Multiple sequence alignment - TraesCS3D01G238100

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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 TraesCS3D01G238100 chr3D 100.000 2255 0 0 1 2255 329499851 329497597 0.000000e+00 4165.0
1 TraesCS3D01G238100 chr3B 93.862 2004 92 13 270 2255 427002099 427000109 0.000000e+00 2990.0
2 TraesCS3D01G238100 chr3A 93.103 1682 72 20 601 2255 444538666 444537002 0.000000e+00 2423.0
3 TraesCS3D01G238100 chr3A 91.156 294 17 5 270 556 444538956 444538665 7.550000e-105 390.0
4 TraesCS3D01G238100 chr1B 78.662 314 66 1 952 1265 662520771 662521083 8.160000e-50 207.0
5 TraesCS3D01G238100 chr1D 78.025 314 68 1 952 1265 476208169 476208481 1.770000e-46 196.0
6 TraesCS3D01G238100 chr1A 77.707 314 69 1 952 1265 571986937 571987249 8.220000e-45 191.0
7 TraesCS3D01G238100 chr7B 90.000 60 6 0 206 265 706115360 706115301 6.680000e-11 78.7
8 TraesCS3D01G238100 chr6D 86.667 60 8 0 206 265 435765923 435765864 1.450000e-07 67.6


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 TraesCS3D01G238100 chr3D 329497597 329499851 2254 True 4165.0 4165 100.0000 1 2255 1 chr3D.!!$R1 2254
1 TraesCS3D01G238100 chr3B 427000109 427002099 1990 True 2990.0 2990 93.8620 270 2255 1 chr3B.!!$R1 1985
2 TraesCS3D01G238100 chr3A 444537002 444538956 1954 True 1406.5 2423 92.1295 270 2255 2 chr3A.!!$R1 1985

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
55 56 0.032017 ACCCTCACGCCTCTCCTATT 60.032 55.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1885 0.158928 GACTTTCGTCGAACGTGCTG 59.841 55.0 20.31 4.32 43.14 4.41 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 4.728058 GAGCGCATGAGAGAGACC 57.272 61.111 11.47 0.00 0.00 3.85
18 19 1.812525 GAGCGCATGAGAGAGACCA 59.187 57.895 11.47 0.00 0.00 4.02
19 20 0.388659 GAGCGCATGAGAGAGACCAT 59.611 55.000 11.47 0.00 0.00 3.55
20 21 0.104487 AGCGCATGAGAGAGACCATG 59.896 55.000 11.47 0.00 42.13 3.66
21 22 0.879400 GCGCATGAGAGAGACCATGG 60.879 60.000 11.19 11.19 40.22 3.66
22 23 0.749049 CGCATGAGAGAGACCATGGA 59.251 55.000 21.47 0.00 40.22 3.41
23 24 1.269673 CGCATGAGAGAGACCATGGAG 60.270 57.143 21.47 0.00 40.22 3.86
24 25 2.037901 GCATGAGAGAGACCATGGAGA 58.962 52.381 21.47 0.00 40.22 3.71
25 26 2.433604 GCATGAGAGAGACCATGGAGAA 59.566 50.000 21.47 0.00 40.22 2.87
26 27 3.493002 GCATGAGAGAGACCATGGAGAAG 60.493 52.174 21.47 0.00 40.22 2.85
27 28 3.746792 TGAGAGAGACCATGGAGAAGA 57.253 47.619 21.47 0.00 0.00 2.87
28 29 4.262891 TGAGAGAGACCATGGAGAAGAT 57.737 45.455 21.47 0.00 0.00 2.40
29 30 4.618635 TGAGAGAGACCATGGAGAAGATT 58.381 43.478 21.47 0.00 0.00 2.40
30 31 5.770919 TGAGAGAGACCATGGAGAAGATTA 58.229 41.667 21.47 0.00 0.00 1.75
31 32 5.832595 TGAGAGAGACCATGGAGAAGATTAG 59.167 44.000 21.47 0.00 0.00 1.73
32 33 6.024563 AGAGAGACCATGGAGAAGATTAGA 57.975 41.667 21.47 0.00 0.00 2.10
33 34 6.439487 AGAGAGACCATGGAGAAGATTAGAA 58.561 40.000 21.47 0.00 0.00 2.10
34 35 6.900186 AGAGAGACCATGGAGAAGATTAGAAA 59.100 38.462 21.47 0.00 0.00 2.52
35 36 6.883744 AGAGACCATGGAGAAGATTAGAAAC 58.116 40.000 21.47 0.00 0.00 2.78
36 37 6.441924 AGAGACCATGGAGAAGATTAGAAACA 59.558 38.462 21.47 0.00 0.00 2.83
37 38 6.410540 AGACCATGGAGAAGATTAGAAACAC 58.589 40.000 21.47 0.00 0.00 3.32
38 39 5.501156 ACCATGGAGAAGATTAGAAACACC 58.499 41.667 21.47 0.00 0.00 4.16
39 40 4.884164 CCATGGAGAAGATTAGAAACACCC 59.116 45.833 5.56 0.00 0.00 4.61
40 41 5.339530 CCATGGAGAAGATTAGAAACACCCT 60.340 44.000 5.56 0.00 0.00 4.34
41 42 5.422214 TGGAGAAGATTAGAAACACCCTC 57.578 43.478 0.00 0.00 0.00 4.30
42 43 4.844085 TGGAGAAGATTAGAAACACCCTCA 59.156 41.667 0.00 0.00 0.00 3.86
43 44 5.179533 GGAGAAGATTAGAAACACCCTCAC 58.820 45.833 0.00 0.00 0.00 3.51
44 45 4.822026 AGAAGATTAGAAACACCCTCACG 58.178 43.478 0.00 0.00 0.00 4.35
45 46 2.973945 AGATTAGAAACACCCTCACGC 58.026 47.619 0.00 0.00 0.00 5.34
46 47 2.007608 GATTAGAAACACCCTCACGCC 58.992 52.381 0.00 0.00 0.00 5.68
47 48 1.053424 TTAGAAACACCCTCACGCCT 58.947 50.000 0.00 0.00 0.00 5.52
48 49 0.606604 TAGAAACACCCTCACGCCTC 59.393 55.000 0.00 0.00 0.00 4.70
49 50 1.122019 AGAAACACCCTCACGCCTCT 61.122 55.000 0.00 0.00 0.00 3.69
50 51 0.670854 GAAACACCCTCACGCCTCTC 60.671 60.000 0.00 0.00 0.00 3.20
51 52 2.113243 AAACACCCTCACGCCTCTCC 62.113 60.000 0.00 0.00 0.00 3.71
52 53 2.681778 CACCCTCACGCCTCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
53 54 1.379977 CACCCTCACGCCTCTCCTA 60.380 63.158 0.00 0.00 0.00 2.94
54 55 0.757188 CACCCTCACGCCTCTCCTAT 60.757 60.000 0.00 0.00 0.00 2.57
55 56 0.032017 ACCCTCACGCCTCTCCTATT 60.032 55.000 0.00 0.00 0.00 1.73
56 57 0.676736 CCCTCACGCCTCTCCTATTC 59.323 60.000 0.00 0.00 0.00 1.75
57 58 0.312416 CCTCACGCCTCTCCTATTCG 59.688 60.000 0.00 0.00 0.00 3.34
58 59 0.318275 CTCACGCCTCTCCTATTCGC 60.318 60.000 0.00 0.00 0.00 4.70
60 61 2.731348 CGCCTCTCCTATTCGCGC 60.731 66.667 0.00 0.00 36.02 6.86
61 62 2.356433 GCCTCTCCTATTCGCGCC 60.356 66.667 0.00 0.00 0.00 6.53
62 63 2.049985 CCTCTCCTATTCGCGCCG 60.050 66.667 0.00 0.00 0.00 6.46
63 64 2.049985 CTCTCCTATTCGCGCCGG 60.050 66.667 0.00 0.00 0.00 6.13
64 65 3.559657 CTCTCCTATTCGCGCCGGG 62.560 68.421 2.18 0.00 0.00 5.73
