Multiple sequence alignment - TraesCS6A01G179700

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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 TraesCS6A01G179700 chr6A 100.000 2147 0 0 1 2147 202340053 202337907 0.000000e+00 3965.0
1 TraesCS6A01G179700 chr6A 89.239 381 36 4 1577 1955 474994884 474994507 2.490000e-129 472.0
2 TraesCS6A01G179700 chr6D 89.798 1088 32 16 380 1442 144544965 144545998 0.000000e+00 1321.0
3 TraesCS6A01G179700 chr6D 89.428 577 52 8 1577 2147 335361488 335360915 0.000000e+00 719.0
4 TraesCS6A01G179700 chr6D 91.111 360 25 1 1602 1954 144563613 144563972 4.140000e-132 481.0
5 TraesCS6A01G179700 chr6D 95.135 185 8 1 1964 2147 144564973 144565157 7.500000e-75 291.0
6 TraesCS6A01G179700 chr6B 87.155 724 21 16 741 1442 257576748 257577421 0.000000e+00 756.0
7 TraesCS6A01G179700 chr6B 92.675 314 11 4 382 693 257576434 257576737 1.960000e-120 442.0
8 TraesCS6A01G179700 chr6B 85.955 356 22 13 1522 1870 257577450 257577784 2.620000e-94 355.0
9 TraesCS6A01G179700 chr6B 94.805 154 6 2 1954 2105 257601013 257601166 2.750000e-59 239.0
10 TraesCS6A01G179700 chr6B 89.394 66 5 2 2083 2147 257601785 257601849 4.910000e-12 82.4
11 TraesCS6A01G179700 chr1A 95.402 261 12 0 72 332 515769139 515768879 1.190000e-112 416.0
12 TraesCS6A01G179700 chr1A 94.253 261 15 0 72 332 100293503 100293763 1.190000e-107 399.0
13 TraesCS6A01G179700 chr5A 94.297 263 14 1 71 332 104620926 104621188 3.320000e-108 401.0
14 TraesCS6A01G179700 chr5A 94.253 261 15 0 72 332 658344957 658345217 1.190000e-107 399.0
15 TraesCS6A01G179700 chr3A 93.985 266 15 1 71 335 474832822 474832557 3.320000e-108 401.0
16 TraesCS6A01G179700 chr3A 94.253 261 15 0 72 332 662939468 662939208 1.190000e-107 399.0
17 TraesCS6A01G179700 chr7A 94.253 261 15 0 72 332 643222595 643222335 1.190000e-107 399.0
18 TraesCS6A01G179700 chr7A 97.260 73 2 0 1 73 392782535 392782607 8.050000e-25 124.0
19 TraesCS6A01G179700 chr7A 96.364 55 1 1 328 381 207289611 207289665 2.930000e-14 89.8
20 TraesCS6A01G179700 chr2A 94.275 262 14 1 72 332 615337626 615337365 1.190000e-107 399.0
21 TraesCS6A01G179700 chr2A 93.633 267 15 2 71 336 7514666 7514401 4.290000e-107 398.0
22 TraesCS6A01G179700 chr3D 95.946 74 2 1 1 73 277927523 277927596 3.740000e-23 119.0
23 TraesCS6A01G179700 chr3D 94.595 74 3 1 1 73 277917812 277917885 1.740000e-21 113.0
24 TraesCS6A01G179700 chr3D 94.521 73 4 0 1 73 432520416 432520344 1.740000e-21 113.0
25 TraesCS6A01G179700 chr2D 95.890 73 3 0 1 73 336520703 336520631 3.740000e-23 119.0
26 TraesCS6A01G179700 chr2D 94.595 74 3 1 4 76 139463568 139463495 1.740000e-21 113.0
27 TraesCS6A01G179700 chr2B 95.890 73 3 0 1 73 123141664 123141736 3.740000e-23 119.0
28 TraesCS6A01G179700 chr2B 100.000 29 0 0 1581 1609 17573043 17573015 1.000000e-03 54.7
29 TraesCS6A01G179700 chr7D 94.595 74 3 1 1 73 21584402 21584475 1.740000e-21 113.0
30 TraesCS6A01G179700 chr1B 94.595 74 3 1 1 73 588815737 588815664 1.740000e-21 113.0
31 TraesCS6A01G179700 chrUn 94.000 50 2 1 331 380 71247073 71247121 8.220000e-10 75.0


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 TraesCS6A01G179700 chr6A 202337907 202340053 2146 True 3965.000000 3965 100.000 1 2147 1 chr6A.!!$R1 2146
1 TraesCS6A01G179700 chr6D 144544965 144545998 1033 False 1321.000000 1321 89.798 380 1442 1 chr6D.!!$F1 1062
2 TraesCS6A01G179700 chr6D 335360915 335361488 573 True 719.000000 719 89.428 1577 2147 1 chr6D.!!$R1 570
3 TraesCS6A01G179700 chr6D 144563613 144565157 1544 False 386.000000 481 93.123 1602 2147 2 chr6D.!!$F2 545
4 TraesCS6A01G179700 chr6B 257576434 257577784 1350 False 517.666667 756 88.595 382 1870 3 chr6B.!!$F1 1488

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
19 20 0.473755 AGGTGGTGTCTTGCATGACA 59.526 50.0 26.52 26.52 43.72 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1271 0.235926 GCCACTTGAAACGCAGAGAC 59.764 55.0 0.0 0.0 0.0 3.36 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.329300 AGGTGGTGTCTTGCATGAC 57.671 52.632 22.34 22.34 37.47 3.06
19 20 0.473755 AGGTGGTGTCTTGCATGACA 59.526 50.000 26.52 26.52 43.72 3.58
20 21 1.133823 AGGTGGTGTCTTGCATGACAA 60.134 47.619 30.38 17.38 46.77 3.18
30 31 3.641437 TTGCATGACAAGCCAACTAAC 57.359 42.857 0.00 0.00 33.24 2.34
31 32 1.885887 TGCATGACAAGCCAACTAACC 59.114 47.619 0.00 0.00 0.00 2.85
32 33 1.202348 GCATGACAAGCCAACTAACCC 59.798 52.381 0.00 0.00 0.00 4.11
33 34 2.795329 CATGACAAGCCAACTAACCCT 58.205 47.619 0.00 0.00 0.00 4.34
34 35 3.872240 GCATGACAAGCCAACTAACCCTA 60.872 47.826 0.00 0.00 0.00 3.53
35 36 3.412237 TGACAAGCCAACTAACCCTAC 57.588 47.619 0.00 0.00 0.00 3.18
36 37 2.706723 TGACAAGCCAACTAACCCTACA 59.293 45.455 0.00 0.00 0.00 2.74
37 38 3.136809 TGACAAGCCAACTAACCCTACAA 59.863 43.478 0.00 0.00 0.00 2.41
38 39 4.202524 TGACAAGCCAACTAACCCTACAAT 60.203 41.667 0.00 0.00 0.00 2.71
39 40 5.013287 TGACAAGCCAACTAACCCTACAATA 59.987 40.000 0.00 0.00 0.00 1.90
40 41 6.074698 ACAAGCCAACTAACCCTACAATAT 57.925 37.500 0.00 0.00 0.00 1.28
41 42 6.120220 ACAAGCCAACTAACCCTACAATATC 58.880 40.000 0.00 0.00 0.00 1.63
42 43 6.069615 ACAAGCCAACTAACCCTACAATATCT 60.070 38.462 0.00 0.00 0.00 1.98
43 44 6.176014 AGCCAACTAACCCTACAATATCTC 57.824 41.667 0.00 0.00 0.00 2.75
