Multiple sequence alignment - TraesCS6D01G158900

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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 TraesCS6D01G158900 chr6D 100.000 2568 0 0 1 2568 135463945 135461378 0.000000e+00 4743.0
1 TraesCS6D01G158900 chr3B 98.645 2214 28 2 357 2568 101912029 101914242 0.000000e+00 3921.0
2 TraesCS6D01G158900 chr3B 98.101 2212 40 2 357 2566 201527878 201530089 0.000000e+00 3851.0
3 TraesCS6D01G158900 chr1A 98.329 2214 35 2 357 2568 554513102 554515315 0.000000e+00 3882.0
4 TraesCS6D01G158900 chr5D 98.105 2216 38 3 357 2568 503219072 503221287 0.000000e+00 3856.0
5 TraesCS6D01G158900 chr5D 97.651 2214 50 2 357 2568 6189794 6192007 0.000000e+00 3799.0
6 TraesCS6D01G158900 chr5D 93.538 325 11 6 1 317 499997324 499997002 2.310000e-130 475.0
7 TraesCS6D01G158900 chr5D 91.331 323 22 4 1 317 20729758 20730080 1.090000e-118 436.0
8 TraesCS6D01G158900 chrUn 97.967 2214 43 2 357 2568 216517749 216515536 0.000000e+00 3838.0
9 TraesCS6D01G158900 chr3A 97.877 2214 42 5 357 2568 672909154 672906944 0.000000e+00 3823.0
10 TraesCS6D01G158900 chr3A 97.787 2214 44 5 357 2568 594898769 594896559 0.000000e+00 3812.0
11 TraesCS6D01G158900 chr1D 97.832 2214 44 4 357 2568 254397256 254395045 0.000000e+00 3819.0
12 TraesCS6D01G158900 chr1D 92.284 324 18 5 1 317 409468804 409469127 1.080000e-123 453.0
13 TraesCS6D01G158900 chr2D 93.808 323 14 4 1 317 138524637 138524315 4.970000e-132 481.0
14 TraesCS6D01G158900 chr2D 91.331 323 22 4 1 317 13469994 13470316 1.090000e-118 436.0
15 TraesCS6D01G158900 chr2D 91.022 323 23 4 1 317 245982018 245981696 5.080000e-117 431.0
16 TraesCS6D01G158900 chr7D 92.879 323 17 4 1 317 625716655 625716977 5.000000e-127 464.0
17 TraesCS6D01G158900 chr4D 92.879 323 17 4 1 317 478169317 478169639 5.000000e-127 464.0
18 TraesCS6D01G158900 chr3D 91.250 320 22 4 4 317 548891407 548891088 5.080000e-117 431.0
19 TraesCS6D01G158900 chr6A 90.938 320 23 4 4 317 207737686 207737367 2.360000e-115 425.0
20 TraesCS6D01G158900 chr5A 89.062 320 29 4 4 317 441713807 441713488 2.400000e-105 392.0
21 TraesCS6D01G158900 chr4A 85.714 322 40 4 4 319 439373732 439374053 4.090000e-88 335.0
22 TraesCS6D01G158900 chr2A 100.000 29 0 0 289 317 716866125 716866153 1.000000e-03 54.7


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 TraesCS6D01G158900 chr6D 135461378 135463945 2567 True 4743 4743 100.000 1 2568 1 chr6D.!!$R1 2567
1 TraesCS6D01G158900 chr3B 101912029 101914242 2213 False 3921 3921 98.645 357 2568 1 chr3B.!!$F1 2211
2 TraesCS6D01G158900 chr3B 201527878 201530089 2211 False 3851 3851 98.101 357 2566 1 chr3B.!!$F2 2209
3 TraesCS6D01G158900 chr1A 554513102 554515315 2213 False 3882 3882 98.329 357 2568 1 chr1A.!!$F1 2211
4 TraesCS6D01G158900 chr5D 503219072 503221287 2215 False 3856 3856 98.105 357 2568 1 chr5D.!!$F3 2211
5 TraesCS6D01G158900 chr5D 6189794 6192007 2213 False 3799 3799 97.651 357 2568 1 chr5D.!!$F1 2211
6 TraesCS6D01G158900 chrUn 216515536 216517749 2213 True 3838 3838 97.967 357 2568 1 chrUn.!!$R1 2211
7 TraesCS6D01G158900 chr3A 672906944 672909154 2210 True 3823 3823 97.877 357 2568 1 chr3A.!!$R2 2211
8 TraesCS6D01G158900 chr3A 594896559 594898769 2210 True 3812 3812 97.787 357 2568 1 chr3A.!!$R1 2211
9 TraesCS6D01G158900 chr1D 254395045 254397256 2211 True 3819 3819 97.832 357 2568 1 chr1D.!!$R1 2211

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
264 265 0.034059 CCTTGACAAGGCTGACGTCT 59.966 55.0 21.1 0.0 42.78 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2231 0.521735 GAGGTCCGTTGGCATTTCAC 59.478 55.0 0.0 0.0 0.0 3.18 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
26 27 4.170062 CAGCATGTTCGGCCGCAG 62.170 66.667 23.51 9.04 0.00 5.18
27 28 4.393155 AGCATGTTCGGCCGCAGA 62.393 61.111 23.51 9.34 0.00 4.26
28 29 3.430862 GCATGTTCGGCCGCAGAA 61.431 61.111 23.51 7.04 0.00 3.02
29 30 2.764314 GCATGTTCGGCCGCAGAAT 61.764 57.895 23.51 8.52 0.00 2.40
30 31 1.802636 CATGTTCGGCCGCAGAATT 59.197 52.632 23.51 0.00 0.00 2.17
31 32 1.013596 CATGTTCGGCCGCAGAATTA 58.986 50.000 23.51 0.00 0.00 1.40
32 33 1.014352 ATGTTCGGCCGCAGAATTAC 58.986 50.000 23.51 9.64 0.00 1.89
33 34 0.036765 TGTTCGGCCGCAGAATTACT 60.037 50.000 23.51 0.00 0.00 2.24
34 35 1.084289 GTTCGGCCGCAGAATTACTT 58.916 50.000 23.51 0.00 0.00 2.24
35 36 2.273557 GTTCGGCCGCAGAATTACTTA 58.726 47.619 23.51 0.00 0.00 2.24
36 37 1.930567 TCGGCCGCAGAATTACTTAC 58.069 50.000 23.51 0.00 0.00 2.34
37 38 0.575390 CGGCCGCAGAATTACTTACG 59.425 55.000 14.67 0.00 0.00 3.18
38 39 1.648504 GGCCGCAGAATTACTTACGT 58.351 50.000 0.00 0.00 0.00 3.57
39 40 1.326548 GGCCGCAGAATTACTTACGTG 59.673 52.381 0.00 0.00 0.00 4.49
40 41 1.326548 GCCGCAGAATTACTTACGTGG 59.673 52.381 0.00 0.00 0.00 4.94
41 42 1.931172 CCGCAGAATTACTTACGTGGG 59.069 52.381 0.00 0.00 0.00 4.61
42 43 2.613691 CGCAGAATTACTTACGTGGGT 58.386 47.619 0.00 0.00 0.00 4.51
43 44 3.429272 CCGCAGAATTACTTACGTGGGTA 60.429 47.826 0.00 0.00 0.00 3.69
44 45 4.365723 CGCAGAATTACTTACGTGGGTAT 58.634 43.478 0.00 0.00 0.00 2.73
45 46 4.443394 CGCAGAATTACTTACGTGGGTATC 59.557 45.833 0.00 0.00 0.00 2.24
