Multiple sequence alignment - TraesCS7D01G290200

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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 TraesCS7D01G290200 chr7D 100.000 6312 0 0 1 6312 339120583 339114272 0.000000e+00 11657.0
1 TraesCS7D01G290200 chr7D 86.170 376 38 9 4 378 547298360 547297998 1.650000e-105 394.0
2 TraesCS7D01G290200 chr7D 94.444 54 3 0 432 485 339120067 339120014 4.060000e-12 84.2
3 TraesCS7D01G290200 chr7D 94.444 54 3 0 517 570 339120152 339120099 4.060000e-12 84.2
4 TraesCS7D01G290200 chr7A 96.697 5449 109 24 888 6312 344674949 344680350 0.000000e+00 8999.0
5 TraesCS7D01G290200 chr7A 81.055 417 33 22 415 822 344643203 344643582 2.230000e-74 291.0
6 TraesCS7D01G290200 chr7A 100.000 32 0 0 812 843 344654388 344654419 6.830000e-05 60.2
7 TraesCS7D01G290200 chr7B 95.794 2663 68 11 922 3553 284150065 284147416 0.000000e+00 4257.0
8 TraesCS7D01G290200 chr7B 96.310 2439 70 8 3550 5976 284147065 284144635 0.000000e+00 3988.0
9 TraesCS7D01G290200 chr7B 87.037 540 43 14 414 927 284152075 284151537 9.120000e-163 584.0
10 TraesCS7D01G290200 chr7B 87.366 372 22 6 5962 6312 284144621 284144254 2.740000e-108 403.0
11 TraesCS7D01G290200 chr7B 82.946 387 54 12 1 379 3388346 3388728 7.840000e-89 339.0
12 TraesCS7D01G290200 chr7B 90.805 87 8 0 415 501 284151989 284151903 4.000000e-22 117.0
13 TraesCS7D01G290200 chr4D 88.830 376 35 7 1 375 125246675 125247044 7.460000e-124 455.0
14 TraesCS7D01G290200 chr4D 86.933 375 47 2 2 375 337056908 337057281 2.720000e-113 420.0
15 TraesCS7D01G290200 chr6A 90.462 346 29 4 1 345 604104927 604105269 2.680000e-123 453.0
16 TraesCS7D01G290200 chr6A 85.882 255 32 2 3264 3518 242203957 242204207 1.040000e-67 268.0
17 TraesCS7D01G290200 chr5D 86.126 382 41 12 2 378 358348532 358348158 9.860000e-108 401.0
18 TraesCS7D01G290200 chr5D 89.916 238 21 3 1765 2001 382871966 382871731 2.860000e-78 303.0
19 TraesCS7D01G290200 chr2A 86.982 338 34 8 1 334 45147705 45147374 7.730000e-99 372.0
20 TraesCS7D01G290200 chr1A 84.916 358 47 7 1 356 29218713 29218361 7.780000e-94 355.0
21 TraesCS7D01G290200 chr5B 83.420 386 51 11 1 378 471846909 471847289 4.680000e-91 346.0
22 TraesCS7D01G290200 chr5A 88.462 260 27 3 1759 2017 493864352 493864095 1.710000e-80 311.0
23 TraesCS7D01G290200 chr5A 85.106 235 31 3 3288 3518 426551201 426551435 2.940000e-58 237.0
24 TraesCS7D01G290200 chr5A 80.702 114 18 4 2926 3037 298314075 298314186 1.130000e-12 86.1
25 TraesCS7D01G290200 chr6B 89.958 239 21 3 1765 2001 439062089 439062326 7.950000e-79 305.0
26 TraesCS7D01G290200 chr6B 76.733 202 32 10 2910 3101 645536753 645536949 1.450000e-16 99.0
27 TraesCS7D01G290200 chr1B 89.958 239 20 1 1767 2001 433422812 433423050 7.950000e-79 305.0
28 TraesCS7D01G290200 chr1B 77.692 130 25 3 2944 3069 456743924 456744053 6.790000e-10 76.8
29 TraesCS7D01G290200 chr1D 89.344 244 22 3 1767 2006 320384414 320384657 2.860000e-78 303.0
30 TraesCS7D01G290200 chr2B 87.692 260 28 4 1761 2019 451836718 451836974 3.700000e-77 300.0
31 TraesCS7D01G290200 chr2B 83.399 253 42 0 3266 3518 494257360 494257612 1.060000e-57 235.0
32 TraesCS7D01G290200 chr2B 82.308 260 44 2 3263 3521 403108005 403107747 2.290000e-54 224.0
33 TraesCS7D01G290200 chr2B 79.730 148 25 5 2926 3069 139078180 139078034 1.120000e-17 102.0
34 TraesCS7D01G290200 chr3D 87.209 258 28 5 1759 2016 394142764 394143016 8.010000e-74 289.0
35 TraesCS7D01G290200 chr3D 84.585 253 38 1 3264 3515 422738342 422738090 3.780000e-62 250.0
36 TraesCS7D01G290200 chr6D 86.434 258 31 3 3264 3521 172118062 172117809 4.820000e-71 279.0
37 TraesCS7D01G290200 chr3A 84.190 253 39 1 3264 3515 566132243 566132495 1.760000e-60 244.0
38 TraesCS7D01G290200 chrUn 80.864 162 25 5 2910 3069 17107240 17107083 8.590000e-24 122.0
39 TraesCS7D01G290200 chrUn 80.864 162 25 5 2910 3069 406467407 406467564 8.590000e-24 122.0
40 TraesCS7D01G290200 chrUn 82.353 136 20 3 2936 3069 17086253 17086120 1.440000e-21 115.0


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 TraesCS7D01G290200 chr7D 339114272 339120583 6311 True 3941.8 11657 96.2960 1 6312 3 chr7D.!!$R2 6311
1 TraesCS7D01G290200 chr7A 344674949 344680350 5401 False 8999.0 8999 96.6970 888 6312 1 chr7A.!!$F3 5424
2 TraesCS7D01G290200 chr7B 284144254 284152075 7821 True 1869.8 4257 91.4624 414 6312 5 chr7B.!!$R1 5898

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
28 29 0.031721 CACGAGGGGCCGTATACTTC 59.968 60.000 0.00 0.00 41.29 3.01 F
195 196 0.031994 CGGACCCACAAGCCTTTTTG 59.968 55.000 0.00 0.00 0.00 2.44 F
262 263 0.098200 GGTTCGCCGGCTGTTATTTC 59.902 55.000 26.68 5.82 0.00 2.17 F
2099 3627 0.108585 TTTGAAGCGGCTTGACCTCT 59.891 50.000 21.70 0.00 33.82 3.69 F
2810 4368 1.079681 GTGCCGACGGTACCAATGA 60.080 57.895 22.93 0.00 32.14 2.57 F
3734 5656 3.883830 ATCAAAGCACACAAAACCACA 57.116 38.095 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 3207 0.615331 GGCAGAGTCATCTTCCACCA 59.385 55.000 0.00 0.00 38.60 4.17 R
1955 3483 1.846007 TTAAGCATGGCAACCCGAAT 58.154 45.000 0.00 0.00 0.00 3.34 R
2212 3740 6.064060 TGTGTGAGTTCTTTCTTCCATGAAT 58.936 36.000 0.00 0.00 0.00 2.57 R
