Multiple sequence alignment - TraesCS5A01G231500

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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 TraesCS5A01G231500 chr5A 100.000 2906 0 0 1 2906 447303758 447306663 0.000000e+00 5367
1 TraesCS5A01G231500 chr5D 93.964 2916 104 31 21 2902 344886337 344883460 0.000000e+00 4344
2 TraesCS5A01G231500 chr5B 92.598 2918 128 36 34 2906 406875141 406878015 0.000000e+00 4111
3 TraesCS5A01G231500 chr7B 96.907 97 3 0 1306 1402 79051426 79051522 2.320000e-36 163
4 TraesCS5A01G231500 chr7A 96.907 97 3 0 1306 1402 122207649 122207745 2.320000e-36 163
5 TraesCS5A01G231500 chr7D 95.876 97 4 0 1306 1402 117792114 117792210 1.080000e-34 158


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 TraesCS5A01G231500 chr5A 447303758 447306663 2905 False 5367 5367 100.000 1 2906 1 chr5A.!!$F1 2905
1 TraesCS5A01G231500 chr5D 344883460 344886337 2877 True 4344 4344 93.964 21 2902 1 chr5D.!!$R1 2881
2 TraesCS5A01G231500 chr5B 406875141 406878015 2874 False 4111 4111 92.598 34 2906 1 chr5B.!!$F1 2872

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
531 532 0.46729 ACCCGCTTCTTTTTCTGGCA 60.467 50.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 2558 0.663153 GCATGGACATTCGTTAGGCC 59.337 55.0 0.0 0.0 0.0 5.19 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
176 177 6.873605 TGAGACACATATAGGTGACAAGTTTG 59.126 38.462 23.38 0.00 41.32 2.93
188 189 5.995897 GGTGACAAGTTTGTAAGACCAGTAT 59.004 40.000 12.19 0.00 42.43 2.12
189 190 7.015877 AGGTGACAAGTTTGTAAGACCAGTATA 59.984 37.037 16.50 0.00 42.43 1.47
254 255 2.170397 CCCAAATTTTAGGTGATGGGGC 59.830 50.000 0.58 0.00 43.06 5.80
255 256 2.836981 CCAAATTTTAGGTGATGGGGCA 59.163 45.455 0.00 0.00 0.00 5.36
306 307 7.642586 CGACAATAATATGTACACTCACTCGAA 59.357 37.037 0.00 0.00 32.57 3.71
324 325 5.648960 ACTCGAAAGTTGAGGGTTAAAACAA 59.351 36.000 0.00 0.00 37.79 2.83
360 361 1.746787 GGACGTTGGTTTGGTTGAACT 59.253 47.619 0.00 0.00 0.00 3.01
446 447 3.381983 TGAGATCACGCGGTGGCT 61.382 61.111 12.47 1.66 36.88 4.75
531 532 0.467290 ACCCGCTTCTTTTTCTGGCA 60.467 50.000 0.00 0.00 0.00 4.92
532 533 0.673437 CCCGCTTCTTTTTCTGGCAA 59.327 50.000 0.00 0.00 0.00 4.52
533 534 1.068434 CCCGCTTCTTTTTCTGGCAAA 59.932 47.619 0.00 0.00 0.00 3.68
534 535 2.289010 CCCGCTTCTTTTTCTGGCAAAT 60.289 45.455 0.00 0.00 0.00 2.32
535 536 3.056891 CCCGCTTCTTTTTCTGGCAAATA 60.057 43.478 0.00 0.00 0.00 1.40