46 47 5.598769 GCAGAATTACTTACGTGGGTATCT 58.401 41.667 0.00 0.00 0.00 1.98
47 48 5.462398 GCAGAATTACTTACGTGGGTATCTG 59.538 44.000 18.48 18.48 32.58 2.90
48 49 5.983720 CAGAATTACTTACGTGGGTATCTGG 59.016 44.000 16.74 6.79 29.00 3.86
49 50 5.895534 AGAATTACTTACGTGGGTATCTGGA 59.104 40.000 0.00 0.00 0.00 3.86
50 51 4.989279 TTACTTACGTGGGTATCTGGAC 57.011 45.455 0.00 0.00 0.00 4.02
51 52 1.747355 ACTTACGTGGGTATCTGGACG 59.253 52.381 0.00 0.00 37.82 4.79
52 53 2.019249 CTTACGTGGGTATCTGGACGA 58.981 52.381 0.00 0.00 35.77 4.20
53 54 2.353357 TACGTGGGTATCTGGACGAT 57.647 50.000 0.00 0.00 35.77 3.73
54 55 1.481871 ACGTGGGTATCTGGACGATT 58.518 50.000 0.00 0.00 35.77 3.34
55 56 1.136305 ACGTGGGTATCTGGACGATTG 59.864 52.381 0.00 0.00 35.77 2.67
56 57 1.136305 CGTGGGTATCTGGACGATTGT 59.864 52.381 0.00 0.00 33.64 2.71
57 58 2.359848 CGTGGGTATCTGGACGATTGTA 59.640 50.000 0.00 0.00 33.64 2.41
58 59 3.550233 CGTGGGTATCTGGACGATTGTAG 60.550 52.174 0.00 0.00 33.64 2.74
59 60 3.383825 GTGGGTATCTGGACGATTGTAGT 59.616 47.826 0.00 0.00 33.48 2.73
60 61 4.028131 TGGGTATCTGGACGATTGTAGTT 58.972 43.478 0.00 0.00 33.48 2.24
61 62 5.068198 GTGGGTATCTGGACGATTGTAGTTA 59.932 44.000 0.00 0.00 33.48 2.24
62 63 5.301045 TGGGTATCTGGACGATTGTAGTTAG 59.699 44.000 0.00 0.00 33.48 2.34
63 64 5.533903 GGGTATCTGGACGATTGTAGTTAGA 59.466 44.000 0.00 0.00 33.48 2.10
64 65 6.437094 GGTATCTGGACGATTGTAGTTAGAC 58.563 44.000 0.00 0.00 33.48 2.59
65 66 4.978083 TCTGGACGATTGTAGTTAGACC 57.022 45.455 0.00 0.00 0.00 3.85
66 67 3.698040 TCTGGACGATTGTAGTTAGACCC 59.302 47.826 0.00 0.00 0.00 4.46
67 68 2.424601 TGGACGATTGTAGTTAGACCCG 59.575 50.000 0.00 0.00 0.00 5.28
68 69 2.457970 GACGATTGTAGTTAGACCCGC 58.542 52.381 0.00 0.00 0.00 6.13
69 70 1.820519 ACGATTGTAGTTAGACCCGCA 59.179 47.619 0.00 0.00 0.00 5.69
70 71 2.429610 ACGATTGTAGTTAGACCCGCAT 59.570 45.455 0.00 0.00 0.00 4.73
71 72 3.050619 CGATTGTAGTTAGACCCGCATC 58.949 50.000 0.00 0.00 0.00 3.91
72 73 2.973694 TTGTAGTTAGACCCGCATCC 57.026 50.000 0.00 0.00 0.00 3.51
73 74 2.154567 TGTAGTTAGACCCGCATCCT 57.845 50.000 0.00 0.00 0.00 3.24
74 75 2.029623 TGTAGTTAGACCCGCATCCTC 58.970 52.381 0.00 0.00 0.00 3.71
75 76 2.029623 GTAGTTAGACCCGCATCCTCA 58.970 52.381 0.00 0.00 0.00 3.86
76 77 1.115467 AGTTAGACCCGCATCCTCAG 58.885 55.000 0.00 0.00 0.00 3.35
77 78 0.824759 GTTAGACCCGCATCCTCAGT 59.175 55.000 0.00 0.00 0.00 3.41
78 79 0.824109 TTAGACCCGCATCCTCAGTG 59.176 55.000 0.00 0.00 0.00 3.66
79 80 1.043116 TAGACCCGCATCCTCAGTGG 61.043 60.000 0.00 0.00 36.41 4.00
80 81 2.607750 ACCCGCATCCTCAGTGGT 60.608 61.111 0.00 0.00 34.86 4.16
81 82 2.124983 CCCGCATCCTCAGTGGTG 60.125 66.667 0.00 0.00 34.86 4.17
82 83 2.665000 CCGCATCCTCAGTGGTGT 59.335 61.111 0.00 0.00 37.07 4.16
83 84 1.448540 CCGCATCCTCAGTGGTGTC 60.449 63.158 0.00 0.00 37.07 3.67
84 85 1.448540 CGCATCCTCAGTGGTGTCC 60.449 63.158 0.00 0.00 37.07 4.02
85 86 1.448540 GCATCCTCAGTGGTGTCCG 60.449 63.158 0.00 0.00 37.07 4.79
86 87 1.219124 CATCCTCAGTGGTGTCCGG 59.781 63.158 0.00 0.00 37.07 5.14
87 88 1.078528 ATCCTCAGTGGTGTCCGGA 59.921 57.895 0.00 0.00 37.07 5.14
88 89 1.258445 ATCCTCAGTGGTGTCCGGAC 61.258 60.000 28.17 28.17 37.07 4.79
89 90 2.207229 CCTCAGTGGTGTCCGGACA 61.207 63.158 33.23 33.23 39.32 4.02
100 101 2.679450 TGTCCGGACACTTTATTCGTG 58.321 47.619 33.23 0.00 36.21 4.35
101 102 2.296752 TGTCCGGACACTTTATTCGTGA 59.703 45.455 33.23 5.69 36.21 4.35
102 103 3.056393 TGTCCGGACACTTTATTCGTGAT 60.056 43.478 33.23 0.00 36.21 3.06
103 104 3.550678 GTCCGGACACTTTATTCGTGATC 59.449 47.826 29.75 0.00 36.29 2.92
104 105 2.864343 CCGGACACTTTATTCGTGATCC 59.136 50.000 0.00 0.00 36.29 3.36
105 106 2.534349 CGGACACTTTATTCGTGATCCG 59.466 50.000 14.62 14.62 42.95 4.18
106 107 3.732774 CGGACACTTTATTCGTGATCCGA 60.733 47.826 19.55 2.65 46.57 4.55
116 117 2.888594 TCGTGATCCGAAGAACAATCC 58.111 47.619 4.13 0.00 44.03 3.01
117 118 2.232696 TCGTGATCCGAAGAACAATCCA 59.767 45.455 4.13 0.00 44.03 3.41
118 119 3.118775 TCGTGATCCGAAGAACAATCCAT 60.119 43.478 4.13 0.00 44.03 3.41
119 120 4.098807 TCGTGATCCGAAGAACAATCCATA 59.901 41.667 4.13 0.00 44.03 2.74
120 121 4.209288 CGTGATCCGAAGAACAATCCATAC 59.791 45.833 0.00 0.00 39.56 2.39
121 122 5.116180 GTGATCCGAAGAACAATCCATACA 58.884 41.667 0.00 0.00 0.00 2.29
122 123 5.760253 GTGATCCGAAGAACAATCCATACAT 59.240 40.000 0.00 0.00 0.00 2.29
123 124 5.991606 TGATCCGAAGAACAATCCATACATC 59.008 40.000 0.00 0.00 0.00 3.06
124 125 5.614324 TCCGAAGAACAATCCATACATCT 57.386 39.130 0.00 0.00 0.00 2.90
125 126 5.601662 TCCGAAGAACAATCCATACATCTC 58.398 41.667 0.00 0.00 0.00 2.75
126 127 5.363868 TCCGAAGAACAATCCATACATCTCT 59.636 40.000 0.00 0.00 0.00 3.10
127 128 6.051717 CCGAAGAACAATCCATACATCTCTT 58.948 40.000 0.00 0.00 0.00 2.85
128 129 6.201806 CCGAAGAACAATCCATACATCTCTTC 59.798 42.308 0.00 0.00 36.03 2.87
129 130 7.171447 GAAGAACAATCCATACATCTCTTCG 57.829 40.000 0.00 0.00 31.27 3.79
130 131 6.471233 AGAACAATCCATACATCTCTTCGA 57.529 37.500 0.00 0.00 0.00 3.71
131 132 6.511416 AGAACAATCCATACATCTCTTCGAG 58.489 40.000 0.00 0.00 0.00 4.04
132 133 4.626042 ACAATCCATACATCTCTTCGAGC 58.374 43.478 0.00 0.00 0.00 5.03
