Multiple sequence alignment - TraesCS7D01G108500

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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 TraesCS7D01G108500 chr7D 100.000 2588 0 0 1 2588 65389363 65391950 0.000000e+00 4780.0
1 TraesCS7D01G108500 chr7D 76.698 648 72 59 789 1408 64893526 64894122 1.170000e-73 287.0
2 TraesCS7D01G108500 chr7D 78.279 488 67 19 448 909 64911890 64912364 7.050000e-71 278.0
3 TraesCS7D01G108500 chr7D 83.502 297 33 9 1119 1407 64912483 64912771 1.970000e-66 263.0
4 TraesCS7D01G108500 chr7B 88.909 1641 112 28 656 2231 6796504 6798139 0.000000e+00 1958.0
5 TraesCS7D01G108500 chr7B 83.459 1457 101 77 271 1656 6922143 6920756 0.000000e+00 1227.0
6 TraesCS7D01G108500 chr7B 89.264 503 35 6 271 768 6795933 6796421 1.700000e-171 612.0
7 TraesCS7D01G108500 chr7B 79.088 636 68 30 296 906 6782502 6783097 6.760000e-101 377.0
8 TraesCS7D01G108500 chr7B 85.634 355 38 8 1641 1984 6920087 6919735 6.810000e-96 361.0
9 TraesCS7D01G108500 chr7B 76.335 824 99 58 789 1574 6755071 6755836 1.140000e-93 353.0
10 TraesCS7D01G108500 chr7B 89.024 246 21 3 2023 2262 6919735 6919490 1.510000e-77 300.0
11 TraesCS7D01G108500 chr7B 88.525 244 28 0 2338 2581 6919174 6918931 1.950000e-76 296.0
12 TraesCS7D01G108500 chr7B 84.727 275 33 7 4 271 603997404 603997132 1.530000e-67 267.0
13 TraesCS7D01G108500 chr7B 80.456 307 40 13 1731 2019 720785621 720785317 1.560000e-52 217.0
14 TraesCS7D01G108500 chr7B 79.412 272 47 4 1146 1414 6783369 6783634 1.580000e-42 183.0
15 TraesCS7D01G108500 chr7A 83.423 2051 184 90 271 2221 69526020 69528014 0.000000e+00 1760.0
16 TraesCS7D01G108500 chr7A 91.592 785 47 9 656 1421 69363564 69364348 0.000000e+00 1066.0
17 TraesCS7D01G108500 chr7A 89.871 464 22 10 348 797 69363055 69363507 8.030000e-160 573.0
18 TraesCS7D01G108500 chr7A 85.390 308 25 9 1114 1408 69225131 69225431 4.190000e-78 302.0
19 TraesCS7D01G108500 chr7A 78.704 432 59 21 494 909 69309802 69310216 9.190000e-65 257.0
20 TraesCS7D01G108500 chr7A 81.340 209 19 10 1817 2018 146975515 146975320 4.460000e-33 152.0
21 TraesCS7D01G108500 chr7A 74.576 295 49 12 1731 2006 554478402 554478689 3.520000e-19 106.0
22 TraesCS7D01G108500 chr7A 97.826 46 1 0 965 1010 69225007 69225052 2.130000e-11 80.5
23 TraesCS7D01G108500 chr5D 89.377 273 17 8 4 271 282376773 282377038 1.480000e-87 333.0
24 TraesCS7D01G108500 chr5D 85.824 261 25 8 6 260 398360779 398361033 1.530000e-67 267.0
25 TraesCS7D01G108500 chr3D 88.686 274 27 2 2 274 566915274 566915004 5.340000e-87 331.0
26 TraesCS7D01G108500 chr1A 87.004 277 32 2 2 274 592142926 592142650 2.500000e-80 309.0
27 TraesCS7D01G108500 chr2D 86.282 277 26 8 4 273 538776150 538776421 9.060000e-75 291.0
28 TraesCS7D01G108500 chr2D 77.157 394 61 18 1731 2099 229633550 229633939 4.370000e-48 202.0
29 TraesCS7D01G108500 chr2D 83.740 123 14 6 1909 2029 603696658 603696776 7.570000e-21 111.0
30 TraesCS7D01G108500 chr6D 88.655 238 21 4 4 236 458536505 458536741 4.220000e-73 285.0
31 TraesCS7D01G108500 chr5B 85.992 257 32 4 21 274 445235544 445235289 3.280000e-69 272.0
32 TraesCS7D01G108500 chr3A 84.982 273 30 5 4 273 534199349 534199613 1.530000e-67 267.0
33 TraesCS7D01G108500 chr3A 77.389 314 51 15 1732 2028 45775100 45775410 4.430000e-38 169.0
34 TraesCS7D01G108500 chr6B 82.085 307 33 13 1732 2019 538944257 538943954 2.570000e-60 243.0
35 TraesCS7D01G108500 chr6B 75.065 385 63 13 1732 2094 633917742 633917369 5.770000e-32 148.0
36 TraesCS7D01G108500 chr4B 80.696 316 33 18 1733 2028 567385619 567385312 1.210000e-53 220.0
37 TraesCS7D01G108500 chr4A 77.612 402 55 22 1733 2102 54725361 54724963 7.260000e-51 211.0
38 TraesCS7D01G108500 chr5A 79.861 288 41 10 1744 2015 692260922 692261208 7.310000e-46 195.0
39 TraesCS7D01G108500 chr6A 74.448 317 54 19 1734 2033 615224820 615225126 7.570000e-21 111.0
40 TraesCS7D01G108500 chrUn 73.186 317 58 19 1734 2033 186947771 186947465 3.550000e-14 89.8
41 TraesCS7D01G108500 chrUn 73.894 226 42 13 1817 2033 451956426 451956209 9.930000e-10 75.0


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 TraesCS7D01G108500 chr7D 65389363 65391950 2587 False 4780.0 4780 100.0000 1 2588 1 chr7D.!!$F2 2587
1 TraesCS7D01G108500 chr7D 64893526 64894122 596 False 287.0 287 76.6980 789 1408 1 chr7D.!!$F1 619
2 TraesCS7D01G108500 chr7D 64911890 64912771 881 False 270.5 278 80.8905 448 1407 2 chr7D.!!$F3 959
3 TraesCS7D01G108500 chr7B 6795933 6798139 2206 False 1285.0 1958 89.0865 271 2231 2 chr7B.!!$F3 1960
4 TraesCS7D01G108500 chr7B 6918931 6922143 3212 True 546.0 1227 86.6605 271 2581 4 chr7B.!!$R3 2310
5 TraesCS7D01G108500 chr7B 6755071 6755836 765 False 353.0 353 76.3350 789 1574 1 chr7B.!!$F1 785
6 TraesCS7D01G108500 chr7B 6782502 6783634 1132 False 280.0 377 79.2500 296 1414 2 chr7B.!!$F2 1118
7 TraesCS7D01G108500 chr7A 69526020 69528014 1994 False 1760.0 1760 83.4230 271 2221 1 chr7A.!!$F2 1950
8 TraesCS7D01G108500 chr7A 69363055 69364348 1293 False 819.5 1066 90.7315 348 1421 2 chr7A.!!$F5 1073

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
