Multiple sequence alignment - TraesCS5A01G407000

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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 TraesCS5A01G407000 chr5A 100.000 2458 0 0 869 3326 597841814 597839357 0.000000e+00 4540.0
1 TraesCS5A01G407000 chr5A 100.000 526 0 0 1 526 597842682 597842157 0.000000e+00 972.0
2 TraesCS5A01G407000 chr5D 88.517 2508 138 74 869 3315 479127143 479124725 0.000000e+00 2898.0
3 TraesCS5A01G407000 chr5B 91.751 1879 67 37 870 2702 586866359 586864523 0.000000e+00 2531.0
4 TraesCS5A01G407000 chr5B 91.704 663 35 9 1804 2447 625120718 625120057 0.000000e+00 902.0
5 TraesCS5A01G407000 chr5B 91.704 663 35 9 1804 2447 628700267 628699606 0.000000e+00 902.0
6 TraesCS5A01G407000 chr5B 79.007 443 24 28 2900 3306 586864346 586863937 4.290000e-59 239.0
7 TraesCS5A01G407000 chr5B 84.181 177 8 9 322 478 586866637 586866461 1.600000e-33 154.0
8 TraesCS5A01G407000 chr2D 87.372 1362 79 40 1804 3141 81516751 81515459 0.000000e+00 1476.0
9 TraesCS5A01G407000 chr2D 77.961 667 111 23 1687 2326 309577676 309578333 5.210000e-103 385.0
10 TraesCS5A01G407000 chr2D 77.376 663 115 23 1001 1653 309576862 309577499 8.770000e-96 361.0
11 TraesCS5A01G407000 chr6B 85.735 1360 93 36 1804 3141 507371888 507373168 0.000000e+00 1343.0
12 TraesCS5A01G407000 chr6B 92.149 726 35 7 1804 2510 615609089 615608367 0.000000e+00 1005.0
13 TraesCS5A01G407000 chr6D 87.093 953 82 13 918 1870 5800685 5799774 0.000000e+00 1040.0
14 TraesCS5A01G407000 chr7A 92.006 663 33 9 1804 2447 487477319 487477980 0.000000e+00 913.0
15 TraesCS5A01G407000 chr2B 76.923 663 124 23 1001 1656 362694158 362693518 1.900000e-92 350.0
16 TraesCS5A01G407000 chr2A 76.772 663 125 23 1001 1656 429718844 429718204 8.830000e-91 344.0
17 TraesCS5A01G407000 chr3B 97.222 36 1 0 118 153 572464235 572464270 9.960000e-06 62.1
18 TraesCS5A01G407000 chr6A 94.286 35 1 1 1867 1900 98355176 98355210 6.000000e-03 52.8


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 TraesCS5A01G407000 chr5A 597839357 597842682 3325 True 2756.000000 4540 100.000000 1 3326 2 chr5A.!!$R1 3325
1 TraesCS5A01G407000 chr5D 479124725 479127143 2418 True 2898.000000 2898 88.517000 869 3315 1 chr5D.!!$R1 2446
2 TraesCS5A01G407000 chr5B 586863937 586866637 2700 True 974.666667 2531 84.979667 322 3306 3 chr5B.!!$R3 2984
3 TraesCS5A01G407000 chr5B 625120057 625120718 661 True 902.000000 902 91.704000 1804 2447 1 chr5B.!!$R1 643
4 TraesCS5A01G407000 chr5B 628699606 628700267 661 True 902.000000 902 91.704000 1804 2447 1 chr5B.!!$R2 643
5 TraesCS5A01G407000 chr2D 81515459 81516751 1292 True 1476.000000 1476 87.372000 1804 3141 1 chr2D.!!$R1 1337
6 TraesCS5A01G407000 chr2D 309576862 309578333 1471 False 373.000000 385 77.668500 1001 2326 2 chr2D.!!$F1 1325
7 TraesCS5A01G407000 chr6B 507371888 507373168 1280 False 1343.000000 1343 85.735000 1804 3141 1 chr6B.!!$F1 1337
8 TraesCS5A01G407000 chr6B 615608367 615609089 722 True 1005.000000 1005 92.149000 1804 2510 1 chr6B.!!$R1 706
9 TraesCS5A01G407000 chr6D 5799774 5800685 911 True 1040.000000 1040 87.093000 918 1870 1 chr6D.!!$R1 952
10 TraesCS5A01G407000 chr7A 487477319 487477980 661 False 913.000000 913 92.006000 1804 2447 1 chr7A.!!$F1 643
11 TraesCS5A01G407000 chr2B 362693518 362694158 640 True 350.000000 350 76.923000 1001 1656 1 chr2B.!!$R1 655
12 TraesCS5A01G407000 chr2A 429718204 429718844 640 True 344.000000 344 76.772000 1001 1656 1 chr2A.!!$R1 655

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
150 151 0.037046 GCGGAGTAAAAAGGACCGGA 60.037 55.0 9.46 0.0 43.15 5.14 F
280 281 0.250467 CACTGACAGTGGAACCCCAG 60.250 60.0 25.22 0.0 44.55 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1666 3.479203 CTGCCCCGGACCTGCATA 61.479 66.667 0.73 0.0 33.97 3.14 R
2336 2590 0.179215 CAGTTTGCTCGTCGGAATGC 60.179 55.000 0.00 0.0 0.00 3.56 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.374220 CGGTTATACTATCCCGCACAA 57.626 47.619 0.00 0.00 33.20 3.33
21 22 3.719924 CGGTTATACTATCCCGCACAAA 58.280 45.455 0.00 0.00 33.20 2.83
22 23 3.492011 CGGTTATACTATCCCGCACAAAC 59.508 47.826 0.00 0.00 33.20 2.93
23 24 4.444536 GGTTATACTATCCCGCACAAACA 58.555 43.478 0.00 0.00 0.00 2.83
24 25 5.061179 GGTTATACTATCCCGCACAAACAT 58.939 41.667 0.00 0.00 0.00 2.71
25 26 6.225318 GGTTATACTATCCCGCACAAACATA 58.775 40.000 0.00 0.00 0.00 2.29
26 27 6.877322 GGTTATACTATCCCGCACAAACATAT 59.123 38.462 0.00 0.00 0.00 1.78
27 28 7.389607 GGTTATACTATCCCGCACAAACATATT 59.610 37.037 0.00 0.00 0.00 1.28
28 29 8.780249 GTTATACTATCCCGCACAAACATATTT 58.220 33.333 0.00 0.00 0.00 1.40
29 30 7.817418 ATACTATCCCGCACAAACATATTTT 57.183 32.000 0.00 0.00 0.00 1.82
30 31 6.131544 ACTATCCCGCACAAACATATTTTC 57.868 37.500 0.00 0.00 0.00 2.29
31 32 5.650266 ACTATCCCGCACAAACATATTTTCA 59.350 36.000 0.00 0.00 0.00 2.69
32 33 4.433186 TCCCGCACAAACATATTTTCAG 57.567 40.909 0.00 0.00 0.00 3.02
33 34 4.075682 TCCCGCACAAACATATTTTCAGA 58.924 39.130 0.00 0.00 0.00 3.27
