Multiple sequence alignment - TraesCS5A01G175900

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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 TraesCS5A01G175900 chr5A 100.000 2498 0 0 1 2498 370108059 370105562 0.000000e+00 4614.0
1 TraesCS5A01G175900 chr5A 100.000 28 0 0 1743 1770 3286476 3286449 4.000000e-03 52.8
2 TraesCS5A01G175900 chr5D 88.721 2119 102 47 195 2195 278440515 278442614 0.000000e+00 2462.0
3 TraesCS5A01G175900 chr5D 91.031 1717 98 24 506 2190 278357881 278359573 0.000000e+00 2266.0
4 TraesCS5A01G175900 chr5D 92.350 183 13 1 2271 2453 319952214 319952395 2.460000e-65 259.0
5 TraesCS5A01G175900 chr5D 82.805 221 23 11 263 478 278357479 278357689 1.530000e-42 183.0
6 TraesCS5A01G175900 chr5D 100.000 32 0 0 2200 2231 278442636 278442667 2.680000e-05 60.2
7 TraesCS5A01G175900 chr5D 100.000 28 0 0 1743 1770 6385594 6385621 4.000000e-03 52.8
8 TraesCS5A01G175900 chr5B 88.991 1735 111 32 246 1934 316530969 316532669 0.000000e+00 2073.0
9 TraesCS5A01G175900 chr5B 87.485 1670 106 44 409 2024 316561032 316562652 0.000000e+00 1831.0
10 TraesCS5A01G175900 chr5B 90.728 151 13 1 246 396 316558944 316559093 1.520000e-47 200.0
11 TraesCS5A01G175900 chr5B 77.193 114 18 6 1743 1855 545190513 545190407 2.680000e-05 60.2
12 TraesCS5A01G175900 chr7A 94.022 184 10 1 2270 2453 202996977 202997159 6.800000e-71 278.0
13 TraesCS5A01G175900 chr7A 92.350 183 12 2 2271 2453 543983273 543983093 2.460000e-65 259.0
14 TraesCS5A01G175900 chr7A 85.000 120 16 2 46 164 215178756 215178874 1.210000e-23 121.0
15 TraesCS5A01G175900 chr7A 84.034 119 19 0 46 164 513991413 513991295 5.650000e-22 115.0
16 TraesCS5A01G175900 chr7A 83.471 121 19 1 46 165 438855313 438855193 7.300000e-21 111.0
17 TraesCS5A01G175900 chr1B 93.443 183 11 1 2271 2453 390618527 390618346 1.140000e-68 270.0
18 TraesCS5A01G175900 chr1B 92.391 184 12 2 2271 2453 323620272 323620454 6.850000e-66 261.0
19 TraesCS5A01G175900 chr2D 92.350 183 13 1 2271 2453 640591839 640592020 2.460000e-65 259.0
20 TraesCS5A01G175900 chr6B 91.803 183 15 0 2271 2453 708269827 708269645 3.190000e-64 255.0
21 TraesCS5A01G175900 chr2A 92.308 182 11 3 2273 2453 166754235 166754056 3.190000e-64 255.0
22 TraesCS5A01G175900 chr2A 85.841 113 14 2 46 157 768997432 768997543 4.360000e-23 119.0
23 TraesCS5A01G175900 chr4B 91.803 183 14 1 2271 2453 215669211 215669392 1.150000e-63 254.0
24 TraesCS5A01G175900 chr4D 87.395 119 15 0 45 163 12510855 12510737 1.200000e-28 137.0
25 TraesCS5A01G175900 chr6D 86.066 122 15 2 46 166 406121280 406121160 2.020000e-26 130.0
26 TraesCS5A01G175900 chr2B 85.593 118 17 0 46 163 518048056 518048173 9.380000e-25 124.0
27 TraesCS5A01G175900 chr7D 84.483 116 18 0 46 161 155295830 155295715 5.650000e-22 115.0
28 TraesCS5A01G175900 chr7D 84.034 119 19 0 46 164 419374961 419375079 5.650000e-22 115.0


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 TraesCS5A01G175900 chr5A 370105562 370108059 2497 True 4614.0 4614 100.0000 1 2498 1 chr5A.!!$R2 2497
1 TraesCS5A01G175900 chr5D 278440515 278442667 2152 False 1261.1 2462 94.3605 195 2231 2 chr5D.!!$F4 2036
2 TraesCS5A01G175900 chr5D 278357479 278359573 2094 False 1224.5 2266 86.9180 263 2190 2 chr5D.!!$F3 1927
3 TraesCS5A01G175900 chr5B 316530969 316532669 1700 False 2073.0 2073 88.9910 246 1934 1 chr5B.!!$F1 1688
4 TraesCS5A01G175900 chr5B 316558944 316562652 3708 False 1015.5 1831 89.1065 246 2024 2 chr5B.!!$F2 1778


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
686 2791 0.095417 GCATCAACCGCTCTTTCGTC 59.905 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 4063 0.031314 ATGCGGATGTCACTCTAGCG 59.969 55.0 0.0 0.0 0.0 4.26 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 3.694535 AAATGTAGTCCTCGAGTAGCG 57.305 47.619 12.31 0.00 42.69 4.26
36 37 1.920762 GCGAATAGCTGTGACGAGC 59.079 57.895 12.75 0.00 44.04 5.03
37 38 1.483424 GCGAATAGCTGTGACGAGCC 61.483 60.000 12.75 0.00 44.04 4.70
38 39 0.179137 CGAATAGCTGTGACGAGCCA 60.179 55.000 0.00 0.00 40.08 4.75
39 40 1.735700 CGAATAGCTGTGACGAGCCAA 60.736 52.381 0.00 0.00 40.08 4.52
40 41 2.346803 GAATAGCTGTGACGAGCCAAA 58.653 47.619 0.00 0.00 40.08 3.28
41 42 2.015736 ATAGCTGTGACGAGCCAAAG 57.984 50.000 0.00 0.00 40.08 2.77
42 43 0.966179 TAGCTGTGACGAGCCAAAGA 59.034 50.000 0.00 0.00 40.08 2.52
43 44 0.320247 AGCTGTGACGAGCCAAAGAG 60.320 55.000 0.00 0.00 40.08 2.85
44 45 0.601311 GCTGTGACGAGCCAAAGAGT 60.601 55.000 0.00 0.00 32.35 3.24
45 46 1.871080 CTGTGACGAGCCAAAGAGTT 58.129 50.000 0.00 0.00 0.00 3.01
46 47 2.866460 GCTGTGACGAGCCAAAGAGTTA 60.866 50.000 0.00 0.00 32.35 2.24
47 48 2.731976 CTGTGACGAGCCAAAGAGTTAC 59.268 50.000 0.00 0.00 0.00 2.50
48 49 2.364324 TGTGACGAGCCAAAGAGTTACT 59.636 45.455 0.00 0.00 0.00 2.24
49 50 2.987821 GTGACGAGCCAAAGAGTTACTC 59.012 50.000 3.85 3.85 0.00 2.59
50 51 2.029290 TGACGAGCCAAAGAGTTACTCC 60.029 50.000 8.96 0.00 0.00 3.85
51 52 1.275573 ACGAGCCAAAGAGTTACTCCC 59.724 52.381 8.96 0.00 0.00 4.30
52 53 1.550976 CGAGCCAAAGAGTTACTCCCT 59.449 52.381 8.96 0.00 0.00 4.20
53 54 2.417515 CGAGCCAAAGAGTTACTCCCTC 60.418 54.545 8.96 6.63 0.00 4.30
54 55 1.909986 AGCCAAAGAGTTACTCCCTCC 59.090 52.381 8.96 0.00 0.00 4.30
55 56 1.405661 GCCAAAGAGTTACTCCCTCCG 60.406 57.143 8.96 0.00 0.00 4.63
56 57 1.900486 CCAAAGAGTTACTCCCTCCGT 59.100 52.381 8.96 0.00 0.00 4.69
