Multiple sequence alignment - TraesCS7A01G530000

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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 TraesCS7A01G530000 chr7A 100.000 1590 0 0 1 1590 709425906 709424317 0.000000e+00 2937.0
1 TraesCS7A01G530000 chr7A 100.000 410 0 0 1951 2360 709423956 709423547 0.000000e+00 758.0
2 TraesCS7A01G530000 chr7A 90.164 427 39 3 933 1358 692503784 692504208 9.530000e-154 553.0
3 TraesCS7A01G530000 chr7A 77.419 217 43 3 1142 1352 78470445 78470229 8.860000e-25 124.0
4 TraesCS7A01G530000 chr7B 95.985 1619 29 10 1 1590 709629998 709628387 0.000000e+00 2597.0
5 TraesCS7A01G530000 chr7B 97.561 410 10 0 1951 2360 709628358 709627949 0.000000e+00 702.0
6 TraesCS7A01G530000 chr7B 87.097 434 49 3 933 1363 735918651 735919080 3.530000e-133 484.0
7 TraesCS7A01G530000 chr7B 78.161 261 37 10 204 446 413249675 413249933 5.260000e-32 148.0
8 TraesCS7A01G530000 chrUn 100.000 422 0 0 439 860 476747797 476747376 0.000000e+00 780.0
9 TraesCS7A01G530000 chr1D 89.227 427 43 3 933 1357 473855232 473854807 4.470000e-147 531.0
10 TraesCS7A01G530000 chr3B 82.313 294 38 8 196 477 779368894 779369185 2.340000e-60 243.0
11 TraesCS7A01G530000 chr2D 84.109 258 29 4 196 441 579754365 579754622 3.030000e-59 239.0
12 TraesCS7A01G530000 chr2D 81.419 296 38 9 196 477 624783267 624782975 2.360000e-55 226.0
13 TraesCS7A01G530000 chr2D 83.077 260 31 5 196 442 334346851 334346592 8.490000e-55 224.0
14 TraesCS7A01G530000 chr2D 80.435 92 6 6 2150 2229 64182661 64182570 2.530000e-05 60.2
15 TraesCS7A01G530000 chr3A 81.757 296 39 8 196 477 96947090 96947384 1.410000e-57 233.0
16 TraesCS7A01G530000 chr3A 86.250 80 7 3 1242 1320 17897048 17897124 1.500000e-12 84.2
17 TraesCS7A01G530000 chr6A 81.695 295 38 8 196 477 37410281 37409990 5.070000e-57 231.0
18 TraesCS7A01G530000 chr6A 81.092 238 37 6 196 426 606283800 606284036 1.440000e-42 183.0
19 TraesCS7A01G530000 chr6B 91.875 160 12 1 196 354 702854894 702855053 3.050000e-54 222.0
20 TraesCS7A01G530000 chr2B 76.271 295 47 8 196 477 222122680 222122396 4.090000e-28 135.0
21 TraesCS7A01G530000 chr7D 77.729 229 36 8 195 409 167939717 167939944 2.460000e-25 126.0


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 TraesCS7A01G530000 chr7A 709423547 709425906 2359 True 1847.5 2937 100.000 1 2360 2 chr7A.!!$R2 2359
1 TraesCS7A01G530000 chr7B 709627949 709629998 2049 True 1649.5 2597 96.773 1 2360 2 chr7B.!!$R1 2359

