Multiple sequence alignment - TraesCS7D01G356700

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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 TraesCS7D01G356700 chr7D 100.000 3422 0 0 1 3422 459874744 459871323 0.000000e+00 6320.0
1 TraesCS7D01G356700 chr7D 93.884 327 18 2 1 326 573961417 573961742 3.070000e-135 492.0
2 TraesCS7D01G356700 chr7D 93.030 330 22 1 1 329 53323918 53323589 6.640000e-132 481.0
3 TraesCS7D01G356700 chr7D 75.477 367 74 13 2063 2421 47910871 47911229 7.600000e-37 165.0
4 TraesCS7D01G356700 chr7D 89.011 91 6 1 2932 3022 44761848 44761934 3.610000e-20 110.0
5 TraesCS7D01G356700 chr7D 88.298 94 7 1 2932 3025 307154214 307154125 3.610000e-20 110.0
6 TraesCS7D01G356700 chr7D 88.298 94 7 1 2932 3025 368996384 368996295 3.610000e-20 110.0
7 TraesCS7D01G356700 chr7B 96.517 2814 78 12 478 3281 482176686 482173883 0.000000e+00 4636.0
8 TraesCS7D01G356700 chr7B 93.913 115 7 0 3306 3420 482173686 482173572 1.260000e-39 174.0
9 TraesCS7D01G356700 chr7A 94.191 2496 86 23 328 2793 539651142 539653608 0.000000e+00 3751.0
10 TraesCS7D01G356700 chr7A 85.106 329 28 9 3102 3414 539654640 539654963 1.980000e-82 316.0
11 TraesCS7D01G356700 chr7A 89.011 91 6 1 2932 3022 91359736 91359822 3.610000e-20 110.0
12 TraesCS7D01G356700 chr7A 100.000 34 0 0 361 394 65619110 65619143 2.850000e-06 63.9
13 TraesCS7D01G356700 chr5D 93.884 327 19 1 1 327 494292794 494293119 3.070000e-135 492.0
14 TraesCS7D01G356700 chr3D 93.865 326 20 0 1 326 32372403 32372728 3.070000e-135 492.0
15 TraesCS7D01G356700 chr5B 93.865 326 18 2 1 326 549165227 549165550 1.100000e-134 490.0
16 TraesCS7D01G356700 chr5B 89.552 67 7 0 328 394 262058106 262058040 6.080000e-13 86.1
17 TraesCS7D01G356700 chr4D 93.519 324 21 0 3 326 388109615 388109292 1.850000e-132 483.0
18 TraesCS7D01G356700 chr4D 87.234 94 8 1 2932 3025 167023639 167023550 1.680000e-18 104.0
19 TraesCS7D01G356700 chr2D 93.009 329 23 0 1 329 588210535 588210207 6.640000e-132 481.0
20 TraesCS7D01G356700 chr2D 92.683 328 24 0 1 328 599600868 599601195 1.110000e-129 473.0
21 TraesCS7D01G356700 chr1D 93.252 326 21 1 1 326 492587794 492587470 2.390000e-131 479.0
22 TraesCS7D01G356700 chr1D 77.778 180 38 2 328 506 223753878 223753700 3.610000e-20 110.0
23 TraesCS7D01G356700 chr6D 76.783 715 147 14 1267 1971 157167882 157167177 1.930000e-102 383.0
24 TraesCS7D01G356700 chr6D 88.172 93 7 1 2933 3025 153952944 153952856 1.300000e-19 108.0
25 TraesCS7D01G356700 chr6D 87.912 91 7 1 2932 3022 429813344 429813430 1.680000e-18 104.0
26 TraesCS7D01G356700 chr6A 76.224 715 151 16 1267 1971 215528184 215528889 9.030000e-96 361.0
27 TraesCS7D01G356700 chr6B 75.978 716 151 16 1267 1971 280049696 280048991 1.950000e-92 350.0
28 TraesCS7D01G356700 chr1A 88.298 94 7 1 2932 3025 430607200 430607111 3.610000e-20 110.0


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 TraesCS7D01G356700 chr7D 459871323 459874744 3421 True 6320.0 6320 100.0000 1 3422 1 chr7D.!!$R4 3421
1 TraesCS7D01G356700 chr7B 482173572 482176686 3114 True 2405.0 4636 95.2150 478 3420 2 chr7B.!!$R1 2942
2 TraesCS7D01G356700 chr7A 539651142 539654963 3821 False 2033.5 3751 89.6485 328 3414 2 chr7A.!!$F3 3086
3 TraesCS7D01G356700 chr6D 157167177 157167882 705 True 383.0 383 76.7830 1267 1971 1 chr6D.!!$R2 704
4 TraesCS7D01G356700 chr6A 215528184 215528889 705 False 361.0 361 76.2240 1267 1971 1 chr6A.!!$F1 704
5 TraesCS7D01G356700 chr6B 280048991 280049696 705 True 350.0 350 75.9780 1267 1971 1 chr6B.!!$R1 704

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
314 315 0.037605 CCGAAGCGTGGTAGTTCCTT 60.038 55.0 0.00 0.0 37.07 3.36 F
317 318 0.107831 AAGCGTGGTAGTTCCTTGCA 59.892 50.0 5.82 0.0 38.71 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2070 1.611673 CCCCATCGGCACCTGATAATC 60.612 57.143 0.0 0.0 0.00 1.75 R
2561 2592 2.271944 ACAAGAACAACCTACAGGGC 57.728 50.000 0.0 0.0 40.27 5.19 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
21 22 4.500116 GGCGGCGACTGGAGAGAC 62.500 72.222 12.98 0.00 0.00 3.36
22 23 4.838486 GCGGCGACTGGAGAGACG 62.838 72.222 12.98 0.00 39.89 4.18
23 24 3.125573 CGGCGACTGGAGAGACGA 61.126 66.667 0.00 0.00 39.36 4.20
24 25 2.795297 GGCGACTGGAGAGACGAG 59.205 66.667 0.00 0.00 39.36 4.18
25 26 2.766400 GGCGACTGGAGAGACGAGG 61.766 68.421 0.00 0.00 39.36 4.63
26 27 2.766400 GCGACTGGAGAGACGAGGG 61.766 68.421 0.00 0.00 39.36 4.30
27 28 2.766400 CGACTGGAGAGACGAGGGC 61.766 68.421 0.00 0.00 39.36 5.19
28 29 2.752238 ACTGGAGAGACGAGGGCG 60.752 66.667 0.00 0.00 44.79 6.13
29 30 2.438614 CTGGAGAGACGAGGGCGA 60.439 66.667 0.00 0.00 41.64 5.54
30 31 1.826054 CTGGAGAGACGAGGGCGAT 60.826 63.158 0.00 0.00 41.64 4.58
31 32 2.069465 CTGGAGAGACGAGGGCGATG 62.069 65.000 0.00 0.00 41.64 3.84
32 33 2.725008 GAGAGACGAGGGCGATGG 59.275 66.667 0.00 0.00 41.64 3.51
33 34 2.835431 AGAGACGAGGGCGATGGG 60.835 66.667 0.00 0.00 41.64 4.00
34 35 3.917760 GAGACGAGGGCGATGGGG 61.918 72.222 0.00 0.00 41.64 4.96
43 44 4.292178 GCGATGGGGCGAGGAGAG 62.292 72.222 0.00 0.00 0.00 3.20
44 45 3.610669 CGATGGGGCGAGGAGAGG 61.611 72.222 0.00 0.00 0.00 3.69