34 35 4.520874 TCCCGCACAAACATATTTTCAGAA 59.479 37.500 0.00 0.00 0.00 3.02
35 36 4.621034 CCCGCACAAACATATTTTCAGAAC 59.379 41.667 0.00 0.00 0.00 3.01
36 37 4.320690 CCGCACAAACATATTTTCAGAACG 59.679 41.667 0.00 0.00 0.00 3.95
37 38 4.909305 CGCACAAACATATTTTCAGAACGT 59.091 37.500 0.00 0.00 0.00 3.99
38 39 5.058008 CGCACAAACATATTTTCAGAACGTC 59.942 40.000 0.00 0.00 0.00 4.34
39 40 5.912396 GCACAAACATATTTTCAGAACGTCA 59.088 36.000 0.00 0.00 0.00 4.35
40 41 6.416455 GCACAAACATATTTTCAGAACGTCAA 59.584 34.615 0.00 0.00 0.00 3.18
41 42 7.043722 GCACAAACATATTTTCAGAACGTCAAA 60.044 33.333 0.00 0.00 0.00 2.69
42 43 8.967218 CACAAACATATTTTCAGAACGTCAAAT 58.033 29.630 0.00 0.00 0.00 2.32
52 53 9.619316 TTTTCAGAACGTCAAATATAACCATTG 57.381 29.630 0.00 0.00 0.00 2.82
53 54 7.915293 TCAGAACGTCAAATATAACCATTGT 57.085 32.000 0.00 0.00 0.00 2.71
54 55 9.438228 TTCAGAACGTCAAATATAACCATTGTA 57.562 29.630 0.00 0.00 0.00 2.41
55 56 9.438228 TCAGAACGTCAAATATAACCATTGTAA 57.562 29.630 0.00 0.00 0.00 2.41
56 57 9.702726 CAGAACGTCAAATATAACCATTGTAAG 57.297 33.333 0.00 0.00 0.00 2.34
57 58 9.444600 AGAACGTCAAATATAACCATTGTAAGT 57.555 29.630 0.00 0.00 0.00 2.24
58 59 9.698617 GAACGTCAAATATAACCATTGTAAGTC 57.301 33.333 0.00 0.00 0.00 3.01
59 60 8.780846 ACGTCAAATATAACCATTGTAAGTCA 57.219 30.769 0.00 0.00 0.00 3.41
60 61 9.391006 ACGTCAAATATAACCATTGTAAGTCAT 57.609 29.630 0.00 0.00 0.00 3.06
61 62 9.650371 CGTCAAATATAACCATTGTAAGTCATG 57.350 33.333 0.00 0.00 0.00 3.07
117 118 6.901081 AAACATATATCTTTTAGGGCCTGC 57.099 37.500 18.53 0.00 0.00 4.85
118 119 5.582950 ACATATATCTTTTAGGGCCTGCA 57.417 39.130 18.53 0.00 0.00 4.41
119 120 5.316987 ACATATATCTTTTAGGGCCTGCAC 58.683 41.667 18.53 0.00 0.00 4.57
120 121 3.951563 ATATCTTTTAGGGCCTGCACA 57.048 42.857 18.53 0.00 0.00 4.57
121 122 2.603075 ATCTTTTAGGGCCTGCACAA 57.397 45.000 18.53 0.00 0.00 3.33
122 123 2.373335 TCTTTTAGGGCCTGCACAAA 57.627 45.000 18.53 5.60 0.00 2.83
123 124 2.888212 TCTTTTAGGGCCTGCACAAAT 58.112 42.857 18.53 0.00 0.00 2.32
124 125 2.562298 TCTTTTAGGGCCTGCACAAATG 59.438 45.455 18.53 10.82 0.00 2.32
125 126 2.008242 TTTAGGGCCTGCACAAATGT 57.992 45.000 18.53 0.00 0.00 2.71
126 127 2.889170 TTAGGGCCTGCACAAATGTA 57.111 45.000 18.53 0.00 0.00 2.29
127 128 2.889170 TAGGGCCTGCACAAATGTAA 57.111 45.000 18.53 0.00 0.00 2.41
128 129 1.256812 AGGGCCTGCACAAATGTAAC 58.743 50.000 4.50 0.00 0.00 2.50
129 130 0.965439 GGGCCTGCACAAATGTAACA 59.035 50.000 0.84 0.00 0.00 2.41
130 131 1.336795 GGGCCTGCACAAATGTAACAC 60.337 52.381 0.84 0.00 0.00 3.32
131 132 1.665735 GGCCTGCACAAATGTAACACG 60.666 52.381 0.00 0.00 0.00 4.49
132 133 1.685302 CCTGCACAAATGTAACACGC 58.315 50.000 0.00 0.00 0.00 5.34
133 134 1.317332 CTGCACAAATGTAACACGCG 58.683 50.000 3.53 3.53 0.00 6.01
134 135 0.040870 TGCACAAATGTAACACGCGG 60.041 50.000 12.47 1.27 0.00 6.46
135 136 0.236187 GCACAAATGTAACACGCGGA 59.764 50.000 12.47 0.00 0.00 5.54
136 137 1.724654 GCACAAATGTAACACGCGGAG 60.725 52.381 12.47 4.93 0.00 4.63
137 138 1.529438 CACAAATGTAACACGCGGAGT 59.471 47.619 12.47 5.72 0.00 3.85
138 139 2.732500 CACAAATGTAACACGCGGAGTA 59.267 45.455 12.47 0.00 0.00 2.59
139 140 3.184783 CACAAATGTAACACGCGGAGTAA 59.815 43.478 12.47 0.00 0.00 2.24
140 141 3.808726 ACAAATGTAACACGCGGAGTAAA 59.191 39.130 12.47 0.00 0.00 2.01
141 142 4.272991 ACAAATGTAACACGCGGAGTAAAA 59.727 37.500 12.47 0.00 0.00 1.52
142 143 5.206299 CAAATGTAACACGCGGAGTAAAAA 58.794 37.500 12.47 0.00 0.00 1.94
143 144 4.657075 ATGTAACACGCGGAGTAAAAAG 57.343 40.909 12.47 0.00 0.00 2.27
144 145 2.801679 TGTAACACGCGGAGTAAAAAGG 59.198 45.455 12.47 0.00 0.00 3.11
145 146 2.243602 AACACGCGGAGTAAAAAGGA 57.756 45.000 12.47 0.00 0.00 3.36
146 147 1.505425 ACACGCGGAGTAAAAAGGAC 58.495 50.000 12.47 0.00 0.00 3.85
147 148 0.794473 CACGCGGAGTAAAAAGGACC 59.206 55.000 12.47 0.00 0.00 4.46
148 149 0.668401 ACGCGGAGTAAAAAGGACCG 60.668 55.000 12.47 0.00 45.26 4.79
149 150 1.356527 CGCGGAGTAAAAAGGACCGG 61.357 60.000 0.00 0.00 43.15 5.28
150 151 0.037046 GCGGAGTAAAAAGGACCGGA 60.037 55.000 9.46 0.00 43.15 5.14
151 152 1.608801 GCGGAGTAAAAAGGACCGGAA 60.609 52.381 9.46 0.00 43.15 4.30
152 153 2.344025 CGGAGTAAAAAGGACCGGAAG 58.656 52.381 9.46 0.00 39.92 3.46
190 191 8.745464 GTAAAATACATTTACCCGCAAAAAGA 57.255 30.769 0.68 0.00 45.02 2.52
191 192 7.883229 AAAATACATTTACCCGCAAAAAGAG 57.117 32.000 0.00 0.00 0.00 2.85
192 193 6.827586 AATACATTTACCCGCAAAAAGAGA 57.172 33.333 0.00 0.00 0.00 3.10
193 194 4.766404 ACATTTACCCGCAAAAAGAGAG 57.234 40.909 0.00 0.00 0.00 3.20
194 195 4.142038 ACATTTACCCGCAAAAAGAGAGT 58.858 39.130 0.00 0.00 0.00 3.24
195 196 5.310451 ACATTTACCCGCAAAAAGAGAGTA 58.690 37.500 0.00 0.00 0.00 2.59
196 197 5.766174 ACATTTACCCGCAAAAAGAGAGTAA 59.234 36.000 0.00 0.00 0.00 2.24
197 198 6.263617 ACATTTACCCGCAAAAAGAGAGTAAA 59.736 34.615 0.00 0.00 34.01 2.01
198 199 6.696441 TTTACCCGCAAAAAGAGAGTAAAA 57.304 33.333 0.00 0.00 0.00 1.52
199 200 6.887626 TTACCCGCAAAAAGAGAGTAAAAT 57.112 33.333 0.00 0.00 0.00 1.82
200 201 7.982761 TTACCCGCAAAAAGAGAGTAAAATA 57.017 32.000 0.00 0.00 0.00 1.40
