Multiple sequence alignment - TraesCS6D01G208800

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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 TraesCS6D01G208800 chr6D 100.000 2348 0 0 1 2348 294963163 294965510 0.000000e+00 4337.0
1 TraesCS6D01G208800 chr6D 96.343 793 27 1 706 1498 294624180 294624970 0.000000e+00 1303.0
2 TraesCS6D01G208800 chr6D 91.880 234 16 1 1045 1275 295045214 295045447 8.090000e-85 324.0
3 TraesCS6D01G208800 chr6D 88.511 235 14 7 1269 1498 295046841 295047067 2.970000e-69 272.0
4 TraesCS6D01G208800 chr6D 86.792 106 7 3 843 945 295045065 295045166 6.860000e-21 111.0
5 TraesCS6D01G208800 chr6A 94.810 790 30 2 1532 2311 220718107 220718895 0.000000e+00 1221.0
6 TraesCS6D01G208800 chr6A 91.595 464 21 8 1045 1498 426215545 426215090 1.980000e-175 625.0
7 TraesCS6D01G208800 chr6A 89.583 240 19 2 715 951 426215823 426215587 1.360000e-77 300.0
8 TraesCS6D01G208800 chr6A 79.286 280 40 13 1505 1769 595766457 595766181 1.850000e-41 180.0
9 TraesCS6D01G208800 chr3A 93.077 780 36 5 1581 2348 572948620 572947847 0.000000e+00 1125.0
10 TraesCS6D01G208800 chr3A 92.000 75 3 3 1508 1579 572948741 572948667 4.130000e-18 102.0
11 TraesCS6D01G208800 chr7D 93.671 711 44 1 1 711 341010788 341011497 0.000000e+00 1062.0
12 TraesCS6D01G208800 chr7D 84.547 563 78 8 149 705 589629397 589629956 1.230000e-152 549.0
13 TraesCS6D01G208800 chr7D 75.456 713 148 21 1531 2225 11616873 11616170 2.910000e-84 322.0
14 TraesCS6D01G208800 chrUn 95.525 648 28 1 1 648 228618594 228617948 0.000000e+00 1035.0
15 TraesCS6D01G208800 chr5A 92.754 690 38 4 1508 2186 522603244 522602556 0.000000e+00 987.0
16 TraesCS6D01G208800 chr5A 93.562 233 14 1 475 706 551499391 551499159 1.730000e-91 346.0
17 TraesCS6D01G208800 chr5A 94.196 224 9 2 501 723 688786113 688785893 2.890000e-89 339.0
18 TraesCS6D01G208800 chr6B 89.849 463 27 8 1045 1498 459148272 459148723 5.630000e-161 577.0
19 TraesCS6D01G208800 chr6B 87.854 247 20 4 706 945 459147981 459148224 4.940000e-72 281.0
20 TraesCS6D01G208800 chr6B 79.298 285 42 12 1499 1769 683489258 683489539 1.430000e-42 183.0
21 TraesCS6D01G208800 chr6B 91.429 105 9 0 604 708 619301755 619301859 6.760000e-31 145.0
22 TraesCS6D01G208800 chr1B 83.107 515 76 2 1511 2015 520561256 520561769 2.130000e-125 459.0
23 TraesCS6D01G208800 chr3D 74.156 770 173 21 1530 2290 565803241 565803993 1.760000e-76 296.0
24 TraesCS6D01G208800 chr2A 76.978 417 77 15 1507 1908 721472497 721472085 1.090000e-53 220.0
25 TraesCS6D01G208800 chr2A 80.000 110 13 7 1530 1634 678829680 678829785 3.240000e-09 73.1