45 46 3.237741 GATGGGGCGAGGAGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
46 47 3.758133 GATGGGGCGAGGAGAGGGA 62.758 68.421 0.00 0.00 0.00 4.20
47 48 4.779733 TGGGGCGAGGAGAGGGAC 62.780 72.222 0.00 0.00 0.00 4.46
48 49 4.779733 GGGGCGAGGAGAGGGACA 62.780 72.222 0.00 0.00 0.00 4.02
49 50 3.151022 GGGCGAGGAGAGGGACAG 61.151 72.222 0.00 0.00 0.00 3.51
50 51 2.043852 GGCGAGGAGAGGGACAGA 60.044 66.667 0.00 0.00 0.00 3.41
51 52 2.124693 GGCGAGGAGAGGGACAGAG 61.125 68.421 0.00 0.00 0.00 3.35
52 53 1.379309 GCGAGGAGAGGGACAGAGT 60.379 63.158 0.00 0.00 0.00 3.24
53 54 1.662438 GCGAGGAGAGGGACAGAGTG 61.662 65.000 0.00 0.00 0.00 3.51
54 55 1.662438 CGAGGAGAGGGACAGAGTGC 61.662 65.000 0.00 0.00 0.00 4.40
55 56 1.662438 GAGGAGAGGGACAGAGTGCG 61.662 65.000 0.00 0.00 0.00 5.34
56 57 2.716017 GGAGAGGGACAGAGTGCGG 61.716 68.421 0.00 0.00 0.00 5.69
57 58 3.363844 GAGAGGGACAGAGTGCGGC 62.364 68.421 0.00 0.00 0.00 6.53
58 59 3.695606 GAGGGACAGAGTGCGGCA 61.696 66.667 0.00 0.00 0.00 5.69
59 60 3.655810 GAGGGACAGAGTGCGGCAG 62.656 68.421 1.18 0.00 0.00 4.85
60 61 4.767255 GGGACAGAGTGCGGCAGG 62.767 72.222 1.18 0.00 0.00 4.85
62 63 4.385405 GACAGAGTGCGGCAGGCT 62.385 66.667 1.18 0.00 44.05 4.58
63 64 4.385405 ACAGAGTGCGGCAGGCTC 62.385 66.667 1.18 7.77 44.05 4.70
73 74 4.660938 GCAGGCTCCGGTTGGGTT 62.661 66.667 0.00 0.00 37.00 4.11
74 75 2.359975 CAGGCTCCGGTTGGGTTC 60.360 66.667 0.00 0.00 37.00 3.62
75 76 4.016706 AGGCTCCGGTTGGGTTCG 62.017 66.667 0.00 0.00 37.00 3.95
76 77 4.011517 GGCTCCGGTTGGGTTCGA 62.012 66.667 0.00 0.00 37.00 3.71
77 78 2.741211 GCTCCGGTTGGGTTCGAC 60.741 66.667 0.00 0.00 37.00 4.20
78 79 2.047560 CTCCGGTTGGGTTCGACC 60.048 66.667 0.00 0.00 42.76 4.79
82 83 2.357881 GGTTGGGTTCGACCGGAC 60.358 66.667 9.46 0.00 39.83 4.79
83 84 2.357881 GTTGGGTTCGACCGGACC 60.358 66.667 9.46 11.30 39.83 4.46
84 85 3.628982 TTGGGTTCGACCGGACCC 61.629 66.667 27.64 27.64 39.83 4.46
95 96 3.151710 CGGACCCGGCTACATGGA 61.152 66.667 0.00 0.00 35.56 3.41
96 97 2.822399 GGACCCGGCTACATGGAG 59.178 66.667 0.00 0.00 0.00 3.86
97 98 2.109181 GACCCGGCTACATGGAGC 59.891 66.667 22.57 22.57 42.05 4.70
98 99 3.792053 GACCCGGCTACATGGAGCG 62.792 68.421 23.61 17.66 43.83 5.03
99 100 3.536917 CCCGGCTACATGGAGCGA 61.537 66.667 23.61 0.00 43.83 4.93
100 101 2.279517 CCGGCTACATGGAGCGAC 60.280 66.667 23.61 9.92 43.83 5.19
101 102 2.279517 CGGCTACATGGAGCGACC 60.280 66.667 23.61 9.17 43.83 4.79
109 110 3.691342 TGGAGCGACCAAGACGGG 61.691 66.667 3.31 0.00 46.75 5.28
110 111 3.692406 GGAGCGACCAAGACGGGT 61.692 66.667 0.00 0.00 46.02 5.28
111 112 2.432628 GAGCGACCAAGACGGGTG 60.433 66.667 0.00 0.00 42.53 4.61
112 113 4.681978 AGCGACCAAGACGGGTGC 62.682 66.667 0.00 0.00 42.53 5.01
114 115 4.351938 CGACCAAGACGGGTGCGA 62.352 66.667 0.00 0.00 42.53 5.10
115 116 2.432628 GACCAAGACGGGTGCGAG 60.433 66.667 0.00 0.00 42.53 5.03
116 117 2.915659 ACCAAGACGGGTGCGAGA 60.916 61.111 0.00 0.00 40.44 4.04
117 118 2.125912 CCAAGACGGGTGCGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
118 119 2.651361 CAAGACGGGTGCGAGAGT 59.349 61.111 0.00 0.00 0.00 3.24
119 120 1.006102 CAAGACGGGTGCGAGAGTT 60.006 57.895 0.00 0.00 0.00 3.01
120 121 0.242825 CAAGACGGGTGCGAGAGTTA 59.757 55.000 0.00 0.00 0.00 2.24
121 122 0.243095 AAGACGGGTGCGAGAGTTAC 59.757 55.000 0.00 0.00 0.00 2.50
122 123 1.153881 GACGGGTGCGAGAGTTACC 60.154 63.158 0.00 0.00 38.96 2.85
123 124 2.202570 CGGGTGCGAGAGTTACCG 60.203 66.667 0.00 0.00 40.05 4.02
124 125 2.693762 CGGGTGCGAGAGTTACCGA 61.694 63.158 0.00 0.00 42.19 4.69
125 126 1.139095 GGGTGCGAGAGTTACCGAG 59.861 63.158 0.00 0.00 40.05 4.63
126 127 1.516603 GGTGCGAGAGTTACCGAGC 60.517 63.158 0.00 0.00 32.48 5.03
127 128 1.868251 GTGCGAGAGTTACCGAGCG 60.868 63.158 0.00 0.00 0.00 5.03
128 129 2.278013 GCGAGAGTTACCGAGCGG 60.278 66.667 7.48 7.48 42.03 5.52
129 130 2.408022 CGAGAGTTACCGAGCGGG 59.592 66.667 14.07 0.00 43.62 6.13
161 162 4.248842 CCACCGTGGCACCTGACA 62.249 66.667 12.86 0.00 0.00 3.58
166 167 2.972505 GTGGCACCTGACACGTGG 60.973 66.667 21.57 4.01 45.07 4.94
167 168 4.248842 TGGCACCTGACACGTGGG 62.249 66.667 21.57 14.04 0.00 4.61
173 174 4.082523 CTGACACGTGGGCCCGAT 62.083 66.667 21.57 0.82 0.00 4.18
174 175 2.680707 TGACACGTGGGCCCGATA 60.681 61.111 21.57 0.00 0.00 2.92
175 176 2.106332 GACACGTGGGCCCGATAG 59.894 66.667 21.57 10.75 0.00 2.08
190 191 3.539431 CGATAGGTCAGATACGTGGTC 57.461 52.381 0.00 0.00 0.00 4.02
191 192 2.876550 CGATAGGTCAGATACGTGGTCA 59.123 50.000 0.00 0.00 0.00 4.02
192 193 3.314357 CGATAGGTCAGATACGTGGTCAA 59.686 47.826 0.00 0.00 0.00 3.18
193 194 4.023107 CGATAGGTCAGATACGTGGTCAAT 60.023 45.833 0.00 0.00 0.00 2.57
194 195 5.180680 CGATAGGTCAGATACGTGGTCAATA 59.819 44.000 0.00 0.00 0.00 1.90
195 196 4.650754 AGGTCAGATACGTGGTCAATAC 57.349 45.455 0.00 0.00 0.00 1.89
196 197 3.066342 AGGTCAGATACGTGGTCAATACG 59.934 47.826 0.00 0.00 46.31 3.06
197 198 2.787680 GTCAGATACGTGGTCAATACGC 59.212 50.000 0.00 0.00 44.87 4.42
198 199 1.779157 CAGATACGTGGTCAATACGCG 59.221 52.381 3.53 3.53 44.87 6.01
199 200 0.501435 GATACGTGGTCAATACGCGC 59.499 55.000 5.73 0.00 44.87 6.86
