Multiple sequence alignment - TraesCS1D01G328200

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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 TraesCS1D01G328200 chr1D 100.000 2993 0 0 1 2993 420011414 420008422 0.000000e+00 5528
1 TraesCS1D01G328200 chr1D 96.041 2728 83 18 275 2993 475528296 475525585 0.000000e+00 4416
2 TraesCS1D01G328200 chr4D 97.869 2722 56 2 274 2993 502867332 502870053 0.000000e+00 4704
3 TraesCS1D01G328200 chr4D 95.493 2729 95 21 275 2993 507114494 507111784 0.000000e+00 4333
4 TraesCS1D01G328200 chr4D 87.215 219 19 6 1 210 215455530 215455312 1.070000e-59 241
5 TraesCS1D01G328200 chr3D 97.943 2722 41 10 275 2993 359622499 359625208 0.000000e+00 4702
6 TraesCS1D01G328200 chr3D 95.604 2730 92 20 275 2993 85226134 85228846 0.000000e+00 4351
7 TraesCS1D01G328200 chr2D 96.754 2742 62 11 261 2993 382702795 382700072 0.000000e+00 4545
8 TraesCS1D01G328200 chr2D 96.586 2724 60 9 275 2993 182632456 182629761 0.000000e+00 4484
9 TraesCS1D01G328200 chr2D 95.999 2749 51 11 275 2993 74953112 74955831 0.000000e+00 4412
10 TraesCS1D01G328200 chr2D 94.980 2729 90 17 269 2989 547563440 547566129 0.000000e+00 4237
11 TraesCS1D01G328200 chr2D 97.286 2321 58 3 677 2992 605551638 605549318 0.000000e+00 3932
12 TraesCS1D01G328200 chr2D 95.868 242 7 2 275 515 74962084 74961845 3.620000e-104 388
13 TraesCS1D01G328200 chr6D 94.340 2721 92 22 274 2989 156246490 156249153 0.000000e+00 4115
14 TraesCS1D01G328200 chr7B 88.143 2412 150 63 275 2619 592365044 592367386 0.000000e+00 2745
15 TraesCS1D01G328200 chr3B 92.670 955 34 12 271 1209 766032542 766033476 0.000000e+00 1343
16 TraesCS1D01G328200 chr3B 80.078 256 31 11 1 249 808488282 808488040 3.970000e-39 172
17 TraesCS1D01G328200 chr5D 94.758 248 11 2 271 517 480816930 480817176 4.680000e-103 385
18 TraesCS1D01G328200 chr1B 89.362 282 22 5 1 274 566988631 566988350 6.140000e-92 348
19 TraesCS1D01G328200 chr1B 82.609 253 36 5 1 245 444347699 444347447 1.810000e-52 217
20 TraesCS1D01G328200 chr7A 82.540 252 32 5 1 242 732056317 732056566 8.410000e-51 211
21 TraesCS1D01G328200 chr7A 83.028 218 28 7 1 209 730767291 730767508 3.940000e-44 189
22 TraesCS1D01G328200 chr5B 84.375 224 25 6 1 215 17588590 17588812 8.410000e-51 211
23 TraesCS1D01G328200 chr5B 82.587 201 27 5 21 213 66037997 66037797 1.430000e-38 171
24 TraesCS1D01G328200 chr5A 81.735 219 31 5 1 210 325806374 325806592 1.100000e-39 174


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 TraesCS1D01G328200 chr1D 420008422 420011414 2992 True 5528 5528 100.000 1 2993 1 chr1D.!!$R1 2992
1 TraesCS1D01G328200 chr1D 475525585 475528296 2711 True 4416 4416 96.041 275 2993 1 chr1D.!!$R2 2718
2 TraesCS1D01G328200 chr4D 502867332 502870053 2721 False 4704 4704 97.869 274 2993 1 chr4D.!!$F1 2719
3 TraesCS1D01G328200 chr4D 507111784 507114494 2710 True 4333 4333 95.493 275 2993 1 chr4D.!!$R2 2718
4 TraesCS1D01G328200 chr3D 359622499 359625208 2709 False 4702 4702 97.943 275 2993 1 chr3D.!!$F2 2718
5 TraesCS1D01G328200 chr3D 85226134 85228846 2712 False 4351 4351 95.604 275 2993 1 chr3D.!!$F1 2718
6 TraesCS1D01G328200 chr2D 382700072 382702795 2723 True 4545 4545 96.754 261 2993 1 chr2D.!!$R3 2732
7 TraesCS1D01G328200 chr2D 182629761 182632456 2695 True 4484 4484 96.586 275 2993 1 chr2D.!!$R2 2718
8 TraesCS1D01G328200 chr2D 74953112 74955831 2719 False 4412 4412 95.999 275 2993 1 chr2D.!!$F1 2718
