Multiple sequence alignment - TraesCS3A01G426900

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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 TraesCS3A01G426900 chr3A 100.000 3266 0 0 1 3266 669987553 669984288 0.000000e+00 6032.0
1 TraesCS3A01G426900 chr3A 99.329 3281 7 1 1 3266 669968701 669971981 0.000000e+00 5923.0
2 TraesCS3A01G426900 chr3A 85.814 1142 152 5 1183 2315 671277414 671278554 0.000000e+00 1203.0
3 TraesCS3A01G426900 chr3A 84.202 1190 175 9 1184 2362 671273571 671274758 0.000000e+00 1144.0
4 TraesCS3A01G426900 chr3A 81.818 572 88 10 1755 2314 671335533 671336100 1.770000e-127 466.0
5 TraesCS3A01G426900 chr3A 96.610 59 2 0 819 877 669969440 669969498 7.460000e-17 99.0
6 TraesCS3A01G426900 chr3A 94.915 59 3 0 740 798 669986735 669986677 3.470000e-15 93.5
7 TraesCS3A01G426900 chr3A 94.915 59 3 0 819 877 669986814 669986756 3.470000e-15 93.5
8 TraesCS3A01G426900 chr3A 93.220 59 4 0 740 798 669969519 669969577 1.610000e-13 87.9
9 TraesCS3A01G426900 chr3A 94.118 51 2 1 916 966 669969261 669969310 3.490000e-10 76.8
10 TraesCS3A01G426900 chr3A 94.118 51 2 1 561 610 669969616 669969666 3.490000e-10 76.8
11 TraesCS3A01G426900 chr3A 94.118 51 2 1 916 966 669986993 669986944 3.490000e-10 76.8
12 TraesCS3A01G426900 chr3D 96.319 2119 41 12 740 2833 534670222 534668116 0.000000e+00 3446.0
13 TraesCS3A01G426900 chr3D 85.071 1132 158 9 1184 2308 535868703 535869830 0.000000e+00 1144.0
14 TraesCS3A01G426900 chr3D 95.265 359 11 1 388 740 534670526 534670168 6.120000e-157 564.0
15 TraesCS3A01G426900 chr3D 88.916 406 9 13 1 372 534674676 534674273 4.930000e-128 468.0
16 TraesCS3A01G426900 chr3D 92.391 276 12 3 2995 3266 534668104 534667834 5.110000e-103 385.0
17 TraesCS3A01G426900 chr3D 90.000 70 7 0 815 884 534670226 534670157 1.250000e-14 91.6
18 TraesCS3A01G426900 chr3D 96.078 51 1 1 561 610 534670047 534669997 7.510000e-12 82.4
19 TraesCS3A01G426900 chr3D 95.652 46 2 0 916 961 534670353 534670308 1.260000e-09 75.0
20 TraesCS3A01G426900 chr3B 95.162 2191 56 14 740 2893 706528829 706526652 0.000000e+00 3413.0
21 TraesCS3A01G426900 chr3B 89.116 1176 119 6 1184 2354 707572382 707573553 0.000000e+00 1454.0
22 TraesCS3A01G426900 chr3B 83.917 1343 170 28 1004 2315 511631011 511632338 0.000000e+00 1242.0
23 TraesCS3A01G426900 chr3B 85.463 1135 150 12 1184 2308 707449748 707450877 0.000000e+00 1168.0
24 TraesCS3A01G426900 chr3B 87.700 1000 116 5 1183 2180 682121800 682120806 0.000000e+00 1158.0
25 TraesCS3A01G426900 chr3B 91.722 749 20 11 31 740 706529520 706528775 0.000000e+00 1002.0
26 TraesCS3A01G426900 chr3B 88.806 402 28 9 744 1139 682122295 682121905 8.200000e-131 477.0
27 TraesCS3A01G426900 chr3B 81.967 610 55 27 155 737 682122829 682122248 1.770000e-127 466.0
28 TraesCS3A01G426900 chr3B 80.656 610 31 25 176 740 511630226 511630793 3.050000e-105 392.0
29 TraesCS3A01G426900 chr3B 91.321 265 13 4 3007 3266 706526573 706526314 1.440000e-93 353.0
30 TraesCS3A01G426900 chr3B 88.571 70 8 0 815 884 706528833 706528764 5.810000e-13 86.1
31 TraesCS3A01G426900 chr3B 96.078 51 1 1 561 610 706528654 706528604 7.510000e-12 82.4
32 TraesCS3A01G426900 chr3B 95.652 46 2 0 916 961 706528960 706528915 1.260000e-09 75.0
33 TraesCS3A01G426900 chrUn 82.353 612 39 22 157 740 119082319 119081749 4.930000e-128 468.0
34 TraesCS3A01G426900 chrUn 89.112 349 18 7 815 1156 119081687 119081352 1.810000e-112 416.0
35 TraesCS3A01G426900 chr7A 98.780 164 2 0 2833 2996 311305900 311306063 3.190000e-75 292.0
36 TraesCS3A01G426900 chr7A 96.000 175 7 0 2830 3004 589994047 589994221 5.330000e-73 285.0
37 TraesCS3A01G426900 chr7A 95.954 173 6 1 2832 3003 655447168 655446996 2.480000e-71 279.0
38 TraesCS3A01G426900 chr7A 94.022 184 8 3 2815 2996 70257943 70258125 3.210000e-70 276.0
39 TraesCS3A01G426900 chr7A 87.500 56 4 2 2624 2676 504220487 504220432 9.780000e-06 62.1
40 TraesCS3A01G426900 chr2A 97.661 171 3 1 2826 2996 318127971 318127802 3.190000e-75 292.0
41 TraesCS3A01G426900 chr2A 97.633 169 4 0 2832 3000 705543009 705543177 1.150000e-74 291.0
42 TraesCS3A01G426900 chr2A 96.067 178 6 1 2833 3010 715386197 715386373 4.120000e-74 289.0
43 TraesCS3A01G426900 chr6A 95.506 178 8 0 2827 3004 469845228 469845405 5.330000e-73 285.0
44 TraesCS3A01G426900 chr1D 90.741 54 5 0 2608 2661 484242374 484242427 4.520000e-09 73.1
45 TraesCS3A01G426900 chr1D 92.000 50 4 0 2612 2661 249030320 249030369 1.630000e-08 71.3
46 TraesCS3A01G426900 chr1D 90.000 50 5 0 2612 2661 372835755 372835804 7.560000e-07 65.8
47 TraesCS3A01G426900 chr1A 100.000 38 0 0 2624 2661 298603676 298603639 1.630000e-08 71.3
48 TraesCS3A01G426900 chr1B 90.385 52 5 0 3000 3051 368590065 368590116 5.850000e-08 69.4
49 TraesCS3A01G426900 chr5A 86.885 61 5 2 2618 2676 37058304 37058245 7.560000e-07 65.8


