Multiple sequence alignment - TraesCS4D01G121500

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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 TraesCS4D01G121500 chr4D 100.000 1883 0 0 853 2735 102534577 102532695 0.000000e+00 3478.0
1 TraesCS4D01G121500 chr4D 100.000 478 0 0 1 478 102535429 102534952 0.000000e+00 883.0
2 TraesCS4D01G121500 chr4B 93.873 1730 71 17 853 2550 147067038 147065312 0.000000e+00 2575.0
3 TraesCS4D01G121500 chr4B 95.862 145 4 2 335 478 147067246 147067103 1.640000e-57 233.0
4 TraesCS4D01G121500 chr4B 97.468 79 1 1 2641 2718 147060809 147060731 1.710000e-27 134.0
5 TraesCS4D01G121500 chr4A 95.144 1318 61 3 877 2193 472398447 472399762 0.000000e+00 2076.0
6 TraesCS4D01G121500 chr4A 90.727 550 29 8 2191 2724 472400052 472400595 0.000000e+00 713.0
7 TraesCS4D01G121500 chr4A 93.210 162 6 5 305 463 472397614 472397773 1.640000e-57 233.0
8 TraesCS4D01G121500 chr5D 79.117 589 74 31 1110 1675 233689153 233688591 7.200000e-96 361.0
9 TraesCS4D01G121500 chr5D 93.011 186 8 2 16 201 30728637 30728817 1.610000e-67 267.0
10 TraesCS4D01G121500 chr5A 78.451 594 81 30 1107 1675 321052021 321052592 7.250000e-91 344.0
11 TraesCS4D01G121500 chr5B 78.305 590 83 28 1107 1675 271182035 271182600 3.370000e-89 339.0
12 TraesCS4D01G121500 chr7D 93.401 197 5 5 9 201 161459251 161459059 4.460000e-73 285.0
13 TraesCS4D01G121500 chr7D 92.147 191 9 3 11 200 574065705 574065520 5.810000e-67 265.0
14 TraesCS4D01G121500 chrUn 92.157 204 8 4 2 202 70301598 70301796 5.770000e-72 281.0
15 TraesCS4D01G121500 chr2D 92.268 194 9 3 10 201 409579375 409579186 1.250000e-68 270.0
16 TraesCS4D01G121500 chr7A 92.188 192 8 4 13 201 730830861 730830674 5.810000e-67 265.0
17 TraesCS4D01G121500 chr7A 91.099 191 10 5 14 201 685223273 685223459 4.520000e-63 252.0
18 TraesCS4D01G121500 chr3D 89.806 206 14 4 8 211 429728135 429728335 9.720000e-65 257.0
19 TraesCS4D01G121500 chr3D 85.227 88 13 0 1116 1203 446109956 446109869 1.040000e-14 91.6
20 TraesCS4D01G121500 chr7B 88.780 205 15 5 7 209 648160315 648160513 7.570000e-61 244.0
21 TraesCS4D01G121500 chr3B 85.227 88 13 0 1116 1203 584985072 584984985 1.040000e-14 91.6
22 TraesCS4D01G121500 chr3B 85.227 88 13 0 1116 1203 585138893 585138806 1.040000e-14 91.6
23 TraesCS4D01G121500 chr3A 84.091 88 14 0 1116 1203 587906162 587906075 4.850000e-13 86.1


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 TraesCS4D01G121500 chr4D 102532695 102535429 2734 True 2180.500000 3478 100.0000 1 2735 2 chr4D.!!$R1 2734
1 TraesCS4D01G121500 chr4B 147065312 147067246 1934 True 1404.000000 2575 94.8675 335 2550 2 chr4B.!!$R2 2215
2 TraesCS4D01G121500 chr4A 472397614 472400595 2981 False 1007.333333 2076 93.0270 305 2724 3 chr4A.!!$F1 2419
3 TraesCS4D01G121500 chr5D 233688591 233689153 562 True 361.000000 361 79.1170 1110 1675 1 chr5D.!!$R1 565
4 TraesCS4D01G121500 chr5A 321052021 321052592 571 False 344.000000 344 78.4510 1107 1675 1 chr5A.!!$F1 568
5 TraesCS4D01G121500 chr5B 271182035 271182600 565 False 339.000000 339 78.3050 1107 1675 1 chr5B.!!$F1 568

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
226 227 0.676466 TACCCTTTGCGCATCACTGG 60.676 55.0 12.75 10.66 0.0 4.00 F
1439 1814 0.671796 TCGTCGTCCAAGCAGAAAGA 59.328 50.0 0.00 0.00 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 2046 2.224885 GCCGAACATCTCGTCGAGC 61.225 63.158 17.61 2.15 46.65 5.03 R
2342 3053 2.477825 CATGAGTCGGTCATAGCCTTG 58.522 52.381 1.44 0.00 44.73 3.61 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
26 27 7.100458 CCCATTTTAATTTGGGTCTGTCTAG 57.900 40.000 12.94 0.00 46.38 2.43
27 28 6.096846 CCCATTTTAATTTGGGTCTGTCTAGG 59.903 42.308 12.94 0.00 46.38 3.02
28 29 6.889722 CCATTTTAATTTGGGTCTGTCTAGGA 59.110 38.462 0.00 0.00 0.00 2.94
29 30 7.148069 CCATTTTAATTTGGGTCTGTCTAGGAC 60.148 40.741 0.00 0.00 0.00 3.85
30 31 6.442541 TTTAATTTGGGTCTGTCTAGGACA 57.557 37.500 0.43 0.43 40.50 4.02
31 32 3.983044 ATTTGGGTCTGTCTAGGACAC 57.017 47.619 0.00 0.00 37.67 3.67
32 33 2.391926 TTGGGTCTGTCTAGGACACA 57.608 50.000 0.00 0.00 44.14 3.72
33 34 2.623418 TGGGTCTGTCTAGGACACAT 57.377 50.000 0.00 0.00 41.46 3.21
34 35 2.457598 TGGGTCTGTCTAGGACACATC 58.542 52.381 0.00 0.00 41.46 3.06
35 36 2.043115 TGGGTCTGTCTAGGACACATCT 59.957 50.000 0.00 0.00 41.46 2.90
36 37 3.268595 TGGGTCTGTCTAGGACACATCTA 59.731 47.826 0.00 0.00 41.46 1.98
37 38 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
38 39 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
