Multiple sequence alignment - TraesCS2D01G191100

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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 TraesCS2D01G191100 chr2D 100.000 2155 0 0 842 2996 135309945 135307791 0.000000e+00 3980
1 TraesCS2D01G191100 chr2D 100.000 426 0 0 1 426 135310786 135310361 0.000000e+00 787
2 TraesCS2D01G191100 chr2A 95.341 2168 73 13 842 2996 143217532 143215380 0.000000e+00 3419
3 TraesCS2D01G191100 chr2A 92.500 320 18 4 112 426 143217883 143217565 1.270000e-123 453
4 TraesCS2D01G191100 chr2B 95.967 2058 66 7 953 2996 192368143 192366089 0.000000e+00 3325
5 TraesCS2D01G191100 chr2B 92.742 372 19 6 60 426 192369122 192368754 5.690000e-147 531
6 TraesCS2D01G191100 chr2B 98.462 65 1 0 842 906 192368697 192368633 6.790000e-22 115


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 TraesCS2D01G191100 chr2D 135307791 135310786 2995 True 2383.500000 3980 100.000000 1 2996 2 chr2D.!!$R1 2995
1 TraesCS2D01G191100 chr2A 143215380 143217883 2503 True 1936.000000 3419 93.920500 112 2996 2 chr2A.!!$R1 2884
2 TraesCS2D01G191100 chr2B 192366089 192369122 3033 True 1323.666667 3325 95.723667 60 2996 3 chr2B.!!$R1 2936

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
31 32 0.037975 TCGCCGAGACAAACCTAACC 60.038 55.0 0.0 0.0 0.0 2.85 F
361 376 0.106708 GTGTCAGGTTCAGTGGCTCA 59.893 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2042 1.472276 GCGCGTACACGATGGAGAAG 61.472 60.0 8.43 0.0 43.02 2.85 R
2060 2518 0.827507 AAAACTGGATGTTGCCCGCT 60.828 50.0 0.00 0.0 39.13 5.52 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
19 20 3.423154 GCCAAACAGGTCGCCGAG 61.423 66.667 0.00 0.00 40.61 4.63
20 21 2.342279 CCAAACAGGTCGCCGAGA 59.658 61.111 0.00 0.00 0.00 4.04
30 31 3.502237 TCGCCGAGACAAACCTAAC 57.498 52.632 0.00 0.00 0.00 2.34
31 32 0.037975 TCGCCGAGACAAACCTAACC 60.038 55.000 0.00 0.00 0.00 2.85
32 33 1.349259 CGCCGAGACAAACCTAACCG 61.349 60.000 0.00 0.00 0.00 4.44
33 34 0.320160 GCCGAGACAAACCTAACCGT 60.320 55.000 0.00 0.00 0.00 4.83
34 35 1.706443 CCGAGACAAACCTAACCGTC 58.294 55.000 0.00 0.00 0.00 4.79
35 36 1.334054 CGAGACAAACCTAACCGTCG 58.666 55.000 0.00 0.00 33.56 5.12
36 37 1.066136 GAGACAAACCTAACCGTCGC 58.934 55.000 0.00 0.00 33.56 5.19
37 38 0.665369 AGACAAACCTAACCGTCGCG 60.665 55.000 0.00 0.00 33.56 5.87
38 39 2.219209 GACAAACCTAACCGTCGCGC 62.219 60.000 0.00 0.00 0.00 6.86
39 40 2.739671 AAACCTAACCGTCGCGCC 60.740 61.111 0.00 0.00 0.00 6.53
40 41 3.230522 AAACCTAACCGTCGCGCCT 62.231 57.895 0.00 0.00 0.00 5.52
41 42 3.927163 AACCTAACCGTCGCGCCTG 62.927 63.158 0.00 0.00 0.00 4.85
73 74 1.250476 CGCGCTTTGCAAGTGTTATC 58.750 50.000 5.56 0.00 46.97 1.75
85 95 5.063438 TGCAAGTGTTATCTAGAATCGTTGC 59.937 40.000 15.53 15.53 37.63 4.17
