Multiple sequence alignment - TraesCS5D01G039200

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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 TraesCS5D01G039200 chr5D 100.000 3309 0 0 1 3309 40699115 40702423 0 6111
1 TraesCS5D01G039200 chr5B 92.240 3402 136 55 1 3305 33998276 34001646 0 4702
2 TraesCS5D01G039200 chr5A 90.292 3420 148 78 2 3309 28663409 28666756 0 4307


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 TraesCS5D01G039200 chr5D 40699115 40702423 3308 False 6111 6111 100.000 1 3309 1 chr5D.!!$F1 3308
1 TraesCS5D01G039200 chr5B 33998276 34001646 3370 False 4702 4702 92.240 1 3305 1 chr5B.!!$F1 3304
2 TraesCS5D01G039200 chr5A 28663409 28666756 3347 False 4307 4307 90.292 2 3309 1 chr5A.!!$F1 3307

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
64 65 0.319211 CTTGTTCGACGGGCTACACA 60.319 55.0 0.00 0.0 0.00 3.72 F
754 798 0.322322 AGGCATGCAAAACCACCATG 59.678 50.0 21.36 0.0 39.38 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1745 0.955428 GCCTCGCTTTCACCATCACA 60.955 55.0 0.00 0.00 0.00 3.58 R
2473 2606 0.111639 TTGAGGTGGGCCCACTTTAC 59.888 55.0 45.38 32.97 45.52 2.01 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
61 62 1.077089 GAGCTTGTTCGACGGGCTAC 61.077 60.000 0.00 0.00 30.96 3.58
64 65 0.319211 CTTGTTCGACGGGCTACACA 60.319 55.000 0.00 0.00 0.00 3.72
73 74 1.073284 ACGGGCTACACATTTGGTCTT 59.927 47.619 0.00 0.00 0.00 3.01
76 77 3.611530 CGGGCTACACATTTGGTCTTTTG 60.612 47.826 0.00 0.00 0.00 2.44
78 79 4.202212 GGGCTACACATTTGGTCTTTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
79 80 5.010213 GGGCTACACATTTGGTCTTTTGTTA 59.990 40.000 0.00 0.00 0.00 2.41
80 81 6.295067 GGGCTACACATTTGGTCTTTTGTTAT 60.295 38.462 0.00 0.00 0.00 1.89
153 159 5.600696 AGGTTTAAATTGCACAAGTTCTGG 58.399 37.500 0.00 0.00 30.75 3.86
211 237 1.094785 GAACCGTGCTTGCATATGGT 58.905 50.000 4.56 10.04 37.80 3.55
212 238 1.472480 GAACCGTGCTTGCATATGGTT 59.528 47.619 21.17 21.17 46.11 3.67
221 247 6.368791 CGTGCTTGCATATGGTTGTACTATAT 59.631 38.462 4.56 0.00 33.30 0.86
222 248 7.544217 CGTGCTTGCATATGGTTGTACTATATA 59.456 37.037 4.56 0.00 31.63 0.86
223 249 8.873830 GTGCTTGCATATGGTTGTACTATATAG 58.126 37.037 8.27 8.27 31.63 1.31
272 300 9.231297 GGCTATCATGTGGTGTGTTATATTTAT 57.769 33.333 0.00 0.00 0.00 1.40
292 328 7.754069 TTTATCATAAAGCAAGCCATTTTCG 57.246 32.000 0.00 0.00 0.00 3.46
