Multiple sequence alignment - TraesCS7B01G393600

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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 TraesCS7B01G393600 chr7B 100.000 1840 0 0 1 1840 660343340 660341501 0.000000e+00 3398
1 TraesCS7B01G393600 chr7B 100.000 475 0 0 2083 2557 660341258 660340784 0.000000e+00 878
2 TraesCS7B01G393600 chr7B 96.429 196 6 1 1 196 660351537 660351343 3.170000e-84 322
3 TraesCS7B01G393600 chr7B 95.408 196 8 1 1 196 699949865 699950059 6.870000e-81 311
4 TraesCS7B01G393600 chr7D 88.049 979 58 35 869 1840 588040809 588039883 0.000000e+00 1105
5 TraesCS7B01G393600 chr7D 87.662 308 23 8 2083 2378 588039867 588039563 6.770000e-91 344
6 TraesCS7B01G393600 chr7A 86.974 998 70 23 869 1833 679900082 679899112 0.000000e+00 1068
7 TraesCS7B01G393600 chr7A 84.129 649 71 17 198 832 679901674 679901044 1.310000e-167 599
8 TraesCS7B01G393600 chr7A 87.318 481 39 8 2090 2557 679899081 679898610 4.840000e-147 531
9 TraesCS7B01G393600 chr6B 95.918 196 6 2 1 196 514630629 514630436 1.480000e-82 316
10 TraesCS7B01G393600 chr3B 95.918 196 6 2 1 196 810204775 810204582 1.480000e-82 316
11 TraesCS7B01G393600 chr3B 94.554 202 8 3 1 202 492603910 492604108 2.470000e-80 309
12 TraesCS7B01G393600 chr4B 95.431 197 7 2 1 197 510857080 510857274 1.910000e-81 313
13 TraesCS7B01G393600 chr2B 95.431 197 7 2 1 197 682215698 682215892 1.910000e-81 313
14 TraesCS7B01G393600 chr5B 95.408 196 7 2 1 196 141931948 141931755 6.870000e-81 311
15 TraesCS7B01G393600 chr1B 95.408 196 7 2 1 196 606350577 606350384 6.870000e-81 311


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 TraesCS7B01G393600 chr7B 660340784 660343340 2556 True 2138.000000 3398 100.000000 1 2557 2 chr7B.!!$R2 2556
1 TraesCS7B01G393600 chr7D 588039563 588040809 1246 True 724.500000 1105 87.855500 869 2378 2 chr7D.!!$R1 1509
2 TraesCS7B01G393600 chr7A 679898610 679901674 3064 True 732.666667 1068 86.140333 198 2557 3 chr7A.!!$R1 2359

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
969 1916 0.109913 AACGTCCCCCACTTTTCCTC 59.89 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2765 1.202348 GGCACACTAAATCCCAAGCAC 59.798 52.381 0.0 0.0 0.0 4.4 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
29 30 7.719778 TCTTGCTATGACATAGTTGCTTATG 57.280 36.000 20.91 6.29 37.13 1.90
30 31 7.275183 TCTTGCTATGACATAGTTGCTTATGT 58.725 34.615 20.91 8.25 44.68 2.29
31 32 7.770433 TCTTGCTATGACATAGTTGCTTATGTT 59.230 33.333 20.91 0.79 42.68 2.71
32 33 7.250445 TGCTATGACATAGTTGCTTATGTTG 57.750 36.000 20.91 0.00 42.68 3.33
33 34 6.138761 GCTATGACATAGTTGCTTATGTTGC 58.861 40.000 20.91 2.28 42.68 4.17
34 35 6.017605 GCTATGACATAGTTGCTTATGTTGCT 60.018 38.462 20.91 3.14 42.68 3.91
35 36 6.764308 ATGACATAGTTGCTTATGTTGCTT 57.236 33.333 9.41 0.00 42.68 3.91
36 37 7.864108 ATGACATAGTTGCTTATGTTGCTTA 57.136 32.000 9.41 0.00 42.68 3.09
37 38 7.307493 TGACATAGTTGCTTATGTTGCTTAG 57.693 36.000 9.41 0.00 42.68 2.18
38 39 6.124088 ACATAGTTGCTTATGTTGCTTAGC 57.876 37.500 0.00 0.00 40.44 3.09
39 40 5.647658 ACATAGTTGCTTATGTTGCTTAGCA 59.352 36.000 1.39 1.39 40.44 3.49
40 41 6.319658 ACATAGTTGCTTATGTTGCTTAGCAT 59.680 34.615 8.05 0.00 40.44 3.79
41 42 7.498900 ACATAGTTGCTTATGTTGCTTAGCATA 59.501 33.333 8.05 0.38 40.44 3.14
42 43 6.949352 AGTTGCTTATGTTGCTTAGCATAT 57.051 33.333 8.05 8.62 42.60 1.78
43 44 6.732154 AGTTGCTTATGTTGCTTAGCATATG 58.268 36.000 8.05 0.00 42.60 1.78
44 45 6.319658 AGTTGCTTATGTTGCTTAGCATATGT 59.680 34.615 8.05 0.00 42.60 2.29
45 46 6.698008 TGCTTATGTTGCTTAGCATATGTT 57.302 33.333 8.05 0.08 38.61 2.71
46 47 6.497437 TGCTTATGTTGCTTAGCATATGTTG 58.503 36.000 8.05 0.00 38.61 3.33
47 48 6.095300 TGCTTATGTTGCTTAGCATATGTTGT 59.905 34.615 8.05 0.00 38.61 3.32
48 49 6.974622 GCTTATGTTGCTTAGCATATGTTGTT 59.025 34.615 8.05 0.00 38.76 2.83
49 50 7.043854 GCTTATGTTGCTTAGCATATGTTGTTG 60.044 37.037 8.05 0.00 38.76 3.33
50 51 5.058149 TGTTGCTTAGCATATGTTGTTGG 57.942 39.130 8.05 0.00 38.76 3.77
51 52 4.522405 TGTTGCTTAGCATATGTTGTTGGT 59.478 37.500 8.05 0.00 38.76 3.67
52 53 4.700268 TGCTTAGCATATGTTGTTGGTG 57.300 40.909 1.39 0.00 31.71 4.17
53 54 3.119531 TGCTTAGCATATGTTGTTGGTGC 60.120 43.478 1.39 0.00 31.71 5.01
54 55 3.119531 GCTTAGCATATGTTGTTGGTGCA 60.120 43.478 4.29 0.00 38.23 4.57
55 56 4.414852 CTTAGCATATGTTGTTGGTGCAC 58.585 43.478 8.80 8.80 38.23 4.57
56 57 2.237643 AGCATATGTTGTTGGTGCACA 58.762 42.857 20.43 1.62 38.23 4.57
57 58 2.827322 AGCATATGTTGTTGGTGCACAT 59.173 40.909 20.43 3.97 38.23 3.21
58 59 4.015764 AGCATATGTTGTTGGTGCACATA 58.984 39.130 20.43 6.28 38.23 2.29
59 60 4.096833 AGCATATGTTGTTGGTGCACATAG 59.903 41.667 20.43 2.17 38.23 2.23
60 61 4.734402 GCATATGTTGTTGGTGCACATAGG 60.734 45.833 20.43 8.68 35.93 2.57
61 62 2.356665 TGTTGTTGGTGCACATAGGT 57.643 45.000 20.43 0.00 0.00 3.08
80 81 4.918588 AGGTGAACCTAATTGTTGTAGGG 58.081 43.478 0.00 0.00 46.48 3.53
81 82 4.352893 AGGTGAACCTAATTGTTGTAGGGT 59.647 41.667 0.00 0.00 46.48 4.34
82 83 5.074804 GGTGAACCTAATTGTTGTAGGGTT 58.925 41.667 2.73 0.00 38.85 4.11
83 84 5.537295 GGTGAACCTAATTGTTGTAGGGTTT 59.463 40.000 2.73 0.00 38.85 3.27
84 85 6.041182 GGTGAACCTAATTGTTGTAGGGTTTT 59.959 38.462 2.73 0.00 38.85 2.43
85 86 6.921307 GTGAACCTAATTGTTGTAGGGTTTTG 59.079 38.462 2.73 0.00 38.85 2.44
