Multiple sequence alignment - TraesCS3A01G377400

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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 TraesCS3A01G377400 chr3A 100.000 2629 0 0 1 2629 627268414 627271042 0.000000e+00 4855.0
1 TraesCS3A01G377400 chr3B 89.497 1828 136 31 759 2576 647169436 647171217 0.000000e+00 2261.0
2 TraesCS3A01G377400 chr3B 89.386 782 65 9 290 1060 647133793 647134567 0.000000e+00 968.0
3 TraesCS3A01G377400 chr3B 88.146 329 30 7 2217 2545 290615134 290615453 1.480000e-102 383.0
4 TraesCS3A01G377400 chr3D 88.185 1879 137 40 761 2629 484339518 484341321 0.000000e+00 2161.0
5 TraesCS3A01G377400 chr3D 87.500 184 17 4 28 209 87414594 87414415 9.540000e-50 207.0
6 TraesCS3A01G377400 chr1A 95.652 414 17 1 1058 1470 468599195 468598782 0.000000e+00 664.0
7 TraesCS3A01G377400 chr1B 95.844 409 17 0 1058 1466 434409086 434409494 0.000000e+00 662.0
8 TraesCS3A01G377400 chr1B 87.850 107 12 1 185 290 159190977 159191083 9.880000e-25 124.0
9 TraesCS3A01G377400 chr1D 95.169 414 19 1 1058 1470 369925926 369925513 0.000000e+00 652.0
10 TraesCS3A01G377400 chr1D 95.355 409 19 0 1058 1466 321704948 321704540 0.000000e+00 651.0
11 TraesCS3A01G377400 chr1D 90.000 140 12 1 150 289 332600561 332600424 2.080000e-41 180.0
12 TraesCS3A01G377400 chr4D 95.355 409 19 0 1058 1466 444177291 444177699 0.000000e+00 651.0
13 TraesCS3A01G377400 chr4A 95.355 409 19 0 1058 1466 23611217 23610809 0.000000e+00 651.0
14 TraesCS3A01G377400 chr6D 94.915 413 20 1 1058 1470 47812384 47812795 0.000000e+00 645.0
15 TraesCS3A01G377400 chr6D 88.971 272 25 3 2274 2545 294698274 294698008 5.420000e-87 331.0
16 TraesCS3A01G377400 chr5D 90.274 329 23 6 2217 2545 79988055 79988374 3.130000e-114 422.0
17 TraesCS3A01G377400 chr6A 88.822 331 28 6 2216 2545 251475484 251475162 5.270000e-107 398.0
18 TraesCS3A01G377400 chr6A 87.842 329 31 7 2217 2545 252021073 252021392 6.870000e-101 377.0
19 TraesCS3A01G377400 chr7D 90.034 291 21 6 4 291 310862285 310862000 1.150000e-98 370.0
20 TraesCS3A01G377400 chr7D 97.143 35 1 0 101 135 107675288 107675322 2.830000e-05 60.2
21 TraesCS3A01G377400 chr5A 90.278 288 20 5 4 290 656235988 656235708 1.150000e-98 370.0
22 TraesCS3A01G377400 chr5B 89.003 291 25 5 4 292 435172063 435171778 1.160000e-93 353.0
23 TraesCS3A01G377400 chr6B 88.542 288 25 6 5 290 79872672 79872953 2.510000e-90 342.0
24 TraesCS3A01G377400 chr6B 90.000 140 14 0 151 290 91035745 91035884 5.780000e-42 182.0
25 TraesCS3A01G377400 chr7B 88.364 275 27 3 2271 2545 601441486 601441755 2.520000e-85 326.0
26 TraesCS3A01G377400 chr7A 87.037 162 20 1 2356 2517 397428945 397428785 5.780000e-42 182.0
27 TraesCS3A01G377400 chr7A 91.509 106 8 1 185 290 9826380 9826276 7.580000e-31 145.0


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 TraesCS3A01G377400 chr3A 627268414 627271042 2628 False 4855 4855 100.000 1 2629 1 chr3A.!!$F1 2628
1 TraesCS3A01G377400 chr3B 647169436 647171217 1781 False 2261 2261 89.497 759 2576 1 chr3B.!!$F3 1817
2 TraesCS3A01G377400 chr3B 647133793 647134567 774 False 968 968 89.386 290 1060 1 chr3B.!!$F2 770
3 TraesCS3A01G377400 chr3D 484339518 484341321 1803 False 2161 2161 88.185 761 2629 1 chr3D.!!$F1 1868

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
224 225 0.031111 AACCGGAGATGGGAGGATGA 60.031 55.0 9.46 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1918 0.304705 AAAATCATGACGCGGCGATC 59.695 50.0 30.94 21.41 0.0 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.803426 GCACGCCGAGAGTGAGGG 62.803 72.222 10.89 0.00 41.83 4.30
18 19 3.062466 CACGCCGAGAGTGAGGGA 61.062 66.667 0.00 0.00 41.83 4.20
19 20 2.752238 ACGCCGAGAGTGAGGGAG 60.752 66.667 0.00 0.00 0.00 4.30
20 21 2.438614 CGCCGAGAGTGAGGGAGA 60.439 66.667 0.00 0.00 0.00 3.71
21 22 2.046864 CGCCGAGAGTGAGGGAGAA 61.047 63.158 0.00 0.00 0.00 2.87
22 23 1.813192 GCCGAGAGTGAGGGAGAAG 59.187 63.158 0.00 0.00 0.00 2.85
23 24 1.671901 GCCGAGAGTGAGGGAGAAGG 61.672 65.000 0.00 0.00 0.00 3.46
24 25 0.323908 CCGAGAGTGAGGGAGAAGGT 60.324 60.000 0.00 0.00 0.00 3.50
25 26 0.814457 CGAGAGTGAGGGAGAAGGTG 59.186 60.000 0.00 0.00 0.00 4.00
26 27 1.190643 GAGAGTGAGGGAGAAGGTGG 58.809 60.000 0.00 0.00 0.00 4.61
27 28 0.252467 AGAGTGAGGGAGAAGGTGGG 60.252 60.000 0.00 0.00 0.00 4.61
28 29 1.229658 AGTGAGGGAGAAGGTGGGG 60.230 63.158 0.00 0.00 0.00 4.96
29 30 2.124996 TGAGGGAGAAGGTGGGGG 59.875 66.667 0.00 0.00 0.00 5.40
30 31 3.412408 GAGGGAGAAGGTGGGGGC 61.412 72.222 0.00 0.00 0.00 5.80
57 58 2.780693 CAGGGTCTGGGGAGGAGA 59.219 66.667 0.00 0.00 0.00 3.71
58 59 1.316266 CAGGGTCTGGGGAGGAGAT 59.684 63.158 0.00 0.00 0.00 2.75
59 60 1.053264 CAGGGTCTGGGGAGGAGATG 61.053 65.000 0.00 0.00 0.00 2.90
60 61 1.768077 GGGTCTGGGGAGGAGATGG 60.768 68.421 0.00 0.00 0.00 3.51
61 62 1.768077 GGTCTGGGGAGGAGATGGG 60.768 68.421 0.00 0.00 0.00 4.00
62 63 1.768077 GTCTGGGGAGGAGATGGGG 60.768 68.421 0.00 0.00 0.00 4.96
63 64 3.174265 CTGGGGAGGAGATGGGGC 61.174 72.222 0.00 0.00 0.00 5.80
117 118 4.623932 TTTGAGGGATATGGAGGAATCG 57.376 45.455 0.00 0.00 0.00 3.34
118 119 1.902508 TGAGGGATATGGAGGAATCGC 59.097 52.381 0.00 0.00 35.81 4.58