133 134 3.567576 ATCCATACATCTCTTCGAGCG 57.432 47.619 0.00 0.00 0.00 5.03
134 135 2.298610 TCCATACATCTCTTCGAGCGT 58.701 47.619 0.00 0.00 0.00 5.07
135 136 2.290916 TCCATACATCTCTTCGAGCGTC 59.709 50.000 0.00 0.00 0.00 5.19
136 137 2.033424 CCATACATCTCTTCGAGCGTCA 59.967 50.000 0.00 0.00 0.00 4.35
137 138 2.826979 TACATCTCTTCGAGCGTCAC 57.173 50.000 0.00 0.00 0.00 3.67
138 139 0.179187 ACATCTCTTCGAGCGTCACG 60.179 55.000 0.00 0.00 0.00 4.35
150 151 2.712077 CGTCACGCCAAAGAATTGC 58.288 52.632 0.00 0.00 35.10 3.56
151 152 0.238289 CGTCACGCCAAAGAATTGCT 59.762 50.000 0.00 0.00 35.10 3.91
152 153 1.689959 GTCACGCCAAAGAATTGCTG 58.310 50.000 0.00 0.00 35.10 4.41
153 154 1.266718 GTCACGCCAAAGAATTGCTGA 59.733 47.619 0.00 0.00 35.10 4.26
154 155 1.952990 TCACGCCAAAGAATTGCTGAA 59.047 42.857 0.00 0.00 35.10 3.02
155 156 2.557924 TCACGCCAAAGAATTGCTGAAT 59.442 40.909 0.00 0.00 35.10 2.57
156 157 3.755905 TCACGCCAAAGAATTGCTGAATA 59.244 39.130 0.00 0.00 35.10 1.75
157 158 4.100529 CACGCCAAAGAATTGCTGAATAG 58.899 43.478 0.00 0.00 35.10 1.73
158 159 3.758554 ACGCCAAAGAATTGCTGAATAGT 59.241 39.130 0.00 0.00 35.10 2.12
159 160 4.218417 ACGCCAAAGAATTGCTGAATAGTT 59.782 37.500 0.00 0.00 35.10 2.24
160 161 4.795278 CGCCAAAGAATTGCTGAATAGTTC 59.205 41.667 0.00 0.00 35.10 3.01
161 162 4.795278 GCCAAAGAATTGCTGAATAGTTCG 59.205 41.667 0.00 0.00 35.10 3.95
162 163 4.795278 CCAAAGAATTGCTGAATAGTTCGC 59.205 41.667 0.00 0.00 35.10 4.70
163 164 3.933155 AGAATTGCTGAATAGTTCGCG 57.067 42.857 0.00 0.00 33.84 5.87
164 165 2.609459 AGAATTGCTGAATAGTTCGCGG 59.391 45.455 6.13 0.00 33.84 6.46
165 166 2.024176 ATTGCTGAATAGTTCGCGGT 57.976 45.000 6.13 0.00 33.84 5.68
166 167 1.355971 TTGCTGAATAGTTCGCGGTC 58.644 50.000 6.13 0.00 33.84 4.79
167 168 0.459585 TGCTGAATAGTTCGCGGTCC 60.460 55.000 6.13 0.00 33.84 4.46
168 169 0.179108 GCTGAATAGTTCGCGGTCCT 60.179 55.000 6.13 1.94 0.00 3.85
169 170 1.739371 GCTGAATAGTTCGCGGTCCTT 60.739 52.381 6.13 0.00 0.00 3.36
170 171 2.194271 CTGAATAGTTCGCGGTCCTTC 58.806 52.381 6.13 4.41 0.00 3.46
171 172 1.822990 TGAATAGTTCGCGGTCCTTCT 59.177 47.619 6.13 0.00 0.00 2.85
172 173 2.194271 GAATAGTTCGCGGTCCTTCTG 58.806 52.381 6.13 0.00 0.00 3.02
173 174 0.460311 ATAGTTCGCGGTCCTTCTGG 59.540 55.000 6.13 0.00 0.00 3.86
174 175 1.601419 TAGTTCGCGGTCCTTCTGGG 61.601 60.000 6.13 0.00 36.81 4.45
175 176 2.920912 TTCGCGGTCCTTCTGGGT 60.921 61.111 6.13 0.00 36.82 4.51
176 177 2.513259 TTCGCGGTCCTTCTGGGTT 61.513 57.895 6.13 0.00 36.82 4.11
177 178 2.725203 TTCGCGGTCCTTCTGGGTTG 62.725 60.000 6.13 0.00 36.82 3.77
178 179 2.747686 GCGGTCCTTCTGGGTTGA 59.252 61.111 0.00 0.00 36.25 3.18
179 180 1.072505 GCGGTCCTTCTGGGTTGAA 59.927 57.895 0.00 0.00 36.25 2.69
180 181 1.235281 GCGGTCCTTCTGGGTTGAAC 61.235 60.000 0.00 0.00 36.25 3.18
181 182 0.396811 CGGTCCTTCTGGGTTGAACT 59.603 55.000 0.00 0.00 36.25 3.01
182 183 1.608283 CGGTCCTTCTGGGTTGAACTC 60.608 57.143 0.00 0.00 36.25 3.01
183 184 1.271434 GGTCCTTCTGGGTTGAACTCC 60.271 57.143 0.00 0.00 36.25 3.85
184 185 1.064825 TCCTTCTGGGTTGAACTCCC 58.935 55.000 0.00 0.00 44.81 4.30
190 191 3.745723 GGGTTGAACTCCCACATGT 57.254 52.632 0.00 0.00 44.05 3.21
191 192 1.247567 GGGTTGAACTCCCACATGTG 58.752 55.000 19.31 19.31 44.05 3.21
202 203 3.425578 CACATGTGGAGAGGTCGAC 57.574 57.895 18.51 7.13 32.23 4.20
203 204 0.456824 CACATGTGGAGAGGTCGACG 60.457 60.000 18.51 0.00 34.25 5.12
204 205 0.894184 ACATGTGGAGAGGTCGACGT 60.894 55.000 11.12 11.12 34.25 4.34
205 206 0.243907 CATGTGGAGAGGTCGACGTT 59.756 55.000 12.67 1.06 34.25 3.99
206 207 0.243907 ATGTGGAGAGGTCGACGTTG 59.756 55.000 12.67 0.00 34.25 4.10
207 208 1.080705 GTGGAGAGGTCGACGTTGG 60.081 63.158 12.67 0.00 0.00 3.77
208 209 2.126031 GGAGAGGTCGACGTTGGC 60.126 66.667 12.67 0.00 0.00 4.52
209 210 2.649034 GAGAGGTCGACGTTGGCA 59.351 61.111 12.67 0.00 0.00 4.92
210 211 1.215647 GAGAGGTCGACGTTGGCAT 59.784 57.895 12.67 0.68 0.00 4.40
211 212 1.078759 GAGAGGTCGACGTTGGCATG 61.079 60.000 12.67 0.00 0.00 4.06
212 213 2.047274 AGGTCGACGTTGGCATGG 60.047 61.111 10.10 0.00 0.00 3.66
213 214 3.799755 GGTCGACGTTGGCATGGC 61.800 66.667 13.29 13.29 0.00 4.40
214 215 3.047280 GTCGACGTTGGCATGGCA 61.047 61.111 19.43 19.43 0.00 4.92
215 216 3.047280 TCGACGTTGGCATGGCAC 61.047 61.111 23.26 15.57 0.00 5.01
216 217 4.444024 CGACGTTGGCATGGCACG 62.444 66.667 28.86 28.86 39.86 5.34
217 218 3.047280 GACGTTGGCATGGCACGA 61.047 61.111 33.59 17.64 37.37 4.35
218 219 3.308878 GACGTTGGCATGGCACGAC 62.309 63.158 33.59 27.49 37.37 4.34
219 220 4.101790 CGTTGGCATGGCACGACC 62.102 66.667 27.67 14.75 35.93 4.79
220 221 3.747976 GTTGGCATGGCACGACCC 61.748 66.667 23.26 3.97 37.83 4.46
225 226 4.429212 CATGGCACGACCCGACGA 62.429 66.667 0.00 0.00 37.83 4.20
226 227 3.687102 ATGGCACGACCCGACGAA 61.687 61.111 0.00 0.00 37.83 3.85
227 228 3.927163 ATGGCACGACCCGACGAAC 62.927 63.158 0.00 0.00 37.83 3.95
228 229 4.353437 GGCACGACCCGACGAACT 62.353 66.667 0.00 0.00 37.03 3.01
229 230 2.562912 GCACGACCCGACGAACTA 59.437 61.111 0.00 0.00 37.03 2.24
230 231 1.513586 GCACGACCCGACGAACTAG 60.514 63.158 0.00 0.00 37.03 2.57
231 232 1.513586 CACGACCCGACGAACTAGC 60.514 63.158 0.00 0.00 37.03 3.42
