Multiple sequence alignment - TraesCS7A01G319300

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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 TraesCS7A01G319300 chr7A 100.000 3633 0 0 1 3633 459622721 459626353 0.000000e+00 6709.0
1 TraesCS7A01G319300 chr7A 91.003 389 30 2 1642 2030 378494676 378495059 1.500000e-143 520.0
2 TraesCS7A01G319300 chr7A 79.130 230 36 8 31 258 711361673 711361454 8.130000e-32 148.0
3 TraesCS7A01G319300 chr7D 94.555 2718 62 18 927 3633 401834204 401836846 0.000000e+00 4120.0
4 TraesCS7A01G319300 chr7D 86.907 527 37 10 285 781 401823111 401823635 2.450000e-156 562.0
5 TraesCS7A01G319300 chr7D 92.112 393 26 2 1642 2034 37621767 37622154 1.910000e-152 549.0
6 TraesCS7A01G319300 chr7D 97.581 124 2 1 769 892 401834089 401834211 1.020000e-50 211.0
7 TraesCS7A01G319300 chr7B 96.879 2467 61 11 927 3389 411490842 411493296 0.000000e+00 4115.0
8 TraesCS7A01G319300 chr7B 91.304 322 16 6 579 892 411490532 411490849 2.590000e-116 429.0
9 TraesCS7A01G319300 chr7B 96.154 208 8 0 3426 3633 411493296 411493503 1.250000e-89 340.0
10 TraesCS7A01G319300 chr7B 86.822 258 19 8 1104 1359 738788074 738787830 1.290000e-69 274.0
11 TraesCS7A01G319300 chr7B 84.286 140 7 5 1445 1584 728163527 728163651 4.930000e-24 122.0
12 TraesCS7A01G319300 chr2B 88.571 665 56 7 1370 2034 12856886 12856242 0.000000e+00 789.0
13 TraesCS7A01G319300 chr2B 79.474 190 27 11 74 257 653690976 653690793 1.370000e-24 124.0
14 TraesCS7A01G319300 chr2B 92.771 83 6 0 2069 2151 12856241 12856159 1.770000e-23 121.0
15 TraesCS7A01G319300 chr2B 82.143 140 10 5 1445 1584 60930371 60930495 4.960000e-19 106.0
16 TraesCS7A01G319300 chr2B 90.000 50 3 2 205 253 441867952 441868000 3.030000e-06 63.9
17 TraesCS7A01G319300 chr6A 92.542 295 22 0 1736 2030 584151660 584151366 1.210000e-114 424.0
18 TraesCS7A01G319300 chr6A 93.491 169 11 0 1866 2034 217043850 217043682 6.020000e-63 252.0
19 TraesCS7A01G319300 chr6A 80.000 240 36 8 24 259 554470042 554470273 2.240000e-37 167.0
20 TraesCS7A01G319300 chr5D 88.660 194 6 3 1445 1638 366924977 366925154 4.720000e-54 222.0
21 TraesCS7A01G319300 chr5D 88.144 194 7 3 1445 1638 28572604 28572781 2.200000e-52 217.0
22 TraesCS7A01G319300 chr6B 86.321 212 17 5 1370 1580 87325068 87325268 1.700000e-53 220.0
23 TraesCS7A01G319300 chr6B 82.018 228 36 5 34 259 502790045 502790269 4.790000e-44 189.0
24 TraesCS7A01G319300 chr5A 83.898 236 32 5 20 253 338221462 338221693 1.700000e-53 220.0
25 TraesCS7A01G319300 chr5A 96.078 102 4 0 1934 2035 486768847 486768746 2.240000e-37 167.0
26 TraesCS7A01G319300 chr5A 85.119 168 10 4 1445 1612 502848505 502848657 1.350000e-34 158.0
27 TraesCS7A01G319300 chrUn 88.144 194 7 3 1445 1638 154748864 154749041 2.200000e-52 217.0
28 TraesCS7A01G319300 chrUn 94.845 97 5 0 1934 2030 17285315 17285411 6.280000e-33 152.0
29 TraesCS7A01G319300 chr6D 89.189 185 5 1 1454 1638 42385177 42385008 2.200000e-52 217.0
30 TraesCS7A01G319300 chr6D 87.113 194 9 3 1445 1638 396278689 396278866 4.760000e-49 206.0
31 TraesCS7A01G319300 chr1D 88.021 192 7 6 1445 1636 79840469 79840294 2.840000e-51 213.0
32 TraesCS7A01G319300 chr1D 87.629 194 8 3 1445 1638 41783212 41783389 1.020000e-50 211.0
33 TraesCS7A01G319300 chr1D 100.000 32 0 0 1275 1306 20517632 20517601 3.920000e-05 60.2
34 TraesCS7A01G319300 chr2A 81.092 238 36 7 18 250 24897132 24897365 8.010000e-42 182.0
35 TraesCS7A01G319300 chr2A 80.000 235 31 11 24 254 760323921 760323699 3.750000e-35 159.0
36 TraesCS7A01G319300 chr2D 79.675 246 39 9 17 256 634331496 634331256 2.240000e-37 167.0
37 TraesCS7A01G319300 chr3D 78.862 246 38 13 23 262 394193433 394193670 1.750000e-33 154.0


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 TraesCS7A01G319300 chr7A 459622721 459626353 3632 False 6709.0 6709 100.000 1 3633 1 chr7A.!!$F2 3632
1 TraesCS7A01G319300 chr7D 401834089 401836846 2757 False 2165.5 4120 96.068 769 3633 2 chr7D.!!$F3 2864
2 TraesCS7A01G319300 chr7D 401823111 401823635 524 False 562.0 562 86.907 285 781 1 chr7D.!!$F2 496
3 TraesCS7A01G319300 chr7B 411490532 411493503 2971 False 1628.0 4115 94.779 579 3633 3 chr7B.!!$F2 3054
4 TraesCS7A01G319300 chr2B 12856159 12856886 727 True 455.0 789 90.671 1370 2151 2 chr2B.!!$R2 781

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
343 344 0.178975 AACCCCGGAGAACAATTGCA 60.179 50.0 0.73 0.0 0.00 4.08 F
373 374 0.179062 CCTGCCTGAGATGTGCCTAC 60.179 60.0 0.00 0.0 0.00 3.18 F
614 637 0.380378 GCGTTCAACCAAACAGCAGA 59.620 50.0 0.00 0.0 32.64 4.26 F
1228 1263 0.565674 GATCCCTCTCTTCCTCCCCT 59.434 60.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1209 1.923909 GAGGGTGCAGGGTAGGGTT 60.924 63.158 0.00 0.0 0.00 4.11 R