200 201 0.101759 ATACGTGGTCAATACGCGCT 59.898 50.000 5.73 0.00 44.87 5.92
201 202 0.109179 TACGTGGTCAATACGCGCTT 60.109 50.000 5.73 0.00 44.87 4.68
202 203 0.109179 ACGTGGTCAATACGCGCTTA 60.109 50.000 5.73 0.00 44.87 3.09
203 204 1.205657 CGTGGTCAATACGCGCTTAT 58.794 50.000 5.73 2.38 34.56 1.73
204 205 2.223548 ACGTGGTCAATACGCGCTTATA 60.224 45.455 5.73 0.00 44.87 0.98
205 206 2.152489 CGTGGTCAATACGCGCTTATAC 59.848 50.000 5.73 2.76 34.56 1.47
206 207 2.152489 GTGGTCAATACGCGCTTATACG 59.848 50.000 5.73 2.20 0.00 3.06
207 208 1.717645 GGTCAATACGCGCTTATACGG 59.282 52.381 5.73 0.89 0.00 4.02
208 209 1.123756 GTCAATACGCGCTTATACGGC 59.876 52.381 5.73 0.00 0.00 5.68
209 210 1.001048 TCAATACGCGCTTATACGGCT 60.001 47.619 5.73 0.00 0.00 5.52
210 211 1.124297 CAATACGCGCTTATACGGCTG 59.876 52.381 5.73 0.00 0.00 4.85
211 212 0.313043 ATACGCGCTTATACGGCTGT 59.687 50.000 5.73 2.42 0.00 4.40
212 213 0.317269 TACGCGCTTATACGGCTGTC 60.317 55.000 5.73 0.00 0.00 3.51
213 214 1.587876 CGCGCTTATACGGCTGTCA 60.588 57.895 0.00 0.00 0.00 3.58
214 215 1.540607 CGCGCTTATACGGCTGTCAG 61.541 60.000 0.00 0.00 0.00 3.51
215 216 0.248907 GCGCTTATACGGCTGTCAGA 60.249 55.000 0.00 0.00 0.00 3.27
216 217 1.478137 CGCTTATACGGCTGTCAGAC 58.522 55.000 0.00 0.00 0.00 3.51
217 218 1.854227 GCTTATACGGCTGTCAGACC 58.146 55.000 0.00 3.66 0.00 3.85
218 219 1.136305 GCTTATACGGCTGTCAGACCA 59.864 52.381 0.00 0.00 0.00 4.02
219 220 2.224066 GCTTATACGGCTGTCAGACCAT 60.224 50.000 0.00 0.00 0.00 3.55
220 221 3.741388 GCTTATACGGCTGTCAGACCATT 60.741 47.826 0.00 0.00 0.00 3.16
221 222 4.442706 CTTATACGGCTGTCAGACCATTT 58.557 43.478 0.00 0.00 0.00 2.32
222 223 2.851263 TACGGCTGTCAGACCATTTT 57.149 45.000 0.00 0.00 0.00 1.82
223 224 1.238439 ACGGCTGTCAGACCATTTTG 58.762 50.000 3.32 0.00 0.00 2.44
224 225 0.109597 CGGCTGTCAGACCATTTTGC 60.110 55.000 3.32 0.00 0.00 3.68
225 226 0.961019 GGCTGTCAGACCATTTTGCA 59.039 50.000 3.32 0.00 0.00 4.08
226 227 1.340889 GGCTGTCAGACCATTTTGCAA 59.659 47.619 3.32 0.00 0.00 4.08
227 228 2.397549 GCTGTCAGACCATTTTGCAAC 58.602 47.619 3.32 0.00 0.00 4.17
228 229 2.223782 GCTGTCAGACCATTTTGCAACA 60.224 45.455 3.32 0.00 0.00 3.33
229 230 3.374745 CTGTCAGACCATTTTGCAACAC 58.625 45.455 0.00 0.00 0.00 3.32
230 231 3.023119 TGTCAGACCATTTTGCAACACT 58.977 40.909 0.00 0.00 0.00 3.55
231 232 3.446873 TGTCAGACCATTTTGCAACACTT 59.553 39.130 0.00 0.00 0.00 3.16
232 233 4.642437 TGTCAGACCATTTTGCAACACTTA 59.358 37.500 0.00 0.00 0.00 2.24
233 234 5.215160 GTCAGACCATTTTGCAACACTTAG 58.785 41.667 0.00 0.00 0.00 2.18
234 235 4.278170 TCAGACCATTTTGCAACACTTAGG 59.722 41.667 0.00 0.00 0.00 2.69
235 236 3.005791 AGACCATTTTGCAACACTTAGGC 59.994 43.478 0.00 0.00 0.00 3.93
236 237 2.965147 ACCATTTTGCAACACTTAGGCT 59.035 40.909 0.00 0.00 0.00 4.58
237 238 3.387699 ACCATTTTGCAACACTTAGGCTT 59.612 39.130 0.00 0.00 0.00 4.35
238 239 4.586841 ACCATTTTGCAACACTTAGGCTTA 59.413 37.500 0.00 0.00 0.00 3.09
239 240 5.163513 CCATTTTGCAACACTTAGGCTTAG 58.836 41.667 0.00 0.00 0.00 2.18
240 241 5.278957 CCATTTTGCAACACTTAGGCTTAGT 60.279 40.000 0.00 0.00 0.00 2.24
241 242 4.829064 TTTGCAACACTTAGGCTTAGTG 57.171 40.909 27.00 27.00 46.56 2.74
249 250 5.148651 CACTTAGGCTTAGTGTTGGTACT 57.851 43.478 22.13 0.00 38.51 2.73
250 251 4.929808 CACTTAGGCTTAGTGTTGGTACTG 59.070 45.833 22.13 0.00 38.51 2.74
251 252 2.474410 AGGCTTAGTGTTGGTACTGC 57.526 50.000 0.00 0.00 32.19 4.40
252 253 1.697432 AGGCTTAGTGTTGGTACTGCA 59.303 47.619 0.00 0.00 32.19 4.41
253 254 2.305927 AGGCTTAGTGTTGGTACTGCAT 59.694 45.455 0.00 0.00 32.19 3.96
254 255 2.420022 GGCTTAGTGTTGGTACTGCATG 59.580 50.000 0.00 0.00 32.19 4.06
255 256 2.420022 GCTTAGTGTTGGTACTGCATGG 59.580 50.000 0.00 0.00 32.19 3.66
256 257 2.107950 TAGTGTTGGTACTGCATGGC 57.892 50.000 0.00 0.00 32.19 4.40
257 258 0.110295 AGTGTTGGTACTGCATGGCA 59.890 50.000 0.00 0.00 36.92 4.92
258 259 0.958091 GTGTTGGTACTGCATGGCAA 59.042 50.000 0.00 0.00 38.41 4.52
259 260 1.339610 GTGTTGGTACTGCATGGCAAA 59.660 47.619 0.00 0.00 38.41 3.68
260 261 2.034878 TGTTGGTACTGCATGGCAAAA 58.965 42.857 0.00 0.00 38.41 2.44
261 262 2.432146 TGTTGGTACTGCATGGCAAAAA 59.568 40.909 0.00 0.00 38.41 1.94
280 281 4.595762 AAAAAGTGACTAGCGGTACTGA 57.404 40.909 5.68 0.00 0.00 3.41
281 282 4.803098 AAAAGTGACTAGCGGTACTGAT 57.197 40.909 5.68 0.47 0.00 2.90
282 283 4.803098 AAAGTGACTAGCGGTACTGATT 57.197 40.909 5.68 0.00 0.00 2.57
283 284 4.373348 AAGTGACTAGCGGTACTGATTC 57.627 45.455 5.68 0.00 0.00 2.52
284 285 2.355132 AGTGACTAGCGGTACTGATTCG 59.645 50.000 5.68 0.00 0.00 3.34
285 286 2.097142 GTGACTAGCGGTACTGATTCGT 59.903 50.000 5.68 0.00 0.00 3.85
286 287 2.353889 TGACTAGCGGTACTGATTCGTC 59.646 50.000 5.68 10.09 0.00 4.20
287 288 2.353889 GACTAGCGGTACTGATTCGTCA 59.646 50.000 5.68 0.00 0.00 4.35
288 289 2.097142 ACTAGCGGTACTGATTCGTCAC 59.903 50.000 5.68 0.00 0.00 3.67
289 290 0.885879 AGCGGTACTGATTCGTCACA 59.114 50.000 5.68 0.00 0.00 3.58
290 291 1.271379 AGCGGTACTGATTCGTCACAA 59.729 47.619 5.68 0.00 0.00 3.33
291 292 1.389106 GCGGTACTGATTCGTCACAAC 59.611 52.381 5.68 0.00 0.00 3.32
292 293 2.668250 CGGTACTGATTCGTCACAACA 58.332 47.619 0.00 0.00 0.00 3.33
