Multiple sequence alignment - TraesCS5D01G156200

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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 TraesCS5D01G156200 chr5D 100.000 3092 0 0 1 3092 244414612 244411521 0.000000e+00 5710
1 TraesCS5D01G156200 chr5D 98.470 2810 36 2 289 3092 480824251 480821443 0.000000e+00 4944
2 TraesCS5D01G156200 chr5D 97.549 2815 56 6 289 3092 565815805 565818617 0.000000e+00 4804
3 TraesCS5D01G156200 chr5D 97.407 2815 60 6 289 3092 260689959 260687147 0.000000e+00 4782
4 TraesCS5D01G156200 chr5D 98.618 217 3 0 74 290 244406976 244406760 4.840000e-103 385
5 TraesCS5D01G156200 chr6D 98.292 2810 42 1 289 3092 472510966 472513775 0.000000e+00 4918
6 TraesCS5D01G156200 chr6D 97.762 2815 51 3 285 3092 367564539 367561730 0.000000e+00 4839
7 TraesCS5D01G156200 chr6D 97.442 2815 59 6 289 3092 51499467 51502279 0.000000e+00 4787
8 TraesCS5D01G156200 chr3D 98.114 2810 46 2 289 3092 574856802 574853994 0.000000e+00 4889
9 TraesCS5D01G156200 chr4D 97.906 2817 45 4 289 3092 398986364 398983549 0.000000e+00 4863
10 TraesCS5D01G156200 chr7D 97.620 2815 55 5 289 3092 245402428 245399615 0.000000e+00 4817
11 TraesCS5D01G156200 chr5B 97.586 290 7 0 1 290 277792870 277792581 5.950000e-137 497


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 TraesCS5D01G156200 chr5D 244411521 244414612 3091 True 5710 5710 100.000 1 3092 1 chr5D.!!$R2 3091
1 TraesCS5D01G156200 chr5D 480821443 480824251 2808 True 4944 4944 98.470 289 3092 1 chr5D.!!$R4 2803
2 TraesCS5D01G156200 chr5D 565815805 565818617 2812 False 4804 4804 97.549 289 3092 1 chr5D.!!$F1 2803
3 TraesCS5D01G156200 chr5D 260687147 260689959 2812 True 4782 4782 97.407 289 3092 1 chr5D.!!$R3 2803
4 TraesCS5D01G156200 chr6D 472510966 472513775 2809 False 4918 4918 98.292 289 3092 1 chr6D.!!$F2 2803
5 TraesCS5D01G156200 chr6D 367561730 367564539 2809 True 4839 4839 97.762 285 3092 1 chr6D.!!$R1 2807
6 TraesCS5D01G156200 chr6D 51499467 51502279 2812 False 4787 4787 97.442 289 3092 1 chr6D.!!$F1 2803
7 TraesCS5D01G156200 chr3D 574853994 574856802 2808 True 4889 4889 98.114 289 3092 1 chr3D.!!$R1 2803
8 TraesCS5D01G156200 chr4D 398983549 398986364 2815 True 4863 4863 97.906 289 3092 1 chr4D.!!$R1 2803
9 TraesCS5D01G156200 chr7D 245399615 245402428 2813 True 4817 4817 97.620 289 3092 1 chr7D.!!$R1 2803

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
31 32 0.032678 CCAGCTATCAGGCGACGAAT 59.967 55.0 0.0 0.0 37.29 3.34 F
278 279 0.035820 GGACTGGTACATCCGCCAAA 60.036 55.0 0.0 0.0 38.20 3.28 F
284 285 0.252197 GTACATCCGCCAAACTCCCT 59.748 55.0 0.0 0.0 0.00 4.20 F
287 288 0.322456 CATCCGCCAAACTCCCTTGA 60.322 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 1595 0.252375 ATTGGATGCCAGGGCTTGTT 60.252 50.000 12.19 0.0 42.51 2.83 R
2028 2047 2.719739 CTTGAATGCCCATCACTCAGT 58.280 47.619 0.00 0.0 32.03 3.41 R
2044 2063 6.757897 TTTCTCAAGTTTCTCTTTGCTTGA 57.242 33.333 0.00 0.0 43.16 3.02 R
2184 2203 9.757227 GACATAGACTAGATTAGCTTCACATTT 57.243 33.333 0.00 0.0 0.00 2.32 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
21 22 3.642141 TGACTCCATACACCAGCTATCA 58.358 45.455 0.00 0.00 0.00 2.15
22 23 3.638627 TGACTCCATACACCAGCTATCAG 59.361 47.826 0.00 0.00 0.00 2.90
23 24 2.968574 ACTCCATACACCAGCTATCAGG 59.031 50.000 0.00 0.00 0.00 3.86
24 25 1.694150 TCCATACACCAGCTATCAGGC 59.306 52.381 0.00 0.00 0.00 4.85
25 26 1.606480 CCATACACCAGCTATCAGGCG 60.606 57.143 0.00 0.00 37.29 5.52
26 27 1.341209 CATACACCAGCTATCAGGCGA 59.659 52.381 0.00 0.00 37.29 5.54
27 28 0.744874 TACACCAGCTATCAGGCGAC 59.255 55.000 0.00 0.00 37.29 5.19
28 29 1.589993 CACCAGCTATCAGGCGACG 60.590 63.158 0.00 0.00 37.29 5.12
29 30 1.753078 ACCAGCTATCAGGCGACGA 60.753 57.895 0.00 0.00 37.29 4.20
30 31 1.320344 ACCAGCTATCAGGCGACGAA 61.320 55.000 0.00 0.00 37.29 3.85
31 32 0.032678 CCAGCTATCAGGCGACGAAT 59.967 55.000 0.00 0.00 37.29 3.34
32 33 1.539065 CCAGCTATCAGGCGACGAATT 60.539 52.381 0.00 0.00 37.29 2.17
33 34 1.524355 CAGCTATCAGGCGACGAATTG 59.476 52.381 0.00 0.00 37.29 2.32
34 35 0.233332 GCTATCAGGCGACGAATTGC 59.767 55.000 0.00 0.00 34.00 3.56
40 41 2.950673 GCGACGAATTGCCACCAA 59.049 55.556 0.00 0.00 35.01 3.67
41 42 1.284408 GCGACGAATTGCCACCAAA 59.716 52.632 0.00 0.00 34.05 3.28
42 43 0.109319 GCGACGAATTGCCACCAAAT 60.109 50.000 0.00 0.00 34.05 2.32
43 44 1.131504 GCGACGAATTGCCACCAAATA 59.868 47.619 0.00 0.00 34.05 1.40
44 45 2.223479 GCGACGAATTGCCACCAAATAT 60.223 45.455 0.00 0.00 34.05 1.28
45 46 3.617669 CGACGAATTGCCACCAAATATC 58.382 45.455 0.00 0.00 34.05 1.63
46 47 3.548014 CGACGAATTGCCACCAAATATCC 60.548 47.826 0.00 0.00 34.05 2.59
47 48 2.357637 ACGAATTGCCACCAAATATCCG 59.642 45.455 0.00 0.00 34.05 4.18
48 49 2.357637 CGAATTGCCACCAAATATCCGT 59.642 45.455 0.00 0.00 34.05 4.69
49 50 3.181491 CGAATTGCCACCAAATATCCGTT 60.181 43.478 0.00 0.00 34.05 4.44
50 51 4.676723 CGAATTGCCACCAAATATCCGTTT 60.677 41.667 0.00 0.00 34.05 3.60
