Multiple sequence alignment - TraesCS6D01G226900

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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 TraesCS6D01G226900 chr6D 100.000 3623 0 0 1 3623 318351869 318348247 0.000000e+00 6691.0
1 TraesCS6D01G226900 chr6B 95.782 3011 104 12 627 3623 505798046 505801047 0.000000e+00 4835.0
2 TraesCS6D01G226900 chr6B 93.590 234 4 7 404 627 505797778 505798010 4.480000e-89 339.0
3 TraesCS6D01G226900 chr6B 88.514 148 11 4 242 384 505797644 505797790 1.340000e-39 174.0
4 TraesCS6D01G226900 chr6A 95.804 3003 108 14 627 3623 455942509 455939519 0.000000e+00 4831.0
5 TraesCS6D01G226900 chr6A 92.887 239 16 1 1 238 212299618 212299380 2.680000e-91 346.0
6 TraesCS6D01G226900 chr6A 93.778 225 8 5 404 627 455942765 455942546 2.080000e-87 333.0
7 TraesCS6D01G226900 chr7A 84.724 1414 208 8 1199 2608 437609362 437610771 0.000000e+00 1408.0
8 TraesCS6D01G226900 chr7A 76.753 813 103 41 981 1762 42011964 42012721 3.420000e-100 375.0
9 TraesCS6D01G226900 chr7D 84.289 1413 216 6 1199 2608 387494734 387496143 0.000000e+00 1375.0
10 TraesCS6D01G226900 chr7D 89.873 237 23 1 1 236 230996659 230996423 1.630000e-78 303.0
11 TraesCS6D01G226900 chr7B 83.864 1413 222 6 1199 2608 382519653 382521062 0.000000e+00 1341.0
12 TraesCS6D01G226900 chr5D 92.050 239 17 2 1 239 520510995 520510759 5.800000e-88 335.0
13 TraesCS6D01G226900 chr5D 87.712 236 27 1 1 236 366736786 366736553 1.280000e-69 274.0
14 TraesCS6D01G226900 chr4B 90.795 239 20 2 1 238 455017455 455017692 5.840000e-83 318.0
15 TraesCS6D01G226900 chr2B 91.739 230 14 5 1 228 102035946 102035720 7.550000e-82 315.0
16 TraesCS6D01G226900 chr2B 88.608 237 25 2 1 236 404747522 404747287 1.650000e-73 287.0
17 TraesCS6D01G226900 chr2B 87.719 57 7 0 2785 2841 53473000 53472944 2.330000e-07 67.6
18 TraesCS6D01G226900 chr3D 88.608 237 27 0 1 237 429913051 429912815 4.580000e-74 289.0
19 TraesCS6D01G226900 chr2D 88.936 235 24 2 3 236 186626840 186627073 4.580000e-74 289.0
20 TraesCS6D01G226900 chr1B 92.453 53 4 0 2789 2841 390622300 390622352 3.880000e-10 76.8
21 TraesCS6D01G226900 chr4D 94.595 37 2 0 2801 2837 43670339 43670375 1.410000e-04 58.4


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 TraesCS6D01G226900 chr6D 318348247 318351869 3622 True 6691.000000 6691 100.000000 1 3623 1 chr6D.!!$R1 3622
1 TraesCS6D01G226900 chr6B 505797644 505801047 3403 False 1782.666667 4835 92.628667 242 3623 3 chr6B.!!$F1 3381
2 TraesCS6D01G226900 chr6A 455939519 455942765 3246 True 2582.000000 4831 94.791000 404 3623 2 chr6A.!!$R2 3219
3 TraesCS6D01G226900 chr7A 437609362 437610771 1409 False 1408.000000 1408 84.724000 1199 2608 1 chr7A.!!$F2 1409
4 TraesCS6D01G226900 chr7A 42011964 42012721 757 False 375.000000 375 76.753000 981 1762 1 chr7A.!!$F1 781
5 TraesCS6D01G226900 chr7D 387494734 387496143 1409 False 1375.000000 1375 84.289000 1199 2608 1 chr7D.!!$F1 1409
6 TraesCS6D01G226900 chr7B 382519653 382521062 1409 False 1341.000000 1341 83.864000 1199 2608 1 chr7B.!!$F1 1409

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
127 128 0.042731 TAGCTAGGGAGGGTTGCTGT 59.957 55.0 0.0 0.0 35.47 4.40 F
128 129 0.042731 AGCTAGGGAGGGTTGCTGTA 59.957 55.0 0.0 0.0 32.32 2.74 F
166 167 0.105039 GGCTTCATGTACCCTCGGAG 59.895 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1715 1.378250 CCAGAAGGCCAGGAAGCAG 60.378 63.158 5.01 0.0 0.00 4.24 R
2512 2603 0.249531 TTGTTGTAGGCTGCGACGAA 60.250 50.000 16.74 10.1 0.00 3.85 R
2629 2720 0.396974 AGGTTTTCTGCAAGCCCACA 60.397 50.000 0.00 0.0 36.38 4.17 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
28 29 2.593346 CTAGGCACCTAGTTCAGCAG 57.407 55.000 14.55 0.00 40.68 4.24
29 30 2.103373 CTAGGCACCTAGTTCAGCAGA 58.897 52.381 14.55 0.00 40.68 4.26
30 31 1.577736 AGGCACCTAGTTCAGCAGAT 58.422 50.000 0.00 0.00 0.00 2.90
31 32 1.484240 AGGCACCTAGTTCAGCAGATC 59.516 52.381 0.00 0.00 0.00 2.75
32 33 1.208052 GGCACCTAGTTCAGCAGATCA 59.792 52.381 0.00 0.00 0.00 2.92
33 34 2.355108 GGCACCTAGTTCAGCAGATCAA 60.355 50.000 0.00 0.00 0.00 2.57
34 35 3.338249 GCACCTAGTTCAGCAGATCAAA 58.662 45.455 0.00 0.00 0.00 2.69
35 36 3.753272 GCACCTAGTTCAGCAGATCAAAA 59.247 43.478 0.00 0.00 0.00 2.44
36 37 4.216257 GCACCTAGTTCAGCAGATCAAAAA 59.784 41.667 0.00 0.00 0.00 1.94
37 38 5.693814 CACCTAGTTCAGCAGATCAAAAAC 58.306 41.667 0.00 0.00 0.00 2.43
38 39 5.471456 CACCTAGTTCAGCAGATCAAAAACT 59.529 40.000 0.00 0.27 0.00 2.66
39 40 6.016777 CACCTAGTTCAGCAGATCAAAAACTT 60.017 38.462 0.00 0.00 0.00 2.66
40 41 6.016777 ACCTAGTTCAGCAGATCAAAAACTTG 60.017 38.462 0.00 0.00 0.00 3.16
41 42 4.614946 AGTTCAGCAGATCAAAAACTTGC 58.385 39.130 0.00 0.00 0.00 4.01
42 43 4.340381 AGTTCAGCAGATCAAAAACTTGCT 59.660 37.500 0.00 0.00 0.00 3.91
43 44 4.924305 TCAGCAGATCAAAAACTTGCTT 57.076 36.364 0.94 0.00 0.00 3.91
