Multiple sequence alignment - TraesCS7A01G416500

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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 TraesCS7A01G416500 chr7A 100.000 2447 0 0 1 2447 608453830 608451384 0.000000e+00 4519
1 TraesCS7A01G416500 chr7A 96.589 2140 67 4 312 2447 40104464 40106601 0.000000e+00 3542
2 TraesCS7A01G416500 chr7A 96.584 2137 69 2 315 2447 19952946 19950810 0.000000e+00 3539
3 TraesCS7A01G416500 chr7A 92.357 314 24 0 1 314 692487036 692487349 4.800000e-122 448
4 TraesCS7A01G416500 chr1A 97.008 2139 59 3 312 2446 3709540 3711677 0.000000e+00 3591
5 TraesCS7A01G416500 chr1A 92.163 319 20 2 1 314 215946579 215946261 1.730000e-121 446
6 TraesCS7A01G416500 chr5A 96.914 2139 60 4 313 2447 462143563 462141427 0.000000e+00 3579
7 TraesCS7A01G416500 chr5A 90.127 314 31 0 1 314 368106800 368107113 2.260000e-110 409
8 TraesCS7A01G416500 chr3A 96.912 2137 61 3 315 2447 30372453 30374588 0.000000e+00 3576
9 TraesCS7A01G416500 chr4A 96.771 2137 64 3 315 2447 15333330 15331195 0.000000e+00 3559
10 TraesCS7A01G416500 chr4A 96.584 2137 69 2 315 2447 608107464 608105328 0.000000e+00 3539
11 TraesCS7A01G416500 chr6A 96.679 2138 66 3 314 2447 596636900 596639036 0.000000e+00 3550
12 TraesCS7A01G416500 chr6A 96.678 2137 65 4 315 2447 546523255 546521121 0.000000e+00 3548
13 TraesCS7A01G416500 chr2A 92.357 314 24 0 1 314 678725757 678725444 4.800000e-122 448
14 TraesCS7A01G416500 chr4D 91.536 319 22 2 1 314 93366675 93366357 3.740000e-118 435
15 TraesCS7A01G416500 chr2B 91.083 314 28 0 1 314 460481255 460480942 2.250000e-115 425
16 TraesCS7A01G416500 chr4B 90.764 314 29 0 1 314 516966572 516966259 1.050000e-113 420
17 TraesCS7A01G416500 chr1D 90.625 320 24 3 1 315 281217072 281216754 1.050000e-113 420
18 TraesCS7A01G416500 chr6D 96.454 141 4 1 1 140 15380246 15380106 5.260000e-57 231


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 TraesCS7A01G416500 chr7A 608451384 608453830 2446 True 4519 4519 100.000 1 2447 1 chr7A.!!$R2 2446
1 TraesCS7A01G416500 chr7A 40104464 40106601 2137 False 3542 3542 96.589 312 2447 1 chr7A.!!$F1 2135
2 TraesCS7A01G416500 chr7A 19950810 19952946 2136 True 3539 3539 96.584 315 2447 1 chr7A.!!$R1 2132
3 TraesCS7A01G416500 chr1A 3709540 3711677 2137 False 3591 3591 97.008 312 2446 1 chr1A.!!$F1 2134
4 TraesCS7A01G416500 chr5A 462141427 462143563 2136 True 3579 3579 96.914 313 2447 1 chr5A.!!$R1 2134
5 TraesCS7A01G416500 chr3A 30372453 30374588 2135 False 3576 3576 96.912 315 2447 1 chr3A.!!$F1 2132
6 TraesCS7A01G416500 chr4A 15331195 15333330 2135 True 3559 3559 96.771 315 2447 1 chr4A.!!$R1 2132
7 TraesCS7A01G416500 chr4A 608105328 608107464 2136 True 3539 3539 96.584 315 2447 1 chr4A.!!$R2 2132
8 TraesCS7A01G416500 chr6A 596636900 596639036 2136 False 3550 3550 96.679 314 2447 1 chr6A.!!$F1 2133
9 TraesCS7A01G416500 chr6A 546521121 546523255 2134 True 3548 3548 96.678 315 2447 1 chr6A.!!$R1 2132

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
115 116 0.108756 GTTGTGGGAGACTCGGCTAC 60.109 60.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1746 0.178903 AGCAGGTGGGAGTGTAGGAA 60.179 55.0 0.0 0.0 0.0 3.36 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
28 29 6.174451 CAATGGTGCATCGATCCTATTTAG 57.826 41.667 0.00 0.00 0.00 1.85
29 30 4.955811 TGGTGCATCGATCCTATTTAGT 57.044 40.909 0.00 0.00 0.00 2.24
30 31 5.290493 TGGTGCATCGATCCTATTTAGTT 57.710 39.130 0.00 0.00 0.00 2.24
31 32 5.297547 TGGTGCATCGATCCTATTTAGTTC 58.702 41.667 0.00 0.00 0.00 3.01
32 33 5.070446 TGGTGCATCGATCCTATTTAGTTCT 59.930 40.000 0.00 0.00 0.00 3.01
33 34 5.406780 GGTGCATCGATCCTATTTAGTTCTG 59.593 44.000 0.00 0.00 0.00 3.02
34 35 5.406780 GTGCATCGATCCTATTTAGTTCTGG 59.593 44.000 0.00 0.00 0.00 3.86
35 36 5.070446 TGCATCGATCCTATTTAGTTCTGGT 59.930 40.000 0.00 0.00 0.00 4.00
36 37 5.992217 GCATCGATCCTATTTAGTTCTGGTT 59.008 40.000 0.00 0.00 0.00 3.67
37 38 6.146347 GCATCGATCCTATTTAGTTCTGGTTC 59.854 42.308 0.00 0.00 0.00 3.62
