Multiple sequence alignment - TraesCS6B01G421200

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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 TraesCS6B01G421200 chr6B 100.000 2740 0 0 1 2740 692045703 692042964 0.000000e+00 5060.0
1 TraesCS6B01G421200 chr6B 97.124 2156 42 7 437 2581 691975634 691977780 0.000000e+00 3620.0
2 TraesCS6B01G421200 chr6B 81.256 1115 148 35 844 1930 691944768 691945849 0.000000e+00 845.0
3 TraesCS6B01G421200 chr6B 83.036 896 111 23 875 1741 692574338 692575221 0.000000e+00 774.0
4 TraesCS6B01G421200 chr6B 95.135 185 5 2 1 185 184811603 184811423 3.450000e-74 289.0
5 TraesCS6B01G421200 chr6B 94.898 98 5 0 2643 2740 691977860 691977957 1.310000e-33 154.0
6 TraesCS6B01G421200 chr6B 93.827 81 5 0 348 428 184804906 184804826 3.710000e-24 122.0
7 TraesCS6B01G421200 chr6D 87.200 2211 183 39 454 2612 454968566 454966404 0.000000e+00 2423.0
8 TraesCS6B01G421200 chr6D 90.407 1720 137 8 893 2601 454962837 454961135 0.000000e+00 2237.0
9 TraesCS6B01G421200 chr6D 82.855 1149 151 28 844 1971 454996670 454995547 0.000000e+00 989.0
10 TraesCS6B01G421200 chr6A 89.379 1883 120 32 670 2528 601241996 601240170 0.000000e+00 2296.0
11 TraesCS6B01G421200 chr6A 86.854 1567 141 35 443 1971 601257575 601256036 0.000000e+00 1692.0
12 TraesCS6B01G421200 chr6A 81.729 1122 146 38 877 1971 601264782 601263693 0.000000e+00 881.0
13 TraesCS6B01G421200 chr6A 79.661 1239 188 43 776 1972 602075402 602076618 0.000000e+00 833.0
14 TraesCS6B01G421200 chr6A 82.106 978 137 27 954 1906 602131438 602132402 0.000000e+00 802.0
15 TraesCS6B01G421200 chr6A 90.120 334 29 2 2 332 580313699 580314031 5.420000e-117 431.0
16 TraesCS6B01G421200 chr6A 92.414 145 11 0 2596 2740 601240149 601240005 9.940000e-50 207.0
17 TraesCS6B01G421200 chr6A 84.541 207 12 6 443 640 601242268 601242073 1.300000e-43 187.0
18 TraesCS6B01G421200 chrUn 87.326 647 40 20 660 1281 79445060 79444431 0.000000e+00 702.0
19 TraesCS6B01G421200 chrUn 86.275 204 11 7 443 640 79445335 79445143 3.580000e-49 206.0
20 TraesCS6B01G421200 chr4A 85.825 388 49 4 2 386 494892733 494893117 9.130000e-110 407.0
21 TraesCS6B01G421200 chr5B 89.062 64 5 2 2000 2061 53534033 53533970 8.130000e-11 78.7
22 TraesCS6B01G421200 chr7D 92.453 53 3 1 379 430 41834109 41834161 1.050000e-09 75.0
23 TraesCS6B01G421200 chr1B 95.000 40 2 0 389 428 47205291 47205330 2.280000e-06 63.9


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 TraesCS6B01G421200 chr6B 692042964 692045703 2739 True 5060.000000 5060 100.0000 1 2740 1 chr6B.!!$R3 2739
1 TraesCS6B01G421200 chr6B 691975634 691977957 2323 False 1887.000000 3620 96.0110 437 2740 2 chr6B.!!$F3 2303
2 TraesCS6B01G421200 chr6B 691944768 691945849 1081 False 845.000000 845 81.2560 844 1930 1 chr6B.!!$F1 1086
3 TraesCS6B01G421200 chr6B 692574338 692575221 883 False 774.000000 774 83.0360 875 1741 1 chr6B.!!$F2 866
4 TraesCS6B01G421200 chr6D 454961135 454968566 7431 True 2330.000000 2423 88.8035 454 2612 2 chr6D.!!$R2 2158
5 TraesCS6B01G421200 chr6D 454995547 454996670 1123 True 989.000000 989 82.8550 844 1971 1 chr6D.!!$R1 1127
6 TraesCS6B01G421200 chr6A 601256036 601257575 1539 True 1692.000000 1692 86.8540 443 1971 1 chr6A.!!$R1 1528
7 TraesCS6B01G421200 chr6A 601240005 601242268 2263 True 896.666667 2296 88.7780 443 2740 3 chr6A.!!$R3 2297
8 TraesCS6B01G421200 chr6A 601263693 601264782 1089 True 881.000000 881 81.7290 877 1971 1 chr6A.!!$R2 1094
9 TraesCS6B01G421200 chr6A 602075402 602076618 1216 False 833.000000 833 79.6610 776 1972 1 chr6A.!!$F2 1196
10 TraesCS6B01G421200 chr6A 602131438 602132402 964 False 802.000000 802 82.1060 954 1906 1 chr6A.!!$F3 952
11 TraesCS6B01G421200 chrUn 79444431 79445335 904 True 454.000000 702 86.8005 443 1281 2 chrUn.!!$R1 838

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
306 307 0.03563 AGCAGAGCACCACATCTTCC 60.036 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 7659 0.605589 CTTTGAGAGACTGAGCCGGT 59.394 55.0 1.9 0.0 0.0 5.28 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
26 27 4.819761 TGAGCATCACCGAGCGCC 62.820 66.667 2.29 0.00 42.56 6.53
42 43 4.944372 CCGCCGCGGTACAGATCC 62.944 72.222 28.70 5.98 42.73 3.36
52 53 3.027974 GGTACAGATCCGAGGTAATGC 57.972 52.381 0.00 0.00 0.00 3.56
53 54 2.288886 GGTACAGATCCGAGGTAATGCC 60.289 54.545 0.00 0.00 37.58 4.40
54 55 1.496060 ACAGATCCGAGGTAATGCCA 58.504 50.000 0.00 0.00 40.61 4.92
55 56 2.050144 ACAGATCCGAGGTAATGCCAT 58.950 47.619 0.00 0.00 40.61 4.40
56 57 3.239449 ACAGATCCGAGGTAATGCCATA 58.761 45.455 0.00 0.00 40.61 2.74
57 58 3.840666 ACAGATCCGAGGTAATGCCATAT 59.159 43.478 0.00 0.00 40.61 1.78
58 59 4.287067 ACAGATCCGAGGTAATGCCATATT 59.713 41.667 0.00 0.00 40.61 1.28
59 60 4.633126 CAGATCCGAGGTAATGCCATATTG 59.367 45.833 0.00 0.00 40.61 1.90
60 61 2.778299 TCCGAGGTAATGCCATATTGC 58.222 47.619 0.00 0.00 40.61 3.56
61 62 1.812571 CCGAGGTAATGCCATATTGCC 59.187 52.381 0.00 0.00 40.61 4.52
62 63 1.812571 CGAGGTAATGCCATATTGCCC 59.187 52.381 3.61 0.00 40.61 5.36
