Multiple sequence alignment - TraesCS2D01G414900

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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 TraesCS2D01G414900 chr2D 100.000 2312 0 0 1 2312 528993739 528996050 0.000000e+00 4270.0
1 TraesCS2D01G414900 chr2D 88.287 1016 78 20 683 1663 527804861 527803852 0.000000e+00 1179.0
2 TraesCS2D01G414900 chr2D 84.489 851 90 32 746 1567 527684525 527683688 0.000000e+00 802.0
3 TraesCS2D01G414900 chr2D 94.186 172 8 2 1569 1739 648401025 648400855 6.340000e-66 261.0
4 TraesCS2D01G414900 chr2D 97.727 44 1 0 224 267 528993918 528993961 2.460000e-10 76.8
5 TraesCS2D01G414900 chr2D 97.727 44 1 0 180 223 528993962 528994005 2.460000e-10 76.8
6 TraesCS2D01G414900 chr2A 90.733 1392 76 29 667 2020 673419642 673421018 0.000000e+00 1807.0
7 TraesCS2D01G414900 chr2A 87.873 973 65 18 636 1564 673417446 673418409 0.000000e+00 1094.0
8 TraesCS2D01G414900 chr2A 87.828 953 60 16 667 1567 672746592 672745644 0.000000e+00 1066.0
9 TraesCS2D01G414900 chr2A 87.942 481 31 17 994 1468 643438487 643438946 2.020000e-150 542.0
10 TraesCS2D01G414900 chr2A 89.818 275 20 6 222 489 673417136 673417409 1.700000e-91 346.0
11 TraesCS2D01G414900 chr2A 88.115 244 24 5 2070 2312 673422070 673422309 3.760000e-73 285.0
12 TraesCS2D01G414900 chr2B 87.042 1065 96 22 630 1659 627317379 627318436 0.000000e+00 1164.0
13 TraesCS2D01G414900 chr2B 87.605 952 81 18 740 1659 625239186 625238240 0.000000e+00 1070.0
14 TraesCS2D01G414900 chr2B 89.796 735 58 9 711 1431 627322844 627323575 0.000000e+00 926.0
15 TraesCS2D01G414900 chr2B 82.556 986 119 29 753 1694 625009286 625008310 0.000000e+00 819.0
16 TraesCS2D01G414900 chr2B 85.983 692 38 18 1320 1997 627324455 627325101 0.000000e+00 686.0
17 TraesCS2D01G414900 chr2B 92.000 300 20 3 2017 2312 627325276 627325575 3.550000e-113 418.0
18 TraesCS2D01G414900 chr2B 89.011 273 24 4 222 489 627317109 627317380 1.320000e-87 333.0
19 TraesCS2D01G414900 chr7D 92.097 658 40 5 663 1312 134467381 134466728 0.000000e+00 917.0
20 TraesCS2D01G414900 chr7A 92.269 595 34 4 727 1313 133627711 133627121 0.000000e+00 833.0
21 TraesCS2D01G414900 chr7A 89.552 67 3 3 54 116 134509269 134509203 5.290000e-12 82.4
22 TraesCS2D01G414900 chr5A 94.737 171 9 0 1569 1739 104951436 104951266 1.360000e-67 267.0
23 TraesCS2D01G414900 chr5A 90.728 151 14 0 2020 2170 104951212 104951062 3.900000e-48 202.0
24 TraesCS2D01G414900 chr5A 86.022 93 7 4 36 127 100622629 100622542 6.800000e-16 95.3
25 TraesCS2D01G414900 chr5D 94.152 171 10 0 1569 1739 309718479 309718309 6.340000e-66 261.0
26 TraesCS2D01G414900 chr5D 92.857 154 11 0 2017 2170 309718258 309718105 8.310000e-55 224.0
27 TraesCS2D01G414900 chr4A 93.529 170 9 2 1569 1737 67425286 67425118 3.810000e-63 252.0
28 TraesCS2D01G414900 chr3A 92.982 171 12 0 1569 1739 620784324 620784154 1.370000e-62 250.0
29 TraesCS2D01G414900 chrUn 79.389 131 16 6 1 125 60937029 60936904 5.290000e-12 82.4


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 TraesCS2D01G414900 chr2D 528993739 528996050 2311 False 1474.533333 4270 98.484667 1 2312 3 chr2D.!!$F1 2311
1 TraesCS2D01G414900 chr2D 527803852 527804861 1009 True 1179.000000 1179 88.287000 683 1663 1 chr2D.!!$R2 980
2 TraesCS2D01G414900 chr2D 527683688 527684525 837 True 802.000000 802 84.489000 746 1567 1 chr2D.!!$R1 821
3 TraesCS2D01G414900 chr2A 672745644 672746592 948 True 1066.000000 1066 87.828000 667 1567 1 chr2A.!!$R1 900
4 TraesCS2D01G414900 chr2A 673417136 673422309 5173 False 883.000000 1807 89.134750 222 2312 4 chr2A.!!$F2 2090
5 TraesCS2D01G414900 chr2B 625238240 625239186 946 True 1070.000000 1070 87.605000 740 1659 1 chr2B.!!$R2 919
6 TraesCS2D01G414900 chr2B 625008310 625009286 976 True 819.000000 819 82.556000 753 1694 1 chr2B.!!$R1 941
7 TraesCS2D01G414900 chr2B 627317109 627318436 1327 False 748.500000 1164 88.026500 222 1659 2 chr2B.!!$F1 1437
8 TraesCS2D01G414900 chr2B 627322844 627325575 2731 False 676.666667 926 89.259667 711 2312 3 chr2B.!!$F2 1601
9 TraesCS2D01G414900 chr7D 134466728 134467381 653 True 917.000000 917 92.097000 663 1312 1 chr7D.!!$R1 649
10 TraesCS2D01G414900 chr7A 133627121 133627711 590 True 833.000000 833 92.269000 727 1313 1 chr7A.!!$R1 586

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
543 552 0.03213 ACGACTCACGATGCTTGTGT 59.968 50.0 0.0 0.0 45.77 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 6812 0.604578 ACCCAAGCTTCGTAACGCTA 59.395 50.0 0.0 0.0 34.96 4.26 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
18 19 3.228085 TTTTGCGAGCACGTCAAAC 57.772 47.368 19.23 0.00 41.23 2.93
19 20 0.730265 TTTTGCGAGCACGTCAAACT 59.270 45.000 19.23 0.00 41.23 2.66
20 21 0.730265 TTTGCGAGCACGTCAAACTT 59.270 45.000 16.95 0.00 38.97 2.66
21 22 0.730265 TTGCGAGCACGTCAAACTTT 59.270 45.000 5.23 0.00 41.98 2.66
22 23 0.730265 TGCGAGCACGTCAAACTTTT 59.270 45.000 5.23 0.00 41.98 2.27
23 24 1.112459 GCGAGCACGTCAAACTTTTG 58.888 50.000 5.23 0.00 41.98 2.44
24 25 1.531058 GCGAGCACGTCAAACTTTTGT 60.531 47.619 5.23 0.00 41.98 2.83
25 26 2.363220 CGAGCACGTCAAACTTTTGTC 58.637 47.619 0.00 0.00 39.18 3.18
26 27 2.222931 CGAGCACGTCAAACTTTTGTCA 60.223 45.455 0.00 0.00 39.18 3.58