38 39 7.437748 CATCGATCCTATTTAGTTCTGGTTCT 58.562 38.462 0.00 0.00 0.00 3.01
39 40 6.806751 TCGATCCTATTTAGTTCTGGTTCTG 58.193 40.000 0.00 0.00 0.00 3.02
40 41 6.380274 TCGATCCTATTTAGTTCTGGTTCTGT 59.620 38.462 0.00 0.00 0.00 3.41
41 42 7.558807 TCGATCCTATTTAGTTCTGGTTCTGTA 59.441 37.037 0.00 0.00 0.00 2.74
42 43 8.361139 CGATCCTATTTAGTTCTGGTTCTGTAT 58.639 37.037 0.00 0.00 0.00 2.29
43 44 9.482627 GATCCTATTTAGTTCTGGTTCTGTATG 57.517 37.037 0.00 0.00 0.00 2.39
44 45 7.272978 TCCTATTTAGTTCTGGTTCTGTATGC 58.727 38.462 0.00 0.00 0.00 3.14
45 46 6.483640 CCTATTTAGTTCTGGTTCTGTATGCC 59.516 42.308 0.00 0.00 0.00 4.40
46 47 5.499004 TTTAGTTCTGGTTCTGTATGCCT 57.501 39.130 0.00 0.00 0.00 4.75
47 48 3.618690 AGTTCTGGTTCTGTATGCCTC 57.381 47.619 0.00 0.00 0.00 4.70
48 49 2.237392 AGTTCTGGTTCTGTATGCCTCC 59.763 50.000 0.00 0.00 0.00 4.30
49 50 1.204146 TCTGGTTCTGTATGCCTCCC 58.796 55.000 0.00 0.00 0.00 4.30
50 51 0.181350 CTGGTTCTGTATGCCTCCCC 59.819 60.000 0.00 0.00 0.00 4.81
51 52 0.548926 TGGTTCTGTATGCCTCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
52 53 0.181350 GGTTCTGTATGCCTCCCCAG 59.819 60.000 0.00 0.00 0.00 4.45
53 54 0.464554 GTTCTGTATGCCTCCCCAGC 60.465 60.000 0.00 0.00 0.00 4.85
54 55 0.621571 TTCTGTATGCCTCCCCAGCT 60.622 55.000 0.00 0.00 0.00 4.24
55 56 0.264657 TCTGTATGCCTCCCCAGCTA 59.735 55.000 0.00 0.00 0.00 3.32
56 57 0.394565 CTGTATGCCTCCCCAGCTAC 59.605 60.000 0.00 0.00 0.00 3.58
57 58 0.326143 TGTATGCCTCCCCAGCTACA 60.326 55.000 0.00 0.00 0.00 2.74
58 59 0.394565 GTATGCCTCCCCAGCTACAG 59.605 60.000 0.00 0.00 0.00 2.74
59 60 1.410850 TATGCCTCCCCAGCTACAGC 61.411 60.000 0.00 0.00 42.49 4.40
102 103 7.709947 AGCATACAAATTGATATCAGTTGTGG 58.290 34.615 29.35 24.29 36.90 4.17
103 104 6.919662 GCATACAAATTGATATCAGTTGTGGG 59.080 38.462 29.35 24.07 36.90 4.61
104 105 7.201812 GCATACAAATTGATATCAGTTGTGGGA 60.202 37.037 29.35 18.86 36.90 4.37
105 106 6.764308 ACAAATTGATATCAGTTGTGGGAG 57.236 37.500 24.88 11.36 35.77 4.30
106 107 6.484288 ACAAATTGATATCAGTTGTGGGAGA 58.516 36.000 24.88 3.25 35.77 3.71
107 108 6.375455 ACAAATTGATATCAGTTGTGGGAGAC 59.625 38.462 24.88 0.00 35.77 3.36
108 109 5.965033 ATTGATATCAGTTGTGGGAGACT 57.035 39.130 5.39 0.00 0.00 3.24
109 110 5.344743 TTGATATCAGTTGTGGGAGACTC 57.655 43.478 5.39 0.00 0.00 3.36
110 111 3.381590 TGATATCAGTTGTGGGAGACTCG 59.618 47.826 0.00 0.00 0.00 4.18
111 112 0.898320 ATCAGTTGTGGGAGACTCGG 59.102 55.000 0.00 0.00 0.00 4.63
112 113 1.374758 CAGTTGTGGGAGACTCGGC 60.375 63.158 0.00 0.00 0.00 5.54
113 114 1.534235 AGTTGTGGGAGACTCGGCT 60.534 57.895 0.00 0.00 0.00 5.52
114 115 0.251653 AGTTGTGGGAGACTCGGCTA 60.252 55.000 0.00 0.00 0.00 3.93
115 116 0.108756 GTTGTGGGAGACTCGGCTAC 60.109 60.000 0.00 0.00 0.00 3.58
116 117 1.592400 TTGTGGGAGACTCGGCTACG 61.592 60.000 0.00 0.00 42.74 3.51
117 118 3.138798 TGGGAGACTCGGCTACGC 61.139 66.667 0.00 0.00 40.69 4.42
118 119 3.902086 GGGAGACTCGGCTACGCC 61.902 72.222 0.00 0.00 46.75 5.68
127 128 3.573491 GGCTACGCCGACAATGCC 61.573 66.667 0.00 0.00 39.62 4.40
128 129 2.511600 GCTACGCCGACAATGCCT 60.512 61.111 0.00 0.00 0.00 4.75
129 130 2.526120 GCTACGCCGACAATGCCTC 61.526 63.158 0.00 0.00 0.00 4.70
130 131 1.883084 CTACGCCGACAATGCCTCC 60.883 63.158 0.00 0.00 0.00 4.30
131 132 2.572095 CTACGCCGACAATGCCTCCA 62.572 60.000 0.00 0.00 0.00 3.86
132 133 2.173758 TACGCCGACAATGCCTCCAA 62.174 55.000 0.00 0.00 0.00 3.53
133 134 2.114670 CGCCGACAATGCCTCCAAT 61.115 57.895 0.00 0.00 0.00 3.16
134 135 1.434696 GCCGACAATGCCTCCAATG 59.565 57.895 0.00 0.00 0.00 2.82
135 136 1.315257 GCCGACAATGCCTCCAATGT 61.315 55.000 0.00 0.00 37.78 2.71
136 137 0.452987 CCGACAATGCCTCCAATGTG 59.547 55.000 0.00 0.00 35.31 3.21
137 138 0.452987 CGACAATGCCTCCAATGTGG 59.547 55.000 0.00 0.00 35.31 4.17
138 139 1.549203 GACAATGCCTCCAATGTGGT 58.451 50.000 0.00 0.00 35.31 4.16
139 140 1.203052 GACAATGCCTCCAATGTGGTG 59.797 52.381 0.00 0.00 35.31 4.17
143 144 2.751436 CCTCCAATGTGGTGGCGG 60.751 66.667 2.59 0.00 43.34 6.13
144 145 2.034066 CTCCAATGTGGTGGCGGT 59.966 61.111 0.00 0.00 39.03 5.68
