Multiple sequence alignment - TraesCS5D01G362200

Loading Multiple Alignment...

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 TraesCS5D01G362200 chr5D 100.000 3561 0 0 982 4542 441017142 441020702 0.000000e+00 6577.0
1 TraesCS5D01G362200 chr5D 100.000 584 0 0 1 584 441016161 441016744 0.000000e+00 1079.0
2 TraesCS5D01G362200 chr5B 93.933 3593 144 30 982 4542 536583801 536587351 0.000000e+00 5360.0
3 TraesCS5D01G362200 chr5B 93.725 255 11 2 326 579 536583517 536583767 1.190000e-100 377.0
4 TraesCS5D01G362200 chr5A 92.523 3210 143 51 982 4141 557123816 557126978 0.000000e+00 4508.0
5 TraesCS5D01G362200 chr5A 94.801 327 11 1 4222 4542 557126976 557127302 5.240000e-139 505.0
6 TraesCS5D01G362200 chr5A 96.277 188 4 2 393 579 557123596 557123781 5.710000e-79 305.0
7 TraesCS5D01G362200 chr5A 100.000 29 0 0 3405 3433 557126194 557126222 2.000000e-03 54.7
8 TraesCS5D01G362200 chr3D 97.154 246 7 0 1 246 592853275 592853520 2.530000e-112 416.0
9 TraesCS5D01G362200 chr3D 98.678 227 3 0 1 227 603054058 603053832 1.970000e-108 403.0
10 TraesCS5D01G362200 chr3D 94.000 100 3 3 4126 4224 22679048 22679145 1.020000e-31 148.0
11 TraesCS5D01G362200 chr3D 94.000 100 3 3 4126 4224 22767910 22767813 1.020000e-31 148.0
12 TraesCS5D01G362200 chr3D 97.647 85 2 0 4139 4223 436676900 436676984 3.660000e-31 147.0
13 TraesCS5D01G362200 chr3D 94.340 53 1 2 283 333 556074315 556074263 3.770000e-11 80.5
14 TraesCS5D01G362200 chr6D 96.552 87 3 0 4139 4225 299191263 299191349 1.320000e-30 145.0
15 TraesCS5D01G362200 chr4A 94.624 93 5 0 4136 4228 9380672 9380764 1.320000e-30 145.0
16 TraesCS5D01G362200 chr4A 80.769 104 11 5 2517 2620 435016425 435016519 6.300000e-09 73.1
17 TraesCS5D01G362200 chr4B 95.556 90 3 1 4134 4223 631527772 631527860 4.740000e-30 143.0
18 TraesCS5D01G362200 chr4B 93.548 93 6 0 4139 4231 20800591 20800499 6.130000e-29 139.0
19 TraesCS5D01G362200 chr1B 96.512 86 3 0 4138 4223 510799093 510799178 4.740000e-30 143.0
20 TraesCS5D01G362200 chr2A 100.000 38 0 0 285 322 360867907 360867944 2.270000e-08 71.3
21 TraesCS5D01G362200 chr2A 93.617 47 2 1 2581 2626 695351587 695351541 8.150000e-08 69.4
22 TraesCS5D01G362200 chr7A 100.000 29 0 0 252 280 728362741 728362713 2.000000e-03 54.7
23 TraesCS5D01G362200 chr7A 96.875 32 0 1 249 280 728361914 728361884 8.000000e-03 52.8
24 TraesCS5D01G362200 chr4D 100.000 29 0 0 253 281 121398859 121398887 2.000000e-03 54.7
25 TraesCS5D01G362200 chr4D 100.000 28 0 0 253 280 450313363 450313390 8.000000e-03 52.8
26 TraesCS5D01G362200 chr7D 100.000 28 0 0 253 280 272237828 272237855 8.000000e-03 52.8
27 TraesCS5D01G362200 chr6A 100.000 28 0 0 253 280 259963597 259963624 8.000000e-03 52.8
28 TraesCS5D01G362200 chr3A 100.000 28 0 0 253 280 365486024 365485997 8.000000e-03 52.8
29 TraesCS5D01G362200 chr2D 100.000 28 0 0 253 280 459340582 459340609 8.000000e-03 52.8


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 TraesCS5D01G362200 chr5D 441016161 441020702 4541 False 3828.000 6577 100.00000 1 4542 2 chr5D.!!$F1 4541
1 TraesCS5D01G362200 chr5B 536583517 536587351 3834 False 2868.500 5360 93.82900 326 4542 2 chr5B.!!$F1 4216
2 TraesCS5D01G362200 chr5A 557123596 557127302 3706 False 1343.175 4508 95.90025 393 4542 4 chr5A.!!$F1 4149

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
230 231 0.038709 TTTTCTTCGCAATTGGGCCG 60.039 50.0 17.19 7.56 0.0 6.13 F
1518 1528 0.106519 AAGTTTGCCTGCTCCTGTGT 60.107 50.0 0.00 0.00 0.0 3.72 F
2203 2227 0.534427 ATGCCTGGACATGCGATCTG 60.534 55.0 0.00 0.00 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1578 0.603707 CAATCCGACATGATCCCCCG 60.604 60.000 0.0 0.0 0.0 5.73 R
2712 2745 2.028130 AGAACAAATGACCACCGCAAA 58.972 42.857 0.0 0.0 0.0 3.68 R
3626 3670 2.093310 CACACTCGTCATGATCAGCAAC 59.907 50.000 0.0 0.0 0.0 4.17 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
30 31 9.887406 TCGTGGTTCTTAGTGAATTTATTTTTC 57.113 29.630 0.00 0.00 36.99 2.29
31 32 9.672086 CGTGGTTCTTAGTGAATTTATTTTTCA 57.328 29.630 0.00 0.00 36.99 2.69
75 76 7.690952 ATAACATATCTCTAGAGGAACGGTC 57.309 40.000 19.67 0.00 0.00 4.79
76 77 5.050126 ACATATCTCTAGAGGAACGGTCA 57.950 43.478 19.67 0.00 0.00 4.02
77 78 5.446860 ACATATCTCTAGAGGAACGGTCAA 58.553 41.667 19.67 0.00 0.00 3.18
78 79 5.892119 ACATATCTCTAGAGGAACGGTCAAA 59.108 40.000 19.67 0.00 0.00 2.69
79 80 6.551601 ACATATCTCTAGAGGAACGGTCAAAT 59.448 38.462 19.67 4.42 0.00 2.32
80 81 7.724506 ACATATCTCTAGAGGAACGGTCAAATA 59.275 37.037 19.67 6.44 0.00 1.40
81 82 8.744652 CATATCTCTAGAGGAACGGTCAAATAT 58.255 37.037 19.67 8.33 0.00 1.28
82 83 6.392625 TCTCTAGAGGAACGGTCAAATATG 57.607 41.667 19.67 0.00 0.00 1.78
83 84 5.892119 TCTCTAGAGGAACGGTCAAATATGT 59.108 40.000 19.67 0.00 0.00 2.29
84 85 6.039493 TCTCTAGAGGAACGGTCAAATATGTC 59.961 42.308 19.67 0.00 0.00 3.06
85 86 5.892119 TCTAGAGGAACGGTCAAATATGTCT 59.108 40.000 1.31 0.00 0.00 3.41
86 87 5.012328 AGAGGAACGGTCAAATATGTCTC 57.988 43.478 1.31 0.00 0.00 3.36
87 88 3.782046 AGGAACGGTCAAATATGTCTCG 58.218 45.455 1.31 0.00 0.00 4.04
88 89 3.194968 AGGAACGGTCAAATATGTCTCGT 59.805 43.478 1.31 0.00 32.47 4.18
89 90 3.930848 GGAACGGTCAAATATGTCTCGTT 59.069 43.478 1.31 0.00 38.77 3.85
90 91 4.390909 GGAACGGTCAAATATGTCTCGTTT 59.609 41.667 1.31 0.00 37.49 3.60
