Multiple sequence alignment - TraesCS7D01G233000

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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 TraesCS7D01G233000 chr7D 100.000 2850 0 0 1 2850 194276742 194273893 0.000000e+00 5264.0
1 TraesCS7D01G233000 chr7B 92.537 1541 79 19 356 1871 158187643 158186114 0.000000e+00 2176.0
2 TraesCS7D01G233000 chr7B 79.724 217 34 9 1869 2076 191676507 191676292 6.360000e-32 148.0
3 TraesCS7D01G233000 chr7B 89.231 65 6 1 356 420 167012314 167012377 2.350000e-11 80.5
4 TraesCS7D01G233000 chr7A 92.697 1027 48 10 651 1661 203976185 203975170 0.000000e+00 1456.0
5 TraesCS7D01G233000 chr7A 92.628 312 20 3 356 666 203978539 203978230 2.010000e-121 446.0
6 TraesCS7D01G233000 chr7A 89.189 222 20 3 1651 1871 203975100 203974882 1.010000e-69 274.0
7 TraesCS7D01G233000 chr7A 94.595 37 2 0 355 391 81954200 81954164 1.100000e-04 58.4
8 TraesCS7D01G233000 chr1D 85.627 654 90 4 1871 2520 298438659 298438006 0.000000e+00 684.0
9 TraesCS7D01G233000 chr1D 94.152 171 9 1 11 180 110021098 110021268 2.820000e-65 259.0
10 TraesCS7D01G233000 chr1D 91.667 180 13 2 1 179 379489765 379489587 6.100000e-62 248.0
11 TraesCS7D01G233000 chr1D 90.323 186 15 3 1 183 54932838 54933023 1.020000e-59 241.0
12 TraesCS7D01G233000 chr4A 83.582 670 95 8 2029 2697 602715811 602716466 5.220000e-172 614.0
13 TraesCS7D01G233000 chr3A 84.310 580 82 8 1871 2444 208266777 208266201 2.480000e-155 558.0
14 TraesCS7D01G233000 chr3A 84.887 397 60 0 2454 2850 208265988 208265592 4.420000e-108 401.0
15 TraesCS7D01G233000 chr3D 91.761 352 21 3 11 362 131641901 131641558 1.540000e-132 483.0
16 TraesCS7D01G233000 chr3D 91.304 184 15 1 1 183 61841897 61841714 1.700000e-62 250.0
17 TraesCS7D01G233000 chr3D 91.160 181 14 2 1 180 419993798 419993977 7.890000e-61 244.0
18 TraesCS7D01G233000 chr6D 88.252 349 39 2 1 348 417501229 417501576 1.580000e-112 416.0
19 TraesCS7D01G233000 chr6D 92.818 181 12 1 1 180 361423494 361423674 7.830000e-66 261.0
20 TraesCS7D01G233000 chr4B 72.936 872 209 22 1980 2840 419643900 419643045 7.780000e-71 278.0
21 TraesCS7D01G233000 chr4B 77.143 175 38 2 2005 2178 442459232 442459405 1.810000e-17 100.0
22 TraesCS7D01G233000 chr4D 91.713 181 14 1 1 180 445099970 445100150 1.700000e-62 250.0
23 TraesCS7D01G233000 chr1A 81.111 270 44 7 1871 2134 493286115 493286383 2.880000e-50 209.0
24 TraesCS7D01G233000 chr2B 72.344 687 166 19 2148 2821 236539397 236538722 8.060000e-46 195.0
25 TraesCS7D01G233000 chr5B 90.323 124 12 0 2067 2190 293533623 293533500 2.270000e-36 163.0
26 TraesCS7D01G233000 chr6B 75.000 168 42 0 2142 2309 281340417 281340584 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 TraesCS7D01G233000 chr7D 194273893 194276742 2849 True 5264.000000 5264 100.000000 1 2850 1 chr7D.!!$R1 2849
1 TraesCS7D01G233000 chr7B 158186114 158187643 1529 True 2176.000000 2176 92.537000 356 1871 1 chr7B.!!$R1 1515
2 TraesCS7D01G233000 chr7A 203974882 203978539 3657 True 725.333333 1456 91.504667 356 1871 3 chr7A.!!$R2 1515
3 TraesCS7D01G233000 chr1D 298438006 298438659 653 True 684.000000 684 85.627000 1871 2520 1 chr1D.!!$R1 649
4 TraesCS7D01G233000 chr4A 602715811 602716466 655 False 614.000000 614 83.582000 2029 2697 1 chr4A.!!$F1 668
5 TraesCS7D01G233000 chr3A 208265592 208266777 1185 True 479.500000 558 84.598500 1871 2850 2 chr3A.!!$R1 979
6 TraesCS7D01G233000 chr4B 419643045 419643900 855 True 278.000000 278 72.936000 1980 2840 1 chr4B.!!$R1 860

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
233 234 0.034767 ATAGATGGATGCATGGCGGG 60.035 55.0 2.46 0.0 0.0 6.13 F
1302 3378 0.106318 AGAAGGGATTGGATGCTGCC 60.106 55.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 3659 0.035317 AGCAGTGCACGAATCTCCAA 59.965 50.0 19.2 0.0 0.00 3.53 R
2319 4486 0.106521 AAAACCACCATGCACTTGCC 59.893 50.0 0.0 0.0 41.18 4.52 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
39 40 9.965824 AAAAGTTTGTTGAAACCTACTCATATG 57.034 29.630 0.00 0.00 42.25 1.78
40 41 7.687941 AGTTTGTTGAAACCTACTCATATGG 57.312 36.000 2.13 0.00 42.25 2.74
41 42 6.659242 AGTTTGTTGAAACCTACTCATATGGG 59.341 38.462 0.00 0.00 42.25 4.00
42 43 6.381498 TTGTTGAAACCTACTCATATGGGA 57.619 37.500 10.29 0.00 0.00 4.37
43 44 6.575244 TGTTGAAACCTACTCATATGGGAT 57.425 37.500 10.29 0.00 0.00 3.85
44 45 6.591935 TGTTGAAACCTACTCATATGGGATC 58.408 40.000 10.29 4.82 0.00 3.36
45 46 6.386927 TGTTGAAACCTACTCATATGGGATCT 59.613 38.462 10.29 0.00 0.00 2.75
46 47 7.567250 TGTTGAAACCTACTCATATGGGATCTA 59.433 37.037 10.29 0.00 0.00 1.98
47 48 7.782897 TGAAACCTACTCATATGGGATCTAG 57.217 40.000 10.29 0.51 0.00 2.43
48 49 7.306013 TGAAACCTACTCATATGGGATCTAGT 58.694 38.462 10.29 3.64 0.00 2.57
49 50 7.789831 TGAAACCTACTCATATGGGATCTAGTT 59.210 37.037 10.29 2.82 0.00 2.24
50 51 8.568617 AAACCTACTCATATGGGATCTAGTTT 57.431 34.615 10.29 8.53 0.00 2.66
51 52 8.568617 AACCTACTCATATGGGATCTAGTTTT 57.431 34.615 10.29 0.00 0.00 2.43
52 53 7.967908 ACCTACTCATATGGGATCTAGTTTTG 58.032 38.462 10.29 0.00 0.00 2.44
53 54 7.789831 ACCTACTCATATGGGATCTAGTTTTGA 59.210 37.037 10.29 0.00 0.00 2.69
54 55 8.651389 CCTACTCATATGGGATCTAGTTTTGAA 58.349 37.037 10.29 0.00 0.00 2.69
55 56 9.703892 CTACTCATATGGGATCTAGTTTTGAAG 57.296 37.037 10.29 0.00 0.00 3.02