297 334 6.703607 TCATAAAGCAAGCCATTTTCGAAAAA 59.296 30.769 25.77 10.76 0.00 1.94
314 351 7.928908 TCGAAAAAGAAAACATGGAAGATTG 57.071 32.000 0.00 0.00 0.00 2.67
324 361 6.845758 AACATGGAAGATTGATGAACATGT 57.154 33.333 0.00 0.00 46.42 3.21
325 362 6.845758 ACATGGAAGATTGATGAACATGTT 57.154 33.333 11.78 11.78 43.22 2.71
326 363 7.235935 ACATGGAAGATTGATGAACATGTTT 57.764 32.000 13.36 0.00 43.22 2.83
354 391 6.801539 TTCGAAAGCTCACTCAATAATGTT 57.198 33.333 0.00 0.00 0.00 2.71
359 396 7.998767 CGAAAGCTCACTCAATAATGTTATACG 59.001 37.037 0.00 0.00 0.00 3.06
377 415 8.452534 TGTTATACGGCGAAAGAAACAAATAAT 58.547 29.630 16.62 0.00 0.00 1.28
498 537 6.264970 GGTATATATAGCTAGGTAGGGTGTGC 59.735 46.154 13.55 0.00 0.00 4.57
557 596 0.454285 CCAAAACGCACAGCCATACG 60.454 55.000 0.00 0.00 0.00 3.06
613 652 4.972733 TGCCGGCCAACATGTGCT 62.973 61.111 26.77 0.00 0.00 4.40
653 694 1.153695 TCTACAGTGTCCCCCTCCCT 61.154 60.000 0.00 0.00 0.00 4.20
683 724 5.163733 GCAAATTGCACCCCAAAATATCAAG 60.164 40.000 13.73 0.00 44.26 3.02
754 798 0.322322 AGGCATGCAAAACCACCATG 59.678 50.000 21.36 0.00 39.38 3.66
788 832 1.065647 ATCTCCATCCATCCAGCCAG 58.934 55.000 0.00 0.00 0.00 4.85
982 1044 5.129155 AGCATGCATTTACTCTCTCTCTCTT 59.871 40.000 21.98 0.00 0.00 2.85
1077 1175 6.064060 ACTCAAATAAGCCATAGCATAGCAA 58.936 36.000 0.00 0.00 43.56 3.91
1195 1293 1.984424 TGATGACCAAGGTGTCCATCA 59.016 47.619 14.57 14.57 33.96 3.07
1443 1544 1.066143 CCAATGGTTAGCGTCTCCAGT 60.066 52.381 0.00 0.00 34.62 4.00
1624 1725 1.686800 TCCTACGCTTACCCCACCC 60.687 63.158 0.00 0.00 0.00 4.61
1644 1745 3.360340 GAGGGTGACGACGACGGT 61.360 66.667 12.58 0.00 44.46 4.83
1980 2081 1.069978 GAGGAGCTACAAGCCTGATCC 59.930 57.143 0.00 0.00 43.77 3.36
2000 2106 3.888930 TCCATGAAACCTCAGTCCAAAAC 59.111 43.478 0.00 0.00 34.23 2.43
2001 2107 3.636300 CCATGAAACCTCAGTCCAAAACA 59.364 43.478 0.00 0.00 34.23 2.83
2019 2126 5.930837 AAACACAAGAATTCCACAGGAAA 57.069 34.783 0.65 0.00 45.41 3.13
2020 2127 5.520376 AACACAAGAATTCCACAGGAAAG 57.480 39.130 0.65 0.00 45.41 2.62
2021 2128 3.891366 ACACAAGAATTCCACAGGAAAGG 59.109 43.478 0.65 0.00 45.41 3.11
2022 2129 4.144297 CACAAGAATTCCACAGGAAAGGA 58.856 43.478 0.65 0.00 45.41 3.36
2024 2131 4.584743 ACAAGAATTCCACAGGAAAGGAAC 59.415 41.667 0.65 0.00 45.41 3.62