91 92 5.445540 GGAACGGTCAAATATGTCTCGTTTC 60.446 44.000 1.31 0.00 37.49 2.78
92 93 4.817517 ACGGTCAAATATGTCTCGTTTCT 58.182 39.130 0.00 0.00 0.00 2.52
93 94 4.625742 ACGGTCAAATATGTCTCGTTTCTG 59.374 41.667 0.00 0.00 0.00 3.02
94 95 4.625742 CGGTCAAATATGTCTCGTTTCTGT 59.374 41.667 0.00 0.00 0.00 3.41
95 96 5.120208 CGGTCAAATATGTCTCGTTTCTGTT 59.880 40.000 0.00 0.00 0.00 3.16
96 97 6.309494 CGGTCAAATATGTCTCGTTTCTGTTA 59.691 38.462 0.00 0.00 0.00 2.41
97 98 7.462856 CGGTCAAATATGTCTCGTTTCTGTTAG 60.463 40.741 0.00 0.00 0.00 2.34
98 99 7.331193 GGTCAAATATGTCTCGTTTCTGTTAGT 59.669 37.037 0.00 0.00 0.00 2.24
99 100 8.709646 GTCAAATATGTCTCGTTTCTGTTAGTT 58.290 33.333 0.00 0.00 0.00 2.24
100 101 8.708742 TCAAATATGTCTCGTTTCTGTTAGTTG 58.291 33.333 0.00 0.00 0.00 3.16
101 102 8.708742 CAAATATGTCTCGTTTCTGTTAGTTGA 58.291 33.333 0.00 0.00 0.00 3.18
102 103 7.813852 ATATGTCTCGTTTCTGTTAGTTGAC 57.186 36.000 0.00 0.00 0.00 3.18
103 104 5.001237 TGTCTCGTTTCTGTTAGTTGACA 57.999 39.130 0.00 0.00 0.00 3.58
104 105 5.412640 TGTCTCGTTTCTGTTAGTTGACAA 58.587 37.500 0.00 0.00 0.00 3.18
105 106 5.518847 TGTCTCGTTTCTGTTAGTTGACAAG 59.481 40.000 0.00 0.00 0.00 3.16
106 107 4.506654 TCTCGTTTCTGTTAGTTGACAAGC 59.493 41.667 0.00 0.00 0.00 4.01
107 108 4.439057 TCGTTTCTGTTAGTTGACAAGCT 58.561 39.130 0.00 0.00 0.00 3.74
108 109 4.873827 TCGTTTCTGTTAGTTGACAAGCTT 59.126 37.500 0.00 0.00 0.00 3.74
109 110 4.963953 CGTTTCTGTTAGTTGACAAGCTTG 59.036 41.667 24.84 24.84 0.00 4.01
110 111 5.447279 CGTTTCTGTTAGTTGACAAGCTTGT 60.447 40.000 31.57 31.57 45.65 3.16
124 125 1.312815 GCTTGTCAGCTTTGTCTGGT 58.687 50.000 0.00 0.00 43.51 4.00
125 126 1.002033 GCTTGTCAGCTTTGTCTGGTG 60.002 52.381 0.00 0.00 43.51 4.17
126 127 1.605710 CTTGTCAGCTTTGTCTGGTGG 59.394 52.381 0.00 0.00 34.91 4.61
127 128 0.546122 TGTCAGCTTTGTCTGGTGGT 59.454 50.000 0.00 0.00 34.91 4.16
128 129 1.064758 TGTCAGCTTTGTCTGGTGGTT 60.065 47.619 0.00 0.00 34.91 3.67
129 130 1.604278 GTCAGCTTTGTCTGGTGGTTC 59.396 52.381 0.00 0.00 34.91 3.62
130 131 1.490490 TCAGCTTTGTCTGGTGGTTCT 59.510 47.619 0.00 0.00 34.91 3.01
131 132 1.605710 CAGCTTTGTCTGGTGGTTCTG 59.394 52.381 0.00 0.00 0.00 3.02
132 133 1.490490 AGCTTTGTCTGGTGGTTCTGA 59.510 47.619 0.00 0.00 0.00 3.27
133 134 1.604278 GCTTTGTCTGGTGGTTCTGAC 59.396 52.381 0.00 0.00 36.54 3.51
134 135 1.867233 CTTTGTCTGGTGGTTCTGACG 59.133 52.381 0.00 0.00 38.09 4.35
135 136 0.828022 TTGTCTGGTGGTTCTGACGT 59.172 50.000 0.00 0.00 38.09 4.34
136 137 0.828022 TGTCTGGTGGTTCTGACGTT 59.172 50.000 0.00 0.00 38.09 3.99
137 138 2.033372 TGTCTGGTGGTTCTGACGTTA 58.967 47.619 0.00 0.00 38.09 3.18
138 139 2.035449 TGTCTGGTGGTTCTGACGTTAG 59.965 50.000 0.00 0.00 38.09 2.34
139 140 1.616865 TCTGGTGGTTCTGACGTTAGG 59.383 52.381 7.57 0.00 0.00 2.69
140 141 1.343465 CTGGTGGTTCTGACGTTAGGT 59.657 52.381 7.57 0.00 0.00 3.08
141 142 1.764134 TGGTGGTTCTGACGTTAGGTT 59.236 47.619 7.57 0.00 0.00 3.50
142 143 2.140717 GGTGGTTCTGACGTTAGGTTG 58.859 52.381 7.57 0.00 0.00 3.77
143 144 1.529865 GTGGTTCTGACGTTAGGTTGC 59.470 52.381 7.57 0.00 0.00 4.17
144 145 1.414919 TGGTTCTGACGTTAGGTTGCT 59.585 47.619 7.57 0.00 0.00 3.91
145 146 1.798813 GGTTCTGACGTTAGGTTGCTG 59.201 52.381 7.57 0.00 0.00 4.41
146 147 2.480845 GTTCTGACGTTAGGTTGCTGT 58.519 47.619 7.57 0.00 0.00 4.40
147 148 3.553508 GGTTCTGACGTTAGGTTGCTGTA 60.554 47.826 7.57 0.00 0.00 2.74
148 149 3.293311 TCTGACGTTAGGTTGCTGTAC 57.707 47.619 7.57 0.00 0.00 2.90
149 150 2.624364 TCTGACGTTAGGTTGCTGTACA 59.376 45.455 7.57 0.00 0.00 2.90
150 151 3.257375 TCTGACGTTAGGTTGCTGTACAT 59.743 43.478 7.57 0.00 0.00 2.29
151 152 3.994392 CTGACGTTAGGTTGCTGTACATT 59.006 43.478 0.00 0.00 0.00 2.71
152 153 4.382291 TGACGTTAGGTTGCTGTACATTT 58.618 39.130 0.00 0.00 0.00 2.32
153 154 4.212425 TGACGTTAGGTTGCTGTACATTTG 59.788 41.667 0.00 0.00 0.00 2.32
154 155 4.382291 ACGTTAGGTTGCTGTACATTTGA 58.618 39.130 0.00 0.00 0.00 2.69
155 156 5.001232 ACGTTAGGTTGCTGTACATTTGAT 58.999 37.500 0.00 0.00 0.00 2.57
156 157 5.106712 ACGTTAGGTTGCTGTACATTTGATG 60.107 40.000 0.00 0.00 0.00 3.07
157 158 5.640732 GTTAGGTTGCTGTACATTTGATGG 58.359 41.667 0.00 0.00 33.60 3.51
158 159 4.032960 AGGTTGCTGTACATTTGATGGA 57.967 40.909 0.00 0.00 33.60 3.41
159 160 4.012374 AGGTTGCTGTACATTTGATGGAG 58.988 43.478 0.00 0.00 33.60 3.86
160 161 3.129287 GGTTGCTGTACATTTGATGGAGG 59.871 47.826 0.00 0.00 33.60 4.30
161 162 3.003394 TGCTGTACATTTGATGGAGGG 57.997 47.619 0.00 0.00 33.60 4.30
162 163 2.308570 TGCTGTACATTTGATGGAGGGT 59.691 45.455 0.00 0.00 33.60 4.34
163 164 3.245229 TGCTGTACATTTGATGGAGGGTT 60.245 43.478 0.00 0.00 33.60 4.11
164 165 3.378427 GCTGTACATTTGATGGAGGGTTC 59.622 47.826 0.00 0.00 33.60 3.62
165 166 3.605634 TGTACATTTGATGGAGGGTTCG 58.394 45.455 0.00 0.00 33.60 3.95
166 167 3.262151 TGTACATTTGATGGAGGGTTCGA 59.738 43.478 0.00 0.00 33.60 3.71
167 168 3.652057 ACATTTGATGGAGGGTTCGAT 57.348 42.857 0.00 0.00 33.60 3.59
168 169 3.968265 ACATTTGATGGAGGGTTCGATT 58.032 40.909 0.00 0.00 33.60 3.34
169 170 3.947834 ACATTTGATGGAGGGTTCGATTC 59.052 43.478 0.00 0.00 33.60 2.52
170 171 2.710096 TTGATGGAGGGTTCGATTCC 57.290 50.000 0.00 0.00 0.00 3.01
171 172 1.879575 TGATGGAGGGTTCGATTCCT 58.120 50.000 6.76 6.76 35.82 3.36