3734 5656 1.615392 GCCCTGCTTTGATTTGTGACT 59.385 47.619 0.00 0.00 0.00 3.41 R
3775 5697 1.656441 CTTGTGCACTTGTGCTCCC 59.344 57.895 23.53 13.32 35.49 4.30 R
5730 7663 0.839946 AACCATCCCAAGATCCCTCG 59.160 55.000 0.00 0.00 0.00 4.63 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
24 25 3.228759 GGCACGAGGGGCCGTATA 61.229 66.667 0.00 0.00 42.39 1.47
25 26 2.028631 GCACGAGGGGCCGTATAC 59.971 66.667 0.00 0.00 41.29 1.47
26 27 2.496291 GCACGAGGGGCCGTATACT 61.496 63.158 0.00 0.00 41.29 2.12
27 28 2.024590 GCACGAGGGGCCGTATACTT 62.025 60.000 0.00 0.00 41.29 2.24
28 29 0.031721 CACGAGGGGCCGTATACTTC 59.968 60.000 0.00 0.00 41.29 3.01
29 30 0.106318 ACGAGGGGCCGTATACTTCT 60.106 55.000 0.00 0.00 41.44 2.85
30 31 1.038280 CGAGGGGCCGTATACTTCTT 58.962 55.000 0.00 0.00 0.00 2.52
31 32 1.000496 CGAGGGGCCGTATACTTCTTC 60.000 57.143 0.00 0.00 0.00 2.87
32 33 1.000496 GAGGGGCCGTATACTTCTTCG 60.000 57.143 0.00 0.00 0.00 3.79
33 34 0.033090 GGGGCCGTATACTTCTTCGG 59.967 60.000 0.00 0.00 44.86 4.30
36 37 3.174790 CCGTATACTTCTTCGGCGG 57.825 57.895 7.21 0.00 36.68 6.13
37 38 0.938168 CCGTATACTTCTTCGGCGGC 60.938 60.000 7.21 0.00 36.68 6.53
38 39 0.248743 CGTATACTTCTTCGGCGGCA 60.249 55.000 10.53 0.00 0.00 5.69
39 40 1.602165 CGTATACTTCTTCGGCGGCAT 60.602 52.381 10.53 0.00 0.00 4.40
40 41 1.792949 GTATACTTCTTCGGCGGCATG 59.207 52.381 10.53 0.00 0.00 4.06
41 42 0.532862 ATACTTCTTCGGCGGCATGG 60.533 55.000 10.53 0.00 0.00 3.66
42 43 3.880846 CTTCTTCGGCGGCATGGC 61.881 66.667 9.69 9.69 40.44 4.40
73 74 4.821589 GTTGGCGCGGAGAGGGAG 62.822 72.222 8.83 0.00 34.27 4.30
78 79 2.440430 CGCGGAGAGGGAGGAGAA 60.440 66.667 0.00 0.00 34.27 2.87
79 80 1.830408 CGCGGAGAGGGAGGAGAAT 60.830 63.158 0.00 0.00 34.27 2.40
80 81 1.745264 GCGGAGAGGGAGGAGAATG 59.255 63.158 0.00 0.00 0.00 2.67
81 82 1.753368 GCGGAGAGGGAGGAGAATGG 61.753 65.000 0.00 0.00 0.00 3.16
82 83 1.753368 CGGAGAGGGAGGAGAATGGC 61.753 65.000 0.00 0.00 0.00 4.40
83 84 1.745264 GAGAGGGAGGAGAATGGCG 59.255 63.158 0.00 0.00 0.00 5.69
84 85 1.753368 GAGAGGGAGGAGAATGGCGG 61.753 65.000 0.00 0.00 0.00 6.13
85 86 2.770048 AGGGAGGAGAATGGCGGG 60.770 66.667 0.00 0.00 0.00 6.13
86 87 2.768344 GGGAGGAGAATGGCGGGA 60.768 66.667 0.00 0.00 0.00 5.14
87 88 2.812619 GGGAGGAGAATGGCGGGAG 61.813 68.421 0.00 0.00 0.00 4.30
88 89 1.762460 GGAGGAGAATGGCGGGAGA 60.762 63.158 0.00 0.00 0.00 3.71
89 90 1.338136 GGAGGAGAATGGCGGGAGAA 61.338 60.000 0.00 0.00 0.00 2.87
90 91 0.179070 GAGGAGAATGGCGGGAGAAC 60.179 60.000 0.00 0.00 0.00 3.01
91 92 0.909610 AGGAGAATGGCGGGAGAACA 60.910 55.000 0.00 0.00 0.00 3.18
92 93 0.035439 GGAGAATGGCGGGAGAACAA 60.035 55.000 0.00 0.00 0.00 2.83
93 94 1.613255 GGAGAATGGCGGGAGAACAAA 60.613 52.381 0.00 0.00 0.00 2.83
94 95 1.740025 GAGAATGGCGGGAGAACAAAG 59.260 52.381 0.00 0.00 0.00 2.77
95 96 0.171231 GAATGGCGGGAGAACAAAGC 59.829 55.000 0.00 0.00 0.00 3.51
96 97 0.539438 AATGGCGGGAGAACAAAGCA 60.539 50.000 0.00 0.00 0.00 3.91
97 98 0.962356 ATGGCGGGAGAACAAAGCAG 60.962 55.000 0.00 0.00 0.00 4.24
98 99 1.302511 GGCGGGAGAACAAAGCAGA 60.303 57.895 0.00 0.00 0.00 4.26
99 100 0.889186 GGCGGGAGAACAAAGCAGAA 60.889 55.000 0.00 0.00 0.00 3.02
100 101 0.238553 GCGGGAGAACAAAGCAGAAC 59.761 55.000 0.00 0.00 0.00 3.01
101 102 0.512952 CGGGAGAACAAAGCAGAACG 59.487 55.000 0.00 0.00 0.00 3.95
102 103 1.872237 CGGGAGAACAAAGCAGAACGA 60.872 52.381 0.00 0.00 0.00 3.85
103 104 1.801178 GGGAGAACAAAGCAGAACGAG 59.199 52.381 0.00 0.00 0.00 4.18
104 105 1.801178 GGAGAACAAAGCAGAACGAGG 59.199 52.381 0.00 0.00 0.00 4.63
105 106 1.801178 GAGAACAAAGCAGAACGAGGG 59.199 52.381 0.00 0.00 0.00 4.30
106 107 0.875059 GAACAAAGCAGAACGAGGGG 59.125 55.000 0.00 0.00 0.00 4.79
107 108 0.537371 AACAAAGCAGAACGAGGGGG 60.537 55.000 0.00 0.00 0.00 5.40
121 122 3.533238 GGGGGTGGGAGGGAAAAT 58.467 61.111 0.00 0.00 0.00 1.82
122 123 1.001631 GGGGGTGGGAGGGAAAATG 59.998 63.158 0.00 0.00 0.00 2.32
123 124 1.001631 GGGGTGGGAGGGAAAATGG 59.998 63.158 0.00 0.00 0.00 3.16
124 125 1.514864 GGGGTGGGAGGGAAAATGGA 61.515 60.000 0.00 0.00 0.00 3.41
125 126 0.033109 GGGTGGGAGGGAAAATGGAG 60.033 60.000 0.00 0.00 0.00 3.86
126 127 0.033109 GGTGGGAGGGAAAATGGAGG 60.033 60.000 0.00 0.00 0.00 4.30
127 128 0.033109 GTGGGAGGGAAAATGGAGGG 60.033 60.000 0.00 0.00 0.00 4.30
128 129 1.221213 TGGGAGGGAAAATGGAGGGG 61.221 60.000 0.00 0.00 0.00 4.79
129 130 0.924226 GGGAGGGAAAATGGAGGGGA 60.924 60.000 0.00 0.00 0.00 4.81
130 131 1.007607 GGAGGGAAAATGGAGGGGAA 58.992 55.000 0.00 0.00 0.00 3.97
131 132 1.361197 GGAGGGAAAATGGAGGGGAAA 59.639 52.381 0.00 0.00 0.00 3.13
132 133 2.624293 GGAGGGAAAATGGAGGGGAAAG 60.624 54.545 0.00 0.00 0.00 2.62
133 134 1.362584 AGGGAAAATGGAGGGGAAAGG 59.637 52.381 0.00 0.00 0.00 3.11
134 135 1.195115 GGAAAATGGAGGGGAAAGGC 58.805 55.000 0.00 0.00 0.00 4.35
135 136 0.817654 GAAAATGGAGGGGAAAGGCG 59.182 55.000 0.00 0.00 0.00 5.52
136 137 0.614697 AAAATGGAGGGGAAAGGCGG 60.615 55.000 0.00 0.00 0.00 6.13
137 138 2.514516 AAATGGAGGGGAAAGGCGGG 62.515 60.000 0.00 0.00 0.00 6.13
141 142 4.779486 AGGGGAAAGGCGGGGGAT 62.779 66.667 0.00 0.00 0.00 3.85
142 143 4.205484 GGGGAAAGGCGGGGGATC 62.205 72.222 0.00 0.00 0.00 3.36
