Multiple sequence alignment - TraesCS5B01G178800

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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 TraesCS5B01G178800 chr5B 100.000 2966 0 0 1 2966 326867522 326864557 0.000000e+00 5478.0
1 TraesCS5B01G178800 chr5B 97.872 47 1 0 312 358 326867181 326867135 6.810000e-12 82.4
2 TraesCS5B01G178800 chr5B 97.872 47 1 0 342 388 326867211 326867165 6.810000e-12 82.4
3 TraesCS5B01G178800 chr5D 92.967 1692 82 18 348 2017 287779443 287777767 0.000000e+00 2431.0
4 TraesCS5B01G178800 chr5D 88.152 709 40 23 2298 2966 287777370 287776666 0.000000e+00 804.0
5 TraesCS5B01G178800 chr5D 98.225 169 3 0 2052 2220 287777687 287777519 2.240000e-76 296.0
6 TraesCS5B01G178800 chr5D 83.784 185 26 4 479 662 502884315 502884134 3.930000e-39 172.0
7 TraesCS5B01G178800 chr5A 91.537 1217 77 16 823 2017 380161597 380160385 0.000000e+00 1653.0
8 TraesCS5B01G178800 chr5A 84.792 480 35 18 2372 2818 380150616 380150142 5.830000e-122 448.0
9 TraesCS5B01G178800 chr5A 82.101 514 45 18 174 670 380163425 380162942 2.140000e-106 396.0
10 TraesCS5B01G178800 chr5A 99.242 132 1 0 2089 2220 380160276 380160145 3.820000e-59 239.0
11 TraesCS5B01G178800 chr5A 84.459 148 15 6 2220 2366 380159925 380159785 3.990000e-29 139.0
12 TraesCS5B01G178800 chr5A 79.459 185 23 10 661 830 380162997 380162813 1.870000e-22 117.0
13 TraesCS5B01G178800 chr6B 98.246 171 3 0 3 173 673603523 673603693 1.730000e-77 300.0
14 TraesCS5B01G178800 chr7B 97.159 176 4 1 3 177 738539432 738539257 2.240000e-76 296.0
15 TraesCS5B01G178800 chr7B 97.159 176 4 1 3 177 738675479 738675304 2.240000e-76 296.0
16 TraesCS5B01G178800 chr7B 97.159 176 4 1 3 177 741065842 741065667 2.240000e-76 296.0
17 TraesCS5B01G178800 chr4B 97.143 175 5 0 3 177 648321501 648321327 2.240000e-76 296.0
18 TraesCS5B01G178800 chr4B 96.610 177 5 1 3 179 628937189 628937014 2.890000e-75 292.0
19 TraesCS5B01G178800 chr1B 96.610 177 6 0 1 177 46687129 46687305 8.040000e-76 294.0
20 TraesCS5B01G178800 chr2B 97.076 171 5 0 3 173 135871679 135871849 3.740000e-74 289.0
21 TraesCS5B01G178800 chr2B 95.082 183 9 0 3 185 435392365 435392547 3.740000e-74 289.0
22 TraesCS5B01G178800 chr7A 86.528 193 25 1 592 784 126365168 126364977 8.330000e-51 211.0
23 TraesCS5B01G178800 chr3B 74.892 462 88 19 174 620 780878448 780878000 5.050000e-43 185.0
24 TraesCS5B01G178800 chr6D 81.529 157 20 7 468 619 321997143 321997295 1.440000e-23 121.0
25 TraesCS5B01G178800 chr2D 81.818 88 10 5 303 388 620479855 620479938 5.300000e-08 69.4


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 TraesCS5B01G178800 chr5B 326864557 326867522 2965 True 1880.933333 5478 98.581333 1 2966 3 chr5B.!!$R1 2965
1 TraesCS5B01G178800 chr5D 287776666 287779443 2777 True 1177.000000 2431 93.114667 348 2966 3 chr5D.!!$R2 2618
2 TraesCS5B01G178800 chr5A 380159785 380163425 3640 True 508.800000 1653 87.359600 174 2366 5 chr5A.!!$R2 2192

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
339 345 0.0293 TTGCTGCAGAACTTTGTCGC 59.971 50.0 20.43 0.0 0.00 5.19 F
698 729 0.1078 GCTGCAGGAGCTTGAGATGA 60.108 55.0 17.12 0.0 45.21 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 2610 0.317269 GTCGTCGACGGTGAAGTCAA 60.317 55.0 35.05 12.03 40.98 3.18 R
1981 3260 0.531753 GGGCGCCAAAACAAACACAT 60.532 50.0 30.85 0.00 0.00 3.21 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
21 22 2.795329 TCCTCTTTAGTACCGGTTCGT 58.205 47.619 15.04 0.00 0.00 3.85
22 23 2.489329 TCCTCTTTAGTACCGGTTCGTG 59.511 50.000 15.04 0.80 0.00 4.35
23 24 2.416431 CCTCTTTAGTACCGGTTCGTGG 60.416 54.545 15.04 1.27 0.00 4.94
24 25 1.067635 TCTTTAGTACCGGTTCGTGGC 60.068 52.381 15.04 0.00 0.00 5.01
25 26 0.678395 TTTAGTACCGGTTCGTGGCA 59.322 50.000 15.04 0.00 0.00 4.92
26 27 0.038343 TTAGTACCGGTTCGTGGCAC 60.038 55.000 15.04 7.79 0.00 5.01
27 28 2.198906 TAGTACCGGTTCGTGGCACG 62.199 60.000 32.75 32.75 44.19 5.34
36 37 2.125832 CGTGGCACGAACCGGTAT 60.126 61.111 34.85 0.00 46.05 2.73
37 38 1.738830 CGTGGCACGAACCGGTATT 60.739 57.895 34.85 0.00 46.05 1.89
38 39 0.458197 CGTGGCACGAACCGGTATTA 60.458 55.000 34.85 0.00 46.05 0.98
39 40 1.803625 CGTGGCACGAACCGGTATTAT 60.804 52.381 34.85 0.00 46.05 1.28
40 41 2.543445 CGTGGCACGAACCGGTATTATA 60.543 50.000 34.85 0.00 46.05 0.98
41 42 3.054878 GTGGCACGAACCGGTATTATAG 58.945 50.000 8.00 0.00 0.00 1.31
42 43 2.036217 TGGCACGAACCGGTATTATAGG 59.964 50.000 8.00 0.00 0.00 2.57
43 44 2.036346 GGCACGAACCGGTATTATAGGT 59.964 50.000 8.00 0.00 40.50 3.08
50 51 4.677673 ACCGGTATTATAGGTTCACCAC 57.322 45.455 4.49 0.00 38.89 4.16
51 52 3.068590 ACCGGTATTATAGGTTCACCACG 59.931 47.826 4.49 0.00 38.89 4.94
52 53 3.318839 CCGGTATTATAGGTTCACCACGA 59.681 47.826 0.00 0.00 38.89 4.35
53 54 4.202141 CCGGTATTATAGGTTCACCACGAA 60.202 45.833 0.00 0.00 38.89 3.85
61 62 2.428834 TTCACCACGAACCGGTACT 58.571 52.632 8.00 0.00 34.02 2.73
