Multiple sequence alignment - TraesCS1A01G010300

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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 TraesCS1A01G010300 chr1A 100.000 2549 0 0 1 2549 6334354 6336902 0.000000e+00 4708.0
1 TraesCS1A01G010300 chr1A 92.353 1543 62 20 408 1902 4504035 4502501 0.000000e+00 2145.0
2 TraesCS1A01G010300 chr1A 92.303 1546 63 20 405 1902 5498539 5500076 0.000000e+00 2145.0
3 TraesCS1A01G010300 chr1A 99.567 924 1 1 982 1902 5500631 5501554 0.000000e+00 1681.0
4 TraesCS1A01G010300 chr1A 90.000 230 7 5 2325 2548 4502337 4502118 1.490000e-72 283.0
5 TraesCS1A01G010300 chr1A 90.000 230 7 5 2325 2548 5500240 5500459 1.490000e-72 283.0
6 TraesCS1A01G010300 chr1A 90.000 230 7 5 2325 2548 5501718 5501937 1.490000e-72 283.0
7 TraesCS1A01G010300 chr1A 97.674 86 1 1 1963 2047 4502509 4502424 2.040000e-31 147.0
8 TraesCS1A01G010300 chr1A 97.674 86 1 1 1963 2047 5500068 5500153 2.040000e-31 147.0
9 TraesCS1A01G010300 chr1A 97.674 86 1 1 1963 2047 5501546 5501631 2.040000e-31 147.0
10 TraesCS1A01G010300 chr1A 97.222 72 2 0 2432 2503 4258706 4258635 3.440000e-24 122.0
11 TraesCS1A01G010300 chr1D 87.589 1958 120 34 501 2374 3968392 3970310 0.000000e+00 2156.0
12 TraesCS1A01G010300 chr1D 88.927 587 38 16 1977 2548 5130307 5130881 0.000000e+00 699.0
13 TraesCS1A01G010300 chr1D 95.094 265 5 3 41 299 440711487 440711225 6.560000e-111 411.0
14 TraesCS1A01G010300 chr1D 83.296 443 48 22 1326 1753 3618231 3617800 3.980000e-103 385.0
15 TraesCS1A01G010300 chr1D 92.920 113 8 0 2436 2548 4235174 4235286 5.640000e-37 165.0
16 TraesCS1A01G010300 chr1B 86.950 1318 106 28 405 1669 6481059 6482363 0.000000e+00 1421.0
17 TraesCS1A01G010300 chr1B 87.469 1213 83 32 501 1669 5760715 5759528 0.000000e+00 1334.0
18 TraesCS1A01G010300 chr1B 81.457 604 47 28 1796 2372 6482427 6482992 3.890000e-118 435.0
19 TraesCS1A01G010300 chr1B 81.445 609 42 29 1796 2372 5759464 5758895 1.400000e-117 433.0
20 TraesCS1A01G010300 chr1B 88.955 335 29 6 2221 2548 22666002 22666335 8.490000e-110 407.0
21 TraesCS1A01G010300 chr1B 85.627 327 22 11 1379 1686 5750003 5749683 1.140000e-83 320.0
22 TraesCS1A01G010300 chr1B 95.763 118 5 0 2431 2548 5990463 5990346 9.310000e-45 191.0
23 TraesCS1A01G010300 chr1B 83.182 220 25 9 2221 2434 6286126 6285913 9.310000e-45 191.0
24 TraesCS1A01G010300 chr1B 94.017 117 7 0 2432 2548 22150031 22150147 7.250000e-41 178.0
25 TraesCS1A01G010300 chr1B 81.364 220 29 8 2221 2434 7697699 7697912 4.360000e-38 169.0
26 TraesCS1A01G010300 chr1B 95.385 65 1 2 395 457 5760797 5760733 4.490000e-18 102.0
27 TraesCS1A01G010300 chr1B 91.781 73 5 1 1701 1772 5759524 5759452 1.610000e-17 100.0
28 TraesCS1A01G010300 chr1B 90.789 76 6 1 1698 1772 6482364 6482439 1.610000e-17 100.0
29 TraesCS1A01G010300 chr1B 85.185 81 10 2 2221 2300 7345271 7345192 5.840000e-12 82.4
30 TraesCS1A01G010300 chr5B 86.674 923 83 22 888 1792 55504708 55503808 0.000000e+00 987.0
31 TraesCS1A01G010300 chr5D 85.618 744 69 25 888 1619 52327702 52326985 0.000000e+00 747.0
32 TraesCS1A01G010300 chr5D 81.933 238 33 6 2163 2395 52326531 52326299 2.590000e-45 193.0
33 TraesCS1A01G010300 chr6B 98.662 299 2 2 1 299 663857608 663857312 1.740000e-146 529.0
34 TraesCS1A01G010300 chr6B 98.780 246 2 1 1 246 692608071 692608315 1.080000e-118 436.0
35 TraesCS1A01G010300 chr3D 95.752 306 9 4 1 305 581060987 581060685 8.200000e-135 490.0
36 TraesCS1A01G010300 chr2A 90.939 309 9 4 1 302 755405450 755405746 5.110000e-107 398.0
37 TraesCS1A01G010300 chr2A 89.305 187 4 2 129 299 706213778 706213592 1.190000e-53 220.0
38 TraesCS1A01G010300 chr2A 86.395 147 9 3 157 298 585248554 585248414 1.580000e-32 150.0
39 TraesCS1A01G010300 chr7A 90.909 308 9 4 1 301 20189020 20188725 1.840000e-106 396.0
40 TraesCS1A01G010300 chr6D 92.568 148 9 2 157 303 69927177 69927323 7.140000e-51 211.0
41 TraesCS1A01G010300 chr7D 89.423 104 7 2 196 298 277504043 277504143 7.400000e-26 128.0


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 TraesCS1A01G010300 chr1A 6334354 6336902 2548 False 4708.000000 4708 100.000000 1 2549 1 chr1A.!!$F1 2548
1 TraesCS1A01G010300 chr1A 4502118 4504035 1917 True 858.333333 2145 93.342333 408 2548 3 chr1A.!!$R2 2140
2 TraesCS1A01G010300 chr1A 5498539 5501937 3398 False 781.000000 2145 94.536333 405 2548 6 chr1A.!!$F2 2143
3 TraesCS1A01G010300 chr1D 3968392 3970310 1918 False 2156.000000 2156 87.589000 501 2374 1 chr1D.!!$F1 1873
4 TraesCS1A01G010300 chr1D 5130307 5130881 574 False 699.000000 699 88.927000 1977 2548 1 chr1D.!!$F3 571
5 TraesCS1A01G010300 chr1B 6481059 6482992 1933 False 652.000000 1421 86.398667 405 2372 3 chr1B.!!$F4 1967
6 TraesCS1A01G010300 chr1B 5758895 5760797 1902 True 492.250000 1334 89.020000 395 2372 4 chr1B.!!$R5 1977
7 TraesCS1A01G010300 chr5B 55503808 55504708 900 True 987.000000 987 86.674000 888 1792 1 chr5B.!!$R1 904
8 TraesCS1A01G010300 chr5D 52326299 52327702 1403 True 470.000000 747 83.775500 888 2395 2 chr5D.!!$R1 1507

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
