Multiple sequence alignment - TraesCS2D01G204500

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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 TraesCS2D01G204500 chr2D 100.000 3953 0 0 1 3953 156598647 156594695 0.000000e+00 7300.0
1 TraesCS2D01G204500 chr2D 81.412 425 55 12 2875 3296 156711074 156710671 3.810000e-85 326.0
2 TraesCS2D01G204500 chr2A 93.605 3675 158 34 302 3953 166260305 166256685 0.000000e+00 5413.0
3 TraesCS2D01G204500 chr2A 80.238 420 57 13 2875 3291 166631690 166631294 3.860000e-75 292.0
4 TraesCS2D01G204500 chr2B 94.479 2735 113 16 302 3015 214287463 214284746 0.000000e+00 4180.0
5 TraesCS2D01G204500 chr2B 88.571 245 21 5 3527 3765 214284677 214284434 1.390000e-74 291.0
6 TraesCS2D01G204500 chr2B 91.753 97 5 1 3839 3935 214283477 214283384 8.910000e-27 132.0
7 TraesCS2D01G204500 chr2B 89.024 82 3 2 3758 3833 214283606 214283525 3.250000e-16 97.1
8 TraesCS2D01G204500 chr7B 92.857 280 19 1 27 305 378300238 378300517 4.760000e-109 405.0
9 TraesCS2D01G204500 chr7B 91.489 282 23 1 25 305 394068908 394068627 1.720000e-103 387.0
10 TraesCS2D01G204500 chr5D 92.500 280 20 1 27 305 365507608 365507329 2.210000e-107 399.0
11 TraesCS2D01G204500 chr1D 91.667 288 23 1 27 313 137147597 137147310 7.960000e-107 398.0
12 TraesCS2D01G204500 chr3D 92.446 278 20 1 29 305 222646143 222645866 2.860000e-106 396.0
13 TraesCS2D01G204500 chr3D 91.398 279 21 3 27 304 481394709 481394985 2.880000e-101 379.0
14 TraesCS2D01G204500 chr3D 100.000 33 0 0 842 874 554717659 554717691 1.190000e-05 62.1
15 TraesCS2D01G204500 chrUn 92.115 279 21 1 25 302 183138221 183137943 3.700000e-105 392.0
16 TraesCS2D01G204500 chr5A 91.519 283 22 2 23 304 126432799 126432518 4.790000e-104 388.0
17 TraesCS2D01G204500 chr6D 91.786 280 20 3 29 305 168723993 168723714 1.720000e-103 387.0


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 TraesCS2D01G204500 chr2D 156594695 156598647 3952 True 7300.000 7300 100.00000 1 3953 1 chr2D.!!$R1 3952
1 TraesCS2D01G204500 chr2A 166256685 166260305 3620 True 5413.000 5413 93.60500 302 3953 1 chr2A.!!$R1 3651
2 TraesCS2D01G204500 chr2B 214283384 214287463 4079 True 1175.025 4180 90.95675 302 3935 4 chr2B.!!$R1 3633

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
317 318 0.744771 GTCTTAGAGGGGGCAAAGCG 60.745 60.0 0.0 0.0 0.00 4.68 F
2103 2123 0.029681 ACTATGGGAGCCTGGTGGAT 60.030 55.0 0.0 0.0 34.57 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2192 0.804544 GCGCACCTAGCACATACGAA 60.805 55.0 0.3 0.0 46.13 3.85 R
3440 3469 0.107410 TGTCCGTGAACAGCAAGGTT 60.107 50.0 0.0 0.0 45.18 3.50 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
22 23 5.695851 CAAAGTCACAGGAACTAGCATTT 57.304 39.130 0.00 0.00 36.02 2.32
23 24 6.076981 CAAAGTCACAGGAACTAGCATTTT 57.923 37.500 0.00 0.00 36.02 1.82
24 25 7.202016 CAAAGTCACAGGAACTAGCATTTTA 57.798 36.000 0.00 0.00 36.02 1.52
25 26 7.301054 CAAAGTCACAGGAACTAGCATTTTAG 58.699 38.462 0.00 0.00 36.02 1.85
26 27 6.115448 AGTCACAGGAACTAGCATTTTAGT 57.885 37.500 0.00 0.00 36.02 2.24
27 28 6.534634 AGTCACAGGAACTAGCATTTTAGTT 58.465 36.000 0.00 0.00 44.38 2.24
28 29 7.676947 AGTCACAGGAACTAGCATTTTAGTTA 58.323 34.615 0.00 0.00 42.38 2.24
29 30 7.819900 AGTCACAGGAACTAGCATTTTAGTTAG 59.180 37.037 0.00 0.00 42.38 2.34
30 31 7.817962 GTCACAGGAACTAGCATTTTAGTTAGA 59.182 37.037 0.00 0.00 42.38 2.10
31 32 7.817962 TCACAGGAACTAGCATTTTAGTTAGAC 59.182 37.037 0.00 0.00 42.38 2.59
32 33 7.819900 CACAGGAACTAGCATTTTAGTTAGACT 59.180 37.037 0.00 0.00 42.38 3.24
33 34 9.032624 ACAGGAACTAGCATTTTAGTTAGACTA 57.967 33.333 0.00 0.00 42.38 2.59
34 35 9.303537 CAGGAACTAGCATTTTAGTTAGACTAC 57.696 37.037 0.00 0.00 42.38 2.73
35 36 8.476447 AGGAACTAGCATTTTAGTTAGACTACC 58.524 37.037 0.00 0.00 42.38 3.18
36 37 7.710044 GGAACTAGCATTTTAGTTAGACTACCC 59.290 40.741 0.00 0.00 42.38 3.69
37 38 7.729124 ACTAGCATTTTAGTTAGACTACCCA 57.271 36.000 0.00 0.00 29.72 4.51
38 39 7.554211 ACTAGCATTTTAGTTAGACTACCCAC 58.446 38.462 0.00 0.00 29.72 4.61
39 40 6.368779 AGCATTTTAGTTAGACTACCCACA 57.631 37.500 0.00 0.00 28.93 4.17
40 41 6.407202 AGCATTTTAGTTAGACTACCCACAG 58.593 40.000 0.00 0.00 28.93 3.66
41 42 6.013639 AGCATTTTAGTTAGACTACCCACAGT 60.014 38.462 0.00 0.00 28.93 3.55
42 43 6.092259 GCATTTTAGTTAGACTACCCACAGTG 59.908 42.308 0.00 0.00 28.93 3.66
43 44 5.733620 TTTAGTTAGACTACCCACAGTGG 57.266 43.478 13.35 13.35 37.25 4.00
58 59 6.090483 CCACAGTGGGAGTAACATAGATAG 57.910 45.833 12.40 0.00 32.67 2.08
59 60 5.598830 CCACAGTGGGAGTAACATAGATAGT 59.401 44.000 12.40 0.00 32.67 2.12
60 61 6.776116 CCACAGTGGGAGTAACATAGATAGTA 59.224 42.308 12.40 0.00 32.67 1.82
61 62 7.287005 CCACAGTGGGAGTAACATAGATAGTAA 59.713 40.741 12.40 0.00 32.67 2.24
62 63 8.136165 CACAGTGGGAGTAACATAGATAGTAAC 58.864 40.741 0.00 0.00 0.00 2.50
63 64 7.837689 ACAGTGGGAGTAACATAGATAGTAACA 59.162 37.037 0.00 0.00 0.00 2.41
64 65 8.861086 CAGTGGGAGTAACATAGATAGTAACAT 58.139 37.037 0.00 0.00 0.00 2.71
65 66 9.080097 AGTGGGAGTAACATAGATAGTAACATC 57.920 37.037 0.00 0.00 0.00 3.06
66 67 8.857098 GTGGGAGTAACATAGATAGTAACATCA 58.143 37.037 0.00 0.00 0.00 3.07
67 68 8.857098 TGGGAGTAACATAGATAGTAACATCAC 58.143 37.037 0.00 0.00 0.00 3.06
68 69 8.857098 GGGAGTAACATAGATAGTAACATCACA 58.143 37.037 0.00 0.00 0.00 3.58
69 70 9.900710 GGAGTAACATAGATAGTAACATCACAG 57.099 37.037 0.00 0.00 0.00 3.66
