Multiple sequence alignment - TraesCS3B01G321200

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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 TraesCS3B01G321200 chr3B 100.000 2243 0 0 1 2243 520374193 520371951 0.000000e+00 4143.0
1 TraesCS3B01G321200 chr3B 90.476 609 36 12 943 1539 520448633 520448035 0.000000e+00 784.0
2 TraesCS3B01G321200 chr3B 86.096 712 43 17 1541 2235 520447965 520447293 0.000000e+00 715.0
3 TraesCS3B01G321200 chr3B 90.127 395 36 1 387 778 520449877 520449483 5.530000e-141 510.0
4 TraesCS3B01G321200 chr3B 91.489 282 21 2 4 282 333292986 333292705 3.490000e-103 385.0
5 TraesCS3B01G321200 chr3B 91.743 109 9 0 149 257 185867605 185867497 3.860000e-33 152.0
6 TraesCS3B01G321200 chr3B 84.146 164 11 8 785 945 520449249 520449098 6.460000e-31 145.0
7 TraesCS3B01G321200 chr3B 97.368 38 1 0 302 339 520454661 520454624 5.170000e-07 65.8
8 TraesCS3B01G321200 chr3A 90.532 1447 69 16 828 2243 515725889 515724480 0.000000e+00 1851.0
9 TraesCS3B01G321200 chr3A 90.058 684 35 16 785 1451 515286064 515285397 0.000000e+00 856.0
10 TraesCS3B01G321200 chr3A 91.767 583 41 5 1664 2243 515285082 515284504 0.000000e+00 804.0
11 TraesCS3B01G321200 chr3A 90.229 481 30 8 302 778 515726512 515726045 1.470000e-171 612.0
12 TraesCS3B01G321200 chr3A 87.500 344 32 6 438 778 515589359 515589024 9.720000e-104 387.0
13 TraesCS3B01G321200 chr3A 83.226 155 7 3 1495 1649 515285396 515285261 8.410000e-25 124.0
14 TraesCS3B01G321200 chr3D 92.487 599 25 11 838 1432 395644494 395643912 0.000000e+00 839.0
15 TraesCS3B01G321200 chr3D 89.474 399 20 2 1837 2235 395643589 395643213 3.350000e-133 484.0
16 TraesCS3B01G321200 chr3D 85.177 479 50 9 307 778 395645322 395644858 2.610000e-129 472.0
17 TraesCS3B01G321200 chr3D 88.690 336 16 7 1479 1798 395643914 395643585 7.510000e-105 390.0
18 TraesCS3B01G321200 chr1D 91.558 308 23 2 1 305 208444865 208444558 2.660000e-114 422.0
19 TraesCS3B01G321200 chr1D 94.361 266 14 1 1 265 370973255 370972990 7.460000e-110 407.0
20 TraesCS3B01G321200 chr4D 95.057 263 12 1 1 262 236579142 236579404 1.600000e-111 412.0
21 TraesCS3B01G321200 chr4D 91.118 304 24 2 1 301 95228369 95228066 2.070000e-110 409.0
22 TraesCS3B01G321200 chr4D 91.579 285 21 2 1 282 506907357 506907073 7.510000e-105 390.0
23 TraesCS3B01G321200 chr7D 94.382 267 13 2 1 265 628383812 628383546 2.070000e-110 409.0
24 TraesCS3B01G321200 chr7D 94.297 263 14 1 1 262 240961581 240961843 3.470000e-108 401.0
25 TraesCS3B01G321200 chr7D 97.297 37 1 0 265 301 628383526 628383490 1.860000e-06 63.9
26 TraesCS3B01G321200 chr2B 89.542 306 28 3 1 302 634315796 634316101 3.490000e-103 385.0
27 TraesCS3B01G321200 chr6D 83.803 142 21 2 117 257 16956066 16956206 1.400000e-27 134.0
28 TraesCS3B01G321200 chr6B 81.690 142 24 2 117 257 703843318 703843458 1.410000e-22 117.0
29 TraesCS3B01G321200 chr6A 80.142 141 28 0 117 257 63327210 63327070 3.050000e-19 106.0


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 TraesCS3B01G321200 chr3B 520371951 520374193 2242 True 4143.000000 4143 100.000000 1 2243 1 chr3B.!!$R3 2242
1 TraesCS3B01G321200 chr3B 520447293 520449877 2584 True 538.500000 784 87.711250 387 2235 4 chr3B.!!$R5 1848
2 TraesCS3B01G321200 chr3A 515724480 515726512 2032 True 1231.500000 1851 90.380500 302 2243 2 chr3A.!!$R3 1941
3 TraesCS3B01G321200 chr3A 515284504 515286064 1560 True 594.666667 856 88.350333 785 2243 3 chr3A.!!$R2 1458
4 TraesCS3B01G321200 chr3D 395643213 395645322 2109 True 546.250000 839 88.957000 307 2235 4 chr3D.!!$R1 1928

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
287 288 0.036765 TGGCGGACGACAAATAAGCT 60.037 50.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 3359 0.107654 CCCTGCTACACCTACTTGGC 60.108 60.0 0.0 0.0 40.22 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
20 21 4.697756 CCTCTTTGCCGTCCGCCA 62.698 66.667 0.00 0.00 36.24 5.69
21 22 3.423154 CTCTTTGCCGTCCGCCAC 61.423 66.667 0.00 0.00 36.24 5.01
35 36 2.671619 CCACCGGTCGGCAAACAT 60.672 61.111 2.59 0.00 39.32 2.71
36 37 2.265182 CCACCGGTCGGCAAACATT 61.265 57.895 2.59 0.00 39.32 2.71
37 38 1.209127 CACCGGTCGGCAAACATTC 59.791 57.895 2.59 0.00 39.32 2.67
38 39 1.072505 ACCGGTCGGCAAACATTCT 59.927 52.632 0.00 0.00 39.32 2.40
39 40 0.536460 ACCGGTCGGCAAACATTCTT 60.536 50.000 0.00 0.00 39.32 2.52
40 41 0.596082 CCGGTCGGCAAACATTCTTT 59.404 50.000 0.00 0.00 0.00 2.52
41 42 1.665735 CCGGTCGGCAAACATTCTTTG 60.666 52.381 0.00 0.00 0.00 2.77
47 48 2.422276 GCAAACATTCTTTGCCGTCT 57.578 45.000 6.53 0.00 46.51 4.18
48 49 2.053627 GCAAACATTCTTTGCCGTCTG 58.946 47.619 6.53 0.00 46.51 3.51
49 50 2.053627 CAAACATTCTTTGCCGTCTGC 58.946 47.619 0.00 0.00 41.77 4.26
50 51 1.609208 AACATTCTTTGCCGTCTGCT 58.391 45.000 0.00 0.00 42.00 4.24