248 249 0.248458 CTTTTTGTGAGGCACGCGTT 60.248 50.0 10.22 0.0 37.14 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 3035 1.292242 TCACCCTCTTAGCATCCTCCT 59.708 52.381 0.0 0.0 0.0 3.69 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
75 76 9.883142 TTTATTTGTGTTTGATCTTCTTGGTTT 57.117 25.926 0.00 0.00 0.00 3.27
76 77 9.883142 TTATTTGTGTTTGATCTTCTTGGTTTT 57.117 25.926 0.00 0.00 0.00 2.43
77 78 7.593875 TTTGTGTTTGATCTTCTTGGTTTTG 57.406 32.000 0.00 0.00 0.00 2.44
78 79 6.279513 TGTGTTTGATCTTCTTGGTTTTGT 57.720 33.333 0.00 0.00 0.00 2.83
79 80 6.696411 TGTGTTTGATCTTCTTGGTTTTGTT 58.304 32.000 0.00 0.00 0.00 2.83
80 81 7.158021 TGTGTTTGATCTTCTTGGTTTTGTTT 58.842 30.769 0.00 0.00 0.00 2.83
81 82 7.117523 TGTGTTTGATCTTCTTGGTTTTGTTTG 59.882 33.333 0.00 0.00 0.00 2.93
82 83 6.593382 TGTTTGATCTTCTTGGTTTTGTTTGG 59.407 34.615 0.00 0.00 0.00 3.28
83 84 6.537453 TTGATCTTCTTGGTTTTGTTTGGA 57.463 33.333 0.00 0.00 0.00 3.53
84 85 6.147864 TGATCTTCTTGGTTTTGTTTGGAG 57.852 37.500 0.00 0.00 0.00 3.86
85 86 5.656416 TGATCTTCTTGGTTTTGTTTGGAGT 59.344 36.000 0.00 0.00 0.00 3.85
86 87 5.323371 TCTTCTTGGTTTTGTTTGGAGTG 57.677 39.130 0.00 0.00 0.00 3.51
87 88 3.518634 TCTTGGTTTTGTTTGGAGTGC 57.481 42.857 0.00 0.00 0.00 4.40
88 89 2.828520 TCTTGGTTTTGTTTGGAGTGCA 59.171 40.909 0.00 0.00 0.00 4.57
89 90 3.450457 TCTTGGTTTTGTTTGGAGTGCAT 59.550 39.130 0.00 0.00 0.00 3.96
90 91 4.646945 TCTTGGTTTTGTTTGGAGTGCATA 59.353 37.500 0.00 0.00 0.00 3.14
91 92 5.304101 TCTTGGTTTTGTTTGGAGTGCATAT 59.696 36.000 0.00 0.00 0.00 1.78
92 93 4.880759 TGGTTTTGTTTGGAGTGCATATG 58.119 39.130 0.00 0.00 0.00 1.78
93 94 4.343526 TGGTTTTGTTTGGAGTGCATATGT 59.656 37.500 4.29 0.00 0.00 2.29
94 95 5.163364 TGGTTTTGTTTGGAGTGCATATGTT 60.163 36.000 4.29 0.00 0.00 2.71
95 96 5.177327 GGTTTTGTTTGGAGTGCATATGTTG 59.823 40.000 4.29 0.00 0.00 3.33
96 97 5.528043 TTTGTTTGGAGTGCATATGTTGT 57.472 34.783 4.29 0.00 0.00 3.32
97 98 5.528043 TTGTTTGGAGTGCATATGTTGTT 57.472 34.783 4.29 0.00 0.00 2.83
98 99 5.528043 TGTTTGGAGTGCATATGTTGTTT 57.472 34.783 4.29 0.00 0.00 2.83
99 100 5.288015 TGTTTGGAGTGCATATGTTGTTTG 58.712 37.500 4.29 0.00 0.00 2.93
100 101 5.163468 TGTTTGGAGTGCATATGTTGTTTGT 60.163 36.000 4.29 0.00 0.00 2.83
101 102 4.502171 TGGAGTGCATATGTTGTTTGTG 57.498 40.909 4.29 0.00 0.00 3.33
102 103 3.244976 GGAGTGCATATGTTGTTTGTGC 58.755 45.455 4.29 0.00 36.39 4.57
103 104 3.057315 GGAGTGCATATGTTGTTTGTGCT 60.057 43.478 4.29 0.00 36.78 4.40
104 105 3.904571 AGTGCATATGTTGTTTGTGCTG 58.095 40.909 4.29 0.00 36.78 4.41
105 106 2.988493 GTGCATATGTTGTTTGTGCTGG 59.012 45.455 4.29 0.00 36.78 4.85
106 107 2.029200 TGCATATGTTGTTTGTGCTGGG 60.029 45.455 4.29 0.00 36.78 4.45
107 108 2.609350 CATATGTTGTTTGTGCTGGGC 58.391 47.619 0.00 0.00 0.00 5.36
108 109 0.595588 TATGTTGTTTGTGCTGGGCG 59.404 50.000 0.00 0.00 0.00 6.13
109 110 2.658268 GTTGTTTGTGCTGGGCGC 60.658 61.111 0.00 0.00 39.75 6.53
110 111 4.263209 TTGTTTGTGCTGGGCGCG 62.263 61.111 0.00 0.00 42.51 6.86
160 161 3.470567 GCTCGCGCGCGCTATATT 61.471 61.111 45.97 0.00 39.59 1.28
161 162 3.000080 GCTCGCGCGCGCTATATTT 62.000 57.895 45.97 0.00 39.59 1.40
162 163 1.487231 CTCGCGCGCGCTATATTTT 59.513 52.632 45.97 0.00 39.59 1.82
163 164 0.782077 CTCGCGCGCGCTATATTTTG 60.782 55.000 45.97 30.36 39.59 2.44
164 165 2.409811 CGCGCGCGCTATATTTTGC 61.410 57.895 45.97 20.58 39.32 3.68
165 166 1.368731 GCGCGCGCTATATTTTGCA 60.369 52.632 44.38 0.00 38.26 4.08
166 167 1.323136 GCGCGCGCTATATTTTGCAG 61.323 55.000 44.38 9.78 38.26 4.41
167 168 1.323136 CGCGCGCTATATTTTGCAGC 61.323 55.000 30.48 0.00 0.00 5.25
171 172 3.479255 GCTATATTTTGCAGCGGCC 57.521 52.632 6.32 0.00 40.13 6.13
172 173 0.385974 GCTATATTTTGCAGCGGCCG 60.386 55.000 24.05 24.05 40.13 6.13
173 174 0.385974 CTATATTTTGCAGCGGCCGC 60.386 55.000 42.34 42.34 40.13 6.53
190 191 2.436292 CTGGAGCCAGCACTCAGC 60.436 66.667 3.18 0.00 46.19 4.26
200 201 4.016629 CACTCAGCTGCGCGCAAA 62.017 61.111 35.50 18.84 42.61 3.68
201 202 3.279116 ACTCAGCTGCGCGCAAAA 61.279 55.556 35.50 18.48 42.61 2.44
202 203 2.051076 CTCAGCTGCGCGCAAAAA 60.051 55.556 35.50 18.84 42.61 1.94
203 204 2.353376 TCAGCTGCGCGCAAAAAC 60.353 55.556 35.50 23.13 42.61 2.43
204 205 2.353839 CAGCTGCGCGCAAAAACT 60.354 55.556 35.50 24.94 42.61 2.66
205 206 2.353839 AGCTGCGCGCAAAAACTG 60.354 55.556 35.50 22.66 42.61 3.16
206 207 3.397317 GCTGCGCGCAAAAACTGG 61.397 61.111 35.50 21.89 38.92 4.00
207 208 3.397317 CTGCGCGCAAAAACTGGC 61.397 61.111 35.50 0.00 0.00 4.85
208 209 3.829272 CTGCGCGCAAAAACTGGCT 62.829 57.895 35.50 0.00 0.00 4.75
209 210 2.254051 GCGCGCAAAAACTGGCTA 59.746 55.556 29.10 0.00 0.00 3.93
210 211 1.154035 GCGCGCAAAAACTGGCTAT 60.154 52.632 29.10 0.00 0.00 2.97
211 212 0.732538 GCGCGCAAAAACTGGCTATT 60.733 50.000 29.10 0.00 0.00 1.73
212 213 1.696988 CGCGCAAAAACTGGCTATTT 58.303 45.000 8.75 0.00 0.00 1.40
213 214 1.648681 CGCGCAAAAACTGGCTATTTC 59.351 47.619 8.75 0.00 0.00 2.17
214 215 2.671596 GCGCAAAAACTGGCTATTTCA 58.328 42.857 0.30 0.00 0.00 2.69
215 216 3.056304 GCGCAAAAACTGGCTATTTCAA 58.944 40.909 0.30 0.00 0.00 2.69
