Multiple sequence alignment - TraesCS7D01G280700

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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 TraesCS7D01G280700 chr7D 100.000 2279 0 0 1 2279 274687015 274689293 0.000000e+00 4209
1 TraesCS7D01G280700 chr7A 93.723 1386 45 9 905 2279 307952433 307953787 0.000000e+00 2039
2 TraesCS7D01G280700 chr7A 91.204 1262 100 6 1 1254 429059598 429058340 0.000000e+00 1705
3 TraesCS7D01G280700 chr4A 91.082 1312 105 8 1 1303 150815286 150813978 0.000000e+00 1764
4 TraesCS7D01G280700 chr5D 91.930 1264 94 3 1 1256 384794136 384795399 0.000000e+00 1762
5 TraesCS7D01G280700 chr4D 90.236 1311 115 8 1 1302 294934599 294933293 0.000000e+00 1700
6 TraesCS7D01G280700 chr7B 97.419 891 17 3 1393 2279 263117143 263116255 0.000000e+00 1513
7 TraesCS7D01G280700 chr7B 92.108 963 63 6 22 972 263119162 263118201 0.000000e+00 1345
8 TraesCS7D01G280700 chr7B 80.895 1319 225 21 1 1302 483805495 483806803 0.000000e+00 1014
9 TraesCS7D01G280700 chr7B 80.667 1319 229 20 1 1302 304088861 304087552 0.000000e+00 1000
10 TraesCS7D01G280700 chr7B 80.455 1320 229 22 1 1302 289654952 289653644 0.000000e+00 981
11 TraesCS7D01G280700 chr7B 81.783 516 41 17 831 1342 263117608 263117142 1.280000e-102 383
12 TraesCS7D01G280700 chr2B 80.516 1319 230 21 1 1302 133003405 133004713 0.000000e+00 987


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 TraesCS7D01G280700 chr7D 274687015 274689293 2278 False 4209.000000 4209 100.000000 1 2279 1 chr7D.!!$F1 2278
1 TraesCS7D01G280700 chr7A 307952433 307953787 1354 False 2039.000000 2039 93.723000 905 2279 1 chr7A.!!$F1 1374
2 TraesCS7D01G280700 chr7A 429058340 429059598 1258 True 1705.000000 1705 91.204000 1 1254 1 chr7A.!!$R1 1253
3 TraesCS7D01G280700 chr4A 150813978 150815286 1308 True 1764.000000 1764 91.082000 1 1303 1 chr4A.!!$R1 1302
4 TraesCS7D01G280700 chr5D 384794136 384795399 1263 False 1762.000000 1762 91.930000 1 1256 1 chr5D.!!$F1 1255
5 TraesCS7D01G280700 chr4D 294933293 294934599 1306 True 1700.000000 1700 90.236000 1 1302 1 chr4D.!!$R1 1301
6 TraesCS7D01G280700 chr7B 263116255 263119162 2907 True 1080.333333 1513 90.436667 22 2279 3 chr7B.!!$R3 2257
7 TraesCS7D01G280700 chr7B 483805495 483806803 1308 False 1014.000000 1014 80.895000 1 1302 1 chr7B.!!$F1 1301
8 TraesCS7D01G280700 chr7B 304087552 304088861 1309 True 1000.000000 1000 80.667000 1 1302 1 chr7B.!!$R2 1301
9 TraesCS7D01G280700 chr7B 289653644 289654952 1308 True 981.000000 981 80.455000 1 1302 1 chr7B.!!$R1 1301
10 TraesCS7D01G280700 chr2B 133003405 133004713 1308 False 987.000000 987 80.516000 1 1302 1 chr2B.!!$F1 1301