63 64 2.553028 CGAGGTAATGCCATATTGCCCT 60.553 50.000 3.61 0.00 40.61 5.19
64 65 3.500343 GAGGTAATGCCATATTGCCCTT 58.500 45.455 3.61 0.00 40.61 3.95
65 66 3.500343 AGGTAATGCCATATTGCCCTTC 58.500 45.455 3.61 0.00 40.61 3.46
66 67 2.562738 GGTAATGCCATATTGCCCTTCC 59.437 50.000 0.00 0.00 37.17 3.46
67 68 2.781403 AATGCCATATTGCCCTTCCT 57.219 45.000 0.00 0.00 0.00 3.36
68 69 2.781403 ATGCCATATTGCCCTTCCTT 57.219 45.000 0.00 0.00 0.00 3.36
69 70 3.901570 ATGCCATATTGCCCTTCCTTA 57.098 42.857 0.00 0.00 0.00 2.69
70 71 3.901570 TGCCATATTGCCCTTCCTTAT 57.098 42.857 0.00 0.00 0.00 1.73
71 72 4.197559 TGCCATATTGCCCTTCCTTATT 57.802 40.909 0.00 0.00 0.00 1.40
72 73 4.151883 TGCCATATTGCCCTTCCTTATTC 58.848 43.478 0.00 0.00 0.00 1.75
73 74 3.511540 GCCATATTGCCCTTCCTTATTCC 59.488 47.826 0.00 0.00 0.00 3.01
74 75 4.089361 CCATATTGCCCTTCCTTATTCCC 58.911 47.826 0.00 0.00 0.00 3.97
75 76 2.775490 ATTGCCCTTCCTTATTCCCC 57.225 50.000 0.00 0.00 0.00 4.81
76 77 1.388174 TTGCCCTTCCTTATTCCCCA 58.612 50.000 0.00 0.00 0.00 4.96
77 78 1.619298 TGCCCTTCCTTATTCCCCAT 58.381 50.000 0.00 0.00 0.00 4.00
78 79 2.795556 TGCCCTTCCTTATTCCCCATA 58.204 47.619 0.00 0.00 0.00 2.74
79 80 2.445525 TGCCCTTCCTTATTCCCCATAC 59.554 50.000 0.00 0.00 0.00 2.39
80 81 2.445525 GCCCTTCCTTATTCCCCATACA 59.554 50.000 0.00 0.00 0.00 2.29
81 82 3.076032 GCCCTTCCTTATTCCCCATACAT 59.924 47.826 0.00 0.00 0.00 2.29
82 83 4.291249 GCCCTTCCTTATTCCCCATACATA 59.709 45.833 0.00 0.00 0.00 2.29
83 84 5.044105 GCCCTTCCTTATTCCCCATACATAT 60.044 44.000 0.00 0.00 0.00 1.78
84 85 6.426587 CCCTTCCTTATTCCCCATACATATG 58.573 44.000 0.00 0.00 0.00 1.78
85 86 6.011628 CCCTTCCTTATTCCCCATACATATGT 60.012 42.308 13.93 13.93 31.82 2.29
86 87 7.470192 CCTTCCTTATTCCCCATACATATGTT 58.530 38.462 14.77 0.00 31.82 2.71
87 88 8.611257 CCTTCCTTATTCCCCATACATATGTTA 58.389 37.037 14.77 0.60 31.82 2.41
88 89 9.449719 CTTCCTTATTCCCCATACATATGTTAC 57.550 37.037 14.77 0.00 31.82 2.50
89 90 8.751215 TCCTTATTCCCCATACATATGTTACT 57.249 34.615 14.77 0.00 31.82 2.24
90 91 9.846725 TCCTTATTCCCCATACATATGTTACTA 57.153 33.333 14.77 0.00 31.82 1.82
112 113 8.668510 ACTAATTAAGTTCCAGTATCATGCAG 57.331 34.615 0.00 0.00 33.35 4.41
113 114 8.486210 ACTAATTAAGTTCCAGTATCATGCAGA 58.514 33.333 0.00 0.00 33.35 4.26
114 115 9.499479 CTAATTAAGTTCCAGTATCATGCAGAT 57.501 33.333 0.00 0.00 40.86 2.90
115 116 7.741027 ATTAAGTTCCAGTATCATGCAGATG 57.259 36.000 8.40 0.00 37.57 2.90
116 117 3.474600 AGTTCCAGTATCATGCAGATGC 58.525 45.455 0.00 0.00 39.38 3.91
128 129 2.591066 GCAGATGCATCGCTTGTATC 57.409 50.000 25.89 7.76 45.01 2.24
133 134 4.708868 GATGCATCGCTTGTATCGTAAA 57.291 40.909 11.68 0.00 37.64 2.01
134 135 5.078153 GATGCATCGCTTGTATCGTAAAA 57.922 39.130 11.68 0.00 37.64 1.52
135 136 4.253352 TGCATCGCTTGTATCGTAAAAC 57.747 40.909 0.00 0.00 0.00 2.43
136 137 3.930229 TGCATCGCTTGTATCGTAAAACT 59.070 39.130 0.00 0.00 0.00 2.66
137 138 4.390603 TGCATCGCTTGTATCGTAAAACTT 59.609 37.500 0.00 0.00 0.00 2.66
138 139 5.106869 TGCATCGCTTGTATCGTAAAACTTT 60.107 36.000 0.00 0.00 0.00 2.66
139 140 5.793457 GCATCGCTTGTATCGTAAAACTTTT 59.207 36.000 0.00 0.00 0.00 2.27
140 141 6.236941 GCATCGCTTGTATCGTAAAACTTTTG 60.237 38.462 0.00 0.00 0.00 2.44
141 142 6.528014 TCGCTTGTATCGTAAAACTTTTGA 57.472 33.333 0.00 0.00 0.00 2.69
142 143 7.124347 TCGCTTGTATCGTAAAACTTTTGAT 57.876 32.000 0.00 0.00 0.00 2.57
143 144 7.012943 TCGCTTGTATCGTAAAACTTTTGATG 58.987 34.615 0.00 0.00 0.00 3.07
144 145 6.236941 CGCTTGTATCGTAAAACTTTTGATGC 60.237 38.462 0.00 0.00 0.00 3.91
145 146 6.580791 GCTTGTATCGTAAAACTTTTGATGCA 59.419 34.615 0.00 0.00 30.68 3.96
146 147 7.114247 GCTTGTATCGTAAAACTTTTGATGCAA 59.886 33.333 13.02 13.02 35.86 4.08
147 148 9.128107 CTTGTATCGTAAAACTTTTGATGCAAT 57.872 29.630 13.60 0.00 36.67 3.56
148 149 9.469807 TTGTATCGTAAAACTTTTGATGCAATT 57.530 25.926 11.07 0.00 34.69 2.32
149 150 9.469807 TGTATCGTAAAACTTTTGATGCAATTT 57.530 25.926 0.00 0.00 30.13 1.82
164 165 8.129161 TGATGCAATTTTATTTAATTCCAGCG 57.871 30.769 0.00 0.00 27.00 5.18
165 166 6.343226 TGCAATTTTATTTAATTCCAGCGC 57.657 33.333 0.00 0.00 0.00 5.92
166 167 6.105333 TGCAATTTTATTTAATTCCAGCGCT 58.895 32.000 2.64 2.64 0.00 5.92
167 168 7.261325 TGCAATTTTATTTAATTCCAGCGCTA 58.739 30.769 10.99 0.00 0.00 4.26
168 169 7.221838 TGCAATTTTATTTAATTCCAGCGCTAC 59.778 33.333 10.99 0.00 0.00 3.58
169 170 7.221838 GCAATTTTATTTAATTCCAGCGCTACA 59.778 33.333 10.99 0.00 0.00 2.74
170 171 9.248291 CAATTTTATTTAATTCCAGCGCTACAT 57.752 29.630 10.99 0.00 0.00 2.29
171 172 8.801715 ATTTTATTTAATTCCAGCGCTACATG 57.198 30.769 10.99 0.00 0.00 3.21
172 173 6.935741 TTATTTAATTCCAGCGCTACATGT 57.064 33.333 10.99 2.69 0.00 3.21
173 174 5.835113 ATTTAATTCCAGCGCTACATGTT 57.165 34.783 10.99 4.48 0.00 2.71
174 175 6.935741 ATTTAATTCCAGCGCTACATGTTA 57.064 33.333 10.99 3.43 0.00 2.41
175 176 6.935741 TTTAATTCCAGCGCTACATGTTAT 57.064 33.333 10.99 0.00 0.00 1.89
176 177 4.818534 AATTCCAGCGCTACATGTTATG 57.181 40.909 10.99 0.00 0.00 1.90
