Multiple sequence alignment - TraesCS7A01G301800

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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 TraesCS7A01G301800 chr7A 100.000 3474 0 0 1 3474 421609606 421613079 0.000000e+00 6416
1 TraesCS7A01G301800 chr6A 95.418 3492 138 15 1 3474 118303832 118307319 0.000000e+00 5542
2 TraesCS7A01G301800 chr3A 95.201 3501 138 20 1 3474 610668920 610672417 0.000000e+00 5507
3 TraesCS7A01G301800 chr3A 94.940 3498 148 17 1 3472 174072939 174069445 0.000000e+00 5452
4 TraesCS7A01G301800 chr3A 93.572 3485 203 16 1 3474 204308730 204305256 0.000000e+00 5175
5 TraesCS7A01G301800 chr3A 93.410 3490 203 18 1 3473 204342959 204339480 0.000000e+00 5145
6 TraesCS7A01G301800 chr3A 96.174 758 23 6 2721 3474 521385967 521386722 0.000000e+00 1234
7 TraesCS7A01G301800 chr4D 94.603 3502 145 26 1 3474 426266278 426262793 0.000000e+00 5380
8 TraesCS7A01G301800 chr6D 94.682 3441 150 24 56 3474 249264292 249267721 0.000000e+00 5310
9 TraesCS7A01G301800 chr2A 93.623 3497 178 20 1 3474 433267547 433271021 0.000000e+00 5180
10 TraesCS7A01G301800 chr2A 94.814 3201 133 18 304 3474 367426807 367423610 0.000000e+00 4961
11 TraesCS7A01G301800 chr1D 93.535 3496 188 22 3 3474 285939050 285942531 0.000000e+00 5169
12 TraesCS7A01G301800 chr3D 94.326 3243 155 19 3 3229 254419840 254416611 0.000000e+00 4942
13 TraesCS7A01G301800 chr5A 95.918 441 15 2 2978 3415 664431851 664431411 0.000000e+00 712
14 TraesCS7A01G301800 chr5A 95.522 67 1 1 3410 3474 664422487 664422421 4.740000e-19 106


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 TraesCS7A01G301800 chr7A 421609606 421613079 3473 False 6416 6416 100.000 1 3474 1 chr7A.!!$F1 3473
1 TraesCS7A01G301800 chr6A 118303832 118307319 3487 False 5542 5542 95.418 1 3474 1 chr6A.!!$F1 3473
2 TraesCS7A01G301800 chr3A 610668920 610672417 3497 False 5507 5507 95.201 1 3474 1 chr3A.!!$F2 3473
3 TraesCS7A01G301800 chr3A 174069445 174072939 3494 True 5452 5452 94.940 1 3472 1 chr3A.!!$R1 3471
4 TraesCS7A01G301800 chr3A 204305256 204308730 3474 True 5175 5175 93.572 1 3474 1 chr3A.!!$R2 3473
5 TraesCS7A01G301800 chr3A 204339480 204342959 3479 True 5145 5145 93.410 1 3473 1 chr3A.!!$R3 3472
6 TraesCS7A01G301800 chr3A 521385967 521386722 755 False 1234 1234 96.174 2721 3474 1 chr3A.!!$F1 753
7 TraesCS7A01G301800 chr4D 426262793 426266278 3485 True 5380 5380 94.603 1 3474 1 chr4D.!!$R1 3473
8 TraesCS7A01G301800 chr6D 249264292 249267721 3429 False 5310 5310 94.682 56 3474 1 chr6D.!!$F1 3418
9 TraesCS7A01G301800 chr2A 433267547 433271021 3474 False 5180 5180 93.623 1 3474 1 chr2A.!!$F1 3473
10 TraesCS7A01G301800 chr2A 367423610 367426807 3197 True 4961 4961 94.814 304 3474 1 chr2A.!!$R1 3170