232 233 1.968017 ACGACCCGACGAACTAGCA 60.968 57.895 0.00 0.00 37.03 3.49
233 234 1.310933 ACGACCCGACGAACTAGCAT 61.311 55.000 0.00 0.00 37.03 3.79
234 235 0.866061 CGACCCGACGAACTAGCATG 60.866 60.000 0.00 0.00 35.09 4.06
235 236 0.454600 GACCCGACGAACTAGCATGA 59.545 55.000 0.00 0.00 0.00 3.07
236 237 0.172803 ACCCGACGAACTAGCATGAC 59.827 55.000 0.00 0.00 0.00 3.06
237 238 0.456221 CCCGACGAACTAGCATGACT 59.544 55.000 0.00 0.00 0.00 3.41
238 239 1.135083 CCCGACGAACTAGCATGACTT 60.135 52.381 0.00 0.00 0.00 3.01
239 240 1.920574 CCGACGAACTAGCATGACTTG 59.079 52.381 0.00 0.00 0.00 3.16
251 252 2.602878 CATGACTTGCATTGCCTTGAC 58.397 47.619 6.12 0.00 34.15 3.18
252 253 1.689984 TGACTTGCATTGCCTTGACA 58.310 45.000 6.12 0.52 0.00 3.58
253 254 2.030371 TGACTTGCATTGCCTTGACAA 58.970 42.857 6.12 0.00 0.00 3.18
254 255 2.034939 TGACTTGCATTGCCTTGACAAG 59.965 45.455 8.31 8.31 42.63 3.16
255 256 6.357404 ATGACTTGCATTGCCTTGACAAGG 62.357 45.833 27.16 27.16 42.54 3.61
262 263 4.779475 CCTTGACAAGGCTGACGT 57.221 55.556 21.10 0.00 42.78 4.34
263 264 2.533318 CCTTGACAAGGCTGACGTC 58.467 57.895 21.10 9.11 42.78 4.34
264 265 0.034059 CCTTGACAAGGCTGACGTCT 59.966 55.000 21.10 0.00 42.78 4.18
265 266 1.423395 CTTGACAAGGCTGACGTCTC 58.577 55.000 17.92 8.42 0.00 3.36
266 267 1.000283 CTTGACAAGGCTGACGTCTCT 60.000 52.381 17.92 8.82 0.00 3.10
267 268 0.598562 TGACAAGGCTGACGTCTCTC 59.401 55.000 17.92 5.84 0.00 3.20
268 269 0.885196 GACAAGGCTGACGTCTCTCT 59.115 55.000 17.92 8.10 0.00 3.10
269 270 1.271102 GACAAGGCTGACGTCTCTCTT 59.729 52.381 17.92 13.43 0.00 2.85
270 271 1.000283 ACAAGGCTGACGTCTCTCTTG 60.000 52.381 27.17 27.17 37.98 3.02
271 272 1.270826 CAAGGCTGACGTCTCTCTTGA 59.729 52.381 25.99 4.84 35.08 3.02
272 273 1.173043 AGGCTGACGTCTCTCTTGAG 58.827 55.000 17.92 4.75 41.51 3.02
273 274 0.172352 GGCTGACGTCTCTCTTGAGG 59.828 60.000 17.92 0.00 40.58 3.86
274 275 1.169577 GCTGACGTCTCTCTTGAGGA 58.830 55.000 17.92 0.00 40.58 3.71
275 276 1.132262 GCTGACGTCTCTCTTGAGGAG 59.868 57.143 17.92 2.44 43.12 3.69
284 285 3.636153 TCTCTTGAGGAGATGTCTCGA 57.364 47.619 4.09 0.00 45.20 4.04
285 286 3.540617 TCTCTTGAGGAGATGTCTCGAG 58.459 50.000 5.93 5.93 45.20 4.04
286 287 3.198853 TCTCTTGAGGAGATGTCTCGAGA 59.801 47.826 12.08 12.08 45.20 4.04
287 288 3.944650 CTCTTGAGGAGATGTCTCGAGAA 59.055 47.826 18.55 8.22 45.76 2.87
288 289 3.944650 TCTTGAGGAGATGTCTCGAGAAG 59.055 47.826 18.55 6.90 44.41 2.85
289 290 3.636153 TGAGGAGATGTCTCGAGAAGA 57.364 47.619 18.55 7.33 43.76 2.87
290 291 3.956744 TGAGGAGATGTCTCGAGAAGAA 58.043 45.455 18.55 6.44 43.76 2.52
291 292 4.336280 TGAGGAGATGTCTCGAGAAGAAA 58.664 43.478 18.55 3.68 43.76 2.52
292 293 4.952957 TGAGGAGATGTCTCGAGAAGAAAT 59.047 41.667 18.55 8.71 43.76 2.17
293 294 5.163571 TGAGGAGATGTCTCGAGAAGAAATG 60.164 44.000 18.55 0.00 43.76 2.32
294 295 4.709397 AGGAGATGTCTCGAGAAGAAATGT 59.291 41.667 18.55 7.32 43.76 2.71
295 296 5.040635 GGAGATGTCTCGAGAAGAAATGTC 58.959 45.833 18.55 15.05 40.01 3.06
296 297 4.667262 AGATGTCTCGAGAAGAAATGTCG 58.333 43.478 18.55 0.00 45.56 4.35
297 298 3.217599 TGTCTCGAGAAGAAATGTCGG 57.782 47.619 18.55 0.00 44.41 4.79
298 299 1.921230 GTCTCGAGAAGAAATGTCGGC 59.079 52.381 18.55 0.00 44.41 5.54
299 300 1.544246 TCTCGAGAAGAAATGTCGGCA 59.456 47.619 14.01 0.00 44.41 5.69
300 301 1.656095 CTCGAGAAGAAATGTCGGCAC 59.344 52.381 6.58 0.00 44.41 5.01
314 315 1.800681 GGCACGTCATTAACTGGCC 59.199 57.895 0.00 0.00 37.51 5.36
315 316 1.654023 GGCACGTCATTAACTGGCCC 61.654 60.000 0.00 0.00 38.25 5.80
316 317 1.654023 GCACGTCATTAACTGGCCCC 61.654 60.000 0.00 0.00 0.00 5.80
317 318 0.322098 CACGTCATTAACTGGCCCCA 60.322 55.000 0.00 0.00 0.00 4.96
318 319 0.623723 ACGTCATTAACTGGCCCCAT 59.376 50.000 0.00 0.00 0.00 4.00
319 320 1.308998 CGTCATTAACTGGCCCCATC 58.691 55.000 0.00 0.00 0.00 3.51
320 321 1.692411 GTCATTAACTGGCCCCATCC 58.308 55.000 0.00 0.00 0.00 3.51
321 322 0.182537 TCATTAACTGGCCCCATCCG 59.817 55.000 0.00 0.00 0.00 4.18
322 323 0.182537 CATTAACTGGCCCCATCCGA 59.817 55.000 0.00 0.00 0.00 4.55
323 324 1.149101 ATTAACTGGCCCCATCCGAT 58.851 50.000 0.00 0.00 0.00 4.18
324 325 0.472471 TTAACTGGCCCCATCCGATC 59.528 55.000 0.00 0.00 0.00 3.69
325 326 0.399949 TAACTGGCCCCATCCGATCT 60.400 55.000 0.00 0.00 0.00 2.75
326 327 1.281925 AACTGGCCCCATCCGATCTT 61.282 55.000 0.00 0.00 0.00 2.40
327 328 1.228063 CTGGCCCCATCCGATCTTG 60.228 63.158 0.00 0.00 0.00 3.02
328 329 1.987807 CTGGCCCCATCCGATCTTGT 61.988 60.000 0.00 0.00 0.00 3.16
329 330 0.692756 TGGCCCCATCCGATCTTGTA 60.693 55.000 0.00 0.00 0.00 2.41
330 331 0.035458 GGCCCCATCCGATCTTGTAG 59.965 60.000 0.00 0.00 0.00 2.74
331 332 0.759346 GCCCCATCCGATCTTGTAGT 59.241 55.000 0.00 0.00 0.00 2.73
332 333 1.541233 GCCCCATCCGATCTTGTAGTG 60.541 57.143 0.00 0.00 0.00 2.74
333 334 2.039418 CCCCATCCGATCTTGTAGTGA 58.961 52.381 0.00 0.00 0.00 3.41
334 335 2.036475 CCCCATCCGATCTTGTAGTGAG 59.964 54.545 0.00 0.00 0.00 3.51
335 336 2.695666 CCCATCCGATCTTGTAGTGAGT 59.304 50.000 0.00 0.00 0.00 3.41
336 337 3.889538 CCCATCCGATCTTGTAGTGAGTA 59.110 47.826 0.00 0.00 0.00 2.59
337 338 4.524714 CCCATCCGATCTTGTAGTGAGTAT 59.475 45.833 0.00 0.00 0.00 2.12
