Multiple sequence alignment - TraesCS1A01G107700

Loading Multiple Alignment...

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 TraesCS1A01G107700 chr1A 100.000 2450 0 0 1 2450 106218869 106216420 0.000000e+00 4525.0
1 TraesCS1A01G107700 chr1A 100.000 81 0 0 2784 2864 106216086 106216006 1.780000e-32 150.0
2 TraesCS1A01G107700 chr1B 88.875 2337 123 49 174 2448 160310727 160308466 0.000000e+00 2748.0
3 TraesCS1A01G107700 chr1D 90.594 2020 97 26 373 2357 106846784 106848745 0.000000e+00 2591.0
4 TraesCS1A01G107700 chr1D 88.889 81 9 0 2784 2864 106849081 106849161 1.820000e-17 100.0
5 TraesCS1A01G107700 chr1D 93.333 45 2 1 322 366 106846749 106846792 6.620000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G107700 chr1A 106216006 106218869 2863 True 2337.500000 4525 100.000000 1 2864 2 chr1A.!!$R1 2863
1 TraesCS1A01G107700 chr1B 160308466 160310727 2261 True 2748.000000 2748 88.875000 174 2448 1 chr1B.!!$R1 2274
2 TraesCS1A01G107700 chr1D 106846749 106849161 2412 False 918.933333 2591 90.938667 322 2864 3 chr1D.!!$F1 2542

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
115 116 0.036199 AGAGTAGACCTCGAGCGTGT 60.036 55.0 6.99 7.86 45.44 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2135 0.039035 ACATAGCCTCCCCGCAAAAA 59.961 50.0 0.0 0.0 0.0 1.94 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
25 26 8.809468 GTAAGGGGTTTGATTCTTAGAGAATT 57.191 34.615 4.81 0.00 44.41 2.17
26 27 7.946381 AAGGGGTTTGATTCTTAGAGAATTC 57.054 36.000 0.00 0.00 44.41 2.17
27 28 7.032598 AGGGGTTTGATTCTTAGAGAATTCA 57.967 36.000 8.44 2.83 44.41 2.57
28 29 6.887002 AGGGGTTTGATTCTTAGAGAATTCAC 59.113 38.462 8.44 0.74 44.41 3.18
29 30 6.183360 GGGGTTTGATTCTTAGAGAATTCACG 60.183 42.308 8.44 0.00 44.41 4.35
30 31 6.251549 GGTTTGATTCTTAGAGAATTCACGC 58.748 40.000 8.44 0.00 44.41 5.34
31 32 6.092807 GGTTTGATTCTTAGAGAATTCACGCT 59.907 38.462 8.44 4.61 44.41 5.07
32 33 7.361286 GGTTTGATTCTTAGAGAATTCACGCTT 60.361 37.037 8.44 0.00 44.41 4.68
33 34 6.653273 TGATTCTTAGAGAATTCACGCTTG 57.347 37.500 8.44 0.00 44.41 4.01
34 35 4.928661 TTCTTAGAGAATTCACGCTTGC 57.071 40.909 8.44 0.00 0.00 4.01
35 36 3.925379 TCTTAGAGAATTCACGCTTGCA 58.075 40.909 8.44 0.00 0.00 4.08
36 37 4.507710 TCTTAGAGAATTCACGCTTGCAT 58.492 39.130 8.44 0.00 0.00 3.96
37 38 5.660460 TCTTAGAGAATTCACGCTTGCATA 58.340 37.500 8.44 0.00 0.00 3.14
38 39 6.283694 TCTTAGAGAATTCACGCTTGCATAT 58.716 36.000 8.44 0.00 0.00 1.78
39 40 7.433680 TCTTAGAGAATTCACGCTTGCATATA 58.566 34.615 8.44 0.00 0.00 0.86
40 41 7.596621 TCTTAGAGAATTCACGCTTGCATATAG 59.403 37.037 8.44 0.00 0.00 1.31
41 42 5.605534 AGAGAATTCACGCTTGCATATAGT 58.394 37.500 8.44 0.00 0.00 2.12
42 43 6.749139 AGAGAATTCACGCTTGCATATAGTA 58.251 36.000 8.44 0.00 0.00 1.82
43 44 6.865726 AGAGAATTCACGCTTGCATATAGTAG 59.134 38.462 8.44 0.00 0.00 2.57
44 45 5.928839 AGAATTCACGCTTGCATATAGTAGG 59.071 40.000 8.44 0.00 0.00 3.18
45 46 4.929819 TTCACGCTTGCATATAGTAGGA 57.070 40.909 0.00 0.00 0.00 2.94
46 47 4.238761 TCACGCTTGCATATAGTAGGAC 57.761 45.455 0.00 0.00 0.00 3.85
47 48 2.980476 CACGCTTGCATATAGTAGGACG 59.020 50.000 0.00 0.00 0.00 4.79
48 49 2.621998 ACGCTTGCATATAGTAGGACGT 59.378 45.455 0.00 0.00 0.00 4.34
49 50 3.817084 ACGCTTGCATATAGTAGGACGTA 59.183 43.478 0.00 0.00 0.00 3.57
50 51 4.276678 ACGCTTGCATATAGTAGGACGTAA 59.723 41.667 0.00 0.00 0.00 3.18
52 53 5.162075 GCTTGCATATAGTAGGACGTAAGG 58.838 45.833 0.00 0.00 46.39 2.69
53 54 5.278858 GCTTGCATATAGTAGGACGTAAGGT 60.279 44.000 0.00 0.00 46.39 3.50
54 55 6.720112 TTGCATATAGTAGGACGTAAGGTT 57.280 37.500 0.00 0.00 46.39 3.50
55 56 6.720112 TGCATATAGTAGGACGTAAGGTTT 57.280 37.500 0.00 0.00 46.39 3.27
56 57 7.116075 TGCATATAGTAGGACGTAAGGTTTT 57.884 36.000 0.00 0.00 46.39 2.43
57 58 8.236585 TGCATATAGTAGGACGTAAGGTTTTA 57.763 34.615 0.00 0.00 46.39 1.52
58 59 8.137437 TGCATATAGTAGGACGTAAGGTTTTAC 58.863 37.037 0.00 0.00 46.39 2.01
59 60 8.355913 GCATATAGTAGGACGTAAGGTTTTACT 58.644 37.037 0.00 0.00 46.39 2.24
60 61 9.890352 CATATAGTAGGACGTAAGGTTTTACTC 57.110 37.037 0.00 0.00 46.39 2.59
61 62 5.302357 AGTAGGACGTAAGGTTTTACTCG 57.698 43.478 0.00 0.00 46.39 4.18
62 63 5.003804 AGTAGGACGTAAGGTTTTACTCGA 58.996 41.667 0.00 0.00 46.39 4.04
63 64 4.431661 AGGACGTAAGGTTTTACTCGAG 57.568 45.455 11.84 11.84 46.39 4.04
64 65 2.919859 GGACGTAAGGTTTTACTCGAGC 59.080 50.000 13.61 0.00 46.39 5.03
65 66 3.568538 GACGTAAGGTTTTACTCGAGCA 58.431 45.455 13.61 0.00 46.39 4.26
66 67 3.572584 ACGTAAGGTTTTACTCGAGCAG 58.427 45.455 13.61 0.00 46.39 4.24
67 68 2.344741 CGTAAGGTTTTACTCGAGCAGC 59.655 50.000 13.61 3.98 37.58 5.25
68 69 1.809684 AAGGTTTTACTCGAGCAGCC 58.190 50.000 13.61 8.45 0.00 4.85
69 70 0.977395 AGGTTTTACTCGAGCAGCCT 59.023 50.000 13.61 10.72 0.00 4.58