51 52 3.584406 TTGCCACCAAATATCCGTTTG 57.416 42.857 0.00 0.00 38.50 2.93
52 53 2.520069 TGCCACCAAATATCCGTTTGT 58.480 42.857 0.00 0.00 37.37 2.83
53 54 2.230025 TGCCACCAAATATCCGTTTGTG 59.770 45.455 0.00 0.00 37.37 3.33
54 55 2.230266 GCCACCAAATATCCGTTTGTGT 59.770 45.455 0.00 0.00 37.37 3.72
55 56 3.672241 GCCACCAAATATCCGTTTGTGTC 60.672 47.826 0.00 0.00 37.37 3.67
56 57 3.504134 CCACCAAATATCCGTTTGTGTCA 59.496 43.478 0.00 0.00 37.37 3.58
57 58 4.472286 CACCAAATATCCGTTTGTGTCAC 58.528 43.478 0.00 0.00 37.37 3.67
58 59 4.023622 CACCAAATATCCGTTTGTGTCACA 60.024 41.667 0.18 0.18 37.37 3.58
59 60 4.764823 ACCAAATATCCGTTTGTGTCACAT 59.235 37.500 6.48 0.00 37.37 3.21
60 61 5.941058 ACCAAATATCCGTTTGTGTCACATA 59.059 36.000 6.48 0.00 37.37 2.29
61 62 6.601613 ACCAAATATCCGTTTGTGTCACATAT 59.398 34.615 6.48 0.00 37.37 1.78
62 63 7.132213 CCAAATATCCGTTTGTGTCACATATC 58.868 38.462 6.48 0.00 37.37 1.63
63 64 7.201688 CCAAATATCCGTTTGTGTCACATATCA 60.202 37.037 6.48 0.00 37.37 2.15
64 65 7.857734 AATATCCGTTTGTGTCACATATCAA 57.142 32.000 6.48 0.00 0.00 2.57
65 66 5.801350 ATCCGTTTGTGTCACATATCAAG 57.199 39.130 6.48 0.00 0.00 3.02
66 67 4.888917 TCCGTTTGTGTCACATATCAAGA 58.111 39.130 6.48 0.00 0.00 3.02
67 68 5.301555 TCCGTTTGTGTCACATATCAAGAA 58.698 37.500 6.48 0.00 0.00 2.52
68 69 5.178623 TCCGTTTGTGTCACATATCAAGAAC 59.821 40.000 6.48 5.52 0.00 3.01
69 70 5.179368 CCGTTTGTGTCACATATCAAGAACT 59.821 40.000 6.48 0.00 0.00 3.01
70 71 6.299604 CGTTTGTGTCACATATCAAGAACTC 58.700 40.000 6.48 0.00 0.00 3.01
71 72 6.073819 CGTTTGTGTCACATATCAAGAACTCA 60.074 38.462 6.48 0.00 0.00 3.41
72 73 7.518211 CGTTTGTGTCACATATCAAGAACTCAA 60.518 37.037 6.48 0.00 0.00 3.02
73 74 6.785488 TGTGTCACATATCAAGAACTCAAC 57.215 37.500 0.18 0.00 0.00 3.18
74 75 6.287525 TGTGTCACATATCAAGAACTCAACA 58.712 36.000 0.18 0.00 0.00 3.33
75 76 6.202762 TGTGTCACATATCAAGAACTCAACAC 59.797 38.462 0.18 0.00 34.29 3.32
76 77 6.202762 GTGTCACATATCAAGAACTCAACACA 59.797 38.462 0.00 0.00 33.98 3.72
77 78 6.936335 TGTCACATATCAAGAACTCAACACAT 59.064 34.615 0.00 0.00 0.00 3.21
78 79 7.095102 TGTCACATATCAAGAACTCAACACATG 60.095 37.037 0.00 0.00 0.00 3.21
79 80 6.936335 TCACATATCAAGAACTCAACACATGT 59.064 34.615 0.00 0.00 0.00 3.21
80 81 7.445096 TCACATATCAAGAACTCAACACATGTT 59.555 33.333 0.00 0.00 39.12 2.71
81 82 7.747799 CACATATCAAGAACTCAACACATGTTC 59.252 37.037 0.00 0.00 40.00 3.18
82 83 5.695851 ATCAAGAACTCAACACATGTTCC 57.304 39.130 0.00 0.00 40.42 3.62
83 84 3.559655 TCAAGAACTCAACACATGTTCCG 59.440 43.478 0.00 0.00 40.42 4.30
84 85 2.494059 AGAACTCAACACATGTTCCGG 58.506 47.619 0.00 0.00 40.42 5.14
85 86 1.535462 GAACTCAACACATGTTCCGGG 59.465 52.381 0.00 0.00 35.83 5.73
86 87 0.762418 ACTCAACACATGTTCCGGGA 59.238 50.000 0.00 0.00 35.83 5.14
87 88 1.142060 ACTCAACACATGTTCCGGGAA 59.858 47.619 5.09 5.09 35.83 3.97
88 89 1.535462 CTCAACACATGTTCCGGGAAC 59.465 52.381 28.87 28.87 42.26 3.62
89 90 0.596082 CAACACATGTTCCGGGAACC 59.404 55.000 31.35 17.10 41.35 3.62
103 104 3.487563 GGGAACCGCTGAATTGTTTAG 57.512 47.619 0.00 0.00 40.86 1.85
104 105 2.817844 GGGAACCGCTGAATTGTTTAGT 59.182 45.455 0.00 0.00 40.86 2.24
105 106 3.119955 GGGAACCGCTGAATTGTTTAGTC 60.120 47.826 0.00 0.00 40.86 2.59
106 107 3.751698 GGAACCGCTGAATTGTTTAGTCT 59.248 43.478 0.00 0.00 0.00 3.24
107 108 4.215613 GGAACCGCTGAATTGTTTAGTCTT 59.784 41.667 0.00 0.00 0.00 3.01
108 109 5.410439 GGAACCGCTGAATTGTTTAGTCTTA 59.590 40.000 0.00 0.00 0.00 2.10
109 110 6.093633 GGAACCGCTGAATTGTTTAGTCTTAT 59.906 38.462 0.00 0.00 0.00 1.73
110 111 6.422776 ACCGCTGAATTGTTTAGTCTTATG 57.577 37.500 0.00 0.00 0.00 1.90
111 112 6.170506 ACCGCTGAATTGTTTAGTCTTATGA 58.829 36.000 0.00 0.00 0.00 2.15
112 113 6.823689 ACCGCTGAATTGTTTAGTCTTATGAT 59.176 34.615 0.00 0.00 0.00 2.45
113 114 7.985184 ACCGCTGAATTGTTTAGTCTTATGATA 59.015 33.333 0.00 0.00 0.00 2.15
114 115 8.993121 CCGCTGAATTGTTTAGTCTTATGATAT 58.007 33.333 0.00 0.00 0.00 1.63
115 116 9.803130 CGCTGAATTGTTTAGTCTTATGATATG 57.197 33.333 0.00 0.00 0.00 1.78
122 123 9.905713 TTGTTTAGTCTTATGATATGGAAGCTT 57.094 29.630 0.00 0.00 0.00 3.74
123 124 9.330063 TGTTTAGTCTTATGATATGGAAGCTTG 57.670 33.333 2.10 0.00 0.00 4.01
124 125 8.778358 GTTTAGTCTTATGATATGGAAGCTTGG 58.222 37.037 2.10 0.00 0.00 3.61
125 126 6.753913 AGTCTTATGATATGGAAGCTTGGA 57.246 37.500 2.10 0.00 0.00 3.53
126 127 6.529220 AGTCTTATGATATGGAAGCTTGGAC 58.471 40.000 2.10 0.00 0.00 4.02
127 128 5.703130 GTCTTATGATATGGAAGCTTGGACC 59.297 44.000 2.10 0.00 0.00 4.46
128 129 2.620251 TGATATGGAAGCTTGGACCG 57.380 50.000 2.10 0.00 0.00 4.79
129 130 1.230324 GATATGGAAGCTTGGACCGC 58.770 55.000 2.10 0.00 0.00 5.68
130 131 0.179018 ATATGGAAGCTTGGACCGCC 60.179 55.000 2.10 0.00 0.00 6.13
131 132 1.271840 TATGGAAGCTTGGACCGCCT 61.272 55.000 2.10 0.00 34.31 5.52
132 133 1.271840 ATGGAAGCTTGGACCGCCTA 61.272 55.000 2.10 0.00 34.31 3.93
133 134 1.271840 TGGAAGCTTGGACCGCCTAT 61.272 55.000 2.10 0.00 34.31 2.57