44 45 4.613944 TCAGCAGATCAAAAACTTGCTTG 58.386 39.130 0.94 0.00 0.00 4.01
45 46 3.739300 CAGCAGATCAAAAACTTGCTTGG 59.261 43.478 0.94 0.00 0.00 3.61
46 47 3.638160 AGCAGATCAAAAACTTGCTTGGA 59.362 39.130 0.00 0.00 0.00 3.53
47 48 3.985925 GCAGATCAAAAACTTGCTTGGAG 59.014 43.478 0.00 0.00 0.00 3.86
48 49 3.985925 CAGATCAAAAACTTGCTTGGAGC 59.014 43.478 0.00 0.00 42.82 4.70
49 50 3.893813 AGATCAAAAACTTGCTTGGAGCT 59.106 39.130 0.00 0.00 42.97 4.09
50 51 3.441496 TCAAAAACTTGCTTGGAGCTG 57.559 42.857 0.00 0.00 42.97 4.24
51 52 2.760092 TCAAAAACTTGCTTGGAGCTGT 59.240 40.909 0.00 0.00 42.97 4.40
52 53 3.118542 CAAAAACTTGCTTGGAGCTGTC 58.881 45.455 0.00 0.00 42.97 3.51
53 54 2.355010 AAACTTGCTTGGAGCTGTCT 57.645 45.000 0.00 0.00 42.97 3.41
54 55 3.492102 AAACTTGCTTGGAGCTGTCTA 57.508 42.857 0.00 0.00 42.97 2.59
55 56 2.758736 ACTTGCTTGGAGCTGTCTAG 57.241 50.000 0.00 0.00 42.97 2.43
56 57 1.277557 ACTTGCTTGGAGCTGTCTAGG 59.722 52.381 0.00 0.00 42.97 3.02
57 58 1.552337 CTTGCTTGGAGCTGTCTAGGA 59.448 52.381 0.00 0.00 42.97 2.94
58 59 1.189752 TGCTTGGAGCTGTCTAGGAG 58.810 55.000 0.00 0.00 42.97 3.69
59 60 0.179086 GCTTGGAGCTGTCTAGGAGC 60.179 60.000 0.00 6.57 38.45 4.70
60 61 1.189752 CTTGGAGCTGTCTAGGAGCA 58.810 55.000 14.74 1.10 39.05 4.26
61 62 0.898320 TTGGAGCTGTCTAGGAGCAC 59.102 55.000 14.74 9.54 39.05 4.40
62 63 0.972983 TGGAGCTGTCTAGGAGCACC 60.973 60.000 18.15 18.15 44.80 5.01
63 64 1.435515 GAGCTGTCTAGGAGCACCG 59.564 63.158 14.74 0.00 41.83 4.94
64 65 1.304547 AGCTGTCTAGGAGCACCGT 60.305 57.895 14.74 0.00 41.83 4.83
65 66 1.153745 GCTGTCTAGGAGCACCGTG 60.154 63.158 9.16 0.00 41.83 4.94
66 67 1.878656 GCTGTCTAGGAGCACCGTGT 61.879 60.000 9.16 0.00 41.83 4.49
67 68 0.109086 CTGTCTAGGAGCACCGTGTG 60.109 60.000 0.00 0.25 41.83 3.82
68 69 1.215647 GTCTAGGAGCACCGTGTGG 59.784 63.158 0.00 0.00 41.83 4.17
78 79 3.115556 CCGTGTGGTTTGGGTGTG 58.884 61.111 0.00 0.00 0.00 3.82
79 80 1.751162 CCGTGTGGTTTGGGTGTGT 60.751 57.895 0.00 0.00 0.00 3.72
80 81 0.464013 CCGTGTGGTTTGGGTGTGTA 60.464 55.000 0.00 0.00 0.00 2.90
81 82 0.941542 CGTGTGGTTTGGGTGTGTAG 59.058 55.000 0.00 0.00 0.00 2.74
82 83 1.314730 GTGTGGTTTGGGTGTGTAGG 58.685 55.000 0.00 0.00 0.00 3.18
83 84 1.134037 GTGTGGTTTGGGTGTGTAGGA 60.134 52.381 0.00 0.00 0.00 2.94
84 85 1.142060 TGTGGTTTGGGTGTGTAGGAG 59.858 52.381 0.00 0.00 0.00 3.69
85 86 1.142262 GTGGTTTGGGTGTGTAGGAGT 59.858 52.381 0.00 0.00 0.00 3.85
86 87 1.142060 TGGTTTGGGTGTGTAGGAGTG 59.858 52.381 0.00 0.00 0.00 3.51
87 88 1.235724 GTTTGGGTGTGTAGGAGTGC 58.764 55.000 0.00 0.00 0.00 4.40
88 89 0.840617 TTTGGGTGTGTAGGAGTGCA 59.159 50.000 0.00 0.00 0.00 4.57
89 90 0.840617 TTGGGTGTGTAGGAGTGCAA 59.159 50.000 0.00 0.00 0.00 4.08
90 91 0.840617 TGGGTGTGTAGGAGTGCAAA 59.159 50.000 0.00 0.00 0.00 3.68
91 92 1.423541 TGGGTGTGTAGGAGTGCAAAT 59.576 47.619 0.00 0.00 0.00 2.32
92 93 2.640332 TGGGTGTGTAGGAGTGCAAATA 59.360 45.455 0.00 0.00 0.00 1.40
93 94 3.073209 TGGGTGTGTAGGAGTGCAAATAA 59.927 43.478 0.00 0.00 0.00 1.40
94 95 4.076394 GGGTGTGTAGGAGTGCAAATAAA 58.924 43.478 0.00 0.00 0.00 1.40
95 96 4.521256 GGGTGTGTAGGAGTGCAAATAAAA 59.479 41.667 0.00 0.00 0.00 1.52
96 97 5.185056 GGGTGTGTAGGAGTGCAAATAAAAT 59.815 40.000 0.00 0.00 0.00 1.82
97 98 6.376018 GGGTGTGTAGGAGTGCAAATAAAATA 59.624 38.462 0.00 0.00 0.00 1.40
98 99 7.415206 GGGTGTGTAGGAGTGCAAATAAAATAG 60.415 40.741 0.00 0.00 0.00 1.73
99 100 6.967199 GTGTGTAGGAGTGCAAATAAAATAGC 59.033 38.462 0.00 0.00 0.00 2.97
100 101 6.657117 TGTGTAGGAGTGCAAATAAAATAGCA 59.343 34.615 0.00 0.00 34.10 3.49
108 109 6.528537 TGCAAATAAAATAGCACATGTCCT 57.471 33.333 0.00 0.00 31.05 3.85
109 110 7.637631 TGCAAATAAAATAGCACATGTCCTA 57.362 32.000 0.00 0.00 31.05 2.94
110 111 7.706159 TGCAAATAAAATAGCACATGTCCTAG 58.294 34.615 2.39 0.00 31.05 3.02
111 112 6.638468 GCAAATAAAATAGCACATGTCCTAGC 59.362 38.462 2.39 0.00 0.00 3.42
112 113 7.469181 GCAAATAAAATAGCACATGTCCTAGCT 60.469 37.037 12.46 12.46 40.92 3.32
113 114 9.056005 CAAATAAAATAGCACATGTCCTAGCTA 57.944 33.333 15.55 15.55 42.99 3.32
114 115 8.839310 AATAAAATAGCACATGTCCTAGCTAG 57.161 34.615 14.20 14.20 42.21 3.42
115 116 4.881019 AATAGCACATGTCCTAGCTAGG 57.119 45.455 30.94 30.94 42.21 3.02
116 117 1.418334 AGCACATGTCCTAGCTAGGG 58.582 55.000 34.43 22.53 43.79 3.53
117 118 1.062886 AGCACATGTCCTAGCTAGGGA 60.063 52.381 34.43 23.43 43.79 4.20
118 119 1.342819 GCACATGTCCTAGCTAGGGAG 59.657 57.143 34.43 23.83 43.79 4.30
119 120 1.967066 CACATGTCCTAGCTAGGGAGG 59.033 57.143 34.43 25.26 43.79 4.30
120 121 1.133009 ACATGTCCTAGCTAGGGAGGG 60.133 57.143 34.43 24.20 43.79 4.30
121 122 1.133009 CATGTCCTAGCTAGGGAGGGT 60.133 57.143 34.43 16.53 43.79 4.34
122 123 1.016415 TGTCCTAGCTAGGGAGGGTT 58.984 55.000 34.43 0.00 43.79 4.11
123 124 1.343075 TGTCCTAGCTAGGGAGGGTTG 60.343 57.143 34.43 10.97 43.79 3.77