216 217 3.121025 GCGCAAAAACTGGCTATTTCAAC 60.121 43.478 0.30 0.00 0.00 3.18
217 218 3.119463 CGCAAAAACTGGCTATTTCAACG 59.881 43.478 0.00 0.00 0.00 4.10
218 219 3.121025 GCAAAAACTGGCTATTTCAACGC 60.121 43.478 0.00 0.00 0.00 4.84
219 220 4.298332 CAAAAACTGGCTATTTCAACGCT 58.702 39.130 0.00 0.00 0.00 5.07
220 221 5.457140 CAAAAACTGGCTATTTCAACGCTA 58.543 37.500 0.00 0.00 0.00 4.26
221 222 5.897377 AAAACTGGCTATTTCAACGCTAT 57.103 34.783 0.00 0.00 0.00 2.97
222 223 6.995511 AAAACTGGCTATTTCAACGCTATA 57.004 33.333 0.00 0.00 0.00 1.31
223 224 6.995511 AAACTGGCTATTTCAACGCTATAA 57.004 33.333 0.00 0.00 0.00 0.98
224 225 6.995511 AACTGGCTATTTCAACGCTATAAA 57.004 33.333 0.00 0.00 0.00 1.40
225 226 6.604735 ACTGGCTATTTCAACGCTATAAAG 57.395 37.500 0.00 0.00 0.00 1.85
226 227 6.346096 ACTGGCTATTTCAACGCTATAAAGA 58.654 36.000 0.00 0.00 0.00 2.52
227 228 6.258068 ACTGGCTATTTCAACGCTATAAAGAC 59.742 38.462 0.00 0.00 0.00 3.01
228 229 5.233476 TGGCTATTTCAACGCTATAAAGACG 59.767 40.000 0.00 0.00 0.00 4.18
229 230 5.131204 GCTATTTCAACGCTATAAAGACGC 58.869 41.667 0.00 0.00 0.00 5.19
230 231 5.050972 GCTATTTCAACGCTATAAAGACGCT 60.051 40.000 0.00 0.00 0.00 5.07
231 232 5.796350 ATTTCAACGCTATAAAGACGCTT 57.204 34.783 0.00 0.00 0.00 4.68
232 233 5.600908 TTTCAACGCTATAAAGACGCTTT 57.399 34.783 9.27 9.27 0.00 3.51
233 234 5.600908 TTCAACGCTATAAAGACGCTTTT 57.399 34.783 9.53 0.77 0.00 2.27
234 235 5.600908 TCAACGCTATAAAGACGCTTTTT 57.399 34.783 9.53 5.64 0.00 1.94
235 236 5.379003 TCAACGCTATAAAGACGCTTTTTG 58.621 37.500 9.53 7.57 0.00 2.44
236 237 5.049954 TCAACGCTATAAAGACGCTTTTTGT 60.050 36.000 9.53 0.00 0.00 2.83
237 238 4.708601 ACGCTATAAAGACGCTTTTTGTG 58.291 39.130 9.53 9.14 0.00 3.33
238 239 4.449743 ACGCTATAAAGACGCTTTTTGTGA 59.550 37.500 9.53 0.00 0.00 3.58
239 240 5.015733 CGCTATAAAGACGCTTTTTGTGAG 58.984 41.667 9.53 3.65 0.00 3.51
240 241 5.324697 GCTATAAAGACGCTTTTTGTGAGG 58.675 41.667 9.53 0.00 0.00 3.86
241 242 2.492019 AAAGACGCTTTTTGTGAGGC 57.508 45.000 0.00 0.00 0.00 4.70
242 243 1.388547 AAGACGCTTTTTGTGAGGCA 58.611 45.000 0.00 0.00 0.00 4.75
243 244 0.663153 AGACGCTTTTTGTGAGGCAC 59.337 50.000 0.00 0.00 34.56 5.01
244 245 0.657368 GACGCTTTTTGTGAGGCACG 60.657 55.000 0.00 0.00 37.14 5.34
245 246 2.010817 CGCTTTTTGTGAGGCACGC 61.011 57.895 0.00 0.00 37.14 5.34
246 247 2.010817 GCTTTTTGTGAGGCACGCG 61.011 57.895 3.53 3.53 37.14 6.01
247 248 1.355210 CTTTTTGTGAGGCACGCGT 59.645 52.632 5.58 5.58 37.14 6.01
248 249 0.248458 CTTTTTGTGAGGCACGCGTT 60.248 50.000 10.22 0.00 37.14 4.84
249 250 0.524392 TTTTTGTGAGGCACGCGTTG 60.524 50.000 10.22 6.68 37.14 4.10
262 263 3.276091 CGTTGCACGCCTGTTGGA 61.276 61.111 0.00 0.00 33.65 3.53
263 264 2.639286 GTTGCACGCCTGTTGGAG 59.361 61.111 0.00 0.00 39.17 3.86
264 265 1.891919 GTTGCACGCCTGTTGGAGA 60.892 57.895 0.00 0.00 36.60 3.71
265 266 1.073025 TTGCACGCCTGTTGGAGAT 59.927 52.632 0.00 0.00 36.60 2.75
266 267 1.236616 TTGCACGCCTGTTGGAGATG 61.237 55.000 0.00 0.00 36.60 2.90
267 268 3.044059 GCACGCCTGTTGGAGATGC 62.044 63.158 0.00 0.00 36.60 3.91
268 269 1.376424 CACGCCTGTTGGAGATGCT 60.376 57.895 0.00 0.00 36.60 3.79
269 270 1.078848 ACGCCTGTTGGAGATGCTC 60.079 57.895 0.00 0.00 36.60 4.26
285 286 1.280710 TGCTCTTAGGCGAATGGGAAA 59.719 47.619 0.00 0.00 34.52 3.13
293 295 1.168714 GCGAATGGGAAACTCTTGCT 58.831 50.000 0.00 0.00 0.00 3.91
487 526 1.492764 ATCCGGGTGAAGATTACGGT 58.507 50.000 0.00 0.00 44.54 4.83
490 529 0.461339 CGGGTGAAGATTACGGTGGG 60.461 60.000 0.00 0.00 0.00 4.61
561 605 7.439381 GGATTTAATTGCTCATGTCATTCCAT 58.561 34.615 0.00 0.00 0.00 3.41
569 613 4.267536 CTCATGTCATTCCATTGGTGACT 58.732 43.478 20.86 9.07 42.03 3.41
570 614 4.264253 TCATGTCATTCCATTGGTGACTC 58.736 43.478 20.86 3.56 42.03 3.36
571 615 4.019051 TCATGTCATTCCATTGGTGACTCT 60.019 41.667 20.86 10.30 42.03 3.24
625 677 3.916761 ACAATGTCAAACATGCATGGAC 58.083 40.909 29.41 24.65 37.97 4.02
633 685 1.453155 ACATGCATGGACGTCTTTCC 58.547 50.000 29.41 0.00 36.03 3.13
717 800 2.169832 GCCAAAGAAAAGAAAGGCCC 57.830 50.000 0.00 0.00 36.17 5.80
724 807 3.402628 GAAAAGAAAGGCCCCTTTTCC 57.597 47.619 27.97 17.90 46.04 3.13
745 829 1.139163 CGTCCAACTTGCCAATTTGC 58.861 50.000 2.23 0.00 0.00 3.68
773 870 8.804912 TTGCAACATGGCATATGTATATATGA 57.195 30.769 20.21 4.00 45.92 2.15
774 871 8.983702 TGCAACATGGCATATGTATATATGAT 57.016 30.769 20.21 5.92 45.92 2.45
775 872 8.842280 TGCAACATGGCATATGTATATATGATG 58.158 33.333 20.21 16.96 45.92 3.07
776 873 9.059260 GCAACATGGCATATGTATATATGATGA 57.941 33.333 20.21 6.00 45.92 2.92
793 890 1.077787 GATGATCACACCGGGCCAA 60.078 57.895 6.32 0.00 0.00 4.52
864 1204 3.590443 CTCGTCGCTGGTTCGTCGT 62.590 63.158 0.00 0.00 40.63 4.34
1052 1419 1.065600 CTAGTGAGAGCTGCGAGGC 59.934 63.158 0.00 0.00 0.00 4.70
1282 1771 2.125310 CAATGCCGCCACCGTCTA 60.125 61.111 0.00 0.00 0.00 2.59
1499 2004 3.532542 GGTGGTAAGTTGGCATCTACTC 58.467 50.000 0.00 0.00 0.00 2.59
1500 2005 3.532542 GTGGTAAGTTGGCATCTACTCC 58.467 50.000 0.00 3.21 0.00 3.85
1521 2042 7.480810 ACTCCGCCAAGAAAAATTATATGTTC 58.519 34.615 0.00 0.00 0.00 3.18
