Multiple sequence alignment - TraesCS3B01G298900

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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 TraesCS3B01G298900 chr3B 100.000 6151 0 0 1 6151 479582719 479576569 0.000000e+00 11359.0
1 TraesCS3B01G298900 chr3B 94.470 217 11 1 33 249 479611151 479610936 3.550000e-87 333.0
2 TraesCS3B01G298900 chr3B 93.814 194 8 3 34 224 810437978 810437786 7.800000e-74 289.0
3 TraesCS3B01G298900 chr3A 94.441 4371 130 45 1856 6151 489754217 489749885 0.000000e+00 6621.0
4 TraesCS3B01G298900 chr3A 94.118 986 51 6 871 1854 489755245 489754265 0.000000e+00 1493.0
5 TraesCS3B01G298900 chr3A 92.366 131 9 1 280 410 489757135 489757006 1.050000e-42 185.0
6 TraesCS3B01G298900 chr3D 87.647 2291 140 55 3913 6132 368227788 368225570 0.000000e+00 2531.0
7 TraesCS3B01G298900 chr3D 90.467 986 51 19 871 1854 368230514 368229570 0.000000e+00 1260.0
8 TraesCS3B01G298900 chr3D 92.503 787 43 8 1856 2636 368229523 368228747 0.000000e+00 1112.0
9 TraesCS3B01G298900 chr3D 92.111 431 25 6 3492 3920 368228257 368227834 3.170000e-167 599.0
10 TraesCS3B01G298900 chr3D 90.287 453 25 11 2967 3403 368228747 368228298 5.350000e-160 575.0
11 TraesCS3B01G298900 chr3D 88.290 427 26 15 444 855 368231014 368230597 1.990000e-134 490.0
12 TraesCS3B01G298900 chr3D 94.652 187 8 2 34 219 603361861 603362046 7.800000e-74 289.0
13 TraesCS3B01G298900 chr7D 90.830 229 17 2 1 225 40732179 40732407 2.790000e-78 303.0
14 TraesCS3B01G298900 chr2B 90.667 225 15 3 1 224 135509167 135509386 1.680000e-75 294.0
15 TraesCS3B01G298900 chr4A 88.936 235 19 5 1 231 30353388 30353619 3.630000e-72 283.0
16 TraesCS3B01G298900 chr5B 92.308 195 15 0 31 225 591183198 591183004 1.690000e-70 278.0
17 TraesCS3B01G298900 chr6B 87.660 235 23 4 1 231 213535774 213535542 1.020000e-67 268.0
18 TraesCS3B01G298900 chr1A 90.000 210 16 3 1 206 167154150 167153942 3.660000e-67 267.0
19 TraesCS3B01G298900 chr7B 100.000 29 0 0 955 983 327638037 327638009 3.000000e-03 54.7


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 TraesCS3B01G298900 chr3B 479576569 479582719 6150 True 11359.000000 11359 100.000000 1 6151 1 chr3B.!!$R1 6150
1 TraesCS3B01G298900 chr3A 489749885 489757135 7250 True 2766.333333 6621 93.641667 280 6151 3 chr3A.!!$R1 5871
2 TraesCS3B01G298900 chr3D 368225570 368231014 5444 True 1094.500000 2531 90.217500 444 6132 6 chr3D.!!$R1 5688

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
640 1991 0.110486 CACCACTAACCACAGGGCTT 59.890 55.0 0.00 0.0 37.90 4.35 F
910 2351 0.250038 CCATCGGCTCCCATACTGTG 60.250 60.0 0.00 0.0 0.00 3.66 F
1324 2777 0.250770 AGCGGTGAGGTTCCCTTTTC 60.251 55.0 0.00 0.0 31.76 2.29 F
2293 3797 0.464036 TGCCTTGTGCTCCTATACCG 59.536 55.0 0.00 0.0 42.00 4.02 F
2786 4292 0.449388 GCGCTGAAGTTGGATTGAGG 59.551 55.0 0.00 0.0 0.00 3.86 F
2789 4295 2.673368 CGCTGAAGTTGGATTGAGGTAC 59.327 50.0 0.00 0.0 0.00 3.34 F
4653 6255 1.138568 CCTCCCTTCATGATCAGCCT 58.861 55.0 0.09 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 2913 0.419865 TCAGGTCCCCCAGAACCATA 59.580 55.000 0.0 0.0 29.47 2.74 R
1846 3301 0.464373 ATCAGCATGGCCCAGTAACG 60.464 55.000 0.0 0.0 36.16 3.18 R
2725 4231 2.223203 GCATGTGAAGTATGCTGCTGAC 60.223 50.000 0.0 0.0 45.64 3.51 R
4191 5767 1.277579 TAATCACCGTTAGTGCCCCA 58.722 50.000 0.0 0.0 46.81 4.96 R
4627 6229 4.365368 TGATCATGAAGGGAGGAGAGAAA 58.635 43.478 0.0 0.0 0.00 2.52 R
4889 6491 0.762418 TTCTCCCTTTTGAGTCCGCA 59.238 50.000 0.0 0.0 33.93 5.69 R
5904 7581 0.463620 GGCTCGATCCTCTCTTTGCT 59.536 55.000 0.0 0.0 0.00 3.91 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 2.964343 AGACGAGGTGGAAGAGTCC 58.036 57.895 0.00 0.00 45.21 3.85
19 20 0.406361 AGACGAGGTGGAAGAGTCCT 59.594 55.000 0.00 0.00 45.22 3.85
20 21 1.203075 AGACGAGGTGGAAGAGTCCTT 60.203 52.381 0.00 0.00 45.22 3.36
21 22 1.202817 GACGAGGTGGAAGAGTCCTTC 59.797 57.143 0.00 0.00 45.22 3.46
22 23 1.203075 ACGAGGTGGAAGAGTCCTTCT 60.203 52.381 0.00 0.00 46.16 2.85
23 24 1.474879 CGAGGTGGAAGAGTCCTTCTC 59.525 57.143 0.00 1.19 46.16 2.87
35 36 5.606348 GAGTCCTTCTCTGAATACCATGT 57.394 43.478 0.00 0.00 39.86 3.21
36 37 5.983540 GAGTCCTTCTCTGAATACCATGTT 58.016 41.667 0.00 0.00 39.86 2.71
37 38 5.738909 AGTCCTTCTCTGAATACCATGTTG 58.261 41.667 0.00 0.00 0.00 3.33
38 39 5.485353 AGTCCTTCTCTGAATACCATGTTGA 59.515 40.000 0.00 0.00 0.00 3.18
39 40 6.013379 AGTCCTTCTCTGAATACCATGTTGAA 60.013 38.462 0.00 0.00 0.00 2.69
40 41 6.825721 GTCCTTCTCTGAATACCATGTTGAAT 59.174 38.462 0.00 0.00 0.00 2.57
41 42 7.987458 GTCCTTCTCTGAATACCATGTTGAATA 59.013 37.037 0.00 0.00 0.00 1.75
42 43 8.548025 TCCTTCTCTGAATACCATGTTGAATAA 58.452 33.333 0.00 0.00 0.00 1.40
43 44 9.347240 CCTTCTCTGAATACCATGTTGAATAAT 57.653 33.333 0.00 0.00 0.00 1.28
53 54 6.810888 CCATGTTGAATAATGGTTTAAGCG 57.189 37.500 0.00 0.00 38.85 4.68
54 55 6.329496 CCATGTTGAATAATGGTTTAAGCGT 58.671 36.000 0.00 0.00 38.85 5.07
55 56 6.472163 CCATGTTGAATAATGGTTTAAGCGTC 59.528 38.462 0.00 0.00 38.85 5.19
56 57 6.811253 TGTTGAATAATGGTTTAAGCGTCT 57.189 33.333 0.00 0.00 0.00 4.18
57 58 6.837992 TGTTGAATAATGGTTTAAGCGTCTC 58.162 36.000 0.00 0.00 0.00 3.36
58 59 6.428465 TGTTGAATAATGGTTTAAGCGTCTCA 59.572 34.615 0.00 0.00 0.00 3.27
59 60 7.041030 TGTTGAATAATGGTTTAAGCGTCTCAA 60.041 33.333 0.00 0.00 0.00 3.02
60 61 7.624360 TGAATAATGGTTTAAGCGTCTCAAT 57.376 32.000 0.00 0.00 0.00 2.57
