Multiple sequence alignment - TraesCS2B01G282200

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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 TraesCS2B01G282200 chr2B 100.000 2522 0 0 1 2522 390806708 390804187 0.000000e+00 4658.0
1 TraesCS2B01G282200 chr2B 95.349 43 0 2 900 941 390805308 390805349 1.620000e-07 67.6
2 TraesCS2B01G282200 chr2B 93.478 46 1 2 1357 1401 390805765 390805809 1.620000e-07 67.6
3 TraesCS2B01G282200 chr2D 92.705 1919 62 25 640 2522 322858822 322856946 0.000000e+00 2697.0
4 TraesCS2B01G282200 chr2D 94.605 519 15 4 1 511 322859538 322859025 0.000000e+00 791.0
5 TraesCS2B01G282200 chr2D 96.512 86 2 1 563 647 322859006 322858921 9.410000e-30 141.0
6 TraesCS2B01G282200 chr2D 95.349 43 0 2 900 941 322858092 322858133 1.620000e-07 67.6
7 TraesCS2B01G282200 chr2A 94.799 1615 46 6 932 2522 408086917 408088517 0.000000e+00 2483.0
8 TraesCS2B01G282200 chr2A 93.173 542 17 7 1 524 408083879 408084418 0.000000e+00 778.0
9 TraesCS2B01G282200 chr2A 89.340 197 8 3 640 823 408084808 408085004 4.190000e-58 235.0
10 TraesCS2B01G282200 chr2A 89.286 140 3 6 519 647 408084446 408084584 5.580000e-37 165.0
11 TraesCS2B01G282200 chr2A 94.286 70 4 0 831 900 408086846 408086915 9.540000e-20 108.0
12 TraesCS2B01G282200 chr2A 97.297 37 0 1 900 935 408087386 408087350 7.530000e-06 62.1


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 TraesCS2B01G282200 chr2B 390804187 390806708 2521 True 4658.000000 4658 100.000000 1 2522 1 chr2B.!!$R1 2521
1 TraesCS2B01G282200 chr2D 322856946 322859538 2592 True 1209.666667 2697 94.607333 1 2522 3 chr2D.!!$R1 2521
2 TraesCS2B01G282200 chr2A 408083879 408088517 4638 False 753.800000 2483 92.176800 1 2522 5 chr2A.!!$F1 2521

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
923 3064 0.320334 CACCATGTACACCGCTGACA 60.32 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 4386 2.099831 GTGCTCCCGTCGTACTCG 59.9 66.667 0.0 0.0 38.55 4.18 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
200 201 8.903820 GGTTACATATTGGCAATTAGACTCTTT 58.096 33.333 19.21 0.00 0.00 2.52
360 371 2.557869 AGTTAGCAACCTGTCCCCATA 58.442 47.619 0.00 0.00 0.00 2.74
450 461 6.280643 ACTTGACATAAGTTTTGGCTTTTCC 58.719 36.000 0.68 0.00 0.00 3.13
637 699 5.010922 CAGCTAGAACAGAGGATTAGCATCT 59.989 44.000 0.00 0.00 39.27 2.90
638 700 5.243730 AGCTAGAACAGAGGATTAGCATCTC 59.756 44.000 0.00 0.00 39.27 2.75
721 1027 4.499758 GCAGCTAGTACTGTTCGTATTCAC 59.500 45.833 5.39 0.00 39.96 3.18
730 1037 6.354039 ACTGTTCGTATTCACTTTTTCGTT 57.646 33.333 0.00 0.00 0.00 3.85
769 1076 5.060662 TCCTCTGTTCTGTTCGTATTCAG 57.939 43.478 0.00 0.00 0.00 3.02
788 1095 3.082548 CAGTTCTTCTGACCCTACGAGA 58.917 50.000 0.00 0.00 46.27 4.04
825 2966 0.525761 TCCGCAATTAAGCCTGCAAC 59.474 50.000 7.50 0.00 38.52 4.17
828 2969 1.067635 CGCAATTAAGCCTGCAACCTT 60.068 47.619 7.50 4.22 38.52 3.50
829 2970 2.610232 CGCAATTAAGCCTGCAACCTTT 60.610 45.455 4.10 0.00 38.52 3.11
896 3037 1.621072 CCACCTGCTCCTACTCCTCTT 60.621 57.143 0.00 0.00 0.00 2.85