44 45 5.905913 AGCCAACTAACCCTACAATATCTCT 59.094 40.000 0.00 0.00 0.00 3.10
45 46 7.073854 AGCCAACTAACCCTACAATATCTCTA 58.926 38.462 0.00 0.00 0.00 2.43
46 47 7.567622 AGCCAACTAACCCTACAATATCTCTAA 59.432 37.037 0.00 0.00 0.00 2.10
47 48 8.208903 GCCAACTAACCCTACAATATCTCTAAA 58.791 37.037 0.00 0.00 0.00 1.85
54 55 8.910351 ACCCTACAATATCTCTAAAAATCAGC 57.090 34.615 0.00 0.00 0.00 4.26
55 56 8.718656 ACCCTACAATATCTCTAAAAATCAGCT 58.281 33.333 0.00 0.00 0.00 4.24
64 65 8.614469 ATCTCTAAAAATCAGCTATACAAGGC 57.386 34.615 0.00 0.00 0.00 4.35
65 66 7.796054 TCTCTAAAAATCAGCTATACAAGGCT 58.204 34.615 0.00 0.00 39.60 4.58
66 67 8.924303 TCTCTAAAAATCAGCTATACAAGGCTA 58.076 33.333 0.00 0.00 37.00 3.93
67 68 9.202273 CTCTAAAAATCAGCTATACAAGGCTAG 57.798 37.037 0.00 0.00 37.00 3.42
68 69 8.924303 TCTAAAAATCAGCTATACAAGGCTAGA 58.076 33.333 0.00 0.00 37.00 2.43
69 70 9.202273 CTAAAAATCAGCTATACAAGGCTAGAG 57.798 37.037 0.00 0.00 37.00 2.43
70 71 6.985653 AAATCAGCTATACAAGGCTAGAGA 57.014 37.500 0.00 0.00 37.00 3.10
71 72 7.552050 AAATCAGCTATACAAGGCTAGAGAT 57.448 36.000 0.00 0.00 37.00 2.75
72 73 8.657387 AAATCAGCTATACAAGGCTAGAGATA 57.343 34.615 0.00 0.00 37.00 1.98
73 74 7.639113 ATCAGCTATACAAGGCTAGAGATAC 57.361 40.000 0.00 0.00 37.00 2.24
74 75 6.785076 TCAGCTATACAAGGCTAGAGATACT 58.215 40.000 0.00 0.00 37.00 2.12
75 76 6.882140 TCAGCTATACAAGGCTAGAGATACTC 59.118 42.308 0.00 0.00 37.00 2.59
76 77 6.094881 CAGCTATACAAGGCTAGAGATACTCC 59.905 46.154 0.00 0.00 37.00 3.85
77 78 5.358725 GCTATACAAGGCTAGAGATACTCCC 59.641 48.000 0.00 0.00 0.00 4.30
78 79 3.983533 ACAAGGCTAGAGATACTCCCT 57.016 47.619 0.00 0.00 33.71 4.20
79 80 3.839778 ACAAGGCTAGAGATACTCCCTC 58.160 50.000 0.00 0.00 31.96 4.30
80 81 3.161866 CAAGGCTAGAGATACTCCCTCC 58.838 54.545 0.00 0.00 31.96 4.30
81 82 1.353022 AGGCTAGAGATACTCCCTCCG 59.647 57.143 0.00 0.00 0.00 4.63
82 83 1.614850 GGCTAGAGATACTCCCTCCGG 60.615 61.905 0.00 0.00 0.00 5.14
83 84 1.074244 GCTAGAGATACTCCCTCCGGT 59.926 57.143 0.00 0.00 0.00 5.28
84 85 2.876892 GCTAGAGATACTCCCTCCGGTC 60.877 59.091 0.00 0.00 0.00 4.79
85 86 0.479378 AGAGATACTCCCTCCGGTCC 59.521 60.000 0.00 0.00 0.00 4.46
86 87 0.479378 GAGATACTCCCTCCGGTCCT 59.521 60.000 0.00 0.00 0.00 3.85
87 88 0.935194 AGATACTCCCTCCGGTCCTT 59.065 55.000 0.00 0.00 0.00 3.36
88 89 1.291335 AGATACTCCCTCCGGTCCTTT 59.709 52.381 0.00 0.00 0.00 3.11
89 90 2.117051 GATACTCCCTCCGGTCCTTTT 58.883 52.381 0.00 0.00 0.00 2.27
90 91 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
91 92 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
92 93 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
93 94 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
94 95 2.305052 CTCCCTCCGGTCCTTTTTAGTT 59.695 50.000 0.00 0.00 0.00 2.24
95 96 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
96 97 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
97 98 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
98 99 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
99 100 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
100 101 3.055963 TCCGGTCCTTTTTAGTTCGCATA 60.056 43.478 0.00 0.00 0.00 3.14
101 102 3.875134 CCGGTCCTTTTTAGTTCGCATAT 59.125 43.478 0.00 0.00 0.00 1.78
102 103 5.051816 CCGGTCCTTTTTAGTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
103 104 5.176958 CCGGTCCTTTTTAGTTCGCATATAG 59.823 44.000 0.00 0.00 0.00 1.31
104 105 5.176958 CGGTCCTTTTTAGTTCGCATATAGG 59.823 44.000 0.00 0.00 0.00 2.57
105 106 6.285990 GGTCCTTTTTAGTTCGCATATAGGA 58.714 40.000 0.00 0.00 0.00 2.94
106 107 6.935208 GGTCCTTTTTAGTTCGCATATAGGAT 59.065 38.462 0.00 0.00 32.42 3.24
107 108 7.444487 GGTCCTTTTTAGTTCGCATATAGGATT 59.556 37.037 0.00 0.00 32.42 3.01
108 109 8.837389 GTCCTTTTTAGTTCGCATATAGGATTT 58.163 33.333 0.00 0.00 32.42 2.17
109 110 8.836413 TCCTTTTTAGTTCGCATATAGGATTTG 58.164 33.333 0.00 0.00 0.00 2.32
110 111 8.836413 CCTTTTTAGTTCGCATATAGGATTTGA 58.164 33.333 0.00 0.00 0.00 2.69
111 112 9.651718 CTTTTTAGTTCGCATATAGGATTTGAC 57.348 33.333 0.00 0.00 0.00 3.18
112 113 8.958119 TTTTAGTTCGCATATAGGATTTGACT 57.042 30.769 0.00 0.00 0.00 3.41
116 117 8.594881 AGTTCGCATATAGGATTTGACTAAAG 57.405 34.615 0.00 0.00 0.00 1.85
117 118 8.204836 AGTTCGCATATAGGATTTGACTAAAGT 58.795 33.333 0.00 0.00 0.00 2.66
118 119 8.488764 GTTCGCATATAGGATTTGACTAAAGTC 58.511 37.037 3.08 3.08 44.97 3.01
132 133 6.723131 GACTAAAGTCAAGCCTCGTAAAAT 57.277 37.500 5.24 0.00 44.18 1.82
133 134 7.130303 GACTAAAGTCAAGCCTCGTAAAATT 57.870 36.000 5.24 0.00 44.18 1.82
134 135 7.506328 ACTAAAGTCAAGCCTCGTAAAATTT 57.494 32.000 0.00 0.00 0.00 1.82
135 136 7.360361 ACTAAAGTCAAGCCTCGTAAAATTTG 58.640 34.615 0.00 0.00 0.00 2.32
136 137 6.385649 AAAGTCAAGCCTCGTAAAATTTGA 57.614 33.333 0.00 0.00 0.00 2.69
137 138 5.358298 AGTCAAGCCTCGTAAAATTTGAC 57.642 39.130 6.98 6.98 42.72 3.18
138 139 4.215613 AGTCAAGCCTCGTAAAATTTGACC 59.784 41.667 10.51 0.00 43.15 4.02
139 140 4.023536 GTCAAGCCTCGTAAAATTTGACCA 60.024 41.667 0.00 0.00 38.79 4.02
140 141 4.580995 TCAAGCCTCGTAAAATTTGACCAA 59.419 37.500 0.00 0.00 0.00 3.67
141 142 4.499037 AGCCTCGTAAAATTTGACCAAC 57.501 40.909 0.00 0.00 0.00 3.77
142 143 4.142038 AGCCTCGTAAAATTTGACCAACT 58.858 39.130 0.00 0.00 0.00 3.16
143 144 4.583073 AGCCTCGTAAAATTTGACCAACTT 59.417 37.500 0.00 0.00 0.00 2.66