145 146 2.033448 TCCAATGTGGTGGCGGTC 59.967 61.111 0.00 0.00 39.03 4.79
146 147 2.282110 CCAATGTGGTGGCGGTCA 60.282 61.111 0.00 0.00 31.35 4.02
147 148 1.678635 CCAATGTGGTGGCGGTCAT 60.679 57.895 0.00 0.00 31.35 3.06
148 149 1.507630 CAATGTGGTGGCGGTCATG 59.492 57.895 0.00 0.00 0.00 3.07
149 150 1.678635 AATGTGGTGGCGGTCATGG 60.679 57.895 0.00 0.00 0.00 3.66
150 151 2.424842 AATGTGGTGGCGGTCATGGT 62.425 55.000 0.00 0.00 0.00 3.55
151 152 3.055719 GTGGTGGCGGTCATGGTG 61.056 66.667 0.00 0.00 0.00 4.17
152 153 4.343323 TGGTGGCGGTCATGGTGG 62.343 66.667 0.00 0.00 0.00 4.61
153 154 4.028490 GGTGGCGGTCATGGTGGA 62.028 66.667 0.00 0.00 0.00 4.02
154 155 2.746277 GTGGCGGTCATGGTGGAC 60.746 66.667 0.00 0.00 37.06 4.02
155 156 4.386951 TGGCGGTCATGGTGGACG 62.387 66.667 0.00 0.00 38.70 4.79
158 159 4.386951 CGGTCATGGTGGACGCCA 62.387 66.667 7.10 7.10 43.48 5.69
167 168 2.347114 TGGACGCCACCATGTGAG 59.653 61.111 0.00 0.00 35.23 3.51
168 169 3.127533 GGACGCCACCATGTGAGC 61.128 66.667 0.00 0.00 35.23 4.26
169 170 2.046892 GACGCCACCATGTGAGCT 60.047 61.111 0.00 0.00 35.23 4.09
170 171 1.672356 GACGCCACCATGTGAGCTT 60.672 57.895 0.00 0.00 35.23 3.74
171 172 1.639298 GACGCCACCATGTGAGCTTC 61.639 60.000 0.00 0.00 35.23 3.86
172 173 2.743752 CGCCACCATGTGAGCTTCG 61.744 63.158 0.00 0.00 35.23 3.79
173 174 2.401766 GCCACCATGTGAGCTTCGG 61.402 63.158 0.00 0.00 35.23 4.30
174 175 2.401766 CCACCATGTGAGCTTCGGC 61.402 63.158 0.00 0.00 42.17 5.54
184 185 4.002797 GCTTCGGCTCATTTGGGT 57.997 55.556 0.00 0.00 38.08 4.51
185 186 1.508088 GCTTCGGCTCATTTGGGTG 59.492 57.895 0.00 0.00 38.08 4.61
186 187 1.244019 GCTTCGGCTCATTTGGGTGT 61.244 55.000 0.00 0.00 38.08 4.16
187 188 1.948611 GCTTCGGCTCATTTGGGTGTA 60.949 52.381 0.00 0.00 38.08 2.90
188 189 2.432444 CTTCGGCTCATTTGGGTGTAA 58.568 47.619 0.00 0.00 0.00 2.41
189 190 1.816074 TCGGCTCATTTGGGTGTAAC 58.184 50.000 0.00 0.00 0.00 2.50
190 191 1.349688 TCGGCTCATTTGGGTGTAACT 59.650 47.619 0.00 0.00 36.74 2.24
191 192 1.468520 CGGCTCATTTGGGTGTAACTG 59.531 52.381 0.00 0.00 36.74 3.16
192 193 1.818674 GGCTCATTTGGGTGTAACTGG 59.181 52.381 0.00 0.00 36.74 4.00
193 194 2.554344 GGCTCATTTGGGTGTAACTGGA 60.554 50.000 0.00 0.00 36.74 3.86
194 195 2.749621 GCTCATTTGGGTGTAACTGGAG 59.250 50.000 0.00 0.00 36.74 3.86
195 196 2.749621 CTCATTTGGGTGTAACTGGAGC 59.250 50.000 0.00 0.00 36.74 4.70
196 197 1.468520 CATTTGGGTGTAACTGGAGCG 59.531 52.381 0.00 0.00 36.74 5.03
197 198 0.759959 TTTGGGTGTAACTGGAGCGA 59.240 50.000 0.00 0.00 36.74 4.93
198 199 0.981183 TTGGGTGTAACTGGAGCGAT 59.019 50.000 0.00 0.00 36.74 4.58
199 200 0.981183 TGGGTGTAACTGGAGCGATT 59.019 50.000 0.00 0.00 36.74 3.34
200 201 1.349688 TGGGTGTAACTGGAGCGATTT 59.650 47.619 0.00 0.00 36.74 2.17
201 202 2.007608 GGGTGTAACTGGAGCGATTTC 58.992 52.381 0.00 0.00 36.74 2.17
202 203 2.007608 GGTGTAACTGGAGCGATTTCC 58.992 52.381 0.00 0.00 36.74 3.13
203 204 2.354805 GGTGTAACTGGAGCGATTTCCT 60.355 50.000 0.00 0.00 38.12 3.36
204 205 3.335579 GTGTAACTGGAGCGATTTCCTT 58.664 45.455 0.00 0.00 38.12 3.36
205 206 3.371285 GTGTAACTGGAGCGATTTCCTTC 59.629 47.826 0.00 0.00 38.12 3.46
206 207 1.726853 AACTGGAGCGATTTCCTTCG 58.273 50.000 0.00 0.00 41.99 3.79
215 216 3.109230 CGATTTCCTTCGCAGTTCAAG 57.891 47.619 0.00 0.00 31.60 3.02
216 217 2.480419 CGATTTCCTTCGCAGTTCAAGT 59.520 45.455 0.00 0.00 31.60 3.16
217 218 3.423645 CGATTTCCTTCGCAGTTCAAGTC 60.424 47.826 0.00 0.00 31.60 3.01
218 219 2.910688 TTCCTTCGCAGTTCAAGTCT 57.089 45.000 0.00 0.00 0.00 3.24
219 220 2.154854 TCCTTCGCAGTTCAAGTCTG 57.845 50.000 0.00 0.00 36.18 3.51
220 221 1.151668 CCTTCGCAGTTCAAGTCTGG 58.848 55.000 0.00 0.00 33.98 3.86
221 222 1.151668 CTTCGCAGTTCAAGTCTGGG 58.848 55.000 0.00 0.00 43.84 4.45
222 223 0.884704 TTCGCAGTTCAAGTCTGGGC 60.885 55.000 5.36 0.00 42.76 5.36
223 224 1.597854 CGCAGTTCAAGTCTGGGCA 60.598 57.895 0.00 0.00 38.57 5.36
224 225 1.572085 CGCAGTTCAAGTCTGGGCAG 61.572 60.000 0.00 0.00 38.57 4.85
225 226 0.536006 GCAGTTCAAGTCTGGGCAGT 60.536 55.000 0.00 0.00 33.98 4.40
226 227 1.972872 CAGTTCAAGTCTGGGCAGTT 58.027 50.000 0.00 0.00 0.00 3.16
