Multiple sequence alignment - TraesCS5D01G364000

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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 TraesCS5D01G364000 chr5D 100.000 3062 0 0 1 3062 441569725 441566664 0.000000e+00 5655.0
1 TraesCS5D01G364000 chr5D 96.522 1639 40 7 961 2592 490431474 490429846 0.000000e+00 2695.0
2 TraesCS5D01G364000 chr5D 97.417 968 22 3 1 965 490437499 490436532 0.000000e+00 1646.0
3 TraesCS5D01G364000 chr5D 84.122 296 16 10 2728 3002 490428869 490428584 1.090000e-64 257.0
4 TraesCS5D01G364000 chr5D 98.601 143 2 0 2590 2732 490429795 490429653 1.410000e-63 254.0
5 TraesCS5D01G364000 chr7D 92.280 2474 108 17 1 2434 44717253 44714823 0.000000e+00 3434.0
6 TraesCS5D01G364000 chr7D 87.213 305 24 5 2295 2591 44714828 44714531 1.760000e-87 333.0
7 TraesCS5D01G364000 chr6D 91.004 2579 111 35 1 2536 28310675 28308175 0.000000e+00 3365.0
8 TraesCS5D01G364000 chr6D 92.636 1548 65 17 657 2194 420225684 420224176 0.000000e+00 2182.0
9 TraesCS5D01G364000 chr6D 95.695 302 9 3 1 302 420228666 420228369 1.650000e-132 483.0
10 TraesCS5D01G364000 chr6D 96.503 143 5 0 2590 2732 28308092 28307950 1.420000e-58 237.0
11 TraesCS5D01G364000 chr6D 92.547 161 8 2 1286 1442 13922058 13922218 8.540000e-56 228.0
12 TraesCS5D01G364000 chr6D 98.148 54 1 0 2197 2250 420224149 420224096 9.040000e-16 95.3
13 TraesCS5D01G364000 chr6A 90.314 2612 120 44 1 2584 29577371 29579877 0.000000e+00 3299.0
14 TraesCS5D01G364000 chr6A 95.000 40 2 0 3023 3062 504621352 504621313 2.550000e-06 63.9
15 TraesCS5D01G364000 chr5A 92.238 2332 98 19 306 2592 611977603 611975310 0.000000e+00 3227.0
16 TraesCS5D01G364000 chr5A 96.013 301 9 2 1 301 611978599 611978302 1.280000e-133 486.0
17 TraesCS5D01G364000 chr5A 97.203 143 3 1 2590 2732 611974472 611974331 1.100000e-59 241.0
18 TraesCS5D01G364000 chr5A 88.889 189 16 4 2728 2911 611973619 611973431 8.540000e-56 228.0
19 TraesCS5D01G364000 chr7A 94.004 2118 78 15 1 2110 47295307 47293231 0.000000e+00 3162.0
20 TraesCS5D01G364000 chr7A 85.225 555 43 20 2065 2591 47293235 47292692 4.490000e-148 534.0
21 TraesCS5D01G364000 chr5B 92.004 2276 90 23 359 2592 604858080 604855855 0.000000e+00 3110.0
22 TraesCS5D01G364000 chr5B 95.801 381 14 1 1 381 604871988 604872366 5.610000e-172 614.0
23 TraesCS5D01G364000 chr5B 95.745 141 6 0 2590 2730 604855804 604855664 8.540000e-56 228.0
24 TraesCS5D01G364000 chr4A 94.702 302 13 2 1 302 581493262 581492964 1.660000e-127 466.0
25 TraesCS5D01G364000 chr4A 100.000 37 0 0 3024 3060 457286100 457286136 5.480000e-08 69.4