2219 2326 2.297597 GGGTAGATCGATCTTCTGGTGG 59.702 54.545 31.55 0.00 38.32 4.61
2346 2476 2.708325 GGAGCAAGGGAGATGGATTAGT 59.292 50.000 0.00 0.00 0.00 2.24
2470 2603 4.263068 GGAAGATCTTGTCCTGTGGAGAAA 60.263 45.833 14.00 0.00 34.57 2.52
2471 2604 5.495640 GAAGATCTTGTCCTGTGGAGAAAT 58.504 41.667 14.00 0.00 34.57 2.17
2473 2606 3.423539 TCTTGTCCTGTGGAGAAATGG 57.576 47.619 0.00 0.00 34.57 3.16
2474 2607 2.711009 TCTTGTCCTGTGGAGAAATGGT 59.289 45.455 0.00 0.00 34.57 3.55
2496 2631 3.650950 TGGGCCCACCTCAAGAGC 61.651 66.667 24.45 0.00 41.11 4.09
2517 2652 9.632638 AAGAGCAAACCATATTTATACACAGAT 57.367 29.630 0.00 0.00 0.00 2.90
2569 2704 7.951530 AATGCTAAAATGGAAACTTGAAGTG 57.048 32.000 0.00 0.00 0.00 3.16
2585 2720 6.092807 ACTTGAAGTGAGTTTCAGAGTTTGTC 59.907 38.462 0.00 0.00 38.25 3.18
2587 2722 6.115446 TGAAGTGAGTTTCAGAGTTTGTCAT 58.885 36.000 0.00 0.00 32.39 3.06
2637 2772 3.498774 ATTCCATATCTGTGGTCTGCC 57.501 47.619 0.00 0.00 40.27 4.85
2662 2810 2.517959 TGGTCTCCTTTGGCAAATCAG 58.482 47.619 13.89 11.91 0.00 2.90
2688 2836 5.047802 TGAAGATCCTCTTTTGCAATCAACC 60.048 40.000 0.00 0.00 36.73 3.77
2892 3041 8.278482 CAGAGCAGCTGCATAAAAATAAATAC 57.722 34.615 38.24 12.00 45.16 1.89
2893 3042 7.916977 CAGAGCAGCTGCATAAAAATAAATACA 59.083 33.333 38.24 0.00 45.16 2.29
2894 3043 8.133627 AGAGCAGCTGCATAAAAATAAATACAG 58.866 33.333 38.24 0.00 45.16 2.74
2975 3126 8.890718 TGCACTATGAGTAGTAAGTAAGTAGTG 58.109 37.037 0.00 0.00 39.12 2.74
2983 3134 8.485976 AGTAGTAAGTAAGTAGTGGTAACTCG 57.514 38.462 0.00 0.00 37.88 4.18
2995 3146 6.770746 AGTGGTAACTCGTGACATAAGTAT 57.229 37.500 0.00 0.00 34.56 2.12
3001 3152 7.012704 GGTAACTCGTGACATAAGTATGGTAGA 59.987 40.741 3.48 0.00 38.00 2.59
3171 3324 5.679734 AACTGTTAAGTGAGCATGAGTTG 57.320 39.130 0.00 0.00 36.51 3.16
3238 3391 9.846248 AGCAAATTAAGCAAATGAGTAAAGTAG 57.154 29.630 5.70 0.00 0.00 2.57
3239 3392 8.587111 GCAAATTAAGCAAATGAGTAAAGTAGC 58.413 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.121768 GTCGAACAAGCTCCTAGCAAAATTA 59.878 40.000 1.22 0.00 45.56 1.40
36 37 0.109272 CGTCGAACAAGCTCCTAGCA 60.109 55.000 1.22 0.00 45.56 3.49
122 125 9.908152 ACTTGTGCAATTTAAACCTATTCTTAC 57.092 29.630 0.00 0.00 0.00 2.34
130 136 5.128663 ACCAGAACTTGTGCAATTTAAACCT 59.871 36.000 0.00 0.00 0.00 3.50
142 148 0.466189 AGGGCACACCAGAACTTGTG 60.466 55.000 4.81 4.81 45.01 3.33
