Multiple sequence alignment - TraesCS6B01G312800

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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 TraesCS6B01G312800 chr6B 100.000 2534 0 0 1 2534 560199649 560197116 0.000000e+00 4680.0
1 TraesCS6B01G312800 chr6B 98.665 1723 17 1 816 2532 540590381 540592103 0.000000e+00 3049.0
2 TraesCS6B01G312800 chr6B 97.733 794 6 2 1 794 540589370 540590151 0.000000e+00 1356.0
3 TraesCS6B01G312800 chr6A 91.725 1583 72 24 857 2413 500505009 500506558 0.000000e+00 2143.0
4 TraesCS6B01G312800 chr6A 92.222 810 27 14 1 800 500503961 500504744 0.000000e+00 1114.0
5 TraesCS6B01G312800 chr6A 100.000 53 0 0 816 868 500504942 500504994 5.770000e-17 99.0
6 TraesCS6B01G312800 chr6D 91.522 1557 81 26 816 2344 358976324 358977857 0.000000e+00 2097.0
7 TraesCS6B01G312800 chr6D 94.692 584 24 5 207 784 358975511 358976093 0.000000e+00 900.0
8 TraesCS6B01G312800 chr6D 92.708 96 7 0 2345 2440 358977931 358978026 3.400000e-29 139.0
9 TraesCS6B01G312800 chr6D 97.727 44 1 0 1 44 358975469 358975512 2.700000e-10 76.8
10 TraesCS6B01G312800 chr5A 96.471 85 3 0 2439 2523 366233788 366233872 9.450000e-30 141.0
11 TraesCS6B01G312800 chr3D 94.444 90 4 1 2438 2526 603266359 603266270 1.220000e-28 137.0
12 TraesCS6B01G312800 chr3D 92.473 93 6 1 2435 2526 455100571 455100663 5.690000e-27 132.0
13 TraesCS6B01G312800 chr2D 94.118 85 5 0 2439 2523 170277823 170277739 2.050000e-26 130.0
14 TraesCS6B01G312800 chr1B 93.182 88 6 0 2439 2526 562890134 562890047 2.050000e-26 130.0
15 TraesCS6B01G312800 chr4A 93.103 87 6 0 2438 2524 709209107 709209193 7.360000e-26 128.0
16 TraesCS6B01G312800 chr3A 91.304 92 8 0 2432 2523 690192215 690192306 2.650000e-25 126.0
17 TraesCS6B01G312800 chr3B 89.109 101 9 2 2430 2529 5532114 5532213 9.520000e-25 124.0


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 TraesCS6B01G312800 chr6B 560197116 560199649 2533 True 4680.000000 4680 100.00000 1 2534 1 chr6B.!!$R1 2533
1 TraesCS6B01G312800 chr6B 540589370 540592103 2733 False 2202.500000 3049 98.19900 1 2532 2 chr6B.!!$F1 2531
2 TraesCS6B01G312800 chr6A 500503961 500506558 2597 False 1118.666667 2143 94.64900 1 2413 3 chr6A.!!$F1 2412
3 TraesCS6B01G312800 chr6D 358975469 358978026 2557 False 803.200000 2097 94.16225 1 2440 4 chr6D.!!$F1 2439

