Multiple sequence alignment - TraesCS2D01G208500

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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 TraesCS2D01G208500 chr2D 100.000 3350 0 0 1 3350 162892110 162888761 0.000000e+00 6187.0
1 TraesCS2D01G208500 chr2A 92.188 2765 91 35 409 3130 173518595 173515913 0.000000e+00 3794.0
2 TraesCS2D01G208500 chr2A 83.491 424 35 19 1 421 173519376 173518985 2.460000e-96 363.0
3 TraesCS2D01G208500 chr2B 96.061 1955 49 11 498 2438 222001953 222000013 0.000000e+00 3158.0
4 TraesCS2D01G208500 chr2B 93.126 902 39 14 2457 3350 221998068 221997182 0.000000e+00 1301.0
5 TraesCS2D01G208500 chr2B 88.317 505 41 11 1 502 222004977 222004488 1.040000e-164 590.0
6 TraesCS2D01G208500 chr1A 80.120 166 29 3 172 335 300833947 300834110 1.630000e-23 121.0
7 TraesCS2D01G208500 chr5B 92.424 66 5 0 1 66 416333994 416334059 9.890000e-16 95.3
8 TraesCS2D01G208500 chr5A 93.443 61 4 0 1 61 616510768 616510828 1.280000e-14 91.6
9 TraesCS2D01G208500 chr7D 89.041 73 7 1 1 73 590425826 590425897 4.600000e-14 89.8
10 TraesCS2D01G208500 chr7B 89.041 73 7 1 1 73 665389233 665389304 4.600000e-14 89.8
11 TraesCS2D01G208500 chr7B 90.909 66 6 0 1 66 698864991 698865056 4.600000e-14 89.8
12 TraesCS2D01G208500 chr4A 87.342 79 8 2 1 78 552720419 552720342 4.600000e-14 89.8
13 TraesCS2D01G208500 chr1B 86.250 80 8 2 1 77 228245661 228245582 2.140000e-12 84.2
14 TraesCS2D01G208500 chr1B 85.185 81 9 2 1 78 548194226 548194306 2.770000e-11 80.5


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 TraesCS2D01G208500 chr2D 162888761 162892110 3349 True 6187.0 6187 100.000000 1 3350 1 chr2D.!!$R1 3349
1 TraesCS2D01G208500 chr2A 173515913 173519376 3463 True 2078.5 3794 87.839500 1 3130 2 chr2A.!!$R1 3129
2 TraesCS2D01G208500 chr2B 221997182 222004977 7795 True 1683.0 3158 92.501333 1 3350 3 chr2B.!!$R1 3349

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
277 281 0.030101 CATTGCCAACGGACGTGTTT 59.97 50.0 0.0 0.0 0.00 2.83 F
578 3533 1.280457 ATCCGAGGGAAGCTCTTGTT 58.72 50.0 0.0 0.0 34.34 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 4926 0.965866 AGTAGTAGTGCAGCGCCTCA 60.966 55.000 2.29 0.0 0.0 3.86 R
2453 5442 1.081509 GCGTGCCAAAAATCGCAGA 60.082 52.632 0.00 0.0 46.4 4.26 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
