Multiple sequence alignment - TraesCS6D01G066400

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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 TraesCS6D01G066400 chr6D 100.000 3043 0 0 483 3525 32641307 32638265 0.000000e+00 5620
1 TraesCS6D01G066400 chr6D 100.000 292 0 0 1 292 32641789 32641498 1.110000e-149 540
2 TraesCS6D01G066400 chr6D 77.436 390 74 10 863 1248 467839409 467839788 1.650000e-53 220
3 TraesCS6D01G066400 chr6D 92.233 103 8 0 172 274 32641307 32641205 2.840000e-31 147
4 TraesCS6D01G066400 chr6D 92.233 103 8 0 483 585 32641618 32641516 2.840000e-31 147
5 TraesCS6D01G066400 chr6A 94.708 2721 107 12 483 3197 36992144 36989455 0.000000e+00 4193
6 TraesCS6D01G066400 chr6A 93.116 276 7 3 3250 3525 36989443 36989180 9.170000e-106 394
7 TraesCS6D01G066400 chr6A 90.411 219 12 7 66 275 36992259 36992041 2.680000e-71 279
8 TraesCS6D01G066400 chr6A 76.570 414 81 10 863 1271 613956642 613957044 2.760000e-51 213
9 TraesCS6D01G066400 chr6A 94.118 119 7 0 172 290 36992294 36992176 7.770000e-42 182
10 TraesCS6D01G066400 chr6A 92.233 103 8 0 483 585 36992294 36992192 2.840000e-31 147
11 TraesCS6D01G066400 chr6B 88.706 1399 123 12 613 1990 68394920 68393536 0.000000e+00 1676
12 TraesCS6D01G066400 chr6B 79.718 1065 157 26 2048 3097 68392200 68391180 0.000000e+00 715
13 TraesCS6D01G066400 chr6B 77.692 390 73 11 863 1248 713838936 713839315 3.540000e-55 226
14 TraesCS6D01G066400 chr4D 77.402 1093 190 32 863 1934 507423921 507422865 6.510000e-167 597
15 TraesCS6D01G066400 chr7D 78.276 580 106 17 1359 1934 3094616 3094053 4.330000e-94 355
16 TraesCS6D01G066400 chr7D 78.276 580 106 17 1359 1934 3169136 3169699 4.330000e-94 355
17 TraesCS6D01G066400 chr5B 79.714 419 73 9 853 1269 25335806 25335398 3.440000e-75 292
18 TraesCS6D01G066400 chr1B 78.934 394 74 6 878 1271 13417207 13416823 3.490000e-65 259
19 TraesCS6D01G066400 chr1B 78.734 395 73 7 878 1271 13391495 13391111 1.620000e-63 254
20 TraesCS6D01G066400 chr1B 78.155 412 77 8 862 1271 13039604 13040004 2.100000e-62 250
21 TraesCS6D01G066400 chr2D 76.301 519 88 20 1424 1938 11148744 11148257 9.770000e-61 244
22 TraesCS6D01G066400 chr2B 76.023 513 88 21 1430 1938 16959599 16959118 2.120000e-57 233
23 TraesCS6D01G066400 chr2B 75.681 514 88 22 1430 1938 16927020 16926539 4.580000e-54 222


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 TraesCS6D01G066400 chr6D 32638265 32641789 3524 True 1613.5 5620 96.1165 1 3525 4 chr6D.!!$R1 3524
1 TraesCS6D01G066400 chr6A 36989180 36992294 3114 True 1039.0 4193 92.9172 66 3525 5 chr6A.!!$R1 3459
2 TraesCS6D01G066400 chr6B 68391180 68394920 3740 True 1195.5 1676 84.2120 613 3097 2 chr6B.!!$R1 2484
3 TraesCS6D01G066400 chr4D 507422865 507423921 1056 True 597.0 597 77.4020 863 1934 1 chr4D.!!$R1 1071
4 TraesCS6D01G066400 chr7D 3094053 3094616 563 True 355.0 355 78.2760 1359 1934 1 chr7D.!!$R1 575
5 TraesCS6D01G066400 chr7D 3169136 3169699 563 False 355.0 355 78.2760 1359 1934 1 chr7D.!!$F1 575

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
37 38 0.096108 GCTGAGCTCGCACTTTAAGC 59.904 55.0 20.64 12.73 36.27 3.09 F
111 112 0.110192 GTTGTCTTGTGCTTAGCGCC 60.110 55.0 15.51 0.82 38.39 6.53 F
843 859 0.112218 CAAACCCCCACCAGACATCA 59.888 55.0 0.00 0.00 0.00 3.07 F
846 862 0.112412 ACCCCCACCAGACATCAAAC 59.888 55.0 0.00 0.00 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1387 0.725686 CTTCCTGATGAAGTGCAGCG 59.274 55.000 0.00 0.0 44.59 5.18 R
1356 1399 2.701551 TCCACCTTTTCCTCTTCCTGA 58.298 47.619 0.00 0.0 0.00 3.86 R
2183 3519 0.594602 GCATGCTGCTGTTTCTCACA 59.405 50.000 11.37 0.0 40.96 3.58 R
2711 4059 1.154225 CAACATTCAGTTCCCGCGC 60.154 57.895 0.00 0.0 38.74 6.86 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 2.932663 AGGTCCACTTGCGAACATG 58.067 52.632 0.00 0.00 0.00 3.21
19 20 1.210155 GGTCCACTTGCGAACATGC 59.790 57.895 0.00 0.00 0.00 4.06
20 21 1.237285 GGTCCACTTGCGAACATGCT 61.237 55.000 0.00 0.00 35.36 3.79
21 22 0.110056 GTCCACTTGCGAACATGCTG 60.110 55.000 0.00 0.00 35.36 4.41
22 23 0.250252 TCCACTTGCGAACATGCTGA 60.250 50.000 0.00 0.00 35.36 4.26
23 24 0.167470 CCACTTGCGAACATGCTGAG 59.833 55.000 0.00 0.00 35.36 3.35
24 25 0.453950 CACTTGCGAACATGCTGAGC 60.454 55.000 0.00 0.00 35.36 4.26
25 26 0.604780 ACTTGCGAACATGCTGAGCT 60.605 50.000 5.83 0.00 35.36 4.09
26 27 0.096628 CTTGCGAACATGCTGAGCTC 59.903 55.000 6.82 6.82 35.36 4.09
27 28 1.629345 TTGCGAACATGCTGAGCTCG 61.629 55.000 9.64 7.77 35.36 5.03
28 29 2.699809 CGAACATGCTGAGCTCGC 59.300 61.111 19.33 19.33 0.00 5.03
29 30 2.096442 CGAACATGCTGAGCTCGCA 61.096 57.895 27.06 27.06 42.25 5.10
30 31 1.423056 GAACATGCTGAGCTCGCAC 59.577 57.895 27.31 15.51 40.65 5.34
31 32 1.004080 AACATGCTGAGCTCGCACT 60.004 52.632 27.31 16.63 40.65 4.40