389 390 0.030092 ATCTGGCTGGCTAACCCCTA 60.03 55.0 2.0 0.0 33.59 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 3766 0.771127 CACCAAAAGACTGGGGAGGA 59.229 55.0 0.0 0.0 43.19 3.71 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
68 69 4.641645 CACAGCGGCCAGTTCCCA 62.642 66.667 2.24 0.00 0.00 4.37
69 70 4.335647 ACAGCGGCCAGTTCCCAG 62.336 66.667 2.24 0.00 0.00 4.45
70 71 4.335647 CAGCGGCCAGTTCCCAGT 62.336 66.667 2.24 0.00 0.00 4.00
71 72 4.021925 AGCGGCCAGTTCCCAGTC 62.022 66.667 2.24 0.00 0.00 3.51
76 77 4.760047 CCAGTTCCCAGTCGCCGG 62.760 72.222 0.00 0.00 0.00 6.13
77 78 4.003788 CAGTTCCCAGTCGCCGGT 62.004 66.667 1.90 0.00 0.00 5.28
78 79 4.003788 AGTTCCCAGTCGCCGGTG 62.004 66.667 9.28 9.28 0.00 4.94
109 110 4.778415 CTCAGCCGTCCGTGGTCG 62.778 72.222 0.00 0.00 0.00 4.79
114 115 4.657824 CCGTCCGTGGTCGCAAGT 62.658 66.667 0.00 0.00 39.48 3.16
115 116 3.103911 CGTCCGTGGTCGCAAGTC 61.104 66.667 0.00 0.00 39.48 3.01
116 117 2.028484 GTCCGTGGTCGCAAGTCA 59.972 61.111 0.00 0.00 39.48 3.41
117 118 1.593209 GTCCGTGGTCGCAAGTCAA 60.593 57.895 0.00 0.00 39.48 3.18
118 119 1.144276 TCCGTGGTCGCAAGTCAAA 59.856 52.632 0.00 0.00 39.48 2.69
119 120 0.878523 TCCGTGGTCGCAAGTCAAAG 60.879 55.000 0.00 0.00 39.48 2.77
120 121 1.569493 CGTGGTCGCAAGTCAAAGG 59.431 57.895 0.00 0.00 39.48 3.11
121 122 1.841663 CGTGGTCGCAAGTCAAAGGG 61.842 60.000 0.00 0.00 39.48 3.95
122 123 1.228124 TGGTCGCAAGTCAAAGGGG 60.228 57.895 0.00 0.00 39.48 4.79
123 124 1.072505 GGTCGCAAGTCAAAGGGGA 59.927 57.895 0.00 0.00 39.48 4.81
124 125 0.536460 GGTCGCAAGTCAAAGGGGAA 60.536 55.000 0.00 0.00 39.48 3.97
125 126 1.314730 GTCGCAAGTCAAAGGGGAAA 58.685 50.000 0.00 0.00 39.48 3.13
126 127 1.679153 GTCGCAAGTCAAAGGGGAAAA 59.321 47.619 0.00 0.00 39.48 2.29
127 128 1.953686 TCGCAAGTCAAAGGGGAAAAG 59.046 47.619 0.00 0.00 39.48 2.27
128 129 1.000274 CGCAAGTCAAAGGGGAAAAGG 60.000 52.381 0.00 0.00 0.00 3.11
129 130 2.316108 GCAAGTCAAAGGGGAAAAGGA 58.684 47.619 0.00 0.00 0.00 3.36
130 131 2.899900 GCAAGTCAAAGGGGAAAAGGAT 59.100 45.455 0.00 0.00 0.00 3.24
131 132 3.324846 GCAAGTCAAAGGGGAAAAGGATT 59.675 43.478 0.00 0.00 0.00 3.01
132 133 4.561530 GCAAGTCAAAGGGGAAAAGGATTC 60.562 45.833 0.00 0.00 0.00 2.52
133 134 4.749048 AGTCAAAGGGGAAAAGGATTCT 57.251 40.909 0.00 0.00 0.00 2.40
134 135 4.411013 AGTCAAAGGGGAAAAGGATTCTG 58.589 43.478 0.00 0.00 0.00 3.02
135 136 3.511540 GTCAAAGGGGAAAAGGATTCTGG 59.488 47.826 0.00 0.00 0.00 3.86
136 137 3.401002 TCAAAGGGGAAAAGGATTCTGGA 59.599 43.478 0.00 0.00 0.00 3.86
137 138 3.746792 AAGGGGAAAAGGATTCTGGAG 57.253 47.619 0.00 0.00 0.00 3.86
138 139 2.648838 AGGGGAAAAGGATTCTGGAGT 58.351 47.619 0.00 0.00 0.00 3.85
139 140 3.815507 AGGGGAAAAGGATTCTGGAGTA 58.184 45.455 0.00 0.00 0.00 2.59
140 141 4.384465 AGGGGAAAAGGATTCTGGAGTAT 58.616 43.478 0.00 0.00 0.00 2.12
141 142 4.166919 AGGGGAAAAGGATTCTGGAGTATG 59.833 45.833 0.00 0.00 0.00 2.39
142 143 4.464947 GGGAAAAGGATTCTGGAGTATGG 58.535 47.826 0.00 0.00 0.00 2.74
143 144 4.166144 GGGAAAAGGATTCTGGAGTATGGA 59.834 45.833 0.00 0.00 0.00 3.41
144 145 5.372373 GGAAAAGGATTCTGGAGTATGGAG 58.628 45.833 0.00 0.00 0.00 3.86
145 146 5.104318 GGAAAAGGATTCTGGAGTATGGAGT 60.104 44.000 0.00 0.00 0.00 3.85
146 147 6.394345 AAAAGGATTCTGGAGTATGGAGTT 57.606 37.500 0.00 0.00 0.00 3.01
147 148 5.365021 AAGGATTCTGGAGTATGGAGTTG 57.635 43.478 0.00 0.00 0.00 3.16
148 149 3.713764 AGGATTCTGGAGTATGGAGTTGG 59.286 47.826 0.00 0.00 0.00 3.77
149 150 3.456277 GGATTCTGGAGTATGGAGTTGGT 59.544 47.826 0.00 0.00 0.00 3.67
150 151 4.443598 GGATTCTGGAGTATGGAGTTGGTC 60.444 50.000 0.00 0.00 0.00 4.02
151 152 2.100197 TCTGGAGTATGGAGTTGGTCG 58.900 52.381 0.00 0.00 0.00 4.79
152 153 0.535335 TGGAGTATGGAGTTGGTCGC 59.465 55.000 0.00 0.00 0.00 5.19
153 154 0.824759 GGAGTATGGAGTTGGTCGCT 59.175 55.000 0.00 0.00 0.00 4.93
154 155 1.471676 GGAGTATGGAGTTGGTCGCTG 60.472 57.143 0.00 0.00 0.00 5.18
155 156 0.108138 AGTATGGAGTTGGTCGCTGC 60.108 55.000 0.00 0.00 0.00 5.25
156 157 0.391130 GTATGGAGTTGGTCGCTGCA 60.391 55.000 0.00 0.00 38.60 4.41
157 158 0.541392 TATGGAGTTGGTCGCTGCAT 59.459 50.000 0.00 4.85 44.93 3.96
158 159 0.745845 ATGGAGTTGGTCGCTGCATC 60.746 55.000 0.00 0.00 40.20 3.91
159 160 2.109126 GGAGTTGGTCGCTGCATCC 61.109 63.158 0.00 1.60 0.00 3.51
160 161 1.375908 GAGTTGGTCGCTGCATCCA 60.376 57.895 8.38 8.38 0.00 3.41
161 162 1.364626 GAGTTGGTCGCTGCATCCAG 61.365 60.000 11.48 0.00 42.13 3.86
162 163 2.046023 TTGGTCGCTGCATCCAGG 60.046 61.111 11.48 0.00 39.54 4.45
168 169 4.119363 GCTGCATCCAGGGCTCCA 62.119 66.667 0.00 0.00 39.54 3.86
169 170 2.192443 CTGCATCCAGGGCTCCAG 59.808 66.667 0.00 0.00 35.38 3.86
170 171 3.414193 TGCATCCAGGGCTCCAGG 61.414 66.667 0.00 0.00 0.00 4.45
171 172 4.891037 GCATCCAGGGCTCCAGGC 62.891 72.222 0.00 0.00 40.90 4.85
172 173 3.414193 CATCCAGGGCTCCAGGCA 61.414 66.667 2.16 0.00 44.01 4.75
173 174 2.369291 ATCCAGGGCTCCAGGCAT 60.369 61.111 2.16 0.00 44.01 4.40
174 175 2.459086 ATCCAGGGCTCCAGGCATC 61.459 63.158 2.16 0.00 44.01 3.91
175 176 4.559063 CCAGGGCTCCAGGCATCG 62.559 72.222 2.16 0.00 44.01 3.84
176 177 3.790437 CAGGGCTCCAGGCATCGT 61.790 66.667 2.16 0.00 44.01 3.73
177 178 2.041922 AGGGCTCCAGGCATCGTA 60.042 61.111 2.16 0.00 44.01 3.43