143 149 1.136828 TAGGGCACACCAGAACTTGT 58.863 50.000 0.00 0.00 43.89 3.16
153 159 0.965363 CACATGGGGTTAGGGCACAC 60.965 60.000 0.00 0.00 0.00 3.82
245 271 4.778213 ATAACACACCACATGATAGCCT 57.222 40.909 0.00 0.00 0.00 4.58
246 272 7.510549 AAATATAACACACCACATGATAGCC 57.489 36.000 0.00 0.00 0.00 3.93
272 300 5.384063 TTCGAAAATGGCTTGCTTTATGA 57.616 34.783 0.00 0.00 0.00 2.15
290 326 7.711846 TCAATCTTCCATGTTTTCTTTTTCGA 58.288 30.769 0.00 0.00 0.00 3.71
291 327 7.928908 TCAATCTTCCATGTTTTCTTTTTCG 57.071 32.000 0.00 0.00 0.00 3.46
292 328 9.480053 TCATCAATCTTCCATGTTTTCTTTTTC 57.520 29.630 0.00 0.00 0.00 2.29
297 334 7.528996 TGTTCATCAATCTTCCATGTTTTCT 57.471 32.000 0.00 0.00 0.00 2.52
359 396 9.952341 GTCAATTTATTATTTGTTTCTTTCGCC 57.048 29.630 0.00 0.00 0.00 5.54
388 426 3.997681 CCATGCATGCTTGTGAAAATTGA 59.002 39.130 26.41 0.63 0.00 2.57
480 519 1.329256 CGCACACCCTACCTAGCTAT 58.671 55.000 0.00 0.00 0.00 2.97
498 537 8.516234 AGAGCATACTTTCTTATATCTACACCG 58.484 37.037 0.00 0.00 0.00 4.94
613 652 3.084536 TGAGAGCAAATGGGCATTGTA 57.915 42.857 0.00 0.00 35.83 2.41
653 694 1.354031 TGGGGTGCAATTTGCTAGAGA 59.646 47.619 21.19 0.00 45.31 3.10
683 724 3.552273 GGATGATGGTGCTGCATTTGATC 60.552 47.826 5.27 5.97 0.00 2.92
754 798 2.025321 TGGAGATGGGGTAAAGAAAGGC 60.025 50.000 0.00 0.00 0.00 4.35
788 832 6.520272 AGTAGCTCTCCAATAATCATGTGTC 58.480 40.000 0.00 0.00 0.00 3.67
982 1044 1.994399 AGGGGGAGAGAGAGAGAGAA 58.006 55.000 0.00 0.00 0.00 2.87
1077 1175 2.881816 GCTTTGGGCTTTCTAGCTTCCT 60.882 50.000 0.00 0.00 46.90 3.36
1602 1703 2.105729 GGGTAAGCGTAGGACGGC 59.894 66.667 0.70 0.00 42.82 5.68
1611 1712 3.659089 CTCACGGGTGGGGTAAGCG 62.659 68.421 0.00 0.00 0.00 4.68
1624 1725 2.126965 GTCGTCGTCACCCTCACG 60.127 66.667 0.00 0.00 38.67 4.35
1644 1745 0.955428 GCCTCGCTTTCACCATCACA 60.955 55.000 0.00 0.00 0.00 3.58
1758 1859 3.246112 TTGTCCTCCACCACGGGG 61.246 66.667 0.00 0.00 41.29 5.73
1759 1860 2.172483 CTCTTGTCCTCCACCACGGG 62.172 65.000 0.00 0.00 34.36 5.28
1760 1861 1.293498 CTCTTGTCCTCCACCACGG 59.707 63.158 0.00 0.00 0.00 4.94
1761 1862 1.374758 GCTCTTGTCCTCCACCACG 60.375 63.158 0.00 0.00 0.00 4.94
1768 1869 1.444553 CGACCACGCTCTTGTCCTC 60.445 63.158 0.00 0.00 0.00 3.71
1980 2081 4.097741 TGTGTTTTGGACTGAGGTTTCATG 59.902 41.667 0.00 0.00 31.68 3.07
2000 2106 4.144297 TCCTTTCCTGTGGAATTCTTGTG 58.856 43.478 5.23 0.00 41.71 3.33