51 52 1.609208 ACATTCTTTGCCGTCTGCTT 58.391 45.000 0.00 0.00 42.00 3.91
52 53 1.267806 ACATTCTTTGCCGTCTGCTTG 59.732 47.619 0.00 0.00 42.00 4.01
53 54 0.242017 ATTCTTTGCCGTCTGCTTGC 59.758 50.000 0.00 0.00 42.00 4.01
54 55 2.116736 TTCTTTGCCGTCTGCTTGCG 62.117 55.000 0.00 0.00 42.00 4.85
69 70 3.423154 GCGGACGGCAAAGAGGTG 61.423 66.667 0.00 0.00 42.87 4.00
70 71 2.742372 CGGACGGCAAAGAGGTGG 60.742 66.667 0.00 0.00 0.00 4.61
71 72 2.359975 GGACGGCAAAGAGGTGGG 60.360 66.667 0.00 0.00 0.00 4.61
72 73 2.359975 GACGGCAAAGAGGTGGGG 60.360 66.667 0.00 0.00 0.00 4.96
73 74 4.660938 ACGGCAAAGAGGTGGGGC 62.661 66.667 0.00 0.00 0.00 5.80
77 78 3.966543 CAAAGAGGTGGGGCCGGT 61.967 66.667 1.90 0.00 43.70 5.28
78 79 3.966543 AAAGAGGTGGGGCCGGTG 61.967 66.667 1.90 0.00 43.70 4.94
91 92 4.596585 CGGTGGGCTTGGGTTGGT 62.597 66.667 0.00 0.00 0.00 3.67
92 93 2.123033 GGTGGGCTTGGGTTGGTT 60.123 61.111 0.00 0.00 0.00 3.67
93 94 1.154221 GGTGGGCTTGGGTTGGTTA 59.846 57.895 0.00 0.00 0.00 2.85
94 95 1.183030 GGTGGGCTTGGGTTGGTTAC 61.183 60.000 0.00 0.00 0.00 2.50
95 96 0.468400 GTGGGCTTGGGTTGGTTACA 60.468 55.000 0.00 0.00 0.00 2.41
96 97 0.468400 TGGGCTTGGGTTGGTTACAC 60.468 55.000 0.00 0.00 0.00 2.90
97 98 0.468400 GGGCTTGGGTTGGTTACACA 60.468 55.000 0.00 0.00 38.76 3.72
104 105 5.776173 TTGGGTTGGTTACACAATAACTG 57.224 39.130 0.00 0.00 45.08 3.16
105 106 4.145807 TGGGTTGGTTACACAATAACTGG 58.854 43.478 0.00 0.00 37.18 4.00
106 107 4.141228 TGGGTTGGTTACACAATAACTGGA 60.141 41.667 0.00 0.00 37.18 3.86
107 108 4.216902 GGGTTGGTTACACAATAACTGGAC 59.783 45.833 0.00 0.00 32.24 4.02
108 109 4.216902 GGTTGGTTACACAATAACTGGACC 59.783 45.833 0.00 0.00 32.24 4.46
109 110 4.023726 TGGTTACACAATAACTGGACCC 57.976 45.455 0.00 0.00 0.00 4.46
110 111 3.394940 TGGTTACACAATAACTGGACCCA 59.605 43.478 0.00 0.00 0.00 4.51
111 112 4.141228 TGGTTACACAATAACTGGACCCAA 60.141 41.667 0.00 0.00 0.00 4.12
112 113 4.216902 GGTTACACAATAACTGGACCCAAC 59.783 45.833 0.00 0.00 0.00 3.77
113 114 3.586470 ACACAATAACTGGACCCAACA 57.414 42.857 0.00 0.00 0.00 3.33
114 115 3.904717 ACACAATAACTGGACCCAACAA 58.095 40.909 0.00 0.00 0.00 2.83
115 116 3.634910 ACACAATAACTGGACCCAACAAC 59.365 43.478 0.00 0.00 0.00 3.32
116 117 3.005367 CACAATAACTGGACCCAACAACC 59.995 47.826 0.00 0.00 0.00 3.77
117 118 3.117284 ACAATAACTGGACCCAACAACCT 60.117 43.478 0.00 0.00 0.00 3.50
118 119 2.943036 TAACTGGACCCAACAACCTC 57.057 50.000 0.00 0.00 0.00 3.85
119 120 1.222567 AACTGGACCCAACAACCTCT 58.777 50.000 0.00 0.00 0.00 3.69
120 121 1.222567 ACTGGACCCAACAACCTCTT 58.777 50.000 0.00 0.00 0.00 2.85
121 122 1.569072 ACTGGACCCAACAACCTCTTT 59.431 47.619 0.00 0.00 0.00 2.52
122 123 1.956477 CTGGACCCAACAACCTCTTTG 59.044 52.381 0.00 0.00 41.49 2.77
123 124 0.673985 GGACCCAACAACCTCTTTGC 59.326 55.000 0.00 0.00 39.01 3.68
124 125 0.673985 GACCCAACAACCTCTTTGCC 59.326 55.000 0.00 0.00 39.01 4.52
125 126 1.106944 ACCCAACAACCTCTTTGCCG 61.107 55.000 0.00 0.00 39.01 5.69
126 127 1.106944 CCCAACAACCTCTTTGCCGT 61.107 55.000 0.00 0.00 39.01 5.68
127 128 0.310854 CCAACAACCTCTTTGCCGTC 59.689 55.000 0.00 0.00 39.01 4.79
128 129 0.310854 CAACAACCTCTTTGCCGTCC 59.689 55.000 0.00 0.00 39.01 4.79
129 130 1.164041 AACAACCTCTTTGCCGTCCG 61.164 55.000 0.00 0.00 39.01 4.79
130 131 2.668550 AACCTCTTTGCCGTCCGC 60.669 61.111 0.00 0.00 38.31 5.54
131 132 3.178540 AACCTCTTTGCCGTCCGCT 62.179 57.895 0.00 0.00 38.78 5.52
132 133 1.823169 AACCTCTTTGCCGTCCGCTA 61.823 55.000 0.00 0.00 38.78 4.26
133 134 1.810030 CCTCTTTGCCGTCCGCTAC 60.810 63.158 0.00 0.00 38.78 3.58
134 135 1.810030 CTCTTTGCCGTCCGCTACC 60.810 63.158 0.00 0.00 38.78 3.18
135 136 3.186047 CTTTGCCGTCCGCTACCG 61.186 66.667 0.00 0.00 38.78 4.02
145 146 2.050351 CGCTACCGGACGGCATAG 60.050 66.667 9.46 7.30 39.32 2.23
146 147 2.842256 CGCTACCGGACGGCATAGT 61.842 63.158 9.46 0.00 39.32 2.12
147 148 1.440476 GCTACCGGACGGCATAGTT 59.560 57.895 9.46 0.00 39.32 2.24
148 149 0.179092 GCTACCGGACGGCATAGTTT 60.179 55.000 9.46 0.00 39.32 2.66
149 150 1.849097 CTACCGGACGGCATAGTTTC 58.151 55.000 9.46 0.00 39.32 2.78
150 151 1.407979 CTACCGGACGGCATAGTTTCT 59.592 52.381 9.46 0.00 39.32 2.52
151 152 0.611714 ACCGGACGGCATAGTTTCTT 59.388 50.000 9.46 0.00 39.32 2.52
152 153 1.002773 ACCGGACGGCATAGTTTCTTT 59.997 47.619 9.46 0.00 39.32 2.52
153 154 1.396996 CCGGACGGCATAGTTTCTTTG 59.603 52.381 0.00 0.00 0.00 2.77
154 155 1.202031 CGGACGGCATAGTTTCTTTGC 60.202 52.381 0.00 4.17 37.63 3.68
158 159 2.544480 GGCATAGTTTCTTTGCCGTC 57.456 50.000 13.44 0.00 45.36 4.79
159 160 1.810151 GGCATAGTTTCTTTGCCGTCA 59.190 47.619 13.44 0.00 45.36 4.35
160 161 2.159517 GGCATAGTTTCTTTGCCGTCAG 60.160 50.000 13.44 0.00 45.36 3.51
161 162 2.729156 GCATAGTTTCTTTGCCGTCAGC 60.729 50.000 1.82 0.00 44.14 4.26
162 163 1.519408 TAGTTTCTTTGCCGTCAGCC 58.481 50.000 0.00 0.00 42.71 4.85
