Multiple sequence alignment - TraesCS2D01G017100

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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 TraesCS2D01G017100 chr2D 100.000 2175 0 0 669 2843 8301108 8303282 0.000000e+00 4017.0
1 TraesCS2D01G017100 chr2D 100.000 266 0 0 1 266 8300440 8300705 2.820000e-135 492.0
2 TraesCS2D01G017100 chr2D 100.000 46 0 0 3101 3146 8303540 8303585 5.590000e-13 86.1
3 TraesCS2D01G017100 chrUn 90.077 2207 143 41 671 2843 170192052 170194216 0.000000e+00 2793.0
4 TraesCS2D01G017100 chrUn 81.930 487 77 6 1886 2362 330901283 330900798 4.890000e-108 401.0
5 TraesCS2D01G017100 chr3D 87.281 228 20 7 1 221 532234868 532234643 5.210000e-63 252.0
6 TraesCS2D01G017100 chr2B 82.456 285 38 7 844 1128 4714162 4714434 4.060000e-59 239.0
7 TraesCS2D01G017100 chr2B 90.000 90 8 1 1675 1764 4721142 4721230 7.130000e-22 115.0
8 TraesCS2D01G017100 chr2B 85.714 91 13 0 1901 1991 4668029 4668119 2.580000e-16 97.1
9 TraesCS2D01G017100 chr3A 85.022 227 26 6 2 221 667495911 667495686 1.140000e-54 224.0
10 TraesCS2D01G017100 chr1B 86.869 198 22 4 27 221 430992934 430993130 5.280000e-53 219.0
11 TraesCS2D01G017100 chr4D 86.500 200 20 5 27 221 478234740 478234937 2.460000e-51 213.0
12 TraesCS2D01G017100 chr4D 86.000 200 21 6 27 221 478034720 478034523 1.140000e-49 207.0
13 TraesCS2D01G017100 chr3B 83.772 228 26 10 1 221 371250967 371251190 4.110000e-49 206.0
14 TraesCS2D01G017100 chr3B 81.407 199 32 3 27 221 169927047 169927244 1.170000e-34 158.0
15 TraesCS2D01G017100 chr7D 84.080 201 25 5 27 221 205727564 205727365 1.490000e-43 187.0
16 TraesCS2D01G017100 chr5B 80.269 223 39 5 3 221 507556235 507556456 2.510000e-36 163.0
17 TraesCS2D01G017100 chr2A 93.103 87 6 0 1674 1760 7329098 7329184 9.160000e-26 128.0


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 TraesCS2D01G017100 chr2D 8300440 8303585 3145 False 1531.7 4017 100.000 1 3146 3 chr2D.!!$F1 3145
1 TraesCS2D01G017100 chrUn 170192052 170194216 2164 False 2793.0 2793 90.077 671 2843 1 chrUn.!!$F1 2172

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
192 193 0.031721 GGACAACGACTGTTCTCGGT 59.968 55.0 0.00 0.0 38.84 4.69 F
884 887 0.105408 GCTCCGGCCGTCCTTAAATA 59.895 55.0 26.12 0.0 0.00 1.40 F
1269 1288 0.604780 CATGCAGGGATCCATCGTCC 60.605 60.0 15.23 0.0 34.92 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1362 0.241749 TAGTGCACAACGGTACCTCG 59.758 55.0 21.04 0.0 0.00 4.63 R
1929 1958 0.902516 AGAGGATGGAGCCTATCGCC 60.903 60.0 0.00 0.0 38.73 5.54 R
3105 3142 0.396974 TTGTGCCCCAAGAACAGCTT 60.397 50.0 0.00 0.0 37.29 3.74 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
25 26 2.235546 GCTTTTATAGCGCCGAGGG 58.764 57.895 2.29 0.00 40.71 4.30
26 27 1.228657 GCTTTTATAGCGCCGAGGGG 61.229 60.000 2.29 1.43 40.71 4.79
45 46 4.221422 GGCGAGCGGATGGTAGCA 62.221 66.667 0.00 0.00 44.67 3.49
46 47 2.659897 GCGAGCGGATGGTAGCAG 60.660 66.667 0.00 0.00 42.76 4.24
47 48 2.808315 CGAGCGGATGGTAGCAGT 59.192 61.111 0.00 0.00 35.48 4.40
48 49 1.589993 CGAGCGGATGGTAGCAGTG 60.590 63.158 0.00 0.00 35.48 3.66
49 50 1.517832 GAGCGGATGGTAGCAGTGT 59.482 57.895 0.00 0.00 35.48 3.55
50 51 0.807667 GAGCGGATGGTAGCAGTGTG 60.808 60.000 0.00 0.00 35.48 3.82
51 52 1.815421 GCGGATGGTAGCAGTGTGG 60.815 63.158 0.00 0.00 0.00 4.17
52 53 1.897423 CGGATGGTAGCAGTGTGGA 59.103 57.895 0.00 0.00 0.00 4.02
53 54 0.460284 CGGATGGTAGCAGTGTGGAC 60.460 60.000 0.00 0.00 0.00 4.02
54 55 0.460284 GGATGGTAGCAGTGTGGACG 60.460 60.000 0.00 0.00 0.00 4.79
55 56 1.079127 ATGGTAGCAGTGTGGACGC 60.079 57.895 0.00 0.00 0.00 5.19
56 57 2.809601 GGTAGCAGTGTGGACGCG 60.810 66.667 3.53 3.53 0.00 6.01
57 58 2.049433 GTAGCAGTGTGGACGCGT 60.049 61.111 13.85 13.85 0.00 6.01
58 59 2.049526 TAGCAGTGTGGACGCGTG 60.050 61.111 20.70 0.00 0.00 5.34
59 60 3.567478 TAGCAGTGTGGACGCGTGG 62.567 63.158 20.70 0.00 0.00 4.94
115 116 3.202001 CGCCGCCCGTGAATCAAT 61.202 61.111 0.00 0.00 0.00 2.57
116 117 2.408835 GCCGCCCGTGAATCAATG 59.591 61.111 0.00 0.00 0.00 2.82
117 118 3.110139 CCGCCCGTGAATCAATGG 58.890 61.111 0.00 0.00 0.00 3.16
118 119 1.451207 CCGCCCGTGAATCAATGGA 60.451 57.895 4.53 0.00 0.00 3.41
119 120 1.029408 CCGCCCGTGAATCAATGGAA 61.029 55.000 4.53 0.00 0.00 3.53
120 121 0.378257 CGCCCGTGAATCAATGGAAG 59.622 55.000 4.53 0.00 0.00 3.46
121 122 0.740737 GCCCGTGAATCAATGGAAGG 59.259 55.000 4.53 0.00 0.00 3.46
122 123 0.740737 CCCGTGAATCAATGGAAGGC 59.259 55.000 4.53 0.00 0.00 4.35
123 124 1.683011 CCCGTGAATCAATGGAAGGCT 60.683 52.381 4.53 0.00 0.00 4.58
124 125 1.402968 CCGTGAATCAATGGAAGGCTG 59.597 52.381 0.00 0.00 0.00 4.85
125 126 2.358957 CGTGAATCAATGGAAGGCTGA 58.641 47.619 0.00 0.00 0.00 4.26
126 127 2.096496 CGTGAATCAATGGAAGGCTGAC 59.904 50.000 0.00 0.00 0.00 3.51
127 128 3.350833 GTGAATCAATGGAAGGCTGACT 58.649 45.455 0.00 0.00 0.00 3.41
128 129 3.128242 GTGAATCAATGGAAGGCTGACTG 59.872 47.826 0.00 0.00 0.00 3.51
129 130 2.431954 ATCAATGGAAGGCTGACTGG 57.568 50.000 0.00 0.00 0.00 4.00
130 131 0.322816 TCAATGGAAGGCTGACTGGC 60.323 55.000 0.00 0.00 42.15 4.85
131 132 0.609957 CAATGGAAGGCTGACTGGCA 60.610 55.000 8.60 0.00 44.55 4.92
133 134 2.045536 GGAAGGCTGACTGGCAGG 60.046 66.667 20.34 1.78 45.03 4.85
