Multiple sequence alignment - TraesCS2B01G539100

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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 TraesCS2B01G539100 chr2B 100.000 2487 0 0 1 2487 734201481 734198995 0.000000e+00 4593.0
1 TraesCS2B01G539100 chr2B 86.989 269 14 9 1220 1485 734185426 734185176 1.460000e-72 283.0
2 TraesCS2B01G539100 chr2B 91.111 45 3 1 1956 1999 30654748 30654792 2.670000e-05 60.2
3 TraesCS2B01G539100 chr2A 91.150 1469 82 16 273 1705 735788767 735787311 0.000000e+00 1949.0
4 TraesCS2B01G539100 chr2A 83.955 268 32 9 1709 1968 735787210 735786946 1.910000e-61 246.0
5 TraesCS2B01G539100 chr2A 92.500 160 12 0 1706 1865 610228060 610228219 1.920000e-56 230.0
6 TraesCS2B01G539100 chr2A 96.774 62 1 1 1938 1998 721520878 721520817 4.380000e-18 102.0
7 TraesCS2B01G539100 chr2D 89.140 1372 100 21 1148 2487 603648558 603647204 0.000000e+00 1663.0
8 TraesCS2B01G539100 chr2D 91.590 868 31 10 273 1110 603649414 603648559 0.000000e+00 1160.0
9 TraesCS2B01G539100 chr2D 80.480 625 55 29 875 1485 603632915 603632344 1.380000e-112 416.0
10 TraesCS2B01G539100 chr2D 93.590 156 10 0 1710 1865 135988930 135988775 1.490000e-57 233.0
11 TraesCS2B01G539100 chr2D 88.194 144 13 1 742 885 603638892 603638753 4.250000e-38 169.0
12 TraesCS2B01G539100 chr7D 94.375 160 9 0 1706 1865 530797182 530797341 1.910000e-61 246.0
13 TraesCS2B01G539100 chr7D 74.263 373 75 19 2060 2421 611215883 611216245 1.200000e-28 137.0
14 TraesCS2B01G539100 chr5D 93.125 160 11 0 1706 1865 503305275 503305116 4.140000e-58 235.0
15 TraesCS2B01G539100 chr5D 72.960 429 84 23 2056 2463 550661691 550662108 1.210000e-23 121.0
16 TraesCS2B01G539100 chr3B 93.125 160 11 0 1706 1865 101926023 101925864 4.140000e-58 235.0
17 TraesCS2B01G539100 chr1D 93.125 160 11 0 1706 1865 254448443 254448284 4.140000e-58 235.0
18 TraesCS2B01G539100 chr4D 91.875 160 13 0 1706 1865 19881858 19881699 8.950000e-55 224.0
19 TraesCS2B01G539100 chr1B 75.467 428 88 13 2063 2477 325287084 325286661 2.520000e-45 193.0
20 TraesCS2B01G539100 chr7A 80.374 214 29 9 2063 2266 443346766 443346976 1.540000e-32 150.0
21 TraesCS2B01G539100 chr5B 84.247 146 17 5 1307 1449 357132390 357132532 1.200000e-28 137.0
22 TraesCS2B01G539100 chr4A 72.627 453 93 20 2056 2485 477792913 477793357 1.210000e-23 121.0
23 TraesCS2B01G539100 chr6B 83.582 67 10 1 1934 1999 182748565 182748499 7.430000e-06 62.1
24 TraesCS2B01G539100 chr3A 89.583 48 3 2 1954 1999 534469789 534469836 2.670000e-05 60.2


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 TraesCS2B01G539100 chr2B 734198995 734201481 2486 True 4593.0 4593 100.0000 1 2487 1 chr2B.!!$R2 2486
1 TraesCS2B01G539100 chr2A 735786946 735788767 1821 True 1097.5 1949 87.5525 273 1968 2 chr2A.!!$R2 1695
2 TraesCS2B01G539100 chr2D 603647204 603649414 2210 True 1411.5 1663 90.3650 273 2487 2 chr2D.!!$R4 2214
3 TraesCS2B01G539100 chr2D 603632344 603632915 571 True 416.0 416 80.4800 875 1485 1 chr2D.!!$R2 610

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
183 184 0.034896 GTTGGCTGAAAGGACTCCGA 59.965 55.0 0.00 0.0 0.00 4.55 F
257 258 0.035317 TGGTGCTCCTGTGATGTGAC 59.965 55.0 6.34 0.0 34.23 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1103 0.179051 GAGCAGGAAGAGGCAGATGG 60.179 60.0 0.0 0.0 0.00 3.51 R
2110 2284 0.308068 CATCTCGTATCGTCAGCCGT 59.692 55.0 0.0 0.0 37.94 5.68 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
19 20 4.728102 CGTAACGCCCGTGAGCCA 62.728 66.667 0.00 0.00 0.00 4.75
20 21 2.125269 GTAACGCCCGTGAGCCAT 60.125 61.111 0.00 0.00 0.00 4.40
21 22 2.171725 GTAACGCCCGTGAGCCATC 61.172 63.158 0.00 0.00 0.00 3.51
22 23 2.651105 TAACGCCCGTGAGCCATCA 61.651 57.895 0.00 0.00 0.00 3.07
23 24 2.173758 TAACGCCCGTGAGCCATCAA 62.174 55.000 0.00 0.00 37.14 2.57
24 25 2.745884 CGCCCGTGAGCCATCAAA 60.746 61.111 0.00 0.00 37.14 2.69
25 26 2.877691 GCCCGTGAGCCATCAAAC 59.122 61.111 0.00 0.00 37.14 2.93
26 27 2.700773 GCCCGTGAGCCATCAAACC 61.701 63.158 0.00 0.00 37.14 3.27
27 28 2.398554 CCCGTGAGCCATCAAACCG 61.399 63.158 0.00 0.00 37.14 4.44
28 29 2.398554 CCGTGAGCCATCAAACCGG 61.399 63.158 0.00 0.00 37.14 5.28
29 30 2.398554 CGTGAGCCATCAAACCGGG 61.399 63.158 6.32 0.00 37.14 5.73
30 31 2.046285 GTGAGCCATCAAACCGGGG 61.046 63.158 6.32 0.00 37.14 5.73
31 32 3.140814 GAGCCATCAAACCGGGGC 61.141 66.667 6.32 7.88 46.77 5.80
35 36 4.374584 CATCAAACCGGGGCCCCA 62.375 66.667 40.06 20.88 35.37 4.96
36 37 3.355344 ATCAAACCGGGGCCCCAT 61.355 61.111 40.06 25.40 35.37 4.00
37 38 3.677480 ATCAAACCGGGGCCCCATG 62.677 63.158 40.06 31.06 35.37 3.66
38 39 4.694987 CAAACCGGGGCCCCATGT 62.695 66.667 40.06 31.76 35.37 3.21
39 40 4.694987 AAACCGGGGCCCCATGTG 62.695 66.667 40.06 25.90 35.37 3.21
56 57 2.203294 GGCTCCACCAACACCGTT 60.203 61.111 0.00 0.00 38.86 4.44
57 58 1.071814 GGCTCCACCAACACCGTTA 59.928 57.895 0.00 0.00 38.86 3.18
58 59 0.953960 GGCTCCACCAACACCGTTAG 60.954 60.000 0.00 0.00 38.86 2.34
59 60 1.574702 GCTCCACCAACACCGTTAGC 61.575 60.000 0.00 0.00 0.00 3.09
60 61 1.289109 CTCCACCAACACCGTTAGCG 61.289 60.000 0.00 0.00 37.95 4.26
61 62 1.595929 CCACCAACACCGTTAGCGT 60.596 57.895 0.00 0.00 36.15 5.07
62 63 1.567537 CACCAACACCGTTAGCGTG 59.432 57.895 0.00 0.00 36.15 5.34
63 64 1.144496 ACCAACACCGTTAGCGTGT 59.856 52.632 0.00 0.05 35.22 4.49
64 65 0.462403 ACCAACACCGTTAGCGTGTT 60.462 50.000 11.81 11.81 40.28 3.32
