Multiple sequence alignment - TraesCS5D01G382700

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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 TraesCS5D01G382700 chr5D 100.000 3071 0 0 1 3071 452483730 452486800 0.000000e+00 5672
1 TraesCS5D01G382700 chr5B 96.811 3042 60 12 58 3071 552748305 552751337 0.000000e+00 5046
2 TraesCS5D01G382700 chr5A 95.000 2880 80 28 51 2887 571325557 571328415 0.000000e+00 4462
3 TraesCS5D01G382700 chr5A 94.792 192 10 0 2880 3071 571328716 571328907 1.790000e-77 300


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 TraesCS5D01G382700 chr5D 452483730 452486800 3070 False 5672 5672 100.000 1 3071 1 chr5D.!!$F1 3070
1 TraesCS5D01G382700 chr5B 552748305 552751337 3032 False 5046 5046 96.811 58 3071 1 chr5B.!!$F1 3013
2 TraesCS5D01G382700 chr5A 571325557 571328907 3350 False 2381 4462 94.896 51 3071 2 chr5A.!!$F1 3020

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
50 51 0.606401 TGGAAGAGCCTTCCTTTGCG 60.606 55.0 25.19 0.0 39.31 4.85 F
555 605 0.899019 GTTCCTGGTCTCCTCTGTCC 59.101 60.0 0.00 0.0 0.00 4.02 F
839 903 1.654023 CGGGGCATTTTTCCGTCCTC 61.654 60.0 0.00 0.0 39.04 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1591 0.836830 TGTACATGGTGGGGAACGGA 60.837 55.000 0.0 0.0 0.00 4.69 R
1963 2027 0.947960 TTCGCATTTGACTTCCGCAA 59.052 45.000 0.0 0.0 0.00 4.85 R
2074 2138 1.588082 CCAAATGTGAGGTGCTGCC 59.412 57.895 0.0 0.0 37.58 4.85 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
33 34 8.320396 AGACACGTATACTATACTACATGTGG 57.680 38.462 9.11 8.41 0.00 4.17
34 35 8.152898 AGACACGTATACTATACTACATGTGGA 58.847 37.037 16.98 0.00 0.00 4.02
35 36 8.681486 ACACGTATACTATACTACATGTGGAA 57.319 34.615 16.98 0.00 0.00 3.53
36 37 8.781196 ACACGTATACTATACTACATGTGGAAG 58.219 37.037 16.98 11.86 0.00 3.46
37 38 8.996271 CACGTATACTATACTACATGTGGAAGA 58.004 37.037 16.98 1.03 0.00 2.87
38 39 9.217278 ACGTATACTATACTACATGTGGAAGAG 57.783 37.037 16.98 11.04 0.00 2.85
39 40 8.176365 CGTATACTATACTACATGTGGAAGAGC 58.824 40.741 16.98 3.66 0.00 4.09
40 41 5.793030 ACTATACTACATGTGGAAGAGCC 57.207 43.478 16.98 0.00 37.10 4.70
41 42 5.459505 ACTATACTACATGTGGAAGAGCCT 58.540 41.667 16.98 0.00 37.63 4.58
42 43 5.900123 ACTATACTACATGTGGAAGAGCCTT 59.100 40.000 16.98 0.00 37.63 4.35
43 44 3.618690 ACTACATGTGGAAGAGCCTTC 57.381 47.619 16.98 6.43 37.63 3.46
44 45 2.237392 ACTACATGTGGAAGAGCCTTCC 59.763 50.000 16.98 20.89 39.03 3.46