86 87 6.608002 TGAACCTAATTGTTGTAGGGTTTTGT 59.392 34.615 2.73 0.00 38.85 2.83
87 88 6.399639 ACCTAATTGTTGTAGGGTTTTGTG 57.600 37.500 2.73 0.00 42.23 3.33
88 89 5.221362 ACCTAATTGTTGTAGGGTTTTGTGC 60.221 40.000 2.73 0.00 42.23 4.57
89 90 5.010617 CCTAATTGTTGTAGGGTTTTGTGCT 59.989 40.000 0.00 0.00 35.41 4.40
90 91 5.351948 AATTGTTGTAGGGTTTTGTGCTT 57.648 34.783 0.00 0.00 0.00 3.91
91 92 3.791973 TGTTGTAGGGTTTTGTGCTTG 57.208 42.857 0.00 0.00 0.00 4.01
92 93 3.357203 TGTTGTAGGGTTTTGTGCTTGA 58.643 40.909 0.00 0.00 0.00 3.02
93 94 3.129638 TGTTGTAGGGTTTTGTGCTTGAC 59.870 43.478 0.00 0.00 0.00 3.18
94 95 3.006112 TGTAGGGTTTTGTGCTTGACA 57.994 42.857 0.00 0.00 0.00 3.58
95 96 3.357203 TGTAGGGTTTTGTGCTTGACAA 58.643 40.909 0.00 0.00 43.11 3.18
104 105 4.640789 TTGTGCTTGACAAATTAACCGT 57.359 36.364 0.00 0.00 41.80 4.83
105 106 4.640789 TGTGCTTGACAAATTAACCGTT 57.359 36.364 0.00 0.00 0.00 4.44
106 107 5.752892 TGTGCTTGACAAATTAACCGTTA 57.247 34.783 0.00 0.00 0.00 3.18
107 108 5.753744 TGTGCTTGACAAATTAACCGTTAG 58.246 37.500 0.00 0.00 0.00 2.34
108 109 5.151389 GTGCTTGACAAATTAACCGTTAGG 58.849 41.667 0.00 0.00 45.13 2.69
122 123 4.625972 CCGTTAGGTTTATTCCGCATTT 57.374 40.909 0.00 0.00 0.00 2.32
123 124 4.347813 CCGTTAGGTTTATTCCGCATTTG 58.652 43.478 0.00 0.00 0.00 2.32
124 125 4.142556 CCGTTAGGTTTATTCCGCATTTGT 60.143 41.667 0.00 0.00 0.00 2.83
125 126 5.395642 CGTTAGGTTTATTCCGCATTTGTT 58.604 37.500 0.00 0.00 0.00 2.83
126 127 5.510323 CGTTAGGTTTATTCCGCATTTGTTC 59.490 40.000 0.00 0.00 0.00 3.18
127 128 6.383415 GTTAGGTTTATTCCGCATTTGTTCA 58.617 36.000 0.00 0.00 0.00 3.18
128 129 5.461032 AGGTTTATTCCGCATTTGTTCAA 57.539 34.783 0.00 0.00 0.00 2.69
129 130 5.469479 AGGTTTATTCCGCATTTGTTCAAG 58.531 37.500 0.00 0.00 0.00 3.02
130 131 4.091365 GGTTTATTCCGCATTTGTTCAAGC 59.909 41.667 0.00 0.00 0.00 4.01
131 132 2.368655 ATTCCGCATTTGTTCAAGCC 57.631 45.000 0.00 0.00 0.00 4.35
132 133 1.327303 TTCCGCATTTGTTCAAGCCT 58.673 45.000 0.00 0.00 0.00 4.58
133 134 0.881118 TCCGCATTTGTTCAAGCCTC 59.119 50.000 0.00 0.00 0.00 4.70
134 135 0.883833 CCGCATTTGTTCAAGCCTCT 59.116 50.000 0.00 0.00 0.00 3.69
135 136 2.083774 CCGCATTTGTTCAAGCCTCTA 58.916 47.619 0.00 0.00 0.00 2.43
136 137 2.159517 CCGCATTTGTTCAAGCCTCTAC 60.160 50.000 0.00 0.00 0.00 2.59
137 138 2.159517 CGCATTTGTTCAAGCCTCTACC 60.160 50.000 0.00 0.00 0.00 3.18
138 139 2.159517 GCATTTGTTCAAGCCTCTACCG 60.160 50.000 0.00 0.00 0.00 4.02
139 140 1.519408 TTTGTTCAAGCCTCTACCGC 58.481 50.000 0.00 0.00 0.00 5.68
140 141 0.394938 TTGTTCAAGCCTCTACCGCA 59.605 50.000 0.00 0.00 0.00 5.69
141 142 0.394938 TGTTCAAGCCTCTACCGCAA 59.605 50.000 0.00 0.00 0.00 4.85
142 143 1.003118 TGTTCAAGCCTCTACCGCAAT 59.997 47.619 0.00 0.00 0.00 3.56
143 144 2.084546 GTTCAAGCCTCTACCGCAATT 58.915 47.619 0.00 0.00 0.00 2.32
144 145 3.267483 GTTCAAGCCTCTACCGCAATTA 58.733 45.455 0.00 0.00 0.00 1.40
145 146 3.838244 TCAAGCCTCTACCGCAATTAT 57.162 42.857 0.00 0.00 0.00 1.28
146 147 4.150897 TCAAGCCTCTACCGCAATTATT 57.849 40.909 0.00 0.00 0.00 1.40
147 148 4.523083 TCAAGCCTCTACCGCAATTATTT 58.477 39.130 0.00 0.00 0.00 1.40
148 149 4.947388 TCAAGCCTCTACCGCAATTATTTT 59.053 37.500 0.00 0.00 0.00 1.82
149 150 5.417580 TCAAGCCTCTACCGCAATTATTTTT 59.582 36.000 0.00 0.00 0.00 1.94
150 151 6.600032 TCAAGCCTCTACCGCAATTATTTTTA 59.400 34.615 0.00 0.00 0.00 1.52
151 152 7.121463 TCAAGCCTCTACCGCAATTATTTTTAA 59.879 33.333 0.00 0.00 0.00 1.52
152 153 7.399245 AGCCTCTACCGCAATTATTTTTAAA 57.601 32.000 0.00 0.00 0.00 1.52
153 154 7.832769 AGCCTCTACCGCAATTATTTTTAAAA 58.167 30.769 0.00 0.00 0.00 1.52
154 155 7.758076 AGCCTCTACCGCAATTATTTTTAAAAC 59.242 33.333 0.00 0.00 0.00 2.43
155 156 7.253519 GCCTCTACCGCAATTATTTTTAAAACG 60.254 37.037 0.00 0.00 0.00 3.60
156 157 7.253519 CCTCTACCGCAATTATTTTTAAAACGC 60.254 37.037 0.00 0.00 0.00 4.84
157 158 5.518529 ACCGCAATTATTTTTAAAACGCC 57.481 34.783 0.00 0.00 0.00 5.68
158 159 5.231702 ACCGCAATTATTTTTAAAACGCCT 58.768 33.333 0.00 0.00 0.00 5.52
159 160 6.388278 ACCGCAATTATTTTTAAAACGCCTA 58.612 32.000 0.00 0.00 0.00 3.93
160 161 7.036829 ACCGCAATTATTTTTAAAACGCCTAT 58.963 30.769 0.00 0.00 0.00 2.57
161 162 7.546316 ACCGCAATTATTTTTAAAACGCCTATT 59.454 29.630 0.00 0.00 0.00 1.73
162 163 8.053653 CCGCAATTATTTTTAAAACGCCTATTC 58.946 33.333 0.00 0.00 0.00 1.75
163 164 8.587950 CGCAATTATTTTTAAAACGCCTATTCA 58.412 29.630 0.00 0.00 0.00 2.57
164 165 9.683651 GCAATTATTTTTAAAACGCCTATTCAC 57.316 29.630 0.00 0.00 0.00 3.18
166 167 8.936070 ATTATTTTTAAAACGCCTATTCACCC 57.064 30.769 0.00 0.00 0.00 4.61
167 168 4.787260 TTTTAAAACGCCTATTCACCCC 57.213 40.909 0.00 0.00 0.00 4.95
168 169 2.423446 TAAAACGCCTATTCACCCCC 57.577 50.000 0.00 0.00 0.00 5.40
183 184 3.460995 CCCCCTCTAGGCGACATC 58.539 66.667 0.00 0.00 0.00 3.06
184 185 2.210711 CCCCCTCTAGGCGACATCC 61.211 68.421 0.00 0.00 0.00 3.51
185 186 1.457643 CCCCTCTAGGCGACATCCA 60.458 63.158 0.00 0.00 0.00 3.41
186 187 1.742768 CCCTCTAGGCGACATCCAC 59.257 63.158 0.00 0.00 0.00 4.02
187 188 1.360551 CCTCTAGGCGACATCCACG 59.639 63.158 0.00 0.00 0.00 4.94
188 189 1.101635 CCTCTAGGCGACATCCACGA 61.102 60.000 0.00 0.00 0.00 4.35
189 190 0.955178 CTCTAGGCGACATCCACGAT 59.045 55.000 0.00 0.00 0.00 3.73
190 191 0.952280 TCTAGGCGACATCCACGATC 59.048 55.000 0.00 0.00 0.00 3.69
