Multiple sequence alignment - TraesCS1A01G178900

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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 TraesCS1A01G178900 chr1A 100.000 2661 0 0 1 2661 323408235 323405575 0.000000e+00 4915
1 TraesCS1A01G178900 chr4B 91.035 2376 191 6 210 2565 513012688 513010315 0.000000e+00 3188
2 TraesCS1A01G178900 chr4B 91.675 2018 144 12 344 2339 213391226 213389211 0.000000e+00 2774
3 TraesCS1A01G178900 chr4B 95.960 99 4 0 2563 2661 141082562 141082660 7.620000e-36 161
4 TraesCS1A01G178900 chr4B 93.939 99 6 0 2563 2661 213388974 213388876 1.650000e-32 150
5 TraesCS1A01G178900 chr4B 89.744 117 9 3 689 803 513012067 513011952 2.130000e-31 147
6 TraesCS1A01G178900 chr4B 83.871 124 20 0 380 503 513012610 513012487 4.650000e-23 119
7 TraesCS1A01G178900 chr3B 90.010 1011 78 10 385 1391 658956570 658957561 0.000000e+00 1286
8 TraesCS1A01G178900 chr3B 92.500 840 45 2 1415 2236 658957551 658958390 0.000000e+00 1186
9 TraesCS1A01G178900 chr3B 92.798 361 25 1 2205 2565 615143996 615143637 3.040000e-144 521
10 TraesCS1A01G178900 chr3B 92.287 363 27 1 1849 2211 615144558 615144197 5.080000e-142 514
11 TraesCS1A01G178900 chr3B 92.529 348 26 0 2218 2565 658958425 658958772 1.420000e-137 499
12 TraesCS1A01G178900 chr3B 91.209 364 29 3 1849 2211 354335768 354335407 2.380000e-135 492
13 TraesCS1A01G178900 chr3B 94.419 215 12 0 2255 2469 383920941 383921155 5.490000e-87 331
14 TraesCS1A01G178900 chr3B 95.960 99 4 0 2563 2661 615143597 615143499 7.620000e-36 161
15 TraesCS1A01G178900 chr3B 93.878 98 6 0 2564 2661 658958813 658958910 5.930000e-32 148
16 TraesCS1A01G178900 chr1B 93.258 356 23 1 1849 2204 349043501 349043855 8.440000e-145 523
17 TraesCS1A01G178900 chr1B 92.222 360 23 5 2207 2565 349044067 349044422 3.060000e-139 505
18 TraesCS1A01G178900 chr1B 95.833 96 4 0 2563 2658 349044462 349044557 3.550000e-34 156
19 TraesCS1A01G178900 chr2B 89.835 364 24 7 1849 2211 20124661 20124310 3.120000e-124 455
20 TraesCS1A01G178900 chr2B 94.444 216 11 1 2255 2469 519070634 519070849 5.490000e-87 331
21 TraesCS1A01G178900 chr2B 94.949 99 5 0 2563 2661 311337063 311337161 3.550000e-34 156
22 TraesCS1A01G178900 chr4D 91.923 260 19 2 2307 2565 270724050 270723792 1.950000e-96 363
23 TraesCS1A01G178900 chr4D 94.083 169 10 0 1 169 215302843 215303011 9.450000e-65 257
24 TraesCS1A01G178900 chr3D 92.248 258 16 4 2309 2565 149909751 149910005 1.950000e-96 363
25 TraesCS1A01G178900 chr3D 94.675 169 9 0 1 169 403648669 403648501 2.030000e-66 263
26 TraesCS1A01G178900 chrUn 85.205 365 39 11 2307 2661 113086160 113085801 7.000000e-96 361
27 TraesCS1A01G178900 chr6D 95.833 168 7 0 2 169 68483291 68483124 3.380000e-69 272
28 TraesCS1A01G178900 chr6D 94.643 168 9 0 2 169 284130284 284130451 7.310000e-66 261
29 TraesCS1A01G178900 chr7D 95.238 168 8 0 2 169 505283230 505283063 1.570000e-67 267
30 TraesCS1A01G178900 chr7D 95.152 165 8 0 5 169 466020066 466019902 7.310000e-66 261
31 TraesCS1A01G178900 chr7D 94.643 168 9 0 2 169 537140827 537140660 7.310000e-66 261
32 TraesCS1A01G178900 chr7D 94.949 99 5 0 2563 2661 195398144 195398242 3.550000e-34 156
33 TraesCS1A01G178900 chr7D 94.000 100 5 1 2563 2661 354529928 354530027 1.650000e-32 150
34 TraesCS1A01G178900 chr4A 95.238 168 8 0 2 169 324734061 324734228 1.570000e-67 267
35 TraesCS1A01G178900 chr5D 94.083 169 10 0 2 170 270620012 270620180 9.450000e-65 257
36 TraesCS1A01G178900 chr5B 95.364 151 7 0 2415 2565 178384700 178384850 9.520000e-60 241
37 TraesCS1A01G178900 chr7B 93.939 99 5 1 2563 2661 253262009 253261912 5.930000e-32 148


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 TraesCS1A01G178900 chr1A 323405575 323408235 2660 True 4915.000000 4915 100.000000 1 2661 1 chr1A.!!$R1 2660
1 TraesCS1A01G178900 chr4B 213388876 213391226 2350 True 1462.000000 2774 92.807000 344 2661 2 chr4B.!!$R1 2317
2 TraesCS1A01G178900 chr4B 513010315 513012688 2373 True 1151.333333 3188 88.216667 210 2565 3 chr4B.!!$R2 2355
3 TraesCS1A01G178900 chr3B 658956570 658958910 2340 False 779.750000 1286 92.229250 385 2661 4 chr3B.!!$F2 2276
4 TraesCS1A01G178900 chr3B 615143499 615144558 1059 True 398.666667 521 93.681667 1849 2661 3 chr3B.!!$R2 812
5 TraesCS1A01G178900 chr1B 349043501 349044557 1056 False 394.666667 523 93.771000 1849 2658 3 chr1B.!!$F1 809

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