9 TraesCS1D01G328200 chr2D 547563440 547566129 2689 False 4237 4237 94.980 269 2989 1 chr2D.!!$F2 2720
10 TraesCS1D01G328200 chr2D 605549318 605551638 2320 True 3932 3932 97.286 677 2992 1 chr2D.!!$R4 2315
11 TraesCS1D01G328200 chr6D 156246490 156249153 2663 False 4115 4115 94.340 274 2989 1 chr6D.!!$F1 2715
12 TraesCS1D01G328200 chr7B 592365044 592367386 2342 False 2745 2745 88.143 275 2619 1 chr7B.!!$F1 2344
13 TraesCS1D01G328200 chr3B 766032542 766033476 934 False 1343 1343 92.670 271 1209 1 chr3B.!!$F1 938

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
251 252 0.032815 GAAGATGCTCGTAGGCTCCC 59.967 60.0 0.0 0.0 0.0 4.30 F
609 674 0.107214 CTCACTCTCCTCTCCGCTCT 60.107 60.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2058 1.499007 ACCTCCTTTTTGCCTTCCTGA 59.501 47.619 0.0 0.0 0.0 3.86 R
2590 2727 1.067295 TTGCCTCCTCACATCCACTT 58.933 50.000 0.0 0.0 0.0 3.16 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
17 18 3.245650 TGTGGTGCTGGGCTGTAA 58.754 55.556 0.00 0.00 0.00 2.41
18 19 1.228124 TGTGGTGCTGGGCTGTAAC 60.228 57.895 0.00 0.00 0.00 2.50
19 20 1.073199 GTGGTGCTGGGCTGTAACT 59.927 57.895 0.00 0.00 0.00 2.24
20 21 0.323629 GTGGTGCTGGGCTGTAACTA 59.676 55.000 0.00 0.00 0.00 2.24
21 22 1.065418 GTGGTGCTGGGCTGTAACTAT 60.065 52.381 0.00 0.00 0.00 2.12
22 23 1.065491 TGGTGCTGGGCTGTAACTATG 60.065 52.381 0.00 0.00 0.00 2.23
23 24 1.017387 GTGCTGGGCTGTAACTATGC 58.983 55.000 0.00 0.00 0.00 3.14
24 25 0.911769 TGCTGGGCTGTAACTATGCT 59.088 50.000 0.00 0.00 0.00 3.79
25 26 2.115427 TGCTGGGCTGTAACTATGCTA 58.885 47.619 0.00 0.00 0.00 3.49
26 27 2.705658 TGCTGGGCTGTAACTATGCTAT 59.294 45.455 0.00 0.00 0.00 2.97
27 28 3.136443 TGCTGGGCTGTAACTATGCTATT 59.864 43.478 0.00 0.00 0.00 1.73
28 29 4.137543 GCTGGGCTGTAACTATGCTATTT 58.862 43.478 0.00 0.00 0.00 1.40
29 30 4.023707 GCTGGGCTGTAACTATGCTATTTG 60.024 45.833 0.00 0.00 0.00 2.32
30 31 5.366482 TGGGCTGTAACTATGCTATTTGA 57.634 39.130 0.00 0.00 0.00 2.69
31 32 5.750524 TGGGCTGTAACTATGCTATTTGAA 58.249 37.500 0.00 0.00 0.00 2.69
32 33 6.364701 TGGGCTGTAACTATGCTATTTGAAT 58.635 36.000 0.00 0.00 0.00 2.57
33 34 6.833416 TGGGCTGTAACTATGCTATTTGAATT 59.167 34.615 0.00 0.00 0.00 2.17
34 35 7.341769 TGGGCTGTAACTATGCTATTTGAATTT 59.658 33.333 0.00 0.00 0.00 1.82
35 36 8.197439 GGGCTGTAACTATGCTATTTGAATTTT 58.803 33.333 0.00 0.00 0.00 1.82
70 71 8.720909 TTGTTTCATATTGTTCGTATGTGTTG 57.279 30.769 0.00 0.00 32.63 3.33
71 72 6.799441 TGTTTCATATTGTTCGTATGTGTTGC 59.201 34.615 0.00 0.00 32.63 4.17
72 73 6.487689 TTCATATTGTTCGTATGTGTTGCA 57.512 33.333 0.00 0.00 32.63 4.08
73 74 6.676237 TCATATTGTTCGTATGTGTTGCAT 57.324 33.333 0.00 0.00 41.42 3.96
74 75 6.714492 TCATATTGTTCGTATGTGTTGCATC 58.286 36.000 0.00 0.00 38.94 3.91
75 76 3.447752 TTGTTCGTATGTGTTGCATCG 57.552 42.857 0.00 0.00 38.94 3.84
76 77 2.409012 TGTTCGTATGTGTTGCATCGT 58.591 42.857 0.00 0.00 38.94 3.73
77 78 3.576648 TGTTCGTATGTGTTGCATCGTA 58.423 40.909 0.00 0.00 38.94 3.43
78 79 3.610677 TGTTCGTATGTGTTGCATCGTAG 59.389 43.478 0.00 0.00 38.94 3.51
79 80 3.497297 TCGTATGTGTTGCATCGTAGT 57.503 42.857 0.00 0.00 38.94 2.73
80 81 4.619437 TCGTATGTGTTGCATCGTAGTA 57.381 40.909 0.00 0.00 38.94 1.82
81 82 4.345288 TCGTATGTGTTGCATCGTAGTAC 58.655 43.478 0.00 0.00 38.94 2.73
82 83 4.099824 CGTATGTGTTGCATCGTAGTACA 58.900 43.478 0.38 0.00 38.94 2.90
83 84 4.204370 CGTATGTGTTGCATCGTAGTACAG 59.796 45.833 0.38 0.00 38.94 2.74
84 85 2.954316 TGTGTTGCATCGTAGTACAGG 58.046 47.619 0.38 0.00 0.00 4.00