27 28 3.726486 CGAGCACGTCAAACTTTTGTCAA 60.726 43.478 0.00 0.00 39.18 3.18
28 29 4.351192 GAGCACGTCAAACTTTTGTCAAT 58.649 39.130 1.75 0.00 39.18 2.57
29 30 4.104776 AGCACGTCAAACTTTTGTCAATG 58.895 39.130 1.75 0.32 39.18 2.82
30 31 3.857093 GCACGTCAAACTTTTGTCAATGT 59.143 39.130 1.75 0.00 39.18 2.71
31 32 4.326009 GCACGTCAAACTTTTGTCAATGTT 59.674 37.500 1.75 0.00 39.18 2.71
32 33 5.164002 GCACGTCAAACTTTTGTCAATGTTT 60.164 36.000 9.87 9.87 39.60 2.83
93 94 7.435068 TTTTAGTTTACTGTTCATCCTGAGC 57.565 36.000 0.00 0.00 0.00 4.26
94 95 4.899352 AGTTTACTGTTCATCCTGAGCT 57.101 40.909 0.00 0.00 0.00 4.09
95 96 4.826556 AGTTTACTGTTCATCCTGAGCTC 58.173 43.478 6.82 6.82 0.00 4.09
96 97 4.284490 AGTTTACTGTTCATCCTGAGCTCA 59.716 41.667 17.19 17.19 0.00 4.26
97 98 4.890158 TTACTGTTCATCCTGAGCTCAA 57.110 40.909 18.85 3.88 0.00 3.02
98 99 3.777106 ACTGTTCATCCTGAGCTCAAA 57.223 42.857 18.85 9.43 0.00 2.69
99 100 4.298103 ACTGTTCATCCTGAGCTCAAAT 57.702 40.909 18.85 11.43 0.00 2.32
100 101 4.008330 ACTGTTCATCCTGAGCTCAAATG 58.992 43.478 23.56 23.56 0.00 2.32
101 102 4.259356 CTGTTCATCCTGAGCTCAAATGA 58.741 43.478 26.25 26.25 0.00 2.57
102 103 4.259356 TGTTCATCCTGAGCTCAAATGAG 58.741 43.478 27.40 14.53 44.75 2.90
110 111 4.547859 CTCAAATGAGCCCGGGAG 57.452 61.111 29.31 5.79 35.13 4.30
111 112 1.821332 CTCAAATGAGCCCGGGAGC 60.821 63.158 29.31 16.09 35.13 4.70
112 113 2.045045 CAAATGAGCCCGGGAGCA 60.045 61.111 29.31 21.92 34.23 4.26
113 114 2.117156 CAAATGAGCCCGGGAGCAG 61.117 63.158 29.31 5.49 34.23 4.24
114 115 2.300967 AAATGAGCCCGGGAGCAGA 61.301 57.895 29.31 1.97 34.23 4.26
115 116 1.852157 AAATGAGCCCGGGAGCAGAA 61.852 55.000 29.31 2.41 34.23 3.02
116 117 2.262774 AATGAGCCCGGGAGCAGAAG 62.263 60.000 29.31 0.00 34.23 2.85
117 118 3.077556 GAGCCCGGGAGCAGAAGA 61.078 66.667 29.31 0.00 34.23 2.87
118 119 2.366167 AGCCCGGGAGCAGAAGAT 60.366 61.111 29.31 0.00 34.23 2.40
119 120 2.203126 GCCCGGGAGCAGAAGATG 60.203 66.667 29.31 0.00 0.00 2.90
120 121 2.735772 GCCCGGGAGCAGAAGATGA 61.736 63.158 29.31 0.00 0.00 2.92
121 122 1.144936 CCCGGGAGCAGAAGATGAC 59.855 63.158 18.48 0.00 0.00 3.06
122 123 1.333636 CCCGGGAGCAGAAGATGACT 61.334 60.000 18.48 0.00 0.00 3.41
123 124 0.539051 CCGGGAGCAGAAGATGACTT 59.461 55.000 0.00 0.00 39.24 3.01
124 125 1.065854 CCGGGAGCAGAAGATGACTTT 60.066 52.381 0.00 0.00 36.39 2.66
125 126 2.616510 CCGGGAGCAGAAGATGACTTTT 60.617 50.000 0.00 0.00 36.39 2.27
126 127 2.417933 CGGGAGCAGAAGATGACTTTTG 59.582 50.000 0.00 0.00 39.98 2.44
127 128 2.751806 GGGAGCAGAAGATGACTTTTGG 59.248 50.000 0.00 0.00 38.26 3.28
128 129 2.751806 GGAGCAGAAGATGACTTTTGGG 59.248 50.000 0.00 0.00 38.26 4.12
129 130 3.416156 GAGCAGAAGATGACTTTTGGGT 58.584 45.455 0.00 0.00 38.26 4.51
130 131 3.823304 GAGCAGAAGATGACTTTTGGGTT 59.177 43.478 0.00 0.00 38.26 4.11
131 132 4.218312 AGCAGAAGATGACTTTTGGGTTT 58.782 39.130 0.00 0.00 38.26 3.27
132 133 4.279420 AGCAGAAGATGACTTTTGGGTTTC 59.721 41.667 0.00 0.00 38.26 2.78
133 134 4.279420 GCAGAAGATGACTTTTGGGTTTCT 59.721 41.667 0.00 0.00 38.26 2.52
134 135 5.473504 GCAGAAGATGACTTTTGGGTTTCTA 59.526 40.000 0.00 0.00 38.26 2.10
135 136 6.151817 GCAGAAGATGACTTTTGGGTTTCTAT 59.848 38.462 0.00 0.00 38.26 1.98
136 137 7.309438 GCAGAAGATGACTTTTGGGTTTCTATT 60.309 37.037 0.00 0.00 38.26 1.73
137 138 8.239998 CAGAAGATGACTTTTGGGTTTCTATTC 58.760 37.037 0.00 0.00 35.47 1.75
138 139 6.743575 AGATGACTTTTGGGTTTCTATTCG 57.256 37.500 0.00 0.00 0.00 3.34
139 140 4.759516 TGACTTTTGGGTTTCTATTCGC 57.240 40.909 0.00 0.00 0.00 4.70
140 141 4.394729 TGACTTTTGGGTTTCTATTCGCT 58.605 39.130 0.00 0.00 0.00 4.93
141 142 5.553123 TGACTTTTGGGTTTCTATTCGCTA 58.447 37.500 0.00 0.00 0.00 4.26
142 143 5.410439 TGACTTTTGGGTTTCTATTCGCTAC 59.590 40.000 0.00 0.00 0.00 3.58
143 144 5.310451 ACTTTTGGGTTTCTATTCGCTACA 58.690 37.500 0.00 0.00 0.00 2.74
144 145 5.944007 ACTTTTGGGTTTCTATTCGCTACAT 59.056 36.000 0.00 0.00 0.00 2.29
145 146 6.093633 ACTTTTGGGTTTCTATTCGCTACATC 59.906 38.462 0.00 0.00 0.00 3.06
146 147 4.067972 TGGGTTTCTATTCGCTACATCC 57.932 45.455 0.00 0.00 0.00 3.51
147 148 3.452990 TGGGTTTCTATTCGCTACATCCA 59.547 43.478 0.00 0.00 0.00 3.41
148 149 4.080807 TGGGTTTCTATTCGCTACATCCAA 60.081 41.667 0.00 0.00 0.00 3.53
149 150 4.879545 GGGTTTCTATTCGCTACATCCAAA 59.120 41.667 0.00 0.00 0.00 3.28
150 151 5.355910 GGGTTTCTATTCGCTACATCCAAAA 59.644 40.000 0.00 0.00 0.00 2.44
151 152 6.039382 GGGTTTCTATTCGCTACATCCAAAAT 59.961 38.462 0.00 0.00 0.00 1.82
152 153 6.912591 GGTTTCTATTCGCTACATCCAAAATG 59.087 38.462 0.00 0.00 0.00 2.32
153 154 7.201696 GGTTTCTATTCGCTACATCCAAAATGA 60.202 37.037 0.00 0.00 0.00 2.57
154 155 6.844696 TCTATTCGCTACATCCAAAATGAC 57.155 37.500 0.00 0.00 0.00 3.06
155 156 4.900635 ATTCGCTACATCCAAAATGACC 57.099 40.909 0.00 0.00 0.00 4.02
156 157 2.276201 TCGCTACATCCAAAATGACCG 58.724 47.619 0.00 0.00 0.00 4.79
157 158 2.006888 CGCTACATCCAAAATGACCGT 58.993 47.619 0.00 0.00 0.00 4.83
158 159 2.030457 CGCTACATCCAAAATGACCGTC 59.970 50.000 0.00 0.00 0.00 4.79
159 160 2.354821 GCTACATCCAAAATGACCGTCC 59.645 50.000 0.00 0.00 0.00 4.79
160 161 1.834188 ACATCCAAAATGACCGTCCC 58.166 50.000 0.00 0.00 0.00 4.46
161 162 1.074727 ACATCCAAAATGACCGTCCCA 59.925 47.619 0.00 0.00 0.00 4.37
162 163 1.745087 CATCCAAAATGACCGTCCCAG 59.255 52.381 0.00 0.00 0.00 4.45