899 3040 1.621072 CCTGCTCCTACTCCTCTTGGT 60.621 57.143 0.00 0.00 34.23 3.67
900 3041 1.754226 CTGCTCCTACTCCTCTTGGTC 59.246 57.143 0.00 0.00 34.23 4.02
901 3042 1.116308 GCTCCTACTCCTCTTGGTCC 58.884 60.000 0.00 0.00 34.23 4.46
902 3043 1.619977 GCTCCTACTCCTCTTGGTCCA 60.620 57.143 0.00 0.00 34.23 4.02
903 3044 2.383855 CTCCTACTCCTCTTGGTCCAG 58.616 57.143 0.00 0.00 34.23 3.86
904 3045 0.827368 CCTACTCCTCTTGGTCCAGC 59.173 60.000 0.00 0.00 34.23 4.85
905 3046 1.561643 CTACTCCTCTTGGTCCAGCA 58.438 55.000 0.00 0.00 34.23 4.41
906 3047 1.205893 CTACTCCTCTTGGTCCAGCAC 59.794 57.143 0.00 0.00 34.23 4.40
915 3056 2.854522 GGTCCAGCACCATGTACAC 58.145 57.895 0.00 0.00 45.98 2.90
916 3057 0.676782 GGTCCAGCACCATGTACACC 60.677 60.000 0.00 0.00 45.98 4.16
917 3058 1.019278 GTCCAGCACCATGTACACCG 61.019 60.000 0.00 0.00 0.00 4.94
918 3059 2.398554 CCAGCACCATGTACACCGC 61.399 63.158 0.00 0.00 0.00 5.68
919 3060 1.375908 CAGCACCATGTACACCGCT 60.376 57.895 0.00 0.61 0.00 5.52
920 3061 1.375908 AGCACCATGTACACCGCTG 60.376 57.895 0.00 0.00 0.00 5.18
921 3062 1.375396 GCACCATGTACACCGCTGA 60.375 57.895 0.00 0.00 0.00 4.26
922 3063 1.635663 GCACCATGTACACCGCTGAC 61.636 60.000 0.00 0.00 0.00 3.51
923 3064 0.320334 CACCATGTACACCGCTGACA 60.320 55.000 0.00 0.00 0.00 3.58
924 3065 0.320421 ACCATGTACACCGCTGACAC 60.320 55.000 0.00 0.00 0.00 3.67
925 3066 1.351430 CCATGTACACCGCTGACACG 61.351 60.000 0.00 0.00 0.00 4.49
926 3067 0.666274 CATGTACACCGCTGACACGT 60.666 55.000 0.00 0.00 0.00 4.49
927 3068 0.388134 ATGTACACCGCTGACACGTC 60.388 55.000 0.00 0.00 0.00 4.34
928 3069 1.731969 GTACACCGCTGACACGTCC 60.732 63.158 0.00 0.00 0.00 4.79
1104 3245 1.800315 CTACTTCGGTGACACGGCG 60.800 63.158 4.80 4.80 0.00 6.46
1241 3382 3.399181 GGTGATCACCGAGGGGCA 61.399 66.667 28.52 0.00 42.29 5.36
1538 3679 2.421424 CCTAGAACAAGTCTGCCATTGC 59.579 50.000 0.00 0.00 37.12 3.56
1604 3757 3.381949 CCGGTTTTAGGATCAGTCGATC 58.618 50.000 0.00 0.00 46.34 3.69
1618 3777 1.819288 GTCGATCTGGGAGAGAACACA 59.181 52.381 0.00 0.00 33.12 3.72
1832 4003 3.319122 ACAACTTGTCATTTCAGCTTCCC 59.681 43.478 0.00 0.00 0.00 3.97
2454 4625 3.060020 GACGCCGACGAATCCCTCA 62.060 63.158 0.00 0.00 43.93 3.86
2463 4634 2.869192 GACGAATCCCTCATTTCTGAGC 59.131 50.000 0.00 0.00 46.39 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.367894 TGGATAGAGGCTGATTGCTGAG 59.632 50.000 0.00 0.00 42.39 3.35
200 201 1.868498 CCTGCACGTAAACGAGGAAAA 59.132 47.619 9.86 0.00 43.02 2.29
214 215 1.270550 CTCAAATGTTCCCACCTGCAC 59.729 52.381 0.00 0.00 0.00 4.57
561 614 1.279271 ACAGAAACTGCCCTTATCGCT 59.721 47.619 0.00 0.00 34.37 4.93
637 699 4.869297 CACACAAGAACAAAGCAATTTGGA 59.131 37.500 5.77 0.00 36.30 3.53
638 700 4.494526 GCACACAAGAACAAAGCAATTTGG 60.495 41.667 5.77 0.00 36.30 3.28
668 962 4.635765 GTCCAGCAGTAAAATATGAGCACA 59.364 41.667 0.00 0.00 0.00 4.57
721 1027 4.324267 ACCATCCCTGTCTAACGAAAAAG 58.676 43.478 0.00 0.00 0.00 2.27
769 1076 4.276431 CCTATCTCGTAGGGTCAGAAGAAC 59.724 50.000 0.00 0.00 45.38 3.01