56 57 8.324191 ACTCATATGGGATCTAGTTTTGAAGA 57.676 34.615 10.29 0.00 0.00 2.87
57 58 8.772250 ACTCATATGGGATCTAGTTTTGAAGAA 58.228 33.333 10.29 0.00 0.00 2.52
58 59 8.964476 TCATATGGGATCTAGTTTTGAAGAAC 57.036 34.615 2.13 0.00 0.00 3.01
59 60 8.772250 TCATATGGGATCTAGTTTTGAAGAACT 58.228 33.333 2.13 0.00 42.27 3.01
60 61 9.050601 CATATGGGATCTAGTTTTGAAGAACTC 57.949 37.037 0.00 0.00 40.24 3.01
61 62 5.479306 TGGGATCTAGTTTTGAAGAACTCG 58.521 41.667 0.00 0.00 40.24 4.18
62 63 5.011738 TGGGATCTAGTTTTGAAGAACTCGT 59.988 40.000 0.00 0.00 40.24 4.18
63 64 5.577554 GGGATCTAGTTTTGAAGAACTCGTC 59.422 44.000 0.00 0.00 40.24 4.20
64 65 5.286558 GGATCTAGTTTTGAAGAACTCGTCG 59.713 44.000 0.00 0.00 40.24 5.12
65 66 3.979495 TCTAGTTTTGAAGAACTCGTCGC 59.021 43.478 0.00 0.00 40.24 5.19
66 67 1.521423 AGTTTTGAAGAACTCGTCGCG 59.479 47.619 0.00 0.00 34.94 5.87
67 68 1.519758 GTTTTGAAGAACTCGTCGCGA 59.480 47.619 3.71 3.71 0.00 5.87
76 77 2.729455 TCGTCGCGAGAAACCCAA 59.271 55.556 10.24 0.00 45.01 4.12
77 78 1.662446 TCGTCGCGAGAAACCCAAC 60.662 57.895 10.24 0.00 45.01 3.77
78 79 2.851104 GTCGCGAGAAACCCAACG 59.149 61.111 10.24 0.00 45.01 4.10
79 80 2.356553 TCGCGAGAAACCCAACGG 60.357 61.111 3.71 0.00 37.03 4.44
80 81 3.154584 TCGCGAGAAACCCAACGGT 62.155 57.895 3.71 0.00 38.96 4.83
81 82 1.373246 CGCGAGAAACCCAACGGTA 60.373 57.895 0.00 0.00 43.71 4.02
82 83 0.945265 CGCGAGAAACCCAACGGTAA 60.945 55.000 0.00 0.00 43.71 2.85
83 84 1.228533 GCGAGAAACCCAACGGTAAA 58.771 50.000 0.00 0.00 43.71 2.01
84 85 1.603326 GCGAGAAACCCAACGGTAAAA 59.397 47.619 0.00 0.00 43.71 1.52
85 86 2.033174 GCGAGAAACCCAACGGTAAAAA 59.967 45.455 0.00 0.00 43.71 1.94
86 87 3.620761 CGAGAAACCCAACGGTAAAAAC 58.379 45.455 0.00 0.00 43.71 2.43
87 88 3.620761 GAGAAACCCAACGGTAAAAACG 58.379 45.455 0.00 0.00 43.71 3.60
88 89 2.358582 AGAAACCCAACGGTAAAAACGG 59.641 45.455 0.00 0.00 43.71 4.44
89 90 2.049888 AACCCAACGGTAAAAACGGA 57.950 45.000 0.00 0.00 43.71 4.69
90 91 2.275134 ACCCAACGGTAAAAACGGAT 57.725 45.000 0.00 0.00 42.18 4.18
91 92 2.585330 ACCCAACGGTAAAAACGGATT 58.415 42.857 0.00 0.00 42.18 3.01
92 93 2.957680 ACCCAACGGTAAAAACGGATTT 59.042 40.909 0.00 0.00 42.18 2.17
93 94 3.243468 ACCCAACGGTAAAAACGGATTTG 60.243 43.478 0.00 0.00 42.18 2.32
94 95 3.004524 CCCAACGGTAAAAACGGATTTGA 59.995 43.478 0.00 0.00 35.23 2.69
95 96 4.499357 CCCAACGGTAAAAACGGATTTGAA 60.499 41.667 0.00 0.00 35.23 2.69
96 97 5.224135 CCAACGGTAAAAACGGATTTGAAT 58.776 37.500 0.00 0.00 35.23 2.57
97 98 5.692654 CCAACGGTAAAAACGGATTTGAATT 59.307 36.000 0.00 0.00 35.23 2.17
98 99 6.201234 CCAACGGTAAAAACGGATTTGAATTT 59.799 34.615 0.00 0.00 35.23 1.82
99 100 7.254488 CCAACGGTAAAAACGGATTTGAATTTT 60.254 33.333 0.00 0.00 35.23 1.82
100 101 7.167831 ACGGTAAAAACGGATTTGAATTTTG 57.832 32.000 0.00 0.00 35.23 2.44
101 102 6.979238 ACGGTAAAAACGGATTTGAATTTTGA 59.021 30.769 0.00 0.00 35.23 2.69
102 103 7.654116 ACGGTAAAAACGGATTTGAATTTTGAT 59.346 29.630 0.00 0.00 35.23 2.57
103 104 9.130312 CGGTAAAAACGGATTTGAATTTTGATA 57.870 29.630 0.00 0.00 0.00 2.15
143 144 9.589111 TTACAAGTGTTTAAAGTTTTTGATCCC 57.411 29.630 0.00 0.00 0.00 3.85
144 145 7.847096 ACAAGTGTTTAAAGTTTTTGATCCCT 58.153 30.769 0.00 0.00 0.00 4.20
145 146 8.973182 ACAAGTGTTTAAAGTTTTTGATCCCTA 58.027 29.630 0.00 0.00 0.00 3.53
146 147 9.810545 CAAGTGTTTAAAGTTTTTGATCCCTAA 57.189 29.630 0.00 0.00 0.00 2.69
156 157 9.603921 AAGTTTTTGATCCCTAATAAATGCATG 57.396 29.630 0.00 0.00 0.00 4.06
157 158 8.761689 AGTTTTTGATCCCTAATAAATGCATGT 58.238 29.630 0.00 0.00 0.00 3.21
158 159 8.819974 GTTTTTGATCCCTAATAAATGCATGTG 58.180 33.333 0.00 0.00 0.00 3.21
159 160 6.653526 TTGATCCCTAATAAATGCATGTGG 57.346 37.500 0.00 0.00 0.00 4.17
160 161 5.078949 TGATCCCTAATAAATGCATGTGGG 58.921 41.667 0.00 1.12 34.98 4.61
161 162 3.843422 TCCCTAATAAATGCATGTGGGG 58.157 45.455 9.59 11.20 34.47 4.96
162 163 3.206412 TCCCTAATAAATGCATGTGGGGT 59.794 43.478 16.21 0.00 34.47 4.95
163 164 4.417183 TCCCTAATAAATGCATGTGGGGTA 59.583 41.667 16.21 5.79 34.47 3.69
164 165 4.766891 CCCTAATAAATGCATGTGGGGTAG 59.233 45.833 0.00 0.00 0.00 3.18
165 166 5.385198 CCTAATAAATGCATGTGGGGTAGT 58.615 41.667 0.00 0.00 0.00 2.73
166 167 5.833131 CCTAATAAATGCATGTGGGGTAGTT 59.167 40.000 0.00 0.00 0.00 2.24
167 168 7.001674 CCTAATAAATGCATGTGGGGTAGTTA 58.998 38.462 0.00 0.00 0.00 2.24
168 169 7.669722 CCTAATAAATGCATGTGGGGTAGTTAT 59.330 37.037 0.00 0.00 0.00 1.89
169 170 6.899393 ATAAATGCATGTGGGGTAGTTATG 57.101 37.500 0.00 0.00 0.00 1.90
170 171 3.951563 ATGCATGTGGGGTAGTTATGT 57.048 42.857 0.00 0.00 0.00 2.29
171 172 2.997980 TGCATGTGGGGTAGTTATGTG 58.002 47.619 0.00 0.00 0.00 3.21
172 173 1.676006 GCATGTGGGGTAGTTATGTGC 59.324 52.381 0.00 0.00 0.00 4.57
173 174 1.939934 CATGTGGGGTAGTTATGTGCG 59.060 52.381 0.00 0.00 0.00 5.34
174 175 0.391927 TGTGGGGTAGTTATGTGCGC 60.392 55.000 0.00 0.00 0.00 6.09
175 176 1.153529 TGGGGTAGTTATGTGCGCG 60.154 57.895 0.00 0.00 0.00 6.86
176 177 2.531376 GGGGTAGTTATGTGCGCGC 61.531 63.158 27.26 27.26 0.00 6.86
177 178 1.812093 GGGTAGTTATGTGCGCGCA 60.812 57.895 33.09 33.09 0.00 6.09
178 179 1.157870 GGGTAGTTATGTGCGCGCAT 61.158 55.000 38.62 35.73 0.00 4.73
179 180 0.042188 GGTAGTTATGTGCGCGCATG 60.042 55.000 39.08 0.00 0.00 4.06
180 181 0.927537 GTAGTTATGTGCGCGCATGA 59.072 50.000 39.08 31.37 0.00 3.07
