Multiple sequence alignment - TraesCS6B01G117200

Loading Multiple Alignment...

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 TraesCS6B01G117200 chr6B 100.000 2549 0 0 1 2549 107039635 107037087 0 4708
1 TraesCS6B01G117200 chr6B 90.490 694 61 3 1 690 7042403 7043095 0 911
2 TraesCS6B01G117200 chr5B 96.518 1867 58 4 687 2549 446193134 446191271 0 3081
3 TraesCS6B01G117200 chr5B 90.843 688 60 1 6 690 396301868 396301181 0 918
4 TraesCS6B01G117200 chr5B 90.634 694 61 2 1 690 396787314 396788007 0 918
5 TraesCS6B01G117200 chr5B 90.490 694 61 3 1 690 271007257 271006565 0 911
6 TraesCS6B01G117200 chr2B 96.364 1870 59 5 687 2549 602077065 602075198 0 3068
7 TraesCS6B01G117200 chr2B 96.144 1867 67 3 687 2549 596962189 596964054 0 3044
8 TraesCS6B01G117200 chr2B 91.014 690 56 4 6 691 558306784 558307471 0 926
9 TraesCS6B01G117200 chr7B 96.193 1865 65 5 687 2549 718488354 718486494 0 3046
10 TraesCS6B01G117200 chr7B 96.041 1869 64 6 687 2549 621924312 621926176 0 3033
11 TraesCS6B01G117200 chr1B 96.197 1867 62 9 687 2549 232740854 232742715 0 3046
12 TraesCS6B01G117200 chr1B 96.086 1865 67 6 687 2549 490563442 490561582 0 3035
13 TraesCS6B01G117200 chr1B 96.084 1864 68 4 687 2549 498442299 498440440 0 3033
14 TraesCS6B01G117200 chr3B 96.195 1866 62 7 687 2549 703251289 703253148 0 3044
15 TraesCS6B01G117200 chr3B 90.647 695 57 2 1 687 699832761 699833455 0 917
16 TraesCS6B01G117200 chr4A 93.064 692 44 3 1 689 715311955 715311265 0 1009
17 TraesCS6B01G117200 chr4B 90.634 694 60 3 1 690 78716402 78715710 0 917
18 TraesCS6B01G117200 chr2D 90.415 699 57 6 1 690 105895863 105895166 0 911


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 TraesCS6B01G117200 chr6B 107037087 107039635 2548 True 4708 4708 100.000 1 2549 1 chr6B.!!$R1 2548
1 TraesCS6B01G117200 chr6B 7042403 7043095 692 False 911 911 90.490 1 690 1 chr6B.!!$F1 689
2 TraesCS6B01G117200 chr5B 446191271 446193134 1863 True 3081 3081 96.518 687 2549 1 chr5B.!!$R3 1862
3 TraesCS6B01G117200 chr5B 396301181 396301868 687 True 918 918 90.843 6 690 1 chr5B.!!$R2 684
4 TraesCS6B01G117200 chr5B 396787314 396788007 693 False 918 918 90.634 1 690 1 chr5B.!!$F1 689
5 TraesCS6B01G117200 chr5B 271006565 271007257 692 True 911 911 90.490 1 690 1 chr5B.!!$R1 689
6 TraesCS6B01G117200 chr2B 602075198 602077065 1867 True 3068 3068 96.364 687 2549 1 chr2B.!!$R1 1862
7 TraesCS6B01G117200 chr2B 596962189 596964054 1865 False 3044 3044 96.144 687 2549 1 chr2B.!!$F2 1862