62 63 1.614996 TTCACCACGAACCGGTACTA 58.385 50.000 8.00 0.00 34.02 1.82
63 64 1.614996 TCACCACGAACCGGTACTAA 58.385 50.000 8.00 0.00 34.02 2.24
64 65 2.170166 TCACCACGAACCGGTACTAAT 58.830 47.619 8.00 0.00 34.02 1.73
65 66 2.094597 TCACCACGAACCGGTACTAATG 60.095 50.000 8.00 2.63 34.02 1.90
66 67 2.094597 CACCACGAACCGGTACTAATGA 60.095 50.000 8.00 0.00 34.02 2.57
67 68 2.165030 ACCACGAACCGGTACTAATGAG 59.835 50.000 8.00 0.00 34.02 2.90
68 69 2.424601 CCACGAACCGGTACTAATGAGA 59.575 50.000 8.00 0.00 0.00 3.27
69 70 3.119388 CCACGAACCGGTACTAATGAGAA 60.119 47.826 8.00 0.00 0.00 2.87
70 71 3.855950 CACGAACCGGTACTAATGAGAAC 59.144 47.826 8.00 0.00 0.00 3.01
71 72 3.103738 CGAACCGGTACTAATGAGAACG 58.896 50.000 8.00 0.00 0.00 3.95
72 73 3.442100 GAACCGGTACTAATGAGAACGG 58.558 50.000 8.00 9.34 40.23 4.44
73 74 1.135721 ACCGGTACTAATGAGAACGGC 59.864 52.381 4.49 0.00 39.00 5.68
74 75 1.537562 CCGGTACTAATGAGAACGGCC 60.538 57.143 0.00 0.00 32.94 6.13
75 76 1.849097 GGTACTAATGAGAACGGCCG 58.151 55.000 26.86 26.86 0.00 6.13
76 77 1.537562 GGTACTAATGAGAACGGCCGG 60.538 57.143 31.76 11.88 0.00 6.13
77 78 0.103572 TACTAATGAGAACGGCCGGC 59.896 55.000 31.76 21.18 0.00 6.13
78 79 1.144057 CTAATGAGAACGGCCGGCT 59.856 57.895 31.76 25.74 0.00 5.52
79 80 0.387929 CTAATGAGAACGGCCGGCTA 59.612 55.000 31.76 11.26 0.00 3.93
80 81 0.387929 TAATGAGAACGGCCGGCTAG 59.612 55.000 31.76 22.69 0.00 3.42
81 82 2.925162 AATGAGAACGGCCGGCTAGC 62.925 60.000 31.76 15.03 0.00 3.42
92 93 2.818274 GGCTAGCCGTTGGAACCG 60.818 66.667 20.16 0.00 0.00 4.44
98 99 2.344500 CCGTTGGAACCGGCACTA 59.656 61.111 0.00 0.00 38.85 2.74
99 100 1.301874 CCGTTGGAACCGGCACTAA 60.302 57.895 0.00 0.00 38.85 2.24
100 101 0.675522 CCGTTGGAACCGGCACTAAT 60.676 55.000 0.00 0.00 38.85 1.73
101 102 0.446222 CGTTGGAACCGGCACTAATG 59.554 55.000 0.00 1.62 0.00 1.90
102 103 0.808755 GTTGGAACCGGCACTAATGG 59.191 55.000 0.00 0.00 0.00 3.16
103 104 0.693622 TTGGAACCGGCACTAATGGA 59.306 50.000 0.00 0.00 0.00 3.41
104 105 0.035820 TGGAACCGGCACTAATGGAC 60.036 55.000 0.00 0.00 0.00 4.02
105 106 0.035820 GGAACCGGCACTAATGGACA 60.036 55.000 0.00 0.00 0.00 4.02
106 107 1.084289 GAACCGGCACTAATGGACAC 58.916 55.000 0.00 0.00 0.00 3.67
107 108 0.398696 AACCGGCACTAATGGACACA 59.601 50.000 0.00 0.00 0.00 3.72
108 109 0.618458 ACCGGCACTAATGGACACAT 59.382 50.000 0.00 0.00 39.54 3.21
110 111 2.237643 ACCGGCACTAATGGACACATTA 59.762 45.455 0.00 0.00 45.17 1.90
121 122 4.615901 CACATTAGTGCCGGCTCA 57.384 55.556 29.70 9.72 39.21 4.26
122 123 2.853159 CACATTAGTGCCGGCTCAA 58.147 52.632 29.70 19.77 39.21 3.02
123 124 1.164411 CACATTAGTGCCGGCTCAAA 58.836 50.000 29.70 18.42 39.21 2.69
124 125 1.539388 CACATTAGTGCCGGCTCAAAA 59.461 47.619 29.70 21.42 39.21 2.44
125 126 1.539827 ACATTAGTGCCGGCTCAAAAC 59.460 47.619 29.70 17.26 0.00 2.43
126 127 1.135402 CATTAGTGCCGGCTCAAAACC 60.135 52.381 29.70 6.44 0.00 3.27
127 128 0.179015 TTAGTGCCGGCTCAAAACCA 60.179 50.000 29.70 2.35 0.00 3.67
128 129 0.179015 TAGTGCCGGCTCAAAACCAA 60.179 50.000 29.70 5.19 0.00 3.67
129 130 1.040339 AGTGCCGGCTCAAAACCAAA 61.040 50.000 29.70 0.00 0.00 3.28
130 131 0.874175 GTGCCGGCTCAAAACCAAAC 60.874 55.000 29.70 9.41 0.00 2.93
131 132 1.300620 GCCGGCTCAAAACCAAACC 60.301 57.895 22.15 0.00 0.00 3.27
132 133 1.007849 CCGGCTCAAAACCAAACCG 60.008 57.895 0.00 0.00 40.30 4.44
133 134 1.007849 CGGCTCAAAACCAAACCGG 60.008 57.895 0.00 0.00 42.50 5.28
134 135 1.300620 GGCTCAAAACCAAACCGGC 60.301 57.895 0.00 0.00 39.03 6.13
135 136 1.439644 GCTCAAAACCAAACCGGCA 59.560 52.632 0.00 0.00 39.03 5.69
136 137 0.874175 GCTCAAAACCAAACCGGCAC 60.874 55.000 0.00 0.00 39.03 5.01
137 138 0.744281 CTCAAAACCAAACCGGCACT 59.256 50.000 0.00 0.00 39.03 4.40
138 139 1.950909 CTCAAAACCAAACCGGCACTA 59.049 47.619 0.00 0.00 39.03 2.74
139 140 2.359531 CTCAAAACCAAACCGGCACTAA 59.640 45.455 0.00 0.00 39.03 2.24
140 141 2.959707 TCAAAACCAAACCGGCACTAAT 59.040 40.909 0.00 0.00 39.03 1.73
141 142 3.056304 CAAAACCAAACCGGCACTAATG 58.944 45.455 0.00 0.00 39.03 1.90
142 143 1.989706 AACCAAACCGGCACTAATGT 58.010 45.000 0.00 0.00 39.03 2.71
143 144 1.243902 ACCAAACCGGCACTAATGTG 58.756 50.000 0.00 0.00 46.37 3.21
144 145 1.243902 CCAAACCGGCACTAATGTGT 58.756 50.000 0.00 0.00 45.44 3.72
145 146 1.199097 CCAAACCGGCACTAATGTGTC 59.801 52.381 0.00 0.00 45.44 3.67
146 147 2.151202 CAAACCGGCACTAATGTGTCT 58.849 47.619 0.00 0.00 45.84 3.41
147 148 2.094762 AACCGGCACTAATGTGTCTC 57.905 50.000 0.00 0.00 45.84 3.36
148 149 0.973632 ACCGGCACTAATGTGTCTCA 59.026 50.000 0.00 0.00 45.84 3.27
149 150 1.555075 ACCGGCACTAATGTGTCTCAT 59.445 47.619 0.00 0.00 45.84 2.90
150 151 2.764010 ACCGGCACTAATGTGTCTCATA 59.236 45.455 0.00 0.00 45.84 2.15
151 152 3.388024 ACCGGCACTAATGTGTCTCATAT 59.612 43.478 0.00 0.00 45.84 1.78
152 153 4.141711 ACCGGCACTAATGTGTCTCATATT 60.142 41.667 0.00 0.00 45.84 1.28
