Multiple sequence alignment - TraesCS7A01G081000

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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 TraesCS7A01G081000 chr7A 100.000 3192 0 0 1 3192 46716433 46713242 0.000000e+00 5895.0
1 TraesCS7A01G081000 chr7A 100.000 43 0 0 1 43 685508244 685508202 2.640000e-11 80.5
2 TraesCS7A01G081000 chr7A 100.000 43 0 0 1 43 685545820 685545778 2.640000e-11 80.5
3 TraesCS7A01G081000 chr7D 88.094 2209 120 50 249 2349 44298202 44296029 0.000000e+00 2490.0
4 TraesCS7A01G081000 chr7D 95.423 852 30 7 2347 3192 44295976 44295128 0.000000e+00 1349.0
5 TraesCS7A01G081000 chr7D 79.399 233 45 3 13 244 563720544 563720774 9.160000e-36 161.0
6 TraesCS7A01G081000 chr4A 89.944 1979 129 40 1259 3192 655256361 655254408 0.000000e+00 2488.0
7 TraesCS7A01G081000 chr4A 78.816 963 115 45 363 1256 655258432 655257490 1.660000e-157 566.0
8 TraesCS7A01G081000 chr1B 82.394 426 54 16 2673 3079 619420234 619419811 5.070000e-93 351.0
9 TraesCS7A01G081000 chr1B 94.595 37 1 1 490 526 9984963 9984928 4.450000e-04 56.5
10 TraesCS7A01G081000 chr1D 81.667 420 62 10 2675 3079 451132204 451131785 5.100000e-88 335.0
11 TraesCS7A01G081000 chr1A 81.928 332 40 16 2766 3079 545891277 545890948 2.440000e-66 263.0
12 TraesCS7A01G081000 chr1A 79.412 238 40 7 12 244 583863486 583863719 3.300000e-35 159.0
13 TraesCS7A01G081000 chr1A 90.244 41 2 2 479 518 281892529 281892568 6.000000e-03 52.8
14 TraesCS7A01G081000 chr7B 82.123 179 30 2 69 245 87817851 87818029 5.510000e-33 152.0
15 TraesCS7A01G081000 chr7B 94.737 38 1 1 491 527 720811335 720811372 1.240000e-04 58.4
16 TraesCS7A01G081000 chr3A 82.558 172 28 2 69 238 745513792 745513621 1.980000e-32 150.0
17 TraesCS7A01G081000 chr2B 80.110 181 33 3 67 245 762508772 762508593 7.180000e-27 132.0
18 TraesCS7A01G081000 chr2B 92.000 50 4 0 198 247 550055836 550055787 1.590000e-08 71.3
19 TraesCS7A01G081000 chr2B 92.683 41 1 2 481 520 645508261 645508300 1.240000e-04 58.4
20 TraesCS7A01G081000 chr6B 78.531 177 36 2 69 243 480853781 480853605 7.240000e-22 115.0
21 TraesCS7A01G081000 chr6B 76.613 124 25 4 116 238 535440076 535439956 7.390000e-07 65.8
22 TraesCS7A01G081000 chr4B 91.667 48 4 0 198 245 14081717 14081670 2.050000e-07 67.6
23 TraesCS7A01G081000 chr4B 97.059 34 1 0 491 524 658516008 658516041 1.240000e-04 58.4
24 TraesCS7A01G081000 chr3B 92.857 42 1 2 479 519 166149057 166149097 3.440000e-05 60.2
25 TraesCS7A01G081000 chr4D 96.970 33 0 1 491 523 335044893 335044862 2.000000e-03 54.7
26 TraesCS7A01G081000 chr3D 96.970 33 0 1 491 523 394765632 394765601 2.000000e-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 TraesCS7A01G081000 chr7A 46713242 46716433 3191 True 5895.0 5895 100.0000 1 3192 1 chr7A.!!$R1 3191
1 TraesCS7A01G081000 chr7D 44295128 44298202 3074 True 1919.5 2490 91.7585 249 3192 2 chr7D.!!$R1 2943
2 TraesCS7A01G081000 chr4A 655254408 655258432 4024 True 1527.0 2488 84.3800 363 3192 2 chr4A.!!$R1 2829

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
185 186 0.250553 GGTTCGTGTGGATTGTGGGA 60.251 55.0 0.00 0.0 0.0 4.37 F
1599 2878 0.679640 TCATCGCACATTGGGGGTTC 60.680 55.0 2.62 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 3028 0.392461 GGCGCCTCCTGTAAATGTCA 60.392 55.000 22.15 0.0 0.0 3.58 R
3098 4472 1.211949 GACTTATAGGGGTGCCAAGCA 59.788 52.381 0.00 0.0 35.6 3.91 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
19 20 2.832672 GACCAGATTTCCGTGATTGC 57.167 50.000 0.00 0.00 0.00 3.56
20 21 2.083774 GACCAGATTTCCGTGATTGCA 58.916 47.619 0.00 0.00 0.00 4.08
21 22 2.086869 ACCAGATTTCCGTGATTGCAG 58.913 47.619 0.00 0.00 0.00 4.41
22 23 1.402968 CCAGATTTCCGTGATTGCAGG 59.597 52.381 0.00 0.00 0.00 4.85
27 28 2.819595 CCGTGATTGCAGGGGACG 60.820 66.667 0.00 0.00 44.40 4.79
28 29 2.047274 CGTGATTGCAGGGGACGT 60.047 61.111 0.00 0.00 0.00 4.34
30 31 2.040544 GTGATTGCAGGGGACGTGG 61.041 63.158 0.00 0.00 45.29 4.94
31 32 2.438434 GATTGCAGGGGACGTGGG 60.438 66.667 0.00 0.00 45.29 4.61
32 33 2.933287 ATTGCAGGGGACGTGGGA 60.933 61.111 0.00 0.00 45.29 4.37
33 34 2.478335 GATTGCAGGGGACGTGGGAA 62.478 60.000 0.00 0.00 45.29 3.97
34 35 1.863155 ATTGCAGGGGACGTGGGAAT 61.863 55.000 0.00 0.00 45.29 3.01
35 36 2.438434 GCAGGGGACGTGGGAATG 60.438 66.667 0.00 0.00 45.29 2.67
36 37 2.272146 CAGGGGACGTGGGAATGG 59.728 66.667 0.00 0.00 40.97 3.16
37 38 2.204090 AGGGGACGTGGGAATGGT 60.204 61.111 0.00 0.00 0.00 3.55
38 39 1.081462 AGGGGACGTGGGAATGGTA 59.919 57.895 0.00 0.00 0.00 3.25
39 40 0.981277 AGGGGACGTGGGAATGGTAG 60.981 60.000 0.00 0.00 0.00 3.18
40 41 1.269703 GGGGACGTGGGAATGGTAGT 61.270 60.000 0.00 0.00 0.00 2.73
41 42 0.616891 GGGACGTGGGAATGGTAGTT 59.383 55.000 0.00 0.00 0.00 2.24
42 43 1.406477 GGGACGTGGGAATGGTAGTTC 60.406 57.143 0.00 0.00 0.00 3.01
43 44 1.406477 GGACGTGGGAATGGTAGTTCC 60.406 57.143 0.00 0.00 45.61 3.62
60 61 9.656323 TGGTAGTTCCAGTATTACATCTTAGAT 57.344 33.333 0.00 0.00 41.93 1.98
61 62 9.915629 GGTAGTTCCAGTATTACATCTTAGATG 57.084 37.037 19.49 19.49 35.97 2.90
65 66 8.983724 GTTCCAGTATTACATCTTAGATGAAGC 58.016 37.037 26.71 12.27 34.87 3.86