57 58 2.094130 CCAAAGAGTTACTCCCTCCGTC 60.094 54.545 8.96 0.00 0.00 4.79
58 59 1.849977 AAGAGTTACTCCCTCCGTCC 58.150 55.000 8.96 0.00 0.00 4.79
59 60 0.702902 AGAGTTACTCCCTCCGTCCA 59.297 55.000 8.96 0.00 0.00 4.02
60 61 1.076677 AGAGTTACTCCCTCCGTCCAA 59.923 52.381 8.96 0.00 0.00 3.53
61 62 1.897802 GAGTTACTCCCTCCGTCCAAA 59.102 52.381 0.00 0.00 0.00 3.28
62 63 2.301009 GAGTTACTCCCTCCGTCCAAAA 59.699 50.000 0.00 0.00 0.00 2.44
63 64 2.707257 AGTTACTCCCTCCGTCCAAAAA 59.293 45.455 0.00 0.00 0.00 1.94
105 106 9.817809 TGTCTCTTAAATGGATGTATCTAACAC 57.182 33.333 0.00 0.00 42.09 3.32
113 114 8.964476 AATGGATGTATCTAACACTAACTTGG 57.036 34.615 0.00 0.00 42.09 3.61
114 115 7.490657 TGGATGTATCTAACACTAACTTGGT 57.509 36.000 0.00 0.00 42.09 3.67
115 116 7.327975 TGGATGTATCTAACACTAACTTGGTG 58.672 38.462 3.83 3.83 42.09 4.17
116 117 6.258068 GGATGTATCTAACACTAACTTGGTGC 59.742 42.308 5.24 0.00 42.09 5.01
117 118 6.354794 TGTATCTAACACTAACTTGGTGCT 57.645 37.500 5.24 0.00 38.14 4.40
118 119 7.470935 TGTATCTAACACTAACTTGGTGCTA 57.529 36.000 5.24 0.00 38.14 3.49
119 120 7.544622 TGTATCTAACACTAACTTGGTGCTAG 58.455 38.462 5.24 7.17 38.14 3.42
120 121 6.852420 ATCTAACACTAACTTGGTGCTAGA 57.148 37.500 16.37 16.37 42.56 2.43
121 122 6.852420 TCTAACACTAACTTGGTGCTAGAT 57.148 37.500 12.12 0.00 37.42 1.98
122 123 7.949690 TCTAACACTAACTTGGTGCTAGATA 57.050 36.000 12.12 0.00 37.42 1.98
123 124 8.534954 TCTAACACTAACTTGGTGCTAGATAT 57.465 34.615 12.12 0.00 37.42 1.63
124 125 9.636789 TCTAACACTAACTTGGTGCTAGATATA 57.363 33.333 12.12 0.00 37.42 0.86
127 128 8.713708 ACACTAACTTGGTGCTAGATATATCT 57.286 34.615 18.99 18.99 38.23 1.98
128 129 9.809395 ACACTAACTTGGTGCTAGATATATCTA 57.191 33.333 19.18 19.18 37.00 1.98
157 158 7.751768 AGGAATAAACTTTTTCAGACAGAGG 57.248 36.000 0.00 0.00 0.00 3.69
158 159 6.717084 AGGAATAAACTTTTTCAGACAGAGGG 59.283 38.462 0.00 0.00 0.00 4.30
159 160 6.715264 GGAATAAACTTTTTCAGACAGAGGGA 59.285 38.462 0.00 0.00 0.00 4.20
160 161 7.094592 GGAATAAACTTTTTCAGACAGAGGGAG 60.095 40.741 0.00 0.00 0.00 4.30
161 162 4.779993 AACTTTTTCAGACAGAGGGAGT 57.220 40.909 0.00 0.00 0.00 3.85
162 163 5.888982 AACTTTTTCAGACAGAGGGAGTA 57.111 39.130 0.00 0.00 0.00 2.59
163 164 5.216614 ACTTTTTCAGACAGAGGGAGTAC 57.783 43.478 0.00 0.00 0.00 2.73
164 165 4.654262 ACTTTTTCAGACAGAGGGAGTACA 59.346 41.667 0.00 0.00 0.00 2.90
165 166 5.308237 ACTTTTTCAGACAGAGGGAGTACAT 59.692 40.000 0.00 0.00 0.00 2.29
166 167 5.407407 TTTTCAGACAGAGGGAGTACATC 57.593 43.478 0.00 0.00 0.00 3.06
167 168 3.739401 TCAGACAGAGGGAGTACATCA 57.261 47.619 0.00 0.00 0.00 3.07
168 169 3.625853 TCAGACAGAGGGAGTACATCAG 58.374 50.000 0.00 0.00 0.00 2.90
169 170 3.267031 TCAGACAGAGGGAGTACATCAGA 59.733 47.826 0.00 0.00 0.00 3.27
170 171 4.019858 CAGACAGAGGGAGTACATCAGAA 58.980 47.826 0.00 0.00 0.00 3.02
171 172 4.097741 CAGACAGAGGGAGTACATCAGAAG 59.902 50.000 0.00 0.00 0.00 2.85
172 173 4.017958 AGACAGAGGGAGTACATCAGAAGA 60.018 45.833 0.00 0.00 0.00 2.87
173 174 4.877773 ACAGAGGGAGTACATCAGAAGAT 58.122 43.478 0.00 0.00 33.87 2.40
174 175 4.892934 ACAGAGGGAGTACATCAGAAGATC 59.107 45.833 0.00 0.00 30.20 2.75
175 176 4.280677 CAGAGGGAGTACATCAGAAGATCC 59.719 50.000 0.00 0.00 30.20 3.36
176 177 4.169856 AGAGGGAGTACATCAGAAGATCCT 59.830 45.833 0.00 0.00 30.20 3.24
177 178 5.374154 AGAGGGAGTACATCAGAAGATCCTA 59.626 44.000 0.00 0.00 30.20 2.94
178 179 6.031964 AGGGAGTACATCAGAAGATCCTAA 57.968 41.667 0.00 0.00 30.20 2.69
179 180 6.444704 AGGGAGTACATCAGAAGATCCTAAA 58.555 40.000 0.00 0.00 30.20 1.85
180 181 6.903534 AGGGAGTACATCAGAAGATCCTAAAA 59.096 38.462 0.00 0.00 30.20 1.52
181 182 7.570607 AGGGAGTACATCAGAAGATCCTAAAAT 59.429 37.037 0.00 0.00 30.20 1.82
182 183 7.875554 GGGAGTACATCAGAAGATCCTAAAATC 59.124 40.741 0.00 0.00 30.20 2.17
183 184 7.875554 GGAGTACATCAGAAGATCCTAAAATCC 59.124 40.741 0.00 0.00 30.20 3.01
184 185 8.560124 AGTACATCAGAAGATCCTAAAATCCT 57.440 34.615 0.00 0.00 30.20 3.24
185 186 8.646900 AGTACATCAGAAGATCCTAAAATCCTC 58.353 37.037 0.00 0.00 30.20 3.71
186 187 7.688918 ACATCAGAAGATCCTAAAATCCTCT 57.311 36.000 0.00 0.00 30.20 3.69
187 188 8.100135 ACATCAGAAGATCCTAAAATCCTCTT 57.900 34.615 0.00 0.00 30.20 2.85
188 189 8.555729 ACATCAGAAGATCCTAAAATCCTCTTT 58.444 33.333 0.00 0.00 30.20 2.52
191 192 8.198109 TCAGAAGATCCTAAAATCCTCTTTACG 58.802 37.037 0.00 0.00 26.37 3.18
192 193 7.439655 CAGAAGATCCTAAAATCCTCTTTACGG 59.560 40.741 0.00 0.00 26.37 4.02
193 194 6.809976 AGATCCTAAAATCCTCTTTACGGT 57.190 37.500 0.00 0.00 0.00 4.83
201 202 5.532664 AATCCTCTTTACGGTAGTCCATC 57.467 43.478 0.00 0.00 0.00 3.51
212 213 2.752903 GGTAGTCCATCGCCACAATTTT 59.247 45.455 0.00 0.00 0.00 1.82
218 219 2.160615 CCATCGCCACAATTTTGTCGTA 59.839 45.455 0.00 0.00 39.91 3.43
238 239 7.399523 GTCGTATGGACATGTTTAGAATGAAC 58.600 38.462 0.00 0.00 45.36 3.18
243 244 5.473162 TGGACATGTTTAGAATGAACCACAG 59.527 40.000 0.00 0.00 33.67 3.66
291 298 6.004574 TCTTTCACTAGTCTTGCTCTCTGTA 58.995 40.000 0.00 0.00 0.00 2.74
305 312 5.105351 TGCTCTCTGTATCGATCCAGAAAAA 60.105 40.000 19.67 8.99 37.27 1.94
331 338 2.230660 CAGGAATTAAAGATCCGGGGC 58.769 52.381 0.00 0.00 40.78 5.80
430 2365 4.861102 AAGAAGGCAAATGACAAGAAGG 57.139 40.909 0.00 0.00 0.00 3.46
435 2370 0.454957 CAAATGACAAGAAGGCGCGG 60.455 55.000 8.83 0.00 0.00 6.46