144 145 5.068591 AGCCTCGTAAAATTTGACCAACTTT 59.931 36.000 0.00 0.00 0.00 2.66
145 146 6.263617 AGCCTCGTAAAATTTGACCAACTTTA 59.736 34.615 0.00 0.00 0.00 1.85
146 147 7.039993 AGCCTCGTAAAATTTGACCAACTTTAT 60.040 33.333 0.00 0.00 0.00 1.40
147 148 8.238631 GCCTCGTAAAATTTGACCAACTTTATA 58.761 33.333 0.00 0.00 0.00 0.98
148 149 9.769093 CCTCGTAAAATTTGACCAACTTTATAG 57.231 33.333 0.00 0.00 0.00 1.31
158 159 8.974060 TTGACCAACTTTATAGAAAAGAGTGT 57.026 30.769 4.59 0.00 0.00 3.55
159 160 8.603242 TGACCAACTTTATAGAAAAGAGTGTC 57.397 34.615 4.59 7.45 0.00 3.67
160 161 8.208224 TGACCAACTTTATAGAAAAGAGTGTCA 58.792 33.333 4.59 9.40 0.00 3.58
161 162 8.974060 ACCAACTTTATAGAAAAGAGTGTCAA 57.026 30.769 4.59 0.00 0.00 3.18
162 163 8.837389 ACCAACTTTATAGAAAAGAGTGTCAAC 58.163 33.333 4.59 0.00 0.00 3.18
163 164 8.836413 CCAACTTTATAGAAAAGAGTGTCAACA 58.164 33.333 4.59 0.00 0.00 3.33
173 174 9.512588 AGAAAAGAGTGTCAACATTCATAATCT 57.487 29.630 8.16 3.91 35.37 2.40
174 175 9.552114 GAAAAGAGTGTCAACATTCATAATCTG 57.448 33.333 8.16 0.00 35.37 2.90
175 176 8.853077 AAAGAGTGTCAACATTCATAATCTGA 57.147 30.769 8.16 0.00 35.37 3.27
177 178 8.853077 AGAGTGTCAACATTCATAATCTGAAA 57.147 30.769 8.16 0.00 46.62 2.69
178 179 9.458727 AGAGTGTCAACATTCATAATCTGAAAT 57.541 29.630 8.16 0.00 46.62 2.17
179 180 9.713740 GAGTGTCAACATTCATAATCTGAAATC 57.286 33.333 1.23 0.00 46.62 2.17
180 181 9.234827 AGTGTCAACATTCATAATCTGAAATCA 57.765 29.630 0.00 0.00 46.62 2.57
181 182 9.844790 GTGTCAACATTCATAATCTGAAATCAA 57.155 29.630 0.00 0.00 46.62 2.57
195 196 8.899427 ATCTGAAATCAATACCACTAGATGTG 57.101 34.615 0.00 0.00 45.80 3.21
196 197 7.851228 TCTGAAATCAATACCACTAGATGTGT 58.149 34.615 0.00 0.00 44.81 3.72
197 198 7.981789 TCTGAAATCAATACCACTAGATGTGTC 59.018 37.037 0.00 0.00 44.81 3.67
198 199 7.619965 TGAAATCAATACCACTAGATGTGTCA 58.380 34.615 0.00 0.00 44.81 3.58
199 200 8.267183 TGAAATCAATACCACTAGATGTGTCAT 58.733 33.333 0.00 0.00 44.81 3.06
200 201 8.442632 AAATCAATACCACTAGATGTGTCATG 57.557 34.615 0.00 0.00 44.81 3.07
201 202 6.790232 TCAATACCACTAGATGTGTCATGA 57.210 37.500 0.00 0.00 44.81 3.07
202 203 6.573434 TCAATACCACTAGATGTGTCATGAC 58.427 40.000 19.27 19.27 44.81 3.06
203 204 6.381133 TCAATACCACTAGATGTGTCATGACT 59.619 38.462 25.55 6.60 44.81 3.41
204 205 6.798427 ATACCACTAGATGTGTCATGACTT 57.202 37.500 25.55 11.29 44.81 3.01
205 206 7.898014 ATACCACTAGATGTGTCATGACTTA 57.102 36.000 25.55 15.01 44.81 2.24
206 207 6.605471 ACCACTAGATGTGTCATGACTTAA 57.395 37.500 25.55 12.04 44.81 1.85
207 208 7.004555 ACCACTAGATGTGTCATGACTTAAA 57.995 36.000 25.55 9.66 44.81 1.52
208 209 7.099764 ACCACTAGATGTGTCATGACTTAAAG 58.900 38.462 25.55 16.54 44.81 1.85
209 210 7.099764 CCACTAGATGTGTCATGACTTAAAGT 58.900 38.462 25.55 17.09 44.81 2.66
210 211 7.604164 CCACTAGATGTGTCATGACTTAAAGTT 59.396 37.037 25.55 8.77 44.81 2.66
211 212 8.993121 CACTAGATGTGTCATGACTTAAAGTTT 58.007 33.333 25.55 7.45 41.53 2.66
212 213 9.209175 ACTAGATGTGTCATGACTTAAAGTTTC 57.791 33.333 25.55 11.27 0.00 2.78
213 214 9.208022 CTAGATGTGTCATGACTTAAAGTTTCA 57.792 33.333 25.55 11.05 0.00 2.69
214 215 8.627208 AGATGTGTCATGACTTAAAGTTTCAT 57.373 30.769 25.55 14.42 0.00 2.57
215 216 9.725019 AGATGTGTCATGACTTAAAGTTTCATA 57.275 29.630 25.55 1.27 0.00 2.15
244 245 9.836864 ATATAACTTTAGCATGACAGATGTTGA 57.163 29.630 0.00 0.00 0.00 3.18
245 246 8.743085 ATAACTTTAGCATGACAGATGTTGAT 57.257 30.769 0.00 0.00 0.00 2.57
246 247 9.836864 ATAACTTTAGCATGACAGATGTTGATA 57.163 29.630 0.00 0.00 0.00 2.15
247 248 8.743085 AACTTTAGCATGACAGATGTTGATAT 57.257 30.769 0.00 0.00 0.00 1.63
248 249 8.743085 ACTTTAGCATGACAGATGTTGATATT 57.257 30.769 0.00 0.00 0.00 1.28
249 250 9.182214 ACTTTAGCATGACAGATGTTGATATTT 57.818 29.630 0.00 0.00 0.00 1.40
295 296 9.447157 AATTTTGTGAAATTTGACTCCAGAAAA 57.553 25.926 9.24 10.68 41.48 2.29
296 297 9.617523 ATTTTGTGAAATTTGACTCCAGAAAAT 57.382 25.926 9.24 12.18 36.52 1.82
297 298 9.447157 TTTTGTGAAATTTGACTCCAGAAAATT 57.553 25.926 9.24 0.00 35.55 1.82
298 299 9.447157 TTTGTGAAATTTGACTCCAGAAAATTT 57.553 25.926 9.24 12.92 42.94 1.82
299 300 9.447157 TTGTGAAATTTGACTCCAGAAAATTTT 57.553 25.926 9.24 2.28 41.29 1.82
323 324 9.603921 TTTAATATGTAGAGTAAAAAGGACCGG 57.396 33.333 0.00 0.00 0.00 5.28
324 325 7.427989 AATATGTAGAGTAAAAAGGACCGGA 57.572 36.000 9.46 0.00 0.00 5.14
325 326 4.796038 TGTAGAGTAAAAAGGACCGGAG 57.204 45.455 9.46 0.00 0.00 4.63
344 345 6.019779 CGGAGGGAGTAATAGAAGAATCAG 57.980 45.833 0.00 0.00 0.00 2.90
345 346 5.536916 CGGAGGGAGTAATAGAAGAATCAGT 59.463 44.000 0.00 0.00 0.00 3.41
346 347 6.294286 CGGAGGGAGTAATAGAAGAATCAGTC 60.294 46.154 0.00 0.00 0.00 3.51
347 348 6.294286 GGAGGGAGTAATAGAAGAATCAGTCG 60.294 46.154 0.00 0.00 0.00 4.18
348 349 6.366340 AGGGAGTAATAGAAGAATCAGTCGA 58.634 40.000 0.00 0.00 0.00 4.20
349 350 6.834451 AGGGAGTAATAGAAGAATCAGTCGAA 59.166 38.462 0.00 0.00 0.00 3.71
350 351 7.342284 AGGGAGTAATAGAAGAATCAGTCGAAA 59.658 37.037 0.00 0.00 0.00 3.46
351 352 7.980099 GGGAGTAATAGAAGAATCAGTCGAAAA 59.020 37.037 0.00 0.00 0.00 2.29
352 353 9.535878 GGAGTAATAGAAGAATCAGTCGAAAAT 57.464 33.333 0.00 0.00 0.00 1.82
474 475 5.852827 ACAACACGGAAATTGGAAAATGAT 58.147 33.333 0.00 0.00 0.00 2.45
475 476 5.695816 ACAACACGGAAATTGGAAAATGATG 59.304 36.000 0.00 0.00 0.00 3.07