191 192 0.955178 CTAGGCGACATCCACGATCT 59.045 55.000 0.00 0.00 0.00 2.75
192 193 1.338337 CTAGGCGACATCCACGATCTT 59.662 52.381 0.00 0.00 0.00 2.40
193 194 0.537188 AGGCGACATCCACGATCTTT 59.463 50.000 0.00 0.00 0.00 2.52
194 195 0.931005 GGCGACATCCACGATCTTTC 59.069 55.000 0.00 0.00 0.00 2.62
195 196 1.640428 GCGACATCCACGATCTTTCA 58.360 50.000 0.00 0.00 0.00 2.69
196 197 1.324736 GCGACATCCACGATCTTTCAC 59.675 52.381 0.00 0.00 0.00 3.18
197 198 1.927174 CGACATCCACGATCTTTCACC 59.073 52.381 0.00 0.00 0.00 4.02
198 199 2.417379 CGACATCCACGATCTTTCACCT 60.417 50.000 0.00 0.00 0.00 4.00
199 200 3.181490 CGACATCCACGATCTTTCACCTA 60.181 47.826 0.00 0.00 0.00 3.08
200 201 4.676986 CGACATCCACGATCTTTCACCTAA 60.677 45.833 0.00 0.00 0.00 2.69
201 202 4.504858 ACATCCACGATCTTTCACCTAAC 58.495 43.478 0.00 0.00 0.00 2.34
202 203 4.223032 ACATCCACGATCTTTCACCTAACT 59.777 41.667 0.00 0.00 0.00 2.24
203 204 4.884668 TCCACGATCTTTCACCTAACTT 57.115 40.909 0.00 0.00 0.00 2.66
204 205 4.817517 TCCACGATCTTTCACCTAACTTC 58.182 43.478 0.00 0.00 0.00 3.01
205 206 4.282449 TCCACGATCTTTCACCTAACTTCA 59.718 41.667 0.00 0.00 0.00 3.02
219 220 1.800805 ACTTCATGGAGACTTGTGCG 58.199 50.000 8.39 0.00 36.87 5.34
220 221 1.081892 CTTCATGGAGACTTGTGCGG 58.918 55.000 0.00 0.00 36.87 5.69
224 225 1.197721 CATGGAGACTTGTGCGGAAAC 59.802 52.381 0.00 0.00 0.00 2.78
227 228 0.232303 GAGACTTGTGCGGAAACACG 59.768 55.000 0.00 0.00 43.74 4.49
244 245 7.570507 CGGAAACACGACAATCTGAATTCTTAA 60.571 37.037 7.05 0.00 35.47 1.85
285 288 4.834357 TGTGTTGATGATTGTCACAAGG 57.166 40.909 0.00 0.00 36.34 3.61
293 296 1.686052 GATTGTCACAAGGCCCAAACA 59.314 47.619 0.00 0.00 0.00 2.83
299 302 1.067916 CAAGGCCCAAACAGTGCAC 59.932 57.895 9.40 9.40 0.00 4.57
305 308 1.885887 GCCCAAACAGTGCACAAGATA 59.114 47.619 21.04 0.00 0.00 1.98
314 317 6.005583 ACAGTGCACAAGATATCAAAACAG 57.994 37.500 21.04 0.00 0.00 3.16
315 318 5.048504 ACAGTGCACAAGATATCAAAACAGG 60.049 40.000 21.04 0.00 0.00 4.00
317 320 3.193267 TGCACAAGATATCAAAACAGGCC 59.807 43.478 5.32 0.00 0.00 5.19
318 321 3.445096 GCACAAGATATCAAAACAGGCCT 59.555 43.478 0.00 0.00 0.00 5.19
361 364 3.058520 CGCGCAATGACAATTCTTCAAAG 59.941 43.478 8.75 0.00 0.00 2.77
369 372 4.343814 TGACAATTCTTCAAAGGTTTCCCC 59.656 41.667 0.00 0.00 0.00 4.81
389 392 3.433598 CCCTTGTTATCATGATCCGGTGT 60.434 47.826 12.53 0.00 0.00 4.16
401 404 1.717194 TCCGGTGTGCGTTTAGAATC 58.283 50.000 0.00 0.00 0.00 2.52
406 409 4.283678 CGGTGTGCGTTTAGAATCAAAAA 58.716 39.130 0.00 0.00 0.00 1.94
480 492 9.727627 CAATACTTATTCTGGAAAAGCTTCATC 57.272 33.333 0.00 1.09 32.75 2.92
486 498 4.186926 TCTGGAAAAGCTTCATCTCATCG 58.813 43.478 0.00 0.00 32.75 3.84
495 507 0.670706 TCATCTCATCGGGAAGAGCG 59.329 55.000 0.00 0.00 0.00 5.03
503 515 0.175760 TCGGGAAGAGCGATTTGAGG 59.824 55.000 0.00 0.00 0.00 3.86
528 540 7.576236 GGAACCATCATTCTACATATTTGTCG 58.424 38.462 0.00 0.00 37.28 4.35
585 597 4.713792 AGTTTCCAAAGTCCAGACAGAT 57.286 40.909 0.00 0.00 0.00 2.90
713 727 6.018669 GTCCATCACTTTATCTCGCCTAAAAG 60.019 42.308 0.00 0.00 35.54 2.27
714 728 5.817816 CCATCACTTTATCTCGCCTAAAAGT 59.182 40.000 0.00 0.00 41.56 2.66
719 733 7.015877 CACTTTATCTCGCCTAAAAGTTCAAC 58.984 38.462 0.00 0.00 39.50 3.18
731 745 7.441458 GCCTAAAAGTTCAACGTCTCCATATAT 59.559 37.037 0.00 0.00 0.00 0.86
782 797 1.495951 CGGCAAAGTAACGCCTGAC 59.504 57.895 0.00 0.00 46.62 3.51
794 809 1.374758 GCCTGACAAGTGGGTCTCG 60.375 63.158 0.00 0.00 38.61 4.04
796 811 1.668294 CTGACAAGTGGGTCTCGCT 59.332 57.895 0.00 0.00 38.61 4.93
802 817 1.053424 AAGTGGGTCTCGCTGGTTAA 58.947 50.000 0.00 0.00 36.17 2.01
809 824 3.119955 GGGTCTCGCTGGTTAATTTTGAC 60.120 47.826 0.00 0.00 0.00 3.18
811 826 4.156008 GGTCTCGCTGGTTAATTTTGACAT 59.844 41.667 0.00 0.00 0.00 3.06
815 830 4.517075 TCGCTGGTTAATTTTGACATCACA 59.483 37.500 0.00 0.00 0.00 3.58
819 834 6.401367 GCTGGTTAATTTTGACATCACAATGC 60.401 38.462 0.00 0.00 36.26 3.56
828 843 4.600032 TGACATCACAATGCGATATTTGC 58.400 39.130 0.00 0.00 36.26 3.68
832 847 2.031560 TCACAATGCGATATTTGCGGTC 59.968 45.455 0.00 0.00 34.24 4.79
833 848 2.032054 CACAATGCGATATTTGCGGTCT 59.968 45.455 0.00 0.00 34.24 3.85
834 849 2.682856 ACAATGCGATATTTGCGGTCTT 59.317 40.909 0.00 0.00 34.24 3.01
835 850 3.038017 CAATGCGATATTTGCGGTCTTG 58.962 45.455 0.00 0.00 34.24 3.02
836 851 1.732941 TGCGATATTTGCGGTCTTGT 58.267 45.000 0.00 0.00 34.24 3.16
837 852 1.663643 TGCGATATTTGCGGTCTTGTC 59.336 47.619 0.00 0.00 34.24 3.18
838 853 1.003866 GCGATATTTGCGGTCTTGTCC 60.004 52.381 0.00 0.00 0.00 4.02
839 854 1.597663 CGATATTTGCGGTCTTGTCCC 59.402 52.381 0.00 0.00 0.00 4.46
840 855 2.639065 GATATTTGCGGTCTTGTCCCA 58.361 47.619 0.00 0.00 0.00 4.37
841 856 2.799126 TATTTGCGGTCTTGTCCCAT 57.201 45.000 0.00 0.00 0.00 4.00
842 857 2.799126 ATTTGCGGTCTTGTCCCATA 57.201 45.000 0.00 0.00 0.00 2.74
843 858 2.570415 TTTGCGGTCTTGTCCCATAA 57.430 45.000 0.00 0.00 0.00 1.90
844 859 2.799126 TTGCGGTCTTGTCCCATAAT 57.201 45.000 0.00 0.00 0.00 1.28
845 860 2.036958 TGCGGTCTTGTCCCATAATG 57.963 50.000 0.00 0.00 0.00 1.90
846 861 0.663153 GCGGTCTTGTCCCATAATGC 59.337 55.000 0.00 0.00 0.00 3.56
847 862 2.016604 GCGGTCTTGTCCCATAATGCA 61.017 52.381 0.00 0.00 0.00 3.96
848 863 2.364632 CGGTCTTGTCCCATAATGCAA 58.635 47.619 0.00 0.00 0.00 4.08