177 178 3.535280 TTCCAGCGCTACATGTTATGA 57.465 42.857 10.99 0.00 0.00 2.15
178 179 2.821546 TCCAGCGCTACATGTTATGAC 58.178 47.619 10.99 0.00 0.00 3.06
179 180 1.867233 CCAGCGCTACATGTTATGACC 59.133 52.381 10.99 0.00 0.00 4.02
180 181 2.483714 CCAGCGCTACATGTTATGACCT 60.484 50.000 10.99 0.00 0.00 3.85
181 182 2.797156 CAGCGCTACATGTTATGACCTC 59.203 50.000 10.99 0.00 0.00 3.85
182 183 2.135933 GCGCTACATGTTATGACCTCC 58.864 52.381 2.30 0.00 0.00 4.30
183 184 2.224066 GCGCTACATGTTATGACCTCCT 60.224 50.000 2.30 0.00 0.00 3.69
184 185 3.643763 CGCTACATGTTATGACCTCCTC 58.356 50.000 2.30 0.00 0.00 3.71
185 186 3.553096 CGCTACATGTTATGACCTCCTCC 60.553 52.174 2.30 0.00 0.00 4.30
186 187 3.388024 GCTACATGTTATGACCTCCTCCA 59.612 47.826 2.30 0.00 0.00 3.86
187 188 4.141711 GCTACATGTTATGACCTCCTCCAA 60.142 45.833 2.30 0.00 0.00 3.53
188 189 4.927267 ACATGTTATGACCTCCTCCAAA 57.073 40.909 0.00 0.00 0.00 3.28
189 190 5.255397 ACATGTTATGACCTCCTCCAAAA 57.745 39.130 0.00 0.00 0.00 2.44
190 191 5.831103 ACATGTTATGACCTCCTCCAAAAT 58.169 37.500 0.00 0.00 0.00 1.82
191 192 5.653769 ACATGTTATGACCTCCTCCAAAATG 59.346 40.000 0.00 0.00 0.00 2.32
192 193 5.255397 TGTTATGACCTCCTCCAAAATGT 57.745 39.130 0.00 0.00 0.00 2.71
193 194 6.381498 TGTTATGACCTCCTCCAAAATGTA 57.619 37.500 0.00 0.00 0.00 2.29
194 195 6.414732 TGTTATGACCTCCTCCAAAATGTAG 58.585 40.000 0.00 0.00 0.00 2.74
195 196 4.510167 ATGACCTCCTCCAAAATGTAGG 57.490 45.455 0.00 0.00 0.00 3.18
196 197 3.256704 TGACCTCCTCCAAAATGTAGGT 58.743 45.455 0.00 0.00 39.99 3.08
197 198 4.431378 TGACCTCCTCCAAAATGTAGGTA 58.569 43.478 0.00 0.00 37.47 3.08
198 199 5.036916 TGACCTCCTCCAAAATGTAGGTAT 58.963 41.667 0.00 0.00 37.47 2.73
199 200 6.206787 TGACCTCCTCCAAAATGTAGGTATA 58.793 40.000 0.00 0.00 37.47 1.47
200 201 6.849697 TGACCTCCTCCAAAATGTAGGTATAT 59.150 38.462 0.00 0.00 37.47 0.86
201 202 7.349859 TGACCTCCTCCAAAATGTAGGTATATT 59.650 37.037 0.00 0.00 37.47 1.28
202 203 7.746703 ACCTCCTCCAAAATGTAGGTATATTC 58.253 38.462 0.00 0.00 35.61 1.75
203 204 7.572861 ACCTCCTCCAAAATGTAGGTATATTCT 59.427 37.037 0.00 0.00 35.61 2.40
204 205 9.101325 CCTCCTCCAAAATGTAGGTATATTCTA 57.899 37.037 0.00 0.00 0.00 2.10
249 250 9.847224 ATATGTTAGTAACCTAGGGAACAATTG 57.153 33.333 14.81 3.24 0.00 2.32
250 251 5.941647 TGTTAGTAACCTAGGGAACAATTGC 59.058 40.000 14.81 0.45 0.00 3.56
251 252 3.964411 AGTAACCTAGGGAACAATTGCC 58.036 45.455 14.81 0.00 42.22 4.52
260 261 4.799564 GGGAACAATTGCCTACAAATGA 57.200 40.909 5.05 0.00 38.71 2.57
261 262 5.146010 GGGAACAATTGCCTACAAATGAA 57.854 39.130 5.05 0.00 38.71 2.57
262 263 5.546526 GGGAACAATTGCCTACAAATGAAA 58.453 37.500 5.05 0.00 38.71 2.69
263 264 6.172630 GGGAACAATTGCCTACAAATGAAAT 58.827 36.000 5.05 0.00 38.71 2.17
264 265 6.654582 GGGAACAATTGCCTACAAATGAAATT 59.345 34.615 5.05 0.00 38.71 1.82
265 266 7.174772 GGGAACAATTGCCTACAAATGAAATTT 59.825 33.333 5.05 0.00 42.09 1.82
281 282 7.888250 ATGAAATTTGAGTCTATTTCCTCCC 57.112 36.000 19.58 5.24 39.08 4.30
282 283 6.187682 TGAAATTTGAGTCTATTTCCTCCCC 58.812 40.000 19.58 4.77 39.08 4.81
283 284 4.797912 ATTTGAGTCTATTTCCTCCCCC 57.202 45.455 0.00 0.00 0.00 5.40
284 285 3.508952 TTGAGTCTATTTCCTCCCCCT 57.491 47.619 0.00 0.00 0.00 4.79
285 286 3.508952 TGAGTCTATTTCCTCCCCCTT 57.491 47.619 0.00 0.00 0.00 3.95
286 287 3.385115 TGAGTCTATTTCCTCCCCCTTC 58.615 50.000 0.00 0.00 0.00 3.46
287 288 3.246350 TGAGTCTATTTCCTCCCCCTTCA 60.246 47.826 0.00 0.00 0.00 3.02
288 289 3.388913 AGTCTATTTCCTCCCCCTTCAG 58.611 50.000 0.00 0.00 0.00 3.02
289 290 2.127708 TCTATTTCCTCCCCCTTCAGC 58.872 52.381 0.00 0.00 0.00 4.26
290 291 1.846439 CTATTTCCTCCCCCTTCAGCA 59.154 52.381 0.00 0.00 0.00 4.41
291 292 0.627986 ATTTCCTCCCCCTTCAGCAG 59.372 55.000 0.00 0.00 0.00 4.24
292 293 0.475632 TTTCCTCCCCCTTCAGCAGA 60.476 55.000 0.00 0.00 0.00 4.26
293 294 0.911525 TTCCTCCCCCTTCAGCAGAG 60.912 60.000 0.00 0.00 0.00 3.35
294 295 2.588989 CTCCCCCTTCAGCAGAGC 59.411 66.667 0.00 0.00 0.00 4.09
295 296 2.203983 TCCCCCTTCAGCAGAGCA 60.204 61.111 0.00 0.00 0.00 4.26
296 297 2.045536 CCCCCTTCAGCAGAGCAC 60.046 66.667 0.00 0.00 0.00 4.40
297 298 2.045536 CCCCTTCAGCAGAGCACC 60.046 66.667 0.00 0.00 0.00 5.01
298 299 2.752358 CCCTTCAGCAGAGCACCA 59.248 61.111 0.00 0.00 0.00 4.17
299 300 1.673665 CCCTTCAGCAGAGCACCAC 60.674 63.158 0.00 0.00 0.00 4.16
300 301 1.071987 CCTTCAGCAGAGCACCACA 59.928 57.895 0.00 0.00 0.00 4.17
301 302 0.322277 CCTTCAGCAGAGCACCACAT 60.322 55.000 0.00 0.00 0.00 3.21
302 303 1.085091 CTTCAGCAGAGCACCACATC 58.915 55.000 0.00 0.00 0.00 3.06
303 304 0.689055 TTCAGCAGAGCACCACATCT 59.311 50.000 0.00 0.00 0.00 2.90
304 305 0.689055 TCAGCAGAGCACCACATCTT 59.311 50.000 0.00 0.00 0.00 2.40
305 306 1.085091 CAGCAGAGCACCACATCTTC 58.915 55.000 0.00 0.00 0.00 2.87
306 307 0.035630 AGCAGAGCACCACATCTTCC 60.036 55.000 0.00 0.00 0.00 3.46
307 308 0.035630 GCAGAGCACCACATCTTCCT 60.036 55.000 0.00 0.00 0.00 3.36
308 309 1.612726 GCAGAGCACCACATCTTCCTT 60.613 52.381 0.00 0.00 0.00 3.36
309 310 2.787994 CAGAGCACCACATCTTCCTTT 58.212 47.619 0.00 0.00 0.00 3.11