201 202 6.250344 ACCCGCAAAAAGAGAGTAAAATAC 57.750 37.500 0.00 0.00 0.00 1.89
202 203 5.766174 ACCCGCAAAAAGAGAGTAAAATACA 59.234 36.000 0.00 0.00 0.00 2.29
203 204 6.084277 CCCGCAAAAAGAGAGTAAAATACAC 58.916 40.000 0.00 0.00 0.00 2.90
204 205 6.084277 CCGCAAAAAGAGAGTAAAATACACC 58.916 40.000 0.00 0.00 0.00 4.16
205 206 6.293735 CCGCAAAAAGAGAGTAAAATACACCA 60.294 38.462 0.00 0.00 0.00 4.17
206 207 7.136119 CGCAAAAAGAGAGTAAAATACACCAA 58.864 34.615 0.00 0.00 0.00 3.67
207 208 7.112984 CGCAAAAAGAGAGTAAAATACACCAAC 59.887 37.037 0.00 0.00 0.00 3.77
208 209 7.918562 GCAAAAAGAGAGTAAAATACACCAACA 59.081 33.333 0.00 0.00 0.00 3.33
209 210 9.450807 CAAAAAGAGAGTAAAATACACCAACAG 57.549 33.333 0.00 0.00 0.00 3.16
210 211 6.803154 AAGAGAGTAAAATACACCAACAGC 57.197 37.500 0.00 0.00 0.00 4.40
211 212 5.246307 AGAGAGTAAAATACACCAACAGCC 58.754 41.667 0.00 0.00 0.00 4.85
212 213 5.013183 AGAGAGTAAAATACACCAACAGCCT 59.987 40.000 0.00 0.00 0.00 4.58
213 214 5.631119 AGAGTAAAATACACCAACAGCCTT 58.369 37.500 0.00 0.00 0.00 4.35
214 215 5.473504 AGAGTAAAATACACCAACAGCCTTG 59.526 40.000 0.00 0.00 0.00 3.61
215 216 5.137551 AGTAAAATACACCAACAGCCTTGT 58.862 37.500 0.00 0.00 39.87 3.16
216 217 6.300703 AGTAAAATACACCAACAGCCTTGTA 58.699 36.000 0.00 0.00 36.23 2.41
217 218 5.705609 AAAATACACCAACAGCCTTGTAG 57.294 39.130 0.00 0.00 36.23 2.74
218 219 4.634012 AATACACCAACAGCCTTGTAGA 57.366 40.909 0.00 0.00 36.23 2.59
219 220 4.634012 ATACACCAACAGCCTTGTAGAA 57.366 40.909 0.00 0.00 36.23 2.10
220 221 3.290948 ACACCAACAGCCTTGTAGAAA 57.709 42.857 0.00 0.00 36.23 2.52
221 222 3.214328 ACACCAACAGCCTTGTAGAAAG 58.786 45.455 0.00 0.00 36.23 2.62
222 223 3.118038 ACACCAACAGCCTTGTAGAAAGA 60.118 43.478 0.00 0.00 36.23 2.52
223 224 3.251004 CACCAACAGCCTTGTAGAAAGAC 59.749 47.826 0.00 0.00 36.23 3.01
224 225 3.118038 ACCAACAGCCTTGTAGAAAGACA 60.118 43.478 0.00 0.00 36.23 3.41
225 226 4.074970 CCAACAGCCTTGTAGAAAGACAT 58.925 43.478 0.00 0.00 36.23 3.06
226 227 4.083110 CCAACAGCCTTGTAGAAAGACATG 60.083 45.833 0.00 0.00 36.23 3.21
227 228 3.077359 ACAGCCTTGTAGAAAGACATGC 58.923 45.455 0.00 0.00 35.25 4.06
228 229 3.244700 ACAGCCTTGTAGAAAGACATGCT 60.245 43.478 0.00 0.00 37.94 3.79
229 230 3.755378 CAGCCTTGTAGAAAGACATGCTT 59.245 43.478 0.00 0.00 36.31 3.91
230 231 4.006319 AGCCTTGTAGAAAGACATGCTTC 58.994 43.478 0.00 0.00 35.45 3.86
231 232 3.127721 GCCTTGTAGAAAGACATGCTTCC 59.872 47.826 0.00 0.00 35.24 3.46
232 233 4.583871 CCTTGTAGAAAGACATGCTTCCT 58.416 43.478 0.00 0.00 35.24 3.36
233 234 4.633565 CCTTGTAGAAAGACATGCTTCCTC 59.366 45.833 0.00 0.00 35.24 3.71
234 235 5.486526 CTTGTAGAAAGACATGCTTCCTCT 58.513 41.667 0.00 1.55 35.24 3.69
235 236 5.078411 TGTAGAAAGACATGCTTCCTCTC 57.922 43.478 0.00 0.00 35.24 3.20
236 237 4.528206 TGTAGAAAGACATGCTTCCTCTCA 59.472 41.667 0.00 0.00 35.24 3.27
237 238 3.936564 AGAAAGACATGCTTCCTCTCAC 58.063 45.455 0.00 0.00 35.24 3.51
238 239 3.326006 AGAAAGACATGCTTCCTCTCACA 59.674 43.478 0.00 0.00 35.24 3.58
239 240 3.996921 AAGACATGCTTCCTCTCACAT 57.003 42.857 0.00 0.00 28.17 3.21
240 241 5.188555 AGAAAGACATGCTTCCTCTCACATA 59.811 40.000 0.00 0.00 35.24 2.29
241 242 4.399004 AGACATGCTTCCTCTCACATAC 57.601 45.455 0.00 0.00 0.00 2.39
242 243 3.771479 AGACATGCTTCCTCTCACATACA 59.229 43.478 0.00 0.00 0.00 2.29
243 244 4.118410 GACATGCTTCCTCTCACATACAG 58.882 47.826 0.00 0.00 0.00 2.74
244 245 3.517100 ACATGCTTCCTCTCACATACAGT 59.483 43.478 0.00 0.00 0.00 3.55
245 246 9.878841 AAGACATGCTTCCTCTCACATACAGTG 62.879 44.444 0.00 0.00 40.31 3.66
257 258 5.791367 CACATACAGTGCCTATGATATGC 57.209 43.478 7.54 0.00 42.15 3.14
258 259 5.485620 CACATACAGTGCCTATGATATGCT 58.514 41.667 7.54 0.00 42.15 3.79
259 260 6.633856 CACATACAGTGCCTATGATATGCTA 58.366 40.000 7.54 0.00 42.15 3.49
260 261 6.533012 CACATACAGTGCCTATGATATGCTAC 59.467 42.308 7.54 0.00 42.15 3.58
261 262 4.543590 ACAGTGCCTATGATATGCTACC 57.456 45.455 1.61 0.00 0.00 3.18
262 263 3.903714 ACAGTGCCTATGATATGCTACCA 59.096 43.478 1.61 0.00 0.00 3.25
263 264 4.248859 CAGTGCCTATGATATGCTACCAC 58.751 47.826 1.61 0.00 0.00 4.16
264 265 4.020751 CAGTGCCTATGATATGCTACCACT 60.021 45.833 1.61 0.00 0.00 4.00
265 266 4.020751 AGTGCCTATGATATGCTACCACTG 60.021 45.833 1.61 0.00 30.65 3.66
266 267 4.021104 GTGCCTATGATATGCTACCACTGA 60.021 45.833 1.61 0.00 0.00 3.41
267 268 4.021104 TGCCTATGATATGCTACCACTGAC 60.021 45.833 1.61 0.00 0.00 3.51
268 269 4.021104 GCCTATGATATGCTACCACTGACA 60.021 45.833 0.00 0.00 0.00 3.58
269 270 5.718146 CCTATGATATGCTACCACTGACAG 58.282 45.833 0.00 0.00 0.00 3.51
270 271 5.244851 CCTATGATATGCTACCACTGACAGT 59.755 44.000 1.07 1.07 0.00 3.55
271 272 4.391405 TGATATGCTACCACTGACAGTG 57.609 45.455 25.83 25.83 45.53 3.66
278 279 4.800554 CACTGACAGTGGAACCCC 57.199 61.111 25.22 0.00 42.35 4.95
279 280 1.836391 CACTGACAGTGGAACCCCA 59.164 57.895 25.22 0.00 42.35 4.96
280 281 0.250467 CACTGACAGTGGAACCCCAG 60.250 60.000 25.22 0.00 44.55 4.45
281 282 1.302832 CTGACAGTGGAACCCCAGC 60.303 63.158 0.00 0.00 44.55 4.85