61 62 7.693952 TGAATAATGGTTTAAGCGTCTCAATC 58.306 34.615 0.00 0.00 0.00 2.67
62 63 7.335673 TGAATAATGGTTTAAGCGTCTCAATCA 59.664 33.333 0.00 0.00 0.00 2.57
63 64 4.946784 ATGGTTTAAGCGTCTCAATCAC 57.053 40.909 0.00 0.00 0.00 3.06
64 65 3.071479 TGGTTTAAGCGTCTCAATCACC 58.929 45.455 0.00 0.00 0.00 4.02
65 66 2.093783 GGTTTAAGCGTCTCAATCACCG 59.906 50.000 0.00 0.00 0.00 4.94
66 67 2.735134 GTTTAAGCGTCTCAATCACCGT 59.265 45.455 0.00 0.00 0.00 4.83
67 68 3.853831 TTAAGCGTCTCAATCACCGTA 57.146 42.857 0.00 0.00 0.00 4.02
68 69 2.736144 AAGCGTCTCAATCACCGTAA 57.264 45.000 0.00 0.00 0.00 3.18
69 70 1.992170 AGCGTCTCAATCACCGTAAC 58.008 50.000 0.00 0.00 0.00 2.50
70 71 1.271379 AGCGTCTCAATCACCGTAACA 59.729 47.619 0.00 0.00 0.00 2.41
71 72 2.094182 AGCGTCTCAATCACCGTAACAT 60.094 45.455 0.00 0.00 0.00 2.71
72 73 2.029244 GCGTCTCAATCACCGTAACATG 59.971 50.000 0.00 0.00 0.00 3.21
73 74 2.603110 CGTCTCAATCACCGTAACATGG 59.397 50.000 0.00 0.00 0.00 3.66
74 75 2.351726 GTCTCAATCACCGTAACATGGC 59.648 50.000 0.00 0.00 0.00 4.40
75 76 1.327460 CTCAATCACCGTAACATGGCG 59.673 52.381 0.00 0.00 0.00 5.69
76 77 1.066787 TCAATCACCGTAACATGGCGA 60.067 47.619 0.00 0.00 0.00 5.54
77 78 1.062002 CAATCACCGTAACATGGCGAC 59.938 52.381 0.00 0.00 0.00 5.19
78 79 0.461339 ATCACCGTAACATGGCGACC 60.461 55.000 0.00 0.00 0.00 4.79
79 80 2.104253 CACCGTAACATGGCGACCC 61.104 63.158 0.00 0.00 0.00 4.46
80 81 2.888534 CCGTAACATGGCGACCCG 60.889 66.667 0.00 0.00 0.00 5.28
100 101 9.076596 CGACCCGCATGTATATATATTGATATG 57.923 37.037 0.00 0.00 30.57 1.78
102 103 9.929180 ACCCGCATGTATATATATTGATATGAC 57.071 33.333 0.00 0.00 30.57 3.06
124 125 3.928727 TGTAGTACAAGAGTTCCGGTG 57.071 47.619 0.00 0.00 0.00 4.94
125 126 2.559668 TGTAGTACAAGAGTTCCGGTGG 59.440 50.000 0.00 0.00 0.00 4.61
126 127 1.713297 AGTACAAGAGTTCCGGTGGT 58.287 50.000 0.00 0.00 0.00 4.16
127 128 2.044758 AGTACAAGAGTTCCGGTGGTT 58.955 47.619 0.00 0.00 0.00 3.67
128 129 3.233507 AGTACAAGAGTTCCGGTGGTTA 58.766 45.455 0.00 0.00 0.00 2.85
129 130 2.538512 ACAAGAGTTCCGGTGGTTAC 57.461 50.000 0.00 0.00 0.00 2.50
130 131 1.764134 ACAAGAGTTCCGGTGGTTACA 59.236 47.619 0.00 0.00 0.00 2.41
131 132 2.171027 ACAAGAGTTCCGGTGGTTACAA 59.829 45.455 0.00 0.00 0.00 2.41
132 133 3.181448 ACAAGAGTTCCGGTGGTTACAAT 60.181 43.478 0.00 0.00 0.00 2.71
133 134 3.329929 AGAGTTCCGGTGGTTACAATC 57.670 47.619 0.00 0.00 0.00 2.67
134 135 2.904434 AGAGTTCCGGTGGTTACAATCT 59.096 45.455 0.00 0.00 0.00 2.40
135 136 4.091549 AGAGTTCCGGTGGTTACAATCTA 58.908 43.478 0.00 0.00 0.00 1.98
136 137 4.529377 AGAGTTCCGGTGGTTACAATCTAA 59.471 41.667 0.00 0.00 0.00 2.10
137 138 4.572909 AGTTCCGGTGGTTACAATCTAAC 58.427 43.478 0.00 0.00 0.00 2.34
138 139 3.615224 TCCGGTGGTTACAATCTAACC 57.385 47.619 0.00 2.77 45.37 2.85
146 147 5.280654 GGTTACAATCTAACCATACGGGA 57.719 43.478 4.67 0.00 44.72 5.14
147 148 5.295152 GGTTACAATCTAACCATACGGGAG 58.705 45.833 4.67 0.00 44.72 4.30
148 149 5.069516 GGTTACAATCTAACCATACGGGAGA 59.930 44.000 4.67 0.00 44.72 3.71
149 150 4.939052 ACAATCTAACCATACGGGAGAG 57.061 45.455 0.00 0.00 41.15 3.20
150 151 4.543689 ACAATCTAACCATACGGGAGAGA 58.456 43.478 0.00 0.00 41.15 3.10
151 152 5.148502 ACAATCTAACCATACGGGAGAGAT 58.851 41.667 0.00 0.00 40.81 2.75
152 153 6.312529 ACAATCTAACCATACGGGAGAGATA 58.687 40.000 0.00 0.00 39.29 1.98
153 154 6.954684 ACAATCTAACCATACGGGAGAGATAT 59.045 38.462 0.00 0.00 39.29 1.63
154 155 8.114102 ACAATCTAACCATACGGGAGAGATATA 58.886 37.037 0.00 0.00 39.29 0.86
155 156 8.407064 CAATCTAACCATACGGGAGAGATATAC 58.593 40.741 0.00 0.00 39.29 1.47
156 157 7.024345 TCTAACCATACGGGAGAGATATACA 57.976 40.000 0.00 0.00 41.15 2.29
157 158 7.464273 TCTAACCATACGGGAGAGATATACAA 58.536 38.462 0.00 0.00 41.15 2.41
158 159 6.591750 AACCATACGGGAGAGATATACAAG 57.408 41.667 0.00 0.00 41.15 3.16
159 160 5.017490 ACCATACGGGAGAGATATACAAGG 58.983 45.833 0.00 0.00 41.15 3.61
160 161 4.402793 CCATACGGGAGAGATATACAAGGG 59.597 50.000 0.00 0.00 40.01 3.95
161 162 3.897657 ACGGGAGAGATATACAAGGGA 57.102 47.619 0.00 0.00 0.00 4.20
162 163 4.194678 ACGGGAGAGATATACAAGGGAA 57.805 45.455 0.00 0.00 0.00 3.97
163 164 4.153411 ACGGGAGAGATATACAAGGGAAG 58.847 47.826 0.00 0.00 0.00 3.46
164 165 3.511934 CGGGAGAGATATACAAGGGAAGG 59.488 52.174 0.00 0.00 0.00 3.46
165 166 4.753186 GGGAGAGATATACAAGGGAAGGA 58.247 47.826 0.00 0.00 0.00 3.36
166 167 4.775253 GGGAGAGATATACAAGGGAAGGAG 59.225 50.000 0.00 0.00 0.00 3.69
167 168 5.459831 GGGAGAGATATACAAGGGAAGGAGA 60.460 48.000 0.00 0.00 0.00 3.71
168 169 6.260663 GGAGAGATATACAAGGGAAGGAGAT 58.739 44.000 0.00 0.00 0.00 2.75
169 170 7.415086 GGAGAGATATACAAGGGAAGGAGATA 58.585 42.308 0.00 0.00 0.00 1.98
170 171 7.896496 GGAGAGATATACAAGGGAAGGAGATAA 59.104 40.741 0.00 0.00 0.00 1.75
171 172 8.893563 AGAGATATACAAGGGAAGGAGATAAG 57.106 38.462 0.00 0.00 0.00 1.73
172 173 7.898636 AGAGATATACAAGGGAAGGAGATAAGG 59.101 40.741 0.00 0.00 0.00 2.69
173 174 7.780822 AGATATACAAGGGAAGGAGATAAGGA 58.219 38.462 0.00 0.00 0.00 3.36
174 175 8.413821 AGATATACAAGGGAAGGAGATAAGGAT 58.586 37.037 0.00 0.00 0.00 3.24
175 176 9.716556 GATATACAAGGGAAGGAGATAAGGATA 57.283 37.037 0.00 0.00 0.00 2.59
176 177 9.722317 ATATACAAGGGAAGGAGATAAGGATAG 57.278 37.037 0.00 0.00 0.00 2.08
177 178 6.044411 ACAAGGGAAGGAGATAAGGATAGA 57.956 41.667 0.00 0.00 0.00 1.98