124 125 0.398664 TCCTAGCTAGGGAGGGTTGC 60.399 60.000 34.43 0.00 43.79 4.17
125 126 0.399233 CCTAGCTAGGGAGGGTTGCT 60.399 60.000 29.47 0.00 39.86 3.91
126 127 0.755686 CTAGCTAGGGAGGGTTGCTG 59.244 60.000 13.32 0.00 35.47 4.41
127 128 0.042731 TAGCTAGGGAGGGTTGCTGT 59.957 55.000 0.00 0.00 35.47 4.40
128 129 0.042731 AGCTAGGGAGGGTTGCTGTA 59.957 55.000 0.00 0.00 32.32 2.74
129 130 0.909623 GCTAGGGAGGGTTGCTGTAA 59.090 55.000 0.00 0.00 0.00 2.41
130 131 1.280998 GCTAGGGAGGGTTGCTGTAAA 59.719 52.381 0.00 0.00 0.00 2.01
131 132 2.092375 GCTAGGGAGGGTTGCTGTAAAT 60.092 50.000 0.00 0.00 0.00 1.40
132 133 2.808906 AGGGAGGGTTGCTGTAAATC 57.191 50.000 0.00 0.00 0.00 2.17
133 134 2.279173 AGGGAGGGTTGCTGTAAATCT 58.721 47.619 0.00 0.00 0.00 2.40
134 135 2.239907 AGGGAGGGTTGCTGTAAATCTC 59.760 50.000 0.00 2.39 0.00 2.75
135 136 2.239907 GGGAGGGTTGCTGTAAATCTCT 59.760 50.000 8.39 0.00 0.00 3.10
136 137 3.308473 GGGAGGGTTGCTGTAAATCTCTT 60.308 47.826 8.39 0.00 0.00 2.85
137 138 4.336280 GGAGGGTTGCTGTAAATCTCTTT 58.664 43.478 8.39 0.00 0.00 2.52
138 139 4.156739 GGAGGGTTGCTGTAAATCTCTTTG 59.843 45.833 8.39 0.00 0.00 2.77
139 140 4.729868 AGGGTTGCTGTAAATCTCTTTGT 58.270 39.130 0.00 0.00 0.00 2.83
140 141 5.876357 AGGGTTGCTGTAAATCTCTTTGTA 58.124 37.500 0.00 0.00 0.00 2.41
141 142 6.303839 AGGGTTGCTGTAAATCTCTTTGTAA 58.696 36.000 0.00 0.00 0.00 2.41
142 143 6.775629 AGGGTTGCTGTAAATCTCTTTGTAAA 59.224 34.615 0.00 0.00 0.00 2.01
143 144 7.286775 AGGGTTGCTGTAAATCTCTTTGTAAAA 59.713 33.333 0.00 0.00 0.00 1.52
144 145 7.381408 GGGTTGCTGTAAATCTCTTTGTAAAAC 59.619 37.037 0.00 0.00 0.00 2.43
145 146 8.135529 GGTTGCTGTAAATCTCTTTGTAAAACT 58.864 33.333 0.00 0.00 0.00 2.66
146 147 9.516314 GTTGCTGTAAATCTCTTTGTAAAACTT 57.484 29.630 0.00 0.00 0.00 2.66
147 148 9.515020 TTGCTGTAAATCTCTTTGTAAAACTTG 57.485 29.630 0.00 0.00 0.00 3.16
148 149 8.134895 TGCTGTAAATCTCTTTGTAAAACTTGG 58.865 33.333 0.00 0.00 0.00 3.61
149 150 7.114953 GCTGTAAATCTCTTTGTAAAACTTGGC 59.885 37.037 0.00 0.00 0.00 4.52
150 151 8.232913 TGTAAATCTCTTTGTAAAACTTGGCT 57.767 30.769 0.00 0.00 0.00 4.75
151 152 8.691797 TGTAAATCTCTTTGTAAAACTTGGCTT 58.308 29.630 0.00 0.00 0.00 4.35
152 153 9.181805 GTAAATCTCTTTGTAAAACTTGGCTTC 57.818 33.333 0.00 0.00 0.00 3.86
153 154 6.959639 ATCTCTTTGTAAAACTTGGCTTCA 57.040 33.333 0.00 0.00 0.00 3.02
154 155 6.959639 TCTCTTTGTAAAACTTGGCTTCAT 57.040 33.333 0.00 0.00 0.00 2.57
155 156 6.738114 TCTCTTTGTAAAACTTGGCTTCATG 58.262 36.000 0.00 0.00 0.00 3.07
156 157 6.321181 TCTCTTTGTAAAACTTGGCTTCATGT 59.679 34.615 0.00 0.00 0.00 3.21
157 158 7.500892 TCTCTTTGTAAAACTTGGCTTCATGTA 59.499 33.333 0.00 0.00 0.00 2.29
158 159 7.422399 TCTTTGTAAAACTTGGCTTCATGTAC 58.578 34.615 0.00 0.00 0.00 2.90
159 160 5.699097 TGTAAAACTTGGCTTCATGTACC 57.301 39.130 0.00 0.00 0.00 3.34
160 161 4.521256 TGTAAAACTTGGCTTCATGTACCC 59.479 41.667 0.00 0.00 0.00 3.69
161 162 3.525800 AAACTTGGCTTCATGTACCCT 57.474 42.857 0.00 0.00 0.00 4.34
162 163 2.789409 ACTTGGCTTCATGTACCCTC 57.211 50.000 0.00 0.00 0.00 4.30
163 164 1.066143 ACTTGGCTTCATGTACCCTCG 60.066 52.381 0.00 0.00 0.00 4.63
164 165 0.251916 TTGGCTTCATGTACCCTCGG 59.748 55.000 0.00 0.00 0.00 4.63
165 166 0.616395 TGGCTTCATGTACCCTCGGA 60.616 55.000 0.00 0.00 0.00 4.55
166 167 0.105039 GGCTTCATGTACCCTCGGAG 59.895 60.000 0.00 0.00 0.00 4.63
167 168 0.824759 GCTTCATGTACCCTCGGAGT 59.175 55.000 4.02 0.00 0.00 3.85
168 169 1.471676 GCTTCATGTACCCTCGGAGTG 60.472 57.143 4.02 0.00 0.00 3.51
169 170 1.825474 CTTCATGTACCCTCGGAGTGT 59.175 52.381 4.02 0.81 0.00 3.55
170 171 1.182667 TCATGTACCCTCGGAGTGTG 58.817 55.000 3.23 0.00 0.00 3.82
171 172 0.895530 CATGTACCCTCGGAGTGTGT 59.104 55.000 3.23 0.92 0.00 3.72
172 173 1.135083 CATGTACCCTCGGAGTGTGTC 60.135 57.143 3.23 0.00 0.00 3.67
173 174 0.896940 TGTACCCTCGGAGTGTGTCC 60.897 60.000 3.23 0.00 42.85 4.02
181 182 4.268687 GAGTGTGTCCGCTCCAAG 57.731 61.111 0.00 0.00 41.45 3.61
182 183 1.374758 GAGTGTGTCCGCTCCAAGG 60.375 63.158 0.00 0.00 41.45 3.61
183 184 2.100879 GAGTGTGTCCGCTCCAAGGT 62.101 60.000 0.00 0.00 41.45 3.50
184 185 1.227853 GTGTGTCCGCTCCAAGGTT 60.228 57.895 0.00 0.00 0.00 3.50
185 186 1.227823 TGTGTCCGCTCCAAGGTTG 60.228 57.895 0.00 0.00 0.00 3.77
186 187 2.281484 TGTCCGCTCCAAGGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
187 188 2.281484 GTCCGCTCCAAGGTTGCA 60.281 61.111 7.38 0.00 0.00 4.08
188 189 2.032528 TCCGCTCCAAGGTTGCAG 59.967 61.111 0.00 0.00 0.00 4.41
189 190 2.032528 CCGCTCCAAGGTTGCAGA 59.967 61.111 0.00 0.00 0.00 4.26
190 191 1.600636 CCGCTCCAAGGTTGCAGAA 60.601 57.895 0.00 0.00 0.00 3.02
191 192 1.580845 CCGCTCCAAGGTTGCAGAAG 61.581 60.000 0.00 0.00 0.00 2.85
192 193 0.603707 CGCTCCAAGGTTGCAGAAGA 60.604 55.000 0.00 0.00 0.00 2.87
193 194 1.163554 GCTCCAAGGTTGCAGAAGAG 58.836 55.000 0.00 0.00 0.00 2.85