119 120 2.183679 GAGGGATATGGAGGAATCGCT 58.816 52.381 2.01 2.01 45.07 4.93
120 121 3.245622 TGAGGGATATGGAGGAATCGCTA 60.246 47.826 2.37 0.00 43.19 4.26
121 122 3.370104 AGGGATATGGAGGAATCGCTAG 58.630 50.000 0.61 0.00 41.87 3.42
122 123 2.432510 GGGATATGGAGGAATCGCTAGG 59.567 54.545 0.00 0.00 33.55 3.02
123 124 3.100671 GGATATGGAGGAATCGCTAGGT 58.899 50.000 0.00 0.00 0.00 3.08
124 125 3.131400 GGATATGGAGGAATCGCTAGGTC 59.869 52.174 0.00 0.00 0.00 3.85
125 126 2.088104 ATGGAGGAATCGCTAGGTCA 57.912 50.000 0.00 0.00 0.00 4.02
126 127 1.403814 TGGAGGAATCGCTAGGTCAG 58.596 55.000 0.00 0.00 0.00 3.51
127 128 0.676736 GGAGGAATCGCTAGGTCAGG 59.323 60.000 0.00 0.00 0.00 3.86
128 129 1.693627 GAGGAATCGCTAGGTCAGGA 58.306 55.000 0.00 0.00 0.00 3.86
129 130 1.611491 GAGGAATCGCTAGGTCAGGAG 59.389 57.143 0.00 0.00 0.00 3.69
130 131 0.676736 GGAATCGCTAGGTCAGGAGG 59.323 60.000 0.00 0.00 0.00 4.30
131 132 1.693627 GAATCGCTAGGTCAGGAGGA 58.306 55.000 0.00 0.00 0.00 3.71
132 133 2.032620 GAATCGCTAGGTCAGGAGGAA 58.967 52.381 0.00 0.00 0.00 3.36
133 134 1.404843 ATCGCTAGGTCAGGAGGAAC 58.595 55.000 0.00 0.00 0.00 3.62
134 135 1.030488 TCGCTAGGTCAGGAGGAACG 61.030 60.000 0.00 0.00 38.65 3.95
135 136 1.313812 CGCTAGGTCAGGAGGAACGT 61.314 60.000 0.00 0.00 38.65 3.99
136 137 0.456628 GCTAGGTCAGGAGGAACGTC 59.543 60.000 0.00 0.00 38.65 4.34
137 138 0.733729 CTAGGTCAGGAGGAACGTCG 59.266 60.000 0.00 0.00 38.65 5.12
138 139 0.679002 TAGGTCAGGAGGAACGTCGG 60.679 60.000 0.00 0.00 38.65 4.79
139 140 2.572284 GTCAGGAGGAACGTCGGG 59.428 66.667 0.00 0.00 0.00 5.14
140 141 2.678934 TCAGGAGGAACGTCGGGG 60.679 66.667 0.00 0.00 0.00 5.73
141 142 2.678934 CAGGAGGAACGTCGGGGA 60.679 66.667 0.00 0.00 0.00 4.81
142 143 2.118951 AGGAGGAACGTCGGGGAA 59.881 61.111 0.00 0.00 0.00 3.97
143 144 1.305887 AGGAGGAACGTCGGGGAAT 60.306 57.895 0.00 0.00 0.00 3.01
144 145 1.143401 GGAGGAACGTCGGGGAATC 59.857 63.158 0.00 0.00 0.00 2.52
145 146 1.226888 GAGGAACGTCGGGGAATCG 60.227 63.158 0.00 0.00 0.00 3.34
146 147 2.889018 GGAACGTCGGGGAATCGC 60.889 66.667 0.00 0.00 0.00 4.58
147 148 2.183555 GAACGTCGGGGAATCGCT 59.816 61.111 0.00 0.00 0.00 4.93
148 149 1.434696 GAACGTCGGGGAATCGCTA 59.565 57.895 0.00 0.00 0.00 4.26
149 150 0.594284 GAACGTCGGGGAATCGCTAG 60.594 60.000 0.00 0.00 0.00 3.42
150 151 2.012902 AACGTCGGGGAATCGCTAGG 62.013 60.000 0.00 0.00 0.00 3.02
151 152 2.487532 CGTCGGGGAATCGCTAGGT 61.488 63.158 0.00 0.00 0.00 3.08
152 153 1.821258 GTCGGGGAATCGCTAGGTT 59.179 57.895 0.00 0.00 0.00 3.50
153 154 0.177373 GTCGGGGAATCGCTAGGTTT 59.823 55.000 0.00 0.00 0.00 3.27
154 155 0.906775 TCGGGGAATCGCTAGGTTTT 59.093 50.000 0.00 0.00 0.00 2.43
155 156 1.279846 TCGGGGAATCGCTAGGTTTTT 59.720 47.619 0.00 0.00 0.00 1.94
171 172 3.752704 TTTTTCGCGGGAGGGTTG 58.247 55.556 6.13 0.00 44.11 3.77
172 173 2.557372 TTTTTCGCGGGAGGGTTGC 61.557 57.895 6.13 0.00 44.11 4.17
173 174 3.776347 TTTTCGCGGGAGGGTTGCA 62.776 57.895 6.13 0.00 44.11 4.08
174 175 3.776347 TTTCGCGGGAGGGTTGCAA 62.776 57.895 6.13 0.00 44.11 4.08
175 176 4.697756 TCGCGGGAGGGTTGCAAG 62.698 66.667 6.13 0.00 44.11 4.01
177 178 2.597510 GCGGGAGGGTTGCAAGTT 60.598 61.111 0.00 0.00 0.00 2.66
178 179 1.302993 GCGGGAGGGTTGCAAGTTA 60.303 57.895 0.00 0.00 0.00 2.24
179 180 0.891904 GCGGGAGGGTTGCAAGTTAA 60.892 55.000 0.00 0.00 0.00 2.01
180 181 0.879090 CGGGAGGGTTGCAAGTTAAC 59.121 55.000 0.00 0.00 0.00 2.01
181 182 0.879090 GGGAGGGTTGCAAGTTAACG 59.121 55.000 0.00 0.00 0.00 3.18
182 183 0.879090 GGAGGGTTGCAAGTTAACGG 59.121 55.000 0.00 0.00 0.00 4.44
183 184 1.543871 GGAGGGTTGCAAGTTAACGGA 60.544 52.381 0.00 0.00 0.00 4.69
184 185 1.804748 GAGGGTTGCAAGTTAACGGAG 59.195 52.381 0.00 0.00 0.00 4.63
185 186 0.879090 GGGTTGCAAGTTAACGGAGG 59.121 55.000 0.00 0.00 0.00 4.30
186 187 1.601166 GGTTGCAAGTTAACGGAGGT 58.399 50.000 0.00 0.00 0.00 3.85
187 188 1.265905 GGTTGCAAGTTAACGGAGGTG 59.734 52.381 0.00 0.00 0.00 4.00
188 189 1.265905 GTTGCAAGTTAACGGAGGTGG 59.734 52.381 0.00 0.00 0.00 4.61
189 190 0.250553 TGCAAGTTAACGGAGGTGGG 60.251 55.000 0.00 0.00 0.00 4.61
190 191 0.035739 GCAAGTTAACGGAGGTGGGA 59.964 55.000 0.00 0.00 0.00 4.37
191 192 1.944430 GCAAGTTAACGGAGGTGGGAG 60.944 57.143 0.00 0.00 0.00 4.30
192 193 0.981943 AAGTTAACGGAGGTGGGAGG 59.018 55.000 0.00 0.00 0.00 4.30
193 194 0.115745 AGTTAACGGAGGTGGGAGGA 59.884 55.000 0.00 0.00 0.00 3.71
194 195 1.201424 GTTAACGGAGGTGGGAGGAT 58.799 55.000 0.00 0.00 0.00 3.24
195 196 1.134491 GTTAACGGAGGTGGGAGGATG 60.134 57.143 0.00 0.00 0.00 3.51
196 197 0.337082 TAACGGAGGTGGGAGGATGA 59.663 55.000 0.00 0.00 0.00 2.92
197 198 1.265454 AACGGAGGTGGGAGGATGAC 61.265 60.000 0.00 0.00 0.00 3.06
198 199 2.786495 CGGAGGTGGGAGGATGACG 61.786 68.421 0.00 0.00 0.00 4.35
199 200 1.381327 GGAGGTGGGAGGATGACGA 60.381 63.158 0.00 0.00 0.00 4.20
200 201 0.976073 GGAGGTGGGAGGATGACGAA 60.976 60.000 0.00 0.00 0.00 3.85
201 202 0.902531 GAGGTGGGAGGATGACGAAA 59.097 55.000 0.00 0.00 0.00 3.46
202 203 1.278127 GAGGTGGGAGGATGACGAAAA 59.722 52.381 0.00 0.00 0.00 2.29
203 204 1.702957 AGGTGGGAGGATGACGAAAAA 59.297 47.619 0.00 0.00 0.00 1.94
220 221 3.978876 AAAAACCGGAGATGGGAGG 57.021 52.632 9.46 0.00 0.00 4.30