178 179 2.136878 AGGGCTCCAGGCATCGTAG 61.137 63.158 2.16 0.00 44.01 3.51
179 180 2.134287 GGGCTCCAGGCATCGTAGA 61.134 63.158 2.16 0.00 44.01 2.59
180 181 1.068250 GGCTCCAGGCATCGTAGAC 59.932 63.158 0.00 0.00 44.01 2.59
181 182 1.395826 GGCTCCAGGCATCGTAGACT 61.396 60.000 0.00 0.00 44.01 3.24
182 183 1.319541 GCTCCAGGCATCGTAGACTA 58.680 55.000 0.00 0.00 42.51 2.59
183 184 1.268352 GCTCCAGGCATCGTAGACTAG 59.732 57.143 0.00 0.00 42.51 2.57
184 185 2.577700 CTCCAGGCATCGTAGACTAGT 58.422 52.381 0.00 0.00 42.51 2.57
185 186 2.550606 CTCCAGGCATCGTAGACTAGTC 59.449 54.545 15.41 15.41 42.51 2.59
186 187 1.609555 CCAGGCATCGTAGACTAGTCC 59.390 57.143 19.38 4.19 42.51 3.85
187 188 2.577700 CAGGCATCGTAGACTAGTCCT 58.422 52.381 19.38 9.34 42.51 3.85
188 189 3.496337 CCAGGCATCGTAGACTAGTCCTA 60.496 52.174 19.38 8.38 42.51 2.94
189 190 3.749088 CAGGCATCGTAGACTAGTCCTAG 59.251 52.174 19.38 10.54 42.51 3.02
191 192 4.136051 GGCATCGTAGACTAGTCCTAGTT 58.864 47.826 19.38 3.00 45.63 2.24
192 193 4.023878 GGCATCGTAGACTAGTCCTAGTTG 60.024 50.000 19.38 14.92 45.63 3.16
193 194 4.815308 GCATCGTAGACTAGTCCTAGTTGA 59.185 45.833 19.38 9.34 45.63 3.18
194 195 5.470777 GCATCGTAGACTAGTCCTAGTTGAT 59.529 44.000 19.38 11.06 45.63 2.57
195 196 6.649973 GCATCGTAGACTAGTCCTAGTTGATA 59.350 42.308 19.38 0.00 45.63 2.15
196 197 7.172875 GCATCGTAGACTAGTCCTAGTTGATAA 59.827 40.741 19.38 0.00 45.63 1.75
197 198 8.714179 CATCGTAGACTAGTCCTAGTTGATAAG 58.286 40.741 19.38 5.38 45.63 1.73
198 199 7.790027 TCGTAGACTAGTCCTAGTTGATAAGT 58.210 38.462 19.38 0.00 45.63 2.24
199 200 7.710044 TCGTAGACTAGTCCTAGTTGATAAGTG 59.290 40.741 19.38 0.00 45.63 3.16
200 201 7.041916 CGTAGACTAGTCCTAGTTGATAAGTGG 60.042 44.444 19.38 0.00 45.63 4.00
201 202 6.130569 AGACTAGTCCTAGTTGATAAGTGGG 58.869 44.000 19.38 0.00 45.63 4.61
202 203 4.650131 ACTAGTCCTAGTTGATAAGTGGGC 59.350 45.833 1.08 0.00 43.35 5.36
203 204 2.772515 AGTCCTAGTTGATAAGTGGGCC 59.227 50.000 0.00 0.00 32.84 5.80
204 205 2.772515 GTCCTAGTTGATAAGTGGGCCT 59.227 50.000 4.53 0.00 32.84 5.19
205 206 2.771943 TCCTAGTTGATAAGTGGGCCTG 59.228 50.000 4.53 0.00 32.84 4.85
206 207 2.505819 CCTAGTTGATAAGTGGGCCTGT 59.494 50.000 4.53 0.00 0.00 4.00
207 208 2.496899 AGTTGATAAGTGGGCCTGTG 57.503 50.000 4.53 0.00 0.00 3.66
208 209 1.004745 AGTTGATAAGTGGGCCTGTGG 59.995 52.381 4.53 0.00 0.00 4.17
209 210 0.331278 TTGATAAGTGGGCCTGTGGG 59.669 55.000 4.53 0.00 0.00 4.61
223 224 4.623932 CCTGTGGGCTGTATGTATACAT 57.376 45.455 21.57 21.57 41.92 2.29
224 225 5.738619 CCTGTGGGCTGTATGTATACATA 57.261 43.478 19.51 19.51 41.92 2.29
225 226 5.724328 CCTGTGGGCTGTATGTATACATAG 58.276 45.833 23.03 16.30 41.92 2.23
226 227 5.337571 CCTGTGGGCTGTATGTATACATAGG 60.338 48.000 23.03 18.86 41.92 2.57
227 228 4.530553 TGTGGGCTGTATGTATACATAGGG 59.469 45.833 23.03 18.57 41.92 3.53
228 229 4.081087 GTGGGCTGTATGTATACATAGGGG 60.081 50.000 23.03 16.58 41.92 4.79
229 230 4.101856 GGGCTGTATGTATACATAGGGGT 58.898 47.826 23.03 2.93 41.92 4.95
230 231 5.222589 TGGGCTGTATGTATACATAGGGGTA 60.223 44.000 23.03 2.96 41.92 3.69
231 232 5.363005 GGGCTGTATGTATACATAGGGGTAG 59.637 48.000 23.03 16.53 41.92 3.18
232 233 5.956563 GGCTGTATGTATACATAGGGGTAGT 59.043 44.000 23.03 0.81 41.92 2.73
233 234 7.121382 GGCTGTATGTATACATAGGGGTAGTA 58.879 42.308 23.03 0.85 41.92 1.82
234 235 7.616935 GGCTGTATGTATACATAGGGGTAGTAA 59.383 40.741 23.03 0.14 41.92 2.24
235 236 9.028284 GCTGTATGTATACATAGGGGTAGTAAA 57.972 37.037 23.03 0.00 41.92 2.01
289 290 4.388499 TTCGCCCCCACGAAGCTC 62.388 66.667 0.00 0.00 46.39 4.09
295 296 4.379243 CCCACGAAGCTCCGCTGT 62.379 66.667 0.00 0.00 39.62 4.40
296 297 2.357517 CCACGAAGCTCCGCTGTT 60.358 61.111 0.00 0.00 39.62 3.16
297 298 2.671177 CCACGAAGCTCCGCTGTTG 61.671 63.158 0.00 0.00 39.62 3.33
298 299 3.044305 ACGAAGCTCCGCTGTTGC 61.044 61.111 0.00 0.00 39.62 4.17
299 300 2.740055 CGAAGCTCCGCTGTTGCT 60.740 61.111 0.00 0.00 39.62 3.91
300 301 2.734673 CGAAGCTCCGCTGTTGCTC 61.735 63.158 0.00 0.00 39.62 4.26
301 302 2.359230 AAGCTCCGCTGTTGCTCC 60.359 61.111 0.00 0.00 39.62 4.70
302 303 2.794820 GAAGCTCCGCTGTTGCTCCT 62.795 60.000 0.00 0.00 39.62 3.69
303 304 3.123620 GCTCCGCTGTTGCTCCTG 61.124 66.667 0.00 0.00 36.97 3.86
304 305 3.123620 CTCCGCTGTTGCTCCTGC 61.124 66.667 0.00 0.00 36.97 4.85
305 306 4.704833 TCCGCTGTTGCTCCTGCC 62.705 66.667 0.00 0.00 38.71 4.85
307 308 2.979676 CGCTGTTGCTCCTGCCAA 60.980 61.111 0.00 0.00 38.71 4.52
308 309 2.338015 CGCTGTTGCTCCTGCCAAT 61.338 57.895 0.00 0.00 38.71 3.16
309 310 1.214589 GCTGTTGCTCCTGCCAATG 59.785 57.895 0.00 0.00 38.71 2.82
310 311 1.530013 GCTGTTGCTCCTGCCAATGT 61.530 55.000 0.00 0.00 38.71 2.71
311 312 0.963962 CTGTTGCTCCTGCCAATGTT 59.036 50.000 0.00 0.00 38.71 2.71
312 313 1.342174 CTGTTGCTCCTGCCAATGTTT 59.658 47.619 0.00 0.00 38.71 2.83
313 314 1.340889 TGTTGCTCCTGCCAATGTTTC 59.659 47.619 0.00 0.00 38.71 2.78
314 315 0.968405 TTGCTCCTGCCAATGTTTCC 59.032 50.000 0.00 0.00 38.71 3.13
315 316 1.243342 TGCTCCTGCCAATGTTTCCG 61.243 55.000 0.00 0.00 38.71 4.30
316 317 1.937546 GCTCCTGCCAATGTTTCCGG 61.938 60.000 0.00 0.00 0.00 5.14
317 318 1.304052 TCCTGCCAATGTTTCCGGG 60.304 57.895 0.00 0.00 0.00 5.73
318 319 1.606313 CCTGCCAATGTTTCCGGGT 60.606 57.895 0.00 0.00 0.00 5.28
