Multiple sequence alignment - TraesCS1B01G166700

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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 TraesCS1B01G166700 chr1B 100.000 2466 0 0 1 2466 292422143 292424608 0.000000e+00 4554
1 TraesCS1B01G166700 chr1B 98.695 2298 29 1 1 2297 292347817 292350114 0.000000e+00 4076
2 TraesCS1B01G166700 chr1B 90.511 137 9 2 1 133 551150195 551150331 7.010000e-41 178
3 TraesCS1B01G166700 chr4B 93.671 2212 117 9 1 2209 161489392 161487201 0.000000e+00 3288
4 TraesCS1B01G166700 chrUn 94.398 1321 65 5 895 2213 49575978 49574665 0.000000e+00 2021
5 TraesCS1B01G166700 chrUn 95.503 845 35 3 1 844 49576817 49575975 0.000000e+00 1347
6 TraesCS1B01G166700 chrUn 90.741 270 23 1 2199 2466 49574639 49574370 2.330000e-95 359
7 TraesCS1B01G166700 chr5D 95.155 1197 39 6 1 1193 393605260 393604079 0.000000e+00 1871
8 TraesCS1B01G166700 chr5D 89.021 337 35 2 1117 1453 443636424 443636090 1.360000e-112 416
9 TraesCS1B01G166700 chr5D 90.511 137 9 3 1 133 486415055 486415191 7.010000e-41 178
10 TraesCS1B01G166700 chr5A 94.906 746 34 3 1464 2209 503685102 503684361 0.000000e+00 1164
11 TraesCS1B01G166700 chr5A 86.119 353 37 10 2120 2466 503684407 503684061 1.080000e-98 370
12 TraesCS1B01G166700 chr5A 94.241 191 10 1 1 190 503685700 503685510 8.630000e-75 291
13 TraesCS1B01G166700 chr2A 88.927 885 45 20 1612 2466 534603514 534602653 0.000000e+00 1042
14 TraesCS1B01G166700 chr2A 94.482 598 31 1 1612 2209 196078951 196078356 0.000000e+00 920
15 TraesCS1B01G166700 chr2A 93.237 414 18 4 1449 1852 560575104 560575517 3.510000e-168 601
16 TraesCS1B01G166700 chr2A 93.976 249 9 2 2218 2466 196078233 196077991 3.000000e-99 372
17 TraesCS1B01G166700 chr4A 94.147 598 33 1 1612 2209 586019515 586018920 0.000000e+00 909
18 TraesCS1B01G166700 chr4A 95.396 543 23 2 1 542 99778220 99777679 0.000000e+00 863
19 TraesCS1B01G166700 chr4A 90.870 471 40 3 614 1083 730355523 730355991 1.610000e-176 628
20 TraesCS1B01G166700 chr4A 95.582 249 9 1 2218 2466 586018834 586018588 4.940000e-107 398
21 TraesCS1B01G166700 chr2D 93.709 604 29 4 1612 2209 430736025 430736625 0.000000e+00 896
22 TraesCS1B01G166700 chr2D 93.688 602 31 3 1612 2209 651121844 651121246 0.000000e+00 894
23 TraesCS1B01G166700 chr2D 87.042 355 37 6 2117 2466 651121292 651120942 2.300000e-105 392
24 TraesCS1B01G166700 chr6A 93.478 598 37 1 1612 2209 257018307 257017712 0.000000e+00 887
25 TraesCS1B01G166700 chr6A 91.667 624 39 7 1080 1693 92340219 92340839 0.000000e+00 852
26 TraesCS1B01G166700 chr6A 94.366 355 19 1 137 490 92300481 92300835 6.000000e-151 544
27 TraesCS1B01G166700 chr6A 85.434 357 35 10 2120 2466 257017758 257017409 3.020000e-94 355
28 TraesCS1B01G166700 chr3A 94.757 534 26 2 719 1251 555513064 555512532 0.000000e+00 830
29 TraesCS1B01G166700 chr3A 90.977 532 42 4 555 1083 725009775 725009247 0.000000e+00 712
30 TraesCS1B01G166700 chr3A 95.067 223 11 0 1431 1653 555512532 555512310 3.900000e-93 351
31 TraesCS1B01G166700 chr7B 91.466 539 36 5 554 1083 383729231 383729768 0.000000e+00 732
32 TraesCS1B01G166700 chr7B 92.800 375 24 3 1080 1453 383729864 383730236 7.760000e-150 540
33 TraesCS1B01G166700 chr7A 90.520 538 41 5 554 1083 438850802 438851337 0.000000e+00 702
34 TraesCS1B01G166700 chr7A 93.333 375 22 3 1080 1453 438851430 438851802 3.580000e-153 551
35 TraesCS1B01G166700 chr7A 89.744 273 21 3 2200 2465 595396746 595396474 2.350000e-90 342
36 TraesCS1B01G166700 chr7D 89.963 538 44 6 554 1083 388692916 388693451 0.000000e+00 686
37 TraesCS1B01G166700 chr7D 93.333 375 22 3 1080 1453 388693547 388693919 3.580000e-153 551
38 TraesCS1B01G166700 chr5B 87.952 415 31 6 1456 1859 664213612 664213206 2.870000e-129 472
39 TraesCS1B01G166700 chr5B 87.200 375 44 4 1080 1453 540253581 540253210 8.150000e-115 424
40 TraesCS1B01G166700 chr1A 87.589 419 37 6 1456 1859 276114698 276114280 2.870000e-129 472
41 TraesCS1B01G166700 chr3D 91.241 274 20 2 2191 2464 41147763 41148032 1.080000e-98 370
42 TraesCS1B01G166700 chr2B 90.370 135 9 2 1 131 514620584 514620450 9.070000e-40 174