65 66 3.602677 CTCCTATTCGCGCCGGGA 61.603 66.667 2.18 0.00 0.00 5.14
66 67 3.559657 CTCCTATTCGCGCCGGGAG 62.560 68.421 17.56 17.56 37.76 4.30
86 87 3.636153 GGAAGGACCTGCTGATTTACT 57.364 47.619 0.00 0.00 35.41 2.24
87 88 4.755266 GGAAGGACCTGCTGATTTACTA 57.245 45.455 0.00 0.00 35.41 1.82
88 89 4.698575 GGAAGGACCTGCTGATTTACTAG 58.301 47.826 0.00 0.00 35.41 2.57
89 90 3.828875 AGGACCTGCTGATTTACTAGC 57.171 47.619 0.00 0.00 40.29 3.42
90 91 2.101582 AGGACCTGCTGATTTACTAGCG 59.898 50.000 0.00 0.00 42.74 4.26
91 92 2.100916 GGACCTGCTGATTTACTAGCGA 59.899 50.000 0.00 0.00 42.74 4.93
92 93 3.243907 GGACCTGCTGATTTACTAGCGAT 60.244 47.826 0.00 0.00 42.74 4.58
93 94 4.022242 GGACCTGCTGATTTACTAGCGATA 60.022 45.833 0.00 0.00 42.74 2.92
94 95 5.336849 GGACCTGCTGATTTACTAGCGATAT 60.337 44.000 0.00 0.00 42.74 1.63
95 96 5.715070 ACCTGCTGATTTACTAGCGATATC 58.285 41.667 0.00 0.00 42.74 1.63
96 97 5.478679 ACCTGCTGATTTACTAGCGATATCT 59.521 40.000 0.34 0.00 42.74 1.98
97 98 6.015010 ACCTGCTGATTTACTAGCGATATCTT 60.015 38.462 0.34 0.00 42.74 2.40
98 99 6.870965 CCTGCTGATTTACTAGCGATATCTTT 59.129 38.462 0.34 0.00 42.74 2.52
99 100 7.386299 CCTGCTGATTTACTAGCGATATCTTTT 59.614 37.037 0.34 0.00 42.74 2.27
100 101 8.076714 TGCTGATTTACTAGCGATATCTTTTG 57.923 34.615 0.34 0.00 42.74 2.44
101 102 7.012358 GCTGATTTACTAGCGATATCTTTTGC 58.988 38.462 0.34 0.00 0.00 3.68
102 103 7.105494 TGATTTACTAGCGATATCTTTTGCG 57.895 36.000 0.34 0.00 0.00 4.85
106 107 3.736581 GCGATATCTTTTGCGCTCC 57.263 52.632 9.73 0.00 45.41 4.70
107 108 1.221414 GCGATATCTTTTGCGCTCCT 58.779 50.000 9.73 0.00 45.41 3.69
108 109 1.193426 GCGATATCTTTTGCGCTCCTC 59.807 52.381 9.73 0.00 45.41 3.71
109 110 2.473816 CGATATCTTTTGCGCTCCTCA 58.526 47.619 9.73 0.00 0.00 3.86
110 111 2.219674 CGATATCTTTTGCGCTCCTCAC 59.780 50.000 9.73 0.00 0.00 3.51
111 112 3.462021 GATATCTTTTGCGCTCCTCACT 58.538 45.455 9.73 0.00 0.00 3.41
112 113 2.191128 ATCTTTTGCGCTCCTCACTT 57.809 45.000 9.73 0.00 0.00 3.16
113 114 1.512926 TCTTTTGCGCTCCTCACTTC 58.487 50.000 9.73 0.00 0.00 3.01
114 115 0.519077 CTTTTGCGCTCCTCACTTCC 59.481 55.000 9.73 0.00 0.00 3.46
115 116 0.108585 TTTTGCGCTCCTCACTTCCT 59.891 50.000 9.73 0.00 0.00 3.36
116 117 0.603707 TTTGCGCTCCTCACTTCCTG 60.604 55.000 9.73 0.00 0.00 3.86
117 118 1.758440 TTGCGCTCCTCACTTCCTGT 61.758 55.000 9.73 0.00 0.00 4.00
118 119 1.446966 GCGCTCCTCACTTCCTGTC 60.447 63.158 0.00 0.00 0.00 3.51
119 120 1.153939 CGCTCCTCACTTCCTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
120 121 1.867919 CGCTCCTCACTTCCTGTCGT 61.868 60.000 0.00 0.00 0.00 4.34
121 122 0.318762 GCTCCTCACTTCCTGTCGTT 59.681 55.000 0.00 0.00 0.00 3.85
122 123 1.270358 GCTCCTCACTTCCTGTCGTTT 60.270 52.381 0.00 0.00 0.00 3.60
123 124 2.408050 CTCCTCACTTCCTGTCGTTTG 58.592 52.381 0.00 0.00 0.00 2.93
124 125 1.070134 TCCTCACTTCCTGTCGTTTGG 59.930 52.381 0.00 0.00 0.00 3.28
125 126 1.070134 CCTCACTTCCTGTCGTTTGGA 59.930 52.381 0.00 0.00 0.00 3.53
126 127 2.135933 CTCACTTCCTGTCGTTTGGAC 58.864 52.381 0.00 0.00 46.27 4.02
127 128 1.202604 TCACTTCCTGTCGTTTGGACC 60.203 52.381 0.00 0.00 45.46 4.46
128 129 1.129058 ACTTCCTGTCGTTTGGACCT 58.871 50.000 0.00 0.00 45.46 3.85
129 130 2.036733 CACTTCCTGTCGTTTGGACCTA 59.963 50.000 0.00 0.00 45.46 3.08
130 131 2.904434 ACTTCCTGTCGTTTGGACCTAT 59.096 45.455 0.00 0.00 45.46 2.57
131 132 3.326880 ACTTCCTGTCGTTTGGACCTATT 59.673 43.478 0.00 0.00 45.46 1.73
132 133 3.604875 TCCTGTCGTTTGGACCTATTC 57.395 47.619 0.00 0.00 45.46 1.75
133 134 2.235402 TCCTGTCGTTTGGACCTATTCC 59.765 50.000 0.00 0.00 45.46 3.01
147 148 7.562454 GGACCTATTCCGTATTTCATTTTCA 57.438 36.000 0.00 0.00 33.46 2.69
148 149 8.166422 GGACCTATTCCGTATTTCATTTTCAT 57.834 34.615 0.00 0.00 33.46 2.57
149 150 8.290325 GGACCTATTCCGTATTTCATTTTCATC 58.710 37.037 0.00 0.00 33.46 2.92
150 151 7.861630 ACCTATTCCGTATTTCATTTTCATCG 58.138 34.615 0.00 0.00 0.00 3.84
151 152 7.041372 ACCTATTCCGTATTTCATTTTCATCGG 60.041 37.037 0.00 0.00 38.36 4.18
152 153 6.693315 ATTCCGTATTTCATTTTCATCGGT 57.307 33.333 0.00 0.00 38.21 4.69
153 154 5.478233 TCCGTATTTCATTTTCATCGGTG 57.522 39.130 0.00 0.00 38.21 4.94
154 155 4.035017 CCGTATTTCATTTTCATCGGTGC 58.965 43.478 0.00 0.00 33.39 5.01
155 156 4.201910 CCGTATTTCATTTTCATCGGTGCT 60.202 41.667 0.00 0.00 33.39 4.40
156 157 4.730042 CGTATTTCATTTTCATCGGTGCTG 59.270 41.667 0.00 0.00 0.00 4.41
157 158 4.789012 ATTTCATTTTCATCGGTGCTGT 57.211 36.364 0.00 0.00 0.00 4.40
158 159 3.829886 TTCATTTTCATCGGTGCTGTC 57.170 42.857 0.00 0.00 0.00 3.51
159 160 2.777094 TCATTTTCATCGGTGCTGTCA 58.223 42.857 0.00 0.00 0.00 3.58
160 161 3.346315 TCATTTTCATCGGTGCTGTCAT 58.654 40.909 0.00 0.00 0.00 3.06
161 162 3.127376 TCATTTTCATCGGTGCTGTCATG 59.873 43.478 0.00 0.00 0.00 3.07
162 163 2.183478 TTTCATCGGTGCTGTCATGT 57.817 45.000 0.00 0.00 0.00 3.21
163 164 3.326836 TTTCATCGGTGCTGTCATGTA 57.673 42.857 0.00 0.00 0.00 2.29
164 165 3.541996 TTCATCGGTGCTGTCATGTAT 57.458 42.857 0.00 0.00 0.00 2.29
165 166 3.097877 TCATCGGTGCTGTCATGTATC 57.902 47.619 0.00 0.00 0.00 2.24
166 167 2.430332 TCATCGGTGCTGTCATGTATCA 59.570 45.455 0.00 0.00 0.00 2.15