1542 2064 6.183360 TGTTCCTCAAACATGAGTTTTGTACC 60.183 38.462 0.00 0.00 45.32 3.34
1582 2107 6.123651 ACGCAAGGGAAATAAATGGTATGTA 58.876 36.000 0.00 0.00 46.39 2.29
1691 2904 2.223021 CGTGCATTAATCCACCGTTGAG 60.223 50.000 3.91 0.00 0.00 3.02
1698 2913 1.593196 ATCCACCGTTGAGTGTGTTG 58.407 50.000 0.00 0.00 35.93 3.33
1786 3015 7.616313 AGAAAACTTTGTGGAAACCATGTTTA 58.384 30.769 0.00 0.00 35.28 2.01
1841 3078 2.308570 AGGGTGATGTTCTATTGGCACA 59.691 45.455 0.00 0.00 0.00 4.57
1880 3117 5.545658 AACACATTACCATTTACGAGCTG 57.454 39.130 0.00 0.00 0.00 4.24
1996 3238 7.362662 TGAACTTGAGAATTTCACATGCTAAC 58.637 34.615 8.84 1.90 34.94 2.34
1998 3240 6.672147 ACTTGAGAATTTCACATGCTAACAC 58.328 36.000 8.84 0.00 34.94 3.32
2020 3262 5.062683 CACAACATCACACTCTTAAGATCCG 59.937 44.000 5.44 0.00 0.00 4.18
2043 3287 7.982354 TCCGGTATTTTTGTGAAACTTCAAAAT 59.018 29.630 0.00 2.01 41.17 1.82
2062 3307 6.748198 TCAAAATACTGTTTTCACGTGGTTTC 59.252 34.615 17.00 5.33 0.00 2.78
2064 3309 1.399089 ACTGTTTTCACGTGGTTTCCG 59.601 47.619 17.00 3.59 0.00 4.30
2113 3362 8.506168 TCCATGTGTATCTCAAGATTAAAACC 57.494 34.615 0.00 0.00 36.05 3.27
2169 3419 9.907229 AAGAAAACCCCTGATAAAGTAGATAAG 57.093 33.333 0.00 0.00 0.00 1.73
2199 3449 6.241207 ACGAGTATGATCTTGTTTTGTTGG 57.759 37.500 0.00 0.00 0.00 3.77
2262 3512 8.964772 AGATGTATCCTTCCTTCAAATTTCTTG 58.035 33.333 0.00 0.00 0.00 3.02
2263 3513 8.884124 ATGTATCCTTCCTTCAAATTTCTTGA 57.116 30.769 0.00 0.00 0.00 3.02
2264 3514 8.884124 TGTATCCTTCCTTCAAATTTCTTGAT 57.116 30.769 0.00 0.00 0.00 2.57
2265 3515 9.312904 TGTATCCTTCCTTCAAATTTCTTGATT 57.687 29.630 0.00 0.00 0.00 2.57
2266 3516 9.578439 GTATCCTTCCTTCAAATTTCTTGATTG 57.422 33.333 0.00 0.00 0.00 2.67
2267 3517 7.601705 TCCTTCCTTCAAATTTCTTGATTGT 57.398 32.000 0.00 0.00 0.00 2.71
2268 3518 8.021898 TCCTTCCTTCAAATTTCTTGATTGTT 57.978 30.769 0.00 0.00 0.00 2.83
2269 3519 7.927629 TCCTTCCTTCAAATTTCTTGATTGTTG 59.072 33.333 0.00 0.00 0.00 3.33
2270 3520 7.172019 CCTTCCTTCAAATTTCTTGATTGTTGG 59.828 37.037 0.00 0.00 0.00 3.77
2271 3521 6.523840 TCCTTCAAATTTCTTGATTGTTGGG 58.476 36.000 0.00 0.00 0.00 4.12
2272 3522 5.179929 CCTTCAAATTTCTTGATTGTTGGGC 59.820 40.000 0.00 0.00 0.00 5.36
2273 3523 4.640364 TCAAATTTCTTGATTGTTGGGCC 58.360 39.130 0.00 0.00 0.00 5.80
2274 3524 4.102210 TCAAATTTCTTGATTGTTGGGCCA 59.898 37.500 0.00 0.00 0.00 5.36
2275 3525 3.967332 ATTTCTTGATTGTTGGGCCAG 57.033 42.857 6.23 0.00 0.00 4.85
2276 3526 0.968405 TTCTTGATTGTTGGGCCAGC 59.032 50.000 14.14 14.14 0.00 4.85
2277 3527 1.213537 CTTGATTGTTGGGCCAGCG 59.786 57.895 15.95 0.00 0.00 5.18
2278 3528 2.824071 CTTGATTGTTGGGCCAGCGC 62.824 60.000 15.95 0.00 0.00 5.92
2279 3529 3.064324 GATTGTTGGGCCAGCGCT 61.064 61.111 15.95 2.64 34.44 5.92
2280 3530 2.601367 ATTGTTGGGCCAGCGCTT 60.601 55.556 7.50 0.00 34.44 4.68
2281 3531 2.824071 GATTGTTGGGCCAGCGCTTG 62.824 60.000 7.50 5.33 34.44 4.01
2282 3532 4.892965 TGTTGGGCCAGCGCTTGT 62.893 61.111 7.50 0.00 34.44 3.16
2283 3533 3.605664 GTTGGGCCAGCGCTTGTT 61.606 61.111 7.50 0.00 34.44 2.83
2284 3534 3.604667 TTGGGCCAGCGCTTGTTG 61.605 61.111 7.50 0.00 34.44 3.33
2294 3544 2.964978 GCTTGTTGGCGGCTCATT 59.035 55.556 11.43 0.00 0.00 2.57
2295 3545 1.290009 GCTTGTTGGCGGCTCATTT 59.710 52.632 11.43 0.00 0.00 2.32
2296 3546 1.010419 GCTTGTTGGCGGCTCATTTG 61.010 55.000 11.43 4.91 0.00 2.32
2297 3547 0.314935 CTTGTTGGCGGCTCATTTGT 59.685 50.000 11.43 0.00 0.00 2.83
2298 3548 0.313672 TTGTTGGCGGCTCATTTGTC 59.686 50.000 11.43 0.00 0.00 3.18
2299 3549 1.154225 GTTGGCGGCTCATTTGTCG 60.154 57.895 11.43 0.00 0.00 4.35
2300 3550 1.302112 TTGGCGGCTCATTTGTCGA 60.302 52.632 11.43 0.00 0.00 4.20
2301 3551 0.886938 TTGGCGGCTCATTTGTCGAA 60.887 50.000 11.43 0.00 0.00 3.71
2302 3552 0.886938 TGGCGGCTCATTTGTCGAAA 60.887 50.000 11.43 0.00 0.00 3.46
2303 3553 0.179189 GGCGGCTCATTTGTCGAAAG 60.179 55.000 0.00 0.00 0.00 2.62
2304 3554 0.179189 GCGGCTCATTTGTCGAAAGG 60.179 55.000 0.00 0.00 0.00 3.11
2305 3555 1.156736 CGGCTCATTTGTCGAAAGGT 58.843 50.000 0.00 0.00 0.00 3.50
2306 3556 1.135972 CGGCTCATTTGTCGAAAGGTG 60.136 52.381 0.00 0.00 0.00 4.00
2307 3557 2.151202 GGCTCATTTGTCGAAAGGTGA 58.849 47.619 0.00 0.00 0.00 4.02
2308 3558 2.552315 GGCTCATTTGTCGAAAGGTGAA 59.448 45.455 0.00 0.00 0.00 3.18
2309 3559 3.365364 GGCTCATTTGTCGAAAGGTGAAG 60.365 47.826 0.00 0.00 0.00 3.02
2310 3560 3.365364 GCTCATTTGTCGAAAGGTGAAGG 60.365 47.826 0.00 0.00 0.00 3.46
2311 3561 3.146066 TCATTTGTCGAAAGGTGAAGGG 58.854 45.455 0.00 0.00 0.00 3.95
2312 3562 1.975660 TTTGTCGAAAGGTGAAGGGG 58.024 50.000 0.00 0.00 0.00 4.79
2313 3563 0.536460 TTGTCGAAAGGTGAAGGGGC 60.536 55.000 0.00 0.00 0.00 5.80
2314 3564 2.033194 GTCGAAAGGTGAAGGGGCG 61.033 63.158 0.00 0.00 0.00 6.13
2315 3565 2.211410 TCGAAAGGTGAAGGGGCGA 61.211 57.895 0.00 0.00 0.00 5.54
2316 3566 1.741770 CGAAAGGTGAAGGGGCGAG 60.742 63.158 0.00 0.00 0.00 5.03
2317 3567 1.377333 GAAAGGTGAAGGGGCGAGG 60.377 63.158 0.00 0.00 0.00 4.63
2318 3568 2.821679 GAAAGGTGAAGGGGCGAGGG 62.822 65.000 0.00 0.00 0.00 4.30
2319 3569 4.658786 AGGTGAAGGGGCGAGGGT 62.659 66.667 0.00 0.00 0.00 4.34
