Multiple sequence alignment - TraesCS6B01G433300

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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 TraesCS6B01G433300 chr6B 100.000 3152 0 0 1 3152 702211516 702208365 0.000000e+00 5821
1 TraesCS6B01G433300 chr4D 95.592 1724 71 4 248 1968 245248076 245249797 0.000000e+00 2758
2 TraesCS6B01G433300 chr4D 93.361 1190 77 2 1964 3152 245256665 245257853 0.000000e+00 1759
3 TraesCS6B01G433300 chr3A 96.993 1530 43 2 418 1945 703885960 703887488 0.000000e+00 2567
4 TraesCS6B01G433300 chr3A 95.858 1159 46 2 1994 3152 703887772 703888928 0.000000e+00 1873
5 TraesCS6B01G433300 chr3A 81.932 797 139 4 486 1279 499682756 499683550 0.000000e+00 669
6 TraesCS6B01G433300 chr3A 94.149 188 7 3 235 421 703849888 703850072 1.850000e-72 283
7 TraesCS6B01G433300 chr1D 97.001 967 29 0 2186 3152 439095170 439094204 0.000000e+00 1626
8 TraesCS6B01G433300 chr5A 77.296 969 183 23 2190 3150 222619132 222618193 1.290000e-148 536
9 TraesCS6B01G433300 chr5A 85.409 514 73 1 2637 3150 416140466 416140977 1.660000e-147 532
10 TraesCS6B01G433300 chr5A 85.236 508 70 3 2643 3150 237962824 237962322 4.660000e-143 518
11 TraesCS6B01G433300 chr6A 85.630 508 71 1 2643 3150 123510071 123509566 1.660000e-147 532
12 TraesCS6B01G433300 chr6A 85.433 508 72 1 2643 3150 283038778 283038273 7.740000e-146 527
13 TraesCS6B01G433300 chr6A 94.118 170 5 2 66 235 607035318 607035482 1.450000e-63 254
14 TraesCS6B01G433300 chr7A 85.859 495 68 1 2656 3150 702615218 702615710 2.780000e-145 525
15 TraesCS6B01G433300 chr6D 92.417 211 6 5 1 210 460772780 460772981 3.070000e-75 292


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 TraesCS6B01G433300 chr6B 702208365 702211516 3151 True 5821 5821 100.0000 1 3152 1 chr6B.!!$R1 3151
1 TraesCS6B01G433300 chr4D 245248076 245249797 1721 False 2758 2758 95.5920 248 1968 1 chr4D.!!$F1 1720
2 TraesCS6B01G433300 chr4D 245256665 245257853 1188 False 1759 1759 93.3610 1964 3152 1 chr4D.!!$F2 1188
3 TraesCS6B01G433300 chr3A 703885960 703888928 2968 False 2220 2567 96.4255 418 3152 2 chr3A.!!$F3 2734
4 TraesCS6B01G433300 chr3A 499682756 499683550 794 False 669 669 81.9320 486 1279 1 chr3A.!!$F1 793
5 TraesCS6B01G433300 chr1D 439094204 439095170 966 True 1626 1626 97.0010 2186 3152 1 chr1D.!!$R1 966
6 TraesCS6B01G433300 chr5A 222618193 222619132 939 True 536 536 77.2960 2190 3150 1 chr5A.!!$R1 960
7 TraesCS6B01G433300 chr5A 416140466 416140977 511 False 532 532 85.4090 2637 3150 1 chr5A.!!$F1 513
8 TraesCS6B01G433300 chr5A 237962322 237962824 502 True 518 518 85.2360 2643 3150 1 chr5A.!!$R2 507
9 TraesCS6B01G433300 chr6A 123509566 123510071 505 True 532 532 85.6300 2643 3150 1 chr6A.!!$R1 507
10 TraesCS6B01G433300 chr6A 283038273 283038778 505 True 527 527 85.4330 2643 3150 1 chr6A.!!$R2 507

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
194 195 0.033504 ATCCGTTGCACTCGTTGTCT 59.966 50.0 9.14 0.0 0.0 3.41 F
204 205 0.179100 CTCGTTGTCTGCCCGATGAT 60.179 55.0 0.00 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2356 0.178953 ACCATCACCAGCAAAAGCCT 60.179 50.000 0.0 0.0 0.00 4.58 R
2197 2436 2.696187 GGCTCCCTTGAGAAGTAGTAGG 59.304 54.545 0.0 0.0 41.42 3.18 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 2.184385 GTGCGCTACACGTATGTACT 57.816 50.000 9.73 0.00 46.11 2.73
25 26 2.523015 GTGCGCTACACGTATGTACTT 58.477 47.619 9.73 0.00 46.11 2.24
26 27 3.683989 GTGCGCTACACGTATGTACTTA 58.316 45.455 9.73 0.00 46.11 2.24
27 28 3.479949 GTGCGCTACACGTATGTACTTAC 59.520 47.826 9.73 8.51 46.11 2.34
28 29 3.374988 TGCGCTACACGTATGTACTTACT 59.625 43.478 9.73 2.07 46.11 2.24
29 30 4.142622 TGCGCTACACGTATGTACTTACTT 60.143 41.667 9.73 5.02 46.11 2.24
30 31 4.435877 GCGCTACACGTATGTACTTACTTC 59.564 45.833 14.83 0.00 46.11 3.01
31 32 5.728898 GCGCTACACGTATGTACTTACTTCT 60.729 44.000 14.83 0.00 46.11 2.85
32 33 6.253746 CGCTACACGTATGTACTTACTTCTT 58.746 40.000 14.83 1.16 40.48 2.52
33 34 7.401860 CGCTACACGTATGTACTTACTTCTTA 58.598 38.462 14.83 2.05 40.48 2.10
34 35 8.066595 CGCTACACGTATGTACTTACTTCTTAT 58.933 37.037 14.83 0.98 40.48 1.73
35 36 9.727627 GCTACACGTATGTACTTACTTCTTATT 57.272 33.333 14.83 0.00 40.48 1.40
63 64 9.646522 AAAGCTAAATATAAACATGACCCAGAT 57.353 29.630 0.00 0.00 0.00 2.90
64 65 8.854614 AGCTAAATATAAACATGACCCAGATC 57.145 34.615 0.00 0.00 0.00 2.75
65 66 8.664079 AGCTAAATATAAACATGACCCAGATCT 58.336 33.333 0.00 0.00 0.00 2.75
66 67 8.940952 GCTAAATATAAACATGACCCAGATCTC 58.059 37.037 0.00 0.00 0.00 2.75
69 70 8.503428 AATATAAACATGACCCAGATCTCTCT 57.497 34.615 0.00 0.00 0.00 3.10
70 71 9.607333 AATATAAACATGACCCAGATCTCTCTA 57.393 33.333 0.00 0.00 0.00 2.43
