Multiple sequence alignment - TraesCS7D01G531700

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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 TraesCS7D01G531700 chr7D 100.000 1565 0 0 968 2532 625662737 625661173 0.000000e+00 2891
1 TraesCS7D01G531700 chr7D 100.000 598 0 0 1 598 625663704 625663107 0.000000e+00 1105
2 TraesCS7D01G531700 chr7D 98.264 288 5 0 302 589 71219438 71219725 2.910000e-139 505
3 TraesCS7D01G531700 chr5D 98.092 1572 22 6 968 2532 399910465 399912035 0.000000e+00 2730
4 TraesCS7D01G531700 chr5D 97.325 1570 37 4 968 2532 47118688 47117119 0.000000e+00 2662
5 TraesCS7D01G531700 chr5D 97.909 287 6 0 303 589 47119052 47118766 4.860000e-137 497
6 TraesCS7D01G531700 chr5D 97.909 287 6 0 303 589 399910100 399910386 4.860000e-137 497
7 TraesCS7D01G531700 chr6D 97.962 1570 27 5 968 2532 390007194 390008763 0.000000e+00 2717
8 TraesCS7D01G531700 chr6D 97.769 1569 29 6 968 2532 8857863 8856297 0.000000e+00 2699
9 TraesCS7D01G531700 chr6D 97.514 1569 34 5 968 2532 2970728 2972295 0.000000e+00 2676
10 TraesCS7D01G531700 chr6D 97.455 1572 29 7 968 2529 465023960 465025530 0.000000e+00 2671
11 TraesCS7D01G531700 chr6D 98.606 287 4 0 303 589 390006827 390007113 2.250000e-140 508
12 TraesCS7D01G531700 chr6D 98.606 287 4 0 303 589 465023254 465023540 2.250000e-140 508
13 TraesCS7D01G531700 chr2D 97.897 1569 29 4 968 2532 396702349 396703917 0.000000e+00 2712
14 TraesCS7D01G531700 chr2D 97.640 1568 34 3 968 2532 70394534 70396101 0.000000e+00 2687
15 TraesCS7D01G531700 chr2D 97.516 1570 33 5 968 2532 640772958 640771390 0.000000e+00 2678
16 TraesCS7D01G531700 chrUn 97.909 287 6 0 303 589 30431623 30431337 4.860000e-137 497
17 TraesCS7D01G531700 chr2B 97.909 287 6 0 303 589 691248387 691248101 4.860000e-137 497
18 TraesCS7D01G531700 chr6B 96.284 296 11 0 294 589 77052389 77052094 1.050000e-133 486
19 TraesCS7D01G531700 chr4B 95.395 304 14 0 295 598 665031618 665031921 3.790000e-133 484
20 TraesCS7D01G531700 chr7B 89.769 303 30 1 1 302 682349232 682349534 1.100000e-103 387
21 TraesCS7D01G531700 chr7A 93.204 206 14 0 97 302 721231070 721230865 1.140000e-78 303


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 TraesCS7D01G531700 chr7D 625661173 625663704 2531 True 1998.0 2891 100.0000 1 2532 2 chr7D.!!$R1 2531
1 TraesCS7D01G531700 chr5D 399910100 399912035 1935 False 1613.5 2730 98.0005 303 2532 2 chr5D.!!$F1 2229
2 TraesCS7D01G531700 chr5D 47117119 47119052 1933 True 1579.5 2662 97.6170 303 2532 2 chr5D.!!$R1 2229
3 TraesCS7D01G531700 chr6D 8856297 8857863 1566 True 2699.0 2699 97.7690 968 2532 1 chr6D.!!$R1 1564
4 TraesCS7D01G531700 chr6D 2970728 2972295 1567 False 2676.0 2676 97.5140 968 2532 1 chr6D.!!$F1 1564
5 TraesCS7D01G531700 chr6D 390006827 390008763 1936 False 1612.5 2717 98.2840 303 2532 2 chr6D.!!$F2 2229
6 TraesCS7D01G531700 chr6D 465023254 465025530 2276 False 1589.5 2671 98.0305 303 2529 2 chr6D.!!$F3 2226
7 TraesCS7D01G531700 chr2D 396702349 396703917 1568 False 2712.0 2712 97.8970 968 2532 1 chr2D.!!$F2 1564
8 TraesCS7D01G531700 chr2D 70394534 70396101 1567 False 2687.0 2687 97.6400 968 2532 1 chr2D.!!$F1 1564
9 TraesCS7D01G531700 chr2D 640771390 640772958 1568 True 2678.0 2678 97.5160 968 2532 1 chr2D.!!$R1 1564

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
179 180 0.031994 GAAAGCTTGGGCGCAAAGAA 59.968 50.0 22.10 3.30 44.37 2.52 F
180 181 0.032540 AAAGCTTGGGCGCAAAGAAG 59.967 50.0 22.10 12.81 44.37 2.85 F
279 280 0.109735 GAAGCAGCGGCAGGTTAAAC 60.110 55.0 12.44 0.00 44.61 2.01 F
1486 1529 0.108138 ATGCAGGAGTTACGGCAGAC 60.108 55.0 0.00 0.00 39.95 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 1418 0.035056 CCAACTTCTCCGCCTCCAAT 60.035 55.000 0.0 0.0 0.0 3.16 R
1477 1520 1.629043 ACTTCTTCAGGTCTGCCGTA 58.371 50.000 0.0 0.0 40.5 4.02 R
1529 1572 3.025978 CCATCAAATTGCCCTGCTTCTA 58.974 45.455 0.0 0.0 0.0 2.10 R
2496 2553 9.732453 TCTATCTATCTATGCTACTAGGGTACT 57.268 37.037 0.0 0.0 0.0 2.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.965805 TTATGGTGTCGTCCGTCCT 58.034 52.632 0.00 0.00 0.00 3.85
19 20 1.259609 TTATGGTGTCGTCCGTCCTT 58.740 50.000 0.00 0.00 0.00 3.36
20 21 0.813184 TATGGTGTCGTCCGTCCTTC 59.187 55.000 0.00 0.00 0.00 3.46
21 22 0.898789 ATGGTGTCGTCCGTCCTTCT 60.899 55.000 0.00 0.00 0.00 2.85
22 23 1.212229 GGTGTCGTCCGTCCTTCTC 59.788 63.158 0.00 0.00 0.00 2.87
23 24 1.212229 GTGTCGTCCGTCCTTCTCC 59.788 63.158 0.00 0.00 0.00 3.71