167 168 3.070015 TCATCGGTGCTGTCATGTATCAT 59.930 43.478 0.00 0.00 0.00 2.45
168 169 3.541996 TCGGTGCTGTCATGTATCATT 57.458 42.857 0.00 0.00 0.00 2.57
169 170 3.872696 TCGGTGCTGTCATGTATCATTT 58.127 40.909 0.00 0.00 0.00 2.32
170 171 3.622612 TCGGTGCTGTCATGTATCATTTG 59.377 43.478 0.00 0.00 0.00 2.32
171 172 3.622612 CGGTGCTGTCATGTATCATTTGA 59.377 43.478 0.00 0.00 0.00 2.69
172 173 4.094739 CGGTGCTGTCATGTATCATTTGAA 59.905 41.667 0.00 0.00 0.00 2.69
173 174 5.335127 GGTGCTGTCATGTATCATTTGAAC 58.665 41.667 0.00 0.00 0.00 3.18
174 175 5.124457 GGTGCTGTCATGTATCATTTGAACT 59.876 40.000 0.00 0.00 0.00 3.01
175 176 6.349611 GGTGCTGTCATGTATCATTTGAACTT 60.350 38.462 0.00 0.00 0.00 2.66
176 177 7.148255 GGTGCTGTCATGTATCATTTGAACTTA 60.148 37.037 0.00 0.00 0.00 2.24
177 178 7.907045 GTGCTGTCATGTATCATTTGAACTTAG 59.093 37.037 0.00 0.00 0.00 2.18
178 179 7.607607 TGCTGTCATGTATCATTTGAACTTAGT 59.392 33.333 0.00 0.00 0.00 2.24
179 180 7.907045 GCTGTCATGTATCATTTGAACTTAGTG 59.093 37.037 0.00 0.00 0.00 2.74
180 181 8.267620 TGTCATGTATCATTTGAACTTAGTGG 57.732 34.615 0.00 0.00 0.00 4.00
181 182 7.882791 TGTCATGTATCATTTGAACTTAGTGGT 59.117 33.333 0.00 0.00 0.00 4.16
182 183 8.730680 GTCATGTATCATTTGAACTTAGTGGTT 58.269 33.333 0.00 0.00 0.00 3.67
183 184 8.729756 TCATGTATCATTTGAACTTAGTGGTTG 58.270 33.333 0.00 0.00 0.00 3.77
184 185 8.514594 CATGTATCATTTGAACTTAGTGGTTGT 58.485 33.333 0.00 0.00 0.00 3.32
185 186 9.733556 ATGTATCATTTGAACTTAGTGGTTGTA 57.266 29.630 0.00 0.00 0.00 2.41
186 187 9.214957 TGTATCATTTGAACTTAGTGGTTGTAG 57.785 33.333 0.00 0.00 0.00 2.74
187 188 7.687941 ATCATTTGAACTTAGTGGTTGTAGG 57.312 36.000 0.00 0.00 0.00 3.18
188 189 6.597562 TCATTTGAACTTAGTGGTTGTAGGT 58.402 36.000 0.00 0.00 0.00 3.08
189 190 7.057894 TCATTTGAACTTAGTGGTTGTAGGTT 58.942 34.615 0.00 0.00 0.00 3.50
190 191 7.558444 TCATTTGAACTTAGTGGTTGTAGGTTT 59.442 33.333 0.00 0.00 0.00 3.27
191 192 6.930667 TTGAACTTAGTGGTTGTAGGTTTC 57.069 37.500 0.00 0.00 0.00 2.78
192 193 5.991861 TGAACTTAGTGGTTGTAGGTTTCA 58.008 37.500 0.00 0.00 0.00 2.69
193 194 6.053005 TGAACTTAGTGGTTGTAGGTTTCAG 58.947 40.000 0.00 0.00 0.00 3.02
194 195 5.625568 ACTTAGTGGTTGTAGGTTTCAGT 57.374 39.130 0.00 0.00 0.00 3.41
195 196 6.736110 ACTTAGTGGTTGTAGGTTTCAGTA 57.264 37.500 0.00 0.00 0.00 2.74
196 197 6.519382 ACTTAGTGGTTGTAGGTTTCAGTAC 58.481 40.000 0.00 0.00 0.00 2.73
197 198 6.325804 ACTTAGTGGTTGTAGGTTTCAGTACT 59.674 38.462 0.00 0.00 0.00 2.73
198 199 5.625568 AGTGGTTGTAGGTTTCAGTACTT 57.374 39.130 0.00 0.00 0.00 2.24
199 200 5.365619 AGTGGTTGTAGGTTTCAGTACTTG 58.634 41.667 0.00 0.00 0.00 3.16
200 201 5.104652 AGTGGTTGTAGGTTTCAGTACTTGT 60.105 40.000 0.00 0.00 0.00 3.16
201 202 5.587443 GTGGTTGTAGGTTTCAGTACTTGTT 59.413 40.000 0.00 0.00 0.00 2.83
202 203 5.818857 TGGTTGTAGGTTTCAGTACTTGTTC 59.181 40.000 0.00 0.00 0.00 3.18
203 204 5.050567 GGTTGTAGGTTTCAGTACTTGTTCG 60.051 44.000 0.00 0.00 0.00 3.95
204 205 5.518848 TGTAGGTTTCAGTACTTGTTCGA 57.481 39.130 0.00 0.00 0.00 3.71
205 206 5.904941 TGTAGGTTTCAGTACTTGTTCGAA 58.095 37.500 0.00 0.00 0.00 3.71
206 207 6.518493 TGTAGGTTTCAGTACTTGTTCGAAT 58.482 36.000 0.00 0.00 0.00 3.34
207 208 5.924475 AGGTTTCAGTACTTGTTCGAATG 57.076 39.130 0.00 0.00 0.00 2.67
208 209 4.213482 AGGTTTCAGTACTTGTTCGAATGC 59.787 41.667 0.00 0.00 0.00 3.56
209 210 4.213482 GGTTTCAGTACTTGTTCGAATGCT 59.787 41.667 0.00 0.00 0.00 3.79
210 211 4.990543 TTCAGTACTTGTTCGAATGCTG 57.009 40.909 0.00 4.65 0.00 4.41
211 212 3.990092 TCAGTACTTGTTCGAATGCTGT 58.010 40.909 12.36 7.54 0.00 4.40
212 213 3.987868 TCAGTACTTGTTCGAATGCTGTC 59.012 43.478 12.36 0.00 0.00 3.51
213 214 3.990469 CAGTACTTGTTCGAATGCTGTCT 59.010 43.478 0.00 0.00 0.00 3.41
214 215 4.449068 CAGTACTTGTTCGAATGCTGTCTT 59.551 41.667 0.00 0.00 0.00 3.01
215 216 5.633601 CAGTACTTGTTCGAATGCTGTCTTA 59.366 40.000 0.00 0.00 0.00 2.10
216 217 6.311445 CAGTACTTGTTCGAATGCTGTCTTAT 59.689 38.462 0.00 0.00 0.00 1.73
217 218 5.536554 ACTTGTTCGAATGCTGTCTTATG 57.463 39.130 0.00 0.00 0.00 1.90
218 219 4.393062 ACTTGTTCGAATGCTGTCTTATGG 59.607 41.667 0.00 0.00 0.00 2.74
219 220 2.677836 TGTTCGAATGCTGTCTTATGGC 59.322 45.455 0.00 0.00 0.00 4.40
220 221 2.939103 GTTCGAATGCTGTCTTATGGCT 59.061 45.455 0.00 0.00 0.00 4.75
221 222 3.266510 TCGAATGCTGTCTTATGGCTT 57.733 42.857 0.00 0.00 0.00 4.35
222 223 3.609853 TCGAATGCTGTCTTATGGCTTT 58.390 40.909 0.00 0.00 0.00 3.51
223 224 4.765273 TCGAATGCTGTCTTATGGCTTTA 58.235 39.130 0.00 0.00 0.00 1.85
224 225 5.368145 TCGAATGCTGTCTTATGGCTTTAT 58.632 37.500 0.00 0.00 0.00 1.40
225 226 5.822519 TCGAATGCTGTCTTATGGCTTTATT 59.177 36.000 0.00 0.00 0.00 1.40
226 227 6.989759 TCGAATGCTGTCTTATGGCTTTATTA 59.010 34.615 0.00 0.00 0.00 0.98
227 228 7.497579 TCGAATGCTGTCTTATGGCTTTATTAA 59.502 33.333 0.00 0.00 0.00 1.40
228 229 8.292448 CGAATGCTGTCTTATGGCTTTATTAAT 58.708 33.333 0.00 0.00 0.00 1.40
229 230 9.971922 GAATGCTGTCTTATGGCTTTATTAATT 57.028 29.630 0.00 0.00 0.00 1.40
241 242 8.450385 TGGCTTTATTAATTTAAAACCGAACG 57.550 30.769 0.00 0.00 32.38 3.95
242 243 7.062022 TGGCTTTATTAATTTAAAACCGAACGC 59.938 33.333 0.00 0.00 32.38 4.84
