Multiple sequence alignment - TraesCS7D01G231300

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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 TraesCS7D01G231300 chr7D 100.000 6442 0 0 1 6442 192375877 192369436 0.000000e+00 11897.0
1 TraesCS7D01G231300 chr7D 90.964 166 13 1 4259 4422 197927008 197927173 8.410000e-54 222.0
2 TraesCS7D01G231300 chr7A 95.583 5932 204 19 563 6442 201990889 201984964 0.000000e+00 9450.0
3 TraesCS7D01G231300 chr7A 93.939 264 12 3 263 524 201991148 201990887 4.680000e-106 396.0
4 TraesCS7D01G231300 chr7A 90.964 166 12 2 4247 4409 462978574 462978739 3.020000e-53 220.0
5 TraesCS7D01G231300 chr7A 82.677 127 21 1 276 401 610151572 610151698 1.900000e-20 111.0
6 TraesCS7D01G231300 chr7A 81.395 129 19 5 276 400 573837110 573837237 4.110000e-17 100.0
7 TraesCS7D01G231300 chr7B 96.661 4403 124 9 2059 6442 155473525 155469127 0.000000e+00 7295.0
8 TraesCS7D01G231300 chr7B 94.095 1829 73 16 245 2062 155475365 155473561 0.000000e+00 2747.0
9 TraesCS7D01G231300 chr7B 96.552 58 2 0 2 59 155475459 155475402 5.320000e-16 97.1
10 TraesCS7D01G231300 chr7B 100.000 31 0 0 193 223 155475393 155475363 2.510000e-04 58.4
11 TraesCS7D01G231300 chr4D 94.409 626 23 2 5818 6442 167197249 167197863 0.000000e+00 952.0
12 TraesCS7D01G231300 chr5A 91.071 168 12 2 4252 4417 86662177 86662011 2.340000e-54 224.0
13 TraesCS7D01G231300 chr5B 92.810 153 9 1 4259 4409 98663330 98663178 3.020000e-53 220.0
14 TraesCS7D01G231300 chr5B 87.368 95 12 0 280 374 489306560 489306466 6.830000e-20 110.0
15 TraesCS7D01G231300 chr1D 91.250 160 11 2 4259 4416 7349704 7349862 1.410000e-51 215.0
16 TraesCS7D01G231300 chr4B 90.244 164 14 2 4252 4413 658773057 658773220 5.060000e-51 213.0
17 TraesCS7D01G231300 chr2D 89.349 169 14 3 4250 4414 88290046 88290214 6.540000e-50 209.0
18 TraesCS7D01G231300 chr2B 90.909 99 9 0 277 375 66962287 66962385 4.050000e-27 134.0
19 TraesCS7D01G231300 chr1A 89.899 99 10 0 276 374 27264132 27264034 1.890000e-25 128.0
20 TraesCS7D01G231300 chr4A 81.890 127 21 1 276 400 210621496 210621622 8.830000e-19 106.0
21 TraesCS7D01G231300 chr3A 80.315 127 22 3 276 400 151650088 151649963 6.880000e-15 93.5


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 TraesCS7D01G231300 chr7D 192369436 192375877 6441 True 11897.000 11897 100.000 1 6442 1 chr7D.!!$R1 6441
1 TraesCS7D01G231300 chr7A 201984964 201991148 6184 True 4923.000 9450 94.761 263 6442 2 chr7A.!!$R1 6179
2 TraesCS7D01G231300 chr7B 155469127 155475459 6332 True 2549.375 7295 96.827 2 6442 4 chr7B.!!$R1 6440
3 TraesCS7D01G231300 chr4D 167197249 167197863 614 False 952.000 952 94.409 5818 6442 1 chr4D.!!$F1 624


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
157 158 0.314935 AACTGAGGTTGCATTTGCCG 59.685 50.000 0.00 0.0 41.18 5.69 F
161 162 0.316841 GAGGTTGCATTTGCCGGAAA 59.683 50.000 5.05 0.0 41.18 3.13 F
639 644 0.538977 AGTGGCATGTGCAAGCTCTT 60.539 50.000 7.36 0.0 44.36 2.85 F
2402 2474 0.179070 GGGAGGATTGAGAAGCCGAC 60.179 60.000 0.00 0.0 43.19 4.79 F