66 67 8.250143 TCCAGTATTACATCTTAGATGAAGCA 57.750 34.615 26.71 9.03 34.87 3.91
67 68 8.874156 TCCAGTATTACATCTTAGATGAAGCAT 58.126 33.333 26.71 14.54 34.87 3.79
68 69 8.933807 CCAGTATTACATCTTAGATGAAGCATG 58.066 37.037 26.71 16.40 34.87 4.06
69 70 8.933807 CAGTATTACATCTTAGATGAAGCATGG 58.066 37.037 26.71 8.90 34.87 3.66
70 71 8.654997 AGTATTACATCTTAGATGAAGCATGGT 58.345 33.333 26.71 6.13 34.87 3.55
71 72 7.976135 ATTACATCTTAGATGAAGCATGGTC 57.024 36.000 26.71 0.00 34.87 4.02
72 73 4.375272 ACATCTTAGATGAAGCATGGTCG 58.625 43.478 26.71 0.00 34.87 4.79
73 74 3.459232 TCTTAGATGAAGCATGGTCGG 57.541 47.619 0.00 0.00 34.87 4.79
74 75 2.766263 TCTTAGATGAAGCATGGTCGGT 59.234 45.455 0.00 0.00 34.87 4.69
75 76 2.890808 TAGATGAAGCATGGTCGGTC 57.109 50.000 0.00 0.00 0.00 4.79
76 77 0.904649 AGATGAAGCATGGTCGGTCA 59.095 50.000 0.00 0.00 0.00 4.02
77 78 1.487976 AGATGAAGCATGGTCGGTCAT 59.512 47.619 9.70 9.70 0.00 3.06
78 79 2.092753 AGATGAAGCATGGTCGGTCATT 60.093 45.455 10.93 1.37 0.00 2.57
79 80 1.452110 TGAAGCATGGTCGGTCATTG 58.548 50.000 0.00 0.00 0.00 2.82
80 81 1.003003 TGAAGCATGGTCGGTCATTGA 59.997 47.619 0.00 0.00 0.00 2.57
81 82 2.083774 GAAGCATGGTCGGTCATTGAA 58.916 47.619 0.00 0.00 0.00 2.69
82 83 2.198827 AGCATGGTCGGTCATTGAAA 57.801 45.000 0.00 0.00 0.00 2.69
83 84 2.513753 AGCATGGTCGGTCATTGAAAA 58.486 42.857 0.00 0.00 0.00 2.29
84 85 3.091545 AGCATGGTCGGTCATTGAAAAT 58.908 40.909 0.00 0.00 0.00 1.82
85 86 3.511146 AGCATGGTCGGTCATTGAAAATT 59.489 39.130 0.00 0.00 0.00 1.82
86 87 3.613737 GCATGGTCGGTCATTGAAAATTG 59.386 43.478 0.00 0.00 0.00 2.32
87 88 4.808558 CATGGTCGGTCATTGAAAATTGT 58.191 39.130 0.00 0.00 0.00 2.71
88 89 4.927978 TGGTCGGTCATTGAAAATTGTT 57.072 36.364 0.00 0.00 0.00 2.83
89 90 6.385843 CATGGTCGGTCATTGAAAATTGTTA 58.614 36.000 0.00 0.00 0.00 2.41
90 91 6.392625 TGGTCGGTCATTGAAAATTGTTAA 57.607 33.333 0.00 0.00 0.00 2.01
91 92 6.442952 TGGTCGGTCATTGAAAATTGTTAAG 58.557 36.000 0.00 0.00 0.00 1.85
92 93 6.039941 TGGTCGGTCATTGAAAATTGTTAAGT 59.960 34.615 0.00 0.00 0.00 2.24
93 94 6.362283 GGTCGGTCATTGAAAATTGTTAAGTG 59.638 38.462 0.00 0.00 0.00 3.16
94 95 6.915843 GTCGGTCATTGAAAATTGTTAAGTGT 59.084 34.615 0.00 0.00 0.00 3.55
95 96 8.071368 GTCGGTCATTGAAAATTGTTAAGTGTA 58.929 33.333 0.00 0.00 0.00 2.90
96 97 8.071368 TCGGTCATTGAAAATTGTTAAGTGTAC 58.929 33.333 0.00 0.00 0.00 2.90
97 98 7.325097 CGGTCATTGAAAATTGTTAAGTGTACC 59.675 37.037 0.00 0.00 0.00 3.34
98 99 8.357402 GGTCATTGAAAATTGTTAAGTGTACCT 58.643 33.333 0.00 0.00 0.00 3.08
126 127 7.902920 AAAATATTAGATCAATGGTGGCTGT 57.097 32.000 0.00 0.00 0.00 4.40
127 128 7.902920 AAATATTAGATCAATGGTGGCTGTT 57.097 32.000 0.00 0.00 0.00 3.16
128 129 8.995027 AAATATTAGATCAATGGTGGCTGTTA 57.005 30.769 0.00 0.00 0.00 2.41
129 130 8.627208 AATATTAGATCAATGGTGGCTGTTAG 57.373 34.615 0.00 0.00 0.00 2.34
130 131 5.692115 TTAGATCAATGGTGGCTGTTAGA 57.308 39.130 0.00 0.00 0.00 2.10
131 132 4.785346 AGATCAATGGTGGCTGTTAGAT 57.215 40.909 0.00 0.00 0.00 1.98
132 133 5.121380 AGATCAATGGTGGCTGTTAGATT 57.879 39.130 0.00 0.00 0.00 2.40
133 134 4.885907 AGATCAATGGTGGCTGTTAGATTG 59.114 41.667 0.00 0.00 0.00 2.67
134 135 4.299586 TCAATGGTGGCTGTTAGATTGA 57.700 40.909 0.00 0.00 0.00 2.57
135 136 4.661222 TCAATGGTGGCTGTTAGATTGAA 58.339 39.130 0.00 0.00 29.23 2.69
136 137 5.076182 TCAATGGTGGCTGTTAGATTGAAA 58.924 37.500 0.00 0.00 29.23 2.69
137 138 5.538053 TCAATGGTGGCTGTTAGATTGAAAA 59.462 36.000 0.00 0.00 29.23 2.29
138 139 5.649782 ATGGTGGCTGTTAGATTGAAAAG 57.350 39.130 0.00 0.00 0.00 2.27
139 140 4.469657 TGGTGGCTGTTAGATTGAAAAGT 58.530 39.130 0.00 0.00 0.00 2.66
140 141 4.278170 TGGTGGCTGTTAGATTGAAAAGTG 59.722 41.667 0.00 0.00 0.00 3.16
141 142 4.278419 GGTGGCTGTTAGATTGAAAAGTGT 59.722 41.667 0.00 0.00 0.00 3.55
142 143 5.215160 GTGGCTGTTAGATTGAAAAGTGTG 58.785 41.667 0.00 0.00 0.00 3.82
143 144 4.278170 TGGCTGTTAGATTGAAAAGTGTGG 59.722 41.667 0.00 0.00 0.00 4.17
144 145 4.321230 GGCTGTTAGATTGAAAAGTGTGGG 60.321 45.833 0.00 0.00 0.00 4.61
145 146 4.278419 GCTGTTAGATTGAAAAGTGTGGGT 59.722 41.667 0.00 0.00 0.00 4.51
146 147 5.562890 GCTGTTAGATTGAAAAGTGTGGGTC 60.563 44.000 0.00 0.00 0.00 4.46
147 148 5.690865 TGTTAGATTGAAAAGTGTGGGTCT 58.309 37.500 0.00 0.00 0.00 3.85
148 149 6.833041 TGTTAGATTGAAAAGTGTGGGTCTA 58.167 36.000 0.00 0.00 0.00 2.59
149 150 7.284074 TGTTAGATTGAAAAGTGTGGGTCTAA 58.716 34.615 0.00 0.00 0.00 2.10
150 151 7.942341 TGTTAGATTGAAAAGTGTGGGTCTAAT 59.058 33.333 0.00 0.00 31.86 1.73
151 152 8.451748 GTTAGATTGAAAAGTGTGGGTCTAATC 58.548 37.037 0.00 0.00 31.86 1.75
152 153 5.643777 AGATTGAAAAGTGTGGGTCTAATCG 59.356 40.000 0.00 0.00 0.00 3.34
153 154 4.345859 TGAAAAGTGTGGGTCTAATCGT 57.654 40.909 0.00 0.00 0.00 3.73
154 155 4.062293 TGAAAAGTGTGGGTCTAATCGTG 58.938 43.478 0.00 0.00 0.00 4.35
155 156 3.764237 AAAGTGTGGGTCTAATCGTGT 57.236 42.857 0.00 0.00 0.00 4.49
156 157 2.743636 AGTGTGGGTCTAATCGTGTG 57.256 50.000 0.00 0.00 0.00 3.82
157 158 1.275291 AGTGTGGGTCTAATCGTGTGG 59.725 52.381 0.00 0.00 0.00 4.17
158 159 1.001633 GTGTGGGTCTAATCGTGTGGT 59.998 52.381 0.00 0.00 0.00 4.16
159 160 1.001520 TGTGGGTCTAATCGTGTGGTG 59.998 52.381 0.00 0.00 0.00 4.17