293 294 3.250744 CGGTACTGATTCGTCACAACAT 58.749 45.455 0.00 0.00 0.00 2.71
294 295 3.060761 CGGTACTGATTCGTCACAACATG 59.939 47.826 0.00 0.00 0.00 3.21
295 296 3.181520 GGTACTGATTCGTCACAACATGC 60.182 47.826 0.00 0.00 0.00 4.06
296 297 1.806542 ACTGATTCGTCACAACATGCC 59.193 47.619 0.00 0.00 0.00 4.40
297 298 0.795698 TGATTCGTCACAACATGCCG 59.204 50.000 0.00 0.00 0.00 5.69
298 299 1.075542 GATTCGTCACAACATGCCGA 58.924 50.000 0.00 0.00 0.00 5.54
299 300 1.463056 GATTCGTCACAACATGCCGAA 59.537 47.619 0.00 0.00 41.16 4.30
300 301 0.865111 TTCGTCACAACATGCCGAAG 59.135 50.000 0.00 0.00 33.13 3.79
301 302 1.154413 CGTCACAACATGCCGAAGC 60.154 57.895 0.00 0.00 40.48 3.86
302 303 1.154413 GTCACAACATGCCGAAGCG 60.154 57.895 0.00 0.00 44.31 4.68
303 304 1.596752 TCACAACATGCCGAAGCGT 60.597 52.632 0.00 0.00 44.31 5.07
309 310 2.978824 ATGCCGAAGCGTGGTAGT 59.021 55.556 0.00 0.00 44.31 2.73
310 311 1.295423 ATGCCGAAGCGTGGTAGTT 59.705 52.632 0.00 0.00 44.31 2.24
311 312 0.739813 ATGCCGAAGCGTGGTAGTTC 60.740 55.000 0.00 0.00 44.31 3.01
312 313 2.098831 GCCGAAGCGTGGTAGTTCC 61.099 63.158 0.00 0.00 0.00 3.62
313 314 1.590147 CCGAAGCGTGGTAGTTCCT 59.410 57.895 0.00 0.00 37.07 3.36
314 315 0.037605 CCGAAGCGTGGTAGTTCCTT 60.038 55.000 0.00 0.00 37.07 3.36
315 316 1.068474 CGAAGCGTGGTAGTTCCTTG 58.932 55.000 0.00 0.00 37.07 3.61
316 317 0.796927 GAAGCGTGGTAGTTCCTTGC 59.203 55.000 0.00 0.00 37.32 4.01
317 318 0.107831 AAGCGTGGTAGTTCCTTGCA 59.892 50.000 5.82 0.00 38.71 4.08
318 319 0.107831 AGCGTGGTAGTTCCTTGCAA 59.892 50.000 0.00 0.00 38.71 4.08
319 320 1.165270 GCGTGGTAGTTCCTTGCAAT 58.835 50.000 0.00 0.00 37.13 3.56
320 321 1.539827 GCGTGGTAGTTCCTTGCAATT 59.460 47.619 0.00 0.00 37.13 2.32
321 322 2.745281 GCGTGGTAGTTCCTTGCAATTA 59.255 45.455 0.00 0.00 37.13 1.40
322 323 3.189702 GCGTGGTAGTTCCTTGCAATTAA 59.810 43.478 0.00 0.00 37.13 1.40
323 324 4.719040 CGTGGTAGTTCCTTGCAATTAAC 58.281 43.478 13.47 13.47 37.07 2.01
324 325 4.454504 CGTGGTAGTTCCTTGCAATTAACT 59.545 41.667 22.65 22.65 36.26 2.24
325 326 5.390567 CGTGGTAGTTCCTTGCAATTAACTC 60.391 44.000 22.70 16.18 34.23 3.01
326 327 5.472137 GTGGTAGTTCCTTGCAATTAACTCA 59.528 40.000 22.70 15.72 34.23 3.41
327 328 6.151144 GTGGTAGTTCCTTGCAATTAACTCAT 59.849 38.462 22.70 8.75 34.23 2.90
328 329 6.374333 TGGTAGTTCCTTGCAATTAACTCATC 59.626 38.462 22.70 16.13 34.23 2.92
329 330 5.904362 AGTTCCTTGCAATTAACTCATCC 57.096 39.130 16.70 0.00 0.00 3.51
330 331 5.574188 AGTTCCTTGCAATTAACTCATCCT 58.426 37.500 16.70 0.19 0.00 3.24
331 332 6.012745 AGTTCCTTGCAATTAACTCATCCTT 58.987 36.000 16.70 0.00 0.00 3.36
332 333 7.175104 AGTTCCTTGCAATTAACTCATCCTTA 58.825 34.615 16.70 0.00 0.00 2.69
333 334 7.121315 AGTTCCTTGCAATTAACTCATCCTTAC 59.879 37.037 16.70 0.00 0.00 2.34
334 335 5.584649 TCCTTGCAATTAACTCATCCTTACG 59.415 40.000 0.00 0.00 0.00 3.18
335 336 5.584649 CCTTGCAATTAACTCATCCTTACGA 59.415 40.000 0.00 0.00 0.00 3.43
354 355 0.530288 AGCACGTGCACAAAGGTTTT 59.470 45.000 39.21 14.41 45.16 2.43
356 357 1.555477 CACGTGCACAAAGGTTTTCC 58.445 50.000 18.64 0.00 41.05 3.13
385 386 0.595095 CAACAAGGTCAAGCTGGCTC 59.405 55.000 0.00 0.00 0.00 4.70
386 387 0.538287 AACAAGGTCAAGCTGGCTCC 60.538 55.000 0.00 0.00 0.00 4.70
391 392 0.249657 GGTCAAGCTGGCTCCGATAG 60.250 60.000 0.00 0.00 0.00 2.08
403 404 2.728817 CGATAGGGGAGCGGTGAC 59.271 66.667 0.00 0.00 31.79 3.67
418 419 0.941542 GTGACAAAGCCACGTTAGCA 59.058 50.000 9.81 0.00 0.00 3.49
422 423 1.602377 ACAAAGCCACGTTAGCAACTC 59.398 47.619 9.81 0.00 0.00 3.01
424 425 1.566018 AAGCCACGTTAGCAACTCGC 61.566 55.000 9.81 0.00 42.91 5.03
434 435 2.605094 GCAACTCGCTCTGACAACA 58.395 52.632 0.00 0.00 37.77 3.33
461 462 2.224257 GGTTGTTTGATGGTGCATGGTT 60.224 45.455 0.00 0.00 0.00 3.67
470 471 1.887854 TGGTGCATGGTTCTTGATGTG 59.112 47.619 0.00 0.00 0.00 3.21
748 758 2.967397 TGGCGACAAGGTACGGAG 59.033 61.111 0.00 0.00 37.44 4.63
866 876 1.663739 CGTTCCTCGTCACCTGGAA 59.336 57.895 0.00 0.00 37.51 3.53
910 920 3.433343 TCACCGTCCTACCTTCATACAA 58.567 45.455 0.00 0.00 0.00 2.41
974 984 4.615961 CGATCGATCCTAACGGTGAATAAC 59.384 45.833 19.51 0.00 0.00 1.89
1224 1234 3.069318 GCCGTTCGGGAGGAGAGT 61.069 66.667 13.16 0.00 38.47 3.24
2475 2499 4.212214 CGATCCCTTCCGAATCTTCAATTC 59.788 45.833 0.00 0.00 0.00 2.17
2476 2500 4.844349 TCCCTTCCGAATCTTCAATTCT 57.156 40.909 0.00 0.00 0.00 2.40
2561 2592 0.978146 ACGGGGTTCAGATCAGAGGG 60.978 60.000 0.00 0.00 0.00 4.30
2583 2614 3.323243 CCCTGTAGGTTGTTCTTGTACG 58.677 50.000 0.00 0.00 0.00 3.67
2738 2774 4.019591 AGGGCCGAGACTAATTTGTTAACT 60.020 41.667 7.22 0.00 0.00 2.24
2773 2810 9.715121 AAGGTTTATCGTCTGTTTATTTCTACA 57.285 29.630 0.00 0.00 0.00 2.74
2897 3743 0.958822 GTTGTTCGGGCTGGACAATT 59.041 50.000 22.54 0.00 35.91 2.32
2915 3761 6.388619 ACAATTACCCACTTCCTACAATCT 57.611 37.500 0.00 0.00 0.00 2.40
2919 3765 1.408822 CCCACTTCCTACAATCTGGCC 60.409 57.143 0.00 0.00 0.00 5.36
2946 3792 0.178992 TTGGGCCAGGTTGTCTCTTG 60.179 55.000 6.23 0.00 0.00 3.02
2957 3803 0.035725 TGTCTCTTGCCTGCTCATGG 60.036 55.000 0.00 0.00 0.00 3.66
2959 3805 1.134159 GTCTCTTGCCTGCTCATGGAT 60.134 52.381 0.00 0.00 0.00 3.41