71 72 7.921041 ATAAACATGACCCAGATCTCTCTAA 57.079 36.000 0.00 0.00 0.00 2.10
72 73 6.627087 AAACATGACCCAGATCTCTCTAAA 57.373 37.500 0.00 0.00 0.00 1.85
73 74 6.821616 AACATGACCCAGATCTCTCTAAAT 57.178 37.500 0.00 0.00 0.00 1.40
74 75 6.418057 ACATGACCCAGATCTCTCTAAATC 57.582 41.667 0.00 0.00 0.00 2.17
75 76 5.901853 ACATGACCCAGATCTCTCTAAATCA 59.098 40.000 0.00 0.00 0.00 2.57
76 77 6.385176 ACATGACCCAGATCTCTCTAAATCAA 59.615 38.462 0.00 0.00 0.00 2.57
77 78 6.874278 TGACCCAGATCTCTCTAAATCAAA 57.126 37.500 0.00 0.00 0.00 2.69
78 79 7.257790 TGACCCAGATCTCTCTAAATCAAAA 57.742 36.000 0.00 0.00 0.00 2.44
79 80 7.106239 TGACCCAGATCTCTCTAAATCAAAAC 58.894 38.462 0.00 0.00 0.00 2.43
80 81 7.020827 ACCCAGATCTCTCTAAATCAAAACA 57.979 36.000 0.00 0.00 0.00 2.83
81 82 6.881602 ACCCAGATCTCTCTAAATCAAAACAC 59.118 38.462 0.00 0.00 0.00 3.32
82 83 6.881065 CCCAGATCTCTCTAAATCAAAACACA 59.119 38.462 0.00 0.00 0.00 3.72
83 84 7.555554 CCCAGATCTCTCTAAATCAAAACACAT 59.444 37.037 0.00 0.00 0.00 3.21
84 85 8.396390 CCAGATCTCTCTAAATCAAAACACATG 58.604 37.037 0.00 0.00 0.00 3.21
85 86 7.909121 CAGATCTCTCTAAATCAAAACACATGC 59.091 37.037 0.00 0.00 0.00 4.06
86 87 7.609146 AGATCTCTCTAAATCAAAACACATGCA 59.391 33.333 0.00 0.00 0.00 3.96
87 88 7.692460 TCTCTCTAAATCAAAACACATGCAT 57.308 32.000 0.00 0.00 0.00 3.96
88 89 7.755591 TCTCTCTAAATCAAAACACATGCATC 58.244 34.615 0.00 0.00 0.00 3.91
89 90 6.855836 TCTCTAAATCAAAACACATGCATCC 58.144 36.000 0.00 0.00 0.00 3.51
90 91 6.433716 TCTCTAAATCAAAACACATGCATCCA 59.566 34.615 0.00 0.00 0.00 3.41
91 92 7.123098 TCTCTAAATCAAAACACATGCATCCAT 59.877 33.333 0.00 0.00 0.00 3.41
92 93 7.613585 TCTAAATCAAAACACATGCATCCATT 58.386 30.769 0.00 0.00 0.00 3.16
93 94 6.730960 AAATCAAAACACATGCATCCATTC 57.269 33.333 0.00 0.00 0.00 2.67
94 95 4.191033 TCAAAACACATGCATCCATTCC 57.809 40.909 0.00 0.00 0.00 3.01
95 96 3.577415 TCAAAACACATGCATCCATTCCA 59.423 39.130 0.00 0.00 0.00 3.53
96 97 4.223255 TCAAAACACATGCATCCATTCCAT 59.777 37.500 0.00 0.00 0.00 3.41
97 98 4.395959 AAACACATGCATCCATTCCATC 57.604 40.909 0.00 0.00 0.00 3.51
98 99 3.021177 ACACATGCATCCATTCCATCA 57.979 42.857 0.00 0.00 0.00 3.07
99 100 3.572642 ACACATGCATCCATTCCATCAT 58.427 40.909 0.00 0.00 0.00 2.45
100 101 3.572682 ACACATGCATCCATTCCATCATC 59.427 43.478 0.00 0.00 0.00 2.92
101 102 3.826729 CACATGCATCCATTCCATCATCT 59.173 43.478 0.00 0.00 0.00 2.90
102 103 4.280929 CACATGCATCCATTCCATCATCTT 59.719 41.667 0.00 0.00 0.00 2.40
103 104 4.523173 ACATGCATCCATTCCATCATCTTC 59.477 41.667 0.00 0.00 0.00 2.87
104 105 4.448720 TGCATCCATTCCATCATCTTCT 57.551 40.909 0.00 0.00 0.00 2.85
105 106 4.800023 TGCATCCATTCCATCATCTTCTT 58.200 39.130 0.00 0.00 0.00 2.52
106 107 4.825634 TGCATCCATTCCATCATCTTCTTC 59.174 41.667 0.00 0.00 0.00 2.87
107 108 5.071370 GCATCCATTCCATCATCTTCTTCT 58.929 41.667 0.00 0.00 0.00 2.85
108 109 5.535406 GCATCCATTCCATCATCTTCTTCTT 59.465 40.000 0.00 0.00 0.00 2.52
109 110 6.713903 GCATCCATTCCATCATCTTCTTCTTA 59.286 38.462 0.00 0.00 0.00 2.10
110 111 7.393796 GCATCCATTCCATCATCTTCTTCTTAT 59.606 37.037 0.00 0.00 0.00 1.73
111 112 8.948145 CATCCATTCCATCATCTTCTTCTTATC 58.052 37.037 0.00 0.00 0.00 1.75
112 113 7.157347 TCCATTCCATCATCTTCTTCTTATCG 58.843 38.462 0.00 0.00 0.00 2.92
113 114 7.015584 TCCATTCCATCATCTTCTTCTTATCGA 59.984 37.037 0.00 0.00 0.00 3.59
114 115 7.117523 CCATTCCATCATCTTCTTCTTATCGAC 59.882 40.741 0.00 0.00 0.00 4.20
115 116 5.763088 TCCATCATCTTCTTCTTATCGACG 58.237 41.667 0.00 0.00 0.00 5.12
116 117 5.531287 TCCATCATCTTCTTCTTATCGACGA 59.469 40.000 0.00 0.00 0.00 4.20
117 118 6.207614 TCCATCATCTTCTTCTTATCGACGAT 59.792 38.462 15.74 15.74 0.00 3.73
118 119 6.865726 CCATCATCTTCTTCTTATCGACGATT 59.134 38.462 16.73 0.30 0.00 3.34
119 120 7.061673 CCATCATCTTCTTCTTATCGACGATTC 59.938 40.741 16.73 0.00 0.00 2.52
120 121 7.265647 TCATCTTCTTCTTATCGACGATTCT 57.734 36.000 16.73 0.00 0.00 2.40
121 122 8.379457 TCATCTTCTTCTTATCGACGATTCTA 57.621 34.615 16.73 0.00 0.00 2.10
122 123 8.283992 TCATCTTCTTCTTATCGACGATTCTAC 58.716 37.037 16.73 0.00 0.00 2.59
123 124 6.647569 TCTTCTTCTTATCGACGATTCTACG 58.352 40.000 16.73 3.02 39.31 3.51
124 125 5.340010 TCTTCTTATCGACGATTCTACGG 57.660 43.478 16.73 3.27 37.61 4.02
125 126 3.532892 TCTTATCGACGATTCTACGGC 57.467 47.619 16.73 0.00 38.00 5.68
126 127 2.225019 TCTTATCGACGATTCTACGGCC 59.775 50.000 16.73 0.00 38.13 6.13
127 128 0.877071 TATCGACGATTCTACGGCCC 59.123 55.000 16.73 0.00 38.13 5.80
128 129 2.126417 ATCGACGATTCTACGGCCCG 62.126 60.000 4.05 0.00 38.13 6.13
129 130 2.027169 GACGATTCTACGGCCCGG 59.973 66.667 8.57 0.00 35.00 5.73
130 131 2.440796 ACGATTCTACGGCCCGGA 60.441 61.111 8.57 0.00 37.61 5.14
131 132 2.008268 GACGATTCTACGGCCCGGAA 62.008 60.000 8.57 2.13 35.00 4.30