310 311 3.869912 GCAGAGCACCACATCTTCCTTTA 60.870 47.826 0.00 0.00 0.00 1.85
311 312 4.521146 CAGAGCACCACATCTTCCTTTAT 58.479 43.478 0.00 0.00 0.00 1.40
312 313 4.946157 CAGAGCACCACATCTTCCTTTATT 59.054 41.667 0.00 0.00 0.00 1.40
313 314 5.065731 CAGAGCACCACATCTTCCTTTATTC 59.934 44.000 0.00 0.00 0.00 1.75
314 315 3.941483 AGCACCACATCTTCCTTTATTCG 59.059 43.478 0.00 0.00 0.00 3.34
315 316 3.938963 GCACCACATCTTCCTTTATTCGA 59.061 43.478 0.00 0.00 0.00 3.71
316 317 4.034510 GCACCACATCTTCCTTTATTCGAG 59.965 45.833 0.00 0.00 0.00 4.04
317 318 5.178797 CACCACATCTTCCTTTATTCGAGT 58.821 41.667 0.00 0.00 0.00 4.18
318 319 5.292101 CACCACATCTTCCTTTATTCGAGTC 59.708 44.000 0.00 0.00 0.00 3.36
319 320 5.187967 ACCACATCTTCCTTTATTCGAGTCT 59.812 40.000 0.00 0.00 0.00 3.24
320 321 6.109359 CCACATCTTCCTTTATTCGAGTCTT 58.891 40.000 0.00 0.00 0.00 3.01
321 322 6.595716 CCACATCTTCCTTTATTCGAGTCTTT 59.404 38.462 0.00 0.00 0.00 2.52
322 323 7.119846 CCACATCTTCCTTTATTCGAGTCTTTT 59.880 37.037 0.00 0.00 0.00 2.27
323 324 8.507249 CACATCTTCCTTTATTCGAGTCTTTTT 58.493 33.333 0.00 0.00 0.00 1.94
345 346 5.873179 TTCAACAGAATTATGGAACGTCC 57.127 39.130 4.88 0.00 36.96 4.79
346 347 3.930229 TCAACAGAATTATGGAACGTCCG 59.070 43.478 4.88 0.00 40.17 4.79
347 348 3.880047 ACAGAATTATGGAACGTCCGA 57.120 42.857 4.88 0.00 40.17 4.55
348 349 3.782046 ACAGAATTATGGAACGTCCGAG 58.218 45.455 4.88 0.00 40.17 4.63
349 350 2.540101 CAGAATTATGGAACGTCCGAGC 59.460 50.000 0.00 0.00 40.17 5.03
350 351 2.431057 AGAATTATGGAACGTCCGAGCT 59.569 45.455 0.00 0.00 40.17 4.09
351 352 2.225068 ATTATGGAACGTCCGAGCTG 57.775 50.000 0.00 0.00 40.17 4.24
352 353 0.892755 TTATGGAACGTCCGAGCTGT 59.107 50.000 0.00 0.00 40.17 4.40
353 354 0.892755 TATGGAACGTCCGAGCTGTT 59.107 50.000 0.00 0.00 40.17 3.16
354 355 0.670546 ATGGAACGTCCGAGCTGTTG 60.671 55.000 0.00 0.00 40.17 3.33
355 356 2.668280 GGAACGTCCGAGCTGTTGC 61.668 63.158 0.00 0.00 40.05 4.17
371 372 6.249035 GCTGTTGCTGTTTTAACTATACCA 57.751 37.500 0.00 0.00 36.03 3.25
372 373 6.084277 GCTGTTGCTGTTTTAACTATACCAC 58.916 40.000 0.00 0.00 36.03 4.16
373 374 6.293735 GCTGTTGCTGTTTTAACTATACCACA 60.294 38.462 0.00 0.00 36.03 4.17
374 375 7.197071 TGTTGCTGTTTTAACTATACCACAG 57.803 36.000 0.00 0.00 35.71 3.66
375 376 6.205853 TGTTGCTGTTTTAACTATACCACAGG 59.794 38.462 0.00 0.00 33.64 4.00
376 377 6.116711 TGCTGTTTTAACTATACCACAGGA 57.883 37.500 0.00 0.00 33.64 3.86
377 378 6.535540 TGCTGTTTTAACTATACCACAGGAA 58.464 36.000 0.00 0.00 33.64 3.36
378 379 7.172342 TGCTGTTTTAACTATACCACAGGAAT 58.828 34.615 0.00 0.00 33.64 3.01
379 380 8.322828 TGCTGTTTTAACTATACCACAGGAATA 58.677 33.333 0.00 0.00 33.64 1.75
380 381 9.169592 GCTGTTTTAACTATACCACAGGAATAA 57.830 33.333 0.00 0.00 33.64 1.40
407 408 2.517609 GACCAATCCGGGCTAGACT 58.482 57.895 0.00 0.00 41.26 3.24
408 409 1.700955 GACCAATCCGGGCTAGACTA 58.299 55.000 0.00 0.00 41.26 2.59
409 410 1.614413 GACCAATCCGGGCTAGACTAG 59.386 57.143 0.00 5.03 41.26 2.57
421 422 4.674281 GCTAGACTAGCCTGTTGGTATT 57.326 45.455 21.82 0.00 45.95 1.89
422 423 5.786264 GCTAGACTAGCCTGTTGGTATTA 57.214 43.478 21.82 0.00 45.95 0.98
423 424 6.347859 GCTAGACTAGCCTGTTGGTATTAT 57.652 41.667 21.82 0.00 45.95 1.28
424 425 6.760291 GCTAGACTAGCCTGTTGGTATTATT 58.240 40.000 21.82 0.00 45.95 1.40
425 426 7.217906 GCTAGACTAGCCTGTTGGTATTATTT 58.782 38.462 21.82 0.00 45.95 1.40
426 427 7.715686 GCTAGACTAGCCTGTTGGTATTATTTT 59.284 37.037 21.82 0.00 45.95 1.82
429 430 8.989131 AGACTAGCCTGTTGGTATTATTTTAGA 58.011 33.333 0.00 0.00 35.27 2.10
430 431 8.959705 ACTAGCCTGTTGGTATTATTTTAGAC 57.040 34.615 0.00 0.00 35.27 2.59
431 432 8.769359 ACTAGCCTGTTGGTATTATTTTAGACT 58.231 33.333 0.00 0.00 35.27 3.24
434 435 9.392259 AGCCTGTTGGTATTATTTTAGACTAAC 57.608 33.333 0.00 0.00 34.81 2.34
435 436 8.618677 GCCTGTTGGTATTATTTTAGACTAACC 58.381 37.037 0.00 0.00 33.70 2.85
458 459 1.341482 TGCAGGAGGACTAGGTCAGAG 60.341 57.143 0.00 0.00 33.68 3.35
487 492 5.366768 CCACCATGGGTTCTATTCTTCTCTA 59.633 44.000 18.09 0.00 31.02 2.43
1998 7555 9.205719 CATTTCAAACATTCCATGACATTTGTA 57.794 29.630 0.00 0.00 30.40 2.41
2221 7778 5.640732 CATCTACAACCACATTAGCCAAAC 58.359 41.667 0.00 0.00 0.00 2.93
2243 7800 3.264450 CCTTACCCCTGAGACATCAAAGT 59.736 47.826 0.00 0.00 34.23 2.66
2321 7878 5.333645 CCAAGATTTGTTCTTCGTGAGACTG 60.334 44.000 0.00 0.00 42.98 3.51
2334 7891 4.088648 CGTGAGACTGAACAACAACAAAC 58.911 43.478 0.00 0.00 0.00 2.93
2405 7972 0.402504 ATAGAAACCACGGCCCAACA 59.597 50.000 0.00 0.00 0.00 3.33
2409 7976 2.648613 AAACCACGGCCCAACATGGA 62.649 55.000 10.66 0.00 40.96 3.41
2410 7977 3.061848 CCACGGCCCAACATGGAC 61.062 66.667 0.00 0.00 40.96 4.02
2450 8017 2.387445 CGCGCGGTCTCATTTCCAA 61.387 57.895 24.84 0.00 0.00 3.53
2508 8075 3.059472 GACAGACGCATCGCACGTG 62.059 63.158 12.28 12.28 45.24 4.49
2526 8093 0.323302 TGCGCTTGTTGTCCATCCTA 59.677 50.000 9.73 0.00 0.00 2.94
2568 8135 2.367486 ACGACCAGCTCCTAGTACTTC 58.633 52.381 0.00 0.00 0.00 3.01
2584 8151 5.839621 AGTACTTCTAAATGTCACACGTGT 58.160 37.500 17.22 17.22 0.00 4.49
