Multiple sequence alignment - TraesCS5D01G447200

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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 TraesCS5D01G447200 chr5D 100.000 1653 0 0 930 2582 497305385 497303733 0.000000e+00 3053.0
1 TraesCS5D01G447200 chr5D 94.913 924 34 3 930 1841 53756526 53757448 0.000000e+00 1434.0
2 TraesCS5D01G447200 chr5D 92.803 931 42 13 931 1841 84452268 84453193 0.000000e+00 1325.0
3 TraesCS5D01G447200 chr5D 100.000 514 0 0 1 514 497306314 497305801 0.000000e+00 950.0
4 TraesCS5D01G447200 chr5D 93.586 343 21 1 173 514 53755582 53755924 6.370000e-141 510.0
5 TraesCS5D01G447200 chr5D 93.675 332 21 0 172 503 359546428 359546759 4.960000e-137 497.0
6 TraesCS5D01G447200 chr5D 81.297 401 70 4 2173 2569 497038452 497038851 1.150000e-83 320.0
7 TraesCS5D01G447200 chr3D 94.118 935 34 11 930 1844 486147212 486146279 0.000000e+00 1402.0
8 TraesCS5D01G447200 chr3D 93.629 926 31 7 941 1841 124070379 124071301 0.000000e+00 1358.0
9 TraesCS5D01G447200 chr3D 93.980 897 40 6 939 1821 338869966 338869070 0.000000e+00 1345.0
10 TraesCS5D01G447200 chr3D 91.715 869 51 8 992 1844 426936962 426936099 0.000000e+00 1186.0
11 TraesCS5D01G447200 chr3D 94.237 295 11 3 177 469 486147831 486147541 1.820000e-121 446.0
12 TraesCS5D01G447200 chr5B 92.872 940 38 14 930 1841 56361516 56362454 0.000000e+00 1338.0
13 TraesCS5D01G447200 chr5B 91.445 339 26 1 175 513 517573192 517572857 1.810000e-126 462.0
14 TraesCS5D01G447200 chr5B 84.840 376 46 7 2211 2582 615741706 615742074 4.060000e-98 368.0
15 TraesCS5D01G447200 chr1D 93.089 926 42 6 930 1841 491907954 491907037 0.000000e+00 1336.0
16 TraesCS5D01G447200 chr1D 86.799 856 68 16 992 1843 13228721 13227907 0.000000e+00 913.0
17 TraesCS5D01G447200 chr1D 89.773 176 16 2 1679 1854 260983558 260983731 9.300000e-55 224.0
18 TraesCS5D01G447200 chr6D 92.973 925 44 10 940 1844 424649069 424648146 0.000000e+00 1328.0
19 TraesCS5D01G447200 chr4B 92.383 919 62 6 930 1841 577063373 577062456 0.000000e+00 1303.0
20 TraesCS5D01G447200 chr4D 92.721 893 44 8 976 1847 92671311 92670419 0.000000e+00 1269.0
21 TraesCS5D01G447200 chr5A 91.518 731 30 6 1871 2582 621527926 621528643 0.000000e+00 977.0
22 TraesCS5D01G447200 chr5A 84.043 376 49 7 2211 2582 621177190 621177558 4.090000e-93 351.0
23 TraesCS5D01G447200 chr5A 95.556 45 2 0 1871 1915 621528020 621528064 3.560000e-09 73.1
24 TraesCS5D01G447200 chrUn 93.510 339 21 1 177 514 470687621 470687959 1.070000e-138 503.0
25 TraesCS5D01G447200 chrUn 93.769 321 19 1 177 496 427412140 427412460 5.000000e-132 481.0
26 TraesCS5D01G447200 chrUn 80.040 506 78 16 2073 2569 335555879 335555388 1.140000e-93 353.0
27 TraesCS5D01G447200 chrUn 79.842 506 79 16 2073 2569 68274195 68273704 5.290000e-92 348.0
28 TraesCS5D01G447200 chrUn 79.842 506 79 16 2073 2569 302517425 302517916 5.290000e-92 348.0
29 TraesCS5D01G447200 chrUn 79.842 506 79 16 2073 2569 310277852 310277361 5.290000e-92 348.0
30 TraesCS5D01G447200 chrUn 79.842 506 79 16 2073 2569 327437883 327438374 5.290000e-92 348.0
31 TraesCS5D01G447200 chr3A 91.124 338 29 1 178 514 308673628 308673965 8.420000e-125 457.0