2496 2568 0.250295 ACATTCCAGTCACCACACCG 60.250 55.000 0.00 0.0 0.00 4.94 F
3846 3921 2.094649 GCTATACCCGTATGAGGCTGAC 60.095 54.545 0.00 0.0 0.00 3.51 F
4513 4594 1.328430 GGTACCGCTGCTTAGGACCT 61.328 60.000 0.00 0.0 0.00 3.85 F
4653 4734 2.570752 CTGGAGAGCCATGCAGGTATAT 59.429 50.000 0.00 0.0 44.91 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1367 0.250038 CTGCATACCTGTATGGCGCT 60.250 55.000 16.71 0.00 42.32 5.92 R
1428 1441 1.652124 CAACGGAACATACGAACCTCG 59.348 52.381 0.00 0.00 46.93 4.63 R
2445 2517 0.178903 TCCTACCCTGGCAAGTGACT 60.179 55.000 0.31 0.00 0.00 3.41 R
3834 3909 1.134965 ACAGAAGCGTCAGCCTCATAC 60.135 52.381 1.61 0.00 46.67 2.39 R
3955 4030 3.325716 AGCGAAGTACCTTGTAAAAGGGA 59.674 43.478 16.40 4.25 44.27 4.20 R
4798 4879 0.319211 TTGCTGACACGTACTTCCCG 60.319 55.000 0.00 0.00 0.00 5.14 R
5436 5521 0.676782 GACGCCCCATGCTGTTAGTT 60.677 55.000 0.00 0.00 38.05 2.24 R
6174 6269 6.105657 TGCAACATCAACAATCTGTATACG 57.894 37.500 0.00 0.00 0.00 3.06 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
30 31 4.833390 ACAGTCCTAATCACCACTAAAGC 58.167 43.478 0.00 0.00 0.00 3.51
59 60 4.736126 TGAATCACATGAGACGGTACAT 57.264 40.909 0.00 0.00 0.00 2.29
60 61 4.682787 TGAATCACATGAGACGGTACATC 58.317 43.478 0.00 0.00 0.00 3.06
62 63 5.592688 TGAATCACATGAGACGGTACATCTA 59.407 40.000 0.00 0.00 21.89 1.98
63 64 4.895224 TCACATGAGACGGTACATCTAC 57.105 45.455 0.00 0.00 21.89 2.59
64 65 4.266714 TCACATGAGACGGTACATCTACA 58.733 43.478 0.00 0.00 21.89 2.74
65 66 4.887655 TCACATGAGACGGTACATCTACAT 59.112 41.667 0.00 1.34 21.89 2.29
66 67 5.008712 TCACATGAGACGGTACATCTACATC 59.991 44.000 0.00 0.00 21.89 3.06
67 68 5.009110 CACATGAGACGGTACATCTACATCT 59.991 44.000 0.00 0.00 21.89 2.90
68 69 6.204882 CACATGAGACGGTACATCTACATCTA 59.795 42.308 0.00 0.00 21.89 1.98
69 70 6.771267 ACATGAGACGGTACATCTACATCTAA 59.229 38.462 0.00 0.00 21.89 2.10
70 71 6.862711 TGAGACGGTACATCTACATCTAAG 57.137 41.667 0.00 0.00 21.89 2.18
71 72 6.354938 TGAGACGGTACATCTACATCTAAGT 58.645 40.000 0.00 0.00 21.89 2.24
72 73 6.482641 TGAGACGGTACATCTACATCTAAGTC 59.517 42.308 0.00 0.00 21.89 3.01
73 74 5.466058 AGACGGTACATCTACATCTAAGTCG 59.534 44.000 0.00 0.00 0.00 4.18
74 75 4.514441 ACGGTACATCTACATCTAAGTCGG 59.486 45.833 0.00 0.00 0.00 4.79
75 76 4.514441 CGGTACATCTACATCTAAGTCGGT 59.486 45.833 0.00 0.00 0.00 4.69
76 77 5.333952 CGGTACATCTACATCTAAGTCGGTC 60.334 48.000 0.00 0.00 0.00 4.79
77 78 5.530171 GGTACATCTACATCTAAGTCGGTCA 59.470 44.000 0.00 0.00 0.00 4.02
78 79 6.039047 GGTACATCTACATCTAAGTCGGTCAA 59.961 42.308 0.00 0.00 0.00 3.18
79 80 6.137794 ACATCTACATCTAAGTCGGTCAAG 57.862 41.667 0.00 0.00 0.00 3.02
80 81 5.067936 ACATCTACATCTAAGTCGGTCAAGG 59.932 44.000 0.00 0.00 0.00 3.61
81 82 4.597004 TCTACATCTAAGTCGGTCAAGGT 58.403 43.478 0.00 0.00 0.00 3.50
82 83 5.014858 TCTACATCTAAGTCGGTCAAGGTT 58.985 41.667 0.00 0.00 0.00 3.50
83 84 4.189639 ACATCTAAGTCGGTCAAGGTTC 57.810 45.455 0.00 0.00 0.00 3.62
84 85 3.833070 ACATCTAAGTCGGTCAAGGTTCT 59.167 43.478 0.00 0.00 0.00 3.01
