Multiple sequence alignment - TraesCS7B01G291300

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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 TraesCS7B01G291300 chr7B 100.000 4209 0 0 1 4209 527961266 527965474 0.000000e+00 7773
1 TraesCS7B01G291300 chr7B 77.807 1906 344 60 498 2372 527979145 527981002 0.000000e+00 1103
2 TraesCS7B01G291300 chr7B 81.191 638 105 12 2646 3273 527981326 527981958 2.260000e-137 499
3 TraesCS7B01G291300 chr7D 97.382 4201 86 9 29 4209 499971061 499975257 0.000000e+00 7127
4 TraesCS7B01G291300 chr7D 78.229 1920 319 67 498 2376 500098177 500100038 0.000000e+00 1138
5 TraesCS7B01G291300 chr7D 81.034 638 106 12 2646 3273 500100358 500100990 1.050000e-135 494
6 TraesCS7B01G291300 chr7D 79.692 325 62 4 1046 1368 499880148 499879826 9.100000e-57 231
7 TraesCS7B01G291300 chr7A 95.486 4010 151 17 29 4022 566007178 566011173 0.000000e+00 6375
8 TraesCS7B01G291300 chr7A 79.679 1496 261 35 890 2372 566017724 566019189 0.000000e+00 1038
9 TraesCS7B01G291300 chr7A 81.191 638 105 11 2646 3273 566019513 566020145 2.260000e-137 499
10 TraesCS7B01G291300 chr7A 91.379 174 10 3 4037 4209 566011232 566011401 2.530000e-57 233
11 TraesCS7B01G291300 chr2B 91.111 360 27 5 29 385 769913347 769912990 2.280000e-132 483
12 TraesCS7B01G291300 chr2B 90.808 359 28 5 29 384 769908052 769907696 3.810000e-130 475
13 TraesCS7B01G291300 chr3A 91.061 358 28 4 29 384 193998973 193999328 8.180000e-132 481
14 TraesCS7B01G291300 chr3A 90.529 359 26 6 29 384 607202100 607202453 6.370000e-128 468
15 TraesCS7B01G291300 chr1B 90.808 359 29 4 29 384 511375259 511375616 1.060000e-130 477
16 TraesCS7B01G291300 chr5B 90.808 359 28 5 29 384 608860506 608860150 3.810000e-130 475
17 TraesCS7B01G291300 chr4B 90.529 359 28 6 29 384 42535214 42535569 1.770000e-128 470


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 TraesCS7B01G291300 chr7B 527961266 527965474 4208 False 7773.0 7773 100.0000 1 4209 1 chr7B.!!$F1 4208
1 TraesCS7B01G291300 chr7B 527979145 527981958 2813 False 801.0 1103 79.4990 498 3273 2 chr7B.!!$F2 2775
2 TraesCS7B01G291300 chr7D 499971061 499975257 4196 False 7127.0 7127 97.3820 29 4209 1 chr7D.!!$F1 4180
3 TraesCS7B01G291300 chr7D 500098177 500100990 2813 False 816.0 1138 79.6315 498 3273 2 chr7D.!!$F2 2775
4 TraesCS7B01G291300 chr7A 566007178 566011401 4223 False 3304.0 6375 93.4325 29 4209 2 chr7A.!!$F1 4180
