Multiple sequence alignment - TraesCS2A01G422800

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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 TraesCS2A01G422800 chr2A 100.000 2549 0 0 1 2549 677959066 677956518 0.000000e+00 4708
1 TraesCS2A01G422800 chr2A 96.238 1967 65 7 588 2549 744582019 744583981 0.000000e+00 3214
2 TraesCS2A01G422800 chr2A 94.672 1952 90 11 598 2543 677413606 677411663 0.000000e+00 3016
3 TraesCS2A01G422800 chr2A 93.130 1965 113 16 598 2549 213959517 213957562 0.000000e+00 2861
4 TraesCS2A01G422800 chr7A 96.370 1956 61 7 598 2549 36946200 36948149 0.000000e+00 3210
5 TraesCS2A01G422800 chr7A 98.905 274 3 0 1 274 552818740 552819013 8.200000e-135 490
6 TraesCS2A01G422800 chr7A 83.092 207 22 7 405 600 75201800 75202004 2.610000e-40 176
7 TraesCS2A01G422800 chr5A 95.906 1954 70 6 598 2549 689446507 689444562 0.000000e+00 3157
8 TraesCS2A01G422800 chr5A 94.118 68 1 3 534 600 446608897 446608962 1.610000e-17 100
9 TraesCS2A01G422800 chr5B 95.814 1959 71 6 598 2549 3450172 3448218 0.000000e+00 3153
10 TraesCS2A01G422800 chr7D 94.944 1958 83 12 598 2549 63995390 63997337 0.000000e+00 3053
11 TraesCS2A01G422800 chr1B 95.206 1940 65 7 598 2529 645321437 645323356 0.000000e+00 3042
12 TraesCS2A01G422800 chr1B 99.632 272 1 0 1 272 604822271 604822542 4.900000e-137 497
13 TraesCS2A01G422800 chr1B 98.545 275 3 1 1 275 209040387 209040660 3.810000e-133 484
14 TraesCS2A01G422800 chr1B 85.408 233 23 10 375 600 616093651 616093879 5.480000e-57 231
15 TraesCS2A01G422800 chr1B 84.127 126 18 2 407 530 616093644 616093769 1.240000e-23 121
16 TraesCS2A01G422800 chr3D 94.563 1968 91 13 588 2549 475106671 475108628 0.000000e+00 3027
17 TraesCS2A01G422800 chr2B 92.202 436 26 5 598 1029 13181551 13181982 6.030000e-171 610
18 TraesCS2A01G422800 chr2B 88.820 161 12 6 444 600 634155370 634155212 2.590000e-45 193
19 TraesCS2A01G422800 chr7B 98.901 273 3 0 1 273 594342819 594343091 2.950000e-134 488
20 TraesCS2A01G422800 chr7B 96.296 297 8 2 1 297 314298642 314298935 3.810000e-133 484
21 TraesCS2A01G422800 chr4A 98.901 273 3 0 1 273 498635472 498635200 2.950000e-134 488
22 TraesCS2A01G422800 chr6B 98.901 273 2 1 1 273 103652010 103651739 1.060000e-133 486
23 TraesCS2A01G422800 chr6B 95.033 302 10 5 1 298 288141113 288140813 1.070000e-128 470
24 TraesCS2A01G422800 chr3A 97.183 284 5 3 1 283 445850366 445850085 6.380000e-131 477
25 TraesCS2A01G422800 chr4D 85.119 336 27 11 268 600 454985686 454985371 3.160000e-84 322
26 TraesCS2A01G422800 chrUn 87.907 215 21 5 388 600 475975972 475975761 5.450000e-62 248
27 TraesCS2A01G422800 chr6D 89.308 159 10 5 444 600 270594354 270594201 2.590000e-45 193
28 TraesCS2A01G422800 chr3B 90.551 127 10 2 475 600 62979317 62979442 1.570000e-37 167
29 TraesCS2A01G422800 chr1D 91.753 97 7 1 505 600 220881404 220881500 1.590000e-27 134


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 TraesCS2A01G422800 chr2A 677956518 677959066 2548 True 4708 4708 100.000 1 2549 1 chr2A.!!$R3 2548
1 TraesCS2A01G422800 chr2A 744582019 744583981 1962 False 3214 3214 96.238 588 2549 1 chr2A.!!$F1 1961
2 TraesCS2A01G422800 chr2A 677411663 677413606 1943 True 3016 3016 94.672 598 2543 1 chr2A.!!$R2 1945
3 TraesCS2A01G422800 chr2A 213957562 213959517 1955 True 2861 2861 93.130 598 2549 1 chr2A.!!$R1 1951
4 TraesCS2A01G422800 chr7A 36946200 36948149 1949 False 3210 3210 96.370 598 2549 1 chr7A.!!$F1 1951
5 TraesCS2A01G422800 chr5A 689444562 689446507 1945 True 3157 3157 95.906 598 2549 1 chr5A.!!$R1 1951
6 TraesCS2A01G422800 chr5B 3448218 3450172 1954 True 3153 3153 95.814 598 2549 1 chr5B.!!$R1 1951
7 TraesCS2A01G422800 chr7D 63995390 63997337 1947 False 3053 3053 94.944 598 2549 1 chr7D.!!$F1 1951
8 TraesCS2A01G422800 chr1B 645321437 645323356 1919 False 3042 3042 95.206 598 2529 1 chr1B.!!$F3 1931
9 TraesCS2A01G422800 chr3D 475106671 475108628 1957 False 3027 3027 94.563 588 2549 1 chr3D.!!$F1 1961

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
149 150 0.035152 TCCGAGACGTAGGGCTGTTA 60.035 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1839 1.473257 CGCAAGAGAATCCCCGAATGA 60.473 52.381 0.0 0.0 43.02 2.57 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
20 21 3.521947 CCTTAAACCCTCTCCTACGTG 57.478 52.381 0.00 0.00 0.00 4.49
21 22 2.167900 CCTTAAACCCTCTCCTACGTGG 59.832 54.545 0.00 0.00 37.10 4.94
22 23 1.856629 TAAACCCTCTCCTACGTGGG 58.143 55.000 12.53 12.53 42.18 4.61
23 24 1.551019 AAACCCTCTCCTACGTGGGC 61.551 60.000 14.07 0.00 40.56 5.36
24 25 2.042843 CCCTCTCCTACGTGGGCT 60.043 66.667 14.07 0.00 36.20 5.19
25 26 2.427245 CCCTCTCCTACGTGGGCTG 61.427 68.421 14.07 8.69 36.20 4.85
26 27 2.427245 CCTCTCCTACGTGGGCTGG 61.427 68.421 14.07 10.83 36.20 4.85
27 28 3.075005 TCTCCTACGTGGGCTGGC 61.075 66.667 14.07 0.00 36.20 4.85
28 29 3.077556 CTCCTACGTGGGCTGGCT 61.078 66.667 14.07 0.00 36.20 4.75
29 30 3.376935 CTCCTACGTGGGCTGGCTG 62.377 68.421 14.07 0.00 36.20 4.85
30 31 4.473520 CCTACGTGGGCTGGCTGG 62.474 72.222 4.50 0.00 0.00 4.85
31 32 4.473520 CTACGTGGGCTGGCTGGG 62.474 72.222 0.00 0.00 0.00 4.45
47 48 3.075005 GGGTCCTGGCGCACTCTA 61.075 66.667 10.83 0.00 0.00 2.43
48 49 2.435693 GGGTCCTGGCGCACTCTAT 61.436 63.158 10.83 0.00 0.00 1.98
49 50 1.113517 GGGTCCTGGCGCACTCTATA 61.114 60.000 10.83 0.00 0.00 1.31