32 33 0.604780 AACATGCTGAGCTCGCACTT 60.605 50.000 27.31 20.13 40.65 3.16
33 34 0.604780 ACATGCTGAGCTCGCACTTT 60.605 50.000 27.31 14.50 40.65 2.66
34 35 1.338105 ACATGCTGAGCTCGCACTTTA 60.338 47.619 27.31 11.19 40.65 1.85
35 36 1.733912 CATGCTGAGCTCGCACTTTAA 59.266 47.619 27.31 10.61 40.65 1.52
36 37 1.432514 TGCTGAGCTCGCACTTTAAG 58.567 50.000 23.20 8.71 31.40 1.85
37 38 0.096108 GCTGAGCTCGCACTTTAAGC 59.904 55.000 20.64 12.73 36.27 3.09
40 41 3.145228 AGCTCGCACTTTAAGCTCC 57.855 52.632 0.00 0.00 42.58 4.70
41 42 0.610687 AGCTCGCACTTTAAGCTCCT 59.389 50.000 0.00 0.00 42.58 3.69
42 43 1.003108 GCTCGCACTTTAAGCTCCTC 58.997 55.000 0.00 0.00 33.23 3.71
43 44 1.404851 GCTCGCACTTTAAGCTCCTCT 60.405 52.381 0.00 0.00 33.23 3.69
44 45 2.933056 GCTCGCACTTTAAGCTCCTCTT 60.933 50.000 0.00 0.00 38.79 2.85
45 46 3.330267 CTCGCACTTTAAGCTCCTCTTT 58.670 45.455 0.00 0.00 36.25 2.52
46 47 3.326747 TCGCACTTTAAGCTCCTCTTTC 58.673 45.455 0.00 0.00 36.25 2.62
47 48 3.006967 TCGCACTTTAAGCTCCTCTTTCT 59.993 43.478 0.00 0.00 36.25 2.52
48 49 3.748568 CGCACTTTAAGCTCCTCTTTCTT 59.251 43.478 0.00 0.00 36.25 2.52
49 50 4.143009 CGCACTTTAAGCTCCTCTTTCTTC 60.143 45.833 0.00 0.00 36.25 2.87
50 51 4.757149 GCACTTTAAGCTCCTCTTTCTTCA 59.243 41.667 0.00 0.00 36.25 3.02
51 52 5.106752 GCACTTTAAGCTCCTCTTTCTTCAG 60.107 44.000 0.00 0.00 36.25 3.02
52 53 5.994668 CACTTTAAGCTCCTCTTTCTTCAGT 59.005 40.000 0.00 0.00 36.25 3.41
53 54 6.147000 CACTTTAAGCTCCTCTTTCTTCAGTC 59.853 42.308 0.00 0.00 36.25 3.51
54 55 3.311486 AAGCTCCTCTTTCTTCAGTCG 57.689 47.619 0.00 0.00 0.00 4.18
55 56 1.067213 AGCTCCTCTTTCTTCAGTCGC 60.067 52.381 0.00 0.00 0.00 5.19
56 57 1.337260 GCTCCTCTTTCTTCAGTCGCA 60.337 52.381 0.00 0.00 0.00 5.10
57 58 2.868044 GCTCCTCTTTCTTCAGTCGCAA 60.868 50.000 0.00 0.00 0.00 4.85
58 59 3.393800 CTCCTCTTTCTTCAGTCGCAAA 58.606 45.455 0.00 0.00 0.00 3.68
59 60 3.804036 TCCTCTTTCTTCAGTCGCAAAA 58.196 40.909 0.00 0.00 0.00 2.44
60 61 4.196193 TCCTCTTTCTTCAGTCGCAAAAA 58.804 39.130 0.00 0.00 0.00 1.94
87 88 9.830975 AAATAAGCTCCTCTTTCTTAATCTCTC 57.169 33.333 0.00 0.00 36.25 3.20
88 89 5.869649 AGCTCCTCTTTCTTAATCTCTCC 57.130 43.478 0.00 0.00 0.00 3.71
89 90 5.528337 AGCTCCTCTTTCTTAATCTCTCCT 58.472 41.667 0.00 0.00 0.00 3.69
90 91 5.963865 AGCTCCTCTTTCTTAATCTCTCCTT 59.036 40.000 0.00 0.00 0.00 3.36
91 92 6.443527 AGCTCCTCTTTCTTAATCTCTCCTTT 59.556 38.462 0.00 0.00 0.00 3.11
92 93 6.538381 GCTCCTCTTTCTTAATCTCTCCTTTG 59.462 42.308 0.00 0.00 0.00 2.77
93 94 7.560796 TCCTCTTTCTTAATCTCTCCTTTGT 57.439 36.000 0.00 0.00 0.00 2.83
94 95 7.978925 TCCTCTTTCTTAATCTCTCCTTTGTT 58.021 34.615 0.00 0.00 0.00 2.83
95 96 7.880195 TCCTCTTTCTTAATCTCTCCTTTGTTG 59.120 37.037 0.00 0.00 0.00 3.33
96 97 7.663493 CCTCTTTCTTAATCTCTCCTTTGTTGT 59.337 37.037 0.00 0.00 0.00 3.32
97 98 8.608844 TCTTTCTTAATCTCTCCTTTGTTGTC 57.391 34.615 0.00 0.00 0.00 3.18
98 99 8.432805 TCTTTCTTAATCTCTCCTTTGTTGTCT 58.567 33.333 0.00 0.00 0.00 3.41
99 100 8.980481 TTTCTTAATCTCTCCTTTGTTGTCTT 57.020 30.769 0.00 0.00 0.00 3.01
100 101 7.969536 TCTTAATCTCTCCTTTGTTGTCTTG 57.030 36.000 0.00 0.00 0.00 3.02
101 102 7.509546 TCTTAATCTCTCCTTTGTTGTCTTGT 58.490 34.615 0.00 0.00 0.00 3.16
102 103 7.442364 TCTTAATCTCTCCTTTGTTGTCTTGTG 59.558 37.037 0.00 0.00 0.00 3.33
103 104 3.206150 TCTCTCCTTTGTTGTCTTGTGC 58.794 45.455 0.00 0.00 0.00 4.57
104 105 3.118261 TCTCTCCTTTGTTGTCTTGTGCT 60.118 43.478 0.00 0.00 0.00 4.40
105 106 3.620488 TCTCCTTTGTTGTCTTGTGCTT 58.380 40.909 0.00 0.00 0.00 3.91
106 107 4.776349 TCTCCTTTGTTGTCTTGTGCTTA 58.224 39.130 0.00 0.00 0.00 3.09
107 108 4.816385 TCTCCTTTGTTGTCTTGTGCTTAG 59.184 41.667 0.00 0.00 0.00 2.18
108 109 3.315191 TCCTTTGTTGTCTTGTGCTTAGC 59.685 43.478 0.00 0.00 0.00 3.09
109 110 3.291585 CTTTGTTGTCTTGTGCTTAGCG 58.708 45.455 0.00 0.00 0.00 4.26
110 111 0.586319 TGTTGTCTTGTGCTTAGCGC 59.414 50.000 11.21 11.21 39.75 5.92
111 112 0.110192 GTTGTCTTGTGCTTAGCGCC 60.110 55.000 15.51 0.82 38.39 6.53
112 113 1.565156 TTGTCTTGTGCTTAGCGCCG 61.565 55.000 15.51 6.57 38.39 6.46
113 114 2.027625 GTCTTGTGCTTAGCGCCGT 61.028 57.895 15.51 0.00 38.39 5.68
114 115 1.301401 TCTTGTGCTTAGCGCCGTT 60.301 52.632 15.51 0.00 38.39 4.44
115 116 1.154413 CTTGTGCTTAGCGCCGTTG 60.154 57.895 15.51 0.00 38.39 4.10
116 117 2.513065 CTTGTGCTTAGCGCCGTTGG 62.513 60.000 15.51 0.00 38.39 3.77
117 118 2.740826 GTGCTTAGCGCCGTTGGA 60.741 61.111 2.29 0.00 38.05 3.53
118 119 2.434185 TGCTTAGCGCCGTTGGAG 60.434 61.111 2.29 0.00 38.05 3.86
119 120 2.125673 GCTTAGCGCCGTTGGAGA 60.126 61.111 2.29 0.00 0.00 3.71
120 121 1.740296 GCTTAGCGCCGTTGGAGAA 60.740 57.895 2.29 0.00 0.00 2.87
121 122 1.967597 GCTTAGCGCCGTTGGAGAAC 61.968 60.000 2.29 0.00 0.00 3.01
136 137 4.266714 TGGAGAACGGATCCAATTAAACC 58.733 43.478 13.41 9.66 43.87 3.27
137 138 3.630769 GGAGAACGGATCCAATTAAACCC 59.369 47.826 13.41 0.00 36.79 4.11