160 161 1.001633 GTGGGTCTAATCGTGTGGTGT 59.998 52.381 0.00 0.00 0.00 4.16
161 162 1.695242 TGGGTCTAATCGTGTGGTGTT 59.305 47.619 0.00 0.00 0.00 3.32
162 163 2.898612 TGGGTCTAATCGTGTGGTGTTA 59.101 45.455 0.00 0.00 0.00 2.41
163 164 3.324268 TGGGTCTAATCGTGTGGTGTTAA 59.676 43.478 0.00 0.00 0.00 2.01
164 165 4.020039 TGGGTCTAATCGTGTGGTGTTAAT 60.020 41.667 0.00 0.00 0.00 1.40
165 166 4.939439 GGGTCTAATCGTGTGGTGTTAATT 59.061 41.667 0.00 0.00 0.00 1.40
166 167 5.163794 GGGTCTAATCGTGTGGTGTTAATTG 60.164 44.000 0.00 0.00 0.00 2.32
167 168 5.163794 GGTCTAATCGTGTGGTGTTAATTGG 60.164 44.000 0.00 0.00 0.00 3.16
168 169 5.410439 GTCTAATCGTGTGGTGTTAATTGGT 59.590 40.000 0.00 0.00 0.00 3.67
169 170 5.998981 TCTAATCGTGTGGTGTTAATTGGTT 59.001 36.000 0.00 0.00 0.00 3.67
170 171 4.759516 ATCGTGTGGTGTTAATTGGTTC 57.240 40.909 0.00 0.00 0.00 3.62
171 172 2.544686 TCGTGTGGTGTTAATTGGTTCG 59.455 45.455 0.00 0.00 0.00 3.95
172 173 2.288458 CGTGTGGTGTTAATTGGTTCGT 59.712 45.455 0.00 0.00 0.00 3.85
173 174 3.623863 GTGTGGTGTTAATTGGTTCGTG 58.376 45.455 0.00 0.00 0.00 4.35
174 175 3.065648 GTGTGGTGTTAATTGGTTCGTGT 59.934 43.478 0.00 0.00 0.00 4.49
175 176 3.065510 TGTGGTGTTAATTGGTTCGTGTG 59.934 43.478 0.00 0.00 0.00 3.82
176 177 2.619177 TGGTGTTAATTGGTTCGTGTGG 59.381 45.455 0.00 0.00 0.00 4.17
177 178 2.879646 GGTGTTAATTGGTTCGTGTGGA 59.120 45.455 0.00 0.00 0.00 4.02
178 179 3.504520 GGTGTTAATTGGTTCGTGTGGAT 59.495 43.478 0.00 0.00 0.00 3.41
179 180 4.022676 GGTGTTAATTGGTTCGTGTGGATT 60.023 41.667 0.00 0.00 0.00 3.01
180 181 4.915085 GTGTTAATTGGTTCGTGTGGATTG 59.085 41.667 0.00 0.00 0.00 2.67
181 182 4.580995 TGTTAATTGGTTCGTGTGGATTGT 59.419 37.500 0.00 0.00 0.00 2.71
182 183 3.641437 AATTGGTTCGTGTGGATTGTG 57.359 42.857 0.00 0.00 0.00 3.33
183 184 1.313772 TTGGTTCGTGTGGATTGTGG 58.686 50.000 0.00 0.00 0.00 4.17
184 185 0.536233 TGGTTCGTGTGGATTGTGGG 60.536 55.000 0.00 0.00 0.00 4.61
185 186 0.250553 GGTTCGTGTGGATTGTGGGA 60.251 55.000 0.00 0.00 0.00 4.37
186 187 0.872388 GTTCGTGTGGATTGTGGGAC 59.128 55.000 0.00 0.00 0.00 4.46
187 188 0.762418 TTCGTGTGGATTGTGGGACT 59.238 50.000 0.00 0.00 0.00 3.85
188 189 1.634960 TCGTGTGGATTGTGGGACTA 58.365 50.000 0.00 0.00 0.00 2.59
189 190 1.972075 TCGTGTGGATTGTGGGACTAA 59.028 47.619 0.00 0.00 0.00 2.24
190 191 2.569853 TCGTGTGGATTGTGGGACTAAT 59.430 45.455 0.00 0.00 0.00 1.73
191 192 3.008594 TCGTGTGGATTGTGGGACTAATT 59.991 43.478 0.00 0.00 0.00 1.40
192 193 3.126858 CGTGTGGATTGTGGGACTAATTG 59.873 47.826 0.00 0.00 0.00 2.32
193 194 3.088532 TGTGGATTGTGGGACTAATTGC 58.911 45.455 0.00 0.00 0.00 3.56
194 195 3.088532 GTGGATTGTGGGACTAATTGCA 58.911 45.455 0.00 0.00 0.00 4.08
195 196 3.509575 GTGGATTGTGGGACTAATTGCAA 59.490 43.478 0.00 0.00 0.00 4.08
196 197 4.021544 GTGGATTGTGGGACTAATTGCAAA 60.022 41.667 1.71 0.00 0.00 3.68
197 198 4.220382 TGGATTGTGGGACTAATTGCAAAG 59.780 41.667 1.71 0.00 0.00 2.77
198 199 4.220602 GGATTGTGGGACTAATTGCAAAGT 59.779 41.667 1.71 2.71 0.00 2.66
199 200 4.582701 TTGTGGGACTAATTGCAAAGTG 57.417 40.909 8.50 1.84 0.00 3.16
200 201 2.295909 TGTGGGACTAATTGCAAAGTGC 59.704 45.455 12.85 12.85 45.29 4.40
217 218 8.314333 GCAAAGTGCATTTAAGAAAGTTTTTG 57.686 30.769 0.00 0.00 44.26 2.44
218 219 7.962373 GCAAAGTGCATTTAAGAAAGTTTTTGT 59.038 29.630 0.00 0.00 44.26 2.83
219 220 9.824534 CAAAGTGCATTTAAGAAAGTTTTTGTT 57.175 25.926 0.00 0.00 0.00 2.83
221 222 9.824534 AAGTGCATTTAAGAAAGTTTTTGTTTG 57.175 25.926 0.00 0.00 0.00 2.93
222 223 9.213799 AGTGCATTTAAGAAAGTTTTTGTTTGA 57.786 25.926 0.00 0.00 0.00 2.69
223 224 9.986833 GTGCATTTAAGAAAGTTTTTGTTTGAT 57.013 25.926 0.00 0.00 0.00 2.57
239 240 9.593134 TTTTGTTTGATTGTTTAATAGCAGTGT 57.407 25.926 0.00 0.00 0.00 3.55
241 242 9.891828 TTGTTTGATTGTTTAATAGCAGTGTAG 57.108 29.630 0.00 0.00 0.00 2.74
242 243 9.278978 TGTTTGATTGTTTAATAGCAGTGTAGA 57.721 29.630 0.00 0.00 0.00 2.59
245 246 8.437360 TGATTGTTTAATAGCAGTGTAGATGG 57.563 34.615 0.00 0.00 0.00 3.51
246 247 8.264347 TGATTGTTTAATAGCAGTGTAGATGGA 58.736 33.333 0.00 0.00 0.00 3.41
247 248 9.277783 GATTGTTTAATAGCAGTGTAGATGGAT 57.722 33.333 0.00 0.00 0.00 3.41
249 250 9.764363 TTGTTTAATAGCAGTGTAGATGGATAG 57.236 33.333 0.00 0.00 0.00 2.08
250 251 8.367911 TGTTTAATAGCAGTGTAGATGGATAGG 58.632 37.037 0.00 0.00 0.00 2.57
251 252 7.482169 TTAATAGCAGTGTAGATGGATAGGG 57.518 40.000 0.00 0.00 0.00 3.53
252 253 3.619900 AGCAGTGTAGATGGATAGGGA 57.380 47.619 0.00 0.00 0.00 4.20
253 254 3.505386 AGCAGTGTAGATGGATAGGGAG 58.495 50.000 0.00 0.00 0.00 4.30
256 257 4.218852 GCAGTGTAGATGGATAGGGAGTAC 59.781 50.000 0.00 0.00 0.00 2.73
273 274 5.648092 GGGAGTACTACATCTTTTGCAATGT 59.352 40.000 7.57 4.09 39.38 2.71
321 322 5.136105 GCTGATTATTCCATTGAGGTTCCT 58.864 41.667 0.00 0.00 39.02 3.36
458 486 6.016943 TCCCCAAATAAGTGTCGTTGTTTTAG 60.017 38.462 0.00 0.00 0.00 1.85
506 534 8.472007 AAAATGACTACACTTATTTTGGGACA 57.528 30.769 0.00 0.00 33.05 4.02
614 654 7.794810 TGTATAACAAGTTCGTGAACATTTTCG 59.205 33.333 14.61 0.02 43.47 3.46
619 659 5.086888 AGTTCGTGAACATTTTCGTAACC 57.913 39.130 14.61 0.00 43.47 2.85
679 726 6.696583 CGTGCATGAAAATGAGCCATATTTTA 59.303 34.615 0.00 0.00 37.73 1.52