65 66 0.041663 CCAACACCGTTAGCGTGTTG 60.042 55.000 25.35 25.35 46.57 3.33
66 67 0.041663 CAACACCGTTAGCGTGTTGG 60.042 55.000 24.96 14.60 45.21 3.77
67 68 1.778027 AACACCGTTAGCGTGTTGGC 61.778 55.000 15.12 0.00 39.19 4.52
68 69 2.109387 ACCGTTAGCGTGTTGGCA 59.891 55.556 0.00 0.00 36.15 4.92
69 70 1.959226 ACCGTTAGCGTGTTGGCAG 60.959 57.895 0.00 0.00 36.15 4.85
70 71 1.959226 CCGTTAGCGTGTTGGCAGT 60.959 57.895 0.00 0.00 36.15 4.40
71 72 1.204062 CGTTAGCGTGTTGGCAGTG 59.796 57.895 0.00 0.00 34.64 3.66
72 73 1.574428 GTTAGCGTGTTGGCAGTGG 59.426 57.895 0.00 0.00 34.64 4.00
73 74 1.599518 TTAGCGTGTTGGCAGTGGG 60.600 57.895 0.00 0.00 34.64 4.61
74 75 2.332312 TTAGCGTGTTGGCAGTGGGT 62.332 55.000 0.00 0.00 34.64 4.51
75 76 3.964875 GCGTGTTGGCAGTGGGTG 61.965 66.667 0.00 0.00 0.00 4.61
76 77 3.286751 CGTGTTGGCAGTGGGTGG 61.287 66.667 0.00 0.00 0.00 4.61
77 78 2.912025 GTGTTGGCAGTGGGTGGG 60.912 66.667 0.00 0.00 0.00 4.61
78 79 3.425014 TGTTGGCAGTGGGTGGGT 61.425 61.111 0.00 0.00 0.00 4.51
79 80 2.123468 GTTGGCAGTGGGTGGGTT 60.123 61.111 0.00 0.00 0.00 4.11
80 81 2.197324 TTGGCAGTGGGTGGGTTC 59.803 61.111 0.00 0.00 0.00 3.62
81 82 2.391130 TTGGCAGTGGGTGGGTTCT 61.391 57.895 0.00 0.00 0.00 3.01
82 83 1.063070 TTGGCAGTGGGTGGGTTCTA 61.063 55.000 0.00 0.00 0.00 2.10
83 84 1.299976 GGCAGTGGGTGGGTTCTAG 59.700 63.158 0.00 0.00 0.00 2.43
84 85 1.377333 GCAGTGGGTGGGTTCTAGC 60.377 63.158 0.00 0.00 0.00 3.42
85 86 1.842381 GCAGTGGGTGGGTTCTAGCT 61.842 60.000 0.00 0.00 0.00 3.32
86 87 1.568504 CAGTGGGTGGGTTCTAGCTA 58.431 55.000 0.00 0.00 0.00 3.32
87 88 1.906574 CAGTGGGTGGGTTCTAGCTAA 59.093 52.381 0.00 0.00 0.00 3.09
88 89 2.304761 CAGTGGGTGGGTTCTAGCTAAA 59.695 50.000 0.00 0.00 0.00 1.85
89 90 2.983898 AGTGGGTGGGTTCTAGCTAAAA 59.016 45.455 0.00 0.00 0.00 1.52
90 91 3.396611 AGTGGGTGGGTTCTAGCTAAAAA 59.603 43.478 0.00 0.00 0.00 1.94
91 92 3.504906 GTGGGTGGGTTCTAGCTAAAAAC 59.495 47.826 9.25 9.25 0.00 2.43
92 93 3.396611 TGGGTGGGTTCTAGCTAAAAACT 59.603 43.478 14.86 0.00 0.00 2.66
93 94 4.598373 TGGGTGGGTTCTAGCTAAAAACTA 59.402 41.667 14.86 0.00 0.00 2.24
94 95 5.073417 TGGGTGGGTTCTAGCTAAAAACTAA 59.927 40.000 14.86 4.96 0.00 2.24
95 96 6.005823 GGGTGGGTTCTAGCTAAAAACTAAA 58.994 40.000 14.86 3.17 0.00 1.85
96 97 6.491062 GGGTGGGTTCTAGCTAAAAACTAAAA 59.509 38.462 14.86 1.39 0.00 1.52
97 98 7.014518 GGGTGGGTTCTAGCTAAAAACTAAAAA 59.985 37.037 14.86 0.14 0.00 1.94
98 99 7.864379 GGTGGGTTCTAGCTAAAAACTAAAAAC 59.136 37.037 14.86 8.58 0.00 2.43
99 100 8.407832 GTGGGTTCTAGCTAAAAACTAAAAACA 58.592 33.333 14.86 0.00 0.00 2.83
100 101 8.968969 TGGGTTCTAGCTAAAAACTAAAAACAA 58.031 29.630 14.86 0.00 0.00 2.83
101 102 9.241317 GGGTTCTAGCTAAAAACTAAAAACAAC 57.759 33.333 14.86 0.00 0.00 3.32
102 103 8.950961 GGTTCTAGCTAAAAACTAAAAACAACG 58.049 33.333 14.86 0.00 0.00 4.10
103 104 9.706846 GTTCTAGCTAAAAACTAAAAACAACGA 57.293 29.630 10.13 0.00 0.00 3.85
104 105 9.706846 TTCTAGCTAAAAACTAAAAACAACGAC 57.293 29.630 0.00 0.00 0.00 4.34
105 106 8.057742 TCTAGCTAAAAACTAAAAACAACGACG 58.942 33.333 0.00 0.00 0.00 5.12
106 107 6.545508 AGCTAAAAACTAAAAACAACGACGT 58.454 32.000 0.00 0.00 0.00 4.34
107 108 7.683746 AGCTAAAAACTAAAAACAACGACGTA 58.316 30.769 0.00 0.00 0.00 3.57
108 109 8.337532 AGCTAAAAACTAAAAACAACGACGTAT 58.662 29.630 0.00 0.00 0.00 3.06
109 110 8.404492 GCTAAAAACTAAAAACAACGACGTATG 58.596 33.333 0.00 4.80 0.00 2.39
110 111 9.424659 CTAAAAACTAAAAACAACGACGTATGT 57.575 29.630 0.00 5.47 0.00 2.29
111 112 7.653523 AAAACTAAAAACAACGACGTATGTG 57.346 32.000 0.00 0.00 0.00 3.21
112 113 6.586868 AACTAAAAACAACGACGTATGTGA 57.413 33.333 0.00 0.00 0.00 3.58
113 114 6.586868 ACTAAAAACAACGACGTATGTGAA 57.413 33.333 0.00 0.00 0.00 3.18
114 115 6.642917 ACTAAAAACAACGACGTATGTGAAG 58.357 36.000 0.00 6.84 0.00 3.02
115 116 5.721876 AAAAACAACGACGTATGTGAAGA 57.278 34.783 0.00 0.00 0.00 2.87
116 117 4.966850 AAACAACGACGTATGTGAAGAG 57.033 40.909 0.00 0.00 0.00 2.85
117 118 3.909776 ACAACGACGTATGTGAAGAGA 57.090 42.857 0.00 0.00 0.00 3.10
118 119 4.233123 ACAACGACGTATGTGAAGAGAA 57.767 40.909 0.00 0.00 0.00 2.87
119 120 4.806330 ACAACGACGTATGTGAAGAGAAT 58.194 39.130 0.00 0.00 0.00 2.40
120 121 4.857588 ACAACGACGTATGTGAAGAGAATC 59.142 41.667 0.00 0.00 0.00 2.52
121 122 4.696899 ACGACGTATGTGAAGAGAATCA 57.303 40.909 0.00 0.00 37.82 2.57
122 123 5.055642 ACGACGTATGTGAAGAGAATCAA 57.944 39.130 0.00 0.00 37.82 2.57
123 124 5.466819 ACGACGTATGTGAAGAGAATCAAA 58.533 37.500 0.00 0.00 37.82 2.69
124 125 6.100004 ACGACGTATGTGAAGAGAATCAAAT 58.900 36.000 0.00 0.00 37.82 2.32
125 126 7.255569 ACGACGTATGTGAAGAGAATCAAATA 58.744 34.615 0.00 0.00 37.82 1.40
126 127 7.220300 ACGACGTATGTGAAGAGAATCAAATAC 59.780 37.037 0.00 7.32 42.97 1.89
127 128 7.220108 CGACGTATGTGAAGAGAATCAAATACA 59.780 37.037 14.64 0.00 45.10 2.29
128 129 8.948631 ACGTATGTGAAGAGAATCAAATACAT 57.051 30.769 14.64 0.00 45.10 2.29
129 130 9.035607 ACGTATGTGAAGAGAATCAAATACATC 57.964 33.333 14.64 0.00 45.10 3.06
130 131 9.034544 CGTATGTGAAGAGAATCAAATACATCA 57.965 33.333 14.64 0.00 45.10 3.07
135 136 9.512435 GTGAAGAGAATCAAATACATCAAATGG 57.488 33.333 0.00 0.00 37.82 3.16
136 137 9.246670 TGAAGAGAATCAAATACATCAAATGGT 57.753 29.630 0.00 0.00 37.82 3.55
155 156 9.832445 CAAATGGTAAAGATACATAGTAGGTGT 57.168 33.333 0.00 0.00 33.45 4.16
157 158 8.777578 ATGGTAAAGATACATAGTAGGTGTCA 57.222 34.615 13.19 0.00 33.45 3.58