536 537 4.555262 CCGCTTCTTTTTCTGGCAAATAA 58.445 39.130 0.00 0.00 0.00 1.40
537 538 5.170748 CCGCTTCTTTTTCTGGCAAATAAT 58.829 37.500 0.00 0.00 0.00 1.28
538 539 5.062558 CCGCTTCTTTTTCTGGCAAATAATG 59.937 40.000 0.00 0.00 0.00 1.90
603 604 3.689161 TGGTGCAGCACATAAATACAGAC 59.311 43.478 26.78 5.53 35.86 3.51
705 706 5.163513 GTTCAACCAATAGCACATTTCCAG 58.836 41.667 0.00 0.00 0.00 3.86
823 825 1.165907 ATGGCCCATACATCAACGCG 61.166 55.000 3.53 3.53 0.00 6.01
824 826 2.327940 GCCCATACATCAACGCGC 59.672 61.111 5.73 0.00 0.00 6.86
1030 1043 1.676635 GAGCAAGATGGGCAGCACA 60.677 57.895 0.00 0.00 0.00 4.57
1449 1480 2.114670 CATGCAAGGCCACTACCCG 61.115 63.158 5.01 0.00 0.00 5.28
1497 1528 1.736645 CTACCACCACCGCTTCGTG 60.737 63.158 0.00 0.00 0.00 4.35
1927 1958 2.739287 CCAAGAACGGCGCGGTTA 60.739 61.111 29.98 0.00 0.00 2.85
1929 1960 1.154543 CAAGAACGGCGCGGTTAAC 60.155 57.895 29.98 19.66 0.00 2.01
1941 1972 1.262417 GCGGTTAACTAATTAGCGGGC 59.738 52.381 12.54 4.44 33.76 6.13
1969 2000 6.148976 GTGAAGCCTAAGAACGAAGGTTAATT 59.851 38.462 0.00 0.00 36.24 1.40
1970 2001 6.370718 TGAAGCCTAAGAACGAAGGTTAATTC 59.629 38.462 0.00 0.00 36.24 2.17
2085 2116 6.434018 TTTCTTTCTCCTACTAGAGTACGC 57.566 41.667 0.00 0.00 35.28 4.42
2171 2202 7.117236 GGAAATAAATGGAACGAAAGGGAAAAC 59.883 37.037 0.00 0.00 0.00 2.43
2195 2226 5.220854 CGGGGAGTGTTGTCATTTTCATATC 60.221 44.000 0.00 0.00 0.00 1.63
2199 2233 7.556275 GGGAGTGTTGTCATTTTCATATCCTTA 59.444 37.037 0.00 0.00 0.00 2.69
2229 2263 6.403527 GCACATTTTCCAGCCATTTTTAATCC 60.404 38.462 0.00 0.00 0.00 3.01
2232 2266 5.675684 TTTCCAGCCATTTTTAATCCTCC 57.324 39.130 0.00 0.00 0.00 4.30
2309 2343 3.424962 GCACTAATTTTCTGGTGCGTCTC 60.425 47.826 0.00 0.00 43.91 3.36
2433 2467 6.753744 CCTTATCATTTGCTTTTTGGAGTAGC 59.246 38.462 0.00 0.00 35.50 3.58
2529 2585 0.524816 GAATGTCCATGCGCTGCTTG 60.525 55.000 9.73 0.81 34.20 4.01
2545 2601 2.231964 TGCTTGCCACTTGAATGATTCC 59.768 45.455 2.26 0.00 0.00 3.01
2562 2618 1.213537 CCTGCCTGCAAATTGACCG 59.786 57.895 0.00 0.00 0.00 4.79
2650 2706 0.329596 AAGTGGGTGCTCCTTGGATC 59.670 55.000 4.53 0.00 36.20 3.36
2732 2788 1.358759 GTTGCCCACGGAAACTGTG 59.641 57.895 0.00 0.00 35.55 3.66
2735 2791 2.908073 GCCCACGGAAACTGTGCTG 61.908 63.158 5.33 1.00 34.82 4.41
2749 2805 1.751544 TGCTGGGCAGTGATGCATC 60.752 57.895 20.14 20.14 33.32 3.91
