Multiple sequence alignment - TraesCS1A01G073900

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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 TraesCS1A01G073900 chr1A 100.000 3407 0 0 1 3407 57633332 57636738 0.000000e+00 6292.0
1 TraesCS1A01G073900 chr1A 96.250 400 9 4 386 779 492637924 492637525 0.000000e+00 651.0
2 TraesCS1A01G073900 chr1A 100.000 45 0 0 343 387 57633717 57633761 2.180000e-12 84.2
3 TraesCS1A01G073900 chr1D 92.577 2142 97 28 770 2890 58756534 58758634 0.000000e+00 3018.0
4 TraesCS1A01G073900 chr1D 91.979 187 12 2 3224 3407 58758955 58759141 3.370000e-65 259.0
5 TraesCS1A01G073900 chr1D 98.148 108 2 0 2890 2997 58758718 58758825 4.490000e-44 189.0
6 TraesCS1A01G073900 chr1D 82.000 150 22 3 3043 3188 460553677 460553825 4.620000e-24 122.0
7 TraesCS1A01G073900 chr1D 81.633 147 20 4 3043 3183 490398807 490398952 7.730000e-22 115.0
8 TraesCS1A01G073900 chr1D 100.000 31 0 0 3185 3215 58758837 58758867 1.320000e-04 58.4
9 TraesCS1A01G073900 chr1B 93.256 1557 62 17 1355 2890 94225897 94227431 0.000000e+00 2254.0
10 TraesCS1A01G073900 chr1B 96.861 223 7 0 3185 3407 94227668 94227890 1.150000e-99 374.0
11 TraesCS1A01G073900 chr1B 90.129 233 14 6 857 1080 94225443 94225675 9.250000e-76 294.0
12 TraesCS1A01G073900 chr1B 93.168 161 11 0 2886 3046 94227511 94227671 1.580000e-58 237.0
13 TraesCS1A01G073900 chr1B 96.809 94 3 0 1245 1338 94225715 94225808 1.270000e-34 158.0
14 TraesCS1A01G073900 chr1B 80.952 147 24 4 3045 3189 642735610 642735466 2.780000e-21 113.0
15 TraesCS1A01G073900 chr1B 97.674 43 1 0 345 387 482340595 482340637 1.310000e-09 75.0
16 TraesCS1A01G073900 chr7A 96.124 387 15 0 1 387 66745314 66744928 1.730000e-177 632.0
17 TraesCS1A01G073900 chr7A 95.652 391 11 2 386 770 66744972 66744582 1.040000e-174 623.0
18 TraesCS1A01G073900 chr7A 90.886 395 32 4 390 781 730302716 730302323 8.370000e-146 527.0
19 TraesCS1A01G073900 chr7A 90.886 395 32 4 390 781 730350700 730350307 8.370000e-146 527.0
20 TraesCS1A01G073900 chr2B 91.885 382 28 3 390 769 546991683 546992063 6.470000e-147 531.0
21 TraesCS1A01G073900 chr2B 88.514 148 15 2 3043 3189 24482653 24482507 9.720000e-41 178.0
22 TraesCS1A01G073900 chr2B 97.674 43 1 0 345 387 278802348 278802306 1.310000e-09 75.0
23 TraesCS1A01G073900 chr2B 97.674 43 1 0 345 387 678958832 678958874 1.310000e-09 75.0
24 TraesCS1A01G073900 chr5A 91.645 383 29 3 390 770 60760808 60761189 8.370000e-146 527.0
25 TraesCS1A01G073900 chr5A 87.608 347 41 2 7 352 130957144 130956799 5.300000e-108 401.0
26 TraesCS1A01G073900 chr7D 92.643 367 22 3 390 752 530044076 530044441 1.080000e-144 523.0
27 TraesCS1A01G073900 chr7D 93.333 330 19 3 390 716 554155456 554155127 5.110000e-133 484.0
28 TraesCS1A01G073900 chr7D 90.294 340 32 1 1 339 471113871 471114210 8.680000e-121 444.0
29 TraesCS1A01G073900 chr7D 89.381 339 34 2 1 337 591230503 591230165 3.140000e-115 425.0
30 TraesCS1A01G073900 chr7D 88.732 142 14 2 3043 3183 30019659 30019799 4.520000e-39 172.0
31 TraesCS1A01G073900 chr7D 79.085 153 28 4 3041 3191 40033463 40033613 6.010000e-18 102.0
32 TraesCS1A01G073900 chr7D 97.561 41 1 0 347 387 530044076 530044116 1.700000e-08 71.3
33 TraesCS1A01G073900 chr5B 90.649 385 29 5 390 770 248667370 248666989 3.920000e-139 505.0
34 TraesCS1A01G073900 chr5B 100.000 41 0 0 347 387 248667370 248667330 3.650000e-10 76.8
35 TraesCS1A01G073900 chr2D 93.255 341 21 1 1 339 8389385 8389725 5.080000e-138 501.0
36 TraesCS1A01G073900 chr2D 82.734 139 21 3 3045 3182 165543257 165543393 1.660000e-23 121.0
37 TraesCS1A01G073900 chr7B 90.616 341 30 2 1 339 692361210 692361550 5.180000e-123 451.0
38 TraesCS1A01G073900 chrUn 90.323 341 31 1 1 339 63532711 63532371 2.410000e-121 446.0
39 TraesCS1A01G073900 chr6D 89.971 339 33 1 2 339 467635598 467635260 1.450000e-118 436.0
40 TraesCS1A01G073900 chr2A 89.181 342 34 2 1 339 763824433 763824092 1.130000e-114 424.0
41 TraesCS1A01G073900 chr2A 97.674 43 1 0 345 387 214714221 214714263 1.310000e-09 75.0
42 TraesCS1A01G073900 chr3D 75.939 852 169 23 1174 2006 578413164 578413998 4.090000e-109 405.0
43 TraesCS1A01G073900 chr3D 89.412 85 8 1 996 1080 578413011 578413094 4.650000e-19 106.0
44 TraesCS1A01G073900 chr3A 79.526 591 103 14 1450 2037 714157211 714156636 4.090000e-109 405.0
45 TraesCS1A01G073900 chr3A 78.771 358 46 18 991 1335 714157753 714157413 2.660000e-51 213.0
46 TraesCS1A01G073900 chr3B 78.863 563 96 17 1450 2007 772401202 772400658 3.230000e-95 359.0
47 TraesCS1A01G073900 chr3B 79.114 158 27 5 3041 3196 768263605 768263452 1.670000e-18 104.0
48 TraesCS1A01G073900 chr6A 87.821 156 11 3 3038 3185 571690914 571691069 3.490000e-40 176.0


