Multiple sequence alignment - TraesCS7B01G498500

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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 TraesCS7B01G498500 chr7B 100.000 2927 0 0 1 2927 749409242 749406316 0.000000e+00 5406
1 TraesCS7B01G498500 chr7D 93.992 1265 41 14 333 1563 633374491 633373228 0.000000e+00 1882
2 TraesCS7B01G498500 chr7D 96.937 653 20 0 1548 2200 633373212 633372560 0.000000e+00 1096
3 TraesCS7B01G498500 chr7D 91.033 736 34 4 2219 2927 633372490 633371760 0.000000e+00 965
4 TraesCS7B01G498500 chr7D 73.481 675 132 27 1247 1899 633369257 633368608 8.220000e-51 211
5 TraesCS7B01G498500 chr6A 81.470 1306 188 28 812 2106 3536542 3537804 0.000000e+00 1022
6 TraesCS7B01G498500 chr6A 75.751 1365 245 47 812 2145 2495906 2494597 2.490000e-170 608
7 TraesCS7B01G498500 chr6A 71.449 1380 270 93 812 2145 2718986 2717685 4.840000e-63 252
8 TraesCS7B01G498500 chrUn 76.510 1358 243 43 812 2145 356527488 356528793 0.000000e+00 671
9 TraesCS7B01G498500 chrUn 76.466 1347 242 42 822 2145 412171405 412170111 0.000000e+00 662
10 TraesCS7B01G498500 chrUn 76.471 901 158 31 1268 2145 70984238 70983369 9.630000e-120 440
11 TraesCS7B01G498500 chrUn 82.576 132 23 0 814 945 51907671 51907802 1.840000e-22 117
12 TraesCS7B01G498500 chrUn 82.576 132 23 0 814 945 290968857 290968988 1.840000e-22 117
13 TraesCS7B01G498500 chr6B 71.670 1126 244 51 812 1920 8451891 8452958 2.910000e-60 243
14 TraesCS7B01G498500 chr6D 73.151 730 159 29 1434 2145 4055113 4054403 8.160000e-56 228
15 TraesCS7B01G498500 chr6D 77.273 264 53 7 1444 1702 4643079 4643340 6.540000e-32 148
16 TraesCS7B01G498500 chr6D 73.611 360 75 14 1559 1905 3836862 3836510 1.420000e-23 121
17 TraesCS7B01G498500 chr4A 97.436 78 2 0 59 136 740085303 740085380 1.830000e-27 134
18 TraesCS7B01G498500 chr4B 78.610 187 30 4 769 945 2691409 2691595 6.630000e-22 115
19 TraesCS7B01G498500 chr4B 81.481 135 24 1 812 945 2702976 2703110 3.080000e-20 110


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 TraesCS7B01G498500 chr7B 749406316 749409242 2926 True 5406.0 5406 100.00000 1 2927 1 chr7B.!!$R1 2926
1 TraesCS7B01G498500 chr7D 633368608 633374491 5883 True 1038.5 1882 88.86075 333 2927 4 chr7D.!!$R1 2594
2 TraesCS7B01G498500 chr6A 3536542 3537804 1262 False 1022.0 1022 81.47000 812 2106 1 chr6A.!!$F1 1294
3 TraesCS7B01G498500 chr6A 2494597 2495906 1309 True 608.0 608 75.75100 812 2145 1 chr6A.!!$R1 1333
4 TraesCS7B01G498500 chr6A 2717685 2718986 1301 True 252.0 252 71.44900 812 2145 1 chr6A.!!$R2 1333
5 TraesCS7B01G498500 chrUn 356527488 356528793 1305 False 671.0 671 76.51000 812 2145 1 chrUn.!!$F3 1333
6 TraesCS7B01G498500 chrUn 412170111 412171405 1294 True 662.0 662 76.46600 822 2145 1 chrUn.!!$R2 1323
7 TraesCS7B01G498500 chrUn 70983369 70984238 869 True 440.0 440 76.47100 1268 2145 1 chrUn.!!$R1 877
8 TraesCS7B01G498500 chr6B 8451891 8452958 1067 False 243.0 243 71.67000 812 1920 1 chr6B.!!$F1 1108
9 TraesCS7B01G498500 chr6D 4054403 4055113 710 True 228.0 228 73.15100 1434 2145 1 chr6D.!!$R2 711

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
128 129 0.038890 GCCTTGAGCCCTTTTCCTCT 59.961 55.0 0.0 0.0 34.35 3.69 F
166 167 0.106708 TCTGGACCTCCGCAATATGC 59.893 55.0 0.0 0.0 40.69 3.14 F
1759 1878 0.175073 GGGGTATGACGAGGACACAC 59.825 60.0 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1808 2.042464 ACTCTGTGTGGAAAGAGCTCA 58.958 47.619 17.77 0.0 43.13 4.26 R
1850 1972 5.036916 TGTAGGGATGAAAGGTGAGGTAAT 58.963 41.667 0.00 0.0 0.00 1.89 R
2731 2951 1.002502 CTCCACTCCCCGGTTTTCC 60.003 63.158 0.00 0.0 0.00 3.13 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
20 21 3.287867 CATAGGGTTCATCAAGTGGCT 57.712 47.619 0.00 0.00 0.00 4.75
21 22 4.422073 CATAGGGTTCATCAAGTGGCTA 57.578 45.455 0.00 0.00 0.00 3.93
22 23 4.978099 CATAGGGTTCATCAAGTGGCTAT 58.022 43.478 0.00 0.00 0.00 2.97
23 24 3.567478 AGGGTTCATCAAGTGGCTATC 57.433 47.619 0.00 0.00 0.00 2.08
24 25 2.846206 AGGGTTCATCAAGTGGCTATCA 59.154 45.455 0.00 0.00 0.00 2.15
25 26 3.461085 AGGGTTCATCAAGTGGCTATCAT 59.539 43.478 0.00 0.00 0.00 2.45
26 27 4.079558 AGGGTTCATCAAGTGGCTATCATT 60.080 41.667 0.00 0.00 0.00 2.57
27 28 4.037208 GGGTTCATCAAGTGGCTATCATTG 59.963 45.833 0.00 0.00 0.00 2.82
28 29 4.641989 GGTTCATCAAGTGGCTATCATTGT 59.358 41.667 0.00 0.00 0.00 2.71
29 30 5.822519 GGTTCATCAAGTGGCTATCATTGTA 59.177 40.000 0.00 0.00 0.00 2.41
30 31 6.488006 GGTTCATCAAGTGGCTATCATTGTAT 59.512 38.462 0.00 0.00 0.00 2.29
31 32 7.308229 GGTTCATCAAGTGGCTATCATTGTATC 60.308 40.741 0.00 0.00 0.00 2.24
