Multiple sequence alignment - TraesCS5B01G313500

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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 TraesCS5B01G313500 chr5B 100.000 3384 0 0 1 3384 495830064 495826681 0.000000e+00 6250.0
1 TraesCS5B01G313500 chr5B 92.073 328 20 4 1 326 299598197 299597874 1.110000e-124 457.0
2 TraesCS5B01G313500 chr5D 88.728 3185 120 65 305 3384 412249773 412246723 0.000000e+00 3672.0
3 TraesCS5B01G313500 chr5A 89.171 1025 42 23 2066 3057 524011368 524010380 0.000000e+00 1214.0
4 TraesCS5B01G313500 chr5A 88.512 766 58 23 1303 2060 524012081 524011338 0.000000e+00 900.0
5 TraesCS5B01G313500 chr5A 86.883 831 54 31 461 1267 524012951 524012152 0.000000e+00 880.0
6 TraesCS5B01G313500 chr5A 82.595 316 19 16 3081 3383 524010394 524010102 2.610000e-61 246.0
7 TraesCS5B01G313500 chr7B 96.078 306 9 3 1 304 380701767 380701463 2.350000e-136 496.0
8 TraesCS5B01G313500 chr7B 93.115 305 19 2 1 304 706458497 706458800 2.400000e-121 446.0
9 TraesCS5B01G313500 chr2B 95.223 314 14 1 1 314 676015629 676015317 2.350000e-136 496.0
10 TraesCS5B01G313500 chr2B 94.771 306 12 4 1 305 44908264 44908566 1.100000e-129 473.0
11 TraesCS5B01G313500 chr4B 94.426 305 15 2 1 304 103051545 103051242 5.110000e-128 468.0
12 TraesCS5B01G313500 chr3B 93.569 311 16 4 1 310 21409259 21408952 8.560000e-126 460.0
13 TraesCS5B01G313500 chr3B 93.770 305 16 3 1 304 504065400 504065098 3.980000e-124 455.0
14 TraesCS5B01G313500 chr3B 97.959 49 0 1 1103 1150 659275883 659275835 2.160000e-12 84.2
15 TraesCS5B01G313500 chr3B 95.918 49 1 1 1103 1150 659297955 659297907 1.010000e-10 78.7
16 TraesCS5B01G313500 chr3B 95.918 49 1 1 1103 1150 659305263 659305215 1.010000e-10 78.7
17 TraesCS5B01G313500 chr1B 93.443 305 17 3 1 304 552309968 552310270 1.850000e-122 449.0
18 TraesCS5B01G313500 chr3A 97.959 49 0 1 1103 1150 638467701 638467653 2.160000e-12 84.2
19 TraesCS5B01G313500 chr3A 97.959 49 0 1 1103 1150 638711299 638711251 2.160000e-12 84.2
20 TraesCS5B01G313500 chr3A 97.872 47 0 1 1105 1150 638446821 638446775 2.800000e-11 80.5
21 TraesCS5B01G313500 chr7D 88.333 60 7 0 1979 2038 25818472 25818413 4.680000e-09 73.1
22 TraesCS5B01G313500 chr4A 88.333 60 7 0 1979 2038 710243801 710243742 4.680000e-09 73.1


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 TraesCS5B01G313500 chr5B 495826681 495830064 3383 True 6250 6250 100.00000 1 3384 1 chr5B.!!$R2 3383
1 TraesCS5B01G313500 chr5D 412246723 412249773 3050 True 3672 3672 88.72800 305 3384 1 chr5D.!!$R1 3079
2 TraesCS5B01G313500 chr5A 524010102 524012951 2849 True 810 1214 86.79025 461 3383 4 chr5A.!!$R1 2922

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
23 24 0.095245 CGTTACAGAAGGCATGCACG 59.905 55.0 21.36 14.02 0.0 5.34 F
725 780 0.107165 CCTCCCTCGTTCCCCAATTC 60.107 60.0 0.00 0.00 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1580 0.674581 CGAGCATCACCAGCTTGGAA 60.675 55.0 8.91 0.0 43.58 3.53 R
2578 2711 0.178947 AGAAAAATGGGGGCGGAACA 60.179 50.0 0.00 0.0 0.00 3.18 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
20 21 2.010145 TCTCGTTACAGAAGGCATGC 57.990 50.000 9.90 9.90 0.00 4.06
21 22 1.275010 TCTCGTTACAGAAGGCATGCA 59.725 47.619 21.36 0.00 0.00 3.96
22 23 1.394917 CTCGTTACAGAAGGCATGCAC 59.605 52.381 21.36 9.10 0.00 4.57
23 24 0.095245 CGTTACAGAAGGCATGCACG 59.905 55.000 21.36 14.02 0.00 5.34
24 25 0.447801 GTTACAGAAGGCATGCACGG 59.552 55.000 21.36 12.88 0.00 4.94
25 26 1.305219 TTACAGAAGGCATGCACGGC 61.305 55.000 21.36 0.00 0.00 5.68
26 27 2.462125 TACAGAAGGCATGCACGGCA 62.462 55.000 21.36 1.01 44.86 5.69
27 28 2.282391 AGAAGGCATGCACGGCAA 60.282 55.556 21.36 0.00 43.62 4.52
28 29 1.902918 AGAAGGCATGCACGGCAAA 60.903 52.632 21.36 0.00 43.62 3.68
29 30 1.006337 GAAGGCATGCACGGCAAAA 60.006 52.632 21.36 0.00 43.62 2.44
30 31 1.284297 GAAGGCATGCACGGCAAAAC 61.284 55.000 21.36 0.00 43.62 2.43
31 32 2.713927 AAGGCATGCACGGCAAAACC 62.714 55.000 21.36 0.00 43.62 3.27
32 33 2.738139 GCATGCACGGCAAAACCC 60.738 61.111 14.21 0.00 43.62 4.11
33 34 3.050339 CATGCACGGCAAAACCCT 58.950 55.556 2.68 0.00 43.62 4.34
34 35 1.373246 CATGCACGGCAAAACCCTG 60.373 57.895 2.68 0.00 43.62 4.45
41 42 2.421314 GCAAAACCCTGCCACACC 59.579 61.111 0.00 0.00 36.25 4.16
42 43 2.133641 GCAAAACCCTGCCACACCT 61.134 57.895 0.00 0.00 36.25 4.00
43 44 1.685355 GCAAAACCCTGCCACACCTT 61.685 55.000 0.00 0.00 36.25 3.50
44 45 1.698506 CAAAACCCTGCCACACCTTA 58.301 50.000 0.00 0.00 0.00 2.69
45 46 1.339929 CAAAACCCTGCCACACCTTAC 59.660 52.381 0.00 0.00 0.00 2.34
46 47 0.178973 AAACCCTGCCACACCTTACC 60.179 55.000 0.00 0.00 0.00 2.85
47 48 2.046314 CCCTGCCACACCTTACCG 60.046 66.667 0.00 0.00 0.00 4.02
48 49 2.746277 CCTGCCACACCTTACCGC 60.746 66.667 0.00 0.00 0.00 5.68
49 50 2.746277 CTGCCACACCTTACCGCC 60.746 66.667 0.00 0.00 0.00 6.13
50 51 3.545124 CTGCCACACCTTACCGCCA 62.545 63.158 0.00 0.00 0.00 5.69
51 52 2.746277 GCCACACCTTACCGCCAG 60.746 66.667 0.00 0.00 0.00 4.85
52 53 3.065306 CCACACCTTACCGCCAGA 58.935 61.111 0.00 0.00 0.00 3.86
53 54 1.079127 CCACACCTTACCGCCAGAG 60.079 63.158 0.00 0.00 0.00 3.35
