Multiple sequence alignment - TraesCS5D01G210900

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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 TraesCS5D01G210900 chr5D 100.000 3014 0 0 1 3014 319253271 319256284 0.000000e+00 5566.0
1 TraesCS5D01G210900 chr5A 90.234 2519 122 45 562 3014 414935293 414932833 0.000000e+00 3175.0
2 TraesCS5D01G210900 chr5A 93.305 239 15 1 303 541 414935518 414935281 4.780000e-93 351.0
3 TraesCS5D01G210900 chr5B 93.450 2122 74 25 562 2647 369484991 369487083 0.000000e+00 3088.0
4 TraesCS5D01G210900 chr5B 93.939 363 17 3 2654 3011 369487388 369487750 7.350000e-151 544.0
5 TraesCS5D01G210900 chr5B 92.188 320 19 5 223 541 369484689 369485003 5.930000e-122 448.0
6 TraesCS5D01G210900 chr7B 91.489 141 11 1 997 1136 128822078 128822218 3.070000e-45 193.0
7 TraesCS5D01G210900 chr7D 91.429 140 11 1 998 1136 165634711 165634850 1.100000e-44 191.0
8 TraesCS5D01G210900 chr7A 90.909 143 12 1 995 1136 167179676 167179818 1.100000e-44 191.0
9 TraesCS5D01G210900 chr6A 90.511 137 11 2 1001 1136 525992595 525992460 2.390000e-41 180.0
10 TraesCS5D01G210900 chr6A 85.821 134 18 1 1429 1561 525992171 525992038 1.130000e-29 141.0
11 TraesCS5D01G210900 chr6D 89.706 136 12 2 1001 1135 383745561 383745427 3.990000e-39 172.0
12 TraesCS5D01G210900 chr6B 88.971 136 13 2 1001 1135 574021484 574021350 1.860000e-37 167.0
13 TraesCS5D01G210900 chr4A 93.684 95 5 1 998 1091 406202731 406202637 1.130000e-29 141.0
14 TraesCS5D01G210900 chr2D 85.714 133 15 4 1300 1430 555395469 555395599 1.460000e-28 137.0
15 TraesCS5D01G210900 chr2D 85.714 126 14 4 1310 1433 165468246 165468123 2.440000e-26 130.0
16 TraesCS5D01G210900 chr2A 86.179 123 13 4 1310 1430 185285018 185285138 2.440000e-26 130.0
17 TraesCS5D01G210900 chr2A 82.609 115 20 0 1300 1414 564218616 564218730 5.320000e-18 102.0
18 TraesCS5D01G210900 chr2B 84.211 133 17 4 1300 1430 662373405 662373535 3.150000e-25 126.0
19 TraesCS5D01G210900 chr2B 73.709 213 46 8 4 212 390810439 390810645 1.160000e-09 75.0
20 TraesCS5D01G210900 chr1A 77.273 176 30 8 1316 1486 569139367 569139197 8.900000e-16 95.3
21 TraesCS5D01G210900 chr1D 90.000 60 6 0 1427 1486 474510215 474510156 8.960000e-11 78.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G210900 chr5D 319253271 319256284 3013 False 5566 5566 100.000000 1 3014 1 chr5D.!!$F1 3013
1 TraesCS5D01G210900 chr5A 414932833 414935518 2685 True 1763 3175 91.769500 303 3014 2 chr5A.!!$R1 2711
2 TraesCS5D01G210900 chr5B 369484689 369487750 3061 False 1360 3088 93.192333 223 3011 3 chr5B.!!$F1 2788

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
43 44 0.032267 GAGGAACTTAGCGCCGCTAT 59.968 55.0 20.79 4.83 41.55 2.97 F
182 183 0.036010 CTCACTCGCCCTCCAAACAT 60.036 55.0 0.00 0.00 0.00 2.71 F
183 184 0.036388 TCACTCGCCCTCCAAACATC 60.036 55.0 0.00 0.00 0.00 3.06 F
184 185 0.036010 CACTCGCCCTCCAAACATCT 60.036 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1293 1.176838 GTCGCAACACGTCAAAACAC 58.823 50.000 0.00 0.00 44.19 3.32 R
1656 1686 1.450312 CATGTCCTCTTCGGCACCC 60.450 63.158 0.00 0.00 0.00 4.61 R
1981 2023 2.286826 CCTGGTGATCGAACAGGGA 58.713 57.895 17.01 0.00 46.24 4.20 R
2297 2341 1.333169 GCATCCACGCATATGTCGTTG 60.333 52.381 18.33 15.86 38.19 4.10 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
24 25 7.545362 ACTTGCTTAATTGCATAGTAGTCAG 57.455 36.000 0.00 0.00 42.96 3.51
25 26 7.331026 ACTTGCTTAATTGCATAGTAGTCAGA 58.669 34.615 0.00 0.00 42.96 3.27
26 27 7.493971 ACTTGCTTAATTGCATAGTAGTCAGAG 59.506 37.037 0.00 0.00 42.96 3.35
27 28 6.283694 TGCTTAATTGCATAGTAGTCAGAGG 58.716 40.000 0.00 0.00 38.12 3.69
28 29 6.098266 TGCTTAATTGCATAGTAGTCAGAGGA 59.902 38.462 0.00 0.00 38.12 3.71
29 30 6.986817 GCTTAATTGCATAGTAGTCAGAGGAA 59.013 38.462 0.00 0.00 0.00 3.36
30 31 7.042389 GCTTAATTGCATAGTAGTCAGAGGAAC 60.042 40.741 0.00 0.00 0.00 3.62
32 33 6.552445 ATTGCATAGTAGTCAGAGGAACTT 57.448 37.500 0.00 0.00 41.55 2.66
33 34 7.661536 ATTGCATAGTAGTCAGAGGAACTTA 57.338 36.000 0.00 0.00 41.55 2.24
34 35 6.701145 TGCATAGTAGTCAGAGGAACTTAG 57.299 41.667 0.00 0.00 41.55 2.18
35 36 5.067936 TGCATAGTAGTCAGAGGAACTTAGC 59.932 44.000 0.00 0.00 41.55 3.09
36 37 5.753744 CATAGTAGTCAGAGGAACTTAGCG 58.246 45.833 0.00 0.00 41.55 4.26
37 38 2.424246 AGTAGTCAGAGGAACTTAGCGC 59.576 50.000 0.00 0.00 41.55 5.92
38 39 0.533032 AGTCAGAGGAACTTAGCGCC 59.467 55.000 2.29 0.00 41.55 6.53
39 40 0.802607 GTCAGAGGAACTTAGCGCCG 60.803 60.000 2.29 0.00 41.55 6.46
40 41 2.167861 CAGAGGAACTTAGCGCCGC 61.168 63.158 2.29 0.00 41.55 6.53
41 42 2.184579 GAGGAACTTAGCGCCGCT 59.815 61.111 18.67 18.67 41.55 5.52