32 33 5.928264 TCATCAAGTGGCTATCATTGTATCG 59.072 40.000 0.00 0.00 0.00 2.92
33 34 4.058124 TCAAGTGGCTATCATTGTATCGC 58.942 43.478 0.00 0.00 0.00 4.58
34 35 3.045601 AGTGGCTATCATTGTATCGCC 57.954 47.619 0.00 0.00 38.02 5.54
35 36 2.634940 AGTGGCTATCATTGTATCGCCT 59.365 45.455 0.00 0.00 38.28 5.52
36 37 2.738846 GTGGCTATCATTGTATCGCCTG 59.261 50.000 0.00 0.00 38.28 4.85
37 38 2.632512 TGGCTATCATTGTATCGCCTGA 59.367 45.455 0.00 0.00 38.28 3.86
38 39 2.996621 GGCTATCATTGTATCGCCTGAC 59.003 50.000 0.00 0.00 35.40 3.51
39 40 2.663602 GCTATCATTGTATCGCCTGACG 59.336 50.000 0.00 0.00 45.62 4.35
40 41 2.890808 ATCATTGTATCGCCTGACGT 57.109 45.000 0.00 0.00 44.19 4.34
41 42 2.203800 TCATTGTATCGCCTGACGTC 57.796 50.000 9.11 9.11 44.19 4.34
42 43 1.474879 TCATTGTATCGCCTGACGTCA 59.525 47.619 18.88 18.88 44.19 4.35
43 44 2.100749 TCATTGTATCGCCTGACGTCAT 59.899 45.455 20.40 6.25 44.19 3.06
44 45 2.203800 TTGTATCGCCTGACGTCATC 57.796 50.000 20.40 12.89 44.19 2.92
45 46 0.384309 TGTATCGCCTGACGTCATCC 59.616 55.000 20.40 11.83 44.19 3.51
46 47 0.660595 GTATCGCCTGACGTCATCCG 60.661 60.000 20.40 22.51 44.19 4.18
47 48 1.792118 TATCGCCTGACGTCATCCGG 61.792 60.000 26.92 22.15 44.19 5.14
48 49 3.822192 CGCCTGACGTCATCCGGA 61.822 66.667 22.65 6.61 42.24 5.14
49 50 2.815308 GCCTGACGTCATCCGGAT 59.185 61.111 22.65 12.38 42.24 4.18
50 51 1.300233 GCCTGACGTCATCCGGATC 60.300 63.158 22.65 4.21 42.24 3.36
51 52 1.739338 GCCTGACGTCATCCGGATCT 61.739 60.000 22.65 0.00 42.24 2.75
52 53 1.605753 CCTGACGTCATCCGGATCTA 58.394 55.000 20.40 2.41 42.24 1.98
53 54 2.163509 CCTGACGTCATCCGGATCTAT 58.836 52.381 20.40 0.00 42.24 1.98
54 55 2.558795 CCTGACGTCATCCGGATCTATT 59.441 50.000 20.40 0.00 42.24 1.73
55 56 3.569548 CTGACGTCATCCGGATCTATTG 58.430 50.000 20.40 4.54 42.24 1.90
56 57 2.296190 TGACGTCATCCGGATCTATTGG 59.704 50.000 15.88 1.88 42.24 3.16
57 58 1.000955 ACGTCATCCGGATCTATTGGC 59.999 52.381 15.88 5.07 42.24 4.52
58 59 1.000843 CGTCATCCGGATCTATTGGCA 59.999 52.381 15.88 0.00 0.00 4.92
59 60 2.547855 CGTCATCCGGATCTATTGGCAA 60.548 50.000 15.88 0.68 0.00 4.52
60 61 3.679389 GTCATCCGGATCTATTGGCAAT 58.321 45.455 15.88 18.01 0.00 3.56
61 62 3.686726 GTCATCCGGATCTATTGGCAATC 59.313 47.826 15.88 2.68 0.00 2.67
62 63 2.455674 TCCGGATCTATTGGCAATCG 57.544 50.000 17.41 13.20 0.00 3.34
63 64 1.691976 TCCGGATCTATTGGCAATCGT 59.308 47.619 17.41 3.76 0.00 3.73
64 65 2.894765 TCCGGATCTATTGGCAATCGTA 59.105 45.455 17.41 3.75 0.00 3.43
65 66 2.993899 CCGGATCTATTGGCAATCGTAC 59.006 50.000 17.41 8.78 0.00 3.67
66 67 3.306088 CCGGATCTATTGGCAATCGTACT 60.306 47.826 17.41 0.00 0.00 2.73
67 68 3.675225 CGGATCTATTGGCAATCGTACTG 59.325 47.826 17.41 9.93 0.00 2.74
68 69 4.558697 CGGATCTATTGGCAATCGTACTGA 60.559 45.833 17.41 7.12 0.00 3.41
69 70 5.297547 GGATCTATTGGCAATCGTACTGAA 58.702 41.667 17.41 0.00 0.00 3.02
70 71 5.177696 GGATCTATTGGCAATCGTACTGAAC 59.822 44.000 17.41 5.70 0.00 3.18
71 72 4.439057 TCTATTGGCAATCGTACTGAACC 58.561 43.478 17.41 0.00 0.00 3.62
72 73 2.851263 TTGGCAATCGTACTGAACCT 57.149 45.000 0.00 0.00 0.00 3.50
73 74 2.851263 TGGCAATCGTACTGAACCTT 57.149 45.000 0.00 0.00 0.00 3.50
74 75 2.422597 TGGCAATCGTACTGAACCTTG 58.577 47.619 0.00 0.00 0.00 3.61
75 76 1.130561 GGCAATCGTACTGAACCTTGC 59.869 52.381 12.20 12.20 40.21 4.01
76 77 2.076863 GCAATCGTACTGAACCTTGCT 58.923 47.619 12.84 0.00 38.92 3.91
77 78 2.484264 GCAATCGTACTGAACCTTGCTT 59.516 45.455 12.84 0.00 38.92 3.91
78 79 3.667960 GCAATCGTACTGAACCTTGCTTG 60.668 47.826 12.84 4.94 38.92 4.01
79 80 2.163818 TCGTACTGAACCTTGCTTGG 57.836 50.000 0.00 0.00 0.00 3.61
80 81 1.414919 TCGTACTGAACCTTGCTTGGT 59.585 47.619 0.00 0.00 43.11 3.67
90 91 2.562738 ACCTTGCTTGGTTTCTATTGGC 59.437 45.455 0.00 0.00 36.89 4.52
91 92 2.562298 CCTTGCTTGGTTTCTATTGGCA 59.438 45.455 0.00 0.00 0.00 4.92
92 93 3.006752 CCTTGCTTGGTTTCTATTGGCAA 59.993 43.478 0.68 0.68 36.86 4.52
93 94 4.322953 CCTTGCTTGGTTTCTATTGGCAAT 60.323 41.667 18.01 18.01 37.53 3.56
94 95 4.454728 TGCTTGGTTTCTATTGGCAATC 57.545 40.909 17.41 1.34 0.00 2.67
95 96 3.195396 TGCTTGGTTTCTATTGGCAATCC 59.805 43.478 17.41 11.76 0.00 3.01
96 97 3.195396 GCTTGGTTTCTATTGGCAATCCA 59.805 43.478 17.41 14.34 41.55 3.41
110 111 2.036572 TCCAATTGGAACCGGGGC 59.963 61.111 25.13 0.00 42.18 5.80
111 112 3.074369 CCAATTGGAACCGGGGCC 61.074 66.667 20.50 7.23 37.39 5.80
112 113 2.037208 CAATTGGAACCGGGGCCT 59.963 61.111 6.32 0.00 0.00 5.19
113 114 1.609210 CAATTGGAACCGGGGCCTT 60.609 57.895 6.32 0.00 0.00 4.35