2773 2829 1.089920 CAAATCTGAAGGGGCACTCG 58.910 55.000 0.00 0.00 0.00 4.18
2847 2903 1.864750 GCGCGTGAATGTGACATGC 60.865 57.895 8.43 0.00 43.94 4.06
2866 2922 1.300971 CGCATCCACCAGTCCTTGTG 61.301 60.000 0.00 0.00 0.00 3.33
2870 2926 2.051334 TCCACCAGTCCTTGTGTTTG 57.949 50.000 0.00 0.00 0.00 2.93
2880 2936 5.473504 CAGTCCTTGTGTTTGCTTAACCTAT 59.526 40.000 0.82 0.00 35.81 2.57
2890 2946 6.036735 TGTTTGCTTAACCTATTCGCTATGAC 59.963 38.462 0.82 0.00 35.81 3.06
2893 2949 6.288294 TGCTTAACCTATTCGCTATGACATT 58.712 36.000 0.00 0.00 0.00 2.71
2902 2958 2.993220 TCGCTATGACATTCACACACAC 59.007 45.455 0.00 0.00 0.00 3.82
2904 2960 3.371898 CGCTATGACATTCACACACACAT 59.628 43.478 0.00 0.00 0.00 3.21
2905 2961 4.566360 CGCTATGACATTCACACACACATA 59.434 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.069165 AATTATGCTCCCCTCGCCCC 62.069 60.000 0.00 0.00 0.00 5.80
13 14 0.178990 AAATTATGCTCCCCTCGCCC 60.179 55.000 0.00 0.00 0.00 6.13
14 15 2.561478 TAAATTATGCTCCCCTCGCC 57.439 50.000 0.00 0.00 0.00 5.54
15 16 5.453567 AAAATAAATTATGCTCCCCTCGC 57.546 39.130 0.00 0.00 0.00 5.03
16 17 9.981114 AATTTAAAATAAATTATGCTCCCCTCG 57.019 29.630 6.35 0.00 0.00 4.63
176 177 7.862648 GCTTTAGCCATTTATACTGGTCTTAC 58.137 38.462 3.16 0.00 36.10 2.34
306 307 6.599356 AGTGTTTGTTTTAACCCTCAACTT 57.401 33.333 0.00 0.00 0.00 2.66
344 345 3.872771 TCGACTAGTTCAACCAAACCAAC 59.127 43.478 0.00 0.00 0.00 3.77
360 361 7.386848 CCCATTTTCTAGTCAACTTTTCGACTA 59.613 37.037 0.00 0.00 42.41 2.59
430 431 2.125512 AAGCCACCGCGTGATCTC 60.126 61.111 4.92 0.00 41.18 2.75
471 472 4.876107 ACTACTTAAGGCACAAATCATCCG 59.124 41.667 7.53 0.00 0.00 4.18
569 570 2.030363 TGCTGCACCAATCTAAAAACCG 60.030 45.455 0.00 0.00 0.00 4.44
603 604 2.535788 TTGTCGTTTTCGTGGCGGG 61.536 57.895 0.00 0.00 44.46 6.13
705 706 4.051922 TGTTTTTGTGTTGTTGGTCACAC 58.948 39.130 0.00 0.00 42.93 3.82
823 825 2.272923 GCTAGGGAGCTAGCTAGGC 58.727 63.158 19.38 13.33 46.32 3.93
1030 1043 2.430367 GGGAAGGCTGTTCGTGGT 59.570 61.111 0.00 0.00 0.00 4.16
1927 1958 1.479323 TCACGAGCCCGCTAATTAGTT 59.521 47.619 13.91 0.00 39.95 2.24
1929 1960 2.128035 CTTCACGAGCCCGCTAATTAG 58.872 52.381 8.20 8.20 39.95 1.73
1941 1972 2.631418 TCGTTCTTAGGCTTCACGAG 57.369 50.000 0.00 0.00 35.05 4.18
1950 1981 8.549338 AAAGAGAATTAACCTTCGTTCTTAGG 57.451 34.615 0.00 0.00 37.56 2.69
1981 2012 1.405821 ACGAATTCACGAGCTAGAGGG 59.594 52.381 6.22 0.00 37.03 4.30