178 179 6.638953 ACAAGGGAAGGAGATAAGGATAGAT 58.361 40.000 0.00 0.00 0.00 1.98
179 180 7.085601 ACAAGGGAAGGAGATAAGGATAGATT 58.914 38.462 0.00 0.00 0.00 2.40
180 181 8.242325 ACAAGGGAAGGAGATAAGGATAGATTA 58.758 37.037 0.00 0.00 0.00 1.75
181 182 8.536175 CAAGGGAAGGAGATAAGGATAGATTAC 58.464 40.741 0.00 0.00 0.00 1.89
182 183 7.780822 AGGGAAGGAGATAAGGATAGATTACA 58.219 38.462 0.00 0.00 0.00 2.41
183 184 7.898636 AGGGAAGGAGATAAGGATAGATTACAG 59.101 40.741 0.00 0.00 0.00 2.74
184 185 7.896496 GGGAAGGAGATAAGGATAGATTACAGA 59.104 40.741 0.00 0.00 0.00 3.41
185 186 8.966868 GGAAGGAGATAAGGATAGATTACAGAG 58.033 40.741 0.00 0.00 0.00 3.35
186 187 9.747898 GAAGGAGATAAGGATAGATTACAGAGA 57.252 37.037 0.00 0.00 0.00 3.10
225 226 9.209175 CTATCTCTTAACAATACCCTTGTATGC 57.791 37.037 0.00 0.00 37.73 3.14
226 227 6.046593 TCTCTTAACAATACCCTTGTATGCG 58.953 40.000 0.00 0.00 37.73 4.73
227 228 4.573201 TCTTAACAATACCCTTGTATGCGC 59.427 41.667 0.00 0.00 37.73 6.09
228 229 2.710096 ACAATACCCTTGTATGCGCT 57.290 45.000 9.73 0.00 37.73 5.92
229 230 2.288666 ACAATACCCTTGTATGCGCTG 58.711 47.619 9.73 0.00 37.73 5.18
230 231 2.093181 ACAATACCCTTGTATGCGCTGA 60.093 45.455 9.73 0.00 37.73 4.26
231 232 3.141398 CAATACCCTTGTATGCGCTGAT 58.859 45.455 9.73 0.00 37.73 2.90
232 233 4.202315 ACAATACCCTTGTATGCGCTGATA 60.202 41.667 9.73 0.00 37.73 2.15
233 234 4.826274 ATACCCTTGTATGCGCTGATAT 57.174 40.909 9.73 0.00 36.32 1.63
234 235 2.771089 ACCCTTGTATGCGCTGATATG 58.229 47.619 9.73 0.00 0.00 1.78
235 236 2.368548 ACCCTTGTATGCGCTGATATGA 59.631 45.455 9.73 0.00 0.00 2.15
236 237 3.008375 ACCCTTGTATGCGCTGATATGAT 59.992 43.478 9.73 0.00 0.00 2.45
237 238 3.373130 CCCTTGTATGCGCTGATATGATG 59.627 47.826 9.73 0.00 0.00 3.07
238 239 3.373130 CCTTGTATGCGCTGATATGATGG 59.627 47.826 9.73 0.00 0.00 3.51
239 240 2.349590 TGTATGCGCTGATATGATGGC 58.650 47.619 9.73 0.00 0.00 4.40
240 241 2.027837 TGTATGCGCTGATATGATGGCT 60.028 45.455 9.73 0.00 0.00 4.75
241 242 1.450025 ATGCGCTGATATGATGGCTG 58.550 50.000 9.73 0.00 0.00 4.85
242 243 0.604511 TGCGCTGATATGATGGCTGG 60.605 55.000 9.73 0.00 0.00 4.85
243 244 0.604780 GCGCTGATATGATGGCTGGT 60.605 55.000 0.00 0.00 0.00 4.00
244 245 1.888215 CGCTGATATGATGGCTGGTT 58.112 50.000 0.00 0.00 0.00 3.67
245 246 2.871637 GCGCTGATATGATGGCTGGTTA 60.872 50.000 0.00 0.00 0.00 2.85
246 247 2.998670 CGCTGATATGATGGCTGGTTAG 59.001 50.000 0.00 0.00 0.00 2.34
330 331 3.433306 TGCGGGGAATATAAATGGGAG 57.567 47.619 0.00 0.00 0.00 4.30
331 332 2.092323 GCGGGGAATATAAATGGGAGC 58.908 52.381 0.00 0.00 0.00 4.70
483 486 1.882623 GCAAACTGAAGAGACCAAGGG 59.117 52.381 0.00 0.00 0.00 3.95
514 517 0.443869 CTGGAAACTGGATGAACGCG 59.556 55.000 3.53 3.53 0.00 6.01
548 551 4.927782 TCGCCCATATGCACGCCC 62.928 66.667 9.90 0.00 0.00 6.13
630 1973 3.053896 GGCCCACGCACCACTAAC 61.054 66.667 0.00 0.00 36.38 2.34
632 1975 2.428187 CCCACGCACCACTAACCA 59.572 61.111 0.00 0.00 0.00 3.67
640 1991 0.110486 CACCACTAACCACAGGGCTT 59.890 55.000 0.00 0.00 37.90 4.35
643 1994 1.074951 ACTAACCACAGGGCTTGGC 59.925 57.895 0.44 0.00 37.69 4.52
730 2094 4.400961 ACCGCTGCTCTTGCCCTC 62.401 66.667 0.00 0.00 38.71 4.30
857 2221 2.765785 CGCGACGCTTCTTCTGTG 59.234 61.111 19.02 0.00 0.00 3.66
859 2223 1.488957 GCGACGCTTCTTCTGTGTG 59.511 57.895 13.73 0.00 0.00 3.82
860 2224 0.939577 GCGACGCTTCTTCTGTGTGA 60.940 55.000 13.73 0.00 0.00 3.58
861 2225 1.702886 CGACGCTTCTTCTGTGTGAT 58.297 50.000 0.00 0.00 0.00 3.06
862 2226 1.388093 CGACGCTTCTTCTGTGTGATG 59.612 52.381 0.00 0.00 0.00 3.07
864 2228 1.270518 ACGCTTCTTCTGTGTGATGCT 60.271 47.619 0.00 0.00 33.14 3.79
865 2229 1.802960 CGCTTCTTCTGTGTGATGCTT 59.197 47.619 0.00 0.00 33.14 3.91
867 2231 3.562505 GCTTCTTCTGTGTGATGCTTTG 58.437 45.455 0.00 0.00 32.74 2.77
869 2233 4.214119 GCTTCTTCTGTGTGATGCTTTGTA 59.786 41.667 0.00 0.00 32.74 2.41
910 2351 0.250038 CCATCGGCTCCCATACTGTG 60.250 60.000 0.00 0.00 0.00 3.66
912 2353 0.465705 ATCGGCTCCCATACTGTGTG 59.534 55.000 0.00 0.00 0.00 3.82
929 2370 5.942236 ACTGTGTGATGCTTTCATATGAGTT 59.058 36.000 5.39 0.00 36.54 3.01
930 2371 7.105588 ACTGTGTGATGCTTTCATATGAGTTA 58.894 34.615 5.39 0.00 36.54 2.24
999 2440 1.228245 TGCCAACAGCTCAACTCCC 60.228 57.895 0.00 0.00 44.23 4.30
1000 2441 1.228245 GCCAACAGCTCAACTCCCA 60.228 57.895 0.00 0.00 38.99 4.37
1001 2442 0.610232 GCCAACAGCTCAACTCCCAT 60.610 55.000 0.00 0.00 38.99 4.00
1002 2443 1.171308 CCAACAGCTCAACTCCCATG 58.829 55.000 0.00 0.00 0.00 3.66
1003 2444 1.171308 CAACAGCTCAACTCCCATGG 58.829 55.000 4.14 4.14 0.00 3.66
1004 2445 0.610232 AACAGCTCAACTCCCATGGC 60.610 55.000 6.09 0.00 0.00 4.40
1005 2446 1.001764 CAGCTCAACTCCCATGGCA 60.002 57.895 6.09 0.00 0.00 4.92
1006 2447 1.030488 CAGCTCAACTCCCATGGCAG 61.030 60.000 6.09 2.72 0.00 4.85
1007 2448 2.413142 GCTCAACTCCCATGGCAGC 61.413 63.158 6.09 2.37 0.00 5.25
1008 2449 2.046023 TCAACTCCCATGGCAGCG 60.046 61.111 6.09 0.00 0.00 5.18
1009 2450 3.136123 CAACTCCCATGGCAGCGG 61.136 66.667 6.09 0.00 0.00 5.52
1086 2539 3.782443 GACCCGGCCTTCGTCCAT 61.782 66.667 0.00 0.00 37.11 3.41
1142 2595 1.272490 GTGAGCCGAATCGATCCCATA 59.728 52.381 3.36 0.00 0.00 2.74
1173 2626 1.571460 CGCATCGCCAGAAATAGCC 59.429 57.895 0.00 0.00 0.00 3.93
1174 2627 1.159713 CGCATCGCCAGAAATAGCCA 61.160 55.000 0.00 0.00 0.00 4.75
1198 2651 2.104331 CATCTCTAACCGGCGCGT 59.896 61.111 8.43 0.00 0.00 6.01