50 51 0.969894 GGTCCTGGCGCACTCTATAT 59.030 55.000 10.83 0.00 0.00 0.86
51 52 2.168496 GGTCCTGGCGCACTCTATATA 58.832 52.381 10.83 0.00 0.00 0.86
52 53 2.561419 GGTCCTGGCGCACTCTATATAA 59.439 50.000 10.83 0.00 0.00 0.98
53 54 3.367498 GGTCCTGGCGCACTCTATATAAG 60.367 52.174 10.83 0.00 0.00 1.73
54 55 2.231478 TCCTGGCGCACTCTATATAAGC 59.769 50.000 10.83 0.00 0.00 3.09
55 56 2.611518 CTGGCGCACTCTATATAAGCC 58.388 52.381 10.83 0.00 43.05 4.35
56 57 2.743636 GGCGCACTCTATATAAGCCA 57.256 50.000 10.83 0.00 42.37 4.75
57 58 2.288825 TGGCGCACTCTATATAAGCCAC 60.289 50.000 10.83 0.00 46.73 5.01
58 59 2.338500 GCGCACTCTATATAAGCCACC 58.662 52.381 0.30 0.00 0.00 4.61
59 60 2.931320 GCGCACTCTATATAAGCCACCC 60.931 54.545 0.30 0.00 0.00 4.61
60 61 2.353803 CGCACTCTATATAAGCCACCCC 60.354 54.545 0.00 0.00 0.00 4.95
61 62 2.027100 GCACTCTATATAAGCCACCCCC 60.027 54.545 0.00 0.00 0.00 5.40
75 76 2.935481 CCCCCTCCACAGGCAGAA 60.935 66.667 0.00 0.00 38.72 3.02
76 77 2.673523 CCCCTCCACAGGCAGAAG 59.326 66.667 0.00 0.00 38.72 2.85
77 78 2.673523 CCCTCCACAGGCAGAAGG 59.326 66.667 0.00 0.00 38.72 3.46
78 79 2.673523 CCTCCACAGGCAGAAGGG 59.326 66.667 0.00 0.00 30.98 3.95
79 80 2.227036 CCTCCACAGGCAGAAGGGT 61.227 63.158 0.00 0.00 30.98 4.34
80 81 1.763770 CTCCACAGGCAGAAGGGTT 59.236 57.895 0.00 0.00 0.00 4.11
81 82 0.322008 CTCCACAGGCAGAAGGGTTC 60.322 60.000 0.00 0.00 0.00 3.62
82 83 1.672356 CCACAGGCAGAAGGGTTCG 60.672 63.158 0.00 0.00 34.02 3.95
83 84 1.672356 CACAGGCAGAAGGGTTCGG 60.672 63.158 0.00 0.00 34.02 4.30
88 89 2.750350 CAGAAGGGTTCGGCACCT 59.250 61.111 0.00 0.00 46.38 4.00
90 91 1.073199 AGAAGGGTTCGGCACCTTG 59.927 57.895 9.60 0.00 46.64 3.61
91 92 1.228154 GAAGGGTTCGGCACCTTGT 60.228 57.895 9.60 0.00 46.64 3.16
92 93 0.035739 GAAGGGTTCGGCACCTTGTA 59.964 55.000 9.60 0.00 46.64 2.41
93 94 0.475044 AAGGGTTCGGCACCTTGTAA 59.525 50.000 0.00 0.00 45.03 2.41
94 95 0.696501 AGGGTTCGGCACCTTGTAAT 59.303 50.000 0.00 0.00 46.38 1.89
95 96 1.074889 AGGGTTCGGCACCTTGTAATT 59.925 47.619 0.00 0.00 46.38 1.40
96 97 1.471287 GGGTTCGGCACCTTGTAATTC 59.529 52.381 0.00 0.00 46.38 2.17
97 98 2.156098 GGTTCGGCACCTTGTAATTCA 58.844 47.619 0.00 0.00 43.29 2.57
98 99 2.752903 GGTTCGGCACCTTGTAATTCAT 59.247 45.455 0.00 0.00 43.29 2.57
99 100 3.942748 GGTTCGGCACCTTGTAATTCATA 59.057 43.478 0.00 0.00 43.29 2.15
100 101 4.201881 GGTTCGGCACCTTGTAATTCATAC 60.202 45.833 0.00 0.00 43.29 2.39
101 102 4.209307 TCGGCACCTTGTAATTCATACA 57.791 40.909 0.00 0.00 42.75 2.29
102 103 4.776349 TCGGCACCTTGTAATTCATACAT 58.224 39.130 0.00 0.00 43.84 2.29
103 104 5.189928 TCGGCACCTTGTAATTCATACATT 58.810 37.500 0.00 0.00 43.84 2.71
104 105 5.295787 TCGGCACCTTGTAATTCATACATTC 59.704 40.000 0.00 0.00 43.84 2.67
105 106 5.065859 CGGCACCTTGTAATTCATACATTCA 59.934 40.000 0.00 0.00 43.84 2.57
106 107 6.238731 CGGCACCTTGTAATTCATACATTCAT 60.239 38.462 0.00 0.00 43.84 2.57
107 108 7.041440 CGGCACCTTGTAATTCATACATTCATA 60.041 37.037 0.00 0.00 43.84 2.15
108 109 8.629158 GGCACCTTGTAATTCATACATTCATAA 58.371 33.333 0.00 0.00 43.84 1.90
118 119 7.946655 TTCATACATTCATAATCCACTCGAC 57.053 36.000 0.00 0.00 0.00 4.20
119 120 6.455647 TCATACATTCATAATCCACTCGACC 58.544 40.000 0.00 0.00 0.00 4.79
120 121 3.717707 ACATTCATAATCCACTCGACCG 58.282 45.455 0.00 0.00 0.00 4.79
121 122 2.218953 TTCATAATCCACTCGACCGC 57.781 50.000 0.00 0.00 0.00 5.68
122 123 0.387929 TCATAATCCACTCGACCGCC 59.612 55.000 0.00 0.00 0.00 6.13
123 124 0.389391 CATAATCCACTCGACCGCCT 59.611 55.000 0.00 0.00 0.00 5.52
124 125 0.674534 ATAATCCACTCGACCGCCTC 59.325 55.000 0.00 0.00 0.00 4.70
125 126 1.389609 TAATCCACTCGACCGCCTCC 61.390 60.000 0.00 0.00 0.00 4.30
143 144 3.217743 GGGCTCCGAGACGTAGGG 61.218 72.222 0.00 0.00 0.00 3.53
144 145 3.902086 GGCTCCGAGACGTAGGGC 61.902 72.222 0.00 0.00 0.00 5.19
145 146 2.829458 GCTCCGAGACGTAGGGCT 60.829 66.667 0.00 0.00 0.00 5.19
146 147 3.111939 CTCCGAGACGTAGGGCTG 58.888 66.667 0.00 0.00 0.00 4.85
147 148 1.749638 CTCCGAGACGTAGGGCTGT 60.750 63.158 0.00 0.00 0.00 4.40
148 149 1.303888 TCCGAGACGTAGGGCTGTT 60.304 57.895 0.00 0.00 0.00 3.16
149 150 0.035152 TCCGAGACGTAGGGCTGTTA 60.035 55.000 0.00 0.00 0.00 2.41
150 151 0.100146 CCGAGACGTAGGGCTGTTAC 59.900 60.000 0.00 0.00 0.00 2.50
151 152 1.093159 CGAGACGTAGGGCTGTTACT 58.907 55.000 0.00 0.00 0.00 2.24
152 153 1.471684 CGAGACGTAGGGCTGTTACTT 59.528 52.381 0.00 0.00 0.00 2.24
153 154 2.477525 CGAGACGTAGGGCTGTTACTTC 60.478 54.545 0.00 0.00 0.00 3.01
154 155 2.754002 GAGACGTAGGGCTGTTACTTCT 59.246 50.000 0.00 4.15 33.78 2.85
155 156 3.163467 AGACGTAGGGCTGTTACTTCTT 58.837 45.455 0.00 0.00 28.63 2.52
156 157 3.193056 AGACGTAGGGCTGTTACTTCTTC 59.807 47.826 0.00 0.00 28.63 2.87
157 158 2.233186 ACGTAGGGCTGTTACTTCTTCC 59.767 50.000 0.00 0.00 0.00 3.46
158 159 2.734492 CGTAGGGCTGTTACTTCTTCCG 60.734 54.545 0.00 0.00 0.00 4.30
159 160 1.640917 AGGGCTGTTACTTCTTCCGA 58.359 50.000 0.00 0.00 0.00 4.55
160 161 1.550976 AGGGCTGTTACTTCTTCCGAG 59.449 52.381 0.00 0.00 0.00 4.63
161 162 1.549170 GGGCTGTTACTTCTTCCGAGA 59.451 52.381 0.00 0.00 0.00 4.04
162 163 2.028385 GGGCTGTTACTTCTTCCGAGAA 60.028 50.000 0.00 0.00 39.54 2.87
168 169 4.561155 TTCTTCCGAGAAGGGCCT 57.439 55.556 0.00 0.00 41.52 5.19
169 170 1.983224 TTCTTCCGAGAAGGGCCTG 59.017 57.895 6.92 0.00 41.52 4.85
170 171 0.544357 TTCTTCCGAGAAGGGCCTGA 60.544 55.000 6.92 0.00 41.52 3.86