32 TraesCS5D01G447200 chr7D 92.628 312 19 4 168 477 549747882 549747573 1.820000e-121 446.0
33 TraesCS5D01G447200 chr2D 89.086 339 32 2 175 512 70817530 70817196 1.430000e-112 416.0
34 TraesCS5D01G447200 chr6B 91.716 169 13 1 1681 1848 4470901 4471069 1.540000e-57 233.0
35 TraesCS5D01G447200 chr7B 92.025 163 13 0 1681 1843 104029069 104029231 2.000000e-56 230.0


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 TraesCS5D01G447200 chr5D 497303733 497306314 2581 True 2001.50 3053 100.0000 1 2582 2 chr5D.!!$R1 2581
1 TraesCS5D01G447200 chr5D 84452268 84453193 925 False 1325.00 1325 92.8030 931 1841 1 chr5D.!!$F1 910
2 TraesCS5D01G447200 chr5D 53755582 53757448 1866 False 972.00 1434 94.2495 173 1841 2 chr5D.!!$F4 1668
3 TraesCS5D01G447200 chr3D 124070379 124071301 922 False 1358.00 1358 93.6290 941 1841 1 chr3D.!!$F1 900
4 TraesCS5D01G447200 chr3D 338869070 338869966 896 True 1345.00 1345 93.9800 939 1821 1 chr3D.!!$R1 882
5 TraesCS5D01G447200 chr3D 426936099 426936962 863 True 1186.00 1186 91.7150 992 1844 1 chr3D.!!$R2 852
6 TraesCS5D01G447200 chr3D 486146279 486147831 1552 True 924.00 1402 94.1775 177 1844 2 chr3D.!!$R3 1667
7 TraesCS5D01G447200 chr5B 56361516 56362454 938 False 1338.00 1338 92.8720 930 1841 1 chr5B.!!$F1 911
8 TraesCS5D01G447200 chr1D 491907037 491907954 917 True 1336.00 1336 93.0890 930 1841 1 chr1D.!!$R2 911
9 TraesCS5D01G447200 chr1D 13227907 13228721 814 True 913.00 913 86.7990 992 1843 1 chr1D.!!$R1 851
10 TraesCS5D01G447200 chr6D 424648146 424649069 923 True 1328.00 1328 92.9730 940 1844 1 chr6D.!!$R1 904
11 TraesCS5D01G447200 chr4B 577062456 577063373 917 True 1303.00 1303 92.3830 930 1841 1 chr4B.!!$R1 911
12 TraesCS5D01G447200 chr4D 92670419 92671311 892 True 1269.00 1269 92.7210 976 1847 1 chr4D.!!$R1 871
13 TraesCS5D01G447200 chr5A 621527926 621528643 717 False 525.05 977 93.5370 1871 2582 2 chr5A.!!$F2 711

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
235 236 0.032912 ACTTTTGGACCGTTTGGGGT 60.033 50.000 0.0 0.0 44.89 4.95 F
1345 1558 2.690778 GCGATGGCGAGGTTTGCTT 61.691 57.895 0.0 0.0 40.82 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1619 0.038890 GGCCCCTTCTTCTTCTGCTT 59.961 55.0 0.00 0.00 0.00 3.91 R
2528 2857 0.179179 GTCGTGGTCGTAGTACTGCC 60.179 60.0 5.39 3.31 38.33 4.85 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
18 19 2.942641 AGACCTTAAAAGCCGCCAC 58.057 52.632 0.00 0.00 0.00 5.01
19 20 0.400594 AGACCTTAAAAGCCGCCACT 59.599 50.000 0.00 0.00 0.00 4.00
20 21 1.626825 AGACCTTAAAAGCCGCCACTA 59.373 47.619 0.00 0.00 0.00 2.74
21 22 2.039348 AGACCTTAAAAGCCGCCACTAA 59.961 45.455 0.00 0.00 0.00 2.24
22 23 2.815503 GACCTTAAAAGCCGCCACTAAA 59.184 45.455 0.00 0.00 0.00 1.85
23 24 3.427573 ACCTTAAAAGCCGCCACTAAAT 58.572 40.909 0.00 0.00 0.00 1.40
24 25 3.830178 ACCTTAAAAGCCGCCACTAAATT 59.170 39.130 0.00 0.00 0.00 1.82
25 26 4.282449 ACCTTAAAAGCCGCCACTAAATTT 59.718 37.500 0.00 0.00 0.00 1.82
26 27 5.221561 ACCTTAAAAGCCGCCACTAAATTTT 60.222 36.000 0.00 0.00 0.00 1.82
27 28 5.120053 CCTTAAAAGCCGCCACTAAATTTTG 59.880 40.000 0.00 0.00 0.00 2.44
28 29 4.329462 AAAAGCCGCCACTAAATTTTGA 57.671 36.364 6.63 0.00 0.00 2.69