70 71 1.079503 GGTTTTACTCGAGCAGCCTG 58.920 55.000 13.61 0.00 0.00 4.85
71 72 1.337823 GGTTTTACTCGAGCAGCCTGA 60.338 52.381 13.61 0.00 0.00 3.86
72 73 2.413837 GTTTTACTCGAGCAGCCTGAA 58.586 47.619 13.61 0.00 0.00 3.02
73 74 2.080286 TTTACTCGAGCAGCCTGAAC 57.920 50.000 13.61 0.00 0.00 3.18
74 75 1.257743 TTACTCGAGCAGCCTGAACT 58.742 50.000 13.61 0.00 0.00 3.01
75 76 1.257743 TACTCGAGCAGCCTGAACTT 58.742 50.000 13.61 0.00 0.00 2.66
76 77 0.320247 ACTCGAGCAGCCTGAACTTG 60.320 55.000 13.61 0.00 0.00 3.16
77 78 1.004560 TCGAGCAGCCTGAACTTGG 60.005 57.895 0.00 0.00 0.00 3.61
78 79 2.037136 CGAGCAGCCTGAACTTGGG 61.037 63.158 0.00 0.00 0.00 4.12
79 80 1.073897 GAGCAGCCTGAACTTGGGT 59.926 57.895 0.00 0.00 35.45 4.51
80 81 0.324943 GAGCAGCCTGAACTTGGGTA 59.675 55.000 0.00 0.00 33.54 3.69
81 82 0.771127 AGCAGCCTGAACTTGGGTAA 59.229 50.000 0.00 0.00 33.54 2.85
82 83 1.144913 AGCAGCCTGAACTTGGGTAAA 59.855 47.619 0.00 0.00 33.54 2.01
83 84 1.960689 GCAGCCTGAACTTGGGTAAAA 59.039 47.619 0.00 0.00 33.54 1.52
84 85 2.288213 GCAGCCTGAACTTGGGTAAAAC 60.288 50.000 0.00 0.00 33.54 2.43
85 86 2.296190 CAGCCTGAACTTGGGTAAAACC 59.704 50.000 0.00 0.00 37.60 3.27
86 87 2.091555 AGCCTGAACTTGGGTAAAACCA 60.092 45.455 0.00 0.00 41.02 3.67
87 88 2.035449 GCCTGAACTTGGGTAAAACCAC 59.965 50.000 0.00 0.00 41.02 4.16
88 89 2.626266 CCTGAACTTGGGTAAAACCACC 59.374 50.000 0.00 0.00 41.02 4.61
89 90 3.292460 CTGAACTTGGGTAAAACCACCA 58.708 45.455 0.00 0.00 41.02 4.17
90 91 3.895041 CTGAACTTGGGTAAAACCACCAT 59.105 43.478 0.00 0.00 41.02 3.55
91 92 3.639094 TGAACTTGGGTAAAACCACCATG 59.361 43.478 0.00 0.00 41.02 3.66
92 93 3.322191 ACTTGGGTAAAACCACCATGT 57.678 42.857 0.00 0.00 41.02 3.21
93 94 3.227614 ACTTGGGTAAAACCACCATGTC 58.772 45.455 0.00 0.00 41.02 3.06
94 95 3.226777 CTTGGGTAAAACCACCATGTCA 58.773 45.455 0.00 0.00 41.02 3.58
95 96 3.534357 TGGGTAAAACCACCATGTCAT 57.466 42.857 0.00 0.00 41.02 3.06
96 97 4.659529 TGGGTAAAACCACCATGTCATA 57.340 40.909 0.00 0.00 41.02 2.15
97 98 4.594970 TGGGTAAAACCACCATGTCATAG 58.405 43.478 0.00 0.00 41.02 2.23
98 99 4.289934 TGGGTAAAACCACCATGTCATAGA 59.710 41.667 0.00 0.00 41.02 1.98
99 100 4.881850 GGGTAAAACCACCATGTCATAGAG 59.118 45.833 0.00 0.00 41.02 2.43
100 101 5.497474 GGTAAAACCACCATGTCATAGAGT 58.503 41.667 0.00 0.00 38.42 3.24
101 102 6.352394 GGGTAAAACCACCATGTCATAGAGTA 60.352 42.308 0.00 0.00 41.02 2.59
102 103 6.761714 GGTAAAACCACCATGTCATAGAGTAG 59.238 42.308 0.00 0.00 38.42 2.57
103 104 6.620877 AAAACCACCATGTCATAGAGTAGA 57.379 37.500 0.00 0.00 0.00 2.59
104 105 5.599999 AACCACCATGTCATAGAGTAGAC 57.400 43.478 0.00 0.00 35.37 2.59
105 106 3.961408 ACCACCATGTCATAGAGTAGACC 59.039 47.826 0.00 0.00 33.89 3.85
106 107 4.219115 CCACCATGTCATAGAGTAGACCT 58.781 47.826 0.00 0.00 33.89 3.85
107 108 4.279671 CCACCATGTCATAGAGTAGACCTC 59.720 50.000 0.00 0.00 40.80 3.85
108 109 4.023622 CACCATGTCATAGAGTAGACCTCG 60.024 50.000 0.00 0.00 45.44 4.63
109 110 4.141459 ACCATGTCATAGAGTAGACCTCGA 60.141 45.833 0.00 0.00 45.44 4.04
110 111 4.454161 CCATGTCATAGAGTAGACCTCGAG 59.546 50.000 5.13 5.13 45.44 4.04
111 112 3.468770 TGTCATAGAGTAGACCTCGAGC 58.531 50.000 6.99 0.00 45.44 5.03
112 113 2.477375 GTCATAGAGTAGACCTCGAGCG 59.523 54.545 6.99 2.92 45.44 5.03
113 114 2.102757 TCATAGAGTAGACCTCGAGCGT 59.897 50.000 6.99 6.58 45.44 5.07
114 115 1.937278 TAGAGTAGACCTCGAGCGTG 58.063 55.000 6.99 0.00 45.44 5.34
115 116 0.036199 AGAGTAGACCTCGAGCGTGT 60.036 55.000 6.99 7.86 45.44 4.49
116 117 0.803740 GAGTAGACCTCGAGCGTGTT 59.196 55.000 6.99 0.62 0.00 3.32
117 118 2.005451 GAGTAGACCTCGAGCGTGTTA 58.995 52.381 6.99 0.00 0.00 2.41
118 119 2.417933 GAGTAGACCTCGAGCGTGTTAA 59.582 50.000 6.99 0.00 0.00 2.01
119 120 2.161211 AGTAGACCTCGAGCGTGTTAAC 59.839 50.000 6.99 0.00 0.00 2.01
128 129 2.948323 CGTGTTAACGCCCCCAAC 59.052 61.111 13.36 0.00 43.98 3.77
129 130 1.892862 CGTGTTAACGCCCCCAACA 60.893 57.895 13.36 0.00 43.98 3.33
130 131 1.847890 CGTGTTAACGCCCCCAACAG 61.848 60.000 13.36 0.00 43.98 3.16
131 132 1.228306 TGTTAACGCCCCCAACAGG 60.228 57.895 0.26 0.00 0.00 4.00
138 139 4.684623 CCCCCAACAGGCAATAGG 57.315 61.111 0.00 0.00 0.00 2.57
139 140 1.076044 CCCCCAACAGGCAATAGGG 60.076 63.158 0.00 0.00 39.29 3.53
140 141 1.580066 CCCCCAACAGGCAATAGGGA 61.580 60.000 6.66 0.00 42.25 4.20
141 142 0.334676 CCCCAACAGGCAATAGGGAA 59.665 55.000 6.66 0.00 42.25 3.97
142 143 1.474330 CCCAACAGGCAATAGGGAAC 58.526 55.000 0.00 0.00 42.25 3.62
155 156 3.056458 GGAACCAAAAAGGGGGCG 58.944 61.111 0.00 0.00 43.89 6.13
156 157 1.835267 GGAACCAAAAAGGGGGCGT 60.835 57.895 0.00 0.00 43.89 5.68
157 158 1.663739 GAACCAAAAAGGGGGCGTC 59.336 57.895 0.00 0.00 43.89 5.19
158 159 0.826256 GAACCAAAAAGGGGGCGTCT 60.826 55.000 0.00 0.00 43.89 4.18
159 160 0.826256 AACCAAAAAGGGGGCGTCTC 60.826 55.000 0.00 0.00 43.89 3.36
