Multiple sequence alignment - TraesCS3D01G112000

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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 TraesCS3D01G112000 chr3D 100.000 3293 0 0 1 3293 66338853 66342145 0.000000e+00 6082.0
1 TraesCS3D01G112000 chr3A 93.561 2050 67 22 313 2347 77470563 77472562 0.000000e+00 2994.0
2 TraesCS3D01G112000 chr3A 98.344 966 13 2 2331 3293 77472597 77473562 0.000000e+00 1692.0
3 TraesCS3D01G112000 chr3A 93.103 87 5 1 1517 1603 77471810 77471895 3.450000e-25 126.0
4 TraesCS3D01G112000 chr3A 92.647 68 3 2 1517 1583 77471834 77471900 2.700000e-16 97.1
5 TraesCS3D01G112000 chr3A 100.000 35 0 0 2336 2370 77472593 77472559 7.630000e-07 65.8
6 TraesCS3D01G112000 chr3B 93.043 2041 88 19 469 2479 109941844 109943860 0.000000e+00 2933.0
7 TraesCS3D01G112000 chr3B 88.916 821 60 18 2486 3293 109944014 109944816 0.000000e+00 983.0
8 TraesCS3D01G112000 chr3B 95.146 103 5 0 1573 1675 109942909 109943011 2.630000e-36 163.0
9 TraesCS3D01G112000 chr1A 89.474 57 4 2 2 57 292088845 292088900 1.640000e-08 71.3


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 TraesCS3D01G112000 chr3D 66338853 66342145 3292 False 6082.000000 6082 100.000000 1 3293 1 chr3D.!!$F1 3292
1 TraesCS3D01G112000 chr3A 77470563 77473562 2999 False 1227.275000 2994 94.413750 313 3293 4 chr3A.!!$F1 2980
2 TraesCS3D01G112000 chr3B 109941844 109944816 2972 False 1359.666667 2933 92.368333 469 3293 3 chr3B.!!$F1 2824

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
33 34 0.178947 TGTTTAGGGGCAAAGTGGGG 60.179 55.0 0.0 0.0 0.0 4.96 F
51 52 0.179081 GGGTCCGGTTGTAGATGCTC 60.179 60.0 0.0 0.0 0.0 4.26 F
1566 1634 0.099259 TACACCGACGCCATCTTACG 59.901 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1563 0.179084 AGTTGGTGTCGGTGTCAGTG 60.179 55.000 0.0 0.0 0.00 3.66 R
1572 1640 0.249573 CCGTAAGTTGGTGTCGGTGT 60.250 55.000 0.0 0.0 36.99 4.16 R
2519 2797 1.755959 TGAAGTGTTTGCTTGCCACAT 59.244 42.857 0.0 0.0 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
18 19 3.935993 CCTGTCCACTCGGATGTTT 57.064 52.632 0.00 0.00 45.33 2.83
20 21 2.893637 CCTGTCCACTCGGATGTTTAG 58.106 52.381 0.00 0.00 45.33 1.85
21 22 2.418746 CCTGTCCACTCGGATGTTTAGG 60.419 54.545 0.00 0.00 45.33 2.69
22 23 1.553248 TGTCCACTCGGATGTTTAGGG 59.447 52.381 0.00 0.00 45.33 3.53
23 24 1.134491 GTCCACTCGGATGTTTAGGGG 60.134 57.143 0.00 0.00 45.33 4.79
24 25 0.463833 CCACTCGGATGTTTAGGGGC 60.464 60.000 0.00 0.00 0.00 5.80
25 26 0.251916 CACTCGGATGTTTAGGGGCA 59.748 55.000 0.00 0.00 0.00 5.36
26 27 0.988832 ACTCGGATGTTTAGGGGCAA 59.011 50.000 0.00 0.00 0.00 4.52
27 28 1.353022 ACTCGGATGTTTAGGGGCAAA 59.647 47.619 0.00 0.00 0.00 3.68
28 29 2.017049 CTCGGATGTTTAGGGGCAAAG 58.983 52.381 0.00 0.00 0.00 2.77
29 30 1.353022 TCGGATGTTTAGGGGCAAAGT 59.647 47.619 0.00 0.00 0.00 2.66
30 31 1.472480 CGGATGTTTAGGGGCAAAGTG 59.528 52.381 0.00 0.00 0.00 3.16
31 32 1.824852 GGATGTTTAGGGGCAAAGTGG 59.175 52.381 0.00 0.00 0.00 4.00
32 33 1.824852 GATGTTTAGGGGCAAAGTGGG 59.175 52.381 0.00 0.00 0.00 4.61
33 34 0.178947 TGTTTAGGGGCAAAGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
34 35 0.902984 GTTTAGGGGCAAAGTGGGGG 60.903 60.000 0.00 0.00 0.00 5.40
35 36 1.373044 TTTAGGGGCAAAGTGGGGGT 61.373 55.000 0.00 0.00 0.00 4.95
36 37 1.795951 TTAGGGGCAAAGTGGGGGTC 61.796 60.000 0.00 0.00 0.00 4.46
37 38 4.696805 GGGGCAAAGTGGGGGTCC 62.697 72.222 0.00 0.00 0.00 4.46
40 41 4.280019 GCAAAGTGGGGGTCCGGT 62.280 66.667 0.00 0.00 35.24 5.28
41 42 2.518933 CAAAGTGGGGGTCCGGTT 59.481 61.111 0.00 0.00 35.24 4.44
42 43 1.901464 CAAAGTGGGGGTCCGGTTG 60.901 63.158 0.00 0.00 35.24 3.77
43 44 2.388610 AAAGTGGGGGTCCGGTTGT 61.389 57.895 0.00 0.00 35.24 3.32
44 45 1.061324 AAAGTGGGGGTCCGGTTGTA 61.061 55.000 0.00 0.00 35.24 2.41
45 46 1.486145 AAGTGGGGGTCCGGTTGTAG 61.486 60.000 0.00 0.00 35.24 2.74
46 47 1.914764 GTGGGGGTCCGGTTGTAGA 60.915 63.158 0.00 0.00 35.24 2.59
47 48 1.081462 TGGGGGTCCGGTTGTAGAT 59.919 57.895 0.00 0.00 35.24 1.98
48 49 1.268992 TGGGGGTCCGGTTGTAGATG 61.269 60.000 0.00 0.00 35.24 2.90
49 50 1.153229 GGGGTCCGGTTGTAGATGC 60.153 63.158 0.00 0.00 0.00 3.91
50 51 1.623542 GGGGTCCGGTTGTAGATGCT 61.624 60.000 0.00 0.00 0.00 3.79
51 52 0.179081 GGGTCCGGTTGTAGATGCTC 60.179 60.000 0.00 0.00 0.00 4.26
52 53 0.824759 GGTCCGGTTGTAGATGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
53 54 2.029623 GGTCCGGTTGTAGATGCTCTA 58.970 52.381 0.00 0.00 0.00 2.43
54 55 2.429610 GGTCCGGTTGTAGATGCTCTAA 59.570 50.000 0.00 0.00 29.58 2.10
55 56 3.118884 GGTCCGGTTGTAGATGCTCTAAA 60.119 47.826 0.00 0.00 29.58 1.85
56 57 4.113354 GTCCGGTTGTAGATGCTCTAAAG 58.887 47.826 0.00 0.00 29.58 1.85
57 58 4.021229 TCCGGTTGTAGATGCTCTAAAGA 58.979 43.478 0.00 0.00 29.58 2.52
58 59 4.113354 CCGGTTGTAGATGCTCTAAAGAC 58.887 47.826 0.00 0.00 29.58 3.01
59 60 4.381612 CCGGTTGTAGATGCTCTAAAGACA 60.382 45.833 0.00 0.00 29.58 3.41
60 61 5.168569 CGGTTGTAGATGCTCTAAAGACAA 58.831 41.667 0.00 0.00 29.58 3.18
61 62 5.062308 CGGTTGTAGATGCTCTAAAGACAAC 59.938 44.000 14.66 14.66 39.59 3.32