693 740 5.569428 GCCATATTTTATGGGCCAGGATTTC 60.569 44.000 13.78 0.00 40.55 2.17
753 800 5.164031 CGAACGAAAATTTACAGATCCGTCA 60.164 40.000 0.00 0.00 0.00 4.35
773 820 6.122782 CGTCATGAACATGTATAAGCTTTCG 58.877 40.000 3.20 0.00 39.72 3.46
910 997 2.589157 CCGGGTGCACTAGGGTTCA 61.589 63.158 17.98 0.00 0.00 3.18
1194 1316 1.359848 GCCGATTTCGCTCAAGAGAA 58.640 50.000 0.32 0.00 38.18 2.87
1256 1378 8.253810 TCTGTGATTGAGAGGAATTAAGTAGTG 58.746 37.037 0.00 0.00 0.00 2.74
1314 2577 3.937706 GGTGAACTGATGAACTCATGAGG 59.062 47.826 26.08 9.27 41.06 3.86
1318 2581 0.807275 TGATGAACTCATGAGGCGCG 60.807 55.000 26.08 0.00 36.57 6.86
1362 2625 4.826274 TCTTGGGAGTAATCTTGTGGAG 57.174 45.455 0.00 0.00 0.00 3.86
1475 2749 3.137176 AGGTATGGCATATGCTGTTCACT 59.863 43.478 26.12 14.69 41.70 3.41
1483 2757 5.407995 GGCATATGCTGTTCACTAGAGATTC 59.592 44.000 26.12 0.51 41.70 2.52
1493 2767 3.056536 TCACTAGAGATTCGCAGTGCTTT 60.057 43.478 14.33 0.00 35.60 3.51
1495 2774 1.354040 AGAGATTCGCAGTGCTTTCG 58.646 50.000 14.33 0.00 0.00 3.46
1506 2785 1.400494 AGTGCTTTCGTCCAACACAAC 59.600 47.619 0.00 0.00 33.69 3.32
1531 2810 8.826710 ACATAAGATGTTGTTACAACCGATATG 58.173 33.333 23.20 23.14 41.63 1.78
1539 2818 4.168014 GTTACAACCGATATGTGACGACA 58.832 43.478 0.00 0.00 36.22 4.35
1543 2822 2.640184 ACCGATATGTGACGACAGAGA 58.360 47.619 0.00 0.00 34.87 3.10
1548 2827 4.745620 CGATATGTGACGACAGAGAGAGTA 59.254 45.833 0.00 0.00 34.87 2.59
1565 2844 7.013274 AGAGAGAGTAGCAGAACAGATTACATC 59.987 40.741 0.00 0.00 0.00 3.06
1566 2845 5.826586 AGAGTAGCAGAACAGATTACATCG 58.173 41.667 0.00 0.00 0.00 3.84
1570 2849 6.973474 AGTAGCAGAACAGATTACATCGTAAC 59.027 38.462 0.00 0.00 0.00 2.50
1575 2854 7.413000 GCAGAACAGATTACATCGTAACAATGT 60.413 37.037 0.00 0.00 40.37 2.71
1599 2878 0.679640 TCATCGCACATTGGGGGTTC 60.680 55.000 2.62 0.00 0.00 3.62
1648 2933 3.389925 TCTTCGTTCCCGTATGTTTGT 57.610 42.857 0.00 0.00 35.01 2.83
1649 2934 3.731089 TCTTCGTTCCCGTATGTTTGTT 58.269 40.909 0.00 0.00 35.01 2.83
1650 2935 3.495377 TCTTCGTTCCCGTATGTTTGTTG 59.505 43.478 0.00 0.00 35.01 3.33
1700 2985 1.135373 CGTTCTGGCTGTCATAGACGT 60.135 52.381 0.00 0.00 37.17 4.34
1743 3028 1.056125 TGCATCTCATCACCCCGGAT 61.056 55.000 0.73 0.00 0.00 4.18
1804 3089 1.304617 CTTCCCCTGCTTTCCCCTC 59.695 63.158 0.00 0.00 0.00 4.30
1807 3092 1.617839 CCCCTGCTTTCCCCTCTCT 60.618 63.158 0.00 0.00 0.00 3.10
1808 3093 1.631071 CCCCTGCTTTCCCCTCTCTC 61.631 65.000 0.00 0.00 0.00 3.20
1809 3094 0.911525 CCCTGCTTTCCCCTCTCTCA 60.912 60.000 0.00 0.00 0.00 3.27
1810 3095 0.987294 CCTGCTTTCCCCTCTCTCAA 59.013 55.000 0.00 0.00 0.00 3.02
1821 3106 4.599241 TCCCCTCTCTCAATTTCTGTTCTT 59.401 41.667 0.00 0.00 0.00 2.52
1842 3127 9.107367 GTTCTTTCAACATTCAAATCTAAGACG 57.893 33.333 0.00 0.00 0.00 4.18
1869 3154 2.679837 TCATCGCAGAAAAGATGGAAGC 59.320 45.455 5.73 0.00 43.58 3.86
1888 3173 9.696917 ATGGAAGCTTTAAGTTAATCTGTTTTG 57.303 29.630 0.00 0.00 0.00 2.44
1896 3181 8.810652 TTAAGTTAATCTGTTTTGAATGGTGC 57.189 30.769 0.00 0.00 0.00 5.01
1953 3238 3.570975 GCACCATGATTATGCCATCTTCA 59.429 43.478 0.00 0.00 33.06 3.02
1954 3239 4.038282 GCACCATGATTATGCCATCTTCAA 59.962 41.667 0.00 0.00 33.06 2.69
1955 3240 5.279306 GCACCATGATTATGCCATCTTCAAT 60.279 40.000 0.00 0.00 33.06 2.57
1956 3241 6.387465 CACCATGATTATGCCATCTTCAATC 58.613 40.000 0.00 0.00 32.79 2.67
2192 3487 1.204146 GAGGCCTGATGGTTGGTAGA 58.796 55.000 12.00 0.00 35.27 2.59
2193 3488 0.912486 AGGCCTGATGGTTGGTAGAC 59.088 55.000 3.11 0.00 35.27 2.59
2196 3491 0.462047 CCTGATGGTTGGTAGACGGC 60.462 60.000 0.00 0.00 0.00 5.68
2198 3493 0.249120 TGATGGTTGGTAGACGGCAG 59.751 55.000 0.00 0.00 0.00 4.85
2199 3494 0.249398 GATGGTTGGTAGACGGCAGT 59.751 55.000 0.00 0.00 0.00 4.40
2201 3496 1.375523 GGTTGGTAGACGGCAGTGG 60.376 63.158 0.00 0.00 0.00 4.00
2202 3497 1.370064 GTTGGTAGACGGCAGTGGT 59.630 57.895 0.00 0.00 0.00 4.16
2204 3499 1.116536 TTGGTAGACGGCAGTGGTGA 61.117 55.000 0.00 0.00 0.00 4.02
2207 3502 1.228769 TAGACGGCAGTGGTGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
2209 3504 2.842462 ACGGCAGTGGTGAGGTGA 60.842 61.111 0.00 0.00 0.00 4.02
2261 3568 5.418840 TCTTTCACCCCAAAGATAAGAATGC 59.581 40.000 0.00 0.00 37.45 3.56
2338 3646 6.478344 CCTATGAAGTGAAGCTGATGAGTTAC 59.522 42.308 0.00 0.00 0.00 2.50
2342 3650 4.489810 AGTGAAGCTGATGAGTTACGAAG 58.510 43.478 0.00 0.00 0.00 3.79
2670 4043 1.364171 CTGAACCGGGCTATCTCCG 59.636 63.158 6.32 0.00 46.43 4.63
2710 4083 6.090483 GTCTTGGCTAGAGCATTGTAGATA 57.910 41.667 3.54 0.00 44.36 1.98
2725 4098 3.318275 TGTAGATATCGCGCTTCCTCTTT 59.682 43.478 5.56 0.00 0.00 2.52
2831 4204 1.587613 GTCGTCTCGCTCTGCATCC 60.588 63.158 0.00 0.00 0.00 3.51
2853 4226 2.964978 GCGCAGGAAGCATGGTTT 59.035 55.556 12.13 0.00 46.13 3.27
2855 4228 0.525761 GCGCAGGAAGCATGGTTTAA 59.474 50.000 12.13 0.00 46.13 1.52
2856 4229 1.732405 GCGCAGGAAGCATGGTTTAAC 60.732 52.381 12.13 5.78 46.13 2.01
2857 4230 1.539388 CGCAGGAAGCATGGTTTAACA 59.461 47.619 12.13 0.00 46.13 2.41
2884 4257 3.807538 CAGTGTGGCGCATGGAGC 61.808 66.667 10.83 0.00 40.87 4.70
2943 4316 1.351017 TCCATGTCAAGGTCCACTTCC 59.649 52.381 0.00 0.00 37.29 3.46