221 222 1.368374 AAAAACCGGAGATGGGAGGA 58.632 50.000 9.46 0.00 0.00 3.71
222 223 1.596496 AAAACCGGAGATGGGAGGAT 58.404 50.000 9.46 0.00 0.00 3.24
223 224 0.839946 AAACCGGAGATGGGAGGATG 59.160 55.000 9.46 0.00 0.00 3.51
224 225 0.031111 AACCGGAGATGGGAGGATGA 60.031 55.000 9.46 0.00 0.00 2.92
225 226 0.760945 ACCGGAGATGGGAGGATGAC 60.761 60.000 9.46 0.00 0.00 3.06
226 227 1.662608 CGGAGATGGGAGGATGACG 59.337 63.158 0.00 0.00 0.00 4.35
227 228 0.823769 CGGAGATGGGAGGATGACGA 60.824 60.000 0.00 0.00 0.00 4.20
228 229 1.414158 GGAGATGGGAGGATGACGAA 58.586 55.000 0.00 0.00 0.00 3.85
229 230 1.762957 GGAGATGGGAGGATGACGAAA 59.237 52.381 0.00 0.00 0.00 3.46
230 231 2.170607 GGAGATGGGAGGATGACGAAAA 59.829 50.000 0.00 0.00 0.00 2.29
231 232 3.370527 GGAGATGGGAGGATGACGAAAAA 60.371 47.826 0.00 0.00 0.00 1.94
250 251 5.743026 AAAAACCCAGCAAAATTAAACCG 57.257 34.783 0.00 0.00 0.00 4.44
251 252 2.448926 ACCCAGCAAAATTAAACCGC 57.551 45.000 0.00 0.00 0.00 5.68
252 253 1.689273 ACCCAGCAAAATTAAACCGCA 59.311 42.857 0.00 0.00 0.00 5.69
253 254 2.065512 CCCAGCAAAATTAAACCGCAC 58.934 47.619 0.00 0.00 0.00 5.34
254 255 2.546795 CCCAGCAAAATTAAACCGCACA 60.547 45.455 0.00 0.00 0.00 4.57
255 256 2.730928 CCAGCAAAATTAAACCGCACAG 59.269 45.455 0.00 0.00 0.00 3.66
256 257 3.551863 CCAGCAAAATTAAACCGCACAGA 60.552 43.478 0.00 0.00 0.00 3.41
257 258 3.425193 CAGCAAAATTAAACCGCACAGAC 59.575 43.478 0.00 0.00 0.00 3.51
258 259 3.317993 AGCAAAATTAAACCGCACAGACT 59.682 39.130 0.00 0.00 0.00 3.24
259 260 4.517453 AGCAAAATTAAACCGCACAGACTA 59.483 37.500 0.00 0.00 0.00 2.59
260 261 5.183140 AGCAAAATTAAACCGCACAGACTAT 59.817 36.000 0.00 0.00 0.00 2.12
261 262 5.861787 GCAAAATTAAACCGCACAGACTATT 59.138 36.000 0.00 0.00 0.00 1.73
262 263 6.033513 GCAAAATTAAACCGCACAGACTATTC 59.966 38.462 0.00 0.00 0.00 1.75
263 264 6.811253 AAATTAAACCGCACAGACTATTCA 57.189 33.333 0.00 0.00 0.00 2.57
264 265 7.391148 AAATTAAACCGCACAGACTATTCAT 57.609 32.000 0.00 0.00 0.00 2.57
265 266 6.604735 ATTAAACCGCACAGACTATTCATC 57.395 37.500 0.00 0.00 0.00 2.92
266 267 3.610040 AACCGCACAGACTATTCATCA 57.390 42.857 0.00 0.00 0.00 3.07
267 268 3.610040 ACCGCACAGACTATTCATCAA 57.390 42.857 0.00 0.00 0.00 2.57
268 269 3.525537 ACCGCACAGACTATTCATCAAG 58.474 45.455 0.00 0.00 0.00 3.02
269 270 3.055819 ACCGCACAGACTATTCATCAAGT 60.056 43.478 0.00 0.00 0.00 3.16
270 271 3.553511 CCGCACAGACTATTCATCAAGTC 59.446 47.826 0.00 0.00 42.02 3.01
271 272 3.241553 CGCACAGACTATTCATCAAGTCG 59.758 47.826 0.00 0.00 45.47 4.18
272 273 4.177026 GCACAGACTATTCATCAAGTCGT 58.823 43.478 0.00 0.00 45.47 4.34
273 274 4.266502 GCACAGACTATTCATCAAGTCGTC 59.733 45.833 0.00 0.00 45.47 4.20
274 275 4.800993 CACAGACTATTCATCAAGTCGTCC 59.199 45.833 0.00 0.00 45.47 4.79
275 276 4.462834 ACAGACTATTCATCAAGTCGTCCA 59.537 41.667 0.00 0.00 45.47 4.02
276 277 5.127845 ACAGACTATTCATCAAGTCGTCCAT 59.872 40.000 0.00 0.00 45.47 3.41
277 278 6.045318 CAGACTATTCATCAAGTCGTCCATT 58.955 40.000 0.00 0.00 45.47 3.16
278 279 7.147897 ACAGACTATTCATCAAGTCGTCCATTA 60.148 37.037 0.00 0.00 45.47 1.90
279 280 7.706607 CAGACTATTCATCAAGTCGTCCATTAA 59.293 37.037 0.00 0.00 45.47 1.40
280 281 7.923344 AGACTATTCATCAAGTCGTCCATTAAG 59.077 37.037 0.00 0.00 45.47 1.85
281 282 7.782049 ACTATTCATCAAGTCGTCCATTAAGA 58.218 34.615 0.00 0.00 0.00 2.10
282 283 8.258007 ACTATTCATCAAGTCGTCCATTAAGAA 58.742 33.333 0.00 0.00 0.00 2.52
283 284 9.265901 CTATTCATCAAGTCGTCCATTAAGAAT 57.734 33.333 0.00 0.00 0.00 2.40
285 286 8.648557 TTCATCAAGTCGTCCATTAAGAATAG 57.351 34.615 0.00 0.00 0.00 1.73
286 287 8.007405 TCATCAAGTCGTCCATTAAGAATAGA 57.993 34.615 0.00 0.00 0.00 1.98
287 288 8.138074 TCATCAAGTCGTCCATTAAGAATAGAG 58.862 37.037 0.00 0.00 0.00 2.43
288 289 7.640597 TCAAGTCGTCCATTAAGAATAGAGA 57.359 36.000 0.00 0.00 0.00 3.10
347 348 3.628487 CACCAAACTACCGTGGAAAAGAA 59.372 43.478 0.00 0.00 38.36 2.52
361 362 6.563381 CGTGGAAAAGAACTGTACATGTACAC 60.563 42.308 30.31 21.73 40.77 2.90
363 364 6.259167 TGGAAAAGAACTGTACATGTACACAC 59.741 38.462 30.31 22.76 40.77 3.82
365 366 7.201661 GGAAAAGAACTGTACATGTACACACAA 60.202 37.037 30.31 12.75 40.77 3.33
373 374 4.829064 ACATGTACACACAAATGTCCAC 57.171 40.909 0.00 0.00 38.42 4.02
450 455 3.617284 TGTGCAGATCAAATGAGCTCAT 58.383 40.909 23.75 23.75 38.98 2.90
457 462 6.625300 GCAGATCAAATGAGCTCATCTTTTGT 60.625 38.462 28.83 18.59 46.02 2.83
468 473 5.009410 AGCTCATCTTTTGTTGTTTCTGGAG 59.991 40.000 0.00 0.00 0.00 3.86
483 488 4.537135 TCTGGAGCACTATTTTTCTCGT 57.463 40.909 0.00 0.00 0.00 4.18
484 489 4.894784 TCTGGAGCACTATTTTTCTCGTT 58.105 39.130 0.00 0.00 0.00 3.85
490 495 4.392138 AGCACTATTTTTCTCGTTGTAGCC 59.608 41.667 0.00 0.00 0.00 3.93
503 508 2.851263 TGTAGCCTACAAACCAGTGG 57.149 50.000 7.91 7.91 35.38 4.00
505 510 2.038033 TGTAGCCTACAAACCAGTGGTC 59.962 50.000 17.06 0.39 35.38 4.02
513 521 4.976224 ACAAACCAGTGGTCAGTAAAAC 57.024 40.909 17.06 0.00 33.12 2.43
514 522 4.595986 ACAAACCAGTGGTCAGTAAAACT 58.404 39.130 17.06 0.00 33.12 2.66
567 575 1.134220 TCCCAGGAACCAATATGACGC 60.134 52.381 0.00 0.00 0.00 5.19
602 610 1.822990 GGACCCACTCGTCATTCACTA 59.177 52.381 0.00 0.00 34.24 2.74