24 25 1.074423 TGTCGTCCGTCCTTCTCCT 59.926 57.895 0.00 0.00 0.00 3.69
25 26 1.241990 TGTCGTCCGTCCTTCTCCTG 61.242 60.000 0.00 0.00 0.00 3.86
26 27 1.677966 TCGTCCGTCCTTCTCCTGG 60.678 63.158 0.00 0.00 0.00 4.45
27 28 2.711922 CGTCCGTCCTTCTCCTGGG 61.712 68.421 0.00 0.00 0.00 4.45
28 29 2.683933 TCCGTCCTTCTCCTGGGC 60.684 66.667 0.00 0.00 0.00 5.36
29 30 2.685380 CCGTCCTTCTCCTGGGCT 60.685 66.667 0.00 0.00 0.00 5.19
30 31 2.581354 CGTCCTTCTCCTGGGCTG 59.419 66.667 0.00 0.00 0.00 4.85
31 32 2.270527 GTCCTTCTCCTGGGCTGC 59.729 66.667 0.00 0.00 0.00 5.25
32 33 2.123632 TCCTTCTCCTGGGCTGCT 59.876 61.111 0.00 0.00 0.00 4.24
33 34 1.992277 TCCTTCTCCTGGGCTGCTC 60.992 63.158 0.00 0.00 0.00 4.26
34 35 2.588989 CTTCTCCTGGGCTGCTCC 59.411 66.667 0.00 0.00 0.00 4.70
35 36 3.382803 CTTCTCCTGGGCTGCTCCG 62.383 68.421 0.00 0.00 34.94 4.63
45 46 4.803426 CTGCTCCGCGACAGGGTC 62.803 72.222 8.23 0.00 0.00 4.46
48 49 3.382832 CTCCGCGACAGGGTCCTT 61.383 66.667 8.23 0.00 0.00 3.36
49 50 2.036098 TCCGCGACAGGGTCCTTA 59.964 61.111 8.23 0.00 0.00 2.69
50 51 2.183555 CCGCGACAGGGTCCTTAC 59.816 66.667 8.23 0.00 0.00 2.34
51 52 2.183555 CGCGACAGGGTCCTTACC 59.816 66.667 0.00 0.00 45.97 2.85
60 61 3.222053 GGTCCTTACCGGTGTTCAC 57.778 57.895 19.93 8.69 35.62 3.18
61 62 0.668401 GGTCCTTACCGGTGTTCACG 60.668 60.000 19.93 0.00 35.62 4.35
62 63 0.314935 GTCCTTACCGGTGTTCACGA 59.685 55.000 19.93 0.65 0.00 4.35
63 64 0.599558 TCCTTACCGGTGTTCACGAG 59.400 55.000 19.93 3.43 0.00 4.18
64 65 0.599558 CCTTACCGGTGTTCACGAGA 59.400 55.000 19.93 0.00 0.00 4.04
65 66 1.203994 CCTTACCGGTGTTCACGAGAT 59.796 52.381 19.93 0.00 0.00 2.75
66 67 2.527100 CTTACCGGTGTTCACGAGATC 58.473 52.381 19.93 0.00 0.00 2.75
67 68 1.830279 TACCGGTGTTCACGAGATCT 58.170 50.000 19.93 0.00 0.00 2.75
68 69 1.830279 ACCGGTGTTCACGAGATCTA 58.170 50.000 6.12 0.00 0.00 1.98
69 70 1.743958 ACCGGTGTTCACGAGATCTAG 59.256 52.381 6.12 0.00 0.00 2.43
70 71 1.534175 CCGGTGTTCACGAGATCTAGC 60.534 57.143 2.33 0.00 0.00 3.42
71 72 1.534175 CGGTGTTCACGAGATCTAGCC 60.534 57.143 2.33 0.00 0.00 3.93
72 73 1.534175 GGTGTTCACGAGATCTAGCCG 60.534 57.143 2.33 1.65 0.00 5.52
73 74 1.132643 GTGTTCACGAGATCTAGCCGT 59.867 52.381 2.33 2.33 36.95 5.68
74 75 1.816835 TGTTCACGAGATCTAGCCGTT 59.183 47.619 5.29 0.00 33.96 4.44
75 76 2.159421 TGTTCACGAGATCTAGCCGTTC 60.159 50.000 5.29 1.63 33.96 3.95
76 77 1.022735 TCACGAGATCTAGCCGTTCC 58.977 55.000 5.29 0.00 33.96 3.62
77 78 1.025812 CACGAGATCTAGCCGTTCCT 58.974 55.000 5.29 0.00 33.96 3.36
78 79 1.002251 CACGAGATCTAGCCGTTCCTC 60.002 57.143 5.29 0.00 33.96 3.71
79 80 0.594110 CGAGATCTAGCCGTTCCTCC 59.406 60.000 0.00 0.00 0.00 4.30
80 81 1.816183 CGAGATCTAGCCGTTCCTCCT 60.816 57.143 0.00 0.00 0.00 3.69
81 82 1.883926 GAGATCTAGCCGTTCCTCCTC 59.116 57.143 0.00 0.00 0.00 3.71
82 83 0.594110 GATCTAGCCGTTCCTCCTCG 59.406 60.000 0.00 0.00 0.00 4.63
84 85 2.441532 TAGCCGTTCCTCCTCGGG 60.442 66.667 5.78 0.00 45.85 5.14
104 105 4.120331 GCGTTGGCTGCCCATGAC 62.120 66.667 17.53 8.70 41.78 3.06
105 106 3.803082 CGTTGGCTGCCCATGACG 61.803 66.667 17.53 16.42 41.78 4.35
106 107 2.359850 GTTGGCTGCCCATGACGA 60.360 61.111 17.53 0.00 41.78 4.20
107 108 1.971167 GTTGGCTGCCCATGACGAA 60.971 57.895 17.53 0.00 41.78 3.85
108 109 1.675310 TTGGCTGCCCATGACGAAG 60.675 57.895 17.53 0.00 41.78 3.79
109 110 3.512516 GGCTGCCCATGACGAAGC 61.513 66.667 7.66 0.00 0.00 3.86
110 111 3.869272 GCTGCCCATGACGAAGCG 61.869 66.667 0.00 0.00 0.00 4.68
111 112 3.197790 CTGCCCATGACGAAGCGG 61.198 66.667 0.00 0.00 0.00 5.52
112 113 3.958147 CTGCCCATGACGAAGCGGT 62.958 63.158 0.00 0.00 0.00 5.68
113 114 3.499737 GCCCATGACGAAGCGGTG 61.500 66.667 0.00 0.00 0.00 4.94
114 115 2.047274 CCCATGACGAAGCGGTGT 60.047 61.111 0.00 0.00 0.00 4.16
115 116 2.100631 CCCATGACGAAGCGGTGTC 61.101 63.158 0.00 0.00 35.67 3.67
116 117 2.444624 CCATGACGAAGCGGTGTCG 61.445 63.158 14.53 14.53 44.10 4.35
134 135 2.584064 CTGCGGTGGAGCATGGTA 59.416 61.111 0.00 0.00 46.97 3.25
135 136 1.522355 CTGCGGTGGAGCATGGTAG 60.522 63.158 0.00 0.00 46.97 3.18
136 137 1.960040 CTGCGGTGGAGCATGGTAGA 61.960 60.000 0.00 0.00 46.97 2.59
137 138 1.227380 GCGGTGGAGCATGGTAGAG 60.227 63.158 0.00 0.00 37.05 2.43
138 139 1.676678 GCGGTGGAGCATGGTAGAGA 61.677 60.000 0.00 0.00 37.05 3.10
139 140 1.043816 CGGTGGAGCATGGTAGAGAT 58.956 55.000 0.00 0.00 0.00 2.75
140 141 1.269988 CGGTGGAGCATGGTAGAGATG 60.270 57.143 0.00 0.00 0.00 2.90
141 142 1.071385 GGTGGAGCATGGTAGAGATGG 59.929 57.143 0.00 0.00 0.00 3.51