850 853 0.027455 TGTGCTTGAGTTTTGCGTCG 59.973 50.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2113 0.248702 GAACCGCTCGAGGATGAGAC 60.249 60.0 15.58 0.0 38.28 3.36 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
17 18 3.263941 AACCGCTTGGACGAATGC 58.736 55.556 0.00 0.00 36.26 3.56
18 19 2.332654 AACCGCTTGGACGAATGCC 61.333 57.895 0.00 0.00 36.26 4.40
19 20 2.436646 CCGCTTGGACGAATGCCT 60.437 61.111 0.00 0.00 34.06 4.75
20 21 2.040544 CCGCTTGGACGAATGCCTT 61.041 57.895 0.00 0.00 34.06 4.35
21 22 1.425428 CGCTTGGACGAATGCCTTC 59.575 57.895 0.00 0.00 34.06 3.46
22 23 1.298157 CGCTTGGACGAATGCCTTCA 61.298 55.000 2.57 0.00 34.06 3.02
23 24 0.169009 GCTTGGACGAATGCCTTCAC 59.831 55.000 2.57 0.00 0.00 3.18
24 25 0.443869 CTTGGACGAATGCCTTCACG 59.556 55.000 2.57 0.00 0.00 4.35
25 26 0.034198 TTGGACGAATGCCTTCACGA 59.966 50.000 2.57 0.00 0.00 4.35
26 27 0.389817 TGGACGAATGCCTTCACGAG 60.390 55.000 2.57 0.00 0.00 4.18
27 28 0.389948 GGACGAATGCCTTCACGAGT 60.390 55.000 2.57 0.00 0.00 4.18
28 29 1.429463 GACGAATGCCTTCACGAGTT 58.571 50.000 2.57 0.00 0.00 3.01
29 30 1.390463 GACGAATGCCTTCACGAGTTC 59.610 52.381 2.57 0.00 0.00 3.01
30 31 1.270094 ACGAATGCCTTCACGAGTTCA 60.270 47.619 2.57 0.00 0.00 3.18
31 32 1.391485 CGAATGCCTTCACGAGTTCAG 59.609 52.381 2.57 0.00 0.00 3.02
32 33 1.734465 GAATGCCTTCACGAGTTCAGG 59.266 52.381 0.00 0.00 0.00 3.86
33 34 3.567473 GCCTTCACGAGTTCAGGC 58.433 61.111 6.68 6.68 45.02 4.85
35 36 2.832931 CCTTCACGAGTTCAGGCAG 58.167 57.895 0.00 0.00 0.00 4.85
36 37 0.318441 CCTTCACGAGTTCAGGCAGA 59.682 55.000 0.00 0.00 0.00 4.26
37 38 1.671261 CCTTCACGAGTTCAGGCAGAG 60.671 57.143 0.00 0.00 0.00 3.35
38 39 0.319900 TTCACGAGTTCAGGCAGAGC 60.320 55.000 0.00 0.00 0.00 4.09
54 55 2.592308 GCCAAGAGCTACCCTGGG 59.408 66.667 12.28 12.28 38.99 4.45
55 56 2.592308 CCAAGAGCTACCCTGGGC 59.408 66.667 14.08 0.00 0.00 5.36
56 57 2.300967 CCAAGAGCTACCCTGGGCA 61.301 63.158 14.08 0.00 0.00 5.36
57 58 1.685224 CAAGAGCTACCCTGGGCAA 59.315 57.895 14.08 0.00 0.00 4.52
58 59 0.393537 CAAGAGCTACCCTGGGCAAG 60.394 60.000 14.08 12.02 0.00 4.01
59 60 1.566298 AAGAGCTACCCTGGGCAAGG 61.566 60.000 14.08 0.00 46.94 3.61
72 73 3.599584 CAAGGGCTGCTGGTCATG 58.400 61.111 0.00 0.00 0.00 3.07
73 74 2.050350 CAAGGGCTGCTGGTCATGG 61.050 63.158 0.00 0.00 0.00 3.66
74 75 2.541907 AAGGGCTGCTGGTCATGGT 61.542 57.895 0.00 0.00 0.00 3.55
75 76 2.439156 GGGCTGCTGGTCATGGTC 60.439 66.667 0.00 0.00 0.00 4.02
76 77 2.673523 GGCTGCTGGTCATGGTCT 59.326 61.111 0.00 0.00 0.00 3.85
77 78 1.451028 GGCTGCTGGTCATGGTCTC 60.451 63.158 0.00 0.00 0.00 3.36
78 79 1.297689 GCTGCTGGTCATGGTCTCA 59.702 57.895 0.00 0.00 0.00 3.27
79 80 0.107312 GCTGCTGGTCATGGTCTCAT 60.107 55.000 0.00 0.00 0.00 2.90
86 87 3.710044 CATGGTCTCATGGACGCG 58.290 61.111 3.53 3.53 45.19 6.01
87 88 1.153568 CATGGTCTCATGGACGCGT 60.154 57.895 13.85 13.85 45.19 6.01
88 89 0.740868 CATGGTCTCATGGACGCGTT 60.741 55.000 15.53 0.00 45.19 4.84
89 90 0.036388 ATGGTCTCATGGACGCGTTT 60.036 50.000 15.53 0.00 45.35 3.60
90 91 0.250124 TGGTCTCATGGACGCGTTTT 60.250 50.000 15.53 0.00 45.35 2.43
91 92 1.001068 TGGTCTCATGGACGCGTTTTA 59.999 47.619 15.53 2.89 45.35 1.52
92 93 2.277084 GGTCTCATGGACGCGTTTTAT 58.723 47.619 15.53 5.54 45.35 1.40
93 94 2.676342 GGTCTCATGGACGCGTTTTATT 59.324 45.455 15.53 0.00 45.35 1.40
94 95 3.126343 GGTCTCATGGACGCGTTTTATTT 59.874 43.478 15.53 0.00 45.35 1.40
95 96 4.379082 GGTCTCATGGACGCGTTTTATTTT 60.379 41.667 15.53 0.00 45.35 1.82
96 97 5.163834 GGTCTCATGGACGCGTTTTATTTTA 60.164 40.000 15.53 0.00 45.35 1.52
97 98 6.308675 GTCTCATGGACGCGTTTTATTTTAA 58.691 36.000 15.53 0.00 35.07 1.52
98 99 6.797995 GTCTCATGGACGCGTTTTATTTTAAA 59.202 34.615 15.53 0.00 35.07 1.52
99 100 7.324135 GTCTCATGGACGCGTTTTATTTTAAAA 59.676 33.333 15.53 2.51 35.07 1.52
100 101 7.861372 TCTCATGGACGCGTTTTATTTTAAAAA 59.139 29.630 15.53 0.00 0.00 1.94
101 102 7.998141 TCATGGACGCGTTTTATTTTAAAAAG 58.002 30.769 15.53 2.59 0.00 2.27
102 103 7.648510 TCATGGACGCGTTTTATTTTAAAAAGT 59.351 29.630 15.53 0.00 0.00 2.66
103 104 7.752557 TGGACGCGTTTTATTTTAAAAAGTT 57.247 28.000 15.53 0.00 0.00 2.66
104 105 7.610509 TGGACGCGTTTTATTTTAAAAAGTTG 58.389 30.769 15.53 0.00 0.00 3.16
105 106 7.275123 TGGACGCGTTTTATTTTAAAAAGTTGT 59.725 29.630 15.53 6.52 0.00 3.32
106 107 8.109391 GGACGCGTTTTATTTTAAAAAGTTGTT 58.891 29.630 15.53 0.00 0.00 2.83
107 108 9.463003 GACGCGTTTTATTTTAAAAAGTTGTTT 57.537 25.926 15.53 0.00 0.00 2.83
108 109 9.463003 ACGCGTTTTATTTTAAAAAGTTGTTTC 57.537 25.926 5.58 0.00 0.00 2.78
