Multiple sequence alignment - TraesCS5B01G108100

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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 TraesCS5B01G108100 chr5B 100.000 2685 0 0 1 2685 147155900 147158584 0 4959
1 TraesCS5B01G108100 chr5D 94.340 2703 98 16 2 2683 135520682 135523350 0 4093
2 TraesCS5B01G108100 chr5A 94.290 2119 81 7 586 2685 169624920 169622823 0 3206
3 TraesCS5B01G108100 chr5A 94.526 548 18 4 2 549 169625459 169624924 0 835


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 TraesCS5B01G108100 chr5B 147155900 147158584 2684 False 4959.0 4959 100.000 1 2685 1 chr5B.!!$F1 2684
1 TraesCS5B01G108100 chr5D 135520682 135523350 2668 False 4093.0 4093 94.340 2 2683 1 chr5D.!!$F1 2681
2 TraesCS5B01G108100 chr5A 169622823 169625459 2636 True 2020.5 3206 94.408 2 2685 2 chr5A.!!$R1 2683

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
349 350 0.516877 TTTGTGGCTCGAAATCAGCG 59.483 50.0 0.0 0.0 37.81 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 1993 0.38539 GTGCACCCTCCAAGTGTTTG 59.615 55.0 5.22 0.0 37.56 2.93 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
64 65 5.221904 TGACTCCAATGTCAAATCTGAAGGA 60.222 40.000 0.00 0.00 43.08 3.36
74 75 8.383318 TGTCAAATCTGAAGGAAAGAACTTAG 57.617 34.615 0.00 0.00 31.88 2.18
81 82 6.326583 TCTGAAGGAAAGAACTTAGTCTCCAA 59.673 38.462 6.00 0.00 0.00 3.53
174 175 5.471424 TCAAGGAGAATCAGATCCCATACT 58.529 41.667 0.00 0.00 36.14 2.12
181 182 6.090186 AGAATCAGATCCCATACTCTCCATT 58.910 40.000 0.00 0.00 0.00 3.16
182 183 7.251936 AGAATCAGATCCCATACTCTCCATTA 58.748 38.462 0.00 0.00 0.00 1.90
246 247 1.141858 GGGGAAGATGGATCAGGTCAC 59.858 57.143 0.00 0.00 0.00 3.67
349 350 0.516877 TTTGTGGCTCGAAATCAGCG 59.483 50.000 0.00 0.00 37.81 5.18
357 358 2.881074 CTCGAAATCAGCGAAGGAAGA 58.119 47.619 0.00 0.00 37.32 2.87
556 557 4.512484 CCATCTCTTCTCCCTTTCTTCAC 58.488 47.826 0.00 0.00 0.00 3.18
558 559 3.497332 TCTCTTCTCCCTTTCTTCACGA 58.503 45.455 0.00 0.00 0.00 4.35
559 560 3.895656 TCTCTTCTCCCTTTCTTCACGAA 59.104 43.478 0.00 0.00 0.00 3.85
711 715 3.157087 GTTCTCATGGTGTTTGGTCCAT 58.843 45.455 0.00 0.00 44.15 3.41
841 845 2.426023 GCAGTCCGTGTGACCCTT 59.574 61.111 0.00 0.00 45.68 3.95
842 846 1.961277 GCAGTCCGTGTGACCCTTG 60.961 63.158 0.00 0.00 45.68 3.61
863 867 1.086696 CATGGTGGTAGCGTTCCAAG 58.913 55.000 7.23 0.90 36.68 3.61
1105 1124 5.939883 AGATTCCAGAACGATGACATTCAAA 59.060 36.000 0.00 0.00 0.00 2.69
1470 1490 2.268730 GCACAGCTGCCTTTGATAAC 57.731 50.000 15.27 0.00 37.45 1.89