163 164 0.465460 AGTTTCTTTGCCGTCAGCCA 60.465 50.000 0.00 0.00 42.71 4.75
164 165 0.040067 GTTTCTTTGCCGTCAGCCAG 60.040 55.000 0.00 0.00 42.71 4.85
165 166 1.795170 TTTCTTTGCCGTCAGCCAGC 61.795 55.000 0.00 0.00 42.71 4.85
166 167 4.093952 CTTTGCCGTCAGCCAGCG 62.094 66.667 0.00 0.00 42.71 5.18
181 182 2.556287 GCGGACGGCAAAGAGTTG 59.444 61.111 0.00 0.00 42.87 3.16
182 183 2.966309 GCGGACGGCAAAGAGTTGG 61.966 63.158 0.00 0.00 42.87 3.77
190 191 2.840296 GCAAAGAGTTGGCTGATAGC 57.160 50.000 0.00 0.00 41.46 2.97
191 192 2.086869 GCAAAGAGTTGGCTGATAGCA 58.913 47.619 2.99 0.00 44.75 3.49
192 193 2.489329 GCAAAGAGTTGGCTGATAGCAA 59.511 45.455 2.99 0.00 44.75 3.91
193 194 3.057315 GCAAAGAGTTGGCTGATAGCAAA 60.057 43.478 2.99 0.00 44.75 3.68
198 199 2.584835 TTGGCTGATAGCAAACACCT 57.415 45.000 2.99 0.00 44.75 4.00
199 200 2.584835 TGGCTGATAGCAAACACCTT 57.415 45.000 2.99 0.00 44.75 3.50
200 201 2.161855 TGGCTGATAGCAAACACCTTG 58.838 47.619 2.99 0.00 44.75 3.61
201 202 2.162681 GGCTGATAGCAAACACCTTGT 58.837 47.619 2.99 0.00 44.75 3.16
202 203 2.558359 GGCTGATAGCAAACACCTTGTT 59.442 45.455 2.99 0.00 44.75 2.83
212 213 0.675633 ACACCTTGTTTGCCATCAGC 59.324 50.000 0.00 0.00 44.14 4.26
213 214 0.037975 CACCTTGTTTGCCATCAGCC 60.038 55.000 0.00 0.00 42.71 4.85
214 215 0.469705 ACCTTGTTTGCCATCAGCCA 60.470 50.000 0.00 0.00 42.71 4.75
215 216 0.037975 CCTTGTTTGCCATCAGCCAC 60.038 55.000 0.00 0.00 42.71 5.01
216 217 0.963962 CTTGTTTGCCATCAGCCACT 59.036 50.000 0.00 0.00 42.71 4.00
217 218 1.342174 CTTGTTTGCCATCAGCCACTT 59.658 47.619 0.00 0.00 42.71 3.16
218 219 0.961019 TGTTTGCCATCAGCCACTTC 59.039 50.000 0.00 0.00 42.71 3.01
219 220 1.251251 GTTTGCCATCAGCCACTTCT 58.749 50.000 0.00 0.00 42.71 2.85
220 221 1.615392 GTTTGCCATCAGCCACTTCTT 59.385 47.619 0.00 0.00 42.71 2.52
221 222 1.999648 TTGCCATCAGCCACTTCTTT 58.000 45.000 0.00 0.00 42.71 2.52
222 223 1.250328 TGCCATCAGCCACTTCTTTG 58.750 50.000 0.00 0.00 42.71 2.77
223 224 1.251251 GCCATCAGCCACTTCTTTGT 58.749 50.000 0.00 0.00 34.35 2.83
224 225 1.200948 GCCATCAGCCACTTCTTTGTC 59.799 52.381 0.00 0.00 34.35 3.18
225 226 1.466167 CCATCAGCCACTTCTTTGTCG 59.534 52.381 0.00 0.00 0.00 4.35
226 227 2.146342 CATCAGCCACTTCTTTGTCGT 58.854 47.619 0.00 0.00 0.00 4.34
227 228 1.865865 TCAGCCACTTCTTTGTCGTC 58.134 50.000 0.00 0.00 0.00 4.20
228 229 0.868406 CAGCCACTTCTTTGTCGTCC 59.132 55.000 0.00 0.00 0.00 4.79
229 230 0.600255 AGCCACTTCTTTGTCGTCCG 60.600 55.000 0.00 0.00 0.00 4.79
230 231 0.878961 GCCACTTCTTTGTCGTCCGT 60.879 55.000 0.00 0.00 0.00 4.69
231 232 1.578583 CCACTTCTTTGTCGTCCGTT 58.421 50.000 0.00 0.00 0.00 4.44
232 233 1.937899 CCACTTCTTTGTCGTCCGTTT 59.062 47.619 0.00 0.00 0.00 3.60
233 234 2.353579 CCACTTCTTTGTCGTCCGTTTT 59.646 45.455 0.00 0.00 0.00 2.43
234 235 3.545426 CCACTTCTTTGTCGTCCGTTTTC 60.545 47.826 0.00 0.00 0.00 2.29
235 236 3.308866 CACTTCTTTGTCGTCCGTTTTCT 59.691 43.478 0.00 0.00 0.00 2.52
236 237 3.937079 ACTTCTTTGTCGTCCGTTTTCTT 59.063 39.130 0.00 0.00 0.00 2.52
237 238 3.936902 TCTTTGTCGTCCGTTTTCTTG 57.063 42.857 0.00 0.00 0.00 3.02
238 239 3.264104 TCTTTGTCGTCCGTTTTCTTGT 58.736 40.909 0.00 0.00 0.00 3.16
239 240 3.685756 TCTTTGTCGTCCGTTTTCTTGTT 59.314 39.130 0.00 0.00 0.00 2.83
240 241 3.392769 TTGTCGTCCGTTTTCTTGTTG 57.607 42.857 0.00 0.00 0.00 3.33
241 242 1.062880 TGTCGTCCGTTTTCTTGTTGC 59.937 47.619 0.00 0.00 0.00 4.17
242 243 1.329599 GTCGTCCGTTTTCTTGTTGCT 59.670 47.619 0.00 0.00 0.00 3.91
243 244 1.329292 TCGTCCGTTTTCTTGTTGCTG 59.671 47.619 0.00 0.00 0.00 4.41
244 245 1.329292 CGTCCGTTTTCTTGTTGCTGA 59.671 47.619 0.00 0.00 0.00 4.26
245 246 2.716398 GTCCGTTTTCTTGTTGCTGAC 58.284 47.619 0.00 0.00 0.00 3.51
246 247 1.329292 TCCGTTTTCTTGTTGCTGACG 59.671 47.619 0.00 0.00 0.00 4.35
247 248 1.596954 CCGTTTTCTTGTTGCTGACGG 60.597 52.381 0.00 0.00 41.89 4.79
248 249 1.477105 GTTTTCTTGTTGCTGACGGC 58.523 50.000 0.00 0.00 42.22 5.68
257 258 3.567473 GCTGACGGCAAAGACCTC 58.433 61.111 0.00 0.00 41.35 3.85
258 259 1.004440 GCTGACGGCAAAGACCTCT 60.004 57.895 0.00 0.00 41.35 3.69
259 260 0.603975 GCTGACGGCAAAGACCTCTT 60.604 55.000 0.00 0.00 41.35 2.85
260 261 1.884235 CTGACGGCAAAGACCTCTTT 58.116 50.000 0.00 0.00 46.23 2.52
270 271 3.601443 AAGACCTCTTTGTCGAGATGG 57.399 47.619 0.00 0.00 40.26 3.51
271 272 1.205893 AGACCTCTTTGTCGAGATGGC 59.794 52.381 0.00 0.00 40.26 4.40
272 273 0.108615 ACCTCTTTGTCGAGATGGCG 60.109 55.000 0.00 0.00 32.74 5.69
273 274 0.807667 CCTCTTTGTCGAGATGGCGG 60.808 60.000 0.00 0.00 32.74 6.13
274 275 0.173481 CTCTTTGTCGAGATGGCGGA 59.827 55.000 0.00 0.00 32.74 5.54
275 276 0.108804 TCTTTGTCGAGATGGCGGAC 60.109 55.000 0.00 0.00 0.00 4.79
276 277 1.413767 CTTTGTCGAGATGGCGGACG 61.414 60.000 0.00 0.00 0.00 4.79
277 278 1.868987 TTTGTCGAGATGGCGGACGA 61.869 55.000 0.00 0.00 0.00 4.20