52 53 5.826586 TGACTTGCACGAAAAACAATACAT 58.173 33.333 0.00 0.00 0.00 2.29
108 109 2.467566 TAACTCTGTCGGGCCTTTTC 57.532 50.000 0.84 0.00 0.00 2.29
113 114 1.982073 CTGTCGGGCCTTTTCGATGC 61.982 60.000 0.84 0.00 37.73 3.91
114 115 2.437716 TCGGGCCTTTTCGATGCC 60.438 61.111 0.84 7.12 44.59 4.40
116 117 1.153249 CGGGCCTTTTCGATGCCTA 60.153 57.895 0.84 0.00 44.71 3.93
129 130 3.128764 TCGATGCCTATATGTCGATGTCC 59.871 47.826 0.00 0.00 38.09 4.02
143 144 2.798145 CGATGTCCGATGTCCGATTTGA 60.798 50.000 0.00 0.00 41.76 2.69
147 148 4.306600 TGTCCGATGTCCGATTTGATATG 58.693 43.478 0.00 0.00 41.76 1.78
153 154 6.414694 CCGATGTCCGATTTGATATGTTTTTG 59.585 38.462 0.00 0.00 41.76 2.44
173 174 2.368548 TGTGCTAACCGGCATGATCTAT 59.631 45.455 0.00 0.00 44.34 1.98
201 204 7.755591 ACTCTGCATGTGTTTGTATGAAATAG 58.244 34.615 0.00 0.00 0.00 1.73
203 206 5.649557 TGCATGTGTTTGTATGAAATAGGC 58.350 37.500 0.00 0.00 0.00 3.93
224 228 1.734388 GCGGGCATATGGGGTTTGTC 61.734 60.000 4.56 0.00 0.00 3.18
231 235 3.880490 GCATATGGGGTTTGTCGTTATGA 59.120 43.478 4.56 0.00 0.00 2.15
260 264 0.252375 AATGGGCTCTGTTTGGGCAT 60.252 50.000 0.00 0.00 0.00 4.40
262 266 1.186917 TGGGCTCTGTTTGGGCATTG 61.187 55.000 0.00 0.00 0.00 2.82
276 280 1.652012 CATTGCCAACGGACGTGTT 59.348 52.632 0.00 0.00 0.00 3.32
277 281 0.030101 CATTGCCAACGGACGTGTTT 59.970 50.000 0.00 0.00 0.00 2.83
301 305 4.379174 GCCCACATGCGTATAGGG 57.621 61.111 15.95 15.95 42.55 3.53
578 3533 1.280457 ATCCGAGGGAAGCTCTTGTT 58.720 50.000 0.00 0.00 34.34 2.83
1251 4227 2.345760 GGTTGCCATGGACCAGCTG 61.346 63.158 18.40 6.78 35.95 4.24
1950 4926 3.546714 CTTCCTGGGCCGGTTCGTT 62.547 63.158 12.30 0.00 0.00 3.85
2271 5247 2.711922 CGGGTGGAAGGACCTCTCG 61.712 68.421 0.00 0.00 46.93 4.04
2272 5248 1.609794 GGGTGGAAGGACCTCTCGT 60.610 63.158 0.00 0.00 39.86 4.18
2351 5327 4.389687 GCAAAAACGCCATGATTCTTGATT 59.610 37.500 0.00 0.00 0.00 2.57
2355 5331 7.992180 AAAACGCCATGATTCTTGATTAATC 57.008 32.000 8.60 8.60 34.55 1.75
2360 5336 6.509656 GCCATGATTCTTGATTAATCTTGCA 58.490 36.000 16.24 6.71 37.26 4.08
2361 5337 6.641314 GCCATGATTCTTGATTAATCTTGCAG 59.359 38.462 16.24 7.41 37.26 4.41
2362 5338 6.641314 CCATGATTCTTGATTAATCTTGCAGC 59.359 38.462 16.24 3.71 37.26 5.25
2363 5339 6.762702 TGATTCTTGATTAATCTTGCAGCA 57.237 33.333 16.24 6.02 34.95 4.41
2364 5340 6.558009 TGATTCTTGATTAATCTTGCAGCAC 58.442 36.000 16.24 3.04 34.95 4.40