282 283 1.770110 TGACAGTGGAACCCCAGCT 60.770 57.895 0.00 0.00 44.55 4.24
283 284 1.302832 GACAGTGGAACCCCAGCTG 60.303 63.158 6.78 6.78 44.55 4.24
284 285 1.768684 GACAGTGGAACCCCAGCTGA 61.769 60.000 17.39 0.00 44.55 4.26
285 286 1.352622 ACAGTGGAACCCCAGCTGAA 61.353 55.000 17.39 0.00 44.55 3.02
286 287 0.890996 CAGTGGAACCCCAGCTGAAC 60.891 60.000 17.39 1.74 44.55 3.18
287 288 1.603739 GTGGAACCCCAGCTGAACC 60.604 63.158 17.39 10.98 44.55 3.62
288 289 2.035783 GGAACCCCAGCTGAACCC 59.964 66.667 17.39 5.08 0.00 4.11
289 290 2.359975 GAACCCCAGCTGAACCCG 60.360 66.667 17.39 0.00 0.00 5.28
290 291 4.660938 AACCCCAGCTGAACCCGC 62.661 66.667 17.39 0.00 0.00 6.13
294 295 4.335647 CCAGCTGAACCCGCCAGT 62.336 66.667 17.39 0.00 34.29 4.00
295 296 2.281761 CAGCTGAACCCGCCAGTT 60.282 61.111 8.42 0.00 34.29 3.16
296 297 2.281761 AGCTGAACCCGCCAGTTG 60.282 61.111 0.00 0.00 34.29 3.16
297 298 4.043200 GCTGAACCCGCCAGTTGC 62.043 66.667 0.00 0.00 34.29 4.17
307 308 4.424566 CCAGTTGCGTGCATGGCC 62.425 66.667 8.27 0.00 0.00 5.36
308 309 4.424566 CAGTTGCGTGCATGGCCC 62.425 66.667 8.27 0.18 0.00 5.80
317 318 4.828296 GCATGGCCCCACTCCCAG 62.828 72.222 0.00 0.00 34.01 4.45
318 319 4.828296 CATGGCCCCACTCCCAGC 62.828 72.222 0.00 0.00 34.01 4.85
327 328 0.674895 CCACTCCCAGCCGAGAAAAG 60.675 60.000 0.39 0.00 33.83 2.27
404 416 2.029666 GATCCATCCGTCCAGGCG 59.970 66.667 0.00 0.00 40.77 5.52
423 435 4.785453 CAGCTCGCCCCCTTCACC 62.785 72.222 0.00 0.00 0.00 4.02
478 499 1.290324 CTCACCCTCACTGACACCG 59.710 63.158 0.00 0.00 0.00 4.94
479 500 1.456892 TCACCCTCACTGACACCGT 60.457 57.895 0.00 0.00 0.00 4.83
481 502 2.357517 CCCTCACTGACACCGTGC 60.358 66.667 0.00 0.00 32.54 5.34
900 962 1.220236 CAATCTCTCTCCCTCCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
985 1056 4.227134 CCGCGGATCCCACCTGAG 62.227 72.222 24.07 0.00 0.00 3.35
987 1058 4.899239 GCGGATCCCACCTGAGCG 62.899 72.222 6.06 0.00 0.00 5.03
988 1059 3.147595 CGGATCCCACCTGAGCGA 61.148 66.667 6.06 0.00 0.00 4.93
989 1060 2.502492 CGGATCCCACCTGAGCGAT 61.502 63.158 6.06 0.00 0.00 4.58
991 1062 1.006805 GATCCCACCTGAGCGATCG 60.007 63.158 11.69 11.69 0.00 3.69
2374 2658 4.495422 ACTGTACAAAGTAGCCGAGAATG 58.505 43.478 0.00 0.00 0.00 2.67
2383 2671 2.853731 AGCCGAGAATGTAGAAGACG 57.146 50.000 0.00 0.00 0.00 4.18
2391 2679 5.399892 CGAGAATGTAGAAGACGATTTAGCC 59.600 44.000 0.00 0.00 0.00 3.93
2405 2704 4.659088 GATTTAGCCGGTTCTTTAGTTGC 58.341 43.478 1.90 0.00 0.00 4.17
2413 2712 0.237235 TTCTTTAGTTGCTTGCGGCG 59.763 50.000 0.51 0.51 45.43 6.46
2414 2713 1.154225 CTTTAGTTGCTTGCGGCGG 60.154 57.895 9.78 0.00 45.43 6.13
2454 2758 3.184541 CGATGGGTTAGTAGTTGGTTCG 58.815 50.000 0.00 0.00 0.00 3.95
2459 2763 3.196254 GGGTTAGTAGTTGGTTCGGATCA 59.804 47.826 0.00 0.00 0.00 2.92
2465 2769 3.771577 AGTTGGTTCGGATCACTTTCT 57.228 42.857 0.00 0.00 0.00 2.52
2466 2770 4.086706 AGTTGGTTCGGATCACTTTCTT 57.913 40.909 0.00 0.00 0.00 2.52
2563 2871 6.545298 AGCTGTTTCCCTCTATGAATCAAATC 59.455 38.462 0.00 0.00 0.00 2.17
2586 2907 5.012046 TCAAACTGAGAGCCTTTGTGATCTA 59.988 40.000 0.00 0.00 0.00 1.98
2622 2943 4.046462 TCGAGTTTGACCTTTGTAGAACG 58.954 43.478 0.00 0.00 0.00 3.95
2636 2963 3.558418 TGTAGAACGAGTCCTTTTGCAAC 59.442 43.478 0.00 0.00 0.00 4.17
2637 2964 1.597663 AGAACGAGTCCTTTTGCAACG 59.402 47.619 0.00 0.00 0.00 4.10
2638 2965 1.595794 GAACGAGTCCTTTTGCAACGA 59.404 47.619 0.00 0.00 0.00 3.85
2654 2984 4.214437 GCAACGAGTGAAAAGATGAACTG 58.786 43.478 0.00 0.00 0.00 3.16
2681 3011 3.930336 ACTCATTTGCGATTGAGACTGA 58.070 40.909 25.69 0.00 41.53 3.41
2683 3013 3.663025 TCATTTGCGATTGAGACTGACA 58.337 40.909 0.00 0.00 0.00 3.58
2721 3051 3.078837 TCCGCAGAGGATAAACCAAAAC 58.921 45.455 0.00 0.00 45.98 2.43
2793 3126 5.087397 GCATATAGTACTAGCCGAAACGAG 58.913 45.833 8.85 0.00 0.00 4.18
2803 3136 1.719780 GCCGAAACGAGTGTCTACAAG 59.280 52.381 0.00 0.00 0.00 3.16
2888 3237 1.662044 CAACCCTGCAAGCAAGGTC 59.338 57.895 15.18 0.00 39.63 3.85
2893 3242 4.269523 TGCAAGCAAGGTCGCCCT 62.270 61.111 0.00 0.00 45.63 5.19
2921 3271 1.892209 TTCGAAGGAAAAGGACCTGC 58.108 50.000 0.00 0.00 37.85 4.85
2990 3340 4.447342 CATGAGGGGTGGGGGCAC 62.447 72.222 0.00 0.00 0.00 5.01
3091 3446 3.279116 GCAGCGAGGCAACACACA 61.279 61.111 0.00 0.00 41.41 3.72
3168 3524 4.176752 CCTAGCGTTGGAGGGGGC 62.177 72.222 0.00 0.00 0.00 5.80
3191 3574 2.456119 GGATTGGCTGTCGTCTGCG 61.456 63.158 5.56 0.00 39.00 5.18
3264 3656 2.418884 GCTCCTTTCGGGTAAAGAGGAG 60.419 54.545 12.23 12.23 46.44 3.69
3265 3657 2.168728 CTCCTTTCGGGTAAAGAGGAGG 59.831 54.545 9.34 0.00 46.44 4.30
3266 3658 2.185387 CCTTTCGGGTAAAGAGGAGGA 58.815 52.381 0.00 0.00 46.44 3.71
3288 3680 2.517875 CCCATGCCAGCTAGTGCC 60.518 66.667 0.00 0.00 40.80 5.01
3298 3690 0.535797 AGCTAGTGCCGTACCTTTCC 59.464 55.000 0.00 0.00 40.80 3.13
3299 3691 0.461516 GCTAGTGCCGTACCTTTCCC 60.462 60.000 0.00 0.00 0.00 3.97
3319 3711 2.869897 CTCGAAAAGGAGAGAGGAACG 58.130 52.381 0.00 0.00 36.65 3.95
3320 3712 1.067776 TCGAAAAGGAGAGAGGAACGC 60.068 52.381 0.00 0.00 0.00 4.84