109 110 8.645844 CGCGTTTTATTTTAAAAAGTTGTTTCG 58.354 29.630 4.44 4.70 0.00 3.46
110 111 9.672864 GCGTTTTATTTTAAAAAGTTGTTTCGA 57.327 25.926 4.44 0.00 0.00 3.71
115 116 9.552114 TTATTTTAAAAAGTTGTTTCGACGTGA 57.448 25.926 4.44 0.00 0.00 4.35
116 117 7.848716 TTTTAAAAAGTTGTTTCGACGTGAA 57.151 28.000 0.00 0.00 33.85 3.18
117 118 8.450385 TTTTAAAAAGTTGTTTCGACGTGAAT 57.550 26.923 0.00 0.00 36.22 2.57
118 119 9.552114 TTTTAAAAAGTTGTTTCGACGTGAATA 57.448 25.926 0.00 0.00 36.22 1.75
119 120 9.552114 TTTAAAAAGTTGTTTCGACGTGAATAA 57.448 25.926 0.00 0.00 36.22 1.40
120 121 7.427238 AAAAAGTTGTTTCGACGTGAATAAC 57.573 32.000 0.00 13.78 36.22 1.89
121 122 5.978934 AAGTTGTTTCGACGTGAATAACT 57.021 34.783 16.50 16.50 41.89 2.24
122 123 5.978934 AGTTGTTTCGACGTGAATAACTT 57.021 34.783 16.50 7.28 39.41 2.66
123 124 6.354039 AGTTGTTTCGACGTGAATAACTTT 57.646 33.333 16.50 4.11 39.41 2.66
124 125 6.189567 AGTTGTTTCGACGTGAATAACTTTG 58.810 36.000 16.50 0.00 39.41 2.77
125 126 5.721876 TGTTTCGACGTGAATAACTTTGT 57.278 34.783 0.00 0.00 36.22 2.83
126 127 6.825284 TGTTTCGACGTGAATAACTTTGTA 57.175 33.333 0.00 0.00 36.22 2.41
127 128 7.410800 TGTTTCGACGTGAATAACTTTGTAT 57.589 32.000 0.00 0.00 36.22 2.29
128 129 7.853524 TGTTTCGACGTGAATAACTTTGTATT 58.146 30.769 0.00 0.00 36.22 1.89
129 130 8.005466 TGTTTCGACGTGAATAACTTTGTATTC 58.995 33.333 0.00 0.00 39.80 1.75
130 131 7.640616 TTCGACGTGAATAACTTTGTATTCA 57.359 32.000 0.00 4.01 44.45 2.57
149 150 9.394767 TGTATTCACAACAATCATAGTATTGCT 57.605 29.630 0.00 0.00 39.93 3.91
150 151 9.869844 GTATTCACAACAATCATAGTATTGCTC 57.130 33.333 0.00 0.00 39.93 4.26
151 152 8.743085 ATTCACAACAATCATAGTATTGCTCT 57.257 30.769 0.00 0.00 39.93 4.09
152 153 7.776933 TCACAACAATCATAGTATTGCTCTC 57.223 36.000 0.00 0.00 39.93 3.20
153 154 7.559486 TCACAACAATCATAGTATTGCTCTCT 58.441 34.615 0.00 0.00 39.93 3.10
154 155 8.043113 TCACAACAATCATAGTATTGCTCTCTT 58.957 33.333 0.00 0.00 39.93 2.85
155 156 8.671921 CACAACAATCATAGTATTGCTCTCTTT 58.328 33.333 0.00 0.00 39.93 2.52
156 157 8.887717 ACAACAATCATAGTATTGCTCTCTTTC 58.112 33.333 0.00 0.00 39.93 2.62
157 158 8.886719 CAACAATCATAGTATTGCTCTCTTTCA 58.113 33.333 0.00 0.00 39.93 2.69
158 159 9.453572 AACAATCATAGTATTGCTCTCTTTCAA 57.546 29.630 0.00 0.00 39.93 2.69
159 160 9.624373 ACAATCATAGTATTGCTCTCTTTCAAT 57.376 29.630 0.00 0.00 39.93 2.57
160 161 9.880064 CAATCATAGTATTGCTCTCTTTCAATG 57.120 33.333 0.00 0.00 34.95 2.82
161 162 9.624373 AATCATAGTATTGCTCTCTTTCAATGT 57.376 29.630 0.00 0.00 34.95 2.71
162 163 8.429493 TCATAGTATTGCTCTCTTTCAATGTG 57.571 34.615 0.00 0.00 34.95 3.21
163 164 8.043113 TCATAGTATTGCTCTCTTTCAATGTGT 58.957 33.333 0.00 0.00 34.95 3.72
164 165 6.492007 AGTATTGCTCTCTTTCAATGTGTG 57.508 37.500 0.00 0.00 34.95 3.82
165 166 6.000219 AGTATTGCTCTCTTTCAATGTGTGT 59.000 36.000 0.00 0.00 34.95 3.72
166 167 7.161404 AGTATTGCTCTCTTTCAATGTGTGTA 58.839 34.615 0.00 0.00 34.95 2.90
167 168 5.673337 TTGCTCTCTTTCAATGTGTGTAC 57.327 39.130 0.00 0.00 0.00 2.90
168 169 4.960938 TGCTCTCTTTCAATGTGTGTACT 58.039 39.130 0.00 0.00 0.00 2.73
169 170 6.096673 TGCTCTCTTTCAATGTGTGTACTA 57.903 37.500 0.00 0.00 0.00 1.82
170 171 6.521162 TGCTCTCTTTCAATGTGTGTACTAA 58.479 36.000 0.00 0.00 0.00 2.24
171 172 6.646653 TGCTCTCTTTCAATGTGTGTACTAAG 59.353 38.462 0.00 0.00 0.00 2.18
172 173 6.401581 GCTCTCTTTCAATGTGTGTACTAAGC 60.402 42.308 0.00 0.00 0.00 3.09
173 174 6.759272 TCTCTTTCAATGTGTGTACTAAGCT 58.241 36.000 0.00 0.00 0.00 3.74
174 175 7.892609 TCTCTTTCAATGTGTGTACTAAGCTA 58.107 34.615 0.00 0.00 0.00 3.32
175 176 8.531982 TCTCTTTCAATGTGTGTACTAAGCTAT 58.468 33.333 0.00 0.00 0.00 2.97
176 177 9.155975 CTCTTTCAATGTGTGTACTAAGCTATT 57.844 33.333 0.00 0.00 0.00 1.73
177 178 9.502091 TCTTTCAATGTGTGTACTAAGCTATTT 57.498 29.630 0.00 0.00 0.00 1.40
180 181 8.942338 TCAATGTGTGTACTAAGCTATTTAGG 57.058 34.615 0.00 0.00 42.57 2.69
181 182 8.755028 TCAATGTGTGTACTAAGCTATTTAGGA 58.245 33.333 0.00 0.00 42.57 2.94
182 183 9.378551 CAATGTGTGTACTAAGCTATTTAGGAA 57.621 33.333 0.00 0.00 42.57 3.36
183 184 8.943909 ATGTGTGTACTAAGCTATTTAGGAAC 57.056 34.615 0.00 0.00 42.57 3.62
184 185 7.325694 TGTGTGTACTAAGCTATTTAGGAACC 58.674 38.462 0.00 0.00 42.57 3.62
185 186 6.760298 GTGTGTACTAAGCTATTTAGGAACCC 59.240 42.308 0.00 0.00 42.57 4.11
186 187 6.126968 TGTGTACTAAGCTATTTAGGAACCCC 60.127 42.308 0.00 0.00 42.57 4.95
187 188 6.099413 GTGTACTAAGCTATTTAGGAACCCCT 59.901 42.308 0.00 0.00 46.62 4.79
188 189 6.675303 TGTACTAAGCTATTTAGGAACCCCTT 59.325 38.462 0.00 0.00 40.78 3.95