243 244 7.274033 GGCTTTATTAATTTAAAACCGAACGCT 59.726 33.333 0.00 0.00 0.00 5.07
244 245 8.309019 GCTTTATTAATTTAAAACCGAACGCTC 58.691 33.333 0.00 0.00 0.00 5.03
245 246 8.672214 TTTATTAATTTAAAACCGAACGCTCC 57.328 30.769 0.00 0.00 0.00 4.70
246 247 5.945466 TTAATTTAAAACCGAACGCTCCT 57.055 34.783 0.00 0.00 0.00 3.69
247 248 7.614124 ATTAATTTAAAACCGAACGCTCCTA 57.386 32.000 0.00 0.00 0.00 2.94
248 249 5.541098 AATTTAAAACCGAACGCTCCTAG 57.459 39.130 0.00 0.00 0.00 3.02
249 250 3.665745 TTAAAACCGAACGCTCCTAGT 57.334 42.857 0.00 0.00 0.00 2.57
250 251 1.792006 AAAACCGAACGCTCCTAGTG 58.208 50.000 0.00 0.00 0.00 2.74
251 252 0.677842 AAACCGAACGCTCCTAGTGT 59.322 50.000 0.00 0.00 41.35 3.55
252 253 0.243095 AACCGAACGCTCCTAGTGTC 59.757 55.000 0.00 0.00 38.11 3.67
253 254 0.608582 ACCGAACGCTCCTAGTGTCT 60.609 55.000 0.00 0.00 38.11 3.41
254 255 0.526662 CCGAACGCTCCTAGTGTCTT 59.473 55.000 0.00 0.00 38.11 3.01
255 256 1.467713 CCGAACGCTCCTAGTGTCTTC 60.468 57.143 0.00 0.00 38.11 2.87
256 257 1.790838 CGAACGCTCCTAGTGTCTTCG 60.791 57.143 0.00 0.00 38.11 3.79
257 258 1.199558 GAACGCTCCTAGTGTCTTCGT 59.800 52.381 0.00 0.00 38.11 3.85
258 259 1.245732 ACGCTCCTAGTGTCTTCGTT 58.754 50.000 0.00 0.00 32.75 3.85
259 260 1.612463 ACGCTCCTAGTGTCTTCGTTT 59.388 47.619 0.00 0.00 32.75 3.60
260 261 2.251893 CGCTCCTAGTGTCTTCGTTTC 58.748 52.381 0.00 0.00 0.00 2.78
261 262 2.351447 CGCTCCTAGTGTCTTCGTTTCA 60.351 50.000 0.00 0.00 0.00 2.69
262 263 3.650139 GCTCCTAGTGTCTTCGTTTCAA 58.350 45.455 0.00 0.00 0.00 2.69
263 264 4.056050 GCTCCTAGTGTCTTCGTTTCAAA 58.944 43.478 0.00 0.00 0.00 2.69
264 265 4.510340 GCTCCTAGTGTCTTCGTTTCAAAA 59.490 41.667 0.00 0.00 0.00 2.44
265 266 5.558463 GCTCCTAGTGTCTTCGTTTCAAAAC 60.558 44.000 0.00 0.00 35.59 2.43
299 300 4.394920 GGTCTCTTGATCGGTTGCATAAAA 59.605 41.667 0.00 0.00 0.00 1.52
300 301 5.106317 GGTCTCTTGATCGGTTGCATAAAAA 60.106 40.000 0.00 0.00 0.00 1.94
322 324 3.837213 AAAGACAATGTGATCAAGCGG 57.163 42.857 0.00 0.00 0.00 5.52
377 379 2.782341 CCCCAATTCCTCTCCATCTTCT 59.218 50.000 0.00 0.00 0.00 2.85
399 401 4.365514 TCTGATTCTGTAGCCACCAAAA 57.634 40.909 0.00 0.00 0.00 2.44
421 423 1.471676 GCATCGAACCAGACTACCAGG 60.472 57.143 0.00 0.00 0.00 4.45
491 499 1.079543 CACTCTGCCTCAACCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
501 509 2.555199 CTCAACCCTCGATCATGAACC 58.445 52.381 0.00 0.00 0.00 3.62
520 528 0.661552 CGCTTGGCATGAAGATCCAG 59.338 55.000 4.32 0.00 0.00 3.86
544 552 5.874810 GGTGCAGTCATCTCACAAACTATTA 59.125 40.000 0.00 0.00 32.69 0.98
567 575 1.962807 TCACCCAAGTTCATGGCAAAG 59.037 47.619 0.00 0.00 39.26 2.77
576 584 4.613437 AGTTCATGGCAAAGGTAATCCAT 58.387 39.130 0.00 0.00 39.72 3.41
591 599 2.335681 TCCATGGACCACCTACAAGA 57.664 50.000 11.44 0.00 37.04 3.02
595 603 1.416243 TGGACCACCTACAAGACGTT 58.584 50.000 0.00 0.00 37.04 3.99
628 638 1.696884 ACCGCATGGAAAAACCCAATT 59.303 42.857 0.00 0.00 40.04 2.32
736 751 2.143458 CGCAACGCAATACAACGGC 61.143 57.895 0.00 0.00 0.00 5.68
740 755 3.794242 CGCAATACAACGGCGGCA 61.794 61.111 13.24 0.00 46.46 5.69
741 756 2.202427 GCAATACAACGGCGGCAC 60.202 61.111 13.24 0.00 0.00 5.01
772 787 5.441700 CTACAAATAGCACACTCAACTCG 57.558 43.478 0.00 0.00 0.00 4.18
782 797 1.664649 CTCAACTCGACGGCAGCAA 60.665 57.895 0.00 0.00 0.00 3.91
849 866 3.057946 ACTCAGCCGCAAATTCTTTCTTC 60.058 43.478 0.00 0.00 0.00 2.87
850 867 2.228822 TCAGCCGCAAATTCTTTCTTCC 59.771 45.455 0.00 0.00 0.00 3.46
859 886 5.936956 GCAAATTCTTTCTTCCTCTCTCTCA 59.063 40.000 0.00 0.00 0.00 3.27
863 890 4.085733 TCTTTCTTCCTCTCTCTCACTGG 58.914 47.826 0.00 0.00 0.00 4.00
912 940 1.668294 CAGCCGGCCACTCCTATAG 59.332 63.158 26.15 0.00 0.00 1.31
1304 1332 7.093322 AGGAATTCAGAACAGTGCATAATTC 57.907 36.000 7.93 8.97 33.30 2.17
1615 1648 0.614979 AGGTCGGTCTGGCTGTGTAT 60.615 55.000 0.00 0.00 0.00 2.29
1619 1652 0.108804 CGGTCTGGCTGTGTATCGTT 60.109 55.000 0.00 0.00 0.00 3.85
1629 1662 5.703592 TGGCTGTGTATCGTTAAAACAAGAT 59.296 36.000 0.00 0.00 0.00 2.40
1649 1682 5.745227 AGATAAAGACATCAACGTTCCCAT 58.255 37.500 0.00 0.00 0.00 4.00
1650 1683 6.884832 AGATAAAGACATCAACGTTCCCATA 58.115 36.000 0.00 0.00 0.00 2.74
1651 1684 7.509546 AGATAAAGACATCAACGTTCCCATAT 58.490 34.615 0.00 0.00 0.00 1.78
1674 1707 3.244112 ACACTACTGTCCTACAAAGGTGC 60.244 47.826 0.00 0.00 44.09 5.01
1752 1786 3.763360 CCCTAATGTCTTGCATGGACAAA 59.237 43.478 21.27 13.97 45.09 2.83
1767 1801 4.055360 TGGACAAACAATAGACACGACTG 58.945 43.478 0.00 0.00 0.00 3.51
1851 1885 5.409214 TGTATAAAGTTGCTACCACGGAAAC 59.591 40.000 0.00 0.00 0.00 2.78
1999 2037 6.415596 GGAGACTTCCGCTCTTCAAGTATTG 61.416 48.000 0.00 0.00 39.84 1.90
2121 2166 1.217585 CTGATCCACGCGGCTACATG 61.218 60.000 12.47 0.00 0.00 3.21
2211 2256 1.251251 AGCAGCACCTTGAATCAACC 58.749 50.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.388659 ATGGTCTCTCTCATGCGCTC 59.611 55.000 9.73 0.00 0.00 5.03
1 2 0.104487 CATGGTCTCTCTCATGCGCT 59.896 55.000 9.73 0.00 35.07 5.92
2 3 0.879400 CCATGGTCTCTCTCATGCGC 60.879 60.000 2.57 0.00 39.36 6.09
3 4 0.749049 TCCATGGTCTCTCTCATGCG 59.251 55.000 12.58 0.00 39.36 4.73
4 5 2.037901 TCTCCATGGTCTCTCTCATGC 58.962 52.381 12.58 0.00 39.36 4.06