1453 1489 2.033141 GCAGGCAAGGCAGTCAGA 59.967 61.111 0.00 0.0 0.00 3.27 R
1463 1499 2.591429 CACGACACCTGCAGGCAA 60.591 61.111 33.06 0.0 39.32 4.52 R
3003 3043 0.191064 AGACCAGTCTCTGAACCCCA 59.809 55.000 0.00 0.0 34.17 4.96 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 4.522722 TGTTGGGGCGGTTTAATTTTAG 57.477 40.909 0.00 0.00 0.00 1.85
23 24 3.258622 TGTTGGGGCGGTTTAATTTTAGG 59.741 43.478 0.00 0.00 0.00 2.69
24 25 3.453059 TGGGGCGGTTTAATTTTAGGA 57.547 42.857 0.00 0.00 0.00 2.94
25 26 3.090790 TGGGGCGGTTTAATTTTAGGAC 58.909 45.455 0.00 0.00 0.00 3.85
26 27 2.428171 GGGGCGGTTTAATTTTAGGACC 59.572 50.000 0.00 0.00 0.00 4.46
27 28 2.428171 GGGCGGTTTAATTTTAGGACCC 59.572 50.000 0.00 0.00 0.00 4.46
28 29 3.359033 GGCGGTTTAATTTTAGGACCCT 58.641 45.455 0.00 0.00 0.00 4.34
29 30 4.525996 GGCGGTTTAATTTTAGGACCCTA 58.474 43.478 0.00 0.00 0.00 3.53
30 31 4.949238 GGCGGTTTAATTTTAGGACCCTAA 59.051 41.667 4.48 4.48 36.81 2.69
31 32 5.595542 GGCGGTTTAATTTTAGGACCCTAAT 59.404 40.000 9.14 0.00 38.20 1.73
32 33 6.772233 GGCGGTTTAATTTTAGGACCCTAATA 59.228 38.462 9.14 5.54 38.20 0.98
33 34 7.285172 GGCGGTTTAATTTTAGGACCCTAATAA 59.715 37.037 9.14 7.37 38.20 1.40
34 35 8.347771 GCGGTTTAATTTTAGGACCCTAATAAG 58.652 37.037 9.14 0.00 38.20 1.73
35 36 9.399797 CGGTTTAATTTTAGGACCCTAATAAGT 57.600 33.333 9.14 8.40 38.20 2.24
40 41 8.803397 AATTTTAGGACCCTAATAAGTGTCAC 57.197 34.615 9.14 0.00 38.20 3.67
41 42 6.938698 TTTAGGACCCTAATAAGTGTCACA 57.061 37.500 9.14 0.00 38.20 3.58
42 43 7.504926 TTTAGGACCCTAATAAGTGTCACAT 57.495 36.000 9.14 0.00 38.20 3.21
43 44 5.359194 AGGACCCTAATAAGTGTCACATG 57.641 43.478 5.62 0.00 0.00 3.21
44 45 4.783227 AGGACCCTAATAAGTGTCACATGT 59.217 41.667 5.62 0.00 0.00 3.21
45 46 4.876107 GGACCCTAATAAGTGTCACATGTG 59.124 45.833 20.18 20.18 0.00 3.21
46 47 5.488341 GACCCTAATAAGTGTCACATGTGT 58.512 41.667 24.63 8.38 0.00 3.72
47 48 5.245531 ACCCTAATAAGTGTCACATGTGTG 58.754 41.667 24.63 6.81 46.91 3.82
48 49 4.635765 CCCTAATAAGTGTCACATGTGTGG 59.364 45.833 24.63 5.56 45.65 4.17
54 55 4.865865 TCACATGTGTGGCACGAA 57.134 50.000 24.63 3.62 45.65 3.85
55 56 2.316237 TCACATGTGTGGCACGAAC 58.684 52.632 24.63 7.16 45.65 3.95
56 57 0.462759 TCACATGTGTGGCACGAACA 60.463 50.000 24.63 13.05 45.65 3.18
57 58 0.316937 CACATGTGTGGCACGAACAC 60.317 55.000 18.03 6.07 46.55 3.32
61 62 4.865865 TGTGGCACGAACACATGA 57.134 50.000 13.77 0.00 43.35 3.07
62 63 2.316237 TGTGGCACGAACACATGAC 58.684 52.632 13.77 0.00 43.35 3.06
63 64 0.462759 TGTGGCACGAACACATGACA 60.463 50.000 13.77 0.00 43.35 3.58
64 65 0.660488 GTGGCACGAACACATGACAA 59.340 50.000 0.00 0.00 35.02 3.18
65 66 0.660488 TGGCACGAACACATGACAAC 59.340 50.000 0.00 0.00 28.30 3.32
66 67 0.944386 GGCACGAACACATGACAACT 59.056 50.000 0.00 0.00 0.00 3.16
67 68 1.069906 GGCACGAACACATGACAACTC 60.070 52.381 0.00 0.00 0.00 3.01
68 69 1.069906 GCACGAACACATGACAACTCC 60.070 52.381 0.00 0.00 0.00 3.85
69 70 1.192312 CACGAACACATGACAACTCCG 59.808 52.381 0.00 0.00 0.00 4.63
70 71 1.067974 ACGAACACATGACAACTCCGA 59.932 47.619 0.00 0.00 0.00 4.55
71 72 2.131972 CGAACACATGACAACTCCGAA 58.868 47.619 0.00 0.00 0.00 4.30
72 73 2.542178 CGAACACATGACAACTCCGAAA 59.458 45.455 0.00 0.00 0.00 3.46
73 74 3.362986 CGAACACATGACAACTCCGAAAG 60.363 47.826 0.00 0.00 0.00 2.62
74 75 3.194005 ACACATGACAACTCCGAAAGT 57.806 42.857 0.00 0.00 41.10 2.66
76 77 3.945285 ACACATGACAACTCCGAAAGTTT 59.055 39.130 0.00 0.00 46.26 2.66
77 78 4.398044 ACACATGACAACTCCGAAAGTTTT 59.602 37.500 0.00 0.00 46.26 2.43
78 79 5.105917 ACACATGACAACTCCGAAAGTTTTT 60.106 36.000 0.00 0.00 46.26 1.94
101 102 9.658475 TTTTTATGACAAATTTAGTGACACGAG 57.342 29.630 0.00 0.00 0.00 4.18
102 103 8.596271 TTTATGACAAATTTAGTGACACGAGA 57.404 30.769 0.00 0.00 0.00 4.04
103 104 8.596271 TTATGACAAATTTAGTGACACGAGAA 57.404 30.769 0.00 0.00 0.00 2.87
104 105 7.672983 ATGACAAATTTAGTGACACGAGAAT 57.327 32.000 0.00 0.00 0.00 2.40
105 106 6.887368 TGACAAATTTAGTGACACGAGAATG 58.113 36.000 0.00 0.00 0.00 2.67
106 107 6.481976 TGACAAATTTAGTGACACGAGAATGT 59.518 34.615 0.00 3.12 34.78 2.71
117 118 6.952935 GACACGAGAATGTCAACTCTAATT 57.047 37.500 1.08 0.00 46.89 1.40
118 119 6.712241 ACACGAGAATGTCAACTCTAATTG 57.288 37.500 0.00 0.00 0.00 2.32
119 120 6.223852 ACACGAGAATGTCAACTCTAATTGT 58.776 36.000 0.00 4.60 0.00 2.71
120 121 6.366332 ACACGAGAATGTCAACTCTAATTGTC 59.634 38.462 0.00 0.00 0.00 3.18
121 122 6.366061 CACGAGAATGTCAACTCTAATTGTCA 59.634 38.462 0.00 0.00 33.25 3.58
122 123 6.929049 ACGAGAATGTCAACTCTAATTGTCAA 59.071 34.615 0.00 0.00 32.62 3.18
123 124 7.116948 ACGAGAATGTCAACTCTAATTGTCAAG 59.883 37.037 0.00 0.00 32.62 3.02
124 125 7.138692 AGAATGTCAACTCTAATTGTCAAGC 57.861 36.000 0.00 0.00 32.62 4.01
125 126 6.712095 AGAATGTCAACTCTAATTGTCAAGCA 59.288 34.615 0.00 0.00 32.62 3.91