227 228 2.301346 CAGTTCAAGTCTGGGCAGTTT 58.699 47.619 0.00 0.00 0.00 2.66
228 229 2.689983 CAGTTCAAGTCTGGGCAGTTTT 59.310 45.455 0.00 0.00 0.00 2.43
229 230 3.131046 CAGTTCAAGTCTGGGCAGTTTTT 59.869 43.478 0.00 0.00 0.00 1.94
248 249 5.906113 TTTTTATGTGCATGTAATCCCGT 57.094 34.783 0.00 0.00 0.00 5.28
249 250 5.906113 TTTTATGTGCATGTAATCCCGTT 57.094 34.783 0.00 0.00 0.00 4.44
250 251 5.906113 TTTATGTGCATGTAATCCCGTTT 57.094 34.783 0.00 0.00 0.00 3.60
251 252 5.906113 TTATGTGCATGTAATCCCGTTTT 57.094 34.783 0.00 0.00 0.00 2.43
252 253 3.567576 TGTGCATGTAATCCCGTTTTG 57.432 42.857 0.00 0.00 0.00 2.44
253 254 2.258755 GTGCATGTAATCCCGTTTTGC 58.741 47.619 0.00 0.00 0.00 3.68
254 255 1.889170 TGCATGTAATCCCGTTTTGCA 59.111 42.857 0.00 0.00 36.37 4.08
255 256 2.258755 GCATGTAATCCCGTTTTGCAC 58.741 47.619 0.00 0.00 0.00 4.57
256 257 2.352225 GCATGTAATCCCGTTTTGCACA 60.352 45.455 0.00 0.00 0.00 4.57
257 258 3.500982 CATGTAATCCCGTTTTGCACAG 58.499 45.455 0.00 0.00 0.00 3.66
258 259 2.577700 TGTAATCCCGTTTTGCACAGT 58.422 42.857 0.00 0.00 0.00 3.55
259 260 2.550606 TGTAATCCCGTTTTGCACAGTC 59.449 45.455 0.00 0.00 0.00 3.51
260 261 0.958822 AATCCCGTTTTGCACAGTCC 59.041 50.000 0.00 0.00 0.00 3.85
261 262 0.893727 ATCCCGTTTTGCACAGTCCC 60.894 55.000 0.00 0.00 0.00 4.46
262 263 1.528309 CCCGTTTTGCACAGTCCCT 60.528 57.895 0.00 0.00 0.00 4.20
263 264 0.250553 CCCGTTTTGCACAGTCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
264 265 1.156736 CCGTTTTGCACAGTCCCTAG 58.843 55.000 0.00 0.00 0.00 3.02
265 266 0.517316 CGTTTTGCACAGTCCCTAGC 59.483 55.000 0.00 0.00 0.00 3.42
266 267 1.604604 GTTTTGCACAGTCCCTAGCA 58.395 50.000 0.00 0.00 34.79 3.49
267 268 2.162681 GTTTTGCACAGTCCCTAGCAT 58.837 47.619 0.00 0.00 36.80 3.79
268 269 2.558359 GTTTTGCACAGTCCCTAGCATT 59.442 45.455 0.00 0.00 36.80 3.56
269 270 3.712016 TTTGCACAGTCCCTAGCATTA 57.288 42.857 0.00 0.00 36.80 1.90
270 271 3.931907 TTGCACAGTCCCTAGCATTAT 57.068 42.857 0.00 0.00 36.80 1.28
271 272 3.931907 TGCACAGTCCCTAGCATTATT 57.068 42.857 0.00 0.00 31.05 1.40
272 273 5.366482 TTGCACAGTCCCTAGCATTATTA 57.634 39.130 0.00 0.00 36.80 0.98
273 274 5.366482 TGCACAGTCCCTAGCATTATTAA 57.634 39.130 0.00 0.00 31.05 1.40
274 275 5.940617 TGCACAGTCCCTAGCATTATTAAT 58.059 37.500 0.00 0.00 31.05 1.40
275 276 6.364701 TGCACAGTCCCTAGCATTATTAATT 58.635 36.000 0.00 0.00 31.05 1.40
276 277 6.833416 TGCACAGTCCCTAGCATTATTAATTT 59.167 34.615 0.00 0.00 31.05 1.82
277 278 7.341769 TGCACAGTCCCTAGCATTATTAATTTT 59.658 33.333 0.00 0.00 31.05 1.82
278 279 8.846211 GCACAGTCCCTAGCATTATTAATTTTA 58.154 33.333 0.00 0.00 0.00 1.52
302 303 9.606631 TTATTTTTCTGCCAATAACAACAAAGT 57.393 25.926 0.00 0.00 0.00 2.66
304 305 9.606631 ATTTTTCTGCCAATAACAACAAAGTAA 57.393 25.926 0.00 0.00 0.00 2.24
305 306 9.606631 TTTTTCTGCCAATAACAACAAAGTAAT 57.393 25.926 0.00 0.00 0.00 1.89
306 307 8.586570 TTTCTGCCAATAACAACAAAGTAATG 57.413 30.769 0.00 0.00 0.00 1.90
307 308 7.283625 TCTGCCAATAACAACAAAGTAATGT 57.716 32.000 0.00 0.00 34.24 2.71
308 309 7.144661 TCTGCCAATAACAACAAAGTAATGTG 58.855 34.615 0.00 0.00 32.81 3.21
309 310 6.810911 TGCCAATAACAACAAAGTAATGTGT 58.189 32.000 0.00 0.00 32.81 3.72
310 311 6.699204 TGCCAATAACAACAAAGTAATGTGTG 59.301 34.615 0.00 0.00 32.81 3.82
329 330 5.465390 TGTGTGCATCACTAGTAGAAAACAC 59.535 40.000 17.12 17.12 46.27 3.32
471 473 2.504367 CGGTTCATCTGGACCTTTTGT 58.496 47.619 6.11 0.00 0.00 2.83
820 822 4.811969 TTTGTCTAGATTTAGCGGTCCA 57.188 40.909 0.00 0.00 0.00 4.02
1115 1117 6.559810 TGTTTATGAAAATTATGCCGACCAG 58.440 36.000 0.00 0.00 0.00 4.00
1171 1173 4.909678 TGGAAATGCCAACCGACA 57.090 50.000 0.00 0.00 45.87 4.35
1288 1293 0.800683 TGTTGCGGATGTCGTCGATC 60.801 55.000 0.00 0.00 41.72 3.69
1336 1341 5.872635 TGCGCTTGAAGATTAGAAAGATTG 58.127 37.500 9.73 0.00 0.00 2.67
1404 1409 4.021544 GGATCAATTGTTACCTTGGTTGCA 60.022 41.667 5.13 0.00 0.00 4.08
1715 1720 1.894466 CCATGCACTGAATGTGGGAAA 59.106 47.619 0.00 0.00 46.27 3.13
1736 1742 2.363683 ACGAGGTCTTACTCTAACCGG 58.636 52.381 0.00 0.00 38.14 5.28