5 6 3.959449 TCTTCTCCATGGTCTCTCTCATG 59.041 47.826 12.58 0.00 40.12 3.07
6 7 4.262891 TCTTCTCCATGGTCTCTCTCAT 57.737 45.455 12.58 0.00 0.00 2.90
7 8 3.746792 TCTTCTCCATGGTCTCTCTCA 57.253 47.619 12.58 0.00 0.00 3.27
8 9 6.068010 TCTAATCTTCTCCATGGTCTCTCTC 58.932 44.000 12.58 0.00 0.00 3.20
9 10 6.024563 TCTAATCTTCTCCATGGTCTCTCT 57.975 41.667 12.58 0.00 0.00 3.10
10 11 6.723298 TTCTAATCTTCTCCATGGTCTCTC 57.277 41.667 12.58 0.00 0.00 3.20
11 12 6.441924 TGTTTCTAATCTTCTCCATGGTCTCT 59.558 38.462 12.58 0.00 0.00 3.10
12 13 6.536941 GTGTTTCTAATCTTCTCCATGGTCTC 59.463 42.308 12.58 0.00 0.00 3.36
13 14 6.410540 GTGTTTCTAATCTTCTCCATGGTCT 58.589 40.000 12.58 0.00 0.00 3.85
14 15 5.586643 GGTGTTTCTAATCTTCTCCATGGTC 59.413 44.000 12.58 0.00 0.00 4.02
15 16 5.501156 GGTGTTTCTAATCTTCTCCATGGT 58.499 41.667 12.58 0.00 0.00 3.55
16 17 4.884164 GGGTGTTTCTAATCTTCTCCATGG 59.116 45.833 4.97 4.97 0.00 3.66
17 18 5.749462 AGGGTGTTTCTAATCTTCTCCATG 58.251 41.667 0.00 0.00 0.00 3.66
18 19 5.488919 TGAGGGTGTTTCTAATCTTCTCCAT 59.511 40.000 0.00 0.00 0.00 3.41
19 20 4.844085 TGAGGGTGTTTCTAATCTTCTCCA 59.156 41.667 0.00 0.00 0.00 3.86
20 21 5.179533 GTGAGGGTGTTTCTAATCTTCTCC 58.820 45.833 0.00 0.00 0.00 3.71
21 22 4.865365 CGTGAGGGTGTTTCTAATCTTCTC 59.135 45.833 0.00 0.00 0.00 2.87
22 23 4.822026 CGTGAGGGTGTTTCTAATCTTCT 58.178 43.478 0.00 0.00 0.00 2.85
23 24 3.371285 GCGTGAGGGTGTTTCTAATCTTC 59.629 47.826 0.00 0.00 0.00 2.87
24 25 3.335579 GCGTGAGGGTGTTTCTAATCTT 58.664 45.455 0.00 0.00 0.00 2.40
25 26 2.354805 GGCGTGAGGGTGTTTCTAATCT 60.355 50.000 0.00 0.00 0.00 2.40
26 27 2.007608 GGCGTGAGGGTGTTTCTAATC 58.992 52.381 0.00 0.00 0.00 1.75
27 28 1.628846 AGGCGTGAGGGTGTTTCTAAT 59.371 47.619 0.00 0.00 0.00 1.73
28 29 1.001633 GAGGCGTGAGGGTGTTTCTAA 59.998 52.381 0.00 0.00 0.00 2.10
29 30 0.606604 GAGGCGTGAGGGTGTTTCTA 59.393 55.000 0.00 0.00 0.00 2.10
30 31 1.122019 AGAGGCGTGAGGGTGTTTCT 61.122 55.000 0.00 0.00 0.00 2.52
31 32 0.670854 GAGAGGCGTGAGGGTGTTTC 60.671 60.000 0.00 0.00 0.00 2.78
32 33 1.371558 GAGAGGCGTGAGGGTGTTT 59.628 57.895 0.00 0.00 0.00 2.83
33 34 2.584391 GGAGAGGCGTGAGGGTGTT 61.584 63.158 0.00 0.00 0.00 3.32
34 35 2.151307 TAGGAGAGGCGTGAGGGTGT 62.151 60.000 0.00 0.00 0.00 4.16
35 36 0.757188 ATAGGAGAGGCGTGAGGGTG 60.757 60.000 0.00 0.00 0.00 4.61
36 37 0.032017 AATAGGAGAGGCGTGAGGGT 60.032 55.000 0.00 0.00 0.00 4.34
37 38 0.676736 GAATAGGAGAGGCGTGAGGG 59.323 60.000 0.00 0.00 0.00 4.30
38 39 0.312416 CGAATAGGAGAGGCGTGAGG 59.688 60.000 0.00 0.00 0.00 3.86
39 40 0.318275 GCGAATAGGAGAGGCGTGAG 60.318 60.000 0.00 0.00 0.00 3.51
40 41 1.734137 GCGAATAGGAGAGGCGTGA 59.266 57.895 0.00 0.00 0.00 4.35
41 42 1.658717 CGCGAATAGGAGAGGCGTG 60.659 63.158 0.00 0.00 41.75 5.34
42 43 2.722487 CGCGAATAGGAGAGGCGT 59.278 61.111 0.00 0.00 41.75 5.68
44 45 2.356433 GGCGCGAATAGGAGAGGC 60.356 66.667 12.10 0.00 0.00 4.70
45 46 2.049985 CGGCGCGAATAGGAGAGG 60.050 66.667 12.10 0.00 0.00 3.69
46 47 2.049985 CCGGCGCGAATAGGAGAG 60.050 66.667 12.10 0.00 0.00 3.20
47 48 3.602677 CCCGGCGCGAATAGGAGA 61.603 66.667 12.10 0.00 0.00 3.71
48 49 3.559657 CTCCCGGCGCGAATAGGAG 62.560 68.421 12.10 15.29 38.32 3.69
49 50 3.602677 CTCCCGGCGCGAATAGGA 61.603 66.667 12.10 8.98 0.00 2.94
50 51 4.664677 CCTCCCGGCGCGAATAGG 62.665 72.222 12.10 6.44 0.00 2.57
51 52 3.146726 TTCCTCCCGGCGCGAATAG 62.147 63.158 12.10 0.00 0.00 1.73
52 53 3.146726 CTTCCTCCCGGCGCGAATA 62.147 63.158 12.10 0.00 0.00 1.75
53 54 4.530857 CTTCCTCCCGGCGCGAAT 62.531 66.667 12.10 0.00 0.00 3.34
59 60 3.787001 CAGGTCCTTCCTCCCGGC 61.787 72.222 0.00 0.00 46.24 6.13
60 61 3.787001 GCAGGTCCTTCCTCCCGG 61.787 72.222 0.00 0.00 46.24 5.73
61 62 2.685380 AGCAGGTCCTTCCTCCCG 60.685 66.667 0.00 0.00 46.24 5.14
62 63 0.985490 ATCAGCAGGTCCTTCCTCCC 60.985 60.000 0.00 0.00 46.24 4.30
63 64 0.915364 AATCAGCAGGTCCTTCCTCC 59.085 55.000 0.00 0.00 46.24 4.30
64 65 2.797177 AAATCAGCAGGTCCTTCCTC 57.203 50.000 0.00 0.00 46.24 3.71
66 67 3.636153 AGTAAATCAGCAGGTCCTTCC 57.364 47.619 0.00 0.00 0.00 3.46
67 68 4.123506 GCTAGTAAATCAGCAGGTCCTTC 58.876 47.826 0.00 0.00 37.73 3.46
68 69 3.430929 CGCTAGTAAATCAGCAGGTCCTT 60.431 47.826 0.00 0.00 37.66 3.36
69 70 2.101582 CGCTAGTAAATCAGCAGGTCCT 59.898 50.000 0.00 0.00 37.66 3.85
70 71 2.100916 TCGCTAGTAAATCAGCAGGTCC 59.899 50.000 0.00 0.00 37.66 4.46
71 72 3.438297 TCGCTAGTAAATCAGCAGGTC 57.562 47.619 0.00 0.00 37.66 3.85
72 73 5.478679 AGATATCGCTAGTAAATCAGCAGGT 59.521 40.000 0.00 0.00 37.66 4.00
73 74 5.960113 AGATATCGCTAGTAAATCAGCAGG 58.040 41.667 0.00 0.00 37.66 4.85
74 75 7.881643 AAAGATATCGCTAGTAAATCAGCAG 57.118 36.000 0.00 0.00 37.66 4.24
75 76 7.307396 GCAAAAGATATCGCTAGTAAATCAGCA 60.307 37.037 0.00 0.00 37.66 4.41
76 77 7.012358 GCAAAAGATATCGCTAGTAAATCAGC 58.988 38.462 0.00 0.00 0.00 4.26
77 78 7.223339 CGCAAAAGATATCGCTAGTAAATCAG 58.777 38.462 0.00 0.00 0.00 2.90
78 79 6.346598 GCGCAAAAGATATCGCTAGTAAATCA 60.347 38.462 0.30 0.00 43.70 2.57
79 80 6.010074 GCGCAAAAGATATCGCTAGTAAATC 58.990 40.000 0.30 0.00 43.70 2.17
80 81 5.916969 GCGCAAAAGATATCGCTAGTAAAT 58.083 37.500 0.30 0.00 43.70 1.40