62 63 5.932303 GGTTGTAGATGCTCTAAAGACAACA 59.068 40.000 19.67 5.80 40.93 3.33
63 64 6.595716 GGTTGTAGATGCTCTAAAGACAACAT 59.404 38.462 19.67 0.00 40.93 2.71
64 65 7.413438 GGTTGTAGATGCTCTAAAGACAACATG 60.413 40.741 19.67 0.00 40.93 3.21
65 66 6.935167 TGTAGATGCTCTAAAGACAACATGA 58.065 36.000 0.00 0.00 29.58 3.07
66 67 7.559486 TGTAGATGCTCTAAAGACAACATGAT 58.441 34.615 0.00 0.00 29.58 2.45
67 68 8.695456 TGTAGATGCTCTAAAGACAACATGATA 58.305 33.333 0.00 0.00 29.58 2.15
68 69 9.534565 GTAGATGCTCTAAAGACAACATGATAA 57.465 33.333 0.00 0.00 29.58 1.75
69 70 8.430801 AGATGCTCTAAAGACAACATGATAAC 57.569 34.615 0.00 0.00 0.00 1.89
70 71 8.043113 AGATGCTCTAAAGACAACATGATAACA 58.957 33.333 0.00 0.00 0.00 2.41
71 72 8.743085 ATGCTCTAAAGACAACATGATAACAT 57.257 30.769 0.00 0.00 37.19 2.71
84 85 6.198650 CATGATAACATGTGTGATGTTGGT 57.801 37.500 0.00 0.06 46.01 3.67
85 86 5.625921 TGATAACATGTGTGATGTTGGTG 57.374 39.130 0.00 0.00 41.73 4.17
86 87 5.312079 TGATAACATGTGTGATGTTGGTGA 58.688 37.500 0.00 0.00 41.73 4.02
87 88 5.767168 TGATAACATGTGTGATGTTGGTGAA 59.233 36.000 0.00 0.00 41.73 3.18
88 89 6.433716 TGATAACATGTGTGATGTTGGTGAAT 59.566 34.615 0.00 0.00 41.73 2.57
89 90 4.771590 ACATGTGTGATGTTGGTGAATC 57.228 40.909 0.00 0.00 0.00 2.52
90 91 4.143543 ACATGTGTGATGTTGGTGAATCA 58.856 39.130 0.00 0.00 0.00 2.57
95 96 3.144657 TGATGTTGGTGAATCACAGCT 57.855 42.857 15.86 0.00 45.86 4.24
96 97 2.815503 TGATGTTGGTGAATCACAGCTG 59.184 45.455 13.48 13.48 45.86 4.24
97 98 0.953727 TGTTGGTGAATCACAGCTGC 59.046 50.000 15.27 0.00 45.86 5.25
98 99 0.953727 GTTGGTGAATCACAGCTGCA 59.046 50.000 15.27 0.00 45.86 4.41
99 100 1.337703 GTTGGTGAATCACAGCTGCAA 59.662 47.619 15.27 6.80 45.86 4.08
100 101 1.913778 TGGTGAATCACAGCTGCAAT 58.086 45.000 15.27 4.42 45.86 3.56
101 102 3.070476 TGGTGAATCACAGCTGCAATA 57.930 42.857 15.27 0.00 45.86 1.90
102 103 3.623703 TGGTGAATCACAGCTGCAATAT 58.376 40.909 15.27 0.00 45.86 1.28
103 104 4.018490 TGGTGAATCACAGCTGCAATATT 58.982 39.130 15.27 8.33 45.86 1.28
104 105 5.192176 TGGTGAATCACAGCTGCAATATTA 58.808 37.500 15.27 0.00 45.86 0.98
105 106 5.829391 TGGTGAATCACAGCTGCAATATTAT 59.171 36.000 15.27 0.00 45.86 1.28
106 107 6.016860 TGGTGAATCACAGCTGCAATATTATC 60.017 38.462 15.27 2.82 45.86 1.75
107 108 6.016860 GGTGAATCACAGCTGCAATATTATCA 60.017 38.462 15.27 5.39 42.84 2.15
108 109 7.309012 GGTGAATCACAGCTGCAATATTATCAT 60.309 37.037 15.27 0.00 42.84 2.45
109 110 8.080417 GTGAATCACAGCTGCAATATTATCATT 58.920 33.333 15.27 0.00 34.08 2.57
110 111 8.079809 TGAATCACAGCTGCAATATTATCATTG 58.920 33.333 15.27 0.00 38.65 2.82
119 120 3.788333 ATATTATCATTGCGGCATGGC 57.212 42.857 9.69 9.69 0.00 4.40
120 121 1.624336 ATTATCATTGCGGCATGGCT 58.376 45.000 18.09 0.00 0.00 4.75
121 122 1.401761 TTATCATTGCGGCATGGCTT 58.598 45.000 18.09 0.00 0.00 4.35
122 123 0.953727 TATCATTGCGGCATGGCTTC 59.046 50.000 18.09 9.40 0.00 3.86
123 124 2.067091 ATCATTGCGGCATGGCTTCG 62.067 55.000 18.09 2.82 0.00 3.79
124 125 3.520862 ATTGCGGCATGGCTTCGG 61.521 61.111 18.09 2.43 0.00 4.30
127 128 3.747976 GCGGCATGGCTTCGGTTT 61.748 61.111 18.09 0.00 0.00 3.27
128 129 2.485122 CGGCATGGCTTCGGTTTC 59.515 61.111 18.09 0.00 0.00 2.78
129 130 2.040544 CGGCATGGCTTCGGTTTCT 61.041 57.895 18.09 0.00 0.00 2.52
130 131 1.586154 CGGCATGGCTTCGGTTTCTT 61.586 55.000 18.09 0.00 0.00 2.52
131 132 1.459450 GGCATGGCTTCGGTTTCTTA 58.541 50.000 12.86 0.00 0.00 2.10
132 133 1.132453 GGCATGGCTTCGGTTTCTTAC 59.868 52.381 12.86 0.00 0.00 2.34
133 134 1.132453 GCATGGCTTCGGTTTCTTACC 59.868 52.381 0.00 0.00 44.03 2.85
134 135 2.711542 CATGGCTTCGGTTTCTTACCT 58.288 47.619 0.00 0.00 45.40 3.08
135 136 2.943036 TGGCTTCGGTTTCTTACCTT 57.057 45.000 0.00 0.00 45.40 3.50
136 137 3.217681 TGGCTTCGGTTTCTTACCTTT 57.782 42.857 0.00 0.00 45.40 3.11
137 138 3.558033 TGGCTTCGGTTTCTTACCTTTT 58.442 40.909 0.00 0.00 45.40 2.27
138 139 3.955551 TGGCTTCGGTTTCTTACCTTTTT 59.044 39.130 0.00 0.00 45.40 1.94
179 180 7.490962 CTGTAAGTAATTCAGACCAACACAA 57.509 36.000 0.00 0.00 0.00 3.33
180 181 7.867305 TGTAAGTAATTCAGACCAACACAAA 57.133 32.000 0.00 0.00 0.00 2.83
181 182 8.282455 TGTAAGTAATTCAGACCAACACAAAA 57.718 30.769 0.00 0.00 0.00 2.44
182 183 8.402472 TGTAAGTAATTCAGACCAACACAAAAG 58.598 33.333 0.00 0.00 0.00 2.27
183 184 7.404671 AAGTAATTCAGACCAACACAAAAGT 57.595 32.000 0.00 0.00 0.00 2.66
184 185 7.404671 AGTAATTCAGACCAACACAAAAGTT 57.595 32.000 0.00 0.00 0.00 2.66
185 186 8.514330 AGTAATTCAGACCAACACAAAAGTTA 57.486 30.769 0.00 0.00 0.00 2.24
186 187 8.403236 AGTAATTCAGACCAACACAAAAGTTAC 58.597 33.333 0.00 0.00 0.00 2.50
187 188 6.767524 ATTCAGACCAACACAAAAGTTACA 57.232 33.333 0.00 0.00 0.00 2.41
188 189 5.811399 TCAGACCAACACAAAAGTTACAG 57.189 39.130 0.00 0.00 0.00 2.74
189 190 4.638421 TCAGACCAACACAAAAGTTACAGG 59.362 41.667 0.00 0.00 0.00 4.00
190 191 4.638421 CAGACCAACACAAAAGTTACAGGA 59.362 41.667 0.00 0.00 0.00 3.86
191 192 5.299279 CAGACCAACACAAAAGTTACAGGAT 59.701 40.000 0.00 0.00 0.00 3.24
192 193 6.485313 CAGACCAACACAAAAGTTACAGGATA 59.515 38.462 0.00 0.00 0.00 2.59
193 194 7.174946 CAGACCAACACAAAAGTTACAGGATAT 59.825 37.037 0.00 0.00 0.00 1.63
