Multiple sequence alignment - TraesCS2D01G199200

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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 TraesCS2D01G199200 chr2D 100.000 2950 0 0 1 2950 148857413 148854464 0.000000e+00 5448
1 TraesCS2D01G199200 chr2D 96.474 794 27 1 2157 2950 617920214 617921006 0.000000e+00 1310
2 TraesCS2D01G199200 chr2D 96.226 795 26 3 2157 2950 88051436 88050645 0.000000e+00 1299
3 TraesCS2D01G199200 chr2D 96.217 793 26 3 2159 2950 5590787 5591576 0.000000e+00 1295
4 TraesCS2D01G199200 chr2D 85.823 790 72 18 1108 1891 490117824 490118579 0.000000e+00 802
5 TraesCS2D01G199200 chr2D 81.030 369 34 22 717 1064 490117132 490117485 8.110000e-66 261
6 TraesCS2D01G199200 chr2D 86.207 232 17 6 1936 2158 490118845 490119070 1.370000e-58 237
7 TraesCS2D01G199200 chr2B 96.896 1514 24 4 646 2158 208212195 208210704 0.000000e+00 2514
8 TraesCS2D01G199200 chr2B 85.679 1201 109 30 718 1889 573974524 573975690 0.000000e+00 1206
9 TraesCS2D01G199200 chr2B 92.576 660 13 13 1 652 208213145 208212514 0.000000e+00 915
10 TraesCS2D01G199200 chr2B 89.914 466 42 4 1426 1889 573985068 573985530 1.960000e-166 595
11 TraesCS2D01G199200 chr2B 82.700 237 21 10 1936 2158 573985877 573986107 3.000000e-45 193
12 TraesCS2D01G199200 chr2B 82.278 237 21 11 1936 2158 573976039 573976268 5.020000e-43 185
13 TraesCS2D01G199200 chr2A 95.531 1186 40 6 977 2158 153452268 153453444 0.000000e+00 1884
14 TraesCS2D01G199200 chr2A 89.496 714 36 13 1 688 153450765 153451465 0.000000e+00 867
15 TraesCS2D01G199200 chr2A 91.273 275 6 6 691 949 153451513 153451785 2.800000e-95 359
16 TraesCS2D01G199200 chr2A 77.928 222 24 11 14 230 633692838 633693039 6.680000e-22 115
17 TraesCS2D01G199200 chr1D 96.380 801 26 3 2152 2950 2168324 2169123 0.000000e+00 1315
18 TraesCS2D01G199200 chr1D 96.226 795 27 3 2158 2950 38746257 38747050 0.000000e+00 1299
19 TraesCS2D01G199200 chr6D 96.478 795 24 3 2157 2950 449925676 449926467 0.000000e+00 1310
20 TraesCS2D01G199200 chr6D 96.348 794 23 4 2159 2950 452852683 452853472 0.000000e+00 1301
21 TraesCS2D01G199200 chr6D 95.875 800 30 3 2152 2950 306348971 306348174 0.000000e+00 1291
22 TraesCS2D01G199200 chr3D 96.343 793 25 3 2159 2950 522515881 522516670 0.000000e+00 1301
23 TraesCS2D01G199200 chrUn 84.263 1201 98 46 719 1891 13023200 13024337 0.000000e+00 1086
24 TraesCS2D01G199200 chrUn 83.682 239 17 6 1936 2158 13024675 13024907 3.850000e-49 206


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 TraesCS2D01G199200 chr2D 148854464 148857413 2949 True 5448.000000 5448 100.000000 1 2950 1 chr2D.!!$R2 2949
1 TraesCS2D01G199200 chr2D 617920214 617921006 792 False 1310.000000 1310 96.474000 2157 2950 1 chr2D.!!$F2 793
2 TraesCS2D01G199200 chr2D 88050645 88051436 791 True 1299.000000 1299 96.226000 2157 2950 1 chr2D.!!$R1 793
3 TraesCS2D01G199200 chr2D 5590787 5591576 789 False 1295.000000 1295 96.217000 2159 2950 1 chr2D.!!$F1 791
4 TraesCS2D01G199200 chr2D 490117132 490119070 1938 False 433.333333 802 84.353333 717 2158 3 chr2D.!!$F3 1441
5 TraesCS2D01G199200 chr2B 208210704 208213145 2441 True 1714.500000 2514 94.736000 1 2158 2 chr2B.!!$R1 2157
6 TraesCS2D01G199200 chr2B 573974524 573976268 1744 False 695.500000 1206 83.978500 718 2158 2 chr2B.!!$F1 1440
7 TraesCS2D01G199200 chr2B 573985068 573986107 1039 False 394.000000 595 86.307000 1426 2158 2 chr2B.!!$F2 732
8 TraesCS2D01G199200 chr2A 153450765 153453444 2679 False 1036.666667 1884 92.100000 1 2158 3 chr2A.!!$F2 2157
9 TraesCS2D01G199200 chr1D 2168324 2169123 799 False 1315.000000 1315 96.380000 2152 2950 1 chr1D.!!$F1 798
10 TraesCS2D01G199200 chr1D 38746257 38747050 793 False 1299.000000 1299 96.226000 2158 2950 1 chr1D.!!$F2 792
11 TraesCS2D01G199200 chr6D 449925676 449926467 791 False 1310.000000 1310 96.478000 2157 2950 1 chr6D.!!$F1 793
12 TraesCS2D01G199200 chr6D 452852683 452853472 789 False 1301.000000 1301 96.348000 2159 2950 1 chr6D.!!$F2 791
13 TraesCS2D01G199200 chr6D 306348174 306348971 797 True 1291.000000 1291 95.875000 2152 2950 1 chr6D.!!$R1 798
14 TraesCS2D01G199200 chr3D 522515881 522516670 789 False 1301.000000 1301 96.343000 2159 2950 1 chr3D.!!$F1 791
15 TraesCS2D01G199200 chrUn 13023200 13024907 1707 False 646.000000 1086 83.972500 719 2158 2 chrUn.!!$F1 1439

