Multiple sequence alignment - TraesCS7D01G147600

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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 TraesCS7D01G147600 chr7D 100.000 2771 0 0 1 2771 94435694 94432924 0.000000e+00 5118
1 TraesCS7D01G147600 chr7B 92.424 2125 73 41 689 2771 48455689 48453611 0.000000e+00 2952
2 TraesCS7D01G147600 chr7B 95.503 378 13 4 1 375 48456442 48456066 3.950000e-168 601
3 TraesCS7D01G147600 chr7B 87.616 323 26 10 362 679 48456046 48455733 2.030000e-96 363
4 TraesCS7D01G147600 chr7A 90.385 2132 83 45 678 2771 97874151 97872104 0.000000e+00 2689
5 TraesCS7D01G147600 chr7A 91.066 638 26 16 1 610 97877027 97876393 0.000000e+00 833


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 TraesCS7D01G147600 chr7D 94432924 94435694 2770 True 5118.000000 5118 100.000000 1 2771 1 chr7D.!!$R1 2770
1 TraesCS7D01G147600 chr7B 48453611 48456442 2831 True 1305.333333 2952 91.847667 1 2771 3 chr7B.!!$R1 2770
2 TraesCS7D01G147600 chr7A 97872104 97877027 4923 True 1761.000000 2689 90.725500 1 2771 2 chr7A.!!$R1 2770

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
456 521 0.46362 AGCGAGAAGAGAATGGAGGC 59.536 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 4553 0.179073 CCGGGAATTCTCTGCGTCAT 60.179 55.0 3.32 0.0 0.0 3.06 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
121 122 2.457366 ACACGAGGTGACTGAAATCC 57.543 50.000 2.29 0.00 44.43 3.01
128 129 1.535462 GGTGACTGAAATCCCACAACG 59.465 52.381 0.00 0.00 0.00 4.10
148 149 2.293399 CGACGGTCATGATATCACAGGA 59.707 50.000 7.78 3.55 0.00 3.86
266 270 0.798776 CTGCTTTTGTAGGGTCAGCG 59.201 55.000 0.00 0.00 0.00 5.18
274 278 1.154197 GTAGGGTCAGCGTGTTTTCC 58.846 55.000 0.00 0.00 0.00 3.13
375 412 1.863880 GCAGAGAGTACACGACGCG 60.864 63.158 3.53 3.53 32.21 6.01
447 512 0.523966 AAGTGACCGAGCGAGAAGAG 59.476 55.000 0.00 0.00 0.00 2.85
456 521 0.463620 AGCGAGAAGAGAATGGAGGC 59.536 55.000 0.00 0.00 0.00 4.70
500 565 2.223876 ACGACGTGGTTGTCATGTACTT 60.224 45.455 0.00 0.00 44.95 2.24
600 1079 4.566488 GGACAGGAATTGAGAGTTGATGGT 60.566 45.833 0.00 0.00 0.00 3.55
629 2826 4.089923 GTGCCATTTAAGCGATGTTCAAAC 59.910 41.667 0.00 0.00 0.00 2.93
923 3160 1.509004 GGTGTCTGCGTCTCTCTCC 59.491 63.158 0.00 0.00 0.00 3.71
930 3167 1.226262 GCGTCTCTCTCCCTCCTCT 59.774 63.158 0.00 0.00 0.00 3.69
946 3183 2.511829 CTCTCTCTCCGCCGACGA 60.512 66.667 0.00 0.00 43.93 4.20
960 3197 4.790962 ACGAGGCGCGAGGGAGTA 62.791 66.667 19.52 0.00 44.57 2.59
961 3198 3.515286 CGAGGCGCGAGGGAGTAA 61.515 66.667 12.10 0.00 44.57 2.24
962 3199 2.413765 GAGGCGCGAGGGAGTAAG 59.586 66.667 12.10 0.00 0.00 2.34
