Multiple sequence alignment - TraesCS1D01G303000

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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 TraesCS1D01G303000 chr1D 100.000 2550 0 0 1 2550 400952156 400949607 0.000000e+00 4710
1 TraesCS1D01G303000 chr1B 94.703 1567 49 10 1000 2550 538155910 538154362 0.000000e+00 2403
2 TraesCS1D01G303000 chr1B 96.301 730 24 3 277 1004 538156705 538155977 0.000000e+00 1195
3 TraesCS1D01G303000 chr1A 92.617 1544 69 16 1029 2550 497182702 497181182 0.000000e+00 2178
4 TraesCS1D01G303000 chr1A 94.493 454 16 4 560 1004 497183474 497183021 0.000000e+00 691
5 TraesCS1D01G303000 chr1A 87.879 330 23 3 238 561 497183953 497183635 3.100000e-99 372
6 TraesCS1D01G303000 chr3D 89.076 238 22 4 3 238 525332485 525332250 2.480000e-75 292
7 TraesCS1D01G303000 chr6B 89.224 232 23 1 3 232 17968076 17967845 3.210000e-74 289
8 TraesCS1D01G303000 chr6B 88.841 233 23 3 3 235 17963952 17963723 1.490000e-72 283
9 TraesCS1D01G303000 chr6B 88.793 232 24 1 3 232 17964777 17964546 1.490000e-72 283
10 TraesCS1D01G303000 chr6B 88.793 232 24 1 3 232 17967251 17967020 1.490000e-72 283
11 TraesCS1D01G303000 chr6B 88.793 232 24 1 3 232 17968901 17968670 1.490000e-72 283
12 TraesCS1D01G303000 chr6B 88.793 232 24 1 3 232 17969726 17969495 1.490000e-72 283
13 TraesCS1D01G303000 chr6B 88.793 232 24 1 3 232 17970291 17970060 1.490000e-72 283
14 TraesCS1D01G303000 chr3B 89.474 228 20 3 3 227 377115347 377115121 4.150000e-73 285


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 TraesCS1D01G303000 chr1D 400949607 400952156 2549 True 4710.000000 4710 100.000000 1 2550 1 chr1D.!!$R1 2549
1 TraesCS1D01G303000 chr1B 538154362 538156705 2343 True 1799.000000 2403 95.502000 277 2550 2 chr1B.!!$R1 2273
2 TraesCS1D01G303000 chr1A 497181182 497183953 2771 True 1080.333333 2178 91.663000 238 2550 3 chr1A.!!$R1 2312
3 TraesCS1D01G303000 chr6B 17963723 17970291 6568 True 283.857143 289 88.861429 3 235 7 chr6B.!!$R1 232

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
179 2395 1.074072 TTGGACGAATGGGTGGTGG 59.926 57.895 0.0 0.0 0.0 4.61 F
1370 5564 0.249398 AGTACCACCGATGTTCTGGC 59.751 55.000 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 5677 0.175989 GGCTTTAGTCAGACGGAGGG 59.824 60.0 0.0 0.0 0.0 4.3 R
2397 7650 2.169832 TTTCGCCCAGAGTTTGAGAG 57.830 50.0 0.0 0.0 0.0 3.2 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
59 2275 5.610235 AAATGTTCATCAAATTTTGCCCG 57.390 34.783 4.19 0.00 0.00 6.13
78 2294 7.266922 TGCCCGTGAATTACCTTATATTTTC 57.733 36.000 0.00 0.00 0.00 2.29
92 2308 9.822185 ACCTTATATTTTCATCAGAAATTTGGC 57.178 29.630 0.00 0.00 42.90 4.52
128 2344 8.990163 AAGTGAAATTGGTTAAGAAGGTAAGA 57.010 30.769 0.00 0.00 0.00 2.10
167 2383 3.328382 TCATACAAGGAAGGTTGGACG 57.672 47.619 0.00 0.00 0.00 4.79
179 2395 1.074072 TTGGACGAATGGGTGGTGG 59.926 57.895 0.00 0.00 0.00 4.61