134 135 0.107165 GGAAGCTTGGACCGCCTATT 60.107 55.000 2.10 0.00 34.31 1.73
135 136 1.017387 GAAGCTTGGACCGCCTATTG 58.983 55.000 2.10 0.00 34.31 1.90
136 137 0.394352 AAGCTTGGACCGCCTATTGG 60.394 55.000 0.00 0.00 34.31 3.16
137 138 1.823899 GCTTGGACCGCCTATTGGG 60.824 63.158 0.00 0.00 38.36 4.12
138 139 1.607612 CTTGGACCGCCTATTGGGT 59.392 57.895 0.00 0.00 39.83 4.51
139 140 0.748005 CTTGGACCGCCTATTGGGTG 60.748 60.000 0.00 0.00 44.75 4.61
146 147 2.331265 GCCTATTGGGTGATTCGGC 58.669 57.895 0.00 0.00 37.43 5.54
147 148 1.507141 GCCTATTGGGTGATTCGGCG 61.507 60.000 0.00 0.00 37.43 6.46
148 149 0.884704 CCTATTGGGTGATTCGGCGG 60.885 60.000 7.21 0.00 0.00 6.13
149 150 0.105964 CTATTGGGTGATTCGGCGGA 59.894 55.000 7.21 0.00 0.00 5.54
150 151 0.105964 TATTGGGTGATTCGGCGGAG 59.894 55.000 7.21 0.00 0.00 4.63
151 152 1.910580 ATTGGGTGATTCGGCGGAGT 61.911 55.000 7.21 0.00 0.00 3.85
152 153 2.511600 GGGTGATTCGGCGGAGTG 60.512 66.667 7.21 0.00 0.00 3.51
153 154 2.577059 GGTGATTCGGCGGAGTGA 59.423 61.111 7.21 0.00 0.00 3.41
154 155 1.810030 GGTGATTCGGCGGAGTGAC 60.810 63.158 7.21 0.00 0.00 3.67
155 156 1.215647 GTGATTCGGCGGAGTGACT 59.784 57.895 7.21 0.00 0.00 3.41
156 157 1.078759 GTGATTCGGCGGAGTGACTG 61.079 60.000 7.21 0.00 0.00 3.51
157 158 1.519455 GATTCGGCGGAGTGACTGG 60.519 63.158 7.21 0.00 0.00 4.00
158 159 1.945354 GATTCGGCGGAGTGACTGGA 61.945 60.000 7.21 0.00 0.00 3.86
159 160 2.227089 ATTCGGCGGAGTGACTGGAC 62.227 60.000 7.21 0.00 0.00 4.02
160 161 4.778415 CGGCGGAGTGACTGGACG 62.778 72.222 0.00 0.00 0.00 4.79
161 162 3.371063 GGCGGAGTGACTGGACGA 61.371 66.667 0.00 0.00 0.00 4.20
162 163 2.126424 GCGGAGTGACTGGACGAC 60.126 66.667 0.00 0.00 0.00 4.34
163 164 2.567049 CGGAGTGACTGGACGACC 59.433 66.667 0.00 0.00 0.00 4.79
164 165 2.971452 GGAGTGACTGGACGACCC 59.029 66.667 0.34 0.00 34.81 4.46
165 166 1.606889 GGAGTGACTGGACGACCCT 60.607 63.158 0.34 0.00 35.38 4.34
166 167 1.596895 GGAGTGACTGGACGACCCTC 61.597 65.000 0.34 0.12 35.38 4.30
167 168 0.894184 GAGTGACTGGACGACCCTCA 60.894 60.000 0.34 0.00 35.38 3.86
168 169 0.251832 AGTGACTGGACGACCCTCAT 60.252 55.000 0.34 0.00 35.38 2.90
169 170 1.005569 AGTGACTGGACGACCCTCATA 59.994 52.381 0.34 0.00 35.38 2.15
170 171 1.405821 GTGACTGGACGACCCTCATAG 59.594 57.143 0.34 0.00 35.38 2.23
171 172 1.033574 GACTGGACGACCCTCATAGG 58.966 60.000 0.34 0.00 35.38 2.57
172 173 0.335361 ACTGGACGACCCTCATAGGT 59.665 55.000 0.34 0.00 45.12 3.08
173 174 1.273098 ACTGGACGACCCTCATAGGTT 60.273 52.381 0.34 0.00 41.42 3.50
174 175 1.137086 CTGGACGACCCTCATAGGTTG 59.863 57.143 0.34 0.00 45.62 3.77
175 176 0.179081 GGACGACCCTCATAGGTTGC 60.179 60.000 0.00 0.00 44.19 4.17
176 177 0.824759 GACGACCCTCATAGGTTGCT 59.175 55.000 0.00 0.00 44.19 3.91
177 178 0.537188 ACGACCCTCATAGGTTGCTG 59.463 55.000 0.00 0.00 44.19 4.41
178 179 0.179073 CGACCCTCATAGGTTGCTGG 60.179 60.000 0.00 0.00 41.42 4.85
179 180 0.912486 GACCCTCATAGGTTGCTGGT 59.088 55.000 0.00 0.00 41.42 4.00
180 181 0.620556 ACCCTCATAGGTTGCTGGTG 59.379 55.000 0.00 0.00 36.44 4.17
181 182 0.749454 CCCTCATAGGTTGCTGGTGC 60.749 60.000 0.00 0.00 34.78 5.01
182 183 3.406836 CCCTCATAGGTTGCTGGTGCA 62.407 57.143 0.00 0.00 39.44 4.57
183 184 4.666767 CCCTCATAGGTTGCTGGTGCAT 62.667 54.545 0.00 0.00 39.88 3.96
191 192 2.260247 TGCTGGTGCATTTCTGAGC 58.740 52.632 0.00 0.00 45.31 4.26
192 193 0.251033 TGCTGGTGCATTTCTGAGCT 60.251 50.000 0.00 0.00 45.31 4.09
193 194 0.450983 GCTGGTGCATTTCTGAGCTC 59.549 55.000 6.82 6.82 39.41 4.09
194 195 1.093159 CTGGTGCATTTCTGAGCTCC 58.907 55.000 12.15 0.00 42.96 4.70
195 196 0.322816 TGGTGCATTTCTGAGCTCCC 60.323 55.000 12.15 1.88 42.21 4.30
196 197 1.372087 GGTGCATTTCTGAGCTCCCG 61.372 60.000 12.15 2.20 38.20 5.14
197 198 0.674895 GTGCATTTCTGAGCTCCCGT 60.675 55.000 12.15 0.00 0.00 5.28
198 199 0.901827 TGCATTTCTGAGCTCCCGTA 59.098 50.000 12.15 0.00 0.00 4.02
199 200 1.134699 TGCATTTCTGAGCTCCCGTAG 60.135 52.381 12.15 1.36 0.00 3.51
209 210 3.527434 CTCCCGTAGCTTTTTCCGT 57.473 52.632 0.00 0.00 0.00 4.69
210 211 2.660189 CTCCCGTAGCTTTTTCCGTA 57.340 50.000 0.00 0.00 0.00 4.02
211 212 3.175109 CTCCCGTAGCTTTTTCCGTAT 57.825 47.619 0.00 0.00 0.00 3.06
212 213 3.121544 CTCCCGTAGCTTTTTCCGTATC 58.878 50.000 0.00 0.00 0.00 2.24
213 214 2.496871 TCCCGTAGCTTTTTCCGTATCA 59.503 45.455 0.00 0.00 0.00 2.15
214 215 3.133362 TCCCGTAGCTTTTTCCGTATCAT 59.867 43.478 0.00 0.00 0.00 2.45
215 216 3.875134 CCCGTAGCTTTTTCCGTATCATT 59.125 43.478 0.00 0.00 0.00 2.57
216 217 4.260620 CCCGTAGCTTTTTCCGTATCATTG 60.261 45.833 0.00 0.00 0.00 2.82
217 218 4.271687 CGTAGCTTTTTCCGTATCATTGC 58.728 43.478 0.00 0.00 0.00 3.56
218 219 4.034048 CGTAGCTTTTTCCGTATCATTGCT 59.966 41.667 0.00 0.00 0.00 3.91
219 220 5.233476 CGTAGCTTTTTCCGTATCATTGCTA 59.767 40.000 0.00 0.00 0.00 3.49
220 221 5.741388 AGCTTTTTCCGTATCATTGCTAG 57.259 39.130 0.00 0.00 0.00 3.42
221 222 4.576463 AGCTTTTTCCGTATCATTGCTAGG 59.424 41.667 0.00 0.00 0.00 3.02
222 223 4.335594 GCTTTTTCCGTATCATTGCTAGGT 59.664 41.667 0.00 0.00 0.00 3.08
