Multiple sequence alignment - TraesCS6D01G036300

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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 TraesCS6D01G036300 chr6D 100.000 2913 0 0 1 2913 14792955 14790043 0.000000e+00 5380.0
1 TraesCS6D01G036300 chr6D 83.121 2038 253 47 361 2364 14727356 14725376 0.000000e+00 1773.0
2 TraesCS6D01G036300 chr6D 85.590 1492 178 25 349 1810 14503307 14504791 0.000000e+00 1530.0
3 TraesCS6D01G036300 chr6D 83.294 1712 212 37 669 2364 14442272 14443925 0.000000e+00 1509.0
4 TraesCS6D01G036300 chr6D 83.248 1558 199 35 401 1918 15344829 15343294 0.000000e+00 1375.0
5 TraesCS6D01G036300 chr6D 83.732 1297 183 21 483 1758 14483810 14485099 0.000000e+00 1201.0
6 TraesCS6D01G036300 chr6D 83.200 1250 173 26 848 2069 14435570 14436810 0.000000e+00 1110.0
7 TraesCS6D01G036300 chr6D 88.190 906 90 12 1141 2036 15349400 15348502 0.000000e+00 1064.0
8 TraesCS6D01G036300 chr6D 83.368 487 54 14 1881 2364 14504788 14505250 2.680000e-115 425.0
9 TraesCS6D01G036300 chr6D 87.819 353 29 9 2575 2913 15351245 15350893 4.520000e-108 401.0
10 TraesCS6D01G036300 chr6D 90.000 110 10 1 6 114 217959351 217959242 1.090000e-29 141.0
11 TraesCS6D01G036300 chr6B 86.192 2600 264 33 365 2909 27065982 27063423 0.000000e+00 2724.0
12 TraesCS6D01G036300 chr6B 86.859 2458 250 30 486 2909 26688111 26685693 0.000000e+00 2682.0
13 TraesCS6D01G036300 chr6B 83.564 2026 242 48 387 2364 26512154 26514136 0.000000e+00 1812.0
14 TraesCS6D01G036300 chr6A 84.292 1999 206 45 381 2364 15700730 15702635 0.000000e+00 1853.0
15 TraesCS6D01G036300 chr6A 83.918 1567 211 23 384 1918 15694602 15696159 0.000000e+00 1459.0
16 TraesCS6D01G036300 chr6A 82.904 427 50 8 2095 2512 16599369 16599781 2.130000e-96 363.0
17 TraesCS6D01G036300 chr6A 77.931 145 26 5 2131 2273 15689215 15689355 5.170000e-13 86.1
18 TraesCS6D01G036300 chr5D 85.216 1434 174 26 365 1767 27985510 27984084 0.000000e+00 1439.0
19 TraesCS6D01G036300 chr5D 80.546 293 33 13 2643 2913 27977781 27977491 1.370000e-48 204.0
20 TraesCS6D01G036300 chr1B 81.886 1612 241 32 349 1918 48062392 48060790 0.000000e+00 1312.0
21 TraesCS6D01G036300 chr1B 91.429 105 7 2 2 105 262748535 262748432 3.030000e-30 143.0
22 TraesCS6D01G036300 chr4B 81.976 749 90 25 1799 2512 575727495 575728233 6.950000e-166 593.0
23 TraesCS6D01G036300 chr4D 92.523 107 7 1 1 106 382308442 382308336 5.030000e-33 152.0
24 TraesCS6D01G036300 chr3D 93.204 103 7 0 2 104 479746501 479746399 5.030000e-33 152.0
25 TraesCS6D01G036300 chr3D 89.189 111 12 0 1 111 5846939 5847049 3.910000e-29 139.0
26 TraesCS6D01G036300 chr2A 92.308 104 8 0 1 104 478504011 478503908 6.500000e-32 148.0
27 TraesCS6D01G036300 chr7D 92.157 102 8 0 3 104 118396182 118396283 8.410000e-31 145.0
28 TraesCS6D01G036300 chr2B 90.826 109 9 1 1 109 92098697 92098590 8.410000e-31 145.0
29 TraesCS6D01G036300 chr4A 91.429 105 8 1 2 105 608476982 608476878 3.030000e-30 143.0


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 TraesCS6D01G036300 chr6D 14790043 14792955 2912 True 5380.000000 5380 100.000 1 2913 1 chr6D.!!$R2 2912
1 TraesCS6D01G036300 chr6D 14725376 14727356 1980 True 1773.000000 1773 83.121 361 2364 1 chr6D.!!$R1 2003
2 TraesCS6D01G036300 chr6D 14442272 14443925 1653 False 1509.000000 1509 83.294 669 2364 1 chr6D.!!$F2 1695
3 TraesCS6D01G036300 chr6D 14483810 14485099 1289 False 1201.000000 1201 83.732 483 1758 1 chr6D.!!$F3 1275
4 TraesCS6D01G036300 chr6D 14435570 14436810 1240 False 1110.000000 1110 83.200 848 2069 1 chr6D.!!$F1 1221
5 TraesCS6D01G036300 chr6D 14503307 14505250 1943 False 977.500000 1530 84.479 349 2364 2 chr6D.!!$F4 2015
6 TraesCS6D01G036300 chr6D 15343294 15351245 7951 True 946.666667 1375 86.419 401 2913 3 chr6D.!!$R4 2512
7 TraesCS6D01G036300 chr6B 27063423 27065982 2559 True 2724.000000 2724 86.192 365 2909 1 chr6B.!!$R2 2544
8 TraesCS6D01G036300 chr6B 26685693 26688111 2418 True 2682.000000 2682 86.859 486 2909 1 chr6B.!!$R1 2423
9 TraesCS6D01G036300 chr6B 26512154 26514136 1982 False 1812.000000 1812 83.564 387 2364 1 chr6B.!!$F1 1977
10 TraesCS6D01G036300 chr6A 15700730 15702635 1905 False 1853.000000 1853 84.292 381 2364 1 chr6A.!!$F3 1983
11 TraesCS6D01G036300 chr6A 15694602 15696159 1557 False 1459.000000 1459 83.918 384 1918 1 chr6A.!!$F2 1534
12 TraesCS6D01G036300 chr5D 27984084 27985510 1426 True 1439.000000 1439 85.216 365 1767 1 chr5D.!!$R2 1402
13 TraesCS6D01G036300 chr1B 48060790 48062392 1602 True 1312.000000 1312 81.886 349 1918 1 chr1B.!!$R1 1569
14 TraesCS6D01G036300 chr4B 575727495 575728233 738 False 593.000000 593 81.976 1799 2512 1 chr4B.!!$F1 713

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
331 332 0.043907 CGACGACATATGCAGTTGCG 60.044 55.0 1.58 3.54 45.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 8463 0.323087 ATCATCAGCTGCAGTTGCCA 60.323 50.0 24.28 9.92 41.18 4.92 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
23 24 6.806120 CCCAGTAAACGAAAAGAAAAGTTG 57.194 37.500 0.00 0.00 0.00 3.16
24 25 6.327154 CCCAGTAAACGAAAAGAAAAGTTGT 58.673 36.000 0.00 0.00 0.00 3.32
25 26 6.809689 CCCAGTAAACGAAAAGAAAAGTTGTT 59.190 34.615 0.00 0.00 0.00 2.83
26 27 7.329962 CCCAGTAAACGAAAAGAAAAGTTGTTT 59.670 33.333 0.00 0.00 33.23 2.83
28 29 9.511022 CAGTAAACGAAAAGAAAAGTTGTTTTG 57.489 29.630 1.09 0.00 36.42 2.44
29 30 8.218441 AGTAAACGAAAAGAAAAGTTGTTTTGC 58.782 29.630 1.09 0.00 36.42 3.68