160 161 1.074951 CCAAAAAGGGGGCGTCTCT 59.925 57.895 0.00 0.00 0.00 3.10
161 162 0.539669 CCAAAAAGGGGGCGTCTCTT 60.540 55.000 0.00 0.00 0.00 2.85
162 163 0.598065 CAAAAAGGGGGCGTCTCTTG 59.402 55.000 0.00 0.00 0.00 3.02
163 164 0.185175 AAAAAGGGGGCGTCTCTTGT 59.815 50.000 0.00 0.00 0.00 3.16
164 165 0.250770 AAAAGGGGGCGTCTCTTGTC 60.251 55.000 0.00 0.00 0.00 3.18
165 166 2.125766 AAAGGGGGCGTCTCTTGTCC 62.126 60.000 0.00 0.00 0.00 4.02
166 167 3.003763 GGGGGCGTCTCTTGTCCT 61.004 66.667 0.00 0.00 0.00 3.85
167 168 2.579738 GGGGCGTCTCTTGTCCTC 59.420 66.667 0.00 0.00 0.00 3.71
168 169 2.283529 GGGGCGTCTCTTGTCCTCA 61.284 63.158 0.00 0.00 0.00 3.86
169 170 1.671742 GGGCGTCTCTTGTCCTCAA 59.328 57.895 0.00 0.00 0.00 3.02
170 171 0.250513 GGGCGTCTCTTGTCCTCAAT 59.749 55.000 0.00 0.00 32.82 2.57
171 172 1.363744 GGCGTCTCTTGTCCTCAATG 58.636 55.000 0.00 0.00 32.82 2.82
172 173 1.338200 GGCGTCTCTTGTCCTCAATGT 60.338 52.381 0.00 0.00 32.82 2.71
173 174 2.417719 GCGTCTCTTGTCCTCAATGTT 58.582 47.619 0.00 0.00 32.82 2.71
174 175 2.413453 GCGTCTCTTGTCCTCAATGTTC 59.587 50.000 0.00 0.00 32.82 3.18
175 176 3.862642 GCGTCTCTTGTCCTCAATGTTCT 60.863 47.826 0.00 0.00 32.82 3.01
176 177 3.677121 CGTCTCTTGTCCTCAATGTTCTG 59.323 47.826 0.00 0.00 32.82 3.02
177 178 4.636249 GTCTCTTGTCCTCAATGTTCTGT 58.364 43.478 0.00 0.00 32.82 3.41
178 179 5.059833 GTCTCTTGTCCTCAATGTTCTGTT 58.940 41.667 0.00 0.00 32.82 3.16
179 180 5.529060 GTCTCTTGTCCTCAATGTTCTGTTT 59.471 40.000 0.00 0.00 32.82 2.83
180 181 6.038714 GTCTCTTGTCCTCAATGTTCTGTTTT 59.961 38.462 0.00 0.00 32.82 2.43
181 182 6.038603 TCTCTTGTCCTCAATGTTCTGTTTTG 59.961 38.462 0.00 0.00 32.82 2.44
182 183 4.305989 TGTCCTCAATGTTCTGTTTTGC 57.694 40.909 0.00 0.00 0.00 3.68
183 184 3.698539 TGTCCTCAATGTTCTGTTTTGCA 59.301 39.130 0.00 0.00 0.00 4.08
184 185 4.044426 GTCCTCAATGTTCTGTTTTGCAC 58.956 43.478 0.00 0.00 0.00 4.57
185 186 3.698539 TCCTCAATGTTCTGTTTTGCACA 59.301 39.130 0.00 0.00 0.00 4.57
186 187 3.798337 CCTCAATGTTCTGTTTTGCACAC 59.202 43.478 0.00 0.00 0.00 3.82
187 188 4.422840 CTCAATGTTCTGTTTTGCACACA 58.577 39.130 0.00 0.00 0.00 3.72
188 189 4.172505 TCAATGTTCTGTTTTGCACACAC 58.827 39.130 0.00 0.00 0.00 3.82
189 190 3.865011 ATGTTCTGTTTTGCACACACA 57.135 38.095 0.00 0.00 30.96 3.72
190 191 3.650070 TGTTCTGTTTTGCACACACAA 57.350 38.095 0.00 0.00 0.00 3.33
191 192 3.312828 TGTTCTGTTTTGCACACACAAC 58.687 40.909 8.59 8.59 37.06 3.32
192 193 3.243535 TGTTCTGTTTTGCACACACAACA 60.244 39.130 12.43 12.43 42.61 3.33
193 194 3.865011 TCTGTTTTGCACACACAACAT 57.135 38.095 0.00 0.00 43.52 2.71
194 195 4.972514 TCTGTTTTGCACACACAACATA 57.027 36.364 0.00 0.00 43.52 2.29
195 196 4.919206 TCTGTTTTGCACACACAACATAG 58.081 39.130 0.00 0.00 43.52 2.23
200 201 0.168788 GCACACACAACATAGCGCAT 59.831 50.000 11.47 0.00 0.00 4.73
238 239 1.066573 CAGGCTGTGTAGACCTTGAGG 60.067 57.143 6.28 0.00 42.17 3.86
253 254 3.686726 CCTTGAGGTTAACATGAGTCAGC 59.313 47.826 8.10 0.00 0.00 4.26
274 275 1.723608 CTTGACCGCAACACTGGCAA 61.724 55.000 0.00 0.00 0.00 4.52
290 291 2.720688 CAAGCAATGCAAGACAGCG 58.279 52.632 8.35 0.00 37.31 5.18
291 292 1.080974 AAGCAATGCAAGACAGCGC 60.081 52.632 8.35 0.00 37.31 5.92
292 293 1.521450 AAGCAATGCAAGACAGCGCT 61.521 50.000 2.64 2.64 40.46 5.92
293 294 1.080974 GCAATGCAAGACAGCGCTT 60.081 52.632 7.50 0.00 37.31 4.68
294 295 1.342082 GCAATGCAAGACAGCGCTTG 61.342 55.000 7.50 4.41 46.18 4.01
297 298 1.580845 ATGCAAGACAGCGCTTGACC 61.581 55.000 7.50 0.00 46.31 4.02
311 328 1.528586 CTTGACCGCAACAGTCAGAAG 59.471 52.381 0.00 0.00 44.60 2.85
313 330 1.344438 TGACCGCAACAGTCAGAAGAT 59.656 47.619 0.00 0.00 39.29 2.40
357 374 1.005037 AACGCGAGCTGAACATGGA 60.005 52.632 15.93 0.00 0.00 3.41
358 375 0.391661 AACGCGAGCTGAACATGGAT 60.392 50.000 15.93 0.00 0.00 3.41
359 376 1.086067 ACGCGAGCTGAACATGGATG 61.086 55.000 15.93 0.00 0.00 3.51
360 377 1.086067 CGCGAGCTGAACATGGATGT 61.086 55.000 0.00 0.00 44.20 3.06
369 386 2.669878 ACATGGATGTTGCAACCCC 58.330 52.632 26.14 24.65 37.90 4.95
370 387 0.904394 ACATGGATGTTGCAACCCCC 60.904 55.000 26.14 24.32 37.90 5.40
410 427 1.302511 GGGCAGCTCCTTTGTCGAA 60.303 57.895 0.00 0.00 34.39 3.71
411 428 0.678048 GGGCAGCTCCTTTGTCGAAT 60.678 55.000 0.00 0.00 34.39 3.34
412 429 0.449388 GGCAGCTCCTTTGTCGAATG 59.551 55.000 0.00 0.00 0.00 2.67
413 430 1.160137 GCAGCTCCTTTGTCGAATGT 58.840 50.000 0.00 0.00 0.00 2.71
414 431 1.129437 GCAGCTCCTTTGTCGAATGTC 59.871 52.381 0.00 0.00 0.00 3.06
415 432 1.391485 CAGCTCCTTTGTCGAATGTCG 59.609 52.381 0.00 0.00 42.10 4.35
577 600 3.797546 GAGGCAACGAGCTGCTGC 61.798 66.667 7.01 7.62 44.79 5.25
596 619 0.460284 CGTGCTCAAGTTCGGCCTAT 60.460 55.000 0.00 0.00 0.00 2.57
597 620 1.202371 CGTGCTCAAGTTCGGCCTATA 60.202 52.381 0.00 0.00 0.00 1.31