172 173 3.040655 TGATGGAGGGTTCGATTCCTA 57.959 47.619 7.01 0.00 32.74 2.94
173 174 2.965831 TGATGGAGGGTTCGATTCCTAG 59.034 50.000 7.01 0.00 32.74 3.02
174 175 2.544844 TGGAGGGTTCGATTCCTAGT 57.455 50.000 7.01 0.00 32.74 2.57
175 176 2.829023 TGGAGGGTTCGATTCCTAGTT 58.171 47.619 7.01 0.00 32.74 2.24
176 177 3.178865 TGGAGGGTTCGATTCCTAGTTT 58.821 45.455 7.01 0.00 32.74 2.66
177 178 3.585732 TGGAGGGTTCGATTCCTAGTTTT 59.414 43.478 7.01 0.00 32.74 2.43
178 179 4.042435 TGGAGGGTTCGATTCCTAGTTTTT 59.958 41.667 7.01 0.00 32.74 1.94
179 180 4.395231 GGAGGGTTCGATTCCTAGTTTTTG 59.605 45.833 7.01 0.00 32.74 2.44
180 181 3.756963 AGGGTTCGATTCCTAGTTTTTGC 59.243 43.478 5.39 0.00 0.00 3.68
181 182 3.425758 GGGTTCGATTCCTAGTTTTTGCG 60.426 47.826 7.03 0.00 0.00 4.85
182 183 3.187842 GGTTCGATTCCTAGTTTTTGCGT 59.812 43.478 0.00 0.00 0.00 5.24
183 184 4.389687 GGTTCGATTCCTAGTTTTTGCGTA 59.610 41.667 0.00 0.00 0.00 4.42
184 185 5.064325 GGTTCGATTCCTAGTTTTTGCGTAT 59.936 40.000 0.00 0.00 0.00 3.06
185 186 6.256321 GGTTCGATTCCTAGTTTTTGCGTATA 59.744 38.462 0.00 0.00 0.00 1.47
186 187 7.042254 GGTTCGATTCCTAGTTTTTGCGTATAT 60.042 37.037 0.00 0.00 0.00 0.86
187 188 8.971321 GTTCGATTCCTAGTTTTTGCGTATATA 58.029 33.333 0.00 0.00 0.00 0.86
188 189 8.511465 TCGATTCCTAGTTTTTGCGTATATAC 57.489 34.615 2.53 2.53 0.00 1.47
189 190 7.596248 TCGATTCCTAGTTTTTGCGTATATACC 59.404 37.037 7.30 1.44 0.00 2.73
190 191 7.383029 CGATTCCTAGTTTTTGCGTATATACCA 59.617 37.037 7.30 3.95 0.00 3.25
191 192 8.603242 ATTCCTAGTTTTTGCGTATATACCAG 57.397 34.615 7.30 0.00 0.00 4.00
192 193 7.116075 TCCTAGTTTTTGCGTATATACCAGT 57.884 36.000 7.30 0.00 0.00 4.00
193 194 8.236585 TCCTAGTTTTTGCGTATATACCAGTA 57.763 34.615 7.30 0.00 0.00 2.74
194 195 8.694540 TCCTAGTTTTTGCGTATATACCAGTAA 58.305 33.333 7.30 0.00 0.00 2.24
195 196 8.975439 CCTAGTTTTTGCGTATATACCAGTAAG 58.025 37.037 7.30 0.00 0.00 2.34
196 197 7.242914 AGTTTTTGCGTATATACCAGTAAGC 57.757 36.000 7.30 4.53 0.00 3.09
197 198 6.819649 AGTTTTTGCGTATATACCAGTAAGCA 59.180 34.615 7.30 6.99 34.37 3.91
198 199 7.497909 AGTTTTTGCGTATATACCAGTAAGCAT 59.502 33.333 7.30 0.00 35.74 3.79
199 200 7.795482 TTTTGCGTATATACCAGTAAGCATT 57.205 32.000 7.30 0.00 35.74 3.56
200 201 7.795482 TTTGCGTATATACCAGTAAGCATTT 57.205 32.000 7.30 0.00 35.74 2.32
201 202 7.795482 TTGCGTATATACCAGTAAGCATTTT 57.205 32.000 7.30 0.00 35.74 1.82
202 203 7.795482 TGCGTATATACCAGTAAGCATTTTT 57.205 32.000 7.30 0.00 31.93 1.94
203 204 7.857569 TGCGTATATACCAGTAAGCATTTTTC 58.142 34.615 7.30 0.00 31.93 2.29
204 205 7.713507 TGCGTATATACCAGTAAGCATTTTTCT 59.286 33.333 7.30 0.00 31.93 2.52
205 206 9.199982 GCGTATATACCAGTAAGCATTTTTCTA 57.800 33.333 7.30 0.00 0.00 2.10
209 210 7.865706 ATACCAGTAAGCATTTTTCTACAGG 57.134 36.000 0.00 0.00 0.00 4.00
210 211 5.631119 ACCAGTAAGCATTTTTCTACAGGT 58.369 37.500 0.00 0.00 0.00 4.00
211 212 6.068670 ACCAGTAAGCATTTTTCTACAGGTT 58.931 36.000 0.00 0.00 0.00 3.50
212 213 6.549736 ACCAGTAAGCATTTTTCTACAGGTTT 59.450 34.615 0.00 0.00 0.00 3.27
213 214 7.069455 ACCAGTAAGCATTTTTCTACAGGTTTT 59.931 33.333 0.00 0.00 0.00 2.43
214 215 7.926018 CCAGTAAGCATTTTTCTACAGGTTTTT 59.074 33.333 0.00 0.00 0.00 1.94
215 216 8.968242 CAGTAAGCATTTTTCTACAGGTTTTTC 58.032 33.333 0.00 0.00 0.00 2.29
216 217 8.914011 AGTAAGCATTTTTCTACAGGTTTTTCT 58.086 29.630 0.00 0.00 0.00 2.52
217 218 9.529325 GTAAGCATTTTTCTACAGGTTTTTCTT 57.471 29.630 0.00 0.00 0.00 2.52
218 219 8.648557 AAGCATTTTTCTACAGGTTTTTCTTC 57.351 30.769 0.00 0.00 0.00 2.87
219 220 6.918022 AGCATTTTTCTACAGGTTTTTCTTCG 59.082 34.615 0.00 0.00 0.00 3.79
220 221 6.345803 GCATTTTTCTACAGGTTTTTCTTCGC 60.346 38.462 0.00 0.00 0.00 4.70
221 222 5.821516 TTTTCTACAGGTTTTTCTTCGCA 57.178 34.783 0.00 0.00 0.00 5.10
222 223 5.821516 TTTCTACAGGTTTTTCTTCGCAA 57.178 34.783 0.00 0.00 0.00 4.85
223 224 6.385649 TTTCTACAGGTTTTTCTTCGCAAT 57.614 33.333 0.00 0.00 0.00 3.56
224 225 6.385649 TTCTACAGGTTTTTCTTCGCAATT 57.614 33.333 0.00 0.00 0.00 2.32
225 226 5.757886 TCTACAGGTTTTTCTTCGCAATTG 58.242 37.500 0.00 0.00 0.00 2.32
226 227 3.716601 ACAGGTTTTTCTTCGCAATTGG 58.283 40.909 7.72 0.00 0.00 3.16
227 228 3.059166 CAGGTTTTTCTTCGCAATTGGG 58.941 45.455 15.98 15.98 0.00 4.12
228 229 1.798223 GGTTTTTCTTCGCAATTGGGC 59.202 47.619 17.19 0.00 0.00 5.36
229 230 1.798223 GTTTTTCTTCGCAATTGGGCC 59.202 47.619 17.19 0.00 0.00 5.80
230 231 0.038709 TTTTCTTCGCAATTGGGCCG 60.039 50.000 17.19 7.56 0.00 6.13
231 232 1.872197 TTTCTTCGCAATTGGGCCGG 61.872 55.000 17.19 0.00 0.00 6.13
232 233 4.496927 CTTCGCAATTGGGCCGGC 62.497 66.667 21.18 21.18 0.00 6.13
248 249 4.554036 GCCCGCTAGCTCCCCTTG 62.554 72.222 13.93 0.00 0.00 3.61
249 250 4.554036 CCCGCTAGCTCCCCTTGC 62.554 72.222 13.93 0.00 38.67 4.01
252 253 2.107953 GCTAGCTCCCCTTGCGAG 59.892 66.667 7.70 0.00 36.48 5.03
272 273 4.880537 CCTGCAGCGCCGACTAGG 62.881 72.222 8.66 1.07 44.97 3.02
273 274 3.826754 CTGCAGCGCCGACTAGGA 61.827 66.667 2.29 0.00 45.00 2.94
274 275 3.764810 CTGCAGCGCCGACTAGGAG 62.765 68.421 2.29 0.00 45.00 3.69
279 280 3.597728 CGCCGACTAGGAGCTCCC 61.598 72.222 29.54 12.87 45.00 4.30
281 282 2.197605 GCCGACTAGGAGCTCCCTC 61.198 68.421 29.54 19.09 43.31 4.30
292 293 2.249139 GAGCTCCCTCCCGTATTATGT 58.751 52.381 0.87 0.00 31.68 2.29
293 294 3.428532 GAGCTCCCTCCCGTATTATGTA 58.571 50.000 0.87 0.00 31.68 2.29