39 40 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
40 41 6.466038 GGGTCTGTCTAGGACACATCTAGATA 60.466 46.154 4.54 1.80 43.25 1.98
41 42 7.172342 GGTCTGTCTAGGACACATCTAGATAT 58.828 42.308 4.54 0.00 43.25 1.63
42 43 7.120579 GGTCTGTCTAGGACACATCTAGATATG 59.879 44.444 9.51 9.51 43.25 1.78
43 44 7.880713 GTCTGTCTAGGACACATCTAGATATGA 59.119 40.741 17.82 0.00 43.25 2.15
44 45 7.880713 TCTGTCTAGGACACATCTAGATATGAC 59.119 40.741 17.82 11.19 43.25 3.06
45 46 7.518188 TGTCTAGGACACATCTAGATATGACA 58.482 38.462 17.82 7.35 43.25 3.58
46 47 8.166726 TGTCTAGGACACATCTAGATATGACAT 58.833 37.037 17.82 11.49 43.25 3.06
47 48 9.674068 GTCTAGGACACATCTAGATATGACATA 57.326 37.037 17.82 12.01 43.25 2.29
48 49 9.898152 TCTAGGACACATCTAGATATGACATAG 57.102 37.037 21.26 21.26 38.50 2.23
49 50 9.679661 CTAGGACACATCTAGATATGACATAGT 57.320 37.037 19.89 5.05 37.08 2.12
50 51 8.948401 AGGACACATCTAGATATGACATAGTT 57.052 34.615 17.82 0.00 0.00 2.24
68 69 8.306313 ACATAGTTATGTCACATCTAACCTGA 57.694 34.615 0.00 0.00 42.96 3.86
69 70 8.928448 ACATAGTTATGTCACATCTAACCTGAT 58.072 33.333 0.00 0.00 42.96 2.90
70 71 9.416794 CATAGTTATGTCACATCTAACCTGATC 57.583 37.037 0.00 0.00 0.00 2.92
71 72 7.667575 AGTTATGTCACATCTAACCTGATCT 57.332 36.000 0.00 0.00 0.00 2.75
72 73 7.721402 AGTTATGTCACATCTAACCTGATCTC 58.279 38.462 0.00 0.00 0.00 2.75
73 74 5.543507 ATGTCACATCTAACCTGATCTCC 57.456 43.478 0.00 0.00 0.00 3.71
74 75 4.352893 TGTCACATCTAACCTGATCTCCA 58.647 43.478 0.00 0.00 0.00 3.86
75 76 4.160439 TGTCACATCTAACCTGATCTCCAC 59.840 45.833 0.00 0.00 0.00 4.02
76 77 4.404073 GTCACATCTAACCTGATCTCCACT 59.596 45.833 0.00 0.00 0.00 4.00
77 78 5.594725 GTCACATCTAACCTGATCTCCACTA 59.405 44.000 0.00 0.00 0.00 2.74
78 79 6.266558 GTCACATCTAACCTGATCTCCACTAT 59.733 42.308 0.00 0.00 0.00 2.12
79 80 6.266330 TCACATCTAACCTGATCTCCACTATG 59.734 42.308 0.00 0.00 0.00 2.23
80 81 5.011533 ACATCTAACCTGATCTCCACTATGC 59.988 44.000 0.00 0.00 0.00 3.14
81 82 4.809193 TCTAACCTGATCTCCACTATGCT 58.191 43.478 0.00 0.00 0.00 3.79
82 83 5.211973 TCTAACCTGATCTCCACTATGCTT 58.788 41.667 0.00 0.00 0.00 3.91
83 84 3.834489 ACCTGATCTCCACTATGCTTG 57.166 47.619 0.00 0.00 0.00 4.01
84 85 3.110705 ACCTGATCTCCACTATGCTTGT 58.889 45.455 0.00 0.00 0.00 3.16
85 86 4.290093 ACCTGATCTCCACTATGCTTGTA 58.710 43.478 0.00 0.00 0.00 2.41
86 87 4.343526 ACCTGATCTCCACTATGCTTGTAG 59.656 45.833 0.00 0.00 0.00 2.74
87 88 4.343526 CCTGATCTCCACTATGCTTGTAGT 59.656 45.833 0.00 0.00 35.34 2.73
88 89 5.508825 CCTGATCTCCACTATGCTTGTAGTC 60.509 48.000 0.00 0.00 32.74 2.59
89 90 5.204292 TGATCTCCACTATGCTTGTAGTCT 58.796 41.667 0.00 0.00 32.74 3.24
90 91 6.365520 TGATCTCCACTATGCTTGTAGTCTA 58.634 40.000 0.00 0.00 32.74 2.59
91 92 7.007116 TGATCTCCACTATGCTTGTAGTCTAT 58.993 38.462 0.00 0.00 32.74 1.98
92 93 7.507277 TGATCTCCACTATGCTTGTAGTCTATT 59.493 37.037 0.00 0.00 32.74 1.73
93 94 7.661536 TCTCCACTATGCTTGTAGTCTATTT 57.338 36.000 0.00 0.00 32.74 1.40
94 95 8.079211 TCTCCACTATGCTTGTAGTCTATTTT 57.921 34.615 0.00 0.00 32.74 1.82
95 96 8.540388 TCTCCACTATGCTTGTAGTCTATTTTT 58.460 33.333 0.00 0.00 32.74 1.94
132 133 3.608316 TTTTGTTCTTTGTTGCTGCCT 57.392 38.095 0.00 0.00 0.00 4.75
133 134 3.608316 TTTGTTCTTTGTTGCTGCCTT 57.392 38.095 0.00 0.00 0.00 4.35
134 135 4.727507 TTTGTTCTTTGTTGCTGCCTTA 57.272 36.364 0.00 0.00 0.00 2.69
135 136 4.935352 TTGTTCTTTGTTGCTGCCTTAT 57.065 36.364 0.00 0.00 0.00 1.73
136 137 4.935352 TGTTCTTTGTTGCTGCCTTATT 57.065 36.364 0.00 0.00 0.00 1.40
137 138 5.275067 TGTTCTTTGTTGCTGCCTTATTT 57.725 34.783 0.00 0.00 0.00 1.40
138 139 5.049167 TGTTCTTTGTTGCTGCCTTATTTG 58.951 37.500 0.00 0.00 0.00 2.32
139 140 4.935352 TCTTTGTTGCTGCCTTATTTGT 57.065 36.364 0.00 0.00 0.00 2.83
140 141 4.619973 TCTTTGTTGCTGCCTTATTTGTG 58.380 39.130 0.00 0.00 0.00 3.33
141 142 3.383620 TTGTTGCTGCCTTATTTGTGG 57.616 42.857 0.00 0.00 0.00 4.17
142 143 1.617850 TGTTGCTGCCTTATTTGTGGG 59.382 47.619 0.00 0.00 0.00 4.61
143 144 1.892474 GTTGCTGCCTTATTTGTGGGA 59.108 47.619 0.00 0.00 0.00 4.37
144 145 1.838112 TGCTGCCTTATTTGTGGGAG 58.162 50.000 0.00 0.00 43.41 4.30
145 146 1.106285 GCTGCCTTATTTGTGGGAGG 58.894 55.000 0.00 0.00 41.30 4.30
146 147 1.616994 GCTGCCTTATTTGTGGGAGGT 60.617 52.381 0.00 0.00 41.30 3.85
147 148 2.807676 CTGCCTTATTTGTGGGAGGTT 58.192 47.619 0.00 0.00 38.01 3.50
148 149 3.876156 GCTGCCTTATTTGTGGGAGGTTA 60.876 47.826 0.00 0.00 41.30 2.85
149 150 3.947834 CTGCCTTATTTGTGGGAGGTTAG 59.052 47.826 0.00 0.00 38.01 2.34
150 151 3.589735 TGCCTTATTTGTGGGAGGTTAGA 59.410 43.478 0.00 0.00 0.00 2.10