138 139 4.524053 GAGAACGGATCCAATTAAACCCT 58.476 43.478 13.41 0.00 0.00 4.34
139 140 5.397109 GGAGAACGGATCCAATTAAACCCTA 60.397 44.000 13.41 0.00 36.79 3.53
140 141 6.069705 AGAACGGATCCAATTAAACCCTAA 57.930 37.500 13.41 0.00 0.00 2.69
141 142 6.486941 AGAACGGATCCAATTAAACCCTAAA 58.513 36.000 13.41 0.00 0.00 1.85
142 143 6.376299 AGAACGGATCCAATTAAACCCTAAAC 59.624 38.462 13.41 0.00 0.00 2.01
143 144 4.951715 ACGGATCCAATTAAACCCTAAACC 59.048 41.667 13.41 0.00 0.00 3.27
144 145 4.340097 CGGATCCAATTAAACCCTAAACCC 59.660 45.833 13.41 0.00 0.00 4.11
145 146 5.525484 GGATCCAATTAAACCCTAAACCCT 58.475 41.667 6.95 0.00 0.00 4.34
146 147 6.635415 CGGATCCAATTAAACCCTAAACCCTA 60.635 42.308 13.41 0.00 0.00 3.53
147 148 7.127405 GGATCCAATTAAACCCTAAACCCTAA 58.873 38.462 6.95 0.00 0.00 2.69
148 149 7.620491 GGATCCAATTAAACCCTAAACCCTAAA 59.380 37.037 6.95 0.00 0.00 1.85
149 150 7.779754 TCCAATTAAACCCTAAACCCTAAAC 57.220 36.000 0.00 0.00 0.00 2.01
150 151 6.725369 TCCAATTAAACCCTAAACCCTAAACC 59.275 38.462 0.00 0.00 0.00 3.27
151 152 6.070653 CCAATTAAACCCTAAACCCTAAACCC 60.071 42.308 0.00 0.00 0.00 4.11
152 153 3.548162 AAACCCTAAACCCTAAACCCC 57.452 47.619 0.00 0.00 0.00 4.95
153 154 2.463671 ACCCTAAACCCTAAACCCCT 57.536 50.000 0.00 0.00 0.00 4.79
154 155 3.601204 ACCCTAAACCCTAAACCCCTA 57.399 47.619 0.00 0.00 0.00 3.53
155 156 4.112548 ACCCTAAACCCTAAACCCCTAT 57.887 45.455 0.00 0.00 0.00 2.57
156 157 4.460973 ACCCTAAACCCTAAACCCCTATT 58.539 43.478 0.00 0.00 0.00 1.73
157 158 4.865592 ACCCTAAACCCTAAACCCCTATTT 59.134 41.667 0.00 0.00 0.00 1.40
158 159 5.043881 ACCCTAAACCCTAAACCCCTATTTC 60.044 44.000 0.00 0.00 0.00 2.17
159 160 5.195146 CCCTAAACCCTAAACCCCTATTTCT 59.805 44.000 0.00 0.00 0.00 2.52
160 161 6.363065 CCTAAACCCTAAACCCCTATTTCTC 58.637 44.000 0.00 0.00 0.00 2.87
161 162 6.159928 CCTAAACCCTAAACCCCTATTTCTCT 59.840 42.308 0.00 0.00 0.00 3.10
162 163 5.712084 AACCCTAAACCCCTATTTCTCTC 57.288 43.478 0.00 0.00 0.00 3.20
163 164 4.974194 ACCCTAAACCCCTATTTCTCTCT 58.026 43.478 0.00 0.00 0.00 3.10
164 165 4.969999 ACCCTAAACCCCTATTTCTCTCTC 59.030 45.833 0.00 0.00 0.00 3.20
165 166 5.220521 CCCTAAACCCCTATTTCTCTCTCT 58.779 45.833 0.00 0.00 0.00 3.10
166 167 5.305902 CCCTAAACCCCTATTTCTCTCTCTC 59.694 48.000 0.00 0.00 0.00 3.20
167 168 6.140377 CCTAAACCCCTATTTCTCTCTCTCT 58.860 44.000 0.00 0.00 0.00 3.10
168 169 6.266786 CCTAAACCCCTATTTCTCTCTCTCTC 59.733 46.154 0.00 0.00 0.00 3.20
169 170 4.890499 ACCCCTATTTCTCTCTCTCTCA 57.110 45.455 0.00 0.00 0.00 3.27
170 171 5.213868 ACCCCTATTTCTCTCTCTCTCAA 57.786 43.478 0.00 0.00 0.00 3.02
171 172 5.594777 ACCCCTATTTCTCTCTCTCTCAAA 58.405 41.667 0.00 0.00 0.00 2.69
172 173 6.026186 ACCCCTATTTCTCTCTCTCTCAAAA 58.974 40.000 0.00 0.00 0.00 2.44
173 174 6.156083 ACCCCTATTTCTCTCTCTCTCAAAAG 59.844 42.308 0.00 0.00 0.00 2.27
174 175 6.382570 CCCCTATTTCTCTCTCTCTCAAAAGA 59.617 42.308 0.00 0.00 0.00 2.52
175 176 7.071071 CCCCTATTTCTCTCTCTCTCAAAAGAT 59.929 40.741 0.00 0.00 0.00 2.40
181 182 5.652014 TCTCTCTCTCTCAAAAGATCCACTC 59.348 44.000 0.00 0.00 0.00 3.51
184 185 2.562738 TCTCTCAAAAGATCCACTCGCA 59.437 45.455 0.00 0.00 0.00 5.10
206 207 3.646554 TGCTGAGCTTGCACTTCG 58.353 55.556 5.83 0.00 35.31 3.79
285 286 4.324022 CGGATCCAACTAAACCCTAAACCT 60.324 45.833 13.41 0.00 0.00 3.50
290 291 6.306199 TCCAACTAAACCCTAAACCTTAACC 58.694 40.000 0.00 0.00 0.00 2.85
561 562 1.238439 TTGCTGTCTTGTGCTTAGCC 58.762 50.000 0.29 0.00 33.60 3.93
585 586 0.613853 TGGAGACCGGACCCAACTAG 60.614 60.000 9.46 0.00 0.00 2.57
586 587 0.614134 GGAGACCGGACCCAACTAGT 60.614 60.000 9.46 0.00 0.00 2.57
661 663 3.909732 ACTAGTTCTCTCCCCATCTCTG 58.090 50.000 0.00 0.00 0.00 3.35
734 736 0.322008 CCAGCCGAGCTCCTCTTTTT 60.322 55.000 8.47 0.00 36.40 1.94
735 737 1.082690 CAGCCGAGCTCCTCTTTTTC 58.917 55.000 8.47 0.00 36.40 2.29
752 754 7.597743 CCTCTTTTTCAATCTCTCATTTGTTGG 59.402 37.037 0.00 0.00 0.00 3.77
754 756 6.409524 TTTTCAATCTCTCATTTGTTGGCT 57.590 33.333 0.00 0.00 0.00 4.75
755 757 6.409524 TTTCAATCTCTCATTTGTTGGCTT 57.590 33.333 0.00 0.00 0.00 4.35
756 758 5.381174 TCAATCTCTCATTTGTTGGCTTG 57.619 39.130 0.00 0.00 0.00 4.01
774 776 3.302555 CTTGTTGTGCTTGTACATGCAG 58.697 45.455 30.38 17.12 41.27 4.41
787 796 0.171903 CATGCAGCCACAGCCTTAAC 59.828 55.000 0.00 0.00 41.25 2.01
790 799 1.087501 GCAGCCACAGCCTTAACTAC 58.912 55.000 0.00 0.00 41.25 2.73
823 832 2.913777 TCACTACCGATCGACACAAG 57.086 50.000 18.66 8.47 0.00 3.16
841 857 1.228862 GCAAACCCCCACCAGACAT 60.229 57.895 0.00 0.00 0.00 3.06
842 858 1.250840 GCAAACCCCCACCAGACATC 61.251 60.000 0.00 0.00 0.00 3.06
843 859 0.112218 CAAACCCCCACCAGACATCA 59.888 55.000 0.00 0.00 0.00 3.07
844 860 0.856982 AAACCCCCACCAGACATCAA 59.143 50.000 0.00 0.00 0.00 2.57
845 861 0.856982 AACCCCCACCAGACATCAAA 59.143 50.000 0.00 0.00 0.00 2.69