42 43 1.035932 AGAGGAACTTAGCGCCGCTA 61.036 55.000 15.99 15.99 41.55 4.26
43 44 0.032267 GAGGAACTTAGCGCCGCTAT 59.968 55.000 20.79 4.83 41.55 2.97
44 45 0.464452 AGGAACTTAGCGCCGCTATT 59.536 50.000 20.79 12.27 41.01 1.73
45 46 1.134491 AGGAACTTAGCGCCGCTATTT 60.134 47.619 20.79 15.69 41.01 1.40
46 47 1.260825 GGAACTTAGCGCCGCTATTTC 59.739 52.381 20.79 22.20 41.01 2.17
47 48 1.931172 GAACTTAGCGCCGCTATTTCA 59.069 47.619 24.81 10.87 41.01 2.69
48 49 2.018542 ACTTAGCGCCGCTATTTCAA 57.981 45.000 20.79 5.28 41.01 2.69
49 50 2.352388 ACTTAGCGCCGCTATTTCAAA 58.648 42.857 20.79 4.48 41.01 2.69
50 51 2.943033 ACTTAGCGCCGCTATTTCAAAT 59.057 40.909 20.79 0.00 41.01 2.32
51 52 3.377172 ACTTAGCGCCGCTATTTCAAATT 59.623 39.130 20.79 0.00 41.01 1.82
52 53 2.193306 AGCGCCGCTATTTCAAATTG 57.807 45.000 11.29 0.00 36.99 2.32
53 54 0.572125 GCGCCGCTATTTCAAATTGC 59.428 50.000 0.00 6.49 0.00 3.56
54 55 1.199624 CGCCGCTATTTCAAATTGCC 58.800 50.000 10.45 0.00 0.00 4.52
55 56 1.202290 CGCCGCTATTTCAAATTGCCT 60.202 47.619 10.45 0.00 0.00 4.75
56 57 2.735126 CGCCGCTATTTCAAATTGCCTT 60.735 45.455 10.45 0.00 0.00 4.35
57 58 3.261580 GCCGCTATTTCAAATTGCCTTT 58.738 40.909 10.45 0.00 0.00 3.11
58 59 3.306973 GCCGCTATTTCAAATTGCCTTTC 59.693 43.478 10.45 0.00 0.00 2.62
59 60 4.493547 CCGCTATTTCAAATTGCCTTTCA 58.506 39.130 10.45 0.00 0.00 2.69
60 61 4.928615 CCGCTATTTCAAATTGCCTTTCAA 59.071 37.500 10.45 0.00 39.32 2.69
61 62 5.581874 CCGCTATTTCAAATTGCCTTTCAAT 59.418 36.000 10.45 0.00 46.82 2.57
62 63 6.455913 CCGCTATTTCAAATTGCCTTTCAATG 60.456 38.462 10.45 0.00 44.23 2.82
63 64 6.455913 CGCTATTTCAAATTGCCTTTCAATGG 60.456 38.462 10.45 0.00 44.23 3.16
64 65 6.594937 GCTATTTCAAATTGCCTTTCAATGGA 59.405 34.615 5.33 0.00 44.23 3.41
65 66 6.806388 ATTTCAAATTGCCTTTCAATGGAC 57.194 33.333 0.00 0.00 44.23 4.02
66 67 4.270245 TCAAATTGCCTTTCAATGGACC 57.730 40.909 0.00 0.00 44.23 4.46
67 68 3.645212 TCAAATTGCCTTTCAATGGACCA 59.355 39.130 0.00 0.00 44.23 4.02
68 69 3.967332 AATTGCCTTTCAATGGACCAG 57.033 42.857 0.00 0.00 44.23 4.00
69 70 2.673775 TTGCCTTTCAATGGACCAGA 57.326 45.000 0.00 0.00 0.00 3.86
70 71 2.673775 TGCCTTTCAATGGACCAGAA 57.326 45.000 0.00 0.00 0.00 3.02
71 72 2.956132 TGCCTTTCAATGGACCAGAAA 58.044 42.857 0.00 4.58 0.00 2.52
72 73 3.303938 TGCCTTTCAATGGACCAGAAAA 58.696 40.909 9.49 4.95 31.59 2.29
73 74 3.321682 TGCCTTTCAATGGACCAGAAAAG 59.678 43.478 14.66 14.66 31.59 2.27
74 75 3.573967 GCCTTTCAATGGACCAGAAAAGA 59.426 43.478 19.90 4.49 31.59 2.52
75 76 4.039124 GCCTTTCAATGGACCAGAAAAGAA 59.961 41.667 19.90 9.12 31.59 2.52
76 77 5.776744 CCTTTCAATGGACCAGAAAAGAAG 58.223 41.667 19.90 10.80 31.59 2.85
77 78 4.853924 TTCAATGGACCAGAAAAGAAGC 57.146 40.909 0.00 0.00 0.00 3.86
78 79 4.104383 TCAATGGACCAGAAAAGAAGCT 57.896 40.909 0.00 0.00 0.00 3.74
79 80 4.473444 TCAATGGACCAGAAAAGAAGCTT 58.527 39.130 0.00 0.00 0.00 3.74
80 81 4.279169 TCAATGGACCAGAAAAGAAGCTTG 59.721 41.667 2.10 0.00 0.00 4.01
81 82 3.297134 TGGACCAGAAAAGAAGCTTGT 57.703 42.857 2.10 0.00 0.00 3.16
82 83 4.431416 TGGACCAGAAAAGAAGCTTGTA 57.569 40.909 2.10 0.00 0.00 2.41
83 84 4.134563 TGGACCAGAAAAGAAGCTTGTAC 58.865 43.478 2.10 0.00 0.00 2.90
84 85 3.502595 GGACCAGAAAAGAAGCTTGTACC 59.497 47.826 2.10 0.00 0.00 3.34
85 86 4.134563 GACCAGAAAAGAAGCTTGTACCA 58.865 43.478 2.10 0.00 0.00 3.25
86 87 4.729868 ACCAGAAAAGAAGCTTGTACCAT 58.270 39.130 2.10 0.00 0.00 3.55
87 88 5.140454 ACCAGAAAAGAAGCTTGTACCATT 58.860 37.500 2.10 0.00 0.00 3.16
88 89 5.598417 ACCAGAAAAGAAGCTTGTACCATTT 59.402 36.000 2.10 0.00 0.00 2.32
89 90 6.098266 ACCAGAAAAGAAGCTTGTACCATTTT 59.902 34.615 2.10 0.00 0.00 1.82
90 91 6.986231 CCAGAAAAGAAGCTTGTACCATTTTT 59.014 34.615 2.10 0.00 0.00 1.94
91 92 7.169813 CCAGAAAAGAAGCTTGTACCATTTTTC 59.830 37.037 2.10 5.89 34.94 2.29
92 93 7.706179 CAGAAAAGAAGCTTGTACCATTTTTCA 59.294 33.333 2.10 0.00 36.35 2.69
93 94 8.424133 AGAAAAGAAGCTTGTACCATTTTTCAT 58.576 29.630 2.10 0.00 36.35 2.57
94 95 8.593492 AAAAGAAGCTTGTACCATTTTTCATC 57.407 30.769 2.10 0.00 0.00 2.92
95 96 6.899393 AGAAGCTTGTACCATTTTTCATCA 57.101 33.333 2.10 0.00 0.00 3.07
96 97 7.472334 AGAAGCTTGTACCATTTTTCATCAT 57.528 32.000 2.10 0.00 0.00 2.45
97 98 7.318141 AGAAGCTTGTACCATTTTTCATCATG 58.682 34.615 2.10 0.00 0.00 3.07
98 99 5.413499 AGCTTGTACCATTTTTCATCATGC 58.587 37.500 0.00 0.00 0.00 4.06
99 100 4.266029 GCTTGTACCATTTTTCATCATGCG 59.734 41.667 0.00 0.00 0.00 4.73
100 101 4.368874 TGTACCATTTTTCATCATGCGG 57.631 40.909 0.00 0.00 0.00 5.69
101 102 2.298411 ACCATTTTTCATCATGCGGC 57.702 45.000 0.00 0.00 0.00 6.53
102 103 1.202203 CCATTTTTCATCATGCGGCG 58.798 50.000 0.51 0.51 0.00 6.46
103 104 1.202203 CATTTTTCATCATGCGGCGG 58.798 50.000 9.78 0.00 0.00 6.13