151 152 4.229582 TGCCTTATTTGTGGGAGGTTAGAT 59.770 41.667 0.00 0.00 0.00 1.98
152 153 4.580580 GCCTTATTTGTGGGAGGTTAGATG 59.419 45.833 0.00 0.00 0.00 2.90
153 154 5.755849 CCTTATTTGTGGGAGGTTAGATGT 58.244 41.667 0.00 0.00 0.00 3.06
154 155 5.590259 CCTTATTTGTGGGAGGTTAGATGTG 59.410 44.000 0.00 0.00 0.00 3.21
155 156 4.927267 ATTTGTGGGAGGTTAGATGTGA 57.073 40.909 0.00 0.00 0.00 3.58
156 157 3.695830 TTGTGGGAGGTTAGATGTGAC 57.304 47.619 0.00 0.00 0.00 3.67
157 158 2.615391 TGTGGGAGGTTAGATGTGACA 58.385 47.619 0.00 0.00 0.00 3.58
158 159 3.181329 TGTGGGAGGTTAGATGTGACAT 58.819 45.455 0.00 0.00 0.00 3.06
159 160 3.197766 TGTGGGAGGTTAGATGTGACATC 59.802 47.826 17.46 17.46 0.00 3.06
160 161 2.771943 TGGGAGGTTAGATGTGACATCC 59.228 50.000 21.05 9.65 43.91 3.51
161 162 3.041946 GGGAGGTTAGATGTGACATCCT 58.958 50.000 21.05 12.23 44.05 3.24
162 163 3.456277 GGGAGGTTAGATGTGACATCCTT 59.544 47.826 21.05 7.22 44.05 3.36
163 164 4.654262 GGGAGGTTAGATGTGACATCCTTA 59.346 45.833 21.05 6.22 44.05 2.69
164 165 5.221541 GGGAGGTTAGATGTGACATCCTTAG 60.222 48.000 21.05 0.00 44.05 2.18
165 166 5.598830 GGAGGTTAGATGTGACATCCTTAGA 59.401 44.000 21.05 1.44 42.00 2.10
166 167 6.098409 GGAGGTTAGATGTGACATCCTTAGAA 59.902 42.308 21.05 6.23 42.00 2.10
167 168 7.364762 GGAGGTTAGATGTGACATCCTTAGAAA 60.365 40.741 21.05 4.81 42.00 2.52
168 169 7.918076 AGGTTAGATGTGACATCCTTAGAAAA 58.082 34.615 21.05 3.24 0.00 2.29
169 170 7.824779 AGGTTAGATGTGACATCCTTAGAAAAC 59.175 37.037 21.05 13.12 0.00 2.43
170 171 7.606456 GGTTAGATGTGACATCCTTAGAAAACA 59.394 37.037 21.05 0.00 0.00 2.83
171 172 9.167311 GTTAGATGTGACATCCTTAGAAAACAT 57.833 33.333 21.05 1.75 0.00 2.71
172 173 7.856145 AGATGTGACATCCTTAGAAAACATC 57.144 36.000 21.05 0.00 41.77 3.06
173 174 7.628234 AGATGTGACATCCTTAGAAAACATCT 58.372 34.615 21.05 8.71 44.92 2.90
174 175 8.762645 AGATGTGACATCCTTAGAAAACATCTA 58.237 33.333 21.05 0.00 46.74 1.98
175 176 8.723942 ATGTGACATCCTTAGAAAACATCTAC 57.276 34.615 0.00 0.00 40.38 2.59
176 177 6.811665 TGTGACATCCTTAGAAAACATCTACG 59.188 38.462 0.00 0.00 40.38 3.51
177 178 6.812160 GTGACATCCTTAGAAAACATCTACGT 59.188 38.462 0.00 0.00 40.38 3.57
178 179 7.972277 GTGACATCCTTAGAAAACATCTACGTA 59.028 37.037 0.00 0.00 40.38 3.57
179 180 8.188799 TGACATCCTTAGAAAACATCTACGTAG 58.811 37.037 16.73 16.73 40.38 3.51
180 181 8.289939 ACATCCTTAGAAAACATCTACGTAGA 57.710 34.615 26.55 26.55 40.38 2.59
181 182 8.915036 ACATCCTTAGAAAACATCTACGTAGAT 58.085 33.333 28.45 28.45 43.51 1.98
196 197 8.906636 TCTACGTAGATGTGAATTAGACAAAC 57.093 34.615 21.25 0.00 0.00 2.93
197 198 8.737175 TCTACGTAGATGTGAATTAGACAAACT 58.263 33.333 21.25 1.44 0.00 2.66
198 199 7.582435 ACGTAGATGTGAATTAGACAAACTG 57.418 36.000 0.00 0.00 0.00 3.16
199 200 7.152645 ACGTAGATGTGAATTAGACAAACTGT 58.847 34.615 0.00 0.00 0.00 3.55
200 201 7.656137 ACGTAGATGTGAATTAGACAAACTGTT 59.344 33.333 0.00 0.00 0.00 3.16
201 202 8.495949 CGTAGATGTGAATTAGACAAACTGTTT 58.504 33.333 0.00 0.00 0.00 2.83
215 216 9.594478 AGACAAACTGTTTTAATTTACCCTTTG 57.406 29.630 2.41 0.00 0.00 2.77
216 217 8.203937 ACAAACTGTTTTAATTTACCCTTTGC 57.796 30.769 2.41 0.00 0.00 3.68
217 218 7.010645 ACAAACTGTTTTAATTTACCCTTTGCG 59.989 33.333 2.41 0.00 0.00 4.85
218 219 4.986034 ACTGTTTTAATTTACCCTTTGCGC 59.014 37.500 0.00 0.00 0.00 6.09
219 220 4.945246 TGTTTTAATTTACCCTTTGCGCA 58.055 34.783 5.66 5.66 0.00 6.09
220 221 5.542779 TGTTTTAATTTACCCTTTGCGCAT 58.457 33.333 12.75 0.00 0.00 4.73
221 222 5.635700 TGTTTTAATTTACCCTTTGCGCATC 59.364 36.000 12.75 0.00 0.00 3.91
222 223 5.392767 TTTAATTTACCCTTTGCGCATCA 57.607 34.783 12.75 0.00 0.00 3.07
223 224 2.939460 ATTTACCCTTTGCGCATCAC 57.061 45.000 12.75 0.00 0.00 3.06
224 225 1.904287 TTTACCCTTTGCGCATCACT 58.096 45.000 12.75 0.00 0.00 3.41
225 226 1.164411 TTACCCTTTGCGCATCACTG 58.836 50.000 12.75 1.46 0.00 3.66
226 227 0.676466 TACCCTTTGCGCATCACTGG 60.676 55.000 12.75 10.66 0.00 4.00
227 228 2.703798 CCCTTTGCGCATCACTGGG 61.704 63.158 12.75 14.66 38.31 4.45
228 229 1.675310 CCTTTGCGCATCACTGGGA 60.675 57.895 12.75 0.00 37.51 4.37
229 230 1.243342 CCTTTGCGCATCACTGGGAA 61.243 55.000 12.75 0.00 37.51 3.97
230 231 0.813184 CTTTGCGCATCACTGGGAAT 59.187 50.000 12.75 0.00 37.51 3.01
231 232 2.016318 CTTTGCGCATCACTGGGAATA 58.984 47.619 12.75 0.00 37.51 1.75
232 233 2.121291 TTGCGCATCACTGGGAATAA 57.879 45.000 12.75 0.00 37.51 1.40
233 234 1.378531 TGCGCATCACTGGGAATAAC 58.621 50.000 5.66 0.00 37.51 1.89
234 235 1.065491 TGCGCATCACTGGGAATAACT 60.065 47.619 5.66 0.00 37.51 2.24
235 236 2.017049 GCGCATCACTGGGAATAACTT 58.983 47.619 0.30 0.00 37.51 2.66