846 862 0.112412 ACCCCCACCAGACATCAAAC 59.888 55.000 0.00 0.00 0.00 2.93
847 863 0.112218 CCCCCACCAGACATCAAACA 59.888 55.000 0.00 0.00 0.00 2.83
865 881 2.504367 ACACCAGCTAAGCGAAAATGT 58.496 42.857 0.00 0.00 0.00 2.71
881 897 1.676678 ATGTAGGCGACGGTGCTGAT 61.677 55.000 0.00 0.00 34.52 2.90
933 949 0.756903 GCTACTCCCAATCCGCCTTA 59.243 55.000 0.00 0.00 0.00 2.69
1098 1114 2.279252 GTCCGCGACGTGGCATAT 60.279 61.111 22.62 0.00 32.51 1.78
1100 1116 3.337889 CCGCGACGTGGCATATGG 61.338 66.667 22.58 11.30 0.00 2.74
1146 1162 1.066430 GCCGTCAGGTTAGATCACCAA 60.066 52.381 5.11 0.00 39.62 3.67
1215 1231 2.174360 GCCAAGGAAATGAAGGAGCTT 58.826 47.619 0.00 0.00 0.00 3.74
1263 1279 0.616891 GGAATGTCCGGTACCACCTT 59.383 55.000 13.54 2.63 35.66 3.50
1344 1387 1.012234 CGCCGAAGCAAAGATACGC 60.012 57.895 0.00 0.00 39.83 4.42
1356 1399 0.179100 AGATACGCGCTGCACTTCAT 60.179 50.000 5.73 0.00 0.00 2.57
1389 1432 1.207791 AGGTGGATCTTGCCGAGATT 58.792 50.000 0.00 0.00 45.17 2.40
2039 3375 3.887741 TCAGTGCATCGTTGTTTTGATG 58.112 40.909 0.00 0.00 43.78 3.07
2248 3584 2.196997 TAGTGGCAGCCGCTTTGGAT 62.197 55.000 32.36 10.14 42.24 3.41
2256 3592 1.065199 AGCCGCTTTGGATGAAGATCA 60.065 47.619 0.00 0.00 42.00 2.92
2508 3856 1.333619 TGGAGACAAAGAAAAGCACGC 59.666 47.619 0.00 0.00 37.44 5.34
2522 3870 0.030638 GCACGCCACTGAAACACAAT 59.969 50.000 0.00 0.00 0.00 2.71
2537 3885 9.743057 CTGAAACACAATAAAGTAACAATGGAA 57.257 29.630 0.00 0.00 0.00 3.53
2690 4038 3.059884 CCATCATCGAAGGACAATACCG 58.940 50.000 0.00 0.00 34.73 4.02
2710 4058 2.738643 CGCTAACCGGATCATTGTCACT 60.739 50.000 9.46 0.00 0.00 3.41
2711 4059 2.609459 GCTAACCGGATCATTGTCACTG 59.391 50.000 9.46 0.00 0.00 3.66
2936 4285 2.112815 GTACTGATGGGCGGGCAAC 61.113 63.158 3.27 0.00 0.00 4.17
3088 4437 8.344831 TGCAGTTCTGTACATATTCATTTATGC 58.655 33.333 0.00 0.00 33.67 3.14
3197 4546 4.895889 TGCTTCACTGAGGCTACATATACT 59.104 41.667 13.76 0.00 35.64 2.12
3198 4547 5.221322 TGCTTCACTGAGGCTACATATACTG 60.221 44.000 13.76 0.00 35.64 2.74
3199 4548 5.010112 GCTTCACTGAGGCTACATATACTGA 59.990 44.000 5.90 0.00 31.81 3.41
3200 4549 6.295011 GCTTCACTGAGGCTACATATACTGAT 60.295 42.308 5.90 0.00 31.81 2.90
3201 4550 6.581171 TCACTGAGGCTACATATACTGATG 57.419 41.667 0.00 0.00 0.00 3.07
3205 4554 6.208402 ACTGAGGCTACATATACTGATGAGTG 59.792 42.308 0.00 0.00 33.21 3.51
3207 4556 6.551227 TGAGGCTACATATACTGATGAGTGTT 59.449 38.462 0.00 0.00 33.21 3.32
3208 4557 6.753180 AGGCTACATATACTGATGAGTGTTG 58.247 40.000 0.00 0.00 33.21 3.33
3209 4558 5.928839 GGCTACATATACTGATGAGTGTTGG 59.071 44.000 0.00 0.00 33.21 3.77
3210 4559 6.463049 GGCTACATATACTGATGAGTGTTGGT 60.463 42.308 0.00 0.00 33.21 3.67
3211 4560 6.642950 GCTACATATACTGATGAGTGTTGGTC 59.357 42.308 0.00 0.00 33.21 4.02
3212 4561 6.798427 ACATATACTGATGAGTGTTGGTCT 57.202 37.500 0.00 0.00 33.21 3.85
3213 4562 7.187824 ACATATACTGATGAGTGTTGGTCTT 57.812 36.000 0.00 0.00 33.21 3.01
3214 4563 8.306313 ACATATACTGATGAGTGTTGGTCTTA 57.694 34.615 0.00 0.00 33.21 2.10
3215 4564 8.198109 ACATATACTGATGAGTGTTGGTCTTAC 58.802 37.037 0.00 0.00 33.21 2.34
3216 4565 6.859112 ATACTGATGAGTGTTGGTCTTACT 57.141 37.500 0.00 0.00 33.21 2.24
3217 4566 5.140747 ACTGATGAGTGTTGGTCTTACTC 57.859 43.478 0.00 0.00 40.85 2.59
3222 4571 4.693283 TGAGTGTTGGTCTTACTCACTTG 58.307 43.478 0.00 0.00 44.10 3.16
3223 4572 4.404394 TGAGTGTTGGTCTTACTCACTTGA 59.596 41.667 0.00 0.00 44.10 3.02
3224 4573 5.070446 TGAGTGTTGGTCTTACTCACTTGAT 59.930 40.000 0.00 0.00 44.10 2.57
3225 4574 5.930135 AGTGTTGGTCTTACTCACTTGATT 58.070 37.500 0.00 0.00 36.17 2.57
3226 4575 7.062749 AGTGTTGGTCTTACTCACTTGATTA 57.937 36.000 0.00 0.00 36.17 1.75
3227 4576 7.680730 AGTGTTGGTCTTACTCACTTGATTAT 58.319 34.615 0.00 0.00 36.17 1.28
3228 4577 7.604164 AGTGTTGGTCTTACTCACTTGATTATG 59.396 37.037 0.00 0.00 36.17 1.90
3229 4578 7.387948 GTGTTGGTCTTACTCACTTGATTATGT 59.612 37.037 0.00 0.00 0.00 2.29
3230 4579 7.602644 TGTTGGTCTTACTCACTTGATTATGTC 59.397 37.037 0.00 0.00 0.00 3.06
3231 4580 6.640518 TGGTCTTACTCACTTGATTATGTCC 58.359 40.000 0.00 0.00 0.00 4.02
3232 4581 6.049790 GGTCTTACTCACTTGATTATGTCCC 58.950 44.000 0.00 0.00 0.00 4.46
3233 4582 6.127026 GGTCTTACTCACTTGATTATGTCCCT 60.127 42.308 0.00 0.00 0.00 4.20
3234 4583 7.331791 GTCTTACTCACTTGATTATGTCCCTT 58.668 38.462 0.00 0.00 0.00 3.95
3235 4584 7.824779 GTCTTACTCACTTGATTATGTCCCTTT 59.175 37.037 0.00 0.00 0.00 3.11
3236 4585 9.042450 TCTTACTCACTTGATTATGTCCCTTTA 57.958 33.333 0.00 0.00 0.00 1.85
3237 4586 9.838339 CTTACTCACTTGATTATGTCCCTTTAT 57.162 33.333 0.00 0.00 0.00 1.40
3239 4588 8.738645 ACTCACTTGATTATGTCCCTTTATTC 57.261 34.615 0.00 0.00 0.00 1.75
3240 4589 8.328758 ACTCACTTGATTATGTCCCTTTATTCA 58.671 33.333 0.00 0.00 0.00 2.57
3241 4590 8.737168 TCACTTGATTATGTCCCTTTATTCAG 57.263 34.615 0.00 0.00 0.00 3.02