477 478 4.283212 ACACGGAAATTGGAAAATGATGGT 59.717 37.500 0.00 0.00 0.00 3.55
478 479 4.626604 CACGGAAATTGGAAAATGATGGTG 59.373 41.667 0.00 0.00 0.00 4.17
479 480 4.526262 ACGGAAATTGGAAAATGATGGTGA 59.474 37.500 0.00 0.00 0.00 4.02
480 481 4.864247 CGGAAATTGGAAAATGATGGTGAC 59.136 41.667 0.00 0.00 0.00 3.67
525 527 3.555324 TGCCAGCGTGAAGACCCA 61.555 61.111 0.00 0.00 0.00 4.51
566 568 3.498397 TCGATGAAAAGCAGAGTTTGACC 59.502 43.478 0.00 0.00 0.00 4.02
567 569 3.365364 CGATGAAAAGCAGAGTTTGACCC 60.365 47.826 0.00 0.00 0.00 4.46
568 570 3.011566 TGAAAAGCAGAGTTTGACCCA 57.988 42.857 0.00 0.00 0.00 4.51
569 571 3.565307 TGAAAAGCAGAGTTTGACCCAT 58.435 40.909 0.00 0.00 0.00 4.00
570 572 3.960102 TGAAAAGCAGAGTTTGACCCATT 59.040 39.130 0.00 0.00 0.00 3.16
571 573 4.405358 TGAAAAGCAGAGTTTGACCCATTT 59.595 37.500 0.00 0.00 0.00 2.32
572 574 4.326504 AAAGCAGAGTTTGACCCATTTG 57.673 40.909 0.00 0.00 0.00 2.32
573 575 3.228188 AGCAGAGTTTGACCCATTTGA 57.772 42.857 0.00 0.00 0.00 2.69
574 576 2.887152 AGCAGAGTTTGACCCATTTGAC 59.113 45.455 0.00 0.00 0.00 3.18
620 622 1.770294 TTTCCTGCGGACAAAACCTT 58.230 45.000 0.00 0.00 0.00 3.50
683 685 3.877508 GGTTATAGCTCCGCTCAAACAAT 59.122 43.478 0.00 0.00 40.44 2.71
684 686 5.054477 GGTTATAGCTCCGCTCAAACAATA 58.946 41.667 0.00 0.00 40.44 1.90
685 687 5.177696 GGTTATAGCTCCGCTCAAACAATAG 59.822 44.000 0.00 0.00 40.44 1.73
686 688 4.672587 ATAGCTCCGCTCAAACAATAGA 57.327 40.909 0.00 0.00 40.44 1.98
689 691 4.265073 AGCTCCGCTCAAACAATAGAAAT 58.735 39.130 0.00 0.00 30.62 2.17
811 815 0.597637 CGATCAAACGAGGCGGCTAT 60.598 55.000 13.24 0.00 35.09 2.97
826 830 2.873472 CGGCTATCGTCTGAAGTCTACT 59.127 50.000 0.00 0.00 0.00 2.57
922 927 1.618837 TCTCTAGCTGCCGAACTTGTT 59.381 47.619 0.00 0.00 0.00 2.83
931 956 2.366266 TGCCGAACTTGTTACCTAGTGT 59.634 45.455 0.00 0.00 0.00 3.55
943 969 1.341581 ACCTAGTGTGAGCTCTCTCCC 60.342 57.143 16.19 4.16 38.58 4.30
1007 1033 4.602259 TTCGATCGGGATGGCGGC 62.602 66.667 16.41 0.00 0.00 6.53
1171 1197 2.932622 GCTACATCGGCTCCCATACATG 60.933 54.545 0.00 0.00 0.00 3.21
1172 1198 1.423584 ACATCGGCTCCCATACATGA 58.576 50.000 0.00 0.00 0.00 3.07
1222 1248 3.611766 AGGATTTTGTTCCGATCGAGT 57.388 42.857 18.66 0.00 40.94 4.18
1223 1249 3.939066 AGGATTTTGTTCCGATCGAGTT 58.061 40.909 18.66 0.00 40.94 3.01
1224 1250 4.324267 AGGATTTTGTTCCGATCGAGTTT 58.676 39.130 18.66 0.00 40.94 2.66
1225 1251 4.154195 AGGATTTTGTTCCGATCGAGTTTG 59.846 41.667 18.66 0.00 40.94 2.93
1226 1252 3.889196 TTTTGTTCCGATCGAGTTTGG 57.111 42.857 18.66 0.00 0.00 3.28
1227 1253 2.536761 TTGTTCCGATCGAGTTTGGT 57.463 45.000 18.66 0.00 0.00 3.67
1228 1254 2.074547 TGTTCCGATCGAGTTTGGTC 57.925 50.000 18.66 0.00 0.00 4.02
1229 1255 0.989890 GTTCCGATCGAGTTTGGTCG 59.010 55.000 18.66 0.00 41.51 4.79
1230 1256 0.734942 TTCCGATCGAGTTTGGTCGC 60.735 55.000 18.66 0.00 39.90 5.19
1231 1257 1.153823 CCGATCGAGTTTGGTCGCT 60.154 57.895 18.66 0.00 39.90 4.93
1232 1258 0.736325 CCGATCGAGTTTGGTCGCTT 60.736 55.000 18.66 0.00 39.90 4.68
1233 1259 1.068474 CGATCGAGTTTGGTCGCTTT 58.932 50.000 10.26 0.00 39.90 3.51
1234 1260 1.059264 CGATCGAGTTTGGTCGCTTTC 59.941 52.381 10.26 0.00 39.90 2.62
1235 1261 1.393883 GATCGAGTTTGGTCGCTTTCC 59.606 52.381 0.00 0.00 39.90 3.13
1236 1262 0.105224 TCGAGTTTGGTCGCTTTCCA 59.895 50.000 0.00 0.00 39.90 3.53
1237 1263 0.234884 CGAGTTTGGTCGCTTTCCAC 59.765 55.000 0.00 0.00 34.45 4.02
1238 1264 0.234884 GAGTTTGGTCGCTTTCCACG 59.765 55.000 0.00 0.00 34.45 4.94
1239 1265 1.164041 AGTTTGGTCGCTTTCCACGG 61.164 55.000 0.00 0.00 34.45 4.94
1240 1266 2.548295 TTTGGTCGCTTTCCACGGC 61.548 57.895 0.00 0.00 34.45 5.68
1247 1273 3.479269 CTTTCCACGGCGCGAGTC 61.479 66.667 12.10 0.00 0.00 3.36
1248 1274 3.916392 CTTTCCACGGCGCGAGTCT 62.916 63.158 12.10 0.00 0.00 3.24
1249 1275 3.909258 TTTCCACGGCGCGAGTCTC 62.909 63.158 12.10 0.00 0.00 3.36
1340 1366 3.110705 TGAGAGAGGAGGGGAGAAAATG 58.889 50.000 0.00 0.00 0.00 2.32
1341 1367 3.246130 TGAGAGAGGAGGGGAGAAAATGA 60.246 47.826 0.00 0.00 0.00 2.57
1342 1368 3.973305 GAGAGAGGAGGGGAGAAAATGAT 59.027 47.826 0.00 0.00 0.00 2.45
1343 1369 5.151454 GAGAGAGGAGGGGAGAAAATGATA 58.849 45.833 0.00 0.00 0.00 2.15
1344 1370 5.736237 AGAGAGGAGGGGAGAAAATGATAT 58.264 41.667 0.00 0.00 0.00 1.63
1345 1371 6.879922 AGAGAGGAGGGGAGAAAATGATATA 58.120 40.000 0.00 0.00 0.00 0.86
1346 1372 6.728632 AGAGAGGAGGGGAGAAAATGATATAC 59.271 42.308 0.00 0.00 0.00 1.47
1419 1445 4.489771 GATGGGACCAGTGGCGGG 62.490 72.222 9.78 0.00 0.00 6.13
1447 1474 4.718940 AAAAATTTATCACGGGGCTGAG 57.281 40.909 0.00 0.00 0.00 3.35
1448 1475 3.366052 AAATTTATCACGGGGCTGAGT 57.634 42.857 0.00 0.00 0.00 3.41
1449 1476 2.332063 ATTTATCACGGGGCTGAGTG 57.668 50.000 0.00 2.15 39.55 3.51
1452 1479 2.981302 TCACGGGGCTGAGTGATG 59.019 61.111 6.23 0.00 41.81 3.07
1453 1480 2.821366 CACGGGGCTGAGTGATGC 60.821 66.667 2.35 0.00 40.56 3.91
1454 1481 3.005539 ACGGGGCTGAGTGATGCT 61.006 61.111 0.00 0.00 0.00 3.79
1455 1482 1.685765 ACGGGGCTGAGTGATGCTA 60.686 57.895 0.00 0.00 0.00 3.49
1456 1483 1.264749 ACGGGGCTGAGTGATGCTAA 61.265 55.000 0.00 0.00 0.00 3.09
1457 1484 0.107703 CGGGGCTGAGTGATGCTAAA 60.108 55.000 0.00 0.00 0.00 1.85
1458 1485 1.678728 CGGGGCTGAGTGATGCTAAAA 60.679 52.381 0.00 0.00 0.00 1.52