3012 4385 1.134371 GCCTTGCTAAGATCTTCCGGT 60.134 52.381 12.24 0.00 0.00 5.28
3153 4532 4.142600 GCAAAAGGCATGAGATAAACGTCT 60.143 41.667 0.00 0.00 43.97 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.083774 TGCAATCACGGAAATCTGGTC 58.916 47.619 0.00 0.00 0.00 4.02
1 2 2.086869 CTGCAATCACGGAAATCTGGT 58.913 47.619 0.00 0.00 0.00 4.00
2 3 1.402968 CCTGCAATCACGGAAATCTGG 59.597 52.381 0.00 0.00 0.00 3.86
3 4 1.402968 CCCTGCAATCACGGAAATCTG 59.597 52.381 0.00 0.00 0.00 2.90
6 7 0.331278 TCCCCTGCAATCACGGAAAT 59.669 50.000 0.00 0.00 0.00 2.17
7 8 0.608035 GTCCCCTGCAATCACGGAAA 60.608 55.000 0.00 0.00 0.00 3.13
8 9 1.002624 GTCCCCTGCAATCACGGAA 60.003 57.895 0.00 0.00 0.00 4.30
9 10 2.668632 GTCCCCTGCAATCACGGA 59.331 61.111 0.00 0.00 0.00 4.69
10 11 2.819595 CGTCCCCTGCAATCACGG 60.820 66.667 0.00 0.00 0.00 4.94
11 12 2.047274 ACGTCCCCTGCAATCACG 60.047 61.111 5.80 5.80 36.54 4.35
12 13 2.040544 CCACGTCCCCTGCAATCAC 61.041 63.158 0.00 0.00 0.00 3.06
13 14 2.350895 CCACGTCCCCTGCAATCA 59.649 61.111 0.00 0.00 0.00 2.57
14 15 2.438434 CCCACGTCCCCTGCAATC 60.438 66.667 0.00 0.00 0.00 2.67
15 16 1.863155 ATTCCCACGTCCCCTGCAAT 61.863 55.000 0.00 0.00 0.00 3.56
16 17 2.534396 ATTCCCACGTCCCCTGCAA 61.534 57.895 0.00 0.00 0.00 4.08
17 18 2.933287 ATTCCCACGTCCCCTGCA 60.933 61.111 0.00 0.00 0.00 4.41
18 19 2.438434 CATTCCCACGTCCCCTGC 60.438 66.667 0.00 0.00 0.00 4.85
19 20 1.268992 TACCATTCCCACGTCCCCTG 61.269 60.000 0.00 0.00 0.00 4.45
20 21 0.981277 CTACCATTCCCACGTCCCCT 60.981 60.000 0.00 0.00 0.00 4.79
21 22 1.269703 ACTACCATTCCCACGTCCCC 61.270 60.000 0.00 0.00 0.00 4.81
22 23 0.616891 AACTACCATTCCCACGTCCC 59.383 55.000 0.00 0.00 0.00 4.46
23 24 1.406477 GGAACTACCATTCCCACGTCC 60.406 57.143 0.00 0.00 42.16 4.79
24 25 1.276989 TGGAACTACCATTCCCACGTC 59.723 52.381 2.19 0.00 46.68 4.34
25 26 1.354101 TGGAACTACCATTCCCACGT 58.646 50.000 2.19 0.00 46.68 4.49
35 36 9.915629 CATCTAAGATGTAATACTGGAACTACC 57.084 37.037 0.00 0.00 39.54 3.18
39 40 8.983724 GCTTCATCTAAGATGTAATACTGGAAC 58.016 37.037 0.00 0.00 37.38 3.62
40 41 8.704668 TGCTTCATCTAAGATGTAATACTGGAA 58.295 33.333 0.00 0.00 37.38 3.53
41 42 8.250143 TGCTTCATCTAAGATGTAATACTGGA 57.750 34.615 0.00 0.00 37.38 3.86
42 43 8.933807 CATGCTTCATCTAAGATGTAATACTGG 58.066 37.037 0.00 0.00 37.38 4.00
43 44 8.933807 CCATGCTTCATCTAAGATGTAATACTG 58.066 37.037 0.00 0.00 37.38 2.74
44 45 8.654997 ACCATGCTTCATCTAAGATGTAATACT 58.345 33.333 0.00 0.00 37.38 2.12
45 46 8.839310 ACCATGCTTCATCTAAGATGTAATAC 57.161 34.615 0.00 0.00 37.38 1.89
46 47 7.814587 CGACCATGCTTCATCTAAGATGTAATA 59.185 37.037 0.00 0.00 37.38 0.98
47 48 6.648310 CGACCATGCTTCATCTAAGATGTAAT 59.352 38.462 0.00 0.00 37.38 1.89
48 49 5.985530 CGACCATGCTTCATCTAAGATGTAA 59.014 40.000 0.00 0.00 37.38 2.41
49 50 5.509670 CCGACCATGCTTCATCTAAGATGTA 60.510 44.000 0.00 0.00 37.38 2.29
50 51 4.375272 CGACCATGCTTCATCTAAGATGT 58.625 43.478 0.00 0.00 37.38 3.06
51 52 3.744942 CCGACCATGCTTCATCTAAGATG 59.255 47.826 0.00 0.00 37.38 2.90
52 53 3.389329 ACCGACCATGCTTCATCTAAGAT 59.611 43.478 0.00 0.00 37.38 2.40
53 54 2.766263 ACCGACCATGCTTCATCTAAGA 59.234 45.455 0.00 0.00 37.38 2.10
54 55 3.126831 GACCGACCATGCTTCATCTAAG 58.873 50.000 0.00 0.00 38.32 2.18
55 56 2.499693 TGACCGACCATGCTTCATCTAA 59.500 45.455 0.00 0.00 0.00 2.10
56 57 2.107366 TGACCGACCATGCTTCATCTA 58.893 47.619 0.00 0.00 0.00 1.98
57 58 0.904649 TGACCGACCATGCTTCATCT 59.095 50.000 0.00 0.00 0.00 2.90
58 59 1.959042 ATGACCGACCATGCTTCATC 58.041 50.000 0.00 0.00 0.00 2.92
59 60 2.019249 CAATGACCGACCATGCTTCAT 58.981 47.619 0.00 0.00 0.00 2.57
60 61 1.003003 TCAATGACCGACCATGCTTCA 59.997 47.619 0.00 0.00 0.00 3.02
61 62 1.737838 TCAATGACCGACCATGCTTC 58.262 50.000 0.00 0.00 0.00 3.86
62 63 2.198827 TTCAATGACCGACCATGCTT 57.801 45.000 0.00 0.00 0.00 3.91
63 64 2.198827 TTTCAATGACCGACCATGCT 57.801 45.000 0.00 0.00 0.00 3.79
64 65 3.508744 ATTTTCAATGACCGACCATGC 57.491 42.857 0.00 0.00 0.00 4.06
65 66 4.808558 ACAATTTTCAATGACCGACCATG 58.191 39.130 0.00 0.00 0.00 3.66
66 67 5.467035 AACAATTTTCAATGACCGACCAT 57.533 34.783 0.00 0.00 0.00 3.55
67 68 4.927978 AACAATTTTCAATGACCGACCA 57.072 36.364 0.00 0.00 0.00 4.02
68 69 6.362283 CACTTAACAATTTTCAATGACCGACC 59.638 38.462 0.00 0.00 0.00 4.79
69 70 6.915843 ACACTTAACAATTTTCAATGACCGAC 59.084 34.615 0.00 0.00 0.00 4.79
70 71 7.033530 ACACTTAACAATTTTCAATGACCGA 57.966 32.000 0.00 0.00 0.00 4.69
71 72 7.325097 GGTACACTTAACAATTTTCAATGACCG 59.675 37.037 0.00 0.00 0.00 4.79
72 73 8.357402 AGGTACACTTAACAATTTTCAATGACC 58.643 33.333 0.00 0.00 0.00 4.02
100 101 9.420118 ACAGCCACCATTGATCTAATATTTTTA 57.580 29.630 0.00 0.00 0.00 1.52
101 102 8.310122 ACAGCCACCATTGATCTAATATTTTT 57.690 30.769 0.00 0.00 0.00 1.94
102 103 7.902920 ACAGCCACCATTGATCTAATATTTT 57.097 32.000 0.00 0.00 0.00 1.82
103 104 7.902920 AACAGCCACCATTGATCTAATATTT 57.097 32.000 0.00 0.00 0.00 1.40
104 105 8.439971 TCTAACAGCCACCATTGATCTAATATT 58.560 33.333 0.00 0.00 0.00 1.28
105 106 7.977818 TCTAACAGCCACCATTGATCTAATAT 58.022 34.615 0.00 0.00 0.00 1.28
106 107 7.373617 TCTAACAGCCACCATTGATCTAATA 57.626 36.000 0.00 0.00 0.00 0.98