142 143 1.765314 GTGGAGCATGGTAGAGATGGT 59.235 52.381 0.00 0.00 34.27 3.55
143 144 1.764723 TGGAGCATGGTAGAGATGGTG 59.235 52.381 0.00 0.00 31.75 4.17
144 145 1.071385 GGAGCATGGTAGAGATGGTGG 59.929 57.143 0.00 0.00 31.75 4.61
145 146 2.042464 GAGCATGGTAGAGATGGTGGA 58.958 52.381 0.00 0.00 31.75 4.02
146 147 2.036992 GAGCATGGTAGAGATGGTGGAG 59.963 54.545 0.00 0.00 31.75 3.86
147 148 1.542108 GCATGGTAGAGATGGTGGAGC 60.542 57.143 0.00 0.00 0.00 4.70
148 149 1.043816 ATGGTAGAGATGGTGGAGCG 58.956 55.000 0.00 0.00 0.00 5.03
149 150 0.324368 TGGTAGAGATGGTGGAGCGT 60.324 55.000 0.00 0.00 0.00 5.07
150 151 0.824759 GGTAGAGATGGTGGAGCGTT 59.175 55.000 0.00 0.00 0.00 4.84
151 152 1.207329 GGTAGAGATGGTGGAGCGTTT 59.793 52.381 0.00 0.00 0.00 3.60
152 153 2.271800 GTAGAGATGGTGGAGCGTTTG 58.728 52.381 0.00 0.00 0.00 2.93
153 154 0.036010 AGAGATGGTGGAGCGTTTGG 60.036 55.000 0.00 0.00 0.00 3.28
154 155 1.002134 AGATGGTGGAGCGTTTGGG 60.002 57.895 0.00 0.00 0.00 4.12
155 156 2.676471 ATGGTGGAGCGTTTGGGC 60.676 61.111 0.00 0.00 0.00 5.36
156 157 3.505790 ATGGTGGAGCGTTTGGGCA 62.506 57.895 0.00 0.00 34.64 5.36
157 158 3.670377 GGTGGAGCGTTTGGGCAC 61.670 66.667 0.00 0.00 34.64 5.01
158 159 4.025401 GTGGAGCGTTTGGGCACG 62.025 66.667 0.00 0.00 43.36 5.34
162 163 4.572571 AGCGTTTGGGCACGGGAA 62.573 61.111 0.00 0.00 40.69 3.97
163 164 3.597728 GCGTTTGGGCACGGGAAA 61.598 61.111 0.00 0.00 40.69 3.13
164 165 2.642700 CGTTTGGGCACGGGAAAG 59.357 61.111 0.00 0.00 36.47 2.62
165 166 2.338620 GTTTGGGCACGGGAAAGC 59.661 61.111 0.00 0.00 0.00 3.51
166 167 2.197324 TTTGGGCACGGGAAAGCT 59.803 55.556 0.00 0.00 0.00 3.74
167 168 1.456705 TTTGGGCACGGGAAAGCTT 60.457 52.632 0.00 0.00 0.00 3.74
168 169 1.743321 TTTGGGCACGGGAAAGCTTG 61.743 55.000 0.00 0.00 0.00 4.01
169 170 3.373565 GGGCACGGGAAAGCTTGG 61.374 66.667 0.00 0.00 0.00 3.61
170 171 3.373565 GGCACGGGAAAGCTTGGG 61.374 66.667 0.00 0.00 0.00 4.12
171 172 4.056125 GCACGGGAAAGCTTGGGC 62.056 66.667 0.00 0.00 39.06 5.36
172 173 3.737172 CACGGGAAAGCTTGGGCG 61.737 66.667 0.00 0.00 44.37 6.13
175 176 3.302344 GGGAAAGCTTGGGCGCAA 61.302 61.111 16.06 16.06 44.37 4.85
176 177 2.733945 GGAAAGCTTGGGCGCAAA 59.266 55.556 17.59 1.45 44.37 3.68
177 178 1.373371 GGAAAGCTTGGGCGCAAAG 60.373 57.895 17.59 13.81 44.37 2.77
178 179 1.659794 GAAAGCTTGGGCGCAAAGA 59.340 52.632 22.10 0.00 44.37 2.52
179 180 0.031994 GAAAGCTTGGGCGCAAAGAA 59.968 50.000 22.10 3.30 44.37 2.52
180 181 0.032540 AAAGCTTGGGCGCAAAGAAG 59.967 50.000 22.10 12.81 44.37 2.85
181 182 0.823356 AAGCTTGGGCGCAAAGAAGA 60.823 50.000 22.10 0.00 44.37 2.87
182 183 0.823356 AGCTTGGGCGCAAAGAAGAA 60.823 50.000 22.10 0.00 44.37 2.52
183 184 0.387750 GCTTGGGCGCAAAGAAGAAG 60.388 55.000 22.10 4.87 0.00 2.85
184 185 1.238439 CTTGGGCGCAAAGAAGAAGA 58.762 50.000 17.59 0.00 0.00 2.87
185 186 1.608590 CTTGGGCGCAAAGAAGAAGAA 59.391 47.619 17.59 0.00 0.00 2.52
186 187 1.238439 TGGGCGCAAAGAAGAAGAAG 58.762 50.000 10.83 0.00 0.00 2.85
187 188 1.202758 TGGGCGCAAAGAAGAAGAAGA 60.203 47.619 10.83 0.00 0.00 2.87
188 189 1.466558 GGGCGCAAAGAAGAAGAAGAG 59.533 52.381 10.83 0.00 0.00 2.85
189 190 1.466558 GGCGCAAAGAAGAAGAAGAGG 59.533 52.381 10.83 0.00 0.00 3.69
190 191 2.417719 GCGCAAAGAAGAAGAAGAGGA 58.582 47.619 0.30 0.00 0.00 3.71
191 192 2.414825 GCGCAAAGAAGAAGAAGAGGAG 59.585 50.000 0.30 0.00 0.00 3.69
192 193 2.414825 CGCAAAGAAGAAGAAGAGGAGC 59.585 50.000 0.00 0.00 0.00 4.70
193 194 2.414825 GCAAAGAAGAAGAAGAGGAGCG 59.585 50.000 0.00 0.00 0.00 5.03
194 195 3.862642 GCAAAGAAGAAGAAGAGGAGCGA 60.863 47.826 0.00 0.00 0.00 4.93
195 196 3.866883 AAGAAGAAGAAGAGGAGCGAG 57.133 47.619 0.00 0.00 0.00 5.03
196 197 3.080300 AGAAGAAGAAGAGGAGCGAGA 57.920 47.619 0.00 0.00 0.00 4.04
197 198 3.016736 AGAAGAAGAAGAGGAGCGAGAG 58.983 50.000 0.00 0.00 0.00 3.20
198 199 1.762708 AGAAGAAGAGGAGCGAGAGG 58.237 55.000 0.00 0.00 0.00 3.69
199 200 0.744281 GAAGAAGAGGAGCGAGAGGG 59.256 60.000 0.00 0.00 0.00 4.30
200 201 0.333312 AAGAAGAGGAGCGAGAGGGA 59.667 55.000 0.00 0.00 0.00 4.20
201 202 0.333312 AGAAGAGGAGCGAGAGGGAA 59.667 55.000 0.00 0.00 0.00 3.97
202 203 1.063266 AGAAGAGGAGCGAGAGGGAAT 60.063 52.381 0.00 0.00 0.00 3.01
203 204 1.068434 GAAGAGGAGCGAGAGGGAATG 59.932 57.143 0.00 0.00 0.00 2.67
204 205 0.758685 AGAGGAGCGAGAGGGAATGG 60.759 60.000 0.00 0.00 0.00 3.16
205 206 1.753368 GAGGAGCGAGAGGGAATGGG 61.753 65.000 0.00 0.00 0.00 4.00
206 207 1.762460 GGAGCGAGAGGGAATGGGA 60.762 63.158 0.00 0.00 0.00 4.37