1740 1746 4.097589 CGAGGTCTTACTCTAACCGGAAAT 59.902 45.833 9.46 0.00 38.14 2.17
1745 1751 6.097412 GGTCTTACTCTAACCGGAAATTCCTA 59.903 42.308 9.46 0.00 33.30 2.94
1779 1785 3.055891 GCTTTACAAGGGTTTCATGCCAT 60.056 43.478 0.00 0.00 0.00 4.40
1855 1864 5.704888 AGAAGAAGACTACGATGACAACTG 58.295 41.667 0.00 0.00 0.00 3.16
1914 1923 3.522750 AGCTGGTGAAGATCAAGAGGAAT 59.477 43.478 0.00 0.00 0.00 3.01
2025 2034 0.099436 GGTCATTGTCGATGCAAGGC 59.901 55.000 0.00 0.00 35.64 4.35
2033 2042 2.887360 GATGCAAGGCCGCAATGT 59.113 55.556 9.50 0.00 46.87 2.71
2065 2074 2.828520 AGGAGAAGCTGAAGTTCGATCA 59.171 45.455 0.00 0.00 0.00 2.92
2136 2145 1.547372 ACACAAAGCTCGGTACCGTAT 59.453 47.619 32.16 17.20 40.74 3.06
2273 2282 2.076863 GCAGCAAAGAAGGTCGTATGT 58.923 47.619 0.00 0.00 0.00 2.29
2310 2319 3.474600 GTGGAGAAGATACATGCATGCT 58.525 45.455 26.53 14.22 0.00 3.79
2369 2378 1.817941 GAACGCATGCCCGGTATGT 60.818 57.895 13.15 0.00 0.00 2.29
2387 2396 2.437413 TGTGGTGCATTGCGGTATAAA 58.563 42.857 3.84 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.702670 ACTAAATAGGATCGATGCACCATTG 59.297 40.000 19.67 7.42 0.00 2.82
6 7 5.869579 ACTAAATAGGATCGATGCACCATT 58.130 37.500 19.67 11.74 0.00 3.16
7 8 5.489792 ACTAAATAGGATCGATGCACCAT 57.510 39.130 19.67 6.30 0.00 3.55
8 9 4.955811 ACTAAATAGGATCGATGCACCA 57.044 40.909 19.67 4.07 0.00 4.17
9 10 5.406780 CAGAACTAAATAGGATCGATGCACC 59.593 44.000 19.67 6.60 0.00 5.01
10 11 5.406780 CCAGAACTAAATAGGATCGATGCAC 59.593 44.000 19.67 1.44 0.00 4.57
11 12 5.070446 ACCAGAACTAAATAGGATCGATGCA 59.930 40.000 19.67 5.64 0.00 3.96
12 13 5.542779 ACCAGAACTAAATAGGATCGATGC 58.457 41.667 9.16 9.16 0.00 3.91
13 14 7.383572 CAGAACCAGAACTAAATAGGATCGATG 59.616 40.741 0.54 0.00 0.00 3.84
14 15 7.070074 ACAGAACCAGAACTAAATAGGATCGAT 59.930 37.037 0.00 0.00 0.00 3.59
15 16 6.380274 ACAGAACCAGAACTAAATAGGATCGA 59.620 38.462 0.00 0.00 0.00 3.59
16 17 6.574350 ACAGAACCAGAACTAAATAGGATCG 58.426 40.000 0.00 0.00 0.00 3.69
17 18 9.482627 CATACAGAACCAGAACTAAATAGGATC 57.517 37.037 0.00 0.00 0.00 3.36
18 19 7.934120 GCATACAGAACCAGAACTAAATAGGAT 59.066 37.037 0.00 0.00 0.00 3.24
19 20 7.272978 GCATACAGAACCAGAACTAAATAGGA 58.727 38.462 0.00 0.00 0.00 2.94
20 21 6.483640 GGCATACAGAACCAGAACTAAATAGG 59.516 42.308 0.00 0.00 0.00 2.57
21 22 7.275920 AGGCATACAGAACCAGAACTAAATAG 58.724 38.462 0.00 0.00 0.00 1.73
22 23 7.195374 AGGCATACAGAACCAGAACTAAATA 57.805 36.000 0.00 0.00 0.00 1.40
23 24 6.067217 AGGCATACAGAACCAGAACTAAAT 57.933 37.500 0.00 0.00 0.00 1.40
24 25 5.488341 GAGGCATACAGAACCAGAACTAAA 58.512 41.667 0.00 0.00 0.00 1.85
25 26 4.081087 GGAGGCATACAGAACCAGAACTAA 60.081 45.833 0.00 0.00 0.00 2.24
26 27 3.451178 GGAGGCATACAGAACCAGAACTA 59.549 47.826 0.00 0.00 0.00 2.24
27 28 2.237392 GGAGGCATACAGAACCAGAACT 59.763 50.000 0.00 0.00 0.00 3.01
28 29 2.633488 GGAGGCATACAGAACCAGAAC 58.367 52.381 0.00 0.00 0.00 3.01
29 30 1.559682 GGGAGGCATACAGAACCAGAA 59.440 52.381 0.00 0.00 0.00 3.02
30 31 1.204146 GGGAGGCATACAGAACCAGA 58.796 55.000 0.00 0.00 0.00 3.86
31 32 0.181350 GGGGAGGCATACAGAACCAG 59.819 60.000 0.00 0.00 0.00 4.00
32 33 0.548926 TGGGGAGGCATACAGAACCA 60.549 55.000 0.00 0.00 0.00 3.67
33 34 0.181350 CTGGGGAGGCATACAGAACC 59.819 60.000 0.00 0.00 32.86 3.62
34 35 0.464554 GCTGGGGAGGCATACAGAAC 60.465 60.000 0.00 0.00 32.86 3.01
35 36 0.621571 AGCTGGGGAGGCATACAGAA 60.622 55.000 0.00 0.00 32.86 3.02
36 37 0.264657 TAGCTGGGGAGGCATACAGA 59.735 55.000 0.00 0.00 32.86 3.41
37 38 0.394565 GTAGCTGGGGAGGCATACAG 59.605 60.000 0.00 0.00 0.00 2.74
38 39 0.326143 TGTAGCTGGGGAGGCATACA 60.326 55.000 0.00 0.00 0.00 2.29
39 40 0.394565 CTGTAGCTGGGGAGGCATAC 59.605 60.000 0.00 0.00 0.00 2.39
40 41 1.410850 GCTGTAGCTGGGGAGGCATA 61.411 60.000 0.00 0.00 38.21 3.14
41 42 2.750657 GCTGTAGCTGGGGAGGCAT 61.751 63.158 0.00 0.00 38.21 4.40
42 43 3.402681 GCTGTAGCTGGGGAGGCA 61.403 66.667 0.00 0.00 38.21 4.75
76 77 8.839343 CCACAACTGATATCAATTTGTATGCTA 58.161 33.333 22.82 0.00 33.11 3.49
77 78 7.201848 CCCACAACTGATATCAATTTGTATGCT 60.202 37.037 22.82 6.54 33.11 3.79