598 621 2.545952 CGTGCTCAAGTTCGGCCTATAT 60.546 50.000 0.00 0.00 0.00 0.86
599 622 3.305131 CGTGCTCAAGTTCGGCCTATATA 60.305 47.826 0.00 0.00 0.00 0.86
647 670 4.127040 CTGCCGAGCTGCGAGACT 62.127 66.667 0.00 0.00 44.57 3.24
648 671 4.426112 TGCCGAGCTGCGAGACTG 62.426 66.667 0.00 0.00 44.57 3.51
681 704 2.665603 GGAAGGCGAGCTGGAACT 59.334 61.111 0.00 0.00 0.00 3.01
684 707 1.576356 GAAGGCGAGCTGGAACTATG 58.424 55.000 0.00 0.00 0.00 2.23
724 758 2.895372 CACGTGCGGCTAATCCCC 60.895 66.667 0.82 0.00 0.00 4.81
864 898 0.446616 CATATACGCGAGCGCTCCTA 59.553 55.000 30.66 17.59 44.19 2.94
896 930 2.486918 TCATCACACTTCACTGCAGTG 58.513 47.619 36.07 36.07 46.18 3.66
903 937 1.449726 CTTCACTGCAGTGCAAGGCA 61.450 55.000 36.76 19.39 45.25 4.75
906 940 1.228337 ACTGCAGTGCAAGGCATCA 60.228 52.632 20.97 0.00 41.91 3.07
927 961 1.091537 CTCTCGACAGACTCCTCACC 58.908 60.000 0.00 0.00 0.00 4.02
930 964 2.574399 GACAGACTCCTCACCGCC 59.426 66.667 0.00 0.00 0.00 6.13
936 970 4.821589 CTCCTCACCGCCGCTTCC 62.822 72.222 0.00 0.00 0.00 3.46
953 987 0.815734 TCCGCTACCGAAAAGAGAGG 59.184 55.000 0.00 0.00 36.29 3.69
954 988 0.179108 CCGCTACCGAAAAGAGAGGG 60.179 60.000 0.00 0.00 36.29 4.30
956 990 1.067071 CGCTACCGAAAAGAGAGGGTT 60.067 52.381 0.00 0.00 36.29 4.11
957 991 2.612221 CGCTACCGAAAAGAGAGGGTTT 60.612 50.000 0.00 0.00 36.29 3.27
958 992 3.409570 GCTACCGAAAAGAGAGGGTTTT 58.590 45.455 0.00 0.00 34.02 2.43
959 993 3.819337 GCTACCGAAAAGAGAGGGTTTTT 59.181 43.478 0.00 0.00 34.02 1.94
988 1023 4.261741 GCTGCTCCTGAAAGAGAGATAGAG 60.262 50.000 0.00 0.00 34.45 2.43
1022 1057 1.237285 GCAACAATGGTCAGAGGCGT 61.237 55.000 0.00 0.00 0.00 5.68
1023 1058 1.943968 GCAACAATGGTCAGAGGCGTA 60.944 52.381 0.00 0.00 0.00 4.42
1081 1116 1.002087 GGAACAAGAAGCTCCGGAAGA 59.998 52.381 5.23 0.00 0.00 2.87
1131 1166 3.384014 GACCGACGAGGAGCACGAG 62.384 68.421 8.56 0.00 45.00 4.18
1160 1195 3.807538 CGCCCTGCACATGTGAGC 61.808 66.667 29.80 21.75 0.00 4.26
1161 1196 3.807538 GCCCTGCACATGTGAGCG 61.808 66.667 29.80 15.70 34.29 5.03
1162 1197 2.046988 CCCTGCACATGTGAGCGA 60.047 61.111 29.80 8.41 34.29 4.93
1194 1244 0.903942 CTGCTCTTTCCTCTCTGCCT 59.096 55.000 0.00 0.00 0.00 4.75
1454 1511 3.647649 CTGACGCCGACATGCTGGA 62.648 63.158 7.96 0.00 0.00 3.86
1674 1737 2.740714 GGTCGATGCGCAACTCCAC 61.741 63.158 17.11 7.26 0.00 4.02
1683 1746 1.165907 CGCAACTCCACAGGCTTCAA 61.166 55.000 0.00 0.00 0.00 2.69
1743 1806 1.000060 ACTTCACATGCACATTGCCAC 60.000 47.619 0.00 0.00 44.23 5.01
1749 1812 2.267426 CATGCACATTGCCACATTCTG 58.733 47.619 0.00 0.00 44.23 3.02
1750 1813 1.618487 TGCACATTGCCACATTCTGA 58.382 45.000 0.00 0.00 44.23 3.27
1759 1822 2.571202 TGCCACATTCTGACATCACCTA 59.429 45.455 0.00 0.00 0.00 3.08
1891 1954 1.401018 CGAACGGCATGGTTTCTTTCC 60.401 52.381 0.00 0.00 0.00 3.13
2050 2121 8.950208 AATTAGTCTTATTCACTCACTTAGGC 57.050 34.615 0.00 0.00 0.00 3.93
2051 2122 7.719871 TTAGTCTTATTCACTCACTTAGGCT 57.280 36.000 0.00 0.00 0.00 4.58
2052 2123 8.818622 TTAGTCTTATTCACTCACTTAGGCTA 57.181 34.615 0.00 0.00 0.00 3.93
2053 2124 7.906199 AGTCTTATTCACTCACTTAGGCTAT 57.094 36.000 0.00 0.00 0.00 2.97
2054 2125 7.721402 AGTCTTATTCACTCACTTAGGCTATG 58.279 38.462 5.91 5.91 0.00 2.23
2055 2126 7.343316 AGTCTTATTCACTCACTTAGGCTATGT 59.657 37.037 7.21 7.21 0.00 2.29
2056 2127 8.630917 GTCTTATTCACTCACTTAGGCTATGTA 58.369 37.037 12.18 0.00 0.00 2.29
2057 2128 8.630917 TCTTATTCACTCACTTAGGCTATGTAC 58.369 37.037 12.18 0.00 0.00 2.90
2058 2129 6.791867 ATTCACTCACTTAGGCTATGTACA 57.208 37.500 12.18 0.00 0.00 2.90
2059 2130 5.836821 TCACTCACTTAGGCTATGTACAG 57.163 43.478 12.18 12.78 0.00 2.74
2060 2131 5.262009 TCACTCACTTAGGCTATGTACAGT 58.738 41.667 12.18 13.30 0.00 3.55
2061 2132 5.125578 TCACTCACTTAGGCTATGTACAGTG 59.874 44.000 26.63 26.63 32.68 3.66
2062 2133 5.017490 ACTCACTTAGGCTATGTACAGTGT 58.983 41.667 18.10 0.00 34.49 3.55
2063 2134 5.480772 ACTCACTTAGGCTATGTACAGTGTT 59.519 40.000 18.10 8.10 34.49 3.32
2064 2135 6.014499 ACTCACTTAGGCTATGTACAGTGTTT 60.014 38.462 18.10 7.83 34.49 2.83
2065 2136 6.765403 TCACTTAGGCTATGTACAGTGTTTT 58.235 36.000 18.10 0.00 34.49 2.43
2066 2137 7.221450 TCACTTAGGCTATGTACAGTGTTTTT 58.779 34.615 18.10 0.00 34.49 1.94
2165 2241 9.716531 CTATTTCATTACCATGCAGAGAAGATA 57.283 33.333 0.00 0.00 0.00 1.98
2295 2372 6.478512 AAGAAACATGTGGCTAAGGAAAAA 57.521 33.333 0.00 0.00 0.00 1.94
2396 2645 6.205658 GTCTCTTCACTAAGCAAGACCAATTT 59.794 38.462 0.00 0.00 33.50 1.82
2448 2697 4.438200 GCAACAGTTTCGTCTCCTTTTTCA 60.438 41.667 0.00 0.00 0.00 2.69
2800 3049 2.895680 TCTGCTTGCCGCTCTAGG 59.104 61.111 0.00 0.00 40.11 3.02
2809 3058 1.987855 CCGCTCTAGGGGTTGGTGA 60.988 63.158 4.95 0.00 42.54 4.02
2814 3063 2.608368 TAGGGGTTGGTGACGGGG 60.608 66.667 0.00 0.00 0.00 5.73
2818 3067 4.029809 GGTTGGTGACGGGGAGGG 62.030 72.222 0.00 0.00 0.00 4.30