95 105 3.325293 AGAATCGTTGCTCATGAGTGT 57.675 42.857 23.38 0.00 0.00 3.55
96 106 3.257393 AGAATCGTTGCTCATGAGTGTC 58.743 45.455 23.38 12.50 0.00 3.67
97 107 3.056250 AGAATCGTTGCTCATGAGTGTCT 60.056 43.478 23.38 12.19 0.00 3.41
98 108 2.354109 TCGTTGCTCATGAGTGTCTC 57.646 50.000 23.38 7.41 0.00 3.36
99 109 1.613437 TCGTTGCTCATGAGTGTCTCA 59.387 47.619 23.38 9.98 44.99 3.27
100 110 1.723542 CGTTGCTCATGAGTGTCTCAC 59.276 52.381 23.38 10.32 43.63 3.51
101 111 2.072298 GTTGCTCATGAGTGTCTCACC 58.928 52.381 23.38 5.27 43.63 4.02
102 112 0.244721 TGCTCATGAGTGTCTCACCG 59.755 55.000 23.38 0.00 43.63 4.94
103 113 0.244994 GCTCATGAGTGTCTCACCGT 59.755 55.000 23.38 0.00 43.63 4.83
104 114 1.734047 GCTCATGAGTGTCTCACCGTC 60.734 57.143 23.38 0.00 43.63 4.79
231 244 3.044305 GCGCCACGAAGCTTCACT 61.044 61.111 25.47 7.52 0.00 3.41
266 281 2.198426 CCCCCACATGCCATACCC 59.802 66.667 0.00 0.00 0.00 3.69
350 365 1.245732 GTCGGTAGTCTGTGTCAGGT 58.754 55.000 0.00 0.00 31.51 4.00
361 376 0.106708 GTGTCAGGTTCAGTGGCTCA 59.893 55.000 0.00 0.00 0.00 4.26
892 907 2.106074 CACTTAGCCGCATTCCGCA 61.106 57.895 0.00 0.00 42.60 5.69
967 1425 2.044352 TCGCCTCGGATCTGACCA 60.044 61.111 0.00 0.00 0.00 4.02
1335 1793 4.200283 CTCACGCTCCTCCTCGCC 62.200 72.222 0.00 0.00 0.00 5.54
1496 1954 4.148825 CCTCGCCACCTTCCTCGG 62.149 72.222 0.00 0.00 0.00 4.63
1584 2042 2.266055 CTCCTCACGGTCCTTGCC 59.734 66.667 0.00 0.00 0.00 4.52
1716 2174 3.758931 GGCCAAACCCATGTCGGC 61.759 66.667 0.00 0.00 42.21 5.54
1905 2363 1.798813 GTGTTCTACTTCACTTGCCGG 59.201 52.381 0.00 0.00 0.00 6.13
2008 2466 6.818644 TGCAGTGAGGTGATTAAGAAGATTAC 59.181 38.462 0.00 0.00 0.00 1.89
2060 2518 7.638444 TCATATTCTGGTGGGAAATAAGTGAA 58.362 34.615 0.00 0.00 0.00 3.18
2062 2520 3.686016 TCTGGTGGGAAATAAGTGAAGC 58.314 45.455 0.00 0.00 0.00 3.86
2074 2532 1.971167 GTGAAGCGGGCAACATCCA 60.971 57.895 0.00 0.00 39.74 3.41
2105 2563 2.253610 AGATTGAAGGGTGTGGTCGTA 58.746 47.619 0.00 0.00 0.00 3.43
2107 2565 2.465860 TTGAAGGGTGTGGTCGTATG 57.534 50.000 0.00 0.00 0.00 2.39
2108 2566 0.611200 TGAAGGGTGTGGTCGTATGG 59.389 55.000 0.00 0.00 0.00 2.74
2187 2645 1.909700 TGCAGTCATTTGGGGTTCTC 58.090 50.000 0.00 0.00 0.00 2.87
2252 2713 8.459635 GGGAAAACTTAGATTGGTGTATTCTTC 58.540 37.037 0.00 0.00 0.00 2.87
2434 2900 6.585695 AACTTGATTCATGAATCTGCACTT 57.414 33.333 36.15 22.07 45.55 3.16
2485 2952 7.840931 TCAAGTCTGTCTTCTAAATGATGCTA 58.159 34.615 0.00 0.00 33.63 3.49
2602 3069 6.179756 ACATTACAGATCACTGCCATGTAAA 58.820 36.000 10.89 0.00 46.95 2.01
2603 3070 6.658816 ACATTACAGATCACTGCCATGTAAAA 59.341 34.615 10.89 0.00 46.95 1.52
2605 3072 4.655963 ACAGATCACTGCCATGTAAAAGT 58.344 39.130 0.00 0.00 46.95 2.66
2606 3073 5.072741 ACAGATCACTGCCATGTAAAAGTT 58.927 37.500 0.00 0.00 46.95 2.66