294 295 3.830755 GAGCTCCCTCCCGTATTATGTAA 59.169 47.826 0.87 0.00 31.68 2.41
295 296 4.426704 AGCTCCCTCCCGTATTATGTAAT 58.573 43.478 0.00 0.00 0.00 1.89
296 297 5.586877 AGCTCCCTCCCGTATTATGTAATA 58.413 41.667 0.00 0.00 0.00 0.98
297 298 6.203072 AGCTCCCTCCCGTATTATGTAATAT 58.797 40.000 0.00 0.00 31.50 1.28
298 299 7.359849 AGCTCCCTCCCGTATTATGTAATATA 58.640 38.462 0.00 0.00 31.50 0.86
299 300 8.011290 AGCTCCCTCCCGTATTATGTAATATAT 58.989 37.037 0.00 0.00 31.50 0.86
300 301 8.648693 GCTCCCTCCCGTATTATGTAATATATT 58.351 37.037 2.97 2.97 31.50 1.28
302 303 9.947189 TCCCTCCCGTATTATGTAATATATTCT 57.053 33.333 0.00 0.00 31.50 2.40
303 304 9.982651 CCCTCCCGTATTATGTAATATATTCTG 57.017 37.037 0.00 0.00 31.50 3.02
304 305 9.982651 CCTCCCGTATTATGTAATATATTCTGG 57.017 37.037 0.00 0.00 31.50 3.86
409 411 3.699894 CCTGTCACGCTCAGGGCT 61.700 66.667 11.67 0.00 46.03 5.19
469 472 2.350484 GCCGCTTAAACAAACAGTCTCC 60.350 50.000 0.00 0.00 0.00 3.71
579 582 3.197549 CCTCCTCTTCCTTCTCCTCTTTG 59.802 52.174 0.00 0.00 0.00 2.77
580 583 2.569404 TCCTCTTCCTTCTCCTCTTTGC 59.431 50.000 0.00 0.00 0.00 3.68
1113 1123 3.503336 CTCGCCGGAGTACTACGCG 62.503 68.421 27.42 27.42 37.62 6.01
1290 1300 7.548427 GGTTCGGTAATTAGGATTATTCTAGCC 59.452 40.741 0.00 0.00 30.84 3.93
1313 1323 1.065854 CGAGAGGGAGAAATGGTGCTT 60.066 52.381 0.00 0.00 0.00 3.91
1360 1370 0.543277 ATGCAGCCGAGGATTCTTCA 59.457 50.000 0.00 0.00 0.00 3.02
1482 1492 2.134287 TCCCGTGGAGAGGCATAGC 61.134 63.158 0.00 0.00 0.00 2.97
1517 1527 0.313043 CAAGTTTGCCTGCTCCTGTG 59.687 55.000 0.00 0.00 0.00 3.66
1518 1528 0.106519 AAGTTTGCCTGCTCCTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
1541 1551 1.930567 TTTATTACTCGGCAGCGGTC 58.069 50.000 0.00 0.00 0.00 4.79
1551 1561 1.493311 GCAGCGGTCGAAGAAACAG 59.507 57.895 0.00 0.00 39.69 3.16
1552 1562 0.944311 GCAGCGGTCGAAGAAACAGA 60.944 55.000 0.00 0.00 39.69 3.41
1554 1564 1.864711 CAGCGGTCGAAGAAACAGAAA 59.135 47.619 0.00 0.00 39.69 2.52
1555 1565 2.096713 CAGCGGTCGAAGAAACAGAAAG 60.097 50.000 0.00 0.00 39.69 2.62
1558 1568 3.639538 CGGTCGAAGAAACAGAAAGAGA 58.360 45.455 0.00 0.00 39.69 3.10
1559 1569 4.049186 CGGTCGAAGAAACAGAAAGAGAA 58.951 43.478 0.00 0.00 39.69 2.87
1560 1570 4.686554 CGGTCGAAGAAACAGAAAGAGAAT 59.313 41.667 0.00 0.00 39.69 2.40
1561 1571 5.164041 CGGTCGAAGAAACAGAAAGAGAATC 60.164 44.000 0.00 0.00 39.69 2.52
1562 1572 5.696724 GGTCGAAGAAACAGAAAGAGAATCA 59.303 40.000 0.00 0.00 39.69 2.57
1563 1573 6.128688 GGTCGAAGAAACAGAAAGAGAATCAG 60.129 42.308 0.00 0.00 39.69 2.90
1564 1574 6.642950 GTCGAAGAAACAGAAAGAGAATCAGA 59.357 38.462 0.00 0.00 39.69 3.27
1565 1575 7.169982 GTCGAAGAAACAGAAAGAGAATCAGAA 59.830 37.037 0.00 0.00 39.69 3.02
1566 1576 7.383572 TCGAAGAAACAGAAAGAGAATCAGAAG 59.616 37.037 0.00 0.00 37.82 2.85
1567 1577 6.799926 AGAAACAGAAAGAGAATCAGAAGC 57.200 37.500 0.00 0.00 37.82 3.86
1568 1578 5.704978 AGAAACAGAAAGAGAATCAGAAGCC 59.295 40.000 0.00 0.00 37.82 4.35
1582 1592 2.996168 GAAGCCGGGGGATCATGTCG 62.996 65.000 2.18 0.00 0.00 4.35
1613 1635 6.140896 CACGAACAAGTGTATTGTAGACAG 57.859 41.667 0.00 0.00 37.35 3.51
1630 1652 4.168101 AGACAGGTCCCTTTGTTGATCTA 58.832 43.478 0.00 0.00 0.00 1.98
1633 1655 5.892348 ACAGGTCCCTTTGTTGATCTAAAT 58.108 37.500 0.00 0.00 0.00 1.40
1638 1661 7.611855 AGGTCCCTTTGTTGATCTAAATAACAG 59.388 37.037 0.00 0.00 35.91 3.16
1659 1682 3.117888 AGGGCCCTTATGTGTATCTTGTG 60.118 47.826 22.28 0.00 0.00 3.33
1661 1684 4.141574 GGGCCCTTATGTGTATCTTGTGTA 60.142 45.833 17.04 0.00 0.00 2.90
1683 1707 8.505625 GTGTAGAGACCTGTATAATAGTGCTAC 58.494 40.741 0.00 0.00 0.00 3.58
1690 1714 5.009310 CCTGTATAATAGTGCTACGTCCACA 59.991 44.000 18.01 2.02 35.69 4.17
1691 1715 6.453926 TGTATAATAGTGCTACGTCCACAA 57.546 37.500 18.01 4.78 35.69 3.33
1692 1716 6.267817 TGTATAATAGTGCTACGTCCACAAC 58.732 40.000 18.01 8.79 35.69 3.32
1735 1759 1.948145 GCTGCCTCAGAAATGATCCTG 59.052 52.381 0.00 0.00 32.44 3.86
1743 1767 4.591929 TCAGAAATGATCCTGTGAATGCA 58.408 39.130 0.00 0.00 0.00 3.96
1893 1917 1.903183 GGAGGGAAGCTATTCGGCTAT 59.097 52.381 0.00 0.00 42.24 2.97
1932 1956 2.737252 CAAGTTTGGCCTCTACGAGTTC 59.263 50.000 3.32 0.00 0.00 3.01
1980 2004 2.320587 GGACAGCAACAGGAGCACG 61.321 63.158 0.00 0.00 0.00 5.34
2154 2178 3.869065 TGGGTAAGCTTCCTTCGTATTG 58.131 45.455 0.00 0.00 32.47 1.90
2196 2220 3.817084 CACTATTGGTATGCCTGGACATG 59.183 47.826 12.08 0.00 35.27 3.21
2203 2227 0.534427 ATGCCTGGACATGCGATCTG 60.534 55.000 0.00 0.00 0.00 2.90
2310 2334 6.483640 GGCGAAATCTTCCATGTAATAACTCT 59.516 38.462 0.00 0.00 0.00 3.24
2326 2350 9.046296 GTAATAACTCTCCCTGTTTCACATATG 57.954 37.037 0.00 0.00 0.00 1.78
2353 2377 2.722094 TCGCAAAATCCTATTGTGCCT 58.278 42.857 8.77 0.00 38.00 4.75
2409 2433 7.825270 TGTGTTAATTTTCCCGCTTAGAAGATA 59.175 33.333 0.00 0.00 0.00 1.98
2420 2444 8.483758 TCCCGCTTAGAAGATAAAATCTAGTTT 58.516 33.333 0.00 0.00 39.08 2.66
2559 2584 8.362639 TCTGTAAAGAAGTGTAAGACCGTTTAT 58.637 33.333 0.00 0.00 0.00 1.40
2560 2585 9.630098 CTGTAAAGAAGTGTAAGACCGTTTATA 57.370 33.333 0.00 0.00 0.00 0.98
2567 2592 4.030977 GTGTAAGACCGTTTATAGCACACG 59.969 45.833 0.00 0.00 0.00 4.49
2598 2623 4.175787 AGTAGTGAGCTAAACGGTCTTG 57.824 45.455 0.00 0.00 40.75 3.02
