Multiple sequence alignment - TraesCS1A01G236300

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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 TraesCS1A01G236300 chr1A 100.000 2150 0 0 1 2150 418916935 418919084 0.000000e+00 3971.0
1 TraesCS1A01G236300 chr1B 93.120 2122 109 20 53 2150 438040262 438038154 0.000000e+00 3075.0
2 TraesCS1A01G236300 chr1B 93.750 48 2 1 1 48 566997631 566997585 1.060000e-08 71.3
3 TraesCS1A01G236300 chr1B 93.750 48 2 1 1 48 666836592 666836638 1.060000e-08 71.3
4 TraesCS1A01G236300 chr1D 94.460 1390 52 15 217 1594 325597895 325596519 0.000000e+00 2117.0
5 TraesCS1A01G236300 chr1D 90.569 562 39 2 1589 2150 325595969 325595422 0.000000e+00 732.0
6 TraesCS1A01G236300 chr1D 95.135 185 6 2 47 228 325598642 325598458 2.700000e-74 289.0
7 TraesCS1A01G236300 chr7B 95.833 48 1 1 1 48 594899741 594899695 2.290000e-10 76.8
8 TraesCS1A01G236300 chrUn 93.750 48 2 1 1 48 51420704 51420750 1.060000e-08 71.3
9 TraesCS1A01G236300 chrUn 91.667 48 3 1 1 48 264394274 264394320 4.950000e-07 65.8
10 TraesCS1A01G236300 chr5B 93.750 48 2 1 1 48 568185659 568185613 1.060000e-08 71.3
11 TraesCS1A01G236300 chr3B 93.750 48 2 1 1 48 16102438 16102484 1.060000e-08 71.3
12 TraesCS1A01G236300 chr5A 93.478 46 1 2 4 48 555570151 555570107 1.380000e-07 67.6
13 TraesCS1A01G236300 chr2A 91.837 49 2 2 1 48 728061833 728061880 1.380000e-07 67.6


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 TraesCS1A01G236300 chr1A 418916935 418919084 2149 False 3971 3971 100.000 1 2150 1 chr1A.!!$F1 2149
1 TraesCS1A01G236300 chr1B 438038154 438040262 2108 True 3075 3075 93.120 53 2150 1 chr1B.!!$R1 2097
2 TraesCS1A01G236300 chr1D 325595422 325598642 3220 True 1046 2117 93.388 47 2150 3 chr1D.!!$R1 2103

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
321 911 0.034477 CACCTAATCCCCACCACCAC 60.034 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1887 0.714439 GGCTTACAGTTTCGACGAGC 59.286 55.0 0.0 0.0 0.0 5.03 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
28 29 8.042515 ACCATGGTTGAAAAATGAATAGATTGG 58.957 33.333 13.00 0.00 0.00 3.16
29 30 8.259411 CCATGGTTGAAAAATGAATAGATTGGA 58.741 33.333 2.57 0.00 0.00 3.53
30 31 9.656040 CATGGTTGAAAAATGAATAGATTGGAA 57.344 29.630 0.00 0.00 0.00 3.53
31 32 9.880157 ATGGTTGAAAAATGAATAGATTGGAAG 57.120 29.630 0.00 0.00 0.00 3.46
32 33 8.869109 TGGTTGAAAAATGAATAGATTGGAAGT 58.131 29.630 0.00 0.00 0.00 3.01
33 34 9.710900 GGTTGAAAAATGAATAGATTGGAAGTT 57.289 29.630 0.00 0.00 0.00 2.66
117 126 3.058501 CCTGATAACAAAACCGTGTCCAC 60.059 47.826 0.00 0.00 0.00 4.02
