Multiple sequence alignment - TraesCS4D01G151800

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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 TraesCS4D01G151800 chr4D 100.000 2501 0 0 1 2501 178587359 178584859 0 4619
1 TraesCS4D01G151800 chr4D 96.088 2505 78 17 1 2501 504400311 504397823 0 4065
2 TraesCS4D01G151800 chr4D 95.605 2503 91 17 1 2501 348405883 348403398 0 3995
3 TraesCS4D01G151800 chr6D 96.846 2505 58 17 1 2501 176859191 176861678 0 4169
4 TraesCS4D01G151800 chr7D 96.513 2524 54 12 2 2501 420794561 420792048 0 4143
5 TraesCS4D01G151800 chr7D 95.569 2505 92 17 1 2501 313362157 313359668 0 3993
6 TraesCS4D01G151800 chr2D 96.249 2506 73 18 1 2501 460887113 460884624 0 4087
7 TraesCS4D01G151800 chr5D 95.331 2506 94 20 1 2501 45854586 45857073 0 3958
8 TraesCS4D01G151800 chr3D 95.286 2503 98 18 1 2501 588800963 588798479 0 3951
9 TraesCS4D01G151800 chr3D 95.284 2502 97 18 1 2501 478614222 478616703 0 3947
10 TraesCS4D01G151800 chr2A 88.353 2301 199 40 209 2501 121072899 121075138 0 2700


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 TraesCS4D01G151800 chr4D 178584859 178587359 2500 True 4619 4619 100.000 1 2501 1 chr4D.!!$R1 2500
1 TraesCS4D01G151800 chr4D 504397823 504400311 2488 True 4065 4065 96.088 1 2501 1 chr4D.!!$R3 2500
2 TraesCS4D01G151800 chr4D 348403398 348405883 2485 True 3995 3995 95.605 1 2501 1 chr4D.!!$R2 2500
3 TraesCS4D01G151800 chr6D 176859191 176861678 2487 False 4169 4169 96.846 1 2501 1 chr6D.!!$F1 2500
4 TraesCS4D01G151800 chr7D 420792048 420794561 2513 True 4143 4143 96.513 2 2501 1 chr7D.!!$R2 2499
5 TraesCS4D01G151800 chr7D 313359668 313362157 2489 True 3993 3993 95.569 1 2501 1 chr7D.!!$R1 2500
6 TraesCS4D01G151800 chr2D 460884624 460887113 2489 True 4087 4087 96.249 1 2501 1 chr2D.!!$R1 2500
7 TraesCS4D01G151800 chr5D 45854586 45857073 2487 False 3958 3958 95.331 1 2501 1 chr5D.!!$F1 2500
8 TraesCS4D01G151800 chr3D 588798479 588800963 2484 True 3951 3951 95.286 1 2501 1 chr3D.!!$R1 2500
9 TraesCS4D01G151800 chr3D 478614222 478616703 2481 False 3947 3947 95.284 1 2501 1 chr3D.!!$F1 2500
10 TraesCS4D01G151800 chr2A 121072899 121075138 2239 False 2700 2700 88.353 209 2501 1 chr2A.!!$F1 2292

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
165 166 0.618458 AGCGTAATGACCACACCCAT 59.382 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1519 0.511221 ACCGCGTGTTGAAATCTTCG 59.489 50.0 4.92 0.0 0.0 3.79 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
99 100 4.081642 ACCAGCTGTACGATATTGTCAAGT 60.082 41.667 13.81 0.00 0.00 3.16
165 166 0.618458 AGCGTAATGACCACACCCAT 59.382 50.000 0.00 0.00 0.00 4.00
248 252 5.033326 TGCTCCGTTTACGTTTTATTTCC 57.967 39.130 0.00 0.00 37.74 3.13
311 315 6.839124 TTTTCATACAGCTCATGTTTGGAT 57.161 33.333 5.05 0.00 39.96 3.41
586 590 6.591935 TGAAGAAATGTGTGAGTACTCCTTT 58.408 36.000 20.11 11.18 0.00 3.11
