Multiple sequence alignment - TraesCS4D01G182500

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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 TraesCS4D01G182500 chr4D 100.000 2021 0 0 1 2021 318927480 318925460 0.000000e+00 3733.0
1 TraesCS4D01G182500 chr4D 100.000 494 0 0 2359 2852 318925122 318924629 0.000000e+00 913.0
2 TraesCS4D01G182500 chr4A 93.772 1702 73 17 338 2021 154925277 154926963 0.000000e+00 2525.0
3 TraesCS4D01G182500 chr4A 91.704 446 19 6 2419 2852 154926977 154927416 1.130000e-168 603.0
4 TraesCS4D01G182500 chr4B 93.539 1687 82 15 344 2021 396450866 396449198 0.000000e+00 2486.0
5 TraesCS4D01G182500 chr4B 96.322 435 10 3 2419 2852 396449174 396448745 0.000000e+00 710.0
6 TraesCS4D01G182500 chr3D 94.955 337 17 0 1 337 137785528 137785192 1.950000e-146 529.0
7 TraesCS4D01G182500 chr3D 94.955 337 17 0 1 337 217716271 217715935 1.950000e-146 529.0
8 TraesCS4D01G182500 chr3D 94.955 337 17 0 1 337 517261499 517261163 1.950000e-146 529.0
9 TraesCS4D01G182500 chr3D 94.659 337 18 0 1 337 570553565 570553229 9.050000e-145 523.0
10 TraesCS4D01G182500 chr1D 94.955 337 17 0 1 337 102404607 102404943 1.950000e-146 529.0
11 TraesCS4D01G182500 chr1D 97.778 45 1 0 1795 1839 81510436 81510480 8.470000e-11 78.7
12 TraesCS4D01G182500 chr1D 92.453 53 1 3 1790 1839 355824351 355824403 3.940000e-09 73.1
13 TraesCS4D01G182500 chr5D 94.955 337 16 1 1 337 256763008 256762673 7.000000e-146 527.0
14 TraesCS4D01G182500 chr5D 77.540 187 32 5 474 653 365728260 365728077 1.400000e-18 104.0
15 TraesCS4D01G182500 chr7D 94.659 337 18 0 1 337 136608897 136609233 9.050000e-145 523.0
16 TraesCS4D01G182500 chr7D 84.800 125 14 4 460 582 554369357 554369236 1.390000e-23 121.0
17 TraesCS4D01G182500 chr2D 94.659 337 18 0 1 337 606761709 606762045 9.050000e-145 523.0
18 TraesCS4D01G182500 chr2D 97.778 45 1 0 1795 1839 637509634 637509678 8.470000e-11 78.7
19 TraesCS4D01G182500 chr1B 94.659 337 18 0 1 337 672705218 672704882 9.050000e-145 523.0
20 TraesCS4D01G182500 chr7B 88.034 117 11 3 469 584 323836184 323836070 4.960000e-28 135.0
21 TraesCS4D01G182500 chr2A 78.974 195 34 5 462 650 572070978 572070785 2.980000e-25 126.0
22 TraesCS4D01G182500 chr2A 97.826 46 0 1 1795 1839 773404528 773404573 8.470000e-11 78.7
23 TraesCS4D01G182500 chr3B 84.921 126 16 3 462 585 425723575 425723451 1.070000e-24 124.0
24 TraesCS4D01G182500 chr6A 85.714 119 14 3 469 585 554782258 554782141 3.860000e-24 122.0
25 TraesCS4D01G182500 chr7A 83.594 128 17 4 462 586 712669024 712668898 1.800000e-22 117.0
26 TraesCS4D01G182500 chr6D 97.778 45 1 0 1795 1839 277850331 277850287 8.470000e-11 78.7
27 TraesCS4D01G182500 chr1A 97.826 46 0 1 1795 1839 456650128 456650173 8.470000e-11 78.7


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 TraesCS4D01G182500 chr4D 318924629 318927480 2851 True 2323 3733 100.0000 1 2852 2 chr4D.!!$R1 2851
1 TraesCS4D01G182500 chr4A 154925277 154927416 2139 False 1564 2525 92.7380 338 2852 2 chr4A.!!$F1 2514
2 TraesCS4D01G182500 chr4B 396448745 396450866 2121 True 1598 2486 94.9305 344 2852 2 chr4B.!!$R1 2508

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
265 266 0.032952 CGGAACACTGGAGACCGAAA 59.967 55.0 0.0 0.0 45.31 3.46 F
1093 1116 0.327000 CCCCATCCCACCTCTTCTCT 60.327 60.0 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1188 0.693767 AGAGCAGGATTAGGCAGCCT 60.694 55.0 20.63 20.63 37.71 4.58 R
2359 2385 0.108138 GAGAGGCATTACAGCACGGT 60.108 55.0 0.00 0.00 35.83 4.83 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
32 33 9.929722 TTTATGCATCTTATTTTGCTTAGTACG 57.070 29.630 0.19 0.00 39.60 3.67
33 34 6.358118 TGCATCTTATTTTGCTTAGTACGG 57.642 37.500 0.00 0.00 39.60 4.02
34 35 5.205565 GCATCTTATTTTGCTTAGTACGGC 58.794 41.667 0.00 2.43 35.95 5.68
35 36 5.432157 CATCTTATTTTGCTTAGTACGGCG 58.568 41.667 4.80 4.80 0.00 6.46
36 37 3.866910 TCTTATTTTGCTTAGTACGGCGG 59.133 43.478 13.24 0.00 0.00 6.13
37 38 2.103537 ATTTTGCTTAGTACGGCGGT 57.896 45.000 13.24 1.39 0.00 5.68
38 39 2.739885 TTTTGCTTAGTACGGCGGTA 57.260 45.000 13.24 0.00 0.00 4.02
39 40 2.282701 TTTGCTTAGTACGGCGGTAG 57.717 50.000 13.24 1.66 0.00 3.18
40 41 0.179129 TTGCTTAGTACGGCGGTAGC 60.179 55.000 13.24 12.41 44.18 3.58
55 56 5.975410 GCGGTAGCATTATAAGATGATCC 57.025 43.478 0.00 0.00 44.35 3.36
56 57 5.419542 GCGGTAGCATTATAAGATGATCCA 58.580 41.667 0.00 0.00 44.35 3.41
57 58 6.051717 GCGGTAGCATTATAAGATGATCCAT 58.948 40.000 0.00 0.00 44.35 3.41
58 59 6.540189 GCGGTAGCATTATAAGATGATCCATT 59.460 38.462 0.00 0.00 44.35 3.16
59 60 7.254590 GCGGTAGCATTATAAGATGATCCATTC 60.255 40.741 0.00 0.00 44.35 2.67
60 61 7.765819 CGGTAGCATTATAAGATGATCCATTCA 59.234 37.037 0.00 0.00 39.12 2.57
61 62 8.887717 GGTAGCATTATAAGATGATCCATTCAC 58.112 37.037 0.00 0.00 37.11 3.18
62 63 9.664332 GTAGCATTATAAGATGATCCATTCACT 57.336 33.333 0.00 0.00 37.11 3.41
73 74 8.910944 AGATGATCCATTCACTAAATTTCAAGG 58.089 33.333 0.00 0.00 37.11 3.61
74 75 8.599624 ATGATCCATTCACTAAATTTCAAGGT 57.400 30.769 0.00 0.00 37.11 3.50
75 76 9.699410 ATGATCCATTCACTAAATTTCAAGGTA 57.301 29.630 0.00 0.00 37.11 3.08
76 77 9.699410 TGATCCATTCACTAAATTTCAAGGTAT 57.301 29.630 0.00 0.00 0.00 2.73
88 89 7.939784 AATTTCAAGGTATAAGTGTTCTCCC 57.060 36.000 0.00 0.00 0.00 4.30
89 90 6.697641 TTTCAAGGTATAAGTGTTCTCCCT 57.302 37.500 0.00 0.00 0.00 4.20
