Multiple sequence alignment - TraesCS3D01G277400

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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 TraesCS3D01G277400 chr3D 100.000 2333 0 0 1 2333 384651721 384649389 0.000000e+00 4309
1 TraesCS3D01G277400 chr4D 97.628 2277 45 2 65 2333 507936176 507938451 0.000000e+00 3897
2 TraesCS3D01G277400 chr4D 97.497 2277 48 2 65 2333 507942139 507939864 0.000000e+00 3880
3 TraesCS3D01G277400 chr2D 97.278 2278 52 7 65 2333 36395873 36398149 0.000000e+00 3855
4 TraesCS3D01G277400 chr2D 97.478 2141 44 7 65 2196 36384951 36387090 0.000000e+00 3646
5 TraesCS3D01G277400 chr6B 77.933 358 75 4 1793 2148 523491237 523490882 1.090000e-53 220
6 TraesCS3D01G277400 chr7B 77.654 358 76 4 1793 2148 466271090 466270735 5.050000e-52 215
7 TraesCS3D01G277400 chr4A 77.841 352 74 4 1793 2142 602139207 602139556 5.050000e-52 215
8 TraesCS3D01G277400 chr3B 77.746 355 75 4 1793 2145 821305101 821305453 5.050000e-52 215
9 TraesCS3D01G277400 chr2A 74.088 548 122 18 1793 2331 733916710 733916174 8.450000e-50 207


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 TraesCS3D01G277400 chr3D 384649389 384651721 2332 True 4309 4309 100.000 1 2333 1 chr3D.!!$R1 2332
1 TraesCS3D01G277400 chr4D 507936176 507938451 2275 False 3897 3897 97.628 65 2333 1 chr4D.!!$F1 2268
2 TraesCS3D01G277400 chr4D 507939864 507942139 2275 True 3880 3880 97.497 65 2333 1 chr4D.!!$R1 2268
3 TraesCS3D01G277400 chr2D 36395873 36398149 2276 False 3855 3855 97.278 65 2333 1 chr2D.!!$F2 2268
4 TraesCS3D01G277400 chr2D 36384951 36387090 2139 False 3646 3646 97.478 65 2196 1 chr2D.!!$F1 2131
5 TraesCS3D01G277400 chr2A 733916174 733916710 536 True 207 207 74.088 1793 2331 1 chr2A.!!$R1 538