181 182 1.071239 GTAGTTATGTGCGCGCATGAG 60.071 52.381 39.08 0.00 0.00 2.90
182 183 1.010797 GTTATGTGCGCGCATGAGG 60.011 57.895 39.08 0.00 0.00 3.86
183 184 1.153469 TTATGTGCGCGCATGAGGA 60.153 52.632 39.08 21.54 0.00 3.71
184 185 0.742635 TTATGTGCGCGCATGAGGAA 60.743 50.000 39.08 25.57 0.00 3.36
185 186 0.742635 TATGTGCGCGCATGAGGAAA 60.743 50.000 39.08 20.46 0.00 3.13
186 187 1.985447 ATGTGCGCGCATGAGGAAAG 61.985 55.000 38.62 0.00 0.00 2.62
187 188 2.358615 TGCGCGCATGAGGAAAGT 60.359 55.556 33.09 0.00 0.00 2.66
188 189 2.099062 GCGCGCATGAGGAAAGTG 59.901 61.111 29.10 0.00 0.00 3.16
189 190 2.680913 GCGCGCATGAGGAAAGTGT 61.681 57.895 29.10 0.00 0.00 3.55
190 191 1.868997 CGCGCATGAGGAAAGTGTT 59.131 52.632 8.75 0.00 0.00 3.32
191 192 0.453282 CGCGCATGAGGAAAGTGTTG 60.453 55.000 8.75 0.00 0.00 3.33
192 193 0.109597 GCGCATGAGGAAAGTGTTGG 60.110 55.000 0.30 0.00 0.00 3.77
193 194 0.109597 CGCATGAGGAAAGTGTTGGC 60.110 55.000 0.00 0.00 0.00 4.52
194 195 1.251251 GCATGAGGAAAGTGTTGGCT 58.749 50.000 0.00 0.00 0.00 4.75
195 196 2.436417 GCATGAGGAAAGTGTTGGCTA 58.564 47.619 0.00 0.00 0.00 3.93
196 197 2.421424 GCATGAGGAAAGTGTTGGCTAG 59.579 50.000 0.00 0.00 0.00 3.42
197 198 2.185004 TGAGGAAAGTGTTGGCTAGC 57.815 50.000 6.04 6.04 0.00 3.42
198 199 1.699634 TGAGGAAAGTGTTGGCTAGCT 59.300 47.619 15.72 0.00 0.00 3.32
199 200 2.079925 GAGGAAAGTGTTGGCTAGCTG 58.920 52.381 15.72 0.00 0.00 4.24
200 201 1.421646 AGGAAAGTGTTGGCTAGCTGT 59.578 47.619 15.72 0.00 0.00 4.40
201 202 2.158608 AGGAAAGTGTTGGCTAGCTGTT 60.159 45.455 15.72 0.00 0.00 3.16
202 203 2.030805 GGAAAGTGTTGGCTAGCTGTTG 60.031 50.000 15.72 0.00 0.00 3.33
203 204 0.954452 AAGTGTTGGCTAGCTGTTGC 59.046 50.000 15.72 2.98 40.05 4.17
208 209 4.972875 GGCTAGCTGTTGCCTGAT 57.027 55.556 15.72 0.00 45.26 2.90
209 210 2.700329 GGCTAGCTGTTGCCTGATC 58.300 57.895 15.72 0.00 45.26 2.92
210 211 0.817229 GGCTAGCTGTTGCCTGATCC 60.817 60.000 15.72 0.00 45.26 3.36
211 212 0.817229 GCTAGCTGTTGCCTGATCCC 60.817 60.000 7.70 0.00 40.80 3.85
212 213 0.835941 CTAGCTGTTGCCTGATCCCT 59.164 55.000 0.00 0.00 40.80 4.20
213 214 0.543277 TAGCTGTTGCCTGATCCCTG 59.457 55.000 0.00 0.00 40.80 4.45
214 215 1.203441 AGCTGTTGCCTGATCCCTGA 61.203 55.000 0.00 0.00 40.80 3.86
215 216 0.106819 GCTGTTGCCTGATCCCTGAT 60.107 55.000 0.00 0.00 0.00 2.90
216 217 1.141657 GCTGTTGCCTGATCCCTGATA 59.858 52.381 0.00 0.00 0.00 2.15
217 218 2.809665 GCTGTTGCCTGATCCCTGATAG 60.810 54.545 0.00 0.00 0.00 2.08
218 219 2.702478 CTGTTGCCTGATCCCTGATAGA 59.298 50.000 0.00 0.00 0.00 1.98
219 220 3.321039 TGTTGCCTGATCCCTGATAGAT 58.679 45.455 0.00 0.00 0.00 1.98
220 221 3.072038 TGTTGCCTGATCCCTGATAGATG 59.928 47.826 0.00 0.00 0.00 2.90
221 222 2.263545 TGCCTGATCCCTGATAGATGG 58.736 52.381 0.00 0.00 0.00 3.51
222 223 2.158112 TGCCTGATCCCTGATAGATGGA 60.158 50.000 0.00 0.00 0.00 3.41
223 224 3.113824 GCCTGATCCCTGATAGATGGAT 58.886 50.000 0.00 0.00 41.54 3.41
224 225 3.118334 GCCTGATCCCTGATAGATGGATG 60.118 52.174 0.00 0.00 38.98 3.51
225 226 3.118334 CCTGATCCCTGATAGATGGATGC 60.118 52.174 0.00 0.00 38.98 3.91
226 227 3.518303 CTGATCCCTGATAGATGGATGCA 59.482 47.826 0.00 0.00 38.98 3.96
227 228 4.109320 TGATCCCTGATAGATGGATGCAT 58.891 43.478 0.00 0.00 38.98 3.96
228 229 3.994931 TCCCTGATAGATGGATGCATG 57.005 47.619 2.46 0.00 0.00 4.06
229 230 2.574824 TCCCTGATAGATGGATGCATGG 59.425 50.000 2.46 0.00 0.00 3.66
230 231 2.366533 CCTGATAGATGGATGCATGGC 58.633 52.381 2.46 0.00 0.00 4.40
231 232 2.007608 CTGATAGATGGATGCATGGCG 58.992 52.381 2.46 0.00 0.00 5.69
232 233 1.339342 TGATAGATGGATGCATGGCGG 60.339 52.381 2.46 0.00 0.00 6.13
233 234 0.034767 ATAGATGGATGCATGGCGGG 60.035 55.000 2.46 0.00 0.00 6.13
234 235 1.418097 TAGATGGATGCATGGCGGGT 61.418 55.000 2.46 0.00 0.00 5.28
235 236 2.520020 ATGGATGCATGGCGGGTG 60.520 61.111 2.46 0.00 0.00 4.61
236 237 2.963928 GATGGATGCATGGCGGGTGA 62.964 60.000 2.46 0.00 0.00 4.02
237 238 2.903855 GGATGCATGGCGGGTGAG 60.904 66.667 2.46 0.00 0.00 3.51
238 239 2.903855 GATGCATGGCGGGTGAGG 60.904 66.667 2.46 0.00 0.00 3.86
239 240 4.511246 ATGCATGGCGGGTGAGGG 62.511 66.667 0.00 0.00 0.00 4.30
247 248 3.953775 CGGGTGAGGGCACTGGTT 61.954 66.667 0.00 0.00 44.52 3.67
248 249 2.282462 GGGTGAGGGCACTGGTTG 60.282 66.667 0.00 0.00 44.52 3.77
249 250 2.515901 GGTGAGGGCACTGGTTGT 59.484 61.111 0.00 0.00 44.52 3.32
262 263 4.193826 ACTGGTTGTGACTACTAGCATG 57.806 45.455 10.07 0.00 38.84 4.06
263 264 2.932614 CTGGTTGTGACTACTAGCATGC 59.067 50.000 10.51 10.51 38.84 4.06
264 265 2.301583 TGGTTGTGACTACTAGCATGCA 59.698 45.455 21.98 5.01 35.66 3.96
265 266 3.055167 TGGTTGTGACTACTAGCATGCAT 60.055 43.478 21.98 7.44 35.66 3.96
266 267 3.941483 GGTTGTGACTACTAGCATGCATT 59.059 43.478 21.98 5.67 31.76 3.56
267 268 4.201851 GGTTGTGACTACTAGCATGCATTG 60.202 45.833 21.98 11.56 31.76 2.82
290 291 4.684134 AGCGGGCCATGGCTGTTT 62.684 61.111 34.70 16.46 38.27 2.83
291 292 4.440127 GCGGGCCATGGCTGTTTG 62.440 66.667 34.70 20.31 41.60 2.93
292 293 4.440127 CGGGCCATGGCTGTTTGC 62.440 66.667 34.70 17.64 41.60 3.68
293 294 2.999063 GGGCCATGGCTGTTTGCT 60.999 61.111 34.70 0.00 42.39 3.91
294 295 2.263540 GGCCATGGCTGTTTGCTG 59.736 61.111 34.70 0.00 42.39 4.41
295 296 2.433664 GCCATGGCTGTTTGCTGC 60.434 61.111 29.98 0.00 42.39 5.25