54 55 1.741770 CACACCTTACCGCCAGAGC 60.742 63.158 0.00 0.00 0.00 4.09
55 56 2.125106 CACCTTACCGCCAGAGCC 60.125 66.667 0.00 0.00 34.57 4.70
56 57 3.771160 ACCTTACCGCCAGAGCCG 61.771 66.667 0.00 0.00 34.57 5.52
57 58 3.771160 CCTTACCGCCAGAGCCGT 61.771 66.667 0.00 0.00 34.67 5.68
58 59 2.264794 CTTACCGCCAGAGCCGTT 59.735 61.111 0.00 0.00 32.48 4.44
59 60 2.047655 TTACCGCCAGAGCCGTTG 60.048 61.111 0.00 0.00 32.48 4.10
60 61 3.599285 TTACCGCCAGAGCCGTTGG 62.599 63.158 0.00 0.00 38.78 3.77
64 65 4.643387 GCCAGAGCCGTTGGTGGT 62.643 66.667 1.31 0.00 38.02 4.16
65 66 3.065306 CCAGAGCCGTTGGTGGTA 58.935 61.111 0.00 0.00 0.00 3.25
66 67 1.079127 CCAGAGCCGTTGGTGGTAG 60.079 63.158 0.00 0.00 0.00 3.18
67 68 1.079127 CAGAGCCGTTGGTGGTAGG 60.079 63.158 0.00 0.00 0.00 3.18
68 69 2.267961 GAGCCGTTGGTGGTAGGG 59.732 66.667 0.00 0.00 0.00 3.53
69 70 2.528378 AGCCGTTGGTGGTAGGGT 60.528 61.111 0.00 0.00 0.00 4.34
70 71 2.120737 GAGCCGTTGGTGGTAGGGTT 62.121 60.000 0.00 0.00 34.28 4.11
71 72 0.837260 AGCCGTTGGTGGTAGGGTTA 60.837 55.000 0.00 0.00 0.00 2.85
72 73 0.392060 GCCGTTGGTGGTAGGGTTAG 60.392 60.000 0.00 0.00 0.00 2.34
73 74 1.269012 CCGTTGGTGGTAGGGTTAGA 58.731 55.000 0.00 0.00 0.00 2.10
74 75 1.066645 CCGTTGGTGGTAGGGTTAGAC 60.067 57.143 0.00 0.00 0.00 2.59
75 76 1.619827 CGTTGGTGGTAGGGTTAGACA 59.380 52.381 0.00 0.00 0.00 3.41
76 77 2.353406 CGTTGGTGGTAGGGTTAGACAG 60.353 54.545 0.00 0.00 0.00 3.51
77 78 1.272807 TGGTGGTAGGGTTAGACAGC 58.727 55.000 0.00 0.00 0.00 4.40
78 79 1.203262 TGGTGGTAGGGTTAGACAGCT 60.203 52.381 0.00 0.00 0.00 4.24
79 80 1.907255 GGTGGTAGGGTTAGACAGCTT 59.093 52.381 0.00 0.00 0.00 3.74
80 81 3.102204 GGTGGTAGGGTTAGACAGCTTA 58.898 50.000 0.00 0.00 0.00 3.09
81 82 3.118847 GGTGGTAGGGTTAGACAGCTTAC 60.119 52.174 0.00 0.00 35.27 2.34
82 83 3.815856 GGTAGGGTTAGACAGCTTACC 57.184 52.381 0.00 0.00 45.39 2.85
83 84 2.100418 GGTAGGGTTAGACAGCTTACCG 59.900 54.545 0.00 0.00 43.49 4.02
84 85 0.535797 AGGGTTAGACAGCTTACCGC 59.464 55.000 0.00 0.00 43.18 5.68
85 86 0.461516 GGGTTAGACAGCTTACCGCC 60.462 60.000 0.00 0.00 43.18 6.13
86 87 0.535797 GGTTAGACAGCTTACCGCCT 59.464 55.000 0.00 0.00 40.39 5.52
87 88 1.641577 GTTAGACAGCTTACCGCCTG 58.358 55.000 0.00 0.00 40.39 4.85
88 89 0.535335 TTAGACAGCTTACCGCCTGG 59.465 55.000 0.00 0.00 40.39 4.45
101 102 3.065306 CCTGGTTGTCTGGCGGTA 58.935 61.111 0.00 0.00 0.00 4.02
102 103 1.373435 CCTGGTTGTCTGGCGGTAA 59.627 57.895 0.00 0.00 0.00 2.85
103 104 0.673644 CCTGGTTGTCTGGCGGTAAG 60.674 60.000 0.00 0.00 0.00 2.34
104 105 0.673644 CTGGTTGTCTGGCGGTAAGG 60.674 60.000 0.00 0.00 0.00 2.69
105 106 1.373812 GGTTGTCTGGCGGTAAGGT 59.626 57.895 0.00 0.00 0.00 3.50
106 107 0.609662 GGTTGTCTGGCGGTAAGGTA 59.390 55.000 0.00 0.00 0.00 3.08
107 108 1.673923 GGTTGTCTGGCGGTAAGGTAC 60.674 57.143 0.00 0.00 0.00 3.34
122 123 1.404391 AGGTACTTATCCACGTCAGCG 59.596 52.381 0.00 0.00 39.38 5.18
123 124 1.197910 GTACTTATCCACGTCAGCGC 58.802 55.000 0.00 0.00 42.83 5.92
124 125 0.248336 TACTTATCCACGTCAGCGCG 60.248 55.000 0.00 0.00 42.83 6.86
125 126 2.860628 CTTATCCACGTCAGCGCGC 61.861 63.158 26.66 26.66 42.83 6.86
150 151 4.755507 GTCCCCGTCTCCCTCCGT 62.756 72.222 0.00 0.00 0.00 4.69
151 152 4.437587 TCCCCGTCTCCCTCCGTC 62.438 72.222 0.00 0.00 0.00 4.79
152 153 4.753662 CCCCGTCTCCCTCCGTCA 62.754 72.222 0.00 0.00 0.00 4.35
153 154 3.450115 CCCGTCTCCCTCCGTCAC 61.450 72.222 0.00 0.00 0.00 3.67
154 155 2.675423 CCGTCTCCCTCCGTCACA 60.675 66.667 0.00 0.00 0.00 3.58
155 156 2.567049 CGTCTCCCTCCGTCACAC 59.433 66.667 0.00 0.00 0.00 3.82
156 157 2.971452 GTCTCCCTCCGTCACACC 59.029 66.667 0.00 0.00 0.00 4.16
157 158 2.283676 TCTCCCTCCGTCACACCC 60.284 66.667 0.00 0.00 0.00 4.61
158 159 2.283966 CTCCCTCCGTCACACCCT 60.284 66.667 0.00 0.00 0.00 4.34
159 160 1.000019 CTCCCTCCGTCACACCCTA 60.000 63.158 0.00 0.00 0.00 3.53
160 161 1.304713 TCCCTCCGTCACACCCTAC 60.305 63.158 0.00 0.00 0.00 3.18
161 162 2.356780 CCCTCCGTCACACCCTACC 61.357 68.421 0.00 0.00 0.00 3.18
162 163 2.707849 CCTCCGTCACACCCTACCG 61.708 68.421 0.00 0.00 0.00 4.02
163 164 3.352338 CTCCGTCACACCCTACCGC 62.352 68.421 0.00 0.00 0.00 5.68
164 165 4.446413 CCGTCACACCCTACCGCC 62.446 72.222 0.00 0.00 0.00 6.13
165 166 3.687102 CGTCACACCCTACCGCCA 61.687 66.667 0.00 0.00 0.00 5.69
166 167 2.264794 GTCACACCCTACCGCCAG 59.735 66.667 0.00 0.00 0.00 4.85
167 168 3.000819 TCACACCCTACCGCCAGG 61.001 66.667 0.00 0.00 45.13 4.45
173 174 3.971894 CCTACCGCCAGGGAATCT 58.028 61.111 0.00 0.00 43.47 2.40
174 175 1.447643 CCTACCGCCAGGGAATCTG 59.552 63.158 0.00 0.00 43.47 2.90
182 183 1.227674 CAGGGAATCTGGCGGTAGC 60.228 63.158 0.00 0.00 39.76 3.58
183 184 1.383248 AGGGAATCTGGCGGTAGCT 60.383 57.895 0.00 0.00 44.37 3.32
184 185 0.983378 AGGGAATCTGGCGGTAGCTT 60.983 55.000 0.00 0.00 44.37 3.74
185 186 0.815615 GGGAATCTGGCGGTAGCTTG 60.816 60.000 0.00 0.00 44.37 4.01
186 187 0.107654 GGAATCTGGCGGTAGCTTGT 60.108 55.000 0.00 0.00 44.37 3.16
187 188 1.291132 GAATCTGGCGGTAGCTTGTC 58.709 55.000 0.00 0.00 44.37 3.18
188 189 0.905357 AATCTGGCGGTAGCTTGTCT 59.095 50.000 0.00 0.00 44.37 3.41