30 31 6.532365 AACGAAAAGAAAAGTTGTTTTGCA 57.468 29.167 1.09 0.00 36.42 4.08
31 32 6.532365 ACGAAAAGAAAAGTTGTTTTGCAA 57.468 29.167 0.00 0.00 36.42 4.08
32 33 6.949449 ACGAAAAGAAAAGTTGTTTTGCAAA 58.051 28.000 8.05 8.05 36.42 3.68
33 34 7.068955 ACGAAAAGAAAAGTTGTTTTGCAAAG 58.931 30.769 12.41 0.00 36.42 2.77
37 38 9.824534 AAAAGAAAAGTTGTTTTGCAAAGTATG 57.175 25.926 12.41 0.00 39.03 2.39
58 59 9.869757 AGTATGCATTAAATTTTACCTTGGAAC 57.130 29.630 3.54 0.00 0.00 3.62
59 60 9.093970 GTATGCATTAAATTTTACCTTGGAACC 57.906 33.333 3.54 0.00 0.00 3.62
61 62 7.158021 TGCATTAAATTTTACCTTGGAACCTG 58.842 34.615 0.00 0.00 0.00 4.00
63 64 8.308207 GCATTAAATTTTACCTTGGAACCTGTA 58.692 33.333 0.00 0.00 0.00 2.74
68 69 6.642707 TTTTACCTTGGAACCTGTAATGTG 57.357 37.500 0.00 0.00 0.00 3.21
69 70 5.570205 TTACCTTGGAACCTGTAATGTGA 57.430 39.130 0.00 0.00 0.00 3.58
70 71 4.021102 ACCTTGGAACCTGTAATGTGAG 57.979 45.455 0.00 0.00 0.00 3.51
71 72 3.394606 ACCTTGGAACCTGTAATGTGAGT 59.605 43.478 0.00 0.00 0.00 3.41
76 77 4.578516 TGGAACCTGTAATGTGAGTTTGTG 59.421 41.667 0.00 0.00 0.00 3.33
77 78 4.023193 GGAACCTGTAATGTGAGTTTGTGG 60.023 45.833 0.00 0.00 0.00 4.17
78 79 2.884639 ACCTGTAATGTGAGTTTGTGGC 59.115 45.455 0.00 0.00 0.00 5.01
79 80 2.228822 CCTGTAATGTGAGTTTGTGGCC 59.771 50.000 0.00 0.00 0.00 5.36
82 83 3.317711 TGTAATGTGAGTTTGTGGCCTTG 59.682 43.478 3.32 0.00 0.00 3.61
84 85 2.719531 TGTGAGTTTGTGGCCTTGTA 57.280 45.000 3.32 0.00 0.00 2.41
85 86 3.222173 TGTGAGTTTGTGGCCTTGTAT 57.778 42.857 3.32 0.00 0.00 2.29
88 89 6.056090 TGTGAGTTTGTGGCCTTGTATATA 57.944 37.500 3.32 0.00 0.00 0.86
89 90 6.477253 TGTGAGTTTGTGGCCTTGTATATAA 58.523 36.000 3.32 0.00 0.00 0.98
90 91 6.943146 TGTGAGTTTGTGGCCTTGTATATAAA 59.057 34.615 3.32 0.00 0.00 1.40
91 92 7.448777 TGTGAGTTTGTGGCCTTGTATATAAAA 59.551 33.333 3.32 0.00 0.00 1.52
92 93 8.301002 GTGAGTTTGTGGCCTTGTATATAAAAA 58.699 33.333 3.32 0.00 0.00 1.94
93 94 9.030452 TGAGTTTGTGGCCTTGTATATAAAAAT 57.970 29.630 3.32 0.00 0.00 1.82
94 95 9.301153 GAGTTTGTGGCCTTGTATATAAAAATG 57.699 33.333 3.32 0.00 0.00 2.32
95 96 8.257306 AGTTTGTGGCCTTGTATATAAAAATGG 58.743 33.333 3.32 0.00 0.00 3.16
96 97 7.962995 TTGTGGCCTTGTATATAAAAATGGA 57.037 32.000 3.32 0.00 0.00 3.41
97 98 7.581213 TGTGGCCTTGTATATAAAAATGGAG 57.419 36.000 3.32 0.00 0.00 3.86
99 100 5.538433 TGGCCTTGTATATAAAAATGGAGGC 59.462 40.000 3.32 4.53 44.81 4.70
101 102 6.294731 GGCCTTGTATATAAAAATGGAGGCAG 60.295 42.308 12.63 0.00 46.76 4.85
103 104 7.447238 GCCTTGTATATAAAAATGGAGGCAGTA 59.553 37.037 7.46 0.00 44.88 2.74
104 105 9.520515 CCTTGTATATAAAAATGGAGGCAGTAT 57.479 33.333 0.00 0.00 0.00 2.12
106 107 9.515226 TTGTATATAAAAATGGAGGCAGTATCC 57.485 33.333 0.00 0.00 37.35 2.59
116 117 6.073447 TGGAGGCAGTATCCAAATTTAAGA 57.927 37.500 0.00 0.00 43.87 2.10
117 118 6.122277 TGGAGGCAGTATCCAAATTTAAGAG 58.878 40.000 0.00 0.00 43.87 2.85
118 119 6.069673 TGGAGGCAGTATCCAAATTTAAGAGA 60.070 38.462 0.00 0.00 43.87 3.10
120 121 5.817816 AGGCAGTATCCAAATTTAAGAGACG 59.182 40.000 8.63 6.27 0.00 4.18
122 123 6.238130 GGCAGTATCCAAATTTAAGAGACGTC 60.238 42.308 7.70 7.70 0.00 4.34
123 124 6.238130 GCAGTATCCAAATTTAAGAGACGTCC 60.238 42.308 13.01 3.77 0.00 4.79
124 125 6.816640 CAGTATCCAAATTTAAGAGACGTCCA 59.183 38.462 13.01 0.00 0.00 4.02
125 126 7.333423 CAGTATCCAAATTTAAGAGACGTCCAA 59.667 37.037 13.01 0.00 0.00 3.53
126 127 7.881232 AGTATCCAAATTTAAGAGACGTCCAAA 59.119 33.333 13.01 8.20 0.00 3.28
127 128 7.703058 ATCCAAATTTAAGAGACGTCCAAAT 57.297 32.000 13.01 10.11 0.00 2.32
128 129 7.141100 TCCAAATTTAAGAGACGTCCAAATC 57.859 36.000 13.01 2.86 0.00 2.17
129 130 6.150474 TCCAAATTTAAGAGACGTCCAAATCC 59.850 38.462 13.01 0.00 0.00 3.01
130 131 6.072175 CCAAATTTAAGAGACGTCCAAATCCA 60.072 38.462 13.01 0.00 0.00 3.41
131 132 7.367285 CAAATTTAAGAGACGTCCAAATCCAA 58.633 34.615 13.01 0.00 0.00 3.53
133 134 7.703058 ATTTAAGAGACGTCCAAATCCAATT 57.297 32.000 13.01 0.00 0.00 2.32
134 135 6.494893 TTAAGAGACGTCCAAATCCAATTG 57.505 37.500 13.01 0.00 0.00 2.32
135 136 2.749621 AGAGACGTCCAAATCCAATTGC 59.250 45.455 13.01 0.00 0.00 3.56
136 137 1.818674 AGACGTCCAAATCCAATTGCC 59.181 47.619 13.01 0.00 0.00 4.52
138 139 1.967066 ACGTCCAAATCCAATTGCCAA 59.033 42.857 0.00 0.00 0.00 4.52
139 140 2.566724 ACGTCCAAATCCAATTGCCAAT 59.433 40.909 0.00 0.00 0.00 3.16
140 141 3.007831 ACGTCCAAATCCAATTGCCAATT 59.992 39.130 0.00 0.00 0.00 2.32
141 142 3.371591 CGTCCAAATCCAATTGCCAATTG 59.628 43.478 20.73 20.73 46.09 2.32
149 150 3.188159 CAATTGCCAATTGGATCTGGG 57.812 47.619 29.02 8.26 43.50 4.45
151 152 2.619697 TTGCCAATTGGATCTGGGAA 57.380 45.000 29.02 5.07 40.33 3.97
154 155 2.566724 TGCCAATTGGATCTGGGAAAAC 59.433 45.455 29.02 6.04 37.39 2.43
155 156 2.566724 GCCAATTGGATCTGGGAAAACA 59.433 45.455 29.02 0.00 37.39 2.83
158 159 5.452356 GCCAATTGGATCTGGGAAAACATAG 60.452 44.000 29.02 0.00 37.39 2.23
159 160 5.658190 CCAATTGGATCTGGGAAAACATAGT 59.342 40.000 20.50 0.00 37.39 2.12
161 162 7.506938 CCAATTGGATCTGGGAAAACATAGTAT 59.493 37.037 20.50 0.00 37.39 2.12
162 163 8.571336 CAATTGGATCTGGGAAAACATAGTATC 58.429 37.037 0.00 0.00 0.00 2.24
163 164 6.823286 TGGATCTGGGAAAACATAGTATCA 57.177 37.500 0.00 0.00 0.00 2.15
164 165 7.392766 TGGATCTGGGAAAACATAGTATCAT 57.607 36.000 0.00 0.00 0.00 2.45
165 166 7.815383 TGGATCTGGGAAAACATAGTATCATT 58.185 34.615 0.00 0.00 0.00 2.57
166 167 8.281531 TGGATCTGGGAAAACATAGTATCATTT 58.718 33.333 0.00 0.00 0.00 2.32
167 168 9.136323 GGATCTGGGAAAACATAGTATCATTTT 57.864 33.333 0.00 2.58 0.00 1.82