1269 2722 2.671177 CGAGGCCTGCAACAACTCG 61.671 63.158 12.00 13.03 43.85 4.18
1320 2773 3.003763 GGAGCGGTGAGGTTCCCT 61.004 66.667 0.00 0.00 36.03 4.20
1324 2777 0.250770 AGCGGTGAGGTTCCCTTTTC 60.251 55.000 0.00 0.00 31.76 2.29
1327 2782 1.610886 CGGTGAGGTTCCCTTTTCTCC 60.611 57.143 0.00 0.00 31.76 3.71
1349 2804 1.608283 CCCTTTCCTGACTCACCGAAC 60.608 57.143 0.00 0.00 0.00 3.95
1360 2815 3.550974 ACCGAACTGCAGGTGTCT 58.449 55.556 19.93 0.00 39.66 3.41
1458 2913 7.881232 TGTTTTATTTCTTTACAGGTCCTCGAT 59.119 33.333 0.00 0.00 0.00 3.59
1469 2924 1.344763 GGTCCTCGATATGGTTCTGGG 59.655 57.143 0.00 0.00 0.00 4.45
1525 2980 3.008485 TGTGGTATGGCTACAATGTGTCA 59.992 43.478 0.00 0.00 35.58 3.58
1553 3008 7.195646 ACAAATGTGCCTGATTAATCATTACG 58.804 34.615 18.26 6.99 36.02 3.18
1641 3096 6.162777 GTGTTCTCAAATCTACTGCTCTCTT 58.837 40.000 0.00 0.00 0.00 2.85
1790 3245 0.685097 AGGTTAGCACTTCCGCTGAA 59.315 50.000 0.00 0.00 43.68 3.02
1804 3259 5.213891 TCCGCTGAATATATCAAAGCTCA 57.786 39.130 10.69 0.00 37.67 4.26
1844 3299 3.016474 GCACCTTCTCAACTCGCGC 62.016 63.158 0.00 0.00 0.00 6.86
1846 3301 2.815647 CCTTCTCAACTCGCGCCC 60.816 66.667 0.00 0.00 0.00 6.13
1854 3309 3.927163 AACTCGCGCCCGTTACTGG 62.927 63.158 0.00 0.00 35.54 4.00
1876 3377 4.202243 GGGCCATGCTGATATTTTTGCTAA 60.202 41.667 4.39 0.00 0.00 3.09
1877 3378 4.746611 GGCCATGCTGATATTTTTGCTAAC 59.253 41.667 0.00 0.00 0.00 2.34
2014 3518 4.591321 TTCAAATGGGCTGAAGGTAGAT 57.409 40.909 0.00 0.00 0.00 1.98
2092 3596 3.581755 TGTTACGGTCAGTACTGCATTC 58.418 45.455 18.45 8.08 35.17 2.67
2293 3797 0.464036 TGCCTTGTGCTCCTATACCG 59.536 55.000 0.00 0.00 42.00 4.02
2310 3814 2.014128 ACCGCATTTAACTCCCAATCG 58.986 47.619 0.00 0.00 0.00 3.34
2356 3861 5.574055 AGCTGCATTAATTTTCACACGAATG 59.426 36.000 1.02 0.00 0.00 2.67
2408 3913 7.039504 ACAGAAAAGGTCATAACATGCTTTCAT 60.040 33.333 0.00 0.00 0.00 2.57
2637 4143 9.877178 ACTATTTCTTATGAGTCGATTTCTTGT 57.123 29.630 0.00 0.00 0.00 3.16
2662 4168 2.025898 TGTATGGATGCACAATGCTGG 58.974 47.619 2.02 0.00 45.31 4.85
2725 4231 5.593968 TGGTGTAATAGTAGCCATTGTACG 58.406 41.667 0.00 0.00 0.00 3.67
2786 4292 0.449388 GCGCTGAAGTTGGATTGAGG 59.551 55.000 0.00 0.00 0.00 3.86
2788 4294 2.935238 GCGCTGAAGTTGGATTGAGGTA 60.935 50.000 0.00 0.00 0.00 3.08
2789 4295 2.673368 CGCTGAAGTTGGATTGAGGTAC 59.327 50.000 0.00 0.00 0.00 3.34
2796 4302 5.359194 AGTTGGATTGAGGTACCATGTAG 57.641 43.478 15.94 0.00 33.56 2.74
2861 4367 7.504911 AGGAGGATTGAAGTGGATCATAATTTG 59.495 37.037 0.00 0.00 0.00 2.32
2913 4419 3.088532 TGCAATTTCCTTTATCCGCAGT 58.911 40.909 0.00 0.00 0.00 4.40
3415 4937 6.553857 TCTGGTCTCTTAAGAGTAAGGTCTT 58.446 40.000 27.59 0.00 42.60 3.01
3504 5028 6.686630 AGAGTGAGCAGAACTGTATATATGC 58.313 40.000 3.77 0.00 0.00 3.14
3556 5080 5.197451 AGGCATATTTCCGTTGTTCCATTA 58.803 37.500 0.00 0.00 0.00 1.90
4069 5645 8.054152 TGTACTTACCATGATTTAGTACGACA 57.946 34.615 13.99 3.18 42.42 4.35
4191 5767 7.907389 TGGACTAATCATTCTTCACACTAGTT 58.093 34.615 0.00 0.00 0.00 2.24
4225 5801 6.659824 ACGGTGATTATAGATGGAAAAGGTT 58.340 36.000 0.00 0.00 0.00 3.50
4282 5858 4.288626 TGGAATGGTACTTAGCAAAGAGGT 59.711 41.667 0.00 0.00 37.24 3.85
4447 6049 4.012374 CCCTGAGCTTGCTCTCATTTTTA 58.988 43.478 21.17 0.37 41.73 1.52
4653 6255 1.138568 CCTCCCTTCATGATCAGCCT 58.861 55.000 0.09 0.00 0.00 4.58
4656 6258 3.495806 CCTCCCTTCATGATCAGCCTTAC 60.496 52.174 0.09 0.00 0.00 2.34
4889 6491 2.271800 GATCGCGAGTTGATCACCTTT 58.728 47.619 16.66 0.00 41.48 3.11
5018 6632 5.742453 CGTACGTGCAACTATTTATCTCTGT 59.258 40.000 7.22 0.00 31.75 3.41
5021 6635 6.398918 ACGTGCAACTATTTATCTCTGTTCT 58.601 36.000 0.00 0.00 31.75 3.01
5024 6638 5.586243 TGCAACTATTTATCTCTGTTCTGCC 59.414 40.000 0.00 0.00 0.00 4.85
5032 6646 0.809385 CTCTGTTCTGCCTGGCATTG 59.191 55.000 23.64 11.95 38.13 2.82
5033 6647 1.214589 CTGTTCTGCCTGGCATTGC 59.785 57.895 23.64 14.78 38.13 3.56
5044 6658 3.514645 CCTGGCATTGCTTATTCACAAC 58.485 45.455 8.82 0.00 0.00 3.32
5048 6662 3.307782 GGCATTGCTTATTCACAACATGC 59.692 43.478 8.82 0.00 33.22 4.06
5067 6681 2.225467 GCAGAGATTAATGGGCTGTCC 58.775 52.381 0.00 0.00 0.00 4.02
5076 6690 2.048601 TGGGCTGTCCACATTTTGC 58.951 52.632 0.00 0.00 41.46 3.68
5154 6769 8.459911 TGACCGTGAAAGATATATGTAGAAGA 57.540 34.615 0.00 0.00 0.00 2.87
5155 6770 8.568794 TGACCGTGAAAGATATATGTAGAAGAG 58.431 37.037 0.00 0.00 0.00 2.85
5156 6771 7.887381 ACCGTGAAAGATATATGTAGAAGAGG 58.113 38.462 0.00 0.00 0.00 3.69
5185 6801 0.317020 GTTTGCTGAACTGTGACGCC 60.317 55.000 0.00 0.00 35.31 5.68
5239 6858 5.989551 AAGCTGCAAAATTACAAACTTGG 57.010 34.783 1.02 0.00 0.00 3.61
5243 6862 5.000012 TGCAAAATTACAAACTTGGACGT 58.000 34.783 0.00 0.00 0.00 4.34
5257 6876 1.202348 TGGACGTGTAGACTGATGCAG 59.798 52.381 0.00 0.00 37.52 4.41
5260 6879 1.275505 CGTGTAGACTGATGCAGCAG 58.724 55.000 29.47 29.47 41.63 4.24
5303 6945 2.467838 CAGCGATCATGTGAGGTAGTG 58.532 52.381 0.00 0.00 0.00 2.74
5305 6947 1.539065 GCGATCATGTGAGGTAGTGGG 60.539 57.143 0.00 0.00 0.00 4.61
5306 6948 1.757118 CGATCATGTGAGGTAGTGGGT 59.243 52.381 0.00 0.00 0.00 4.51
5326 6977 1.265568 GTGCTTCATCAATTGCTGCG 58.734 50.000 4.37 0.12 0.00 5.18
5330 6981 2.727777 CTTCATCAATTGCTGCGGATG 58.272 47.619 4.37 13.65 38.73 3.51
5331 6982 1.026584 TCATCAATTGCTGCGGATGG 58.973 50.000 17.34 4.39 38.11 3.51
5366 7018 4.764172 TGTAAAATTGCAGCAAACTTGGT 58.236 34.783 12.97 0.00 39.91 3.67
