Multiple sequence alignment - TraesCS3B01G011000

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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 TraesCS3B01G011000 chr3B 100.000 3080 0 0 1 3080 5084557 5081478 0.000000e+00 5688.0
1 TraesCS3B01G011000 chr3B 99.120 2160 18 1 1 2160 92264440 92266598 0.000000e+00 3882.0
2 TraesCS3B01G011000 chr3B 98.565 2160 29 1 1 2160 92145509 92147666 0.000000e+00 3816.0
3 TraesCS3B01G011000 chr3B 98.878 891 7 1 2190 3080 4226972 4226085 0.000000e+00 1587.0
4 TraesCS3B01G011000 chr3B 82.716 162 27 1 2236 2396 3612253 3612092 3.200000e-30 143.0
5 TraesCS3B01G011000 chr3B 82.716 162 27 1 2236 2396 5224439 5224600 3.200000e-30 143.0
6 TraesCS3B01G011000 chr3B 98.000 50 1 0 2190 2239 273303111 273303160 1.520000e-13 87.9
7 TraesCS3B01G011000 chr3B 94.545 55 2 1 2190 2243 99666501 99666447 1.970000e-12 84.2
8 TraesCS3B01G011000 chr1B 99.352 2160 13 1 1 2160 683731558 683729400 0.000000e+00 3910.0
9 TraesCS3B01G011000 chr1B 96.970 165 5 0 2873 3037 268402863 268402699 8.410000e-71 278.0
10 TraesCS3B01G011000 chr6B 99.074 2160 19 1 1 2160 128914700 128916858 0.000000e+00 3877.0
11 TraesCS3B01G011000 chr7B 99.028 2160 20 1 1 2160 698142745 698144903 0.000000e+00 3871.0
12 TraesCS3B01G011000 chrUn 98.889 2160 22 2 1 2160 40088445 40090602 0.000000e+00 3855.0
13 TraesCS3B01G011000 chr2A 98.889 2160 23 1 1 2160 563259225 563261383 0.000000e+00 3855.0
14 TraesCS3B01G011000 chr2A 87.616 323 36 4 2232 2553 35471650 35471969 3.750000e-99 372.0
15 TraesCS3B01G011000 chr5B 98.797 2161 24 2 1 2160 713079636 713077477 0.000000e+00 3845.0
16 TraesCS3B01G011000 chr5B 98.612 2162 27 3 1 2160 713129078 713131238 0.000000e+00 3823.0
17 TraesCS3B01G011000 chr3A 93.729 303 18 1 2236 2537 714469939 714469637 1.300000e-123 453.0
18 TraesCS3B01G011000 chr7D 93.841 276 16 1 2426 2701 43198928 43199202 6.140000e-112 414.0
19 TraesCS3B01G011000 chr7D 90.957 188 13 2 2237 2424 43197475 43197658 1.830000e-62 250.0
20 TraesCS3B01G011000 chr6A 83.527 431 61 4 2237 2658 522483247 522482818 8.010000e-106 394.0
21 TraesCS3B01G011000 chr6A 94.444 54 3 0 2190 2243 224620546 224620493 1.970000e-12 84.2
22 TraesCS3B01G011000 chr2B 87.781 311 38 0 2243 2553 53054932 53055242 6.280000e-97 364.0
23 TraesCS3B01G011000 chr2B 97.024 168 5 0 2870 3037 47170743 47170910 1.810000e-72 283.0
24 TraesCS3B01G011000 chr2B 87.783 221 22 5 2829 3047 21914697 21914480 1.420000e-63 254.0
25 TraesCS3B01G011000 chr2B 98.000 50 1 0 2190 2239 214828164 214828213 1.520000e-13 87.9
26 TraesCS3B01G011000 chr2B 94.643 56 1 1 2190 2243 585937288 585937233 5.470000e-13 86.1
27 TraesCS3B01G011000 chr5D 96.450 169 6 0 2869 3037 66671781 66671949 2.340000e-71 279.0