963 3200 3.140225 GAGGCGCGAGGGAGTAAGG 62.140 68.421 12.10 0.00 0.00 2.69
968 3205 2.408022 CGAGGGAGTAAGGACGCG 59.592 66.667 3.53 3.53 0.00 6.01
1041 3284 2.750637 GCCTCCTCGTCCTCGTCA 60.751 66.667 0.00 0.00 38.33 4.35
1888 4151 6.648192 AGATTAAGATTTGTGCTCTGCTAGT 58.352 36.000 0.00 0.00 0.00 2.57
1889 4152 7.786030 AGATTAAGATTTGTGCTCTGCTAGTA 58.214 34.615 0.00 0.00 0.00 1.82
1890 4153 7.925483 AGATTAAGATTTGTGCTCTGCTAGTAG 59.075 37.037 0.63 0.63 0.00 2.57
1891 4154 5.413309 AAGATTTGTGCTCTGCTAGTAGT 57.587 39.130 7.77 0.00 0.00 2.73
1892 4155 6.531503 AAGATTTGTGCTCTGCTAGTAGTA 57.468 37.500 7.77 0.00 0.00 1.82
1893 4156 6.142818 AGATTTGTGCTCTGCTAGTAGTAG 57.857 41.667 8.86 8.86 0.00 2.57
1974 4237 4.935808 CCGAATTTGTCTGGCTTTACTACT 59.064 41.667 0.00 0.00 0.00 2.57
1975 4238 6.071221 TCCGAATTTGTCTGGCTTTACTACTA 60.071 38.462 0.00 0.00 0.00 1.82
1976 4239 6.035758 CCGAATTTGTCTGGCTTTACTACTAC 59.964 42.308 0.00 0.00 0.00 2.73
2012 4275 2.972505 CTGTGTGCCCGTGTCACC 60.973 66.667 0.00 0.00 33.71 4.02
2013 4276 4.901123 TGTGTGCCCGTGTCACCG 62.901 66.667 0.00 0.00 33.71 4.94
2016 4279 4.295119 GTGCCCGTGTCACCGTCT 62.295 66.667 0.00 0.00 0.00 4.18
2105 4368 4.778842 AACGACGTCTATCATGCAATTC 57.221 40.909 14.70 0.00 0.00 2.17
2119 4384 1.522258 GCAATTCTTTGTTGTGTGGCG 59.478 47.619 0.00 0.00 35.17 5.69
2204 4469 8.606040 CATTCTTTGGAATAAACAACCATTGT 57.394 30.769 0.00 0.00 41.82 2.71
2205 4470 9.703892 CATTCTTTGGAATAAACAACCATTGTA 57.296 29.630 0.00 0.00 40.41 2.41
2206 4471 9.705290 ATTCTTTGGAATAAACAACCATTGTAC 57.295 29.630 0.00 0.00 40.51 2.90
2207 4472 8.472007 TCTTTGGAATAAACAACCATTGTACT 57.528 30.769 0.00 0.00 44.59 2.73
2221 4486 2.386661 TGTACTAGCTGAAGCCTTGC 57.613 50.000 0.00 0.00 43.38 4.01
2244 4511 9.912634 TTGCTTTGGATTTTCAACTAGATAAAG 57.087 29.630 0.00 0.00 0.00 1.85
2248 4515 7.865706 TGGATTTTCAACTAGATAAAGGCTC 57.134 36.000 0.00 0.00 0.00 4.70
2251 4520 7.339466 GGATTTTCAACTAGATAAAGGCTCCAA 59.661 37.037 0.00 0.00 0.00 3.53
2263 4532 1.796796 GCTCCAAAGCTAAGCACGG 59.203 57.895 0.00 0.00 45.55 4.94
2264 4533 1.796796 CTCCAAAGCTAAGCACGGC 59.203 57.895 0.00 0.00 0.00 5.68
2265 4534 1.648467 CTCCAAAGCTAAGCACGGCC 61.648 60.000 0.00 0.00 0.00 6.13
2266 4535 2.480555 CAAAGCTAAGCACGGCCG 59.519 61.111 26.86 26.86 0.00 6.13
2267 4536 2.032634 CAAAGCTAAGCACGGCCGA 61.033 57.895 35.90 7.96 0.00 5.54
2268 4537 1.078426 AAAGCTAAGCACGGCCGAT 60.078 52.632 35.90 17.06 0.00 4.18
2269 4538 1.090052 AAAGCTAAGCACGGCCGATC 61.090 55.000 35.90 22.26 0.00 3.69
2270 4539 3.330853 GCTAAGCACGGCCGATCG 61.331 66.667 35.90 20.56 0.00 3.69
2271 4540 2.411701 CTAAGCACGGCCGATCGA 59.588 61.111 35.90 14.36 0.00 3.59
