Multiple sequence alignment - TraesCS5D01G079600

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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 TraesCS5D01G079600 chr5D 100.000 2786 0 0 1 2786 80020428 80017643 0 5145
1 TraesCS5D01G079600 chr7B 97.203 2789 74 2 1 2785 742950732 742947944 0 4715
2 TraesCS5D01G079600 chr7A 97.167 2789 75 2 1 2785 60170761 60167973 0 4710
3 TraesCS5D01G079600 chr2A 97.168 2790 74 2 1 2785 755478554 755481343 0 4710
4 TraesCS5D01G079600 chr5A 97.060 2789 77 3 1 2785 420183709 420186496 0 4691
5 TraesCS5D01G079600 chr4D 96.915 2788 83 2 1 2785 123348128 123350915 0 4669
6 TraesCS5D01G079600 chr1D 96.845 2789 83 3 1 2785 185745755 185742968 0 4658
7 TraesCS5D01G079600 chr1B 96.869 2779 82 3 1 2775 583563542 583560765 0 4645
8 TraesCS5D01G079600 chr6A 96.701 2789 88 2 1 2785 155855305 155858093 0 4638
9 TraesCS5D01G079600 chr2D 96.701 2789 88 2 1 2785 200924303 200927091 0 4638


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 TraesCS5D01G079600 chr5D 80017643 80020428 2785 True 5145 5145 100.000 1 2786 1 chr5D.!!$R1 2785
1 TraesCS5D01G079600 chr7B 742947944 742950732 2788 True 4715 4715 97.203 1 2785 1 chr7B.!!$R1 2784
2 TraesCS5D01G079600 chr7A 60167973 60170761 2788 True 4710 4710 97.167 1 2785 1 chr7A.!!$R1 2784
3 TraesCS5D01G079600 chr2A 755478554 755481343 2789 False 4710 4710 97.168 1 2785 1 chr2A.!!$F1 2784
4 TraesCS5D01G079600 chr5A 420183709 420186496 2787 False 4691 4691 97.060 1 2785 1 chr5A.!!$F1 2784
5 TraesCS5D01G079600 chr4D 123348128 123350915 2787 False 4669 4669 96.915 1 2785 1 chr4D.!!$F1 2784
6 TraesCS5D01G079600 chr1D 185742968 185745755 2787 True 4658 4658 96.845 1 2785 1 chr1D.!!$R1 2784
7 TraesCS5D01G079600 chr1B 583560765 583563542 2777 True 4645 4645 96.869 1 2775 1 chr1B.!!$R1 2774
8 TraesCS5D01G079600 chr6A 155855305 155858093 2788 False 4638 4638 96.701 1 2785 1 chr6A.!!$F1 2784
9 TraesCS5D01G079600 chr2D 200924303 200927091 2788 False 4638 4638 96.701 1 2785 1 chr2D.!!$F1 2784