1459 1486 1.745653 GGGGCTGAGTGATGCTAAAAC 59.254 52.381 0.00 0.00 0.00 2.43
1460 1487 2.436417 GGGCTGAGTGATGCTAAAACA 58.564 47.619 0.00 0.00 0.00 2.83
1461 1488 2.421424 GGGCTGAGTGATGCTAAAACAG 59.579 50.000 0.00 0.00 0.00 3.16
1462 1489 3.338249 GGCTGAGTGATGCTAAAACAGA 58.662 45.455 0.00 0.00 0.00 3.41
1463 1490 3.944015 GGCTGAGTGATGCTAAAACAGAT 59.056 43.478 0.00 0.00 0.00 2.90
1471 1498 5.415701 GTGATGCTAAAACAGATTGGGAAGA 59.584 40.000 0.00 0.00 0.00 2.87
1473 1500 3.758554 TGCTAAAACAGATTGGGAAGAGC 59.241 43.478 0.00 0.00 0.00 4.09
1483 1510 3.603965 TTGGGAAGAGCCAAAACCTAA 57.396 42.857 0.00 0.00 38.95 2.69
1509 1536 8.436046 AAAAATGAGTTTTTAGCTGCAAATGA 57.564 26.923 1.02 0.00 43.70 2.57
1510 1537 7.412137 AAATGAGTTTTTAGCTGCAAATGAC 57.588 32.000 1.02 3.67 0.00 3.06
1511 1538 4.870363 TGAGTTTTTAGCTGCAAATGACC 58.130 39.130 1.02 0.31 0.00 4.02
1512 1539 3.900941 AGTTTTTAGCTGCAAATGACCG 58.099 40.909 1.02 0.00 0.00 4.79
1513 1540 2.986479 GTTTTTAGCTGCAAATGACCGG 59.014 45.455 0.00 0.00 0.00 5.28
1514 1541 1.904287 TTTAGCTGCAAATGACCGGT 58.096 45.000 6.92 6.92 0.00 5.28
1515 1542 2.772077 TTAGCTGCAAATGACCGGTA 57.228 45.000 7.34 0.00 0.00 4.02
1516 1543 2.772077 TAGCTGCAAATGACCGGTAA 57.228 45.000 7.34 0.00 0.00 2.85
1517 1544 2.128771 AGCTGCAAATGACCGGTAAT 57.871 45.000 7.34 1.12 0.00 1.89
1518 1545 2.446435 AGCTGCAAATGACCGGTAATT 58.554 42.857 11.79 11.79 0.00 1.40
1519 1546 3.616219 AGCTGCAAATGACCGGTAATTA 58.384 40.909 17.95 1.45 0.00 1.40
1520 1547 4.207165 AGCTGCAAATGACCGGTAATTAT 58.793 39.130 17.95 5.66 0.00 1.28
1521 1548 4.036734 AGCTGCAAATGACCGGTAATTATG 59.963 41.667 17.95 17.09 0.00 1.90
1522 1549 4.202010 GCTGCAAATGACCGGTAATTATGT 60.202 41.667 17.95 0.00 0.00 2.29
1563 1590 9.995003 AATTAGCATGAAATCCTTGTTGTTAAA 57.005 25.926 0.00 0.00 0.00 1.52
1567 1594 5.799827 TGAAATCCTTGTTGTTAAAGGGG 57.200 39.130 2.54 0.00 43.78 4.79
1569 1596 2.003937 TCCTTGTTGTTAAAGGGGCC 57.996 50.000 0.00 0.00 43.78 5.80
1571 1598 0.038618 CTTGTTGTTAAAGGGGCCGC 60.039 55.000 12.88 12.88 0.00 6.53
1572 1599 0.755698 TTGTTGTTAAAGGGGCCGCA 60.756 50.000 23.39 0.00 0.00 5.69
1573 1600 0.540830 TGTTGTTAAAGGGGCCGCAT 60.541 50.000 23.39 7.26 0.00 4.73
1574 1601 0.108851 GTTGTTAAAGGGGCCGCATG 60.109 55.000 23.39 0.00 0.00 4.06
1575 1602 1.254284 TTGTTAAAGGGGCCGCATGG 61.254 55.000 23.39 0.00 38.77 3.66
1599 1626 1.515954 GCCGGTCCTGAGATTTCGA 59.484 57.895 1.90 0.00 0.00 3.71
1610 1638 3.338250 ATTTCGAGGGCCAGGGCA 61.338 61.111 16.36 0.00 44.11 5.36
1753 1783 4.587262 TCCAGAGCACAGAAGTAAAGTGTA 59.413 41.667 0.00 0.00 35.75 2.90
1887 1924 0.316772 CACGTGTATAGCCCTCGTCG 60.317 60.000 7.58 0.00 32.47 5.12
1930 1967 1.795768 TGCTAAGTCGCCAAACTCAG 58.204 50.000 0.00 0.00 0.00 3.35
1944 1981 5.393461 GCCAAACTCAGAATTCATAACCCAG 60.393 44.000 8.44 0.00 0.00 4.45
1955 1992 9.561069 AGAATTCATAACCCAGACAATGTATAC 57.439 33.333 8.44 0.00 0.00 1.47
1957 1994 6.816616 TCATAACCCAGACAATGTATACCA 57.183 37.500 0.00 0.00 0.00 3.25
1962 2990 9.793259 ATAACCCAGACAATGTATACCAATAAG 57.207 33.333 0.00 0.00 0.00 1.73
2005 3033 1.134729 GCAACGACGGGGAGGTAATAA 60.135 52.381 0.00 0.00 0.00 1.40
2141 3171 0.389948 GTGATCGCGTCTTCAGGGTT 60.390 55.000 5.77 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.473755 TGTCATGCAAGACACCACCT 59.526 50.000 20.17 0.00 43.18 4.00
1 2 3.019964 TGTCATGCAAGACACCACC 57.980 52.632 20.17 0.00 43.18 4.61
10 11 2.295909 GGTTAGTTGGCTTGTCATGCAA 59.704 45.455 12.33 0.00 35.50 4.08
11 12 1.885887 GGTTAGTTGGCTTGTCATGCA 59.114 47.619 12.33 0.00 0.00 3.96
12 13 1.202348 GGGTTAGTTGGCTTGTCATGC 59.798 52.381 2.09 2.09 0.00 4.06
13 14 2.795329 AGGGTTAGTTGGCTTGTCATG 58.205 47.619 0.00 0.00 0.00 3.07
14 15 3.329520 TGTAGGGTTAGTTGGCTTGTCAT 59.670 43.478 0.00 0.00 0.00 3.06
15 16 2.706723 TGTAGGGTTAGTTGGCTTGTCA 59.293 45.455 0.00 0.00 0.00 3.58
16 17 3.412237 TGTAGGGTTAGTTGGCTTGTC 57.588 47.619 0.00 0.00 0.00 3.18
17 18 3.868619 TTGTAGGGTTAGTTGGCTTGT 57.131 42.857 0.00 0.00 0.00 3.16
18 19 6.357367 AGATATTGTAGGGTTAGTTGGCTTG 58.643 40.000 0.00 0.00 0.00 4.01
19 20 6.387220 AGAGATATTGTAGGGTTAGTTGGCTT 59.613 38.462 0.00 0.00 0.00 4.35
20 21 5.905913 AGAGATATTGTAGGGTTAGTTGGCT 59.094 40.000 0.00 0.00 0.00 4.75
21 22 6.176014 AGAGATATTGTAGGGTTAGTTGGC 57.824 41.667 0.00 0.00 0.00 4.52
28 29 9.343539 GCTGATTTTTAGAGATATTGTAGGGTT 57.656 33.333 0.00 0.00 0.00 4.11
29 30 8.718656 AGCTGATTTTTAGAGATATTGTAGGGT 58.281 33.333 0.00 0.00 0.00 4.34
38 39 9.712305 GCCTTGTATAGCTGATTTTTAGAGATA 57.288 33.333 0.00 0.00 0.00 1.98
39 40 8.435982 AGCCTTGTATAGCTGATTTTTAGAGAT 58.564 33.333 0.00 0.00 38.11 2.75
40 41 7.796054 AGCCTTGTATAGCTGATTTTTAGAGA 58.204 34.615 0.00 0.00 38.11 3.10
41 42 9.202273 CTAGCCTTGTATAGCTGATTTTTAGAG 57.798 37.037 0.00 0.00 40.28 2.43
42 43 8.924303 TCTAGCCTTGTATAGCTGATTTTTAGA 58.076 33.333 0.00 0.00 40.28 2.10
43 44 9.202273 CTCTAGCCTTGTATAGCTGATTTTTAG 57.798 37.037 0.00 0.00 40.28 1.85
44 45 8.924303 TCTCTAGCCTTGTATAGCTGATTTTTA 58.076 33.333 0.00 0.00 40.28 1.52
45 46 7.796054 TCTCTAGCCTTGTATAGCTGATTTTT 58.204 34.615 0.00 0.00 40.28 1.94
46 47 7.366847 TCTCTAGCCTTGTATAGCTGATTTT 57.633 36.000 0.00 0.00 40.28 1.82
47 48 6.985653 TCTCTAGCCTTGTATAGCTGATTT 57.014 37.500 0.00 0.00 40.28 2.17