278 279 2.278013 GTCGAGATGGCGGACGAC 60.278 66.667 0.00 0.00 45.51 4.34
279 280 2.748647 TCGAGATGGCGGACGACA 60.749 61.111 1.44 1.44 37.65 4.35
280 281 2.180769 CGAGATGGCGGACGACAA 59.819 61.111 3.64 0.00 36.35 3.18
281 282 1.445410 CGAGATGGCGGACGACAAA 60.445 57.895 3.64 0.00 36.35 2.83
282 283 0.806102 CGAGATGGCGGACGACAAAT 60.806 55.000 3.64 0.00 36.35 2.32
283 284 1.535226 CGAGATGGCGGACGACAAATA 60.535 52.381 3.64 0.00 36.35 1.40
284 285 2.546778 GAGATGGCGGACGACAAATAA 58.453 47.619 3.64 0.00 36.35 1.40
285 286 2.540101 GAGATGGCGGACGACAAATAAG 59.460 50.000 3.64 0.00 36.35 1.73
286 287 1.003866 GATGGCGGACGACAAATAAGC 60.004 52.381 3.64 0.00 36.35 3.09
287 288 0.036765 TGGCGGACGACAAATAAGCT 60.037 50.000 0.00 0.00 0.00 3.74
288 289 1.205179 TGGCGGACGACAAATAAGCTA 59.795 47.619 0.00 0.00 0.00 3.32
289 290 2.273557 GGCGGACGACAAATAAGCTAA 58.726 47.619 0.00 0.00 0.00 3.09
290 291 2.870411 GGCGGACGACAAATAAGCTAAT 59.130 45.455 0.00 0.00 0.00 1.73
291 292 3.311596 GGCGGACGACAAATAAGCTAATT 59.688 43.478 0.00 0.00 0.00 1.40
292 293 4.201881 GGCGGACGACAAATAAGCTAATTT 60.202 41.667 0.00 0.00 0.00 1.82
293 294 4.962151 GCGGACGACAAATAAGCTAATTTC 59.038 41.667 0.00 0.00 0.00 2.17
294 295 5.446741 GCGGACGACAAATAAGCTAATTTCA 60.447 40.000 0.00 0.00 0.00 2.69
295 296 6.185399 CGGACGACAAATAAGCTAATTTCAG 58.815 40.000 0.00 0.00 0.00 3.02
296 297 6.183360 CGGACGACAAATAAGCTAATTTCAGT 60.183 38.462 0.00 0.00 0.00 3.41
297 298 7.009815 CGGACGACAAATAAGCTAATTTCAGTA 59.990 37.037 0.00 0.00 0.00 2.74
298 299 8.328864 GGACGACAAATAAGCTAATTTCAGTAG 58.671 37.037 0.00 0.00 0.00 2.57
299 300 8.773404 ACGACAAATAAGCTAATTTCAGTAGT 57.227 30.769 0.00 0.00 0.00 2.73
300 301 8.656849 ACGACAAATAAGCTAATTTCAGTAGTG 58.343 33.333 0.00 0.00 0.00 2.74
336 338 8.462016 CAATCTAGCAAGGCATACTTTTTAGTT 58.538 33.333 0.00 0.00 37.29 2.24
382 388 5.454966 AGGCGGGTTCTCCAAATTTTATAT 58.545 37.500 0.00 0.00 34.36 0.86
383 389 5.897250 AGGCGGGTTCTCCAAATTTTATATT 59.103 36.000 0.00 0.00 34.36 1.28
384 390 5.983118 GGCGGGTTCTCCAAATTTTATATTG 59.017 40.000 0.00 0.00 34.36 1.90
385 391 5.462068 GCGGGTTCTCCAAATTTTATATTGC 59.538 40.000 0.00 0.00 34.36 3.56
448 454 3.558931 TCGCACCATATTCCTGTCAAT 57.441 42.857 0.00 0.00 0.00 2.57
496 502 5.718039 AGGTAAATTCCAGTTTTAACCCCA 58.282 37.500 0.00 0.00 28.45 4.96
499 505 8.126385 AGGTAAATTCCAGTTTTAACCCCATAT 58.874 33.333 0.00 0.00 28.45 1.78
507 513 7.901861 TCCAGTTTTAACCCCATATTTTGGTAT 59.098 33.333 0.00 0.00 44.83 2.73
561 568 5.772393 TTCATACAGGTCACCCATTTAGT 57.228 39.130 0.00 0.00 0.00 2.24
568 575 5.222130 ACAGGTCACCCATTTAGTGATTTCT 60.222 40.000 0.00 0.00 45.45 2.52
661 671 6.033966 GCCGTTGGAGTTATTTCTAAAATGG 58.966 40.000 0.00 0.00 0.00 3.16
733 743 6.238566 CGAATAAGGAGTTGCATGACATGAAT 60.239 38.462 19.76 0.00 0.00 2.57
743 753 6.110543 TGCATGACATGAATAAGAAACTCG 57.889 37.500 19.76 0.00 0.00 4.18
754 764 1.420430 AGAAACTCGTCAAGGTGGGA 58.580 50.000 0.00 0.00 0.00 4.37
763 773 1.153046 CAAGGTGGGACGGTGTGTT 60.153 57.895 0.00 0.00 0.00 3.32
780 790 3.318017 GTGTTTGTACACGAGATGAGCT 58.682 45.455 0.00 0.00 44.66 4.09
782 792 3.740832 TGTTTGTACACGAGATGAGCTTG 59.259 43.478 0.00 0.00 0.00 4.01
783 793 1.996292 TGTACACGAGATGAGCTTGC 58.004 50.000 0.00 0.00 0.00 4.01
822 1226 5.407502 GGTAAAAACAGGAATTCATTCGGG 58.592 41.667 7.93 0.00 37.67 5.14
823 1227 4.535526 AAAAACAGGAATTCATTCGGGG 57.464 40.909 7.93 0.00 37.67 5.73
824 1228 2.143876 AACAGGAATTCATTCGGGGG 57.856 50.000 7.93 0.00 37.67 5.40
895 1301 4.013267 CCACAAAGGGCCTATAGATCTG 57.987 50.000 6.41 0.00 0.00 2.90
896 1302 3.244700 CCACAAAGGGCCTATAGATCTGG 60.245 52.174 6.41 0.00 0.00 3.86
900 1306 0.547712 GGGCCTATAGATCTGGGGCA 60.548 60.000 26.41 2.94 44.69 5.36
923 1332 1.064952 CGCAAACCACTTCCTTCGTTT 59.935 47.619 0.00 0.00 0.00 3.60
929 1338 1.593196 CACTTCCTTCGTTTGGCTCA 58.407 50.000 0.00 0.00 0.00 4.26
1223 2106 3.062466 CCCTGACCTCTGCGACGA 61.062 66.667 0.00 0.00 0.00 4.20
1227 2110 0.803117 CTGACCTCTGCGACGACTTA 59.197 55.000 0.00 0.00 0.00 2.24
1228 2111 1.402259 CTGACCTCTGCGACGACTTAT 59.598 52.381 0.00 0.00 0.00 1.73
1229 2112 1.816835 TGACCTCTGCGACGACTTATT 59.183 47.619 0.00 0.00 0.00 1.40
1230 2113 2.186076 GACCTCTGCGACGACTTATTG 58.814 52.381 0.00 0.00 0.00 1.90
1231 2114 1.816835 ACCTCTGCGACGACTTATTGA 59.183 47.619 0.00 0.00 0.00 2.57
1244 2127 9.454585 CGACGACTTATTGATTGGTAATTAGTA 57.545 33.333 0.00 0.00 30.27 1.82
1335 2218 6.069331 CCAGAGCTAGACTACCCTAAATGTA 58.931 44.000 0.00 0.00 0.00 2.29
1336 2219 6.550108 CCAGAGCTAGACTACCCTAAATGTAA 59.450 42.308 0.00 0.00 0.00 2.41
1337 2220 7.233757 CCAGAGCTAGACTACCCTAAATGTAAT 59.766 40.741 0.00 0.00 0.00 1.89
1338 2221 8.085296 CAGAGCTAGACTACCCTAAATGTAATG 58.915 40.741 0.00 0.00 0.00 1.90