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 TraesCS1B01G166700 chr1B 292422143 292424608 2465 False 4554.000000 4554 100.000000 1 2466 1 chr1B.!!$F2 2465
1 TraesCS1B01G166700 chr1B 292347817 292350114 2297 False 4076.000000 4076 98.695000 1 2297 1 chr1B.!!$F1 2296
2 TraesCS1B01G166700 chr4B 161487201 161489392 2191 True 3288.000000 3288 93.671000 1 2209 1 chr4B.!!$R1 2208
3 TraesCS1B01G166700 chrUn 49574370 49576817 2447 True 1242.333333 2021 93.547333 1 2466 3 chrUn.!!$R1 2465
4 TraesCS1B01G166700 chr5D 393604079 393605260 1181 True 1871.000000 1871 95.155000 1 1193 1 chr5D.!!$R1 1192
5 TraesCS1B01G166700 chr5A 503684061 503685700 1639 True 608.333333 1164 91.755333 1 2466 3 chr5A.!!$R1 2465
6 TraesCS1B01G166700 chr2A 534602653 534603514 861 True 1042.000000 1042 88.927000 1612 2466 1 chr2A.!!$R1 854
7 TraesCS1B01G166700 chr2A 196077991 196078951 960 True 646.000000 920 94.229000 1612 2466 2 chr2A.!!$R2 854
8 TraesCS1B01G166700 chr4A 99777679 99778220 541 True 863.000000 863 95.396000 1 542 1 chr4A.!!$R1 541
9 TraesCS1B01G166700 chr4A 586018588 586019515 927 True 653.500000 909 94.864500 1612 2466 2 chr4A.!!$R2 854
10 TraesCS1B01G166700 chr2D 430736025 430736625 600 False 896.000000 896 93.709000 1612 2209 1 chr2D.!!$F1 597
11 TraesCS1B01G166700 chr2D 651120942 651121844 902 True 643.000000 894 90.365000 1612 2466 2 chr2D.!!$R1 854
12 TraesCS1B01G166700 chr6A 92340219 92340839 620 False 852.000000 852 91.667000 1080 1693 1 chr6A.!!$F2 613
13 TraesCS1B01G166700 chr6A 257017409 257018307 898 True 621.000000 887 89.456000 1612 2466 2 chr6A.!!$R1 854
14 TraesCS1B01G166700 chr3A 725009247 725009775 528 True 712.000000 712 90.977000 555 1083 1 chr3A.!!$R1 528
15 TraesCS1B01G166700 chr3A 555512310 555513064 754 True 590.500000 830 94.912000 719 1653 2 chr3A.!!$R2 934
16 TraesCS1B01G166700 chr7B 383729231 383730236 1005 False 636.000000 732 92.133000 554 1453 2 chr7B.!!$F1 899
17 TraesCS1B01G166700 chr7A 438850802 438851802 1000 False 626.500000 702 91.926500 554 1453 2 chr7A.!!$F1 899
18 TraesCS1B01G166700 chr7D 388692916 388693919 1003 False 618.500000 686 91.648000 554 1453 2 chr7D.!!$F1 899

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
874 891 1.963515 ACAAGGCAGTTCCATTGTTCC 59.036 47.619 0.0 0.0 34.64 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2584 1.410737 CGTAACCCTGTGTCGATGCG 61.411 60.0 0.0 0.0 0.0 4.73 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
354 356 9.787532 CCATGTGGTGTAAAAAGAAATATGTAG 57.212 33.333 0.00 0.00 0.00 2.74
874 891 1.963515 ACAAGGCAGTTCCATTGTTCC 59.036 47.619 0.00 0.00 34.64 3.62
1234 1352 4.141846 GGTTGATGTGGATCTAGCTTCTGA 60.142 45.833 0.00 0.00 31.53 3.27
1931 2333 7.769044 GGTCTGTTAGGAACTGCTTATAATTCA 59.231 37.037 0.38 0.00 41.52 2.57
1932 2334 9.331282 GTCTGTTAGGAACTGCTTATAATTCAT 57.669 33.333 0.38 0.00 41.52 2.57
2048 2452 6.097915 TCTTTTGAGTTCCTAGTAGTGGTG 57.902 41.667 0.00 0.00 0.00 4.17
2172 2584 2.535984 GACGATGATGACGACAACATCC 59.464 50.000 24.22 12.88 46.43 3.51
2197 2609 2.340809 CACAGGGTTACGACGGCA 59.659 61.111 0.00 0.00 0.00 5.69
2292 2849 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
2297 2854 2.743928 TGTGTGTGTGTGTGCGCA 60.744 55.556 5.66 5.66 0.00 6.09
2457 3021 4.647853 AGTAGCGTGGGTGTATCATAGAAA 59.352 41.667 0.00 0.00 0.00 2.52
2460 3024 3.120792 CGTGGGTGTATCATAGAAACGG 58.879 50.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
874 891 1.337260 ACCACTGTTAAGAGCTGCTCG 60.337 52.381 22.77 10.75 35.36 5.03
1234 1352 1.995376 AATCTTTGCTTTCCACCGGT 58.005 45.000 0.00 0.00 0.00 5.28
2172 2584 1.410737 CGTAACCCTGTGTCGATGCG 61.411 60.000 0.00 0.00 0.00 4.73
2197 2609 2.132762 GGTGTTGATGTCGTCTTCGTT 58.867 47.619 0.00 0.00 38.33 3.85
2242 2697 1.426621 GTCTATGTCGTCGGCGTCA 59.573 57.895 12.36 12.36 40.03 4.35
2297 2854 7.494298 TGATGTAGATAATTAACACACGCACAT 59.506 33.333 0.00 0.00 0.00 3.21
2433 2997 2.890808 ATGATACACCCACGCTACTG 57.109 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.