132 133 1.299926 CGATTCTACGGCCCGGAAG 60.300 63.158 8.57 4.55 0.00 3.46
144 145 4.303257 CGGAAGGCTTGGAAGACC 57.697 61.111 3.46 0.00 33.27 3.85
145 146 1.377333 CGGAAGGCTTGGAAGACCC 60.377 63.158 3.46 0.00 33.27 4.46
146 147 1.377333 GGAAGGCTTGGAAGACCCG 60.377 63.158 3.46 0.00 37.93 5.28
147 148 1.677552 GAAGGCTTGGAAGACCCGA 59.322 57.895 3.46 0.00 37.93 5.14
149 150 1.842381 AAGGCTTGGAAGACCCGAGG 61.842 60.000 0.00 0.00 45.14 4.63
150 151 2.291043 GGCTTGGAAGACCCGAGGA 61.291 63.158 0.00 0.00 45.14 3.71
151 152 1.219393 GCTTGGAAGACCCGAGGAG 59.781 63.158 0.00 0.00 45.14 3.69
152 153 1.901085 CTTGGAAGACCCGAGGAGG 59.099 63.158 0.00 0.00 41.91 4.30
153 154 0.614979 CTTGGAAGACCCGAGGAGGA 60.615 60.000 0.00 0.00 45.00 3.71
154 155 0.178915 TTGGAAGACCCGAGGAGGAA 60.179 55.000 0.00 0.00 45.00 3.36
155 156 0.042731 TGGAAGACCCGAGGAGGAAT 59.957 55.000 0.00 0.00 45.00 3.01
156 157 0.753867 GGAAGACCCGAGGAGGAATC 59.246 60.000 0.00 0.00 45.00 2.52
157 158 0.753867 GAAGACCCGAGGAGGAATCC 59.246 60.000 0.00 0.00 45.00 3.01
158 159 0.691413 AAGACCCGAGGAGGAATCCC 60.691 60.000 0.00 0.00 45.00 3.85
159 160 1.382695 GACCCGAGGAGGAATCCCA 60.383 63.158 0.00 0.00 45.00 4.37
160 161 0.764752 GACCCGAGGAGGAATCCCAT 60.765 60.000 0.00 0.00 45.00 4.00
161 162 1.056700 ACCCGAGGAGGAATCCCATG 61.057 60.000 0.00 0.00 45.00 3.66
162 163 0.764369 CCCGAGGAGGAATCCCATGA 60.764 60.000 0.00 0.00 45.00 3.07
163 164 1.131638 CCGAGGAGGAATCCCATGAA 58.868 55.000 0.00 0.00 45.00 2.57
164 165 1.071385 CCGAGGAGGAATCCCATGAAG 59.929 57.143 0.00 0.00 45.00 3.02
165 166 2.042464 CGAGGAGGAATCCCATGAAGA 58.958 52.381 0.00 0.00 33.88 2.87
166 167 2.435805 CGAGGAGGAATCCCATGAAGAA 59.564 50.000 0.00 0.00 33.88 2.52
167 168 3.742640 CGAGGAGGAATCCCATGAAGAAC 60.743 52.174 0.00 0.00 33.88 3.01
168 169 2.511637 AGGAGGAATCCCATGAAGAACC 59.488 50.000 0.00 0.00 33.88 3.62
169 170 2.242196 GGAGGAATCCCATGAAGAACCA 59.758 50.000 0.00 0.00 33.88 3.67
170 171 3.282885 GAGGAATCCCATGAAGAACCAC 58.717 50.000 0.00 0.00 33.88 4.16
171 172 2.024941 AGGAATCCCATGAAGAACCACC 60.025 50.000 0.00 0.00 33.88 4.61
172 173 2.291540 GGAATCCCATGAAGAACCACCA 60.292 50.000 0.00 0.00 0.00 4.17
173 174 2.514458 ATCCCATGAAGAACCACCAC 57.486 50.000 0.00 0.00 0.00 4.16
174 175 0.404040 TCCCATGAAGAACCACCACC 59.596 55.000 0.00 0.00 0.00 4.61
175 176 0.112218 CCCATGAAGAACCACCACCA 59.888 55.000 0.00 0.00 0.00 4.17
176 177 1.272648 CCCATGAAGAACCACCACCAT 60.273 52.381 0.00 0.00 0.00 3.55
177 178 2.094675 CCATGAAGAACCACCACCATC 58.905 52.381 0.00 0.00 0.00 3.51
178 179 2.094675 CATGAAGAACCACCACCATCC 58.905 52.381 0.00 0.00 0.00 3.51
179 180 0.036164 TGAAGAACCACCACCATCCG 59.964 55.000 0.00 0.00 0.00 4.18
180 181 0.036306 GAAGAACCACCACCATCCGT 59.964 55.000 0.00 0.00 0.00 4.69
181 182 0.476771 AAGAACCACCACCATCCGTT 59.523 50.000 0.00 0.00 0.00 4.44
182 183 0.250727 AGAACCACCACCATCCGTTG 60.251 55.000 0.00 0.00 0.00 4.10
183 184 1.862602 GAACCACCACCATCCGTTGC 61.863 60.000 0.00 0.00 0.00 4.17
184 185 2.282110 CCACCACCATCCGTTGCA 60.282 61.111 0.00 0.00 0.00 4.08
185 186 2.625823 CCACCACCATCCGTTGCAC 61.626 63.158 0.00 0.00 0.00 4.57
186 187 1.600636 CACCACCATCCGTTGCACT 60.601 57.895 0.00 0.00 0.00 4.40
187 188 1.302511 ACCACCATCCGTTGCACTC 60.303 57.895 0.00 0.00 0.00 3.51
188 189 2.390599 CCACCATCCGTTGCACTCG 61.391 63.158 3.83 3.83 0.00 4.18
189 190 1.667830 CACCATCCGTTGCACTCGT 60.668 57.895 9.14 0.00 0.00 4.18
190 191 1.070786 ACCATCCGTTGCACTCGTT 59.929 52.632 9.14 0.00 0.00 3.85
191 192 1.227999 ACCATCCGTTGCACTCGTTG 61.228 55.000 9.14 6.68 0.00 4.10
192 193 1.227999 CCATCCGTTGCACTCGTTGT 61.228 55.000 9.14 0.00 0.00 3.32
193 194 0.163788 CATCCGTTGCACTCGTTGTC 59.836 55.000 9.14 0.00 0.00 3.18
194 195 0.033504 ATCCGTTGCACTCGTTGTCT 59.966 50.000 9.14 0.00 0.00 3.41
195 196 0.874175 TCCGTTGCACTCGTTGTCTG 60.874 55.000 9.14 0.00 0.00 3.51
196 197 1.083401 CGTTGCACTCGTTGTCTGC 60.083 57.895 0.00 0.00 0.00 4.26
197 198 1.279840 GTTGCACTCGTTGTCTGCC 59.720 57.895 0.00 0.00 0.00 4.85
198 199 1.891919 TTGCACTCGTTGTCTGCCC 60.892 57.895 0.00 0.00 0.00 5.36
199 200 3.414700 GCACTCGTTGTCTGCCCG 61.415 66.667 0.00 0.00 0.00 6.13
200 201 2.338620 CACTCGTTGTCTGCCCGA 59.661 61.111 0.00 0.00 0.00 5.14
201 202 1.079819 CACTCGTTGTCTGCCCGAT 60.080 57.895 0.00 0.00 0.00 4.18
202 203 1.079819 ACTCGTTGTCTGCCCGATG 60.080 57.895 0.00 0.00 0.00 3.84
203 204 1.215382 CTCGTTGTCTGCCCGATGA 59.785 57.895 0.00 0.00 0.00 2.92
204 205 0.179100 CTCGTTGTCTGCCCGATGAT 60.179 55.000 0.00 0.00 0.00 2.45
205 206 1.067060 CTCGTTGTCTGCCCGATGATA 59.933 52.381 0.00 0.00 0.00 2.15
206 207 1.478916 TCGTTGTCTGCCCGATGATAA 59.521 47.619 0.00 0.00 0.00 1.75
207 208 2.102420 TCGTTGTCTGCCCGATGATAAT 59.898 45.455 0.00 0.00 0.00 1.28