151 152 3.357504 GCAGCCTTGGCATTGATTC 57.642 52.632 14.54 0.00 0.00 2.52
152 153 0.179092 GCAGCCTTGGCATTGATTCC 60.179 55.000 14.54 0.00 0.00 3.01
153 154 0.462789 CAGCCTTGGCATTGATTCCC 59.537 55.000 14.54 0.00 0.00 3.97
154 155 0.688749 AGCCTTGGCATTGATTCCCC 60.689 55.000 14.54 0.00 0.00 4.81
155 156 1.689243 GCCTTGGCATTGATTCCCCC 61.689 60.000 6.79 0.00 0.00 5.40
156 157 1.394266 CCTTGGCATTGATTCCCCCG 61.394 60.000 0.00 0.00 0.00 5.73
157 158 1.381056 TTGGCATTGATTCCCCCGG 60.381 57.895 0.00 0.00 0.00 5.73
158 159 2.521708 GGCATTGATTCCCCCGGG 60.522 66.667 15.80 15.80 0.00 5.73
159 160 2.600731 GCATTGATTCCCCCGGGA 59.399 61.111 26.32 0.92 43.52 5.14
175 176 2.822215 GGAACCTAGGCGATGAGGA 58.178 57.895 9.30 0.00 36.61 3.71
176 177 0.389757 GGAACCTAGGCGATGAGGAC 59.610 60.000 9.30 0.00 36.61 3.85
177 178 1.112113 GAACCTAGGCGATGAGGACA 58.888 55.000 9.30 0.00 36.61 4.02
178 179 1.480954 GAACCTAGGCGATGAGGACAA 59.519 52.381 9.30 0.00 36.61 3.18
179 180 0.824759 ACCTAGGCGATGAGGACAAC 59.175 55.000 9.30 0.00 36.61 3.32
180 181 0.249073 CCTAGGCGATGAGGACAACG 60.249 60.000 0.00 0.00 43.34 4.10
181 182 0.738975 CTAGGCGATGAGGACAACGA 59.261 55.000 0.00 0.00 43.20 3.85
182 183 3.782042 GGCGATGAGGACAACGAC 58.218 61.111 0.00 0.00 43.20 4.34
183 184 1.215647 GGCGATGAGGACAACGACT 59.784 57.895 0.00 0.00 44.82 4.18
184 185 1.078759 GGCGATGAGGACAACGACTG 61.079 60.000 0.00 0.00 44.82 3.51
185 186 0.388649 GCGATGAGGACAACGACTGT 60.389 55.000 0.00 0.00 43.20 3.55
186 187 1.935300 GCGATGAGGACAACGACTGTT 60.935 52.381 0.00 0.00 43.20 3.16
187 188 1.986378 CGATGAGGACAACGACTGTTC 59.014 52.381 0.00 0.00 43.20 3.18
190 191 3.867723 AGGACAACGACTGTTCTCG 57.132 52.632 0.00 0.00 40.11 4.04
191 192 0.314302 AGGACAACGACTGTTCTCGG 59.686 55.000 0.00 0.00 40.11 4.63
192 193 0.031721 GGACAACGACTGTTCTCGGT 59.968 55.000 0.00 0.00 38.84 4.69
194 195 3.267900 CAACGACTGTTCTCGGTGT 57.732 52.632 0.00 0.00 44.73 4.16
195 196 1.129326 CAACGACTGTTCTCGGTGTC 58.871 55.000 0.00 0.00 44.73 3.67
196 197 4.132426 CGACTGTTCTCGGTGTCG 57.868 61.111 0.00 0.00 44.41 4.35
197 198 2.081212 CGACTGTTCTCGGTGTCGC 61.081 63.158 0.00 0.00 44.00 5.19
198 199 1.733399 GACTGTTCTCGGTGTCGCC 60.733 63.158 0.00 0.00 36.13 5.54
199 200 2.432628 CTGTTCTCGGTGTCGCCC 60.433 66.667 0.00 0.00 36.13 6.13
200 201 3.220999 CTGTTCTCGGTGTCGCCCA 62.221 63.158 0.00 0.00 36.13 5.36
201 202 2.432628 GTTCTCGGTGTCGCCCAG 60.433 66.667 0.00 0.00 36.13 4.45
202 203 2.915659 TTCTCGGTGTCGCCCAGT 60.916 61.111 0.00 0.00 36.13 4.00
203 204 3.220999 TTCTCGGTGTCGCCCAGTG 62.221 63.158 0.00 0.00 36.13 3.66
207 208 4.314440 GGTGTCGCCCAGTGCTGA 62.314 66.667 0.02 0.00 38.05 4.26
208 209 3.044305 GTGTCGCCCAGTGCTGAC 61.044 66.667 0.02 0.00 41.08 3.51
209 210 3.233980 TGTCGCCCAGTGCTGACT 61.234 61.111 0.02 0.00 41.19 3.41
210 211 2.433318 GTCGCCCAGTGCTGACTC 60.433 66.667 0.02 0.00 39.11 3.36
211 212 4.056125 TCGCCCAGTGCTGACTCG 62.056 66.667 0.02 1.83 38.05 4.18
221 222 3.461773 CTGACTCGGCGGGTCCAT 61.462 66.667 34.54 1.42 33.22 3.41
222 223 3.723235 CTGACTCGGCGGGTCCATG 62.723 68.421 34.54 21.23 33.22 3.66
227 228 4.155733 CGGCGGGTCCATGCTGTA 62.156 66.667 0.00 0.00 32.78 2.74
228 229 2.513897 GGCGGGTCCATGCTGTAC 60.514 66.667 5.43 0.00 34.01 2.90
229 230 2.890474 GCGGGTCCATGCTGTACG 60.890 66.667 0.00 0.00 0.00 3.67
230 231 2.889617 CGGGTCCATGCTGTACGA 59.110 61.111 0.00 0.00 0.00 3.43
231 232 1.441729 CGGGTCCATGCTGTACGAT 59.558 57.895 0.00 0.00 0.00 3.73
232 233 0.179084 CGGGTCCATGCTGTACGATT 60.179 55.000 0.00 0.00 0.00 3.34
233 234 1.742411 CGGGTCCATGCTGTACGATTT 60.742 52.381 0.00 0.00 0.00 2.17
234 235 2.365582 GGGTCCATGCTGTACGATTTT 58.634 47.619 0.00 0.00 0.00 1.82
235 236 2.097466 GGGTCCATGCTGTACGATTTTG 59.903 50.000 0.00 0.00 0.00 2.44
236 237 2.747446 GGTCCATGCTGTACGATTTTGT 59.253 45.455 0.00 0.00 0.00 2.83
237 238 3.190535 GGTCCATGCTGTACGATTTTGTT 59.809 43.478 0.00 0.00 0.00 2.83
238 239 4.320935 GGTCCATGCTGTACGATTTTGTTT 60.321 41.667 0.00 0.00 0.00 2.83
239 240 5.219633 GTCCATGCTGTACGATTTTGTTTT 58.780 37.500 0.00 0.00 0.00 2.43
240 241 5.689961 GTCCATGCTGTACGATTTTGTTTTT 59.310 36.000 0.00 0.00 0.00 1.94
241 242 5.689514 TCCATGCTGTACGATTTTGTTTTTG 59.310 36.000 0.00 0.00 0.00 2.44
242 243 5.365133 CATGCTGTACGATTTTGTTTTTGC 58.635 37.500 0.00 0.00 0.00 3.68
243 244 3.799420 TGCTGTACGATTTTGTTTTTGCC 59.201 39.130 0.00 0.00 0.00 4.52
244 245 3.799420 GCTGTACGATTTTGTTTTTGCCA 59.201 39.130 0.00 0.00 0.00 4.92
245 246 4.268884 GCTGTACGATTTTGTTTTTGCCAA 59.731 37.500 0.00 0.00 0.00 4.52
246 247 5.220491 GCTGTACGATTTTGTTTTTGCCAAA 60.220 36.000 0.00 0.00 0.00 3.28
247 248 6.510960 GCTGTACGATTTTGTTTTTGCCAAAT 60.511 34.615 0.00 0.00 32.28 2.32
248 249 7.308782 TGTACGATTTTGTTTTTGCCAAATT 57.691 28.000 0.00 0.00 32.28 1.82
249 250 7.402640 TGTACGATTTTGTTTTTGCCAAATTC 58.597 30.769 0.00 0.00 32.28 2.17
251 252 5.497273 CGATTTTGTTTTTGCCAAATTCGT 58.503 33.333 16.02 0.00 43.50 3.85
252 253 5.962423 CGATTTTGTTTTTGCCAAATTCGTT 59.038 32.000 16.02 0.00 43.50 3.85
253 254 6.467364 CGATTTTGTTTTTGCCAAATTCGTTT 59.533 30.769 16.02 0.00 43.50 3.60