319 320 1.595093 CCTGCCAATGTTTCCGGGTC 61.595 60.000 0.00 0.00 0.00 4.46
320 321 0.609131 CTGCCAATGTTTCCGGGTCT 60.609 55.000 0.00 0.00 0.00 3.85
321 322 0.893270 TGCCAATGTTTCCGGGTCTG 60.893 55.000 0.00 0.00 0.00 3.51
322 323 1.883021 CCAATGTTTCCGGGTCTGC 59.117 57.895 0.00 0.00 0.00 4.26
323 324 0.609131 CCAATGTTTCCGGGTCTGCT 60.609 55.000 0.00 0.00 0.00 4.24
324 325 0.804989 CAATGTTTCCGGGTCTGCTC 59.195 55.000 0.00 0.00 0.00 4.26
325 326 0.322546 AATGTTTCCGGGTCTGCTCC 60.323 55.000 0.00 0.00 0.00 4.70
326 327 2.434359 GTTTCCGGGTCTGCTCCG 60.434 66.667 0.00 0.00 46.43 4.63
331 332 3.691342 CGGGTCTGCTCCGGACAA 61.691 66.667 0.00 0.00 41.15 3.18
332 333 2.990479 GGGTCTGCTCCGGACAAT 59.010 61.111 0.00 0.00 41.15 2.71
333 334 1.450312 GGGTCTGCTCCGGACAATG 60.450 63.158 0.00 0.00 41.15 2.82
334 335 1.296715 GGTCTGCTCCGGACAATGT 59.703 57.895 0.00 0.00 41.15 2.71
335 336 0.321653 GGTCTGCTCCGGACAATGTT 60.322 55.000 0.00 0.00 41.15 2.71
336 337 1.523758 GTCTGCTCCGGACAATGTTT 58.476 50.000 0.00 0.00 39.36 2.83
337 338 1.464997 GTCTGCTCCGGACAATGTTTC 59.535 52.381 0.00 0.00 39.36 2.78
338 339 0.443869 CTGCTCCGGACAATGTTTCG 59.556 55.000 0.00 0.00 0.00 3.46
339 340 0.953471 TGCTCCGGACAATGTTTCGG 60.953 55.000 18.32 18.32 43.42 4.30
340 341 1.794222 CTCCGGACAATGTTTCGGC 59.206 57.895 19.17 0.00 41.98 5.54
341 342 1.644786 CTCCGGACAATGTTTCGGCC 61.645 60.000 19.17 0.00 41.98 6.13
342 343 1.674322 CCGGACAATGTTTCGGCCT 60.674 57.895 14.03 0.00 35.95 5.19
343 344 1.644786 CCGGACAATGTTTCGGCCTC 61.645 60.000 14.03 0.00 35.95 4.70
344 345 1.644786 CGGACAATGTTTCGGCCTCC 61.645 60.000 0.00 0.00 0.00 4.30
354 355 4.473520 CGGCCTCCGGACAATGCT 62.474 66.667 0.00 0.00 44.15 3.79
355 356 2.514824 GGCCTCCGGACAATGCTC 60.515 66.667 0.00 0.00 0.00 4.26
356 357 2.514824 GCCTCCGGACAATGCTCC 60.515 66.667 0.00 0.00 0.00 4.70
362 363 4.713946 GGACAATGCTCCGGACAA 57.286 55.556 0.00 0.00 0.00 3.18
363 364 2.471255 GGACAATGCTCCGGACAAG 58.529 57.895 0.00 4.37 0.00 3.16
364 365 0.321653 GGACAATGCTCCGGACAAGT 60.322 55.000 0.00 7.54 0.00 3.16
365 366 1.523758 GACAATGCTCCGGACAAGTT 58.476 50.000 0.00 0.00 0.00 2.66
366 367 1.880027 GACAATGCTCCGGACAAGTTT 59.120 47.619 0.00 0.00 0.00 2.66
367 368 3.071479 GACAATGCTCCGGACAAGTTTA 58.929 45.455 0.00 0.00 0.00 2.01
368 369 3.686016 ACAATGCTCCGGACAAGTTTAT 58.314 40.909 0.00 0.00 0.00 1.40
369 370 3.440173 ACAATGCTCCGGACAAGTTTATG 59.560 43.478 0.00 0.00 0.00 1.90
370 371 3.627395 ATGCTCCGGACAAGTTTATGA 57.373 42.857 0.00 0.00 0.00 2.15
371 372 3.627395 TGCTCCGGACAAGTTTATGAT 57.373 42.857 0.00 0.00 0.00 2.45
372 373 3.531538 TGCTCCGGACAAGTTTATGATC 58.468 45.455 0.00 0.00 0.00 2.92
373 374 3.197766 TGCTCCGGACAAGTTTATGATCT 59.802 43.478 0.00 0.00 0.00 2.75
374 375 3.557595 GCTCCGGACAAGTTTATGATCTG 59.442 47.826 0.00 0.00 0.00 2.90
375 376 4.122776 CTCCGGACAAGTTTATGATCTGG 58.877 47.826 0.00 0.00 37.20 3.86
376 377 2.614057 CCGGACAAGTTTATGATCTGGC 59.386 50.000 0.00 0.00 0.00 4.85
377 378 3.535561 CGGACAAGTTTATGATCTGGCT 58.464 45.455 0.00 0.00 0.00 4.75
378 379 3.310774 CGGACAAGTTTATGATCTGGCTG 59.689 47.826 0.00 0.00 0.00 4.85
379 380 3.629398 GGACAAGTTTATGATCTGGCTGG 59.371 47.826 0.00 0.00 0.00 4.85
380 381 3.019564 ACAAGTTTATGATCTGGCTGGC 58.980 45.455 0.00 0.00 0.00 4.85
381 382 3.285484 CAAGTTTATGATCTGGCTGGCT 58.715 45.455 2.00 0.00 0.00 4.75
382 383 4.080356 ACAAGTTTATGATCTGGCTGGCTA 60.080 41.667 2.00 0.00 0.00 3.93
383 384 4.778213 AGTTTATGATCTGGCTGGCTAA 57.222 40.909 2.00 0.00 0.00 3.09
384 385 4.455606 AGTTTATGATCTGGCTGGCTAAC 58.544 43.478 2.00 0.00 0.00 2.34
385 386 3.492102 TTATGATCTGGCTGGCTAACC 57.508 47.619 2.00 0.00 0.00 2.85
386 387 0.475906 ATGATCTGGCTGGCTAACCC 59.524 55.000 2.00 0.00 33.59 4.11
387 388 1.149401 GATCTGGCTGGCTAACCCC 59.851 63.158 2.00 0.00 33.59 4.95
388 389 1.308216 ATCTGGCTGGCTAACCCCT 60.308 57.895 2.00 0.00 33.59 4.79
389 390 0.030092 ATCTGGCTGGCTAACCCCTA 60.030 55.000 2.00 0.00 33.59 3.53
390 391 0.030092 TCTGGCTGGCTAACCCCTAT 60.030 55.000 2.00 0.00 33.59 2.57
391 392 0.398318 CTGGCTGGCTAACCCCTATC 59.602 60.000 2.00 0.00 33.59 2.08
392 393 1.060163 TGGCTGGCTAACCCCTATCC 61.060 60.000 2.00 0.00 33.59 2.59
393 394 1.060163 GGCTGGCTAACCCCTATCCA 61.060 60.000 0.00 0.00 33.59 3.41
394 395 0.843984 GCTGGCTAACCCCTATCCAA 59.156 55.000 0.00 0.00 33.59 3.53
395 396 1.214424 GCTGGCTAACCCCTATCCAAA 59.786 52.381 0.00 0.00 33.59 3.28
396 397 2.357777 GCTGGCTAACCCCTATCCAAAA 60.358 50.000 0.00 0.00 33.59 2.44
397 398 3.691311 GCTGGCTAACCCCTATCCAAAAT 60.691 47.826 0.00 0.00 33.59 1.82
398 399 4.546674 CTGGCTAACCCCTATCCAAAATT 58.453 43.478 0.00 0.00 33.59 1.82
399 400 5.701224 CTGGCTAACCCCTATCCAAAATTA 58.299 41.667 0.00 0.00 33.59 1.40
435 436 5.960704 TCATCTCCAATCCATTCATCCATT 58.039 37.500 0.00 0.00 0.00 3.16
537 558 5.307976 CCATCCACTCCTCAATAAGTATGGA 59.692 44.000 0.00 0.00 35.18 3.41
691 722 6.549433 AATGAAATGGTGACCATGCTAATT 57.451 33.333 19.32 8.10 44.40 1.40
697 728 2.887152 GGTGACCATGCTAATTGATCCC 59.113 50.000 0.00 0.00 0.00 3.85
768 799 8.400947 CCTCATGTTGTTAATGTAGAATTCAGG 58.599 37.037 8.44 0.00 0.00 3.86