616 624 5.038683 TCATTCACTATAAACGCTACCACG 58.961 41.667 0.00 0.00 39.50 4.94
620 628 1.856597 CTATAAACGCTACCACGCCAC 59.143 52.381 0.00 0.00 36.19 5.01
628 642 2.081462 GCTACCACGCCACAACTATTT 58.919 47.619 0.00 0.00 0.00 1.40
687 701 2.480932 CCACAGTCAGATCATCCAGTCG 60.481 54.545 0.00 0.00 0.00 4.18
705 719 1.597461 GGAACCGAGGAACCTCCAG 59.403 63.158 14.25 9.09 39.61 3.86
708 722 1.831652 AACCGAGGAACCTCCAGCTG 61.832 60.000 6.78 6.78 39.61 4.24
842 856 0.392998 CACCCCAAGACCCAATCTCG 60.393 60.000 0.00 0.00 36.27 4.04
847 861 2.291043 AAGACCCAATCTCGGCCGT 61.291 57.895 27.15 1.97 36.27 5.68
895 909 0.041238 TCCATCTTCCCTCCACTCGT 59.959 55.000 0.00 0.00 0.00 4.18
999 1013 1.387737 CAGCTCCCAAATCCCCCAA 59.612 57.895 0.00 0.00 0.00 4.12
1000 1014 0.685458 CAGCTCCCAAATCCCCCAAG 60.685 60.000 0.00 0.00 0.00 3.61
1012 1029 1.005394 CCCCAAGCAAGCAAGCAAG 60.005 57.895 3.19 0.00 36.85 4.01
1015 1032 0.944311 CCAAGCAAGCAAGCAAGCAG 60.944 55.000 10.52 3.81 36.85 4.24
1392 1410 2.031163 GACACCAACCTCTGCGCT 59.969 61.111 9.73 0.00 0.00 5.92
1504 1522 1.330779 CGTGCGTTGTCAGAGAGTCG 61.331 60.000 0.00 0.00 0.00 4.18
1506 1524 0.317854 TGCGTTGTCAGAGAGTCGTG 60.318 55.000 0.00 0.00 0.00 4.35
1522 1540 1.626654 CGTGCTGTGATGTTCCGGTC 61.627 60.000 0.00 0.00 0.00 4.79
1524 1542 0.396435 TGCTGTGATGTTCCGGTCTT 59.604 50.000 0.00 0.00 0.00 3.01
1572 1591 3.173240 GTCCGCTCTCGTCGTTGC 61.173 66.667 0.00 0.00 0.00 4.17
1588 1607 1.338020 GTTGCCTTGCCATATGTAGCC 59.662 52.381 1.24 0.00 0.00 3.93
1628 1647 7.792374 TTATCAATGAAGAGTGCAGTTATCC 57.208 36.000 0.00 0.00 0.00 2.59
1642 1661 6.309980 GTGCAGTTATCCTCATATGAATCTCG 59.690 42.308 6.90 0.00 0.00 4.04
1654 1673 4.910746 ATGAATCTCGTTTCAGTGTTCG 57.089 40.909 0.00 0.00 38.90 3.95
1660 1679 4.889241 TCTCGTTTCAGTGTTCGTTTTTC 58.111 39.130 0.00 0.00 0.00 2.29
1661 1680 4.628333 TCTCGTTTCAGTGTTCGTTTTTCT 59.372 37.500 0.00 0.00 0.00 2.52
1662 1681 4.643953 TCGTTTCAGTGTTCGTTTTTCTG 58.356 39.130 0.00 0.00 0.00 3.02
1663 1682 4.389382 TCGTTTCAGTGTTCGTTTTTCTGA 59.611 37.500 0.00 0.00 34.08 3.27
1664 1683 5.083389 CGTTTCAGTGTTCGTTTTTCTGAA 58.917 37.500 0.00 0.00 41.36 3.02
1665 1684 5.737290 CGTTTCAGTGTTCGTTTTTCTGAAT 59.263 36.000 6.72 0.00 42.18 2.57
1667 1686 6.677781 TTCAGTGTTCGTTTTTCTGAATCT 57.322 33.333 0.00 0.00 39.27 2.40
1668 1687 6.287107 TCAGTGTTCGTTTTTCTGAATCTC 57.713 37.500 0.00 0.00 33.18 2.75
1669 1688 5.815222 TCAGTGTTCGTTTTTCTGAATCTCA 59.185 36.000 0.00 0.00 33.18 3.27
1675 1694 7.857389 TGTTCGTTTTTCTGAATCTCATTTCTG 59.143 33.333 0.00 0.00 0.00 3.02
1677 1696 7.930217 TCGTTTTTCTGAATCTCATTTCTGTT 58.070 30.769 0.00 0.00 0.00 3.16
1678 1697 7.857389 TCGTTTTTCTGAATCTCATTTCTGTTG 59.143 33.333 0.00 0.00 0.00 3.33
1683 1702 6.479006 TCTGAATCTCATTTCTGTTGGATGT 58.521 36.000 0.00 0.00 0.00 3.06
1690 1709 5.620206 TCATTTCTGTTGGATGTGTACTGT 58.380 37.500 0.00 0.00 0.00 3.55
1691 1710 5.700832 TCATTTCTGTTGGATGTGTACTGTC 59.299 40.000 0.00 0.00 0.00 3.51
1694 1713 5.290493 TCTGTTGGATGTGTACTGTCTTT 57.710 39.130 0.00 0.00 0.00 2.52
1695 1714 5.297547 TCTGTTGGATGTGTACTGTCTTTC 58.702 41.667 0.00 0.00 0.00 2.62
1726 1745 3.927142 AGTTTCGTTGTCTAGCTGTATGC 59.073 43.478 0.00 0.00 43.29 3.14
1755 1774 1.051008 TGTGAAGCAGAGGAAGAGCA 58.949 50.000 0.00 0.00 0.00 4.26
1757 1776 0.322975 TGAAGCAGAGGAAGAGCACC 59.677 55.000 0.00 0.00 0.00 5.01
1758 1777 0.322975 GAAGCAGAGGAAGAGCACCA 59.677 55.000 0.00 0.00 0.00 4.17
1759 1778 0.036022 AAGCAGAGGAAGAGCACCAC 59.964 55.000 0.00 0.00 0.00 4.16
1774 1793 2.350772 GCACCACTGCCGCATAATAATC 60.351 50.000 0.00 0.00 37.45 1.75
1782 1801 3.684305 TGCCGCATAATAATCTTCATCCG 59.316 43.478 0.00 0.00 0.00 4.18
1784 1803 4.154195 GCCGCATAATAATCTTCATCCGTT 59.846 41.667 0.00 0.00 0.00 4.44
1791 1810 9.979270 CATAATAATCTTCATCCGTTGATTAGC 57.021 33.333 0.00 0.00 35.66 3.09
1793 1812 3.194005 TCTTCATCCGTTGATTAGCCC 57.806 47.619 0.00 0.00 33.34 5.19
1811 1830 0.740737 CCCTTCCGTCATTGGATTGC 59.259 55.000 0.00 0.00 38.00 3.56
1812 1831 0.378257 CCTTCCGTCATTGGATTGCG 59.622 55.000 0.00 0.00 38.00 4.85
1813 1832 1.086696 CTTCCGTCATTGGATTGCGT 58.913 50.000 0.00 0.00 38.00 5.24
1824 1843 1.000145 GGATTGCGTCCTTCGTCTTC 59.000 55.000 0.91 0.00 44.16 2.87
1832 1854 2.683867 CGTCCTTCGTCTTCCACTCTAT 59.316 50.000 0.00 0.00 34.52 1.98
1837 1859 7.095270 GTCCTTCGTCTTCCACTCTATTTTAA 58.905 38.462 0.00 0.00 0.00 1.52
1840 1862 8.604890 CCTTCGTCTTCCACTCTATTTTAATTC 58.395 37.037 0.00 0.00 0.00 2.17
1873 1895 9.465985 TTTTTCTTAATTTTCGGATGGTGTTAC 57.534 29.630 0.00 0.00 0.00 2.50
1874 1896 6.411630 TCTTAATTTTCGGATGGTGTTACG 57.588 37.500 0.00 0.00 0.00 3.18
1875 1897 3.481112 AATTTTCGGATGGTGTTACGC 57.519 42.857 0.00 0.00 0.00 4.42
1895 1918 3.204526 GCTGATGGAGATGAAGAACAGG 58.795 50.000 0.00 0.00 0.00 4.00
1904 1927 2.509336 AAGAACAGGATCGCCGCG 60.509 61.111 6.39 6.39 39.96 6.46
1914 1937 0.304705 GATCGCCGCGTCATGATTTT 59.695 50.000 13.39 0.00 0.00 1.82
1930 1964 2.886862 TTTTCGTCTCACCGTGGTTA 57.113 45.000 0.00 0.00 0.00 2.85
1937 1971 3.135994 GTCTCACCGTGGTTATGTTGTT 58.864 45.455 0.00 0.00 0.00 2.83
1938 1972 3.185797 GTCTCACCGTGGTTATGTTGTTC 59.814 47.826 0.00 0.00 0.00 3.18
