Multiple sequence alignment - TraesCS3A01G189200

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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 TraesCS3A01G189200 chr3A 100.000 3128 0 0 1 3128 231668951 231672078 0 5777
1 TraesCS3A01G189200 chr3D 94.077 3157 92 34 1 3128 182593455 182596545 0 4706
2 TraesCS3A01G189200 chr3B 93.428 3180 99 41 1 3128 261785503 261788624 0 4614


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 TraesCS3A01G189200 chr3A 231668951 231672078 3127 False 5777 5777 100.000 1 3128 1 chr3A.!!$F1 3127
1 TraesCS3A01G189200 chr3D 182593455 182596545 3090 False 4706 4706 94.077 1 3128 1 chr3D.!!$F1 3127
2 TraesCS3A01G189200 chr3B 261785503 261788624 3121 False 4614 4614 93.428 1 3128 1 chr3B.!!$F1 3127

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
890 906 0.108329 TGGCTTCCGATTCTTCCGAC 60.108 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2154 0.392193 ATCCAAACGGAGCAGAGCAG 60.392 55.0 0.0 0.0 35.52 4.24 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
138 139 3.119673 GGTCATGCTCGATGATCGTAGAT 60.120 47.826 15.06 2.42 43.20 1.98
159 160 3.774702 GCGTTCTCCGTTGTCGCC 61.775 66.667 0.00 0.00 40.83 5.54
167 168 4.072088 CGTTGTCGCCCTCGCAAC 62.072 66.667 11.78 11.78 42.98 4.17
168 169 2.665185 GTTGTCGCCCTCGCAACT 60.665 61.111 13.43 0.00 43.03 3.16
235 238 3.264450 GTCCTATATCTGGGTTGGATGGG 59.736 52.174 0.00 0.00 0.00 4.00
288 291 0.811616 AGCGGCGCAGAAGAAATAGG 60.812 55.000 35.02 0.00 0.00 2.57
295 298 4.295051 GCGCAGAAGAAATAGGACTAGAG 58.705 47.826 0.30 0.00 0.00 2.43
331 334 8.189119 AGTTTGTTTTATGGAGAAATAAGGCA 57.811 30.769 0.00 0.00 0.00 4.75
435 438 9.476928 AAACGTGTATCTATATATTAGGAGCCT 57.523 33.333 0.00 0.00 0.00 4.58
436 439 8.453238 ACGTGTATCTATATATTAGGAGCCTG 57.547 38.462 0.00 0.00 0.00 4.85
571 575 3.568443 TCAACCATCCATCAATCCATGG 58.432 45.455 4.97 4.97 44.45 3.66
583 587 5.270893 TCAATCCATGGATGATGCTTTTG 57.729 39.130 27.97 19.10 34.70 2.44
641 645 3.009033 TCATTCTCCTCCGATTTGGTTGT 59.991 43.478 0.00 0.00 39.52 3.32
887 903 1.066152 GCATTGGCTTCCGATTCTTCC 59.934 52.381 0.00 0.00 36.96 3.46
890 906 0.108329 TGGCTTCCGATTCTTCCGAC 60.108 55.000 0.00 0.00 0.00 4.79
893 909 1.803252 GCTTCCGATTCTTCCGACTCC 60.803 57.143 0.00 0.00 0.00 3.85
902 918 0.745845 CTTCCGACTCCTGGCCATTG 60.746 60.000 5.51 0.00 0.00 2.82
934 950 2.486370 GCTCTAATCTTCCCCTTCCTGC 60.486 54.545 0.00 0.00 0.00 4.85
942 958 0.253044 TCCCCTTCCTGCTTGATTCG 59.747 55.000 0.00 0.00 0.00 3.34