85 86 2.297880 TGTGTTGCATCGTAGTACAGGT 59.702 45.455 0.38 0.00 0.00 4.00
86 87 3.243941 TGTGTTGCATCGTAGTACAGGTT 60.244 43.478 0.38 0.00 0.00 3.50
87 88 3.122948 GTGTTGCATCGTAGTACAGGTTG 59.877 47.826 0.38 0.00 0.00 3.77
88 89 2.004583 TGCATCGTAGTACAGGTTGC 57.995 50.000 0.38 4.30 37.94 4.17
89 90 1.548719 TGCATCGTAGTACAGGTTGCT 59.451 47.619 15.44 0.00 38.16 3.91
90 91 2.194271 GCATCGTAGTACAGGTTGCTC 58.806 52.381 0.38 0.00 35.70 4.26
91 92 2.451132 CATCGTAGTACAGGTTGCTCG 58.549 52.381 0.38 0.00 0.00 5.03
92 93 0.169672 TCGTAGTACAGGTTGCTCGC 59.830 55.000 0.38 0.00 0.00 5.03
93 94 1.132199 CGTAGTACAGGTTGCTCGCG 61.132 60.000 0.00 0.00 0.00 5.87
94 95 1.153901 TAGTACAGGTTGCTCGCGC 60.154 57.895 0.00 0.00 0.00 6.86
95 96 2.860690 TAGTACAGGTTGCTCGCGCG 62.861 60.000 26.76 26.76 39.65 6.86
101 102 4.759096 GTTGCTCGCGCGCCATTT 62.759 61.111 27.95 0.00 39.65 2.32
102 103 4.036804 TTGCTCGCGCGCCATTTT 62.037 55.556 27.95 0.00 39.65 1.82
103 104 3.550339 TTGCTCGCGCGCCATTTTT 62.550 52.632 27.95 0.00 39.65 1.94
104 105 3.535491 GCTCGCGCGCCATTTTTG 61.535 61.111 27.95 9.81 0.00 2.44
105 106 3.535491 CTCGCGCGCCATTTTTGC 61.535 61.111 27.95 0.00 0.00 3.68
106 107 4.334109 TCGCGCGCCATTTTTGCA 62.334 55.556 27.95 0.00 0.00 4.08
107 108 3.829975 CGCGCGCCATTTTTGCAG 61.830 61.111 27.72 2.72 0.00 4.41
108 109 4.138109 GCGCGCCATTTTTGCAGC 62.138 61.111 23.24 0.00 0.00 5.25
109 110 2.733969 CGCGCCATTTTTGCAGCA 60.734 55.556 0.00 0.00 0.00 4.41
110 111 2.855325 GCGCCATTTTTGCAGCAC 59.145 55.556 0.00 0.00 0.00 4.40
111 112 2.670210 GCGCCATTTTTGCAGCACC 61.670 57.895 0.00 0.00 0.00 5.01
112 113 1.005867 CGCCATTTTTGCAGCACCT 60.006 52.632 0.00 0.00 0.00 4.00
113 114 0.243365 CGCCATTTTTGCAGCACCTA 59.757 50.000 0.00 0.00 0.00 3.08
114 115 1.713597 GCCATTTTTGCAGCACCTAC 58.286 50.000 0.00 0.00 0.00 3.18
115 116 1.273327 GCCATTTTTGCAGCACCTACT 59.727 47.619 0.00 0.00 0.00 2.57
116 117 2.927871 GCCATTTTTGCAGCACCTACTG 60.928 50.000 0.00 0.00 40.80 2.74
117 118 2.353011 CCATTTTTGCAGCACCTACTGG 60.353 50.000 0.00 0.00 38.16 4.00
118 119 2.356665 TTTTTGCAGCACCTACTGGA 57.643 45.000 0.00 0.00 38.16 3.86
119 120 1.896220 TTTTGCAGCACCTACTGGAG 58.104 50.000 0.00 0.00 39.32 3.86
124 125 2.985456 GCACCTACTGGAGCTGCT 59.015 61.111 6.82 0.00 44.80 4.24
125 126 1.153469 GCACCTACTGGAGCTGCTC 60.153 63.158 21.17 21.17 44.80 4.26
126 127 1.140589 CACCTACTGGAGCTGCTCG 59.859 63.158 22.25 12.63 37.04 5.03
127 128 2.105930 CCTACTGGAGCTGCTCGC 59.894 66.667 22.25 15.63 39.57 5.03
128 129 2.278466 CTACTGGAGCTGCTCGCG 60.278 66.667 22.25 17.25 45.59 5.87
129 130 4.498520 TACTGGAGCTGCTCGCGC 62.499 66.667 22.25 10.16 45.59 6.86
137 138 3.341043 CTGCTCGCGCGCCATATT 61.341 61.111 27.95 0.00 39.65 1.28
138 139 2.885676 CTGCTCGCGCGCCATATTT 61.886 57.895 27.95 0.00 39.65 1.40
139 140 2.327940 GCTCGCGCGCCATATTTT 59.672 55.556 27.95 0.00 0.00 1.82
140 141 2.005537 GCTCGCGCGCCATATTTTG 61.006 57.895 27.95 8.96 0.00 2.44
166 167 4.536316 GCTGGAGCCAGTGATCTG 57.464 61.111 17.23 0.00 45.24 2.90
167 168 1.818785 GCTGGAGCCAGTGATCTGC 60.819 63.158 17.23 0.00 45.24 4.26
168 169 1.906253 CTGGAGCCAGTGATCTGCT 59.094 57.895 8.38 0.00 40.09 4.24
169 170 0.462225 CTGGAGCCAGTGATCTGCTG 60.462 60.000 8.38 9.83 40.09 4.41
170 171 1.818785 GGAGCCAGTGATCTGCTGC 60.819 63.158 10.92 7.36 40.09 5.25
171 172 2.125229 AGCCAGTGATCTGCTGCG 60.125 61.111 10.92 6.98 40.09 5.18
172 173 2.435586 GCCAGTGATCTGCTGCGT 60.436 61.111 10.92 0.00 40.09 5.24
