Multiple sequence alignment - TraesCS1B01G192100

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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 TraesCS1B01G192100 chr1B 100.000 4248 0 0 1 4248 343665738 343661491 0.000000e+00 7845.0
1 TraesCS1B01G192100 chr1B 100.000 46 0 0 391 436 576029140 576029095 7.570000e-13 86.1
2 TraesCS1B01G192100 chr1D 93.765 2422 112 17 919 3325 270024014 270021617 0.000000e+00 3600.0
3 TraesCS1B01G192100 chr1D 97.401 885 23 0 3364 4248 270021618 270020734 0.000000e+00 1507.0
4 TraesCS1B01G192100 chr1D 86.354 491 46 13 2 482 270024704 270024225 2.260000e-142 516.0
5 TraesCS1B01G192100 chr1D 88.506 261 25 5 47 305 430320475 430320218 1.150000e-80 311.0
6 TraesCS1B01G192100 chr1A 94.395 1784 73 9 819 2584 343621942 343620168 0.000000e+00 2715.0
7 TraesCS1B01G192100 chr1A 96.105 1669 54 7 2581 4248 343619141 343617483 0.000000e+00 2712.0
8 TraesCS1B01G192100 chr1A 90.228 307 20 7 473 775 525024586 525024886 3.980000e-105 392.0
9 TraesCS1B01G192100 chr5D 95.063 790 34 5 2334 3123 325957147 325956363 0.000000e+00 1238.0
10 TraesCS1B01G192100 chr5D 86.447 546 33 9 832 1366 325958850 325959365 1.030000e-155 560.0
11 TraesCS1B01G192100 chr5D 85.821 268 36 2 47 313 520111444 520111710 2.500000e-72 283.0
12 TraesCS1B01G192100 chr7B 93.561 792 40 5 2334 3123 5917895 5917113 0.000000e+00 1170.0
13 TraesCS1B01G192100 chr7B 89.902 307 22 2 475 774 739246388 739246084 1.850000e-103 387.0
14 TraesCS1B01G192100 chr7B 86.590 261 32 3 47 305 104298591 104298332 6.950000e-73 285.0
15 TraesCS1B01G192100 chr7B 91.667 60 3 2 384 442 701637092 701637034 9.790000e-12 82.4
16 TraesCS1B01G192100 chr7B 95.745 47 1 1 389 434 683166851 683166897 1.640000e-09 75.0
17 TraesCS1B01G192100 chr5A 94.861 720 35 2 2404 3123 430641801 430642518 0.000000e+00 1123.0
18 TraesCS1B01G192100 chr5A 95.833 72 3 0 2334 2405 430641463 430641534 2.680000e-22 117.0
19 TraesCS1B01G192100 chr5B 92.484 306 16 2 475 773 124716393 124716698 8.440000e-117 431.0
20 TraesCS1B01G192100 chr5B 85.338 266 37 2 48 312 703850174 703849910 1.500000e-69 274.0
21 TraesCS1B01G192100 chr5B 84.758 269 41 0 41 309 511291327 511291595 1.950000e-68 270.0
22 TraesCS1B01G192100 chr4A 92.459 305 17 1 474 772 10642050 10641746 8.440000e-117 431.0
23 TraesCS1B01G192100 chr4A 90.909 55 4 1 389 442 143238944 143238890 5.890000e-09 73.1
24 TraesCS1B01G192100 chr2B 90.203 296 25 4 478 773 30230368 30230077 2.400000e-102 383.0
25 TraesCS1B01G192100 chr2B 91.071 56 3 2 384 439 30299019 30298966 1.640000e-09 75.0
26 TraesCS1B01G192100 chr6A 89.404 302 27 3 474 772 504938819 504939118 4.010000e-100 375.0
27 TraesCS1B01G192100 chr6A 95.833 48 0 1 390 435 456781875 456781922 4.550000e-10 76.8
28 TraesCS1B01G192100 chrUn 89.527 296 27 2 478 773 178511019 178511310 5.190000e-99 372.0
29 TraesCS1B01G192100 chrUn 88.851 296 29 2 478 773 178494292 178494583 1.120000e-95 361.0
30 TraesCS1B01G192100 chr6B 88.026 309 29 6 476 781 233671702 233671399 4.040000e-95 359.0
31 TraesCS1B01G192100 chr7D 86.364 264 34 2 43 305 515486967 515487229 1.930000e-73 287.0
32 TraesCS1B01G192100 chr7D 100.000 43 0 0 392 434 235530992 235530950 3.520000e-11 80.5
33 TraesCS1B01G192100 chr4D 84.871 271 37 4 49 317 12696149 12695881 1.950000e-68 270.0
34 TraesCS1B01G192100 chr3A 84.871 271 38 3 47 315 134257424 134257693 1.950000e-68 270.0
35 TraesCS1B01G192100 chr2A 97.778 45 0 1 391 434 43462451 43462495 4.550000e-10 76.8
36 TraesCS1B01G192100 chr4B 95.745 47 1 1 391 436 591486555 591486601 1.640000e-09 75.0


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 TraesCS1B01G192100 chr1B 343661491 343665738 4247 True 7845.000000 7845 100.000000 1 4248 1 chr1B.!!$R1 4247
1 TraesCS1B01G192100 chr1D 270020734 270024704 3970 True 1874.333333 3600 92.506667 2 4248 3 chr1D.!!$R2 4246
2 TraesCS1B01G192100 chr1A 343617483 343621942 4459 True 2713.500000 2715 95.250000 819 4248 2 chr1A.!!$R1 3429
3 TraesCS1B01G192100 chr5D 325956363 325957147 784 True 1238.000000 1238 95.063000 2334 3123 1 chr5D.!!$R1 789
4 TraesCS1B01G192100 chr5D 325958850 325959365 515 False 560.000000 560 86.447000 832 1366 1 chr5D.!!$F1 534
5 TraesCS1B01G192100 chr7B 5917113 5917895 782 True 1170.000000 1170 93.561000 2334 3123 1 chr7B.!!$R1 789
6 TraesCS1B01G192100 chr5A 430641463 430642518 1055 False 620.000000 1123 95.347000 2334 3123 2 chr5A.!!$F1 789


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
520 528 0.102300 AGCGCTCATATACACGTGCA 59.898 50.0 17.22 2.06 35.49 4.57 F
551 559 0.179250 CTATGAACGCACACACGCAC 60.179 55.0 0.00 0.00 36.19 5.34 F
1393 1535 0.240945 GTCCGAAACCGAGGTAACGA 59.759 55.0 17.60 1.34 46.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2107 0.682209 AGCCATTGTCACCCAGCATC 60.682 55.0 0.0 0.0 0.0 3.91 R
1953 2108 0.968901 CAGCCATTGTCACCCAGCAT 60.969 55.0 0.0 0.0 0.0 3.79 R
3260 4718 0.966920 TCCTTCTCTGACCCGTGTTC 59.033 55.0 0.0 0.0 0.0 3.18 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.