1650 1670 8.725148 CAGTGTTAAACTCTGCATTAATCTTCT 58.275 33.333 0.00 0.00 36.83 2.85
1721 1741 9.874205 CACCTGATTGTAATATTTGGAACATTT 57.126 29.630 0.00 0.00 39.30 2.32
1741 1761 9.516314 AACATTTTGAGCTAACAGTTTTAACTC 57.484 29.630 0.00 0.00 37.08 3.01
1763 1783 6.980397 ACTCTCAACCTTGTTGCAAAAATTAG 59.020 34.615 1.65 0.00 0.00 1.73
1848 1868 4.803329 AGAAATTATGCAGGGGAGTCAT 57.197 40.909 0.00 0.00 0.00 3.06
1859 1879 2.915604 AGGGGAGTCATGAGTTCACAAT 59.084 45.455 13.78 0.00 0.00 2.71
1881 1901 7.329226 ACAATAGTGCTCAATGTTTTTATGCAC 59.671 33.333 0.00 0.00 46.38 4.57
1972 1993 9.533253 TTACAGGTACTTAACAAGAGTAACAAC 57.467 33.333 2.59 0.00 39.28 3.32
1982 2003 5.949735 ACAAGAGTAACAACAAACACTTGG 58.050 37.500 14.21 1.41 43.93 3.61
2039 2060 8.099364 ACAATATTAGCCAAATATGAAGACCG 57.901 34.615 3.37 0.00 39.41 4.79
2041 2062 9.214957 CAATATTAGCCAAATATGAAGACCGTA 57.785 33.333 3.37 0.00 39.41 4.02
2056 2077 3.429881 AGACCGTAATCCGAAACGAAAAC 59.570 43.478 7.92 0.00 41.55 2.43
2058 2079 3.559242 ACCGTAATCCGAAACGAAAACAA 59.441 39.130 7.92 0.00 41.55 2.83
2191 2213 1.342819 GGTAACATTGCCTGTGCCAAA 59.657 47.619 0.00 0.00 38.39 3.28
2236 2258 4.142881 GCCATAAGGACGAGACTTTTCAAC 60.143 45.833 0.00 0.00 36.89 3.18
2237 2259 4.994852 CCATAAGGACGAGACTTTTCAACA 59.005 41.667 0.00 0.00 36.89 3.33
2238 2260 5.468746 CCATAAGGACGAGACTTTTCAACAA 59.531 40.000 0.00 0.00 36.89 2.83
2239 2261 6.347725 CCATAAGGACGAGACTTTTCAACAAG 60.348 42.308 0.00 0.00 36.89 3.16
2240 2262 2.872858 AGGACGAGACTTTTCAACAAGC 59.127 45.455 0.00 0.00 0.00 4.01
2241 2263 2.031944 GGACGAGACTTTTCAACAAGCC 60.032 50.000 0.00 0.00 0.00 4.35
2242 2264 1.947456 ACGAGACTTTTCAACAAGCCC 59.053 47.619 0.00 0.00 0.00 5.19
2243 2265 2.222027 CGAGACTTTTCAACAAGCCCT 58.778 47.619 0.00 0.00 0.00 5.19
2244 2266 2.031682 CGAGACTTTTCAACAAGCCCTG 60.032 50.000 0.00 0.00 0.00 4.45
2245 2267 2.294512 GAGACTTTTCAACAAGCCCTGG 59.705 50.000 0.00 0.00 0.00 4.45
2246 2268 0.752658 ACTTTTCAACAAGCCCTGGC 59.247 50.000 0.00 0.00 42.33 4.85
2363 2385 2.525105 TTCCAAAGCCCCATCCTAAC 57.475 50.000 0.00 0.00 0.00 2.34
2396 2418 0.250467 CGCATCCCCCACCTATTCAG 60.250 60.000 0.00 0.00 0.00 3.02
2418 2440 7.879070 TCAGAAAGAGGAAATTCAATTCAGTG 58.121 34.615 0.00 0.00 0.00 3.66
2440 2462 7.928167 CAGTGCCAATTTACTCTAGATGATGTA 59.072 37.037 0.00 0.00 0.00 2.29
2441 2463 8.147058 AGTGCCAATTTACTCTAGATGATGTAG 58.853 37.037 0.00 0.00 0.00 2.74
2442 2464 7.928706 GTGCCAATTTACTCTAGATGATGTAGT 59.071 37.037 0.00 0.00 0.00 2.73
2443 2465 8.486210 TGCCAATTTACTCTAGATGATGTAGTT 58.514 33.333 0.00 0.00 0.00 2.24
