Multiple sequence alignment - TraesCS2D01G244300

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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 TraesCS2D01G244300 chr2D 100.000 3511 0 0 1 3511 273055742 273059252 0.000000e+00 6484
1 TraesCS2D01G244300 chr2D 93.333 3525 173 27 1 3511 184179401 184175925 0.000000e+00 5151
2 TraesCS2D01G244300 chr7D 94.041 3541 172 20 1 3511 234393523 234397054 0.000000e+00 5334
3 TraesCS2D01G244300 chr7D 90.229 3541 270 40 1 3511 341105399 341108893 0.000000e+00 4553
4 TraesCS2D01G244300 chr7D 93.238 1686 94 10 1 1668 370465172 370463489 0.000000e+00 2464
5 TraesCS2D01G244300 chr7A 93.830 3533 190 14 1 3511 315495815 315492289 0.000000e+00 5291
6 TraesCS2D01G244300 chr7A 92.561 3468 220 23 69 3511 583021591 583025045 0.000000e+00 4940
7 TraesCS2D01G244300 chr1D 93.217 3538 192 22 1 3511 238010214 238013730 0.000000e+00 5160
8 TraesCS2D01G244300 chr1D 90.123 243 14 1 1 233 238009965 238010207 1.220000e-79 307
9 TraesCS2D01G244300 chr1D 89.712 243 15 1 1 233 238010048 238010290 5.700000e-78 302
10 TraesCS2D01G244300 chr1D 88.889 243 17 1 1 233 238010131 238010373 1.230000e-74 291
11 TraesCS2D01G244300 chr3D 92.225 3550 203 24 1 3511 323154446 323157961 0.000000e+00 4959
12 TraesCS2D01G244300 chr3D 96.012 2031 72 5 1488 3511 428373413 428375441 0.000000e+00 3293
13 TraesCS2D01G244300 chr3A 92.353 3531 192 17 1 3510 217243227 217239754 0.000000e+00 4953
14 TraesCS2D01G244300 chr6A 92.003 3539 227 23 1 3511 446428169 446431679 0.000000e+00 4916
15 TraesCS2D01G244300 chr6A 92.211 2465 180 9 1055 3511 175158607 175156147 0.000000e+00 3478
16 TraesCS2D01G244300 chr2A 91.869 3468 230 29 69 3511 378112026 378115466 0.000000e+00 4795
17 TraesCS2D01G244300 chr6D 93.628 2260 107 9 1 2248 186932770 186930536 0.000000e+00 3341
18 TraesCS2D01G244300 chr1A 93.523 1544 96 3 331 1871 379613305 379614847 0.000000e+00 2294
19 TraesCS2D01G244300 chr1A 89.796 245 13 3 1 233 379612404 379612648 1.580000e-78 303
20 TraesCS2D01G244300 chr1A 88.163 245 17 2 1 233 379612321 379612565 7.420000e-72 281
21 TraesCS2D01G244300 chr5D 93.999 1483 85 4 294 1772 205326670 205328152 0.000000e+00 2242
22 TraesCS2D01G244300 chr5D 89.286 196 11 1 1 186 205326112 205326307 1.630000e-58 237
23 TraesCS2D01G244300 chr5D 90.265 113 1 1 1 103 205326195 205326307 4.730000e-29 139


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 TraesCS2D01G244300 chr2D 273055742 273059252 3510 False 6484.000000 6484 100.000000 1 3511 1 chr2D.!!$F1 3510