158 159 8.234136 TGGTAAAGATACATAGTAGGTGTCAG 57.766 38.462 13.19 0.00 33.45 3.51
159 160 7.146648 GGTAAAGATACATAGTAGGTGTCAGC 58.853 42.308 13.19 0.00 33.45 4.26
160 161 5.440234 AAGATACATAGTAGGTGTCAGCG 57.560 43.478 13.19 0.00 0.00 5.18
161 162 4.462133 AGATACATAGTAGGTGTCAGCGT 58.538 43.478 13.19 0.00 0.00 5.07
162 163 2.941453 ACATAGTAGGTGTCAGCGTG 57.059 50.000 0.00 0.00 0.00 5.34
163 164 2.168496 ACATAGTAGGTGTCAGCGTGT 58.832 47.619 0.00 0.00 0.00 4.49
164 165 2.094700 ACATAGTAGGTGTCAGCGTGTG 60.095 50.000 0.00 0.00 0.00 3.82
165 166 1.612676 TAGTAGGTGTCAGCGTGTGT 58.387 50.000 0.00 0.00 0.00 3.72
166 167 0.750850 AGTAGGTGTCAGCGTGTGTT 59.249 50.000 0.00 0.00 0.00 3.32
167 168 0.859232 GTAGGTGTCAGCGTGTGTTG 59.141 55.000 0.00 0.00 0.00 3.33
168 169 0.249699 TAGGTGTCAGCGTGTGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
169 170 2.327940 GTGTCAGCGTGTGTTGGC 59.672 61.111 0.00 0.00 0.00 4.52
170 171 2.180204 GTGTCAGCGTGTGTTGGCT 61.180 57.895 0.00 0.00 40.90 4.75
174 175 4.234019 AGCGTGTGTTGGCTGAAA 57.766 50.000 0.00 0.00 38.27 2.69
175 176 2.024918 AGCGTGTGTTGGCTGAAAG 58.975 52.632 0.00 0.00 38.27 2.62
176 177 1.008538 GCGTGTGTTGGCTGAAAGG 60.009 57.895 0.00 0.00 0.00 3.11
177 178 1.444119 GCGTGTGTTGGCTGAAAGGA 61.444 55.000 0.00 0.00 0.00 3.36
178 179 0.307760 CGTGTGTTGGCTGAAAGGAC 59.692 55.000 0.00 0.00 0.00 3.85
179 180 1.680338 GTGTGTTGGCTGAAAGGACT 58.320 50.000 0.00 0.00 0.00 3.85
180 181 1.604278 GTGTGTTGGCTGAAAGGACTC 59.396 52.381 0.00 0.00 0.00 3.36
181 182 1.239347 GTGTTGGCTGAAAGGACTCC 58.761 55.000 0.00 0.00 0.00 3.85
182 183 0.250295 TGTTGGCTGAAAGGACTCCG 60.250 55.000 0.00 0.00 0.00 4.63
183 184 0.034896 GTTGGCTGAAAGGACTCCGA 59.965 55.000 0.00 0.00 0.00 4.55
184 185 0.984230 TTGGCTGAAAGGACTCCGAT 59.016 50.000 0.00 0.00 0.00 4.18
185 186 1.860641 TGGCTGAAAGGACTCCGATA 58.139 50.000 0.00 0.00 0.00 2.92
186 187 2.184533 TGGCTGAAAGGACTCCGATAA 58.815 47.619 0.00 0.00 0.00 1.75
187 188 2.771943 TGGCTGAAAGGACTCCGATAAT 59.228 45.455 0.00 0.00 0.00 1.28
188 189 3.199946 TGGCTGAAAGGACTCCGATAATT 59.800 43.478 0.00 0.00 0.00 1.40
189 190 4.200092 GGCTGAAAGGACTCCGATAATTT 58.800 43.478 0.00 0.00 0.00 1.82
190 191 4.640647 GGCTGAAAGGACTCCGATAATTTT 59.359 41.667 0.00 0.00 0.00 1.82
191 192 5.125578 GGCTGAAAGGACTCCGATAATTTTT 59.874 40.000 0.00 0.00 0.00 1.94
230 231 3.469564 TGTTCCACGAAACACTGCT 57.530 47.368 0.00 0.00 34.31 4.24
231 232 2.605837 TGTTCCACGAAACACTGCTA 57.394 45.000 0.00 0.00 34.31 3.49
232 233 3.120321 TGTTCCACGAAACACTGCTAT 57.880 42.857 0.00 0.00 34.31 2.97
233 234 4.260139 TGTTCCACGAAACACTGCTATA 57.740 40.909 0.00 0.00 34.31 1.31
234 235 4.827692 TGTTCCACGAAACACTGCTATAT 58.172 39.130 0.00 0.00 34.31 0.86
235 236 5.968254 TGTTCCACGAAACACTGCTATATA 58.032 37.500 0.00 0.00 34.31 0.86
236 237 6.578944 TGTTCCACGAAACACTGCTATATAT 58.421 36.000 0.00 0.00 34.31 0.86
237 238 7.718525 TGTTCCACGAAACACTGCTATATATA 58.281 34.615 0.00 0.00 34.31 0.86
238 239 8.364894 TGTTCCACGAAACACTGCTATATATAT 58.635 33.333 0.00 0.00 34.31 0.86
239 240 8.648097 GTTCCACGAAACACTGCTATATATATG 58.352 37.037 5.44 0.00 0.00 1.78
240 241 7.320399 TCCACGAAACACTGCTATATATATGG 58.680 38.462 5.44 3.57 0.00 2.74
241 242 7.039293 TCCACGAAACACTGCTATATATATGGT 60.039 37.037 5.44 0.00 0.00 3.55
242 243 7.063426 CCACGAAACACTGCTATATATATGGTG 59.937 40.741 5.44 10.58 0.00 4.17
243 244 6.590292 ACGAAACACTGCTATATATATGGTGC 59.410 38.462 5.44 7.64 0.00 5.01
244 245 6.813649 CGAAACACTGCTATATATATGGTGCT 59.186 38.462 5.44 0.00 0.00 4.40
245 246 7.009631 CGAAACACTGCTATATATATGGTGCTC 59.990 40.741 5.44 8.21 0.00 4.26
246 247 6.227298 ACACTGCTATATATATGGTGCTCC 57.773 41.667 5.44 0.00 0.00 4.70
247 248 5.960811 ACACTGCTATATATATGGTGCTCCT 59.039 40.000 6.34 0.00 34.23 3.69
248 249 6.127225 ACACTGCTATATATATGGTGCTCCTG 60.127 42.308 6.34 6.63 34.23 3.86
249 250 5.960811 ACTGCTATATATATGGTGCTCCTGT 59.039 40.000 6.34 0.00 34.23 4.00
250 251 6.127225 ACTGCTATATATATGGTGCTCCTGTG 60.127 42.308 6.34 0.35 34.23 3.66
251 252 5.957774 TGCTATATATATGGTGCTCCTGTGA 59.042 40.000 6.34 0.00 34.23 3.58
252 253 6.612863 TGCTATATATATGGTGCTCCTGTGAT 59.387 38.462 6.34 0.00 34.23 3.06
253 254 6.927936 GCTATATATATGGTGCTCCTGTGATG 59.072 42.308 6.34 0.00 34.23 3.07
254 255 6.881067 ATATATATGGTGCTCCTGTGATGT 57.119 37.500 6.34 0.00 34.23 3.06
255 256 2.696989 TATGGTGCTCCTGTGATGTG 57.303 50.000 6.34 0.00 34.23 3.21
256 257 0.986527 ATGGTGCTCCTGTGATGTGA 59.013 50.000 6.34 0.00 34.23 3.58
257 258 0.035317 TGGTGCTCCTGTGATGTGAC 59.965 55.000 6.34 0.00 34.23 3.67
258 259 0.674895 GGTGCTCCTGTGATGTGACC 60.675 60.000 0.00 0.00 0.00 4.02
259 260 0.035317 GTGCTCCTGTGATGTGACCA 59.965 55.000 0.00 0.00 0.00 4.02
260 261 0.986527 TGCTCCTGTGATGTGACCAT 59.013 50.000 0.00 0.00 0.00 3.55
261 262 2.093500 GTGCTCCTGTGATGTGACCATA 60.093 50.000 0.00 0.00 0.00 2.74
262 263 2.773661 TGCTCCTGTGATGTGACCATAT 59.226 45.455 0.00 0.00 0.00 1.78
263 264 3.181462 TGCTCCTGTGATGTGACCATATC 60.181 47.826 0.55 0.55 0.00 1.63
264 265 3.070734 GCTCCTGTGATGTGACCATATCT 59.929 47.826 7.96 0.00 31.27 1.98
265 266 4.444022 GCTCCTGTGATGTGACCATATCTT 60.444 45.833 7.96 0.00 31.27 2.40
266 267 5.221521 GCTCCTGTGATGTGACCATATCTTA 60.222 44.000 7.96 0.00 31.27 2.10
267 268 6.161855 TCCTGTGATGTGACCATATCTTAC 57.838 41.667 7.96 0.97 31.27 2.34