223 224 5.163652 GCTTTTTCCGTATCATTGCTAGGTT 60.164 40.000 0.00 0.00 0.00 3.50
224 225 6.625081 GCTTTTTCCGTATCATTGCTAGGTTT 60.625 38.462 0.00 0.00 0.00 3.27
225 226 6.827586 TTTTCCGTATCATTGCTAGGTTTT 57.172 33.333 0.00 0.00 0.00 2.43
226 227 7.925043 TTTTCCGTATCATTGCTAGGTTTTA 57.075 32.000 0.00 0.00 0.00 1.52
227 228 7.548196 TTTCCGTATCATTGCTAGGTTTTAG 57.452 36.000 0.00 0.00 0.00 1.85
228 229 6.229936 TCCGTATCATTGCTAGGTTTTAGT 57.770 37.500 0.00 0.00 0.00 2.24
229 230 6.278363 TCCGTATCATTGCTAGGTTTTAGTC 58.722 40.000 0.00 0.00 0.00 2.59
230 231 6.046593 CCGTATCATTGCTAGGTTTTAGTCA 58.953 40.000 0.00 0.00 0.00 3.41
231 232 6.201044 CCGTATCATTGCTAGGTTTTAGTCAG 59.799 42.308 0.00 0.00 0.00 3.51
232 233 6.292381 CGTATCATTGCTAGGTTTTAGTCAGC 60.292 42.308 0.00 0.00 0.00 4.26
233 234 4.905429 TCATTGCTAGGTTTTAGTCAGCA 58.095 39.130 0.00 0.00 40.31 4.41
236 237 3.408634 TGCTAGGTTTTAGTCAGCAACC 58.591 45.455 0.00 0.00 39.18 3.77
237 238 2.415512 GCTAGGTTTTAGTCAGCAACCG 59.584 50.000 0.00 0.00 44.16 4.44
238 239 1.235724 AGGTTTTAGTCAGCAACCGC 58.764 50.000 0.00 0.00 44.16 5.68
239 240 0.948678 GGTTTTAGTCAGCAACCGCA 59.051 50.000 0.00 0.00 42.27 5.69
240 241 1.539827 GGTTTTAGTCAGCAACCGCAT 59.460 47.619 0.00 0.00 42.27 4.73
241 242 2.030274 GGTTTTAGTCAGCAACCGCATT 60.030 45.455 0.00 0.00 42.27 3.56
242 243 3.189702 GGTTTTAGTCAGCAACCGCATTA 59.810 43.478 0.00 0.00 42.27 1.90
243 244 4.403453 GTTTTAGTCAGCAACCGCATTAG 58.597 43.478 0.00 0.00 42.27 1.73
244 245 1.651987 TAGTCAGCAACCGCATTAGC 58.348 50.000 0.00 0.00 42.27 3.09
245 246 0.321564 AGTCAGCAACCGCATTAGCA 60.322 50.000 0.00 0.00 42.27 3.49
246 247 0.521291 GTCAGCAACCGCATTAGCAA 59.479 50.000 0.00 0.00 42.27 3.91
247 248 0.521291 TCAGCAACCGCATTAGCAAC 59.479 50.000 0.00 0.00 42.27 4.17
248 249 0.240678 CAGCAACCGCATTAGCAACA 59.759 50.000 0.00 0.00 42.27 3.33
249 250 1.135315 CAGCAACCGCATTAGCAACAT 60.135 47.619 0.00 0.00 42.27 2.71
250 251 1.133025 AGCAACCGCATTAGCAACATC 59.867 47.619 0.00 0.00 42.27 3.06
251 252 1.135431 GCAACCGCATTAGCAACATCA 60.135 47.619 0.00 0.00 42.27 3.07
252 253 2.670789 GCAACCGCATTAGCAACATCAA 60.671 45.455 0.00 0.00 42.27 2.57
253 254 3.772932 CAACCGCATTAGCAACATCAAT 58.227 40.909 0.00 0.00 42.27 2.57
254 255 3.698029 ACCGCATTAGCAACATCAATC 57.302 42.857 0.00 0.00 42.27 2.67
255 256 3.282021 ACCGCATTAGCAACATCAATCT 58.718 40.909 0.00 0.00 42.27 2.40
256 257 3.313526 ACCGCATTAGCAACATCAATCTC 59.686 43.478 0.00 0.00 42.27 2.75
257 258 3.313249 CCGCATTAGCAACATCAATCTCA 59.687 43.478 0.00 0.00 42.27 3.27
258 259 4.201940 CCGCATTAGCAACATCAATCTCAA 60.202 41.667 0.00 0.00 42.27 3.02
259 260 4.968181 CGCATTAGCAACATCAATCTCAAG 59.032 41.667 0.00 0.00 42.27 3.02
260 261 5.279384 GCATTAGCAACATCAATCTCAAGG 58.721 41.667 0.00 0.00 41.58 3.61
261 262 5.066893 GCATTAGCAACATCAATCTCAAGGA 59.933 40.000 0.00 0.00 41.58 3.36
262 263 6.493116 CATTAGCAACATCAATCTCAAGGAC 58.507 40.000 0.00 0.00 0.00 3.85
263 264 4.298103 AGCAACATCAATCTCAAGGACT 57.702 40.909 0.00 0.00 0.00 3.85
264 265 4.008330 AGCAACATCAATCTCAAGGACTG 58.992 43.478 0.00 0.00 0.00 3.51
265 266 3.128242 GCAACATCAATCTCAAGGACTGG 59.872 47.826 0.00 0.00 0.00 4.00
266 267 4.330250 CAACATCAATCTCAAGGACTGGT 58.670 43.478 0.00 0.00 0.00 4.00
267 268 5.491070 CAACATCAATCTCAAGGACTGGTA 58.509 41.667 0.00 0.00 0.00 3.25
268 269 5.091261 ACATCAATCTCAAGGACTGGTAC 57.909 43.478 0.00 0.00 0.00 3.34
269 270 4.532126 ACATCAATCTCAAGGACTGGTACA 59.468 41.667 0.00 0.00 0.00 2.90
270 271 5.190528 ACATCAATCTCAAGGACTGGTACAT 59.809 40.000 0.00 0.00 38.20 2.29
271 272 5.344743 TCAATCTCAAGGACTGGTACATC 57.655 43.478 0.00 0.00 38.20 3.06
272 273 4.162320 TCAATCTCAAGGACTGGTACATCC 59.838 45.833 0.00 0.00 38.20 3.51
273 274 2.100197 TCTCAAGGACTGGTACATCCG 58.900 52.381 0.00 0.00 39.71 4.18
274 275 0.535335 TCAAGGACTGGTACATCCGC 59.465 55.000 0.00 0.00 39.71 5.54
275 276 0.462047 CAAGGACTGGTACATCCGCC 60.462 60.000 0.00 0.00 39.71 6.13
276 277 0.907704 AAGGACTGGTACATCCGCCA 60.908 55.000 0.00 0.00 39.71 5.69
277 278 0.907704 AGGACTGGTACATCCGCCAA 60.908 55.000 0.00 0.00 39.71 4.52
278 279 0.035820 GGACTGGTACATCCGCCAAA 60.036 55.000 0.00 0.00 38.20 3.28
279 280 1.084289 GACTGGTACATCCGCCAAAC 58.916 55.000 0.00 0.00 38.20 2.93
280 281 0.690762 ACTGGTACATCCGCCAAACT 59.309 50.000 0.00 0.00 38.20 2.66
281 282 1.338769 ACTGGTACATCCGCCAAACTC 60.339 52.381 0.00 0.00 38.20 3.01
282 283 0.035820 TGGTACATCCGCCAAACTCC 60.036 55.000 0.00 0.00 39.52 3.85
283 284 0.746923 GGTACATCCGCCAAACTCCC 60.747 60.000 0.00 0.00 0.00 4.30
284 285 0.252197 GTACATCCGCCAAACTCCCT 59.748 55.000 0.00 0.00 0.00 4.20
285 286 0.988832 TACATCCGCCAAACTCCCTT 59.011 50.000 0.00 0.00 0.00 3.95
286 287 0.609131 ACATCCGCCAAACTCCCTTG 60.609 55.000 0.00 0.00 0.00 3.61
287 288 0.322456 CATCCGCCAAACTCCCTTGA 60.322 55.000 0.00 0.00 0.00 3.02
633 646 0.916086 TCTCGCTCCTCTCCTCTCTT 59.084 55.000 0.00 0.00 0.00 2.85