2365 5341 4.970662 TCTTGATTAATCTTGCAGCACC 57.029 40.909 16.24 0.00 0.00 5.01
2366 5342 4.592942 TCTTGATTAATCTTGCAGCACCT 58.407 39.130 16.24 0.00 0.00 4.00
2367 5343 5.012239 TCTTGATTAATCTTGCAGCACCTT 58.988 37.500 16.24 0.00 0.00 3.50
2368 5344 5.477984 TCTTGATTAATCTTGCAGCACCTTT 59.522 36.000 16.24 0.00 0.00 3.11
2369 5345 5.063180 TGATTAATCTTGCAGCACCTTTG 57.937 39.130 16.24 0.00 0.00 2.77
2399 5375 5.991861 TGGCCCGTAATTATTAGAAGTTCA 58.008 37.500 0.00 0.00 0.00 3.18
2422 5398 8.712228 TCATGATATAATCGTATAGGCTCCAT 57.288 34.615 0.00 0.00 0.00 3.41
2432 5408 4.142381 CGTATAGGCTCCATCGATCATTCA 60.142 45.833 0.00 0.00 0.00 2.57
2444 5433 6.293298 CCATCGATCATTCATTCTCAAGGTTC 60.293 42.308 0.00 0.00 0.00 3.62
2453 5442 5.759059 TCATTCTCAAGGTTCAGGCATAAT 58.241 37.500 0.00 0.00 0.00 1.28
2499 7402 0.601558 TAGCCGTGTGTTCAGAGACC 59.398 55.000 0.00 0.00 0.00 3.85
2525 7428 1.553248 TGTGTTTCGGATAGGGAGGTG 59.447 52.381 0.00 0.00 0.00 4.00
2526 7429 1.829222 GTGTTTCGGATAGGGAGGTGA 59.171 52.381 0.00 0.00 0.00 4.02
2527 7430 2.108168 TGTTTCGGATAGGGAGGTGAG 58.892 52.381 0.00 0.00 0.00 3.51
2528 7431 1.413077 GTTTCGGATAGGGAGGTGAGG 59.587 57.143 0.00 0.00 0.00 3.86
2529 7432 0.635009 TTCGGATAGGGAGGTGAGGT 59.365 55.000 0.00 0.00 0.00 3.85
2530 7433 0.106167 TCGGATAGGGAGGTGAGGTG 60.106 60.000 0.00 0.00 0.00 4.00
2531 7434 0.106167 CGGATAGGGAGGTGAGGTGA 60.106 60.000 0.00 0.00 0.00 4.02
2532 7435 1.415200 GGATAGGGAGGTGAGGTGAC 58.585 60.000 0.00 0.00 0.00 3.67
2533 7436 1.343075 GGATAGGGAGGTGAGGTGACA 60.343 57.143 0.00 0.00 0.00 3.58
2534 7437 2.035632 GATAGGGAGGTGAGGTGACAG 58.964 57.143 0.00 0.00 0.00 3.51
2591 7494 6.128472 CCGTTGTGTTTAATACTCCTGGTTAC 60.128 42.308 0.00 0.00 0.00 2.50
2603 7506 6.696441 ACTCCTGGTTACGATTAGAGTAAG 57.304 41.667 0.00 0.00 35.09 2.34
2660 7563 3.256879 CAGGACAAGAACAGAGACAGCTA 59.743 47.826 0.00 0.00 0.00 3.32
2671 7574 4.078516 ACAGCTAACCCGTCGGCC 62.079 66.667 5.50 0.00 0.00 6.13
2811 7719 1.853319 CGACGGTGCTTGTGTCTTC 59.147 57.895 0.00 0.00 0.00 2.87
2825 7733 1.212688 TGTCTTCCATGGCATGTAGGG 59.787 52.381 24.80 10.78 0.00 3.53
2865 7773 7.010923 CAGAGGAATTTCGAAGAAACCTAGATG 59.989 40.741 12.67 9.58 45.90 2.90
2874 7783 5.960105 CGAAGAAACCTAGATGAAAAATCGC 59.040 40.000 0.00 0.00 0.00 4.58