194 195 7.174946 AGACCAACACAAAAGTTACAGGATATG 59.825 37.037 0.00 0.00 0.00 1.78
195 196 6.092748 CCAACACAAAAGTTACAGGATATGC 58.907 40.000 0.00 0.00 0.00 3.14
196 197 6.294453 CCAACACAAAAGTTACAGGATATGCA 60.294 38.462 0.00 0.00 0.00 3.96
197 198 6.254281 ACACAAAAGTTACAGGATATGCAC 57.746 37.500 0.00 0.00 0.00 4.57
198 199 6.003950 ACACAAAAGTTACAGGATATGCACT 58.996 36.000 0.00 0.00 0.00 4.40
199 200 7.165485 ACACAAAAGTTACAGGATATGCACTA 58.835 34.615 0.00 0.00 0.00 2.74
200 201 7.119262 ACACAAAAGTTACAGGATATGCACTAC 59.881 37.037 0.00 0.00 0.00 2.73
201 202 7.119116 CACAAAAGTTACAGGATATGCACTACA 59.881 37.037 0.00 0.00 0.00 2.74
202 203 7.663905 ACAAAAGTTACAGGATATGCACTACAA 59.336 33.333 0.00 0.00 0.00 2.41
203 204 7.611213 AAAGTTACAGGATATGCACTACAAC 57.389 36.000 0.00 0.00 0.00 3.32
204 205 6.294361 AGTTACAGGATATGCACTACAACA 57.706 37.500 0.00 0.00 0.00 3.33
205 206 6.106673 AGTTACAGGATATGCACTACAACAC 58.893 40.000 0.00 0.00 0.00 3.32
206 207 4.826274 ACAGGATATGCACTACAACACT 57.174 40.909 0.00 0.00 0.00 3.55
207 208 5.932619 ACAGGATATGCACTACAACACTA 57.067 39.130 0.00 0.00 0.00 2.74
208 209 5.907207 ACAGGATATGCACTACAACACTAG 58.093 41.667 0.00 0.00 0.00 2.57
209 210 5.656859 ACAGGATATGCACTACAACACTAGA 59.343 40.000 0.00 0.00 0.00 2.43
210 211 6.154534 ACAGGATATGCACTACAACACTAGAA 59.845 38.462 0.00 0.00 0.00 2.10
211 212 7.147655 ACAGGATATGCACTACAACACTAGAAT 60.148 37.037 0.00 0.00 0.00 2.40
212 213 7.170489 CAGGATATGCACTACAACACTAGAATG 59.830 40.741 0.00 0.00 0.00 2.67
213 214 6.986817 GGATATGCACTACAACACTAGAATGT 59.013 38.462 0.00 0.81 0.00 2.71
214 215 7.495934 GGATATGCACTACAACACTAGAATGTT 59.504 37.037 0.00 0.00 43.67 2.71
215 216 8.792830 ATATGCACTACAACACTAGAATGTTT 57.207 30.769 0.00 0.00 40.89 2.83
216 217 6.935741 TGCACTACAACACTAGAATGTTTT 57.064 33.333 0.00 0.00 40.89 2.43
217 218 7.328277 TGCACTACAACACTAGAATGTTTTT 57.672 32.000 0.00 0.00 40.89 1.94
240 241 7.412853 TTTTTACCAAAAGACAGCCTTAAGT 57.587 32.000 0.97 0.00 34.00 2.24
241 242 6.385649 TTTACCAAAAGACAGCCTTAAGTG 57.614 37.500 0.97 0.00 34.00 3.16
242 243 3.898482 ACCAAAAGACAGCCTTAAGTGT 58.102 40.909 0.97 0.00 34.00 3.55
243 244 4.278310 ACCAAAAGACAGCCTTAAGTGTT 58.722 39.130 0.97 0.00 34.00 3.32
244 245 4.097892 ACCAAAAGACAGCCTTAAGTGTTG 59.902 41.667 0.97 4.27 34.00 3.33
245 246 4.097892 CCAAAAGACAGCCTTAAGTGTTGT 59.902 41.667 11.34 11.34 34.00 3.32
246 247 5.298276 CCAAAAGACAGCCTTAAGTGTTGTA 59.702 40.000 11.45 0.00 34.00 2.41
247 248 6.016276 CCAAAAGACAGCCTTAAGTGTTGTAT 60.016 38.462 11.45 7.49 34.00 2.29
248 249 7.425606 CAAAAGACAGCCTTAAGTGTTGTATT 58.574 34.615 11.45 11.69 34.00 1.89
249 250 7.582667 AAAGACAGCCTTAAGTGTTGTATTT 57.417 32.000 18.50 18.50 34.00 1.40
250 251 6.803154 AGACAGCCTTAAGTGTTGTATTTC 57.197 37.500 11.45 3.04 0.00 2.17
251 252 6.296026 AGACAGCCTTAAGTGTTGTATTTCA 58.704 36.000 11.45 0.00 0.00 2.69
252 253 6.942576 AGACAGCCTTAAGTGTTGTATTTCAT 59.057 34.615 11.45 0.00 0.00 2.57
253 254 7.448469 AGACAGCCTTAAGTGTTGTATTTCATT 59.552 33.333 11.45 0.00 0.00 2.57
254 255 7.370383 ACAGCCTTAAGTGTTGTATTTCATTG 58.630 34.615 10.28 0.00 0.00 2.82
255 256 7.230510 ACAGCCTTAAGTGTTGTATTTCATTGA 59.769 33.333 10.28 0.00 0.00 2.57
256 257 8.246180 CAGCCTTAAGTGTTGTATTTCATTGAT 58.754 33.333 0.97 0.00 0.00 2.57
257 258 8.246180 AGCCTTAAGTGTTGTATTTCATTGATG 58.754 33.333 0.97 0.00 0.00 3.07
258 259 8.243426 GCCTTAAGTGTTGTATTTCATTGATGA 58.757 33.333 0.97 0.00 34.44 2.92
262 263 7.765695 AGTGTTGTATTTCATTGATGAAGGT 57.234 32.000 6.53 3.59 46.34 3.50
263 264 8.862325 AGTGTTGTATTTCATTGATGAAGGTA 57.138 30.769 6.53 2.79 46.34 3.08
264 265 8.950210 AGTGTTGTATTTCATTGATGAAGGTAG 58.050 33.333 6.53 0.00 46.34 3.18
265 266 8.946085 GTGTTGTATTTCATTGATGAAGGTAGA 58.054 33.333 6.53 1.79 46.34 2.59
266 267 9.513906 TGTTGTATTTCATTGATGAAGGTAGAA 57.486 29.630 6.53 6.61 46.34 2.10
269 270 8.664798 TGTATTTCATTGATGAAGGTAGAAACG 58.335 33.333 6.53 0.00 46.34 3.60
270 271 7.921786 ATTTCATTGATGAAGGTAGAAACGA 57.078 32.000 6.53 0.00 46.34 3.85
271 272 7.737972 TTTCATTGATGAAGGTAGAAACGAA 57.262 32.000 6.53 0.00 46.34 3.85
272 273 7.921786 TTCATTGATGAAGGTAGAAACGAAT 57.078 32.000 2.39 0.00 41.51 3.34
273 274 7.539712 TCATTGATGAAGGTAGAAACGAATC 57.460 36.000 0.00 0.00 33.08 2.52
274 275 7.102993 TCATTGATGAAGGTAGAAACGAATCA 58.897 34.615 0.00 0.00 33.08 2.57
275 276 7.606073 TCATTGATGAAGGTAGAAACGAATCAA 59.394 33.333 0.00 0.00 37.25 2.57
276 277 7.737972 TTGATGAAGGTAGAAACGAATCAAA 57.262 32.000 0.00 0.00 31.72 2.69
277 278 7.737972 TGATGAAGGTAGAAACGAATCAAAA 57.262 32.000 0.00 0.00 0.00 2.44
278 279 7.806690 TGATGAAGGTAGAAACGAATCAAAAG 58.193 34.615 0.00 0.00 0.00 2.27
279 280 6.554334 TGAAGGTAGAAACGAATCAAAAGG 57.446 37.500 0.00 0.00 0.00 3.11
280 281 6.292923 TGAAGGTAGAAACGAATCAAAAGGA 58.707 36.000 0.00 0.00 0.00 3.36
281 282 6.768861 TGAAGGTAGAAACGAATCAAAAGGAA 59.231 34.615 0.00 0.00 0.00 3.36
282 283 6.555812 AGGTAGAAACGAATCAAAAGGAAC 57.444 37.500 0.00 0.00 0.00 3.62
284 285 6.204882 AGGTAGAAACGAATCAAAAGGAACTG 59.795 38.462 0.00 0.00 40.86 3.16
285 286 6.204108 GGTAGAAACGAATCAAAAGGAACTGA 59.796 38.462 0.00 0.00 40.86 3.41