3321 3713 1.067495 CGAAAAGGAGAGAGGAACGCT 60.067 52.381 0.00 0.00 44.68 5.07
3322 3714 2.342179 GAAAAGGAGAGAGGAACGCTG 58.658 52.381 0.00 0.00 39.71 5.18
3323 3715 1.633774 AAAGGAGAGAGGAACGCTGA 58.366 50.000 0.00 0.00 39.71 4.26
3324 3716 0.892063 AAGGAGAGAGGAACGCTGAC 59.108 55.000 0.00 0.00 39.71 3.51
3325 3717 1.137825 GGAGAGAGGAACGCTGACG 59.862 63.158 0.00 0.00 39.71 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.374220 TTGTGCGGGATAGTATAACCG 57.626 47.619 17.23 17.23 44.66 4.44
1 2 4.444536 TGTTTGTGCGGGATAGTATAACC 58.555 43.478 0.00 0.00 31.81 2.85
2 3 7.900782 ATATGTTTGTGCGGGATAGTATAAC 57.099 36.000 0.00 0.00 0.00 1.89
3 4 8.911918 AAATATGTTTGTGCGGGATAGTATAA 57.088 30.769 0.00 0.00 0.00 0.98
4 5 8.911918 AAAATATGTTTGTGCGGGATAGTATA 57.088 30.769 0.00 0.00 0.00 1.47
5 6 7.500892 TGAAAATATGTTTGTGCGGGATAGTAT 59.499 33.333 0.00 0.00 0.00 2.12
6 7 6.824196 TGAAAATATGTTTGTGCGGGATAGTA 59.176 34.615 0.00 0.00 0.00 1.82
7 8 5.650266 TGAAAATATGTTTGTGCGGGATAGT 59.350 36.000 0.00 0.00 0.00 2.12
8 9 6.038161 TCTGAAAATATGTTTGTGCGGGATAG 59.962 38.462 0.00 0.00 0.00 2.08
9 10 5.883115 TCTGAAAATATGTTTGTGCGGGATA 59.117 36.000 0.00 0.00 0.00 2.59
10 11 4.704540 TCTGAAAATATGTTTGTGCGGGAT 59.295 37.500 0.00 0.00 0.00 3.85
11 12 4.075682 TCTGAAAATATGTTTGTGCGGGA 58.924 39.130 0.00 0.00 0.00 5.14
12 13 4.433186 TCTGAAAATATGTTTGTGCGGG 57.567 40.909 0.00 0.00 0.00 6.13
13 14 4.320690 CGTTCTGAAAATATGTTTGTGCGG 59.679 41.667 0.00 0.00 0.00 5.69
14 15 4.909305 ACGTTCTGAAAATATGTTTGTGCG 59.091 37.500 0.00 0.00 0.00 5.34
15 16 5.912396 TGACGTTCTGAAAATATGTTTGTGC 59.088 36.000 0.00 0.00 0.00 4.57
16 17 7.906611 TTGACGTTCTGAAAATATGTTTGTG 57.093 32.000 0.00 0.00 0.00 3.33
26 27 9.619316 CAATGGTTATATTTGACGTTCTGAAAA 57.381 29.630 0.00 0.00 0.00 2.29
27 28 8.788806 ACAATGGTTATATTTGACGTTCTGAAA 58.211 29.630 0.00 0.00 0.00 2.69
28 29 8.330466 ACAATGGTTATATTTGACGTTCTGAA 57.670 30.769 0.00 0.00 0.00 3.02
29 30 7.915293 ACAATGGTTATATTTGACGTTCTGA 57.085 32.000 0.00 0.00 0.00 3.27
30 31 9.702726 CTTACAATGGTTATATTTGACGTTCTG 57.297 33.333 0.00 0.00 0.00 3.02
31 32 9.444600 ACTTACAATGGTTATATTTGACGTTCT 57.555 29.630 0.00 0.00 0.00 3.01
32 33 9.698617 GACTTACAATGGTTATATTTGACGTTC 57.301 33.333 0.00 0.00 0.00 3.95
33 34 9.221933 TGACTTACAATGGTTATATTTGACGTT 57.778 29.630 0.00 0.00 0.00 3.99
34 35 8.780846 TGACTTACAATGGTTATATTTGACGT 57.219 30.769 0.00 0.00 0.00 4.34
35 36 9.650371 CATGACTTACAATGGTTATATTTGACG 57.350 33.333 0.00 0.00 0.00 4.35
91 92 9.025041 GCAGGCCCTAAAAGATATATGTTTAAT 57.975 33.333 8.17 0.00 0.00 1.40
92 93 8.001875 TGCAGGCCCTAAAAGATATATGTTTAA 58.998 33.333 8.17 0.00 0.00 1.52
93 94 7.447238 GTGCAGGCCCTAAAAGATATATGTTTA 59.553 37.037 8.17 3.83 0.00 2.01
94 95 6.265422 GTGCAGGCCCTAAAAGATATATGTTT 59.735 38.462 0.00 2.10 0.00 2.83
95 96 5.770162 GTGCAGGCCCTAAAAGATATATGTT 59.230 40.000 0.00 0.00 0.00 2.71
96 97 5.163099 TGTGCAGGCCCTAAAAGATATATGT 60.163 40.000 0.00 0.00 0.00 2.29
97 98 5.316167 TGTGCAGGCCCTAAAAGATATATG 58.684 41.667 0.00 0.00 0.00 1.78
98 99 5.582950 TGTGCAGGCCCTAAAAGATATAT 57.417 39.130 0.00 0.00 0.00 0.86
99 100 5.381184 TTGTGCAGGCCCTAAAAGATATA 57.619 39.130 0.00 0.00 0.00 0.86
100 101 3.951563 TGTGCAGGCCCTAAAAGATAT 57.048 42.857 0.00 0.00 0.00 1.63
101 102 3.730215 TTGTGCAGGCCCTAAAAGATA 57.270 42.857 0.00 0.00 0.00 1.98
102 103 2.603075 TTGTGCAGGCCCTAAAAGAT 57.397 45.000 0.00 0.00 0.00 2.40
103 104 2.373335 TTTGTGCAGGCCCTAAAAGA 57.627 45.000 0.00 0.00 0.00 2.52
104 105 2.299867 ACATTTGTGCAGGCCCTAAAAG 59.700 45.455 0.00 0.00 0.00 2.27
105 106 2.324541 ACATTTGTGCAGGCCCTAAAA 58.675 42.857 0.00 0.00 0.00 1.52
106 107 2.008242 ACATTTGTGCAGGCCCTAAA 57.992 45.000 0.00 0.00 0.00 1.85
107 108 2.823154 GTTACATTTGTGCAGGCCCTAA 59.177 45.455 0.00 0.00 0.00 2.69
108 109 2.224892 TGTTACATTTGTGCAGGCCCTA 60.225 45.455 0.00 0.00 0.00 3.53
109 110 1.256812 GTTACATTTGTGCAGGCCCT 58.743 50.000 0.00 0.00 0.00 5.19
110 111 0.965439 TGTTACATTTGTGCAGGCCC 59.035 50.000 0.00 0.00 0.00 5.80
111 112 1.665735 CGTGTTACATTTGTGCAGGCC 60.666 52.381 0.00 0.00 0.00 5.19
112 113 1.685302 CGTGTTACATTTGTGCAGGC 58.315 50.000 0.00 0.00 0.00 4.85
113 114 1.685302 GCGTGTTACATTTGTGCAGG 58.315 50.000 0.00 0.53 0.00 4.85
114 115 1.317332 CGCGTGTTACATTTGTGCAG 58.683 50.000 0.00 0.00 0.00 4.41
115 116 0.040870 CCGCGTGTTACATTTGTGCA 60.041 50.000 4.92 0.00 0.00 4.57
116 117 0.236187 TCCGCGTGTTACATTTGTGC 59.764 50.000 4.92 0.00 0.00 4.57
117 118 1.529438 ACTCCGCGTGTTACATTTGTG 59.471 47.619 4.92 0.00 0.00 3.33
118 119 1.873698 ACTCCGCGTGTTACATTTGT 58.126 45.000 4.92 0.00 0.00 2.83
119 120 4.392619 TTTACTCCGCGTGTTACATTTG 57.607 40.909 4.92 0.00 0.00 2.32
120 121 5.421212 TTTTTACTCCGCGTGTTACATTT 57.579 34.783 4.92 0.00 0.00 2.32
121 122 4.083696 CCTTTTTACTCCGCGTGTTACATT 60.084 41.667 4.92 0.00 0.00 2.71
122 123 3.434299 CCTTTTTACTCCGCGTGTTACAT 59.566 43.478 4.92 0.00 0.00 2.29
123 124 2.801679 CCTTTTTACTCCGCGTGTTACA 59.198 45.455 4.92 0.00 0.00 2.41