2272 4541 1.007271 CTAAGCACGGCCGATCGAT 60.007 57.895 35.90 15.99 0.00 3.59
2284 4553 3.932710 GGCCGATCGATATATGCTTTTGA 59.067 43.478 18.66 0.00 0.00 2.69
2288 4557 6.700020 CCGATCGATATATGCTTTTGATGAC 58.300 40.000 18.66 0.00 0.00 3.06
2302 4571 1.212616 GATGACGCAGAGAATTCCCG 58.787 55.000 0.65 3.06 0.00 5.14
2433 4707 0.536006 GAAATGCGGAGGGAGGGATG 60.536 60.000 0.00 0.00 0.00 3.51
2447 4721 3.626217 GGAGGGATGATTTTAACGTGACC 59.374 47.826 0.00 0.00 0.00 4.02
2590 4872 2.202756 GCGGCGTAGGGTCAGAAG 60.203 66.667 9.37 0.00 0.00 2.85
2701 5003 0.319900 CGGGCCACTATCGATCCTTG 60.320 60.000 4.39 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 2.287393 TATCATGACCGTCGTTGTGG 57.713 50.000 0.00 0.00 0.00 4.17
128 129 4.322080 TTCCTGTGATATCATGACCGTC 57.678 45.455 9.02 0.00 0.00 4.79
219 223 2.540101 CGTAGAAATGATGGCTCGAACC 59.460 50.000 0.00 0.00 0.00 3.62
266 270 2.971261 GAGAATTTGTCGCGGAAAACAC 59.029 45.455 6.13 0.00 0.00 3.32
274 278 1.906966 GCACAATGAGAATTTGTCGCG 59.093 47.619 0.00 0.00 35.18 5.87
318 322 2.229062 CGACACTGAGAGTTCTTGCCTA 59.771 50.000 0.00 0.00 0.00 3.93
375 412 1.298859 GGTGTTGGCCTCACGATCAC 61.299 60.000 19.63 8.53 36.76 3.06
447 512 2.692041 CAAAGATTCTGGGCCTCCATTC 59.308 50.000 4.53 0.00 43.11 2.67
456 521 3.766545 TCTTTCCACCAAAGATTCTGGG 58.233 45.455 3.68 3.68 44.78 4.45
478 543 2.129607 GTACATGACAACCACGTCGTT 58.870 47.619 0.00 0.00 38.84 3.85
500 565 8.306038 AGACTTTGCAATTTTGTAATCAGCATA 58.694 29.630 0.00 0.00 35.77 3.14
629 2826 1.884235 GGGATGATTTACAGCTCCCG 58.116 55.000 0.00 0.00 37.86 5.14
698 2935 3.430862 GCCGCCAAGATTCGTGCA 61.431 61.111 0.00 0.00 0.00 4.57
923 3160 1.528309 GGCGGAGAGAGAGAGGAGG 60.528 68.421 0.00 0.00 0.00 4.30
930 3167 2.511829 CTCGTCGGCGGAGAGAGA 60.512 66.667 21.70 6.68 38.89 3.10
946 3183 3.148279 CCTTACTCCCTCGCGCCT 61.148 66.667 0.00 0.00 0.00 5.52
1032 3275 0.612453 AGGAGGAGGTTGACGAGGAC 60.612 60.000 0.00 0.00 0.00 3.85
1035 3278 1.658686 CCGAGGAGGAGGTTGACGAG 61.659 65.000 0.00 0.00 45.00 4.18
1038 3281 2.579738 GCCGAGGAGGAGGTTGAC 59.420 66.667 0.00 0.00 45.00 3.18
1131 3383 1.047739 CGTCGTACACGTTGAGGAAC 58.952 55.000 1.19 0.00 44.07 3.62
1888 4151 3.758425 TGGTGACAGTGCAGTACTACTA 58.242 45.455 0.00 0.00 37.60 1.82
1889 4152 2.594131 TGGTGACAGTGCAGTACTACT 58.406 47.619 0.00 0.00 37.60 2.57
1974 4237 2.958818 CCAGCCAGGTGTATCTAGGTA 58.041 52.381 0.00 0.00 0.00 3.08
1975 4238 1.794714 CCAGCCAGGTGTATCTAGGT 58.205 55.000 0.00 0.00 0.00 3.08
1976 4239 0.394565 GCCAGCCAGGTGTATCTAGG 59.605 60.000 0.00 0.00 40.61 3.02
2004 4267 3.406361 GCAGCAGACGGTGACACG 61.406 66.667 0.00 0.00 43.56 4.49
2012 4275 2.099062 GCGATTTGGCAGCAGACG 59.901 61.111 0.00 0.00 0.00 4.18