8 TraesCS6B01G117200 chr2B 558306784 558307471 687 False 926 926 91.014 6 691 1 chr2B.!!$F1 685
9 TraesCS6B01G117200 chr7B 718486494 718488354 1860 True 3046 3046 96.193 687 2549 1 chr7B.!!$R1 1862
10 TraesCS6B01G117200 chr7B 621924312 621926176 1864 False 3033 3033 96.041 687 2549 1 chr7B.!!$F1 1862
11 TraesCS6B01G117200 chr1B 232740854 232742715 1861 False 3046 3046 96.197 687 2549 1 chr1B.!!$F1 1862
12 TraesCS6B01G117200 chr1B 490561582 490563442 1860 True 3035 3035 96.086 687 2549 1 chr1B.!!$R1 1862
13 TraesCS6B01G117200 chr1B 498440440 498442299 1859 True 3033 3033 96.084 687 2549 1 chr1B.!!$R2 1862
14 TraesCS6B01G117200 chr3B 703251289 703253148 1859 False 3044 3044 96.195 687 2549 1 chr3B.!!$F2 1862
15 TraesCS6B01G117200 chr3B 699832761 699833455 694 False 917 917 90.647 1 687 1 chr3B.!!$F1 686
16 TraesCS6B01G117200 chr4A 715311265 715311955 690 True 1009 1009 93.064 1 689 1 chr4A.!!$R1 688
17 TraesCS6B01G117200 chr4B 78715710 78716402 692 True 917 917 90.634 1 690 1 chr4B.!!$R1 689
18 TraesCS6B01G117200 chr2D 105895166 105895863 697 True 911 911 90.415 1 690 1 chr2D.!!$R1 689

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
600 610 0.734889 AAGGCGAAATTCCAGATGCG 59.265 50.0 0.0 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2012 2.291346 GCCCTAAACACCACTAACCCAT 60.291 50.0 0.0 0.0 0.0 4.0 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
41 47 2.292587 GGGGAGGAGAAGAAGAGGAAGA 60.293 54.545 0.00 0.00 0.00 2.87
45 51 2.041891 AGGAGAAGAAGAGGAAGACCGA 59.958 50.000 0.00 0.00 41.83 4.69
86 92 1.303561 TCCAAGAAAGCGGCTGCAT 60.304 52.632 21.93 4.33 46.23 3.96
271 278 1.340017 CGAAGAAGGGAAAGGCATCCA 60.340 52.381 10.94 0.00 41.55 3.41
295 302 2.185310 GAATCACTCCACCACGGCCT 62.185 60.000 0.00 0.00 33.14 5.19
406 416 6.255020 ACTTCATAGTTTGTAATAACGCCGAG 59.745 38.462 0.00 0.00 33.26 4.63
423 433 3.812203 GCACGCATATGCAGTCCA 58.188 55.556 26.52 0.00 45.39 4.02
427 437 1.524393 CGCATATGCAGTCCAGCCA 60.524 57.895 26.52 0.00 42.21 4.75
434 444 2.608988 CAGTCCAGCCAGGTCCCT 60.609 66.667 0.00 0.00 39.02 4.20
438 448 1.920325 TCCAGCCAGGTCCCTTCTG 60.920 63.158 5.71 5.71 39.02 3.02
525 535 3.499737 CGGCTTGCGGATGACACC 61.500 66.667 0.00 0.00 0.00 4.16
550 560 1.979308 TGTTGTCCCAAAGGATACCGA 59.021 47.619 0.00 0.00 46.41 4.69
600 610 0.734889 AAGGCGAAATTCCAGATGCG 59.265 50.000 0.00 0.00 0.00 4.73
601 611 1.097547 AGGCGAAATTCCAGATGCGG 61.098 55.000 0.00 0.00 0.00 5.69
612 623 4.820744 GATGCGGGGCACATGGGT 62.821 66.667 0.00 0.00 43.04 4.51
631 642 2.638363 GGTGGTAAGATCCCCATAGACC 59.362 54.545 0.22 0.00 32.32 3.85