163 164 0.768622 TCCAAAATGACCGTCCCAGT 59.231 50.000 0.00 0.00 0.00 4.00
164 165 1.144093 TCCAAAATGACCGTCCCAGTT 59.856 47.619 0.00 0.00 0.00 3.16
165 166 1.269448 CCAAAATGACCGTCCCAGTTG 59.731 52.381 0.00 0.00 0.00 3.16
166 167 1.269448 CAAAATGACCGTCCCAGTTGG 59.731 52.381 0.00 0.00 0.00 3.77
167 168 0.476771 AAATGACCGTCCCAGTTGGT 59.523 50.000 0.00 0.00 39.12 3.67
168 169 1.354101 AATGACCGTCCCAGTTGGTA 58.646 50.000 0.00 0.00 35.75 3.25
169 170 0.902531 ATGACCGTCCCAGTTGGTAG 59.097 55.000 0.00 0.00 35.75 3.18
170 171 1.189524 TGACCGTCCCAGTTGGTAGG 61.190 60.000 0.00 0.47 35.75 3.18
171 172 2.267961 CCGTCCCAGTTGGTAGGC 59.732 66.667 0.00 0.00 34.77 3.93
172 173 2.291043 CCGTCCCAGTTGGTAGGCT 61.291 63.158 0.00 0.00 34.77 4.58
173 174 1.218316 CGTCCCAGTTGGTAGGCTC 59.782 63.158 0.00 0.00 34.77 4.70
174 175 1.218316 GTCCCAGTTGGTAGGCTCG 59.782 63.158 0.00 0.00 34.77 5.03
175 176 1.077805 TCCCAGTTGGTAGGCTCGA 59.922 57.895 0.00 0.00 34.77 4.04
176 177 1.218316 CCCAGTTGGTAGGCTCGAC 59.782 63.158 0.00 0.00 0.00 4.20
177 178 1.541310 CCCAGTTGGTAGGCTCGACA 61.541 60.000 0.00 0.00 0.00 4.35
178 179 0.320374 CCAGTTGGTAGGCTCGACAA 59.680 55.000 0.00 0.00 0.00 3.18
179 180 1.066143 CCAGTTGGTAGGCTCGACAAT 60.066 52.381 0.00 0.00 0.00 2.71
180 181 2.615493 CCAGTTGGTAGGCTCGACAATT 60.615 50.000 0.00 0.00 0.00 2.32
181 182 3.074412 CAGTTGGTAGGCTCGACAATTT 58.926 45.455 0.00 0.00 0.00 1.82
182 183 4.250464 CAGTTGGTAGGCTCGACAATTTA 58.750 43.478 0.00 0.00 0.00 1.40
183 184 4.876107 CAGTTGGTAGGCTCGACAATTTAT 59.124 41.667 0.00 0.00 0.00 1.40
184 185 5.354234 CAGTTGGTAGGCTCGACAATTTATT 59.646 40.000 0.00 0.00 0.00 1.40
185 186 5.944007 AGTTGGTAGGCTCGACAATTTATTT 59.056 36.000 0.00 0.00 0.00 1.40
186 187 6.433093 AGTTGGTAGGCTCGACAATTTATTTT 59.567 34.615 0.00 0.00 0.00 1.82
187 188 7.608761 AGTTGGTAGGCTCGACAATTTATTTTA 59.391 33.333 0.00 0.00 0.00 1.52
188 189 7.311364 TGGTAGGCTCGACAATTTATTTTAC 57.689 36.000 0.00 0.00 0.00 2.01
189 190 6.316890 TGGTAGGCTCGACAATTTATTTTACC 59.683 38.462 0.00 0.00 0.00 2.85
190 191 5.830000 AGGCTCGACAATTTATTTTACCC 57.170 39.130 0.00 0.00 0.00 3.69
191 192 4.643334 AGGCTCGACAATTTATTTTACCCC 59.357 41.667 0.00 0.00 0.00 4.95
192 193 4.496840 GGCTCGACAATTTATTTTACCCCG 60.497 45.833 0.00 0.00 0.00 5.73
193 194 4.095334 GCTCGACAATTTATTTTACCCCGT 59.905 41.667 0.00 0.00 0.00 5.28
194 195 5.728621 GCTCGACAATTTATTTTACCCCGTC 60.729 44.000 0.00 0.00 0.00 4.79
195 196 5.243981 TCGACAATTTATTTTACCCCGTCA 58.756 37.500 0.00 0.00 0.00 4.35
196 197 5.704515 TCGACAATTTATTTTACCCCGTCAA 59.295 36.000 0.00 0.00 0.00 3.18
197 198 6.206243 TCGACAATTTATTTTACCCCGTCAAA 59.794 34.615 0.00 0.00 0.00 2.69
198 199 6.862090 CGACAATTTATTTTACCCCGTCAAAA 59.138 34.615 0.00 0.00 0.00 2.44
199 200 7.381678 CGACAATTTATTTTACCCCGTCAAAAA 59.618 33.333 0.00 0.00 0.00 1.94
216 217 2.470057 AAAAGAAAAGAGGGGTGCCA 57.530 45.000 0.00 0.00 0.00 4.92
217 218 2.470057 AAAGAAAAGAGGGGTGCCAA 57.530 45.000 0.00 0.00 0.00 4.52
218 219 2.470057 AAGAAAAGAGGGGTGCCAAA 57.530 45.000 0.00 0.00 0.00 3.28
219 220 2.001076 AGAAAAGAGGGGTGCCAAAG 57.999 50.000 0.00 0.00 0.00 2.77
220 221 0.969149 GAAAAGAGGGGTGCCAAAGG 59.031 55.000 0.00 0.00 0.00 3.11
221 222 0.560688 AAAAGAGGGGTGCCAAAGGA 59.439 50.000 0.00 0.00 0.00 3.36
222 223 0.786435 AAAGAGGGGTGCCAAAGGAT 59.214 50.000 0.00 0.00 0.00 3.24
223 224 0.786435 AAGAGGGGTGCCAAAGGATT 59.214 50.000 0.00 0.00 0.00 3.01
224 225 0.786435 AGAGGGGTGCCAAAGGATTT 59.214 50.000 0.00 0.00 40.26 2.17
225 226 1.149923 AGAGGGGTGCCAAAGGATTTT 59.850 47.619 0.00 0.00 35.03 1.82
226 227 2.381961 AGAGGGGTGCCAAAGGATTTTA 59.618 45.455 0.00 0.00 35.03 1.52
236 237 5.113383 GCCAAAGGATTTTATTTTACCCCG 58.887 41.667 0.00 0.00 35.03 5.73
239 240 6.071278 CCAAAGGATTTTATTTTACCCCGTCA 60.071 38.462 0.00 0.00 35.03 4.35
240 241 7.379750 CAAAGGATTTTATTTTACCCCGTCAA 58.620 34.615 0.00 0.00 35.03 3.18
306 311 5.612725 TTTCCTTCTTCCTTGCATGTTTT 57.387 34.783 0.00 0.00 0.00 2.43
314 319 5.236911 TCTTCCTTGCATGTTTTTCATTTGC 59.763 36.000 0.00 0.00 34.09 3.68
315 320 4.449131 TCCTTGCATGTTTTTCATTTGCA 58.551 34.783 0.00 0.00 39.37 4.08
355 360 8.874156 AGGAGTCAGCTCATTGTAATGATTATA 58.126 33.333 7.67 0.00 43.87 0.98
478 487 5.571784 AGGAAATACAACGATACGACTCA 57.428 39.130 0.00 0.00 0.00 3.41
489 498 2.551270 CGACTCACGGTTTGCAGC 59.449 61.111 0.00 0.00 38.46 5.25
491 500 1.891919 GACTCACGGTTTGCAGCCA 60.892 57.895 9.58 0.00 0.00 4.75
492 501 1.845809 GACTCACGGTTTGCAGCCAG 61.846 60.000 9.58 5.36 0.00 4.85
493 502 2.594303 TCACGGTTTGCAGCCAGG 60.594 61.111 9.58 1.79 0.00 4.45
494 503 3.673484 CACGGTTTGCAGCCAGGG 61.673 66.667 9.58 1.08 0.00 4.45
495 504 3.884774 ACGGTTTGCAGCCAGGGA 61.885 61.111 9.58 0.00 0.00 4.20
496 505 3.058160 CGGTTTGCAGCCAGGGAG 61.058 66.667 9.58 0.00 0.00 4.30
497 506 2.436109 GGTTTGCAGCCAGGGAGA 59.564 61.111 4.72 0.00 0.00 3.71
498 507 1.228552 GGTTTGCAGCCAGGGAGAA 60.229 57.895 4.72 0.00 0.00 2.87
499 508 1.527433 GGTTTGCAGCCAGGGAGAAC 61.527 60.000 4.72 0.00 0.00 3.01
500 509 1.228552 TTTGCAGCCAGGGAGAACC 60.229 57.895 0.00 0.00 40.67 3.62
501 510 3.551496 TTGCAGCCAGGGAGAACCG 62.551 63.158 0.00 0.00 46.96 4.44
502 511 4.785453 GCAGCCAGGGAGAACCGG 62.785 72.222 0.00 0.00 46.96 5.28
