Multiple sequence alignment - TraesCS4A01G406700

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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 TraesCS4A01G406700 chr4A 100.000 3953 0 0 1 3953 679659897 679655945 0.000000e+00 7300
1 TraesCS4A01G406700 chr6A 98.384 3961 50 6 4 3953 517540469 517536512 0.000000e+00 6948
2 TraesCS4A01G406700 chr5A 98.384 3961 48 7 4 3953 427854229 427850274 0.000000e+00 6946
3 TraesCS4A01G406700 chr5A 93.666 1926 82 6 339 2252 554988124 554986227 0.000000e+00 2844
4 TraesCS4A01G406700 chr5A 97.953 342 7 0 1 342 65997440 65997781 9.460000e-166 593
5 TraesCS4A01G406700 chr7D 97.293 2955 67 5 25 2968 83434474 83437426 0.000000e+00 5001
6 TraesCS4A01G406700 chr7D 96.954 2955 75 6 25 2968 292322600 292325550 0.000000e+00 4944
7 TraesCS4A01G406700 chr7D 95.332 964 28 2 2990 3953 83451118 83452064 0.000000e+00 1515
8 TraesCS4A01G406700 chr7D 94.819 965 31 4 2990 3953 292339363 292340309 0.000000e+00 1487
9 TraesCS4A01G406700 chr7D 94.069 843 33 4 2997 3839 86840439 86841264 0.000000e+00 1264
10 TraesCS4A01G406700 chrUn 97.124 2956 71 6 25 2968 19136336 19139289 0.000000e+00 4975
11 TraesCS4A01G406700 chrUn 95.228 964 29 2 2990 3953 19153054 19154000 0.000000e+00 1509
12 TraesCS4A01G406700 chr2D 97.090 2955 72 6 25 2968 142216011 142218962 0.000000e+00 4968
13 TraesCS4A01G406700 chr2D 94.001 2217 113 9 339 2540 89876608 89874397 0.000000e+00 3339
14 TraesCS4A01G406700 chr2D 94.566 957 35 6 2997 3953 203148265 203149204 0.000000e+00 1463
15 TraesCS4A01G406700 chr4D 97.057 2956 68 9 25 2968 215025786 215022838 0.000000e+00 4959
16 TraesCS4A01G406700 chr2A 94.319 2218 103 9 339 2540 89491533 89489323 0.000000e+00 3376
17 TraesCS4A01G406700 chr1D 94.375 1671 50 10 1316 2968 460574411 460572767 0.000000e+00 2525
18 TraesCS4A01G406700 chr1D 94.710 964 34 2 2990 3953 460559281 460558335 0.000000e+00 1482
19 TraesCS4A01G406700 chr7A 89.162 895 94 3 3061 3953 689301473 689302366 0.000000e+00 1112
20 TraesCS4A01G406700 chr5D 94.816 598 14 2 3356 3953 13284138 13284718 0.000000e+00 917
21 TraesCS4A01G406700 chr3D 95.622 434 17 2 2535 2968 48644531 48644962 0.000000e+00 695
22 TraesCS4A01G406700 chr3D 94.051 353 4 2 3601 3953 46929638 46929303 1.630000e-143 520
23 TraesCS4A01G406700 chr3B 95.280 339 16 0 4 342 17319538 17319876 4.490000e-149 538


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 TraesCS4A01G406700 chr4A 679655945 679659897 3952 True 7300 7300 100.000 1 3953 1 chr4A.!!$R1 3952
1 TraesCS4A01G406700 chr6A 517536512 517540469 3957 True 6948 6948 98.384 4 3953 1 chr6A.!!$R1 3949