5374 7026 2.650608 CAGCAAACTTGGTCGTTAAGC 58.349 47.619 0.00 0.00 36.65 3.09
5446 7099 4.398988 TCACTTCATTAATGTGGGTCATGC 59.601 41.667 14.97 0.00 36.81 4.06
5572 7233 3.428413 AGTAATTACCACCGCCACTTT 57.572 42.857 12.05 0.00 0.00 2.66
5638 7299 2.066262 CCAGCAAAGGTGTAGTACGTG 58.934 52.381 0.00 0.00 0.00 4.49
5639 7300 1.459592 CAGCAAAGGTGTAGTACGTGC 59.540 52.381 0.00 0.00 34.37 5.34
5640 7301 0.794473 GCAAAGGTGTAGTACGTGCC 59.206 55.000 0.00 0.00 0.00 5.01
5641 7302 1.874739 GCAAAGGTGTAGTACGTGCCA 60.875 52.381 0.00 0.00 0.00 4.92
5642 7303 1.796459 CAAAGGTGTAGTACGTGCCAC 59.204 52.381 0.00 0.88 0.00 5.01
5716 7377 1.302366 ACCACGCATGCTATGTCATG 58.698 50.000 17.13 0.00 44.93 3.07
5723 7384 2.159037 GCATGCTATGTCATGTCCATCG 59.841 50.000 11.37 1.06 44.20 3.84
5801 7474 1.443802 CGAGGTTGCTTCCTTCCTTC 58.556 55.000 2.13 0.00 38.02 3.46
5811 7484 1.529744 TCCTTCCTTCCTTTGGTGGT 58.470 50.000 0.00 0.00 0.00 4.16
5829 7504 2.412421 GTAGTATTCGTGCTACCCGG 57.588 55.000 0.00 0.00 33.41 5.73
5830 7505 1.678101 GTAGTATTCGTGCTACCCGGT 59.322 52.381 0.00 0.00 33.41 5.28
5831 7506 2.057137 AGTATTCGTGCTACCCGGTA 57.943 50.000 0.00 0.00 0.00 4.02
5902 7579 3.594134 AGATTGTGCGGAGAAGAAGAAG 58.406 45.455 0.00 0.00 0.00 2.85
5903 7580 3.259374 AGATTGTGCGGAGAAGAAGAAGA 59.741 43.478 0.00 0.00 0.00 2.87
5904 7581 3.469008 TTGTGCGGAGAAGAAGAAGAA 57.531 42.857 0.00 0.00 0.00 2.52
5908 7585 2.224281 TGCGGAGAAGAAGAAGAAGCAA 60.224 45.455 0.00 0.00 0.00 3.91
5922 7599 2.159114 AGAAGCAAAGAGAGGATCGAGC 60.159 50.000 0.00 0.00 42.67 5.03
6132 7813 2.854736 AAATTCCCCATCTCCCCTTG 57.145 50.000 0.00 0.00 0.00 3.61
6133 7814 1.698874 AATTCCCCATCTCCCCTTGT 58.301 50.000 0.00 0.00 0.00 3.16
6138 7819 1.565390 CCCATCTCCCCTTGTGAGCA 61.565 60.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.406361 AGGACTCTTCCACCTCGTCT 59.594 55.000 0.00 0.00 45.72 4.18
1 2 1.202817 GAAGGACTCTTCCACCTCGTC 59.797 57.143 0.00 0.00 45.72 4.20
2 3 1.258676 GAAGGACTCTTCCACCTCGT 58.741 55.000 0.00 0.00 45.72 4.18
13 14 5.606348 ACATGGTATTCAGAGAAGGACTC 57.394 43.478 0.00 0.00 45.22 3.36
14 15 5.485353 TCAACATGGTATTCAGAGAAGGACT 59.515 40.000 0.00 0.00 0.00 3.85
15 16 5.734720 TCAACATGGTATTCAGAGAAGGAC 58.265 41.667 0.00 0.00 0.00 3.85
16 17 6.373005 TTCAACATGGTATTCAGAGAAGGA 57.627 37.500 0.00 0.00 0.00 3.36
17 18 8.737168 TTATTCAACATGGTATTCAGAGAAGG 57.263 34.615 0.00 0.00 0.00 3.46
19 20 9.123902 CCATTATTCAACATGGTATTCAGAGAA 57.876 33.333 0.00 0.00 36.01 2.87
20 21 8.681486 CCATTATTCAACATGGTATTCAGAGA 57.319 34.615 0.00 0.00 36.01 3.10
30 31 6.329496 ACGCTTAAACCATTATTCAACATGG 58.671 36.000 0.00 0.00 45.01 3.66
31 32 7.250569 AGACGCTTAAACCATTATTCAACATG 58.749 34.615 0.00 0.00 0.00 3.21
32 33 7.120579 TGAGACGCTTAAACCATTATTCAACAT 59.879 33.333 0.00 0.00 0.00 2.71
33 34 6.428465 TGAGACGCTTAAACCATTATTCAACA 59.572 34.615 0.00 0.00 0.00 3.33
34 35 6.837992 TGAGACGCTTAAACCATTATTCAAC 58.162 36.000 0.00 0.00 0.00 3.18
35 36 7.441890 TTGAGACGCTTAAACCATTATTCAA 57.558 32.000 0.00 0.00 0.00 2.69
36 37 7.335673 TGATTGAGACGCTTAAACCATTATTCA 59.664 33.333 0.00 0.00 0.00 2.57
37 38 7.640240 GTGATTGAGACGCTTAAACCATTATTC 59.360 37.037 0.00 0.00 0.00 1.75
38 39 7.415206 GGTGATTGAGACGCTTAAACCATTATT 60.415 37.037 0.00 0.00 0.00 1.40
39 40 6.038271 GGTGATTGAGACGCTTAAACCATTAT 59.962 38.462 0.00 0.00 0.00 1.28
40 41 5.353123 GGTGATTGAGACGCTTAAACCATTA 59.647 40.000 0.00 0.00 0.00 1.90
41 42 4.156008 GGTGATTGAGACGCTTAAACCATT 59.844 41.667 0.00 0.00 0.00 3.16
42 43 3.689649 GGTGATTGAGACGCTTAAACCAT 59.310 43.478 0.00 0.00 0.00 3.55
43 44 3.071479 GGTGATTGAGACGCTTAAACCA 58.929 45.455 0.00 0.00 0.00 3.67
44 45 2.093783 CGGTGATTGAGACGCTTAAACC 59.906 50.000 0.00 0.00 0.00 3.27
45 46 2.735134 ACGGTGATTGAGACGCTTAAAC 59.265 45.455 0.00 0.00 0.00 2.01
46 47 3.034721 ACGGTGATTGAGACGCTTAAA 57.965 42.857 0.00 0.00 0.00 1.52
47 48 2.736144 ACGGTGATTGAGACGCTTAA 57.264 45.000 0.00 0.00 0.00 1.85
48 49 3.057386 TGTTACGGTGATTGAGACGCTTA 60.057 43.478 0.00 0.00 0.00 3.09
49 50 2.288579 TGTTACGGTGATTGAGACGCTT 60.289 45.455 0.00 0.00 0.00 4.68
50 51 1.271379 TGTTACGGTGATTGAGACGCT 59.729 47.619 0.00 0.00 0.00 5.07
51 52 1.705256 TGTTACGGTGATTGAGACGC 58.295 50.000 0.00 0.00 0.00 5.19
52 53 2.603110 CCATGTTACGGTGATTGAGACG 59.397 50.000 0.00 0.00 0.00 4.18
53 54 2.351726 GCCATGTTACGGTGATTGAGAC 59.648 50.000 0.00 0.00 0.00 3.36
54 55 2.627945 GCCATGTTACGGTGATTGAGA 58.372 47.619 0.00 0.00 0.00 3.27
55 56 1.327460 CGCCATGTTACGGTGATTGAG 59.673 52.381 0.00 0.00 36.02 3.02
56 57 1.066787 TCGCCATGTTACGGTGATTGA 60.067 47.619 0.00 0.00 38.12 2.57
57 58 1.062002 GTCGCCATGTTACGGTGATTG 59.938 52.381 0.00 0.00 44.50 2.67
58 59 1.365699 GTCGCCATGTTACGGTGATT 58.634 50.000 0.00 0.00 44.50 2.57
59 60 0.461339 GGTCGCCATGTTACGGTGAT 60.461 55.000 0.00 0.00 44.50 3.06
60 61 1.079681 GGTCGCCATGTTACGGTGA 60.080 57.895 0.00 0.00 40.71 4.02
61 62 2.104253 GGGTCGCCATGTTACGGTG 61.104 63.158 0.00 0.00 35.24 4.94
62 63 2.266689 GGGTCGCCATGTTACGGT 59.733 61.111 0.00 0.00 0.00 4.83
63 64 2.888534 CGGGTCGCCATGTTACGG 60.889 66.667 0.00 0.00 0.00 4.02
74 75 9.076596 CATATCAATATATATACATGCGGGTCG 57.923 37.037 0.00 0.00 0.00 4.79
76 77 9.929180 GTCATATCAATATATATACATGCGGGT 57.071 33.333 0.00 0.00 0.00 5.28
103 104 3.006110 CCACCGGAACTCTTGTACTACAA 59.994 47.826 9.46 1.67 36.54 2.41