296 297 2.126228 CCATGGCTGTTTGCTGCG 60.126 61.111 0.00 0.00 42.39 5.18
297 298 2.646719 CATGGCTGTTTGCTGCGT 59.353 55.556 0.00 0.00 42.39 5.24
298 299 1.731613 CATGGCTGTTTGCTGCGTG 60.732 57.895 0.00 0.00 42.39 5.34
299 300 3.562779 ATGGCTGTTTGCTGCGTGC 62.563 57.895 0.00 0.00 42.39 5.34
301 302 4.612536 GCTGTTTGCTGCGTGCGT 62.613 61.111 0.00 0.00 46.63 5.24
302 303 2.723271 CTGTTTGCTGCGTGCGTG 60.723 61.111 0.00 0.00 46.63 5.34
303 304 4.249020 TGTTTGCTGCGTGCGTGG 62.249 61.111 0.00 0.00 46.63 4.94
304 305 3.947841 GTTTGCTGCGTGCGTGGA 61.948 61.111 0.00 0.00 46.63 4.02
305 306 3.648982 TTTGCTGCGTGCGTGGAG 61.649 61.111 0.00 0.00 46.63 3.86
317 318 4.803426 GTGGAGGGTGCGCTCGAG 62.803 72.222 9.73 8.45 0.00 4.04
328 329 4.778415 GCTCGAGGCAGCGAACGA 62.778 66.667 15.58 6.93 40.13 3.85
329 330 2.578178 CTCGAGGCAGCGAACGAG 60.578 66.667 16.02 16.02 44.10 4.18
330 331 4.778415 TCGAGGCAGCGAACGAGC 62.778 66.667 0.00 1.11 37.35 5.03
354 355 2.815647 GCACTGGCTAGCCACGTC 60.816 66.667 32.88 18.88 41.89 4.34
449 450 0.678950 TGCCAGGCCTAAAAACTTGC 59.321 50.000 3.98 0.00 0.00 4.01
457 458 2.292292 GCCTAAAAACTTGCCGTCAGAA 59.708 45.455 0.00 0.00 0.00 3.02
469 470 3.003897 TGCCGTCAGAATTTTAGCGTTTT 59.996 39.130 0.00 0.00 0.00 2.43
500 501 7.754851 TTTAAAAGCTTAACTAGACAAGGGG 57.245 36.000 0.00 0.00 0.00 4.79
591 592 3.685139 AATCTCAGACGCCTTCAAAGA 57.315 42.857 0.00 0.00 0.00 2.52
697 2756 2.057137 TTTGCTTTGCTCACCTCACT 57.943 45.000 0.00 0.00 0.00 3.41
705 2764 4.680237 TCACCTCACTTGGCCGCG 62.680 66.667 0.00 0.00 0.00 6.46
919 2978 3.383761 CCCAGAAACATGCACAAAAGTC 58.616 45.455 0.00 0.00 0.00 3.01
1008 3078 2.049063 ACACGAAGCAGACCGAGC 60.049 61.111 0.00 0.00 0.00 5.03
1013 3083 0.371645 CGAAGCAGACCGAGCATTTC 59.628 55.000 0.00 0.00 0.00 2.17
1090 3166 1.040646 CGGCAGCTACTATCCTTCCA 58.959 55.000 0.00 0.00 0.00 3.53
1295 3371 0.469917 GATGCGGAGAAGGGATTGGA 59.530 55.000 0.00 0.00 0.00 3.53
1297 3373 0.181114 TGCGGAGAAGGGATTGGATG 59.819 55.000 0.00 0.00 0.00 3.51
1302 3378 0.106318 AGAAGGGATTGGATGCTGCC 60.106 55.000 0.00 0.00 0.00 4.85
1368 3444 1.516386 GCACGACATGGACGACGAT 60.516 57.895 18.41 0.00 34.70 3.73
1628 3710 2.930040 CAACAAAGTAGATGATCGCCGT 59.070 45.455 0.00 0.00 0.00 5.68
1652 3734 5.634896 ACGATGTTTCTCGATAGTACGTTT 58.365 37.500 0.00 0.00 41.12 3.60
1661 3743 9.669353 TTTCTCGATAGTACGTTTCAATATACC 57.331 33.333 0.00 0.00 37.40 2.73
1663 3745 9.006839 TCTCGATAGTACGTTTCAATATACCAT 57.993 33.333 0.00 0.00 37.40 3.55
1675 3837 9.925268 GTTTCAATATACCATTAAACTACACCG 57.075 33.333 0.00 0.00 0.00 4.94
1754 3916 3.120786 CGTTTCCAGTTACAGTTTAGCCG 60.121 47.826 0.00 0.00 0.00 5.52
1760 3922 3.617263 CAGTTACAGTTTAGCCGTGGATC 59.383 47.826 0.00 0.00 0.00 3.36
1775 3937 1.335145 GGATCCGAACGAGGGGAATA 58.665 55.000 0.00 0.00 35.60 1.75
1776 3938 1.000618 GGATCCGAACGAGGGGAATAC 59.999 57.143 0.00 0.00 35.60 1.89
1795 3957 1.156736 CACGTGGTCCTTGTGATTCC 58.843 55.000 7.95 0.00 35.66 3.01
1901 4065 3.368739 CCCCGACCGTAGAACAATAGTTT 60.369 47.826 0.00 0.00 38.30 2.66
1904 4068 6.044682 CCCGACCGTAGAACAATAGTTTTAT 58.955 40.000 0.00 0.00 38.30 1.40
1906 4070 6.753279 CCGACCGTAGAACAATAGTTTTATGA 59.247 38.462 0.00 0.00 38.30 2.15
1952 4118 3.963383 ACAAGTTACAAAAGACCTGCG 57.037 42.857 0.00 0.00 0.00 5.18
1953 4119 2.616842 ACAAGTTACAAAAGACCTGCGG 59.383 45.455 0.00 0.00 0.00 5.69
1969 4135 3.003763 GGGAGGGCGTGAGGAAGT 61.004 66.667 0.00 0.00 0.00 3.01
1973 4139 0.175989 GAGGGCGTGAGGAAGTAAGG 59.824 60.000 0.00 0.00 0.00 2.69
1978 4144 3.344515 GGCGTGAGGAAGTAAGGAAAAT 58.655 45.455 0.00 0.00 0.00 1.82
1997 4163 7.841222 AGGAAAATCTATCCTATGCCTGTTTTT 59.159 33.333 0.00 0.00 45.51 1.94
2011 4178 6.355747 TGCCTGTTTTTGGAAAAAGATCATT 58.644 32.000 0.00 0.00 38.44 2.57
2183 4350 0.250234 TCCAGATGTTCCAGCTTCCG 59.750 55.000 0.00 0.00 0.00 4.30
2185 4352 1.649664 CAGATGTTCCAGCTTCCGAG 58.350 55.000 0.00 0.00 0.00 4.63
2201 4368 4.527509 TCCGAGAATGATAATCTCTGCC 57.472 45.455 2.47 0.00 40.93 4.85
2250 4417 5.067954 TGGCAAGAATGATGTCCTCATATG 58.932 41.667 0.00 0.00 44.03 1.78
2259 4426 7.565190 ATGATGTCCTCATATGTGGAAGTAT 57.435 36.000 24.44 18.72 42.96 2.12
2296 4463 3.359950 GAATCAGGGAGTTCCAGCATTT 58.640 45.455 0.00 0.00 38.24 2.32
2319 4486 4.582701 TGTGCAAAATTACACTCCCAAG 57.417 40.909 0.00 0.00 37.68 3.61
2324 4491 4.559153 CAAAATTACACTCCCAAGGCAAG 58.441 43.478 0.00 0.00 0.00 4.01
2338 4505 0.106521 GGCAAGTGCATGGTGGTTTT 59.893 50.000 5.52 0.00 44.36 2.43
2348 4515 1.981256 TGGTGGTTTTCTCAGCCTTC 58.019 50.000 0.00 0.00 32.25 3.46
2411 4580 1.270907 TCCCCTGAAGAAGTGCTCTC 58.729 55.000 0.00 0.00 31.02 3.20
2426 4595 3.244814 GTGCTCTCGTATTGATTCTGCAG 59.755 47.826 7.63 7.63 0.00 4.41
2472 4845 3.249917 GTGTTTCAGTCTGCTAGAGCTC 58.750 50.000 5.27 5.27 42.66 4.09
2511 4884 5.405935 AAATAGGGTGTTCATCCTTTTGC 57.594 39.130 10.02 0.00 34.75 3.68
2550 4923 8.052748 TGGTAAATGTGGATAGCTGAGTATTTT 58.947 33.333 0.00 0.00 0.00 1.82
2570 4943 4.335400 TTCCTTTTTGACCTTGGATTGC 57.665 40.909 0.00 0.00 0.00 3.56
2592 4965 4.385310 GCCCATTTATCCTTAGTGTCTGGT 60.385 45.833 0.00 0.00 0.00 4.00
2675 5048 3.057526 GGAAGGTGGAAATTTTCAGACCG 60.058 47.826 17.43 0.00 38.25 4.79
2682 5055 4.160626 TGGAAATTTTCAGACCGGTTTTGT 59.839 37.500 9.42 0.00 0.00 2.83