189 190 7.845800 TGTACTAAGCTATTTAGGAACCCCTTA 59.154 37.037 0.00 0.00 40.78 2.69
190 191 7.760400 ACTAAGCTATTTAGGAACCCCTTAA 57.240 36.000 0.00 0.00 40.78 1.85
191 192 8.166479 ACTAAGCTATTTAGGAACCCCTTAAA 57.834 34.615 0.00 0.00 40.78 1.52
192 193 8.051535 ACTAAGCTATTTAGGAACCCCTTAAAC 58.948 37.037 0.00 0.00 40.78 2.01
193 194 6.653790 AGCTATTTAGGAACCCCTTAAACT 57.346 37.500 0.00 0.00 40.78 2.66
194 195 7.760400 AGCTATTTAGGAACCCCTTAAACTA 57.240 36.000 0.00 0.00 40.78 2.24
195 196 7.803131 AGCTATTTAGGAACCCCTTAAACTAG 58.197 38.462 0.00 0.00 40.78 2.57
196 197 7.626487 AGCTATTTAGGAACCCCTTAAACTAGA 59.374 37.037 0.00 0.00 40.78 2.43
197 198 7.714377 GCTATTTAGGAACCCCTTAAACTAGAC 59.286 40.741 0.00 0.00 40.78 2.59
198 199 7.578458 ATTTAGGAACCCCTTAAACTAGACA 57.422 36.000 0.00 0.00 40.78 3.41
199 200 7.391388 TTTAGGAACCCCTTAAACTAGACAA 57.609 36.000 0.00 0.00 40.78 3.18
200 201 5.917545 AGGAACCCCTTAAACTAGACAAA 57.082 39.130 0.00 0.00 40.78 2.83
201 202 5.877491 AGGAACCCCTTAAACTAGACAAAG 58.123 41.667 0.00 0.00 40.78 2.77
202 203 5.008331 GGAACCCCTTAAACTAGACAAAGG 58.992 45.833 0.00 5.81 38.58 3.11
203 204 5.221986 GGAACCCCTTAAACTAGACAAAGGA 60.222 44.000 17.64 0.00 40.85 3.36
204 205 6.464530 AACCCCTTAAACTAGACAAAGGAT 57.535 37.500 17.64 7.51 40.85 3.24
205 206 6.063496 ACCCCTTAAACTAGACAAAGGATC 57.937 41.667 17.64 0.00 40.85 3.36
206 207 5.045066 ACCCCTTAAACTAGACAAAGGATCC 60.045 44.000 17.64 2.48 40.85 3.36
207 208 5.116882 CCCTTAAACTAGACAAAGGATCCG 58.883 45.833 17.64 0.00 40.85 4.18
208 209 5.105064 CCCTTAAACTAGACAAAGGATCCGA 60.105 44.000 17.64 0.00 40.85 4.55
213 214 0.970937 AGACAAAGGATCCGAGCCGA 60.971 55.000 5.98 0.00 0.00 5.54
227 228 3.060866 CCGAATCCCGATCCCTCC 58.939 66.667 0.00 0.00 41.76 4.30
259 260 0.248289 CACCCCTACAAATCCGACGT 59.752 55.000 0.00 0.00 0.00 4.34
261 262 0.822164 CCCCTACAAATCCGACGTCT 59.178 55.000 14.70 0.00 0.00 4.18
271 272 1.008424 CCGACGTCTGATCCCATCG 60.008 63.158 14.70 0.00 0.00 3.84
276 277 1.252175 CGTCTGATCCCATCGATCCT 58.748 55.000 0.00 0.00 46.06 3.24
278 279 2.421775 CGTCTGATCCCATCGATCCTAG 59.578 54.545 0.00 0.00 46.06 3.02
280 281 2.174360 CTGATCCCATCGATCCTAGCA 58.826 52.381 0.00 0.00 46.06 3.49
282 283 2.762887 TGATCCCATCGATCCTAGCATC 59.237 50.000 0.00 0.00 46.06 3.91
301 302 1.291637 TCGATTCCCCCACCTAACCTA 59.708 52.381 0.00 0.00 0.00 3.08
304 305 4.101856 CGATTCCCCCACCTAACCTATAT 58.898 47.826 0.00 0.00 0.00 0.86
308 309 5.179881 TCCCCCACCTAACCTATATCTTT 57.820 43.478 0.00 0.00 0.00 2.52
309 310 4.911522 TCCCCCACCTAACCTATATCTTTG 59.088 45.833 0.00 0.00 0.00 2.77
313 314 7.168905 CCCCACCTAACCTATATCTTTGAATC 58.831 42.308 0.00 0.00 0.00 2.52
401 402 3.773119 CCCCTACCTAACTTGTAGCTTCA 59.227 47.826 0.00 0.00 35.44 3.02
410 411 3.074412 ACTTGTAGCTTCAAATCCACCG 58.926 45.455 7.22 0.00 0.00 4.94
537 538 0.465705 ATCCGCTTCGTCATGATGGT 59.534 50.000 14.91 0.00 0.00 3.55
550 551 4.907457 ATGGTGGCCATCGATTCC 57.093 55.556 9.72 4.43 40.74 3.01
608 610 1.005340 GCTTTGGATCTCTCACTGCG 58.995 55.000 0.00 0.00 0.00 5.18
723 726 1.225855 CGTGCAGTTAGCTGGTTTGA 58.774 50.000 8.78 0.00 45.94 2.69
797 800 2.906389 ACATTCAGTTAGCTCTGTGGGA 59.094 45.455 0.00 0.00 36.85 4.37
849 852 2.111756 CTTGTGCTTGAGTTTTGCGTC 58.888 47.619 0.00 0.00 0.00 5.19
850 853 0.027455 TGTGCTTGAGTTTTGCGTCG 59.973 50.000 0.00 0.00 0.00 5.12
871 874 2.170607 GAGTTAGCTGGTTGCATCCCTA 59.829 50.000 11.33 3.84 45.94 3.53
1029 1033 4.279420 CCTGATGAAGACGATGATGACCTA 59.721 45.833 0.00 0.00 0.00 3.08
1036 1040 4.207955 AGACGATGATGACCTAACTAGCA 58.792 43.478 0.00 0.00 0.00 3.49
1040 1044 4.219507 CGATGATGACCTAACTAGCAGGAT 59.780 45.833 16.08 2.27 36.61 3.24
1055 1059 3.118629 AGCAGGATTGTATGTGTCGACAT 60.119 43.478 23.12 9.40 45.24 3.06
1065 1069 2.560504 TGTGTCGACATGCAAAACTCT 58.439 42.857 23.12 0.00 0.00 3.24
1089 1094 2.159627 CGTGCAGAATGACCCAGTTTAC 59.840 50.000 0.00 0.00 39.69 2.01
1162 1167 6.096001 GCCAATGAATGAAAGAGTTACTGGAT 59.904 38.462 0.00 0.00 0.00 3.41
1171 1176 2.679837 AGAGTTACTGGATGCAATTGCG 59.320 45.455 24.58 12.76 45.83 4.85
1177 1182 2.016318 CTGGATGCAATTGCGAACCTA 58.984 47.619 27.63 18.42 45.83 3.08
1255 1261 6.041637 TGAGGTAGAGTGTGACAATTAACTGT 59.958 38.462 0.00 0.00 0.00 3.55
1311 1317 8.106247 AGAGTTTTCAAATTTCCGCAGTTATA 57.894 30.769 0.00 0.00 0.00 0.98
1364 1371 7.938563 TTGTGTTTGTGAATAAATTAGGTGC 57.061 32.000 0.00 0.00 0.00 5.01
1409 1416 0.251253 TGAACACATGGATGCTGCCA 60.251 50.000 0.00 0.59 43.23 4.92