126 127 7.392673 AGAATGTCAACTCTAATTGTCAAGCAT 59.607 33.333 0.00 0.00 32.62 3.79
127 128 6.245115 TGTCAACTCTAATTGTCAAGCATG 57.755 37.500 0.00 0.00 0.00 4.06
128 129 5.181811 TGTCAACTCTAATTGTCAAGCATGG 59.818 40.000 0.00 0.00 0.00 3.66
129 130 4.156556 TCAACTCTAATTGTCAAGCATGGC 59.843 41.667 0.00 0.00 0.00 4.40
130 131 3.689347 ACTCTAATTGTCAAGCATGGCA 58.311 40.909 0.00 0.00 40.01 4.92
141 142 7.507733 TGTCAAGCATGGCAAATTTATTTTT 57.492 28.000 0.00 0.00 38.47 1.94
142 143 7.583230 TGTCAAGCATGGCAAATTTATTTTTC 58.417 30.769 0.00 0.00 38.47 2.29
143 144 6.737750 GTCAAGCATGGCAAATTTATTTTTCG 59.262 34.615 0.00 0.00 0.00 3.46
144 145 5.799681 AGCATGGCAAATTTATTTTTCGG 57.200 34.783 0.00 0.00 0.00 4.30
145 146 5.486526 AGCATGGCAAATTTATTTTTCGGA 58.513 33.333 0.00 0.00 0.00 4.55
146 147 6.114767 AGCATGGCAAATTTATTTTTCGGAT 58.885 32.000 0.00 0.00 0.00 4.18
147 148 6.037391 AGCATGGCAAATTTATTTTTCGGATG 59.963 34.615 0.00 0.00 0.00 3.51
148 149 6.717413 CATGGCAAATTTATTTTTCGGATGG 58.283 36.000 0.00 0.00 0.00 3.51
149 150 4.633565 TGGCAAATTTATTTTTCGGATGGC 59.366 37.500 0.00 0.00 0.00 4.40
150 151 4.633565 GGCAAATTTATTTTTCGGATGGCA 59.366 37.500 0.00 0.00 0.00 4.92
151 152 5.123027 GGCAAATTTATTTTTCGGATGGCAA 59.877 36.000 0.00 0.00 0.00 4.52
152 153 6.250089 GCAAATTTATTTTTCGGATGGCAAG 58.750 36.000 0.00 0.00 0.00 4.01
153 154 6.128309 GCAAATTTATTTTTCGGATGGCAAGT 60.128 34.615 0.00 0.00 0.00 3.16
154 155 7.572910 GCAAATTTATTTTTCGGATGGCAAGTT 60.573 33.333 0.00 0.00 0.00 2.66
155 156 7.977789 AATTTATTTTTCGGATGGCAAGTTT 57.022 28.000 0.00 0.00 0.00 2.66
156 157 7.977789 ATTTATTTTTCGGATGGCAAGTTTT 57.022 28.000 0.00 0.00 0.00 2.43
157 158 9.495572 AATTTATTTTTCGGATGGCAAGTTTTA 57.504 25.926 0.00 0.00 0.00 1.52
158 159 8.527567 TTTATTTTTCGGATGGCAAGTTTTAG 57.472 30.769 0.00 0.00 0.00 1.85
159 160 5.523438 TTTTTCGGATGGCAAGTTTTAGT 57.477 34.783 0.00 0.00 0.00 2.24
160 161 5.523438 TTTTCGGATGGCAAGTTTTAGTT 57.477 34.783 0.00 0.00 0.00 2.24
161 162 5.523438 TTTCGGATGGCAAGTTTTAGTTT 57.477 34.783 0.00 0.00 0.00 2.66
162 163 5.523438 TTCGGATGGCAAGTTTTAGTTTT 57.477 34.783 0.00 0.00 0.00 2.43
163 164 5.523438 TCGGATGGCAAGTTTTAGTTTTT 57.477 34.783 0.00 0.00 0.00 1.94
164 165 5.525199 TCGGATGGCAAGTTTTAGTTTTTC 58.475 37.500 0.00 0.00 0.00 2.29
165 166 4.381566 CGGATGGCAAGTTTTAGTTTTTCG 59.618 41.667 0.00 0.00 0.00 3.46
166 167 4.684242 GGATGGCAAGTTTTAGTTTTTCGG 59.316 41.667 0.00 0.00 0.00 4.30
167 168 4.048241 TGGCAAGTTTTAGTTTTTCGGG 57.952 40.909 0.00 0.00 0.00 5.14
168 169 3.447944 TGGCAAGTTTTAGTTTTTCGGGT 59.552 39.130 0.00 0.00 0.00 5.28
169 170 4.081586 TGGCAAGTTTTAGTTTTTCGGGTT 60.082 37.500 0.00 0.00 0.00 4.11
170 171 4.871557 GGCAAGTTTTAGTTTTTCGGGTTT 59.128 37.500 0.00 0.00 0.00 3.27
171 172 5.220510 GGCAAGTTTTAGTTTTTCGGGTTTG 60.221 40.000 0.00 0.00 0.00 2.93
172 173 5.349270 GCAAGTTTTAGTTTTTCGGGTTTGT 59.651 36.000 0.00 0.00 0.00 2.83
173 174 6.128499 GCAAGTTTTAGTTTTTCGGGTTTGTT 60.128 34.615 0.00 0.00 0.00 2.83
174 175 7.571613 GCAAGTTTTAGTTTTTCGGGTTTGTTT 60.572 33.333 0.00 0.00 0.00 2.83
175 176 7.966246 AGTTTTAGTTTTTCGGGTTTGTTTT 57.034 28.000 0.00 0.00 0.00 2.43
176 177 8.380743 AGTTTTAGTTTTTCGGGTTTGTTTTT 57.619 26.923 0.00 0.00 0.00 1.94
199 200 9.883142 TTTTTCTTTGTGGATGACAACTTTAAT 57.117 25.926 0.00 0.00 44.53 1.40
200 201 9.883142 TTTTCTTTGTGGATGACAACTTTAATT 57.117 25.926 0.00 0.00 44.53 1.40
201 202 8.870160 TTCTTTGTGGATGACAACTTTAATTG 57.130 30.769 0.00 0.00 44.53 2.32
202 203 8.006298 TCTTTGTGGATGACAACTTTAATTGT 57.994 30.769 0.00 0.00 44.53 2.71
203 204 8.474025 TCTTTGTGGATGACAACTTTAATTGTT 58.526 29.630 0.00 0.00 44.53 2.83
204 205 9.743057 CTTTGTGGATGACAACTTTAATTGTTA 57.257 29.630 0.00 0.00 44.53 2.41
218 219 9.476202 ACTTTAATTGTTAAAAACATCAGAGGC 57.524 29.630 0.00 0.00 41.79 4.70
219 220 9.474920 CTTTAATTGTTAAAAACATCAGAGGCA 57.525 29.630 0.00 0.00 41.79 4.75
220 221 9.474920 TTTAATTGTTAAAAACATCAGAGGCAG 57.525 29.630 0.00 0.00 41.79 4.85
221 222 6.899393 ATTGTTAAAAACATCAGAGGCAGA 57.101 33.333 0.00 0.00 41.79 4.26
222 223 5.947228 TGTTAAAAACATCAGAGGCAGAG 57.053 39.130 0.00 0.00 36.25 3.35
223 224 5.376625 TGTTAAAAACATCAGAGGCAGAGT 58.623 37.500 0.00 0.00 36.25 3.24
224 225 5.239306 TGTTAAAAACATCAGAGGCAGAGTG 59.761 40.000 0.00 0.00 36.25 3.51
225 226 1.818642 AAACATCAGAGGCAGAGTGC 58.181 50.000 0.00 0.00 44.08 4.40
226 227 0.982704 AACATCAGAGGCAGAGTGCT 59.017 50.000 0.00 0.00 44.28 4.40
227 228 0.982704 ACATCAGAGGCAGAGTGCTT 59.017 50.000 0.00 0.00 44.28 3.91
232 233 4.315588 AGGCAGAGTGCTTCATGC 57.684 55.556 0.00 0.00 44.28 4.06
234 235 3.991999 GCAGAGTGCTTCATGCCA 58.008 55.556 0.00 0.00 40.96 4.92
235 236 1.505353 GCAGAGTGCTTCATGCCAC 59.495 57.895 0.00 0.00 40.96 5.01
236 237 1.239296 GCAGAGTGCTTCATGCCACA 61.239 55.000 11.68 0.00 40.96 4.17