114 115 1.609210 AATTGGAACCGGGGCCTTG 60.609 57.895 6.32 0.00 0.00 3.61
115 116 2.087857 AATTGGAACCGGGGCCTTGA 62.088 55.000 6.32 0.00 0.00 3.02
116 117 2.499303 ATTGGAACCGGGGCCTTGAG 62.499 60.000 6.32 0.00 0.00 3.02
126 127 4.852388 GCCTTGAGCCCTTTTCCT 57.148 55.556 0.00 0.00 34.35 3.36
127 128 2.572733 GCCTTGAGCCCTTTTCCTC 58.427 57.895 0.00 0.00 34.35 3.71
128 129 0.038890 GCCTTGAGCCCTTTTCCTCT 59.961 55.000 0.00 0.00 34.35 3.69
129 130 1.282157 GCCTTGAGCCCTTTTCCTCTA 59.718 52.381 0.00 0.00 34.35 2.43
130 131 2.290960 GCCTTGAGCCCTTTTCCTCTAA 60.291 50.000 0.00 0.00 34.35 2.10
131 132 3.814316 GCCTTGAGCCCTTTTCCTCTAAA 60.814 47.826 0.00 0.00 34.35 1.85
132 133 4.407365 CCTTGAGCCCTTTTCCTCTAAAA 58.593 43.478 0.00 0.00 35.74 1.52
133 134 4.832823 CCTTGAGCCCTTTTCCTCTAAAAA 59.167 41.667 0.00 0.00 36.64 1.94
151 152 2.024176 AAAACGTCATCCGGATCTGG 57.976 50.000 15.88 15.09 42.24 3.86
152 153 1.191535 AAACGTCATCCGGATCTGGA 58.808 50.000 25.60 25.60 43.58 3.86
153 154 0.460311 AACGTCATCCGGATCTGGAC 59.540 55.000 25.91 17.77 41.85 4.02
154 155 1.364171 CGTCATCCGGATCTGGACC 59.636 63.158 25.91 14.83 41.85 4.46
155 156 1.109920 CGTCATCCGGATCTGGACCT 61.110 60.000 25.91 8.24 41.85 3.85
156 157 0.676736 GTCATCCGGATCTGGACCTC 59.323 60.000 25.91 14.03 41.85 3.85
157 158 0.470080 TCATCCGGATCTGGACCTCC 60.470 60.000 25.91 0.00 41.85 4.30
160 161 3.147595 CGGATCTGGACCTCCGCA 61.148 66.667 7.65 0.00 46.87 5.69
161 162 2.721167 CGGATCTGGACCTCCGCAA 61.721 63.158 7.65 0.00 46.87 4.85
162 163 1.832912 GGATCTGGACCTCCGCAAT 59.167 57.895 0.00 0.00 39.43 3.56
163 164 1.048601 GGATCTGGACCTCCGCAATA 58.951 55.000 0.00 0.00 39.43 1.90
164 165 1.625818 GGATCTGGACCTCCGCAATAT 59.374 52.381 0.00 0.00 39.43 1.28
165 166 2.613977 GGATCTGGACCTCCGCAATATG 60.614 54.545 0.00 0.00 39.43 1.78
166 167 0.106708 TCTGGACCTCCGCAATATGC 59.893 55.000 0.00 0.00 40.69 3.14
167 168 0.179048 CTGGACCTCCGCAATATGCA 60.179 55.000 2.99 0.00 45.36 3.96
168 169 0.473755 TGGACCTCCGCAATATGCAT 59.526 50.000 3.79 3.79 45.36 3.96
169 170 1.696884 TGGACCTCCGCAATATGCATA 59.303 47.619 9.27 9.27 45.36 3.14
170 171 2.305635 TGGACCTCCGCAATATGCATAT 59.694 45.455 13.63 13.63 45.36 1.78
171 172 2.679837 GGACCTCCGCAATATGCATATG 59.320 50.000 19.77 14.13 45.36 1.78
172 173 3.338249 GACCTCCGCAATATGCATATGT 58.662 45.455 19.77 11.10 45.36 2.29
173 174 3.076621 ACCTCCGCAATATGCATATGTG 58.923 45.455 19.77 18.37 45.36 3.21
174 175 3.076621 CCTCCGCAATATGCATATGTGT 58.923 45.455 19.77 1.66 45.36 3.72
175 176 3.503363 CCTCCGCAATATGCATATGTGTT 59.497 43.478 19.77 2.16 45.36 3.32
176 177 4.022935 CCTCCGCAATATGCATATGTGTTT 60.023 41.667 19.77 1.77 45.36 2.83
177 178 5.107109 TCCGCAATATGCATATGTGTTTC 57.893 39.130 19.77 0.00 45.36 2.78
178 179 4.821260 TCCGCAATATGCATATGTGTTTCT 59.179 37.500 19.77 0.00 45.36 2.52
179 180 5.299028 TCCGCAATATGCATATGTGTTTCTT 59.701 36.000 19.77 0.00 45.36 2.52
180 181 5.978919 CCGCAATATGCATATGTGTTTCTTT 59.021 36.000 19.77 0.00 45.36 2.52
181 182 6.476380 CCGCAATATGCATATGTGTTTCTTTT 59.524 34.615 19.77 0.00 45.36 2.27
182 183 7.010367 CCGCAATATGCATATGTGTTTCTTTTT 59.990 33.333 19.77 0.00 45.36 1.94
183 184 8.051909 CGCAATATGCATATGTGTTTCTTTTTC 58.948 33.333 19.77 4.45 45.36 2.29
184 185 9.090692 GCAATATGCATATGTGTTTCTTTTTCT 57.909 29.630 19.77 0.00 44.26 2.52
187 188 9.793252 ATATGCATATGTGTTTCTTTTTCTGTC 57.207 29.630 18.45 0.00 0.00 3.51
188 189 7.036996 TGCATATGTGTTTCTTTTTCTGTCA 57.963 32.000 4.29 0.00 0.00 3.58
189 190 7.487484 TGCATATGTGTTTCTTTTTCTGTCAA 58.513 30.769 4.29 0.00 0.00 3.18
190 191 8.143193 TGCATATGTGTTTCTTTTTCTGTCAAT 58.857 29.630 4.29 0.00 0.00 2.57
191 192 8.981647 GCATATGTGTTTCTTTTTCTGTCAATT 58.018 29.630 4.29 0.00 0.00 2.32
207 208 9.541143 TTCTGTCAATTATTGAAAGTTTTTCCC 57.459 29.630 20.70 2.40 43.94 3.97
208 209 8.147704 TCTGTCAATTATTGAAAGTTTTTCCCC 58.852 33.333 20.70 1.97 43.94 4.81
209 210 6.926272 TGTCAATTATTGAAAGTTTTTCCCCG 59.074 34.615 9.39 0.00 42.15 5.73
210 211 5.929415 TCAATTATTGAAAGTTTTTCCCCGC 59.071 36.000 5.03 0.00 36.59 6.13
211 212 4.939052 TTATTGAAAGTTTTTCCCCGCA 57.061 36.364 0.00 0.00 0.00 5.69
212 213 3.828875 ATTGAAAGTTTTTCCCCGCAA 57.171 38.095 0.00 0.00 0.00 4.85
213 214 3.828875 TTGAAAGTTTTTCCCCGCAAT 57.171 38.095 0.00 0.00 0.00 3.56
214 215 3.828875 TGAAAGTTTTTCCCCGCAATT 57.171 38.095 0.00 0.00 0.00 2.32
215 216 4.143986 TGAAAGTTTTTCCCCGCAATTT 57.856 36.364 0.00 0.00 0.00 1.82
216 217 4.518249 TGAAAGTTTTTCCCCGCAATTTT 58.482 34.783 0.00 0.00 0.00 1.82
217 218 4.944317 TGAAAGTTTTTCCCCGCAATTTTT 59.056 33.333 0.00 0.00 0.00 1.94