1518 1525 1.434555 CCTAAAACACGATGTCCGCA 58.565 50.000 0.00 0.00 43.32 5.69
1556 1563 2.889170 AGACCAGTCTAGTCAGAGCA 57.111 50.000 0.00 0.00 38.35 4.26
1568 1575 4.434545 AGTCAGAGCAATGATAAGGCAT 57.565 40.909 0.00 0.00 0.00 4.40
1588 1595 4.033358 GCATGTGCAGATACTTGTACAGAC 59.967 45.833 0.00 0.00 44.79 3.51
1725 1749 6.439375 TGAGTGCATAAGGGAGTTAGAAACTA 59.561 38.462 0.00 0.00 43.03 2.24
1768 1792 9.520204 AATAATGCAGTTATGTGATAAAGCAAC 57.480 29.630 0.00 0.00 39.68 4.17
1847 1871 5.919272 ACGAAAAAGGCAGTTAACTAGAC 57.081 39.130 8.04 5.33 0.00 2.59
1888 1912 1.382629 GCACCCTTCTTTAGGCCCA 59.617 57.895 0.00 0.00 43.27 5.36
1957 1981 2.203640 TCCAGCTCCGGTGACACT 60.204 61.111 7.92 0.00 32.22 3.55
1976 2000 2.305927 ACTTTCCCCATGTCATCGTTCT 59.694 45.455 0.00 0.00 0.00 3.01
1999 2023 0.673644 GGAGGCGCAGAAGCTTGTTA 60.674 55.000 10.83 0.00 39.10 2.41
2006 2030 1.068954 GCAGAAGCTTGTTACAGTGGC 60.069 52.381 2.10 0.00 37.91 5.01
2089 2113 2.702478 TGCTCTTCATGTCCTAGATGGG 59.298 50.000 0.00 0.00 36.20 4.00
2094 2118 3.688049 TCATGTCCTAGATGGGTCTCA 57.312 47.619 0.00 0.00 35.87 3.27
2104 2128 1.459455 ATGGGTCTCATCCTCGAGCG 61.459 60.000 6.99 0.19 32.75 5.03
2241 2733 7.865385 TCTTACTTGCAAAATAATGTTGTGTCC 59.135 33.333 0.00 0.00 0.00 4.02
2259 2751 3.245622 TGTCCAGAGTCAAGACATCCCTA 60.246 47.826 10.31 0.00 35.67 3.53
2262 2754 4.078922 TCCAGAGTCAAGACATCCCTATCT 60.079 45.833 2.72 0.00 0.00 1.98
2297 2789 7.838079 TTTGGGGATCCAGTGAATATTATTG 57.162 36.000 15.23 0.00 45.04 1.90
2330 2822 3.503363 CAGTTAACTTCTGCTCCATTGCA 59.497 43.478 5.07 0.00 41.05 4.08
2402 2894 2.878406 GACCTCTCTACAGCTAGCTCAG 59.122 54.545 16.15 15.02 0.00 3.35
2567 3103 3.753272 TCAGTTTCATGGAGCAGTTAAGC 59.247 43.478 0.00 0.00 0.00 3.09
2572 3108 1.003116 CATGGAGCAGTTAAGCGATGC 60.003 52.381 0.00 0.00 40.15 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.332654 GGCATTCGTCCAAGCGGTT 61.333 57.895 0.00 0.00 0.00 4.44
1 2 2.746277 GGCATTCGTCCAAGCGGT 60.746 61.111 0.00 0.00 0.00 5.68
2 3 1.982073 GAAGGCATTCGTCCAAGCGG 61.982 60.000 0.00 0.00 0.00 5.52
3 4 1.298157 TGAAGGCATTCGTCCAAGCG 61.298 55.000 6.62 0.00 38.34 4.68
4 5 0.169009 GTGAAGGCATTCGTCCAAGC 59.831 55.000 6.62 0.00 38.34 4.01
5 6 0.443869 CGTGAAGGCATTCGTCCAAG 59.556 55.000 6.62 0.00 38.34 3.61
6 7 0.034198 TCGTGAAGGCATTCGTCCAA 59.966 50.000 6.62 0.00 38.34 3.53
7 8 0.389817 CTCGTGAAGGCATTCGTCCA 60.390 55.000 6.62 0.00 38.34 4.02
8 9 0.389948 ACTCGTGAAGGCATTCGTCC 60.390 55.000 6.62 0.00 38.34 4.79
9 10 1.390463 GAACTCGTGAAGGCATTCGTC 59.610 52.381 6.62 1.57 38.34 4.20
10 11 1.270094 TGAACTCGTGAAGGCATTCGT 60.270 47.619 6.62 0.00 38.34 3.85
11 12 1.391485 CTGAACTCGTGAAGGCATTCG 59.609 52.381 6.62 0.00 38.34 3.34
12 13 1.734465 CCTGAACTCGTGAAGGCATTC 59.266 52.381 3.66 3.66 35.87 2.67
13 14 1.813513 CCTGAACTCGTGAAGGCATT 58.186 50.000 0.00 0.00 0.00 3.56
14 15 3.540211 CCTGAACTCGTGAAGGCAT 57.460 52.632 0.00 0.00 0.00 4.40
17 18 0.318441 TCTGCCTGAACTCGTGAAGG 59.682 55.000 0.00 0.00 0.00 3.46
18 19 1.707632 CTCTGCCTGAACTCGTGAAG 58.292 55.000 0.00 0.00 0.00 3.02
19 20 0.319900 GCTCTGCCTGAACTCGTGAA 60.320 55.000 0.00 0.00 0.00 3.18
20 21 1.290324 GCTCTGCCTGAACTCGTGA 59.710 57.895 0.00 0.00 0.00 4.35
21 22 1.739562 GGCTCTGCCTGAACTCGTG 60.740 63.158 0.73 0.00 46.69 4.35
22 23 2.659610 GGCTCTGCCTGAACTCGT 59.340 61.111 0.73 0.00 46.69 4.18
37 38 2.592308 CCCAGGGTAGCTCTTGGC 59.408 66.667 0.00 0.00 42.19 4.52
38 39 1.852157 TTGCCCAGGGTAGCTCTTGG 61.852 60.000 7.55 0.00 0.00 3.61
39 40 0.393537 CTTGCCCAGGGTAGCTCTTG 60.394 60.000 7.55 0.00 0.00 3.02
40 41 1.566298 CCTTGCCCAGGGTAGCTCTT 61.566 60.000 7.55 0.00 39.39 2.85
41 42 1.997874 CCTTGCCCAGGGTAGCTCT 60.998 63.158 7.55 0.00 39.39 4.09
42 43 2.592308 CCTTGCCCAGGGTAGCTC 59.408 66.667 7.55 0.00 39.39 4.09
55 56 2.050350 CCATGACCAGCAGCCCTTG 61.050 63.158 0.00 0.00 0.00 3.61
56 57 2.357836 CCATGACCAGCAGCCCTT 59.642 61.111 0.00 0.00 0.00 3.95
57 58 2.937689 ACCATGACCAGCAGCCCT 60.938 61.111 0.00 0.00 0.00 5.19
58 59 2.439156 GACCATGACCAGCAGCCC 60.439 66.667 0.00 0.00 0.00 5.19
59 60 1.451028 GAGACCATGACCAGCAGCC 60.451 63.158 0.00 0.00 0.00 4.85
60 61 0.107312 ATGAGACCATGACCAGCAGC 60.107 55.000 0.00 0.00 0.00 5.25
70 71 0.036388 AAACGCGTCCATGAGACCAT 60.036 50.000 14.44 0.00 43.08 3.55
71 72 0.250124 AAAACGCGTCCATGAGACCA 60.250 50.000 14.44 0.00 43.08 4.02
72 73 1.717194 TAAAACGCGTCCATGAGACC 58.283 50.000 14.44 0.00 43.08 3.85