771 802 7.447374 TGTTGTTAATGTAGAATTCAGGGTG 57.553 36.000 8.44 0.00 0.00 4.61
789 823 3.837355 GGTGGAGCCCAGATATTCATTT 58.163 45.455 0.00 0.00 32.34 2.32
831 865 5.105635 TGCATCCATGAGACCTTCAATTTTC 60.106 40.000 0.00 0.00 39.77 2.29
846 883 5.901552 TCAATTTTCGAACTGGAAAGCTTT 58.098 33.333 12.53 12.53 37.24 3.51
848 885 4.974368 TTTTCGAACTGGAAAGCTTTCA 57.026 36.364 33.88 21.29 38.92 2.69
869 906 5.771469 TCATGTTCAAGATTTGTGCGATTT 58.229 33.333 0.00 0.00 0.00 2.17
892 929 4.615949 TGTTGTTAATGCACACCATTCAC 58.384 39.130 0.00 0.00 42.99 3.18
897 958 1.171308 ATGCACACCATTCACTCTGC 58.829 50.000 0.00 0.00 0.00 4.26
922 983 3.571590 ACATGCTTGGGACCTTTGTTTA 58.428 40.909 4.44 0.00 0.00 2.01
931 992 6.155475 TGGGACCTTTGTTTACTTGAATTG 57.845 37.500 0.00 0.00 0.00 2.32
980 1044 2.056577 GACTTTTGCTTGTGATGCTGC 58.943 47.619 0.00 0.00 0.00 5.25
1942 3460 3.628032 TGAATCGCGGGTGCAAATTAATA 59.372 39.130 6.13 0.00 42.97 0.98
1967 3485 4.849329 GCTTCAGCTGCGGCATGC 62.849 66.667 21.93 9.90 46.70 4.06
2126 3787 0.478507 CCTCCCCAGTCTTTTGGTGT 59.521 55.000 0.00 0.00 36.45 4.16
2237 3908 0.746063 CAGGCAACAGCAAACCAGAA 59.254 50.000 0.00 0.00 41.41 3.02
2241 3912 2.615869 GCAACAGCAAACCAGAACAAA 58.384 42.857 0.00 0.00 0.00 2.83
2255 3926 5.222007 ACCAGAACAAAGATGAGATGGTCTT 60.222 40.000 0.00 0.00 39.03 3.01
2306 3977 4.099170 GACGCCAAGCAGCAGCAG 62.099 66.667 3.17 0.00 45.49 4.24
2318 3989 4.393155 CAGCAGCCGCCCTACACA 62.393 66.667 0.00 0.00 39.83 3.72
2319 3990 3.402681 AGCAGCCGCCCTACACAT 61.403 61.111 0.00 0.00 39.83 3.21
2320 3991 3.204827 GCAGCCGCCCTACACATG 61.205 66.667 0.00 0.00 0.00 3.21
2321 3992 3.204827 CAGCCGCCCTACACATGC 61.205 66.667 0.00 0.00 0.00 4.06
2322 3993 4.489771 AGCCGCCCTACACATGCC 62.490 66.667 0.00 0.00 0.00 4.40
2323 3994 4.794648 GCCGCCCTACACATGCCA 62.795 66.667 0.00 0.00 0.00 4.92
2406 4091 0.320596 GCAGAGCAGAACAGAGCAGT 60.321 55.000 0.00 0.00 0.00 4.40
2411 4096 0.237761 GCAGAACAGAGCAGTGCAAG 59.762 55.000 19.20 8.89 34.18 4.01
2548 4239 3.889196 TTGAATTCCGTTACTGCACAC 57.111 42.857 2.27 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.641645 TGGGAACTGGCCGCTGTG 62.642 66.667 0.00 0.00 0.00 3.66
52 53 4.335647 CTGGGAACTGGCCGCTGT 62.336 66.667 0.00 0.00 0.00 4.40
53 54 4.335647 ACTGGGAACTGGCCGCTG 62.336 66.667 0.00 0.00 0.00 5.18
54 55 4.021925 GACTGGGAACTGGCCGCT 62.022 66.667 0.00 0.00 0.00 5.52
59 60 4.760047 CCGGCGACTGGGAACTGG 62.760 72.222 9.30 0.00 0.00 4.00
60 61 4.003788 ACCGGCGACTGGGAACTG 62.004 66.667 9.30 0.00 0.00 3.16
61 62 4.003788 CACCGGCGACTGGGAACT 62.004 66.667 9.30 0.00 0.00 3.01
92 93 4.778415 CGACCACGGACGGCTGAG 62.778 72.222 2.64 0.00 35.72 3.35
97 98 4.657824 ACTTGCGACCACGGACGG 62.658 66.667 9.84 0.00 39.93 4.79
98 99 3.103911 GACTTGCGACCACGGACG 61.104 66.667 3.52 3.52 39.93 4.79
99 100 1.155424 TTTGACTTGCGACCACGGAC 61.155 55.000 0.00 0.00 39.93 4.79
100 101 0.878523 CTTTGACTTGCGACCACGGA 60.879 55.000 0.00 0.00 40.15 4.69
101 102 1.569493 CTTTGACTTGCGACCACGG 59.431 57.895 0.00 0.00 40.15 4.94
102 103 1.569493 CCTTTGACTTGCGACCACG 59.431 57.895 0.00 0.00 42.93 4.94
103 104 1.515521 CCCCTTTGACTTGCGACCAC 61.516 60.000 0.00 0.00 0.00 4.16
104 105 1.228124 CCCCTTTGACTTGCGACCA 60.228 57.895 0.00 0.00 0.00 4.02
105 106 0.536460 TTCCCCTTTGACTTGCGACC 60.536 55.000 0.00 0.00 0.00 4.79
106 107 1.314730 TTTCCCCTTTGACTTGCGAC 58.685 50.000 0.00 0.00 0.00 5.19
107 108 1.953686 CTTTTCCCCTTTGACTTGCGA 59.046 47.619 0.00 0.00 0.00 5.10
108 109 1.000274 CCTTTTCCCCTTTGACTTGCG 60.000 52.381 0.00 0.00 0.00 4.85
109 110 2.316108 TCCTTTTCCCCTTTGACTTGC 58.684 47.619 0.00 0.00 0.00 4.01
110 111 4.835056 AGAATCCTTTTCCCCTTTGACTTG 59.165 41.667 0.00 0.00 0.00 3.16
111 112 4.835056 CAGAATCCTTTTCCCCTTTGACTT 59.165 41.667 0.00 0.00 0.00 3.01
112 113 4.411013 CAGAATCCTTTTCCCCTTTGACT 58.589 43.478 0.00 0.00 0.00 3.41
113 114 3.511540 CCAGAATCCTTTTCCCCTTTGAC 59.488 47.826 0.00 0.00 0.00 3.18
114 115 3.401002 TCCAGAATCCTTTTCCCCTTTGA 59.599 43.478 0.00 0.00 0.00 2.69
115 116 3.766051 CTCCAGAATCCTTTTCCCCTTTG 59.234 47.826 0.00 0.00 0.00 2.77
116 117 3.402708 ACTCCAGAATCCTTTTCCCCTTT 59.597 43.478 0.00 0.00 0.00 3.11
117 118 2.996742 ACTCCAGAATCCTTTTCCCCTT 59.003 45.455 0.00 0.00 0.00 3.95
118 119 2.648838 ACTCCAGAATCCTTTTCCCCT 58.351 47.619 0.00 0.00 0.00 4.79
119 120 4.464947 CATACTCCAGAATCCTTTTCCCC 58.535 47.826 0.00 0.00 0.00 4.81
120 121 4.166144 TCCATACTCCAGAATCCTTTTCCC 59.834 45.833 0.00 0.00 0.00 3.97
121 122 5.104318 ACTCCATACTCCAGAATCCTTTTCC 60.104 44.000 0.00 0.00 0.00 3.13
122 123 5.995446 ACTCCATACTCCAGAATCCTTTTC 58.005 41.667 0.00 0.00 0.00 2.29
123 124 6.183347 CAACTCCATACTCCAGAATCCTTTT 58.817 40.000 0.00 0.00 0.00 2.27
124 125 5.339530 CCAACTCCATACTCCAGAATCCTTT 60.340 44.000 0.00 0.00 0.00 3.11
125 126 4.164988 CCAACTCCATACTCCAGAATCCTT 59.835 45.833 0.00 0.00 0.00 3.36
126 127 3.713764 CCAACTCCATACTCCAGAATCCT 59.286 47.826 0.00 0.00 0.00 3.24
127 128 3.456277 ACCAACTCCATACTCCAGAATCC 59.544 47.826 0.00 0.00 0.00 3.01
128 129 4.698575 GACCAACTCCATACTCCAGAATC 58.301 47.826 0.00 0.00 0.00 2.52
129 130 3.133003 CGACCAACTCCATACTCCAGAAT 59.867 47.826 0.00 0.00 0.00 2.40