2320 3570 2.686106 GGTGAAGGGGCGAGGGTA 60.686 66.667 0.00 0.00 0.00 3.69
2321 3571 2.295602 GGTGAAGGGGCGAGGGTAA 61.296 63.158 0.00 0.00 0.00 2.85
2322 3572 1.221021 GTGAAGGGGCGAGGGTAAG 59.779 63.158 0.00 0.00 0.00 2.34
2323 3573 1.079621 TGAAGGGGCGAGGGTAAGA 59.920 57.895 0.00 0.00 0.00 2.10
2324 3574 0.545787 TGAAGGGGCGAGGGTAAGAA 60.546 55.000 0.00 0.00 0.00 2.52
2325 3575 0.616891 GAAGGGGCGAGGGTAAGAAA 59.383 55.000 0.00 0.00 0.00 2.52
2326 3576 1.003928 GAAGGGGCGAGGGTAAGAAAA 59.996 52.381 0.00 0.00 0.00 2.29
2327 3577 0.618981 AGGGGCGAGGGTAAGAAAAG 59.381 55.000 0.00 0.00 0.00 2.27
2328 3578 0.616891 GGGGCGAGGGTAAGAAAAGA 59.383 55.000 0.00 0.00 0.00 2.52
2329 3579 1.003928 GGGGCGAGGGTAAGAAAAGAA 59.996 52.381 0.00 0.00 0.00 2.52
2330 3580 2.553685 GGGGCGAGGGTAAGAAAAGAAA 60.554 50.000 0.00 0.00 0.00 2.52
2331 3581 2.747989 GGGCGAGGGTAAGAAAAGAAAG 59.252 50.000 0.00 0.00 0.00 2.62
2332 3582 2.161808 GGCGAGGGTAAGAAAAGAAAGC 59.838 50.000 0.00 0.00 0.00 3.51
2333 3583 3.075148 GCGAGGGTAAGAAAAGAAAGCT 58.925 45.455 0.00 0.00 0.00 3.74
2334 3584 4.251268 GCGAGGGTAAGAAAAGAAAGCTA 58.749 43.478 0.00 0.00 0.00 3.32
2335 3585 4.876679 GCGAGGGTAAGAAAAGAAAGCTAT 59.123 41.667 0.00 0.00 0.00 2.97
2336 3586 5.220681 GCGAGGGTAAGAAAAGAAAGCTATG 60.221 44.000 0.00 0.00 0.00 2.23
2351 3841 3.743521 AGCTATGCTTGTCTTTGACACA 58.256 40.909 0.00 0.00 42.60 3.72
2353 3843 4.763793 AGCTATGCTTGTCTTTGACACAAT 59.236 37.500 0.00 0.00 42.60 2.71
2356 3846 4.717233 TGCTTGTCTTTGACACAATTGT 57.283 36.364 4.92 4.92 42.60 2.71
2363 3853 4.032786 GTCTTTGACACAATTGTTGGTTGC 59.967 41.667 8.77 0.00 35.47 4.17
2364 3854 3.883830 TTGACACAATTGTTGGTTGCT 57.116 38.095 8.77 0.00 35.47 3.91
2380 3870 2.275880 GCTGACAGCAGAGAGACCT 58.724 57.895 22.62 0.00 45.17 3.85
2399 3889 5.185056 AGACCTAGAGAAGTGAAAGAGAAGC 59.815 44.000 0.00 0.00 0.00 3.86
2414 3904 7.601886 TGAAAGAGAAGCAGAAATAAGACTCTG 59.398 37.037 0.00 0.00 41.71 3.35
2417 3907 5.729510 AGAAGCAGAAATAAGACTCTGACC 58.270 41.667 3.32 0.00 41.38 4.02
2431 3921 2.663602 CTCTGACCAGAAACGTGATTCG 59.336 50.000 1.08 0.00 40.26 3.34
2433 3923 3.253921 TCTGACCAGAAACGTGATTCGTA 59.746 43.478 0.00 0.00 41.95 3.43
2444 3934 2.268298 GTGATTCGTAACGGCAGACAT 58.732 47.619 0.00 0.00 0.00 3.06
2447 3937 0.604073 TTCGTAACGGCAGACATGGA 59.396 50.000 0.00 0.00 0.00 3.41
2479 3969 1.939934 CAGGAAACAAGTTCGAGTGCA 59.060 47.619 0.00 0.00 37.08 4.57
2481 3971 1.334149 GGAAACAAGTTCGAGTGCAGC 60.334 52.381 0.00 0.00 37.08 5.25
2501 3991 2.501881 CGTGGTTTATGTTTGCGCTAC 58.498 47.619 9.73 7.68 0.00 3.58
2555 4045 3.679980 GTGATACATATGTGTGATCGCCC 59.320 47.826 18.81 0.00 39.39 6.13
2562 4052 1.218047 GTGTGATCGCCCACTAGCA 59.782 57.895 3.31 0.00 37.89 3.49
2573 4063 2.094675 CCCACTAGCATTCAAGTTGGG 58.905 52.381 2.34 0.00 31.91 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.883142 AAACCAAGAAGATCAAACACAAATAAA 57.117 25.926 0.00 0.00 0.00 1.40
50 51 9.883142 AAAACCAAGAAGATCAAACACAAATAA 57.117 25.926 0.00 0.00 0.00 1.40
51 52 9.311916 CAAAACCAAGAAGATCAAACACAAATA 57.688 29.630 0.00 0.00 0.00 1.40
52 53 7.823799 ACAAAACCAAGAAGATCAAACACAAAT 59.176 29.630 0.00 0.00 0.00 2.32
53 54 7.158021 ACAAAACCAAGAAGATCAAACACAAA 58.842 30.769 0.00 0.00 0.00 2.83
54 55 6.696411 ACAAAACCAAGAAGATCAAACACAA 58.304 32.000 0.00 0.00 0.00 3.33
55 56 6.279513 ACAAAACCAAGAAGATCAAACACA 57.720 33.333 0.00 0.00 0.00 3.72
56 57 7.412891 CCAAACAAAACCAAGAAGATCAAACAC 60.413 37.037 0.00 0.00 0.00 3.32
57 58 6.593382 CCAAACAAAACCAAGAAGATCAAACA 59.407 34.615 0.00 0.00 0.00 2.83
58 59 6.816140 TCCAAACAAAACCAAGAAGATCAAAC 59.184 34.615 0.00 0.00 0.00 2.93
59 60 6.940739 TCCAAACAAAACCAAGAAGATCAAA 58.059 32.000 0.00 0.00 0.00 2.69
60 61 6.154363 ACTCCAAACAAAACCAAGAAGATCAA 59.846 34.615 0.00 0.00 0.00 2.57
61 62 5.656416 ACTCCAAACAAAACCAAGAAGATCA 59.344 36.000 0.00 0.00 0.00 2.92
62 63 5.979517 CACTCCAAACAAAACCAAGAAGATC 59.020 40.000 0.00 0.00 0.00 2.75
63 64 5.682212 GCACTCCAAACAAAACCAAGAAGAT 60.682 40.000 0.00 0.00 0.00 2.40
64 65 4.381505 GCACTCCAAACAAAACCAAGAAGA 60.382 41.667 0.00 0.00 0.00 2.87
65 66 3.865164 GCACTCCAAACAAAACCAAGAAG 59.135 43.478 0.00 0.00 0.00 2.85
66 67 3.259374 TGCACTCCAAACAAAACCAAGAA 59.741 39.130 0.00 0.00 0.00 2.52
67 68 2.828520 TGCACTCCAAACAAAACCAAGA 59.171 40.909 0.00 0.00 0.00 3.02
68 69 3.244033 TGCACTCCAAACAAAACCAAG 57.756 42.857 0.00 0.00 0.00 3.61
69 70 3.902881 ATGCACTCCAAACAAAACCAA 57.097 38.095 0.00 0.00 0.00 3.67
70 71 4.343526 ACATATGCACTCCAAACAAAACCA 59.656 37.500 1.58 0.00 0.00 3.67
71 72 4.881920 ACATATGCACTCCAAACAAAACC 58.118 39.130 1.58 0.00 0.00 3.27
72 73 5.752955 ACAACATATGCACTCCAAACAAAAC 59.247 36.000 1.58 0.00 0.00 2.43
73 74 5.911752 ACAACATATGCACTCCAAACAAAA 58.088 33.333 1.58 0.00 0.00 2.44
74 75 5.528043 ACAACATATGCACTCCAAACAAA 57.472 34.783 1.58 0.00 0.00 2.83
75 76 5.528043 AACAACATATGCACTCCAAACAA 57.472 34.783 1.58 0.00 0.00 2.83
76 77 5.163468 ACAAACAACATATGCACTCCAAACA 60.163 36.000 1.58 0.00 0.00 2.83
77 78 5.175491 CACAAACAACATATGCACTCCAAAC 59.825 40.000 1.58 0.00 0.00 2.93
78 79 5.288015 CACAAACAACATATGCACTCCAAA 58.712 37.500 1.58 0.00 0.00 3.28