90 91 5.677319 TCAAGGTATAAGTGTTCTCCCTG 57.323 43.478 0.00 0.00 0.00 4.45
91 92 5.338632 TCAAGGTATAAGTGTTCTCCCTGA 58.661 41.667 0.00 0.00 0.00 3.86
92 93 5.422331 TCAAGGTATAAGTGTTCTCCCTGAG 59.578 44.000 0.00 0.00 0.00 3.35
93 94 4.949121 AGGTATAAGTGTTCTCCCTGAGT 58.051 43.478 0.00 0.00 0.00 3.41
94 95 6.088541 AGGTATAAGTGTTCTCCCTGAGTA 57.911 41.667 0.00 0.00 0.00 2.59
95 96 6.684538 AGGTATAAGTGTTCTCCCTGAGTAT 58.315 40.000 0.00 0.00 0.00 2.12
96 97 6.551601 AGGTATAAGTGTTCTCCCTGAGTATG 59.448 42.308 0.00 0.00 0.00 2.39
97 98 3.618690 AAGTGTTCTCCCTGAGTATGC 57.381 47.619 0.00 0.00 0.00 3.14
98 99 2.540383 AGTGTTCTCCCTGAGTATGCA 58.460 47.619 0.00 0.00 0.00 3.96
99 100 2.234908 AGTGTTCTCCCTGAGTATGCAC 59.765 50.000 0.00 0.00 0.00 4.57
100 101 1.555075 TGTTCTCCCTGAGTATGCACC 59.445 52.381 0.00 0.00 0.00 5.01
101 102 0.824109 TTCTCCCTGAGTATGCACCG 59.176 55.000 0.00 0.00 0.00 4.94
102 103 0.324368 TCTCCCTGAGTATGCACCGT 60.324 55.000 0.00 0.00 0.00 4.83
103 104 0.537188 CTCCCTGAGTATGCACCGTT 59.463 55.000 0.00 0.00 0.00 4.44
104 105 0.249120 TCCCTGAGTATGCACCGTTG 59.751 55.000 0.00 0.00 0.00 4.10
114 115 2.914379 GCACCGTTGCTACAGTTCT 58.086 52.632 0.00 0.00 46.17 3.01
115 116 1.226746 GCACCGTTGCTACAGTTCTT 58.773 50.000 0.00 0.00 46.17 2.52
116 117 1.194772 GCACCGTTGCTACAGTTCTTC 59.805 52.381 0.00 0.00 46.17 2.87
117 118 1.455786 CACCGTTGCTACAGTTCTTCG 59.544 52.381 0.00 0.00 0.00 3.79
118 119 1.068127 ACCGTTGCTACAGTTCTTCGT 59.932 47.619 0.00 0.00 0.00 3.85
119 120 2.132762 CCGTTGCTACAGTTCTTCGTT 58.867 47.619 0.00 0.00 0.00 3.85
120 121 2.542595 CCGTTGCTACAGTTCTTCGTTT 59.457 45.455 0.00 0.00 0.00 3.60
121 122 3.362693 CCGTTGCTACAGTTCTTCGTTTC 60.363 47.826 0.00 0.00 0.00 2.78
122 123 3.658342 CGTTGCTACAGTTCTTCGTTTCG 60.658 47.826 0.00 0.00 0.00 3.46
123 124 3.358707 TGCTACAGTTCTTCGTTTCGA 57.641 42.857 0.00 0.00 0.00 3.71
124 125 3.305964 TGCTACAGTTCTTCGTTTCGAG 58.694 45.455 0.00 0.00 37.14 4.04
125 126 3.004002 TGCTACAGTTCTTCGTTTCGAGA 59.996 43.478 0.00 0.00 37.14 4.04
126 127 3.361348 GCTACAGTTCTTCGTTTCGAGAC 59.639 47.826 0.00 0.00 37.14 3.36
127 128 3.431922 ACAGTTCTTCGTTTCGAGACA 57.568 42.857 6.91 0.00 37.14 3.41
128 129 3.114065 ACAGTTCTTCGTTTCGAGACAC 58.886 45.455 6.91 0.00 37.14 3.67
129 130 2.471743 CAGTTCTTCGTTTCGAGACACC 59.528 50.000 6.91 0.00 37.14 4.16
130 131 2.100252 AGTTCTTCGTTTCGAGACACCA 59.900 45.455 6.91 0.00 37.14 4.17
131 132 2.129823 TCTTCGTTTCGAGACACCAC 57.870 50.000 6.91 0.00 37.14 4.16
132 133 0.776451 CTTCGTTTCGAGACACCACG 59.224 55.000 6.91 0.66 37.14 4.94
133 134 0.101040 TTCGTTTCGAGACACCACGT 59.899 50.000 6.91 0.00 37.14 4.49
134 135 0.593008 TCGTTTCGAGACACCACGTG 60.593 55.000 9.08 9.08 39.75 4.49
135 136 0.593008 CGTTTCGAGACACCACGTGA 60.593 55.000 19.30 0.00 36.96 4.35
136 137 1.779569 GTTTCGAGACACCACGTGAT 58.220 50.000 19.30 0.00 36.96 3.06
137 138 1.455786 GTTTCGAGACACCACGTGATG 59.544 52.381 19.30 14.17 36.96 3.07
138 139 0.955905 TTCGAGACACCACGTGATGA 59.044 50.000 19.08 0.63 36.96 2.92
139 140 1.173913 TCGAGACACCACGTGATGAT 58.826 50.000 19.08 4.23 36.96 2.45
140 141 1.132453 TCGAGACACCACGTGATGATC 59.868 52.381 19.08 13.01 36.96 2.92
141 142 1.135402 CGAGACACCACGTGATGATCA 60.135 52.381 19.08 0.00 36.96 2.92
142 143 2.534298 GAGACACCACGTGATGATCAG 58.466 52.381 19.08 0.00 36.96 2.90
143 144 1.205655 AGACACCACGTGATGATCAGG 59.794 52.381 19.08 13.06 38.16 3.86
144 145 0.976641 ACACCACGTGATGATCAGGT 59.023 50.000 19.08 14.39 45.17 4.00
151 152 4.313277 ACGTGATGATCAGGTGTGATAG 57.687 45.455 18.73 0.00 43.92 2.08
152 153 3.954258 ACGTGATGATCAGGTGTGATAGA 59.046 43.478 18.73 0.00 43.92 1.98
153 154 4.202060 ACGTGATGATCAGGTGTGATAGAC 60.202 45.833 18.73 0.00 43.92 2.59
154 155 4.037327 CGTGATGATCAGGTGTGATAGACT 59.963 45.833 6.95 0.00 43.92 3.24
155 156 5.527951 GTGATGATCAGGTGTGATAGACTC 58.472 45.833 0.09 0.00 43.92 3.36
156 157 5.301551 GTGATGATCAGGTGTGATAGACTCT 59.698 44.000 0.09 0.00 43.92 3.24
157 158 6.488344 GTGATGATCAGGTGTGATAGACTCTA 59.512 42.308 0.09 0.00 43.92 2.43
158 159 6.488344 TGATGATCAGGTGTGATAGACTCTAC 59.512 42.308 0.09 0.00 43.92 2.59
159 160 4.816925 TGATCAGGTGTGATAGACTCTACG 59.183 45.833 0.00 0.00 43.92 3.51
160 161 4.217836 TCAGGTGTGATAGACTCTACGT 57.782 45.455 0.00 0.00 0.00 3.57
161 162 4.586884 TCAGGTGTGATAGACTCTACGTT 58.413 43.478 0.00 0.00 0.00 3.99
162 163 4.634883 TCAGGTGTGATAGACTCTACGTTC 59.365 45.833 0.00 0.00 0.00 3.95
163 164 4.395231 CAGGTGTGATAGACTCTACGTTCA 59.605 45.833 0.00 0.00 0.00 3.18
164 165 4.395542 AGGTGTGATAGACTCTACGTTCAC 59.604 45.833 0.00 9.86 35.27 3.18
165 166 4.155462 GGTGTGATAGACTCTACGTTCACA 59.845 45.833 13.55 13.55 40.64 3.58
166 167 5.163642 GGTGTGATAGACTCTACGTTCACAT 60.164 44.000 17.93 0.00 43.54 3.21
167 168 6.037940 GGTGTGATAGACTCTACGTTCACATA 59.962 42.308 17.93 1.48 43.54 2.29
168 169 6.906143 GTGTGATAGACTCTACGTTCACATAC 59.094 42.308 17.93 7.95 43.54 2.39
169 170 6.596497 TGTGATAGACTCTACGTTCACATACA 59.404 38.462 13.55 0.00 38.71 2.29
170 171 7.120138 TGTGATAGACTCTACGTTCACATACAA 59.880 37.037 13.55 0.00 38.71 2.41
171 172 7.428761 GTGATAGACTCTACGTTCACATACAAC 59.571 40.741 11.21 0.00 34.92 3.32
177 178 1.504359 CGTTCACATACAACGGGTGT 58.496 50.000 3.29 3.29 42.36 4.16
178 179 2.674954 CGTTCACATACAACGGGTGTA 58.325 47.619 8.56 8.56 46.72 2.90