237 238 0.520404 CAGAGTGCTTCATGCCACAC 59.480 55.000 11.68 8.21 42.00 3.82
238 239 0.952497 AGAGTGCTTCATGCCACACG 60.952 55.000 11.68 0.00 42.00 4.49
239 240 1.227943 AGTGCTTCATGCCACACGT 60.228 52.632 11.68 0.00 42.00 4.49
240 241 1.081906 GTGCTTCATGCCACACGTG 60.082 57.895 15.48 15.48 42.00 4.49
241 242 1.525765 TGCTTCATGCCACACGTGT 60.526 52.632 17.22 17.22 42.00 4.49
242 243 1.081906 GCTTCATGCCACACGTGTG 60.082 57.895 36.13 36.13 45.23 3.82
256 257 5.342806 ACACGTGTGACACTTATCAATTG 57.657 39.130 22.71 0.00 31.34 2.32
257 258 4.213270 ACACGTGTGACACTTATCAATTGG 59.787 41.667 22.71 0.00 31.34 3.16
258 259 3.751175 ACGTGTGACACTTATCAATTGGG 59.249 43.478 14.42 0.00 31.34 4.12
259 260 3.751175 CGTGTGACACTTATCAATTGGGT 59.249 43.478 14.42 0.00 31.34 4.51
260 261 4.932799 CGTGTGACACTTATCAATTGGGTA 59.067 41.667 14.42 0.00 31.34 3.69
261 262 5.410132 CGTGTGACACTTATCAATTGGGTAA 59.590 40.000 14.42 5.02 31.34 2.85
262 263 6.093495 CGTGTGACACTTATCAATTGGGTAAT 59.907 38.462 14.42 0.00 31.34 1.89
263 264 7.361713 CGTGTGACACTTATCAATTGGGTAATT 60.362 37.037 14.42 0.00 32.94 1.40
264 265 8.303876 GTGTGACACTTATCAATTGGGTAATTT 58.696 33.333 8.76 0.00 34.34 1.82
265 266 8.865090 TGTGACACTTATCAATTGGGTAATTTT 58.135 29.630 5.42 0.00 34.34 1.82
310 311 7.989947 ATTAAGAAATGGAGGTAGTACAGGA 57.010 36.000 2.06 0.00 0.00 3.86
343 344 0.178975 AACCCCGGAGAACAATTGCA 60.179 50.000 0.73 0.00 0.00 4.08
372 373 0.618680 ACCTGCCTGAGATGTGCCTA 60.619 55.000 0.00 0.00 0.00 3.93
373 374 0.179062 CCTGCCTGAGATGTGCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
393 394 6.357367 CCTACATATTGTTTGGTTAGAGGCT 58.643 40.000 0.00 0.00 0.00 4.58
402 403 5.221422 TGTTTGGTTAGAGGCTTGGAATTTG 60.221 40.000 0.00 0.00 0.00 2.32
405 406 3.563479 GGTTAGAGGCTTGGAATTTGGGA 60.563 47.826 0.00 0.00 0.00 4.37
437 438 2.324541 CCTAGAACTGATAGCCTGGCT 58.675 52.381 26.52 26.52 43.41 4.75
438 439 2.703007 CCTAGAACTGATAGCCTGGCTT 59.297 50.000 28.55 14.60 40.44 4.35
499 521 3.187700 CACTCGGGACTAATTAGTGCAC 58.812 50.000 30.65 21.09 45.16 4.57
530 552 8.005192 TGTGATTATTTATGGTTTGCATGCTA 57.995 30.769 20.33 8.83 0.00 3.49
537 559 0.456653 GGTTTGCATGCTAACTGCCG 60.457 55.000 33.29 0.00 42.00 5.69
564 586 3.755378 ACTCAACCTGACATGCTGATTTC 59.245 43.478 0.00 0.00 0.00 2.17
575 598 8.510243 TGACATGCTGATTTCTTATTGTGTAT 57.490 30.769 0.00 0.00 0.00 2.29
577 600 9.869844 GACATGCTGATTTCTTATTGTGTATAC 57.130 33.333 0.00 0.00 0.00 1.47
614 637 0.380378 GCGTTCAACCAAACAGCAGA 59.620 50.000 0.00 0.00 32.64 4.26
616 639 2.225491 GCGTTCAACCAAACAGCAGATA 59.775 45.455 0.00 0.00 32.64 1.98
643 671 2.760092 GCAAGCCAGACATATTTTCCCA 59.240 45.455 0.00 0.00 0.00 4.37
724 754 4.074970 CAGACCCACAATTTGTAAGCTCT 58.925 43.478 0.86 0.00 0.00 4.09
725 755 4.520492 CAGACCCACAATTTGTAAGCTCTT 59.480 41.667 0.86 0.00 0.00 2.85
812 844 5.308237 CCCATTACTAACCTTCTCTAGCCAT 59.692 44.000 0.00 0.00 0.00 4.40
841 873 1.217057 ACCATTCTGGCCCATCTGGT 61.217 55.000 10.46 10.46 42.67 4.00
884 916 6.449830 TTAGCCTTCCTTCTCTAACCTTTT 57.550 37.500 0.00 0.00 0.00 2.27
885 917 4.912586 AGCCTTCCTTCTCTAACCTTTTC 58.087 43.478 0.00 0.00 0.00 2.29
886 918 4.011023 GCCTTCCTTCTCTAACCTTTTCC 58.989 47.826 0.00 0.00 0.00 3.13
887 919 4.590918 CCTTCCTTCTCTAACCTTTTCCC 58.409 47.826 0.00 0.00 0.00 3.97
888 920 4.567958 CCTTCCTTCTCTAACCTTTTCCCC 60.568 50.000 0.00 0.00 0.00 4.81
889 921 3.604787 TCCTTCTCTAACCTTTTCCCCA 58.395 45.455 0.00 0.00 0.00 4.96
890 922 3.984770 TCCTTCTCTAACCTTTTCCCCAA 59.015 43.478 0.00 0.00 0.00 4.12
891 923 4.042934 TCCTTCTCTAACCTTTTCCCCAAG 59.957 45.833 0.00 0.00 0.00 3.61
892 924 4.202577 CCTTCTCTAACCTTTTCCCCAAGT 60.203 45.833 0.00 0.00 0.00 3.16
893 925 4.635699 TCTCTAACCTTTTCCCCAAGTC 57.364 45.455 0.00 0.00 0.00 3.01
894 926 4.240323 TCTCTAACCTTTTCCCCAAGTCT 58.760 43.478 0.00 0.00 0.00 3.24
895 927 4.663592 TCTCTAACCTTTTCCCCAAGTCTT 59.336 41.667 0.00 0.00 0.00 3.01
896 928 5.133830 TCTCTAACCTTTTCCCCAAGTCTTT 59.866 40.000 0.00 0.00 0.00 2.52
897 929 5.382616 TCTAACCTTTTCCCCAAGTCTTTC 58.617 41.667 0.00 0.00 0.00 2.62
898 930 3.973472 ACCTTTTCCCCAAGTCTTTCT 57.027 42.857 0.00 0.00 0.00 2.52
899 931 3.833732 ACCTTTTCCCCAAGTCTTTCTC 58.166 45.455 0.00 0.00 0.00 2.87
900 932 3.204382 ACCTTTTCCCCAAGTCTTTCTCA 59.796 43.478 0.00 0.00 0.00 3.27
901 933 4.215109 CCTTTTCCCCAAGTCTTTCTCAA 58.785 43.478 0.00 0.00 0.00 3.02
902 934 4.649218 CCTTTTCCCCAAGTCTTTCTCAAA 59.351 41.667 0.00 0.00 0.00 2.69
903 935 5.128663 CCTTTTCCCCAAGTCTTTCTCAAAA 59.871 40.000 0.00 0.00 0.00 2.44
904 936 6.351796 CCTTTTCCCCAAGTCTTTCTCAAAAA 60.352 38.462 0.00 0.00 0.00 1.94
1180 1215 1.802553 GCAGGTATCTCCCAACCCTA 58.197 55.000 0.00 0.00 36.34 3.53
1185 1220 2.047830 GTATCTCCCAACCCTACCCTG 58.952 57.143 0.00 0.00 0.00 4.45