171 172 0.544357 TCTTCCGAGAAGGGCCTGAA 60.544 55.000 6.92 4.77 41.52 3.02
172 173 0.391793 CTTCCGAGAAGGGCCTGAAC 60.392 60.000 6.92 1.62 41.52 3.18
173 174 0.836400 TTCCGAGAAGGGCCTGAACT 60.836 55.000 6.92 7.41 41.52 3.01
174 175 1.219393 CCGAGAAGGGCCTGAACTC 59.781 63.158 6.92 15.44 35.97 3.01
175 176 1.153745 CGAGAAGGGCCTGAACTCG 60.154 63.158 29.13 29.13 42.77 4.18
176 177 1.878656 CGAGAAGGGCCTGAACTCGT 61.879 60.000 31.25 9.99 43.19 4.18
177 178 1.183549 GAGAAGGGCCTGAACTCGTA 58.816 55.000 6.92 0.00 0.00 3.43
178 179 0.896226 AGAAGGGCCTGAACTCGTAC 59.104 55.000 6.92 0.00 0.00 3.67
179 180 0.606604 GAAGGGCCTGAACTCGTACA 59.393 55.000 6.92 0.00 0.00 2.90
180 181 1.207329 GAAGGGCCTGAACTCGTACAT 59.793 52.381 6.92 0.00 0.00 2.29
181 182 0.824759 AGGGCCTGAACTCGTACATC 59.175 55.000 4.50 0.00 0.00 3.06
182 183 0.179081 GGGCCTGAACTCGTACATCC 60.179 60.000 0.84 0.00 0.00 3.51
183 184 0.824759 GGCCTGAACTCGTACATCCT 59.175 55.000 0.00 0.00 0.00 3.24
184 185 1.207329 GGCCTGAACTCGTACATCCTT 59.793 52.381 0.00 0.00 0.00 3.36
185 186 2.354805 GGCCTGAACTCGTACATCCTTT 60.355 50.000 0.00 0.00 0.00 3.11
186 187 2.673368 GCCTGAACTCGTACATCCTTTG 59.327 50.000 0.00 0.00 0.00 2.77
187 188 3.864921 GCCTGAACTCGTACATCCTTTGT 60.865 47.826 0.00 0.00 42.62 2.83
188 189 3.679980 CCTGAACTCGTACATCCTTTGTG 59.320 47.826 0.00 0.00 39.48 3.33
189 190 3.064207 TGAACTCGTACATCCTTTGTGC 58.936 45.455 0.00 0.00 39.48 4.57
190 191 3.244078 TGAACTCGTACATCCTTTGTGCT 60.244 43.478 0.00 0.00 38.66 4.40
191 192 3.402628 ACTCGTACATCCTTTGTGCTT 57.597 42.857 0.00 0.00 38.66 3.91
192 193 4.530710 ACTCGTACATCCTTTGTGCTTA 57.469 40.909 0.00 0.00 38.66 3.09
193 194 4.243270 ACTCGTACATCCTTTGTGCTTAC 58.757 43.478 0.00 0.00 38.66 2.34
194 195 4.242475 CTCGTACATCCTTTGTGCTTACA 58.758 43.478 0.00 0.00 38.66 2.41
195 196 4.633175 TCGTACATCCTTTGTGCTTACAA 58.367 39.130 0.00 0.00 38.66 2.41
196 197 4.449743 TCGTACATCCTTTGTGCTTACAAC 59.550 41.667 0.00 0.00 38.66 3.32
197 198 4.378046 CGTACATCCTTTGTGCTTACAACC 60.378 45.833 0.00 0.00 38.66 3.77
198 199 3.832527 ACATCCTTTGTGCTTACAACCT 58.167 40.909 0.00 0.00 37.11 3.50
199 200 3.821033 ACATCCTTTGTGCTTACAACCTC 59.179 43.478 0.00 0.00 37.11 3.85
200 201 3.857157 TCCTTTGTGCTTACAACCTCT 57.143 42.857 0.00 0.00 0.00 3.69
201 202 3.740115 TCCTTTGTGCTTACAACCTCTC 58.260 45.455 0.00 0.00 0.00 3.20
202 203 2.814336 CCTTTGTGCTTACAACCTCTCC 59.186 50.000 0.00 0.00 0.00 3.71
203 204 3.476552 CTTTGTGCTTACAACCTCTCCA 58.523 45.455 0.00 0.00 0.00 3.86
204 205 3.788227 TTGTGCTTACAACCTCTCCAT 57.212 42.857 0.00 0.00 0.00 3.41
205 206 4.901197 TTGTGCTTACAACCTCTCCATA 57.099 40.909 0.00 0.00 0.00 2.74
206 207 4.471904 TGTGCTTACAACCTCTCCATAG 57.528 45.455 0.00 0.00 0.00 2.23
207 208 3.198872 GTGCTTACAACCTCTCCATAGC 58.801 50.000 0.00 0.00 0.00 2.97
208 209 3.107601 TGCTTACAACCTCTCCATAGCT 58.892 45.455 0.00 0.00 0.00 3.32
209 210 4.099573 GTGCTTACAACCTCTCCATAGCTA 59.900 45.833 0.00 0.00 0.00 3.32
210 211 4.342378 TGCTTACAACCTCTCCATAGCTAG 59.658 45.833 0.00 0.00 0.00 3.42
211 212 4.262249 GCTTACAACCTCTCCATAGCTAGG 60.262 50.000 0.00 0.00 35.14 3.02
212 213 3.689872 ACAACCTCTCCATAGCTAGGA 57.310 47.619 7.04 9.11 33.16 2.94
213 214 3.995636 ACAACCTCTCCATAGCTAGGAA 58.004 45.455 7.04 0.00 34.08 3.36
214 215 3.707102 ACAACCTCTCCATAGCTAGGAAC 59.293 47.826 7.04 0.00 34.08 3.62
215 216 3.964031 CAACCTCTCCATAGCTAGGAACT 59.036 47.826 7.04 0.00 46.37 3.01
216 217 4.273300 ACCTCTCCATAGCTAGGAACTT 57.727 45.455 7.04 0.00 41.75 2.66
217 218 3.964031 ACCTCTCCATAGCTAGGAACTTG 59.036 47.826 7.04 0.00 41.75 3.16
228 229 4.329462 CTAGGAACTTGCCTCTCCATAC 57.671 50.000 0.00 0.00 41.75 2.39
229 230 1.840635 AGGAACTTGCCTCTCCATACC 59.159 52.381 0.00 0.00 27.25 2.73
230 231 1.840635 GGAACTTGCCTCTCCATACCT 59.159 52.381 0.00 0.00 0.00 3.08
231 232 3.039011 GGAACTTGCCTCTCCATACCTA 58.961 50.000 0.00 0.00 0.00 3.08
232 233 3.181464 GGAACTTGCCTCTCCATACCTAC 60.181 52.174 0.00 0.00 0.00 3.18
233 234 2.399580 ACTTGCCTCTCCATACCTACC 58.600 52.381 0.00 0.00 0.00 3.18
234 235 1.694696 CTTGCCTCTCCATACCTACCC 59.305 57.143 0.00 0.00 0.00 3.69
235 236 0.105142 TGCCTCTCCATACCTACCCC 60.105 60.000 0.00 0.00 0.00 4.95
236 237 0.836830 GCCTCTCCATACCTACCCCC 60.837 65.000 0.00 0.00 0.00 5.40
251 252 2.596776 CCCCCACTCTACTGTCAGG 58.403 63.158 4.53 0.00 0.00 3.86
252 253 1.617947 CCCCCACTCTACTGTCAGGC 61.618 65.000 4.53 0.00 0.00 4.85
253 254 0.616111 CCCCACTCTACTGTCAGGCT 60.616 60.000 4.53 0.00 0.00 4.58
254 255 1.270907 CCCACTCTACTGTCAGGCTT 58.729 55.000 4.53 0.00 0.00 4.35
255 256 2.457598 CCCACTCTACTGTCAGGCTTA 58.542 52.381 4.53 0.00 0.00 3.09
256 257 2.428890 CCCACTCTACTGTCAGGCTTAG 59.571 54.545 4.53 0.00 0.00 2.18
257 258 3.357203 CCACTCTACTGTCAGGCTTAGA 58.643 50.000 4.53 2.00 0.00 2.10
258 259 3.764434 CCACTCTACTGTCAGGCTTAGAA 59.236 47.826 4.53 0.00 0.00 2.10
259 260 4.381079 CCACTCTACTGTCAGGCTTAGAAC 60.381 50.000 4.53 0.00 0.00 3.01
260 261 3.764972 ACTCTACTGTCAGGCTTAGAACC 59.235 47.826 4.53 0.00 0.00 3.62
261 262 3.764434 CTCTACTGTCAGGCTTAGAACCA 59.236 47.826 4.53 0.00 0.00 3.67
262 263 2.841442 ACTGTCAGGCTTAGAACCAC 57.159 50.000 4.53 0.00 0.00 4.16
263 264 1.000955 ACTGTCAGGCTTAGAACCACG 59.999 52.381 4.53 0.00 0.00 4.94
264 265 1.272490 CTGTCAGGCTTAGAACCACGA 59.728 52.381 0.00 0.00 0.00 4.35
265 266 1.000506 TGTCAGGCTTAGAACCACGAC 59.999 52.381 0.00 0.00 34.27 4.34