48 49 7.893302 AGTATCTCTAGCCTTGTATAGCTGATT 59.107 37.037 0.00 0.00 40.28 2.57
49 50 7.410174 AGTATCTCTAGCCTTGTATAGCTGAT 58.590 38.462 0.00 0.00 40.28 2.90
50 51 6.785076 AGTATCTCTAGCCTTGTATAGCTGA 58.215 40.000 0.00 0.00 40.28 4.26
51 52 6.094881 GGAGTATCTCTAGCCTTGTATAGCTG 59.905 46.154 0.00 0.00 35.92 4.24
52 53 6.184789 GGAGTATCTCTAGCCTTGTATAGCT 58.815 44.000 0.00 0.00 38.06 3.32
53 54 5.358725 GGGAGTATCTCTAGCCTTGTATAGC 59.641 48.000 0.00 0.00 33.73 2.97
77 78 1.730612 GCGAACTAAAAAGGACCGGAG 59.269 52.381 9.46 0.00 0.00 4.63
78 79 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
79 80 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
80 81 5.176958 CCTATATGCGAACTAAAAAGGACCG 59.823 44.000 0.00 0.00 0.00 4.79
81 82 6.285990 TCCTATATGCGAACTAAAAAGGACC 58.714 40.000 0.00 0.00 0.00 4.46
82 83 7.964604 ATCCTATATGCGAACTAAAAAGGAC 57.035 36.000 0.00 0.00 33.67 3.85
83 84 8.836413 CAAATCCTATATGCGAACTAAAAAGGA 58.164 33.333 0.00 0.00 35.24 3.36
84 85 8.836413 TCAAATCCTATATGCGAACTAAAAAGG 58.164 33.333 0.00 0.00 0.00 3.11
85 86 9.651718 GTCAAATCCTATATGCGAACTAAAAAG 57.348 33.333 0.00 0.00 0.00 2.27
86 87 9.391006 AGTCAAATCCTATATGCGAACTAAAAA 57.609 29.630 0.00 0.00 0.00 1.94
87 88 8.958119 AGTCAAATCCTATATGCGAACTAAAA 57.042 30.769 0.00 0.00 0.00 1.52
90 91 9.692749 CTTTAGTCAAATCCTATATGCGAACTA 57.307 33.333 0.00 0.00 0.00 2.24
91 92 8.204836 ACTTTAGTCAAATCCTATATGCGAACT 58.795 33.333 0.00 0.00 0.00 3.01
92 93 8.366671 ACTTTAGTCAAATCCTATATGCGAAC 57.633 34.615 0.00 0.00 0.00 3.95
93 94 8.589335 GACTTTAGTCAAATCCTATATGCGAA 57.411 34.615 5.04 0.00 44.18 4.70
109 110 6.723131 ATTTTACGAGGCTTGACTTTAGTC 57.277 37.500 9.20 2.92 44.97 2.59
110 111 7.227910 TCAAATTTTACGAGGCTTGACTTTAGT 59.772 33.333 9.20 0.00 0.00 2.24
111 112 7.534239 GTCAAATTTTACGAGGCTTGACTTTAG 59.466 37.037 9.20 0.00 39.54 1.85
112 113 7.357303 GTCAAATTTTACGAGGCTTGACTTTA 58.643 34.615 9.20 0.00 39.54 1.85
113 114 6.206498 GTCAAATTTTACGAGGCTTGACTTT 58.794 36.000 9.20 0.00 39.54 2.66
114 115 5.278315 GGTCAAATTTTACGAGGCTTGACTT 60.278 40.000 9.20 0.00 41.40 3.01
115 116 4.215613 GGTCAAATTTTACGAGGCTTGACT 59.784 41.667 9.20 0.00 41.40 3.41
116 117 4.023536 TGGTCAAATTTTACGAGGCTTGAC 60.024 41.667 9.20 5.19 41.09 3.18
117 118 4.138290 TGGTCAAATTTTACGAGGCTTGA 58.862 39.130 9.20 0.00 0.00 3.02
118 119 4.497473 TGGTCAAATTTTACGAGGCTTG 57.503 40.909 0.00 0.00 0.00 4.01
119 120 4.583073 AGTTGGTCAAATTTTACGAGGCTT 59.417 37.500 0.00 0.00 0.00 4.35
120 121 4.142038 AGTTGGTCAAATTTTACGAGGCT 58.858 39.130 0.00 0.00 0.00 4.58
121 122 4.499037 AGTTGGTCAAATTTTACGAGGC 57.501 40.909 0.00 0.00 0.00 4.70
122 123 9.769093 CTATAAAGTTGGTCAAATTTTACGAGG 57.231 33.333 13.08 0.00 39.07 4.63
132 133 9.403583 ACACTCTTTTCTATAAAGTTGGTCAAA 57.596 29.630 0.00 0.00 0.00 2.69
133 134 8.974060 ACACTCTTTTCTATAAAGTTGGTCAA 57.026 30.769 0.00 0.00 0.00 3.18
134 135 8.208224 TGACACTCTTTTCTATAAAGTTGGTCA 58.792 33.333 0.00 0.00 33.64 4.02
135 136 8.603242 TGACACTCTTTTCTATAAAGTTGGTC 57.397 34.615 0.00 0.00 0.00 4.02
136 137 8.837389 GTTGACACTCTTTTCTATAAAGTTGGT 58.163 33.333 0.00 0.00 0.00 3.67
137 138 8.836413 TGTTGACACTCTTTTCTATAAAGTTGG 58.164 33.333 0.00 0.00 0.00 3.77
147 148 9.512588 AGATTATGAATGTTGACACTCTTTTCT 57.487 29.630 0.00 0.00 0.00 2.52
148 149 9.552114 CAGATTATGAATGTTGACACTCTTTTC 57.448 33.333 0.00 0.00 0.00 2.29
149 150 9.288576 TCAGATTATGAATGTTGACACTCTTTT 57.711 29.630 0.00 0.00 34.02 2.27
150 151 8.853077 TCAGATTATGAATGTTGACACTCTTT 57.147 30.769 0.00 0.00 34.02 2.52
151 152 8.853077 TTCAGATTATGAATGTTGACACTCTT 57.147 30.769 0.00 0.00 43.09 2.85
169 170 9.334947 CACATCTAGTGGTATTGATTTCAGATT 57.665 33.333 0.00 0.00 44.69 2.40
170 171 8.899427 CACATCTAGTGGTATTGATTTCAGAT 57.101 34.615 0.00 0.00 44.69 2.90
186 187 9.209175 GAAACTTTAAGTCATGACACATCTAGT 57.791 33.333 27.02 17.46 0.00 2.57
187 188 9.208022 TGAAACTTTAAGTCATGACACATCTAG 57.792 33.333 27.02 16.90 0.00 2.43
188 189 9.725019 ATGAAACTTTAAGTCATGACACATCTA 57.275 29.630 27.02 7.86 30.84 1.98
189 190 8.627208 ATGAAACTTTAAGTCATGACACATCT 57.373 30.769 27.02 3.53 30.84 2.90
218 219 9.836864 TCAACATCTGTCATGCTAAAGTTATAT 57.163 29.630 0.00 0.00 0.00 0.86
219 220 9.836864 ATCAACATCTGTCATGCTAAAGTTATA 57.163 29.630 0.00 0.00 0.00 0.98
220 221 8.743085 ATCAACATCTGTCATGCTAAAGTTAT 57.257 30.769 0.00 0.00 0.00 1.89
221 222 9.836864 ATATCAACATCTGTCATGCTAAAGTTA 57.163 29.630 0.00 0.00 0.00 2.24
222 223 8.743085 ATATCAACATCTGTCATGCTAAAGTT 57.257 30.769 0.00 0.00 0.00 2.66
223 224 8.743085 AATATCAACATCTGTCATGCTAAAGT 57.257 30.769 0.00 0.00 0.00 2.66
269 270 9.447157 TTTTCTGGAGTCAAATTTCACAAAATT 57.553 25.926 0.00 0.00 44.97 1.82
270 271 9.617523 ATTTTCTGGAGTCAAATTTCACAAAAT 57.382 25.926 0.00 0.00 36.64 1.82
271 272 9.447157 AATTTTCTGGAGTCAAATTTCACAAAA 57.553 25.926 0.00 0.00 27.77 2.44
272 273 9.447157 AAATTTTCTGGAGTCAAATTTCACAAA 57.553 25.926 0.00 0.00 35.98 2.83
273 274 9.447157 AAAATTTTCTGGAGTCAAATTTCACAA 57.553 25.926 10.41 0.00 38.54 3.33
297 298 9.603921 CCGGTCCTTTTTACTCTACATATTAAA 57.396 33.333 0.00 0.00 0.00 1.52
298 299 8.980596 TCCGGTCCTTTTTACTCTACATATTAA 58.019 33.333 0.00 0.00 0.00 1.40
299 300 8.537728 TCCGGTCCTTTTTACTCTACATATTA 57.462 34.615 0.00 0.00 0.00 0.98
300 301 7.418712 CCTCCGGTCCTTTTTACTCTACATATT 60.419 40.741 0.00 0.00 0.00 1.28