2829 3078 2.597903 GGGAGGGGAATGTCAGGC 59.402 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.809468 AATTCTCTAAGAATCAAACCCCTTAC 57.191 34.615 2.84 0.00 43.67 2.34
1 2 8.611257 TGAATTCTCTAAGAATCAAACCCCTTA 58.389 33.333 7.05 0.00 43.67 2.69
2 3 7.394641 GTGAATTCTCTAAGAATCAAACCCCTT 59.605 37.037 7.05 0.00 43.67 3.95
3 4 6.887002 GTGAATTCTCTAAGAATCAAACCCCT 59.113 38.462 7.05 0.00 43.67 4.79
4 5 6.183360 CGTGAATTCTCTAAGAATCAAACCCC 60.183 42.308 7.05 0.00 43.67 4.95
5 6 6.675728 GCGTGAATTCTCTAAGAATCAAACCC 60.676 42.308 7.05 0.00 43.67 4.11
6 7 6.092807 AGCGTGAATTCTCTAAGAATCAAACC 59.907 38.462 7.05 0.00 43.67 3.27
7 8 7.066374 AGCGTGAATTCTCTAAGAATCAAAC 57.934 36.000 7.05 2.31 43.67 2.93
8 9 7.521529 CAAGCGTGAATTCTCTAAGAATCAAA 58.478 34.615 7.05 0.00 43.67 2.69
9 10 6.402550 GCAAGCGTGAATTCTCTAAGAATCAA 60.403 38.462 2.99 0.00 43.67 2.57
10 11 5.063944 GCAAGCGTGAATTCTCTAAGAATCA 59.936 40.000 2.99 1.56 43.67 2.57
11 12 5.063944 TGCAAGCGTGAATTCTCTAAGAATC 59.936 40.000 2.99 0.00 43.67 2.52
13 14 4.314961 TGCAAGCGTGAATTCTCTAAGAA 58.685 39.130 2.99 0.00 38.78 2.52
14 15 3.925379 TGCAAGCGTGAATTCTCTAAGA 58.075 40.909 2.99 0.00 0.00 2.10
15 16 4.871993 ATGCAAGCGTGAATTCTCTAAG 57.128 40.909 2.99 0.45 0.00 2.18
16 17 7.210174 ACTATATGCAAGCGTGAATTCTCTAA 58.790 34.615 2.99 0.00 0.00 2.10
17 18 6.749139 ACTATATGCAAGCGTGAATTCTCTA 58.251 36.000 2.99 0.00 0.00 2.43
19 20 5.914085 ACTATATGCAAGCGTGAATTCTC 57.086 39.130 2.99 1.90 0.00 2.87
20 21 5.928839 CCTACTATATGCAAGCGTGAATTCT 59.071 40.000 2.99 0.00 0.00 2.40
21 22 5.926542 TCCTACTATATGCAAGCGTGAATTC 59.073 40.000 2.99 0.00 0.00 2.17
22 23 5.696724 GTCCTACTATATGCAAGCGTGAATT 59.303 40.000 2.99 0.00 0.00 2.17
23 24 5.230942 GTCCTACTATATGCAAGCGTGAAT 58.769 41.667 2.99 0.00 0.00 2.57
24 25 4.617959 GTCCTACTATATGCAAGCGTGAA 58.382 43.478 2.99 0.00 0.00 3.18
25 26 3.304458 CGTCCTACTATATGCAAGCGTGA 60.304 47.826 2.99 0.00 0.00 4.35
26 27 2.980476 CGTCCTACTATATGCAAGCGTG 59.020 50.000 0.00 0.00 0.00 5.34
27 28 2.621998 ACGTCCTACTATATGCAAGCGT 59.378 45.455 0.00 0.00 0.00 5.07
28 29 3.284323 ACGTCCTACTATATGCAAGCG 57.716 47.619 0.00 0.00 0.00 4.68
29 30 5.162075 CCTTACGTCCTACTATATGCAAGC 58.838 45.833 0.00 0.00 0.00 4.01
30 31 6.328641 ACCTTACGTCCTACTATATGCAAG 57.671 41.667 0.00 0.00 0.00 4.01
31 32 6.720112 AACCTTACGTCCTACTATATGCAA 57.280 37.500 0.00 0.00 0.00 4.08
32 33 6.720112 AAACCTTACGTCCTACTATATGCA 57.280 37.500 0.00 0.00 0.00 3.96
33 34 8.355913 AGTAAAACCTTACGTCCTACTATATGC 58.644 37.037 0.00 0.00 42.02 3.14
34 35 9.890352 GAGTAAAACCTTACGTCCTACTATATG 57.110 37.037 0.00 0.00 42.02 1.78
35 36 8.778358 CGAGTAAAACCTTACGTCCTACTATAT 58.222 37.037 0.00 0.00 42.02 0.86
36 37 7.985184 TCGAGTAAAACCTTACGTCCTACTATA 59.015 37.037 0.00 0.00 42.02 1.31
37 38 6.823689 TCGAGTAAAACCTTACGTCCTACTAT 59.176 38.462 0.00 0.00 42.02 2.12
38 39 6.170506 TCGAGTAAAACCTTACGTCCTACTA 58.829 40.000 0.00 0.00 42.02 1.82
39 40 5.003804 TCGAGTAAAACCTTACGTCCTACT 58.996 41.667 0.00 0.00 42.02 2.57
40 41 5.296813 TCGAGTAAAACCTTACGTCCTAC 57.703 43.478 0.00 0.00 42.02 3.18
41 42 4.142600 GCTCGAGTAAAACCTTACGTCCTA 60.143 45.833 15.13 0.00 42.02 2.94
42 43 3.366781 GCTCGAGTAAAACCTTACGTCCT 60.367 47.826 15.13 0.00 42.02 3.85
43 44 2.919859 GCTCGAGTAAAACCTTACGTCC 59.080 50.000 15.13 0.00 42.02 4.79
44 45 3.568538 TGCTCGAGTAAAACCTTACGTC 58.431 45.455 15.13 0.00 42.02 4.34
45 46 3.572584 CTGCTCGAGTAAAACCTTACGT 58.427 45.455 15.13 0.00 42.02 3.57
46 47 2.344741 GCTGCTCGAGTAAAACCTTACG 59.655 50.000 15.13 0.00 42.02 3.18
47 48 2.671888 GGCTGCTCGAGTAAAACCTTAC 59.328 50.000 15.13 0.00 38.16 2.34
48 49 2.565834 AGGCTGCTCGAGTAAAACCTTA 59.434 45.455 15.13 0.00 0.00 2.69
49 50 1.348036 AGGCTGCTCGAGTAAAACCTT 59.652 47.619 15.13 0.00 0.00 3.50
50 51 0.977395 AGGCTGCTCGAGTAAAACCT 59.023 50.000 15.13 13.23 0.00 3.50
51 52 1.079503 CAGGCTGCTCGAGTAAAACC 58.920 55.000 15.13 11.15 0.00 3.27
52 53 2.080286 TCAGGCTGCTCGAGTAAAAC 57.920 50.000 15.13 2.55 0.00 2.43
53 54 2.037251 AGTTCAGGCTGCTCGAGTAAAA 59.963 45.455 15.13 0.00 0.00 1.52
54 55 1.618837 AGTTCAGGCTGCTCGAGTAAA 59.381 47.619 15.13 0.00 0.00 2.01
55 56 1.257743 AGTTCAGGCTGCTCGAGTAA 58.742 50.000 15.13 1.83 0.00 2.24
56 57 1.067565 CAAGTTCAGGCTGCTCGAGTA 60.068 52.381 15.13 8.96 0.00 2.59
57 58 0.320247 CAAGTTCAGGCTGCTCGAGT 60.320 55.000 15.13 0.00 0.00 4.18
58 59 1.018226 CCAAGTTCAGGCTGCTCGAG 61.018 60.000 10.34 8.45 0.00 4.04
59 60 1.004560 CCAAGTTCAGGCTGCTCGA 60.005 57.895 10.34 0.00 0.00 4.04
60 61 2.037136 CCCAAGTTCAGGCTGCTCG 61.037 63.158 10.34 0.00 0.00 5.03
61 62 0.324943 TACCCAAGTTCAGGCTGCTC 59.675 55.000 10.34 5.13 0.00 4.26
62 63 0.771127 TTACCCAAGTTCAGGCTGCT 59.229 50.000 10.34 0.00 0.00 4.24