26 TraesCS5D01G364000 chr4A 97.368 38 1 0 3023 3060 292923732 292923695 7.090000e-07 65.8
27 TraesCS5D01G364000 chr4A 97.143 35 1 0 3026 3060 617910491 617910457 3.300000e-05 60.2
28 TraesCS5D01G364000 chr3A 78.808 604 65 34 1737 2292 128521175 128520587 6.280000e-92 348.0
29 TraesCS5D01G364000 chr6B 90.496 242 21 1 561 802 25279063 25279302 4.930000e-83 318.0
30 TraesCS5D01G364000 chr6B 100.000 36 0 0 3025 3060 107879847 107879812 1.970000e-07 67.6
31 TraesCS5D01G364000 chr1A 95.882 170 6 1 2026 2194 389877111 389877280 1.080000e-69 274.0
32 TraesCS5D01G364000 chr1A 92.708 96 4 1 2197 2292 389877472 389877564 5.330000e-28 135.0
33 TraesCS5D01G364000 chr1A 93.023 43 3 0 3018 3060 384069743 384069701 2.550000e-06 63.9
34 TraesCS5D01G364000 chr1A 100.000 29 0 0 2915 2943 113250781 113250809 2.000000e-03 54.7
35 TraesCS5D01G364000 chr2B 82.935 293 38 5 294 575 138115682 138115391 1.410000e-63 254.0
36 TraesCS5D01G364000 chr2B 97.368 38 1 0 3025 3062 420197799 420197762 7.090000e-07 65.8
37 TraesCS5D01G364000 chr2B 95.000 40 1 1 3021 3060 677017674 677017712 9.170000e-06 62.1
38 TraesCS5D01G364000 chr1D 82.958 311 24 15 1737 2041 310148264 310148551 1.410000e-63 254.0
39 TraesCS5D01G364000 chr4D 87.560 209 19 3 918 1125 55035065 55035267 5.100000e-58 235.0
40 TraesCS5D01G364000 chr4D 94.595 37 2 0 2837 2873 322259936 322259972 1.190000e-04 58.4
41 TraesCS5D01G364000 chr2A 85.882 170 21 1 402 568 46323254 46323085 8.720000e-41 178.0
42 TraesCS5D01G364000 chr7B 89.583 48 3 2 3014 3060 130268589 130268635 3.300000e-05 60.2


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 TraesCS5D01G364000 chr5D 441566664 441569725 3061 True 5655.000000 5655 100.000000 1 3062 1 chr5D.!!$R1 3061
1 TraesCS5D01G364000 chr5D 490436532 490437499 967 True 1646.000000 1646 97.417000 1 965 1 chr5D.!!$R2 964
2 TraesCS5D01G364000 chr5D 490428584 490431474 2890 True 1068.666667 2695 93.081667 961 3002 3 chr5D.!!$R3 2041
3 TraesCS5D01G364000 chr7D 44714531 44717253 2722 True 1883.500000 3434 89.746500 1 2591 2 chr7D.!!$R1 2590
4 TraesCS5D01G364000 chr6D 28307950 28310675 2725 True 1801.000000 3365 93.753500 1 2732 2 chr6D.!!$R1 2731
5 TraesCS5D01G364000 chr6D 420224096 420228666 4570 True 920.100000 2182 95.493000 1 2250 3 chr6D.!!$R2 2249
6 TraesCS5D01G364000 chr6A 29577371 29579877 2506 False 3299.000000 3299 90.314000 1 2584 1 chr6A.!!$F1 2583
7 TraesCS5D01G364000 chr5A 611973431 611978599 5168 True 1045.500000 3227 93.585750 1 2911 4 chr5A.!!$R1 2910
8 TraesCS5D01G364000 chr7A 47292692 47295307 2615 True 1848.000000 3162 89.614500 1 2591 2 chr7A.!!$R1 2590