171 172 9.927668 CTGGGAAAACATAGTATCATTTTTGTT 57.072 29.630 4.05 0.00 0.00 2.83
187 188 9.670719 TCATTTTTGTTTTTGTTTTTCTGGAAC 57.329 25.926 0.00 0.00 0.00 3.62
188 189 9.455847 CATTTTTGTTTTTGTTTTTCTGGAACA 57.544 25.926 0.00 0.00 35.36 3.18
193 194 4.912528 TTTGTTTTTCTGGAACAAACGC 57.087 36.364 10.15 0.00 46.32 4.84
194 195 3.577649 TGTTTTTCTGGAACAAACGCA 57.422 38.095 11.98 0.00 38.70 5.24
196 197 4.109050 TGTTTTTCTGGAACAAACGCATC 58.891 39.130 11.98 0.00 38.70 3.91
198 199 4.647424 TTTTCTGGAACAAACGCATCTT 57.353 36.364 0.00 0.00 38.70 2.40
199 200 5.759506 TTTTCTGGAACAAACGCATCTTA 57.240 34.783 0.00 0.00 38.70 2.10
200 201 5.356882 TTTCTGGAACAAACGCATCTTAG 57.643 39.130 0.00 0.00 38.70 2.18
202 203 4.385825 TCTGGAACAAACGCATCTTAGTT 58.614 39.130 0.00 0.00 38.70 2.24
204 205 5.298276 TCTGGAACAAACGCATCTTAGTTTT 59.702 36.000 0.00 0.00 38.37 2.43
205 206 5.897050 TGGAACAAACGCATCTTAGTTTTT 58.103 33.333 0.00 0.00 38.37 1.94
233 234 5.188751 GGGGGAACAAAAACATATCCATCAA 59.811 40.000 0.00 0.00 31.63 2.57
234 235 6.126796 GGGGGAACAAAAACATATCCATCAAT 60.127 38.462 0.00 0.00 31.63 2.57
236 237 7.828717 GGGGAACAAAAACATATCCATCAATTT 59.171 33.333 0.00 0.00 31.63 1.82
246 247 8.413309 ACATATCCATCAATTTTATGGGTCAG 57.587 34.615 14.04 7.78 43.52 3.51
247 248 7.452501 ACATATCCATCAATTTTATGGGTCAGG 59.547 37.037 14.04 5.68 43.52 3.86
248 249 5.205517 TCCATCAATTTTATGGGTCAGGT 57.794 39.130 14.04 0.00 43.52 4.00
250 251 4.342092 CCATCAATTTTATGGGTCAGGTCC 59.658 45.833 8.24 0.00 40.27 4.46
252 253 5.004361 TCAATTTTATGGGTCAGGTCCAA 57.996 39.130 0.00 0.00 37.87 3.53
253 254 5.588845 TCAATTTTATGGGTCAGGTCCAAT 58.411 37.500 0.00 0.00 37.87 3.16
254 255 6.736581 TCAATTTTATGGGTCAGGTCCAATA 58.263 36.000 0.00 0.00 37.87 1.90
255 256 6.833416 TCAATTTTATGGGTCAGGTCCAATAG 59.167 38.462 0.00 0.00 37.87 1.73
256 257 6.590656 ATTTTATGGGTCAGGTCCAATAGA 57.409 37.500 0.00 0.00 37.87 1.98
257 258 5.630415 TTTATGGGTCAGGTCCAATAGAG 57.370 43.478 0.00 0.00 37.87 2.43
258 259 1.204146 TGGGTCAGGTCCAATAGAGC 58.796 55.000 0.00 0.00 43.67 4.09
259 260 0.470341 GGGTCAGGTCCAATAGAGCC 59.530 60.000 0.00 0.00 44.46 4.70
260 261 0.470341 GGTCAGGTCCAATAGAGCCC 59.530 60.000 0.00 0.00 44.46 5.19
261 262 1.204146 GTCAGGTCCAATAGAGCCCA 58.796 55.000 0.00 0.00 44.46 5.36
264 265 1.281867 CAGGTCCAATAGAGCCCACAA 59.718 52.381 0.00 0.00 44.46 3.33
265 266 1.992557 AGGTCCAATAGAGCCCACAAA 59.007 47.619 0.00 0.00 44.46 2.83
266 267 2.092323 GGTCCAATAGAGCCCACAAAC 58.908 52.381 0.00 0.00 36.99 2.93
267 268 2.554344 GGTCCAATAGAGCCCACAAACA 60.554 50.000 0.00 0.00 36.99 2.83
268 269 2.488153 GTCCAATAGAGCCCACAAACAC 59.512 50.000 0.00 0.00 0.00 3.32
269 270 2.107378 TCCAATAGAGCCCACAAACACA 59.893 45.455 0.00 0.00 0.00 3.72
270 271 2.489329 CCAATAGAGCCCACAAACACAG 59.511 50.000 0.00 0.00 0.00 3.66
273 274 1.680338 AGAGCCCACAAACACAGAAC 58.320 50.000 0.00 0.00 0.00 3.01
275 276 1.956477 GAGCCCACAAACACAGAACAT 59.044 47.619 0.00 0.00 0.00 2.71
276 277 1.956477 AGCCCACAAACACAGAACATC 59.044 47.619 0.00 0.00 0.00 3.06
278 279 1.266718 CCCACAAACACAGAACATCCG 59.733 52.381 0.00 0.00 0.00 4.18
279 280 2.217750 CCACAAACACAGAACATCCGA 58.782 47.619 0.00 0.00 0.00 4.55
280 281 2.616376 CCACAAACACAGAACATCCGAA 59.384 45.455 0.00 0.00 0.00 4.30
281 282 3.066064 CCACAAACACAGAACATCCGAAA 59.934 43.478 0.00 0.00 0.00 3.46
282 283 4.282068 CACAAACACAGAACATCCGAAAG 58.718 43.478 0.00 0.00 0.00 2.62
283 284 4.035091 CACAAACACAGAACATCCGAAAGA 59.965 41.667 0.00 0.00 0.00 2.52
284 285 4.638421 ACAAACACAGAACATCCGAAAGAA 59.362 37.500 0.00 0.00 0.00 2.52
285 286 5.207768 CAAACACAGAACATCCGAAAGAAG 58.792 41.667 0.00 0.00 0.00 2.85
286 287 4.336889 ACACAGAACATCCGAAAGAAGA 57.663 40.909 0.00 0.00 0.00 2.87
287 288 4.310769 ACACAGAACATCCGAAAGAAGAG 58.689 43.478 0.00 0.00 0.00 2.85
288 289 4.039245 ACACAGAACATCCGAAAGAAGAGA 59.961 41.667 0.00 0.00 0.00 3.10
289 290 5.174395 CACAGAACATCCGAAAGAAGAGAT 58.826 41.667 0.00 0.00 0.00 2.75
290 291 5.063186 CACAGAACATCCGAAAGAAGAGATG 59.937 44.000 0.00 0.00 0.00 2.90
291 292 4.033817 CAGAACATCCGAAAGAAGAGATGC 59.966 45.833 0.00 0.00 0.00 3.91
293 294 3.529533 ACATCCGAAAGAAGAGATGCAG 58.470 45.455 0.00 0.00 0.00 4.41
294 295 2.015736 TCCGAAAGAAGAGATGCAGC 57.984 50.000 0.00 0.00 0.00 5.25
296 297 1.012841 CGAAAGAAGAGATGCAGCCC 58.987 55.000 0.00 0.00 0.00 5.19
297 298 1.676916 CGAAAGAAGAGATGCAGCCCA 60.677 52.381 0.00 0.00 0.00 5.36
298 299 2.652590 GAAAGAAGAGATGCAGCCCAT 58.347 47.619 0.00 0.00 36.70 4.00
299 300 2.822707 AAGAAGAGATGCAGCCCATT 57.177 45.000 0.00 0.00 33.29 3.16
300 301 2.345124 AGAAGAGATGCAGCCCATTC 57.655 50.000 0.00 0.43 33.29 2.67
301 302 1.845143 AGAAGAGATGCAGCCCATTCT 59.155 47.619 0.00 3.07 33.29 2.40
302 303 1.948145 GAAGAGATGCAGCCCATTCTG 59.052 52.381 0.00 0.00 33.29 3.02
303 304 1.210538 AGAGATGCAGCCCATTCTGA 58.789 50.000 0.00 0.00 36.19 3.27
304 305 1.141254 AGAGATGCAGCCCATTCTGAG 59.859 52.381 0.00 0.00 36.19 3.35
305 306 0.465824 AGATGCAGCCCATTCTGAGC 60.466 55.000 0.00 0.00 36.19 4.26
306 307 0.750546 GATGCAGCCCATTCTGAGCA 60.751 55.000 0.00 0.00 36.19 4.26
307 308 0.323999 ATGCAGCCCATTCTGAGCAA 60.324 50.000 0.00 0.00 36.19 3.91
308 309 0.540133 TGCAGCCCATTCTGAGCAAA 60.540 50.000 0.00 0.00 36.19 3.68
309 310 0.108945 GCAGCCCATTCTGAGCAAAC 60.109 55.000 0.00 0.00 36.19 2.93
310 311 0.169672 CAGCCCATTCTGAGCAAACG 59.830 55.000 0.00 0.00 36.19 3.60
311 312 1.153958 GCCCATTCTGAGCAAACGC 60.154 57.895 0.00 0.00 0.00 4.84