194 195 1.271054 GCTCCAAGGTTGCAGAAGAGA 60.271 52.381 0.00 0.00 0.00 3.10
195 196 2.617532 GCTCCAAGGTTGCAGAAGAGAT 60.618 50.000 0.00 0.00 0.00 2.75
196 197 3.008330 CTCCAAGGTTGCAGAAGAGATG 58.992 50.000 0.00 0.00 0.00 2.90
197 198 2.639347 TCCAAGGTTGCAGAAGAGATGA 59.361 45.455 0.00 0.00 0.00 2.92
198 199 3.072915 TCCAAGGTTGCAGAAGAGATGAA 59.927 43.478 0.00 0.00 0.00 2.57
199 200 3.190118 CCAAGGTTGCAGAAGAGATGAAC 59.810 47.826 0.00 0.00 0.00 3.18
200 201 4.070716 CAAGGTTGCAGAAGAGATGAACT 58.929 43.478 0.00 0.00 0.00 3.01
201 202 3.936564 AGGTTGCAGAAGAGATGAACTC 58.063 45.455 0.00 0.00 45.22 3.01
215 216 7.840342 GAGATGAACTCTGAATAAAAGAGCA 57.160 36.000 0.42 0.00 44.22 4.26
216 217 8.261492 GAGATGAACTCTGAATAAAAGAGCAA 57.739 34.615 0.42 0.00 44.22 3.91
217 218 8.038492 AGATGAACTCTGAATAAAAGAGCAAC 57.962 34.615 0.42 0.00 44.22 4.17
218 219 7.882271 AGATGAACTCTGAATAAAAGAGCAACT 59.118 33.333 0.42 0.00 44.22 3.16
219 220 7.194607 TGAACTCTGAATAAAAGAGCAACTG 57.805 36.000 0.42 0.00 44.22 3.16
220 221 6.767902 TGAACTCTGAATAAAAGAGCAACTGT 59.232 34.615 0.42 0.00 44.22 3.55
221 222 7.283127 TGAACTCTGAATAAAAGAGCAACTGTT 59.717 33.333 0.42 0.00 44.22 3.16
222 223 7.573968 ACTCTGAATAAAAGAGCAACTGTTT 57.426 32.000 0.42 0.00 44.22 2.83
223 224 8.000780 ACTCTGAATAAAAGAGCAACTGTTTT 57.999 30.769 7.49 7.49 44.22 2.43
224 225 8.131731 ACTCTGAATAAAAGAGCAACTGTTTTC 58.868 33.333 5.82 0.00 44.22 2.29
225 226 7.425606 TCTGAATAAAAGAGCAACTGTTTTCC 58.574 34.615 5.82 0.00 37.88 3.13
226 227 6.512297 TGAATAAAAGAGCAACTGTTTTCCC 58.488 36.000 5.82 0.00 37.88 3.97
227 228 3.819564 AAAAGAGCAACTGTTTTCCCC 57.180 42.857 0.00 0.00 32.73 4.81
228 229 2.755952 AAGAGCAACTGTTTTCCCCT 57.244 45.000 0.00 0.00 0.00 4.79
229 230 3.876309 AAGAGCAACTGTTTTCCCCTA 57.124 42.857 0.00 0.00 0.00 3.53
230 231 3.876309 AGAGCAACTGTTTTCCCCTAA 57.124 42.857 0.00 0.00 0.00 2.69
231 232 4.178956 AGAGCAACTGTTTTCCCCTAAA 57.821 40.909 0.00 0.00 0.00 1.85
232 233 4.542697 AGAGCAACTGTTTTCCCCTAAAA 58.457 39.130 0.00 0.00 34.66 1.52
233 234 4.959839 AGAGCAACTGTTTTCCCCTAAAAA 59.040 37.500 0.00 0.00 38.76 1.94
259 260 1.134037 TGGCCTACGTGTTGGAAAAGT 60.134 47.619 3.32 0.00 0.00 2.66
264 265 4.501559 GCCTACGTGTTGGAAAAGTTTTTC 59.498 41.667 1.64 8.48 44.38 2.29
285 290 3.827302 TCCTGCGTAAGAAAACTCTCTCT 59.173 43.478 0.00 0.00 43.02 3.10
286 291 5.008331 TCCTGCGTAAGAAAACTCTCTCTA 58.992 41.667 0.00 0.00 43.02 2.43
295 300 2.853731 AACTCTCTCTAACCGCATCG 57.146 50.000 0.00 0.00 0.00 3.84
375 381 9.825972 TTACTCAAAGAAAAAGCTAATCATTCG 57.174 29.630 0.00 0.00 0.00 3.34
376 382 7.875971 ACTCAAAGAAAAAGCTAATCATTCGT 58.124 30.769 0.00 0.00 0.00 3.85
377 383 8.352942 ACTCAAAGAAAAAGCTAATCATTCGTT 58.647 29.630 0.00 0.00 0.00 3.85
378 384 9.185192 CTCAAAGAAAAAGCTAATCATTCGTTT 57.815 29.630 0.00 0.00 0.00 3.60
379 385 8.967218 TCAAAGAAAAAGCTAATCATTCGTTTG 58.033 29.630 0.00 2.28 0.00 2.93
380 386 8.755018 CAAAGAAAAAGCTAATCATTCGTTTGT 58.245 29.630 0.00 0.00 0.00 2.83
381 387 9.959749 AAAGAAAAAGCTAATCATTCGTTTGTA 57.040 25.926 0.00 0.00 0.00 2.41
383 389 9.774742 AGAAAAAGCTAATCATTCGTTTGTATC 57.225 29.630 0.00 0.00 0.00 2.24
384 390 9.774742 GAAAAAGCTAATCATTCGTTTGTATCT 57.225 29.630 0.00 0.00 0.00 1.98
457 471 5.349543 CGTGGTTAACTGGTTATGGACTTAC 59.650 44.000 5.42 0.00 0.00 2.34
458 472 6.470278 GTGGTTAACTGGTTATGGACTTACT 58.530 40.000 5.42 0.00 0.00 2.24
459 473 7.577426 CGTGGTTAACTGGTTATGGACTTACTA 60.577 40.741 5.42 0.00 0.00 1.82
460 474 8.262933 GTGGTTAACTGGTTATGGACTTACTAT 58.737 37.037 5.42 0.00 0.00 2.12
461 475 9.491406 TGGTTAACTGGTTATGGACTTACTATA 57.509 33.333 5.42 0.00 0.00 1.31
537 552 6.882610 ATAAACAATGCTCAAGTTGAGTGA 57.117 33.333 28.95 18.63 45.94 3.41
540 555 3.434641 ACAATGCTCAAGTTGAGTGATCG 59.565 43.478 28.95 17.96 45.94 3.69
656 713 2.351641 CCAACAAATCACCATCACACCG 60.352 50.000 0.00 0.00 0.00 4.94
658 715 2.426522 ACAAATCACCATCACACCGAG 58.573 47.619 0.00 0.00 0.00 4.63
683 742 0.119155 TCCCAACACTCCAGATCCCT 59.881 55.000 0.00 0.00 0.00 4.20
775 834 0.178767 CTGCCGTCCATTCCTCATCA 59.821 55.000 0.00 0.00 0.00 3.07
812 871 0.400213 TTGGACAGCGAGGAACCATT 59.600 50.000 0.00 0.00 0.00 3.16
849 909 1.066303 GGAATCTGATCTCGCTGTCGT 59.934 52.381 0.00 0.00 36.96 4.34
960 1020 3.324993 CAACAAGTCAAGAGCTCTCTCC 58.675 50.000 18.55 7.52 39.39 3.71
979 1040 2.456443 GCCCCATCTCCTTCCCCTC 61.456 68.421 0.00 0.00 0.00 4.30
1275 1352 3.723235 CTGGATCGGCCTCGTGGTG 62.723 68.421 0.00 0.00 37.63 4.17
1317 1394 3.138798 GGCAGCCTCGTCGACCTA 61.139 66.667 10.58 0.00 0.00 3.08
1762 1853 1.982395 CTCACCTGGGCCTACGTGA 60.982 63.158 17.59 17.59 34.26 4.35
2133 2224 1.295357 CCAACATCGCTGCCAACGTA 61.295 55.000 0.00 0.00 0.00 3.57
2511 2602 2.262915 CCGAGTGTCTCCAGTGCC 59.737 66.667 0.00 0.00 0.00 5.01