9 TraesCS5D01G364000 chr5B 604855664 604858080 2416 True 1669.000000 3110 93.874500 359 2730 2 chr5B.!!$R1 2371
10 TraesCS5D01G364000 chr3A 128520587 128521175 588 True 348.000000 348 78.808000 1737 2292 1 chr3A.!!$R1 555


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
695 3085 0.24746 TGTGCAGTGCGAGCTAAGAT 59.753 50.0 11.2 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 4907 0.24912 CATCAACTCCAGGTACCGCA 59.751 55.0 6.18 0.0 0.0 5.69 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
214 216 2.358737 GTCCAGTGGGGTTGCTCG 60.359 66.667 9.92 0.00 38.11 5.03
441 1143 7.466746 AGACAACTAATTTGCATACAATGGT 57.533 32.000 0.00 0.00 39.01 3.55
502 1597 9.829507 CTTATTTCAGAGATGATTGGAGTAACT 57.170 33.333 0.00 0.00 0.00 2.24
695 3085 0.247460 TGTGCAGTGCGAGCTAAGAT 59.753 50.000 11.20 0.00 0.00 2.40
750 3154 5.929697 TTCAGTCATGATTGTCAAGTGTC 57.070 39.130 16.80 0.00 34.73 3.67
928 3335 2.452600 ACTTTGGAATGTGTGGGTGT 57.547 45.000 0.00 0.00 0.00 4.16
971 3381 7.718314 TGATCTAATCATCTTGAATTGACAGGG 59.282 37.037 0.00 0.00 33.59 4.45
1102 3512 0.106268 TCCAGGTTTGCTTTGCCTCA 60.106 50.000 0.00 0.00 0.00 3.86
1162 3572 4.500127 TGTACCGGATAACATGTGTTGAG 58.500 43.478 9.46 0.00 38.90 3.02
1457 3870 6.148811 CACCAATTTTAGTGTATGTTCGAGGT 59.851 38.462 0.00 0.00 0.00 3.85
1507 3926 4.178540 GTGTCATTGCTTCATCAAATGGG 58.821 43.478 0.00 0.00 0.00 4.00
1519 3938 9.822185 GCTTCATCAAATGGGAATTTAAGTAAT 57.178 29.630 0.00 0.00 0.00 1.89
1550 3969 8.894768 ATTCGTCAAATGGAAATTTAAACCAA 57.105 26.923 1.55 0.00 37.24 3.67
2194 4708 7.164122 GGATGCTCCTCATACTCATTATGAAA 58.836 38.462 0.00 0.00 44.98 2.69
2195 4709 7.118971 GGATGCTCCTCATACTCATTATGAAAC 59.881 40.741 0.00 0.00 44.98 2.78
2356 4903 2.095768 CACTGTAGTTTGGCCAACATCG 60.096 50.000 20.35 5.33 37.93 3.84
2357 4904 2.224426 ACTGTAGTTTGGCCAACATCGA 60.224 45.455 20.35 0.00 37.93 3.59
2358 4905 2.416547 CTGTAGTTTGGCCAACATCGAG 59.583 50.000 20.35 8.13 37.93 4.04
2359 4906 1.130561 GTAGTTTGGCCAACATCGAGC 59.869 52.381 20.35 0.00 37.93 5.03
2360 4907 0.250901 AGTTTGGCCAACATCGAGCT 60.251 50.000 20.35 0.00 37.93 4.09
2361 4908 0.109597 GTTTGGCCAACATCGAGCTG 60.110 55.000 20.35 0.00 35.18 4.24
2362 4909 1.865788 TTTGGCCAACATCGAGCTGC 61.866 55.000 20.35 0.00 0.00 5.25
2372 4926 3.449227 CGAGCTGCGGTACCTGGA 61.449 66.667 10.90 4.08 36.03 3.86
2546 5261 8.610035 GCTAAACTTGAACTTAAGTTGTAGTGT 58.390 33.333 25.17 21.25 46.96 3.55
2786 7140 9.094578 TGATCTATCTAATTTACCTCTTCCTGG 57.905 37.037 0.00 0.00 0.00 4.45
2827 7184 5.593909 CAGGGACAATGGCAGATAATTAACA 59.406 40.000 0.00 0.00 0.00 2.41
2965 7342 9.981114 AAAAATCGATCTAAAGTTGTCCAAAAT 57.019 25.926 0.00 0.00 0.00 1.82