254 255 7.304566 CGATTTTGTTTTTGCCAAATTCGTTTC 60.305 33.333 16.02 0.00 43.50 2.78
255 256 4.866682 TGTTTTTGCCAAATTCGTTTCC 57.133 36.364 0.00 0.00 0.00 3.13
256 257 3.623510 TGTTTTTGCCAAATTCGTTTCCC 59.376 39.130 0.00 0.00 0.00 3.97
257 258 2.535012 TTTGCCAAATTCGTTTCCCC 57.465 45.000 0.00 0.00 0.00 4.81
258 259 0.315568 TTGCCAAATTCGTTTCCCCG 59.684 50.000 0.00 0.00 0.00 5.73
259 260 1.214325 GCCAAATTCGTTTCCCCGG 59.786 57.895 0.00 0.00 0.00 5.73
260 261 1.887301 CCAAATTCGTTTCCCCGGG 59.113 57.895 15.80 15.80 0.00 5.73
261 262 1.214325 CAAATTCGTTTCCCCGGGC 59.786 57.895 17.73 0.00 0.00 6.13
262 263 2.337246 AAATTCGTTTCCCCGGGCG 61.337 57.895 17.73 14.12 0.00 6.13
263 264 4.789123 ATTCGTTTCCCCGGGCGG 62.789 66.667 17.73 1.63 0.00 6.13
754 755 1.758122 CCCAGGTAAAGCCATGGCC 60.758 63.158 33.14 17.44 43.17 5.36
755 756 2.120909 CCAGGTAAAGCCATGGCCG 61.121 63.158 33.14 12.39 43.17 6.13
756 757 2.120909 CAGGTAAAGCCATGGCCGG 61.121 63.158 33.14 14.08 43.17 6.13
779 780 3.121019 GGACTCGATCCGGTCAGG 58.879 66.667 0.00 0.00 37.88 3.86
884 887 0.105408 GCTCCGGCCGTCCTTAAATA 59.895 55.000 26.12 0.00 0.00 1.40
891 894 0.806884 CCGTCCTTAAATACCGCGCA 60.807 55.000 8.75 0.00 0.00 6.09
894 897 1.061566 GTCCTTAAATACCGCGCACAC 59.938 52.381 8.75 0.00 0.00 3.82
928 933 4.421479 CACGTCTCCGGCGAGCTT 62.421 66.667 9.30 0.00 38.78 3.74
929 934 4.117661 ACGTCTCCGGCGAGCTTC 62.118 66.667 9.30 0.00 38.78 3.86
931 936 2.103340 GTCTCCGGCGAGCTTCTC 59.897 66.667 9.30 0.00 35.94 2.87
932 937 2.044848 TCTCCGGCGAGCTTCTCT 60.045 61.111 9.30 0.00 35.94 3.10
933 938 2.103934 CTCCGGCGAGCTTCTCTG 59.896 66.667 9.30 0.00 0.00 3.35
934 939 4.135153 TCCGGCGAGCTTCTCTGC 62.135 66.667 9.30 0.00 32.46 4.26
938 943 2.099431 GGCGAGCTTCTCTGCTGTG 61.099 63.158 0.00 0.00 44.17 3.66
946 951 2.548875 CTTCTCTGCTGTGATAGTGCC 58.451 52.381 0.00 0.00 0.00 5.01
948 953 1.479730 TCTCTGCTGTGATAGTGCCAG 59.520 52.381 0.00 0.00 0.00 4.85
952 957 1.910722 CTGTGATAGTGCCAGGCCT 59.089 57.895 9.64 0.00 0.00 5.19
1092 1111 5.651530 TGTAAGCTTAGTTTGATCTCTCCG 58.348 41.667 6.38 0.00 0.00 4.63
1107 1126 5.932619 TCTCTCCGGTTCATTAATTCAGA 57.067 39.130 0.00 0.00 0.00 3.27
1121 1140 2.010145 TTCAGAGCAACGCTGGTATC 57.990 50.000 0.00 0.00 39.88 2.24
1123 1142 1.134995 TCAGAGCAACGCTGGTATCTG 60.135 52.381 0.00 0.00 39.88 2.90
1124 1143 1.134995 CAGAGCAACGCTGGTATCTGA 60.135 52.381 1.63 0.00 39.88 3.27
1125 1144 1.759445 AGAGCAACGCTGGTATCTGAT 59.241 47.619 0.00 0.00 39.88 2.90
1126 1145 2.959030 AGAGCAACGCTGGTATCTGATA 59.041 45.455 0.00 0.00 39.88 2.15
1127 1146 3.576118 AGAGCAACGCTGGTATCTGATAT 59.424 43.478 0.00 0.00 39.88 1.63
1131 1150 4.988540 GCAACGCTGGTATCTGATATGTAA 59.011 41.667 0.00 0.00 0.00 2.41
1132 1151 5.639506 GCAACGCTGGTATCTGATATGTAAT 59.360 40.000 0.00 0.00 0.00 1.89
1133 1152 6.811665 GCAACGCTGGTATCTGATATGTAATA 59.188 38.462 0.00 0.00 0.00 0.98
1134 1153 7.492669 GCAACGCTGGTATCTGATATGTAATAT 59.507 37.037 0.00 0.00 43.59 1.28
1135 1154 8.811378 CAACGCTGGTATCTGATATGTAATATG 58.189 37.037 0.00 0.00 40.26 1.78
1136 1155 7.492524 ACGCTGGTATCTGATATGTAATATGG 58.507 38.462 0.00 0.00 40.26 2.74
1137 1156 7.342026 ACGCTGGTATCTGATATGTAATATGGA 59.658 37.037 0.00 0.00 40.26 3.41
1138 1157 7.864882 CGCTGGTATCTGATATGTAATATGGAG 59.135 40.741 0.00 0.00 40.26 3.86
1180 1199 9.753674 ACTCCCTTCATAGAGAGATATAAAGAG 57.246 37.037 0.00 0.00 34.13 2.85
1181 1200 8.588290 TCCCTTCATAGAGAGATATAAAGAGC 57.412 38.462 0.00 0.00 0.00 4.09
1183 1202 7.122055 CCCTTCATAGAGAGATATAAAGAGCGT 59.878 40.741 0.00 0.00 0.00 5.07
1184 1203 8.519526 CCTTCATAGAGAGATATAAAGAGCGTT 58.480 37.037 0.00 0.00 0.00 4.84
1185 1204 9.906660 CTTCATAGAGAGATATAAAGAGCGTTT 57.093 33.333 0.00 0.00 0.00 3.60
1191 1210 9.290988 AGAGAGATATAAAGAGCGTTTAGATCA 57.709 33.333 21.34 3.11 37.82 2.92
1192 1211 9.337091 GAGAGATATAAAGAGCGTTTAGATCAC 57.663 37.037 21.34 17.49 37.82 3.06
1199 1218 7.706281 AAAGAGCGTTTAGATCACTATCATG 57.294 36.000 0.00 0.00 37.82 3.07
1200 1219 5.777802 AGAGCGTTTAGATCACTATCATGG 58.222 41.667 0.00 0.00 37.82 3.66
1201 1220 5.536538 AGAGCGTTTAGATCACTATCATGGA 59.463 40.000 0.00 0.00 37.82 3.41
1220 1239 6.820152 TCATGGACAAAGAAGATACACTCATG 59.180 38.462 0.00 0.00 0.00 3.07
1241 1260 2.736400 GCAAGCAATTCTACCATGCACC 60.736 50.000 0.00 0.00 42.45 5.01
1256 1275 3.696281 TGCACCGAATATTTCATGCAG 57.304 42.857 14.10 0.00 42.85 4.41
1264 1283 4.703575 CGAATATTTCATGCAGGGATCCAT 59.296 41.667 15.23 2.55 0.00 3.41
1269 1288 0.604780 CATGCAGGGATCCATCGTCC 60.605 60.000 15.23 0.00 34.92 4.79
1294 1313 2.785681 GCGTGATTTGAGATTCGTGCTG 60.786 50.000 0.00 0.00 0.00 4.41
1319 1338 3.408288 TTTTCAGGTTTGGACGTTTCG 57.592 42.857 0.00 0.00 0.00 3.46
1350 1369 8.193250 TCTATCAAAATGTTTTAGCGAGGTAC 57.807 34.615 0.00 0.00 0.00 3.34
1360 1379 2.664436 GCGAGGTACCGTTGTGCAC 61.664 63.158 10.75 10.75 0.00 4.57
1368 1387 4.706476 AGGTACCGTTGTGCACTAGTAATA 59.294 41.667 19.41 0.95 0.00 0.98
1405 1424 8.818057 CAAGTGCACTCTTATTTATAGGTACAC 58.182 37.037 21.95 0.00 0.00 2.90
1423 1443 5.287035 GGTACACACGAAATCTTAAGGTACG 59.713 44.000 11.82 11.82 31.75 3.67
1425 1445 3.061697 CACACGAAATCTTAAGGTACGCC 59.938 47.826 12.89 0.00 0.00 5.68
1438 1458 4.838904 AGGTACGCCTTAGGAAAAGATT 57.161 40.909 0.69 0.00 44.18 2.40