506 515 3.971894 CCAGGGAGAACCGGCTAT 58.028 61.111 0.00 0.00 46.96 2.97
507 516 1.447643 CCAGGGAGAACCGGCTATG 59.552 63.158 0.00 0.00 46.96 2.23
508 517 1.227674 CAGGGAGAACCGGCTATGC 60.228 63.158 0.00 0.00 46.96 3.14
509 518 2.111251 GGGAGAACCGGCTATGCC 59.889 66.667 0.00 0.00 46.75 4.40
525 534 6.496524 GCTATGCCATTTGAAAAACGATAC 57.503 37.500 0.00 0.00 0.00 2.24
526 535 5.171337 GCTATGCCATTTGAAAAACGATACG 59.829 40.000 0.00 0.00 0.00 3.06
527 536 4.750952 TGCCATTTGAAAAACGATACGA 57.249 36.364 0.00 0.00 0.00 3.43
528 537 4.468643 TGCCATTTGAAAAACGATACGAC 58.531 39.130 0.00 0.00 0.00 4.34
529 538 4.214545 TGCCATTTGAAAAACGATACGACT 59.785 37.500 0.00 0.00 0.00 4.18
530 539 4.786575 GCCATTTGAAAAACGATACGACTC 59.213 41.667 0.00 0.00 0.00 3.36
531 540 5.615984 GCCATTTGAAAAACGATACGACTCA 60.616 40.000 0.00 0.00 0.00 3.41
532 541 5.788531 CCATTTGAAAAACGATACGACTCAC 59.211 40.000 0.00 0.00 0.00 3.51
534 543 3.887741 TGAAAAACGATACGACTCACGA 58.112 40.909 0.00 0.00 45.77 4.35
535 544 4.478699 TGAAAAACGATACGACTCACGAT 58.521 39.130 0.00 0.00 45.77 3.73
536 545 4.322539 TGAAAAACGATACGACTCACGATG 59.677 41.667 0.00 0.00 45.77 3.84
537 546 1.823828 AACGATACGACTCACGATGC 58.176 50.000 0.00 0.00 45.77 3.91
538 547 1.015109 ACGATACGACTCACGATGCT 58.985 50.000 0.00 0.00 45.77 3.79
539 548 1.400846 ACGATACGACTCACGATGCTT 59.599 47.619 0.00 0.00 45.77 3.91
540 549 1.775770 CGATACGACTCACGATGCTTG 59.224 52.381 0.00 0.00 45.77 4.01
541 550 2.791503 CGATACGACTCACGATGCTTGT 60.792 50.000 0.00 0.00 45.77 3.16
542 551 1.977188 TACGACTCACGATGCTTGTG 58.023 50.000 0.00 0.00 45.77 3.33
543 552 0.032130 ACGACTCACGATGCTTGTGT 59.968 50.000 0.00 0.00 45.77 3.72
544 553 1.268625 ACGACTCACGATGCTTGTGTA 59.731 47.619 0.00 0.00 45.77 2.90
545 554 2.094700 ACGACTCACGATGCTTGTGTAT 60.095 45.455 0.00 0.00 45.77 2.29
546 555 2.279921 CGACTCACGATGCTTGTGTATG 59.720 50.000 0.00 0.00 45.77 2.39
547 556 3.254060 GACTCACGATGCTTGTGTATGT 58.746 45.455 0.00 2.92 38.48 2.29
548 557 2.995939 ACTCACGATGCTTGTGTATGTG 59.004 45.455 0.00 0.00 38.48 3.21
549 558 2.345876 TCACGATGCTTGTGTATGTGG 58.654 47.619 0.00 0.00 38.48 4.17
550 559 1.398041 CACGATGCTTGTGTATGTGGG 59.602 52.381 0.00 0.00 32.68 4.61
551 560 1.277842 ACGATGCTTGTGTATGTGGGA 59.722 47.619 0.00 0.00 0.00 4.37
552 561 2.092968 ACGATGCTTGTGTATGTGGGAT 60.093 45.455 0.00 0.00 0.00 3.85
553 562 2.288729 CGATGCTTGTGTATGTGGGATG 59.711 50.000 0.00 0.00 0.00 3.51
554 563 2.127271 TGCTTGTGTATGTGGGATGG 57.873 50.000 0.00 0.00 0.00 3.51
555 564 0.740737 GCTTGTGTATGTGGGATGGC 59.259 55.000 0.00 0.00 0.00 4.40
556 565 1.392589 CTTGTGTATGTGGGATGGCC 58.607 55.000 0.00 0.00 0.00 5.36
557 566 0.393673 TTGTGTATGTGGGATGGCCG 60.394 55.000 0.00 0.00 33.83 6.13
558 567 1.223487 GTGTATGTGGGATGGCCGT 59.777 57.895 0.00 0.00 33.83 5.68
559 568 1.095228 GTGTATGTGGGATGGCCGTG 61.095 60.000 0.00 0.00 33.83 4.94
560 569 1.223487 GTATGTGGGATGGCCGTGT 59.777 57.895 0.00 0.00 33.83 4.49
561 570 0.466543 GTATGTGGGATGGCCGTGTA 59.533 55.000 0.00 0.00 33.83 2.90
562 571 1.071699 GTATGTGGGATGGCCGTGTAT 59.928 52.381 0.00 0.00 33.83 2.29
563 572 0.179020 ATGTGGGATGGCCGTGTATG 60.179 55.000 0.00 0.00 33.83 2.39
564 573 1.223487 GTGGGATGGCCGTGTATGT 59.777 57.895 0.00 0.00 33.83 2.29
565 574 1.095228 GTGGGATGGCCGTGTATGTG 61.095 60.000 0.00 0.00 33.83 3.21
566 575 1.268283 TGGGATGGCCGTGTATGTGA 61.268 55.000 0.00 0.00 33.83 3.58
567 576 0.532862 GGGATGGCCGTGTATGTGAG 60.533 60.000 0.00 0.00 33.83 3.51
568 577 0.532862 GGATGGCCGTGTATGTGAGG 60.533 60.000 0.00 0.00 0.00 3.86
569 578 0.532862 GATGGCCGTGTATGTGAGGG 60.533 60.000 0.00 0.00 0.00 4.30
570 579 0.980754 ATGGCCGTGTATGTGAGGGA 60.981 55.000 0.00 0.00 0.00 4.20
571 580 1.153429 GGCCGTGTATGTGAGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
573 582 0.249398 GCCGTGTATGTGAGGGACTT 59.751 55.000 0.00 0.00 41.55 3.01
574 583 1.338769 GCCGTGTATGTGAGGGACTTT 60.339 52.381 0.00 0.00 41.55 2.66
575 584 2.093869 GCCGTGTATGTGAGGGACTTTA 60.094 50.000 0.00 0.00 41.55 1.85
576 585 3.618019 GCCGTGTATGTGAGGGACTTTAA 60.618 47.826 0.00 0.00 41.55 1.52
577 586 4.766375 CCGTGTATGTGAGGGACTTTAAT 58.234 43.478 0.00 0.00 41.55 1.40
578 587 5.183228 CCGTGTATGTGAGGGACTTTAATT 58.817 41.667 0.00 0.00 41.55 1.40
579 588 5.064707 CCGTGTATGTGAGGGACTTTAATTG 59.935 44.000 0.00 0.00 41.55 2.32
580 589 5.642063 CGTGTATGTGAGGGACTTTAATTGT 59.358 40.000 0.00 0.00 41.55 2.71
581 590 6.814644 CGTGTATGTGAGGGACTTTAATTGTA 59.185 38.462 0.00 0.00 41.55 2.41
582 591 7.201496 CGTGTATGTGAGGGACTTTAATTGTAC 60.201 40.741 0.00 0.00 41.55 2.90
583 592 7.822822 GTGTATGTGAGGGACTTTAATTGTACT 59.177 37.037 0.00 0.00 41.55 2.73
584 593 7.822334 TGTATGTGAGGGACTTTAATTGTACTG 59.178 37.037 0.00 0.00 41.55 2.74
585 594 6.182507 TGTGAGGGACTTTAATTGTACTGT 57.817 37.500 0.00 0.00 41.55 3.55
586 595 5.995282 TGTGAGGGACTTTAATTGTACTGTG 59.005 40.000 0.00 0.00 41.55 3.66
587 596 6.183361 TGTGAGGGACTTTAATTGTACTGTGA 60.183 38.462 0.00 0.00 41.55 3.58
588 597 6.879458 GTGAGGGACTTTAATTGTACTGTGAT 59.121 38.462 0.00 0.00 41.55 3.06
589 598 8.038944 GTGAGGGACTTTAATTGTACTGTGATA 58.961 37.037 0.00 0.00 41.55 2.15
590 599 8.598916 TGAGGGACTTTAATTGTACTGTGATAA 58.401 33.333 0.00 0.00 41.55 1.75
591 600 9.444600 GAGGGACTTTAATTGTACTGTGATAAA 57.555 33.333 0.00 0.00 41.55 1.40