153 154 5.069914 ACCGGCACTAATGTGTCTCATATTA 59.930 40.000 0.00 0.00 45.84 0.98
154 155 5.635280 CCGGCACTAATGTGTCTCATATTAG 59.365 44.000 17.96 17.96 45.84 1.73
155 156 5.635280 CGGCACTAATGTGTCTCATATTAGG 59.365 44.000 21.16 14.61 44.30 2.69
156 157 6.525629 GGCACTAATGTGTCTCATATTAGGT 58.474 40.000 21.16 10.60 44.30 3.08
157 158 6.425114 GGCACTAATGTGTCTCATATTAGGTG 59.575 42.308 21.16 17.90 44.30 4.00
158 159 6.073548 GCACTAATGTGTCTCATATTAGGTGC 60.074 42.308 21.16 21.15 44.30 5.01
159 160 7.212976 CACTAATGTGTCTCATATTAGGTGCT 58.787 38.462 21.16 6.37 44.30 4.40
160 161 7.712639 CACTAATGTGTCTCATATTAGGTGCTT 59.287 37.037 21.16 6.12 44.30 3.91
161 162 8.267894 ACTAATGTGTCTCATATTAGGTGCTTT 58.732 33.333 21.16 5.64 44.30 3.51
162 163 7.944729 AATGTGTCTCATATTAGGTGCTTTT 57.055 32.000 0.00 0.00 35.48 2.27
163 164 7.944729 ATGTGTCTCATATTAGGTGCTTTTT 57.055 32.000 0.00 0.00 34.67 1.94
164 165 7.377766 TGTGTCTCATATTAGGTGCTTTTTC 57.622 36.000 0.00 0.00 0.00 2.29
165 166 7.168219 TGTGTCTCATATTAGGTGCTTTTTCT 58.832 34.615 0.00 0.00 0.00 2.52
166 167 8.318412 TGTGTCTCATATTAGGTGCTTTTTCTA 58.682 33.333 0.00 0.00 0.00 2.10
167 168 8.604890 GTGTCTCATATTAGGTGCTTTTTCTAC 58.395 37.037 0.00 0.00 0.00 2.59
168 169 8.540388 TGTCTCATATTAGGTGCTTTTTCTACT 58.460 33.333 0.00 0.00 0.00 2.57
172 173 9.817809 TCATATTAGGTGCTTTTTCTACTAGTG 57.182 33.333 5.39 0.00 0.00 2.74
194 195 5.353123 GTGATTGGATGTACATGTTAACGGT 59.647 40.000 14.43 4.63 0.00 4.83
198 199 4.452795 TGGATGTACATGTTAACGGTTGTG 59.547 41.667 14.43 6.21 0.00 3.33
210 211 1.600107 GGTTGTGCGATCTACCCCA 59.400 57.895 0.00 0.00 0.00 4.96
261 262 0.834687 TGGTGTCGTAGAAGGCCCTT 60.835 55.000 0.00 0.00 39.69 3.95
274 275 2.644992 CCCTTCGCAACAACCAGC 59.355 61.111 0.00 0.00 0.00 4.85
289 291 3.719268 ACCAGCTTGTTGTATCATCCA 57.281 42.857 0.00 0.00 0.00 3.41
293 295 4.095483 CCAGCTTGTTGTATCATCCAAGTC 59.905 45.833 0.00 0.00 37.28 3.01
301 303 7.450074 TGTTGTATCATCCAAGTCTGTACTTT 58.550 34.615 0.00 0.00 43.60 2.66
302 304 8.590204 TGTTGTATCATCCAAGTCTGTACTTTA 58.410 33.333 0.00 0.00 43.60 1.85
312 318 7.918562 TCCAAGTCTGTACTTTATTTTTGCAAC 59.081 33.333 0.00 0.00 43.60 4.17
313 319 7.704472 CCAAGTCTGTACTTTATTTTTGCAACA 59.296 33.333 0.00 0.00 43.60 3.33
319 325 8.413899 TGTACTTTATTTTTGCAACAAAGGTC 57.586 30.769 18.65 13.62 31.89 3.85
320 326 8.254508 TGTACTTTATTTTTGCAACAAAGGTCT 58.745 29.630 18.65 1.83 31.89 3.85
321 327 9.093970 GTACTTTATTTTTGCAACAAAGGTCTT 57.906 29.630 18.65 7.17 31.89 3.01
322 328 7.973601 ACTTTATTTTTGCAACAAAGGTCTTG 58.026 30.769 18.65 5.05 31.89 3.02
323 329 4.880886 ATTTTTGCAACAAAGGTCTTGC 57.119 36.364 0.00 0.00 42.67 4.01
324 330 3.608316 TTTTGCAACAAAGGTCTTGCT 57.392 38.095 0.00 0.00 42.77 3.91
325 331 2.582728 TTGCAACAAAGGTCTTGCTG 57.417 45.000 0.00 0.00 42.77 4.41
326 332 0.102844 TGCAACAAAGGTCTTGCTGC 59.897 50.000 6.03 6.03 42.77 5.25
327 333 0.102844 GCAACAAAGGTCTTGCTGCA 59.897 50.000 0.00 0.00 39.79 4.41
328 334 1.866880 GCAACAAAGGTCTTGCTGCAG 60.867 52.381 10.11 10.11 39.79 4.41
329 335 1.677576 CAACAAAGGTCTTGCTGCAGA 59.322 47.619 20.43 0.00 0.00 4.26
330 336 2.057137 ACAAAGGTCTTGCTGCAGAA 57.943 45.000 20.43 2.96 0.00 3.02
331 337 1.678101 ACAAAGGTCTTGCTGCAGAAC 59.322 47.619 20.43 9.09 0.00 3.01
332 338 1.952296 CAAAGGTCTTGCTGCAGAACT 59.048 47.619 20.43 12.02 43.15 3.01
333 339 2.355010 AAGGTCTTGCTGCAGAACTT 57.645 45.000 20.43 19.67 44.62 2.66
334 340 2.355010 AGGTCTTGCTGCAGAACTTT 57.645 45.000 20.43 0.10 37.59 2.66
335 341 1.952296 AGGTCTTGCTGCAGAACTTTG 59.048 47.619 20.43 0.50 37.59 2.77
336 342 1.678101 GGTCTTGCTGCAGAACTTTGT 59.322 47.619 20.43 0.00 0.00 2.83
337 343 2.287248 GGTCTTGCTGCAGAACTTTGTC 60.287 50.000 20.43 0.00 0.00 3.18
338 344 1.599071 TCTTGCTGCAGAACTTTGTCG 59.401 47.619 20.43 0.00 0.00 4.35
339 345 0.029300 TTGCTGCAGAACTTTGTCGC 59.971 50.000 20.43 0.00 0.00 5.19
340 346 1.439365 GCTGCAGAACTTTGTCGCG 60.439 57.895 20.43 0.00 0.00 5.87
341 347 1.831389 GCTGCAGAACTTTGTCGCGA 61.831 55.000 20.43 3.71 0.00 5.87
342 348 0.111089 CTGCAGAACTTTGTCGCGAC 60.111 55.000 31.66 31.66 0.00 5.19
343 349 0.808060 TGCAGAACTTTGTCGCGACA 60.808 50.000 36.40 36.40 39.98 4.35
361 367 1.678101 ACAAAGGTCTTGCTGCAGAAC 59.322 47.619 20.43 9.09 0.00 3.01
370 376 1.439365 GCTGCAGAACTTTGTCGCG 60.439 57.895 20.43 0.00 0.00 5.87
389 395 3.354089 CGACAAAGGTCTTGTTGCATT 57.646 42.857 0.00 0.00 42.05 3.56
390 396 3.705604 CGACAAAGGTCTTGTTGCATTT 58.294 40.909 0.00 0.00 42.05 2.32
532 550 3.933332 GTGCAAGAGAGTACATGTTACCC 59.067 47.826 2.30 0.00 0.00 3.69
533 551 3.838317 TGCAAGAGAGTACATGTTACCCT 59.162 43.478 2.30 0.00 0.00 4.34
534 552 4.286032 TGCAAGAGAGTACATGTTACCCTT 59.714 41.667 2.30 0.00 0.00 3.95
535 553 5.221843 TGCAAGAGAGTACATGTTACCCTTT 60.222 40.000 2.30 0.00 0.00 3.11
576 594 0.612732 ACCGTGACGTGAAGGGGATA 60.613 55.000 12.01 0.00 0.00 2.59