2965 3811 0.465824 GCCTGCTCATGGATTCAGCT 60.466 55.000 5.11 0.00 34.03 4.24
2982 3828 7.094634 GGATTCAGCTGTCAGTTCAAAAGATTA 60.095 37.037 14.67 0.00 0.00 1.75
3009 3855 7.723172 ACCTATTTGAAATGGAATCTCTGGATC 59.277 37.037 2.62 0.00 0.00 3.36
3122 3968 6.174760 ACCAATTAGTTAGCAACGTTCCATA 58.825 36.000 0.00 0.00 36.23 2.74
3123 3969 6.655848 ACCAATTAGTTAGCAACGTTCCATAA 59.344 34.615 0.00 0.00 36.23 1.90
3196 4084 7.701501 TGACACTTAATTTAACGTGGAAAAACC 59.298 33.333 16.26 0.00 39.54 3.27
3297 4344 0.459411 GCAACAACAACCACCACCAC 60.459 55.000 0.00 0.00 0.00 4.16
3420 4480 6.036408 CACACATACACACGAATTCATGAGAT 59.964 38.462 8.78 0.00 0.00 2.75
3421 4481 6.256539 ACACATACACACGAATTCATGAGATC 59.743 38.462 8.78 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.500116 GTCTCTCCAGTCGCCGCC 62.500 72.222 0.00 0.00 0.00 6.13
7 8 2.766400 CCTCGTCTCTCCAGTCGCC 61.766 68.421 0.00 0.00 31.97 5.54
9 10 2.766400 GCCCTCGTCTCTCCAGTCG 61.766 68.421 0.00 0.00 33.05 4.18
10 11 2.766400 CGCCCTCGTCTCTCCAGTC 61.766 68.421 0.00 0.00 0.00 3.51
11 12 2.559922 ATCGCCCTCGTCTCTCCAGT 62.560 60.000 0.00 0.00 36.96 4.00
12 13 1.826054 ATCGCCCTCGTCTCTCCAG 60.826 63.158 0.00 0.00 36.96 3.86
13 14 2.121538 CATCGCCCTCGTCTCTCCA 61.122 63.158 0.00 0.00 36.96 3.86
14 15 2.725008 CATCGCCCTCGTCTCTCC 59.275 66.667 0.00 0.00 36.96 3.71
15 16 2.725008 CCATCGCCCTCGTCTCTC 59.275 66.667 0.00 0.00 36.96 3.20
16 17 2.835431 CCCATCGCCCTCGTCTCT 60.835 66.667 0.00 0.00 36.96 3.10
17 18 3.917760 CCCCATCGCCCTCGTCTC 61.918 72.222 0.00 0.00 36.96 3.36
26 27 4.292178 CTCTCCTCGCCCCATCGC 62.292 72.222 0.00 0.00 0.00 4.58
27 28 3.610669 CCTCTCCTCGCCCCATCG 61.611 72.222 0.00 0.00 0.00 3.84
28 29 3.237741 CCCTCTCCTCGCCCCATC 61.238 72.222 0.00 0.00 0.00 3.51
29 30 3.767268 TCCCTCTCCTCGCCCCAT 61.767 66.667 0.00 0.00 0.00 4.00
30 31 4.779733 GTCCCTCTCCTCGCCCCA 62.780 72.222 0.00 0.00 0.00 4.96
31 32 4.779733 TGTCCCTCTCCTCGCCCC 62.780 72.222 0.00 0.00 0.00 5.80
32 33 3.151022 CTGTCCCTCTCCTCGCCC 61.151 72.222 0.00 0.00 0.00 6.13
33 34 2.043852 TCTGTCCCTCTCCTCGCC 60.044 66.667 0.00 0.00 0.00 5.54
34 35 1.379309 ACTCTGTCCCTCTCCTCGC 60.379 63.158 0.00 0.00 0.00 5.03
35 36 1.662438 GCACTCTGTCCCTCTCCTCG 61.662 65.000 0.00 0.00 0.00 4.63
36 37 1.662438 CGCACTCTGTCCCTCTCCTC 61.662 65.000 0.00 0.00 0.00 3.71
37 38 1.680651 CGCACTCTGTCCCTCTCCT 60.681 63.158 0.00 0.00 0.00 3.69
38 39 2.716017 CCGCACTCTGTCCCTCTCC 61.716 68.421 0.00 0.00 0.00 3.71
39 40 2.888863 CCGCACTCTGTCCCTCTC 59.111 66.667 0.00 0.00 0.00 3.20
40 41 3.386237 GCCGCACTCTGTCCCTCT 61.386 66.667 0.00 0.00 0.00 3.69
41 42 3.655810 CTGCCGCACTCTGTCCCTC 62.656 68.421 0.00 0.00 0.00 4.30
42 43 3.699894 CTGCCGCACTCTGTCCCT 61.700 66.667 0.00 0.00 0.00 4.20
43 44 4.767255 CCTGCCGCACTCTGTCCC 62.767 72.222 0.00 0.00 0.00 4.46
45 46 4.385405 AGCCTGCCGCACTCTGTC 62.385 66.667 0.00 0.00 41.38 3.51
46 47 4.385405 GAGCCTGCCGCACTCTGT 62.385 66.667 4.19 0.00 41.38 3.41
56 57 4.660938 AACCCAACCGGAGCCTGC 62.661 66.667 9.46 0.00 34.64 4.85
57 58 2.359975 GAACCCAACCGGAGCCTG 60.360 66.667 9.46 0.00 34.64 4.85
58 59 4.016706 CGAACCCAACCGGAGCCT 62.017 66.667 9.46 0.00 34.64 4.58
59 60 4.011517 TCGAACCCAACCGGAGCC 62.012 66.667 9.46 0.00 34.64 4.70
60 61 2.741211 GTCGAACCCAACCGGAGC 60.741 66.667 9.46 0.00 34.64 4.70
61 62 2.047560 GGTCGAACCCAACCGGAG 60.048 66.667 9.46 0.00 34.64 4.63
65 66 2.357881 GTCCGGTCGAACCCAACC 60.358 66.667 0.00 0.00 33.75 3.77
66 67 2.357881 GGTCCGGTCGAACCCAAC 60.358 66.667 0.00 0.00 33.75 3.77
78 79 3.151710 TCCATGTAGCCGGGTCCG 61.152 66.667 10.79 1.86 39.44 4.79
79 80 2.822399 CTCCATGTAGCCGGGTCC 59.178 66.667 10.79 0.00 0.00 4.46
80 81 2.109181 GCTCCATGTAGCCGGGTC 59.891 66.667 10.79 2.32 36.45 4.46
81 82 3.849951 CGCTCCATGTAGCCGGGT 61.850 66.667 12.58 12.58 39.43 5.28
82 83 3.536917 TCGCTCCATGTAGCCGGG 61.537 66.667 2.18 0.00 39.43 5.73
83 84 2.279517 GTCGCTCCATGTAGCCGG 60.280 66.667 4.51 0.00 39.43 6.13
84 85 2.279517 GGTCGCTCCATGTAGCCG 60.280 66.667 4.51 0.52 39.43 5.52
85 86 0.811616 CTTGGTCGCTCCATGTAGCC 60.812 60.000 4.51 0.00 46.60 3.93
86 87 0.175760 TCTTGGTCGCTCCATGTAGC 59.824 55.000 0.00 0.00 46.60 3.58
87 88 1.799181 CGTCTTGGTCGCTCCATGTAG 60.799 57.143 10.38 0.00 46.60 2.74
88 89 0.172578 CGTCTTGGTCGCTCCATGTA 59.827 55.000 10.38 0.00 46.60 2.29
89 90 1.079819 CGTCTTGGTCGCTCCATGT 60.080 57.895 10.38 0.00 46.60 3.21
90 91 1.811266 CCGTCTTGGTCGCTCCATG 60.811 63.158 0.37 3.66 46.60 3.66
91 92 2.579201 CCGTCTTGGTCGCTCCAT 59.421 61.111 0.37 0.00 46.60 3.41
92 93 3.691342 CCCGTCTTGGTCGCTCCA 61.691 66.667 0.00 0.00 45.60 3.86
93 94 3.692406 ACCCGTCTTGGTCGCTCC 61.692 66.667 0.00 0.00 31.15 4.70
94 95 2.432628 CACCCGTCTTGGTCGCTC 60.433 66.667 0.00 0.00 36.12 5.03
95 96 4.681978 GCACCCGTCTTGGTCGCT 62.682 66.667 0.00 0.00 36.12 4.93
97 98 4.351938 TCGCACCCGTCTTGGTCG 62.352 66.667 0.00 0.00 36.12 4.79
98 99 2.432628 CTCGCACCCGTCTTGGTC 60.433 66.667 0.00 0.00 36.12 4.02
99 100 2.915659 TCTCGCACCCGTCTTGGT 60.916 61.111 0.00 0.00 39.96 3.67
100 101 2.125912 CTCTCGCACCCGTCTTGG 60.126 66.667 0.00 0.00 35.54 3.61