143 144 4.564110 GGGAAAGGCGGGGGATCG 62.564 72.222 0.00 0.00 0.00 3.69
144 145 3.476419 GGAAAGGCGGGGGATCGA 61.476 66.667 0.00 0.00 0.00 3.59
145 146 2.203029 GAAAGGCGGGGGATCGAC 60.203 66.667 0.00 0.00 38.69 4.20
146 147 4.157120 AAAGGCGGGGGATCGACG 62.157 66.667 0.00 0.00 44.03 5.12
151 152 3.463585 CGGGGGATCGACGGGAAA 61.464 66.667 0.00 0.00 0.00 3.13
152 153 2.992164 GGGGGATCGACGGGAAAA 59.008 61.111 0.00 0.00 0.00 2.29
153 154 1.300634 GGGGGATCGACGGGAAAAA 59.699 57.895 0.00 0.00 0.00 1.94
154 155 0.746923 GGGGGATCGACGGGAAAAAG 60.747 60.000 0.00 0.00 0.00 2.27
155 156 0.035725 GGGGATCGACGGGAAAAAGT 60.036 55.000 0.00 0.00 0.00 2.66
156 157 1.084289 GGGATCGACGGGAAAAAGTG 58.916 55.000 0.00 0.00 0.00 3.16
157 158 0.446616 GGATCGACGGGAAAAAGTGC 59.553 55.000 0.00 0.00 0.00 4.40
158 159 0.446616 GATCGACGGGAAAAAGTGCC 59.553 55.000 0.00 0.00 0.00 5.01
159 160 0.036306 ATCGACGGGAAAAAGTGCCT 59.964 50.000 0.00 0.00 34.95 4.75
160 161 0.179040 TCGACGGGAAAAAGTGCCTT 60.179 50.000 0.00 0.00 34.95 4.35
161 162 0.237498 CGACGGGAAAAAGTGCCTTC 59.763 55.000 0.00 0.00 34.95 3.46
162 163 1.314730 GACGGGAAAAAGTGCCTTCA 58.685 50.000 0.00 0.00 36.16 3.02
163 164 1.001706 GACGGGAAAAAGTGCCTTCAC 60.002 52.381 0.00 0.00 43.44 3.18
171 172 2.125512 GTGCCTTCACTCGCCGAT 60.126 61.111 0.00 0.00 40.03 4.18
172 173 1.141019 GTGCCTTCACTCGCCGATA 59.859 57.895 0.00 0.00 40.03 2.92
173 174 0.872021 GTGCCTTCACTCGCCGATAG 60.872 60.000 0.00 0.00 40.03 2.08
174 175 1.035385 TGCCTTCACTCGCCGATAGA 61.035 55.000 0.00 0.00 39.76 1.98
175 176 0.318275 GCCTTCACTCGCCGATAGAG 60.318 60.000 0.00 0.00 41.27 2.43
176 177 0.318275 CCTTCACTCGCCGATAGAGC 60.318 60.000 0.00 0.00 39.23 4.09
185 186 3.521605 CGATAGAGCGGACCCACA 58.478 61.111 0.00 0.00 39.76 4.17
186 187 1.813859 CGATAGAGCGGACCCACAA 59.186 57.895 0.00 0.00 39.76 3.33
187 188 0.249073 CGATAGAGCGGACCCACAAG 60.249 60.000 0.00 0.00 39.76 3.16
188 189 0.530870 GATAGAGCGGACCCACAAGC 60.531 60.000 0.00 0.00 0.00 4.01
189 190 1.972660 ATAGAGCGGACCCACAAGCC 61.973 60.000 0.00 0.00 0.00 4.35
190 191 4.021925 GAGCGGACCCACAAGCCT 62.022 66.667 0.00 0.00 0.00 4.58
191 192 3.553095 GAGCGGACCCACAAGCCTT 62.553 63.158 0.00 0.00 0.00 4.35
192 193 2.597510 GCGGACCCACAAGCCTTT 60.598 61.111 0.00 0.00 0.00 3.11
193 194 2.200337 GCGGACCCACAAGCCTTTT 61.200 57.895 0.00 0.00 0.00 2.27
194 195 1.744320 GCGGACCCACAAGCCTTTTT 61.744 55.000 0.00 0.00 0.00 1.94
195 196 0.031994 CGGACCCACAAGCCTTTTTG 59.968 55.000 0.00 0.00 0.00 2.44
196 197 0.249868 GGACCCACAAGCCTTTTTGC 60.250 55.000 0.00 0.00 0.00 3.68
197 198 0.752658 GACCCACAAGCCTTTTTGCT 59.247 50.000 0.00 0.00 45.43 3.91
204 205 1.662044 AGCCTTTTTGCTTCAGCCG 59.338 52.632 0.00 0.00 38.85 5.52
205 206 1.373371 GCCTTTTTGCTTCAGCCGG 60.373 57.895 0.00 0.00 41.18 6.13
206 207 1.373371 CCTTTTTGCTTCAGCCGGC 60.373 57.895 21.89 21.89 41.18 6.13
207 208 1.730547 CTTTTTGCTTCAGCCGGCG 60.731 57.895 23.20 16.49 41.18 6.46
208 209 3.839642 TTTTTGCTTCAGCCGGCGC 62.840 57.895 23.20 19.20 41.18 6.53
245 246 4.016706 CTTGGGTTCGGCTCGGGT 62.017 66.667 0.00 0.00 0.00 5.28
246 247 3.546714 CTTGGGTTCGGCTCGGGTT 62.547 63.158 0.00 0.00 0.00 4.11
247 248 3.540367 TTGGGTTCGGCTCGGGTTC 62.540 63.158 0.00 0.00 0.00 3.62
258 259 4.745751 CGGGTTCGCCGGCTGTTA 62.746 66.667 26.68 3.97 38.45 2.41
259 260 2.124860 GGGTTCGCCGGCTGTTAT 60.125 61.111 26.68 0.00 38.45 1.89
260 261 1.747745 GGGTTCGCCGGCTGTTATT 60.748 57.895 26.68 0.00 38.45 1.40
261 262 1.310216 GGGTTCGCCGGCTGTTATTT 61.310 55.000 26.68 0.00 38.45 1.40
262 263 0.098200 GGTTCGCCGGCTGTTATTTC 59.902 55.000 26.68 5.82 0.00 2.17
263 264 0.247537 GTTCGCCGGCTGTTATTTCG 60.248 55.000 26.68 5.22 0.00 3.46
264 265 1.363145 TTCGCCGGCTGTTATTTCGG 61.363 55.000 26.68 4.37 44.70 4.30
271 272 2.959507 GCTGTTATTTCGGCCCAAAT 57.040 45.000 13.15 13.15 34.02 2.32
272 273 3.245518 GCTGTTATTTCGGCCCAAATT 57.754 42.857 13.83 0.00 34.02 1.82
273 274 2.929398 GCTGTTATTTCGGCCCAAATTG 59.071 45.455 13.83 4.06 34.02 2.32
274 275 3.520569 CTGTTATTTCGGCCCAAATTGG 58.479 45.455 13.83 4.74 37.25 3.16
283 284 2.663826 GCCCAAATTGGCGATAAACA 57.336 45.000 6.48 0.00 42.54 2.83
284 285 2.966050 GCCCAAATTGGCGATAAACAA 58.034 42.857 6.48 0.00 42.54 2.83
285 286 2.929398 GCCCAAATTGGCGATAAACAAG 59.071 45.455 6.48 0.00 42.54 3.16
286 287 3.520569 CCCAAATTGGCGATAAACAAGG 58.479 45.455 6.48 0.00 35.79 3.61
287 288 3.056179 CCCAAATTGGCGATAAACAAGGT 60.056 43.478 6.48 0.00 35.79 3.50
288 289 4.173256 CCAAATTGGCGATAAACAAGGTC 58.827 43.478 0.00 0.00 0.00 3.85
289 290 4.173256 CAAATTGGCGATAAACAAGGTCC 58.827 43.478 0.00 0.00 0.00 4.46
290 291 2.871096 TTGGCGATAAACAAGGTCCT 57.129 45.000 0.00 0.00 0.00 3.85
291 292 2.107950 TGGCGATAAACAAGGTCCTG 57.892 50.000 0.00 0.00 0.00 3.86
292 293 1.339631 TGGCGATAAACAAGGTCCTGG 60.340 52.381 0.00 0.00 0.00 4.45
293 294 1.339727 GGCGATAAACAAGGTCCTGGT 60.340 52.381 0.00 0.00 0.00 4.00
294 295 1.737793 GCGATAAACAAGGTCCTGGTG 59.262 52.381 0.00 0.00 0.00 4.17
295 296 2.356135 CGATAAACAAGGTCCTGGTGG 58.644 52.381 0.00 0.00 0.00 4.61
296 297 2.092323 GATAAACAAGGTCCTGGTGGC 58.908 52.381 0.00 0.00 0.00 5.01