240 241 5.488645 TTTCTTCGAAAGTTTACCACACC 57.511 39.130 0.00 0.00 0.00 4.16
241 242 4.411256 TCTTCGAAAGTTTACCACACCT 57.589 40.909 0.00 0.00 0.00 4.00
242 243 4.773013 TCTTCGAAAGTTTACCACACCTT 58.227 39.130 0.00 0.00 0.00 3.50
243 244 5.187687 TCTTCGAAAGTTTACCACACCTTT 58.812 37.500 0.00 0.00 0.00 3.11
244 245 5.648960 TCTTCGAAAGTTTACCACACCTTTT 59.351 36.000 0.00 0.00 0.00 2.27
245 246 5.900865 TCGAAAGTTTACCACACCTTTTT 57.099 34.783 0.00 0.00 0.00 1.94
261 262 2.838637 TTTTTATGGGGATTCCGCCT 57.161 45.000 16.43 9.72 44.95 5.52
262 263 2.358322 TTTTATGGGGATTCCGCCTC 57.642 50.000 16.43 0.00 44.95 4.70
263 264 0.476771 TTTATGGGGATTCCGCCTCC 59.523 55.000 16.43 3.23 44.95 4.30
268 269 2.998949 GGATTCCGCCTCCCAAGT 59.001 61.111 0.00 0.00 0.00 3.16
269 270 1.303282 GGATTCCGCCTCCCAAGTT 59.697 57.895 0.00 0.00 0.00 2.66
270 271 0.544697 GGATTCCGCCTCCCAAGTTA 59.455 55.000 0.00 0.00 0.00 2.24
271 272 1.143073 GGATTCCGCCTCCCAAGTTAT 59.857 52.381 0.00 0.00 0.00 1.89
272 273 2.422945 GGATTCCGCCTCCCAAGTTATT 60.423 50.000 0.00 0.00 0.00 1.40
273 274 2.122783 TTCCGCCTCCCAAGTTATTG 57.877 50.000 0.00 0.00 36.09 1.90
274 275 1.281419 TCCGCCTCCCAAGTTATTGA 58.719 50.000 0.00 0.00 38.83 2.57
275 276 1.631388 TCCGCCTCCCAAGTTATTGAA 59.369 47.619 0.00 0.00 38.83 2.69
276 277 2.040545 TCCGCCTCCCAAGTTATTGAAA 59.959 45.455 0.00 0.00 38.83 2.69
277 278 2.423538 CCGCCTCCCAAGTTATTGAAAG 59.576 50.000 0.00 0.00 38.83 2.62
278 279 3.081804 CGCCTCCCAAGTTATTGAAAGT 58.918 45.455 0.00 0.00 38.83 2.66
279 280 3.506067 CGCCTCCCAAGTTATTGAAAGTT 59.494 43.478 0.00 0.00 38.83 2.66
280 281 4.379499 CGCCTCCCAAGTTATTGAAAGTTC 60.379 45.833 0.00 0.00 38.83 3.01
281 282 4.767409 GCCTCCCAAGTTATTGAAAGTTCT 59.233 41.667 0.00 0.00 38.83 3.01
282 283 5.944007 GCCTCCCAAGTTATTGAAAGTTCTA 59.056 40.000 0.00 0.00 38.83 2.10
283 284 6.127980 GCCTCCCAAGTTATTGAAAGTTCTAC 60.128 42.308 0.00 0.00 38.83 2.59
284 285 6.374613 CCTCCCAAGTTATTGAAAGTTCTACC 59.625 42.308 0.00 0.00 38.83 3.18
285 286 6.243148 TCCCAAGTTATTGAAAGTTCTACCC 58.757 40.000 0.00 0.00 38.83 3.69
286 287 5.417894 CCCAAGTTATTGAAAGTTCTACCCC 59.582 44.000 0.00 0.00 38.83 4.95
287 288 6.246163 CCAAGTTATTGAAAGTTCTACCCCT 58.754 40.000 0.00 0.00 38.83 4.79
288 289 7.399634 CCAAGTTATTGAAAGTTCTACCCCTA 58.600 38.462 0.00 0.00 38.83 3.53
289 290 7.886446 CCAAGTTATTGAAAGTTCTACCCCTAA 59.114 37.037 0.00 0.00 38.83 2.69
290 291 9.292195 CAAGTTATTGAAAGTTCTACCCCTAAA 57.708 33.333 0.00 0.00 38.83 1.85
291 292 9.871175 AAGTTATTGAAAGTTCTACCCCTAAAA 57.129 29.630 0.00 0.00 0.00 1.52
292 293 9.871175 AGTTATTGAAAGTTCTACCCCTAAAAA 57.129 29.630 0.00 0.00 0.00 1.94
316 317 8.494016 AAAAAGTTATTGAGAGTTCTATCCGG 57.506 34.615 0.00 0.00 0.00 5.14
317 318 7.419711 AAAGTTATTGAGAGTTCTATCCGGA 57.580 36.000 6.61 6.61 0.00 5.14
318 319 7.419711 AAGTTATTGAGAGTTCTATCCGGAA 57.580 36.000 9.01 0.00 0.00 4.30
319 320 7.419711 AGTTATTGAGAGTTCTATCCGGAAA 57.580 36.000 9.01 0.00 0.00 3.13
320 321 7.493367 AGTTATTGAGAGTTCTATCCGGAAAG 58.507 38.462 9.01 0.00 0.00 2.62
321 322 4.737855 TTGAGAGTTCTATCCGGAAAGG 57.262 45.455 9.01 1.20 42.97 3.11
487 509 3.753070 CTACGCGCTCCTCCCGTTC 62.753 68.421 5.73 0.00 36.51 3.95
507 529 4.832608 CGCCACGCCTCCCCTTAC 62.833 72.222 0.00 0.00 0.00 2.34
508 530 4.832608 GCCACGCCTCCCCTTACG 62.833 72.222 0.00 0.00 0.00 3.18
509 531 4.157120 CCACGCCTCCCCTTACGG 62.157 72.222 0.00 0.00 0.00 4.02
673 696 0.588730 CAGTTTGGTTCGCGTGTGTG 60.589 55.000 5.77 0.00 0.00 3.82
745 768 1.065102 CAAGATTGAAGCATGAGCCGG 59.935 52.381 0.00 0.00 43.56 6.13
767 790 1.663379 ATGTTCCTCGGTCGCGATCA 61.663 55.000 21.02 5.76 0.00 2.92
915 948 2.625823 CCGTTTCCGCAAGCACCAT 61.626 57.895 0.00 0.00 0.00 3.55
959 998 7.416213 CGGCTTCTTCAATGGGAATATTTACAA 60.416 37.037 0.00 0.00 34.32 2.41
1002 1041 2.887568 GACTCGCCCGACTGCATG 60.888 66.667 0.00 0.00 0.00 4.06
1237 1285 4.953010 ATGCTGCGGTGGTGTGCA 62.953 61.111 0.00 0.00 39.13 4.57
1328 1376 4.464597 GGTCACTGAGAACCTAGAAGACAT 59.535 45.833 0.00 0.00 0.00 3.06
1506 1579 7.709149 TGTATTTGATCTTCAGAGTCAGAGA 57.291 36.000 0.00 0.00 0.00 3.10
1689 1808 5.486735 TGCAGAAAACCATTCAATTGGAT 57.513 34.783 5.42 0.00 39.25 3.41
1704 1823 2.479566 TGGATGAGCTCTTTCCACAC 57.520 50.000 25.87 8.70 0.00 3.82
1759 1878 0.175073 GGGGTATGACGAGGACACAC 59.825 60.000 0.00 0.00 0.00 3.82
1824 1943 4.232188 ACTTGACTCCATGCAGATCAAT 57.768 40.909 0.00 0.00 0.00 2.57
1832 1951 7.605309 TGACTCCATGCAGATCAATCATATTAC 59.395 37.037 0.00 0.00 0.00 1.89
1894 2016 8.204836 CCTACACAAATTTCTATACTACAGGCT 58.795 37.037 0.00 0.00 0.00 4.58