622 640 2.753849 GTGGCGGCCATGGCTAAA 60.754 61.111 34.70 16.25 41.60 1.85
623 641 2.440065 TGGCGGCCATGGCTAAAG 60.440 61.111 34.70 23.27 41.60 1.85
624 642 3.219198 GGCGGCCATGGCTAAAGG 61.219 66.667 34.70 19.48 41.60 3.11
628 646 3.219198 GCCATGGCTAAAGGCGGG 61.219 66.667 29.98 9.00 44.42 6.13
698 729 0.107800 GCTGCAGGAGCTTGAGATGA 60.108 55.000 17.12 0.00 45.21 2.92
732 763 1.427020 GCGTTGCTGAAGGAGATGC 59.573 57.895 0.00 0.00 0.00 3.91
820 2080 2.970324 GGCGCACAACCAAGACGA 60.970 61.111 10.83 0.00 0.00 4.20
821 2081 2.325082 GGCGCACAACCAAGACGAT 61.325 57.895 10.83 0.00 0.00 3.73
864 2124 6.029607 CCACCTGTTGATGTTAATCATTTCG 58.970 40.000 0.00 0.00 42.41 3.46
933 2199 7.676683 AAAGTAAATACCTGCAGGATCTCTA 57.323 36.000 39.19 20.52 38.94 2.43
935 2201 6.377912 AGTAAATACCTGCAGGATCTCTACT 58.622 40.000 39.19 28.55 38.94 2.57
936 2202 5.543507 AAATACCTGCAGGATCTCTACTG 57.456 43.478 39.19 8.80 38.94 2.74
940 2206 4.036518 ACCTGCAGGATCTCTACTGATTT 58.963 43.478 39.19 8.45 36.86 2.17
942 2208 4.100653 CCTGCAGGATCTCTACTGATTTGA 59.899 45.833 29.88 0.00 36.86 2.69
944 2210 6.014755 CCTGCAGGATCTCTACTGATTTGATA 60.015 42.308 29.88 0.00 36.86 2.15
945 2211 7.310547 CCTGCAGGATCTCTACTGATTTGATAT 60.311 40.741 29.88 0.00 36.86 1.63
996 2267 9.639563 TCAGGTATTTATTTCATGCCTATTTCA 57.360 29.630 0.00 0.00 34.72 2.69
1177 2456 2.281761 CGGGCAAGTCCAAGCTGT 60.282 61.111 0.00 0.00 36.21 4.40
1506 2785 0.107945 GCCTCTTCGTCTGGCTTGAT 60.108 55.000 0.00 0.00 43.05 2.57
1967 3246 1.419387 GATCAACCTGCTGCCCTAGAT 59.581 52.381 0.00 0.00 0.00 1.98
1969 3248 1.099879 CAACCTGCTGCCCTAGATGC 61.100 60.000 0.00 0.00 0.00 3.91
1974 3253 1.690893 CTGCTGCCCTAGATGCTAGAA 59.309 52.381 0.00 0.00 0.00 2.10
1976 3255 1.691434 GCTGCCCTAGATGCTAGAACT 59.309 52.381 0.00 0.00 0.00 3.01
1981 3260 4.145807 GCCCTAGATGCTAGAACTACTCA 58.854 47.826 0.00 0.00 0.00 3.41
1988 3267 6.940739 AGATGCTAGAACTACTCATGTGTTT 58.059 36.000 5.63 0.00 0.00 2.83
1999 3278 0.581053 CATGTGTTTGTTTTGGCGCC 59.419 50.000 22.73 22.73 0.00 6.53
2006 3285 2.010582 TTGTTTTGGCGCCCTGTGTC 62.011 55.000 26.77 10.12 0.00 3.67
2017 3296 2.811431 CGCCCTGTGTCAGTTTTGAATA 59.189 45.455 0.00 0.00 34.49 1.75
2018 3297 3.440173 CGCCCTGTGTCAGTTTTGAATAT 59.560 43.478 0.00 0.00 34.49 1.28
2019 3298 4.437390 CGCCCTGTGTCAGTTTTGAATATC 60.437 45.833 0.00 0.00 34.49 1.63
2020 3299 4.437390 GCCCTGTGTCAGTTTTGAATATCG 60.437 45.833 0.00 0.00 34.49 2.92
2021 3300 4.935205 CCCTGTGTCAGTTTTGAATATCGA 59.065 41.667 0.00 0.00 34.49 3.59
2023 3302 6.402550 CCCTGTGTCAGTTTTGAATATCGAAG 60.403 42.308 0.00 0.00 34.49 3.79
2024 3303 6.368791 CCTGTGTCAGTTTTGAATATCGAAGA 59.631 38.462 0.00 0.00 36.32 2.87
2025 3304 7.095229 CCTGTGTCAGTTTTGAATATCGAAGAA 60.095 37.037 0.00 0.00 35.63 2.52
2026 3305 8.148807 TGTGTCAGTTTTGAATATCGAAGAAA 57.851 30.769 0.00 0.00 35.63 2.52
2027 3306 8.783093 TGTGTCAGTTTTGAATATCGAAGAAAT 58.217 29.630 0.00 0.00 35.63 2.17
2044 3352 5.344743 AGAAATTGAGGAGCTTCATCGTA 57.655 39.130 0.00 0.00 28.20 3.43
2050 3358 3.706594 TGAGGAGCTTCATCGTAAAGGAT 59.293 43.478 0.00 0.00 28.20 3.24
2079 3404 5.121221 ACTCCTTTATTGCGTTTCCAAAG 57.879 39.130 0.00 0.00 0.00 2.77
2261 3806 2.948979 CGAAGTCTGTCTGATAGCTCCT 59.051 50.000 0.00 0.00 0.00 3.69
2268 3813 6.609212 AGTCTGTCTGATAGCTCCTTCAATTA 59.391 38.462 0.00 0.00 0.00 1.40
2277 3822 9.935241 TGATAGCTCCTTCAATTATATCTTGAC 57.065 33.333 0.00 0.00 32.57 3.18
2281 3826 9.064706 AGCTCCTTCAATTATATCTTGACATTG 57.935 33.333 1.21 0.00 32.57 2.82
2291 3836 4.853924 ATCTTGACATTGTTGGTTCACC 57.146 40.909 0.00 0.00 0.00 4.02
2292 3837 3.625853 TCTTGACATTGTTGGTTCACCA 58.374 40.909 0.00 0.00 45.94 4.17
2304 3849 4.916041 TGGTTCACCAGAAGAAGATGAT 57.084 40.909 0.00 0.00 42.01 2.45
2349 3904 1.401552 CATATGAACAGCCAACCACCG 59.598 52.381 0.00 0.00 0.00 4.94
2352 3907 3.485346 GAACAGCCAACCACCGGGA 62.485 63.158 6.32 0.00 38.05 5.14
2369 3924 3.261643 CCGGGATGAGAATATGTCCATCA 59.738 47.826 0.00 0.00 36.44 3.07
2370 3925 4.248859 CGGGATGAGAATATGTCCATCAC 58.751 47.826 0.00 0.00 36.44 3.06
2376 3931 6.405278 TGAGAATATGTCCATCACACGTAT 57.595 37.500 0.00 0.00 38.04 3.06
2404 3959 1.963190 GCACTAAGGGTTGTACGCGC 61.963 60.000 5.73 0.00 36.04 6.86
2406 3961 0.319405 ACTAAGGGTTGTACGCGCTT 59.681 50.000 5.73 18.44 41.12 4.68
2457 4012 1.780309 TGTGGGGAAGGTGATGAAGTT 59.220 47.619 0.00 0.00 0.00 2.66
2459 4014 3.230976 GTGGGGAAGGTGATGAAGTTTT 58.769 45.455 0.00 0.00 0.00 2.43
2482 4041 3.998099 TTTTCATGATGCGGTGTTTCA 57.002 38.095 0.00 0.00 0.00 2.69
2487 4046 0.888736 TGATGCGGTGTTTCAGTGGG 60.889 55.000 0.00 0.00 0.00 4.61
2495 4054 3.219281 GGTGTTTCAGTGGGCTTTCTTA 58.781 45.455 0.00 0.00 0.00 2.10
2507 4066 3.119955 GGGCTTTCTTAACGGTGTGATTC 60.120 47.826 0.00 0.00 0.00 2.52
2508 4067 3.119955 GGCTTTCTTAACGGTGTGATTCC 60.120 47.826 0.00 0.00 0.00 3.01