45 46 1.366319 ACATGTGGAAGAGCCTTCCT 58.634 50.000 25.19 10.38 39.31 3.36
46 47 1.707427 ACATGTGGAAGAGCCTTCCTT 59.293 47.619 25.19 13.37 39.31 3.36
47 48 2.108952 ACATGTGGAAGAGCCTTCCTTT 59.891 45.455 25.19 13.12 39.31 3.11
48 49 2.276732 TGTGGAAGAGCCTTCCTTTG 57.723 50.000 25.19 0.00 39.31 2.77
49 50 0.884514 GTGGAAGAGCCTTCCTTTGC 59.115 55.000 25.19 14.20 39.31 3.68
50 51 0.606401 TGGAAGAGCCTTCCTTTGCG 60.606 55.000 25.19 0.00 39.31 4.85
51 52 1.503994 GAAGAGCCTTCCTTTGCGC 59.496 57.895 0.00 0.00 0.00 6.09
52 53 2.245714 GAAGAGCCTTCCTTTGCGCG 62.246 60.000 0.00 0.00 32.19 6.86
53 54 2.731691 AAGAGCCTTCCTTTGCGCGA 62.732 55.000 12.10 0.00 32.19 5.87
54 55 2.281484 AGCCTTCCTTTGCGCGAA 60.281 55.556 12.10 10.26 0.00 4.70
55 56 2.176792 GCCTTCCTTTGCGCGAAG 59.823 61.111 27.46 27.46 36.13 3.79
86 87 2.882777 CGCGTCAAGATCAGCGCT 60.883 61.111 2.64 2.64 46.56 5.92
90 91 1.522580 GTCAAGATCAGCGCTCCCC 60.523 63.158 7.13 0.00 0.00 4.81
555 605 0.899019 GTTCCTGGTCTCCTCTGTCC 59.101 60.000 0.00 0.00 0.00 4.02
839 903 1.654023 CGGGGCATTTTTCCGTCCTC 61.654 60.000 0.00 0.00 39.04 3.71
1607 1671 4.562347 CCACCGCAGCTTCATAGAGATAAT 60.562 45.833 0.00 0.00 0.00 1.28
1963 2027 1.611673 CGGCAAACTTGATCAGGGAGT 60.612 52.381 9.90 1.01 0.00 3.85
1966 2030 2.352127 GCAAACTTGATCAGGGAGTTGC 60.352 50.000 19.74 19.74 34.13 4.17
2074 2138 0.311165 CATCCTACGTGACTAGGCCG 59.689 60.000 0.00 5.08 34.25 6.13
2095 2159 1.331214 CAGCACCTCACATTTGGGTT 58.669 50.000 0.00 0.00 0.00 4.11
2433 2497 4.889832 AGTGCTTTTTCAGTGAAGTGAG 57.110 40.909 5.56 6.74 0.00 3.51
2519 2583 6.096141 GTCTCTCTGGATTATTGTCAGACTCA 59.904 42.308 1.31 0.00 34.33 3.41
2680 2744 0.038251 TGAACAGGCACGAGCTAGTG 60.038 55.000 21.27 21.27 44.47 2.74
2768 2832 1.479323 GGTAATAGACGGTGCTGGTCA 59.521 52.381 5.43 0.00 36.87 4.02
2824 2888 3.728845 AGTATGCTGTTTGAACACGACT 58.271 40.909 0.00 0.00 34.70 4.18
2881 3253 7.718334 ATGATCATCCTATGTATTACACGGA 57.282 36.000 15.26 15.26 36.09 4.69
2897 3269 0.811616 CGGACTTAGAGGCACCATGC 60.812 60.000 0.00 0.00 44.08 4.06
2961 3333 5.862924 ATATAATATGTCACGCCTGTTGC 57.137 39.130 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.781196 CCACATGTAGTATAGTATACGTGTCTT 58.219 37.037 13.43 0.00 44.78 3.01
8 9 8.152898 TCCACATGTAGTATAGTATACGTGTCT 58.847 37.037 13.43 0.00 44.78 3.41
9 10 8.315391 TCCACATGTAGTATAGTATACGTGTC 57.685 38.462 13.43 7.18 44.78 3.67
11 12 8.996271 TCTTCCACATGTAGTATAGTATACGTG 58.004 37.037 13.43 13.70 42.20 4.49