2653 8238 1.213296 CAGTAACCCTAGCCCACCAT 58.787 55.000 0.00 0.00 0.00 3.55
2700 8285 3.371063 GGGAGCACGACCACGAGA 61.371 66.667 0.00 0.00 42.66 4.04
2714 8299 2.265182 CGAGATCGGCTCCTCCTCC 61.265 68.421 0.00 0.00 40.70 4.30
2715 8300 1.152652 GAGATCGGCTCCTCCTCCA 60.153 63.158 0.00 0.00 37.69 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.891936 TGATGCTCATGCCGCGTC 60.892 61.111 17.15 17.15 42.33 5.19
2 3 3.945434 GGTGATGCTCATGCCGCG 61.945 66.667 0.00 0.00 38.71 6.46
3 4 3.945434 CGGTGATGCTCATGCCGC 61.945 66.667 8.70 0.00 38.71 6.53
4 5 2.202919 TCGGTGATGCTCATGCCG 60.203 61.111 13.02 13.02 43.32 5.69
5 6 2.541120 GCTCGGTGATGCTCATGCC 61.541 63.158 0.00 0.00 38.71 4.40
6 7 2.879070 CGCTCGGTGATGCTCATGC 61.879 63.158 0.00 0.00 40.20 4.06
7 8 2.879070 GCGCTCGGTGATGCTCATG 61.879 63.158 0.00 0.00 0.00 3.07
8 9 2.587194 GCGCTCGGTGATGCTCAT 60.587 61.111 0.00 0.00 0.00 2.90
9 10 4.819761 GGCGCTCGGTGATGCTCA 62.820 66.667 7.64 0.00 0.00 4.26
32 33 2.288886 GGCATTACCTCGGATCTGTACC 60.289 54.545 0.42 0.00 34.51 3.34
33 34 2.364324 TGGCATTACCTCGGATCTGTAC 59.636 50.000 0.42 0.00 40.22 2.90
34 35 2.673258 TGGCATTACCTCGGATCTGTA 58.327 47.619 0.42 0.00 40.22 2.74
35 36 1.496060 TGGCATTACCTCGGATCTGT 58.504 50.000 0.42 0.00 40.22 3.41
36 37 2.847327 ATGGCATTACCTCGGATCTG 57.153 50.000 0.00 0.00 40.22 2.90
37 38 4.836825 CAATATGGCATTACCTCGGATCT 58.163 43.478 4.78 0.00 40.22 2.75
38 39 3.375299 GCAATATGGCATTACCTCGGATC 59.625 47.826 4.78 0.00 40.22 3.36
39 40 3.347216 GCAATATGGCATTACCTCGGAT 58.653 45.455 4.78 0.00 40.22 4.18
40 41 2.552155 GGCAATATGGCATTACCTCGGA 60.552 50.000 4.78 0.00 43.14 4.55
41 42 1.812571 GGCAATATGGCATTACCTCGG 59.187 52.381 4.78 0.00 43.14 4.63
42 43 1.812571 GGGCAATATGGCATTACCTCG 59.187 52.381 4.78 0.00 45.76 4.63
43 44 3.160679 AGGGCAATATGGCATTACCTC 57.839 47.619 4.78 0.00 45.76 3.85
44 45 3.500343 GAAGGGCAATATGGCATTACCT 58.500 45.455 4.78 3.84 46.73 3.08
45 46 2.562738 GGAAGGGCAATATGGCATTACC 59.437 50.000 4.78 2.14 46.73 2.85
46 47 3.500343 AGGAAGGGCAATATGGCATTAC 58.500 45.455 4.78 5.50 46.73 1.89
47 48 3.901570 AGGAAGGGCAATATGGCATTA 57.098 42.857 4.78 0.00 46.73 1.90
49 50 2.781403 AAGGAAGGGCAATATGGCAT 57.219 45.000 4.88 4.88 45.76 4.40
50 51 3.901570 ATAAGGAAGGGCAATATGGCA 57.098 42.857 4.05 0.00 45.76 4.92
51 52 3.511540 GGAATAAGGAAGGGCAATATGGC 59.488 47.826 0.00 0.00 42.88 4.40
52 53 4.089361 GGGAATAAGGAAGGGCAATATGG 58.911 47.826 0.00 0.00 0.00 2.74
53 54 4.089361 GGGGAATAAGGAAGGGCAATATG 58.911 47.826 0.00 0.00 0.00 1.78
54 55 3.732204 TGGGGAATAAGGAAGGGCAATAT 59.268 43.478 0.00 0.00 0.00 1.28
55 56 3.135279 TGGGGAATAAGGAAGGGCAATA 58.865 45.455 0.00 0.00 0.00 1.90
56 57 1.936631 TGGGGAATAAGGAAGGGCAAT 59.063 47.619 0.00 0.00 0.00 3.56
57 58 1.388174 TGGGGAATAAGGAAGGGCAA 58.612 50.000 0.00 0.00 0.00 4.52
58 59 1.619298 ATGGGGAATAAGGAAGGGCA 58.381 50.000 0.00 0.00 0.00 5.36
59 60 2.445525 TGTATGGGGAATAAGGAAGGGC 59.554 50.000 0.00 0.00 0.00 5.19
60 61 6.011628 ACATATGTATGGGGAATAAGGAAGGG 60.012 42.308 6.56 0.00 38.00 3.95
61 62 7.032598 ACATATGTATGGGGAATAAGGAAGG 57.967 40.000 6.56 0.00 38.00 3.46
62 63 9.449719 GTAACATATGTATGGGGAATAAGGAAG 57.550 37.037 9.21 0.00 38.00 3.46
63 64 9.177927 AGTAACATATGTATGGGGAATAAGGAA 57.822 33.333 9.21 0.00 38.00 3.36
64 65 8.751215 AGTAACATATGTATGGGGAATAAGGA 57.249 34.615 9.21 0.00 38.00 3.36
86 87 9.764363 CTGCATGATACTGGAACTTAATTAGTA 57.236 33.333 0.00 0.00 35.54 1.82
87 88 8.486210 TCTGCATGATACTGGAACTTAATTAGT 58.514 33.333 0.00 0.00 39.32 2.24
88 89 8.893219 TCTGCATGATACTGGAACTTAATTAG 57.107 34.615 0.00 0.00 0.00 1.73
89 90 9.276590 CATCTGCATGATACTGGAACTTAATTA 57.723 33.333 0.00 0.00 33.36 1.40
90 91 7.255381 GCATCTGCATGATACTGGAACTTAATT 60.255 37.037 0.00 0.00 41.59 1.40
91 92 6.206243 GCATCTGCATGATACTGGAACTTAAT 59.794 38.462 0.00 0.00 41.59 1.40
92 93 5.528690 GCATCTGCATGATACTGGAACTTAA 59.471 40.000 0.00 0.00 41.59 1.85
93 94 5.059161 GCATCTGCATGATACTGGAACTTA 58.941 41.667 0.00 0.00 41.59 2.24
94 95 3.881688 GCATCTGCATGATACTGGAACTT 59.118 43.478 0.00 0.00 41.59 2.66
95 96 3.474600 GCATCTGCATGATACTGGAACT 58.525 45.455 0.00 0.00 41.59 3.01
96 97 3.892918 GCATCTGCATGATACTGGAAC 57.107 47.619 0.00 0.00 41.59 3.62
109 110 1.136419 CGATACAAGCGATGCATCTGC 60.136 52.381 25.86 25.86 42.50 4.26
110 111 2.130395 ACGATACAAGCGATGCATCTG 58.870 47.619 23.73 17.34 30.72 2.90
111 112 2.515926 ACGATACAAGCGATGCATCT 57.484 45.000 23.73 7.83 30.72 2.90
112 113 4.708868 TTTACGATACAAGCGATGCATC 57.291 40.909 17.10 17.10 0.00 3.91
113 114 4.570772 AGTTTTACGATACAAGCGATGCAT 59.429 37.500 0.00 0.00 0.00 3.96
114 115 3.930229 AGTTTTACGATACAAGCGATGCA 59.070 39.130 0.00 0.00 0.00 3.96
115 116 4.516092 AGTTTTACGATACAAGCGATGC 57.484 40.909 0.00 0.00 0.00 3.91
116 117 7.012943 TCAAAAGTTTTACGATACAAGCGATG 58.987 34.615 0.00 0.00 0.00 3.84
117 118 7.124347 TCAAAAGTTTTACGATACAAGCGAT 57.876 32.000 0.00 0.00 0.00 4.58
118 119 6.528014 TCAAAAGTTTTACGATACAAGCGA 57.472 33.333 0.00 0.00 0.00 4.93