2696 2729 7.259882 ACACAGGTTGCATTTATATCACAATG 58.740 34.615 0.00 0.00 34.09 2.82
2785 2818 4.970662 TTGCTTCTGATACATGGAAAGC 57.029 40.909 5.28 5.28 0.00 3.51
2793 2826 8.442632 TTCTGATACATGGAAAGCTATCTTTG 57.557 34.615 0.00 0.00 42.24 2.77
2841 2881 8.046708 AGTTAATTAGTCCATTAGTGCATCACA 58.953 33.333 0.00 0.00 36.74 3.58
3112 3152 8.736751 AAAAGGCTAAAAACGTTATACATGTG 57.263 30.769 9.11 0.00 0.00 3.21
3130 3170 2.022195 GTGAGGATGCGACTGTACCTA 58.978 52.381 0.00 0.00 0.00 3.08
3339 3380 6.892658 ATTTACTGGATTGTAAGTGTGCAA 57.107 33.333 0.00 0.00 34.43 4.08
3626 3670 6.710744 AGTATTTTACCCACAGTTCTGAGTTG 59.289 38.462 6.83 0.00 0.00 3.16
3854 3908 3.429543 GTCATTTTGTCGTGCATGCAAAT 59.570 39.130 24.58 14.48 33.00 2.32
3864 3918 1.605232 TGCATGCAAATGATCGGCTAG 59.395 47.619 20.30 0.00 0.00 3.42
3904 3958 2.270352 TGCGAAGGATGAAAACTGGT 57.730 45.000 0.00 0.00 0.00 4.00
3911 3965 6.073548 GCGAAGGATGAAAACTGGTATCATAG 60.074 42.308 0.00 0.00 34.10 2.23
3972 4029 4.925646 GTGATCAAATTCCCTTGCAAGTTC 59.074 41.667 24.35 4.27 0.00 3.01
4019 4078 7.760340 GGTAAGTAACACTTTGGATACTCTCAG 59.240 40.741 0.00 0.00 39.51 3.35
4106 4169 6.320926 TCTCATCAACACAGGAACAAAATGAA 59.679 34.615 0.00 0.00 0.00 2.57
4107 4170 6.506147 TCATCAACACAGGAACAAAATGAAG 58.494 36.000 0.00 0.00 0.00 3.02
4148 4212 0.684805 ACTTCCTGCTACTCCCTCCG 60.685 60.000 0.00 0.00 0.00 4.63
4165 4229 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
4200 4264 7.870445 CACTACTTTAGGGATCTAAATGCTCTC 59.130 40.741 0.00 0.00 42.52 3.20
4260 4324 8.348507 CAGGAATTCAGTAAATAATTCTGAGGC 58.651 37.037 7.93 0.00 40.41 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.887406 GAAAAATAAATTCACTAAGAACCACGA 57.113 29.630 0.00 0.00 39.49 4.35
5 6 9.672086 TGAAAAATAAATTCACTAAGAACCACG 57.328 29.630 0.00 0.00 39.49 4.94
49 50 9.398538 GACCGTTCCTCTAGAGATATGTTATAT 57.601 37.037 21.76 0.00 0.00 0.86
50 51 8.380867 TGACCGTTCCTCTAGAGATATGTTATA 58.619 37.037 21.76 0.00 0.00 0.98
51 52 7.232188 TGACCGTTCCTCTAGAGATATGTTAT 58.768 38.462 21.76 0.00 0.00 1.89
52 53 6.598503 TGACCGTTCCTCTAGAGATATGTTA 58.401 40.000 21.76 5.70 0.00 2.41
53 54 5.446860 TGACCGTTCCTCTAGAGATATGTT 58.553 41.667 21.76 2.43 0.00 2.71
54 55 5.050126 TGACCGTTCCTCTAGAGATATGT 57.950 43.478 21.76 10.86 0.00 2.29
55 56 6.392625 TTTGACCGTTCCTCTAGAGATATG 57.607 41.667 21.76 12.66 0.00 1.78
56 57 8.744652 CATATTTGACCGTTCCTCTAGAGATAT 58.255 37.037 21.76 8.97 0.00 1.63
57 58 7.724506 ACATATTTGACCGTTCCTCTAGAGATA 59.275 37.037 21.76 6.00 0.00 1.98
58 59 6.551601 ACATATTTGACCGTTCCTCTAGAGAT 59.448 38.462 21.76 5.03 0.00 2.75
59 60 5.892119 ACATATTTGACCGTTCCTCTAGAGA 59.108 40.000 21.76 4.61 0.00 3.10
60 61 6.039941 AGACATATTTGACCGTTCCTCTAGAG 59.960 42.308 13.18 13.18 0.00 2.43
61 62 5.892119 AGACATATTTGACCGTTCCTCTAGA 59.108 40.000 0.00 0.00 0.00 2.43
62 63 6.150396 AGACATATTTGACCGTTCCTCTAG 57.850 41.667 0.00 0.00 0.00 2.43
63 64 5.220989 CGAGACATATTTGACCGTTCCTCTA 60.221 44.000 0.00 0.00 0.00 2.43
64 65 4.440250 CGAGACATATTTGACCGTTCCTCT 60.440 45.833 0.00 0.00 0.00 3.69
65 66 3.797256 CGAGACATATTTGACCGTTCCTC 59.203 47.826 0.00 0.00 0.00 3.71
66 67 3.194968 ACGAGACATATTTGACCGTTCCT 59.805 43.478 0.00 0.00 0.00 3.36
67 68 3.518590 ACGAGACATATTTGACCGTTCC 58.481 45.455 0.00 0.00 0.00 3.62
68 69 5.347907 AGAAACGAGACATATTTGACCGTTC 59.652 40.000 0.00 0.00 35.38 3.95
69 70 5.120208 CAGAAACGAGACATATTTGACCGTT 59.880 40.000 0.00 0.00 36.68 4.44
70 71 4.625742 CAGAAACGAGACATATTTGACCGT 59.374 41.667 0.00 0.00 0.00 4.83
71 72 4.625742 ACAGAAACGAGACATATTTGACCG 59.374 41.667 0.00 0.00 0.00 4.79
72 73 6.481954 AACAGAAACGAGACATATTTGACC 57.518 37.500 0.00 0.00 0.00 4.02
73 74 8.240883 ACTAACAGAAACGAGACATATTTGAC 57.759 34.615 0.00 0.00 0.00 3.18
74 75 8.708742 CAACTAACAGAAACGAGACATATTTGA 58.291 33.333 0.00 0.00 0.00 2.69
75 76 8.708742 TCAACTAACAGAAACGAGACATATTTG 58.291 33.333 0.00 0.00 0.00 2.32
76 77 8.709646 GTCAACTAACAGAAACGAGACATATTT 58.290 33.333 0.00 0.00 0.00 1.40
77 78 7.870954 TGTCAACTAACAGAAACGAGACATATT 59.129 33.333 0.00 0.00 0.00 1.28
78 79 7.375834 TGTCAACTAACAGAAACGAGACATAT 58.624 34.615 0.00 0.00 0.00 1.78
79 80 6.741109 TGTCAACTAACAGAAACGAGACATA 58.259 36.000 0.00 0.00 0.00 2.29
80 81 5.597806 TGTCAACTAACAGAAACGAGACAT 58.402 37.500 0.00 0.00 0.00 3.06
81 82 5.001237 TGTCAACTAACAGAAACGAGACA 57.999 39.130 0.00 0.00 0.00 3.41
82 83 5.556570 GCTTGTCAACTAACAGAAACGAGAC 60.557 44.000 0.00 0.00 0.00 3.36
83 84 4.506654 GCTTGTCAACTAACAGAAACGAGA 59.493 41.667 0.00 0.00 0.00 4.04
84 85 4.508124 AGCTTGTCAACTAACAGAAACGAG 59.492 41.667 0.00 0.00 0.00 4.18
85 86 4.439057 AGCTTGTCAACTAACAGAAACGA 58.561 39.130 0.00 0.00 0.00 3.85
86 87 4.795970 AGCTTGTCAACTAACAGAAACG 57.204 40.909 0.00 0.00 0.00 3.60
87 88 5.880341 ACAAGCTTGTCAACTAACAGAAAC 58.120 37.500 26.36 0.00 36.50 2.78
106 107 1.605710 CCACCAGACAAAGCTGACAAG 59.394 52.381 0.00 0.00 38.14 3.16
107 108 1.064758 ACCACCAGACAAAGCTGACAA 60.065 47.619 0.00 0.00 38.14 3.18
108 109 0.546122 ACCACCAGACAAAGCTGACA 59.454 50.000 0.00 0.00 38.14 3.58
109 110 1.604278 GAACCACCAGACAAAGCTGAC 59.396 52.381 0.00 0.00 38.14 3.51
110 111 1.490490 AGAACCACCAGACAAAGCTGA 59.510 47.619 0.00 0.00 38.14 4.26
111 112 1.605710 CAGAACCACCAGACAAAGCTG 59.394 52.381 0.00 0.00 35.66 4.24