268 269 5.660864 TCCTGTGATGTGACCATATCTTACA 59.339 40.000 7.96 4.71 31.27 2.41
269 270 6.156083 TCCTGTGATGTGACCATATCTTACAA 59.844 38.462 7.96 0.00 31.27 2.41
270 271 6.481313 CCTGTGATGTGACCATATCTTACAAG 59.519 42.308 7.96 0.00 31.27 3.16
271 272 6.348498 TGTGATGTGACCATATCTTACAAGG 58.652 40.000 7.96 0.00 31.27 3.61
288 289 3.763897 ACAAGGTTGTTCAAAGAAGCTGT 59.236 39.130 5.27 4.01 38.80 4.40
301 302 0.951040 AAGCTGTTGCAGACGTAGGC 60.951 55.000 4.09 4.09 42.74 3.93
308 309 2.987413 TGCAGACGTAGGCAAATTTG 57.013 45.000 14.03 14.03 37.03 2.32
332 340 8.017587 TGCATGCTTAAAGATGTATACGTATG 57.982 34.615 20.33 0.00 0.00 2.39
531 563 0.964860 CACGGCATCCAATCAACCCA 60.965 55.000 0.00 0.00 0.00 4.51
548 580 1.405391 CCCATCCCAATTTCAAACCGC 60.405 52.381 0.00 0.00 0.00 5.68
563 595 4.157656 TCAAACCGCAGAGAAAATAATGGG 59.842 41.667 0.00 0.00 0.00 4.00
566 598 1.002468 CGCAGAGAAAATAATGGGCGG 60.002 52.381 0.00 0.00 39.59 6.13
575 607 2.265467 ATAATGGGCGGGCGTCACTT 62.265 55.000 0.00 0.00 0.00 3.16
636 668 2.954318 CCTGGATACCAAAGAAGCCATG 59.046 50.000 0.00 0.00 30.80 3.66
664 696 3.150848 CGTTCATCGGTTGATCTCTCA 57.849 47.619 0.00 0.00 33.34 3.27
665 697 3.511699 CGTTCATCGGTTGATCTCTCAA 58.488 45.455 0.00 0.00 36.11 3.02
728 760 2.049802 CGTGGTTGCGACGGTACT 60.050 61.111 0.00 0.00 32.29 2.73
799 831 3.392947 TCCATATTCCCTACGCAATCCAA 59.607 43.478 0.00 0.00 0.00 3.53
1046 1088 3.498661 CCCCAGTTCTATATCCCTTTGCC 60.499 52.174 0.00 0.00 0.00 4.52
1054 1096 1.140312 TATCCCTTTGCCCCAGCTAG 58.860 55.000 0.00 0.00 40.80 3.42
1055 1097 2.290021 ATCCCTTTGCCCCAGCTAGC 62.290 60.000 6.62 6.62 40.80 3.42
1056 1098 2.679716 CCTTTGCCCCAGCTAGCT 59.320 61.111 12.68 12.68 40.80 3.32
1057 1099 1.635817 CCCTTTGCCCCAGCTAGCTA 61.636 60.000 18.86 0.00 40.80 3.32
1061 1103 0.541863 TTGCCCCAGCTAGCTACTTC 59.458 55.000 18.86 8.02 40.80 3.01
1084 1134 0.176219 CTGCCTCTTCCTGCTCAGAG 59.824 60.000 0.00 0.00 36.96 3.35
1085 1135 0.251967 TGCCTCTTCCTGCTCAGAGA 60.252 55.000 0.00 0.00 39.21 3.10
1086 1136 0.461135 GCCTCTTCCTGCTCAGAGAG 59.539 60.000 0.00 8.03 39.21 3.20
1127 1178 6.161855 TCTGTTATCCATGTCCAGTATCAC 57.838 41.667 0.00 0.00 0.00 3.06
1135 1186 4.565444 CCATGTCCAGTATCACTTTGTCCA 60.565 45.833 0.00 0.00 0.00 4.02
1160 1215 2.596904 TGCCGGTAGAATTCAGCTAC 57.403 50.000 8.44 1.61 37.96 3.58
1223 1278 3.009723 GGGAATTTCATCTGTGCGAAGA 58.990 45.455 0.00 0.00 0.00 2.87
1336 1394 4.722700 GGGAAGAAGGCAGCGGCA 62.723 66.667 11.88 0.00 43.71 5.69
1492 1553 0.323451 TCCTCGCCTTCTAGCTGTCA 60.323 55.000 0.00 0.00 0.00 3.58
1509 1570 2.872245 TGTCAGCGTTCTTCAAAAGGAG 59.128 45.455 0.00 0.00 0.00 3.69
1660 1724 5.362143 ACACATGCAGTACTATCTGTCTCAT 59.638 40.000 0.00 0.00 37.70 2.90
1673 1737 1.344438 TGTCTCATCCGTGAACTTGCT 59.656 47.619 0.00 0.00 33.05 3.91
1705 1769 3.881089 TCCTGATATTAGAAGTGACGCGA 59.119 43.478 15.93 0.00 0.00 5.87
1706 1770 4.337274 TCCTGATATTAGAAGTGACGCGAA 59.663 41.667 15.93 0.00 0.00 4.70
1798 1959 2.436417 CGAAGGACCCACAACAATGAT 58.564 47.619 0.00 0.00 0.00 2.45
1817 1978 4.283337 TGATAGAACACCCCGAGTAATCA 58.717 43.478 0.00 0.00 0.00 2.57
1842 2003 0.320771 TTTCCCAAGCAGAGTCTCGC 60.321 55.000 8.15 8.15 0.00 5.03
1844 2005 2.507992 CCAAGCAGAGTCTCGCGG 60.508 66.667 6.13 0.00 0.00 6.46
1946 2114 5.686159 AGTCACTTCTTCAGAAATGCTTG 57.314 39.130 0.00 0.00 31.96 4.01
1950 2118 4.212004 CACTTCTTCAGAAATGCTTGTCGA 59.788 41.667 0.00 0.00 33.07 4.20
1952 2120 4.997905 TCTTCAGAAATGCTTGTCGAAG 57.002 40.909 13.41 13.41 0.00 3.79
1958 2126 5.469760 TCAGAAATGCTTGTCGAAGAAATGA 59.530 36.000 0.00 0.00 39.69 2.57
1970 2139 8.420374 TGTCGAAGAAATGAATGTATCTAACC 57.580 34.615 0.00 0.00 39.69 2.85
2034 2208 9.602568 TGCTATATAATTAAGTTGTTTCGGTCA 57.397 29.630 0.00 0.00 0.00 4.02
2057 2231 9.646427 GTCATATAAGATGACTTTATGGACTCC 57.354 37.037 9.36 0.00 43.62 3.85
2060 2234 7.698163 ATAAGATGACTTTATGGACTCCCTT 57.302 36.000 0.00 0.00 37.53 3.95
2078 2252 2.165641 CCTTAAAACTGGATTTCGCCCC 59.834 50.000 0.00 0.00 0.00 5.80
2079 2253 1.455248 TAAAACTGGATTTCGCCCCG 58.545 50.000 0.00 0.00 0.00 5.73
2116 2290 3.059188 ACAATCGAAAAAGTACACGGCTG 60.059 43.478 0.00 0.00 0.00 4.85
2117 2291 2.512485 TCGAAAAAGTACACGGCTGA 57.488 45.000 0.00 0.00 0.00 4.26
2157 2336 1.922447 AGCCCTCATACAACATCCCAA 59.078 47.619 0.00 0.00 0.00 4.12
2177 2356 2.851263 AATAACCGGAGCACACAGAA 57.149 45.000 9.46 0.00 0.00 3.02
2179 2358 0.319211 TAACCGGAGCACACAGAACG 60.319 55.000 9.46 0.00 0.00 3.95
2190 2369 1.301716 ACAGAACGCAAGCGACCAT 60.302 52.632 22.30 4.07 42.83 3.55
2192 2371 2.202349 GAACGCAAGCGACCATGC 60.202 61.111 22.30 0.00 42.83 4.06
2197 2376 1.745115 GCAAGCGACCATGCTACCA 60.745 57.895 0.00 0.00 46.60 3.25
2217 2396 7.041372 GCTACCAAAAGAGTACAAATGAAGACA 60.041 37.037 0.00 0.00 0.00 3.41
2218 2397 7.639113 ACCAAAAGAGTACAAATGAAGACAA 57.361 32.000 0.00 0.00 0.00 3.18
2229 2408 6.715464 ACAAATGAAGACAAAGTACAACGAG 58.285 36.000 0.00 0.00 0.00 4.18
2248 2427 1.336125 AGACGCTACGCCCTATAACAC 59.664 52.381 0.00 0.00 0.00 3.32
2270 2449 0.478072 AAGCTCCATGACAACACCCA 59.522 50.000 0.00 0.00 0.00 4.51
2273 2452 1.887956 GCTCCATGACAACACCCACAT 60.888 52.381 0.00 0.00 0.00 3.21
2283 2462 0.984230 ACACCCACATGACGGAGAAT 59.016 50.000 0.00 0.00 0.00 2.40
2284 2463 1.351017 ACACCCACATGACGGAGAATT 59.649 47.619 0.00 0.00 0.00 2.17
2290 2469 3.365264 CCACATGACGGAGAATTGTGTTG 60.365 47.826 0.00 0.00 0.00 3.33