29 30 4.535526 AAAGCCGCCACTAAATTTTGAT 57.464 36.364 6.63 0.00 0.00 2.57
30 31 4.535526 AAGCCGCCACTAAATTTTGATT 57.464 36.364 6.63 0.00 0.00 2.57
31 32 5.652994 AAGCCGCCACTAAATTTTGATTA 57.347 34.783 6.63 0.00 0.00 1.75
32 33 5.852282 AGCCGCCACTAAATTTTGATTAT 57.148 34.783 6.63 0.00 0.00 1.28
33 34 5.831997 AGCCGCCACTAAATTTTGATTATC 58.168 37.500 6.63 0.00 0.00 1.75
34 35 4.982295 GCCGCCACTAAATTTTGATTATCC 59.018 41.667 6.63 0.00 0.00 2.59
35 36 5.451242 GCCGCCACTAAATTTTGATTATCCA 60.451 40.000 6.63 0.00 0.00 3.41
36 37 5.977129 CCGCCACTAAATTTTGATTATCCAC 59.023 40.000 6.63 0.00 0.00 4.02
37 38 6.405286 CCGCCACTAAATTTTGATTATCCACA 60.405 38.462 6.63 0.00 0.00 4.17
38 39 6.692681 CGCCACTAAATTTTGATTATCCACAG 59.307 38.462 6.63 0.00 0.00 3.66
39 40 7.415095 CGCCACTAAATTTTGATTATCCACAGA 60.415 37.037 6.63 0.00 0.00 3.41
40 41 8.250332 GCCACTAAATTTTGATTATCCACAGAA 58.750 33.333 6.63 0.00 0.00 3.02
41 42 9.793252 CCACTAAATTTTGATTATCCACAGAAG 57.207 33.333 6.63 0.00 0.00 2.85
42 43 9.793252 CACTAAATTTTGATTATCCACAGAAGG 57.207 33.333 6.63 0.00 0.00 3.46
43 44 8.470002 ACTAAATTTTGATTATCCACAGAAGGC 58.530 33.333 6.63 0.00 0.00 4.35
44 45 5.859205 ATTTTGATTATCCACAGAAGGCC 57.141 39.130 0.00 0.00 0.00 5.19
45 46 2.620251 TGATTATCCACAGAAGGCCG 57.380 50.000 0.00 0.00 0.00 6.13
46 47 1.837439 TGATTATCCACAGAAGGCCGT 59.163 47.619 0.00 0.00 0.00 5.68
47 48 2.238646 TGATTATCCACAGAAGGCCGTT 59.761 45.455 0.00 0.00 0.00 4.44
48 49 3.452990 TGATTATCCACAGAAGGCCGTTA 59.547 43.478 0.00 0.00 0.00 3.18
49 50 3.536956 TTATCCACAGAAGGCCGTTAG 57.463 47.619 0.00 0.00 0.00 2.34
50 51 1.568504 ATCCACAGAAGGCCGTTAGA 58.431 50.000 0.00 0.00 0.00 2.10
51 52 1.344065 TCCACAGAAGGCCGTTAGAA 58.656 50.000 0.00 0.00 0.00 2.10
52 53 1.275291 TCCACAGAAGGCCGTTAGAAG 59.725 52.381 0.00 0.00 0.00 2.85
53 54 1.002087 CCACAGAAGGCCGTTAGAAGT 59.998 52.381 0.00 0.00 0.00 3.01
54 55 2.069273 CACAGAAGGCCGTTAGAAGTG 58.931 52.381 0.00 0.00 0.00 3.16
55 56 1.968493 ACAGAAGGCCGTTAGAAGTGA 59.032 47.619 0.00 0.00 0.00 3.41
56 57 2.567615 ACAGAAGGCCGTTAGAAGTGAT 59.432 45.455 0.00 0.00 0.00 3.06
57 58 3.190874 CAGAAGGCCGTTAGAAGTGATC 58.809 50.000 0.00 0.00 0.00 2.92
58 59 2.832129 AGAAGGCCGTTAGAAGTGATCA 59.168 45.455 0.00 0.00 0.00 2.92
59 60 3.260884 AGAAGGCCGTTAGAAGTGATCAA 59.739 43.478 0.00 0.00 0.00 2.57
60 61 3.914426 AGGCCGTTAGAAGTGATCAAT 57.086 42.857 0.00 0.00 0.00 2.57
61 62 3.535561 AGGCCGTTAGAAGTGATCAATG 58.464 45.455 0.00 0.00 0.00 2.82
62 63 3.055094 AGGCCGTTAGAAGTGATCAATGT 60.055 43.478 0.00 0.00 0.00 2.71
63 64 4.161565 AGGCCGTTAGAAGTGATCAATGTA 59.838 41.667 0.00 0.00 0.00 2.29
64 65 4.508124 GGCCGTTAGAAGTGATCAATGTAG 59.492 45.833 0.00 0.00 0.00 2.74
65 66 5.348986 GCCGTTAGAAGTGATCAATGTAGA 58.651 41.667 0.00 0.00 0.00 2.59
66 67 5.986135 GCCGTTAGAAGTGATCAATGTAGAT 59.014 40.000 0.00 0.00 0.00 1.98
67 68 6.480320 GCCGTTAGAAGTGATCAATGTAGATT 59.520 38.462 0.00 0.00 0.00 2.40
68 69 7.011482 GCCGTTAGAAGTGATCAATGTAGATTT 59.989 37.037 0.00 0.00 0.00 2.17
69 70 9.529325 CCGTTAGAAGTGATCAATGTAGATTTA 57.471 33.333 0.00 0.00 0.00 1.40
76 77 8.915057 AGTGATCAATGTAGATTTAATCCAGG 57.085 34.615 0.00 0.00 0.00 4.45
77 78 8.717717 AGTGATCAATGTAGATTTAATCCAGGA 58.282 33.333 0.00 0.00 0.00 3.86