649 662 3.626680 CTTCTCTTCGACGCCGGCA 62.627 63.158 28.98 2.89 36.24 5.69
994 1013 6.939730 TGTGAGCTAAGGTGATTTTGTTGATA 59.060 34.615 0.00 0.00 0.00 2.15
1576 1595 3.039743 TGTGGTGTTACTGAGTGGGTTA 58.960 45.455 0.00 0.00 0.00 2.85
1983 2002 5.513962 GGAGGTTGAACAGGAGAGAGATTTT 60.514 44.000 0.00 0.00 0.00 1.82
2028 2047 2.236893 TGAGCATGTGGTGAATGAGCTA 59.763 45.455 0.00 0.00 0.00 3.32
2044 2063 1.842562 AGCTACTGAGTGATGGGCATT 59.157 47.619 0.00 0.00 0.00 3.56
2052 2071 2.231964 GAGTGATGGGCATTCAAGCAAA 59.768 45.455 0.00 0.00 33.75 3.68
2184 2203 4.480537 AGATATGGGGTGTACATTTTGGGA 59.519 41.667 0.00 0.00 0.00 4.37
2592 2612 3.557903 GAGGAGGCAGTGCAGGCAA 62.558 63.158 18.61 0.00 36.37 4.52
2608 2628 1.442526 GCAATGGATGTGAGGAGGCG 61.443 60.000 0.00 0.00 0.00 5.52
2642 2662 2.142761 AGTGCAGGCAGTGGAGTGA 61.143 57.895 0.00 0.00 0.00 3.41
2723 2743 1.507140 TCACAGTTCTTGTCCCTGGT 58.493 50.000 0.00 0.00 38.16 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.006323 CCTGATAGCTGGTGTATGGAGTC 59.994 52.174 0.00 0.00 0.00 3.36
2 3 2.968574 CCTGATAGCTGGTGTATGGAGT 59.031 50.000 0.00 0.00 0.00 3.85
3 4 2.289320 GCCTGATAGCTGGTGTATGGAG 60.289 54.545 5.75 0.00 35.68 3.86
4 5 1.694150 GCCTGATAGCTGGTGTATGGA 59.306 52.381 5.75 0.00 35.68 3.41
5 6 1.606480 CGCCTGATAGCTGGTGTATGG 60.606 57.143 9.12 0.00 38.42 2.74
6 7 1.341209 TCGCCTGATAGCTGGTGTATG 59.659 52.381 15.84 0.00 42.35 2.39
7 8 1.341531 GTCGCCTGATAGCTGGTGTAT 59.658 52.381 15.84 0.00 42.35 2.29
8 9 0.744874 GTCGCCTGATAGCTGGTGTA 59.255 55.000 15.84 2.23 42.35 2.90
9 10 1.517832 GTCGCCTGATAGCTGGTGT 59.482 57.895 15.84 0.00 42.35 4.16
10 11 1.589993 CGTCGCCTGATAGCTGGTG 60.590 63.158 10.89 10.89 42.89 4.17
11 12 1.320344 TTCGTCGCCTGATAGCTGGT 61.320 55.000 5.75 0.00 35.68 4.00
12 13 0.032678 ATTCGTCGCCTGATAGCTGG 59.967 55.000 0.00 0.00 36.29 4.85
13 14 1.524355 CAATTCGTCGCCTGATAGCTG 59.476 52.381 0.00 0.00 0.00 4.24
14 15 1.858091 CAATTCGTCGCCTGATAGCT 58.142 50.000 0.00 0.00 0.00 3.32
15 16 0.233332 GCAATTCGTCGCCTGATAGC 59.767 55.000 0.00 0.00 0.00 2.97
16 17 0.861837 GGCAATTCGTCGCCTGATAG 59.138 55.000 0.00 0.00 45.29 2.08
17 18 2.986311 GGCAATTCGTCGCCTGATA 58.014 52.632 0.00 0.00 45.29 2.15
18 19 3.813596 GGCAATTCGTCGCCTGAT 58.186 55.556 0.00 0.00 45.29 2.90
23 24 0.109319 ATTTGGTGGCAATTCGTCGC 60.109 50.000 0.00 0.00 0.00 5.19
24 25 3.548014 GGATATTTGGTGGCAATTCGTCG 60.548 47.826 0.00 0.00 0.00 5.12
25 26 3.548014 CGGATATTTGGTGGCAATTCGTC 60.548 47.826 0.00 0.00 0.00 4.20
26 27 2.357637 CGGATATTTGGTGGCAATTCGT 59.642 45.455 0.00 0.00 0.00 3.85
27 28 2.357637 ACGGATATTTGGTGGCAATTCG 59.642 45.455 0.00 0.00 0.00 3.34
28 29 4.385358 AACGGATATTTGGTGGCAATTC 57.615 40.909 0.00 0.00 0.00 2.17
29 30 4.020662 ACAAACGGATATTTGGTGGCAATT 60.021 37.500 0.00 0.00 42.74 2.32
30 31 3.513515 ACAAACGGATATTTGGTGGCAAT 59.486 39.130 0.00 0.00 42.74 3.56
31 32 2.894126 ACAAACGGATATTTGGTGGCAA 59.106 40.909 0.00 0.00 42.74 4.52
32 33 2.230025 CACAAACGGATATTTGGTGGCA 59.770 45.455 3.52 0.00 42.74 4.92
33 34 2.230266 ACACAAACGGATATTTGGTGGC 59.770 45.455 3.52 0.00 42.74 5.01
34 35 3.504134 TGACACAAACGGATATTTGGTGG 59.496 43.478 3.52 0.00 42.74 4.61
35 36 4.023622 TGTGACACAAACGGATATTTGGTG 60.024 41.667 5.62 0.00 42.74 4.17
36 37 4.138290 TGTGACACAAACGGATATTTGGT 58.862 39.130 5.62 0.00 42.74 3.67
37 38 4.757799 TGTGACACAAACGGATATTTGG 57.242 40.909 5.62 0.00 42.74 3.28
38 39 7.693020 TGATATGTGACACAAACGGATATTTG 58.307 34.615 13.23 0.00 43.81 2.32
39 40 7.857734 TGATATGTGACACAAACGGATATTT 57.142 32.000 13.23 0.00 0.00 1.40
40 41 7.768582 TCTTGATATGTGACACAAACGGATATT 59.231 33.333 13.23 0.00 0.00 1.28
41 42 7.272244 TCTTGATATGTGACACAAACGGATAT 58.728 34.615 13.23 4.63 0.00 1.63
42 43 6.635755 TCTTGATATGTGACACAAACGGATA 58.364 36.000 13.23 0.00 0.00 2.59
43 44 5.487433 TCTTGATATGTGACACAAACGGAT 58.513 37.500 13.23 1.50 0.00 4.18
44 45 4.888917 TCTTGATATGTGACACAAACGGA 58.111 39.130 13.23 4.10 0.00 4.69
45 46 5.179368 AGTTCTTGATATGTGACACAAACGG 59.821 40.000 13.23 1.81 0.00 4.44
46 47 6.073819 TGAGTTCTTGATATGTGACACAAACG 60.074 38.462 13.23 0.00 0.00 3.60
47 48 7.189693 TGAGTTCTTGATATGTGACACAAAC 57.810 36.000 13.23 10.31 0.00 2.93
48 49 7.281999 TGTTGAGTTCTTGATATGTGACACAAA 59.718 33.333 13.23 1.16 0.00 2.83
49 50 6.765512 TGTTGAGTTCTTGATATGTGACACAA 59.234 34.615 13.23 2.71 0.00 3.33
50 51 6.202762 GTGTTGAGTTCTTGATATGTGACACA 59.797 38.462 11.41 11.41 34.33 3.72
51 52 6.202762 TGTGTTGAGTTCTTGATATGTGACAC 59.797 38.462 0.00 0.00 34.65 3.67
52 53 6.287525 TGTGTTGAGTTCTTGATATGTGACA 58.712 36.000 0.00 0.00 0.00 3.58
53 54 6.785488 TGTGTTGAGTTCTTGATATGTGAC 57.215 37.500 0.00 0.00 0.00 3.67
54 55 6.936335 ACATGTGTTGAGTTCTTGATATGTGA 59.064 34.615 0.00 0.00 0.00 3.58
55 56 7.137490 ACATGTGTTGAGTTCTTGATATGTG 57.863 36.000 0.00 0.00 0.00 3.21
56 57 7.094634 GGAACATGTGTTGAGTTCTTGATATGT 60.095 37.037 0.00 0.00 40.97 2.29
57 58 7.246311 GGAACATGTGTTGAGTTCTTGATATG 58.754 38.462 0.00 0.00 40.97 1.78