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
954 1392 0.983378 CCCTCTAACCTCCCCACCAG 60.983 65.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 4079 1.106944 TCGCCGATGTGCTGGATCTA 61.107 55.0 0.0 0.0 0.0 1.98 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
82 88 3.184178 CACCACGCATCAAATTCAAAACC 59.816 43.478 0.00 0.00 0.00 3.27
110 116 8.965172 CGTAGTTGCCTGTATAACTATAAACTG 58.035 37.037 0.00 0.00 40.36 3.16
263 269 2.425668 CCACTAACCCCCAAATTAAGCG 59.574 50.000 0.00 0.00 0.00 4.68
266 272 2.517998 AACCCCCAAATTAAGCGCTA 57.482 45.000 12.05 0.00 0.00 4.26
511 534 4.558538 ACTGAACTTGCTGAAACATGTC 57.441 40.909 0.00 0.00 0.00 3.06
517 540 4.392047 ACTTGCTGAAACATGTCATCAGA 58.608 39.130 30.89 19.33 42.48 3.27
520 543 4.644498 TGCTGAAACATGTCATCAGAAGA 58.356 39.130 30.89 17.94 42.48 2.87
534 557 7.499232 TGTCATCAGAAGAAGATATGTACTCGA 59.501 37.037 0.00 0.00 0.00 4.04
808 1228 8.980481 GCACCTTTGCCACCTATATATATTAT 57.020 34.615 0.00 0.00 43.66 1.28
949 1387 1.074395 CCTCCCCTCTAACCTCCCC 60.074 68.421 0.00 0.00 0.00 4.81
950 1388 1.710341 CTCCCCTCTAACCTCCCCA 59.290 63.158 0.00 0.00 0.00 4.96
954 1392 0.983378 CCCTCTAACCTCCCCACCAG 60.983 65.000 0.00 0.00 0.00 4.00
955 1393 0.983378 CCTCTAACCTCCCCACCAGG 60.983 65.000 0.00 0.00 37.03 4.45
1140 2328 2.966309 GCTTCAGTTTCACCGGCCG 61.966 63.158 21.04 21.04 0.00 6.13
1339 2532 3.649277 GACCGACGAGCAGGTGCAT 62.649 63.158 4.48 0.00 45.16 3.96
1561 2754 2.039818 TCGAGAACGAGGTATGCTCT 57.960 50.000 0.00 0.00 43.81 4.09
1562 2755 1.941294 TCGAGAACGAGGTATGCTCTC 59.059 52.381 0.00 0.00 43.81 3.20
1563 2756 1.944024 CGAGAACGAGGTATGCTCTCT 59.056 52.381 0.00 0.00 42.66 3.10
1565 2758 2.946329 GAGAACGAGGTATGCTCTCTCA 59.054 50.000 0.00 0.00 31.71 3.27
1569 2762 1.268285 CGAGGTATGCTCTCTCACACG 60.268 57.143 0.00 0.00 0.00 4.49
2207 3745 0.938168 GAGCCGTTCGTTTGTCTCGT 60.938 55.000 0.00 0.00 0.00 4.18
2337 3875 1.885887 CCCTCTCGTCCAATGCAAAAA 59.114 47.619 0.00 0.00 0.00 1.94
2341 3879 0.665835 TCGTCCAATGCAAAAACGCT 59.334 45.000 0.00 0.00 33.58 5.07
2378 3916 4.717313 AAACCGCCGCCCTTCTCC 62.717 66.667 0.00 0.00 0.00 3.71
2513 4053 0.477597 ACATCCACCCCCTCTTCCAA 60.478 55.000 0.00 0.00 0.00 3.53
2518 4058 1.386772 ACCCCCTCTTCCAACCACA 60.387 57.895 0.00 0.00 0.00 4.17
2558 4098 1.106944 TAGATCCAGCACATCGGCGA 61.107 55.000 13.87 13.87 39.27 5.54
2693 4233 5.801947 GGTTTCACAACATATTGCAGATGAC 59.198 40.000 15.46 3.73 39.66 3.06
2816 4357 4.838152 GCGATGGAGCAGGCCGAA 62.838 66.667 0.00 0.00 37.05 4.30