112 113 1.490490 TCAGAACCACCAGACAAAGCT 59.510 47.619 0.00 0.00 0.00 3.74
113 114 1.604278 GTCAGAACCACCAGACAAAGC 59.396 52.381 0.00 0.00 0.00 3.51
114 115 1.867233 CGTCAGAACCACCAGACAAAG 59.133 52.381 0.00 0.00 0.00 2.77
115 116 1.208535 ACGTCAGAACCACCAGACAAA 59.791 47.619 0.00 0.00 0.00 2.83
116 117 0.828022 ACGTCAGAACCACCAGACAA 59.172 50.000 0.00 0.00 0.00 3.18
117 118 0.828022 AACGTCAGAACCACCAGACA 59.172 50.000 0.00 0.00 0.00 3.41
118 119 2.609737 CCTAACGTCAGAACCACCAGAC 60.610 54.545 0.00 0.00 0.00 3.51
119 120 1.616865 CCTAACGTCAGAACCACCAGA 59.383 52.381 0.00 0.00 0.00 3.86
120 121 1.343465 ACCTAACGTCAGAACCACCAG 59.657 52.381 0.00 0.00 0.00 4.00
121 122 1.416243 ACCTAACGTCAGAACCACCA 58.584 50.000 0.00 0.00 0.00 4.17
122 123 2.140717 CAACCTAACGTCAGAACCACC 58.859 52.381 0.00 0.00 0.00 4.61
123 124 1.529865 GCAACCTAACGTCAGAACCAC 59.470 52.381 0.00 0.00 0.00 4.16
124 125 1.414919 AGCAACCTAACGTCAGAACCA 59.585 47.619 0.00 0.00 0.00 3.67
125 126 1.798813 CAGCAACCTAACGTCAGAACC 59.201 52.381 0.00 0.00 0.00 3.62
126 127 2.480845 ACAGCAACCTAACGTCAGAAC 58.519 47.619 0.00 0.00 0.00 3.01
127 128 2.902705 ACAGCAACCTAACGTCAGAA 57.097 45.000 0.00 0.00 0.00 3.02
128 129 2.624364 TGTACAGCAACCTAACGTCAGA 59.376 45.455 0.00 0.00 0.00 3.27
129 130 3.021269 TGTACAGCAACCTAACGTCAG 57.979 47.619 0.00 0.00 0.00 3.51
130 131 3.671008 ATGTACAGCAACCTAACGTCA 57.329 42.857 0.33 0.00 0.00 4.35
131 132 4.449743 TCAAATGTACAGCAACCTAACGTC 59.550 41.667 0.33 0.00 0.00 4.34
132 133 4.382291 TCAAATGTACAGCAACCTAACGT 58.618 39.130 0.33 0.00 0.00 3.99
133 134 5.323900 CATCAAATGTACAGCAACCTAACG 58.676 41.667 0.33 0.00 0.00 3.18
134 135 5.414454 TCCATCAAATGTACAGCAACCTAAC 59.586 40.000 0.33 0.00 0.00 2.34
135 136 5.565509 TCCATCAAATGTACAGCAACCTAA 58.434 37.500 0.33 0.00 0.00 2.69
136 137 5.172687 TCCATCAAATGTACAGCAACCTA 57.827 39.130 0.33 0.00 0.00 3.08
137 138 4.012374 CTCCATCAAATGTACAGCAACCT 58.988 43.478 0.33 0.00 0.00 3.50
138 139 3.129287 CCTCCATCAAATGTACAGCAACC 59.871 47.826 0.33 0.00 0.00 3.77
139 140 3.129287 CCCTCCATCAAATGTACAGCAAC 59.871 47.826 0.33 0.00 0.00 4.17
140 141 3.245229 ACCCTCCATCAAATGTACAGCAA 60.245 43.478 0.33 0.00 0.00 3.91
141 142 2.308570 ACCCTCCATCAAATGTACAGCA 59.691 45.455 0.33 0.00 0.00 4.41
142 143 3.004752 ACCCTCCATCAAATGTACAGC 57.995 47.619 0.33 0.00 0.00 4.40
143 144 3.623060 CGAACCCTCCATCAAATGTACAG 59.377 47.826 0.33 0.00 0.00 2.74
144 145 3.262151 TCGAACCCTCCATCAAATGTACA 59.738 43.478 0.00 0.00 0.00 2.90
145 146 3.869065 TCGAACCCTCCATCAAATGTAC 58.131 45.455 0.00 0.00 0.00 2.90
146 147 4.771114 ATCGAACCCTCCATCAAATGTA 57.229 40.909 0.00 0.00 0.00 2.29
147 148 3.652057 ATCGAACCCTCCATCAAATGT 57.348 42.857 0.00 0.00 0.00 2.71
148 149 3.316308 GGAATCGAACCCTCCATCAAATG 59.684 47.826 0.00 0.00 0.00 2.32
149 150 3.203040 AGGAATCGAACCCTCCATCAAAT 59.797 43.478 8.14 0.00 0.00 2.32
150 151 2.576191 AGGAATCGAACCCTCCATCAAA 59.424 45.455 8.14 0.00 0.00 2.69
151 152 2.196595 AGGAATCGAACCCTCCATCAA 58.803 47.619 8.14 0.00 0.00 2.57
152 153 1.879575 AGGAATCGAACCCTCCATCA 58.120 50.000 8.14 0.00 0.00 3.07
153 154 2.966516 ACTAGGAATCGAACCCTCCATC 59.033 50.000 11.64 0.00 34.11 3.51
154 155 3.047695 ACTAGGAATCGAACCCTCCAT 57.952 47.619 11.64 0.00 34.11 3.41
155 156 2.544844 ACTAGGAATCGAACCCTCCA 57.455 50.000 11.64 0.00 34.11 3.86
156 157 3.908643 AAACTAGGAATCGAACCCTCC 57.091 47.619 11.64 5.36 34.11 4.30
157 158 4.142665 GCAAAAACTAGGAATCGAACCCTC 60.143 45.833 11.64 0.00 34.11 4.30
158 159 3.756963 GCAAAAACTAGGAATCGAACCCT 59.243 43.478 12.71 12.71 36.60 4.34
159 160 3.425758 CGCAAAAACTAGGAATCGAACCC 60.426 47.826 8.14 3.67 0.00 4.11
160 161 3.187842 ACGCAAAAACTAGGAATCGAACC 59.812 43.478 0.00 0.00 0.00 3.62
161 162 4.400036 ACGCAAAAACTAGGAATCGAAC 57.600 40.909 0.00 0.00 0.00 3.95
162 163 8.971321 GTATATACGCAAAAACTAGGAATCGAA 58.029 33.333 0.00 0.00 0.00 3.71
163 164 7.596248 GGTATATACGCAAAAACTAGGAATCGA 59.404 37.037 6.79 0.00 0.00 3.59
164 165 7.383029 TGGTATATACGCAAAAACTAGGAATCG 59.617 37.037 6.79 0.00 0.00 3.34
165 166 8.597662 TGGTATATACGCAAAAACTAGGAATC 57.402 34.615 6.79 0.00 0.00 2.52
166 167 8.208903 ACTGGTATATACGCAAAAACTAGGAAT 58.791 33.333 6.79 0.00 0.00 3.01
167 168 7.558604 ACTGGTATATACGCAAAAACTAGGAA 58.441 34.615 6.79 0.00 0.00 3.36
168 169 7.116075 ACTGGTATATACGCAAAAACTAGGA 57.884 36.000 6.79 0.00 0.00 2.94
169 170 8.876275 TTACTGGTATATACGCAAAAACTAGG 57.124 34.615 6.79 0.00 0.00 3.02
170 171 8.485591 GCTTACTGGTATATACGCAAAAACTAG 58.514 37.037 6.79 0.00 0.00 2.57
171 172 7.980662 TGCTTACTGGTATATACGCAAAAACTA 59.019 33.333 6.79 0.00 0.00 2.24
172 173 6.819649 TGCTTACTGGTATATACGCAAAAACT 59.180 34.615 6.79 0.00 0.00 2.66
173 174 7.007313 TGCTTACTGGTATATACGCAAAAAC 57.993 36.000 6.79 0.00 0.00 2.43
174 175 7.795482 ATGCTTACTGGTATATACGCAAAAA 57.205 32.000 12.76 6.48 0.00 1.94
175 176 7.795482 AATGCTTACTGGTATATACGCAAAA 57.205 32.000 12.76 6.73 0.00 2.44
176 177 7.795482 AAATGCTTACTGGTATATACGCAAA 57.205 32.000 12.76 2.97 0.00 3.68
177 178 7.795482 AAAATGCTTACTGGTATATACGCAA 57.205 32.000 12.76 2.41 0.00 4.85
178 179 7.713507 AGAAAAATGCTTACTGGTATATACGCA 59.286 33.333 11.60 11.60 0.00 5.24
179 180 8.084590 AGAAAAATGCTTACTGGTATATACGC 57.915 34.615 6.79 4.32 0.00 4.42
