Multiple sequence alignment - TraesCS7A01G277800

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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 TraesCS7A01G277800 chr7A 100.000 2291 0 0 1 2291 292781287 292783577 0 4231
1 TraesCS7A01G277800 chr7A 96.686 2293 72 3 1 2291 292773242 292775532 0 3810
2 TraesCS7A01G277800 chr7A 92.000 2300 154 18 1 2291 424618841 424621119 0 3201
3 TraesCS7A01G277800 chr7A 91.562 2299 172 14 1 2291 424610901 424613185 0 3151
4 TraesCS7A01G277800 chr7A 95.597 863 24 1 1 849 292789334 292790196 0 1371
5 TraesCS7A01G277800 chr4A 95.508 2293 90 4 1 2291 489643941 489646222 0 3651
6 TraesCS7A01G277800 chr4A 90.700 2301 167 24 1 2291 253433006 253435269 0 3020
7 TraesCS7A01G277800 chr4A 89.030 1969 184 24 334 2291 201269566 201271513 0 2410
8 TraesCS7A01G277800 chr1A 91.565 2300 161 21 1 2291 202033921 202031646 0 3142
9 TraesCS7A01G277800 chr1A 91.091 2301 169 20 1 2291 202027132 202024858 0 3081
10 TraesCS7A01G277800 chr5A 90.949 2298 191 14 1 2291 266469383 266467096 0 3075
11 TraesCS7A01G277800 chr5A 90.517 2320 185 13 1 2291 266461440 266459127 0 3033


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 TraesCS7A01G277800 chr7A 292781287 292783577 2290 False 4231 4231 100.000 1 2291 1 chr7A.!!$F2 2290
1 TraesCS7A01G277800 chr7A 292773242 292775532 2290 False 3810 3810 96.686 1 2291 1 chr7A.!!$F1 2290
2 TraesCS7A01G277800 chr7A 424618841 424621119 2278 False 3201 3201 92.000 1 2291 1 chr7A.!!$F5 2290
3 TraesCS7A01G277800 chr7A 424610901 424613185 2284 False 3151 3151 91.562 1 2291 1 chr7A.!!$F4 2290
4 TraesCS7A01G277800 chr7A 292789334 292790196 862 False 1371 1371 95.597 1 849 1 chr7A.!!$F3 848
5 TraesCS7A01G277800 chr4A 489643941 489646222 2281 False 3651 3651 95.508 1 2291 1 chr4A.!!$F3 2290
6 TraesCS7A01G277800 chr4A 253433006 253435269 2263 False 3020 3020 90.700 1 2291 1 chr4A.!!$F2 2290
7 TraesCS7A01G277800 chr4A 201269566 201271513 1947 False 2410 2410 89.030 334 2291 1 chr4A.!!$F1 1957
8 TraesCS7A01G277800 chr1A 202031646 202033921 2275 True 3142 3142 91.565 1 2291 1 chr1A.!!$R2 2290
9 TraesCS7A01G277800 chr1A 202024858 202027132 2274 True 3081 3081 91.091 1 2291 1 chr1A.!!$R1 2290
10 TraesCS7A01G277800 chr5A 266467096 266469383 2287 True 3075 3075 90.949 1 2291 1 chr5A.!!$R2 2290
11 TraesCS7A01G277800 chr5A 266459127 266461440 2313 True 3033 3033 90.517 1 2291 1 chr5A.!!$R1 2290