2883 4424 0.466124 GGGTAGAGCATCCACTGGAC 59.534 60.000 0.00 0.00 32.98 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 52 1.337728 CGTGGTGTGCTACTCCATGAA 60.338 52.381 17.48 0.0 46.36 2.57
58 64 2.702898 TGAATTTGATGCGTGGTGTG 57.297 45.000 0.00 0.0 0.00 3.82
110 116 2.099427 CGGTCCTTAACTCACTCTAGCC 59.901 54.545 0.00 0.0 0.00 3.93
263 269 1.537202 GTCGGGATGGCATTTGATAGC 59.463 52.381 0.00 0.0 0.00 2.97
266 272 1.477558 GGAGTCGGGATGGCATTTGAT 60.478 52.381 0.00 0.0 0.00 2.57
511 534 9.179552 CTTTCGAGTACATATCTTCTTCTGATG 57.820 37.037 0.00 0.0 0.00 3.07
517 540 8.821894 GCATTTCTTTCGAGTACATATCTTCTT 58.178 33.333 0.00 0.0 0.00 2.52
520 543 7.981789 TCTGCATTTCTTTCGAGTACATATCTT 59.018 33.333 0.00 0.0 0.00 2.40
534 557 8.169977 TGATTTACTGAGTTCTGCATTTCTTT 57.830 30.769 0.00 0.0 0.00 2.52
592 623 2.539338 GCGGGTGTTTGCTGACGAA 61.539 57.895 0.00 0.0 0.00 3.85
808 1228 1.491332 CTCGAGGGAGAGACCTAGGAA 59.509 57.143 17.98 0.0 43.27 3.36
1142 2330 3.129502 CATGCGTGTCCTGGGCTG 61.130 66.667 0.00 0.0 0.00 4.85
1339 2532 1.548357 GGAAGCTCAGCTCCAGACCA 61.548 60.000 0.00 0.0 38.25 4.02
1417 2610 1.741401 CGCGACTTGCTTGGGATCA 60.741 57.895 0.00 0.0 43.27 2.92
1523 2716 0.251341 AGGTGGCATTTGTGGAGGAC 60.251 55.000 0.00 0.0 0.00 3.85
1560 2753 0.249031 TGTGAGTGTGCGTGTGAGAG 60.249 55.000 0.00 0.0 0.00 3.20
1561 2754 0.527600 GTGTGAGTGTGCGTGTGAGA 60.528 55.000 0.00 0.0 0.00 3.27
1562 2755 0.528466 AGTGTGAGTGTGCGTGTGAG 60.528 55.000 0.00 0.0 0.00 3.51
1563 2756 0.805711 CAGTGTGAGTGTGCGTGTGA 60.806 55.000 0.00 0.0 0.00 3.58
1565 2758 1.521457 CCAGTGTGAGTGTGCGTGT 60.521 57.895 0.00 0.0 0.00 4.49
1569 2762 0.798776 GTATGCCAGTGTGAGTGTGC 59.201 55.000 0.00 0.0 0.00 4.57
1943 3459 5.070446 ACCCAGCTCGTCTCAATATCAAATA 59.930 40.000 0.00 0.0 0.00 1.40
2207 3745 2.223548 ACGTATGTATGCGCCGTTAGAA 60.224 45.455 4.18 0.0 39.55 2.10
2341 3879 2.683465 GCATTGGAGGAGAGGGGCA 61.683 63.158 0.00 0.0 0.00 5.36
2373 3911 1.549203 GGCTTTGCATTGGAGGAGAA 58.451 50.000 0.00 0.0 0.00 2.87
2378 3916 1.135315 CGACGGCTTTGCATTGGAG 59.865 57.895 0.00 0.0 0.00 3.86
2513 4053 1.208052 CCATCGAGGATCTTGTGTGGT 59.792 52.381 0.00 0.0 41.22 4.16
2539 4079 1.106944 TCGCCGATGTGCTGGATCTA 61.107 55.000 0.00 0.0 0.00 1.98
2816 4357 3.000819 TCCACGGGCTGGACGAAT 61.001 61.111 0.00 0.0 44.99 3.34
2841 4382 2.185310 ATCTGAACGCCCACCACCTC 62.185 60.000 0.00 0.0 0.00 3.85
2883 4424 4.263572 TGCACCGTGGGTTCCTGG 62.264 66.667 0.00 0.0 31.02 4.45


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

AutoCloner maintained by Alex Coulton.