124 125 3.059166 TCCTTTTTACTCCGCGTGTTAC 58.941 45.455 4.92 0.00 0.00 2.50
125 126 3.059166 GTCCTTTTTACTCCGCGTGTTA 58.941 45.455 4.92 0.00 0.00 2.41
126 127 1.869132 GTCCTTTTTACTCCGCGTGTT 59.131 47.619 4.92 0.00 0.00 3.32
127 128 1.505425 GTCCTTTTTACTCCGCGTGT 58.495 50.000 4.92 6.28 0.00 4.49
128 129 0.794473 GGTCCTTTTTACTCCGCGTG 59.206 55.000 4.92 0.00 0.00 5.34
129 130 0.668401 CGGTCCTTTTTACTCCGCGT 60.668 55.000 4.92 0.00 35.01 6.01
130 131 1.356527 CCGGTCCTTTTTACTCCGCG 61.357 60.000 0.00 0.00 39.87 6.46
131 132 0.037046 TCCGGTCCTTTTTACTCCGC 60.037 55.000 0.00 0.00 39.87 5.54
132 133 2.344025 CTTCCGGTCCTTTTTACTCCG 58.656 52.381 0.00 0.00 40.72 4.63
133 134 2.303890 TCCTTCCGGTCCTTTTTACTCC 59.696 50.000 0.00 0.00 0.00 3.85
134 135 3.690475 TCCTTCCGGTCCTTTTTACTC 57.310 47.619 0.00 0.00 0.00 2.59
135 136 4.652679 ATTCCTTCCGGTCCTTTTTACT 57.347 40.909 0.00 0.00 0.00 2.24
136 137 9.212641 GTATATATTCCTTCCGGTCCTTTTTAC 57.787 37.037 0.00 0.00 0.00 2.01
137 138 8.090214 CGTATATATTCCTTCCGGTCCTTTTTA 58.910 37.037 0.00 0.00 0.00 1.52
138 139 6.932960 CGTATATATTCCTTCCGGTCCTTTTT 59.067 38.462 0.00 0.00 0.00 1.94
139 140 6.268387 TCGTATATATTCCTTCCGGTCCTTTT 59.732 38.462 0.00 0.00 0.00 2.27
140 141 5.776716 TCGTATATATTCCTTCCGGTCCTTT 59.223 40.000 0.00 0.00 0.00 3.11
141 142 5.327732 TCGTATATATTCCTTCCGGTCCTT 58.672 41.667 0.00 0.00 0.00 3.36
142 143 4.927049 TCGTATATATTCCTTCCGGTCCT 58.073 43.478 0.00 0.00 0.00 3.85
143 144 4.704057 ACTCGTATATATTCCTTCCGGTCC 59.296 45.833 0.00 0.00 0.00 4.46
144 145 5.893897 ACTCGTATATATTCCTTCCGGTC 57.106 43.478 0.00 0.00 0.00 4.79
145 146 7.765695 TTTACTCGTATATATTCCTTCCGGT 57.234 36.000 0.00 0.00 0.00 5.28
163 164 8.745464 TTTTTGCGGGTAAATGTATTTTACTC 57.255 30.769 7.83 3.75 45.96 2.59
164 165 8.578151 TCTTTTTGCGGGTAAATGTATTTTACT 58.422 29.630 7.83 0.00 45.96 2.24
165 166 8.745464 TCTTTTTGCGGGTAAATGTATTTTAC 57.255 30.769 0.00 0.66 45.97 2.01
166 167 8.794553 TCTCTTTTTGCGGGTAAATGTATTTTA 58.205 29.630 0.00 0.00 0.00 1.52
167 168 7.662897 TCTCTTTTTGCGGGTAAATGTATTTT 58.337 30.769 0.00 0.00 0.00 1.82
168 169 7.039993 ACTCTCTTTTTGCGGGTAAATGTATTT 60.040 33.333 0.00 0.00 0.00 1.40
169 170 6.433093 ACTCTCTTTTTGCGGGTAAATGTATT 59.567 34.615 0.00 0.00 0.00 1.89
170 171 5.944007 ACTCTCTTTTTGCGGGTAAATGTAT 59.056 36.000 0.00 0.00 0.00 2.29
171 172 5.310451 ACTCTCTTTTTGCGGGTAAATGTA 58.690 37.500 0.00 0.00 0.00 2.29
172 173 4.142038 ACTCTCTTTTTGCGGGTAAATGT 58.858 39.130 0.00 0.00 0.00 2.71
173 174 4.766404 ACTCTCTTTTTGCGGGTAAATG 57.234 40.909 0.00 0.00 0.00 2.32
174 175 6.887626 TTTACTCTCTTTTTGCGGGTAAAT 57.112 33.333 0.00 0.00 0.00 1.40
175 176 6.696441 TTTTACTCTCTTTTTGCGGGTAAA 57.304 33.333 0.00 0.00 0.00 2.01
176 177 6.887626 ATTTTACTCTCTTTTTGCGGGTAA 57.112 33.333 0.00 0.00 0.00 2.85
177 178 6.935771 TGTATTTTACTCTCTTTTTGCGGGTA 59.064 34.615 0.00 0.00 0.00 3.69
178 179 5.766174 TGTATTTTACTCTCTTTTTGCGGGT 59.234 36.000 0.00 0.00 0.00 5.28
179 180 6.084277 GTGTATTTTACTCTCTTTTTGCGGG 58.916 40.000 0.00 0.00 0.00 6.13
180 181 6.084277 GGTGTATTTTACTCTCTTTTTGCGG 58.916 40.000 0.00 0.00 0.00 5.69
181 182 6.664515 TGGTGTATTTTACTCTCTTTTTGCG 58.335 36.000 0.00 0.00 0.00 4.85
182 183 7.918562 TGTTGGTGTATTTTACTCTCTTTTTGC 59.081 33.333 0.00 0.00 0.00 3.68
183 184 9.450807 CTGTTGGTGTATTTTACTCTCTTTTTG 57.549 33.333 0.00 0.00 0.00 2.44
184 185 8.135529 GCTGTTGGTGTATTTTACTCTCTTTTT 58.864 33.333 0.00 0.00 0.00 1.94
185 186 7.255486 GGCTGTTGGTGTATTTTACTCTCTTTT 60.255 37.037 0.00 0.00 0.00 2.27
186 187 6.206829 GGCTGTTGGTGTATTTTACTCTCTTT 59.793 38.462 0.00 0.00 0.00 2.52
187 188 5.705905 GGCTGTTGGTGTATTTTACTCTCTT 59.294 40.000 0.00 0.00 0.00 2.85
188 189 5.013183 AGGCTGTTGGTGTATTTTACTCTCT 59.987 40.000 0.00 0.00 0.00 3.10
189 190 5.246307 AGGCTGTTGGTGTATTTTACTCTC 58.754 41.667 0.00 0.00 0.00 3.20
190 191 5.242795 AGGCTGTTGGTGTATTTTACTCT 57.757 39.130 0.00 0.00 0.00 3.24
191 192 5.240844 ACAAGGCTGTTGGTGTATTTTACTC 59.759 40.000 0.00 0.00 28.57 2.59
192 193 5.137551 ACAAGGCTGTTGGTGTATTTTACT 58.862 37.500 0.00 0.00 28.57 2.24
193 194 5.447624 ACAAGGCTGTTGGTGTATTTTAC 57.552 39.130 0.00 0.00 28.57 2.01
194 195 6.535540 TCTACAAGGCTGTTGGTGTATTTTA 58.464 36.000 0.00 0.00 36.96 1.52
195 196 5.381757 TCTACAAGGCTGTTGGTGTATTTT 58.618 37.500 0.00 0.00 36.96 1.82
196 197 4.980573 TCTACAAGGCTGTTGGTGTATTT 58.019 39.130 0.00 0.00 36.96 1.40
197 198 4.634012 TCTACAAGGCTGTTGGTGTATT 57.366 40.909 0.00 0.00 36.96 1.89
198 199 4.634012 TTCTACAAGGCTGTTGGTGTAT 57.366 40.909 0.00 0.00 36.96 2.29
199 200 4.101898 TCTTTCTACAAGGCTGTTGGTGTA 59.898 41.667 0.00 0.00 36.96 2.90
200 201 3.118038 TCTTTCTACAAGGCTGTTGGTGT 60.118 43.478 0.00 0.00 36.96 4.16
201 202 3.251004 GTCTTTCTACAAGGCTGTTGGTG 59.749 47.826 0.00 0.00 36.96 4.17
202 203 3.118038 TGTCTTTCTACAAGGCTGTTGGT 60.118 43.478 0.00 0.00 36.96 3.67
203 204 3.476552 TGTCTTTCTACAAGGCTGTTGG 58.523 45.455 0.00 0.00 36.96 3.77
204 205 4.614535 GCATGTCTTTCTACAAGGCTGTTG 60.615 45.833 0.00 0.00 36.96 3.33