81 82 5.324739 GCGCAAAAGATATCGCTAGTAAA 57.675 39.130 0.30 0.00 43.70 2.01
82 83 4.966850 GCGCAAAAGATATCGCTAGTAA 57.033 40.909 0.30 0.00 43.70 2.24
88 89 1.193426 GAGGAGCGCAAAAGATATCGC 59.807 52.381 11.47 0.00 46.95 4.58
89 90 2.219674 GTGAGGAGCGCAAAAGATATCG 59.780 50.000 11.47 0.00 0.00 2.92
90 91 3.462021 AGTGAGGAGCGCAAAAGATATC 58.538 45.455 11.47 0.00 0.00 1.63
91 92 3.550437 AGTGAGGAGCGCAAAAGATAT 57.450 42.857 11.47 0.00 0.00 1.63
92 93 3.262420 GAAGTGAGGAGCGCAAAAGATA 58.738 45.455 11.47 0.00 0.00 1.98
93 94 2.079925 GAAGTGAGGAGCGCAAAAGAT 58.920 47.619 11.47 0.00 0.00 2.40
94 95 1.512926 GAAGTGAGGAGCGCAAAAGA 58.487 50.000 11.47 0.00 0.00 2.52
95 96 0.519077 GGAAGTGAGGAGCGCAAAAG 59.481 55.000 11.47 0.00 0.00 2.27
96 97 0.108585 AGGAAGTGAGGAGCGCAAAA 59.891 50.000 11.47 0.00 0.00 2.44
97 98 0.603707 CAGGAAGTGAGGAGCGCAAA 60.604 55.000 11.47 0.00 0.00 3.68
98 99 1.004560 CAGGAAGTGAGGAGCGCAA 60.005 57.895 11.47 0.00 0.00 4.85
99 100 2.159819 GACAGGAAGTGAGGAGCGCA 62.160 60.000 11.47 0.00 0.00 6.09
100 101 1.446966 GACAGGAAGTGAGGAGCGC 60.447 63.158 0.00 0.00 0.00 5.92
101 102 1.153939 CGACAGGAAGTGAGGAGCG 60.154 63.158 0.00 0.00 0.00 5.03
102 103 0.318762 AACGACAGGAAGTGAGGAGC 59.681 55.000 0.00 0.00 0.00 4.70
103 104 2.408050 CAAACGACAGGAAGTGAGGAG 58.592 52.381 0.00 0.00 0.00 3.69
104 105 1.070134 CCAAACGACAGGAAGTGAGGA 59.930 52.381 0.00 0.00 0.00 3.71
105 106 1.070134 TCCAAACGACAGGAAGTGAGG 59.930 52.381 0.00 0.00 0.00 3.86
106 107 2.135933 GTCCAAACGACAGGAAGTGAG 58.864 52.381 0.00 0.00 41.54 3.51
107 108 1.202604 GGTCCAAACGACAGGAAGTGA 60.203 52.381 0.00 0.00 43.95 3.41
108 109 1.202651 AGGTCCAAACGACAGGAAGTG 60.203 52.381 0.00 0.00 43.95 3.16
109 110 1.129058 AGGTCCAAACGACAGGAAGT 58.871 50.000 0.00 0.00 43.95 3.01
110 111 3.611766 ATAGGTCCAAACGACAGGAAG 57.388 47.619 0.00 0.00 43.95 3.46
111 112 3.307199 GGAATAGGTCCAAACGACAGGAA 60.307 47.826 0.00 0.00 46.97 3.36
112 113 2.235402 GGAATAGGTCCAAACGACAGGA 59.765 50.000 0.00 0.00 46.97 3.86
113 114 2.629051 GGAATAGGTCCAAACGACAGG 58.371 52.381 0.00 0.00 46.97 4.00
123 124 7.562454 TGAAAATGAAATACGGAATAGGTCC 57.438 36.000 0.00 0.00 43.90 4.46
124 125 8.009974 CGATGAAAATGAAATACGGAATAGGTC 58.990 37.037 0.00 0.00 0.00 3.85
125 126 7.041372 CCGATGAAAATGAAATACGGAATAGGT 60.041 37.037 0.00 0.00 41.30 3.08
126 127 7.041372 ACCGATGAAAATGAAATACGGAATAGG 60.041 37.037 0.00 0.00 41.30 2.57
127 128 7.798516 CACCGATGAAAATGAAATACGGAATAG 59.201 37.037 0.00 0.00 41.30 1.73
128 129 7.635423 CACCGATGAAAATGAAATACGGAATA 58.365 34.615 0.00 0.00 41.30 1.75
129 130 6.494842 CACCGATGAAAATGAAATACGGAAT 58.505 36.000 0.00 0.00 41.30 3.01
130 131 5.675071 GCACCGATGAAAATGAAATACGGAA 60.675 40.000 0.00 0.00 41.30 4.30
131 132 4.201871 GCACCGATGAAAATGAAATACGGA 60.202 41.667 0.00 0.00 41.30 4.69
132 133 4.035017 GCACCGATGAAAATGAAATACGG 58.965 43.478 0.00 0.00 43.79 4.02
133 134 4.730042 CAGCACCGATGAAAATGAAATACG 59.270 41.667 0.00 0.00 0.00 3.06
134 135 5.640732 ACAGCACCGATGAAAATGAAATAC 58.359 37.500 0.00 0.00 0.00 1.89
135 136 5.414144 TGACAGCACCGATGAAAATGAAATA 59.586 36.000 0.00 0.00 0.00 1.40
136 137 4.218200 TGACAGCACCGATGAAAATGAAAT 59.782 37.500 0.00 0.00 0.00 2.17
137 138 3.567585 TGACAGCACCGATGAAAATGAAA 59.432 39.130 0.00 0.00 0.00 2.69
138 139 3.145286 TGACAGCACCGATGAAAATGAA 58.855 40.909 0.00 0.00 0.00 2.57
139 140 2.777094 TGACAGCACCGATGAAAATGA 58.223 42.857 0.00 0.00 0.00 2.57
140 141 3.119743 ACATGACAGCACCGATGAAAATG 60.120 43.478 0.00 0.00 0.00 2.32
141 142 3.084039 ACATGACAGCACCGATGAAAAT 58.916 40.909 0.00 0.00 0.00 1.82
142 143 2.503331 ACATGACAGCACCGATGAAAA 58.497 42.857 0.00 0.00 0.00 2.29
143 144 2.183478 ACATGACAGCACCGATGAAA 57.817 45.000 0.00 0.00 0.00 2.69
144 145 3.118811 TGATACATGACAGCACCGATGAA 60.119 43.478 0.00 0.00 0.00 2.57
145 146 2.430332 TGATACATGACAGCACCGATGA 59.570 45.455 0.00 0.00 0.00 2.92
146 147 2.825205 TGATACATGACAGCACCGATG 58.175 47.619 0.00 0.00 0.00 3.84
147 148 3.758755 ATGATACATGACAGCACCGAT 57.241 42.857 0.00 0.00 0.00 4.18
148 149 3.541996 AATGATACATGACAGCACCGA 57.458 42.857 0.00 0.00 0.00 4.69
149 150 3.622612 TCAAATGATACATGACAGCACCG 59.377 43.478 0.00 0.00 0.00 4.94
150 151 5.124457 AGTTCAAATGATACATGACAGCACC 59.876 40.000 0.00 0.00 0.00 5.01
151 152 6.187125 AGTTCAAATGATACATGACAGCAC 57.813 37.500 0.00 0.00 0.00 4.40
152 153 6.822667 AAGTTCAAATGATACATGACAGCA 57.177 33.333 0.00 0.00 0.00 4.41
153 154 7.907045 CACTAAGTTCAAATGATACATGACAGC 59.093 37.037 0.00 0.00 0.00 4.40
154 155 8.393366 CCACTAAGTTCAAATGATACATGACAG 58.607 37.037 0.00 0.00 0.00 3.51
155 156 7.882791 ACCACTAAGTTCAAATGATACATGACA 59.117 33.333 0.00 0.00 0.00 3.58
156 157 8.268850 ACCACTAAGTTCAAATGATACATGAC 57.731 34.615 0.00 0.00 0.00 3.06
157 158 8.729756 CAACCACTAAGTTCAAATGATACATGA 58.270 33.333 0.00 0.00 0.00 3.07
158 159 8.514594 ACAACCACTAAGTTCAAATGATACATG 58.485 33.333 0.00 0.00 0.00 3.21
159 160 8.635765 ACAACCACTAAGTTCAAATGATACAT 57.364 30.769 0.00 0.00 0.00 2.29
160 161 9.214957 CTACAACCACTAAGTTCAAATGATACA 57.785 33.333 0.00 0.00 0.00 2.29
161 162 8.665685 CCTACAACCACTAAGTTCAAATGATAC 58.334 37.037 0.00 0.00 0.00 2.24
