Multiple sequence alignment - TraesCS2D01G042600

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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 TraesCS2D01G042600 chr2D 100.000 3664 0 0 1 3664 15263456 15267119 0.000000e+00 6767
1 TraesCS2D01G042600 chr2D 99.622 3174 12 0 491 3664 15228235 15231408 0.000000e+00 5795
2 TraesCS2D01G042600 chr2D 99.837 2460 4 0 1 2460 15248548 15251007 0.000000e+00 4521
3 TraesCS2D01G042600 chr2D 99.535 1076 5 0 2589 3664 15251569 15252644 0.000000e+00 1960
4 TraesCS2D01G042600 chr2D 94.599 574 23 6 3097 3664 397664556 397663985 0.000000e+00 881
5 TraesCS2D01G042600 chr2D 97.018 503 6 2 1 494 15218058 15218560 0.000000e+00 837
6 TraesCS2D01G042600 chr2D 92.490 253 18 1 2 254 15330252 15330503 9.670000e-96 361
7 TraesCS2D01G042600 chr2D 91.304 253 21 1 2 254 19851237 19850986 9.740000e-91 344
8 TraesCS2D01G042600 chr2D 83.193 357 27 11 280 627 19849952 19849620 2.770000e-76 296
9 TraesCS2D01G042600 chr2D 85.484 186 17 3 280 455 15331572 15331757 6.250000e-43 185
10 TraesCS2D01G042600 chr2D 88.276 145 6 5 617 760 15333464 15333598 2.930000e-36 163
11 TraesCS2D01G042600 chrUn 99.319 3672 17 1 1 3664 266172191 266168520 0.000000e+00 6636
12 TraesCS2D01G042600 chrUn 87.871 2828 179 64 340 3098 16444887 16442155 0.000000e+00 3171
13 TraesCS2D01G042600 chrUn 88.418 2737 177 57 340 3018 233477867 233475213 0.000000e+00 3169
14 TraesCS2D01G042600 chrUn 99.763 1687 4 0 1543 3229 379234394 379232708 0.000000e+00 3094
15 TraesCS2D01G042600 chrUn 99.704 1687 5 0 1543 3229 379211163 379209477 0.000000e+00 3088
16 TraesCS2D01G042600 chrUn 99.442 1076 6 0 2589 3664 344072929 344074004 0.000000e+00 1954
17 TraesCS2D01G042600 chrUn 98.816 1098 5 1 1 1090 375770771 375769674 0.000000e+00 1949
18 TraesCS2D01G042600 chrUn 85.161 1806 125 57 340 2083 366814639 366812915 0.000000e+00 1718
19 TraesCS2D01G042600 chrUn 83.234 334 26 10 291 624 16611322 16611625 2.790000e-71 279
20 TraesCS2D01G042600 chrUn 82.036 334 27 13 291 624 16656939 16657239 1.690000e-63 254
21 TraesCS2D01G042600 chr2A 91.490 3161 137 50 4 3098 17299120 17302214 0.000000e+00 4226
22 TraesCS2D01G042600 chr2A 87.090 1828 125 49 280 2063 20364764 20366524 0.000000e+00 1965
23 TraesCS2D01G042600 chr2A 93.333 255 17 0 2 256 20363456 20363710 9.600000e-101 377
24 TraesCS2D01G042600 chr2B 92.886 2010 82 30 1103 3098 27287690 27289652 0.000000e+00 2863
25 TraesCS2D01G042600 chr2B 94.438 1834 78 13 1103 2925 27355997 27357817 0.000000e+00 2800
26 TraesCS2D01G042600 chr2B 90.704 398 26 7 768 1160 27406651 27407042 1.510000e-143 520
27 TraesCS2D01G042600 chr2B 86.266 466 37 6 2 455 27352811 27353261 7.120000e-132 481
28 TraesCS2D01G042600 chr2B 86.022 465 39 5 2 455 27403830 27404279 3.310000e-130 475
29 TraesCS2D01G042600 chr2B 85.591 465 40 9 2 455 27284498 27284946 2.580000e-126 462
30 TraesCS2D01G042600 chr2B 94.558 147 6 1 2954 3098 27408857 27409003 3.680000e-55 226
31 TraesCS2D01G042600 chr2B 82.569 218 14 13 505 722 27249506 27249699 1.750000e-38 171
32 TraesCS2D01G042600 chr2B 82.569 218 14 13 505 722 27287100 27287293 1.750000e-38 171
33 TraesCS2D01G042600 chr6B 93.296 1939 105 19 1171 3098 549029331 549031255 0.000000e+00 2837
34 TraesCS2D01G042600 chr6D 96.497 571 16 2 3098 3664 215532366 215532936 0.000000e+00 941
35 TraesCS2D01G042600 chr5D 95.752 565 18 4 3104 3664 305195445 305196007 0.000000e+00 905
36 TraesCS2D01G042600 chr7D 95.271 571 24 1 3097 3664 573900406 573900976 0.000000e+00 902
37 TraesCS2D01G042600 chr7D 94.957 575 23 2 3096 3664 102993160 102992586 0.000000e+00 896