266 267 1.000506 GTCAGGCTTAGAACCACGACA 59.999 52.381 0.00 0.00 34.01 4.35
267 268 1.000506 TCAGGCTTAGAACCACGACAC 59.999 52.381 0.00 0.00 0.00 3.67
268 269 0.038526 AGGCTTAGAACCACGACACG 60.039 55.000 0.00 0.00 0.00 4.49
269 270 1.623973 GGCTTAGAACCACGACACGC 61.624 60.000 0.00 0.00 0.00 5.34
271 272 1.342082 CTTAGAACCACGACACGCGG 61.342 60.000 12.47 1.27 46.49 6.46
272 273 3.902162 TAGAACCACGACACGCGGC 62.902 63.158 12.47 0.00 46.49 6.53
326 327 2.811317 CGAACACGCTGGAGAGCC 60.811 66.667 0.00 0.00 42.91 4.70
327 328 2.435059 GAACACGCTGGAGAGCCC 60.435 66.667 0.00 0.00 42.91 5.19
328 329 2.925170 AACACGCTGGAGAGCCCT 60.925 61.111 0.00 0.00 42.91 5.19
329 330 3.245668 AACACGCTGGAGAGCCCTG 62.246 63.158 0.00 0.00 42.91 4.45
330 331 3.699894 CACGCTGGAGAGCCCTGT 61.700 66.667 0.00 0.00 42.91 4.00
331 332 3.386237 ACGCTGGAGAGCCCTGTC 61.386 66.667 0.00 0.00 42.91 3.51
332 333 4.154347 CGCTGGAGAGCCCTGTCC 62.154 72.222 4.61 4.61 42.91 4.02
333 334 2.686835 GCTGGAGAGCCCTGTCCT 60.687 66.667 12.10 0.00 42.94 3.85
334 335 3.028921 GCTGGAGAGCCCTGTCCTG 62.029 68.421 12.10 12.16 42.94 3.86
335 336 2.284921 TGGAGAGCCCTGTCCTGG 60.285 66.667 12.10 0.00 42.94 4.45
336 337 2.039624 GGAGAGCCCTGTCCTGGA 59.960 66.667 4.35 0.00 39.70 3.86
337 338 2.063378 GGAGAGCCCTGTCCTGGAG 61.063 68.421 0.00 0.00 39.70 3.86
338 339 1.000993 GAGAGCCCTGTCCTGGAGA 59.999 63.158 0.00 0.00 0.00 3.71
339 340 1.001503 AGAGCCCTGTCCTGGAGAG 59.998 63.158 13.68 13.68 0.00 3.20
340 341 2.040278 AGCCCTGTCCTGGAGAGG 59.960 66.667 28.49 28.49 41.99 3.69
341 342 2.284995 GCCCTGTCCTGGAGAGGT 60.285 66.667 31.38 0.00 40.93 3.85
342 343 1.920835 GCCCTGTCCTGGAGAGGTT 60.921 63.158 31.38 0.00 40.93 3.50
343 344 1.986413 CCCTGTCCTGGAGAGGTTG 59.014 63.158 31.38 17.71 40.93 3.77
344 345 0.545309 CCCTGTCCTGGAGAGGTTGA 60.545 60.000 31.38 0.00 40.93 3.18
345 346 1.577736 CCTGTCCTGGAGAGGTTGAT 58.422 55.000 27.43 0.00 38.17 2.57
346 347 1.484240 CCTGTCCTGGAGAGGTTGATC 59.516 57.143 27.43 0.18 38.17 2.92
347 348 1.135915 CTGTCCTGGAGAGGTTGATCG 59.864 57.143 12.86 0.00 40.76 3.69
348 349 0.179097 GTCCTGGAGAGGTTGATCGC 60.179 60.000 0.00 0.00 40.76 4.58
349 350 0.324738 TCCTGGAGAGGTTGATCGCT 60.325 55.000 0.00 0.00 40.76 4.93
350 351 0.179089 CCTGGAGAGGTTGATCGCTG 60.179 60.000 0.00 0.00 34.16 5.18
351 352 0.534412 CTGGAGAGGTTGATCGCTGT 59.466 55.000 0.00 0.00 0.00 4.40
352 353 0.532573 TGGAGAGGTTGATCGCTGTC 59.467 55.000 0.00 0.00 0.00 3.51
353 354 0.532573 GGAGAGGTTGATCGCTGTCA 59.467 55.000 0.00 0.00 0.00 3.58
354 355 1.634702 GAGAGGTTGATCGCTGTCAC 58.365 55.000 0.00 0.00 0.00 3.67
355 356 0.109086 AGAGGTTGATCGCTGTCACG 60.109 55.000 0.00 0.00 0.00 4.35
356 357 1.078759 GAGGTTGATCGCTGTCACGG 61.079 60.000 0.00 0.00 0.00 4.94
357 358 2.740714 GGTTGATCGCTGTCACGGC 61.741 63.158 0.00 0.00 0.00 5.68
378 379 4.736896 GGAGGCGGACCACGTGAC 62.737 72.222 19.30 10.61 46.52 3.67
471 472 4.156622 CGTACGGTCGCGAGCAGA 62.157 66.667 34.30 20.40 0.00 4.26
472 473 2.408022 GTACGGTCGCGAGCAGAT 59.592 61.111 34.30 22.24 0.00 2.90
473 474 1.939785 GTACGGTCGCGAGCAGATG 60.940 63.158 34.30 21.65 0.00 2.90
474 475 3.120979 TACGGTCGCGAGCAGATGG 62.121 63.158 34.30 21.30 0.00 3.51
495 496 4.139420 CGGACGCGAGCAAGCAAG 62.139 66.667 15.93 0.00 36.85 4.01
496 497 3.793144 GGACGCGAGCAAGCAAGG 61.793 66.667 15.93 0.00 36.85 3.61
497 498 4.451652 GACGCGAGCAAGCAAGGC 62.452 66.667 15.93 0.00 36.85 4.35
499 500 4.748679 CGCGAGCAAGCAAGGCAC 62.749 66.667 0.00 0.00 36.85 5.01
500 501 4.748679 GCGAGCAAGCAAGGCACG 62.749 66.667 9.07 9.07 45.86 5.34
501 502 4.093952 CGAGCAAGCAAGGCACGG 62.094 66.667 6.28 0.00 40.77 4.94
502 503 3.741476 GAGCAAGCAAGGCACGGG 61.741 66.667 0.00 0.00 0.00 5.28
545 546 2.656646 CACTAGCTGTGCACCGGA 59.343 61.111 15.69 0.00 40.06 5.14
546 547 1.446792 CACTAGCTGTGCACCGGAG 60.447 63.158 15.69 0.00 40.06 4.63
547 548 2.510238 CTAGCTGTGCACCGGAGC 60.510 66.667 17.78 17.78 0.00 4.70
548 549 3.300934 CTAGCTGTGCACCGGAGCA 62.301 63.158 23.37 23.37 43.35 4.26
554 555 3.645660 TGCACCGGAGCAATCCCA 61.646 61.111 24.92 0.00 42.46 4.37
555 556 3.134127 GCACCGGAGCAATCCCAC 61.134 66.667 19.70 0.00 0.00 4.61
556 557 2.438434 CACCGGAGCAATCCCACC 60.438 66.667 9.46 0.00 0.00 4.61
557 558 4.096003 ACCGGAGCAATCCCACCG 62.096 66.667 9.46 0.00 44.16 4.94
559 560 3.781307 CGGAGCAATCCCACCGGA 61.781 66.667 9.46 0.00 44.33 5.14
560 561 2.124695 GGAGCAATCCCACCGGAC 60.125 66.667 9.46 0.00 42.48 4.79
561 562 2.124695 GAGCAATCCCACCGGACC 60.125 66.667 9.46 0.00 42.48 4.46
562 563 4.096003 AGCAATCCCACCGGACCG 62.096 66.667 9.46 6.99 42.48 4.79
572 573 3.849951 CCGGACCGGTGGGAGATG 61.850 72.222 25.54 0.00 42.73 2.90
573 574 2.758327 CGGACCGGTGGGAGATGA 60.758 66.667 14.63 0.00 36.97 2.92
574 575 2.355986 CGGACCGGTGGGAGATGAA 61.356 63.158 14.63 0.00 36.97 2.57
575 576 1.522569 GGACCGGTGGGAGATGAAG 59.477 63.158 14.63 0.00 36.97 3.02
576 577 1.522569 GACCGGTGGGAGATGAAGG 59.477 63.158 14.63 0.00 36.97 3.46
577 578 1.229529 ACCGGTGGGAGATGAAGGT 60.230 57.895 6.12 0.00 36.97 3.50
578 579 1.265454 ACCGGTGGGAGATGAAGGTC 61.265 60.000 6.12 0.00 36.97 3.85
579 580 1.522569 CGGTGGGAGATGAAGGTCC 59.477 63.158 0.00 0.00 0.00 4.46
580 581 0.978146 CGGTGGGAGATGAAGGTCCT 60.978 60.000 0.00 0.00 32.90 3.85
581 582 0.543749 GGTGGGAGATGAAGGTCCTG 59.456 60.000 0.00 0.00 32.90 3.86