2 TraesCS4A01G406700 chr5A 427850274 427854229 3955 True 6946 6946 98.384 4 3953 1 chr5A.!!$R1 3949
3 TraesCS4A01G406700 chr5A 554986227 554988124 1897 True 2844 2844 93.666 339 2252 1 chr5A.!!$R2 1913
4 TraesCS4A01G406700 chr7D 83434474 83437426 2952 False 5001 5001 97.293 25 2968 1 chr7D.!!$F1 2943
5 TraesCS4A01G406700 chr7D 292322600 292325550 2950 False 4944 4944 96.954 25 2968 1 chr7D.!!$F4 2943
6 TraesCS4A01G406700 chr7D 83451118 83452064 946 False 1515 1515 95.332 2990 3953 1 chr7D.!!$F2 963
7 TraesCS4A01G406700 chr7D 292339363 292340309 946 False 1487 1487 94.819 2990 3953 1 chr7D.!!$F5 963
8 TraesCS4A01G406700 chr7D 86840439 86841264 825 False 1264 1264 94.069 2997 3839 1 chr7D.!!$F3 842
9 TraesCS4A01G406700 chrUn 19136336 19139289 2953 False 4975 4975 97.124 25 2968 1 chrUn.!!$F1 2943
10 TraesCS4A01G406700 chrUn 19153054 19154000 946 False 1509 1509 95.228 2990 3953 1 chrUn.!!$F2 963
11 TraesCS4A01G406700 chr2D 142216011 142218962 2951 False 4968 4968 97.090 25 2968 1 chr2D.!!$F1 2943
12 TraesCS4A01G406700 chr2D 89874397 89876608 2211 True 3339 3339 94.001 339 2540 1 chr2D.!!$R1 2201
13 TraesCS4A01G406700 chr2D 203148265 203149204 939 False 1463 1463 94.566 2997 3953 1 chr2D.!!$F2 956
14 TraesCS4A01G406700 chr4D 215022838 215025786 2948 True 4959 4959 97.057 25 2968 1 chr4D.!!$R1 2943
15 TraesCS4A01G406700 chr2A 89489323 89491533 2210 True 3376 3376 94.319 339 2540 1 chr2A.!!$R1 2201
16 TraesCS4A01G406700 chr1D 460572767 460574411 1644 True 2525 2525 94.375 1316 2968 1 chr1D.!!$R2 1652
17 TraesCS4A01G406700 chr1D 460558335 460559281 946 True 1482 1482 94.710 2990 3953 1 chr1D.!!$R1 963
18 TraesCS4A01G406700 chr7A 689301473 689302366 893 False 1112 1112 89.162 3061 3953 1 chr7A.!!$F1 892
19 TraesCS4A01G406700 chr5D 13284138 13284718 580 False 917 917 94.816 3356 3953 1 chr5D.!!$F1 597

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
989 998 0.318699 CGTCAGCGTCTTTCAGTCCA 60.319 55.000 0.0 0.0 0.00 4.02 F
1766 1786 2.169144 AGCAAGCCAAGCTGAAGTTTTT 59.831 40.909 0.0 0.0 41.61 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2121 3.405831 CATCTTCAGAAGCCTGTGAACA 58.594 45.455 5.15 0.0 41.16 3.18 R
3450 3485 0.039165 CTTTGCTTTCTGAACGCCCC 60.039 55.000 15.14 0.0 0.00 5.80 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
165 166 6.350780 GGGAGCAACAAATCTGAATCAAAGAT 60.351 38.462 0.00 0.0 35.89 2.40
361 362 2.500504 GTTAGTTGGTTCTCCCGATCCT 59.499 50.000 0.00 0.0 35.15 3.24
531 532 2.235155 GAGGGGAGAACTCTTCCACTTC 59.765 54.545 6.38 0.0 43.79 3.01