1441 1461 6.008331 AGGTACGCCTTAGGAAAAGATTTTT 58.992 36.000 0.69 0.00 44.18 1.94
1472 1494 5.567138 AGCAAAACATTATGTAGCACTCC 57.433 39.130 15.82 0.00 0.00 3.85
1477 1499 5.796350 AACATTATGTAGCACTCCGAAAC 57.204 39.130 0.00 0.00 0.00 2.78
1486 1508 3.013921 AGCACTCCGAAACAAGACAAAA 58.986 40.909 0.00 0.00 0.00 2.44
1487 1509 3.632145 AGCACTCCGAAACAAGACAAAAT 59.368 39.130 0.00 0.00 0.00 1.82
1488 1510 4.819630 AGCACTCCGAAACAAGACAAAATA 59.180 37.500 0.00 0.00 0.00 1.40
1490 1512 6.016276 AGCACTCCGAAACAAGACAAAATATT 60.016 34.615 0.00 0.00 0.00 1.28
1492 1514 6.582295 CACTCCGAAACAAGACAAAATATTGG 59.418 38.462 0.00 0.00 41.01 3.16
1521 1543 9.986833 AAAACAAAACAAAAGCATAAATCTCAC 57.013 25.926 0.00 0.00 0.00 3.51
1529 1551 1.596464 GCATAAATCTCACAGCAGCGC 60.596 52.381 0.00 0.00 0.00 5.92
1540 1562 2.510238 GCAGCGCTGGACTGTAGG 60.510 66.667 36.47 10.44 37.47 3.18
1542 1564 3.775654 AGCGCTGGACTGTAGGCC 61.776 66.667 10.39 0.00 0.00 5.19
1550 1572 0.882042 GGACTGTAGGCCGATGCATG 60.882 60.000 2.46 0.00 40.13 4.06
1579 1605 3.573967 CCCTTGCACAGTAGAAAAACCAT 59.426 43.478 0.00 0.00 0.00 3.55
1584 1610 2.095263 CACAGTAGAAAAACCATGCCCG 60.095 50.000 0.00 0.00 0.00 6.13
1585 1611 2.224670 ACAGTAGAAAAACCATGCCCGA 60.225 45.455 0.00 0.00 0.00 5.14
1654 1683 7.454260 AAGATAAGTGGGCTTCTTTTAACAG 57.546 36.000 0.92 0.00 36.22 3.16
1656 1685 3.229697 AGTGGGCTTCTTTTAACAGCT 57.770 42.857 0.00 0.00 33.76 4.24
1683 1712 0.806868 CATGTGCAACCTACAGGCTG 59.193 55.000 14.16 14.16 39.32 4.85
1717 1746 2.264480 CCGTGCATCACCTTCGGA 59.736 61.111 3.74 0.00 43.22 4.55
1860 1889 8.131100 GTGTCCGTATCAATGAATGAATGAATT 58.869 33.333 0.00 0.00 42.54 2.17
1876 1905 8.027524 TGAATGAATTCTACTATTGCTCTCCT 57.972 34.615 7.05 0.00 37.67 3.69
1905 1934 2.202932 GCGAGTGGGACGATGCAT 60.203 61.111 0.00 0.00 0.00 3.96
1929 1958 4.760047 CAGGGCTTGGGGACGTCG 62.760 72.222 9.92 0.00 0.00 5.12
1960 1989 0.529337 CATCCTCTACCACTGCTGCG 60.529 60.000 0.00 0.00 0.00 5.18
1962 1991 0.684479 TCCTCTACCACTGCTGCGAT 60.684 55.000 0.00 0.00 0.00 4.58
1965 1994 1.139734 CTACCACTGCTGCGATCGT 59.860 57.895 17.81 0.00 0.00 3.73
2070 2103 0.318275 GGAGTATCGCGAGCTCAAGG 60.318 60.000 30.95 1.70 34.37 3.61
2081 2114 2.358737 CTCAAGGGTCGCGGCTTT 60.359 61.111 11.94 2.45 0.00 3.51
2129 2162 0.719015 TGGAGAGGATGGGGAAGACT 59.281 55.000 0.00 0.00 0.00 3.24
2236 2271 0.240145 TGTCAACGTCCAGCTACTCG 59.760 55.000 0.00 0.00 0.00 4.18
2238 2273 0.956633 TCAACGTCCAGCTACTCGTT 59.043 50.000 13.48 13.48 45.16 3.85
2299 2334 2.754552 AGCTGTTGCAAGTTGTTCTTCA 59.245 40.909 0.00 0.00 42.74 3.02
2324 2359 0.401738 CCAGTCACTTCCCACCATGT 59.598 55.000 0.00 0.00 0.00 3.21
2350 2385 6.974622 GTCAAATCTATGTGCAACCAATAAGG 59.025 38.462 0.00 0.00 45.67 2.69
2352 2387 3.961849 TCTATGTGCAACCAATAAGGCA 58.038 40.909 0.00 0.00 43.14 4.75
2384 2419 9.645059 TCATATCTTTGTGTAGAAGAAACAGAG 57.355 33.333 0.00 0.00 36.77 3.35
2392 2427 1.157585 GAAGAAACAGAGGTTCGCCC 58.842 55.000 0.00 0.00 35.82 6.13
2394 2429 2.032071 AAACAGAGGTTCGCCCCG 59.968 61.111 0.00 0.00 35.82 5.73
2445 2480 6.936279 TGTAATATCTATGGCAGCTACCTTC 58.064 40.000 4.19 0.00 0.00 3.46
2458 2493 6.393171 GCAGCTACCTTCAATCTTCAAAAAT 58.607 36.000 0.00 0.00 0.00 1.82
2461 2496 8.706035 CAGCTACCTTCAATCTTCAAAAATTTG 58.294 33.333 0.00 0.00 39.48 2.32
2468 2503 8.436046 TTCAATCTTCAAAAATTTGTTGAGGG 57.564 30.769 10.54 5.28 39.18 4.30
2489 2524 5.921962 GGAACCTTAAATCTCCAAATGCT 57.078 39.130 0.00 0.00 0.00 3.79
2491 2526 7.588497 GGAACCTTAAATCTCCAAATGCTAT 57.412 36.000 0.00 0.00 0.00 2.97
2492 2527 8.011844 GGAACCTTAAATCTCCAAATGCTATT 57.988 34.615 0.00 0.00 0.00 1.73
2511 2546 6.126911 TGCTATTAATGGATGTAGTGACCACA 60.127 38.462 2.52 0.00 36.49 4.17
2528 2563 2.605818 CCACACGTATTTGTATGGGTCG 59.394 50.000 0.00 0.00 0.00 4.79
2549 2584 5.914635 GTCGCATGGTTTGGACATTTATATG 59.085 40.000 0.00 0.00 37.79 1.78
2552 2587 6.572519 GCATGGTTTGGACATTTATATGTGT 58.427 36.000 3.33 0.00 44.90 3.72
2619 2655 3.093057 CGGGATCCCAAAACAAACCATA 58.907 45.455 30.42 0.00 35.37 2.74
2645 2681 2.687935 ACAACGTCAAATTGCAGAGGTT 59.312 40.909 6.07 6.07 41.79 3.50
2671 2707 8.322828 TGCTACATGGGTTAAAATAGTCTTGTA 58.677 33.333 0.00 0.00 0.00 2.41
2708 2744 7.308782 ACCAGCTAAGTGAATTAATTTCTCG 57.691 36.000 1.43 2.08 35.23 4.04
2709 2745 6.879458 ACCAGCTAAGTGAATTAATTTCTCGT 59.121 34.615 1.43 0.00 35.23 4.18
2718 2754 9.831737 AGTGAATTAATTTCTCGTGAAAAGATG 57.168 29.630 15.80 0.00 44.22 2.90
2760 2796 5.484173 TGTCCTTGCGCATTTATTAAGAG 57.516 39.130 12.75 1.12 0.00 2.85
2770 2806 7.436970 TGCGCATTTATTAAGAGATCTCGTAAA 59.563 33.333 27.48 22.58 37.17 2.01
2771 2807 7.736448 GCGCATTTATTAAGAGATCTCGTAAAC 59.264 37.037 27.48 15.20 37.17 2.01
3121 3158 4.179361 CAAGCTGTTCTTGGGGCA 57.821 55.556 0.00 0.00 46.50 5.36
3122 3159 1.662044 CAAGCTGTTCTTGGGGCAC 59.338 57.895 0.00 0.00 46.50 5.01
3123 3160 1.108727 CAAGCTGTTCTTGGGGCACA 61.109 55.000 0.00 0.00 46.50 4.57
3124 3161 0.396974 AAGCTGTTCTTGGGGCACAA 60.397 50.000 0.51 0.51 37.55 3.33
3125 3162 1.109323 AGCTGTTCTTGGGGCACAAC 61.109 55.000 0.00 0.00 34.76 3.32
3126 3163 1.109323 GCTGTTCTTGGGGCACAACT 61.109 55.000 0.00 0.00 34.76 3.16