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
922 924 1.073897 GAGCCTCTGTTTGTGCCCT 59.926 57.895 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1874 3.067833 TGTTGCGAAATCGGTTGATACA 58.932 40.909 4.84 0.0 40.23 2.29 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
27 28 9.798994 AGGAATTATTGTACTGTAGAAACTACG 57.201 33.333 1.28 0.00 0.00 3.51
28 29 9.028185 GGAATTATTGTACTGTAGAAACTACGG 57.972 37.037 13.92 13.92 0.00 4.02
29 30 9.793252 GAATTATTGTACTGTAGAAACTACGGA 57.207 33.333 20.09 3.97 0.00 4.69
30 31 9.578439 AATTATTGTACTGTAGAAACTACGGAC 57.422 33.333 20.09 13.58 0.00 4.79
31 32 6.830873 ATTGTACTGTAGAAACTACGGACT 57.169 37.500 20.09 5.72 0.00 3.85
32 33 6.639632 TTGTACTGTAGAAACTACGGACTT 57.360 37.500 20.09 5.15 0.00 3.01
33 34 6.005583 TGTACTGTAGAAACTACGGACTTG 57.994 41.667 20.09 3.78 0.00 3.16
34 35 5.532406 TGTACTGTAGAAACTACGGACTTGT 59.468 40.000 20.09 4.58 0.00 3.16
35 36 6.710295 TGTACTGTAGAAACTACGGACTTGTA 59.290 38.462 20.09 3.80 0.00 2.41
36 37 6.830873 ACTGTAGAAACTACGGACTTGTAT 57.169 37.500 20.09 0.00 0.00 2.29
37 38 6.618811 ACTGTAGAAACTACGGACTTGTATG 58.381 40.000 20.09 0.00 0.00 2.39
38 39 5.957798 TGTAGAAACTACGGACTTGTATGG 58.042 41.667 0.00 0.00 0.00 2.74
39 40 5.711506 TGTAGAAACTACGGACTTGTATGGA 59.288 40.000 0.00 0.00 0.00 3.41
40 41 5.326200 AGAAACTACGGACTTGTATGGAG 57.674 43.478 0.00 0.00 0.00 3.86
41 42 4.771054 AGAAACTACGGACTTGTATGGAGT 59.229 41.667 0.00 0.00 0.00 3.85
42 43 5.948162 AGAAACTACGGACTTGTATGGAGTA 59.052 40.000 0.00 0.00 0.00 2.59
43 44 5.831702 AACTACGGACTTGTATGGAGTAG 57.168 43.478 0.00 0.00 36.93 2.57
44 45 4.853007 ACTACGGACTTGTATGGAGTAGT 58.147 43.478 0.19 0.19 38.59 2.73
45 46 5.994250 ACTACGGACTTGTATGGAGTAGTA 58.006 41.667 3.87 0.00 40.69 1.82
46 47 6.599445 ACTACGGACTTGTATGGAGTAGTAT 58.401 40.000 3.87 0.00 40.69 2.12
47 48 7.059156 ACTACGGACTTGTATGGAGTAGTATT 58.941 38.462 3.87 0.00 40.69 1.89
48 49 8.213679 ACTACGGACTTGTATGGAGTAGTATTA 58.786 37.037 3.87 0.00 40.69 0.98
49 50 9.228949 CTACGGACTTGTATGGAGTAGTATTAT 57.771 37.037 0.00 0.00 0.00 1.28
51 52 9.750783 ACGGACTTGTATGGAGTAGTATTATAT 57.249 33.333 0.00 0.00 0.00 0.86
345 346 1.314867 GAGACAGGAGGGATGGGGA 59.685 63.158 0.00 0.00 0.00 4.81
664 665 1.544825 CCTCGGTTCTTCCTGCTCCA 61.545 60.000 0.00 0.00 0.00 3.86
704 705 1.439228 GACCGCTCTGCTGATGCTA 59.561 57.895 11.23 0.00 40.48 3.49
782 783 2.542907 CCGGCTTGTTTGTCGCTGT 61.543 57.895 0.00 0.00 33.25 4.40
922 924 1.073897 GAGCCTCTGTTTGTGCCCT 59.926 57.895 0.00 0.00 0.00 5.19
1082 1084 1.068588 GAAGAAAGTGGGGTTTGCCAC 59.931 52.381 0.00 0.00 39.12 5.01
1224 1226 4.083164 CCAGAAAATATCATGCATGCGCTA 60.083 41.667 22.25 12.89 39.64 4.26
1638 1640 2.433838 CGAGGCTGTGCAGGTCTG 60.434 66.667 0.00 0.00 0.00 3.51
1655 1665 5.997746 CAGGTCTGAGATGTTTACCTTTTGA 59.002 40.000 0.00 0.00 38.51 2.69
1742 1752 1.118838 CGGCCTCCTCTCTGAAGAAT 58.881 55.000 0.00 0.00 0.00 2.40
1745 1755 2.705127 GGCCTCCTCTCTGAAGAATGAT 59.295 50.000 0.00 0.00 0.00 2.45
1864 1874 1.076332 GCGAAACATCAACCGTAGCT 58.924 50.000 0.00 0.00 0.00 3.32
2033 2043 2.417339 TTCAGTTCTCACGTCCTTCG 57.583 50.000 0.00 0.00 46.00 3.79
2204 2214 2.509336 CCACGCTGAGCCTTACCG 60.509 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.798994 CGTAGTTTCTACAGTACAATAATTCCT 57.201 33.333 0.00 0.00 0.00 3.36
2 3 9.028185 CCGTAGTTTCTACAGTACAATAATTCC 57.972 37.037 0.00 0.00 0.00 3.01
3 4 9.793252 TCCGTAGTTTCTACAGTACAATAATTC 57.207 33.333 0.00 0.00 0.00 2.17