107 108 6.252599 TCTAACAGCCACCATTGATCTAAT 57.747 37.500 0.00 0.00 0.00 1.73
108 109 5.692115 TCTAACAGCCACCATTGATCTAA 57.308 39.130 0.00 0.00 0.00 2.10
109 110 5.894298 ATCTAACAGCCACCATTGATCTA 57.106 39.130 0.00 0.00 0.00 1.98
110 111 4.785346 ATCTAACAGCCACCATTGATCT 57.215 40.909 0.00 0.00 0.00 2.75
111 112 4.883585 TCAATCTAACAGCCACCATTGATC 59.116 41.667 0.00 0.00 0.00 2.92
112 113 4.858850 TCAATCTAACAGCCACCATTGAT 58.141 39.130 0.00 0.00 0.00 2.57
113 114 4.299586 TCAATCTAACAGCCACCATTGA 57.700 40.909 0.00 0.00 0.00 2.57
114 115 5.389859 TTTCAATCTAACAGCCACCATTG 57.610 39.130 0.00 0.00 0.00 2.82
115 116 5.539955 ACTTTTCAATCTAACAGCCACCATT 59.460 36.000 0.00 0.00 0.00 3.16
116 117 5.047802 CACTTTTCAATCTAACAGCCACCAT 60.048 40.000 0.00 0.00 0.00 3.55
117 118 4.278170 CACTTTTCAATCTAACAGCCACCA 59.722 41.667 0.00 0.00 0.00 4.17
118 119 4.278419 ACACTTTTCAATCTAACAGCCACC 59.722 41.667 0.00 0.00 0.00 4.61
119 120 5.215160 CACACTTTTCAATCTAACAGCCAC 58.785 41.667 0.00 0.00 0.00 5.01
120 121 4.278170 CCACACTTTTCAATCTAACAGCCA 59.722 41.667 0.00 0.00 0.00 4.75
121 122 4.321230 CCCACACTTTTCAATCTAACAGCC 60.321 45.833 0.00 0.00 0.00 4.85
122 123 4.278419 ACCCACACTTTTCAATCTAACAGC 59.722 41.667 0.00 0.00 0.00 4.40
123 124 5.765182 AGACCCACACTTTTCAATCTAACAG 59.235 40.000 0.00 0.00 0.00 3.16
124 125 5.690865 AGACCCACACTTTTCAATCTAACA 58.309 37.500 0.00 0.00 0.00 2.41
125 126 7.739498 TTAGACCCACACTTTTCAATCTAAC 57.261 36.000 0.00 0.00 0.00 2.34
126 127 7.333423 CGATTAGACCCACACTTTTCAATCTAA 59.667 37.037 0.00 0.00 33.32 2.10
127 128 6.816640 CGATTAGACCCACACTTTTCAATCTA 59.183 38.462 0.00 0.00 0.00 1.98
128 129 5.643777 CGATTAGACCCACACTTTTCAATCT 59.356 40.000 0.00 0.00 0.00 2.40
129 130 5.411669 ACGATTAGACCCACACTTTTCAATC 59.588 40.000 0.00 0.00 0.00 2.67
130 131 5.181245 CACGATTAGACCCACACTTTTCAAT 59.819 40.000 0.00 0.00 0.00 2.57
131 132 4.513692 CACGATTAGACCCACACTTTTCAA 59.486 41.667 0.00 0.00 0.00 2.69
132 133 4.062293 CACGATTAGACCCACACTTTTCA 58.938 43.478 0.00 0.00 0.00 2.69
133 134 4.062991 ACACGATTAGACCCACACTTTTC 58.937 43.478 0.00 0.00 0.00 2.29
134 135 3.813166 CACACGATTAGACCCACACTTTT 59.187 43.478 0.00 0.00 0.00 2.27
135 136 3.399330 CACACGATTAGACCCACACTTT 58.601 45.455 0.00 0.00 0.00 2.66
136 137 2.289444 CCACACGATTAGACCCACACTT 60.289 50.000 0.00 0.00 0.00 3.16
137 138 1.275291 CCACACGATTAGACCCACACT 59.725 52.381 0.00 0.00 0.00 3.55
138 139 1.001633 ACCACACGATTAGACCCACAC 59.998 52.381 0.00 0.00 0.00 3.82
139 140 1.001520 CACCACACGATTAGACCCACA 59.998 52.381 0.00 0.00 0.00 4.17
140 141 1.001633 ACACCACACGATTAGACCCAC 59.998 52.381 0.00 0.00 0.00 4.61
141 142 1.344065 ACACCACACGATTAGACCCA 58.656 50.000 0.00 0.00 0.00 4.51
142 143 2.467566 AACACCACACGATTAGACCC 57.532 50.000 0.00 0.00 0.00 4.46
143 144 5.163794 CCAATTAACACCACACGATTAGACC 60.164 44.000 0.00 0.00 0.00 3.85
144 145 5.410439 ACCAATTAACACCACACGATTAGAC 59.590 40.000 0.00 0.00 0.00 2.59
145 146 5.553123 ACCAATTAACACCACACGATTAGA 58.447 37.500 0.00 0.00 0.00 2.10
146 147 5.873179 ACCAATTAACACCACACGATTAG 57.127 39.130 0.00 0.00 0.00 1.73
147 148 5.107026 CGAACCAATTAACACCACACGATTA 60.107 40.000 0.00 0.00 0.00 1.75
148 149 4.319911 CGAACCAATTAACACCACACGATT 60.320 41.667 0.00 0.00 0.00 3.34
149 150 3.187637 CGAACCAATTAACACCACACGAT 59.812 43.478 0.00 0.00 0.00 3.73
150 151 2.544686 CGAACCAATTAACACCACACGA 59.455 45.455 0.00 0.00 0.00 4.35
151 152 2.288458 ACGAACCAATTAACACCACACG 59.712 45.455 0.00 0.00 0.00 4.49
152 153 3.065648 ACACGAACCAATTAACACCACAC 59.934 43.478 0.00 0.00 0.00 3.82
153 154 3.065510 CACACGAACCAATTAACACCACA 59.934 43.478 0.00 0.00 0.00 4.17
154 155 3.549221 CCACACGAACCAATTAACACCAC 60.549 47.826 0.00 0.00 0.00 4.16
155 156 2.619177 CCACACGAACCAATTAACACCA 59.381 45.455 0.00 0.00 0.00 4.17
156 157 2.879646 TCCACACGAACCAATTAACACC 59.120 45.455 0.00 0.00 0.00 4.16
157 158 4.759516 ATCCACACGAACCAATTAACAC 57.240 40.909 0.00 0.00 0.00 3.32
158 159 4.580995 ACAATCCACACGAACCAATTAACA 59.419 37.500 0.00 0.00 0.00 2.41
159 160 4.915085 CACAATCCACACGAACCAATTAAC 59.085 41.667 0.00 0.00 0.00 2.01
160 161 4.022762 CCACAATCCACACGAACCAATTAA 60.023 41.667 0.00 0.00 0.00 1.40
161 162 3.504134 CCACAATCCACACGAACCAATTA 59.496 43.478 0.00 0.00 0.00 1.40
162 163 2.295909 CCACAATCCACACGAACCAATT 59.704 45.455 0.00 0.00 0.00 2.32
163 164 1.885887 CCACAATCCACACGAACCAAT 59.114 47.619 0.00 0.00 0.00 3.16
164 165 1.313772 CCACAATCCACACGAACCAA 58.686 50.000 0.00 0.00 0.00 3.67
165 166 0.536233 CCCACAATCCACACGAACCA 60.536 55.000 0.00 0.00 0.00 3.67
166 167 0.250553 TCCCACAATCCACACGAACC 60.251 55.000 0.00 0.00 0.00 3.62
167 168 0.872388 GTCCCACAATCCACACGAAC 59.128 55.000 0.00 0.00 0.00 3.95
168 169 0.762418 AGTCCCACAATCCACACGAA 59.238 50.000 0.00 0.00 0.00 3.85
169 170 1.634960 TAGTCCCACAATCCACACGA 58.365 50.000 0.00 0.00 0.00 4.35
170 171 2.465860 TTAGTCCCACAATCCACACG 57.534 50.000 0.00 0.00 0.00 4.49
171 172 3.119495 GCAATTAGTCCCACAATCCACAC 60.119 47.826 0.00 0.00 0.00 3.82
172 173 3.088532 GCAATTAGTCCCACAATCCACA 58.911 45.455 0.00 0.00 0.00 4.17
173 174 3.088532 TGCAATTAGTCCCACAATCCAC 58.911 45.455 0.00 0.00 0.00 4.02