1982 2013 2.853731 ACGAATTCACGAGCTAGAGG 57.146 50.000 6.22 0.00 37.03 3.69
2053 2084 5.437060 AGTAGGAGAAAGAAAAACACTGCA 58.563 37.500 0.00 0.00 0.00 4.41
2054 2085 6.929606 TCTAGTAGGAGAAAGAAAAACACTGC 59.070 38.462 0.00 0.00 0.00 4.40
2055 2086 8.145122 ACTCTAGTAGGAGAAAGAAAAACACTG 58.855 37.037 0.00 0.00 37.13 3.66
2056 2087 8.252624 ACTCTAGTAGGAGAAAGAAAAACACT 57.747 34.615 0.00 0.00 37.13 3.55
2057 2088 9.409312 GTACTCTAGTAGGAGAAAGAAAAACAC 57.591 37.037 0.00 0.00 37.13 3.32
2058 2089 8.295288 CGTACTCTAGTAGGAGAAAGAAAAACA 58.705 37.037 4.23 0.00 38.32 2.83
2059 2090 7.273164 GCGTACTCTAGTAGGAGAAAGAAAAAC 59.727 40.741 12.71 0.00 38.32 2.43
2060 2091 7.040201 TGCGTACTCTAGTAGGAGAAAGAAAAA 60.040 37.037 12.71 0.00 38.32 1.94
2085 2116 2.094286 AGAAGAGCAGGACGAATGAGTG 60.094 50.000 0.00 0.00 0.00 3.51
2171 2202 2.226330 TGAAAATGACAACACTCCCCG 58.774 47.619 0.00 0.00 0.00 5.73
2195 2226 5.105392 TGGCTGGAAAATGTGCTTAATAAGG 60.105 40.000 1.88 0.00 0.00 2.69
2199 2233 5.425196 AATGGCTGGAAAATGTGCTTAAT 57.575 34.783 0.00 0.00 0.00 1.40
2202 2236 3.775261 AAATGGCTGGAAAATGTGCTT 57.225 38.095 0.00 0.00 0.00 3.91
2229 2263 8.240682 CCTATCGATGTGAAATTAGTAGAGGAG 58.759 40.741 8.54 0.00 0.00 3.69
2309 2343 5.520376 ACTTTTGGTTTGAATGGACAGAG 57.480 39.130 0.00 0.00 0.00 3.35
2502 2558 0.663153 GCATGGACATTCGTTAGGCC 59.337 55.000 0.00 0.00 0.00 5.19
2529 2585 1.135721 GGCAGGAATCATTCAAGTGGC 59.864 52.381 0.00 2.37 0.00 5.01
2545 2601 0.387622 CACGGTCAATTTGCAGGCAG 60.388 55.000 0.00 0.00 0.00 4.85
2562 2618 1.105457 TAGCTGGGAAATGCATGCAC 58.895 50.000 25.37 10.69 0.00 4.57
2621 2677 2.046285 CACCCACTTTCGGATGCCC 61.046 63.158 0.00 0.00 0.00 5.36
2680 2736 3.055963 TGCATTATGTTGCCAAAAGGAGG 60.056 43.478 0.00 0.00 42.06 4.30
2749 2805 0.529378 GCCCCTTCAGATTTGTGCAG 59.471 55.000 0.00 0.00 0.00 4.41
2764 2820 4.120331 GCATGTTGCGAGTGCCCC 62.120 66.667 0.00 0.00 41.78 5.80
2773 2829 1.001487 TGTTACTGCTGTGCATGTTGC 60.001 47.619 6.48 0.00 45.29 4.17
2833 2889 1.532505 GGATGCGCATGTCACATTCAC 60.533 52.381 30.76 8.83 0.00 3.18
2847 2903 1.003355 ACAAGGACTGGTGGATGCG 60.003 57.895 0.00 0.00 0.00 4.73
2866 2922 6.036735 TGTCATAGCGAATAGGTTAAGCAAAC 59.963 38.462 7.52 0.00 37.36 2.93
2870 2926 6.423905 TGAATGTCATAGCGAATAGGTTAAGC 59.576 38.462 0.00 0.00 0.00 3.09
2880 2936 3.431912 GTGTGTGTGAATGTCATAGCGAA 59.568 43.478 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.