60.431 52.174 0.00 0.00 0.00 3.51
725 735 1.024579 CACCATCGCCGGTAAAAGCT 61.025 55.000 1.90 0.00 37.07 3.74
726 736 0.538118 ACCATCGCCGGTAAAAGCTA 59.462 50.000 1.90 0.00 37.57 3.32
727 737 0.935196 CCATCGCCGGTAAAAGCTAC 59.065 55.000 1.90 0.00 0.00 3.58
728 738 1.472728 CCATCGCCGGTAAAAGCTACT 60.473 52.381 1.90 0.00 0.00 2.57
729 739 1.859080 CATCGCCGGTAAAAGCTACTC 59.141 52.381 1.90 0.00 0.00 2.59
730 740 0.179156 TCGCCGGTAAAAGCTACTCG 60.179 55.000 1.90 0.00 0.00 4.18
767 777 6.211587 TCCATTGCATCTCAATTCGATTTT 57.788 33.333 0.00 0.00 42.48 1.82
944 956 2.127297 CCTCCCTTTCCCCTCCCA 59.873 66.667 0.00 0.00 0.00 4.37
1827 4246 1.664649 CTTCTTCGCTCACACGCCA 60.665 57.895 0.00 0.00 0.00 5.69
1830 4249 1.664649 CTTCGCTCACACGCCAGAA 60.665 57.895 0.00 0.00 0.00 3.02
1923 4342 0.253113 TGGGGATGGGACTGTCATCA 60.253 55.000 10.38 7.75 41.89 3.07
1978 4397 2.606587 GGTGGAGGGAGTGGCATGT 61.607 63.158 0.00 0.00 0.00 3.21
2532 4951 3.605749 CTGGGGTGCCGACAACGAT 62.606 63.158 0.00 0.00 42.66 3.73
2570 4989 1.132199 CGGTCGTCCTCGTTTGATCG 61.132 60.000 0.00 0.00 38.33 3.69
3072 5494 2.429610 CAAATGGAGGAAATGGAGCCTG 59.570 50.000 0.00 0.00 33.84 4.85
3289 5722 6.842676 AGGGGAGAAGGATATTACATCAAAC 58.157 40.000 0.00 0.00 0.00 2.93
3379 5812 5.831103 ACCATGATTGATGTAAAGTTCCCT 58.169 37.500 0.00 0.00 0.00 4.20
3382 5815 6.261826 CCATGATTGATGTAAAGTTCCCTCTC 59.738 42.308 0.00 0.00 0.00 3.20
3499 5932 5.027293 AGCATCACACAGCATTACATCTA 57.973 39.130 0.00 0.00 0.00 1.98
3500 5933 4.813161 AGCATCACACAGCATTACATCTAC 59.187 41.667 0.00 0.00 0.00 2.59
3501 5934 4.813161 GCATCACACAGCATTACATCTACT 59.187 41.667 0.00 0.00 0.00 2.57
3502 5935 5.050499 GCATCACACAGCATTACATCTACTC 60.050 44.000 0.00 0.00 0.00 2.59
3503 5936 5.921962 TCACACAGCATTACATCTACTCT 57.078 39.130 0.00 0.00 0.00 3.24
3525 5958 6.330278 TCTATGTGGAGTAATCGTTGTTCAG 58.670 40.000 0.00 0.00 0.00 3.02
3549 5982 0.031857 TGTTGCTGGTTCCAAATGCG 59.968 50.000 0.00 0.00 0.00 4.73
3647 6080 4.572985 TTGACAAAGATTGTGCTTGGAG 57.427 40.909 0.00 0.00 45.52 3.86
3673 6106 1.751924 ACGGATCCCTTCTCTTTCTCG 59.248 52.381 6.06 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.459539 CCGAAGAGGCCCCTCCATA 60.460 63.158 10.64 0.00 43.70 2.74
43 44 2.770048 CCGAAGAGGCCCCTCCAT 60.770 66.667 10.64 0.51 43.70 3.41
119 120 4.214971 CAGTGGTCATTGAAAGGTCTTCAG 59.785 45.833 0.00 0.00 0.00 3.02
132 133 3.457380 ACTCTATGATGGCAGTGGTCATT 59.543 43.478 6.63 0.00 40.06 2.57
141 142 4.106502 ACCTCCTACTACTCTATGATGGCA 59.893 45.833 0.00 0.00 0.00 4.92
170 171 2.097629 GCGATGACTACAGACTGTGCTA 59.902 50.000 18.58 2.54 0.00 3.49
177 178 1.002684 CGGGTAGCGATGACTACAGAC 60.003 57.143 4.29 0.00 43.61 3.51