236 237 2.032178 GCGCATCACTGGGAATAACTTC 59.968 50.000 0.30 0.00 37.51 3.01
250 251 7.389603 GGAATAACTTCCGTTTTGTTCTTTG 57.610 36.000 0.00 0.00 41.60 2.77
251 252 6.074516 GGAATAACTTCCGTTTTGTTCTTTGC 60.075 38.462 0.00 0.00 41.60 3.68
252 253 3.159353 ACTTCCGTTTTGTTCTTTGCC 57.841 42.857 0.00 0.00 0.00 4.52
253 254 2.116366 CTTCCGTTTTGTTCTTTGCCG 58.884 47.619 0.00 0.00 0.00 5.69
254 255 1.380524 TCCGTTTTGTTCTTTGCCGA 58.619 45.000 0.00 0.00 0.00 5.54
255 256 1.743958 TCCGTTTTGTTCTTTGCCGAA 59.256 42.857 0.00 0.00 0.00 4.30
256 257 2.163815 TCCGTTTTGTTCTTTGCCGAAA 59.836 40.909 0.00 0.00 0.00 3.46
257 258 3.120041 CCGTTTTGTTCTTTGCCGAAAT 58.880 40.909 0.00 0.00 0.00 2.17
258 259 4.036498 TCCGTTTTGTTCTTTGCCGAAATA 59.964 37.500 0.00 0.00 0.00 1.40
259 260 4.920927 CCGTTTTGTTCTTTGCCGAAATAT 59.079 37.500 0.00 0.00 0.00 1.28
260 261 5.164100 CCGTTTTGTTCTTTGCCGAAATATG 60.164 40.000 0.00 0.00 0.00 1.78
261 262 5.608146 GTTTTGTTCTTTGCCGAAATATGC 58.392 37.500 0.00 0.00 0.00 3.14
262 263 4.511617 TTGTTCTTTGCCGAAATATGCA 57.488 36.364 0.00 0.00 35.27 3.96
263 264 3.832276 TGTTCTTTGCCGAAATATGCAC 58.168 40.909 0.00 0.00 37.18 4.57
264 265 3.254411 TGTTCTTTGCCGAAATATGCACA 59.746 39.130 0.00 0.00 37.18 4.57
265 266 4.082300 TGTTCTTTGCCGAAATATGCACAT 60.082 37.500 0.00 0.00 37.18 3.21
266 267 4.031418 TCTTTGCCGAAATATGCACATG 57.969 40.909 0.00 0.00 37.18 3.21
267 268 3.443329 TCTTTGCCGAAATATGCACATGT 59.557 39.130 0.00 0.00 37.18 3.21
268 269 2.847959 TGCCGAAATATGCACATGTG 57.152 45.000 21.83 21.83 31.31 3.21
269 270 1.404748 TGCCGAAATATGCACATGTGG 59.595 47.619 26.55 8.27 31.31 4.17
270 271 1.405105 GCCGAAATATGCACATGTGGT 59.595 47.619 26.55 0.00 0.00 4.16
271 272 2.159254 GCCGAAATATGCACATGTGGTT 60.159 45.455 26.55 3.69 0.00 3.67
272 273 3.066064 GCCGAAATATGCACATGTGGTTA 59.934 43.478 26.55 5.54 0.00 2.85
273 274 4.439426 GCCGAAATATGCACATGTGGTTAA 60.439 41.667 26.55 0.09 0.00 2.01
274 275 5.034152 CCGAAATATGCACATGTGGTTAAC 58.966 41.667 26.55 10.44 0.00 2.01
275 276 5.163663 CCGAAATATGCACATGTGGTTAACT 60.164 40.000 26.55 3.46 0.00 2.24
276 277 6.037720 CCGAAATATGCACATGTGGTTAACTA 59.962 38.462 26.55 0.00 0.00 2.24
277 278 7.255104 CCGAAATATGCACATGTGGTTAACTAT 60.255 37.037 26.55 8.64 0.00 2.12
278 279 7.798516 CGAAATATGCACATGTGGTTAACTATC 59.201 37.037 26.55 7.59 0.00 2.08
279 280 7.510549 AATATGCACATGTGGTTAACTATCC 57.489 36.000 26.55 6.88 0.00 2.59
280 281 4.293662 TGCACATGTGGTTAACTATCCA 57.706 40.909 26.55 9.40 0.00 3.41
281 282 4.657013 TGCACATGTGGTTAACTATCCAA 58.343 39.130 26.55 0.00 35.38 3.53
282 283 4.699735 TGCACATGTGGTTAACTATCCAAG 59.300 41.667 26.55 0.00 35.38 3.61
283 284 4.700213 GCACATGTGGTTAACTATCCAAGT 59.300 41.667 26.55 0.00 41.49 3.16
284 285 5.163754 GCACATGTGGTTAACTATCCAAGTC 60.164 44.000 26.55 0.40 37.50 3.01
285 286 5.937540 CACATGTGGTTAACTATCCAAGTCA 59.062 40.000 18.51 0.00 37.50 3.41
286 287 6.429692 CACATGTGGTTAACTATCCAAGTCAA 59.570 38.462 18.51 0.00 37.50 3.18
287 288 7.001674 ACATGTGGTTAACTATCCAAGTCAAA 58.998 34.615 5.42 0.00 37.50 2.69
288 289 6.870971 TGTGGTTAACTATCCAAGTCAAAC 57.129 37.500 5.42 0.00 37.50 2.93
289 290 6.597562 TGTGGTTAACTATCCAAGTCAAACT 58.402 36.000 5.42 0.00 37.50 2.66
290 291 7.057894 TGTGGTTAACTATCCAAGTCAAACTT 58.942 34.615 5.42 0.00 39.39 2.66
291 292 7.227910 TGTGGTTAACTATCCAAGTCAAACTTC 59.772 37.037 5.42 0.00 36.03 3.01
292 293 6.713450 TGGTTAACTATCCAAGTCAAACTTCC 59.287 38.462 5.42 0.00 36.03 3.46
293 294 6.150641 GGTTAACTATCCAAGTCAAACTTCCC 59.849 42.308 5.42 0.00 36.03 3.97
294 295 5.584551 AACTATCCAAGTCAAACTTCCCT 57.415 39.130 0.00 0.00 36.03 4.20
295 296 5.167303 ACTATCCAAGTCAAACTTCCCTC 57.833 43.478 0.00 0.00 36.03 4.30
296 297 4.597507 ACTATCCAAGTCAAACTTCCCTCA 59.402 41.667 0.00 0.00 36.03 3.86
297 298 3.943671 TCCAAGTCAAACTTCCCTCAA 57.056 42.857 0.00 0.00 36.03 3.02
298 299 4.243793 TCCAAGTCAAACTTCCCTCAAA 57.756 40.909 0.00 0.00 36.03 2.69
299 300 4.605183 TCCAAGTCAAACTTCCCTCAAAA 58.395 39.130 0.00 0.00 36.03 2.44
300 301 5.020132 TCCAAGTCAAACTTCCCTCAAAAA 58.980 37.500 0.00 0.00 36.03 1.94
329 330 9.520515 ACTATCAAAGTCAAACATTTATGTCCT 57.479 29.630 0.00 0.00 34.70 3.85
369 372 3.886505 TCGTGCAACTTTTCCATAAGGTT 59.113 39.130 0.00 0.00 32.34 3.50
456 819 2.402305 CGCTGAGGATAGCAATCAGTC 58.598 52.381 12.35 5.88 43.87 3.51
1323 1695 2.293318 CCTGGCAGAGCACTGGGTA 61.293 63.158 17.94 0.00 43.62 3.69
1439 1814 0.671796 TCGTCGTCCAAGCAGAAAGA 59.328 50.000 0.00 0.00 0.00 2.52
1656 2046 1.962822 CATGGGGATCGTCATGGCG 60.963 63.158 14.91 14.91 37.63 5.69