63 64 1.616159 TTTACCCAAGTTCAGGCTGC 58.384 50.000 10.34 0.00 0.00 5.25
64 65 2.296190 GGTTTTACCCAAGTTCAGGCTG 59.704 50.000 8.58 8.58 30.04 4.85
65 66 2.091555 TGGTTTTACCCAAGTTCAGGCT 60.092 45.455 0.00 0.00 37.50 4.58
66 67 2.035449 GTGGTTTTACCCAAGTTCAGGC 59.965 50.000 0.00 0.00 37.50 4.85
67 68 2.626266 GGTGGTTTTACCCAAGTTCAGG 59.374 50.000 0.00 0.00 37.50 3.86
68 69 3.292460 TGGTGGTTTTACCCAAGTTCAG 58.708 45.455 0.00 0.00 40.09 3.02
69 70 3.383698 TGGTGGTTTTACCCAAGTTCA 57.616 42.857 0.00 0.00 40.09 3.18
70 71 3.639561 ACATGGTGGTTTTACCCAAGTTC 59.360 43.478 0.00 0.00 40.09 3.01
71 72 3.639561 GACATGGTGGTTTTACCCAAGTT 59.360 43.478 0.00 0.00 40.09 2.66
72 73 3.227614 GACATGGTGGTTTTACCCAAGT 58.772 45.455 0.00 0.00 40.09 3.16
73 74 3.226777 TGACATGGTGGTTTTACCCAAG 58.773 45.455 0.00 0.00 40.09 3.61
74 75 3.314307 TGACATGGTGGTTTTACCCAA 57.686 42.857 0.00 0.00 40.09 4.12
75 76 3.534357 ATGACATGGTGGTTTTACCCA 57.466 42.857 0.00 0.00 40.09 4.51
76 77 4.850680 TCTATGACATGGTGGTTTTACCC 58.149 43.478 0.00 0.00 40.09 3.69
77 78 5.497474 ACTCTATGACATGGTGGTTTTACC 58.503 41.667 0.00 0.00 41.24 2.85
78 79 7.491696 GTCTACTCTATGACATGGTGGTTTTAC 59.508 40.741 0.00 0.00 33.75 2.01
79 80 7.364408 GGTCTACTCTATGACATGGTGGTTTTA 60.364 40.741 0.00 0.00 35.11 1.52
80 81 6.407202 GTCTACTCTATGACATGGTGGTTTT 58.593 40.000 0.00 0.00 33.75 2.43
81 82 5.104900 GGTCTACTCTATGACATGGTGGTTT 60.105 44.000 0.00 0.00 35.11 3.27
82 83 4.406003 GGTCTACTCTATGACATGGTGGTT 59.594 45.833 0.00 0.00 35.11 3.67
83 84 3.961408 GGTCTACTCTATGACATGGTGGT 59.039 47.826 0.00 2.35 35.11 4.16
84 85 4.219115 AGGTCTACTCTATGACATGGTGG 58.781 47.826 0.00 0.00 35.11 4.61
85 86 4.023622 CGAGGTCTACTCTATGACATGGTG 60.024 50.000 0.00 0.00 44.33 4.17
86 87 4.138290 CGAGGTCTACTCTATGACATGGT 58.862 47.826 0.00 0.00 44.33 3.55
87 88 4.390264 TCGAGGTCTACTCTATGACATGG 58.610 47.826 0.00 0.00 44.33 3.66
88 89 4.083537 GCTCGAGGTCTACTCTATGACATG 60.084 50.000 15.58 0.00 44.33 3.21
89 90 4.069304 GCTCGAGGTCTACTCTATGACAT 58.931 47.826 15.58 0.00 44.33 3.06
90 91 3.468770 GCTCGAGGTCTACTCTATGACA 58.531 50.000 15.58 0.00 44.33 3.58
91 92 2.477375 CGCTCGAGGTCTACTCTATGAC 59.523 54.545 15.58 0.00 44.33 3.06
92 93 2.102757 ACGCTCGAGGTCTACTCTATGA 59.897 50.000 15.58 0.00 44.33 2.15
93 94 2.222213 CACGCTCGAGGTCTACTCTATG 59.778 54.545 15.58 0.00 44.33 2.23
94 95 2.158928 ACACGCTCGAGGTCTACTCTAT 60.159 50.000 15.58 0.00 44.33 1.98
95 96 1.206610 ACACGCTCGAGGTCTACTCTA 59.793 52.381 15.58 0.00 44.33 2.43
96 97 0.036199 ACACGCTCGAGGTCTACTCT 60.036 55.000 15.58 0.00 44.33 3.24
97 98 0.803740 AACACGCTCGAGGTCTACTC 59.196 55.000 15.58 0.00 43.02 2.59
98 99 2.105006 TAACACGCTCGAGGTCTACT 57.895 50.000 15.58 0.00 0.00 2.57
99 100 2.513893 GTTAACACGCTCGAGGTCTAC 58.486 52.381 15.58 2.37 0.00 2.59
100 101 1.129251 CGTTAACACGCTCGAGGTCTA 59.871 52.381 15.58 2.12 40.18 2.59
101 102 0.109873 CGTTAACACGCTCGAGGTCT 60.110 55.000 15.58 3.01 40.18 3.85
102 103 2.346884 CGTTAACACGCTCGAGGTC 58.653 57.895 15.58 0.00 40.18 3.85
103 104 4.546637 CGTTAACACGCTCGAGGT 57.453 55.556 15.58 7.66 40.18 3.85
112 113 1.520600 CCTGTTGGGGGCGTTAACAC 61.521 60.000 6.39 0.00 31.64 3.32
113 114 1.228306 CCTGTTGGGGGCGTTAACA 60.228 57.895 6.39 0.00 33.67 2.41
114 115 2.632544 GCCTGTTGGGGGCGTTAAC 61.633 63.158 0.00 0.00 40.19 2.01
115 116 2.282603 GCCTGTTGGGGGCGTTAA 60.283 61.111 0.00 0.00 40.19 2.01
121 122 1.076044 CCCTATTGCCTGTTGGGGG 60.076 63.158 0.00 0.00 34.46 5.40
122 123 0.334676 TTCCCTATTGCCTGTTGGGG 59.665 55.000 0.00 0.00 38.43 4.96
123 124 1.474330 GTTCCCTATTGCCTGTTGGG 58.526 55.000 0.00 0.00 39.22 4.12
124 125 1.272425 TGGTTCCCTATTGCCTGTTGG 60.272 52.381 0.00 0.00 0.00 3.77
125 126 2.214376 TGGTTCCCTATTGCCTGTTG 57.786 50.000 0.00 0.00 0.00 3.33
126 127 2.990740 TTGGTTCCCTATTGCCTGTT 57.009 45.000 0.00 0.00 0.00 3.16
127 128 2.990740 TTTGGTTCCCTATTGCCTGT 57.009 45.000 0.00 0.00 0.00 4.00
128 129 3.055891 CCTTTTTGGTTCCCTATTGCCTG 60.056 47.826 0.00 0.00 0.00 4.85
129 130 3.173151 CCTTTTTGGTTCCCTATTGCCT 58.827 45.455 0.00 0.00 0.00 4.75
130 131 2.236146 CCCTTTTTGGTTCCCTATTGCC 59.764 50.000 0.00 0.00 0.00 4.52
131 132 2.236146 CCCCTTTTTGGTTCCCTATTGC 59.764 50.000 0.00 0.00 0.00 3.56
132 133 2.837591 CCCCCTTTTTGGTTCCCTATTG 59.162 50.000 0.00 0.00 0.00 1.90
133 134 2.829335 GCCCCCTTTTTGGTTCCCTATT 60.829 50.000 0.00 0.00 0.00 1.73
134 135 1.273609 GCCCCCTTTTTGGTTCCCTAT 60.274 52.381 0.00 0.00 0.00 2.57
135 136 0.115547 GCCCCCTTTTTGGTTCCCTA 59.884 55.000 0.00 0.00 0.00 3.53
136 137 1.152118 GCCCCCTTTTTGGTTCCCT 60.152 57.895 0.00 0.00 0.00 4.20
137 138 2.579657 CGCCCCCTTTTTGGTTCCC 61.580 63.158 0.00 0.00 0.00 3.97
138 139 1.812686 GACGCCCCCTTTTTGGTTCC 61.813 60.000 0.00 0.00 0.00 3.62
139 140 0.826256 AGACGCCCCCTTTTTGGTTC 60.826 55.000 0.00 0.00 0.00 3.62