207 208 1.745264 GAGCGAGAGGGAATGGGAG 59.255 63.158 0.00 0.00 0.00 4.30
208 209 2.110006 GCGAGAGGGAATGGGAGC 59.890 66.667 0.00 0.00 0.00 4.70
209 210 2.419198 CGAGAGGGAATGGGAGCG 59.581 66.667 0.00 0.00 0.00 5.03
210 211 2.825264 GAGAGGGAATGGGAGCGG 59.175 66.667 0.00 0.00 0.00 5.52
211 212 1.762460 GAGAGGGAATGGGAGCGGA 60.762 63.158 0.00 0.00 0.00 5.54
212 213 1.306997 AGAGGGAATGGGAGCGGAA 60.307 57.895 0.00 0.00 0.00 4.30
213 214 0.914417 AGAGGGAATGGGAGCGGAAA 60.914 55.000 0.00 0.00 0.00 3.13
214 215 0.748367 GAGGGAATGGGAGCGGAAAC 60.748 60.000 0.00 0.00 0.00 2.78
215 216 1.753078 GGGAATGGGAGCGGAAACC 60.753 63.158 0.00 0.00 0.00 3.27
216 217 1.303282 GGAATGGGAGCGGAAACCT 59.697 57.895 0.00 0.00 0.00 3.50
217 218 0.323451 GGAATGGGAGCGGAAACCTT 60.323 55.000 0.00 0.00 0.00 3.50
218 219 1.095600 GAATGGGAGCGGAAACCTTC 58.904 55.000 0.00 0.00 0.00 3.46
219 220 0.323451 AATGGGAGCGGAAACCTTCC 60.323 55.000 0.00 0.00 46.62 3.46
231 232 5.595257 GGAAACCTTCCTTCGTATCTACT 57.405 43.478 0.00 0.00 46.57 2.57
232 233 6.705863 GGAAACCTTCCTTCGTATCTACTA 57.294 41.667 0.00 0.00 46.57 1.82
233 234 7.287512 GGAAACCTTCCTTCGTATCTACTAT 57.712 40.000 0.00 0.00 46.57 2.12
234 235 7.724287 GGAAACCTTCCTTCGTATCTACTATT 58.276 38.462 0.00 0.00 46.57 1.73
235 236 7.866898 GGAAACCTTCCTTCGTATCTACTATTC 59.133 40.741 0.00 0.00 46.57 1.75
236 237 6.897706 ACCTTCCTTCGTATCTACTATTCC 57.102 41.667 0.00 0.00 0.00 3.01
237 238 5.774184 ACCTTCCTTCGTATCTACTATTCCC 59.226 44.000 0.00 0.00 0.00 3.97
238 239 6.011481 CCTTCCTTCGTATCTACTATTCCCT 58.989 44.000 0.00 0.00 0.00 4.20
239 240 6.494146 CCTTCCTTCGTATCTACTATTCCCTT 59.506 42.308 0.00 0.00 0.00 3.95
240 241 6.896021 TCCTTCGTATCTACTATTCCCTTG 57.104 41.667 0.00 0.00 0.00 3.61
241 242 6.371278 TCCTTCGTATCTACTATTCCCTTGT 58.629 40.000 0.00 0.00 0.00 3.16
242 243 7.520798 TCCTTCGTATCTACTATTCCCTTGTA 58.479 38.462 0.00 0.00 0.00 2.41
243 244 8.168725 TCCTTCGTATCTACTATTCCCTTGTAT 58.831 37.037 0.00 0.00 0.00 2.29
244 245 9.458727 CCTTCGTATCTACTATTCCCTTGTATA 57.541 37.037 0.00 0.00 0.00 1.47
246 247 9.458727 TTCGTATCTACTATTCCCTTGTATAGG 57.541 37.037 0.00 0.00 44.33 2.57
257 258 4.200447 CCTTGTATAGGGGAAGAGGAGA 57.800 50.000 0.00 0.00 40.67 3.71
258 259 4.156477 CCTTGTATAGGGGAAGAGGAGAG 58.844 52.174 0.00 0.00 40.67 3.20
259 260 4.388118 CCTTGTATAGGGGAAGAGGAGAGT 60.388 50.000 0.00 0.00 40.67 3.24
260 261 4.186077 TGTATAGGGGAAGAGGAGAGTG 57.814 50.000 0.00 0.00 0.00 3.51
261 262 3.792114 TGTATAGGGGAAGAGGAGAGTGA 59.208 47.826 0.00 0.00 0.00 3.41
262 263 4.232122 TGTATAGGGGAAGAGGAGAGTGAA 59.768 45.833 0.00 0.00 0.00 3.18
263 264 2.246091 AGGGGAAGAGGAGAGTGAAG 57.754 55.000 0.00 0.00 0.00 3.02
264 265 0.539518 GGGGAAGAGGAGAGTGAAGC 59.460 60.000 0.00 0.00 0.00 3.86
265 266 1.270907 GGGAAGAGGAGAGTGAAGCA 58.729 55.000 0.00 0.00 0.00 3.91
266 267 1.206849 GGGAAGAGGAGAGTGAAGCAG 59.793 57.143 0.00 0.00 0.00 4.24
267 268 1.405391 GGAAGAGGAGAGTGAAGCAGC 60.405 57.143 0.00 0.00 0.00 5.25
268 269 0.246086 AAGAGGAGAGTGAAGCAGCG 59.754 55.000 0.00 0.00 0.00 5.18
269 270 1.153667 GAGGAGAGTGAAGCAGCGG 60.154 63.158 0.00 0.00 0.00 5.52
270 271 2.817396 GGAGAGTGAAGCAGCGGC 60.817 66.667 0.00 0.00 41.61 6.53
271 272 2.047844 GAGAGTGAAGCAGCGGCA 60.048 61.111 12.44 0.00 44.61 5.69
272 273 2.047465 AGAGTGAAGCAGCGGCAG 60.047 61.111 12.44 0.00 44.61 4.85
273 274 3.123620 GAGTGAAGCAGCGGCAGG 61.124 66.667 12.44 0.00 44.61 4.85
274 275 3.890936 GAGTGAAGCAGCGGCAGGT 62.891 63.158 12.44 0.00 44.61 4.00
275 276 2.980233 GTGAAGCAGCGGCAGGTT 60.980 61.111 12.44 9.62 44.61 3.50
276 277 1.671054 GTGAAGCAGCGGCAGGTTA 60.671 57.895 12.44 0.00 44.61 2.85
277 278 1.072332 TGAAGCAGCGGCAGGTTAA 59.928 52.632 12.44 0.00 44.61 2.01
278 279 0.536233 TGAAGCAGCGGCAGGTTAAA 60.536 50.000 12.44 0.00 44.61 1.52
279 280 0.109735 GAAGCAGCGGCAGGTTAAAC 60.110 55.000 12.44 0.00 44.61 2.01
280 281 1.524008 AAGCAGCGGCAGGTTAAACC 61.524 55.000 12.44 0.00 44.61 3.27
290 291 1.953772 GGTTAAACCTGCGGTGTGG 59.046 57.895 0.94 0.00 35.34 4.17
291 292 1.284715 GTTAAACCTGCGGTGTGGC 59.715 57.895 0.94 0.00 35.34 5.01
292 293 1.152943 TTAAACCTGCGGTGTGGCA 60.153 52.632 0.94 0.00 41.45 4.92
293 294 0.538516 TTAAACCTGCGGTGTGGCAT 60.539 50.000 0.94 0.00 42.99 4.40
294 295 0.958382 TAAACCTGCGGTGTGGCATC 60.958 55.000 0.94 0.00 42.99 3.91
295 296 2.974692 AAACCTGCGGTGTGGCATCA 62.975 55.000 0.94 0.00 42.99 3.07
296 297 2.672651 CCTGCGGTGTGGCATCAA 60.673 61.111 0.00 0.00 42.99 2.57