189 190 1.776662 ATCTGGCGGTAGCTTGTCTA 58.223 50.000 0.00 0.00 44.37 2.59
190 191 1.552578 TCTGGCGGTAGCTTGTCTAA 58.447 50.000 0.00 0.00 44.37 2.10
191 192 1.203994 TCTGGCGGTAGCTTGTCTAAC 59.796 52.381 0.00 0.00 44.37 2.34
192 193 0.248289 TGGCGGTAGCTTGTCTAACC 59.752 55.000 0.00 0.00 44.37 2.85
193 194 0.461516 GGCGGTAGCTTGTCTAACCC 60.462 60.000 0.00 0.00 44.37 4.11
194 195 0.535797 GCGGTAGCTTGTCTAACCCT 59.464 55.000 0.00 0.00 41.01 4.34
195 196 1.753073 GCGGTAGCTTGTCTAACCCTA 59.247 52.381 0.00 0.00 41.01 3.53
196 197 2.480932 GCGGTAGCTTGTCTAACCCTAC 60.481 54.545 0.00 0.00 41.01 3.18
197 198 2.100418 CGGTAGCTTGTCTAACCCTACC 59.900 54.545 0.00 0.00 42.80 3.18
198 199 2.100418 GGTAGCTTGTCTAACCCTACCG 59.900 54.545 0.00 0.00 38.82 4.02
199 200 0.535797 AGCTTGTCTAACCCTACCGC 59.464 55.000 0.00 0.00 0.00 5.68
200 201 0.461516 GCTTGTCTAACCCTACCGCC 60.462 60.000 0.00 0.00 0.00 6.13
201 202 0.899720 CTTGTCTAACCCTACCGCCA 59.100 55.000 0.00 0.00 0.00 5.69
202 203 0.899720 TTGTCTAACCCTACCGCCAG 59.100 55.000 0.00 0.00 0.00 4.85
203 204 0.974010 TGTCTAACCCTACCGCCAGG 60.974 60.000 0.00 0.00 45.13 4.45
209 210 2.042843 CCTACCGCCAGGGACTCT 60.043 66.667 0.00 0.00 43.47 3.24
210 211 2.427245 CCTACCGCCAGGGACTCTG 61.427 68.421 0.00 0.00 43.47 3.35
217 218 3.211288 CAGGGACTCTGGCGGTAG 58.789 66.667 0.00 0.00 39.76 3.18
218 219 2.760385 AGGGACTCTGGCGGTAGC 60.760 66.667 0.00 0.00 44.18 3.58
228 229 4.390048 GCGGTAGCAAAAGGGTCA 57.610 55.556 0.00 0.00 44.35 4.02
229 230 2.636299 GCGGTAGCAAAAGGGTCAA 58.364 52.632 0.00 0.00 44.35 3.18
230 231 0.955905 GCGGTAGCAAAAGGGTCAAA 59.044 50.000 0.00 0.00 44.35 2.69
231 232 1.544246 GCGGTAGCAAAAGGGTCAAAT 59.456 47.619 0.00 0.00 44.35 2.32
232 233 2.415491 GCGGTAGCAAAAGGGTCAAATC 60.415 50.000 0.00 0.00 44.35 2.17
233 234 2.163613 CGGTAGCAAAAGGGTCAAATCC 59.836 50.000 0.00 0.00 0.00 3.01
234 235 3.431415 GGTAGCAAAAGGGTCAAATCCT 58.569 45.455 0.00 0.00 35.88 3.24
235 236 3.193479 GGTAGCAAAAGGGTCAAATCCTG 59.807 47.826 0.00 0.00 34.34 3.86
236 237 3.243359 AGCAAAAGGGTCAAATCCTGA 57.757 42.857 0.00 0.00 34.34 3.86
237 238 3.575805 AGCAAAAGGGTCAAATCCTGAA 58.424 40.909 0.00 0.00 35.22 3.02
238 239 4.162651 AGCAAAAGGGTCAAATCCTGAAT 58.837 39.130 0.00 0.00 35.22 2.57
239 240 4.594491 AGCAAAAGGGTCAAATCCTGAATT 59.406 37.500 0.00 0.00 35.22 2.17
240 241 5.072193 AGCAAAAGGGTCAAATCCTGAATTT 59.928 36.000 0.00 0.00 38.11 1.82
241 242 5.764686 GCAAAAGGGTCAAATCCTGAATTTT 59.235 36.000 0.00 0.00 35.32 1.82
242 243 6.262944 GCAAAAGGGTCAAATCCTGAATTTTT 59.737 34.615 0.00 0.00 35.32 1.94
266 267 7.737972 TTTTTAAACGTGGATCAGATCTTGA 57.262 32.000 10.36 0.00 40.85 3.02
268 269 7.921786 TTTAAACGTGGATCAGATCTTGATT 57.078 32.000 10.36 4.61 46.51 2.57
269 270 7.921786 TTAAACGTGGATCAGATCTTGATTT 57.078 32.000 10.36 8.77 46.51 2.17
270 271 6.824305 AAACGTGGATCAGATCTTGATTTT 57.176 33.333 10.36 2.04 46.51 1.82
271 272 5.808042 ACGTGGATCAGATCTTGATTTTG 57.192 39.130 10.36 0.00 46.51 2.44
272 273 5.248640 ACGTGGATCAGATCTTGATTTTGT 58.751 37.500 10.36 0.00 46.51 2.83
273 274 5.707298 ACGTGGATCAGATCTTGATTTTGTT 59.293 36.000 10.36 0.00 46.51 2.83
274 275 6.207417 ACGTGGATCAGATCTTGATTTTGTTT 59.793 34.615 10.36 0.00 46.51 2.83
275 276 7.390440 ACGTGGATCAGATCTTGATTTTGTTTA 59.610 33.333 10.36 0.00 46.51 2.01
276 277 8.236586 CGTGGATCAGATCTTGATTTTGTTTAA 58.763 33.333 10.36 0.00 46.51 1.52
277 278 9.912634 GTGGATCAGATCTTGATTTTGTTTAAA 57.087 29.630 10.36 0.00 46.51 1.52
299 300 6.656314 AAAAAGGGTCAAAACACGAAATTC 57.344 33.333 0.00 0.00 32.44 2.17
300 301 4.993029 AAGGGTCAAAACACGAAATTCA 57.007 36.364 0.00 0.00 32.44 2.57
301 302 4.568152 AGGGTCAAAACACGAAATTCAG 57.432 40.909 0.00 0.00 32.44 3.02
302 303 3.049912 GGGTCAAAACACGAAATTCAGC 58.950 45.455 0.00 0.00 0.00 4.26
303 304 3.049912 GGTCAAAACACGAAATTCAGCC 58.950 45.455 0.00 0.00 0.00 4.85
348 351 1.915141 CTGGCCACTTTTCTGGTCAT 58.085 50.000 0.00 0.00 45.05 3.06
356 359 4.144297 CACTTTTCTGGTCATGGGAAAGA 58.856 43.478 7.28 0.00 31.88 2.52
374 377 4.580551 GCATGCAGAATGGCGGGC 62.581 66.667 14.21 0.00 36.71 6.13
411 414 1.520787 CGGGCCCGATATATTCCGC 60.521 63.158 41.82 0.00 42.83 5.54
414 417 1.520787 GCCCGATATATTCCGCCGG 60.521 63.158 0.00 0.00 39.85 6.13
419 422 0.527817 GATATATTCCGCCGGCCTCG 60.528 60.000 23.46 8.87 0.00 4.63
495 531 0.320946 TTGCCCCGTTTCTTACTCCG 60.321 55.000 0.00 0.00 0.00 4.63
504 540 3.615592 CGTTTCTTACTCCGGAATCCACA 60.616 47.826 5.23 0.00 0.00 4.17
505 541 4.514401 GTTTCTTACTCCGGAATCCACAT 58.486 43.478 5.23 0.00 0.00 3.21
593 637 1.207791 CCCTGTCCCTGAGCTGTATT 58.792 55.000 0.00 0.00 0.00 1.89
627 682 2.609610 TACCCTCCCCACCTGTGC 60.610 66.667 0.00 0.00 0.00 4.57
711 766 2.122189 CCCCTGATCCCTCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
714 769 1.532794 CCTGATCCCTCCTCCCTCG 60.533 68.421 0.00 0.00 0.00 4.63
725 780 0.107165 CCTCCCTCGTTCCCCAATTC 60.107 60.000 0.00 0.00 0.00 2.17
813 873 1.135286 CCAGCAAATTCGCCTCTTTCC 60.135 52.381 0.00 0.00 0.00 3.13
815 875 2.229784 CAGCAAATTCGCCTCTTTCCTT 59.770 45.455 0.00 0.00 0.00 3.36
817 877 2.228822 GCAAATTCGCCTCTTTCCTTCA 59.771 45.455 0.00 0.00 0.00 3.02