2512 2603 2.279069 CCGAGTGTCTCCAGTGCCT 61.279 63.158 0.00 0.00 0.00 4.75
2627 2718 7.448469 AGTGAAATACCAAAGCAGTTGATAGTT 59.552 33.333 1.93 0.00 39.87 2.24
2629 2720 9.461312 TGAAATACCAAAGCAGTTGATAGTTAT 57.539 29.630 1.93 0.00 39.87 1.89
2654 2745 2.546584 GGCTTGCAGAAAACCTTTGGAG 60.547 50.000 0.00 0.00 0.00 3.86
2692 2783 7.654022 ACTTTTGAAAGTGGGTTTCTGAATA 57.346 32.000 8.24 0.00 46.80 1.75
2703 2794 3.424962 GGTTTCTGAATAGCACGCTGAAC 60.425 47.826 0.72 0.00 0.00 3.18
2802 2893 7.553881 AAGTATTCCATCCGTTCACAAATAG 57.446 36.000 0.00 0.00 0.00 1.73
2974 3072 4.162320 TCAGGCCTCGATTTAGTTCAAGAT 59.838 41.667 0.00 0.00 0.00 2.40
3059 3157 5.439721 AGCTATCACAAAGGCAACATATGA 58.560 37.500 10.38 0.00 41.41 2.15
3078 3176 8.280497 ACATATGAAGTTCGTAACAAAGACAAC 58.720 33.333 10.38 0.00 0.00 3.32
3079 3177 6.671614 ATGAAGTTCGTAACAAAGACAACA 57.328 33.333 0.00 0.00 0.00 3.33
3088 3186 2.851195 ACAAAGACAACATCGAAGCCT 58.149 42.857 0.00 0.00 0.00 4.58
3103 3201 4.954092 GAAGCCTCGAAATGACAAGATT 57.046 40.909 0.00 0.00 0.00 2.40
3109 3207 5.233263 GCCTCGAAATGACAAGATTCTCTAC 59.767 44.000 0.00 0.00 0.00 2.59
3149 3251 5.986135 ACTCAGTCTCAAATGTGTCACTAAC 59.014 40.000 4.27 0.00 0.00 2.34
3452 3557 7.093596 CCTCTAGATGCCTTTTTCTCCATTTTT 60.094 37.037 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.231716 TCTGCTGAACTAGGTGCCTA 57.768 50.000 0.00 0.00 0.00 3.93
11 12 1.484240 GATCTGCTGAACTAGGTGCCT 59.516 52.381 0.00 0.00 0.00 4.75
12 13 1.208052 TGATCTGCTGAACTAGGTGCC 59.792 52.381 0.00 0.00 0.00 5.01
13 14 2.680312 TGATCTGCTGAACTAGGTGC 57.320 50.000 0.00 0.00 0.00 5.01
14 15 5.471456 AGTTTTTGATCTGCTGAACTAGGTG 59.529 40.000 0.00 0.00 0.00 4.00
15 16 5.625150 AGTTTTTGATCTGCTGAACTAGGT 58.375 37.500 0.00 0.00 0.00 3.08
16 17 6.376978 CAAGTTTTTGATCTGCTGAACTAGG 58.623 40.000 0.00 0.00 36.36 3.02
17 18 5.855395 GCAAGTTTTTGATCTGCTGAACTAG 59.145 40.000 0.00 0.00 36.36 2.57
18 19 5.532406 AGCAAGTTTTTGATCTGCTGAACTA 59.468 36.000 2.85 0.00 36.36 2.24
19 20 4.340381 AGCAAGTTTTTGATCTGCTGAACT 59.660 37.500 2.85 0.00 36.36 3.01
20 21 4.614946 AGCAAGTTTTTGATCTGCTGAAC 58.385 39.130 2.85 0.00 36.36 3.18
21 22 4.924305 AGCAAGTTTTTGATCTGCTGAA 57.076 36.364 2.85 0.00 36.36 3.02
22 23 4.500205 CCAAGCAAGTTTTTGATCTGCTGA 60.500 41.667 4.34 0.00 36.36 4.26
23 24 3.739300 CCAAGCAAGTTTTTGATCTGCTG 59.261 43.478 4.34 0.57 36.36 4.41
24 25 3.638160 TCCAAGCAAGTTTTTGATCTGCT 59.362 39.130 0.00 0.00 36.36 4.24
25 26 3.981211 TCCAAGCAAGTTTTTGATCTGC 58.019 40.909 0.00 0.00 36.36 4.26
26 27 3.985925 GCTCCAAGCAAGTTTTTGATCTG 59.014 43.478 0.00 0.00 41.89 2.90
27 28 3.893813 AGCTCCAAGCAAGTTTTTGATCT 59.106 39.130 1.29 0.00 45.56 2.75
28 29 3.985925 CAGCTCCAAGCAAGTTTTTGATC 59.014 43.478 1.29 0.00 45.56 2.92
29 30 3.385755 ACAGCTCCAAGCAAGTTTTTGAT 59.614 39.130 1.29 0.00 45.56 2.57
30 31 2.760092 ACAGCTCCAAGCAAGTTTTTGA 59.240 40.909 1.29 0.00 45.56 2.69
31 32 3.118542 GACAGCTCCAAGCAAGTTTTTG 58.881 45.455 1.29 0.00 45.56 2.44
32 33 3.026694 AGACAGCTCCAAGCAAGTTTTT 58.973 40.909 1.29 0.00 45.56 1.94
33 34 2.659428 AGACAGCTCCAAGCAAGTTTT 58.341 42.857 1.29 0.00 45.56 2.43
34 35 2.355010 AGACAGCTCCAAGCAAGTTT 57.645 45.000 1.29 0.00 45.56 2.66
35 36 2.289945 CCTAGACAGCTCCAAGCAAGTT 60.290 50.000 1.29 0.00 45.56 2.66
36 37 1.277557 CCTAGACAGCTCCAAGCAAGT 59.722 52.381 1.29 0.00 45.56 3.16
37 38 1.552337 TCCTAGACAGCTCCAAGCAAG 59.448 52.381 1.29 0.00 45.56 4.01
38 39 1.552337 CTCCTAGACAGCTCCAAGCAA 59.448 52.381 1.29 0.00 45.56 3.91
39 40 1.189752 CTCCTAGACAGCTCCAAGCA 58.810 55.000 1.29 0.00 45.56 3.91
40 41 0.179086 GCTCCTAGACAGCTCCAAGC 60.179 60.000 6.44 0.00 42.84 4.01
41 42 1.134848 GTGCTCCTAGACAGCTCCAAG 60.135 57.143 13.11 0.00 37.79 3.61
42 43 0.898320 GTGCTCCTAGACAGCTCCAA 59.102 55.000 13.11 0.00 37.79 3.53
43 44 0.972983 GGTGCTCCTAGACAGCTCCA 60.973 60.000 21.12 0.86 45.87 3.86
44 45 1.819905 GGTGCTCCTAGACAGCTCC 59.180 63.158 15.07 15.07 41.89 4.70
45 46 1.316706 ACGGTGCTCCTAGACAGCTC 61.317 60.000 13.11 9.99 37.79 4.09
46 47 1.304547 ACGGTGCTCCTAGACAGCT 60.305 57.895 13.11 0.00 37.79 4.24
47 48 1.153745 CACGGTGCTCCTAGACAGC 60.154 63.158 2.85 6.69 37.40 4.40
48 49 0.109086 CACACGGTGCTCCTAGACAG 60.109 60.000 8.30 0.00 0.00 3.51
49 50 1.532604 CCACACGGTGCTCCTAGACA 61.533 60.000 8.30 0.00 31.34 3.41
50 51 1.215647 CCACACGGTGCTCCTAGAC 59.784 63.158 8.30 0.00 31.34 2.59
51 52 1.228769 ACCACACGGTGCTCCTAGA 60.229 57.895 8.30 0.00 46.79 2.43
52 53 3.377656 ACCACACGGTGCTCCTAG 58.622 61.111 8.30 0.00 46.79 3.02
61 62 0.464013 TACACACCCAAACCACACGG 60.464 55.000 0.00 0.00 38.77 4.94
62 63 0.941542 CTACACACCCAAACCACACG 59.058 55.000 0.00 0.00 0.00 4.49
63 64 1.134037 TCCTACACACCCAAACCACAC 60.134 52.381 0.00 0.00 0.00 3.82
64 65 1.142060 CTCCTACACACCCAAACCACA 59.858 52.381 0.00 0.00 0.00 4.17
