Multiple sequence alignment - TraesCS6B01G420600

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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 TraesCS6B01G420600 chr6B 100.000 3263 0 0 1 3263 691862848 691866110 0.000000e+00 6026.0
1 TraesCS6B01G420600 chr6B 97.978 3264 48 9 1 3256 692195804 692192551 0.000000e+00 5646.0
2 TraesCS6B01G420600 chr6B 90.285 1719 125 24 576 2280 692488851 692490541 0.000000e+00 2211.0
3 TraesCS6B01G420600 chr6B 90.941 287 22 3 2550 2833 151599592 151599307 1.840000e-102 383.0
4 TraesCS6B01G420600 chr6B 81.364 220 28 6 2505 2721 714633569 714633360 2.010000e-37 167.0
5 TraesCS6B01G420600 chr6D 91.112 2554 153 33 2 2509 455087245 455084720 0.000000e+00 3391.0
6 TraesCS6B01G420600 chr6D 88.746 1786 113 25 569 2280 455311355 455313126 0.000000e+00 2104.0
7 TraesCS6B01G420600 chr6D 91.289 287 21 3 2550 2833 372261928 372261643 3.950000e-104 388.0
8 TraesCS6B01G420600 chr6D 90.909 154 14 0 3106 3259 455084492 455084339 1.190000e-49 207.0
9 TraesCS6B01G420600 chr6A 90.353 2550 154 35 1 2509 601399367 601396869 0.000000e+00 3262.0
10 TraesCS6B01G420600 chr6A 89.708 1749 131 25 569 2282 601967712 601969446 0.000000e+00 2187.0
11 TraesCS6B01G420600 chr6A 87.931 232 24 4 3029 3260 601395662 601395435 1.490000e-68 270.0
12 TraesCS6B01G420600 chr6A 89.189 148 15 1 2852 2999 601395807 601395661 2.000000e-42 183.0
13 TraesCS6B01G420600 chr6A 92.500 40 3 0 2394 2433 601397083 601397044 1.260000e-04 58.4
14 TraesCS6B01G420600 chrUn 100.000 388 0 0 1666 2053 480245409 480245796 0.000000e+00 717.0
15 TraesCS6B01G420600 chr2A 91.608 286 20 3 2550 2832 20010445 20010729 3.050000e-105 392.0
16 TraesCS6B01G420600 chr2A 79.088 373 70 4 2895 3262 765662728 765662359 1.940000e-62 250.0
17 TraesCS6B01G420600 chr7D 90.301 299 26 2 2550 2846 186509544 186509247 3.950000e-104 388.0
18 TraesCS6B01G420600 chr5D 91.259 286 21 3 2550 2832 127068916 127069200 1.420000e-103 387.0
19 TraesCS6B01G420600 chr5D 76.737 331 59 12 2900 3221 227733199 227732878 5.600000e-38 169.0
20 TraesCS6B01G420600 chr5D 84.483 174 22 4 3057 3227 5412543 5412372 2.010000e-37 167.0
21 TraesCS6B01G420600 chr4A 91.549 284 18 5 2550 2830 584933028 584933308 1.420000e-103 387.0
22 TraesCS6B01G420600 chr4A 90.941 287 21 4 2550 2832 61740110 61740395 6.610000e-102 381.0
23 TraesCS6B01G420600 chr2D 91.034 290 21 4 2550 2835 256866319 256866031 1.420000e-103 387.0
24 TraesCS6B01G420600 chr4B 87.387 333 25 10 2506 2833 247896220 247895900 1.850000e-97 366.0
25 TraesCS6B01G420600 chr1B 86.333 300 26 7 2499 2794 415684231 415683943 2.440000e-81 313.0
26 TraesCS6B01G420600 chr7A 79.186 442 76 12 2830 3261 20690865 20691300 3.180000e-75 292.0
27 TraesCS6B01G420600 chr5B 77.701 435 88 5 2832 3260 450111327 450110896 1.160000e-64 257.0
28 TraesCS6B01G420600 chr3D 78.676 272 53 2 2996 3262 449302449 449302720 3.350000e-40 176.0
29 TraesCS6B01G420600 chr5A 82.967 182 22 5 2987 3159 556384391 556384210 4.360000e-34 156.0
30 TraesCS6B01G420600 chr3A 82.069 145 25 1 2891 3035 517992962 517992819 4.420000e-24 122.0
31 TraesCS6B01G420600 chr3A 83.871 124 16 3 176 296 645643092 645643214 7.400000e-22 115.0
32 TraesCS6B01G420600 chr7B 77.723 202 40 5 2836 3034 666536632 666536433 5.720000e-23 119.0
33 TraesCS6B01G420600 chr1D 76.699 206 41 5 2829 3030 488137623 488137825 1.240000e-19 108.0
34 TraesCS6B01G420600 chr1D 82.692 104 16 2 2829 2931 478908975 478908873 1.250000e-14 91.6
35 TraesCS6B01G420600 chr2B 83.505 97 16 0 2830 2926 263078899 263078995 1.250000e-14 91.6