5 TraesCS7B01G291300 chr7A 566017724 566020145 2421 False 768.5 1038 80.4350 890 3273 2 chr7A.!!$F2 2383

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
43 44 0.247185 GTGATGCCCCAATTGTGTGG 59.753 55.000 4.43 3.25 38.51 4.17 F
207 208 2.031245 TGCCTTTCGTGTTTGCATACTG 60.031 45.455 8.78 1.86 0.00 2.74 F
1298 1324 4.077300 TGCTGCCCTCTTATGAAGTATG 57.923 45.455 0.00 0.00 0.00 2.39 F
2448 2534 2.871096 AGACTTGCCATTCCGGTAAA 57.129 45.000 0.00 0.00 39.10 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1083 1.065126 GCAGGGGTTAGAGTCAAGCAT 60.065 52.381 0.0 0.0 0.0 3.79 R
1510 1541 1.948611 GCCAAGAAACGCCATCCTGTA 60.949 52.381 0.0 0.0 0.0 2.74 R
2785 2890 3.006430 TGTGATTCCTACTCTGCGACAAA 59.994 43.478 0.0 0.0 0.0 2.83 R
4030 4180 2.017049 GTGGTATTGCTCGCTGGAAAT 58.983 47.619 0.0 0.0 0.0 2.17 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
19 20 2.855660 GCGAAGAGGGAAGTAGTCTC 57.144 55.000 0.00 0.00 0.00 3.36
20 21 1.064357 GCGAAGAGGGAAGTAGTCTCG 59.936 57.143 0.00 0.00 33.16 4.04
21 22 2.630158 CGAAGAGGGAAGTAGTCTCGA 58.370 52.381 0.00 0.00 33.16 4.04
22 23 3.207778 CGAAGAGGGAAGTAGTCTCGAT 58.792 50.000 0.00 0.00 33.16 3.59
23 24 3.628487 CGAAGAGGGAAGTAGTCTCGATT 59.372 47.826 0.00 0.00 33.16 3.34
24 25 4.496673 CGAAGAGGGAAGTAGTCTCGATTG 60.497 50.000 0.00 0.00 33.16 2.67
25 26 3.970842 AGAGGGAAGTAGTCTCGATTGT 58.029 45.455 0.00 0.00 33.16 2.71
26 27 3.697045 AGAGGGAAGTAGTCTCGATTGTG 59.303 47.826 0.00 0.00 33.16 3.33
27 28 3.695060 GAGGGAAGTAGTCTCGATTGTGA 59.305 47.826 0.00 0.00 0.00 3.58
32 33 2.101582 AGTAGTCTCGATTGTGATGCCC 59.898 50.000 0.00 0.00 0.00 5.36
43 44 0.247185 GTGATGCCCCAATTGTGTGG 59.753 55.000 4.43 3.25 38.51 4.17
139 140 9.946165 TTAGTTTAGAAAAGCTTAAAACTGAGC 57.054 29.630 24.68 12.32 39.86 4.26
154 155 4.050852 ACTGAGCTCTTTTTGCTTTTGG 57.949 40.909 16.19 0.00 41.30 3.28
183 184 5.066117 CAGTCAGCCTACTTCGTAGTAATCA 59.934 44.000 3.40 0.00 36.46 2.57
184 185 5.297278 AGTCAGCCTACTTCGTAGTAATCAG 59.703 44.000 3.40 0.00 36.46 2.90
196 197 2.699954 AGTAATCAGGTGCCTTTCGTG 58.300 47.619 0.00 0.00 0.00 4.35
207 208 2.031245 TGCCTTTCGTGTTTGCATACTG 60.031 45.455 8.78 1.86 0.00 2.74
276 277 7.231317 TGGCTCTCTAATTTGTTTGAACTGATT 59.769 33.333 0.00 0.00 0.00 2.57
937 959 4.372656 AGAGAGACTGCACTTTGTGTTAC 58.627 43.478 0.00 0.00 35.75 2.50
997 1023 7.608153 TCACGGAAACTATCAGAACAATAGAA 58.392 34.615 0.00 0.00 32.22 2.10