592 601 9.802039 AGGGACTTTAATTGTACTGTGATAAAA 57.198 29.630 0.00 0.00 27.25 1.52
654 696 3.032017 TCTTTTCTCTGAACGCTGAGG 57.968 47.619 0.00 0.00 39.68 3.86
696 742 0.038166 TCACTCCTGGCCCAAATCAC 59.962 55.000 0.00 0.00 0.00 3.06
701 747 1.707989 TCCTGGCCCAAATCACTGTAA 59.292 47.619 0.00 0.00 0.00 2.41
816 873 2.290260 ACCTTCTGATCGCAATCCAACA 60.290 45.455 0.00 0.00 0.00 3.33
826 883 1.915141 CAATCCAACAGCCCAACTCT 58.085 50.000 0.00 0.00 0.00 3.24
929 1006 1.475392 CGCCCCATATAAACCCGTCAA 60.475 52.381 0.00 0.00 0.00 3.18
988 1078 0.908198 CCACTCCCTTCTTCTCCCAG 59.092 60.000 0.00 0.00 0.00 4.45
994 1095 2.021639 TCCCTTCTTCTCCCAGATCCAT 60.022 50.000 0.00 0.00 0.00 3.41
1086 1187 2.047274 CGCGACAACATCCAGGGT 60.047 61.111 0.00 0.00 0.00 4.34
1167 1268 0.545171 TCATCTACGAGGAGACCCGT 59.455 55.000 0.00 0.00 42.15 5.28
1352 3655 0.861837 CCTCGTTTGCTCTGTGTGAC 59.138 55.000 0.00 0.00 0.00 3.67
1357 3660 2.799978 CGTTTGCTCTGTGTGACATGTA 59.200 45.455 0.00 0.00 0.00 2.29
1358 3661 3.433274 CGTTTGCTCTGTGTGACATGTAT 59.567 43.478 0.00 0.00 0.00 2.29
1359 3662 4.434725 CGTTTGCTCTGTGTGACATGTATC 60.435 45.833 0.00 0.00 0.00 2.24
1505 4789 8.410030 TGTTGAATTGTGATTTGTTTTCTCTG 57.590 30.769 0.00 0.00 0.00 3.35
1526 4963 2.863137 GAGACCGACTGATTTGATCTGC 59.137 50.000 0.00 0.00 0.00 4.26
1567 5026 9.283768 TGCAGTGAATCAGTCTTTTATTTCTTA 57.716 29.630 0.00 0.00 0.00 2.10
1577 5036 9.931210 CAGTCTTTTATTTCTTAACACTCGTTT 57.069 29.630 0.00 0.00 36.52 3.60
1637 5096 6.705381 TGGCTTTCATTTGTTCAAGTATTTGG 59.295 34.615 0.00 0.00 34.97 3.28
1644 5103 2.418628 TGTTCAAGTATTTGGCGCTAGC 59.581 45.455 7.64 4.06 44.18 3.42
1696 5155 7.561356 TGTACTGAATCATCCTTCTATCTGACA 59.439 37.037 0.00 0.00 0.00 3.58
1708 5167 4.424626 TCTATCTGACACTCGTTGCAATC 58.575 43.478 0.59 0.00 0.00 2.67
1713 5172 3.317150 TGACACTCGTTGCAATCTGTAG 58.683 45.455 0.59 0.00 0.00 2.74
1728 5187 6.073873 GCAATCTGTAGAAGAGATGGAATTCG 60.074 42.308 0.00 0.00 38.67 3.34
1743 5213 1.949847 ATTCGTCCGCTCAGGTCCAG 61.950 60.000 0.00 0.00 41.99 3.86
1764 5234 3.957497 AGTGTTTTGGTTTGGCATCACTA 59.043 39.130 0.00 0.00 33.96 2.74
1814 5284 6.653020 TGCTTTCAGTGGTATGAATACTCAT 58.347 36.000 0.00 0.00 44.71 2.90
1953 5423 4.646945 TCGAGGAATGAGCAGTAGAGATTT 59.353 41.667 0.00 0.00 0.00 2.17
2061 5686 1.728971 GAGCAGGAATTGTGTGACTCG 59.271 52.381 0.00 0.00 0.00 4.18
2147 6758 9.469807 GTATGTATTTCATGTCACCTAGAGAAG 57.530 37.037 0.00 0.00 37.91 2.85
2183 6795 4.458295 GTCATGCAATGGATTATCTCTGGG 59.542 45.833 0.00 0.00 46.73 4.45
2188 6800 5.360714 TGCAATGGATTATCTCTGGGTTTTC 59.639 40.000 0.00 0.00 0.00 2.29
2197 6809 4.106029 TCTCTGGGTTTTCGTTATCGAG 57.894 45.455 0.00 0.00 46.81 4.04
2200 6812 3.508793 TCTGGGTTTTCGTTATCGAGAGT 59.491 43.478 0.00 0.00 46.81 3.24
2215 6827 2.475852 CGAGAGTAGCGTTACGAAGCTT 60.476 50.000 9.62 0.00 44.15 3.74
2248 6860 3.680937 GCACCTGCGTGTACAGTAAATTA 59.319 43.478 0.00 0.00 42.39 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.730265 AGTTTGACGTGCTCGCAAAA 59.270 45.000 22.53 14.88 40.98 2.44
4 5 1.112459 CAAAAGTTTGACGTGCTCGC 58.888 50.000 8.29 1.97 40.55 5.03
7 8 3.840890 TTGACAAAAGTTTGACGTGCT 57.159 38.095 10.66 0.00 40.55 4.40
8 9 3.857093 ACATTGACAAAAGTTTGACGTGC 59.143 39.130 10.66 0.00 40.55 5.34
76 77 8.274161 CTCATTTGAGCTCAGGATGAACAGTAA 61.274 40.741 29.32 15.35 37.77 2.24
77 78 6.851363 CTCATTTGAGCTCAGGATGAACAGTA 60.851 42.308 29.32 16.17 37.77 2.74
78 79 6.088103 CTCATTTGAGCTCAGGATGAACAGT 61.088 44.000 29.32 7.78 37.77 3.55
79 80 4.333095 CTCATTTGAGCTCAGGATGAACAG 59.667 45.833 29.32 20.62 37.77 3.16
80 81 4.259356 CTCATTTGAGCTCAGGATGAACA 58.741 43.478 29.32 17.12 37.77 3.18
81 82 4.879104 CTCATTTGAGCTCAGGATGAAC 57.121 45.455 29.32 2.18 37.77 3.18
93 94 1.821332 GCTCCCGGGCTCATTTGAG 60.821 63.158 18.49 6.38 44.75 3.02
94 95 2.272146 GCTCCCGGGCTCATTTGA 59.728 61.111 18.49 0.00 0.00 2.69
95 96 2.045045 TGCTCCCGGGCTCATTTG 60.045 61.111 18.49 0.33 0.00 2.32
96 97 1.852157 TTCTGCTCCCGGGCTCATTT 61.852 55.000 18.49 0.00 0.00 2.32
97 98 2.262774 CTTCTGCTCCCGGGCTCATT 62.263 60.000 18.49 0.00 0.00 2.57
98 99 2.688666 TTCTGCTCCCGGGCTCAT 60.689 61.111 18.49 0.00 0.00 2.90
99 100 3.393970 CTTCTGCTCCCGGGCTCA 61.394 66.667 18.49 15.04 0.00 4.26
100 101 2.439104 ATCTTCTGCTCCCGGGCTC 61.439 63.158 18.49 10.53 0.00 4.70
101 102 2.366167 ATCTTCTGCTCCCGGGCT 60.366 61.111 18.49 0.00 0.00 5.19
102 103 2.203126 CATCTTCTGCTCCCGGGC 60.203 66.667 18.49 5.48 0.00 6.13
103 104 1.144936 GTCATCTTCTGCTCCCGGG 59.855 63.158 16.85 16.85 0.00 5.73
104 105 0.539051 AAGTCATCTTCTGCTCCCGG 59.461 55.000 0.00 0.00 0.00 5.73
105 106 2.393271 AAAGTCATCTTCTGCTCCCG 57.607 50.000 0.00 0.00 32.90 5.14
106 107 2.751806 CCAAAAGTCATCTTCTGCTCCC 59.248 50.000 0.00 0.00 32.90 4.30
107 108 2.751806 CCCAAAAGTCATCTTCTGCTCC 59.248 50.000 0.00 0.00 32.90 4.70
108 109 3.416156 ACCCAAAAGTCATCTTCTGCTC 58.584 45.455 0.00 0.00 32.90 4.26
109 110 3.515602 ACCCAAAAGTCATCTTCTGCT 57.484 42.857 0.00 0.00 32.90 4.24
110 111 4.279420 AGAAACCCAAAAGTCATCTTCTGC 59.721 41.667 0.00 0.00 32.90 4.26
111 112 7.693969 ATAGAAACCCAAAAGTCATCTTCTG 57.306 36.000 0.00 0.00 32.90 3.02
112 113 7.119846 CGAATAGAAACCCAAAAGTCATCTTCT 59.880 37.037 0.00 0.00 32.90 2.85