582 583 1.573108 GTGGGAGATGAAGGTCCTGA 58.427 55.000 0.00 0.00 32.90 3.86
583 584 2.122768 GTGGGAGATGAAGGTCCTGAT 58.877 52.381 0.00 0.00 32.90 2.90
584 585 2.507471 GTGGGAGATGAAGGTCCTGATT 59.493 50.000 0.00 0.00 32.90 2.57
585 586 2.507058 TGGGAGATGAAGGTCCTGATTG 59.493 50.000 0.00 0.00 32.90 2.67
586 587 2.570135 GGAGATGAAGGTCCTGATTGC 58.430 52.381 0.00 0.00 0.00 3.56
596 597 7.378181 TGAAGGTCCTGATTGCTTTTATTTTC 58.622 34.615 0.00 0.00 0.00 2.29
932 937 0.461163 CACGGCGAGAGAGAGAGAGA 60.461 60.000 16.62 0.00 0.00 3.10
933 938 0.179084 ACGGCGAGAGAGAGAGAGAG 60.179 60.000 16.62 0.00 0.00 3.20
991 996 0.462759 GTTGAGATCCCCTTCGGCTG 60.463 60.000 0.00 0.00 0.00 4.85
1018 1023 1.649664 CATGTCTTCCTCAAGCTCCG 58.350 55.000 0.00 0.00 0.00 4.63
1294 1299 3.626670 GGCCAAGACTCTGATGAATGAAG 59.373 47.826 0.00 0.00 0.00 3.02
1406 1411 2.616376 CACGCACTGATAGAGAGCTAGT 59.384 50.000 0.00 0.00 36.21 2.57
1490 1496 4.103943 ACCCATTTGCAAATACTTTTGGGT 59.896 37.500 32.30 32.30 42.09 4.51
1827 1839 2.381911 CCAACTGCATCCAATTAGGCT 58.618 47.619 0.00 0.00 37.29 4.58
1837 1849 1.142870 CCAATTAGGCTCATTCGGGGA 59.857 52.381 0.00 0.00 0.00 4.81
1947 1959 5.828299 TTATTCCGGAGCCAAACAATTAG 57.172 39.130 3.34 0.00 0.00 1.73
2184 2205 1.911766 GGACTCGAACCCAGGACCA 60.912 63.158 0.00 0.00 0.00 4.02
2230 2251 0.248289 GCTGGTAACCGCTAGGACAA 59.752 55.000 0.00 0.00 41.02 3.18
2444 2474 4.745783 GCACTTGGTTTAGGGTTAGAGTGT 60.746 45.833 0.00 0.00 36.53 3.55
2461 2492 5.941788 AGAGTGTCACTTGGTTTAGGATTT 58.058 37.500 7.00 0.00 0.00 2.17
2466 2497 7.996644 AGTGTCACTTGGTTTAGGATTTAAAGA 59.003 33.333 0.00 0.00 0.00 2.52
2467 2498 8.626526 GTGTCACTTGGTTTAGGATTTAAAGAA 58.373 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.167900 CCACGTAGGAGAGGGTTTAAGG 59.832 54.545 0.00 0.00 41.22 2.69
1 2 2.167900 CCCACGTAGGAGAGGGTTTAAG 59.832 54.545 0.00 0.00 41.22 1.85
5 6 1.988406 GCCCACGTAGGAGAGGGTT 60.988 63.158 3.45 0.00 43.42 4.11
6 7 2.363925 GCCCACGTAGGAGAGGGT 60.364 66.667 3.45 0.00 43.42 4.34
7 8 2.042843 AGCCCACGTAGGAGAGGG 60.043 66.667 3.45 2.64 44.37 4.30
8 9 2.427245 CCAGCCCACGTAGGAGAGG 61.427 68.421 3.45 0.00 41.22 3.69
9 10 3.082579 GCCAGCCCACGTAGGAGAG 62.083 68.421 3.45 0.00 41.22 3.20
10 11 3.075005 GCCAGCCCACGTAGGAGA 61.075 66.667 3.45 0.00 41.22 3.71
11 12 3.077556 AGCCAGCCCACGTAGGAG 61.078 66.667 3.45 0.00 41.22 3.69
12 13 3.390521 CAGCCAGCCCACGTAGGA 61.391 66.667 3.45 0.00 41.22 2.94
13 14 4.473520 CCAGCCAGCCCACGTAGG 62.474 72.222 0.00 0.00 37.03 3.18
14 15 4.473520 CCCAGCCAGCCCACGTAG 62.474 72.222 0.00 0.00 0.00 3.51
30 31 1.113517 TATAGAGTGCGCCAGGACCC 61.114 60.000 4.18 0.00 39.75 4.46
31 32 0.969894 ATATAGAGTGCGCCAGGACC 59.030 55.000 4.18 0.00 39.75 4.46
32 33 3.839293 CTTATATAGAGTGCGCCAGGAC 58.161 50.000 4.18 0.00 39.15 3.85
33 34 2.231478 GCTTATATAGAGTGCGCCAGGA 59.769 50.000 4.18 0.00 0.00 3.86
34 35 2.611518 GCTTATATAGAGTGCGCCAGG 58.388 52.381 4.18 0.00 0.00 4.45
35 36 2.029020 TGGCTTATATAGAGTGCGCCAG 60.029 50.000 4.18 0.00 40.76 4.85
36 37 1.967779 TGGCTTATATAGAGTGCGCCA 59.032 47.619 4.18 0.00 43.12 5.69
37 38 2.338500 GTGGCTTATATAGAGTGCGCC 58.662 52.381 4.18 0.00 36.64 6.53
38 39 2.338500 GGTGGCTTATATAGAGTGCGC 58.662 52.381 0.00 0.00 0.00 6.09
39 40 2.353803 GGGGTGGCTTATATAGAGTGCG 60.354 54.545 0.00 0.00 0.00 5.34
40 41 2.027100 GGGGGTGGCTTATATAGAGTGC 60.027 54.545 0.00 0.00 0.00 4.40
41 42 3.983044 GGGGGTGGCTTATATAGAGTG 57.017 52.381 0.00 0.00 0.00 3.51
58 59 2.935481 TTCTGCCTGTGGAGGGGG 60.935 66.667 0.00 0.00 40.19 5.40
59 60 2.673523 CTTCTGCCTGTGGAGGGG 59.326 66.667 0.00 0.00 40.19 4.79
60 61 2.673523 CCTTCTGCCTGTGGAGGG 59.326 66.667 0.00 0.00 40.19 4.30
61 62 1.783250 AACCCTTCTGCCTGTGGAGG 61.783 60.000 0.00 0.00 43.19 4.30
62 63 0.322008 GAACCCTTCTGCCTGTGGAG 60.322 60.000 0.00 0.00 0.00 3.86
63 64 1.761174 GAACCCTTCTGCCTGTGGA 59.239 57.895 0.00 0.00 0.00 4.02
64 65 1.672356 CGAACCCTTCTGCCTGTGG 60.672 63.158 0.00 0.00 0.00 4.17
65 66 1.672356 CCGAACCCTTCTGCCTGTG 60.672 63.158 0.00 0.00 0.00 3.66
66 67 2.750350 CCGAACCCTTCTGCCTGT 59.250 61.111 0.00 0.00 0.00 4.00
67 68 2.747855 GCCGAACCCTTCTGCCTG 60.748 66.667 0.00 0.00 34.33 4.85
68 69 3.249189 TGCCGAACCCTTCTGCCT 61.249 61.111 0.00 0.00 38.88 4.75
69 70 3.056328 GTGCCGAACCCTTCTGCC 61.056 66.667 0.00 0.00 38.88 4.85
70 71 3.056328 GGTGCCGAACCCTTCTGC 61.056 66.667 0.00 0.00 44.02 4.26
77 78 6.600078 TGTATGAATTACAAGGTGCCGAACC 61.600 44.000 0.00 0.00 41.56 3.62
78 79 4.393680 TGTATGAATTACAAGGTGCCGAAC 59.606 41.667 0.00 0.00 37.87 3.95
79 80 4.580868 TGTATGAATTACAAGGTGCCGAA 58.419 39.130 0.00 0.00 37.87 4.30
80 81 4.209307 TGTATGAATTACAAGGTGCCGA 57.791 40.909 0.00 0.00 37.87 5.54
81 82 5.065859 TGAATGTATGAATTACAAGGTGCCG 59.934 40.000 0.00 0.00 43.84 5.69
82 83 6.449635 TGAATGTATGAATTACAAGGTGCC 57.550 37.500 0.00 0.00 43.84 5.01
92 93 8.993121 GTCGAGTGGATTATGAATGTATGAATT 58.007 33.333 0.00 0.00 0.00 2.17
93 94 7.604164 GGTCGAGTGGATTATGAATGTATGAAT 59.396 37.037 0.00 0.00 0.00 2.57
94 95 6.929049 GGTCGAGTGGATTATGAATGTATGAA 59.071 38.462 0.00 0.00 0.00 2.57
95 96 6.455647 GGTCGAGTGGATTATGAATGTATGA 58.544 40.000 0.00 0.00 0.00 2.15
96 97 5.346011 CGGTCGAGTGGATTATGAATGTATG 59.654 44.000 0.00 0.00 0.00 2.39
97 98 5.470368 CGGTCGAGTGGATTATGAATGTAT 58.530 41.667 0.00 0.00 0.00 2.29
98 99 4.794981 GCGGTCGAGTGGATTATGAATGTA 60.795 45.833 0.00 0.00 0.00 2.29