79 80 4.795635 GCACAAACAACATATGCACTCCAA 60.796 41.667 1.58 0.00 36.30 3.53
80 81 3.305267 GCACAAACAACATATGCACTCCA 60.305 43.478 1.58 0.00 36.30 3.86
81 82 3.057315 AGCACAAACAACATATGCACTCC 60.057 43.478 1.58 0.00 38.79 3.85
82 83 3.916172 CAGCACAAACAACATATGCACTC 59.084 43.478 1.58 0.00 38.79 3.51
83 84 3.305539 CCAGCACAAACAACATATGCACT 60.306 43.478 1.58 0.00 38.79 4.40
84 85 2.988493 CCAGCACAAACAACATATGCAC 59.012 45.455 1.58 0.00 38.79 4.57
85 86 2.029200 CCCAGCACAAACAACATATGCA 60.029 45.455 1.58 0.00 38.79 3.96
86 87 2.609350 CCCAGCACAAACAACATATGC 58.391 47.619 1.58 0.00 36.52 3.14
87 88 2.609350 GCCCAGCACAAACAACATATG 58.391 47.619 0.00 0.00 0.00 1.78
88 89 1.202114 CGCCCAGCACAAACAACATAT 59.798 47.619 0.00 0.00 0.00 1.78
89 90 0.595588 CGCCCAGCACAAACAACATA 59.404 50.000 0.00 0.00 0.00 2.29
90 91 1.363443 CGCCCAGCACAAACAACAT 59.637 52.632 0.00 0.00 0.00 2.71
91 92 2.804167 CGCCCAGCACAAACAACA 59.196 55.556 0.00 0.00 0.00 3.33
147 148 1.323136 CTGCAAAATATAGCGCGCGC 61.323 55.000 45.10 45.10 42.33 6.86
148 149 1.323136 GCTGCAAAATATAGCGCGCG 61.323 55.000 28.44 28.44 0.00 6.86
149 150 2.413924 GCTGCAAAATATAGCGCGC 58.586 52.632 26.66 26.66 0.00 6.86
153 154 0.385974 CGGCCGCTGCAAAATATAGC 60.386 55.000 14.67 0.00 40.13 2.97
154 155 0.385974 GCGGCCGCTGCAAAATATAG 60.386 55.000 41.71 0.75 40.13 1.31
155 156 1.652012 GCGGCCGCTGCAAAATATA 59.348 52.632 41.71 0.00 40.13 0.86
156 157 2.412937 GCGGCCGCTGCAAAATAT 59.587 55.556 41.71 0.00 40.13 1.28
173 174 2.436292 GCTGAGTGCTGGCTCCAG 60.436 66.667 11.47 11.47 46.15 3.86
190 191 2.456594 TAGCCAGTTTTTGCGCGCAG 62.457 55.000 34.25 21.27 0.00 5.18
191 192 1.861542 ATAGCCAGTTTTTGCGCGCA 61.862 50.000 33.09 33.09 0.00 6.09
192 193 0.732538 AATAGCCAGTTTTTGCGCGC 60.733 50.000 27.26 27.26 0.00 6.86
193 194 1.648681 GAAATAGCCAGTTTTTGCGCG 59.351 47.619 0.00 0.00 0.00 6.86
194 195 2.671596 TGAAATAGCCAGTTTTTGCGC 58.328 42.857 0.00 0.00 0.00 6.09
195 196 3.119463 CGTTGAAATAGCCAGTTTTTGCG 59.881 43.478 0.00 0.00 0.00 4.85
196 197 3.121025 GCGTTGAAATAGCCAGTTTTTGC 60.121 43.478 0.00 0.00 0.00 3.68
197 198 4.298332 AGCGTTGAAATAGCCAGTTTTTG 58.702 39.130 0.00 0.00 0.00 2.44
198 199 4.584327 AGCGTTGAAATAGCCAGTTTTT 57.416 36.364 0.00 0.00 0.00 1.94
199 200 5.897377 ATAGCGTTGAAATAGCCAGTTTT 57.103 34.783 0.00 0.00 0.00 2.43
200 201 6.995511 TTATAGCGTTGAAATAGCCAGTTT 57.004 33.333 0.00 0.00 0.00 2.66
201 202 6.821665 TCTTTATAGCGTTGAAATAGCCAGTT 59.178 34.615 0.00 0.00 0.00 3.16
202 203 6.258068 GTCTTTATAGCGTTGAAATAGCCAGT 59.742 38.462 0.00 0.00 0.00 4.00
203 204 6.562270 CGTCTTTATAGCGTTGAAATAGCCAG 60.562 42.308 0.00 0.00 0.00 4.85
204 205 5.233476 CGTCTTTATAGCGTTGAAATAGCCA 59.767 40.000 0.00 0.00 0.00 4.75
205 206 5.667175 CGTCTTTATAGCGTTGAAATAGCC 58.333 41.667 0.00 0.00 0.00 3.93
206 207 5.050972 AGCGTCTTTATAGCGTTGAAATAGC 60.051 40.000 0.00 0.00 35.78 2.97
207 208 6.512177 AGCGTCTTTATAGCGTTGAAATAG 57.488 37.500 0.00 0.00 35.78 1.73
208 209 6.897259 AAGCGTCTTTATAGCGTTGAAATA 57.103 33.333 0.00 0.00 35.78 1.40
209 210 5.796350 AAGCGTCTTTATAGCGTTGAAAT 57.204 34.783 0.00 0.00 35.78 2.17
210 211 5.600908 AAAGCGTCTTTATAGCGTTGAAA 57.399 34.783 3.48 0.00 31.93 2.69
211 212 5.600908 AAAAGCGTCTTTATAGCGTTGAA 57.399 34.783 5.47 0.00 33.31 2.69
212 213 5.049954 ACAAAAAGCGTCTTTATAGCGTTGA 60.050 36.000 13.82 0.00 33.31 3.18
213 214 5.058008 CACAAAAAGCGTCTTTATAGCGTTG 59.942 40.000 5.47 7.53 33.31 4.10
214 215 5.049954 TCACAAAAAGCGTCTTTATAGCGTT 60.050 36.000 5.47 0.00 34.34 4.84
215 216 4.449743 TCACAAAAAGCGTCTTTATAGCGT 59.550 37.500 5.47 0.00 35.78 5.07
216 217 4.953269 TCACAAAAAGCGTCTTTATAGCG 58.047 39.130 5.47 0.00 35.78 4.26
217 218 5.324697 CCTCACAAAAAGCGTCTTTATAGC 58.675 41.667 5.47 0.00 0.00 2.97
218 219 5.106712 TGCCTCACAAAAAGCGTCTTTATAG 60.107 40.000 5.47 2.69 0.00 1.31
219 220 4.757657 TGCCTCACAAAAAGCGTCTTTATA 59.242 37.500 5.47 0.00 0.00 0.98
220 221 3.568007 TGCCTCACAAAAAGCGTCTTTAT 59.432 39.130 5.47 0.00 0.00 1.40
221 222 2.946329 TGCCTCACAAAAAGCGTCTTTA 59.054 40.909 5.47 0.00 0.00 1.85
222 223 1.748493 TGCCTCACAAAAAGCGTCTTT 59.252 42.857 0.00 0.00 0.00 2.52
223 224 1.065551 GTGCCTCACAAAAAGCGTCTT 59.934 47.619 0.00 0.00 34.08 3.01
224 225 0.663153 GTGCCTCACAAAAAGCGTCT 59.337 50.000 0.00 0.00 34.08 4.18
225 226 0.657368 CGTGCCTCACAAAAAGCGTC 60.657 55.000 0.00 0.00 33.40 5.19
226 227 1.355210 CGTGCCTCACAAAAAGCGT 59.645 52.632 0.00 0.00 33.40 5.07
227 228 2.010817 GCGTGCCTCACAAAAAGCG 61.011 57.895 0.00 0.00 33.40 4.68
228 229 2.010817 CGCGTGCCTCACAAAAAGC 61.011 57.895 0.00 0.00 33.40 3.51
229 230 0.248458 AACGCGTGCCTCACAAAAAG 60.248 50.000 14.98 0.00 33.40 2.27
230 231 0.524392 CAACGCGTGCCTCACAAAAA 60.524 50.000 14.98 0.00 33.40 1.94
231 232 1.063327 CAACGCGTGCCTCACAAAA 59.937 52.632 14.98 0.00 33.40 2.44
232 233 2.712539 CAACGCGTGCCTCACAAA 59.287 55.556 14.98 0.00 33.40 2.83
246 247 1.237285 ATCTCCAACAGGCGTGCAAC 61.237 55.000 6.26 0.00 0.00 4.17
247 248 1.073025 ATCTCCAACAGGCGTGCAA 59.927 52.632 6.26 0.00 0.00 4.08
248 249 1.672030 CATCTCCAACAGGCGTGCA 60.672 57.895 6.26 0.00 0.00 4.57