719 730 4.280677 TCAATGTTTTGACTTGGCCCTTAG 59.719 41.667 0.00 0.00 36.94 2.18
774 785 2.049526 AGATCGTTGCACGCGTGA 60.050 55.556 41.19 23.48 42.21 4.35
956 967 3.019003 GCGGTGGGAAGCTAGCTGA 62.019 63.158 20.16 0.00 0.00 4.26
1128 1139 0.105964 CTCACACACCGAGGAACCAA 59.894 55.000 0.00 0.00 0.00 3.67
1284 1295 0.540923 ATGCTCTGGCCAAGACTCTC 59.459 55.000 7.01 0.00 37.74 3.20
1375 1386 2.028130 GAGCTCCGGAAGAAGAGATGA 58.972 52.381 5.23 0.00 0.00 2.92
1504 1515 5.083821 ACTTTTGGGCATTTGTAGGTATGT 58.916 37.500 0.00 0.00 0.00 2.29
1628 1639 9.877178 ATGTTGGTCAAAGTTGTTTAAATGTTA 57.123 25.926 0.00 0.00 0.00 2.41
1728 1742 5.766670 TGCAGCTAATGAATTATTCCAGAGG 59.233 40.000 2.22 0.00 0.00 3.69
1996 2012 2.342279 CTCGAACCCAAGACCGCA 59.658 61.111 0.00 0.00 0.00 5.69
2317 2338 0.249114 TTTGCACACGCGTGAGAGTA 60.249 50.000 42.94 27.17 46.80 2.59
2442 2464 4.875561 AGAGTCTCACTTGGTTTAGGAC 57.124 45.455 1.94 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 172 3.837731 GGAATTTCTTCATGTTTCCCCCA 59.162 43.478 0.00 0.00 32.70 4.96
271 278 2.355108 CCGTGGTGGAGTGATTCAGAAT 60.355 50.000 0.00 0.00 42.00 2.40
275 282 1.003839 GCCGTGGTGGAGTGATTCA 60.004 57.895 0.00 0.00 42.00 2.57
295 302 1.616865 CAACCACTCCTCGTTGTAGGA 59.383 52.381 0.00 0.00 43.58 2.94
406 416 1.645455 CTGGACTGCATATGCGTGC 59.355 57.895 25.45 25.45 45.83 5.34
550 560 4.123545 AAGCGCCGCCCCCTATTT 62.124 61.111 4.98 0.00 0.00 1.40
600 610 1.379843 CTTACCACCCATGTGCCCC 60.380 63.158 0.00 0.00 41.35 5.80
601 611 0.258774 ATCTTACCACCCATGTGCCC 59.741 55.000 0.00 0.00 41.35 5.36
612 623 3.717507 TGGTCTATGGGGATCTTACCA 57.282 47.619 6.76 6.76 41.76 3.25
631 642 3.260483 GCGGCTCTCGTCAGCATG 61.260 66.667 9.96 0.00 41.65 4.06
774 785 4.335647 CTGCTGGGTCCCGCAAGT 62.336 66.667 22.34 0.00 34.13 3.16
889 900 1.504446 GTCGTGCTCTCGCTCTCTT 59.496 57.895 0.00 0.00 36.97 2.85
1051 1062 0.976641 ACGAAGACAGGCATCTCCAA 59.023 50.000 0.00 0.00 37.29 3.53
1128 1139 2.322161 CACACGTAGAACCGACGATTT 58.678 47.619 6.61 0.00 42.98 2.17
1136 1147 2.206750 TCTTGTTGCACACGTAGAACC 58.793 47.619 0.00 0.00 0.00 3.62
1284 1295 5.946298 TGCTCTTCTTGCAGTTCATTTATG 58.054 37.500 0.00 0.00 35.31 1.90
1504 1515 5.470437 TCAACATTACAACCAGTGCGATTAA 59.530 36.000 0.00 0.00 0.00 1.40
1996 2012 2.291346 GCCCTAAACACCACTAACCCAT 60.291 50.000 0.00 0.00 0.00 4.00
2317 2338 5.146010 TCAGTGCAAAACAAAGGAAAACT 57.854 34.783 0.00 0.00 0.00 2.66
2501 2533 4.044571 TCATTCAAAAGAGGGGGTGAGAAT 59.955 41.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.