58 59 6.092670 CGGAACATGTGTTGAGTTCTTGATAT 59.907 38.462 0.00 0.00 40.97 1.63
59 60 5.408299 CGGAACATGTGTTGAGTTCTTGATA 59.592 40.000 0.00 0.00 40.97 2.15
60 61 4.214119 CGGAACATGTGTTGAGTTCTTGAT 59.786 41.667 0.00 0.00 40.97 2.57
61 62 3.559655 CGGAACATGTGTTGAGTTCTTGA 59.440 43.478 0.00 0.00 40.97 3.02
62 63 3.303990 CCGGAACATGTGTTGAGTTCTTG 60.304 47.826 0.00 0.00 40.97 3.02
63 64 2.878406 CCGGAACATGTGTTGAGTTCTT 59.122 45.455 0.00 0.00 40.97 2.52
64 65 2.494059 CCGGAACATGTGTTGAGTTCT 58.506 47.619 0.00 0.00 40.97 3.01
65 66 1.535462 CCCGGAACATGTGTTGAGTTC 59.465 52.381 0.73 0.00 38.56 3.01
66 67 1.142060 TCCCGGAACATGTGTTGAGTT 59.858 47.619 0.73 0.00 38.56 3.01
67 68 0.762418 TCCCGGAACATGTGTTGAGT 59.238 50.000 0.73 0.00 38.56 3.41
68 69 1.535462 GTTCCCGGAACATGTGTTGAG 59.465 52.381 23.14 0.00 41.62 3.02
69 70 1.600023 GTTCCCGGAACATGTGTTGA 58.400 50.000 23.14 0.00 41.62 3.18
70 71 0.596082 GGTTCCCGGAACATGTGTTG 59.404 55.000 27.76 0.00 43.54 3.33
71 72 0.887387 CGGTTCCCGGAACATGTGTT 60.887 55.000 27.76 0.00 43.54 3.32
72 73 1.302192 CGGTTCCCGGAACATGTGT 60.302 57.895 27.76 0.00 43.54 3.72
73 74 3.573558 CGGTTCCCGGAACATGTG 58.426 61.111 27.76 12.99 43.54 3.21
83 84 2.817844 ACTAAACAATTCAGCGGTTCCC 59.182 45.455 0.00 0.00 0.00 3.97
84 85 3.751698 AGACTAAACAATTCAGCGGTTCC 59.248 43.478 0.00 0.00 0.00 3.62
85 86 5.358298 AAGACTAAACAATTCAGCGGTTC 57.642 39.130 0.00 0.00 0.00 3.62
86 87 6.653320 TCATAAGACTAAACAATTCAGCGGTT 59.347 34.615 0.00 0.00 0.00 4.44
87 88 6.170506 TCATAAGACTAAACAATTCAGCGGT 58.829 36.000 0.00 0.00 0.00 5.68
88 89 6.662414 TCATAAGACTAAACAATTCAGCGG 57.338 37.500 0.00 0.00 0.00 5.52
89 90 9.803130 CATATCATAAGACTAAACAATTCAGCG 57.197 33.333 0.00 0.00 0.00 5.18
96 97 9.905713 AAGCTTCCATATCATAAGACTAAACAA 57.094 29.630 0.00 0.00 0.00 2.83
97 98 9.330063 CAAGCTTCCATATCATAAGACTAAACA 57.670 33.333 0.00 0.00 0.00 2.83
98 99 8.778358 CCAAGCTTCCATATCATAAGACTAAAC 58.222 37.037 0.00 0.00 0.00 2.01
99 100 8.713971 TCCAAGCTTCCATATCATAAGACTAAA 58.286 33.333 0.00 0.00 0.00 1.85
100 101 8.150945 GTCCAAGCTTCCATATCATAAGACTAA 58.849 37.037 0.00 0.00 0.00 2.24
101 102 7.256332 GGTCCAAGCTTCCATATCATAAGACTA 60.256 40.741 0.00 0.00 0.00 2.59
102 103 6.465035 GGTCCAAGCTTCCATATCATAAGACT 60.465 42.308 0.00 0.00 0.00 3.24
103 104 5.703130 GGTCCAAGCTTCCATATCATAAGAC 59.297 44.000 0.00 0.00 0.00 3.01
104 105 5.511373 CGGTCCAAGCTTCCATATCATAAGA 60.511 44.000 0.00 0.00 0.00 2.10
105 106 4.692625 CGGTCCAAGCTTCCATATCATAAG 59.307 45.833 0.00 0.00 0.00 1.73
106 107 4.641396 CGGTCCAAGCTTCCATATCATAA 58.359 43.478 0.00 0.00 0.00 1.90
107 108 3.557054 GCGGTCCAAGCTTCCATATCATA 60.557 47.826 0.00 0.00 0.00 2.15
108 109 2.811873 GCGGTCCAAGCTTCCATATCAT 60.812 50.000 0.00 0.00 0.00 2.45
109 110 1.475034 GCGGTCCAAGCTTCCATATCA 60.475 52.381 0.00 0.00 0.00 2.15
110 111 1.230324 GCGGTCCAAGCTTCCATATC 58.770 55.000 0.00 0.00 0.00 1.63
111 112 0.179018 GGCGGTCCAAGCTTCCATAT 60.179 55.000 0.00 0.00 34.52 1.78
112 113 1.223487 GGCGGTCCAAGCTTCCATA 59.777 57.895 0.00 0.00 34.52 2.74
113 114 1.271840 TAGGCGGTCCAAGCTTCCAT 61.272 55.000 0.00 0.00 33.74 3.41
114 115 1.271840 ATAGGCGGTCCAAGCTTCCA 61.272 55.000 0.00 0.00 33.74 3.53
115 116 0.107165 AATAGGCGGTCCAAGCTTCC 60.107 55.000 0.00 0.00 33.74 3.46
116 117 1.017387 CAATAGGCGGTCCAAGCTTC 58.983 55.000 0.00 0.00 33.74 3.86
117 118 0.394352 CCAATAGGCGGTCCAAGCTT 60.394 55.000 0.00 0.00 33.74 3.74
118 119 1.224592 CCAATAGGCGGTCCAAGCT 59.775 57.895 0.00 0.00 33.74 3.74
119 120 1.823899 CCCAATAGGCGGTCCAAGC 60.824 63.158 0.00 0.00 33.74 4.01
120 121 0.748005 CACCCAATAGGCGGTCCAAG 60.748 60.000 0.00 0.00 40.58 3.61
121 122 1.202099 TCACCCAATAGGCGGTCCAA 61.202 55.000 0.00 0.00 40.58 3.53
122 123 0.986019 ATCACCCAATAGGCGGTCCA 60.986 55.000 0.00 0.00 40.58 4.02
123 124 0.182775 AATCACCCAATAGGCGGTCC 59.817 55.000 0.00 0.00 40.58 4.46
124 125 1.594331 GAATCACCCAATAGGCGGTC 58.406 55.000 0.00 0.00 40.58 4.79
125 126 0.179056 CGAATCACCCAATAGGCGGT 60.179 55.000 0.00 0.00 40.58 5.68
126 127 0.884704 CCGAATCACCCAATAGGCGG 60.885 60.000 0.00 0.00 40.58 6.13
127 128 1.507141 GCCGAATCACCCAATAGGCG 61.507 60.000 0.00 0.00 40.58 5.52
128 129 1.507141 CGCCGAATCACCCAATAGGC 61.507 60.000 0.00 0.00 40.58 3.93
129 130 0.884704 CCGCCGAATCACCCAATAGG 60.885 60.000 0.00 0.00 43.78 2.57
130 131 0.105964 TCCGCCGAATCACCCAATAG 59.894 55.000 0.00 0.00 0.00 1.73
131 132 0.105964 CTCCGCCGAATCACCCAATA 59.894 55.000 0.00 0.00 0.00 1.90
132 133 1.153168 CTCCGCCGAATCACCCAAT 60.153 57.895 0.00 0.00 0.00 3.16
133 134 2.267642 CTCCGCCGAATCACCCAA 59.732 61.111 0.00 0.00 0.00 4.12
134 135 3.000819 ACTCCGCCGAATCACCCA 61.001 61.111 0.00 0.00 0.00 4.51
135 136 2.511600 CACTCCGCCGAATCACCC 60.512 66.667 0.00 0.00 0.00 4.61
136 137 1.810030 GTCACTCCGCCGAATCACC 60.810 63.158 0.00 0.00 0.00 4.02
137 138 1.078759 CAGTCACTCCGCCGAATCAC 61.079 60.000 0.00 0.00 0.00 3.06
138 139 1.215382 CAGTCACTCCGCCGAATCA 59.785 57.895 0.00 0.00 0.00 2.57