119 128 2.414994 TAACAAAACCGTGTCCACCA 57.585 45.000 0.00 0.00 0.00 4.17
196 206 1.135632 ACGCTCGCTTGTCTTCTAGTC 60.136 52.381 0.00 0.00 0.00 2.59
208 218 4.395542 TGTCTTCTAGTCTTAGACGAAGCC 59.604 45.833 18.67 12.10 40.86 4.35
255 845 0.519077 CTTGGCGCTTCTTCAGTTCC 59.481 55.000 7.64 0.00 0.00 3.62
281 871 3.195610 CCAAATTCCCAGAAAACCCTAGC 59.804 47.826 0.00 0.00 0.00 3.42
313 903 0.258774 ACATGCACCACCTAATCCCC 59.741 55.000 0.00 0.00 0.00 4.81
320 910 1.211567 CCACCTAATCCCCACCACCA 61.212 60.000 0.00 0.00 0.00 4.17
321 911 0.034477 CACCTAATCCCCACCACCAC 60.034 60.000 0.00 0.00 0.00 4.16
322 912 1.212250 ACCTAATCCCCACCACCACC 61.212 60.000 0.00 0.00 0.00 4.61
364 957 1.753956 GTGTTTCACATTCACACCGC 58.246 50.000 0.00 0.00 35.72 5.68
367 960 0.865111 TTTCACATTCACACCGCGAG 59.135 50.000 8.23 1.37 0.00 5.03
396 989 2.353889 GCTACGTACGTTCTCTCCATCA 59.646 50.000 27.92 2.89 0.00 3.07
446 1047 2.812011 ACAAGTAGCCATCAACCGTTTC 59.188 45.455 0.00 0.00 0.00 2.78
454 1055 3.674753 GCCATCAACCGTTTCAATTTCAG 59.325 43.478 0.00 0.00 0.00 3.02
500 1101 5.393461 GCCCTTTGATCCTGTACTTTTCATG 60.393 44.000 0.00 0.00 0.00 3.07
527 1128 6.578023 TGTATACACATCACCATCGATCAAA 58.422 36.000 0.08 0.00 0.00 2.69
533 1134 5.854866 CACATCACCATCGATCAAATATTGC 59.145 40.000 0.00 0.00 0.00 3.56
572 1173 1.006825 CGAATCGCCGTCAAGTGACA 61.007 55.000 11.77 0.00 44.99 3.58
579 1180 1.354337 CCGTCAAGTGACAGCATCCG 61.354 60.000 11.77 0.00 44.99 4.18
862 1466 1.441311 CAACAAACTGGCCACACCC 59.559 57.895 0.00 0.00 37.83 4.61
952 1556 0.387929 TTCGTCTGACCACCACTGAC 59.612 55.000 1.55 0.00 34.49 3.51
1192 1796 1.774217 TGGTTGCTGGGAGGAAGGT 60.774 57.895 0.00 0.00 0.00 3.50
1193 1797 1.360393 TGGTTGCTGGGAGGAAGGTT 61.360 55.000 0.00 0.00 0.00 3.50
1194 1798 0.696501 GGTTGCTGGGAGGAAGGTTA 59.303 55.000 0.00 0.00 0.00 2.85
1213 1817 4.258543 GTTATTCGGTTGTTCATGGGAGA 58.741 43.478 0.00 0.00 0.00 3.71
1308 1913 4.553938 CGTCGAAACTGTAAGCCATGTTTT 60.554 41.667 0.00 0.00 37.60 2.43
1309 1914 5.333492 CGTCGAAACTGTAAGCCATGTTTTA 60.333 40.000 0.00 0.00 37.60 1.52
1310 1915 6.608610 GTCGAAACTGTAAGCCATGTTTTAT 58.391 36.000 0.00 0.00 37.60 1.40
1311 1916 6.741358 GTCGAAACTGTAAGCCATGTTTTATC 59.259 38.462 0.00 0.00 37.60 1.75
1313 1918 5.560966 AACTGTAAGCCATGTTTTATCGG 57.439 39.130 0.00 0.00 37.60 4.18
1314 1919 4.585879 ACTGTAAGCCATGTTTTATCGGT 58.414 39.130 0.00 0.00 37.60 4.69
1315 1920 5.736813 ACTGTAAGCCATGTTTTATCGGTA 58.263 37.500 0.00 0.00 37.60 4.02
1316 1921 6.354130 ACTGTAAGCCATGTTTTATCGGTAT 58.646 36.000 0.00 0.00 37.60 2.73