28 TraesCS3B01G011000 chr5D 93.820 178 9 2 2873 3049 100549542 100549366 1.820000e-67 267.0
29 TraesCS3B01G011000 chr5D 81.481 189 26 8 2235 2418 319685339 319685523 2.470000e-31 147.0
30 TraesCS3B01G011000 chr5D 96.154 52 2 0 2190 2241 389438751 389438802 5.470000e-13 86.1
31 TraesCS3B01G011000 chr4B 96.970 165 5 0 2872 3036 549133881 549133717 8.410000e-71 278.0
32 TraesCS3B01G011000 chr4B 93.855 179 10 1 2869 3047 658178329 658178152 5.060000e-68 268.0
33 TraesCS3B01G011000 chr4B 96.154 52 2 0 2190 2241 666597954 666598005 5.470000e-13 86.1
34 TraesCS3B01G011000 chr4D 91.623 191 12 4 2858 3044 216066927 216067117 8.470000e-66 261.0
35 TraesCS3B01G011000 chr4D 92.857 56 4 0 2190 2245 298543520 298543575 7.080000e-12 82.4


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 TraesCS3B01G011000 chr3B 5081478 5084557 3079 True 5688 5688 100.000 1 3080 1 chr3B.!!$R3 3079
1 TraesCS3B01G011000 chr3B 92264440 92266598 2158 False 3882 3882 99.120 1 2160 1 chr3B.!!$F3 2159
2 TraesCS3B01G011000 chr3B 92145509 92147666 2157 False 3816 3816 98.565 1 2160 1 chr3B.!!$F2 2159
3 TraesCS3B01G011000 chr3B 4226085 4226972 887 True 1587 1587 98.878 2190 3080 1 chr3B.!!$R2 890
4 TraesCS3B01G011000 chr1B 683729400 683731558 2158 True 3910 3910 99.352 1 2160 1 chr1B.!!$R2 2159
5 TraesCS3B01G011000 chr6B 128914700 128916858 2158 False 3877 3877 99.074 1 2160 1 chr6B.!!$F1 2159
6 TraesCS3B01G011000 chr7B 698142745 698144903 2158 False 3871 3871 99.028 1 2160 1 chr7B.!!$F1 2159
7 TraesCS3B01G011000 chrUn 40088445 40090602 2157 False 3855 3855 98.889 1 2160 1 chrUn.!!$F1 2159
8 TraesCS3B01G011000 chr2A 563259225 563261383 2158 False 3855 3855 98.889 1 2160 1 chr2A.!!$F2 2159
9 TraesCS3B01G011000 chr5B 713077477 713079636 2159 True 3845 3845 98.797 1 2160 1 chr5B.!!$R1 2159
10 TraesCS3B01G011000 chr5B 713129078 713131238 2160 False 3823 3823 98.612 1 2160 1 chr5B.!!$F1 2159
11 TraesCS3B01G011000 chr7D 43197475 43199202 1727 False 332 414 92.399 2237 2701 2 chr7D.!!$F1 464

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
126 127 0.250513 GAGGCAGAAACTCGTCCCAT 59.749 55.000 0.00 0.00 0.00 4.00 F
250 251 2.858644 ACTCCATATGGGGAAGGAACA 58.141 47.619 28.98 0.99 38.16 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1405 2.170397 TCTATTGGAAGAGATGGCGCAA 59.830 45.455 10.83 0.0 0.00 4.85 R
2160 2163 1.076192 TCCCTCGACTAAGGAGCCC 60.076 63.158 0.00 0.0 38.87 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
126 127 0.250513 GAGGCAGAAACTCGTCCCAT 59.749 55.000 0.00 0.00 0.00 4.00
188 189 3.196039 TGCGGCTTAGGTCAACTAATACA 59.804 43.478 0.00 0.00 40.71 2.29