1939 1973 2.482721 CTCACCGTGGTTATGTTGTTCC 59.517 50.000 0.00 0.00 0.00 3.62
1940 1974 2.158798 TCACCGTGGTTATGTTGTTCCA 60.159 45.455 0.00 0.00 0.00 3.53
1942 1976 4.004314 CACCGTGGTTATGTTGTTCCATA 58.996 43.478 0.00 0.00 32.45 2.74
1945 1979 5.124776 ACCGTGGTTATGTTGTTCCATATTG 59.875 40.000 0.00 0.00 32.45 1.90
1946 1980 5.355630 CCGTGGTTATGTTGTTCCATATTGA 59.644 40.000 0.00 0.00 32.45 2.57
1947 1981 6.458206 CCGTGGTTATGTTGTTCCATATTGAG 60.458 42.308 0.00 0.00 32.45 3.02
1948 1982 6.315144 CGTGGTTATGTTGTTCCATATTGAGA 59.685 38.462 0.00 0.00 32.45 3.27
1949 1983 7.012327 CGTGGTTATGTTGTTCCATATTGAGAT 59.988 37.037 0.00 0.00 32.45 2.75
1950 1984 9.337396 GTGGTTATGTTGTTCCATATTGAGATA 57.663 33.333 0.00 0.00 32.45 1.98
2005 2039 1.005394 TTTCCAGGTTCTCCGCGTC 60.005 57.895 4.92 0.00 39.05 5.19
2020 2054 3.435186 GTCTGCCTCTTTGCCGCC 61.435 66.667 0.00 0.00 0.00 6.13
2024 2058 4.416738 GCCTCTTTGCCGCCTCCT 62.417 66.667 0.00 0.00 0.00 3.69
2519 2557 2.823147 GATCTGCTTGCCGCTGCT 60.823 61.111 0.70 0.00 40.11 4.24
2589 2627 2.609491 GGTTTGGACTGATTTTTCCGGC 60.609 50.000 0.00 0.00 34.24 6.13
2604 2642 2.435059 GGCGGTCAGTCTTCTGCC 60.435 66.667 8.38 8.38 46.60 4.85
2610 2648 1.837051 TCAGTCTTCTGCCACGGGT 60.837 57.895 0.00 0.00 41.10 5.28
2613 2651 1.122019 AGTCTTCTGCCACGGGTCTT 61.122 55.000 0.00 0.00 0.00 3.01
2614 2652 0.606604 GTCTTCTGCCACGGGTCTTA 59.393 55.000 0.00 0.00 0.00 2.10
2616 2654 0.736325 CTTCTGCCACGGGTCTTACG 60.736 60.000 0.00 0.00 37.36 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.803426 CCCTCACTCTCGGCGTGC 62.803 72.222 6.85 0.00 32.54 5.34
1 2 3.057547 CTCCCTCACTCTCGGCGTG 62.058 68.421 6.85 4.24 0.00 5.34
2 3 2.752238 CTCCCTCACTCTCGGCGT 60.752 66.667 6.85 0.00 0.00 5.68
3 4 1.999071 CTTCTCCCTCACTCTCGGCG 61.999 65.000 0.00 0.00 0.00 6.46
4 5 1.671901 CCTTCTCCCTCACTCTCGGC 61.672 65.000 0.00 0.00 0.00 5.54
5 6 0.323908 ACCTTCTCCCTCACTCTCGG 60.324 60.000 0.00 0.00 0.00 4.63
6 7 0.814457 CACCTTCTCCCTCACTCTCG 59.186 60.000 0.00 0.00 0.00 4.04
7 8 1.190643 CCACCTTCTCCCTCACTCTC 58.809 60.000 0.00 0.00 0.00 3.20
8 9 0.252467 CCCACCTTCTCCCTCACTCT 60.252 60.000 0.00 0.00 0.00 3.24
9 10 1.268283 CCCCACCTTCTCCCTCACTC 61.268 65.000 0.00 0.00 0.00 3.51
10 11 1.229658 CCCCACCTTCTCCCTCACT 60.230 63.158 0.00 0.00 0.00 3.41
11 12 2.301738 CCCCCACCTTCTCCCTCAC 61.302 68.421 0.00 0.00 0.00 3.51
12 13 2.124996 CCCCCACCTTCTCCCTCA 59.875 66.667 0.00 0.00 0.00 3.86
13 14 3.412408 GCCCCCACCTTCTCCCTC 61.412 72.222 0.00 0.00 0.00 4.30
40 41 1.053264 CATCTCCTCCCCAGACCCTG 61.053 65.000 0.00 0.00 0.00 4.45
41 42 1.316266 CATCTCCTCCCCAGACCCT 59.684 63.158 0.00 0.00 0.00 4.34
42 43 1.768077 CCATCTCCTCCCCAGACCC 60.768 68.421 0.00 0.00 0.00 4.46
43 44 1.768077 CCCATCTCCTCCCCAGACC 60.768 68.421 0.00 0.00 0.00 3.85
44 45 1.768077 CCCCATCTCCTCCCCAGAC 60.768 68.421 0.00 0.00 0.00 3.51
45 46 2.705410 CCCCATCTCCTCCCCAGA 59.295 66.667 0.00 0.00 0.00 3.86
46 47 3.174265 GCCCCATCTCCTCCCCAG 61.174 72.222 0.00 0.00 0.00 4.45
94 95 5.376625 CGATTCCTCCATATCCCTCAAAAA 58.623 41.667 0.00 0.00 0.00 1.94
95 96 4.746702 GCGATTCCTCCATATCCCTCAAAA 60.747 45.833 0.00 0.00 0.00 2.44
96 97 3.244561 GCGATTCCTCCATATCCCTCAAA 60.245 47.826 0.00 0.00 0.00 2.69
97 98 2.303022 GCGATTCCTCCATATCCCTCAA 59.697 50.000 0.00 0.00 0.00 3.02
98 99 1.902508 GCGATTCCTCCATATCCCTCA 59.097 52.381 0.00 0.00 0.00 3.86
99 100 2.183679 AGCGATTCCTCCATATCCCTC 58.816 52.381 0.00 0.00 0.00 4.30
100 101 2.334006 AGCGATTCCTCCATATCCCT 57.666 50.000 0.00 0.00 0.00 4.20
101 102 2.432510 CCTAGCGATTCCTCCATATCCC 59.567 54.545 0.00 0.00 0.00 3.85
102 103 3.100671 ACCTAGCGATTCCTCCATATCC 58.899 50.000 0.00 0.00 0.00 2.59
103 104 3.764434 TGACCTAGCGATTCCTCCATATC 59.236 47.826 0.00 0.00 0.00 1.63
104 105 3.766591 CTGACCTAGCGATTCCTCCATAT 59.233 47.826 0.00 0.00 0.00 1.78
105 106 3.157881 CTGACCTAGCGATTCCTCCATA 58.842 50.000 0.00 0.00 0.00 2.74
106 107 1.967066 CTGACCTAGCGATTCCTCCAT 59.033 52.381 0.00 0.00 0.00 3.41
107 108 1.403814 CTGACCTAGCGATTCCTCCA 58.596 55.000 0.00 0.00 0.00 3.86
108 109 0.676736 CCTGACCTAGCGATTCCTCC 59.323 60.000 0.00 0.00 0.00 4.30
109 110 1.611491 CTCCTGACCTAGCGATTCCTC 59.389 57.143 0.00 0.00 0.00 3.71
110 111 1.698506 CTCCTGACCTAGCGATTCCT 58.301 55.000 0.00 0.00 0.00 3.36
111 112 0.676736 CCTCCTGACCTAGCGATTCC 59.323 60.000 0.00 0.00 0.00 3.01
112 113 1.693627 TCCTCCTGACCTAGCGATTC 58.306 55.000 0.00 0.00 0.00 2.52
113 114 1.757699 GTTCCTCCTGACCTAGCGATT 59.242 52.381 0.00 0.00 0.00 3.34
114 115 1.404843 GTTCCTCCTGACCTAGCGAT 58.595 55.000 0.00 0.00 0.00 4.58
115 116 1.030488 CGTTCCTCCTGACCTAGCGA 61.030 60.000 0.00 0.00 0.00 4.93
116 117 1.313812 ACGTTCCTCCTGACCTAGCG 61.314 60.000 0.00 0.00 0.00 4.26
117 118 0.456628 GACGTTCCTCCTGACCTAGC 59.543 60.000 0.00 0.00 0.00 3.42
118 119 0.733729 CGACGTTCCTCCTGACCTAG 59.266 60.000 0.00 0.00 0.00 3.02
119 120 0.679002 CCGACGTTCCTCCTGACCTA 60.679 60.000 0.00 0.00 0.00 3.08
120 121 1.977544 CCGACGTTCCTCCTGACCT 60.978 63.158 0.00 0.00 0.00 3.85
121 122 2.572284 CCGACGTTCCTCCTGACC 59.428 66.667 0.00 0.00 0.00 4.02
122 123 2.572284 CCCGACGTTCCTCCTGAC 59.428 66.667 0.00 0.00 0.00 3.51
123 124 2.678934 CCCCGACGTTCCTCCTGA 60.679 66.667 0.00 0.00 0.00 3.86