119 120 6.236941 GCATCAAAAGTTTTACGATACAAGCG 60.237 38.462 0.00 0.00 0.00 4.68
120 121 6.580791 TGCATCAAAAGTTTTACGATACAAGC 59.419 34.615 0.00 2.13 0.00 4.01
121 122 8.500837 TTGCATCAAAAGTTTTACGATACAAG 57.499 30.769 0.00 0.00 0.00 3.16
122 123 9.469807 AATTGCATCAAAAGTTTTACGATACAA 57.530 25.926 12.93 12.93 0.00 2.41
123 124 9.469807 AAATTGCATCAAAAGTTTTACGATACA 57.530 25.926 0.00 0.00 0.00 2.29
138 139 8.602328 CGCTGGAATTAAATAAAATTGCATCAA 58.398 29.630 4.36 0.00 43.41 2.57
139 140 7.254387 GCGCTGGAATTAAATAAAATTGCATCA 60.254 33.333 0.00 0.00 43.41 3.07
140 141 7.042523 AGCGCTGGAATTAAATAAAATTGCATC 60.043 33.333 10.39 0.66 43.41 3.91
141 142 6.762661 AGCGCTGGAATTAAATAAAATTGCAT 59.237 30.769 10.39 0.00 43.41 3.96
142 143 6.105333 AGCGCTGGAATTAAATAAAATTGCA 58.895 32.000 10.39 3.95 42.59 4.08
143 144 6.588348 AGCGCTGGAATTAAATAAAATTGC 57.412 33.333 10.39 0.00 37.60 3.56
144 145 8.627487 TGTAGCGCTGGAATTAAATAAAATTG 57.373 30.769 22.90 0.00 0.00 2.32
145 146 9.248291 CATGTAGCGCTGGAATTAAATAAAATT 57.752 29.630 22.90 0.00 0.00 1.82
146 147 8.413229 ACATGTAGCGCTGGAATTAAATAAAAT 58.587 29.630 22.90 0.00 0.00 1.82
147 148 7.767261 ACATGTAGCGCTGGAATTAAATAAAA 58.233 30.769 22.90 0.00 0.00 1.52
148 149 7.328277 ACATGTAGCGCTGGAATTAAATAAA 57.672 32.000 22.90 0.00 0.00 1.40
149 150 6.935741 ACATGTAGCGCTGGAATTAAATAA 57.064 33.333 22.90 0.00 0.00 1.40
150 151 6.935741 AACATGTAGCGCTGGAATTAAATA 57.064 33.333 22.90 0.00 0.00 1.40
151 152 5.835113 AACATGTAGCGCTGGAATTAAAT 57.165 34.783 22.90 0.00 0.00 1.40
152 153 6.540551 TCATAACATGTAGCGCTGGAATTAAA 59.459 34.615 22.90 0.00 0.00 1.52
153 154 6.018262 GTCATAACATGTAGCGCTGGAATTAA 60.018 38.462 22.90 0.67 0.00 1.40
154 155 5.465390 GTCATAACATGTAGCGCTGGAATTA 59.535 40.000 22.90 12.29 0.00 1.40
155 156 4.273480 GTCATAACATGTAGCGCTGGAATT 59.727 41.667 22.90 10.40 0.00 2.17
156 157 3.809832 GTCATAACATGTAGCGCTGGAAT 59.190 43.478 22.90 7.89 0.00 3.01
157 158 3.194861 GTCATAACATGTAGCGCTGGAA 58.805 45.455 22.90 5.45 0.00 3.53
158 159 2.483013 GGTCATAACATGTAGCGCTGGA 60.483 50.000 22.90 6.39 0.00 3.86
159 160 1.867233 GGTCATAACATGTAGCGCTGG 59.133 52.381 22.90 9.45 0.00 4.85
160 161 2.797156 GAGGTCATAACATGTAGCGCTG 59.203 50.000 22.90 6.48 0.00 5.18
161 162 2.224066 GGAGGTCATAACATGTAGCGCT 60.224 50.000 17.26 17.26 0.00 5.92
162 163 2.135933 GGAGGTCATAACATGTAGCGC 58.864 52.381 0.00 0.00 0.00 5.92
163 164 3.553096 GGAGGAGGTCATAACATGTAGCG 60.553 52.174 0.00 0.00 0.00 4.26
164 165 3.388024 TGGAGGAGGTCATAACATGTAGC 59.612 47.826 0.00 0.00 0.00 3.58
165 166 5.614324 TTGGAGGAGGTCATAACATGTAG 57.386 43.478 0.00 0.00 0.00 2.74
166 167 6.381498 TTTTGGAGGAGGTCATAACATGTA 57.619 37.500 0.00 0.00 0.00 2.29
167 168 4.927267 TTTGGAGGAGGTCATAACATGT 57.073 40.909 0.00 0.00 0.00 3.21
168 169 5.653769 ACATTTTGGAGGAGGTCATAACATG 59.346 40.000 0.00 0.00 0.00 3.21
169 170 5.831103 ACATTTTGGAGGAGGTCATAACAT 58.169 37.500 0.00 0.00 0.00 2.71
170 171 5.255397 ACATTTTGGAGGAGGTCATAACA 57.745 39.130 0.00 0.00 0.00 2.41
171 172 6.927294 CTACATTTTGGAGGAGGTCATAAC 57.073 41.667 0.00 0.00 0.00 1.89
223 224 9.847224 CAATTGTTCCCTAGGTTACTAACATAT 57.153 33.333 8.29 4.74 0.00 1.78
224 225 7.771826 GCAATTGTTCCCTAGGTTACTAACATA 59.228 37.037 8.29 0.00 0.00 2.29
225 226 6.602009 GCAATTGTTCCCTAGGTTACTAACAT 59.398 38.462 8.29 0.00 0.00 2.71
226 227 5.941647 GCAATTGTTCCCTAGGTTACTAACA 59.058 40.000 8.29 7.31 0.00 2.41
227 228 5.356190 GGCAATTGTTCCCTAGGTTACTAAC 59.644 44.000 8.29 4.86 0.00 2.34
228 229 5.252164 AGGCAATTGTTCCCTAGGTTACTAA 59.748 40.000 8.29 3.58 0.00 2.24
229 230 4.786454 AGGCAATTGTTCCCTAGGTTACTA 59.214 41.667 8.29 2.71 0.00 1.82
230 231 3.591977 AGGCAATTGTTCCCTAGGTTACT 59.408 43.478 8.29 0.00 0.00 2.24
231 232 3.964411 AGGCAATTGTTCCCTAGGTTAC 58.036 45.455 8.29 5.81 0.00 2.50
232 233 4.536888 TGTAGGCAATTGTTCCCTAGGTTA 59.463 41.667 8.29 0.00 32.19 2.85
233 234 3.332485 TGTAGGCAATTGTTCCCTAGGTT 59.668 43.478 8.29 0.00 32.19 3.50
234 235 2.916934 TGTAGGCAATTGTTCCCTAGGT 59.083 45.455 8.29 0.00 32.19 3.08
235 236 3.644966 TGTAGGCAATTGTTCCCTAGG 57.355 47.619 7.40 0.06 32.19 3.02
236 237 5.652014 TCATTTGTAGGCAATTGTTCCCTAG 59.348 40.000 7.40 0.00 37.30 3.02
237 238 5.575157 TCATTTGTAGGCAATTGTTCCCTA 58.425 37.500 7.40 6.75 37.30 3.53
238 239 4.415596 TCATTTGTAGGCAATTGTTCCCT 58.584 39.130 7.40 7.76 37.30 4.20
239 240 4.799564 TCATTTGTAGGCAATTGTTCCC 57.200 40.909 7.40 0.00 37.30 3.97
240 241 7.671495 AATTTCATTTGTAGGCAATTGTTCC 57.329 32.000 7.40 0.30 37.30 3.62
241 242 8.938047 CAAATTTCATTTGTAGGCAATTGTTC 57.062 30.769 7.40 0.08 43.47 3.18
255 256 8.753133 GGGAGGAAATAGACTCAAATTTCATTT 58.247 33.333 14.25 0.00 41.70 2.32
256 257 7.343057 GGGGAGGAAATAGACTCAAATTTCATT 59.657 37.037 14.25 6.25 41.70 2.57
257 258 6.836007 GGGGAGGAAATAGACTCAAATTTCAT 59.164 38.462 14.25 9.79 41.70 2.57
258 259 6.187682 GGGGAGGAAATAGACTCAAATTTCA 58.812 40.000 14.25 0.00 41.70 2.69
259 260 5.594725 GGGGGAGGAAATAGACTCAAATTTC 59.405 44.000 7.75 7.75 40.03 2.17