174 175 3.448093 TGCAATTAGTCCCACAATCCA 57.552 42.857 0.00 0.00 0.00 3.41
175 176 4.220602 ACTTTGCAATTAGTCCCACAATCC 59.779 41.667 0.00 0.00 0.00 3.01
176 177 5.163513 CACTTTGCAATTAGTCCCACAATC 58.836 41.667 0.00 0.00 0.00 2.67
177 178 4.561326 GCACTTTGCAATTAGTCCCACAAT 60.561 41.667 0.00 0.00 44.26 2.71
178 179 3.243704 GCACTTTGCAATTAGTCCCACAA 60.244 43.478 0.00 0.00 44.26 3.33
179 180 2.295909 GCACTTTGCAATTAGTCCCACA 59.704 45.455 0.00 0.00 44.26 4.17
180 181 2.946564 GCACTTTGCAATTAGTCCCAC 58.053 47.619 0.00 0.00 44.26 4.61
192 193 7.962373 ACAAAAACTTTCTTAAATGCACTTTGC 59.038 29.630 0.00 0.00 45.29 3.68
193 194 9.824534 AACAAAAACTTTCTTAAATGCACTTTG 57.175 25.926 0.00 0.00 0.00 2.77
195 196 9.824534 CAAACAAAAACTTTCTTAAATGCACTT 57.175 25.926 0.00 0.00 0.00 3.16
196 197 9.213799 TCAAACAAAAACTTTCTTAAATGCACT 57.786 25.926 0.00 0.00 0.00 4.40
197 198 9.986833 ATCAAACAAAAACTTTCTTAAATGCAC 57.013 25.926 0.00 0.00 0.00 4.57
213 214 9.593134 ACACTGCTATTAAACAATCAAACAAAA 57.407 25.926 0.00 0.00 0.00 2.44
215 216 9.891828 CTACACTGCTATTAAACAATCAAACAA 57.108 29.630 0.00 0.00 0.00 2.83
216 217 9.278978 TCTACACTGCTATTAAACAATCAAACA 57.721 29.630 0.00 0.00 0.00 2.83
219 220 8.892723 CCATCTACACTGCTATTAAACAATCAA 58.107 33.333 0.00 0.00 0.00 2.57
220 221 8.264347 TCCATCTACACTGCTATTAAACAATCA 58.736 33.333 0.00 0.00 0.00 2.57
221 222 8.662781 TCCATCTACACTGCTATTAAACAATC 57.337 34.615 0.00 0.00 0.00 2.67
223 224 9.764363 CTATCCATCTACACTGCTATTAAACAA 57.236 33.333 0.00 0.00 0.00 2.83
224 225 8.367911 CCTATCCATCTACACTGCTATTAAACA 58.632 37.037 0.00 0.00 0.00 2.83
225 226 7.819900 CCCTATCCATCTACACTGCTATTAAAC 59.180 40.741 0.00 0.00 0.00 2.01
226 227 7.733047 TCCCTATCCATCTACACTGCTATTAAA 59.267 37.037 0.00 0.00 0.00 1.52
227 228 7.246027 TCCCTATCCATCTACACTGCTATTAA 58.754 38.462 0.00 0.00 0.00 1.40
228 229 6.800890 TCCCTATCCATCTACACTGCTATTA 58.199 40.000 0.00 0.00 0.00 0.98
229 230 5.655394 TCCCTATCCATCTACACTGCTATT 58.345 41.667 0.00 0.00 0.00 1.73
230 231 5.222442 ACTCCCTATCCATCTACACTGCTAT 60.222 44.000 0.00 0.00 0.00 2.97
231 232 4.106502 ACTCCCTATCCATCTACACTGCTA 59.893 45.833 0.00 0.00 0.00 3.49
232 233 3.116939 ACTCCCTATCCATCTACACTGCT 60.117 47.826 0.00 0.00 0.00 4.24
233 234 3.235200 ACTCCCTATCCATCTACACTGC 58.765 50.000 0.00 0.00 0.00 4.40
234 235 5.636123 AGTACTCCCTATCCATCTACACTG 58.364 45.833 0.00 0.00 0.00 3.66
235 236 5.933846 AGTACTCCCTATCCATCTACACT 57.066 43.478 0.00 0.00 0.00 3.55
236 237 6.540995 TGTAGTACTCCCTATCCATCTACAC 58.459 44.000 0.00 0.00 33.96 2.90
237 238 6.775234 TGTAGTACTCCCTATCCATCTACA 57.225 41.667 0.00 0.00 35.66 2.74
238 239 7.635648 AGATGTAGTACTCCCTATCCATCTAC 58.364 42.308 0.00 0.00 32.91 2.59
239 240 7.832473 AGATGTAGTACTCCCTATCCATCTA 57.168 40.000 0.00 0.00 32.91 1.98
240 241 6.728366 AGATGTAGTACTCCCTATCCATCT 57.272 41.667 0.00 3.93 31.22 2.90
241 242 7.784470 AAAGATGTAGTACTCCCTATCCATC 57.216 40.000 0.00 1.75 0.00 3.51
242 243 7.473511 GCAAAAGATGTAGTACTCCCTATCCAT 60.474 40.741 0.00 0.00 0.00 3.41
243 244 6.183360 GCAAAAGATGTAGTACTCCCTATCCA 60.183 42.308 0.00 0.00 0.00 3.41
244 245 6.183360 TGCAAAAGATGTAGTACTCCCTATCC 60.183 42.308 0.00 0.00 0.00 2.59
245 246 6.817184 TGCAAAAGATGTAGTACTCCCTATC 58.183 40.000 0.00 0.00 0.00 2.08
246 247 6.808321 TGCAAAAGATGTAGTACTCCCTAT 57.192 37.500 0.00 0.00 0.00 2.57
247 248 6.614694 TTGCAAAAGATGTAGTACTCCCTA 57.385 37.500 0.00 0.00 0.00 3.53
248 249 5.499004 TTGCAAAAGATGTAGTACTCCCT 57.501 39.130 0.00 0.00 0.00 4.20
249 250 5.648092 ACATTGCAAAAGATGTAGTACTCCC 59.352 40.000 1.71 0.00 34.88 4.30
250 251 6.743575 ACATTGCAAAAGATGTAGTACTCC 57.256 37.500 1.71 0.00 34.88 3.85
273 274 9.762933 GCAAGGGCAAAAATGAGAATTATTATA 57.237 29.630 0.00 0.00 40.72 0.98
337 338 4.020662 GTGAAACCAGGGATGCCATTTAAA 60.021 41.667 5.86 0.00 0.00 1.52
485 513 6.428083 TCTGTCCCAAAATAAGTGTAGTCA 57.572 37.500 0.00 0.00 0.00 3.41
486 514 5.875359 CCTCTGTCCCAAAATAAGTGTAGTC 59.125 44.000 0.00 0.00 0.00 2.59
506 534 9.220906 TGTGGTATTTAAATATGTACTCCCTCT 57.779 33.333 11.00 0.00 0.00 3.69
597 637 4.571580 TGGTTACGAAAATGTTCACGAACT 59.428 37.500 11.01 0.00 41.67 3.01
648 695 4.500477 GGCTCATTTTCATGCACGTATTTC 59.500 41.667 0.00 0.00 0.00 2.17
655 702 6.913873 AAAATATGGCTCATTTTCATGCAC 57.086 33.333 0.00 0.00 31.54 4.57
657 704 7.118680 CCCATAAAATATGGCTCATTTTCATGC 59.881 37.037 10.32 0.00 36.99 4.06
679 726 1.824852 GAAAACGAAATCCTGGCCCAT 59.175 47.619 0.00 0.00 0.00 4.00
753 800 6.985188 ACACGAAAGCTTATACATGTTCAT 57.015 33.333 2.30 0.00 0.00 2.57
843 916 4.519906 CTCCAGGGAGCCCTTTTATTTA 57.480 45.455 5.03 0.00 45.70 1.40
899 986 3.981071 TTGACCTGATGAACCCTAGTG 57.019 47.619 0.00 0.00 0.00 2.74
935 1024 3.036075 ACGAACCCTAGTACACTTTGC 57.964 47.619 0.00 0.00 0.00 3.68
1174 1296 0.460284 TCTCTTGAGCGAAATCGGCC 60.460 55.000 4.84 0.00 40.23 6.13
1194 1316 9.950496 TCTTAATTTCTGCTAAAAGATCAGAGT 57.050 29.630 0.00 0.00 38.02 3.24
1236 1358 8.312669 ACTAGCACTACTTAATTCCTCTCAAT 57.687 34.615 0.00 0.00 0.00 2.57
1240 1362 9.649316 AAGATACTAGCACTACTTAATTCCTCT 57.351 33.333 0.00 0.00 0.00 3.69