104 105 2.559668 CCACCGGAACTCTTGTACTACA 59.440 50.000 9.46 0.00 0.00 2.74
105 106 2.560105 ACCACCGGAACTCTTGTACTAC 59.440 50.000 9.46 0.00 0.00 2.73
106 107 2.880443 ACCACCGGAACTCTTGTACTA 58.120 47.619 9.46 0.00 0.00 1.82
107 108 1.713297 ACCACCGGAACTCTTGTACT 58.287 50.000 9.46 0.00 0.00 2.73
108 109 2.538512 AACCACCGGAACTCTTGTAC 57.461 50.000 9.46 0.00 0.00 2.90
109 110 2.964464 TGTAACCACCGGAACTCTTGTA 59.036 45.455 9.46 0.00 0.00 2.41
110 111 1.764134 TGTAACCACCGGAACTCTTGT 59.236 47.619 9.46 0.00 0.00 3.16
111 112 2.536761 TGTAACCACCGGAACTCTTG 57.463 50.000 9.46 0.00 0.00 3.02
112 113 3.326880 AGATTGTAACCACCGGAACTCTT 59.673 43.478 9.46 0.00 0.00 2.85
113 114 2.904434 AGATTGTAACCACCGGAACTCT 59.096 45.455 9.46 0.00 0.00 3.24
114 115 3.329929 AGATTGTAACCACCGGAACTC 57.670 47.619 9.46 0.00 0.00 3.01
115 116 4.564199 GGTTAGATTGTAACCACCGGAACT 60.564 45.833 9.46 0.00 44.72 3.01
116 117 3.686241 GGTTAGATTGTAACCACCGGAAC 59.314 47.826 9.46 0.00 44.72 3.62
117 118 3.941573 GGTTAGATTGTAACCACCGGAA 58.058 45.455 9.46 0.00 44.72 4.30
118 119 3.615224 GGTTAGATTGTAACCACCGGA 57.385 47.619 9.46 0.00 44.72 5.14
124 125 5.069516 TCTCCCGTATGGTTAGATTGTAACC 59.930 44.000 14.30 14.30 45.37 2.85
125 126 6.040166 TCTCTCCCGTATGGTTAGATTGTAAC 59.960 42.308 0.00 0.00 34.77 2.50
126 127 6.131264 TCTCTCCCGTATGGTTAGATTGTAA 58.869 40.000 0.00 0.00 34.77 2.41
127 128 5.698104 TCTCTCCCGTATGGTTAGATTGTA 58.302 41.667 0.00 0.00 34.77 2.41
128 129 4.543689 TCTCTCCCGTATGGTTAGATTGT 58.456 43.478 0.00 0.00 34.77 2.71
129 130 5.730296 ATCTCTCCCGTATGGTTAGATTG 57.270 43.478 0.00 0.00 34.86 2.67
130 131 8.114102 TGTATATCTCTCCCGTATGGTTAGATT 58.886 37.037 12.62 4.42 37.63 2.40
131 132 7.640313 TGTATATCTCTCCCGTATGGTTAGAT 58.360 38.462 12.22 12.22 38.95 1.98
132 133 7.024345 TGTATATCTCTCCCGTATGGTTAGA 57.976 40.000 0.00 1.92 34.77 2.10
133 134 7.148052 CCTTGTATATCTCTCCCGTATGGTTAG 60.148 44.444 0.00 0.00 34.77 2.34
134 135 6.662234 CCTTGTATATCTCTCCCGTATGGTTA 59.338 42.308 0.00 0.00 34.77 2.85
135 136 5.480772 CCTTGTATATCTCTCCCGTATGGTT 59.519 44.000 0.00 0.00 34.77 3.67
136 137 5.017490 CCTTGTATATCTCTCCCGTATGGT 58.983 45.833 0.00 0.00 34.77 3.55
137 138 4.402793 CCCTTGTATATCTCTCCCGTATGG 59.597 50.000 0.00 0.00 0.00 2.74
138 139 5.262009 TCCCTTGTATATCTCTCCCGTATG 58.738 45.833 0.00 0.00 0.00 2.39
139 140 5.531753 TCCCTTGTATATCTCTCCCGTAT 57.468 43.478 0.00 0.00 0.00 3.06
140 141 5.322754 CTTCCCTTGTATATCTCTCCCGTA 58.677 45.833 0.00 0.00 0.00 4.02
141 142 3.897657 TCCCTTGTATATCTCTCCCGT 57.102 47.619 0.00 0.00 0.00 5.28
142 143 3.511934 CCTTCCCTTGTATATCTCTCCCG 59.488 52.174 0.00 0.00 0.00 5.14
143 144 4.753186 TCCTTCCCTTGTATATCTCTCCC 58.247 47.826 0.00 0.00 0.00 4.30
144 145 5.646215 TCTCCTTCCCTTGTATATCTCTCC 58.354 45.833 0.00 0.00 0.00 3.71
145 146 8.887264 TTATCTCCTTCCCTTGTATATCTCTC 57.113 38.462 0.00 0.00 0.00 3.20
146 147 7.898636 CCTTATCTCCTTCCCTTGTATATCTCT 59.101 40.741 0.00 0.00 0.00 3.10
147 148 7.896496 TCCTTATCTCCTTCCCTTGTATATCTC 59.104 40.741 0.00 0.00 0.00 2.75
148 149 7.780822 TCCTTATCTCCTTCCCTTGTATATCT 58.219 38.462 0.00 0.00 0.00 1.98
149 150 8.616799 ATCCTTATCTCCTTCCCTTGTATATC 57.383 38.462 0.00 0.00 0.00 1.63
150 151 9.722317 CTATCCTTATCTCCTTCCCTTGTATAT 57.278 37.037 0.00 0.00 0.00 0.86
151 152 8.912285 TCTATCCTTATCTCCTTCCCTTGTATA 58.088 37.037 0.00 0.00 0.00 1.47
152 153 7.780822 TCTATCCTTATCTCCTTCCCTTGTAT 58.219 38.462 0.00 0.00 0.00 2.29
153 154 7.175635 TCTATCCTTATCTCCTTCCCTTGTA 57.824 40.000 0.00 0.00 0.00 2.41
154 155 6.044411 TCTATCCTTATCTCCTTCCCTTGT 57.956 41.667 0.00 0.00 0.00 3.16
155 156 7.566658 AATCTATCCTTATCTCCTTCCCTTG 57.433 40.000 0.00 0.00 0.00 3.61
156 157 8.242325 TGTAATCTATCCTTATCTCCTTCCCTT 58.758 37.037 0.00 0.00 0.00 3.95
157 158 7.780822 TGTAATCTATCCTTATCTCCTTCCCT 58.219 38.462 0.00 0.00 0.00 4.20
158 159 7.896496 TCTGTAATCTATCCTTATCTCCTTCCC 59.104 40.741 0.00 0.00 0.00 3.97
159 160 8.887264 TCTGTAATCTATCCTTATCTCCTTCC 57.113 38.462 0.00 0.00 0.00 3.46
160 161 9.747898 TCTCTGTAATCTATCCTTATCTCCTTC 57.252 37.037 0.00 0.00 0.00 3.46
199 200 9.209175 GCATACAAGGGTATTGTTAAGAGATAG 57.791 37.037 0.00 0.00 38.14 2.08
200 201 7.870954 CGCATACAAGGGTATTGTTAAGAGATA 59.129 37.037 0.00 0.00 38.14 1.98
201 202 6.706270 CGCATACAAGGGTATTGTTAAGAGAT 59.294 38.462 0.00 0.00 38.14 2.75
202 203 6.046593 CGCATACAAGGGTATTGTTAAGAGA 58.953 40.000 0.00 0.00 38.14 3.10
203 204 5.277345 GCGCATACAAGGGTATTGTTAAGAG 60.277 44.000 0.30 0.00 38.14 2.85
204 205 4.573201 GCGCATACAAGGGTATTGTTAAGA 59.427 41.667 0.30 0.00 38.14 2.10
205 206 4.574828 AGCGCATACAAGGGTATTGTTAAG 59.425 41.667 11.47 0.00 38.14 1.85
206 207 4.334203 CAGCGCATACAAGGGTATTGTTAA 59.666 41.667 11.47 0.00 38.14 2.01
207 208 3.874543 CAGCGCATACAAGGGTATTGTTA 59.125 43.478 11.47 0.00 38.14 2.41
208 209 2.682856 CAGCGCATACAAGGGTATTGTT 59.317 45.455 11.47 0.00 38.14 2.83
209 210 2.093181 TCAGCGCATACAAGGGTATTGT 60.093 45.455 11.47 0.00 38.14 2.71
210 211 2.560504 TCAGCGCATACAAGGGTATTG 58.439 47.619 11.47 0.00 38.14 1.90
211 212 3.492102 ATCAGCGCATACAAGGGTATT 57.508 42.857 11.47 0.00 38.14 1.89
212 213 4.222810 TCATATCAGCGCATACAAGGGTAT 59.777 41.667 11.47 0.00 40.86 2.73
213 214 3.576550 TCATATCAGCGCATACAAGGGTA 59.423 43.478 11.47 0.00 0.00 3.69
214 215 2.368548 TCATATCAGCGCATACAAGGGT 59.631 45.455 11.47 0.00 0.00 4.34