1794 2184 4.391405 TGTCATCTATAGCACAGTGTGG 57.609 45.455 24.24 7.70 33.64 4.17
1858 2248 6.171006 GCACGAAATAAAAATGAATCTTGCG 58.829 36.000 0.00 0.00 0.00 4.85
1951 2342 3.772025 GGAGAAGAGAGGAGGAACATTGA 59.228 47.826 0.00 0.00 0.00 2.57
1977 2368 0.400975 AGCATCATGATCAGGAGGGC 59.599 55.000 21.80 21.96 0.00 5.19
1978 2369 0.400975 GCATCATGATCAGGAGGGCT 59.599 55.000 21.80 0.00 0.00 5.19
2124 2521 9.994432 AAATGCTTTCAGAAATTCTTATACTCG 57.006 29.630 0.00 0.00 0.00 4.18
2125 2522 8.948631 ATGCTTTCAGAAATTCTTATACTCGA 57.051 30.769 0.00 0.00 0.00 4.04
2134 2531 4.941325 TTCTTATACTCGATCCGATCCG 57.059 45.455 2.69 0.00 34.61 4.18
2136 2533 3.683340 TCTTATACTCGATCCGATCCGTG 59.317 47.826 2.69 2.71 34.61 4.94
2143 2540 3.377439 TCGATCCGATCCGTGTTAATTG 58.623 45.455 2.69 0.00 0.00 2.32
2145 2542 3.060540 CGATCCGATCCGTGTTAATTGTG 60.061 47.826 2.69 0.00 0.00 3.33
2361 3072 1.414181 CCAAGGCTATGACCGACTCAT 59.586 52.381 0.00 1.75 42.68 2.90
2368 3079 4.380655 GGCTATGACCGACTCATGGTATAC 60.381 50.000 5.96 0.00 40.12 1.47
2394 3108 6.883217 ACATATTTTCTGCTCTCAAGACACAT 59.117 34.615 0.00 0.00 0.00 3.21
2404 3118 6.183360 TGCTCTCAAGACACATTTTTACGTTT 60.183 34.615 0.00 0.00 0.00 3.60
2405 3119 6.691388 GCTCTCAAGACACATTTTTACGTTTT 59.309 34.615 0.00 0.00 0.00 2.43
2492 3206 5.346281 CGGTTTTGTTTCAGCAAAGTTTACA 59.654 36.000 0.00 0.00 39.20 2.41
2554 3270 3.587797 TCCAGAGATTTACGTCACCAC 57.412 47.619 0.00 0.00 0.00 4.16
2555 3271 2.894765 TCCAGAGATTTACGTCACCACA 59.105 45.455 0.00 0.00 0.00 4.17
2568 3284 5.209240 ACGTCACCACAATTTACATTTTCG 58.791 37.500 0.00 0.00 0.00 3.46
2576 3292 9.103861 ACCACAATTTACATTTTCGTCAATTTT 57.896 25.926 0.00 0.00 0.00 1.82
2618 3344 0.904649 TGTGTGACAGGCTAGGATGG 59.095 55.000 0.00 0.00 0.00 3.51
2682 3408 7.095229 GGCTCAAAATTAATGGGAAAACTTGAC 60.095 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.889722 TCCTAGACAGACCCAAATTAAAATGG 59.110 38.462 0.00 3.48 36.42 3.16
4 5 7.393234 TGTCCTAGACAGACCCAAATTAAAATG 59.607 37.037 0.00 0.00 37.67 2.32
5 6 7.393515 GTGTCCTAGACAGACCCAAATTAAAAT 59.606 37.037 0.00 0.00 43.57 1.82
6 7 6.713450 GTGTCCTAGACAGACCCAAATTAAAA 59.287 38.462 0.00 0.00 43.57 1.52
7 8 6.183361 TGTGTCCTAGACAGACCCAAATTAAA 60.183 38.462 0.00 0.00 43.57 1.52
8 9 5.308497 TGTGTCCTAGACAGACCCAAATTAA 59.692 40.000 0.00 0.00 43.57 1.40
9 10 4.841813 TGTGTCCTAGACAGACCCAAATTA 59.158 41.667 0.00 0.00 43.57 1.40
10 11 3.650942 TGTGTCCTAGACAGACCCAAATT 59.349 43.478 0.00 0.00 43.57 1.82
11 12 3.248024 TGTGTCCTAGACAGACCCAAAT 58.752 45.455 0.00 0.00 43.57 2.32
12 13 2.684943 TGTGTCCTAGACAGACCCAAA 58.315 47.619 0.00 0.00 43.57 3.28
13 14 2.391926 TGTGTCCTAGACAGACCCAA 57.608 50.000 0.00 0.00 43.57 4.12
14 15 2.043115 AGATGTGTCCTAGACAGACCCA 59.957 50.000 0.00 0.00 43.57 4.51
15 16 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
16 17 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
17 18 7.880713 TCATATCTAGATGTGTCCTAGACAGAC 59.119 40.741 23.88 0.00 43.57 3.51
18 19 7.880713 GTCATATCTAGATGTGTCCTAGACAGA 59.119 40.741 23.88 0.00 43.57 3.41
19 20 7.663493 TGTCATATCTAGATGTGTCCTAGACAG 59.337 40.741 23.88 0.73 43.57 3.51
20 21 7.518188 TGTCATATCTAGATGTGTCCTAGACA 58.482 38.462 23.88 17.81 43.57 3.41
21 22 7.987750 TGTCATATCTAGATGTGTCCTAGAC 57.012 40.000 23.88 15.91 43.57 2.59
22 23 9.898152 CTATGTCATATCTAGATGTGTCCTAGA 57.102 37.037 23.88 8.33 44.50 2.43
23 24 9.679661 ACTATGTCATATCTAGATGTGTCCTAG 57.320 37.037 23.88 23.41 35.97 3.02
25 26 8.948401 AACTATGTCATATCTAGATGTGTCCT 57.052 34.615 23.88 15.89 32.61 3.85
44 45 9.416794 GATCAGGTTAGATGTGACATAACTATG 57.583 37.037 10.13 9.49 39.55 2.23
45 46 9.373450 AGATCAGGTTAGATGTGACATAACTAT 57.627 33.333 10.13 3.77 31.53 2.12
46 47 8.768501 AGATCAGGTTAGATGTGACATAACTA 57.231 34.615 10.13 1.46 31.53 2.24
47 48 7.201956 GGAGATCAGGTTAGATGTGACATAACT 60.202 40.741 10.13 2.33 31.53 2.24
48 49 6.926272 GGAGATCAGGTTAGATGTGACATAAC 59.074 42.308 0.00 0.00 0.00 1.89
49 50 6.611236 TGGAGATCAGGTTAGATGTGACATAA 59.389 38.462 0.00 0.00 0.00 1.90
50 51 6.040955 GTGGAGATCAGGTTAGATGTGACATA 59.959 42.308 0.00 0.00 0.00 2.29
51 52 4.964897 TGGAGATCAGGTTAGATGTGACAT 59.035 41.667 0.00 0.00 0.00 3.06
52 53 4.160439 GTGGAGATCAGGTTAGATGTGACA 59.840 45.833 0.00 0.00 0.00 3.58
53 54 4.404073 AGTGGAGATCAGGTTAGATGTGAC 59.596 45.833 0.00 0.00 0.00 3.67
54 55 4.614475 AGTGGAGATCAGGTTAGATGTGA 58.386 43.478 0.00 0.00 0.00 3.58
55 56 6.453943 CATAGTGGAGATCAGGTTAGATGTG 58.546 44.000 0.00 0.00 0.00 3.21