297 298 0.250553 TAAACAAGGTCCTGGTGGCG 60.251 55.000 0.00 0.00 0.00 5.69
298 299 4.643387 ACAAGGTCCTGGTGGCGC 62.643 66.667 0.00 0.00 0.00 6.53
313 314 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
314 315 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
315 316 1.136774 GCGACTGGGCCGATTTTTC 59.863 57.895 0.00 0.00 0.00 2.29
316 317 1.423845 CGACTGGGCCGATTTTTCG 59.576 57.895 0.00 0.00 0.00 3.46
323 324 3.492545 CCGATTTTTCGGCGCCGA 61.493 61.111 45.37 45.37 46.76 5.54
354 355 3.987638 CCTAGGGGGCCTGTTAGG 58.012 66.667 0.84 8.72 38.80 2.69
355 356 1.770518 CCTAGGGGGCCTGTTAGGG 60.771 68.421 16.08 0.00 35.37 3.53
356 357 1.770518 CTAGGGGGCCTGTTAGGGG 60.771 68.421 0.84 0.00 35.37 4.79
375 376 3.780173 GCGGCTGGAGAGGCTCTT 61.780 66.667 19.80 1.95 42.73 2.85
376 377 2.427245 GCGGCTGGAGAGGCTCTTA 61.427 63.158 19.80 10.18 42.73 2.10
377 378 1.739049 CGGCTGGAGAGGCTCTTAG 59.261 63.158 19.80 19.64 42.73 2.18
378 379 1.040339 CGGCTGGAGAGGCTCTTAGT 61.040 60.000 19.80 0.00 42.73 2.24
379 380 0.750249 GGCTGGAGAGGCTCTTAGTC 59.250 60.000 19.80 17.19 41.64 2.59
380 381 1.479709 GCTGGAGAGGCTCTTAGTCA 58.520 55.000 19.80 13.28 0.00 3.41
381 382 1.408702 GCTGGAGAGGCTCTTAGTCAG 59.591 57.143 19.80 21.43 0.00 3.51
382 383 2.031120 CTGGAGAGGCTCTTAGTCAGG 58.969 57.143 19.80 1.78 0.00 3.86
383 384 0.750249 GGAGAGGCTCTTAGTCAGGC 59.250 60.000 19.80 2.60 36.69 4.85
384 385 0.750249 GAGAGGCTCTTAGTCAGGCC 59.250 60.000 19.80 0.00 44.38 5.19
386 387 3.617368 GGCTCTTAGTCAGGCCGA 58.383 61.111 0.00 0.00 35.08 5.54
387 388 1.898154 GGCTCTTAGTCAGGCCGAA 59.102 57.895 0.00 0.00 35.08 4.30
388 389 0.249398 GGCTCTTAGTCAGGCCGAAA 59.751 55.000 0.00 0.00 35.08 3.46
389 390 1.338769 GGCTCTTAGTCAGGCCGAAAA 60.339 52.381 0.00 0.00 35.08 2.29
390 391 2.423577 GCTCTTAGTCAGGCCGAAAAA 58.576 47.619 0.00 0.00 0.00 1.94
428 429 6.995511 TTTTGTGTGTGCTATATTAGGGTC 57.004 37.500 0.00 0.00 0.00 4.46
443 444 1.380246 GGTCAGCCCATCCATGCAA 60.380 57.895 0.00 0.00 0.00 4.08
445 446 0.672342 GTCAGCCCATCCATGCAATC 59.328 55.000 0.00 0.00 0.00 2.67
447 448 1.152398 AGCCCATCCATGCAATCCC 60.152 57.895 0.00 0.00 0.00 3.85
464 465 2.438434 CGCCAAGGCCCAAGTAGG 60.438 66.667 5.34 0.00 37.98 3.18
526 527 2.592861 GAGCCGACCCATCCATGC 60.593 66.667 0.00 0.00 0.00 4.06
528 529 2.203394 GCCGACCCATCCATGCAT 60.203 61.111 0.00 0.00 0.00 3.96
532 533 0.670162 CGACCCATCCATGCATTTCC 59.330 55.000 0.00 0.00 0.00 3.13
539 540 0.323269 TCCATGCATTTCCGCCAAGA 60.323 50.000 0.00 0.00 0.00 3.02
543 544 1.976474 GCATTTCCGCCAAGACCCA 60.976 57.895 0.00 0.00 0.00 4.51
547 548 0.766131 TTTCCGCCAAGACCCAAGTA 59.234 50.000 0.00 0.00 0.00 2.24
559 560 1.361543 ACCCAAGTAGGCTCCTAGTCA 59.638 52.381 3.90 0.00 35.39 3.41
560 561 2.035632 CCCAAGTAGGCTCCTAGTCAG 58.964 57.143 3.90 1.24 35.39 3.51
561 562 1.410882 CCAAGTAGGCTCCTAGTCAGC 59.589 57.143 3.90 2.83 36.02 4.26
568 569 2.770164 GCTCCTAGTCAGCCTTTTCA 57.230 50.000 0.24 0.00 0.00 2.69
569 570 3.274095 GCTCCTAGTCAGCCTTTTCAT 57.726 47.619 0.24 0.00 0.00 2.57
570 571 4.408182 GCTCCTAGTCAGCCTTTTCATA 57.592 45.455 0.24 0.00 0.00 2.15
571 572 4.123506 GCTCCTAGTCAGCCTTTTCATAC 58.876 47.826 0.24 0.00 0.00 2.39
572 573 4.698575 CTCCTAGTCAGCCTTTTCATACC 58.301 47.826 0.00 0.00 0.00 2.73
573 574 4.362677 TCCTAGTCAGCCTTTTCATACCT 58.637 43.478 0.00 0.00 0.00 3.08
574 575 4.406003 TCCTAGTCAGCCTTTTCATACCTC 59.594 45.833 0.00 0.00 0.00 3.85
575 576 3.252974 AGTCAGCCTTTTCATACCTCG 57.747 47.619 0.00 0.00 0.00 4.63
576 577 1.666189 GTCAGCCTTTTCATACCTCGC 59.334 52.381 0.00 0.00 0.00 5.03
577 578 1.277842 TCAGCCTTTTCATACCTCGCA 59.722 47.619 0.00 0.00 0.00 5.10
578 579 2.083774 CAGCCTTTTCATACCTCGCAA 58.916 47.619 0.00 0.00 0.00 4.85
579 580 2.487762 CAGCCTTTTCATACCTCGCAAA 59.512 45.455 0.00 0.00 0.00 3.68
580 581 3.057596 CAGCCTTTTCATACCTCGCAAAA 60.058 43.478 0.00 0.00 0.00 2.44
581 582 3.572255 AGCCTTTTCATACCTCGCAAAAA 59.428 39.130 0.00 0.00 0.00 1.94
639 686 3.181500 ACGAAGTTGTCAAAGAACAAGCC 60.181 43.478 0.00 0.00 37.78 4.35
645 692 5.639082 AGTTGTCAAAGAACAAGCCTTTTTG 59.361 36.000 0.00 0.00 39.69 2.44
646 693 5.398603 TGTCAAAGAACAAGCCTTTTTGA 57.601 34.783 0.00 0.00 35.93 2.69
706 755 2.907236 GAGGAGAGGGGCAAGCTC 59.093 66.667 0.00 0.00 0.00 4.09
713 762 1.101331 GAGGGGCAAGCTCAAGAATG 58.899 55.000 0.00 0.00 0.00 2.67
851 900 6.129062 TGTGTTGTTAAAAAGTTTGCGTCAAG 60.129 34.615 0.00 0.00 0.00 3.02
861 910 9.961266 AAAAAGTTTGCGTCAAGTTTAATTAAC 57.039 25.926 0.00 0.00 36.99 2.01
995 2522 2.357760 TGTTAGGGTTCGTGCCGC 60.358 61.111 0.00 0.00 0.00 6.53
1414 2941 0.755686 AGGATCTGGTCTTCGATGCC 59.244 55.000 0.00 0.00 0.00 4.40
1526 3053 2.416202 CTCGCTGTTGCATAATGTGTCA 59.584 45.455 0.00 0.00 39.64 3.58
1540 3067 7.148289 GCATAATGTGTCAGATCATTAGATGGG 60.148 40.741 13.03 5.57 39.04 4.00
1672 3199 4.037089 TGGCATGCAAGAATTATGTGCTAG 59.963 41.667 21.36 0.00 39.09 3.42
1680 3207 3.200825 AGAATTATGTGCTAGGGCTGTGT 59.799 43.478 0.00 0.00 39.59 3.72
1714 3241 1.911357 TCTGCCCATCATCTGTGAACT 59.089 47.619 0.00 0.00 38.01 3.01
1791 3318 3.196039 TCCCGATAATTCCTGAACGTTCA 59.804 43.478 28.07 28.07 35.57 3.18