12 13 9.217278 CTCTTCCACATGTAGTATAGTATACGT 57.783 37.037 13.43 0.00 0.00 3.57
13 14 8.176365 GCTCTTCCACATGTAGTATAGTATACG 58.824 40.741 13.43 3.33 0.00 3.06
14 15 8.460428 GGCTCTTCCACATGTAGTATAGTATAC 58.540 40.741 11.73 11.73 34.01 1.47
15 16 8.391699 AGGCTCTTCCACATGTAGTATAGTATA 58.608 37.037 0.00 0.00 37.29 1.47
16 17 7.242359 AGGCTCTTCCACATGTAGTATAGTAT 58.758 38.462 0.00 0.00 37.29 2.12
17 18 6.611785 AGGCTCTTCCACATGTAGTATAGTA 58.388 40.000 0.00 0.00 37.29 1.82
18 19 5.459505 AGGCTCTTCCACATGTAGTATAGT 58.540 41.667 0.00 0.00 37.29 2.12
19 20 6.412362 AAGGCTCTTCCACATGTAGTATAG 57.588 41.667 0.00 0.00 37.29 1.31
20 21 5.304614 GGAAGGCTCTTCCACATGTAGTATA 59.695 44.000 22.10 0.00 38.45 1.47
21 22 4.101741 GGAAGGCTCTTCCACATGTAGTAT 59.898 45.833 22.10 0.00 38.45 2.12
22 23 3.451178 GGAAGGCTCTTCCACATGTAGTA 59.549 47.826 22.10 0.00 38.45 1.82
23 24 2.237392 GGAAGGCTCTTCCACATGTAGT 59.763 50.000 22.10 0.00 38.45 2.73
24 25 2.503356 AGGAAGGCTCTTCCACATGTAG 59.497 50.000 26.22 0.00 41.00 2.74
25 26 2.551270 AGGAAGGCTCTTCCACATGTA 58.449 47.619 26.22 0.00 41.00 2.29
26 27 1.366319 AGGAAGGCTCTTCCACATGT 58.634 50.000 26.22 10.28 41.00 3.21
27 28 2.490903 CAAAGGAAGGCTCTTCCACATG 59.509 50.000 26.22 19.47 41.00 3.21
28 29 2.800250 CAAAGGAAGGCTCTTCCACAT 58.200 47.619 26.22 14.64 41.00 3.21
29 30 1.819305 GCAAAGGAAGGCTCTTCCACA 60.819 52.381 26.22 0.00 41.00 4.17
30 31 0.884514 GCAAAGGAAGGCTCTTCCAC 59.115 55.000 26.22 14.28 41.00 4.02
31 32 0.606401 CGCAAAGGAAGGCTCTTCCA 60.606 55.000 26.22 0.00 41.00 3.53
32 33 1.927608 GCGCAAAGGAAGGCTCTTCC 61.928 60.000 20.39 20.39 38.86 3.46
33 34 1.503994 GCGCAAAGGAAGGCTCTTC 59.496 57.895 0.30 6.43 0.00 2.87
34 35 2.328099 CGCGCAAAGGAAGGCTCTT 61.328 57.895 8.75 0.00 0.00 2.85
35 36 2.731691 TTCGCGCAAAGGAAGGCTCT 62.732 55.000 8.75 0.00 0.00 4.09
36 37 2.245714 CTTCGCGCAAAGGAAGGCTC 62.246 60.000 8.75 0.00 36.78 4.70
37 38 2.281484 TTCGCGCAAAGGAAGGCT 60.281 55.556 8.75 0.00 0.00 4.58
38 39 2.176792 CTTCGCGCAAAGGAAGGC 59.823 61.111 8.75 0.00 36.78 4.35
39 40 1.639298 CCTCTTCGCGCAAAGGAAGG 61.639 60.000 18.62 11.19 40.00 3.46
40 41 1.790387 CCTCTTCGCGCAAAGGAAG 59.210 57.895 8.48 11.97 40.74 3.46
41 42 2.325082 GCCTCTTCGCGCAAAGGAA 61.325 57.895 20.21 1.55 0.00 3.36
42 43 2.731691 AAGCCTCTTCGCGCAAAGGA 62.732 55.000 20.21 0.00 0.00 3.36
43 44 2.245714 GAAGCCTCTTCGCGCAAAGG 62.246 60.000 8.48 8.99 0.00 3.11
44 45 1.133458 GAAGCCTCTTCGCGCAAAG 59.867 57.895 8.75 4.48 0.00 2.77