78 79 9.512588 GTGATCAATGTAGATTTAATCCAGGAT 57.487 33.333 0.00 0.00 0.00 3.24
104 105 3.987594 GGATTCTCCTGGCTGGTTT 57.012 52.632 10.44 0.00 37.07 3.27
105 106 1.467920 GGATTCTCCTGGCTGGTTTG 58.532 55.000 10.44 2.89 37.07 2.93
106 107 1.004745 GGATTCTCCTGGCTGGTTTGA 59.995 52.381 10.44 5.10 37.07 2.69
107 108 2.087646 GATTCTCCTGGCTGGTTTGAC 58.912 52.381 10.44 0.00 37.07 3.18
108 109 1.140312 TTCTCCTGGCTGGTTTGACT 58.860 50.000 10.44 0.00 37.07 3.41
109 110 2.024176 TCTCCTGGCTGGTTTGACTA 57.976 50.000 10.44 0.00 37.07 2.59
110 111 2.334977 TCTCCTGGCTGGTTTGACTAA 58.665 47.619 10.44 0.00 37.07 2.24
111 112 2.912956 TCTCCTGGCTGGTTTGACTAAT 59.087 45.455 10.44 0.00 37.07 1.73
112 113 3.012518 CTCCTGGCTGGTTTGACTAATG 58.987 50.000 10.44 0.00 37.07 1.90
113 114 2.375174 TCCTGGCTGGTTTGACTAATGT 59.625 45.455 10.44 0.00 37.07 2.71
114 115 2.489329 CCTGGCTGGTTTGACTAATGTG 59.511 50.000 1.62 0.00 0.00 3.21
115 116 1.885887 TGGCTGGTTTGACTAATGTGC 59.114 47.619 0.00 0.00 0.00 4.57
116 117 1.885887 GGCTGGTTTGACTAATGTGCA 59.114 47.619 0.00 0.00 0.00 4.57
117 118 2.493278 GGCTGGTTTGACTAATGTGCAT 59.507 45.455 0.00 0.00 0.00 3.96
118 119 3.694072 GGCTGGTTTGACTAATGTGCATA 59.306 43.478 0.00 0.00 0.00 3.14
119 120 4.157656 GGCTGGTTTGACTAATGTGCATAA 59.842 41.667 0.00 0.00 0.00 1.90
120 121 5.335127 GCTGGTTTGACTAATGTGCATAAG 58.665 41.667 0.00 0.00 0.00 1.73
121 122 5.123820 GCTGGTTTGACTAATGTGCATAAGA 59.876 40.000 0.00 0.00 0.00 2.10
122 123 6.676456 GCTGGTTTGACTAATGTGCATAAGAG 60.676 42.308 0.00 0.00 0.00 2.85
123 124 5.123820 TGGTTTGACTAATGTGCATAAGAGC 59.876 40.000 0.00 0.00 0.00 4.09
124 125 5.123820 GGTTTGACTAATGTGCATAAGAGCA 59.876 40.000 0.00 0.00 43.35 4.26
134 135 3.466836 TGCATAAGAGCATCCTTAACCG 58.533 45.455 0.00 0.00 40.11 4.44
135 136 3.133901 TGCATAAGAGCATCCTTAACCGA 59.866 43.478 0.00 0.00 40.11 4.69
136 137 4.202357 TGCATAAGAGCATCCTTAACCGAT 60.202 41.667 0.00 0.00 40.11 4.18
137 138 4.757149 GCATAAGAGCATCCTTAACCGATT 59.243 41.667 0.00 0.00 33.66 3.34
138 139 5.106908 GCATAAGAGCATCCTTAACCGATTC 60.107 44.000 0.00 0.00 33.66 2.52
139 140 3.477210 AGAGCATCCTTAACCGATTCC 57.523 47.619 0.00 0.00 33.66 3.01
140 141 2.104963 AGAGCATCCTTAACCGATTCCC 59.895 50.000 0.00 0.00 33.66 3.97
141 142 2.104963 GAGCATCCTTAACCGATTCCCT 59.895 50.000 0.00 0.00 0.00 4.20
142 143 3.314693 AGCATCCTTAACCGATTCCCTA 58.685 45.455 0.00 0.00 0.00 3.53
143 144 3.910627 AGCATCCTTAACCGATTCCCTAT 59.089 43.478 0.00 0.00 0.00 2.57
144 145 5.091552 AGCATCCTTAACCGATTCCCTATA 58.908 41.667 0.00 0.00 0.00 1.31
145 146 5.546499 AGCATCCTTAACCGATTCCCTATAA 59.454 40.000 0.00 0.00 0.00 0.98
146 147 6.215636 AGCATCCTTAACCGATTCCCTATAAT 59.784 38.462 0.00 0.00 0.00 1.28
147 148 6.884836 GCATCCTTAACCGATTCCCTATAATT 59.115 38.462 0.00 0.00 0.00 1.40
148 149 7.393515 GCATCCTTAACCGATTCCCTATAATTT 59.606 37.037 0.00 0.00 0.00 1.82
149 150 9.953565 CATCCTTAACCGATTCCCTATAATTTA 57.046 33.333 0.00 0.00 0.00 1.40
151 152 9.383578 TCCTTAACCGATTCCCTATAATTTAGA 57.616 33.333 0.00 0.00 0.00 2.10
156 157 8.437274 ACCGATTCCCTATAATTTAGATGAGT 57.563 34.615 0.00 0.00 0.00 3.41
157 158 9.543231 ACCGATTCCCTATAATTTAGATGAGTA 57.457 33.333 0.00 0.00 0.00 2.59