208 209 3.319689 TCGTTGTCTGCCCGATGATAATA 59.680 43.478 0.00 0.00 0.00 0.98
209 210 4.055360 CGTTGTCTGCCCGATGATAATAA 58.945 43.478 0.00 0.00 0.00 1.40
210 211 4.690748 CGTTGTCTGCCCGATGATAATAAT 59.309 41.667 0.00 0.00 0.00 1.28
211 212 5.389830 CGTTGTCTGCCCGATGATAATAATG 60.390 44.000 0.00 0.00 0.00 1.90
212 213 5.482163 TGTCTGCCCGATGATAATAATGA 57.518 39.130 0.00 0.00 0.00 2.57
213 214 5.237815 TGTCTGCCCGATGATAATAATGAC 58.762 41.667 0.00 0.00 0.00 3.06
214 215 5.012046 TGTCTGCCCGATGATAATAATGACT 59.988 40.000 0.00 0.00 0.00 3.41
215 216 5.578727 GTCTGCCCGATGATAATAATGACTC 59.421 44.000 0.00 0.00 0.00 3.36
216 217 5.481824 TCTGCCCGATGATAATAATGACTCT 59.518 40.000 0.00 0.00 0.00 3.24
217 218 5.482006 TGCCCGATGATAATAATGACTCTG 58.518 41.667 0.00 0.00 0.00 3.35
218 219 4.331168 GCCCGATGATAATAATGACTCTGC 59.669 45.833 0.00 0.00 0.00 4.26
219 220 4.564372 CCCGATGATAATAATGACTCTGCG 59.436 45.833 0.00 0.00 0.00 5.18
220 221 5.402398 CCGATGATAATAATGACTCTGCGA 58.598 41.667 0.00 0.00 0.00 5.10
221 222 6.038985 CCGATGATAATAATGACTCTGCGAT 58.961 40.000 0.00 0.00 0.00 4.58
222 223 6.020041 CCGATGATAATAATGACTCTGCGATG 60.020 42.308 0.00 0.00 0.00 3.84
223 224 6.020041 CGATGATAATAATGACTCTGCGATGG 60.020 42.308 0.00 0.00 0.00 3.51
224 225 6.345096 TGATAATAATGACTCTGCGATGGA 57.655 37.500 0.00 0.00 0.00 3.41
225 226 6.939622 TGATAATAATGACTCTGCGATGGAT 58.060 36.000 0.00 0.00 0.00 3.41
226 227 7.038048 TGATAATAATGACTCTGCGATGGATC 58.962 38.462 0.00 0.00 0.00 3.36
227 228 4.879197 ATAATGACTCTGCGATGGATCA 57.121 40.909 0.00 0.00 0.00 2.92
228 229 3.548745 AATGACTCTGCGATGGATCAA 57.451 42.857 0.00 0.00 0.00 2.57
229 230 2.591571 TGACTCTGCGATGGATCAAG 57.408 50.000 0.00 0.00 0.00 3.02
230 231 1.137675 TGACTCTGCGATGGATCAAGG 59.862 52.381 0.00 0.00 0.00 3.61
231 232 1.410517 GACTCTGCGATGGATCAAGGA 59.589 52.381 0.00 0.00 0.00 3.36
232 233 1.411977 ACTCTGCGATGGATCAAGGAG 59.588 52.381 0.00 0.00 0.00 3.69
233 234 1.685517 CTCTGCGATGGATCAAGGAGA 59.314 52.381 0.00 0.00 0.00 3.71
234 235 2.299582 CTCTGCGATGGATCAAGGAGAT 59.700 50.000 0.00 0.00 40.48 2.75
235 236 2.702478 TCTGCGATGGATCAAGGAGATT 59.298 45.455 0.00 0.00 37.00 2.40
236 237 3.065655 CTGCGATGGATCAAGGAGATTC 58.934 50.000 0.00 0.00 37.00 2.52
237 238 2.702478 TGCGATGGATCAAGGAGATTCT 59.298 45.455 0.00 0.00 37.00 2.40
238 239 3.244009 TGCGATGGATCAAGGAGATTCTC 60.244 47.826 5.03 5.03 37.00 2.87
250 251 1.765904 GAGATTCTCCCCTGTTCCTCC 59.234 57.143 1.97 0.00 0.00 4.30
338 340 3.287867 TCTTTGCCATCTCCATTCTCC 57.712 47.619 0.00 0.00 0.00 3.71
345 347 1.210478 CATCTCCATTCTCCCGGTTGT 59.790 52.381 0.00 0.00 0.00 3.32
348 350 1.279271 CTCCATTCTCCCGGTTGTTCT 59.721 52.381 0.00 0.00 0.00 3.01
362 364 4.207955 GGTTGTTCTTTCCTTCTCTGGTT 58.792 43.478 0.00 0.00 0.00 3.67
405 407 3.568430 ACTTTTCCCCTTTTGCTAGTTCG 59.432 43.478 0.00 0.00 0.00 3.95
430 432 4.722526 TTGAGATGGAAAGACAAAGGGA 57.277 40.909 0.00 0.00 0.00 4.20
473 475 2.022527 AGGAGAGGAAGTGAATAGGGCT 60.023 50.000 0.00 0.00 0.00 5.19
526 528 6.119240 TGATCCTGGGATTGAGATCAATAC 57.881 41.667 8.98 8.98 45.72 1.89
734 736 5.883685 ATGGAATCTCACAGCTATCAAGA 57.116 39.130 0.00 0.00 0.00 3.02
782 784 4.009675 CCTTGGAAGCTGCTATGTTTGTA 58.990 43.478 0.90 0.00 0.00 2.41
841 843 5.191323 ACTTCTTGATTGAGTGGATGGATCT 59.809 40.000 0.00 0.00 0.00 2.75
842 844 5.032327 TCTTGATTGAGTGGATGGATCTG 57.968 43.478 0.00 0.00 0.00 2.90
1173 1177 5.730550 TGTGGAGTTATGTTCCATAGTGTC 58.269 41.667 0.00 0.00 45.85 3.67
1269 1273 5.867903 CAAATAGGTTTGGCCAATGGATA 57.132 39.130 21.26 10.58 40.78 2.59
1322 1326 5.890419 CAGGAGCTAATTTCCAGGAAGATTT 59.110 40.000 1.07 1.12 37.18 2.17
1374 1378 4.937620 CAGTTAGCCAGATTACAGAAGCAA 59.062 41.667 0.00 0.00 0.00 3.91
1787 1791 3.370315 CCCCCTATCTCTGCTATTCATGC 60.370 52.174 0.00 0.00 0.00 4.06
1844 1848 8.348285 ACAAATATTAATCCCATTCATACCCG 57.652 34.615 0.00 0.00 0.00 5.28
1845 1849 7.093945 ACAAATATTAATCCCATTCATACCCGC 60.094 37.037 0.00 0.00 0.00 6.13
1846 1850 3.866703 TTAATCCCATTCATACCCGCA 57.133 42.857 0.00 0.00 0.00 5.69
1957 1961 0.745845 AGTGATTCCTCATGGTGCGC 60.746 55.000 0.00 0.00 32.98 6.09
1985 1989 6.836242 AGAATTCAGATAAGATTCCTGGGTC 58.164 40.000 8.44 0.00 0.00 4.46
1986 1990 6.388100 AGAATTCAGATAAGATTCCTGGGTCA 59.612 38.462 8.44 0.00 0.00 4.02
2022 2261 1.227249 TTCCCAACTCTGGTTCCCAA 58.773 50.000 0.00 0.00 41.72 4.12
2026 2265 1.479389 CCAACTCTGGTTCCCAAGCTT 60.479 52.381 0.00 0.00 38.00 3.74
2037 2276 4.098807 GGTTCCCAAGCTTTACAAAGTTCA 59.901 41.667 0.00 0.00 38.28 3.18
2117 2356 0.696501 GGTTTGGGGTCTGCCTTAGA 59.303 55.000 0.00 0.00 34.45 2.10
2197 2436 3.723348 GCAACGCGGTTCCTGGAC 61.723 66.667 12.47 0.00 0.00 4.02