2013 4276 2.486966 GGCGATTTGGCAGCAGAC 59.513 61.111 0.00 0.00 44.08 3.51
2105 4368 0.667993 ATCCACGCCACACAACAAAG 59.332 50.000 0.00 0.00 0.00 2.77
2119 4384 3.070018 CGCCAGATAGAATTGGATCCAC 58.930 50.000 15.91 2.84 36.55 4.02
2190 4455 7.148239 GCTTCAGCTAGTACAATGGTTGTTTAT 60.148 37.037 0.20 0.00 40.46 1.40
2202 4467 1.902508 AGCAAGGCTTCAGCTAGTACA 59.097 47.619 10.07 0.00 41.70 2.90
2221 4486 8.743714 AGCCTTTATCTAGTTGAAAATCCAAAG 58.256 33.333 0.00 0.00 0.00 2.77
2248 4515 2.877691 GGCCGTGCTTAGCTTTGG 59.122 61.111 5.60 5.70 0.00 3.28
2251 4520 1.521681 GATCGGCCGTGCTTAGCTT 60.522 57.895 27.15 0.00 0.00 3.74
2254 4523 0.240145 TATCGATCGGCCGTGCTTAG 59.760 55.000 27.15 11.84 0.00 2.18
2255 4524 0.885879 ATATCGATCGGCCGTGCTTA 59.114 50.000 27.15 5.24 0.00 3.09
2256 4525 0.885879 TATATCGATCGGCCGTGCTT 59.114 50.000 27.15 8.79 0.00 3.91
2258 4527 1.200483 CATATATCGATCGGCCGTGC 58.800 55.000 27.15 17.12 0.00 5.34
2259 4528 1.200483 GCATATATCGATCGGCCGTG 58.800 55.000 27.15 16.45 0.00 4.94
2260 4529 1.103803 AGCATATATCGATCGGCCGT 58.896 50.000 27.15 12.96 0.00 5.68
2262 4531 3.932710 TCAAAAGCATATATCGATCGGCC 59.067 43.478 16.41 0.00 0.00 6.13
2263 4532 5.291858 TCATCAAAAGCATATATCGATCGGC 59.708 40.000 16.41 9.50 0.00 5.54
2264 4533 6.506984 CGTCATCAAAAGCATATATCGATCGG 60.507 42.308 16.41 0.00 0.00 4.18
2265 4534 6.398037 CGTCATCAAAAGCATATATCGATCG 58.602 40.000 9.36 9.36 0.00 3.69
2266 4535 6.181255 GCGTCATCAAAAGCATATATCGATC 58.819 40.000 0.00 0.00 0.00 3.69
2267 4536 5.639082 TGCGTCATCAAAAGCATATATCGAT 59.361 36.000 2.16 2.16 34.39 3.59
2268 4537 4.987912 TGCGTCATCAAAAGCATATATCGA 59.012 37.500 0.00 0.00 34.39 3.59
2269 4538 5.119125 TCTGCGTCATCAAAAGCATATATCG 59.881 40.000 0.00 0.00 39.02 2.92
2270 4539 6.367149 TCTCTGCGTCATCAAAAGCATATATC 59.633 38.462 0.00 0.00 39.02 1.63
2271 4540 6.226052 TCTCTGCGTCATCAAAAGCATATAT 58.774 36.000 0.00 0.00 39.02 0.86
2272 4541 5.600696 TCTCTGCGTCATCAAAAGCATATA 58.399 37.500 0.00 0.00 39.02 0.86
2284 4553 0.179073 CCGGGAATTCTCTGCGTCAT 60.179 55.000 3.32 0.00 0.00 3.06
2288 4557 1.079127 ACACCGGGAATTCTCTGCG 60.079 57.895 6.32 0.00 0.00 5.18
2316 4585 0.957395 GCCAGTGTGATGACAGGTGG 60.957 60.000 8.76 8.76 39.21 4.61
2433 4707 2.477375 TGCGACAGGTCACGTTAAAATC 59.523 45.455 0.00 0.00 0.00 2.17
2468 4742 2.426522 CCCAAGATTTCTGTCGAAGCA 58.573 47.619 0.00 0.00 0.00 3.91
2579 4861 1.198759 GGTGCCCACTTCTGACCCTA 61.199 60.000 0.00 0.00 0.00 3.53
2617 4902 2.034558 CACATTGGTGTCCTCCACAAAC 59.965 50.000 0.00 0.00 46.44 2.93


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

AutoCloner maintained by Alex Coulton.