2703 5076 9.436957 TTTTGTACTTCCAAAAAGTTTTGCATA 57.563 25.926 10.41 0.00 44.62 3.14
2705 5078 8.001881 TGTACTTCCAAAAAGTTTTGCATAGA 57.998 30.769 10.41 1.20 44.62 1.98
2744 5117 4.574013 GGCATATGAGTGAAGTTCAGGAAG 59.426 45.833 5.62 0.00 0.00 3.46
2745 5118 4.574013 GCATATGAGTGAAGTTCAGGAAGG 59.426 45.833 5.62 0.00 0.00 3.46
2746 5119 3.710209 ATGAGTGAAGTTCAGGAAGGG 57.290 47.619 5.62 0.00 0.00 3.95
2751 5124 1.494721 TGAAGTTCAGGAAGGGCTTGT 59.505 47.619 0.08 0.00 0.00 3.16
2753 5126 1.986882 AGTTCAGGAAGGGCTTGTTG 58.013 50.000 0.00 0.00 0.00 3.33
2763 5136 3.577805 AGGGCTTGTTGTAGAGTTTGT 57.422 42.857 0.00 0.00 0.00 2.83
2773 5146 5.184096 TGTTGTAGAGTTTGTTCAAGCCAAA 59.816 36.000 0.00 0.00 0.00 3.28
2775 5148 5.830912 TGTAGAGTTTGTTCAAGCCAAATG 58.169 37.500 0.00 0.00 34.59 2.32
2787 5160 4.347583 TCAAGCCAAATGTCCTTCCAAAAT 59.652 37.500 0.00 0.00 0.00 1.82
2792 5165 6.441604 AGCCAAATGTCCTTCCAAAATAGAAT 59.558 34.615 0.00 0.00 0.00 2.40
2796 5169 9.143631 CAAATGTCCTTCCAAAATAGAATTGTC 57.856 33.333 0.00 0.00 0.00 3.18
2798 5171 9.753674 AATGTCCTTCCAAAATAGAATTGTCTA 57.246 29.630 0.00 0.00 40.68 2.59
2799 5172 8.561738 TGTCCTTCCAAAATAGAATTGTCTAC 57.438 34.615 0.00 0.00 39.20 2.59
2803 5176 8.272173 CCTTCCAAAATAGAATTGTCTACCCTA 58.728 37.037 0.00 0.00 39.20 3.53
2821 5194 4.776837 ACCCTAATCCAATTGTGCATTTGA 59.223 37.500 4.43 0.00 0.00 2.69
2826 5199 6.918892 AATCCAATTGTGCATTTGATCATG 57.081 33.333 4.43 0.00 28.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.965824 CATATGAGTAGGTTTCAACAAACTTTT 57.034 29.630 0.00 0.00 41.61 2.27
14 15 8.576442 CCATATGAGTAGGTTTCAACAAACTTT 58.424 33.333 3.65 0.00 41.61 2.66
15 16 7.176690 CCCATATGAGTAGGTTTCAACAAACTT 59.823 37.037 3.65 0.00 41.61 2.66
16 17 6.659242 CCCATATGAGTAGGTTTCAACAAACT 59.341 38.462 3.65 0.00 41.61 2.66
17 18 6.657541 TCCCATATGAGTAGGTTTCAACAAAC 59.342 38.462 3.65 0.00 41.22 2.93
18 19 6.785076 TCCCATATGAGTAGGTTTCAACAAA 58.215 36.000 3.65 0.00 0.00 2.83
19 20 6.381498 TCCCATATGAGTAGGTTTCAACAA 57.619 37.500 3.65 0.00 0.00 2.83
20 21 6.386927 AGATCCCATATGAGTAGGTTTCAACA 59.613 38.462 3.65 0.00 0.00 3.33
21 22 6.831976 AGATCCCATATGAGTAGGTTTCAAC 58.168 40.000 3.65 0.00 0.00 3.18
22 23 7.789831 ACTAGATCCCATATGAGTAGGTTTCAA 59.210 37.037 3.65 0.00 0.00 2.69
23 24 7.306013 ACTAGATCCCATATGAGTAGGTTTCA 58.694 38.462 3.65 0.00 0.00 2.69
24 25 7.784470 ACTAGATCCCATATGAGTAGGTTTC 57.216 40.000 3.65 0.00 0.00 2.78
25 26 8.568617 AAACTAGATCCCATATGAGTAGGTTT 57.431 34.615 3.65 4.29 0.00 3.27
26 27 8.432805 CAAAACTAGATCCCATATGAGTAGGTT 58.567 37.037 3.65 0.01 0.00 3.50
27 28 7.789831 TCAAAACTAGATCCCATATGAGTAGGT 59.210 37.037 3.65 0.00 0.00 3.08
28 29 8.195165 TCAAAACTAGATCCCATATGAGTAGG 57.805 38.462 3.65 0.00 0.00 3.18
29 30 9.703892 CTTCAAAACTAGATCCCATATGAGTAG 57.296 37.037 3.65 0.49 0.00 2.57
30 31 9.434275 TCTTCAAAACTAGATCCCATATGAGTA 57.566 33.333 3.65 0.00 0.00 2.59
31 32 8.324191 TCTTCAAAACTAGATCCCATATGAGT 57.676 34.615 3.65 0.00 0.00 3.41
32 33 9.050601 GTTCTTCAAAACTAGATCCCATATGAG 57.949 37.037 3.65 0.00 0.00 2.90
33 34 8.772250 AGTTCTTCAAAACTAGATCCCATATGA 58.228 33.333 3.65 0.00 37.71 2.15
34 35 8.970859 AGTTCTTCAAAACTAGATCCCATATG 57.029 34.615 0.00 0.00 37.71 1.78
35 36 7.928706 CGAGTTCTTCAAAACTAGATCCCATAT 59.071 37.037 0.00 0.00 39.55 1.78
36 37 7.093465 ACGAGTTCTTCAAAACTAGATCCCATA 60.093 37.037 0.00 0.00 39.55 2.74
37 38 6.109359 CGAGTTCTTCAAAACTAGATCCCAT 58.891 40.000 0.00 0.00 39.55 4.00
38 39 5.011738 ACGAGTTCTTCAAAACTAGATCCCA 59.988 40.000 0.00 0.00 39.55 4.37
39 40 5.480205 ACGAGTTCTTCAAAACTAGATCCC 58.520 41.667 0.00 0.00 39.55 3.85
40 41 5.286558 CGACGAGTTCTTCAAAACTAGATCC 59.713 44.000 0.00 0.00 39.55 3.36
41 42 5.220061 GCGACGAGTTCTTCAAAACTAGATC 60.220 44.000 0.00 0.00 39.55 2.75
42 43 4.621886 GCGACGAGTTCTTCAAAACTAGAT 59.378 41.667 0.00 0.00 39.55 1.98
43 44 3.979495 GCGACGAGTTCTTCAAAACTAGA 59.021 43.478 0.00 0.00 39.55 2.43
44 45 3.181552 CGCGACGAGTTCTTCAAAACTAG 60.182 47.826 0.00 0.00 39.55 2.57
45 46 2.722629 CGCGACGAGTTCTTCAAAACTA 59.277 45.455 0.00 0.00 39.55 2.24
46 47 1.521423 CGCGACGAGTTCTTCAAAACT 59.479 47.619 0.00 0.00 42.10 2.66
47 48 1.519758 TCGCGACGAGTTCTTCAAAAC 59.480 47.619 3.71 0.00 0.00 2.43
48 49 1.842720 TCGCGACGAGTTCTTCAAAA 58.157 45.000 3.71 0.00 0.00 2.44
49 50 3.555401 TCGCGACGAGTTCTTCAAA 57.445 47.368 3.71 0.00 0.00 2.69
59 60 1.662446 GTTGGGTTTCTCGCGACGA 60.662 57.895 3.71 4.19 34.51 4.20
60 61 2.851104 GTTGGGTTTCTCGCGACG 59.149 61.111 3.71 1.32 34.51 5.12
61 62 2.664436 CCGTTGGGTTTCTCGCGAC 61.664 63.158 3.71 0.00 39.21 5.19
62 63 2.356553 CCGTTGGGTTTCTCGCGA 60.357 61.111 9.26 9.26 0.00 5.87
72 73 3.004524 TCAAATCCGTTTTTACCGTTGGG 59.995 43.478 0.00 0.00 40.11 4.12
73 74 4.226113 TCAAATCCGTTTTTACCGTTGG 57.774 40.909 0.00 0.00 0.00 3.77
74 75 6.757026 AATTCAAATCCGTTTTTACCGTTG 57.243 33.333 0.00 0.00 0.00 4.10
75 76 7.491696 TCAAAATTCAAATCCGTTTTTACCGTT 59.508 29.630 0.00 0.00 0.00 4.44
76 77 6.979238 TCAAAATTCAAATCCGTTTTTACCGT 59.021 30.769 0.00 0.00 0.00 4.83
77 78 7.396190 TCAAAATTCAAATCCGTTTTTACCG 57.604 32.000 0.00 0.00 0.00 4.02
117 118 9.589111 GGGATCAAAAACTTTAAACACTTGTAA 57.411 29.630 0.00 0.00 0.00 2.41
118 119 8.973182 AGGGATCAAAAACTTTAAACACTTGTA 58.027 29.630 0.00 0.00 0.00 2.41