2222 2461 2.607750 TTCTCAAGGGAGCCGCCT 60.608 61.111 0.00 0.00 41.13 5.52
2289 2528 0.180406 GTGGTATGCGTTCCCATCCT 59.820 55.000 0.00 0.00 0.00 3.24
2325 2564 0.613777 ATCGTCCTGGTTCTTCCACC 59.386 55.000 0.00 0.00 41.93 4.61
2530 2769 5.700722 TGTCAGTACAGGTACAGTTAGTG 57.299 43.478 11.78 1.06 38.48 2.74
2535 2774 4.196965 GGTACAGTTAGTGCCCGC 57.803 61.111 0.00 0.00 46.25 6.13
2600 2839 4.014569 TGGATTTCGATGTTGGTCAAGA 57.985 40.909 0.00 0.00 0.00 3.02
2615 2854 3.369052 GGTCAAGATATGTGTGGTTCCGA 60.369 47.826 0.00 0.00 0.00 4.55
2977 3217 4.398988 TGATATGGCTAACAGCTTTGTTGG 59.601 41.667 1.78 0.17 41.99 3.77
3053 3293 2.234908 AGTTTCTGTTCATAGCGCCTCT 59.765 45.455 2.29 0.00 0.00 3.69
3071 3311 5.279006 CGCCTCTTTTCACTATATCCTAGCA 60.279 44.000 0.00 0.00 0.00 3.49
3139 3379 9.791781 TTGTATATATGGTGACCCCTATCATAA 57.208 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.184385 AGTACATACGTGTAGCGCAC 57.816 50.000 11.47 6.60 46.11 5.34
6 7 2.925578 AAGTACATACGTGTAGCGCA 57.074 45.000 11.47 0.00 46.11 6.09
7 8 3.945179 AGTAAGTACATACGTGTAGCGC 58.055 45.455 0.00 0.00 46.11 5.92
8 9 5.804173 AGAAGTAAGTACATACGTGTAGCG 58.196 41.667 0.00 0.00 41.29 4.26
9 10 9.727627 AATAAGAAGTAAGTACATACGTGTAGC 57.272 33.333 0.00 0.00 41.29 3.58
37 38 9.646522 ATCTGGGTCATGTTTATATTTAGCTTT 57.353 29.630 0.00 0.00 0.00 3.51
38 39 9.289782 GATCTGGGTCATGTTTATATTTAGCTT 57.710 33.333 0.00 0.00 0.00 3.74
39 40 8.664079 AGATCTGGGTCATGTTTATATTTAGCT 58.336 33.333 0.00 0.00 0.00 3.32
40 41 8.854614 AGATCTGGGTCATGTTTATATTTAGC 57.145 34.615 0.00 0.00 0.00 3.09
43 44 8.943085 AGAGAGATCTGGGTCATGTTTATATTT 58.057 33.333 0.00 0.00 0.00 1.40
44 45 8.503428 AGAGAGATCTGGGTCATGTTTATATT 57.497 34.615 0.00 0.00 0.00 1.28
45 46 9.607333 TTAGAGAGATCTGGGTCATGTTTATAT 57.393 33.333 0.00 0.00 0.00 0.86
46 47 9.434275 TTTAGAGAGATCTGGGTCATGTTTATA 57.566 33.333 0.00 0.00 0.00 0.98
47 48 7.921041 TTAGAGAGATCTGGGTCATGTTTAT 57.079 36.000 0.00 0.00 0.00 1.40
48 49 7.733773 TTTAGAGAGATCTGGGTCATGTTTA 57.266 36.000 0.00 0.00 0.00 2.01
49 50 6.627087 TTTAGAGAGATCTGGGTCATGTTT 57.373 37.500 0.00 0.00 0.00 2.83
50 51 6.385176 TGATTTAGAGAGATCTGGGTCATGTT 59.615 38.462 0.00 0.00 0.00 2.71
51 52 5.901853 TGATTTAGAGAGATCTGGGTCATGT 59.098 40.000 0.00 0.00 0.00 3.21
52 53 6.416631 TGATTTAGAGAGATCTGGGTCATG 57.583 41.667 0.00 0.00 0.00 3.07
53 54 7.443302 TTTGATTTAGAGAGATCTGGGTCAT 57.557 36.000 0.00 0.00 0.00 3.06
54 55 6.874278 TTTGATTTAGAGAGATCTGGGTCA 57.126 37.500 0.00 0.00 0.00 4.02
55 56 7.065204 GTGTTTTGATTTAGAGAGATCTGGGTC 59.935 40.741 0.00 0.00 0.00 4.46
56 57 6.881602 GTGTTTTGATTTAGAGAGATCTGGGT 59.118 38.462 0.00 0.00 0.00 4.51
57 58 6.881065 TGTGTTTTGATTTAGAGAGATCTGGG 59.119 38.462 0.00 0.00 0.00 4.45
58 59 7.912056 TGTGTTTTGATTTAGAGAGATCTGG 57.088 36.000 0.00 0.00 0.00 3.86
59 60 7.909121 GCATGTGTTTTGATTTAGAGAGATCTG 59.091 37.037 0.00 0.00 0.00 2.90
60 61 7.609146 TGCATGTGTTTTGATTTAGAGAGATCT 59.391 33.333 0.00 0.00 0.00 2.75
61 62 7.755591 TGCATGTGTTTTGATTTAGAGAGATC 58.244 34.615 0.00 0.00 0.00 2.75
62 63 7.692460 TGCATGTGTTTTGATTTAGAGAGAT 57.308 32.000 0.00 0.00 0.00 2.75
63 64 7.148188 GGATGCATGTGTTTTGATTTAGAGAGA 60.148 37.037 2.46 0.00 0.00 3.10
64 65 6.971184 GGATGCATGTGTTTTGATTTAGAGAG 59.029 38.462 2.46 0.00 0.00 3.20
65 66 6.433716 TGGATGCATGTGTTTTGATTTAGAGA 59.566 34.615 2.46 0.00 0.00 3.10
66 67 6.623486 TGGATGCATGTGTTTTGATTTAGAG 58.377 36.000 2.46 0.00 0.00 2.43
67 68 6.587206 TGGATGCATGTGTTTTGATTTAGA 57.413 33.333 2.46 0.00 0.00 2.10
68 69 7.010738 GGAATGGATGCATGTGTTTTGATTTAG 59.989 37.037 2.46 0.00 0.00 1.85
69 70 6.817641 GGAATGGATGCATGTGTTTTGATTTA 59.182 34.615 2.46 0.00 0.00 1.40
70 71 5.644636 GGAATGGATGCATGTGTTTTGATTT 59.355 36.000 2.46 0.00 0.00 2.17
71 72 5.180271 GGAATGGATGCATGTGTTTTGATT 58.820 37.500 2.46 0.00 0.00 2.57
72 73 4.223255 TGGAATGGATGCATGTGTTTTGAT 59.777 37.500 2.46 0.00 0.00 2.57
73 74 3.577415 TGGAATGGATGCATGTGTTTTGA 59.423 39.130 2.46 0.00 0.00 2.69
74 75 3.927854 TGGAATGGATGCATGTGTTTTG 58.072 40.909 2.46 0.00 0.00 2.44
75 76 4.223255 TGATGGAATGGATGCATGTGTTTT 59.777 37.500 2.46 0.00 40.61 2.43
76 77 3.770388 TGATGGAATGGATGCATGTGTTT 59.230 39.130 2.46 0.00 40.61 2.83
77 78 3.367321 TGATGGAATGGATGCATGTGTT 58.633 40.909 2.46 0.00 40.61 3.32
78 79 3.021177 TGATGGAATGGATGCATGTGT 57.979 42.857 2.46 0.00 40.61 3.72
79 80 3.826729 AGATGATGGAATGGATGCATGTG 59.173 43.478 2.46 0.00 40.61 3.21
80 81 4.114015 AGATGATGGAATGGATGCATGT 57.886 40.909 2.46 0.00 40.61 3.21
81 82 4.767409 AGAAGATGATGGAATGGATGCATG 59.233 41.667 2.46 0.00 40.61 4.06
82 83 4.999310 AGAAGATGATGGAATGGATGCAT 58.001 39.130 0.00 0.00 43.60 3.96
83 84 4.448720 AGAAGATGATGGAATGGATGCA 57.551 40.909 0.00 0.00 0.00 3.96