78 79 6.919662 CCCACAACTGATATCAATTTGTATGC 59.080 38.462 22.82 0.00 33.11 3.14
79 80 8.224389 TCCCACAACTGATATCAATTTGTATG 57.776 34.615 22.82 18.25 33.11 2.39
80 81 8.274322 TCTCCCACAACTGATATCAATTTGTAT 58.726 33.333 22.82 7.59 33.11 2.29
81 82 7.552687 GTCTCCCACAACTGATATCAATTTGTA 59.447 37.037 22.82 12.75 33.11 2.41
82 83 6.375455 GTCTCCCACAACTGATATCAATTTGT 59.625 38.462 19.74 19.74 34.37 2.83
83 84 6.600822 AGTCTCCCACAACTGATATCAATTTG 59.399 38.462 18.77 18.77 0.00 2.32
84 85 6.725364 AGTCTCCCACAACTGATATCAATTT 58.275 36.000 6.90 0.23 0.00 1.82
85 86 6.319048 AGTCTCCCACAACTGATATCAATT 57.681 37.500 6.90 0.00 0.00 2.32
86 87 5.452496 CGAGTCTCCCACAACTGATATCAAT 60.452 44.000 6.90 0.00 0.00 2.57
87 88 4.142160 CGAGTCTCCCACAACTGATATCAA 60.142 45.833 6.90 0.00 0.00 2.57
88 89 3.381590 CGAGTCTCCCACAACTGATATCA 59.618 47.826 5.07 5.07 0.00 2.15
89 90 3.243569 CCGAGTCTCCCACAACTGATATC 60.244 52.174 0.00 0.00 0.00 1.63
90 91 2.695666 CCGAGTCTCCCACAACTGATAT 59.304 50.000 0.00 0.00 0.00 1.63
91 92 2.100197 CCGAGTCTCCCACAACTGATA 58.900 52.381 0.00 0.00 0.00 2.15
92 93 0.898320 CCGAGTCTCCCACAACTGAT 59.102 55.000 0.00 0.00 0.00 2.90
93 94 1.816863 GCCGAGTCTCCCACAACTGA 61.817 60.000 0.00 0.00 0.00 3.41
94 95 1.374758 GCCGAGTCTCCCACAACTG 60.375 63.158 0.00 0.00 0.00 3.16
95 96 0.251653 TAGCCGAGTCTCCCACAACT 60.252 55.000 0.00 0.00 0.00 3.16
96 97 0.108756 GTAGCCGAGTCTCCCACAAC 60.109 60.000 0.00 0.00 0.00 3.32
97 98 1.592400 CGTAGCCGAGTCTCCCACAA 61.592 60.000 0.00 0.00 35.63 3.33
98 99 2.044555 CGTAGCCGAGTCTCCCACA 61.045 63.158 0.00 0.00 35.63 4.17
99 100 2.799371 CGTAGCCGAGTCTCCCAC 59.201 66.667 0.00 0.00 35.63 4.61
112 113 1.883084 GGAGGCATTGTCGGCGTAG 60.883 63.158 6.85 0.00 36.37 3.51
113 114 2.173758 TTGGAGGCATTGTCGGCGTA 62.174 55.000 6.85 0.00 36.37 4.42
114 115 2.819984 ATTGGAGGCATTGTCGGCGT 62.820 55.000 6.85 0.00 36.37 5.68
115 116 2.114670 ATTGGAGGCATTGTCGGCG 61.115 57.895 0.00 0.00 36.37 6.46
116 117 1.315257 ACATTGGAGGCATTGTCGGC 61.315 55.000 0.00 0.00 0.00 5.54
117 118 0.452987 CACATTGGAGGCATTGTCGG 59.547 55.000 0.00 0.00 0.00 4.79
118 119 0.452987 CCACATTGGAGGCATTGTCG 59.547 55.000 0.00 0.00 40.96 4.35
119 120 1.203052 CACCACATTGGAGGCATTGTC 59.797 52.381 0.00 0.00 40.96 3.18
120 121 1.259609 CACCACATTGGAGGCATTGT 58.740 50.000 0.00 0.00 40.96 2.71
121 122 0.533491 CCACCACATTGGAGGCATTG 59.467 55.000 0.00 0.00 41.28 2.82
122 123 2.980541 CCACCACATTGGAGGCATT 58.019 52.632 0.00 0.00 41.28 3.56
123 124 4.770540 CCACCACATTGGAGGCAT 57.229 55.556 0.00 0.00 41.28 4.40
127 128 2.034066 ACCGCCACCACATTGGAG 59.966 61.111 0.00 0.00 40.96 3.86
128 129 2.033448 GACCGCCACCACATTGGA 59.967 61.111 0.00 0.00 40.96 3.53
129 130 1.678635 ATGACCGCCACCACATTGG 60.679 57.895 0.00 0.00 45.02 3.16
130 131 1.507630 CATGACCGCCACCACATTG 59.492 57.895 0.00 0.00 0.00 2.82
131 132 1.678635 CCATGACCGCCACCACATT 60.679 57.895 0.00 0.00 0.00 2.71
132 133 2.045045 CCATGACCGCCACCACAT 60.045 61.111 0.00 0.00 0.00 3.21
133 134 3.565214 ACCATGACCGCCACCACA 61.565 61.111 0.00 0.00 0.00 4.17
134 135 3.055719 CACCATGACCGCCACCAC 61.056 66.667 0.00 0.00 0.00 4.16
135 136 4.343323 CCACCATGACCGCCACCA 62.343 66.667 0.00 0.00 0.00 4.17
136 137 4.028490 TCCACCATGACCGCCACC 62.028 66.667 0.00 0.00 0.00 4.61
137 138 2.746277 GTCCACCATGACCGCCAC 60.746 66.667 0.00 0.00 0.00 5.01
138 139 4.386951 CGTCCACCATGACCGCCA 62.387 66.667 0.00 0.00 31.35 5.69
141 142 4.386951 TGGCGTCCACCATGACCG 62.387 66.667 0.00 0.00 33.75 4.79
150 151 2.347114 CTCACATGGTGGCGTCCA 59.653 61.111 0.00 3.82 42.01 4.02
151 152 3.127533 GCTCACATGGTGGCGTCC 61.128 66.667 0.00 0.00 33.87 4.79
152 153 1.639298 GAAGCTCACATGGTGGCGTC 61.639 60.000 0.00 2.15 35.81 5.19
153 154 1.672356 GAAGCTCACATGGTGGCGT 60.672 57.895 0.00 0.00 35.81 5.68
154 155 2.743752 CGAAGCTCACATGGTGGCG 61.744 63.158 0.00 0.00 35.81 5.69
155 156 2.401766 CCGAAGCTCACATGGTGGC 61.402 63.158 0.00 0.00 33.87 5.01
156 157 2.401766 GCCGAAGCTCACATGGTGG 61.402 63.158 0.00 0.00 33.87 4.61
157 158 3.181367 GCCGAAGCTCACATGGTG 58.819 61.111 0.00 0.00 35.50 4.17