286 287 6.693315 AGAAACGAATCAAAAGGAACTGAA 57.307 33.333 0.00 0.00 40.86 3.02
287 288 7.095695 AGAAACGAATCAAAAGGAACTGAAA 57.904 32.000 0.00 0.00 40.86 2.69
288 289 6.972901 AGAAACGAATCAAAAGGAACTGAAAC 59.027 34.615 0.00 0.00 40.86 2.78
289 290 6.451064 AACGAATCAAAAGGAACTGAAACT 57.549 33.333 0.00 0.00 40.86 2.66
290 291 6.451064 ACGAATCAAAAGGAACTGAAACTT 57.549 33.333 0.00 0.00 40.86 2.66
291 292 6.863275 ACGAATCAAAAGGAACTGAAACTTT 58.137 32.000 0.00 0.00 40.86 2.66
292 293 7.320399 ACGAATCAAAAGGAACTGAAACTTTT 58.680 30.769 0.00 0.00 43.10 2.27
297 298 3.443099 AGGAACTGAAACTTTTGCAGC 57.557 42.857 0.00 0.00 37.18 5.25
298 299 2.760092 AGGAACTGAAACTTTTGCAGCA 59.240 40.909 0.00 0.00 37.18 4.41
299 300 2.860136 GGAACTGAAACTTTTGCAGCAC 59.140 45.455 0.00 0.00 33.03 4.40
300 301 3.510719 GAACTGAAACTTTTGCAGCACA 58.489 40.909 0.00 0.00 33.03 4.57
301 302 3.591196 ACTGAAACTTTTGCAGCACAA 57.409 38.095 0.00 0.00 36.13 3.33
302 303 4.127566 ACTGAAACTTTTGCAGCACAAT 57.872 36.364 0.00 0.00 38.31 2.71
303 304 5.261209 ACTGAAACTTTTGCAGCACAATA 57.739 34.783 0.00 0.00 38.31 1.90
304 305 5.043248 ACTGAAACTTTTGCAGCACAATAC 58.957 37.500 0.00 0.00 38.31 1.89
305 306 5.163519 ACTGAAACTTTTGCAGCACAATACT 60.164 36.000 0.00 0.00 38.31 2.12
306 307 5.042593 TGAAACTTTTGCAGCACAATACTG 58.957 37.500 0.00 0.00 38.31 2.74
307 308 4.654091 AACTTTTGCAGCACAATACTGT 57.346 36.364 0.00 0.00 38.31 3.55
308 309 4.228912 ACTTTTGCAGCACAATACTGTC 57.771 40.909 0.00 0.00 38.31 3.51
309 310 3.631686 ACTTTTGCAGCACAATACTGTCA 59.368 39.130 0.00 0.00 38.31 3.58
310 311 4.097741 ACTTTTGCAGCACAATACTGTCAA 59.902 37.500 0.00 0.00 38.31 3.18
311 312 4.645762 TTTGCAGCACAATACTGTCAAA 57.354 36.364 0.00 0.00 38.31 2.69
351 352 9.423061 ACAAATCTGTGGTAATAAGCAAAATTC 57.577 29.630 0.00 0.00 34.25 2.17
352 353 8.872845 CAAATCTGTGGTAATAAGCAAAATTCC 58.127 33.333 0.00 0.00 34.25 3.01
353 354 7.961326 ATCTGTGGTAATAAGCAAAATTCCT 57.039 32.000 0.00 0.00 34.25 3.36
355 356 7.601856 TCTGTGGTAATAAGCAAAATTCCTTG 58.398 34.615 0.00 0.00 34.25 3.61
358 359 7.870445 TGTGGTAATAAGCAAAATTCCTTGTTC 59.130 33.333 0.00 0.00 34.25 3.18
359 360 7.870445 GTGGTAATAAGCAAAATTCCTTGTTCA 59.130 33.333 0.00 0.00 34.25 3.18
360 361 7.870445 TGGTAATAAGCAAAATTCCTTGTTCAC 59.130 33.333 0.00 0.00 0.00 3.18
362 363 9.423061 GTAATAAGCAAAATTCCTTGTTCACAT 57.577 29.630 0.00 0.00 0.00 3.21
363 364 8.907222 AATAAGCAAAATTCCTTGTTCACATT 57.093 26.923 0.00 0.00 0.00 2.71
387 388 4.840401 TCTAAAGATGAAATGCACGACG 57.160 40.909 0.00 0.00 0.00 5.12
388 389 4.242475 TCTAAAGATGAAATGCACGACGT 58.758 39.130 0.00 0.00 0.00 4.34
390 391 3.896648 AAGATGAAATGCACGACGTTT 57.103 38.095 0.00 0.00 40.26 3.60
400 401 2.126467 GCACGACGTTTACAGGTGTTA 58.874 47.619 0.00 0.00 0.00 2.41
432 439 0.321653 AAGCAGACCGAATCACCACC 60.322 55.000 0.00 0.00 0.00 4.61
450 457 2.100749 CACCTTCCAGTTGGACCAAAAC 59.899 50.000 8.94 0.00 45.39 2.43
467 474 4.142491 CCAAAACACAGCTTCAGTAACACA 60.142 41.667 0.00 0.00 0.00 3.72
471 478 5.637006 ACACAGCTTCAGTAACACAAAAA 57.363 34.783 0.00 0.00 0.00 1.94
554 562 3.534357 AACATACCCCACCATGTTTCA 57.466 42.857 0.00 0.00 41.43 2.69
686 694 2.889045 CCGGAGAGTATTCCATTCCGTA 59.111 50.000 0.00 0.00 46.97 4.02
688 696 3.317149 CGGAGAGTATTCCATTCCGTACA 59.683 47.826 6.32 0.00 44.23 2.90
817 832 5.411361 TCAGATGAAGAATTGGGTTAACACG 59.589 40.000 8.10 0.00 0.00 4.49
840 856 4.081087 GGGCTCTAAAATACTCACAGTGGA 60.081 45.833 0.00 0.00 0.00 4.02
855 871 0.318762 GTGGAAGCTTGGTCGAGAGT 59.681 55.000 2.10 0.00 0.00 3.24
941 970 9.371136 CAACTACTAACAGTGTGATGAACATAT 57.629 33.333 0.00 0.00 41.97 1.78
948 977 6.711277 ACAGTGTGATGAACATATACAGGTT 58.289 36.000 0.00 0.00 41.97 3.50
1015 1044 6.294787 CCACTCTCGTGTATAAATAGGCATCT 60.295 42.308 0.00 0.00 39.55 2.90
1102 1136 1.071228 TCTGCACACACTGAGAGCAAT 59.929 47.619 0.82 0.00 34.45 3.56
1126 1160 1.815003 GGTGGCAAGGTTCTTCTGATG 59.185 52.381 0.00 0.00 0.00 3.07
1291 1335 3.321968 ACTGCATCTATTACAGCGATCCA 59.678 43.478 0.00 0.00 34.72 3.41
1298 1342 6.456795 TCTATTACAGCGATCCATGGATAG 57.543 41.667 27.38 26.53 34.60 2.08
1338 1382 4.816385 TGCATCTACCTAGCTAATGCAAAC 59.184 41.667 21.91 0.85 46.92 2.93
1435 1479 5.791336 TCATGCTATCTAGATTTCACGGT 57.209 39.130 11.25 0.00 0.00 4.83
1517 1561 1.686110 AGGAGGAGGCTACAACCCG 60.686 63.158 0.00 0.00 0.00 5.28
1518 1562 1.684734 GGAGGAGGCTACAACCCGA 60.685 63.158 0.00 0.00 0.00 5.14
1519 1563 1.516423 GAGGAGGCTACAACCCGAC 59.484 63.158 0.00 0.00 0.00 4.79
1520 1564 1.229082 AGGAGGCTACAACCCGACA 60.229 57.895 0.00 0.00 0.00 4.35
1521 1565 1.079336 GGAGGCTACAACCCGACAC 60.079 63.158 0.00 0.00 0.00 3.67
1522 1566 1.542187 GGAGGCTACAACCCGACACT 61.542 60.000 0.00 0.00 0.00 3.55
1563 1631 0.108804 CACTACACCGACGCCATCTT 60.109 55.000 0.00 0.00 0.00 2.40
1564 1632 1.133598 CACTACACCGACGCCATCTTA 59.866 52.381 0.00 0.00 0.00 2.10
1565 1633 1.133790 ACTACACCGACGCCATCTTAC 59.866 52.381 0.00 0.00 0.00 2.34
1566 1634 0.099259 TACACCGACGCCATCTTACG 59.901 55.000 0.00 0.00 0.00 3.18
1568 1636 2.960129 CCGACGCCATCTTACGGC 60.960 66.667 0.00 0.00 46.62 5.68