215 216 3.044235 TCATATCAGCGCATACAAGGG 57.956 47.619 11.47 0.00 0.00 3.95
216 217 3.373130 CCATCATATCAGCGCATACAAGG 59.627 47.826 11.47 0.00 0.00 3.61
217 218 3.181513 GCCATCATATCAGCGCATACAAG 60.182 47.826 11.47 0.00 0.00 3.16
218 219 2.743664 GCCATCATATCAGCGCATACAA 59.256 45.455 11.47 0.00 0.00 2.41
219 220 2.027837 AGCCATCATATCAGCGCATACA 60.028 45.455 11.47 0.00 0.00 2.29
220 221 2.350804 CAGCCATCATATCAGCGCATAC 59.649 50.000 11.47 0.00 0.00 2.39
221 222 2.624636 CAGCCATCATATCAGCGCATA 58.375 47.619 11.47 0.00 0.00 3.14
222 223 1.450025 CAGCCATCATATCAGCGCAT 58.550 50.000 11.47 0.00 0.00 4.73
223 224 0.604511 CCAGCCATCATATCAGCGCA 60.605 55.000 11.47 0.00 0.00 6.09
224 225 0.604780 ACCAGCCATCATATCAGCGC 60.605 55.000 0.00 0.00 0.00 5.92
225 226 1.888215 AACCAGCCATCATATCAGCG 58.112 50.000 0.00 0.00 0.00 5.18
226 227 2.746362 GCTAACCAGCCATCATATCAGC 59.254 50.000 0.00 0.00 42.37 4.26
254 255 9.537192 TCGTCGTTAATGGATTAATGAATAGTT 57.463 29.630 13.27 0.00 44.94 2.24
255 256 9.706691 ATCGTCGTTAATGGATTAATGAATAGT 57.293 29.630 13.27 1.94 44.94 2.12
259 260 9.315525 TGTTATCGTCGTTAATGGATTAATGAA 57.684 29.630 13.27 3.12 44.94 2.57
260 261 8.874744 TGTTATCGTCGTTAATGGATTAATGA 57.125 30.769 9.14 9.14 42.70 2.57
266 267 9.084164 GCTTATATGTTATCGTCGTTAATGGAT 57.916 33.333 0.00 0.00 0.00 3.41
267 268 7.271868 CGCTTATATGTTATCGTCGTTAATGGA 59.728 37.037 0.00 0.00 0.00 3.41
268 269 7.381079 CGCTTATATGTTATCGTCGTTAATGG 58.619 38.462 0.00 0.00 0.00 3.16
269 270 7.381079 CCGCTTATATGTTATCGTCGTTAATG 58.619 38.462 0.00 0.00 0.00 1.90
270 271 6.529125 CCCGCTTATATGTTATCGTCGTTAAT 59.471 38.462 0.00 0.00 0.00 1.40
271 272 5.858049 CCCGCTTATATGTTATCGTCGTTAA 59.142 40.000 0.00 0.00 0.00 2.01
272 273 5.181056 TCCCGCTTATATGTTATCGTCGTTA 59.819 40.000 0.00 0.00 0.00 3.18
273 274 4.022935 TCCCGCTTATATGTTATCGTCGTT 60.023 41.667 0.00 0.00 0.00 3.85
274 275 3.503363 TCCCGCTTATATGTTATCGTCGT 59.497 43.478 0.00 0.00 0.00 4.34
275 276 4.087510 TCCCGCTTATATGTTATCGTCG 57.912 45.455 0.00 0.00 0.00 5.12
276 277 6.588756 TCATTTCCCGCTTATATGTTATCGTC 59.411 38.462 0.00 0.00 0.00 4.20
277 278 6.460781 TCATTTCCCGCTTATATGTTATCGT 58.539 36.000 0.00 0.00 0.00 3.73
278 279 6.961359 TCATTTCCCGCTTATATGTTATCG 57.039 37.500 0.00 0.00 0.00 2.92
308 309 4.148838 CTCCCATTTATATTCCCCGCAAA 58.851 43.478 0.00 0.00 0.00 3.68
318 319 7.696981 ACAATCTCATCAGCTCCCATTTATAT 58.303 34.615 0.00 0.00 0.00 0.86
325 326 3.265221 AGAAACAATCTCATCAGCTCCCA 59.735 43.478 0.00 0.00 30.46 4.37
330 331 9.286946 CATTCTTTTAGAAACAATCTCATCAGC 57.713 33.333 0.00 0.00 37.82 4.26
461 462 2.291741 CCTTGGTCTCTTCAGTTTGCAC 59.708 50.000 0.00 0.00 0.00 4.57
491 494 3.338249 CGTTCATCCAGTTTCCAGTGAT 58.662 45.455 0.00 0.00 0.00 3.06
492 495 2.766313 CGTTCATCCAGTTTCCAGTGA 58.234 47.619 0.00 0.00 0.00 3.41
498 501 1.134694 GGCGCGTTCATCCAGTTTC 59.865 57.895 8.43 0.00 0.00 2.78
530 533 2.899838 GGCGTGCATATGGGCGAA 60.900 61.111 4.56 0.00 36.28 4.70
548 551 2.163818 TAGTTGAGGAAACGCACAGG 57.836 50.000 0.00 0.00 44.04 4.00
630 1973 3.850098 AACGAGCCAAGCCCTGTGG 62.850 63.158 0.00 0.00 39.33 4.17
632 1975 0.605589 GTAAACGAGCCAAGCCCTGT 60.606 55.000 0.00 0.00 0.00 4.00
855 2219 8.668353 TCTTGATTTCTATACAAAGCATCACAC 58.332 33.333 0.00 0.00 31.96 3.82
856 2220 8.791327 TCTTGATTTCTATACAAAGCATCACA 57.209 30.769 0.00 0.00 31.96 3.58
857 2221 9.102757 TCTCTTGATTTCTATACAAAGCATCAC 57.897 33.333 0.00 0.00 31.96 3.06
898 2339 4.864219 TGAAAGCATCACACAGTATGGGAG 60.864 45.833 0.00 0.00 46.52 4.30
1086 2539 1.384989 GCGAGGATCTGAGACGGGAA 61.385 60.000 0.00 0.00 0.00 3.97
1173 2626 2.798680 CCGGTTAGAGATGAGTTCGTG 58.201 52.381 0.00 0.00 0.00 4.35
1174 2627 1.134560 GCCGGTTAGAGATGAGTTCGT 59.865 52.381 1.90 0.00 0.00 3.85
1198 2651 0.515127 CTGCGCAACACAATACCGAA 59.485 50.000 13.05 0.00 0.00 4.30
1327 2782 1.685820 GGTGAGTCAGGAAAGGGGG 59.314 63.158 0.00 0.00 0.00 5.40
1334 2789 1.112916 TGCAGTTCGGTGAGTCAGGA 61.113 55.000 0.00 0.00 0.00 3.86
1343 2798 0.532862 CAAGACACCTGCAGTTCGGT 60.533 55.000 13.81 0.35 0.00 4.69
1349 2804 2.880268 TCATCAAACAAGACACCTGCAG 59.120 45.455 6.78 6.78 0.00 4.41
1360 2815 4.211584 GCACATGCACATTTCATCAAACAA 59.788 37.500 0.00 0.00 41.59 2.83
1458 2913 0.419865 TCAGGTCCCCCAGAACCATA 59.580 55.000 0.00 0.00 29.47 2.74
1469 2924 1.210722 GATGTTCCTCCTTCAGGTCCC 59.789 57.143 0.00 0.00 43.95 4.46
1525 2980 7.886629 ATGATTAATCAGGCACATTTGTAGT 57.113 32.000 21.97 0.00 40.64 2.73
1553 3008 4.130857 GCATCGGTTGCGTTTCAC 57.869 55.556 0.00 0.00 42.54 3.18
1610 3065 5.991606 CAGTAGATTTGAGAACACACAAGGA 59.008 40.000 0.00 0.00 0.00 3.36
1615 3070 5.233988 AGAGCAGTAGATTTGAGAACACAC 58.766 41.667 0.00 0.00 0.00 3.82
1668 3123 5.342259 GCAAGTTTAACAAGCGAGTAAATGG 59.658 40.000 0.00 0.00 0.00 3.16
1790 3245 9.638176 ATTGGAAGAAAGTGAGCTTTGATATAT 57.362 29.630 0.00 0.00 44.25 0.86
1804 3259 5.774690 TGCCACATAAAGATTGGAAGAAAGT 59.225 36.000 0.00 0.00 31.39 2.66
1846 3301 0.464373 ATCAGCATGGCCCAGTAACG 60.464 55.000 0.00 0.00 36.16 3.18
1854 3309 3.464111 AGCAAAAATATCAGCATGGCC 57.536 42.857 0.00 0.00 36.16 5.36
1876 3377 5.983540 TGGCAATTTCCTAAAAACACAAGT 58.016 33.333 0.00 0.00 0.00 3.16
1877 3378 5.466393 CCTGGCAATTTCCTAAAAACACAAG 59.534 40.000 0.00 0.00 0.00 3.16
2014 3518 9.574516 AAGAAGCCTAAATAAGAAGACTTTCAA 57.425 29.630 0.00 0.00 37.53 2.69
2280 3784 4.377897 AGTTAAATGCGGTATAGGAGCAC 58.622 43.478 0.00 0.00 44.12 4.40