113 114 7.244192 CGAATAGAAACCCAAAAGTCATCTTC 58.756 38.462 0.00 0.00 32.90 2.87
114 115 6.349363 GCGAATAGAAACCCAAAAGTCATCTT 60.349 38.462 0.00 0.00 35.14 2.40
115 116 5.123979 GCGAATAGAAACCCAAAAGTCATCT 59.876 40.000 0.00 0.00 0.00 2.90
116 117 5.123979 AGCGAATAGAAACCCAAAAGTCATC 59.876 40.000 0.00 0.00 0.00 2.92
117 118 5.010282 AGCGAATAGAAACCCAAAAGTCAT 58.990 37.500 0.00 0.00 0.00 3.06
118 119 4.394729 AGCGAATAGAAACCCAAAAGTCA 58.605 39.130 0.00 0.00 0.00 3.41
119 120 5.410439 TGTAGCGAATAGAAACCCAAAAGTC 59.590 40.000 0.00 0.00 0.00 3.01
120 121 5.310451 TGTAGCGAATAGAAACCCAAAAGT 58.690 37.500 0.00 0.00 0.00 2.66
121 122 5.873179 TGTAGCGAATAGAAACCCAAAAG 57.127 39.130 0.00 0.00 0.00 2.27
122 123 5.355910 GGATGTAGCGAATAGAAACCCAAAA 59.644 40.000 0.00 0.00 0.00 2.44
123 124 4.879545 GGATGTAGCGAATAGAAACCCAAA 59.120 41.667 0.00 0.00 0.00 3.28
124 125 4.080807 TGGATGTAGCGAATAGAAACCCAA 60.081 41.667 0.00 0.00 0.00 4.12
125 126 3.452990 TGGATGTAGCGAATAGAAACCCA 59.547 43.478 0.00 0.00 0.00 4.51
126 127 4.067972 TGGATGTAGCGAATAGAAACCC 57.932 45.455 0.00 0.00 0.00 4.11
127 128 6.431198 TTTTGGATGTAGCGAATAGAAACC 57.569 37.500 0.00 0.00 0.00 3.27
128 129 7.640240 GTCATTTTGGATGTAGCGAATAGAAAC 59.360 37.037 0.00 0.00 0.00 2.78
129 130 7.201696 GGTCATTTTGGATGTAGCGAATAGAAA 60.202 37.037 0.00 0.00 0.00 2.52
130 131 6.260050 GGTCATTTTGGATGTAGCGAATAGAA 59.740 38.462 0.00 0.00 0.00 2.10
131 132 5.758296 GGTCATTTTGGATGTAGCGAATAGA 59.242 40.000 0.00 0.00 0.00 1.98
132 133 5.333339 CGGTCATTTTGGATGTAGCGAATAG 60.333 44.000 0.00 0.00 0.00 1.73
133 134 4.509970 CGGTCATTTTGGATGTAGCGAATA 59.490 41.667 0.00 0.00 0.00 1.75
134 135 3.312421 CGGTCATTTTGGATGTAGCGAAT 59.688 43.478 0.00 0.00 0.00 3.34
135 136 2.675844 CGGTCATTTTGGATGTAGCGAA 59.324 45.455 0.00 0.00 0.00 4.70
136 137 2.276201 CGGTCATTTTGGATGTAGCGA 58.724 47.619 0.00 0.00 0.00 4.93
137 138 2.006888 ACGGTCATTTTGGATGTAGCG 58.993 47.619 0.00 0.00 0.00 4.26
138 139 2.354821 GGACGGTCATTTTGGATGTAGC 59.645 50.000 10.76 0.00 0.00 3.58
139 140 2.943033 GGGACGGTCATTTTGGATGTAG 59.057 50.000 10.76 0.00 0.00 2.74
140 141 2.306219 TGGGACGGTCATTTTGGATGTA 59.694 45.455 10.76 0.00 0.00 2.29
141 142 1.074727 TGGGACGGTCATTTTGGATGT 59.925 47.619 10.76 0.00 0.00 3.06
142 143 1.745087 CTGGGACGGTCATTTTGGATG 59.255 52.381 10.76 0.00 0.00 3.51
143 144 2.128771 CTGGGACGGTCATTTTGGAT 57.871 50.000 10.76 0.00 0.00 3.41
144 145 3.642938 CTGGGACGGTCATTTTGGA 57.357 52.632 10.76 0.00 0.00 3.53
154 155 2.240162 GAGCCTACCAACTGGGACGG 62.240 65.000 0.00 0.00 41.15 4.79
155 156 1.218316 GAGCCTACCAACTGGGACG 59.782 63.158 0.00 0.00 41.15 4.79
156 157 1.218316 CGAGCCTACCAACTGGGAC 59.782 63.158 0.00 0.00 41.15 4.46
157 158 1.077805 TCGAGCCTACCAACTGGGA 59.922 57.895 0.00 0.00 41.15 4.37
158 159 1.218316 GTCGAGCCTACCAACTGGG 59.782 63.158 0.00 0.00 44.81 4.45
159 160 0.320374 TTGTCGAGCCTACCAACTGG 59.680 55.000 0.00 0.00 42.17 4.00
160 161 2.386661 ATTGTCGAGCCTACCAACTG 57.613 50.000 0.00 0.00 0.00 3.16
161 162 3.418684 AAATTGTCGAGCCTACCAACT 57.581 42.857 0.00 0.00 0.00 3.16
162 163 5.813080 AATAAATTGTCGAGCCTACCAAC 57.187 39.130 0.00 0.00 0.00 3.77
163 164 6.827586 AAAATAAATTGTCGAGCCTACCAA 57.172 33.333 0.00 0.00 0.00 3.67
164 165 6.316890 GGTAAAATAAATTGTCGAGCCTACCA 59.683 38.462 0.00 0.00 0.00 3.25
165 166 6.238566 GGGTAAAATAAATTGTCGAGCCTACC 60.239 42.308 0.00 0.00 0.00 3.18
166 167 6.238566 GGGGTAAAATAAATTGTCGAGCCTAC 60.239 42.308 0.00 0.00 0.00 3.18
167 168 5.824097 GGGGTAAAATAAATTGTCGAGCCTA 59.176 40.000 0.00 0.00 0.00 3.93
168 169 4.643334 GGGGTAAAATAAATTGTCGAGCCT 59.357 41.667 0.00 0.00 0.00 4.58
169 170 4.496840 CGGGGTAAAATAAATTGTCGAGCC 60.497 45.833 0.00 0.00 0.00 4.70
170 171 4.095334 ACGGGGTAAAATAAATTGTCGAGC 59.905 41.667 0.00 0.00 0.00 5.03
171 172 5.352016 TGACGGGGTAAAATAAATTGTCGAG 59.648 40.000 0.00 0.00 0.00 4.04
172 173 5.243981 TGACGGGGTAAAATAAATTGTCGA 58.756 37.500 0.00 0.00 0.00 4.20
173 174 5.548706 TGACGGGGTAAAATAAATTGTCG 57.451 39.130 0.00 0.00 0.00 4.35
174 175 8.590719 TTTTTGACGGGGTAAAATAAATTGTC 57.409 30.769 0.00 0.00 0.00 3.18
196 197 2.758130 TGGCACCCCTCTTTTCTTTTT 58.242 42.857 0.00 0.00 0.00 1.94
197 198 2.470057 TGGCACCCCTCTTTTCTTTT 57.530 45.000 0.00 0.00 0.00 2.27
198 199 2.470057 TTGGCACCCCTCTTTTCTTT 57.530 45.000 0.00 0.00 0.00 2.52
199 200 2.319844 CTTTGGCACCCCTCTTTTCTT 58.680 47.619 0.00 0.00 0.00 2.52
200 201 1.481242 CCTTTGGCACCCCTCTTTTCT 60.481 52.381 0.00 0.00 0.00 2.52
201 202 0.969149 CCTTTGGCACCCCTCTTTTC 59.031 55.000 0.00 0.00 0.00 2.29
202 203 0.560688 TCCTTTGGCACCCCTCTTTT 59.439 50.000 0.00 0.00 0.00 2.27
203 204 0.786435 ATCCTTTGGCACCCCTCTTT 59.214 50.000 0.00 0.00 0.00 2.52
204 205 0.786435 AATCCTTTGGCACCCCTCTT 59.214 50.000 0.00 0.00 0.00 2.85
205 206 0.786435 AAATCCTTTGGCACCCCTCT 59.214 50.000 0.00 0.00 0.00 3.69
206 207 1.644509 AAAATCCTTTGGCACCCCTC 58.355 50.000 0.00 0.00 0.00 4.30
207 208 3.490060 ATAAAATCCTTTGGCACCCCT 57.510 42.857 0.00 0.00 0.00 4.79
208 209 4.568072 AAATAAAATCCTTTGGCACCCC 57.432 40.909 0.00 0.00 0.00 4.95
209 210 5.878116 GGTAAAATAAAATCCTTTGGCACCC 59.122 40.000 0.00 0.00 0.00 4.61
210 211 5.878116 GGGTAAAATAAAATCCTTTGGCACC 59.122 40.000 0.00 0.00 0.00 5.01
211 212 5.878116 GGGGTAAAATAAAATCCTTTGGCAC 59.122 40.000 0.00 0.00 0.00 5.01