179 180 3.058450 CGTTCACATACAACGGGTGTAA 58.942 45.455 10.35 0.00 45.81 2.41
180 181 3.122278 CGTTCACATACAACGGGTGTAAG 59.878 47.826 10.35 8.47 45.81 2.34
181 182 4.309099 GTTCACATACAACGGGTGTAAGA 58.691 43.478 14.69 8.48 45.81 2.10
182 183 3.916761 TCACATACAACGGGTGTAAGAC 58.083 45.455 14.69 0.00 45.81 3.01
183 184 3.321396 TCACATACAACGGGTGTAAGACA 59.679 43.478 14.69 0.00 45.81 3.41
184 185 3.678072 CACATACAACGGGTGTAAGACAG 59.322 47.826 14.69 4.00 45.81 3.51
185 186 3.322828 ACATACAACGGGTGTAAGACAGT 59.677 43.478 14.69 4.55 45.81 3.55
186 187 2.994186 ACAACGGGTGTAAGACAGTT 57.006 45.000 0.00 0.00 39.29 3.16
187 188 3.271055 ACAACGGGTGTAAGACAGTTT 57.729 42.857 0.00 0.00 39.29 2.66
188 189 3.613030 ACAACGGGTGTAAGACAGTTTT 58.387 40.909 0.00 0.00 39.29 2.43
189 190 4.768583 ACAACGGGTGTAAGACAGTTTTA 58.231 39.130 0.00 0.00 39.29 1.52
190 191 4.571984 ACAACGGGTGTAAGACAGTTTTAC 59.428 41.667 0.00 6.98 39.29 2.01
191 192 4.405116 ACGGGTGTAAGACAGTTTTACA 57.595 40.909 11.72 11.72 38.36 2.41
198 199 6.299023 TGTAAGACAGTTTTACACATGCAG 57.701 37.500 11.72 0.00 36.41 4.41
199 200 6.052360 TGTAAGACAGTTTTACACATGCAGA 58.948 36.000 11.72 0.00 36.41 4.26
200 201 6.540551 TGTAAGACAGTTTTACACATGCAGAA 59.459 34.615 11.72 0.00 36.41 3.02
201 202 6.639632 AAGACAGTTTTACACATGCAGAAT 57.360 33.333 0.00 0.00 0.00 2.40
202 203 7.744087 AAGACAGTTTTACACATGCAGAATA 57.256 32.000 0.00 0.00 0.00 1.75
203 204 7.133891 AGACAGTTTTACACATGCAGAATAC 57.866 36.000 0.00 0.00 0.00 1.89
204 205 6.936900 AGACAGTTTTACACATGCAGAATACT 59.063 34.615 0.00 0.00 0.00 2.12
205 206 7.445402 AGACAGTTTTACACATGCAGAATACTT 59.555 33.333 0.00 0.00 0.00 2.24
206 207 7.362662 ACAGTTTTACACATGCAGAATACTTG 58.637 34.615 0.00 0.00 0.00 3.16
207 208 6.803320 CAGTTTTACACATGCAGAATACTTGG 59.197 38.462 0.00 0.00 0.00 3.61
208 209 5.895636 TTTACACATGCAGAATACTTGGG 57.104 39.130 0.00 0.00 0.00 4.12
209 210 3.439857 ACACATGCAGAATACTTGGGT 57.560 42.857 0.00 0.00 0.00 4.51
210 211 3.766545 ACACATGCAGAATACTTGGGTT 58.233 40.909 0.00 0.00 0.00 4.11
211 212 4.917385 ACACATGCAGAATACTTGGGTTA 58.083 39.130 0.00 0.00 0.00 2.85
212 213 5.321102 ACACATGCAGAATACTTGGGTTAA 58.679 37.500 0.00 0.00 0.00 2.01
213 214 5.772672 ACACATGCAGAATACTTGGGTTAAA 59.227 36.000 0.00 0.00 0.00 1.52
214 215 6.092748 CACATGCAGAATACTTGGGTTAAAC 58.907 40.000 0.00 0.00 0.00 2.01
215 216 6.010219 ACATGCAGAATACTTGGGTTAAACT 58.990 36.000 0.00 0.00 0.00 2.66
216 217 6.493458 ACATGCAGAATACTTGGGTTAAACTT 59.507 34.615 0.00 0.00 0.00 2.66
217 218 6.325919 TGCAGAATACTTGGGTTAAACTTG 57.674 37.500 0.00 0.00 0.00 3.16
218 219 6.065374 TGCAGAATACTTGGGTTAAACTTGA 58.935 36.000 0.00 0.00 0.00 3.02
219 220 6.016610 TGCAGAATACTTGGGTTAAACTTGAC 60.017 38.462 0.00 0.00 0.00 3.18
220 221 6.599437 CAGAATACTTGGGTTAAACTTGACG 58.401 40.000 0.00 0.00 0.00 4.35
221 222 6.425721 CAGAATACTTGGGTTAAACTTGACGA 59.574 38.462 0.00 0.00 0.00 4.20
222 223 6.649557 AGAATACTTGGGTTAAACTTGACGAG 59.350 38.462 0.00 0.00 0.00 4.18
223 224 4.411256 ACTTGGGTTAAACTTGACGAGA 57.589 40.909 0.00 0.00 0.00 4.04
224 225 4.124970 ACTTGGGTTAAACTTGACGAGAC 58.875 43.478 0.00 0.00 0.00 3.36
225 226 2.746269 TGGGTTAAACTTGACGAGACG 58.254 47.619 0.00 0.00 0.00 4.18
226 227 2.361757 TGGGTTAAACTTGACGAGACGA 59.638 45.455 0.00 0.00 0.00 4.20
227 228 2.985139 GGGTTAAACTTGACGAGACGAG 59.015 50.000 0.00 0.00 0.00 4.18
228 229 2.407696 GGTTAAACTTGACGAGACGAGC 59.592 50.000 0.00 0.00 0.00 5.03
229 230 3.047796 GTTAAACTTGACGAGACGAGCA 58.952 45.455 0.00 0.00 0.00 4.26
230 231 2.440539 AAACTTGACGAGACGAGCAT 57.559 45.000 0.00 0.00 0.00 3.79
231 232 1.702886 AACTTGACGAGACGAGCATG 58.297 50.000 0.00 0.00 0.00 4.06
232 233 0.598562 ACTTGACGAGACGAGCATGT 59.401 50.000 0.00 0.00 0.00 3.21
233 234 1.810755 ACTTGACGAGACGAGCATGTA 59.189 47.619 0.00 0.00 0.00 2.29
234 235 2.177977 CTTGACGAGACGAGCATGTAC 58.822 52.381 0.00 0.00 0.00 2.90
235 236 1.161843 TGACGAGACGAGCATGTACA 58.838 50.000 0.00 0.00 0.00 2.90
236 237 1.130561 TGACGAGACGAGCATGTACAG 59.869 52.381 0.33 0.00 0.00 2.74
237 238 1.397343 GACGAGACGAGCATGTACAGA 59.603 52.381 0.33 0.00 0.00 3.41
238 239 1.130749 ACGAGACGAGCATGTACAGAC 59.869 52.381 0.33 0.00 0.00 3.51
239 240 1.130561 CGAGACGAGCATGTACAGACA 59.869 52.381 0.33 0.00 40.72 3.41
249 250 2.209690 TGTACAGACATGACCTCGGA 57.790 50.000 0.00 0.00 0.00 4.55
250 251 2.521126 TGTACAGACATGACCTCGGAA 58.479 47.619 0.00 0.00 0.00 4.30
251 252 2.230508 TGTACAGACATGACCTCGGAAC 59.769 50.000 0.00 0.00 0.00 3.62
252 253 1.338107 ACAGACATGACCTCGGAACA 58.662 50.000 0.00 0.00 0.00 3.18
253 254 1.000955 ACAGACATGACCTCGGAACAC 59.999 52.381 0.00 0.00 0.00 3.32
254 255 1.273606 CAGACATGACCTCGGAACACT 59.726 52.381 0.00 0.00 0.00 3.55
255 256 1.273606 AGACATGACCTCGGAACACTG 59.726 52.381 0.00 0.00 0.00 3.66
256 257 0.321671 ACATGACCTCGGAACACTGG 59.678 55.000 0.00 0.00 0.00 4.00
257 258 0.608130 CATGACCTCGGAACACTGGA 59.392 55.000 0.00 0.00 0.00 3.86
258 259 0.898320 ATGACCTCGGAACACTGGAG 59.102 55.000 0.00 0.00 0.00 3.86
259 260 0.178973 TGACCTCGGAACACTGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
260 261 0.244178 GACCTCGGAACACTGGAGAC 59.756 60.000 0.00 0.00 0.00 3.36
261 262 1.186267 ACCTCGGAACACTGGAGACC 61.186 60.000 0.00 0.00 0.00 3.85
262 263 1.213013 CTCGGAACACTGGAGACCG 59.787 63.158 0.00 0.00 44.09 4.79