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 TraesCS3A01G426900 chr3A 669984288 669987553 3265 True 1573.950000 6032 95.987000 1 3266 4 chr3A.!!$R1 3265
1 TraesCS3A01G426900 chr3A 669968701 669971981 3280 False 1252.700000 5923 95.479000 1 3266 5 chr3A.!!$F2 3265
2 TraesCS3A01G426900 chr3A 671273571 671278554 4983 False 1173.500000 1203 85.008000 1183 2362 2 chr3A.!!$F3 1179
3 TraesCS3A01G426900 chr3A 671335533 671336100 567 False 466.000000 466 81.818000 1755 2314 1 chr3A.!!$F1 559
4 TraesCS3A01G426900 chr3D 535868703 535869830 1127 False 1144.000000 1144 85.071000 1184 2308 1 chr3D.!!$F1 1124
5 TraesCS3A01G426900 chr3D 534667834 534674676 6842 True 730.285714 3446 93.517286 1 3266 7 chr3D.!!$R1 3265
6 TraesCS3A01G426900 chr3B 707572382 707573553 1171 False 1454.000000 1454 89.116000 1184 2354 1 chr3B.!!$F2 1170
7 TraesCS3A01G426900 chr3B 707449748 707450877 1129 False 1168.000000 1168 85.463000 1184 2308 1 chr3B.!!$F1 1124
8 TraesCS3A01G426900 chr3B 706526314 706529520 3206 True 835.250000 3413 93.084333 31 3266 6 chr3B.!!$R2 3235
9 TraesCS3A01G426900 chr3B 511630226 511632338 2112 False 817.000000 1242 82.286500 176 2315 2 chr3B.!!$F3 2139
10 TraesCS3A01G426900 chr3B 682120806 682122829 2023 True 700.333333 1158 86.157667 155 2180 3 chr3B.!!$R1 2025
11 TraesCS3A01G426900 chrUn 119081352 119082319 967 True 442.000000 468 85.732500 157 1156 2 chrUn.!!$R1 999

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
1489 9332 3.802418 GACCACAACCACGTCCGCT 62.802 63.158 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 10188 6.015688 CACTCAAATGCTAGCAATAATGGGAT 60.016 38.462 23.54 0.0 0.0 3.85 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
1489 9332 3.802418 GACCACAACCACGTCCGCT 62.802 63.158 0.00 0.0 0.00 5.52
2321 10188 6.947158 TGAATGGCTATGCAATATGGACATTA 59.053 34.615 3.47 0.0 0.00 1.90
2386 10256 4.023365 GCTGAAGCTGAATCAACTCTTTGT 60.023 41.667 0.00 0.0 38.21 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1489 9332 2.664851 CGTGAGCGGGTTGAGCAA 60.665 61.111 0.00 0.0 37.01 3.91
2321 10188 6.015688 CACTCAAATGCTAGCAATAATGGGAT 60.016 38.462 23.54 0.0 0.00 3.85
2386 10256 6.952773 ACAGGTACAGAATTTTTAGCACAA 57.047 33.333 0.00 0.0 0.00 3.33


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

AutoCloner maintained by Alex Coulton.