85 86 4.283722 ACATCTAAGTCGGTCAAGGTTCTT 59.716 41.667 0.00 0.00 0.00 2.52
86 87 4.950205 TCTAAGTCGGTCAAGGTTCTTT 57.050 40.909 0.00 0.00 0.00 2.52
87 88 4.879598 TCTAAGTCGGTCAAGGTTCTTTC 58.120 43.478 0.00 0.00 0.00 2.62
88 89 3.840124 AAGTCGGTCAAGGTTCTTTCT 57.160 42.857 0.00 0.00 0.00 2.52
89 90 3.840124 AGTCGGTCAAGGTTCTTTCTT 57.160 42.857 0.00 0.00 0.00 2.52
90 91 4.152284 AGTCGGTCAAGGTTCTTTCTTT 57.848 40.909 0.00 0.00 0.00 2.52
91 92 4.524053 AGTCGGTCAAGGTTCTTTCTTTT 58.476 39.130 0.00 0.00 0.00 2.27
92 93 4.948004 AGTCGGTCAAGGTTCTTTCTTTTT 59.052 37.500 0.00 0.00 0.00 1.94
93 94 5.066117 AGTCGGTCAAGGTTCTTTCTTTTTC 59.934 40.000 0.00 0.00 0.00 2.29
94 95 4.034742 TCGGTCAAGGTTCTTTCTTTTTCG 59.965 41.667 0.00 0.00 0.00 3.46
95 96 4.034742 CGGTCAAGGTTCTTTCTTTTTCGA 59.965 41.667 0.00 0.00 0.00 3.71
96 97 5.448089 CGGTCAAGGTTCTTTCTTTTTCGAA 60.448 40.000 0.00 0.00 0.00 3.71
97 98 5.971792 GGTCAAGGTTCTTTCTTTTTCGAAG 59.028 40.000 0.00 0.00 0.00 3.79
98 99 5.455849 GTCAAGGTTCTTTCTTTTTCGAAGC 59.544 40.000 0.00 0.00 34.94 3.86
99 100 4.569761 AGGTTCTTTCTTTTTCGAAGCC 57.430 40.909 0.00 0.00 35.21 4.35
100 101 3.951680 AGGTTCTTTCTTTTTCGAAGCCA 59.048 39.130 0.00 0.00 35.21 4.75
101 102 4.036852 AGGTTCTTTCTTTTTCGAAGCCAG 59.963 41.667 0.00 0.00 35.21 4.85
102 103 4.202020 GGTTCTTTCTTTTTCGAAGCCAGT 60.202 41.667 0.00 0.00 0.00 4.00
103 104 5.340803 GTTCTTTCTTTTTCGAAGCCAGTT 58.659 37.500 0.00 0.00 0.00 3.16
104 105 5.576447 TCTTTCTTTTTCGAAGCCAGTTT 57.424 34.783 0.00 0.00 0.00 2.66
105 106 5.961272 TCTTTCTTTTTCGAAGCCAGTTTT 58.039 33.333 0.00 0.00 0.00 2.43
106 107 5.804979 TCTTTCTTTTTCGAAGCCAGTTTTG 59.195 36.000 0.00 0.00 0.00 2.44
107 108 4.974368 TCTTTTTCGAAGCCAGTTTTGA 57.026 36.364 0.00 0.00 0.00 2.69
108 109 5.317733 TCTTTTTCGAAGCCAGTTTTGAA 57.682 34.783 0.00 0.00 0.00 2.69
109 110 5.715070 TCTTTTTCGAAGCCAGTTTTGAAA 58.285 33.333 0.00 5.76 38.21 2.69
110 111 6.159988 TCTTTTTCGAAGCCAGTTTTGAAAA 58.840 32.000 14.71 14.71 43.53 2.29
112 113 6.976636 TTTTCGAAGCCAGTTTTGAAAAAT 57.023 29.167 15.78 0.00 42.85 1.82
113 114 5.964887 TTCGAAGCCAGTTTTGAAAAATG 57.035 34.783 10.79 10.79 29.63 2.32
114 115 3.801594 TCGAAGCCAGTTTTGAAAAATGC 59.198 39.130 12.13 8.15 0.00 3.56
115 116 3.555139 CGAAGCCAGTTTTGAAAAATGCA 59.445 39.130 12.13 0.00 0.00 3.96
116 117 4.033817 CGAAGCCAGTTTTGAAAAATGCAA 59.966 37.500 12.13 0.00 0.00 4.08
117 118 5.277442 CGAAGCCAGTTTTGAAAAATGCAAT 60.277 36.000 12.13 0.86 0.00 3.56
118 119 6.453926 AAGCCAGTTTTGAAAAATGCAATT 57.546 29.167 12.13 4.25 38.98 2.32
132 133 6.930667 AAATGCAATTTCAGCTTCACTTTT 57.069 29.167 0.00 0.00 44.81 2.27
133 134 6.535274 AATGCAATTTCAGCTTCACTTTTC 57.465 33.333 0.00 0.00 26.74 2.29
134 135 5.008619 TGCAATTTCAGCTTCACTTTTCA 57.991 34.783 0.00 0.00 0.00 2.69
135 136 4.805192 TGCAATTTCAGCTTCACTTTTCAC 59.195 37.500 0.00 0.00 0.00 3.18
136 137 4.805192 GCAATTTCAGCTTCACTTTTCACA 59.195 37.500 0.00 0.00 0.00 3.58
137 138 5.291614 GCAATTTCAGCTTCACTTTTCACAA 59.708 36.000 0.00 0.00 0.00 3.33
138 139 6.183360 GCAATTTCAGCTTCACTTTTCACAAA 60.183 34.615 0.00 0.00 0.00 2.83