686 2791 0.095417 GCATCAACCGCTCTTTCGTC 59.905 55.000 0.00 0.00 0.00 4.20
705 2810 2.864343 GTCCATGCAATGTACGTACTCC 59.136 50.000 25.12 11.68 44.81 3.85
738 2843 1.264288 CCGTTGTTTCTTGAGAGGCAC 59.736 52.381 0.00 0.00 0.00 5.01
832 2941 5.560005 CGCAATTGGATCGACAAATAATACG 59.440 40.000 7.72 0.00 33.48 3.06
888 2997 1.198094 TGGACCCGCAAATCTCCAGA 61.198 55.000 0.00 0.00 0.00 3.86
971 3081 1.409427 AGTGATACGGACTAGCAAGCC 59.591 52.381 0.00 0.00 0.00 4.35
987 3097 1.729586 AGCCCTGTTGTCTTCCACTA 58.270 50.000 0.00 0.00 0.00 2.74
988 3098 1.348036 AGCCCTGTTGTCTTCCACTAC 59.652 52.381 0.00 0.00 0.00 2.73
989 3099 1.348036 GCCCTGTTGTCTTCCACTACT 59.652 52.381 0.00 0.00 32.43 2.57
998 3108 1.006758 TCTTCCACTACTCATCCCGGT 59.993 52.381 0.00 0.00 0.00 5.28
1030 3140 3.530910 AAGCTCAACCCCACGTCCG 62.531 63.158 0.00 0.00 0.00 4.79
1133 3243 0.528470 TACATGCACGACGTGATGGA 59.472 50.000 31.08 22.49 38.75 3.41
1161 3271 4.408821 ATGATGGTGGTGCGCGGT 62.409 61.111 8.83 0.00 0.00 5.68
1281 3391 4.475135 GTCGCCTCCTCCAAGGGC 62.475 72.222 0.00 0.00 42.18 5.19
1431 3541 2.464459 GCAGTTCCGGATGGCGAAG 61.464 63.158 4.15 0.00 34.14 3.79
1522 3639 2.267642 CCCACTCGGCCGATTCAA 59.732 61.111 31.19 5.64 0.00 2.69
1549 3670 2.741092 GTCGGTGACCTCTGGCAA 59.259 61.111 0.00 0.00 0.00 4.52
1567 3688 2.725490 CAACATTGCGTAAGTGTTGCA 58.275 42.857 19.65 0.00 44.00 4.08
1615 3736 3.119316 TGTTGCACCTTGTGTTACAAAGG 60.119 43.478 18.06 18.06 37.69 3.11
1645 3769 6.861055 ACGTGGATGTTTGTGATATTGTTTTC 59.139 34.615 0.00 0.00 0.00 2.29
1646 3770 6.307800 CGTGGATGTTTGTGATATTGTTTTCC 59.692 38.462 0.00 0.00 0.00 3.13
1647 3771 6.307800 GTGGATGTTTGTGATATTGTTTTCCG 59.692 38.462 0.00 0.00 0.00 4.30
1651 3775 6.565234 TGTTTGTGATATTGTTTTCCGTGTT 58.435 32.000 0.00 0.00 0.00 3.32
1653 3777 7.221067 TGTTTGTGATATTGTTTTCCGTGTTTC 59.779 33.333 0.00 0.00 0.00 2.78
1655 3779 7.033530 TGTGATATTGTTTTCCGTGTTTCTT 57.966 32.000 0.00 0.00 0.00 2.52
1681 3835 9.528018 TTTATCTTGTCATTCTTTTTGTTGGTC 57.472 29.630 0.00 0.00 0.00 4.02
1682 3836 6.773976 TCTTGTCATTCTTTTTGTTGGTCT 57.226 33.333 0.00 0.00 0.00 3.85
1683 3837 7.873719 TCTTGTCATTCTTTTTGTTGGTCTA 57.126 32.000 0.00 0.00 0.00 2.59
1934 4095 0.533085 TCCGCATTGTCCGTTTCACA 60.533 50.000 0.00 0.00 0.00 3.58
1963 4134 1.810606 CGCCGATGTCTCCTAGGCAT 61.811 60.000 2.96 1.45 44.40 4.40
1970 4141 0.461961 GTCTCCTAGGCATGCTTCGT 59.538 55.000 18.92 2.64 0.00 3.85
2032 4208 0.608640 GGATCCACAACTCGGTGACT 59.391 55.000 6.95 0.00 41.32 3.41
2061 4250 4.388499 CTTCGGGTGGGTCGTGGG 62.388 72.222 0.00 0.00 0.00 4.61
2101 4290 0.680618 TGTGGGGTTATCGTCGTGTT 59.319 50.000 0.00 0.00 0.00 3.32
2127 4336 1.441016 GCCATATTGCGCGCTAAGC 60.441 57.895 33.29 21.16 43.95 3.09
2233 4463 4.990288 GTGTCGTTCACCTCCCTC 57.010 61.111 3.00 0.00 40.84 4.30
2234 4464 1.292541 GTGTCGTTCACCTCCCTCC 59.707 63.158 3.00 0.00 40.84 4.30
2235 4465 1.152419 TGTCGTTCACCTCCCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
2236 4466 0.761323 TGTCGTTCACCTCCCTCCAA 60.761 55.000 0.00 0.00 0.00 3.53
2237 4467 0.320508 GTCGTTCACCTCCCTCCAAC 60.321 60.000 0.00 0.00 0.00 3.77
2238 4468 0.761323 TCGTTCACCTCCCTCCAACA 60.761 55.000 0.00 0.00 0.00 3.33
2239 4469 0.602905 CGTTCACCTCCCTCCAACAC 60.603 60.000 0.00 0.00 0.00 3.32
2240 4470 0.472471 GTTCACCTCCCTCCAACACA 59.528 55.000 0.00 0.00 0.00 3.72
2241 4471 1.133915 GTTCACCTCCCTCCAACACAA 60.134 52.381 0.00 0.00 0.00 3.33
2242 4472 1.444933 TCACCTCCCTCCAACACAAT 58.555 50.000 0.00 0.00 0.00 2.71
2243 4473 2.626785 TCACCTCCCTCCAACACAATA 58.373 47.619 0.00 0.00 0.00 1.90
2244 4474 2.983192 TCACCTCCCTCCAACACAATAA 59.017 45.455 0.00 0.00 0.00 1.40
2245 4475 3.396276 TCACCTCCCTCCAACACAATAAA 59.604 43.478 0.00 0.00 0.00 1.40
2246 4476 3.758554 CACCTCCCTCCAACACAATAAAG 59.241 47.826 0.00 0.00 0.00 1.85
2247 4477 2.755103 CCTCCCTCCAACACAATAAAGC 59.245 50.000 0.00 0.00 0.00 3.51
2248 4478 3.420893 CTCCCTCCAACACAATAAAGCA 58.579 45.455 0.00 0.00 0.00 3.91
2249 4479 3.826157 CTCCCTCCAACACAATAAAGCAA 59.174 43.478 0.00 0.00 0.00 3.91
2250 4480 4.219115 TCCCTCCAACACAATAAAGCAAA 58.781 39.130 0.00 0.00 0.00 3.68
2251 4481 4.651503 TCCCTCCAACACAATAAAGCAAAA 59.348 37.500 0.00 0.00 0.00 2.44
2252 4482 4.990426 CCCTCCAACACAATAAAGCAAAAG 59.010 41.667 0.00 0.00 0.00 2.27
2253 4483 4.448732 CCTCCAACACAATAAAGCAAAAGC 59.551 41.667 0.00 0.00 0.00 3.51
2254 4484 4.047822 TCCAACACAATAAAGCAAAAGCG 58.952 39.130 0.00 0.00 0.00 4.68
2255 4485 3.184178 CCAACACAATAAAGCAAAAGCGG 59.816 43.478 0.00 0.00 0.00 5.52
2256 4486 3.025287 ACACAATAAAGCAAAAGCGGG 57.975 42.857 0.00 0.00 0.00 6.13
2257 4487 2.625790 ACACAATAAAGCAAAAGCGGGA 59.374 40.909 0.00 0.00 0.00 5.14
2258 4488 2.986479 CACAATAAAGCAAAAGCGGGAC 59.014 45.455 0.00 0.00 0.00 4.46
2259 4489 2.625790 ACAATAAAGCAAAAGCGGGACA 59.374 40.909 0.00 0.00 0.00 4.02
2260 4490 3.258123 ACAATAAAGCAAAAGCGGGACAT 59.742 39.130 0.00 0.00 0.00 3.06
2261 4491 4.461081 ACAATAAAGCAAAAGCGGGACATA 59.539 37.500 0.00 0.00 0.00 2.29
2262 4492 5.127031 ACAATAAAGCAAAAGCGGGACATAT 59.873 36.000 0.00 0.00 0.00 1.78
2263 4493 6.320164 ACAATAAAGCAAAAGCGGGACATATA 59.680 34.615 0.00 0.00 0.00 0.86
2264 4494 4.900635 AAAGCAAAAGCGGGACATATAG 57.099 40.909 0.00 0.00 0.00 1.31
2265 4495 3.560636 AGCAAAAGCGGGACATATAGT 57.439 42.857 0.00 0.00 0.00 2.12
2266 4496 3.206150 AGCAAAAGCGGGACATATAGTG 58.794 45.455 0.00 0.00 0.00 2.74