1576 1644 1.935933 CCATCTTACGGCACTACACC 58.064 55.000 0.00 0.00 0.00 4.16
1583 1651 2.738480 GGCACTACACCGACACCA 59.262 61.111 0.00 0.00 0.00 4.17
1584 1652 1.070105 GGCACTACACCGACACCAA 59.930 57.895 0.00 0.00 0.00 3.67
1585 1653 1.226030 GGCACTACACCGACACCAAC 61.226 60.000 0.00 0.00 0.00 3.77
1586 1654 0.249741 GCACTACACCGACACCAACT 60.250 55.000 0.00 0.00 0.00 3.16
1594 1662 0.672401 CCGACACCAACTTACGGCAT 60.672 55.000 0.00 0.00 37.32 4.40
1661 1729 2.029623 ACTACACCGACGCCATCTTAT 58.970 47.619 0.00 0.00 0.00 1.73
1822 1895 9.320352 GGTTCTTAAATGGTTTTCTTTTGCTTA 57.680 29.630 0.00 0.00 0.00 3.09
1879 1952 0.255890 TTGCAGCTATTGGGTCCCTC 59.744 55.000 10.00 0.00 0.00 4.30
2071 2144 1.757306 CCAGCAGGTGAAGGACTGT 59.243 57.895 0.00 0.00 37.07 3.55
2156 2229 7.121315 AGGCAAATGAATTCCACTACTAGTTTC 59.879 37.037 0.00 0.00 0.00 2.78
2163 2236 8.035394 TGAATTCCACTACTAGTTTCAGTCATC 58.965 37.037 0.00 0.00 0.00 2.92
2305 2378 6.855763 TTTTGAGTGCAATAAATCCATCCT 57.144 33.333 0.00 0.00 33.25 3.24
2325 2398 6.455360 TCCTTTTCCATTGCTTGATATCAC 57.545 37.500 4.48 0.00 0.00 3.06
2797 3076 9.679661 AAAATCCTGTAACAAAACCATCTTTTT 57.320 25.926 0.00 0.00 0.00 1.94
3212 3493 3.118298 TGGATGTGCTATGTGCTATGTGT 60.118 43.478 0.00 0.00 43.37 3.72
3213 3494 3.879295 GGATGTGCTATGTGCTATGTGTT 59.121 43.478 0.00 0.00 43.37 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.463833 GCCCCTAAACATCCGAGTGG 60.464 60.000 0.00 0.00 0.00 4.00
6 7 0.251916 TGCCCCTAAACATCCGAGTG 59.748 55.000 0.00 0.00 0.00 3.51
7 8 0.988832 TTGCCCCTAAACATCCGAGT 59.011 50.000 0.00 0.00 0.00 4.18
8 9 2.017049 CTTTGCCCCTAAACATCCGAG 58.983 52.381 0.00 0.00 0.00 4.63
9 10 1.353022 ACTTTGCCCCTAAACATCCGA 59.647 47.619 0.00 0.00 0.00 4.55
10 11 1.472480 CACTTTGCCCCTAAACATCCG 59.528 52.381 0.00 0.00 0.00 4.18
11 12 1.824852 CCACTTTGCCCCTAAACATCC 59.175 52.381 0.00 0.00 0.00 3.51
12 13 1.824852 CCCACTTTGCCCCTAAACATC 59.175 52.381 0.00 0.00 0.00 3.06
13 14 1.552254 CCCCACTTTGCCCCTAAACAT 60.552 52.381 0.00 0.00 0.00 2.71
14 15 0.178947 CCCCACTTTGCCCCTAAACA 60.179 55.000 0.00 0.00 0.00 2.83
15 16 0.902984 CCCCCACTTTGCCCCTAAAC 60.903 60.000 0.00 0.00 0.00 2.01
16 17 1.373044 ACCCCCACTTTGCCCCTAAA 61.373 55.000 0.00 0.00 0.00 1.85
17 18 1.780911 ACCCCCACTTTGCCCCTAA 60.781 57.895 0.00 0.00 0.00 2.69
18 19 2.121228 ACCCCCACTTTGCCCCTA 60.121 61.111 0.00 0.00 0.00 3.53
19 20 3.590574 GACCCCCACTTTGCCCCT 61.591 66.667 0.00 0.00 0.00 4.79
20 21 4.696805 GGACCCCCACTTTGCCCC 62.697 72.222 0.00 0.00 0.00 5.80
23 24 3.802852 AACCGGACCCCCACTTTGC 62.803 63.158 9.46 0.00 0.00 3.68
24 25 1.901464 CAACCGGACCCCCACTTTG 60.901 63.158 9.46 0.00 0.00 2.77
25 26 1.061324 TACAACCGGACCCCCACTTT 61.061 55.000 9.46 0.00 0.00 2.66
26 27 1.461849 TACAACCGGACCCCCACTT 60.462 57.895 9.46 0.00 0.00 3.16
27 28 1.916777 CTACAACCGGACCCCCACT 60.917 63.158 9.46 0.00 0.00 4.00
28 29 1.269703 ATCTACAACCGGACCCCCAC 61.270 60.000 9.46 0.00 0.00 4.61
29 30 1.081462 ATCTACAACCGGACCCCCA 59.919 57.895 9.46 0.00 0.00 4.96
30 31 1.525442 CATCTACAACCGGACCCCC 59.475 63.158 9.46 0.00 0.00 5.40
31 32 1.153229 GCATCTACAACCGGACCCC 60.153 63.158 9.46 0.00 0.00 4.95
32 33 0.179081 GAGCATCTACAACCGGACCC 60.179 60.000 9.46 0.00 0.00 4.46
33 34 3.364277 GAGCATCTACAACCGGACC 57.636 57.895 9.46 0.00 0.00 4.46
45 46 8.201554 TGTTATCATGTTGTCTTTAGAGCATC 57.798 34.615 0.00 0.00 0.00 3.91
46 47 8.618677 CATGTTATCATGTTGTCTTTAGAGCAT 58.381 33.333 5.72 0.00 44.37 3.79
47 48 7.977904 CATGTTATCATGTTGTCTTTAGAGCA 58.022 34.615 5.72 0.00 44.37 4.26
62 63 5.945191 TCACCAACATCACACATGTTATCAT 59.055 36.000 0.00 0.00 39.94 2.45
63 64 5.312079 TCACCAACATCACACATGTTATCA 58.688 37.500 0.00 0.00 39.94 2.15
64 65 5.878332 TCACCAACATCACACATGTTATC 57.122 39.130 0.00 0.00 39.94 1.75
65 66 6.433716 TGATTCACCAACATCACACATGTTAT 59.566 34.615 0.00 0.00 39.94 1.89
66 67 5.767168 TGATTCACCAACATCACACATGTTA 59.233 36.000 0.00 0.00 39.94 2.41
67 68 4.583907 TGATTCACCAACATCACACATGTT 59.416 37.500 0.00 0.00 42.38 2.71
68 69 4.022935 GTGATTCACCAACATCACACATGT 60.023 41.667 5.44 0.00 45.90 3.21
69 70 4.478699 GTGATTCACCAACATCACACATG 58.521 43.478 5.44 0.00 45.90 3.21
70 71 4.771590 GTGATTCACCAACATCACACAT 57.228 40.909 5.44 0.00 45.90 3.21
74 75 2.816087 AGCTGTGATTCACCAACATCAC 59.184 45.455 14.05 2.42 46.53 3.06
75 76 2.815503 CAGCTGTGATTCACCAACATCA 59.184 45.455 14.05 0.00 32.73 3.07
76 77 2.415090 GCAGCTGTGATTCACCAACATC 60.415 50.000 16.64 0.00 32.73 3.06
77 78 1.542915 GCAGCTGTGATTCACCAACAT 59.457 47.619 16.64 0.00 32.73 2.71
78 79 0.953727 GCAGCTGTGATTCACCAACA 59.046 50.000 16.64 0.00 32.73 3.33
79 80 0.953727 TGCAGCTGTGATTCACCAAC 59.046 50.000 16.64 3.84 32.73 3.77
80 81 1.689984 TTGCAGCTGTGATTCACCAA 58.310 45.000 16.64 5.31 32.73 3.67
81 82 1.913778 ATTGCAGCTGTGATTCACCA 58.086 45.000 16.64 0.00 32.73 4.17
82 83 4.644103 AATATTGCAGCTGTGATTCACC 57.356 40.909 16.64 0.00 32.73 4.02
83 84 6.962686 TGATAATATTGCAGCTGTGATTCAC 58.037 36.000 16.64 9.93 34.56 3.18
84 85 7.754851 ATGATAATATTGCAGCTGTGATTCA 57.245 32.000 16.64 10.05 0.00 2.57
85 86 8.449085 CAATGATAATATTGCAGCTGTGATTC 57.551 34.615 16.64 5.03 31.96 2.52