212 213 5.337652 CGGGGTAAAATAAAATCCTTTGGCA 60.338 40.000 0.00 0.00 0.00 4.92
213 214 5.113383 CGGGGTAAAATAAAATCCTTTGGC 58.887 41.667 0.00 0.00 0.00 4.52
214 215 6.071278 TGACGGGGTAAAATAAAATCCTTTGG 60.071 38.462 0.00 0.00 0.00 3.28
215 216 6.926313 TGACGGGGTAAAATAAAATCCTTTG 58.074 36.000 0.00 0.00 0.00 2.77
216 217 7.541916 TTGACGGGGTAAAATAAAATCCTTT 57.458 32.000 0.00 0.00 0.00 3.11
217 218 7.541916 TTTGACGGGGTAAAATAAAATCCTT 57.458 32.000 0.00 0.00 0.00 3.36
218 219 7.541916 TTTTGACGGGGTAAAATAAAATCCT 57.458 32.000 0.00 0.00 0.00 3.24
240 241 1.686587 CGGCACCCCTCTTTTCTTTTT 59.313 47.619 0.00 0.00 0.00 1.94
306 311 6.700960 CCTTGAAACTACATTGTGCAAATGAA 59.299 34.615 20.96 8.14 0.00 2.57
314 319 5.334414 GCTGACTCCTTGAAACTACATTGTG 60.334 44.000 0.00 0.00 0.00 3.33
315 320 4.757149 GCTGACTCCTTGAAACTACATTGT 59.243 41.667 0.00 0.00 0.00 2.71
376 382 9.672086 TGACTACATTTATGTAAAAACAGCAAC 57.328 29.630 4.32 0.00 42.20 4.17
478 487 3.850098 CTCCCTGGCTGCAAACCGT 62.850 63.158 0.50 0.00 0.00 4.83
483 492 2.436109 GGTTCTCCCTGGCTGCAA 59.564 61.111 0.50 0.00 0.00 4.08
489 498 1.447643 CATAGCCGGTTCTCCCTGG 59.552 63.158 1.90 0.00 0.00 4.45
491 500 2.444256 GGCATAGCCGGTTCTCCCT 61.444 63.158 1.90 0.00 39.62 4.20
492 501 2.111251 GGCATAGCCGGTTCTCCC 59.889 66.667 1.90 0.00 39.62 4.30
502 511 5.171337 CGTATCGTTTTTCAAATGGCATAGC 59.829 40.000 0.00 0.00 0.00 2.97
503 512 6.410914 GTCGTATCGTTTTTCAAATGGCATAG 59.589 38.462 0.00 0.00 0.00 2.23
504 513 6.092944 AGTCGTATCGTTTTTCAAATGGCATA 59.907 34.615 0.00 0.00 0.00 3.14
505 514 5.092781 GTCGTATCGTTTTTCAAATGGCAT 58.907 37.500 0.00 0.00 0.00 4.40
506 515 4.214545 AGTCGTATCGTTTTTCAAATGGCA 59.785 37.500 0.00 0.00 0.00 4.92
507 516 4.719040 AGTCGTATCGTTTTTCAAATGGC 58.281 39.130 0.00 0.00 0.00 4.40
508 517 5.788531 GTGAGTCGTATCGTTTTTCAAATGG 59.211 40.000 0.00 0.00 0.00 3.16
509 518 5.499955 CGTGAGTCGTATCGTTTTTCAAATG 59.500 40.000 0.00 0.00 34.52 2.32
510 519 5.403166 TCGTGAGTCGTATCGTTTTTCAAAT 59.597 36.000 0.00 0.00 40.80 2.32
511 520 4.739228 TCGTGAGTCGTATCGTTTTTCAAA 59.261 37.500 0.00 0.00 40.80 2.69
512 521 4.289342 TCGTGAGTCGTATCGTTTTTCAA 58.711 39.130 0.00 0.00 40.80 2.69
513 522 3.887741 TCGTGAGTCGTATCGTTTTTCA 58.112 40.909 0.00 0.00 40.80 2.69
514 523 4.775083 GCATCGTGAGTCGTATCGTTTTTC 60.775 45.833 0.00 0.00 40.80 2.29
515 524 3.060363 GCATCGTGAGTCGTATCGTTTTT 59.940 43.478 0.00 0.00 40.80 1.94
516 525 2.597305 GCATCGTGAGTCGTATCGTTTT 59.403 45.455 0.00 0.00 40.80 2.43
517 526 2.159421 AGCATCGTGAGTCGTATCGTTT 60.159 45.455 0.00 0.00 40.80 3.60
518 527 1.400846 AGCATCGTGAGTCGTATCGTT 59.599 47.619 0.00 0.00 40.80 3.85
519 528 1.015109 AGCATCGTGAGTCGTATCGT 58.985 50.000 0.00 0.00 40.80 3.73
520 529 1.775770 CAAGCATCGTGAGTCGTATCG 59.224 52.381 0.00 0.00 40.80 2.92
521 530 2.531912 CACAAGCATCGTGAGTCGTATC 59.468 50.000 0.00 0.00 40.80 2.24
522 531 2.094700 ACACAAGCATCGTGAGTCGTAT 60.095 45.455 7.11 0.00 40.80 3.06
523 532 1.268625 ACACAAGCATCGTGAGTCGTA 59.731 47.619 7.11 0.00 40.80 3.43
524 533 0.032130 ACACAAGCATCGTGAGTCGT 59.968 50.000 7.11 0.00 40.80 4.34
525 534 1.977188 TACACAAGCATCGTGAGTCG 58.023 50.000 7.11 0.00 37.80 4.18
526 535 3.061295 CACATACACAAGCATCGTGAGTC 59.939 47.826 7.11 0.00 37.80 3.36
527 536 2.995939 CACATACACAAGCATCGTGAGT 59.004 45.455 7.11 0.00 37.80 3.41
528 537 2.349580 CCACATACACAAGCATCGTGAG 59.650 50.000 7.11 0.64 37.80 3.51
529 538 2.345876 CCACATACACAAGCATCGTGA 58.654 47.619 7.11 0.00 37.80 4.35
530 539 1.398041 CCCACATACACAAGCATCGTG 59.602 52.381 0.00 0.00 40.32 4.35
531 540 1.277842 TCCCACATACACAAGCATCGT 59.722 47.619 0.00 0.00 0.00 3.73
532 541 2.022764 TCCCACATACACAAGCATCG 57.977 50.000 0.00 0.00 0.00 3.84
533 542 2.620115 CCATCCCACATACACAAGCATC 59.380 50.000 0.00 0.00 0.00 3.91
534 543 2.658285 CCATCCCACATACACAAGCAT 58.342 47.619 0.00 0.00 0.00 3.79
535 544 1.954733 GCCATCCCACATACACAAGCA 60.955 52.381 0.00 0.00 0.00 3.91
536 545 0.740737 GCCATCCCACATACACAAGC 59.259 55.000 0.00 0.00 0.00 4.01
537 546 1.392589 GGCCATCCCACATACACAAG 58.607 55.000 0.00 0.00 0.00 3.16
538 547 0.393673 CGGCCATCCCACATACACAA 60.394 55.000 2.24 0.00 0.00 3.33
539 548 1.223211 CGGCCATCCCACATACACA 59.777 57.895 2.24 0.00 0.00 3.72
540 549 1.095228 CACGGCCATCCCACATACAC 61.095 60.000 2.24 0.00 0.00 2.90
541 550 1.223211 CACGGCCATCCCACATACA 59.777 57.895 2.24 0.00 0.00 2.29
542 551 0.466543 TACACGGCCATCCCACATAC 59.533 55.000 2.24 0.00 0.00 2.39
543 552 1.071542 CATACACGGCCATCCCACATA 59.928 52.381 2.24 0.00 0.00 2.29
544 553 0.179020 CATACACGGCCATCCCACAT 60.179 55.000 2.24 0.00 0.00 3.21
545 554 1.223211 CATACACGGCCATCCCACA 59.777 57.895 2.24 0.00 0.00 4.17
546 555 1.095228 CACATACACGGCCATCCCAC 61.095 60.000 2.24 0.00 0.00 4.61
547 556 1.223211 CACATACACGGCCATCCCA 59.777 57.895 2.24 0.00 0.00 4.37
548 557 0.532862 CTCACATACACGGCCATCCC 60.533 60.000 2.24 0.00 0.00 3.85
549 558 0.532862 CCTCACATACACGGCCATCC 60.533 60.000 2.24 0.00 0.00 3.51
550 559 0.532862 CCCTCACATACACGGCCATC 60.533 60.000 2.24 0.00 0.00 3.51
551 560 0.980754 TCCCTCACATACACGGCCAT 60.981 55.000 2.24 0.00 0.00 4.40
552 561 1.610967 TCCCTCACATACACGGCCA 60.611 57.895 2.24 0.00 0.00 5.36
553 562 1.153429 GTCCCTCACATACACGGCC 60.153 63.158 0.00 0.00 0.00 6.13
