Multiple sequence alignment - TraesCS7A01G062900

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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 TraesCS7A01G062900 chr7A 100.000 2768 0 0 1 2768 31512989 31510222 0.000000e+00 5112.0
1 TraesCS7A01G062900 chr7A 99.673 2751 9 0 1 2751 31549231 31546481 0.000000e+00 5031.0
2 TraesCS7A01G062900 chr7A 99.494 2765 8 3 1 2759 31530791 31528027 0.000000e+00 5024.0
3 TraesCS7A01G062900 chr7A 79.470 151 27 4 2316 2465 31739430 31739577 1.360000e-18 104.0
4 TraesCS7A01G062900 chr7D 96.547 1332 40 2 1360 2685 31055811 31054480 0.000000e+00 2200.0
5 TraesCS7A01G062900 chr7D 86.722 1205 103 27 652 1820 31099397 31098214 0.000000e+00 1286.0
6 TraesCS7A01G062900 chr7D 88.574 1059 114 5 1000 2058 30984559 30983508 0.000000e+00 1279.0
7 TraesCS7A01G062900 chr7D 88.089 1083 114 10 1000 2078 31102029 31100958 0.000000e+00 1271.0
8 TraesCS7A01G062900 chr7D 87.849 716 78 5 989 1700 31070809 31070099 0.000000e+00 832.0
9 TraesCS7A01G062900 chr7D 87.252 353 45 0 989 1341 31056242 31055890 1.190000e-108 403.0
10 TraesCS7A01G062900 chr7D 75.223 674 132 25 1395 2058 31337731 31338379 1.250000e-73 287.0
11 TraesCS7A01G062900 chr7D 75.037 673 135 24 1395 2058 31206251 31206899 5.840000e-72 281.0
12 TraesCS7A01G062900 chr7D 86.885 244 23 4 2333 2568 31063129 31062887 5.880000e-67 265.0
13 TraesCS7A01G062900 chr7D 85.581 215 22 5 558 771 30985000 30984794 1.670000e-52 217.0
14 TraesCS7A01G062900 chr7D 75.786 541 67 30 463 973 31102612 31102106 6.000000e-52 215.0
15 TraesCS7A01G062900 chr7D 81.860 215 28 5 558 771 31092560 31092356 1.320000e-38 171.0
16 TraesCS7A01G062900 chr7D 76.241 282 32 19 688 955 31056574 31056314 1.740000e-22 117.0
17 TraesCS7A01G062900 chrUn 98.836 773 3 3 1993 2759 341131052 341130280 0.000000e+00 1373.0
18 TraesCS7A01G062900 chr4A 88.458 1057 106 9 1000 2055 697432863 697433904 0.000000e+00 1262.0
19 TraesCS7A01G062900 chr4A 88.788 990 100 5 1000 1984 697439302 697440285 0.000000e+00 1203.0
20 TraesCS7A01G062900 chr4A 85.393 267 25 8 2314 2568 697440337 697440601 5.880000e-67 265.0
21 TraesCS7A01G062900 chr4A 89.623 106 10 1 688 792 697499963 697500068 1.730000e-27 134.0
22 TraesCS7A01G062900 chr4A 86.667 90 9 3 327 415 496578307 496578394 2.270000e-16 97.1
23 TraesCS7A01G062900 chr5D 85.066 837 89 21 1220 2053 37207820 37208623 0.000000e+00 821.0
24 TraesCS7A01G062900 chr5D 84.348 575 58 13 631 1178 37207577 37207008 4.060000e-148 534.0
25 TraesCS7A01G062900 chr2A 99.036 415 4 0 1 415 510816809 510817223 0.000000e+00 745.0
26 TraesCS7A01G062900 chr3A 99.031 413 4 0 1 413 39235922 39235510 0.000000e+00 741.0
27 TraesCS7A01G062900 chr3A 95.884 413 9 1 1 413 481864292 481863888 0.000000e+00 662.0
28 TraesCS7A01G062900 chr3A 93.833 227 14 0 2091 2317 137577310 137577084 2.640000e-90 342.0
29 TraesCS7A01G062900 chr3A 86.245 269 34 2 2054 2322 475281056 475281321 3.490000e-74 289.0
30 TraesCS7A01G062900 chr3A 85.294 272 39 1 2047 2317 706867793 706868064 2.100000e-71 279.0
31 TraesCS7A01G062900 chr1A 86.517 267 32 2 2054 2317 434422674 434422939 9.700000e-75 291.0
32 TraesCS7A01G062900 chr3B 86.245 269 32 2 2050 2317 97755878 97756142 1.250000e-73 287.0
33 TraesCS7A01G062900 chr3B 91.503 153 11 1 24 176 735541710 735541560 2.790000e-50 209.0
34 TraesCS7A01G062900 chr3B 89.773 88 9 0 325 412 299563140 299563227 2.250000e-21 113.0
35 TraesCS7A01G062900 chr2D 80.235 425 42 24 23 413 336434777 336434361 5.840000e-72 281.0
36 TraesCS7A01G062900 chr3D 86.235 247 21 10 176 413 204745499 204745257 3.540000e-64 255.0
37 TraesCS7A01G062900 chr3D 93.478 138 7 1 23 160 204751102 204750967 1.300000e-48 204.0
38 TraesCS7A01G062900 chr2B 85.425 247 25 8 176 414 3604666 3604909 2.130000e-61 246.0
39 TraesCS7A01G062900 chr2B 92.810 153 9 1 24 176 3604482 3604632 1.290000e-53 220.0