1186 1221 0.988678 ATCTCCCAACCCTACCCTGC 60.989 60.000 0.00 0.00 0.00 4.85
1187 1222 1.923395 CTCCCAACCCTACCCTGCA 60.923 63.158 0.00 0.00 0.00 4.41
1188 1223 2.198304 CTCCCAACCCTACCCTGCAC 62.198 65.000 0.00 0.00 0.00 4.57
1189 1224 2.355115 CCAACCCTACCCTGCACC 59.645 66.667 0.00 0.00 0.00 5.01
1190 1225 2.355115 CAACCCTACCCTGCACCC 59.645 66.667 0.00 0.00 0.00 4.61
1191 1226 2.210102 AACCCTACCCTGCACCCT 59.790 61.111 0.00 0.00 0.00 4.34
1192 1227 1.923909 AACCCTACCCTGCACCCTC 60.924 63.158 0.00 0.00 0.00 4.30
1193 1228 2.041265 CCCTACCCTGCACCCTCT 59.959 66.667 0.00 0.00 0.00 3.69
1213 1248 2.280865 GCAACCCGATCCCGATCC 60.281 66.667 0.00 0.00 38.22 3.36
1214 1249 2.426023 CAACCCGATCCCGATCCC 59.574 66.667 0.00 0.00 38.22 3.85
1217 1252 2.118513 CCCGATCCCGATCCCTCT 59.881 66.667 0.00 0.00 38.22 3.69
1228 1263 0.565674 GATCCCTCTCTTCCTCCCCT 59.434 60.000 0.00 0.00 0.00 4.79
1229 1264 1.031112 ATCCCTCTCTTCCTCCCCTT 58.969 55.000 0.00 0.00 0.00 3.95
1394 1430 2.478134 CGATCGATCTTGATTCTTGGCC 59.522 50.000 22.43 0.00 0.00 5.36
1398 1434 1.680207 GATCTTGATTCTTGGCCTGCC 59.320 52.381 3.32 0.00 0.00 4.85
1399 1435 0.700564 TCTTGATTCTTGGCCTGCCT 59.299 50.000 9.97 0.00 36.94 4.75
1400 1436 1.915489 TCTTGATTCTTGGCCTGCCTA 59.085 47.619 9.97 0.35 36.94 3.93
1463 1499 0.900182 TGATCCGTGTCTGACTGCCT 60.900 55.000 9.51 0.00 0.00 4.75
1804 1843 2.030027 TGACTGGGAGGTCTTGATGT 57.970 50.000 0.00 0.00 37.16 3.06
1945 1984 2.758979 TGAACTAGGAACGCTAGAAGGG 59.241 50.000 0.00 0.00 0.00 3.95
1970 2009 7.120579 GGTATGATGTGGTTGTATCAGTTTCAA 59.879 37.037 0.00 0.00 36.81 2.69
2045 2084 5.355910 ACAGTGTTTCGTTTAGGTTGACATT 59.644 36.000 0.00 0.00 0.00 2.71
2256 2295 7.698836 ATGACACTGTTTCATTTAGTTTTGC 57.301 32.000 3.68 0.00 28.83 3.68
2370 2409 7.658575 AGTTTTGTATGTTTCCGTTTAGCTCTA 59.341 33.333 0.00 0.00 0.00 2.43
2384 2423 9.609950 CCGTTTAGCTCTACTAGAACATTATAC 57.390 37.037 0.00 0.00 30.79 1.47
2526 2566 2.161410 TGCTAACGCACCATTGTTGATC 59.839 45.455 0.00 0.00 42.25 2.92
2629 2669 0.694771 TGTGAGCAGGCCAGAAGAAT 59.305 50.000 5.01 0.00 0.00 2.40
2802 2842 6.374417 TTTCTCTACTATGGGTTTGCTCTT 57.626 37.500 0.00 0.00 0.00 2.85
2833 2873 2.030893 ACGATGTTCATGTTTGCACCTG 60.031 45.455 0.00 0.00 0.00 4.00
2881 2921 4.098501 TCAGTCTATCAGTTCGCACATGAT 59.901 41.667 0.00 5.74 37.44 2.45
3002 3042 4.630644 TGAGGCCTGGAATTATGATCTC 57.369 45.455 12.00 0.00 0.00 2.75
3003 3043 4.237843 TGAGGCCTGGAATTATGATCTCT 58.762 43.478 12.00 0.00 0.00 3.10
3103 3144 4.688879 CCTGACTTGATAACTGCGTGTTTA 59.311 41.667 0.32 0.00 39.89 2.01
3229 3271 1.209621 TAGGCACATTCACCTACCCC 58.790 55.000 0.00 0.00 37.50 4.95
3369 3413 7.609918 TCTCATGCCTAATGCTAACAGTTTTTA 59.390 33.333 0.00 0.00 42.00 1.52
3390 3434 8.599055 TTTTATTTGCATGTCACATTTGCTTA 57.401 26.923 5.02 0.00 37.28 3.09
3403 3447 6.208402 TCACATTTGCTTAATGAACCAAGCTA 59.792 34.615 15.87 0.00 45.35 3.32
3503 3547 2.032799 TCAACATTCGAAGCAACACACC 59.967 45.455 3.35 0.00 0.00 4.16
3579 3623 9.781633 TTCTTTAGGTAATGTAAAAGCACAGTA 57.218 29.630 0.00 0.00 0.00 2.74
3587 3631 6.780706 ATGTAAAAGCACAGTACAGTACAC 57.219 37.500 13.37 0.00 31.61 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.081365 CCTAAAATTAAACCGCCCCAACAT 60.081 41.667 0.00 0.00 0.00 2.71
1 2 3.258622 CCTAAAATTAAACCGCCCCAACA 59.741 43.478 0.00 0.00 0.00 3.33
2 3 3.510753 TCCTAAAATTAAACCGCCCCAAC 59.489 43.478 0.00 0.00 0.00 3.77
3 4 3.510753 GTCCTAAAATTAAACCGCCCCAA 59.489 43.478 0.00 0.00 0.00 4.12
4 5 3.090790 GTCCTAAAATTAAACCGCCCCA 58.909 45.455 0.00 0.00 0.00 4.96
5 6 2.428171 GGTCCTAAAATTAAACCGCCCC 59.572 50.000 0.00 0.00 0.00 5.80
6 7 2.428171 GGGTCCTAAAATTAAACCGCCC 59.572 50.000 0.00 0.00 0.00 6.13
7 8 3.359033 AGGGTCCTAAAATTAAACCGCC 58.641 45.455 0.00 0.00 0.00 6.13
8 9 6.704289 ATTAGGGTCCTAAAATTAAACCGC 57.296 37.500 12.83 0.00 41.21 5.68
9 10 9.399797 ACTTATTAGGGTCCTAAAATTAAACCG 57.600 33.333 12.83 1.21 41.21 4.44
24 25 5.499004 ACACATGTGACACTTATTAGGGT 57.501 39.130 31.94 1.18 41.95 4.34
38 39 0.316937 GTGTTCGTGCCACACATGTG 60.317 55.000 24.25 24.25 43.52 3.21
39 40 2.021722 GTGTTCGTGCCACACATGT 58.978 52.632 0.00 0.00 43.52 3.21
40 41 4.920662 GTGTTCGTGCCACACATG 57.079 55.556 0.00 0.00 43.52 3.21
43 44 0.041312 GTCATGTGTTCGTGCCACAC 60.041 55.000 0.00 5.23 44.90 3.82
44 45 0.462759 TGTCATGTGTTCGTGCCACA 60.463 50.000 0.00 6.93 46.03 4.17
45 46 0.660488 TTGTCATGTGTTCGTGCCAC 59.340 50.000 0.00 0.00 0.00 5.01
46 47 0.660488 GTTGTCATGTGTTCGTGCCA 59.340 50.000 0.00 0.00 0.00 4.92
47 48 0.944386 AGTTGTCATGTGTTCGTGCC 59.056 50.000 0.00 0.00 0.00 5.01
48 49 1.069906 GGAGTTGTCATGTGTTCGTGC 60.070 52.381 0.00 0.00 0.00 5.34
49 50 1.192312 CGGAGTTGTCATGTGTTCGTG 59.808 52.381 0.00 0.00 0.00 4.35
50 51 1.067974 TCGGAGTTGTCATGTGTTCGT 59.932 47.619 0.00 0.00 0.00 3.85