2267 4497 2.943033 GCAAAAGCGGGACATATAGTGT 59.057 45.455 0.00 0.00 45.83 3.55
2268 4498 3.377172 GCAAAAGCGGGACATATAGTGTT 59.623 43.478 0.00 0.00 42.36 3.32
2269 4499 4.142469 GCAAAAGCGGGACATATAGTGTTT 60.142 41.667 0.00 0.00 42.36 2.83
2270 4500 5.621329 GCAAAAGCGGGACATATAGTGTTTT 60.621 40.000 0.00 0.00 42.36 2.43
2271 4501 6.403855 GCAAAAGCGGGACATATAGTGTTTTA 60.404 38.462 0.00 0.00 42.36 1.52
2272 4502 6.673154 AAAGCGGGACATATAGTGTTTTAC 57.327 37.500 0.00 0.00 42.36 2.01
2273 4503 5.609533 AGCGGGACATATAGTGTTTTACT 57.390 39.130 0.00 0.00 42.36 2.24
2274 4504 5.598769 AGCGGGACATATAGTGTTTTACTC 58.401 41.667 0.00 0.00 42.36 2.59
2275 4505 4.748600 GCGGGACATATAGTGTTTTACTCC 59.251 45.833 0.00 0.00 42.36 3.85
2276 4506 5.295152 CGGGACATATAGTGTTTTACTCCC 58.705 45.833 0.00 0.00 42.36 4.30
2277 4507 5.070047 CGGGACATATAGTGTTTTACTCCCT 59.930 44.000 0.00 0.00 42.36 4.20
2278 4508 6.522946 GGGACATATAGTGTTTTACTCCCTC 58.477 44.000 0.00 0.00 42.36 4.30
2279 4509 6.099269 GGGACATATAGTGTTTTACTCCCTCA 59.901 42.308 0.00 0.00 42.36 3.86
2280 4510 7.365295 GGGACATATAGTGTTTTACTCCCTCAA 60.365 40.741 0.00 0.00 42.36 3.02
2281 4511 8.211629 GGACATATAGTGTTTTACTCCCTCAAT 58.788 37.037 0.00 0.00 42.36 2.57
2282 4512 9.614792 GACATATAGTGTTTTACTCCCTCAATT 57.385 33.333 0.00 0.00 42.36 2.32
2283 4513 9.975218 ACATATAGTGTTTTACTCCCTCAATTT 57.025 29.630 0.00 0.00 38.01 1.82
2287 4517 7.898014 AGTGTTTTACTCCCTCAATTTCTTT 57.102 32.000 0.00 0.00 33.17 2.52
2288 4518 8.306313 AGTGTTTTACTCCCTCAATTTCTTTT 57.694 30.769 0.00 0.00 33.17 2.27
2289 4519 8.414003 AGTGTTTTACTCCCTCAATTTCTTTTC 58.586 33.333 0.00 0.00 33.17 2.29
2290 4520 8.194769 GTGTTTTACTCCCTCAATTTCTTTTCA 58.805 33.333 0.00 0.00 0.00 2.69
2291 4521 8.413229 TGTTTTACTCCCTCAATTTCTTTTCAG 58.587 33.333 0.00 0.00 0.00 3.02
2292 4522 8.414003 GTTTTACTCCCTCAATTTCTTTTCAGT 58.586 33.333 0.00 0.00 0.00 3.41
2293 4523 8.533569 TTTACTCCCTCAATTTCTTTTCAGTT 57.466 30.769 0.00 0.00 0.00 3.16
2294 4524 8.533569 TTACTCCCTCAATTTCTTTTCAGTTT 57.466 30.769 0.00 0.00 0.00 2.66
2295 4525 6.809869 ACTCCCTCAATTTCTTTTCAGTTTG 58.190 36.000 0.00 0.00 0.00 2.93
2296 4526 5.600696 TCCCTCAATTTCTTTTCAGTTTGC 58.399 37.500 0.00 0.00 0.00 3.68
2297 4527 5.128499 TCCCTCAATTTCTTTTCAGTTTGCA 59.872 36.000 0.00 0.00 0.00 4.08
2298 4528 5.993441 CCCTCAATTTCTTTTCAGTTTGCAT 59.007 36.000 0.00 0.00 0.00 3.96
2299 4529 7.015098 TCCCTCAATTTCTTTTCAGTTTGCATA 59.985 33.333 0.00 0.00 0.00 3.14
2300 4530 7.820872 CCCTCAATTTCTTTTCAGTTTGCATAT 59.179 33.333 0.00 0.00 0.00 1.78
2301 4531 9.859427 CCTCAATTTCTTTTCAGTTTGCATATA 57.141 29.630 0.00 0.00 0.00 0.86
2309 4539 9.859427 TCTTTTCAGTTTGCATATAAGATTTGG 57.141 29.630 0.00 0.00 0.00 3.28
2310 4540 9.643693 CTTTTCAGTTTGCATATAAGATTTGGT 57.356 29.630 0.00 0.00 0.00 3.67
2311 4541 9.638239 TTTTCAGTTTGCATATAAGATTTGGTC 57.362 29.630 0.00 0.00 0.00 4.02
2312 4542 7.936496 TCAGTTTGCATATAAGATTTGGTCA 57.064 32.000 0.00 0.00 0.00 4.02
2313 4543 8.347004 TCAGTTTGCATATAAGATTTGGTCAA 57.653 30.769 0.00 0.00 0.00 3.18
2314 4544 8.801299 TCAGTTTGCATATAAGATTTGGTCAAA 58.199 29.630 0.00 0.00 34.46 2.69
2315 4545 9.421806 CAGTTTGCATATAAGATTTGGTCAAAA 57.578 29.630 0.00 0.00 33.56 2.44
2316 4546 9.643693 AGTTTGCATATAAGATTTGGTCAAAAG 57.356 29.630 0.00 0.00 33.56 2.27
2317 4547 9.423061 GTTTGCATATAAGATTTGGTCAAAAGT 57.577 29.630 0.00 0.00 33.56 2.66
2318 4548 9.638239 TTTGCATATAAGATTTGGTCAAAAGTC 57.362 29.630 0.00 0.00 33.56 3.01
2319 4549 8.347004 TGCATATAAGATTTGGTCAAAAGTCA 57.653 30.769 0.00 0.00 33.56 3.41
2320 4550 8.801299 TGCATATAAGATTTGGTCAAAAGTCAA 58.199 29.630 0.00 0.00 33.56 3.18
2321 4551 9.638239 GCATATAAGATTTGGTCAAAAGTCAAA 57.362 29.630 0.00 0.00 35.30 2.69
2326 4556 7.832503 AGATTTGGTCAAAAGTCAAACTTTG 57.167 32.000 5.88 0.00 46.78 2.77
2327 4557 7.386059 AGATTTGGTCAAAAGTCAAACTTTGT 58.614 30.769 5.88 0.00 46.78 2.83
2328 4558 8.527810 AGATTTGGTCAAAAGTCAAACTTTGTA 58.472 29.630 5.88 0.00 46.78 2.41
2329 4559 9.145865 GATTTGGTCAAAAGTCAAACTTTGTAA 57.854 29.630 5.88 0.00 46.78 2.41
2330 4560 8.888579 TTTGGTCAAAAGTCAAACTTTGTAAA 57.111 26.923 5.88 2.41 46.78 2.01
2331 4561 8.527567 TTGGTCAAAAGTCAAACTTTGTAAAG 57.472 30.769 5.88 2.94 46.78 1.85
2332 4562 7.662897 TGGTCAAAAGTCAAACTTTGTAAAGT 58.337 30.769 5.88 4.25 46.78 2.66
2346 4576 8.051901 ACTTTGTAAAGTTTGACTAGCTTTGT 57.948 30.769 8.55 0.00 46.52 2.83
2347 4577 9.169592 ACTTTGTAAAGTTTGACTAGCTTTGTA 57.830 29.630 8.55 0.00 46.52 2.41
2348 4578 9.651718 CTTTGTAAAGTTTGACTAGCTTTGTAG 57.348 33.333 8.55 0.00 34.69 2.74
2349 4579 7.724305 TGTAAAGTTTGACTAGCTTTGTAGG 57.276 36.000 8.55 0.00 34.69 3.18
2350 4580 7.502696 TGTAAAGTTTGACTAGCTTTGTAGGA 58.497 34.615 8.55 0.00 34.69 2.94
2351 4581 7.988599 TGTAAAGTTTGACTAGCTTTGTAGGAA 59.011 33.333 8.55 0.00 34.69 3.36
2352 4582 7.875327 AAAGTTTGACTAGCTTTGTAGGAAA 57.125 32.000 0.00 0.00 32.03 3.13
2353 4583 7.875327 AAGTTTGACTAGCTTTGTAGGAAAA 57.125 32.000 0.00 0.00 0.00 2.29
2354 4584 7.497925 AGTTTGACTAGCTTTGTAGGAAAAG 57.502 36.000 0.00 0.00 39.66 2.27
2355 4585 7.280356 AGTTTGACTAGCTTTGTAGGAAAAGA 58.720 34.615 0.00 0.00 39.12 2.52
2356 4586 7.939588 AGTTTGACTAGCTTTGTAGGAAAAGAT 59.060 33.333 0.00 0.00 39.12 2.40
2357 4587 9.216117 GTTTGACTAGCTTTGTAGGAAAAGATA 57.784 33.333 0.00 0.00 39.12 1.98