312 313 1.508088 CCCATTCTGAGCAAACGCC 59.492 57.895 0.00 0.00 0.00 5.68
315 316 0.179215 CATTCTGAGCAAACGCCGAC 60.179 55.000 0.00 0.00 0.00 4.79
317 318 2.686956 TTCTGAGCAAACGCCGACGA 62.687 55.000 0.00 0.00 43.93 4.20
318 319 3.000080 CTGAGCAAACGCCGACGAC 62.000 63.158 0.00 0.00 43.93 4.34
319 320 3.033764 GAGCAAACGCCGACGACA 61.034 61.111 0.00 0.00 43.93 4.35
320 321 2.357034 AGCAAACGCCGACGACAT 60.357 55.556 0.00 0.00 43.93 3.06
321 322 1.074319 GAGCAAACGCCGACGACATA 61.074 55.000 0.00 0.00 43.93 2.29
323 324 0.315059 GCAAACGCCGACGACATATG 60.315 55.000 0.00 0.00 43.93 1.78
324 325 0.315059 CAAACGCCGACGACATATGC 60.315 55.000 0.00 0.00 43.93 3.14
327 328 1.588932 CGCCGACGACATATGCAGT 60.589 57.895 1.58 2.78 43.93 4.40
328 329 1.145759 CGCCGACGACATATGCAGTT 61.146 55.000 1.58 0.00 43.93 3.16
329 330 0.301687 GCCGACGACATATGCAGTTG 59.698 55.000 1.58 6.99 0.00 3.16
330 331 0.301687 CCGACGACATATGCAGTTGC 59.698 55.000 1.58 0.00 42.50 4.17
331 332 0.043907 CGACGACATATGCAGTTGCG 60.044 55.000 1.58 3.54 45.83 4.85
333 334 0.999406 ACGACATATGCAGTTGCGAC 59.001 50.000 1.58 0.00 45.83 5.19
334 335 1.280982 CGACATATGCAGTTGCGACT 58.719 50.000 0.00 0.00 45.83 4.18
335 336 1.660607 CGACATATGCAGTTGCGACTT 59.339 47.619 3.02 0.00 45.83 3.01
336 337 2.535534 CGACATATGCAGTTGCGACTTG 60.536 50.000 3.02 2.30 45.83 3.16
337 338 1.131126 ACATATGCAGTTGCGACTTGC 59.869 47.619 16.94 16.94 45.83 4.01
354 355 1.006337 GCAACCGCAGCAAATCCAA 60.006 52.632 0.00 0.00 38.36 3.53
412 6429 0.107993 CATGCTCCGCCTCAAGAAGA 60.108 55.000 0.00 0.00 0.00 2.87
430 6447 4.579340 AGAAGAGCGTCGTTTCCTATATCA 59.421 41.667 0.00 0.00 0.00 2.15
495 6542 4.382320 TCCGCCGTTTCCCCGAAG 62.382 66.667 0.00 0.00 0.00 3.79
511 6558 3.393970 AGCCTAGCAGCTTCGCCA 61.394 61.111 0.00 0.00 41.41 5.69
534 6581 0.324285 AGGAGTACCTCGTCGACACT 59.676 55.000 17.16 10.82 44.13 3.55
595 6642 0.907230 GCTCTCCCACCTCAAGTCCT 60.907 60.000 0.00 0.00 0.00 3.85
603 6651 1.201429 ACCTCAAGTCCTCCGCCAAT 61.201 55.000 0.00 0.00 0.00 3.16
711 6760 1.135257 CGCACCAAAGTGGACAAAACA 60.135 47.619 0.18 0.00 44.69 2.83
750 6799 1.455217 GCTCACCGGCCTAGGTCTA 60.455 63.158 12.53 0.00 43.89 2.59
752 6801 1.547223 GCTCACCGGCCTAGGTCTATA 60.547 57.143 12.53 0.00 43.89 1.31
862 6911 0.721718 CTTCGGCTCATTCGACAACC 59.278 55.000 0.00 0.00 36.30 3.77
1083 7132 2.034879 CCGTGGCTCTGCGATGTTT 61.035 57.895 0.00 0.00 0.00 2.83
1149 7198 2.370519 TGCTGCCAAACTGGACTACTTA 59.629 45.455 0.00 0.00 40.96 2.24
1184 7233 0.391661 TGGTCTGATGCCGAAGCTTC 60.392 55.000 16.84 16.84 42.16 3.86
1218 7267 0.324368 AGTATCCGGGTGTGCTGAGA 60.324 55.000 0.00 0.00 0.00 3.27
1227 7276 2.687935 GGGTGTGCTGAGAAAGTCAAAA 59.312 45.455 0.00 0.00 33.60 2.44
1249 7298 0.908198 ATCTCTGAAGCACAGGTCCC 59.092 55.000 10.23 0.00 45.76 4.46
1325 7374 7.450074 TCGGAAATACTTTCATATAGCATGGT 58.550 34.615 1.62 1.62 41.43 3.55
1425 7474 1.068281 AGCGCGATCAAGATGACTGAT 59.932 47.619 12.10 0.00 0.00 2.90
1666 7728 2.663826 TGTTGGTTGTTTTCTGTGGC 57.336 45.000 0.00 0.00 0.00 5.01
1686 7766 2.675889 GCATGCCTGTTGCTAAATGCTT 60.676 45.455 6.36 0.00 41.34 3.91
1797 7886 8.954350 AGTTCATGGATATTTTGTCTTTCTGAG 58.046 33.333 0.00 0.00 0.00 3.35
1898 7989 3.364964 CCAAAAGAGTAATGTGGTGTCGC 60.365 47.826 0.00 0.00 0.00 5.19
2111 8264 4.260172 CCTTCCGCAAATTGTTGTGTTTTC 60.260 41.667 0.00 0.00 42.60 2.29
2143 8297 8.880878 AATTAATGTTTCCTGGTTGTGTTTAC 57.119 30.769 0.00 0.00 0.00 2.01
2196 8357 6.712095 ACTGTCACCATGCCATTATATACAAG 59.288 38.462 0.00 0.00 0.00 3.16
2208 8369 7.605449 CCATTATATACAAGCATTTTCCCTGG 58.395 38.462 0.00 0.00 0.00 4.45
2219 8380 1.801242 TTTCCCTGGTCAGAGACACA 58.199 50.000 0.00 0.00 33.68 3.72
2230 8391 4.999950 GGTCAGAGACACAAAAGATGACAT 59.000 41.667 0.00 0.00 37.82 3.06
2297 8459 1.001487 TCGTGTGAAAGCTGCAAATGG 60.001 47.619 1.02 0.00 0.00 3.16
2298 8460 1.142474 GTGTGAAAGCTGCAAATGGC 58.858 50.000 1.02 0.00 45.13 4.40
2331 8499 3.377485 GCAGCTGATGATCAACAAGATGT 59.623 43.478 20.43 0.00 37.00 3.06
2405 8575 4.576463 CAGTTATACCAAGGTCATGAAGCC 59.424 45.833 0.00 0.00 0.00 4.35
2415 8585 1.141657 GTCATGAAGCCCCTATCTGCA 59.858 52.381 0.00 0.00 0.00 4.41
2423 8593 0.625849 CCCCTATCTGCAAACTGGGT 59.374 55.000 11.86 0.00 33.13 4.51
2427 8597 2.290260 CCTATCTGCAAACTGGGTGTCA 60.290 50.000 0.00 0.00 0.00 3.58
2507 8683 0.468226 TCCGAAGAGTGTTGTGCCTT 59.532 50.000 0.00 0.00 0.00 4.35
2524 8700 3.964031 TGCCTTGGTTCAAAAATACCAGT 59.036 39.130 0.00 0.00 44.68 4.00
2525 8701 4.038642 TGCCTTGGTTCAAAAATACCAGTC 59.961 41.667 0.00 0.00 44.68 3.51
2527 8703 5.475564 GCCTTGGTTCAAAAATACCAGTCTA 59.524 40.000 0.00 0.00 44.68 2.59
2528 8704 6.349363 GCCTTGGTTCAAAAATACCAGTCTAG 60.349 42.308 0.00 0.00 44.68 2.43
2530 8706 7.094762 CCTTGGTTCAAAAATACCAGTCTAGAC 60.095 40.741 15.41 15.41 44.68 2.59
2533 8709 7.016268 TGGTTCAAAAATACCAGTCTAGACTCT 59.984 37.037 22.76 12.89 39.44 3.24
2543 8730 6.926313 ACCAGTCTAGACTCTGTTTATGAAC 58.074 40.000 22.76 0.00 40.20 3.18
2552 8739 6.989169 AGACTCTGTTTATGAACTGCATATCC 59.011 38.462 1.75 0.00 39.15 2.59
2553 8740 5.755375 ACTCTGTTTATGAACTGCATATCCG 59.245 40.000 1.75 0.00 39.15 4.18
2571 8758 2.251642 GCGCGGTGACTCCAACTTT 61.252 57.895 8.83 0.00 35.57 2.66
2573 8760 0.661020 CGCGGTGACTCCAACTTTTT 59.339 50.000 0.00 0.00 35.57 1.94
2646 8833 1.093159 CAACAGATCTGGGCTTCTGC 58.907 55.000 26.08 0.00 42.51 4.26
2648 8835 1.871418 ACAGATCTGGGCTTCTGCTA 58.129 50.000 26.08 0.00 42.51 3.49