2294 2473 1.126846 GACGGAGAATTGTGTTGAGCG 59.873 52.381 0.00 0.00 0.00 5.03
2299 2478 2.802816 GAGAATTGTGTTGAGCGTCACT 59.197 45.455 0.00 0.00 35.82 3.41
2301 2480 1.953559 ATTGTGTTGAGCGTCACTGT 58.046 45.000 0.00 0.00 35.82 3.55
2316 2495 1.374758 CTGTTGCCGAGTCCAGGAC 60.375 63.158 12.25 12.25 0.00 3.85
2347 2526 4.394712 CACCCGGAGCCCTGACAC 62.395 72.222 0.73 0.00 0.00 3.67
2392 2571 3.191581 TCATTGAGAAGAGAGTGTCGTCC 59.808 47.826 0.00 0.00 34.40 4.79
2411 2590 3.458579 CGAGTGTCGTTGTCGCCG 61.459 66.667 0.00 0.00 34.72 6.46
2412 2591 3.103911 GAGTGTCGTTGTCGCCGG 61.104 66.667 0.00 0.00 36.96 6.13
2425 2604 3.793144 GCCGGCGACAAAGCTCAG 61.793 66.667 12.58 0.00 37.29 3.35
2452 2631 4.051167 TCGGTAGCTCCCCCGTGA 62.051 66.667 16.21 0.00 44.51 4.35
2477 2656 2.727123 TGAGGTTTCCAGAACAAGCA 57.273 45.000 0.00 0.00 0.00 3.91
2478 2657 2.297701 TGAGGTTTCCAGAACAAGCAC 58.702 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.728102 TGGCTCACGGGCGTTACG 62.728 66.667 0.00 0.00 44.11 3.18
3 4 2.125269 ATGGCTCACGGGCGTTAC 60.125 61.111 0.00 0.00 44.11 2.50
5 6 3.545124 TTGATGGCTCACGGGCGTT 62.545 57.895 0.00 0.00 44.11 4.84
6 7 3.545124 TTTGATGGCTCACGGGCGT 62.545 57.895 0.00 0.00 44.11 5.68
7 8 2.745884 TTTGATGGCTCACGGGCG 60.746 61.111 0.00 0.00 44.11 6.13
8 9 2.700773 GGTTTGATGGCTCACGGGC 61.701 63.158 0.00 0.00 41.27 6.13
9 10 2.398554 CGGTTTGATGGCTCACGGG 61.399 63.158 0.00 0.00 0.00 5.28
10 11 2.398554 CCGGTTTGATGGCTCACGG 61.399 63.158 0.00 0.00 33.79 4.94
11 12 2.398554 CCCGGTTTGATGGCTCACG 61.399 63.158 0.00 0.00 0.00 4.35
12 13 2.046285 CCCCGGTTTGATGGCTCAC 61.046 63.158 0.00 0.00 0.00 3.51
13 14 2.354729 CCCCGGTTTGATGGCTCA 59.645 61.111 0.00 0.00 0.00 4.26
14 15 3.140814 GCCCCGGTTTGATGGCTC 61.141 66.667 9.65 0.00 40.77 4.70
15 16 4.759205 GGCCCCGGTTTGATGGCT 62.759 66.667 15.53 0.00 43.50 4.75
18 19 3.677480 ATGGGGCCCCGGTTTGATG 62.677 63.158 36.00 0.00 39.42 3.07
19 20 3.355344 ATGGGGCCCCGGTTTGAT 61.355 61.111 36.00 19.92 39.42 2.57
20 21 4.374584 CATGGGGCCCCGGTTTGA 62.375 66.667 36.00 18.31 39.42 2.69
21 22 4.694987 ACATGGGGCCCCGGTTTG 62.695 66.667 36.00 29.00 39.42 2.93
22 23 4.694987 CACATGGGGCCCCGGTTT 62.695 66.667 36.00 17.52 39.42 3.27
39 40 0.953960 CTAACGGTGTTGGTGGAGCC 60.954 60.000 0.00 0.00 37.90 4.70
40 41 1.574702 GCTAACGGTGTTGGTGGAGC 61.575 60.000 0.00 0.00 0.00 4.70
41 42 1.289109 CGCTAACGGTGTTGGTGGAG 61.289 60.000 0.00 0.00 34.97 3.86
42 43 1.301087 CGCTAACGGTGTTGGTGGA 60.301 57.895 0.00 0.00 34.97 4.02
43 44 1.595929 ACGCTAACGGTGTTGGTGG 60.596 57.895 10.58 0.00 46.04 4.61
44 45 1.155424 ACACGCTAACGGTGTTGGTG 61.155 55.000 5.25 5.25 46.04 4.17
45 46 0.462403 AACACGCTAACGGTGTTGGT 60.462 50.000 9.27 0.00 46.04 3.67
46 47 0.041663 CAACACGCTAACGGTGTTGG 60.042 55.000 23.13 9.97 46.10 3.77
47 48 3.431068 CAACACGCTAACGGTGTTG 57.569 52.632 19.38 19.38 45.45 3.33
48 49 1.778027 GCCAACACGCTAACGGTGTT 61.778 55.000 4.60 4.60 46.04 3.32
49 50 2.248835 GCCAACACGCTAACGGTGT 61.249 57.895 0.00 0.00 46.04 4.16
50 51 2.170260 CTGCCAACACGCTAACGGTG 62.170 60.000 0.00 0.00 46.04 4.94
51 52 1.959226 CTGCCAACACGCTAACGGT 60.959 57.895 0.00 0.00 46.04 4.83
52 53 1.959226 ACTGCCAACACGCTAACGG 60.959 57.895 0.00 0.00 46.04 4.44
54 55 1.574428 CCACTGCCAACACGCTAAC 59.426 57.895 0.00 0.00 0.00 2.34
55 56 1.599518 CCCACTGCCAACACGCTAA 60.600 57.895 0.00 0.00 0.00 3.09
56 57 2.031919 CCCACTGCCAACACGCTA 59.968 61.111 0.00 0.00 0.00 4.26
57 58 4.189580 ACCCACTGCCAACACGCT 62.190 61.111 0.00 0.00 0.00 5.07
58 59 3.964875 CACCCACTGCCAACACGC 61.965 66.667 0.00 0.00 0.00 5.34
59 60 3.286751 CCACCCACTGCCAACACG 61.287 66.667 0.00 0.00 0.00 4.49
60 61 2.912025 CCCACCCACTGCCAACAC 60.912 66.667 0.00 0.00 0.00 3.32
61 62 2.920076 GAACCCACCCACTGCCAACA 62.920 60.000 0.00 0.00 0.00 3.33
62 63 2.123468 AACCCACCCACTGCCAAC 60.123 61.111 0.00 0.00 0.00 3.77
63 64 1.063070 TAGAACCCACCCACTGCCAA 61.063 55.000 0.00 0.00 0.00 4.52
64 65 1.462432 TAGAACCCACCCACTGCCA 60.462 57.895 0.00 0.00 0.00 4.92
65 66 1.299976 CTAGAACCCACCCACTGCC 59.700 63.158 0.00 0.00 0.00 4.85
66 67 1.377333 GCTAGAACCCACCCACTGC 60.377 63.158 0.00 0.00 0.00 4.40
67 68 1.568504 TAGCTAGAACCCACCCACTG 58.431 55.000 0.00 0.00 0.00 3.66
68 69 2.337359 TTAGCTAGAACCCACCCACT 57.663 50.000 0.00 0.00 0.00 4.00
69 70 3.428413 TTTTAGCTAGAACCCACCCAC 57.572 47.619 0.00 0.00 0.00 4.61
70 71 3.396611 AGTTTTTAGCTAGAACCCACCCA 59.603 43.478 14.79 0.00 0.00 4.51
71 72 4.030314 AGTTTTTAGCTAGAACCCACCC 57.970 45.455 14.79 0.00 0.00 4.61
72 73 7.514784 TTTTAGTTTTTAGCTAGAACCCACC 57.485 36.000 14.79 0.00 0.00 4.61
73 74 8.407832 TGTTTTTAGTTTTTAGCTAGAACCCAC 58.592 33.333 14.79 4.47 0.00 4.61
74 75 8.522542 TGTTTTTAGTTTTTAGCTAGAACCCA 57.477 30.769 14.79 4.92 0.00 4.51
75 76 9.241317 GTTGTTTTTAGTTTTTAGCTAGAACCC 57.759 33.333 14.79 2.77 0.00 4.11
76 77 8.950961 CGTTGTTTTTAGTTTTTAGCTAGAACC 58.049 33.333 14.79 1.71 0.00 3.62
77 78 9.706846 TCGTTGTTTTTAGTTTTTAGCTAGAAC 57.293 29.630 11.92 11.92 0.00 3.01
78 79 9.706846 GTCGTTGTTTTTAGTTTTTAGCTAGAA 57.293 29.630 0.00 0.00 0.00 2.10
79 80 8.057742 CGTCGTTGTTTTTAGTTTTTAGCTAGA 58.942 33.333 0.00 0.00 0.00 2.43
80 81 7.847564 ACGTCGTTGTTTTTAGTTTTTAGCTAG 59.152 33.333 0.00 0.00 0.00 3.42
81 82 7.683746 ACGTCGTTGTTTTTAGTTTTTAGCTA 58.316 30.769 0.00 0.00 0.00 3.32
82 83 6.545508 ACGTCGTTGTTTTTAGTTTTTAGCT 58.454 32.000 0.00 0.00 0.00 3.32