3242 4591 8.548025 TCACTTGATTATGTCCCTTTATTCAGA 58.452 33.333 0.00 0.00 0.00 3.27
3243 4592 9.177608 CACTTGATTATGTCCCTTTATTCAGAA 57.822 33.333 0.00 0.00 0.00 3.02
3244 4593 9.927081 ACTTGATTATGTCCCTTTATTCAGAAT 57.073 29.630 0.20 0.20 0.00 2.40
3246 4595 9.919416 TTGATTATGTCCCTTTATTCAGAATCA 57.081 29.630 0.00 9.07 42.55 2.57
3247 4596 9.919416 TGATTATGTCCCTTTATTCAGAATCAA 57.081 29.630 0.00 0.00 41.87 2.57
3285 4634 3.056107 TGCAAACTAGAATGTACCTCGCT 60.056 43.478 0.00 0.00 0.00 4.93
3331 4680 7.389053 AGAATTCATTCAGAGTACACTTTGACC 59.611 37.037 8.44 0.00 36.91 4.02
3332 4681 5.545063 TCATTCAGAGTACACTTTGACCA 57.455 39.130 2.31 0.00 36.91 4.02
3333 4682 5.924356 TCATTCAGAGTACACTTTGACCAA 58.076 37.500 2.31 0.00 36.91 3.67
3350 4699 4.754618 TGACCAACAACTACTATGCAACAG 59.245 41.667 0.00 0.00 0.00 3.16
3362 4711 7.883311 ACTACTATGCAACAGAAACCTTATGTT 59.117 33.333 5.74 0.00 39.43 2.71
3371 4720 5.940470 ACAGAAACCTTATGTTGTGAGATCC 59.060 40.000 0.00 0.00 37.23 3.36
3372 4721 5.063944 CAGAAACCTTATGTTGTGAGATCCG 59.936 44.000 0.00 0.00 37.23 4.18
3373 4722 4.553330 AACCTTATGTTGTGAGATCCGT 57.447 40.909 0.00 0.00 35.31 4.69
3374 4723 5.670792 AACCTTATGTTGTGAGATCCGTA 57.329 39.130 0.00 0.00 35.31 4.02
3375 4724 5.871396 ACCTTATGTTGTGAGATCCGTAT 57.129 39.130 0.00 0.00 0.00 3.06
3376 4725 6.235231 ACCTTATGTTGTGAGATCCGTATT 57.765 37.500 0.00 0.00 0.00 1.89
3377 4726 6.281405 ACCTTATGTTGTGAGATCCGTATTC 58.719 40.000 0.00 0.00 0.00 1.75
3378 4727 5.696724 CCTTATGTTGTGAGATCCGTATTCC 59.303 44.000 0.00 0.00 0.00 3.01
3379 4728 4.753516 ATGTTGTGAGATCCGTATTCCA 57.246 40.909 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.210155 GCATGTTCGCAAGTGGACC 59.790 57.895 0.00 0.00 39.48 4.46
3 4 0.250252 TCAGCATGTTCGCAAGTGGA 60.250 50.000 0.00 0.00 37.40 4.02
4 5 0.167470 CTCAGCATGTTCGCAAGTGG 59.833 55.000 0.00 0.00 37.40 4.00
5 6 0.453950 GCTCAGCATGTTCGCAAGTG 60.454 55.000 0.00 0.00 37.40 3.16
6 7 0.604780 AGCTCAGCATGTTCGCAAGT 60.605 50.000 0.00 0.00 37.40 3.16
7 8 0.096628 GAGCTCAGCATGTTCGCAAG 59.903 55.000 9.40 0.00 37.40 4.01
8 9 1.629345 CGAGCTCAGCATGTTCGCAA 61.629 55.000 15.40 0.00 37.40 4.85
9 10 2.096442 CGAGCTCAGCATGTTCGCA 61.096 57.895 15.40 0.00 37.40 5.10
10 11 2.699809 CGAGCTCAGCATGTTCGC 59.300 61.111 15.40 0.00 37.40 4.70
11 12 2.096442 TGCGAGCTCAGCATGTTCG 61.096 57.895 23.20 0.00 40.01 3.95
12 13 1.018226 AGTGCGAGCTCAGCATGTTC 61.018 55.000 27.41 18.07 46.96 3.18
13 14 0.604780 AAGTGCGAGCTCAGCATGTT 60.605 50.000 27.41 21.85 46.96 2.71
14 15 0.604780 AAAGTGCGAGCTCAGCATGT 60.605 50.000 27.41 18.58 46.96 3.21
15 16 1.362768 TAAAGTGCGAGCTCAGCATG 58.637 50.000 27.41 8.55 46.96 4.06
16 17 2.005451 CTTAAAGTGCGAGCTCAGCAT 58.995 47.619 27.41 18.07 46.96 3.79
17 18 1.432514 CTTAAAGTGCGAGCTCAGCA 58.567 50.000 23.20 23.20 42.99 4.41
18 19 0.096108 GCTTAAAGTGCGAGCTCAGC 59.904 55.000 15.40 17.75 33.72 4.26
19 20 1.719600 AGCTTAAAGTGCGAGCTCAG 58.280 50.000 15.40 7.85 42.80 3.35
20 21 3.914984 AGCTTAAAGTGCGAGCTCA 57.085 47.368 15.40 0.00 42.80 4.26
23 24 1.003108 GAGGAGCTTAAAGTGCGAGC 58.997 55.000 0.00 0.00 36.68 5.03
24 25 2.663826 AGAGGAGCTTAAAGTGCGAG 57.336 50.000 0.00 0.00 35.28 5.03
25 26 3.006967 AGAAAGAGGAGCTTAAAGTGCGA 59.993 43.478 0.00 0.00 35.24 5.10
26 27 3.330267 AGAAAGAGGAGCTTAAAGTGCG 58.670 45.455 0.00 0.00 35.24 5.34
27 28 4.757149 TGAAGAAAGAGGAGCTTAAAGTGC 59.243 41.667 0.00 0.00 35.24 4.40
28 29 5.994668 ACTGAAGAAAGAGGAGCTTAAAGTG 59.005 40.000 0.00 0.00 35.24 3.16
29 30 6.181206 ACTGAAGAAAGAGGAGCTTAAAGT 57.819 37.500 0.00 0.00 35.24 2.66
30 31 5.347364 CGACTGAAGAAAGAGGAGCTTAAAG 59.653 44.000 0.00 0.00 35.24 1.85
31 32 5.230942 CGACTGAAGAAAGAGGAGCTTAAA 58.769 41.667 0.00 0.00 35.24 1.52
32 33 4.810790 CGACTGAAGAAAGAGGAGCTTAA 58.189 43.478 0.00 0.00 35.24 1.85
33 34 3.367498 GCGACTGAAGAAAGAGGAGCTTA 60.367 47.826 0.00 0.00 35.24 3.09
34 35 2.611722 GCGACTGAAGAAAGAGGAGCTT 60.612 50.000 0.00 0.00 38.88 3.74
35 36 1.067213 GCGACTGAAGAAAGAGGAGCT 60.067 52.381 0.00 0.00 0.00 4.09
36 37 1.337260 TGCGACTGAAGAAAGAGGAGC 60.337 52.381 0.00 0.00 0.00 4.70
37 38 2.732412 TGCGACTGAAGAAAGAGGAG 57.268 50.000 0.00 0.00 0.00 3.69
38 39 3.469008 TTTGCGACTGAAGAAAGAGGA 57.531 42.857 0.00 0.00 0.00 3.71
39 40 4.552166 TTTTTGCGACTGAAGAAAGAGG 57.448 40.909 0.00 0.00 0.00 3.69
61 62 9.830975 GAGAGATTAAGAAAGAGGAGCTTATTT 57.169 33.333 0.00 0.00 35.24 1.40
62 63 8.428852 GGAGAGATTAAGAAAGAGGAGCTTATT 58.571 37.037 0.00 0.00 35.24 1.40
63 64 7.789349 AGGAGAGATTAAGAAAGAGGAGCTTAT 59.211 37.037 0.00 0.00 35.24 1.73
64 65 7.129425 AGGAGAGATTAAGAAAGAGGAGCTTA 58.871 38.462 0.00 0.00 35.24 3.09
65 66 5.963865 AGGAGAGATTAAGAAAGAGGAGCTT 59.036 40.000 0.00 0.00 38.88 3.74
66 67 5.528337 AGGAGAGATTAAGAAAGAGGAGCT 58.472 41.667 0.00 0.00 0.00 4.09