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 TraesCS7A01G062900 chr7A 31510222 31512989 2767 True 5112.000000 5112 100.000000 1 2768 1 chr7A.!!$R1 2767
1 TraesCS7A01G062900 chr7A 31546481 31549231 2750 True 5031.000000 5031 99.673000 1 2751 1 chr7A.!!$R3 2750
2 TraesCS7A01G062900 chr7A 31528027 31530791 2764 True 5024.000000 5024 99.494000 1 2759 1 chr7A.!!$R2 2758
3 TraesCS7A01G062900 chr7D 31098214 31102612 4398 True 924.000000 1286 83.532333 463 2078 3 chr7D.!!$R6 1615
4 TraesCS7A01G062900 chr7D 31054480 31056574 2094 True 906.666667 2200 86.680000 688 2685 3 chr7D.!!$R5 1997
5 TraesCS7A01G062900 chr7D 31070099 31070809 710 True 832.000000 832 87.849000 989 1700 1 chr7D.!!$R2 711
6 TraesCS7A01G062900 chr7D 30983508 30985000 1492 True 748.000000 1279 87.077500 558 2058 2 chr7D.!!$R4 1500
7 TraesCS7A01G062900 chr7D 31337731 31338379 648 False 287.000000 287 75.223000 1395 2058 1 chr7D.!!$F2 663
8 TraesCS7A01G062900 chr7D 31206251 31206899 648 False 281.000000 281 75.037000 1395 2058 1 chr7D.!!$F1 663
9 TraesCS7A01G062900 chrUn 341130280 341131052 772 True 1373.000000 1373 98.836000 1993 2759 1 chrUn.!!$R1 766
10 TraesCS7A01G062900 chr4A 697432863 697433904 1041 False 1262.000000 1262 88.458000 1000 2055 1 chr4A.!!$F2 1055
11 TraesCS7A01G062900 chr4A 697439302 697440601 1299 False 734.000000 1203 87.090500 1000 2568 2 chr4A.!!$F4 1568
12 TraesCS7A01G062900 chr5D 37207820 37208623 803 False 821.000000 821 85.066000 1220 2053 1 chr5D.!!$F1 833
13 TraesCS7A01G062900 chr5D 37207008 37207577 569 True 534.000000 534 84.348000 631 1178 1 chr5D.!!$R1 547

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
329 330 0.178301 TAGTGAAACCACCGTGCACA 59.822 50.0 18.64 0.0 37.8 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2071 1.003545 CACGGACACTCAAAGCAACAG 60.004 52.381 0.0 0.0 0.0 3.16 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
272 273 2.829206 CGGCGCACAGAACCAAACA 61.829 57.895 10.83 0.00 0.00 2.83
329 330 0.178301 TAGTGAAACCACCGTGCACA 59.822 50.000 18.64 0.00 37.80 4.57
343 344 1.367665 GCACACGTGTCGCTCAAAC 60.368 57.895 25.72 6.01 0.00 2.93
2184 2596 7.859377 CCAAACATGTATCATTAGATTCAGCAC 59.141 37.037 0.00 0.00 35.42 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 0.485099 TGGTGGGGTTGTTTAGGCAT 59.515 50.000 0.0 0.0 0.0 4.40
329 330 1.157870 CCCTTGTTTGAGCGACACGT 61.158 55.000 0.0 0.0 0.0 4.49
1879 2071 1.003545 CACGGACACTCAAAGCAACAG 60.004 52.381 0.0 0.0 0.0 3.16


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

AutoCloner maintained by Alex Coulton.