74 75 8.988546 ACATAGATAGTAACATCACAGTCTCT 57.011 34.615 0.00 0.00 0.00 3.10
77 78 9.733556 ATAGATAGTAACATCACAGTCTCTAGG 57.266 37.037 0.00 0.00 0.00 3.02
78 79 4.993029 AGTAACATCACAGTCTCTAGGC 57.007 45.455 0.00 0.00 0.00 3.93
79 80 4.344978 AGTAACATCACAGTCTCTAGGCA 58.655 43.478 0.00 0.00 0.00 4.75
80 81 4.772624 AGTAACATCACAGTCTCTAGGCAA 59.227 41.667 0.00 0.00 0.00 4.52
81 82 4.623932 AACATCACAGTCTCTAGGCAAA 57.376 40.909 0.00 0.00 0.00 3.68
82 83 4.623932 ACATCACAGTCTCTAGGCAAAA 57.376 40.909 0.00 0.00 0.00 2.44
83 84 4.319177 ACATCACAGTCTCTAGGCAAAAC 58.681 43.478 0.00 0.00 0.00 2.43
84 85 4.202357 ACATCACAGTCTCTAGGCAAAACA 60.202 41.667 0.00 0.00 0.00 2.83
85 86 3.995199 TCACAGTCTCTAGGCAAAACAG 58.005 45.455 0.00 0.00 0.00 3.16
86 87 3.641436 TCACAGTCTCTAGGCAAAACAGA 59.359 43.478 0.00 0.00 0.00 3.41
87 88 4.284490 TCACAGTCTCTAGGCAAAACAGAT 59.716 41.667 0.00 0.00 0.00 2.90
88 89 4.391216 CACAGTCTCTAGGCAAAACAGATG 59.609 45.833 0.00 0.00 0.00 2.90
89 90 4.284490 ACAGTCTCTAGGCAAAACAGATGA 59.716 41.667 0.00 0.00 0.00 2.92
90 91 5.046014 ACAGTCTCTAGGCAAAACAGATGAT 60.046 40.000 0.00 0.00 0.00 2.45
91 92 5.293814 CAGTCTCTAGGCAAAACAGATGATG 59.706 44.000 0.00 0.00 0.00 3.07
92 93 5.046014 AGTCTCTAGGCAAAACAGATGATGT 60.046 40.000 0.00 0.00 46.97 3.06
93 94 5.064452 GTCTCTAGGCAAAACAGATGATGTG 59.936 44.000 0.00 0.00 43.00 3.21
94 95 4.264253 TCTAGGCAAAACAGATGATGTGG 58.736 43.478 0.00 0.00 43.00 4.17
95 96 1.547372 AGGCAAAACAGATGATGTGGC 59.453 47.619 0.00 0.00 43.00 5.01
96 97 1.273048 GGCAAAACAGATGATGTGGCA 59.727 47.619 2.47 0.00 43.00 4.92
97 98 2.288948 GGCAAAACAGATGATGTGGCAA 60.289 45.455 2.47 0.00 43.00 4.52
98 99 2.991190 GCAAAACAGATGATGTGGCAAG 59.009 45.455 0.00 0.00 43.00 4.01
99 100 3.553508 GCAAAACAGATGATGTGGCAAGT 60.554 43.478 0.00 0.00 43.00 3.16
100 101 4.321156 GCAAAACAGATGATGTGGCAAGTA 60.321 41.667 0.00 0.00 43.00 2.24
101 102 5.771469 CAAAACAGATGATGTGGCAAGTAA 58.229 37.500 0.00 0.00 43.00 2.24
102 103 6.392354 CAAAACAGATGATGTGGCAAGTAAT 58.608 36.000 0.00 0.00 43.00 1.89
103 104 6.594788 AAACAGATGATGTGGCAAGTAATT 57.405 33.333 0.00 0.00 43.00 1.40
104 105 7.701539 AAACAGATGATGTGGCAAGTAATTA 57.298 32.000 0.00 0.00 43.00 1.40
105 106 7.701539 AACAGATGATGTGGCAAGTAATTAA 57.298 32.000 0.00 0.00 43.00 1.40
106 107 7.886629 ACAGATGATGTGGCAAGTAATTAAT 57.113 32.000 0.00 0.00 41.91 1.40
107 108 7.709947 ACAGATGATGTGGCAAGTAATTAATG 58.290 34.615 0.00 0.00 41.91 1.90
108 109 7.557358 ACAGATGATGTGGCAAGTAATTAATGA 59.443 33.333 0.00 0.00 41.91 2.57
109 110 8.074370 CAGATGATGTGGCAAGTAATTAATGAG 58.926 37.037 0.00 0.00 0.00 2.90
110 111 6.698008 TGATGTGGCAAGTAATTAATGAGG 57.302 37.500 0.00 0.00 0.00 3.86
111 112 6.422333 TGATGTGGCAAGTAATTAATGAGGA 58.578 36.000 0.00 0.00 0.00 3.71
112 113 6.889177 TGATGTGGCAAGTAATTAATGAGGAA 59.111 34.615 0.00 0.00 0.00 3.36
113 114 7.395772 TGATGTGGCAAGTAATTAATGAGGAAA 59.604 33.333 0.00 0.00 0.00 3.13
114 115 7.156876 TGTGGCAAGTAATTAATGAGGAAAG 57.843 36.000 0.00 0.00 0.00 2.62
115 116 6.945435 TGTGGCAAGTAATTAATGAGGAAAGA 59.055 34.615 0.00 0.00 0.00 2.52
116 117 7.121168 TGTGGCAAGTAATTAATGAGGAAAGAG 59.879 37.037 0.00 0.00 0.00 2.85
117 118 7.336931 GTGGCAAGTAATTAATGAGGAAAGAGA 59.663 37.037 0.00 0.00 0.00 3.10
118 119 7.554118 TGGCAAGTAATTAATGAGGAAAGAGAG 59.446 37.037 4.19 0.00 0.00 3.20
119 120 7.012799 GGCAAGTAATTAATGAGGAAAGAGAGG 59.987 40.741 4.19 0.00 0.00 3.69
120 121 7.467947 GCAAGTAATTAATGAGGAAAGAGAGGC 60.468 40.741 4.19 0.00 0.00 4.70
121 122 7.200434 AGTAATTAATGAGGAAAGAGAGGCA 57.800 36.000 0.00 0.00 0.00 4.75
122 123 7.810260 AGTAATTAATGAGGAAAGAGAGGCAT 58.190 34.615 0.00 0.00 0.00 4.40
123 124 6.956202 AATTAATGAGGAAAGAGAGGCATG 57.044 37.500 0.00 0.00 0.00 4.06
124 125 5.441718 TTAATGAGGAAAGAGAGGCATGT 57.558 39.130 0.00 0.00 0.00 3.21
125 126 2.775911 TGAGGAAAGAGAGGCATGTG 57.224 50.000 0.00 0.00 0.00 3.21
126 127 1.280133 TGAGGAAAGAGAGGCATGTGG 59.720 52.381 0.00 0.00 0.00 4.17
127 128 1.280421 GAGGAAAGAGAGGCATGTGGT 59.720 52.381 0.00 0.00 0.00 4.16
128 129 2.501723 GAGGAAAGAGAGGCATGTGGTA 59.498 50.000 0.00 0.00 0.00 3.25
129 130 2.912956 AGGAAAGAGAGGCATGTGGTAA 59.087 45.455 0.00 0.00 0.00 2.85
130 131 3.010420 GGAAAGAGAGGCATGTGGTAAC 58.990 50.000 0.00 0.00 0.00 2.50
149 150 8.352137 TGGTAACATAGCTAGTTACTGTAACA 57.648 34.615 27.12 19.73 46.49 2.41
150 151 8.974238 TGGTAACATAGCTAGTTACTGTAACAT 58.026 33.333 27.12 16.67 46.49 2.71
151 152 9.460906 GGTAACATAGCTAGTTACTGTAACATC 57.539 37.037 27.12 16.94 46.49 3.06
153 154 8.928270 AACATAGCTAGTTACTGTAACATCAC 57.072 34.615 27.12 15.70 41.07 3.06
154 155 8.063200 ACATAGCTAGTTACTGTAACATCACA 57.937 34.615 27.12 12.96 41.07 3.58
155 156 8.696374 ACATAGCTAGTTACTGTAACATCACAT 58.304 33.333 27.12 14.32 41.07 3.21
160 161 9.408069 GCTAGTTACTGTAACATCACATATACC 57.592 37.037 27.12 1.55 41.07 2.73
163 164 9.817809 AGTTACTGTAACATCACATATACCAAG 57.182 33.333 27.12 0.00 41.07 3.61
164 165 9.811995 GTTACTGTAACATCACATATACCAAGA 57.188 33.333 22.30 0.00 38.52 3.02
165 166 9.811995 TTACTGTAACATCACATATACCAAGAC 57.188 33.333 0.00 0.00 0.00 3.01
166 167 7.847096 ACTGTAACATCACATATACCAAGACA 58.153 34.615 0.00 0.00 0.00 3.41
167 168 8.318412 ACTGTAACATCACATATACCAAGACAA 58.682 33.333 0.00 0.00 0.00 3.18
168 169 8.716646 TGTAACATCACATATACCAAGACAAG 57.283 34.615 0.00 0.00 0.00 3.16
169 170 8.536175 TGTAACATCACATATACCAAGACAAGA 58.464 33.333 0.00 0.00 0.00 3.02