1339 2222 7.785506 AGAGCTAGACTACCCTAAATGTAATGT 59.214 37.037 0.00 0.00 0.00 2.71
1348 2232 7.625828 ACCCTAAATGTAATGTTGTTCTAGC 57.374 36.000 0.00 0.00 0.00 3.42
1381 2265 2.952310 GGTCCCTGGTTATGCTTGATTC 59.048 50.000 0.00 0.00 0.00 2.52
1382 2266 2.952310 GTCCCTGGTTATGCTTGATTCC 59.048 50.000 0.00 0.00 0.00 3.01
1383 2267 1.949525 CCCTGGTTATGCTTGATTCCG 59.050 52.381 0.00 0.00 0.00 4.30
1452 2337 5.397899 CCTTGGAATACCTGATTTCTGCCTA 60.398 44.000 0.00 0.00 37.04 3.93
1453 2338 5.912149 TGGAATACCTGATTTCTGCCTAT 57.088 39.130 0.00 0.00 37.04 2.57
1454 2339 5.624159 TGGAATACCTGATTTCTGCCTATG 58.376 41.667 0.00 0.00 37.04 2.23
1455 2340 5.132648 TGGAATACCTGATTTCTGCCTATGT 59.867 40.000 0.00 0.00 37.04 2.29
1471 2356 9.555411 TCTGCCTATGTCTTTATATAACCCATA 57.445 33.333 0.00 2.17 0.00 2.74
1538 2493 6.700081 TCTCATGTTATTCCAGTACGCAATAC 59.300 38.462 0.00 0.00 0.00 1.89
1609 2634 8.840867 GTCAACGATAAATGAATTGACTGAAAC 58.159 33.333 7.90 0.00 43.68 2.78
1655 2839 2.158842 CCAGGCTCCATCCTAGTTCAAG 60.159 54.545 0.00 0.00 33.95 3.02
1686 2875 2.746904 TGACCCTGCATTGTATTGAACG 59.253 45.455 0.00 0.00 0.00 3.95
1967 3159 0.320374 TTCAGTACTCGGCTTGTGGG 59.680 55.000 0.00 0.00 0.00 4.61
2056 3252 2.614829 AGGTAAGACGTGCACTTTGT 57.385 45.000 16.19 5.31 0.00 2.83
2068 3264 5.106712 ACGTGCACTTTGTAATCACATTAGG 60.107 40.000 16.19 0.00 33.76 2.69
2113 3309 0.639392 ATCCTGTCCTGCCTAGACCT 59.361 55.000 0.00 0.00 33.09 3.85
2163 3359 2.418333 CGTGACACGACGAAGCTCG 61.418 63.158 23.39 4.36 46.05 5.03
2183 3379 0.107654 CCAAGTAGGTGTAGCAGGGC 60.108 60.000 0.00 0.00 0.00 5.19
2235 3431 4.562963 GGAATGTCCCTTCAGACGTAACTT 60.563 45.833 0.00 0.00 39.77 2.66
2237 3433 2.960384 TGTCCCTTCAGACGTAACTTGA 59.040 45.455 0.00 0.00 39.77 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.195123 GAATGTTTGCCGACCGGTGG 62.195 60.000 14.63 12.00 37.65 4.61
19 20 1.209127 GAATGTTTGCCGACCGGTG 59.791 57.895 14.63 4.10 37.65 4.94
20 21 0.536460 AAGAATGTTTGCCGACCGGT 60.536 50.000 6.92 6.92 37.65 5.28
21 22 0.596082 AAAGAATGTTTGCCGACCGG 59.404 50.000 0.00 0.00 38.57 5.28
22 23 1.685302 CAAAGAATGTTTGCCGACCG 58.315 50.000 0.00 0.00 0.00 4.79
23 24 1.418373 GCAAAGAATGTTTGCCGACC 58.582 50.000 15.83 0.00 46.51 4.79
29 30 2.053627 GCAGACGGCAAAGAATGTTTG 58.946 47.619 0.00 0.00 43.97 2.93
30 31 2.422276 GCAGACGGCAAAGAATGTTT 57.578 45.000 0.00 0.00 43.97 2.83
52 53 3.423154 CACCTCTTTGCCGTCCGC 61.423 66.667 0.00 0.00 38.31 5.54
53 54 2.742372 CCACCTCTTTGCCGTCCG 60.742 66.667 0.00 0.00 0.00 4.79
54 55 2.359975 CCCACCTCTTTGCCGTCC 60.360 66.667 0.00 0.00 0.00 4.79
55 56 2.359975 CCCCACCTCTTTGCCGTC 60.360 66.667 0.00 0.00 0.00 4.79
56 57 4.660938 GCCCCACCTCTTTGCCGT 62.661 66.667 0.00 0.00 0.00 5.68
60 61 3.966543 ACCGGCCCCACCTCTTTG 61.967 66.667 0.00 0.00 35.61 2.77
61 62 3.966543 CACCGGCCCCACCTCTTT 61.967 66.667 0.00 0.00 35.61 2.52
74 75 2.700407 TAACCAACCCAAGCCCACCG 62.700 60.000 0.00 0.00 0.00 4.94
75 76 1.154221 TAACCAACCCAAGCCCACC 59.846 57.895 0.00 0.00 0.00 4.61
76 77 0.468400 TGTAACCAACCCAAGCCCAC 60.468 55.000 0.00 0.00 0.00 4.61
77 78 0.468400 GTGTAACCAACCCAAGCCCA 60.468 55.000 0.00 0.00 0.00 5.36
78 79 0.468400 TGTGTAACCAACCCAAGCCC 60.468 55.000 0.00 0.00 34.36 5.19
79 80 1.404843 TTGTGTAACCAACCCAAGCC 58.595 50.000 0.00 0.00 34.36 4.35
80 81 4.279922 AGTTATTGTGTAACCAACCCAAGC 59.720 41.667 0.00 0.00 34.36 4.01
81 82 5.278758 CCAGTTATTGTGTAACCAACCCAAG 60.279 44.000 0.00 0.00 34.36 3.61
82 83 4.585162 CCAGTTATTGTGTAACCAACCCAA 59.415 41.667 0.00 0.00 34.36 4.12
83 84 4.141228 TCCAGTTATTGTGTAACCAACCCA 60.141 41.667 0.00 0.00 34.36 4.51
84 85 4.216902 GTCCAGTTATTGTGTAACCAACCC 59.783 45.833 0.00 0.00 34.36 4.11
85 86 4.216902 GGTCCAGTTATTGTGTAACCAACC 59.783 45.833 0.00 0.00 34.36 3.77
86 87 4.216902 GGGTCCAGTTATTGTGTAACCAAC 59.783 45.833 0.00 0.00 34.36 3.77
87 88 4.141228 TGGGTCCAGTTATTGTGTAACCAA 60.141 41.667 0.00 0.00 34.36 3.67
88 89 3.394940 TGGGTCCAGTTATTGTGTAACCA 59.605 43.478 0.00 0.00 34.36 3.67
89 90 4.023726 TGGGTCCAGTTATTGTGTAACC 57.976 45.455 0.00 0.00 34.36 2.85
90 91 4.822896 TGTTGGGTCCAGTTATTGTGTAAC 59.177 41.667 0.00 0.00 37.35 2.50
91 92 5.050126 TGTTGGGTCCAGTTATTGTGTAA 57.950 39.130 0.00 0.00 0.00 2.41
92 93 4.708576 TGTTGGGTCCAGTTATTGTGTA 57.291 40.909 0.00 0.00 0.00 2.90
93 94 3.586470 TGTTGGGTCCAGTTATTGTGT 57.414 42.857 0.00 0.00 0.00 3.72
94 95 3.005367 GGTTGTTGGGTCCAGTTATTGTG 59.995 47.826 0.00 0.00 0.00 3.33
95 96 3.117284 AGGTTGTTGGGTCCAGTTATTGT 60.117 43.478 0.00 0.00 0.00 2.71
96 97 3.496331 AGGTTGTTGGGTCCAGTTATTG 58.504 45.455 0.00 0.00 0.00 1.90
97 98 3.397955 AGAGGTTGTTGGGTCCAGTTATT 59.602 43.478 0.00 0.00 0.00 1.40
98 99 2.986728 AGAGGTTGTTGGGTCCAGTTAT 59.013 45.455 0.00 0.00 0.00 1.89
99 100 2.414612 AGAGGTTGTTGGGTCCAGTTA 58.585 47.619 0.00 0.00 0.00 2.24