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
918 921 1.072505 CCTGGGCTAAACACACGGT 59.927 57.895 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2332 1.415672 AAAGGTGGCGGAGAACCTGA 61.416 55.0 0.0 0.0 43.83 3.86 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
58 60 2.358898 AGGTGTTTTATGATCGCATGCC 59.641 45.455 13.15 0.0 35.94 4.40
172 174 1.299976 GGGGATATGGGATCACGCC 59.700 63.158 0.00 0.0 0.00 5.68
174 176 1.079127 GGATATGGGATCACGCCGG 60.079 63.158 0.00 0.0 0.00 6.13
194 196 1.609320 GCGCCCTGGAAATCCTAGATC 60.609 57.143 0.00 0.0 36.82 2.75
210 212 6.231211 TCCTAGATCTTTTTGCGAGAAAACT 58.769 36.000 0.00 0.0 0.00 2.66
261 263 9.662947 GGTACTACAACAACCAGTAGAAATAAT 57.337 33.333 6.60 0.0 40.02 1.28
346 348 2.581354 GCAGCTGTCATCGTCCCT 59.419 61.111 16.64 0.0 0.00 4.20
353 355 2.833582 TCATCGTCCCTCCCTCGC 60.834 66.667 0.00 0.0 0.00 5.03
372 374 7.122055 TCCCTCGCAAAATTTGTTGTAATAGAT 59.878 33.333 7.60 0.0 0.00 1.98
437 440 2.736721 AGAACAACAATCACCGTCGATG 59.263 45.455 0.00 0.0 0.00 3.84
860 863 9.689501 TCCCCGTAAAAATAAAATTATGTCTCT 57.310 29.630 0.00 0.0 0.00 3.10
901 904 3.650461 AGGGAGAGAGATATTTGAAGCCC 59.350 47.826 0.00 0.0 0.00 5.19
918 921 1.072505 CCTGGGCTAAACACACGGT 59.927 57.895 0.00 0.0 0.00 4.83
1060 1063 1.000506 GGTCGAACTTGCCACTGACTA 59.999 52.381 0.00 0.0 0.00 2.59
1093 1096 1.036481 TGCCAAACTGCTGCAACTGA 61.036 50.000 3.02 0.0 30.85 3.41
1094 1097 0.316204 GCCAAACTGCTGCAACTGAT 59.684 50.000 3.02 0.0 0.00 2.90
1095 1098 1.269936 GCCAAACTGCTGCAACTGATT 60.270 47.619 3.02 0.0 0.00 2.57
1170 1173 5.259632 AGAATGATTCTGGTCCAAGAAAGG 58.740 41.667 6.93 0.0 39.54 3.11
1201 1204 7.286215 AGTTTAGCTAAGATTAGTCGGCATA 57.714 36.000 6.24 0.0 33.32 3.14
1222 1225 0.107214 TAATGCTGCTAGCCACACCC 60.107 55.000 13.29 0.0 41.51 4.61
1223 1226 1.856539 AATGCTGCTAGCCACACCCT 61.857 55.000 13.29 0.0 41.51 4.34
1224 1227 1.856539 ATGCTGCTAGCCACACCCTT 61.857 55.000 13.29 0.0 41.51 3.95
1225 1228 1.198094 TGCTGCTAGCCACACCCTTA 61.198 55.000 13.29 0.0 41.51 2.69
1555 1587 0.320374 TTGCCTCAACTACTCCCGTG 59.680 55.000 0.00 0.0 0.00 4.94
1577 1609 3.110358 GCCTTTAACGTTGTTTGGACAC 58.890 45.455 11.99 0.0 34.98 3.67
2096 2128 5.878116 GTCAAAGGGTTAGCACATACATACA 59.122 40.000 0.00 0.0 0.00 2.29
2159 2191 2.026641 TGTGCCTACGGTATGTACTCC 58.973 52.381 11.50 0.0 0.00 3.85
2162 2194 1.885233 GCCTACGGTATGTACTCCCTC 59.115 57.143 0.00 0.0 0.00 4.30
2180 2212 8.588290 ACTCCCTCTGTAAGCTAATATATGAG 57.412 38.462 0.00 0.0 0.00 2.90
2182 2214 8.354711 TCCCTCTGTAAGCTAATATATGAGTG 57.645 38.462 0.00 0.0 0.00 3.51
2250 2282 7.979786 ACTATTTTCTCCTAGGAACAGATCA 57.020 36.000 13.77 0.0 0.00 2.92
2296 2328 3.255149 ACACGTGACTAGAAACCTACCTG 59.745 47.826 25.01 0.0 0.00 4.00
2300 2332 3.505293 GTGACTAGAAACCTACCTGTCGT 59.495 47.826 0.00 0.0 0.00 4.34