2708 8895 8.575649 TGTTAACTTTCTTTTCCTGAACTTCT 57.424 30.769 7.22 0.00 0.00 2.85
2713 8900 8.980481 ACTTTCTTTTCCTGAACTTCTTGATA 57.020 30.769 0.00 0.00 0.00 2.15
2737 8924 6.937436 AAAATGGAGAAGAACGTAACACTT 57.063 33.333 0.00 0.00 0.00 3.16
2738 8925 5.924475 AATGGAGAAGAACGTAACACTTG 57.076 39.130 0.00 0.00 0.00 3.16
2739 8926 3.724374 TGGAGAAGAACGTAACACTTGG 58.276 45.455 0.00 0.00 0.00 3.61
2740 8927 3.133362 TGGAGAAGAACGTAACACTTGGT 59.867 43.478 0.00 0.00 0.00 3.67
2741 8928 4.124970 GGAGAAGAACGTAACACTTGGTT 58.875 43.478 0.00 0.00 43.62 3.67
2742 8929 4.025145 GGAGAAGAACGTAACACTTGGTTG 60.025 45.833 0.00 0.00 40.73 3.77
2743 8930 3.875134 AGAAGAACGTAACACTTGGTTGG 59.125 43.478 0.00 0.00 40.73 3.77
2744 8931 1.944709 AGAACGTAACACTTGGTTGGC 59.055 47.619 0.00 0.00 40.73 4.52
2745 8932 1.671845 GAACGTAACACTTGGTTGGCA 59.328 47.619 0.00 0.00 40.73 4.92
2746 8933 1.975660 ACGTAACACTTGGTTGGCAT 58.024 45.000 0.00 0.00 40.73 4.40
2747 8934 1.877443 ACGTAACACTTGGTTGGCATC 59.123 47.619 0.00 0.00 40.73 3.91
2748 8935 2.151202 CGTAACACTTGGTTGGCATCT 58.849 47.619 0.00 0.00 40.73 2.90
2749 8936 2.095768 CGTAACACTTGGTTGGCATCTG 60.096 50.000 0.00 0.00 40.73 2.90
2750 8937 1.331214 AACACTTGGTTGGCATCTGG 58.669 50.000 0.00 0.00 38.60 3.86
2751 8938 0.185901 ACACTTGGTTGGCATCTGGT 59.814 50.000 0.00 0.00 0.00 4.00
2752 8939 1.331214 CACTTGGTTGGCATCTGGTT 58.669 50.000 0.00 0.00 0.00 3.67
2753 8940 1.688197 CACTTGGTTGGCATCTGGTTT 59.312 47.619 0.00 0.00 0.00 3.27
2754 8941 2.890311 CACTTGGTTGGCATCTGGTTTA 59.110 45.455 0.00 0.00 0.00 2.01
2755 8942 3.511146 CACTTGGTTGGCATCTGGTTTAT 59.489 43.478 0.00 0.00 0.00 1.40
2756 8943 4.704540 CACTTGGTTGGCATCTGGTTTATA 59.295 41.667 0.00 0.00 0.00 0.98
2757 8944 4.949856 ACTTGGTTGGCATCTGGTTTATAG 59.050 41.667 0.00 0.00 0.00 1.31
2758 8945 4.584638 TGGTTGGCATCTGGTTTATAGT 57.415 40.909 0.00 0.00 0.00 2.12
2759 8946 4.929479 TGGTTGGCATCTGGTTTATAGTT 58.071 39.130 0.00 0.00 0.00 2.24
2760 8947 6.068461 TGGTTGGCATCTGGTTTATAGTTA 57.932 37.500 0.00 0.00 0.00 2.24
2787 8974 7.591421 TGGAGATGAATGCATTGAATGTTAT 57.409 32.000 18.59 0.00 34.11 1.89
2788 8975 8.694581 TGGAGATGAATGCATTGAATGTTATA 57.305 30.769 18.59 0.00 34.11 0.98
2814 9001 9.830186 ATTCTGATATGATAGGTACAACTAGGT 57.170 33.333 0.00 0.00 0.00 3.08
2816 9003 7.606839 TCTGATATGATAGGTACAACTAGGTCG 59.393 40.741 0.00 0.00 0.00 4.79
2818 9005 8.107729 TGATATGATAGGTACAACTAGGTCGAT 58.892 37.037 0.00 0.00 0.00 3.59
2820 9007 9.970553 ATATGATAGGTACAACTAGGTCGATTA 57.029 33.333 0.00 0.00 0.00 1.75
2855 9042 2.189594 TCACCCTGCTGTTCAGATTG 57.810 50.000 3.84 0.00 45.72 2.67
2909 9097 7.848223 AGCAAAAATAATGGTTAAGATTGGC 57.152 32.000 0.00 0.00 0.00 4.52
2910 9098 7.623630 AGCAAAAATAATGGTTAAGATTGGCT 58.376 30.769 0.00 0.00 0.00 4.75
2911 9099 8.757877 AGCAAAAATAATGGTTAAGATTGGCTA 58.242 29.630 0.00 0.00 0.00 3.93
2912 9100 9.377312 GCAAAAATAATGGTTAAGATTGGCTAA 57.623 29.630 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.327154 ACAACTTTTCTTTTCGTTTACTGGG 58.673 36.000 0.00 0.00 0.00 4.45
1 2 7.806149 AACAACTTTTCTTTTCGTTTACTGG 57.194 32.000 0.00 0.00 0.00 4.00
2 3 9.511022 CAAAACAACTTTTCTTTTCGTTTACTG 57.489 29.630 0.00 0.00 0.00 2.74
3 4 8.218441 GCAAAACAACTTTTCTTTTCGTTTACT 58.782 29.630 0.00 0.00 0.00 2.24
4 5 8.004905 TGCAAAACAACTTTTCTTTTCGTTTAC 58.995 29.630 0.00 0.00 0.00 2.01
6 7 6.949449 TGCAAAACAACTTTTCTTTTCGTTT 58.051 28.000 0.00 0.00 0.00 3.60
7 8 6.532365 TGCAAAACAACTTTTCTTTTCGTT 57.468 29.167 0.00 0.00 0.00 3.85
8 9 6.532365 TTGCAAAACAACTTTTCTTTTCGT 57.468 29.167 0.00 0.00 31.73 3.85
11 12 9.824534 CATACTTTGCAAAACAACTTTTCTTTT 57.175 25.926 13.84 0.00 38.23 2.27
32 33 9.869757 GTTCCAAGGTAAAATTTAATGCATACT 57.130 29.630 0.00 0.00 0.00 2.12
33 34 9.093970 GGTTCCAAGGTAAAATTTAATGCATAC 57.906 33.333 0.00 0.00 0.00 2.39
37 38 7.158697 ACAGGTTCCAAGGTAAAATTTAATGC 58.841 34.615 0.00 0.00 0.00 3.56
42 43 8.147704 CACATTACAGGTTCCAAGGTAAAATTT 58.852 33.333 0.00 0.00 30.41 1.82
43 44 7.507616 TCACATTACAGGTTCCAAGGTAAAATT 59.492 33.333 0.00 0.00 30.41 1.82
44 45 7.007723 TCACATTACAGGTTCCAAGGTAAAAT 58.992 34.615 0.00 0.00 30.41 1.82
45 46 6.366340 TCACATTACAGGTTCCAAGGTAAAA 58.634 36.000 0.00 0.00 30.41 1.52
46 47 5.942961 TCACATTACAGGTTCCAAGGTAAA 58.057 37.500 0.00 0.00 30.41 2.01
47 48 5.072600 ACTCACATTACAGGTTCCAAGGTAA 59.927 40.000 0.00 0.00 0.00 2.85
48 49 4.595781 ACTCACATTACAGGTTCCAAGGTA 59.404 41.667 0.00 0.00 0.00 3.08
49 50 3.394606 ACTCACATTACAGGTTCCAAGGT 59.605 43.478 0.00 0.00 0.00 3.50
51 52 5.299279 ACAAACTCACATTACAGGTTCCAAG 59.701 40.000 0.00 0.00 0.00 3.61
53 54 4.578516 CACAAACTCACATTACAGGTTCCA 59.421 41.667 0.00 0.00 0.00 3.53
54 55 4.023193 CCACAAACTCACATTACAGGTTCC 60.023 45.833 0.00 0.00 0.00 3.62
55 56 4.556699 GCCACAAACTCACATTACAGGTTC 60.557 45.833 0.00 0.00 0.00 3.62
56 57 3.317993 GCCACAAACTCACATTACAGGTT 59.682 43.478 0.00 0.00 0.00 3.50
58 59 2.228822 GGCCACAAACTCACATTACAGG 59.771 50.000 0.00 0.00 0.00 4.00
59 60 3.149196 AGGCCACAAACTCACATTACAG 58.851 45.455 5.01 0.00 0.00 2.74
61 62 3.317993 ACAAGGCCACAAACTCACATTAC 59.682 43.478 5.01 0.00 0.00 1.89
63 64 2.387757 ACAAGGCCACAAACTCACATT 58.612 42.857 5.01 0.00 0.00 2.71
64 65 2.071778 ACAAGGCCACAAACTCACAT 57.928 45.000 5.01 0.00 0.00 3.21
65 66 2.719531 TACAAGGCCACAAACTCACA 57.280 45.000 5.01 0.00 0.00 3.58
66 67 6.995511 TTATATACAAGGCCACAAACTCAC 57.004 37.500 5.01 0.00 0.00 3.51