167 168 1.244019 ACACCCAAATGAGCCGAAGC 61.244 55.000 0.00 0.00 40.32 3.86
168 169 2.107950 TACACCCAAATGAGCCGAAG 57.892 50.000 0.00 0.00 0.00 3.79
169 170 2.156098 GTTACACCCAAATGAGCCGAA 58.844 47.619 0.00 0.00 0.00 4.30
170 171 1.349688 AGTTACACCCAAATGAGCCGA 59.650 47.619 0.00 0.00 0.00 5.54
171 172 1.468520 CAGTTACACCCAAATGAGCCG 59.531 52.381 0.00 0.00 0.00 5.52
172 173 1.818674 CCAGTTACACCCAAATGAGCC 59.181 52.381 0.00 0.00 0.00 4.70
173 174 2.749621 CTCCAGTTACACCCAAATGAGC 59.250 50.000 0.00 0.00 0.00 4.26
174 175 2.749621 GCTCCAGTTACACCCAAATGAG 59.250 50.000 0.00 0.00 0.00 2.90
175 176 2.790433 GCTCCAGTTACACCCAAATGA 58.210 47.619 0.00 0.00 0.00 2.57
176 177 1.468520 CGCTCCAGTTACACCCAAATG 59.531 52.381 0.00 0.00 0.00 2.32
177 178 1.349688 TCGCTCCAGTTACACCCAAAT 59.650 47.619 0.00 0.00 0.00 2.32
178 179 0.759959 TCGCTCCAGTTACACCCAAA 59.240 50.000 0.00 0.00 0.00 3.28
179 180 0.981183 ATCGCTCCAGTTACACCCAA 59.019 50.000 0.00 0.00 0.00 4.12
180 181 0.981183 AATCGCTCCAGTTACACCCA 59.019 50.000 0.00 0.00 0.00 4.51
181 182 2.007608 GAAATCGCTCCAGTTACACCC 58.992 52.381 0.00 0.00 0.00 4.61
182 183 2.007608 GGAAATCGCTCCAGTTACACC 58.992 52.381 0.00 0.00 35.36 4.16
183 184 2.973945 AGGAAATCGCTCCAGTTACAC 58.026 47.619 1.58 0.00 38.02 2.90
184 185 3.596214 GAAGGAAATCGCTCCAGTTACA 58.404 45.455 1.58 0.00 38.02 2.41
185 186 2.603560 CGAAGGAAATCGCTCCAGTTAC 59.396 50.000 1.58 0.00 38.02 2.50
186 187 2.888594 CGAAGGAAATCGCTCCAGTTA 58.111 47.619 1.58 0.00 38.02 2.24
187 188 1.726853 CGAAGGAAATCGCTCCAGTT 58.273 50.000 1.58 0.00 38.02 3.16
188 189 3.442996 CGAAGGAAATCGCTCCAGT 57.557 52.632 1.58 0.00 38.02 4.00
195 196 2.480419 ACTTGAACTGCGAAGGAAATCG 59.520 45.455 0.00 0.00 45.41 3.34
196 197 3.748568 AGACTTGAACTGCGAAGGAAATC 59.251 43.478 0.00 0.00 0.00 2.17
197 198 3.499918 CAGACTTGAACTGCGAAGGAAAT 59.500 43.478 0.00 0.00 0.00 2.17
198 199 2.872245 CAGACTTGAACTGCGAAGGAAA 59.128 45.455 0.00 0.00 0.00 3.13
199 200 2.483876 CAGACTTGAACTGCGAAGGAA 58.516 47.619 0.00 0.00 0.00 3.36
200 201 1.270305 CCAGACTTGAACTGCGAAGGA 60.270 52.381 0.00 0.00 34.47 3.36
201 202 1.151668 CCAGACTTGAACTGCGAAGG 58.848 55.000 0.00 0.00 34.47 3.46
202 203 1.151668 CCCAGACTTGAACTGCGAAG 58.848 55.000 0.00 0.00 34.47 3.79
203 204 0.884704 GCCCAGACTTGAACTGCGAA 60.885 55.000 0.00 0.00 34.47 4.70
204 205 1.301716 GCCCAGACTTGAACTGCGA 60.302 57.895 0.00 0.00 34.47 5.10
205 206 1.572085 CTGCCCAGACTTGAACTGCG 61.572 60.000 0.00 0.00 34.47 5.18
206 207 0.536006 ACTGCCCAGACTTGAACTGC 60.536 55.000 1.69 0.00 34.47 4.40
207 208 1.972872 AACTGCCCAGACTTGAACTG 58.027 50.000 1.69 0.00 35.43 3.16
208 209 2.736670 AAACTGCCCAGACTTGAACT 57.263 45.000 1.69 0.00 0.00 3.01
209 210 3.801114 AAAAACTGCCCAGACTTGAAC 57.199 42.857 1.69 0.00 0.00 3.18
226 227 5.906113 ACGGGATTACATGCACATAAAAA 57.094 34.783 0.00 0.00 0.00 1.94
227 228 5.906113 AACGGGATTACATGCACATAAAA 57.094 34.783 0.00 0.00 0.00 1.52
228 229 5.906113 AAACGGGATTACATGCACATAAA 57.094 34.783 0.00 0.00 0.00 1.40
229 230 5.645624 CAAAACGGGATTACATGCACATAA 58.354 37.500 0.00 0.00 0.00 1.90
230 231 4.439426 GCAAAACGGGATTACATGCACATA 60.439 41.667 0.00 0.00 32.80 2.29
231 232 3.675775 GCAAAACGGGATTACATGCACAT 60.676 43.478 0.00 0.00 32.80 3.21
232 233 2.352225 GCAAAACGGGATTACATGCACA 60.352 45.455 0.00 0.00 32.80 4.57
233 234 2.258755 GCAAAACGGGATTACATGCAC 58.741 47.619 0.00 0.00 32.80 4.57
234 235 1.889170 TGCAAAACGGGATTACATGCA 59.111 42.857 0.00 0.00 39.73 3.96
235 236 2.258755 GTGCAAAACGGGATTACATGC 58.741 47.619 0.00 0.00 0.00 4.06
236 237 3.057596 ACTGTGCAAAACGGGATTACATG 60.058 43.478 0.00 0.00 39.74 3.21
237 238 3.153919 ACTGTGCAAAACGGGATTACAT 58.846 40.909 0.00 0.00 39.74 2.29
238 239 2.550606 GACTGTGCAAAACGGGATTACA 59.449 45.455 0.00 0.00 39.74 2.41
239 240 2.095415 GGACTGTGCAAAACGGGATTAC 60.095 50.000 0.00 0.00 39.74 1.89
240 241 2.156098 GGACTGTGCAAAACGGGATTA 58.844 47.619 0.00 0.00 39.74 1.75
241 242 0.958822 GGACTGTGCAAAACGGGATT 59.041 50.000 0.00 0.00 39.74 3.01