124 125 1.614241 ATTCCCCGACGTTCCTCCTG 61.614 60.000 0.00 0.00 0.00 3.86
125 126 1.305887 ATTCCCCGACGTTCCTCCT 60.306 57.895 0.00 0.00 0.00 3.69
126 127 1.143401 GATTCCCCGACGTTCCTCC 59.857 63.158 0.00 0.00 0.00 4.30
127 128 1.226888 CGATTCCCCGACGTTCCTC 60.227 63.158 0.00 0.00 0.00 3.71
128 129 2.890371 CGATTCCCCGACGTTCCT 59.110 61.111 0.00 0.00 0.00 3.36
129 130 2.008268 TAGCGATTCCCCGACGTTCC 62.008 60.000 0.00 0.00 0.00 3.62
130 131 0.594284 CTAGCGATTCCCCGACGTTC 60.594 60.000 0.00 0.00 0.00 3.95
131 132 1.436336 CTAGCGATTCCCCGACGTT 59.564 57.895 0.00 0.00 0.00 3.99
132 133 2.487532 CCTAGCGATTCCCCGACGT 61.488 63.158 0.00 0.00 0.00 4.34
133 134 2.012902 AACCTAGCGATTCCCCGACG 62.013 60.000 0.00 0.00 0.00 5.12
134 135 0.177373 AAACCTAGCGATTCCCCGAC 59.823 55.000 0.00 0.00 0.00 4.79
135 136 0.906775 AAAACCTAGCGATTCCCCGA 59.093 50.000 0.00 0.00 0.00 5.14
136 137 1.746470 AAAAACCTAGCGATTCCCCG 58.254 50.000 0.00 0.00 0.00 5.73
154 155 2.557372 GCAACCCTCCCGCGAAAAA 61.557 57.895 8.23 0.00 0.00 1.94
155 156 2.981350 GCAACCCTCCCGCGAAAA 60.981 61.111 8.23 0.00 0.00 2.29
156 157 3.776347 TTGCAACCCTCCCGCGAAA 62.776 57.895 8.23 0.00 0.00 3.46
157 158 4.257654 TTGCAACCCTCCCGCGAA 62.258 61.111 8.23 0.00 0.00 4.70
158 159 4.697756 CTTGCAACCCTCCCGCGA 62.698 66.667 8.23 0.00 0.00 5.87
160 161 0.891904 TTAACTTGCAACCCTCCCGC 60.892 55.000 0.00 0.00 0.00 6.13
161 162 0.879090 GTTAACTTGCAACCCTCCCG 59.121 55.000 0.00 0.00 0.00 5.14
162 163 0.879090 CGTTAACTTGCAACCCTCCC 59.121 55.000 3.71 0.00 0.00 4.30
163 164 0.879090 CCGTTAACTTGCAACCCTCC 59.121 55.000 3.71 0.00 0.00 4.30
164 165 1.804748 CTCCGTTAACTTGCAACCCTC 59.195 52.381 3.71 0.00 0.00 4.30
165 166 1.544759 CCTCCGTTAACTTGCAACCCT 60.545 52.381 3.71 0.00 0.00 4.34
166 167 0.879090 CCTCCGTTAACTTGCAACCC 59.121 55.000 3.71 0.00 0.00 4.11
167 168 1.265905 CACCTCCGTTAACTTGCAACC 59.734 52.381 3.71 0.00 0.00 3.77
168 169 1.265905 CCACCTCCGTTAACTTGCAAC 59.734 52.381 3.71 0.00 0.00 4.17
169 170 1.600023 CCACCTCCGTTAACTTGCAA 58.400 50.000 3.71 0.00 0.00 4.08
170 171 0.250553 CCCACCTCCGTTAACTTGCA 60.251 55.000 3.71 0.00 0.00 4.08
171 172 0.035739 TCCCACCTCCGTTAACTTGC 59.964 55.000 3.71 0.00 0.00 4.01
172 173 1.338769 CCTCCCACCTCCGTTAACTTG 60.339 57.143 3.71 0.00 0.00 3.16
173 174 0.981943 CCTCCCACCTCCGTTAACTT 59.018 55.000 3.71 0.00 0.00 2.66
174 175 0.115745 TCCTCCCACCTCCGTTAACT 59.884 55.000 3.71 0.00 0.00 2.24
175 176 1.134491 CATCCTCCCACCTCCGTTAAC 60.134 57.143 0.00 0.00 0.00 2.01
176 177 1.200519 CATCCTCCCACCTCCGTTAA 58.799 55.000 0.00 0.00 0.00 2.01
177 178 0.337082 TCATCCTCCCACCTCCGTTA 59.663 55.000 0.00 0.00 0.00 3.18
178 179 1.080354 TCATCCTCCCACCTCCGTT 59.920 57.895 0.00 0.00 0.00 4.44
179 180 1.686110 GTCATCCTCCCACCTCCGT 60.686 63.158 0.00 0.00 0.00 4.69
180 181 2.786495 CGTCATCCTCCCACCTCCG 61.786 68.421 0.00 0.00 0.00 4.63
181 182 0.976073 TTCGTCATCCTCCCACCTCC 60.976 60.000 0.00 0.00 0.00 4.30
182 183 0.902531 TTTCGTCATCCTCCCACCTC 59.097 55.000 0.00 0.00 0.00 3.85
183 184 1.358152 TTTTCGTCATCCTCCCACCT 58.642 50.000 0.00 0.00 0.00 4.00
184 185 2.194201 TTTTTCGTCATCCTCCCACC 57.806 50.000 0.00 0.00 0.00 4.61
202 203 1.368374 TCCTCCCATCTCCGGTTTTT 58.632 50.000 0.00 0.00 0.00 1.94
203 204 1.212935 CATCCTCCCATCTCCGGTTTT 59.787 52.381 0.00 0.00 0.00 2.43
204 205 0.839946 CATCCTCCCATCTCCGGTTT 59.160 55.000 0.00 0.00 0.00 3.27
205 206 0.031111 TCATCCTCCCATCTCCGGTT 60.031 55.000 0.00 0.00 0.00 4.44
206 207 0.760945 GTCATCCTCCCATCTCCGGT 60.761 60.000 0.00 0.00 0.00 5.28
207 208 1.810606 CGTCATCCTCCCATCTCCGG 61.811 65.000 0.00 0.00 0.00 5.14
208 209 0.823769 TCGTCATCCTCCCATCTCCG 60.824 60.000 0.00 0.00 0.00 4.63
209 210 1.414158 TTCGTCATCCTCCCATCTCC 58.586 55.000 0.00 0.00 0.00 3.71
210 211 3.543680 TTTTCGTCATCCTCCCATCTC 57.456 47.619 0.00 0.00 0.00 2.75
228 229 4.035792 GCGGTTTAATTTTGCTGGGTTTTT 59.964 37.500 0.00 0.00 0.00 1.94
229 230 3.562141 GCGGTTTAATTTTGCTGGGTTTT 59.438 39.130 0.00 0.00 0.00 2.43
230 231 3.135225 GCGGTTTAATTTTGCTGGGTTT 58.865 40.909 0.00 0.00 0.00 3.27
231 232 2.103263 TGCGGTTTAATTTTGCTGGGTT 59.897 40.909 0.00 0.00 0.00 4.11
232 233 1.689273 TGCGGTTTAATTTTGCTGGGT 59.311 42.857 0.00 0.00 0.00 4.51
233 234 2.065512 GTGCGGTTTAATTTTGCTGGG 58.934 47.619 0.00 0.00 0.00 4.45
234 235 2.730928 CTGTGCGGTTTAATTTTGCTGG 59.269 45.455 0.00 0.00 0.00 4.85
235 236 3.425193 GTCTGTGCGGTTTAATTTTGCTG 59.575 43.478 0.00 0.00 0.00 4.41
236 237 3.317993 AGTCTGTGCGGTTTAATTTTGCT 59.682 39.130 0.00 0.00 0.00 3.91
237 238 3.638484 AGTCTGTGCGGTTTAATTTTGC 58.362 40.909 0.00 0.00 0.00 3.68
238 239 7.081349 TGAATAGTCTGTGCGGTTTAATTTTG 58.919 34.615 0.00 0.00 0.00 2.44
239 240 7.209471 TGAATAGTCTGTGCGGTTTAATTTT 57.791 32.000 0.00 0.00 0.00 1.82
240 241 6.811253 TGAATAGTCTGTGCGGTTTAATTT 57.189 33.333 0.00 0.00 0.00 1.82
241 242 6.597672 TGATGAATAGTCTGTGCGGTTTAATT 59.402 34.615 0.00 0.00 0.00 1.40
242 243 6.112734 TGATGAATAGTCTGTGCGGTTTAAT 58.887 36.000 0.00 0.00 0.00 1.40
243 244 5.483811 TGATGAATAGTCTGTGCGGTTTAA 58.516 37.500 0.00 0.00 0.00 1.52
244 245 5.079689 TGATGAATAGTCTGTGCGGTTTA 57.920 39.130 0.00 0.00 0.00 2.01