249 250 3.044059 GCATCTCCAACAGGCGTGC 62.044 63.158 6.26 0.00 0.00 5.34
250 251 1.364626 GAGCATCTCCAACAGGCGTG 61.365 60.000 4.53 4.53 0.00 5.34
251 252 1.078848 GAGCATCTCCAACAGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
252 253 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
263 264 1.070758 TCCCATTCGCCTAAGAGCATC 59.929 52.381 0.00 0.00 0.00 3.91
264 265 1.131638 TCCCATTCGCCTAAGAGCAT 58.868 50.000 0.00 0.00 0.00 3.79
265 266 0.908910 TTCCCATTCGCCTAAGAGCA 59.091 50.000 0.00 0.00 0.00 4.26
266 267 1.671328 GTTTCCCATTCGCCTAAGAGC 59.329 52.381 0.00 0.00 0.00 4.09
267 268 3.118592 AGAGTTTCCCATTCGCCTAAGAG 60.119 47.826 0.00 0.00 0.00 2.85
268 269 2.838202 AGAGTTTCCCATTCGCCTAAGA 59.162 45.455 0.00 0.00 0.00 2.10
269 270 3.268023 AGAGTTTCCCATTCGCCTAAG 57.732 47.619 0.00 0.00 0.00 2.18
285 286 4.502962 GAGTCATTGAGCTAAGCAAGAGT 58.497 43.478 0.00 0.00 0.00 3.24
293 295 2.089201 TCGGTCGAGTCATTGAGCTAA 58.911 47.619 0.00 0.00 35.51 3.09
375 381 4.319333 GCCATTGATATGTCAAAGAGCGAG 60.319 45.833 9.08 0.00 46.67 5.03
376 382 3.561310 GCCATTGATATGTCAAAGAGCGA 59.439 43.478 9.08 0.00 46.67 4.93
377 383 3.605461 CGCCATTGATATGTCAAAGAGCG 60.605 47.826 22.46 22.46 46.67 5.03
378 384 3.313526 ACGCCATTGATATGTCAAAGAGC 59.686 43.478 9.08 10.75 46.67 4.09
506 545 1.490490 GGTATCTTGGGCCAGATCACA 59.510 52.381 17.94 0.00 35.08 3.58
561 605 7.649533 TTATCGATAGGTTTAGAGTCACCAA 57.350 36.000 5.09 0.00 35.25 3.67
569 613 8.094548 CCAACCATCATTATCGATAGGTTTAGA 58.905 37.037 18.48 7.72 35.98 2.10
570 614 7.878127 ACCAACCATCATTATCGATAGGTTTAG 59.122 37.037 18.48 15.72 35.98 1.85
571 615 7.741785 ACCAACCATCATTATCGATAGGTTTA 58.258 34.615 18.48 0.51 35.98 2.01
717 800 1.269051 GCAAGTTGGACGTGGAAAAGG 60.269 52.381 4.75 0.00 0.00 3.11
724 807 2.126467 CAAATTGGCAAGTTGGACGTG 58.874 47.619 27.55 6.47 33.17 4.49
764 861 6.925718 CCCGGTGTGATCATCATCATATATAC 59.074 42.308 0.00 0.00 41.26 1.47
765 862 6.462909 GCCCGGTGTGATCATCATCATATATA 60.463 42.308 0.00 0.00 41.26 0.86
773 870 1.149174 GGCCCGGTGTGATCATCAT 59.851 57.895 0.00 0.00 0.00 2.45
774 871 1.846712 TTGGCCCGGTGTGATCATCA 61.847 55.000 0.00 0.00 0.00 3.07
775 872 1.077787 TTGGCCCGGTGTGATCATC 60.078 57.895 0.00 0.00 0.00 2.92
776 873 1.077501 CTTGGCCCGGTGTGATCAT 60.078 57.895 0.00 0.00 0.00 2.45
777 874 2.184020 CTCTTGGCCCGGTGTGATCA 62.184 60.000 0.00 0.00 0.00 2.92
793 890 3.584733 AACTGGACAAGCCTTTTCTCT 57.415 42.857 0.00 0.00 37.63 3.10
1499 2004 6.805713 AGGAACATATAATTTTTCTTGGCGG 58.194 36.000 0.00 0.00 0.00 6.13
1500 2005 7.479980 TGAGGAACATATAATTTTTCTTGGCG 58.520 34.615 0.00 0.00 0.00 5.69
1542 2064 1.340657 GCGTGCTTCAGAGACACGAG 61.341 60.000 24.02 4.25 46.55 4.18
1582 2107 3.930848 GGGAAACGTGAACGATCAAGTAT 59.069 43.478 14.03 3.35 45.70 2.12
1592 2117 2.312436 CGGGTCGGGAAACGTGAAC 61.312 63.158 0.00 0.00 44.69 3.18
1613 2138 2.557056 TCCCGTTGTATCTCCATCGATC 59.443 50.000 0.00 0.00 30.97 3.69
1691 2904 7.381139 CACTAAATTCCAAATGTACCAACACAC 59.619 37.037 0.00 0.00 38.78 3.82
1770 2995 9.372369 CTTAAACTTTTAAACATGGTTTCCACA 57.628 29.630 0.00 0.00 32.43 4.17
1804 3033 2.507471 CACCCTCTTAGCATCCTCCTTT 59.493 50.000 0.00 0.00 0.00 3.11
1805 3034 2.122768 CACCCTCTTAGCATCCTCCTT 58.877 52.381 0.00 0.00 0.00 3.36
1806 3035 1.292242 TCACCCTCTTAGCATCCTCCT 59.708 52.381 0.00 0.00 0.00 3.69
1807 3036 1.794714 TCACCCTCTTAGCATCCTCC 58.205 55.000 0.00 0.00 0.00 4.30
1808 3037 2.703007 ACATCACCCTCTTAGCATCCTC 59.297 50.000 0.00 0.00 0.00 3.71
1947 3189 7.709182 TCAAATGCATTACTACTTACGTGCTAT 59.291 33.333 13.39 0.00 33.95 2.97
1958 3200 9.846248 AATTCTCAAGTTCAAATGCATTACTAC 57.154 29.630 13.39 10.53 0.00 2.73
1960 3202 9.415544 GAAATTCTCAAGTTCAAATGCATTACT 57.584 29.630 13.39 9.95 35.68 2.24
1968 3210 7.439381 AGCATGTGAAATTCTCAAGTTCAAAT 58.561 30.769 1.72 0.00 45.59 2.32
1996 3238 5.062683 CGGATCTTAAGAGTGTGATGTTGTG 59.937 44.000 11.53 0.00 0.00 3.33
1998 3240 4.568359 CCGGATCTTAAGAGTGTGATGTTG 59.432 45.833 11.53 0.00 0.00 3.33
2043 3287 2.608546 CGGAAACCACGTGAAAACAGTA 59.391 45.455 19.30 0.00 0.00 2.74
2062 3307 3.220447 TTTCAGTAGAAACCGGCGG 57.780 52.632 27.06 27.06 38.76 6.13
2125 3374 5.633830 TTCTTGTTTCAGGATGCATCTTC 57.366 39.130 25.28 10.56 34.76 2.87
2169 3419 9.907576 CAAAACAAGATCATACTCGTTAGATTC 57.092 33.333 0.00 0.00 0.00 2.52
2262 3512 2.639327 AAGCGCTGGCCCAACAATC 61.639 57.895 12.58 0.00 41.24 2.67
2263 3513 2.601367 AAGCGCTGGCCCAACAAT 60.601 55.556 12.58 0.00 41.24 2.71
2264 3514 3.604667 CAAGCGCTGGCCCAACAA 61.605 61.111 12.58 0.00 41.24 2.83
2265 3515 4.892965 ACAAGCGCTGGCCCAACA 62.893 61.111 12.58 0.00 41.24 3.33
2266 3516 3.605664 AACAAGCGCTGGCCCAAC 61.606 61.111 12.58 0.00 41.24 3.77
2267 3517 3.604667 CAACAAGCGCTGGCCCAA 61.605 61.111 12.58 0.00 41.24 4.12
2277 3527 1.010419 CAAATGAGCCGCCAACAAGC 61.010 55.000 0.00 0.00 0.00 4.01
2278 3528 0.314935 ACAAATGAGCCGCCAACAAG 59.685 50.000 0.00 0.00 0.00 3.16
2279 3529 0.313672 GACAAATGAGCCGCCAACAA 59.686 50.000 0.00 0.00 0.00 2.83
2280 3530 1.851021 CGACAAATGAGCCGCCAACA 61.851 55.000 0.00 0.00 0.00 3.33