1256 1378 8.572185 TCATCAGAGACATACAAAGATACTAGC 58.428 37.037 0.00 0.00 0.00 3.42
1271 2519 5.703130 CACCTAGATACGATCATCAGAGACA 59.297 44.000 0.00 0.00 0.00 3.41
1272 2520 5.935206 TCACCTAGATACGATCATCAGAGAC 59.065 44.000 0.00 0.00 0.00 3.36
1314 2577 3.438905 TTCATCAGCAATCGCGCGC 62.439 57.895 27.95 23.91 45.49 6.86
1318 2581 1.267235 CGTCAGTTCATCAGCAATCGC 60.267 52.381 0.00 0.00 38.99 4.58
1362 2625 1.467734 CTTCACAGGCTGCACAAGATC 59.532 52.381 15.89 0.00 0.00 2.75
1465 2730 2.231235 TGCGAATCTCTAGTGAACAGCA 59.769 45.455 13.61 13.61 0.00 4.41
1475 2749 2.094700 ACGAAAGCACTGCGAATCTCTA 60.095 45.455 0.00 0.00 0.00 2.43
1483 2757 1.082756 GTTGGACGAAAGCACTGCG 60.083 57.895 0.00 0.00 0.00 5.18
1493 2767 4.637276 ACATCTTATGTTGTGTTGGACGA 58.363 39.130 0.00 0.00 41.63 4.20
1506 2785 8.826710 ACATATCGGTTGTAACAACATCTTATG 58.173 33.333 5.09 8.31 0.00 1.90
1517 2796 4.168014 TGTCGTCACATATCGGTTGTAAC 58.832 43.478 0.00 0.00 0.00 2.50
1531 2810 2.077627 TGCTACTCTCTCTGTCGTCAC 58.922 52.381 0.00 0.00 0.00 3.67
1539 2818 6.184068 TGTAATCTGTTCTGCTACTCTCTCT 58.816 40.000 0.00 0.00 0.00 3.10
1543 2822 5.358442 ACGATGTAATCTGTTCTGCTACTCT 59.642 40.000 0.00 0.00 42.58 3.24
1548 2827 5.720202 TGTTACGATGTAATCTGTTCTGCT 58.280 37.500 0.00 0.00 42.58 4.24
1565 2844 2.030457 GCGATGAAGGGACATTGTTACG 59.970 50.000 0.00 0.00 34.98 3.18
1566 2845 3.006940 TGCGATGAAGGGACATTGTTAC 58.993 45.455 0.00 0.00 34.98 2.50
1570 2849 1.452110 TGTGCGATGAAGGGACATTG 58.548 50.000 0.00 0.00 35.45 2.82
1575 2854 0.394216 CCCAATGTGCGATGAAGGGA 60.394 55.000 0.00 0.00 36.96 4.20
1599 2878 2.673368 GAGTGACAACCTAAATCAGCGG 59.327 50.000 0.00 0.00 0.00 5.52
1700 2985 1.066858 GCATCGTCTCCTTGTTCTCCA 60.067 52.381 0.00 0.00 0.00 3.86
1743 3028 0.392461 GGCGCCTCCTGTAAATGTCA 60.392 55.000 22.15 0.00 0.00 3.58
1804 3089 9.178427 GAATGTTGAAAGAACAGAAATTGAGAG 57.822 33.333 0.00 0.00 33.18 3.20
1807 3092 9.650539 TTTGAATGTTGAAAGAACAGAAATTGA 57.349 25.926 0.00 0.00 33.18 2.57
1821 3106 9.663904 CTTTTCGTCTTAGATTTGAATGTTGAA 57.336 29.630 0.00 0.00 0.00 2.69
1837 3122 3.026630 TCTGCGATGACTTTTCGTCTT 57.973 42.857 0.00 0.00 43.25 3.01
1838 3123 2.724977 TCTGCGATGACTTTTCGTCT 57.275 45.000 0.00 0.00 43.25 4.18
1842 3127 5.091431 CCATCTTTTCTGCGATGACTTTTC 58.909 41.667 0.00 0.00 39.43 2.29
1881 3166 0.667184 GGCGGCACCATTCAAAACAG 60.667 55.000 3.07 0.00 38.86 3.16
1888 3173 2.929398 CAAAATAAAGGCGGCACCATTC 59.071 45.455 13.08 0.00 43.14 2.67
1896 3181 3.743911 GGGAACAAACAAAATAAAGGCGG 59.256 43.478 0.00 0.00 0.00 6.13
1953 3238 0.681564 ACGTCCCTGCGAGAGAGATT 60.682 55.000 0.00 0.00 35.59 2.40
1954 3239 0.681564 AACGTCCCTGCGAGAGAGAT 60.682 55.000 0.00 0.00 35.59 2.75
1955 3240 1.303398 AACGTCCCTGCGAGAGAGA 60.303 57.895 0.00 0.00 35.59 3.10
1956 3241 1.137825 GAACGTCCCTGCGAGAGAG 59.862 63.158 0.00 0.00 35.59 3.20
2077 3366 7.922278 AGCATAATGAAACAACATTCGCAATAT 59.078 29.630 0.33 0.00 40.36 1.28
2080 3369 5.468592 AGCATAATGAAACAACATTCGCAA 58.531 33.333 0.33 0.00 40.36 4.85
2115 3406 6.128172 GCAAGATACCATACATTAGCATCACC 60.128 42.308 0.00 0.00 0.00 4.02
2192 3487 2.439960 TTCACCTCACCACTGCCGT 61.440 57.895 0.00 0.00 0.00 5.68
2193 3488 1.961277 GTTCACCTCACCACTGCCG 60.961 63.158 0.00 0.00 0.00 5.69
2201 3496 5.335661 GGTTTGATTGTATGGTTCACCTCAC 60.336 44.000 0.00 0.00 36.82 3.51
2202 3497 4.764823 GGTTTGATTGTATGGTTCACCTCA 59.235 41.667 0.00 0.00 36.82 3.86
2204 3499 4.086457 GGGTTTGATTGTATGGTTCACCT 58.914 43.478 0.00 0.00 36.82 4.00
2207 3502 4.396357 AGGGGTTTGATTGTATGGTTCA 57.604 40.909 0.00 0.00 0.00 3.18
2209 3504 5.151454 TCAAAGGGGTTTGATTGTATGGTT 58.849 37.500 0.00 0.00 36.15 3.67
2338 3646 7.119262 ACAGAGGTTATTCATTGGTAAACTTCG 59.881 37.037 3.06 0.00 33.05 3.79
2342 3650 7.882179 ACAACAGAGGTTATTCATTGGTAAAC 58.118 34.615 0.00 0.00 34.87 2.01
2531 3902 2.303022 CACACCTGACCTGGTCTAATGT 59.697 50.000 26.03 21.71 38.45 2.71
2710 4083 3.490890 GCAAAGAGGAAGCGCGAT 58.509 55.556 12.10 0.00 0.00 4.58
2725 4098 1.928653 CAAGACCGACGAAAACGCA 59.071 52.632 0.00 0.00 0.00 5.24
2760 4133 3.113514 TTGGAGCGACAGGCCAACA 62.114 57.895 5.01 0.00 45.17 3.33
2853 4226 6.087522 GCGCCACACTGTTTATAAAATGTTA 58.912 36.000 0.00 0.00 0.00 2.41
2855 4228 4.022762 TGCGCCACACTGTTTATAAAATGT 60.023 37.500 4.18 2.70 0.00 2.71
2856 4229 4.480541 TGCGCCACACTGTTTATAAAATG 58.519 39.130 4.18 2.09 0.00 2.32
2857 4230 4.775058 TGCGCCACACTGTTTATAAAAT 57.225 36.364 4.18 0.00 0.00 1.82
2884 4257 4.271776 CCTTTATTCTAAACCCTAACCGCG 59.728 45.833 0.00 0.00 0.00 6.46
2943 4316 3.993081 CTGACTTCCAAACTACAGCAGAG 59.007 47.826 0.00 0.00 0.00 3.35
3012 4385 2.230664 AGGTCTTTGCCACCTGACA 58.769 52.632 0.00 0.00 43.10 3.58
3082 4456 6.583050 GTGCCAAGCATAAAAACGTTACAATA 59.417 34.615 0.00 0.00 41.91 1.90
3084 4458 4.740695 GTGCCAAGCATAAAAACGTTACAA 59.259 37.500 0.00 0.00 41.91 2.41
3085 4459 4.291783 GTGCCAAGCATAAAAACGTTACA 58.708 39.130 0.00 0.00 41.91 2.41
3098 4472 1.211949 GACTTATAGGGGTGCCAAGCA 59.788 52.381 0.00 0.00 35.60 3.91
3153 4532 5.047590 TCAGAGATGCAGGTACGTCTTAAAA 60.048 40.000 0.00 0.00 36.04 1.52


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

AutoCloner maintained by Alex Coulton.