849 864 2.355756 CGGTCTTGTCCCATAATGCAAG 59.644 50.000 0.00 0.00 39.52 4.01
850 865 3.620488 GGTCTTGTCCCATAATGCAAGA 58.380 45.455 0.00 0.00 43.16 3.02
852 867 3.620488 TCTTGTCCCATAATGCAAGACC 58.380 45.455 0.00 0.00 41.33 3.85
853 868 3.266772 TCTTGTCCCATAATGCAAGACCT 59.733 43.478 0.00 0.00 41.33 3.85
854 869 4.473196 TCTTGTCCCATAATGCAAGACCTA 59.527 41.667 0.00 0.00 41.33 3.08
856 871 4.523083 TGTCCCATAATGCAAGACCTAAC 58.477 43.478 0.00 0.00 0.00 2.34
866 1224 7.944729 AATGCAAGACCTAACTCAAATATGT 57.055 32.000 0.00 0.00 0.00 2.29
867 1225 6.741992 TGCAAGACCTAACTCAAATATGTG 57.258 37.500 0.00 0.00 0.00 3.21
892 1833 5.685520 TTTTTGCCAGTCCCTAAAGTTTT 57.314 34.783 0.00 0.00 0.00 2.43
911 1852 3.859411 TTGGGTTATGTGAAATTCGCC 57.141 42.857 3.93 0.00 0.00 5.54
923 1870 5.064198 TGTGAAATTCGCCCTCGTAAATAAG 59.936 40.000 3.93 0.00 36.96 1.73
925 1872 5.292589 TGAAATTCGCCCTCGTAAATAAGAC 59.707 40.000 0.00 0.00 36.96 3.01
939 1886 2.614829 TAAGACGATAAGCAAGGGGC 57.385 50.000 0.00 0.00 45.30 5.80
965 1912 3.120796 GGAAACGTCCCCCACTTTT 57.879 52.632 0.00 0.00 38.08 2.27
966 1913 0.956633 GGAAACGTCCCCCACTTTTC 59.043 55.000 0.00 0.00 40.80 2.29
967 1914 0.956633 GAAACGTCCCCCACTTTTCC 59.043 55.000 0.00 0.00 37.31 3.13
968 1915 0.554305 AAACGTCCCCCACTTTTCCT 59.446 50.000 0.00 0.00 0.00 3.36
969 1916 0.109913 AACGTCCCCCACTTTTCCTC 59.890 55.000 0.00 0.00 0.00 3.71
970 1917 0.767060 ACGTCCCCCACTTTTCCTCT 60.767 55.000 0.00 0.00 0.00 3.69
999 1946 4.083862 GCGGCCTCTTCCTTCCGT 62.084 66.667 0.00 0.00 43.45 4.69
1000 1947 2.663196 CGGCCTCTTCCTTCCGTT 59.337 61.111 0.00 0.00 37.33 4.44
1001 1948 1.448013 CGGCCTCTTCCTTCCGTTC 60.448 63.158 0.00 0.00 37.33 3.95
1002 1949 1.078356 GGCCTCTTCCTTCCGTTCC 60.078 63.158 0.00 0.00 0.00 3.62
1003 1950 1.448013 GCCTCTTCCTTCCGTTCCG 60.448 63.158 0.00 0.00 0.00 4.30
1053 2000 0.895530 AGCCATCGGAGAACTTTCGA 59.104 50.000 0.00 0.00 43.58 3.71
1422 2370 5.408299 GCTTTTTGGGCGATTGAAGTTTTAT 59.592 36.000 0.00 0.00 0.00 1.40
1424 2372 3.502191 TGGGCGATTGAAGTTTTATGC 57.498 42.857 0.00 0.00 0.00 3.14
1433 2381 6.566564 CGATTGAAGTTTTATGCACTGACTGT 60.567 38.462 0.00 0.00 0.00 3.55
1436 2384 6.264832 TGAAGTTTTATGCACTGACTGTTTG 58.735 36.000 0.00 0.00 0.00 2.93
1441 2389 0.808125 TGCACTGACTGTTTGCGTTT 59.192 45.000 5.78 0.00 39.22 3.60
1448 2396 5.171337 CACTGACTGTTTGCGTTTGTTATTC 59.829 40.000 0.00 0.00 0.00 1.75
1488 2436 0.782384 GTAGTTCGTGCCGAGTGTTG 59.218 55.000 0.00 0.00 37.14 3.33
1523 2471 1.278985 TCCCTGTTGTCTGCTGTATGG 59.721 52.381 0.00 0.00 0.00 2.74
1524 2472 1.278985 CCCTGTTGTCTGCTGTATGGA 59.721 52.381 0.00 0.00 0.00 3.41
1568 2517 7.992180 AACTGTTGTGAGATTTTAGCTTTTG 57.008 32.000 0.00 0.00 0.00 2.44
1597 2552 3.016736 CCATGGGGTGTATGTTTCAGTC 58.983 50.000 2.85 0.00 0.00 3.51
1623 2578 5.640147 TCCAAGTGGGAACTATGATTTTGT 58.360 37.500 0.00 0.00 44.80 2.83
1635 2590 4.535526 ATGATTTTGTTGCTTGGTACCC 57.464 40.909 10.07 0.00 0.00 3.69
1643 2598 0.611618 TGCTTGGTACCCTGCCAATG 60.612 55.000 19.35 1.03 44.06 2.82
1664 2619 9.614792 CCAATGCTACCTTAGTTTACTATCTTT 57.385 33.333 0.00 0.00 0.00 2.52
1684 2657 5.580691 TCTTTGGTTACGAAGTGCATCTATG 59.419 40.000 0.00 0.00 45.73 2.23
1705 2678 8.923270 TCTATGGAAGTCTGGAAATTTTGTTTT 58.077 29.630 0.00 0.00 0.00 2.43
1725 2698 2.316108 TCCTGACAGTGTTGTGCTAGA 58.684 47.619 0.00 0.00 37.76 2.43
1727 2700 2.054363 CTGACAGTGTTGTGCTAGACG 58.946 52.381 0.00 0.00 37.76 4.18
1779 2755 0.323542 ATCGGTCGAGGAAGGAGTGT 60.324 55.000 0.00 0.00 0.00 3.55
1789 2765 4.006319 GAGGAAGGAGTGTGGAAATTGAG 58.994 47.826 0.00 0.00 0.00 3.02
2125 3101 8.848474 AGTCAAGTATAAATACACTGCAAAGT 57.152 30.769 3.13 0.00 35.74 2.66
2154 3130 6.583562 ACTCTGATTATAAGTGGTAGGTTGC 58.416 40.000 0.00 0.00 0.00 4.17
2205 3181 8.055279 CCGGATTGGTTAATGAGCATAATAAT 57.945 34.615 0.00 0.00 35.33 1.28
2228 3204 2.507407 TAGGTTCCTGTTTGGGCATC 57.493 50.000 1.12 0.00 36.20 3.91
2247 3227 3.650070 TCTGTTGCTGTGAGTGAGTAG 57.350 47.619 0.00 0.00 0.00 2.57
2322 3305 2.860136 GTTGTTCAGCAGCTTTTGGTTC 59.140 45.455 0.00 0.00 34.69 3.62
2328 3311 1.208642 GCAGCTTTTGGTTCGTGTGC 61.209 55.000 0.00 0.00 0.00 4.57
2329 3312 0.381801 CAGCTTTTGGTTCGTGTGCT 59.618 50.000 0.00 0.00 0.00 4.40
2369 3357 7.770897 AGAACTTTTTAGTCACATCTCAACTGT 59.229 33.333 0.00 0.00 0.00 3.55
2402 3390 2.303311 GTTGACCTAGGAGGCTGAGTTT 59.697 50.000 17.98 0.00 39.63 2.66
2415 3403 3.371285 GGCTGAGTTTACTTGAATCGGAC 59.629 47.826 0.00 0.00 0.00 4.79
2419 3407 4.182339 GAGTTTACTTGAATCGGACCCTC 58.818 47.826 0.00 0.00 0.00 4.30
2432 3420 2.965831 CGGACCCTCCTGAGAATTCATA 59.034 50.000 8.44 0.00 33.30 2.15
2444 3432 9.739276 TCCTGAGAATTCATATTTGTACTTGTT 57.261 29.630 8.44 0.00 31.68 2.83
2487 3476 8.910351 AGAGTTAAATTGTAGTTCAGCTTTCT 57.090 30.769 0.00 0.00 0.00 2.52
2490 3479 8.352942 AGTTAAATTGTAGTTCAGCTTTCTTGG 58.647 33.333 0.00 0.00 0.00 3.61
2532 3521 4.944619 TCCTGTAGGAACTATGCTGATG 57.055 45.455 0.00 0.00 45.60 3.07
2533 3522 3.070159 TCCTGTAGGAACTATGCTGATGC 59.930 47.826 0.00 0.00 45.60 3.91
2534 3523 3.181462 CCTGTAGGAACTATGCTGATGCA 60.181 47.826 0.00 0.00 45.60 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.428097 CATAAGCAACTATGTCATAGCAAGATA 57.572 33.333 18.12 8.26 36.30 1.98