99 100 3.717707 CGGTCGAGTGGATTATGAATGT 58.282 45.455 0.00 0.00 0.00 2.71
100 101 2.476619 GCGGTCGAGTGGATTATGAATG 59.523 50.000 0.00 0.00 0.00 2.67
101 102 2.548067 GGCGGTCGAGTGGATTATGAAT 60.548 50.000 0.00 0.00 0.00 2.57
102 103 1.202486 GGCGGTCGAGTGGATTATGAA 60.202 52.381 0.00 0.00 0.00 2.57
103 104 0.387929 GGCGGTCGAGTGGATTATGA 59.612 55.000 0.00 0.00 0.00 2.15
104 105 0.389391 AGGCGGTCGAGTGGATTATG 59.611 55.000 0.00 0.00 0.00 1.90
105 106 0.674534 GAGGCGGTCGAGTGGATTAT 59.325 55.000 0.00 0.00 0.00 1.28
106 107 1.389609 GGAGGCGGTCGAGTGGATTA 61.390 60.000 0.00 0.00 0.00 1.75
107 108 2.722201 GGAGGCGGTCGAGTGGATT 61.722 63.158 0.00 0.00 0.00 3.01
108 109 3.148279 GGAGGCGGTCGAGTGGAT 61.148 66.667 0.00 0.00 0.00 3.41
126 127 3.217743 CCCTACGTCTCGGAGCCC 61.218 72.222 0.00 0.00 36.34 5.19
127 128 3.902086 GCCCTACGTCTCGGAGCC 61.902 72.222 0.00 0.00 36.34 4.70
128 129 2.829458 AGCCCTACGTCTCGGAGC 60.829 66.667 0.00 0.00 36.34 4.70
129 130 1.313812 AACAGCCCTACGTCTCGGAG 61.314 60.000 0.00 0.00 37.59 4.63
130 131 0.035152 TAACAGCCCTACGTCTCGGA 60.035 55.000 0.00 0.00 0.00 4.55
131 132 0.100146 GTAACAGCCCTACGTCTCGG 59.900 60.000 0.00 0.00 0.00 4.63
132 133 1.093159 AGTAACAGCCCTACGTCTCG 58.907 55.000 0.00 0.00 0.00 4.04
133 134 2.754002 AGAAGTAACAGCCCTACGTCTC 59.246 50.000 0.00 0.00 34.34 3.36
134 135 2.805194 AGAAGTAACAGCCCTACGTCT 58.195 47.619 0.00 1.70 34.54 4.18
135 136 3.509740 GAAGAAGTAACAGCCCTACGTC 58.490 50.000 0.00 0.00 0.00 4.34
136 137 2.233186 GGAAGAAGTAACAGCCCTACGT 59.767 50.000 0.00 0.00 0.00 3.57
137 138 2.734492 CGGAAGAAGTAACAGCCCTACG 60.734 54.545 0.00 0.00 0.00 3.51
138 139 2.494870 TCGGAAGAAGTAACAGCCCTAC 59.505 50.000 0.00 0.00 37.03 3.18
139 140 2.758979 CTCGGAAGAAGTAACAGCCCTA 59.241 50.000 0.00 0.00 41.32 3.53
140 141 1.550976 CTCGGAAGAAGTAACAGCCCT 59.449 52.381 0.00 0.00 41.32 5.19
141 142 1.549170 TCTCGGAAGAAGTAACAGCCC 59.451 52.381 0.00 0.00 41.32 5.19
142 143 3.314541 TTCTCGGAAGAAGTAACAGCC 57.685 47.619 0.00 0.00 41.32 4.85
151 152 0.544357 TCAGGCCCTTCTCGGAAGAA 60.544 55.000 13.28 1.41 41.32 2.52
152 153 0.544357 TTCAGGCCCTTCTCGGAAGA 60.544 55.000 13.28 0.00 39.12 2.87
153 154 0.391793 GTTCAGGCCCTTCTCGGAAG 60.392 60.000 0.00 6.66 33.16 3.46
154 155 0.836400 AGTTCAGGCCCTTCTCGGAA 60.836 55.000 0.00 0.00 33.16 4.30
155 156 1.229209 AGTTCAGGCCCTTCTCGGA 60.229 57.895 0.00 0.00 33.16 4.55
156 157 1.219393 GAGTTCAGGCCCTTCTCGG 59.781 63.158 0.00 0.00 0.00 4.63
157 158 1.153745 CGAGTTCAGGCCCTTCTCG 60.154 63.158 17.87 17.87 41.02 4.04
158 159 1.135053 GTACGAGTTCAGGCCCTTCTC 60.135 57.143 0.00 1.73 0.00 2.87
159 160 0.896226 GTACGAGTTCAGGCCCTTCT 59.104 55.000 0.00 0.00 0.00 2.85
160 161 0.606604 TGTACGAGTTCAGGCCCTTC 59.393 55.000 0.00 0.00 0.00 3.46
161 162 1.207329 GATGTACGAGTTCAGGCCCTT 59.793 52.381 0.00 0.00 0.00 3.95
162 163 0.824759 GATGTACGAGTTCAGGCCCT 59.175 55.000 0.00 0.00 0.00 5.19
163 164 0.179081 GGATGTACGAGTTCAGGCCC 60.179 60.000 0.00 0.00 0.00 5.80
164 165 0.824759 AGGATGTACGAGTTCAGGCC 59.175 55.000 0.00 0.00 0.00 5.19
165 166 2.673368 CAAAGGATGTACGAGTTCAGGC 59.327 50.000 0.00 0.00 0.00 4.85
166 167 3.679980 CACAAAGGATGTACGAGTTCAGG 59.320 47.826 0.00 0.00 41.46 3.86
167 168 3.123621 GCACAAAGGATGTACGAGTTCAG 59.876 47.826 0.00 0.00 41.46 3.02
168 169 3.064207 GCACAAAGGATGTACGAGTTCA 58.936 45.455 0.00 0.00 41.46 3.18
169 170 3.326747 AGCACAAAGGATGTACGAGTTC 58.673 45.455 0.00 0.00 41.46 3.01
170 171 3.402628 AGCACAAAGGATGTACGAGTT 57.597 42.857 0.00 0.00 41.46 3.01
171 172 3.402628 AAGCACAAAGGATGTACGAGT 57.597 42.857 0.00 0.00 41.46 4.18
172 173 4.242475 TGTAAGCACAAAGGATGTACGAG 58.758 43.478 0.00 0.00 41.46 4.18
173 174 4.260139 TGTAAGCACAAAGGATGTACGA 57.740 40.909 0.00 0.00 41.46 3.43
174 175 4.378046 GGTTGTAAGCACAAAGGATGTACG 60.378 45.833 0.00 0.00 45.99 3.67
175 176 4.760204 AGGTTGTAAGCACAAAGGATGTAC 59.240 41.667 0.00 0.00 45.99 2.90
176 177 4.980573 AGGTTGTAAGCACAAAGGATGTA 58.019 39.130 0.00 0.00 45.99 2.29
177 178 3.821033 GAGGTTGTAAGCACAAAGGATGT 59.179 43.478 0.00 0.00 45.99 3.06
178 179 4.074970 AGAGGTTGTAAGCACAAAGGATG 58.925 43.478 0.00 0.00 45.99 3.51
179 180 4.327680 GAGAGGTTGTAAGCACAAAGGAT 58.672 43.478 0.00 0.00 45.99 3.24
180 181 3.496160 GGAGAGGTTGTAAGCACAAAGGA 60.496 47.826 0.00 0.00 45.99 3.36
181 182 2.814336 GGAGAGGTTGTAAGCACAAAGG 59.186 50.000 0.00 0.00 45.99 3.11
182 183 3.476552 TGGAGAGGTTGTAAGCACAAAG 58.523 45.455 0.00 0.00 45.99 2.77
183 184 3.569194 TGGAGAGGTTGTAAGCACAAA 57.431 42.857 0.00 0.00 45.99 2.83
184 185 3.788227 ATGGAGAGGTTGTAAGCACAA 57.212 42.857 0.00 0.00 42.39 3.33
185 186 3.369471 GCTATGGAGAGGTTGTAAGCACA 60.369 47.826 0.00 0.00 0.00 4.57
186 187 3.118592 AGCTATGGAGAGGTTGTAAGCAC 60.119 47.826 0.00 0.00 0.00 4.40
187 188 3.107601 AGCTATGGAGAGGTTGTAAGCA 58.892 45.455 0.00 0.00 0.00 3.91
188 189 3.828875 AGCTATGGAGAGGTTGTAAGC 57.171 47.619 0.00 0.00 0.00 3.09
189 190 5.141182 TCCTAGCTATGGAGAGGTTGTAAG 58.859 45.833 7.59 0.00 0.00 2.34
190 191 5.138758 TCCTAGCTATGGAGAGGTTGTAA 57.861 43.478 7.59 0.00 0.00 2.41
191 192 4.808767 TCCTAGCTATGGAGAGGTTGTA 57.191 45.455 7.59 0.00 0.00 2.41
192 193 3.689872 TCCTAGCTATGGAGAGGTTGT 57.310 47.619 7.59 0.00 0.00 3.32
193 194 3.964031 AGTTCCTAGCTATGGAGAGGTTG 59.036 47.826 10.56 0.00 34.76 3.77