1581 1597 4.218578 CAGCTGGCCGAGAGCGAT 62.219 66.667 5.57 0.00 45.17 4.58
1779 1795 2.672996 ATTGTGCCGTGGCTGGAC 60.673 61.111 12.84 2.61 42.51 4.02
1893 1912 0.529378 CCACCACCTACGTCACCTAC 59.471 60.000 0.00 0.00 0.00 3.18
2086 2105 1.561076 CATCACCATCCTCCACTTCCA 59.439 52.381 0.00 0.00 0.00 3.53
2087 2106 0.984230 TCACCATCCTCCACTTCCAC 59.016 55.000 0.00 0.00 0.00 4.02
2088 2107 0.987294 CACCATCCTCCACTTCCACT 59.013 55.000 0.00 0.00 0.00 4.00
2089 2108 1.352352 CACCATCCTCCACTTCCACTT 59.648 52.381 0.00 0.00 0.00 3.16
2090 2109 1.630878 ACCATCCTCCACTTCCACTTC 59.369 52.381 0.00 0.00 0.00 3.01
2091 2110 1.065126 CCATCCTCCACTTCCACTTCC 60.065 57.143 0.00 0.00 0.00 3.46
2132 2151 3.372206 CGGCACTTTGAGGACTAAATCTG 59.628 47.826 0.00 0.00 0.00 2.90
2133 2152 3.127721 GGCACTTTGAGGACTAAATCTGC 59.872 47.826 0.00 0.00 0.00 4.26
2134 2153 4.006319 GCACTTTGAGGACTAAATCTGCT 58.994 43.478 0.00 0.00 0.00 4.24
2135 2154 4.094146 GCACTTTGAGGACTAAATCTGCTC 59.906 45.833 0.00 0.00 0.00 4.26
2136 2155 5.486526 CACTTTGAGGACTAAATCTGCTCT 58.513 41.667 0.00 0.00 0.00 4.09
2338 2372 7.335673 TGTTCATCAGTTTTCAAACTCTACACA 59.664 33.333 1.76 0.79 45.65 3.72
2342 2376 5.870433 TCAGTTTTCAAACTCTACACAACGA 59.130 36.000 1.76 0.00 45.65 3.85
2350 2384 8.014322 TCAAACTCTACACAACGATAATCAAC 57.986 34.615 0.00 0.00 0.00 3.18
2353 2387 5.187186 ACTCTACACAACGATAATCAACCCT 59.813 40.000 0.00 0.00 0.00 4.34
2354 2388 5.416083 TCTACACAACGATAATCAACCCTG 58.584 41.667 0.00 0.00 0.00 4.45
2355 2389 4.015872 ACACAACGATAATCAACCCTGT 57.984 40.909 0.00 0.00 0.00 4.00
2356 2390 3.751175 ACACAACGATAATCAACCCTGTG 59.249 43.478 0.00 0.00 39.02 3.66
2357 2391 2.747446 ACAACGATAATCAACCCTGTGC 59.253 45.455 0.00 0.00 0.00 4.57
2358 2392 2.038387 ACGATAATCAACCCTGTGCC 57.962 50.000 0.00 0.00 0.00 5.01
2359 2393 1.280710 ACGATAATCAACCCTGTGCCA 59.719 47.619 0.00 0.00 0.00 4.92
2361 2395 2.419990 CGATAATCAACCCTGTGCCAGA 60.420 50.000 4.00 0.00 32.44 3.86
2362 2396 3.620488 GATAATCAACCCTGTGCCAGAA 58.380 45.455 4.00 0.00 32.44 3.02
2363 2397 2.610438 AATCAACCCTGTGCCAGAAT 57.390 45.000 4.00 0.00 32.44 2.40
2364 2398 2.610438 ATCAACCCTGTGCCAGAATT 57.390 45.000 4.00 0.00 32.44 2.17
2365 2399 1.909700 TCAACCCTGTGCCAGAATTC 58.090 50.000 0.00 0.00 32.44 2.17
2367 2401 1.962807 CAACCCTGTGCCAGAATTCAA 59.037 47.619 8.44 0.00 32.44 2.69
2368 2402 1.915141 ACCCTGTGCCAGAATTCAAG 58.085 50.000 8.44 0.00 32.44 3.02
2369 2403 1.425066 ACCCTGTGCCAGAATTCAAGA 59.575 47.619 8.44 0.00 32.44 3.02