104 105 0.102844 ATTTTTCATCATGCGGCGGG 59.897 50.000 9.78 0.00 0.00 6.13
105 106 2.555565 TTTTTCATCATGCGGCGGGC 62.556 55.000 9.78 0.00 43.96 6.13
115 116 2.673687 CGGCGGGCCAAAACCTAA 60.674 61.111 4.39 0.00 35.37 2.69
116 117 2.967397 GGCGGGCCAAAACCTAAC 59.033 61.111 4.39 0.00 35.81 2.34
117 118 2.642254 GGCGGGCCAAAACCTAACC 61.642 63.158 4.39 0.00 35.81 2.85
118 119 1.904378 GCGGGCCAAAACCTAACCA 60.904 57.895 4.39 0.00 0.00 3.67
119 120 1.254975 GCGGGCCAAAACCTAACCAT 61.255 55.000 4.39 0.00 0.00 3.55
120 121 1.956159 GCGGGCCAAAACCTAACCATA 60.956 52.381 4.39 0.00 0.00 2.74
121 122 2.448453 CGGGCCAAAACCTAACCATAA 58.552 47.619 4.39 0.00 0.00 1.90
122 123 2.826725 CGGGCCAAAACCTAACCATAAA 59.173 45.455 4.39 0.00 0.00 1.40
123 124 3.119280 CGGGCCAAAACCTAACCATAAAG 60.119 47.826 4.39 0.00 0.00 1.85
124 125 3.369052 GGGCCAAAACCTAACCATAAAGC 60.369 47.826 4.39 0.00 0.00 3.51
125 126 3.259625 GGCCAAAACCTAACCATAAAGCA 59.740 43.478 0.00 0.00 0.00 3.91
126 127 4.494484 GCCAAAACCTAACCATAAAGCAG 58.506 43.478 0.00 0.00 0.00 4.24
127 128 4.494484 CCAAAACCTAACCATAAAGCAGC 58.506 43.478 0.00 0.00 0.00 5.25
128 129 4.165779 CAAAACCTAACCATAAAGCAGCG 58.834 43.478 0.00 0.00 0.00 5.18
129 130 2.781681 ACCTAACCATAAAGCAGCGT 57.218 45.000 0.00 0.00 0.00 5.07
130 131 3.067684 ACCTAACCATAAAGCAGCGTT 57.932 42.857 0.00 0.00 0.00 4.84
131 132 2.747446 ACCTAACCATAAAGCAGCGTTG 59.253 45.455 3.53 0.00 0.00 4.10
132 133 2.097466 CCTAACCATAAAGCAGCGTTGG 59.903 50.000 3.53 0.52 0.00 3.77
133 134 0.243636 AACCATAAAGCAGCGTTGGC 59.756 50.000 3.53 0.00 40.37 4.52
134 135 0.893270 ACCATAAAGCAGCGTTGGCA 60.893 50.000 3.53 0.00 43.41 4.92
135 136 0.456653 CCATAAAGCAGCGTTGGCAC 60.457 55.000 3.53 0.00 43.41 5.01
136 137 0.240678 CATAAAGCAGCGTTGGCACA 59.759 50.000 3.53 0.00 43.41 4.57
137 138 1.135315 CATAAAGCAGCGTTGGCACAT 60.135 47.619 3.53 0.00 43.41 3.21
138 139 1.814793 TAAAGCAGCGTTGGCACATA 58.185 45.000 3.53 0.00 43.41 2.29
139 140 0.523072 AAAGCAGCGTTGGCACATAG 59.477 50.000 0.16 0.00 43.41 2.23
140 141 0.321564 AAGCAGCGTTGGCACATAGA 60.322 50.000 0.16 0.00 43.41 1.98
141 142 0.321564 AGCAGCGTTGGCACATAGAA 60.322 50.000 0.16 0.00 43.41 2.10
142 143 0.521291 GCAGCGTTGGCACATAGAAA 59.479 50.000 0.16 0.00 43.41 2.52
143 144 1.729149 GCAGCGTTGGCACATAGAAAC 60.729 52.381 0.16 0.00 43.41 2.78
144 145 1.135689 CAGCGTTGGCACATAGAAACC 60.136 52.381 0.00 0.00 43.41 3.27
145 146 0.170339 GCGTTGGCACATAGAAACCC 59.830 55.000 0.00 0.00 39.30 4.11
146 147 1.821216 CGTTGGCACATAGAAACCCT 58.179 50.000 0.00 0.00 39.30 4.34
147 148 2.937873 GCGTTGGCACATAGAAACCCTA 60.938 50.000 0.00 0.00 39.30 3.53
148 149 2.936498 CGTTGGCACATAGAAACCCTAG 59.064 50.000 0.00 0.00 39.30 3.02
149 150 3.279434 GTTGGCACATAGAAACCCTAGG 58.721 50.000 0.06 0.06 39.30 3.02
150 151 1.211949 TGGCACATAGAAACCCTAGGC 59.788 52.381 2.05 0.00 32.68 3.93
151 152 1.477014 GGCACATAGAAACCCTAGGCC 60.477 57.143 2.05 0.00 36.51 5.19
152 153 1.490910 GCACATAGAAACCCTAGGCCT 59.509 52.381 11.78 11.78 32.68 5.19
153 154 2.704065 GCACATAGAAACCCTAGGCCTA 59.296 50.000 13.09 13.09 32.68 3.93
154 155 3.244249 GCACATAGAAACCCTAGGCCTAG 60.244 52.174 30.05 30.05 32.68 3.02
155 156 2.973406 ACATAGAAACCCTAGGCCTAGC 59.027 50.000 31.33 18.42 32.68 3.42
166 167 3.660724 GCCTAGCCATTCCCCTCA 58.339 61.111 0.00 0.00 0.00 3.86
167 168 1.149401 GCCTAGCCATTCCCCTCAC 59.851 63.158 0.00 0.00 0.00 3.51
168 169 1.348775 GCCTAGCCATTCCCCTCACT 61.349 60.000 0.00 0.00 0.00 3.41
169 170 0.761802 CCTAGCCATTCCCCTCACTC 59.238 60.000 0.00 0.00 0.00 3.51
170 171 0.390860 CTAGCCATTCCCCTCACTCG 59.609 60.000 0.00 0.00 0.00 4.18
171 172 1.686325 TAGCCATTCCCCTCACTCGC 61.686 60.000 0.00 0.00 0.00 5.03
172 173 2.190578 CCATTCCCCTCACTCGCC 59.809 66.667 0.00 0.00 0.00 5.54
173 174 2.190578 CATTCCCCTCACTCGCCC 59.809 66.667 0.00 0.00 0.00 6.13
174 175 2.041265 ATTCCCCTCACTCGCCCT 59.959 61.111 0.00 0.00 0.00 5.19
175 176 2.066999 ATTCCCCTCACTCGCCCTC 61.067 63.158 0.00 0.00 0.00 4.30
176 177 4.779733 TCCCCTCACTCGCCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
178 179 3.003173 CCCTCACTCGCCCTCCAA 61.003 66.667 0.00 0.00 0.00 3.53
179 180 2.592993 CCCTCACTCGCCCTCCAAA 61.593 63.158 0.00 0.00 0.00 3.28
180 181 1.376037 CCTCACTCGCCCTCCAAAC 60.376 63.158 0.00 0.00 0.00 2.93
181 182 1.371183 CTCACTCGCCCTCCAAACA 59.629 57.895 0.00 0.00 0.00 2.83
182 183 0.036010 CTCACTCGCCCTCCAAACAT 60.036 55.000 0.00 0.00 0.00 2.71
183 184 0.036388 TCACTCGCCCTCCAAACATC 60.036 55.000 0.00 0.00 0.00 3.06
184 185 0.036010 CACTCGCCCTCCAAACATCT 60.036 55.000 0.00 0.00 0.00 2.90
185 186 1.207089 CACTCGCCCTCCAAACATCTA 59.793 52.381 0.00 0.00 0.00 1.98