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
42 43 1.002430 TCACAGAAGCGAATGCCTCTT 59.998 47.619 0.00 0.0 38.80 2.85 F
1638 1644 1.066303 TGCGATTGGACAAAAACGCTT 59.934 42.857 23.16 0.0 39.77 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1718 0.032615 AGAGGAGCAGGATCCGAAGT 60.033 55.0 5.98 0.0 44.65 3.01 R
2741 2747 0.902048 GGTATAGGTAGGGGGTCCGC 60.902 65.0 0.00 0.0 38.33 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
25 26 5.672856 CGTTGCTTCGCTTATTAAAGATCAC 59.327 40.000 0.00 0.00 34.37 3.06
42 43 1.002430 TCACAGAAGCGAATGCCTCTT 59.998 47.619 0.00 0.00 38.80 2.85
311 312 5.163447 CGGTAGATTCCATTCAACTGGTAGA 60.163 44.000 0.00 0.00 37.57 2.59
534 535 4.653341 AGGAAGACTCGGAATCATTCTCAT 59.347 41.667 0.00 0.00 0.00 2.90
714 718 1.939974 CAATTCTCGCGGGAATCTCA 58.060 50.000 32.80 7.31 35.19 3.27
921 925 7.758980 CGGTTCACCAAATGATAATTCAAATCA 59.241 33.333 0.00 0.00 37.11 2.57
982 986 7.446625 CGGATTTCTCCCTTCAAAATATCATCT 59.553 37.037 0.00 0.00 38.45 2.90
1127 1131 1.718757 GGAGATGGGATTGCACGTGC 61.719 60.000 33.11 33.11 42.50 5.34
1140 1144 3.016031 TGCACGTGCTTATGGATTGAAT 58.984 40.909 37.59 0.00 42.66 2.57
1178 1182 3.680156 GGTGGAATTTGCCAGCGA 58.320 55.556 0.00 0.00 45.32 4.93
1302 1306 4.445448 GGATCTATTGTGGATGTTCCTGCT 60.445 45.833 0.00 0.00 37.46 4.24
1415 1419 1.566231 AGTGAAAGCCCCAGGGATTAG 59.434 52.381 7.25 0.00 43.82 1.73
1432 1436 5.293569 GGGATTAGTGAACGTAAATCTGTGG 59.706 44.000 0.00 0.00 0.00 4.17
1517 1521 3.119029 CGAGAACTTATAACCGGGGACAA 60.119 47.826 6.32 0.00 0.00 3.18
1534 1538 5.105269 GGGGACAAACAAACTGGAAAAACTA 60.105 40.000 0.00 0.00 0.00 2.24
1584 1588 2.978156 AGCAAATGAACTCAAGGGGA 57.022 45.000 0.00 0.00 0.00 4.81
1599 1603 4.043310 TCAAGGGGAACAAATGAGAGTGAT 59.957 41.667 0.00 0.00 0.00 3.06
1638 1644 1.066303 TGCGATTGGACAAAAACGCTT 59.934 42.857 23.16 0.00 39.77 4.68
1704 1710 7.768582 TGCTTTCGAATATTCCATTCTTGTAGA 59.231 33.333 9.87 0.00 0.00 2.59
1712 1718 2.642311 TCCATTCTTGTAGAAGCCACCA 59.358 45.455 0.00 0.00 37.69 4.17
1752 1758 3.113824 TGCAATTTCTGGCCCCATATTT 58.886 40.909 0.00 0.00 0.00 1.40
1763 1769 1.499007 CCCCATATTTAGGGTGTGCCT 59.501 52.381 0.00 0.00 45.28 4.75
1833 1839 3.536956 TGATCTAAGTAAACAGGCGGG 57.463 47.619 0.00 0.00 0.00 6.13
1841 1847 0.553819 TAAACAGGCGGGGGCATATT 59.446 50.000 0.00 0.00 0.00 1.28
1917 1923 7.654022 GGGATGTTTTCTATTTACATTCCCA 57.346 36.000 0.00 0.00 40.58 4.37
1971 1977 1.066303 GACAGGTGCAGGTATCTCGAG 59.934 57.143 5.93 5.93 0.00 4.04
1975 1981 0.173481 GTGCAGGTATCTCGAGTGCA 59.827 55.000 20.06 20.06 41.72 4.57
2010 2016 3.402628 AACACAAGCTGGAGACGTATT 57.597 42.857 0.00 0.00 0.00 1.89
2082 2088 8.862325 TGTTTGGAAATAGAGCTCTTTTATCA 57.138 30.769 23.84 17.38 0.00 2.15
2114 2120 5.823045 AGACCAGCTATTAATGTTGGCTTAC 59.177 40.000 15.57 8.69 39.03 2.34
2118 2124 3.304458 GCTATTAATGTTGGCTTACCCGC 60.304 47.826 0.00 0.00 35.87 6.13
2206 2212 2.588027 TGGCACAATATCGCGAAGTA 57.412 45.000 15.24 1.35 31.92 2.24
2208 2214 2.159156 TGGCACAATATCGCGAAGTAGT 60.159 45.455 15.24 7.40 31.92 2.73