2370 2404 2.089980 CCCTGTGCCAGAATTCAAGAG 58.910 52.381 8.44 0.00 32.44 2.85
2371 2405 2.553904 CCCTGTGCCAGAATTCAAGAGT 60.554 50.000 8.44 0.00 32.44 3.24
2374 2410 2.880268 TGTGCCAGAATTCAAGAGTGTG 59.120 45.455 8.44 0.00 0.00 3.82
2381 2417 2.592102 ATTCAAGAGTGTGTGGGCAT 57.408 45.000 0.00 0.00 0.00 4.40
2390 2426 4.080129 AGAGTGTGTGGGCATAATTGATCT 60.080 41.667 0.00 0.00 0.00 2.75
2402 2438 7.538678 GGGCATAATTGATCTAACGCTTTTATG 59.461 37.037 0.00 0.00 0.00 1.90
2403 2439 8.076178 GGCATAATTGATCTAACGCTTTTATGT 58.924 33.333 0.00 0.00 31.60 2.29
2407 2443 8.895932 AATTGATCTAACGCTTTTATGTTGTC 57.104 30.769 0.00 0.00 0.00 3.18
2415 2459 5.640732 ACGCTTTTATGTTGTCAATCATCC 58.359 37.500 4.55 0.00 0.00 3.51
2417 2461 6.071952 ACGCTTTTATGTTGTCAATCATCCTT 60.072 34.615 4.55 0.00 0.00 3.36
2442 2486 9.793259 TTCTTCACCATTTTGAGATAAACTAGT 57.207 29.630 0.00 0.00 0.00 2.57
2446 2490 9.871238 TCACCATTTTGAGATAAACTAGTAGAC 57.129 33.333 3.59 0.00 0.00 2.59
2447 2491 9.099454 CACCATTTTGAGATAAACTAGTAGACC 57.901 37.037 3.59 0.00 0.00 3.85
2448 2492 8.822805 ACCATTTTGAGATAAACTAGTAGACCA 58.177 33.333 3.59 0.00 0.00 4.02
2449 2493 9.667107 CCATTTTGAGATAAACTAGTAGACCAA 57.333 33.333 3.59 0.00 0.00 3.67
2484 2537 1.134848 ACGCAAACAACAGGCAAACAT 60.135 42.857 0.00 0.00 0.00 2.71
2498 2551 4.157289 AGGCAAACATATGAAGTGAAGCAG 59.843 41.667 10.38 0.00 0.00 4.24
2517 2570 4.406972 AGCAGCTATCAGGTAGTTCAATCA 59.593 41.667 0.00 0.00 32.72 2.57
2530 2583 9.632638 AGGTAGTTCAATCATTGCATATAAGTT 57.367 29.630 0.00 0.00 0.00 2.66
2744 2815 2.192187 TTGCATTGTCGCTGCCACA 61.192 52.632 0.00 0.00 38.89 4.17
2880 2951 2.347490 GCCTCTTCCGTGGCTTCA 59.653 61.111 0.00 0.00 44.42 3.02
2937 3008 1.300233 GATCACGCCCCTCACGATC 60.300 63.158 0.00 0.00 0.00 3.69
3099 3170 1.479323 ACCAAGATAAGCGTCGCCTTA 59.521 47.619 14.86 11.99 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.892723 CCATCTCAGCAAACATTTGTTACTATA 58.107 33.333 6.24 0.00 40.24 1.31
179 180 9.710900 AGGCTCAAGGAAAACATTTTATTTTAG 57.289 29.630 0.00 0.00 29.44 1.85
288 291 3.957508 ACTACTTCCCTCCCTCTAGTC 57.042 52.381 0.00 0.00 0.00 2.59
295 298 5.417894 CCATAAAACAAACTACTTCCCTCCC 59.582 44.000 0.00 0.00 0.00 4.30
331 334 7.895759 TGCTCTGGCATTTCTAATTTTAAACT 58.104 30.769 0.00 0.00 44.28 2.66
435 438 2.300956 TCCTTGGGTTAATTGCTGCA 57.699 45.000 0.00 0.00 0.00 4.41
436 439 3.588955 CTTTCCTTGGGTTAATTGCTGC 58.411 45.455 0.00 0.00 0.00 5.25
571 575 5.244785 TGCTGAATCTCAAAAGCATCATC 57.755 39.130 0.00 0.00 40.59 2.92