67 68 5.869649 AGGAGAGATTAAGAAAGAGGAGC 57.130 43.478 0.00 0.00 0.00 4.70
68 69 7.619965 ACAAAGGAGAGATTAAGAAAGAGGAG 58.380 38.462 0.00 0.00 0.00 3.69
69 70 7.560796 ACAAAGGAGAGATTAAGAAAGAGGA 57.439 36.000 0.00 0.00 0.00 3.71
70 71 7.663493 ACAACAAAGGAGAGATTAAGAAAGAGG 59.337 37.037 0.00 0.00 0.00 3.69
71 72 8.614469 ACAACAAAGGAGAGATTAAGAAAGAG 57.386 34.615 0.00 0.00 0.00 2.85
72 73 8.432805 AGACAACAAAGGAGAGATTAAGAAAGA 58.567 33.333 0.00 0.00 0.00 2.52
73 74 8.614469 AGACAACAAAGGAGAGATTAAGAAAG 57.386 34.615 0.00 0.00 0.00 2.62
74 75 8.840321 CAAGACAACAAAGGAGAGATTAAGAAA 58.160 33.333 0.00 0.00 0.00 2.52
75 76 7.993183 ACAAGACAACAAAGGAGAGATTAAGAA 59.007 33.333 0.00 0.00 0.00 2.52
76 77 7.442364 CACAAGACAACAAAGGAGAGATTAAGA 59.558 37.037 0.00 0.00 0.00 2.10
77 78 7.579726 CACAAGACAACAAAGGAGAGATTAAG 58.420 38.462 0.00 0.00 0.00 1.85
78 79 6.017109 GCACAAGACAACAAAGGAGAGATTAA 60.017 38.462 0.00 0.00 0.00 1.40
79 80 5.470098 GCACAAGACAACAAAGGAGAGATTA 59.530 40.000 0.00 0.00 0.00 1.75
80 81 4.276926 GCACAAGACAACAAAGGAGAGATT 59.723 41.667 0.00 0.00 0.00 2.40
81 82 3.817647 GCACAAGACAACAAAGGAGAGAT 59.182 43.478 0.00 0.00 0.00 2.75
82 83 3.118261 AGCACAAGACAACAAAGGAGAGA 60.118 43.478 0.00 0.00 0.00 3.10
83 84 3.209410 AGCACAAGACAACAAAGGAGAG 58.791 45.455 0.00 0.00 0.00 3.20
84 85 3.281727 AGCACAAGACAACAAAGGAGA 57.718 42.857 0.00 0.00 0.00 3.71
85 86 4.555511 GCTAAGCACAAGACAACAAAGGAG 60.556 45.833 0.00 0.00 0.00 3.69
86 87 3.315191 GCTAAGCACAAGACAACAAAGGA 59.685 43.478 0.00 0.00 0.00 3.36
87 88 3.632189 GCTAAGCACAAGACAACAAAGG 58.368 45.455 0.00 0.00 0.00 3.11
88 89 3.291585 CGCTAAGCACAAGACAACAAAG 58.708 45.455 0.00 0.00 0.00 2.77
89 90 3.332761 CGCTAAGCACAAGACAACAAA 57.667 42.857 0.00 0.00 0.00 2.83
103 104 2.079049 GTTCTCCAACGGCGCTAAG 58.921 57.895 6.90 1.39 0.00 2.18
104 105 4.272100 GTTCTCCAACGGCGCTAA 57.728 55.556 6.90 0.00 0.00 3.09
114 115 4.266714 GGTTTAATTGGATCCGTTCTCCA 58.733 43.478 7.39 0.00 41.03 3.86
115 116 3.630769 GGGTTTAATTGGATCCGTTCTCC 59.369 47.826 7.39 7.87 0.00 3.71
116 117 4.524053 AGGGTTTAATTGGATCCGTTCTC 58.476 43.478 7.39 0.00 0.00 2.87
117 118 4.586306 AGGGTTTAATTGGATCCGTTCT 57.414 40.909 7.39 0.00 0.00 3.01
118 119 6.405065 GGTTTAGGGTTTAATTGGATCCGTTC 60.405 42.308 7.39 0.00 0.00 3.95
119 120 5.419788 GGTTTAGGGTTTAATTGGATCCGTT 59.580 40.000 7.39 7.33 0.00 4.44
120 121 4.951715 GGTTTAGGGTTTAATTGGATCCGT 59.048 41.667 7.39 0.00 0.00 4.69
121 122 4.340097 GGGTTTAGGGTTTAATTGGATCCG 59.660 45.833 7.39 0.00 0.00 4.18
122 123 5.525484 AGGGTTTAGGGTTTAATTGGATCC 58.475 41.667 4.20 4.20 0.00 3.36
123 124 8.472413 GTTTAGGGTTTAGGGTTTAATTGGATC 58.528 37.037 0.00 0.00 0.00 3.36
124 125 7.400915 GGTTTAGGGTTTAGGGTTTAATTGGAT 59.599 37.037 0.00 0.00 0.00 3.41
125 126 6.725369 GGTTTAGGGTTTAGGGTTTAATTGGA 59.275 38.462 0.00 0.00 0.00 3.53
126 127 6.070653 GGGTTTAGGGTTTAGGGTTTAATTGG 60.071 42.308 0.00 0.00 0.00 3.16
127 128 6.070653 GGGGTTTAGGGTTTAGGGTTTAATTG 60.071 42.308 0.00 0.00 0.00 2.32
128 129 6.024893 GGGGTTTAGGGTTTAGGGTTTAATT 58.975 40.000 0.00 0.00 0.00 1.40
129 130 5.319434 AGGGGTTTAGGGTTTAGGGTTTAAT 59.681 40.000 0.00 0.00 0.00 1.40
130 131 4.674097 AGGGGTTTAGGGTTTAGGGTTTAA 59.326 41.667 0.00 0.00 0.00 1.52
131 132 4.258775 AGGGGTTTAGGGTTTAGGGTTTA 58.741 43.478 0.00 0.00 0.00 2.01
132 133 3.073631 AGGGGTTTAGGGTTTAGGGTTT 58.926 45.455 0.00 0.00 0.00 3.27
133 134 2.734428 AGGGGTTTAGGGTTTAGGGTT 58.266 47.619 0.00 0.00 0.00 4.11
134 135 2.463671 AGGGGTTTAGGGTTTAGGGT 57.536 50.000 0.00 0.00 0.00 4.34
135 136 5.195146 AGAAATAGGGGTTTAGGGTTTAGGG 59.805 44.000 0.00 0.00 0.00 3.53
136 137 6.159928 AGAGAAATAGGGGTTTAGGGTTTAGG 59.840 42.308 0.00 0.00 0.00 2.69
137 138 7.127493 AGAGAGAAATAGGGGTTTAGGGTTTAG 59.873 40.741 0.00 0.00 0.00 1.85
138 139 6.970041 AGAGAGAAATAGGGGTTTAGGGTTTA 59.030 38.462 0.00 0.00 0.00 2.01
139 140 5.796399 AGAGAGAAATAGGGGTTTAGGGTTT 59.204 40.000 0.00 0.00 0.00 3.27
140 141 5.360041 AGAGAGAAATAGGGGTTTAGGGTT 58.640 41.667 0.00 0.00 0.00 4.11
141 142 4.969999 GAGAGAGAAATAGGGGTTTAGGGT 59.030 45.833 0.00 0.00 0.00 4.34
142 143 5.220521 AGAGAGAGAAATAGGGGTTTAGGG 58.779 45.833 0.00 0.00 0.00 3.53
143 144 6.140377 AGAGAGAGAGAAATAGGGGTTTAGG 58.860 44.000 0.00 0.00 0.00 2.69
144 145 6.836527 TGAGAGAGAGAGAAATAGGGGTTTAG 59.163 42.308 0.00 0.00 0.00 1.85
145 146 6.742756 TGAGAGAGAGAGAAATAGGGGTTTA 58.257 40.000 0.00 0.00 0.00 2.01
146 147 5.594777 TGAGAGAGAGAGAAATAGGGGTTT 58.405 41.667 0.00 0.00 0.00 3.27
147 148 5.213868 TGAGAGAGAGAGAAATAGGGGTT 57.786 43.478 0.00 0.00 0.00 4.11
148 149 4.890499 TGAGAGAGAGAGAAATAGGGGT 57.110 45.455 0.00 0.00 0.00 4.95
149 150 6.382570 TCTTTTGAGAGAGAGAGAAATAGGGG 59.617 42.308 0.00 0.00 0.00 4.79
150 151 7.416964 TCTTTTGAGAGAGAGAGAAATAGGG 57.583 40.000 0.00 0.00 0.00 3.53
151 152 8.143835 GGATCTTTTGAGAGAGAGAGAAATAGG 58.856 40.741 0.00 0.00 0.00 2.57