194 195 4.273300 AGTTCCTAGCTATGGAGAGGTT 57.727 45.455 10.56 0.00 34.76 3.50
195 196 3.964031 CAAGTTCCTAGCTATGGAGAGGT 59.036 47.826 10.56 0.00 34.76 3.85
196 197 3.244044 GCAAGTTCCTAGCTATGGAGAGG 60.244 52.174 10.56 2.40 34.76 3.69
197 198 3.244044 GGCAAGTTCCTAGCTATGGAGAG 60.244 52.174 10.56 5.56 34.76 3.20
198 199 2.700897 GGCAAGTTCCTAGCTATGGAGA 59.299 50.000 10.56 0.00 34.76 3.71
199 200 2.703007 AGGCAAGTTCCTAGCTATGGAG 59.297 50.000 10.56 3.32 33.95 3.86
200 201 2.700897 GAGGCAAGTTCCTAGCTATGGA 59.299 50.000 7.59 7.59 36.38 3.41
201 202 2.703007 AGAGGCAAGTTCCTAGCTATGG 59.297 50.000 0.00 0.00 36.38 2.74
202 203 3.244044 GGAGAGGCAAGTTCCTAGCTATG 60.244 52.174 0.00 0.00 36.38 2.23
203 204 2.969262 GGAGAGGCAAGTTCCTAGCTAT 59.031 50.000 0.00 0.00 36.38 2.97
204 205 2.292257 TGGAGAGGCAAGTTCCTAGCTA 60.292 50.000 0.00 0.00 36.38 3.32
205 206 1.199615 GGAGAGGCAAGTTCCTAGCT 58.800 55.000 0.00 0.00 36.38 3.32
206 207 0.905357 TGGAGAGGCAAGTTCCTAGC 59.095 55.000 0.00 0.00 36.38 3.42
207 208 3.070302 GGTATGGAGAGGCAAGTTCCTAG 59.930 52.174 0.00 0.00 36.38 3.02
208 209 3.039011 GGTATGGAGAGGCAAGTTCCTA 58.961 50.000 0.00 0.00 36.38 2.94
209 210 1.840635 GGTATGGAGAGGCAAGTTCCT 59.159 52.381 0.00 0.00 39.67 3.36
210 211 1.840635 AGGTATGGAGAGGCAAGTTCC 59.159 52.381 0.00 0.00 0.00 3.62
211 212 3.181464 GGTAGGTATGGAGAGGCAAGTTC 60.181 52.174 0.00 0.00 0.00 3.01
212 213 2.772515 GGTAGGTATGGAGAGGCAAGTT 59.227 50.000 0.00 0.00 0.00 2.66
213 214 2.399580 GGTAGGTATGGAGAGGCAAGT 58.600 52.381 0.00 0.00 0.00 3.16
214 215 1.694696 GGGTAGGTATGGAGAGGCAAG 59.305 57.143 0.00 0.00 0.00 4.01
215 216 1.694693 GGGGTAGGTATGGAGAGGCAA 60.695 57.143 0.00 0.00 0.00 4.52
216 217 0.105142 GGGGTAGGTATGGAGAGGCA 60.105 60.000 0.00 0.00 0.00 4.75
217 218 0.836830 GGGGGTAGGTATGGAGAGGC 60.837 65.000 0.00 0.00 0.00 4.70
218 219 3.477783 GGGGGTAGGTATGGAGAGG 57.522 63.158 0.00 0.00 0.00 3.69
233 234 1.617947 GCCTGACAGTAGAGTGGGGG 61.618 65.000 0.93 0.00 0.00 5.40
234 235 0.616111 AGCCTGACAGTAGAGTGGGG 60.616 60.000 0.93 0.00 0.00 4.96
235 236 1.270907 AAGCCTGACAGTAGAGTGGG 58.729 55.000 0.93 0.00 0.00 4.61
236 237 3.357203 TCTAAGCCTGACAGTAGAGTGG 58.643 50.000 0.93 0.00 0.00 4.00
237 238 4.381079 GGTTCTAAGCCTGACAGTAGAGTG 60.381 50.000 0.93 0.00 0.00 3.51
238 239 3.764972 GGTTCTAAGCCTGACAGTAGAGT 59.235 47.826 0.93 0.00 0.00 3.24
239 240 3.764434 TGGTTCTAAGCCTGACAGTAGAG 59.236 47.826 0.93 0.00 0.00 2.43
240 241 3.510360 GTGGTTCTAAGCCTGACAGTAGA 59.490 47.826 0.93 0.00 0.00 2.59
241 242 3.673594 CGTGGTTCTAAGCCTGACAGTAG 60.674 52.174 0.93 0.00 0.00 2.57
242 243 2.230508 CGTGGTTCTAAGCCTGACAGTA 59.769 50.000 0.93 0.00 0.00 2.74
243 244 1.000955 CGTGGTTCTAAGCCTGACAGT 59.999 52.381 0.93 0.00 0.00 3.55
244 245 1.272490 TCGTGGTTCTAAGCCTGACAG 59.728 52.381 0.00 0.00 0.00 3.51
245 246 1.000506 GTCGTGGTTCTAAGCCTGACA 59.999 52.381 8.06 0.00 34.53 3.58
246 247 1.000506 TGTCGTGGTTCTAAGCCTGAC 59.999 52.381 6.65 6.65 34.77 3.51
247 248 1.000506 GTGTCGTGGTTCTAAGCCTGA 59.999 52.381 0.00 0.00 0.00 3.86
248 249 1.429463 GTGTCGTGGTTCTAAGCCTG 58.571 55.000 0.00 0.00 0.00 4.85
249 250 0.038526 CGTGTCGTGGTTCTAAGCCT 60.039 55.000 0.00 0.00 0.00 4.58
250 251 1.623973 GCGTGTCGTGGTTCTAAGCC 61.624 60.000 0.00 0.00 0.00 4.35
251 252 1.779683 GCGTGTCGTGGTTCTAAGC 59.220 57.895 0.00 0.00 0.00 3.09
252 253 2.059575 CGCGTGTCGTGGTTCTAAG 58.940 57.895 0.00 0.00 33.47 2.18
253 254 4.231753 CGCGTGTCGTGGTTCTAA 57.768 55.556 0.00 0.00 33.47 2.10
316 317 2.686835 AGGACAGGGCTCTCCAGC 60.687 66.667 0.00 0.00 46.06 4.85
317 318 2.365586 CCAGGACAGGGCTCTCCAG 61.366 68.421 0.00 0.00 38.24 3.86
318 319 2.284921 CCAGGACAGGGCTCTCCA 60.285 66.667 0.00 0.00 38.24 3.86
319 320 2.039624 TCCAGGACAGGGCTCTCC 59.960 66.667 0.00 0.00 0.00 3.71
320 321 1.000993 TCTCCAGGACAGGGCTCTC 59.999 63.158 0.00 0.00 0.00 3.20
321 322 1.001503 CTCTCCAGGACAGGGCTCT 59.998 63.158 0.00 0.00 0.00 4.09
322 323 2.063378 CCTCTCCAGGACAGGGCTC 61.063 68.421 2.64 0.00 43.65 4.70
323 324 2.040278 CCTCTCCAGGACAGGGCT 59.960 66.667 2.64 0.00 43.65 5.19
324 325 1.920835 AACCTCTCCAGGACAGGGC 60.921 63.158 15.00 0.00 43.65 5.19
325 326 0.545309 TCAACCTCTCCAGGACAGGG 60.545 60.000 15.00 5.97 43.65 4.45
326 327 1.484240 GATCAACCTCTCCAGGACAGG 59.516 57.143 9.25 9.25 43.65 4.00
327 328 1.135915 CGATCAACCTCTCCAGGACAG 59.864 57.143 0.00 0.00 43.65 3.51
328 329 1.186200 CGATCAACCTCTCCAGGACA 58.814 55.000 0.00 0.00 43.65 4.02
329 330 0.179097 GCGATCAACCTCTCCAGGAC 60.179 60.000 0.00 0.00 43.65 3.85
330 331 0.324738 AGCGATCAACCTCTCCAGGA 60.325 55.000 0.00 0.00 43.65 3.86
331 332 0.179089 CAGCGATCAACCTCTCCAGG 60.179 60.000 0.00 0.00 46.87 4.45
332 333 0.534412 ACAGCGATCAACCTCTCCAG 59.466 55.000 0.00 0.00 0.00 3.86
333 334 0.532573 GACAGCGATCAACCTCTCCA 59.467 55.000 0.00 0.00 0.00 3.86
334 335 0.532573 TGACAGCGATCAACCTCTCC 59.467 55.000 0.00 0.00 0.00 3.71
335 336 1.634702 GTGACAGCGATCAACCTCTC 58.365 55.000 0.00 0.00 0.00 3.20
336 337 0.109086 CGTGACAGCGATCAACCTCT 60.109 55.000 0.00 0.00 0.00 3.69
337 338 1.078759 CCGTGACAGCGATCAACCTC 61.079 60.000 0.00 0.00 0.00 3.85
338 339 1.079819 CCGTGACAGCGATCAACCT 60.080 57.895 0.00 0.00 0.00 3.50
339 340 2.740714 GCCGTGACAGCGATCAACC 61.741 63.158 0.00 0.00 0.00 3.77
340 341 2.778679 GCCGTGACAGCGATCAAC 59.221 61.111 0.00 0.00 0.00 3.18
361 362 4.736896 GTCACGTGGTCCGCCTCC 62.737 72.222 17.00 0.00 41.42 4.30