1 TraesCS2D01G244300 chr2D 184175925 184179401 3476 True 5151.000000 5151 93.333000 1 3511 1 chr2D.!!$R1 3510
2 TraesCS2D01G244300 chr7D 234393523 234397054 3531 False 5334.000000 5334 94.041000 1 3511 1 chr7D.!!$F1 3510
3 TraesCS2D01G244300 chr7D 341105399 341108893 3494 False 4553.000000 4553 90.229000 1 3511 1 chr7D.!!$F2 3510
4 TraesCS2D01G244300 chr7D 370463489 370465172 1683 True 2464.000000 2464 93.238000 1 1668 1 chr7D.!!$R1 1667
5 TraesCS2D01G244300 chr7A 315492289 315495815 3526 True 5291.000000 5291 93.830000 1 3511 1 chr7A.!!$R1 3510
6 TraesCS2D01G244300 chr7A 583021591 583025045 3454 False 4940.000000 4940 92.561000 69 3511 1 chr7A.!!$F1 3442
7 TraesCS2D01G244300 chr1D 238009965 238013730 3765 False 1515.000000 5160 90.485250 1 3511 4 chr1D.!!$F1 3510
8 TraesCS2D01G244300 chr3D 323154446 323157961 3515 False 4959.000000 4959 92.225000 1 3511 1 chr3D.!!$F1 3510
9 TraesCS2D01G244300 chr3D 428373413 428375441 2028 False 3293.000000 3293 96.012000 1488 3511 1 chr3D.!!$F2 2023
10 TraesCS2D01G244300 chr3A 217239754 217243227 3473 True 4953.000000 4953 92.353000 1 3510 1 chr3A.!!$R1 3509
11 TraesCS2D01G244300 chr6A 446428169 446431679 3510 False 4916.000000 4916 92.003000 1 3511 1 chr6A.!!$F1 3510
12 TraesCS2D01G244300 chr6A 175156147 175158607 2460 True 3478.000000 3478 92.211000 1055 3511 1 chr6A.!!$R1 2456
13 TraesCS2D01G244300 chr2A 378112026 378115466 3440 False 4795.000000 4795 91.869000 69 3511 1 chr2A.!!$F1 3442
14 TraesCS2D01G244300 chr6D 186930536 186932770 2234 True 3341.000000 3341 93.628000 1 2248 1 chr6D.!!$R1 2247
15 TraesCS2D01G244300 chr1A 379612321 379614847 2526 False 959.333333 2294 90.494000 1 1871 3 chr1A.!!$F1 1870
16 TraesCS2D01G244300 chr5D 205326112 205328152 2040 False 872.666667 2242 91.183333 1 1772 3 chr5D.!!$F1 1771

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
682 2022 1.066143 AGACGTGCAAGTGGGATAAGG 60.066 52.381 10.87 0.0 0.0 2.69 F
1310 2664 0.165944 CAATTGTGCGTCGAGGAACC 59.834 55.000 13.56 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 3651 2.608090 GCCAAGGAGTCGTAGTATTTGC 59.392 50.000 0.0 0.0 0.00 3.68 R
3138 4562 2.552315 GGAATGCGAACTGAAACTTCCA 59.448 45.455 0.0 0.0 32.73 3.53 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
182 614 8.629158 TCAACTACTAAAATGCAACAAGTTCAT 58.371 29.630 0.00 0.00 0.00 2.57
525 1863 3.560068 ACTAGTTTTGAGCAACAACTCCG 59.440 43.478 11.34 8.52 38.29 4.63
682 2022 1.066143 AGACGTGCAAGTGGGATAAGG 60.066 52.381 10.87 0.00 0.00 2.69