867 876 8.870116 GCCATCAAAAATAAATTCCCTACCTAT 58.130 33.333 0.00 0.0 0.00 2.57
989 998 0.318699 CGTCAGCGTCTTTCAGTCCA 60.319 55.000 0.00 0.0 0.00 4.02
1249 1258 6.647895 GCTGGCAAATATAAGGATGAAATTGG 59.352 38.462 0.00 0.0 0.00 3.16
1766 1786 2.169144 AGCAAGCCAAGCTGAAGTTTTT 59.831 40.909 0.00 0.0 41.61 1.94
2387 2419 3.314693 ACTCCCCTTGACTTCTGTACAA 58.685 45.455 0.00 0.0 0.00 2.41
2463 2498 6.762333 TCTATGTACTGCATCATACAGCAAT 58.238 36.000 10.33 0.0 40.73 3.56
2520 2555 0.524862 GTCCAGATGCTGTGCTTTGG 59.475 55.000 0.00 0.0 0.00 3.28
2567 2602 9.757227 ACTCATTGTATTACTTGCTCTATCTTC 57.243 33.333 0.00 0.0 0.00 2.87
3224 3259 6.183360 GGAGGATATGTTGATTCATTATGCGG 60.183 42.308 0.00 0.0 0.00 5.69
3450 3485 7.716998 ACATTAGTTCCTATTGTAATCCAGCAG 59.283 37.037 0.00 0.0 31.51 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.021396 GGAACCATTCTAATAGAAAACACACAC 58.979 37.037 6.82 0.00 37.82 3.82
2 3 7.942341 AGGAACCATTCTAATAGAAAACACACA 59.058 33.333 6.82 0.00 37.82 3.72
165 166 8.739039 CCATAGAAGATCCACAACAAAACATAA 58.261 33.333 0.00 0.00 0.00 1.90
361 362 4.020218 ACAGACCTGCATTAGAAGCAACTA 60.020 41.667 0.00 0.00 42.17 2.24
531 532 1.467035 GCTGATGAAAAGGCAGAAGCG 60.467 52.381 0.00 0.00 43.41 4.68
867 876 6.551975 TGACTATCCCATTCGTACCATTCTTA 59.448 38.462 0.00 0.00 0.00 2.10
989 998 2.483877 TCAAATTTCATTGCGAGCTCGT 59.516 40.909 34.46 14.96 42.22 4.18
1022 1031 8.035394 CCTCGTTAGATAATAATGTGGCAGTAT 58.965 37.037 0.00 0.00 0.00 2.12
1163 1172 2.136298 TCAGAAGGATGTCTCGCTCT 57.864 50.000 0.00 0.00 0.00 4.09
1249 1258 3.326880 ACCAACCATAGATACCGATTCCC 59.673 47.826 0.00 0.00 0.00 3.97
1402 1420 5.603170 AACAAAGGGATGATTTAGGCATG 57.397 39.130 0.00 0.00 0.00 4.06
1766 1786 3.943671 TTCAGAAGTCCCAACAAAGGA 57.056 42.857 0.00 0.00 0.00 3.36
1854 1874 4.815973 ACCATCGGCAGGCCCCTA 62.816 66.667 0.00 0.00 0.00 3.53
2089 2121 3.405831 CATCTTCAGAAGCCTGTGAACA 58.594 45.455 5.15 0.00 41.16 3.18
2216 2248 9.807921 TTACCTCCTTTCTAATTCTTTGTGAAT 57.192 29.630 0.00 0.00 46.49 2.57
2387 2419 6.048732 ACCACTGGTTTTGAACAGAAAAAT 57.951 33.333 0.00 0.00 38.09 1.82
2443 2478 6.160576 TCTATTGCTGTATGATGCAGTACA 57.839 37.500 12.05 8.52 40.46 2.90
2463 2498 3.873801 GCAAAGTTGGGCAGGAAGATCTA 60.874 47.826 0.00 0.00 0.00 1.98
2520 2555 6.371548 TGAGTATAACAAATTGAGGACAGTGC 59.628 38.462 0.00 0.00 0.00 4.40
2650 2685 5.664294 ATTGCATGAGGACAAAATGCTTA 57.336 34.783 0.00 0.00 45.51 3.09
2751 2786 5.789643 ATTAAGTGTTTCAACATGCCAGT 57.210 34.783 0.00 0.00 41.59 4.00
3450 3485 0.039165 CTTTGCTTTCTGAACGCCCC 60.039 55.000 15.14 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.