1317 1922 7.502696 ACTGTAAGCCATGTTTTATCGGTATA 58.497 34.615 0.00 0.00 37.60 1.47
1318 1923 8.154856 ACTGTAAGCCATGTTTTATCGGTATAT 58.845 33.333 0.00 0.00 37.60 0.86
1412 2021 6.151985 TGTTATGTTGTTTTCACTTGTCCTGT 59.848 34.615 0.00 0.00 0.00 4.00
1420 2029 1.420138 TCACTTGTCCTGTTCCCTTCC 59.580 52.381 0.00 0.00 0.00 3.46
1440 2049 5.011982 TCCCTCTTTCTCTCCTCTGTTTA 57.988 43.478 0.00 0.00 0.00 2.01
1489 2100 8.437360 TTGATATGATCGTAACAGAAAAGCAT 57.563 30.769 5.22 0.00 0.00 3.79
1493 2104 9.935241 ATATGATCGTAACAGAAAAGCATAGAT 57.065 29.630 0.00 0.00 0.00 1.98
1512 2123 4.122776 AGATGCTTGGTTATCTGTTAGCG 58.877 43.478 0.00 0.00 32.65 4.26
1580 2191 4.698201 TGGTGATCAAGTGGTTCTGTAA 57.302 40.909 0.00 0.00 0.00 2.41
1594 2205 2.752030 TCTGTAATGACTCCAGGAGGG 58.248 52.381 21.31 0.00 33.35 4.30
1748 2914 7.373493 AGACCATCATTCAACTGTTTGATTTC 58.627 34.615 3.98 4.57 41.50 2.17
1785 2951 9.504710 GTTACTGTAGATAACTGTCAGTACATG 57.495 37.037 5.77 3.94 40.52 3.21
1847 3013 4.437390 CGGTTCATGGTTATCTCTGTTTGC 60.437 45.833 0.00 0.00 0.00 3.68
1850 3016 6.374333 GGTTCATGGTTATCTCTGTTTGCTTA 59.626 38.462 0.00 0.00 0.00 3.09
1928 3094 1.116308 GTCTCCAGAAGGGCCTCTAC 58.884 60.000 6.46 1.34 36.21 2.59
1970 3137 7.418942 CCCCTTTTCTGAATTTTTCTCCTTTCA 60.419 37.037 0.00 0.00 0.00 2.69
1971 3138 7.439356 CCCTTTTCTGAATTTTTCTCCTTTCAC 59.561 37.037 0.00 0.00 0.00 3.18
1989 3156 6.536224 CCTTTCACATAATTTTCCAGGAATGC 59.464 38.462 1.58 0.00 0.00 3.56
2029 3196 5.877012 TCAGGAATCTTGCTTGCTAGTTTAG 59.123 40.000 4.25 0.00 0.00 1.85
2057 3224 3.372897 TCCATGAAGATCTGCTCAGTCT 58.627 45.455 1.43 0.00 0.00 3.24
2062 3229 5.417754 TGAAGATCTGCTCAGTCTTCAAT 57.582 39.130 25.05 5.00 43.71 2.57
2071 3238 5.900425 TGCTCAGTCTTCAATATCTCACTC 58.100 41.667 0.00 0.00 0.00 3.51
2123 3290 5.407407 TTCACACTTCAGTTCTATCCTCC 57.593 43.478 0.00 0.00 0.00 4.30
2131 3298 3.318275 TCAGTTCTATCCTCCGAATTCCG 59.682 47.826 0.00 0.00 38.18 4.30
2147 3314 0.034896 TCCGGCACTGAAACTCCTTC 59.965 55.000 0.00 0.00 34.31 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.042515 CCAATCTATTCATTTTTCAACCATGGT 58.957 33.333 13.00 13.00 0.00 3.55
3 4 8.259411 TCCAATCTATTCATTTTTCAACCATGG 58.741 33.333 11.19 11.19 0.00 3.66
4 5 9.656040 TTCCAATCTATTCATTTTTCAACCATG 57.344 29.630 0.00 0.00 0.00 3.66
5 6 9.880157 CTTCCAATCTATTCATTTTTCAACCAT 57.120 29.630 0.00 0.00 0.00 3.55
6 7 8.869109 ACTTCCAATCTATTCATTTTTCAACCA 58.131 29.630 0.00 0.00 0.00 3.67
7 8 9.710900 AACTTCCAATCTATTCATTTTTCAACC 57.289 29.630 0.00 0.00 0.00 3.77