1955 3483 6.533367 GTGAACTAAAGTTGCCATGAAAAACA 59.467 34.615 0.00 0.00 38.56 2.83
2099 3627 0.108585 TTTGAAGCGGCTTGACCTCT 59.891 50.000 21.70 0.00 33.82 3.69
2212 3740 3.719268 ATGTAGGATTGGTGCTGACAA 57.281 42.857 0.00 0.00 0.00 3.18
2761 4319 3.969976 TCTTCAGTTATATGGCAGCTCCT 59.030 43.478 0.00 0.00 35.26 3.69
2810 4368 1.079681 GTGCCGACGGTACCAATGA 60.080 57.895 22.93 0.00 32.14 2.57
3109 4669 6.339587 TGGGCTAAAATCAAAGTACCAAAG 57.660 37.500 0.00 0.00 0.00 2.77
3262 4822 6.943981 TCATTACACTTGTTTTCTTGAGTCG 58.056 36.000 0.00 0.00 0.00 4.18
3328 4888 9.338291 CAGTATATTAATTGCATGCACATCTTC 57.662 33.333 22.58 5.88 0.00 2.87
3641 5563 7.625828 ACACTCACTTTTAAGCACTTAAAGT 57.374 32.000 13.61 11.54 43.36 2.66
3733 5655 4.391523 ACAAATCAAAGCACACAAAACCAC 59.608 37.500 0.00 0.00 0.00 4.16
3734 5656 3.883830 ATCAAAGCACACAAAACCACA 57.116 38.095 0.00 0.00 0.00 4.17
3813 5735 2.039624 GGCAGGGGAGGAGAGACA 59.960 66.667 0.00 0.00 0.00 3.41
3906 5828 0.901124 GCCAGAGGAAGAGAGCAGAA 59.099 55.000 0.00 0.00 0.00 3.02
3934 5856 4.227197 TCCTCTCTTAGGGATGCCTTAAG 58.773 47.826 12.53 12.82 46.55 1.85
3963 5885 4.021368 TGCACTTGAGTACCTTCCTAAGAC 60.021 45.833 0.00 0.00 0.00 3.01
4037 5959 9.664332 CTTGATCTTATTAATACTGGATCCCTG 57.336 37.037 9.90 4.71 31.55 4.45
4085 6007 4.113354 AGTTCAACTGTCGAGAAGTGAAC 58.887 43.478 21.31 21.31 36.73 3.18
4309 6231 9.125026 GTCTATTGAAATGACTGTTGGGATAAT 57.875 33.333 0.00 0.00 0.00 1.28
4437 6359 6.064060 TCTAGTGGGCATATGAAATTCCAAG 58.936 40.000 6.97 1.92 0.00 3.61
4636 6560 3.217626 CATGAAAGATAACCCTCCCTGC 58.782 50.000 0.00 0.00 0.00 4.85
5027 6959 4.481368 CACCATACTTTACAGGGTGCTA 57.519 45.455 0.00 0.00 42.11 3.49
5112 7044 7.905604 TGGTTTCATGTATCAAGTACTTCAG 57.094 36.000 4.77 0.00 34.27 3.02
5559 7491 1.975660 GTGGTTTGACAAGGCCACTA 58.024 50.000 24.76 3.92 45.64 2.74
5738 7671 3.190874 GACAATTCAGTGTCGAGGGATC 58.809 50.000 0.00 0.00 38.68 3.36
5845 7780 4.101585 TGATGAACTCTGGAACACTCTGTT 59.898 41.667 0.00 0.00 44.37 3.16
5846 7781 4.487714 TGAACTCTGGAACACTCTGTTT 57.512 40.909 0.00 0.00 41.28 2.83
5847 7782 4.191544 TGAACTCTGGAACACTCTGTTTG 58.808 43.478 0.00 0.00 41.28 2.93
5848 7783 3.914426 ACTCTGGAACACTCTGTTTGT 57.086 42.857 0.00 0.00 41.28 2.83
6028 7992 4.081642 TGCAGTTAATTCGCTAAGAGGAGT 60.082 41.667 0.00 0.00 0.00 3.85
6066 8030 3.467863 AGGTAGGCTAGTCCATAGAGGTT 59.532 47.826 0.00 0.00 39.02 3.50
6087 8051 0.833287 TGCAGATGGAGAGGTAAGCC 59.167 55.000 0.00 0.00 0.00 4.35
6091 8056 2.503356 CAGATGGAGAGGTAAGCCAAGT 59.497 50.000 0.00 0.00 34.95 3.16
6118 8087 6.166279 ACATAAGTGATGCGGATAGTTATGG 58.834 40.000 22.43 13.33 39.93 2.74
6122 8091 4.345257 AGTGATGCGGATAGTTATGGAAGT 59.655 41.667 0.00 0.00 0.00 3.01
6215 8200 3.104843 TGCTTGGTTTTGTTGGTATGC 57.895 42.857 0.00 0.00 0.00 3.14
6243 8228 9.733556 ATGAATATTAGTTTTATGCGGACCATA 57.266 29.630 0.00 0.00 35.34 2.74
6274 8259 4.263905 TGAATCTGGATAGGCACAAACCTT 60.264 41.667 0.00 0.00 41.50 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.228759 TATACGGCCCCTCGTGCC 61.229 66.667 0.00 0.00 43.70 5.01
8 9 2.024590 AAGTATACGGCCCCTCGTGC 62.025 60.000 0.00 0.00 43.70 5.34
9 10 0.031721 GAAGTATACGGCCCCTCGTG 59.968 60.000 0.00 0.00 43.70 4.35
10 11 0.106318 AGAAGTATACGGCCCCTCGT 60.106 55.000 0.00 0.00 45.88 4.18
11 12 1.000496 GAAGAAGTATACGGCCCCTCG 60.000 57.143 0.00 0.00 0.00 4.63
12 13 1.000496 CGAAGAAGTATACGGCCCCTC 60.000 57.143 0.00 0.00 0.00 4.30
13 14 1.038280 CGAAGAAGTATACGGCCCCT 58.962 55.000 0.00 0.00 0.00 4.79
14 15 0.033090 CCGAAGAAGTATACGGCCCC 59.967 60.000 0.00 0.00 38.98 5.80
15 16 3.582743 CCGAAGAAGTATACGGCCC 57.417 57.895 0.00 0.00 38.98 5.80
18 19 0.938168 GCCGCCGAAGAAGTATACGG 60.938 60.000 0.00 0.00 46.74 4.02
19 20 0.248743 TGCCGCCGAAGAAGTATACG 60.249 55.000 0.00 0.00 0.00 3.06
20 21 1.792949 CATGCCGCCGAAGAAGTATAC 59.207 52.381 0.00 0.00 0.00 1.47
21 22 1.270094 CCATGCCGCCGAAGAAGTATA 60.270 52.381 0.00 0.00 0.00 1.47
22 23 0.532862 CCATGCCGCCGAAGAAGTAT 60.533 55.000 0.00 0.00 0.00 2.12
23 24 1.153449 CCATGCCGCCGAAGAAGTA 60.153 57.895 0.00 0.00 0.00 2.24
24 25 2.436646 CCATGCCGCCGAAGAAGT 60.437 61.111 0.00 0.00 0.00 3.01
25 26 3.880846 GCCATGCCGCCGAAGAAG 61.881 66.667 0.00 0.00 0.00 2.85
56 57 4.821589 CTCCCTCTCCGCGCCAAC 62.822 72.222 0.00 0.00 0.00 3.77
61 62 1.830408 ATTCTCCTCCCTCTCCGCG 60.830 63.158 0.00 0.00 0.00 6.46
62 63 1.745264 CATTCTCCTCCCTCTCCGC 59.255 63.158 0.00 0.00 0.00 5.54
63 64 1.753368 GCCATTCTCCTCCCTCTCCG 61.753 65.000 0.00 0.00 0.00 4.63
64 65 1.753368 CGCCATTCTCCTCCCTCTCC 61.753 65.000 0.00 0.00 0.00 3.71
65 66 1.745264 CGCCATTCTCCTCCCTCTC 59.255 63.158 0.00 0.00 0.00 3.20
66 67 1.764054 CCGCCATTCTCCTCCCTCT 60.764 63.158 0.00 0.00 0.00 3.69
67 68 2.812619 CCCGCCATTCTCCTCCCTC 61.813 68.421 0.00 0.00 0.00 4.30
68 69 2.770048 CCCGCCATTCTCCTCCCT 60.770 66.667 0.00 0.00 0.00 4.20
69 70 2.768344 TCCCGCCATTCTCCTCCC 60.768 66.667 0.00 0.00 0.00 4.30
70 71 1.338136 TTCTCCCGCCATTCTCCTCC 61.338 60.000 0.00 0.00 0.00 4.30
71 72 0.179070 GTTCTCCCGCCATTCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
72 73 0.909610 TGTTCTCCCGCCATTCTCCT 60.910 55.000 0.00 0.00 0.00 3.69