196 2412 3.640967 TGGTGGAAAGAAAGGTGAAATGG 59.359 43.478 0.00 0.00 0.00 3.16
274 2490 9.790389 ACGAAAAATGTACAACATGTAAAAGAA 57.210 25.926 0.00 0.00 37.97 2.52
382 2782 7.432350 AAAATTAGACTCACTGAAGCTTCTG 57.568 36.000 26.40 26.40 0.00 3.02
397 2797 2.285083 CTTCTGAAACCGTGTGAACCA 58.715 47.619 0.00 0.00 0.00 3.67
419 2819 4.818546 CAGTCCATATAAGCTTCCCACAAG 59.181 45.833 0.00 0.00 0.00 3.16
445 2845 2.439507 CCAGGATGCTACAGTATTGGGT 59.560 50.000 0.00 0.00 31.97 4.51
739 3301 6.432783 TGGTCTTCAAATCGTTCCAACATATT 59.567 34.615 0.00 0.00 0.00 1.28
1001 3807 9.002600 TGCTTATATTGTATCATTGTCCATCAC 57.997 33.333 0.00 0.00 0.00 3.06
1004 3810 5.739752 ATTGTATCATTGTCCATCACACG 57.260 39.130 0.00 0.00 33.41 4.49
1005 3811 2.935849 TGTATCATTGTCCATCACACGC 59.064 45.455 0.00 0.00 33.41 5.34
1006 3812 1.009078 ATCATTGTCCATCACACGCG 58.991 50.000 3.53 3.53 33.41 6.01
1013 5120 2.127646 CATCACACGCGCACACAC 60.128 61.111 5.73 0.00 0.00 3.82
1014 5121 2.587473 ATCACACGCGCACACACA 60.587 55.556 5.73 0.00 0.00 3.72
1255 5449 1.093972 CATGCCGCAGTGAACCATAA 58.906 50.000 0.00 0.00 0.00 1.90
1370 5564 0.249398 AGTACCACCGATGTTCTGGC 59.751 55.000 0.00 0.00 0.00 4.85
1462 5656 1.230281 ACACCCACCCCAGATCCAT 60.230 57.895 0.00 0.00 0.00 3.41
1483 5677 1.407025 GCACCTAAGTTGGTAGAGGCC 60.407 57.143 0.00 0.00 38.45 5.19
1610 6347 6.249260 GCACAAGTGTCTTTATTAGCGATTTG 59.751 38.462 1.79 0.00 0.00 2.32
1706 6443 6.259167 TCGGGTTCCATTATCAAAAGATAACG 59.741 38.462 0.46 0.00 30.81 3.18
1793 6530 1.662876 CGAAAAGTGTCGCCAACCATG 60.663 52.381 0.00 0.00 33.66 3.66
1794 6531 1.336755 GAAAAGTGTCGCCAACCATGT 59.663 47.619 0.00 0.00 0.00 3.21
1798 6543 1.149401 TGTCGCCAACCATGTTCCA 59.851 52.632 0.00 0.00 0.00 3.53
1966 7172 5.587443 TCATGTTCCTTCATCACATCATCAC 59.413 40.000 0.00 0.00 0.00 3.06
1969 7175 4.783560 TCCTTCATCACATCATCACCAT 57.216 40.909 0.00 0.00 0.00 3.55
2119 7334 2.287547 GCTCGTTCACCTTCATTTTGCA 60.288 45.455 0.00 0.00 0.00 4.08
2424 7677 1.549170 ACTCTGGGCGAAAACGATACT 59.451 47.619 0.00 0.00 0.00 2.12
2469 7722 5.850557 TTTGATCATGTTGTCTTTGGTGT 57.149 34.783 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.517770 ACACTATTACGAACAGGTAAATCGC 59.482 40.000 0.00 0.00 40.09 4.58
1 2 6.748658 TCACACTATTACGAACAGGTAAATCG 59.251 38.462 0.00 0.00 42.05 3.34
9 10 6.706055 ACACAATCACACTATTACGAACAG 57.294 37.500 0.00 0.00 0.00 3.16
44 45 5.063312 GGTAATTCACGGGCAAAATTTGATG 59.937 40.000 10.26 2.11 0.00 3.07
50 2266 7.833285 ATATAAGGTAATTCACGGGCAAAAT 57.167 32.000 0.00 0.00 0.00 1.82
138 2354 8.917088 CCAACCTTCCTTGTATGATAATCAATT 58.083 33.333 0.00 0.00 0.00 2.32
160 2376 1.241315 CCACCACCCATTCGTCCAAC 61.241 60.000 0.00 0.00 0.00 3.77
167 2383 2.562738 CCTTTCTTTCCACCACCCATTC 59.437 50.000 0.00 0.00 0.00 2.67
179 2395 4.588951 AGGTTCCCATTTCACCTTTCTTTC 59.411 41.667 0.00 0.00 37.70 2.62
227 2443 7.767745 TCGTACACACACTAATCTCTACTAG 57.232 40.000 0.00 0.00 0.00 2.57