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 TraesCS6D01G208800 chr6D 294963163 294965510 2347 False 4337.000000 4337 100.0000 1 2348 1 chr6D.!!$F2 2347
1 TraesCS6D01G208800 chr6D 294624180 294624970 790 False 1303.000000 1303 96.3430 706 1498 1 chr6D.!!$F1 792
2 TraesCS6D01G208800 chr6D 295045065 295047067 2002 False 235.666667 324 89.0610 843 1498 3 chr6D.!!$F3 655
3 TraesCS6D01G208800 chr6A 220718107 220718895 788 False 1221.000000 1221 94.8100 1532 2311 1 chr6A.!!$F1 779
4 TraesCS6D01G208800 chr6A 426215090 426215823 733 True 462.500000 625 90.5890 715 1498 2 chr6A.!!$R2 783
5 TraesCS6D01G208800 chr3A 572947847 572948741 894 True 613.500000 1125 92.5385 1508 2348 2 chr3A.!!$R1 840
6 TraesCS6D01G208800 chr7D 341010788 341011497 709 False 1062.000000 1062 93.6710 1 711 1 chr7D.!!$F1 710
7 TraesCS6D01G208800 chr7D 589629397 589629956 559 False 549.000000 549 84.5470 149 705 1 chr7D.!!$F2 556
8 TraesCS6D01G208800 chr7D 11616170 11616873 703 True 322.000000 322 75.4560 1531 2225 1 chr7D.!!$R1 694
9 TraesCS6D01G208800 chrUn 228617948 228618594 646 True 1035.000000 1035 95.5250 1 648 1 chrUn.!!$R1 647
10 TraesCS6D01G208800 chr5A 522602556 522603244 688 True 987.000000 987 92.7540 1508 2186 1 chr5A.!!$R1 678
11 TraesCS6D01G208800 chr6B 459147981 459148723 742 False 429.000000 577 88.8515 706 1498 2 chr6B.!!$F3 792
12 TraesCS6D01G208800 chr1B 520561256 520561769 513 False 459.000000 459 83.1070 1511 2015 1 chr1B.!!$F1 504
13 TraesCS6D01G208800 chr3D 565803241 565803993 752 False 296.000000 296 74.1560 1530 2290 1 chr3D.!!$F1 760