297 298 2.267351 CCTGCGGTGTGGCATCAAA 61.267 57.895 0.00 0.00 42.99 2.69
298 299 1.597797 CCTGCGGTGTGGCATCAAAT 61.598 55.000 0.00 0.00 42.99 2.32
299 300 0.179156 CTGCGGTGTGGCATCAAATC 60.179 55.000 0.00 0.00 42.99 2.17
300 301 1.139520 GCGGTGTGGCATCAAATCC 59.860 57.895 0.00 0.00 0.00 3.01
301 302 1.809207 CGGTGTGGCATCAAATCCC 59.191 57.895 0.00 0.00 0.00 3.85
333 334 1.444724 CCATGCGACGTCGTTGGTA 60.445 57.895 34.49 21.29 42.22 3.25
393 394 0.389687 TCATGCGACATCTGCGTTGA 60.390 50.000 0.00 0.00 34.24 3.18
429 430 0.460987 GCGACACTGCTGCCTAATCT 60.461 55.000 0.00 0.00 0.00 2.40
1301 1344 5.498069 CGATTTCAGAAATTGAAGCAATGCG 60.498 40.000 15.82 4.95 46.01 4.73
1375 1418 0.830648 CAGGGGAGCTCGATTTACCA 59.169 55.000 7.83 0.00 0.00 3.25
1427 1470 3.838271 GCGCGTCTGGATCTGGGA 61.838 66.667 8.43 0.00 0.00 4.37
1477 1520 1.852157 TGTGGGGGATGCAGGAGTT 60.852 57.895 0.00 0.00 0.00 3.01
1486 1529 0.108138 ATGCAGGAGTTACGGCAGAC 60.108 55.000 0.00 0.00 39.95 3.51
1496 1539 1.629043 TACGGCAGACCTGAAGAAGT 58.371 50.000 0.47 0.00 0.00 3.01
1594 1641 2.096466 TGTTTGTGTAATTGCTCTCGCG 60.096 45.455 0.00 0.00 39.65 5.87
1754 1802 3.113322 CAGTTCTTCAGTTCGTCGTCAA 58.887 45.455 0.00 0.00 0.00 3.18
1814 1866 1.652563 GTCCACAGTTGCCCGAAAC 59.347 57.895 0.00 0.00 0.00 2.78
2206 2262 4.640789 TTGTGCTACGGTGTTTTCAAAT 57.359 36.364 0.00 0.00 0.00 2.32
2292 2349 2.829120 GCCCCTAGTAGCATCTCCTTAG 59.171 54.545 0.00 0.00 0.00 2.18
2496 2553 0.106708 GCACAATAGAGGGGCATCGA 59.893 55.000 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.203052 GAAGGACGGACGACACCATAA 59.797 52.381 0.00 0.00 0.00 1.90
1 2 0.813184 GAAGGACGGACGACACCATA 59.187 55.000 0.00 0.00 0.00 2.74
2 3 0.898789 AGAAGGACGGACGACACCAT 60.899 55.000 0.00 0.00 0.00 3.55
3 4 1.521450 GAGAAGGACGGACGACACCA 61.521 60.000 0.00 0.00 0.00 4.17
4 5 1.212229 GAGAAGGACGGACGACACC 59.788 63.158 0.00 0.00 0.00 4.16
5 6 1.212229 GGAGAAGGACGGACGACAC 59.788 63.158 0.00 0.00 0.00 3.67
6 7 1.074423 AGGAGAAGGACGGACGACA 59.926 57.895 0.00 0.00 0.00 4.35
7 8 1.507174 CAGGAGAAGGACGGACGAC 59.493 63.158 0.00 0.00 0.00 4.34
8 9 1.677966 CCAGGAGAAGGACGGACGA 60.678 63.158 0.00 0.00 0.00 4.20
9 10 2.711922 CCCAGGAGAAGGACGGACG 61.712 68.421 0.00 0.00 0.00 4.79
10 11 3.020237 GCCCAGGAGAAGGACGGAC 62.020 68.421 0.00 0.00 0.00 4.79
11 12 2.683933 GCCCAGGAGAAGGACGGA 60.684 66.667 0.00 0.00 0.00 4.69
12 13 2.685380 AGCCCAGGAGAAGGACGG 60.685 66.667 0.00 0.00 0.00 4.79
13 14 2.581354 CAGCCCAGGAGAAGGACG 59.419 66.667 0.00 0.00 0.00 4.79
14 15 2.250741 GAGCAGCCCAGGAGAAGGAC 62.251 65.000 0.00 0.00 0.00 3.85
15 16 1.992277 GAGCAGCCCAGGAGAAGGA 60.992 63.158 0.00 0.00 0.00 3.36
16 17 2.588989 GAGCAGCCCAGGAGAAGG 59.411 66.667 0.00 0.00 0.00 3.46
17 18 2.588989 GGAGCAGCCCAGGAGAAG 59.411 66.667 0.00 0.00 0.00 2.85
18 19 3.393970 CGGAGCAGCCCAGGAGAA 61.394 66.667 0.00 0.00 0.00 2.87
31 32 2.050350 TAAGGACCCTGTCGCGGAG 61.050 63.158 6.13 2.18 32.65 4.63
32 33 2.036098 TAAGGACCCTGTCGCGGA 59.964 61.111 6.13 0.00 32.65 5.54
33 34 2.183555 GTAAGGACCCTGTCGCGG 59.816 66.667 6.13 0.00 32.65 6.46
34 35 2.183555 GGTAAGGACCCTGTCGCG 59.816 66.667 0.00 0.00 40.23 5.87
35 36 2.183555 CGGTAAGGACCCTGTCGC 59.816 66.667 0.00 0.00 43.64 5.19
36 37 1.980772 ACCGGTAAGGACCCTGTCG 60.981 63.158 4.49 0.00 43.64 4.35
37 38 1.190178 ACACCGGTAAGGACCCTGTC 61.190 60.000 6.87 0.00 43.64 3.51
38 39 0.765519 AACACCGGTAAGGACCCTGT 60.766 55.000 6.87 0.00 43.64 4.00
39 40 0.036671 GAACACCGGTAAGGACCCTG 60.037 60.000 6.87 0.00 43.64 4.45
40 41 0.472352 TGAACACCGGTAAGGACCCT 60.472 55.000 6.87 0.00 43.64 4.34
41 42 0.321034 GTGAACACCGGTAAGGACCC 60.321 60.000 6.87 0.00 43.64 4.46
42 43 0.668401 CGTGAACACCGGTAAGGACC 60.668 60.000 6.87 0.00 45.00 4.46
43 44 0.314935 TCGTGAACACCGGTAAGGAC 59.685 55.000 6.87 0.85 45.00 3.85
44 45 0.599558 CTCGTGAACACCGGTAAGGA 59.400 55.000 6.87 3.91 45.00 3.36
46 47 2.163815 AGATCTCGTGAACACCGGTAAG 59.836 50.000 6.87 0.00 0.00 2.34
47 48 2.165167 AGATCTCGTGAACACCGGTAA 58.835 47.619 6.87 0.00 0.00 2.85
48 49 1.830279 AGATCTCGTGAACACCGGTA 58.170 50.000 6.87 0.00 0.00 4.02
49 50 1.743958 CTAGATCTCGTGAACACCGGT 59.256 52.381 0.00 0.00 0.00 5.28
50 51 1.534175 GCTAGATCTCGTGAACACCGG 60.534 57.143 0.00 0.00 0.00 5.28
51 52 1.534175 GGCTAGATCTCGTGAACACCG 60.534 57.143 0.00 0.00 0.00 4.94
52 53 1.534175 CGGCTAGATCTCGTGAACACC 60.534 57.143 0.00 0.00 0.00 4.16
53 54 1.132643 ACGGCTAGATCTCGTGAACAC 59.867 52.381 7.11 0.00 35.70 3.32