84 85 5.071370 AGAAGAAGATGATGGAATGGATGC 58.929 41.667 0.00 0.00 0.00 3.91
85 86 8.865420 ATAAGAAGAAGATGATGGAATGGATG 57.135 34.615 0.00 0.00 0.00 3.51
86 87 7.823310 CGATAAGAAGAAGATGATGGAATGGAT 59.177 37.037 0.00 0.00 0.00 3.41
87 88 7.015584 TCGATAAGAAGAAGATGATGGAATGGA 59.984 37.037 0.00 0.00 0.00 3.41
88 89 7.117523 GTCGATAAGAAGAAGATGATGGAATGG 59.882 40.741 0.00 0.00 0.00 3.16
89 90 7.148836 CGTCGATAAGAAGAAGATGATGGAATG 60.149 40.741 0.00 0.00 0.00 2.67
90 91 6.865726 CGTCGATAAGAAGAAGATGATGGAAT 59.134 38.462 0.00 0.00 0.00 3.01
91 92 6.039382 TCGTCGATAAGAAGAAGATGATGGAA 59.961 38.462 0.00 0.00 34.50 3.53
92 93 5.531287 TCGTCGATAAGAAGAAGATGATGGA 59.469 40.000 0.00 0.00 34.50 3.41
93 94 5.763088 TCGTCGATAAGAAGAAGATGATGG 58.237 41.667 0.00 0.00 34.50 3.51
94 95 7.807433 AGAATCGTCGATAAGAAGAAGATGATG 59.193 37.037 8.43 0.00 40.56 3.07
95 96 7.881142 AGAATCGTCGATAAGAAGAAGATGAT 58.119 34.615 8.43 0.00 40.56 2.45
96 97 7.265647 AGAATCGTCGATAAGAAGAAGATGA 57.734 36.000 8.43 0.00 40.56 2.92
97 98 7.267388 CGTAGAATCGTCGATAAGAAGAAGATG 59.733 40.741 8.43 0.00 40.56 2.90
98 99 7.292292 CGTAGAATCGTCGATAAGAAGAAGAT 58.708 38.462 8.43 0.00 40.56 2.40
99 100 6.292757 CCGTAGAATCGTCGATAAGAAGAAGA 60.293 42.308 8.43 0.00 40.56 2.87
100 101 5.846994 CCGTAGAATCGTCGATAAGAAGAAG 59.153 44.000 8.43 0.00 40.56 2.85
101 102 5.745514 CCGTAGAATCGTCGATAAGAAGAA 58.254 41.667 8.43 0.00 40.56 2.52
102 103 4.319333 GCCGTAGAATCGTCGATAAGAAGA 60.319 45.833 8.43 0.00 41.37 2.87
103 104 3.907194 GCCGTAGAATCGTCGATAAGAAG 59.093 47.826 8.43 0.97 0.00 2.85
104 105 3.304257 GGCCGTAGAATCGTCGATAAGAA 60.304 47.826 8.43 0.00 0.00 2.52
105 106 2.225019 GGCCGTAGAATCGTCGATAAGA 59.775 50.000 8.43 0.00 0.00 2.10
106 107 2.582687 GGCCGTAGAATCGTCGATAAG 58.417 52.381 8.43 0.00 0.00 1.73
107 108 1.267806 GGGCCGTAGAATCGTCGATAA 59.732 52.381 8.43 0.00 0.00 1.75
108 109 0.877071 GGGCCGTAGAATCGTCGATA 59.123 55.000 8.43 0.00 0.00 2.92
109 110 1.658673 GGGCCGTAGAATCGTCGAT 59.341 57.895 0.75 0.75 0.00 3.59
110 111 2.827051 CGGGCCGTAGAATCGTCGA 61.827 63.158 19.97 0.00 0.00 4.20
111 112 2.353145 CGGGCCGTAGAATCGTCG 60.353 66.667 19.97 0.00 0.00 5.12
112 113 2.008268 TTCCGGGCCGTAGAATCGTC 62.008 60.000 26.32 0.00 0.00 4.20
113 114 2.012902 CTTCCGGGCCGTAGAATCGT 62.013 60.000 26.32 0.00 0.00 3.73
114 115 1.299926 CTTCCGGGCCGTAGAATCG 60.300 63.158 26.32 7.53 0.00 3.34
115 116 1.069258 CCTTCCGGGCCGTAGAATC 59.931 63.158 26.32 0.00 0.00 2.52
116 117 3.227250 CCTTCCGGGCCGTAGAAT 58.773 61.111 26.32 0.00 0.00 2.40
125 126 1.377333 GTCTTCCAAGCCTTCCGGG 60.377 63.158 0.00 0.00 38.36 5.73
126 127 1.377333 GGTCTTCCAAGCCTTCCGG 60.377 63.158 0.00 0.00 0.00 5.14
127 128 1.377333 GGGTCTTCCAAGCCTTCCG 60.377 63.158 0.00 0.00 33.89 4.30
128 129 1.377333 CGGGTCTTCCAAGCCTTCC 60.377 63.158 0.00 0.00 34.56 3.46
129 130 0.391793 CTCGGGTCTTCCAAGCCTTC 60.392 60.000 0.00 0.00 34.56 3.46
130 131 1.679898 CTCGGGTCTTCCAAGCCTT 59.320 57.895 0.00 0.00 34.56 4.35
131 132 2.294078 CCTCGGGTCTTCCAAGCCT 61.294 63.158 0.00 0.00 34.56 4.58
132 133 2.245438 CTCCTCGGGTCTTCCAAGCC 62.245 65.000 0.00 0.00 34.36 4.35
133 134 1.219393 CTCCTCGGGTCTTCCAAGC 59.781 63.158 0.00 0.00 34.36 4.01
134 135 0.614979 TCCTCCTCGGGTCTTCCAAG 60.615 60.000 0.00 0.00 34.36 3.61
135 136 0.178915 TTCCTCCTCGGGTCTTCCAA 60.179 55.000 0.00 0.00 34.36 3.53
136 137 0.042731 ATTCCTCCTCGGGTCTTCCA 59.957 55.000 0.00 0.00 34.36 3.53
137 138 0.753867 GATTCCTCCTCGGGTCTTCC 59.246 60.000 0.00 0.00 0.00 3.46
138 139 0.753867 GGATTCCTCCTCGGGTCTTC 59.246 60.000 0.00 0.00 38.65 2.87
139 140 0.691413 GGGATTCCTCCTCGGGTCTT 60.691 60.000 2.01 0.00 41.74 3.01
140 141 1.075151 GGGATTCCTCCTCGGGTCT 60.075 63.158 2.01 0.00 41.74 3.85
141 142 0.764752 ATGGGATTCCTCCTCGGGTC 60.765 60.000 2.01 0.00 41.74 4.46
142 143 1.056700 CATGGGATTCCTCCTCGGGT 61.057 60.000 2.01 0.00 41.74 5.28
143 144 0.764369 TCATGGGATTCCTCCTCGGG 60.764 60.000 2.01 0.00 41.74 5.14
144 145 1.071385 CTTCATGGGATTCCTCCTCGG 59.929 57.143 2.01 0.00 41.74 4.63
145 146 2.042464 TCTTCATGGGATTCCTCCTCG 58.958 52.381 2.01 0.00 41.74 4.63
146 147 3.434310 GGTTCTTCATGGGATTCCTCCTC 60.434 52.174 2.01 0.00 41.74 3.71
147 148 2.511637 GGTTCTTCATGGGATTCCTCCT 59.488 50.000 2.01 0.00 41.74 3.69
148 149 2.242196 TGGTTCTTCATGGGATTCCTCC 59.758 50.000 2.01 0.00 41.26 4.30
149 150 3.282885 GTGGTTCTTCATGGGATTCCTC 58.717 50.000 2.01 0.00 0.00 3.71
150 151 2.024941 GGTGGTTCTTCATGGGATTCCT 60.025 50.000 2.01 0.00 0.00 3.36
151 152 2.291540 TGGTGGTTCTTCATGGGATTCC 60.292 50.000 0.00 0.00 0.00 3.01
152 153 2.755103 GTGGTGGTTCTTCATGGGATTC 59.245 50.000 0.00 0.00 0.00 2.52
153 154 2.557452 GGTGGTGGTTCTTCATGGGATT 60.557 50.000 0.00 0.00 0.00 3.01