51 52 1.778334 TCGGAGTTGTCATGTGTTCG 58.222 50.000 0.00 0.00 0.00 3.95
52 53 3.560068 ACTTTCGGAGTTGTCATGTGTTC 59.440 43.478 0.00 0.00 33.92 3.18
53 54 3.541632 ACTTTCGGAGTTGTCATGTGTT 58.458 40.909 0.00 0.00 33.92 3.32
54 55 3.194005 ACTTTCGGAGTTGTCATGTGT 57.806 42.857 0.00 0.00 33.92 3.72
75 76 9.658475 CTCGTGTCACTAAATTTGTCATAAAAA 57.342 29.630 0.00 0.00 0.00 1.94
76 77 9.047371 TCTCGTGTCACTAAATTTGTCATAAAA 57.953 29.630 0.00 0.00 0.00 1.52
77 78 8.596271 TCTCGTGTCACTAAATTTGTCATAAA 57.404 30.769 0.00 0.00 0.00 1.40
78 79 8.596271 TTCTCGTGTCACTAAATTTGTCATAA 57.404 30.769 0.00 0.00 0.00 1.90
79 80 8.655970 CATTCTCGTGTCACTAAATTTGTCATA 58.344 33.333 0.00 0.00 0.00 2.15
80 81 7.173218 ACATTCTCGTGTCACTAAATTTGTCAT 59.827 33.333 0.00 0.00 0.00 3.06
81 82 6.481976 ACATTCTCGTGTCACTAAATTTGTCA 59.518 34.615 0.00 0.00 0.00 3.58
82 83 6.888430 ACATTCTCGTGTCACTAAATTTGTC 58.112 36.000 0.00 0.00 0.00 3.18
83 84 6.861065 ACATTCTCGTGTCACTAAATTTGT 57.139 33.333 0.00 0.00 0.00 2.83
94 95 6.366332 ACAATTAGAGTTGACATTCTCGTGTC 59.634 38.462 0.30 0.30 46.75 3.67
95 96 6.223852 ACAATTAGAGTTGACATTCTCGTGT 58.776 36.000 0.00 0.00 36.03 4.49
96 97 6.366061 TGACAATTAGAGTTGACATTCTCGTG 59.634 38.462 0.00 0.00 36.03 4.35
97 98 6.455647 TGACAATTAGAGTTGACATTCTCGT 58.544 36.000 0.00 0.00 36.03 4.18
98 99 6.951256 TGACAATTAGAGTTGACATTCTCG 57.049 37.500 0.00 0.00 36.03 4.04
99 100 7.095060 TGCTTGACAATTAGAGTTGACATTCTC 60.095 37.037 0.00 1.41 34.67 2.87
100 101 6.712095 TGCTTGACAATTAGAGTTGACATTCT 59.288 34.615 0.00 0.00 34.67 2.40
101 102 6.902341 TGCTTGACAATTAGAGTTGACATTC 58.098 36.000 0.00 0.00 34.67 2.67
102 103 6.882610 TGCTTGACAATTAGAGTTGACATT 57.117 33.333 0.00 0.00 34.67 2.71
103 104 6.127814 CCATGCTTGACAATTAGAGTTGACAT 60.128 38.462 0.22 0.00 34.67 3.06
104 105 5.181811 CCATGCTTGACAATTAGAGTTGACA 59.818 40.000 0.22 0.00 33.26 3.58
105 106 5.634896 CCATGCTTGACAATTAGAGTTGAC 58.365 41.667 0.22 0.00 33.37 3.18
106 107 4.156556 GCCATGCTTGACAATTAGAGTTGA 59.843 41.667 0.22 0.00 33.37 3.18
107 108 4.082625 TGCCATGCTTGACAATTAGAGTTG 60.083 41.667 0.22 0.00 35.25 3.16
108 109 4.081406 TGCCATGCTTGACAATTAGAGTT 58.919 39.130 0.22 0.00 0.00 3.01
109 110 3.689347 TGCCATGCTTGACAATTAGAGT 58.311 40.909 0.22 0.00 0.00 3.24
110 111 4.707030 TTGCCATGCTTGACAATTAGAG 57.293 40.909 0.22 0.00 0.00 2.43
111 112 5.664294 ATTTGCCATGCTTGACAATTAGA 57.336 34.783 2.24 0.00 0.00 2.10
112 113 6.730960 AAATTTGCCATGCTTGACAATTAG 57.269 33.333 2.24 0.00 0.00 1.73
113 114 8.789825 AATAAATTTGCCATGCTTGACAATTA 57.210 26.923 0.00 0.80 0.00 1.40
114 115 7.690952 AATAAATTTGCCATGCTTGACAATT 57.309 28.000 0.00 0.00 0.00 2.32
115 116 7.690952 AAATAAATTTGCCATGCTTGACAAT 57.309 28.000 0.00 0.00 0.00 2.71
116 117 7.507733 AAAATAAATTTGCCATGCTTGACAA 57.492 28.000 0.00 0.00 0.00 3.18
117 118 7.507733 AAAAATAAATTTGCCATGCTTGACA 57.492 28.000 0.00 0.00 0.00 3.58
118 119 6.737750 CGAAAAATAAATTTGCCATGCTTGAC 59.262 34.615 0.00 0.00 0.00 3.18
119 120 6.128336 CCGAAAAATAAATTTGCCATGCTTGA 60.128 34.615 0.00 0.00 0.00 3.02
120 121 6.022821 CCGAAAAATAAATTTGCCATGCTTG 58.977 36.000 0.00 0.00 0.00 4.01
121 122 5.936956 TCCGAAAAATAAATTTGCCATGCTT 59.063 32.000 0.00 0.00 0.00 3.91
122 123 5.486526 TCCGAAAAATAAATTTGCCATGCT 58.513 33.333 0.00 0.00 0.00 3.79
123 124 5.793026 TCCGAAAAATAAATTTGCCATGC 57.207 34.783 0.00 0.00 0.00 4.06
124 125 6.717413 CCATCCGAAAAATAAATTTGCCATG 58.283 36.000 0.00 0.00 0.00 3.66
125 126 5.296531 GCCATCCGAAAAATAAATTTGCCAT 59.703 36.000 0.00 0.00 0.00 4.40
126 127 4.633565 GCCATCCGAAAAATAAATTTGCCA 59.366 37.500 0.00 0.00 0.00 4.92
127 128 4.633565 TGCCATCCGAAAAATAAATTTGCC 59.366 37.500 0.00 0.00 0.00 4.52
128 129 5.793026 TGCCATCCGAAAAATAAATTTGC 57.207 34.783 0.00 0.00 0.00 3.68
129 130 7.363205 ACTTGCCATCCGAAAAATAAATTTG 57.637 32.000 0.00 0.00 0.00 2.32
130 131 7.977789 AACTTGCCATCCGAAAAATAAATTT 57.022 28.000 0.00 0.00 0.00 1.82
131 132 7.977789 AAACTTGCCATCCGAAAAATAAATT 57.022 28.000 0.00 0.00 0.00 1.82
132 133 7.977789 AAAACTTGCCATCCGAAAAATAAAT 57.022 28.000 0.00 0.00 0.00 1.40
133 134 8.145122 ACTAAAACTTGCCATCCGAAAAATAAA 58.855 29.630 0.00 0.00 0.00 1.40
134 135 7.662897 ACTAAAACTTGCCATCCGAAAAATAA 58.337 30.769 0.00 0.00 0.00 1.40
135 136 7.222000 ACTAAAACTTGCCATCCGAAAAATA 57.778 32.000 0.00 0.00 0.00 1.40
136 137 6.096673 ACTAAAACTTGCCATCCGAAAAAT 57.903 33.333 0.00 0.00 0.00 1.82
137 138 5.523438 ACTAAAACTTGCCATCCGAAAAA 57.477 34.783 0.00 0.00 0.00 1.94
138 139 5.523438 AACTAAAACTTGCCATCCGAAAA 57.477 34.783 0.00 0.00 0.00 2.29
139 140 5.523438 AAACTAAAACTTGCCATCCGAAA 57.477 34.783 0.00 0.00 0.00 3.46
140 141 5.523438 AAAACTAAAACTTGCCATCCGAA 57.477 34.783 0.00 0.00 0.00 4.30
141 142 5.523438 AAAAACTAAAACTTGCCATCCGA 57.477 34.783 0.00 0.00 0.00 4.55