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
550 557 0.385751 CGCCTCTATCGAAGCAGGAA 59.614 55.0 10.33 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1693 1.592131 CGACAACGTTCCGGTTCCA 60.592 57.895 0.0 0.0 34.56 3.53 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
296 301 4.329545 TCCTTTTGCGCCGCCTCT 62.330 61.111 6.63 0.00 0.00 3.69
318 323 2.444895 GACCCCCATCTCTCGCCT 60.445 66.667 0.00 0.00 0.00 5.52
530 537 3.429141 GACCTCGTCGCTCACCGA 61.429 66.667 0.00 0.00 45.15 4.69
542 549 1.153309 TCACCGACGCCTCTATCGA 60.153 57.895 0.00 0.00 40.86 3.59
550 557 0.385751 CGCCTCTATCGAAGCAGGAA 59.614 55.000 10.33 0.00 0.00 3.36
1052 1093 1.310933 GCTCCCGACCGAGACAGTTA 61.311 60.000 0.00 0.00 30.97 2.24
1086 1128 1.079405 GACACGCCAAATCCCTCGA 60.079 57.895 0.00 0.00 0.00 4.04
1088 1130 1.815421 CACGCCAAATCCCTCGAGG 60.815 63.158 25.36 25.36 0.00 4.63
1146 1188 2.360852 GACACCGGGAGTCCTCGA 60.361 66.667 18.27 0.00 0.00 4.04
1178 1220 4.082354 AGTTCCACTACGAGATGTACAACC 60.082 45.833 0.00 0.00 0.00 3.77
1342 1384 3.463944 CCGTTGAGTGAACAAACTACCT 58.536 45.455 0.00 0.00 33.73 3.08
1343 1385 3.493503 CCGTTGAGTGAACAAACTACCTC 59.506 47.826 0.00 0.00 33.73 3.85
1374 1416 4.754372 TGACTACTTCGTGAACGTGTAT 57.246 40.909 2.37 0.22 40.80 2.29
1422 1464 2.283298 CTACTTCTACTACCACCGCGA 58.717 52.381 8.23 0.00 0.00 5.87
1651 1693 2.223971 ACCGACGTCTCAATGAGTTGTT 60.224 45.455 14.70 0.00 36.69 2.83
1681 1724 1.430228 GTTGTCGTGGCACCGTTTT 59.570 52.632 12.86 0.00 0.00 2.43
1687 1730 0.111001 CGTGGCACCGTTTTCGTTAG 60.111 55.000 12.86 0.00 42.35 2.34
1808 1853 4.512571 TCATCCGCATCATGATAACAACTG 59.487 41.667 8.15 2.84 0.00 3.16
2025 2073 3.435327 GTGTTCCGTCAATATGCAACTCA 59.565 43.478 0.00 0.00 0.00 3.41
2051 2099 8.518430 TTGCATATTGAGCTCCACTTAATTTA 57.482 30.769 12.15 0.00 36.16 1.40
2100 2148 3.634448 CCATGCATATTTAACCCGGACAA 59.366 43.478 0.73 0.00 0.00 3.18
2239 2289 1.136085 CCGTTCGACTACGTCCGTTTA 60.136 52.381 8.68 0.00 39.81 2.01
2250 2300 7.383102 ACTACGTCCGTTTATCTTCTTTAGA 57.617 36.000 0.00 0.00 37.28 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 262 0.032615 AGCGAAGGGAGAGGAGATGT 60.033 55.000 0.00 0.00 0.00 3.06
296 301 4.414956 AGAGATGGGGGTCGGGCA 62.415 66.667 0.00 0.00 0.00 5.36
318 323 0.537188 GAGAGGGCGAAAGGATCACA 59.463 55.000 0.00 0.00 0.00 3.58
542 549 2.032681 GGCGACAGGTTCCTGCTT 59.967 61.111 17.55 0.40 37.57 3.91
550 557 1.985116 GAAGGAGAGGGCGACAGGT 60.985 63.158 0.00 0.00 0.00 4.00
1052 1093 1.535462 GTGTCCAAAACGTAGCAGCAT 59.465 47.619 0.00 0.00 0.00 3.79
1078 1120 2.865598 CGCATCTGCCTCGAGGGAT 61.866 63.158 32.06 22.99 37.91 3.85
1086 1128 1.078848 GGTCTTGACGCATCTGCCT 60.079 57.895 0.00 0.00 37.91 4.75
1088 1130 3.084579 CGGTCTTGACGCATCTGC 58.915 61.111 0.00 0.00 37.78 4.26
1178 1220 1.666872 GTCTTTGGGGTCGACGGTG 60.667 63.158 9.92 0.00 0.00 4.94
1342 1384 3.999001 ACGAAGTAGTCATACACGTCAGA 59.001 43.478 0.00 0.00 41.94 3.27
1343 1385 4.089341 CACGAAGTAGTCATACACGTCAG 58.911 47.826 0.00 0.00 41.61 3.51
1374 1416 3.376078 GGTCCACGCCGGTAGTGA 61.376 66.667 26.41 13.91 41.83 3.41
1422 1464 4.015764 GGGAGTAGAGGAAGTAGTCGTTT 58.984 47.826 0.00 0.00 0.00 3.60
1651 1693 1.592131 CGACAACGTTCCGGTTCCA 60.592 57.895 0.00 0.00 34.56 3.53
1681 1724 2.017783 GCCACGACAACGCTAACGA 61.018 57.895 0.00 0.00 43.93 3.85
1808 1853 6.632434 GCAACAACAATTTTAACCAATCTTGC 59.368 34.615 0.00 0.00 0.00 4.01
1997 2044 3.874543 GCATATTGACGGAACACCACATA 59.125 43.478 0.00 0.00 0.00 2.29
2025 2073 7.592885 AATTAAGTGGAGCTCAATATGCAAT 57.407 32.000 17.19 0.00 0.00 3.56
2051 2099 2.299867 CAAGGGGCACAAACAAAGCTAT 59.700 45.455 0.00 0.00 0.00 2.97
2100 2148 2.794103 TGCACAACCAAGTATGATGCT 58.206 42.857 0.00 0.00 32.81 3.79
2157 2207 2.737039 GCAACACCGGAAAGAAGCAAAA 60.737 45.455 9.46 0.00 0.00 2.44
2250 2300 3.594134 CGCAAGGAAGAAGAATGAGTCT 58.406 45.455 0.00 0.00 38.69 3.24


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

AutoCloner maintained by Alex Coulton.