869 929 2.164624 CGACAGGAGGAGAGATTTTCGT 59.835 50.000 0.00 0.00 0.00 3.85
882 942 3.690139 AGATTTTCGTAGCTGAGACTCGA 59.310 43.478 0.00 0.00 0.00 4.04
883 943 3.473093 TTTTCGTAGCTGAGACTCGAG 57.527 47.619 11.84 11.84 32.39 4.04
884 944 2.381725 TTCGTAGCTGAGACTCGAGA 57.618 50.000 21.68 0.00 32.39 4.04
885 945 1.929230 TCGTAGCTGAGACTCGAGAG 58.071 55.000 21.68 6.99 0.00 3.20
888 948 2.417239 CGTAGCTGAGACTCGAGAGTTT 59.583 50.000 21.68 1.30 42.66 2.66
930 1001 1.302192 GTTGCCGAGGGTAGTGCAA 60.302 57.895 0.00 0.00 41.08 4.08
963 1034 2.622942 TGCTCGGTTGATTCTTTGCTTT 59.377 40.909 0.00 0.00 0.00 3.51
964 1035 3.818210 TGCTCGGTTGATTCTTTGCTTTA 59.182 39.130 0.00 0.00 0.00 1.85
965 1036 4.159120 GCTCGGTTGATTCTTTGCTTTAC 58.841 43.478 0.00 0.00 0.00 2.01
966 1037 4.083271 GCTCGGTTGATTCTTTGCTTTACT 60.083 41.667 0.00 0.00 0.00 2.24
967 1038 5.562890 GCTCGGTTGATTCTTTGCTTTACTT 60.563 40.000 0.00 0.00 0.00 2.24
1056 1127 0.176680 CCATGAAGGAGACCACCTCG 59.823 60.000 0.00 0.00 42.89 4.63
1269 1360 2.362077 GGCATCCTTCGGTAATGCAAAT 59.638 45.455 8.61 0.00 45.95 2.32
1288 1389 6.847956 CAAATCAATTGCTTTGGTTTCTCA 57.152 33.333 21.60 0.00 43.61 3.27
1343 1450 0.962356 CTGAGGGTGAATGGTGGTGC 60.962 60.000 0.00 0.00 0.00 5.01
1344 1451 1.074775 GAGGGTGAATGGTGGTGCA 59.925 57.895 0.00 0.00 0.00 4.57
1449 1562 0.830648 CCAAGGCCTTCCTCGACATA 59.169 55.000 17.29 0.00 43.40 2.29
1480 1593 1.070786 GACCGTTCCAAGCTGGTGA 59.929 57.895 0.00 0.00 39.03 4.02
1631 1744 4.666512 ACTTAATCACCACTGGATTGCTT 58.333 39.130 0.71 0.00 36.45 3.91
1632 1745 4.460382 ACTTAATCACCACTGGATTGCTTG 59.540 41.667 0.71 0.00 36.45 4.01
1633 1746 1.180029 ATCACCACTGGATTGCTTGC 58.820 50.000 0.71 0.00 0.00 4.01
1634 1747 0.895100 TCACCACTGGATTGCTTGCC 60.895 55.000 0.71 0.00 0.00 4.52
1635 1748 0.896940 CACCACTGGATTGCTTGCCT 60.897 55.000 0.71 0.00 0.00 4.75
1636 1749 0.178953 ACCACTGGATTGCTTGCCTT 60.179 50.000 0.71 0.00 0.00 4.35
1638 1751 0.169672 CACTGGATTGCTTGCCTTCG 59.830 55.000 0.00 0.00 0.00 3.79
1639 1752 0.036732 ACTGGATTGCTTGCCTTCGA 59.963 50.000 0.00 0.00 0.00 3.71
1641 1754 0.677731 TGGATTGCTTGCCTTCGAGG 60.678 55.000 0.00 0.00 38.80 4.63
1642 1755 0.392998 GGATTGCTTGCCTTCGAGGA 60.393 55.000 0.00 0.00 37.67 3.71
1643 1756 0.729690 GATTGCTTGCCTTCGAGGAC 59.270 55.000 0.00 0.00 37.67 3.85
1645 1758 0.320771 TTGCTTGCCTTCGAGGACTC 60.321 55.000 0.00 0.00 37.67 3.36
1648 1761 0.108424 CTTGCCTTCGAGGACTCTGG 60.108 60.000 0.00 0.00 37.67 3.86
1649 1762 2.172483 TTGCCTTCGAGGACTCTGGC 62.172 60.000 15.78 15.78 37.67 4.85
1671 1784 1.798735 GTTCGTCTCGTCGATGGGA 59.201 57.895 2.15 2.15 39.57 4.37
1674 1787 0.661552 TCGTCTCGTCGATGGGATTC 59.338 55.000 11.09 0.00 34.85 2.52
1684 1797 0.034477 GATGGGATTCGGTGGGTGTT 60.034 55.000 0.00 0.00 0.00 3.32
1726 1845 4.457496 CAGGTGTCGGCGCTGGAT 62.457 66.667 17.88 0.00 0.00 3.41
1727 1846 2.758327 AGGTGTCGGCGCTGGATA 60.758 61.111 17.88 5.33 0.00 2.59
1875 1994 2.257371 GGTCAGCACGTACGCTCA 59.743 61.111 16.72 0.00 41.38 4.26
1918 2037 1.705256 TCCGTTGACGAGCACATTAC 58.295 50.000 4.91 0.00 43.02 1.89
1933 2059 0.034089 ATTACTTGCCCACAGGAGCC 60.034 55.000 0.00 0.00 33.47 4.70
1977 2103 3.067320 GGCTCTATGAATCTTTTGGTGGC 59.933 47.826 0.00 0.00 0.00 5.01
2343 2469 1.226831 CGGCCACCAACAACAACAC 60.227 57.895 2.24 0.00 0.00 3.32
2452 2581 1.806542 GCTTGATTCCTTTCTCGTGCA 59.193 47.619 0.00 0.00 0.00 4.57
2490 2619 0.323633 TCTCTGCTCTGCTCTGCTCT 60.324 55.000 0.00 0.00 0.00 4.09
2491 2620 0.179121 CTCTGCTCTGCTCTGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
2492 2621 1.812093 CTGCTCTGCTCTGCTCTGC 60.812 63.158 0.00 0.00 0.00 4.26
2493 2622 2.233605 CTGCTCTGCTCTGCTCTGCT 62.234 60.000 0.00 0.00 0.00 4.24
2494 2623 1.519898 GCTCTGCTCTGCTCTGCTC 60.520 63.158 0.00 0.00 0.00 4.26
2495 2624 1.952102 GCTCTGCTCTGCTCTGCTCT 61.952 60.000 0.00 0.00 0.00 4.09
2496 2625 0.179121 CTCTGCTCTGCTCTGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
2497 2626 1.812093 CTGCTCTGCTCTGCTCTGC 60.812 63.158 0.00 0.00 0.00 4.26
2498 2627 2.233605 CTGCTCTGCTCTGCTCTGCT 62.234 60.000 0.00 0.00 0.00 4.24
2499 2628 1.519898 GCTCTGCTCTGCTCTGCTC 60.520 63.158 0.00 0.00 0.00 4.26
2500 2629 1.952102 GCTCTGCTCTGCTCTGCTCT 61.952 60.000 0.00 0.00 0.00 4.09
2501 2630 0.179121 CTCTGCTCTGCTCTGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
2502 2631 1.153529 CTGCTCTGCTCTGCTCTGG 60.154 63.158 0.00 0.00 0.00 3.86
2503 2632 1.890625 CTGCTCTGCTCTGCTCTGGT 61.891 60.000 0.00 0.00 0.00 4.00
2537 2666 2.028112 TCTAGTGCCGATTGTTTGCTCT 60.028 45.455 0.00 0.00 33.80 4.09
2583 2716 3.658351 CGATGGATCGTTTCTTGTTCC 57.342 47.619 0.70 0.00 44.74 3.62
2584 2717 2.029244 CGATGGATCGTTTCTTGTTCCG 59.971 50.000 0.70 0.00 44.74 4.30
2606 2739 4.688879 CGCCCCCATTTTTCTTTCTTTTAC 59.311 41.667 0.00 0.00 0.00 2.01
2611 2744 8.783093 CCCCCATTTTTCTTTCTTTTACATTTC 58.217 33.333 0.00 0.00 0.00 2.17
2659 2796 6.543465 ACATCAAACAACAGAAGATGAACAGA 59.457 34.615 7.62 0.00 38.62 3.41
2724 2871 0.447801 CCGTGCAGAAAATAAGCGCT 59.552 50.000 2.64 2.64 36.68 5.92
2852 3025 1.482182 GCTTGGTTGATTCCCCCATTC 59.518 52.381 0.00 0.00 0.00 2.67