2563 4122 1.519408 ACTTTGGTGTCCGCATGTAC 58.481 50.000 0.00 0.00 0.00 2.90
2575 4134 5.703592 TGTCCGCATGTACTTTATTTGTCTT 59.296 36.000 0.00 0.00 0.00 3.01
2578 4137 6.035220 TCCGCATGTACTTTATTTGTCTTACG 59.965 38.462 0.00 0.00 0.00 3.18
2586 4145 5.467735 ACTTTATTTGTCTTACGGTGTCACC 59.532 40.000 12.40 12.40 34.05 4.02
2593 4152 0.533308 TTACGGTGTCACCTGTTGGC 60.533 55.000 19.82 0.00 35.66 4.52
2595 4154 2.203153 GGTGTCACCTGTTGGCGT 60.203 61.111 15.22 0.00 34.73 5.68
2598 4157 0.028902 GTGTCACCTGTTGGCGTTTC 59.971 55.000 0.00 0.00 36.63 2.78
2657 4216 5.473846 TGTATTTTTACGGATTGGTTGCTGA 59.526 36.000 0.00 0.00 0.00 4.26
2659 4218 1.434555 TTACGGATTGGTTGCTGACG 58.565 50.000 0.00 0.00 0.00 4.35
2672 4231 5.471797 TGGTTGCTGACGATTAATTTGAGAA 59.528 36.000 0.00 0.00 0.00 2.87
2674 4233 7.029563 GGTTGCTGACGATTAATTTGAGAAAT 58.970 34.615 0.00 0.00 0.00 2.17
2802 4373 9.099071 AGTAAGGAGCATAGTGAATTAGATGAT 57.901 33.333 0.00 0.00 0.00 2.45
2805 4376 8.427902 AGGAGCATAGTGAATTAGATGATACA 57.572 34.615 0.00 0.00 0.00 2.29
2822 4393 9.601217 AGATGATACACTTATTTTAGGACACAC 57.399 33.333 0.00 0.00 0.00 3.82
2823 4394 9.378551 GATGATACACTTATTTTAGGACACACA 57.621 33.333 0.00 0.00 0.00 3.72
2824 4395 8.542497 TGATACACTTATTTTAGGACACACAC 57.458 34.615 0.00 0.00 0.00 3.82
2825 4396 8.151596 TGATACACTTATTTTAGGACACACACA 58.848 33.333 0.00 0.00 0.00 3.72
2826 4397 9.162764 GATACACTTATTTTAGGACACACACAT 57.837 33.333 0.00 0.00 0.00 3.21
2829 4400 9.344772 ACACTTATTTTAGGACACACACATAAA 57.655 29.630 0.00 0.00 0.00 1.40
2854 4448 7.979444 ATATAATGGTACGTTTTGGATCCAG 57.021 36.000 15.53 5.82 0.00 3.86
2891 4485 4.463891 ACATTCCAAGTTTAGATGGCCTTG 59.536 41.667 3.32 0.00 36.62 3.61
2956 4550 4.363999 CCGACTTGCTCCTATTAGTGAAG 58.636 47.826 0.00 0.00 0.00 3.02
2963 4557 8.734386 ACTTGCTCCTATTAGTGAAGAAAAATG 58.266 33.333 0.00 0.00 0.00 2.32
2964 4558 7.088589 TGCTCCTATTAGTGAAGAAAAATGC 57.911 36.000 0.00 0.00 0.00 3.56
2965 4559 6.886459 TGCTCCTATTAGTGAAGAAAAATGCT 59.114 34.615 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.129988 CACGAACCGGTACTAAAGAGGAT 59.870 47.826 8.00 0.00 0.00 3.24
1 2 2.489329 CACGAACCGGTACTAAAGAGGA 59.511 50.000 8.00 0.00 0.00 3.71
2 3 2.416431 CCACGAACCGGTACTAAAGAGG 60.416 54.545 8.00 0.17 0.00 3.69
3 4 2.872370 CCACGAACCGGTACTAAAGAG 58.128 52.381 8.00 0.00 0.00 2.85
4 5 1.067635 GCCACGAACCGGTACTAAAGA 60.068 52.381 8.00 0.00 0.00 2.52
5 6 1.337074 TGCCACGAACCGGTACTAAAG 60.337 52.381 8.00 0.00 0.00 1.85
6 7 0.678395 TGCCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
7 8 0.038343 GTGCCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 36.33 2.24
8 9 1.586028 GTGCCACGAACCGGTACTA 59.414 57.895 8.00 0.00 36.33 1.82
9 10 2.341176 GTGCCACGAACCGGTACT 59.659 61.111 8.00 0.00 36.33 2.73
10 11 3.107661 CGTGCCACGAACCGGTAC 61.108 66.667 12.85 0.00 46.05 3.34
19 20 0.458197 TAATACCGGTTCGTGCCACG 60.458 55.000 15.04 11.80 44.19 4.94
20 21 1.944032 ATAATACCGGTTCGTGCCAC 58.056 50.000 15.04 0.00 0.00 5.01
21 22 2.036217 CCTATAATACCGGTTCGTGCCA 59.964 50.000 15.04 0.00 0.00 4.92
22 23 2.036346 ACCTATAATACCGGTTCGTGCC 59.964 50.000 15.04 0.00 0.00 5.01
23 24 3.375782 ACCTATAATACCGGTTCGTGC 57.624 47.619 15.04 0.00 0.00 5.34
28 29 4.441913 CGTGGTGAACCTATAATACCGGTT 60.442 45.833 15.04 0.00 43.32 4.44
29 30 3.068590 CGTGGTGAACCTATAATACCGGT 59.931 47.826 13.98 13.98 36.82 5.28
30 31 3.318839 TCGTGGTGAACCTATAATACCGG 59.681 47.826 0.00 0.00 36.82 5.28
31 32 4.572985 TCGTGGTGAACCTATAATACCG 57.427 45.455 0.37 0.00 36.82 4.02
43 44 1.614996 TAGTACCGGTTCGTGGTGAA 58.385 50.000 15.04 0.00 40.73 3.18
44 45 1.614996 TTAGTACCGGTTCGTGGTGA 58.385 50.000 15.04 0.00 40.73 4.02
45 46 2.094597 TCATTAGTACCGGTTCGTGGTG 60.095 50.000 15.04 7.47 40.73 4.17
46 47 2.165030 CTCATTAGTACCGGTTCGTGGT 59.835 50.000 15.04 0.00 43.62 4.16
47 48 2.424601 TCTCATTAGTACCGGTTCGTGG 59.575 50.000 15.04 0.29 0.00 4.94
48 49 3.770263 TCTCATTAGTACCGGTTCGTG 57.230 47.619 15.04 10.08 0.00 4.35
49 50 3.426695 CGTTCTCATTAGTACCGGTTCGT 60.427 47.826 15.04 0.00 0.00 3.85
50 51 3.103738 CGTTCTCATTAGTACCGGTTCG 58.896 50.000 15.04 0.00 0.00 3.95
51 52 3.442100 CCGTTCTCATTAGTACCGGTTC 58.558 50.000 15.04 8.12 0.00 3.62
52 53 2.417787 GCCGTTCTCATTAGTACCGGTT 60.418 50.000 15.04 0.00 0.00 4.44
53 54 1.135721 GCCGTTCTCATTAGTACCGGT 59.864 52.381 13.98 13.98 0.00 5.28
54 55 1.537562 GGCCGTTCTCATTAGTACCGG 60.538 57.143 0.00 0.00 0.00 5.28
55 56 1.849097 GGCCGTTCTCATTAGTACCG 58.151 55.000 0.00 0.00 0.00 4.02
56 57 1.537562 CCGGCCGTTCTCATTAGTACC 60.538 57.143 26.12 0.00 0.00 3.34
57 58 1.849097 CCGGCCGTTCTCATTAGTAC 58.151 55.000 26.12 0.00 0.00 2.73
58 59 0.103572 GCCGGCCGTTCTCATTAGTA 59.896 55.000 26.12 0.00 0.00 1.82
59 60 1.153429 GCCGGCCGTTCTCATTAGT 60.153 57.895 26.12 0.00 0.00 2.24
60 61 0.387929 TAGCCGGCCGTTCTCATTAG 59.612 55.000 26.15 6.10 0.00 1.73