68 69 9.301153 CATTTTTATATACAAGGCCACAAACTC 57.699 33.333 5.01 0.00 0.00 3.01
69 70 8.257306 CCATTTTTATATACAAGGCCACAAACT 58.743 33.333 5.01 0.00 0.00 2.66
70 71 8.254508 TCCATTTTTATATACAAGGCCACAAAC 58.745 33.333 5.01 0.00 0.00 2.93
71 72 8.367660 TCCATTTTTATATACAAGGCCACAAA 57.632 30.769 5.01 0.00 0.00 2.83
76 77 5.538433 TGCCTCCATTTTTATATACAAGGCC 59.462 40.000 0.00 0.00 44.82 5.19
77 78 6.265422 ACTGCCTCCATTTTTATATACAAGGC 59.735 38.462 0.00 0.00 45.46 4.35
78 79 7.823745 ACTGCCTCCATTTTTATATACAAGG 57.176 36.000 0.00 0.00 0.00 3.61
82 83 9.515226 TTGGATACTGCCTCCATTTTTATATAC 57.485 33.333 0.23 0.00 42.26 1.47
84 85 9.605951 ATTTGGATACTGCCTCCATTTTTATAT 57.394 29.630 0.23 0.00 42.26 0.86
85 86 9.432982 AATTTGGATACTGCCTCCATTTTTATA 57.567 29.630 0.23 0.00 42.26 0.98
88 89 6.625532 AATTTGGATACTGCCTCCATTTTT 57.374 33.333 0.23 0.00 42.26 1.94
89 90 6.625532 AAATTTGGATACTGCCTCCATTTT 57.374 33.333 0.00 2.26 42.26 1.82
90 91 7.619302 TCTTAAATTTGGATACTGCCTCCATTT 59.381 33.333 0.00 2.59 42.26 2.32
91 92 7.125391 TCTTAAATTTGGATACTGCCTCCATT 58.875 34.615 0.00 0.00 42.26 3.16
92 93 6.672593 TCTTAAATTTGGATACTGCCTCCAT 58.327 36.000 0.00 0.00 42.26 3.41
93 94 6.069673 TCTCTTAAATTTGGATACTGCCTCCA 60.070 38.462 0.00 0.00 41.03 3.86
94 95 6.261158 GTCTCTTAAATTTGGATACTGCCTCC 59.739 42.308 0.00 0.00 37.61 4.30
95 96 6.018669 CGTCTCTTAAATTTGGATACTGCCTC 60.019 42.308 0.00 0.00 37.61 4.70
96 97 5.817816 CGTCTCTTAAATTTGGATACTGCCT 59.182 40.000 0.00 0.00 37.61 4.75
97 98 5.585047 ACGTCTCTTAAATTTGGATACTGCC 59.415 40.000 0.00 0.00 37.61 4.85
99 100 6.816640 TGGACGTCTCTTAAATTTGGATACTG 59.183 38.462 16.46 2.78 37.61 2.74
101 102 7.605410 TTGGACGTCTCTTAAATTTGGATAC 57.395 36.000 16.46 1.98 0.00 2.24
103 104 7.148069 GGATTTGGACGTCTCTTAAATTTGGAT 60.148 37.037 16.46 0.00 0.00 3.41
104 105 6.150474 GGATTTGGACGTCTCTTAAATTTGGA 59.850 38.462 16.46 0.00 0.00 3.53
106 107 6.908825 TGGATTTGGACGTCTCTTAAATTTG 58.091 36.000 16.46 0.00 0.00 2.32
107 108 7.519032 TTGGATTTGGACGTCTCTTAAATTT 57.481 32.000 16.46 0.00 0.00 1.82
109 110 7.538575 CAATTGGATTTGGACGTCTCTTAAAT 58.461 34.615 16.46 15.67 0.00 1.40
110 111 6.569610 GCAATTGGATTTGGACGTCTCTTAAA 60.570 38.462 16.46 11.92 0.00 1.52
115 116 2.159379 GGCAATTGGATTTGGACGTCTC 60.159 50.000 16.46 4.66 0.00 3.36
116 117 1.818674 GGCAATTGGATTTGGACGTCT 59.181 47.619 16.46 0.00 0.00 4.18
117 118 1.543802 TGGCAATTGGATTTGGACGTC 59.456 47.619 7.13 7.13 0.00 4.34
118 119 1.626686 TGGCAATTGGATTTGGACGT 58.373 45.000 7.72 0.00 0.00 4.34
120 121 4.950434 CAATTGGCAATTGGATTTGGAC 57.050 40.909 34.65 0.00 43.50 4.02
129 130 2.767394 TCCCAGATCCAATTGGCAATTG 59.233 45.455 35.08 35.08 46.09 2.32
130 131 3.119009 TCCCAGATCCAATTGGCAATT 57.881 42.857 20.33 19.39 32.98 2.32
131 132 2.852714 TCCCAGATCCAATTGGCAAT 57.147 45.000 20.33 6.96 32.98 3.56
133 134 2.566724 GTTTTCCCAGATCCAATTGGCA 59.433 45.455 20.33 9.23 32.98 4.92
134 135 2.566724 TGTTTTCCCAGATCCAATTGGC 59.433 45.455 20.33 6.80 32.98 4.52
135 136 5.658190 ACTATGTTTTCCCAGATCCAATTGG 59.342 40.000 19.08 19.08 0.00 3.16
136 137 6.780457 ACTATGTTTTCCCAGATCCAATTG 57.220 37.500 0.00 0.00 0.00 2.32
138 139 7.815383 TGATACTATGTTTTCCCAGATCCAAT 58.185 34.615 0.00 0.00 0.00 3.16
139 140 7.206789 TGATACTATGTTTTCCCAGATCCAA 57.793 36.000 0.00 0.00 0.00 3.53
140 141 6.823286 TGATACTATGTTTTCCCAGATCCA 57.177 37.500 0.00 0.00 0.00 3.41
141 142 8.697507 AAATGATACTATGTTTTCCCAGATCC 57.302 34.615 0.00 0.00 0.00 3.36
145 146 9.927668 AACAAAAATGATACTATGTTTTCCCAG 57.072 29.630 0.00 0.00 0.00 4.45
161 162 9.670719 GTTCCAGAAAAACAAAAACAAAAATGA 57.329 25.926 0.00 0.00 0.00 2.57
162 163 9.455847 TGTTCCAGAAAAACAAAAACAAAAATG 57.544 25.926 0.00 0.00 33.86 2.32
173 174 3.914312 TGCGTTTGTTCCAGAAAAACAA 58.086 36.364 13.51 0.00 43.03 2.83
174 175 3.577649 TGCGTTTGTTCCAGAAAAACA 57.422 38.095 13.51 0.00 34.23 2.83
175 176 4.359706 AGATGCGTTTGTTCCAGAAAAAC 58.640 39.130 7.52 7.52 0.00 2.43
177 178 4.647424 AAGATGCGTTTGTTCCAGAAAA 57.353 36.364 0.00 0.00 0.00 2.29
178 179 4.819630 ACTAAGATGCGTTTGTTCCAGAAA 59.180 37.500 0.00 0.00 0.00 2.52
181 182 4.749245 AACTAAGATGCGTTTGTTCCAG 57.251 40.909 0.00 0.00 0.00 3.86
209 210 4.714308 TGATGGATATGTTTTTGTTCCCCC 59.286 41.667 0.00 0.00 0.00 5.40
211 212 8.791327 AAATTGATGGATATGTTTTTGTTCCC 57.209 30.769 0.00 0.00 0.00 3.97
219 220 9.211410 TGACCCATAAAATTGATGGATATGTTT 57.789 29.630 10.99 0.00 45.89 2.83
220 221 8.780616 TGACCCATAAAATTGATGGATATGTT 57.219 30.769 10.99 0.00 45.89 2.71
222 223 7.452501 ACCTGACCCATAAAATTGATGGATATG 59.547 37.037 10.99 0.00 45.89 1.78
223 224 7.538402 ACCTGACCCATAAAATTGATGGATAT 58.462 34.615 10.99 0.00 45.89 1.63
225 226 5.780731 ACCTGACCCATAAAATTGATGGAT 58.219 37.500 10.99 0.00 45.89 3.41
226 227 5.200483 GACCTGACCCATAAAATTGATGGA 58.800 41.667 10.99 0.00 45.89 3.41
227 228 4.342092 GGACCTGACCCATAAAATTGATGG 59.658 45.833 2.18 2.18 43.12 3.51
228 229 4.955450 TGGACCTGACCCATAAAATTGATG 59.045 41.667 0.00 0.00 0.00 3.07
229 230 5.205517 TGGACCTGACCCATAAAATTGAT 57.794 39.130 0.00 0.00 0.00 2.57
233 234 6.590656 TCTATTGGACCTGACCCATAAAAT 57.409 37.500 0.00 0.00 33.04 1.82
234 235 5.631481 GCTCTATTGGACCTGACCCATAAAA 60.631 44.000 0.00 0.00 33.04 1.52
236 237 3.391296 GCTCTATTGGACCTGACCCATAA 59.609 47.826 0.00 0.00 33.04 1.90
238 239 1.771255 GCTCTATTGGACCTGACCCAT 59.229 52.381 0.00 0.00 33.04 4.00
239 240 1.204146 GCTCTATTGGACCTGACCCA 58.796 55.000 0.00 0.00 0.00 4.51
240 241 0.470341 GGCTCTATTGGACCTGACCC 59.530 60.000 0.00 0.00 0.00 4.46