2394 2589 8.634335 TTTTGTCCATCATTTCTCATACTCAA 57.366 30.769 0.00 0.00 0.00 3.02
2413 2608 9.851686 ATACTCAATATTTTAGAATGTGCTCCA 57.148 29.630 2.30 0.00 0.00 3.86
2416 2611 7.118723 TCAATATTTTAGAATGTGCTCCAGGT 58.881 34.615 0.00 0.00 0.00 4.00
2426 2621 2.320587 GCTCCAGGTGTGCAAGACG 61.321 63.158 0.00 0.00 33.65 4.18
2452 2647 8.862325 AAACATTCACACAGAGGATGTATTTA 57.138 30.769 0.00 0.00 41.41 1.40
2506 2726 3.195825 AGAGTGAAAATAGAGTGTCCCGG 59.804 47.826 0.00 0.00 0.00 5.73
2550 2770 2.097954 CCATGTTACATTCATGCGCTGT 59.902 45.455 9.73 6.72 40.63 4.40
2568 2788 1.755959 TGTGCCATTCAACTGCAAAGT 59.244 42.857 0.00 0.00 36.65 2.66
2582 2802 1.477923 GCAAAGTGTACTTGACCCCCA 60.478 52.381 0.00 0.00 36.12 4.96
2585 2805 3.895041 CAAAGTGTACTTGACCCCCAAAT 59.105 43.478 0.00 0.00 36.12 2.32
2588 2808 4.918588 AGTGTACTTGACCCCCAAATAAG 58.081 43.478 0.00 0.00 33.76 1.73
2599 2819 6.069088 TGACCCCCAAATAAGTCTTGATGTAT 60.069 38.462 0.00 0.00 0.00 2.29
2600 2820 6.129179 ACCCCCAAATAAGTCTTGATGTATG 58.871 40.000 0.00 0.00 0.00 2.39
2652 2872 6.860023 GGATCTTGCCATCAAATATTTTCTCG 59.140 38.462 0.00 0.00 0.00 4.04
2669 2889 5.401531 TTCTCGTTCCAAGTAGCACTAAT 57.598 39.130 0.00 0.00 0.00 1.73
2672 2892 7.812690 TCTCGTTCCAAGTAGCACTAATATA 57.187 36.000 0.00 0.00 0.00 0.86
2731 2951 6.866770 TCCATAAAGTCACTAAGTTCTTGACG 59.133 38.462 9.87 0.00 43.69 4.35
2758 2978 4.240323 ACCGGGGAGTGGAGAATAATAAT 58.760 43.478 6.32 0.00 0.00 1.28
2788 3008 6.897966 AGTGTCTAAATCTCCTTATCCTGTGA 59.102 38.462 0.00 0.00 0.00 3.58
2791 3011 9.434275 TGTCTAAATCTCCTTATCCTGTGATTA 57.566 33.333 0.00 0.00 32.18 1.75
2792 3012 9.699703 GTCTAAATCTCCTTATCCTGTGATTAC 57.300 37.037 0.00 0.00 32.18 1.89
2807 3027 6.918892 TGTGATTACAGTGTAATATGTGCC 57.081 37.500 24.95 13.81 31.91 5.01
2814 3034 4.225042 ACAGTGTAATATGTGCCCTCTTGA 59.775 41.667 0.00 0.00 0.00 3.02
2845 3065 6.241207 ACATTGATGAGTTGGTAAAAGACG 57.759 37.500 0.00 0.00 0.00 4.18
2857 3077 3.734231 GGTAAAAGACGCAAAAAGGCTTC 59.266 43.478 0.00 0.00 35.59 3.86
2863 3083 4.833390 AGACGCAAAAAGGCTTCTATACT 58.167 39.130 0.00 0.00 40.19 2.12
2876 3096 9.438228 AAGGCTTCTATACTGTTTCTTTTCTAC 57.562 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.287867 AGCCACTTGATGAACCCTATG 57.712 47.619 0.00 0.00 0.00 2.23
1 2 4.660303 TGATAGCCACTTGATGAACCCTAT 59.340 41.667 0.00 0.00 0.00 2.57
2 3 4.037222 TGATAGCCACTTGATGAACCCTA 58.963 43.478 0.00 0.00 0.00 3.53
3 4 2.846206 TGATAGCCACTTGATGAACCCT 59.154 45.455 0.00 0.00 0.00 4.34
4 5 3.281727 TGATAGCCACTTGATGAACCC 57.718 47.619 0.00 0.00 0.00 4.11
5 6 4.641989 ACAATGATAGCCACTTGATGAACC 59.358 41.667 0.00 0.00 0.00 3.62
6 7 5.824904 ACAATGATAGCCACTTGATGAAC 57.175 39.130 0.00 0.00 0.00 3.18
7 8 6.424812 CGATACAATGATAGCCACTTGATGAA 59.575 38.462 0.00 0.00 0.00 2.57
8 9 5.928264 CGATACAATGATAGCCACTTGATGA 59.072 40.000 0.00 0.00 0.00 2.92
9 10 5.390251 GCGATACAATGATAGCCACTTGATG 60.390 44.000 0.00 0.00 0.00 3.07
10 11 4.692625 GCGATACAATGATAGCCACTTGAT 59.307 41.667 0.00 0.00 0.00 2.57
11 12 4.058124 GCGATACAATGATAGCCACTTGA 58.942 43.478 0.00 0.00 0.00 3.02
12 13 3.187227 GGCGATACAATGATAGCCACTTG 59.813 47.826 10.20 0.00 44.53 3.16
13 14 3.071602 AGGCGATACAATGATAGCCACTT 59.928 43.478 14.88 0.00 46.77 3.16
14 15 2.634940 AGGCGATACAATGATAGCCACT 59.365 45.455 14.88 0.00 46.77 4.00
15 16 2.738846 CAGGCGATACAATGATAGCCAC 59.261 50.000 14.88 0.00 46.77 5.01
16 17 2.632512 TCAGGCGATACAATGATAGCCA 59.367 45.455 14.88 0.00 46.77 4.75
17 18 2.996621 GTCAGGCGATACAATGATAGCC 59.003 50.000 8.08 8.08 45.24 3.93
18 19 2.663602 CGTCAGGCGATACAATGATAGC 59.336 50.000 0.00 0.00 44.77 2.97
19 20 3.902150 ACGTCAGGCGATACAATGATAG 58.098 45.455 0.00 0.00 44.77 2.08
20 21 3.316868 TGACGTCAGGCGATACAATGATA 59.683 43.478 15.76 0.00 44.77 2.15
21 22 2.100749 TGACGTCAGGCGATACAATGAT 59.899 45.455 15.76 0.00 44.77 2.45
22 23 1.474879 TGACGTCAGGCGATACAATGA 59.525 47.619 15.76 0.00 44.77 2.57
23 24 1.921243 TGACGTCAGGCGATACAATG 58.079 50.000 15.76 0.00 44.77 2.82
24 25 2.545952 GGATGACGTCAGGCGATACAAT 60.546 50.000 24.41 2.19 44.77 2.71
25 26 1.202371 GGATGACGTCAGGCGATACAA 60.202 52.381 24.41 0.00 44.77 2.41
26 27 0.384309 GGATGACGTCAGGCGATACA 59.616 55.000 24.41 0.00 44.77 2.29
27 28 0.660595 CGGATGACGTCAGGCGATAC 60.661 60.000 24.41 6.32 44.77 2.24
28 29 1.652563 CGGATGACGTCAGGCGATA 59.347 57.895 24.41 0.00 44.77 2.92
29 30 2.413351 CGGATGACGTCAGGCGAT 59.587 61.111 24.41 6.33 44.77 4.58
30 31 3.822192 CCGGATGACGTCAGGCGA 61.822 66.667 24.41 0.00 44.77 5.54
31 32 3.138930 ATCCGGATGACGTCAGGCG 62.139 63.158 24.41 10.94 41.44 5.52