73 74 0.035439 TTGTTCTCCCGCCATTCTCC 60.035 55.000 0.00 0.00 0.00 3.71
74 75 1.740025 CTTTGTTCTCCCGCCATTCTC 59.260 52.381 0.00 0.00 0.00 2.87
75 76 1.826385 CTTTGTTCTCCCGCCATTCT 58.174 50.000 0.00 0.00 0.00 2.40
76 77 0.171231 GCTTTGTTCTCCCGCCATTC 59.829 55.000 0.00 0.00 0.00 2.67
77 78 0.539438 TGCTTTGTTCTCCCGCCATT 60.539 50.000 0.00 0.00 0.00 3.16
78 79 0.962356 CTGCTTTGTTCTCCCGCCAT 60.962 55.000 0.00 0.00 0.00 4.40
79 80 1.600636 CTGCTTTGTTCTCCCGCCA 60.601 57.895 0.00 0.00 0.00 5.69
80 81 0.889186 TTCTGCTTTGTTCTCCCGCC 60.889 55.000 0.00 0.00 0.00 6.13
81 82 0.238553 GTTCTGCTTTGTTCTCCCGC 59.761 55.000 0.00 0.00 0.00 6.13
82 83 0.512952 CGTTCTGCTTTGTTCTCCCG 59.487 55.000 0.00 0.00 0.00 5.14
83 84 1.801178 CTCGTTCTGCTTTGTTCTCCC 59.199 52.381 0.00 0.00 0.00 4.30
84 85 1.801178 CCTCGTTCTGCTTTGTTCTCC 59.199 52.381 0.00 0.00 0.00 3.71
85 86 1.801178 CCCTCGTTCTGCTTTGTTCTC 59.199 52.381 0.00 0.00 0.00 2.87
86 87 1.543429 CCCCTCGTTCTGCTTTGTTCT 60.543 52.381 0.00 0.00 0.00 3.01
87 88 0.875059 CCCCTCGTTCTGCTTTGTTC 59.125 55.000 0.00 0.00 0.00 3.18
88 89 0.537371 CCCCCTCGTTCTGCTTTGTT 60.537 55.000 0.00 0.00 0.00 2.83
89 90 1.073199 CCCCCTCGTTCTGCTTTGT 59.927 57.895 0.00 0.00 0.00 2.83
90 91 3.987404 CCCCCTCGTTCTGCTTTG 58.013 61.111 0.00 0.00 0.00 2.77
104 105 1.001631 CATTTTCCCTCCCACCCCC 59.998 63.158 0.00 0.00 0.00 5.40
105 106 1.001631 CCATTTTCCCTCCCACCCC 59.998 63.158 0.00 0.00 0.00 4.95
106 107 0.033109 CTCCATTTTCCCTCCCACCC 60.033 60.000 0.00 0.00 0.00 4.61
107 108 0.033109 CCTCCATTTTCCCTCCCACC 60.033 60.000 0.00 0.00 0.00 4.61
108 109 0.033109 CCCTCCATTTTCCCTCCCAC 60.033 60.000 0.00 0.00 0.00 4.61
109 110 1.221213 CCCCTCCATTTTCCCTCCCA 61.221 60.000 0.00 0.00 0.00 4.37
110 111 0.924226 TCCCCTCCATTTTCCCTCCC 60.924 60.000 0.00 0.00 0.00 4.30
111 112 1.007607 TTCCCCTCCATTTTCCCTCC 58.992 55.000 0.00 0.00 0.00 4.30
112 113 2.624293 CCTTTCCCCTCCATTTTCCCTC 60.624 54.545 0.00 0.00 0.00 4.30
113 114 1.362584 CCTTTCCCCTCCATTTTCCCT 59.637 52.381 0.00 0.00 0.00 4.20
114 115 1.866015 CCTTTCCCCTCCATTTTCCC 58.134 55.000 0.00 0.00 0.00 3.97
115 116 1.195115 GCCTTTCCCCTCCATTTTCC 58.805 55.000 0.00 0.00 0.00 3.13
116 117 0.817654 CGCCTTTCCCCTCCATTTTC 59.182 55.000 0.00 0.00 0.00 2.29
117 118 0.614697 CCGCCTTTCCCCTCCATTTT 60.615 55.000 0.00 0.00 0.00 1.82
118 119 1.000359 CCGCCTTTCCCCTCCATTT 60.000 57.895 0.00 0.00 0.00 2.32
119 120 2.683475 CCGCCTTTCCCCTCCATT 59.317 61.111 0.00 0.00 0.00 3.16
120 121 3.420482 CCCGCCTTTCCCCTCCAT 61.420 66.667 0.00 0.00 0.00 3.41
124 125 4.779486 ATCCCCCGCCTTTCCCCT 62.779 66.667 0.00 0.00 0.00 4.79
125 126 4.205484 GATCCCCCGCCTTTCCCC 62.205 72.222 0.00 0.00 0.00 4.81
126 127 4.564110 CGATCCCCCGCCTTTCCC 62.564 72.222 0.00 0.00 0.00 3.97
127 128 3.476419 TCGATCCCCCGCCTTTCC 61.476 66.667 0.00 0.00 0.00 3.13
128 129 2.203029 GTCGATCCCCCGCCTTTC 60.203 66.667 0.00 0.00 0.00 2.62
129 130 4.157120 CGTCGATCCCCCGCCTTT 62.157 66.667 0.00 0.00 0.00 3.11
134 135 2.524951 TTTTTCCCGTCGATCCCCCG 62.525 60.000 0.00 0.00 0.00 5.73
135 136 0.746923 CTTTTTCCCGTCGATCCCCC 60.747 60.000 0.00 0.00 0.00 5.40
136 137 0.035725 ACTTTTTCCCGTCGATCCCC 60.036 55.000 0.00 0.00 0.00 4.81
137 138 1.084289 CACTTTTTCCCGTCGATCCC 58.916 55.000 0.00 0.00 0.00 3.85
138 139 0.446616 GCACTTTTTCCCGTCGATCC 59.553 55.000 0.00 0.00 0.00 3.36
139 140 0.446616 GGCACTTTTTCCCGTCGATC 59.553 55.000 0.00 0.00 0.00 3.69
140 141 0.036306 AGGCACTTTTTCCCGTCGAT 59.964 50.000 0.00 0.00 27.25 3.59
141 142 1.448497 AGGCACTTTTTCCCGTCGA 59.552 52.632 0.00 0.00 27.25 4.20
142 143 4.058797 AGGCACTTTTTCCCGTCG 57.941 55.556 0.00 0.00 27.25 5.12
154 155 0.872021 CTATCGGCGAGTGAAGGCAC 60.872 60.000 17.22 0.00 45.49 5.01
155 156 1.035385 TCTATCGGCGAGTGAAGGCA 61.035 55.000 17.22 0.00 0.00 4.75
156 157 0.318275 CTCTATCGGCGAGTGAAGGC 60.318 60.000 17.22 0.00 0.00 4.35
157 158 0.318275 GCTCTATCGGCGAGTGAAGG 60.318 60.000 17.22 6.31 0.00 3.46
158 159 3.171705 GCTCTATCGGCGAGTGAAG 57.828 57.895 17.22 11.03 0.00 3.02
168 169 0.249073 CTTGTGGGTCCGCTCTATCG 60.249 60.000 2.07 0.00 0.00 2.92
169 170 0.530870 GCTTGTGGGTCCGCTCTATC 60.531 60.000 2.07 0.00 0.00 2.08
170 171 1.522569 GCTTGTGGGTCCGCTCTAT 59.477 57.895 2.07 0.00 0.00 1.98
171 172 2.656069 GGCTTGTGGGTCCGCTCTA 61.656 63.158 2.07 0.00 0.00 2.43
172 173 4.021925 GGCTTGTGGGTCCGCTCT 62.022 66.667 2.07 0.00 0.00 4.09
173 174 3.553095 AAGGCTTGTGGGTCCGCTC 62.553 63.158 0.00 0.00 0.00 5.03
174 175 2.640581 AAAAGGCTTGTGGGTCCGCT 62.641 55.000 0.00 0.00 0.00 5.52
175 176 1.744320 AAAAAGGCTTGTGGGTCCGC 61.744 55.000 0.00 0.00 0.00 5.54
176 177 0.031994 CAAAAAGGCTTGTGGGTCCG 59.968 55.000 0.00 0.00 0.00 4.79
177 178 0.249868 GCAAAAAGGCTTGTGGGTCC 60.250 55.000 0.00 0.00 0.00 4.46
178 179 0.752658 AGCAAAAAGGCTTGTGGGTC 59.247 50.000 0.00 0.00 42.71 4.46
179 180 2.914908 AGCAAAAAGGCTTGTGGGT 58.085 47.368 0.00 0.00 42.71 4.51
187 188 1.373371 CCGGCTGAAGCAAAAAGGC 60.373 57.895 4.43 0.00 44.36 4.35
188 189 1.373371 GCCGGCTGAAGCAAAAAGG 60.373 57.895 22.15 0.84 44.36 3.11
189 190 1.730547 CGCCGGCTGAAGCAAAAAG 60.731 57.895 26.68 0.00 44.36 2.27