2281 3531 1.154225 CGACAAATGAGCCGCCAAC 60.154 57.895 0.00 0.00 0.00 3.77
2282 3532 0.886938 TTCGACAAATGAGCCGCCAA 60.887 50.000 0.00 0.00 0.00 4.52
2283 3533 0.886938 TTTCGACAAATGAGCCGCCA 60.887 50.000 0.00 0.00 0.00 5.69
2284 3534 0.179189 CTTTCGACAAATGAGCCGCC 60.179 55.000 0.00 0.00 0.00 6.13
2285 3535 0.179189 CCTTTCGACAAATGAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
2286 3536 1.135972 CACCTTTCGACAAATGAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
2287 3537 2.151202 TCACCTTTCGACAAATGAGCC 58.849 47.619 0.00 0.00 0.00 4.70
2288 3538 3.365364 CCTTCACCTTTCGACAAATGAGC 60.365 47.826 0.00 0.00 0.00 4.26
2289 3539 3.189287 CCCTTCACCTTTCGACAAATGAG 59.811 47.826 0.00 0.00 0.00 2.90
2290 3540 3.146066 CCCTTCACCTTTCGACAAATGA 58.854 45.455 0.00 0.00 0.00 2.57
2291 3541 2.228822 CCCCTTCACCTTTCGACAAATG 59.771 50.000 0.00 0.00 0.00 2.32
2292 3542 2.514803 CCCCTTCACCTTTCGACAAAT 58.485 47.619 0.00 0.00 0.00 2.32
2293 3543 1.975660 CCCCTTCACCTTTCGACAAA 58.024 50.000 0.00 0.00 0.00 2.83
2294 3544 0.536460 GCCCCTTCACCTTTCGACAA 60.536 55.000 0.00 0.00 0.00 3.18
2295 3545 1.072505 GCCCCTTCACCTTTCGACA 59.927 57.895 0.00 0.00 0.00 4.35
2296 3546 2.033194 CGCCCCTTCACCTTTCGAC 61.033 63.158 0.00 0.00 0.00 4.20
2297 3547 2.167398 CTCGCCCCTTCACCTTTCGA 62.167 60.000 0.00 0.00 0.00 3.71
2298 3548 1.741770 CTCGCCCCTTCACCTTTCG 60.742 63.158 0.00 0.00 0.00 3.46
2299 3549 1.377333 CCTCGCCCCTTCACCTTTC 60.377 63.158 0.00 0.00 0.00 2.62
2300 3550 2.757077 CCTCGCCCCTTCACCTTT 59.243 61.111 0.00 0.00 0.00 3.11
2301 3551 2.758852 TACCCTCGCCCCTTCACCTT 62.759 60.000 0.00 0.00 0.00 3.50
2302 3552 2.758852 TTACCCTCGCCCCTTCACCT 62.759 60.000 0.00 0.00 0.00 4.00
2303 3553 2.253403 CTTACCCTCGCCCCTTCACC 62.253 65.000 0.00 0.00 0.00 4.02
2304 3554 1.221021 CTTACCCTCGCCCCTTCAC 59.779 63.158 0.00 0.00 0.00 3.18
2305 3555 0.545787 TTCTTACCCTCGCCCCTTCA 60.546 55.000 0.00 0.00 0.00 3.02
2306 3556 0.616891 TTTCTTACCCTCGCCCCTTC 59.383 55.000 0.00 0.00 0.00 3.46
2307 3557 1.004394 CTTTTCTTACCCTCGCCCCTT 59.996 52.381 0.00 0.00 0.00 3.95
2308 3558 0.618981 CTTTTCTTACCCTCGCCCCT 59.381 55.000 0.00 0.00 0.00 4.79
2309 3559 0.616891 TCTTTTCTTACCCTCGCCCC 59.383 55.000 0.00 0.00 0.00 5.80
2310 3560 2.484742 TTCTTTTCTTACCCTCGCCC 57.515 50.000 0.00 0.00 0.00 6.13
2311 3561 2.161808 GCTTTCTTTTCTTACCCTCGCC 59.838 50.000 0.00 0.00 0.00 5.54
2312 3562 3.075148 AGCTTTCTTTTCTTACCCTCGC 58.925 45.455 0.00 0.00 0.00 5.03
2313 3563 5.220681 GCATAGCTTTCTTTTCTTACCCTCG 60.221 44.000 0.00 0.00 0.00 4.63
2314 3564 5.883115 AGCATAGCTTTCTTTTCTTACCCTC 59.117 40.000 0.00 0.00 33.89 4.30
2315 3565 5.821097 AGCATAGCTTTCTTTTCTTACCCT 58.179 37.500 0.00 0.00 33.89 4.34
2330 3580 3.743521 TGTGTCAAAGACAAGCATAGCT 58.256 40.909 0.82 0.00 44.49 3.32
2331 3581 4.488126 TTGTGTCAAAGACAAGCATAGC 57.512 40.909 0.82 0.00 44.49 2.97
2332 3582 6.441274 ACAATTGTGTCAAAGACAAGCATAG 58.559 36.000 11.07 0.00 44.49 2.23
2333 3583 6.389830 ACAATTGTGTCAAAGACAAGCATA 57.610 33.333 11.07 0.00 44.49 3.14
2334 3584 5.266733 ACAATTGTGTCAAAGACAAGCAT 57.733 34.783 11.07 0.00 44.49 3.79
2335 3585 4.717233 ACAATTGTGTCAAAGACAAGCA 57.283 36.364 11.07 0.00 44.49 3.91
2336 3586 4.268405 CCAACAATTGTGTCAAAGACAAGC 59.732 41.667 12.82 0.00 44.49 4.01
2342 3832 4.033129 CAGCAACCAACAATTGTGTCAAAG 59.967 41.667 12.82 2.56 36.80 2.77
2350 3840 2.129607 GCTGTCAGCAACCAACAATTG 58.870 47.619 20.16 3.24 41.89 2.32
2351 3841 2.514205 GCTGTCAGCAACCAACAATT 57.486 45.000 20.16 0.00 41.89 2.32
2363 3853 2.945008 CTCTAGGTCTCTCTGCTGTCAG 59.055 54.545 0.00 0.00 41.67 3.51
2364 3854 2.573915 TCTCTAGGTCTCTCTGCTGTCA 59.426 50.000 0.00 0.00 0.00 3.58
2375 3865 5.185056 GCTTCTCTTTCACTTCTCTAGGTCT 59.815 44.000 0.00 0.00 0.00 3.85
2376 3866 5.047660 TGCTTCTCTTTCACTTCTCTAGGTC 60.048 44.000 0.00 0.00 0.00 3.85
2380 3870 6.656632 TTCTGCTTCTCTTTCACTTCTCTA 57.343 37.500 0.00 0.00 0.00 2.43
2399 3889 6.090088 CGTTTCTGGTCAGAGTCTTATTTCTG 59.910 42.308 0.75 0.00 41.67 3.02
2431 3921 2.000447 GACTTCCATGTCTGCCGTTAC 59.000 52.381 0.00 0.00 34.39 2.50
2433 3923 0.321653 GGACTTCCATGTCTGCCGTT 60.322 55.000 0.00 0.00 37.16 4.44
2436 3926 0.393537 CCTGGACTTCCATGTCTGCC 60.394 60.000 0.00 0.00 46.46 4.85
2437 3927 0.615331 TCCTGGACTTCCATGTCTGC 59.385 55.000 0.00 0.00 46.46 4.26
2438 3928 2.938756 GCTTCCTGGACTTCCATGTCTG 60.939 54.545 0.00 0.00 46.46 3.51
2444 3934 0.473694 TCCTGCTTCCTGGACTTCCA 60.474 55.000 0.00 0.00 45.30 3.53
2447 3937 1.494721 TGTTTCCTGCTTCCTGGACTT 59.505 47.619 0.00 0.00 38.62 3.01
2461 3951 1.334149 GCTGCACTCGAACTTGTTTCC 60.334 52.381 0.00 0.00 0.00 3.13
2479 3969 0.386731 GCGCAAACATAAACCACGCT 60.387 50.000 0.30 0.00 41.50 5.07
2481 3971 2.501881 GTAGCGCAAACATAAACCACG 58.498 47.619 11.47 0.00 0.00 4.94
2501 3991 8.785329 AATAGCTCAAACTCTAAAAGAAGAGG 57.215 34.615 0.00 0.00 46.11 3.69
2550 4040 0.613260 ACTTGAATGCTAGTGGGCGA 59.387 50.000 0.00 0.00 34.52 5.54
2555 4045 1.474077 GGCCCAACTTGAATGCTAGTG 59.526 52.381 0.00 0.00 30.50 2.74
2562 4052 2.679996 GGCCGGCCCAACTTGAAT 60.680 61.111 36.64 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.