229 2445 7.444629 TTTCGTACACACACTAATCTCTACT 57.555 36.000 0.00 0.00 0.00 2.57
230 2446 8.511465 TTTTTCGTACACACACTAATCTCTAC 57.489 34.615 0.00 0.00 0.00 2.59
231 2447 9.135843 CATTTTTCGTACACACACTAATCTCTA 57.864 33.333 0.00 0.00 0.00 2.43
232 2448 7.656137 ACATTTTTCGTACACACACTAATCTCT 59.344 33.333 0.00 0.00 0.00 3.10
233 2449 7.793902 ACATTTTTCGTACACACACTAATCTC 58.206 34.615 0.00 0.00 0.00 2.75
234 2450 7.724305 ACATTTTTCGTACACACACTAATCT 57.276 32.000 0.00 0.00 0.00 2.40
235 2451 8.489559 TGTACATTTTTCGTACACACACTAATC 58.510 33.333 0.00 0.00 43.19 1.75
236 2452 8.367943 TGTACATTTTTCGTACACACACTAAT 57.632 30.769 0.00 0.00 43.19 1.73
242 2458 6.908284 ACATGTTGTACATTTTTCGTACACAC 59.092 34.615 0.00 5.97 46.61 3.82
357 2757 8.367911 TCAGAAGCTTCAGTGAGTCTAATTTTA 58.632 33.333 27.57 0.00 0.00 1.52
382 2782 0.942252 GGACTGGTTCACACGGTTTC 59.058 55.000 0.00 0.00 0.00 2.78
397 2797 4.687219 GCTTGTGGGAAGCTTATATGGACT 60.687 45.833 0.00 0.00 40.01 3.85
419 2819 0.539051 ACTGTAGCATCCTGGAGTGC 59.461 55.000 17.80 17.80 41.57 4.40
445 2845 1.141019 CGCTCCGCTAACTAGCCAA 59.859 57.895 3.18 0.00 46.34 4.52
503 2903 1.082117 AGAAAACCGCGATGCCTACG 61.082 55.000 8.23 0.00 0.00 3.51
739 3301 5.192722 TCCATCCCACTACCATCAATACAAA 59.807 40.000 0.00 0.00 0.00 2.83
995 3801 3.345011 TGTGTGCGCGTGTGATGG 61.345 61.111 8.43 0.00 0.00 3.51
1001 3807 4.918060 CGTGTGTGTGTGCGCGTG 62.918 66.667 8.43 0.00 34.41 5.34
1004 3810 4.589700 CACCGTGTGTGTGTGCGC 62.590 66.667 0.00 0.00 40.26 6.09
1013 5120 1.581934 TCTTCTTGAAGCACCGTGTG 58.418 50.000 5.56 0.25 36.51 3.82
1014 5121 2.325583 TTCTTCTTGAAGCACCGTGT 57.674 45.000 5.56 0.00 0.00 4.49
1240 5434 1.369625 GTCCTTATGGTTCACTGCGG 58.630 55.000 0.00 0.00 34.23 5.69
1370 5564 7.196331 CCTGGAAAGAAAACTGAAGTGTTAAG 58.804 38.462 0.00 0.00 0.00 1.85
1448 5642 1.454479 GTGCATGGATCTGGGGTGG 60.454 63.158 0.00 0.00 0.00 4.61
1462 5656 1.278127 GCCTCTACCAACTTAGGTGCA 59.722 52.381 0.00 0.00 43.14 4.57
1483 5677 0.175989 GGCTTTAGTCAGACGGAGGG 59.824 60.000 0.00 0.00 0.00 4.30
1579 6316 6.293955 GCTAATAAAGACACTTGTGCCAAAGA 60.294 38.462 0.10 0.00 0.00 2.52
1598 6335 1.508632 GCCCGCTCAAATCGCTAATA 58.491 50.000 0.00 0.00 0.00 0.98
1610 6347 7.661437 TGATATATCATATAAAATGGCCCGCTC 59.339 37.037 11.49 0.00 0.00 5.03
1760 6497 5.513849 CGACACTTTTCGTTTAAGCCTTTTT 59.486 36.000 0.00 0.00 34.16 1.94
1774 6511 1.336755 ACATGGTTGGCGACACTTTTC 59.663 47.619 7.28 0.00 42.67 2.29
1793 6530 9.447040 GTTTCTTACTTCTATTTGTTGTGGAAC 57.553 33.333 0.00 0.00 37.35 3.62
1794 6531 9.403583 AGTTTCTTACTTCTATTTGTTGTGGAA 57.596 29.630 0.00 0.00 31.29 3.53
2067 7279 3.857052 ACATGTGGTGGTTGTATAGACG 58.143 45.455 0.00 0.00 0.00 4.18
2397 7650 2.169832 TTTCGCCCAGAGTTTGAGAG 57.830 50.000 0.00 0.00 0.00 3.20
2469 7722 3.765381 TCTGGCTTTGGAATGTCATTGA 58.235 40.909 1.88 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.