119 120 7.847096 AGGGATCAAAAACTTTAAACACTTGT 58.153 30.769 0.00 0.00 0.00 3.16
120 121 9.810545 TTAGGGATCAAAAACTTTAAACACTTG 57.189 29.630 0.00 0.00 0.00 3.16
130 131 9.603921 CATGCATTTATTAGGGATCAAAAACTT 57.396 29.630 0.00 0.00 0.00 2.66
131 132 8.761689 ACATGCATTTATTAGGGATCAAAAACT 58.238 29.630 0.00 0.00 0.00 2.66
132 133 8.819974 CACATGCATTTATTAGGGATCAAAAAC 58.180 33.333 0.00 0.00 0.00 2.43
133 134 7.986320 CCACATGCATTTATTAGGGATCAAAAA 59.014 33.333 0.00 0.00 0.00 1.94
134 135 7.418827 CCCACATGCATTTATTAGGGATCAAAA 60.419 37.037 0.00 0.00 37.22 2.44
135 136 6.041865 CCCACATGCATTTATTAGGGATCAAA 59.958 38.462 0.00 0.00 37.22 2.69
136 137 5.539574 CCCACATGCATTTATTAGGGATCAA 59.460 40.000 0.00 0.00 37.22 2.57
137 138 5.078949 CCCACATGCATTTATTAGGGATCA 58.921 41.667 0.00 0.00 37.22 2.92
138 139 4.463891 CCCCACATGCATTTATTAGGGATC 59.536 45.833 7.40 0.00 37.22 3.36
139 140 4.140710 ACCCCACATGCATTTATTAGGGAT 60.141 41.667 16.79 0.00 37.22 3.85
140 141 3.206412 ACCCCACATGCATTTATTAGGGA 59.794 43.478 16.79 0.00 37.22 4.20
141 142 3.575805 ACCCCACATGCATTTATTAGGG 58.424 45.455 0.00 4.44 38.04 3.53
142 143 5.385198 ACTACCCCACATGCATTTATTAGG 58.615 41.667 0.00 0.00 0.00 2.69
143 144 6.959639 AACTACCCCACATGCATTTATTAG 57.040 37.500 0.00 0.00 0.00 1.73
144 145 8.001875 ACATAACTACCCCACATGCATTTATTA 58.998 33.333 0.00 0.00 0.00 0.98
145 146 6.838612 ACATAACTACCCCACATGCATTTATT 59.161 34.615 0.00 0.00 0.00 1.40
146 147 6.265196 CACATAACTACCCCACATGCATTTAT 59.735 38.462 0.00 0.00 0.00 1.40
147 148 5.592282 CACATAACTACCCCACATGCATTTA 59.408 40.000 0.00 0.00 0.00 1.40
148 149 4.402155 CACATAACTACCCCACATGCATTT 59.598 41.667 0.00 0.00 0.00 2.32
149 150 3.953612 CACATAACTACCCCACATGCATT 59.046 43.478 0.00 0.00 0.00 3.56
150 151 3.554934 CACATAACTACCCCACATGCAT 58.445 45.455 0.00 0.00 0.00 3.96
151 152 2.943646 GCACATAACTACCCCACATGCA 60.944 50.000 0.00 0.00 0.00 3.96
152 153 1.676006 GCACATAACTACCCCACATGC 59.324 52.381 0.00 0.00 0.00 4.06
153 154 1.939934 CGCACATAACTACCCCACATG 59.060 52.381 0.00 0.00 0.00 3.21
154 155 1.745827 GCGCACATAACTACCCCACAT 60.746 52.381 0.30 0.00 0.00 3.21
155 156 0.391927 GCGCACATAACTACCCCACA 60.392 55.000 0.30 0.00 0.00 4.17
156 157 1.426041 CGCGCACATAACTACCCCAC 61.426 60.000 8.75 0.00 0.00 4.61
157 158 1.153529 CGCGCACATAACTACCCCA 60.154 57.895 8.75 0.00 0.00 4.96
158 159 2.531376 GCGCGCACATAACTACCCC 61.531 63.158 29.10 0.00 0.00 4.95
159 160 1.157870 ATGCGCGCACATAACTACCC 61.158 55.000 39.05 0.00 0.00 3.69
160 161 0.042188 CATGCGCGCACATAACTACC 60.042 55.000 39.05 0.00 0.00 3.18
161 162 0.927537 TCATGCGCGCACATAACTAC 59.072 50.000 39.05 0.00 0.00 2.73
162 163 1.208259 CTCATGCGCGCACATAACTA 58.792 50.000 39.05 11.72 0.00 2.24
163 164 1.431488 CCTCATGCGCGCACATAACT 61.431 55.000 39.05 17.70 0.00 2.24
164 165 1.010797 CCTCATGCGCGCACATAAC 60.011 57.895 39.05 2.60 0.00 1.89
165 166 0.742635 TTCCTCATGCGCGCACATAA 60.743 50.000 39.05 22.37 0.00 1.90
166 167 0.742635 TTTCCTCATGCGCGCACATA 60.743 50.000 39.05 23.03 0.00 2.29
167 168 1.985447 CTTTCCTCATGCGCGCACAT 61.985 55.000 39.05 20.43 0.00 3.21
168 169 2.667874 TTTCCTCATGCGCGCACA 60.668 55.556 39.05 24.89 0.00 4.57
169 170 2.099062 CTTTCCTCATGCGCGCAC 59.901 61.111 39.05 6.30 0.00 5.34
170 171 2.358615 ACTTTCCTCATGCGCGCA 60.359 55.556 38.27 38.27 0.00 6.09
171 172 2.099062 CACTTTCCTCATGCGCGC 59.901 61.111 27.26 27.26 0.00 6.86
172 173 0.453282 CAACACTTTCCTCATGCGCG 60.453 55.000 0.00 0.00 0.00 6.86
173 174 0.109597 CCAACACTTTCCTCATGCGC 60.110 55.000 0.00 0.00 0.00 6.09
174 175 0.109597 GCCAACACTTTCCTCATGCG 60.110 55.000 0.00 0.00 0.00 4.73
175 176 1.251251 AGCCAACACTTTCCTCATGC 58.749 50.000 0.00 0.00 0.00 4.06
176 177 2.421424 GCTAGCCAACACTTTCCTCATG 59.579 50.000 2.29 0.00 0.00 3.07
177 178 2.307098 AGCTAGCCAACACTTTCCTCAT 59.693 45.455 12.13 0.00 0.00 2.90
178 179 1.699634 AGCTAGCCAACACTTTCCTCA 59.300 47.619 12.13 0.00 0.00 3.86
179 180 2.079925 CAGCTAGCCAACACTTTCCTC 58.920 52.381 12.13 0.00 0.00 3.71
180 181 1.421646 ACAGCTAGCCAACACTTTCCT 59.578 47.619 12.13 0.00 0.00 3.36
181 182 1.897560 ACAGCTAGCCAACACTTTCC 58.102 50.000 12.13 0.00 0.00 3.13
182 183 2.605580 GCAACAGCTAGCCAACACTTTC 60.606 50.000 12.13 0.00 0.00 2.62
183 184 1.338020 GCAACAGCTAGCCAACACTTT 59.662 47.619 12.13 0.00 0.00 2.66
184 185 0.954452 GCAACAGCTAGCCAACACTT 59.046 50.000 12.13 0.00 0.00 3.16
185 186 2.633860 GCAACAGCTAGCCAACACT 58.366 52.632 12.13 0.00 0.00 3.55
192 193 0.817229 GGGATCAGGCAACAGCTAGC 60.817 60.000 6.62 6.62 41.41 3.42
193 194 0.835941 AGGGATCAGGCAACAGCTAG 59.164 55.000 0.00 0.00 41.41 3.42
194 195 0.543277 CAGGGATCAGGCAACAGCTA 59.457 55.000 0.00 0.00 41.41 3.32
195 196 1.203441 TCAGGGATCAGGCAACAGCT 61.203 55.000 0.00 0.00 41.41 4.24
196 197 0.106819 ATCAGGGATCAGGCAACAGC 60.107 55.000 0.00 0.00 41.41 4.40
197 198 2.702478 TCTATCAGGGATCAGGCAACAG 59.298 50.000 0.00 0.00 41.41 3.16
198 199 2.763039 TCTATCAGGGATCAGGCAACA 58.237 47.619 0.00 0.00 41.41 3.33
199 200 3.558746 CCATCTATCAGGGATCAGGCAAC 60.559 52.174 0.00 0.00 0.00 4.17
200 201 2.641321 CCATCTATCAGGGATCAGGCAA 59.359 50.000 0.00 0.00 0.00 4.52
201 202 2.158112 TCCATCTATCAGGGATCAGGCA 60.158 50.000 0.00 0.00 0.00 4.75
202 203 2.544721 TCCATCTATCAGGGATCAGGC 58.455 52.381 0.00 0.00 0.00 4.85