44 45 9.754382 TCTATCTTCGTAACGGCTAAATATTTT 57.246 29.630 5.91 0.00 0.00 1.82
45 46 9.754382 TTCTATCTTCGTAACGGCTAAATATTT 57.246 29.630 5.89 5.89 0.00 1.40
119 128 1.066787 GCTAAGCGGAGTCCAACTTCT 60.067 52.381 15.85 0.00 0.00 2.85
208 218 0.810648 ATGTGCCATGTTGCCTTACG 59.189 50.000 0.00 0.00 0.00 3.18
241 825 0.391793 GGGGAGGAACTGAAGAAGCG 60.392 60.000 0.00 0.00 41.55 4.68
242 826 0.693049 TGGGGAGGAACTGAAGAAGC 59.307 55.000 0.00 0.00 41.55 3.86
255 845 2.567169 GGTTTTCTGGGAATTTGGGGAG 59.433 50.000 0.00 0.00 0.00 4.30
281 871 2.555782 CATGTTGCGTGTCGGTGG 59.444 61.111 0.00 0.00 0.00 4.61
313 903 5.363868 TCTCTATCTATTTGAGGTGGTGGTG 59.636 44.000 0.00 0.00 0.00 4.17
320 910 4.140994 TCCCCGTCTCTATCTATTTGAGGT 60.141 45.833 0.00 0.00 0.00 3.85
321 911 4.218852 GTCCCCGTCTCTATCTATTTGAGG 59.781 50.000 0.00 0.00 0.00 3.86
322 912 4.083217 CGTCCCCGTCTCTATCTATTTGAG 60.083 50.000 0.00 0.00 0.00 3.02
364 957 1.585261 TACGTAGCGTGCATGCTCG 60.585 57.895 35.61 33.53 45.87 5.03
367 960 1.680105 AACGTACGTAGCGTGCATGC 61.680 55.000 23.12 23.58 42.16 4.06
377 970 2.679837 GGTGATGGAGAGAACGTACGTA 59.320 50.000 23.12 4.01 0.00 3.57
378 971 1.471684 GGTGATGGAGAGAACGTACGT 59.528 52.381 16.72 16.72 0.00 3.57
379 972 1.471287 TGGTGATGGAGAGAACGTACG 59.529 52.381 15.01 15.01 0.00 3.67
380 973 3.130516 TGATGGTGATGGAGAGAACGTAC 59.869 47.826 0.00 0.00 0.00 3.67
396 989 2.170397 TGTCCGATAGCATTGTGATGGT 59.830 45.455 0.00 0.00 45.39 3.55
446 1047 5.618236 TCTGATATCCTCCTGCTGAAATTG 58.382 41.667 0.00 0.00 0.00 2.32
454 1055 4.622695 GCTGGTATTCTGATATCCTCCTGC 60.623 50.000 0.00 5.86 0.00 4.85
527 1128 5.197451 TGAAAATTACGGGGACAGCAATAT 58.803 37.500 0.00 0.00 0.00 1.28
533 1134 2.612212 CGGATGAAAATTACGGGGACAG 59.388 50.000 0.00 0.00 0.00 3.51
572 1173 2.590007 GGCGATCTTGCGGATGCT 60.590 61.111 0.00 0.00 43.34 3.79
689 1290 4.234550 ACTGCCCCAGATGTTGAGATATA 58.765 43.478 0.00 0.00 35.18 0.86
690 1291 3.051581 ACTGCCCCAGATGTTGAGATAT 58.948 45.455 0.00 0.00 35.18 1.63
952 1556 3.774528 TGCTGCCTACGCTGGAGG 61.775 66.667 0.00 2.76 37.12 4.30
1044 1648 1.377856 GAGCCCCAGGAAGCTGAAC 60.378 63.158 8.60 0.00 40.11 3.18
1084 1688 1.735386 CAGAGGAGCATGAACACCAG 58.265 55.000 0.00 0.00 0.00 4.00
1124 1728 1.141019 CACGGGTAGATGGTGACGG 59.859 63.158 0.00 0.00 33.58 4.79
1192 1796 4.224147 TCTCTCCCATGAACAACCGAATAA 59.776 41.667 0.00 0.00 0.00 1.40
1193 1797 3.772572 TCTCTCCCATGAACAACCGAATA 59.227 43.478 0.00 0.00 0.00 1.75
1194 1798 2.571653 TCTCTCCCATGAACAACCGAAT 59.428 45.455 0.00 0.00 0.00 3.34
1213 1817 2.044252 CATTGCCTGGCCTGCTCT 60.044 61.111 17.53 3.78 0.00 4.09