101 102 0.242825 TAACTCTCGCACCCGTCTTG 59.757 55.000 0.00 0.00 35.54 3.02
102 103 0.243095 GTAACTCTCGCACCCGTCTT 59.757 55.000 0.00 0.00 35.54 3.01
103 104 1.593296 GGTAACTCTCGCACCCGTCT 61.593 60.000 0.00 0.00 35.54 4.18
104 105 1.153881 GGTAACTCTCGCACCCGTC 60.154 63.158 0.00 0.00 35.54 4.79
105 106 2.968206 GGTAACTCTCGCACCCGT 59.032 61.111 0.00 0.00 35.54 5.28
106 107 2.202570 CGGTAACTCTCGCACCCG 60.203 66.667 0.00 0.00 0.00 5.28
107 108 1.139095 CTCGGTAACTCTCGCACCC 59.861 63.158 0.00 0.00 0.00 4.61
108 109 1.516603 GCTCGGTAACTCTCGCACC 60.517 63.158 0.00 0.00 0.00 5.01
109 110 1.868251 CGCTCGGTAACTCTCGCAC 60.868 63.158 0.00 0.00 0.00 5.34
110 111 2.483745 CGCTCGGTAACTCTCGCA 59.516 61.111 0.00 0.00 0.00 5.10
111 112 2.278013 CCGCTCGGTAACTCTCGC 60.278 66.667 0.00 0.00 0.00 5.03
112 113 2.404995 ACCCGCTCGGTAACTCTCG 61.405 63.158 7.59 0.00 45.97 4.04
113 114 1.139095 CACCCGCTCGGTAACTCTC 59.861 63.158 7.59 0.00 46.14 3.20
114 115 3.003113 GCACCCGCTCGGTAACTCT 62.003 63.158 7.59 0.00 46.14 3.24
115 116 2.508663 GCACCCGCTCGGTAACTC 60.509 66.667 7.59 0.00 46.14 3.01
116 117 4.430765 CGCACCCGCTCGGTAACT 62.431 66.667 7.59 0.00 46.14 2.24
144 145 4.248842 TGTCAGGTGCCACGGTGG 62.249 66.667 22.87 22.87 41.55 4.61
145 146 2.972505 GTGTCAGGTGCCACGGTG 60.973 66.667 0.00 0.00 0.00 4.94
149 150 2.972505 CCACGTGTCAGGTGCCAC 60.973 66.667 18.22 0.00 33.03 5.01
150 151 4.248842 CCCACGTGTCAGGTGCCA 62.249 66.667 18.22 0.00 33.03 4.92
156 157 2.629050 CTATCGGGCCCACGTGTCAG 62.629 65.000 24.92 1.98 34.94 3.51
157 158 2.680707 TATCGGGCCCACGTGTCA 60.681 61.111 24.92 0.00 34.94 3.58
158 159 2.106332 CTATCGGGCCCACGTGTC 59.894 66.667 24.92 5.64 34.94 3.67
159 160 3.467226 CCTATCGGGCCCACGTGT 61.467 66.667 24.92 4.49 34.94 4.49
160 161 3.441011 GACCTATCGGGCCCACGTG 62.441 68.421 24.92 9.08 39.10 4.49
161 162 3.152400 GACCTATCGGGCCCACGT 61.152 66.667 24.92 9.38 39.10 4.49
162 163 3.151710 TGACCTATCGGGCCCACG 61.152 66.667 24.92 9.15 37.62 4.94
163 164 1.122019 ATCTGACCTATCGGGCCCAC 61.122 60.000 24.92 4.02 37.62 4.61
164 165 0.485543 TATCTGACCTATCGGGCCCA 59.514 55.000 24.92 9.77 37.62 5.36
165 166 0.896226 GTATCTGACCTATCGGGCCC 59.104 60.000 13.57 13.57 37.62 5.80
166 167 0.526662 CGTATCTGACCTATCGGGCC 59.473 60.000 0.00 0.00 37.62 5.80
167 168 1.068472 CACGTATCTGACCTATCGGGC 60.068 57.143 0.00 0.00 39.55 6.13
168 169 1.540267 CCACGTATCTGACCTATCGGG 59.460 57.143 0.00 0.00 41.89 5.14
169 170 2.225963 GACCACGTATCTGACCTATCGG 59.774 54.545 0.00 0.00 0.00 4.18
170 171 2.876550 TGACCACGTATCTGACCTATCG 59.123 50.000 0.00 0.00 0.00 2.92
171 172 4.913335 TTGACCACGTATCTGACCTATC 57.087 45.455 0.00 0.00 0.00 2.08
172 173 5.048921 CGTATTGACCACGTATCTGACCTAT 60.049 44.000 0.00 0.00 34.74 2.57
173 174 4.274214 CGTATTGACCACGTATCTGACCTA 59.726 45.833 0.00 0.00 34.74 3.08
174 175 3.066342 CGTATTGACCACGTATCTGACCT 59.934 47.826 0.00 0.00 34.74 3.85
175 176 3.369385 CGTATTGACCACGTATCTGACC 58.631 50.000 0.00 0.00 34.74 4.02
176 177 2.787680 GCGTATTGACCACGTATCTGAC 59.212 50.000 0.00 0.00 41.41 3.51
177 178 2.540157 CGCGTATTGACCACGTATCTGA 60.540 50.000 0.00 0.00 41.41 3.27
178 179 1.779157 CGCGTATTGACCACGTATCTG 59.221 52.381 0.00 0.00 41.41 2.90
179 180 1.862815 GCGCGTATTGACCACGTATCT 60.863 52.381 8.43 0.00 41.41 1.98
180 181 0.501435 GCGCGTATTGACCACGTATC 59.499 55.000 8.43 0.00 41.41 2.24
181 182 0.101759 AGCGCGTATTGACCACGTAT 59.898 50.000 8.43 0.00 41.41 3.06
182 183 0.109179 AAGCGCGTATTGACCACGTA 60.109 50.000 8.43 0.00 41.41 3.57
183 184 0.109179 TAAGCGCGTATTGACCACGT 60.109 50.000 8.43 0.00 41.41 4.49
184 185 1.205657 ATAAGCGCGTATTGACCACG 58.794 50.000 10.21 0.00 42.24 4.94
185 186 2.152489 CGTATAAGCGCGTATTGACCAC 59.848 50.000 20.71 11.39 0.00 4.16
186 187 2.387185 CGTATAAGCGCGTATTGACCA 58.613 47.619 20.71 0.00 0.00 4.02
187 188 1.717645 CCGTATAAGCGCGTATTGACC 59.282 52.381 20.71 6.56 0.00 4.02
188 189 1.123756 GCCGTATAAGCGCGTATTGAC 59.876 52.381 20.71 12.74 0.00 3.18
189 190 1.001048 AGCCGTATAAGCGCGTATTGA 60.001 47.619 20.71 1.31 34.64 2.57
190 191 1.124297 CAGCCGTATAAGCGCGTATTG 59.876 52.381 20.71 13.37 34.64 1.90
191 192 1.269413 ACAGCCGTATAAGCGCGTATT 60.269 47.619 20.71 5.91 34.64 1.89
192 193 0.313043 ACAGCCGTATAAGCGCGTAT 59.687 50.000 19.53 19.53 34.64 3.06
193 194 0.317269 GACAGCCGTATAAGCGCGTA 60.317 55.000 8.43 5.30 34.64 4.42
194 195 1.588139 GACAGCCGTATAAGCGCGT 60.588 57.895 8.43 0.00 34.64 6.01
195 196 1.540607 CTGACAGCCGTATAAGCGCG 61.541 60.000 0.00 0.00 34.64 6.86
196 197 0.248907 TCTGACAGCCGTATAAGCGC 60.249 55.000 0.00 0.00 34.64 5.92
197 198 1.478137 GTCTGACAGCCGTATAAGCG 58.522 55.000 2.24 0.00 34.64 4.68
198 199 1.136305 TGGTCTGACAGCCGTATAAGC 59.864 52.381 10.38 0.00 0.00 3.09
199 200 3.735237 ATGGTCTGACAGCCGTATAAG 57.265 47.619 10.38 0.00 0.00 1.73
200 201 4.481368 AAATGGTCTGACAGCCGTATAA 57.519 40.909 10.38 0.00 0.00 0.98
201 202 4.188462 CAAAATGGTCTGACAGCCGTATA 58.812 43.478 10.38 0.00 0.00 1.47
202 203 3.009723 CAAAATGGTCTGACAGCCGTAT 58.990 45.455 10.38 2.44 0.00 3.06
203 204 2.422597 CAAAATGGTCTGACAGCCGTA 58.577 47.619 10.38 0.00 0.00 4.02
204 205 1.238439 CAAAATGGTCTGACAGCCGT 58.762 50.000 10.38 1.25 0.00 5.68