2358 4588 9.959721 TTTGACTAGCTTTGTAGGAAAAGATAT 57.040 29.630 0.00 0.00 37.39 1.63
2359 4589 9.601217 TTGACTAGCTTTGTAGGAAAAGATATC 57.399 33.333 0.00 0.00 37.39 1.63
2360 4590 8.758829 TGACTAGCTTTGTAGGAAAAGATATCA 58.241 33.333 5.32 3.18 37.39 2.15
2361 4591 9.601217 GACTAGCTTTGTAGGAAAAGATATCAA 57.399 33.333 5.32 0.00 37.39 2.57
2466 4696 3.625314 TTTTTGTGGGGGCAGACTT 57.375 47.368 0.00 0.00 0.00 3.01
2467 4697 1.408969 TTTTTGTGGGGGCAGACTTC 58.591 50.000 0.00 0.00 0.00 3.01
2468 4698 0.260230 TTTTGTGGGGGCAGACTTCA 59.740 50.000 0.00 0.00 0.00 3.02
2469 4699 0.467290 TTTGTGGGGGCAGACTTCAC 60.467 55.000 0.00 0.00 0.00 3.18
2470 4700 2.034221 GTGGGGGCAGACTTCACC 59.966 66.667 0.00 0.00 0.00 4.02
2471 4701 2.121963 TGGGGGCAGACTTCACCT 60.122 61.111 0.00 0.00 0.00 4.00
2472 4702 1.774217 TGGGGGCAGACTTCACCTT 60.774 57.895 0.00 0.00 0.00 3.50
2473 4703 1.002011 GGGGGCAGACTTCACCTTC 60.002 63.158 0.00 0.00 0.00 3.46
2474 4704 1.761174 GGGGCAGACTTCACCTTCA 59.239 57.895 0.00 0.00 0.00 3.02
2475 4705 0.329596 GGGGCAGACTTCACCTTCAT 59.670 55.000 0.00 0.00 0.00 2.57
2476 4706 1.559682 GGGGCAGACTTCACCTTCATA 59.440 52.381 0.00 0.00 0.00 2.15
2477 4707 2.173569 GGGGCAGACTTCACCTTCATAT 59.826 50.000 0.00 0.00 0.00 1.78
2478 4708 3.391296 GGGGCAGACTTCACCTTCATATA 59.609 47.826 0.00 0.00 0.00 0.86
2479 4709 4.141482 GGGGCAGACTTCACCTTCATATAA 60.141 45.833 0.00 0.00 0.00 0.98
2480 4710 4.816925 GGGCAGACTTCACCTTCATATAAC 59.183 45.833 0.00 0.00 0.00 1.89
2481 4711 4.508124 GGCAGACTTCACCTTCATATAACG 59.492 45.833 0.00 0.00 0.00 3.18
2482 4712 5.109903 GCAGACTTCACCTTCATATAACGT 58.890 41.667 0.00 0.00 0.00 3.99
2483 4713 6.270815 GCAGACTTCACCTTCATATAACGTA 58.729 40.000 0.00 0.00 0.00 3.57
2484 4714 6.755141 GCAGACTTCACCTTCATATAACGTAA 59.245 38.462 0.00 0.00 0.00 3.18
2485 4715 7.254017 GCAGACTTCACCTTCATATAACGTAAC 60.254 40.741 0.00 0.00 0.00 2.50
2486 4716 7.222224 CAGACTTCACCTTCATATAACGTAACC 59.778 40.741 0.00 0.00 0.00 2.85
2487 4717 6.038356 ACTTCACCTTCATATAACGTAACCG 58.962 40.000 0.00 0.00 40.83 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.276857 TCGCTACTCGAGGACTACATTT 58.723 45.455 18.41 0.00 43.16 2.32
1 2 2.915349 TCGCTACTCGAGGACTACATT 58.085 47.619 18.41 0.00 43.16 2.71
18 19 1.483424 GGCTCGTCACAGCTATTCGC 61.483 60.000 0.00 0.00 39.58 4.70
19 20 0.179137 TGGCTCGTCACAGCTATTCG 60.179 55.000 0.00 0.00 39.58 3.34
20 21 2.010145 TTGGCTCGTCACAGCTATTC 57.990 50.000 0.00 0.00 39.58 1.75
21 22 2.028112 TCTTTGGCTCGTCACAGCTATT 60.028 45.455 0.00 0.00 39.58 1.73
22 23 1.550524 TCTTTGGCTCGTCACAGCTAT 59.449 47.619 0.00 0.00 39.58 2.97
23 24 0.966179 TCTTTGGCTCGTCACAGCTA 59.034 50.000 0.00 0.00 39.58 3.32
24 25 0.320247 CTCTTTGGCTCGTCACAGCT 60.320 55.000 0.21 0.00 39.58 4.24
25 26 0.601311 ACTCTTTGGCTCGTCACAGC 60.601 55.000 0.00 0.00 38.84 4.40
26 27 1.871080 AACTCTTTGGCTCGTCACAG 58.129 50.000 0.00 0.00 0.00 3.66
27 28 2.364324 AGTAACTCTTTGGCTCGTCACA 59.636 45.455 0.00 0.00 0.00 3.58
28 29 2.987821 GAGTAACTCTTTGGCTCGTCAC 59.012 50.000 0.00 0.00 0.00 3.67
29 30 2.029290 GGAGTAACTCTTTGGCTCGTCA 60.029 50.000 0.00 0.00 0.00 4.35
30 31 2.608268 GGAGTAACTCTTTGGCTCGTC 58.392 52.381 0.00 0.00 0.00 4.20
31 32 1.275573 GGGAGTAACTCTTTGGCTCGT 59.724 52.381 0.00 0.00 0.00 4.18
32 33 1.550976 AGGGAGTAACTCTTTGGCTCG 59.449 52.381 0.00 0.00 0.00 5.03
33 34 2.093394 GGAGGGAGTAACTCTTTGGCTC 60.093 54.545 0.00 0.00 35.34 4.70
34 35 1.909986 GGAGGGAGTAACTCTTTGGCT 59.090 52.381 0.00 0.00 35.34 4.75
35 36 1.405661 CGGAGGGAGTAACTCTTTGGC 60.406 57.143 0.00 0.00 35.34 4.52
36 37 1.900486 ACGGAGGGAGTAACTCTTTGG 59.100 52.381 0.00 0.00 35.34 3.28
37 38 2.094130 GGACGGAGGGAGTAACTCTTTG 60.094 54.545 0.00 0.00 35.34 2.77
38 39 2.177734 GGACGGAGGGAGTAACTCTTT 58.822 52.381 0.00 0.00 35.34 2.52
39 40 1.076677 TGGACGGAGGGAGTAACTCTT 59.923 52.381 0.00 0.00 35.34 2.85
40 41 0.702902 TGGACGGAGGGAGTAACTCT 59.297 55.000 0.00 0.00 35.34 3.24
41 42 1.553706 TTGGACGGAGGGAGTAACTC 58.446 55.000 0.00 0.00 0.00 3.01
42 43 2.019807 TTTGGACGGAGGGAGTAACT 57.980 50.000 0.00 0.00 0.00 2.24
43 44 2.845363 TTTTGGACGGAGGGAGTAAC 57.155 50.000 0.00 0.00 0.00 2.50
79 80 9.817809 GTGTTAGATACATCCATTTAAGAGACA 57.182 33.333 0.00 0.00 39.39 3.41
87 88 9.396022 CCAAGTTAGTGTTAGATACATCCATTT 57.604 33.333 0.00 0.00 39.39 2.32
88 89 8.548877 ACCAAGTTAGTGTTAGATACATCCATT 58.451 33.333 0.00 0.00 39.39 3.16
89 90 7.987458 CACCAAGTTAGTGTTAGATACATCCAT 59.013 37.037 0.00 0.00 39.39 3.41
90 91 7.327975 CACCAAGTTAGTGTTAGATACATCCA 58.672 38.462 0.00 0.00 39.39 3.41
91 92 6.258068 GCACCAAGTTAGTGTTAGATACATCC 59.742 42.308 3.37 0.00 39.39 3.51
92 93 7.042335 AGCACCAAGTTAGTGTTAGATACATC 58.958 38.462 3.37 0.00 39.39 3.06
93 94 6.947464 AGCACCAAGTTAGTGTTAGATACAT 58.053 36.000 3.37 0.00 39.39 2.29
94 95 6.354794 AGCACCAAGTTAGTGTTAGATACA 57.645 37.500 3.37 0.00 37.56 2.29
95 96 7.769220 TCTAGCACCAAGTTAGTGTTAGATAC 58.231 38.462 18.99 0.00 46.54 2.24
96 97 7.949690 TCTAGCACCAAGTTAGTGTTAGATA 57.050 36.000 18.99 4.07 46.54 1.98
97 98 6.852420 TCTAGCACCAAGTTAGTGTTAGAT 57.148 37.500 18.99 0.00 46.54 1.98
101 102 9.148879 AGATATATCTAGCACCAAGTTAGTGTT 57.851 33.333 13.76 0.00 34.97 3.32
102 103 8.713708 AGATATATCTAGCACCAAGTTAGTGT 57.286 34.615 13.76 0.00 34.97 3.55
131 132 9.284968 CCTCTGTCTGAAAAAGTTTATTCCTTA 57.715 33.333 0.00 0.00 0.00 2.69