170 171 9.547753 GTAACATCACATATACCAAGACAAGAT 57.452 33.333 0.00 0.00 0.00 2.40
171 172 8.442632 AACATCACATATACCAAGACAAGATG 57.557 34.615 0.00 0.00 36.24 2.90
172 173 7.795047 ACATCACATATACCAAGACAAGATGA 58.205 34.615 0.00 0.00 34.73 2.92
173 174 7.930325 ACATCACATATACCAAGACAAGATGAG 59.070 37.037 0.00 0.00 34.73 2.90
174 175 7.423844 TCACATATACCAAGACAAGATGAGT 57.576 36.000 0.00 0.00 0.00 3.41
175 176 7.492524 TCACATATACCAAGACAAGATGAGTC 58.507 38.462 0.00 0.00 36.26 3.36
177 178 8.633561 CACATATACCAAGACAAGATGAGTCTA 58.366 37.037 0.00 0.00 45.11 2.59
178 179 9.373450 ACATATACCAAGACAAGATGAGTCTAT 57.627 33.333 0.00 0.00 45.11 1.98
182 183 6.879400 ACCAAGACAAGATGAGTCTATAACC 58.121 40.000 0.00 0.00 45.11 2.85
183 184 6.670027 ACCAAGACAAGATGAGTCTATAACCT 59.330 38.462 0.00 0.00 45.11 3.50
184 185 7.839705 ACCAAGACAAGATGAGTCTATAACCTA 59.160 37.037 0.00 0.00 45.11 3.08
185 186 8.696374 CCAAGACAAGATGAGTCTATAACCTAA 58.304 37.037 0.00 0.00 45.11 2.69
204 205 7.701539 ACCTAATAAATGAAGTGTTGCATGA 57.298 32.000 0.00 0.00 0.00 3.07
205 206 7.538575 ACCTAATAAATGAAGTGTTGCATGAC 58.461 34.615 0.00 0.00 0.00 3.06
206 207 7.176515 ACCTAATAAATGAAGTGTTGCATGACA 59.823 33.333 0.00 0.00 0.00 3.58
213 214 1.308047 GTGTTGCATGACACCTCACA 58.692 50.000 10.05 0.00 43.16 3.58
214 215 1.881973 GTGTTGCATGACACCTCACAT 59.118 47.619 10.05 0.00 43.16 3.21
215 216 3.073678 GTGTTGCATGACACCTCACATA 58.926 45.455 10.05 0.00 43.16 2.29
216 217 3.691118 GTGTTGCATGACACCTCACATAT 59.309 43.478 10.05 0.00 43.16 1.78
217 218 3.690628 TGTTGCATGACACCTCACATATG 59.309 43.478 0.00 0.00 0.00 1.78
218 219 3.632643 TGCATGACACCTCACATATGT 57.367 42.857 1.41 1.41 0.00 2.29
219 220 3.954200 TGCATGACACCTCACATATGTT 58.046 40.909 5.37 0.00 0.00 2.71
220 221 3.690628 TGCATGACACCTCACATATGTTG 59.309 43.478 5.37 4.62 0.00 3.33
221 222 3.488047 GCATGACACCTCACATATGTTGC 60.488 47.826 5.37 6.62 0.00 4.17
222 223 3.701205 TGACACCTCACATATGTTGCT 57.299 42.857 5.37 0.00 0.00 3.91
223 224 4.817318 TGACACCTCACATATGTTGCTA 57.183 40.909 5.37 0.00 0.00 3.49
224 225 4.503910 TGACACCTCACATATGTTGCTAC 58.496 43.478 5.37 0.00 0.00 3.58
225 226 3.871594 GACACCTCACATATGTTGCTACC 59.128 47.826 5.37 0.00 0.00 3.18
226 227 3.206150 CACCTCACATATGTTGCTACCC 58.794 50.000 5.37 0.00 0.00 3.69
227 228 2.843730 ACCTCACATATGTTGCTACCCA 59.156 45.455 5.37 0.00 0.00 4.51
228 229 3.206150 CCTCACATATGTTGCTACCCAC 58.794 50.000 5.37 0.00 0.00 4.61
229 230 3.118261 CCTCACATATGTTGCTACCCACT 60.118 47.826 5.37 0.00 0.00 4.00
230 231 3.872696 TCACATATGTTGCTACCCACTG 58.127 45.455 5.37 0.00 0.00 3.66
231 232 3.263170 TCACATATGTTGCTACCCACTGT 59.737 43.478 5.37 0.00 0.00 3.55
232 233 3.374988 CACATATGTTGCTACCCACTGTG 59.625 47.826 5.37 0.00 0.00 3.66
233 234 3.263170 ACATATGTTGCTACCCACTGTGA 59.737 43.478 9.86 0.00 0.00 3.58
234 235 2.949177 ATGTTGCTACCCACTGTGAA 57.051 45.000 9.86 0.00 0.00 3.18
235 236 2.254546 TGTTGCTACCCACTGTGAAG 57.745 50.000 9.86 5.00 0.00 3.02
236 237 1.202758 TGTTGCTACCCACTGTGAAGG 60.203 52.381 9.86 5.43 0.00 3.46
237 238 1.136828 TTGCTACCCACTGTGAAGGT 58.863 50.000 9.86 11.38 37.69 3.50
238 239 2.018355 TGCTACCCACTGTGAAGGTA 57.982 50.000 9.86 11.91 35.02 3.08
243 244 5.934402 CTACCCACTGTGAAGGTAGTAAT 57.066 43.478 23.95 2.54 45.39 1.89
245 246 7.598759 CTACCCACTGTGAAGGTAGTAATAT 57.401 40.000 23.95 1.45 45.39 1.28
246 247 8.701908 CTACCCACTGTGAAGGTAGTAATATA 57.298 38.462 23.95 4.07 45.39 0.86
247 248 7.598759 ACCCACTGTGAAGGTAGTAATATAG 57.401 40.000 9.86 0.00 30.13 1.31
248 249 7.359849 ACCCACTGTGAAGGTAGTAATATAGA 58.640 38.462 9.86 0.00 30.13 1.98
249 250 8.011290 ACCCACTGTGAAGGTAGTAATATAGAT 58.989 37.037 9.86 0.00 30.13 1.98
250 251 8.871125 CCCACTGTGAAGGTAGTAATATAGATT 58.129 37.037 9.86 0.00 0.00 2.40
287 288 9.473640 GCATGTTACTACTCTAAGTTATTACCC 57.526 37.037 0.00 0.00 0.00 3.69
294 295 9.263446 ACTACTCTAAGTTATTACCCATTGTGA 57.737 33.333 0.00 0.00 0.00 3.58
295 296 9.530633 CTACTCTAAGTTATTACCCATTGTGAC 57.469 37.037 0.00 0.00 0.00 3.67
296 297 8.147244 ACTCTAAGTTATTACCCATTGTGACT 57.853 34.615 0.00 0.00 0.00 3.41
297 298 9.263446 ACTCTAAGTTATTACCCATTGTGACTA 57.737 33.333 0.00 0.00 0.00 2.59
298 299 9.751542 CTCTAAGTTATTACCCATTGTGACTAG 57.248 37.037 0.00 0.00 0.00 2.57
299 300 9.263446 TCTAAGTTATTACCCATTGTGACTAGT 57.737 33.333 0.00 0.00 0.00 2.57
300 301 9.530633 CTAAGTTATTACCCATTGTGACTAGTC 57.469 37.037 16.32 16.32 0.00 2.59
317 318 0.744771 GTCTTAGAGGGGGCAAAGCG 60.745 60.000 0.00 0.00 0.00 4.68
396 410 2.415825 CGAGGAAGTCGGCTATGGA 58.584 57.895 0.00 0.00 45.58 3.41
564 578 1.062121 AGCAGTAGGGGCTAAGATCCA 60.062 52.381 0.00 0.00 40.47 3.41
622 637 2.692741 GGTGGGGAGGAGGAAGGG 60.693 72.222 0.00 0.00 0.00 3.95
628 643 1.147153 GGAGGAGGAAGGGAATGCG 59.853 63.158 0.00 0.00 0.00 4.73
852 867 3.741476 GCTTGGCAGTTGGCTCCG 61.741 66.667 7.23 0.00 44.01 4.63
969 988 7.256332 GCAATCTACTTCCACATCCTCCTATTA 60.256 40.741 0.00 0.00 0.00 0.98
1000 1020 1.213094 CCACGTATCATTCGGTCGCC 61.213 60.000 0.00 0.00 0.00 5.54
1381 1401 0.321564 CTCCAACGGCTTCATCCACA 60.322 55.000 0.00 0.00 0.00 4.17
1761 1781 2.207229 CGCCGGTAGGATGGATGGA 61.207 63.158 1.90 0.00 41.02 3.41
1981 2001 1.202758 ACGAGGTCACCTTCATTTGCA 60.203 47.619 0.00 0.00 31.76 4.08
2103 2123 0.029681 ACTATGGGAGCCTGGTGGAT 60.030 55.000 0.00 0.00 34.57 3.41
2178 2198 1.374252 GATGCGGCCCGATTCGTAT 60.374 57.895 7.68 0.00 34.66 3.06