139 140 1.519455 CCAGTCACTCCGCCGAATC 60.519 63.158 0.00 0.00 0.00 2.52
140 141 1.982395 TCCAGTCACTCCGCCGAAT 60.982 57.895 0.00 0.00 0.00 3.34
141 142 2.599281 TCCAGTCACTCCGCCGAA 60.599 61.111 0.00 0.00 0.00 4.30
142 143 3.371063 GTCCAGTCACTCCGCCGA 61.371 66.667 0.00 0.00 0.00 5.54
143 144 4.778415 CGTCCAGTCACTCCGCCG 62.778 72.222 0.00 0.00 0.00 6.46
144 145 3.371063 TCGTCCAGTCACTCCGCC 61.371 66.667 0.00 0.00 0.00 6.13
145 146 2.126424 GTCGTCCAGTCACTCCGC 60.126 66.667 0.00 0.00 0.00 5.54
146 147 2.567049 GGTCGTCCAGTCACTCCG 59.433 66.667 0.00 0.00 0.00 4.63
147 148 1.596895 GAGGGTCGTCCAGTCACTCC 61.597 65.000 0.04 0.00 33.24 3.85
148 149 0.894184 TGAGGGTCGTCCAGTCACTC 60.894 60.000 0.04 0.00 38.62 3.51
149 150 0.251832 ATGAGGGTCGTCCAGTCACT 60.252 55.000 0.04 0.00 38.24 3.41
150 151 1.405821 CTATGAGGGTCGTCCAGTCAC 59.594 57.143 0.04 0.00 38.24 3.67
151 152 1.685180 CCTATGAGGGTCGTCCAGTCA 60.685 57.143 0.04 3.35 38.24 3.41
152 153 1.033574 CCTATGAGGGTCGTCCAGTC 58.966 60.000 0.04 0.00 38.24 3.51
153 154 0.335361 ACCTATGAGGGTCGTCCAGT 59.665 55.000 0.04 0.00 40.58 4.00
154 155 1.137086 CAACCTATGAGGGTCGTCCAG 59.863 57.143 0.04 0.00 40.58 3.86
155 156 1.191535 CAACCTATGAGGGTCGTCCA 58.808 55.000 0.04 0.00 40.58 4.02
156 157 0.179081 GCAACCTATGAGGGTCGTCC 60.179 60.000 0.00 0.00 40.58 4.79
157 158 0.824759 AGCAACCTATGAGGGTCGTC 59.175 55.000 0.00 0.00 40.58 4.20
158 159 0.537188 CAGCAACCTATGAGGGTCGT 59.463 55.000 0.00 0.00 40.58 4.34
159 160 0.179073 CCAGCAACCTATGAGGGTCG 60.179 60.000 0.00 0.00 40.58 4.79
160 161 0.912486 ACCAGCAACCTATGAGGGTC 59.088 55.000 0.00 0.00 40.58 4.46
161 162 0.620556 CACCAGCAACCTATGAGGGT 59.379 55.000 0.00 0.00 40.58 4.34
162 163 0.749454 GCACCAGCAACCTATGAGGG 60.749 60.000 0.00 0.00 39.39 4.30
163 164 2.785868 GCACCAGCAACCTATGAGG 58.214 57.895 0.00 0.00 40.39 3.86
174 175 0.450983 GAGCTCAGAAATGCACCAGC 59.549 55.000 9.40 0.00 42.57 4.85
175 176 1.093159 GGAGCTCAGAAATGCACCAG 58.907 55.000 17.19 0.00 39.24 4.00
176 177 0.322816 GGGAGCTCAGAAATGCACCA 60.323 55.000 17.19 0.00 40.79 4.17
177 178 1.372087 CGGGAGCTCAGAAATGCACC 61.372 60.000 17.19 2.82 38.82 5.01
178 179 0.674895 ACGGGAGCTCAGAAATGCAC 60.675 55.000 17.19 0.00 0.00 4.57
179 180 0.901827 TACGGGAGCTCAGAAATGCA 59.098 50.000 17.19 0.00 0.00 3.96
180 181 1.576356 CTACGGGAGCTCAGAAATGC 58.424 55.000 17.19 0.00 0.00 3.56
191 192 2.660189 TACGGAAAAAGCTACGGGAG 57.340 50.000 0.00 0.00 0.00 4.30
192 193 2.496871 TGATACGGAAAAAGCTACGGGA 59.503 45.455 0.00 0.00 0.00 5.14
193 194 2.896168 TGATACGGAAAAAGCTACGGG 58.104 47.619 0.00 0.00 0.00 5.28
194 195 4.785341 GCAATGATACGGAAAAAGCTACGG 60.785 45.833 0.00 0.00 0.00 4.02
195 196 4.034048 AGCAATGATACGGAAAAAGCTACG 59.966 41.667 0.00 0.00 0.00 3.51
196 197 5.485662 AGCAATGATACGGAAAAAGCTAC 57.514 39.130 0.00 0.00 0.00 3.58
197 198 5.758296 CCTAGCAATGATACGGAAAAAGCTA 59.242 40.000 0.00 0.00 0.00 3.32
198 199 4.576463 CCTAGCAATGATACGGAAAAAGCT 59.424 41.667 0.00 0.00 0.00 3.74
199 200 4.335594 ACCTAGCAATGATACGGAAAAAGC 59.664 41.667 2.06 0.00 0.00 3.51
200 201 6.436843 AACCTAGCAATGATACGGAAAAAG 57.563 37.500 2.06 0.00 0.00 2.27
201 202 6.827586 AAACCTAGCAATGATACGGAAAAA 57.172 33.333 2.06 0.00 0.00 1.94
202 203 6.827586 AAAACCTAGCAATGATACGGAAAA 57.172 33.333 2.06 0.00 0.00 2.29
203 204 7.107542 ACTAAAACCTAGCAATGATACGGAAA 58.892 34.615 2.06 0.00 0.00 3.13
204 205 6.646267 ACTAAAACCTAGCAATGATACGGAA 58.354 36.000 2.06 0.00 0.00 4.30
205 206 6.127281 TGACTAAAACCTAGCAATGATACGGA 60.127 38.462 2.06 0.00 0.00 4.69
206 207 6.046593 TGACTAAAACCTAGCAATGATACGG 58.953 40.000 0.00 0.00 0.00 4.02
207 208 6.292381 GCTGACTAAAACCTAGCAATGATACG 60.292 42.308 0.00 0.00 34.64 3.06
208 209 6.538742 TGCTGACTAAAACCTAGCAATGATAC 59.461 38.462 0.00 0.00 40.99 2.24
209 210 6.649155 TGCTGACTAAAACCTAGCAATGATA 58.351 36.000 0.00 0.00 40.99 2.15
210 211 5.500234 TGCTGACTAAAACCTAGCAATGAT 58.500 37.500 0.00 0.00 40.99 2.45
211 212 4.905429 TGCTGACTAAAACCTAGCAATGA 58.095 39.130 0.00 0.00 40.99 2.57
212 213 5.627499 TTGCTGACTAAAACCTAGCAATG 57.373 39.130 5.92 0.00 46.02 2.82
215 216 3.408634 GGTTGCTGACTAAAACCTAGCA 58.591 45.455 0.00 0.00 42.09 3.49
216 217 2.415512 CGGTTGCTGACTAAAACCTAGC 59.584 50.000 2.64 0.00 41.03 3.42
217 218 2.415512 GCGGTTGCTGACTAAAACCTAG 59.584 50.000 2.64 0.00 41.03 3.02
218 219 2.224329 TGCGGTTGCTGACTAAAACCTA 60.224 45.455 2.64 0.00 41.03 3.08
219 220 1.235724 GCGGTTGCTGACTAAAACCT 58.764 50.000 2.64 0.00 41.03 3.50
220 221 0.948678 TGCGGTTGCTGACTAAAACC 59.051 50.000 0.00 0.00 43.34 3.27
221 222 2.989422 ATGCGGTTGCTGACTAAAAC 57.011 45.000 0.00 0.00 43.34 2.43
222 223 3.119990 GCTAATGCGGTTGCTGACTAAAA 60.120 43.478 0.00 0.00 43.34 1.52
223 224 2.418628 GCTAATGCGGTTGCTGACTAAA 59.581 45.455 0.00 0.00 43.34 1.85
224 225 2.006888 GCTAATGCGGTTGCTGACTAA 58.993 47.619 0.00 0.00 43.34 2.24
225 226 1.066502 TGCTAATGCGGTTGCTGACTA 60.067 47.619 0.00 0.00 43.34 2.59