241 242 0.470341 GGGCTCTATTGGACCTGACC 59.530 60.000 0.00 0.00 0.00 4.02
243 244 1.204146 GTGGGCTCTATTGGACCTGA 58.796 55.000 0.00 0.00 0.00 3.86
244 245 0.911769 TGTGGGCTCTATTGGACCTG 59.088 55.000 0.00 0.00 0.00 4.00
246 247 2.092323 GTTTGTGGGCTCTATTGGACC 58.908 52.381 0.00 0.00 0.00 4.46
247 248 2.488153 GTGTTTGTGGGCTCTATTGGAC 59.512 50.000 0.00 0.00 0.00 4.02
248 249 2.107378 TGTGTTTGTGGGCTCTATTGGA 59.893 45.455 0.00 0.00 0.00 3.53
250 251 3.411446 TCTGTGTTTGTGGGCTCTATTG 58.589 45.455 0.00 0.00 0.00 1.90
252 253 3.181445 TGTTCTGTGTTTGTGGGCTCTAT 60.181 43.478 0.00 0.00 0.00 1.98
253 254 2.171659 TGTTCTGTGTTTGTGGGCTCTA 59.828 45.455 0.00 0.00 0.00 2.43
254 255 1.064758 TGTTCTGTGTTTGTGGGCTCT 60.065 47.619 0.00 0.00 0.00 4.09
255 256 1.388547 TGTTCTGTGTTTGTGGGCTC 58.611 50.000 0.00 0.00 0.00 4.70
256 257 1.956477 GATGTTCTGTGTTTGTGGGCT 59.044 47.619 0.00 0.00 0.00 5.19
257 258 1.000274 GGATGTTCTGTGTTTGTGGGC 60.000 52.381 0.00 0.00 0.00 5.36
258 259 1.266718 CGGATGTTCTGTGTTTGTGGG 59.733 52.381 0.00 0.00 0.00 4.61
259 260 2.217750 TCGGATGTTCTGTGTTTGTGG 58.782 47.619 0.00 0.00 0.00 4.17
260 261 3.961477 TTCGGATGTTCTGTGTTTGTG 57.039 42.857 0.00 0.00 0.00 3.33
261 262 4.196193 TCTTTCGGATGTTCTGTGTTTGT 58.804 39.130 0.00 0.00 0.00 2.83
264 265 4.703897 TCTTCTTTCGGATGTTCTGTGTT 58.296 39.130 0.00 0.00 0.00 3.32
265 266 4.039245 TCTCTTCTTTCGGATGTTCTGTGT 59.961 41.667 0.00 0.00 0.00 3.72
266 267 4.560128 TCTCTTCTTTCGGATGTTCTGTG 58.440 43.478 0.00 0.00 0.00 3.66
267 268 4.873746 TCTCTTCTTTCGGATGTTCTGT 57.126 40.909 0.00 0.00 0.00 3.41
268 269 4.033817 GCATCTCTTCTTTCGGATGTTCTG 59.966 45.833 0.00 0.00 38.16 3.02
269 270 4.187694 GCATCTCTTCTTTCGGATGTTCT 58.812 43.478 0.00 0.00 38.16 3.01
270 271 3.935203 TGCATCTCTTCTTTCGGATGTTC 59.065 43.478 0.00 0.00 38.16 3.18
273 274 2.287373 GCTGCATCTCTTCTTTCGGATG 59.713 50.000 0.00 0.00 38.69 3.51
275 276 1.406069 GGCTGCATCTCTTCTTTCGGA 60.406 52.381 0.50 0.00 0.00 4.55
276 277 1.012841 GGCTGCATCTCTTCTTTCGG 58.987 55.000 0.50 0.00 0.00 4.30
278 279 2.119801 TGGGCTGCATCTCTTCTTTC 57.880 50.000 0.50 0.00 0.00 2.62
279 280 2.822707 ATGGGCTGCATCTCTTCTTT 57.177 45.000 0.50 0.00 0.00 2.52
280 281 2.241685 AGAATGGGCTGCATCTCTTCTT 59.758 45.455 0.50 0.00 0.00 2.52
281 282 1.845143 AGAATGGGCTGCATCTCTTCT 59.155 47.619 0.50 3.94 0.00 2.85
282 283 1.948145 CAGAATGGGCTGCATCTCTTC 59.052 52.381 0.50 1.87 0.00 2.87
283 284 1.562942 TCAGAATGGGCTGCATCTCTT 59.437 47.619 0.50 0.00 36.16 2.85
284 285 1.141254 CTCAGAATGGGCTGCATCTCT 59.859 52.381 0.50 0.00 36.16 3.10
285 286 1.595466 CTCAGAATGGGCTGCATCTC 58.405 55.000 0.50 0.00 36.16 2.75
286 287 3.802862 CTCAGAATGGGCTGCATCT 57.197 52.632 0.50 0.00 36.16 2.90
294 295 1.508088 GGCGTTTGCTCAGAATGGG 59.492 57.895 0.00 0.00 42.01 4.00
296 297 0.179215 GTCGGCGTTTGCTCAGAATG 60.179 55.000 6.85 0.00 42.25 2.67
297 298 1.626654 CGTCGGCGTTTGCTCAGAAT 61.627 55.000 6.85 0.00 42.25 2.40
298 299 2.307309 CGTCGGCGTTTGCTCAGAA 61.307 57.895 6.85 0.00 42.25 3.02
299 300 2.733218 CGTCGGCGTTTGCTCAGA 60.733 61.111 6.85 0.00 42.25 3.27
300 301 2.733218 TCGTCGGCGTTTGCTCAG 60.733 61.111 10.18 0.00 42.25 3.35
301 302 3.033764 GTCGTCGGCGTTTGCTCA 61.034 61.111 10.18 0.00 42.25 4.26
302 303 1.074319 TATGTCGTCGGCGTTTGCTC 61.074 55.000 10.18 0.00 42.25 4.26
303 304 0.459585 ATATGTCGTCGGCGTTTGCT 60.460 50.000 10.18 0.00 42.25 3.91
304 305 0.315059 CATATGTCGTCGGCGTTTGC 60.315 55.000 10.18 0.00 39.49 3.68
305 306 0.315059 GCATATGTCGTCGGCGTTTG 60.315 55.000 10.18 0.44 39.49 2.93
306 307 0.738063 TGCATATGTCGTCGGCGTTT 60.738 50.000 10.18 0.00 39.49 3.60
307 308 1.145759 CTGCATATGTCGTCGGCGTT 61.146 55.000 10.18 0.00 39.49 4.84
308 309 1.588932 CTGCATATGTCGTCGGCGT 60.589 57.895 10.18 0.00 39.49 5.68
309 310 1.145759 AACTGCATATGTCGTCGGCG 61.146 55.000 1.15 1.15 39.92 6.46
310 311 0.301687 CAACTGCATATGTCGTCGGC 59.698 55.000 4.29 0.00 0.00 5.54
311 312 0.301687 GCAACTGCATATGTCGTCGG 59.698 55.000 4.29 0.00 41.59 4.79
312 313 0.043907 CGCAACTGCATATGTCGTCG 60.044 55.000 4.29 0.00 42.21 5.12
315 316 1.280982 AGTCGCAACTGCATATGTCG 58.719 50.000 4.29 0.00 42.21 4.35
316 317 2.789092 GCAAGTCGCAACTGCATATGTC 60.789 50.000 4.29 0.00 42.21 3.06
317 318 1.131126 GCAAGTCGCAACTGCATATGT 59.869 47.619 4.29 0.00 42.21 2.29
318 319 1.818850 GCAAGTCGCAACTGCATATG 58.181 50.000 0.00 0.00 42.21 1.78
336 337 1.006337 TTGGATTTGCTGCGGTTGC 60.006 52.632 0.00 0.00 43.20 4.17
337 338 1.003262 CGTTGGATTTGCTGCGGTTG 61.003 55.000 0.00 0.00 0.00 3.77
338 339 1.285641 CGTTGGATTTGCTGCGGTT 59.714 52.632 0.00 0.00 0.00 4.44
339 340 2.625823 CCGTTGGATTTGCTGCGGT 61.626 57.895 0.00 0.00 35.11 5.68
340 341 1.861542 TTCCGTTGGATTTGCTGCGG 61.862 55.000 0.00 0.00 40.43 5.69
341 342 0.039617 TTTCCGTTGGATTTGCTGCG 60.040 50.000 0.00 0.00 0.00 5.18
342 343 2.094545 AGATTTCCGTTGGATTTGCTGC 60.095 45.455 0.00 0.00 0.00 5.25
343 344 3.428045 GGAGATTTCCGTTGGATTTGCTG 60.428 47.826 0.00 0.00 32.79 4.41
345 346 3.150848 GGAGATTTCCGTTGGATTTGC 57.849 47.619 0.00 0.00 32.79 3.68
407 6424 4.579340 TGATATAGGAAACGACGCTCTTCT 59.421 41.667 0.00 0.00 0.00 2.85
412 6429 4.762765 AGAGATGATATAGGAAACGACGCT 59.237 41.667 0.00 0.00 0.00 5.07
430 6447 3.373830 CAGAGGTGGAGGAAGAAGAGAT 58.626 50.000 0.00 0.00 0.00 2.75
667 6716 0.392998 AACAGCGGATCTTTGGCGAT 60.393 50.000 0.00 0.00 0.00 4.58
711 6760 1.912971 GACGACCTTAGGGGCCAAT 59.087 57.895 4.39 0.00 37.32 3.16