2535 2555 2.487428 CGTCACCTCGAGGAGCTG 59.513 66.667 37.69 24.60 38.94 4.24
2588 2608 2.430921 CTCAGGTCGTCGCACACC 60.431 66.667 0.00 0.00 0.00 4.16
2620 2640 5.193679 GCCTCTTATAAGTTGGAACACCAT 58.806 41.667 22.34 0.00 39.29 3.55
2624 2644 7.362056 CCTCTTATAAGTTGGAACACCATGTTG 60.362 40.741 12.19 0.00 41.28 3.33
2655 2675 3.230134 ACCACAACTACACATGGCAAAT 58.770 40.909 0.00 0.00 35.49 2.32
2671 2691 3.859386 GGCAAATATTGTTCAGCCGAAAG 59.141 43.478 0.00 0.00 31.43 2.62
2808 2833 4.704833 GGAGCTTCACCGCTGGCA 62.705 66.667 0.00 0.00 41.08 4.92
2865 2890 2.439701 TACCGCCGAGACCTCTGG 60.440 66.667 0.00 0.00 0.00 3.86
2884 2909 6.446649 CTCTGGAGAGGAATCCTTACAGAGG 61.447 52.000 30.27 20.33 43.70 3.69
2911 2936 8.631797 TGTATGGAATGATTACCAAATGTGATG 58.368 33.333 0.00 0.00 39.69 3.07
2923 2948 3.475566 AATGTGATGTATCTCCACGGG 57.524 47.619 0.00 0.00 33.78 5.28
2939 2964 0.527565 CGGGTTCCTTCAGGCATTTG 59.472 55.000 0.00 0.00 34.44 2.32
2956 2981 6.944862 AGGCATTTGAGAAGTTGATAAAGAGT 59.055 34.615 0.00 0.00 0.00 3.24
3015 3040 5.048991 CCGTAGCATCAACTAACAGGTTTTT 60.049 40.000 0.00 0.00 0.00 1.94
3101 3126 3.441496 AATGTGCCAGTTTGTCAGTTG 57.559 42.857 0.00 0.00 0.00 3.16
3104 3129 1.008538 GCCAGTTTGTCAGTTGCCG 60.009 57.895 0.00 0.00 0.00 5.69
3118 3143 4.451096 TCAGTTGCCGTAATCAGAAACTTC 59.549 41.667 0.00 0.00 0.00 3.01
3137 3162 4.574013 ACTTCTCAAGTTCTTCAGCACTTG 59.426 41.667 11.77 11.77 45.99 3.16
3144 3171 5.993106 AGTTCTTCAGCACTTGTTAGAAC 57.007 39.130 0.00 0.00 42.76 3.01
3154 3181 5.414454 AGCACTTGTTAGAACAGAAAACACA 59.586 36.000 0.00 0.00 40.50 3.72
3156 3183 7.282224 AGCACTTGTTAGAACAGAAAACACATA 59.718 33.333 0.00 0.00 40.50 2.29
3199 3228 7.881775 ACACTTTTCAACTTATCCTTCAGTT 57.118 32.000 0.00 0.00 33.29 3.16
3203 3232 7.556275 ACTTTTCAACTTATCCTTCAGTTGTCA 59.444 33.333 10.90 0.00 46.76 3.58
3214 3243 6.601332 TCCTTCAGTTGTCAACCTATCTTTT 58.399 36.000 12.17 0.00 0.00 2.27
3215 3244 6.710744 TCCTTCAGTTGTCAACCTATCTTTTC 59.289 38.462 12.17 0.00 0.00 2.29
3216 3245 6.072452 CCTTCAGTTGTCAACCTATCTTTTCC 60.072 42.308 12.17 0.00 0.00 3.13
3231 3260 4.843728 TCTTTTCCGCAGTTCATCCTAAT 58.156 39.130 0.00 0.00 0.00 1.73
3293 3322 3.257127 CCTCAGATTACTAGCAGCTACCC 59.743 52.174 0.00 0.00 0.00 3.69
3335 3364 1.016130 CAGCACGCTACCCTGTTCAG 61.016 60.000 0.00 0.00 0.00 3.02
3337 3366 1.014564 GCACGCTACCCTGTTCAGAC 61.015 60.000 1.00 0.00 0.00 3.51
3344 3373 2.425592 CCTGTTCAGACGGTGGCA 59.574 61.111 1.00 0.00 0.00 4.92
3345 3374 1.669115 CCTGTTCAGACGGTGGCAG 60.669 63.158 1.00 0.00 32.66 4.85
3353 3382 1.003718 GACGGTGGCAGCCTAAGTT 60.004 57.895 14.15 0.00 0.00 2.66
3364 3393 2.877168 CAGCCTAAGTTCAGATGATGGC 59.123 50.000 0.00 0.00 39.40 4.40
3365 3394 2.158696 AGCCTAAGTTCAGATGATGGCC 60.159 50.000 0.00 0.00 39.90 5.36
3366 3395 2.856222 CCTAAGTTCAGATGATGGCCC 58.144 52.381 0.00 0.00 0.00 5.80
3367 3396 2.441001 CCTAAGTTCAGATGATGGCCCT 59.559 50.000 0.00 0.00 0.00 5.19
3368 3397 2.725221 AAGTTCAGATGATGGCCCTC 57.275 50.000 0.00 0.00 0.00 4.30
3369 3398 0.467384 AGTTCAGATGATGGCCCTCG 59.533 55.000 0.00 0.00 0.00 4.63
3370 3399 0.533755 GTTCAGATGATGGCCCTCGG 60.534 60.000 0.00 0.00 0.00 4.63
3384 3413 1.005748 CTCGGTGTTGAGCAGCTCA 60.006 57.895 21.85 21.85 42.99 4.26
3388 3417 0.250038 GGTGTTGAGCAGCTCAGTGA 60.250 55.000 24.15 8.21 41.75 3.41
3411 3440 3.270960 AGGACCTCCTCAAGATGTCTACT 59.729 47.826 0.00 0.00 44.77 2.57
3440 3469 6.428083 TTTGGAGTTCTCCATGTTAGTGTA 57.572 37.500 20.26 1.80 39.86 2.90
3472 3501 0.963962 ACGGACAACCACTACGACAT 59.036 50.000 0.00 0.00 35.59 3.06
3475 3504 2.416836 CGGACAACCACTACGACATCAT 60.417 50.000 0.00 0.00 35.59 2.45
3481 3510 3.899726 ACCACTACGACATCATCTACCT 58.100 45.455 0.00 0.00 0.00 3.08
3496 3525 4.571369 TCTACCTATAGATCTCCCGTGG 57.429 50.000 0.00 0.00 32.16 4.94
3629 3658 4.770795 ACTGCTAGTACCAATGGATTGAC 58.229 43.478 6.16 0.00 40.14 3.18
3630 3659 4.471386 ACTGCTAGTACCAATGGATTGACT 59.529 41.667 6.16 6.23 40.14 3.41
3632 3661 5.914033 TGCTAGTACCAATGGATTGACTAC 58.086 41.667 6.16 0.00 40.14 2.73
3681 3710 8.645814 TTTAGTCTGATTAGTTCCTGTGACTA 57.354 34.615 0.00 0.00 35.52 2.59
3686 3715 6.719829 TCTGATTAGTTCCTGTGACTAGTTCA 59.280 38.462 0.00 0.00 31.74 3.18
3715 3759 6.517013 ACTACTCCTGTGTATATCCTCTCA 57.483 41.667 0.00 0.00 0.00 3.27
3787 4667 4.497006 GCTTGTGCCTGAACATGTATGATC 60.497 45.833 0.00 0.00 0.00 2.92
3846 4774 6.875948 ACAGCAATGTACTTGTTGATACAA 57.124 33.333 20.30 0.00 45.87 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.695851 AAATGCTAGTTCCTGTGACTTTG 57.304 39.130 0.00 0.00 0.00 2.77
1 2 6.998673 ACTAAAATGCTAGTTCCTGTGACTTT 59.001 34.615 0.00 0.00 0.00 2.66
3 4 6.115448 ACTAAAATGCTAGTTCCTGTGACT 57.885 37.500 0.00 0.00 0.00 3.41
4 5 6.803154 AACTAAAATGCTAGTTCCTGTGAC 57.197 37.500 0.00 0.00 37.53 3.67
5 6 7.817962 GTCTAACTAAAATGCTAGTTCCTGTGA 59.182 37.037 0.00 0.00 40.49 3.58
6 7 7.819900 AGTCTAACTAAAATGCTAGTTCCTGTG 59.180 37.037 0.00 0.00 40.49 3.66
7 8 7.908453 AGTCTAACTAAAATGCTAGTTCCTGT 58.092 34.615 0.00 0.00 40.49 4.00
8 9 9.303537 GTAGTCTAACTAAAATGCTAGTTCCTG 57.696 37.037 0.00 0.00 40.49 3.86
9 10 8.476447 GGTAGTCTAACTAAAATGCTAGTTCCT 58.524 37.037 0.00 0.00 40.49 3.36
10 11 7.710044 GGGTAGTCTAACTAAAATGCTAGTTCC 59.290 40.741 0.00 0.00 40.49 3.62
11 12 8.255905 TGGGTAGTCTAACTAAAATGCTAGTTC 58.744 37.037 0.00 0.00 40.49 3.01
12 13 8.039538 GTGGGTAGTCTAACTAAAATGCTAGTT 58.960 37.037 0.00 2.17 43.12 2.24