731 2074 5.747197 ACTACTCAGTGTGACAGTAAAAACG 59.253 40.000 0.00 0.00 32.25 3.60
904 2250 1.566231 ACCCCATTGTCTTCCATCTCC 59.434 52.381 0.00 0.00 0.00 3.71
1004 2356 1.078143 GCTGAAGGAAGGCGATGGT 60.078 57.895 0.00 0.00 0.00 3.55
1006 2358 0.250234 CTGAAGGAAGGCGATGGTGA 59.750 55.000 0.00 0.00 0.00 4.02
1107 2459 1.154263 GCGCGAGTACACGAGAACT 60.154 57.895 19.30 0.00 35.31 3.01
1143 2495 0.975556 TCCATGGCAAGGAGACGCTA 60.976 55.000 7.49 0.00 0.00 4.26
1169 2521 0.176680 ATCTGCACTAGCGAACCAGG 59.823 55.000 0.00 0.00 46.23 4.45
1192 2544 2.013483 GCCGACGAGATGATGAGCG 61.013 63.158 0.00 0.00 0.00 5.03
1221 2573 2.033602 AAGGGCGGTGGCTTGTAC 59.966 61.111 0.00 0.00 39.81 2.90
1234 2586 2.355108 GGCTTGTACCTGAGCTTCATCA 60.355 50.000 11.29 0.00 38.89 3.07
1246 2598 1.728971 GCTTCATCAGAGTTGACGTGG 59.271 52.381 0.00 0.00 35.83 4.94
1247 2599 2.610479 GCTTCATCAGAGTTGACGTGGA 60.610 50.000 0.00 0.00 35.83 4.02
1310 2664 0.165944 CAATTGTGCGTCGAGGAACC 59.834 55.000 13.56 0.00 0.00 3.62
1470 2825 3.188460 GTGGATGCACGAGTACATGTTTT 59.812 43.478 2.30 0.00 0.00 2.43
1706 3093 9.822727 TGAAGTGGTATAGGTCATATCTTGATA 57.177 33.333 0.00 0.00 36.54 2.15
1796 3183 9.802039 ACTGGTATAGGTCTTTTATTCAACAAA 57.198 29.630 0.00 0.00 0.00 2.83
1886 3278 2.028748 GGTGAAGCATTTGGTGAAGCAT 60.029 45.455 0.00 0.00 0.00 3.79
1926 3319 9.744468 AAAGAAAAATAACATGGTGTAGTTGAC 57.256 29.630 0.00 0.00 0.00 3.18
2239 3642 1.446907 CAGCGCAAGTGGAAAGATCT 58.553 50.000 11.47 0.00 41.68 2.75
2406 3810 3.751479 ATGCAGGAATAGATGCGTACA 57.249 42.857 0.00 0.00 45.54 2.90
2525 3930 4.142227 GCAGGATGAAGATGCATGAAAGTT 60.142 41.667 2.46 0.00 39.69 2.66
2651 4056 3.383505 AGGGTTTGAACAAGTTTGCCTAC 59.616 43.478 0.00 0.00 0.00 3.18
2796 4204 5.046910 AGTAATGGAGCAACAAAATCACG 57.953 39.130 0.00 0.00 0.00 4.35
2914 4333 9.070149 CGGTAGTACTATCAAACTAAAAGTCAC 57.930 37.037 13.53 0.00 30.32 3.67
3112 4535 4.695396 ACACTTGAACACACGGTACATTA 58.305 39.130 0.00 0.00 0.00 1.90
3184 4608 7.307989 CCCTAAAACAGTGACACACTAAGAATG 60.308 40.741 8.59 0.00 43.43 2.67
3186 4610 7.807977 AAAACAGTGACACACTAAGAATGAT 57.192 32.000 8.59 0.00 43.43 2.45
3375 4803 0.171007 GCATCAACCCACATTGACCG 59.829 55.000 0.00 0.00 41.29 4.79
3380 4808 0.536460 AACCCACATTGACCGGTGAC 60.536 55.000 14.63 0.00 37.18 3.67
3401 4829 6.420008 GTGACGTACTAGATTCAAACAACACT 59.580 38.462 0.00 0.00 0.00 3.55
3402 4830 6.982141 TGACGTACTAGATTCAAACAACACTT 59.018 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 580 6.655062 TGCATTTTAGTAGTTGAACTTGTCG 58.345 36.000 1.97 0.00 0.00 4.35