6 7 7.488187 ACATAAGCAACTATGTCATAGCAAG 57.512 36.000 18.12 10.15 37.90 4.01
7 8 7.679400 GCAACATAAGCAACTATGTCATAGCAA 60.679 37.037 18.12 1.16 40.79 3.91
8 9 6.238456 GCAACATAAGCAACTATGTCATAGCA 60.238 38.462 18.12 0.00 40.79 3.49
9 10 6.017605 AGCAACATAAGCAACTATGTCATAGC 60.018 38.462 18.12 7.05 40.79 2.97
10 11 7.488187 AGCAACATAAGCAACTATGTCATAG 57.512 36.000 16.85 16.85 40.79 2.23
11 12 7.864108 AAGCAACATAAGCAACTATGTCATA 57.136 32.000 6.59 0.00 40.79 2.15
12 13 6.764308 AAGCAACATAAGCAACTATGTCAT 57.236 33.333 6.59 0.00 40.79 3.06
13 14 6.183360 GCTAAGCAACATAAGCAACTATGTCA 60.183 38.462 6.59 0.00 40.79 3.58
14 15 6.183360 TGCTAAGCAACATAAGCAACTATGTC 60.183 38.462 6.59 0.00 40.79 3.06
15 16 5.647658 TGCTAAGCAACATAAGCAACTATGT 59.352 36.000 0.00 1.47 42.95 2.29
16 17 6.122850 TGCTAAGCAACATAAGCAACTATG 57.877 37.500 0.00 0.00 41.74 2.23
23 24 6.498304 ACAACATATGCTAAGCAACATAAGC 58.502 36.000 1.58 0.00 43.62 3.09
24 25 7.433131 CCAACAACATATGCTAAGCAACATAAG 59.567 37.037 1.58 0.00 43.62 1.73
25 26 7.093988 ACCAACAACATATGCTAAGCAACATAA 60.094 33.333 1.58 0.00 43.62 1.90
26 27 6.376864 ACCAACAACATATGCTAAGCAACATA 59.623 34.615 1.58 0.00 43.62 2.29
27 28 5.185635 ACCAACAACATATGCTAAGCAACAT 59.814 36.000 1.58 0.00 43.62 2.71
28 29 4.522405 ACCAACAACATATGCTAAGCAACA 59.478 37.500 1.58 0.00 43.62 3.33
29 30 4.858692 CACCAACAACATATGCTAAGCAAC 59.141 41.667 1.58 0.00 43.62 4.17
30 31 4.617995 GCACCAACAACATATGCTAAGCAA 60.618 41.667 1.58 0.00 43.62 3.91
31 32 3.119531 GCACCAACAACATATGCTAAGCA 60.120 43.478 1.58 0.00 44.86 3.91
32 33 3.119531 TGCACCAACAACATATGCTAAGC 60.120 43.478 1.58 0.00 37.20 3.09
33 34 4.082841 TGTGCACCAACAACATATGCTAAG 60.083 41.667 15.69 0.00 37.20 2.18
34 35 3.823304 TGTGCACCAACAACATATGCTAA 59.177 39.130 15.69 0.00 37.20 3.09
35 36 3.416156 TGTGCACCAACAACATATGCTA 58.584 40.909 15.69 0.00 37.20 3.49
36 37 2.237643 TGTGCACCAACAACATATGCT 58.762 42.857 15.69 0.00 37.20 3.79
37 38 2.721274 TGTGCACCAACAACATATGC 57.279 45.000 15.69 0.00 36.81 3.14
38 39 4.398988 ACCTATGTGCACCAACAACATATG 59.601 41.667 15.69 0.00 32.81 1.78
39 40 4.398988 CACCTATGTGCACCAACAACATAT 59.601 41.667 15.69 0.00 35.31 1.78
40 41 3.755905 CACCTATGTGCACCAACAACATA 59.244 43.478 15.69 2.57 35.31 2.29
41 42 2.557924 CACCTATGTGCACCAACAACAT 59.442 45.455 15.69 1.33 35.31 2.71
42 43 1.952990 CACCTATGTGCACCAACAACA 59.047 47.619 15.69 0.00 35.31 3.33
43 44 2.226330 TCACCTATGTGCACCAACAAC 58.774 47.619 15.69 0.00 42.46 3.32
44 45 2.621055 GTTCACCTATGTGCACCAACAA 59.379 45.455 15.69 0.00 42.46 2.83
45 46 2.226330 GTTCACCTATGTGCACCAACA 58.774 47.619 15.69 0.00 42.46 3.33
46 47 2.989422 GTTCACCTATGTGCACCAAC 57.011 50.000 15.69 2.26 42.46 3.77
57 58 5.548836 ACCCTACAACAATTAGGTTCACCTA 59.451 40.000 1.18 1.18 46.48 3.08
59 60 4.659115 ACCCTACAACAATTAGGTTCACC 58.341 43.478 0.00 0.00 35.21 4.02
60 61 6.644248 AAACCCTACAACAATTAGGTTCAC 57.356 37.500 0.00 0.00 35.21 3.18
61 62 6.608002 ACAAAACCCTACAACAATTAGGTTCA 59.392 34.615 0.00 0.00 35.21 3.18
62 63 6.921307 CACAAAACCCTACAACAATTAGGTTC 59.079 38.462 0.00 0.00 35.21 3.62
63 64 6.684362 GCACAAAACCCTACAACAATTAGGTT 60.684 38.462 0.00 0.00 35.21 3.50
64 65 5.221362 GCACAAAACCCTACAACAATTAGGT 60.221 40.000 0.00 0.00 35.21 3.08
65 66 5.010617 AGCACAAAACCCTACAACAATTAGG 59.989 40.000 0.00 0.00 36.58 2.69
66 67 6.084326 AGCACAAAACCCTACAACAATTAG 57.916 37.500 0.00 0.00 0.00 1.73
67 68 6.096987 TCAAGCACAAAACCCTACAACAATTA 59.903 34.615 0.00 0.00 0.00 1.40
68 69 5.105146 TCAAGCACAAAACCCTACAACAATT 60.105 36.000 0.00 0.00 0.00 2.32
69 70 4.404073 TCAAGCACAAAACCCTACAACAAT 59.596 37.500 0.00 0.00 0.00 2.71
70 71 3.764434 TCAAGCACAAAACCCTACAACAA 59.236 39.130 0.00 0.00 0.00 2.83
71 72 3.129638 GTCAAGCACAAAACCCTACAACA 59.870 43.478 0.00 0.00 0.00 3.33
72 73 3.129638 TGTCAAGCACAAAACCCTACAAC 59.870 43.478 0.00 0.00 29.30 3.32
73 74 3.357203 TGTCAAGCACAAAACCCTACAA 58.643 40.909 0.00 0.00 29.30 2.41
74 75 3.006112 TGTCAAGCACAAAACCCTACA 57.994 42.857 0.00 0.00 29.30 2.74
83 84 4.640789 ACGGTTAATTTGTCAAGCACAA 57.359 36.364 0.00 0.00 43.68 3.33
84 85 4.640789 AACGGTTAATTTGTCAAGCACA 57.359 36.364 0.00 0.00 0.00 4.57
85 86 5.151389 CCTAACGGTTAATTTGTCAAGCAC 58.849 41.667 1.79 0.00 0.00 4.40
86 87 4.822896 ACCTAACGGTTAATTTGTCAAGCA 59.177 37.500 1.79 0.00 42.13 3.91
87 88 5.366829 ACCTAACGGTTAATTTGTCAAGC 57.633 39.130 1.79 0.00 42.13 4.01
101 102 4.142556 ACAAATGCGGAATAAACCTAACGG 60.143 41.667 0.00 0.00 0.00 4.44
102 103 4.976987 ACAAATGCGGAATAAACCTAACG 58.023 39.130 0.00 0.00 0.00 3.18
103 104 6.383415 TGAACAAATGCGGAATAAACCTAAC 58.617 36.000 0.00 0.00 0.00 2.34
104 105 6.576662 TGAACAAATGCGGAATAAACCTAA 57.423 33.333 0.00 0.00 0.00 2.69
105 106 6.576662 TTGAACAAATGCGGAATAAACCTA 57.423 33.333 0.00 0.00 0.00 3.08
106 107 5.461032 TTGAACAAATGCGGAATAAACCT 57.539 34.783 0.00 0.00 0.00 3.50
107 108 4.091365 GCTTGAACAAATGCGGAATAAACC 59.909 41.667 0.00 0.00 0.00 3.27
108 109 4.091365 GGCTTGAACAAATGCGGAATAAAC 59.909 41.667 0.00 0.00 0.00 2.01
109 110 4.021544 AGGCTTGAACAAATGCGGAATAAA 60.022 37.500 0.00 0.00 0.00 1.40
110 111 3.509575 AGGCTTGAACAAATGCGGAATAA 59.490 39.130 0.00 0.00 0.00 1.40
111 112 3.088532 AGGCTTGAACAAATGCGGAATA 58.911 40.909 0.00 0.00 0.00 1.75
112 113 1.895131 AGGCTTGAACAAATGCGGAAT 59.105 42.857 0.00 0.00 0.00 3.01