13 14 7.179694 TGTGGGTAGTCTAACTAAAATGCTAGT 59.820 37.037 0.00 0.00 31.62 2.57
14 15 7.553334 TGTGGGTAGTCTAACTAAAATGCTAG 58.447 38.462 0.00 0.00 31.62 3.42
15 16 7.179694 ACTGTGGGTAGTCTAACTAAAATGCTA 59.820 37.037 0.00 0.00 31.62 3.49
16 17 6.013639 ACTGTGGGTAGTCTAACTAAAATGCT 60.014 38.462 0.00 0.00 31.62 3.79
17 18 6.092259 CACTGTGGGTAGTCTAACTAAAATGC 59.908 42.308 0.00 0.00 31.62 3.56
18 19 6.594159 CCACTGTGGGTAGTCTAACTAAAATG 59.406 42.308 19.23 0.00 31.62 2.32
19 20 6.708285 CCACTGTGGGTAGTCTAACTAAAAT 58.292 40.000 19.23 0.00 31.62 1.82
20 21 6.105397 CCACTGTGGGTAGTCTAACTAAAA 57.895 41.667 19.23 0.00 31.62 1.52
21 22 5.733620 CCACTGTGGGTAGTCTAACTAAA 57.266 43.478 19.23 0.00 31.62 1.85
35 36 5.598830 ACTATCTATGTTACTCCCACTGTGG 59.401 44.000 20.01 20.01 37.25 4.17
36 37 6.716934 ACTATCTATGTTACTCCCACTGTG 57.283 41.667 0.00 0.00 0.00 3.66
37 38 7.837689 TGTTACTATCTATGTTACTCCCACTGT 59.162 37.037 0.00 0.00 0.00 3.55
38 39 8.234136 TGTTACTATCTATGTTACTCCCACTG 57.766 38.462 0.00 0.00 0.00 3.66
39 40 9.080097 GATGTTACTATCTATGTTACTCCCACT 57.920 37.037 0.00 0.00 0.00 4.00
40 41 8.857098 TGATGTTACTATCTATGTTACTCCCAC 58.143 37.037 0.00 0.00 0.00 4.61
41 42 8.857098 GTGATGTTACTATCTATGTTACTCCCA 58.143 37.037 0.00 0.00 0.00 4.37
42 43 8.857098 TGTGATGTTACTATCTATGTTACTCCC 58.143 37.037 0.00 0.00 0.00 4.30
43 44 9.900710 CTGTGATGTTACTATCTATGTTACTCC 57.099 37.037 0.00 0.00 0.00 3.85
48 49 9.415008 AGAGACTGTGATGTTACTATCTATGTT 57.585 33.333 0.00 0.00 0.00 2.71
49 50 8.988546 AGAGACTGTGATGTTACTATCTATGT 57.011 34.615 0.00 0.00 0.00 2.29
51 52 9.733556 CCTAGAGACTGTGATGTTACTATCTAT 57.266 37.037 0.00 0.00 0.00 1.98
52 53 7.662258 GCCTAGAGACTGTGATGTTACTATCTA 59.338 40.741 0.00 0.00 0.00 1.98
53 54 6.488683 GCCTAGAGACTGTGATGTTACTATCT 59.511 42.308 0.00 0.00 0.00 1.98
54 55 6.263392 TGCCTAGAGACTGTGATGTTACTATC 59.737 42.308 0.00 0.00 0.00 2.08
55 56 6.129874 TGCCTAGAGACTGTGATGTTACTAT 58.870 40.000 0.00 0.00 0.00 2.12
56 57 5.506708 TGCCTAGAGACTGTGATGTTACTA 58.493 41.667 0.00 0.00 0.00 1.82
57 58 4.344978 TGCCTAGAGACTGTGATGTTACT 58.655 43.478 0.00 0.00 0.00 2.24
58 59 4.720649 TGCCTAGAGACTGTGATGTTAC 57.279 45.455 0.00 0.00 0.00 2.50
59 60 5.738619 TTTGCCTAGAGACTGTGATGTTA 57.261 39.130 0.00 0.00 0.00 2.41
60 61 4.623932 TTTGCCTAGAGACTGTGATGTT 57.376 40.909 0.00 0.00 0.00 2.71
61 62 4.202357 TGTTTTGCCTAGAGACTGTGATGT 60.202 41.667 0.00 0.00 0.00 3.06
62 63 4.318332 TGTTTTGCCTAGAGACTGTGATG 58.682 43.478 0.00 0.00 0.00 3.07
63 64 4.284490 TCTGTTTTGCCTAGAGACTGTGAT 59.716 41.667 0.00 0.00 0.00 3.06
64 65 3.641436 TCTGTTTTGCCTAGAGACTGTGA 59.359 43.478 0.00 0.00 0.00 3.58
65 66 3.995199 TCTGTTTTGCCTAGAGACTGTG 58.005 45.455 0.00 0.00 0.00 3.66
66 67 4.284490 TCATCTGTTTTGCCTAGAGACTGT 59.716 41.667 0.00 0.00 0.00 3.55
67 68 4.825422 TCATCTGTTTTGCCTAGAGACTG 58.175 43.478 0.00 0.00 0.00 3.51
68 69 5.046014 ACATCATCTGTTTTGCCTAGAGACT 60.046 40.000 0.00 0.00 32.90 3.24
69 70 5.064452 CACATCATCTGTTTTGCCTAGAGAC 59.936 44.000 0.00 0.00 35.29 3.36
70 71 5.181009 CACATCATCTGTTTTGCCTAGAGA 58.819 41.667 0.00 0.00 35.29 3.10
71 72 4.334759 CCACATCATCTGTTTTGCCTAGAG 59.665 45.833 0.00 0.00 35.29 2.43
72 73 4.264253 CCACATCATCTGTTTTGCCTAGA 58.736 43.478 0.00 0.00 35.29 2.43
73 74 3.181493 GCCACATCATCTGTTTTGCCTAG 60.181 47.826 0.00 0.00 35.29 3.02
74 75 2.754552 GCCACATCATCTGTTTTGCCTA 59.245 45.455 0.00 0.00 35.29 3.93
75 76 1.547372 GCCACATCATCTGTTTTGCCT 59.453 47.619 0.00 0.00 35.29 4.75
76 77 1.273048 TGCCACATCATCTGTTTTGCC 59.727 47.619 0.00 0.00 35.29 4.52
77 78 2.728690 TGCCACATCATCTGTTTTGC 57.271 45.000 0.00 0.00 35.29 3.68
78 79 4.247267 ACTTGCCACATCATCTGTTTTG 57.753 40.909 0.00 0.00 35.29 2.44
79 80 6.594788 ATTACTTGCCACATCATCTGTTTT 57.405 33.333 0.00 0.00 35.29 2.43
80 81 6.594788 AATTACTTGCCACATCATCTGTTT 57.405 33.333 0.00 0.00 35.29 2.83
81 82 7.701539 TTAATTACTTGCCACATCATCTGTT 57.298 32.000 0.00 0.00 35.29 3.16
82 83 7.557358 TCATTAATTACTTGCCACATCATCTGT 59.443 33.333 0.00 0.00 39.20 3.41
83 84 7.933396 TCATTAATTACTTGCCACATCATCTG 58.067 34.615 0.00 0.00 0.00 2.90
84 85 7.230108 CCTCATTAATTACTTGCCACATCATCT 59.770 37.037 0.00 0.00 0.00 2.90
85 86 7.229306 TCCTCATTAATTACTTGCCACATCATC 59.771 37.037 0.00 0.00 0.00 2.92
86 87 7.062322 TCCTCATTAATTACTTGCCACATCAT 58.938 34.615 0.00 0.00 0.00 2.45
87 88 6.422333 TCCTCATTAATTACTTGCCACATCA 58.578 36.000 0.00 0.00 0.00 3.07
88 89 6.942532 TCCTCATTAATTACTTGCCACATC 57.057 37.500 0.00 0.00 0.00 3.06
89 90 7.615365 TCTTTCCTCATTAATTACTTGCCACAT 59.385 33.333 0.00 0.00 0.00 3.21
90 91 6.945435 TCTTTCCTCATTAATTACTTGCCACA 59.055 34.615 0.00 0.00 0.00 4.17
91 92 7.336931 TCTCTTTCCTCATTAATTACTTGCCAC 59.663 37.037 0.00 0.00 0.00 5.01
92 93 7.402054 TCTCTTTCCTCATTAATTACTTGCCA 58.598 34.615 0.00 0.00 0.00 4.92
93 94 7.012799 CCTCTCTTTCCTCATTAATTACTTGCC 59.987 40.741 0.00 0.00 0.00 4.52
94 95 7.467947 GCCTCTCTTTCCTCATTAATTACTTGC 60.468 40.741 0.00 0.00 0.00 4.01
95 96 7.554118 TGCCTCTCTTTCCTCATTAATTACTTG 59.446 37.037 0.00 0.00 0.00 3.16
96 97 7.633789 TGCCTCTCTTTCCTCATTAATTACTT 58.366 34.615 0.00 0.00 0.00 2.24
97 98 7.200434 TGCCTCTCTTTCCTCATTAATTACT 57.800 36.000 0.00 0.00 0.00 2.24
98 99 7.500559 ACATGCCTCTCTTTCCTCATTAATTAC 59.499 37.037 0.00 0.00 0.00 1.89
99 100 7.500227 CACATGCCTCTCTTTCCTCATTAATTA 59.500 37.037 0.00 0.00 0.00 1.40
100 101 6.320672 CACATGCCTCTCTTTCCTCATTAATT 59.679 38.462 0.00 0.00 0.00 1.40