83 84 6.779385 ACGTCGTTGTTTTTAGTTTTTAGC 57.221 33.333 0.00 0.00 0.00 3.09
84 85 9.424659 ACATACGTCGTTGTTTTTAGTTTTTAG 57.575 29.630 1.78 0.00 0.00 1.85
85 86 9.208169 CACATACGTCGTTGTTTTTAGTTTTTA 57.792 29.630 1.78 0.00 0.00 1.52
86 87 7.961827 TCACATACGTCGTTGTTTTTAGTTTTT 59.038 29.630 1.78 0.00 0.00 1.94
87 88 7.462731 TCACATACGTCGTTGTTTTTAGTTTT 58.537 30.769 1.78 0.00 0.00 2.43
88 89 7.002816 TCACATACGTCGTTGTTTTTAGTTT 57.997 32.000 1.78 0.00 0.00 2.66
89 90 6.586868 TCACATACGTCGTTGTTTTTAGTT 57.413 33.333 1.78 0.00 0.00 2.24
90 91 6.476380 TCTTCACATACGTCGTTGTTTTTAGT 59.524 34.615 1.78 0.00 0.00 2.24
91 92 6.869473 TCTTCACATACGTCGTTGTTTTTAG 58.131 36.000 1.78 3.42 0.00 1.85
92 93 6.696583 TCTCTTCACATACGTCGTTGTTTTTA 59.303 34.615 1.78 0.00 0.00 1.52
93 94 5.521010 TCTCTTCACATACGTCGTTGTTTTT 59.479 36.000 1.78 0.00 0.00 1.94
94 95 5.045215 TCTCTTCACATACGTCGTTGTTTT 58.955 37.500 1.78 0.00 0.00 2.43
95 96 4.613944 TCTCTTCACATACGTCGTTGTTT 58.386 39.130 1.78 0.00 0.00 2.83
96 97 4.233123 TCTCTTCACATACGTCGTTGTT 57.767 40.909 1.78 0.00 0.00 2.83
97 98 3.909776 TCTCTTCACATACGTCGTTGT 57.090 42.857 1.78 5.30 0.00 3.32
98 99 4.857037 TGATTCTCTTCACATACGTCGTTG 59.143 41.667 1.78 4.64 0.00 4.10
99 100 5.055642 TGATTCTCTTCACATACGTCGTT 57.944 39.130 1.78 0.00 0.00 3.85
100 101 4.696899 TGATTCTCTTCACATACGTCGT 57.303 40.909 2.21 2.21 0.00 4.34
101 102 6.575083 ATTTGATTCTCTTCACATACGTCG 57.425 37.500 0.00 0.00 0.00 5.12
102 103 8.407457 TGTATTTGATTCTCTTCACATACGTC 57.593 34.615 0.00 0.00 40.05 4.34
103 104 8.948631 ATGTATTTGATTCTCTTCACATACGT 57.051 30.769 0.00 0.00 40.05 3.57
104 105 9.034544 TGATGTATTTGATTCTCTTCACATACG 57.965 33.333 6.37 0.00 40.05 3.06
109 110 9.512435 CCATTTGATGTATTTGATTCTCTTCAC 57.488 33.333 0.00 0.00 0.00 3.18
110 111 9.246670 ACCATTTGATGTATTTGATTCTCTTCA 57.753 29.630 0.00 0.00 0.00 3.02
129 130 9.832445 ACACCTACTATGTATCTTTACCATTTG 57.168 33.333 0.00 0.00 0.00 2.32
131 132 9.209048 TGACACCTACTATGTATCTTTACCATT 57.791 33.333 0.00 0.00 0.00 3.16
132 133 8.777578 TGACACCTACTATGTATCTTTACCAT 57.222 34.615 0.00 0.00 0.00 3.55
133 134 7.201884 GCTGACACCTACTATGTATCTTTACCA 60.202 40.741 0.00 0.00 0.00 3.25
134 135 7.146648 GCTGACACCTACTATGTATCTTTACC 58.853 42.308 0.00 0.00 0.00 2.85
135 136 6.856938 CGCTGACACCTACTATGTATCTTTAC 59.143 42.308 0.00 0.00 0.00 2.01
136 137 6.544931 ACGCTGACACCTACTATGTATCTTTA 59.455 38.462 0.00 0.00 0.00 1.85
137 138 5.360144 ACGCTGACACCTACTATGTATCTTT 59.640 40.000 0.00 0.00 0.00 2.52
138 139 4.888239 ACGCTGACACCTACTATGTATCTT 59.112 41.667 0.00 0.00 0.00 2.40
139 140 4.276183 CACGCTGACACCTACTATGTATCT 59.724 45.833 0.00 0.00 0.00 1.98
140 141 4.036498 ACACGCTGACACCTACTATGTATC 59.964 45.833 0.00 0.00 0.00 2.24
141 142 3.952323 ACACGCTGACACCTACTATGTAT 59.048 43.478 0.00 0.00 0.00 2.29
142 143 3.128068 CACACGCTGACACCTACTATGTA 59.872 47.826 0.00 0.00 0.00 2.29
143 144 2.094700 CACACGCTGACACCTACTATGT 60.095 50.000 0.00 0.00 0.00 2.29
144 145 2.094700 ACACACGCTGACACCTACTATG 60.095 50.000 0.00 0.00 0.00 2.23
145 146 2.168496 ACACACGCTGACACCTACTAT 58.832 47.619 0.00 0.00 0.00 2.12
146 147 1.612676 ACACACGCTGACACCTACTA 58.387 50.000 0.00 0.00 0.00 1.82
147 148 0.750850 AACACACGCTGACACCTACT 59.249 50.000 0.00 0.00 0.00 2.57
148 149 0.859232 CAACACACGCTGACACCTAC 59.141 55.000 0.00 0.00 0.00 3.18
149 150 0.249699 CCAACACACGCTGACACCTA 60.250 55.000 0.00 0.00 0.00 3.08
150 151 1.523711 CCAACACACGCTGACACCT 60.524 57.895 0.00 0.00 0.00 4.00
151 152 3.022287 CCAACACACGCTGACACC 58.978 61.111 0.00 0.00 0.00 4.16
152 153 2.180204 AGCCAACACACGCTGACAC 61.180 57.895 0.00 0.00 32.98 3.67
153 154 2.189257 AGCCAACACACGCTGACA 59.811 55.556 0.00 0.00 32.98 3.58
157 158 1.447317 CCTTTCAGCCAACACACGCT 61.447 55.000 0.00 0.00 35.10 5.07
158 159 1.008538 CCTTTCAGCCAACACACGC 60.009 57.895 0.00 0.00 0.00 5.34
159 160 0.307760 GTCCTTTCAGCCAACACACG 59.692 55.000 0.00 0.00 0.00 4.49
160 161 1.604278 GAGTCCTTTCAGCCAACACAC 59.396 52.381 0.00 0.00 0.00 3.82
161 162 1.476833 GGAGTCCTTTCAGCCAACACA 60.477 52.381 0.41 0.00 0.00 3.72
162 163 1.239347 GGAGTCCTTTCAGCCAACAC 58.761 55.000 0.41 0.00 0.00 3.32
163 164 0.250295 CGGAGTCCTTTCAGCCAACA 60.250 55.000 7.77 0.00 0.00 3.33
164 165 0.034896 TCGGAGTCCTTTCAGCCAAC 59.965 55.000 7.77 0.00 0.00 3.77
165 166 0.984230 ATCGGAGTCCTTTCAGCCAA 59.016 50.000 7.77 0.00 0.00 4.52
166 167 1.860641 TATCGGAGTCCTTTCAGCCA 58.139 50.000 7.77 0.00 0.00 4.75
167 168 2.981859 TTATCGGAGTCCTTTCAGCC 57.018 50.000 7.77 0.00 0.00 4.85
168 169 5.819825 AAAATTATCGGAGTCCTTTCAGC 57.180 39.130 7.77 0.00 0.00 4.26
212 213 2.605837 TAGCAGTGTTTCGTGGAACA 57.394 45.000 0.00 0.00 37.20 3.18
213 214 8.648097 CATATATATAGCAGTGTTTCGTGGAAC 58.352 37.037 0.00 0.00 0.00 3.62
214 215 7.817478 CCATATATATAGCAGTGTTTCGTGGAA 59.183 37.037 0.00 0.00 0.00 3.53
215 216 7.039293 ACCATATATATAGCAGTGTTTCGTGGA 60.039 37.037 7.33 0.00 0.00 4.02
216 217 7.063426 CACCATATATATAGCAGTGTTTCGTGG 59.937 40.741 0.00 0.00 0.00 4.94
217 218 7.411912 GCACCATATATATAGCAGTGTTTCGTG 60.412 40.741 15.52 7.24 0.00 4.35
218 219 6.590292 GCACCATATATATAGCAGTGTTTCGT 59.410 38.462 15.52 0.00 0.00 3.85
219 220 6.813649 AGCACCATATATATAGCAGTGTTTCG 59.186 38.462 15.52 0.00 0.00 3.46
220 221 7.278868 GGAGCACCATATATATAGCAGTGTTTC 59.721 40.741 15.52 13.62 35.97 2.78