588 592 5.230942 AGAAATGTGTGAGTACTCCTTTCG 58.769 41.667 20.11 0.00 38.64 3.46
723 727 9.199982 CATGTAAAATGACTTCTGATTTGCTTT 57.800 29.630 0.00 0.00 0.00 3.51
755 759 2.552315 ACCTATGTGGCAACTTCAAACG 59.448 45.455 0.00 0.00 40.22 3.60
778 782 5.164196 CGAAAATACATGGCAACTTTGTTCG 60.164 40.000 0.00 0.00 35.64 3.95
857 861 1.768275 ACTTTTTCTTTGGCCCCTTGG 59.232 47.619 0.00 0.00 0.00 3.61
960 965 4.815533 TCTTAATGTGAGCTCTGCTTCT 57.184 40.909 16.19 0.00 39.88 2.85
1035 1041 1.027255 CACCACACGACCCACACAAA 61.027 55.000 0.00 0.00 0.00 2.83
1178 1184 2.711009 ACCTCAAAGAGACATGGAACCA 59.289 45.455 0.00 0.00 0.00 3.67
1298 1304 0.804989 GTCCTCCAAACCAATGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
1376 1386 7.110155 TCTTGTGAGTTAACCTGACTCTTTTT 58.890 34.615 0.88 0.00 43.07 1.94
1450 1460 2.567497 GGTCGACGGGTTCCTGTCA 61.567 63.158 24.66 12.82 34.78 3.58
1499 1509 5.473846 TCCGCAAAATTTACACATGGAACTA 59.526 36.000 0.00 0.00 0.00 2.24
1509 1519 7.667043 TTACACATGGAACTAGTTGATGAAC 57.333 36.000 22.54 6.29 0.00 3.18
1691 1706 7.941795 AAACTATGTCCGTGTAATATGCTAC 57.058 36.000 0.00 0.00 0.00 3.58
1717 1732 2.792878 CATCTCCCCGTACCCTAGTAG 58.207 57.143 0.00 0.00 0.00 2.57
1748 1763 3.482786 GCGTGTGAGTGACATTTGAATC 58.517 45.455 0.00 0.00 36.78 2.52
1998 2019 4.392940 GGCTAGCATGGTAGTTTGATCAT 58.607 43.478 27.79 0.00 0.00 2.45
1999 2020 5.551233 GGCTAGCATGGTAGTTTGATCATA 58.449 41.667 27.79 0.00 0.00 2.15
2048 2069 2.612212 GAGACCGTTTCAGCTTGTTTCA 59.388 45.455 0.00 0.00 0.00 2.69
2140 2184 7.148407 GGTGAAGATTCAGTACAACTAACATGG 60.148 40.741 0.00 0.00 37.98 3.66
2141 2185 6.371548 TGAAGATTCAGTACAACTAACATGGC 59.628 38.462 0.00 0.00 32.50 4.40
2142 2186 5.804639 AGATTCAGTACAACTAACATGGCA 58.195 37.500 0.00 0.00 0.00 4.92
2143 2187 6.418101 AGATTCAGTACAACTAACATGGCAT 58.582 36.000 0.00 0.00 0.00 4.40
2144 2188 5.878332 TTCAGTACAACTAACATGGCATG 57.122 39.130 25.31 25.31 0.00 4.06
2159 2203 7.141100 ACATGGCATGTTTAGTACAACTAAC 57.859 36.000 26.78 0.00 40.12 2.34
2160 2204 6.712998 ACATGGCATGTTTAGTACAACTAACA 59.287 34.615 26.78 0.29 40.12 2.41
2161 2205 7.393234 ACATGGCATGTTTAGTACAACTAACAT 59.607 33.333 26.78 0.00 40.12 2.71
2162 2206 7.139896 TGGCATGTTTAGTACAACTAACATG 57.860 36.000 23.53 23.53 43.39 3.21
2269 2408 2.203470 TGCATGGCAGATTCAGTTCA 57.797 45.000 0.00 0.00 33.32 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.705658 ACTTCCGGCTCATAATCATCCA 59.294 45.455 0.00 0.00 0.00 3.41
99 100 0.881118 GACCTCGCATTTCCAAAGCA 59.119 50.000 0.00 0.00 0.00 3.91
165 166 6.886459 AGAGCAAAGCAAATGAGAGGTTTATA 59.114 34.615 0.00 0.00 34.09 0.98
223 226 7.281549 AGGAAATAAAACGTAAACGGAGCATAT 59.718 33.333 7.50 0.00 44.95 1.78
311 315 7.227314 GCATCACATTGTATGATCTTGGTTCTA 59.773 37.037 0.00 0.00 34.49 2.10
663 667 4.500205 CCACATGAAACAGCTGTCACAAAT 60.500 41.667 21.95 12.14 0.00 2.32