101 102 5.826737 CACATGCCTCTCTTTCCTCATTAAT 59.173 40.000 0.00 0.00 0.00 1.40
102 103 5.188434 CACATGCCTCTCTTTCCTCATTAA 58.812 41.667 0.00 0.00 0.00 1.40
103 104 4.384537 CCACATGCCTCTCTTTCCTCATTA 60.385 45.833 0.00 0.00 0.00 1.90
104 105 3.618351 CACATGCCTCTCTTTCCTCATT 58.382 45.455 0.00 0.00 0.00 2.57
105 106 2.092538 CCACATGCCTCTCTTTCCTCAT 60.093 50.000 0.00 0.00 0.00 2.90
106 107 1.280133 CCACATGCCTCTCTTTCCTCA 59.720 52.381 0.00 0.00 0.00 3.86
107 108 1.280421 ACCACATGCCTCTCTTTCCTC 59.720 52.381 0.00 0.00 0.00 3.71
108 109 1.366319 ACCACATGCCTCTCTTTCCT 58.634 50.000 0.00 0.00 0.00 3.36
109 110 3.010420 GTTACCACATGCCTCTCTTTCC 58.990 50.000 0.00 0.00 0.00 3.13
110 111 3.674997 TGTTACCACATGCCTCTCTTTC 58.325 45.455 0.00 0.00 0.00 2.62
111 112 3.788227 TGTTACCACATGCCTCTCTTT 57.212 42.857 0.00 0.00 0.00 2.52
112 113 4.684485 GCTATGTTACCACATGCCTCTCTT 60.684 45.833 0.00 0.00 43.92 2.85
113 114 3.181461 GCTATGTTACCACATGCCTCTCT 60.181 47.826 0.00 0.00 43.92 3.10
114 115 3.134458 GCTATGTTACCACATGCCTCTC 58.866 50.000 0.00 0.00 43.92 3.20
115 116 2.774234 AGCTATGTTACCACATGCCTCT 59.226 45.455 0.00 0.00 43.92 3.69
116 117 3.199880 AGCTATGTTACCACATGCCTC 57.800 47.619 0.00 0.00 43.92 4.70
117 118 3.711704 ACTAGCTATGTTACCACATGCCT 59.288 43.478 0.00 0.00 43.92 4.75
118 119 4.073293 ACTAGCTATGTTACCACATGCC 57.927 45.455 0.00 0.00 43.92 4.40
119 120 6.201044 CAGTAACTAGCTATGTTACCACATGC 59.799 42.308 25.92 11.98 46.31 4.06
120 121 7.265673 ACAGTAACTAGCTATGTTACCACATG 58.734 38.462 25.92 22.03 46.31 3.21
121 122 7.419711 ACAGTAACTAGCTATGTTACCACAT 57.580 36.000 25.92 14.84 46.31 3.21
122 123 6.845758 ACAGTAACTAGCTATGTTACCACA 57.154 37.500 25.92 6.86 46.31 4.17
123 124 8.246180 TGTTACAGTAACTAGCTATGTTACCAC 58.754 37.037 25.92 20.75 46.31 4.16
124 125 8.352137 TGTTACAGTAACTAGCTATGTTACCA 57.648 34.615 25.92 19.04 46.31 3.25
125 126 9.460906 GATGTTACAGTAACTAGCTATGTTACC 57.539 37.037 25.92 17.65 46.31 2.85
128 129 8.528643 TGTGATGTTACAGTAACTAGCTATGTT 58.471 33.333 21.56 7.75 39.38 2.71
129 130 8.063200 TGTGATGTTACAGTAACTAGCTATGT 57.937 34.615 21.56 0.00 39.38 2.29
134 135 9.408069 GGTATATGTGATGTTACAGTAACTAGC 57.592 37.037 21.56 12.59 39.38 3.42
137 138 9.817809 CTTGGTATATGTGATGTTACAGTAACT 57.182 33.333 21.56 9.41 39.38 2.24
138 139 9.811995 TCTTGGTATATGTGATGTTACAGTAAC 57.188 33.333 15.58 15.58 39.11 2.50
139 140 9.811995 GTCTTGGTATATGTGATGTTACAGTAA 57.188 33.333 0.00 0.00 33.44 2.24
140 141 8.973182 TGTCTTGGTATATGTGATGTTACAGTA 58.027 33.333 0.00 0.00 33.44 2.74
141 142 7.847096 TGTCTTGGTATATGTGATGTTACAGT 58.153 34.615 0.00 0.00 33.44 3.55
142 143 8.716646 TTGTCTTGGTATATGTGATGTTACAG 57.283 34.615 0.00 0.00 33.44 2.74
143 144 8.536175 TCTTGTCTTGGTATATGTGATGTTACA 58.464 33.333 0.00 0.00 34.63 2.41
144 145 8.942338 TCTTGTCTTGGTATATGTGATGTTAC 57.058 34.615 0.00 0.00 0.00 2.50
145 146 9.546428 CATCTTGTCTTGGTATATGTGATGTTA 57.454 33.333 0.00 0.00 0.00 2.41
146 147 8.267183 TCATCTTGTCTTGGTATATGTGATGTT 58.733 33.333 0.00 0.00 32.21 2.71
147 148 7.795047 TCATCTTGTCTTGGTATATGTGATGT 58.205 34.615 0.00 0.00 32.21 3.06
148 149 7.930325 ACTCATCTTGTCTTGGTATATGTGATG 59.070 37.037 0.00 0.00 0.00 3.07
149 150 8.027524 ACTCATCTTGTCTTGGTATATGTGAT 57.972 34.615 0.00 0.00 0.00 3.06
150 151 7.343057 AGACTCATCTTGTCTTGGTATATGTGA 59.657 37.037 0.00 0.00 41.45 3.58
151 152 7.495901 AGACTCATCTTGTCTTGGTATATGTG 58.504 38.462 0.00 0.00 41.45 3.21
152 153 7.667575 AGACTCATCTTGTCTTGGTATATGT 57.332 36.000 0.00 0.00 41.45 2.29
156 157 8.643324 GGTTATAGACTCATCTTGTCTTGGTAT 58.357 37.037 1.67 0.00 41.45 2.73
157 158 7.839705 AGGTTATAGACTCATCTTGTCTTGGTA 59.160 37.037 1.67 0.00 41.45 3.25
158 159 6.670027 AGGTTATAGACTCATCTTGTCTTGGT 59.330 38.462 1.67 0.00 41.45 3.67
159 160 7.118496 AGGTTATAGACTCATCTTGTCTTGG 57.882 40.000 1.67 0.00 41.45 3.61
178 179 9.237187 TCATGCAACACTTCATTTATTAGGTTA 57.763 29.630 0.00 0.00 0.00 2.85
179 180 8.028938 GTCATGCAACACTTCATTTATTAGGTT 58.971 33.333 0.00 0.00 0.00 3.50
180 181 7.176515 TGTCATGCAACACTTCATTTATTAGGT 59.823 33.333 0.00 0.00 0.00 3.08
181 182 7.485913 GTGTCATGCAACACTTCATTTATTAGG 59.514 37.037 13.31 0.00 44.90 2.69
182 183 7.485913 GGTGTCATGCAACACTTCATTTATTAG 59.514 37.037 18.55 0.00 46.96 1.73
183 184 7.176515 AGGTGTCATGCAACACTTCATTTATTA 59.823 33.333 18.55 0.00 46.96 0.98
184 185 6.015180 AGGTGTCATGCAACACTTCATTTATT 60.015 34.615 18.55 0.00 46.96 1.40
185 186 5.477984 AGGTGTCATGCAACACTTCATTTAT 59.522 36.000 18.55 0.00 46.96 1.40
186 187 4.826733 AGGTGTCATGCAACACTTCATTTA 59.173 37.500 18.55 0.00 46.96 1.40
187 188 3.638160 AGGTGTCATGCAACACTTCATTT 59.362 39.130 18.55 0.00 46.96 2.32
188 189 3.225104 AGGTGTCATGCAACACTTCATT 58.775 40.909 18.55 1.19 46.96 2.57
189 190 2.867624 AGGTGTCATGCAACACTTCAT 58.132 42.857 18.55 3.44 46.96 2.57
190 191 2.346766 AGGTGTCATGCAACACTTCA 57.653 45.000 18.55 0.00 46.96 3.02
191 192 2.977405 GAGGTGTCATGCAACACTTC 57.023 50.000 18.55 16.95 46.96 3.01
192 193 1.949525 GTGAGGTGTCATGCAACACTT 59.050 47.619 18.55 12.83 46.96 3.16
193 194 1.134128 TGTGAGGTGTCATGCAACACT 60.134 47.619 18.55 7.29 46.96 3.55
195 196 2.275134 ATGTGAGGTGTCATGCAACA 57.725 45.000 7.72 0.00 37.23 3.33
196 197 3.691118 ACATATGTGAGGTGTCATGCAAC 59.309 43.478 7.78 0.00 34.36 4.17
197 198 3.954200 ACATATGTGAGGTGTCATGCAA 58.046 40.909 7.78 0.00 34.36 4.08