454 455 3.450559 ATCTGCTCGCGACCGTACG 62.451 63.158 3.71 8.69 35.54 3.67
455 456 1.939785 CATCTGCTCGCGACCGTAC 60.940 63.158 3.71 0.00 35.54 3.67
456 457 2.407616 CATCTGCTCGCGACCGTA 59.592 61.111 3.71 0.00 35.54 4.02
457 458 4.498520 CCATCTGCTCGCGACCGT 62.499 66.667 3.71 0.00 35.54 4.83
478 479 4.139420 CTTGCTTGCTCGCGTCCG 62.139 66.667 5.77 0.00 0.00 4.79
479 480 3.793144 CCTTGCTTGCTCGCGTCC 61.793 66.667 5.77 0.00 0.00 4.79
480 481 4.451652 GCCTTGCTTGCTCGCGTC 62.452 66.667 5.77 0.00 0.00 5.19
482 483 4.748679 GTGCCTTGCTTGCTCGCG 62.749 66.667 0.00 0.00 0.00 5.87
483 484 4.748679 CGTGCCTTGCTTGCTCGC 62.749 66.667 4.73 0.00 38.61 5.03
484 485 4.093952 CCGTGCCTTGCTTGCTCG 62.094 66.667 9.18 9.18 43.19 5.03
485 486 3.741476 CCCGTGCCTTGCTTGCTC 61.741 66.667 0.00 0.00 0.00 4.26
529 530 2.973899 CTCCGGTGCACAGCTAGT 59.026 61.111 20.43 0.00 0.00 2.57
530 531 2.510238 GCTCCGGTGCACAGCTAG 60.510 66.667 23.09 15.06 0.00 3.42
531 532 2.184020 ATTGCTCCGGTGCACAGCTA 62.184 55.000 29.62 15.92 43.20 3.32
532 533 3.557903 ATTGCTCCGGTGCACAGCT 62.558 57.895 29.62 12.61 43.20 4.24
533 534 3.044059 GATTGCTCCGGTGCACAGC 62.044 63.158 29.62 19.12 43.20 4.40
534 535 2.401766 GGATTGCTCCGGTGCACAG 61.402 63.158 29.62 15.33 43.20 3.66
535 536 2.359850 GGATTGCTCCGGTGCACA 60.360 61.111 29.62 20.23 43.20 4.57
536 537 3.134127 GGGATTGCTCCGGTGCAC 61.134 66.667 29.62 19.04 43.11 4.57
537 538 3.645660 TGGGATTGCTCCGGTGCA 61.646 61.111 26.46 26.46 43.11 4.57
538 539 3.134127 GTGGGATTGCTCCGGTGC 61.134 66.667 21.41 21.41 43.11 5.01
539 540 2.438434 GGTGGGATTGCTCCGGTG 60.438 66.667 0.00 0.00 43.11 4.94
540 541 4.096003 CGGTGGGATTGCTCCGGT 62.096 66.667 0.00 0.00 43.11 5.28
542 543 3.781307 TCCGGTGGGATTGCTCCG 61.781 66.667 0.00 0.00 43.11 4.63
543 544 2.124695 GTCCGGTGGGATTGCTCC 60.125 66.667 0.00 0.00 46.14 4.70
544 545 2.124695 GGTCCGGTGGGATTGCTC 60.125 66.667 0.00 0.00 46.14 4.26
545 546 4.096003 CGGTCCGGTGGGATTGCT 62.096 66.667 2.34 0.00 46.14 3.91
556 557 2.298158 CTTCATCTCCCACCGGTCCG 62.298 65.000 2.59 3.60 0.00 4.79
557 558 1.522569 CTTCATCTCCCACCGGTCC 59.477 63.158 2.59 0.00 0.00 4.46
558 559 1.265454 ACCTTCATCTCCCACCGGTC 61.265 60.000 2.59 0.00 0.00 4.79
559 560 1.229529 ACCTTCATCTCCCACCGGT 60.230 57.895 0.00 0.00 0.00 5.28
560 561 1.522569 GACCTTCATCTCCCACCGG 59.477 63.158 0.00 0.00 0.00 5.28
561 562 0.978146 AGGACCTTCATCTCCCACCG 60.978 60.000 0.00 0.00 0.00 4.94
562 563 0.543749 CAGGACCTTCATCTCCCACC 59.456 60.000 0.00 0.00 0.00 4.61
563 564 1.573108 TCAGGACCTTCATCTCCCAC 58.427 55.000 0.00 0.00 0.00 4.61
564 565 2.507058 CAATCAGGACCTTCATCTCCCA 59.493 50.000 0.00 0.00 0.00 4.37
565 566 2.747799 GCAATCAGGACCTTCATCTCCC 60.748 54.545 0.00 0.00 0.00 4.30
566 567 2.172293 AGCAATCAGGACCTTCATCTCC 59.828 50.000 0.00 0.00 0.00 3.71
567 568 3.557228 AGCAATCAGGACCTTCATCTC 57.443 47.619 0.00 0.00 0.00 2.75
568 569 4.313020 AAAGCAATCAGGACCTTCATCT 57.687 40.909 0.00 0.00 0.00 2.90
569 570 6.705863 ATAAAAGCAATCAGGACCTTCATC 57.294 37.500 0.00 0.00 0.00 2.92
570 571 7.486407 AAATAAAAGCAATCAGGACCTTCAT 57.514 32.000 0.00 0.00 0.00 2.57
571 572 6.916360 AAATAAAAGCAATCAGGACCTTCA 57.084 33.333 0.00 0.00 0.00 3.02
572 573 6.528072 CGAAAATAAAAGCAATCAGGACCTTC 59.472 38.462 0.00 0.00 0.00 3.46
573 574 6.389906 CGAAAATAAAAGCAATCAGGACCTT 58.610 36.000 0.00 0.00 0.00 3.50
574 575 5.105756 CCGAAAATAAAAGCAATCAGGACCT 60.106 40.000 0.00 0.00 0.00 3.85
575 576 5.102313 CCGAAAATAAAAGCAATCAGGACC 58.898 41.667 0.00 0.00 0.00 4.46
576 577 5.102313 CCCGAAAATAAAAGCAATCAGGAC 58.898 41.667 0.00 0.00 0.00 3.85
577 578 4.770010 ACCCGAAAATAAAAGCAATCAGGA 59.230 37.500 0.00 0.00 0.00 3.86
578 579 5.072040 ACCCGAAAATAAAAGCAATCAGG 57.928 39.130 0.00 0.00 0.00 3.86
579 580 8.702163 ATTAACCCGAAAATAAAAGCAATCAG 57.298 30.769 0.00 0.00 0.00 2.90
583 584 9.589111 GGATAATTAACCCGAAAATAAAAGCAA 57.411 29.630 0.24 0.00 0.00 3.91
584 585 8.973182 AGGATAATTAACCCGAAAATAAAAGCA 58.027 29.630 8.09 0.00 0.00 3.91
585 586 9.811995 AAGGATAATTAACCCGAAAATAAAAGC 57.188 29.630 8.09 0.00 0.00 3.51
596 597 3.958147 AGGGCAAAAGGATAATTAACCCG 59.042 43.478 8.09 0.00 39.89 5.28
829 830 0.392193 CCAACGGCTCTCTGCTCAAT 60.392 55.000 0.00 0.00 42.39 2.57
991 996 0.529555 GAGGAAGACATGGAGCTCGC 60.530 60.000 7.83 1.18 0.00 5.03
1294 1299 4.413087 CATTCTTCATGCTCTTCTTGCAC 58.587 43.478 0.00 0.00 43.59 4.57
1406 1411 5.620206 TCTTCAACATCCTAAGCTCAACAA 58.380 37.500 0.00 0.00 0.00 2.83
1490 1496 7.439955 CCAGTGCGATTACCATACTTACAAATA 59.560 37.037 0.00 0.00 0.00 1.40
1498 1504 3.055385 ACAACCAGTGCGATTACCATACT 60.055 43.478 0.00 0.00 0.00 2.12
1762 1774 2.898705 CTCTACGCTCTGAATTTGGCT 58.101 47.619 0.00 0.00 0.00 4.75
1827 1839 1.473257 CGCAAGAGAATCCCCGAATGA 60.473 52.381 0.00 0.00 43.02 2.57
1837 1849 8.352942 AGAAAACAGAAAAATACGCAAGAGAAT 58.647 29.630 0.00 0.00 43.62 2.40
1911 1923 6.205658 GCTCCGGAATAATTCAATTAGCTTCT 59.794 38.462 5.23 0.00 0.00 2.85
1994 2006 9.829507 ACATTTTGGTCTTTGATTTAAATCACA 57.170 25.926 26.69 20.43 44.54 3.58
2127 2148 5.486735 TTTGTGCATTTTCCATCCTTCAT 57.513 34.783 0.00 0.00 0.00 2.57
2184 2205 2.018515 CTAAACACCACAAACCCACGT 58.981 47.619 0.00 0.00 0.00 4.49
2230 2251 2.564062 CCCATGTCAAAGTCTTGCCATT 59.436 45.455 0.00 0.00 28.75 3.16


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

AutoCloner maintained by Alex Coulton.