2607 3074 5.182001 ACAGATCACTGCCATGTAAAAGTTC 59.818 40.000 0.00 0.00 46.95 3.01
2608 3075 4.702131 AGATCACTGCCATGTAAAAGTTCC 59.298 41.667 0.00 0.00 0.00 3.62
2610 3077 4.072131 TCACTGCCATGTAAAAGTTCCTC 58.928 43.478 0.00 0.00 0.00 3.71
2628 3099 7.331791 AGTTCCTCTGAGACATGGTTAATTAC 58.668 38.462 6.17 0.00 0.00 1.89
2632 3103 7.400339 TCCTCTGAGACATGGTTAATTACTCTT 59.600 37.037 6.17 0.00 0.00 2.85
2645 3116 8.178313 GGTTAATTACTCTTCTTGCATCAGAAC 58.822 37.037 0.00 0.00 0.00 3.01
2664 3135 3.064900 ACTGGAGTTCTCCATTTGCTC 57.935 47.619 19.96 0.00 39.34 4.26
2837 3308 0.736325 CGAGGCGGTAGTTGAACTGG 60.736 60.000 8.33 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.423154 CTCGGCGACCTGTTTGGC 61.423 66.667 4.99 0.00 40.22 4.52
3 4 2.027625 GTCTCGGCGACCTGTTTGG 61.028 63.158 4.99 0.00 42.93 3.28
4 5 0.878523 TTGTCTCGGCGACCTGTTTG 60.879 55.000 4.99 0.00 42.13 2.93
5 6 0.179067 TTTGTCTCGGCGACCTGTTT 60.179 50.000 4.99 0.00 42.13 2.83
6 7 0.878961 GTTTGTCTCGGCGACCTGTT 60.879 55.000 4.99 0.00 42.13 3.16
7 8 1.300697 GTTTGTCTCGGCGACCTGT 60.301 57.895 4.99 0.00 42.13 4.00
8 9 2.027625 GGTTTGTCTCGGCGACCTG 61.028 63.158 4.99 0.00 42.13 4.00
9 10 0.896940 TAGGTTTGTCTCGGCGACCT 60.897 55.000 18.01 18.01 42.13 3.85
10 11 0.037975 TTAGGTTTGTCTCGGCGACC 60.038 55.000 4.99 5.09 42.13 4.79
11 12 1.066136 GTTAGGTTTGTCTCGGCGAC 58.934 55.000 4.99 0.00 43.14 5.19
12 13 0.037975 GGTTAGGTTTGTCTCGGCGA 60.038 55.000 10.14 10.14 0.00 5.54
13 14 1.349259 CGGTTAGGTTTGTCTCGGCG 61.349 60.000 0.00 0.00 0.00 6.46
14 15 0.320160 ACGGTTAGGTTTGTCTCGGC 60.320 55.000 0.00 0.00 0.00 5.54
15 16 1.706443 GACGGTTAGGTTTGTCTCGG 58.294 55.000 0.00 0.00 0.00 4.63
16 17 1.334054 CGACGGTTAGGTTTGTCTCG 58.666 55.000 0.00 0.00 0.00 4.04
17 18 1.066136 GCGACGGTTAGGTTTGTCTC 58.934 55.000 0.00 0.00 0.00 3.36
18 19 0.665369 CGCGACGGTTAGGTTTGTCT 60.665 55.000 0.00 0.00 0.00 3.41
19 20 1.777199 CGCGACGGTTAGGTTTGTC 59.223 57.895 0.00 0.00 0.00 3.18
20 21 2.312436 GCGCGACGGTTAGGTTTGT 61.312 57.895 12.10 0.00 0.00 2.83
21 22 2.472934 GCGCGACGGTTAGGTTTG 59.527 61.111 12.10 0.00 0.00 2.93
22 23 2.739671 GGCGCGACGGTTAGGTTT 60.740 61.111 12.10 0.00 0.00 3.27
23 24 3.688159 AGGCGCGACGGTTAGGTT 61.688 61.111 12.10 0.00 0.00 3.50
24 25 4.430765 CAGGCGCGACGGTTAGGT 62.431 66.667 12.10 0.00 0.00 3.08
73 74 4.428209 ACACTCATGAGCAACGATTCTAG 58.572 43.478 22.83 0.00 0.00 2.43
85 95 1.815613 AGACGGTGAGACACTCATGAG 59.184 52.381 21.37 21.37 42.73 2.90
95 105 1.118965 TTTGGGCAGAGACGGTGAGA 61.119 55.000 0.00 0.00 0.00 3.27
96 106 0.250295 TTTTGGGCAGAGACGGTGAG 60.250 55.000 0.00 0.00 0.00 3.51
97 107 0.400213 ATTTTGGGCAGAGACGGTGA 59.600 50.000 0.00 0.00 0.00 4.02
98 108 0.523072 CATTTTGGGCAGAGACGGTG 59.477 55.000 0.00 0.00 0.00 4.94