32 33 1.300233 GATCCGGATGACGTCAGGC 60.300 63.158 24.82 17.35 41.44 4.85
33 34 1.605753 TAGATCCGGATGACGTCAGG 58.394 55.000 24.82 19.07 42.86 3.86
34 35 3.569548 CAATAGATCCGGATGACGTCAG 58.430 50.000 24.82 10.28 42.24 3.51
35 36 2.296190 CCAATAGATCCGGATGACGTCA 59.704 50.000 24.82 22.48 42.24 4.35
36 37 2.927014 GCCAATAGATCCGGATGACGTC 60.927 54.545 24.82 9.11 42.24 4.34
37 38 1.000955 GCCAATAGATCCGGATGACGT 59.999 52.381 24.82 6.05 42.24 4.34
38 39 1.000843 TGCCAATAGATCCGGATGACG 59.999 52.381 24.82 5.32 43.80 4.35
39 40 2.839486 TGCCAATAGATCCGGATGAC 57.161 50.000 24.82 8.57 0.00 3.06
40 41 3.617288 CGATTGCCAATAGATCCGGATGA 60.617 47.826 24.82 10.18 0.00 2.92
41 42 2.674852 CGATTGCCAATAGATCCGGATG 59.325 50.000 24.82 8.57 0.00 3.51
42 43 2.303022 ACGATTGCCAATAGATCCGGAT 59.697 45.455 19.21 19.21 0.00 4.18
43 44 1.691976 ACGATTGCCAATAGATCCGGA 59.308 47.619 6.61 6.61 0.00 5.14
44 45 2.169832 ACGATTGCCAATAGATCCGG 57.830 50.000 4.47 0.00 0.00 5.14
45 46 3.675225 CAGTACGATTGCCAATAGATCCG 59.325 47.826 4.47 0.00 0.00 4.18
46 47 4.883083 TCAGTACGATTGCCAATAGATCC 58.117 43.478 4.47 0.00 0.00 3.36
47 48 5.177696 GGTTCAGTACGATTGCCAATAGATC 59.822 44.000 4.47 0.00 0.00 2.75
48 49 5.057149 GGTTCAGTACGATTGCCAATAGAT 58.943 41.667 4.47 0.00 0.00 1.98
49 50 4.161565 AGGTTCAGTACGATTGCCAATAGA 59.838 41.667 4.47 0.00 0.00 1.98
50 51 4.442706 AGGTTCAGTACGATTGCCAATAG 58.557 43.478 0.00 0.00 0.00 1.73
51 52 4.481368 AGGTTCAGTACGATTGCCAATA 57.519 40.909 0.00 0.00 0.00 1.90
52 53 3.350219 AGGTTCAGTACGATTGCCAAT 57.650 42.857 0.00 0.00 0.00 3.16
53 54 2.811431 CAAGGTTCAGTACGATTGCCAA 59.189 45.455 0.00 0.00 0.00 4.52
54 55 2.422597 CAAGGTTCAGTACGATTGCCA 58.577 47.619 0.00 0.00 0.00 4.92
55 56 1.130561 GCAAGGTTCAGTACGATTGCC 59.869 52.381 10.65 2.46 41.02 4.52
56 57 2.076863 AGCAAGGTTCAGTACGATTGC 58.923 47.619 12.49 12.49 44.29 3.56
57 58 3.120199 CCAAGCAAGGTTCAGTACGATTG 60.120 47.826 0.00 0.00 0.00 2.67
58 59 3.074412 CCAAGCAAGGTTCAGTACGATT 58.926 45.455 0.00 0.00 0.00 3.34
59 60 2.038557 ACCAAGCAAGGTTCAGTACGAT 59.961 45.455 0.00 0.00 39.34 3.73
60 61 1.414919 ACCAAGCAAGGTTCAGTACGA 59.585 47.619 0.00 0.00 39.34 3.43
61 62 1.878953 ACCAAGCAAGGTTCAGTACG 58.121 50.000 0.00 0.00 39.34 3.67
69 70 2.562738 GCCAATAGAAACCAAGCAAGGT 59.437 45.455 0.00 0.00 45.91 3.50
70 71 2.562298 TGCCAATAGAAACCAAGCAAGG 59.438 45.455 0.00 0.00 0.00 3.61
71 72 3.940209 TGCCAATAGAAACCAAGCAAG 57.060 42.857 0.00 0.00 0.00 4.01
72 73 4.322650 GGATTGCCAATAGAAACCAAGCAA 60.323 41.667 0.00 0.00 42.31 3.91
73 74 3.195396 GGATTGCCAATAGAAACCAAGCA 59.805 43.478 0.00 0.00 0.00 3.91
74 75 3.195396 TGGATTGCCAATAGAAACCAAGC 59.805 43.478 0.00 0.00 42.49 4.01
87 88 0.894141 CGGTTCCAATTGGATTGCCA 59.106 50.000 27.53 9.91 44.98 4.92
88 89 0.175531 CCGGTTCCAATTGGATTGCC 59.824 55.000 27.53 24.81 44.98 4.52
89 90 0.175531 CCCGGTTCCAATTGGATTGC 59.824 55.000 27.53 19.02 44.98 3.56
90 91 0.823460 CCCCGGTTCCAATTGGATTG 59.177 55.000 27.53 18.61 44.98 2.67
91 92 0.975556 GCCCCGGTTCCAATTGGATT 60.976 55.000 27.53 0.00 44.98 3.01
92 93 1.381191 GCCCCGGTTCCAATTGGAT 60.381 57.895 27.53 0.00 44.98 3.41
93 94 2.036572 GCCCCGGTTCCAATTGGA 59.963 61.111 23.63 23.63 43.73 3.53
94 95 3.074369 GGCCCCGGTTCCAATTGG 61.074 66.667 19.08 19.08 0.00 3.16
95 96 1.609210 AAGGCCCCGGTTCCAATTG 60.609 57.895 0.00 0.00 0.00 2.32
96 97 1.609210 CAAGGCCCCGGTTCCAATT 60.609 57.895 0.00 0.00 0.00 2.32
97 98 2.037208 CAAGGCCCCGGTTCCAAT 59.963 61.111 0.00 0.00 0.00 3.16
98 99 3.179339 TCAAGGCCCCGGTTCCAA 61.179 61.111 0.00 0.00 0.00 3.53
99 100 3.646715 CTCAAGGCCCCGGTTCCA 61.647 66.667 0.00 0.00 0.00 3.53
109 110 0.038890 AGAGGAAAAGGGCTCAAGGC 59.961 55.000 0.00 0.00 40.90 4.35
110 111 3.721087 TTAGAGGAAAAGGGCTCAAGG 57.279 47.619 0.00 0.00 0.00 3.61
131 132 2.027561 TCCAGATCCGGATGACGTTTTT 60.028 45.455 24.82 0.00 42.24 1.94
132 133 1.553248 TCCAGATCCGGATGACGTTTT 59.447 47.619 24.82 0.00 42.24 2.43
133 134 1.134788 GTCCAGATCCGGATGACGTTT 60.135 52.381 24.82 0.00 42.24 3.60
134 135 0.460311 GTCCAGATCCGGATGACGTT 59.540 55.000 24.82 0.00 42.24 3.99
135 136 1.392710 GGTCCAGATCCGGATGACGT 61.393 60.000 24.82 0.00 42.24 4.34
136 137 1.109920 AGGTCCAGATCCGGATGACG 61.110 60.000 24.82 9.56 37.41 4.35
137 138 0.676736 GAGGTCCAGATCCGGATGAC 59.323 60.000 24.82 21.87 37.41 3.06
138 139 0.470080 GGAGGTCCAGATCCGGATGA 60.470 60.000 24.82 10.60 37.41 2.92
139 140 2.053618 GGAGGTCCAGATCCGGATG 58.946 63.158 24.82 10.32 37.41 3.51
140 141 4.629442 GGAGGTCCAGATCCGGAT 57.371 61.111 19.21 19.21 37.41 4.18