250 251 2.858644 ACTCCATATGGGGAAGGAACA 58.141 47.619 28.98 0.99 38.16 3.18
289 290 4.347876 TCTCGATCATTTACATGGACCCAT 59.652 41.667 0.00 0.00 37.08 4.00
1228 1230 4.474226 GAAGAAATCGATACCATGGTGC 57.526 45.455 28.17 17.51 0.00 5.01
1403 1405 1.357420 TGGTGATTGGCCTTGTATGGT 59.643 47.619 3.32 0.00 0.00 3.55
1599 1602 7.766278 GTCTGTGTGGATTTGAGTCATAGTATT 59.234 37.037 0.00 0.00 0.00 1.89
2160 2163 5.223449 TGTCCTACTTTGTGAAGTAAGGG 57.777 43.478 1.26 0.88 45.20 3.95
2161 2164 4.041198 TGTCCTACTTTGTGAAGTAAGGGG 59.959 45.833 1.26 0.30 45.20 4.79
2162 2165 3.585732 TCCTACTTTGTGAAGTAAGGGGG 59.414 47.826 1.26 0.00 45.20 5.40
2163 2166 2.287977 ACTTTGTGAAGTAAGGGGGC 57.712 50.000 0.00 0.00 44.13 5.80
2164 2167 1.780919 ACTTTGTGAAGTAAGGGGGCT 59.219 47.619 0.00 0.00 44.13 5.19
2165 2168 2.224793 ACTTTGTGAAGTAAGGGGGCTC 60.225 50.000 0.00 0.00 44.13 4.70
2166 2169 0.696501 TTGTGAAGTAAGGGGGCTCC 59.303 55.000 0.00 0.00 0.00 4.70
2174 2177 3.106736 AGGGGGCTCCTTAGTCGA 58.893 61.111 0.00 0.00 45.47 4.20
2175 2178 1.075896 AGGGGGCTCCTTAGTCGAG 60.076 63.158 0.00 0.00 45.47 4.04
2176 2179 2.134933 GGGGGCTCCTTAGTCGAGG 61.135 68.421 0.52 0.00 38.20 4.63
2177 2180 2.134933 GGGGCTCCTTAGTCGAGGG 61.135 68.421 0.00 0.00 37.41 4.30
2178 2181 1.076192 GGGCTCCTTAGTCGAGGGA 60.076 63.158 0.00 0.00 37.41 4.20
2179 2182 1.110518 GGGCTCCTTAGTCGAGGGAG 61.111 65.000 15.22 15.22 46.65 4.30
2180 2183 0.396001 GGCTCCTTAGTCGAGGGAGT 60.396 60.000 18.54 0.00 45.91 3.85
2181 2184 1.133853 GGCTCCTTAGTCGAGGGAGTA 60.134 57.143 18.54 0.00 45.91 2.59
2182 2185 2.489437 GGCTCCTTAGTCGAGGGAGTAT 60.489 54.545 18.54 0.00 45.91 2.12
2183 2186 3.224269 GCTCCTTAGTCGAGGGAGTATT 58.776 50.000 18.54 0.00 45.91 1.89
2184 2187 3.637694 GCTCCTTAGTCGAGGGAGTATTT 59.362 47.826 18.54 0.00 45.91 1.40
2185 2188 4.099727 GCTCCTTAGTCGAGGGAGTATTTT 59.900 45.833 18.54 0.00 45.91 1.82
2186 2189 5.395435 GCTCCTTAGTCGAGGGAGTATTTTT 60.395 44.000 18.54 0.00 45.91 1.94
2187 2190 5.974108 TCCTTAGTCGAGGGAGTATTTTTG 58.026 41.667 0.00 0.00 37.41 2.44
2188 2191 5.105064 TCCTTAGTCGAGGGAGTATTTTTGG 60.105 44.000 0.00 0.00 37.41 3.28
2193 2196 5.001874 GTCGAGGGAGTATTTTTGGAAAGT 58.998 41.667 0.00 0.00 0.00 2.66
2338 2341 0.748450 GTGTATCGTCCCGGATCCAA 59.252 55.000 13.41 0.00 0.00 3.53
2374 2377 4.712051 TGGCTAACCTATCAGCATCATT 57.288 40.909 0.00 0.00 39.63 2.57
2375 2378 4.392047 TGGCTAACCTATCAGCATCATTG 58.608 43.478 0.00 0.00 39.63 2.82
2376 2379 4.141413 TGGCTAACCTATCAGCATCATTGT 60.141 41.667 0.00 0.00 39.63 2.71
2827 4098 8.372459 TGTGTTGTAACCAAAGATAGTAGATGT 58.628 33.333 0.00 0.00 30.94 3.06
2878 4149 5.450818 TTTGCTAATTCCCATGTACTCCT 57.549 39.130 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 9.436957 AATCGTTGAGTGAACTGTATCTTATTT 57.563 29.630 0.00 0.00 31.70 1.40
