Multiple sequence alignment - TraesCS5A01G083800

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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 TraesCS5A01G083800 chr5A 100.000 2351 0 0 1 2351 109667491 109669841 0.000000e+00 4342
1 TraesCS5A01G083800 chr5A 97.276 2239 56 3 118 2351 268344304 268346542 0.000000e+00 3792
2 TraesCS5A01G083800 chr5A 89.881 168 14 3 1 166 163458276 163458110 1.830000e-51 213
3 TraesCS5A01G083800 chr6A 96.653 2241 64 7 121 2351 204306933 204304694 0.000000e+00 3712
4 TraesCS5A01G083800 chr6A 96.339 2240 76 4 118 2351 136164323 136162084 0.000000e+00 3677
5 TraesCS5A01G083800 chr6A 96.161 2240 79 5 118 2351 328875925 328878163 0.000000e+00 3653
6 TraesCS5A01G083800 chr6A 96.159 2239 80 4 118 2351 518075640 518073403 0.000000e+00 3653
7 TraesCS5A01G083800 chr6A 96.204 2239 72 6 118 2351 213994228 213991998 0.000000e+00 3651
8 TraesCS5A01G083800 chr6A 97.031 1987 53 5 370 2351 473515388 473517373 0.000000e+00 3338
9 TraesCS5A01G083800 chr6A 91.444 187 15 1 1 187 312146637 312146452 3.000000e-64 255
10 TraesCS5A01G083800 chr2A 96.381 2238 74 5 121 2351 616456350 616454113 0.000000e+00 3677
11 TraesCS5A01G083800 chr2A 92.903 155 7 4 1 153 352444457 352444305 3.040000e-54 222
12 TraesCS5A01G083800 chr2A 91.667 156 7 6 1 153 352444847 352444695 6.580000e-51 211
13 TraesCS5A01G083800 chr3A 95.002 2261 81 11 118 2351 134617333 134619588 0.000000e+00 3520
14 TraesCS5A01G083800 chr3A 89.820 167 13 3 1 166 649157275 649157112 6.580000e-51 211
15 TraesCS5A01G083800 chr1A 97.006 1837 48 5 520 2351 465251795 465253629 0.000000e+00 3081
16 TraesCS5A01G083800 chr1A 90.323 155 12 3 1 153 358828787 358828940 1.420000e-47 200
17 TraesCS5A01G083800 chr4A 92.308 195 10 4 1 192 148262780 148262972 2.980000e-69 272
18 TraesCS5A01G083800 chr4A 87.500 200 20 3 1 199 260224947 260224752 2.350000e-55 226
19 TraesCS5A01G083800 chr7A 89.024 164 12 6 1 159 717178426 717178264 5.120000e-47 198


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 TraesCS5A01G083800 chr5A 109667491 109669841 2350 False 4342.0 4342 100.000 1 2351 1 chr5A.!!$F1 2350
1 TraesCS5A01G083800 chr5A 268344304 268346542 2238 False 3792.0 3792 97.276 118 2351 1 chr5A.!!$F2 2233
2 TraesCS5A01G083800 chr6A 204304694 204306933 2239 True 3712.0 3712 96.653 121 2351 1 chr6A.!!$R2 2230
3 TraesCS5A01G083800 chr6A 136162084 136164323 2239 True 3677.0 3677 96.339 118 2351 1 chr6A.!!$R1 2233
4 TraesCS5A01G083800 chr6A 328875925 328878163 2238 False 3653.0 3653 96.161 118 2351 1 chr6A.!!$F1 2233
5 TraesCS5A01G083800 chr6A 518073403 518075640 2237 True 3653.0 3653 96.159 118 2351 1 chr6A.!!$R5 2233
6 TraesCS5A01G083800 chr6A 213991998 213994228 2230 True 3651.0 3651 96.204 118 2351 1 chr6A.!!$R3 2233
7 TraesCS5A01G083800 chr6A 473515388 473517373 1985 False 3338.0 3338 97.031 370 2351 1 chr6A.!!$F2 1981
8 TraesCS5A01G083800 chr2A 616454113 616456350 2237 True 3677.0 3677 96.381 121 2351 1 chr2A.!!$R1 2230
9 TraesCS5A01G083800 chr2A 352444305 352444847 542 True 216.5 222 92.285 1 153 2 chr2A.!!$R2 152