100 101 1.222567 AGAGGTTGTTGGGTCCAGTT 58.777 50.000 0.00 0.00 0.00 3.16
101 102 1.222567 AAGAGGTTGTTGGGTCCAGT 58.777 50.000 0.00 0.00 0.00 4.00
102 103 1.956477 CAAAGAGGTTGTTGGGTCCAG 59.044 52.381 0.00 0.00 32.08 3.86
103 104 2.026905 GCAAAGAGGTTGTTGGGTCCA 61.027 52.381 0.00 0.00 39.63 4.02
104 105 0.673985 GCAAAGAGGTTGTTGGGTCC 59.326 55.000 0.00 0.00 39.63 4.46
105 106 0.673985 GGCAAAGAGGTTGTTGGGTC 59.326 55.000 0.00 0.00 39.63 4.46
106 107 1.106944 CGGCAAAGAGGTTGTTGGGT 61.107 55.000 0.00 0.00 39.63 4.51
107 108 1.106944 ACGGCAAAGAGGTTGTTGGG 61.107 55.000 0.00 0.00 39.63 4.12
108 109 0.310854 GACGGCAAAGAGGTTGTTGG 59.689 55.000 0.00 0.00 39.63 3.77
109 110 0.310854 GGACGGCAAAGAGGTTGTTG 59.689 55.000 0.00 0.00 39.63 3.33
110 111 1.164041 CGGACGGCAAAGAGGTTGTT 61.164 55.000 0.00 0.00 39.63 2.83
111 112 1.597027 CGGACGGCAAAGAGGTTGT 60.597 57.895 0.00 0.00 39.63 3.32
112 113 2.966309 GCGGACGGCAAAGAGGTTG 61.966 63.158 0.00 0.00 42.87 3.77
113 114 2.668550 GCGGACGGCAAAGAGGTT 60.669 61.111 0.00 0.00 42.87 3.50
128 129 2.050351 CTATGCCGTCCGGTAGCG 60.050 66.667 7.49 7.49 37.65 4.26
129 130 0.179092 AAACTATGCCGTCCGGTAGC 60.179 55.000 7.66 3.48 37.65 3.58
130 131 1.407979 AGAAACTATGCCGTCCGGTAG 59.592 52.381 7.66 4.87 37.65 3.18
131 132 1.477553 AGAAACTATGCCGTCCGGTA 58.522 50.000 7.66 2.85 37.65 4.02
132 133 0.611714 AAGAAACTATGCCGTCCGGT 59.388 50.000 7.66 0.00 37.65 5.28
133 134 1.396996 CAAAGAAACTATGCCGTCCGG 59.603 52.381 0.24 0.24 38.57 5.14
134 135 1.202031 GCAAAGAAACTATGCCGTCCG 60.202 52.381 0.00 0.00 34.03 4.79
135 136 2.544480 GCAAAGAAACTATGCCGTCC 57.456 50.000 0.00 0.00 34.03 4.79
140 141 2.729156 GCTGACGGCAAAGAAACTATGC 60.729 50.000 0.00 0.00 41.35 3.14
141 142 2.159517 GGCTGACGGCAAAGAAACTATG 60.160 50.000 8.86 0.00 44.01 2.23
142 143 2.084546 GGCTGACGGCAAAGAAACTAT 58.915 47.619 8.86 0.00 44.01 2.12
143 144 1.202710 TGGCTGACGGCAAAGAAACTA 60.203 47.619 8.86 0.00 43.40 2.24
144 145 0.465460 TGGCTGACGGCAAAGAAACT 60.465 50.000 8.86 0.00 43.40 2.66
145 146 0.040067 CTGGCTGACGGCAAAGAAAC 60.040 55.000 8.86 0.00 45.84 2.78
146 147 2.330254 CTGGCTGACGGCAAAGAAA 58.670 52.632 8.86 0.00 45.84 2.52
147 148 4.063529 CTGGCTGACGGCAAAGAA 57.936 55.556 8.86 0.00 45.84 2.52
161 162 3.121030 CTCTTTGCCGTCCGCTGG 61.121 66.667 0.00 0.00 38.78 4.85
162 163 1.961277 AACTCTTTGCCGTCCGCTG 60.961 57.895 0.00 0.00 38.78 5.18
163 164 1.961277 CAACTCTTTGCCGTCCGCT 60.961 57.895 0.00 0.00 38.78 5.52
164 165 2.556287 CAACTCTTTGCCGTCCGC 59.444 61.111 0.00 0.00 38.31 5.54
165 166 2.966309 GCCAACTCTTTGCCGTCCG 61.966 63.158 0.00 0.00 0.00 4.79
166 167 1.600916 AGCCAACTCTTTGCCGTCC 60.601 57.895 0.00 0.00 0.00 4.79
167 168 0.884704 TCAGCCAACTCTTTGCCGTC 60.885 55.000 0.00 0.00 0.00 4.79
168 169 0.250901 ATCAGCCAACTCTTTGCCGT 60.251 50.000 0.00 0.00 0.00 5.68
169 170 1.667724 CTATCAGCCAACTCTTTGCCG 59.332 52.381 0.00 0.00 0.00 5.69
170 171 1.403323 GCTATCAGCCAACTCTTTGCC 59.597 52.381 0.00 0.00 34.48 4.52
171 172 2.086869 TGCTATCAGCCAACTCTTTGC 58.913 47.619 0.00 0.00 41.51 3.68
172 173 4.022935 TGTTTGCTATCAGCCAACTCTTTG 60.023 41.667 14.02 0.00 44.40 2.77
173 174 4.022849 GTGTTTGCTATCAGCCAACTCTTT 60.023 41.667 14.02 0.00 44.40 2.52
174 175 3.503748 GTGTTTGCTATCAGCCAACTCTT 59.496 43.478 14.02 0.00 44.40 2.85
175 176 3.077359 GTGTTTGCTATCAGCCAACTCT 58.923 45.455 14.02 0.00 44.40 3.24
176 177 2.162408 GGTGTTTGCTATCAGCCAACTC 59.838 50.000 14.02 10.97 44.40 3.01
177 178 2.162681 GGTGTTTGCTATCAGCCAACT 58.837 47.619 14.02 0.00 44.40 3.16
178 179 2.162681 AGGTGTTTGCTATCAGCCAAC 58.837 47.619 7.88 7.88 44.36 3.77
179 180 2.557924 CAAGGTGTTTGCTATCAGCCAA 59.442 45.455 5.06 0.00 41.51 4.52
180 181 2.161855 CAAGGTGTTTGCTATCAGCCA 58.838 47.619 5.06 0.00 41.51 4.75
181 182 2.162681 ACAAGGTGTTTGCTATCAGCC 58.837 47.619 5.06 0.00 41.51 4.85
182 183 3.923017 AACAAGGTGTTTGCTATCAGC 57.077 42.857 0.91 0.91 37.26 4.26
192 193 1.069049 GCTGATGGCAAACAAGGTGTT 59.931 47.619 0.00 0.00 43.41 3.32
193 194 0.675633 GCTGATGGCAAACAAGGTGT 59.324 50.000 0.00 0.00 41.35 4.16
194 195 0.037975 GGCTGATGGCAAACAAGGTG 60.038 55.000 0.00 0.00 44.01 4.00
195 196 0.469705 TGGCTGATGGCAAACAAGGT 60.470 50.000 0.00 0.00 46.03 3.50
196 197 2.353858 TGGCTGATGGCAAACAAGG 58.646 52.632 0.00 0.00 46.03 3.61
203 204 1.250328 CAAAGAAGTGGCTGATGGCA 58.750 50.000 0.00 0.00 46.87 4.92
204 205 1.200948 GACAAAGAAGTGGCTGATGGC 59.799 52.381 0.00 0.00 40.90 4.40
205 206 1.466167 CGACAAAGAAGTGGCTGATGG 59.534 52.381 0.00 0.00 0.00 3.51
206 207 2.146342 ACGACAAAGAAGTGGCTGATG 58.854 47.619 0.00 0.00 0.00 3.07
207 208 2.417719 GACGACAAAGAAGTGGCTGAT 58.582 47.619 0.00 0.00 0.00 2.90
208 209 1.540363 GGACGACAAAGAAGTGGCTGA 60.540 52.381 0.00 0.00 0.00 4.26
209 210 0.868406 GGACGACAAAGAAGTGGCTG 59.132 55.000 0.00 0.00 0.00 4.85