65 66 1.142262 ACTCCTACACACCCAAACCAC 59.858 52.381 0.00 0.00 0.00 4.16
66 67 1.142060 CACTCCTACACACCCAAACCA 59.858 52.381 0.00 0.00 0.00 3.67
67 68 1.892209 CACTCCTACACACCCAAACC 58.108 55.000 0.00 0.00 0.00 3.27
68 69 1.235724 GCACTCCTACACACCCAAAC 58.764 55.000 0.00 0.00 0.00 2.93
69 70 0.840617 TGCACTCCTACACACCCAAA 59.159 50.000 0.00 0.00 0.00 3.28
70 71 0.840617 TTGCACTCCTACACACCCAA 59.159 50.000 0.00 0.00 0.00 4.12
71 72 0.840617 TTTGCACTCCTACACACCCA 59.159 50.000 0.00 0.00 0.00 4.51
72 73 2.200373 ATTTGCACTCCTACACACCC 57.800 50.000 0.00 0.00 0.00 4.61
73 74 5.699097 TTTTATTTGCACTCCTACACACC 57.301 39.130 0.00 0.00 0.00 4.16
74 75 6.967199 GCTATTTTATTTGCACTCCTACACAC 59.033 38.462 0.00 0.00 0.00 3.82
75 76 6.657117 TGCTATTTTATTTGCACTCCTACACA 59.343 34.615 0.00 0.00 0.00 3.72
76 77 7.083875 TGCTATTTTATTTGCACTCCTACAC 57.916 36.000 0.00 0.00 0.00 2.90
85 86 6.528537 AGGACATGTGCTATTTTATTTGCA 57.471 33.333 19.35 0.00 0.00 4.08
86 87 6.638468 GCTAGGACATGTGCTATTTTATTTGC 59.362 38.462 25.07 18.25 33.06 3.68
87 88 7.934457 AGCTAGGACATGTGCTATTTTATTTG 58.066 34.615 25.07 13.14 33.06 2.32
88 89 9.277783 CTAGCTAGGACATGTGCTATTTTATTT 57.722 33.333 25.07 9.93 37.39 1.40
89 90 7.880195 CCTAGCTAGGACATGTGCTATTTTATT 59.120 37.037 32.79 11.08 46.63 1.40
90 91 7.390027 CCTAGCTAGGACATGTGCTATTTTAT 58.610 38.462 32.79 12.86 46.63 1.40
91 92 6.239600 CCCTAGCTAGGACATGTGCTATTTTA 60.240 42.308 36.80 16.32 46.63 1.52
92 93 5.455326 CCCTAGCTAGGACATGTGCTATTTT 60.455 44.000 36.80 16.10 46.63 1.82
93 94 4.040952 CCCTAGCTAGGACATGTGCTATTT 59.959 45.833 36.80 18.21 46.63 1.40
94 95 3.580458 CCCTAGCTAGGACATGTGCTATT 59.420 47.826 36.80 18.52 46.63 1.73
95 96 3.169099 CCCTAGCTAGGACATGTGCTAT 58.831 50.000 36.80 15.14 46.63 2.97
96 97 2.177016 TCCCTAGCTAGGACATGTGCTA 59.823 50.000 36.80 23.66 46.63 3.49
97 98 1.062886 TCCCTAGCTAGGACATGTGCT 60.063 52.381 36.80 24.00 46.63 4.40
98 99 1.342819 CTCCCTAGCTAGGACATGTGC 59.657 57.143 36.80 9.70 46.63 4.57
99 100 1.967066 CCTCCCTAGCTAGGACATGTG 59.033 57.143 36.80 20.74 46.63 3.21
100 101 1.133009 CCCTCCCTAGCTAGGACATGT 60.133 57.143 36.80 0.00 46.63 3.21
101 102 1.133009 ACCCTCCCTAGCTAGGACATG 60.133 57.143 36.80 24.09 46.63 3.21
102 103 1.246294 ACCCTCCCTAGCTAGGACAT 58.754 55.000 36.80 16.72 46.63 3.06
103 104 1.016415 AACCCTCCCTAGCTAGGACA 58.984 55.000 36.80 22.73 46.63 4.02
104 105 1.415200 CAACCCTCCCTAGCTAGGAC 58.585 60.000 36.80 0.00 46.63 3.85
105 106 0.398664 GCAACCCTCCCTAGCTAGGA 60.399 60.000 36.80 22.46 46.63 2.94
106 107 0.399233 AGCAACCCTCCCTAGCTAGG 60.399 60.000 30.05 30.05 43.25 3.02
107 108 0.755686 CAGCAACCCTCCCTAGCTAG 59.244 60.000 14.20 14.20 33.59 3.42
108 109 0.042731 ACAGCAACCCTCCCTAGCTA 59.957 55.000 0.00 0.00 33.59 3.32
109 110 0.042731 TACAGCAACCCTCCCTAGCT 59.957 55.000 0.00 0.00 35.63 3.32
110 111 0.909623 TTACAGCAACCCTCCCTAGC 59.090 55.000 0.00 0.00 0.00 3.42
111 112 3.456277 AGATTTACAGCAACCCTCCCTAG 59.544 47.826 0.00 0.00 0.00 3.02
112 113 3.454812 GAGATTTACAGCAACCCTCCCTA 59.545 47.826 0.00 0.00 0.00 3.53
113 114 2.239907 GAGATTTACAGCAACCCTCCCT 59.760 50.000 0.00 0.00 0.00 4.20
114 115 2.239907 AGAGATTTACAGCAACCCTCCC 59.760 50.000 0.00 0.00 0.00 4.30
115 116 3.636153 AGAGATTTACAGCAACCCTCC 57.364 47.619 0.00 0.00 0.00 4.30
116 117 4.762251 ACAAAGAGATTTACAGCAACCCTC 59.238 41.667 0.00 0.00 0.00 4.30
117 118 4.729868 ACAAAGAGATTTACAGCAACCCT 58.270 39.130 0.00 0.00 0.00 4.34
118 119 6.569179 TTACAAAGAGATTTACAGCAACCC 57.431 37.500 0.00 0.00 0.00 4.11
119 120 8.135529 AGTTTTACAAAGAGATTTACAGCAACC 58.864 33.333 0.00 0.00 0.00 3.77
120 121 9.516314 AAGTTTTACAAAGAGATTTACAGCAAC 57.484 29.630 0.00 0.00 0.00 4.17
121 122 9.515020 CAAGTTTTACAAAGAGATTTACAGCAA 57.485 29.630 0.00 0.00 0.00 3.91
122 123 8.134895 CCAAGTTTTACAAAGAGATTTACAGCA 58.865 33.333 0.00 0.00 0.00 4.41
123 124 7.114953 GCCAAGTTTTACAAAGAGATTTACAGC 59.885 37.037 0.00 0.00 0.00 4.40
124 125 8.352942 AGCCAAGTTTTACAAAGAGATTTACAG 58.647 33.333 0.00 0.00 0.00 2.74
125 126 8.232913 AGCCAAGTTTTACAAAGAGATTTACA 57.767 30.769 0.00 0.00 0.00 2.41
126 127 9.181805 GAAGCCAAGTTTTACAAAGAGATTTAC 57.818 33.333 0.00 0.00 0.00 2.01
127 128 8.908903 TGAAGCCAAGTTTTACAAAGAGATTTA 58.091 29.630 0.00 0.00 0.00 1.40
128 129 7.781056 TGAAGCCAAGTTTTACAAAGAGATTT 58.219 30.769 0.00 0.00 0.00 2.17
129 130 7.346751 TGAAGCCAAGTTTTACAAAGAGATT 57.653 32.000 0.00 0.00 0.00 2.40
130 131 6.959639 TGAAGCCAAGTTTTACAAAGAGAT 57.040 33.333 0.00 0.00 0.00 2.75
131 132 6.321181 ACATGAAGCCAAGTTTTACAAAGAGA 59.679 34.615 0.00 0.00 0.00 3.10
132 133 6.507023 ACATGAAGCCAAGTTTTACAAAGAG 58.493 36.000 0.00 0.00 0.00 2.85
133 134 6.463995 ACATGAAGCCAAGTTTTACAAAGA 57.536 33.333 0.00 0.00 0.00 2.52
134 135 6.640907 GGTACATGAAGCCAAGTTTTACAAAG 59.359 38.462 0.00 0.00 0.00 2.77
135 136 6.461788 GGGTACATGAAGCCAAGTTTTACAAA 60.462 38.462 0.00 0.00 36.99 2.83