242 243 0.893727 GGGACTGTGCAAAACGGGAT 60.894 55.000 0.77 0.00 39.74 3.85
243 244 1.527380 GGGACTGTGCAAAACGGGA 60.527 57.895 0.77 0.00 39.74 5.14
244 245 0.250553 TAGGGACTGTGCAAAACGGG 60.251 55.000 0.77 0.00 41.52 5.28
245 246 1.156736 CTAGGGACTGTGCAAAACGG 58.843 55.000 0.77 0.00 41.52 4.44
246 247 0.517316 GCTAGGGACTGTGCAAAACG 59.483 55.000 0.77 0.00 41.52 3.60
247 248 1.604604 TGCTAGGGACTGTGCAAAAC 58.395 50.000 0.77 0.00 43.59 2.43
252 253 6.884280 AATTAATAATGCTAGGGACTGTGC 57.116 37.500 0.00 0.00 41.52 4.57
276 277 9.606631 ACTTTGTTGTTATTGGCAGAAAAATAA 57.393 25.926 0.00 0.00 0.00 1.40
278 279 9.606631 TTACTTTGTTGTTATTGGCAGAAAAAT 57.393 25.926 0.00 0.00 0.00 1.82
279 280 9.606631 ATTACTTTGTTGTTATTGGCAGAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
280 281 9.039870 CATTACTTTGTTGTTATTGGCAGAAAA 57.960 29.630 0.00 0.00 0.00 2.29
281 282 8.200792 ACATTACTTTGTTGTTATTGGCAGAAA 58.799 29.630 0.00 0.00 0.00 2.52
282 283 7.651304 CACATTACTTTGTTGTTATTGGCAGAA 59.349 33.333 0.00 0.00 0.00 3.02
283 284 7.144661 CACATTACTTTGTTGTTATTGGCAGA 58.855 34.615 0.00 0.00 0.00 4.26
284 285 6.922957 ACACATTACTTTGTTGTTATTGGCAG 59.077 34.615 0.00 0.00 0.00 4.85
285 286 6.699204 CACACATTACTTTGTTGTTATTGGCA 59.301 34.615 0.00 0.00 0.00 4.92
286 287 6.346518 GCACACATTACTTTGTTGTTATTGGC 60.347 38.462 0.00 0.00 0.00 4.52
287 288 6.699204 TGCACACATTACTTTGTTGTTATTGG 59.301 34.615 0.00 0.00 0.00 3.16
288 289 7.691430 TGCACACATTACTTTGTTGTTATTG 57.309 32.000 0.00 0.00 0.00 1.90
289 290 8.140628 TGATGCACACATTACTTTGTTGTTATT 58.859 29.630 0.00 0.00 36.35 1.40
290 291 7.656412 TGATGCACACATTACTTTGTTGTTAT 58.344 30.769 0.00 0.00 36.35 1.89
291 292 7.032377 TGATGCACACATTACTTTGTTGTTA 57.968 32.000 0.00 0.00 36.35 2.41
292 293 5.900425 TGATGCACACATTACTTTGTTGTT 58.100 33.333 0.00 0.00 36.35 2.83
293 294 5.512753 TGATGCACACATTACTTTGTTGT 57.487 34.783 0.00 0.00 36.35 3.32
307 308 4.684242 CGTGTTTTCTACTAGTGATGCACA 59.316 41.667 5.39 0.33 36.74 4.57
308 309 4.091509 CCGTGTTTTCTACTAGTGATGCAC 59.908 45.833 5.39 6.38 34.10 4.57
309 310 4.242475 CCGTGTTTTCTACTAGTGATGCA 58.758 43.478 5.39 0.00 0.00 3.96
310 311 3.062234 GCCGTGTTTTCTACTAGTGATGC 59.938 47.826 5.39 0.00 0.00 3.91
1142 1144 5.735285 TGGCATTTCCAATTCACATACAA 57.265 34.783 0.00 0.00 43.21 2.41
1154 1156 0.179004 AGTGTCGGTTGGCATTTCCA 60.179 50.000 0.00 0.00 44.85 3.53
1288 1293 4.578928 TGCATCCATCTTGATCTTGTGATG 59.421 41.667 0.00 3.04 36.87 3.07
1336 1341 5.106157 CCTCGGTATGAATGGCATATTTTCC 60.106 44.000 0.00 0.71 41.29 3.13
1404 1409 5.804473 TGCGAAAACAAATGCGATCATAATT 59.196 32.000 0.00 0.00 31.46 1.40
1475 1480 7.290813 TCTAACAACATATAGCTCTCCAGAGA 58.709 38.462 7.84 0.00 44.74 3.10
1569 1574 4.452114 TCGGTTCATCTGCATGCATTATAC 59.548 41.667 22.97 14.91 0.00 1.47
1579 1584 1.003003 TCCATTGTCGGTTCATCTGCA 59.997 47.619 0.00 0.00 0.00 4.41
1715 1720 2.751806 CCGGTTAGAGTAAGACCTCGTT 59.248 50.000 0.00 0.00 36.56 3.85
1736 1742 3.610911 CAGGTGGGAGTGTAGGAATTTC 58.389 50.000 0.00 0.00 0.00 2.17
1740 1746 0.178903 AGCAGGTGGGAGTGTAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
1745 1751 1.136828 TGTAAAGCAGGTGGGAGTGT 58.863 50.000 0.00 0.00 0.00 3.55
1779 1785 5.989168 CGTGCCTCATCCAAACATTATAGTA 59.011 40.000 0.00 0.00 0.00 1.82
1855 1864 1.451387 CCGTATTCAGGGGGCACAC 60.451 63.158 0.00 0.00 0.00 3.82
1914 1923 0.612744 TCATTGGGCACATCGTCTGA 59.387 50.000 0.00 0.00 0.00 3.27
2025 2034 3.052036 CCTTTTGACTTTCACATTGCGG 58.948 45.455 0.00 0.00 0.00 5.69
2033 2042 4.780815 TCAGCTTCTCCTTTTGACTTTCA 58.219 39.130 0.00 0.00 0.00 2.69
2136 2145 1.614903 CTTCCACTGCAGCAATTCCAA 59.385 47.619 15.27 0.00 0.00 3.53
2172 2181 4.723309 AGCTTCTCAAATCCTTTGTCAGT 58.277 39.130 0.04 0.00 41.36 3.41
2220 2229 4.338118 GTCGGGCAATTCATTATCCTTTGA 59.662 41.667 0.00 0.00 0.00 2.69
2310 2319 3.570125 CGGTAGAGGATGCAGTCATTAGA 59.430 47.826 0.00 0.00 31.96 2.10
2369 2378 3.696548 TGATTTTATACCGCAATGCACCA 59.303 39.130 5.91 0.00 0.00 4.17
2387 2396 1.759445 CCAGGGTCATCTCGTCTGATT 59.241 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.