210 211 0.600255 CGGACGACAAAGAAGTGGCT 60.600 55.000 0.00 0.00 0.00 4.75
211 212 0.878961 ACGGACGACAAAGAAGTGGC 60.879 55.000 0.00 0.00 0.00 5.01
212 213 1.578583 AACGGACGACAAAGAAGTGG 58.421 50.000 0.00 0.00 0.00 4.00
213 214 3.308866 AGAAAACGGACGACAAAGAAGTG 59.691 43.478 0.00 0.00 0.00 3.16
214 215 3.528532 AGAAAACGGACGACAAAGAAGT 58.471 40.909 0.00 0.00 0.00 3.01
215 216 4.201783 ACAAGAAAACGGACGACAAAGAAG 60.202 41.667 0.00 0.00 0.00 2.85
216 217 3.685756 ACAAGAAAACGGACGACAAAGAA 59.314 39.130 0.00 0.00 0.00 2.52
217 218 3.264104 ACAAGAAAACGGACGACAAAGA 58.736 40.909 0.00 0.00 0.00 2.52
218 219 3.668596 ACAAGAAAACGGACGACAAAG 57.331 42.857 0.00 0.00 0.00 2.77
219 220 3.749404 CAACAAGAAAACGGACGACAAA 58.251 40.909 0.00 0.00 0.00 2.83
220 221 2.476519 GCAACAAGAAAACGGACGACAA 60.477 45.455 0.00 0.00 0.00 3.18
221 222 1.062880 GCAACAAGAAAACGGACGACA 59.937 47.619 0.00 0.00 0.00 4.35
222 223 1.329599 AGCAACAAGAAAACGGACGAC 59.670 47.619 0.00 0.00 0.00 4.34
223 224 1.329292 CAGCAACAAGAAAACGGACGA 59.671 47.619 0.00 0.00 0.00 4.20
224 225 1.329292 TCAGCAACAAGAAAACGGACG 59.671 47.619 0.00 0.00 0.00 4.79
225 226 2.716398 GTCAGCAACAAGAAAACGGAC 58.284 47.619 0.00 0.00 0.00 4.79
226 227 1.329292 CGTCAGCAACAAGAAAACGGA 59.671 47.619 0.00 0.00 0.00 4.69
227 228 1.596954 CCGTCAGCAACAAGAAAACGG 60.597 52.381 0.00 0.00 41.70 4.44
228 229 1.741993 CCGTCAGCAACAAGAAAACG 58.258 50.000 0.00 0.00 0.00 3.60
229 230 1.477105 GCCGTCAGCAACAAGAAAAC 58.523 50.000 0.00 0.00 42.97 2.43
230 231 3.936585 GCCGTCAGCAACAAGAAAA 57.063 47.368 0.00 0.00 42.97 2.29
240 241 0.603975 AAGAGGTCTTTGCCGTCAGC 60.604 55.000 0.00 0.00 44.14 4.26
241 242 1.884235 AAAGAGGTCTTTGCCGTCAG 58.116 50.000 4.13 0.00 43.87 3.51
249 250 3.866449 GCCATCTCGACAAAGAGGTCTTT 60.866 47.826 0.00 0.00 46.23 2.52
250 251 2.354203 GCCATCTCGACAAAGAGGTCTT 60.354 50.000 0.00 0.00 38.71 3.01
251 252 1.205893 GCCATCTCGACAAAGAGGTCT 59.794 52.381 0.00 0.00 38.71 3.85
252 253 1.646189 GCCATCTCGACAAAGAGGTC 58.354 55.000 0.00 0.00 38.71 3.85
253 254 0.108615 CGCCATCTCGACAAAGAGGT 60.109 55.000 0.00 0.00 38.71 3.85
254 255 0.807667 CCGCCATCTCGACAAAGAGG 60.808 60.000 0.00 0.00 38.71 3.69
255 256 0.173481 TCCGCCATCTCGACAAAGAG 59.827 55.000 0.00 0.00 39.52 2.85
256 257 0.108804 GTCCGCCATCTCGACAAAGA 60.109 55.000 0.00 0.00 0.00 2.52
257 258 1.413767 CGTCCGCCATCTCGACAAAG 61.414 60.000 0.00 0.00 0.00 2.77
258 259 1.445410 CGTCCGCCATCTCGACAAA 60.445 57.895 0.00 0.00 0.00 2.83
259 260 2.180769 CGTCCGCCATCTCGACAA 59.819 61.111 0.00 0.00 0.00 3.18
260 261 2.748647 TCGTCCGCCATCTCGACA 60.749 61.111 0.00 0.00 0.00 4.35
261 262 2.278013 GTCGTCCGCCATCTCGAC 60.278 66.667 0.00 0.00 43.81 4.20
262 263 1.868987 TTTGTCGTCCGCCATCTCGA 61.869 55.000 0.00 0.00 0.00 4.04
263 264 0.806102 ATTTGTCGTCCGCCATCTCG 60.806 55.000 0.00 0.00 0.00 4.04
264 265 2.218953 TATTTGTCGTCCGCCATCTC 57.781 50.000 0.00 0.00 0.00 2.75
265 266 2.550978 CTTATTTGTCGTCCGCCATCT 58.449 47.619 0.00 0.00 0.00 2.90
266 267 1.003866 GCTTATTTGTCGTCCGCCATC 60.004 52.381 0.00 0.00 0.00 3.51
267 268 1.014352 GCTTATTTGTCGTCCGCCAT 58.986 50.000 0.00 0.00 0.00 4.40
268 269 0.036765 AGCTTATTTGTCGTCCGCCA 60.037 50.000 0.00 0.00 0.00 5.69
269 270 1.930567 TAGCTTATTTGTCGTCCGCC 58.069 50.000 0.00 0.00 0.00 6.13
270 271 4.531659 AATTAGCTTATTTGTCGTCCGC 57.468 40.909 0.00 0.00 0.00 5.54
271 272 6.102006 TGAAATTAGCTTATTTGTCGTCCG 57.898 37.500 15.00 0.00 0.00 4.79
272 273 7.073342 ACTGAAATTAGCTTATTTGTCGTCC 57.927 36.000 15.00 1.14 0.00 4.79
273 274 8.870879 ACTACTGAAATTAGCTTATTTGTCGTC 58.129 33.333 15.00 1.78 0.00 4.20
274 275 8.656849 CACTACTGAAATTAGCTTATTTGTCGT 58.343 33.333 15.00 10.77 0.00 4.34
275 276 8.656849 ACACTACTGAAATTAGCTTATTTGTCG 58.343 33.333 15.00 6.94 0.00 4.35
281 282 9.765795 GGTCATACACTACTGAAATTAGCTTAT 57.234 33.333 0.00 0.00 0.00 1.73
282 283 8.202137 GGGTCATACACTACTGAAATTAGCTTA 58.798 37.037 0.00 0.00 0.00 3.09
283 284 7.048512 GGGTCATACACTACTGAAATTAGCTT 58.951 38.462 0.00 0.00 0.00 3.74
284 285 6.156256 TGGGTCATACACTACTGAAATTAGCT 59.844 38.462 0.00 0.00 0.00 3.32
285 286 6.258068 GTGGGTCATACACTACTGAAATTAGC 59.742 42.308 0.00 0.00 35.98 3.09
286 287 7.327975 TGTGGGTCATACACTACTGAAATTAG 58.672 38.462 0.00 0.00 39.52 1.73
287 288 7.247456 TGTGGGTCATACACTACTGAAATTA 57.753 36.000 0.00 0.00 39.52 1.40
288 289 6.121776 TGTGGGTCATACACTACTGAAATT 57.878 37.500 0.00 0.00 39.52 1.82
289 290 5.755409 TGTGGGTCATACACTACTGAAAT 57.245 39.130 0.00 0.00 39.52 2.17
290 291 5.554437 TTGTGGGTCATACACTACTGAAA 57.446 39.130 0.00 0.00 39.52 2.69
291 292 5.483937 AGATTGTGGGTCATACACTACTGAA 59.516 40.000 0.00 0.00 39.52 3.02
292 293 5.023452 AGATTGTGGGTCATACACTACTGA 58.977 41.667 0.00 0.00 39.52 3.41
293 294 5.344743 AGATTGTGGGTCATACACTACTG 57.655 43.478 0.00 0.00 39.52 2.74
