Multiple sequence alignment - TraesCS2A01G217100

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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 TraesCS2A01G217100 chr2A 100.000 3396 0 0 1 3396 203788558 203785163 0.000000e+00 6272
1 TraesCS2A01G217100 chr2A 99.735 3396 9 0 1 3396 203847267 203843872 0.000000e+00 6222
2 TraesCS2A01G217100 chr2A 93.610 313 18 2 919 1229 34479654 34479966 1.850000e-127 466
3 TraesCS2A01G217100 chr2A 92.834 307 21 1 922 1227 444413091 444412785 8.650000e-121 444
4 TraesCS2A01G217100 chr2A 99.286 140 1 0 3257 3396 612979244 612979105 1.560000e-63 254
5 TraesCS2A01G217100 chr2A 100.000 136 0 0 3261 3396 203776034 203775899 5.630000e-63 252
6 TraesCS2A01G217100 chr2A 100.000 136 0 0 3261 3396 203856382 203856247 5.630000e-63 252
7 TraesCS2A01G217100 chr2A 91.011 178 8 6 3226 3396 277588483 277588307 2.040000e-57 233
8 TraesCS2A01G217100 chr2A 87.117 163 20 1 2611 2772 734270036 734269874 2.080000e-42 183
9 TraesCS2A01G217100 chrUn 99.903 2066 2 0 1071 3136 356072859 356074924 0.000000e+00 3805
10 TraesCS2A01G217100 chr3A 85.928 1201 127 23 1229 2413 382364623 382365797 0.000000e+00 1243
11 TraesCS2A01G217100 chr3A 94.485 272 12 2 3 271 192822588 192822859 1.890000e-112 416
12 TraesCS2A01G217100 chr3D 87.843 765 74 12 1229 1989 290189132 290189881 0.000000e+00 880
13 TraesCS2A01G217100 chr3D 88.525 427 30 10 1998 2413 290189919 290190337 1.820000e-137 499
14 TraesCS2A01G217100 chr3D 91.640 311 25 1 920 1229 38194647 38194337 2.420000e-116 429
15 TraesCS2A01G217100 chr3D 88.235 238 19 7 2941 3175 38041363 38041594 3.340000e-70 276
16 TraesCS2A01G217100 chr3D 81.272 283 45 6 320 598 43650244 43650522 4.410000e-54 222
17 TraesCS2A01G217100 chr3D 87.821 156 15 3 2940 3092 38146833 38146987 2.690000e-41 180
18 TraesCS2A01G217100 chr4A 93.248 311 20 1 918 1227 463545726 463545416 1.110000e-124 457
19 TraesCS2A01G217100 chr4A 96.283 269 9 1 3 270 607331584 607331316 1.120000e-119 440
20 TraesCS2A01G217100 chr4A 85.542 166 20 4 2610 2771 47740257 47740092 1.620000e-38 171
21 TraesCS2A01G217100 chr6D 96.703 273 7 1 3 273 29755061 29754789 1.440000e-123 453
22 TraesCS2A01G217100 chr5A 96.071 280 4 2 3 277 535244155 535244432 1.860000e-122 449
23 TraesCS2A01G217100 chr5A 92.283 311 23 1 918 1227 6628757 6628447 1.120000e-119 440
24 TraesCS2A01G217100 chr5A 97.917 144 1 2 3254 3396 313626254 313626112 7.280000e-62 248
25 TraesCS2A01G217100 chr5A 98.582 141 1 1 3256 3396 629631959 629632098 7.280000e-62 248
26 TraesCS2A01G217100 chr1A 95.956 272 8 3 1 270 36784825 36784555 4.020000e-119 438
27 TraesCS2A01G217100 chr1A 96.078 153 4 2 3244 3396 552913376 552913526 7.280000e-62 248
28 TraesCS2A01G217100 chr3B 92.182 307 23 1 922 1227 592595914 592595608 1.870000e-117 433
29 TraesCS2A01G217100 chr3B 82.143 224 28 9 2941 3159 580887388 580887172 7.490000e-42 182
30 TraesCS2A01G217100 chr3B 86.585 164 21 1 2611 2773 77702430 77702267 2.690000e-41 180
31 TraesCS2A01G217100 chr2D 95.572 271 10 1 3 271 359387405 359387135 1.870000e-117 433
32 TraesCS2A01G217100 chr2D 93.262 282 17 2 317 598 547687495 547687774 6.780000e-112 414
33 TraesCS2A01G217100 chr1B 91.667 312 24 2 920 1229 622367154 622367465 6.730000e-117 431
34 TraesCS2A01G217100 chr1B 82.632 190 22 9 2938 3120 375389674 375389859 1.260000e-34 158
35 TraesCS2A01G217100 chr6A 95.221 272 10 2 1 270 608260818 608260548 8.710000e-116 427
36 TraesCS2A01G217100 chr6A 100.000 136 0 0 3261 3396 69318847 69318712 5.630000e-63 252
37 TraesCS2A01G217100 chr7D 93.972 282 16 1 317 598 89947530 89947810 3.130000e-115 425
38 TraesCS2A01G217100 chr7D 81.882 287 42 9 320 601 442672045 442671764 2.040000e-57 233
39 TraesCS2A01G217100 chr7D 87.037 162 20 1 2611 2771 511213042 511213203 7.490000e-42 182
40 TraesCS2A01G217100 chr7D 86.076 158 17 2 2938 3092 421362189 421362344 7.540000e-37 165
41 TraesCS2A01G217100 chr1D 94.776 268 13 1 3 270 299555003 299554737 1.890000e-112 416
42 TraesCS2A01G217100 chr1D 82.105 190 23 9 2938 3120 276061057 276061242 5.870000e-33 152
43 TraesCS2A01G217100 chr5B 80.903 288 49 6 320 604 402755497 402755213 4.410000e-54 222
44 TraesCS2A01G217100 chr2B 83.051 236 30 9 367 598 324660193 324660422 4.440000e-49 206
45 TraesCS2A01G217100 chr2B 85.870 184 20 4 2941 3120 14514865 14514684 1.240000e-44 191
46 TraesCS2A01G217100 chr2B 93.478 92 6 0 511 602 64784305 64784214 1.640000e-28 137
47 TraesCS2A01G217100 chr7B 79.787 282 51 6 320 598 50357373 50357095 2.070000e-47 200
48 TraesCS2A01G217100 chr7A 88.272 162 18 1 2611 2771 524701417 524701256 3.460000e-45 193
49 TraesCS2A01G217100 chr4D 85.455 165 20 4 2611 2771 500724662 500724498 5.830000e-38 169
50 TraesCS2A01G217100 chr5D 84.431 167 23 3 2609 2773 315204634 315204799 9.750000e-36 161