144 145 1.048601 TATTGCGGAGGTCCAGATCC 58.951 55.000 0.00 0.00 35.14 3.36
145 146 2.693069 CATATTGCGGAGGTCCAGATC 58.307 52.381 0.00 0.00 35.14 2.75
146 147 1.271054 GCATATTGCGGAGGTCCAGAT 60.271 52.381 0.00 0.00 31.71 2.90
147 148 0.106708 GCATATTGCGGAGGTCCAGA 59.893 55.000 0.00 0.00 31.71 3.86
148 149 2.621763 GCATATTGCGGAGGTCCAG 58.378 57.895 0.00 0.00 31.71 3.86
149 150 4.876701 GCATATTGCGGAGGTCCA 57.123 55.556 0.00 0.00 31.71 4.02
158 159 9.090692 AGAAAAAGAAACACATATGCATATTGC 57.909 29.630 16.71 2.13 45.29 3.56
161 162 9.793252 GACAGAAAAAGAAACACATATGCATAT 57.207 29.630 13.63 13.63 0.00 1.78
162 163 8.791675 TGACAGAAAAAGAAACACATATGCATA 58.208 29.630 9.27 9.27 0.00 3.14
163 164 7.660112 TGACAGAAAAAGAAACACATATGCAT 58.340 30.769 3.79 3.79 0.00 3.96
164 165 7.036996 TGACAGAAAAAGAAACACATATGCA 57.963 32.000 1.58 0.00 0.00 3.96
165 166 7.928908 TTGACAGAAAAAGAAACACATATGC 57.071 32.000 1.58 0.00 0.00 3.14
181 182 9.541143 GGGAAAAACTTTCAATAATTGACAGAA 57.459 29.630 0.00 0.00 39.28 3.02
182 183 8.147704 GGGGAAAAACTTTCAATAATTGACAGA 58.852 33.333 0.00 0.00 39.28 3.41
183 184 7.116233 CGGGGAAAAACTTTCAATAATTGACAG 59.884 37.037 0.00 0.00 41.90 3.51
184 185 6.926272 CGGGGAAAAACTTTCAATAATTGACA 59.074 34.615 1.88 0.00 39.87 3.58
185 186 6.128661 GCGGGGAAAAACTTTCAATAATTGAC 60.129 38.462 1.88 0.00 39.87 3.18
186 187 5.929415 GCGGGGAAAAACTTTCAATAATTGA 59.071 36.000 1.88 0.00 38.04 2.57
187 188 5.698545 TGCGGGGAAAAACTTTCAATAATTG 59.301 36.000 1.88 0.00 0.00 2.32
188 189 5.859495 TGCGGGGAAAAACTTTCAATAATT 58.141 33.333 1.88 0.00 0.00 1.40
189 190 5.476091 TGCGGGGAAAAACTTTCAATAAT 57.524 34.783 1.88 0.00 0.00 1.28
190 191 4.939052 TGCGGGGAAAAACTTTCAATAA 57.061 36.364 1.88 0.00 0.00 1.40
191 192 4.939052 TTGCGGGGAAAAACTTTCAATA 57.061 36.364 1.88 0.00 0.00 1.90
192 193 3.828875 TTGCGGGGAAAAACTTTCAAT 57.171 38.095 1.88 0.00 0.00 2.57
193 194 3.828875 ATTGCGGGGAAAAACTTTCAA 57.171 38.095 1.88 0.00 0.00 2.69
194 195 3.828875 AATTGCGGGGAAAAACTTTCA 57.171 38.095 1.88 0.00 0.00 2.69
195 196 5.493133 AAAAATTGCGGGGAAAAACTTTC 57.507 34.783 0.00 0.00 0.00 2.62
216 217 6.151480 AGGTGTGGTAAACTTTCGAAGAAAAA 59.849 34.615 0.00 0.00 45.90 1.94
217 218 5.648960 AGGTGTGGTAAACTTTCGAAGAAAA 59.351 36.000 0.00 0.00 45.90 2.29
218 219 5.187687 AGGTGTGGTAAACTTTCGAAGAAA 58.812 37.500 0.00 0.00 45.90 2.52
219 220 4.773013 AGGTGTGGTAAACTTTCGAAGAA 58.227 39.130 0.00 0.00 45.90 2.52
220 221 4.411256 AGGTGTGGTAAACTTTCGAAGA 57.589 40.909 0.00 0.00 0.00 2.87
221 222 5.494632 AAAGGTGTGGTAAACTTTCGAAG 57.505 39.130 0.00 0.00 0.00 3.79
222 223 5.900865 AAAAGGTGTGGTAAACTTTCGAA 57.099 34.783 0.00 0.00 32.44 3.71
223 224 5.900865 AAAAAGGTGTGGTAAACTTTCGA 57.099 34.783 0.00 0.00 32.44 3.71
242 243 2.661718 GAGGCGGAATCCCCATAAAAA 58.338 47.619 9.05 0.00 34.14 1.94
243 244 1.133606 GGAGGCGGAATCCCCATAAAA 60.134 52.381 9.05 0.00 34.14 1.52
244 245 0.476771 GGAGGCGGAATCCCCATAAA 59.523 55.000 9.05 0.00 34.14 1.40
245 246 2.151369 GGAGGCGGAATCCCCATAA 58.849 57.895 9.05 0.00 34.14 1.90
246 247 3.900888 GGAGGCGGAATCCCCATA 58.099 61.111 9.05 0.00 34.14 2.74
251 252 0.544697 TAACTTGGGAGGCGGAATCC 59.455 55.000 0.00 0.00 35.99 3.01
252 253 2.618709 CAATAACTTGGGAGGCGGAATC 59.381 50.000 0.00 0.00 0.00 2.52
253 254 2.241176 TCAATAACTTGGGAGGCGGAAT 59.759 45.455 0.00 0.00 32.95 3.01
254 255 1.631388 TCAATAACTTGGGAGGCGGAA 59.369 47.619 0.00 0.00 32.95 4.30
255 256 1.281419 TCAATAACTTGGGAGGCGGA 58.719 50.000 0.00 0.00 32.95 5.54
256 257 2.122783 TTCAATAACTTGGGAGGCGG 57.877 50.000 0.00 0.00 32.95 6.13
257 258 3.081804 ACTTTCAATAACTTGGGAGGCG 58.918 45.455 0.00 0.00 32.95 5.52
258 259 4.767409 AGAACTTTCAATAACTTGGGAGGC 59.233 41.667 0.00 0.00 32.95 4.70
259 260 6.374613 GGTAGAACTTTCAATAACTTGGGAGG 59.625 42.308 0.00 0.00 32.95 4.30
260 261 6.374613 GGGTAGAACTTTCAATAACTTGGGAG 59.625 42.308 0.00 0.00 32.95 4.30
261 262 6.243148 GGGTAGAACTTTCAATAACTTGGGA 58.757 40.000 0.00 0.00 32.95 4.37
262 263 5.417894 GGGGTAGAACTTTCAATAACTTGGG 59.582 44.000 0.00 0.00 32.95 4.12
263 264 6.246163 AGGGGTAGAACTTTCAATAACTTGG 58.754 40.000 0.00 0.00 32.95 3.61
264 265 8.857694 TTAGGGGTAGAACTTTCAATAACTTG 57.142 34.615 0.00 0.00 0.00 3.16
265 266 9.871175 TTTTAGGGGTAGAACTTTCAATAACTT 57.129 29.630 0.00 0.00 0.00 2.66
266 267 9.871175 TTTTTAGGGGTAGAACTTTCAATAACT 57.129 29.630 0.00 0.00 0.00 2.24
291 292 8.319146 TCCGGATAGAACTCTCAATAACTTTTT 58.681 33.333 0.00 0.00 0.00 1.94
292 293 7.848128 TCCGGATAGAACTCTCAATAACTTTT 58.152 34.615 0.00 0.00 0.00 2.27