198 199 3.632643 ACATATGTGAGGTGTCATGCA 57.367 42.857 7.78 0.00 34.36 3.96
199 200 3.488047 GCAACATATGTGAGGTGTCATGC 60.488 47.826 9.63 8.30 34.36 4.06
200 201 3.943381 AGCAACATATGTGAGGTGTCATG 59.057 43.478 9.63 1.55 34.36 3.07
201 202 4.226427 AGCAACATATGTGAGGTGTCAT 57.774 40.909 9.63 0.00 34.36 3.06
202 203 3.701205 AGCAACATATGTGAGGTGTCA 57.299 42.857 9.63 0.00 0.00 3.58
203 204 3.871594 GGTAGCAACATATGTGAGGTGTC 59.128 47.826 9.63 8.58 0.00 3.67
204 205 3.370527 GGGTAGCAACATATGTGAGGTGT 60.371 47.826 9.63 0.00 0.00 4.16
205 206 3.206150 GGGTAGCAACATATGTGAGGTG 58.794 50.000 9.63 4.98 0.00 4.00
206 207 2.843730 TGGGTAGCAACATATGTGAGGT 59.156 45.455 9.63 13.02 0.00 3.85
207 208 3.118261 AGTGGGTAGCAACATATGTGAGG 60.118 47.826 9.63 3.66 0.00 3.86
208 209 3.873361 CAGTGGGTAGCAACATATGTGAG 59.127 47.826 9.63 6.66 0.00 3.51
209 210 3.263170 ACAGTGGGTAGCAACATATGTGA 59.737 43.478 9.63 0.00 0.00 3.58
210 211 3.374988 CACAGTGGGTAGCAACATATGTG 59.625 47.826 9.63 4.24 33.75 3.21
211 212 3.263170 TCACAGTGGGTAGCAACATATGT 59.737 43.478 1.41 1.41 0.00 2.29
212 213 3.872696 TCACAGTGGGTAGCAACATATG 58.127 45.455 1.58 0.00 0.00 1.78
213 214 4.517285 CTTCACAGTGGGTAGCAACATAT 58.483 43.478 1.58 0.00 0.00 1.78
214 215 3.307410 CCTTCACAGTGGGTAGCAACATA 60.307 47.826 1.58 0.00 0.00 2.29
215 216 2.553028 CCTTCACAGTGGGTAGCAACAT 60.553 50.000 1.58 0.00 0.00 2.71
216 217 1.202758 CCTTCACAGTGGGTAGCAACA 60.203 52.381 1.58 0.00 0.00 3.33
217 218 1.202770 ACCTTCACAGTGGGTAGCAAC 60.203 52.381 0.00 0.00 0.00 4.17
218 219 1.136828 ACCTTCACAGTGGGTAGCAA 58.863 50.000 0.00 0.00 0.00 3.91
219 220 1.899814 CTACCTTCACAGTGGGTAGCA 59.100 52.381 18.09 0.00 43.70 3.49
220 221 2.674796 CTACCTTCACAGTGGGTAGC 57.325 55.000 18.09 0.00 43.70 3.58
222 223 8.505246 TCTATATTACTACCTTCACAGTGGGTA 58.495 37.037 0.00 4.71 34.86 3.69
223 224 7.359849 TCTATATTACTACCTTCACAGTGGGT 58.640 38.462 0.00 3.68 37.16 4.51
224 225 7.834881 TCTATATTACTACCTTCACAGTGGG 57.165 40.000 0.00 0.00 0.00 4.61
261 262 9.473640 GGGTAATAACTTAGAGTAGTAACATGC 57.526 37.037 0.00 0.00 0.00 4.06
268 269 9.263446 TCACAATGGGTAATAACTTAGAGTAGT 57.737 33.333 0.00 0.00 0.00 2.73
269 270 9.530633 GTCACAATGGGTAATAACTTAGAGTAG 57.469 37.037 0.00 0.00 0.00 2.57
270 271 9.263446 AGTCACAATGGGTAATAACTTAGAGTA 57.737 33.333 0.00 0.00 0.00 2.59
271 272 8.147244 AGTCACAATGGGTAATAACTTAGAGT 57.853 34.615 0.00 0.00 0.00 3.24
272 273 9.751542 CTAGTCACAATGGGTAATAACTTAGAG 57.248 37.037 0.00 0.00 0.00 2.43
273 274 9.263446 ACTAGTCACAATGGGTAATAACTTAGA 57.737 33.333 0.00 0.00 0.00 2.10
274 275 9.530633 GACTAGTCACAATGGGTAATAACTTAG 57.469 37.037 18.20 0.00 0.00 2.18
275 276 9.263446 AGACTAGTCACAATGGGTAATAACTTA 57.737 33.333 24.44 0.00 0.00 2.24
276 277 8.147244 AGACTAGTCACAATGGGTAATAACTT 57.853 34.615 24.44 0.00 0.00 2.66
277 278 7.735326 AGACTAGTCACAATGGGTAATAACT 57.265 36.000 24.44 0.00 0.00 2.24
278 279 9.530633 CTAAGACTAGTCACAATGGGTAATAAC 57.469 37.037 24.44 0.00 0.00 1.89
279 280 9.483489 TCTAAGACTAGTCACAATGGGTAATAA 57.517 33.333 24.44 0.00 0.00 1.40
280 281 9.132923 CTCTAAGACTAGTCACAATGGGTAATA 57.867 37.037 24.44 0.59 0.00 0.98
281 282 7.070074 CCTCTAAGACTAGTCACAATGGGTAAT 59.930 40.741 24.44 0.00 0.00 1.89
282 283 6.380274 CCTCTAAGACTAGTCACAATGGGTAA 59.620 42.308 24.44 0.00 0.00 2.85
283 284 5.892119 CCTCTAAGACTAGTCACAATGGGTA 59.108 44.000 24.44 3.30 0.00 3.69
284 285 4.712337 CCTCTAAGACTAGTCACAATGGGT 59.288 45.833 24.44 0.00 0.00 4.51
285 286 4.100189 CCCTCTAAGACTAGTCACAATGGG 59.900 50.000 24.44 22.30 0.00 4.00
286 287 4.100189 CCCCTCTAAGACTAGTCACAATGG 59.900 50.000 24.44 18.19 0.00 3.16
287 288 4.100189 CCCCCTCTAAGACTAGTCACAATG 59.900 50.000 24.44 11.07 0.00 2.82
288 289 4.290942 CCCCCTCTAAGACTAGTCACAAT 58.709 47.826 24.44 10.13 0.00 2.71
289 290 3.709587 CCCCCTCTAAGACTAGTCACAA 58.290 50.000 24.44 8.44 0.00 3.33
290 291 2.623502 GCCCCCTCTAAGACTAGTCACA 60.624 54.545 24.44 10.55 0.00 3.58
291 292 2.033372 GCCCCCTCTAAGACTAGTCAC 58.967 57.143 24.44 0.00 0.00 3.67
292 293 1.644337 TGCCCCCTCTAAGACTAGTCA 59.356 52.381 24.44 4.18 0.00 3.41
293 294 2.456073 TGCCCCCTCTAAGACTAGTC 57.544 55.000 15.41 15.41 0.00 2.59
294 295 2.942604 TTGCCCCCTCTAAGACTAGT 57.057 50.000 0.00 0.00 0.00 2.57
295 296 2.158885 GCTTTGCCCCCTCTAAGACTAG 60.159 54.545 0.00 0.00 0.00 2.57
296 297 1.838077 GCTTTGCCCCCTCTAAGACTA 59.162 52.381 0.00 0.00 0.00 2.59
297 298 0.621082 GCTTTGCCCCCTCTAAGACT 59.379 55.000 0.00 0.00 0.00 3.24
298 299 0.744771 CGCTTTGCCCCCTCTAAGAC 60.745 60.000 0.00 0.00 0.00 3.01
299 300 1.602237 CGCTTTGCCCCCTCTAAGA 59.398 57.895 0.00 0.00 0.00 2.10
300 301 2.115291 GCGCTTTGCCCCCTCTAAG 61.115 63.158 0.00 0.00 37.76 2.18
396 410 0.251165 ACTGCACAGGCCCGTATTTT 60.251 50.000 0.00 0.00 40.13 1.82
480 494 9.364653 GGGAATTAGAACTCTTGATACCTAGTA 57.635 37.037 0.00 0.00 0.00 1.82
481 495 7.290481 GGGGAATTAGAACTCTTGATACCTAGT 59.710 40.741 0.00 0.00 0.00 2.57
482 496 7.524038 CGGGGAATTAGAACTCTTGATACCTAG 60.524 44.444 0.00 0.00 0.00 3.02
505 519 2.032030 GTGATTTATTCCACGCATCGGG 60.032 50.000 0.00 0.00 0.00 5.14
564 578 4.708177 CCTCAGTACGATTGGATTGGATT 58.292 43.478 0.00 0.00 0.00 3.01
622 637 1.109323 CCATTTCCCTCCCCGCATTC 61.109 60.000 0.00 0.00 0.00 2.67
628 643 0.702706 AGATCCCCATTTCCCTCCCC 60.703 60.000 0.00 0.00 0.00 4.81
852 867 1.227383 CCATTAGTGGGTGGGGAGC 59.773 63.158 0.00 0.00 42.11 4.70
938 957 0.392461 GTGGAAGTAGATTGCCGGCA 60.392 55.000 29.03 29.03 0.00 5.69