788 1095 3.069729 GCGGAGTAATTGTGGAGTCCTAT 59.930 47.826 11.33 0.00 33.60 2.57
802 1109 2.014128 GCAGGCTTAATTGCGGAGTAA 58.986 47.619 0.00 0.00 35.99 2.24
825 2966 1.703411 TGGGTTGGAGAAAGCAAAGG 58.297 50.000 0.00 0.00 38.05 3.11
828 2969 2.238521 GTGATGGGTTGGAGAAAGCAA 58.761 47.619 0.00 0.00 38.05 3.91
829 2970 1.144708 TGTGATGGGTTGGAGAAAGCA 59.855 47.619 0.00 0.00 38.05 3.91
899 3040 1.295101 CGGTGTACATGGTGCTGGA 59.705 57.895 0.00 0.00 0.00 3.86
900 3041 2.398554 GCGGTGTACATGGTGCTGG 61.399 63.158 0.00 0.00 0.00 4.85
901 3042 1.375908 AGCGGTGTACATGGTGCTG 60.376 57.895 11.64 0.13 0.00 4.41
902 3043 1.375908 CAGCGGTGTACATGGTGCT 60.376 57.895 14.61 11.30 0.00 4.40
903 3044 1.375396 TCAGCGGTGTACATGGTGC 60.375 57.895 15.22 12.38 0.00 5.01
904 3045 0.320334 TGTCAGCGGTGTACATGGTG 60.320 55.000 15.22 18.71 0.00 4.17
905 3046 0.320421 GTGTCAGCGGTGTACATGGT 60.320 55.000 15.22 0.00 0.00 3.55
906 3047 1.351430 CGTGTCAGCGGTGTACATGG 61.351 60.000 21.43 14.10 0.00 3.66
907 3048 0.666274 ACGTGTCAGCGGTGTACATG 60.666 55.000 24.67 24.67 36.44 3.21
908 3049 0.388134 GACGTGTCAGCGGTGTACAT 60.388 55.000 15.22 3.78 35.98 2.29
909 3050 1.008194 GACGTGTCAGCGGTGTACA 60.008 57.895 15.22 14.14 35.98 2.90
910 3051 1.731969 GGACGTGTCAGCGGTGTAC 60.732 63.158 15.22 13.57 35.98 2.90
911 3052 1.859427 GAGGACGTGTCAGCGGTGTA 61.859 60.000 15.22 2.24 35.98 2.90
912 3053 3.208884 GAGGACGTGTCAGCGGTGT 62.209 63.158 15.22 0.00 35.98 4.16
913 3054 2.430921 GAGGACGTGTCAGCGGTG 60.431 66.667 8.67 8.67 35.98 4.94
914 3055 4.039357 CGAGGACGTGTCAGCGGT 62.039 66.667 0.00 0.00 35.98 5.68
925 3066 4.415332 TTGAGCGACGGCGAGGAC 62.415 66.667 18.90 1.71 46.35 3.85
926 3067 4.415332 GTTGAGCGACGGCGAGGA 62.415 66.667 18.90 0.00 46.35 3.71
927 3068 4.421479 AGTTGAGCGACGGCGAGG 62.421 66.667 18.90 5.63 46.35 4.63
928 3069 2.876645 GAGTTGAGCGACGGCGAG 60.877 66.667 18.90 8.50 46.35 5.03
1080 3221 0.541063 TGTCACCGAAGTAGCTCCCA 60.541 55.000 0.00 0.00 0.00 4.37
1104 3245 1.030488 TCAGGAGGTCGTCGATCACC 61.030 60.000 13.50 13.50 0.00 4.02
1241 3382 3.066198 GGGTGCTCCCGTTGTACT 58.934 61.111 8.37 0.00 44.74 2.73
1341 3482 4.673298 CACAGCACGTGCCCGGTA 62.673 66.667 35.51 0.00 43.38 4.02
1354 3495 4.135153 CTCGGCCGTCCTCCACAG 62.135 72.222 27.15 8.60 0.00 3.66
1478 3619 1.303561 GACATGTTCCTGCTGCCCA 60.304 57.895 0.00 0.00 0.00 5.36
1511 3652 4.041567 TGGCAGACTTGTTCTAGGAATCAA 59.958 41.667 0.00 0.00 31.12 2.57
1538 3679 0.462047 GTGGGAGATACAAGTGGCGG 60.462 60.000 0.00 0.00 0.00 6.13
1570 3723 0.601841 AAACCGGCAAGACCAGTACG 60.602 55.000 0.00 0.00 39.03 3.67
1579 3732 2.678336 GACTGATCCTAAAACCGGCAAG 59.322 50.000 0.00 0.00 0.00 4.01
1604 3757 1.081892 CGCATTGTGTTCTCTCCCAG 58.918 55.000 0.00 0.00 0.00 4.45
1618 3777 0.953471 TGAAAGCTACGCACCGCATT 60.953 50.000 0.00 0.00 0.00 3.56
2215 4386 2.099831 GTGCTCCCGTCGTACTCG 59.900 66.667 0.00 0.00 38.55 4.18
2253 4424 2.196382 CTCCTTCTTGGACGCGTCGA 62.196 60.000 30.99 26.08 40.56 4.20
2463 4634 5.277154 CGTCCATTAGTATTTTTAGCGTGGG 60.277 44.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.