10 TraesCS5A01G083800 chr3A 134617333 134619588 2255 False 3520.0 3520 95.002 118 2351 1 chr3A.!!$F1 2233
11 TraesCS5A01G083800 chr1A 465251795 465253629 1834 False 3081.0 3081 97.006 520 2351 1 chr1A.!!$F2 1831

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
113 114 0.317854 CAGGATGACGAATAGCGCGA 60.318 55.0 12.1 0.00 46.04 5.87 F
114 115 0.317938 AGGATGACGAATAGCGCGAC 60.318 55.0 12.1 0.04 46.04 5.19 F
1030 1062 1.191489 TGATCTGCGACCACCTTGGA 61.191 55.0 0.0 0.00 40.96 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1137 0.324091 CCTGCCAGAAGATGCCCTTT 60.324 55.000 0.00 0.00 34.68 3.11 R
1254 1286 4.094646 ATGACCATGGCGTCGGCA 62.095 61.111 24.58 24.58 43.52 5.69 R
2320 2370 9.883142 AAACAATCAAACAAAAGAAGGACATAA 57.117 25.926 0.00 0.00 0.00 1.90 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
30 31 6.129115 CGTCGGAAATAAGACAAAACTTACGA 60.129 38.462 0.00 0.00 37.23 3.43
90 91 6.710597 GGGGGTGAAAAATAACTATTCCTC 57.289 41.667 0.00 0.00 0.00 3.71
91 92 6.192044 GGGGGTGAAAAATAACTATTCCTCA 58.808 40.000 0.00 0.00 0.00 3.86
92 93 6.096423 GGGGGTGAAAAATAACTATTCCTCAC 59.904 42.308 11.75 11.75 36.94 3.51
93 94 6.096423 GGGGTGAAAAATAACTATTCCTCACC 59.904 42.308 21.43 21.43 45.36 4.02
94 95 7.096884 GGTGAAAAATAACTATTCCTCACCC 57.903 40.000 20.20 10.64 43.27 4.61
95 96 6.661805 GGTGAAAAATAACTATTCCTCACCCA 59.338 38.462 20.20 0.00 43.27 4.51
96 97 7.148069 GGTGAAAAATAACTATTCCTCACCCAG 60.148 40.741 20.20 0.00 43.27 4.45
97 98 6.889722 TGAAAAATAACTATTCCTCACCCAGG 59.110 38.462 0.00 0.00 45.15 4.45
108 109 3.377346 CTCACCCAGGATGACGAATAG 57.623 52.381 0.00 0.00 39.69 1.73
109 110 1.412710 TCACCCAGGATGACGAATAGC 59.587 52.381 0.00 0.00 39.69 2.97
111 112 0.946221 CCCAGGATGACGAATAGCGC 60.946 60.000 0.00 0.00 46.04 5.92
112 113 1.278172 CCAGGATGACGAATAGCGCG 61.278 60.000 0.00 0.00 46.04 6.86
113 114 0.317854 CAGGATGACGAATAGCGCGA 60.318 55.000 12.10 0.00 46.04 5.87
114 115 0.317938 AGGATGACGAATAGCGCGAC 60.318 55.000 12.10 0.04 46.04 5.19
115 116 1.276145 GGATGACGAATAGCGCGACC 61.276 60.000 12.10 0.00 46.04 4.79
116 117 1.276145 GATGACGAATAGCGCGACCC 61.276 60.000 12.10 0.00 46.04 4.46
124 125 3.125829 CGAATAGCGCGACCCTATAGTAA 59.874 47.826 12.10 0.00 0.00 2.24
194 195 2.292323 CCTATATAGGGCCCGAAGAGGT 60.292 54.545 18.44 0.00 39.86 3.85
201 202 1.671742 GCCCGAAGAGGTGTTCTCA 59.328 57.895 0.00 0.00 44.81 3.27
227 228 1.346479 TGAGAAAACCCACCCGACCA 61.346 55.000 0.00 0.00 0.00 4.02
673 683 1.402896 ATGTCATCGTCCATCGCCCT 61.403 55.000 0.00 0.00 39.67 5.19
1030 1062 1.191489 TGATCTGCGACCACCTTGGA 61.191 55.000 0.00 0.00 40.96 3.53
1105 1137 3.551454 CGTTCGTGAACCTGAAGGAGTAA 60.551 47.826 2.62 0.00 38.03 2.24
1254 1286 2.093447 CGACCCCTACTTCATCAAGCTT 60.093 50.000 0.00 0.00 32.09 3.74
1479 1519 2.146342 CAGGTTCAGGCTGTTGTGTAG 58.854 52.381 15.27 0.00 0.00 2.74
1673 1718 1.014352 GAGCGGCAAAACGATGGTAT 58.986 50.000 1.45 0.00 35.47 2.73
2320 2370 5.007921 GCAACAAGCAGGAAACAATTGAAAT 59.992 36.000 13.59 0.00 44.79 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.277974 CCTCTATTTTACCATCAATGCACCG 60.278 44.000 0.00 0.00 0.00 4.94