139 140 7.623925 GCAATTTCAGCTTCACTTTTCACAAAA 60.624 33.333 0.00 0.00 0.00 2.44
140 141 6.704512 TTTCAGCTTCACTTTTCACAAAAC 57.295 33.333 0.00 0.00 0.00 2.43
141 142 5.643379 TCAGCTTCACTTTTCACAAAACT 57.357 34.783 0.00 0.00 0.00 2.66
142 143 5.401550 TCAGCTTCACTTTTCACAAAACTG 58.598 37.500 0.00 0.00 0.00 3.16
143 144 5.182950 TCAGCTTCACTTTTCACAAAACTGA 59.817 36.000 0.00 0.00 0.00 3.41
144 145 5.514204 CAGCTTCACTTTTCACAAAACTGAG 59.486 40.000 0.00 0.00 29.28 3.35
145 146 4.800471 GCTTCACTTTTCACAAAACTGAGG 59.200 41.667 0.00 0.00 29.28 3.86
146 147 5.622233 GCTTCACTTTTCACAAAACTGAGGT 60.622 40.000 0.00 0.00 29.46 3.85
147 148 5.975693 TCACTTTTCACAAAACTGAGGTT 57.024 34.783 0.00 0.00 37.24 3.50
148 149 5.708948 TCACTTTTCACAAAACTGAGGTTG 58.291 37.500 0.00 0.00 35.63 3.77
149 150 4.327087 CACTTTTCACAAAACTGAGGTTGC 59.673 41.667 0.00 0.00 35.63 4.17
150 151 4.021544 ACTTTTCACAAAACTGAGGTTGCA 60.022 37.500 0.00 0.00 35.63 4.08
151 152 4.734398 TTTCACAAAACTGAGGTTGCAT 57.266 36.364 0.00 0.00 35.63 3.96
152 153 4.734398 TTCACAAAACTGAGGTTGCATT 57.266 36.364 0.00 0.00 35.63 3.56
153 154 4.734398 TCACAAAACTGAGGTTGCATTT 57.266 36.364 0.00 0.00 35.63 2.32
154 155 4.431809 TCACAAAACTGAGGTTGCATTTG 58.568 39.130 4.12 4.12 35.63 2.32
155 156 3.001533 CACAAAACTGAGGTTGCATTTGC 59.998 43.478 5.32 0.00 42.50 3.68
156 157 2.531522 AAACTGAGGTTGCATTTGCC 57.468 45.000 0.00 0.00 41.18 4.52
157 158 0.314935 AACTGAGGTTGCATTTGCCG 59.685 50.000 0.00 0.00 41.18 5.69
158 159 1.213537 CTGAGGTTGCATTTGCCGG 59.786 57.895 0.00 0.00 41.18 6.13
159 160 1.228398 TGAGGTTGCATTTGCCGGA 60.228 52.632 5.05 0.00 41.18 5.14
160 161 0.825425 TGAGGTTGCATTTGCCGGAA 60.825 50.000 5.05 0.00 41.18 4.30
161 162 0.316841 GAGGTTGCATTTGCCGGAAA 59.683 50.000 5.05 0.00 41.18 3.13
162 163 0.975887 AGGTTGCATTTGCCGGAAAT 59.024 45.000 5.05 5.80 41.18 2.17
163 164 2.165437 GAGGTTGCATTTGCCGGAAATA 59.835 45.455 5.05 0.00 41.18 1.40
164 165 2.166254 AGGTTGCATTTGCCGGAAATAG 59.834 45.455 5.05 0.00 41.18 1.73
165 166 2.165437 GGTTGCATTTGCCGGAAATAGA 59.835 45.455 5.05 0.00 41.18 1.98
166 167 3.179048 GTTGCATTTGCCGGAAATAGAC 58.821 45.455 5.05 4.78 41.18 2.59
167 168 2.722094 TGCATTTGCCGGAAATAGACT 58.278 42.857 5.05 0.00 41.18 3.24
168 169 3.088532 TGCATTTGCCGGAAATAGACTT 58.911 40.909 5.05 0.00 41.18 3.01
169 170 4.265893 TGCATTTGCCGGAAATAGACTTA 58.734 39.130 5.05 0.00 41.18 2.24
170 171 4.702612 TGCATTTGCCGGAAATAGACTTAA 59.297 37.500 5.05 0.00 41.18 1.85
171 172 5.184096 TGCATTTGCCGGAAATAGACTTAAA 59.816 36.000 5.05 0.00 41.18 1.52
172 173 5.515270 GCATTTGCCGGAAATAGACTTAAAC 59.485 40.000 5.05 0.00 32.65 2.01
173 174 4.932268 TTGCCGGAAATAGACTTAAACG 57.068 40.909 5.05 0.00 0.00 3.60
174 175 3.929094 TGCCGGAAATAGACTTAAACGT 58.071 40.909 5.05 0.00 0.00 3.99
175 176 4.317488 TGCCGGAAATAGACTTAAACGTT 58.683 39.130 5.05 0.00 0.00 3.99
176 177 5.477510 TGCCGGAAATAGACTTAAACGTTA 58.522 37.500 5.05 0.00 0.00 3.18
177 178 5.577945 TGCCGGAAATAGACTTAAACGTTAG 59.422 40.000 5.05 0.00 0.00 2.34