162 163 8.380099 ACCTACAACCACTAAGTTCAAATGATA 58.620 33.333 0.00 0.00 0.00 2.15
163 164 7.231467 ACCTACAACCACTAAGTTCAAATGAT 58.769 34.615 0.00 0.00 0.00 2.45
164 165 6.597562 ACCTACAACCACTAAGTTCAAATGA 58.402 36.000 0.00 0.00 0.00 2.57
165 166 6.877611 ACCTACAACCACTAAGTTCAAATG 57.122 37.500 0.00 0.00 0.00 2.32
166 167 7.558444 TGAAACCTACAACCACTAAGTTCAAAT 59.442 33.333 0.00 0.00 0.00 2.32
167 168 6.885376 TGAAACCTACAACCACTAAGTTCAAA 59.115 34.615 0.00 0.00 0.00 2.69
168 169 6.416415 TGAAACCTACAACCACTAAGTTCAA 58.584 36.000 0.00 0.00 0.00 2.69
169 170 5.991861 TGAAACCTACAACCACTAAGTTCA 58.008 37.500 0.00 0.00 0.00 3.18
170 171 6.053650 ACTGAAACCTACAACCACTAAGTTC 58.946 40.000 0.00 0.00 0.00 3.01
171 172 5.997843 ACTGAAACCTACAACCACTAAGTT 58.002 37.500 0.00 0.00 0.00 2.66
172 173 5.625568 ACTGAAACCTACAACCACTAAGT 57.374 39.130 0.00 0.00 0.00 2.24
173 174 6.756221 AGTACTGAAACCTACAACCACTAAG 58.244 40.000 0.00 0.00 0.00 2.18
174 175 6.736110 AGTACTGAAACCTACAACCACTAA 57.264 37.500 0.00 0.00 0.00 2.24
175 176 6.098695 ACAAGTACTGAAACCTACAACCACTA 59.901 38.462 0.00 0.00 0.00 2.74
176 177 5.104652 ACAAGTACTGAAACCTACAACCACT 60.105 40.000 0.00 0.00 0.00 4.00
177 178 5.121105 ACAAGTACTGAAACCTACAACCAC 58.879 41.667 0.00 0.00 0.00 4.16
178 179 5.362105 ACAAGTACTGAAACCTACAACCA 57.638 39.130 0.00 0.00 0.00 3.67
179 180 5.050567 CGAACAAGTACTGAAACCTACAACC 60.051 44.000 0.00 0.00 0.00 3.77
180 181 5.750067 TCGAACAAGTACTGAAACCTACAAC 59.250 40.000 0.00 0.00 0.00 3.32
181 182 5.904941 TCGAACAAGTACTGAAACCTACAA 58.095 37.500 0.00 0.00 0.00 2.41
182 183 5.518848 TCGAACAAGTACTGAAACCTACA 57.481 39.130 0.00 0.00 0.00 2.74
183 184 6.617953 GCATTCGAACAAGTACTGAAACCTAC 60.618 42.308 0.00 0.00 0.00 3.18
184 185 5.407387 GCATTCGAACAAGTACTGAAACCTA 59.593 40.000 0.00 0.00 0.00 3.08
185 186 4.213482 GCATTCGAACAAGTACTGAAACCT 59.787 41.667 0.00 0.00 0.00 3.50
186 187 4.213482 AGCATTCGAACAAGTACTGAAACC 59.787 41.667 0.00 0.00 0.00 3.27
187 188 5.140177 CAGCATTCGAACAAGTACTGAAAC 58.860 41.667 0.00 0.00 0.00 2.78
188 189 4.814234 ACAGCATTCGAACAAGTACTGAAA 59.186 37.500 0.00 0.00 0.00 2.69
189 190 4.377021 ACAGCATTCGAACAAGTACTGAA 58.623 39.130 0.00 0.00 0.00 3.02
190 191 3.987868 GACAGCATTCGAACAAGTACTGA 59.012 43.478 0.00 0.00 0.00 3.41
191 192 3.990469 AGACAGCATTCGAACAAGTACTG 59.010 43.478 0.00 4.80 0.00 2.74
192 193 4.258702 AGACAGCATTCGAACAAGTACT 57.741 40.909 0.00 0.00 0.00 2.73
193 194 4.992381 AAGACAGCATTCGAACAAGTAC 57.008 40.909 0.00 0.00 0.00 2.73
194 195 5.580691 CCATAAGACAGCATTCGAACAAGTA 59.419 40.000 0.00 0.00 0.00 2.24
195 196 4.393062 CCATAAGACAGCATTCGAACAAGT 59.607 41.667 0.00 0.00 0.00 3.16
196 197 4.728882 GCCATAAGACAGCATTCGAACAAG 60.729 45.833 0.00 0.00 0.00 3.16
197 198 3.126858 GCCATAAGACAGCATTCGAACAA 59.873 43.478 0.00 0.00 0.00 2.83
198 199 2.677836 GCCATAAGACAGCATTCGAACA 59.322 45.455 0.00 0.00 0.00 3.18
199 200 2.939103 AGCCATAAGACAGCATTCGAAC 59.061 45.455 0.00 0.00 0.00 3.95
200 201 3.266510 AGCCATAAGACAGCATTCGAA 57.733 42.857 0.00 0.00 0.00 3.71
201 202 2.988010 AGCCATAAGACAGCATTCGA 57.012 45.000 0.00 0.00 0.00 3.71
202 203 5.679734 ATAAAGCCATAAGACAGCATTCG 57.320 39.130 0.00 0.00 0.00 3.34
203 204 9.971922 AATTAATAAAGCCATAAGACAGCATTC 57.028 29.630 0.00 0.00 0.00 2.67
215 216 9.078753 CGTTCGGTTTTAAATTAATAAAGCCAT 57.921 29.630 13.73 0.00 42.80 4.40
216 217 7.062022 GCGTTCGGTTTTAAATTAATAAAGCCA 59.938 33.333 13.73 0.00 42.80 4.75
217 218 7.274033 AGCGTTCGGTTTTAAATTAATAAAGCC 59.726 33.333 6.54 6.54 40.64 4.35
218 219 8.165212 AGCGTTCGGTTTTAAATTAATAAAGC 57.835 30.769 0.00 0.00 0.00 3.51
219 220 8.791605 GGAGCGTTCGGTTTTAAATTAATAAAG 58.208 33.333 0.00 0.00 0.00 1.85
220 221 8.513774 AGGAGCGTTCGGTTTTAAATTAATAAA 58.486 29.630 0.00 0.00 0.00 1.40
221 222 8.042944 AGGAGCGTTCGGTTTTAAATTAATAA 57.957 30.769 0.00 0.00 0.00 1.40
222 223 7.614124 AGGAGCGTTCGGTTTTAAATTAATA 57.386 32.000 0.00 0.00 0.00 0.98
223 224 6.505044 AGGAGCGTTCGGTTTTAAATTAAT 57.495 33.333 0.00 0.00 0.00 1.40
224 225 5.945466 AGGAGCGTTCGGTTTTAAATTAA 57.055 34.783 0.00 0.00 0.00 1.40
225 226 6.091169 CACTAGGAGCGTTCGGTTTTAAATTA 59.909 38.462 0.00 0.00 0.00 1.40
226 227 4.999311 ACTAGGAGCGTTCGGTTTTAAATT 59.001 37.500 0.00 0.00 0.00 1.82
227 228 4.390909 CACTAGGAGCGTTCGGTTTTAAAT 59.609 41.667 0.00 0.00 0.00 1.40
228 229 3.742369 CACTAGGAGCGTTCGGTTTTAAA 59.258 43.478 0.00 0.00 0.00 1.52
229 230 3.243839 ACACTAGGAGCGTTCGGTTTTAA 60.244 43.478 0.00 0.00 0.00 1.52
230 231 2.297033 ACACTAGGAGCGTTCGGTTTTA 59.703 45.455 0.00 0.00 0.00 1.52
231 232 1.069668 ACACTAGGAGCGTTCGGTTTT 59.930 47.619 0.00 0.00 0.00 2.43
232 233 0.677842 ACACTAGGAGCGTTCGGTTT 59.322 50.000 0.00 0.00 0.00 3.27
233 234 0.243095 GACACTAGGAGCGTTCGGTT 59.757 55.000 0.00 0.00 0.00 4.44
234 235 0.608582 AGACACTAGGAGCGTTCGGT 60.609 55.000 0.00 0.00 0.00 4.69
235 236 0.526662 AAGACACTAGGAGCGTTCGG 59.473 55.000 0.00 0.00 0.00 4.30
236 237 1.790838 CGAAGACACTAGGAGCGTTCG 60.791 57.143 0.00 1.64 0.00 3.95
237 238 1.199558 ACGAAGACACTAGGAGCGTTC 59.800 52.381 0.00 0.00 0.00 3.95
238 239 1.245732 ACGAAGACACTAGGAGCGTT 58.754 50.000 0.00 0.00 0.00 4.84