221 222 7.038017 AGGAGCACCATATATATAGCAGTGTTT 60.038 37.037 2.07 8.59 38.94 2.83
222 223 6.441924 AGGAGCACCATATATATAGCAGTGTT 59.558 38.462 2.07 11.95 38.94 3.32
223 224 5.960811 AGGAGCACCATATATATAGCAGTGT 59.039 40.000 2.07 7.38 38.94 3.55
224 225 6.127225 ACAGGAGCACCATATATATAGCAGTG 60.127 42.308 2.07 12.15 38.94 3.66
225 226 5.960811 ACAGGAGCACCATATATATAGCAGT 59.039 40.000 2.07 0.00 38.94 4.40
226 227 6.097412 TCACAGGAGCACCATATATATAGCAG 59.903 42.308 2.07 0.00 38.94 4.24
227 228 5.957774 TCACAGGAGCACCATATATATAGCA 59.042 40.000 2.07 0.00 38.94 3.49
228 229 6.471233 TCACAGGAGCACCATATATATAGC 57.529 41.667 2.07 0.90 38.94 2.97
229 230 7.924947 CACATCACAGGAGCACCATATATATAG 59.075 40.741 2.07 0.00 38.94 1.31
230 231 7.619302 TCACATCACAGGAGCACCATATATATA 59.381 37.037 2.07 0.00 38.94 0.86
231 232 6.441604 TCACATCACAGGAGCACCATATATAT 59.558 38.462 2.07 0.00 38.94 0.86
232 233 5.779771 TCACATCACAGGAGCACCATATATA 59.220 40.000 2.07 0.00 38.94 0.86
233 234 4.594491 TCACATCACAGGAGCACCATATAT 59.406 41.667 2.07 0.00 38.94 0.86
234 235 3.966665 TCACATCACAGGAGCACCATATA 59.033 43.478 2.07 0.00 38.94 0.86
235 236 2.773661 TCACATCACAGGAGCACCATAT 59.226 45.455 2.07 0.00 38.94 1.78
236 237 2.093500 GTCACATCACAGGAGCACCATA 60.093 50.000 2.07 0.00 38.94 2.74
237 238 0.986527 TCACATCACAGGAGCACCAT 59.013 50.000 2.07 0.00 38.94 3.55
238 239 0.035317 GTCACATCACAGGAGCACCA 59.965 55.000 2.07 0.00 38.94 4.17
239 240 0.674895 GGTCACATCACAGGAGCACC 60.675 60.000 0.00 0.00 0.00 5.01
240 241 0.035317 TGGTCACATCACAGGAGCAC 59.965 55.000 0.00 0.00 34.47 4.40
241 242 0.986527 ATGGTCACATCACAGGAGCA 59.013 50.000 0.00 0.00 42.43 4.26
242 243 2.988010 TATGGTCACATCACAGGAGC 57.012 50.000 0.00 0.00 38.53 4.70
243 244 4.952071 AGATATGGTCACATCACAGGAG 57.048 45.455 0.00 0.00 38.53 3.69
244 245 5.660864 TGTAAGATATGGTCACATCACAGGA 59.339 40.000 0.00 0.00 38.53 3.86
245 246 5.917462 TGTAAGATATGGTCACATCACAGG 58.083 41.667 0.00 0.00 38.53 4.00
246 247 6.481313 CCTTGTAAGATATGGTCACATCACAG 59.519 42.308 0.00 0.00 38.53 3.66
247 248 6.070251 ACCTTGTAAGATATGGTCACATCACA 60.070 38.462 0.00 0.00 38.53 3.58
248 249 6.349300 ACCTTGTAAGATATGGTCACATCAC 58.651 40.000 0.00 0.00 38.53 3.06
249 250 6.560003 ACCTTGTAAGATATGGTCACATCA 57.440 37.500 0.00 0.00 38.53 3.07
250 251 6.823689 ACAACCTTGTAAGATATGGTCACATC 59.176 38.462 0.00 0.00 40.16 3.06
251 252 6.721318 ACAACCTTGTAAGATATGGTCACAT 58.279 36.000 0.00 0.00 40.16 3.21
252 253 6.121776 ACAACCTTGTAAGATATGGTCACA 57.878 37.500 0.00 0.00 40.16 3.58
253 254 6.653320 TGAACAACCTTGTAAGATATGGTCAC 59.347 38.462 7.46 0.00 41.31 3.67
254 255 6.774673 TGAACAACCTTGTAAGATATGGTCA 58.225 36.000 7.46 7.46 41.31 4.02
255 256 7.681939 TTGAACAACCTTGTAAGATATGGTC 57.318 36.000 0.00 0.00 41.31 4.02
256 257 7.942341 TCTTTGAACAACCTTGTAAGATATGGT 59.058 33.333 0.00 0.00 41.31 3.55
257 258 8.335532 TCTTTGAACAACCTTGTAAGATATGG 57.664 34.615 0.00 0.00 41.31 2.74
258 259 9.831737 CTTCTTTGAACAACCTTGTAAGATATG 57.168 33.333 3.74 0.00 41.31 1.78
259 260 8.515414 GCTTCTTTGAACAACCTTGTAAGATAT 58.485 33.333 3.74 0.00 41.31 1.63
260 261 7.719633 AGCTTCTTTGAACAACCTTGTAAGATA 59.280 33.333 3.74 0.00 41.31 1.98
261 262 6.547510 AGCTTCTTTGAACAACCTTGTAAGAT 59.452 34.615 3.74 0.00 41.31 2.40
262 263 5.885912 AGCTTCTTTGAACAACCTTGTAAGA 59.114 36.000 0.00 0.00 41.31 2.10
263 264 5.973565 CAGCTTCTTTGAACAACCTTGTAAG 59.026 40.000 0.00 0.00 41.31 2.34
264 265 5.417580 ACAGCTTCTTTGAACAACCTTGTAA 59.582 36.000 0.00 0.00 41.31 2.41
265 266 4.947388 ACAGCTTCTTTGAACAACCTTGTA 59.053 37.500 0.00 0.00 41.31 2.41
266 267 3.763897 ACAGCTTCTTTGAACAACCTTGT 59.236 39.130 0.00 0.00 44.72 3.16
267 268 4.376340 ACAGCTTCTTTGAACAACCTTG 57.624 40.909 0.00 0.00 0.00 3.61
268 269 4.747810 CAACAGCTTCTTTGAACAACCTT 58.252 39.130 0.00 0.00 0.00 3.50
269 270 3.429410 GCAACAGCTTCTTTGAACAACCT 60.429 43.478 4.06 0.00 0.00 3.50
270 271 2.860136 GCAACAGCTTCTTTGAACAACC 59.140 45.455 4.06 0.00 0.00 3.77
271 272 3.510719 TGCAACAGCTTCTTTGAACAAC 58.489 40.909 4.06 0.00 0.00 3.32
288 289 3.281341 CAAATTTGCCTACGTCTGCAA 57.719 42.857 17.66 17.66 45.12 4.08
304 305 7.930217 ACGTATACATCTTTAAGCATGCAAAT 58.070 30.769 21.98 8.21 0.00 2.32
308 309 8.239681 TCATACGTATACATCTTTAAGCATGC 57.760 34.615 10.51 10.51 0.00 4.06
316 324 8.565416 TCGAGTCATTCATACGTATACATCTTT 58.435 33.333 7.96 0.00 0.00 2.52
319 327 8.789743 CAATCGAGTCATTCATACGTATACATC 58.210 37.037 7.96 2.28 0.00 3.06
325 333 8.347035 TGATTACAATCGAGTCATTCATACGTA 58.653 33.333 0.00 0.00 38.26 3.57
332 340 8.443160 TGAAGTTTGATTACAATCGAGTCATTC 58.557 33.333 0.00 1.30 38.26 2.67
371 391 1.608590 CGCCATTTGTCAACTTCCTGT 59.391 47.619 0.00 0.00 0.00 4.00
402 422 1.870901 CGCCTACTCGCAACGGTAC 60.871 63.158 0.00 0.00 0.00 3.34
460 480 1.632920 TGTGGGCTGTGGATGATGTTA 59.367 47.619 0.00 0.00 0.00 2.41
531 563 2.493278 CTCTGCGGTTTGAAATTGGGAT 59.507 45.455 0.00 0.00 0.00 3.85
548 580 1.338020 GCCCGCCCATTATTTTCTCTG 59.662 52.381 0.00 0.00 0.00 3.35
563 595 3.479269 CGAGAAAGTGACGCCCGC 61.479 66.667 0.00 0.00 0.00 6.13
566 598 1.891060 CTGCACGAGAAAGTGACGCC 61.891 60.000 0.88 0.00 44.43 5.68
654 686 6.219473 GTTCAGACTTGAGTTGAGAGATCAA 58.781 40.000 0.00 0.00 34.15 2.57
664 696 1.221414 GCAGCGTTCAGACTTGAGTT 58.779 50.000 0.00 0.00 34.15 3.01
665 697 0.104855 TGCAGCGTTCAGACTTGAGT 59.895 50.000 0.00 0.00 34.15 3.41
666 698 1.436600 ATGCAGCGTTCAGACTTGAG 58.563 50.000 0.00 0.00 34.15 3.02