45 46 0.037697 TAGAAGCCTCTTCGCGCAAA 60.038 50.000 8.75 0.00 32.70 3.68
46 47 0.458543 CTAGAAGCCTCTTCGCGCAA 60.459 55.000 8.75 0.00 32.70 4.85
47 48 1.139734 CTAGAAGCCTCTTCGCGCA 59.860 57.895 8.75 0.00 32.70 6.09
48 49 0.868177 GTCTAGAAGCCTCTTCGCGC 60.868 60.000 0.00 0.00 32.70 6.86
49 50 0.590230 CGTCTAGAAGCCTCTTCGCG 60.590 60.000 0.00 0.00 32.70 5.87
50 51 0.868177 GCGTCTAGAAGCCTCTTCGC 60.868 60.000 18.67 11.37 37.64 4.70
51 52 0.590230 CGCGTCTAGAAGCCTCTTCG 60.590 60.000 22.52 7.79 32.70 3.79
52 53 0.868177 GCGCGTCTAGAAGCCTCTTC 60.868 60.000 22.52 5.65 32.70 2.87
53 54 1.139947 GCGCGTCTAGAAGCCTCTT 59.860 57.895 22.52 0.00 32.70 2.85
54 55 2.802106 GCGCGTCTAGAAGCCTCT 59.198 61.111 22.52 0.00 35.52 3.69
55 56 2.652496 CGCGCGTCTAGAAGCCTC 60.652 66.667 24.19 14.30 32.09 4.70
310 333 1.671901 GAGGCCGAGAAGAGGAGGTG 61.672 65.000 0.00 0.00 0.00 4.00
316 339 0.739112 GCTTGTGAGGCCGAGAAGAG 60.739 60.000 16.07 5.12 0.00 2.85
408 442 4.547367 GGGGACGGGAGAATGGCG 62.547 72.222 0.00 0.00 0.00 5.69
443 484 3.803368 GCCCCAACAACCAAAAGAATCAG 60.803 47.826 0.00 0.00 0.00 2.90
712 774 4.663444 GGATCAATCCGAGGAGCG 57.337 61.111 0.00 0.00 37.19 5.03
839 903 2.919043 CGGAGGAATTGGGGAGGG 59.081 66.667 0.00 0.00 0.00 4.30
1527 1591 0.836830 TGTACATGGTGGGGAACGGA 60.837 55.000 0.00 0.00 0.00 4.69
1947 2011 2.154462 CGCAACTCCCTGATCAAGTTT 58.846 47.619 8.28 0.00 31.04 2.66
1963 2027 0.947960 TTCGCATTTGACTTCCGCAA 59.052 45.000 0.00 0.00 0.00 4.85
1966 2030 4.092821 TGAGTATTTCGCATTTGACTTCCG 59.907 41.667 0.00 0.00 0.00 4.30
2074 2138 1.588082 CCAAATGTGAGGTGCTGCC 59.412 57.895 0.00 0.00 37.58 4.85
2095 2159 6.220726 TCATCATCTCAGTTTATCCGACAA 57.779 37.500 0.00 0.00 0.00 3.18
2433 2497 5.277250 GCTAGAATAAGAGCAACAGATGTGC 60.277 44.000 0.00 0.00 38.62 4.57
2519 2583 6.752168 AGCAAATCAAATTACTTCAGTGCTT 58.248 32.000 0.00 0.00 35.16 3.91
2680 2744 6.603940 AGAAAGATCTGTAGGGATAGATGC 57.396 41.667 0.00 0.00 33.95 3.91
2768 2832 4.290093 TCAGTTGCCATACCATACTCTCT 58.710 43.478 0.00 0.00 0.00 3.10
2824 2888 5.252547 TGATATGTTACTTGCCAAGAAGCA 58.747 37.500 12.25 6.74 42.17 3.91
2897 3269 1.447317 GCCGCCACTGGATGTATTGG 61.447 60.000 0.00 0.00 0.00 3.16
2914 3286 7.420184 ACATGCAATAAAAACTACAAAAGCC 57.580 32.000 0.00 0.00 0.00 4.35
2961 3333 5.890424 ACAACCCCAAAATACAGTATTCG 57.110 39.130 6.26 1.63 0.00 3.34


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

AutoCloner maintained by Alex Coulton.