2853 3026 2.110578 CTTGGTTGATTCCCCCATTCC 58.889 52.381 0.00 0.00 0.00 3.01
2854 3027 0.338120 TGGTTGATTCCCCCATTCCC 59.662 55.000 0.00 0.00 0.00 3.97
2886 3059 0.460284 GTGATCGTACTGCTGGGTGG 60.460 60.000 0.00 0.00 0.00 4.61
2956 3133 2.255406 TGATTGATTGGTTGGGGTTGG 58.745 47.619 0.00 0.00 0.00 3.77
2957 3134 1.554617 GATTGATTGGTTGGGGTTGGG 59.445 52.381 0.00 0.00 0.00 4.12
2959 3136 1.612146 GATTGGTTGGGGTTGGGGG 60.612 63.158 0.00 0.00 0.00 5.40
3084 3265 2.328099 GCGAGTTGGTTCCAGGCAG 61.328 63.158 0.00 0.00 0.00 4.85
3191 3373 3.133691 TGGTAAGAAGCGCATGATGATC 58.866 45.455 11.47 0.00 0.00 2.92
3252 3434 0.322322 TAGTTTGGTCGGTCGGCAAT 59.678 50.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.093500 TGCATGCCTTCTGTAACGAGAT 60.093 45.455 16.68 0.00 0.00 2.75
1 2 1.275010 TGCATGCCTTCTGTAACGAGA 59.725 47.619 16.68 0.00 0.00 4.04
2 3 1.394917 GTGCATGCCTTCTGTAACGAG 59.605 52.381 16.68 0.00 0.00 4.18
3 4 1.438651 GTGCATGCCTTCTGTAACGA 58.561 50.000 16.68 0.00 0.00 3.85
4 5 0.095245 CGTGCATGCCTTCTGTAACG 59.905 55.000 16.68 11.84 0.00 3.18
5 6 0.447801 CCGTGCATGCCTTCTGTAAC 59.552 55.000 16.68 2.61 0.00 2.50
6 7 1.305219 GCCGTGCATGCCTTCTGTAA 61.305 55.000 16.68 0.00 0.00 2.41
7 8 1.745115 GCCGTGCATGCCTTCTGTA 60.745 57.895 16.68 0.00 0.00 2.74
8 9 3.058160 GCCGTGCATGCCTTCTGT 61.058 61.111 16.68 0.00 0.00 3.41
9 10 2.144833 TTTGCCGTGCATGCCTTCTG 62.145 55.000 16.68 3.63 38.76 3.02
10 11 1.462731 TTTTGCCGTGCATGCCTTCT 61.463 50.000 16.68 0.00 38.76 2.85
11 12 1.006337 TTTTGCCGTGCATGCCTTC 60.006 52.632 16.68 4.90 38.76 3.46
12 13 1.300853 GTTTTGCCGTGCATGCCTT 60.301 52.632 16.68 0.00 38.76 4.35
13 14 2.339712 GTTTTGCCGTGCATGCCT 59.660 55.556 16.68 0.00 38.76 4.75
14 15 2.738139 GGTTTTGCCGTGCATGCC 60.738 61.111 16.68 5.63 38.76 4.40
15 16 2.738139 GGGTTTTGCCGTGCATGC 60.738 61.111 11.82 11.82 38.76 4.06
16 17 1.373246 CAGGGTTTTGCCGTGCATG 60.373 57.895 0.00 0.00 44.82 4.06
17 18 3.050339 CAGGGTTTTGCCGTGCAT 58.950 55.556 0.00 0.00 44.82 3.96
24 25 1.685355 AAGGTGTGGCAGGGTTTTGC 61.685 55.000 0.00 0.00 43.34 3.68
25 26 1.339929 GTAAGGTGTGGCAGGGTTTTG 59.660 52.381 0.00 0.00 0.00 2.44
26 27 1.699730 GTAAGGTGTGGCAGGGTTTT 58.300 50.000 0.00 0.00 0.00 2.43
27 28 0.178973 GGTAAGGTGTGGCAGGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
28 29 1.458927 GGTAAGGTGTGGCAGGGTT 59.541 57.895 0.00 0.00 0.00 4.11
29 30 2.890766 CGGTAAGGTGTGGCAGGGT 61.891 63.158 0.00 0.00 0.00 4.34
30 31 2.046314 CGGTAAGGTGTGGCAGGG 60.046 66.667 0.00 0.00 0.00 4.45
31 32 2.746277 GCGGTAAGGTGTGGCAGG 60.746 66.667 0.00 0.00 0.00 4.85
32 33 2.746277 GGCGGTAAGGTGTGGCAG 60.746 66.667 0.00 0.00 0.00 4.85
33 34 3.545124 CTGGCGGTAAGGTGTGGCA 62.545 63.158 0.00 0.00 35.46 4.92
34 35 2.746277 CTGGCGGTAAGGTGTGGC 60.746 66.667 0.00 0.00 0.00 5.01
35 36 1.079127 CTCTGGCGGTAAGGTGTGG 60.079 63.158 0.00 0.00 0.00 4.17
36 37 1.741770 GCTCTGGCGGTAAGGTGTG 60.742 63.158 0.00 0.00 0.00 3.82
37 38 2.663196 GCTCTGGCGGTAAGGTGT 59.337 61.111 0.00 0.00 0.00 4.16
38 39 2.125106 GGCTCTGGCGGTAAGGTG 60.125 66.667 0.00 0.00 39.81 4.00
47 48 3.248446 TACCACCAACGGCTCTGGC 62.248 63.158 1.92 0.00 37.48 4.85
48 49 1.079127 CTACCACCAACGGCTCTGG 60.079 63.158 0.54 0.54 40.05 3.86
49 50 1.079127 CCTACCACCAACGGCTCTG 60.079 63.158 0.00 0.00 0.00 3.35
50 51 2.291043 CCCTACCACCAACGGCTCT 61.291 63.158 0.00 0.00 0.00 4.09
51 52 2.120737 AACCCTACCACCAACGGCTC 62.121 60.000 0.00 0.00 0.00 4.70
52 53 0.837260 TAACCCTACCACCAACGGCT 60.837 55.000 0.00 0.00 0.00 5.52
53 54 0.392060 CTAACCCTACCACCAACGGC 60.392 60.000 0.00 0.00 0.00 5.68
54 55 1.066645 GTCTAACCCTACCACCAACGG 60.067 57.143 0.00 0.00 0.00 4.44
55 56 1.619827 TGTCTAACCCTACCACCAACG 59.380 52.381 0.00 0.00 0.00 4.10
56 57 2.614734 GCTGTCTAACCCTACCACCAAC 60.615 54.545 0.00 0.00 0.00 3.77
57 58 1.626825 GCTGTCTAACCCTACCACCAA 59.373 52.381 0.00 0.00 0.00 3.67
58 59 1.203262 AGCTGTCTAACCCTACCACCA 60.203 52.381 0.00 0.00 0.00 4.17
59 60 1.569653 AGCTGTCTAACCCTACCACC 58.430 55.000 0.00 0.00 0.00 4.61
60 61 3.118847 GGTAAGCTGTCTAACCCTACCAC 60.119 52.174 0.00 0.00 0.00 4.16
61 62 3.102204 GGTAAGCTGTCTAACCCTACCA 58.898 50.000 0.00 0.00 0.00 3.25
62 63 2.100418 CGGTAAGCTGTCTAACCCTACC 59.900 54.545 0.00 0.00 0.00 3.18
63 64 2.480932 GCGGTAAGCTGTCTAACCCTAC 60.481 54.545 0.00 0.00 44.04 3.18
64 65 1.753073 GCGGTAAGCTGTCTAACCCTA 59.247 52.381 0.00 0.00 44.04 3.53
65 66 0.535797 GCGGTAAGCTGTCTAACCCT 59.464 55.000 0.00 0.00 44.04 4.34
66 67 3.061093 GCGGTAAGCTGTCTAACCC 57.939 57.895 0.00 0.00 44.04 4.11
68 69 4.304419 ACCAGGCGGTAAGCTGTCTAAC 62.304 54.545 0.00 0.00 46.71 2.34
69 70 2.169540 ACCAGGCGGTAAGCTGTCTAA 61.170 52.381 0.00 0.00 46.71 2.10
70 71 0.613853 ACCAGGCGGTAAGCTGTCTA 60.614 55.000 0.00 0.00 46.71 2.59
71 72 1.913762 ACCAGGCGGTAAGCTGTCT 60.914 57.895 0.00 0.00 46.71 3.41
72 73 2.663196 ACCAGGCGGTAAGCTGTC 59.337 61.111 0.00 0.00 46.71 3.51
83 84 2.741486 TTACCGCCAGACAACCAGGC 62.741 60.000 0.00 0.00 44.89 4.85
84 85 0.673644 CTTACCGCCAGACAACCAGG 60.674 60.000 0.00 0.00 0.00 4.45
85 86 0.673644 CCTTACCGCCAGACAACCAG 60.674 60.000 0.00 0.00 0.00 4.00