173 174 2.747822 GCCAGTGATCTGCTGCGTG 61.748 63.158 10.92 0.00 40.09 5.34
174 175 2.747822 CCAGTGATCTGCTGCGTGC 61.748 63.158 10.92 0.00 40.09 5.34
201 202 5.915812 AAAAATTCGGCGCTGTAAAAATT 57.084 30.435 17.37 11.69 0.00 1.82
203 204 7.589574 AAAAATTCGGCGCTGTAAAAATTAT 57.410 28.000 17.37 5.07 0.00 1.28
204 205 7.589574 AAAATTCGGCGCTGTAAAAATTATT 57.410 28.000 17.37 8.77 0.00 1.40
205 206 7.589574 AAATTCGGCGCTGTAAAAATTATTT 57.410 28.000 17.37 7.56 0.00 1.40
206 207 8.690680 AAATTCGGCGCTGTAAAAATTATTTA 57.309 26.923 17.37 0.00 0.00 1.40
207 208 7.908193 ATTCGGCGCTGTAAAAATTATTTAG 57.092 32.000 17.37 0.00 0.00 1.85
208 209 5.267776 TCGGCGCTGTAAAAATTATTTAGC 58.732 37.500 17.37 1.33 0.00 3.09
209 210 4.144051 CGGCGCTGTAAAAATTATTTAGCG 59.856 41.667 21.15 21.15 44.60 4.26
210 211 5.032220 GGCGCTGTAAAAATTATTTAGCGT 58.968 37.500 24.04 2.73 43.82 5.07
211 212 5.052633 GGCGCTGTAAAAATTATTTAGCGTG 60.053 40.000 24.04 7.26 43.82 5.34
212 213 5.551920 GCGCTGTAAAAATTATTTAGCGTGC 60.552 40.000 24.04 11.74 43.82 5.34
213 214 5.052633 CGCTGTAAAAATTATTTAGCGTGCC 60.053 40.000 18.65 0.00 38.27 5.01
214 215 5.052633 GCTGTAAAAATTATTTAGCGTGCCG 60.053 40.000 0.00 0.00 0.00 5.69
215 216 5.940595 TGTAAAAATTATTTAGCGTGCCGT 58.059 33.333 0.00 0.00 0.00 5.68
216 217 5.795939 TGTAAAAATTATTTAGCGTGCCGTG 59.204 36.000 0.00 0.00 0.00 4.94
217 218 4.428615 AAAATTATTTAGCGTGCCGTGT 57.571 36.364 0.00 0.00 0.00 4.49
218 219 3.398954 AATTATTTAGCGTGCCGTGTG 57.601 42.857 0.00 0.00 0.00 3.82
219 220 1.798283 TTATTTAGCGTGCCGTGTGT 58.202 45.000 0.00 0.00 0.00 3.72
220 221 1.798283 TATTTAGCGTGCCGTGTGTT 58.202 45.000 0.00 0.00 0.00 3.32
221 222 0.237235 ATTTAGCGTGCCGTGTGTTG 59.763 50.000 0.00 0.00 0.00 3.33
222 223 2.381665 TTTAGCGTGCCGTGTGTTGC 62.382 55.000 0.00 0.00 0.00 4.17
230 231 3.487202 CGTGTGTTGCGCGCCTAT 61.487 61.111 30.77 0.00 44.35 2.57
231 232 2.867472 GTGTGTTGCGCGCCTATT 59.133 55.556 30.77 0.00 0.00 1.73
232 233 1.511887 GTGTGTTGCGCGCCTATTG 60.512 57.895 30.77 0.00 0.00 1.90
233 234 1.669437 TGTGTTGCGCGCCTATTGA 60.669 52.632 30.77 5.30 0.00 2.57
234 235 1.231296 TGTGTTGCGCGCCTATTGAA 61.231 50.000 30.77 12.43 0.00 2.69
235 236 0.521242 GTGTTGCGCGCCTATTGAAG 60.521 55.000 30.77 0.00 0.00 3.02
236 237 0.672091 TGTTGCGCGCCTATTGAAGA 60.672 50.000 30.77 10.74 0.00 2.87
237 238 0.657840 GTTGCGCGCCTATTGAAGAT 59.342 50.000 30.77 0.00 0.00 2.40
238 239 0.657312 TTGCGCGCCTATTGAAGATG 59.343 50.000 30.77 0.00 0.00 2.90
239 240 1.082496 GCGCGCCTATTGAAGATGC 60.082 57.895 23.24 0.00 0.00 3.91
240 241 1.502163 GCGCGCCTATTGAAGATGCT 61.502 55.000 23.24 0.00 0.00 3.79
241 242 0.510359 CGCGCCTATTGAAGATGCTC 59.490 55.000 0.00 0.00 0.00 4.26
242 243 0.510359 GCGCCTATTGAAGATGCTCG 59.490 55.000 0.00 0.00 0.00 5.03
243 244 1.858091 CGCCTATTGAAGATGCTCGT 58.142 50.000 0.00 0.00 0.00 4.18
244 245 2.862530 GCGCCTATTGAAGATGCTCGTA 60.863 50.000 0.00 0.00 0.00 3.43
245 246 2.983136 CGCCTATTGAAGATGCTCGTAG 59.017 50.000 0.00 0.00 0.00 3.51
246 247 3.321497 GCCTATTGAAGATGCTCGTAGG 58.679 50.000 0.00 0.00 33.02 3.18
247 248 3.321497 CCTATTGAAGATGCTCGTAGGC 58.679 50.000 0.00 0.00 0.00 3.93
248 249 3.006323 CCTATTGAAGATGCTCGTAGGCT 59.994 47.826 0.00 0.00 0.00 4.58
249 250 2.586258 TTGAAGATGCTCGTAGGCTC 57.414 50.000 0.00 0.00 0.00 4.70
250 251 0.747255 TGAAGATGCTCGTAGGCTCC 59.253 55.000 0.00 0.00 0.00 4.70
251 252 0.032815 GAAGATGCTCGTAGGCTCCC 59.967 60.000 0.00 0.00 0.00 4.30
252 253 0.397816 AAGATGCTCGTAGGCTCCCT 60.398 55.000 0.00 0.00 37.71 4.20