136 137 5.010213 GGGTACATGAAGCCAAGTTTTACAA 59.990 40.000 0.00 0.00 36.99 2.41
137 138 4.521256 GGGTACATGAAGCCAAGTTTTACA 59.479 41.667 0.00 0.00 36.99 2.41
138 139 4.765339 AGGGTACATGAAGCCAAGTTTTAC 59.235 41.667 0.00 0.00 39.59 2.01
139 140 4.993028 AGGGTACATGAAGCCAAGTTTTA 58.007 39.130 0.00 0.00 39.59 1.52
140 141 3.826729 GAGGGTACATGAAGCCAAGTTTT 59.173 43.478 0.00 0.00 39.59 2.43
141 142 3.421844 GAGGGTACATGAAGCCAAGTTT 58.578 45.455 0.00 0.00 39.59 2.66
142 143 2.615493 CGAGGGTACATGAAGCCAAGTT 60.615 50.000 0.00 0.00 39.59 2.66
143 144 1.066143 CGAGGGTACATGAAGCCAAGT 60.066 52.381 0.00 0.00 39.59 3.16
144 145 1.656652 CGAGGGTACATGAAGCCAAG 58.343 55.000 0.00 0.00 39.59 3.61
145 146 0.251916 CCGAGGGTACATGAAGCCAA 59.748 55.000 0.00 0.00 39.59 4.52
146 147 0.616395 TCCGAGGGTACATGAAGCCA 60.616 55.000 0.00 0.00 39.59 4.75
147 148 0.105039 CTCCGAGGGTACATGAAGCC 59.895 60.000 0.00 0.00 37.29 4.35
148 149 0.824759 ACTCCGAGGGTACATGAAGC 59.175 55.000 0.00 0.00 0.00 3.86
149 150 1.825474 ACACTCCGAGGGTACATGAAG 59.175 52.381 0.00 0.00 23.74 3.02
150 151 1.548719 CACACTCCGAGGGTACATGAA 59.451 52.381 2.09 0.00 25.53 2.57
151 152 1.182667 CACACTCCGAGGGTACATGA 58.817 55.000 2.09 0.00 25.53 3.07
152 153 0.895530 ACACACTCCGAGGGTACATG 59.104 55.000 2.09 0.00 25.53 3.21
153 154 1.183549 GACACACTCCGAGGGTACAT 58.816 55.000 2.09 0.00 25.53 2.29
154 155 0.896940 GGACACACTCCGAGGGTACA 60.897 60.000 2.09 0.00 25.53 2.90
155 156 1.888736 GGACACACTCCGAGGGTAC 59.111 63.158 2.09 0.93 25.53 3.34
156 157 4.428845 GGACACACTCCGAGGGTA 57.571 61.111 2.09 0.00 25.53 3.69
164 165 1.374758 CCTTGGAGCGGACACACTC 60.375 63.158 0.00 0.00 0.00 3.51
165 166 1.696097 AACCTTGGAGCGGACACACT 61.696 55.000 0.00 0.00 0.00 3.55
166 167 1.227853 AACCTTGGAGCGGACACAC 60.228 57.895 0.00 0.00 0.00 3.82
167 168 1.227823 CAACCTTGGAGCGGACACA 60.228 57.895 0.00 0.00 0.00 3.72
168 169 2.617274 GCAACCTTGGAGCGGACAC 61.617 63.158 0.00 0.00 0.00 3.67
169 170 2.281484 GCAACCTTGGAGCGGACA 60.281 61.111 0.00 0.00 0.00 4.02
170 171 2.281484 TGCAACCTTGGAGCGGAC 60.281 61.111 0.00 0.00 0.00 4.79
171 172 2.032528 CTGCAACCTTGGAGCGGA 59.967 61.111 10.49 0.00 39.74 5.54
172 173 1.580845 CTTCTGCAACCTTGGAGCGG 61.581 60.000 1.83 9.98 45.01 5.52
173 174 0.603707 TCTTCTGCAACCTTGGAGCG 60.604 55.000 1.83 0.00 45.01 5.03
174 175 1.163554 CTCTTCTGCAACCTTGGAGC 58.836 55.000 1.83 0.00 45.01 4.70
175 176 2.847327 TCTCTTCTGCAACCTTGGAG 57.153 50.000 0.28 0.28 46.51 3.86
176 177 2.639347 TCATCTCTTCTGCAACCTTGGA 59.361 45.455 0.00 0.00 0.00 3.53
177 178 3.063510 TCATCTCTTCTGCAACCTTGG 57.936 47.619 0.00 0.00 0.00 3.61
178 179 4.070716 AGTTCATCTCTTCTGCAACCTTG 58.929 43.478 0.00 0.00 0.00 3.61
179 180 4.322567 GAGTTCATCTCTTCTGCAACCTT 58.677 43.478 0.00 0.00 39.86 3.50
180 181 3.936564 GAGTTCATCTCTTCTGCAACCT 58.063 45.455 0.00 0.00 39.86 3.50
191 192 7.840342 TGCTCTTTTATTCAGAGTTCATCTC 57.160 36.000 0.00 0.00 40.13 2.75
192 193 7.882271 AGTTGCTCTTTTATTCAGAGTTCATCT 59.118 33.333 0.00 0.00 40.13 2.90
193 194 7.961827 CAGTTGCTCTTTTATTCAGAGTTCATC 59.038 37.037 0.00 0.00 40.13 2.92
194 195 7.446625 ACAGTTGCTCTTTTATTCAGAGTTCAT 59.553 33.333 0.00 0.00 40.13 2.57
195 196 6.767902 ACAGTTGCTCTTTTATTCAGAGTTCA 59.232 34.615 0.00 0.00 40.13 3.18
196 197 7.195839 ACAGTTGCTCTTTTATTCAGAGTTC 57.804 36.000 0.00 0.00 40.13 3.01
197 198 7.573968 AACAGTTGCTCTTTTATTCAGAGTT 57.426 32.000 0.00 0.00 40.13 3.01
198 199 7.573968 AAACAGTTGCTCTTTTATTCAGAGT 57.426 32.000 0.00 0.00 40.13 3.24
199 200 7.592903 GGAAAACAGTTGCTCTTTTATTCAGAG 59.407 37.037 0.00 0.00 40.84 3.35
200 201 7.425606 GGAAAACAGTTGCTCTTTTATTCAGA 58.574 34.615 0.00 0.00 0.00 3.27
201 202 6.642540 GGGAAAACAGTTGCTCTTTTATTCAG 59.357 38.462 0.00 0.00 0.00 3.02
202 203 6.462347 GGGGAAAACAGTTGCTCTTTTATTCA 60.462 38.462 0.00 0.00 0.00 2.57
203 204 5.926542 GGGGAAAACAGTTGCTCTTTTATTC 59.073 40.000 0.00 0.00 0.00 1.75
204 205 5.602561 AGGGGAAAACAGTTGCTCTTTTATT 59.397 36.000 0.00 0.00 0.00 1.40
205 206 5.147767 AGGGGAAAACAGTTGCTCTTTTAT 58.852 37.500 0.00 0.00 0.00 1.40
206 207 4.542697 AGGGGAAAACAGTTGCTCTTTTA 58.457 39.130 0.00 0.00 0.00 1.52
207 208 3.374764 AGGGGAAAACAGTTGCTCTTTT 58.625 40.909 0.00 0.00 0.00 2.27
208 209 3.032265 AGGGGAAAACAGTTGCTCTTT 57.968 42.857 0.00 0.00 0.00 2.52
209 210 2.755952 AGGGGAAAACAGTTGCTCTT 57.244 45.000 0.00 0.00 0.00 2.85
210 211 3.876309 TTAGGGGAAAACAGTTGCTCT 57.124 42.857 0.00 0.00 0.00 4.09
211 212 4.929819 TTTTAGGGGAAAACAGTTGCTC 57.070 40.909 0.00 0.00 31.90 4.26
231 232 2.616842 CAACACGTAGGCCAGTCTTTTT 59.383 45.455 5.01 0.00 0.00 1.94
232 233 2.218603 CAACACGTAGGCCAGTCTTTT 58.781 47.619 5.01 0.00 0.00 2.27
233 234 1.542547 CCAACACGTAGGCCAGTCTTT 60.543 52.381 5.01 0.00 0.00 2.52
234 235 0.034896 CCAACACGTAGGCCAGTCTT 59.965 55.000 5.01 0.00 0.00 3.01