175 176 9.440761 AGATGAGTAAACCATCTAGTATCCTTT 57.559 33.333 10.50 0.00 46.26 3.11
235 236 0.032912 ACTTTTGGACCGTTTGGGGT 60.033 50.000 0.00 0.00 44.89 4.95
1269 1473 3.258123 TCAACATGAAGGAGATCACGACA 59.742 43.478 0.00 0.00 30.82 4.35
1345 1558 2.690778 GCGATGGCGAGGTTTGCTT 61.691 57.895 0.00 0.00 40.82 3.91
1476 1693 0.631753 TCCCCATCGAGTCCTCTTCT 59.368 55.000 0.00 0.00 0.00 2.85
1592 1832 6.711194 TCCGATGAGGAGTAGTTTATCTAGTG 59.289 42.308 0.00 0.00 45.98 2.74
1688 1946 8.742777 TGGACTAGTAGTATGTCGTTTTACATT 58.257 33.333 1.88 0.00 40.52 2.71
1736 2045 2.352127 GCTCTTTTGGACCATCTGTTGC 60.352 50.000 0.00 0.00 0.00 4.17
1804 2114 6.265649 TCCAAATTTTACATCTCCGGTTTTGA 59.734 34.615 0.00 0.00 0.00 2.69
1848 2158 7.523293 TCTATTGAAGATGCTCTTAGAGGAG 57.477 40.000 11.54 0.00 36.73 3.69
1849 2159 7.066142 TCTATTGAAGATGCTCTTAGAGGAGT 58.934 38.462 11.54 0.00 36.73 3.85
1850 2160 8.221251 TCTATTGAAGATGCTCTTAGAGGAGTA 58.779 37.037 11.54 0.00 36.73 2.59
1851 2161 7.854166 ATTGAAGATGCTCTTAGAGGAGTAT 57.146 36.000 11.54 0.00 40.39 2.12
1866 2176 6.864360 GAGGAGTATCTTCGCTACTCTAAA 57.136 41.667 9.24 0.00 43.00 1.85
1867 2177 7.261829 GAGGAGTATCTTCGCTACTCTAAAA 57.738 40.000 9.24 0.00 43.00 1.52
1868 2178 7.642082 AGGAGTATCTTCGCTACTCTAAAAA 57.358 36.000 9.24 0.00 43.00 1.94
1957 2267 4.624024 TCAGAAGAAATAACGCGTTACAGG 59.376 41.667 32.10 15.82 0.00 4.00
2021 2348 3.565482 TCCATCAGCTTGAATTATTCCGC 59.435 43.478 2.22 5.49 0.00 5.54
2105 2432 5.948742 AGCTTAGAGTTAGAGAAGCCATT 57.051 39.130 2.02 0.00 44.32 3.16
2109 2436 6.202570 GCTTAGAGTTAGAGAAGCCATTGATG 59.797 42.308 0.00 0.00 38.68 3.07
2140 2467 5.129485 AGGCAGTATAAATACACAGCTCACT 59.871 40.000 3.13 0.00 35.74 3.41
2159 2486 2.304180 ACTGTGGCAGCCTATATCATCC 59.696 50.000 14.15 0.00 34.37 3.51
2179 2506 7.840931 TCATCCTTACAGATACATTCGCATAT 58.159 34.615 0.00 0.00 0.00 1.78
2204 2531 5.245977 ACATCTTCCCACCCTTAATTTTGTG 59.754 40.000 0.00 0.00 0.00 3.33
2205 2532 5.068215 TCTTCCCACCCTTAATTTTGTGA 57.932 39.130 0.00 0.00 0.00 3.58
2206 2533 5.459505 TCTTCCCACCCTTAATTTTGTGAA 58.540 37.500 0.00 0.00 0.00 3.18
2214 2543 5.095490 CCCTTAATTTTGTGAAGCTTAGCG 58.905 41.667 0.00 0.00 0.00 4.26
2256 2585 0.528684 CAGCGGTACTGCTCTTAGCC 60.529 60.000 26.48 0.00 45.23 3.93
2276 2605 4.735132 CGCGTCCGTCATGGTGGT 62.735 66.667 0.00 0.00 39.52 4.16
2476 2805 2.676232 CTCTTCAGAGGCAGTGGGA 58.324 57.895 0.00 0.00 38.48 4.37
2477 2806 0.536260 CTCTTCAGAGGCAGTGGGAG 59.464 60.000 0.00 0.00 38.48 4.30
2478 2807 0.178921 TCTTCAGAGGCAGTGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
2479 2808 0.036577 CTTCAGAGGCAGTGGGAGTG 60.037 60.000 0.00 0.00 0.00 3.51
2480 2809 1.483595 TTCAGAGGCAGTGGGAGTGG 61.484 60.000 0.00 0.00 0.00 4.00
2481 2810 2.608988 AGAGGCAGTGGGAGTGGG 60.609 66.667 0.00 0.00 0.00 4.61
2482 2811 2.607750 GAGGCAGTGGGAGTGGGA 60.608 66.667 0.00 0.00 0.00 4.37
2528 2857 2.310233 CGCTGTGGGTGTCGAACAG 61.310 63.158 9.38 9.38 43.37 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.400594 AGTGGCGGCTTTTAAGGTCT 59.599 50.000 11.43 0.00 0.00 3.85
1 2 2.103537 TAGTGGCGGCTTTTAAGGTC 57.896 50.000 11.43 0.00 0.00 3.85