253 254 1.112315 AGATGCTCGTAGGCTCCCTG 61.112 60.000 0.00 0.00 34.61 4.45
254 255 1.075970 ATGCTCGTAGGCTCCCTGA 60.076 57.895 0.00 0.00 34.61 3.86
255 256 0.470833 ATGCTCGTAGGCTCCCTGAT 60.471 55.000 0.00 0.00 34.61 2.90
256 257 1.365633 GCTCGTAGGCTCCCTGATG 59.634 63.158 0.00 0.00 34.61 3.07
257 258 1.109920 GCTCGTAGGCTCCCTGATGA 61.110 60.000 0.00 0.00 34.61 2.92
258 259 1.403814 CTCGTAGGCTCCCTGATGAA 58.596 55.000 0.00 0.00 34.61 2.57
259 260 1.067821 CTCGTAGGCTCCCTGATGAAC 59.932 57.143 0.00 0.00 34.61 3.18
269 270 0.541392 CCTGATGAACACCCGGATGA 59.459 55.000 0.36 0.00 0.00 2.92
270 271 1.473965 CCTGATGAACACCCGGATGAG 60.474 57.143 0.36 0.00 0.00 2.90
271 272 1.482182 CTGATGAACACCCGGATGAGA 59.518 52.381 0.36 0.00 0.00 3.27
272 273 2.103771 CTGATGAACACCCGGATGAGAT 59.896 50.000 0.36 0.00 0.00 2.75
559 617 1.473677 CTCACTCTGCTCTCACTCTGG 59.526 57.143 0.00 0.00 0.00 3.86
605 670 1.436195 CGCTCTCACTCTCCTCTCCG 61.436 65.000 0.00 0.00 0.00 4.63
608 673 0.107410 TCTCACTCTCCTCTCCGCTC 60.107 60.000 0.00 0.00 0.00 5.03
609 674 0.107214 CTCACTCTCCTCTCCGCTCT 60.107 60.000 0.00 0.00 0.00 4.09
610 675 0.393673 TCACTCTCCTCTCCGCTCTG 60.394 60.000 0.00 0.00 0.00 3.35
611 676 1.752694 ACTCTCCTCTCCGCTCTGC 60.753 63.158 0.00 0.00 0.00 4.26
612 677 1.453745 CTCTCCTCTCCGCTCTGCT 60.454 63.158 0.00 0.00 0.00 4.24
613 678 1.447317 CTCTCCTCTCCGCTCTGCTC 61.447 65.000 0.00 0.00 0.00 4.26
614 679 1.453745 CTCCTCTCCGCTCTGCTCT 60.454 63.158 0.00 0.00 0.00 4.09
615 680 1.000270 TCCTCTCCGCTCTGCTCTT 60.000 57.895 0.00 0.00 0.00 2.85
616 681 1.141449 CCTCTCCGCTCTGCTCTTG 59.859 63.158 0.00 0.00 0.00 3.02
617 682 1.141449 CTCTCCGCTCTGCTCTTGG 59.859 63.158 0.00 0.00 0.00 3.61
618 683 1.304464 TCTCCGCTCTGCTCTTGGA 60.304 57.895 0.00 0.00 0.00 3.53
619 684 1.141449 CTCCGCTCTGCTCTTGGAG 59.859 63.158 0.00 0.00 40.19 3.86
620 685 1.603236 CTCCGCTCTGCTCTTGGAGT 61.603 60.000 0.00 0.00 41.04 3.85
621 686 0.323451 TCCGCTCTGCTCTTGGAGTA 60.323 55.000 0.00 0.00 33.13 2.59
622 687 0.179124 CCGCTCTGCTCTTGGAGTAC 60.179 60.000 0.00 0.00 33.13 2.73
623 688 0.814457 CGCTCTGCTCTTGGAGTACT 59.186 55.000 0.00 0.00 33.13 2.73
624 689 1.202245 CGCTCTGCTCTTGGAGTACTC 60.202 57.143 14.87 14.87 33.13 2.59
1158 1249 2.904866 GGTTGTCCAGTGCCGCAA 60.905 61.111 0.00 0.00 0.00 4.85
1758 1867 5.591877 GCTTGTCCAAGATGTATCCAAGATT 59.408 40.000 11.12 0.00 40.79 2.40
2140 2257 7.354312 ACATCCAAGGCCTTTATAAGTATGTT 58.646 34.615 17.61 0.00 0.00 2.71
2185 2302 1.076350 TGGGGTGTACATTTTGGGGAG 59.924 52.381 0.00 0.00 0.00 4.30
2226 2343 8.147058 AGTCTATGTCTATGCCAATGTTAAGAG 58.853 37.037 0.00 0.00 0.00 2.85
2507 2644 0.252467 CCTCCTCCCTCCAGAACACT 60.252 60.000 0.00 0.00 0.00 3.55
2590 2727 0.251354 GAAGAGGAGGCAGTGCATGA 59.749 55.000 18.61 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.228124 GTTACAGCCCAGCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
1 2 0.323629 TAGTTACAGCCCAGCACCAC 59.676 55.000 0.00 0.00 0.00 4.16
3 4 1.668419 CATAGTTACAGCCCAGCACC 58.332 55.000 0.00 0.00 0.00 5.01
4 5 1.017387 GCATAGTTACAGCCCAGCAC 58.983 55.000 0.00 0.00 0.00 4.40
5 6 0.911769 AGCATAGTTACAGCCCAGCA 59.088 50.000 0.00 0.00 0.00 4.41
6 7 2.910688 TAGCATAGTTACAGCCCAGC 57.089 50.000 0.00 0.00 0.00 4.85
7 8 5.368145 TCAAATAGCATAGTTACAGCCCAG 58.632 41.667 0.00 0.00 0.00 4.45
8 9 5.366482 TCAAATAGCATAGTTACAGCCCA 57.634 39.130 0.00 0.00 0.00 5.36
9 10 6.884280 ATTCAAATAGCATAGTTACAGCCC 57.116 37.500 0.00 0.00 0.00 5.19