2908 7817 4.389576 CGTGCCAGGCTTTCACGC 62.390 66.667 20.43 3.47 45.22 5.34
2927 7844 1.763968 CACTGTAGGGATCACGAGGA 58.236 55.000 0.00 0.00 0.00 3.71
2929 7846 2.496070 CACTGTAGGGATCACGAGGAAA 59.504 50.000 0.00 0.00 0.00 3.13
2945 7862 0.664224 GAAACAGGAACGCGGGAAAA 59.336 50.000 12.47 0.00 0.00 2.29
3073 7990 2.222027 CCAAAAGCTCGTGGTCTTCTT 58.778 47.619 7.35 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.474920 TCAACCATTTGAATGTTTTATCAAGAC 57.525 29.630 3.30 0.00 38.87 3.01
11 12 7.714377 TGCAAGTCAACCATTTGAATGTTTTAT 59.286 29.630 3.30 0.00 43.52 1.40
13 14 5.879223 TGCAAGTCAACCATTTGAATGTTTT 59.121 32.000 3.30 0.00 43.52 2.43
108 109 3.439293 GGACATCGACATATAGGCATCG 58.561 50.000 0.00 0.00 35.91 3.84
129 130 6.966632 ACAAAAACATATCAAATCGGACATCG 59.033 34.615 0.00 0.00 40.90 3.84
136 137 7.253288 CGGTTAGCACAAAAACATATCAAATCG 60.253 37.037 0.00 0.00 0.00 3.34
143 144 3.508012 TGCCGGTTAGCACAAAAACATAT 59.492 39.130 1.90 0.00 38.00 1.78
147 148 3.949031 TGCCGGTTAGCACAAAAAC 57.051 47.368 1.90 0.00 38.00 2.43
173 174 5.546526 TCATACAAACACATGCAGAGTACA 58.453 37.500 0.00 0.00 0.00 2.90
203 206 1.455587 AAACCCCATATGCCCGCAG 60.456 57.895 0.00 0.00 0.00 5.18
218 222 9.103048 CATTTTACTCACTTCATAACGACAAAC 57.897 33.333 0.00 0.00 0.00 2.93
224 228 5.354234 AGCCCATTTTACTCACTTCATAACG 59.646 40.000 0.00 0.00 0.00 3.18
231 235 4.373156 ACAGAGCCCATTTTACTCACTT 57.627 40.909 0.00 0.00 32.71 3.16
260 264 1.429825 CAAACACGTCCGTTGGCAA 59.570 52.632 0.00 0.00 0.00 4.52
262 266 2.181521 TCCAAACACGTCCGTTGGC 61.182 57.895 14.01 0.00 0.00 4.52
266 270 2.963320 GCGTCCAAACACGTCCGT 60.963 61.111 0.00 0.00 42.04 4.69
301 305 5.197682 ACCACGATTACCTATTCTACTGC 57.802 43.478 0.00 0.00 0.00 4.40
388 393 0.966920 ACGGGTGGTAGAGACAACAG 59.033 55.000 0.00 0.00 30.07 3.16
389 394 0.677288 CACGGGTGGTAGAGACAACA 59.323 55.000 0.00 0.00 30.07 3.33
390 395 0.037605 CCACGGGTGGTAGAGACAAC 60.038 60.000 9.72 0.00 45.53 3.32
623 3578 0.751643 CATTTGATGGGGGACGGGAC 60.752 60.000 0.00 0.00 0.00 4.46
626 3581 1.609208 GATCATTTGATGGGGGACGG 58.391 55.000 0.00 0.00 34.37 4.79
1236 4212 4.746309 GGCAGCTGGTCCATGGCA 62.746 66.667 17.12 0.00 39.18 4.92
1950 4926 0.965866 AGTAGTAGTGCAGCGCCTCA 60.966 55.000 2.29 0.00 0.00 3.86
2373 5349 7.393796 TGAACTTCTAATAATTACGGGCCAAAA 59.606 33.333 4.39 0.00 0.00 2.44