3003 7380 7.321745 GGTAACAAGGAAACCATTCTATCTG 57.678 40.000 0.00 0.00 35.79 2.90
3004 7381 5.904362 AACAAGGAAACCATTCTATCTGC 57.096 39.130 0.00 0.00 35.79 4.26
3005 7382 4.273318 ACAAGGAAACCATTCTATCTGCC 58.727 43.478 0.00 0.00 35.79 4.85
3006 7383 3.199880 AGGAAACCATTCTATCTGCCG 57.800 47.619 0.00 0.00 35.79 5.69
3007 7384 2.158755 AGGAAACCATTCTATCTGCCGG 60.159 50.000 0.00 0.00 35.79 6.13
3008 7385 2.158813 GGAAACCATTCTATCTGCCGGA 60.159 50.000 5.05 0.00 35.79 5.14
3009 7386 3.496870 GGAAACCATTCTATCTGCCGGAT 60.497 47.826 5.05 0.00 35.79 4.18
3010 7387 2.847327 ACCATTCTATCTGCCGGATG 57.153 50.000 5.05 0.00 35.98 3.51
3011 7388 1.349026 ACCATTCTATCTGCCGGATGG 59.651 52.381 5.05 9.55 35.98 3.51
3012 7389 1.339438 CCATTCTATCTGCCGGATGGG 60.339 57.143 5.05 0.00 35.98 4.00
3013 7390 1.625315 CATTCTATCTGCCGGATGGGA 59.375 52.381 5.05 0.00 38.47 4.37
3014 7391 2.030027 TTCTATCTGCCGGATGGGAT 57.970 50.000 5.05 4.85 38.47 3.85
3015 7392 1.561643 TCTATCTGCCGGATGGGATC 58.438 55.000 5.05 0.00 38.47 3.36
3016 7393 0.539051 CTATCTGCCGGATGGGATCC 59.461 60.000 5.05 1.92 46.22 3.36
3024 7401 2.998493 GGATGGGATCCGGATAGCT 58.002 57.895 19.15 2.13 40.13 3.32
3025 7402 1.280457 GGATGGGATCCGGATAGCTT 58.720 55.000 19.15 2.75 40.13 3.74
3026 7403 2.467880 GGATGGGATCCGGATAGCTTA 58.532 52.381 19.15 2.78 40.13 3.09
3027 7404 3.041946 GGATGGGATCCGGATAGCTTAT 58.958 50.000 19.15 7.84 40.13 1.73
3028 7405 4.223953 GGATGGGATCCGGATAGCTTATA 58.776 47.826 19.15 0.11 40.13 0.98
3029 7406 4.282195 GGATGGGATCCGGATAGCTTATAG 59.718 50.000 19.15 0.00 40.13 1.31
3030 7407 3.031736 TGGGATCCGGATAGCTTATAGC 58.968 50.000 19.15 0.64 42.84 2.97
3041 7418 0.663153 GCTTATAGCTGGCCAAACGG 59.337 55.000 7.01 0.00 38.45 4.44
3042 7419 1.308998 CTTATAGCTGGCCAAACGGG 58.691 55.000 7.01 0.00 40.85 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.295518 TCAGTATGGCTATGATGAGAACCATC 60.296 42.308 0.00 0.00 43.91 3.51
214 216 8.947115 ACTGTAAGCCTAAATTCTGTAATTCAC 58.053 33.333 0.00 0.00 37.60 3.18
502 1597 1.891919 GCTGCTGAACCGGTCAACA 60.892 57.895 8.04 8.67 35.22 3.33
695 3085 3.552132 TGCTGAATGATTAACCGGCTA 57.448 42.857 0.00 0.00 32.47 3.93
928 3335 3.258372 AGATCAACTAGTCGAAACCAGCA 59.742 43.478 0.00 0.00 0.00 4.41
971 3381 5.554696 GCGACTTGCGAGTATATTCAGAAAC 60.555 44.000 6.58 0.00 44.57 2.78
1162 3572 0.745845 CTAGCCAGTGCATCCACACC 60.746 60.000 0.00 0.00 44.53 4.16
1238 3648 2.703416 CACTGACTCTGCAAGGCAATA 58.297 47.619 6.02 0.00 44.52 1.90
1457 3870 7.681939 AAAAAGATCCGTAAAATCTGCTACA 57.318 32.000 0.00 0.00 33.78 2.74
1483 3900 4.624024 CCATTTGATGAAGCAATGACACAC 59.376 41.667 0.00 0.00 0.00 3.82