554 563 0.249398 AAGTCCCTCACATACACGGC 59.751 55.000 0.00 0.00 0.00 5.68
555 564 2.762535 AAAGTCCCTCACATACACGG 57.237 50.000 0.00 0.00 0.00 4.94
556 565 5.642063 ACAATTAAAGTCCCTCACATACACG 59.358 40.000 0.00 0.00 0.00 4.49
557 566 7.822822 AGTACAATTAAAGTCCCTCACATACAC 59.177 37.037 0.00 0.00 0.00 2.90
558 567 7.822334 CAGTACAATTAAAGTCCCTCACATACA 59.178 37.037 0.00 0.00 0.00 2.29
559 568 7.822822 ACAGTACAATTAAAGTCCCTCACATAC 59.177 37.037 0.00 0.00 0.00 2.39
560 569 7.822334 CACAGTACAATTAAAGTCCCTCACATA 59.178 37.037 0.00 0.00 0.00 2.29
561 570 6.655003 CACAGTACAATTAAAGTCCCTCACAT 59.345 38.462 0.00 0.00 0.00 3.21
562 571 5.995282 CACAGTACAATTAAAGTCCCTCACA 59.005 40.000 0.00 0.00 0.00 3.58
563 572 6.228258 TCACAGTACAATTAAAGTCCCTCAC 58.772 40.000 0.00 0.00 0.00 3.51
564 573 6.428083 TCACAGTACAATTAAAGTCCCTCA 57.572 37.500 0.00 0.00 0.00 3.86
565 574 9.444600 TTTATCACAGTACAATTAAAGTCCCTC 57.555 33.333 0.00 0.00 0.00 4.30
566 575 9.802039 TTTTATCACAGTACAATTAAAGTCCCT 57.198 29.630 0.00 0.00 0.00 4.20
617 626 7.280205 AGAGAAAAGAACACTCGCTTCTAAAAA 59.720 33.333 0.00 0.00 36.03 1.94
618 627 6.761714 AGAGAAAAGAACACTCGCTTCTAAAA 59.238 34.615 0.00 0.00 36.03 1.52
619 628 6.201044 CAGAGAAAAGAACACTCGCTTCTAAA 59.799 38.462 0.00 0.00 36.03 1.85
620 629 5.692204 CAGAGAAAAGAACACTCGCTTCTAA 59.308 40.000 0.00 0.00 36.03 2.10
621 630 5.009710 TCAGAGAAAAGAACACTCGCTTCTA 59.990 40.000 0.00 0.00 36.03 2.10
622 631 4.054671 CAGAGAAAAGAACACTCGCTTCT 58.945 43.478 0.00 0.00 36.03 2.85
623 632 4.051922 TCAGAGAAAAGAACACTCGCTTC 58.948 43.478 0.00 0.00 36.03 3.86
624 633 4.060038 TCAGAGAAAAGAACACTCGCTT 57.940 40.909 0.00 0.00 36.03 4.68
625 634 3.735237 TCAGAGAAAAGAACACTCGCT 57.265 42.857 0.00 0.00 36.03 4.93
626 635 3.362110 CGTTCAGAGAAAAGAACACTCGC 60.362 47.826 0.00 0.00 43.20 5.03
627 636 3.362110 GCGTTCAGAGAAAAGAACACTCG 60.362 47.826 0.00 0.00 43.20 4.18
628 637 3.804873 AGCGTTCAGAGAAAAGAACACTC 59.195 43.478 0.00 0.00 43.20 3.51
629 638 3.557595 CAGCGTTCAGAGAAAAGAACACT 59.442 43.478 0.00 0.00 43.20 3.55
630 639 3.555956 TCAGCGTTCAGAGAAAAGAACAC 59.444 43.478 0.00 0.00 43.20 3.32
631 640 3.792401 TCAGCGTTCAGAGAAAAGAACA 58.208 40.909 0.00 0.00 43.20 3.18
632 641 3.185391 CCTCAGCGTTCAGAGAAAAGAAC 59.815 47.826 0.00 0.00 40.45 3.01
654 696 4.222847 GGTCGATCTGCCGGTCCC 62.223 72.222 1.90 0.00 0.00 4.46
665 708 1.759445 CAGGAGTGATTGGAGGTCGAT 59.241 52.381 0.00 0.00 0.00 3.59
696 742 0.593128 GTGGGCTGCTTGTGTTACAG 59.407 55.000 0.00 0.00 34.48 2.74
701 747 0.675633 GAAATGTGGGCTGCTTGTGT 59.324 50.000 0.00 0.00 0.00 3.72
737 793 0.179048 TGGCGGAGATGTTGGCATAG 60.179 55.000 0.00 0.00 35.07 2.23
738 794 0.463654 GTGGCGGAGATGTTGGCATA 60.464 55.000 0.00 0.00 40.46 3.14
744 800 1.374252 GTGACGTGGCGGAGATGTT 60.374 57.895 0.00 0.00 0.00 2.71
785 841 0.749454 ATCAGAAGGTTGGATGCGGC 60.749 55.000 0.00 0.00 0.00 6.53
794 850 2.749621 GTTGGATTGCGATCAGAAGGTT 59.250 45.455 15.92 0.00 33.77 3.50
816 873 0.830444 TGTGACGGTAGAGTTGGGCT 60.830 55.000 0.00 0.00 0.00 5.19
929 1006 1.421646 GATGGATTGGGGAATCGGAGT 59.578 52.381 0.00 0.00 0.00 3.85
988 1078 0.387367 CCGGACATCGTCGATGGATC 60.387 60.000 32.48 23.20 43.60 3.36
1167 1268 0.537188 GGAAGATCTTGAGGACGCCA 59.463 55.000 14.00 0.00 0.00 5.69
1352 3655 3.942130 TCCCATCTAGCACGATACATG 57.058 47.619 0.00 0.00 0.00 3.21
1357 3660 4.800914 GCAGTAAATCCCATCTAGCACGAT 60.801 45.833 0.00 0.00 0.00 3.73
1358 3661 3.492656 GCAGTAAATCCCATCTAGCACGA 60.493 47.826 0.00 0.00 0.00 4.35
1359 3662 2.802816 GCAGTAAATCCCATCTAGCACG 59.197 50.000 0.00 0.00 0.00 5.34
1505 4789 2.863137 GCAGATCAAATCAGTCGGTCTC 59.137 50.000 0.00 0.00 0.00 3.36
1567 5026 3.771577 ATCTGGGAAGAAACGAGTGTT 57.228 42.857 0.00 0.00 40.98 3.32
1577 5036 5.663106 AGCAGTACAATCTAATCTGGGAAGA 59.337 40.000 0.00 0.00 0.00 2.87
1696 5155 4.218635 TCTCTTCTACAGATTGCAACGAGT 59.781 41.667 0.00 2.77 0.00 4.18
1708 5167 5.285651 GGACGAATTCCATCTCTTCTACAG 58.714 45.833 0.00 0.00 45.10 2.74
1713 5172 1.861575 GCGGACGAATTCCATCTCTTC 59.138 52.381 0.00 0.00 46.29 2.87
1728 5187 2.100879 AACACTGGACCTGAGCGGAC 62.101 60.000 5.22 0.00 36.31 4.79
1743 5213 3.177997 AGTGATGCCAAACCAAAACAC 57.822 42.857 0.00 0.00 0.00 3.32
1764 5234 8.511604 ACAGAAATATTCGAAGTTCATTCCAT 57.488 30.769 16.71 0.00 34.10 3.41
1814 5284 5.584649 CGTTCAGGAACAGAAGCCATATTTA 59.415 40.000 12.22 0.00 41.20 1.40
1964 5434 6.261826 ACAGTGAGGAACAAGATTTTGAAGAG 59.738 38.462 2.48 0.00 37.73 2.85
1969 5439 5.756195 TCACAGTGAGGAACAAGATTTTG 57.244 39.130 0.00 0.00 40.24 2.44
2061 5686 6.227298 TGATCAGTGAAGATCTAAGGAACC 57.773 41.667 0.00 0.00 43.76 3.62
2121 6732 9.469807 CTTCTCTAGGTGACATGAAATACATAC 57.530 37.037 0.00 0.00 37.46 2.39
2140 6751 7.415541 GCATGACATGTTTTATTGCCTTCTCTA 60.416 37.037 16.62 0.00 0.00 2.43
2147 6758 5.220700 CCATTGCATGACATGTTTTATTGCC 60.221 40.000 16.62 0.00 0.00 4.52
2157 6769 6.349363 CCAGAGATAATCCATTGCATGACATG 60.349 42.308 11.27 11.27 0.00 3.21
2188 6800 3.060940 TCGTAACGCTACTCTCGATAACG 60.061 47.826 0.00 0.00 41.26 3.18
2197 6809 1.918609 CCAAGCTTCGTAACGCTACTC 59.081 52.381 0.00 0.00 34.96 2.59
2200 6812 0.604578 ACCCAAGCTTCGTAACGCTA 59.395 50.000 0.00 0.00 34.96 4.26


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

AutoCloner maintained by Alex Coulton.