152 153 8.694540 TGGATCTTTTGAGAGAGAGAGAAATAG 58.305 37.037 0.00 0.00 0.00 1.73
153 154 8.474025 GTGGATCTTTTGAGAGAGAGAGAAATA 58.526 37.037 0.00 0.00 0.00 1.40
154 155 7.180766 AGTGGATCTTTTGAGAGAGAGAGAAAT 59.819 37.037 0.00 0.00 0.00 2.17
155 156 6.496565 AGTGGATCTTTTGAGAGAGAGAGAAA 59.503 38.462 0.00 0.00 0.00 2.52
156 157 6.015918 AGTGGATCTTTTGAGAGAGAGAGAA 58.984 40.000 0.00 0.00 0.00 2.87
157 158 5.579047 AGTGGATCTTTTGAGAGAGAGAGA 58.421 41.667 0.00 0.00 0.00 3.10
158 159 5.449041 CGAGTGGATCTTTTGAGAGAGAGAG 60.449 48.000 0.00 0.00 0.00 3.20
159 160 4.397730 CGAGTGGATCTTTTGAGAGAGAGA 59.602 45.833 0.00 0.00 0.00 3.10
160 161 4.671377 CGAGTGGATCTTTTGAGAGAGAG 58.329 47.826 0.00 0.00 0.00 3.20
161 162 3.119316 GCGAGTGGATCTTTTGAGAGAGA 60.119 47.826 0.00 0.00 0.00 3.10
162 163 3.186119 GCGAGTGGATCTTTTGAGAGAG 58.814 50.000 0.00 0.00 0.00 3.20
163 164 2.562738 TGCGAGTGGATCTTTTGAGAGA 59.437 45.455 0.00 0.00 0.00 3.10
164 165 2.964740 TGCGAGTGGATCTTTTGAGAG 58.035 47.619 0.00 0.00 0.00 3.20
165 166 3.401033 TTGCGAGTGGATCTTTTGAGA 57.599 42.857 0.00 0.00 0.00 3.27
166 167 3.665323 CGTTTGCGAGTGGATCTTTTGAG 60.665 47.826 0.00 0.00 41.33 3.02
167 168 2.223144 CGTTTGCGAGTGGATCTTTTGA 59.777 45.455 0.00 0.00 41.33 2.69
168 169 2.032030 ACGTTTGCGAGTGGATCTTTTG 60.032 45.455 0.00 0.00 42.00 2.44
169 170 2.032030 CACGTTTGCGAGTGGATCTTTT 60.032 45.455 0.00 0.00 42.00 2.27
170 171 1.531149 CACGTTTGCGAGTGGATCTTT 59.469 47.619 0.00 0.00 42.00 2.52
171 172 1.148310 CACGTTTGCGAGTGGATCTT 58.852 50.000 0.00 0.00 42.00 2.40
172 173 1.291877 GCACGTTTGCGAGTGGATCT 61.292 55.000 0.00 0.00 39.50 2.75
173 174 1.132640 GCACGTTTGCGAGTGGATC 59.867 57.895 0.00 0.00 39.50 3.36
174 175 3.253955 GCACGTTTGCGAGTGGAT 58.746 55.556 0.00 0.00 39.50 3.41
184 185 3.826221 TGCAAGCTCAGCACGTTT 58.174 50.000 9.50 0.00 37.02 3.60
206 207 5.598417 AGGAGAGATTAAGAAAGAGGAGCTC 59.402 44.000 4.71 4.71 0.00 4.09
257 258 3.329814 AGGGTTTAGTTGGATCCGTTCTT 59.670 43.478 7.39 0.00 0.00 2.52
512 513 2.378445 AAGAAAGAGGAGCTCGAAGC 57.622 50.000 7.83 0.00 42.84 3.86
561 562 2.590092 GGTCCGGTCTCCAATGGG 59.410 66.667 0.00 0.00 0.00 4.00
609 610 6.142798 CAGCGGATTTCATAAATTTTCATCGG 59.857 38.462 0.00 0.00 0.00 4.18
611 612 7.202526 TCCAGCGGATTTCATAAATTTTCATC 58.797 34.615 0.00 0.00 0.00 2.92
672 674 1.881973 CAAGTTGGCTTTGCTCTGCTA 59.118 47.619 0.00 0.00 31.49 3.49
734 736 4.828939 ACAAGCCAACAAATGAGAGATTGA 59.171 37.500 0.00 0.00 0.00 2.57
735 737 5.130292 ACAAGCCAACAAATGAGAGATTG 57.870 39.130 0.00 0.00 0.00 2.67
752 754 2.053627 GCATGTACAAGCACAACAAGC 58.946 47.619 17.73 0.00 31.71 4.01
754 756 2.543445 GCTGCATGTACAAGCACAACAA 60.543 45.455 21.06 0.15 36.62 2.83
755 757 1.001487 GCTGCATGTACAAGCACAACA 60.001 47.619 21.06 0.87 36.62 3.33
756 758 1.666888 GGCTGCATGTACAAGCACAAC 60.667 52.381 21.06 13.18 36.62 3.32
774 776 2.076863 CACTGTAGTTAAGGCTGTGGC 58.923 52.381 0.00 0.00 37.82 5.01
787 796 0.670239 TGATGGCGTGCACACTGTAG 60.670 55.000 18.64 0.00 0.00 2.74
790 799 0.670239 TAGTGATGGCGTGCACACTG 60.670 55.000 18.64 1.23 42.37 3.66
823 832 1.228862 ATGTCTGGTGGGGGTTTGC 60.229 57.895 0.00 0.00 0.00 3.68
841 857 2.248280 TTCGCTTAGCTGGTGTTTGA 57.752 45.000 1.76 0.00 0.00 2.69
842 858 3.347958 TTTTCGCTTAGCTGGTGTTTG 57.652 42.857 1.76 0.00 0.00 2.93
843 859 3.317993 ACATTTTCGCTTAGCTGGTGTTT 59.682 39.130 1.76 0.00 0.00 2.83
844 860 2.884639 ACATTTTCGCTTAGCTGGTGTT 59.115 40.909 1.76 0.00 0.00 3.32
845 861 2.504367 ACATTTTCGCTTAGCTGGTGT 58.496 42.857 1.76 0.00 0.00 4.16
846 862 3.063997 CCTACATTTTCGCTTAGCTGGTG 59.936 47.826 1.76 0.00 0.00 4.17
847 863 3.270877 CCTACATTTTCGCTTAGCTGGT 58.729 45.455 1.76 0.00 0.00 4.00
865 881 2.805546 GATCAGCACCGTCGCCTA 59.194 61.111 0.00 0.00 0.00 3.93
919 935 2.915869 GGCTAAGGCGGATTGGGA 59.084 61.111 0.00 0.00 39.81 4.37
1146 1162 1.214589 GATACGCCACCACGACTGT 59.785 57.895 0.00 0.00 36.70 3.55
1263 1279 3.889815 CTGCCCAGATGTTTCCTTGATA 58.110 45.455 0.00 0.00 0.00 2.15
1273 1289 2.191375 CGATGGCTGCCCAGATGT 59.809 61.111 17.53 0.00 46.24 3.06
1344 1387 0.725686 CTTCCTGATGAAGTGCAGCG 59.274 55.000 0.00 0.00 44.59 5.18
1356 1399 2.701551 TCCACCTTTTCCTCTTCCTGA 58.298 47.619 0.00 0.00 0.00 3.86
1389 1432 3.157881 GTCATCTCCATCCTCGGTGATA 58.842 50.000 0.00 0.00 37.20 2.15
1707 1756 6.097554 CCAAGTACCTCTTCTCAGTCACATAT 59.902 42.308 0.00 0.00 33.63 1.78
1920 1969 6.824704 GCATACTTATGGTTACCTTGTGGTAA 59.175 38.462 2.07 3.80 42.88 2.85
1944 2002 4.576216 TCAAGACGAAGAGGAGATATGC 57.424 45.455 0.00 0.00 0.00 3.14
2014 3330 4.036144 TCAAAACAACGATGCACTGATTCA 59.964 37.500 0.00 0.00 0.00 2.57
2028 3344 7.011482 CCTGCTAGATACCTACATCAAAACAAC 59.989 40.741 0.00 0.00 0.00 3.32
2039 3375 7.008021 ACTACTCTACCTGCTAGATACCTAC 57.992 44.000 0.00 0.00 30.60 3.18