2 3 2.572209 TTAGTGGCGGCTTTTAAGGT 57.428 45.000 11.43 0.00 0.00 3.50
3 4 4.450082 AATTTAGTGGCGGCTTTTAAGG 57.550 40.909 11.43 0.00 0.00 2.69
4 5 5.923684 TCAAAATTTAGTGGCGGCTTTTAAG 59.076 36.000 11.43 0.00 0.00 1.85
5 6 5.844004 TCAAAATTTAGTGGCGGCTTTTAA 58.156 33.333 11.43 3.48 0.00 1.52
6 7 5.455056 TCAAAATTTAGTGGCGGCTTTTA 57.545 34.783 11.43 0.00 0.00 1.52
7 8 4.329462 TCAAAATTTAGTGGCGGCTTTT 57.671 36.364 11.43 4.48 0.00 2.27
8 9 4.535526 ATCAAAATTTAGTGGCGGCTTT 57.464 36.364 11.43 0.00 0.00 3.51
9 10 4.535526 AATCAAAATTTAGTGGCGGCTT 57.464 36.364 11.43 0.60 0.00 4.35
10 11 5.221244 GGATAATCAAAATTTAGTGGCGGCT 60.221 40.000 11.43 0.00 0.00 5.52
11 12 4.982295 GGATAATCAAAATTTAGTGGCGGC 59.018 41.667 0.00 0.00 0.00 6.53
12 13 5.977129 GTGGATAATCAAAATTTAGTGGCGG 59.023 40.000 0.00 0.00 0.00 6.13
13 14 6.559810 TGTGGATAATCAAAATTTAGTGGCG 58.440 36.000 0.00 0.00 0.00 5.69
14 15 7.771183 TCTGTGGATAATCAAAATTTAGTGGC 58.229 34.615 0.00 0.00 0.00 5.01
15 16 9.793252 CTTCTGTGGATAATCAAAATTTAGTGG 57.207 33.333 0.00 0.00 0.00 4.00
16 17 9.793252 CCTTCTGTGGATAATCAAAATTTAGTG 57.207 33.333 0.00 0.00 0.00 2.74
17 18 8.470002 GCCTTCTGTGGATAATCAAAATTTAGT 58.530 33.333 0.00 0.00 0.00 2.24
18 19 7.922811 GGCCTTCTGTGGATAATCAAAATTTAG 59.077 37.037 0.00 0.00 0.00 1.85
19 20 7.416213 CGGCCTTCTGTGGATAATCAAAATTTA 60.416 37.037 0.00 0.00 0.00 1.40
20 21 6.627953 CGGCCTTCTGTGGATAATCAAAATTT 60.628 38.462 0.00 0.00 0.00 1.82
21 22 5.163519 CGGCCTTCTGTGGATAATCAAAATT 60.164 40.000 0.00 0.00 0.00 1.82
22 23 4.339247 CGGCCTTCTGTGGATAATCAAAAT 59.661 41.667 0.00 0.00 0.00 1.82
23 24 3.694072 CGGCCTTCTGTGGATAATCAAAA 59.306 43.478 0.00 0.00 0.00 2.44
24 25 3.278574 CGGCCTTCTGTGGATAATCAAA 58.721 45.455 0.00 0.00 0.00 2.69
25 26 2.238646 ACGGCCTTCTGTGGATAATCAA 59.761 45.455 0.00 0.00 0.00 2.57
26 27 1.837439 ACGGCCTTCTGTGGATAATCA 59.163 47.619 0.00 0.00 0.00 2.57
27 28 2.622064 ACGGCCTTCTGTGGATAATC 57.378 50.000 0.00 0.00 0.00 1.75
28 29 3.709653 TCTAACGGCCTTCTGTGGATAAT 59.290 43.478 0.00 0.00 0.00 1.28
29 30 3.101437 TCTAACGGCCTTCTGTGGATAA 58.899 45.455 0.00 0.00 0.00 1.75
30 31 2.742348 TCTAACGGCCTTCTGTGGATA 58.258 47.619 0.00 0.00 0.00 2.59
31 32 1.568504 TCTAACGGCCTTCTGTGGAT 58.431 50.000 0.00 0.00 0.00 3.41
32 33 1.275291 CTTCTAACGGCCTTCTGTGGA 59.725 52.381 0.00 0.00 0.00 4.02
33 34 1.002087 ACTTCTAACGGCCTTCTGTGG 59.998 52.381 0.00 0.00 0.00 4.17
34 35 2.069273 CACTTCTAACGGCCTTCTGTG 58.931 52.381 0.00 0.00 0.00 3.66
35 36 1.968493 TCACTTCTAACGGCCTTCTGT 59.032 47.619 0.00 0.00 0.00 3.41
36 37 2.743636 TCACTTCTAACGGCCTTCTG 57.256 50.000 0.00 0.00 0.00 3.02
37 38 2.832129 TGATCACTTCTAACGGCCTTCT 59.168 45.455 0.00 0.00 0.00 2.85
38 39 3.247006 TGATCACTTCTAACGGCCTTC 57.753 47.619 0.00 0.00 0.00 3.46
39 40 3.695830 TTGATCACTTCTAACGGCCTT 57.304 42.857 0.00 0.00 0.00 4.35
40 41 3.055094 ACATTGATCACTTCTAACGGCCT 60.055 43.478 0.00 0.00 0.00 5.19
41 42 3.270877 ACATTGATCACTTCTAACGGCC 58.729 45.455 0.00 0.00 0.00 6.13
42 43 5.348986 TCTACATTGATCACTTCTAACGGC 58.651 41.667 0.00 0.00 0.00 5.68
43 44 8.425577 AAATCTACATTGATCACTTCTAACGG 57.574 34.615 0.00 0.00 0.00 4.44
50 51 9.347240 CCTGGATTAAATCTACATTGATCACTT 57.653 33.333 0.00 0.00 0.00 3.16