235 236 0.830444 TCCAACACGTAGGCCAGTCT 60.830 55.000 5.01 0.00 0.00 3.24
236 237 0.034337 TTCCAACACGTAGGCCAGTC 59.966 55.000 5.01 0.00 0.00 3.51
237 238 0.470766 TTTCCAACACGTAGGCCAGT 59.529 50.000 5.01 0.00 0.00 4.00
238 239 1.535462 CTTTTCCAACACGTAGGCCAG 59.465 52.381 5.01 0.00 0.00 4.85
239 240 1.134037 ACTTTTCCAACACGTAGGCCA 60.134 47.619 5.01 0.00 0.00 5.36
240 241 1.601166 ACTTTTCCAACACGTAGGCC 58.399 50.000 0.00 0.00 0.00 5.19
259 260 5.820947 AGAGAGTTTTCTTACGCAGGAAAAA 59.179 36.000 7.19 0.00 41.19 1.94
264 265 4.181309 AGAGAGAGTTTTCTTACGCAGG 57.819 45.455 0.00 0.00 32.53 4.85
269 270 5.467705 TGCGGTTAGAGAGAGTTTTCTTAC 58.532 41.667 0.00 0.00 32.53 2.34
270 271 5.717078 TGCGGTTAGAGAGAGTTTTCTTA 57.283 39.130 0.00 0.00 32.53 2.10
271 272 4.602340 TGCGGTTAGAGAGAGTTTTCTT 57.398 40.909 0.00 0.00 32.53 2.52
272 273 4.675671 CGATGCGGTTAGAGAGAGTTTTCT 60.676 45.833 0.00 0.00 36.01 2.52
273 274 3.548268 CGATGCGGTTAGAGAGAGTTTTC 59.452 47.826 0.00 0.00 0.00 2.29
353 359 8.967218 CAAACGAATGATTAGCTTTTTCTTTGA 58.033 29.630 0.00 0.00 0.00 2.69
391 397 2.359531 ACAAACGAATCTCCCGCAAAAA 59.640 40.909 0.00 0.00 0.00 1.94
392 398 1.950909 ACAAACGAATCTCCCGCAAAA 59.049 42.857 0.00 0.00 0.00 2.44
393 399 1.600023 ACAAACGAATCTCCCGCAAA 58.400 45.000 0.00 0.00 0.00 3.68
394 400 2.459060 TACAAACGAATCTCCCGCAA 57.541 45.000 0.00 0.00 0.00 4.85
395 401 2.093921 TGATACAAACGAATCTCCCGCA 60.094 45.455 0.00 0.00 0.00 5.69
396 402 2.546778 TGATACAAACGAATCTCCCGC 58.453 47.619 0.00 0.00 0.00 6.13
397 403 4.085055 CGAATGATACAAACGAATCTCCCG 60.085 45.833 0.00 0.00 0.00 5.14
398 404 5.047847 TCGAATGATACAAACGAATCTCCC 58.952 41.667 0.00 0.00 0.00 4.30
399 405 5.749109 AGTCGAATGATACAAACGAATCTCC 59.251 40.000 0.00 0.00 34.91 3.71
400 406 6.814076 AGTCGAATGATACAAACGAATCTC 57.186 37.500 0.00 0.00 34.91 2.75
401 407 6.020599 CGAAGTCGAATGATACAAACGAATCT 60.021 38.462 0.00 0.00 43.02 2.40
402 408 6.020916 TCGAAGTCGAATGATACAAACGAATC 60.021 38.462 0.00 0.00 46.30 2.52
459 473 9.244292 ACCAACGACTATGAGTGTATATCATAT 57.756 33.333 0.00 0.00 38.59 1.78
460 474 8.631480 ACCAACGACTATGAGTGTATATCATA 57.369 34.615 0.00 0.00 38.36 2.15
461 475 7.230712 TGACCAACGACTATGAGTGTATATCAT 59.769 37.037 0.00 0.00 40.45 2.45
462 476 6.544564 TGACCAACGACTATGAGTGTATATCA 59.455 38.462 0.00 0.00 0.00 2.15
463 477 6.967135 TGACCAACGACTATGAGTGTATATC 58.033 40.000 0.00 0.00 0.00 1.63
464 478 6.954487 TGACCAACGACTATGAGTGTATAT 57.046 37.500 0.00 0.00 0.00 0.86
465 479 6.320418 ACATGACCAACGACTATGAGTGTATA 59.680 38.462 0.00 0.00 0.00 1.47
537 552 1.067974 TCGACGCATAATTGGACCGAT 59.932 47.619 0.00 0.00 0.00 4.18
540 555 1.531149 CCATCGACGCATAATTGGACC 59.469 52.381 0.00 0.00 0.00 4.46
656 713 3.769844 TCTGGAGTGTTGGGAGATAACTC 59.230 47.826 0.00 0.00 41.94 3.01
658 715 4.443598 GGATCTGGAGTGTTGGGAGATAAC 60.444 50.000 0.00 0.00 0.00 1.89
742 801 1.442526 CGGCAGTGGATTGATCAGGC 61.443 60.000 0.00 0.00 0.00 4.85
775 834 1.000283 CAAGAGTGAGCTGAACCGTCT 60.000 52.381 0.00 0.00 0.00 4.18
960 1020 3.878667 GGGGAAGGAGATGGGGCG 61.879 72.222 0.00 0.00 0.00 6.13
1629 1715 1.378250 CCAGAAGGCCAGGAAGCAG 60.378 63.158 5.01 0.00 0.00 4.24
2511 2602 0.666274 TGTTGTAGGCTGCGACGAAG 60.666 55.000 16.74 0.00 0.00 3.79
2512 2603 0.249531 TTGTTGTAGGCTGCGACGAA 60.250 50.000 16.74 10.10 0.00 3.85
2627 2718 1.892474 GGTTTTCTGCAAGCCCACATA 59.108 47.619 0.00 0.00 29.24 2.29
2629 2720 0.396974 AGGTTTTCTGCAAGCCCACA 60.397 50.000 0.00 0.00 36.38 4.17
2692 2783 1.334869 CCTTCTTTTGTTCAGCGTGCT 59.665 47.619 0.00 0.00 0.00 4.40
2730 2821 4.709250 GGTTTAATTTTGGGCAAGAACCA 58.291 39.130 0.00 0.00 36.27 3.67
2731 2822 3.743911 CGGTTTAATTTTGGGCAAGAACC 59.256 43.478 0.00 0.00 33.67 3.62
2787 2878 7.106239 AGAACATCTTCTATTTGTGAACGGAT 58.894 34.615 0.00 0.00 34.74 4.18
2910 3008 9.905713 TTGCAGGACAGATAAGAGTAATAATTT 57.094 29.630 0.00 0.00 0.00 1.82
2917 3015 5.939764 ACATTGCAGGACAGATAAGAGTA 57.060 39.130 0.00 0.00 0.00 2.59
3014 3112 7.323420 AGCTAAAAATTTCATTAGGAAGTGCC 58.677 34.615 10.30 0.00 36.72 5.01
3034 3132 7.053498 TCATATGTTGCCTTTGTGATAGCTAA 58.947 34.615 0.00 0.00 0.00 3.09
3041 3139 5.334802 CGAACTTCATATGTTGCCTTTGTGA 60.335 40.000 1.90 0.00 0.00 3.58
3059 3157 5.521010 TCGATGTTGTCTTTGTTACGAACTT 59.479 36.000 0.00 0.00 0.00 2.66
3126 3228 5.985530 TGTTAGTGACACATTTGAGACTGAG 59.014 40.000 8.59 0.00 32.00 3.35
3149 3251 1.064463 AGGCATGGTAACCCAGACATG 60.064 52.381 0.00 0.00 46.15 3.21
3191 3293 8.340757 TGGTATTTGTATATTTCCTGACCCTTT 58.659 33.333 0.00 0.00 0.00 3.11
3452 3557 4.153411 AGAAGTCTCGAAAGAAGAGGGAA 58.847 43.478 0.00 0.00 41.32 3.97
3558 3663 6.014327 AGAGGTAAAATAGACCACGTACCAAA 60.014 38.462 0.00 0.00 39.65 3.28


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

AutoCloner maintained by Alex Coulton.