11 TraesCS7A01G301800 chr1D 285939050 285942531 3481 False 5169 5169 93.535 3 3474 1 chr1D.!!$F1 3471
12 TraesCS7A01G301800 chr3D 254416611 254419840 3229 True 4942 4942 94.326 3 3229 1 chr3D.!!$R1 3226

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
355 370 0.760567 TCAGTCAGGCCACTCACACT 60.761 55.000 5.01 0.0 0.0 3.55 F
720 735 2.093500 TGACAAGACAAGTCAGTGCAGT 60.093 45.455 2.72 0.0 40.8 4.40 F
1179 1202 0.321653 GTGAACCAGACAAGGCCGAT 60.322 55.000 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1184 0.321564 CATCGGCCTTGTCTGGTTCA 60.322 55.000 0.0 0.0 0.00 3.18 R
2327 2394 1.877680 CGTGATGAGGTTGTCTGGCAA 60.878 52.381 0.0 0.0 34.16 4.52 R
2892 2972 1.066787 AGTCCTCGGCTGAAACTTAGC 60.067 52.381 0.0 0.0 40.41 3.09 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
257 264 3.469739 ACGGTCTGGTCGTAAAACAATT 58.530 40.909 0.00 0.00 39.22 2.32
276 284 5.121811 CAATTTCAATCCCCACAAAACACA 58.878 37.500 0.00 0.00 0.00 3.72
355 370 0.760567 TCAGTCAGGCCACTCACACT 60.761 55.000 5.01 0.00 0.00 3.55
578 593 8.603242 GTCTATAAGACTTCAGTGGAAAAACA 57.397 34.615 0.00 0.00 41.88 2.83
696 711 6.069905 TGGGATTTAGCAGGTCATAAGTACAA 60.070 38.462 0.00 0.00 0.00 2.41
720 735 2.093500 TGACAAGACAAGTCAGTGCAGT 60.093 45.455 2.72 0.00 40.80 4.40
788 803 2.113139 CCACCCACTGAGCGGTTT 59.887 61.111 0.00 0.00 0.00 3.27
848 870 4.308458 CACGCCCCTGACGAACCA 62.308 66.667 0.00 0.00 0.00 3.67
928 951 3.834231 CTCATTCCCAGAAACCACCATTT 59.166 43.478 0.00 0.00 0.00 2.32
956 979 2.346766 ATCTCCACTGCACACAAACA 57.653 45.000 0.00 0.00 0.00 2.83
1035 1058 4.223800 GCCAAGCGTCATCATGGA 57.776 55.556 0.00 0.00 34.82 3.41
1161 1184 0.900182 TGGAGATCGTCTGCACCAGT 60.900 55.000 5.39 0.00 39.98 4.00
1179 1202 0.321653 GTGAACCAGACAAGGCCGAT 60.322 55.000 0.00 0.00 0.00 4.18
1251 1274 3.007940 TCATCGGAGTTGATGTGGAGTTT 59.992 43.478 3.90 0.00 44.82 2.66
1252 1275 2.766313 TCGGAGTTGATGTGGAGTTTG 58.234 47.619 0.00 0.00 0.00 2.93
1263 1286 0.674581 TGGAGTTTGCCAGCGATGAG 60.675 55.000 0.06 0.00 33.10 2.90
1291 1314 1.130054 ACAGATGGTGGCAGTCCTGT 61.130 55.000 6.09 6.09 0.00 4.00
1496 1520 6.446318 TCAACTTACATGCAATTCTGAAACC 58.554 36.000 0.00 0.00 0.00 3.27
1576 1603 9.421806 CTGAACTTGATGCACCAAATTAATTTA 57.578 29.630 12.98 0.00 0.00 1.40
1728 1757 8.885494 ATTTCTGAACTTGATATAGAGCTGAC 57.115 34.615 0.00 0.00 0.00 3.51
2049 2106 1.073763 CTTCAATGTGTGTCTCCCCCA 59.926 52.381 0.00 0.00 0.00 4.96
2271 2332 2.550978 CGTCATCCACCCATTCTACAC 58.449 52.381 0.00 0.00 0.00 2.90
2274 2335 2.916269 TCATCCACCCATTCTACACCAA 59.084 45.455 0.00 0.00 0.00 3.67
2513 2580 0.529773 TCGTGTTGCTCGCACTTCTT 60.530 50.000 0.00 0.00 34.91 2.52