260 261 5.256389 AGGGGGAGGAAATAGACTCAAATTT 59.744 40.000 0.00 0.00 35.45 1.82
261 262 4.796265 AGGGGGAGGAAATAGACTCAAATT 59.204 41.667 0.00 0.00 35.45 1.82
262 263 4.384465 AGGGGGAGGAAATAGACTCAAAT 58.616 43.478 0.00 0.00 35.45 2.32
263 264 3.815507 AGGGGGAGGAAATAGACTCAAA 58.184 45.455 0.00 0.00 35.45 2.69
264 265 3.508952 AGGGGGAGGAAATAGACTCAA 57.491 47.619 0.00 0.00 35.45 3.02
265 266 3.246350 TGAAGGGGGAGGAAATAGACTCA 60.246 47.826 0.00 0.00 35.45 3.41
266 267 3.385115 TGAAGGGGGAGGAAATAGACTC 58.615 50.000 0.00 0.00 0.00 3.36
267 268 3.388913 CTGAAGGGGGAGGAAATAGACT 58.611 50.000 0.00 0.00 0.00 3.24
268 269 2.158740 GCTGAAGGGGGAGGAAATAGAC 60.159 54.545 0.00 0.00 0.00 2.59
269 270 2.127708 GCTGAAGGGGGAGGAAATAGA 58.872 52.381 0.00 0.00 0.00 1.98
270 271 1.846439 TGCTGAAGGGGGAGGAAATAG 59.154 52.381 0.00 0.00 0.00 1.73
271 272 1.846439 CTGCTGAAGGGGGAGGAAATA 59.154 52.381 0.00 0.00 0.00 1.40
272 273 0.627986 CTGCTGAAGGGGGAGGAAAT 59.372 55.000 0.00 0.00 0.00 2.17
273 274 0.475632 TCTGCTGAAGGGGGAGGAAA 60.476 55.000 0.00 0.00 0.00 3.13
274 275 0.911525 CTCTGCTGAAGGGGGAGGAA 60.912 60.000 0.00 0.00 0.00 3.36
275 276 1.306482 CTCTGCTGAAGGGGGAGGA 60.306 63.158 0.00 0.00 0.00 3.71
276 277 3.041469 GCTCTGCTGAAGGGGGAGG 62.041 68.421 0.00 0.00 0.00 4.30
277 278 2.296365 TGCTCTGCTGAAGGGGGAG 61.296 63.158 0.00 0.00 0.00 4.30
278 279 2.203983 TGCTCTGCTGAAGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
279 280 2.045536 GTGCTCTGCTGAAGGGGG 60.046 66.667 0.00 0.00 0.00 5.40
280 281 2.045536 GGTGCTCTGCTGAAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
281 282 1.673665 GTGGTGCTCTGCTGAAGGG 60.674 63.158 0.00 0.00 0.00 3.95
282 283 0.322277 ATGTGGTGCTCTGCTGAAGG 60.322 55.000 0.00 0.00 0.00 3.46
283 284 1.085091 GATGTGGTGCTCTGCTGAAG 58.915 55.000 0.00 0.00 0.00 3.02
284 285 0.689055 AGATGTGGTGCTCTGCTGAA 59.311 50.000 0.00 0.00 0.00 3.02
285 286 0.689055 AAGATGTGGTGCTCTGCTGA 59.311 50.000 0.00 0.00 0.00 4.26
286 287 1.085091 GAAGATGTGGTGCTCTGCTG 58.915 55.000 0.00 0.00 0.00 4.41
287 288 0.035630 GGAAGATGTGGTGCTCTGCT 60.036 55.000 0.00 0.00 0.00 4.24
288 289 0.035630 AGGAAGATGTGGTGCTCTGC 60.036 55.000 0.00 0.00 0.00 4.26
289 290 2.486472 AAGGAAGATGTGGTGCTCTG 57.514 50.000 0.00 0.00 0.00 3.35
290 291 4.851639 ATAAAGGAAGATGTGGTGCTCT 57.148 40.909 0.00 0.00 0.00 4.09
291 292 4.034510 CGAATAAAGGAAGATGTGGTGCTC 59.965 45.833 0.00 0.00 0.00 4.26
292 293 3.941483 CGAATAAAGGAAGATGTGGTGCT 59.059 43.478 0.00 0.00 0.00 4.40
293 294 3.938963 TCGAATAAAGGAAGATGTGGTGC 59.061 43.478 0.00 0.00 0.00 5.01
294 295 5.178797 ACTCGAATAAAGGAAGATGTGGTG 58.821 41.667 0.00 0.00 0.00 4.17
295 296 5.187967 AGACTCGAATAAAGGAAGATGTGGT 59.812 40.000 0.00 0.00 0.00 4.16
296 297 5.665459 AGACTCGAATAAAGGAAGATGTGG 58.335 41.667 0.00 0.00 0.00 4.17
297 298 7.602517 AAAGACTCGAATAAAGGAAGATGTG 57.397 36.000 0.00 0.00 0.00 3.21
298 299 8.622948 AAAAAGACTCGAATAAAGGAAGATGT 57.377 30.769 0.00 0.00 0.00 3.06
320 321 7.142680 GGACGTTCCATAATTCTGTTGAAAAA 58.857 34.615 0.00 0.00 36.28 1.94
321 322 6.566942 CGGACGTTCCATAATTCTGTTGAAAA 60.567 38.462 0.00 0.00 35.91 2.29
322 323 5.106869 CGGACGTTCCATAATTCTGTTGAAA 60.107 40.000 0.00 0.00 35.91 2.69
323 324 4.390603 CGGACGTTCCATAATTCTGTTGAA 59.609 41.667 0.00 0.00 35.91 2.69
324 325 3.930229 CGGACGTTCCATAATTCTGTTGA 59.070 43.478 0.00 0.00 35.91 3.18
325 326 3.930229 TCGGACGTTCCATAATTCTGTTG 59.070 43.478 0.00 0.00 35.91 3.33
326 327 4.181578 CTCGGACGTTCCATAATTCTGTT 58.818 43.478 0.00 0.00 35.91 3.16
327 328 3.782046 CTCGGACGTTCCATAATTCTGT 58.218 45.455 0.00 0.00 35.91 3.41
328 329 2.540101 GCTCGGACGTTCCATAATTCTG 59.460 50.000 0.00 0.00 35.91 3.02
329 330 2.431057 AGCTCGGACGTTCCATAATTCT 59.569 45.455 0.00 0.00 35.91 2.40
330 331 2.540101 CAGCTCGGACGTTCCATAATTC 59.460 50.000 0.00 0.00 35.91 2.17
331 332 2.093658 ACAGCTCGGACGTTCCATAATT 60.094 45.455 0.00 0.00 35.91 1.40
332 333 1.480954 ACAGCTCGGACGTTCCATAAT 59.519 47.619 0.00 0.00 35.91 1.28
333 334 0.892755 ACAGCTCGGACGTTCCATAA 59.107 50.000 0.00 0.00 35.91 1.90
334 335 0.892755 AACAGCTCGGACGTTCCATA 59.107 50.000 0.00 0.00 35.91 2.74
335 336 0.670546 CAACAGCTCGGACGTTCCAT 60.671 55.000 0.00 0.00 35.91 3.41
336 337 1.300620 CAACAGCTCGGACGTTCCA 60.301 57.895 0.00 0.00 35.91 3.53
337 338 2.668280 GCAACAGCTCGGACGTTCC 61.668 63.158 0.00 0.00 0.00 3.62
338 339 1.664965 AGCAACAGCTCGGACGTTC 60.665 57.895 0.00 0.00 31.68 3.95
339 340 1.956170 CAGCAACAGCTCGGACGTT 60.956 57.895 0.00 0.00 36.19 3.99
340 341 2.356313 CAGCAACAGCTCGGACGT 60.356 61.111 0.00 0.00 36.19 4.34
341 342 1.498865 AAACAGCAACAGCTCGGACG 61.499 55.000 0.00 0.00 36.19 4.79
342 343 0.663153 AAAACAGCAACAGCTCGGAC 59.337 50.000 0.00 0.00 36.19 4.79
343 344 2.248280 TAAAACAGCAACAGCTCGGA 57.752 45.000 0.00 0.00 36.19 4.55
344 345 2.290641 AGTTAAAACAGCAACAGCTCGG 59.709 45.455 0.00 0.00 36.19 4.63
345 346 3.609103 AGTTAAAACAGCAACAGCTCG 57.391 42.857 0.00 0.00 36.19 5.03
346 347 6.148811 TGGTATAGTTAAAACAGCAACAGCTC 59.851 38.462 0.00 0.00 36.19 4.09