186 187 1.207329 ACTCGCCCTCCAAACATCTAC 59.793 52.381 0.00 0.00 0.00 2.59
187 188 0.174845 TCGCCCTCCAAACATCTACG 59.825 55.000 0.00 0.00 0.00 3.51
188 189 0.810031 CGCCCTCCAAACATCTACGG 60.810 60.000 0.00 0.00 0.00 4.02
189 190 1.095807 GCCCTCCAAACATCTACGGC 61.096 60.000 0.00 0.00 0.00 5.68
190 191 0.810031 CCCTCCAAACATCTACGGCG 60.810 60.000 4.80 4.80 0.00 6.46
191 192 0.108329 CCTCCAAACATCTACGGCGT 60.108 55.000 19.64 19.64 0.00 5.68
192 193 1.278238 CTCCAAACATCTACGGCGTC 58.722 55.000 19.21 0.00 0.00 5.19
193 194 0.892755 TCCAAACATCTACGGCGTCT 59.107 50.000 19.21 0.00 0.00 4.18
194 195 0.999406 CCAAACATCTACGGCGTCTG 59.001 55.000 19.21 15.52 0.00 3.51
195 196 1.403647 CCAAACATCTACGGCGTCTGA 60.404 52.381 19.21 17.10 0.00 3.27
196 197 1.920574 CAAACATCTACGGCGTCTGAG 59.079 52.381 19.21 9.25 0.00 3.35
197 198 0.456221 AACATCTACGGCGTCTGAGG 59.544 55.000 19.21 19.90 0.00 3.86
198 199 0.680280 ACATCTACGGCGTCTGAGGT 60.680 55.000 19.21 20.58 0.00 3.85
199 200 0.248661 CATCTACGGCGTCTGAGGTG 60.249 60.000 19.21 11.97 0.00 4.00
200 201 1.384989 ATCTACGGCGTCTGAGGTGG 61.385 60.000 19.21 0.00 0.00 4.61
201 202 3.701604 CTACGGCGTCTGAGGTGGC 62.702 68.421 19.21 0.00 0.00 5.01
205 206 4.687215 GCGTCTGAGGTGGCTGCA 62.687 66.667 0.50 0.00 0.00 4.41
206 207 2.031012 CGTCTGAGGTGGCTGCAA 59.969 61.111 0.50 0.00 0.00 4.08
207 208 1.597854 CGTCTGAGGTGGCTGCAAA 60.598 57.895 0.50 0.00 0.00 3.68
208 209 1.845809 CGTCTGAGGTGGCTGCAAAC 61.846 60.000 0.50 0.00 0.00 2.93
209 210 0.536006 GTCTGAGGTGGCTGCAAACT 60.536 55.000 0.00 0.00 0.00 2.66
210 211 0.535780 TCTGAGGTGGCTGCAAACTG 60.536 55.000 0.00 0.00 0.00 3.16
211 212 2.138656 CTGAGGTGGCTGCAAACTGC 62.139 60.000 0.00 0.00 45.29 4.40
217 218 2.647297 GCTGCAAACTGCCACTCC 59.353 61.111 0.00 0.00 44.23 3.85
218 219 2.924105 GCTGCAAACTGCCACTCCC 61.924 63.158 0.00 0.00 44.23 4.30
219 220 1.228367 CTGCAAACTGCCACTCCCT 60.228 57.895 0.00 0.00 44.23 4.20
220 221 1.228245 TGCAAACTGCCACTCCCTC 60.228 57.895 0.00 0.00 44.23 4.30
221 222 1.973812 GCAAACTGCCACTCCCTCC 60.974 63.158 0.00 0.00 37.42 4.30
225 226 0.984995 AACTGCCACTCCCTCCTTAC 59.015 55.000 0.00 0.00 0.00 2.34
236 237 2.568509 TCCCTCCTTACCTAAAACCACG 59.431 50.000 0.00 0.00 0.00 4.94
250 251 1.453155 ACCACGCCATGACAAGAATC 58.547 50.000 0.00 0.00 0.00 2.52
275 276 4.141574 TGGAACGGAGGGATTACCATTTAG 60.142 45.833 0.00 0.00 43.89 1.85
278 279 2.552373 CGGAGGGATTACCATTTAGCCC 60.552 54.545 0.00 0.00 43.89 5.19
280 281 1.423921 AGGGATTACCATTTAGCCCGG 59.576 52.381 0.00 0.00 43.89 5.73
286 287 5.537295 GGATTACCATTTAGCCCGGTATTTT 59.463 40.000 0.00 0.00 35.27 1.82
287 288 6.041182 GGATTACCATTTAGCCCGGTATTTTT 59.959 38.462 0.00 0.00 35.27 1.94
327 328 6.981722 ACAAAATGAAGGACCTTGATACAAC 58.018 36.000 12.68 0.00 0.00 3.32
331 332 3.325425 TGAAGGACCTTGATACAACGGAA 59.675 43.478 12.68 0.00 0.00 4.30
403 404 2.033299 GGAATGGACACATTACATGCCG 59.967 50.000 0.00 0.00 46.89 5.69
494 495 4.347453 GGCCAGCACTTGCAACGG 62.347 66.667 0.00 2.17 45.16 4.44
532 533 3.818787 CAGCAGCCCGGCAATGTC 61.819 66.667 13.15 0.00 35.83 3.06
638 639 0.918799 TCATCCTTGGCTAGCCCCAA 60.919 55.000 30.81 18.07 42.37 4.12
658 659 1.191535 TACTGGTCCAAGGTCCATCG 58.808 55.000 5.55 0.00 33.27 3.84
659 660 0.836400 ACTGGTCCAAGGTCCATCGT 60.836 55.000 5.55 0.00 33.27 3.73
660 661 0.108138 CTGGTCCAAGGTCCATCGTC 60.108 60.000 5.55 0.00 33.27 4.20
835 858 1.401905 GCTAAAGCGCCATTTGCTAGT 59.598 47.619 18.02 0.00 43.14 2.57
851 874 2.872858 GCTAGTTAGCTATTGTGCACCC 59.127 50.000 15.69 0.00 45.62 4.61
976 1000 4.318333 CGAGTGAAGTGATCTTTGTGTGTG 60.318 45.833 0.00 0.00 33.64 3.82
977 1001 3.313526 AGTGAAGTGATCTTTGTGTGTGC 59.686 43.478 0.00 0.00 33.64 4.57
978 1002 2.287644 TGAAGTGATCTTTGTGTGTGCG 59.712 45.455 0.00 0.00 33.64 5.34
979 1003 2.238942 AGTGATCTTTGTGTGTGCGA 57.761 45.000 0.00 0.00 0.00 5.10
980 1004 2.560504 AGTGATCTTTGTGTGTGCGAA 58.439 42.857 0.00 0.00 0.00 4.70
1151 1175 1.004440 GTGGGTCACTCACTGCCTC 60.004 63.158 0.00 0.00 32.78 4.70
1162 1186 4.790962 CTGCCTCCACATGCGCCT 62.791 66.667 4.18 0.00 0.00 5.52
1163 1187 3.390183 CTGCCTCCACATGCGCCTA 62.390 63.158 4.18 0.00 0.00 3.93
1263 1293 3.365364 GCGACCTTTCTTTGATTGACCAG 60.365 47.826 0.00 0.00 0.00 4.00
1286 1316 1.080298 TTTGACGTGTTGCGACTTGT 58.920 45.000 5.50 3.53 44.77 3.16
1298 1328 2.421775 TGCGACTTGTGTTTGTGTGAAT 59.578 40.909 0.00 0.00 0.00 2.57
1488 1518 3.254060 CGACAACGAGATCAAGAACCAT 58.746 45.455 0.00 0.00 42.66 3.55
1656 1686 2.432628 GCCACGGGAAGTCAGTCG 60.433 66.667 0.00 0.00 0.00 4.18
2042 2084 0.523546 CTCGTCGTCGTTGATCCCAG 60.524 60.000 1.33 0.00 38.33 4.45
2257 2301 7.381948 TCATTTGTCGTTCATTTTTCATCCTTG 59.618 33.333 0.00 0.00 0.00 3.61