61 62 0.387929 CTAGCCGGCCGTTCTCATTA 59.612 55.000 26.15 4.22 0.00 1.90
62 63 1.144057 CTAGCCGGCCGTTCTCATT 59.856 57.895 26.15 2.97 0.00 2.57
63 64 2.815308 CTAGCCGGCCGTTCTCAT 59.185 61.111 26.15 3.86 0.00 2.90
64 65 4.143333 GCTAGCCGGCCGTTCTCA 62.143 66.667 26.15 8.60 0.00 3.27
65 66 4.893601 GGCTAGCCGGCCGTTCTC 62.894 72.222 26.15 10.10 42.82 2.87
75 76 2.818274 CGGTTCCAACGGCTAGCC 60.818 66.667 24.75 24.75 0.00 3.93
76 77 2.818274 CCGGTTCCAACGGCTAGC 60.818 66.667 6.04 6.04 45.34 3.42
82 83 0.446222 CATTAGTGCCGGTTCCAACG 59.554 55.000 1.90 0.00 0.00 4.10
83 84 0.808755 CCATTAGTGCCGGTTCCAAC 59.191 55.000 1.90 0.00 0.00 3.77
84 85 0.693622 TCCATTAGTGCCGGTTCCAA 59.306 50.000 1.90 0.00 0.00 3.53
85 86 0.035820 GTCCATTAGTGCCGGTTCCA 60.036 55.000 1.90 0.00 0.00 3.53
86 87 0.035820 TGTCCATTAGTGCCGGTTCC 60.036 55.000 1.90 0.00 0.00 3.62
87 88 1.084289 GTGTCCATTAGTGCCGGTTC 58.916 55.000 1.90 0.00 0.00 3.62
88 89 0.398696 TGTGTCCATTAGTGCCGGTT 59.601 50.000 1.90 0.00 0.00 4.44
89 90 0.618458 ATGTGTCCATTAGTGCCGGT 59.382 50.000 1.90 0.00 0.00 5.28
90 91 1.750193 AATGTGTCCATTAGTGCCGG 58.250 50.000 0.00 0.00 39.52 6.13
97 98 2.912771 CCGGCACTAATGTGTCCATTA 58.087 47.619 0.00 0.00 45.29 1.90
98 99 1.750193 CCGGCACTAATGTGTCCATT 58.250 50.000 0.00 0.00 45.29 3.16
99 100 0.748005 GCCGGCACTAATGTGTCCAT 60.748 55.000 24.80 0.00 45.29 3.41
100 101 1.376683 GCCGGCACTAATGTGTCCA 60.377 57.895 24.80 0.00 45.29 4.02
101 102 1.078426 AGCCGGCACTAATGTGTCC 60.078 57.895 31.54 0.00 45.29 4.02
102 103 0.391130 TGAGCCGGCACTAATGTGTC 60.391 55.000 31.54 14.56 45.44 3.67
103 104 0.036164 TTGAGCCGGCACTAATGTGT 59.964 50.000 31.54 3.33 45.44 3.72
104 105 1.164411 TTTGAGCCGGCACTAATGTG 58.836 50.000 31.54 0.00 46.37 3.21
105 106 1.539827 GTTTTGAGCCGGCACTAATGT 59.460 47.619 31.54 5.22 0.00 2.71
106 107 1.135402 GGTTTTGAGCCGGCACTAATG 60.135 52.381 31.54 0.00 0.00 1.90
107 108 1.173913 GGTTTTGAGCCGGCACTAAT 58.826 50.000 31.54 7.13 0.00 1.73
108 109 0.179015 TGGTTTTGAGCCGGCACTAA 60.179 50.000 31.54 22.93 0.00 2.24
109 110 0.179015 TTGGTTTTGAGCCGGCACTA 60.179 50.000 31.54 17.63 0.00 2.74
110 111 1.040339 TTTGGTTTTGAGCCGGCACT 61.040 50.000 31.54 9.09 0.00 4.40
111 112 0.874175 GTTTGGTTTTGAGCCGGCAC 60.874 55.000 31.54 24.60 0.00 5.01
112 113 1.439644 GTTTGGTTTTGAGCCGGCA 59.560 52.632 31.54 5.56 0.00 5.69
113 114 1.300620 GGTTTGGTTTTGAGCCGGC 60.301 57.895 21.89 21.89 0.00 6.13
114 115 1.007849 CGGTTTGGTTTTGAGCCGG 60.008 57.895 0.00 0.00 36.05 6.13
115 116 1.007849 CCGGTTTGGTTTTGAGCCG 60.008 57.895 0.00 0.00 38.99 5.52
116 117 1.300620 GCCGGTTTGGTTTTGAGCC 60.301 57.895 1.90 0.00 41.21 4.70
117 118 0.874175 GTGCCGGTTTGGTTTTGAGC 60.874 55.000 1.90 0.00 41.21 4.26
118 119 0.744281 AGTGCCGGTTTGGTTTTGAG 59.256 50.000 1.90 0.00 41.21 3.02
119 120 2.054232 TAGTGCCGGTTTGGTTTTGA 57.946 45.000 1.90 0.00 41.21 2.69
120 121 2.873133 TTAGTGCCGGTTTGGTTTTG 57.127 45.000 1.90 0.00 41.21 2.44
121 122 2.696187 ACATTAGTGCCGGTTTGGTTTT 59.304 40.909 1.90 0.00 41.21 2.43
122 123 2.035321 CACATTAGTGCCGGTTTGGTTT 59.965 45.455 1.90 0.00 39.21 3.27
123 124 1.611491 CACATTAGTGCCGGTTTGGTT 59.389 47.619 1.90 0.00 39.21 3.67
124 125 1.243902 CACATTAGTGCCGGTTTGGT 58.756 50.000 1.90 0.00 39.21 3.67
135 136 7.366847 AGCACCTAATATGAGACACATTAGT 57.633 36.000 8.34 0.00 40.07 2.24
136 137 8.668510 AAAGCACCTAATATGAGACACATTAG 57.331 34.615 0.00 0.00 40.07 1.73
137 138 9.461312 AAAAAGCACCTAATATGAGACACATTA 57.539 29.630 0.00 0.00 40.07 1.90
138 139 7.944729 AAAAGCACCTAATATGAGACACATT 57.055 32.000 0.00 0.00 40.07 2.71
139 140 7.831193 AGAAAAAGCACCTAATATGAGACACAT 59.169 33.333 0.00 0.00 42.39 3.21
140 141 7.168219 AGAAAAAGCACCTAATATGAGACACA 58.832 34.615 0.00 0.00 0.00 3.72
141 142 7.617041 AGAAAAAGCACCTAATATGAGACAC 57.383 36.000 0.00 0.00 0.00 3.67
142 143 8.540388 AGTAGAAAAAGCACCTAATATGAGACA 58.460 33.333 0.00 0.00 0.00 3.41
143 144 8.950208 AGTAGAAAAAGCACCTAATATGAGAC 57.050 34.615 0.00 0.00 0.00 3.36
146 147 9.817809 CACTAGTAGAAAAAGCACCTAATATGA 57.182 33.333 3.59 0.00 0.00 2.15
147 148 9.817809 TCACTAGTAGAAAAAGCACCTAATATG 57.182 33.333 3.59 0.00 0.00 1.78
150 151 9.167311 CAATCACTAGTAGAAAAAGCACCTAAT 57.833 33.333 3.59 0.00 0.00 1.73
151 152 7.606456 CCAATCACTAGTAGAAAAAGCACCTAA 59.394 37.037 3.59 0.00 0.00 2.69
152 153 7.038587 TCCAATCACTAGTAGAAAAAGCACCTA 60.039 37.037 3.59 0.00 0.00 3.08
153 154 5.940470 CCAATCACTAGTAGAAAAAGCACCT 59.060 40.000 3.59 0.00 0.00 4.00
154 155 5.938125 TCCAATCACTAGTAGAAAAAGCACC 59.062 40.000 3.59 0.00 0.00 5.01
155 156 7.119846 ACATCCAATCACTAGTAGAAAAAGCAC 59.880 37.037 3.59 0.00 0.00 4.40
156 157 7.168219 ACATCCAATCACTAGTAGAAAAAGCA 58.832 34.615 3.59 0.00 0.00 3.91
157 158 7.617041 ACATCCAATCACTAGTAGAAAAAGC 57.383 36.000 3.59 0.00 0.00 3.51
158 159 9.653287 TGTACATCCAATCACTAGTAGAAAAAG 57.347 33.333 3.59 0.00 0.00 2.27