2444 2466 8.983724 GCCAATTTACTCTAGATGATGTAGTTC 58.016 37.037 0.00 0.00 0.00 3.01
2517 2539 4.079253 GAGGCATTCCTGTGGTAGAAAAA 58.921 43.478 0.00 0.00 44.46 1.94
2521 2543 5.222631 GCATTCCTGTGGTAGAAAAACAAG 58.777 41.667 0.00 0.00 0.00 3.16
2552 2574 9.590451 AGCATGTTATTTTCTTACAATGAATGG 57.410 29.630 0.00 0.00 0.00 3.16
2553 2575 8.819974 GCATGTTATTTTCTTACAATGAATGGG 58.180 33.333 0.00 0.00 0.00 4.00
2588 2610 9.745880 ATAAGGAATAGTTACTGACGTACAATG 57.254 33.333 0.00 0.00 0.00 2.82
2620 2642 5.745227 ACTCTTCAAAGAAAGTCTGTTCCA 58.255 37.500 0.00 0.00 34.03 3.53
2629 2651 9.586435 CAAAGAAAGTCTGTTCCAGTAAATTTT 57.414 29.630 0.00 0.00 32.61 1.82
2632 2654 9.190317 AGAAAGTCTGTTCCAGTAAATTTTTCT 57.810 29.630 0.00 0.00 32.61 2.52
2633 2655 9.803315 GAAAGTCTGTTCCAGTAAATTTTTCTT 57.197 29.630 0.00 0.00 32.61 2.52
2639 2661 7.414436 TGTTCCAGTAAATTTTTCTTCAGACG 58.586 34.615 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.765219 GGCAAGAAAAAGAGAATAAGGTTTTTC 58.235 33.333 9.92 9.92 44.08 2.29
6 7 5.948758 AGAGGGCAAGAAAAAGAGAATAAGG 59.051 40.000 0.00 0.00 0.00 2.69
64 65 4.254492 GCGGATTGGAGACTAAGTTCTTT 58.746 43.478 0.00 0.00 0.00 2.52
74 75 3.195698 GTGCGGCGGATTGGAGAC 61.196 66.667 9.78 0.00 0.00 3.36
81 82 2.509336 CTCTTTCGTGCGGCGGAT 60.509 61.111 9.78 0.00 41.72 4.18
93 94 4.614946 GCATTTCAGTTGCTTGTCTCTTT 58.385 39.130 0.00 0.00 37.14 2.52
159 160 9.741198 ATATAATGGAGAGTATGGGATCTGATT 57.259 33.333 0.00 0.00 0.00 2.57
246 247 4.746951 TGCGCGTACGGTGTCTCG 62.747 66.667 18.39 11.69 40.57 4.04
349 350 9.255304 GATTATACATCTGTTGAGTCTTCCTTC 57.745 37.037 0.00 0.00 0.00 3.46
357 358 6.098838 TCAGGCAGATTATACATCTGTTGAGT 59.901 38.462 18.21 0.00 45.38 3.41
513 514 3.381590 GGGAACACAGCTTGAAGAAAAGT 59.618 43.478 0.00 0.00 0.00 2.66
556 557 4.084013 AGCAACGAAGGAATACAGTTTTCG 60.084 41.667 3.69 3.69 44.33 3.46
558 559 6.261381 TGTTAGCAACGAAGGAATACAGTTTT 59.739 34.615 0.00 0.00 0.00 2.43
559 560 5.761234 TGTTAGCAACGAAGGAATACAGTTT 59.239 36.000 0.00 0.00 0.00 2.66
841 845 1.376683 GAACGCTACCACCATGGCA 60.377 57.895 13.04 0.00 42.67 4.92
842 846 2.112815 GGAACGCTACCACCATGGC 61.113 63.158 13.04 0.00 42.67 4.40
1470 1490 5.221185 CCTCTTATGCATTCACAGAAATGGG 60.221 44.000 3.54 0.00 37.17 4.00
1650 1670 7.926674 TCAGTGAAAATGAGAATGCAATAGA 57.073 32.000 0.00 0.00 35.16 1.98
1721 1741 7.012044 GGTTGAGAGTTAAAACTGTTAGCTCAA 59.988 37.037 14.86 14.86 40.00 3.02
1741 1761 5.050159 GGCTAATTTTTGCAACAAGGTTGAG 60.050 40.000 12.90 0.53 0.00 3.02
1791 1811 6.280643 GGAAACAAAACTGAAGGCTGTATTT 58.719 36.000 0.00 0.00 0.00 1.40