86 87 1.373435 CCTTACCGCCAGACAACCA 59.627 57.895 0.00 0.00 0.00 3.67
87 88 0.609662 TACCTTACCGCCAGACAACC 59.390 55.000 0.00 0.00 0.00 3.77
88 89 1.274447 AGTACCTTACCGCCAGACAAC 59.726 52.381 0.00 0.00 0.00 3.32
89 90 1.636148 AGTACCTTACCGCCAGACAA 58.364 50.000 0.00 0.00 0.00 3.18
90 91 1.636148 AAGTACCTTACCGCCAGACA 58.364 50.000 0.00 0.00 0.00 3.41
91 92 3.243670 GGATAAGTACCTTACCGCCAGAC 60.244 52.174 0.00 0.00 0.00 3.51
92 93 2.961062 GGATAAGTACCTTACCGCCAGA 59.039 50.000 0.00 0.00 0.00 3.86
93 94 2.696707 TGGATAAGTACCTTACCGCCAG 59.303 50.000 0.00 0.00 0.00 4.85
94 95 2.431782 GTGGATAAGTACCTTACCGCCA 59.568 50.000 0.00 0.00 29.80 5.69
95 96 2.544486 CGTGGATAAGTACCTTACCGCC 60.544 54.545 0.00 0.00 31.00 6.13
96 97 2.099756 ACGTGGATAAGTACCTTACCGC 59.900 50.000 0.00 0.00 31.20 5.68
97 98 3.378112 TGACGTGGATAAGTACCTTACCG 59.622 47.826 0.00 0.00 0.00 4.02
98 99 4.735873 GCTGACGTGGATAAGTACCTTACC 60.736 50.000 0.00 0.00 0.00 2.85
99 100 4.357996 GCTGACGTGGATAAGTACCTTAC 58.642 47.826 0.00 0.00 0.00 2.34
100 101 3.065786 CGCTGACGTGGATAAGTACCTTA 59.934 47.826 0.00 0.00 33.53 2.69
101 102 2.159282 CGCTGACGTGGATAAGTACCTT 60.159 50.000 0.00 0.00 33.53 3.50
102 103 1.404391 CGCTGACGTGGATAAGTACCT 59.596 52.381 0.00 0.00 33.53 3.08
103 104 1.836383 CGCTGACGTGGATAAGTACC 58.164 55.000 0.00 0.00 33.53 3.34
104 105 1.197910 GCGCTGACGTGGATAAGTAC 58.802 55.000 0.00 0.00 42.83 2.73
105 106 0.248336 CGCGCTGACGTGGATAAGTA 60.248 55.000 5.56 0.00 45.93 2.24
106 107 1.516386 CGCGCTGACGTGGATAAGT 60.516 57.895 5.56 0.00 45.93 2.24
107 108 3.299585 CGCGCTGACGTGGATAAG 58.700 61.111 5.56 0.00 45.93 1.73
133 134 4.755507 ACGGAGGGAGACGGGGAC 62.756 72.222 0.00 0.00 0.00 4.46
134 135 4.437587 GACGGAGGGAGACGGGGA 62.438 72.222 0.00 0.00 0.00 4.81
135 136 4.753662 TGACGGAGGGAGACGGGG 62.754 72.222 0.00 0.00 0.00 5.73
136 137 3.450115 GTGACGGAGGGAGACGGG 61.450 72.222 0.00 0.00 0.00 5.28
137 138 2.675423 TGTGACGGAGGGAGACGG 60.675 66.667 0.00 0.00 0.00 4.79
138 139 2.567049 GTGTGACGGAGGGAGACG 59.433 66.667 0.00 0.00 0.00 4.18
139 140 2.647158 GGGTGTGACGGAGGGAGAC 61.647 68.421 0.00 0.00 0.00 3.36
140 141 1.503401 TAGGGTGTGACGGAGGGAGA 61.503 60.000 0.00 0.00 0.00 3.71
141 142 1.000019 TAGGGTGTGACGGAGGGAG 60.000 63.158 0.00 0.00 0.00 4.30
142 143 1.304713 GTAGGGTGTGACGGAGGGA 60.305 63.158 0.00 0.00 0.00 4.20
143 144 2.356780 GGTAGGGTGTGACGGAGGG 61.357 68.421 0.00 0.00 0.00 4.30
144 145 2.707849 CGGTAGGGTGTGACGGAGG 61.708 68.421 0.00 0.00 0.00 4.30
145 146 2.882876 CGGTAGGGTGTGACGGAG 59.117 66.667 0.00 0.00 0.00 4.63
146 147 3.376078 GCGGTAGGGTGTGACGGA 61.376 66.667 0.00 0.00 0.00 4.69
147 148 4.446413 GGCGGTAGGGTGTGACGG 62.446 72.222 0.00 0.00 0.00 4.79
148 149 3.642778 CTGGCGGTAGGGTGTGACG 62.643 68.421 0.00 0.00 0.00 4.35
149 150 2.264794 CTGGCGGTAGGGTGTGAC 59.735 66.667 0.00 0.00 0.00 3.67
150 151 3.000819 CCTGGCGGTAGGGTGTGA 61.001 66.667 0.00 0.00 34.06 3.58
156 157 1.447643 CAGATTCCCTGGCGGTAGG 59.552 63.158 0.00 0.00 39.23 3.18
164 165 1.227674 GCTACCGCCAGATTCCCTG 60.228 63.158 0.00 0.00 42.55 4.45
165 166 0.983378 AAGCTACCGCCAGATTCCCT 60.983 55.000 0.00 0.00 36.60 4.20
166 167 0.815615 CAAGCTACCGCCAGATTCCC 60.816 60.000 0.00 0.00 36.60 3.97
167 168 0.107654 ACAAGCTACCGCCAGATTCC 60.108 55.000 0.00 0.00 36.60 3.01
168 169 1.134670 AGACAAGCTACCGCCAGATTC 60.135 52.381 0.00 0.00 36.60 2.52
169 170 0.905357 AGACAAGCTACCGCCAGATT 59.095 50.000 0.00 0.00 36.60 2.40
170 171 1.776662 TAGACAAGCTACCGCCAGAT 58.223 50.000 0.00 0.00 36.60 2.90
171 172 1.203994 GTTAGACAAGCTACCGCCAGA 59.796 52.381 0.00 0.00 36.60 3.86
172 173 1.641577 GTTAGACAAGCTACCGCCAG 58.358 55.000 0.00 0.00 36.60 4.85
173 174 0.248289 GGTTAGACAAGCTACCGCCA 59.752 55.000 0.00 0.00 36.60 5.69
174 175 0.461516 GGGTTAGACAAGCTACCGCC 60.462 60.000 0.00 0.00 36.60 6.13
175 176 0.535797 AGGGTTAGACAAGCTACCGC 59.464 55.000 0.00 0.00 32.59 5.68
176 177 2.100418 GGTAGGGTTAGACAAGCTACCG 59.900 54.545 0.00 0.00 31.97 4.02
177 178 2.100418 CGGTAGGGTTAGACAAGCTACC 59.900 54.545 0.00 0.00 35.20 3.18
178 179 2.480932 GCGGTAGGGTTAGACAAGCTAC 60.481 54.545 0.00 0.00 32.59 3.58
179 180 1.753073 GCGGTAGGGTTAGACAAGCTA 59.247 52.381 0.00 0.00 32.59 3.32
180 181 0.535797 GCGGTAGGGTTAGACAAGCT 59.464 55.000 0.00 0.00 32.59 3.74
181 182 0.461516 GGCGGTAGGGTTAGACAAGC 60.462 60.000 0.00 0.00 0.00 4.01
182 183 0.899720 TGGCGGTAGGGTTAGACAAG 59.100 55.000 0.00 0.00 0.00 3.16
183 184 0.899720 CTGGCGGTAGGGTTAGACAA 59.100 55.000 0.00 0.00 0.00 3.18
184 185 0.974010 CCTGGCGGTAGGGTTAGACA 60.974 60.000 0.00 0.00 34.06 3.41
185 186 1.821258 CCTGGCGGTAGGGTTAGAC 59.179 63.158 0.00 0.00 34.06 2.59
186 187 4.368003 CCTGGCGGTAGGGTTAGA 57.632 61.111 0.00 0.00 34.06 2.10
192 193 2.042843 AGAGTCCCTGGCGGTAGG 60.043 66.667 0.00 0.00 37.59 3.18
193 194 3.211288 CAGAGTCCCTGGCGGTAG 58.789 66.667 0.00 0.00 39.23 3.18
200 201 3.082579 GCTACCGCCAGAGTCCCTG 62.083 68.421 0.00 0.00 42.55 4.45
201 202 2.760385 GCTACCGCCAGAGTCCCT 60.760 66.667 0.00 0.00 0.00 4.20
202 203 2.180159 TTTGCTACCGCCAGAGTCCC 62.180 60.000 0.00 0.00 34.43 4.46