140 141 0.826256 GAGACGCCCCCTTTTTGGTT 60.826 55.000 0.00 0.00 0.00 3.67
141 142 1.228459 GAGACGCCCCCTTTTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
142 143 0.539669 AAGAGACGCCCCCTTTTTGG 60.540 55.000 0.00 0.00 0.00 3.28
143 144 0.598065 CAAGAGACGCCCCCTTTTTG 59.402 55.000 0.00 0.00 0.00 2.44
144 145 0.185175 ACAAGAGACGCCCCCTTTTT 59.815 50.000 0.00 0.00 0.00 1.94
145 146 0.250770 GACAAGAGACGCCCCCTTTT 60.251 55.000 0.00 0.00 0.00 2.27
146 147 1.375326 GACAAGAGACGCCCCCTTT 59.625 57.895 0.00 0.00 0.00 3.11
147 148 2.593956 GGACAAGAGACGCCCCCTT 61.594 63.158 0.00 0.00 0.00 3.95
148 149 3.003763 GGACAAGAGACGCCCCCT 61.004 66.667 0.00 0.00 0.00 4.79
149 150 3.003763 AGGACAAGAGACGCCCCC 61.004 66.667 0.00 0.00 0.00 5.40
150 151 1.827399 TTGAGGACAAGAGACGCCCC 61.827 60.000 0.00 0.00 0.00 5.80
151 152 0.250513 ATTGAGGACAAGAGACGCCC 59.749 55.000 0.00 0.00 39.46 6.13
152 153 1.338200 ACATTGAGGACAAGAGACGCC 60.338 52.381 0.00 0.00 39.46 5.68
153 154 2.086054 ACATTGAGGACAAGAGACGC 57.914 50.000 0.00 0.00 39.46 5.19
154 155 3.677121 CAGAACATTGAGGACAAGAGACG 59.323 47.826 0.00 0.00 39.46 4.18
155 156 4.636249 ACAGAACATTGAGGACAAGAGAC 58.364 43.478 0.00 0.00 39.46 3.36
156 157 4.963318 ACAGAACATTGAGGACAAGAGA 57.037 40.909 0.00 0.00 39.46 3.10
157 158 6.204359 CAAAACAGAACATTGAGGACAAGAG 58.796 40.000 0.00 0.00 39.46 2.85
158 159 5.450412 GCAAAACAGAACATTGAGGACAAGA 60.450 40.000 0.00 0.00 39.46 3.02
159 160 4.741676 GCAAAACAGAACATTGAGGACAAG 59.258 41.667 0.00 0.00 39.46 3.16
160 161 4.159321 TGCAAAACAGAACATTGAGGACAA 59.841 37.500 0.00 0.00 40.42 3.18
161 162 3.698539 TGCAAAACAGAACATTGAGGACA 59.301 39.130 0.00 0.00 0.00 4.02
162 163 4.044426 GTGCAAAACAGAACATTGAGGAC 58.956 43.478 0.00 0.00 0.00 3.85
163 164 3.698539 TGTGCAAAACAGAACATTGAGGA 59.301 39.130 0.00 0.00 33.78 3.71
164 165 3.798337 GTGTGCAAAACAGAACATTGAGG 59.202 43.478 0.00 0.00 40.26 3.86
165 166 4.266029 GTGTGTGCAAAACAGAACATTGAG 59.734 41.667 3.79 0.00 32.31 3.02
166 167 4.172505 GTGTGTGCAAAACAGAACATTGA 58.827 39.130 3.79 0.00 32.31 2.57
167 168 3.925299 TGTGTGTGCAAAACAGAACATTG 59.075 39.130 3.79 0.00 32.31 2.82
168 169 4.185467 TGTGTGTGCAAAACAGAACATT 57.815 36.364 3.79 0.00 32.31 2.71
169 170 3.865011 TGTGTGTGCAAAACAGAACAT 57.135 38.095 3.79 0.00 32.31 2.71
170 171 3.650070 TTGTGTGTGCAAAACAGAACA 57.350 38.095 8.73 0.39 32.31 3.18
172 173 3.650070 TGTTGTGTGTGCAAAACAGAA 57.350 38.095 8.73 8.73 45.13 3.02
176 177 2.467305 CGCTATGTTGTGTGTGCAAAAC 59.533 45.455 0.00 0.00 41.91 2.43
177 178 2.725490 CGCTATGTTGTGTGTGCAAAA 58.275 42.857 0.00 0.00 0.00 2.44
178 179 1.599171 GCGCTATGTTGTGTGTGCAAA 60.599 47.619 0.00 0.00 36.16 3.68
179 180 0.040514 GCGCTATGTTGTGTGTGCAA 60.041 50.000 0.00 0.00 36.16 4.08
180 181 1.162800 TGCGCTATGTTGTGTGTGCA 61.163 50.000 9.73 0.00 42.49 4.57
181 182 0.168788 ATGCGCTATGTTGTGTGTGC 59.831 50.000 9.73 0.00 36.59 4.57
182 183 1.464219 TCATGCGCTATGTTGTGTGTG 59.536 47.619 9.73 0.00 38.01 3.82
183 184 1.464608 GTCATGCGCTATGTTGTGTGT 59.535 47.619 9.73 0.00 38.01 3.72
184 185 1.464219 TGTCATGCGCTATGTTGTGTG 59.536 47.619 9.73 0.00 38.01 3.82
185 186 1.733912 CTGTCATGCGCTATGTTGTGT 59.266 47.619 9.73 0.00 38.01 3.72
186 187 1.530441 GCTGTCATGCGCTATGTTGTG 60.530 52.381 9.73 5.12 38.01 3.33
187 188 0.729116 GCTGTCATGCGCTATGTTGT 59.271 50.000 9.73 0.00 38.01 3.32
188 189 0.028505 GGCTGTCATGCGCTATGTTG 59.971 55.000 9.73 6.95 38.01 3.33
189 190 1.431488 CGGCTGTCATGCGCTATGTT 61.431 55.000 9.73 0.00 38.01 2.71
190 191 1.884464 CGGCTGTCATGCGCTATGT 60.884 57.895 9.73 0.00 38.01 2.29
191 192 1.554891 CTCGGCTGTCATGCGCTATG 61.555 60.000 9.73 11.14 38.17 2.23
192 193 1.300465 CTCGGCTGTCATGCGCTAT 60.300 57.895 9.73 0.00 0.00 2.97
193 194 2.104928 CTCGGCTGTCATGCGCTA 59.895 61.111 9.73 0.00 0.00 4.26
212 213 1.667830 TCTACACAGCCTGCGTTGC 60.668 57.895 0.00 0.00 0.00 4.17
220 221 3.842869 CCTCAAGGTCTACACAGCC 57.157 57.895 0.00 0.00 0.00 4.85
238 239 2.736721 TCAAGCGCTGACTCATGTTAAC 59.263 45.455 12.58 0.00 0.00 2.01
239 240 3.038788 TCAAGCGCTGACTCATGTTAA 57.961 42.857 12.58 0.00 0.00 2.01
253 254 2.249309 CAGTGTTGCGGTCAAGCG 59.751 61.111 0.00 0.00 40.67 4.68
274 275 1.521450 AAGCGCTGTCTTGCATTGCT 61.521 50.000 12.58 0.00 38.54 3.91
286 287 3.584250 CTGTTGCGGTCAAGCGCTG 62.584 63.158 24.53 5.47 40.67 5.18
290 291 3.731136 TGACTGTTGCGGTCAAGC 58.269 55.556 8.19 0.00 45.32 4.01
293 294 0.750249 TCTTCTGACTGTTGCGGTCA 59.250 50.000 9.98 9.98 45.99 4.02
294 295 1.728971 CATCTTCTGACTGTTGCGGTC 59.271 52.381 1.44 1.44 39.93 4.79
297 298 1.128136 CAGCATCTTCTGACTGTTGCG 59.872 52.381 0.00 0.00 36.19 4.85
367 384 4.621832 GCAATTGCAACATGGGGG 57.378 55.556 25.36 0.00 41.59 5.40
450 467 1.202580 AGACTGCTGCTTCGTTGTTCT 60.203 47.619 0.00 0.00 0.00 3.01