263 264 3.362262 CGGAACACTGGAGACCGA 58.638 61.111 0.00 0.00 45.31 4.69
264 265 1.663739 CGGAACACTGGAGACCGAA 59.336 57.895 0.00 0.00 45.31 4.30
265 266 0.032952 CGGAACACTGGAGACCGAAA 59.967 55.000 0.00 0.00 45.31 3.46
266 267 1.797025 GGAACACTGGAGACCGAAAG 58.203 55.000 0.00 0.00 0.00 2.62
281 282 3.870723 CGAAAGGTCAAACGTGAATCA 57.129 42.857 0.00 0.00 34.87 2.57
282 283 4.404507 CGAAAGGTCAAACGTGAATCAT 57.595 40.909 0.00 0.00 34.87 2.45
283 284 5.524511 CGAAAGGTCAAACGTGAATCATA 57.475 39.130 0.00 0.00 34.87 2.15
284 285 6.106877 CGAAAGGTCAAACGTGAATCATAT 57.893 37.500 0.00 0.00 34.87 1.78
285 286 7.229228 CGAAAGGTCAAACGTGAATCATATA 57.771 36.000 0.00 0.00 34.87 0.86
286 287 7.337718 CGAAAGGTCAAACGTGAATCATATAG 58.662 38.462 0.00 0.00 34.87 1.31
287 288 7.010183 CGAAAGGTCAAACGTGAATCATATAGT 59.990 37.037 0.00 0.00 34.87 2.12
288 289 9.309516 GAAAGGTCAAACGTGAATCATATAGTA 57.690 33.333 0.00 0.00 34.87 1.82
289 290 8.873215 AAGGTCAAACGTGAATCATATAGTAG 57.127 34.615 0.00 0.00 34.87 2.57
290 291 8.234136 AGGTCAAACGTGAATCATATAGTAGA 57.766 34.615 0.00 0.00 34.87 2.59
291 292 8.861086 AGGTCAAACGTGAATCATATAGTAGAT 58.139 33.333 0.00 0.00 34.87 1.98
323 324 7.943079 ACATAAAGATGTTCACCATTGATGA 57.057 32.000 0.00 0.00 44.18 2.92
324 325 8.529424 ACATAAAGATGTTCACCATTGATGAT 57.471 30.769 0.00 0.00 44.18 2.45
325 326 8.974238 ACATAAAGATGTTCACCATTGATGATT 58.026 29.630 0.00 0.00 44.18 2.57
328 329 6.949352 AGATGTTCACCATTGATGATTACC 57.051 37.500 0.00 0.00 32.56 2.85
329 330 5.829924 AGATGTTCACCATTGATGATTACCC 59.170 40.000 0.00 0.00 32.56 3.69
330 331 4.277476 TGTTCACCATTGATGATTACCCC 58.723 43.478 0.00 0.00 0.00 4.95
331 332 4.264128 TGTTCACCATTGATGATTACCCCA 60.264 41.667 0.00 0.00 0.00 4.96
332 333 4.812403 TCACCATTGATGATTACCCCAT 57.188 40.909 0.00 0.00 0.00 4.00
333 334 4.728772 TCACCATTGATGATTACCCCATC 58.271 43.478 0.00 0.00 40.48 3.51
334 335 4.416513 TCACCATTGATGATTACCCCATCT 59.583 41.667 0.00 0.00 40.65 2.90
335 336 4.763793 CACCATTGATGATTACCCCATCTC 59.236 45.833 0.00 0.00 40.65 2.75
336 337 4.416513 ACCATTGATGATTACCCCATCTCA 59.583 41.667 0.00 0.00 40.65 3.27
423 427 4.508124 GGTCATACTATGCCGAAGTTCTTG 59.492 45.833 0.56 0.00 0.00 3.02
460 466 6.762077 TTCACATCCATTCCTATGTCCATA 57.238 37.500 0.00 0.00 34.12 2.74
465 471 8.517878 CACATCCATTCCTATGTCCATATTTTC 58.482 37.037 0.00 0.00 34.12 2.29
520 526 9.355215 TCATCGAAAGTAGAAAGTATCTCAAAC 57.645 33.333 0.00 0.00 39.71 2.93
599 606 0.683504 AGTCGTTGCTCCCCTATCGT 60.684 55.000 0.00 0.00 0.00 3.73
661 668 2.895372 CGCGCCCCTTATGTCCAC 60.895 66.667 0.00 0.00 0.00 4.02
901 908 1.794116 GTGTCACACATGCAAAATGGC 59.206 47.619 2.00 0.00 34.08 4.40
965 972 1.447489 CGGCAGCACAGAGGAGAAG 60.447 63.158 0.00 0.00 0.00 2.85
972 984 3.257873 CAGCACAGAGGAGAAGAAGAAGA 59.742 47.826 0.00 0.00 0.00 2.87
973 985 3.900601 AGCACAGAGGAGAAGAAGAAGAA 59.099 43.478 0.00 0.00 0.00 2.52
1093 1116 0.327000 CCCCATCCCACCTCTTCTCT 60.327 60.000 0.00 0.00 0.00 3.10
1162 1185 3.254166 AGGCAACAACAATCAGATCACAC 59.746 43.478 0.00 0.00 41.41 3.82
1163 1186 3.004629 GGCAACAACAATCAGATCACACA 59.995 43.478 0.00 0.00 0.00 3.72
1164 1187 3.976942 GCAACAACAATCAGATCACACAC 59.023 43.478 0.00 0.00 0.00 3.82
1165 1188 4.497842 GCAACAACAATCAGATCACACACA 60.498 41.667 0.00 0.00 0.00 3.72
1361 1384 4.243008 TTCCAAGTGGCGGACGCA 62.243 61.111 18.95 1.95 44.11 5.24
1940 1963 4.164843 AGTTAGCCTCTCCTCTCTAGTG 57.835 50.000 0.00 0.00 0.00 2.74
2018 2044 2.812011 ACTCTGGTGATTTAAACCGTGC 59.188 45.455 0.00 0.00 40.86 5.34
2019 2045 3.074412 CTCTGGTGATTTAAACCGTGCT 58.926 45.455 0.00 0.00 40.86 4.40
2020 2046 2.811431 TCTGGTGATTTAAACCGTGCTG 59.189 45.455 0.00 0.00 40.86 4.41
2381 2407 1.135915 CGTGCTGTAATGCCTCTCTCT 59.864 52.381 0.00 0.00 0.00 3.10
2382 2408 2.797792 CGTGCTGTAATGCCTCTCTCTC 60.798 54.545 0.00 0.00 0.00 3.20
2383 2409 2.430332 GTGCTGTAATGCCTCTCTCTCT 59.570 50.000 0.00 0.00 0.00 3.10
2384 2410 2.692557 TGCTGTAATGCCTCTCTCTCTC 59.307 50.000 0.00 0.00 0.00 3.20
2385 2411 2.958355 GCTGTAATGCCTCTCTCTCTCT 59.042 50.000 0.00 0.00 0.00 3.10
2386 2412 3.004734 GCTGTAATGCCTCTCTCTCTCTC 59.995 52.174 0.00 0.00 0.00 3.20
2387 2413 4.464008 CTGTAATGCCTCTCTCTCTCTCT 58.536 47.826 0.00 0.00 0.00 3.10
2388 2414 4.460263 TGTAATGCCTCTCTCTCTCTCTC 58.540 47.826 0.00 0.00 0.00 3.20
2389 2415 3.959495 AATGCCTCTCTCTCTCTCTCT 57.041 47.619 0.00 0.00 0.00 3.10
2390 2416 3.498774 ATGCCTCTCTCTCTCTCTCTC 57.501 52.381 0.00 0.00 0.00 3.20
2391 2417 1.138859 TGCCTCTCTCTCTCTCTCTCG 59.861 57.143 0.00 0.00 0.00 4.04
2392 2418 1.871080 CCTCTCTCTCTCTCTCTCGC 58.129 60.000 0.00 0.00 0.00 5.03
2393 2419 1.414181 CCTCTCTCTCTCTCTCTCGCT 59.586 57.143 0.00 0.00 0.00 4.93
2394 2420 2.477825 CTCTCTCTCTCTCTCTCGCTG 58.522 57.143 0.00 0.00 0.00 5.18
2395 2421 1.831106 TCTCTCTCTCTCTCTCGCTGT 59.169 52.381 0.00 0.00 0.00 4.40
2396 2422 2.159099 TCTCTCTCTCTCTCTCGCTGTC 60.159 54.545 0.00 0.00 0.00 3.51
2397 2423 1.831106 TCTCTCTCTCTCTCGCTGTCT 59.169 52.381 0.00 0.00 0.00 3.41
2398 2424 1.935873 CTCTCTCTCTCTCGCTGTCTG 59.064 57.143 0.00 0.00 0.00 3.51
2399 2425 1.016627 CTCTCTCTCTCGCTGTCTGG 58.983 60.000 0.00 0.00 0.00 3.86
2400 2426 0.326595 TCTCTCTCTCGCTGTCTGGT 59.673 55.000 0.00 0.00 0.00 4.00
2401 2427 1.173043 CTCTCTCTCGCTGTCTGGTT 58.827 55.000 0.00 0.00 0.00 3.67