2326 2358 0.875059 CTCCGCCACCTTTTTCTGAC 59.125 55.000 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 3.195698 GCCTTTCGCGTGGCTAGG 61.196 66.667 24.68 17.17 45.26 3.02
172 174 2.996168 CTAGGATTTCCAGGGCGCCG 62.996 65.000 22.54 7.47 38.89 6.46
174 176 0.398318 ATCTAGGATTTCCAGGGCGC 59.602 55.000 0.00 0.00 38.89 6.53
194 196 7.455331 AGATTGAAAGTTTTCTCGCAAAAAG 57.545 32.000 6.21 0.00 38.02 2.27
261 263 9.832445 GGTCTACAGATCTGGATGTAATTTTTA 57.168 33.333 26.08 4.61 31.81 1.52
346 348 4.920640 TTACAACAAATTTTGCGAGGGA 57.079 36.364 9.04 0.00 0.00 4.20
353 355 9.716507 CCCGACTATCTATTACAACAAATTTTG 57.283 33.333 7.59 7.59 0.00 2.44
372 374 1.830279 ACACGATGACTTCCCGACTA 58.170 50.000 0.00 0.00 0.00 2.59
437 440 5.316327 CCCTTTTGGTCAAAGCTATCTTC 57.684 43.478 0.00 0.00 40.75 2.87
860 863 6.013293 TCTCCCTCTCTCGATCATATACAGAA 60.013 42.308 0.00 0.00 0.00 3.02
901 904 0.034896 AGACCGTGTGTTTAGCCCAG 59.965 55.000 0.00 0.00 0.00 4.45
918 921 4.989168 GCACCTTCGTTTCTAAAGAAGAGA 59.011 41.667 14.02 1.20 42.75 3.10
952 955 2.455674 AAGAGCACACAAGTCGCATA 57.544 45.000 0.00 0.00 0.00 3.14
961 964 3.882288 TCAGCACAATTAAAGAGCACACA 59.118 39.130 4.16 0.00 0.00 3.72
1093 1096 0.178068 CCAACATCCCTCGACGGAAT 59.822 55.000 7.25 0.00 34.93 3.01
1094 1097 1.189524 ACCAACATCCCTCGACGGAA 61.190 55.000 7.25 0.00 34.93 4.30
1095 1098 0.323633 TACCAACATCCCTCGACGGA 60.324 55.000 5.58 5.58 36.02 4.69
1160 1163 7.231467 AGCTAAACTAATGTTCCTTTCTTGGA 58.769 34.615 0.00 0.00 34.96 3.53
1201 1204 1.407437 GGTGTGGCTAGCAGCATTAGT 60.407 52.381 18.24 0.00 44.75 2.24
1222 1225 3.214328 GCACCCATCCCATACAAGTAAG 58.786 50.000 0.00 0.00 0.00 2.34
1223 1226 2.578480 TGCACCCATCCCATACAAGTAA 59.422 45.455 0.00 0.00 0.00 2.24
1224 1227 2.200955 TGCACCCATCCCATACAAGTA 58.799 47.619 0.00 0.00 0.00 2.24
1225 1228 0.998928 TGCACCCATCCCATACAAGT 59.001 50.000 0.00 0.00 0.00 3.16
1405 1437 5.969435 CGCTTTGTCAGTTCAGTACGATATA 59.031 40.000 0.00 0.00 0.00 0.86
1406 1438 4.798907 CGCTTTGTCAGTTCAGTACGATAT 59.201 41.667 0.00 0.00 0.00 1.63
1555 1587 2.099427 TGTCCAAACAACGTTAAAGGCC 59.901 45.455 0.00 0.00 30.70 5.19
1956 1988 5.523552 ACAACCTTTAAGTAAAGCGTACGTT 59.476 36.000 17.90 8.23 40.93 3.99
2159 2191 9.988815 AAACACTCATATATTAGCTTACAGAGG 57.011 33.333 0.00 0.00 0.00 3.69
2180 2212 9.769093 ATATGAGCGTTTAGACAATTTAAACAC 57.231 29.630 10.39 2.96 39.71 3.32
2250 2282 3.193691 CCCTAGACAGAAACGAGTCACAT 59.806 47.826 0.00 0.00 37.23 3.21
2296 2328 2.126031 GGCGGAGAACCTGACGAC 60.126 66.667 0.00 0.00 0.00 4.34
2300 2332 1.415672 AAAGGTGGCGGAGAACCTGA 61.416 55.000 0.00 0.00 43.83 3.86
2326 2358 4.189188 CGTCGGTGTAGGAGCCCG 62.189 72.222 0.00 0.00 43.03 6.13


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

AutoCloner maintained by Alex Coulton.