160 161 9.599866 CATGTACATCCAATCACTAGTAGAAAA 57.400 33.333 5.07 0.00 0.00 2.29
161 162 8.758829 ACATGTACATCCAATCACTAGTAGAAA 58.241 33.333 5.07 0.00 0.00 2.52
162 163 8.306313 ACATGTACATCCAATCACTAGTAGAA 57.694 34.615 5.07 0.00 0.00 2.10
163 164 7.898014 ACATGTACATCCAATCACTAGTAGA 57.102 36.000 5.07 0.00 0.00 2.59
165 166 9.811995 GTTAACATGTACATCCAATCACTAGTA 57.188 33.333 5.07 0.00 0.00 1.82
166 167 7.491372 CGTTAACATGTACATCCAATCACTAGT 59.509 37.037 5.07 0.00 0.00 2.57
167 168 7.042725 CCGTTAACATGTACATCCAATCACTAG 60.043 40.741 5.07 0.00 0.00 2.57
168 169 6.759356 CCGTTAACATGTACATCCAATCACTA 59.241 38.462 5.07 0.00 0.00 2.74
169 170 5.584649 CCGTTAACATGTACATCCAATCACT 59.415 40.000 5.07 0.00 0.00 3.41
170 171 5.353123 ACCGTTAACATGTACATCCAATCAC 59.647 40.000 5.07 0.00 0.00 3.06
171 172 5.492895 ACCGTTAACATGTACATCCAATCA 58.507 37.500 5.07 0.00 0.00 2.57
172 173 6.128117 ACAACCGTTAACATGTACATCCAATC 60.128 38.462 5.07 0.00 0.00 2.67
194 195 1.067974 CGTATGGGGTAGATCGCACAA 59.932 52.381 3.38 0.00 32.46 3.33
198 199 2.670509 GCTTACGTATGGGGTAGATCGC 60.671 54.545 10.17 0.00 0.00 4.58
210 211 4.083484 GCAAAGAAGTGGTTGCTTACGTAT 60.083 41.667 0.00 0.00 45.34 3.06
274 275 7.099764 AGTACAGACTTGGATGATACAACAAG 58.900 38.462 13.68 13.68 44.32 3.16
287 289 7.704472 TGTTGCAAAAATAAAGTACAGACTTGG 59.296 33.333 0.00 0.00 45.50 3.61
293 295 8.419076 ACCTTTGTTGCAAAAATAAAGTACAG 57.581 30.769 2.11 0.00 0.00 2.74
312 318 1.952296 AGTTCTGCAGCAAGACCTTTG 59.048 47.619 9.47 0.00 0.00 2.77
313 319 2.355010 AGTTCTGCAGCAAGACCTTT 57.645 45.000 9.47 0.00 0.00 3.11
319 325 1.923316 GCGACAAAGTTCTGCAGCAAG 60.923 52.381 9.47 0.00 0.00 4.01
320 326 0.029300 GCGACAAAGTTCTGCAGCAA 59.971 50.000 9.47 1.36 0.00 3.91
321 327 1.648720 GCGACAAAGTTCTGCAGCA 59.351 52.632 9.47 0.00 0.00 4.41
322 328 1.439365 CGCGACAAAGTTCTGCAGC 60.439 57.895 9.47 0.00 0.00 5.25
323 329 0.111089 GTCGCGACAAAGTTCTGCAG 60.111 55.000 33.09 7.63 0.00 4.41
324 330 0.808060 TGTCGCGACAAAGTTCTGCA 60.808 50.000 37.68 12.12 38.56 4.41
325 331 1.931551 TGTCGCGACAAAGTTCTGC 59.068 52.632 37.68 9.34 38.56 4.26
334 340 1.495584 GCAAGACCTTTGTCGCGACA 61.496 55.000 36.40 36.40 46.51 4.35
335 341 1.204312 GCAAGACCTTTGTCGCGAC 59.796 57.895 31.66 31.66 46.51 5.19
336 342 1.069090 AGCAAGACCTTTGTCGCGA 59.931 52.632 3.71 3.71 46.51 5.87
337 343 1.205064 CAGCAAGACCTTTGTCGCG 59.795 57.895 0.00 0.00 46.51 5.87
338 344 1.081840 GCAGCAAGACCTTTGTCGC 60.082 57.895 0.00 0.00 46.51 5.19
339 345 0.236711 CTGCAGCAAGACCTTTGTCG 59.763 55.000 0.00 0.00 46.51 4.35
340 346 1.597742 TCTGCAGCAAGACCTTTGTC 58.402 50.000 9.47 0.00 42.09 3.18
341 347 1.678101 GTTCTGCAGCAAGACCTTTGT 59.322 47.619 9.47 0.00 0.00 2.83
342 348 1.952296 AGTTCTGCAGCAAGACCTTTG 59.048 47.619 9.47 0.00 0.00 2.77
343 349 2.355010 AGTTCTGCAGCAAGACCTTT 57.645 45.000 9.47 0.00 0.00 3.11
344 350 2.355010 AAGTTCTGCAGCAAGACCTT 57.645 45.000 9.47 0.00 0.00 3.50
345 351 1.952296 CAAAGTTCTGCAGCAAGACCT 59.048 47.619 9.47 0.00 0.00 3.85
346 352 1.678101 ACAAAGTTCTGCAGCAAGACC 59.322 47.619 9.47 0.00 0.00 3.85
426 441 6.369065 TCTGCAACAAAACCGTTACAAAATTT 59.631 30.769 0.00 0.00 0.00 1.82
427 442 5.869888 TCTGCAACAAAACCGTTACAAAATT 59.130 32.000 0.00 0.00 0.00 1.82
428 443 5.411781 TCTGCAACAAAACCGTTACAAAAT 58.588 33.333 0.00 0.00 0.00 1.82
535 553 8.138712 ACGGTCTCTATTTGCAAAACATAAAAA 58.861 29.630 17.19 0.00 0.00 1.94
540 558 4.759693 TCACGGTCTCTATTTGCAAAACAT 59.240 37.500 17.19 2.12 0.00 2.71
542 560 4.464112 GTCACGGTCTCTATTTGCAAAAC 58.536 43.478 17.19 9.16 0.00 2.43
619 637 2.709883 GCAGCAATGCCCGCCTTTA 61.710 57.895 0.00 0.00 0.00 1.85
620 638 4.073200 GCAGCAATGCCCGCCTTT 62.073 61.111 0.00 0.00 0.00 3.11
692 723 1.970114 CCATGGCCGCCATCATCTC 60.970 63.158 22.62 0.00 43.15 2.75
761 792 0.247736 CTTCCTCAACCTCTGTCCCG 59.752 60.000 0.00 0.00 0.00 5.14
808 845 0.949105 GCGTCCATCGTCTTGGTTGT 60.949 55.000 2.60 0.00 42.13 3.32
920 2186 5.273674 TCAAATCAGTAGAGATCCTGCAG 57.726 43.478 6.78 6.78 0.00 4.41
921 2187 5.883685 ATCAAATCAGTAGAGATCCTGCA 57.116 39.130 0.00 0.00 0.00 4.41
973 2239 9.143631 GCATGAAATAGGCATGAAATAAATACC 57.856 33.333 7.68 0.00 44.49 2.73
987 2258 1.066002 ACACGCATGCATGAAATAGGC 59.934 47.619 30.64 11.78 36.42 3.93
996 2267 4.498009 GCTTTTATAGGAACACGCATGCAT 60.498 41.667 19.57 0.00 0.00 3.96
1039 2310 3.648009 GTGATTGCCGGATTGTTGAAAA 58.352 40.909 5.05 0.00 0.00 2.29
1331 2610 0.317269 GTCGTCGACGGTGAAGTCAA 60.317 55.000 35.05 12.03 40.98 3.18
1967 3246 5.853936 ACAAACACATGAGTAGTTCTAGCA 58.146 37.500 0.00 0.00 0.00 3.49
1969 3248 8.070171 CCAAAACAAACACATGAGTAGTTCTAG 58.930 37.037 0.00 1.42 0.00 2.43
1974 3253 4.497340 CGCCAAAACAAACACATGAGTAGT 60.497 41.667 0.00 0.00 0.00 2.73
1976 3255 3.793801 GCGCCAAAACAAACACATGAGTA 60.794 43.478 0.00 0.00 0.00 2.59
1981 3260 0.531753 GGGCGCCAAAACAAACACAT 60.532 50.000 30.85 0.00 0.00 3.21