999 1025 8.169268 CACGGAAACTATCAGAACAATAGAAAC 58.831 37.037 0.00 0.00 32.22 2.78
1143 1169 4.163458 GGTATACCATGTCCAGTTTCTCCA 59.837 45.833 17.44 0.00 35.64 3.86
1289 1315 4.828939 CCATGATAAAATGCTGCCCTCTTA 59.171 41.667 0.00 0.00 0.00 2.10
1298 1324 4.077300 TGCTGCCCTCTTATGAAGTATG 57.923 45.455 0.00 0.00 0.00 2.39
1509 1540 5.831702 AGCTGAATCAAATGTCTGGATTC 57.168 39.130 0.00 0.00 44.43 2.52
1510 1541 5.507637 AGCTGAATCAAATGTCTGGATTCT 58.492 37.500 12.97 0.00 44.46 2.40
2131 2164 5.674318 GCTTATTGGAAATTGCCACATTTGC 60.674 40.000 3.97 2.85 37.75 3.68
2247 2282 8.966194 GGTATCTTTACTACGACTGCTAATTTC 58.034 37.037 0.00 0.00 0.00 2.17
2347 2382 8.654997 ACTTATTGATTATGAGTAGAGGTGCAT 58.345 33.333 0.00 0.00 31.79 3.96
2372 2407 9.715121 ATGTGTTTAAGATTTTCTACGAGGTTA 57.285 29.630 0.00 0.00 0.00 2.85
2448 2534 2.871096 AGACTTGCCATTCCGGTAAA 57.129 45.000 0.00 0.00 39.10 2.01
2785 2890 8.361139 CCTACGTCTATGAGAAACCTTATTCAT 58.639 37.037 0.00 0.00 34.81 2.57
2799 2904 5.812642 ACCTTATTCATTTGTCGCAGAGTAG 59.187 40.000 0.00 0.00 36.95 2.57
2815 2920 6.054295 GCAGAGTAGGAATCACAATCAGAAT 58.946 40.000 0.00 0.00 0.00 2.40
2816 2921 6.541641 GCAGAGTAGGAATCACAATCAGAATT 59.458 38.462 0.00 0.00 0.00 2.17
2878 2987 4.096984 ACTTTTCTCATCCCGATTTGCATC 59.903 41.667 0.00 0.00 0.00 3.91
3224 3335 4.280174 GTCACTGAGGGTTACTACTTCACA 59.720 45.833 0.00 0.00 0.00 3.58
3236 3347 8.035394 GGTTACTACTTCACATCTCTTCATGAA 58.965 37.037 8.12 8.12 0.00 2.57
3273 3386 0.698238 TGGTTCCAGCCTATGCAACT 59.302 50.000 0.00 0.00 41.13 3.16
3360 3473 3.069300 GTCAGGCTGATCATGCTAGAGAA 59.931 47.826 21.84 0.00 0.00 2.87
3548 3661 5.365314 ACTGGGTTTTGTGGATGTTTATGTT 59.635 36.000 0.00 0.00 0.00 2.71
3632 3747 7.584108 TCATACTGTTGTGAAAAGCTGTTATG 58.416 34.615 0.00 0.00 0.00 1.90
3779 3900 0.456221 GCTCTTAGGTAGACGCAGCA 59.544 55.000 0.00 0.00 31.43 4.41
3936 4057 5.977725 GCAGATATAGCTACTTTGTTCGACA 59.022 40.000 0.00 0.00 0.00 4.35
4030 4180 3.709141 TCAACAGGATGATTGGTCCGATA 59.291 43.478 0.00 0.00 39.69 2.92
4073 4239 3.516615 CTCGAATCTTCTTGTCTCCACC 58.483 50.000 0.00 0.00 0.00 4.61
4108 4274 4.455606 GGATCAAGGGGTTCTGAACTATG 58.544 47.826 19.05 12.73 0.00 2.23
4128 4294 2.124403 GGAGACCTCCTACGCCGA 60.124 66.667 8.76 0.00 46.16 5.54
4158 4324 6.655078 AGTTTGCAAGACCAGTTATTTGAT 57.345 33.333 0.00 0.00 0.00 2.57
4159 4325 7.054491 AGTTTGCAAGACCAGTTATTTGATT 57.946 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.064357 CGAGACTACTTCCCTCTTCGC 59.936 57.143 0.00 0.00 0.00 4.70