132 133 7.231519 CCCTCTGTCTGAAAAAGTTTATTCCTT 59.768 37.037 0.00 0.00 0.00 3.36
133 134 6.717084 CCCTCTGTCTGAAAAAGTTTATTCCT 59.283 38.462 0.00 0.00 0.00 3.36
134 135 6.715264 TCCCTCTGTCTGAAAAAGTTTATTCC 59.285 38.462 0.00 0.00 0.00 3.01
135 136 7.445707 ACTCCCTCTGTCTGAAAAAGTTTATTC 59.554 37.037 0.00 0.00 0.00 1.75
136 137 7.290813 ACTCCCTCTGTCTGAAAAAGTTTATT 58.709 34.615 0.00 0.00 0.00 1.40
137 138 6.842676 ACTCCCTCTGTCTGAAAAAGTTTAT 58.157 36.000 0.00 0.00 0.00 1.40
138 139 6.248569 ACTCCCTCTGTCTGAAAAAGTTTA 57.751 37.500 0.00 0.00 0.00 2.01
139 140 5.117406 ACTCCCTCTGTCTGAAAAAGTTT 57.883 39.130 0.00 0.00 0.00 2.66
140 141 4.779993 ACTCCCTCTGTCTGAAAAAGTT 57.220 40.909 0.00 0.00 0.00 2.66
141 142 4.654262 TGTACTCCCTCTGTCTGAAAAAGT 59.346 41.667 0.00 0.00 0.00 2.66
142 143 5.215252 TGTACTCCCTCTGTCTGAAAAAG 57.785 43.478 0.00 0.00 0.00 2.27
143 144 5.306937 TGATGTACTCCCTCTGTCTGAAAAA 59.693 40.000 0.00 0.00 0.00 1.94
144 145 4.838423 TGATGTACTCCCTCTGTCTGAAAA 59.162 41.667 0.00 0.00 0.00 2.29
145 146 4.416516 TGATGTACTCCCTCTGTCTGAAA 58.583 43.478 0.00 0.00 0.00 2.69
146 147 4.019858 CTGATGTACTCCCTCTGTCTGAA 58.980 47.826 0.00 0.00 0.00 3.02
147 148 3.267031 TCTGATGTACTCCCTCTGTCTGA 59.733 47.826 0.00 0.00 0.00 3.27
148 149 3.625853 TCTGATGTACTCCCTCTGTCTG 58.374 50.000 0.00 0.00 0.00 3.51
149 150 4.017958 TCTTCTGATGTACTCCCTCTGTCT 60.018 45.833 0.00 0.00 0.00 3.41
150 151 4.274147 TCTTCTGATGTACTCCCTCTGTC 58.726 47.826 0.00 0.00 0.00 3.51
151 152 4.323569 TCTTCTGATGTACTCCCTCTGT 57.676 45.455 0.00 0.00 0.00 3.41
152 153 4.280677 GGATCTTCTGATGTACTCCCTCTG 59.719 50.000 0.00 0.00 32.19 3.35
153 154 4.169856 AGGATCTTCTGATGTACTCCCTCT 59.830 45.833 0.00 0.00 32.19 3.69
154 155 4.479158 AGGATCTTCTGATGTACTCCCTC 58.521 47.826 0.00 0.00 32.19 4.30
155 156 4.551215 AGGATCTTCTGATGTACTCCCT 57.449 45.455 0.00 0.00 32.19 4.20
156 157 6.732896 TTTAGGATCTTCTGATGTACTCCC 57.267 41.667 0.00 0.00 32.19 4.30
157 158 7.875554 GGATTTTAGGATCTTCTGATGTACTCC 59.124 40.741 0.00 0.00 32.19 3.85
158 159 8.646900 AGGATTTTAGGATCTTCTGATGTACTC 58.353 37.037 0.00 0.00 32.19 2.59
159 160 8.560124 AGGATTTTAGGATCTTCTGATGTACT 57.440 34.615 0.00 0.00 32.19 2.73
160 161 8.646900 AGAGGATTTTAGGATCTTCTGATGTAC 58.353 37.037 0.00 0.00 39.95 2.90
161 162 8.789767 AGAGGATTTTAGGATCTTCTGATGTA 57.210 34.615 0.00 0.00 39.95 2.29
162 163 7.688918 AGAGGATTTTAGGATCTTCTGATGT 57.311 36.000 0.00 0.00 39.95 3.06
163 164 8.977267 AAAGAGGATTTTAGGATCTTCTGATG 57.023 34.615 1.05 0.00 40.38 3.07
165 166 8.198109 CGTAAAGAGGATTTTAGGATCTTCTGA 58.802 37.037 1.05 0.00 40.38 3.27
166 167 7.439655 CCGTAAAGAGGATTTTAGGATCTTCTG 59.560 40.741 1.05 0.00 40.38 3.02
167 168 7.125963 ACCGTAAAGAGGATTTTAGGATCTTCT 59.874 37.037 0.00 0.00 42.29 2.85
168 169 7.273712 ACCGTAAAGAGGATTTTAGGATCTTC 58.726 38.462 0.00 0.00 32.79 2.87
169 170 7.196637 ACCGTAAAGAGGATTTTAGGATCTT 57.803 36.000 0.00 0.00 32.79 2.40
170 171 6.809976 ACCGTAAAGAGGATTTTAGGATCT 57.190 37.500 0.00 0.00 32.79 2.75
171 172 7.724287 ACTACCGTAAAGAGGATTTTAGGATC 58.276 38.462 0.00 0.00 32.79 3.36
172 173 7.201983 GGACTACCGTAAAGAGGATTTTAGGAT 60.202 40.741 1.16 0.00 32.79 3.24
173 174 6.097412 GGACTACCGTAAAGAGGATTTTAGGA 59.903 42.308 1.16 0.00 32.79 2.94
174 175 6.127253 TGGACTACCGTAAAGAGGATTTTAGG 60.127 42.308 0.00 0.00 39.42 2.69
175 176 6.870769 TGGACTACCGTAAAGAGGATTTTAG 58.129 40.000 0.00 0.00 39.42 1.85
176 177 6.855763 TGGACTACCGTAAAGAGGATTTTA 57.144 37.500 0.00 0.00 39.42 1.52
177 178 5.750352 TGGACTACCGTAAAGAGGATTTT 57.250 39.130 0.00 0.00 39.42 1.82
178 179 5.451520 CGATGGACTACCGTAAAGAGGATTT 60.452 44.000 0.00 0.00 39.42 2.17
179 180 4.037684 CGATGGACTACCGTAAAGAGGATT 59.962 45.833 0.00 0.00 39.42 3.01
180 181 3.568853 CGATGGACTACCGTAAAGAGGAT 59.431 47.826 0.00 0.00 39.42 3.24
181 182 2.947652 CGATGGACTACCGTAAAGAGGA 59.052 50.000 0.00 0.00 39.42 3.71
182 183 2.543238 GCGATGGACTACCGTAAAGAGG 60.543 54.545 0.00 0.00 39.42 3.69
183 184 2.543238 GGCGATGGACTACCGTAAAGAG 60.543 54.545 0.00 0.00 39.42 2.85
184 185 1.406539 GGCGATGGACTACCGTAAAGA 59.593 52.381 0.00 0.00 39.42 2.52
185 186 1.135527 TGGCGATGGACTACCGTAAAG 59.864 52.381 0.00 0.00 39.42 1.85
186 187 1.135024 GTGGCGATGGACTACCGTAAA 60.135 52.381 0.00 0.00 39.42 2.01
187 188 0.457035 GTGGCGATGGACTACCGTAA 59.543 55.000 0.00 0.00 39.42 3.18
188 189 0.680601 TGTGGCGATGGACTACCGTA 60.681 55.000 0.00 0.00 39.42 4.02
189 190 1.537814 TTGTGGCGATGGACTACCGT 61.538 55.000 0.00 0.00 39.42 4.83
190 191 0.179084 ATTGTGGCGATGGACTACCG 60.179 55.000 0.00 0.00 39.42 4.02
191 192 2.038387 AATTGTGGCGATGGACTACC 57.962 50.000 0.00 0.00 0.00 3.18
192 193 3.190535 ACAAAATTGTGGCGATGGACTAC 59.809 43.478 0.00 0.00 40.49 2.73
193 194 3.417101 ACAAAATTGTGGCGATGGACTA 58.583 40.909 0.00 0.00 40.49 2.59
218 219 6.009589 TGTGGTTCATTCTAAACATGTCCAT 58.990 36.000 0.00 0.00 33.20 3.41
268 275 5.132897 ACAGAGAGCAAGACTAGTGAAAG 57.867 43.478 0.00 0.00 0.00 2.62
305 312 5.185056 CCCGGATCTTTAATTCCTGTTGTTT 59.815 40.000 0.73 0.00 0.00 2.83
314 321 1.145119 AGGGCCCCGGATCTTTAATTC 59.855 52.381 21.43 0.00 0.00 2.17
318 325 2.076184 CCAGGGCCCCGGATCTTTA 61.076 63.158 20.77 0.00 0.00 1.85
331 338 3.625897 TGAGGTGTCGTGCCAGGG 61.626 66.667 0.00 0.00 0.00 4.45
430 2365 1.369091 ATTTGTCTGGTGATCCGCGC 61.369 55.000 0.00 0.00 36.30 6.86