154 155 1.005924 GGTGGTGGTTCTTCATGGGAT 59.994 52.381 0.00 0.00 0.00 3.85
155 156 0.404040 GGTGGTGGTTCTTCATGGGA 59.596 55.000 0.00 0.00 0.00 4.37
156 157 0.112218 TGGTGGTGGTTCTTCATGGG 59.888 55.000 0.00 0.00 0.00 4.00
157 158 2.094675 GATGGTGGTGGTTCTTCATGG 58.905 52.381 0.00 0.00 0.00 3.66
158 159 2.094675 GGATGGTGGTGGTTCTTCATG 58.905 52.381 0.00 0.00 0.00 3.07
159 160 1.340017 CGGATGGTGGTGGTTCTTCAT 60.340 52.381 0.00 0.00 0.00 2.57
160 161 0.036164 CGGATGGTGGTGGTTCTTCA 59.964 55.000 0.00 0.00 0.00 3.02
161 162 0.036306 ACGGATGGTGGTGGTTCTTC 59.964 55.000 0.00 0.00 0.00 2.87
162 163 0.476771 AACGGATGGTGGTGGTTCTT 59.523 50.000 0.00 0.00 0.00 2.52
163 164 0.250727 CAACGGATGGTGGTGGTTCT 60.251 55.000 0.00 0.00 0.00 3.01
164 165 1.862602 GCAACGGATGGTGGTGGTTC 61.863 60.000 0.00 0.00 0.00 3.62
165 166 1.901464 GCAACGGATGGTGGTGGTT 60.901 57.895 0.00 0.00 0.00 3.67
166 167 2.282180 GCAACGGATGGTGGTGGT 60.282 61.111 0.00 0.00 0.00 4.16
167 168 2.282110 TGCAACGGATGGTGGTGG 60.282 61.111 0.00 0.00 0.00 4.61
168 169 1.577328 GAGTGCAACGGATGGTGGTG 61.577 60.000 0.00 0.00 45.86 4.17
169 170 1.302511 GAGTGCAACGGATGGTGGT 60.303 57.895 0.00 0.00 45.86 4.16
170 171 2.390599 CGAGTGCAACGGATGGTGG 61.391 63.158 6.65 0.00 45.86 4.61
171 172 1.227999 AACGAGTGCAACGGATGGTG 61.228 55.000 16.63 0.00 45.86 4.17
172 173 1.070786 AACGAGTGCAACGGATGGT 59.929 52.632 16.63 0.00 45.86 3.55
173 174 1.227999 ACAACGAGTGCAACGGATGG 61.228 55.000 16.63 7.24 45.86 3.51
174 175 0.163788 GACAACGAGTGCAACGGATG 59.836 55.000 16.63 15.91 45.86 3.51
175 176 0.033504 AGACAACGAGTGCAACGGAT 59.966 50.000 16.63 4.87 45.86 4.18
176 177 0.874175 CAGACAACGAGTGCAACGGA 60.874 55.000 16.63 0.00 45.86 4.69
177 178 1.564622 CAGACAACGAGTGCAACGG 59.435 57.895 16.63 4.87 45.86 4.44
178 179 1.083401 GCAGACAACGAGTGCAACG 60.083 57.895 11.98 11.98 45.86 4.10
179 180 1.279840 GGCAGACAACGAGTGCAAC 59.720 57.895 0.00 0.00 39.05 4.17
180 181 1.891919 GGGCAGACAACGAGTGCAA 60.892 57.895 0.00 0.00 39.05 4.08
181 182 2.280797 GGGCAGACAACGAGTGCA 60.281 61.111 0.00 0.00 39.05 4.57
182 183 3.414700 CGGGCAGACAACGAGTGC 61.415 66.667 0.00 0.00 36.42 4.40
183 184 1.079819 ATCGGGCAGACAACGAGTG 60.080 57.895 0.00 0.00 40.21 3.51
184 185 1.079819 CATCGGGCAGACAACGAGT 60.080 57.895 0.00 0.00 40.21 4.18
185 186 0.179100 ATCATCGGGCAGACAACGAG 60.179 55.000 0.00 0.00 40.21 4.18
186 187 1.107945 TATCATCGGGCAGACAACGA 58.892 50.000 0.00 0.00 41.20 3.85
187 188 1.934589 TTATCATCGGGCAGACAACG 58.065 50.000 0.00 0.00 0.00 4.10
188 189 5.700832 TCATTATTATCATCGGGCAGACAAC 59.299 40.000 0.00 0.00 0.00 3.32
189 190 5.700832 GTCATTATTATCATCGGGCAGACAA 59.299 40.000 0.00 0.00 0.00 3.18
190 191 5.012046 AGTCATTATTATCATCGGGCAGACA 59.988 40.000 0.00 0.00 0.00 3.41
191 192 5.482908 AGTCATTATTATCATCGGGCAGAC 58.517 41.667 0.00 0.00 0.00 3.51
192 193 5.481824 AGAGTCATTATTATCATCGGGCAGA 59.518 40.000 0.00 0.00 0.00 4.26
193 194 5.579904 CAGAGTCATTATTATCATCGGGCAG 59.420 44.000 0.00 0.00 0.00 4.85
194 195 5.482006 CAGAGTCATTATTATCATCGGGCA 58.518 41.667 0.00 0.00 0.00 5.36
195 196 4.331168 GCAGAGTCATTATTATCATCGGGC 59.669 45.833 0.00 0.00 0.00 6.13
196 197 4.564372 CGCAGAGTCATTATTATCATCGGG 59.436 45.833 0.00 0.00 0.00 5.14
197 198 5.402398 TCGCAGAGTCATTATTATCATCGG 58.598 41.667 0.00 0.00 0.00 4.18
198 199 6.020041 CCATCGCAGAGTCATTATTATCATCG 60.020 42.308 0.00 0.00 43.63 3.84
199 200 7.038048 TCCATCGCAGAGTCATTATTATCATC 58.962 38.462 0.00 0.00 43.63 2.92
200 201 6.939622 TCCATCGCAGAGTCATTATTATCAT 58.060 36.000 0.00 0.00 43.63 2.45
201 202 6.345096 TCCATCGCAGAGTCATTATTATCA 57.655 37.500 0.00 0.00 43.63 2.15
202 203 7.038048 TGATCCATCGCAGAGTCATTATTATC 58.962 38.462 0.00 0.00 43.63 1.75
203 204 6.939622 TGATCCATCGCAGAGTCATTATTAT 58.060 36.000 0.00 0.00 43.63 1.28
204 205 6.345096 TGATCCATCGCAGAGTCATTATTA 57.655 37.500 0.00 0.00 43.63 0.98
205 206 5.219343 TGATCCATCGCAGAGTCATTATT 57.781 39.130 0.00 0.00 43.63 1.40
206 207 4.879197 TGATCCATCGCAGAGTCATTAT 57.121 40.909 0.00 0.00 43.63 1.28
207 208 4.502087 CCTTGATCCATCGCAGAGTCATTA 60.502 45.833 0.00 0.00 43.63 1.90
208 209 3.464907 CTTGATCCATCGCAGAGTCATT 58.535 45.455 0.00 0.00 43.63 2.57
209 210 2.224233 CCTTGATCCATCGCAGAGTCAT 60.224 50.000 0.00 0.00 43.63 3.06
210 211 1.137675 CCTTGATCCATCGCAGAGTCA 59.862 52.381 0.00 0.00 43.63 3.41
211 212 1.410517 TCCTTGATCCATCGCAGAGTC 59.589 52.381 0.00 0.00 43.63 3.36
212 213 1.411977 CTCCTTGATCCATCGCAGAGT 59.588 52.381 0.00 0.00 43.63 3.24
213 214 1.685517 TCTCCTTGATCCATCGCAGAG 59.314 52.381 0.00 0.00 43.63 3.35
214 215 1.780503 TCTCCTTGATCCATCGCAGA 58.219 50.000 0.00 0.00 45.75 4.26
215 216 2.835580 ATCTCCTTGATCCATCGCAG 57.164 50.000 0.00 0.00 0.00 5.18