239 240 1.245732 AACGAAGACACTAGGAGCGT 58.754 50.000 0.00 0.00 0.00 5.07
240 241 2.251893 GAAACGAAGACACTAGGAGCG 58.748 52.381 0.00 0.00 0.00 5.03
241 242 3.299340 TGAAACGAAGACACTAGGAGC 57.701 47.619 0.00 0.00 0.00 4.70
242 243 5.975442 GTTTTGAAACGAAGACACTAGGAG 58.025 41.667 0.00 0.00 0.00 3.69
243 244 5.978934 GTTTTGAAACGAAGACACTAGGA 57.021 39.130 0.00 0.00 0.00 2.94
256 257 4.866921 ACCTTCTATTGCCGTTTTGAAAC 58.133 39.130 0.00 0.00 35.59 2.78
257 258 4.825085 AGACCTTCTATTGCCGTTTTGAAA 59.175 37.500 0.00 0.00 0.00 2.69
258 259 4.394729 AGACCTTCTATTGCCGTTTTGAA 58.605 39.130 0.00 0.00 0.00 2.69
259 260 4.000988 GAGACCTTCTATTGCCGTTTTGA 58.999 43.478 0.00 0.00 0.00 2.69
260 261 4.003648 AGAGACCTTCTATTGCCGTTTTG 58.996 43.478 0.00 0.00 33.23 2.44
261 262 4.287766 AGAGACCTTCTATTGCCGTTTT 57.712 40.909 0.00 0.00 33.23 2.43
262 263 3.983044 AGAGACCTTCTATTGCCGTTT 57.017 42.857 0.00 0.00 33.23 3.60
263 264 3.260884 TCAAGAGACCTTCTATTGCCGTT 59.739 43.478 5.80 0.00 43.33 4.44
264 265 2.832129 TCAAGAGACCTTCTATTGCCGT 59.168 45.455 5.80 0.00 43.33 5.68
265 266 3.526931 TCAAGAGACCTTCTATTGCCG 57.473 47.619 5.80 0.00 43.33 5.69
266 267 4.054671 CGATCAAGAGACCTTCTATTGCC 58.945 47.826 5.80 0.97 43.33 4.52
267 268 4.054671 CCGATCAAGAGACCTTCTATTGC 58.945 47.826 5.80 0.00 43.33 3.56
268 269 5.269505 ACCGATCAAGAGACCTTCTATTG 57.730 43.478 4.50 4.50 44.57 1.90
300 301 4.549458 CCGCTTGATCACATTGTCTTTTT 58.451 39.130 0.00 0.00 0.00 1.94
307 308 0.447406 TTCGCCGCTTGATCACATTG 59.553 50.000 0.00 0.00 0.00 2.82
322 324 4.056125 GTTTGCCTGGGCCTTCGC 62.056 66.667 4.53 3.91 41.09 4.70
377 379 4.365514 TTTGGTGGCTACAGAATCAGAA 57.634 40.909 1.52 0.00 0.00 3.02
399 401 1.831106 TGGTAGTCTGGTTCGATGCAT 59.169 47.619 0.00 0.00 0.00 3.96
421 423 5.123820 TCGATTCATGACTCAATTTGGTTCC 59.876 40.000 12.93 0.00 0.00 3.62
491 499 1.027357 ATGCCAAGCGGTTCATGATC 58.973 50.000 0.00 0.00 33.28 2.92
501 509 0.661552 CTGGATCTTCATGCCAAGCG 59.338 55.000 0.00 0.00 0.00 4.68
520 528 2.498167 AGTTTGTGAGATGACTGCACC 58.502 47.619 0.00 0.00 0.00 5.01
544 552 1.355381 TGCCATGAACTTGGGTGATCT 59.645 47.619 0.00 0.00 37.24 2.75
567 575 2.775384 TGTAGGTGGTCCATGGATTACC 59.225 50.000 29.47 29.47 34.98 2.85
576 584 1.416243 AACGTCTTGTAGGTGGTCCA 58.584 50.000 0.00 0.00 35.89 4.02
591 599 1.268899 CGGTTGGAGTCTGAGTAACGT 59.731 52.381 0.00 0.00 0.00 3.99
595 603 1.204704 CATGCGGTTGGAGTCTGAGTA 59.795 52.381 0.00 0.00 0.00 2.59
618 626 8.869109 TCAGTTCTGATTTGATAATTGGGTTTT 58.131 29.630 0.00 0.00 0.00 2.43
622 632 6.316140 TCGTCAGTTCTGATTTGATAATTGGG 59.684 38.462 5.80 0.00 0.00 4.12
628 638 5.931724 TGCTTTCGTCAGTTCTGATTTGATA 59.068 36.000 5.80 0.97 0.00 2.15
737 752 4.697756 TGTAGCCGTGCTGGTGCC 62.698 66.667 8.44 0.00 40.10 5.01
738 753 1.586154 ATTTGTAGCCGTGCTGGTGC 61.586 55.000 8.44 0.00 40.10 5.01
739 754 1.665679 CTATTTGTAGCCGTGCTGGTG 59.334 52.381 8.44 0.00 40.10 4.17
740 755 2.012051 GCTATTTGTAGCCGTGCTGGT 61.012 52.381 8.44 0.00 40.10 4.00
741 756 0.657840 GCTATTTGTAGCCGTGCTGG 59.342 55.000 8.44 0.00 40.10 4.85
782 797 2.847234 TCAGGGACGTTGTGGCCT 60.847 61.111 3.32 0.00 0.00 5.19
849 866 2.493973 GCGCCAGTGAGAGAGAGG 59.506 66.667 0.00 0.00 0.00 3.69
850 867 1.674764 ATGGCGCCAGTGAGAGAGAG 61.675 60.000 35.36 0.00 0.00 3.20
859 886 2.310327 TATTCGAGCATGGCGCCAGT 62.310 55.000 35.36 21.71 44.04 4.00
863 890 0.588252 ACATTATTCGAGCATGGCGC 59.412 50.000 0.00 0.00 42.91 6.53
914 942 0.320771 CACCAGGTGGCACTAGTGAC 60.321 60.000 27.08 24.87 39.32 3.67
1119 1147 3.267860 GCCTGCAAGATCGCGAGG 61.268 66.667 16.66 9.62 34.07 4.63
1304 1332 8.932945 ATGCATAGATTTATATACACCTCACG 57.067 34.615 0.00 0.00 0.00 4.35
1442 1475 1.261619 GGCAGACATATACGCACAAGC 59.738 52.381 0.00 0.00 37.42 4.01
1468 1501 5.867174 TGTACCGTCTTGATCTGTACATTTG 59.133 40.000 0.00 0.00 0.00 2.32
1615 1648 9.872757 GTTGATGTCTTTATCTTGTTTTAACGA 57.127 29.630 0.00 0.00 0.00 3.85
1619 1652 9.872757 GAACGTTGATGTCTTTATCTTGTTTTA 57.127 29.630 5.00 0.00 0.00 1.52
1629 1662 7.493320 GTGTATATGGGAACGTTGATGTCTTTA 59.507 37.037 5.00 0.00 0.00 1.85
1649 1682 6.127535 GCACCTTTGTAGGACAGTAGTGTATA 60.128 42.308 2.39 0.00 45.05 1.47
1650 1683 5.337330 GCACCTTTGTAGGACAGTAGTGTAT 60.337 44.000 2.39 0.00 45.05 2.29
1651 1684 4.021719 GCACCTTTGTAGGACAGTAGTGTA 60.022 45.833 2.39 0.00 45.05 2.90
1674 1707 4.682860 ACAATTTCGCTTCTTCTGCAATTG 59.317 37.500 0.00 0.00 38.56 2.32
1722 1755 5.902613 TGCAAGACATTAGGGAATTTCTG 57.097 39.130 0.00 0.00 33.32 3.02
1752 1786 5.414765 TCTGTATGTCAGTCGTGTCTATTGT 59.585 40.000 0.00 0.00 43.97 2.71
1767 1801 2.744202 CAAGCTGGTGGTTCTGTATGTC 59.256 50.000 0.00 0.00 0.00 3.06
1802 1836 6.738832 AAGCATCATTTCTCATCATATCCG 57.261 37.500 0.00 0.00 0.00 4.18
1851 1885 0.158928 GACTTTCGTCGAACGTGCTG 59.841 55.000 20.31 4.32 43.14 4.41
1999 2037 3.003378 GTCTTGTTTGGTACTCTGGCAAC 59.997 47.826 0.00 0.00 0.00 4.17
2108 2153 0.452618 CACAAACATGTAGCCGCGTG 60.453 55.000 4.92 0.00 0.00 5.34
2121 2166 5.837586 TCTTGCTCAACAAAAACACAAAC 57.162 34.783 0.00 0.00 37.96 2.93


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

AutoCloner maintained by Alex Coulton.