1848 1868 5.308014 ACATTGAGCACTATTGTGAACTCA 58.692 37.500 11.66 11.56 46.55 3.41
1946 1967 9.533253 GTTGTTACTCTTGTTAAGTACCTGTAA 57.467 33.333 0.00 0.00 0.00 2.41
1948 1969 7.558604 TGTTGTTACTCTTGTTAAGTACCTGT 58.441 34.615 0.00 0.00 0.00 4.00
1972 1993 0.385390 GTGCACCCTCCAAGTGTTTG 59.615 55.000 5.22 0.00 37.56 2.93
2032 2053 2.867429 TCGTTTCGGATTACGGTCTTC 58.133 47.619 11.57 0.00 44.45 2.87
2039 2060 7.217447 CCATGTATTGTTTTCGTTTCGGATTAC 59.783 37.037 0.00 0.00 0.00 1.89
2041 2062 6.072397 TCCATGTATTGTTTTCGTTTCGGATT 60.072 34.615 0.00 0.00 0.00 3.01
2056 2077 8.859236 ACAGAATGAGGATAATCCATGTATTG 57.141 34.615 0.00 0.00 38.32 1.90
2058 2079 9.950496 GTAACAGAATGAGGATAATCCATGTAT 57.050 33.333 0.00 0.00 38.32 2.29
2078 2100 8.783093 TGAACTTGGACATTTTCATAGTAACAG 58.217 33.333 0.00 0.00 0.00 3.16
2093 2115 6.462552 TTGATGTTTTGATGAACTTGGACA 57.537 33.333 0.00 0.00 0.00 4.02
2236 2258 2.985282 TTGCTTCGCCAGGGCTTG 60.985 61.111 8.91 0.00 39.32 4.01
2237 2259 2.674380 CTTGCTTCGCCAGGGCTT 60.674 61.111 8.91 0.00 39.32 4.35
2240 2262 2.270986 AAAGCTTGCTTCGCCAGGG 61.271 57.895 8.39 0.00 0.00 4.45
2241 2263 1.080974 CAAAGCTTGCTTCGCCAGG 60.081 57.895 8.39 0.00 0.00 4.45
2242 2264 1.080974 CCAAAGCTTGCTTCGCCAG 60.081 57.895 8.39 0.00 0.00 4.85
2243 2265 1.827789 ACCAAAGCTTGCTTCGCCA 60.828 52.632 8.39 0.00 0.00 5.69
2244 2266 1.372128 CACCAAAGCTTGCTTCGCC 60.372 57.895 8.39 0.00 0.00 5.54
2245 2267 2.018324 GCACCAAAGCTTGCTTCGC 61.018 57.895 8.39 5.92 35.74 4.70
2246 2268 4.233408 GCACCAAAGCTTGCTTCG 57.767 55.556 8.39 4.83 35.74 3.79
2363 2385 1.002134 ATGCGGAGTTGGTCTTGGG 60.002 57.895 0.00 0.00 0.00 4.12
2396 2418 5.866092 GGCACTGAATTGAATTTCCTCTTTC 59.134 40.000 0.00 0.00 0.00 2.62
2418 2440 8.894768 AACTACATCATCTAGAGTAAATTGGC 57.105 34.615 0.00 0.00 0.00 4.52
2552 2574 9.209175 CAGTAACTATTCCTTATTGACTATGCC 57.791 37.037 0.00 0.00 0.00 4.40
2553 2575 9.982651 TCAGTAACTATTCCTTATTGACTATGC 57.017 33.333 0.00 0.00 0.00 3.14
2588 2610 6.004574 ACTTTCTTTGAAGAGTTATGGTCCC 58.995 40.000 0.00 0.00 36.22 4.46
2620 2642 7.227910 TGGCTTACGTCTGAAGAAAAATTTACT 59.772 33.333 0.00 0.00 0.00 2.24
2629 2651 3.746045 AACTGGCTTACGTCTGAAGAA 57.254 42.857 0.00 0.00 0.00 2.52
2632 2654 4.325028 TTGTAACTGGCTTACGTCTGAA 57.675 40.909 0.00 0.00 38.08 3.02
2633 2655 4.325028 TTTGTAACTGGCTTACGTCTGA 57.675 40.909 0.00 0.00 38.08 3.27
2639 2661 7.683437 AATAGAGGTTTTGTAACTGGCTTAC 57.317 36.000 0.00 0.00 36.06 2.34


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

AutoCloner maintained by Alex Coulton.