4 5 9.578439 GTCCGTAGTTTCTACAGTACAATAATT 57.422 33.333 0.00 0.00 0.00 1.40
5 6 8.964772 AGTCCGTAGTTTCTACAGTACAATAAT 58.035 33.333 0.00 0.00 0.00 1.28
6 7 8.340618 AGTCCGTAGTTTCTACAGTACAATAA 57.659 34.615 0.00 0.00 0.00 1.40
7 8 7.928307 AGTCCGTAGTTTCTACAGTACAATA 57.072 36.000 0.00 0.00 0.00 1.90
8 9 6.830873 AGTCCGTAGTTTCTACAGTACAAT 57.169 37.500 0.00 0.00 0.00 2.71
9 10 6.039717 ACAAGTCCGTAGTTTCTACAGTACAA 59.960 38.462 0.00 0.00 0.00 2.41
10 11 5.532406 ACAAGTCCGTAGTTTCTACAGTACA 59.468 40.000 0.00 0.00 0.00 2.90
11 12 6.006759 ACAAGTCCGTAGTTTCTACAGTAC 57.993 41.667 7.53 0.00 0.00 2.73
12 13 7.148188 CCATACAAGTCCGTAGTTTCTACAGTA 60.148 40.741 7.53 0.00 0.00 2.74
13 14 6.349944 CCATACAAGTCCGTAGTTTCTACAGT 60.350 42.308 7.53 0.00 0.00 3.55
14 15 6.034591 CCATACAAGTCCGTAGTTTCTACAG 58.965 44.000 7.53 0.00 0.00 2.74
15 16 5.711506 TCCATACAAGTCCGTAGTTTCTACA 59.288 40.000 7.53 0.00 0.00 2.74
16 17 6.127786 ACTCCATACAAGTCCGTAGTTTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
17 18 5.948162 ACTCCATACAAGTCCGTAGTTTCTA 59.052 40.000 0.00 0.00 0.00 2.10
18 19 4.771054 ACTCCATACAAGTCCGTAGTTTCT 59.229 41.667 0.00 0.00 0.00 2.52
19 20 5.069501 ACTCCATACAAGTCCGTAGTTTC 57.930 43.478 0.00 0.00 0.00 2.78
20 21 5.713861 ACTACTCCATACAAGTCCGTAGTTT 59.286 40.000 0.00 0.00 34.19 2.66
21 22 5.259632 ACTACTCCATACAAGTCCGTAGTT 58.740 41.667 0.00 0.00 34.19 2.24
22 23 4.853007 ACTACTCCATACAAGTCCGTAGT 58.147 43.478 0.00 0.00 33.35 2.73
23 24 7.507733 AATACTACTCCATACAAGTCCGTAG 57.492 40.000 0.00 0.00 0.00 3.51
25 26 9.750783 ATATAATACTACTCCATACAAGTCCGT 57.249 33.333 0.00 0.00 0.00 4.69
52 53 9.310449 GGACTGAAGTCTTCCTTATATATACCA 57.690 37.037 10.12 0.00 44.20 3.25
53 54 9.536510 AGGACTGAAGTCTTCCTTATATATACC 57.463 37.037 10.12 0.00 44.20 2.73
56 57 9.836179 ATCAGGACTGAAGTCTTCCTTATATAT 57.164 33.333 10.12 0.00 43.58 0.86
57 58 9.083422 CATCAGGACTGAAGTCTTCCTTATATA 57.917 37.037 10.12 0.00 43.58 0.86
58 59 7.472663 GCATCAGGACTGAAGTCTTCCTTATAT 60.473 40.741 10.12 0.00 43.58 0.86
59 60 6.183360 GCATCAGGACTGAAGTCTTCCTTATA 60.183 42.308 10.12 0.00 43.58 0.98
60 61 5.396213 GCATCAGGACTGAAGTCTTCCTTAT 60.396 44.000 10.12 0.00 43.58 1.73
61 62 4.081420 GCATCAGGACTGAAGTCTTCCTTA 60.081 45.833 10.12 0.00 43.58 2.69
62 63 3.307339 GCATCAGGACTGAAGTCTTCCTT 60.307 47.826 10.12 0.00 43.58 3.36
63 64 2.235898 GCATCAGGACTGAAGTCTTCCT 59.764 50.000 10.12 0.00 43.58 3.36
94 95 0.040067 GCCTTGCACTTTGAGGAACG 60.040 55.000 5.53 0.00 32.11 3.95
339 340 1.644437 TTCATGCCGACCATCCCCAT 61.644 55.000 0.00 0.00 29.71 4.00
345 346 4.963878 GGTCTTCATGCCGACCAT 57.036 55.556 21.35 0.00 46.98 3.55
664 665 2.437359 GCACGCCTGGAGCTCATT 60.437 61.111 17.19 0.00 40.39 2.57
811 813 1.104577 GGCGTTGGTGAGTTCCCAAA 61.105 55.000 0.00 0.00 43.30 3.28
822 824 0.687354 AGATGACAGAAGGCGTTGGT 59.313 50.000 0.00 0.00 0.00 3.67
1082 1084 1.154205 CGCCTCCTTTGCCATAGACG 61.154 60.000 0.00 0.00 0.00 4.18
1224 1226 1.902508 TCAATCTTGAAGAGGCCTCGT 59.097 47.619 26.95 24.59 33.55 4.18
1638 1640 6.371389 CGGAAAGTCAAAAGGTAAACATCTC 58.629 40.000 0.00 0.00 0.00 2.75
1655 1665 3.193056 GGACTAAGACAGTAGCGGAAAGT 59.807 47.826 0.00 0.00 37.72 2.66
1864 1874 3.067833 TGTTGCGAAATCGGTTGATACA 58.932 40.909 4.84 0.00 40.23 2.29
2204 2214 3.386768 TGAGCTTATGGAATAGCCGTC 57.613 47.619 0.00 0.00 40.66 4.79


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

AutoCloner maintained by Alex Coulton.