44 45 9.340695 CAACACATACGAACAATATGAAACAAT 57.659 29.630 0.00 0.00 34.65 2.71
45 46 7.324856 GCAACACATACGAACAATATGAAACAA 59.675 33.333 0.00 0.00 34.65 2.83
46 47 6.799441 GCAACACATACGAACAATATGAAACA 59.201 34.615 0.00 0.00 34.65 2.83
47 48 6.799441 TGCAACACATACGAACAATATGAAAC 59.201 34.615 0.00 0.00 34.65 2.78
48 49 6.903419 TGCAACACATACGAACAATATGAAA 58.097 32.000 0.00 0.00 34.65 2.69
49 50 6.487689 TGCAACACATACGAACAATATGAA 57.512 33.333 0.00 0.00 34.65 2.57
50 51 6.509358 CGATGCAACACATACGAACAATATGA 60.509 38.462 0.00 0.00 39.84 2.15
51 52 5.616785 CGATGCAACACATACGAACAATATG 59.383 40.000 0.00 0.00 39.84 1.78
52 53 5.293324 ACGATGCAACACATACGAACAATAT 59.707 36.000 0.00 0.00 39.84 1.28
53 54 4.627900 ACGATGCAACACATACGAACAATA 59.372 37.500 0.00 0.00 39.84 1.90
54 55 3.435327 ACGATGCAACACATACGAACAAT 59.565 39.130 0.00 0.00 39.84 2.71
55 56 2.803386 ACGATGCAACACATACGAACAA 59.197 40.909 0.00 0.00 39.84 2.83
56 57 2.409012 ACGATGCAACACATACGAACA 58.591 42.857 0.00 0.00 39.84 3.18
57 58 3.611113 ACTACGATGCAACACATACGAAC 59.389 43.478 0.00 0.00 39.84 3.95
58 59 3.840468 ACTACGATGCAACACATACGAA 58.160 40.909 0.00 0.00 39.84 3.85
59 60 3.497297 ACTACGATGCAACACATACGA 57.503 42.857 0.00 0.00 39.84 3.43
60 61 4.099824 TGTACTACGATGCAACACATACG 58.900 43.478 0.00 0.00 39.84 3.06
61 62 4.503007 CCTGTACTACGATGCAACACATAC 59.497 45.833 0.00 0.00 39.84 2.39
62 63 4.158949 ACCTGTACTACGATGCAACACATA 59.841 41.667 0.00 0.00 39.84 2.29
63 64 3.056107 ACCTGTACTACGATGCAACACAT 60.056 43.478 0.00 0.00 43.54 3.21
64 65 2.297880 ACCTGTACTACGATGCAACACA 59.702 45.455 0.00 0.00 0.00 3.72
65 66 2.955614 ACCTGTACTACGATGCAACAC 58.044 47.619 0.00 0.00 0.00 3.32
66 67 3.322369 CAACCTGTACTACGATGCAACA 58.678 45.455 0.00 0.00 0.00 3.33
67 68 2.093783 GCAACCTGTACTACGATGCAAC 59.906 50.000 0.00 0.00 32.80 4.17
68 69 2.028476 AGCAACCTGTACTACGATGCAA 60.028 45.455 0.00 0.00 34.89 4.08
69 70 1.548719 AGCAACCTGTACTACGATGCA 59.451 47.619 11.68 0.00 34.89 3.96
70 71 2.194271 GAGCAACCTGTACTACGATGC 58.806 52.381 0.00 0.00 0.00 3.91
71 72 2.451132 CGAGCAACCTGTACTACGATG 58.549 52.381 0.00 0.00 0.00 3.84
72 73 1.202268 GCGAGCAACCTGTACTACGAT 60.202 52.381 0.00 0.00 0.00 3.73
73 74 0.169672 GCGAGCAACCTGTACTACGA 59.830 55.000 0.00 0.00 0.00 3.43
74 75 1.132199 CGCGAGCAACCTGTACTACG 61.132 60.000 0.00 0.00 0.00 3.51
75 76 2.650163 CGCGAGCAACCTGTACTAC 58.350 57.895 0.00 0.00 0.00 2.73
88 89 3.535491 GCAAAAATGGCGCGCGAG 61.535 61.111 37.18 8.39 0.00 5.03
89 90 4.334109 TGCAAAAATGGCGCGCGA 62.334 55.556 37.18 23.73 0.00 5.87
90 91 3.829975 CTGCAAAAATGGCGCGCG 61.830 61.111 28.44 28.44 0.00 6.86
91 92 4.138109 GCTGCAAAAATGGCGCGC 62.138 61.111 25.94 25.94 0.00 6.86
92 93 2.733969 TGCTGCAAAAATGGCGCG 60.734 55.556 0.00 0.00 34.91 6.86
93 94 2.670210 GGTGCTGCAAAAATGGCGC 61.670 57.895 2.77 0.00 34.89 6.53
94 95 0.243365 TAGGTGCTGCAAAAATGGCG 59.757 50.000 2.77 0.00 0.00 5.69
95 96 1.273327 AGTAGGTGCTGCAAAAATGGC 59.727 47.619 2.77 0.00 0.00 4.40
96 97 2.353011 CCAGTAGGTGCTGCAAAAATGG 60.353 50.000 2.77 8.02 35.28 3.16
97 98 2.557924 TCCAGTAGGTGCTGCAAAAATG 59.442 45.455 2.77 2.23 35.28 2.32
98 99 2.821969 CTCCAGTAGGTGCTGCAAAAAT 59.178 45.455 2.77 0.00 35.28 1.82
99 100 2.229792 CTCCAGTAGGTGCTGCAAAAA 58.770 47.619 2.77 0.00 35.28 1.94
100 101 1.896220 CTCCAGTAGGTGCTGCAAAA 58.104 50.000 2.77 0.00 35.28 2.44
101 102 3.631453 CTCCAGTAGGTGCTGCAAA 57.369 52.632 2.77 0.00 35.28 3.68
109 110 2.716017 GCGAGCAGCTCCAGTAGGT 61.716 63.158 17.16 0.00 44.04 3.08