301 302 6.041751 CCTCCGGTCCTTTTTACTCTACATAT 59.958 42.308 0.00 0.00 0.00 1.78
302 303 5.361857 CCTCCGGTCCTTTTTACTCTACATA 59.638 44.000 0.00 0.00 0.00 2.29
303 304 4.161754 CCTCCGGTCCTTTTTACTCTACAT 59.838 45.833 0.00 0.00 0.00 2.29
304 305 3.512724 CCTCCGGTCCTTTTTACTCTACA 59.487 47.826 0.00 0.00 0.00 2.74
305 306 3.118847 CCCTCCGGTCCTTTTTACTCTAC 60.119 52.174 0.00 0.00 0.00 2.59
306 307 3.102204 CCCTCCGGTCCTTTTTACTCTA 58.898 50.000 0.00 0.00 0.00 2.43
307 308 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
308 309 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
309 310 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
310 311 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
311 312 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
312 313 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
313 314 2.034436 TTACTCCCTCCGGTCCTTTT 57.966 50.000 0.00 0.00 0.00 2.27
314 315 2.265526 ATTACTCCCTCCGGTCCTTT 57.734 50.000 0.00 0.00 0.00 3.11
315 316 2.517127 TCTATTACTCCCTCCGGTCCTT 59.483 50.000 0.00 0.00 0.00 3.36
316 317 2.141911 TCTATTACTCCCTCCGGTCCT 58.858 52.381 0.00 0.00 0.00 3.85
317 318 2.671896 TCTATTACTCCCTCCGGTCC 57.328 55.000 0.00 0.00 0.00 4.46
318 319 3.830121 TCTTCTATTACTCCCTCCGGTC 58.170 50.000 0.00 0.00 0.00 4.79
319 320 3.967467 TCTTCTATTACTCCCTCCGGT 57.033 47.619 0.00 0.00 0.00 5.28
320 321 4.833380 TGATTCTTCTATTACTCCCTCCGG 59.167 45.833 0.00 0.00 0.00 5.14
321 322 5.536916 ACTGATTCTTCTATTACTCCCTCCG 59.463 44.000 0.00 0.00 0.00 4.63
322 323 6.294286 CGACTGATTCTTCTATTACTCCCTCC 60.294 46.154 0.00 0.00 0.00 4.30
323 324 6.487331 TCGACTGATTCTTCTATTACTCCCTC 59.513 42.308 0.00 0.00 0.00 4.30
324 325 6.366340 TCGACTGATTCTTCTATTACTCCCT 58.634 40.000 0.00 0.00 0.00 4.20
325 326 6.636562 TCGACTGATTCTTCTATTACTCCC 57.363 41.667 0.00 0.00 0.00 4.30
326 327 8.928270 TTTTCGACTGATTCTTCTATTACTCC 57.072 34.615 0.00 0.00 0.00 3.85
354 355 9.187455 GGTGTTGAAACGTGATATTTTTGTATT 57.813 29.630 0.00 0.00 0.00 1.89
355 356 8.353684 TGGTGTTGAAACGTGATATTTTTGTAT 58.646 29.630 0.00 0.00 0.00 2.29
356 357 7.704271 TGGTGTTGAAACGTGATATTTTTGTA 58.296 30.769 0.00 0.00 0.00 2.41
357 358 6.565234 TGGTGTTGAAACGTGATATTTTTGT 58.435 32.000 0.00 0.00 0.00 2.83
358 359 7.409238 CGATGGTGTTGAAACGTGATATTTTTG 60.409 37.037 0.00 0.00 0.00 2.44
359 360 6.580791 CGATGGTGTTGAAACGTGATATTTTT 59.419 34.615 0.00 0.00 0.00 1.94
360 361 6.072948 TCGATGGTGTTGAAACGTGATATTTT 60.073 34.615 0.00 0.00 0.00 1.82
361 362 5.410132 TCGATGGTGTTGAAACGTGATATTT 59.590 36.000 0.00 0.00 0.00 1.40
362 363 4.932799 TCGATGGTGTTGAAACGTGATATT 59.067 37.500 0.00 0.00 0.00 1.28
363 364 4.500127 TCGATGGTGTTGAAACGTGATAT 58.500 39.130 0.00 0.00 0.00 1.63
364 365 3.915536 TCGATGGTGTTGAAACGTGATA 58.084 40.909 0.00 0.00 0.00 2.15
365 366 2.761559 TCGATGGTGTTGAAACGTGAT 58.238 42.857 0.00 0.00 0.00 3.06
366 367 2.226602 TCGATGGTGTTGAAACGTGA 57.773 45.000 0.00 0.00 0.00 4.35
367 368 3.059257 TCATTCGATGGTGTTGAAACGTG 60.059 43.478 0.00 0.00 33.95 4.49
368 369 3.135225 TCATTCGATGGTGTTGAAACGT 58.865 40.909 0.00 0.00 33.95 3.99
369 370 3.186409 ACTCATTCGATGGTGTTGAAACG 59.814 43.478 0.00 0.00 33.95 3.60
370 371 4.749245 ACTCATTCGATGGTGTTGAAAC 57.251 40.909 0.00 0.00 33.95 2.78
371 372 5.278266 GGAAACTCATTCGATGGTGTTGAAA 60.278 40.000 5.43 0.00 39.05 2.69
372 373 4.215399 GGAAACTCATTCGATGGTGTTGAA 59.785 41.667 5.43 0.00 39.05 2.69
373 374 3.751175 GGAAACTCATTCGATGGTGTTGA 59.249 43.478 5.43 0.00 39.05 3.18
374 375 3.424829 CGGAAACTCATTCGATGGTGTTG 60.425 47.826 5.43 0.00 39.05 3.33
375 376 2.742053 CGGAAACTCATTCGATGGTGTT 59.258 45.455 0.00 0.00 39.05 3.32
376 377 2.346803 CGGAAACTCATTCGATGGTGT 58.653 47.619 0.00 0.00 39.05 4.16
377 378 1.062587 GCGGAAACTCATTCGATGGTG 59.937 52.381 0.00 0.00 39.05 4.17
378 379 1.066143 AGCGGAAACTCATTCGATGGT 60.066 47.619 0.00 0.00 39.05 3.55
432 433 2.166130 TTGCCGCGATGAGAACCAGA 62.166 55.000 8.23 0.00 0.00 3.86
474 475 1.059098 ACAATGCCTCTCTGTCACCA 58.941 50.000 0.00 0.00 0.00 4.17
475 476 2.191128 AACAATGCCTCTCTGTCACC 57.809 50.000 0.00 0.00 0.00 4.02
525 527 0.398318 AAGAGAAACCCAGCTTCGCT 59.602 50.000 0.00 0.00 40.77 4.93
566 568 2.158559 TGTCAATCGTGGGTCAAATGG 58.841 47.619 0.00 0.00 0.00 3.16
567 569 3.913548 TTGTCAATCGTGGGTCAAATG 57.086 42.857 0.00 0.00 0.00 2.32
568 570 4.098654 TGTTTTGTCAATCGTGGGTCAAAT 59.901 37.500 0.00 0.00 0.00 2.32
569 571 3.444034 TGTTTTGTCAATCGTGGGTCAAA 59.556 39.130 0.00 0.00 0.00 2.69
570 572 3.017442 TGTTTTGTCAATCGTGGGTCAA 58.983 40.909 0.00 0.00 0.00 3.18
571 573 2.644676 TGTTTTGTCAATCGTGGGTCA 58.355 42.857 0.00 0.00 0.00 4.02
572 574 3.915437 ATGTTTTGTCAATCGTGGGTC 57.085 42.857 0.00 0.00 0.00 4.46
573 575 3.190535 GCTATGTTTTGTCAATCGTGGGT 59.809 43.478 0.00 0.00 0.00 4.51
574 576 3.440173 AGCTATGTTTTGTCAATCGTGGG 59.560 43.478 0.00 0.00 0.00 4.61
620 622 4.037565 CGGAATATATATGGCTGGCGTAGA 59.962 45.833 9.13 4.80 0.00 2.59
683 685 5.163131 GCAGGGAATAACCTACCCATTTCTA 60.163 44.000 0.00 0.00 45.43 2.10
684 686 4.386424 GCAGGGAATAACCTACCCATTTCT 60.386 45.833 0.00 0.00 45.43 2.52
685 687 3.889538 GCAGGGAATAACCTACCCATTTC 59.110 47.826 0.00 0.00 45.43 2.17
686 688 3.270960 TGCAGGGAATAACCTACCCATTT 59.729 43.478 0.00 0.00 45.43 2.32