1507 3926 8.433421 TGACGAATCTCCCATTACTTAAATTC 57.567 34.615 0.00 0.00 0.00 2.17
1519 3938 3.712016 TTCCATTTGACGAATCTCCCA 57.288 42.857 0.00 0.00 0.00 4.37
1759 4182 4.469586 TGTCCAGCTAGGTTTACATGATGA 59.530 41.667 0.00 0.00 39.02 2.92
2194 4708 4.380841 TCGCCATAGTTATGAAGAACGT 57.619 40.909 0.74 0.00 35.75 3.99
2195 4709 5.462068 TGATTCGCCATAGTTATGAAGAACG 59.538 40.000 0.74 0.00 35.75 3.95
2356 4903 1.889530 AACTCCAGGTACCGCAGCTC 61.890 60.000 6.18 0.00 30.72 4.09
2357 4904 1.913762 AACTCCAGGTACCGCAGCT 60.914 57.895 6.18 0.00 34.51 4.24
2358 4905 1.741770 CAACTCCAGGTACCGCAGC 60.742 63.158 6.18 0.00 0.00 5.25
2359 4906 0.537188 ATCAACTCCAGGTACCGCAG 59.463 55.000 6.18 6.26 0.00 5.18
2360 4907 0.249120 CATCAACTCCAGGTACCGCA 59.751 55.000 6.18 0.00 0.00 5.69
2361 4908 0.249398 ACATCAACTCCAGGTACCGC 59.751 55.000 6.18 0.00 0.00 5.68
2362 4909 1.405526 CCACATCAACTCCAGGTACCG 60.406 57.143 6.18 1.26 0.00 4.02
2372 4926 3.395941 AGGTCTTTTCCTCCACATCAACT 59.604 43.478 0.00 0.00 31.32 3.16
2732 6288 7.595819 TTTTTGTCCAGTAGTTCCAATCAAT 57.404 32.000 0.00 0.00 0.00 2.57
2775 7129 2.382649 ACTACCAGTACCAGGAAGAGGT 59.617 50.000 8.83 0.00 43.14 3.85
2827 7184 5.779771 TGTTCTTGGCTTATCAAGGGATTTT 59.220 36.000 4.99 0.00 43.05 1.82
2900 7277 6.588756 AGATTAATTCTGCACACATTTGCTTG 59.411 34.615 0.00 0.00 43.41 4.01
2969 7346 6.155393 TGGTTTCCTTGTTACCAGAATTGTTT 59.845 34.615 0.00 0.00 37.04 2.83
2970 7347 5.659079 TGGTTTCCTTGTTACCAGAATTGTT 59.341 36.000 0.00 0.00 37.04 2.83
2971 7348 5.205056 TGGTTTCCTTGTTACCAGAATTGT 58.795 37.500 0.00 0.00 37.04 2.71
2972 7349 5.782893 TGGTTTCCTTGTTACCAGAATTG 57.217 39.130 0.00 0.00 37.04 2.32
2973 7350 6.782494 AGAATGGTTTCCTTGTTACCAGAATT 59.218 34.615 0.00 0.00 44.53 2.17
2974 7351 6.314917 AGAATGGTTTCCTTGTTACCAGAAT 58.685 36.000 0.00 0.00 44.53 2.40
2975 7352 5.701224 AGAATGGTTTCCTTGTTACCAGAA 58.299 37.500 0.00 0.00 44.53 3.02
3006 7383 1.280457 AAGCTATCCGGATCCCATCC 58.720 55.000 23.08 4.10 46.22 3.51
3007 7384 4.262249 GCTATAAGCTATCCGGATCCCATC 60.262 50.000 23.08 6.71 38.45 3.51
3008 7385 3.643792 GCTATAAGCTATCCGGATCCCAT 59.356 47.826 23.08 10.75 38.45 4.00
3009 7386 3.031736 GCTATAAGCTATCCGGATCCCA 58.968 50.000 23.08 2.02 38.45 4.37
3010 7387 3.737032 GCTATAAGCTATCCGGATCCC 57.263 52.381 23.08 13.18 38.45 3.85
3022 7399 0.663153 CCGTTTGGCCAGCTATAAGC 59.337 55.000 5.11 0.00 42.84 3.09
3023 7400 1.308998 CCCGTTTGGCCAGCTATAAG 58.691 55.000 5.11 0.00 0.00 1.73
3024 7401 3.487576 CCCGTTTGGCCAGCTATAA 57.512 52.632 5.11 0.00 0.00 0.98



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

AutoCloner maintained by Alex Coulton.