73 74 4.336532 AAATAAAACGCGTCCATGAGAC 57.663 40.909 14.44 0.00 42.54 3.36
74 75 6.483385 TTAAAATAAAACGCGTCCATGAGA 57.517 33.333 14.44 0.00 0.00 3.27
75 76 7.555639 TTTTAAAATAAAACGCGTCCATGAG 57.444 32.000 14.44 0.00 0.00 2.90
76 77 7.648510 ACTTTTTAAAATAAAACGCGTCCATGA 59.351 29.630 14.44 0.00 0.00 3.07
77 78 7.779349 ACTTTTTAAAATAAAACGCGTCCATG 58.221 30.769 14.44 0.00 0.00 3.66
78 79 7.933728 ACTTTTTAAAATAAAACGCGTCCAT 57.066 28.000 14.44 4.16 0.00 3.41
79 80 7.275123 ACAACTTTTTAAAATAAAACGCGTCCA 59.725 29.630 14.44 0.00 0.00 4.02
80 81 7.611387 ACAACTTTTTAAAATAAAACGCGTCC 58.389 30.769 14.44 0.00 0.00 4.79
81 82 9.463003 AAACAACTTTTTAAAATAAAACGCGTC 57.537 25.926 14.44 0.00 0.00 5.19
82 83 9.463003 GAAACAACTTTTTAAAATAAAACGCGT 57.537 25.926 5.58 5.58 0.00 6.01
83 84 8.645844 CGAAACAACTTTTTAAAATAAAACGCG 58.354 29.630 3.53 3.53 0.00 6.01
84 85 9.672864 TCGAAACAACTTTTTAAAATAAAACGC 57.327 25.926 0.55 0.00 0.00 4.84
89 90 9.552114 TCACGTCGAAACAACTTTTTAAAATAA 57.448 25.926 0.55 0.00 0.00 1.40
90 91 9.552114 TTCACGTCGAAACAACTTTTTAAAATA 57.448 25.926 0.55 0.00 0.00 1.40
91 92 8.450385 TTCACGTCGAAACAACTTTTTAAAAT 57.550 26.923 0.55 0.00 0.00 1.82
92 93 7.848716 TTCACGTCGAAACAACTTTTTAAAA 57.151 28.000 0.00 0.00 0.00 1.52
93 94 9.552114 TTATTCACGTCGAAACAACTTTTTAAA 57.448 25.926 0.00 0.00 37.12 1.52
94 95 8.997960 GTTATTCACGTCGAAACAACTTTTTAA 58.002 29.630 0.00 3.30 37.12 1.52
95 96 8.389603 AGTTATTCACGTCGAAACAACTTTTTA 58.610 29.630 16.34 0.38 38.69 1.52
96 97 7.245604 AGTTATTCACGTCGAAACAACTTTTT 58.754 30.769 16.34 0.00 38.69 1.94
97 98 6.778108 AGTTATTCACGTCGAAACAACTTTT 58.222 32.000 16.34 5.27 38.69 2.27
98 99 6.354039 AGTTATTCACGTCGAAACAACTTT 57.646 33.333 16.34 5.68 38.69 2.66
99 100 5.978934 AGTTATTCACGTCGAAACAACTT 57.021 34.783 16.34 8.33 38.69 2.66
100 101 5.978934 AAGTTATTCACGTCGAAACAACT 57.021 34.783 16.34 16.34 41.31 3.16
101 102 5.961263 ACAAAGTTATTCACGTCGAAACAAC 59.039 36.000 0.00 14.00 37.12 3.32
102 103 6.109320 ACAAAGTTATTCACGTCGAAACAA 57.891 33.333 0.00 1.26 37.12 2.83
103 104 5.721876 ACAAAGTTATTCACGTCGAAACA 57.278 34.783 0.00 0.00 37.12 2.83
104 105 8.005466 TGAATACAAAGTTATTCACGTCGAAAC 58.995 33.333 0.00 0.00 37.66 2.78
105 106 8.005466 GTGAATACAAAGTTATTCACGTCGAAA 58.995 33.333 16.27 0.00 46.76 3.46
106 107 7.503991 GTGAATACAAAGTTATTCACGTCGAA 58.496 34.615 16.27 3.49 46.76 3.71
107 108 7.041187 GTGAATACAAAGTTATTCACGTCGA 57.959 36.000 16.27 0.00 46.76 4.20
123 124 9.394767 AGCAATACTATGATTGTTGTGAATACA 57.605 29.630 0.00 0.00 38.77 2.29
124 125 9.869844 GAGCAATACTATGATTGTTGTGAATAC 57.130 33.333 0.00 0.00 38.77 1.89
125 126 9.836864 AGAGCAATACTATGATTGTTGTGAATA 57.163 29.630 0.00 0.00 38.77 1.75
126 127 8.743085 AGAGCAATACTATGATTGTTGTGAAT 57.257 30.769 0.00 0.00 38.77 2.57
127 128 8.043113 AGAGAGCAATACTATGATTGTTGTGAA 58.957 33.333 0.00 0.00 38.77 3.18
128 129 7.559486 AGAGAGCAATACTATGATTGTTGTGA 58.441 34.615 0.00 0.00 38.77 3.58
129 130 7.783090 AGAGAGCAATACTATGATTGTTGTG 57.217 36.000 0.00 0.00 38.77 3.33
130 131 8.798859 AAAGAGAGCAATACTATGATTGTTGT 57.201 30.769 0.00 0.00 38.77 3.32
131 132 8.886719 TGAAAGAGAGCAATACTATGATTGTTG 58.113 33.333 0.00 0.00 38.77 3.33
132 133 9.453572 TTGAAAGAGAGCAATACTATGATTGTT 57.546 29.630 0.00 0.00 38.77 2.83
133 134 9.624373 ATTGAAAGAGAGCAATACTATGATTGT 57.376 29.630 0.00 0.00 38.77 2.71
134 135 9.880064 CATTGAAAGAGAGCAATACTATGATTG 57.120 33.333 0.00 0.00 39.41 2.67
135 136 9.624373 ACATTGAAAGAGAGCAATACTATGATT 57.376 29.630 0.00 0.00 33.68 2.57
136 137 9.053840 CACATTGAAAGAGAGCAATACTATGAT 57.946 33.333 0.00 0.00 33.68 2.45
137 138 8.043113 ACACATTGAAAGAGAGCAATACTATGA 58.957 33.333 0.00 0.00 33.68 2.15
138 139 8.121086 CACACATTGAAAGAGAGCAATACTATG 58.879 37.037 0.00 0.00 33.68 2.23
139 140 7.826252 ACACACATTGAAAGAGAGCAATACTAT 59.174 33.333 0.00 0.00 33.68 2.12
140 141 7.161404 ACACACATTGAAAGAGAGCAATACTA 58.839 34.615 0.00 0.00 33.68 1.82
141 142 6.000219 ACACACATTGAAAGAGAGCAATACT 59.000 36.000 0.00 0.00 33.68 2.12
142 143 6.246420 ACACACATTGAAAGAGAGCAATAC 57.754 37.500 0.00 0.00 33.68 1.89
143 144 7.161404 AGTACACACATTGAAAGAGAGCAATA 58.839 34.615 0.00 0.00 33.68 1.90
144 145 6.000219 AGTACACACATTGAAAGAGAGCAAT 59.000 36.000 0.00 0.00 35.24 3.56
145 146 5.368145 AGTACACACATTGAAAGAGAGCAA 58.632 37.500 0.00 0.00 0.00 3.91
146 147 4.960938 AGTACACACATTGAAAGAGAGCA 58.039 39.130 0.00 0.00 0.00 4.26
147 148 6.401581 GCTTAGTACACACATTGAAAGAGAGC 60.402 42.308 0.00 0.00 0.00 4.09