435 2370 6.650807 TCTGTTCAGTAATTTGTCTGGTGATC 59.349 38.462 0.00 0.00 33.13 2.92
594 2699 5.336372 GCTGTCTTGTCAGTATTGTCTCTCT 60.336 44.000 0.00 0.00 37.70 3.10
686 2791 3.179443 AGGAGTACGTACATTGCATGG 57.821 47.619 26.55 0.00 33.60 3.66
699 2804 5.131594 ACGGAGAAAGTTTGTAGGAGTAC 57.868 43.478 0.00 0.00 0.00 2.73
700 2805 5.069516 ACAACGGAGAAAGTTTGTAGGAGTA 59.930 40.000 0.00 0.00 0.00 2.59
701 2806 4.141779 ACAACGGAGAAAGTTTGTAGGAGT 60.142 41.667 0.00 0.00 0.00 3.85
702 2807 4.377897 ACAACGGAGAAAGTTTGTAGGAG 58.622 43.478 0.00 0.00 0.00 3.69
703 2808 4.411256 ACAACGGAGAAAGTTTGTAGGA 57.589 40.909 0.00 0.00 0.00 2.94
704 2809 5.296035 AGAAACAACGGAGAAAGTTTGTAGG 59.704 40.000 0.00 0.00 34.62 3.18
705 2810 6.359480 AGAAACAACGGAGAAAGTTTGTAG 57.641 37.500 0.00 0.00 34.62 2.74
832 2941 4.090761 TCCTTGATAATGGACATGAGGC 57.909 45.455 0.00 0.00 0.00 4.70
888 2997 3.009473 ACAGTAGGATTGCATCTGTGGTT 59.991 43.478 0.00 0.00 37.85 3.67
971 3081 4.499183 GATGAGTAGTGGAAGACAACAGG 58.501 47.826 0.00 0.00 0.00 4.00
987 3097 1.274703 AAGCCATGACCGGGATGAGT 61.275 55.000 15.47 1.74 0.00 3.41
988 3098 0.816825 CAAGCCATGACCGGGATGAG 60.817 60.000 15.47 8.07 0.00 2.90
989 3099 1.224315 CAAGCCATGACCGGGATGA 59.776 57.895 15.47 0.00 0.00 2.92
1133 3243 2.583319 CCATCATCGCGCTGTCGT 60.583 61.111 10.07 0.00 38.14 4.34
1261 3371 2.182030 CTTGGAGGAGGCGACGAC 59.818 66.667 0.00 0.00 0.00 4.34
1281 3391 1.811266 CACCATCAGCTCGAACCCG 60.811 63.158 0.00 0.00 37.07 5.28
1549 3670 1.333702 CGTGCAACACTTACGCAATGT 60.334 47.619 0.00 0.00 37.41 2.71
1588 3709 2.057137 ACACAAGGTGCAACACTCAT 57.943 45.000 3.64 0.00 39.98 2.90
1615 3736 0.179225 CACAAACATCCACGTAGCGC 60.179 55.000 0.00 0.00 0.00 5.92
1645 3769 7.584987 AGAATGACAAGATAAAAGAAACACGG 58.415 34.615 0.00 0.00 0.00 4.94
1646 3770 9.450807 AAAGAATGACAAGATAAAAGAAACACG 57.549 29.630 0.00 0.00 0.00 4.49
1655 3779 9.528018 GACCAACAAAAAGAATGACAAGATAAA 57.472 29.630 0.00 0.00 0.00 1.40
1681 3835 5.175856 GCTCATAATCCGTTGCACTTAGTAG 59.824 44.000 0.00 0.00 0.00 2.57
1682 3836 5.047847 GCTCATAATCCGTTGCACTTAGTA 58.952 41.667 0.00 0.00 0.00 1.82
1683 3837 3.871594 GCTCATAATCCGTTGCACTTAGT 59.128 43.478 0.00 0.00 0.00 2.24
1901 4062 1.946650 GCGGATGTCACTCTAGCGC 60.947 63.158 0.00 0.00 0.00 5.92
1902 4063 0.031314 ATGCGGATGTCACTCTAGCG 59.969 55.000 0.00 0.00 0.00 4.26
1938 4099 4.796231 GAGACATCGGCGCCACGT 62.796 66.667 28.98 19.81 34.94 4.49
1942 4103 2.336809 CTAGGAGACATCGGCGCC 59.663 66.667 19.07 19.07 0.00 6.53
1995 4171 4.382320 CCGAGGAAAACCGGCCGA 62.382 66.667 30.73 0.00 39.22 5.54
2068 4257 4.722700 CACAGGAAGGTGGGCCCG 62.723 72.222 19.37 1.73 38.74 6.13
2101 4290 4.473643 GCAATATGGCGCCCACTA 57.526 55.556 26.77 13.54 35.80 2.74
2122 4331 2.509336 CTGTCACGGGCGGCTTAG 60.509 66.667 9.56 3.37 0.00 2.18
2127 4336 4.742201 CTCACCTGTCACGGGCGG 62.742 72.222 1.07 0.00 32.02 6.13
2190 4403 3.122250 GAGTCGGGCGTATGCGAGT 62.122 63.158 7.60 0.00 44.10 4.18
2231 4461 4.148696 CGCTTTTGCTTTATTGTGTTGGAG 59.851 41.667 0.00 0.00 44.80 3.86
2232 4462 4.047822 CGCTTTTGCTTTATTGTGTTGGA 58.952 39.130 0.00 0.00 44.80 3.53
2233 4463 3.184178 CCGCTTTTGCTTTATTGTGTTGG 59.816 43.478 0.00 0.00 44.80 3.77
2234 4464 3.184178 CCCGCTTTTGCTTTATTGTGTTG 59.816 43.478 0.00 0.00 44.80 3.33
2235 4465 3.068873 TCCCGCTTTTGCTTTATTGTGTT 59.931 39.130 0.00 0.00 44.80 3.32
2236 4466 2.625790 TCCCGCTTTTGCTTTATTGTGT 59.374 40.909 0.00 0.00 44.80 3.72
2237 4467 2.986479 GTCCCGCTTTTGCTTTATTGTG 59.014 45.455 0.00 0.00 44.80 3.33
2238 4468 2.625790 TGTCCCGCTTTTGCTTTATTGT 59.374 40.909 0.00 0.00 44.80 2.71
2239 4469 3.296322 TGTCCCGCTTTTGCTTTATTG 57.704 42.857 0.00 0.00 44.80 1.90
2240 4470 5.852282 ATATGTCCCGCTTTTGCTTTATT 57.148 34.783 0.00 0.00 44.80 1.40
2241 4471 6.017109 CACTATATGTCCCGCTTTTGCTTTAT 60.017 38.462 0.00 0.00 44.80 1.40
2242 4472 5.295787 CACTATATGTCCCGCTTTTGCTTTA 59.704 40.000 0.00 0.00 44.80 1.85
2243 4473 4.096382 CACTATATGTCCCGCTTTTGCTTT 59.904 41.667 0.00 0.00 44.80 3.51
2244 4474 3.627577 CACTATATGTCCCGCTTTTGCTT 59.372 43.478 0.00 0.00 44.80 3.91
2245 4475 3.206150 CACTATATGTCCCGCTTTTGCT 58.794 45.455 0.00 0.00 44.80 3.91
2246 4476 2.943033 ACACTATATGTCCCGCTTTTGC 59.057 45.455 0.00 0.00 36.54 3.68
2247 4477 5.560966 AAACACTATATGTCCCGCTTTTG 57.439 39.130 0.00 0.00 42.31 2.44
2248 4478 6.882678 AGTAAAACACTATATGTCCCGCTTTT 59.117 34.615 0.00 0.00 42.31 2.27
2249 4479 6.412214 AGTAAAACACTATATGTCCCGCTTT 58.588 36.000 0.00 0.00 42.31 3.51
2250 4480 5.985911 AGTAAAACACTATATGTCCCGCTT 58.014 37.500 0.00 0.00 42.31 4.68
2251 4481 5.452917 GGAGTAAAACACTATATGTCCCGCT 60.453 44.000 0.00 0.00 42.31 5.52
2252 4482 4.748600 GGAGTAAAACACTATATGTCCCGC 59.251 45.833 0.00 0.00 42.31 6.13
2253 4483 5.070047 AGGGAGTAAAACACTATATGTCCCG 59.930 44.000 0.00 0.00 42.31 5.14
2254 4484 6.099269 TGAGGGAGTAAAACACTATATGTCCC 59.901 42.308 0.00 0.00 42.31 4.46
2255 4485 7.120923 TGAGGGAGTAAAACACTATATGTCC 57.879 40.000 0.00 0.00 42.31 4.02
2256 4486 9.614792 AATTGAGGGAGTAAAACACTATATGTC 57.385 33.333 0.00 0.00 42.31 3.06
2257 4487 9.975218 AAATTGAGGGAGTAAAACACTATATGT 57.025 29.630 0.00 0.00 46.42 2.29
2261 4491 9.588096 AAAGAAATTGAGGGAGTAAAACACTAT 57.412 29.630 0.00 0.00 37.72 2.12
2262 4492 8.990163 AAAGAAATTGAGGGAGTAAAACACTA 57.010 30.769 0.00 0.00 37.72 2.74
2263 4493 7.898014 AAAGAAATTGAGGGAGTAAAACACT 57.102 32.000 0.00 0.00 41.47 3.55