338 339 5.465051 CCATCCGATCTTGTAGTGAGTATG 58.535 45.833 0.00 0.00 0.00 2.39
339 340 4.569761 TCCGATCTTGTAGTGAGTATGC 57.430 45.455 0.00 0.00 0.00 3.14
340 341 3.951680 TCCGATCTTGTAGTGAGTATGCA 59.048 43.478 0.00 0.00 0.00 3.96
341 342 4.401202 TCCGATCTTGTAGTGAGTATGCAA 59.599 41.667 0.00 0.00 0.00 4.08
342 343 5.105513 TCCGATCTTGTAGTGAGTATGCAAA 60.106 40.000 0.00 0.00 0.00 3.68
343 344 5.005779 CCGATCTTGTAGTGAGTATGCAAAC 59.994 44.000 0.00 0.00 0.00 2.93
344 345 5.807520 CGATCTTGTAGTGAGTATGCAAACT 59.192 40.000 0.00 0.00 0.00 2.66
345 346 6.972901 CGATCTTGTAGTGAGTATGCAAACTA 59.027 38.462 0.00 0.00 0.00 2.24
346 347 7.488150 CGATCTTGTAGTGAGTATGCAAACTAA 59.512 37.037 0.00 0.00 0.00 2.24
347 348 9.151471 GATCTTGTAGTGAGTATGCAAACTAAA 57.849 33.333 0.00 0.00 0.00 1.85
348 349 8.896320 TCTTGTAGTGAGTATGCAAACTAAAA 57.104 30.769 0.00 0.00 0.00 1.52
349 350 9.502091 TCTTGTAGTGAGTATGCAAACTAAAAT 57.498 29.630 0.00 0.00 0.00 1.82
352 353 9.891828 TGTAGTGAGTATGCAAACTAAAATTTG 57.108 29.630 0.00 0.00 41.62 2.32
355 356 9.630098 AGTGAGTATGCAAACTAAAATTTGATG 57.370 29.630 0.00 0.00 41.28 3.07
390 391 6.699575 ATTGATTCTTCCCCAATAAACGAG 57.300 37.500 0.00 0.00 0.00 4.18
462 463 2.246067 TCCCTCCTATGCTCTGAGTTCT 59.754 50.000 6.53 0.00 0.00 3.01
932 933 5.452078 TTAGCAAAGAATGACCTTGGTTG 57.548 39.130 0.00 0.00 0.00 3.77
975 976 7.394816 CGGGATCCATTTACTTATGATACCTT 58.605 38.462 15.23 0.00 0.00 3.50
1138 1140 2.438800 TGGAAACCCTTTTCGTTCCA 57.561 45.000 0.00 0.00 41.97 3.53
1143 1145 4.338964 GGAAACCCTTTTCGTTCCACTTAA 59.661 41.667 0.00 0.00 41.97 1.85
1343 1346 4.448210 TGTTCCATACTAAAGGATTCGGC 58.552 43.478 0.00 0.00 33.10 5.54
1361 1364 1.207329 GGCTCCATAACCACGAGTTCT 59.793 52.381 0.00 0.00 40.05 3.01
1841 1846 6.544650 CCTATTAGAGGTAGAAGGTGCTCTA 58.455 44.000 0.00 0.00 40.98 2.43
2002 2007 8.394121 GCTATATGAAAAGAAGTGGAGTTTGAG 58.606 37.037 0.00 0.00 0.00 3.02
2054 2059 6.128172 ACTGCTAGAGGAACGAATTTTCAATG 60.128 38.462 0.00 0.00 0.00 2.82
2120 2125 4.751767 TTTGATTGCAGGGTTTTGTTCT 57.248 36.364 0.00 0.00 0.00 3.01
2247 2252 1.626321 TGAAATGCCAACGGACCTCTA 59.374 47.619 0.00 0.00 0.00 2.43
2509 2516 5.990668 ACTAGTCTTCACTCTTGTGGTTTT 58.009 37.500 0.00 0.00 43.94 2.43
2537 2544 7.501225 TCTTCCTCGGTTTCTGTTTTCTTATTT 59.499 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.000274 GGCCGAACATGCTGTCTTTTT 60.000 47.619 0.00 0.00 0.00 1.94
5 6 2.034879 CGGCCGAACATGCTGTCTT 61.035 57.895 24.07 0.00 0.00 3.01
6 7 2.434884 CGGCCGAACATGCTGTCT 60.435 61.111 24.07 0.00 0.00 3.41
7 8 4.166011 GCGGCCGAACATGCTGTC 62.166 66.667 33.48 2.06 37.43 3.51
9 10 4.170062 CTGCGGCCGAACATGCTG 62.170 66.667 33.48 10.13 38.16 4.41
10 11 3.899981 TTCTGCGGCCGAACATGCT 62.900 57.895 33.48 0.00 0.00 3.79
11 12 2.270297 AATTCTGCGGCCGAACATGC 62.270 55.000 33.48 10.77 0.00 4.06
12 13 1.013596 TAATTCTGCGGCCGAACATG 58.986 50.000 33.48 7.00 0.00 3.21
13 14 1.014352 GTAATTCTGCGGCCGAACAT 58.986 50.000 33.48 8.55 0.00 2.71
14 15 0.036765 AGTAATTCTGCGGCCGAACA 60.037 50.000 33.48 18.03 0.00 3.18
15 16 1.084289 AAGTAATTCTGCGGCCGAAC 58.916 50.000 33.48 13.46 0.00 3.95
16 17 2.273557 GTAAGTAATTCTGCGGCCGAA 58.726 47.619 33.48 20.72 0.00 4.30
17 18 1.799917 CGTAAGTAATTCTGCGGCCGA 60.800 52.381 33.48 13.59 0.00 5.54
18 19 0.575390 CGTAAGTAATTCTGCGGCCG 59.425 55.000 24.05 24.05 0.00 6.13
27 28 8.822484 ATCGTCCAGATACCCACGTAAGTAATT 61.822 40.741 0.00 0.00 44.26 1.40
28 29 7.417513 ATCGTCCAGATACCCACGTAAGTAAT 61.418 42.308 0.00 0.00 44.26 1.89
29 30 6.152103 ATCGTCCAGATACCCACGTAAGTAA 61.152 44.000 0.00 0.00 44.26 2.24
30 31 4.686944 ATCGTCCAGATACCCACGTAAGTA 60.687 45.833 0.00 0.00 44.26 2.24
31 32 3.938595 ATCGTCCAGATACCCACGTAAGT 60.939 47.826 0.00 0.00 46.30 2.24
32 33 2.621998 ATCGTCCAGATACCCACGTAAG 59.378 50.000 0.00 0.00 37.93 2.34
33 34 2.127271 TCGTCCAGATACCCACGTAA 57.873 50.000 0.00 0.00 33.89 3.18
34 35 2.353357 ATCGTCCAGATACCCACGTA 57.647 50.000 0.00 0.00 37.93 3.57
35 36 1.136305 CAATCGTCCAGATACCCACGT 59.864 52.381 0.00 0.00 38.98 4.49
36 37 1.136305 ACAATCGTCCAGATACCCACG 59.864 52.381 0.00 0.00 38.98 4.94
37 38 2.981859 ACAATCGTCCAGATACCCAC 57.018 50.000 0.00 0.00 38.98 4.61
38 39 3.638860 ACTACAATCGTCCAGATACCCA 58.361 45.455 0.00 0.00 38.98 4.51
39 40 4.667519 AACTACAATCGTCCAGATACCC 57.332 45.455 0.00 0.00 38.98 3.69
40 41 6.437094 GTCTAACTACAATCGTCCAGATACC 58.563 44.000 0.00 0.00 38.98 2.73
41 42 6.437094 GGTCTAACTACAATCGTCCAGATAC 58.563 44.000 0.00 0.00 38.98 2.24
42 43 5.533903 GGGTCTAACTACAATCGTCCAGATA 59.466 44.000 0.00 0.00 38.98 1.98
43 44 4.341520 GGGTCTAACTACAATCGTCCAGAT 59.658 45.833 0.00 0.00 42.43 2.90
44 45 3.698040 GGGTCTAACTACAATCGTCCAGA 59.302 47.826 0.00 0.00 0.00 3.86
45 46 3.488721 CGGGTCTAACTACAATCGTCCAG 60.489 52.174 0.00 0.00 0.00 3.86
46 47 2.424601 CGGGTCTAACTACAATCGTCCA 59.575 50.000 0.00 0.00 0.00 4.02
47 48 2.797439 GCGGGTCTAACTACAATCGTCC 60.797 54.545 0.00 0.00 0.00 4.79
48 49 2.159338 TGCGGGTCTAACTACAATCGTC 60.159 50.000 0.00 0.00 0.00 4.20
49 50 1.820519 TGCGGGTCTAACTACAATCGT 59.179 47.619 0.00 0.00 0.00 3.73
50 51 2.572191 TGCGGGTCTAACTACAATCG 57.428 50.000 0.00 0.00 0.00 3.34