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
904 1168 0.038526 GACCACACCACTACTCACGG 60.039 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 2874 6.661805 CCTAAGAGATATACTCCCTCTGTTCC 59.338 46.154 0.0 0.0 45.96 3.62 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
629 635 0.249657 CAGTAGGCGCTCATTCCTCC 60.250 60.000 7.64 0.0 34.02 4.30
767 792 2.267426 GCAACGTCCAAAAGCAAAAGT 58.733 42.857 0.00 0.0 0.00 2.66
794 819 3.357919 GCCAGCAGCACATCACAA 58.642 55.556 0.00 0.0 42.97 3.33
803 840 0.662374 GCACATCACAACACAGCAGC 60.662 55.000 0.00 0.0 0.00 5.25
804 841 0.664224 CACATCACAACACAGCAGCA 59.336 50.000 0.00 0.0 0.00 4.41
806 843 0.664224 CATCACAACACAGCAGCACA 59.336 50.000 0.00 0.0 0.00 4.57
807 844 0.949397 ATCACAACACAGCAGCACAG 59.051 50.000 0.00 0.0 0.00 3.66
808 845 1.298863 CACAACACAGCAGCACAGC 60.299 57.895 0.00 0.0 0.00 4.40
810 847 1.298863 CAACACAGCAGCACAGCAC 60.299 57.895 0.00 0.0 36.85 4.40
811 848 1.750018 AACACAGCAGCACAGCACA 60.750 52.632 0.00 0.0 36.85 4.57
812 849 1.105167 AACACAGCAGCACAGCACAT 61.105 50.000 0.00 0.0 36.85 3.21
814 851 1.228033 ACAGCAGCACAGCACATCA 60.228 52.632 0.00 0.0 36.85 3.07
884 1148 1.341482 TGCCCCGCTCCATCATAAAAA 60.341 47.619 0.00 0.0 0.00 1.94
904 1168 0.038526 GACCACACCACTACTCACGG 60.039 60.000 0.00 0.0 0.00 4.94
948 1212 4.570505 CCATTTCCATTCCCTTCCTTGAGA 60.571 45.833 0.00 0.0 0.00 3.27
957 1222 3.973973 TCCCTTCCTTGAGAAACAGAGAA 59.026 43.478 0.00 0.0 32.88 2.87
1340 1610 2.508439 GATCAAGTTCGCGCCGGA 60.508 61.111 5.05 0.0 0.00 5.14
1604 1888 3.341823 AGAGTGTCTGCTAGGCAATTTG 58.658 45.455 0.00 0.0 38.41 2.32
1708 1992 3.791320 AGTTCCCAGTCACTTCCAGATA 58.209 45.455 0.00 0.0 0.00 1.98
2532 2898 7.235079 TGGAACAGAGGGAGTATATCTCTTAG 58.765 42.308 0.00 0.0 39.60 2.18
2533 2899 6.661805 GGAACAGAGGGAGTATATCTCTTAGG 59.338 46.154 0.00 0.0 39.60 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
520 526 3.118884 TGACATCTTAGGCGTAGGGTTTC 60.119 47.826 0.00 0.00 0.00 2.78
767 792 1.220206 GCTGCTGGCTTGCTCTCTA 59.780 57.895 0.00 0.00 38.06 2.43
789 814 1.717791 GCTGTGCTGCTGTGTTGTGA 61.718 55.000 0.00 0.00 0.00 3.58
794 819 1.512996 GATGTGCTGTGCTGCTGTGT 61.513 55.000 0.00 0.00 0.00 3.72
803 840 2.104859 CCCTCGCTGATGTGCTGTG 61.105 63.158 0.00 0.00 0.00 3.66
804 841 2.267006 CCCTCGCTGATGTGCTGT 59.733 61.111 0.00 0.00 0.00 4.40
806 843 4.827087 CGCCCTCGCTGATGTGCT 62.827 66.667 0.00 0.00 0.00 4.40
807 844 4.819761 TCGCCCTCGCTGATGTGC 62.820 66.667 0.00 0.00 35.26 4.57
808 845 1.298157 TTTTCGCCCTCGCTGATGTG 61.298 55.000 0.00 0.00 35.26 3.21
810 847 1.709147 CCTTTTCGCCCTCGCTGATG 61.709 60.000 0.00 0.00 35.26 3.07
811 848 1.450312 CCTTTTCGCCCTCGCTGAT 60.450 57.895 0.00 0.00 35.26 2.90
812 849 2.047274 CCTTTTCGCCCTCGCTGA 60.047 61.111 0.00 0.00 35.26 4.26
814 851 0.322546 AATTCCTTTTCGCCCTCGCT 60.323 50.000 0.00 0.00 35.26 4.93
884 1148 0.959553 CGTGAGTAGTGGTGTGGTCT 59.040 55.000 0.00 0.00 0.00 3.85
957 1222 3.476552 CCTCTCAGCTCTCGAGAACTAT 58.523 50.000 17.59 0.51 38.99 2.12
1375 1645 2.281761 CTGGCGCCCTCTGTTGTT 60.282 61.111 26.77 0.00 0.00 2.83
1425 1701 0.664761 CGGCGTACTCCTTCGGAATA 59.335 55.000 0.00 0.00 0.00 1.75
1428 1704 3.136123 CCGGCGTACTCCTTCGGA 61.136 66.667 6.01 0.00 42.94 4.55
1604 1888 2.641305 GATGGATCATGGATGCCTAGC 58.359 52.381 0.00 0.00 29.18 3.42
2508 2874 6.661805 CCTAAGAGATATACTCCCTCTGTTCC 59.338 46.154 0.00 0.00 45.96 3.62


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

AutoCloner maintained by Alex Coulton.