216 217 2.702478 AGAATCTCCTTGATCCATCGCA 59.298 45.455 0.00 0.00 33.57 5.10
217 218 3.324993 GAGAATCTCCTTGATCCATCGC 58.675 50.000 0.00 0.00 33.57 4.58
218 219 3.924144 GGAGAATCTCCTTGATCCATCG 58.076 50.000 21.48 0.00 46.41 3.84
230 231 1.765904 GGAGGAACAGGGGAGAATCTC 59.234 57.143 0.71 0.71 33.73 2.75
231 232 1.626631 GGGAGGAACAGGGGAGAATCT 60.627 57.143 0.00 0.00 33.73 2.40
232 233 0.840617 GGGAGGAACAGGGGAGAATC 59.159 60.000 0.00 0.00 0.00 2.52
233 234 0.423544 AGGGAGGAACAGGGGAGAAT 59.576 55.000 0.00 0.00 0.00 2.40
234 235 0.252742 GAGGGAGGAACAGGGGAGAA 60.253 60.000 0.00 0.00 0.00 2.87
235 236 1.156322 AGAGGGAGGAACAGGGGAGA 61.156 60.000 0.00 0.00 0.00 3.71
236 237 0.689412 GAGAGGGAGGAACAGGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
237 238 1.156322 AGAGAGGGAGGAACAGGGGA 61.156 60.000 0.00 0.00 0.00 4.81
238 239 0.689412 GAGAGAGGGAGGAACAGGGG 60.689 65.000 0.00 0.00 0.00 4.79
239 240 0.338120 AGAGAGAGGGAGGAACAGGG 59.662 60.000 0.00 0.00 0.00 4.45
240 241 1.287739 AGAGAGAGAGGGAGGAACAGG 59.712 57.143 0.00 0.00 0.00 4.00
241 242 2.242196 AGAGAGAGAGAGGGAGGAACAG 59.758 54.545 0.00 0.00 0.00 3.16
242 243 2.241176 GAGAGAGAGAGAGGGAGGAACA 59.759 54.545 0.00 0.00 0.00 3.18
243 244 2.422945 GGAGAGAGAGAGAGGGAGGAAC 60.423 59.091 0.00 0.00 0.00 3.62
244 245 1.850345 GGAGAGAGAGAGAGGGAGGAA 59.150 57.143 0.00 0.00 0.00 3.36
245 246 1.274708 TGGAGAGAGAGAGAGGGAGGA 60.275 57.143 0.00 0.00 0.00 3.71
246 247 1.143684 CTGGAGAGAGAGAGAGGGAGG 59.856 61.905 0.00 0.00 0.00 4.30
250 251 4.443978 AGAATCTGGAGAGAGAGAGAGG 57.556 50.000 0.00 0.00 0.00 3.69
338 340 2.808543 CAGAGAAGGAAAGAACAACCGG 59.191 50.000 0.00 0.00 0.00 5.28
345 347 3.864789 AGCAACCAGAGAAGGAAAGAA 57.135 42.857 0.00 0.00 0.00 2.52
348 350 4.536765 AGAAAAGCAACCAGAGAAGGAAA 58.463 39.130 0.00 0.00 0.00 3.13
362 364 0.687354 AAGAGGAGGCGAGAAAAGCA 59.313 50.000 0.00 0.00 36.08 3.91
405 407 5.507985 CCCTTTGTCTTTCCATCTCAAACAC 60.508 44.000 0.00 0.00 0.00 3.32
473 475 1.344953 CCCGAGGATGGACCATGGAA 61.345 60.000 21.47 3.61 42.04 3.53
526 528 0.870393 ATGGATTGATAGCGCTTGCG 59.130 50.000 18.68 10.90 45.69 4.85
841 843 2.214376 ATTTTTGCCACGATCCTCCA 57.786 45.000 0.00 0.00 0.00 3.86
842 844 4.338118 TGAATATTTTTGCCACGATCCTCC 59.662 41.667 0.00 0.00 0.00 4.30
850 852 8.034804 ACTTGTAATCCTGAATATTTTTGCCAC 58.965 33.333 0.00 0.00 0.00 5.01
1173 1177 4.377021 TGTTTCTAGCAGTACAGTGTTGG 58.623 43.478 0.00 0.00 0.00 3.77
1269 1273 1.282157 GGAATCAGCCCCACACTAGTT 59.718 52.381 0.00 0.00 0.00 2.24
1305 1309 8.884124 ATGAAGTCAAATCTTCCTGGAAATTA 57.116 30.769 10.86 0.00 41.96 1.40
1309 1313 6.546484 AGAATGAAGTCAAATCTTCCTGGAA 58.454 36.000 9.14 9.14 41.96 3.53
1322 1326 7.661847 GGTTAAGAAAGGAAGAGAATGAAGTCA 59.338 37.037 0.00 0.00 0.00 3.41
1374 1378 8.339247 TCTTTTCCTTTAGAATCCTCCATGAAT 58.661 33.333 0.00 0.00 33.44 2.57
1443 1447 9.857656 TGCTCATTAATTTCCTTGAGAGATAAT 57.142 29.630 5.82 0.00 38.25 1.28
1568 1572 3.718434 AGTCTGATGGCCCAAATCTGATA 59.282 43.478 12.39 0.00 35.36 2.15
1787 1791 9.817365 CACTAAGATGTTTGTCTATCAAAGTTG 57.183 33.333 0.00 0.00 45.15 3.16
1844 1848 3.137360 AGGGGGAGATGAAGAAACTATGC 59.863 47.826 0.00 0.00 0.00 3.14
1845 1849 5.104360 TGAAGGGGGAGATGAAGAAACTATG 60.104 44.000 0.00 0.00 0.00 2.23
1846 1850 5.039645 TGAAGGGGGAGATGAAGAAACTAT 58.960 41.667 0.00 0.00 0.00 2.12
1957 1961 5.931146 CAGGAATCTTATCTGAATTCTCCCG 59.069 44.000 7.05 0.00 0.00 5.14
2022 2261 4.889995 AGAAGGCTTGAACTTTGTAAAGCT 59.110 37.500 3.46 0.00 43.58 3.74
2037 2276 2.360475 GGCGCTCCAAGAAGGCTT 60.360 61.111 7.64 0.00 37.29 4.35
2117 2356 0.178953 ACCATCACCAGCAAAAGCCT 60.179 50.000 0.00 0.00 0.00 4.58
2149 2388 3.198068 GTTCTTCACTGTGAGTGCTTCA 58.802 45.455 10.77 0.00 45.54 3.02
2197 2436 2.696187 GGCTCCCTTGAGAAGTAGTAGG 59.304 54.545 0.00 0.00 41.42 3.18
2222 2461 0.039180 TCTGCTACCTCCAGACCGAA 59.961 55.000 0.00 0.00 34.59 4.30
2289 2528 0.458669 GATAGCGAAGAACCCCGTGA 59.541 55.000 0.00 0.00 0.00 4.35
2325 2564 2.675056 GCTGCTGTCACGCTTCCAG 61.675 63.158 0.00 0.00 0.00 3.86
2358 2597 9.967451 TTGATTCCAGTCAAATTAATGGTACTA 57.033 29.630 0.00 0.00 35.31 1.82
2366 2605 9.142014 TCTTTCCTTTGATTCCAGTCAAATTAA 57.858 29.630 2.91 0.00 44.48 1.40
2461 2700 5.541484 GCCATGGATCATAATTTCCTCCTTT 59.459 40.000 18.40 0.00 32.95 3.11
2586 2825 4.034394 CCACACATATCTTGACCAACATCG 59.966 45.833 0.00 0.00 0.00 3.84
2600 2839 2.236146 TGAGCTTCGGAACCACACATAT 59.764 45.455 0.00 0.00 0.00 1.78
2615 2854 6.008960 AGATTCTCCATTGTTCTTTGAGCTT 58.991 36.000 0.00 0.00 0.00 3.74
3071 3311 4.336433 CCCGATGCTTGATGAACTACATTT 59.664 41.667 0.00 0.00 39.56 2.32


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

AutoCloner maintained by Alex Coulton.