1282 1887 0.714439 GGCTTACAGTTTCGACGAGC 59.286 55.000 0.00 0.00 0.00 5.03
1308 1913 8.777578 ATGGACAGCCTAATAATATACCGATA 57.222 34.615 0.00 0.00 34.31 2.92
1309 1914 7.565398 AGATGGACAGCCTAATAATATACCGAT 59.435 37.037 0.00 0.00 34.31 4.18
1310 1915 6.895756 AGATGGACAGCCTAATAATATACCGA 59.104 38.462 0.00 0.00 34.31 4.69
1311 1916 7.113658 AGATGGACAGCCTAATAATATACCG 57.886 40.000 0.00 0.00 34.31 4.02
1313 1918 8.079211 TGGAGATGGACAGCCTAATAATATAC 57.921 38.462 0.00 0.00 34.31 1.47
1314 1919 8.860517 ATGGAGATGGACAGCCTAATAATATA 57.139 34.615 0.00 0.00 34.31 0.86
1315 1920 7.626890 AGATGGAGATGGACAGCCTAATAATAT 59.373 37.037 0.00 0.00 34.31 1.28
1316 1921 6.962311 AGATGGAGATGGACAGCCTAATAATA 59.038 38.462 0.00 0.00 34.31 0.98
1317 1922 5.789575 AGATGGAGATGGACAGCCTAATAAT 59.210 40.000 0.00 0.00 34.31 1.28
1318 1923 5.012458 CAGATGGAGATGGACAGCCTAATAA 59.988 44.000 0.00 0.00 34.31 1.40
1412 2021 2.114506 AGGAGAGAAAGAGGGAAGGGAA 59.885 50.000 0.00 0.00 0.00 3.97
1420 2029 8.628630 AAAAATAAACAGAGGAGAGAAAGAGG 57.371 34.615 0.00 0.00 0.00 3.69
1489 2100 5.289595 CGCTAACAGATAACCAAGCATCTA 58.710 41.667 0.00 0.00 30.32 1.98
1493 2104 2.006888 GCGCTAACAGATAACCAAGCA 58.993 47.619 0.00 0.00 0.00 3.91
1500 2111 1.473257 CCTGGCTGCGCTAACAGATAA 60.473 52.381 21.49 0.00 40.25 1.75
1512 2123 2.965572 TTTAATTGCATCCTGGCTGC 57.034 45.000 15.33 15.33 40.10 5.25
1580 2191 1.229625 TGCACCCTCCTGGAGTCAT 60.230 57.895 21.70 4.49 38.00 3.06
1633 2799 5.876357 ACTATTTTGTAGCCCTGTTTCTGA 58.124 37.500 0.00 0.00 0.00 3.27
1773 2939 2.348666 GCGGCTTAACATGTACTGACAG 59.651 50.000 0.00 0.00 39.50 3.51
1781 2947 0.960364 CCTGGTGCGGCTTAACATGT 60.960 55.000 0.00 0.00 0.00 3.21
1785 2951 2.399356 GCTCCTGGTGCGGCTTAAC 61.399 63.158 4.83 0.00 0.00 2.01
1847 3013 2.300437 CGGGGGAAAGAGCCTAGATAAG 59.700 54.545 0.00 0.00 0.00 1.73
1850 3016 0.764752 CCGGGGGAAAGAGCCTAGAT 60.765 60.000 0.00 0.00 0.00 1.98
1928 3094 0.962356 GGGGTGACATTCTGCAGGTG 60.962 60.000 15.13 15.40 0.00 4.00
1989 3156 1.134461 CCTGAATCTGGAGAGTGCAGG 60.134 57.143 0.00 0.00 36.40 4.85
2029 3196 2.780714 CAGATCTTCATGGATCCCTGC 58.219 52.381 9.90 0.00 42.02 4.85
2057 3224 3.885724 TGCACCGAGTGAGATATTGAA 57.114 42.857 8.04 0.00 35.23 2.69
2062 3229 1.170442 TCGTTGCACCGAGTGAGATA 58.830 50.000 0.74 0.00 35.23 1.98
2071 3238 1.325640 CATGAAGAGATCGTTGCACCG 59.674 52.381 0.00 0.00 0.00 4.94
2123 3290 1.128692 GAGTTTCAGTGCCGGAATTCG 59.871 52.381 5.05 0.00 38.88 3.34


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

AutoCloner maintained by Alex Coulton.