641 645 7.267128 ACAGAATCAATTCACAAGCAGAAAAA 58.733 30.769 5.59 0.00 39.23 1.94
784 797 2.928334 ACCACATGAGATGAGATTGCC 58.072 47.619 0.00 0.00 0.00 4.52
785 798 4.024218 GCTAACCACATGAGATGAGATTGC 60.024 45.833 0.00 0.00 0.00 3.56
786 799 5.366460 AGCTAACCACATGAGATGAGATTG 58.634 41.667 0.00 0.00 0.00 2.67
787 800 5.627182 AGCTAACCACATGAGATGAGATT 57.373 39.130 0.00 0.00 0.00 2.40
788 801 5.279406 GCTAGCTAACCACATGAGATGAGAT 60.279 44.000 7.70 0.00 0.00 2.75
789 802 4.038522 GCTAGCTAACCACATGAGATGAGA 59.961 45.833 7.70 0.00 0.00 3.27
790 803 4.039004 AGCTAGCTAACCACATGAGATGAG 59.961 45.833 17.69 0.00 0.00 2.90
791 804 3.963374 AGCTAGCTAACCACATGAGATGA 59.037 43.478 17.69 0.00 0.00 2.92
792 805 4.333913 AGCTAGCTAACCACATGAGATG 57.666 45.455 17.69 0.00 0.00 2.90
887 903 2.110967 CAGCAATGGCCAGGAGTCG 61.111 63.158 13.05 0.00 42.56 4.18
890 906 2.050350 CACCAGCAATGGCCAGGAG 61.050 63.158 13.05 4.32 42.56 3.69
893 909 2.693762 CGACACCAGCAATGGCCAG 61.694 63.158 13.05 0.00 42.56 4.85
902 918 1.407258 AGATTAGAGCTCGACACCAGC 59.593 52.381 8.37 0.00 37.12 4.85
934 950 3.426695 GGATTTGGCACTGACGAATCAAG 60.427 47.826 21.85 0.00 41.85 3.02
942 958 4.525912 AATTCTTGGATTTGGCACTGAC 57.474 40.909 0.00 0.00 0.00 3.51
1450 1466 0.393537 AATGGGCTGTAGTGCTCTGC 60.394 55.000 0.00 0.00 33.90 4.26
1653 1669 3.691342 TCCTCCTCGTTGCACCCG 61.691 66.667 0.00 0.00 0.00 5.28
1779 1795 3.138798 GGGCAGGAGCTGTGCATG 61.139 66.667 17.30 0.90 43.12 4.06
1893 1912 1.278172 CGTTCACCTCAGCACTGACG 61.278 60.000 0.00 0.00 35.46 4.35
2016 2035 3.071837 TGTATGGACGCCGGCAGA 61.072 61.111 28.98 6.70 0.00 4.26
2132 2151 1.375268 AAACGGAGCAGAGCAGAGC 60.375 57.895 0.00 0.00 0.00 4.09
2133 2152 1.018226 CCAAACGGAGCAGAGCAGAG 61.018 60.000 0.00 0.00 0.00 3.35
2134 2153 1.004560 CCAAACGGAGCAGAGCAGA 60.005 57.895 0.00 0.00 0.00 4.26
2135 2154 0.392193 ATCCAAACGGAGCAGAGCAG 60.392 55.000 0.00 0.00 35.52 4.24
2136 2155 0.674581 CATCCAAACGGAGCAGAGCA 60.675 55.000 0.00 0.00 35.52 4.26
2187 2210 1.199558 GAGAAAAGCTCCAAGCAGCAG 59.800 52.381 1.29 0.00 45.56 4.24
2338 2372 2.290641 TGGCACAGGGTTGATTATCGTT 60.291 45.455 0.00 0.00 0.00 3.85
2353 2387 2.880268 CACACTCTTGAATTCTGGCACA 59.120 45.455 7.05 0.00 0.00 4.57
2354 2388 2.880890 ACACACTCTTGAATTCTGGCAC 59.119 45.455 7.05 0.00 0.00 5.01
2355 2389 2.880268 CACACACTCTTGAATTCTGGCA 59.120 45.455 7.05 0.00 0.00 4.92
2356 2390 2.227388 CCACACACTCTTGAATTCTGGC 59.773 50.000 7.05 0.00 0.00 4.85
2357 2391 2.816087 CCCACACACTCTTGAATTCTGG 59.184 50.000 7.05 2.49 0.00 3.86