1191 1211 3.090532 GGGAGGAATGCGGGGAGT 61.091 66.667 0.00 0.00 0.00 3.85
1516 1536 2.535485 ATTCCATCGAACAGGGCGCA 62.535 55.000 10.83 0.00 0.00 6.09
1601 1621 3.665675 AACACCTCGAGCGCATCCC 62.666 63.158 11.47 0.00 0.00 3.85
1818 1838 3.426568 GCTGCGAACACCTGCCTC 61.427 66.667 0.00 0.00 0.00 4.70
1981 2001 2.515523 GGCACATGCGCTGAGGAT 60.516 61.111 9.73 0.00 43.26 3.24
2172 2192 0.804544 GCGCACCTAGCACATACGAA 60.805 55.000 0.30 0.00 46.13 3.85
2178 2198 3.939837 GAGCAGCGCACCTAGCACA 62.940 63.158 11.47 0.00 46.13 4.57
2223 2243 1.667830 CTTTCCGAGCTTCACGCCA 60.668 57.895 0.00 0.00 40.39 5.69
2535 2555 0.605589 AAGCCTACGCCAAGTTGGAC 60.606 55.000 26.52 15.20 46.59 4.02
2588 2608 4.124851 ACTTATAAGAGGCCAAGACACG 57.875 45.455 19.38 0.00 0.00 4.49
2620 2640 0.747852 TGTGGTACGAGTCTGCAACA 59.252 50.000 0.00 0.00 0.00 3.33
2624 2644 2.030540 TGTAGTTGTGGTACGAGTCTGC 60.031 50.000 0.00 0.00 0.00 4.26
2655 2675 1.340600 CCCCCTTTCGGCTGAACAATA 60.341 52.381 7.69 0.00 32.71 1.90
2671 2691 2.129785 GCAATGGATCTGTGCCCCC 61.130 63.158 0.00 0.00 31.94 5.40
2677 2697 3.199289 TGTCATCTGAGCAATGGATCTGT 59.801 43.478 0.00 0.00 31.27 3.41
2884 2909 7.995289 TCACATTTGGTAATCATTCCATACAC 58.005 34.615 0.00 0.00 33.50 2.90
2911 2936 1.829222 TGAAGGAACCCGTGGAGATAC 59.171 52.381 0.00 0.00 0.00 2.24
2923 2948 3.823304 ACTTCTCAAATGCCTGAAGGAAC 59.177 43.478 0.00 0.00 39.90 3.62
2939 2964 9.030301 GCTCATTAGACTCTTTATCAACTTCTC 57.970 37.037 0.00 0.00 0.00 2.87
2956 2981 4.323028 CCTTGTGTCTTCCAGCTCATTAGA 60.323 45.833 0.00 0.00 0.00 2.10
3015 3040 7.254252 CGGAATTGCAGAAAAACAAACATGTAA 60.254 33.333 0.00 0.00 0.00 2.41
3016 3041 6.199908 CGGAATTGCAGAAAAACAAACATGTA 59.800 34.615 0.00 0.00 0.00 2.29
3017 3042 5.006552 CGGAATTGCAGAAAAACAAACATGT 59.993 36.000 0.00 0.00 0.00 3.21
3018 3043 5.433855 CGGAATTGCAGAAAAACAAACATG 58.566 37.500 0.00 0.00 0.00 3.21
3101 3126 4.691216 ACTTGAGAAGTTTCTGATTACGGC 59.309 41.667 0.00 0.00 39.04 5.68
3162 3189 7.433680 AGTTGAAAAGTGTTTTCTCACTGTTT 58.566 30.769 12.15 4.15 46.25 2.83
3165 3192 9.226345 GATAAGTTGAAAAGTGTTTTCTCACTG 57.774 33.333 12.15 0.00 46.25 3.66
3167 3194 8.406297 AGGATAAGTTGAAAAGTGTTTTCTCAC 58.594 33.333 12.15 9.21 47.00 3.51
3168 3195 8.519799 AGGATAAGTTGAAAAGTGTTTTCTCA 57.480 30.769 12.15 0.00 47.00 3.27
3169 3196 9.452065 GAAGGATAAGTTGAAAAGTGTTTTCTC 57.548 33.333 12.15 6.70 47.00 2.87
3170 3197 8.966868 TGAAGGATAAGTTGAAAAGTGTTTTCT 58.033 29.630 12.15 0.00 47.00 2.52
3173 3200 8.293699 ACTGAAGGATAAGTTGAAAAGTGTTT 57.706 30.769 0.00 0.00 0.00 2.83
3184 3213 5.941788 AGGTTGACAACTGAAGGATAAGTT 58.058 37.500 17.52 0.00 37.09 2.66
3199 3228 3.244422 ACTGCGGAAAAGATAGGTTGACA 60.244 43.478 0.00 0.00 0.00 3.58
3203 3232 4.015872 TGAACTGCGGAAAAGATAGGTT 57.984 40.909 0.00 0.00 0.00 3.50
3214 3243 3.904800 TGAATTAGGATGAACTGCGGA 57.095 42.857 0.00 0.00 0.00 5.54
3215 3244 3.879295 ACATGAATTAGGATGAACTGCGG 59.121 43.478 0.00 0.00 0.00 5.69
3216 3245 5.490139 AACATGAATTAGGATGAACTGCG 57.510 39.130 0.00 0.00 0.00 5.18
3254 3283 5.996644 TCTGAGGAAAACTAAAACTGACCA 58.003 37.500 0.00 0.00 0.00 4.02
3255 3284 7.511959 AATCTGAGGAAAACTAAAACTGACC 57.488 36.000 0.00 0.00 0.00 4.02
3265 3294 5.188751 AGCTGCTAGTAATCTGAGGAAAACT 59.811 40.000 0.00 0.00 0.00 2.66
3293 3322 1.016130 GCACCACTGTGACATCTCCG 61.016 60.000 9.86 0.00 45.76 4.63
3335 3364 1.003718 AACTTAGGCTGCCACCGTC 60.004 57.895 22.65 0.00 33.69 4.79
3337 3366 1.003839 TGAACTTAGGCTGCCACCG 60.004 57.895 22.65 10.37 33.69 4.94
3344 3373 2.158696 GGCCATCATCTGAACTTAGGCT 60.159 50.000 0.00 0.00 40.61 4.58
3345 3374 2.225467 GGCCATCATCTGAACTTAGGC 58.775 52.381 0.00 0.00 40.08 3.93
3353 3382 1.383109 ACCGAGGGCCATCATCTGA 60.383 57.895 19.00 0.00 0.00 3.27
3364 3393 2.743928 GCTGCTCAACACCGAGGG 60.744 66.667 0.00 0.00 33.36 4.30
3365 3394 1.739562 GAGCTGCTCAACACCGAGG 60.740 63.158 24.02 0.00 33.36 4.63
3366 3395 1.005748 TGAGCTGCTCAACACCGAG 60.006 57.895 28.72 0.00 37.57 4.63
3367 3396 1.005748 CTGAGCTGCTCAACACCGA 60.006 57.895 30.00 8.46 40.18 4.69
3368 3397 1.301244 ACTGAGCTGCTCAACACCG 60.301 57.895 30.00 20.87 40.18 4.94
3369 3398 0.250038 TCACTGAGCTGCTCAACACC 60.250 55.000 30.00 5.34 40.18 4.16
3370 3399 1.530293 CTTCACTGAGCTGCTCAACAC 59.470 52.381 30.00 6.08 40.18 3.32
3440 3469 0.107410 TGTCCGTGAACAGCAAGGTT 60.107 50.000 0.00 0.00 45.18 3.50
3472 3501 5.339282 CCACGGGAGATCTATAGGTAGATGA 60.339 48.000 0.00 0.00 45.47 2.92
3475 3504 4.173594 TCCACGGGAGATCTATAGGTAGA 58.826 47.826 0.00 0.00 41.03 2.59
3656 3685 7.540474 AGTCACAGGAACTAATCAGACTAAA 57.460 36.000 0.00 0.00 36.02 1.85
3659 3688 6.249951 ACTAGTCACAGGAACTAATCAGACT 58.750 40.000 0.00 0.00 36.02 3.24
3660 3689 6.518208 ACTAGTCACAGGAACTAATCAGAC 57.482 41.667 0.00 0.00 36.02 3.51
3672 3701 8.453238 AGTAGTACATATGAACTAGTCACAGG 57.547 38.462 10.38 0.00 39.72 4.00
3681 3710 8.998277 ATACACAGGAGTAGTACATATGAACT 57.002 34.615 10.38 7.06 0.00 3.01
3686 3715 9.908747 GAGGATATACACAGGAGTAGTACATAT 57.091 37.037 2.52 0.00 0.00 1.78
3715 3759 7.721399 AGAACCAGAAAGAAACAACATAGACAT 59.279 33.333 0.00 0.00 0.00 3.06
3787 4667 4.201841 TGCAAGTCATCGCACAATTAGATG 60.202 41.667 0.00 0.00 42.11 2.90
3798 4678 3.404978 TTGCATTGCAAGTCATCGC 57.595 47.368 19.77 1.23 43.99 4.58
3846 4774 4.640771 TCCAAAGAAGCCAGTCTATTGT 57.359 40.909 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.