178 179 5.807011 GCCGGAAATAGACTTAAACGTTAGA 59.193 40.000 5.05 0.00 0.00 2.10
179 180 6.311200 GCCGGAAATAGACTTAAACGTTAGAA 59.689 38.462 5.05 0.00 0.00 2.10
180 181 7.148590 GCCGGAAATAGACTTAAACGTTAGAAA 60.149 37.037 5.05 0.00 0.00 2.52
181 182 8.711457 CCGGAAATAGACTTAAACGTTAGAAAA 58.289 33.333 0.00 0.00 0.00 2.29
221 222 8.240682 AGTAGTAGCATAGCGATCTCTTATTTG 58.759 37.037 0.00 0.00 0.00 2.32
222 223 6.987386 AGTAGCATAGCGATCTCTTATTTGT 58.013 36.000 0.00 0.00 0.00 2.83
223 224 7.437748 AGTAGCATAGCGATCTCTTATTTGTT 58.562 34.615 0.00 0.00 0.00 2.83
224 225 6.536731 AGCATAGCGATCTCTTATTTGTTG 57.463 37.500 0.00 0.00 0.00 3.33
225 226 5.468072 AGCATAGCGATCTCTTATTTGTTGG 59.532 40.000 0.00 0.00 0.00 3.77
226 227 5.334414 GCATAGCGATCTCTTATTTGTTGGG 60.334 44.000 0.00 0.00 0.00 4.12
227 228 4.487714 AGCGATCTCTTATTTGTTGGGA 57.512 40.909 0.00 0.00 0.00 4.37
228 229 4.192317 AGCGATCTCTTATTTGTTGGGAC 58.808 43.478 0.00 0.00 0.00 4.46
229 230 3.938963 GCGATCTCTTATTTGTTGGGACA 59.061 43.478 0.00 0.00 0.00 4.02
230 231 4.576463 GCGATCTCTTATTTGTTGGGACAT 59.424 41.667 0.00 0.00 39.30 3.06
231 232 5.066505 GCGATCTCTTATTTGTTGGGACATT 59.933 40.000 0.00 0.00 39.30 2.71
232 233 6.260050 GCGATCTCTTATTTGTTGGGACATTA 59.740 38.462 0.00 0.00 39.30 1.90
233 234 7.519008 GCGATCTCTTATTTGTTGGGACATTAG 60.519 40.741 0.00 0.00 39.30 1.73
234 235 7.519008 CGATCTCTTATTTGTTGGGACATTAGC 60.519 40.741 0.00 0.00 39.30 3.09
235 236 6.480763 TCTCTTATTTGTTGGGACATTAGCA 58.519 36.000 0.00 0.00 39.30 3.49
236 237 6.945435 TCTCTTATTTGTTGGGACATTAGCAA 59.055 34.615 0.00 0.00 39.30 3.91
237 238 7.450014 TCTCTTATTTGTTGGGACATTAGCAAA 59.550 33.333 0.00 0.00 39.30 3.68
238 239 8.133024 TCTTATTTGTTGGGACATTAGCAAAT 57.867 30.769 0.00 0.00 39.30 2.32
239 240 8.592809 TCTTATTTGTTGGGACATTAGCAAATT 58.407 29.630 0.00 0.00 39.30 1.82
240 241 9.868277 CTTATTTGTTGGGACATTAGCAAATTA 57.132 29.630 0.00 0.00 39.30 1.40
244 245 8.588290 TTGTTGGGACATTAGCAAATTATAGT 57.412 30.769 0.00 0.00 39.30 2.12
293 294 8.508875 ACATGCAATTTGATTCAAAGGATTTTC 58.491 29.630 16.34 2.81 35.03 2.29
484 488 6.584563 CGAGAAAAGAACACTTTGTTTTTCCA 59.415 34.615 10.50 0.00 41.28 3.53
542 546 3.347958 TTGAAAAATGAGCACGACACC 57.652 42.857 0.00 0.00 0.00 4.16
554 558 2.866460 GCACGACACCGCAATCCTATAT 60.866 50.000 0.00 0.00 39.95 0.86
555 559 3.390135 CACGACACCGCAATCCTATATT 58.610 45.455 0.00 0.00 39.95 1.28
598 603 2.403252 ATTCCGCGAATCAAAGAGGT 57.597 45.000 8.23 0.00 0.00 3.85
599 604 1.438651 TTCCGCGAATCAAAGAGGTG 58.561 50.000 8.23 0.00 0.00 4.00
602 607 1.640428 CGCGAATCAAAGAGGTGCTA 58.360 50.000 0.00 0.00 0.00 3.49
639 644 0.538977 AGTGGCATGTGCAAGCTCTT 60.539 50.000 7.36 0.00 44.36 2.85
673 678 2.420547 CCCATTTCTTCATCCTCTGCGA 60.421 50.000 0.00 0.00 0.00 5.10
708 714 0.972983 ACTAGAGCCATGCACGACCT 60.973 55.000 0.00 0.00 0.00 3.85
760 766 2.276869 TGGAGTGAGTGATCCACCG 58.723 57.895 0.00 0.00 40.70 4.94
801 807 1.619669 GTCCCTCCCACCATCCCTT 60.620 63.158 0.00 0.00 0.00 3.95
853 866 1.959042 CGAGAATCCATCCAACCCAG 58.041 55.000 0.00 0.00 0.00 4.45