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 TraesCS2A01G217100 chr2A 203785163 203788558 3395 True 6272.0 6272 100.000 1 3396 1 chr2A.!!$R2 3395
1 TraesCS2A01G217100 chr2A 203843872 203847267 3395 True 6222.0 6222 99.735 1 3396 1 chr2A.!!$R3 3395
2 TraesCS2A01G217100 chrUn 356072859 356074924 2065 False 3805.0 3805 99.903 1071 3136 1 chrUn.!!$F1 2065
3 TraesCS2A01G217100 chr3A 382364623 382365797 1174 False 1243.0 1243 85.928 1229 2413 1 chr3A.!!$F2 1184
4 TraesCS2A01G217100 chr3D 290189132 290190337 1205 False 689.5 880 88.184 1229 2413 2 chr3D.!!$F4 1184

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
437 438 1.019805 GTAAGTGGCAGCTCGGGAAC 61.02 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 2534 7.708998 TCCTAACAGTTTGGTTGTGATAAAAC 58.291 34.615 12.83 0.0 33.65 2.43 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
437 438 1.019805 GTAAGTGGCAGCTCGGGAAC 61.020 60.000 0.00 0.0 0.00 3.62
943 944 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.0 39.94 3.24
2487 2534 1.072331 AGGTAAATAGGGCTGGCATCG 59.928 52.381 2.88 0.0 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 308 2.229302 CTCTCGTTCGTTCCTCTCCTTT 59.771 50.000 0.00 0.00 0.00 3.11
437 438 4.429788 CCGGAATCAGCGATTTCGTTGG 62.430 54.545 21.88 9.94 46.13 3.77
519 520 7.572523 AATCTGATTCTCAAACAAACAGTCA 57.427 32.000 0.00 0.00 0.00 3.41
2487 2534 7.708998 TCCTAACAGTTTGGTTGTGATAAAAC 58.291 34.615 12.83 0.00 33.65 2.43


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

AutoCloner maintained by Alex Coulton.