667 699 2.337583 GTATGCAGCGTTCAGACTTGA 58.662 47.619 0.00 0.00 0.00 3.02
728 760 3.235157 ACAAAGCGCTATAACCACGTA 57.765 42.857 12.05 0.00 0.00 3.57
799 831 1.816835 TCGGCGCGAGGAATAATATCT 59.183 47.619 12.10 0.00 0.00 1.98
1046 1088 2.036992 CAGATGGAAGTAGCTAGCTGGG 59.963 54.545 27.68 0.67 30.38 4.45
1054 1096 2.484594 GGAAGAGGCAGATGGAAGTAGC 60.485 54.545 0.00 0.00 0.00 3.58
1055 1097 3.037549 AGGAAGAGGCAGATGGAAGTAG 58.962 50.000 0.00 0.00 0.00 2.57
1056 1098 2.768527 CAGGAAGAGGCAGATGGAAGTA 59.231 50.000 0.00 0.00 0.00 2.24
1057 1099 1.558756 CAGGAAGAGGCAGATGGAAGT 59.441 52.381 0.00 0.00 0.00 3.01
1061 1103 0.179051 GAGCAGGAAGAGGCAGATGG 60.179 60.000 0.00 0.00 0.00 3.51
1084 1134 2.674796 AACAAGATGGTACCTCGCTC 57.325 50.000 14.36 4.96 0.00 5.03
1085 1135 2.567615 AGAAACAAGATGGTACCTCGCT 59.432 45.455 14.36 4.70 0.00 4.93
1086 1136 2.673368 CAGAAACAAGATGGTACCTCGC 59.327 50.000 14.36 2.22 0.00 5.03
1087 1137 3.926616 ACAGAAACAAGATGGTACCTCG 58.073 45.455 14.36 0.00 0.00 4.63
1088 1138 6.539103 GGATAACAGAAACAAGATGGTACCTC 59.461 42.308 14.36 8.28 0.00 3.85
1127 1178 2.644992 GGCAACGGCTGGACAAAG 59.355 61.111 0.00 0.00 40.87 2.77
1160 1215 2.129823 CAAGTTGCCAGTTGCTGAAG 57.870 50.000 0.00 0.00 42.00 3.02
1223 1278 1.547820 CATCACCATCGATCGATCCCT 59.452 52.381 27.20 9.97 31.62 4.20
1264 1319 4.436998 GACCTCAGCCCGTCCACG 62.437 72.222 0.00 0.00 39.44 4.94
1340 1398 2.407616 CATCTGCTCGTACGCCGA 59.592 61.111 11.24 4.31 45.00 5.54
1492 1553 2.772287 CTCCTCCTTTTGAAGAACGCT 58.228 47.619 0.00 0.00 0.00 5.07
1509 1570 2.037251 TGTTAGAACAGGACACAGCTCC 59.963 50.000 0.00 0.00 34.30 4.70
1689 1753 4.033019 CGTGATTCGCGTCACTTCTAATA 58.967 43.478 22.54 0.00 44.89 0.98
1705 1769 9.906660 TTTTTCAGCTATTTGTAATTCGTGATT 57.093 25.926 0.00 0.00 0.00 2.57
1706 1770 9.559958 CTTTTTCAGCTATTTGTAATTCGTGAT 57.440 29.630 0.00 0.00 0.00 3.06
1798 1959 3.196254 GGTTGATTACTCGGGGTGTTCTA 59.804 47.826 0.00 0.00 0.00 2.10
1817 1978 1.215423 ACTCTGCTTGGGAAACAGGTT 59.785 47.619 0.00 0.00 32.19 3.50
1844 2005 3.073209 AGGAAGGTCAAGAGGAAAGGTTC 59.927 47.826 0.00 0.00 0.00 3.62
1858 2019 1.001706 GTGCGAACCAAAAGGAAGGTC 60.002 52.381 0.00 0.00 37.07 3.85
1928 2096 4.380531 TCGACAAGCATTTCTGAAGAAGT 58.619 39.130 0.00 0.00 35.21 3.01
1931 2099 4.631131 TCTTCGACAAGCATTTCTGAAGA 58.369 39.130 7.69 7.69 38.32 2.87
1933 2101 5.749596 TTTCTTCGACAAGCATTTCTGAA 57.250 34.783 0.00 0.00 0.00 3.02
1942 2110 7.009568 AGATACATTCATTTCTTCGACAAGC 57.990 36.000 0.00 0.00 0.00 4.01
1946 2114 8.649973 AGGTTAGATACATTCATTTCTTCGAC 57.350 34.615 0.00 0.00 0.00 4.20
2008 2178 9.602568 TGACCGAAACAACTTAATTATATAGCA 57.397 29.630 0.00 0.00 0.00 3.49
2018 2188 9.878667 TCATCTTATATGACCGAAACAACTTAA 57.121 29.630 0.00 0.00 0.00 1.85
2034 2208 8.980832 AGGGAGTCCATAAAGTCATCTTATAT 57.019 34.615 12.30 0.00 32.33 0.86
2037 2211 8.618240 TTAAGGGAGTCCATAAAGTCATCTTA 57.382 34.615 12.30 2.55 32.33 2.10
2038 2212 7.510675 TTAAGGGAGTCCATAAAGTCATCTT 57.489 36.000 12.30 3.52 34.83 2.40
2040 2214 7.829706 AGTTTTAAGGGAGTCCATAAAGTCATC 59.170 37.037 12.30 5.93 37.46 2.92
2057 2231 2.165641 GGGGCGAAATCCAGTTTTAAGG 59.834 50.000 0.00 0.00 0.00 2.69
2060 2234 1.455248 CGGGGCGAAATCCAGTTTTA 58.545 50.000 0.00 0.00 0.00 1.52
2092 2266 3.662186 GCCGTGTACTTTTTCGATTGTTG 59.338 43.478 0.00 0.00 0.00 3.33
2098 2272 2.129607 GTCAGCCGTGTACTTTTTCGA 58.870 47.619 0.00 0.00 0.00 3.71
2106 2280 0.374758 TCGTATCGTCAGCCGTGTAC 59.625 55.000 0.00 0.00 37.94 2.90
2110 2284 0.308068 CATCTCGTATCGTCAGCCGT 59.692 55.000 0.00 0.00 37.94 5.68
2116 2290 4.436317 GCTACCTCATCATCTCGTATCGTC 60.436 50.000 0.00 0.00 0.00 4.20
2117 2291 3.437395 GCTACCTCATCATCTCGTATCGT 59.563 47.826 0.00 0.00 0.00 3.73
2157 2336 2.812011 GTTCTGTGTGCTCCGGTTATTT 59.188 45.455 0.00 0.00 0.00 1.40
2177 2356 2.100631 GTAGCATGGTCGCTTGCGT 61.101 57.895 14.70 0.00 43.56 5.24
2179 2358 1.305219 TTGGTAGCATGGTCGCTTGC 61.305 55.000 0.00 0.00 43.56 4.01
2190 2369 6.995686 TCTTCATTTGTACTCTTTTGGTAGCA 59.004 34.615 0.00 0.00 0.00 3.49
2192 2371 8.378172 TGTCTTCATTTGTACTCTTTTGGTAG 57.622 34.615 0.00 0.00 0.00 3.18
2217 2396 2.578495 CGTAGCGTCTCGTTGTACTTT 58.422 47.619 0.00 0.00 0.00 2.66
2218 2397 2.238245 CGTAGCGTCTCGTTGTACTT 57.762 50.000 0.00 0.00 0.00 2.24
2248 2427 2.359900 GGTGTTGTCATGGAGCTTAGG 58.640 52.381 0.00 0.00 0.00 2.69
2270 2449 3.738982 TCAACACAATTCTCCGTCATGT 58.261 40.909 0.00 0.00 0.00 3.21
2273 2452 2.143122 GCTCAACACAATTCTCCGTCA 58.857 47.619 0.00 0.00 0.00 4.35
2283 2462 1.396648 CAACAGTGACGCTCAACACAA 59.603 47.619 0.00 0.00 39.18 3.33
2284 2463 1.006086 CAACAGTGACGCTCAACACA 58.994 50.000 0.00 0.00 39.18 3.72
2294 2473 0.946221 CTGGACTCGGCAACAGTGAC 60.946 60.000 0.00 0.00 0.00 3.67
2299 2478 2.741092 GTCCTGGACTCGGCAACA 59.259 61.111 19.53 0.00 0.00 3.33
2301 2480 3.691342 CCGTCCTGGACTCGGCAA 61.691 66.667 23.49 0.00 42.00 4.52
2316 2495 4.695560 GGTGAAGACCCTTGTCCG 57.304 61.111 0.00 0.00 42.81 4.79
2347 2526 2.281208 TCGTGGTGCCCCTTTTCG 60.281 61.111 0.00 0.00 0.00 3.46
2409 2588 2.048222 TCTGAGCTTTGTCGCCGG 60.048 61.111 0.00 0.00 0.00 6.13
2411 2590 3.172919 GCTCTGAGCTTTGTCGCC 58.827 61.111 21.93 0.00 38.45 5.54
2439 2618 2.043248 GGTCTCACGGGGGAGCTA 60.043 66.667 10.12 0.00 34.84 3.32


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

AutoCloner maintained by Alex Coulton.