51 52 3.069729 AGGATGCGGGTCTAACTACAATC 59.930 47.826 0.00 0.00 0.00 2.67
52 53 3.039011 AGGATGCGGGTCTAACTACAAT 58.961 45.455 0.00 0.00 0.00 2.71
53 54 2.429610 GAGGATGCGGGTCTAACTACAA 59.570 50.000 0.00 0.00 0.00 2.41
54 55 2.029623 GAGGATGCGGGTCTAACTACA 58.970 52.381 0.00 0.00 0.00 2.74
55 56 2.029623 TGAGGATGCGGGTCTAACTAC 58.970 52.381 0.00 0.00 0.00 2.73
56 57 2.307768 CTGAGGATGCGGGTCTAACTA 58.692 52.381 0.00 0.00 0.00 2.24
57 58 1.115467 CTGAGGATGCGGGTCTAACT 58.885 55.000 0.00 0.00 0.00 2.24
58 59 0.824759 ACTGAGGATGCGGGTCTAAC 59.175 55.000 0.00 0.00 0.00 2.34
59 60 0.824109 CACTGAGGATGCGGGTCTAA 59.176 55.000 0.00 0.00 0.00 2.10
60 61 1.043116 CCACTGAGGATGCGGGTCTA 61.043 60.000 0.00 0.00 41.22 2.59
61 62 2.362369 CCACTGAGGATGCGGGTCT 61.362 63.158 0.00 0.00 41.22 3.85
62 63 2.187946 CCACTGAGGATGCGGGTC 59.812 66.667 0.00 0.00 41.22 4.46
63 64 2.607750 ACCACTGAGGATGCGGGT 60.608 61.111 0.00 0.00 41.22 5.28
64 65 2.124983 CACCACTGAGGATGCGGG 60.125 66.667 0.00 0.00 41.22 6.13
65 66 1.448540 GACACCACTGAGGATGCGG 60.449 63.158 0.00 0.00 41.22 5.69
66 67 1.448540 GGACACCACTGAGGATGCG 60.449 63.158 0.00 0.00 41.22 4.73
67 68 1.448540 CGGACACCACTGAGGATGC 60.449 63.158 0.00 0.00 41.22 3.91
68 69 1.219124 CCGGACACCACTGAGGATG 59.781 63.158 0.00 0.00 41.22 3.51
69 70 1.078528 TCCGGACACCACTGAGGAT 59.921 57.895 0.00 0.00 41.22 3.24
70 71 1.906824 GTCCGGACACCACTGAGGA 60.907 63.158 29.75 0.00 41.22 3.71
71 72 2.207229 TGTCCGGACACCACTGAGG 61.207 63.158 33.23 0.00 45.67 3.86
72 73 3.455152 TGTCCGGACACCACTGAG 58.545 61.111 33.23 0.00 36.21 3.35
80 81 2.296752 TCACGAATAAAGTGTCCGGACA 59.703 45.455 33.23 33.23 40.28 4.02
81 82 2.950433 TCACGAATAAAGTGTCCGGAC 58.050 47.619 28.17 28.17 40.28 4.79
82 83 3.429822 GGATCACGAATAAAGTGTCCGGA 60.430 47.826 0.00 0.00 40.28 5.14
83 84 2.864343 GGATCACGAATAAAGTGTCCGG 59.136 50.000 0.00 0.00 40.28 5.14
97 98 2.616960 TGGATTGTTCTTCGGATCACG 58.383 47.619 0.00 0.00 46.11 4.35
98 99 5.116180 TGTATGGATTGTTCTTCGGATCAC 58.884 41.667 0.00 0.00 0.00 3.06
99 100 5.351948 TGTATGGATTGTTCTTCGGATCA 57.648 39.130 0.00 0.00 0.00 2.92
100 101 6.226787 AGATGTATGGATTGTTCTTCGGATC 58.773 40.000 0.00 0.00 0.00 3.36
101 102 6.042552 AGAGATGTATGGATTGTTCTTCGGAT 59.957 38.462 0.00 0.00 0.00 4.18
102 103 5.363868 AGAGATGTATGGATTGTTCTTCGGA 59.636 40.000 0.00 0.00 0.00 4.55
103 104 5.605534 AGAGATGTATGGATTGTTCTTCGG 58.394 41.667 0.00 0.00 0.00 4.30
104 105 7.171447 GAAGAGATGTATGGATTGTTCTTCG 57.829 40.000 0.00 0.00 32.74 3.79
105 106 6.980978 TCGAAGAGATGTATGGATTGTTCTTC 59.019 38.462 0.00 0.00 37.19 2.87
106 107 6.878317 TCGAAGAGATGTATGGATTGTTCTT 58.122 36.000 0.00 0.00 0.00 2.52
107 108 6.471233 TCGAAGAGATGTATGGATTGTTCT 57.529 37.500 0.00 0.00 0.00 3.01
132 133 0.238289 AGCAATTCTTTGGCGTGACG 59.762 50.000 0.00 0.00 33.22 4.35
133 134 1.266718 TCAGCAATTCTTTGGCGTGAC 59.733 47.619 0.00 0.00 33.22 3.67
134 135 1.603456 TCAGCAATTCTTTGGCGTGA 58.397 45.000 0.00 0.00 33.22 4.35
135 136 2.420628 TTCAGCAATTCTTTGGCGTG 57.579 45.000 0.00 0.00 33.22 5.34
136 137 3.758554 ACTATTCAGCAATTCTTTGGCGT 59.241 39.130 0.00 0.00 33.22 5.68
137 138 4.361451 ACTATTCAGCAATTCTTTGGCG 57.639 40.909 0.00 0.00 33.22 5.69
138 139 4.795278 CGAACTATTCAGCAATTCTTTGGC 59.205 41.667 0.00 0.00 33.22 4.52
139 140 4.795278 GCGAACTATTCAGCAATTCTTTGG 59.205 41.667 0.00 0.00 33.22 3.28
140 141 4.493350 CGCGAACTATTCAGCAATTCTTTG 59.507 41.667 0.00 0.00 35.85 2.77
141 142 4.437390 CCGCGAACTATTCAGCAATTCTTT 60.437 41.667 8.23 0.00 32.28 2.52
142 143 3.063997 CCGCGAACTATTCAGCAATTCTT 59.936 43.478 8.23 0.00 32.28 2.52
143 144 2.609459 CCGCGAACTATTCAGCAATTCT 59.391 45.455 8.23 0.00 32.28 2.40
144 145 2.351726 ACCGCGAACTATTCAGCAATTC 59.648 45.455 8.23 0.00 32.28 2.17
145 146 2.351726 GACCGCGAACTATTCAGCAATT 59.648 45.455 8.23 0.00 32.28 2.32
146 147 1.933853 GACCGCGAACTATTCAGCAAT 59.066 47.619 8.23 0.00 32.28 3.56
147 148 1.355971 GACCGCGAACTATTCAGCAA 58.644 50.000 8.23 0.00 32.28 3.91
148 149 0.459585 GGACCGCGAACTATTCAGCA 60.460 55.000 8.23 0.00 32.28 4.41
149 150 0.179108 AGGACCGCGAACTATTCAGC 60.179 55.000 8.23 0.00 0.00 4.26
150 151 2.159226 AGAAGGACCGCGAACTATTCAG 60.159 50.000 8.23 0.00 0.00 3.02
151 152 1.822990 AGAAGGACCGCGAACTATTCA 59.177 47.619 8.23 0.00 0.00 2.57
152 153 2.194271 CAGAAGGACCGCGAACTATTC 58.806 52.381 8.23 5.28 0.00 1.75
153 154 1.134788 CCAGAAGGACCGCGAACTATT 60.135 52.381 8.23 0.00 36.89 1.73
154 155 0.460311 CCAGAAGGACCGCGAACTAT 59.540 55.000 8.23 0.00 36.89 2.12
155 156 1.601419 CCCAGAAGGACCGCGAACTA 61.601 60.000 8.23 0.00 38.24 2.24
156 157 2.657237 CCAGAAGGACCGCGAACT 59.343 61.111 8.23 0.00 36.89 3.01
157 158 2.434359 CCCAGAAGGACCGCGAAC 60.434 66.667 8.23 0.00 38.24 3.95
158 159 2.513259 AACCCAGAAGGACCGCGAA 61.513 57.895 8.23 0.00 39.89 4.70
159 160 2.920912 AACCCAGAAGGACCGCGA 60.921 61.111 8.23 0.00 39.89 5.87
160 161 2.725203 TTCAACCCAGAAGGACCGCG 62.725 60.000 0.00 0.00 39.89 6.46
161 162 1.072505 TTCAACCCAGAAGGACCGC 59.927 57.895 0.00 0.00 39.89 5.68
162 163 0.396811 AGTTCAACCCAGAAGGACCG 59.603 55.000 0.00 0.00 39.89 4.79