2293 3797 2.423538 ACAGCGATTGGGAGTTAAATGC 59.576 45.455 0.00 0.00 0.00 3.56
2310 3814 7.594015 CAGCTGATATTCAATAAAATGGACAGC 59.406 37.037 8.42 0.00 38.73 4.40
2356 3861 6.545504 ACAATTAGACAACTCATGACACAC 57.454 37.500 0.00 0.00 0.00 3.82
2725 4231 2.223203 GCATGTGAAGTATGCTGCTGAC 60.223 50.000 0.00 0.00 45.64 3.51
2786 4292 7.843490 TTGCTGATAGAAAACTACATGGTAC 57.157 36.000 0.00 0.00 0.00 3.34
2788 4294 7.611467 TCATTTGCTGATAGAAAACTACATGGT 59.389 33.333 0.00 0.00 0.00 3.55
2789 4295 7.988737 TCATTTGCTGATAGAAAACTACATGG 58.011 34.615 0.00 0.00 0.00 3.66
2796 4302 6.500684 TGTCCTCATTTGCTGATAGAAAAC 57.499 37.500 0.00 0.00 32.10 2.43
2861 4367 8.041323 TCCTATGGAACTACAGAATTGAAAGTC 58.959 37.037 0.00 0.00 0.00 3.01
2867 4373 7.921786 TGTTTCCTATGGAACTACAGAATTG 57.078 36.000 0.00 0.00 41.87 2.32
2906 4412 3.071479 GACTTTTCCAATACACTGCGGA 58.929 45.455 0.00 0.00 0.00 5.54
3389 4911 7.186268 AGACCTTACTCTTAAGAGACCAGATT 58.814 38.462 33.94 15.42 44.74 2.40
3432 4954 9.387123 CATGTCTTTCTTAGTTCTTTTAGCAAC 57.613 33.333 0.00 0.00 0.00 4.17
3765 5290 3.817647 GACACCACTCTGAAGCTGAAAAT 59.182 43.478 0.00 0.00 0.00 1.82
3767 5292 2.170397 TGACACCACTCTGAAGCTGAAA 59.830 45.455 0.00 0.00 0.00 2.69
4069 5645 3.845109 ACTCATACCAACCCCCATTTT 57.155 42.857 0.00 0.00 0.00 1.82
4191 5767 1.277579 TAATCACCGTTAGTGCCCCA 58.722 50.000 0.00 0.00 46.81 4.96
4225 5801 7.225784 ACAACATGGAAATGCTATTAACACA 57.774 32.000 0.00 0.00 0.00 3.72
4282 5858 7.786046 TTGGACAGATACTACTCCAAAAGTA 57.214 36.000 0.00 0.00 39.55 2.24
4447 6049 8.948631 ACTTGATATACTGAACACGAAATGAT 57.051 30.769 0.00 0.00 0.00 2.45
4627 6229 4.365368 TGATCATGAAGGGAGGAGAGAAA 58.635 43.478 0.00 0.00 0.00 2.52
4889 6491 0.762418 TTCTCCCTTTTGAGTCCGCA 59.238 50.000 0.00 0.00 33.93 5.69
5018 6632 2.148446 ATAAGCAATGCCAGGCAGAA 57.852 45.000 21.51 0.00 43.65 3.02
5021 6635 1.477700 GTGAATAAGCAATGCCAGGCA 59.522 47.619 18.99 18.99 44.86 4.75
5024 6638 4.177165 TGTTGTGAATAAGCAATGCCAG 57.823 40.909 0.00 0.00 0.00 4.85
5032 6646 4.952262 TCTCTGCATGTTGTGAATAAGC 57.048 40.909 0.00 0.00 0.00 3.09
5033 6647 9.447040 CATTAATCTCTGCATGTTGTGAATAAG 57.553 33.333 0.00 0.00 0.00 1.73
5044 6658 3.220110 ACAGCCCATTAATCTCTGCATG 58.780 45.455 0.00 0.00 0.00 4.06
5048 6662 3.565764 TGGACAGCCCATTAATCTCTG 57.434 47.619 6.59 6.59 40.82 3.35
5067 6681 3.577667 ACACCATCATTCGCAAAATGTG 58.422 40.909 8.26 6.57 0.00 3.21
5076 6690 5.808042 ATCAAGAGAAACACCATCATTCG 57.192 39.130 0.00 0.00 0.00 3.34
5154 6769 3.788227 TCAGCAAACACATAGGAACCT 57.212 42.857 0.00 0.00 0.00 3.50
5155 6770 3.821033 AGTTCAGCAAACACATAGGAACC 59.179 43.478 0.00 0.00 40.56 3.62
5156 6771 4.275936 ACAGTTCAGCAAACACATAGGAAC 59.724 41.667 5.00 0.00 40.56 3.62
5185 6801 6.347402 CCATTACTACTTGAACCACTGAAACG 60.347 42.308 0.00 0.00 0.00 3.60
5239 6858 1.272781 GCTGCATCAGTCTACACGTC 58.727 55.000 0.00 0.00 33.43 4.34
5243 6862 1.895131 TCACTGCTGCATCAGTCTACA 59.105 47.619 19.92 2.55 44.81 2.74
5303 6945 1.547372 AGCAATTGATGAAGCACACCC 59.453 47.619 10.34 0.00 0.00 4.61
5305 6947 1.990563 GCAGCAATTGATGAAGCACAC 59.009 47.619 27.03 3.73 32.25 3.82
5306 6948 1.401800 CGCAGCAATTGATGAAGCACA 60.402 47.619 27.03 0.00 32.25 4.57
5326 6977 1.063717 ACATGTTCACATCCCCCATCC 60.064 52.381 0.00 0.00 33.61 3.51
5330 6981 5.418676 CAATTTTACATGTTCACATCCCCC 58.581 41.667 2.30 0.00 33.61 5.40
5331 6982 4.869861 GCAATTTTACATGTTCACATCCCC 59.130 41.667 2.30 0.00 33.61 4.81
5374 7026 1.564207 TCAGCAATGAAGCGATCTCG 58.436 50.000 0.00 0.00 40.15 4.04
5406 7058 8.723942 ATGAAGTGATAGATAAAACGAAAGCT 57.276 30.769 0.00 0.00 0.00 3.74
5592 7253 0.868406 GCTGGTTCAACTTGGACTCG 59.132 55.000 0.07 0.00 0.00 4.18
5638 7299 4.077184 TGGATCGACCCACGTGGC 62.077 66.667 29.75 15.52 43.13 5.01
5639 7300 2.184322 CTGGATCGACCCACGTGG 59.816 66.667 28.26 28.26 43.13 4.94
5640 7301 2.184322 CCTGGATCGACCCACGTG 59.816 66.667 9.08 9.08 43.13 4.49
5641 7302 3.771160 GCCTGGATCGACCCACGT 61.771 66.667 0.00 0.00 43.13 4.49
5642 7303 3.770040 TGCCTGGATCGACCCACG 61.770 66.667 0.00 0.00 44.09 4.94
5643 7304 2.125106 GTGCCTGGATCGACCCAC 60.125 66.667 0.00 0.00 38.00 4.61
5644 7305 2.284625 AGTGCCTGGATCGACCCA 60.285 61.111 0.00 0.00 38.00 4.51
5716 7377 2.029666 CCGGATGCCTCGATGGAC 59.970 66.667 0.00 0.00 38.35 4.02
5723 7384 4.899239 CACGCCTCCGGATGCCTC 62.899 72.222 23.81 0.00 39.22 4.70
5746 7407 2.029964 GCGATTCCCCGGCGAATA 59.970 61.111 14.26 0.00 32.56 1.75
5801 7474 2.676342 GCACGAATACTACCACCAAAGG 59.324 50.000 0.00 0.00 0.00 3.11
5811 7484 2.057137 ACCGGGTAGCACGAATACTA 57.943 50.000 6.32 0.00 0.00 1.82
5828 7503 6.870439 ACAGAACGAAATACCTTTGTACTACC 59.130 38.462 0.00 0.00 30.83 3.18
5829 7504 7.880059 ACAGAACGAAATACCTTTGTACTAC 57.120 36.000 0.00 0.00 30.83 2.73
5830 7505 8.362639 AGAACAGAACGAAATACCTTTGTACTA 58.637 33.333 0.00 0.00 30.83 1.82
5831 7506 7.170998 CAGAACAGAACGAAATACCTTTGTACT 59.829 37.037 0.00 0.00 30.83 2.73
5902 7579 2.200899 GCTCGATCCTCTCTTTGCTTC 58.799 52.381 0.00 0.00 0.00 3.86
5903 7580 1.134551 GGCTCGATCCTCTCTTTGCTT 60.135 52.381 0.00 0.00 0.00 3.91
5904 7581 0.463620 GGCTCGATCCTCTCTTTGCT 59.536 55.000 0.00 0.00 0.00 3.91
5908 7585 1.415659 CCATTGGCTCGATCCTCTCTT 59.584 52.381 6.88 0.00 0.00 2.85
5922 7599 1.224592 CCTCCTCCCGAACCATTGG 59.775 63.158 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.