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
253 255 1.110518 AATGTTGACGGCGGGGTTTT 61.111 50.0 13.24 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 3055 1.191535 ATGACTTGGATCGGTTCGGA 58.808 50.0 0.0 0.0 0.0 4.55 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
99 100 2.029307 GCTAGAATCCCTTCCGGCGT 62.029 60.000 6.01 0.00 31.27 5.68
130 131 1.969923 CAAGCCCAGGTTTCCATTTGA 59.030 47.619 0.00 0.00 0.00 2.69
132 133 2.906568 AGCCCAGGTTTCCATTTGAAT 58.093 42.857 0.00 0.00 31.67 2.57
175 177 2.446848 CGGAGGATCTGCATGGGGT 61.447 63.158 0.00 0.00 32.86 4.95
183 185 2.079170 TCTGCATGGGGTTGTTTCAA 57.921 45.000 0.00 0.00 0.00 2.69
253 255 1.110518 AATGTTGACGGCGGGGTTTT 61.111 50.000 13.24 0.00 0.00 2.43
649 654 6.116126 GGCTCTCTAATTTGCCCGATATTAT 58.884 40.000 0.00 0.00 39.49 1.28
696 701 6.944862 AGACTCTGAATAAAAGGATGCAGTTT 59.055 34.615 0.00 0.00 34.46 2.66
697 702 7.449704 AGACTCTGAATAAAAGGATGCAGTTTT 59.550 33.333 8.69 8.69 34.46 2.43
698 703 7.955918 ACTCTGAATAAAAGGATGCAGTTTTT 58.044 30.769 8.90 9.26 34.46 1.94
699 704 9.077885 ACTCTGAATAAAAGGATGCAGTTTTTA 57.922 29.630 12.38 12.38 34.46 1.52
700 705 9.912634 CTCTGAATAAAAGGATGCAGTTTTTAA 57.087 29.630 13.42 0.00 34.46 1.52
767 773 6.585322 GCGTAATCCGAGTATTAGCAAACTAT 59.415 38.462 0.00 0.00 39.56 2.12
781 787 9.865321 ATTAGCAAACTATTCTTCTACGTAACA 57.135 29.630 0.00 0.00 0.00 2.41
807 813 2.350804 CACGAGGACGACTCTAATTCGA 59.649 50.000 9.49 0.00 44.33 3.71
835 841 1.376683 GCGTTCATACAGCCACCCA 60.377 57.895 0.00 0.00 0.00 4.51
882 894 1.472552 CGACACCACAAAGTCTCACCA 60.473 52.381 0.00 0.00 32.68 4.17
986 998 1.314730 GTGCAAGAACCGGGAAAGAA 58.685 50.000 6.32 0.00 0.00 2.52
1173 1188 2.585153 GGGGAGGCGGAAGAGAAC 59.415 66.667 0.00 0.00 0.00 3.01
1498 2917 6.816140 TGACGTATGCAGATTCTTTATGTGAA 59.184 34.615 0.00 0.00 29.12 3.18
1499 2918 7.495606 TGACGTATGCAGATTCTTTATGTGAAT 59.504 33.333 0.00 0.00 36.91 2.57
1500 2919 8.213518 ACGTATGCAGATTCTTTATGTGAATT 57.786 30.769 0.00 0.00 34.67 2.17
1501 2920 8.677300 ACGTATGCAGATTCTTTATGTGAATTT 58.323 29.630 0.00 0.00 34.67 1.82
1502 2921 9.507280 CGTATGCAGATTCTTTATGTGAATTTT 57.493 29.630 0.00 0.00 34.67 1.82
1590 3055 3.777522 CAACTCAAGGACCTTAGGAGGAT 59.222 47.826 20.27 9.95 46.74 3.24
1749 3246 7.059788 GCATAGACTGATCTATCTATCTCCCA 58.940 42.308 13.40 0.00 44.89 4.37
1783 3280 0.038526 CAACCGCCGTAAGTGAGTCT 60.039 55.000 0.00 0.00 0.00 3.24
1967 3464 4.621274 CGGCTGATCCATTTTGTCCAAATT 60.621 41.667 0.00 0.00 32.24 1.82
2303 3800 5.363939 CACTCCTTCCCTGTATGAAAGATC 58.636 45.833 0.00 0.00 0.00 2.75
2338 3835 1.402787 AACCTCCACACTTTTGCCAG 58.597 50.000 0.00 0.00 0.00 4.85
2340 3837 0.954452 CCTCCACACTTTTGCCAGAC 59.046 55.000 0.00 0.00 0.00 3.51
2341 3838 1.477558 CCTCCACACTTTTGCCAGACT 60.478 52.381 0.00 0.00 0.00 3.24
2342 3839 2.301346 CTCCACACTTTTGCCAGACTT 58.699 47.619 0.00 0.00 0.00 3.01
2343 3840 3.476552 CTCCACACTTTTGCCAGACTTA 58.523 45.455 0.00 0.00 0.00 2.24
2345 3842 5.235850 TCCACACTTTTGCCAGACTTATA 57.764 39.130 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 2.517875 GCATGCCGCTGGGAGATT 60.518 61.111 6.36 0.0 37.77 2.40
132 133 3.800833 ATGCATGCCGCTGGGAGA 61.801 61.111 16.68 0.0 43.06 3.71
175 177 5.975693 AGTTTTCTGGACACTTGAAACAA 57.024 34.783 0.00 0.0 30.66 2.83
183 185 3.118038 TGCCAAGTAGTTTTCTGGACACT 60.118 43.478 0.00 0.0 0.00 3.55
253 255 0.546747 ACCTCTGGTTCCATCCCGAA 60.547 55.000 0.00 0.0 27.29 4.30
284 286 1.003580 CCATGCTTGTCCCTACACACT 59.996 52.381 0.00 0.0 34.61 3.55
672 677 6.749923 AACTGCATCCTTTTATTCAGAGTC 57.250 37.500 0.00 0.0 0.00 3.36
703 708 8.511321 GTTTGACCCAAGTTTTCTTCAATTTTT 58.489 29.630 0.00 0.0 38.17 1.94
704 709 7.148490 CGTTTGACCCAAGTTTTCTTCAATTTT 60.148 33.333 0.00 0.0 38.17 1.82
707 712 5.348164 CGTTTGACCCAAGTTTTCTTCAAT 58.652 37.500 0.00 0.0 38.17 2.57
781 787 0.883814 AGAGTCGTCCTCGTGTCGTT 60.884 55.000 0.41 0.0 45.44 3.85
807 813 2.604914 CTGTATGAACGCGCTGATTTCT 59.395 45.455 5.73 0.0 0.00 2.52
882 894 3.697166 GTGGTCCTCTCTTCTCTTCTCT 58.303 50.000 0.00 0.0 0.00 3.10
986 998 4.021544 GCCTCTTCATGGATCTAACTCGAT 60.022 45.833 0.00 0.0 0.00 3.59
1590 3055 1.191535 ATGACTTGGATCGGTTCGGA 58.808 50.000 0.00 0.0 0.00 4.55
1749 3246 2.095059 GCGGTTGCAATGATTCAGAAGT 60.095 45.455 0.59 0.0 42.15 3.01
1783 3280 6.544197 GTGATCTTCCTATAGCCATCGAGATA 59.456 42.308 0.00 0.0 0.00 1.98
1967 3464 5.001232 GGTTAAGTTGAACACTGATGGCTA 58.999 41.667 0.00 0.0 35.12 3.93
2096 3593 2.235155 TGGGACTAAGCTGAATACGCAA 59.765 45.455 0.00 0.0 0.00 4.85
2303 3800 3.131396 GAGGTTACCAGCCATTGATACG 58.869 50.000 3.51 0.0 0.00 3.06


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

AutoCloner maintained by Alex Coulton.