2402 2428 1.543802 CTCTCTCTCGCTGTCTGGTTT 59.456 52.381 0.00 0.00 0.00 3.27
2403 2429 1.964223 TCTCTCTCGCTGTCTGGTTTT 59.036 47.619 0.00 0.00 0.00 2.43
2404 2430 2.365617 TCTCTCTCGCTGTCTGGTTTTT 59.634 45.455 0.00 0.00 0.00 1.94
2482 2518 0.396435 TTCTCGCTTGGCTTTCTCCA 59.604 50.000 0.00 0.00 0.00 3.86
2600 2640 0.041047 TTCGTCGAGTACCGTGTGTG 60.041 55.000 0.00 0.00 39.75 3.82
2601 2641 1.159713 TCGTCGAGTACCGTGTGTGT 61.160 55.000 0.00 0.00 39.75 3.72
2602 2642 0.995234 CGTCGAGTACCGTGTGTGTG 60.995 60.000 0.00 0.00 39.75 3.82
2603 2643 0.029834 GTCGAGTACCGTGTGTGTGT 59.970 55.000 0.00 0.00 39.75 3.72
2619 2659 3.411351 GTTCTTTCCTGCGCGCGA 61.411 61.111 37.18 16.12 0.00 5.87
2736 2788 2.073307 CGTGATCCTCTGCAACACG 58.927 57.895 0.00 0.00 45.46 4.49
2791 2843 4.931661 TCCATCTCGGTAGGTAAATCAC 57.068 45.455 0.00 0.00 35.57 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.929722 CGTACTAAGCAAAATAAGATGCATAAA 57.070 29.630 0.00 0.00 44.95 1.40
7 8 8.556194 CCGTACTAAGCAAAATAAGATGCATAA 58.444 33.333 0.00 0.00 44.95 1.90
8 9 7.307751 GCCGTACTAAGCAAAATAAGATGCATA 60.308 37.037 0.00 0.00 44.95 3.14
9 10 6.513393 GCCGTACTAAGCAAAATAAGATGCAT 60.513 38.462 0.00 0.00 44.95 3.96
10 11 5.220777 GCCGTACTAAGCAAAATAAGATGCA 60.221 40.000 0.00 0.00 44.95 3.96
11 12 5.205565 GCCGTACTAAGCAAAATAAGATGC 58.794 41.667 0.00 0.00 42.87 3.91
12 13 5.432157 CGCCGTACTAAGCAAAATAAGATG 58.568 41.667 0.00 0.00 0.00 2.90
13 14 4.510340 CCGCCGTACTAAGCAAAATAAGAT 59.490 41.667 0.00 0.00 0.00 2.40
14 15 3.866910 CCGCCGTACTAAGCAAAATAAGA 59.133 43.478 0.00 0.00 0.00 2.10
15 16 3.619929 ACCGCCGTACTAAGCAAAATAAG 59.380 43.478 0.00 0.00 0.00 1.73
16 17 3.598299 ACCGCCGTACTAAGCAAAATAA 58.402 40.909 0.00 0.00 0.00 1.40
17 18 3.249986 ACCGCCGTACTAAGCAAAATA 57.750 42.857 0.00 0.00 0.00 1.40
18 19 2.103537 ACCGCCGTACTAAGCAAAAT 57.896 45.000 0.00 0.00 0.00 1.82
19 20 2.609350 CTACCGCCGTACTAAGCAAAA 58.391 47.619 0.00 0.00 0.00 2.44
20 21 1.736696 GCTACCGCCGTACTAAGCAAA 60.737 52.381 0.00 0.00 0.00 3.68
21 22 0.179129 GCTACCGCCGTACTAAGCAA 60.179 55.000 0.00 0.00 0.00 3.91
22 23 1.314534 TGCTACCGCCGTACTAAGCA 61.315 55.000 0.00 0.00 34.43 3.91
23 24 0.031721 ATGCTACCGCCGTACTAAGC 59.968 55.000 0.00 0.00 34.43 3.09
24 25 2.503920 AATGCTACCGCCGTACTAAG 57.496 50.000 0.00 0.00 34.43 2.18
25 26 5.473162 TCTTATAATGCTACCGCCGTACTAA 59.527 40.000 0.00 0.00 34.43 2.24
26 27 5.003160 TCTTATAATGCTACCGCCGTACTA 58.997 41.667 0.00 0.00 34.43 1.82
27 28 3.822735 TCTTATAATGCTACCGCCGTACT 59.177 43.478 0.00 0.00 34.43 2.73
28 29 4.164822 TCTTATAATGCTACCGCCGTAC 57.835 45.455 0.00 0.00 34.43 3.67
29 30 4.460034 TCATCTTATAATGCTACCGCCGTA 59.540 41.667 0.00 0.00 34.43 4.02
30 31 3.257375 TCATCTTATAATGCTACCGCCGT 59.743 43.478 0.00 0.00 34.43 5.68
31 32 3.845178 TCATCTTATAATGCTACCGCCG 58.155 45.455 0.00 0.00 34.43 6.46
32 33 4.811557 GGATCATCTTATAATGCTACCGCC 59.188 45.833 0.00 0.00 34.43 6.13
33 34 5.419542 TGGATCATCTTATAATGCTACCGC 58.580 41.667 0.00 0.00 0.00 5.68
34 35 7.765819 TGAATGGATCATCTTATAATGCTACCG 59.234 37.037 0.00 0.00 31.50 4.02
35 36 8.887717 GTGAATGGATCATCTTATAATGCTACC 58.112 37.037 0.00 0.00 40.97 3.18
36 37 9.664332 AGTGAATGGATCATCTTATAATGCTAC 57.336 33.333 0.00 0.00 40.97 3.58
47 48 8.910944 CCTTGAAATTTAGTGAATGGATCATCT 58.089 33.333 0.00 0.00 40.97 2.90
48 49 8.689972 ACCTTGAAATTTAGTGAATGGATCATC 58.310 33.333 0.00 0.00 40.97 2.92
49 50 8.599624 ACCTTGAAATTTAGTGAATGGATCAT 57.400 30.769 0.00 0.00 40.97 2.45
50 51 9.699410 ATACCTTGAAATTTAGTGAATGGATCA 57.301 29.630 0.00 0.00 35.05 2.92
62 63 9.457436 GGGAGAACACTTATACCTTGAAATTTA 57.543 33.333 0.00 0.00 0.00 1.40
63 64 8.170730 AGGGAGAACACTTATACCTTGAAATTT 58.829 33.333 0.00 0.00 0.00 1.82
64 65 7.611855 CAGGGAGAACACTTATACCTTGAAATT 59.388 37.037 0.00 0.00 0.00 1.82
65 66 7.037586 TCAGGGAGAACACTTATACCTTGAAAT 60.038 37.037 0.00 0.00 32.30 2.17
66 67 6.271391 TCAGGGAGAACACTTATACCTTGAAA 59.729 38.462 0.00 0.00 32.30 2.69
67 68 5.783360 TCAGGGAGAACACTTATACCTTGAA 59.217 40.000 0.00 0.00 32.30 2.69
68 69 5.338632 TCAGGGAGAACACTTATACCTTGA 58.661 41.667 0.00 0.00 32.67 3.02
69 70 5.187967 ACTCAGGGAGAACACTTATACCTTG 59.812 44.000 0.00 0.00 33.32 3.61
70 71 5.342866 ACTCAGGGAGAACACTTATACCTT 58.657 41.667 0.00 0.00 33.32 3.50
71 72 4.949121 ACTCAGGGAGAACACTTATACCT 58.051 43.478 0.00 0.00 33.32 3.08
72 73 6.739008 GCATACTCAGGGAGAACACTTATACC 60.739 46.154 0.00 0.00 33.32 2.73
73 74 6.183360 TGCATACTCAGGGAGAACACTTATAC 60.183 42.308 0.00 0.00 33.32 1.47
74 75 5.897250 TGCATACTCAGGGAGAACACTTATA 59.103 40.000 0.00 0.00 33.32 0.98
75 76 4.716784 TGCATACTCAGGGAGAACACTTAT 59.283 41.667 0.00 0.00 33.32 1.73
76 77 4.081642 GTGCATACTCAGGGAGAACACTTA 60.082 45.833 0.00 0.00 33.32 2.24
77 78 2.906389 TGCATACTCAGGGAGAACACTT 59.094 45.455 0.00 0.00 33.32 3.16
78 79 2.234908 GTGCATACTCAGGGAGAACACT 59.765 50.000 0.00 0.00 33.32 3.55
79 80 2.622436 GTGCATACTCAGGGAGAACAC 58.378 52.381 0.00 0.00 33.32 3.32
80 81 1.555075 GGTGCATACTCAGGGAGAACA 59.445 52.381 0.00 0.00 33.32 3.18
81 82 1.471676 CGGTGCATACTCAGGGAGAAC 60.472 57.143 0.00 0.00 33.32 3.01
82 83 0.824109 CGGTGCATACTCAGGGAGAA 59.176 55.000 0.00 0.00 33.32 2.87
83 84 0.324368 ACGGTGCATACTCAGGGAGA 60.324 55.000 0.00 0.00 33.32 3.71
84 85 0.537188 AACGGTGCATACTCAGGGAG 59.463 55.000 0.00 0.00 35.52 4.30
85 86 0.249120 CAACGGTGCATACTCAGGGA 59.751 55.000 0.00 0.00 0.00 4.20