3127 3164 1.402787 CTGTTCTTGGGGCACAACTT 58.597 50.000 0.00 0.00 34.76 2.66
3128 3165 1.067516 CTGTTCTTGGGGCACAACTTG 59.932 52.381 0.00 0.00 34.76 3.16
3129 3166 1.341482 TGTTCTTGGGGCACAACTTGA 60.341 47.619 0.00 0.00 34.76 3.02
3130 3167 1.067060 GTTCTTGGGGCACAACTTGAC 59.933 52.381 0.00 0.00 34.76 3.18
3135 3172 4.579127 GGCACAACTTGACCACCT 57.421 55.556 0.00 0.00 0.00 4.00
3136 3173 2.807247 GGCACAACTTGACCACCTT 58.193 52.632 0.00 0.00 0.00 3.50
3137 3174 0.668535 GGCACAACTTGACCACCTTC 59.331 55.000 0.00 0.00 0.00 3.46
3138 3175 0.668535 GCACAACTTGACCACCTTCC 59.331 55.000 0.00 0.00 0.00 3.46
3139 3176 0.944386 CACAACTTGACCACCTTCCG 59.056 55.000 0.00 0.00 0.00 4.30
3140 3177 0.179029 ACAACTTGACCACCTTCCGG 60.179 55.000 0.00 0.00 0.00 5.14
3141 3178 0.107831 CAACTTGACCACCTTCCGGA 59.892 55.000 0.00 0.00 0.00 5.14
3142 3179 0.841289 AACTTGACCACCTTCCGGAA 59.159 50.000 17.73 17.73 0.00 4.30
3143 3180 0.841289 ACTTGACCACCTTCCGGAAA 59.159 50.000 19.39 0.00 0.00 3.13
3144 3181 1.202770 ACTTGACCACCTTCCGGAAAG 60.203 52.381 19.39 15.27 34.52 2.62
3145 3182 1.071699 CTTGACCACCTTCCGGAAAGA 59.928 52.381 19.71 0.00 37.12 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.914379 CCCCTCGGCGCTATAAAAG 58.086 57.895 7.64 0.00 0.00 2.27
28 29 4.221422 TGCTACCATCCGCTCGCC 62.221 66.667 0.00 0.00 0.00 5.54
29 30 2.659897 CTGCTACCATCCGCTCGC 60.660 66.667 0.00 0.00 0.00 5.03
30 31 1.589993 CACTGCTACCATCCGCTCG 60.590 63.158 0.00 0.00 0.00 5.03
31 32 0.807667 CACACTGCTACCATCCGCTC 60.808 60.000 0.00 0.00 0.00 5.03
32 33 1.219124 CACACTGCTACCATCCGCT 59.781 57.895 0.00 0.00 0.00 5.52
33 34 1.815421 CCACACTGCTACCATCCGC 60.815 63.158 0.00 0.00 0.00 5.54
34 35 0.460284 GTCCACACTGCTACCATCCG 60.460 60.000 0.00 0.00 0.00 4.18
35 36 0.460284 CGTCCACACTGCTACCATCC 60.460 60.000 0.00 0.00 0.00 3.51
36 37 1.084370 GCGTCCACACTGCTACCATC 61.084 60.000 0.00 0.00 0.00 3.51
37 38 1.079127 GCGTCCACACTGCTACCAT 60.079 57.895 0.00 0.00 0.00 3.55
38 39 2.342279 GCGTCCACACTGCTACCA 59.658 61.111 0.00 0.00 0.00 3.25
39 40 2.809601 CGCGTCCACACTGCTACC 60.810 66.667 0.00 0.00 0.00 3.18
40 41 2.049433 ACGCGTCCACACTGCTAC 60.049 61.111 5.58 0.00 0.00 3.58
41 42 2.049526 CACGCGTCCACACTGCTA 60.050 61.111 9.86 0.00 0.00 3.49
42 43 4.969196 CCACGCGTCCACACTGCT 62.969 66.667 9.86 0.00 0.00 4.24
98 99 3.202001 ATTGATTCACGGGCGGCG 61.202 61.111 0.51 0.51 0.00 6.46
99 100 2.408835 CATTGATTCACGGGCGGC 59.591 61.111 0.00 0.00 0.00 6.53
100 101 1.029408 TTCCATTGATTCACGGGCGG 61.029 55.000 2.29 0.00 0.00 6.13
101 102 0.378257 CTTCCATTGATTCACGGGCG 59.622 55.000 2.29 0.00 0.00 6.13
102 103 0.740737 CCTTCCATTGATTCACGGGC 59.259 55.000 2.29 0.00 0.00 6.13
103 104 0.740737 GCCTTCCATTGATTCACGGG 59.259 55.000 2.29 0.01 0.00 5.28
104 105 1.402968 CAGCCTTCCATTGATTCACGG 59.597 52.381 0.00 0.00 0.00 4.94
105 106 2.096496 GTCAGCCTTCCATTGATTCACG 59.904 50.000 0.00 0.00 0.00 4.35
106 107 3.128242 CAGTCAGCCTTCCATTGATTCAC 59.872 47.826 0.00 0.00 0.00 3.18
107 108 3.349927 CAGTCAGCCTTCCATTGATTCA 58.650 45.455 0.00 0.00 0.00 2.57
108 109 2.686915 CCAGTCAGCCTTCCATTGATTC 59.313 50.000 0.00 0.00 0.00 2.52
109 110 2.731572 CCAGTCAGCCTTCCATTGATT 58.268 47.619 0.00 0.00 0.00 2.57
110 111 1.684248 GCCAGTCAGCCTTCCATTGAT 60.684 52.381 0.00 0.00 0.00 2.57
111 112 0.322816 GCCAGTCAGCCTTCCATTGA 60.323 55.000 0.00 0.00 0.00 2.57
112 113 0.609957 TGCCAGTCAGCCTTCCATTG 60.610 55.000 0.00 0.00 0.00 2.82
113 114 0.323178 CTGCCAGTCAGCCTTCCATT 60.323 55.000 0.00 0.00 35.78 3.16
114 115 1.302285 CTGCCAGTCAGCCTTCCAT 59.698 57.895 0.00 0.00 35.78 3.41
115 116 2.752358 CTGCCAGTCAGCCTTCCA 59.248 61.111 0.00 0.00 35.78 3.53
116 117 2.045536 CCTGCCAGTCAGCCTTCC 60.046 66.667 0.00 0.00 41.50 3.46
117 118 2.749441 GCCTGCCAGTCAGCCTTC 60.749 66.667 0.00 0.00 41.50 3.46
118 119 3.564345 CTGCCTGCCAGTCAGCCTT 62.564 63.158 0.00 0.00 41.50 4.35
119 120 4.031129 CTGCCTGCCAGTCAGCCT 62.031 66.667 0.00 0.00 41.50 4.58
129 130 3.387947 AATGCCAAGGCTGCCTGC 61.388 61.111 24.16 22.12 42.51 4.85
130 131 1.327690 ATCAATGCCAAGGCTGCCTG 61.328 55.000 24.16 15.76 42.51 4.85
131 132 0.616679 AATCAATGCCAAGGCTGCCT 60.617 50.000 17.22 17.22 42.51 4.75
132 133 0.179092 GAATCAATGCCAAGGCTGCC 60.179 55.000 11.65 11.65 42.51 4.85
133 134 0.179092 GGAATCAATGCCAAGGCTGC 60.179 55.000 12.96 0.00 42.51 5.25
134 135 0.462789 GGGAATCAATGCCAAGGCTG 59.537 55.000 12.96 3.28 39.85 4.85
135 136 0.688749 GGGGAATCAATGCCAAGGCT 60.689 55.000 12.96 0.00 42.44 4.58
136 137 1.689243 GGGGGAATCAATGCCAAGGC 61.689 60.000 3.61 3.61 42.44 4.35
137 138 1.394266 CGGGGGAATCAATGCCAAGG 61.394 60.000 0.00 0.00 42.44 3.61
138 139 1.394266 CCGGGGGAATCAATGCCAAG 61.394 60.000 0.00 0.00 42.44 3.61
139 140 1.381056 CCGGGGGAATCAATGCCAA 60.381 57.895 0.00 0.00 42.44 4.52
140 141 2.278404 CCGGGGGAATCAATGCCA 59.722 61.111 0.00 0.00 42.44 4.92
141 142 2.521708 CCCGGGGGAATCAATGCC 60.522 66.667 14.71 0.00 39.22 4.40
142 143 2.600731 TCCCGGGGGAATCAATGC 59.399 61.111 23.50 0.00 42.05 3.56
150 151 4.810184 GCCTAGGTTCCCGGGGGA 62.810 72.222 23.50 7.08 43.52 4.81
153 154 2.842936 ATCGCCTAGGTTCCCGGG 60.843 66.667 16.85 16.85 0.00 5.73