56 57 5.011533 GCATAGTGGAGATCAGGTTAGATGT 59.988 44.000 0.00 0.00 0.00 3.06
57 58 5.245751 AGCATAGTGGAGATCAGGTTAGATG 59.754 44.000 0.00 0.00 0.00 2.90
58 59 5.401750 AGCATAGTGGAGATCAGGTTAGAT 58.598 41.667 0.00 0.00 0.00 1.98
59 60 4.809193 AGCATAGTGGAGATCAGGTTAGA 58.191 43.478 0.00 0.00 0.00 2.10
60 61 5.163364 ACAAGCATAGTGGAGATCAGGTTAG 60.163 44.000 0.00 0.00 0.00 2.34
61 62 4.716784 ACAAGCATAGTGGAGATCAGGTTA 59.283 41.667 0.00 0.00 0.00 2.85
62 63 3.521126 ACAAGCATAGTGGAGATCAGGTT 59.479 43.478 0.00 0.00 0.00 3.50
63 64 3.110705 ACAAGCATAGTGGAGATCAGGT 58.889 45.455 0.00 0.00 0.00 4.00
64 65 3.834489 ACAAGCATAGTGGAGATCAGG 57.166 47.619 0.00 0.00 0.00 3.86
65 66 5.301551 AGACTACAAGCATAGTGGAGATCAG 59.698 44.000 0.00 0.00 35.48 2.90
66 67 5.204292 AGACTACAAGCATAGTGGAGATCA 58.796 41.667 0.00 0.00 35.48 2.92
67 68 5.782893 AGACTACAAGCATAGTGGAGATC 57.217 43.478 0.52 0.00 35.48 2.75
68 69 7.847711 AATAGACTACAAGCATAGTGGAGAT 57.152 36.000 0.52 0.00 35.48 2.75
69 70 7.661536 AAATAGACTACAAGCATAGTGGAGA 57.338 36.000 0.52 0.00 35.48 3.71
70 71 8.723942 AAAAATAGACTACAAGCATAGTGGAG 57.276 34.615 0.52 0.00 35.48 3.86
111 112 3.936564 AGGCAGCAACAAAGAACAAAAA 58.063 36.364 0.00 0.00 0.00 1.94
112 113 3.608316 AGGCAGCAACAAAGAACAAAA 57.392 38.095 0.00 0.00 0.00 2.44
113 114 3.608316 AAGGCAGCAACAAAGAACAAA 57.392 38.095 0.00 0.00 0.00 2.83
114 115 4.935352 ATAAGGCAGCAACAAAGAACAA 57.065 36.364 0.00 0.00 0.00 2.83
115 116 4.935352 AATAAGGCAGCAACAAAGAACA 57.065 36.364 0.00 0.00 0.00 3.18
116 117 5.049828 ACAAATAAGGCAGCAACAAAGAAC 58.950 37.500 0.00 0.00 0.00 3.01
117 118 5.049167 CACAAATAAGGCAGCAACAAAGAA 58.951 37.500 0.00 0.00 0.00 2.52
118 119 4.501229 CCACAAATAAGGCAGCAACAAAGA 60.501 41.667 0.00 0.00 0.00 2.52
119 120 3.742369 CCACAAATAAGGCAGCAACAAAG 59.258 43.478 0.00 0.00 0.00 2.77
120 121 3.494048 CCCACAAATAAGGCAGCAACAAA 60.494 43.478 0.00 0.00 0.00 2.83
121 122 2.036992 CCCACAAATAAGGCAGCAACAA 59.963 45.455 0.00 0.00 0.00 2.83
122 123 1.617850 CCCACAAATAAGGCAGCAACA 59.382 47.619 0.00 0.00 0.00 3.33
123 124 1.892474 TCCCACAAATAAGGCAGCAAC 59.108 47.619 0.00 0.00 0.00 4.17
124 125 2.170166 CTCCCACAAATAAGGCAGCAA 58.830 47.619 0.00 0.00 0.00 3.91
125 126 1.616725 CCTCCCACAAATAAGGCAGCA 60.617 52.381 0.00 0.00 0.00 4.41
126 127 1.106285 CCTCCCACAAATAAGGCAGC 58.894 55.000 0.00 0.00 0.00 5.25
127 128 2.514458 ACCTCCCACAAATAAGGCAG 57.486 50.000 0.00 0.00 31.79 4.85
128 129 2.990740 AACCTCCCACAAATAAGGCA 57.009 45.000 0.00 0.00 31.79 4.75
129 130 4.230745 TCTAACCTCCCACAAATAAGGC 57.769 45.455 0.00 0.00 31.79 4.35
130 131 5.590259 CACATCTAACCTCCCACAAATAAGG 59.410 44.000 0.00 0.00 34.94 2.69
131 132 6.316390 GTCACATCTAACCTCCCACAAATAAG 59.684 42.308 0.00 0.00 0.00 1.73
132 133 6.177610 GTCACATCTAACCTCCCACAAATAA 58.822 40.000 0.00 0.00 0.00 1.40
133 134 5.249622 TGTCACATCTAACCTCCCACAAATA 59.750 40.000 0.00 0.00 0.00 1.40
134 135 4.042809 TGTCACATCTAACCTCCCACAAAT 59.957 41.667 0.00 0.00 0.00 2.32
135 136 3.392947 TGTCACATCTAACCTCCCACAAA 59.607 43.478 0.00 0.00 0.00 2.83
136 137 2.976185 TGTCACATCTAACCTCCCACAA 59.024 45.455 0.00 0.00 0.00 3.33
137 138 2.615391 TGTCACATCTAACCTCCCACA 58.385 47.619 0.00 0.00 0.00 4.17
138 139 3.432326 GGATGTCACATCTAACCTCCCAC 60.432 52.174 17.46 0.00 0.00 4.61
139 140 2.771943 GGATGTCACATCTAACCTCCCA 59.228 50.000 17.46 0.00 0.00 4.37
140 141 3.041946 AGGATGTCACATCTAACCTCCC 58.958 50.000 17.46 0.00 32.42 4.30
141 142 4.762289 AAGGATGTCACATCTAACCTCC 57.238 45.455 17.46 0.18 32.24 4.30
142 143 6.716934 TCTAAGGATGTCACATCTAACCTC 57.283 41.667 17.46 0.00 0.00 3.85
143 144 7.496346 TTTCTAAGGATGTCACATCTAACCT 57.504 36.000 17.46 3.80 0.00 3.50
144 145 7.606456 TGTTTTCTAAGGATGTCACATCTAACC 59.394 37.037 17.46 1.26 0.00 2.85
145 146 8.547967 TGTTTTCTAAGGATGTCACATCTAAC 57.452 34.615 17.46 10.31 0.00 2.34
146 147 9.383519 GATGTTTTCTAAGGATGTCACATCTAA 57.616 33.333 17.46 2.83 37.41 2.10
147 148 8.762645 AGATGTTTTCTAAGGATGTCACATCTA 58.237 33.333 17.46 2.37 44.89 1.98
148 149 7.628234 AGATGTTTTCTAAGGATGTCACATCT 58.372 34.615 17.46 1.18 42.98 2.90
149 150 7.856145 AGATGTTTTCTAAGGATGTCACATC 57.144 36.000 9.53 9.53 39.62 3.06
150 151 7.492669 CGTAGATGTTTTCTAAGGATGTCACAT 59.507 37.037 0.00 0.00 38.67 3.21
151 152 6.811665 CGTAGATGTTTTCTAAGGATGTCACA 59.188 38.462 0.00 0.00 38.67 3.58
152 153 6.812160 ACGTAGATGTTTTCTAAGGATGTCAC 59.188 38.462 0.00 0.00 39.79 3.67
153 154 6.931838 ACGTAGATGTTTTCTAAGGATGTCA 58.068 36.000 0.00 0.00 39.79 3.58
154 155 8.404000 TCTACGTAGATGTTTTCTAAGGATGTC 58.596 37.037 21.25 0.00 39.79 3.06