750 6799 1.333177 GGGCGATGTCAGGACTCTAT 58.667 55.000 0.65 0.00 0.00 1.98
752 6801 2.418910 CGGGCGATGTCAGGACTCT 61.419 63.158 0.65 0.00 0.00 3.24
862 6911 0.459237 CACTTGAGCAGCCGGAGTAG 60.459 60.000 5.05 0.00 0.00 2.57
960 7009 3.065786 ACAGCTTGGCAATATCACAATCG 59.934 43.478 0.00 0.00 0.00 3.34
1039 7088 1.750193 CCAATACCTTCGGTGCATGT 58.250 50.000 0.00 0.00 36.19 3.21
1045 7094 1.743995 GCACGCCAATACCTTCGGT 60.744 57.895 0.00 0.00 40.16 4.69
1076 7125 4.577687 TGTAGCGCTTTTCTAAACATCG 57.422 40.909 18.68 0.00 0.00 3.84
1131 7180 5.298989 TCTTTAAGTAGTCCAGTTTGGCA 57.701 39.130 0.00 0.00 37.47 4.92
1218 7267 6.319658 TGTGCTTCAGAGATTCTTTTGACTTT 59.680 34.615 2.40 0.00 0.00 2.66
1227 7276 2.235898 GGACCTGTGCTTCAGAGATTCT 59.764 50.000 10.22 0.00 46.27 2.40
1325 7374 2.680352 GAGGTCTGAGTCGGCCCA 60.680 66.667 1.10 0.00 0.00 5.36
1401 7450 3.605916 CAGTCATCTTGATCGCGCTATAC 59.394 47.826 5.56 0.00 0.00 1.47
1411 7460 9.334947 CACAAATACCTTATCAGTCATCTTGAT 57.665 33.333 0.00 0.00 0.00 2.57
1425 7474 5.755409 TGAGCTTCTCCACAAATACCTTA 57.245 39.130 0.00 0.00 0.00 2.69
1551 7601 6.737254 ATACACTGTAACCAACTTGCATAC 57.263 37.500 0.00 0.00 0.00 2.39
1556 7606 5.212194 GCACAATACACTGTAACCAACTTG 58.788 41.667 0.00 0.00 0.00 3.16
1710 7795 7.235399 ACATGAACAAATAAGGGTTGAGGAATT 59.765 33.333 0.00 0.00 0.00 2.17
1717 7802 6.511416 TGACAACATGAACAAATAAGGGTTG 58.489 36.000 0.00 0.00 39.99 3.77
1821 7910 4.329638 AATTGGTCCAACCCACATATCA 57.670 40.909 6.41 0.00 37.50 2.15
1898 7989 8.279970 TCATACTGATACATTTTGGTGGAAAG 57.720 34.615 0.00 0.00 0.00 2.62
2040 8137 1.051812 AGGTGGAAGGTCTCAGTGTG 58.948 55.000 0.00 0.00 0.00 3.82
2111 8264 8.522830 ACAACCAGGAAACATTAATTACATCAG 58.477 33.333 0.00 0.00 0.00 2.90
2143 8297 0.693049 AGGTTACCCCTGTTGCTCAG 59.307 55.000 0.00 3.18 44.08 3.35
2162 8316 3.157518 TGGTGACAGTAGCAGGGAA 57.842 52.632 0.00 0.00 35.01 3.97
2196 8357 2.087646 GTCTCTGACCAGGGAAAATGC 58.912 52.381 0.46 0.00 40.10 3.56
2208 8369 5.121454 GGATGTCATCTTTTGTGTCTCTGAC 59.879 44.000 12.54 0.00 33.79 3.51
2219 8380 9.118300 GTCAGATCTAAATGGATGTCATCTTTT 57.882 33.333 12.54 13.74 34.44 2.27
2297 8459 1.736645 CAGCTGCAGTTGCCAATGC 60.737 57.895 18.01 2.87 42.86 3.56
2298 8460 0.530744 ATCAGCTGCAGTTGCCAATG 59.469 50.000 24.28 8.06 41.18 2.82
2299 8461 0.530744 CATCAGCTGCAGTTGCCAAT 59.469 50.000 24.28 11.10 41.18 3.16
2300 8462 0.537828 TCATCAGCTGCAGTTGCCAA 60.538 50.000 24.28 9.18 41.18 4.52
2301 8463 0.323087 ATCATCAGCTGCAGTTGCCA 60.323 50.000 24.28 9.92 41.18 4.92
2302 8464 0.381089 GATCATCAGCTGCAGTTGCC 59.619 55.000 24.28 3.19 41.18 4.52
2383 8553 4.385310 GGGCTTCATGACCTTGGTATAACT 60.385 45.833 0.00 0.00 41.93 2.24
2397 8567 2.353357 TTGCAGATAGGGGCTTCATG 57.647 50.000 0.00 0.00 0.00 3.07
2405 8575 1.004745 ACACCCAGTTTGCAGATAGGG 59.995 52.381 13.42 13.42 42.07 3.53
2415 8585 4.907457 CTGGCTGACACCCAGTTT 57.093 55.556 8.46 0.00 43.86 2.66
2462 8638 3.470567 CTCGAACACAGGTCGCGC 61.471 66.667 0.00 0.00 0.00 6.86
2466 8642 1.264288 CCAAAAGCTCGAACACAGGTC 59.736 52.381 0.00 0.00 0.00 3.85
2507 8683 7.016268 AGAGTCTAGACTGGTATTTTTGAACCA 59.984 37.037 29.84 0.00 42.66 3.67
2524 8700 6.590234 TGCAGTTCATAAACAGAGTCTAGA 57.410 37.500 0.00 0.00 37.88 2.43
2525 8701 9.190858 GATATGCAGTTCATAAACAGAGTCTAG 57.809 37.037 0.00 0.00 40.73 2.43
2527 8703 6.989169 GGATATGCAGTTCATAAACAGAGTCT 59.011 38.462 0.00 0.00 40.73 3.24
2528 8704 6.074088 CGGATATGCAGTTCATAAACAGAGTC 60.074 42.308 0.00 0.00 40.73 3.36
2530 8706 5.333645 GCGGATATGCAGTTCATAAACAGAG 60.334 44.000 0.00 0.00 40.73 3.35
2533 8709 3.247411 CGCGGATATGCAGTTCATAAACA 59.753 43.478 0.00 0.00 40.73 2.83
2553 8740 1.782028 AAAAGTTGGAGTCACCGCGC 61.782 55.000 0.00 0.00 42.61 6.86
2573 8760 3.153130 TGCATCCGATGGTCAAGAAAAA 58.847 40.909 10.41 0.00 0.00 1.94
2574 8761 2.789213 TGCATCCGATGGTCAAGAAAA 58.211 42.857 10.41 0.00 0.00 2.29
2582 8769 0.548031 AGGTGATTGCATCCGATGGT 59.452 50.000 10.41 0.00 0.00 3.55
2669 8856 8.608844 AGAAAGTTAACATACCTCAGTTCAAG 57.391 34.615 8.61 0.00 0.00 3.02
2708 8895 9.058174 TGTTACGTTCTTCTCCATTTTTATCAA 57.942 29.630 0.00 0.00 0.00 2.57
2713 8900 6.937436 AGTGTTACGTTCTTCTCCATTTTT 57.063 33.333 0.00 0.00 0.00 1.94
2728 8915 2.095768 CAGATGCCAACCAAGTGTTACG 60.096 50.000 0.00 0.00 34.69 3.18
2737 8924 4.584638 ACTATAAACCAGATGCCAACCA 57.415 40.909 0.00 0.00 0.00 3.67
2738 8925 8.730680 CATATAACTATAAACCAGATGCCAACC 58.269 37.037 0.00 0.00 0.00 3.77
2739 8926 8.730680 CCATATAACTATAAACCAGATGCCAAC 58.269 37.037 0.00 0.00 0.00 3.77
2740 8927 8.664992 TCCATATAACTATAAACCAGATGCCAA 58.335 33.333 0.00 0.00 0.00 4.52
2741 8928 8.213489 TCCATATAACTATAAACCAGATGCCA 57.787 34.615 0.00 0.00 0.00 4.92
2742 8929 8.540388 TCTCCATATAACTATAAACCAGATGCC 58.460 37.037 0.00 0.00 0.00 4.40
2756 8943 8.929260 TTCAATGCATTCATCTCCATATAACT 57.071 30.769 9.53 0.00 31.27 2.24
2757 8944 9.569167 CATTCAATGCATTCATCTCCATATAAC 57.431 33.333 9.53 0.00 31.27 1.89
2758 8945 9.304335 ACATTCAATGCATTCATCTCCATATAA 57.696 29.630 9.53 0.00 31.27 0.98
2759 8946 8.873186 ACATTCAATGCATTCATCTCCATATA 57.127 30.769 9.53 0.00 31.27 0.86
2760 8947 7.776618 ACATTCAATGCATTCATCTCCATAT 57.223 32.000 9.53 0.00 31.27 1.78
2788 8975 9.830186 ACCTAGTTGTACCTATCATATCAGAAT 57.170 33.333 0.00 0.00 0.00 2.40
2792 8979 7.455891 TCGACCTAGTTGTACCTATCATATCA 58.544 38.462 0.00 0.00 0.00 2.15
2884 9071 8.102676 AGCCAATCTTAACCATTATTTTTGCTT 58.897 29.630 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.