97 98 3.861113 GCCATGCCGCAATGATAATATTG 59.139 43.478 0.00 0.00 40.25 1.90
98 99 3.765511 AGCCATGCCGCAATGATAATATT 59.234 39.130 0.00 0.00 0.00 1.28
99 100 3.359033 AGCCATGCCGCAATGATAATAT 58.641 40.909 0.00 0.00 0.00 1.28
100 101 2.794103 AGCCATGCCGCAATGATAATA 58.206 42.857 0.00 0.00 0.00 0.98
101 102 1.624336 AGCCATGCCGCAATGATAAT 58.376 45.000 0.00 0.00 0.00 1.28
102 103 1.337703 GAAGCCATGCCGCAATGATAA 59.662 47.619 0.00 0.00 0.00 1.75
103 104 0.953727 GAAGCCATGCCGCAATGATA 59.046 50.000 0.00 0.00 0.00 2.15
104 105 1.737816 GAAGCCATGCCGCAATGAT 59.262 52.632 0.00 0.00 0.00 2.45
105 106 2.763273 CGAAGCCATGCCGCAATGA 61.763 57.895 0.00 0.00 0.00 2.57
106 107 2.278336 CGAAGCCATGCCGCAATG 60.278 61.111 0.00 0.00 0.00 2.82
107 108 3.520862 CCGAAGCCATGCCGCAAT 61.521 61.111 0.00 0.00 0.00 3.56
110 111 3.683587 GAAACCGAAGCCATGCCGC 62.684 63.158 0.00 0.00 0.00 6.53
111 112 1.586154 AAGAAACCGAAGCCATGCCG 61.586 55.000 0.00 0.00 0.00 5.69
112 113 1.132453 GTAAGAAACCGAAGCCATGCC 59.868 52.381 0.00 0.00 0.00 4.40
113 114 1.132453 GGTAAGAAACCGAAGCCATGC 59.868 52.381 0.00 0.00 38.88 4.06
149 150 9.654663 GTTGGTCTGAATTACTTACAGTAGAAT 57.345 33.333 0.00 0.00 31.47 2.40
150 151 8.644216 TGTTGGTCTGAATTACTTACAGTAGAA 58.356 33.333 0.00 0.00 31.47 2.10
151 152 8.086522 GTGTTGGTCTGAATTACTTACAGTAGA 58.913 37.037 0.00 0.00 31.47 2.59
152 153 7.870954 TGTGTTGGTCTGAATTACTTACAGTAG 59.129 37.037 0.00 0.00 31.47 2.57
153 154 7.728148 TGTGTTGGTCTGAATTACTTACAGTA 58.272 34.615 0.00 0.00 33.93 2.74
154 155 6.588204 TGTGTTGGTCTGAATTACTTACAGT 58.412 36.000 0.00 0.00 33.93 3.55
155 156 7.490962 TTGTGTTGGTCTGAATTACTTACAG 57.509 36.000 0.00 0.00 0.00 2.74
156 157 7.867305 TTTGTGTTGGTCTGAATTACTTACA 57.133 32.000 0.00 0.00 0.00 2.41
157 158 8.403236 ACTTTTGTGTTGGTCTGAATTACTTAC 58.597 33.333 0.00 0.00 0.00 2.34
158 159 8.514330 ACTTTTGTGTTGGTCTGAATTACTTA 57.486 30.769 0.00 0.00 0.00 2.24
159 160 7.404671 ACTTTTGTGTTGGTCTGAATTACTT 57.595 32.000 0.00 0.00 0.00 2.24
160 161 7.404671 AACTTTTGTGTTGGTCTGAATTACT 57.595 32.000 0.00 0.00 0.00 2.24
161 162 8.185505 TGTAACTTTTGTGTTGGTCTGAATTAC 58.814 33.333 0.00 0.00 0.00 1.89
162 163 8.282455 TGTAACTTTTGTGTTGGTCTGAATTA 57.718 30.769 0.00 0.00 0.00 1.40
163 164 7.164230 TGTAACTTTTGTGTTGGTCTGAATT 57.836 32.000 0.00 0.00 0.00 2.17
164 165 6.183360 CCTGTAACTTTTGTGTTGGTCTGAAT 60.183 38.462 0.00 0.00 0.00 2.57
165 166 5.124776 CCTGTAACTTTTGTGTTGGTCTGAA 59.875 40.000 0.00 0.00 0.00 3.02
166 167 4.638421 CCTGTAACTTTTGTGTTGGTCTGA 59.362 41.667 0.00 0.00 0.00 3.27
167 168 4.638421 TCCTGTAACTTTTGTGTTGGTCTG 59.362 41.667 0.00 0.00 0.00 3.51
168 169 4.850680 TCCTGTAACTTTTGTGTTGGTCT 58.149 39.130 0.00 0.00 0.00 3.85
169 170 5.767816 ATCCTGTAACTTTTGTGTTGGTC 57.232 39.130 0.00 0.00 0.00 4.02
170 171 6.294508 GCATATCCTGTAACTTTTGTGTTGGT 60.295 38.462 0.00 0.00 0.00 3.67
171 172 6.092748 GCATATCCTGTAACTTTTGTGTTGG 58.907 40.000 0.00 0.00 0.00 3.77
172 173 6.582295 GTGCATATCCTGTAACTTTTGTGTTG 59.418 38.462 0.00 0.00 0.00 3.33
173 174 6.490040 AGTGCATATCCTGTAACTTTTGTGTT 59.510 34.615 0.00 0.00 0.00 3.32
174 175 6.003950 AGTGCATATCCTGTAACTTTTGTGT 58.996 36.000 0.00 0.00 0.00 3.72
175 176 6.500684 AGTGCATATCCTGTAACTTTTGTG 57.499 37.500 0.00 0.00 0.00 3.33
176 177 7.165485 TGTAGTGCATATCCTGTAACTTTTGT 58.835 34.615 0.00 0.00 0.00 2.83
177 178 7.609760 TGTAGTGCATATCCTGTAACTTTTG 57.390 36.000 0.00 0.00 0.00 2.44
178 179 7.663905 TGTTGTAGTGCATATCCTGTAACTTTT 59.336 33.333 0.00 0.00 0.00 2.27
179 180 7.119262 GTGTTGTAGTGCATATCCTGTAACTTT 59.881 37.037 0.00 0.00 0.00 2.66
180 181 6.594159 GTGTTGTAGTGCATATCCTGTAACTT 59.406 38.462 0.00 0.00 0.00 2.66
181 182 6.070767 AGTGTTGTAGTGCATATCCTGTAACT 60.071 38.462 0.00 0.00 0.00 2.24
182 183 6.106673 AGTGTTGTAGTGCATATCCTGTAAC 58.893 40.000 0.00 0.00 0.00 2.50
183 184 6.294361 AGTGTTGTAGTGCATATCCTGTAA 57.706 37.500 0.00 0.00 0.00 2.41
184 185 5.932619 AGTGTTGTAGTGCATATCCTGTA 57.067 39.130 0.00 0.00 0.00 2.74
185 186 4.826274 AGTGTTGTAGTGCATATCCTGT 57.174 40.909 0.00 0.00 0.00 4.00
186 187 6.149129 TCTAGTGTTGTAGTGCATATCCTG 57.851 41.667 0.00 0.00 0.00 3.86
187 188 6.791867 TTCTAGTGTTGTAGTGCATATCCT 57.208 37.500 0.00 0.00 0.00 3.24
188 189 6.986817 ACATTCTAGTGTTGTAGTGCATATCC 59.013 38.462 0.00 0.00 0.00 2.59
189 190 8.425577 AACATTCTAGTGTTGTAGTGCATATC 57.574 34.615 0.00 0.00 40.60 1.63
190 191 8.792830 AAACATTCTAGTGTTGTAGTGCATAT 57.207 30.769 0.00 0.00 41.22 1.78
191 192 8.615878 AAAACATTCTAGTGTTGTAGTGCATA 57.384 30.769 0.00 0.00 41.22 3.14
192 193 7.510549 AAAACATTCTAGTGTTGTAGTGCAT 57.489 32.000 0.00 0.00 41.22 3.96
193 194 6.935741 AAAACATTCTAGTGTTGTAGTGCA 57.064 33.333 0.00 0.00 41.22 4.57
216 217 7.093684 ACACTTAAGGCTGTCTTTTGGTAAAAA 60.094 33.333 7.53 0.00 36.93 1.94
217 218 6.378848 ACACTTAAGGCTGTCTTTTGGTAAAA 59.621 34.615 7.53 0.00 36.93 1.52
218 219 5.889289 ACACTTAAGGCTGTCTTTTGGTAAA 59.111 36.000 7.53 0.00 36.93 2.01
219 220 5.442391 ACACTTAAGGCTGTCTTTTGGTAA 58.558 37.500 7.53 0.00 36.93 2.85
220 221 5.043737 ACACTTAAGGCTGTCTTTTGGTA 57.956 39.130 7.53 0.00 36.93 3.25