113 114 1.269448 GAGGCTTGAACAAATGCGGAA 59.731 47.619 0.00 0.00 0.00 4.30
114 115 0.881118 GAGGCTTGAACAAATGCGGA 59.119 50.000 0.00 0.00 0.00 5.54
115 116 0.883833 AGAGGCTTGAACAAATGCGG 59.116 50.000 0.00 0.00 0.00 5.69
116 117 2.159517 GGTAGAGGCTTGAACAAATGCG 60.160 50.000 0.00 0.00 0.00 4.73
117 118 2.159517 CGGTAGAGGCTTGAACAAATGC 60.160 50.000 0.00 0.00 0.00 3.56
118 119 2.159517 GCGGTAGAGGCTTGAACAAATG 60.160 50.000 0.00 0.00 0.00 2.32
119 120 2.084546 GCGGTAGAGGCTTGAACAAAT 58.915 47.619 0.00 0.00 0.00 2.32
120 121 1.202710 TGCGGTAGAGGCTTGAACAAA 60.203 47.619 0.00 0.00 0.00 2.83
121 122 0.394938 TGCGGTAGAGGCTTGAACAA 59.605 50.000 0.00 0.00 0.00 2.83
122 123 0.394938 TTGCGGTAGAGGCTTGAACA 59.605 50.000 0.00 0.00 0.00 3.18
123 124 1.739067 ATTGCGGTAGAGGCTTGAAC 58.261 50.000 0.00 0.00 0.00 3.18
124 125 2.489938 AATTGCGGTAGAGGCTTGAA 57.510 45.000 0.00 0.00 0.00 2.69
125 126 3.838244 ATAATTGCGGTAGAGGCTTGA 57.162 42.857 0.00 0.00 0.00 3.02
126 127 4.900635 AAATAATTGCGGTAGAGGCTTG 57.099 40.909 0.00 0.00 0.00 4.01
127 128 5.914898 AAAAATAATTGCGGTAGAGGCTT 57.085 34.783 0.00 0.00 0.00 4.35
128 129 7.399245 TTTAAAAATAATTGCGGTAGAGGCT 57.601 32.000 0.00 0.00 0.00 4.58
129 130 7.253519 CGTTTTAAAAATAATTGCGGTAGAGGC 60.254 37.037 1.31 0.00 0.00 4.70
130 131 7.253519 GCGTTTTAAAAATAATTGCGGTAGAGG 60.254 37.037 1.31 0.00 0.00 3.69
131 132 7.253519 GGCGTTTTAAAAATAATTGCGGTAGAG 60.254 37.037 1.31 0.00 0.00 2.43
132 133 6.527372 GGCGTTTTAAAAATAATTGCGGTAGA 59.473 34.615 1.31 0.00 0.00 2.59
133 134 6.528774 AGGCGTTTTAAAAATAATTGCGGTAG 59.471 34.615 1.31 0.00 0.00 3.18
134 135 6.388278 AGGCGTTTTAAAAATAATTGCGGTA 58.612 32.000 1.31 0.00 0.00 4.02
135 136 5.231702 AGGCGTTTTAAAAATAATTGCGGT 58.768 33.333 1.31 0.00 0.00 5.68
136 137 5.771602 AGGCGTTTTAAAAATAATTGCGG 57.228 34.783 1.31 0.00 0.00 5.69
137 138 8.587950 TGAATAGGCGTTTTAAAAATAATTGCG 58.412 29.630 1.31 1.57 0.00 4.85
138 139 9.683651 GTGAATAGGCGTTTTAAAAATAATTGC 57.316 29.630 1.31 0.88 0.00 3.56
140 141 9.373603 GGGTGAATAGGCGTTTTAAAAATAATT 57.626 29.630 1.31 0.00 0.00 1.40
141 142 7.982919 GGGGTGAATAGGCGTTTTAAAAATAAT 59.017 33.333 1.31 0.00 0.00 1.28
142 143 7.321908 GGGGTGAATAGGCGTTTTAAAAATAA 58.678 34.615 1.31 0.00 0.00 1.40
143 144 6.127394 GGGGGTGAATAGGCGTTTTAAAAATA 60.127 38.462 1.31 0.00 0.00 1.40
144 145 5.337733 GGGGGTGAATAGGCGTTTTAAAAAT 60.338 40.000 1.31 0.00 0.00 1.82
145 146 4.021280 GGGGGTGAATAGGCGTTTTAAAAA 60.021 41.667 1.31 0.00 0.00 1.94
146 147 3.510753 GGGGGTGAATAGGCGTTTTAAAA 59.489 43.478 0.00 0.00 0.00 1.52
147 148 3.090790 GGGGGTGAATAGGCGTTTTAAA 58.909 45.455 0.00 0.00 0.00 1.52
148 149 2.725637 GGGGGTGAATAGGCGTTTTAA 58.274 47.619 0.00 0.00 0.00 1.52
149 150 2.423446 GGGGGTGAATAGGCGTTTTA 57.577 50.000 0.00 0.00 0.00 1.52
150 151 3.276281 GGGGGTGAATAGGCGTTTT 57.724 52.632 0.00 0.00 0.00 2.43
166 167 2.210711 GGATGTCGCCTAGAGGGGG 61.211 68.421 12.32 0.23 46.90 5.40
168 169 1.742768 GTGGATGTCGCCTAGAGGG 59.257 63.158 0.00 0.00 35.18 4.30
169 170 1.101635 TCGTGGATGTCGCCTAGAGG 61.102 60.000 0.00 0.00 38.53 3.69
170 171 0.955178 ATCGTGGATGTCGCCTAGAG 59.045 55.000 0.00 0.00 0.00 2.43
171 172 0.952280 GATCGTGGATGTCGCCTAGA 59.048 55.000 0.00 0.00 0.00 2.43
172 173 0.955178 AGATCGTGGATGTCGCCTAG 59.045 55.000 0.00 0.00 0.00 3.02
173 174 1.399714 AAGATCGTGGATGTCGCCTA 58.600 50.000 0.00 0.00 0.00 3.93
174 175 0.537188 AAAGATCGTGGATGTCGCCT 59.463 50.000 0.00 0.00 0.00 5.52
175 176 0.931005 GAAAGATCGTGGATGTCGCC 59.069 55.000 0.00 0.00 0.00 5.54
176 177 1.324736 GTGAAAGATCGTGGATGTCGC 59.675 52.381 0.00 0.00 0.00 5.19
177 178 1.927174 GGTGAAAGATCGTGGATGTCG 59.073 52.381 0.00 0.00 0.00 4.35
178 179 3.252974 AGGTGAAAGATCGTGGATGTC 57.747 47.619 0.00 0.00 0.00 3.06
179 180 4.223032 AGTTAGGTGAAAGATCGTGGATGT 59.777 41.667 0.00 0.00 0.00 3.06
180 181 4.759782 AGTTAGGTGAAAGATCGTGGATG 58.240 43.478 0.00 0.00 0.00 3.51
181 182 5.046591 TGAAGTTAGGTGAAAGATCGTGGAT 60.047 40.000 0.00 0.00 0.00 3.41
182 183 4.282449 TGAAGTTAGGTGAAAGATCGTGGA 59.718 41.667 0.00 0.00 0.00 4.02
183 184 4.566004 TGAAGTTAGGTGAAAGATCGTGG 58.434 43.478 0.00 0.00 0.00 4.94
184 185 5.063944 CCATGAAGTTAGGTGAAAGATCGTG 59.936 44.000 0.00 0.00 0.00 4.35
185 186 5.046591 TCCATGAAGTTAGGTGAAAGATCGT 60.047 40.000 0.00 0.00 0.00 3.73
186 187 5.419542 TCCATGAAGTTAGGTGAAAGATCG 58.580 41.667 0.00 0.00 0.00 3.69
187 188 6.536941 GTCTCCATGAAGTTAGGTGAAAGATC 59.463 42.308 0.00 0.00 0.00 2.75
188 189 6.214412 AGTCTCCATGAAGTTAGGTGAAAGAT 59.786 38.462 0.00 0.00 0.00 2.40
189 190 5.544176 AGTCTCCATGAAGTTAGGTGAAAGA 59.456 40.000 0.00 0.00 0.00 2.52
190 191 5.799213 AGTCTCCATGAAGTTAGGTGAAAG 58.201 41.667 0.00 0.00 0.00 2.62
191 192 5.825593 AGTCTCCATGAAGTTAGGTGAAA 57.174 39.130 0.00 0.00 0.00 2.69
192 193 5.071788 ACAAGTCTCCATGAAGTTAGGTGAA 59.928 40.000 0.00 0.00 0.00 3.18
193 194 4.593206 ACAAGTCTCCATGAAGTTAGGTGA 59.407 41.667 0.00 0.00 0.00 4.02
194 195 4.692625 CACAAGTCTCCATGAAGTTAGGTG 59.307 45.833 0.00 0.00 0.00 4.00
195 196 4.804261 GCACAAGTCTCCATGAAGTTAGGT 60.804 45.833 0.00 0.00 0.00 3.08
196 197 3.686726 GCACAAGTCTCCATGAAGTTAGG 59.313 47.826 0.00 0.00 0.00 2.69
197 198 3.369147 CGCACAAGTCTCCATGAAGTTAG 59.631 47.826 0.00 0.00 0.00 2.34
198 199 3.325870 CGCACAAGTCTCCATGAAGTTA 58.674 45.455 0.00 0.00 0.00 2.24