1354 1367 2.203337 GCCACCACAAGGAGCACA 60.203 61.111 0.00 0.00 37.56 4.57
1428 1441 2.088423 AGTGAGATGGTCGACTGAGAC 58.912 52.381 16.46 5.33 40.25 3.36
1838 1858 9.246670 ACATACATAAATGCATGCCACTATATT 57.753 29.630 16.68 3.90 35.45 1.28
1901 1922 1.802960 CTGATTATTAGGCCAGCTGCG 59.197 52.381 8.66 2.70 42.61 5.18
2108 2180 9.832445 TTTTAGTCTTCTATTAGCATACAAGGG 57.168 33.333 0.00 0.00 0.00 3.95
2118 2190 2.961062 AGCATACAAGGGATTGAATGGC 59.039 45.455 0.00 0.00 0.00 4.40
2182 2254 4.002982 CCATTCCCCATCACATATACACG 58.997 47.826 0.00 0.00 0.00 4.49
2200 2272 1.344438 ACGCCATGAGTGAGTTCTTCA 59.656 47.619 0.00 0.00 0.00 3.02
2202 2274 2.158449 CGCCATGAGTGAGTTCTTCAAC 59.842 50.000 0.00 0.00 37.61 3.18
2314 2386 0.249699 TCAAGAAAAGCTCGCCGACA 60.250 50.000 0.00 0.00 0.00 4.35
2385 2457 3.391382 GGTCTGGGTGACTCGGGG 61.391 72.222 0.00 0.00 44.74 5.73
2402 2474 0.179070 GGGAGGATTGAGAAGCCGAC 60.179 60.000 0.00 0.00 43.19 4.79
2411 2483 1.964223 TGAGAAGCCGACAGAAGAAGT 59.036 47.619 0.00 0.00 0.00 3.01
2412 2484 3.154710 TGAGAAGCCGACAGAAGAAGTA 58.845 45.455 0.00 0.00 0.00 2.24
2426 2498 3.710209 AGAAGTAGCCAACAAGCTGAT 57.290 42.857 0.00 0.00 44.67 2.90
2439 2511 1.489481 AGCTGATGACATTCTCGGGA 58.511 50.000 0.00 0.00 0.00 5.14
2445 2517 1.602237 GACATTCTCGGGAAGGGCA 59.398 57.895 11.43 0.00 40.58 5.36
2460 2532 2.113986 GCAGTCACTTGCCAGGGT 59.886 61.111 0.00 0.00 38.13 4.34
2496 2568 0.250295 ACATTCCAGTCACCACACCG 60.250 55.000 0.00 0.00 0.00 4.94
2706 2778 5.567430 ACATATCGGTAGGTGTAGCTGATA 58.433 41.667 0.00 0.00 32.21 2.15
2709 2781 3.894759 TCGGTAGGTGTAGCTGATAACT 58.105 45.455 0.00 0.00 0.00 2.24
2886 2958 8.781196 AGTTATCACATATAAGCAATGCTGAAG 58.219 33.333 9.14 0.00 39.62 3.02
2891 2963 6.412943 CACATATAAGCAATGCTGAAGAAACG 59.587 38.462 9.14 0.00 39.62 3.60
3032 3104 6.149142 ACTTGAGAAGATCTGAAGCATTTCAC 59.851 38.462 6.50 0.00 40.65 3.18
3095 3167 5.430089 ACTTCCTCTTAATAGGCAATCAGGT 59.570 40.000 1.97 0.00 36.51 4.00
3834 3909 6.612247 TTATTGTCAATGTTGCTATACCCG 57.388 37.500 8.39 0.00 0.00 5.28
3846 3921 2.094649 GCTATACCCGTATGAGGCTGAC 60.095 54.545 0.00 0.00 0.00 3.51
3934 4009 6.710597 AGTCGTTATCACTTCCTAATAGCA 57.289 37.500 0.00 0.00 0.00 3.49
3955 4030 7.934855 AGCAATCAGAAACATCATTCTAACT 57.065 32.000 0.00 0.00 37.56 2.24
4120 4198 4.274459 GCTTTGTAGCCAGGTAATCAGATG 59.726 45.833 0.00 0.00 41.74 2.90
4276 4354 3.002038 ACTACTCCCTCCGTTCACTAG 57.998 52.381 0.00 0.00 0.00 2.57
4326 4405 5.977635 TGGACTACATACAGACTGAAATGG 58.022 41.667 10.08 3.93 0.00 3.16
4465 4546 8.875803 CAATGATGGTGTTTAATTTGGAATGAG 58.124 33.333 0.00 0.00 0.00 2.90
4513 4594 1.328430 GGTACCGCTGCTTAGGACCT 61.328 60.000 0.00 0.00 0.00 3.85
4653 4734 2.570752 CTGGAGAGCCATGCAGGTATAT 59.429 50.000 0.00 0.00 44.91 0.86
4713 4794 8.740906 TGTTCTTCAGACTTCTTATAGGTACTG 58.259 37.037 0.00 0.00 41.52 2.74
4717 4798 8.824756 TTCAGACTTCTTATAGGTACTGATGT 57.175 34.615 0.00 0.00 41.52 3.06
4798 4879 5.335661 GGACATAAACCACATTGTCAACCTC 60.336 44.000 4.52 0.00 40.14 3.85
5436 5521 5.468540 TCCTTTTCATGAAGTCGAAGAGA 57.531 39.130 15.95 10.19 36.95 3.10