183 184 9.561069 CCTGTAGAAAAATGCTTACTGGTATAT 57.439 33.333 0.00 0.00 0.00 0.86
184 185 8.545472 ACCTGTAGAAAAATGCTTACTGGTATA 58.455 33.333 9.41 0.00 37.77 1.47
185 186 7.402862 ACCTGTAGAAAAATGCTTACTGGTAT 58.597 34.615 9.41 0.00 37.77 2.73
186 187 6.775708 ACCTGTAGAAAAATGCTTACTGGTA 58.224 36.000 9.41 0.00 37.77 3.25
187 188 5.631119 ACCTGTAGAAAAATGCTTACTGGT 58.369 37.500 6.32 6.32 35.76 4.00
188 189 6.575162 AACCTGTAGAAAAATGCTTACTGG 57.425 37.500 5.28 5.28 34.23 4.00
189 190 8.871686 AAAAACCTGTAGAAAAATGCTTACTG 57.128 30.769 0.00 0.00 0.00 2.74
190 191 8.914011 AGAAAAACCTGTAGAAAAATGCTTACT 58.086 29.630 0.00 0.00 0.00 2.24
191 192 9.529325 AAGAAAAACCTGTAGAAAAATGCTTAC 57.471 29.630 0.00 0.00 0.00 2.34
192 193 9.744468 GAAGAAAAACCTGTAGAAAAATGCTTA 57.256 29.630 0.00 0.00 0.00 3.09
193 194 7.435192 CGAAGAAAAACCTGTAGAAAAATGCTT 59.565 33.333 0.00 0.00 0.00 3.91
194 195 6.918022 CGAAGAAAAACCTGTAGAAAAATGCT 59.082 34.615 0.00 0.00 0.00 3.79
195 196 6.345803 GCGAAGAAAAACCTGTAGAAAAATGC 60.346 38.462 0.00 0.00 0.00 3.56
196 197 6.695278 TGCGAAGAAAAACCTGTAGAAAAATG 59.305 34.615 0.00 0.00 0.00 2.32
197 198 6.801575 TGCGAAGAAAAACCTGTAGAAAAAT 58.198 32.000 0.00 0.00 0.00 1.82
198 199 6.197364 TGCGAAGAAAAACCTGTAGAAAAA 57.803 33.333 0.00 0.00 0.00 1.94
199 200 5.821516 TGCGAAGAAAAACCTGTAGAAAA 57.178 34.783 0.00 0.00 0.00 2.29
200 201 5.821516 TTGCGAAGAAAAACCTGTAGAAA 57.178 34.783 0.00 0.00 0.00 2.52
201 202 6.205784 CAATTGCGAAGAAAAACCTGTAGAA 58.794 36.000 0.00 0.00 0.00 2.10
202 203 5.278266 CCAATTGCGAAGAAAAACCTGTAGA 60.278 40.000 0.00 0.00 0.00 2.59
203 204 4.917415 CCAATTGCGAAGAAAAACCTGTAG 59.083 41.667 0.00 0.00 0.00 2.74
204 205 4.261825 CCCAATTGCGAAGAAAAACCTGTA 60.262 41.667 0.00 0.00 0.00 2.74
205 206 3.492482 CCCAATTGCGAAGAAAAACCTGT 60.492 43.478 0.00 0.00 0.00 4.00
206 207 3.059166 CCCAATTGCGAAGAAAAACCTG 58.941 45.455 0.00 0.00 0.00 4.00
207 208 2.547855 GCCCAATTGCGAAGAAAAACCT 60.548 45.455 0.00 0.00 0.00 3.50
208 209 1.798223 GCCCAATTGCGAAGAAAAACC 59.202 47.619 0.00 0.00 0.00 3.27
209 210 1.798223 GGCCCAATTGCGAAGAAAAAC 59.202 47.619 0.00 0.00 0.00 2.43
210 211 1.604185 CGGCCCAATTGCGAAGAAAAA 60.604 47.619 0.00 0.00 0.00 1.94
211 212 0.038709 CGGCCCAATTGCGAAGAAAA 60.039 50.000 0.00 0.00 0.00 2.29
212 213 1.583986 CGGCCCAATTGCGAAGAAA 59.416 52.632 0.00 0.00 0.00 2.52
213 214 2.339556 CCGGCCCAATTGCGAAGAA 61.340 57.895 0.00 0.00 0.00 2.52
214 215 2.749839 CCGGCCCAATTGCGAAGA 60.750 61.111 0.00 0.00 0.00 2.87
215 216 4.496927 GCCGGCCCAATTGCGAAG 62.497 66.667 18.11 0.00 0.00 3.79
231 232 4.554036 CAAGGGGAGCTAGCGGGC 62.554 72.222 9.55 2.80 0.00 6.13
232 233 4.554036 GCAAGGGGAGCTAGCGGG 62.554 72.222 9.55 0.00 0.00 6.13
233 234 4.899239 CGCAAGGGGAGCTAGCGG 62.899 72.222 9.55 0.00 44.20 5.52
235 236 2.107953 CTCGCAAGGGGAGCTAGC 59.892 66.667 6.62 6.62 35.94 3.42
255 256 4.880537 CCTAGTCGGCGCTGCAGG 62.881 72.222 17.12 13.74 0.00 4.85
256 257 3.764810 CTCCTAGTCGGCGCTGCAG 62.765 68.421 12.58 10.11 0.00 4.41
257 258 3.826754 CTCCTAGTCGGCGCTGCA 61.827 66.667 12.58 0.00 0.00 4.41
261 262 4.273257 GGAGCTCCTAGTCGGCGC 62.273 72.222 26.25 0.00 43.98 6.53
262 263 3.597728 GGGAGCTCCTAGTCGGCG 61.598 72.222 31.36 0.00 35.95 6.46
263 264 2.123640 AGGGAGCTCCTAGTCGGC 60.124 66.667 31.36 13.49 45.98 5.54
271 272 1.550976 CATAATACGGGAGGGAGCTCC 59.449 57.143 25.59 25.59 42.62 4.70
272 273 2.249139 ACATAATACGGGAGGGAGCTC 58.751 52.381 4.71 4.71 0.00 4.09
273 274 2.400467 ACATAATACGGGAGGGAGCT 57.600 50.000 0.00 0.00 0.00 4.09
274 275 4.820894 ATTACATAATACGGGAGGGAGC 57.179 45.455 0.00 0.00 0.00 4.70
276 277 9.947189 AGAATATATTACATAATACGGGAGGGA 57.053 33.333 0.00 0.00 31.57 4.20
277 278 9.982651 CAGAATATATTACATAATACGGGAGGG 57.017 37.037 0.00 0.00 31.57 4.30
278 279 9.982651 CCAGAATATATTACATAATACGGGAGG 57.017 37.037 0.00 0.00 31.57 4.30
321 322 4.386424 GGGCTGTCCTATGGGTCTATTTTT 60.386 45.833 0.00 0.00 0.00 1.94
322 323 3.138468 GGGCTGTCCTATGGGTCTATTTT 59.862 47.826 0.00 0.00 0.00 1.82
323 324 2.711547 GGGCTGTCCTATGGGTCTATTT 59.288 50.000 0.00 0.00 0.00 1.40
324 325 2.339769 GGGCTGTCCTATGGGTCTATT 58.660 52.381 0.00 0.00 0.00 1.73
336 337 1.095807 GTTAATCGCCTGGGCTGTCC 61.096 60.000 10.04 0.00 39.32 4.02
337 338 1.095807 GGTTAATCGCCTGGGCTGTC 61.096 60.000 10.04 0.00 39.32 3.51
374 375 7.094162 CGTGACAGGTGGAGATATGAATATAGT 60.094 40.741 0.00 0.00 0.00 2.12
409 411 0.320374 CCTTGAACCCTAGTCGCACA 59.680 55.000 0.00 0.00 0.00 4.57
469 472 2.671177 CGTGGCTTCGTCTTGCTGG 61.671 63.158 0.00 0.00 0.00 4.85
1061 1065 2.686106 TCCCTACCCCAACGCCTC 60.686 66.667 0.00 0.00 0.00 4.70
1068 1072 1.632164 CATCCCTCTCCCTACCCCA 59.368 63.158 0.00 0.00 0.00 4.96
1071 1075 2.210711 CCGCATCCCTCTCCCTACC 61.211 68.421 0.00 0.00 0.00 3.18
1290 1300 1.227380 CCATTTCTCCCTCTCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
1482 1492 3.266686 TTGGTCATGGGCCTCGTGG 62.267 63.158 4.53 0.00 33.31 4.94
1483 1493 1.746615 CTTGGTCATGGGCCTCGTG 60.747 63.158 4.53 4.80 0.00 4.35
1484 1494 1.779061 AACTTGGTCATGGGCCTCGT 61.779 55.000 4.53 0.00 0.00 4.18
1485 1495 0.609131 AAACTTGGTCATGGGCCTCG 60.609 55.000 4.53 0.00 0.00 4.63
1486 1496 0.890683 CAAACTTGGTCATGGGCCTC 59.109 55.000 4.53 0.00 0.00 4.70
1487 1497 1.187567 GCAAACTTGGTCATGGGCCT 61.188 55.000 4.53 0.00 0.00 5.19