51 52 8.717717 TCCTGGATTAAATCTACATTGATCACT 58.282 33.333 0.00 0.00 0.00 3.41
52 53 8.908786 TCCTGGATTAAATCTACATTGATCAC 57.091 34.615 0.00 0.00 0.00 3.06
87 88 2.087646 GTCAAACCAGCCAGGAGAATC 58.912 52.381 0.00 0.00 41.22 2.52
88 89 1.707427 AGTCAAACCAGCCAGGAGAAT 59.293 47.619 0.00 0.00 41.22 2.40
89 90 1.140312 AGTCAAACCAGCCAGGAGAA 58.860 50.000 0.00 0.00 41.22 2.87
90 91 2.024176 TAGTCAAACCAGCCAGGAGA 57.976 50.000 0.00 0.00 41.22 3.71
91 92 2.859165 TTAGTCAAACCAGCCAGGAG 57.141 50.000 0.00 0.00 41.22 3.69
92 93 2.375174 ACATTAGTCAAACCAGCCAGGA 59.625 45.455 0.00 0.00 41.22 3.86
93 94 2.489329 CACATTAGTCAAACCAGCCAGG 59.511 50.000 0.00 0.00 45.67 4.45
94 95 2.095059 GCACATTAGTCAAACCAGCCAG 60.095 50.000 0.00 0.00 0.00 4.85
95 96 1.885887 GCACATTAGTCAAACCAGCCA 59.114 47.619 0.00 0.00 0.00 4.75
96 97 1.885887 TGCACATTAGTCAAACCAGCC 59.114 47.619 0.00 0.00 0.00 4.85
97 98 3.855689 ATGCACATTAGTCAAACCAGC 57.144 42.857 0.00 0.00 0.00 4.85
98 99 6.676456 GCTCTTATGCACATTAGTCAAACCAG 60.676 42.308 0.00 0.00 0.00 4.00
99 100 5.123820 GCTCTTATGCACATTAGTCAAACCA 59.876 40.000 0.00 0.00 0.00 3.67
100 101 5.123820 TGCTCTTATGCACATTAGTCAAACC 59.876 40.000 0.00 0.00 38.12 3.27
101 102 6.182039 TGCTCTTATGCACATTAGTCAAAC 57.818 37.500 0.00 0.00 38.12 2.93
102 103 6.038603 GGATGCTCTTATGCACATTAGTCAAA 59.961 38.462 0.00 0.00 46.33 2.69
103 104 5.528690 GGATGCTCTTATGCACATTAGTCAA 59.471 40.000 0.00 0.00 46.33 3.18
104 105 5.059161 GGATGCTCTTATGCACATTAGTCA 58.941 41.667 0.00 0.00 46.33 3.41
105 106 5.303971 AGGATGCTCTTATGCACATTAGTC 58.696 41.667 0.00 0.00 46.33 2.59
106 107 5.301835 AGGATGCTCTTATGCACATTAGT 57.698 39.130 0.00 0.00 46.33 2.24
107 108 7.308229 GGTTAAGGATGCTCTTATGCACATTAG 60.308 40.741 0.00 0.00 46.33 1.73
108 109 6.486657 GGTTAAGGATGCTCTTATGCACATTA 59.513 38.462 0.00 0.00 46.33 1.90
109 110 5.300286 GGTTAAGGATGCTCTTATGCACATT 59.700 40.000 0.00 0.00 46.33 2.71
110 111 4.823989 GGTTAAGGATGCTCTTATGCACAT 59.176 41.667 0.00 0.00 46.33 3.21
111 112 4.199310 GGTTAAGGATGCTCTTATGCACA 58.801 43.478 0.00 0.00 46.33 4.57
112 113 3.248602 CGGTTAAGGATGCTCTTATGCAC 59.751 47.826 0.00 0.00 46.33 4.57
114 115 3.728845 TCGGTTAAGGATGCTCTTATGC 58.271 45.455 0.00 0.00 0.00 3.14
115 116 5.409826 GGAATCGGTTAAGGATGCTCTTATG 59.590 44.000 0.00 0.00 0.00 1.90
116 117 5.513267 GGGAATCGGTTAAGGATGCTCTTAT 60.513 44.000 0.00 0.00 0.00 1.73
117 118 4.202326 GGGAATCGGTTAAGGATGCTCTTA 60.202 45.833 0.00 0.00 0.00 2.10
118 119 3.433740 GGGAATCGGTTAAGGATGCTCTT 60.434 47.826 0.00 0.00 0.00 2.85
119 120 2.104963 GGGAATCGGTTAAGGATGCTCT 59.895 50.000 0.00 0.00 0.00 4.09
120 121 2.104963 AGGGAATCGGTTAAGGATGCTC 59.895 50.000 0.00 0.00 0.00 4.26
121 122 2.127708 AGGGAATCGGTTAAGGATGCT 58.872 47.619 0.00 0.00 0.00 3.79
122 123 2.640316 AGGGAATCGGTTAAGGATGC 57.360 50.000 0.00 0.00 0.00 3.91
123 124 8.863872 AAATTATAGGGAATCGGTTAAGGATG 57.136 34.615 0.00 0.00 0.00 3.51
125 126 9.383578 TCTAAATTATAGGGAATCGGTTAAGGA 57.616 33.333 0.00 0.00 0.00 3.36
130 131 8.881262 ACTCATCTAAATTATAGGGAATCGGTT 58.119 33.333 0.00 0.00 0.00 4.44
131 132 8.437274 ACTCATCTAAATTATAGGGAATCGGT 57.563 34.615 0.00 0.00 0.00 4.69