54 55 1.460504 ACGGCTAGATCTCGTGAACA 58.539 50.000 7.11 0.00 35.70 3.18
55 56 2.452105 GAACGGCTAGATCTCGTGAAC 58.548 52.381 8.52 1.65 37.20 3.18
56 57 1.404391 GGAACGGCTAGATCTCGTGAA 59.596 52.381 8.52 0.00 37.20 3.18
57 58 1.022735 GGAACGGCTAGATCTCGTGA 58.977 55.000 8.52 0.00 37.20 4.35
58 59 1.002251 GAGGAACGGCTAGATCTCGTG 60.002 57.143 8.52 0.00 37.20 4.35
59 60 1.310904 GAGGAACGGCTAGATCTCGT 58.689 55.000 0.00 0.00 38.89 4.18
60 61 0.594110 GGAGGAACGGCTAGATCTCG 59.406 60.000 0.00 0.00 0.00 4.04
61 62 1.883926 GAGGAGGAACGGCTAGATCTC 59.116 57.143 0.00 0.00 0.00 2.75
62 63 1.816183 CGAGGAGGAACGGCTAGATCT 60.816 57.143 0.00 0.00 0.00 2.75
63 64 0.594110 CGAGGAGGAACGGCTAGATC 59.406 60.000 0.00 0.00 0.00 2.75
64 65 0.824182 CCGAGGAGGAACGGCTAGAT 60.824 60.000 0.00 0.00 45.00 1.98
65 66 1.453379 CCGAGGAGGAACGGCTAGA 60.453 63.158 0.00 0.00 45.00 2.43
66 67 2.491022 CCCGAGGAGGAACGGCTAG 61.491 68.421 0.00 0.00 46.59 3.42
67 68 2.441532 CCCGAGGAGGAACGGCTA 60.442 66.667 0.00 0.00 46.59 3.93
87 88 4.120331 GTCATGGGCAGCCAACGC 62.120 66.667 15.19 0.00 0.00 4.84
88 89 3.803082 CGTCATGGGCAGCCAACG 61.803 66.667 15.19 13.15 0.00 4.10
89 90 1.926511 CTTCGTCATGGGCAGCCAAC 61.927 60.000 15.19 4.61 0.00 3.77
90 91 1.675310 CTTCGTCATGGGCAGCCAA 60.675 57.895 15.19 0.58 0.00 4.52
91 92 2.046023 CTTCGTCATGGGCAGCCA 60.046 61.111 15.19 0.00 0.00 4.75
92 93 3.512516 GCTTCGTCATGGGCAGCC 61.513 66.667 1.26 1.26 0.00 4.85
93 94 3.869272 CGCTTCGTCATGGGCAGC 61.869 66.667 0.00 0.00 0.00 5.25
94 95 3.197790 CCGCTTCGTCATGGGCAG 61.198 66.667 0.00 0.00 0.00 4.85
95 96 4.015406 ACCGCTTCGTCATGGGCA 62.015 61.111 0.00 0.00 0.00 5.36
96 97 3.499737 CACCGCTTCGTCATGGGC 61.500 66.667 0.00 0.00 0.00 5.36
97 98 2.047274 ACACCGCTTCGTCATGGG 60.047 61.111 0.00 0.00 0.00 4.00
98 99 2.444624 CGACACCGCTTCGTCATGG 61.445 63.158 0.00 0.00 32.24 3.66
99 100 3.072598 CGACACCGCTTCGTCATG 58.927 61.111 0.00 0.00 32.24 3.07
116 117 3.680620 TACCATGCTCCACCGCAGC 62.681 63.158 0.00 0.00 44.10 5.25
117 118 1.522355 CTACCATGCTCCACCGCAG 60.522 63.158 0.00 0.00 44.10 5.18
118 119 1.960040 CTCTACCATGCTCCACCGCA 61.960 60.000 0.00 0.00 45.10 5.69
119 120 1.227380 CTCTACCATGCTCCACCGC 60.227 63.158 0.00 0.00 0.00 5.68
120 121 1.043816 ATCTCTACCATGCTCCACCG 58.956 55.000 0.00 0.00 0.00 4.94
121 122 1.071385 CCATCTCTACCATGCTCCACC 59.929 57.143 0.00 0.00 0.00 4.61
122 123 1.765314 ACCATCTCTACCATGCTCCAC 59.235 52.381 0.00 0.00 0.00 4.02
123 124 1.764723 CACCATCTCTACCATGCTCCA 59.235 52.381 0.00 0.00 0.00 3.86
124 125 1.071385 CCACCATCTCTACCATGCTCC 59.929 57.143 0.00 0.00 0.00 4.70
125 126 2.036992 CTCCACCATCTCTACCATGCTC 59.963 54.545 0.00 0.00 0.00 4.26
126 127 2.045524 CTCCACCATCTCTACCATGCT 58.954 52.381 0.00 0.00 0.00 3.79
127 128 1.542108 GCTCCACCATCTCTACCATGC 60.542 57.143 0.00 0.00 0.00 4.06
128 129 1.269988 CGCTCCACCATCTCTACCATG 60.270 57.143 0.00 0.00 0.00 3.66
129 130 1.043816 CGCTCCACCATCTCTACCAT 58.956 55.000 0.00 0.00 0.00 3.55
130 131 0.324368 ACGCTCCACCATCTCTACCA 60.324 55.000 0.00 0.00 0.00 3.25
131 132 0.824759 AACGCTCCACCATCTCTACC 59.175 55.000 0.00 0.00 0.00 3.18
132 133 2.271800 CAAACGCTCCACCATCTCTAC 58.728 52.381 0.00 0.00 0.00 2.59
133 134 1.207089 CCAAACGCTCCACCATCTCTA 59.793 52.381 0.00 0.00 0.00 2.43
134 135 0.036010 CCAAACGCTCCACCATCTCT 60.036 55.000 0.00 0.00 0.00 3.10
135 136 1.026718 CCCAAACGCTCCACCATCTC 61.027 60.000 0.00 0.00 0.00 2.75
136 137 1.002134 CCCAAACGCTCCACCATCT 60.002 57.895 0.00 0.00 0.00 2.90
137 138 2.700773 GCCCAAACGCTCCACCATC 61.701 63.158 0.00 0.00 0.00 3.51
138 139 2.676471 GCCCAAACGCTCCACCAT 60.676 61.111 0.00 0.00 0.00 3.55
139 140 4.196778 TGCCCAAACGCTCCACCA 62.197 61.111 0.00 0.00 0.00 4.17
140 141 3.670377 GTGCCCAAACGCTCCACC 61.670 66.667 0.00 0.00 0.00 4.61
141 142 4.025401 CGTGCCCAAACGCTCCAC 62.025 66.667 0.00 0.00 36.65 4.02
145 146 4.572571 TTCCCGTGCCCAAACGCT 62.573 61.111 0.00 0.00 42.23 5.07
146 147 3.551887 CTTTCCCGTGCCCAAACGC 62.552 63.158 0.00 0.00 42.23 4.84
147 148 2.642700 CTTTCCCGTGCCCAAACG 59.357 61.111 0.00 0.00 43.20 3.60
148 149 1.744320 AAGCTTTCCCGTGCCCAAAC 61.744 55.000 0.00 0.00 0.00 2.93
149 150 1.456705 AAGCTTTCCCGTGCCCAAA 60.457 52.632 0.00 0.00 0.00 3.28
150 151 2.197324 AAGCTTTCCCGTGCCCAA 59.803 55.556 0.00 0.00 0.00 4.12
151 152 2.597217 CAAGCTTTCCCGTGCCCA 60.597 61.111 0.00 0.00 0.00 5.36
152 153 3.373565 CCAAGCTTTCCCGTGCCC 61.374 66.667 0.00 0.00 0.00 5.36