2394 5370 8.634444 GGAGCCTATACGATTATATCATGAACT 58.366 37.037 0.00 0.00 0.00 3.01
2399 5375 7.665974 TCGATGGAGCCTATACGATTATATCAT 59.334 37.037 0.00 0.00 0.00 2.45
2413 5389 4.529769 AGAATGAATGATCGATGGAGCCTA 59.470 41.667 0.54 0.00 0.00 3.93
2422 5398 5.733676 TGAACCTTGAGAATGAATGATCGA 58.266 37.500 0.00 0.00 0.00 3.59
2432 5408 5.826737 CAGATTATGCCTGAACCTTGAGAAT 59.173 40.000 0.00 0.00 33.65 2.40
2453 5442 1.081509 GCGTGCCAAAAATCGCAGA 60.082 52.632 0.00 0.00 46.40 4.26
2499 7402 2.259618 CCTATCCGAAACACAGTCACG 58.740 52.381 0.00 0.00 0.00 4.35
2525 7428 1.174783 TTAGGCTCGTCTGTCACCTC 58.825 55.000 0.00 0.00 31.79 3.85
2526 7429 1.853963 ATTAGGCTCGTCTGTCACCT 58.146 50.000 0.00 0.00 34.42 4.00
2527 7430 2.674796 AATTAGGCTCGTCTGTCACC 57.325 50.000 0.00 0.00 0.00 4.02
2528 7431 3.125316 CCAAAATTAGGCTCGTCTGTCAC 59.875 47.826 0.00 0.00 0.00 3.67
2529 7432 3.334691 CCAAAATTAGGCTCGTCTGTCA 58.665 45.455 0.00 0.00 0.00 3.58
2591 7494 5.406649 GGAGGATGATGCTTACTCTAATCG 58.593 45.833 0.00 0.00 0.00 3.34
2637 7540 2.036475 GCTGTCTCTGTTCTTGTCCTGA 59.964 50.000 0.00 0.00 0.00 3.86
2803 7706 2.356022 CCTACATGCCATGGAAGACACA 60.356 50.000 18.40 2.37 33.60 3.72
2807 7710 0.846015 CCCCTACATGCCATGGAAGA 59.154 55.000 18.40 0.00 33.60 2.87
2811 7719 1.457604 CCTCCCCTACATGCCATGG 59.542 63.158 7.63 7.63 33.60 3.66
2825 7733 3.736482 CTCTGTCGTACGCGCCTCC 62.736 68.421 11.24 0.00 38.14 4.30
2842 7750 6.947464 TCATCTAGGTTTCTTCGAAATTCCT 58.053 36.000 0.00 7.57 0.00 3.36
2865 7773 1.940613 AGCATCCTACGGCGATTTTTC 59.059 47.619 16.62 0.00 34.54 2.29
2874 7783 1.082038 CGACGCTAGCATCCTACGG 60.082 63.158 16.45 0.00 0.00 4.02
2908 7817 1.763968 TCCTCGTGATCCCTACAGTG 58.236 55.000 0.00 0.00 0.00 3.66
2927 7844 0.666374 CTTTTCCCGCGTTCCTGTTT 59.334 50.000 4.92 0.00 0.00 2.83
2929 7846 0.179040 TTCTTTTCCCGCGTTCCTGT 60.179 50.000 4.92 0.00 0.00 4.00
2987 7904 6.602410 TTCCATTTCACAGGCATGATAAAA 57.398 33.333 4.84 2.69 0.00 1.52
3073 7990 8.853077 AAATCAACTATCAACTCTGTTCATCA 57.147 30.769 0.00 0.00 0.00 3.07
3216 8133 8.633561 TGACACTGACGATTAGATCAAATAGAT 58.366 33.333 0.00 0.00 40.48 1.98
3224 8141 5.763088 TGCTATGACACTGACGATTAGATC 58.237 41.667 0.00 0.00 0.00 2.75
3255 8173 7.710676 ACTATAGCTAGTGATTGACATAGGG 57.289 40.000 0.00 0.00 36.81 3.53


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

AutoCloner maintained by Alex Coulton.