577 600 0.460284 ATAGGCCGAACTTGAGCACG 60.460 55.000 0.00 0.00 0.00 5.34
596 619 0.178981 ACCGAGGGCGCCTAACTATA 60.179 55.000 28.56 0.00 31.76 1.31
597 620 1.457079 ACCGAGGGCGCCTAACTAT 60.457 57.895 28.56 5.00 31.76 2.12
598 621 2.043652 ACCGAGGGCGCCTAACTA 60.044 61.111 28.56 0.00 31.76 2.24
599 622 3.459063 GACCGAGGGCGCCTAACT 61.459 66.667 28.56 15.75 31.76 2.24
646 669 1.524621 CCTTCCGGTATGCCTGCAG 60.525 63.158 6.78 6.78 0.00 4.41
647 670 2.589540 CCTTCCGGTATGCCTGCA 59.410 61.111 0.00 0.00 0.00 4.41
648 671 2.203209 CCCTTCCGGTATGCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
681 704 4.501071 GAAAGAAGGACACGGCTTACATA 58.499 43.478 0.00 0.00 0.00 2.29
684 707 1.725164 CGAAAGAAGGACACGGCTTAC 59.275 52.381 0.00 0.00 0.00 2.34
864 898 1.059098 TGTGATGAACTGAGGTGGCT 58.941 50.000 0.00 0.00 0.00 4.75
896 930 1.153489 TCGAGAGCTGATGCCTTGC 60.153 57.895 0.00 0.00 40.80 4.01
903 937 1.064758 AGGAGTCTGTCGAGAGCTGAT 60.065 52.381 4.35 0.00 0.00 2.90
906 940 0.326595 TGAGGAGTCTGTCGAGAGCT 59.673 55.000 4.35 5.48 0.00 4.09
936 970 0.531200 ACCCTCTCTTTTCGGTAGCG 59.469 55.000 8.29 8.29 0.00 4.26
956 990 0.534877 TCAGGAGCAGCGCTGAAAAA 60.535 50.000 40.21 16.66 39.88 1.94
957 991 0.534877 TTCAGGAGCAGCGCTGAAAA 60.535 50.000 40.21 19.52 39.88 2.29
958 992 0.534877 TTTCAGGAGCAGCGCTGAAA 60.535 50.000 40.21 25.86 39.88 2.69
959 993 0.952497 CTTTCAGGAGCAGCGCTGAA 60.952 55.000 40.21 21.61 39.88 3.02
988 1023 2.688507 TGTTGCCATCGTCTTCTTCTC 58.311 47.619 0.00 0.00 0.00 2.87
1051 1086 3.702048 CTTGTTCCTCCCCGCCGA 61.702 66.667 0.00 0.00 0.00 5.54
1081 1116 1.136147 GCCTCGTGATCGTGTACGT 59.864 57.895 4.20 0.00 40.87 3.57
1134 1169 3.329889 TGCAGGGCGTGGAGGAAT 61.330 61.111 9.49 0.00 0.00 3.01
1162 1197 0.469705 AGAGCAGCTGATCGAGGGAT 60.470 55.000 25.12 4.77 35.26 3.85
1194 1244 3.005897 GTCAGTTCAGAGCTCCAAGTACA 59.994 47.826 10.93 0.00 0.00 2.90
1329 1380 1.818642 CCTTGAGGAAGTGCTTCTGG 58.181 55.000 11.18 3.95 39.45 3.86
1454 1511 3.790437 CCCAGTCCATGCTCGGCT 61.790 66.667 0.00 0.00 0.00 5.52
1674 1737 2.633509 GCCCTGCAGTTGAAGCCTG 61.634 63.158 13.81 0.00 0.00 4.85
1743 1806 3.464907 CCAGCTAGGTGATGTCAGAATG 58.535 50.000 23.31 0.00 37.54 2.67
1749 1812 1.147153 GGGCCAGCTAGGTGATGTC 59.853 63.158 23.31 8.78 40.61 3.06
1750 1813 1.207488 TTGGGCCAGCTAGGTGATGT 61.207 55.000 23.31 0.00 40.61 3.06
1759 1822 2.036256 GGACACATTGGGCCAGCT 59.964 61.111 6.23 0.00 0.00 4.24
1825 1888 4.752101 CGCTTCCAGATTCCTTAATACCAG 59.248 45.833 0.00 0.00 0.00 4.00
1830 1893 4.080299 AGGTTCGCTTCCAGATTCCTTAAT 60.080 41.667 0.00 0.00 0.00 1.40
1831 1894 3.263425 AGGTTCGCTTCCAGATTCCTTAA 59.737 43.478 0.00 0.00 0.00 1.85
1891 1954 3.485378 GCTTCGAATTCTCTGTCGATGAG 59.515 47.826 0.00 10.86 45.03 2.90
1910 1973 1.227999 CCATGTGACCGAACGTGCTT 61.228 55.000 0.00 0.00 36.02 3.91
2064 2135 0.039035 ACATAGCCTCCCCGCAAAAA 59.961 50.000 0.00 0.00 0.00 1.94
2065 2136 0.913205 TACATAGCCTCCCCGCAAAA 59.087 50.000 0.00 0.00 0.00 2.44
2066 2137 0.179468 GTACATAGCCTCCCCGCAAA 59.821 55.000 0.00 0.00 0.00 3.68
2067 2138 0.978667 TGTACATAGCCTCCCCGCAA 60.979 55.000 0.00 0.00 0.00 4.85
2068 2139 1.382009 TGTACATAGCCTCCCCGCA 60.382 57.895 0.00 0.00 0.00 5.69
2069 2140 1.367840 CTGTACATAGCCTCCCCGC 59.632 63.158 0.00 0.00 0.00 6.13
2070 2141 0.389391 CACTGTACATAGCCTCCCCG 59.611 60.000 0.00 0.00 0.00 5.73
2071 2142 1.497161 ACACTGTACATAGCCTCCCC 58.503 55.000 0.00 0.00 0.00 4.81
2072 2143 3.055385 TCAAACACTGTACATAGCCTCCC 60.055 47.826 0.00 0.00 0.00 4.30
2073 2144 4.202245 TCAAACACTGTACATAGCCTCC 57.798 45.455 0.00 0.00 0.00 4.30
2074 2145 5.459107 CGTATCAAACACTGTACATAGCCTC 59.541 44.000 0.00 0.00 0.00 4.70
2323 2401 7.571059 GCATTTTTAACCATTGTGCGAGATTTT 60.571 33.333 0.00 0.00 0.00 1.82
2370 2619 3.641436 TGGTCTTGCTTAGTGAAGAGACA 59.359 43.478 0.00 0.00 37.88 3.41
2400 2649 7.493971 GCATAATGTTTGAGCTAGAAGAGAGAA 59.506 37.037 0.00 0.00 0.00 2.87
2410 2659 6.573664 AACTGTTGCATAATGTTTGAGCTA 57.426 33.333 0.00 0.00 0.00 3.32
2412 2661 5.164158 CGAAACTGTTGCATAATGTTTGAGC 60.164 40.000 10.75 0.00 32.01 4.26
2792 3041 1.218316 GTCACCAACCCCTAGAGCG 59.782 63.158 0.00 0.00 0.00 5.03
2797 3046 2.608368 CCCCGTCACCAACCCCTA 60.608 66.667 0.00 0.00 0.00 3.53
2798 3047 4.585216 TCCCCGTCACCAACCCCT 62.585 66.667 0.00 0.00 0.00 4.79
2800 3049 4.029809 CCTCCCCGTCACCAACCC 62.030 72.222 0.00 0.00 0.00 4.11
2803 3052 3.795977 TTCCCCTCCCCGTCACCAA 62.796 63.158 0.00 0.00 0.00 3.67
2809 3058 1.995626 CTGACATTCCCCTCCCCGT 60.996 63.158 0.00 0.00 0.00 5.28
2814 3063 2.597903 GGGCCTGACATTCCCCTC 59.402 66.667 0.84 0.00 34.59 4.30
2818 3067 0.919710 AGTTAGGGGCCTGACATTCC 59.080 55.000 0.84 0.00 35.36 3.01
2829 3078 3.933332 GTGTCGAATTCTTCAGTTAGGGG 59.067 47.826 3.52 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.