2001 2107 4.453480 TCCTTTCCTGTGGAATTCTTGT 57.547 40.909 5.23 0.00 41.71 3.16
2205 2312 2.034878 CCATCTCCACCAGAAGATCGA 58.965 52.381 0.00 0.00 33.62 3.59
2206 2313 2.034878 TCCATCTCCACCAGAAGATCG 58.965 52.381 0.00 0.00 33.62 3.69
2207 2314 3.037549 ACTCCATCTCCACCAGAAGATC 58.962 50.000 0.00 0.00 33.62 2.75
2208 2315 2.770802 CACTCCATCTCCACCAGAAGAT 59.229 50.000 0.00 0.00 33.62 2.40
2219 2326 2.951642 CCTCTCACTCTCACTCCATCTC 59.048 54.545 0.00 0.00 0.00 2.75
2470 2603 1.146544 AGGTGGGCCCACTTTACCAT 61.147 55.000 45.38 21.25 45.52 3.55
2471 2604 1.776710 AGGTGGGCCCACTTTACCA 60.777 57.895 45.38 12.88 45.52 3.25
2473 2606 0.111639 TTGAGGTGGGCCCACTTTAC 59.888 55.000 45.38 32.97 45.52 2.01
2474 2607 0.404040 CTTGAGGTGGGCCCACTTTA 59.596 55.000 45.38 36.09 45.52 1.85
2496 2631 9.567776 TGGGTATCTGTGTATAAATATGGTTTG 57.432 33.333 0.00 0.00 0.00 2.93
2564 2699 6.610741 ATGACAAACTCTGAAACTCACTTC 57.389 37.500 0.00 0.00 0.00 3.01
2569 2704 7.020914 AGACAAATGACAAACTCTGAAACTC 57.979 36.000 0.00 0.00 0.00 3.01
2637 2772 0.178992 TGCCAAAGGAGACCAAGTGG 60.179 55.000 0.00 0.00 42.17 4.00
2644 2779 2.094854 CAGCTGATTTGCCAAAGGAGAC 60.095 50.000 8.42 0.00 0.00 3.36
2688 2836 3.504863 CATTGCAAAACAAGATCCCTCG 58.495 45.455 1.71 0.00 42.87 4.63
2811 2960 7.642669 AGGCAGATGAAACAATAAATGATACG 58.357 34.615 0.00 0.00 0.00 3.06
2889 3038 5.336849 GCTGTTTCACTGTCTCCTACTGTAT 60.337 44.000 0.00 0.00 38.11 2.29
2890 3039 4.022242 GCTGTTTCACTGTCTCCTACTGTA 60.022 45.833 0.00 0.00 38.11 2.74
2892 3041 3.006323 AGCTGTTTCACTGTCTCCTACTG 59.994 47.826 0.00 0.00 0.00 2.74
2893 3042 3.235200 AGCTGTTTCACTGTCTCCTACT 58.765 45.455 0.00 0.00 0.00 2.57
2894 3043 3.580731 GAGCTGTTTCACTGTCTCCTAC 58.419 50.000 0.00 0.00 0.00 3.18
2970 3121 5.947443 ACTTATGTCACGAGTTACCACTAC 58.053 41.667 0.00 0.00 31.22 2.73
2975 3126 5.899299 ACCATACTTATGTCACGAGTTACC 58.101 41.667 0.00 0.00 31.82 2.85
2995 3146 6.031964 AGGGACTGAGATCTAAATCTACCA 57.968 41.667 0.00 0.00 42.46 3.25
3124 3276 4.892934 ACACCACCAAATAACAGTGAACAT 59.107 37.500 0.00 0.00 33.21 2.71
3171 3324 6.264518 TCCTTGTGTTAAGATGGGAAAGAAAC 59.735 38.462 0.00 0.00 0.00 2.78
3238 3391 7.222999 CAGCTAAGTAGTAAGTGATTGGTTAGC 59.777 40.741 0.00 0.00 39.96 3.09
3239 3392 7.707035 CCAGCTAAGTAGTAAGTGATTGGTTAG 59.293 40.741 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.