130 131 2.496070 CGACCAACTCCATACTCCAGAA 59.504 50.000 0.00 0.00 0.00 3.02
131 132 2.100197 CGACCAACTCCATACTCCAGA 58.900 52.381 0.00 0.00 0.00 3.86
132 133 1.471676 GCGACCAACTCCATACTCCAG 60.472 57.143 0.00 0.00 0.00 3.86
133 134 0.535335 GCGACCAACTCCATACTCCA 59.465 55.000 0.00 0.00 0.00 3.86
134 135 0.824759 AGCGACCAACTCCATACTCC 59.175 55.000 0.00 0.00 0.00 3.85
135 136 1.927895 CAGCGACCAACTCCATACTC 58.072 55.000 0.00 0.00 0.00 2.59
136 137 0.108138 GCAGCGACCAACTCCATACT 60.108 55.000 0.00 0.00 0.00 2.12
137 138 0.391130 TGCAGCGACCAACTCCATAC 60.391 55.000 0.00 0.00 0.00 2.39
138 139 0.541392 ATGCAGCGACCAACTCCATA 59.459 50.000 0.00 0.00 0.00 2.74
139 140 0.745845 GATGCAGCGACCAACTCCAT 60.746 55.000 0.00 0.00 0.00 3.41
140 141 1.375908 GATGCAGCGACCAACTCCA 60.376 57.895 0.00 0.00 0.00 3.86
141 142 2.109126 GGATGCAGCGACCAACTCC 61.109 63.158 0.00 0.00 0.00 3.85
142 143 1.364626 CTGGATGCAGCGACCAACTC 61.365 60.000 0.00 0.00 33.14 3.01
143 144 1.376424 CTGGATGCAGCGACCAACT 60.376 57.895 0.00 0.00 33.14 3.16
144 145 2.401766 CCTGGATGCAGCGACCAAC 61.402 63.158 9.03 0.00 33.14 3.77
145 146 2.046023 CCTGGATGCAGCGACCAA 60.046 61.111 9.03 0.00 33.14 3.67
146 147 4.100084 CCCTGGATGCAGCGACCA 62.100 66.667 9.03 9.54 0.00 4.02
148 149 4.479993 AGCCCTGGATGCAGCGAC 62.480 66.667 9.03 0.00 0.00 5.19
149 150 4.166888 GAGCCCTGGATGCAGCGA 62.167 66.667 9.03 0.00 0.00 4.93
151 152 4.119363 TGGAGCCCTGGATGCAGC 62.119 66.667 9.03 0.00 0.00 5.25
152 153 2.192443 CTGGAGCCCTGGATGCAG 59.808 66.667 8.57 8.57 42.83 4.41
153 154 3.414193 CCTGGAGCCCTGGATGCA 61.414 66.667 10.45 0.00 44.09 3.96
154 155 4.891037 GCCTGGAGCCCTGGATGC 62.891 72.222 17.59 0.00 44.09 3.91
155 156 2.693896 GATGCCTGGAGCCCTGGATG 62.694 65.000 17.59 0.00 44.09 3.51
156 157 2.369291 ATGCCTGGAGCCCTGGAT 60.369 61.111 17.59 8.09 44.09 3.41
157 158 3.092511 GATGCCTGGAGCCCTGGA 61.093 66.667 17.59 6.56 44.09 3.86
158 159 4.559063 CGATGCCTGGAGCCCTGG 62.559 72.222 0.00 11.33 44.16 4.45
159 160 2.374830 CTACGATGCCTGGAGCCCTG 62.375 65.000 0.00 0.00 42.71 4.45
160 161 2.041922 TACGATGCCTGGAGCCCT 60.042 61.111 0.00 0.00 42.71 5.19
161 162 2.134287 TCTACGATGCCTGGAGCCC 61.134 63.158 0.00 0.00 42.71 5.19
162 163 1.068250 GTCTACGATGCCTGGAGCC 59.932 63.158 0.00 0.00 42.71 4.70
163 164 1.268352 CTAGTCTACGATGCCTGGAGC 59.732 57.143 0.00 0.00 44.14 4.70
164 165 2.550606 GACTAGTCTACGATGCCTGGAG 59.449 54.545 15.91 0.00 0.00 3.86
165 166 2.573369 GACTAGTCTACGATGCCTGGA 58.427 52.381 15.91 0.00 0.00 3.86
166 167 1.609555 GGACTAGTCTACGATGCCTGG 59.390 57.143 21.88 0.00 0.00 4.45
167 168 2.577700 AGGACTAGTCTACGATGCCTG 58.422 52.381 21.88 0.00 0.00 4.85
168 169 3.391955 ACTAGGACTAGTCTACGATGCCT 59.608 47.826 21.88 11.24 42.30 4.75
169 170 3.742385 ACTAGGACTAGTCTACGATGCC 58.258 50.000 21.88 3.89 42.30 4.40
170 171 4.815308 TCAACTAGGACTAGTCTACGATGC 59.185 45.833 21.88 4.01 44.96 3.91
171 172 8.604640 TTATCAACTAGGACTAGTCTACGATG 57.395 38.462 21.88 15.12 44.96 3.84
172 173 8.431222 ACTTATCAACTAGGACTAGTCTACGAT 58.569 37.037 21.88 15.89 44.96 3.73
173 174 7.710044 CACTTATCAACTAGGACTAGTCTACGA 59.290 40.741 21.88 10.66 44.96 3.43
174 175 7.041916 CCACTTATCAACTAGGACTAGTCTACG 60.042 44.444 21.88 12.35 44.96 3.51
175 176 7.229106 CCCACTTATCAACTAGGACTAGTCTAC 59.771 44.444 21.88 6.92 44.96 2.59
176 177 7.288560 CCCACTTATCAACTAGGACTAGTCTA 58.711 42.308 21.88 11.33 44.96 2.59
177 178 6.130569 CCCACTTATCAACTAGGACTAGTCT 58.869 44.000 21.88 10.81 44.96 3.24
178 179 5.221283 GCCCACTTATCAACTAGGACTAGTC 60.221 48.000 14.87 14.87 44.96 2.59
180 181 4.039366 GGCCCACTTATCAACTAGGACTAG 59.961 50.000 4.86 4.86 39.04 2.57
181 182 3.965347 GGCCCACTTATCAACTAGGACTA 59.035 47.826 0.00 0.00 0.00 2.59
182 183 2.772515 GGCCCACTTATCAACTAGGACT 59.227 50.000 0.00 0.00 0.00 3.85
183 184 2.772515 AGGCCCACTTATCAACTAGGAC 59.227 50.000 0.00 0.00 0.00 3.85
184 185 2.771943 CAGGCCCACTTATCAACTAGGA 59.228 50.000 0.00 0.00 0.00 2.94
185 186 2.505819 ACAGGCCCACTTATCAACTAGG 59.494 50.000 0.00 0.00 0.00 3.02
186 187 3.535561 CACAGGCCCACTTATCAACTAG 58.464 50.000 0.00 0.00 0.00 2.57
187 188 2.238646 CCACAGGCCCACTTATCAACTA 59.761 50.000 0.00 0.00 0.00 2.24
188 189 1.004745 CCACAGGCCCACTTATCAACT 59.995 52.381 0.00 0.00 0.00 3.16
189 190 1.463674 CCACAGGCCCACTTATCAAC 58.536 55.000 0.00 0.00 0.00 3.18
190 191 0.331278 CCCACAGGCCCACTTATCAA 59.669 55.000 0.00 0.00 0.00 2.57
191 192 1.998530 CCCACAGGCCCACTTATCA 59.001 57.895 0.00 0.00 0.00 2.15
192 193 4.986467 CCCACAGGCCCACTTATC 57.014 61.111 0.00 0.00 0.00 1.75
202 203 4.623932 ATGTATACATACAGCCCACAGG 57.376 45.455 16.85 0.00 45.46 4.00
203 204 5.337571 CCCTATGTATACATACAGCCCACAG 60.338 48.000 19.51 9.76 45.46 3.66
204 205 4.530553 CCCTATGTATACATACAGCCCACA 59.469 45.833 19.51 0.90 45.46 4.17
205 206 4.081087 CCCCTATGTATACATACAGCCCAC 60.081 50.000 19.51 0.00 45.46 4.61
206 207 4.101114 CCCCTATGTATACATACAGCCCA 58.899 47.826 19.51 2.25 45.46 5.36
207 208 4.101856 ACCCCTATGTATACATACAGCCC 58.898 47.826 19.51 0.00 45.46 5.19
208 209 5.956563 ACTACCCCTATGTATACATACAGCC 59.043 44.000 19.51 0.00 45.46 4.85
209 210 8.585471 TTACTACCCCTATGTATACATACAGC 57.415 38.462 19.51 0.00 45.46 4.40
