Multiple sequence alignment - TraesCS6D01G232500

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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 TraesCS6D01G232500 chr6D 100.000 2546 0 0 1 2546 326295841 326293296 0 4702
1 TraesCS6D01G232500 chr6B 93.717 2499 150 5 3 2495 496413130 496415627 0 3738
2 TraesCS6D01G232500 chr7D 89.765 2550 249 11 1 2546 208835139 208832598 0 3253
3 TraesCS6D01G232500 chr7A 88.789 2551 274 12 1 2546 221975589 221973046 0 3116
4 TraesCS6D01G232500 chrUn 88.122 2551 293 10 1 2546 86159511 86162056 0 3024


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 TraesCS6D01G232500 chr6D 326293296 326295841 2545 True 4702 4702 100.000 1 2546 1 chr6D.!!$R1 2545
1 TraesCS6D01G232500 chr6B 496413130 496415627 2497 False 3738 3738 93.717 3 2495 1 chr6B.!!$F1 2492
2 TraesCS6D01G232500 chr7D 208832598 208835139 2541 True 3253 3253 89.765 1 2546 1 chr7D.!!$R1 2545
3 TraesCS6D01G232500 chr7A 221973046 221975589 2543 True 3116 3116 88.789 1 2546 1 chr7A.!!$R1 2545
4 TraesCS6D01G232500 chrUn 86159511 86162056 2545 False 3024 3024 88.122 1 2546 1 chrUn.!!$F1 2545