163 164 1.271434 GGAGTTCAACCCAGAAGGACC 60.271 57.143 0.00 0.00 39.89 4.46
164 165 1.271434 GGGAGTTCAACCCAGAAGGAC 60.271 57.143 0.00 0.00 46.05 3.85
165 166 1.064825 GGGAGTTCAACCCAGAAGGA 58.935 55.000 0.00 0.00 46.05 3.36
166 167 3.652581 GGGAGTTCAACCCAGAAGG 57.347 57.895 0.00 0.00 46.05 3.46
172 173 1.247567 CACATGTGGGAGTTCAACCC 58.752 55.000 18.51 0.00 46.87 4.11
173 174 1.247567 CCACATGTGGGAGTTCAACC 58.752 55.000 33.56 0.00 46.81 3.77
184 185 0.456824 CGTCGACCTCTCCACATGTG 60.457 60.000 19.31 19.31 0.00 3.21
185 186 0.894184 ACGTCGACCTCTCCACATGT 60.894 55.000 10.58 0.00 0.00 3.21
186 187 0.243907 AACGTCGACCTCTCCACATG 59.756 55.000 10.58 0.00 0.00 3.21
187 188 0.243907 CAACGTCGACCTCTCCACAT 59.756 55.000 10.58 0.00 0.00 3.21
188 189 1.658114 CAACGTCGACCTCTCCACA 59.342 57.895 10.58 0.00 0.00 4.17
189 190 1.080705 CCAACGTCGACCTCTCCAC 60.081 63.158 10.58 0.00 0.00 4.02
190 191 2.927580 GCCAACGTCGACCTCTCCA 61.928 63.158 10.58 0.00 0.00 3.86
191 192 2.126031 GCCAACGTCGACCTCTCC 60.126 66.667 10.58 0.00 0.00 3.71
192 193 1.078759 CATGCCAACGTCGACCTCTC 61.079 60.000 10.58 0.00 0.00 3.20
193 194 1.079819 CATGCCAACGTCGACCTCT 60.080 57.895 10.58 0.00 0.00 3.69
194 195 2.100631 CCATGCCAACGTCGACCTC 61.101 63.158 10.58 0.00 0.00 3.85
195 196 2.047274 CCATGCCAACGTCGACCT 60.047 61.111 10.58 0.00 0.00 3.85
196 197 3.799755 GCCATGCCAACGTCGACC 61.800 66.667 10.58 0.00 0.00 4.79
197 198 3.047280 TGCCATGCCAACGTCGAC 61.047 61.111 5.18 5.18 0.00 4.20
198 199 3.047280 GTGCCATGCCAACGTCGA 61.047 61.111 0.00 0.00 0.00 4.20
199 200 4.444024 CGTGCCATGCCAACGTCG 62.444 66.667 0.00 0.00 0.00 5.12
200 201 3.047280 TCGTGCCATGCCAACGTC 61.047 61.111 11.26 0.00 0.00 4.34
201 202 3.353836 GTCGTGCCATGCCAACGT 61.354 61.111 11.26 0.00 0.00 3.99
202 203 4.101790 GGTCGTGCCATGCCAACG 62.102 66.667 6.69 6.69 37.17 4.10
203 204 3.747976 GGGTCGTGCCATGCCAAC 61.748 66.667 0.00 0.00 39.65 3.77
208 209 3.925362 TTCGTCGGGTCGTGCCATG 62.925 63.158 0.00 0.00 39.65 3.66
209 210 3.687102 TTCGTCGGGTCGTGCCAT 61.687 61.111 0.00 0.00 39.65 4.40
210 211 4.651008 GTTCGTCGGGTCGTGCCA 62.651 66.667 0.00 0.00 39.65 4.92
211 212 2.862347 CTAGTTCGTCGGGTCGTGCC 62.862 65.000 0.00 0.00 0.00 5.01
212 213 1.513586 CTAGTTCGTCGGGTCGTGC 60.514 63.158 0.00 0.00 0.00 5.34
213 214 1.513586 GCTAGTTCGTCGGGTCGTG 60.514 63.158 0.00 0.00 0.00 4.35
214 215 1.310933 ATGCTAGTTCGTCGGGTCGT 61.311 55.000 0.00 0.00 0.00 4.34
215 216 0.866061 CATGCTAGTTCGTCGGGTCG 60.866 60.000 0.00 0.00 0.00 4.79
216 217 0.454600 TCATGCTAGTTCGTCGGGTC 59.545 55.000 0.00 0.00 0.00 4.46
217 218 0.172803 GTCATGCTAGTTCGTCGGGT 59.827 55.000 0.00 0.00 0.00 5.28
218 219 0.456221 AGTCATGCTAGTTCGTCGGG 59.544 55.000 0.00 0.00 0.00 5.14
219 220 1.920574 CAAGTCATGCTAGTTCGTCGG 59.079 52.381 0.00 0.00 0.00 4.79
231 232 2.029739 TGTCAAGGCAATGCAAGTCATG 60.030 45.455 7.79 0.00 35.13 3.07
232 233 2.241160 TGTCAAGGCAATGCAAGTCAT 58.759 42.857 7.79 0.00 36.87 3.06
233 234 1.689984 TGTCAAGGCAATGCAAGTCA 58.310 45.000 7.79 0.00 0.00 3.41
234 235 2.608752 CCTTGTCAAGGCAATGCAAGTC 60.609 50.000 18.66 0.00 42.78 3.01
235 236 1.342174 CCTTGTCAAGGCAATGCAAGT 59.658 47.619 18.66 0.00 42.78 3.16
236 237 2.074547 CCTTGTCAAGGCAATGCAAG 57.925 50.000 18.66 0.38 42.78 4.01
246 247 1.000283 AGAGACGTCAGCCTTGTCAAG 60.000 52.381 19.50 5.53 35.09 3.02
247 248 1.000163 GAGAGACGTCAGCCTTGTCAA 60.000 52.381 19.50 0.00 35.09 3.18
248 249 0.598562 GAGAGACGTCAGCCTTGTCA 59.401 55.000 19.50 0.00 35.09 3.58
249 250 0.885196 AGAGAGACGTCAGCCTTGTC 59.115 55.000 19.50 4.52 0.00 3.18
250 251 1.000283 CAAGAGAGACGTCAGCCTTGT 60.000 52.381 23.66 3.97 0.00 3.16
251 252 1.270826 TCAAGAGAGACGTCAGCCTTG 59.729 52.381 24.93 24.93 32.58 3.61
252 253 1.543802 CTCAAGAGAGACGTCAGCCTT 59.456 52.381 19.50 13.57 44.98 4.35
253 254 1.173043 CTCAAGAGAGACGTCAGCCT 58.827 55.000 19.50 11.44 44.98 4.58
254 255 0.172352 CCTCAAGAGAGACGTCAGCC 59.828 60.000 19.50 6.42 44.98 4.85
255 256 1.132262 CTCCTCAAGAGAGACGTCAGC 59.868 57.143 19.50 9.38 46.50 4.26
264 265 9.636348 TTCTTCTCGAGACATCTCCTCAAGAGA 62.636 44.444 16.36 7.57 44.48 3.10
265 266 3.540617 TCTCGAGACATCTCCTCAAGAG 58.459 50.000 12.08 4.31 44.75 2.85
266 267 3.636153 TCTCGAGACATCTCCTCAAGA 57.364 47.619 12.08 0.00 39.79 3.02
267 268 3.944650 TCTTCTCGAGACATCTCCTCAAG 59.055 47.826 16.36 5.85 39.79 3.02
268 269 3.956744 TCTTCTCGAGACATCTCCTCAA 58.043 45.455 16.36 0.00 39.79 3.02
269 270 3.636153 TCTTCTCGAGACATCTCCTCA 57.364 47.619 16.36 0.00 39.79 3.86
270 271 4.974368 TTTCTTCTCGAGACATCTCCTC 57.026 45.455 16.36 0.00 39.79 3.71
271 272 4.709397 ACATTTCTTCTCGAGACATCTCCT 59.291 41.667 16.36 0.00 39.79 3.69
272 273 5.004922 ACATTTCTTCTCGAGACATCTCC 57.995 43.478 16.36 0.00 39.79 3.71
273 274 4.732923 CGACATTTCTTCTCGAGACATCTC 59.267 45.833 16.36 2.90 39.55 2.75
274 275 4.439426 CCGACATTTCTTCTCGAGACATCT 60.439 45.833 16.36 0.00 33.02 2.90
275 276 3.794028 CCGACATTTCTTCTCGAGACATC 59.206 47.826 16.36 4.37 33.02 3.06
276 277 3.775202 CCGACATTTCTTCTCGAGACAT 58.225 45.455 16.36 2.14 33.02 3.06
277 278 2.671351 GCCGACATTTCTTCTCGAGACA 60.671 50.000 16.36 1.25 33.02 3.41