205 206 3.503748 GCATGTCTTTCTACAAGGCTGTT 59.496 43.478 0.00 0.00 36.96 3.16
206 207 3.077359 GCATGTCTTTCTACAAGGCTGT 58.923 45.455 0.00 0.00 39.75 4.40
207 208 3.341823 AGCATGTCTTTCTACAAGGCTG 58.658 45.455 0.00 0.00 40.44 4.85
208 209 3.710209 AGCATGTCTTTCTACAAGGCT 57.290 42.857 0.00 0.00 38.49 4.58
209 210 3.127721 GGAAGCATGTCTTTCTACAAGGC 59.872 47.826 0.00 0.00 34.56 4.35
210 211 4.583871 AGGAAGCATGTCTTTCTACAAGG 58.416 43.478 8.43 0.00 38.87 3.61
211 212 5.486526 AGAGGAAGCATGTCTTTCTACAAG 58.513 41.667 9.76 0.00 40.74 3.16
212 213 5.012046 TGAGAGGAAGCATGTCTTTCTACAA 59.988 40.000 9.76 0.00 40.74 2.41
213 214 4.528206 TGAGAGGAAGCATGTCTTTCTACA 59.472 41.667 9.76 10.16 40.74 2.74
214 215 4.867608 GTGAGAGGAAGCATGTCTTTCTAC 59.132 45.833 9.76 8.37 40.74 2.59
215 216 4.528206 TGTGAGAGGAAGCATGTCTTTCTA 59.472 41.667 9.76 0.00 40.74 2.10
216 217 3.326006 TGTGAGAGGAAGCATGTCTTTCT 59.674 43.478 9.60 9.60 43.35 2.52
217 218 3.668447 TGTGAGAGGAAGCATGTCTTTC 58.332 45.455 0.00 0.00 34.56 2.62
218 219 3.777106 TGTGAGAGGAAGCATGTCTTT 57.223 42.857 0.00 0.00 34.56 2.52
219 220 3.996921 ATGTGAGAGGAAGCATGTCTT 57.003 42.857 0.00 0.00 37.83 3.01
220 221 3.771479 TGTATGTGAGAGGAAGCATGTCT 59.229 43.478 0.00 0.00 0.00 3.41
221 222 4.118410 CTGTATGTGAGAGGAAGCATGTC 58.882 47.826 0.00 0.00 0.00 3.06
222 223 3.517100 ACTGTATGTGAGAGGAAGCATGT 59.483 43.478 0.00 0.00 0.00 3.21
223 224 4.134379 ACTGTATGTGAGAGGAAGCATG 57.866 45.455 0.00 0.00 0.00 4.06
236 237 5.752036 AGCATATCATAGGCACTGTATGT 57.248 39.130 3.76 0.00 41.52 2.29
237 238 6.045318 GGTAGCATATCATAGGCACTGTATG 58.955 44.000 3.76 0.00 41.52 2.39
238 239 5.721480 TGGTAGCATATCATAGGCACTGTAT 59.279 40.000 3.76 0.00 41.52 2.29
239 240 5.047306 GTGGTAGCATATCATAGGCACTGTA 60.047 44.000 3.76 0.00 41.52 2.74
240 241 3.903714 TGGTAGCATATCATAGGCACTGT 59.096 43.478 3.76 0.00 41.52 3.55
241 242 4.020751 AGTGGTAGCATATCATAGGCACTG 60.021 45.833 3.76 0.00 41.52 3.66
242 243 4.020751 CAGTGGTAGCATATCATAGGCACT 60.021 45.833 3.76 0.00 46.37 4.40
243 244 4.021104 TCAGTGGTAGCATATCATAGGCAC 60.021 45.833 3.76 0.18 32.11 5.01
244 245 4.021104 GTCAGTGGTAGCATATCATAGGCA 60.021 45.833 3.76 0.00 32.11 4.75
245 246 4.021104 TGTCAGTGGTAGCATATCATAGGC 60.021 45.833 0.00 0.00 32.11 3.93
246 247 5.244851 ACTGTCAGTGGTAGCATATCATAGG 59.755 44.000 4.21 0.00 32.11 2.57
247 248 6.155136 CACTGTCAGTGGTAGCATATCATAG 58.845 44.000 23.09 0.00 42.35 2.23
248 249 6.089249 CACTGTCAGTGGTAGCATATCATA 57.911 41.667 23.09 0.00 42.35 2.15
249 250 4.953667 CACTGTCAGTGGTAGCATATCAT 58.046 43.478 23.09 0.00 42.35 2.45
250 251 4.391405 CACTGTCAGTGGTAGCATATCA 57.609 45.455 23.09 0.00 42.35 2.15
261 262 0.250467 CTGGGGTTCCACTGTCAGTG 60.250 60.000 23.72 23.72 45.53 3.66
262 263 2.056906 GCTGGGGTTCCACTGTCAGT 62.057 60.000 0.00 0.00 38.32 3.41
263 264 1.302832 GCTGGGGTTCCACTGTCAG 60.303 63.158 0.00 0.00 38.32 3.51
264 265 1.770110 AGCTGGGGTTCCACTGTCA 60.770 57.895 0.00 0.00 38.32 3.58
265 266 1.302832 CAGCTGGGGTTCCACTGTC 60.303 63.158 5.57 0.00 38.32 3.51
266 267 1.352622 TTCAGCTGGGGTTCCACTGT 61.353 55.000 15.13 0.00 40.18 3.55
267 268 0.890996 GTTCAGCTGGGGTTCCACTG 60.891 60.000 15.13 0.00 40.40 3.66
268 269 1.456287 GTTCAGCTGGGGTTCCACT 59.544 57.895 15.13 0.00 38.32 4.00
269 270 1.603739 GGTTCAGCTGGGGTTCCAC 60.604 63.158 15.13 0.00 38.32 4.02
270 271 2.840753 GGGTTCAGCTGGGGTTCCA 61.841 63.158 15.13 0.00 41.58 3.53
271 272 2.035783 GGGTTCAGCTGGGGTTCC 59.964 66.667 15.13 9.12 0.00 3.62
272 273 2.359975 CGGGTTCAGCTGGGGTTC 60.360 66.667 15.13 0.00 0.00 3.62
273 274 4.660938 GCGGGTTCAGCTGGGGTT 62.661 66.667 15.13 0.00 0.00 4.11
277 278 3.850098 AACTGGCGGGTTCAGCTGG 62.850 63.158 15.13 0.00 35.78 4.85
278 279 2.281761 AACTGGCGGGTTCAGCTG 60.282 61.111 7.63 7.63 35.78 4.24
279 280 2.281761 CAACTGGCGGGTTCAGCT 60.282 61.111 0.00 0.00 35.78 4.24
280 281 4.043200 GCAACTGGCGGGTTCAGC 62.043 66.667 0.00 0.00 35.78 4.26
290 291 4.424566 GGCCATGCACGCAACTGG 62.425 66.667 9.63 7.21 31.24 4.00
291 292 4.424566 GGGCCATGCACGCAACTG 62.425 66.667 4.39 0.00 0.00 3.16
300 301 4.828296 CTGGGAGTGGGGCCATGC 62.828 72.222 4.39 0.00 0.00 4.06
301 302 4.828296 GCTGGGAGTGGGGCCATG 62.828 72.222 4.39 0.00 0.00 3.66
307 308 2.124507 TTTTCTCGGCTGGGAGTGGG 62.125 60.000 0.00 0.00 35.52 4.61
308 309 0.674895 CTTTTCTCGGCTGGGAGTGG 60.675 60.000 0.00 0.00 35.52 4.00
309 310 0.674895 CCTTTTCTCGGCTGGGAGTG 60.675 60.000 0.00 0.00 35.52 3.51
310 311 0.836400 TCCTTTTCTCGGCTGGGAGT 60.836 55.000 0.00 0.00 35.52 3.85
311 312 0.107945 CTCCTTTTCTCGGCTGGGAG 60.108 60.000 0.00 0.00 35.16 4.30
312 313 1.553690 CCTCCTTTTCTCGGCTGGGA 61.554 60.000 0.00 0.00 0.00 4.37
313 314 1.078143 CCTCCTTTTCTCGGCTGGG 60.078 63.158 0.00 0.00 0.00 4.45
314 315 1.078143 CCCTCCTTTTCTCGGCTGG 60.078 63.158 0.00 0.00 0.00 4.85
315 316 0.324943 TTCCCTCCTTTTCTCGGCTG 59.675 55.000 0.00 0.00 0.00 4.85
316 317 1.065126 CATTCCCTCCTTTTCTCGGCT 60.065 52.381 0.00 0.00 0.00 5.52
317 318 1.065418 TCATTCCCTCCTTTTCTCGGC 60.065 52.381 0.00 0.00 0.00 5.54