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 TraesCS6B01G420600 chr6B 691862848 691866110 3262 False 6026.00 6026 100.00000 1 3263 1 chr6B.!!$F1 3262
1 TraesCS6B01G420600 chr6B 692192551 692195804 3253 True 5646.00 5646 97.97800 1 3256 1 chr6B.!!$R2 3255
2 TraesCS6B01G420600 chr6B 692488851 692490541 1690 False 2211.00 2211 90.28500 576 2280 1 chr6B.!!$F2 1704
3 TraesCS6B01G420600 chr6D 455311355 455313126 1771 False 2104.00 2104 88.74600 569 2280 1 chr6D.!!$F1 1711
4 TraesCS6B01G420600 chr6D 455084339 455087245 2906 True 1799.00 3391 91.01050 2 3259 2 chr6D.!!$R2 3257
5 TraesCS6B01G420600 chr6A 601967712 601969446 1734 False 2187.00 2187 89.70800 569 2282 1 chr6A.!!$F1 1713
6 TraesCS6B01G420600 chr6A 601395435 601399367 3932 True 943.35 3262 89.99325 1 3260 4 chr6A.!!$R1 3259

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
658 688 3.891049 AGAACAGAAAAGACCAAGCACT 58.109 40.909 0.0 0.0 0.0 4.40 F
769 841 4.065214 AGTCAATCCAATCCAACCCAAT 57.935 40.909 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1601 4.093556 GGAATCCAGCGAAAGTTCTAACAG 59.906 45.833 0.0 0.0 0.0 3.16 R
2580 2710 5.099042 TCTCCTCTTAATTACCTTGCCAC 57.901 43.478 0.0 0.0 0.0 5.01 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
217 218 5.459536 AGTCGATGCTATGCTCATAAGAA 57.540 39.130 0.00 0.00 0.00 2.52
487 505 9.715121 CCATTAATTTTATCCATTTGATCAGGG 57.285 33.333 0.00 0.00 34.76 4.45
557 575 4.083271 GCTGGCGAAAATTACTCTTCAACT 60.083 41.667 0.00 0.00 0.00 3.16
657 687 4.096382 TGAAGAACAGAAAAGACCAAGCAC 59.904 41.667 0.00 0.00 0.00 4.40
658 688 3.891049 AGAACAGAAAAGACCAAGCACT 58.109 40.909 0.00 0.00 0.00 4.40
769 841 4.065214 AGTCAATCCAATCCAACCCAAT 57.935 40.909 0.00 0.00 0.00 3.16
1477 1601 1.646189 GTCCAAGTCGGCAGAAGATC 58.354 55.000 0.00 0.00 33.14 2.75
1503 1627 0.323451 AACTTTCGCTGGATTCCCCC 60.323 55.000 0.00 0.00 0.00 5.40
2526 2656 3.078843 GCCCCTCCCAATGCTCCAT 62.079 63.158 0.00 0.00 0.00 3.41
2539 2669 8.448008 TCCCAATGCTCCATCTTATACTAAATT 58.552 33.333 0.00 0.00 0.00 1.82
2609 2741 7.936301 GCAAGGTAATTAAGAGGAGAGATGAAT 59.064 37.037 0.00 0.00 0.00 2.57
2610 2742 9.844257 CAAGGTAATTAAGAGGAGAGATGAATT 57.156 33.333 0.00 0.00 0.00 2.17
2679 2811 4.082125 ACACTTAAATGGAAGAAGCCCAG 58.918 43.478 0.00 0.00 37.08 4.45
2689 2821 0.323999 AGAAGCCCAGCAATGCATGA 60.324 50.000 8.35 0.00 0.00 3.07
3159 4335 2.332654 GCCGGAATTGAAGTGGCGT 61.333 57.895 5.05 0.00 35.77 5.68
3212 4388 1.255667 TGGTGTAGGCGACTTCTCCC 61.256 60.000 12.80 5.54 39.75 4.30
3260 4436 8.190784 GTCCATTGCCCTACATTAATATTATGC 58.809 37.037 0.00 0.00 0.00 3.14
3261 4437 7.066887 TCCATTGCCCTACATTAATATTATGCG 59.933 37.037 0.00 0.00 0.00 4.73
3262 4438 7.148086 CCATTGCCCTACATTAATATTATGCGT 60.148 37.037 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 218 7.645058 AATTTTCACGGATCTCCATGTAAAT 57.355 32.000 4.65 4.65 39.62 1.40
557 575 9.627123 AGTTTAGCCACTGCATTTCTATTATTA 57.373 29.630 0.00 0.00 41.13 0.98
657 687 4.833380 TCCTTCTATTATCGACCCCTTGAG 59.167 45.833 0.00 0.00 0.00 3.02
658 688 4.811498 TCCTTCTATTATCGACCCCTTGA 58.189 43.478 0.00 0.00 0.00 3.02
769 841 1.214923 AGTAAAACGGGTTGGGTTGGA 59.785 47.619 0.00 0.00 0.00 3.53
1477 1601 4.093556 GGAATCCAGCGAAAGTTCTAACAG 59.906 45.833 0.00 0.00 0.00 3.16
2539 2669 6.364701 ACATGGCAGCCTTAGTAAATCATTA 58.635 36.000 14.15 0.00 0.00 1.90
2580 2710 5.099042 TCTCCTCTTAATTACCTTGCCAC 57.901 43.478 0.00 0.00 0.00 5.01
2584 2714 9.844257 AATTCATCTCTCCTCTTAATTACCTTG 57.156 33.333 0.00 0.00 0.00 3.61
2679 2811 7.083858 TGTAACTAAAGTTCTTCATGCATTGC 58.916 34.615 0.00 0.46 39.31 3.56
2838 2970 1.611491 GTTTGAGGATTGGCGTTGGAA 59.389 47.619 0.00 0.00 0.00 3.53
2881 4057 1.489881 GCAAAACACGTACGGACCGT 61.490 55.000 25.14 25.14 44.35 4.83
3159 4335 4.742201 GCGCTCTCTTGGCCGACA 62.742 66.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.