99 109 0.609131 CCATTTTGGGCAGAGACGGT 60.609 55.000 0.00 0.00 32.67 4.83
100 110 0.322456 TCCATTTTGGGCAGAGACGG 60.322 55.000 0.00 0.00 38.32 4.79
101 111 1.089920 CTCCATTTTGGGCAGAGACG 58.910 55.000 0.00 0.00 38.32 4.18
102 112 1.004745 TCCTCCATTTTGGGCAGAGAC 59.995 52.381 0.00 0.00 38.32 3.36
103 113 1.283029 CTCCTCCATTTTGGGCAGAGA 59.717 52.381 0.00 0.00 38.32 3.10
104 114 1.283029 TCTCCTCCATTTTGGGCAGAG 59.717 52.381 0.00 0.00 38.32 3.35
350 365 2.224159 GGGAGGGTGAGCCACTGAA 61.224 63.158 2.50 0.00 34.40 3.02
387 402 2.618045 CGAGGGTAGGGCTTTTGTTGAT 60.618 50.000 0.00 0.00 0.00 2.57
942 957 1.152652 ATCCGAGGCGAGATCAGGT 60.153 57.895 0.00 0.00 0.00 4.00
1584 2042 1.472276 GCGCGTACACGATGGAGAAG 61.472 60.000 8.43 0.00 43.02 2.85
1638 2096 2.049433 ACGTCCTCAAGAACGGCG 60.049 61.111 4.80 4.80 0.00 6.46
1905 2363 2.012673 AGAATTGCCAAGCTCGATGAC 58.987 47.619 0.00 0.00 0.00 3.06
2008 2466 6.148480 CAGATACACCTTGAGAAAGAAACCTG 59.852 42.308 0.00 0.00 0.00 4.00
2060 2518 0.827507 AAAACTGGATGTTGCCCGCT 60.828 50.000 0.00 0.00 39.13 5.52
2062 2520 1.782044 CAAAAACTGGATGTTGCCCG 58.218 50.000 0.00 0.00 39.13 6.13
2074 2532 3.711190 ACCCTTCAATCTTGGCAAAAACT 59.289 39.130 0.00 0.00 0.00 2.66
2105 2563 2.057137 AAGCGTGTAATCATGGCCAT 57.943 45.000 14.09 14.09 0.00 4.40
2107 2565 3.315191 ACATTAAGCGTGTAATCATGGCC 59.685 43.478 0.00 0.00 0.00 5.36
2108 2566 4.282068 CACATTAAGCGTGTAATCATGGC 58.718 43.478 0.00 0.00 0.00 4.40
2187 2645 1.224069 CGCCATTACATGAGCCTCGG 61.224 60.000 0.00 0.00 0.00 4.63
2252 2713 2.798853 CGGATCACTGCTGAGACAGATG 60.799 54.545 10.14 5.84 40.25 2.90
2434 2900 8.786826 AGTCACTGTAAAATAAATTCGGATCA 57.213 30.769 0.00 0.00 0.00 2.92
2485 2952 6.431234 GGTTACCATGTCTCAGACTCAAAATT 59.569 38.462 6.33 0.00 33.15 1.82
2495 2962 5.812642 GTCTTATGTGGTTACCATGTCTCAG 59.187 44.000 7.58 0.00 35.28 3.35
2602 3069 5.825593 TTAACCATGTCTCAGAGGAACTT 57.174 39.130 0.00 0.00 41.55 2.66
2605 3072 7.400339 AGAGTAATTAACCATGTCTCAGAGGAA 59.600 37.037 0.00 0.00 0.00 3.36
2606 3073 6.897966 AGAGTAATTAACCATGTCTCAGAGGA 59.102 38.462 0.00 0.00 0.00 3.71
2607 3074 7.118496 AGAGTAATTAACCATGTCTCAGAGG 57.882 40.000 0.00 0.00 0.00 3.69
2608 3075 8.474025 AGAAGAGTAATTAACCATGTCTCAGAG 58.526 37.037 0.00 0.00 0.00 3.35
2610 3077 8.877779 CAAGAAGAGTAATTAACCATGTCTCAG 58.122 37.037 0.00 0.00 0.00 3.35
2628 3099 3.933955 CTCCAGTTCTGATGCAAGAAGAG 59.066 47.826 0.97 2.19 36.86 2.85
2632 3103 3.777106 AACTCCAGTTCTGATGCAAGA 57.223 42.857 0.00 0.00 31.64 3.02
2664 3135 2.303022 TGGGTTTTCTAGAGTCCAGCAG 59.697 50.000 10.56 0.00 0.00 4.24
2837 3308 7.298507 TCTGTCATATAAAAACAGCGGTTAC 57.701 36.000 1.70 0.00 40.15 2.50


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

AutoCloner maintained by Alex Coulton.