318 319 3.350219 TTCATTCCCTCCTTTTCTCGG 57.650 47.619 0.00 0.00 0.00 4.63
319 320 3.440522 GGTTTCATTCCCTCCTTTTCTCG 59.559 47.826 0.00 0.00 0.00 4.04
320 321 4.407365 TGGTTTCATTCCCTCCTTTTCTC 58.593 43.478 0.00 0.00 0.00 2.87
327 328 2.604139 TGGTTTGGTTTCATTCCCTCC 58.396 47.619 0.00 0.00 0.00 4.30
423 435 4.596585 GGGTGGTGTGTGTGGGGG 62.597 72.222 0.00 0.00 0.00 5.40
461 482 1.456892 ACGGTGTCAGTGAGGGTGA 60.457 57.895 0.00 0.00 0.00 4.02
462 483 1.300931 CACGGTGTCAGTGAGGGTG 60.301 63.158 0.00 0.00 41.83 4.61
900 962 1.146566 GGAGACCCGGGAGATAAGGTA 59.853 57.143 32.02 0.00 31.10 3.08
987 1058 3.928779 TCCATGGCGCCTCCGATC 61.929 66.667 29.70 0.00 37.80 3.69
988 1059 4.241555 GTCCATGGCGCCTCCGAT 62.242 66.667 29.70 9.98 37.80 4.18
1581 1666 3.479203 CTGCCCCGGACCTGCATA 61.479 66.667 0.73 0.00 33.97 3.14
2331 2585 2.809174 CTCGTCGGAATGCGTGCA 60.809 61.111 0.00 0.00 0.00 4.57
2334 2588 1.666553 TTTGCTCGTCGGAATGCGT 60.667 52.632 0.00 0.00 0.00 5.24
2335 2589 1.225745 GTTTGCTCGTCGGAATGCG 60.226 57.895 0.00 0.00 0.00 4.73
2336 2590 0.179215 CAGTTTGCTCGTCGGAATGC 60.179 55.000 0.00 0.00 0.00 3.56
2374 2658 3.433513 ACCGGCTAAATCGTCTTCTAC 57.566 47.619 0.00 0.00 0.00 2.59
2383 2671 4.395231 AGCAACTAAAGAACCGGCTAAATC 59.605 41.667 0.00 0.00 0.00 2.17
2391 2679 1.399727 CCGCAAGCAACTAAAGAACCG 60.400 52.381 0.00 0.00 0.00 4.44
2405 2704 3.894547 AACTACCACCCGCCGCAAG 62.895 63.158 0.00 0.00 0.00 4.01
2413 2712 1.471287 GCCAAAATCGAACTACCACCC 59.529 52.381 0.00 0.00 0.00 4.61
2414 2713 1.129811 CGCCAAAATCGAACTACCACC 59.870 52.381 0.00 0.00 0.00 4.61
2417 2716 2.031683 CCATCGCCAAAATCGAACTACC 59.968 50.000 0.00 0.00 39.54 3.18
2563 2871 4.070716 AGATCACAAAGGCTCTCAGTTTG 58.929 43.478 0.00 0.00 37.23 2.93
2586 2907 6.388278 GTCAAACTCGAAATGGAGTAGTAGT 58.612 40.000 0.00 0.00 46.21 2.73
2622 2943 2.210116 TCACTCGTTGCAAAAGGACTC 58.790 47.619 0.00 0.00 0.00 3.36
2636 2963 5.230942 ACTACCAGTTCATCTTTTCACTCG 58.769 41.667 0.00 0.00 0.00 4.18
2637 2964 7.379750 AGTACTACCAGTTCATCTTTTCACTC 58.620 38.462 0.00 0.00 0.00 3.51
2638 2965 7.015292 TGAGTACTACCAGTTCATCTTTTCACT 59.985 37.037 0.00 0.00 0.00 3.41
2654 2984 5.232414 GTCTCAATCGCAAATGAGTACTACC 59.768 44.000 0.00 0.00 42.86 3.18
2681 3011 2.615493 GGAATCACGGGTTCATGTCTGT 60.615 50.000 0.00 0.00 0.00 3.41
2683 3013 1.405526 CGGAATCACGGGTTCATGTCT 60.406 52.381 0.00 0.00 0.00 3.41
2721 3051 2.836262 TGCAGACAAAAATGCTTTGGG 58.164 42.857 2.45 0.00 42.98 4.12
2773 3103 5.118990 ACACTCGTTTCGGCTAGTACTATA 58.881 41.667 2.33 0.00 0.00 1.31
2780 3113 2.161012 TGTAGACACTCGTTTCGGCTAG 59.839 50.000 0.00 0.00 0.00 3.42
2781 3114 2.153645 TGTAGACACTCGTTTCGGCTA 58.846 47.619 0.00 0.00 0.00 3.93
2782 3115 0.956633 TGTAGACACTCGTTTCGGCT 59.043 50.000 0.00 0.00 0.00 5.52
2785 3118 3.179795 CACACTTGTAGACACTCGTTTCG 59.820 47.826 0.00 0.00 0.00 3.46
2793 3126 6.844696 TCTGAAAATCACACTTGTAGACAC 57.155 37.500 0.00 0.00 0.00 3.67
2803 3136 6.698766 AGCTTTTGTTCATCTGAAAATCACAC 59.301 34.615 0.00 0.00 35.58 3.82
2846 3195 0.957888 GACCAGTTGCTCCTCCAAGC 60.958 60.000 0.00 0.00 42.82 4.01
2888 3237 5.744666 TCCTTCGAAAAATATTAAGGGCG 57.255 39.130 12.12 3.06 37.81 6.13
2893 3242 9.304335 AGGTCCTTTTCCTTCGAAAAATATTAA 57.696 29.630 0.00 0.00 45.12 1.40
2895 3244 7.602753 CAGGTCCTTTTCCTTCGAAAAATATT 58.397 34.615 0.00 0.00 45.12 1.28
2904 3254 0.320421 TCGCAGGTCCTTTTCCTTCG 60.320 55.000 0.00 0.00 41.52 3.79
2918 3268 2.032528 TGTTGCTCCCCTTCGCAG 59.967 61.111 0.00 0.00 37.46 5.18
2921 3271 2.045926 CCCTGTTGCTCCCCTTCG 60.046 66.667 0.00 0.00 0.00 3.79
2960 3310 1.142748 CTCATGCACCTCGTCCTCC 59.857 63.158 0.00 0.00 0.00 4.30
2961 3311 1.142748 CCTCATGCACCTCGTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
2962 3312 2.362369 CCCTCATGCACCTCGTCCT 61.362 63.158 0.00 0.00 0.00 3.85
2963 3313 2.187946 CCCTCATGCACCTCGTCC 59.812 66.667 0.00 0.00 0.00 4.79
2964 3314 2.187946 CCCCTCATGCACCTCGTC 59.812 66.667 0.00 0.00 0.00 4.20
2965 3315 2.607750 ACCCCTCATGCACCTCGT 60.608 61.111 0.00 0.00 0.00 4.18
2966 3316 2.124983 CACCCCTCATGCACCTCG 60.125 66.667 0.00 0.00 0.00 4.63
2994 3344 4.408821 TCCACCACGCCTGCCATC 62.409 66.667 0.00 0.00 0.00 3.51
3003 3353 2.882876 CCGTACTCCTCCACCACG 59.117 66.667 0.00 0.00 0.00 4.94
3071 3426 4.030452 GTGTTGCCTCGCTGCCAC 62.030 66.667 0.00 0.00 0.00 5.01
3072 3427 4.560743 TGTGTTGCCTCGCTGCCA 62.561 61.111 0.00 0.00 0.00 4.92
3073 3428 4.030452 GTGTGTTGCCTCGCTGCC 62.030 66.667 0.00 0.00 0.00 4.85
3087 3442 4.562425 CACCCCACTGGCGTGTGT 62.562 66.667 4.85 3.82 39.55 3.72
3119 3475 4.426313 GGTAGCCAGCCCCACACC 62.426 72.222 0.00 0.00 0.00 4.16
3168 3524 1.635663 GACGACAGCCAATCCCAACG 61.636 60.000 0.00 0.00 0.00 4.10
3234 3626 4.468689 GAAAGGAGCGGACCGGGG 62.469 72.222 17.22 0.00 34.73 5.73
3282 3674 1.188863 GAGGGAAAGGTACGGCACTA 58.811 55.000 0.00 0.00 0.00 2.74
3288 3680 2.028748 TCCTTTTCGAGGGAAAGGTACG 60.029 50.000 21.06 2.62 46.31 3.67
3299 3691 2.869897 CGTTCCTCTCTCCTTTTCGAG 58.130 52.381 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.