203 204 0.321298 TTTTGCTACCGCCAGAGTCC 60.321 55.000 0.00 0.00 34.43 3.85
204 205 1.079503 CTTTTGCTACCGCCAGAGTC 58.920 55.000 0.00 0.00 34.43 3.36
205 206 0.321653 CCTTTTGCTACCGCCAGAGT 60.322 55.000 0.00 0.00 34.43 3.24
206 207 1.026718 CCCTTTTGCTACCGCCAGAG 61.027 60.000 0.00 0.00 34.43 3.35
207 208 1.002624 CCCTTTTGCTACCGCCAGA 60.003 57.895 0.00 0.00 34.43 3.86
208 209 1.303317 ACCCTTTTGCTACCGCCAG 60.303 57.895 0.00 0.00 34.43 4.85
209 210 1.302993 GACCCTTTTGCTACCGCCA 60.303 57.895 0.00 0.00 34.43 5.69
210 211 0.891904 TTGACCCTTTTGCTACCGCC 60.892 55.000 0.00 0.00 34.43 6.13
211 212 0.955905 TTTGACCCTTTTGCTACCGC 59.044 50.000 0.00 0.00 0.00 5.68
212 213 2.163613 GGATTTGACCCTTTTGCTACCG 59.836 50.000 0.00 0.00 0.00 4.02
213 214 3.193479 CAGGATTTGACCCTTTTGCTACC 59.807 47.826 0.00 0.00 0.00 3.18
214 215 4.079253 TCAGGATTTGACCCTTTTGCTAC 58.921 43.478 0.00 0.00 0.00 3.58
215 216 4.380843 TCAGGATTTGACCCTTTTGCTA 57.619 40.909 0.00 0.00 0.00 3.49
216 217 3.243359 TCAGGATTTGACCCTTTTGCT 57.757 42.857 0.00 0.00 0.00 3.91
217 218 4.541973 ATTCAGGATTTGACCCTTTTGC 57.458 40.909 0.00 0.00 34.94 3.68
218 219 7.806409 AAAAATTCAGGATTTGACCCTTTTG 57.194 32.000 0.00 0.00 37.98 2.44
242 243 7.737972 TCAAGATCTGATCCACGTTTAAAAA 57.262 32.000 13.83 0.00 0.00 1.94
243 244 7.921786 ATCAAGATCTGATCCACGTTTAAAA 57.078 32.000 13.83 0.00 41.13 1.52
244 245 7.921786 AATCAAGATCTGATCCACGTTTAAA 57.078 32.000 13.83 0.00 44.43 1.52
245 246 7.921786 AAATCAAGATCTGATCCACGTTTAA 57.078 32.000 13.83 0.00 44.43 1.52
246 247 7.390440 ACAAAATCAAGATCTGATCCACGTTTA 59.610 33.333 13.83 0.00 44.43 2.01
247 248 6.207417 ACAAAATCAAGATCTGATCCACGTTT 59.793 34.615 13.83 8.08 44.43 3.60
248 249 5.707298 ACAAAATCAAGATCTGATCCACGTT 59.293 36.000 13.83 0.00 44.43 3.99
249 250 5.248640 ACAAAATCAAGATCTGATCCACGT 58.751 37.500 13.83 0.00 44.43 4.49
250 251 5.808042 ACAAAATCAAGATCTGATCCACG 57.192 39.130 13.83 3.48 44.43 4.94
251 252 9.912634 TTTAAACAAAATCAAGATCTGATCCAC 57.087 29.630 13.83 0.00 44.43 4.02
276 277 6.166982 TGAATTTCGTGTTTTGACCCTTTTT 58.833 32.000 0.00 0.00 0.00 1.94
277 278 5.725362 TGAATTTCGTGTTTTGACCCTTTT 58.275 33.333 0.00 0.00 0.00 2.27
278 279 5.331876 TGAATTTCGTGTTTTGACCCTTT 57.668 34.783 0.00 0.00 0.00 3.11
279 280 4.736464 GCTGAATTTCGTGTTTTGACCCTT 60.736 41.667 0.00 0.00 0.00 3.95
280 281 3.243401 GCTGAATTTCGTGTTTTGACCCT 60.243 43.478 0.00 0.00 0.00 4.34
281 282 3.049912 GCTGAATTTCGTGTTTTGACCC 58.950 45.455 0.00 0.00 0.00 4.46
282 283 3.049912 GGCTGAATTTCGTGTTTTGACC 58.950 45.455 0.00 0.00 0.00 4.02
283 284 3.964909 AGGCTGAATTTCGTGTTTTGAC 58.035 40.909 0.00 0.00 0.00 3.18
284 285 3.004315 GGAGGCTGAATTTCGTGTTTTGA 59.996 43.478 0.00 0.00 0.00 2.69
285 286 3.243367 TGGAGGCTGAATTTCGTGTTTTG 60.243 43.478 0.00 0.00 0.00 2.44
286 287 2.955660 TGGAGGCTGAATTTCGTGTTTT 59.044 40.909 0.00 0.00 0.00 2.43
287 288 2.293399 GTGGAGGCTGAATTTCGTGTTT 59.707 45.455 0.00 0.00 0.00 2.83
288 289 1.880027 GTGGAGGCTGAATTTCGTGTT 59.120 47.619 0.00 0.00 0.00 3.32
289 290 1.523758 GTGGAGGCTGAATTTCGTGT 58.476 50.000 0.00 0.00 0.00 4.49
290 291 0.443869 CGTGGAGGCTGAATTTCGTG 59.556 55.000 0.00 0.00 0.00 4.35
291 292 1.298859 GCGTGGAGGCTGAATTTCGT 61.299 55.000 0.00 0.00 0.00 3.85
292 293 1.425428 GCGTGGAGGCTGAATTTCG 59.575 57.895 0.00 0.00 0.00 3.46
293 294 1.019278 TCGCGTGGAGGCTGAATTTC 61.019 55.000 5.77 0.00 0.00 2.17
294 295 0.605319 TTCGCGTGGAGGCTGAATTT 60.605 50.000 5.77 0.00 0.00 1.82
295 296 1.003839 TTCGCGTGGAGGCTGAATT 60.004 52.632 5.77 0.00 0.00 2.17
296 297 1.741770 GTTCGCGTGGAGGCTGAAT 60.742 57.895 5.77 0.00 31.74 2.57
297 298 2.357034 GTTCGCGTGGAGGCTGAA 60.357 61.111 5.77 0.00 0.00 3.02
298 299 4.717629 CGTTCGCGTGGAGGCTGA 62.718 66.667 5.77 0.00 35.57 4.26
322 323 1.452145 GAAAAGTGGCCAGCGGACAA 61.452 55.000 5.11 0.00 45.35 3.18
348 351 2.097036 CATTCTGCATGCTCTTTCCCA 58.903 47.619 20.33 0.00 0.00 4.37
356 359 2.831742 CCCGCCATTCTGCATGCT 60.832 61.111 20.33 0.00 0.00 3.79
403 406 4.681978 GCGAGGCCGGCGGAATAT 62.682 66.667 33.44 11.62 36.06 1.28
495 531 2.093288 TGAGTGAGAGCATGTGGATTCC 60.093 50.000 0.00 0.00 0.00 3.01
504 540 0.323816 TCGGGAGTGAGTGAGAGCAT 60.324 55.000 0.00 0.00 0.00 3.79
505 541 0.962855 CTCGGGAGTGAGTGAGAGCA 60.963 60.000 0.00 0.00 0.00 4.26
593 637 2.244252 GGGTACAAGGAGGAGGAGACTA 59.756 54.545 0.00 0.00 44.43 2.59
627 682 2.152016 GAGAGGTGGGGAAAGAAAACG 58.848 52.381 0.00 0.00 0.00 3.60
711 766 1.067142 TCGACTGAATTGGGGAACGAG 60.067 52.381 0.00 0.00 0.00 4.18
714 769 1.076332 CGTCGACTGAATTGGGGAAC 58.924 55.000 14.70 0.00 0.00 3.62
725 780 4.135153 CTCCCCTGGCGTCGACTG 62.135 72.222 14.70 8.46 0.00 3.51
869 929 3.011119 GGAAACTCTCGAGTCTCAGCTA 58.989 50.000 13.13 0.00 41.58 3.32
882 942 2.154462 CAATCCAAGCACGGAAACTCT 58.846 47.619 0.00 0.00 38.95 3.24
883 943 1.880027 ACAATCCAAGCACGGAAACTC 59.120 47.619 0.00 0.00 38.95 3.01
884 944 1.981256 ACAATCCAAGCACGGAAACT 58.019 45.000 0.00 0.00 38.95 2.66
885 945 2.293399 AGAACAATCCAAGCACGGAAAC 59.707 45.455 0.00 0.00 38.95 2.78
888 948 1.879380 CAAGAACAATCCAAGCACGGA 59.121 47.619 0.00 0.00 40.07 4.69