221 222 3.898482 ACACTTAAGGCTGTCTTTTGGT 58.102 40.909 7.53 0.00 36.93 3.67
222 223 4.097892 ACAACACTTAAGGCTGTCTTTTGG 59.902 41.667 7.53 0.00 36.93 3.28
223 224 5.248870 ACAACACTTAAGGCTGTCTTTTG 57.751 39.130 7.53 0.72 36.93 2.44
224 225 7.582667 AATACAACACTTAAGGCTGTCTTTT 57.417 32.000 7.53 0.72 36.93 2.27
225 226 7.284489 TGAAATACAACACTTAAGGCTGTCTTT 59.716 33.333 7.53 10.93 36.93 2.52
226 227 6.770785 TGAAATACAACACTTAAGGCTGTCTT 59.229 34.615 7.53 0.00 39.40 3.01
227 228 6.296026 TGAAATACAACACTTAAGGCTGTCT 58.704 36.000 7.53 0.00 0.00 3.41
228 229 6.554334 TGAAATACAACACTTAAGGCTGTC 57.446 37.500 7.53 0.00 0.00 3.51
229 230 7.230510 TCAATGAAATACAACACTTAAGGCTGT 59.769 33.333 7.53 9.14 0.00 4.40
230 231 7.592938 TCAATGAAATACAACACTTAAGGCTG 58.407 34.615 7.53 3.50 0.00 4.85
231 232 7.759489 TCAATGAAATACAACACTTAAGGCT 57.241 32.000 7.53 0.00 0.00 4.58
232 233 8.243426 TCATCAATGAAATACAACACTTAAGGC 58.757 33.333 7.53 0.00 33.08 4.35
236 237 9.295825 ACCTTCATCAATGAAATACAACACTTA 57.704 29.630 6.85 0.00 45.26 2.24
237 238 8.181904 ACCTTCATCAATGAAATACAACACTT 57.818 30.769 6.85 0.00 45.26 3.16
238 239 7.765695 ACCTTCATCAATGAAATACAACACT 57.234 32.000 6.85 0.00 45.26 3.55
239 240 8.946085 TCTACCTTCATCAATGAAATACAACAC 58.054 33.333 6.85 0.00 45.26 3.32
240 241 9.513906 TTCTACCTTCATCAATGAAATACAACA 57.486 29.630 6.85 0.00 45.26 3.33
243 244 8.664798 CGTTTCTACCTTCATCAATGAAATACA 58.335 33.333 6.85 0.00 45.26 2.29
244 245 8.879759 TCGTTTCTACCTTCATCAATGAAATAC 58.120 33.333 6.85 0.00 45.26 1.89
245 246 9.443323 TTCGTTTCTACCTTCATCAATGAAATA 57.557 29.630 6.85 2.67 45.26 1.40
246 247 7.921786 TCGTTTCTACCTTCATCAATGAAAT 57.078 32.000 6.85 1.72 45.26 2.17
247 248 7.737972 TTCGTTTCTACCTTCATCAATGAAA 57.262 32.000 6.85 0.00 45.26 2.69
248 249 7.606073 TGATTCGTTTCTACCTTCATCAATGAA 59.394 33.333 5.38 5.38 43.94 2.57
249 250 7.102993 TGATTCGTTTCTACCTTCATCAATGA 58.897 34.615 0.00 0.00 34.44 2.57
250 251 7.307493 TGATTCGTTTCTACCTTCATCAATG 57.693 36.000 0.00 0.00 0.00 2.82
251 252 7.921786 TTGATTCGTTTCTACCTTCATCAAT 57.078 32.000 0.00 0.00 0.00 2.57
252 253 7.737972 TTTGATTCGTTTCTACCTTCATCAA 57.262 32.000 0.00 0.00 0.00 2.57
253 254 7.094805 CCTTTTGATTCGTTTCTACCTTCATCA 60.095 37.037 0.00 0.00 0.00 3.07
254 255 7.119262 TCCTTTTGATTCGTTTCTACCTTCATC 59.881 37.037 0.00 0.00 0.00 2.92
255 256 6.940298 TCCTTTTGATTCGTTTCTACCTTCAT 59.060 34.615 0.00 0.00 0.00 2.57
256 257 6.292923 TCCTTTTGATTCGTTTCTACCTTCA 58.707 36.000 0.00 0.00 0.00 3.02
257 258 6.796705 TCCTTTTGATTCGTTTCTACCTTC 57.203 37.500 0.00 0.00 0.00 3.46
258 259 6.771267 AGTTCCTTTTGATTCGTTTCTACCTT 59.229 34.615 0.00 0.00 0.00 3.50
259 260 6.204882 CAGTTCCTTTTGATTCGTTTCTACCT 59.795 38.462 0.00 0.00 0.00 3.08
260 261 6.204108 TCAGTTCCTTTTGATTCGTTTCTACC 59.796 38.462 0.00 0.00 0.00 3.18
261 262 7.186021 TCAGTTCCTTTTGATTCGTTTCTAC 57.814 36.000 0.00 0.00 0.00 2.59
262 263 7.795482 TTCAGTTCCTTTTGATTCGTTTCTA 57.205 32.000 0.00 0.00 0.00 2.10
263 264 6.693315 TTCAGTTCCTTTTGATTCGTTTCT 57.307 33.333 0.00 0.00 0.00 2.52
264 265 6.972901 AGTTTCAGTTCCTTTTGATTCGTTTC 59.027 34.615 0.00 0.00 0.00 2.78
265 266 6.863275 AGTTTCAGTTCCTTTTGATTCGTTT 58.137 32.000 0.00 0.00 0.00 3.60
266 267 6.451064 AGTTTCAGTTCCTTTTGATTCGTT 57.549 33.333 0.00 0.00 0.00 3.85
267 268 6.451064 AAGTTTCAGTTCCTTTTGATTCGT 57.549 33.333 0.00 0.00 0.00 3.85
268 269 7.755582 AAAAGTTTCAGTTCCTTTTGATTCG 57.244 32.000 0.00 0.00 37.11 3.34
274 275 4.631377 GCTGCAAAAGTTTCAGTTCCTTTT 59.369 37.500 0.00 0.00 38.56 2.27
275 276 4.183865 GCTGCAAAAGTTTCAGTTCCTTT 58.816 39.130 0.00 0.00 0.00 3.11
276 277 3.195396 TGCTGCAAAAGTTTCAGTTCCTT 59.805 39.130 0.00 0.00 0.00 3.36
277 278 2.760092 TGCTGCAAAAGTTTCAGTTCCT 59.240 40.909 0.00 0.00 0.00 3.36
278 279 2.860136 GTGCTGCAAAAGTTTCAGTTCC 59.140 45.455 2.77 0.00 0.00 3.62
279 280 3.510719 TGTGCTGCAAAAGTTTCAGTTC 58.489 40.909 2.77 0.00 0.00 3.01
280 281 3.591196 TGTGCTGCAAAAGTTTCAGTT 57.409 38.095 2.77 0.00 0.00 3.16
281 282 3.591196 TTGTGCTGCAAAAGTTTCAGT 57.409 38.095 2.77 0.00 33.53 3.41
282 283 5.174398 CAGTATTGTGCTGCAAAAGTTTCAG 59.826 40.000 11.41 0.94 40.91 3.02
283 284 5.042593 CAGTATTGTGCTGCAAAAGTTTCA 58.957 37.500 11.41 0.00 40.91 2.69
284 285 5.043248 ACAGTATTGTGCTGCAAAAGTTTC 58.957 37.500 11.41 1.95 40.91 2.78
285 286 5.009854 ACAGTATTGTGCTGCAAAAGTTT 57.990 34.783 11.41 0.00 40.91 2.66
286 287 4.097741 TGACAGTATTGTGCTGCAAAAGTT 59.902 37.500 11.41 0.00 40.91 2.66
287 288 3.631686 TGACAGTATTGTGCTGCAAAAGT 59.368 39.130 11.41 3.24 40.91 2.66
288 289 4.227512 TGACAGTATTGTGCTGCAAAAG 57.772 40.909 11.41 0.00 40.91 2.27
289 290 4.645762 TTGACAGTATTGTGCTGCAAAA 57.354 36.364 7.85 7.85 40.91 2.44
290 291 4.645762 TTTGACAGTATTGTGCTGCAAA 57.354 36.364 2.77 0.00 40.91 3.68
291 292 4.645762 TTTTGACAGTATTGTGCTGCAA 57.354 36.364 2.77 0.00 41.89 4.08
292 293 4.645762 TTTTTGACAGTATTGTGCTGCA 57.354 36.364 0.00 0.00 37.76 4.41
336 337 8.810652 TGTGAACAAGGAATTTTGCTTATTAC 57.189 30.769 0.00 0.00 36.67 1.89
358 359 8.950961 CGTGCATTTCATCTTTAGATAAATGTG 58.049 33.333 20.53 14.02 37.54 3.21