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
45 46 0.035056 CACCAATCCCACTCCAGTCC 60.035 60.0 0.0 0.0 0.00 3.85 F
1313 1315 0.036765 TTCGTTGGCGCCTCTTACAT 60.037 50.0 29.7 0.0 38.14 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1349 2.164219 CAGGTACAGCGCATTGGAAATT 59.836 45.455 11.47 0.0 0.0 1.82 R
2238 2248 0.035739 AGTACGTCGTGGGCCAAAAT 59.964 50.000 8.40 0.0 0.0 1.82 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
40 41 1.000896 CCACCACCAATCCCACTCC 60.001 63.158 0.00 0.00 0.00 3.85
45 46 0.035056 CACCAATCCCACTCCAGTCC 60.035 60.000 0.00 0.00 0.00 3.85
130 131 5.243060 TCATCGGACATAGATCGTAACCAAT 59.757 40.000 0.00 0.00 0.00 3.16
278 279 1.446792 CAGCGCCTTGATCAGACGT 60.447 57.895 2.29 0.00 0.00 4.34
305 306 7.048512 AGTGCACTACCTATTTTTGGTATCTC 58.951 38.462 20.16 0.00 39.10 2.75
326 327 3.876914 TCCGTAGATCATGGACATTTTGC 59.123 43.478 0.00 0.00 37.41 3.68
327 328 3.627123 CCGTAGATCATGGACATTTTGCA 59.373 43.478 0.00 0.00 34.93 4.08
549 551 2.352422 GCTCACTGTGCATCCCCA 59.648 61.111 2.12 0.00 0.00 4.96
636 638 2.436646 CACCATCACCTCGGCACC 60.437 66.667 0.00 0.00 0.00 5.01
795 797 1.817520 CATCAACGGTGCCGGCATA 60.818 57.895 35.23 7.61 44.69 3.14
986 988 1.256376 GCGATGCTACTTCACGACATG 59.744 52.381 0.00 0.00 0.00 3.21
1023 1025 1.758122 ATTGGATTTGAGCCCGGGC 60.758 57.895 39.29 39.29 42.33 6.13
1135 1137 1.302366 TGATCGAATGCTCATGGTGC 58.698 50.000 0.00 0.00 0.00 5.01
1309 1311 2.690778 GCATTCGTTGGCGCCTCTT 61.691 57.895 29.70 3.39 38.14 2.85
1313 1315 0.036765 TTCGTTGGCGCCTCTTACAT 60.037 50.000 29.70 0.00 38.14 2.29
1347 1349 4.714802 TCCACTGAGAAATTCCCTCGAATA 59.285 41.667 0.00 0.00 37.76 1.75
1360 1362 3.300009 CCTCGAATAATTTCCAATGCGC 58.700 45.455 0.00 0.00 0.00 6.09
1423 1425 4.759782 TGCTACCTACTGCTTTGAAGATC 58.240 43.478 0.00 0.00 0.00 2.75
1491 1493 0.403271 ACTCTCCTTGTGCTTGCCAT 59.597 50.000 0.00 0.00 0.00 4.40
1498 1500 1.186917 TTGTGCTTGCCATTGGGAGG 61.187 55.000 4.53 3.03 35.59 4.30
1686 1688 8.459635 GGAAACTCCCTCTATCAAATGTTAAAC 58.540 37.037 0.00 0.00 0.00 2.01
1803 1807 3.696051 TGCTTCACAGGAATATTCTTGGC 59.304 43.478 25.95 20.20 38.46 4.52
1835 1839 7.039011 AGCCATATCTTACCATCGTGATTTAGA 60.039 37.037 0.00 0.00 0.00 2.10
1929 1933 6.670233 CATGCCATGTTTTTACTGCATTTTT 58.330 32.000 0.00 0.00 37.34 1.94
1984 1990 9.967559 AGGAACCCTAATTTATTATGGGATTTT 57.032 29.630 16.96 7.16 35.78 1.82
2090 2096 8.380099 TCTATAATAGCCCCAATATTTTCACGT 58.620 33.333 0.00 0.00 0.00 4.49
2092 2098 5.767816 ATAGCCCCAATATTTTCACGTTC 57.232 39.130 0.00 0.00 0.00 3.95
2170 2176 4.387256 CAGAACACGGATCAGAGAGAAAAC 59.613 45.833 0.00 0.00 0.00 2.43
2201 2211 0.533032 TATTCACCATGCCGACGACA 59.467 50.000 0.00 0.00 0.00 4.35
2224 2234 1.557269 CCCAGTAGCACTTCCCAGCT 61.557 60.000 0.00 0.00 44.55 4.24
2289 2299 2.802414 GGTACGCACGACACGACC 60.802 66.667 0.00 0.00 0.00 4.79
2401 2411 6.922407 TCATCAACAATCTTTTGCGATTTTGA 59.078 30.769 0.00 0.00 36.32 2.69
2403 2413 5.172951 TCAACAATCTTTTGCGATTTTGACG 59.827 36.000 0.00 0.00 36.22 4.35
2412 2422 1.882198 CGATTTTGACGGCACATGTC 58.118 50.000 0.00 0.00 0.00 3.06
2415 2425 0.179004 TTTTGACGGCACATGTCCCT 60.179 50.000 3.84 0.00 0.00 4.20
2416 2426 0.888736 TTTGACGGCACATGTCCCTG 60.889 55.000 3.84 2.35 0.00 4.45
2434 2444 1.741770 GTGCACGATCCCACACCTC 60.742 63.158 0.00 0.00 32.37 3.85
2455 2465 1.972752 ATGATGCAGCGCACCAACA 60.973 52.632 11.47 11.45 43.04 3.33
2467 2477 2.350895 CCAACAGCCATCCCGACA 59.649 61.111 0.00 0.00 0.00 4.35
2501 2511 3.905678 CTCGGCGCCCTAGACTGG 61.906 72.222 23.46 3.72 0.00 4.00
2504 2514 3.851128 GGCGCCCTAGACTGGTCC 61.851 72.222 18.11 0.00 0.00 4.46
2507 2517 2.128507 CGCCCTAGACTGGTCCTCC 61.129 68.421 0.00 0.00 0.00 4.30
2508 2518 1.001760 GCCCTAGACTGGTCCTCCA 59.998 63.158 0.00 0.00 42.05 3.86
2533 2543 1.272490 CTAGTCGCTCACTTCCACCAA 59.728 52.381 0.00 0.00 36.43 3.67