2297 2341 7.923878 GTCTAGATTTGATACCTCAACTCTTCC 59.076 40.741 11.76 0.97 44.50 3.46
2314 2359 0.533032 TCCAACGACATATGCGTGGA 59.467 50.000 21.27 22.29 41.75 4.02
2349 2394 3.128764 ACATGCATGCAAAGTGAGATGAG 59.871 43.478 26.68 5.43 0.00 2.90
2381 2426 9.478238 TCTGGATAATGAAATGAAGGAAAATGA 57.522 29.630 0.00 0.00 0.00 2.57
2461 2513 1.240256 TTGGGTTATGCACACCGTTC 58.760 50.000 10.19 0.00 34.79 3.95
2507 2559 0.244450 TCCGCCTAGTTACACGTTGG 59.756 55.000 0.00 0.00 0.00 3.77
2547 2599 3.270027 TCGGGTTTGACATAGAGCATTG 58.730 45.455 0.00 0.00 0.00 2.82
2617 2669 4.455533 GTCACAACATCTTGAGCATGGTTA 59.544 41.667 0.00 0.00 0.00 2.85
2648 2700 5.250200 TGGGTAACAAAATGCTAGTACTGG 58.750 41.667 5.39 3.15 39.74 4.00
2703 3056 8.726988 AGTATTAACTGCTGCTCGAAAATAAAA 58.273 29.630 0.00 0.00 33.57 1.52
2704 3057 9.337091 GTATTAACTGCTGCTCGAAAATAAAAA 57.663 29.630 0.00 0.00 0.00 1.94
2705 3058 8.986477 ATTAACTGCTGCTCGAAAATAAAAAT 57.014 26.923 0.00 0.00 0.00 1.82
2706 3059 8.810652 TTAACTGCTGCTCGAAAATAAAAATT 57.189 26.923 0.00 0.00 0.00 1.82
2707 3060 6.695292 ACTGCTGCTCGAAAATAAAAATTG 57.305 33.333 0.00 0.00 0.00 2.32
2709 3062 6.583806 ACTGCTGCTCGAAAATAAAAATTGAG 59.416 34.615 0.00 0.00 0.00 3.02
2712 3067 7.326789 TGCTGCTCGAAAATAAAAATTGAGAAG 59.673 33.333 0.00 0.00 32.00 2.85
2753 3108 5.544136 GAGCAGAAAGGTCTTCTCAAATC 57.456 43.478 0.00 0.00 42.03 2.17
2973 3333 7.549488 ACGGAAAATGTACTAGGATTTTCTCTG 59.451 37.037 22.80 18.16 43.52 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.516718 TCCTCTGACTACTATGCAATTAAGC 58.483 40.000 0.00 0.00 0.00 3.09
5 6 8.200792 AGTTCCTCTGACTACTATGCAATTAAG 58.799 37.037 0.00 0.00 0.00 1.85
6 7 8.079211 AGTTCCTCTGACTACTATGCAATTAA 57.921 34.615 0.00 0.00 0.00 1.40
7 8 7.661536 AGTTCCTCTGACTACTATGCAATTA 57.338 36.000 0.00 0.00 0.00 1.40
8 9 6.552445 AGTTCCTCTGACTACTATGCAATT 57.448 37.500 0.00 0.00 0.00 2.32
9 10 6.552445 AAGTTCCTCTGACTACTATGCAAT 57.448 37.500 0.00 0.00 0.00 3.56
10 11 6.405953 GCTAAGTTCCTCTGACTACTATGCAA 60.406 42.308 0.00 0.00 0.00 4.08
11 12 5.067936 GCTAAGTTCCTCTGACTACTATGCA 59.932 44.000 0.00 0.00 0.00 3.96
12 13 5.525199 GCTAAGTTCCTCTGACTACTATGC 58.475 45.833 0.00 0.00 0.00 3.14
13 14 5.753744 CGCTAAGTTCCTCTGACTACTATG 58.246 45.833 0.00 0.00 0.00 2.23
14 15 4.276431 GCGCTAAGTTCCTCTGACTACTAT 59.724 45.833 0.00 0.00 0.00 2.12
15 16 3.626670 GCGCTAAGTTCCTCTGACTACTA 59.373 47.826 0.00 0.00 0.00 1.82
16 17 2.424246 GCGCTAAGTTCCTCTGACTACT 59.576 50.000 0.00 0.00 0.00 2.57
17 18 2.479901 GGCGCTAAGTTCCTCTGACTAC 60.480 54.545 7.64 0.00 0.00 2.73
18 19 1.749634 GGCGCTAAGTTCCTCTGACTA 59.250 52.381 7.64 0.00 0.00 2.59
19 20 0.533032 GGCGCTAAGTTCCTCTGACT 59.467 55.000 7.64 0.00 0.00 3.41
20 21 0.802607 CGGCGCTAAGTTCCTCTGAC 60.803 60.000 7.64 0.00 0.00 3.51
21 22 1.511305 CGGCGCTAAGTTCCTCTGA 59.489 57.895 7.64 0.00 0.00 3.27
22 23 2.167861 GCGGCGCTAAGTTCCTCTG 61.168 63.158 26.86 0.00 0.00 3.35
23 24 1.035932 TAGCGGCGCTAAGTTCCTCT 61.036 55.000 36.64 13.59 38.27 3.69
24 25 0.032267 ATAGCGGCGCTAAGTTCCTC 59.968 55.000 40.67 5.66 44.62 3.71
25 26 0.464452 AATAGCGGCGCTAAGTTCCT 59.536 50.000 40.67 23.43 44.62 3.36
26 27 1.260825 GAAATAGCGGCGCTAAGTTCC 59.739 52.381 40.67 25.02 44.62 3.62
27 28 1.931172 TGAAATAGCGGCGCTAAGTTC 59.069 47.619 36.56 36.56 44.62 3.01
28 29 2.018542 TGAAATAGCGGCGCTAAGTT 57.981 45.000 40.67 34.48 44.62 2.66
29 30 2.018542 TTGAAATAGCGGCGCTAAGT 57.981 45.000 40.67 31.13 44.62 2.24
30 31 3.609103 ATTTGAAATAGCGGCGCTAAG 57.391 42.857 40.67 0.00 44.62 2.18
31 32 3.690422 CAATTTGAAATAGCGGCGCTAA 58.310 40.909 40.67 27.45 44.62 3.09
32 33 2.540769 GCAATTTGAAATAGCGGCGCTA 60.541 45.455 39.52 39.52 45.55 4.26
33 34 1.798813 GCAATTTGAAATAGCGGCGCT 60.799 47.619 37.84 37.84 43.41 5.92
34 35 0.572125 GCAATTTGAAATAGCGGCGC 59.428 50.000 26.86 26.86 0.00 6.53
35 36 1.199624 GGCAATTTGAAATAGCGGCG 58.800 50.000 0.51 0.51 0.00 6.46
36 37 2.584492 AGGCAATTTGAAATAGCGGC 57.416 45.000 0.00 0.00 0.00 6.53
37 38 4.493547 TGAAAGGCAATTTGAAATAGCGG 58.506 39.130 0.00 0.00 0.00 5.52
38 39 6.455913 CCATTGAAAGGCAATTTGAAATAGCG 60.456 38.462 0.00 0.00 44.68 4.26
39 40 6.594937 TCCATTGAAAGGCAATTTGAAATAGC 59.405 34.615 0.00 0.00 44.68 2.97
40 41 7.064966 GGTCCATTGAAAGGCAATTTGAAATAG 59.935 37.037 0.00 0.00 44.68 1.73
41 42 6.878389 GGTCCATTGAAAGGCAATTTGAAATA 59.122 34.615 0.00 0.00 44.68 1.40
42 43 5.706833 GGTCCATTGAAAGGCAATTTGAAAT 59.293 36.000 0.00 0.00 44.68 2.17
43 44 5.062528 GGTCCATTGAAAGGCAATTTGAAA 58.937 37.500 0.00 0.00 44.68 2.69
44 45 4.102210 TGGTCCATTGAAAGGCAATTTGAA 59.898 37.500 0.00 0.00 44.68 2.69
45 46 3.645212 TGGTCCATTGAAAGGCAATTTGA 59.355 39.130 0.00 0.00 44.68 2.69