359 360 8.892723 TCGTGCATTTCATCTTTAGATAAATGT 58.107 29.630 20.53 0.00 37.54 2.71
360 361 9.162793 GTCGTGCATTTCATCTTTAGATAAATG 57.837 33.333 18.23 18.23 37.82 2.32
362 363 7.064134 ACGTCGTGCATTTCATCTTTAGATAAA 59.936 33.333 0.00 0.00 32.63 1.40
363 364 6.533723 ACGTCGTGCATTTCATCTTTAGATAA 59.466 34.615 0.00 0.00 32.63 1.75
387 388 5.987347 TGCTACAAGTCTAACACCTGTAAAC 59.013 40.000 0.00 0.00 0.00 2.01
388 389 6.164417 TGCTACAAGTCTAACACCTGTAAA 57.836 37.500 0.00 0.00 0.00 2.01
390 391 5.794726 TTGCTACAAGTCTAACACCTGTA 57.205 39.130 0.00 0.00 0.00 2.74
471 478 5.997129 CCAACCCATTTTACTCTTGCATTTT 59.003 36.000 0.00 0.00 0.00 1.82
686 694 3.297134 TTTGGACAGGCTTCTTTCTGT 57.703 42.857 0.00 0.00 45.70 3.41
688 696 3.381590 GTGTTTTGGACAGGCTTCTTTCT 59.618 43.478 0.00 0.00 39.39 2.52
737 745 3.319926 GAGCACTGGAGCTTTGCGC 62.320 63.158 0.00 0.00 46.75 6.09
817 832 4.081087 TCCACTGTGAGTATTTTAGAGCCC 60.081 45.833 9.86 0.00 0.00 5.19
840 856 1.373497 CGCACTCTCGACCAAGCTT 60.373 57.895 0.00 0.00 0.00 3.74
855 871 1.948721 ATGACGGTGATCTGCTCGCA 61.949 55.000 0.00 0.00 36.01 5.10
941 970 4.112716 CATTTGCATGCATGAACCTGTA 57.887 40.909 30.64 0.60 0.00 2.74
976 1005 0.249489 GAGTGGCACTCGACAGTTGT 60.249 55.000 29.91 0.00 32.23 3.32
1015 1044 5.087323 AGTTGATGAACTGAAGGGTCTCTA 58.913 41.667 0.00 0.00 41.12 2.43
1102 1136 1.992557 AGAAGAACCTTGCCACCCATA 59.007 47.619 0.00 0.00 0.00 2.74
1126 1160 2.358737 CCCACCAAGACGGCACTC 60.359 66.667 0.00 0.00 39.03 3.51
1338 1382 6.772770 TGTTCAGCACAAATTCATTTCATG 57.227 33.333 0.00 0.00 29.87 3.07
1435 1479 7.233553 AGGTATACAGAATTGCAGCTATCAGTA 59.766 37.037 5.01 0.00 0.00 2.74
1517 1561 0.179094 TTGGTGTCGGTGTCAGTGTC 60.179 55.000 0.00 0.00 0.00 3.67
1518 1562 0.461339 GTTGGTGTCGGTGTCAGTGT 60.461 55.000 0.00 0.00 0.00 3.55
1519 1563 0.179084 AGTTGGTGTCGGTGTCAGTG 60.179 55.000 0.00 0.00 0.00 3.66
1520 1564 0.539986 AAGTTGGTGTCGGTGTCAGT 59.460 50.000 0.00 0.00 0.00 3.41
1521 1565 2.132762 GTAAGTTGGTGTCGGTGTCAG 58.867 52.381 0.00 0.00 0.00 3.51
1522 1566 1.536496 CGTAAGTTGGTGTCGGTGTCA 60.536 52.381 0.00 0.00 0.00 3.58
1566 1634 1.070105 TTGGTGTCGGTGTAGTGCC 59.930 57.895 0.00 0.00 0.00 5.01
1567 1635 0.249741 AGTTGGTGTCGGTGTAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
1568 1636 2.234300 AAGTTGGTGTCGGTGTAGTG 57.766 50.000 0.00 0.00 0.00 2.74
1569 1637 2.287788 CGTAAGTTGGTGTCGGTGTAGT 60.288 50.000 0.00 0.00 0.00 2.73
1570 1638 2.322161 CGTAAGTTGGTGTCGGTGTAG 58.678 52.381 0.00 0.00 0.00 2.74
1571 1639 1.000385 CCGTAAGTTGGTGTCGGTGTA 60.000 52.381 0.00 0.00 36.99 2.90
1572 1640 0.249573 CCGTAAGTTGGTGTCGGTGT 60.250 55.000 0.00 0.00 36.99 4.16
1573 1641 1.562575 GCCGTAAGTTGGTGTCGGTG 61.563 60.000 0.00 0.00 42.62 4.94
1574 1642 1.301165 GCCGTAAGTTGGTGTCGGT 60.301 57.895 0.00 0.00 42.62 4.69
1575 1643 0.672401 ATGCCGTAAGTTGGTGTCGG 60.672 55.000 0.00 0.00 43.37 4.79
1576 1644 1.153353 AATGCCGTAAGTTGGTGTCG 58.847 50.000 0.00 0.00 0.00 4.35
1577 1645 3.068560 TGTAATGCCGTAAGTTGGTGTC 58.931 45.455 0.00 0.00 0.00 3.67
1578 1646 2.809696 GTGTAATGCCGTAAGTTGGTGT 59.190 45.455 0.00 0.00 0.00 4.16
1579 1647 2.160813 GGTGTAATGCCGTAAGTTGGTG 59.839 50.000 0.00 0.00 0.00 4.17
1580 1648 2.429478 GGTGTAATGCCGTAAGTTGGT 58.571 47.619 0.00 0.00 0.00 3.67
1581 1649 1.395608 CGGTGTAATGCCGTAAGTTGG 59.604 52.381 0.00 0.00 43.84 3.77
1582 1650 2.798834 CGGTGTAATGCCGTAAGTTG 57.201 50.000 0.00 0.00 43.84 3.16
1594 1662 1.782044 GTAAGTTGGCGTCGGTGTAA 58.218 50.000 0.00 0.00 0.00 2.41
1661 1729 2.342279 GTGCTCGGTGTAGTGCCA 59.658 61.111 0.00 0.00 0.00 4.92
1686 1754 0.753111 GGGACATCATGGGAAGGTGC 60.753 60.000 0.00 0.00 0.00 5.01
1822 1895 5.012239 TGATTCTTCCAGTAGCTGCATTTT 58.988 37.500 4.12 0.00 0.00 1.82
1823 1896 4.397417 GTGATTCTTCCAGTAGCTGCATTT 59.603 41.667 4.12 0.00 0.00 2.32
1824 1897 3.944015 GTGATTCTTCCAGTAGCTGCATT 59.056 43.478 4.12 0.00 0.00 3.56
1825 1898 3.539604 GTGATTCTTCCAGTAGCTGCAT 58.460 45.455 4.12 0.00 0.00 3.96
1826 1899 2.355108 GGTGATTCTTCCAGTAGCTGCA 60.355 50.000 4.12 0.00 0.00 4.41
1879 1952 1.647545 ATGTCTTGCCGATGTTGCCG 61.648 55.000 0.00 0.00 0.00 5.69
2071 2144 2.486504 GTCACGGCCACGACGATA 59.513 61.111 2.24 0.00 44.60 2.92
2122 2195 5.990996 GTGGAATTCATTTGCCTTCTTGAAA 59.009 36.000 7.93 0.00 32.35 2.69
2156 2229 1.197721 GCCAAGAAACACCGATGACTG 59.802 52.381 0.00 0.00 0.00 3.51
2163 2236 5.121221 AGAAATTTAGCCAAGAAACACCG 57.879 39.130 0.00 0.00 0.00 4.94
2279 2352 6.018507 GGATGGATTTATTGCACTCAAAATGC 60.019 38.462 0.00 0.00 43.68 3.56
2305 2378 6.839124 ACAGTGATATCAAGCAATGGAAAA 57.161 33.333 7.07 0.00 41.18 2.29
2325 2398 9.325198 TGTGTTACTAATCCAGCATAATAACAG 57.675 33.333 0.00 0.00 33.31 3.16
2519 2797 1.755959 TGAAGTGTTTGCTTGCCACAT 59.244 42.857 0.00 0.00 0.00 3.21
2662 2941 4.100808 TCAATTTGCCAAACCTTTGCTAGT 59.899 37.500 0.00 0.00 36.86 2.57
3212 3493 9.251792 CATTCAACAATTCTGAATCAGACAAAA 57.748 29.630 13.17 0.00 40.69 2.44
3213 3494 7.383029 GCATTCAACAATTCTGAATCAGACAAA 59.617 33.333 13.17 0.00 40.69 2.83


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

AutoCloner maintained by Alex Coulton.