689 691 1.974028 TGCAGGGAATAACCTACCCA 58.026 50.000 0.00 0.00 45.43 4.51
775 779 2.357396 GGGGCTTGCCTTTTTGCG 60.357 61.111 11.71 0.00 0.00 4.85
811 815 1.199327 CGCCAAGTAGACTTCAGACGA 59.801 52.381 0.00 0.00 33.11 4.20
881 885 1.228552 GGTTGATGCCCTGGTGTGT 60.229 57.895 0.00 0.00 0.00 3.72
922 927 2.092321 GGGAGAGAGCTCACACTAGGTA 60.092 54.545 17.77 0.00 44.25 3.08
931 956 0.612229 CTTGCTTGGGAGAGAGCTCA 59.388 55.000 17.77 0.00 43.14 4.26
943 969 1.863267 CCGATCCTAGAGCTTGCTTG 58.137 55.000 0.00 0.00 0.00 4.01
1171 1197 2.978010 CGGCCGCCCATGGTATTC 60.978 66.667 14.67 0.00 0.00 1.75
1172 1198 4.579384 CCGGCCGCCCATGGTATT 62.579 66.667 22.85 0.00 0.00 1.89
1222 1248 2.548295 GCCGTGGAAAGCGACCAAA 61.548 57.895 0.00 0.00 39.22 3.28
1223 1249 2.975799 GCCGTGGAAAGCGACCAA 60.976 61.111 0.00 0.00 39.22 3.67
1230 1256 3.479269 GACTCGCGCCGTGGAAAG 61.479 66.667 0.00 0.00 0.00 2.62
1231 1257 3.909258 GAGACTCGCGCCGTGGAAA 62.909 63.158 0.00 0.00 0.00 3.13
1232 1258 4.415332 GAGACTCGCGCCGTGGAA 62.415 66.667 0.00 0.00 0.00 3.53
1241 1267 0.436531 CTTGAAACGCAGAGACTCGC 59.563 55.000 8.62 8.62 0.00 5.03
1242 1268 1.453524 CACTTGAAACGCAGAGACTCG 59.546 52.381 0.00 0.00 0.00 4.18
1243 1269 1.795286 CCACTTGAAACGCAGAGACTC 59.205 52.381 0.00 0.00 0.00 3.36
1244 1270 1.871080 CCACTTGAAACGCAGAGACT 58.129 50.000 0.00 0.00 0.00 3.24
1245 1271 0.235926 GCCACTTGAAACGCAGAGAC 59.764 55.000 0.00 0.00 0.00 3.36
1246 1272 0.884704 GGCCACTTGAAACGCAGAGA 60.885 55.000 0.00 0.00 0.00 3.10
1247 1273 1.576421 GGCCACTTGAAACGCAGAG 59.424 57.895 0.00 0.00 0.00 3.35
1248 1274 2.250939 CGGCCACTTGAAACGCAGA 61.251 57.895 2.24 0.00 0.00 4.26
1249 1275 2.252260 CGGCCACTTGAAACGCAG 59.748 61.111 2.24 0.00 0.00 5.18
1442 1469 5.330295 CAATCTGTTTTAGCATCACTCAGC 58.670 41.667 0.00 0.00 0.00 4.26
1443 1470 5.163683 CCCAATCTGTTTTAGCATCACTCAG 60.164 44.000 0.00 0.00 0.00 3.35
1444 1471 4.701651 CCCAATCTGTTTTAGCATCACTCA 59.298 41.667 0.00 0.00 0.00 3.41
1445 1472 4.943705 TCCCAATCTGTTTTAGCATCACTC 59.056 41.667 0.00 0.00 0.00 3.51
1446 1473 4.922206 TCCCAATCTGTTTTAGCATCACT 58.078 39.130 0.00 0.00 0.00 3.41
1447 1474 5.415701 TCTTCCCAATCTGTTTTAGCATCAC 59.584 40.000 0.00 0.00 0.00 3.06
1448 1475 5.569355 TCTTCCCAATCTGTTTTAGCATCA 58.431 37.500 0.00 0.00 0.00 3.07
1449 1476 5.449725 GCTCTTCCCAATCTGTTTTAGCATC 60.450 44.000 0.00 0.00 0.00 3.91
1450 1477 4.400567 GCTCTTCCCAATCTGTTTTAGCAT 59.599 41.667 0.00 0.00 0.00 3.79
1451 1478 3.758554 GCTCTTCCCAATCTGTTTTAGCA 59.241 43.478 0.00 0.00 0.00 3.49
1452 1479 3.129462 GGCTCTTCCCAATCTGTTTTAGC 59.871 47.826 0.00 0.00 0.00 3.09
1453 1480 4.335416 TGGCTCTTCCCAATCTGTTTTAG 58.665 43.478 0.00 0.00 30.32 1.85
1454 1481 4.380843 TGGCTCTTCCCAATCTGTTTTA 57.619 40.909 0.00 0.00 30.32 1.52
1455 1482 3.243359 TGGCTCTTCCCAATCTGTTTT 57.757 42.857 0.00 0.00 30.32 2.43
1456 1483 2.978156 TGGCTCTTCCCAATCTGTTT 57.022 45.000 0.00 0.00 30.32 2.83
1457 1484 2.978156 TTGGCTCTTCCCAATCTGTT 57.022 45.000 0.00 0.00 39.85 3.16
1458 1485 2.893489 GTTTTGGCTCTTCCCAATCTGT 59.107 45.455 0.00 0.00 43.91 3.41
1459 1486 2.232208 GGTTTTGGCTCTTCCCAATCTG 59.768 50.000 0.00 0.00 43.91 2.90
1460 1487 2.110721 AGGTTTTGGCTCTTCCCAATCT 59.889 45.455 0.00 0.00 43.91 2.40
1461 1488 2.529632 AGGTTTTGGCTCTTCCCAATC 58.470 47.619 0.00 0.00 43.91 2.67
1462 1489 2.702270 AGGTTTTGGCTCTTCCCAAT 57.298 45.000 0.00 0.00 43.91 3.16
1463 1490 3.603965 TTAGGTTTTGGCTCTTCCCAA 57.396 42.857 0.00 0.00 42.87 4.12
1494 1521 2.235016 ACCGGTCATTTGCAGCTAAAA 58.765 42.857 0.00 0.00 0.00 1.52
1495 1522 1.904287 ACCGGTCATTTGCAGCTAAA 58.096 45.000 0.00 0.00 0.00 1.85
1496 1523 2.772077 TACCGGTCATTTGCAGCTAA 57.228 45.000 12.40 0.00 0.00 3.09
1497 1524 2.772077 TTACCGGTCATTTGCAGCTA 57.228 45.000 12.40 0.00 0.00 3.32
1498 1525 2.128771 ATTACCGGTCATTTGCAGCT 57.871 45.000 12.40 0.00 0.00 4.24
1499 1526 2.939460 AATTACCGGTCATTTGCAGC 57.061 45.000 12.40 0.00 0.00 5.25
1500 1527 5.499139 ACATAATTACCGGTCATTTGCAG 57.501 39.130 18.67 9.26 0.00 4.41
1501 1528 6.116806 AGTACATAATTACCGGTCATTTGCA 58.883 36.000 18.67 2.26 0.00 4.08
1502 1529 6.613755 AGTACATAATTACCGGTCATTTGC 57.386 37.500 18.67 5.62 0.00 3.68
1542 1569 5.639082 CCCTTTAACAACAAGGATTTCATGC 59.361 40.000 0.00 0.00 43.32 4.06
1610 1638 2.152016 GGGCGTTTGAGTCTAGCTTTT 58.848 47.619 0.00 0.00 0.00 2.27
1771 1808 9.691362 AGGTATTTGTTTTTACTACAATGCTTG 57.309 29.630 0.00 0.00 35.60 4.01
1835 1872 8.046107 TCAACATGGATGATAACAACATGAGTA 58.954 33.333 20.35 8.05 42.50 2.59
1896 1933 7.224949 GGCGACTTAGCAATAGTTTCTAATCTT 59.775 37.037 0.00 0.00 39.27 2.40
1911 1948 1.343142 TCTGAGTTTGGCGACTTAGCA 59.657 47.619 7.47 0.00 39.27 3.49
1913 1950 4.690748 TGAATTCTGAGTTTGGCGACTTAG 59.309 41.667 7.05 6.36 35.30 2.18
1916 1953 3.126001 TGAATTCTGAGTTTGGCGACT 57.874 42.857 7.05 0.00 0.00 4.18
1930 1967 8.784043 GGTATACATTGTCTGGGTTATGAATTC 58.216 37.037 5.01 0.00 0.00 2.17
1955 1992 6.036517 GGTCGCAGATAGATATTGCTTATTGG 59.963 42.308 0.00 0.00 40.67 3.16
1957 1994 5.807520 CGGTCGCAGATAGATATTGCTTATT 59.192 40.000 0.00 0.00 40.67 1.40
1962 2990 2.263077 CCGGTCGCAGATAGATATTGC 58.737 52.381 0.00 0.00 40.67 3.56
1990 3018 4.884668 TCATCATTATTACCTCCCCGTC 57.115 45.455 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.