110 111 2.105930 GCGAGCAGCTCCAGTAGG 59.894 66.667 17.16 2.59 44.04 3.18
111 112 2.278466 CGCGAGCAGCTCCAGTAG 60.278 66.667 17.16 3.34 45.59 2.57
123 124 1.369209 CCAAAATATGGCGCGCGAG 60.369 57.895 37.18 8.39 43.80 5.03
124 125 2.712539 CCAAAATATGGCGCGCGA 59.287 55.556 37.18 23.73 43.80 5.87
151 152 1.600638 CAGCAGATCACTGGCTCCA 59.399 57.895 7.67 0.00 43.62 3.86
152 153 1.818785 GCAGCAGATCACTGGCTCC 60.819 63.158 15.24 0.00 43.62 4.70
153 154 2.172372 CGCAGCAGATCACTGGCTC 61.172 63.158 15.24 1.39 43.62 4.70
154 155 2.125229 CGCAGCAGATCACTGGCT 60.125 61.111 15.24 6.63 43.62 4.75
155 156 2.435586 ACGCAGCAGATCACTGGC 60.436 61.111 15.24 4.61 43.62 4.85
156 157 2.747822 GCACGCAGCAGATCACTGG 61.748 63.158 15.24 9.22 43.62 4.00
157 158 2.783275 GCACGCAGCAGATCACTG 59.217 61.111 10.56 10.56 45.91 3.66
179 180 5.915812 AATTTTTACAGCGCCGAATTTTT 57.084 30.435 2.29 0.00 0.00 1.94
180 181 7.589574 AATAATTTTTACAGCGCCGAATTTT 57.410 28.000 2.29 0.00 0.00 1.82
181 182 7.589574 AAATAATTTTTACAGCGCCGAATTT 57.410 28.000 2.29 0.00 0.00 1.82
182 183 7.043656 GCTAAATAATTTTTACAGCGCCGAATT 60.044 33.333 2.29 4.76 0.00 2.17
183 184 6.416750 GCTAAATAATTTTTACAGCGCCGAAT 59.583 34.615 2.29 0.00 0.00 3.34
184 185 5.740099 GCTAAATAATTTTTACAGCGCCGAA 59.260 36.000 2.29 0.00 0.00 4.30
185 186 5.267776 GCTAAATAATTTTTACAGCGCCGA 58.732 37.500 2.29 0.00 0.00 5.54
186 187 4.144051 CGCTAAATAATTTTTACAGCGCCG 59.856 41.667 17.85 0.00 39.29 6.46
187 188 5.032220 ACGCTAAATAATTTTTACAGCGCC 58.968 37.500 24.28 0.00 45.02 6.53
188 189 5.551920 GCACGCTAAATAATTTTTACAGCGC 60.552 40.000 24.28 0.00 45.02 5.92
189 190 5.052633 GGCACGCTAAATAATTTTTACAGCG 60.053 40.000 23.45 23.45 45.88 5.18
190 191 6.255884 GGCACGCTAAATAATTTTTACAGC 57.744 37.500 5.57 5.57 0.00 4.40
213 214 3.022401 AATAGGCGCGCAACACACG 62.022 57.895 34.42 0.00 0.00 4.49
214 215 1.511887 CAATAGGCGCGCAACACAC 60.512 57.895 34.42 14.51 0.00 3.82
215 216 1.231296 TTCAATAGGCGCGCAACACA 61.231 50.000 34.42 12.64 0.00 3.72
216 217 0.521242 CTTCAATAGGCGCGCAACAC 60.521 55.000 34.42 15.77 0.00 3.32
217 218 0.672091 TCTTCAATAGGCGCGCAACA 60.672 50.000 34.42 17.44 0.00 3.33
218 219 0.657840 ATCTTCAATAGGCGCGCAAC 59.342 50.000 34.42 17.03 0.00 4.17
219 220 0.657312 CATCTTCAATAGGCGCGCAA 59.343 50.000 34.42 21.08 0.00 4.85
220 221 1.775039 GCATCTTCAATAGGCGCGCA 61.775 55.000 34.42 14.59 0.00 6.09
221 222 1.082496 GCATCTTCAATAGGCGCGC 60.082 57.895 25.94 25.94 0.00 6.86
222 223 0.510359 GAGCATCTTCAATAGGCGCG 59.490 55.000 0.00 0.00 0.00 6.86
223 224 0.510359 CGAGCATCTTCAATAGGCGC 59.490 55.000 0.00 0.00 0.00 6.53
224 225 1.858091 ACGAGCATCTTCAATAGGCG 58.142 50.000 0.00 0.00 0.00 5.52
225 226 3.321497 CCTACGAGCATCTTCAATAGGC 58.679 50.000 0.00 0.00 0.00 3.93
226 227 3.006323 AGCCTACGAGCATCTTCAATAGG 59.994 47.826 0.00 0.00 32.50 2.57
227 228 4.233789 GAGCCTACGAGCATCTTCAATAG 58.766 47.826 0.00 0.00 34.23 1.73
228 229 3.005897 GGAGCCTACGAGCATCTTCAATA 59.994 47.826 0.00 0.00 34.23 1.90
229 230 2.224161 GGAGCCTACGAGCATCTTCAAT 60.224 50.000 0.00 0.00 34.23 2.57
230 231 1.137086 GGAGCCTACGAGCATCTTCAA 59.863 52.381 0.00 0.00 34.23 2.69
231 232 0.747255 GGAGCCTACGAGCATCTTCA 59.253 55.000 0.00 0.00 34.23 3.02
232 233 0.032815 GGGAGCCTACGAGCATCTTC 59.967 60.000 0.00 0.00 34.23 2.87
233 234 0.397816 AGGGAGCCTACGAGCATCTT 60.398 55.000 0.00 0.00 34.23 2.40
234 235 1.112315 CAGGGAGCCTACGAGCATCT 61.112 60.000 0.00 0.00 34.23 2.90