2180 3516 2.042686 TGCTGCTGTTTCTCACAAGT 57.957 45.000 0.00 0.00 33.87 3.16
2183 3519 0.594602 GCATGCTGCTGTTTCTCACA 59.405 50.000 11.37 0.00 40.96 3.58
2248 3584 2.034685 CCGGTCGATAAGCTGATCTTCA 59.965 50.000 9.49 0.00 36.25 3.02
2256 3592 3.090219 GCCACCCGGTCGATAAGCT 62.090 63.158 0.00 0.00 33.28 3.74
2508 3856 8.967218 CATTGTTACTTTATTGTGTTTCAGTGG 58.033 33.333 0.00 0.00 0.00 4.00
2522 3870 7.284074 TGTGTCTCCTTTCCATTGTTACTTTA 58.716 34.615 0.00 0.00 0.00 1.85
2537 3885 4.855340 TCTTTCTTTGGTTGTGTCTCCTT 58.145 39.130 0.00 0.00 0.00 3.36
2690 4038 2.609459 CAGTGACAATGATCCGGTTAGC 59.391 50.000 0.00 0.00 0.00 3.09
2710 4058 1.599518 AACATTCAGTTCCCGCGCA 60.600 52.632 8.75 0.00 34.74 6.09
2711 4059 1.154225 CAACATTCAGTTCCCGCGC 60.154 57.895 0.00 0.00 38.74 6.86
2936 4285 5.357032 ACTGCTTTTACGAAATAAGGATGGG 59.643 40.000 0.00 0.00 0.00 4.00
3161 4510 6.691754 TCAGTGAAGCACAAACTGAAATTA 57.308 33.333 8.53 0.00 45.45 1.40
3173 4522 2.393271 ATGTAGCCTCAGTGAAGCAC 57.607 50.000 15.93 11.63 34.10 4.40
3200 4549 4.404394 TCAAGTGAGTAAGACCAACACTCA 59.596 41.667 0.00 0.00 44.78 3.41
3201 4550 4.945246 TCAAGTGAGTAAGACCAACACTC 58.055 43.478 0.00 0.00 40.23 3.51
3205 4554 7.064728 GGACATAATCAAGTGAGTAAGACCAAC 59.935 40.741 7.34 0.00 31.98 3.77
3207 4556 6.351881 GGGACATAATCAAGTGAGTAAGACCA 60.352 42.308 12.12 0.00 32.78 4.02
3208 4557 6.049790 GGGACATAATCAAGTGAGTAAGACC 58.950 44.000 4.66 4.66 31.31 3.85
3209 4558 6.879400 AGGGACATAATCAAGTGAGTAAGAC 58.121 40.000 0.00 0.00 0.00 3.01
3210 4559 7.496346 AAGGGACATAATCAAGTGAGTAAGA 57.504 36.000 0.00 0.00 0.00 2.10
3211 4560 9.838339 ATAAAGGGACATAATCAAGTGAGTAAG 57.162 33.333 0.00 0.00 0.00 2.34
3213 4562 9.832445 GAATAAAGGGACATAATCAAGTGAGTA 57.168 33.333 0.00 0.00 0.00 2.59
3214 4563 8.328758 TGAATAAAGGGACATAATCAAGTGAGT 58.671 33.333 0.00 0.00 0.00 3.41
3215 4564 8.737168 TGAATAAAGGGACATAATCAAGTGAG 57.263 34.615 0.00 0.00 0.00 3.51
3216 4565 8.548025 TCTGAATAAAGGGACATAATCAAGTGA 58.452 33.333 0.00 0.00 0.00 3.41
3217 4566 8.737168 TCTGAATAAAGGGACATAATCAAGTG 57.263 34.615 0.00 0.00 0.00 3.16
3218 4567 9.927081 ATTCTGAATAAAGGGACATAATCAAGT 57.073 29.630 0.00 0.00 0.00 3.16
3220 4569 9.919416 TGATTCTGAATAAAGGGACATAATCAA 57.081 29.630 2.28 0.00 35.00 2.57
3221 4570 9.919416 TTGATTCTGAATAAAGGGACATAATCA 57.081 29.630 2.28 0.00 35.60 2.57
3224 4573 9.354673 GGATTGATTCTGAATAAAGGGACATAA 57.645 33.333 2.28 0.00 0.00 1.90
3225 4574 8.501904 TGGATTGATTCTGAATAAAGGGACATA 58.498 33.333 2.28 0.00 0.00 2.29
3226 4575 7.356680 TGGATTGATTCTGAATAAAGGGACAT 58.643 34.615 2.28 0.00 0.00 3.06
3227 4576 6.730447 TGGATTGATTCTGAATAAAGGGACA 58.270 36.000 2.28 0.00 0.00 4.02
3228 4577 7.286316 ACATGGATTGATTCTGAATAAAGGGAC 59.714 37.037 2.28 0.00 0.00 4.46
3229 4578 7.356680 ACATGGATTGATTCTGAATAAAGGGA 58.643 34.615 2.28 0.00 0.00 4.20
3230 4579 7.592885 ACATGGATTGATTCTGAATAAAGGG 57.407 36.000 2.28 0.00 0.00 3.95
3231 4580 9.525409 GAAACATGGATTGATTCTGAATAAAGG 57.475 33.333 2.28 0.00 35.02 3.11
3235 4584 9.411189 TCATGAAACATGGATTGATTCTGAATA 57.589 29.630 2.28 0.00 37.83 1.75
3236 4585 8.301252 TCATGAAACATGGATTGATTCTGAAT 57.699 30.769 1.81 1.81 37.83 2.57
3237 4586 7.706100 TCATGAAACATGGATTGATTCTGAA 57.294 32.000 11.04 0.00 37.83 3.02
3238 4587 7.706100 TTCATGAAACATGGATTGATTCTGA 57.294 32.000 5.45 0.00 37.83 3.27
3239 4588 7.042725 GCATTCATGAAACATGGATTGATTCTG 60.043 37.037 13.09 1.35 37.83 3.02
3240 4589 6.984474 GCATTCATGAAACATGGATTGATTCT 59.016 34.615 13.09 0.00 37.83 2.40
3241 4590 6.759356 TGCATTCATGAAACATGGATTGATTC 59.241 34.615 13.09 0.00 37.57 2.52
3242 4591 6.645306 TGCATTCATGAAACATGGATTGATT 58.355 32.000 13.09 0.00 0.00 2.57
3243 4592 6.228616 TGCATTCATGAAACATGGATTGAT 57.771 33.333 13.09 0.00 0.00 2.57
3244 4593 5.662674 TGCATTCATGAAACATGGATTGA 57.337 34.783 13.09 0.00 0.00 2.57
3245 4594 6.370442 AGTTTGCATTCATGAAACATGGATTG 59.630 34.615 13.09 4.67 33.89 2.67
3246 4595 6.469410 AGTTTGCATTCATGAAACATGGATT 58.531 32.000 13.09 0.00 33.89 3.01
3247 4596 6.045072 AGTTTGCATTCATGAAACATGGAT 57.955 33.333 13.09 5.89 33.89 3.41
3248 4597 5.471556 AGTTTGCATTCATGAAACATGGA 57.528 34.783 13.09 4.88 33.89 3.41
3260 4609 5.502544 GCGAGGTACATTCTAGTTTGCATTC 60.503 44.000 0.00 0.00 0.00 2.67
3328 4677 4.994852 TCTGTTGCATAGTAGTTGTTGGTC 59.005 41.667 0.00 0.00 0.00 4.02
3331 4680 6.017109 AGGTTTCTGTTGCATAGTAGTTGTTG 60.017 38.462 0.00 0.00 0.00 3.33
3332 4681 6.062095 AGGTTTCTGTTGCATAGTAGTTGTT 58.938 36.000 0.00 0.00 0.00 2.83
3333 4682 5.621193 AGGTTTCTGTTGCATAGTAGTTGT 58.379 37.500 0.00 0.00 0.00 3.32
3350 4699 4.935808 ACGGATCTCACAACATAAGGTTTC 59.064 41.667 0.00 0.00 37.72 2.78
3362 4711 5.833667 AGTATCTTGGAATACGGATCTCACA 59.166 40.000 0.00 0.00 37.23 3.58


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

AutoCloner maintained by Alex Coulton.