930 1001 2.581354 CGAGCAACCCTAGCAGCT 59.419 61.111 0.00 0.00 40.60 4.24
1269 1360 5.596836 AACTGAGAAACCAAAGCAATTGA 57.403 34.783 10.34 0.00 41.85 2.57
1288 1389 5.047847 TCGAGTCGAGTCAAATCAAAAACT 58.952 37.500 19.87 0.00 0.00 2.66
1343 1450 3.606595 TCATCTTCTTCAGCTCACCTG 57.393 47.619 0.00 0.00 43.17 4.00
1344 1451 3.518705 ACATCATCTTCTTCAGCTCACCT 59.481 43.478 0.00 0.00 0.00 4.00
1449 1562 4.143333 CGGTCCTTGACGCCGGAT 62.143 66.667 5.05 0.00 41.60 4.18
1467 1580 0.674581 CGAGCATCACCAGCTTGGAA 60.675 55.000 8.91 0.00 43.58 3.53
1480 1593 3.148279 GTCGGGGTCCTCGAGCAT 61.148 66.667 15.96 0.00 37.31 3.79
1631 1744 2.650116 GCCAGAGTCCTCGAAGGCA 61.650 63.158 17.63 0.00 42.34 4.75
1632 1745 2.185608 GCCAGAGTCCTCGAAGGC 59.814 66.667 10.96 10.96 38.77 4.35
1633 1746 1.515020 CAGCCAGAGTCCTCGAAGG 59.485 63.158 0.00 0.00 36.46 3.46
1634 1747 1.153667 GCAGCCAGAGTCCTCGAAG 60.154 63.158 0.00 0.00 34.09 3.79
1635 1748 2.973899 GCAGCCAGAGTCCTCGAA 59.026 61.111 0.00 0.00 34.09 3.71
1636 1749 3.443925 CGCAGCCAGAGTCCTCGA 61.444 66.667 0.00 0.00 34.09 4.04
1638 1751 1.446966 GAACGCAGCCAGAGTCCTC 60.447 63.158 0.00 0.00 0.00 3.71
1639 1752 2.659610 GAACGCAGCCAGAGTCCT 59.340 61.111 0.00 0.00 0.00 3.85
1641 1754 2.049063 ACGAACGCAGCCAGAGTC 60.049 61.111 0.00 0.00 0.00 3.36
1642 1755 2.049063 GACGAACGCAGCCAGAGT 60.049 61.111 0.00 0.00 0.00 3.24
1643 1756 1.803519 GAGACGAACGCAGCCAGAG 60.804 63.158 0.00 0.00 0.00 3.35
1645 1758 3.175240 CGAGACGAACGCAGCCAG 61.175 66.667 0.00 0.00 0.00 4.85
1648 1761 3.524759 CGACGAGACGAACGCAGC 61.525 66.667 0.00 0.00 35.09 5.25
1649 1762 1.226046 ATCGACGAGACGAACGCAG 60.226 57.895 3.01 0.00 45.16 5.18
1671 1784 1.002659 TCGATCAAACACCCACCGAAT 59.997 47.619 0.00 0.00 0.00 3.34
1674 1787 1.448985 ATTCGATCAAACACCCACCG 58.551 50.000 0.00 0.00 0.00 4.94
1684 1797 1.543802 GCACCACCCAAATTCGATCAA 59.456 47.619 0.00 0.00 0.00 2.57
1726 1845 2.125310 CCCTTGCGCACGATGGTA 60.125 61.111 16.43 0.00 0.00 3.25
1875 1994 0.746923 GCGGGGAACTTAATTCGGCT 60.747 55.000 0.00 0.00 38.31 5.52
1918 2037 3.965539 CTCGGCTCCTGTGGGCAAG 62.966 68.421 0.00 0.00 0.00 4.01
1933 2059 1.016130 AGCGGATTCAGTTGTGCTCG 61.016 55.000 0.00 0.00 0.00 5.03
2331 2457 0.380378 CGAGGTGGTGTTGTTGTTGG 59.620 55.000 0.00 0.00 0.00 3.77
2452 2581 3.246301 AGAGGTCGATTGATGGATGGAT 58.754 45.455 0.00 0.00 0.00 3.41
2490 2619 1.670949 GGATCGACCAGAGCAGAGCA 61.671 60.000 0.00 0.00 36.90 4.26
2491 2620 1.067250 GGATCGACCAGAGCAGAGC 59.933 63.158 0.00 0.00 36.90 4.09
2492 2621 1.098129 TCGGATCGACCAGAGCAGAG 61.098 60.000 0.00 0.00 34.71 3.35
2493 2622 1.077716 TCGGATCGACCAGAGCAGA 60.078 57.895 0.00 0.00 37.14 4.26
2494 2623 3.514417 TCGGATCGACCAGAGCAG 58.486 61.111 0.00 0.00 36.90 4.24
2503 2632 1.337071 GCACTAGATTGGTCGGATCGA 59.663 52.381 0.00 0.00 0.00 3.59
2537 2666 8.446599 AGAAAAAGGAAAGAATAAACAGACGA 57.553 30.769 0.00 0.00 0.00 4.20
2576 2709 0.684535 AAAAATGGGGGCGGAACAAG 59.315 50.000 0.00 0.00 0.00 3.16
2577 2710 0.682292 GAAAAATGGGGGCGGAACAA 59.318 50.000 0.00 0.00 0.00 2.83
2578 2711 0.178947 AGAAAAATGGGGGCGGAACA 60.179 50.000 0.00 0.00 0.00 3.18
2579 2712 0.973632 AAGAAAAATGGGGGCGGAAC 59.026 50.000 0.00 0.00 0.00 3.62
2580 2713 1.621317 GAAAGAAAAATGGGGGCGGAA 59.379 47.619 0.00 0.00 0.00 4.30
2581 2714 1.203125 AGAAAGAAAAATGGGGGCGGA 60.203 47.619 0.00 0.00 0.00 5.54
2582 2715 1.266178 AGAAAGAAAAATGGGGGCGG 58.734 50.000 0.00 0.00 0.00 6.13
2583 2716 3.401033 AAAGAAAGAAAAATGGGGGCG 57.599 42.857 0.00 0.00 0.00 6.13
2584 2717 5.616270 TGTAAAAGAAAGAAAAATGGGGGC 58.384 37.500 0.00 0.00 0.00 5.80
2606 2739 8.703336 CATACATACATACACTCGGAAGAAATG 58.297 37.037 0.00 0.00 41.32 2.32
2611 2744 7.645402 TGTACATACATACATACACTCGGAAG 58.355 38.462 0.00 0.00 29.97 3.46
2659 2796 3.953775 CACTTCACCGGCCAGGGT 61.954 66.667 16.44 7.51 46.96 4.34
2724 2871 3.497763 CCTTCACATTAAGACCACCACCA 60.498 47.826 0.00 0.00 0.00 4.17
2852 3025 2.556840 ATCACCACTTGCGATGGGGG 62.557 60.000 3.35 0.00 41.39 5.40
2853 3026 1.077501 ATCACCACTTGCGATGGGG 60.078 57.895 5.76 1.41 42.55 4.96
2854 3027 1.431488 CGATCACCACTTGCGATGGG 61.431 60.000 5.76 0.00 41.97 4.00
2886 3059 2.009774 CAAATCTCACACCCCGATGAC 58.990 52.381 0.00 0.00 0.00 3.06
2963 3140 3.279116 GACACAAGCACAGCGGCA 61.279 61.111 1.45 0.00 35.83 5.69
2966 3143 2.246397 CACGACACAAGCACAGCG 59.754 61.111 0.00 0.00 0.00 5.18
3057 3238 2.113243 AACCAACTCGCTCCTGTCCC 62.113 60.000 0.00 0.00 0.00 4.46
3058 3239 0.670854 GAACCAACTCGCTCCTGTCC 60.671 60.000 0.00 0.00 0.00 4.02
3059 3240 0.670854 GGAACCAACTCGCTCCTGTC 60.671 60.000 0.00 0.00 0.00 3.51
3084 3265 1.379044 CTGTCAATGGACCCAGCCC 60.379 63.158 0.00 0.00 43.65 5.19
3142 3323 2.171840 CACACCCACAGAGTACTAGCT 58.828 52.381 0.00 0.00 0.00 3.32
3147 3328 0.037232 GAGCCACACCCACAGAGTAC 60.037 60.000 0.00 0.00 0.00 2.73
3191 3373 2.025441 CCACACCCAAACGCAACG 59.975 61.111 0.00 0.00 0.00 4.10
3252 3434 0.398696 ACACCCAAGAACATGGCGTA 59.601 50.000 0.00 0.00 39.26 4.42
3264 3446 2.938838 CCAGTTCAGGTTAACACCCAA 58.061 47.619 8.10 0.00 45.63 4.12


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

AutoCloner maintained by Alex Coulton.