205 206 0.109597 GCAAAATGGTCTGACAGCCG 60.110 55.000 10.38 0.00 0.00 5.52
206 207 0.961019 TGCAAAATGGTCTGACAGCC 59.039 50.000 10.38 3.31 0.00 4.85
207 208 2.223782 TGTTGCAAAATGGTCTGACAGC 60.224 45.455 10.38 4.25 0.00 4.40
208 209 3.067180 AGTGTTGCAAAATGGTCTGACAG 59.933 43.478 10.38 0.00 0.00 3.51
209 210 3.023119 AGTGTTGCAAAATGGTCTGACA 58.977 40.909 10.38 0.00 0.00 3.58
210 211 3.715628 AGTGTTGCAAAATGGTCTGAC 57.284 42.857 0.00 0.00 0.00 3.51
211 212 4.278170 CCTAAGTGTTGCAAAATGGTCTGA 59.722 41.667 0.00 0.00 0.00 3.27
212 213 4.549458 CCTAAGTGTTGCAAAATGGTCTG 58.451 43.478 0.00 0.00 0.00 3.51
213 214 3.005791 GCCTAAGTGTTGCAAAATGGTCT 59.994 43.478 0.00 0.00 0.00 3.85
214 215 3.005791 AGCCTAAGTGTTGCAAAATGGTC 59.994 43.478 0.00 0.00 0.00 4.02
215 216 2.965147 AGCCTAAGTGTTGCAAAATGGT 59.035 40.909 0.00 0.00 0.00 3.55
216 217 3.665745 AGCCTAAGTGTTGCAAAATGG 57.334 42.857 0.00 0.00 0.00 3.16
217 218 5.630680 CACTAAGCCTAAGTGTTGCAAAATG 59.369 40.000 0.00 0.00 39.61 2.32
218 219 5.772521 CACTAAGCCTAAGTGTTGCAAAAT 58.227 37.500 0.00 0.00 39.61 1.82
219 220 5.181690 CACTAAGCCTAAGTGTTGCAAAA 57.818 39.130 0.00 0.00 39.61 2.44
220 221 4.829064 CACTAAGCCTAAGTGTTGCAAA 57.171 40.909 0.00 0.00 39.61 3.68
228 229 4.562963 GCAGTACCAACACTAAGCCTAAGT 60.563 45.833 0.00 0.00 0.00 2.24
229 230 3.933332 GCAGTACCAACACTAAGCCTAAG 59.067 47.826 0.00 0.00 0.00 2.18
230 231 3.325425 TGCAGTACCAACACTAAGCCTAA 59.675 43.478 0.00 0.00 0.00 2.69
231 232 2.901192 TGCAGTACCAACACTAAGCCTA 59.099 45.455 0.00 0.00 0.00 3.93
232 233 1.697432 TGCAGTACCAACACTAAGCCT 59.303 47.619 0.00 0.00 0.00 4.58
233 234 2.178912 TGCAGTACCAACACTAAGCC 57.821 50.000 0.00 0.00 0.00 4.35
234 235 2.420022 CCATGCAGTACCAACACTAAGC 59.580 50.000 0.00 0.00 0.00 3.09
235 236 2.420022 GCCATGCAGTACCAACACTAAG 59.580 50.000 0.00 0.00 0.00 2.18
236 237 2.224646 TGCCATGCAGTACCAACACTAA 60.225 45.455 0.00 0.00 33.32 2.24
237 238 1.349357 TGCCATGCAGTACCAACACTA 59.651 47.619 0.00 0.00 33.32 2.74
238 239 0.110295 TGCCATGCAGTACCAACACT 59.890 50.000 0.00 0.00 33.32 3.55
239 240 0.958091 TTGCCATGCAGTACCAACAC 59.042 50.000 0.00 0.00 40.61 3.32
240 241 1.697284 TTTGCCATGCAGTACCAACA 58.303 45.000 0.00 0.00 40.61 3.33
241 242 2.810439 TTTTGCCATGCAGTACCAAC 57.190 45.000 0.00 0.00 40.61 3.77
259 260 4.595762 TCAGTACCGCTAGTCACTTTTT 57.404 40.909 0.00 0.00 0.00 1.94
260 261 4.803098 ATCAGTACCGCTAGTCACTTTT 57.197 40.909 0.00 0.00 0.00 2.27
261 262 4.674623 CGAATCAGTACCGCTAGTCACTTT 60.675 45.833 0.00 0.00 0.00 2.66
262 263 3.181499 CGAATCAGTACCGCTAGTCACTT 60.181 47.826 0.00 0.00 0.00 3.16
263 264 2.355132 CGAATCAGTACCGCTAGTCACT 59.645 50.000 0.00 0.00 0.00 3.41
264 265 2.097142 ACGAATCAGTACCGCTAGTCAC 59.903 50.000 0.00 0.00 0.00 3.67
265 266 2.353889 GACGAATCAGTACCGCTAGTCA 59.646 50.000 0.00 0.00 0.00 3.41
266 267 2.353889 TGACGAATCAGTACCGCTAGTC 59.646 50.000 0.00 0.00 0.00 2.59
267 268 2.097142 GTGACGAATCAGTACCGCTAGT 59.903 50.000 0.00 0.00 34.75 2.57
268 269 2.096980 TGTGACGAATCAGTACCGCTAG 59.903 50.000 0.00 0.00 34.75 3.42
269 270 2.086094 TGTGACGAATCAGTACCGCTA 58.914 47.619 0.00 0.00 34.75 4.26
270 271 0.885879 TGTGACGAATCAGTACCGCT 59.114 50.000 0.00 0.00 34.75 5.52
271 272 1.389106 GTTGTGACGAATCAGTACCGC 59.611 52.381 0.00 0.00 34.75 5.68
272 273 2.668250 TGTTGTGACGAATCAGTACCG 58.332 47.619 0.00 0.00 34.75 4.02
273 274 3.181520 GCATGTTGTGACGAATCAGTACC 60.182 47.826 0.00 0.00 34.75 3.34
274 275 3.181520 GGCATGTTGTGACGAATCAGTAC 60.182 47.826 0.00 0.00 34.75 2.73
275 276 3.000041 GGCATGTTGTGACGAATCAGTA 59.000 45.455 0.00 0.00 34.75 2.74
276 277 1.806542 GGCATGTTGTGACGAATCAGT 59.193 47.619 0.00 0.00 34.75 3.41
277 278 2.532531 GGCATGTTGTGACGAATCAG 57.467 50.000 0.00 0.00 34.75 2.90
284 285 1.154413 CGCTTCGGCATGTTGTGAC 60.154 57.895 0.00 0.00 41.88 3.67
285 286 1.596752 ACGCTTCGGCATGTTGTGA 60.597 52.632 0.00 0.00 41.88 3.58
286 287 1.440850 CACGCTTCGGCATGTTGTG 60.441 57.895 0.00 0.00 41.88 3.33
287 288 2.616330 CCACGCTTCGGCATGTTGT 61.616 57.895 0.00 0.00 41.88 3.32
288 289 1.295357 TACCACGCTTCGGCATGTTG 61.295 55.000 0.00 0.00 41.88 3.33
289 290 1.004320 TACCACGCTTCGGCATGTT 60.004 52.632 0.00 0.00 41.88 2.71
290 291 1.447838 CTACCACGCTTCGGCATGT 60.448 57.895 0.00 0.00 41.88 3.21
291 292 1.019278 AACTACCACGCTTCGGCATG 61.019 55.000 0.00 0.00 41.88 4.06
292 293 0.739813 GAACTACCACGCTTCGGCAT 60.740 55.000 0.00 0.00 41.88 4.40
293 294 1.373748 GAACTACCACGCTTCGGCA 60.374 57.895 0.00 0.00 41.88 5.69
294 295 2.098831 GGAACTACCACGCTTCGGC 61.099 63.158 0.00 0.00 38.79 5.54
295 296 0.037605 AAGGAACTACCACGCTTCGG 60.038 55.000 0.00 0.00 38.49 4.30
296 297 1.068474 CAAGGAACTACCACGCTTCG 58.932 55.000 0.00 0.00 38.49 3.79
297 298 0.796927 GCAAGGAACTACCACGCTTC 59.203 55.000 0.00 0.00 38.49 3.86
298 299 0.107831 TGCAAGGAACTACCACGCTT 59.892 50.000 0.00 0.00 38.49 4.68
299 300 0.107831 TTGCAAGGAACTACCACGCT 59.892 50.000 0.00 0.00 38.49 5.07
300 301 1.165270 ATTGCAAGGAACTACCACGC 58.835 50.000 4.94 0.00 38.49 5.34
301 302 4.454504 AGTTAATTGCAAGGAACTACCACG 59.545 41.667 21.26 0.00 38.49 4.94