203 204 3.118334 GCATCCATCTATCAGGGATCAGG 60.118 52.174 0.00 0.00 39.36 3.86
204 205 3.518303 TGCATCCATCTATCAGGGATCAG 59.482 47.826 0.00 0.00 39.36 2.90
205 206 3.523792 TGCATCCATCTATCAGGGATCA 58.476 45.455 0.00 0.00 39.36 2.92
206 207 4.452825 CATGCATCCATCTATCAGGGATC 58.547 47.826 0.00 0.00 39.36 3.36
207 208 3.202373 CCATGCATCCATCTATCAGGGAT 59.798 47.826 0.00 0.00 42.04 3.85
208 209 2.574824 CCATGCATCCATCTATCAGGGA 59.425 50.000 0.00 0.00 30.93 4.20
209 210 2.944542 GCCATGCATCCATCTATCAGGG 60.945 54.545 0.00 0.00 0.00 4.45
210 211 2.366533 GCCATGCATCCATCTATCAGG 58.633 52.381 0.00 0.00 0.00 3.86
211 212 2.007608 CGCCATGCATCCATCTATCAG 58.992 52.381 0.00 0.00 0.00 2.90
212 213 1.339342 CCGCCATGCATCCATCTATCA 60.339 52.381 0.00 0.00 0.00 2.15
213 214 1.376543 CCGCCATGCATCCATCTATC 58.623 55.000 0.00 0.00 0.00 2.08
214 215 0.034767 CCCGCCATGCATCCATCTAT 60.035 55.000 0.00 0.00 0.00 1.98
215 216 1.376086 CCCGCCATGCATCCATCTA 59.624 57.895 0.00 0.00 0.00 1.98
216 217 2.114625 CCCGCCATGCATCCATCT 59.885 61.111 0.00 0.00 0.00 2.90
217 218 2.203394 ACCCGCCATGCATCCATC 60.203 61.111 0.00 0.00 0.00 3.51
218 219 2.520020 CACCCGCCATGCATCCAT 60.520 61.111 0.00 0.00 0.00 3.41
219 220 3.702529 CTCACCCGCCATGCATCCA 62.703 63.158 0.00 0.00 0.00 3.41
220 221 2.903855 CTCACCCGCCATGCATCC 60.904 66.667 0.00 0.00 0.00 3.51
221 222 2.903855 CCTCACCCGCCATGCATC 60.904 66.667 0.00 0.00 0.00 3.91
222 223 4.511246 CCCTCACCCGCCATGCAT 62.511 66.667 0.00 0.00 0.00 3.96
230 231 3.953775 AACCAGTGCCCTCACCCG 61.954 66.667 0.00 0.00 44.16 5.28
231 232 2.282462 CAACCAGTGCCCTCACCC 60.282 66.667 0.00 0.00 44.16 4.61
232 233 1.898574 CACAACCAGTGCCCTCACC 60.899 63.158 0.00 0.00 44.16 4.02
233 234 3.749981 CACAACCAGTGCCCTCAC 58.250 61.111 0.00 0.00 42.15 3.51
241 242 3.617531 GCATGCTAGTAGTCACAACCAGT 60.618 47.826 11.37 0.00 0.00 4.00
242 243 2.932614 GCATGCTAGTAGTCACAACCAG 59.067 50.000 11.37 0.00 0.00 4.00
243 244 2.301583 TGCATGCTAGTAGTCACAACCA 59.698 45.455 20.33 0.00 0.00 3.67
244 245 2.972625 TGCATGCTAGTAGTCACAACC 58.027 47.619 20.33 0.00 0.00 3.77
245 246 4.901814 CAATGCATGCTAGTAGTCACAAC 58.098 43.478 20.33 0.00 0.00 3.32
273 274 4.684134 AAACAGCCATGGCCCGCT 62.684 61.111 33.14 13.50 43.17 5.52
274 275 4.440127 CAAACAGCCATGGCCCGC 62.440 66.667 33.14 8.47 43.17 6.13
275 276 4.440127 GCAAACAGCCATGGCCCG 62.440 66.667 33.14 25.77 43.17 6.13
284 285 4.612536 ACGCACGCAGCAAACAGC 62.613 61.111 0.00 0.00 46.13 4.40
285 286 2.723271 CACGCACGCAGCAAACAG 60.723 61.111 0.00 0.00 46.13 3.16
286 287 4.249020 CCACGCACGCAGCAAACA 62.249 61.111 0.00 0.00 46.13 2.83
287 288 3.862063 CTCCACGCACGCAGCAAAC 62.862 63.158 0.00 0.00 46.13 2.93
288 289 3.648982 CTCCACGCACGCAGCAAA 61.649 61.111 0.00 0.00 46.13 3.68
300 301 4.803426 CTCGAGCGCACCCTCCAC 62.803 72.222 11.47 0.00 0.00 4.02
311 312 4.778415 TCGTTCGCTGCCTCGAGC 62.778 66.667 6.99 3.23 39.82 5.03
312 313 2.578178 CTCGTTCGCTGCCTCGAG 60.578 66.667 5.13 5.13 42.36 4.04
313 314 4.778415 GCTCGTTCGCTGCCTCGA 62.778 66.667 0.00 1.30 36.60 4.04
341 342 1.476845 TTTCTGGACGTGGCTAGCCA 61.477 55.000 32.88 32.88 45.02 4.75
342 343 0.321298 TTTTCTGGACGTGGCTAGCC 60.321 55.000 27.71 27.71 0.00 3.93
343 344 1.739067 ATTTTCTGGACGTGGCTAGC 58.261 50.000 6.04 6.04 0.00 3.42
344 345 2.159517 GCAATTTTCTGGACGTGGCTAG 60.160 50.000 0.00 0.00 0.00 3.42
345 346 1.810151 GCAATTTTCTGGACGTGGCTA 59.190 47.619 0.00 0.00 0.00 3.93
346 347 0.598065 GCAATTTTCTGGACGTGGCT 59.402 50.000 0.00 0.00 0.00 4.75
347 348 0.388520 GGCAATTTTCTGGACGTGGC 60.389 55.000 0.00 0.00 0.00 5.01
348 349 0.109781 CGGCAATTTTCTGGACGTGG 60.110 55.000 0.00 0.00 0.00 4.94
349 350 0.591170 ACGGCAATTTTCTGGACGTG 59.409 50.000 0.00 0.00 0.00 4.49
350 351 0.591170 CACGGCAATTTTCTGGACGT 59.409 50.000 0.00 0.00 0.00 4.34
351 352 0.729140 GCACGGCAATTTTCTGGACG 60.729 55.000 0.00 0.00 0.00 4.79
352 353 0.598065 AGCACGGCAATTTTCTGGAC 59.402 50.000 0.00 0.00 0.00 4.02
353 354 1.000385 CAAGCACGGCAATTTTCTGGA 60.000 47.619 0.00 0.00 0.00 3.86
354 355 1.269726 ACAAGCACGGCAATTTTCTGG 60.270 47.619 0.00 0.00 0.00 3.86
387 388 9.061435 TGACAATTTATATTGGTGCGATTATGA 57.939 29.630 10.17 0.00 44.42 2.15
435 436 0.955905 TGACGGCAAGTTTTTAGGCC 59.044 50.000 0.00 0.00 42.98 5.19
449 450 3.838550 CGAAAACGCTAAAATTCTGACGG 59.161 43.478 0.00 0.00 0.00 4.79
500 501 6.327177 TGATTACGTGACGCTAAAAATCTC 57.673 37.500 4.25 0.00 0.00 2.75
581 582 2.293399 TCTTCGGCTTTTCTTTGAAGGC 59.707 45.455 0.85 0.85 43.81 4.35
582 583 3.607078 CGTCTTCGGCTTTTCTTTGAAGG 60.607 47.826 0.98 0.00 37.30 3.46
591 592 2.814280 TTCTCTCGTCTTCGGCTTTT 57.186 45.000 0.00 0.00 37.69 2.27
679 2738 1.677576 CAAGTGAGGTGAGCAAAGCAA 59.322 47.619 0.00 0.00 0.00 3.91
705 2764 2.050077 GCACCGGAACAAAGCAGC 60.050 61.111 9.46 0.00 0.00 5.25
1008 3078 2.301902 GACTCCTGCAGCGCGAAATG 62.302 60.000 12.10 6.11 0.00 2.32
1072 3148 1.070914 GGTGGAAGGATAGTAGCTGCC 59.929 57.143 0.00 0.00 0.00 4.85
1230 3306 0.903454 ACTTTCCCCTGGACGACGAT 60.903 55.000 0.00 0.00 0.00 3.73
1275 3351 0.882042 CCAATCCCTTCTCCGCATCG 60.882 60.000 0.00 0.00 0.00 3.84
1344 3420 1.080366 GTCCATGTCGTGCACCGTA 60.080 57.895 12.15 0.00 37.94 4.02
1368 3444 3.424198 CGAACTTGATCTCGAAAACGTCA 59.576 43.478 0.00 0.00 37.23 4.35
1408 3484 2.033602 GTGTTTCTCCCACCCCGG 59.966 66.667 0.00 0.00 0.00 5.73