142 143 4.381566 CGAAAAACTAAAACTTGCCATCCG 59.618 41.667 0.00 0.00 0.00 4.18
143 144 4.684242 CCGAAAAACTAAAACTTGCCATCC 59.316 41.667 0.00 0.00 0.00 3.51
144 145 4.684242 CCCGAAAAACTAAAACTTGCCATC 59.316 41.667 0.00 0.00 0.00 3.51
145 146 4.100344 ACCCGAAAAACTAAAACTTGCCAT 59.900 37.500 0.00 0.00 0.00 4.40
146 147 3.447944 ACCCGAAAAACTAAAACTTGCCA 59.552 39.130 0.00 0.00 0.00 4.92
147 148 4.049546 ACCCGAAAAACTAAAACTTGCC 57.950 40.909 0.00 0.00 0.00 4.52
148 149 5.349270 ACAAACCCGAAAAACTAAAACTTGC 59.651 36.000 0.00 0.00 0.00 4.01
149 150 6.954616 ACAAACCCGAAAAACTAAAACTTG 57.045 33.333 0.00 0.00 0.00 3.16
150 151 7.966246 AAACAAACCCGAAAAACTAAAACTT 57.034 28.000 0.00 0.00 0.00 2.66
151 152 7.966246 AAAACAAACCCGAAAAACTAAAACT 57.034 28.000 0.00 0.00 0.00 2.66
173 174 9.883142 ATTAAAGTTGTCATCCACAAAGAAAAA 57.117 25.926 0.00 0.00 46.90 1.94
174 175 9.883142 AATTAAAGTTGTCATCCACAAAGAAAA 57.117 25.926 0.00 0.00 46.90 2.29
175 176 9.311916 CAATTAAAGTTGTCATCCACAAAGAAA 57.688 29.630 0.00 0.00 46.90 2.52
176 177 8.474025 ACAATTAAAGTTGTCATCCACAAAGAA 58.526 29.630 0.00 0.00 46.90 2.52
177 178 8.006298 ACAATTAAAGTTGTCATCCACAAAGA 57.994 30.769 0.00 0.00 46.90 2.52
178 179 8.647143 AACAATTAAAGTTGTCATCCACAAAG 57.353 30.769 0.00 0.00 46.90 2.77
192 193 9.476202 GCCTCTGATGTTTTTAACAATTAAAGT 57.524 29.630 0.00 0.00 45.86 2.66
193 194 9.474920 TGCCTCTGATGTTTTTAACAATTAAAG 57.525 29.630 0.00 0.00 45.86 1.85
194 195 9.474920 CTGCCTCTGATGTTTTTAACAATTAAA 57.525 29.630 0.00 0.00 45.86 1.52
195 196 8.855110 TCTGCCTCTGATGTTTTTAACAATTAA 58.145 29.630 0.00 0.00 45.86 1.40
196 197 8.402798 TCTGCCTCTGATGTTTTTAACAATTA 57.597 30.769 0.00 0.00 45.86 1.40
197 198 7.014615 ACTCTGCCTCTGATGTTTTTAACAATT 59.985 33.333 0.00 0.00 45.86 2.32
198 199 6.491403 ACTCTGCCTCTGATGTTTTTAACAAT 59.509 34.615 0.00 0.00 45.86 2.71
199 200 5.827797 ACTCTGCCTCTGATGTTTTTAACAA 59.172 36.000 0.00 0.00 45.86 2.83
200 201 5.239306 CACTCTGCCTCTGATGTTTTTAACA 59.761 40.000 0.00 0.00 46.94 2.41
201 202 5.693814 CACTCTGCCTCTGATGTTTTTAAC 58.306 41.667 0.00 0.00 0.00 2.01
202 203 4.216257 GCACTCTGCCTCTGATGTTTTTAA 59.784 41.667 0.00 0.00 37.42 1.52
203 204 3.753272 GCACTCTGCCTCTGATGTTTTTA 59.247 43.478 0.00 0.00 37.42 1.52
204 205 2.555757 GCACTCTGCCTCTGATGTTTTT 59.444 45.455 0.00 0.00 37.42 1.94
205 206 2.157738 GCACTCTGCCTCTGATGTTTT 58.842 47.619 0.00 0.00 37.42 2.43
206 207 1.350351 AGCACTCTGCCTCTGATGTTT 59.650 47.619 0.00 0.00 46.52 2.83
207 208 0.982704 AGCACTCTGCCTCTGATGTT 59.017 50.000 0.00 0.00 46.52 2.71
208 209 0.982704 AAGCACTCTGCCTCTGATGT 59.017 50.000 0.00 0.00 46.52 3.06
209 210 1.066358 TGAAGCACTCTGCCTCTGATG 60.066 52.381 0.00 0.00 46.52 3.07
210 211 1.273759 TGAAGCACTCTGCCTCTGAT 58.726 50.000 0.00 0.00 46.52 2.90
211 212 1.066358 CATGAAGCACTCTGCCTCTGA 60.066 52.381 0.00 0.00 46.52 3.27
212 213 1.370609 CATGAAGCACTCTGCCTCTG 58.629 55.000 0.00 0.00 46.52 3.35
213 214 0.392729 GCATGAAGCACTCTGCCTCT 60.393 55.000 0.00 0.00 46.52 3.69
214 215 2.096596 GCATGAAGCACTCTGCCTC 58.903 57.895 0.00 0.00 46.52 4.70
215 216 4.315588 GCATGAAGCACTCTGCCT 57.684 55.556 0.00 0.00 46.52 4.75
216 217 3.194719 GGCATGAAGCACTCTGCC 58.805 61.111 0.00 4.88 46.52 4.85
224 225 1.081906 CACACGTGTGGCATGAAGC 60.082 57.895 35.65 0.00 42.10 3.86
225 226 2.615774 TCACACGTGTGGCATGAAG 58.384 52.632 39.88 18.65 45.65 3.02
226 227 4.865865 TCACACGTGTGGCATGAA 57.134 50.000 39.88 22.46 45.65 2.57
232 233 2.749776 TGATAAGTGTCACACGTGTGG 58.250 47.619 39.88 25.18 45.65 4.17
233 234 4.990543 ATTGATAAGTGTCACACGTGTG 57.009 40.909 37.04 37.04 46.91 3.82
234 235 4.213270 CCAATTGATAAGTGTCACACGTGT 59.787 41.667 17.22 17.22 39.64 4.49
235 236 4.378356 CCCAATTGATAAGTGTCACACGTG 60.378 45.833 15.48 15.48 39.64 4.49
236 237 3.751175 CCCAATTGATAAGTGTCACACGT 59.249 43.478 7.12 1.06 39.64 4.49
237 238 3.751175 ACCCAATTGATAAGTGTCACACG 59.249 43.478 7.12 0.00 39.64 4.49
238 239 6.811253 TTACCCAATTGATAAGTGTCACAC 57.189 37.500 7.12 0.00 34.10 3.82
239 240 8.415950 AAATTACCCAATTGATAAGTGTCACA 57.584 30.769 7.12 0.00 34.53 3.58
291 292 5.615925 ACATCCTGTACTACCTCCATTTC 57.384 43.478 0.00 0.00 0.00 2.17
292 293 7.691993 AATACATCCTGTACTACCTCCATTT 57.308 36.000 0.00 0.00 35.42 2.32
322 323 0.243636 CAATTGTTCTCCGGGGTTGC 59.756 55.000 0.00 0.00 0.00 4.17
329 330 0.179129 GGCCATGCAATTGTTCTCCG 60.179 55.000 7.40 0.00 0.00 4.63
372 373 5.418840 CCAAGCCTCTAACCAAACAATATGT 59.581 40.000 0.00 0.00 0.00 2.29
373 374 5.652014 TCCAAGCCTCTAACCAAACAATATG 59.348 40.000 0.00 0.00 0.00 1.78
383 384 2.760650 CCCAAATTCCAAGCCTCTAACC 59.239 50.000 0.00 0.00 0.00 2.85
405 406 1.581149 AGTTCTAGGCCAGGGAGGTAT 59.419 52.381 5.01 0.00 40.61 2.73
414 415 2.042464 CAGGCTATCAGTTCTAGGCCA 58.958 52.381 5.01 0.00 41.39 5.36