302 303 5.472137 TGAGTTAATTGCAAGGAACTACCAC 59.528 40.000 22.16 13.65 38.49 4.16
303 304 5.626142 TGAGTTAATTGCAAGGAACTACCA 58.374 37.500 22.16 16.20 38.49 3.25
304 305 6.183360 GGATGAGTTAATTGCAAGGAACTACC 60.183 42.308 22.16 20.29 38.49 3.18
305 306 6.599638 AGGATGAGTTAATTGCAAGGAACTAC 59.400 38.462 22.16 17.04 38.49 2.73
306 307 6.721318 AGGATGAGTTAATTGCAAGGAACTA 58.279 36.000 22.16 14.00 38.49 2.24
308 309 5.904362 AGGATGAGTTAATTGCAAGGAAC 57.096 39.130 15.19 15.19 0.00 3.62
309 310 6.093495 CGTAAGGATGAGTTAATTGCAAGGAA 59.907 38.462 4.94 0.00 0.00 3.36
310 311 5.584649 CGTAAGGATGAGTTAATTGCAAGGA 59.415 40.000 4.94 0.00 0.00 3.36
311 312 5.584649 TCGTAAGGATGAGTTAATTGCAAGG 59.415 40.000 4.94 0.00 38.47 3.61
312 313 6.662414 TCGTAAGGATGAGTTAATTGCAAG 57.338 37.500 4.94 0.00 38.47 4.01
313 314 5.064707 GCTCGTAAGGATGAGTTAATTGCAA 59.935 40.000 0.00 0.00 38.47 4.08
314 315 4.570772 GCTCGTAAGGATGAGTTAATTGCA 59.429 41.667 0.00 0.00 38.47 4.08
315 316 4.570772 TGCTCGTAAGGATGAGTTAATTGC 59.429 41.667 0.00 0.00 38.47 3.56
316 317 5.276395 CGTGCTCGTAAGGATGAGTTAATTG 60.276 44.000 0.00 0.00 31.85 2.32
317 318 4.804139 CGTGCTCGTAAGGATGAGTTAATT 59.196 41.667 0.00 0.00 31.85 1.40
318 319 4.360563 CGTGCTCGTAAGGATGAGTTAAT 58.639 43.478 0.00 0.00 31.85 1.40
319 320 3.766151 CGTGCTCGTAAGGATGAGTTAA 58.234 45.455 0.00 0.00 31.85 2.01
320 321 3.416119 CGTGCTCGTAAGGATGAGTTA 57.584 47.619 0.00 0.00 31.85 2.24
321 322 2.279582 CGTGCTCGTAAGGATGAGTT 57.720 50.000 0.00 0.00 31.85 3.01
333 334 2.047151 AACCTTTGTGCACGTGCTCG 62.047 55.000 37.59 23.66 42.66 5.03
334 335 0.100503 AAACCTTTGTGCACGTGCTC 59.899 50.000 37.59 33.79 42.66 4.26
335 336 0.530288 AAAACCTTTGTGCACGTGCT 59.470 45.000 37.59 16.06 42.66 4.40
354 355 1.421268 ACCTTGTTGATGACAGCTGGA 59.579 47.619 19.93 4.16 39.94 3.86
356 357 2.497138 TGACCTTGTTGATGACAGCTG 58.503 47.619 13.48 13.48 39.94 4.24
386 387 1.672854 TTGTCACCGCTCCCCTATCG 61.673 60.000 0.00 0.00 0.00 2.92
391 392 3.056328 GCTTTGTCACCGCTCCCC 61.056 66.667 0.00 0.00 0.00 4.81
400 401 1.332375 GTTGCTAACGTGGCTTTGTCA 59.668 47.619 13.55 0.00 0.00 3.58
401 402 1.602377 AGTTGCTAACGTGGCTTTGTC 59.398 47.619 13.55 2.46 36.23 3.18
403 404 1.398451 CGAGTTGCTAACGTGGCTTTG 60.398 52.381 13.55 2.42 36.23 2.77
418 419 3.990469 CACTATTGTTGTCAGAGCGAGTT 59.010 43.478 0.00 0.00 0.00 3.01
422 423 2.688507 ACCACTATTGTTGTCAGAGCG 58.311 47.619 0.00 0.00 0.00 5.03
434 435 3.894427 TGCACCATCAAACAACCACTATT 59.106 39.130 0.00 0.00 0.00 1.73
447 448 2.583024 TCAAGAACCATGCACCATCA 57.417 45.000 0.00 0.00 0.00 3.07
452 453 4.445452 AATCACATCAAGAACCATGCAC 57.555 40.909 0.00 0.00 0.00 4.57
482 483 2.427095 AGAAGCACAAACCACCTCAAAC 59.573 45.455 0.00 0.00 0.00 2.93
522 523 9.549078 GGAAAGAACCGAGATCTATTTTCTATT 57.451 33.333 10.93 8.53 0.00 1.73
575 583 4.699257 GTGAGGGCATCATCTTGATTATCC 59.301 45.833 4.69 0.00 40.92 2.59
582 590 4.217767 CCATAATGTGAGGGCATCATCTTG 59.782 45.833 4.69 0.00 40.92 3.02
745 755 3.869272 CAACTCGCGCATGCCTCC 61.869 66.667 13.15 0.00 38.08 4.30
866 876 0.107508 CCATCAGGGACATTGCTCGT 60.108 55.000 0.00 0.00 40.01 4.18
910 920 4.331968 TCGTGATGGCCTTGATTTTTAGT 58.668 39.130 3.32 0.00 0.00 2.24
1224 1234 1.827399 GCAACTTCCTCCTCGACCCA 61.827 60.000 0.00 0.00 0.00 4.51
1276 1286 2.582498 GATCGGGTTCGTCGCCTG 60.582 66.667 0.00 0.00 37.69 4.85
1392 1402 2.357952 CGTGACGATGTAGATCTTCCCA 59.642 50.000 0.00 0.00 0.00 4.37
2043 2057 3.696051 GGCACCTGATAATCAAGCAAGAA 59.304 43.478 0.00 0.00 0.00 2.52
2052 2070 1.611673 CCCCATCGGCACCTGATAATC 60.612 57.143 0.00 0.00 0.00 1.75
2561 2592 2.271944 ACAAGAACAACCTACAGGGC 57.728 50.000 0.00 0.00 40.27 5.19
2583 2614 2.476051 CTGACACGGCGAATGCAC 59.524 61.111 16.62 1.04 45.35 4.57
2813 2855 0.029300 GCACACATGTTCACTTGCGT 59.971 50.000 0.00 0.00 0.00 5.24
2878 3724 0.958822 AATTGTCCAGCCCGAACAAC 59.041 50.000 0.00 0.00 35.87 3.32
2884 3730 1.029947 GTGGGTAATTGTCCAGCCCG 61.030 60.000 2.34 0.00 42.10 6.13
2897 3743 2.504175 GCCAGATTGTAGGAAGTGGGTA 59.496 50.000 0.00 0.00 0.00 3.69
2915 3761 2.203625 GCCCAAAGGTTCAGGCCA 60.204 61.111 5.01 0.00 39.60 5.36
2919 3765 1.153756 ACCTGGCCCAAAGGTTCAG 59.846 57.895 7.44 0.00 46.14 3.02
2946 3792 0.465824 AGCTGAATCCATGAGCAGGC 60.466 55.000 6.17 0.00 35.03 4.85
2957 3803 5.679734 TCTTTTGAACTGACAGCTGAATC 57.320 39.130 23.35 9.26 0.00 2.52
2959 3805 7.417612 GTTAATCTTTTGAACTGACAGCTGAA 58.582 34.615 23.35 7.24 0.00 3.02
2982 3828 7.413446 TCCAGAGATTCCATTTCAAATAGGTT 58.587 34.615 0.00 0.00 0.00 3.50
3032 3878 6.862711 TGTATATTTGTTGTGTCGGTGAAA 57.137 33.333 0.00 0.00 0.00 2.69
3142 4019 7.935520 TGTGCATGTTGTTTGACTTTATTCTA 58.064 30.769 0.00 0.00 0.00 2.10
3196 4084 0.943835 TCGTGTGAGCCACAACGATG 60.944 55.000 18.76 0.00 46.28 3.84
3198 4086 1.590525 GTCGTGTGAGCCACAACGA 60.591 57.895 18.76 18.76 46.28 3.85
3199 4087 1.151777 AAGTCGTGTGAGCCACAACG 61.152 55.000 9.23 13.55 46.28 4.10
3297 4344 0.795085 CTCTGCTTTGCTTCTCGTGG 59.205 55.000 0.00 0.00 0.00 4.94
3332 4392 5.867166 GCAGTTTGCAAAATTCAGAAACAA 58.133 33.333 14.67 0.00 44.26 2.83


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

AutoCloner maintained by Alex Coulton.