5542 5627 5.411781 AGAAAGCATGCACTACACTACTAC 58.588 41.667 21.98 0.00 0.00 2.73
5599 5684 4.165779 GCATTCAAATGTACCGTTTGGAG 58.834 43.478 16.28 10.14 39.82 3.86
5600 5685 4.083003 GCATTCAAATGTACCGTTTGGAGA 60.083 41.667 16.28 7.47 39.82 3.71
5601 5686 5.631026 CATTCAAATGTACCGTTTGGAGAG 58.369 41.667 16.28 5.85 39.82 3.20
5676 5764 9.362151 TCCAACTAGTTTTCCATGTAAGAATTT 57.638 29.630 5.07 0.00 0.00 1.82
5937 6025 3.439857 AGCTCAACTAGGGATGCAAAA 57.560 42.857 0.00 0.00 0.00 2.44
6174 6269 4.839668 AGTAAGCACATACGAGATCCTC 57.160 45.455 0.00 0.00 0.00 3.71
6204 6299 6.183360 ACAGATTGTTGATGTTGCAGTTAACA 60.183 34.615 8.61 0.00 43.93 2.41
6265 6360 9.838975 TGTTCAAACATAGCATATTACAACTTG 57.161 29.630 0.00 0.00 33.17 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.794103 TCATGCATGTGCTTTAGTGGT 58.206 42.857 25.43 0.00 42.66 4.16
59 60 4.597004 ACCTTGACCGACTTAGATGTAGA 58.403 43.478 0.00 0.00 0.00 2.59
60 61 4.985538 ACCTTGACCGACTTAGATGTAG 57.014 45.455 0.00 0.00 0.00 2.74
62 63 3.833070 AGAACCTTGACCGACTTAGATGT 59.167 43.478 0.00 0.00 0.00 3.06
63 64 4.457834 AGAACCTTGACCGACTTAGATG 57.542 45.455 0.00 0.00 0.00 2.90
64 65 5.246429 AGAAAGAACCTTGACCGACTTAGAT 59.754 40.000 0.00 0.00 0.00 1.98
65 66 4.587684 AGAAAGAACCTTGACCGACTTAGA 59.412 41.667 0.00 0.00 0.00 2.10
66 67 4.884247 AGAAAGAACCTTGACCGACTTAG 58.116 43.478 0.00 0.00 0.00 2.18
67 68 4.950205 AGAAAGAACCTTGACCGACTTA 57.050 40.909 0.00 0.00 0.00 2.24
68 69 3.840124 AGAAAGAACCTTGACCGACTT 57.160 42.857 0.00 0.00 0.00 3.01
69 70 3.840124 AAGAAAGAACCTTGACCGACT 57.160 42.857 0.00 0.00 0.00 4.18
70 71 4.895224 AAAAGAAAGAACCTTGACCGAC 57.105 40.909 0.00 0.00 0.00 4.79
71 72 4.034742 CGAAAAAGAAAGAACCTTGACCGA 59.965 41.667 0.00 0.00 0.00 4.69
72 73 4.034742 TCGAAAAAGAAAGAACCTTGACCG 59.965 41.667 0.00 0.00 0.00 4.79
73 74 5.494632 TCGAAAAAGAAAGAACCTTGACC 57.505 39.130 0.00 0.00 0.00 4.02
74 75 5.455849 GCTTCGAAAAAGAAAGAACCTTGAC 59.544 40.000 0.00 0.00 0.00 3.18
75 76 5.449999 GGCTTCGAAAAAGAAAGAACCTTGA 60.450 40.000 0.00 0.00 0.00 3.02
76 77 4.740205 GGCTTCGAAAAAGAAAGAACCTTG 59.260 41.667 0.00 0.00 0.00 3.61
77 78 4.401202 TGGCTTCGAAAAAGAAAGAACCTT 59.599 37.500 0.00 0.00 0.00 3.50
78 79 3.951680 TGGCTTCGAAAAAGAAAGAACCT 59.048 39.130 0.00 0.00 0.00 3.50
79 80 4.202020 ACTGGCTTCGAAAAAGAAAGAACC 60.202 41.667 0.00 0.00 0.00 3.62
80 81 4.921547 ACTGGCTTCGAAAAAGAAAGAAC 58.078 39.130 0.00 0.00 0.00 3.01
81 82 5.576447 AACTGGCTTCGAAAAAGAAAGAA 57.424 34.783 0.00 0.00 0.00 2.52
82 83 5.576447 AAACTGGCTTCGAAAAAGAAAGA 57.424 34.783 0.00 0.00 0.00 2.52
83 84 5.804979 TCAAAACTGGCTTCGAAAAAGAAAG 59.195 36.000 0.00 0.00 0.00 2.62
84 85 5.715070 TCAAAACTGGCTTCGAAAAAGAAA 58.285 33.333 0.00 0.00 0.00 2.52
85 86 5.317733 TCAAAACTGGCTTCGAAAAAGAA 57.682 34.783 0.00 0.00 0.00 2.52
86 87 4.974368 TCAAAACTGGCTTCGAAAAAGA 57.026 36.364 0.00 0.00 0.00 2.52
87 88 6.401955 TTTTCAAAACTGGCTTCGAAAAAG 57.598 33.333 0.00 0.00 31.45 2.27
88 89 6.787085 TTTTTCAAAACTGGCTTCGAAAAA 57.213 29.167 0.00 0.00 39.00 1.94