420 421 1.211457 CCAAGCCAGGCTATCAGTTCT 59.789 52.381 16.56 0.00 38.25 3.01
473 495 3.454812 ACTAATTAGTCCCGAGTGGCATT 59.545 43.478 12.50 0.00 0.00 3.56
481 503 2.167693 CAGGTGCACTAATTAGTCCCGA 59.832 50.000 17.98 0.00 33.46 5.14
499 521 6.201425 GCAAACCATAAATAATCACATGCAGG 59.799 38.462 0.00 0.00 0.00 4.85
514 536 4.108699 GCAGTTAGCATGCAAACCATAA 57.891 40.909 21.98 5.56 43.31 1.90
530 552 0.818040 GGTTGAGTTGACCGGCAGTT 60.818 55.000 0.00 0.00 0.00 3.16
537 559 1.537202 GCATGTCAGGTTGAGTTGACC 59.463 52.381 0.00 0.00 42.30 4.02
564 586 7.171508 CCTGGCACACATAGTATACACAATAAG 59.828 40.741 5.50 0.00 0.00 1.73
575 598 1.065491 CCTTGCCTGGCACACATAGTA 60.065 52.381 23.30 2.67 38.71 1.82
577 600 2.485677 CCTTGCCTGGCACACATAG 58.514 57.895 23.30 15.51 38.71 2.23
614 637 0.692476 TGTCTGGCTTGCCTGTGTAT 59.308 50.000 13.18 0.00 0.00 2.29
616 639 0.692476 TATGTCTGGCTTGCCTGTGT 59.308 50.000 13.18 5.93 0.00 3.72
643 671 0.548510 GCCTGGTAGCCTGGAGAAAT 59.451 55.000 14.14 0.00 44.09 2.17
686 716 2.554344 GGTCTGTTTGGTTGATGCCCTA 60.554 50.000 0.00 0.00 0.00 3.53
841 873 3.951563 ATAAATGGGCTGGCTAAGACA 57.048 42.857 0.00 0.00 34.40 3.41
908 940 2.775384 GGGACTTGGGGAAAAGGTTTTT 59.225 45.455 0.00 0.00 0.00 1.94
909 941 2.404559 GGGACTTGGGGAAAAGGTTTT 58.595 47.619 0.00 0.00 0.00 2.43
910 942 1.413953 GGGGACTTGGGGAAAAGGTTT 60.414 52.381 0.00 0.00 0.00 3.27
911 943 0.190069 GGGGACTTGGGGAAAAGGTT 59.810 55.000 0.00 0.00 0.00 3.50
912 944 1.002242 TGGGGACTTGGGGAAAAGGT 61.002 55.000 0.00 0.00 0.00 3.50
913 945 0.189822 TTGGGGACTTGGGGAAAAGG 59.810 55.000 0.00 0.00 0.00 3.11
914 946 1.632589 CTTGGGGACTTGGGGAAAAG 58.367 55.000 0.00 0.00 0.00 2.27
915 947 0.189822 CCTTGGGGACTTGGGGAAAA 59.810 55.000 0.00 0.00 33.58 2.29
916 948 0.703056 TCCTTGGGGACTTGGGGAAA 60.703 55.000 0.00 0.00 36.57 3.13
917 949 1.072538 TCCTTGGGGACTTGGGGAA 60.073 57.895 0.00 0.00 36.57 3.97
918 950 1.541368 CTCCTTGGGGACTTGGGGA 60.541 63.158 0.00 0.00 36.57 4.81
919 951 1.541368 TCTCCTTGGGGACTTGGGG 60.541 63.158 0.00 0.00 36.57 4.96
920 952 0.547712 TCTCTCCTTGGGGACTTGGG 60.548 60.000 0.00 0.00 36.57 4.12
921 953 1.362224 TTCTCTCCTTGGGGACTTGG 58.638 55.000 0.00 0.00 36.57 3.61
922 954 2.784347 GTTTCTCTCCTTGGGGACTTG 58.216 52.381 0.00 0.00 36.57 3.16
923 955 1.348036 CGTTTCTCTCCTTGGGGACTT 59.652 52.381 0.00 0.00 36.57 3.01
924 956 0.977395 CGTTTCTCTCCTTGGGGACT 59.023 55.000 0.00 0.00 36.57 3.85
925 957 0.974383 TCGTTTCTCTCCTTGGGGAC 59.026 55.000 0.00 0.00 36.57 4.46
1174 1209 1.923909 GAGGGTGCAGGGTAGGGTT 60.924 63.158 0.00 0.00 0.00 4.11
1175 1210 2.285442 GAGGGTGCAGGGTAGGGT 60.285 66.667 0.00 0.00 0.00 4.34
1186 1221 4.760047 CGGGTTGCGGAGAGGGTG 62.760 72.222 0.00 0.00 0.00 4.61
1188 1223 3.447025 GATCGGGTTGCGGAGAGGG 62.447 68.421 0.00 0.00 0.00 4.30
1189 1224 2.107141 GATCGGGTTGCGGAGAGG 59.893 66.667 0.00 0.00 0.00 3.69
1190 1225 2.107141 GGATCGGGTTGCGGAGAG 59.893 66.667 0.00 0.00 0.00 3.20
1191 1226 3.467226 GGGATCGGGTTGCGGAGA 61.467 66.667 0.00 0.00 0.00 3.71
1192 1227 4.891727 CGGGATCGGGTTGCGGAG 62.892 72.222 0.00 0.00 0.00 4.63
1213 1248 2.262266 AGAAAGGGGAGGAAGAGAGG 57.738 55.000 0.00 0.00 0.00 3.69
1214 1249 5.966853 ATTTAGAAAGGGGAGGAAGAGAG 57.033 43.478 0.00 0.00 0.00 3.20
1217 1252 5.104652 CCGTAATTTAGAAAGGGGAGGAAGA 60.105 44.000 0.00 0.00 0.00 2.87
1453 1489 2.033141 GCAGGCAAGGCAGTCAGA 59.967 61.111 0.00 0.00 0.00 3.27
1463 1499 2.591429 CACGACACCTGCAGGCAA 60.591 61.111 33.06 0.00 39.32 4.52
1804 1843 5.076182 TCCAAATTCACTCAAGTGGCATAA 58.924 37.500 10.13 0.00 45.65 1.90
1945 1984 7.609760 TGAAACTGATACAACCACATCATAC 57.390 36.000 0.00 0.00 31.05 2.39
2045 2084 7.151999 TGTTTTGTGAGAGCTAAACAGAAAA 57.848 32.000 13.88 13.88 38.46 2.29
2384 2423 7.809546 TCAACACTACTGGAGATACTATCAG 57.190 40.000 0.00 0.00 0.00 2.90
2526 2566 6.730960 AAATACTTTCATGCAGGCAATTTG 57.269 33.333 0.00 0.00 0.00 2.32
2629 2669 5.555017 AGCTTATGCAGAAGTCTTCTTCAA 58.445 37.500 21.36 5.30 44.00 2.69
2802 2842 7.148639 GCAAACATGAACATCGTAGAGAAACTA 60.149 37.037 0.00 0.00 43.63 2.24
2833 2873 5.959618 AGTACTGGCATTTAGTTTTCCAC 57.040 39.130 0.00 0.00 0.00 4.02
2881 2921 9.491675 TTTTTACGGTCATTGAATACTTACAGA 57.508 29.630 0.00 0.00 0.00 3.41
3002 3042 0.610687 GACCAGTCTCTGAACCCCAG 59.389 60.000 0.00 0.00 44.27 4.45
3003 3043 0.191064 AGACCAGTCTCTGAACCCCA 59.809 55.000 0.00 0.00 34.17 4.96
3103 3144 8.707449 ACATAGCATCAAAATAATGACCCAAAT 58.293 29.630 0.00 0.00 30.82 2.32
3369 3413 6.874664 TCATTAAGCAAATGTGACATGCAAAT 59.125 30.769 13.00 9.15 44.58 2.32
3390 3434 6.964807 TGCATGATATTAGCTTGGTTCATT 57.035 33.333 0.00 0.00 0.00 2.57
3579 3623 6.070938 CCTTAAGGCCTTAAGTAGTGTACTGT 60.071 42.308 42.43 14.55 46.42 3.55


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

AutoCloner maintained by Alex Coulton.