46 47 3.998341 CTGGTCCATTGAAAGGCAATTTG 59.002 43.478 0.00 0.00 44.68 2.32
47 48 3.903090 TCTGGTCCATTGAAAGGCAATTT 59.097 39.130 0.00 0.00 44.68 1.82
48 49 3.509442 TCTGGTCCATTGAAAGGCAATT 58.491 40.909 0.00 0.00 44.68 2.32
50 51 2.673775 TCTGGTCCATTGAAAGGCAA 57.326 45.000 0.00 0.00 41.53 4.52
51 52 2.673775 TTCTGGTCCATTGAAAGGCA 57.326 45.000 0.00 0.00 0.00 4.75
52 53 3.573967 TCTTTTCTGGTCCATTGAAAGGC 59.426 43.478 15.93 0.00 32.36 4.35
53 54 5.776744 CTTCTTTTCTGGTCCATTGAAAGG 58.223 41.667 15.93 12.57 32.36 3.11
54 55 5.010415 AGCTTCTTTTCTGGTCCATTGAAAG 59.990 40.000 12.31 12.31 32.36 2.62
55 56 4.895297 AGCTTCTTTTCTGGTCCATTGAAA 59.105 37.500 2.85 2.85 0.00 2.69
56 57 4.473444 AGCTTCTTTTCTGGTCCATTGAA 58.527 39.130 0.00 0.00 0.00 2.69
57 58 4.104383 AGCTTCTTTTCTGGTCCATTGA 57.896 40.909 0.00 0.00 0.00 2.57
58 59 4.038402 ACAAGCTTCTTTTCTGGTCCATTG 59.962 41.667 0.00 0.00 0.00 2.82
59 60 4.218312 ACAAGCTTCTTTTCTGGTCCATT 58.782 39.130 0.00 0.00 0.00 3.16
60 61 3.837355 ACAAGCTTCTTTTCTGGTCCAT 58.163 40.909 0.00 0.00 0.00 3.41
61 62 3.297134 ACAAGCTTCTTTTCTGGTCCA 57.703 42.857 0.00 0.00 0.00 4.02
62 63 3.502595 GGTACAAGCTTCTTTTCTGGTCC 59.497 47.826 0.00 0.00 0.00 4.46
63 64 4.134563 TGGTACAAGCTTCTTTTCTGGTC 58.865 43.478 0.00 0.00 31.92 4.02
64 65 4.164843 TGGTACAAGCTTCTTTTCTGGT 57.835 40.909 0.00 0.00 31.92 4.00
80 81 3.115554 GCCGCATGATGAAAAATGGTAC 58.884 45.455 0.00 0.00 0.00 3.34
81 82 2.223456 CGCCGCATGATGAAAAATGGTA 60.223 45.455 0.00 0.00 0.00 3.25
82 83 1.469595 CGCCGCATGATGAAAAATGGT 60.470 47.619 0.00 0.00 0.00 3.55
83 84 1.202203 CGCCGCATGATGAAAAATGG 58.798 50.000 0.00 0.00 0.00 3.16
84 85 1.202203 CCGCCGCATGATGAAAAATG 58.798 50.000 0.00 0.00 0.00 2.32
85 86 0.102844 CCCGCCGCATGATGAAAAAT 59.897 50.000 0.00 0.00 0.00 1.82
86 87 1.510383 CCCGCCGCATGATGAAAAA 59.490 52.632 0.00 0.00 0.00 1.94
87 88 3.062500 GCCCGCCGCATGATGAAAA 62.063 57.895 0.00 0.00 37.47 2.29
88 89 3.517140 GCCCGCCGCATGATGAAA 61.517 61.111 0.00 0.00 37.47 2.69
98 99 2.673687 TTAGGTTTTGGCCCGCCG 60.674 61.111 0.00 0.00 39.42 6.46
99 100 2.642254 GGTTAGGTTTTGGCCCGCC 61.642 63.158 0.00 0.00 0.00 6.13
100 101 1.254975 ATGGTTAGGTTTTGGCCCGC 61.255 55.000 0.00 0.00 0.00 6.13
101 102 2.131776 TATGGTTAGGTTTTGGCCCG 57.868 50.000 0.00 0.00 0.00 6.13
102 103 3.369052 GCTTTATGGTTAGGTTTTGGCCC 60.369 47.826 0.00 0.00 0.00 5.80
103 104 3.259625 TGCTTTATGGTTAGGTTTTGGCC 59.740 43.478 0.00 0.00 0.00 5.36
104 105 4.494484 CTGCTTTATGGTTAGGTTTTGGC 58.506 43.478 0.00 0.00 0.00 4.52
105 106 4.494484 GCTGCTTTATGGTTAGGTTTTGG 58.506 43.478 0.00 0.00 0.00 3.28
106 107 4.165779 CGCTGCTTTATGGTTAGGTTTTG 58.834 43.478 0.00 0.00 0.00 2.44
107 108 3.824443 ACGCTGCTTTATGGTTAGGTTTT 59.176 39.130 0.00 0.00 0.00 2.43
108 109 3.418047 ACGCTGCTTTATGGTTAGGTTT 58.582 40.909 0.00 0.00 0.00 3.27
109 110 3.067684 ACGCTGCTTTATGGTTAGGTT 57.932 42.857 0.00 0.00 0.00 3.50
110 111 2.747446 CAACGCTGCTTTATGGTTAGGT 59.253 45.455 0.00 0.00 0.00 3.08
111 112 2.097466 CCAACGCTGCTTTATGGTTAGG 59.903 50.000 0.00 0.00 0.00 2.69
112 113 2.477863 GCCAACGCTGCTTTATGGTTAG 60.478 50.000 0.00 0.00 33.63 2.34
113 114 1.470890 GCCAACGCTGCTTTATGGTTA 59.529 47.619 0.00 0.00 33.63 2.85
114 115 0.243636 GCCAACGCTGCTTTATGGTT 59.756 50.000 0.00 0.00 33.63 3.67
115 116 0.893270 TGCCAACGCTGCTTTATGGT 60.893 50.000 0.00 0.00 35.36 3.55
116 117 0.456653 GTGCCAACGCTGCTTTATGG 60.457 55.000 0.00 1.95 35.36 2.74
117 118 0.240678 TGTGCCAACGCTGCTTTATG 59.759 50.000 0.00 0.00 35.36 1.90
118 119 1.176527 ATGTGCCAACGCTGCTTTAT 58.823 45.000 0.00 0.00 35.36 1.40
119 120 1.737236 CTATGTGCCAACGCTGCTTTA 59.263 47.619 0.00 0.00 35.36 1.85
120 121 0.523072 CTATGTGCCAACGCTGCTTT 59.477 50.000 0.00 0.00 35.36 3.51
121 122 0.321564 TCTATGTGCCAACGCTGCTT 60.322 50.000 0.00 0.00 35.36 3.91
122 123 0.321564 TTCTATGTGCCAACGCTGCT 60.322 50.000 0.00 0.00 35.36 4.24
123 124 0.521291 TTTCTATGTGCCAACGCTGC 59.479 50.000 0.00 0.00 35.36 5.25
124 125 1.135689 GGTTTCTATGTGCCAACGCTG 60.136 52.381 0.00 0.00 35.36 5.18
125 126 1.165270 GGTTTCTATGTGCCAACGCT 58.835 50.000 0.00 0.00 35.36 5.07
126 127 0.170339 GGGTTTCTATGTGCCAACGC 59.830 55.000 0.00 0.00 0.00 4.84
127 128 1.821216 AGGGTTTCTATGTGCCAACG 58.179 50.000 0.00 0.00 0.00 4.10
128 129 3.279434 CCTAGGGTTTCTATGTGCCAAC 58.721 50.000 0.00 0.00 0.00 3.77
129 130 2.356741 GCCTAGGGTTTCTATGTGCCAA 60.357 50.000 11.72 0.00 0.00 4.52
130 131 1.211949 GCCTAGGGTTTCTATGTGCCA 59.788 52.381 11.72 0.00 0.00 4.92
131 132 1.477014 GGCCTAGGGTTTCTATGTGCC 60.477 57.143 11.72 0.00 33.18 5.01
132 133 1.490910 AGGCCTAGGGTTTCTATGTGC 59.509 52.381 1.29 0.00 0.00 4.57