2264 4494 8.194769 TGAAAAGAAATTGAGGGAGTAAAACAC 58.805 33.333 0.00 0.00 0.00 3.32
2265 4495 8.299990 TGAAAAGAAATTGAGGGAGTAAAACA 57.700 30.769 0.00 0.00 0.00 2.83
2266 4496 8.414003 ACTGAAAAGAAATTGAGGGAGTAAAAC 58.586 33.333 0.00 0.00 0.00 2.43
2267 4497 8.533569 ACTGAAAAGAAATTGAGGGAGTAAAA 57.466 30.769 0.00 0.00 0.00 1.52
2268 4498 8.533569 AACTGAAAAGAAATTGAGGGAGTAAA 57.466 30.769 0.00 0.00 0.00 2.01
2269 4499 8.413229 CAAACTGAAAAGAAATTGAGGGAGTAA 58.587 33.333 0.00 0.00 0.00 2.24
2270 4500 7.470009 GCAAACTGAAAAGAAATTGAGGGAGTA 60.470 37.037 0.00 0.00 0.00 2.59
2271 4501 6.683861 GCAAACTGAAAAGAAATTGAGGGAGT 60.684 38.462 0.00 0.00 0.00 3.85
2272 4502 5.693555 GCAAACTGAAAAGAAATTGAGGGAG 59.306 40.000 0.00 0.00 0.00 4.30
2273 4503 5.128499 TGCAAACTGAAAAGAAATTGAGGGA 59.872 36.000 0.00 0.00 0.00 4.20
2274 4504 5.358922 TGCAAACTGAAAAGAAATTGAGGG 58.641 37.500 0.00 0.00 0.00 4.30
2275 4505 8.767478 ATATGCAAACTGAAAAGAAATTGAGG 57.233 30.769 0.00 0.00 0.00 3.86
2283 4513 9.859427 CCAAATCTTATATGCAAACTGAAAAGA 57.141 29.630 0.00 0.00 0.00 2.52
2284 4514 9.643693 ACCAAATCTTATATGCAAACTGAAAAG 57.356 29.630 0.00 0.00 0.00 2.27
2285 4515 9.638239 GACCAAATCTTATATGCAAACTGAAAA 57.362 29.630 0.00 0.00 0.00 2.29
2286 4516 8.801299 TGACCAAATCTTATATGCAAACTGAAA 58.199 29.630 0.00 0.00 0.00 2.69
2287 4517 8.347004 TGACCAAATCTTATATGCAAACTGAA 57.653 30.769 0.00 0.00 0.00 3.02
2288 4518 7.936496 TGACCAAATCTTATATGCAAACTGA 57.064 32.000 0.00 0.00 0.00 3.41
2289 4519 8.984891 TTTGACCAAATCTTATATGCAAACTG 57.015 30.769 0.00 0.00 0.00 3.16
2290 4520 9.643693 CTTTTGACCAAATCTTATATGCAAACT 57.356 29.630 0.00 0.00 0.00 2.66
2291 4521 9.423061 ACTTTTGACCAAATCTTATATGCAAAC 57.577 29.630 0.00 0.00 0.00 2.93
2292 4522 9.638239 GACTTTTGACCAAATCTTATATGCAAA 57.362 29.630 0.00 0.00 0.00 3.68
2293 4523 8.801299 TGACTTTTGACCAAATCTTATATGCAA 58.199 29.630 0.00 0.00 0.00 4.08
2294 4524 8.347004 TGACTTTTGACCAAATCTTATATGCA 57.653 30.769 0.00 0.00 0.00 3.96
2295 4525 9.638239 TTTGACTTTTGACCAAATCTTATATGC 57.362 29.630 0.00 0.00 0.00 3.14
2300 4530 9.364989 CAAAGTTTGACTTTTGACCAAATCTTA 57.635 29.630 10.19 0.00 45.38 2.10
2301 4531 7.877612 ACAAAGTTTGACTTTTGACCAAATCTT 59.122 29.630 22.23 0.00 45.38 2.40
2302 4532 7.386059 ACAAAGTTTGACTTTTGACCAAATCT 58.614 30.769 22.23 0.00 45.38 2.40
2303 4533 7.595311 ACAAAGTTTGACTTTTGACCAAATC 57.405 32.000 22.23 0.00 45.38 2.17
2304 4534 9.495572 TTTACAAAGTTTGACTTTTGACCAAAT 57.504 25.926 22.23 0.00 45.38 2.32
2305 4535 8.888579 TTTACAAAGTTTGACTTTTGACCAAA 57.111 26.923 22.23 3.97 45.38 3.28
2306 4536 8.145122 ACTTTACAAAGTTTGACTTTTGACCAA 58.855 29.630 22.23 0.00 45.38 3.67
2307 4537 7.662897 ACTTTACAAAGTTTGACTTTTGACCA 58.337 30.769 22.23 0.00 45.38 4.02
2322 4552 9.651718 CTACAAAGCTAGTCAAACTTTACAAAG 57.348 33.333 0.13 0.13 41.73 2.77
2323 4553 8.617809 CCTACAAAGCTAGTCAAACTTTACAAA 58.382 33.333 0.00 0.00 32.54 2.83
2324 4554 7.988599 TCCTACAAAGCTAGTCAAACTTTACAA 59.011 33.333 0.00 0.00 32.54 2.41
2325 4555 7.502696 TCCTACAAAGCTAGTCAAACTTTACA 58.497 34.615 0.00 0.00 32.54 2.41
2326 4556 7.958053 TCCTACAAAGCTAGTCAAACTTTAC 57.042 36.000 0.00 0.00 32.54 2.01
2327 4557 8.967664 TTTCCTACAAAGCTAGTCAAACTTTA 57.032 30.769 0.00 0.00 32.54 1.85
2328 4558 7.875327 TTTCCTACAAAGCTAGTCAAACTTT 57.125 32.000 0.00 0.00 34.03 2.66
2329 4559 7.773690 TCTTTTCCTACAAAGCTAGTCAAACTT 59.226 33.333 0.00 0.00 34.26 2.66
2330 4560 7.280356 TCTTTTCCTACAAAGCTAGTCAAACT 58.720 34.615 0.00 0.00 34.26 2.66
2331 4561 7.492352 TCTTTTCCTACAAAGCTAGTCAAAC 57.508 36.000 0.00 0.00 34.26 2.93
2332 4562 9.959721 ATATCTTTTCCTACAAAGCTAGTCAAA 57.040 29.630 0.00 0.00 34.26 2.69
2333 4563 9.601217 GATATCTTTTCCTACAAAGCTAGTCAA 57.399 33.333 0.00 0.00 34.26 3.18
2334 4564 8.758829 TGATATCTTTTCCTACAAAGCTAGTCA 58.241 33.333 3.98 0.00 34.26 3.41
2335 4565 9.601217 TTGATATCTTTTCCTACAAAGCTAGTC 57.399 33.333 3.98 0.00 34.26 2.59
2448 4678 1.342474 TGAAGTCTGCCCCCACAAAAA 60.342 47.619 0.00 0.00 0.00 1.94
2449 4679 0.260230 TGAAGTCTGCCCCCACAAAA 59.740 50.000 0.00 0.00 0.00 2.44
2450 4680 0.467290 GTGAAGTCTGCCCCCACAAA 60.467 55.000 0.00 0.00 0.00 2.83
2451 4681 1.150536 GTGAAGTCTGCCCCCACAA 59.849 57.895 0.00 0.00 0.00 3.33
2452 4682 2.829384 GGTGAAGTCTGCCCCCACA 61.829 63.158 0.00 0.00 0.00 4.17
2453 4683 2.034221 GGTGAAGTCTGCCCCCAC 59.966 66.667 0.00 0.00 0.00 4.61
2454 4684 1.774217 AAGGTGAAGTCTGCCCCCA 60.774 57.895 0.00 0.00 0.00 4.96
2455 4685 1.002011 GAAGGTGAAGTCTGCCCCC 60.002 63.158 0.00 0.00 0.00 5.40
2456 4686 0.329596 ATGAAGGTGAAGTCTGCCCC 59.670 55.000 0.00 0.00 0.00 5.80
2457 4687 3.567478 ATATGAAGGTGAAGTCTGCCC 57.433 47.619 0.00 0.00 0.00 5.36
2458 4688 4.508124 CGTTATATGAAGGTGAAGTCTGCC 59.492 45.833 0.00 0.00 0.00 4.85
2459 4689 5.109903 ACGTTATATGAAGGTGAAGTCTGC 58.890 41.667 0.00 0.00 0.00 4.26
2460 4690 7.222224 GGTTACGTTATATGAAGGTGAAGTCTG 59.778 40.741 0.00 0.00 0.00 3.51
2461 4691 7.263496 GGTTACGTTATATGAAGGTGAAGTCT 58.737 38.462 0.00 0.00 0.00 3.24
2462 4692 6.197842 CGGTTACGTTATATGAAGGTGAAGTC 59.802 42.308 0.00 0.00 34.81 3.01
2463 4693 6.038356 CGGTTACGTTATATGAAGGTGAAGT 58.962 40.000 0.00 0.00 34.81 3.01
2464 4694 6.506464 CGGTTACGTTATATGAAGGTGAAG 57.494 41.667 0.00 0.00 34.81 3.02



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

AutoCloner maintained by Alex Coulton.