268 269 4.323477 TTCGTGGGGGCGAACCTG 62.323 66.667 0.00 0.00 44.55 4.00
269 270 4.016706 CTTCGTGGGGGCGAACCT 62.017 66.667 0.00 0.00 44.55 3.50
271 272 4.699522 AGCTTCGTGGGGGCGAAC 62.700 66.667 0.00 0.00 44.55 3.95
272 273 4.388499 GAGCTTCGTGGGGGCGAA 62.388 66.667 0.00 1.08 46.78 4.70
287 288 3.123620 GCAGGAGCAACAGCGGAG 61.124 66.667 0.00 0.00 41.58 4.63
288 289 4.704833 GGCAGGAGCAACAGCGGA 62.705 66.667 0.00 0.00 44.61 5.54
290 291 2.338015 ATTGGCAGGAGCAACAGCG 61.338 57.895 0.00 0.00 44.61 5.18
291 292 1.214589 CATTGGCAGGAGCAACAGC 59.785 57.895 0.00 0.00 44.61 4.40
292 293 0.963962 AACATTGGCAGGAGCAACAG 59.036 50.000 0.00 0.00 44.61 3.16
293 294 1.340889 GAAACATTGGCAGGAGCAACA 59.659 47.619 0.00 0.00 44.61 3.33
294 295 1.337167 GGAAACATTGGCAGGAGCAAC 60.337 52.381 0.00 0.00 44.61 4.17
295 296 0.968405 GGAAACATTGGCAGGAGCAA 59.032 50.000 0.00 0.00 44.61 3.91
296 297 1.243342 CGGAAACATTGGCAGGAGCA 61.243 55.000 0.00 0.00 44.61 4.26
297 298 1.508088 CGGAAACATTGGCAGGAGC 59.492 57.895 0.00 0.00 41.10 4.70
298 299 1.315257 CCCGGAAACATTGGCAGGAG 61.315 60.000 0.73 0.00 0.00 3.69
299 300 1.304052 CCCGGAAACATTGGCAGGA 60.304 57.895 0.73 0.00 0.00 3.86
300 301 1.595093 GACCCGGAAACATTGGCAGG 61.595 60.000 0.73 0.00 0.00 4.85
301 302 0.609131 AGACCCGGAAACATTGGCAG 60.609 55.000 0.73 0.00 0.00 4.85
302 303 0.893270 CAGACCCGGAAACATTGGCA 60.893 55.000 0.73 0.00 0.00 4.92
303 304 1.883021 CAGACCCGGAAACATTGGC 59.117 57.895 0.73 0.00 0.00 4.52
304 305 0.609131 AGCAGACCCGGAAACATTGG 60.609 55.000 0.73 0.00 0.00 3.16
305 306 0.804989 GAGCAGACCCGGAAACATTG 59.195 55.000 0.73 0.00 0.00 2.82
306 307 0.322546 GGAGCAGACCCGGAAACATT 60.323 55.000 0.73 0.00 0.00 2.71
307 308 1.299976 GGAGCAGACCCGGAAACAT 59.700 57.895 0.73 0.00 0.00 2.71
308 309 2.747686 GGAGCAGACCCGGAAACA 59.252 61.111 0.73 0.00 0.00 2.83
309 310 2.434359 CGGAGCAGACCCGGAAAC 60.434 66.667 0.73 0.00 43.05 2.78
314 315 3.019003 ATTGTCCGGAGCAGACCCG 62.019 63.158 3.06 0.00 46.10 5.28
315 316 1.450312 CATTGTCCGGAGCAGACCC 60.450 63.158 3.06 0.00 0.00 4.46
316 317 0.321653 AACATTGTCCGGAGCAGACC 60.322 55.000 3.06 0.00 0.00 3.85
317 318 1.464997 GAAACATTGTCCGGAGCAGAC 59.535 52.381 3.06 0.00 0.00 3.51
318 319 1.808411 GAAACATTGTCCGGAGCAGA 58.192 50.000 3.06 0.00 0.00 4.26
319 320 0.443869 CGAAACATTGTCCGGAGCAG 59.556 55.000 3.06 0.00 0.00 4.24
320 321 0.953471 CCGAAACATTGTCCGGAGCA 60.953 55.000 19.69 3.03 44.29 4.26
321 322 1.794222 CCGAAACATTGTCCGGAGC 59.206 57.895 19.69 0.00 44.29 4.70
322 323 1.644786 GGCCGAAACATTGTCCGGAG 61.645 60.000 25.32 0.00 44.29 4.63
323 324 1.673009 GGCCGAAACATTGTCCGGA 60.673 57.895 25.32 0.00 44.29 5.14
324 325 1.644786 GAGGCCGAAACATTGTCCGG 61.645 60.000 19.94 19.94 44.34 5.14
325 326 1.644786 GGAGGCCGAAACATTGTCCG 61.645 60.000 0.00 0.00 0.00 4.79
326 327 2.180674 GGAGGCCGAAACATTGTCC 58.819 57.895 0.00 0.00 0.00 4.02
345 346 0.321653 ACTTGTCCGGAGCATTGTCC 60.322 55.000 3.06 0.00 0.00 4.02
346 347 1.523758 AACTTGTCCGGAGCATTGTC 58.476 50.000 3.06 0.00 0.00 3.18
347 348 1.981256 AAACTTGTCCGGAGCATTGT 58.019 45.000 3.06 5.96 0.00 2.71
348 349 3.689161 TCATAAACTTGTCCGGAGCATTG 59.311 43.478 3.06 5.35 0.00 2.82
349 350 3.950397 TCATAAACTTGTCCGGAGCATT 58.050 40.909 3.06 0.00 0.00 3.56
350 351 3.627395 TCATAAACTTGTCCGGAGCAT 57.373 42.857 3.06 0.00 0.00 3.79
351 352 3.197766 AGATCATAAACTTGTCCGGAGCA 59.802 43.478 3.06 3.03 0.00 4.26
352 353 3.557595 CAGATCATAAACTTGTCCGGAGC 59.442 47.826 3.06 0.00 0.00 4.70
353 354 4.122776 CCAGATCATAAACTTGTCCGGAG 58.877 47.826 3.06 0.00 0.00 4.63
354 355 3.681594 GCCAGATCATAAACTTGTCCGGA 60.682 47.826 0.00 0.00 0.00 5.14
355 356 2.614057 GCCAGATCATAAACTTGTCCGG 59.386 50.000 0.00 0.00 0.00 5.14
356 357 3.310774 CAGCCAGATCATAAACTTGTCCG 59.689 47.826 0.00 0.00 0.00 4.79
357 358 3.629398 CCAGCCAGATCATAAACTTGTCC 59.371 47.826 0.00 0.00 0.00 4.02
358 359 3.065925 GCCAGCCAGATCATAAACTTGTC 59.934 47.826 0.00 0.00 0.00 3.18
359 360 3.019564 GCCAGCCAGATCATAAACTTGT 58.980 45.455 0.00 0.00 0.00 3.16
360 361 3.285484 AGCCAGCCAGATCATAAACTTG 58.715 45.455 0.00 0.00 0.00 3.16
361 362 3.659183 AGCCAGCCAGATCATAAACTT 57.341 42.857 0.00 0.00 0.00 2.66
362 363 4.455606 GTTAGCCAGCCAGATCATAAACT 58.544 43.478 0.00 0.00 0.00 2.66
363 364 3.565902 GGTTAGCCAGCCAGATCATAAAC 59.434 47.826 0.00 0.00 34.09 2.01
364 365 3.435026 GGGTTAGCCAGCCAGATCATAAA 60.435 47.826 0.00 0.00 43.39 1.40
365 366 2.106511 GGGTTAGCCAGCCAGATCATAA 59.893 50.000 0.00 0.00 43.39 1.90
366 367 1.699634 GGGTTAGCCAGCCAGATCATA 59.300 52.381 0.00 0.00 43.39 2.15
367 368 0.475906 GGGTTAGCCAGCCAGATCAT 59.524 55.000 0.00 0.00 43.39 2.45
368 369 1.635817 GGGGTTAGCCAGCCAGATCA 61.636 60.000 1.94 0.00 46.10 2.92
369 370 1.149401 GGGGTTAGCCAGCCAGATC 59.851 63.158 1.94 0.00 46.10 2.75
370 371 0.030092 TAGGGGTTAGCCAGCCAGAT 60.030 55.000 1.94 0.00 46.10 2.90
371 372 0.030092 ATAGGGGTTAGCCAGCCAGA 60.030 55.000 1.94 0.00 46.10 3.86
372 373 0.398318 GATAGGGGTTAGCCAGCCAG 59.602 60.000 1.94 0.00 46.10 4.85
373 374 1.060163 GGATAGGGGTTAGCCAGCCA 61.060 60.000 1.94 0.00 46.10 4.75
374 375 1.060163 TGGATAGGGGTTAGCCAGCC 61.060 60.000 1.94 0.00 42.76 4.85
375 376 2.539983 TGGATAGGGGTTAGCCAGC 58.460 57.895 1.94 0.00 42.76 4.85