148 149 6.870965 AGCTTAGTACACACATTGAAAGAGAG 59.129 38.462 0.00 0.00 0.00 3.20
149 150 6.759272 AGCTTAGTACACACATTGAAAGAGA 58.241 36.000 0.00 0.00 0.00 3.10
150 151 8.709386 ATAGCTTAGTACACACATTGAAAGAG 57.291 34.615 0.00 0.00 0.00 2.85
151 152 9.502091 AAATAGCTTAGTACACACATTGAAAGA 57.498 29.630 0.00 0.00 0.00 2.52
154 155 9.378551 CCTAAATAGCTTAGTACACACATTGAA 57.621 33.333 0.00 0.00 36.06 2.69
155 156 8.755028 TCCTAAATAGCTTAGTACACACATTGA 58.245 33.333 0.00 0.00 36.06 2.57
156 157 8.942338 TCCTAAATAGCTTAGTACACACATTG 57.058 34.615 0.00 0.00 36.06 2.82
157 158 9.379791 GTTCCTAAATAGCTTAGTACACACATT 57.620 33.333 0.00 0.00 36.06 2.71
158 159 7.985752 GGTTCCTAAATAGCTTAGTACACACAT 59.014 37.037 0.00 0.00 36.06 3.21
159 160 7.325694 GGTTCCTAAATAGCTTAGTACACACA 58.674 38.462 0.00 0.00 36.06 3.72
160 161 6.760298 GGGTTCCTAAATAGCTTAGTACACAC 59.240 42.308 0.00 0.00 36.06 3.82
161 162 6.126968 GGGGTTCCTAAATAGCTTAGTACACA 60.127 42.308 0.00 0.00 36.06 3.72
162 163 6.099413 AGGGGTTCCTAAATAGCTTAGTACAC 59.901 42.308 0.00 0.00 42.75 2.90
163 164 6.207532 AGGGGTTCCTAAATAGCTTAGTACA 58.792 40.000 0.00 0.00 42.75 2.90
164 165 6.744175 AGGGGTTCCTAAATAGCTTAGTAC 57.256 41.667 0.00 0.00 42.75 2.73
165 166 8.858944 TTAAGGGGTTCCTAAATAGCTTAGTA 57.141 34.615 0.00 0.00 44.07 1.82
166 167 7.760400 TTAAGGGGTTCCTAAATAGCTTAGT 57.240 36.000 0.00 0.00 44.07 2.24
167 168 8.272889 AGTTTAAGGGGTTCCTAAATAGCTTAG 58.727 37.037 0.00 0.00 44.07 2.18
168 169 8.166479 AGTTTAAGGGGTTCCTAAATAGCTTA 57.834 34.615 0.00 0.00 44.07 3.09
169 170 7.040913 AGTTTAAGGGGTTCCTAAATAGCTT 57.959 36.000 0.00 0.00 44.07 3.74
170 171 6.653790 AGTTTAAGGGGTTCCTAAATAGCT 57.346 37.500 0.00 0.00 44.07 3.32
171 172 7.714377 GTCTAGTTTAAGGGGTTCCTAAATAGC 59.286 40.741 0.00 0.00 44.07 2.97
172 173 8.765517 TGTCTAGTTTAAGGGGTTCCTAAATAG 58.234 37.037 0.00 0.00 44.07 1.73
173 174 8.683776 TGTCTAGTTTAAGGGGTTCCTAAATA 57.316 34.615 0.00 0.00 44.07 1.40
174 175 7.578458 TGTCTAGTTTAAGGGGTTCCTAAAT 57.422 36.000 0.00 0.00 44.07 1.40
175 176 7.391388 TTGTCTAGTTTAAGGGGTTCCTAAA 57.609 36.000 0.00 0.00 44.07 1.85
176 177 7.391388 TTTGTCTAGTTTAAGGGGTTCCTAA 57.609 36.000 0.00 0.00 44.07 2.69
177 178 6.013119 CCTTTGTCTAGTTTAAGGGGTTCCTA 60.013 42.308 9.99 0.00 44.07 2.94
179 180 5.008331 CCTTTGTCTAGTTTAAGGGGTTCC 58.992 45.833 9.99 0.00 34.77 3.62
180 181 5.872963 TCCTTTGTCTAGTTTAAGGGGTTC 58.127 41.667 14.91 0.00 38.14 3.62
181 182 5.917545 TCCTTTGTCTAGTTTAAGGGGTT 57.082 39.130 14.91 0.00 38.14 4.11
182 183 5.045066 GGATCCTTTGTCTAGTTTAAGGGGT 60.045 44.000 3.84 5.35 38.14 4.95
183 184 5.437946 GGATCCTTTGTCTAGTTTAAGGGG 58.562 45.833 3.84 5.86 38.14 4.79
184 185 5.105064 TCGGATCCTTTGTCTAGTTTAAGGG 60.105 44.000 10.75 8.19 38.14 3.95
185 186 5.974108 TCGGATCCTTTGTCTAGTTTAAGG 58.026 41.667 10.75 11.05 38.78 2.69
186 187 5.520649 GCTCGGATCCTTTGTCTAGTTTAAG 59.479 44.000 10.75 0.00 0.00 1.85
187 188 5.416947 GCTCGGATCCTTTGTCTAGTTTAA 58.583 41.667 10.75 0.00 0.00 1.52
188 189 4.142004 GGCTCGGATCCTTTGTCTAGTTTA 60.142 45.833 10.75 0.00 0.00 2.01
189 190 3.369576 GGCTCGGATCCTTTGTCTAGTTT 60.370 47.826 10.75 0.00 0.00 2.66
190 191 2.168728 GGCTCGGATCCTTTGTCTAGTT 59.831 50.000 10.75 0.00 0.00 2.24
191 192 1.757699 GGCTCGGATCCTTTGTCTAGT 59.242 52.381 10.75 0.00 0.00 2.57
192 193 1.269309 CGGCTCGGATCCTTTGTCTAG 60.269 57.143 10.75 0.00 0.00 2.43
193 194 0.744874 CGGCTCGGATCCTTTGTCTA 59.255 55.000 10.75 0.00 0.00 2.59
194 195 0.970937 TCGGCTCGGATCCTTTGTCT 60.971 55.000 10.75 0.00 0.00 3.41
195 196 0.108329 TTCGGCTCGGATCCTTTGTC 60.108 55.000 10.75 0.03 0.00 3.18
196 197 0.541863 ATTCGGCTCGGATCCTTTGT 59.458 50.000 10.75 0.00 0.00 2.83
197 198 1.221414 GATTCGGCTCGGATCCTTTG 58.779 55.000 10.75 0.58 36.00 2.77
198 199 3.688553 GATTCGGCTCGGATCCTTT 57.311 52.632 10.75 0.00 36.00 3.11
202 203 1.878656 ATCGGGATTCGGCTCGGATC 61.879 60.000 7.19 7.19 40.77 3.36
203 204 1.878656 GATCGGGATTCGGCTCGGAT 61.879 60.000 0.00 0.00 39.77 4.18
204 205 2.520982 ATCGGGATTCGGCTCGGA 60.521 61.111 0.00 0.00 39.77 4.55
205 206 2.049063 GATCGGGATTCGGCTCGG 60.049 66.667 0.00 0.00 39.77 4.63
206 207 2.049063 GGATCGGGATTCGGCTCG 60.049 66.667 0.00 0.00 39.77 5.03
207 208 2.161078 GAGGGATCGGGATTCGGCTC 62.161 65.000 0.00 0.00 39.77 4.70
208 209 2.122813 AGGGATCGGGATTCGGCT 60.123 61.111 0.00 0.00 39.77 5.52
231 232 0.838987 TTGTAGGGGTGAGGTGGGAC 60.839 60.000 0.00 0.00 0.00 4.46
234 235 1.064685 GGATTTGTAGGGGTGAGGTGG 60.065 57.143 0.00 0.00 0.00 4.61
241 242 0.533951 GACGTCGGATTTGTAGGGGT 59.466 55.000 0.00 0.00 0.00 4.95