154 155 2.088674 CTCATCGCCTAGGTTCCCGG 62.089 65.000 11.31 0.00 0.00 5.73
155 156 1.364171 CTCATCGCCTAGGTTCCCG 59.636 63.158 11.31 5.35 0.00 5.14
156 157 0.759436 TCCTCATCGCCTAGGTTCCC 60.759 60.000 11.31 0.00 34.30 3.97
157 158 0.389757 GTCCTCATCGCCTAGGTTCC 59.610 60.000 11.31 0.00 34.30 3.62
158 159 1.112113 TGTCCTCATCGCCTAGGTTC 58.888 55.000 11.31 0.00 34.30 3.62
159 160 1.207329 GTTGTCCTCATCGCCTAGGTT 59.793 52.381 11.31 0.00 34.30 3.50
160 161 0.824759 GTTGTCCTCATCGCCTAGGT 59.175 55.000 11.31 0.00 34.30 3.08
161 162 0.249073 CGTTGTCCTCATCGCCTAGG 60.249 60.000 3.67 3.67 31.64 3.02
162 163 0.738975 TCGTTGTCCTCATCGCCTAG 59.261 55.000 0.00 0.00 36.90 3.02
163 164 0.454600 GTCGTTGTCCTCATCGCCTA 59.545 55.000 0.00 0.00 36.90 3.93
164 165 1.215647 GTCGTTGTCCTCATCGCCT 59.784 57.895 0.00 0.00 36.90 5.52
165 166 1.078759 CAGTCGTTGTCCTCATCGCC 61.079 60.000 0.00 0.00 36.90 5.54
166 167 0.388649 ACAGTCGTTGTCCTCATCGC 60.389 55.000 0.00 0.00 33.87 4.58
167 168 1.986378 GAACAGTCGTTGTCCTCATCG 59.014 52.381 0.00 0.00 39.73 3.84
168 169 3.246619 GAGAACAGTCGTTGTCCTCATC 58.753 50.000 4.71 0.00 39.03 2.92
169 170 2.351835 CGAGAACAGTCGTTGTCCTCAT 60.352 50.000 8.98 0.00 41.26 2.90
170 171 1.001706 CGAGAACAGTCGTTGTCCTCA 60.002 52.381 8.98 0.00 41.26 3.86
171 172 1.666311 CCGAGAACAGTCGTTGTCCTC 60.666 57.143 0.45 0.45 41.26 3.71
172 173 0.314302 CCGAGAACAGTCGTTGTCCT 59.686 55.000 0.00 0.00 41.26 3.85
173 174 0.031721 ACCGAGAACAGTCGTTGTCC 59.968 55.000 0.00 0.00 41.26 4.02
174 175 1.129326 CACCGAGAACAGTCGTTGTC 58.871 55.000 0.00 0.00 39.73 3.18
175 176 0.458669 ACACCGAGAACAGTCGTTGT 59.541 50.000 0.00 0.00 40.33 3.32
176 177 1.129326 GACACCGAGAACAGTCGTTG 58.871 55.000 0.00 0.00 38.25 4.10
177 178 0.317603 CGACACCGAGAACAGTCGTT 60.318 55.000 0.00 0.00 46.17 3.85
178 179 1.281960 CGACACCGAGAACAGTCGT 59.718 57.895 0.00 0.00 46.17 4.34
179 180 4.132426 CGACACCGAGAACAGTCG 57.868 61.111 0.00 0.00 46.12 4.18
180 181 1.733399 GGCGACACCGAGAACAGTC 60.733 63.158 0.00 0.00 38.22 3.51
181 182 2.338984 GGCGACACCGAGAACAGT 59.661 61.111 0.00 0.00 38.22 3.55
182 183 2.432628 GGGCGACACCGAGAACAG 60.433 66.667 0.00 0.00 40.62 3.16
183 184 3.220999 CTGGGCGACACCGAGAACA 62.221 63.158 0.00 0.00 46.90 3.18
184 185 2.432628 CTGGGCGACACCGAGAAC 60.433 66.667 0.00 0.00 46.90 3.01
185 186 2.915659 ACTGGGCGACACCGAGAA 60.916 61.111 0.00 0.00 46.90 2.87
186 187 3.680786 CACTGGGCGACACCGAGA 61.681 66.667 0.00 0.00 46.90 4.04
204 205 3.461773 ATGGACCCGCCGAGTCAG 61.462 66.667 0.14 0.00 40.66 3.51
205 206 3.770040 CATGGACCCGCCGAGTCA 61.770 66.667 0.14 0.00 40.66 3.41
210 211 4.155733 TACAGCATGGACCCGCCG 62.156 66.667 0.00 0.00 43.62 6.46
211 212 2.513897 GTACAGCATGGACCCGCC 60.514 66.667 0.00 0.00 46.98 6.13
217 218 5.446143 AAAACAAAATCGTACAGCATGGA 57.554 34.783 0.00 0.00 43.62 3.41
218 219 5.612276 GCAAAAACAAAATCGTACAGCATGG 60.612 40.000 0.00 0.00 43.62 3.66
219 220 5.365133 GCAAAAACAAAATCGTACAGCATG 58.635 37.500 0.00 0.00 46.00 4.06
220 221 4.447389 GGCAAAAACAAAATCGTACAGCAT 59.553 37.500 0.00 0.00 0.00 3.79
221 222 3.799420 GGCAAAAACAAAATCGTACAGCA 59.201 39.130 0.00 0.00 0.00 4.41
222 223 3.799420 TGGCAAAAACAAAATCGTACAGC 59.201 39.130 0.00 0.00 0.00 4.40
223 224 5.957910 TTGGCAAAAACAAAATCGTACAG 57.042 34.783 0.00 0.00 0.00 2.74
224 225 6.910536 ATTTGGCAAAAACAAAATCGTACA 57.089 29.167 17.70 0.00 40.74 2.90
225 226 7.814972 GAATTTGGCAAAAACAAAATCGTAC 57.185 32.000 17.70 0.00 40.74 3.67
229 230 7.044380 GGAAACGAATTTGGCAAAAACAAAATC 60.044 33.333 17.70 9.91 40.74 2.17
230 231 6.749578 GGAAACGAATTTGGCAAAAACAAAAT 59.250 30.769 17.70 1.10 40.74 1.82
231 232 6.086871 GGAAACGAATTTGGCAAAAACAAAA 58.913 32.000 17.70 0.00 40.74 2.44
232 233 5.392057 GGGAAACGAATTTGGCAAAAACAAA 60.392 36.000 17.70 0.00 41.50 2.83
233 234 4.095036 GGGAAACGAATTTGGCAAAAACAA 59.905 37.500 17.70 0.00 0.00 2.83
234 235 3.623510 GGGAAACGAATTTGGCAAAAACA 59.376 39.130 17.70 0.00 0.00 2.83
235 236 3.002862 GGGGAAACGAATTTGGCAAAAAC 59.997 43.478 17.70 12.42 0.00 2.43
236 237 3.206964 GGGGAAACGAATTTGGCAAAAA 58.793 40.909 17.70 0.00 0.00 1.94
237 238 2.803492 CGGGGAAACGAATTTGGCAAAA 60.803 45.455 17.70 0.44 35.47 2.44
238 239 1.269831 CGGGGAAACGAATTTGGCAAA 60.270 47.619 16.01 16.01 35.47 3.68
239 240 0.315568 CGGGGAAACGAATTTGGCAA 59.684 50.000 0.00 0.00 35.47 4.52
240 241 1.528292 CCGGGGAAACGAATTTGGCA 61.528 55.000 0.00 0.00 35.47 4.92
241 242 1.214325 CCGGGGAAACGAATTTGGC 59.786 57.895 0.00 0.00 35.47 4.52
242 243 1.887301 CCCGGGGAAACGAATTTGG 59.113 57.895 14.71 0.00 35.47 3.28
243 244 1.214325 GCCCGGGGAAACGAATTTG 59.786 57.895 25.28 0.00 35.47 2.32
244 245 2.337246 CGCCCGGGGAAACGAATTT 61.337 57.895 25.28 0.00 35.47 1.82
245 246 2.748647 CGCCCGGGGAAACGAATT 60.749 61.111 25.28 0.00 35.47 2.17
246 247 4.789123 CCGCCCGGGGAAACGAAT 62.789 66.667 25.28 0.00 35.47 3.34
668 669 3.625764 TCCTTCTCGCCGGAAAATATTTG 59.374 43.478 5.05 0.00 0.00 2.32
669 670 3.877508 CTCCTTCTCGCCGGAAAATATTT 59.122 43.478 5.05 0.00 0.00 1.40
670 671 3.134081 TCTCCTTCTCGCCGGAAAATATT 59.866 43.478 5.05 0.00 0.00 1.28
671 672 2.698797 TCTCCTTCTCGCCGGAAAATAT 59.301 45.455 5.05 0.00 0.00 1.28
672 673 2.104967 TCTCCTTCTCGCCGGAAAATA 58.895 47.619 5.05 0.00 0.00 1.40