1988 3267 2.441164 ACACAGGGCGCCAAAACA 60.441 55.556 30.85 0.00 0.00 2.83
1999 3278 6.368791 TCTTCGATATTCAAAACTGACACAGG 59.631 38.462 0.00 0.00 35.51 4.00
2006 3285 9.282247 CCTCAATTTCTTCGATATTCAAAACTG 57.718 33.333 0.00 0.00 0.00 3.16
2017 3296 4.836825 TGAAGCTCCTCAATTTCTTCGAT 58.163 39.130 0.00 0.00 36.77 3.59
2018 3297 4.271696 TGAAGCTCCTCAATTTCTTCGA 57.728 40.909 0.00 0.00 36.77 3.71
2019 3298 4.260132 CGATGAAGCTCCTCAATTTCTTCG 60.260 45.833 0.00 6.87 39.28 3.79
2020 3299 4.633565 ACGATGAAGCTCCTCAATTTCTTC 59.366 41.667 0.00 0.00 35.12 2.87
2021 3300 4.583871 ACGATGAAGCTCCTCAATTTCTT 58.416 39.130 0.00 0.00 0.00 2.52
2023 3302 6.422776 TTTACGATGAAGCTCCTCAATTTC 57.577 37.500 0.00 0.00 0.00 2.17
2024 3303 5.355350 CCTTTACGATGAAGCTCCTCAATTT 59.645 40.000 0.00 0.00 0.00 1.82
2025 3304 4.878397 CCTTTACGATGAAGCTCCTCAATT 59.122 41.667 0.00 0.00 0.00 2.32
2026 3305 4.162320 TCCTTTACGATGAAGCTCCTCAAT 59.838 41.667 0.00 0.00 0.00 2.57
2027 3306 3.513912 TCCTTTACGATGAAGCTCCTCAA 59.486 43.478 0.00 0.00 0.00 3.02
2050 3358 8.205512 TGGAAACGCAATAAAGGAGTATATGTA 58.794 33.333 0.00 0.00 0.00 2.29
2268 3813 6.009589 TGGTGAACCAACAATGTCAAGATAT 58.990 36.000 0.00 0.00 44.35 1.63
2277 3822 4.580167 TCTTCTTCTGGTGAACCAACAATG 59.420 41.667 3.33 0.00 46.97 2.82
2281 3826 4.389374 TCATCTTCTTCTGGTGAACCAAC 58.611 43.478 3.33 0.00 46.97 3.77
2284 3829 7.362142 GGTTAAATCATCTTCTTCTGGTGAACC 60.362 40.741 0.00 0.00 0.00 3.62
2289 3834 7.461749 TCAAGGTTAAATCATCTTCTTCTGGT 58.538 34.615 0.00 0.00 0.00 4.00
2290 3835 7.928307 TCAAGGTTAAATCATCTTCTTCTGG 57.072 36.000 0.00 0.00 0.00 3.86
2291 3836 9.224267 TCTTCAAGGTTAAATCATCTTCTTCTG 57.776 33.333 0.00 0.00 0.00 3.02
2292 3837 9.972106 ATCTTCAAGGTTAAATCATCTTCTTCT 57.028 29.630 0.00 0.00 0.00 2.85
2349 3904 4.999950 GTGTGATGGACATATTCTCATCCC 59.000 45.833 0.00 0.00 36.78 3.85
2352 3907 5.282055 ACGTGTGATGGACATATTCTCAT 57.718 39.130 0.00 0.00 36.78 2.90
2369 3924 6.704493 CCCTTAGTGCATATGTAAATACGTGT 59.296 38.462 4.29 0.00 0.00 4.49
2370 3925 6.704493 ACCCTTAGTGCATATGTAAATACGTG 59.296 38.462 4.29 0.00 0.00 4.49
2376 3931 6.535865 CGTACAACCCTTAGTGCATATGTAAA 59.464 38.462 4.29 0.00 0.00 2.01
2404 3959 3.038017 CAACATCAACAACGCAGTGAAG 58.962 45.455 0.00 0.00 45.00 3.02
2406 3961 2.013400 ACAACATCAACAACGCAGTGA 58.987 42.857 0.00 0.00 45.00 3.41
2464 4019 2.226200 CACTGAAACACCGCATCATGAA 59.774 45.455 0.00 0.00 0.00 2.57
2482 4041 1.142262 ACACCGTTAAGAAAGCCCACT 59.858 47.619 0.00 0.00 0.00 4.00
2487 4046 3.424433 CGGAATCACACCGTTAAGAAAGC 60.424 47.826 0.00 0.00 44.57 3.51
2507 4066 6.529829 CCACATAATTATTGGTTGAAACACGG 59.470 38.462 13.99 0.00 0.00 4.94
2508 4067 7.309177 TCCACATAATTATTGGTTGAAACACG 58.691 34.615 18.32 0.00 0.00 4.49
2563 4122 5.699458 AGGTGACACCGTAAGACAAATAAAG 59.301 40.000 18.93 0.00 44.90 1.85
2575 4134 1.070105 GCCAACAGGTGACACCGTA 59.930 57.895 18.93 0.00 44.90 4.02
2578 4137 1.381165 AAACGCCAACAGGTGACACC 61.381 55.000 17.43 17.43 38.99 4.16
2657 4216 8.960591 AGGACAATGATTTCTCAAATTAATCGT 58.039 29.630 0.00 0.00 34.37 3.73
2708 4267 9.790344 TGGTTTATGATTTTGACCATTCAATTT 57.210 25.926 0.00 0.00 41.50 1.82
2709 4268 9.790344 TTGGTTTATGATTTTGACCATTCAATT 57.210 25.926 0.00 0.00 41.50 2.32
2711 4270 9.434420 GATTGGTTTATGATTTTGACCATTCAA 57.566 29.630 9.56 0.00 39.87 2.69
2712 4271 8.040132 GGATTGGTTTATGATTTTGACCATTCA 58.960 33.333 14.10 0.00 40.16 2.57
2713 4272 8.040132 TGGATTGGTTTATGATTTTGACCATTC 58.960 33.333 0.00 0.00 39.87 2.67
2716 4275 6.924913 TGGATTGGTTTATGATTTTGACCA 57.075 33.333 0.00 0.00 38.54 4.02
2717 4276 8.614469 TTTTGGATTGGTTTATGATTTTGACC 57.386 30.769 0.00 0.00 0.00 4.02
2732 4303 6.870769 ACTGAGCTATTCAATTTTGGATTGG 58.129 36.000 0.00 0.00 34.81 3.16
2748 4319 2.489329 GCTTTGCCATTCAACTGAGCTA 59.511 45.455 0.00 0.00 34.70 3.32
2802 4373 9.999660 TTATGTGTGTGTCCTAAAATAAGTGTA 57.000 29.630 0.00 0.00 0.00 2.90
2817 4388 9.386010 ACGTACCATTATATTTTATGTGTGTGT 57.614 29.630 0.00 0.00 0.00 3.72
2827 4398 9.191479 TGGATCCAAAACGTACCATTATATTTT 57.809 29.630 13.46 0.00 0.00 1.82
2829 4400 7.447238 CCTGGATCCAAAACGTACCATTATATT 59.553 37.037 17.00 0.00 0.00 1.28
2830 4401 6.940298 CCTGGATCCAAAACGTACCATTATAT 59.060 38.462 17.00 0.00 0.00 0.86
2831 4402 6.292923 CCTGGATCCAAAACGTACCATTATA 58.707 40.000 17.00 0.00 0.00 0.98
2833 4404 4.519213 CCTGGATCCAAAACGTACCATTA 58.481 43.478 17.00 0.00 0.00 1.90
2854 4448 2.019984 GGAATGTCCAGATTCAGTGCC 58.980 52.381 0.00 0.00 36.28 5.01
2870 4464 4.934356 TCAAGGCCATCTAAACTTGGAAT 58.066 39.130 5.01 0.00 40.41 3.01
2910 4504 6.459923 GCCTTAGAGAGGGTTGACTATTATG 58.540 44.000 0.00 0.00 46.40 1.90
2917 4511 0.175989 CGGCCTTAGAGAGGGTTGAC 59.824 60.000 0.00 0.00 46.40 3.18
2918 4512 0.040646 TCGGCCTTAGAGAGGGTTGA 59.959 55.000 0.00 0.00 46.40 3.18


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

AutoCloner maintained by Alex Coulton.