190 191 2.334653 CGCCGGCTGAAGCAAAAA 59.665 55.556 26.68 0.00 44.36 1.94
191 192 4.341502 GCGCCGGCTGAAGCAAAA 62.342 61.111 26.68 0.00 44.36 2.44
228 229 3.546714 AACCCGAGCCGAACCCAAG 62.547 63.158 0.00 0.00 0.00 3.61
229 230 3.540367 GAACCCGAGCCGAACCCAA 62.540 63.158 0.00 0.00 0.00 4.12
230 231 4.011517 GAACCCGAGCCGAACCCA 62.012 66.667 0.00 0.00 0.00 4.51
242 243 1.310216 AAATAACAGCCGGCGAACCC 61.310 55.000 23.20 0.00 0.00 4.11
243 244 0.098200 GAAATAACAGCCGGCGAACC 59.902 55.000 23.20 2.30 0.00 3.62
244 245 0.247537 CGAAATAACAGCCGGCGAAC 60.248 55.000 23.20 7.03 0.00 3.95
245 246 1.363145 CCGAAATAACAGCCGGCGAA 61.363 55.000 23.20 8.26 35.29 4.70
246 247 1.812093 CCGAAATAACAGCCGGCGA 60.812 57.895 23.20 8.45 35.29 5.54
247 248 2.707039 CCGAAATAACAGCCGGCG 59.293 61.111 23.20 18.60 35.29 6.46
249 250 2.478033 GGGCCGAAATAACAGCCGG 61.478 63.158 0.00 0.00 46.75 6.13
250 251 1.309499 TTGGGCCGAAATAACAGCCG 61.309 55.000 0.00 0.00 46.75 5.52
251 252 0.892063 TTTGGGCCGAAATAACAGCC 59.108 50.000 9.10 0.00 44.99 4.85
252 253 2.929398 CAATTTGGGCCGAAATAACAGC 59.071 45.455 24.00 0.00 0.00 4.40
253 254 3.520569 CCAATTTGGGCCGAAATAACAG 58.479 45.455 24.00 14.50 32.67 3.16
254 255 3.601443 CCAATTTGGGCCGAAATAACA 57.399 42.857 24.00 0.00 32.67 2.41
265 266 3.056179 ACCTTGTTTATCGCCAATTTGGG 60.056 43.478 17.03 7.46 38.19 4.12
266 267 4.173256 GACCTTGTTTATCGCCAATTTGG 58.827 43.478 11.27 11.27 41.55 3.28
267 268 4.082245 AGGACCTTGTTTATCGCCAATTTG 60.082 41.667 0.00 0.00 0.00 2.32
268 269 4.082245 CAGGACCTTGTTTATCGCCAATTT 60.082 41.667 0.00 0.00 0.00 1.82
269 270 3.443681 CAGGACCTTGTTTATCGCCAATT 59.556 43.478 0.00 0.00 0.00 2.32
270 271 3.016736 CAGGACCTTGTTTATCGCCAAT 58.983 45.455 0.00 0.00 0.00 3.16
271 272 2.432444 CAGGACCTTGTTTATCGCCAA 58.568 47.619 0.00 0.00 0.00 4.52
272 273 1.339631 CCAGGACCTTGTTTATCGCCA 60.340 52.381 0.00 0.00 0.00 5.69
273 274 1.339727 ACCAGGACCTTGTTTATCGCC 60.340 52.381 0.00 0.00 0.00 5.54
274 275 1.737793 CACCAGGACCTTGTTTATCGC 59.262 52.381 0.00 0.00 0.00 4.58
275 276 2.356135 CCACCAGGACCTTGTTTATCG 58.644 52.381 0.00 0.00 36.89 2.92
276 277 2.092323 GCCACCAGGACCTTGTTTATC 58.908 52.381 0.00 0.00 36.89 1.75
277 278 1.613255 CGCCACCAGGACCTTGTTTAT 60.613 52.381 0.00 0.00 36.89 1.40
278 279 0.250553 CGCCACCAGGACCTTGTTTA 60.251 55.000 0.00 0.00 36.89 2.01
279 280 1.528309 CGCCACCAGGACCTTGTTT 60.528 57.895 0.00 0.00 36.89 2.83
280 281 2.113139 CGCCACCAGGACCTTGTT 59.887 61.111 0.00 0.00 36.89 2.83
281 282 4.643387 GCGCCACCAGGACCTTGT 62.643 66.667 0.00 0.00 36.89 3.16
296 297 2.577763 GAAAAATCGGCCCAGTCGCG 62.578 60.000 0.00 0.00 0.00 5.87
297 298 1.136774 GAAAAATCGGCCCAGTCGC 59.863 57.895 0.00 0.00 0.00 5.19
298 299 1.423845 CGAAAAATCGGCCCAGTCG 59.576 57.895 0.00 0.00 0.00 4.18
299 300 1.800681 CCGAAAAATCGGCCCAGTC 59.199 57.895 4.12 0.00 46.76 3.51
300 301 3.996614 CCGAAAAATCGGCCCAGT 58.003 55.556 4.12 0.00 46.76 4.00
337 338 1.770518 CCCTAACAGGCCCCCTAGG 60.771 68.421 12.71 12.71 32.73 3.02
338 339 1.770518 CCCCTAACAGGCCCCCTAG 60.771 68.421 0.00 0.00 32.73 3.02
339 340 2.375173 CCCCTAACAGGCCCCCTA 59.625 66.667 0.00 0.00 32.73 3.53
358 359 2.362329 CTAAGAGCCTCTCCAGCCGC 62.362 65.000 0.00 0.00 0.00 6.53
359 360 1.040339 ACTAAGAGCCTCTCCAGCCG 61.040 60.000 0.00 0.00 0.00 5.52
360 361 0.750249 GACTAAGAGCCTCTCCAGCC 59.250 60.000 0.00 0.00 0.00 4.85
361 362 1.408702 CTGACTAAGAGCCTCTCCAGC 59.591 57.143 0.00 0.00 0.00 4.85
362 363 2.031120 CCTGACTAAGAGCCTCTCCAG 58.969 57.143 0.00 0.00 0.00 3.86
363 364 1.962402 GCCTGACTAAGAGCCTCTCCA 60.962 57.143 0.00 0.00 0.00 3.86
364 365 0.750249 GCCTGACTAAGAGCCTCTCC 59.250 60.000 0.00 0.00 0.00 3.71
365 366 0.750249 GGCCTGACTAAGAGCCTCTC 59.250 60.000 0.00 0.00 38.52 3.20
366 367 1.040339 CGGCCTGACTAAGAGCCTCT 61.040 60.000 0.00 0.00 39.07 3.69
367 368 1.038130 TCGGCCTGACTAAGAGCCTC 61.038 60.000 0.00 0.00 39.07 4.70
368 369 0.614979 TTCGGCCTGACTAAGAGCCT 60.615 55.000 0.00 0.00 39.07 4.58
369 370 0.249398 TTTCGGCCTGACTAAGAGCC 59.751 55.000 0.00 0.00 38.31 4.70
370 371 2.094762 TTTTCGGCCTGACTAAGAGC 57.905 50.000 0.00 0.00 0.00 4.09
404 405 6.943146 TGACCCTAATATAGCACACACAAAAA 59.057 34.615 0.00 0.00 0.00 1.94
405 406 6.477253 TGACCCTAATATAGCACACACAAAA 58.523 36.000 0.00 0.00 0.00 2.44
406 407 6.056090 TGACCCTAATATAGCACACACAAA 57.944 37.500 0.00 0.00 0.00 2.83
407 408 5.670485 CTGACCCTAATATAGCACACACAA 58.330 41.667 0.00 0.00 0.00 3.33
408 409 4.442893 GCTGACCCTAATATAGCACACACA 60.443 45.833 0.00 0.00 34.64 3.72
409 410 4.058817 GCTGACCCTAATATAGCACACAC 58.941 47.826 0.00 0.00 34.64 3.82
410 411 3.071023 GGCTGACCCTAATATAGCACACA 59.929 47.826 0.00 0.00 36.15 3.72
411 412 3.665190 GGCTGACCCTAATATAGCACAC 58.335 50.000 0.00 0.00 36.15 3.82
428 429 1.469335 GGGATTGCATGGATGGGCTG 61.469 60.000 0.00 0.00 0.00 4.85
443 444 4.447342 CTTGGGCCTTGGCGGGAT 62.447 66.667 4.53 0.00 0.00 3.85
445 446 3.995506 CTACTTGGGCCTTGGCGGG 62.996 68.421 4.53 0.00 0.00 6.13
447 448 2.438434 CCTACTTGGGCCTTGGCG 60.438 66.667 4.53 0.00 0.00 5.69
464 465 2.770164 TGAAAAGGCTGACTAGGAGC 57.230 50.000 7.35 7.35 35.57 4.70
507 508 3.550431 ATGGATGGGTCGGCTCCG 61.550 66.667 1.14 1.14 41.35 4.63