153 154 3.373565 CCCAAGCTTTCCCGTGCC 61.374 66.667 0.00 0.00 0.00 5.01
154 155 4.056125 GCCCAAGCTTTCCCGTGC 62.056 66.667 0.00 0.00 35.50 5.34
155 156 3.737172 CGCCCAAGCTTTCCCGTG 61.737 66.667 0.00 0.00 36.60 4.94
158 159 2.770132 CTTTGCGCCCAAGCTTTCCC 62.770 60.000 4.18 0.00 38.13 3.97
159 160 1.373371 CTTTGCGCCCAAGCTTTCC 60.373 57.895 4.18 0.00 38.13 3.13
160 161 0.031994 TTCTTTGCGCCCAAGCTTTC 59.968 50.000 4.18 0.00 38.13 2.62
161 162 0.032540 CTTCTTTGCGCCCAAGCTTT 59.967 50.000 4.18 0.00 38.13 3.51
162 163 0.823356 TCTTCTTTGCGCCCAAGCTT 60.823 50.000 4.18 0.00 38.13 3.74
163 164 0.823356 TTCTTCTTTGCGCCCAAGCT 60.823 50.000 4.18 0.00 38.13 3.74
164 165 0.387750 CTTCTTCTTTGCGCCCAAGC 60.388 55.000 4.18 0.00 37.71 4.01
165 166 1.238439 TCTTCTTCTTTGCGCCCAAG 58.762 50.000 4.18 7.60 31.52 3.61
166 167 1.608590 CTTCTTCTTCTTTGCGCCCAA 59.391 47.619 4.18 0.00 0.00 4.12
167 168 1.202758 TCTTCTTCTTCTTTGCGCCCA 60.203 47.619 4.18 0.00 0.00 5.36
168 169 1.466558 CTCTTCTTCTTCTTTGCGCCC 59.533 52.381 4.18 0.00 0.00 6.13
169 170 1.466558 CCTCTTCTTCTTCTTTGCGCC 59.533 52.381 4.18 0.00 0.00 6.53
170 171 2.414825 CTCCTCTTCTTCTTCTTTGCGC 59.585 50.000 0.00 0.00 0.00 6.09
171 172 2.414825 GCTCCTCTTCTTCTTCTTTGCG 59.585 50.000 0.00 0.00 0.00 4.85
172 173 2.414825 CGCTCCTCTTCTTCTTCTTTGC 59.585 50.000 0.00 0.00 0.00 3.68
173 174 3.919216 TCGCTCCTCTTCTTCTTCTTTG 58.081 45.455 0.00 0.00 0.00 2.77
174 175 3.829601 TCTCGCTCCTCTTCTTCTTCTTT 59.170 43.478 0.00 0.00 0.00 2.52
175 176 3.426615 TCTCGCTCCTCTTCTTCTTCTT 58.573 45.455 0.00 0.00 0.00 2.52
176 177 3.016736 CTCTCGCTCCTCTTCTTCTTCT 58.983 50.000 0.00 0.00 0.00 2.85
177 178 2.099098 CCTCTCGCTCCTCTTCTTCTTC 59.901 54.545 0.00 0.00 0.00 2.87
178 179 2.099405 CCTCTCGCTCCTCTTCTTCTT 58.901 52.381 0.00 0.00 0.00 2.52
179 180 1.684869 CCCTCTCGCTCCTCTTCTTCT 60.685 57.143 0.00 0.00 0.00 2.85
180 181 0.744281 CCCTCTCGCTCCTCTTCTTC 59.256 60.000 0.00 0.00 0.00 2.87
181 182 0.333312 TCCCTCTCGCTCCTCTTCTT 59.667 55.000 0.00 0.00 0.00 2.52
182 183 0.333312 TTCCCTCTCGCTCCTCTTCT 59.667 55.000 0.00 0.00 0.00 2.85
183 184 1.068434 CATTCCCTCTCGCTCCTCTTC 59.932 57.143 0.00 0.00 0.00 2.87
184 185 1.118838 CATTCCCTCTCGCTCCTCTT 58.881 55.000 0.00 0.00 0.00 2.85
185 186 0.758685 CCATTCCCTCTCGCTCCTCT 60.759 60.000 0.00 0.00 0.00 3.69
186 187 1.745264 CCATTCCCTCTCGCTCCTC 59.255 63.158 0.00 0.00 0.00 3.71
187 188 1.764054 CCCATTCCCTCTCGCTCCT 60.764 63.158 0.00 0.00 0.00 3.69
188 189 1.753368 CTCCCATTCCCTCTCGCTCC 61.753 65.000 0.00 0.00 0.00 4.70
189 190 1.745264 CTCCCATTCCCTCTCGCTC 59.255 63.158 0.00 0.00 0.00 5.03
190 191 2.439104 GCTCCCATTCCCTCTCGCT 61.439 63.158 0.00 0.00 0.00 4.93
191 192 2.110006 GCTCCCATTCCCTCTCGC 59.890 66.667 0.00 0.00 0.00 5.03
192 193 2.419198 CGCTCCCATTCCCTCTCG 59.581 66.667 0.00 0.00 0.00 4.04
193 194 1.338136 TTCCGCTCCCATTCCCTCTC 61.338 60.000 0.00 0.00 0.00 3.20
194 195 0.914417 TTTCCGCTCCCATTCCCTCT 60.914 55.000 0.00 0.00 0.00 3.69
195 196 0.748367 GTTTCCGCTCCCATTCCCTC 60.748 60.000 0.00 0.00 0.00 4.30
196 197 1.303282 GTTTCCGCTCCCATTCCCT 59.697 57.895 0.00 0.00 0.00 4.20
197 198 1.753078 GGTTTCCGCTCCCATTCCC 60.753 63.158 0.00 0.00 0.00 3.97
198 199 0.323451 AAGGTTTCCGCTCCCATTCC 60.323 55.000 0.00 0.00 0.00 3.01
199 200 1.095600 GAAGGTTTCCGCTCCCATTC 58.904 55.000 0.00 0.00 0.00 2.67
200 201 0.323451 GGAAGGTTTCCGCTCCCATT 60.323 55.000 0.00 0.00 40.59 3.16
201 202 1.303282 GGAAGGTTTCCGCTCCCAT 59.697 57.895 0.00 0.00 40.59 4.00
202 203 2.754375 GGAAGGTTTCCGCTCCCA 59.246 61.111 0.00 0.00 40.59 4.37
210 211 7.866898 GGAATAGTAGATACGAAGGAAGGTTTC 59.133 40.741 0.00 0.00 0.00 2.78
211 212 7.201983 GGGAATAGTAGATACGAAGGAAGGTTT 60.202 40.741 0.00 0.00 0.00 3.27
212 213 6.267242 GGGAATAGTAGATACGAAGGAAGGTT 59.733 42.308 0.00 0.00 0.00 3.50
213 214 5.774184 GGGAATAGTAGATACGAAGGAAGGT 59.226 44.000 0.00 0.00 0.00 3.50
214 215 6.011481 AGGGAATAGTAGATACGAAGGAAGG 58.989 44.000 0.00 0.00 0.00 3.46
215 216 7.014422 ACAAGGGAATAGTAGATACGAAGGAAG 59.986 40.741 0.00 0.00 0.00 3.46
216 217 6.837568 ACAAGGGAATAGTAGATACGAAGGAA 59.162 38.462 0.00 0.00 0.00 3.36
217 218 6.371278 ACAAGGGAATAGTAGATACGAAGGA 58.629 40.000 0.00 0.00 0.00 3.36
218 219 6.651975 ACAAGGGAATAGTAGATACGAAGG 57.348 41.667 0.00 0.00 0.00 3.46
220 221 9.458727 CCTATACAAGGGAATAGTAGATACGAA 57.541 37.037 0.00 0.00 42.32 3.85
236 237 4.156477 CTCTCCTCTTCCCCTATACAAGG 58.844 52.174 0.00 0.00 46.09 3.61
237 238 4.586841 CACTCTCCTCTTCCCCTATACAAG 59.413 50.000 0.00 0.00 0.00 3.16