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
227 235 1.336609 ACGGTTCGGTCAGCTTACTTC 60.337 52.381 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2809 0.174389 CCGTGAGCACAGATAGCAGT 59.826 55.0 1.2 0.0 0.0 4.4 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
79 87 4.275936 CCTTATCAATCCGGTCACCAATTC 59.724 45.833 0.00 0.00 0.00 2.17
83 91 3.081061 CAATCCGGTCACCAATTCTTGA 58.919 45.455 0.00 0.00 0.00 3.02
115 123 6.952773 TTTAGTAAGACAAACATTGTGGCT 57.047 33.333 0.00 0.00 45.52 4.75
192 200 9.778993 CAGATTTCATTACTTGGAATTACACAG 57.221 33.333 0.00 0.00 33.40 3.66
197 205 8.547967 TCATTACTTGGAATTACACAGAGAAC 57.452 34.615 0.00 0.00 0.00 3.01
227 235 1.336609 ACGGTTCGGTCAGCTTACTTC 60.337 52.381 0.00 0.00 0.00 3.01
420 434 9.249457 TGCTAATAGACATATGAAAGTTTCTCG 57.751 33.333 16.33 5.17 0.00 4.04
447 461 2.923121 CCCATCATGTTCGAATGGACT 58.077 47.619 14.87 0.00 34.46 3.85
461 475 9.099454 GTTCGAATGGACTAGAAGATACAAAAT 57.901 33.333 0.00 0.00 0.00 1.82
480 494 8.948853 ACAAAATACATGTTGTTTCTATGTCG 57.051 30.769 2.30 0.00 34.29 4.35
563 577 3.371097 GATCGTGCGGGAGAGGCAA 62.371 63.158 0.00 0.00 42.92 4.52
635 649 2.498481 ACCCAGAATGCACATGAATTGG 59.502 45.455 0.00 0.00 31.97 3.16
639 653 4.561938 CCAGAATGCACATGAATTGGTTGT 60.562 41.667 0.00 0.00 31.97 3.32
726 741 1.946984 TACCAAACCTCGATGGGAGT 58.053 50.000 7.65 1.72 41.46 3.85
845 861 6.258230 TGAATGTCGATGCTTCTTTTGATT 57.742 33.333 0.00 0.00 0.00 2.57
871 887 1.938585 TGCTTAGAGGTACAGCAGGT 58.061 50.000 0.95 0.00 38.65 4.00
1005 1022 1.090052 GCACAGAAGGCGGGATGTAC 61.090 60.000 0.00 0.00 0.00 2.90
1018 1042 2.093869 GGGATGTACGTTGTTAGCTCCA 60.094 50.000 0.00 0.00 0.00 3.86
1063 1822 8.859090 ACACAATGAAGAATAAAGGACATTCAA 58.141 29.630 0.00 0.00 35.30 2.69
1119 1878 3.840890 TTTATGGCGTGCGATTTTCTT 57.159 38.095 0.00 0.00 0.00 2.52
1124 1883 2.095213 TGGCGTGCGATTTTCTTCATAC 59.905 45.455 0.00 0.00 0.00 2.39
1127 1886 4.033587 GGCGTGCGATTTTCTTCATACTAA 59.966 41.667 0.00 0.00 0.00 2.24
1345 2110 2.034558 AGATTTCAGGTGGCAAAACACG 59.965 45.455 0.00 0.00 42.23 4.49
1354 2119 2.852180 GCAAAACACGACCCCACCC 61.852 63.158 0.00 0.00 0.00 4.61
1355 2120 2.196502 AAAACACGACCCCACCCC 59.803 61.111 0.00 0.00 0.00 4.95
1356 2121 2.691779 AAAACACGACCCCACCCCA 61.692 57.895 0.00 0.00 0.00 4.96
1357 2122 2.634193 AAAACACGACCCCACCCCAG 62.634 60.000 0.00 0.00 0.00 4.45
1358 2123 4.567597 ACACGACCCCACCCCAGA 62.568 66.667 0.00 0.00 0.00 3.86
1359 2124 3.009115 CACGACCCCACCCCAGAT 61.009 66.667 0.00 0.00 0.00 2.90
1390 2155 2.515854 ACCTAGTCGCATATCCGTGAT 58.484 47.619 0.00 0.00 0.00 3.06
1392 2157 2.488153 CCTAGTCGCATATCCGTGATCA 59.512 50.000 0.00 0.00 0.00 2.92