508 509 2.111878 CATGGATGGGTCGGCTCC 59.888 66.667 0.00 0.00 0.00 4.70
510 511 2.288642 AATGCATGGATGGGTCGGCT 62.289 55.000 0.00 0.00 0.00 5.52
512 513 0.670162 GAAATGCATGGATGGGTCGG 59.330 55.000 0.00 0.00 0.00 4.79
515 516 1.394266 GCGGAAATGCATGGATGGGT 61.394 55.000 0.00 0.00 34.15 4.51
526 527 0.527565 CTTGGGTCTTGGCGGAAATG 59.472 55.000 0.00 0.00 0.00 2.32
528 529 0.766131 TACTTGGGTCTTGGCGGAAA 59.234 50.000 0.00 0.00 0.00 3.13
532 533 1.745489 GCCTACTTGGGTCTTGGCG 60.745 63.158 0.00 0.00 36.00 5.69
559 560 2.489938 TTGCGAGGTATGAAAAGGCT 57.510 45.000 0.00 0.00 0.00 4.58
560 561 3.569250 TTTTGCGAGGTATGAAAAGGC 57.431 42.857 0.00 0.00 0.00 4.35
603 604 8.541133 TGACAACTTCGTCACATATTCAATAA 57.459 30.769 0.00 0.00 40.94 1.40
645 692 7.285401 TGCCTGATCCTCCACTTATTAATTTTC 59.715 37.037 0.00 0.00 0.00 2.29
646 693 7.125391 TGCCTGATCCTCCACTTATTAATTTT 58.875 34.615 0.00 0.00 0.00 1.82
668 715 5.352569 CCTCGTTTATCCATAGATTCATGCC 59.647 44.000 0.00 0.00 33.67 4.40
732 781 2.501316 AGCAAAAGAGCCCACTTGTTTT 59.499 40.909 0.00 0.00 34.23 2.43
733 782 2.110578 AGCAAAAGAGCCCACTTGTTT 58.889 42.857 0.00 0.00 34.23 2.83
736 785 2.227388 CACTAGCAAAAGAGCCCACTTG 59.773 50.000 0.00 0.00 34.23 3.16
861 910 5.183140 AGGTTTGGTTTCGGTGATAATCAAG 59.817 40.000 0.00 0.00 0.00 3.02
1414 2941 4.421479 AGCGCCGACTTGGTCTCG 62.421 66.667 2.29 0.00 41.21 4.04
1526 3053 6.212388 AGCGTATTTCTCCCATCTAATGATCT 59.788 38.462 0.00 0.00 0.00 2.75
1540 3067 4.454504 TCTGACCCAAAAAGCGTATTTCTC 59.545 41.667 0.00 0.00 0.00 2.87
1672 3199 0.962356 CATCTTCCACCACACAGCCC 60.962 60.000 0.00 0.00 0.00 5.19
1680 3207 0.615331 GGCAGAGTCATCTTCCACCA 59.385 55.000 0.00 0.00 38.60 4.17
1714 3241 9.066892 GCCATAATTCCTCATTAGTTCACATTA 57.933 33.333 0.00 0.00 30.48 1.90
1791 3318 4.780815 TCGGGATGACATGCTTAAAATCT 58.219 39.130 6.91 0.00 0.00 2.40
1798 3325 2.425143 ATGTTCGGGATGACATGCTT 57.575 45.000 6.91 0.00 0.00 3.91
1827 3354 5.501712 TCACCTCGTGTCAACTAAAGTTGC 61.502 45.833 16.34 12.28 42.25 4.17
1955 3483 1.846007 TTAAGCATGGCAACCCGAAT 58.154 45.000 0.00 0.00 0.00 3.34
2030 3558 8.362639 AGCAACATGAATAAGAAAAGACACAAT 58.637 29.630 0.00 0.00 0.00 2.71
2212 3740 6.064060 TGTGTGAGTTCTTTCTTCCATGAAT 58.936 36.000 0.00 0.00 0.00 2.57
2761 4319 5.045578 GCCAGCATAAGGATTATAAGGAGGA 60.046 44.000 0.00 0.00 39.78 3.71
2810 4368 0.398318 GGCACAGGAGAAGGTGAAGT 59.602 55.000 0.00 0.00 37.18 3.01
3096 4656 5.633655 TTAGGGTGTCTTTGGTACTTTGA 57.366 39.130 0.00 0.00 0.00 2.69
3109 4669 4.799564 TGGAAAATGCATTTAGGGTGTC 57.200 40.909 24.35 16.19 0.00 3.67
3262 4822 9.938280 TGCATTACCCATATACATTTACTAGTC 57.062 33.333 0.00 0.00 0.00 2.59
3328 4888 1.844357 CGCGCGAATAATATCCTACCG 59.156 52.381 28.94 0.00 0.00 4.02
3733 5655 2.608752 GCCCTGCTTTGATTTGTGACTG 60.609 50.000 0.00 0.00 0.00 3.51
3734 5656 1.615392 GCCCTGCTTTGATTTGTGACT 59.385 47.619 0.00 0.00 0.00 3.41
3775 5697 1.656441 CTTGTGCACTTGTGCTCCC 59.344 57.895 23.53 13.32 35.49 4.30
3794 5716 4.465446 TCTCTCCTCCCCTGCCCG 62.465 72.222 0.00 0.00 0.00 6.13
3934 5856 4.083271 GGAAGGTACTCAAGTGCATTGTTC 60.083 45.833 2.93 0.00 38.49 3.18
4037 5959 2.191128 ACAAGTCTGAGACCAATGCC 57.809 50.000 9.33 0.00 32.18 4.40
4164 6086 9.751542 AATACGTTAAATTCACCAAACAAATGA 57.248 25.926 0.00 0.00 0.00 2.57
4288 6210 8.328758 AGAGTATTATCCCAACAGTCATTTCAA 58.671 33.333 0.00 0.00 0.00 2.69
4298 6220 8.160765 TCAAAACTGAAGAGTATTATCCCAACA 58.839 33.333 0.00 0.00 0.00 3.33
4437 6359 8.858003 TTCATCAAGTATCTAACGATCTTGAC 57.142 34.615 7.83 0.00 41.28 3.18
4636 6560 7.550196 CCAAGATTTCCAATGAAAAGGGTATTG 59.450 37.037 0.00 0.00 43.37 1.90
4830 6762 6.378564 TCATTTGTTTGAAACCAGGTTGTCTA 59.621 34.615 5.30 0.50 0.00 2.59
5027 6959 1.679032 GCGGCCAGAACTAGGAACAAT 60.679 52.381 2.24 0.00 0.00 2.71
5549 7481 3.118112 AGGAGACATTCATAGTGGCCTTG 60.118 47.826 3.32 0.00 0.00 3.61
5559 7491 6.183360 CCAAATGCATGTTAGGAGACATTCAT 60.183 38.462 0.00 0.00 42.81 2.57
5730 7663 0.839946 AACCATCCCAAGATCCCTCG 59.160 55.000 0.00 0.00 0.00 4.63
5738 7671 8.863086 ACAAATAATGATATGAACCATCCCAAG 58.137 33.333 0.00 0.00 0.00 3.61
5846 7781 0.609957 CCTGCATGCTTCTTGGGACA 60.610 55.000 20.33 0.00 0.00 4.02
5847 7782 1.941999 GCCTGCATGCTTCTTGGGAC 61.942 60.000 20.33 4.70 0.00 4.46
5848 7783 1.679977 GCCTGCATGCTTCTTGGGA 60.680 57.895 20.33 0.00 0.00 4.37
5994 7958 5.390613 CGAATTAACTGCAACAACTTAGGG 58.609 41.667 0.00 0.00 0.00 3.53
6028 7992 3.072038 CCTACCTCCATCAGCATCATGAA 59.928 47.826 0.00 0.00 31.76 2.57
6066 8030 1.208052 GCTTACCTCTCCATCTGCACA 59.792 52.381 0.00 0.00 0.00 4.57
6087 8051 3.663464 CGCATCACTTATGTGGACTTG 57.337 47.619 8.74 4.03 43.94 3.16
6118 8087 6.587273 AGCTGATATAAACCTTCCTCACTTC 58.413 40.000 0.00 0.00 0.00 3.01
6122 8091 9.561069 GAATAAAGCTGATATAAACCTTCCTCA 57.439 33.333 0.00 0.00 0.00 3.86
6169 8154 8.443953 AACATCAGGTTTATAGAAGATTCAGC 57.556 34.615 0.00 0.00 35.82 4.26
6215 8200 7.040755 TGGTCCGCATAAAACTAATATTCATGG 60.041 37.037 0.00 0.00 0.00 3.66
6243 8228 4.596212 TGCCTATCCAGATTCATCTCACAT 59.404 41.667 0.00 0.00 34.22 3.21
6274 8259 0.958382 GCCGACCATGTTACTGCCAA 60.958 55.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.