2819 2897 3.238108 AGTAGAATTGGACGCTCAGTG 57.762 47.619 0.00 0.00 0.00 3.66
2918 3007 3.830755 AGTTTCAGCCGAGGACTACTAAA 59.169 43.478 0.00 0.00 0.00 1.85
3045 3135 5.708230 AGTTCTGGTACACTTGAACAAAACA 59.292 36.000 16.17 0.00 40.62 2.83
3049 3139 7.051623 TCTGGTACACTTGAACAAAACAGTAT 58.948 34.615 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 223 3.450578 GTTCGTTGAGGTGTGTACAGAA 58.549 45.455 0.00 0.00 0.00 3.02
257 264 3.636679 TCTGTGTTTTGTGGGGATTGAA 58.363 40.909 0.00 0.00 0.00 2.69
355 370 6.511444 CGGTTTTGAAATTTGGTGTCGTAGTA 60.511 38.462 0.00 0.00 0.00 1.82
578 593 8.950007 TTTTCCCTGAGGATGTTAAGTATTTT 57.050 30.769 0.00 0.00 43.54 1.82
788 803 1.619654 CATTTGCAGTCCCTTGTGGA 58.380 50.000 0.00 0.00 42.41 4.02
848 870 3.009115 CGGGGATGTGTGGGAGGT 61.009 66.667 0.00 0.00 0.00 3.85
928 951 1.699083 TGCAGTGGAGATTGAAGTGGA 59.301 47.619 0.00 0.00 0.00 4.02
956 979 3.481453 GCTTGGGAGAGAGAAGTTTGTT 58.519 45.455 0.00 0.00 0.00 2.83
1035 1058 2.995872 GCTCTTGTCCGACGGCTCT 61.996 63.158 9.66 0.00 0.00 4.09
1161 1184 0.321564 CATCGGCCTTGTCTGGTTCA 60.322 55.000 0.00 0.00 0.00 3.18
1179 1202 0.906282 TGAGCCTGCTCATCACCTCA 60.906 55.000 17.46 0.00 46.80 3.86
1251 1274 2.244117 GAGGTTCCTCATCGCTGGCA 62.244 60.000 13.31 0.00 33.58 4.92
1252 1275 1.522580 GAGGTTCCTCATCGCTGGC 60.523 63.158 13.31 0.00 33.58 4.85
1291 1314 0.956633 AGTTCCTCGACGCACAACTA 59.043 50.000 4.05 0.00 0.00 2.24
1418 1442 9.250624 CAAAGTATAGTAGTTCATCTAGTTGGC 57.749 37.037 1.00 0.00 34.51 4.52
1496 1520 2.616376 TGGTGAAACAATCCACTTCACG 59.384 45.455 7.79 0.00 46.42 4.35
1549 1576 4.942761 AATTTGGTGCATCAAGTTCAGT 57.057 36.364 14.14 0.00 0.00 3.41
1576 1603 5.922053 TCTATGCTAGCACATCAAGTTCAT 58.078 37.500 22.07 1.47 0.00 2.57
1723 1752 2.672874 TGATACATCTTTGTGCGTCAGC 59.327 45.455 0.00 0.00 45.41 4.26
1728 1757 3.125829 AGTGCTTGATACATCTTTGTGCG 59.874 43.478 0.00 0.00 36.53 5.34
2134 2191 3.068590 CCAAACCAGACTTGTTCAGCATT 59.931 43.478 0.00 0.00 0.00 3.56
2271 2332 5.005740 TGTCCATCTTCTTCTTCATGTTGG 58.994 41.667 0.00 0.00 0.00 3.77
2274 2335 5.251764 CCTTGTCCATCTTCTTCTTCATGT 58.748 41.667 0.00 0.00 0.00 3.21
2327 2394 1.877680 CGTGATGAGGTTGTCTGGCAA 60.878 52.381 0.00 0.00 34.16 4.52
2513 2580 8.160765 TCTGAAACAACAATATTAAGGACAGGA 58.839 33.333 0.00 0.00 0.00 3.86
2543 2610 8.675504 TGGTTCAACATAACGAAAGAAAACTAA 58.324 29.630 0.00 0.00 0.00 2.24
2819 2897 4.430908 ACTACCGTAAATGTCTAAGCTGC 58.569 43.478 0.00 0.00 0.00 5.25
2892 2972 1.066787 AGTCCTCGGCTGAAACTTAGC 60.067 52.381 0.00 0.00 40.41 3.09
2964 3053 7.333528 TGTACTGATTGTTCTTTGCTTTTCT 57.666 32.000 0.00 0.00 0.00 2.52
3068 3160 2.226674 CTGAAGCTTCCCGTTCCTTTTC 59.773 50.000 23.42 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.