238 239 4.232122 TCACTCTCCTCTTCCCCTATACAA 59.768 45.833 0.00 0.00 0.00 2.41
239 240 3.792114 TCACTCTCCTCTTCCCCTATACA 59.208 47.826 0.00 0.00 0.00 2.29
240 241 4.456662 TCACTCTCCTCTTCCCCTATAC 57.543 50.000 0.00 0.00 0.00 1.47
241 242 4.693058 GCTTCACTCTCCTCTTCCCCTATA 60.693 50.000 0.00 0.00 0.00 1.31
242 243 3.922375 CTTCACTCTCCTCTTCCCCTAT 58.078 50.000 0.00 0.00 0.00 2.57
243 244 2.624557 GCTTCACTCTCCTCTTCCCCTA 60.625 54.545 0.00 0.00 0.00 3.53
244 245 1.899438 GCTTCACTCTCCTCTTCCCCT 60.899 57.143 0.00 0.00 0.00 4.79
245 246 0.539518 GCTTCACTCTCCTCTTCCCC 59.460 60.000 0.00 0.00 0.00 4.81
246 247 1.206849 CTGCTTCACTCTCCTCTTCCC 59.793 57.143 0.00 0.00 0.00 3.97
247 248 1.405391 GCTGCTTCACTCTCCTCTTCC 60.405 57.143 0.00 0.00 0.00 3.46
248 249 1.735369 CGCTGCTTCACTCTCCTCTTC 60.735 57.143 0.00 0.00 0.00 2.87
249 250 0.246086 CGCTGCTTCACTCTCCTCTT 59.754 55.000 0.00 0.00 0.00 2.85
250 251 1.603236 CCGCTGCTTCACTCTCCTCT 61.603 60.000 0.00 0.00 0.00 3.69
251 252 1.153667 CCGCTGCTTCACTCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
252 253 2.977178 CCGCTGCTTCACTCTCCT 59.023 61.111 0.00 0.00 0.00 3.69
253 254 2.817396 GCCGCTGCTTCACTCTCC 60.817 66.667 0.00 0.00 33.53 3.71
254 255 2.047844 TGCCGCTGCTTCACTCTC 60.048 61.111 0.70 0.00 38.71 3.20
255 256 2.047465 CTGCCGCTGCTTCACTCT 60.047 61.111 0.70 0.00 38.71 3.24
256 257 3.123620 CCTGCCGCTGCTTCACTC 61.124 66.667 0.70 0.00 38.71 3.51
257 258 2.111999 TAACCTGCCGCTGCTTCACT 62.112 55.000 0.70 0.00 38.71 3.41
258 259 1.234615 TTAACCTGCCGCTGCTTCAC 61.235 55.000 0.70 0.00 38.71 3.18
259 260 0.536233 TTTAACCTGCCGCTGCTTCA 60.536 50.000 0.70 0.00 38.71 3.02
260 261 0.109735 GTTTAACCTGCCGCTGCTTC 60.110 55.000 0.70 0.00 38.71 3.86
261 262 1.524008 GGTTTAACCTGCCGCTGCTT 61.524 55.000 6.92 0.00 38.71 3.91
262 263 1.971695 GGTTTAACCTGCCGCTGCT 60.972 57.895 6.92 0.00 38.71 4.24
263 264 2.566529 GGTTTAACCTGCCGCTGC 59.433 61.111 6.92 0.00 34.73 5.25
280 281 0.179156 GATTTGATGCCACACCGCAG 60.179 55.000 0.00 0.00 43.26 5.18
281 282 1.594194 GGATTTGATGCCACACCGCA 61.594 55.000 0.00 0.00 44.35 5.69
282 283 1.139520 GGATTTGATGCCACACCGC 59.860 57.895 0.00 0.00 0.00 5.68
283 284 1.809207 GGGATTTGATGCCACACCG 59.191 57.895 0.00 0.00 40.99 4.94
284 285 1.666209 CCGGGATTTGATGCCACACC 61.666 60.000 0.00 0.00 41.46 4.16
285 286 1.666209 CCCGGGATTTGATGCCACAC 61.666 60.000 18.48 0.00 41.46 3.82
286 287 1.379710 CCCGGGATTTGATGCCACA 60.380 57.895 18.48 0.00 41.46 4.17
287 288 2.785425 GCCCGGGATTTGATGCCAC 61.785 63.158 29.31 0.00 41.46 5.01
288 289 2.441901 GCCCGGGATTTGATGCCA 60.442 61.111 29.31 0.00 41.46 4.92
289 290 3.595758 CGCCCGGGATTTGATGCC 61.596 66.667 29.31 0.79 37.42 4.40
290 291 1.455383 ATTCGCCCGGGATTTGATGC 61.455 55.000 29.31 4.51 0.00 3.91
291 292 1.806542 CTATTCGCCCGGGATTTGATG 59.193 52.381 29.31 3.76 0.00 3.07
292 293 1.882352 GCTATTCGCCCGGGATTTGAT 60.882 52.381 29.31 12.42 0.00 2.57
293 294 0.534203 GCTATTCGCCCGGGATTTGA 60.534 55.000 29.31 13.25 0.00 2.69
294 295 0.535102 AGCTATTCGCCCGGGATTTG 60.535 55.000 29.31 10.73 40.39 2.32
295 296 0.250338 GAGCTATTCGCCCGGGATTT 60.250 55.000 29.31 7.89 40.39 2.17
296 297 1.371558 GAGCTATTCGCCCGGGATT 59.628 57.895 29.31 7.48 40.39 3.01
297 298 2.584391 GGAGCTATTCGCCCGGGAT 61.584 63.158 29.31 12.20 40.39 3.85
298 299 3.231736 GGAGCTATTCGCCCGGGA 61.232 66.667 29.31 2.74 40.39 5.14
299 300 4.315941 GGGAGCTATTCGCCCGGG 62.316 72.222 19.09 19.09 45.06 5.73
333 334 2.862536 CGTCGCATGAGAGACAATTCAT 59.137 45.455 0.00 0.00 43.73 2.57
429 430 9.872757 GATTCGAGTTTTAAACATGTGTCTTTA 57.127 29.630 10.60 0.00 0.00 1.85
1301 1344 2.128771 TCTAGCCACTCAAAATGGGC 57.871 50.000 0.00 0.00 46.77 5.36
1375 1418 0.035056 CCAACTTCTCCGCCTCCAAT 60.035 55.000 0.00 0.00 0.00 3.16
1427 1470 4.843331 ATGGGCGGATCCAGGGGT 62.843 66.667 13.41 0.00 40.56 4.95
1477 1520 1.629043 ACTTCTTCAGGTCTGCCGTA 58.371 50.000 0.00 0.00 40.50 4.02
1486 1529 3.879295 TCTGCTTGTTCAACTTCTTCAGG 59.121 43.478 0.00 0.00 0.00 3.86
1496 1539 5.589855 TGAGTTTCTTCATCTGCTTGTTCAA 59.410 36.000 0.00 0.00 0.00 2.69
1529 1572 3.025978 CCATCAAATTGCCCTGCTTCTA 58.974 45.455 0.00 0.00 0.00 2.10
1754 1802 4.597507 TCCCTCTACCACTGAAACTGAAAT 59.402 41.667 0.00 0.00 0.00 2.17
1851 1903 3.686227 TCAATGGGCCTGGATATGTTT 57.314 42.857 4.53 0.00 0.00 2.83
2496 2553 9.732453 TCTATCTATCTATGCTACTAGGGTACT 57.268 37.037 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.