245 246 3.937814 TGATGAATAGTCTGTGCGGTTT 58.062 40.909 0.00 0.00 0.00 3.27
246 247 3.610040 TGATGAATAGTCTGTGCGGTT 57.390 42.857 0.00 0.00 0.00 4.44
247 248 3.055819 ACTTGATGAATAGTCTGTGCGGT 60.056 43.478 0.00 0.00 0.00 5.68
248 249 3.525537 ACTTGATGAATAGTCTGTGCGG 58.474 45.455 0.00 0.00 0.00 5.69
249 250 3.241553 CGACTTGATGAATAGTCTGTGCG 59.758 47.826 0.00 0.00 38.86 5.34
250 251 4.177026 ACGACTTGATGAATAGTCTGTGC 58.823 43.478 0.00 0.00 38.86 4.57
251 252 4.800993 GGACGACTTGATGAATAGTCTGTG 59.199 45.833 0.00 0.00 38.86 3.66
252 253 4.462834 TGGACGACTTGATGAATAGTCTGT 59.537 41.667 0.00 0.00 38.86 3.41
253 254 4.998788 TGGACGACTTGATGAATAGTCTG 58.001 43.478 0.00 0.00 38.86 3.51
254 255 5.860941 ATGGACGACTTGATGAATAGTCT 57.139 39.130 0.00 0.00 38.86 3.24
255 256 7.921214 TCTTAATGGACGACTTGATGAATAGTC 59.079 37.037 0.00 0.00 37.90 2.59
256 257 7.782049 TCTTAATGGACGACTTGATGAATAGT 58.218 34.615 0.00 0.00 0.00 2.12
257 258 8.648557 TTCTTAATGGACGACTTGATGAATAG 57.351 34.615 0.00 0.00 0.00 1.73
259 260 9.265901 CTATTCTTAATGGACGACTTGATGAAT 57.734 33.333 0.00 0.00 0.00 2.57
260 261 8.474831 TCTATTCTTAATGGACGACTTGATGAA 58.525 33.333 0.00 0.00 0.00 2.57
261 262 8.007405 TCTATTCTTAATGGACGACTTGATGA 57.993 34.615 0.00 0.00 0.00 2.92
262 263 8.138074 TCTCTATTCTTAATGGACGACTTGATG 58.862 37.037 0.00 0.00 0.00 3.07
263 264 8.239038 TCTCTATTCTTAATGGACGACTTGAT 57.761 34.615 0.00 0.00 0.00 2.57
264 265 7.640597 TCTCTATTCTTAATGGACGACTTGA 57.359 36.000 0.00 0.00 0.00 3.02
265 266 8.879342 AATCTCTATTCTTAATGGACGACTTG 57.121 34.615 0.00 0.00 0.00 3.16
307 308 8.919145 AGTTTGGTGTCCATAGAAATGTTTTTA 58.081 29.630 0.00 0.00 31.53 1.52
318 319 3.259064 CACGGTAGTTTGGTGTCCATAG 58.741 50.000 0.00 0.00 31.53 2.23
347 348 5.468746 GGACATTTGTGTGTACATGTACAGT 59.531 40.000 33.58 25.66 45.61 3.55
361 362 7.495135 TGTATGCATATAGTGGACATTTGTG 57.505 36.000 10.16 0.00 0.00 3.33
363 364 9.970395 AATTTGTATGCATATAGTGGACATTTG 57.030 29.630 10.16 0.00 0.00 2.32
391 392 9.384764 TCACGTATGAAAATACATATTTGGTGA 57.615 29.630 0.00 0.00 36.14 4.02
419 420 9.529325 CTCATTTGATCTGCACATTTTTCATAT 57.471 29.630 0.00 0.00 0.00 1.78
430 435 3.878103 AGATGAGCTCATTTGATCTGCAC 59.122 43.478 29.26 12.86 36.57 4.57
450 455 4.016444 AGTGCTCCAGAAACAACAAAAGA 58.984 39.130 0.00 0.00 0.00 2.52
457 462 6.293407 CGAGAAAAATAGTGCTCCAGAAACAA 60.293 38.462 0.00 0.00 0.00 2.83
468 473 4.392138 AGGCTACAACGAGAAAAATAGTGC 59.608 41.667 0.00 0.00 0.00 4.40
483 488 2.440253 ACCACTGGTTTGTAGGCTACAA 59.560 45.455 30.85 30.85 46.13 2.41
484 489 2.038033 GACCACTGGTTTGTAGGCTACA 59.962 50.000 22.96 22.96 35.25 2.74
490 495 5.820947 AGTTTTACTGACCACTGGTTTGTAG 59.179 40.000 1.13 2.19 35.25 2.74
497 502 7.562454 TCTTAAAAGTTTTACTGACCACTGG 57.438 36.000 7.58 0.00 0.00 4.00
524 532 7.549134 GGGAGTTTCAAACAAGAACTCAAAATT 59.451 33.333 14.95 0.00 32.35 1.82
526 534 6.015010 TGGGAGTTTCAAACAAGAACTCAAAA 60.015 34.615 14.95 0.73 32.35 2.44
548 556 1.134098 AGCGTCATATTGGTTCCTGGG 60.134 52.381 0.00 0.00 0.00 4.45
591 599 5.038683 TGGTAGCGTTTATAGTGAATGACG 58.961 41.667 0.00 0.00 33.88 4.35
602 610 0.037139 TGTGGCGTGGTAGCGTTTAT 60.037 50.000 0.00 0.00 38.18 1.40
646 660 2.479219 GGGTCTTGTAGTACGCTGTAGC 60.479 54.545 0.00 0.00 37.78 3.58
651 665 1.544691 CTGTGGGTCTTGTAGTACGCT 59.455 52.381 0.00 0.00 0.00 5.07
687 701 1.597461 CTGGAGGTTCCTCGGTTCC 59.403 63.158 12.01 0.68 37.46 3.62
691 705 1.544825 TTCAGCTGGAGGTTCCTCGG 61.545 60.000 15.13 8.82 37.46 4.63
716 730 3.506844 CCCGGGTTCCTCGAAAATTTTAA 59.493 43.478 14.18 0.00 0.00 1.52
717 731 3.083293 CCCGGGTTCCTCGAAAATTTTA 58.917 45.455 14.18 0.00 0.00 1.52
718 732 1.890489 CCCGGGTTCCTCGAAAATTTT 59.110 47.619 14.18 2.28 0.00 1.82
719 733 1.541379 CCCGGGTTCCTCGAAAATTT 58.459 50.000 14.18 0.00 0.00 1.82
720 734 0.963856 GCCCGGGTTCCTCGAAAATT 60.964 55.000 24.63 0.00 0.00 1.82
721 735 1.378119 GCCCGGGTTCCTCGAAAAT 60.378 57.895 24.63 0.00 0.00 1.82
722 736 2.032987 GCCCGGGTTCCTCGAAAA 59.967 61.111 24.63 0.00 0.00 2.29
864 878 1.405463 GAAGATGGATTTGGGGCGTTC 59.595 52.381 0.00 0.00 0.00 3.95
908 922 2.225267 GGGAGACTGGGAAATTTTGGGA 60.225 50.000 0.00 0.00 0.00 4.37
911 925 1.202348 GCGGGAGACTGGGAAATTTTG 59.798 52.381 0.00 0.00 37.13 2.44
999 1013 2.338984 GCTGCTTGCTTGCTTGCT 59.661 55.556 0.00 0.00 38.95 3.91
1000 1014 2.737376 GGCTGCTTGCTTGCTTGC 60.737 61.111 0.00 7.11 42.39 4.01
1045 1063 3.508840 CGCCATTGCTTCGGGGTC 61.509 66.667 0.00 0.00 34.43 4.46
1481 1499 2.202810 TCTGACAACGCACGCACA 60.203 55.556 0.00 0.00 0.00 4.57
1504 1522 0.320771 AGACCGGAACATCACAGCAC 60.321 55.000 9.46 0.00 0.00 4.40
1506 1524 2.094182 TCTAAGACCGGAACATCACAGC 60.094 50.000 9.46 0.00 0.00 4.40
1522 1540 2.234908 AGCTACACCACCAAGCTCTAAG 59.765 50.000 0.00 0.00 42.89 2.18
1524 1542 1.938585 AGCTACACCACCAAGCTCTA 58.061 50.000 0.00 0.00 42.89 2.43
1572 1591 0.773644 AGGGGCTACATATGGCAAGG 59.226 55.000 7.80 0.00 32.95 3.61
1588 1607 2.880268 TGATAATTCATCGCAGCAAGGG 59.120 45.455 0.00 0.00 36.33 3.95
1628 1647 7.514280 CGAACACTGAAACGAGATTCATATGAG 60.514 40.741 5.39 0.00 38.55 2.90
1642 1661 6.967199 AGATTCAGAAAAACGAACACTGAAAC 59.033 34.615 0.00 0.00 45.89 2.78