86 87 2.767536 CAACGGTGCATACTCAGGG 58.232 57.895 0.00 0.00 0.00 4.45
97 98 1.455786 CGAAGAACTGTAGCAACGGTG 59.544 52.381 0.00 0.00 44.70 4.94
99 100 1.779569 ACGAAGAACTGTAGCAACGG 58.220 50.000 0.00 0.00 38.04 4.44
100 101 3.658342 CGAAACGAAGAACTGTAGCAACG 60.658 47.826 0.00 0.00 0.00 4.10
101 102 3.488310 TCGAAACGAAGAACTGTAGCAAC 59.512 43.478 0.00 0.00 31.06 4.17
102 103 3.708890 TCGAAACGAAGAACTGTAGCAA 58.291 40.909 0.00 0.00 31.06 3.91
103 104 3.004002 TCTCGAAACGAAGAACTGTAGCA 59.996 43.478 0.00 0.00 34.74 3.49
104 105 3.361348 GTCTCGAAACGAAGAACTGTAGC 59.639 47.826 0.00 0.00 34.74 3.58
105 106 4.379204 GTGTCTCGAAACGAAGAACTGTAG 59.621 45.833 0.00 0.00 34.74 2.74
106 107 4.285292 GTGTCTCGAAACGAAGAACTGTA 58.715 43.478 0.00 0.00 34.74 2.74
107 108 3.114065 GTGTCTCGAAACGAAGAACTGT 58.886 45.455 0.00 0.00 34.74 3.55
108 109 2.471743 GGTGTCTCGAAACGAAGAACTG 59.528 50.000 0.00 0.00 34.74 3.16
109 110 2.100252 TGGTGTCTCGAAACGAAGAACT 59.900 45.455 0.00 0.00 34.74 3.01
110 111 2.218075 GTGGTGTCTCGAAACGAAGAAC 59.782 50.000 0.00 0.00 34.74 3.01
111 112 2.466846 GTGGTGTCTCGAAACGAAGAA 58.533 47.619 0.00 0.00 34.74 2.52
112 113 1.598676 CGTGGTGTCTCGAAACGAAGA 60.599 52.381 0.00 0.00 36.38 2.87
113 114 0.776451 CGTGGTGTCTCGAAACGAAG 59.224 55.000 0.00 0.00 36.38 3.79
114 115 0.101040 ACGTGGTGTCTCGAAACGAA 59.899 50.000 0.00 0.00 37.66 3.85
115 116 0.593008 CACGTGGTGTCTCGAAACGA 60.593 55.000 7.95 0.00 37.66 3.85
116 117 0.593008 TCACGTGGTGTCTCGAAACG 60.593 55.000 17.00 0.00 40.00 3.60
117 118 1.455786 CATCACGTGGTGTCTCGAAAC 59.544 52.381 20.85 0.00 34.79 2.78
118 119 1.338655 TCATCACGTGGTGTCTCGAAA 59.661 47.619 27.10 4.29 34.79 3.46
119 120 0.955905 TCATCACGTGGTGTCTCGAA 59.044 50.000 27.10 5.07 34.79 3.71
120 121 1.132453 GATCATCACGTGGTGTCTCGA 59.868 52.381 27.10 9.16 34.79 4.04
121 122 1.135402 TGATCATCACGTGGTGTCTCG 60.135 52.381 27.10 2.49 34.79 4.04
122 123 2.534298 CTGATCATCACGTGGTGTCTC 58.466 52.381 27.10 23.04 34.79 3.36
123 124 1.205655 CCTGATCATCACGTGGTGTCT 59.794 52.381 27.10 16.35 34.79 3.41
124 125 1.066858 ACCTGATCATCACGTGGTGTC 60.067 52.381 27.10 22.16 34.79 3.67
125 126 0.976641 ACCTGATCATCACGTGGTGT 59.023 50.000 27.10 15.24 34.79 4.16
126 127 1.362768 CACCTGATCATCACGTGGTG 58.637 55.000 23.01 23.01 38.87 4.17
127 128 0.976641 ACACCTGATCATCACGTGGT 59.023 50.000 17.00 5.26 37.60 4.16
128 129 1.066929 TCACACCTGATCATCACGTGG 60.067 52.381 17.00 5.91 37.60 4.94
129 130 2.368655 TCACACCTGATCATCACGTG 57.631 50.000 9.94 9.94 38.68 4.49
130 131 3.954258 TCTATCACACCTGATCATCACGT 59.046 43.478 0.00 0.00 38.21 4.49
131 132 4.037327 AGTCTATCACACCTGATCATCACG 59.963 45.833 0.00 0.00 38.21 4.35
132 133 5.301551 AGAGTCTATCACACCTGATCATCAC 59.698 44.000 0.00 0.00 38.21 3.06
133 134 5.453158 AGAGTCTATCACACCTGATCATCA 58.547 41.667 0.00 0.00 38.21 3.07
134 135 6.348132 CGTAGAGTCTATCACACCTGATCATC 60.348 46.154 2.51 0.00 38.21 2.92
135 136 5.471797 CGTAGAGTCTATCACACCTGATCAT 59.528 44.000 2.51 0.00 38.21 2.45
136 137 4.816925 CGTAGAGTCTATCACACCTGATCA 59.183 45.833 2.51 0.00 38.21 2.92
137 138 4.817464 ACGTAGAGTCTATCACACCTGATC 59.183 45.833 2.51 0.00 38.21 2.92
138 139 4.783055 ACGTAGAGTCTATCACACCTGAT 58.217 43.478 2.51 0.00 40.47 2.90
139 140 4.217836 ACGTAGAGTCTATCACACCTGA 57.782 45.455 2.51 0.00 0.00 3.86
140 141 4.395231 TGAACGTAGAGTCTATCACACCTG 59.605 45.833 2.51 0.00 0.00 4.00
141 142 4.395542 GTGAACGTAGAGTCTATCACACCT 59.604 45.833 20.32 0.00 37.65 4.00
142 143 4.155462 TGTGAACGTAGAGTCTATCACACC 59.845 45.833 22.60 6.32 41.39 4.16
143 144 5.292671 TGTGAACGTAGAGTCTATCACAC 57.707 43.478 22.60 19.02 41.39 3.82
145 146 7.012959 TGTATGTGAACGTAGAGTCTATCAC 57.987 40.000 19.15 19.15 38.08 3.06
146 147 7.470079 GTTGTATGTGAACGTAGAGTCTATCA 58.530 38.462 2.51 0.42 0.00 2.15
147 148 6.628065 CGTTGTATGTGAACGTAGAGTCTATC 59.372 42.308 2.51 0.00 41.00 2.08
148 149 6.457934 CCGTTGTATGTGAACGTAGAGTCTAT 60.458 42.308 2.51 0.00 43.70 1.98
149 150 5.163824 CCGTTGTATGTGAACGTAGAGTCTA 60.164 44.000 0.00 0.00 43.70 2.59
150 151 4.379186 CCGTTGTATGTGAACGTAGAGTCT 60.379 45.833 0.00 0.00 43.70 3.24
151 152 3.850273 CCGTTGTATGTGAACGTAGAGTC 59.150 47.826 0.00 0.00 43.70 3.36
152 153 3.366679 CCCGTTGTATGTGAACGTAGAGT 60.367 47.826 0.00 0.00 43.70 3.24
153 154 3.176708 CCCGTTGTATGTGAACGTAGAG 58.823 50.000 0.00 0.00 43.70 2.43
154 155 2.557924 ACCCGTTGTATGTGAACGTAGA 59.442 45.455 0.00 0.00 43.70 2.59
155 156 2.664568 CACCCGTTGTATGTGAACGTAG 59.335 50.000 0.00 0.00 43.70 3.51
156 157 2.035704 ACACCCGTTGTATGTGAACGTA 59.964 45.455 0.00 0.00 43.70 3.57
157 158 1.202557 ACACCCGTTGTATGTGAACGT 60.203 47.619 0.00 0.00 43.70 3.99
158 159 1.504359 ACACCCGTTGTATGTGAACG 58.496 50.000 0.00 0.00 44.59 3.95
159 160 4.151157 GTCTTACACCCGTTGTATGTGAAC 59.849 45.833 0.00 0.00 40.53 3.18
160 161 4.202233 TGTCTTACACCCGTTGTATGTGAA 60.202 41.667 0.00 0.00 40.53 3.18
161 162 3.321396 TGTCTTACACCCGTTGTATGTGA 59.679 43.478 0.00 0.68 40.53 3.58
162 163 3.655486 TGTCTTACACCCGTTGTATGTG 58.345 45.455 7.01 0.00 40.53 3.21
163 164 3.322828 ACTGTCTTACACCCGTTGTATGT 59.677 43.478 7.01 0.00 40.53 2.29
164 165 3.921677 ACTGTCTTACACCCGTTGTATG 58.078 45.455 0.00 0.00 40.53 2.39
165 166 4.612264 AACTGTCTTACACCCGTTGTAT 57.388 40.909 0.00 0.00 40.53 2.29