235 236 1.109920 TCAGGGAGCCTACGAGCATC 61.110 60.000 0.00 0.00 34.23 3.91
236 237 0.470833 ATCAGGGAGCCTACGAGCAT 60.471 55.000 0.00 0.00 34.23 3.79
237 238 1.075970 ATCAGGGAGCCTACGAGCA 60.076 57.895 0.00 0.00 34.23 4.26
238 239 1.109920 TCATCAGGGAGCCTACGAGC 61.110 60.000 0.00 0.00 29.64 5.03
239 240 1.067821 GTTCATCAGGGAGCCTACGAG 59.932 57.143 0.00 0.00 29.64 4.18
240 241 1.112113 GTTCATCAGGGAGCCTACGA 58.888 55.000 0.00 0.00 29.64 3.43
241 242 0.824109 TGTTCATCAGGGAGCCTACG 59.176 55.000 0.00 0.00 29.64 3.51
242 243 1.134371 GGTGTTCATCAGGGAGCCTAC 60.134 57.143 0.00 0.00 29.64 3.18
243 244 1.204146 GGTGTTCATCAGGGAGCCTA 58.796 55.000 0.00 0.00 29.64 3.93
244 245 1.566298 GGGTGTTCATCAGGGAGCCT 61.566 60.000 0.00 0.00 0.00 4.58
245 246 1.077429 GGGTGTTCATCAGGGAGCC 60.077 63.158 0.00 0.00 0.00 4.70
246 247 1.450312 CGGGTGTTCATCAGGGAGC 60.450 63.158 0.00 0.00 0.00 4.70
247 248 1.221840 CCGGGTGTTCATCAGGGAG 59.778 63.158 0.00 0.00 0.00 4.30
248 249 0.620410 ATCCGGGTGTTCATCAGGGA 60.620 55.000 0.00 0.91 0.00 4.20
249 250 0.464373 CATCCGGGTGTTCATCAGGG 60.464 60.000 6.53 0.00 0.00 4.45
250 251 0.541392 TCATCCGGGTGTTCATCAGG 59.459 55.000 15.92 0.00 0.00 3.86
251 252 1.482182 TCTCATCCGGGTGTTCATCAG 59.518 52.381 15.92 3.28 0.00 2.90
252 253 1.567357 TCTCATCCGGGTGTTCATCA 58.433 50.000 15.92 0.00 0.00 3.07
253 254 2.874701 CAATCTCATCCGGGTGTTCATC 59.125 50.000 15.92 0.00 0.00 2.92
254 255 2.505407 TCAATCTCATCCGGGTGTTCAT 59.495 45.455 15.92 2.17 0.00 2.57
255 256 1.905894 TCAATCTCATCCGGGTGTTCA 59.094 47.619 15.92 0.00 0.00 3.18
256 257 2.093447 ACTCAATCTCATCCGGGTGTTC 60.093 50.000 15.92 0.00 0.00 3.18
257 258 1.909302 ACTCAATCTCATCCGGGTGTT 59.091 47.619 15.92 0.00 0.00 3.32
258 259 1.573108 ACTCAATCTCATCCGGGTGT 58.427 50.000 15.92 0.00 0.00 4.16
259 260 3.819564 TTACTCAATCTCATCCGGGTG 57.180 47.619 8.97 8.97 0.00 4.61
272 273 9.953565 AGTGGTAGTTTTATGCTATTTACTCAA 57.046 29.630 0.00 0.00 0.00 3.02
329 343 7.012894 TGGTAGGTATCAGTCACAAACAAAAAG 59.987 37.037 0.00 0.00 0.00 2.27
392 407 1.003331 CGGTTCAAAACGCTAGCAACA 60.003 47.619 16.45 0.00 0.00 3.33
605 670 2.577449 GAGTACTCCAAGAGCAGAGC 57.423 55.000 12.13 0.00 33.18 4.09
617 682 1.133407 CGTCCAAGAGCAGGAGTACTC 59.867 57.143 14.87 14.87 35.42 2.59
618 683 1.178276 CGTCCAAGAGCAGGAGTACT 58.822 55.000 0.00 0.00 35.42 2.73
619 684 0.458716 GCGTCCAAGAGCAGGAGTAC 60.459 60.000 0.00 0.00 35.42 2.73
620 685 1.605058 GGCGTCCAAGAGCAGGAGTA 61.605 60.000 0.00 0.00 35.42 2.59
621 686 2.659610 GCGTCCAAGAGCAGGAGT 59.340 61.111 0.00 0.00 35.42 3.85
622 687 2.125350 GGCGTCCAAGAGCAGGAG 60.125 66.667 0.00 0.00 35.42 3.69
623 688 4.069232 CGGCGTCCAAGAGCAGGA 62.069 66.667 0.00 0.00 34.54 3.86
675 757 1.140852 CCGTCATTCCAGGAAGGCATA 59.859 52.381 9.14 0.00 37.29 3.14
1191 1282 6.780901 TCCTTGTAAATACATGTGTGGGTTA 58.219 36.000 9.11 0.00 35.89 2.85
1758 1867 3.364549 CCTACCATCCTGCCAATCAAAA 58.635 45.455 0.00 0.00 0.00 2.44
1943 2058 1.499007 ACCTCCTTTTTGCCTTCCTGA 59.501 47.619 0.00 0.00 0.00 3.86
2140 2257 5.164620 TCTTCACATCAGATTGTTAGGCA 57.835 39.130 0.00 0.00 0.00 4.75
2185 2302 7.936584 AGACATAGACTAGATTAGCTTCACAC 58.063 38.462 0.00 0.00 0.00 3.82
2226 2343 4.271291 GGTTCTAGCAGCATAAACTACAGC 59.729 45.833 0.00 0.00 0.00 4.40
2590 2727 1.067295 TTGCCTCCTCACATCCACTT 58.933 50.000 0.00 0.00 0.00 3.16
2887 3028 4.347000 GTGGAAGGGGTACATAGCTCATAA 59.653 45.833 0.00 0.00 0.00 1.90
2901 3042 3.146847 GTTGTACAGAAAGTGGAAGGGG 58.853 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.