278 279 1.921230 GCCGACATTTCTTCTCGAGAC 59.079 52.381 16.36 0.00 33.02 3.36
279 280 1.544246 TGCCGACATTTCTTCTCGAGA 59.456 47.619 12.08 12.08 0.00 4.04
280 281 1.656095 GTGCCGACATTTCTTCTCGAG 59.344 52.381 5.93 5.93 0.00 4.04
281 282 1.710013 GTGCCGACATTTCTTCTCGA 58.290 50.000 0.00 0.00 0.00 4.04
282 283 0.366871 CGTGCCGACATTTCTTCTCG 59.633 55.000 0.00 0.00 0.00 4.04
283 284 1.390463 GACGTGCCGACATTTCTTCTC 59.610 52.381 0.00 0.00 0.00 2.87
284 285 1.270094 TGACGTGCCGACATTTCTTCT 60.270 47.619 0.00 0.00 0.00 2.85
285 286 1.144969 TGACGTGCCGACATTTCTTC 58.855 50.000 0.00 0.00 0.00 2.87
286 287 1.808411 ATGACGTGCCGACATTTCTT 58.192 45.000 0.00 0.00 38.83 2.52
287 288 1.808411 AATGACGTGCCGACATTTCT 58.192 45.000 15.25 0.48 45.84 2.52
288 289 3.124636 AGTTAATGACGTGCCGACATTTC 59.875 43.478 21.91 17.00 45.84 2.17
289 290 3.071479 AGTTAATGACGTGCCGACATTT 58.929 40.909 21.91 8.93 45.84 2.32
291 292 1.999735 CAGTTAATGACGTGCCGACAT 59.000 47.619 0.00 6.70 42.88 3.06
292 293 1.424403 CAGTTAATGACGTGCCGACA 58.576 50.000 0.00 2.25 35.99 4.35
293 294 0.719465 CCAGTTAATGACGTGCCGAC 59.281 55.000 0.00 0.00 0.00 4.79
294 295 1.017177 GCCAGTTAATGACGTGCCGA 61.017 55.000 0.00 0.00 0.00 5.54
295 296 1.423845 GCCAGTTAATGACGTGCCG 59.576 57.895 0.00 0.00 0.00 5.69
296 297 1.654023 GGGCCAGTTAATGACGTGCC 61.654 60.000 4.39 0.00 44.31 5.01
297 298 1.654023 GGGGCCAGTTAATGACGTGC 61.654 60.000 4.39 0.00 0.00 5.34
298 299 0.322098 TGGGGCCAGTTAATGACGTG 60.322 55.000 4.39 0.00 0.00 4.49
299 300 0.623723 ATGGGGCCAGTTAATGACGT 59.376 50.000 4.39 0.00 0.00 4.34
300 301 1.308998 GATGGGGCCAGTTAATGACG 58.691 55.000 4.39 0.00 0.00 4.35
301 302 1.692411 GGATGGGGCCAGTTAATGAC 58.308 55.000 4.39 0.00 0.00 3.06
302 303 0.182537 CGGATGGGGCCAGTTAATGA 59.817 55.000 4.39 0.00 0.00 2.57
303 304 0.182537 TCGGATGGGGCCAGTTAATG 59.817 55.000 4.39 0.00 0.00 1.90
304 305 1.073923 GATCGGATGGGGCCAGTTAAT 59.926 52.381 4.39 0.00 0.00 1.40
305 306 0.472471 GATCGGATGGGGCCAGTTAA 59.528 55.000 4.39 0.00 0.00 2.01
306 307 0.399949 AGATCGGATGGGGCCAGTTA 60.400 55.000 4.39 0.00 0.00 2.24
307 308 1.281925 AAGATCGGATGGGGCCAGTT 61.282 55.000 4.39 0.00 0.00 3.16
308 309 1.694169 AAGATCGGATGGGGCCAGT 60.694 57.895 4.39 0.00 0.00 4.00
309 310 1.228063 CAAGATCGGATGGGGCCAG 60.228 63.158 4.39 0.00 0.00 4.85
310 311 0.692756 TACAAGATCGGATGGGGCCA 60.693 55.000 4.39 0.00 0.00 5.36
311 312 0.035458 CTACAAGATCGGATGGGGCC 59.965 60.000 0.00 0.00 0.00 5.80
312 313 0.759346 ACTACAAGATCGGATGGGGC 59.241 55.000 0.00 0.00 0.00 5.80
313 314 2.036475 CTCACTACAAGATCGGATGGGG 59.964 54.545 0.00 0.00 0.00 4.96
314 315 2.695666 ACTCACTACAAGATCGGATGGG 59.304 50.000 0.00 0.00 0.00 4.00
315 316 5.465051 CATACTCACTACAAGATCGGATGG 58.535 45.833 0.00 0.00 0.00 3.51
316 317 4.920340 GCATACTCACTACAAGATCGGATG 59.080 45.833 0.00 0.00 0.00 3.51
317 318 4.584743 TGCATACTCACTACAAGATCGGAT 59.415 41.667 0.00 0.00 0.00 4.18
318 319 3.951680 TGCATACTCACTACAAGATCGGA 59.048 43.478 0.00 0.00 0.00 4.55
319 320 4.307443 TGCATACTCACTACAAGATCGG 57.693 45.455 0.00 0.00 0.00 4.18
320 321 5.807520 AGTTTGCATACTCACTACAAGATCG 59.192 40.000 3.73 0.00 0.00 3.69
321 322 8.703604 TTAGTTTGCATACTCACTACAAGATC 57.296 34.615 13.38 0.00 0.00 2.75
322 323 9.502091 TTTTAGTTTGCATACTCACTACAAGAT 57.498 29.630 13.38 0.00 0.00 2.40
323 324 8.896320 TTTTAGTTTGCATACTCACTACAAGA 57.104 30.769 13.38 0.00 0.00 3.02
326 327 9.891828 CAAATTTTAGTTTGCATACTCACTACA 57.108 29.630 13.38 0.00 32.90 2.74
329 330 9.630098 CATCAAATTTTAGTTTGCATACTCACT 57.370 29.630 13.38 1.08 38.61 3.41
330 331 9.624697 TCATCAAATTTTAGTTTGCATACTCAC 57.375 29.630 13.38 0.00 38.61 3.51
932 933 2.030274 CCCGGTTGTTCAATCCTTTGAC 60.030 50.000 0.00 0.00 41.50 3.18
975 976 5.263599 AGATCCTTGTTATCAATGCCAACA 58.736 37.500 0.00 0.00 32.82 3.33
1026 1027 7.171678 GCAAGGAATATACGTCTTTCTGCTAAT 59.828 37.037 0.00 0.00 0.00 1.73
1343 1346 4.673441 CACTAGAACTCGTGGTTATGGAG 58.327 47.826 0.00 0.00 38.41 3.86
1361 1364 5.250235 GTGCTACAAGATCTAGTGCACTA 57.750 43.478 24.63 24.63 43.79 2.74
1826 1831 1.825474 TGCACTAGAGCACCTTCTACC 59.175 52.381 11.06 0.00 40.11 3.18
1841 1846 1.899814 TCTGTCGGTAAGGATTGCACT 59.100 47.619 0.00 0.00 29.70 4.40
2002 2007 1.821216 TGAGCATTCCGTTCCCTTTC 58.179 50.000 0.00 0.00 0.00 2.62
2054 2059 1.768870 TCTAGGAGCCCAAGTTATGCC 59.231 52.381 0.00 0.00 0.00 4.40
2120 2125 1.138069 TCCGCGGATATCTTTGCTTCA 59.862 47.619 27.28 0.00 0.00 3.02
2188 2193 3.954258 CAGGGCCTATCCGAAAGAAAATT 59.046 43.478 5.28 0.00 34.94 1.82
2192 2197 1.874129 TCAGGGCCTATCCGAAAGAA 58.126 50.000 5.28 0.00 34.94 2.52
2223 2228 1.605165 TCCGTTGGCATTTCACCCC 60.605 57.895 0.00 0.00 0.00 4.95
2226 2231 0.521735 GAGGTCCGTTGGCATTTCAC 59.478 55.000 0.00 0.00 0.00 3.18
2247 2252 6.127591 CGGATCGGGTGAATTAGAGAATAGAT 60.128 42.308 0.00 0.00 0.00 1.98
2329 2334 3.119495 CCGATTTGTCAAAGGGATTGGAC 60.119 47.826 11.10 0.00 39.62 4.02
2405 2412 6.767524 TGCCGACCAAAAATTCTATATGTT 57.232 33.333 0.00 0.00 0.00 2.71
2509 2516 4.101119 AGAAAACAGAAACCGAGGAAGAGA 59.899 41.667 0.00 0.00 0.00 3.10
2537 2544 3.173953 ACCATGAAAAGCAAGATCCCA 57.826 42.857 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.