2537 2547 1.134220 TCGCTCACTTCCACCAAGTTT 60.134 47.619 0.00 0.00 43.38 2.66
2540 2550 2.952310 GCTCACTTCCACCAAGTTTCTT 59.048 45.455 0.00 0.00 43.38 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.818142 ACCAAATTCAAAGAAAACAAGGACTG 59.182 34.615 0.00 0.00 0.00 3.51
106 107 4.139038 TGGTTACGATCTATGTCCGATGA 58.861 43.478 0.00 0.00 0.00 2.92
130 131 0.971386 GGGTGTTCGTACCTCTGGAA 59.029 55.000 0.00 0.00 40.66 3.53
210 211 9.574516 AGGTCAAATTAGGTATACAATGGAATC 57.425 33.333 5.01 0.00 0.00 2.52
278 279 8.545472 AGATACCAAAAATAGGTAGTGCACTTA 58.455 33.333 27.06 12.19 44.29 2.24
282 283 6.354130 GGAGATACCAAAAATAGGTAGTGCA 58.646 40.000 0.00 0.00 44.29 4.57
284 285 6.579865 ACGGAGATACCAAAAATAGGTAGTG 58.420 40.000 0.00 0.00 44.29 2.74
289 290 7.667557 TGATCTACGGAGATACCAAAAATAGG 58.332 38.462 10.98 0.00 42.80 2.57
305 306 3.627123 TGCAAAATGTCCATGATCTACGG 59.373 43.478 0.00 0.00 0.00 4.02
326 327 1.180456 TTTGTGCTGGCATGGGAGTG 61.180 55.000 0.00 0.00 0.00 3.51
327 328 0.469705 TTTTGTGCTGGCATGGGAGT 60.470 50.000 0.00 0.00 0.00 3.85
549 551 3.665675 GAGAAGGGTGCGGCGTGAT 62.666 63.158 9.37 0.00 0.00 3.06
795 797 1.924731 TGGGAACAGTCGAGTCATCT 58.075 50.000 0.00 0.00 35.01 2.90
948 950 2.359975 CCTCCAAAGGTCACCGGC 60.360 66.667 0.00 0.00 37.94 6.13
986 988 4.082787 CCAATGTCATTATTATGCCGTCCC 60.083 45.833 0.00 0.00 0.00 4.46
1143 1145 9.685979 CCTTTCTGGAGAAGGTTCATACCGAAT 62.686 44.444 0.00 0.00 43.56 3.34
1309 1311 6.610830 TCTCAGTGGATACCATGACTATGTA 58.389 40.000 0.00 0.00 35.28 2.29
1313 1315 7.419057 GGAATTTCTCAGTGGATACCATGACTA 60.419 40.741 0.00 0.00 35.28 2.59
1347 1349 2.164219 CAGGTACAGCGCATTGGAAATT 59.836 45.455 11.47 0.00 0.00 1.82
1360 1362 6.183360 CCTTGCATTGAATAGTTCAGGTACAG 60.183 42.308 0.00 0.00 41.38 2.74
1423 1425 5.009911 AGTCTCTTGCAGATATAGCTGTCTG 59.990 44.000 18.68 16.69 41.98 3.51
1491 1493 7.775093 CACATAAGATAATCTTCAACCTCCCAA 59.225 37.037 0.00 0.00 37.89 4.12
1803 1807 4.564372 CGATGGTAAGATATGGCTTGATCG 59.436 45.833 0.00 0.00 32.14 3.69
2021 2027 3.860641 CCCCAATGCATGTTTTAGGAAC 58.139 45.455 0.00 0.00 0.00 3.62
2177 2187 2.356135 GTCGGCATGGTGAATACTGTT 58.644 47.619 0.00 0.00 0.00 3.16
2178 2188 1.739035 CGTCGGCATGGTGAATACTGT 60.739 52.381 0.00 0.00 0.00 3.55
2189 2199 1.956170 GGGCTATGTCGTCGGCATG 60.956 63.158 22.16 12.71 0.00 4.06
2201 2211 1.132500 GGGAAGTGCTACTGGGCTAT 58.868 55.000 0.00 0.00 0.00 2.97
2224 2234 2.506061 AAAATTGCTGTGGCGGCCA 61.506 52.632 19.77 19.77 42.25 5.36
2234 2244 1.665442 GTCGTGGGCCAAAATTGCT 59.335 52.632 8.40 0.00 0.00 3.91
2238 2248 0.035739 AGTACGTCGTGGGCCAAAAT 59.964 50.000 8.40 0.00 0.00 1.82
2289 2299 3.753294 AGACCAGACACCTACAACTTG 57.247 47.619 0.00 0.00 0.00 3.16
2366 2376 5.384145 AGATTGTTGATGATGGGATCAGT 57.616 39.130 0.00 0.00 43.53 3.41
2401 2411 2.032528 CACAGGGACATGTGCCGT 59.967 61.111 28.23 24.54 46.59 5.68
2412 2422 2.436646 GTGGGATCGTGCACAGGG 60.437 66.667 18.64 0.04 0.00 4.45
2415 2425 2.031919 GGTGTGGGATCGTGCACA 59.968 61.111 18.64 4.45 33.88 4.57
2416 2426 1.741770 GAGGTGTGGGATCGTGCAC 60.742 63.158 6.82 6.82 0.00 4.57
2421 2431 1.884464 CATGCGAGGTGTGGGATCG 60.884 63.158 0.00 0.00 39.40 3.69
2449 2459 2.351276 GTCGGGATGGCTGTTGGT 59.649 61.111 0.00 0.00 0.00 3.67
2455 2465 0.691078 ACTATGGTGTCGGGATGGCT 60.691 55.000 0.00 0.00 0.00 4.75
2467 2477 3.244457 GCCGAGGGCTATTTAACTATGGT 60.244 47.826 0.00 0.00 46.69 3.55
2501 2511 1.385756 GCGACTAGGGTCTGGAGGAC 61.386 65.000 0.00 0.00 43.79 3.85
2504 2514 0.394488 TGAGCGACTAGGGTCTGGAG 60.394 60.000 0.00 0.00 40.10 3.86
2507 2517 1.133407 GAAGTGAGCGACTAGGGTCTG 59.867 57.143 0.00 0.00 40.10 3.51
2508 2518 1.465794 GAAGTGAGCGACTAGGGTCT 58.534 55.000 0.00 0.00 40.10 3.85
2519 2529 2.576615 AGAAACTTGGTGGAAGTGAGC 58.423 47.619 0.00 0.00 44.68 4.26


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

AutoCloner maintained by Alex Coulton.