199 200 2.146342 CGCACAAGTCTCCATGAAGTT 58.854 47.619 0.00 0.00 0.00 2.66
200 201 1.609061 CCGCACAAGTCTCCATGAAGT 60.609 52.381 0.00 0.00 0.00 3.01
201 202 1.081892 CCGCACAAGTCTCCATGAAG 58.918 55.000 0.00 0.00 0.00 3.02
202 203 0.684535 TCCGCACAAGTCTCCATGAA 59.315 50.000 0.00 0.00 0.00 2.57
203 204 0.684535 TTCCGCACAAGTCTCCATGA 59.315 50.000 0.00 0.00 0.00 3.07
204 205 1.197721 GTTTCCGCACAAGTCTCCATG 59.802 52.381 0.00 0.00 0.00 3.66
205 206 1.202758 TGTTTCCGCACAAGTCTCCAT 60.203 47.619 0.00 0.00 0.00 3.41
219 220 5.613358 AGAATTCAGATTGTCGTGTTTCC 57.387 39.130 8.44 0.00 0.00 3.13
220 221 9.445786 TTTTAAGAATTCAGATTGTCGTGTTTC 57.554 29.630 8.44 0.00 0.00 2.78
224 225 9.778993 ATGATTTTAAGAATTCAGATTGTCGTG 57.221 29.630 8.44 0.00 31.04 4.35
260 263 6.702723 CCTTGTGACAATCATCAACACAAATT 59.297 34.615 0.00 0.00 45.93 1.82
261 264 6.218019 CCTTGTGACAATCATCAACACAAAT 58.782 36.000 0.00 0.00 45.93 2.32
268 271 2.170166 GGGCCTTGTGACAATCATCAA 58.830 47.619 0.84 0.00 0.00 2.57
293 296 4.082571 GCCTGTTTTGATATCTTGTGCACT 60.083 41.667 19.41 0.00 0.00 4.40
299 302 3.633986 GGGAGGCCTGTTTTGATATCTTG 59.366 47.826 12.00 0.00 0.00 3.02
305 308 0.625849 ATCGGGAGGCCTGTTTTGAT 59.374 50.000 12.00 3.07 0.00 2.57
314 317 3.090532 AAGTGGGATCGGGAGGCC 61.091 66.667 0.00 0.00 0.00 5.19
315 318 2.190578 CAAGTGGGATCGGGAGGC 59.809 66.667 0.00 0.00 0.00 4.70
317 320 0.613260 TTGACAAGTGGGATCGGGAG 59.387 55.000 0.00 0.00 0.00 4.30
318 321 0.613260 CTTGACAAGTGGGATCGGGA 59.387 55.000 7.05 0.00 0.00 5.14
369 372 3.002656 GCACACCGGATCATGATAACAAG 59.997 47.826 9.46 1.95 0.00 3.16
376 379 0.321210 AAACGCACACCGGATCATGA 60.321 50.000 9.46 0.00 42.52 3.07
380 383 1.717194 TTCTAAACGCACACCGGATC 58.283 50.000 9.46 0.00 42.52 3.36
465 477 3.311871 CCGATGAGATGAAGCTTTTCCAG 59.688 47.826 0.00 0.00 0.00 3.86
480 492 1.863454 CAAATCGCTCTTCCCGATGAG 59.137 52.381 3.79 3.79 43.90 2.90
486 498 0.541863 TCCCTCAAATCGCTCTTCCC 59.458 55.000 0.00 0.00 0.00 3.97
495 507 6.122277 TGTAGAATGATGGTTCCCTCAAATC 58.878 40.000 1.36 3.94 0.00 2.17
503 515 7.226720 ACGACAAATATGTAGAATGATGGTTCC 59.773 37.037 0.00 0.00 40.74 3.62
555 567 7.549134 GTCTGGACTTTGGAAACTTTGATTTTT 59.451 33.333 0.00 0.00 0.00 1.94
556 568 7.041721 GTCTGGACTTTGGAAACTTTGATTTT 58.958 34.615 0.00 0.00 0.00 1.82
557 569 6.154363 TGTCTGGACTTTGGAAACTTTGATTT 59.846 34.615 2.38 0.00 0.00 2.17
558 570 5.656416 TGTCTGGACTTTGGAAACTTTGATT 59.344 36.000 2.38 0.00 0.00 2.57
559 571 5.200483 TGTCTGGACTTTGGAAACTTTGAT 58.800 37.500 2.38 0.00 0.00 2.57
561 573 4.640201 TCTGTCTGGACTTTGGAAACTTTG 59.360 41.667 2.38 0.00 0.00 2.77
562 574 4.855340 TCTGTCTGGACTTTGGAAACTTT 58.145 39.130 2.38 0.00 0.00 2.66
563 575 4.503714 TCTGTCTGGACTTTGGAAACTT 57.496 40.909 2.38 0.00 0.00 2.66
564 576 4.713792 ATCTGTCTGGACTTTGGAAACT 57.286 40.909 2.38 0.00 0.00 2.66
565 577 4.821805 TCAATCTGTCTGGACTTTGGAAAC 59.178 41.667 2.38 0.00 0.00 2.78
566 578 5.047566 TCAATCTGTCTGGACTTTGGAAA 57.952 39.130 2.38 0.00 0.00 3.13
567 579 4.347876 TCTCAATCTGTCTGGACTTTGGAA 59.652 41.667 2.38 0.00 0.00 3.53
568 580 3.903714 TCTCAATCTGTCTGGACTTTGGA 59.096 43.478 2.38 2.44 0.00 3.53
569 581 4.277515 TCTCAATCTGTCTGGACTTTGG 57.722 45.455 2.38 0.66 0.00 3.28
570 582 6.624352 TTTTCTCAATCTGTCTGGACTTTG 57.376 37.500 2.38 4.44 0.00 2.77
571 583 7.000472 TGATTTTCTCAATCTGTCTGGACTTT 59.000 34.615 2.38 0.00 0.00 2.66
572 584 6.537355 TGATTTTCTCAATCTGTCTGGACTT 58.463 36.000 2.38 0.00 0.00 3.01
573 585 6.119240 TGATTTTCTCAATCTGTCTGGACT 57.881 37.500 2.38 0.00 0.00 3.85
574 586 6.128063 CCTTGATTTTCTCAATCTGTCTGGAC 60.128 42.308 0.00 0.00 42.87 4.02
577 589 7.444629 TTCCTTGATTTTCTCAATCTGTCTG 57.555 36.000 0.00 0.00 42.87 3.51
616 629 7.650104 GCGCTAGATTTTCTCAGAATAGTAACT 59.350 37.037 0.00 0.00 0.00 2.24
621 634 7.418840 AATGCGCTAGATTTTCTCAGAATAG 57.581 36.000 9.73 0.00 0.00 1.73
623 636 6.493116 CAAATGCGCTAGATTTTCTCAGAAT 58.507 36.000 9.73 0.00 0.00 2.40
627 640 4.019919 GCAAATGCGCTAGATTTTCTCA 57.980 40.909 9.73 0.00 0.00 3.27
649 662 9.875675 GAACTATGATTCTCATAAAATGCTCAC 57.124 33.333 0.00 0.00 38.72 3.51
698 712 5.232463 ACGTTGAACTTTTAGGCGAGATAA 58.768 37.500 0.00 0.00 0.00 1.75
699 713 4.813027 ACGTTGAACTTTTAGGCGAGATA 58.187 39.130 0.00 0.00 0.00 1.98
746 760 2.096174 GCCGCGGTGATAAATAACAACA 59.904 45.455 28.70 0.00 0.00 3.33
748 762 2.357075 TGCCGCGGTGATAAATAACAA 58.643 42.857 28.70 0.00 0.00 2.83
749 763 2.025589 TGCCGCGGTGATAAATAACA 57.974 45.000 28.70 8.98 0.00 2.41
782 797 0.320374 TAACCAGCGAGACCCACTTG 59.680 55.000 0.00 0.00 0.00 3.16
794 809 6.401367 GCATTGTGATGTCAAAATTAACCAGC 60.401 38.462 0.00 0.00 31.69 4.85
796 811 5.632764 CGCATTGTGATGTCAAAATTAACCA 59.367 36.000 0.00 0.00 31.69 3.67
802 817 7.254185 GCAAATATCGCATTGTGATGTCAAAAT 60.254 33.333 20.33 4.40 34.24 1.82
809 824 2.975193 CCGCAAATATCGCATTGTGATG 59.025 45.455 20.33 8.27 38.91 3.07
811 826 2.013400 ACCGCAAATATCGCATTGTGA 58.987 42.857 1.78 1.78 38.91 3.58
815 830 2.682856 ACAAGACCGCAAATATCGCATT 59.317 40.909 0.00 0.00 0.00 3.56
819 834 1.597663 GGGACAAGACCGCAAATATCG 59.402 52.381 0.00 0.00 0.00 2.92
835 850 4.781934 AGTTAGGTCTTGCATTATGGGAC 58.218 43.478 0.00 0.00 0.00 4.46
836 851 4.473196 TGAGTTAGGTCTTGCATTATGGGA 59.527 41.667 0.00 0.00 0.00 4.37