1 2 2.630158 TCGAGACTACTTCCCTCTTCG 58.370 52.381 0.00 0.00 0.00 3.79
2 3 4.399934 ACAATCGAGACTACTTCCCTCTTC 59.600 45.833 0.00 0.00 0.00 2.87
3 4 4.158764 CACAATCGAGACTACTTCCCTCTT 59.841 45.833 0.00 0.00 0.00 2.85
4 5 3.697045 CACAATCGAGACTACTTCCCTCT 59.303 47.826 0.00 0.00 0.00 3.69
5 6 3.695060 TCACAATCGAGACTACTTCCCTC 59.305 47.826 0.00 0.00 0.00 4.30
6 7 3.698289 TCACAATCGAGACTACTTCCCT 58.302 45.455 0.00 0.00 0.00 4.20
7 8 4.363999 CATCACAATCGAGACTACTTCCC 58.636 47.826 0.00 0.00 0.00 3.97
8 9 3.799420 GCATCACAATCGAGACTACTTCC 59.201 47.826 0.00 0.00 0.00 3.46
9 10 3.799420 GGCATCACAATCGAGACTACTTC 59.201 47.826 0.00 0.00 0.00 3.01
10 11 3.430929 GGGCATCACAATCGAGACTACTT 60.431 47.826 0.00 0.00 0.00 2.24
11 12 2.101582 GGGCATCACAATCGAGACTACT 59.898 50.000 0.00 0.00 0.00 2.57
12 13 2.474816 GGGCATCACAATCGAGACTAC 58.525 52.381 0.00 0.00 0.00 2.73
13 14 1.412710 GGGGCATCACAATCGAGACTA 59.587 52.381 0.00 0.00 0.00 2.59
14 15 0.179000 GGGGCATCACAATCGAGACT 59.821 55.000 0.00 0.00 0.00 3.24
15 16 0.107703 TGGGGCATCACAATCGAGAC 60.108 55.000 0.00 0.00 0.00 3.36
16 17 0.617935 TTGGGGCATCACAATCGAGA 59.382 50.000 0.00 0.00 0.00 4.04
17 18 1.683943 ATTGGGGCATCACAATCGAG 58.316 50.000 0.00 0.00 32.12 4.04
18 19 1.750206 CAATTGGGGCATCACAATCGA 59.250 47.619 0.00 0.00 36.36 3.59
19 20 1.477700 ACAATTGGGGCATCACAATCG 59.522 47.619 10.83 0.00 36.36 3.34
20 21 2.234414 ACACAATTGGGGCATCACAATC 59.766 45.455 13.35 0.00 36.36 2.67
21 22 2.027929 CACACAATTGGGGCATCACAAT 60.028 45.455 13.35 0.00 38.85 2.71
22 23 1.343789 CACACAATTGGGGCATCACAA 59.656 47.619 13.35 0.00 0.00 3.33
23 24 0.967662 CACACAATTGGGGCATCACA 59.032 50.000 13.35 0.00 0.00 3.58
24 25 0.247185 CCACACAATTGGGGCATCAC 59.753 55.000 13.35 0.00 40.36 3.06
25 26 2.668612 CCACACAATTGGGGCATCA 58.331 52.632 13.35 0.00 40.36 3.07
32 33 0.667993 AGCAACGACCACACAATTGG 59.332 50.000 10.83 1.35 43.04 3.16
43 44 1.071605 CTAACCTCAGCAGCAACGAC 58.928 55.000 0.00 0.00 0.00 4.34
128 129 7.064490 CCAAAAGCAAAAAGAGCTCAGTTTTAA 59.936 33.333 21.11 0.00 42.53 1.52
154 155 1.734047 CGAAGTAGGCTGACTGTCTGC 60.734 57.143 25.74 25.74 40.10 4.26
183 184 1.034838 TGCAAACACGAAAGGCACCT 61.035 50.000 0.00 0.00 0.00 4.00
184 185 0.031994 ATGCAAACACGAAAGGCACC 59.968 50.000 0.00 0.00 37.30 5.01
196 197 1.332377 GCTCGCGATCAGTATGCAAAC 60.332 52.381 10.36 0.00 34.76 2.93