133 134 3.244249 GCTAGGCCTAGGGTTTCTATGTG 60.244 52.174 35.44 11.59 33.87 3.21
134 135 2.973406 GCTAGGCCTAGGGTTTCTATGT 59.027 50.000 35.44 0.00 33.87 2.29
135 136 2.303311 GGCTAGGCCTAGGGTTTCTATG 59.697 54.545 35.44 12.28 46.69 2.23
136 137 2.622210 GGCTAGGCCTAGGGTTTCTAT 58.378 52.381 35.44 0.00 46.69 1.98
137 138 2.098618 GGCTAGGCCTAGGGTTTCTA 57.901 55.000 35.44 3.80 46.69 2.10
138 139 2.932404 GGCTAGGCCTAGGGTTTCT 58.068 57.895 35.44 0.83 46.69 2.52
149 150 1.149401 GTGAGGGGAATGGCTAGGC 59.851 63.158 9.85 9.85 0.00 3.93
150 151 0.761802 GAGTGAGGGGAATGGCTAGG 59.238 60.000 0.00 0.00 0.00 3.02
151 152 0.390860 CGAGTGAGGGGAATGGCTAG 59.609 60.000 0.00 0.00 0.00 3.42
152 153 1.686325 GCGAGTGAGGGGAATGGCTA 61.686 60.000 0.00 0.00 0.00 3.93
153 154 3.036429 GCGAGTGAGGGGAATGGCT 62.036 63.158 0.00 0.00 0.00 4.75
154 155 2.514824 GCGAGTGAGGGGAATGGC 60.515 66.667 0.00 0.00 0.00 4.40
155 156 2.190578 GGCGAGTGAGGGGAATGG 59.809 66.667 0.00 0.00 0.00 3.16
156 157 2.190578 GGGCGAGTGAGGGGAATG 59.809 66.667 0.00 0.00 0.00 2.67
157 158 2.041265 AGGGCGAGTGAGGGGAAT 59.959 61.111 0.00 0.00 0.00 3.01
158 159 2.683933 GAGGGCGAGTGAGGGGAA 60.684 66.667 0.00 0.00 0.00 3.97
159 160 4.779733 GGAGGGCGAGTGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
161 162 2.592993 TTTGGAGGGCGAGTGAGGG 61.593 63.158 0.00 0.00 0.00 4.30
162 163 1.376037 GTTTGGAGGGCGAGTGAGG 60.376 63.158 0.00 0.00 0.00 3.86
163 164 0.036010 ATGTTTGGAGGGCGAGTGAG 60.036 55.000 0.00 0.00 0.00 3.51
164 165 0.036388 GATGTTTGGAGGGCGAGTGA 60.036 55.000 0.00 0.00 0.00 3.41
165 166 0.036010 AGATGTTTGGAGGGCGAGTG 60.036 55.000 0.00 0.00 0.00 3.51
166 167 1.207329 GTAGATGTTTGGAGGGCGAGT 59.793 52.381 0.00 0.00 0.00 4.18
167 168 1.802880 CGTAGATGTTTGGAGGGCGAG 60.803 57.143 0.00 0.00 0.00 5.03
168 169 0.174845 CGTAGATGTTTGGAGGGCGA 59.825 55.000 0.00 0.00 0.00 5.54
169 170 0.810031 CCGTAGATGTTTGGAGGGCG 60.810 60.000 0.00 0.00 0.00 6.13
170 171 1.095807 GCCGTAGATGTTTGGAGGGC 61.096 60.000 0.00 0.00 35.87 5.19
171 172 0.810031 CGCCGTAGATGTTTGGAGGG 60.810 60.000 0.00 0.00 0.00 4.30
172 173 0.108329 ACGCCGTAGATGTTTGGAGG 60.108 55.000 0.00 0.00 0.00 4.30
173 174 1.135083 AGACGCCGTAGATGTTTGGAG 60.135 52.381 0.00 0.00 0.00 3.86
174 175 0.892755 AGACGCCGTAGATGTTTGGA 59.107 50.000 0.00 0.00 0.00 3.53
175 176 0.999406 CAGACGCCGTAGATGTTTGG 59.001 55.000 0.00 0.00 0.00 3.28
176 177 1.920574 CTCAGACGCCGTAGATGTTTG 59.079 52.381 0.00 0.00 0.00 2.93
177 178 1.135083 CCTCAGACGCCGTAGATGTTT 60.135 52.381 0.00 0.00 0.00 2.83
178 179 0.456221 CCTCAGACGCCGTAGATGTT 59.544 55.000 0.00 0.00 0.00 2.71
179 180 0.680280 ACCTCAGACGCCGTAGATGT 60.680 55.000 0.00 0.00 0.00 3.06
180 181 0.248661 CACCTCAGACGCCGTAGATG 60.249 60.000 0.00 0.00 0.00 2.90
181 182 1.384989 CCACCTCAGACGCCGTAGAT 61.385 60.000 0.00 0.00 0.00 1.98
182 183 2.044555 CCACCTCAGACGCCGTAGA 61.045 63.158 0.00 0.00 0.00 2.59
183 184 2.490217 CCACCTCAGACGCCGTAG 59.510 66.667 0.00 0.00 0.00 3.51
184 185 3.755628 GCCACCTCAGACGCCGTA 61.756 66.667 0.00 0.00 0.00 4.02
188 189 4.687215 TGCAGCCACCTCAGACGC 62.687 66.667 0.00 0.00 0.00 5.19
189 190 1.597854 TTTGCAGCCACCTCAGACG 60.598 57.895 0.00 0.00 0.00 4.18
190 191 0.536006 AGTTTGCAGCCACCTCAGAC 60.536 55.000 0.00 0.00 0.00 3.51
191 192 0.535780 CAGTTTGCAGCCACCTCAGA 60.536 55.000 0.00 0.00 0.00 3.27
192 193 1.954528 CAGTTTGCAGCCACCTCAG 59.045 57.895 0.00 0.00 0.00 3.35
193 194 2.195567 GCAGTTTGCAGCCACCTCA 61.196 57.895 0.00 0.00 44.26 3.86
194 195 2.647297 GCAGTTTGCAGCCACCTC 59.353 61.111 0.00 0.00 44.26 3.85
203 204 1.973812 GGAGGGAGTGGCAGTTTGC 60.974 63.158 0.00 0.00 44.08 3.68
204 205 0.111253 AAGGAGGGAGTGGCAGTTTG 59.889 55.000 0.00 0.00 0.00 2.93
205 206 1.351350 GTAAGGAGGGAGTGGCAGTTT 59.649 52.381 0.00 0.00 0.00 2.66
206 207 0.984995 GTAAGGAGGGAGTGGCAGTT 59.015 55.000 0.00 0.00 0.00 3.16
207 208 0.910088 GGTAAGGAGGGAGTGGCAGT 60.910 60.000 0.00 0.00 0.00 4.40
208 209 0.618968 AGGTAAGGAGGGAGTGGCAG 60.619 60.000 0.00 0.00 0.00 4.85
209 210 0.714180 TAGGTAAGGAGGGAGTGGCA 59.286 55.000 0.00 0.00 0.00 4.92
210 211 1.875488 TTAGGTAAGGAGGGAGTGGC 58.125 55.000 0.00 0.00 0.00 5.01
211 212 3.054582 GGTTTTAGGTAAGGAGGGAGTGG 60.055 52.174 0.00 0.00 0.00 4.00
212 213 3.585732 TGGTTTTAGGTAAGGAGGGAGTG 59.414 47.826 0.00 0.00 0.00 3.51
213 214 3.586174 GTGGTTTTAGGTAAGGAGGGAGT 59.414 47.826 0.00 0.00 0.00 3.85
214 215 3.369157 CGTGGTTTTAGGTAAGGAGGGAG 60.369 52.174 0.00 0.00 0.00 4.30
215 216 2.568509 CGTGGTTTTAGGTAAGGAGGGA 59.431 50.000 0.00 0.00 0.00 4.20
216 217 2.938314 GCGTGGTTTTAGGTAAGGAGGG 60.938 54.545 0.00 0.00 0.00 4.30
217 218 2.353323 GCGTGGTTTTAGGTAAGGAGG 58.647 52.381 0.00 0.00 0.00 4.30