166 167 4.405116 AAACTGTCTTACACCCGTTGTA 57.595 40.909 0.00 0.00 39.91 2.41
167 168 2.994186 AACTGTCTTACACCCGTTGT 57.006 45.000 0.00 0.00 42.84 3.32
168 169 4.571580 TGTAAAACTGTCTTACACCCGTTG 59.428 41.667 2.69 0.00 34.99 4.10
169 170 4.768583 TGTAAAACTGTCTTACACCCGTT 58.231 39.130 2.69 0.00 34.99 4.44
170 171 4.405116 TGTAAAACTGTCTTACACCCGT 57.595 40.909 2.69 0.00 34.99 5.28
175 176 6.052360 TCTGCATGTGTAAAACTGTCTTACA 58.948 36.000 2.69 2.69 37.01 2.41
176 177 6.539649 TCTGCATGTGTAAAACTGTCTTAC 57.460 37.500 0.00 0.00 0.00 2.34
177 178 7.744087 ATTCTGCATGTGTAAAACTGTCTTA 57.256 32.000 0.00 0.00 0.00 2.10
178 179 6.639632 ATTCTGCATGTGTAAAACTGTCTT 57.360 33.333 0.00 0.00 0.00 3.01
179 180 6.936900 AGTATTCTGCATGTGTAAAACTGTCT 59.063 34.615 0.00 0.00 0.00 3.41
180 181 7.133891 AGTATTCTGCATGTGTAAAACTGTC 57.866 36.000 0.00 0.00 0.00 3.51
181 182 7.362662 CAAGTATTCTGCATGTGTAAAACTGT 58.637 34.615 0.00 0.00 0.00 3.55
182 183 6.803320 CCAAGTATTCTGCATGTGTAAAACTG 59.197 38.462 0.00 0.00 0.00 3.16
183 184 6.071952 CCCAAGTATTCTGCATGTGTAAAACT 60.072 38.462 0.00 0.00 0.00 2.66
184 185 6.092748 CCCAAGTATTCTGCATGTGTAAAAC 58.907 40.000 0.00 0.00 0.00 2.43
185 186 5.772672 ACCCAAGTATTCTGCATGTGTAAAA 59.227 36.000 0.00 0.00 0.00 1.52
186 187 5.321102 ACCCAAGTATTCTGCATGTGTAAA 58.679 37.500 0.00 0.00 0.00 2.01
187 188 4.917385 ACCCAAGTATTCTGCATGTGTAA 58.083 39.130 0.00 0.00 0.00 2.41
188 189 4.568072 ACCCAAGTATTCTGCATGTGTA 57.432 40.909 0.00 0.00 0.00 2.90
189 190 3.439857 ACCCAAGTATTCTGCATGTGT 57.560 42.857 0.00 0.00 0.00 3.72
190 191 5.895636 TTAACCCAAGTATTCTGCATGTG 57.104 39.130 0.00 0.00 0.00 3.21
191 192 6.010219 AGTTTAACCCAAGTATTCTGCATGT 58.990 36.000 0.00 0.00 0.00 3.21
192 193 6.515272 AGTTTAACCCAAGTATTCTGCATG 57.485 37.500 0.00 0.00 0.00 4.06
193 194 6.719370 TCAAGTTTAACCCAAGTATTCTGCAT 59.281 34.615 0.00 0.00 0.00 3.96
194 195 6.016610 GTCAAGTTTAACCCAAGTATTCTGCA 60.017 38.462 0.00 0.00 0.00 4.41
195 196 6.379386 GTCAAGTTTAACCCAAGTATTCTGC 58.621 40.000 0.00 0.00 0.00 4.26
196 197 6.425721 TCGTCAAGTTTAACCCAAGTATTCTG 59.574 38.462 0.00 0.00 0.00 3.02
197 198 6.527423 TCGTCAAGTTTAACCCAAGTATTCT 58.473 36.000 0.00 0.00 0.00 2.40
198 199 6.647895 TCTCGTCAAGTTTAACCCAAGTATTC 59.352 38.462 0.00 0.00 0.00 1.75
199 200 6.426025 GTCTCGTCAAGTTTAACCCAAGTATT 59.574 38.462 0.00 0.00 0.00 1.89
200 201 5.930569 GTCTCGTCAAGTTTAACCCAAGTAT 59.069 40.000 0.00 0.00 0.00 2.12
201 202 5.291971 GTCTCGTCAAGTTTAACCCAAGTA 58.708 41.667 0.00 0.00 0.00 2.24
202 203 4.124970 GTCTCGTCAAGTTTAACCCAAGT 58.875 43.478 0.00 0.00 0.00 3.16
203 204 3.183775 CGTCTCGTCAAGTTTAACCCAAG 59.816 47.826 0.00 0.00 0.00 3.61
204 205 3.125316 CGTCTCGTCAAGTTTAACCCAA 58.875 45.455 0.00 0.00 0.00 4.12
205 206 2.361757 TCGTCTCGTCAAGTTTAACCCA 59.638 45.455 0.00 0.00 0.00 4.51
206 207 2.985139 CTCGTCTCGTCAAGTTTAACCC 59.015 50.000 0.00 0.00 0.00 4.11
207 208 2.407696 GCTCGTCTCGTCAAGTTTAACC 59.592 50.000 0.00 0.00 0.00 2.85
208 209 3.047796 TGCTCGTCTCGTCAAGTTTAAC 58.952 45.455 0.00 0.00 0.00 2.01
209 210 3.358707 TGCTCGTCTCGTCAAGTTTAA 57.641 42.857 0.00 0.00 0.00 1.52
210 211 3.242518 CATGCTCGTCTCGTCAAGTTTA 58.757 45.455 0.00 0.00 0.00 2.01
211 212 2.061773 CATGCTCGTCTCGTCAAGTTT 58.938 47.619 0.00 0.00 0.00 2.66
212 213 1.000163 ACATGCTCGTCTCGTCAAGTT 60.000 47.619 0.00 0.00 0.00 2.66
213 214 0.598562 ACATGCTCGTCTCGTCAAGT 59.401 50.000 0.00 0.00 0.00 3.16
214 215 2.177977 GTACATGCTCGTCTCGTCAAG 58.822 52.381 0.00 0.00 0.00 3.02
215 216 1.538075 TGTACATGCTCGTCTCGTCAA 59.462 47.619 0.00 0.00 0.00 3.18
216 217 1.130561 CTGTACATGCTCGTCTCGTCA 59.869 52.381 0.00 0.00 0.00 4.35
217 218 1.397343 TCTGTACATGCTCGTCTCGTC 59.603 52.381 0.00 0.00 0.00 4.20
218 219 1.130749 GTCTGTACATGCTCGTCTCGT 59.869 52.381 0.00 0.00 0.00 4.18
219 220 1.130561 TGTCTGTACATGCTCGTCTCG 59.869 52.381 0.00 0.00 0.00 4.04
220 221 2.921634 TGTCTGTACATGCTCGTCTC 57.078 50.000 0.00 0.00 0.00 3.36
230 231 2.209690 TCCGAGGTCATGTCTGTACA 57.790 50.000 0.00 0.00 40.69 2.90
231 232 2.230508 TGTTCCGAGGTCATGTCTGTAC 59.769 50.000 0.00 0.00 0.00 2.90
232 233 2.230508 GTGTTCCGAGGTCATGTCTGTA 59.769 50.000 0.00 0.00 0.00 2.74
233 234 1.000955 GTGTTCCGAGGTCATGTCTGT 59.999 52.381 0.00 0.00 0.00 3.41
234 235 1.273606 AGTGTTCCGAGGTCATGTCTG 59.726 52.381 0.00 0.00 0.00 3.51
235 236 1.273606 CAGTGTTCCGAGGTCATGTCT 59.726 52.381 0.00 0.00 0.00 3.41
236 237 1.673033 CCAGTGTTCCGAGGTCATGTC 60.673 57.143 0.00 0.00 0.00 3.06
237 238 0.321671 CCAGTGTTCCGAGGTCATGT 59.678 55.000 0.00 0.00 0.00 3.21
238 239 0.608130 TCCAGTGTTCCGAGGTCATG 59.392 55.000 0.00 0.00 0.00 3.07
239 240 0.898320 CTCCAGTGTTCCGAGGTCAT 59.102 55.000 0.00 0.00 0.00 3.06
240 241 0.178973 TCTCCAGTGTTCCGAGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
241 242 0.244178 GTCTCCAGTGTTCCGAGGTC 59.756 60.000 0.00 0.00 0.00 3.85
242 243 1.186267 GGTCTCCAGTGTTCCGAGGT 61.186 60.000 0.00 0.00 0.00 3.85
243 244 1.592223 GGTCTCCAGTGTTCCGAGG 59.408 63.158 0.00 0.00 0.00 4.63
244 245 1.213013 CGGTCTCCAGTGTTCCGAG 59.787 63.158 0.00 0.00 43.22 4.63
245 246 0.824595 TTCGGTCTCCAGTGTTCCGA 60.825 55.000 9.86 9.86 46.54 4.55
246 247 0.032952 TTTCGGTCTCCAGTGTTCCG 59.967 55.000 0.00 0.00 42.12 4.30
247 248 1.608283 CCTTTCGGTCTCCAGTGTTCC 60.608 57.143 0.00 0.00 0.00 3.62
248 249 1.070289 ACCTTTCGGTCTCCAGTGTTC 59.930 52.381 0.00 0.00 40.27 3.18