673 674 0.902531 TCTCCTTCTCGCCGGAAAAT 59.097 50.000 5.05 0.00 0.00 1.82
686 687 4.099170 CGCCGTCGACGTCTCCTT 62.099 66.667 33.49 0.00 38.10 3.36
719 720 2.047560 GGTGACCCCACGCACTAC 60.048 66.667 0.00 0.00 44.09 2.73
737 738 2.120909 CGGCCATGGCTTTACCTGG 61.121 63.158 34.70 11.13 41.60 4.45
762 763 1.448922 CTCCTGACCGGATCGAGTCC 61.449 65.000 9.46 0.00 42.12 3.85
765 766 2.851071 GCCTCCTGACCGGATCGAG 61.851 68.421 9.46 7.04 42.12 4.04
766 767 2.833582 GCCTCCTGACCGGATCGA 60.834 66.667 9.46 0.00 42.12 3.59
767 768 4.271816 CGCCTCCTGACCGGATCG 62.272 72.222 9.46 0.00 42.12 3.69
768 769 2.833582 TCGCCTCCTGACCGGATC 60.834 66.667 9.46 2.18 42.12 3.36
769 770 3.148279 GTCGCCTCCTGACCGGAT 61.148 66.667 9.46 0.00 42.12 4.18
770 771 4.671590 TGTCGCCTCCTGACCGGA 62.672 66.667 9.46 0.00 40.30 5.14
771 772 4.135153 CTGTCGCCTCCTGACCGG 62.135 72.222 0.00 0.00 35.46 5.28
772 773 4.803426 GCTGTCGCCTCCTGACCG 62.803 72.222 0.00 0.00 35.46 4.79
773 774 4.803426 CGCTGTCGCCTCCTGACC 62.803 72.222 0.00 0.00 35.46 4.02
797 798 2.416260 CGGGCTAACGTCCTAGGC 59.584 66.667 2.96 11.36 42.32 3.93
869 872 1.493134 GCGGTATTTAAGGACGGCCG 61.493 60.000 26.86 26.86 39.96 6.13
928 933 1.479730 CTGGCACTATCACAGCAGAGA 59.520 52.381 0.00 0.00 0.00 3.10
929 934 1.472904 CCTGGCACTATCACAGCAGAG 60.473 57.143 0.00 0.00 0.00 3.35
931 936 1.094073 GCCTGGCACTATCACAGCAG 61.094 60.000 15.17 0.00 0.00 4.24
932 937 1.078214 GCCTGGCACTATCACAGCA 60.078 57.895 15.17 0.00 0.00 4.41
933 938 1.821332 GGCCTGGCACTATCACAGC 60.821 63.158 22.05 0.00 0.00 4.40
934 939 0.463295 CAGGCCTGGCACTATCACAG 60.463 60.000 26.14 0.00 0.00 3.66
938 943 0.462759 GTCACAGGCCTGGCACTATC 60.463 60.000 35.42 14.66 34.19 2.08
971 990 4.681978 GGCAGACGGTCGCCTTGT 62.682 66.667 25.95 0.00 45.29 3.16
982 1001 4.754667 GGGAACGTCGGGGCAGAC 62.755 72.222 0.00 2.74 37.76 3.51
1092 1111 4.098416 GCGTTGCTCTGAATTAATGAACC 58.902 43.478 0.00 0.00 0.00 3.62
1107 1126 3.070159 ACATATCAGATACCAGCGTTGCT 59.930 43.478 0.00 0.00 40.77 3.91
1137 1156 9.263446 TGAAGGGAGTACTTATTATGTTGTACT 57.737 33.333 0.00 0.00 45.39 2.73
1166 1185 9.337091 GTGATCTAAACGCTCTTTATATCTCTC 57.663 37.037 0.00 0.00 0.00 3.20
1177 1196 5.536538 TCCATGATAGTGATCTAAACGCTCT 59.463 40.000 0.00 0.00 32.79 4.09
1178 1197 5.631512 GTCCATGATAGTGATCTAAACGCTC 59.368 44.000 0.00 0.00 32.79 5.03
1179 1198 5.069119 TGTCCATGATAGTGATCTAAACGCT 59.931 40.000 0.00 0.00 32.79 5.07
1180 1199 5.289595 TGTCCATGATAGTGATCTAAACGC 58.710 41.667 0.00 0.00 32.79 4.84
1181 1200 7.706607 TCTTTGTCCATGATAGTGATCTAAACG 59.293 37.037 0.00 0.00 32.79 3.60
1183 1202 9.605275 CTTCTTTGTCCATGATAGTGATCTAAA 57.395 33.333 0.00 0.00 32.79 1.85
1184 1203 8.981659 TCTTCTTTGTCCATGATAGTGATCTAA 58.018 33.333 0.00 0.00 32.79 2.10
1185 1204 8.539117 TCTTCTTTGTCCATGATAGTGATCTA 57.461 34.615 0.00 0.00 32.79 1.98
1186 1205 7.429374 TCTTCTTTGTCCATGATAGTGATCT 57.571 36.000 0.00 0.00 32.79 2.75
1187 1206 9.202273 GTATCTTCTTTGTCCATGATAGTGATC 57.798 37.037 0.00 0.00 0.00 2.92
1188 1207 8.708378 TGTATCTTCTTTGTCCATGATAGTGAT 58.292 33.333 0.00 0.00 0.00 3.06
1189 1208 7.981789 GTGTATCTTCTTTGTCCATGATAGTGA 59.018 37.037 0.00 0.00 0.00 3.41
1190 1209 7.984050 AGTGTATCTTCTTTGTCCATGATAGTG 59.016 37.037 0.00 0.00 0.00 2.74
1191 1210 8.083828 AGTGTATCTTCTTTGTCCATGATAGT 57.916 34.615 0.00 0.00 0.00 2.12
1192 1211 8.200120 TGAGTGTATCTTCTTTGTCCATGATAG 58.800 37.037 0.00 0.00 0.00 2.08
1194 1213 6.950842 TGAGTGTATCTTCTTTGTCCATGAT 58.049 36.000 0.00 0.00 0.00 2.45
1195 1214 6.358974 TGAGTGTATCTTCTTTGTCCATGA 57.641 37.500 0.00 0.00 0.00 3.07
1196 1215 6.457934 GCATGAGTGTATCTTCTTTGTCCATG 60.458 42.308 0.00 0.00 0.00 3.66
1197 1216 5.587844 GCATGAGTGTATCTTCTTTGTCCAT 59.412 40.000 0.00 0.00 0.00 3.41
1198 1217 4.937620 GCATGAGTGTATCTTCTTTGTCCA 59.062 41.667 0.00 0.00 0.00 4.02
1199 1218 4.937620 TGCATGAGTGTATCTTCTTTGTCC 59.062 41.667 0.00 0.00 0.00 4.02
1200 1219 6.486253 TTGCATGAGTGTATCTTCTTTGTC 57.514 37.500 0.00 0.00 0.00 3.18
1201 1220 5.106396 GCTTGCATGAGTGTATCTTCTTTGT 60.106 40.000 3.33 0.00 0.00 2.83
1220 1239 2.533266 GTGCATGGTAGAATTGCTTGC 58.467 47.619 0.00 0.00 37.28 4.01
1241 1260 4.074259 TGGATCCCTGCATGAAATATTCG 58.926 43.478 9.90 0.00 0.00 3.34
1269 1288 1.267038 CGAATCTCAAATCACGCGGTG 60.267 52.381 12.47 6.71 34.45 4.94
1343 1362 0.241749 TAGTGCACAACGGTACCTCG 59.758 55.000 21.04 0.00 0.00 4.63
1346 1365 3.302365 TTACTAGTGCACAACGGTACC 57.698 47.619 21.04 0.16 0.00 3.34
1350 1369 9.687210 TTAGATTATATTACTAGTGCACAACGG 57.313 33.333 21.04 8.13 0.00 4.44
1382 1401 7.043590 CGTGTGTACCTATAAATAAGAGTGCAC 60.044 40.741 9.40 9.40 40.04 4.57
1383 1402 6.976349 CGTGTGTACCTATAAATAAGAGTGCA 59.024 38.462 0.00 0.00 0.00 4.57
1384 1403 7.198390 TCGTGTGTACCTATAAATAAGAGTGC 58.802 38.462 0.00 0.00 0.00 4.40
1398 1417 5.479124 ACCTTAAGATTTCGTGTGTACCT 57.521 39.130 3.36 0.00 0.00 3.08
1405 1424 3.920112 GGCGTACCTTAAGATTTCGTG 57.080 47.619 3.36 0.00 0.00 4.35
1443 1463 6.481313 TGCTACATAATGTTTTGCTTGCAAAA 59.519 30.769 24.07 24.07 0.00 2.44
1451 1473 4.094294 TCGGAGTGCTACATAATGTTTTGC 59.906 41.667 0.00 0.00 0.00 3.68
1452 1474 5.794687 TCGGAGTGCTACATAATGTTTTG 57.205 39.130 0.00 0.00 0.00 2.44