71 72 7.148069 CCTGGGTGAGGAATAGTTATTTTTCAC 60.148 40.741 14.68 14.68 46.33 3.18
72 73 6.889722 CCTGGGTGAGGAATAGTTATTTTTCA 59.110 38.462 0.00 0.00 46.33 2.69
73 74 7.334844 CCTGGGTGAGGAATAGTTATTTTTC 57.665 40.000 0.00 0.00 46.33 2.29
87 88 0.833287 ATTCGTCATCCTGGGTGAGG 59.167 55.000 20.81 20.81 44.45 3.86
88 89 2.546795 GCTATTCGTCATCCTGGGTGAG 60.547 54.545 10.58 5.05 0.00 3.51
89 90 1.412710 GCTATTCGTCATCCTGGGTGA 59.587 52.381 5.31 5.31 0.00 4.02
90 91 1.869754 CGCTATTCGTCATCCTGGGTG 60.870 57.143 0.00 0.00 0.00 4.61
91 92 0.389391 CGCTATTCGTCATCCTGGGT 59.611 55.000 0.00 0.00 0.00 4.51
92 93 0.946221 GCGCTATTCGTCATCCTGGG 60.946 60.000 0.00 0.00 41.07 4.45
93 94 1.278172 CGCGCTATTCGTCATCCTGG 61.278 60.000 5.56 0.00 41.07 4.45
94 95 0.317854 TCGCGCTATTCGTCATCCTG 60.318 55.000 5.56 0.00 41.07 3.86
95 96 0.317938 GTCGCGCTATTCGTCATCCT 60.318 55.000 5.56 0.00 41.07 3.24
96 97 1.276145 GGTCGCGCTATTCGTCATCC 61.276 60.000 5.56 0.00 41.07 3.51
97 98 1.276145 GGGTCGCGCTATTCGTCATC 61.276 60.000 5.56 0.00 41.07 2.92
98 99 1.299926 GGGTCGCGCTATTCGTCAT 60.300 57.895 5.56 0.00 41.07 3.06
99 100 1.096967 TAGGGTCGCGCTATTCGTCA 61.097 55.000 5.56 0.00 41.07 4.35
100 101 0.240411 ATAGGGTCGCGCTATTCGTC 59.760 55.000 5.56 0.00 36.44 4.20
101 102 1.467734 CTATAGGGTCGCGCTATTCGT 59.532 52.381 17.00 0.00 39.65 3.85
102 103 1.467734 ACTATAGGGTCGCGCTATTCG 59.532 52.381 17.00 12.63 39.65 3.34
103 104 4.083110 TGTTACTATAGGGTCGCGCTATTC 60.083 45.833 17.00 0.00 39.65 1.75
104 105 3.822735 TGTTACTATAGGGTCGCGCTATT 59.177 43.478 17.00 7.24 39.65 1.73
105 106 3.190118 GTGTTACTATAGGGTCGCGCTAT 59.810 47.826 5.56 16.35 41.39 2.97
106 107 2.549754 GTGTTACTATAGGGTCGCGCTA 59.450 50.000 5.56 0.00 33.62 4.26
107 108 1.336125 GTGTTACTATAGGGTCGCGCT 59.664 52.381 5.56 0.00 0.00 5.92
108 109 1.336125 AGTGTTACTATAGGGTCGCGC 59.664 52.381 0.00 0.00 0.00 6.86
109 110 5.180868 AGAATAGTGTTACTATAGGGTCGCG 59.819 44.000 0.00 0.00 40.32 5.87
110 111 6.572167 AGAATAGTGTTACTATAGGGTCGC 57.428 41.667 4.43 0.83 40.32 5.19
113 114 9.544579 GGGATTAGAATAGTGTTACTATAGGGT 57.455 37.037 4.43 0.00 40.32 4.34
114 115 9.543231 TGGGATTAGAATAGTGTTACTATAGGG 57.457 37.037 4.43 0.00 40.32 3.53
201 202 2.424379 GGGTGGGTTTTCTCAGGAGTTT 60.424 50.000 0.00 0.00 0.00 2.66
247 250 2.122769 TCGTGGGAAGTGGGTGGA 60.123 61.111 0.00 0.00 0.00 4.02
538 547 3.426568 GCGGAGTTGCAGCTGGAC 61.427 66.667 17.12 7.75 34.66 4.02
660 670 3.770040 CCACAGGGCGATGGACGA 61.770 66.667 0.00 0.00 45.77 4.20
935 967 5.006358 ACTCAAAGACGATGTGTGTGTTTAC 59.994 40.000 0.00 0.00 31.85 2.01
1030 1062 0.971447 GCCCCGTCTTGACTCCTAGT 60.971 60.000 0.00 0.00 0.00 2.57
1077 1109 0.812412 CAGGTTCACGAACGGGTTGT 60.812 55.000 3.95 0.00 42.02 3.32
1105 1137 0.324091 CCTGCCAGAAGATGCCCTTT 60.324 55.000 0.00 0.00 34.68 3.11
1254 1286 4.094646 ATGACCATGGCGTCGGCA 62.095 61.111 24.58 24.58 43.52 5.69
1479 1519 4.766404 ACAGGCAGCTAATGTTTTGTAC 57.234 40.909 0.00 0.00 0.00 2.90
2320 2370 9.883142 AAACAATCAAACAAAAGAAGGACATAA 57.117 25.926 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.