314 315 7.883391 ATAGAAACTGTTAGAGAATCGGAGA 57.117 36.000 0.00 0.00 42.67 3.71
427 432 8.953990 GCATTAACGTATTTACAAAGCTAATGG 58.046 33.333 9.14 0.00 0.00 3.16
462 467 3.907894 TCCAAAACACTATTTCACCGC 57.092 42.857 0.00 0.00 0.00 5.68
467 472 7.359514 GCAAGCAAGATTCCAAAACACTATTTC 60.360 37.037 0.00 0.00 0.00 2.17
472 478 3.721035 GCAAGCAAGATTCCAAAACACT 58.279 40.909 0.00 0.00 0.00 3.55
544 553 2.896745 AAGGGTAGGCGGTATTTACG 57.103 50.000 0.00 0.00 0.00 3.18
594 604 8.539117 TCACACTGAAGATTCATCCTATTAGA 57.461 34.615 0.00 0.00 36.46 2.10
704 714 0.725117 CTTTTACCGGCGATGGTGTC 59.275 55.000 9.30 0.00 43.68 3.67
716 726 7.490402 TCATAGCTTTTACGAGTAGCTTTTACC 59.510 37.037 10.29 0.00 42.30 2.85
725 735 7.042051 GCAATGGATTCATAGCTTTTACGAGTA 60.042 37.037 0.00 0.00 32.44 2.59
726 736 6.238484 GCAATGGATTCATAGCTTTTACGAGT 60.238 38.462 0.00 0.00 32.44 4.18
727 737 6.138761 GCAATGGATTCATAGCTTTTACGAG 58.861 40.000 0.00 0.00 32.44 4.18
728 738 5.588246 TGCAATGGATTCATAGCTTTTACGA 59.412 36.000 0.00 0.00 32.44 3.43
729 739 5.820131 TGCAATGGATTCATAGCTTTTACG 58.180 37.500 0.00 0.00 32.44 3.18
730 740 7.655490 AGATGCAATGGATTCATAGCTTTTAC 58.345 34.615 0.00 0.00 32.44 2.01
829 839 4.370364 AATGTCGTTTTCACAGCTTTGT 57.630 36.364 0.00 0.00 0.00 2.83
944 956 1.789576 AATGGTGGAAAGCGGGGAGT 61.790 55.000 0.00 0.00 0.00 3.85
1914 4333 1.482593 GAAGATCCCGGTGATGACAGT 59.517 52.381 9.80 0.00 32.41 3.55
1923 4342 1.214589 CGTGAACGAAGATCCCGGT 59.785 57.895 0.00 2.94 43.02 5.28
2532 4951 1.004560 CTTGAGACGGCCAAGCTCA 60.005 57.895 13.44 13.44 35.23 4.26
2829 5251 2.937519 ACTACCATCTCATCGAGCTGA 58.062 47.619 0.00 0.00 28.47 4.26
3204 5626 4.593634 GGGGCAACAGATAAGATAGTACCT 59.406 45.833 0.00 0.00 39.74 3.08
3289 5722 1.067283 AGTCGAGTCATGGAGCAACAG 60.067 52.381 0.00 0.00 0.00 3.16
3379 5812 5.527582 GGAGCTTAATTTTGGAATAGCGAGA 59.472 40.000 0.00 0.00 33.84 4.04
3382 5815 4.035208 ACGGAGCTTAATTTTGGAATAGCG 59.965 41.667 0.00 0.00 33.84 4.26
3500 5933 6.330278 TGAACAACGATTACTCCACATAGAG 58.670 40.000 0.00 0.00 39.91 2.43
3501 5934 6.275494 TGAACAACGATTACTCCACATAGA 57.725 37.500 0.00 0.00 0.00 1.98
3502 5935 5.005779 GCTGAACAACGATTACTCCACATAG 59.994 44.000 0.00 0.00 0.00 2.23
3503 5936 4.868171 GCTGAACAACGATTACTCCACATA 59.132 41.667 0.00 0.00 0.00 2.29
3525 5958 1.737355 TTGGAACCAGCAACAGCAGC 61.737 55.000 0.00 0.00 0.00 5.25
3549 5982 6.877236 TGCAGGAATGAAGAAAATAATTCCC 58.123 36.000 9.15 0.00 46.17 3.97
3610 6043 4.431131 AATGCCCCTGCCGACCTG 62.431 66.667 0.00 0.00 36.33 4.00
3673 6106 2.098117 CGATCCTTTTCAATGCCTCCAC 59.902 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.