218 219 2.289819 TGGCGTGGTTTTAGGTAAGGAG 60.290 50.000 0.00 0.00 0.00 3.69
219 220 1.698532 TGGCGTGGTTTTAGGTAAGGA 59.301 47.619 0.00 0.00 0.00 3.36
220 221 2.188062 TGGCGTGGTTTTAGGTAAGG 57.812 50.000 0.00 0.00 0.00 2.69
221 222 3.126343 GTCATGGCGTGGTTTTAGGTAAG 59.874 47.826 6.90 0.00 0.00 2.34
225 226 1.529226 TGTCATGGCGTGGTTTTAGG 58.471 50.000 6.90 0.00 0.00 2.69
250 251 1.488812 TGGTAATCCCTCCGTTCCATG 59.511 52.381 0.00 0.00 0.00 3.66
259 260 2.552373 CCGGGCTAAATGGTAATCCCTC 60.552 54.545 0.00 0.00 0.00 4.30
317 318 4.634004 TGTATTGGCTTCCGTTGTATCAAG 59.366 41.667 0.00 0.00 0.00 3.02
327 328 4.036734 ACATGCTAATTGTATTGGCTTCCG 59.963 41.667 8.80 0.00 0.00 4.30
331 332 7.880160 TCTAAACATGCTAATTGTATTGGCT 57.120 32.000 8.80 0.00 0.00 4.75
403 404 8.560355 AGGGTTTTCAATGGTATTAATTTTGC 57.440 30.769 0.00 0.00 0.00 3.68
494 495 1.821136 CTCATGGGTCCCTTTTGCTTC 59.179 52.381 10.00 0.00 0.00 3.86
559 560 1.768112 CGTCGGCGTCACCACTTTTT 61.768 55.000 6.85 0.00 39.03 1.94
560 561 2.241880 CGTCGGCGTCACCACTTTT 61.242 57.895 6.85 0.00 39.03 2.27
561 562 2.660552 CGTCGGCGTCACCACTTT 60.661 61.111 6.85 0.00 39.03 2.66
617 618 1.635817 GGGGCTAGCCAAGGATGACA 61.636 60.000 34.09 0.00 37.98 3.58
638 639 1.762957 CGATGGACCTTGGACCAGTAT 59.237 52.381 15.22 0.43 39.62 2.12
703 704 9.026121 ACTGATGACTAGCTAGAAGTAGAAAAA 57.974 33.333 27.45 1.69 0.00 1.94
704 705 8.582657 ACTGATGACTAGCTAGAAGTAGAAAA 57.417 34.615 27.45 2.98 0.00 2.29
724 727 1.077501 CCGGTGGCCATCAACTGAT 60.078 57.895 18.15 0.00 34.56 2.90
725 728 2.350895 CCGGTGGCCATCAACTGA 59.649 61.111 18.15 0.00 0.00 3.41
835 858 1.732941 CACGGGTGCACAATAGCTAA 58.267 50.000 20.43 0.00 34.99 3.09
847 870 2.348605 CTGTTTTGGTGGCACGGGTG 62.349 60.000 12.17 0.00 0.00 4.61
851 874 1.008538 GCTCTGTTTTGGTGGCACG 60.009 57.895 12.17 0.00 0.00 5.34
878 901 6.554334 ACAGCTGCGAACTTTTTCTTTATA 57.446 33.333 15.27 0.00 0.00 0.98
879 902 5.438761 ACAGCTGCGAACTTTTTCTTTAT 57.561 34.783 15.27 0.00 0.00 1.40
880 903 4.893424 ACAGCTGCGAACTTTTTCTTTA 57.107 36.364 15.27 0.00 0.00 1.85
883 906 3.438360 CAAACAGCTGCGAACTTTTTCT 58.562 40.909 15.27 0.00 0.00 2.52
884 907 2.034591 GCAAACAGCTGCGAACTTTTTC 60.035 45.455 15.27 0.00 41.15 2.29
885 908 1.926510 GCAAACAGCTGCGAACTTTTT 59.073 42.857 15.27 1.65 41.15 1.94
976 1000 2.392206 GAGCTTCGTTCGCTTCGC 59.608 61.111 0.00 0.00 37.96 4.70
977 1001 2.683965 CGAGCTTCGTTCGCTTCG 59.316 61.111 0.00 0.00 37.96 3.79
1151 1175 1.958205 GCTAGCTAGGCGCATGTGG 60.958 63.158 22.10 0.00 42.61 4.17
1162 1186 1.793134 GCCGGCGAAGTAGCTAGCTA 61.793 60.000 20.67 20.67 37.29 3.32
1163 1187 3.121019 CCGGCGAAGTAGCTAGCT 58.879 61.111 23.12 23.12 37.29 3.32
1241 1271 2.552315 TGGTCAATCAAAGAAAGGTCGC 59.448 45.455 0.00 0.00 0.00 5.19
1263 1293 1.176838 GTCGCAACACGTCAAAACAC 58.823 50.000 0.00 0.00 44.19 3.32
1286 1316 3.561143 AGCAACCCTATTCACACAAACA 58.439 40.909 0.00 0.00 0.00 2.83
1298 1328 4.077184 CGCACCGGAGCAACCCTA 62.077 66.667 23.87 0.00 34.64 3.53
1425 1455 1.882352 GCGATCTTGGACCACCTGTTT 60.882 52.381 0.00 0.00 37.04 2.83
1488 1518 1.960417 TCTTGATGTGCGTGTTCCAA 58.040 45.000 0.00 0.00 0.00 3.53
1656 1686 1.450312 CATGTCCTCTTCGGCACCC 60.450 63.158 0.00 0.00 0.00 4.61
1981 2023 2.286826 CCTGGTGATCGAACAGGGA 58.713 57.895 17.01 0.00 46.24 4.20
2297 2341 1.333169 GCATCCACGCATATGTCGTTG 60.333 52.381 18.33 15.86 38.19 4.10
2314 2359 2.104132 CATGTGCGCATGCTGCAT 59.896 55.556 29.91 20.89 45.36 3.96
2325 2370 1.068125 TCTCACTTTGCATGCATGTGC 60.068 47.619 32.09 16.62 45.25 4.57
2349 2394 7.941238 TCCTTCATTTCATTATCCAGATTCCTC 59.059 37.037 0.00 0.00 0.00 3.71
2507 2559 2.164422 CGAAAAAGGGAGGAGAAATGCC 59.836 50.000 0.00 0.00 0.00 4.40
2547 2599 5.702349 ATAATGGCTTTCATCAGCTTAGC 57.298 39.130 0.00 0.00 39.97 3.09
2617 2669 4.649218 AGCATTTTGTTACCCAGTCAAACT 59.351 37.500 0.00 0.00 32.08 2.66
2648 2700 9.382244 GAAATGGACGCAGAATGTTATTAATAC 57.618 33.333 0.00 0.00 39.31 1.89
2687 3037 7.327032 ACTTCTCAATTTTTATTTTCGAGCAGC 59.673 33.333 0.00 0.00 0.00 5.25
2703 3056 9.270640 GCTGATAGATCATGTAACTTCTCAATT 57.729 33.333 0.00 0.00 36.02 2.32
2704 3057 8.427276 TGCTGATAGATCATGTAACTTCTCAAT 58.573 33.333 0.00 0.00 36.02 2.57
2705 3058 7.785033 TGCTGATAGATCATGTAACTTCTCAA 58.215 34.615 0.00 0.00 36.02 3.02
2706 3059 7.286316 TCTGCTGATAGATCATGTAACTTCTCA 59.714 37.037 0.00 0.00 36.02 3.27
2707 3060 7.656412 TCTGCTGATAGATCATGTAACTTCTC 58.344 38.462 0.00 0.00 36.02 2.87
2709 3062 6.365789 GCTCTGCTGATAGATCATGTAACTTC 59.634 42.308 0.00 0.00 36.02 3.01
2712 3067 5.536260 TGCTCTGCTGATAGATCATGTAAC 58.464 41.667 0.00 0.00 36.02 2.50


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

AutoCloner maintained by Alex Coulton.