347 348 6.001460 TGGTATAGTTAAAACAGCAACAGCT 58.999 36.000 0.00 0.00 39.75 4.24
348 349 6.084277 GTGGTATAGTTAAAACAGCAACAGC 58.916 40.000 0.00 0.00 0.00 4.40
349 350 7.197071 TGTGGTATAGTTAAAACAGCAACAG 57.803 36.000 0.00 0.00 0.00 3.16
350 351 6.205853 CCTGTGGTATAGTTAAAACAGCAACA 59.794 38.462 0.00 0.00 34.95 3.33
351 352 6.428771 TCCTGTGGTATAGTTAAAACAGCAAC 59.571 38.462 0.00 0.00 34.95 4.17
352 353 6.535540 TCCTGTGGTATAGTTAAAACAGCAA 58.464 36.000 0.00 0.00 34.95 3.91
353 354 6.116711 TCCTGTGGTATAGTTAAAACAGCA 57.883 37.500 0.00 0.00 34.95 4.41
354 355 7.625828 ATTCCTGTGGTATAGTTAAAACAGC 57.374 36.000 0.00 0.00 34.95 4.40
381 382 1.824852 GCCCGGATTGGTCTCATTTTT 59.175 47.619 0.73 0.00 35.15 1.94
382 383 1.005924 AGCCCGGATTGGTCTCATTTT 59.994 47.619 0.73 0.00 35.15 1.82
383 384 0.625849 AGCCCGGATTGGTCTCATTT 59.374 50.000 0.73 0.00 35.15 2.32
384 385 1.417890 CTAGCCCGGATTGGTCTCATT 59.582 52.381 0.73 0.00 35.15 2.57
385 386 1.051812 CTAGCCCGGATTGGTCTCAT 58.948 55.000 0.73 0.00 35.15 2.90
386 387 0.032515 TCTAGCCCGGATTGGTCTCA 60.033 55.000 0.73 0.00 35.15 3.27
387 388 0.389757 GTCTAGCCCGGATTGGTCTC 59.610 60.000 0.73 0.00 35.15 3.36
388 389 0.032017 AGTCTAGCCCGGATTGGTCT 60.032 55.000 0.73 0.00 35.15 3.85
389 390 1.614413 CTAGTCTAGCCCGGATTGGTC 59.386 57.143 0.73 0.00 35.15 4.02
390 391 1.705873 CTAGTCTAGCCCGGATTGGT 58.294 55.000 0.73 0.00 35.15 3.67
391 392 0.318762 GCTAGTCTAGCCCGGATTGG 59.681 60.000 19.57 0.00 45.95 3.16
392 393 3.896317 GCTAGTCTAGCCCGGATTG 57.104 57.895 19.57 0.00 45.95 2.67
403 404 8.989131 TCTAAAATAATACCAACAGGCTAGTCT 58.011 33.333 0.00 0.00 0.00 3.24
404 405 9.043079 GTCTAAAATAATACCAACAGGCTAGTC 57.957 37.037 0.00 0.00 0.00 2.59
405 406 8.769359 AGTCTAAAATAATACCAACAGGCTAGT 58.231 33.333 0.00 0.00 0.00 2.57
408 409 9.392259 GTTAGTCTAAAATAATACCAACAGGCT 57.608 33.333 0.00 0.00 0.00 4.58
409 410 8.618677 GGTTAGTCTAAAATAATACCAACAGGC 58.381 37.037 0.00 0.00 0.00 4.85
410 411 9.117183 GGGTTAGTCTAAAATAATACCAACAGG 57.883 37.037 0.00 0.00 0.00 4.00
411 412 9.675464 TGGGTTAGTCTAAAATAATACCAACAG 57.325 33.333 0.00 0.00 0.00 3.16
414 415 9.127277 GCATGGGTTAGTCTAAAATAATACCAA 57.873 33.333 0.00 0.00 30.02 3.67
415 416 8.275758 TGCATGGGTTAGTCTAAAATAATACCA 58.724 33.333 0.00 0.00 0.00 3.25
416 417 8.685838 TGCATGGGTTAGTCTAAAATAATACC 57.314 34.615 0.00 0.00 0.00 2.73
417 418 8.784043 CCTGCATGGGTTAGTCTAAAATAATAC 58.216 37.037 0.00 0.00 0.00 1.89
418 419 8.719596 TCCTGCATGGGTTAGTCTAAAATAATA 58.280 33.333 0.00 0.00 36.20 0.98
419 420 7.582719 TCCTGCATGGGTTAGTCTAAAATAAT 58.417 34.615 0.00 0.00 36.20 1.28
420 421 6.964464 TCCTGCATGGGTTAGTCTAAAATAA 58.036 36.000 0.00 0.00 36.20 1.40
421 422 6.409234 CCTCCTGCATGGGTTAGTCTAAAATA 60.409 42.308 0.00 0.00 36.20 1.40
422 423 5.440610 CTCCTGCATGGGTTAGTCTAAAAT 58.559 41.667 0.00 0.00 36.20 1.82
423 424 4.324254 CCTCCTGCATGGGTTAGTCTAAAA 60.324 45.833 0.00 0.00 36.20 1.52
424 425 3.199946 CCTCCTGCATGGGTTAGTCTAAA 59.800 47.826 0.00 0.00 36.20 1.85
425 426 2.771943 CCTCCTGCATGGGTTAGTCTAA 59.228 50.000 0.00 0.00 36.20 2.10
426 427 2.023404 TCCTCCTGCATGGGTTAGTCTA 60.023 50.000 0.00 0.00 36.20 2.59
427 428 1.207791 CCTCCTGCATGGGTTAGTCT 58.792 55.000 0.00 0.00 36.20 3.24
428 429 1.134371 GTCCTCCTGCATGGGTTAGTC 60.134 57.143 0.00 0.00 36.20 2.59
429 430 0.912486 GTCCTCCTGCATGGGTTAGT 59.088 55.000 0.00 0.00 36.20 2.24
430 431 1.207791 AGTCCTCCTGCATGGGTTAG 58.792 55.000 0.00 0.00 36.20 2.34
431 432 2.398588 CTAGTCCTCCTGCATGGGTTA 58.601 52.381 0.00 0.00 36.20 2.85
432 433 1.207791 CTAGTCCTCCTGCATGGGTT 58.792 55.000 0.00 0.00 36.20 4.11
433 434 0.692419 CCTAGTCCTCCTGCATGGGT 60.692 60.000 0.00 0.00 36.20 4.51
434 435 0.692419 ACCTAGTCCTCCTGCATGGG 60.692 60.000 0.00 0.00 36.20 4.00
435 436 0.755686 GACCTAGTCCTCCTGCATGG 59.244 60.000 0.00 0.00 37.10 3.66
458 459 5.449553 AGAATAGAACCCATGGTGGAATTC 58.550 41.667 11.73 12.30 40.96 2.17
2013 7570 2.550978 CACTGCCCTTCTAACCATACG 58.449 52.381 0.00 0.00 0.00 3.06
2102 7659 0.605589 CTTTGAGAGACTGAGCCGGT 59.394 55.000 1.90 0.00 0.00 5.28
2221 7778 3.264450 ACTTTGATGTCTCAGGGGTAAGG 59.736 47.826 0.00 0.00 31.68 2.69
2243 7800 8.865090 ACAAGGTAACAAATGTAATCATGGAAA 58.135 29.630 0.00 0.00 41.41 3.13
2321 7878 5.713822 AGAGTAGACGTTTGTTGTTGTTC 57.286 39.130 0.00 0.00 0.00 3.18
2334 7891 2.034812 GGAGTTGCCCATAGAGTAGACG 59.965 54.545 0.00 0.00 0.00 4.18
2405 7972 3.186409 CGAAACGTGAAATGAGTGTCCAT 59.814 43.478 0.00 0.00 0.00 3.41
2508 8075 1.009829 CTAGGATGGACAACAAGCGC 58.990 55.000 0.00 0.00 0.00 5.92
2515 8082 1.622607 CGTGGGCCTAGGATGGACAA 61.623 60.000 14.75 0.00 36.67 3.18
2624 8191 2.751688 GGTTACTGTTGGCCGGGA 59.248 61.111 2.18 0.00 0.00 5.14
2628 8195 0.393944 GGCTAGGGTTACTGTTGGCC 60.394 60.000 0.00 0.00 0.00 5.36
2653 8238 2.020720 ACTTCCACAACATTGCGACAA 58.979 42.857 0.00 0.00 0.00 3.18
2700 8285 2.123077 CCTGGAGGAGGAGCCGAT 60.123 66.667 0.00 0.00 46.33 4.18


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

AutoCloner maintained by Alex Coulton.