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 TraesCS2D01G042600 chr2D 15263456 15267119 3663 False 6767.000000 6767 100.000000 1 3664 1 chr2D.!!$F3 3663
1 TraesCS2D01G042600 chr2D 15228235 15231408 3173 False 5795.000000 5795 99.622000 491 3664 1 chr2D.!!$F2 3173
2 TraesCS2D01G042600 chr2D 15248548 15252644 4096 False 3240.500000 4521 99.686000 1 3664 2 chr2D.!!$F4 3663
3 TraesCS2D01G042600 chr2D 397663985 397664556 571 True 881.000000 881 94.599000 3097 3664 1 chr2D.!!$R1 567
4 TraesCS2D01G042600 chr2D 15218058 15218560 502 False 837.000000 837 97.018000 1 494 1 chr2D.!!$F1 493
5 TraesCS2D01G042600 chr2D 19849620 19851237 1617 True 320.000000 344 87.248500 2 627 2 chr2D.!!$R2 625
6 TraesCS2D01G042600 chr2D 15330252 15333598 3346 False 236.333333 361 88.750000 2 760 3 chr2D.!!$F5 758
7 TraesCS2D01G042600 chrUn 266168520 266172191 3671 True 6636.000000 6636 99.319000 1 3664 1 chrUn.!!$R3 3663
8 TraesCS2D01G042600 chrUn 16442155 16444887 2732 True 3171.000000 3171 87.871000 340 3098 1 chrUn.!!$R1 2758
9 TraesCS2D01G042600 chrUn 233475213 233477867 2654 True 3169.000000 3169 88.418000 340 3018 1 chrUn.!!$R2 2678
10 TraesCS2D01G042600 chrUn 379232708 379234394 1686 True 3094.000000 3094 99.763000 1543 3229 1 chrUn.!!$R7 1686
11 TraesCS2D01G042600 chrUn 379209477 379211163 1686 True 3088.000000 3088 99.704000 1543 3229 1 chrUn.!!$R6 1686
12 TraesCS2D01G042600 chrUn 344072929 344074004 1075 False 1954.000000 1954 99.442000 2589 3664 1 chrUn.!!$F3 1075
13 TraesCS2D01G042600 chrUn 375769674 375770771 1097 True 1949.000000 1949 98.816000 1 1090 1 chrUn.!!$R5 1089
14 TraesCS2D01G042600 chrUn 366812915 366814639 1724 True 1718.000000 1718 85.161000 340 2083 1 chrUn.!!$R4 1743
15 TraesCS2D01G042600 chr2A 17299120 17302214 3094 False 4226.000000 4226 91.490000 4 3098 1 chr2A.!!$F1 3094
16 TraesCS2D01G042600 chr2A 20363456 20366524 3068 False 1171.000000 1965 90.211500 2 2063 2 chr2A.!!$F2 2061
17 TraesCS2D01G042600 chr2B 27352811 27357817 5006 False 1640.500000 2800 90.352000 2 2925 2 chr2B.!!$F3 2923
18 TraesCS2D01G042600 chr2B 27284498 27289652 5154 False 1165.333333 2863 87.015333 2 3098 3 chr2B.!!$F2 3096
19 TraesCS2D01G042600 chr2B 27403830 27409003 5173 False 407.000000 520 90.428000 2 3098 3 chr2B.!!$F4 3096
20 TraesCS2D01G042600 chr6B 549029331 549031255 1924 False 2837.000000 2837 93.296000 1171 3098 1 chr6B.!!$F1 1927
21 TraesCS2D01G042600 chr6D 215532366 215532936 570 False 941.000000 941 96.497000 3098 3664 1 chr6D.!!$F1 566
22 TraesCS2D01G042600 chr5D 305195445 305196007 562 False 905.000000 905 95.752000 3104 3664 1 chr5D.!!$F1 560
23 TraesCS2D01G042600 chr7D 573900406 573900976 570 False 902.000000 902 95.271000 3097 3664 1 chr7D.!!$F1 567
24 TraesCS2D01G042600 chr7D 102992586 102993160 574 True 896.000000 896 94.957000 3096 3664 1 chr7D.!!$R1 568

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
141 143 1.272816 TGTAGGAGAACGTCATGGGGA 60.273 52.381 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3044 8469 4.046286 TCACCAATAAGATGCCCTTTGT 57.954 40.909 0.0 0.0 36.34 2.83 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
141 143 1.272816 TGTAGGAGAACGTCATGGGGA 60.273 52.381 0.0 0.0 0.0 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 143 4.221262 AGCATTCTACACCATTGCAACAAT 59.779 37.500 0.0 0.0 35.79 2.71
203 205 3.955524 ATCGGTCCTCTCTCCTCTAAA 57.044 47.619 0.0 0.0 0.00 1.85
3044 8469 4.046286 TCACCAATAAGATGCCCTTTGT 57.954 40.909 0.0 0.0 36.34 2.83


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

AutoCloner maintained by Alex Coulton.