226 227 0.321564 TGCTAATGCGGTTGCTGACT 60.322 50.000 0.00 0.00 43.34 3.41
227 228 0.521291 TTGCTAATGCGGTTGCTGAC 59.479 50.000 0.00 0.00 43.34 3.51
228 229 0.521291 GTTGCTAATGCGGTTGCTGA 59.479 50.000 0.00 0.00 43.34 4.26
229 230 0.240678 TGTTGCTAATGCGGTTGCTG 59.759 50.000 0.00 0.00 43.34 4.41
230 231 1.133025 GATGTTGCTAATGCGGTTGCT 59.867 47.619 0.00 0.00 43.34 3.91
231 232 1.135431 TGATGTTGCTAATGCGGTTGC 60.135 47.619 0.00 0.00 43.34 4.17
232 233 2.917701 TGATGTTGCTAATGCGGTTG 57.082 45.000 0.00 0.00 43.34 3.77
233 234 3.696051 AGATTGATGTTGCTAATGCGGTT 59.304 39.130 0.00 0.00 43.34 4.44
234 235 3.282021 AGATTGATGTTGCTAATGCGGT 58.718 40.909 0.00 0.00 43.34 5.68
235 236 3.313249 TGAGATTGATGTTGCTAATGCGG 59.687 43.478 0.00 0.00 43.34 5.69
236 237 4.541085 TGAGATTGATGTTGCTAATGCG 57.459 40.909 0.00 0.00 43.34 4.73
237 238 5.066893 TCCTTGAGATTGATGTTGCTAATGC 59.933 40.000 0.00 0.00 40.20 3.56
238 239 6.318144 AGTCCTTGAGATTGATGTTGCTAATG 59.682 38.462 0.00 0.00 0.00 1.90
239 240 6.318144 CAGTCCTTGAGATTGATGTTGCTAAT 59.682 38.462 0.00 0.00 34.18 1.73
240 241 5.645067 CAGTCCTTGAGATTGATGTTGCTAA 59.355 40.000 0.00 0.00 34.18 3.09
241 242 5.181009 CAGTCCTTGAGATTGATGTTGCTA 58.819 41.667 0.00 0.00 34.18 3.49
242 243 4.008330 CAGTCCTTGAGATTGATGTTGCT 58.992 43.478 0.00 0.00 34.18 3.91
243 244 3.128242 CCAGTCCTTGAGATTGATGTTGC 59.872 47.826 0.00 0.00 34.18 4.17
244 245 4.330250 ACCAGTCCTTGAGATTGATGTTG 58.670 43.478 0.00 0.00 34.18 3.33
245 246 4.647564 ACCAGTCCTTGAGATTGATGTT 57.352 40.909 0.00 0.00 34.18 2.71
246 247 4.532126 TGTACCAGTCCTTGAGATTGATGT 59.468 41.667 0.00 0.00 34.18 3.06
247 248 5.089970 TGTACCAGTCCTTGAGATTGATG 57.910 43.478 0.00 0.00 34.18 3.07
248 249 5.163258 GGATGTACCAGTCCTTGAGATTGAT 60.163 44.000 0.00 0.00 34.18 2.57
249 250 4.162320 GGATGTACCAGTCCTTGAGATTGA 59.838 45.833 0.00 0.00 34.18 2.57
250 251 4.446371 GGATGTACCAGTCCTTGAGATTG 58.554 47.826 0.00 0.00 38.79 2.67
251 252 3.133003 CGGATGTACCAGTCCTTGAGATT 59.867 47.826 7.26 0.00 38.90 2.40
252 253 2.695666 CGGATGTACCAGTCCTTGAGAT 59.304 50.000 7.26 0.00 38.90 2.75
253 254 2.100197 CGGATGTACCAGTCCTTGAGA 58.900 52.381 7.26 0.00 38.90 3.27
254 255 1.471676 GCGGATGTACCAGTCCTTGAG 60.472 57.143 7.26 0.00 38.90 3.02
255 256 0.535335 GCGGATGTACCAGTCCTTGA 59.465 55.000 7.26 0.00 38.90 3.02
256 257 0.462047 GGCGGATGTACCAGTCCTTG 60.462 60.000 7.26 0.00 38.90 3.61
257 258 0.907704 TGGCGGATGTACCAGTCCTT 60.908 55.000 7.26 0.00 38.90 3.36
258 259 0.907704 TTGGCGGATGTACCAGTCCT 60.908 55.000 7.26 0.00 37.24 3.85
259 260 0.035820 TTTGGCGGATGTACCAGTCC 60.036 55.000 0.00 0.00 37.24 3.85
260 261 1.084289 GTTTGGCGGATGTACCAGTC 58.916 55.000 0.00 0.00 37.24 3.51
261 262 0.690762 AGTTTGGCGGATGTACCAGT 59.309 50.000 0.00 0.00 37.24 4.00
262 263 1.369625 GAGTTTGGCGGATGTACCAG 58.630 55.000 0.00 0.00 37.24 4.00
263 264 0.035820 GGAGTTTGGCGGATGTACCA 60.036 55.000 0.00 0.00 38.90 3.25
264 265 0.746923 GGGAGTTTGGCGGATGTACC 60.747 60.000 0.00 0.00 0.00 3.34
265 266 0.252197 AGGGAGTTTGGCGGATGTAC 59.748 55.000 0.00 0.00 0.00 2.90
266 267 0.988832 AAGGGAGTTTGGCGGATGTA 59.011 50.000 0.00 0.00 0.00 2.29
267 268 0.609131 CAAGGGAGTTTGGCGGATGT 60.609 55.000 0.00 0.00 0.00 3.06
268 269 0.322456 TCAAGGGAGTTTGGCGGATG 60.322 55.000 0.00 0.00 0.00 3.51
269 270 0.625849 ATCAAGGGAGTTTGGCGGAT 59.374 50.000 0.00 0.00 0.00 4.18
270 271 1.281419 TATCAAGGGAGTTTGGCGGA 58.719 50.000 0.00 0.00 0.00 5.54
271 272 2.122783 TTATCAAGGGAGTTTGGCGG 57.877 50.000 0.00 0.00 0.00 6.13
272 273 4.261197 GCTATTTATCAAGGGAGTTTGGCG 60.261 45.833 0.00 0.00 0.00 5.69
273 274 4.644685 TGCTATTTATCAAGGGAGTTTGGC 59.355 41.667 0.00 0.00 0.00 4.52
274 275 6.966534 ATGCTATTTATCAAGGGAGTTTGG 57.033 37.500 0.00 0.00 0.00 3.28
277 278 9.700831 AGTTTTATGCTATTTATCAAGGGAGTT 57.299 29.630 0.00 0.00 0.00 3.01
280 281 9.569122 GGTAGTTTTATGCTATTTATCAAGGGA 57.431 33.333 0.00 0.00 0.00 4.20
281 282 9.349713 TGGTAGTTTTATGCTATTTATCAAGGG 57.650 33.333 0.00 0.00 0.00 3.95
633 646 4.116328 CTGCCGGCGTCGAAGAGA 62.116 66.667 23.90 0.00 36.95 3.10
652 665 3.966215 GCTTCCACAGCGCAAGTA 58.034 55.556 11.47 0.00 39.29 2.24
859 878 0.960364 ACAGCAACCATAACCCTGCG 60.960 55.000 0.00 0.00 39.80 5.18
994 1013 0.257039 GGGGTCTCCTGCATGAACAT 59.743 55.000 0.00 0.00 0.00 2.71
1059 1078 1.996786 GCATCATGCAGGTGGGTTCG 61.997 60.000 4.20 0.00 44.26 3.95
1576 1595 0.252375 ATTGGATGCCAGGGCTTGTT 60.252 50.000 12.19 0.00 42.51 2.83
1983 2002 4.965532 AGCTTGGCCTTCTCTATCTTAAGA 59.034 41.667 7.82 7.82 0.00 2.10
2028 2047 2.719739 CTTGAATGCCCATCACTCAGT 58.280 47.619 0.00 0.00 32.03 3.41
2044 2063 6.757897 TTTCTCAAGTTTCTCTTTGCTTGA 57.242 33.333 0.00 0.00 43.16 3.02
2184 2203 9.757227 GACATAGACTAGATTAGCTTCACATTT 57.243 33.333 0.00 0.00 0.00 2.32
2592 2612 0.467384 CTTCGCCTCCTCACATCCAT 59.533 55.000 0.00 0.00 0.00 3.41
2642 2662 2.178580 CTCCTCTTGAACTCCAGCTCT 58.821 52.381 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.