293 294 7.419711 TCCGGATAGAACTCTCAATAACTTT 57.580 36.000 0.00 0.00 0.00 2.66
294 295 7.419711 TTCCGGATAGAACTCTCAATAACTT 57.580 36.000 4.15 0.00 0.00 2.66
295 296 7.418025 CCTTTCCGGATAGAACTCTCAATAACT 60.418 40.741 22.00 0.00 33.16 2.24
296 297 6.702282 CCTTTCCGGATAGAACTCTCAATAAC 59.298 42.308 22.00 0.00 33.16 1.89
297 298 6.610020 TCCTTTCCGGATAGAACTCTCAATAA 59.390 38.462 22.00 0.00 36.69 1.40
298 299 6.134055 TCCTTTCCGGATAGAACTCTCAATA 58.866 40.000 22.00 0.00 36.69 1.90
299 300 4.962995 TCCTTTCCGGATAGAACTCTCAAT 59.037 41.667 22.00 0.00 36.69 2.57
300 301 4.350245 TCCTTTCCGGATAGAACTCTCAA 58.650 43.478 22.00 0.63 36.69 3.02
301 302 3.977312 TCCTTTCCGGATAGAACTCTCA 58.023 45.455 22.00 0.00 36.69 3.27
302 303 5.340439 TTTCCTTTCCGGATAGAACTCTC 57.660 43.478 22.00 0.00 42.70 3.20
303 304 5.757099 TTTTCCTTTCCGGATAGAACTCT 57.243 39.130 22.00 0.00 42.70 3.24
323 324 6.128526 GCGCTCTCTAGAACTATTGTGTTTTT 60.129 38.462 0.00 0.00 0.00 1.94
324 325 5.348997 GCGCTCTCTAGAACTATTGTGTTTT 59.651 40.000 0.00 0.00 0.00 2.43
325 326 4.865365 GCGCTCTCTAGAACTATTGTGTTT 59.135 41.667 0.00 0.00 0.00 2.83
326 327 4.082190 TGCGCTCTCTAGAACTATTGTGTT 60.082 41.667 9.73 0.00 0.00 3.32
327 328 3.444034 TGCGCTCTCTAGAACTATTGTGT 59.556 43.478 9.73 0.00 0.00 3.72
328 329 3.794028 GTGCGCTCTCTAGAACTATTGTG 59.206 47.826 9.73 0.00 0.00 3.33
329 330 3.487711 CGTGCGCTCTCTAGAACTATTGT 60.488 47.826 9.73 0.00 0.00 2.71
330 331 3.039405 CGTGCGCTCTCTAGAACTATTG 58.961 50.000 9.73 0.00 0.00 1.90
331 332 2.683867 ACGTGCGCTCTCTAGAACTATT 59.316 45.455 9.73 0.00 0.00 1.73
346 347 4.459331 CCCAATGGCGAACGTGCG 62.459 66.667 12.84 12.84 35.06 5.34
476 498 3.839432 GGCGGAGAACGGGAGGAG 61.839 72.222 0.00 0.00 44.51 3.69
593 616 3.723348 GCGCTCACCGTTTGTCCC 61.723 66.667 0.00 0.00 39.71 4.46
959 998 4.039366 GGACAGAAGTGAAGTGGTACTCTT 59.961 45.833 0.00 0.00 45.41 2.85
1237 1285 2.440409 GTGCCCATCTTCATTGTCAGT 58.560 47.619 0.00 0.00 0.00 3.41
1506 1579 3.258372 TCGGCTTCTTGATCACACTAAGT 59.742 43.478 0.00 0.00 0.00 2.24
1689 1808 2.042464 ACTCTGTGTGGAAAGAGCTCA 58.958 47.619 17.77 0.00 43.13 4.26
1704 1823 7.134815 CCATTTTGAAGTCACTAAACACTCTG 58.865 38.462 0.00 0.00 0.00 3.35
1759 1878 5.523552 TCACCGCAGACAGAATAATAACATG 59.476 40.000 0.00 0.00 0.00 3.21
1850 1972 5.036916 TGTAGGGATGAAAGGTGAGGTAAT 58.963 41.667 0.00 0.00 0.00 1.89
2368 2563 8.634335 TGAGTATGAGAAATGATGGACAAAAA 57.366 30.769 0.00 0.00 0.00 1.94
2370 2565 8.812513 ATTGAGTATGAGAAATGATGGACAAA 57.187 30.769 0.00 0.00 0.00 2.83
2394 2589 6.319658 CACACCTGGAGCACATTCTAAAATAT 59.680 38.462 0.00 0.00 0.00 1.28
2413 2608 1.967319 ATGTTTCGTCTTGCACACCT 58.033 45.000 0.00 0.00 0.00 4.00
2416 2611 2.680339 TGTGAATGTTTCGTCTTGCACA 59.320 40.909 0.00 0.00 33.18 4.57
2426 2621 6.992063 ATACATCCTCTGTGTGAATGTTTC 57.008 37.500 0.00 0.00 38.92 2.78
2452 2647 5.826208 CAGAGTAAGTTTAACCCACAAAGGT 59.174 40.000 0.00 0.00 44.00 3.50
2506 2726 4.631377 GGCCCATTCAGAAATAAAAAGCAC 59.369 41.667 0.00 0.00 0.00 4.40
2550 2770 1.755959 ACACTTTGCAGTTGAATGGCA 59.244 42.857 0.00 0.00 35.41 4.92
2568 2788 4.600111 AGACTTATTTGGGGGTCAAGTACA 59.400 41.667 0.00 0.00 36.62 2.90
2588 2808 9.507280 CCATTTGAAATACACATACATCAAGAC 57.493 33.333 0.00 0.00 0.00 3.01
2599 2819 4.148079 TGGACTGCCATTTGAAATACACA 58.852 39.130 0.00 0.00 39.92 3.72
2600 2820 4.782019 TGGACTGCCATTTGAAATACAC 57.218 40.909 0.00 0.00 39.92 2.90
2637 2857 8.398665 GCTACTTGGAACGAGAAAATATTTGAT 58.601 33.333 0.39 0.00 0.00 2.57
2678 2898 7.193595 GTCGGAAATTGTATATCCAAAACCAG 58.806 38.462 0.00 0.00 32.58 4.00
2731 2951 1.002502 CTCCACTCCCCGGTTTTCC 60.003 63.158 0.00 0.00 0.00 3.13
2788 3008 6.500589 AGAGGGCACATATTACACTGTAAT 57.499 37.500 16.81 16.81 0.00 1.89
2791 3011 4.225042 TCAAGAGGGCACATATTACACTGT 59.775 41.667 0.00 0.00 0.00 3.55
2792 3012 4.769688 TCAAGAGGGCACATATTACACTG 58.230 43.478 0.00 0.00 0.00 3.66
2794 3014 5.126067 ACATCAAGAGGGCACATATTACAC 58.874 41.667 0.00 0.00 0.00 2.90
2797 3017 6.186957 ACAAACATCAAGAGGGCACATATTA 58.813 36.000 0.00 0.00 0.00 0.98
2807 3027 7.120285 ACTCATCAATGTACAAACATCAAGAGG 59.880 37.037 0.00 0.00 45.79 3.69
2845 3065 6.914259 AGAAACAGTATAGAAGCCTTTTTGC 58.086 36.000 0.00 0.00 0.00 3.68
2863 3083 7.333528 AGCAAAGACATGTAGAAAAGAAACA 57.666 32.000 0.00 0.00 0.00 2.83
2893 3113 7.757097 ACAACGAGCAGTGAAATAATAGTAG 57.243 36.000 0.00 0.00 0.00 2.57
2894 3114 7.601130 ACAACAACGAGCAGTGAAATAATAGTA 59.399 33.333 0.00 0.00 0.00 1.82
2895 3115 6.426937 ACAACAACGAGCAGTGAAATAATAGT 59.573 34.615 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.