1654 1673 8.137437 TCCAACAGAAATGAGATTCAGAAAAAC 58.863 33.333 0.00 0.00 0.00 2.43
1660 1679 6.150641 ACACATCCAACAGAAATGAGATTCAG 59.849 38.462 0.00 0.00 0.00 3.02
1661 1680 6.005823 ACACATCCAACAGAAATGAGATTCA 58.994 36.000 0.00 0.00 0.00 2.57
1662 1681 6.506500 ACACATCCAACAGAAATGAGATTC 57.493 37.500 0.00 0.00 0.00 2.52
1663 1682 7.120285 CAGTACACATCCAACAGAAATGAGATT 59.880 37.037 0.00 0.00 0.00 2.40
1664 1683 6.596888 CAGTACACATCCAACAGAAATGAGAT 59.403 38.462 0.00 0.00 0.00 2.75
1665 1684 5.934043 CAGTACACATCCAACAGAAATGAGA 59.066 40.000 0.00 0.00 0.00 3.27
1667 1686 5.620206 ACAGTACACATCCAACAGAAATGA 58.380 37.500 0.00 0.00 0.00 2.57
1668 1687 5.702670 AGACAGTACACATCCAACAGAAATG 59.297 40.000 0.00 0.00 0.00 2.32
1669 1688 5.869579 AGACAGTACACATCCAACAGAAAT 58.130 37.500 0.00 0.00 0.00 2.17
1675 1694 5.057149 ACAGAAAGACAGTACACATCCAAC 58.943 41.667 0.00 0.00 0.00 3.77
1677 1696 4.955811 ACAGAAAGACAGTACACATCCA 57.044 40.909 0.00 0.00 0.00 3.41
1678 1697 5.542779 AGAACAGAAAGACAGTACACATCC 58.457 41.667 0.00 0.00 0.00 3.51
1755 1774 3.492102 AGATTATTATGCGGCAGTGGT 57.508 42.857 9.25 0.00 0.00 4.16
1757 1776 5.391310 GGATGAAGATTATTATGCGGCAGTG 60.391 44.000 9.25 0.00 0.00 3.66
1758 1777 4.697352 GGATGAAGATTATTATGCGGCAGT 59.303 41.667 9.25 0.00 0.00 4.40
1759 1778 4.201753 CGGATGAAGATTATTATGCGGCAG 60.202 45.833 9.25 0.00 31.95 4.85
1774 1793 2.158755 AGGGGCTAATCAACGGATGAAG 60.159 50.000 0.00 0.00 42.54 3.02
1782 1801 1.065709 TGACGGAAGGGGCTAATCAAC 60.066 52.381 0.00 0.00 0.00 3.18
1784 1803 1.507140 ATGACGGAAGGGGCTAATCA 58.493 50.000 0.00 0.00 0.00 2.57
1791 1810 1.392589 CAATCCAATGACGGAAGGGG 58.607 55.000 0.00 0.00 38.95 4.79
1793 1812 0.378257 CGCAATCCAATGACGGAAGG 59.622 55.000 0.00 0.00 38.95 3.46
1812 1831 4.722361 AATAGAGTGGAAGACGAAGGAC 57.278 45.455 0.00 0.00 0.00 3.85
1813 1832 5.740290 AAAATAGAGTGGAAGACGAAGGA 57.260 39.130 0.00 0.00 0.00 3.36
1818 1837 7.764443 TCCAGAATTAAAATAGAGTGGAAGACG 59.236 37.037 0.00 0.00 29.85 4.18
1819 1838 9.620259 ATCCAGAATTAAAATAGAGTGGAAGAC 57.380 33.333 0.00 0.00 36.46 3.01
1851 1873 5.163834 GCGTAACACCATCCGAAAATTAAGA 60.164 40.000 0.00 0.00 0.00 2.10
1856 1878 2.418628 CAGCGTAACACCATCCGAAAAT 59.581 45.455 0.00 0.00 0.00 1.82
1857 1879 1.801771 CAGCGTAACACCATCCGAAAA 59.198 47.619 0.00 0.00 0.00 2.29
1861 1883 0.930310 CATCAGCGTAACACCATCCG 59.070 55.000 0.00 0.00 0.00 4.18
1862 1884 1.134521 TCCATCAGCGTAACACCATCC 60.135 52.381 0.00 0.00 0.00 3.51
1863 1885 2.159099 TCTCCATCAGCGTAACACCATC 60.159 50.000 0.00 0.00 0.00 3.51
1864 1886 1.831106 TCTCCATCAGCGTAACACCAT 59.169 47.619 0.00 0.00 0.00 3.55
1865 1887 1.262417 TCTCCATCAGCGTAACACCA 58.738 50.000 0.00 0.00 0.00 4.17
1866 1888 2.159099 TCATCTCCATCAGCGTAACACC 60.159 50.000 0.00 0.00 0.00 4.16
1868 1890 3.447229 TCTTCATCTCCATCAGCGTAACA 59.553 43.478 0.00 0.00 0.00 2.41
1869 1891 4.046938 TCTTCATCTCCATCAGCGTAAC 57.953 45.455 0.00 0.00 0.00 2.50
1870 1892 4.081697 TGTTCTTCATCTCCATCAGCGTAA 60.082 41.667 0.00 0.00 0.00 3.18
1871 1893 3.447229 TGTTCTTCATCTCCATCAGCGTA 59.553 43.478 0.00 0.00 0.00 4.42
1872 1894 2.234661 TGTTCTTCATCTCCATCAGCGT 59.765 45.455 0.00 0.00 0.00 5.07
1873 1895 2.864946 CTGTTCTTCATCTCCATCAGCG 59.135 50.000 0.00 0.00 0.00 5.18
1874 1896 3.118482 TCCTGTTCTTCATCTCCATCAGC 60.118 47.826 0.00 0.00 0.00 4.26
1875 1897 4.750021 TCCTGTTCTTCATCTCCATCAG 57.250 45.455 0.00 0.00 0.00 2.90
1895 1918 0.304705 AAAATCATGACGCGGCGATC 59.695 50.000 30.94 21.41 0.00 3.69
1904 1927 2.993899 ACGGTGAGACGAAAATCATGAC 59.006 45.455 0.00 0.00 37.61 3.06
1914 1937 1.250328 ACATAACCACGGTGAGACGA 58.750 50.000 10.28 0.00 37.61 4.20
1942 1976 9.525826 GGGAACAAATATGGAAGATATCTCAAT 57.474 33.333 5.51 3.14 0.00 2.57
1945 1979 7.461749 TGGGGAACAAATATGGAAGATATCTC 58.538 38.462 5.51 0.00 0.00 2.75
1946 1980 7.295672 TCTGGGGAACAAATATGGAAGATATCT 59.704 37.037 0.00 0.00 0.00 1.98
1947 1981 7.461749 TCTGGGGAACAAATATGGAAGATATC 58.538 38.462 0.00 0.00 0.00 1.63
1948 1982 7.406620 TCTGGGGAACAAATATGGAAGATAT 57.593 36.000 0.00 0.00 0.00 1.63
1949 1983 6.840090 TCTGGGGAACAAATATGGAAGATA 57.160 37.500 0.00 0.00 0.00 1.98
1950 1984 5.732331 TCTGGGGAACAAATATGGAAGAT 57.268 39.130 0.00 0.00 0.00 2.40
1951 1985 5.732331 ATCTGGGGAACAAATATGGAAGA 57.268 39.130 0.00 0.00 0.00 2.87
1952 1986 6.796785 AAATCTGGGGAACAAATATGGAAG 57.203 37.500 0.00 0.00 0.00 3.46
1953 1987 6.500049 ACAAAATCTGGGGAACAAATATGGAA 59.500 34.615 0.00 0.00 0.00 3.53
1996 2030 2.276116 AAAGAGGCAGACGCGGAGA 61.276 57.895 12.47 0.00 39.92 3.71
2005 2039 3.130160 GAGGCGGCAAAGAGGCAG 61.130 66.667 13.08 0.00 44.47 4.85
2020 2054 2.260869 CGCCAACCACCAACAGGAG 61.261 63.158 0.00 0.00 0.00 3.69
2024 2058 1.826054 CTTCCGCCAACCACCAACA 60.826 57.895 0.00 0.00 0.00 3.33
2050 2084 3.064931 AGCGTTGGTTTTCAGCTACTAC 58.935 45.455 0.00 0.00 36.28 2.73
2489 2527 1.760086 CAGATCTGAGGAGGGGCGT 60.760 63.158 18.34 0.00 0.00 5.68
2519 2557 8.880991 ATCACAAAGTAAACTAGACCTAGAGA 57.119 34.615 10.74 0.00 36.97 3.10
2604 2642 2.030007 TCAAACTACCGTAAGACCCGTG 60.030 50.000 0.00 0.00 43.02 4.94


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

AutoCloner maintained by Alex Coulton.