155 156 8.289939 TCTACGTAGATGTTTTCTAAGGATGT 57.710 34.615 21.25 0.00 39.79 3.06
170 171 9.517609 GTTTGTCTAATTCACATCTACGTAGAT 57.482 33.333 28.45 28.45 43.51 1.98
171 172 8.737175 AGTTTGTCTAATTCACATCTACGTAGA 58.263 33.333 26.55 26.55 36.65 2.59
172 173 8.799091 CAGTTTGTCTAATTCACATCTACGTAG 58.201 37.037 16.73 16.73 0.00 3.51
173 174 8.301720 ACAGTTTGTCTAATTCACATCTACGTA 58.698 33.333 0.00 0.00 0.00 3.57
174 175 7.152645 ACAGTTTGTCTAATTCACATCTACGT 58.847 34.615 0.00 0.00 0.00 3.57
175 176 7.582435 ACAGTTTGTCTAATTCACATCTACG 57.418 36.000 0.00 0.00 0.00 3.51
189 190 9.594478 CAAAGGGTAAATTAAAACAGTTTGTCT 57.406 29.630 0.00 0.00 0.00 3.41
190 191 8.332464 GCAAAGGGTAAATTAAAACAGTTTGTC 58.668 33.333 0.00 0.00 0.00 3.18
191 192 7.010645 CGCAAAGGGTAAATTAAAACAGTTTGT 59.989 33.333 0.00 0.00 0.00 2.83
192 193 7.341446 CGCAAAGGGTAAATTAAAACAGTTTG 58.659 34.615 0.00 0.00 0.00 2.93
193 194 6.018588 GCGCAAAGGGTAAATTAAAACAGTTT 60.019 34.615 0.30 0.00 0.00 2.66
194 195 5.464057 GCGCAAAGGGTAAATTAAAACAGTT 59.536 36.000 0.30 0.00 0.00 3.16
195 196 4.986034 GCGCAAAGGGTAAATTAAAACAGT 59.014 37.500 0.30 0.00 0.00 3.55
196 197 4.985409 TGCGCAAAGGGTAAATTAAAACAG 59.015 37.500 8.16 0.00 0.00 3.16
197 198 4.945246 TGCGCAAAGGGTAAATTAAAACA 58.055 34.783 8.16 0.00 0.00 2.83
198 199 5.635700 TGATGCGCAAAGGGTAAATTAAAAC 59.364 36.000 17.11 0.00 0.00 2.43
199 200 5.635700 GTGATGCGCAAAGGGTAAATTAAAA 59.364 36.000 17.11 0.00 0.00 1.52
200 201 5.047660 AGTGATGCGCAAAGGGTAAATTAAA 60.048 36.000 17.11 0.00 0.00 1.52
201 202 4.461081 AGTGATGCGCAAAGGGTAAATTAA 59.539 37.500 17.11 0.00 0.00 1.40
202 203 4.013728 AGTGATGCGCAAAGGGTAAATTA 58.986 39.130 17.11 0.00 0.00 1.40
203 204 2.825532 AGTGATGCGCAAAGGGTAAATT 59.174 40.909 17.11 0.00 0.00 1.82
204 205 2.164219 CAGTGATGCGCAAAGGGTAAAT 59.836 45.455 17.11 0.00 0.00 1.40
205 206 1.539388 CAGTGATGCGCAAAGGGTAAA 59.461 47.619 17.11 0.00 0.00 2.01
206 207 1.164411 CAGTGATGCGCAAAGGGTAA 58.836 50.000 17.11 0.00 0.00 2.85
207 208 0.676466 CCAGTGATGCGCAAAGGGTA 60.676 55.000 17.11 0.00 0.00 3.69
208 209 1.973281 CCAGTGATGCGCAAAGGGT 60.973 57.895 17.11 0.00 0.00 4.34
209 210 2.703798 CCCAGTGATGCGCAAAGGG 61.704 63.158 17.11 17.41 36.76 3.95
210 211 1.243342 TTCCCAGTGATGCGCAAAGG 61.243 55.000 17.11 12.02 0.00 3.11
211 212 0.813184 ATTCCCAGTGATGCGCAAAG 59.187 50.000 17.11 2.22 0.00 2.77
212 213 2.121291 TATTCCCAGTGATGCGCAAA 57.879 45.000 17.11 2.20 0.00 3.68
213 214 1.742831 GTTATTCCCAGTGATGCGCAA 59.257 47.619 17.11 0.00 0.00 4.85
214 215 1.065491 AGTTATTCCCAGTGATGCGCA 60.065 47.619 14.96 14.96 0.00 6.09
215 216 1.668419 AGTTATTCCCAGTGATGCGC 58.332 50.000 0.00 0.00 0.00 6.09
216 217 3.951979 GAAGTTATTCCCAGTGATGCG 57.048 47.619 0.00 0.00 0.00 4.73
233 234 2.116366 CGGCAAAGAACAAAACGGAAG 58.884 47.619 0.00 0.00 0.00 3.46
234 235 1.743958 TCGGCAAAGAACAAAACGGAA 59.256 42.857 0.00 0.00 0.00 4.30
235 236 1.380524 TCGGCAAAGAACAAAACGGA 58.619 45.000 0.00 0.00 0.00 4.69
236 237 2.196295 TTCGGCAAAGAACAAAACGG 57.804 45.000 0.00 0.00 0.00 4.44
237 238 5.665217 GCATATTTCGGCAAAGAACAAAACG 60.665 40.000 0.00 0.00 0.00 3.60
238 239 5.176590 TGCATATTTCGGCAAAGAACAAAAC 59.823 36.000 0.00 0.00 37.03 2.43
239 240 5.176590 GTGCATATTTCGGCAAAGAACAAAA 59.823 36.000 0.00 0.00 42.45 2.44
240 241 4.683781 GTGCATATTTCGGCAAAGAACAAA 59.316 37.500 0.00 0.00 42.45 2.83
241 242 4.233789 GTGCATATTTCGGCAAAGAACAA 58.766 39.130 0.00 0.00 42.45 2.83
242 243 3.254411 TGTGCATATTTCGGCAAAGAACA 59.746 39.130 0.00 0.00 42.45 3.18
243 244 3.832276 TGTGCATATTTCGGCAAAGAAC 58.168 40.909 0.00 0.00 42.45 3.01
244 245 4.082300 ACATGTGCATATTTCGGCAAAGAA 60.082 37.500 0.00 0.00 42.45 2.52
245 246 3.443329 ACATGTGCATATTTCGGCAAAGA 59.557 39.130 0.00 0.00 42.45 2.52
246 247 3.548668 CACATGTGCATATTTCGGCAAAG 59.451 43.478 13.94 0.00 42.45 2.77
247 248 3.509740 CACATGTGCATATTTCGGCAAA 58.490 40.909 13.94 0.00 42.45 3.68
248 249 2.159268 CCACATGTGCATATTTCGGCAA 60.159 45.455 20.81 0.00 42.45 4.52
249 250 1.404748 CCACATGTGCATATTTCGGCA 59.595 47.619 20.81 0.00 37.77 5.69
250 251 1.405105 ACCACATGTGCATATTTCGGC 59.595 47.619 20.81 0.00 0.00 5.54
251 252 3.781079 AACCACATGTGCATATTTCGG 57.219 42.857 20.81 5.92 0.00 4.30
252 253 5.879237 AGTTAACCACATGTGCATATTTCG 58.121 37.500 20.81 6.62 0.00 3.46
253 254 8.076178 GGATAGTTAACCACATGTGCATATTTC 58.924 37.037 20.81 9.27 0.00 2.17
254 255 7.559533 TGGATAGTTAACCACATGTGCATATTT 59.440 33.333 20.81 9.63 0.00 1.40
255 256 7.059788 TGGATAGTTAACCACATGTGCATATT 58.940 34.615 20.81 12.97 0.00 1.28