2358 2392 2.227388 GCCCACACACTCTTGAATTCTG 59.773 50.000 7.05 0.00 0.00 3.02
2359 2393 2.158623 TGCCCACACACTCTTGAATTCT 60.159 45.455 7.05 0.00 0.00 2.40
2361 2395 2.363306 TGCCCACACACTCTTGAATT 57.637 45.000 0.00 0.00 0.00 2.17
2362 2396 2.592102 ATGCCCACACACTCTTGAAT 57.408 45.000 0.00 0.00 0.00 2.57
2363 2397 3.500448 TTATGCCCACACACTCTTGAA 57.500 42.857 0.00 0.00 0.00 2.69
2364 2398 3.719268 ATTATGCCCACACACTCTTGA 57.281 42.857 0.00 0.00 0.00 3.02
2365 2399 3.758023 TCAATTATGCCCACACACTCTTG 59.242 43.478 0.00 0.00 0.00 3.02
2367 2401 3.719268 TCAATTATGCCCACACACTCT 57.281 42.857 0.00 0.00 0.00 3.24
2368 2402 4.202441 AGATCAATTATGCCCACACACTC 58.798 43.478 0.00 0.00 0.00 3.51
2369 2403 4.240881 AGATCAATTATGCCCACACACT 57.759 40.909 0.00 0.00 0.00 3.55
2370 2404 5.504010 CGTTAGATCAATTATGCCCACACAC 60.504 44.000 0.00 0.00 0.00 3.82
2371 2405 4.574421 CGTTAGATCAATTATGCCCACACA 59.426 41.667 0.00 0.00 0.00 3.72
2374 2410 3.815401 AGCGTTAGATCAATTATGCCCAC 59.185 43.478 0.00 0.00 0.00 4.61
2381 2417 9.982291 GACAACATAAAAGCGTTAGATCAATTA 57.018 29.630 0.00 0.00 0.00 1.40
2390 2426 7.120579 AGGATGATTGACAACATAAAAGCGTTA 59.879 33.333 0.00 0.00 0.00 3.18
2402 2438 4.761739 TGGTGAAGAAGGATGATTGACAAC 59.238 41.667 0.00 0.00 0.00 3.32
2403 2439 4.984295 TGGTGAAGAAGGATGATTGACAA 58.016 39.130 0.00 0.00 0.00 3.18
2405 2441 6.521151 AAATGGTGAAGAAGGATGATTGAC 57.479 37.500 0.00 0.00 0.00 3.18
2407 2443 6.927416 TCAAAATGGTGAAGAAGGATGATTG 58.073 36.000 0.00 0.00 0.00 2.67
2442 2486 9.602568 TGCGTTATATTTCTAACATTTGGTCTA 57.397 29.630 0.00 0.00 32.27 2.59
2443 2487 8.500753 TGCGTTATATTTCTAACATTTGGTCT 57.499 30.769 0.00 0.00 32.27 3.85
2444 2488 9.562583 TTTGCGTTATATTTCTAACATTTGGTC 57.437 29.630 0.00 0.00 32.27 4.02
2445 2489 9.349145 GTTTGCGTTATATTTCTAACATTTGGT 57.651 29.630 0.00 0.00 32.27 3.67
2446 2490 9.347934 TGTTTGCGTTATATTTCTAACATTTGG 57.652 29.630 0.00 0.00 32.27 3.28
2449 2493 9.900710 TGTTGTTTGCGTTATATTTCTAACATT 57.099 25.926 0.00 0.00 32.27 2.71
2484 2537 4.406972 ACCTGATAGCTGCTTCACTTCATA 59.593 41.667 7.79 0.00 0.00 2.15
2498 2551 5.528690 TGCAATGATTGAACTACCTGATAGC 59.471 40.000 9.76 0.00 33.73 2.97
2530 2583 6.903883 GCAGCTTGTTTTGCTACTACTATA 57.096 37.500 0.00 0.00 38.92 1.31
2744 2815 1.344763 AGCTCTTGACCGTGTAAGCTT 59.655 47.619 3.48 3.48 36.75 3.74
2880 2951 1.447317 CTGCCAAGGCGTTTGACAGT 61.447 55.000 6.60 0.00 40.97 3.55


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

AutoCloner maintained by Alex Coulton.