250 251 1.531149 CGAGACCTCGCAAACAACAAT 59.469 47.619 6.49 0.00 46.50 2.71
674 676 2.366167 AGCCTCCCGATGAAGCCT 60.366 61.111 0.00 0.00 30.16 4.58
1228 1230 5.227908 AGAATAACCTTCGTGTATATGCGG 58.772 41.667 0.00 0.00 0.00 5.69
1403 1405 2.170397 TCTATTGGAAGAGATGGCGCAA 59.830 45.455 10.83 0.00 0.00 4.85
1599 1602 2.487762 ACGTTCCGTAGAAACATACCGA 59.512 45.455 0.00 0.00 38.73 4.69
2160 2163 1.076192 TCCCTCGACTAAGGAGCCC 60.076 63.158 0.00 0.00 38.87 5.19
2161 2164 2.421220 CTCCCTCGACTAAGGAGCC 58.579 63.158 3.78 0.00 40.75 4.70
2164 2167 5.105064 CCAAAAATACTCCCTCGACTAAGGA 60.105 44.000 0.00 0.00 38.87 3.36
2165 2168 5.105064 TCCAAAAATACTCCCTCGACTAAGG 60.105 44.000 0.00 0.00 36.08 2.69
2166 2169 5.974108 TCCAAAAATACTCCCTCGACTAAG 58.026 41.667 0.00 0.00 0.00 2.18
2167 2170 6.363167 TTCCAAAAATACTCCCTCGACTAA 57.637 37.500 0.00 0.00 0.00 2.24
2168 2171 6.013984 ACTTTCCAAAAATACTCCCTCGACTA 60.014 38.462 0.00 0.00 0.00 2.59
2169 2172 4.903045 TTCCAAAAATACTCCCTCGACT 57.097 40.909 0.00 0.00 0.00 4.18
2170 2173 5.001874 ACTTTCCAAAAATACTCCCTCGAC 58.998 41.667 0.00 0.00 0.00 4.20
2171 2174 5.237236 ACTTTCCAAAAATACTCCCTCGA 57.763 39.130 0.00 0.00 0.00 4.04
2172 2175 5.959618 AACTTTCCAAAAATACTCCCTCG 57.040 39.130 0.00 0.00 0.00 4.63
2173 2176 7.997773 ACTAACTTTCCAAAAATACTCCCTC 57.002 36.000 0.00 0.00 0.00 4.30
2174 2177 8.442374 TGTACTAACTTTCCAAAAATACTCCCT 58.558 33.333 0.00 0.00 0.00 4.20
2175 2178 8.625786 TGTACTAACTTTCCAAAAATACTCCC 57.374 34.615 0.00 0.00 0.00 4.30
2181 2184 9.594478 CCAACTTTGTACTAACTTTCCAAAAAT 57.406 29.630 0.00 0.00 0.00 1.82
2182 2185 8.035984 CCCAACTTTGTACTAACTTTCCAAAAA 58.964 33.333 0.00 0.00 0.00 1.94
2183 2186 7.178805 ACCCAACTTTGTACTAACTTTCCAAAA 59.821 33.333 0.00 0.00 0.00 2.44
2184 2187 6.664384 ACCCAACTTTGTACTAACTTTCCAAA 59.336 34.615 0.00 0.00 0.00 3.28
2185 2188 6.189133 ACCCAACTTTGTACTAACTTTCCAA 58.811 36.000 0.00 0.00 0.00 3.53
2186 2189 5.757988 ACCCAACTTTGTACTAACTTTCCA 58.242 37.500 0.00 0.00 0.00 3.53
2187 2190 5.824097 TGACCCAACTTTGTACTAACTTTCC 59.176 40.000 0.00 0.00 0.00 3.13
2188 2191 6.930667 TGACCCAACTTTGTACTAACTTTC 57.069 37.500 0.00 0.00 0.00 2.62
2193 2196 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2338 2341 5.539955 AGGTTAGCCATGTTTTCACATTCTT 59.460 36.000 0.00 0.00 41.16 2.52
2374 2377 7.472804 TCAAGTTTGAAGGTAGAGCATCTAACA 60.473 37.037 11.65 0.00 44.40 2.41
2375 2378 6.874134 TCAAGTTTGAAGGTAGAGCATCTAAC 59.126 38.462 4.03 4.03 43.25 2.34
2376 2379 7.004555 TCAAGTTTGAAGGTAGAGCATCTAA 57.995 36.000 0.00 0.00 41.18 2.10
2878 4149 8.857694 AGAAAGACAAATATTTAGGAACGGAA 57.142 30.769 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.