377 378 4.618378 AATTTTGGATAGGGGTTAGCCA 57.382 40.909 1.94 0.00 45.83 4.75
378 379 4.831155 GGTAATTTTGGATAGGGGTTAGCC 59.169 45.833 0.00 0.00 38.36 3.93
379 380 5.451354 TGGTAATTTTGGATAGGGGTTAGC 58.549 41.667 0.00 0.00 0.00 3.09
380 381 6.906848 TCTGGTAATTTTGGATAGGGGTTAG 58.093 40.000 0.00 0.00 0.00 2.34
381 382 6.911993 TCTGGTAATTTTGGATAGGGGTTA 57.088 37.500 0.00 0.00 0.00 2.85
382 383 5.806955 TCTGGTAATTTTGGATAGGGGTT 57.193 39.130 0.00 0.00 0.00 4.11
383 384 5.676811 AGATCTGGTAATTTTGGATAGGGGT 59.323 40.000 0.00 0.00 0.00 4.95
384 385 6.206180 AGATCTGGTAATTTTGGATAGGGG 57.794 41.667 0.00 0.00 0.00 4.79
385 386 8.001292 AGAAAGATCTGGTAATTTTGGATAGGG 58.999 37.037 0.00 0.00 33.59 3.53
386 387 8.986929 AGAAAGATCTGGTAATTTTGGATAGG 57.013 34.615 0.00 0.00 33.59 2.57
388 389 9.973661 TGAAGAAAGATCTGGTAATTTTGGATA 57.026 29.630 0.00 0.00 35.59 2.59
389 390 8.884124 TGAAGAAAGATCTGGTAATTTTGGAT 57.116 30.769 0.00 0.00 35.59 3.41
390 391 8.884124 ATGAAGAAAGATCTGGTAATTTTGGA 57.116 30.769 0.00 0.00 35.59 3.53
391 392 8.964772 AGATGAAGAAAGATCTGGTAATTTTGG 58.035 33.333 0.00 0.00 35.59 3.28
393 394 9.183368 GGAGATGAAGAAAGATCTGGTAATTTT 57.817 33.333 0.00 0.00 35.59 1.82
394 395 8.331740 TGGAGATGAAGAAAGATCTGGTAATTT 58.668 33.333 0.00 0.00 35.59 1.82
395 396 7.865820 TGGAGATGAAGAAAGATCTGGTAATT 58.134 34.615 0.00 0.00 35.59 1.40
396 397 7.443302 TGGAGATGAAGAAAGATCTGGTAAT 57.557 36.000 0.00 0.00 35.59 1.89
397 398 6.874278 TGGAGATGAAGAAAGATCTGGTAA 57.126 37.500 0.00 0.00 35.59 2.85
398 399 6.874278 TTGGAGATGAAGAAAGATCTGGTA 57.126 37.500 0.00 0.00 35.59 3.25
399 400 5.768980 TTGGAGATGAAGAAAGATCTGGT 57.231 39.130 0.00 0.00 35.59 4.00
572 593 2.658285 CAACATTCAAGACACAGCAGC 58.342 47.619 0.00 0.00 0.00 5.25
666 697 4.895668 AGCATGGTCACCATTTCATTTT 57.104 36.364 6.58 0.00 42.23 1.82
691 722 3.913799 TCCAGTTAAAAGGTCAGGGATCA 59.086 43.478 0.00 0.00 0.00 2.92
697 728 8.622948 AGAATACTTTCCAGTTAAAAGGTCAG 57.377 34.615 0.00 0.00 37.91 3.51
728 759 4.864334 GAGGGCAGGGCATCCACG 62.864 72.222 0.00 0.00 34.83 4.94
768 799 3.515602 AATGAATATCTGGGCTCCACC 57.484 47.619 0.00 0.00 37.93 4.61
771 802 5.859205 AACAAAATGAATATCTGGGCTCC 57.141 39.130 0.00 0.00 0.00 4.70
800 834 4.858850 AGGTCTCATGGATGCATGTTAAA 58.141 39.130 24.37 6.62 34.39 1.52
801 835 4.508551 AGGTCTCATGGATGCATGTTAA 57.491 40.909 24.37 10.22 34.39 2.01
802 836 4.080413 TGAAGGTCTCATGGATGCATGTTA 60.080 41.667 24.37 12.49 34.39 2.41
803 837 3.285484 GAAGGTCTCATGGATGCATGTT 58.715 45.455 24.37 12.54 34.39 2.71
804 838 2.240414 TGAAGGTCTCATGGATGCATGT 59.760 45.455 24.37 6.29 34.39 3.21
807 841 3.657398 ATTGAAGGTCTCATGGATGCA 57.343 42.857 0.00 0.00 32.78 3.96
819 853 5.736207 GCTTTCCAGTTCGAAAATTGAAGGT 60.736 40.000 0.00 0.00 31.56 3.50
831 865 3.904136 ACATGAAAGCTTTCCAGTTCG 57.096 42.857 31.14 17.16 36.36 3.95
846 883 5.375417 AATCGCACAAATCTTGAACATGA 57.625 34.783 0.00 0.00 0.00 3.07
848 885 5.984926 ACAAAATCGCACAAATCTTGAACAT 59.015 32.000 0.00 0.00 0.00 2.71
892 929 0.809385 CCCAAGCATGTCAAGCAGAG 59.191 55.000 2.46 0.00 0.00 3.35
897 958 1.915141 AAGGTCCCAAGCATGTCAAG 58.085 50.000 0.00 0.00 0.00 3.02
922 983 7.309438 GCAAGATTTAAGGAGGTCAATTCAAGT 60.309 37.037 0.00 0.00 0.00 3.16
931 992 7.201741 GGATTAACAGCAAGATTTAAGGAGGTC 60.202 40.741 0.00 0.00 0.00 3.85
980 1044 3.063510 TGGCAGACAAGAATCCTGAAG 57.936 47.619 0.00 0.00 0.00 3.02
2093 3750 4.202441 CTGGGGAGGATACAAGATGTTTG 58.798 47.826 0.00 0.00 41.41 2.93
2096 3754 3.041946 GACTGGGGAGGATACAAGATGT 58.958 50.000 0.00 0.00 41.41 3.06
2105 3765 1.355720 CACCAAAAGACTGGGGAGGAT 59.644 52.381 0.00 0.00 43.19 3.24
2106 3766 0.771127 CACCAAAAGACTGGGGAGGA 59.229 55.000 0.00 0.00 43.19 3.71
2132 3793 8.292444 AGCTTCTTGCACCATACAATATTTAA 57.708 30.769 0.00 0.00 45.94 1.52
2133 3794 7.880160 AGCTTCTTGCACCATACAATATTTA 57.120 32.000 0.00 0.00 45.94 1.40
2134 3795 6.780457 AGCTTCTTGCACCATACAATATTT 57.220 33.333 0.00 0.00 45.94 1.40
2135 3796 8.469309 AATAGCTTCTTGCACCATACAATATT 57.531 30.769 0.00 0.00 45.94 1.28
2136 3797 7.720957 TGAATAGCTTCTTGCACCATACAATAT 59.279 33.333 0.00 0.00 45.94 1.28
2137 3798 7.053498 TGAATAGCTTCTTGCACCATACAATA 58.947 34.615 0.00 0.00 45.94 1.90
2224 3895 3.953612 TCATCTTTGTTCTGGTTTGCTGT 59.046 39.130 0.00 0.00 0.00 4.40
2237 3908 3.350833 GCCAAGACCATCTCATCTTTGT 58.649 45.455 0.00 0.00 32.77 2.83
2241 3912 1.890552 AGGCCAAGACCATCTCATCT 58.109 50.000 5.01 0.00 0.00 2.90
2255 3926 3.114606 TCTGAATCAACATCCTAGGCCA 58.885 45.455 5.01 0.00 0.00 5.36
2305 3976 4.489771 GGCATGTGTAGGGCGGCT 62.490 66.667 9.56 0.00 0.00 5.52
2306 3977 4.794648 TGGCATGTGTAGGGCGGC 62.795 66.667 0.00 0.00 35.73 6.53
2307 3978 1.447317 GAATGGCATGTGTAGGGCGG 61.447 60.000 0.00 0.00 35.73 6.13
2322 3993 1.336440 AGTCGCTCTCCATCGAGAATG 59.664 52.381 0.00 0.00 44.62 2.67
2323 3994 1.336440 CAGTCGCTCTCCATCGAGAAT 59.664 52.381 0.00 0.00 44.62 2.40
2345 4030 4.703897 TGCTTCTACAACTTAACTGTGCT 58.296 39.130 0.00 0.00 0.00 4.40
2383 4068 1.476085 GCTCTGTTCTGCTCTGCTAGA 59.524 52.381 0.00 0.00 0.00 2.43
2406 4091 1.409241 GCCTGATCCCTGATTCTTGCA 60.409 52.381 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.