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 TraesCS1A01G073900 chr1A 57633332 57636738 3406 False 3188.1 6292 100.0000 1 3407 2 chr1A.!!$F1 3406
1 TraesCS1A01G073900 chr1D 58756534 58759141 2607 False 881.1 3018 95.6760 770 3407 4 chr1D.!!$F3 2637
2 TraesCS1A01G073900 chr1B 94225443 94227890 2447 False 663.4 2254 94.0446 857 3407 5 chr1B.!!$F2 2550
3 TraesCS1A01G073900 chr7A 66744582 66745314 732 True 627.5 632 95.8880 1 770 2 chr7A.!!$R3 769
4 TraesCS1A01G073900 chr3D 578413011 578413998 987 False 255.5 405 82.6755 996 2006 2 chr3D.!!$F1 1010
5 TraesCS1A01G073900 chr3A 714156636 714157753 1117 True 309.0 405 79.1485 991 2037 2 chr3A.!!$R1 1046
6 TraesCS1A01G073900 chr3B 772400658 772401202 544 True 359.0 359 78.8630 1450 2007 1 chr3B.!!$R2 557


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
694 695 0.030705 CATGGGAGGAGGAGAGGGAA 60.031 60.0 0.0 0.0 0.0 3.97 F
701 702 0.043485 GGAGGAGAGGGAAGGGTCTT 59.957 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 2825 0.251354 GGAAGGTTCGGTAGTTCCCC 59.749 60.0 0.0 0.0 33.6 4.81 R
2442 2921 0.538057 ACACATGGCAGTCTTGGTGG 60.538 55.0 0.0 0.0 0.0 4.61 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)



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AutoCloner maintained by Alex Coulton.