2367 2373 1.571460 CTGTCAACGGCTTCTGTGC 59.429 57.895 0.00 0.00 0.00 4.57
2370 2376 0.880278 GTCAACGGCTTCTGTGCTCA 60.880 55.000 0.00 0.00 0.00 4.26
2504 2510 6.916360 TGGAACCAGATGCTTCTTTAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
2578 2584 5.186198 GCAGATGTAGGAAGAAGGCTTTTA 58.814 41.667 0.00 0.00 33.61 1.52
2580 2586 6.319911 GCAGATGTAGGAAGAAGGCTTTTATT 59.680 38.462 0.00 0.00 33.61 1.40
2619 2625 3.913089 AGGCTATTTTGGACTTTTTGCG 58.087 40.909 0.00 0.00 0.00 4.85
2702 2708 2.204059 ACAAGGGGGAGCTGCTCT 60.204 61.111 27.09 6.46 0.00 4.09
2724 2730 2.318207 AGTAGTTCAGGATACCCCACCT 59.682 50.000 0.00 0.00 37.41 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.153513 GCGAGCACTTTTCAATCAATTACA 58.846 37.500 0.00 0.00 0.00 2.41
311 312 3.527665 AGTGTTATGGGTAAGGGCTTGAT 59.472 43.478 0.00 0.00 0.00 2.57
714 718 1.534729 GAATCGGCCCAAACAAGACT 58.465 50.000 0.00 0.00 0.00 3.24
790 794 1.075525 TCGTAGGGGCCAGCATACT 60.076 57.895 4.39 0.00 0.00 2.12
1140 1144 4.263639 ACCATTTCTCCTGCTTGAATCTCA 60.264 41.667 0.00 0.00 0.00 3.27
1415 1419 5.390567 GGTTCATCCACAGATTTACGTTCAC 60.391 44.000 0.00 0.00 35.97 3.18
1432 1436 1.404583 GCCTGTTTGCATGGGTTCATC 60.405 52.381 0.00 0.00 0.00 2.92
1508 1512 0.466555 TCCAGTTTGTTTGTCCCCGG 60.467 55.000 0.00 0.00 0.00 5.73
1517 1521 8.007405 AGCTATTGTAGTTTTTCCAGTTTGTT 57.993 30.769 0.00 0.00 0.00 2.83
1599 1603 4.991687 TCGCAACAGACACAATACAATGTA 59.008 37.500 0.00 0.00 30.84 2.29
1638 1644 3.814625 TGAACTAATTGTGCCACAGTCA 58.185 40.909 0.00 0.00 0.00 3.41
1684 1690 6.483307 TGGCTTCTACAAGAATGGAATATTCG 59.517 38.462 9.32 0.00 33.13 3.34
1704 1710 1.201429 AGGATCCGAAGTGGTGGCTT 61.201 55.000 5.98 0.00 39.52 4.35
1712 1718 0.032615 AGAGGAGCAGGATCCGAAGT 60.033 55.000 5.98 0.00 44.65 3.01
1752 1758 2.938798 CCCCCAAGGCACACCCTA 60.939 66.667 0.00 0.00 45.62 3.53
1971 1977 3.057876 TGTTTCAATCACGGGTAATGCAC 60.058 43.478 0.00 0.00 0.00 4.57
1975 1981 4.320935 GCTTGTGTTTCAATCACGGGTAAT 60.321 41.667 0.00 0.00 38.48 1.89
2010 2016 1.710244 CATTGGTGGGGATATAGGCCA 59.290 52.381 5.01 0.00 0.00 5.36
2082 2088 9.113838 CAACATTAATAGCTGGTCTAATTCTGT 57.886 33.333 0.00 0.00 0.00 3.41
2118 2124 4.778415 CAGACCCGACGCGACTGG 62.778 72.222 15.93 16.25 0.00 4.00
2208 2214 0.602562 CCCAAATTGAGCGAAGGCAA 59.397 50.000 0.00 0.00 43.41 4.52
2347 2353 0.882042 CACAGAAGCCGTTGACAGCT 60.882 55.000 0.00 0.00 42.40 4.24
2367 2373 6.373774 AGAAATTCTGTCTAGTGGCATTTGAG 59.626 38.462 0.00 0.00 0.00 3.02
2370 2376 6.240894 TGAGAAATTCTGTCTAGTGGCATTT 58.759 36.000 0.00 0.00 0.00 2.32
2504 2510 3.568007 CACAGGTAAGGCAAAGTGCTTTA 59.432 43.478 1.12 1.12 41.04 1.85
2578 2584 2.028561 ATTGGGGTTCAGTTGGCAAT 57.971 45.000 1.92 0.00 0.00 3.56
2580 2586 1.272425 CCTATTGGGGTTCAGTTGGCA 60.272 52.381 0.00 0.00 0.00 4.92
2642 2648 1.857318 TTGGTTTACGCATGGCACGG 61.857 55.000 2.51 0.00 34.00 4.94
2702 2708 3.534747 AGGTGGGGTATCCTGAACTACTA 59.465 47.826 0.00 0.00 36.20 1.82
2741 2747 0.902048 GGTATAGGTAGGGGGTCCGC 60.902 65.000 0.00 0.00 38.33 5.54


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

AutoCloner maintained by Alex Coulton.