837 852 4.780815 TGAGTTAGGTCTTGCATTATGGG 58.219 43.478 0.00 0.00 0.00 4.00
838 853 6.757897 TTTGAGTTAGGTCTTGCATTATGG 57.242 37.500 0.00 0.00 0.00 2.74
839 854 9.888878 CATATTTGAGTTAGGTCTTGCATTATG 57.111 33.333 0.00 0.00 0.00 1.90
840 855 9.632638 ACATATTTGAGTTAGGTCTTGCATTAT 57.367 29.630 0.00 0.00 0.00 1.28
841 856 8.892723 CACATATTTGAGTTAGGTCTTGCATTA 58.107 33.333 0.00 0.00 0.00 1.90
842 857 7.394359 ACACATATTTGAGTTAGGTCTTGCATT 59.606 33.333 0.00 0.00 0.00 3.56
843 858 6.886459 ACACATATTTGAGTTAGGTCTTGCAT 59.114 34.615 0.00 0.00 0.00 3.96
844 859 6.237901 ACACATATTTGAGTTAGGTCTTGCA 58.762 36.000 0.00 0.00 0.00 4.08
845 860 6.743575 ACACATATTTGAGTTAGGTCTTGC 57.256 37.500 0.00 0.00 0.00 4.01
846 861 9.965824 AAAAACACATATTTGAGTTAGGTCTTG 57.034 29.630 0.00 0.00 35.90 3.02
883 1824 8.911662 CGAATTTCACATAACCCAAAACTTTAG 58.088 33.333 0.00 0.00 0.00 1.85
892 1833 2.096248 GGGCGAATTTCACATAACCCA 58.904 47.619 0.00 0.00 36.07 4.51
923 1870 2.417719 CTATGCCCCTTGCTTATCGTC 58.582 52.381 0.00 0.00 42.00 4.20
925 1872 1.160137 GCTATGCCCCTTGCTTATCG 58.840 55.000 0.00 0.00 42.00 2.92
947 1894 0.956633 GAAAAGTGGGGGACGTTTCC 59.043 55.000 0.00 0.00 43.41 3.13
957 1904 0.846870 AGGGGGAGAGGAAAAGTGGG 60.847 60.000 0.00 0.00 0.00 4.61
998 1945 2.677979 GCGCAAGGAAGGACGGAAC 61.678 63.158 0.30 0.00 38.28 3.62
999 1946 2.358247 GCGCAAGGAAGGACGGAA 60.358 61.111 0.30 0.00 38.28 4.30
1000 1947 2.879233 AAGCGCAAGGAAGGACGGA 61.879 57.895 11.47 0.00 38.28 4.69
1001 1948 2.358737 AAGCGCAAGGAAGGACGG 60.359 61.111 11.47 0.00 38.28 4.79
1002 1949 2.863153 CAAGCGCAAGGAAGGACG 59.137 61.111 11.47 0.00 38.28 4.79
1003 1950 2.563427 GCAAGCGCAAGGAAGGAC 59.437 61.111 11.47 0.00 38.36 3.85
1035 1982 1.281899 CTCGAAAGTTCTCCGATGGC 58.718 55.000 0.00 0.00 0.00 4.40
1045 1992 1.842381 CTGGCTCCCCCTCGAAAGTT 61.842 60.000 0.00 0.00 0.00 2.66
1053 2000 4.505970 CCCTAGCTGGCTCCCCCT 62.506 72.222 0.00 0.00 0.00 4.79
1422 2370 0.808125 AAACGCAAACAGTCAGTGCA 59.192 45.000 5.07 0.00 38.19 4.57
1424 2372 2.542766 ACAAACGCAAACAGTCAGTG 57.457 45.000 0.00 0.00 0.00 3.66
1433 2381 7.432545 TGATTTCTTTCGAATAACAAACGCAAA 59.567 29.630 0.00 0.00 0.00 3.68
1436 2384 6.904954 TGATTTCTTTCGAATAACAAACGC 57.095 33.333 0.00 0.00 0.00 4.84
1441 2389 6.811170 GGCCAAATGATTTCTTTCGAATAACA 59.189 34.615 0.00 0.00 0.00 2.41
1448 2396 2.916716 CACGGCCAAATGATTTCTTTCG 59.083 45.455 2.24 0.00 0.00 3.46
1488 2436 6.745116 ACAACAGGGAAAAACTTATTACAGC 58.255 36.000 0.00 0.00 0.00 4.40
1550 2499 7.086376 GCTTCATCAAAAGCTAAAATCTCACA 58.914 34.615 1.51 0.00 46.51 3.58
1597 2552 3.981071 TCATAGTTCCCACTTGGACAG 57.019 47.619 0.00 0.00 45.11 3.51
1635 2590 5.186198 AGTAAACTAAGGTAGCATTGGCAG 58.814 41.667 0.00 0.00 44.61 4.85
1664 2619 3.449377 TCCATAGATGCACTTCGTAACCA 59.551 43.478 0.00 0.00 0.00 3.67
1665 2620 4.054780 TCCATAGATGCACTTCGTAACC 57.945 45.455 0.00 0.00 0.00 2.85
1705 2678 2.035961 GTCTAGCACAACACTGTCAGGA 59.964 50.000 4.53 0.00 31.64 3.86
1711 2684 2.729882 GGTTACGTCTAGCACAACACTG 59.270 50.000 0.00 0.00 0.00 3.66
1725 2698 4.792057 GCATAGATAAGCAGTCGGTTACGT 60.792 45.833 0.00 0.00 37.89 3.57
1727 2700 3.988517 GGCATAGATAAGCAGTCGGTTAC 59.011 47.826 0.00 0.00 37.89 2.50
1779 2755 2.673775 TCCCAAGCACTCAATTTCCA 57.326 45.000 0.00 0.00 0.00 3.53
1789 2765 1.202348 GGCACACTAAATCCCAAGCAC 59.798 52.381 0.00 0.00 0.00 4.40
2082 3058 6.770785 ACTTGACTTACTCAGGTAAATGCAAA 59.229 34.615 0.00 0.00 37.44 3.68
2083 3059 6.296026 ACTTGACTTACTCAGGTAAATGCAA 58.704 36.000 0.00 0.00 37.44 4.08
2084 3060 5.865085 ACTTGACTTACTCAGGTAAATGCA 58.135 37.500 0.00 0.00 37.44 3.96
2085 3061 9.595823 TTATACTTGACTTACTCAGGTAAATGC 57.404 33.333 0.00 0.00 42.87 3.56
2125 3101 7.402071 ACCTACCACTTATAATCAGAGTTCCAA 59.598 37.037 0.00 0.00 0.00 3.53
2180 3156 5.964958 ATTATGCTCATTAACCAATCCGG 57.035 39.130 0.00 0.00 42.50 5.14
2205 3181 4.390129 TGCCCAAACAGGAACCTATTAA 57.610 40.909 0.00 0.00 41.22 1.40
2228 3204 3.377346 ACTACTCACTCACAGCAACAG 57.623 47.619 0.00 0.00 0.00 3.16
2234 3210 4.792521 AAAGGCTACTACTCACTCACAG 57.207 45.455 0.00 0.00 0.00 3.66
2247 3227 7.417456 CCAGGGGATAACAATTTAAAAGGCTAC 60.417 40.741 0.00 0.00 0.00 3.58
2328 3311 9.845305 CTAAAAAGTTCTTAACGTGTCTTGTAG 57.155 33.333 0.00 0.00 36.23 2.74
2329 3312 9.369904 ACTAAAAAGTTCTTAACGTGTCTTGTA 57.630 29.630 0.00 0.00 36.23 2.41
2369 3357 7.673082 GCCTCCTAGGTCAACTATAGGTAATTA 59.327 40.741 9.08 0.00 37.80 1.40
2384 3372 3.367321 AGTAAACTCAGCCTCCTAGGTC 58.633 50.000 9.08 0.00 37.80 3.85
2402 3390 2.108168 CAGGAGGGTCCGATTCAAGTA 58.892 52.381 0.00 0.00 42.75 2.24
2415 3403 7.512992 AGTACAAATATGAATTCTCAGGAGGG 58.487 38.462 7.05 0.00 34.23 4.30
2419 3407 9.994432 GAACAAGTACAAATATGAATTCTCAGG 57.006 33.333 7.05 0.00 34.23 3.86
2468 3457 6.715347 ACCAAGAAAGCTGAACTACAATTT 57.285 33.333 0.00 0.00 0.00 1.82
2474 3463 6.169557 TGAGTAACCAAGAAAGCTGAACTA 57.830 37.500 0.00 0.00 0.00 2.24
2487 3476 2.026262 GCCCCTGAGAATGAGTAACCAA 60.026 50.000 0.00 0.00 0.00 3.67
2490 3479 3.350219 TTGCCCCTGAGAATGAGTAAC 57.650 47.619 0.00 0.00 0.00 2.50
2532 3521 5.391736 GCTCTCAATAAGTGGATGCATATGC 60.392 44.000 21.09 21.09 42.50 3.14
2533 3522 6.179504 GCTCTCAATAAGTGGATGCATATG 57.820 41.667 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.