1550 2319 7.472543 TCAAAGAACAAGAACTAAACTGCTTC 58.527 34.615 0.00 0.00 0.00 3.86
1637 2406 5.815581 ACAGAAGCTACATTATTCAACCCA 58.184 37.500 0.00 0.00 0.00 4.51
2039 2809 2.687935 GGTTGAGTTCCTTGTGCTTTCA 59.312 45.455 0.00 0.00 0.00 2.69
2166 2936 3.130869 CCCAAATTCATCAAATCTGCGGA 59.869 43.478 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.543277 TGATAGCAGGTGCCCTCTTG 59.457 55.000 0.00 0.0 43.38 3.02
177 185 4.315803 CCGTTCTCTGTGTAATTCCAAGT 58.684 43.478 0.00 0.0 0.00 3.16
192 200 0.531311 ACCGTGAAACACCCGTTCTC 60.531 55.000 0.00 0.0 35.74 2.87
197 205 2.600475 CCGAACCGTGAAACACCCG 61.600 63.158 0.00 0.0 35.74 5.28
227 235 3.980646 TGTTGTTTGTTCCATTCCTCG 57.019 42.857 0.00 0.0 0.00 4.63
420 434 0.309922 CGAACATGATGGGCAGATGC 59.690 55.000 0.00 0.0 41.14 3.91
461 475 5.872617 CCTTCCGACATAGAAACAACATGTA 59.127 40.000 0.00 0.0 33.16 2.29
480 494 2.226674 CTCCAAACTTCTTTCGCCTTCC 59.773 50.000 0.00 0.0 0.00 3.46
563 577 9.077885 TGGCATAAGAAGTAAAAACTCAAGAAT 57.922 29.630 0.00 0.0 0.00 2.40
639 653 8.664992 TCCACCATAAATATCAGGCTGTTATAA 58.335 33.333 15.27 8.4 0.00 0.98
652 666 6.823689 GCGACCATCTATTCCACCATAAATAT 59.176 38.462 0.00 0.0 0.00 1.28
726 741 3.275617 AATTTGCCACTATAGCACGGA 57.724 42.857 0.00 0.0 40.69 4.69
845 861 3.637229 GCTGTACCTCTAAGCATGTCCTA 59.363 47.826 0.00 0.0 36.91 2.94
871 887 4.761739 CCTTTGTCATCTTTAAGGACAGCA 59.238 41.667 0.00 0.0 41.99 4.41
882 898 7.175641 CAGTAATGAACCTTCCTTTGTCATCTT 59.824 37.037 0.00 0.0 0.00 2.40
1018 1042 8.514594 CATTGTGTCAACTACTTCCATATTGTT 58.485 33.333 0.00 0.0 0.00 2.83
1127 1886 7.839907 TGCTTCCTTATTACAATGCTCAAAAT 58.160 30.769 0.00 0.0 0.00 1.82
1256 2018 9.294030 GCCTTTATTCATTAGAAATGACAGTTG 57.706 33.333 1.90 0.0 37.29 3.16
1345 2110 1.926426 CTTGGATCTGGGGTGGGGTC 61.926 65.000 0.00 0.0 0.00 4.46
1354 2119 3.769844 ACTAGGTACACACTTGGATCTGG 59.230 47.826 0.00 0.0 0.00 3.86
1355 2120 4.438880 CGACTAGGTACACACTTGGATCTG 60.439 50.000 0.00 0.0 0.00 2.90
1356 2121 3.695060 CGACTAGGTACACACTTGGATCT 59.305 47.826 0.00 0.0 0.00 2.75
1357 2122 3.734293 GCGACTAGGTACACACTTGGATC 60.734 52.174 0.00 0.0 0.00 3.36
1358 2123 2.165845 GCGACTAGGTACACACTTGGAT 59.834 50.000 0.00 0.0 0.00 3.41
1359 2124 1.542915 GCGACTAGGTACACACTTGGA 59.457 52.381 0.00 0.0 0.00 3.53
1550 2319 1.126846 GAGTCGTGTTCCAGAAATGCG 59.873 52.381 0.00 0.0 0.00 4.73
1637 2406 6.933514 ACATTTTATTGATGTGGAGGGTTT 57.066 33.333 0.00 0.0 36.43 3.27
1771 2541 3.985925 GTCGTACACTGACCAAAGTAAGG 59.014 47.826 0.00 0.0 0.00 2.69
2039 2809 0.174389 CCGTGAGCACAGATAGCAGT 59.826 55.000 1.20 0.0 0.00 4.40
2166 2936 8.489676 AGAGATCACATTACAGATAACCTCAT 57.510 34.615 0.00 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.