1453 1475 6.205853 TGTTTCGGAGTGCTACATAATGTTTT 59.794 34.615 0.00 0.00 0.00 2.43
1460 1482 4.021807 TGTCTTGTTTCGGAGTGCTACATA 60.022 41.667 0.00 0.00 0.00 2.29
1472 1494 8.514136 TTTAGCCAATATTTTGTCTTGTTTCG 57.486 30.769 0.00 0.00 0.00 3.46
1486 1508 8.443953 TGCTTTTGTTTTGTTTTAGCCAATAT 57.556 26.923 0.00 0.00 0.00 1.28
1487 1509 7.849804 TGCTTTTGTTTTGTTTTAGCCAATA 57.150 28.000 0.00 0.00 0.00 1.90
1488 1510 6.749923 TGCTTTTGTTTTGTTTTAGCCAAT 57.250 29.167 0.00 0.00 0.00 3.16
1490 1512 7.849804 TTATGCTTTTGTTTTGTTTTAGCCA 57.150 28.000 0.00 0.00 0.00 4.75
1498 1520 7.042523 GCTGTGAGATTTATGCTTTTGTTTTGT 60.043 33.333 0.00 0.00 0.00 2.83
1529 1551 1.227380 GCATCGGCCTACAGTCCAG 60.227 63.158 0.00 0.00 0.00 3.86
1535 1557 1.418097 ATCCCATGCATCGGCCTACA 61.418 55.000 5.31 0.00 40.13 2.74
1540 1562 2.785868 GGATATCCCATGCATCGGC 58.214 57.895 11.02 0.00 36.12 5.54
1566 1592 2.871096 TCGGGCATGGTTTTTCTACT 57.129 45.000 0.00 0.00 0.00 2.57
1569 1595 2.214376 TCATCGGGCATGGTTTTTCT 57.786 45.000 0.00 0.00 32.64 2.52
1579 1605 3.904800 TCTTGTTTCTATCATCGGGCA 57.095 42.857 0.00 0.00 0.00 5.36
1683 1712 1.376553 GGGCAGAAGAGTGTCAGGC 60.377 63.158 0.00 0.00 0.00 4.85
1717 1746 1.655329 GACGATCTCGGCGATCCTT 59.345 57.895 11.27 0.00 44.66 3.36
1740 1769 1.063717 CAAACTCACATATGGCCCCCT 60.064 52.381 7.80 0.00 0.00 4.79
1860 1889 3.903467 TGCTGAGGAGAGCAATAGTAGA 58.097 45.455 0.00 0.00 46.05 2.59
1905 1934 4.980702 CCCAAGCCCTGCAGCACA 62.981 66.667 8.66 0.00 34.23 4.57
1929 1958 0.902516 AGAGGATGGAGCCTATCGCC 60.903 60.000 0.00 0.00 38.73 5.54
2070 2103 2.480555 CATGTCAAAGCCGCGACC 59.519 61.111 8.23 0.00 0.00 4.79
2075 2108 2.180017 GCCTGCATGTCAAAGCCG 59.820 61.111 0.00 0.00 0.00 5.52
2081 2114 2.124612 CATCCCGCCTGCATGTCA 60.125 61.111 0.00 0.00 0.00 3.58
2129 2162 3.700970 TTCATCTGGGGCGCGACA 61.701 61.111 17.00 6.32 0.00 4.35
2299 2334 1.073923 GTGGGAAGTGACTGGTTGGAT 59.926 52.381 0.00 0.00 0.00 3.41
2324 2359 5.981088 ATTGGTTGCACATAGATTTGACA 57.019 34.783 0.00 0.00 0.00 3.58
2384 2419 1.523032 CTCATTACCGGGGCGAACC 60.523 63.158 6.32 0.00 39.11 3.62
2392 2427 1.327460 CGTGATTGCACTCATTACCGG 59.673 52.381 10.21 0.00 42.93 5.28
2394 2429 4.158384 CAAACGTGATTGCACTCATTACC 58.842 43.478 10.21 0.00 42.93 2.85
2445 2480 8.337532 GTTCCCTCAACAAATTTTTGAAGATTG 58.662 33.333 9.88 4.39 40.55 2.67
2458 2493 5.773176 GGAGATTTAAGGTTCCCTCAACAAA 59.227 40.000 0.00 0.00 36.61 2.83
2461 2496 4.918588 TGGAGATTTAAGGTTCCCTCAAC 58.081 43.478 0.00 0.00 30.89 3.18
2485 2520 6.936900 GTGGTCACTACATCCATTAATAGCAT 59.063 38.462 0.00 0.00 33.68 3.79
2486 2521 6.126911 TGTGGTCACTACATCCATTAATAGCA 60.127 38.462 0.00 0.00 33.68 3.49
2487 2522 6.202954 GTGTGGTCACTACATCCATTAATAGC 59.797 42.308 0.00 0.00 40.98 2.97
2488 2523 6.420903 CGTGTGGTCACTACATCCATTAATAG 59.579 42.308 0.00 0.00 41.89 1.73
2489 2524 6.127281 ACGTGTGGTCACTACATCCATTAATA 60.127 38.462 0.00 0.00 41.89 0.98
2490 2525 5.116180 CGTGTGGTCACTACATCCATTAAT 58.884 41.667 0.00 0.00 41.89 1.40
2491 2526 4.020928 ACGTGTGGTCACTACATCCATTAA 60.021 41.667 0.00 0.00 41.89 1.40
2492 2527 3.512329 ACGTGTGGTCACTACATCCATTA 59.488 43.478 0.00 0.00 41.89 1.90
2511 2546 2.676632 TGCGACCCATACAAATACGT 57.323 45.000 0.00 0.00 0.00 3.57
2528 2563 6.572519 ACACATATAAATGTCCAAACCATGC 58.427 36.000 0.00 0.00 44.70 4.06
2558 2593 6.151648 CAGGAACACATATATAAATGGCCCTG 59.848 42.308 0.00 16.32 0.00 4.45
2559 2594 6.045459 TCAGGAACACATATATAAATGGCCCT 59.955 38.462 0.00 0.00 0.00 5.19
2619 2655 2.796031 CTGCAATTTGACGTTGTGCATT 59.204 40.909 11.29 0.00 43.73 3.56
2645 2681 7.172342 ACAAGACTATTTTAACCCATGTAGCA 58.828 34.615 0.00 0.00 0.00 3.49
2671 2707 5.880332 CACTTAGCTGGTTGTACCACATTAT 59.120 40.000 0.00 0.00 44.79 1.28
2718 2754 7.765307 AGGACAATCATCATGATTTGTGTAAC 58.235 34.615 23.95 12.96 44.03 2.50
3105 3142 0.396974 TTGTGCCCCAAGAACAGCTT 60.397 50.000 0.00 0.00 37.29 3.74
3106 3143 1.109323 GTTGTGCCCCAAGAACAGCT 61.109 55.000 0.00 0.00 32.51 4.24
3107 3144 1.109323 AGTTGTGCCCCAAGAACAGC 61.109 55.000 0.00 0.00 32.51 4.40
3108 3145 1.067516 CAAGTTGTGCCCCAAGAACAG 59.932 52.381 0.00 0.00 32.51 3.16
3109 3146 1.110442 CAAGTTGTGCCCCAAGAACA 58.890 50.000 0.00 0.00 32.51 3.18
3110 3147 1.067060 GTCAAGTTGTGCCCCAAGAAC 59.933 52.381 2.11 0.00 32.51 3.01
3111 3148 1.398692 GTCAAGTTGTGCCCCAAGAA 58.601 50.000 2.11 0.00 32.51 2.52
3112 3149 0.467290 GGTCAAGTTGTGCCCCAAGA 60.467 55.000 2.11 0.00 32.51 3.02
3113 3150 0.754957 TGGTCAAGTTGTGCCCCAAG 60.755 55.000 13.75 0.00 32.51 3.61
3114 3151 1.040339 GTGGTCAAGTTGTGCCCCAA 61.040 55.000 13.75 0.00 31.94 4.12
3115 3152 1.454847 GTGGTCAAGTTGTGCCCCA 60.455 57.895 13.75 8.69 0.00 4.96
3116 3153 2.200337 GGTGGTCAAGTTGTGCCCC 61.200 63.158 13.75 11.26 0.00 5.80
3117 3154 0.755327 AAGGTGGTCAAGTTGTGCCC 60.755 55.000 13.75 8.65 0.00 5.36
3118 3155 0.668535 GAAGGTGGTCAAGTTGTGCC 59.331 55.000 2.11 7.43 0.00 5.01
3119 3156 0.668535 GGAAGGTGGTCAAGTTGTGC 59.331 55.000 2.11 0.00 0.00 4.57
3120 3157 0.944386 CGGAAGGTGGTCAAGTTGTG 59.056 55.000 2.11 0.00 0.00 3.33
3121 3158 3.396951 CGGAAGGTGGTCAAGTTGT 57.603 52.632 2.11 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.