505 1843 3.799366 TCGGAGTTGTTGCTCAAAACTA 58.201 40.909 8.84 0.00 37.81 2.24
525 1863 4.692228 TCAAAACATTTTTCAGTGCCCTC 58.308 39.130 0.00 0.00 0.00 4.30
561 1900 9.057089 AGTATTGTTTTTCCACTGAAGTCTTAG 57.943 33.333 0.00 0.00 0.00 2.18
682 2022 7.221838 GTCTTGTCAAGCTGTACTTATGATCTC 59.778 40.741 7.78 0.00 36.04 2.75
731 2074 0.605589 ACTAACCGTCCAAGCCAAGC 60.606 55.000 0.00 0.00 0.00 4.01
904 2250 0.798776 GTGGTTCTGTGAATGAGGCG 59.201 55.000 0.00 0.00 0.00 5.52
1004 2356 2.725203 CTTGGCGGACGGTTCCTTCA 62.725 60.000 0.00 0.00 40.23 3.02
1006 2358 2.032071 CTTGGCGGACGGTTCCTT 59.968 61.111 0.00 0.00 40.23 3.36
1027 2379 0.816421 TCCGACGTCTCGCCATGATA 60.816 55.000 14.70 0.00 38.70 2.15
1107 2459 1.008327 TGGAGCTCAACCCCTATGAGA 59.992 52.381 17.19 0.00 45.74 3.27
1143 2495 2.580962 TCGCTAGTGCAGATGATCTCT 58.419 47.619 0.00 0.00 39.64 3.10
1169 2521 1.227380 ATCATCTCGTCGGCCTTGC 60.227 57.895 0.00 0.00 0.00 4.01
1192 2544 1.817099 CGCCCTTCATCCTGAGCAC 60.817 63.158 0.00 0.00 0.00 4.40
1221 2573 3.260740 GTCAACTCTGATGAAGCTCAGG 58.739 50.000 1.28 0.00 42.42 3.86
1234 2586 1.612463 GGTGTACTCCACGTCAACTCT 59.388 52.381 9.12 0.00 45.52 3.24
1242 2594 0.732880 CTTCGCTGGTGTACTCCACG 60.733 60.000 22.07 22.07 45.52 4.94
1246 2598 2.924290 GTTCATCTTCGCTGGTGTACTC 59.076 50.000 0.00 0.00 0.00 2.59
1247 2599 2.353803 GGTTCATCTTCGCTGGTGTACT 60.354 50.000 0.00 0.00 0.00 2.73
1293 2647 1.375523 GGGTTCCTCGACGCACAAT 60.376 57.895 0.00 0.00 33.16 2.71
1470 2825 7.648908 CAGTTTCAGAAATGCATGTAACTTGAA 59.351 33.333 0.00 0.88 35.61 2.69
1706 3093 8.143193 TCAGAAATTAATTTGAGCAACATGTGT 58.857 29.630 17.98 0.00 0.00 3.72
1797 3184 9.651913 TGCTTGATTCAAGTTTAGTTTTCTTTT 57.348 25.926 23.66 0.00 42.77 2.27
2239 3642 4.221262 AGTCGTAGTATTTGCTGGTGGTTA 59.779 41.667 0.00 0.00 0.00 2.85
2248 3651 2.608090 GCCAAGGAGTCGTAGTATTTGC 59.392 50.000 0.00 0.00 0.00 3.68
2298 3702 6.169094 TCTTCTTCTTCATGCCTTTGTAGAG 58.831 40.000 0.00 0.00 0.00 2.43
2406 3810 2.631062 TCTTCCATGACTTGTACGTGGT 59.369 45.455 0.00 0.00 42.85 4.16
2525 3930 2.892334 GCGAGCAACACGAAGGCAA 61.892 57.895 0.00 0.00 0.00 4.52
2651 4056 4.798907 AGCAAACGATGTACTTGATAGACG 59.201 41.667 0.00 0.00 0.00 4.18
3138 4562 2.552315 GGAATGCGAACTGAAACTTCCA 59.448 45.455 0.00 0.00 32.73 3.53
3375 4803 5.693104 TGTTGTTTGAATCTAGTACGTCACC 59.307 40.000 0.00 0.00 0.00 4.02
3451 4888 7.702772 GGTATCATCATAGCACTTACCGAATAG 59.297 40.741 0.00 0.00 33.75 1.73


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

AutoCloner maintained by Alex Coulton.