294 295 5.069251 GCTAGATTGTGGGTCATACACTACT 59.931 44.000 0.00 0.00 39.52 2.57
295 296 5.163447 TGCTAGATTGTGGGTCATACACTAC 60.163 44.000 0.00 0.00 39.52 2.73
296 297 4.959839 TGCTAGATTGTGGGTCATACACTA 59.040 41.667 0.00 0.00 39.52 2.74
297 298 3.774766 TGCTAGATTGTGGGTCATACACT 59.225 43.478 0.00 0.00 39.52 3.55
298 299 4.137116 TGCTAGATTGTGGGTCATACAC 57.863 45.455 0.00 0.00 39.26 2.90
299 300 4.384098 CCTTGCTAGATTGTGGGTCATACA 60.384 45.833 0.00 0.00 0.00 2.29
300 301 4.130118 CCTTGCTAGATTGTGGGTCATAC 58.870 47.826 0.00 0.00 0.00 2.39
305 306 0.698238 TGCCTTGCTAGATTGTGGGT 59.302 50.000 0.00 0.00 0.00 4.51
336 338 3.008266 CCCCGAGTACAAAGAACCCTTAA 59.992 47.826 0.00 0.00 31.15 1.85
382 388 6.696441 TACATCATGTAAAGCATCATGCAA 57.304 33.333 13.38 0.00 39.32 4.08
383 389 6.319405 ACTTACATCATGTAAAGCATCATGCA 59.681 34.615 13.38 0.00 39.32 3.96
384 390 6.732154 ACTTACATCATGTAAAGCATCATGC 58.268 36.000 11.43 0.00 39.32 4.06
385 391 8.068380 CAGACTTACATCATGTAAAGCATCATG 58.932 37.037 11.43 0.41 41.70 3.07
396 402 7.936847 TGAGGTTTAAACAGACTTACATCATGT 59.063 33.333 19.57 0.00 0.00 3.21
638 648 7.027161 CACCATTTTAGAAATAACTCCAACGG 58.973 38.462 0.00 0.00 0.00 4.44
661 671 4.399303 ACCATATTTGCTTCTAGGTTGCAC 59.601 41.667 5.06 0.00 36.37 4.57
680 690 9.699410 TGATTTCACCTTATTCTTATTCACCAT 57.301 29.630 0.00 0.00 0.00 3.55
733 743 2.967201 TCCCACCTTGACGAGTTTCTTA 59.033 45.455 0.00 0.00 0.00 2.10
743 753 1.597027 CACACCGTCCCACCTTGAC 60.597 63.158 0.00 0.00 0.00 3.18
763 773 2.288763 TGCAAGCTCATCTCGTGTACAA 60.289 45.455 0.00 0.00 0.00 2.41
771 781 4.082895 ACTTGAACATTGCAAGCTCATCTC 60.083 41.667 4.94 0.00 45.00 2.75
778 788 3.119708 CCCTCTACTTGAACATTGCAAGC 60.120 47.826 4.94 0.00 45.00 4.01
780 790 4.098914 ACCCTCTACTTGAACATTGCAA 57.901 40.909 0.00 0.00 0.00 4.08
782 792 6.569179 TTTTACCCTCTACTTGAACATTGC 57.431 37.500 0.00 0.00 0.00 3.56
783 793 7.936584 TGTTTTTACCCTCTACTTGAACATTG 58.063 34.615 0.00 0.00 0.00 2.82
822 1226 1.539157 CTTCTGCTTCTGTTTCCCCC 58.461 55.000 0.00 0.00 0.00 5.40
823 1227 1.073923 TCCTTCTGCTTCTGTTTCCCC 59.926 52.381 0.00 0.00 0.00 4.81
824 1228 2.568623 TCCTTCTGCTTCTGTTTCCC 57.431 50.000 0.00 0.00 0.00 3.97
825 1229 3.625313 GCTATCCTTCTGCTTCTGTTTCC 59.375 47.826 0.00 0.00 0.00 3.13
826 1230 4.256920 TGCTATCCTTCTGCTTCTGTTTC 58.743 43.478 0.00 0.00 0.00 2.78
893 1299 3.365265 GGTTTGCGACTGCCCCAG 61.365 66.667 0.00 0.00 41.78 4.45
895 1301 3.670377 GTGGTTTGCGACTGCCCC 61.670 66.667 0.00 0.00 41.78 5.80
896 1302 2.130073 GAAGTGGTTTGCGACTGCCC 62.130 60.000 0.00 0.00 41.78 5.36
900 1306 1.594331 GAAGGAAGTGGTTTGCGACT 58.406 50.000 0.00 0.00 35.11 4.18
923 1332 0.247460 CTTGACGTGAGGATGAGCCA 59.753 55.000 0.00 0.00 40.02 4.75
929 1338 2.990479 GGGCCTTGACGTGAGGAT 59.010 61.111 16.67 0.00 36.33 3.24
1227 2110 7.715657 TCCGTACGTACTAATTACCAATCAAT 58.284 34.615 22.55 0.00 0.00 2.57
1228 2111 7.094508 TCCGTACGTACTAATTACCAATCAA 57.905 36.000 22.55 0.00 0.00 2.57
1229 2112 6.691754 TCCGTACGTACTAATTACCAATCA 57.308 37.500 22.55 0.00 0.00 2.57
1230 2113 7.536622 CAGATCCGTACGTACTAATTACCAATC 59.463 40.741 22.55 11.26 0.00 2.67
1231 2114 7.365741 CAGATCCGTACGTACTAATTACCAAT 58.634 38.462 22.55 3.86 0.00 3.16
1244 2127 1.379443 TCCTGCCAGATCCGTACGT 60.379 57.895 15.21 0.00 0.00 3.57
1335 2218 7.243487 CGTTATTGACATGCTAGAACAACATT 58.757 34.615 0.00 0.00 0.00 2.71
1336 2219 6.183360 CCGTTATTGACATGCTAGAACAACAT 60.183 38.462 0.00 0.00 0.00 2.71
1337 2220 5.121611 CCGTTATTGACATGCTAGAACAACA 59.878 40.000 0.00 0.00 0.00 3.33
1338 2221 5.121768 ACCGTTATTGACATGCTAGAACAAC 59.878 40.000 0.00 0.00 0.00 3.32
1339 2222 5.242434 ACCGTTATTGACATGCTAGAACAA 58.758 37.500 0.00 0.00 0.00 2.83
1348 2232 2.288666 CCAGGGACCGTTATTGACATG 58.711 52.381 0.00 0.00 0.00 3.21
1381 2265 3.315191 ACATGAGTTTCAAACAAGGACGG 59.685 43.478 2.41 0.00 0.00 4.79
1382 2266 4.273480 AGACATGAGTTTCAAACAAGGACG 59.727 41.667 2.41 0.00 0.00 4.79
1383 2267 5.757850 AGACATGAGTTTCAAACAAGGAC 57.242 39.130 2.41 0.00 0.00 3.85
1538 2493 4.349663 TTCGTAGCCCAAATCAAATTCG 57.650 40.909 0.00 0.00 0.00 3.34
1609 2634 6.267817 CCCATATGCAACACAAACTCTATTG 58.732 40.000 0.00 0.00 36.37 1.90
1655 2839 2.464459 GCAGGGTCAGCGCACATAC 61.464 63.158 11.47 1.01 0.00 2.39
1709 2898 3.249799 GCAATTACCGCACTGCACATATA 59.750 43.478 1.11 0.00 34.87 0.86
1877 3069 4.216257 GCTTACAAGCCAGATTGACAGAAA 59.784 41.667 2.12 0.00 46.20 2.52
2079 3275 5.036737 GGACAGGATTTGATGTAAAATGCG 58.963 41.667 0.00 0.00 41.29 4.73
2113 3309 1.214589 GCGGTGCTCGGTAAGAAGA 59.785 57.895 2.61 0.00 39.69 2.87
2163 3359 0.107654 CCCTGCTACACCTACTTGGC 60.108 60.000 0.00 0.00 40.22 4.52
2183 3379 4.699192 TGGAGGTCCAGGATACCG 57.301 61.111 0.00 0.00 42.01 4.02


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

AutoCloner maintained by Alex Coulton.