207 208 0.102481 TGAAGGTAAGGCTCGCGATC 59.898 55.000 10.36 4.94 0.00 3.69
276 277 9.716507 GTTGCGCTTATCTGAAATTCTTAAATA 57.283 29.630 9.73 0.00 0.00 1.40
485 486 7.114882 CTTCATTAAGAAGTATCTGGATGCG 57.885 40.000 0.00 0.00 46.97 4.73
937 959 0.749454 GCAGGGTGCAAGGATAGTGG 60.749 60.000 0.00 0.00 44.26 4.00
997 1023 7.663081 AGCCATCGAAATATGTAGAATCATGTT 59.337 33.333 0.00 0.00 32.17 2.71
999 1025 7.606858 AGCCATCGAAATATGTAGAATCATG 57.393 36.000 0.00 0.00 0.00 3.07
1054 1080 4.843728 CAGGGGTTAGAGTCAAGCATAAA 58.156 43.478 0.00 0.00 0.00 1.40
1057 1083 1.065126 GCAGGGGTTAGAGTCAAGCAT 60.065 52.381 0.00 0.00 0.00 3.79
1143 1169 4.575885 ACTTGCACATAGTAAACGGATGT 58.424 39.130 0.00 0.00 34.11 3.06
1289 1315 9.277783 GCCATAGATTTAGACAACATACTTCAT 57.722 33.333 0.00 0.00 0.00 2.57
1298 1324 5.294552 GTGACCTGCCATAGATTTAGACAAC 59.705 44.000 0.00 0.00 0.00 3.32
1509 1540 2.009774 CCAAGAAACGCCATCCTGTAG 58.990 52.381 0.00 0.00 0.00 2.74
1510 1541 1.948611 GCCAAGAAACGCCATCCTGTA 60.949 52.381 0.00 0.00 0.00 2.74
2247 2282 5.009610 TGCTGCCTTTTGTTCCTACTTAAAG 59.990 40.000 0.00 0.00 31.87 1.85
2347 2382 9.715121 ATAACCTCGTAGAAAATCTTAAACACA 57.285 29.630 0.00 0.00 34.09 3.72
2372 2407 6.682423 TCACATTGAAATTCATACAGCGAT 57.318 33.333 0.00 0.00 0.00 4.58
2448 2534 3.071602 AGCACATTAGGAGTTGTGACTGT 59.928 43.478 7.20 0.00 44.74 3.55
2785 2890 3.006430 TGTGATTCCTACTCTGCGACAAA 59.994 43.478 0.00 0.00 0.00 2.83
2815 2920 6.757162 GCTTTGAACAAGCGAAAACTTAAAA 58.243 32.000 0.00 0.00 33.20 1.52
2816 2921 6.325849 GCTTTGAACAAGCGAAAACTTAAA 57.674 33.333 0.00 0.00 33.20 1.52
3094 3203 5.276461 AGTATTGCACCTCGATGTTATCA 57.724 39.130 0.00 0.00 0.00 2.15
3224 3335 3.940221 GCTGAAGCTGTTCATGAAGAGAT 59.060 43.478 30.89 24.41 41.96 2.75
3360 3473 8.937634 AAACCGACTATTTGATCGTAGTTTAT 57.062 30.769 6.67 0.00 33.72 1.40
3548 3661 8.267894 AGCTTTAAGCCTTCAGATATAAAGACA 58.732 33.333 13.84 0.00 43.77 3.41
3779 3900 6.481313 CAGAACGAAGGACATAATCATCACAT 59.519 38.462 0.00 0.00 0.00 3.21
3870 3991 3.192422 TCTCCACAACCAATAAAATGCCG 59.808 43.478 0.00 0.00 0.00 5.69
4030 4180 2.017049 GTGGTATTGCTCGCTGGAAAT 58.983 47.619 0.00 0.00 0.00 2.17
4126 4292 3.250762 TGGTCTTGCAAACTTCAGATTCG 59.749 43.478 0.00 0.00 0.00 3.34
4128 4294 4.210331 ACTGGTCTTGCAAACTTCAGATT 58.790 39.130 19.01 2.64 0.00 2.40


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

AutoCloner maintained by Alex Coulton.