256 257 6.600388 TGGATAGTTAACCACATGTGCATAT 58.400 36.000 20.81 10.48 0.00 1.78
257 258 5.995446 TGGATAGTTAACCACATGTGCATA 58.005 37.500 20.81 11.96 0.00 3.14
258 259 4.854173 TGGATAGTTAACCACATGTGCAT 58.146 39.130 20.81 12.96 0.00 3.96
259 260 4.293662 TGGATAGTTAACCACATGTGCA 57.706 40.909 20.81 5.88 0.00 4.57
260 261 4.700213 ACTTGGATAGTTAACCACATGTGC 59.300 41.667 20.81 6.31 35.81 4.57
261 262 5.937540 TGACTTGGATAGTTAACCACATGTG 59.062 40.000 19.31 19.31 37.17 3.21
262 263 6.121776 TGACTTGGATAGTTAACCACATGT 57.878 37.500 0.88 0.00 37.17 3.21
263 264 7.174946 AGTTTGACTTGGATAGTTAACCACATG 59.825 37.037 0.88 0.00 37.17 3.21
264 265 7.231467 AGTTTGACTTGGATAGTTAACCACAT 58.769 34.615 0.88 0.00 37.17 3.21
265 266 6.597562 AGTTTGACTTGGATAGTTAACCACA 58.402 36.000 0.88 0.00 37.17 4.17
266 267 7.308408 GGAAGTTTGACTTGGATAGTTAACCAC 60.308 40.741 0.88 0.00 38.80 4.16
267 268 6.713450 GGAAGTTTGACTTGGATAGTTAACCA 59.287 38.462 0.88 0.00 38.80 3.67
268 269 6.150641 GGGAAGTTTGACTTGGATAGTTAACC 59.849 42.308 0.88 0.00 38.80 2.85
269 270 6.940867 AGGGAAGTTTGACTTGGATAGTTAAC 59.059 38.462 0.00 0.00 38.80 2.01
270 271 7.086685 AGGGAAGTTTGACTTGGATAGTTAA 57.913 36.000 0.00 0.00 38.80 2.01
271 272 6.271391 TGAGGGAAGTTTGACTTGGATAGTTA 59.729 38.462 0.00 0.00 38.80 2.24
272 273 5.073144 TGAGGGAAGTTTGACTTGGATAGTT 59.927 40.000 0.00 0.00 38.80 2.24
273 274 4.597507 TGAGGGAAGTTTGACTTGGATAGT 59.402 41.667 0.00 0.00 38.80 2.12
274 275 5.165961 TGAGGGAAGTTTGACTTGGATAG 57.834 43.478 0.00 0.00 38.80 2.08
275 276 5.576563 TTGAGGGAAGTTTGACTTGGATA 57.423 39.130 0.00 0.00 38.80 2.59
276 277 4.453480 TTGAGGGAAGTTTGACTTGGAT 57.547 40.909 0.00 0.00 38.80 3.41
277 278 3.943671 TTGAGGGAAGTTTGACTTGGA 57.056 42.857 0.00 0.00 38.80 3.53
278 279 5.337578 TTTTTGAGGGAAGTTTGACTTGG 57.662 39.130 0.00 0.00 38.80 3.61
303 304 9.520515 AGGACATAAATGTTTGACTTTGATAGT 57.479 29.630 0.00 0.00 41.95 2.12
309 310 8.918202 TGTAGAGGACATAAATGTTTGACTTT 57.082 30.769 0.00 0.00 41.95 2.66
322 323 8.885693 AATCAGCATATACTGTAGAGGACATA 57.114 34.615 2.85 0.00 37.45 2.29
323 324 7.362487 CGAATCAGCATATACTGTAGAGGACAT 60.362 40.741 2.85 0.00 37.45 3.06
324 325 6.072452 CGAATCAGCATATACTGTAGAGGACA 60.072 42.308 2.85 0.00 38.84 4.02
325 326 6.072397 ACGAATCAGCATATACTGTAGAGGAC 60.072 42.308 2.85 0.00 38.84 3.85
326 327 6.004574 ACGAATCAGCATATACTGTAGAGGA 58.995 40.000 2.85 0.00 38.84 3.71
328 329 5.570973 GCACGAATCAGCATATACTGTAGAG 59.429 44.000 2.85 0.00 38.84 2.43
329 330 5.009610 TGCACGAATCAGCATATACTGTAGA 59.990 40.000 2.85 0.00 38.84 2.59
369 372 0.180171 CATTGGATGCGTGGGGTCTA 59.820 55.000 0.00 0.00 0.00 2.59
456 819 0.667184 GGTTTCAATTGGCCAGCGTG 60.667 55.000 5.11 5.75 0.00 5.34
862 1225 4.104183 GATGGGGGAAACGCGGGA 62.104 66.667 12.47 0.00 45.87 5.14
864 1227 2.737881 TAGGATGGGGGAAACGCGG 61.738 63.158 12.47 0.00 45.87 6.46
870 1233 1.320512 GAGGGGTAGGATGGGGGAA 59.679 63.158 0.00 0.00 0.00 3.97
967 1330 2.581246 TGTCCTCTGTCTTCCCTAGCTA 59.419 50.000 0.00 0.00 0.00 3.32
1323 1695 2.406401 CCGTCGCCGTCGTAGATT 59.594 61.111 2.78 0.00 40.67 2.40
1656 2046 2.224885 GCCGAACATCTCGTCGAGC 61.225 63.158 17.61 2.15 46.65 5.03
1794 2184 3.353836 TTCTTCCCTTGTGCGCGC 61.354 61.111 27.26 27.26 0.00 6.86
1951 2342 2.901192 CCTGATCATGATGCTCTCCTCT 59.099 50.000 14.30 0.00 0.00 3.69
1977 2368 4.142381 GGGCAACTAAAGCATCCTTGTTAG 60.142 45.833 0.00 0.00 0.00 2.34
1978 2369 3.761752 GGGCAACTAAAGCATCCTTGTTA 59.238 43.478 0.00 0.00 0.00 2.41
2124 2521 3.247648 CCACAATTAACACGGATCGGATC 59.752 47.826 9.54 9.54 0.00 3.36
2125 2522 3.202906 CCACAATTAACACGGATCGGAT 58.797 45.455 7.35 0.00 0.00 4.18
2134 2531 7.812648 TGTACTAAATCAGCCACAATTAACAC 58.187 34.615 0.00 0.00 0.00 3.32
2136 2533 7.480542 CGTTGTACTAAATCAGCCACAATTAAC 59.519 37.037 0.00 0.00 35.86 2.01
2143 2540 4.689345 ACTTCGTTGTACTAAATCAGCCAC 59.311 41.667 0.00 0.00 0.00 5.01
2145 2542 6.589139 AGTTACTTCGTTGTACTAAATCAGCC 59.411 38.462 0.00 0.00 0.00 4.85
2342 3053 2.477825 CATGAGTCGGTCATAGCCTTG 58.522 52.381 1.44 0.00 44.73 3.61
2361 3072 7.791029 TGAGAGCAGAAAATATGTGTATACCA 58.209 34.615 0.00 0.00 0.00 3.25
2368 3079 6.148315 TGTGTCTTGAGAGCAGAAAATATGTG 59.852 38.462 0.00 0.00 0.00 3.21
2585 3301 6.605849 CCTGTCACACAAAATTGATGTCTAG 58.394 40.000 0.00 0.00 0.00 2.43
2593 3309 3.820467 TCCTAGCCTGTCACACAAAATTG 59.180 43.478 0.00 0.00 0.00 2.32
2651 3377 5.857471 TCCCATTAATTTTGAGCCTCATG 57.143 39.130 0.00 0.00 0.00 3.07
2682 3408 3.281727 TGGCTAGACTATTTGCTTGGG 57.718 47.619 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.