723 727 5.702065 TGCCACATAGGTTGTATTAGGAA 57.298 39.130 0.00 0.00 40.61 3.36
755 759 5.689961 ACGAACAAAGTTGCCATGTATTTTC 59.310 36.000 0.00 0.00 0.00 2.29
778 782 2.094762 AGAAGTTGCCGTCCATGTAC 57.905 50.000 0.00 0.00 0.00 2.90
857 861 3.318017 ACATGAGTGACTACGAAAGCAC 58.682 45.455 0.00 0.00 34.42 4.40
960 965 8.571336 TGCAAACAAAAATGAAGGAAAGAAAAA 58.429 25.926 0.00 0.00 0.00 1.94
1178 1184 6.542821 TGGACCTTTGAGTTTTCATAGTGAT 58.457 36.000 0.00 0.00 32.44 3.06
1376 1386 1.508632 GCAGTCGTGCCTAAACAAGA 58.491 50.000 0.00 0.00 44.72 3.02
1450 1460 0.615331 ACGACCATTCCAGCTGTGAT 59.385 50.000 13.81 2.96 0.00 3.06
1499 1509 6.430451 GTGTTGAAATCTTCGTTCATCAACT 58.570 36.000 15.02 0.00 44.18 3.16
1509 1519 0.511221 ACCGCGTGTTGAAATCTTCG 59.489 50.000 4.92 0.00 0.00 3.79
1662 1676 8.178964 GCATATTACACGGACATAGTTTTGAAA 58.821 33.333 0.00 0.00 0.00 2.69
1691 1706 1.065928 GTACGGGGAGATGCAGTCG 59.934 63.158 0.00 0.00 0.00 4.18
1717 1732 1.956170 CTCACACGCCACCACTGTC 60.956 63.158 0.00 0.00 0.00 3.51
1748 1763 8.137210 TCACATCCACACATATATTACAAACG 57.863 34.615 0.00 0.00 0.00 3.60
2048 2069 6.985188 ATTGTATTCTCGTGCAAACTATGT 57.015 33.333 0.00 0.00 0.00 2.29
2140 2184 6.027749 GCCATGTTAGTTGTACTAAACATGC 58.972 40.000 20.32 15.01 41.80 4.06
2141 2185 7.119116 TCTGCCATGTTAGTTGTACTAAACATG 59.881 37.037 19.45 19.45 41.80 3.21
2142 2186 7.165485 TCTGCCATGTTAGTTGTACTAAACAT 58.835 34.615 1.15 0.00 41.80 2.71
2143 2187 6.526526 TCTGCCATGTTAGTTGTACTAAACA 58.473 36.000 1.15 0.00 41.80 2.83
2144 2188 7.611213 ATCTGCCATGTTAGTTGTACTAAAC 57.389 36.000 1.15 0.00 41.80 2.01
2145 2189 7.880713 TGAATCTGCCATGTTAGTTGTACTAAA 59.119 33.333 1.15 0.00 41.80 1.85
2146 2190 7.390823 TGAATCTGCCATGTTAGTTGTACTAA 58.609 34.615 0.00 0.00 38.28 2.24
2147 2191 6.941857 TGAATCTGCCATGTTAGTTGTACTA 58.058 36.000 0.00 0.00 0.00 1.82
2148 2192 5.804639 TGAATCTGCCATGTTAGTTGTACT 58.195 37.500 0.00 0.00 0.00 2.73
2149 2193 5.643777 ACTGAATCTGCCATGTTAGTTGTAC 59.356 40.000 0.00 0.00 0.00 2.90
2150 2194 5.804639 ACTGAATCTGCCATGTTAGTTGTA 58.195 37.500 0.00 0.00 0.00 2.41
2151 2195 4.655963 ACTGAATCTGCCATGTTAGTTGT 58.344 39.130 0.00 0.00 0.00 3.32
2152 2196 6.741992 TTACTGAATCTGCCATGTTAGTTG 57.258 37.500 0.00 0.00 0.00 3.16
2153 2197 7.759489 TTTTACTGAATCTGCCATGTTAGTT 57.241 32.000 0.00 0.00 0.00 2.24
2154 2198 7.759489 TTTTTACTGAATCTGCCATGTTAGT 57.241 32.000 0.00 0.00 0.00 2.24
2209 2302 5.394883 CCATGCCATTTCTACTCAATTTGCT 60.395 40.000 0.00 0.00 0.00 3.91
2269 2408 4.990426 GCACTGAATTTGCCATGTTACTTT 59.010 37.500 0.00 0.00 33.58 2.66
2409 2552 4.860802 TGACTTGGTTCCATGGTGATAT 57.139 40.909 12.58 0.00 0.00 1.63
2410 2553 4.649267 TTGACTTGGTTCCATGGTGATA 57.351 40.909 12.58 0.00 0.00 2.15
2411 2554 3.524095 TTGACTTGGTTCCATGGTGAT 57.476 42.857 12.58 0.00 0.00 3.06
2458 2602 2.173996 AGAAACCAAAGAAAGGGACGGA 59.826 45.455 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.