249 250 1.129058 ACCTTTCGGTCTCCAGTGTT 58.871 50.000 0.00 0.00 40.27 3.32
250 251 2.836020 ACCTTTCGGTCTCCAGTGT 58.164 52.632 0.00 0.00 40.27 3.55
260 261 2.546368 TGATTCACGTTTGACCTTTCGG 59.454 45.455 0.00 0.00 0.00 4.30
261 262 3.870723 TGATTCACGTTTGACCTTTCG 57.129 42.857 0.00 0.00 0.00 3.46
262 263 8.197988 ACTATATGATTCACGTTTGACCTTTC 57.802 34.615 0.00 0.00 0.00 2.62
263 264 9.314321 CTACTATATGATTCACGTTTGACCTTT 57.686 33.333 0.00 0.00 0.00 3.11
264 265 8.692710 TCTACTATATGATTCACGTTTGACCTT 58.307 33.333 0.00 0.00 0.00 3.50
265 266 8.234136 TCTACTATATGATTCACGTTTGACCT 57.766 34.615 0.00 0.00 0.00 3.85
302 303 8.902806 GGTAATCATCAATGGTGAACATCTTTA 58.097 33.333 0.00 0.00 39.40 1.85
303 304 7.147846 GGGTAATCATCAATGGTGAACATCTTT 60.148 37.037 0.00 0.00 39.40 2.52
304 305 6.322201 GGGTAATCATCAATGGTGAACATCTT 59.678 38.462 0.00 0.00 39.40 2.40
305 306 5.829924 GGGTAATCATCAATGGTGAACATCT 59.170 40.000 0.00 0.00 39.40 2.90
306 307 5.010012 GGGGTAATCATCAATGGTGAACATC 59.990 44.000 0.00 0.00 39.40 3.06
307 308 4.895297 GGGGTAATCATCAATGGTGAACAT 59.105 41.667 0.00 0.00 43.07 2.71
308 309 4.264128 TGGGGTAATCATCAATGGTGAACA 60.264 41.667 0.00 0.00 37.30 3.18
309 310 4.277476 TGGGGTAATCATCAATGGTGAAC 58.723 43.478 0.00 0.00 37.30 3.18
310 311 4.599720 TGGGGTAATCATCAATGGTGAA 57.400 40.909 0.00 0.00 37.30 3.18
311 312 4.416513 AGATGGGGTAATCATCAATGGTGA 59.583 41.667 0.00 0.00 42.38 4.02
312 313 4.733165 AGATGGGGTAATCATCAATGGTG 58.267 43.478 6.80 0.00 42.38 4.17
313 314 4.416513 TGAGATGGGGTAATCATCAATGGT 59.583 41.667 6.80 0.00 42.38 3.55
314 315 4.989277 TGAGATGGGGTAATCATCAATGG 58.011 43.478 6.80 0.00 42.38 3.16
315 316 5.417894 CCATGAGATGGGGTAATCATCAATG 59.582 44.000 0.00 8.84 46.86 2.82
316 317 5.577100 CCATGAGATGGGGTAATCATCAAT 58.423 41.667 0.00 0.00 46.86 2.57
317 318 4.989277 CCATGAGATGGGGTAATCATCAA 58.011 43.478 0.00 0.00 46.86 2.57
318 319 4.645863 CCATGAGATGGGGTAATCATCA 57.354 45.455 0.00 0.00 46.86 3.07
369 370 9.817809 GTCCTTGTGACATAATATTCTTAGACA 57.182 33.333 0.00 0.00 43.85 3.41
399 403 3.961408 AGAACTTCGGCATAGTATGACCT 59.039 43.478 14.52 0.00 33.66 3.85
444 450 8.696043 TTCAGAAAATATGGACATAGGAATGG 57.304 34.615 0.00 0.00 37.43 3.16
599 606 0.320073 CGACAAGGTCAAACCGGCTA 60.320 55.000 0.00 0.00 44.90 3.93
824 831 1.338020 GGTTTGGACTTTGTGGCTCAG 59.662 52.381 0.00 0.00 0.00 3.35
901 908 8.822652 ATGAATTTTCTTTGCTTTTGGTCTAG 57.177 30.769 0.00 0.00 0.00 2.43
1005 1017 2.435586 GACAGCAGTGATGCCGCT 60.436 61.111 8.62 0.00 36.10 5.52
1093 1116 1.814429 TGAGTTGGGACTTGGGAGAA 58.186 50.000 0.00 0.00 35.88 2.87
1162 1185 3.091318 CAGGATTAGGCAGCCTGTG 57.909 57.895 25.59 9.45 43.25 3.66
1165 1188 0.693767 AGAGCAGGATTAGGCAGCCT 60.694 55.000 20.63 20.63 37.71 4.58
1361 1384 2.180862 TAGATCTCGTGCTCGCGCT 61.181 57.895 5.56 0.86 36.97 5.92
1940 1963 3.477210 ACCTGAGAAACAAGAGGACAC 57.523 47.619 0.00 0.00 0.00 3.67
2358 2384 0.324943 AGAGGCATTACAGCACGGTT 59.675 50.000 0.00 0.00 35.83 4.44
2359 2385 0.108138 GAGAGGCATTACAGCACGGT 60.108 55.000 0.00 0.00 35.83 4.83
2360 2386 0.176680 AGAGAGGCATTACAGCACGG 59.823 55.000 0.00 0.00 35.83 4.94
2361 2387 1.135915 AGAGAGAGGCATTACAGCACG 59.864 52.381 0.00 0.00 35.83 5.34
2362 2388 2.430332 AGAGAGAGAGGCATTACAGCAC 59.570 50.000 0.00 0.00 35.83 4.40
2363 2389 2.692557 GAGAGAGAGAGGCATTACAGCA 59.307 50.000 0.00 0.00 35.83 4.41
2364 2390 2.958355 AGAGAGAGAGAGGCATTACAGC 59.042 50.000 0.00 0.00 0.00 4.40
2381 2407 0.326595 ACCAGACAGCGAGAGAGAGA 59.673 55.000 0.00 0.00 0.00 3.10
2382 2408 1.173043 AACCAGACAGCGAGAGAGAG 58.827 55.000 0.00 0.00 0.00 3.20
2383 2409 1.621992 AAACCAGACAGCGAGAGAGA 58.378 50.000 0.00 0.00 0.00 3.10
2384 2410 2.447244 AAAACCAGACAGCGAGAGAG 57.553 50.000 0.00 0.00 0.00 3.20
2385 2411 2.910688 AAAAACCAGACAGCGAGAGA 57.089 45.000 0.00 0.00 0.00 3.10
2407 2433 4.537135 AGACAGCGAGATACCTCAAAAA 57.463 40.909 0.00 0.00 39.39 1.94
2408 2434 4.705507 ACTAGACAGCGAGATACCTCAAAA 59.294 41.667 0.00 0.00 39.39 2.44
2409 2435 4.270834 ACTAGACAGCGAGATACCTCAAA 58.729 43.478 0.00 0.00 39.39 2.69
2410 2436 3.887352 ACTAGACAGCGAGATACCTCAA 58.113 45.455 0.00 0.00 39.39 3.02
2411 2437 3.562343 ACTAGACAGCGAGATACCTCA 57.438 47.619 0.00 0.00 39.39 3.86
2412 2438 3.628487 ACAACTAGACAGCGAGATACCTC 59.372 47.826 0.00 0.00 36.08 3.85
2413 2439 3.378742 CACAACTAGACAGCGAGATACCT 59.621 47.826 0.00 0.00 0.00 3.08
2414 2440 3.489398 CCACAACTAGACAGCGAGATACC 60.489 52.174 0.00 0.00 0.00 2.73
2415 2441 3.377485 TCCACAACTAGACAGCGAGATAC 59.623 47.826 0.00 0.00 0.00 2.24
2416 2442 3.617284 TCCACAACTAGACAGCGAGATA 58.383 45.455 0.00 0.00 0.00 1.98
2417 2443 2.425312 CTCCACAACTAGACAGCGAGAT 59.575 50.000 0.00 0.00 0.00 2.75
2482 2518 2.101582 CACGAAAGAATCCCGAGGAGAT 59.898 50.000 0.00 0.00 34.05 2.75
2600 2640 2.127232 GCGCGCAGGAAAGAACAC 60.127 61.111 29.10 0.00 0.00 3.32
2601 2641 3.711842 CGCGCGCAGGAAAGAACA 61.712 61.111 32.61 0.00 0.00 3.18
2602 2642 2.740714 ATCGCGCGCAGGAAAGAAC 61.741 57.895 32.61 0.00 0.00 3.01
2603 2643 2.434185 ATCGCGCGCAGGAAAGAA 60.434 55.556 32.61 4.34 0.00 2.52
2736 2788 2.691526 TGGCATCATTTCATTCAGGCTC 59.308 45.455 0.00 0.00 0.00 4.70
2791 2843 0.530650 CGATTGGGATCCAGGACACG 60.531 60.000 15.23 7.43 33.81 4.49


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

AutoCloner maintained by Alex Coulton.