1412 3488 3.047877 CGCCGTGTTTCTCCCACC 61.048 66.667 0.00 0.00 0.00 4.61
1577 3659 0.035317 AGCAGTGCACGAATCTCCAA 59.965 50.000 19.20 0.00 0.00 3.53
1628 3710 5.973651 ACGTACTATCGAGAAACATCGTA 57.026 39.130 0.00 0.00 43.20 3.43
1652 3734 7.927629 GGACGGTGTAGTTTAATGGTATATTGA 59.072 37.037 0.00 0.00 0.00 2.57
1661 3743 7.977853 ACTATTACAGGACGGTGTAGTTTAATG 59.022 37.037 0.00 0.00 34.41 1.90
1663 3745 7.394359 AGACTATTACAGGACGGTGTAGTTTAA 59.606 37.037 0.00 0.00 34.41 1.52
1665 3747 5.713861 AGACTATTACAGGACGGTGTAGTTT 59.286 40.000 0.00 0.00 34.41 2.66
1673 3835 4.082408 TGTTCACAGACTATTACAGGACGG 60.082 45.833 0.00 0.00 0.00 4.79
1675 3837 7.097192 TCAATGTTCACAGACTATTACAGGAC 58.903 38.462 0.00 0.00 0.00 3.85
1754 3916 1.610554 TTCCCCTCGTTCGGATCCAC 61.611 60.000 13.41 1.97 0.00 4.02
1760 3922 0.526954 CGTGTATTCCCCTCGTTCGG 60.527 60.000 0.00 0.00 0.00 4.30
1775 3937 1.542547 GGAATCACAAGGACCACGTGT 60.543 52.381 15.65 2.26 42.69 4.49
1776 3938 1.156736 GGAATCACAAGGACCACGTG 58.843 55.000 9.08 9.08 34.52 4.49
1795 3957 6.621737 TTCGCAAATAGTTACAGTCTTACG 57.378 37.500 0.00 0.00 0.00 3.18
1927 4091 7.577979 CGCAGGTCTTTTGTAACTTGTAATTA 58.422 34.615 0.00 0.00 0.00 1.40
1930 4096 5.412526 CGCAGGTCTTTTGTAACTTGTAA 57.587 39.130 0.00 0.00 0.00 2.41
1952 4118 1.262640 TTACTTCCTCACGCCCTCCC 61.263 60.000 0.00 0.00 0.00 4.30
1953 4119 0.175989 CTTACTTCCTCACGCCCTCC 59.824 60.000 0.00 0.00 0.00 4.30
1958 4124 4.254492 AGATTTTCCTTACTTCCTCACGC 58.746 43.478 0.00 0.00 0.00 5.34
1960 4126 7.797062 AGGATAGATTTTCCTTACTTCCTCAC 58.203 38.462 0.00 0.00 40.84 3.51
1962 4128 9.936759 CATAGGATAGATTTTCCTTACTTCCTC 57.063 37.037 0.00 0.00 40.84 3.71
1964 4130 7.608376 GGCATAGGATAGATTTTCCTTACTTCC 59.392 40.741 0.00 0.00 40.84 3.46
1967 4133 7.293535 ACAGGCATAGGATAGATTTTCCTTACT 59.706 37.037 0.00 0.00 40.84 2.24
1969 4135 7.633018 ACAGGCATAGGATAGATTTTCCTTA 57.367 36.000 0.00 0.00 40.84 2.69
1973 4139 7.922811 CCAAAAACAGGCATAGGATAGATTTTC 59.077 37.037 0.00 0.00 0.00 2.29
1978 4144 5.708736 TCCAAAAACAGGCATAGGATAGA 57.291 39.130 0.00 0.00 0.00 1.98
2020 4187 7.482169 TTCTCACAGTGGATAGACAATAACT 57.518 36.000 0.00 0.00 0.00 2.24
2117 4284 2.884012 TGCACAACAACCATCCTTACAG 59.116 45.455 0.00 0.00 0.00 2.74
2183 4350 3.657634 TGCGGCAGAGATTATCATTCTC 58.342 45.455 0.00 0.00 39.96 2.87
2185 4352 4.818534 TTTGCGGCAGAGATTATCATTC 57.181 40.909 1.67 0.00 0.00 2.67
2201 4368 2.671596 CACCTACCCAAACAATTTGCG 58.328 47.619 0.00 0.00 39.31 4.85
2238 4405 7.015680 AGAGATACTTCCACATATGAGGACAT 58.984 38.462 20.10 13.65 40.16 3.06
2250 4417 6.073003 CCAAACAGACAAAGAGATACTTCCAC 60.073 42.308 0.00 0.00 37.93 4.02
2259 4426 5.065914 CCTGATTCCAAACAGACAAAGAGA 58.934 41.667 0.00 0.00 36.38 3.10
2296 4463 5.344743 TTGGGAGTGTAATTTTGCACAAA 57.655 34.783 12.91 0.00 44.73 2.83
2312 4479 1.601419 CCATGCACTTGCCTTGGGAG 61.601 60.000 10.91 0.00 38.74 4.30
2319 4486 0.106521 AAAACCACCATGCACTTGCC 59.893 50.000 0.00 0.00 41.18 4.52
2324 4491 1.336240 GCTGAGAAAACCACCATGCAC 60.336 52.381 0.00 0.00 0.00 4.57
2356 4523 4.665451 AGATGATCCACATTGTCCAAACA 58.335 39.130 0.00 0.00 39.56 2.83
2411 4580 3.043635 GCACACTGCAGAATCAATACG 57.956 47.619 23.35 0.00 44.26 3.06
2449 4620 3.260380 AGCTCTAGCAGACTGAAACACAT 59.740 43.478 6.65 0.00 45.16 3.21
2457 4830 2.098614 TGGAAGAGCTCTAGCAGACTG 58.901 52.381 18.59 0.00 45.16 3.51
2472 4845 7.175641 CACCCTATTTTCAGCCTAATATGGAAG 59.824 40.741 0.00 0.00 30.86 3.46
2511 4884 6.543465 TCCACATTTACCATCTATTGCTTGAG 59.457 38.462 0.00 0.00 0.00 3.02
2550 4923 2.632512 GGCAATCCAAGGTCAAAAAGGA 59.367 45.455 0.00 0.00 0.00 3.36
2570 4943 5.373812 ACCAGACACTAAGGATAAATGGG 57.626 43.478 0.00 0.00 0.00 4.00
2592 4965 5.186021 TGGAACTTTTAACCTTGAAGTGCAA 59.814 36.000 0.00 0.00 34.13 4.08
2675 5048 7.018826 GCAAAACTTTTTGGAAGTACAAAACC 58.981 34.615 14.67 0.00 46.52 3.27
2730 5103 1.882623 CAAGCCCTTCCTGAACTTCAC 59.117 52.381 0.00 0.00 0.00 3.18
2744 5117 3.630312 TGAACAAACTCTACAACAAGCCC 59.370 43.478 0.00 0.00 0.00 5.19
2745 5118 4.893424 TGAACAAACTCTACAACAAGCC 57.107 40.909 0.00 0.00 0.00 4.35
2746 5119 4.735338 GCTTGAACAAACTCTACAACAAGC 59.265 41.667 0.00 0.00 46.88 4.01
2751 5124 5.906113 TTTGGCTTGAACAAACTCTACAA 57.094 34.783 0.00 0.00 33.26 2.41
2753 5126 5.831997 ACATTTGGCTTGAACAAACTCTAC 58.168 37.500 0.00 0.00 40.25 2.59
2763 5136 2.956132 TGGAAGGACATTTGGCTTGAA 58.044 42.857 0.00 0.00 0.00 2.69
2773 5146 9.178758 GTAGACAATTCTATTTTGGAAGGACAT 57.821 33.333 0.00 0.00 36.69 3.06
2775 5148 7.067129 GGGTAGACAATTCTATTTTGGAAGGAC 59.933 40.741 0.00 0.00 36.69 3.85
2787 5160 8.778059 ACAATTGGATTAGGGTAGACAATTCTA 58.222 33.333 10.83 0.00 36.67 2.10
2792 5165 4.947388 GCACAATTGGATTAGGGTAGACAA 59.053 41.667 10.83 0.00 0.00 3.18
2796 5169 6.096705 TCAAATGCACAATTGGATTAGGGTAG 59.903 38.462 10.83 0.00 42.54 3.18
2798 5171 4.776837 TCAAATGCACAATTGGATTAGGGT 59.223 37.500 10.83 0.00 42.54 4.34
2799 5172 5.341872 TCAAATGCACAATTGGATTAGGG 57.658 39.130 10.83 0.00 42.54 3.53
2803 5176 5.820423 CCATGATCAAATGCACAATTGGATT 59.180 36.000 10.83 2.33 45.07 3.01
2821 5194 5.797051 ACTGCACAAATTTAAAGCCATGAT 58.203 33.333 0.00 0.00 0.00 2.45
2826 5199 6.407475 CCATTACTGCACAAATTTAAAGCC 57.593 37.500 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.