167 168 8.128322 TCTATTGGAGATGCTCTAAAGGATAC 57.872 38.462 0.00 0.00 34.82 2.24
168 169 8.907829 ATCTATTGGAGATGCTCTAAAGGATA 57.092 34.615 0.00 0.00 43.71 2.59
169 170 7.811482 ATCTATTGGAGATGCTCTAAAGGAT 57.189 36.000 0.00 0.00 43.71 3.24
287 289 3.937814 TGCATTTTACATCACGAGGAGT 58.062 40.909 0.00 0.00 0.00 3.85
1061 1265 4.263572 CCACACCCCAGTTGCCGA 62.264 66.667 0.00 0.00 0.00 5.54
1269 1473 4.709250 ACGGCTTCTTCTTCTTCTTCTTT 58.291 39.130 0.00 0.00 0.00 2.52
1345 1558 2.125326 CGTACTCCGGATGCTCCCA 61.125 63.158 3.57 0.00 31.13 4.37
1402 1619 0.038890 GGCCCCTTCTTCTTCTGCTT 59.961 55.000 0.00 0.00 0.00 3.91
1453 1670 0.965439 GAGGACTCGATGGGGATCAG 59.035 60.000 0.00 0.00 0.00 2.90
1476 1693 1.610673 GTCTGCCCAGTCCTCCTCA 60.611 63.158 0.00 0.00 0.00 3.86
1620 1860 9.773328 ACATCAAATTCAACATAGTTTCATACG 57.227 29.630 0.00 0.00 0.00 3.06
1750 2059 1.586154 AATGCGTTTTGGAGCTCCGG 61.586 55.000 27.43 14.52 39.43 5.14
1931 2241 6.097356 TGTAACGCGTTATTTCTTCTGAGAT 58.903 36.000 32.03 4.53 0.00 2.75
2021 2348 5.726729 AACTTAAAATTTGCAAACCGTGG 57.273 34.783 15.41 6.22 0.00 4.94
2092 2419 6.003326 TGAACAACATCAATGGCTTCTCTAA 58.997 36.000 0.00 0.00 0.00 2.10
2093 2420 5.559770 TGAACAACATCAATGGCTTCTCTA 58.440 37.500 0.00 0.00 0.00 2.43
2094 2421 4.401022 TGAACAACATCAATGGCTTCTCT 58.599 39.130 0.00 0.00 0.00 3.10
2095 2422 4.380233 CCTGAACAACATCAATGGCTTCTC 60.380 45.833 0.00 0.00 0.00 2.87
2096 2423 3.508793 CCTGAACAACATCAATGGCTTCT 59.491 43.478 0.00 0.00 0.00 2.85
2097 2424 3.841643 CCTGAACAACATCAATGGCTTC 58.158 45.455 0.00 0.00 0.00 3.86
2105 2432 7.826744 TGTATTTATACTGCCTGAACAACATCA 59.173 33.333 1.95 0.00 34.41 3.07
2109 2436 7.372451 TGTGTATTTATACTGCCTGAACAAC 57.628 36.000 1.95 0.00 34.41 3.32
2140 2467 2.624495 AGGATGATATAGGCTGCCACA 58.376 47.619 22.65 8.58 0.00 4.17
2159 2486 9.794685 AGATGTATATGCGAATGTATCTGTAAG 57.205 33.333 0.00 0.00 0.00 2.34
2179 2506 6.435904 CACAAAATTAAGGGTGGGAAGATGTA 59.564 38.462 0.00 0.00 0.00 2.29
2204 2531 3.634283 GAGTACTCCATCGCTAAGCTTC 58.366 50.000 12.13 0.00 0.00 3.86
2205 2532 2.033550 CGAGTACTCCATCGCTAAGCTT 59.966 50.000 17.23 3.48 31.42 3.74
2206 2533 1.604755 CGAGTACTCCATCGCTAAGCT 59.395 52.381 17.23 0.00 31.42 3.74
2214 2543 0.595310 GCTTCGGCGAGTACTCCATC 60.595 60.000 17.23 6.60 0.00 3.51
2256 2585 4.129737 ACCATGACGGACGCGAGG 62.130 66.667 15.93 3.28 38.63 4.63
2276 2605 4.373116 GCGAGTTCTGGGCCGTGA 62.373 66.667 0.00 0.00 0.00 4.35
2298 2627 2.342279 TGGGCTTCCACGAAGTCG 59.658 61.111 0.00 0.00 44.23 4.18
2476 2805 1.908793 CTGTCCAGTCGGTCCCACT 60.909 63.158 0.00 0.00 0.00 4.00
2477 2806 2.657237 CTGTCCAGTCGGTCCCAC 59.343 66.667 0.00 0.00 0.00 4.61
2478 2807 3.311110 GCTGTCCAGTCGGTCCCA 61.311 66.667 0.00 0.00 0.00 4.37
2479 2808 4.436998 CGCTGTCCAGTCGGTCCC 62.437 72.222 0.00 0.00 0.00 4.46
2480 2809 4.436998 CCGCTGTCCAGTCGGTCC 62.437 72.222 16.73 0.00 40.59 4.46
2509 2838 2.279918 GTTCGACACCCACAGCGT 60.280 61.111 0.00 0.00 0.00 5.07
2511 2840 1.961277 CCTGTTCGACACCCACAGC 60.961 63.158 8.40 0.00 37.24 4.40
2528 2857 0.179179 GTCGTGGTCGTAGTACTGCC 60.179 60.000 5.39 3.31 38.33 4.85


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

AutoCloner maintained by Alex Coulton.