271 272 1.208293 GGGGGAATCGATGCTAGGATC 59.792 57.143 13.90 13.90 0.00 3.36
276 277 0.399949 AGGTGGGGGAATCGATGCTA 60.400 55.000 2.72 0.00 0.00 3.49
278 279 0.472471 TTAGGTGGGGGAATCGATGC 59.528 55.000 0.00 0.00 0.00 3.91
280 281 1.137697 GGTTAGGTGGGGGAATCGAT 58.862 55.000 0.00 0.00 0.00 3.59
282 283 1.797320 TAGGTTAGGTGGGGGAATCG 58.203 55.000 0.00 0.00 0.00 3.34
301 302 2.417719 GCGAGGCGGATTCAAAGATAT 58.582 47.619 0.00 0.00 0.00 1.63
304 305 4.201951 GCGAGGCGGATTCAAAGA 57.798 55.556 0.00 0.00 0.00 2.52
323 324 2.413437 CTATCGCCACTGCTCCCTCG 62.413 65.000 0.00 0.00 34.43 4.63
326 327 2.280457 GCTATCGCCACTGCTCCC 60.280 66.667 0.00 0.00 34.43 4.30
336 337 2.807045 CCTCGCATCGGCTATCGC 60.807 66.667 0.00 0.00 39.05 4.58
383 384 6.877322 GTGGATTTGAAGCTACAAGTTAGGTA 59.123 38.462 0.00 0.00 0.00 3.08
401 402 3.118454 CTCGCACGCGGTGGATTT 61.118 61.111 12.47 0.00 40.25 2.17
469 470 1.665137 CTACAGGTTAGGTGGGGGTT 58.335 55.000 0.00 0.00 0.00 4.11
537 538 1.338890 TAACCGGGAATCGATGGCCA 61.339 55.000 8.56 8.56 42.43 5.36
543 544 3.005472 GTGATGATCTAACCGGGAATCGA 59.995 47.826 6.32 0.00 42.43 3.59
550 551 3.384789 TCCAGAAGTGATGATCTAACCGG 59.615 47.826 0.00 0.00 0.00 5.28
608 610 4.034285 TGGGGGAATCAAAGAAGAAGAC 57.966 45.455 0.00 0.00 0.00 3.01
723 726 2.979678 ACATTACCAACTGACAGGGACT 59.020 45.455 7.51 0.00 43.88 3.85
769 772 4.629200 CAGAGCTAACTGAATGTTGTCTCC 59.371 45.833 0.00 0.00 39.55 3.71
797 800 8.292448 CACATTTTCTAGCTCAAACTACACAAT 58.708 33.333 0.00 0.00 0.00 2.71
849 852 1.009829 GGATGCAACCAGCTAACTCG 58.990 55.000 8.36 0.00 45.94 4.18
850 853 1.065126 AGGGATGCAACCAGCTAACTC 60.065 52.381 15.68 0.00 45.94 3.01
897 900 6.542821 TGGTTTCTCCAACAGATAACTTCAT 58.457 36.000 0.00 0.00 44.12 2.57
919 922 2.636830 CCCACAGAGCTAACTGAATGG 58.363 52.381 9.28 7.14 40.63 3.16
1029 1033 4.159693 TCGACACATACAATCCTGCTAGTT 59.840 41.667 0.00 0.00 0.00 2.24
1036 1040 3.198068 GCATGTCGACACATACAATCCT 58.802 45.455 22.71 0.00 41.69 3.24
1040 1044 4.274705 AGTTTTGCATGTCGACACATACAA 59.725 37.500 22.71 18.51 42.30 2.41
1055 1059 1.153066 TGCACGGGAGAGTTTTGCA 60.153 52.632 0.00 0.00 40.81 4.08
1065 1069 2.184020 CTGGGTCATTCTGCACGGGA 62.184 60.000 0.00 0.00 0.00 5.14
1162 1167 0.455410 GGCATAGGTTCGCAATTGCA 59.545 50.000 28.77 14.00 42.21 4.08
1171 1176 3.272334 CAGGCGCGGCATAGGTTC 61.272 66.667 34.94 0.00 0.00 3.62
1177 1182 3.127533 GTTCTTCAGGCGCGGCAT 61.128 61.111 34.94 16.89 0.00 4.40
1281 1287 3.826729 CGGAAATTTGAAAACTCTCCCCT 59.173 43.478 0.00 0.00 0.00 4.79
1326 1333 8.129161 TCACAAACACAATTGCTTTTATGAAG 57.871 30.769 5.05 0.00 33.52 3.02
1341 1348 7.043961 TGCACCTAATTTATTCACAAACACA 57.956 32.000 0.00 0.00 0.00 3.72
1364 1371 2.118313 TCTTGTGCAGGTCCATCATG 57.882 50.000 0.00 0.00 0.00 3.07
1518 1525 5.189180 GGTCTTCTTGAGCTTGTGGATATT 58.811 41.667 0.00 0.00 39.86 1.28
1556 1563 5.628130 AGTATCTGCACATGCCTTATCATT 58.372 37.500 0.49 0.00 41.18 2.57
1568 1575 4.864704 TGTCTGTACAAGTATCTGCACA 57.135 40.909 0.00 0.00 30.91 4.57
1588 1595 4.084118 GCAGTTCTAGCTTTCTCACAGTTG 60.084 45.833 0.00 0.00 0.00 3.16
1725 1749 5.011023 GCATTATTTAAGCTAACTGCCCCAT 59.989 40.000 0.00 0.00 44.23 4.00
1888 1912 2.001269 GGAGTAGGCCACCCACCAT 61.001 63.158 5.01 0.00 0.00 3.55
1938 1962 2.203640 TGTCACCGGAGCTGGAGT 60.204 61.111 9.46 0.00 0.00 3.85
1957 1981 3.517901 ACTAGAACGATGACATGGGGAAA 59.482 43.478 0.00 0.00 0.00 3.13
1976 2000 1.544825 AAGCTTCTGCGCCTCCACTA 61.545 55.000 4.18 0.00 45.42 2.74
1999 2023 2.031163 GCAGGAAGTCGCCACTGT 59.969 61.111 0.00 0.00 31.06 3.55
2089 2113 0.248702 GAACCGCTCGAGGATGAGAC 60.249 60.000 15.58 0.00 38.28 3.36
2094 2118 1.330655 ACCATGAACCGCTCGAGGAT 61.331 55.000 15.58 0.00 34.73 3.24
2104 2128 1.743772 CGGAGATCCACACCATGAACC 60.744 57.143 0.00 0.00 35.14 3.62
2241 2733 4.039004 CCAGATAGGGATGTCTTGACTCTG 59.961 50.000 2.35 5.03 0.00 3.35
2259 2751 7.369434 TGGATCCCCAAAATAATAAACCAGAT 58.631 34.615 9.90 0.00 40.09 2.90
2262 2754 6.382570 CACTGGATCCCCAAAATAATAAACCA 59.617 38.462 9.90 0.00 42.98 3.67
2330 2822 4.437587 ACCTCGTCGATCCCCGGT 62.438 66.667 0.00 0.00 39.14 5.28
2402 2894 9.989869 GAAACTAAGCTAACTTATCCATGAAAC 57.010 33.333 0.00 0.00 37.73 2.78
2524 3018 2.497173 ATTGGCAAACTGCGCACCA 61.497 52.632 5.66 9.76 46.21 4.17
2567 3103 4.263677 GCAAAATCATAGTTGTGTGCATCG 59.736 41.667 0.00 0.00 0.00 3.84
2572 3108 4.386652 GCTTGGCAAAATCATAGTTGTGTG 59.613 41.667 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.