1488 1498 1.293179 GCAAACTTGGTCATGGGCC 59.707 57.895 0.00 0.00 0.00 5.80
1489 1499 1.187567 AGGCAAACTTGGTCATGGGC 61.188 55.000 0.00 0.00 0.00 5.36
1490 1500 0.604578 CAGGCAAACTTGGTCATGGG 59.395 55.000 0.00 0.00 0.00 4.00
1517 1527 2.153247 CGCTGCCGAGTAATAAATCGAC 59.847 50.000 0.00 0.00 41.40 4.20
1518 1528 2.390938 CGCTGCCGAGTAATAAATCGA 58.609 47.619 0.00 0.00 41.40 3.59
1536 1546 2.132762 TCTTTCTGTTTCTTCGACCGC 58.867 47.619 0.00 0.00 0.00 5.68
1541 1551 7.413475 TTCTGATTCTCTTTCTGTTTCTTCG 57.587 36.000 0.00 0.00 0.00 3.79
1551 1561 2.284190 CCCGGCTTCTGATTCTCTTTC 58.716 52.381 0.00 0.00 0.00 2.62
1552 1562 1.065126 CCCCGGCTTCTGATTCTCTTT 60.065 52.381 0.00 0.00 0.00 2.52
1554 1564 1.341156 CCCCCGGCTTCTGATTCTCT 61.341 60.000 0.00 0.00 0.00 3.10
1555 1565 1.147153 CCCCCGGCTTCTGATTCTC 59.853 63.158 0.00 0.00 0.00 2.87
1558 1568 0.988145 TGATCCCCCGGCTTCTGATT 60.988 55.000 0.00 0.00 0.00 2.57
1559 1569 0.769776 ATGATCCCCCGGCTTCTGAT 60.770 55.000 0.00 0.00 0.00 2.90
1560 1570 1.384502 ATGATCCCCCGGCTTCTGA 60.385 57.895 0.00 0.00 0.00 3.27
1561 1571 1.228063 CATGATCCCCCGGCTTCTG 60.228 63.158 0.00 0.00 0.00 3.02
1562 1572 1.694169 ACATGATCCCCCGGCTTCT 60.694 57.895 0.00 0.00 0.00 2.85
1563 1573 1.227973 GACATGATCCCCCGGCTTC 60.228 63.158 0.00 0.00 0.00 3.86
1564 1574 2.919043 GACATGATCCCCCGGCTT 59.081 61.111 0.00 0.00 0.00 4.35
1565 1575 3.550431 CGACATGATCCCCCGGCT 61.550 66.667 0.00 0.00 0.00 5.52
1566 1576 4.626081 CCGACATGATCCCCCGGC 62.626 72.222 0.00 0.00 33.47 6.13
1567 1577 1.768684 AATCCGACATGATCCCCCGG 61.769 60.000 0.00 0.00 41.36 5.73
1568 1578 0.603707 CAATCCGACATGATCCCCCG 60.604 60.000 0.00 0.00 0.00 5.73
1582 1592 2.218603 ACACTTGTTCGTGTCCAATCC 58.781 47.619 0.00 0.00 44.32 3.01
1613 1635 7.148069 CCTGTTATTTAGATCAACAAAGGGACC 60.148 40.741 0.00 0.00 32.16 4.46
1630 1652 4.331159 ACACATAAGGGCCCTGTTATTT 57.669 40.909 29.50 11.55 0.00 1.40
1633 1655 4.303794 AGATACACATAAGGGCCCTGTTA 58.696 43.478 29.50 16.43 0.00 2.41
1638 1661 3.214328 CACAAGATACACATAAGGGCCC 58.786 50.000 16.46 16.46 0.00 5.80
1659 1682 7.387397 ACGTAGCACTATTATACAGGTCTCTAC 59.613 40.741 0.00 0.00 0.00 2.59
1661 1684 6.297582 ACGTAGCACTATTATACAGGTCTCT 58.702 40.000 0.00 0.00 0.00 3.10
1677 1701 4.735662 TTAATTGTTGTGGACGTAGCAC 57.264 40.909 0.00 0.00 0.00 4.40
1683 1707 3.848272 AGGCATTAATTGTTGTGGACG 57.152 42.857 0.00 0.00 0.00 4.79
1729 1753 1.002033 GCCGAATGCATTCACAGGATC 60.002 52.381 32.72 14.33 40.77 3.36
1735 1759 7.698836 AAATTATAAAGCCGAATGCATTCAC 57.301 32.000 32.72 24.99 44.83 3.18
1743 1767 9.719355 AAAAGGAACAAAATTATAAAGCCGAAT 57.281 25.926 0.00 0.00 0.00 3.34
1932 1956 5.502058 CGCATCAGAATACTGCTTCTTGAAG 60.502 44.000 6.04 6.04 43.17 3.02
1980 2004 2.159558 GGCGCTGCTAAGAAAGTAAACC 60.160 50.000 7.64 0.00 0.00 3.27
2076 2100 3.810310 TCGACCAAACCTTTTGCAAAT 57.190 38.095 13.65 0.00 0.00 2.32
2196 2220 2.685897 ACTCAGGAAGACTACAGATCGC 59.314 50.000 0.00 0.00 0.00 4.58
2203 2227 9.092876 CATAAATTCAGAACTCAGGAAGACTAC 57.907 37.037 0.00 0.00 0.00 2.73
2286 2310 7.307455 GGAGAGTTATTACATGGAAGATTTCGC 60.307 40.741 0.00 0.00 0.00 4.70
2326 2350 6.454186 GCACAATAGGATTTTGCGAACAATTC 60.454 38.462 0.00 0.00 35.21 2.17
2527 2552 6.015265 GTCTTACACTTCTTTACAGAGGGAGT 60.015 42.308 0.00 0.00 30.09 3.85
2559 2584 5.835257 ACTACTTTAGTGTTTCGTGTGCTA 58.165 37.500 0.00 0.00 37.69 3.49
2560 2585 4.690122 ACTACTTTAGTGTTTCGTGTGCT 58.310 39.130 0.00 0.00 37.69 4.40
2598 2623 5.735766 AGTACTCCCTCTGTAAAGAAATGC 58.264 41.667 0.00 0.00 0.00 3.56
2712 2745 2.028130 AGAACAAATGACCACCGCAAA 58.972 42.857 0.00 0.00 0.00 3.68
2716 2749 3.659786 TGAGTAGAACAAATGACCACCG 58.340 45.455 0.00 0.00 0.00 4.94
2793 2826 7.813645 AACTTGGAAAGGTTCGATTATAACAC 58.186 34.615 0.00 0.00 45.56 3.32
2803 2836 6.428771 TGGACTAATTAACTTGGAAAGGTTCG 59.571 38.462 0.00 0.00 45.56 3.95
3001 3041 2.865119 TATATCCAGCCAGGCATGTG 57.135 50.000 15.80 2.75 37.29 3.21
3112 3152 2.229302 GGATAGGTACAGTCGCATCCTC 59.771 54.545 0.00 0.00 31.23 3.71
3130 3170 8.592809 TGAAATTAACTAATTTGTTGGCTGGAT 58.407 29.630 14.41 0.00 43.67 3.41
3365 3406 9.186837 AGAAAATACGGTCTGTAGATAAGAAGA 57.813 33.333 0.00 0.00 36.25 2.87
3366 3407 9.239002 CAGAAAATACGGTCTGTAGATAAGAAG 57.761 37.037 0.00 0.00 37.16 2.85
3382 3426 5.408604 AGAGCTACCAACAACAGAAAATACG 59.591 40.000 0.00 0.00 0.00 3.06
3436 3480 4.000331 TCCACAAGAGAGCTTTCAAGAG 58.000 45.455 7.06 0.00 30.14 2.85
3626 3670 2.093310 CACACTCGTCATGATCAGCAAC 59.907 50.000 0.00 0.00 0.00 4.17
3820 3874 6.638063 CACGACAAAATGACATTTTCTCACAT 59.362 34.615 20.73 7.16 40.27 3.21
3854 3908 3.234353 ACAATGGATCTCTAGCCGATCA 58.766 45.455 17.90 8.93 39.17 2.92
3864 3918 7.639039 TCGCAACATTATTTACAATGGATCTC 58.361 34.615 0.00 0.00 39.71 2.75
3972 4029 9.712305 CTTACCCCTGAATATAGTGTAAATGAG 57.288 37.037 0.00 0.00 0.00 2.90
4165 4229 7.942990 AGATCCCTAAAGTAGTGATCTAAACG 58.057 38.462 8.07 0.00 44.60 3.60
4179 4243 9.956640 AATATGAGAGCATTTAGATCCCTAAAG 57.043 33.333 0.00 0.00 45.07 1.85
4200 4264 9.319143 CTTGTACTCCCTCTGTAAAGAAATATG 57.681 37.037 0.00 0.00 0.00 1.78
4260 4324 4.035091 TGAAACACTTCTTCATGTTCCACG 59.965 41.667 0.00 0.00 38.08 4.94


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

AutoCloner maintained by Alex Coulton.