89 90 6.674278 GCATTTTTCAAAACTGGCTTCGAAAA 60.674 34.615 0.00 0.00 32.25 2.29
90 91 5.220567 GCATTTTTCAAAACTGGCTTCGAAA 60.221 36.000 0.00 0.00 0.00 3.46
91 92 4.269844 GCATTTTTCAAAACTGGCTTCGAA 59.730 37.500 0.00 0.00 0.00 3.71
92 93 3.801594 GCATTTTTCAAAACTGGCTTCGA 59.198 39.130 2.70 0.00 0.00 3.71
93 94 3.555139 TGCATTTTTCAAAACTGGCTTCG 59.445 39.130 2.70 0.00 0.00 3.79
94 95 5.482686 TTGCATTTTTCAAAACTGGCTTC 57.517 34.783 2.70 0.00 0.00 3.86
95 96 6.453926 AATTGCATTTTTCAAAACTGGCTT 57.546 29.167 2.70 0.00 0.00 4.35
96 97 6.095160 TGAAATTGCATTTTTCAAAACTGGCT 59.905 30.769 18.03 0.00 39.46 4.75
97 98 6.264088 TGAAATTGCATTTTTCAAAACTGGC 58.736 32.000 18.03 0.00 39.46 4.85
98 99 6.415573 GCTGAAATTGCATTTTTCAAAACTGG 59.584 34.615 19.77 11.83 41.23 4.00
99 100 7.190871 AGCTGAAATTGCATTTTTCAAAACTG 58.809 30.769 19.77 12.31 41.23 3.16
100 101 7.324354 AGCTGAAATTGCATTTTTCAAAACT 57.676 28.000 19.77 15.65 41.23 2.66
101 102 7.697291 TGAAGCTGAAATTGCATTTTTCAAAAC 59.303 29.630 19.77 14.31 41.23 2.43
102 103 7.697291 GTGAAGCTGAAATTGCATTTTTCAAAA 59.303 29.630 19.77 7.19 41.23 2.44
103 104 7.066043 AGTGAAGCTGAAATTGCATTTTTCAAA 59.934 29.630 19.77 5.25 41.23 2.69
104 105 6.539464 AGTGAAGCTGAAATTGCATTTTTCAA 59.461 30.769 19.77 7.78 41.23 2.69
105 106 6.050432 AGTGAAGCTGAAATTGCATTTTTCA 58.950 32.000 18.78 18.78 39.96 2.69
106 107 6.535274 AGTGAAGCTGAAATTGCATTTTTC 57.465 33.333 13.14 13.14 34.40 2.29
107 108 6.930667 AAGTGAAGCTGAAATTGCATTTTT 57.069 29.167 7.92 1.73 31.47 1.94
108 109 6.930667 AAAGTGAAGCTGAAATTGCATTTT 57.069 29.167 6.29 6.29 31.47 1.82
109 110 6.539464 TGAAAAGTGAAGCTGAAATTGCATTT 59.461 30.769 0.00 0.00 34.64 2.32
110 111 6.018507 GTGAAAAGTGAAGCTGAAATTGCATT 60.019 34.615 0.00 0.00 0.00 3.56
111 112 5.464389 GTGAAAAGTGAAGCTGAAATTGCAT 59.536 36.000 0.00 0.00 0.00 3.96
112 113 4.805192 GTGAAAAGTGAAGCTGAAATTGCA 59.195 37.500 0.00 0.00 0.00 4.08
113 114 4.805192 TGTGAAAAGTGAAGCTGAAATTGC 59.195 37.500 0.00 0.00 0.00 3.56
114 115 6.890663 TTGTGAAAAGTGAAGCTGAAATTG 57.109 33.333 0.00 0.00 0.00 2.32
115 116 7.603784 AGTTTTGTGAAAAGTGAAGCTGAAATT 59.396 29.630 0.00 0.00 32.98 1.82
116 117 7.099120 AGTTTTGTGAAAAGTGAAGCTGAAAT 58.901 30.769 0.00 0.00 32.98 2.17
117 118 6.454795 AGTTTTGTGAAAAGTGAAGCTGAAA 58.545 32.000 0.00 0.00 32.98 2.69
118 119 6.024552 AGTTTTGTGAAAAGTGAAGCTGAA 57.975 33.333 0.00 0.00 32.98 3.02
119 120 5.643379 AGTTTTGTGAAAAGTGAAGCTGA 57.357 34.783 0.00 0.00 32.98 4.26
127 128 4.021544 TGCAACCTCAGTTTTGTGAAAAGT 60.022 37.500 0.00 0.00 32.45 2.66
128 129 4.493547 TGCAACCTCAGTTTTGTGAAAAG 58.506 39.130 0.00 0.00 32.45 2.27
129 130 4.527509 TGCAACCTCAGTTTTGTGAAAA 57.472 36.364 0.00 0.00 32.45 2.29
130 131 4.734398 ATGCAACCTCAGTTTTGTGAAA 57.266 36.364 0.00 0.00 32.45 2.69
131 132 4.734398 AATGCAACCTCAGTTTTGTGAA 57.266 36.364 0.00 0.00 32.45 3.18
132 133 4.431809 CAAATGCAACCTCAGTTTTGTGA 58.568 39.130 0.00 0.00 32.45 3.58
133 134 3.001533 GCAAATGCAACCTCAGTTTTGTG 59.998 43.478 0.00 0.00 41.59 3.33
134 135 3.197265 GCAAATGCAACCTCAGTTTTGT 58.803 40.909 0.00 0.00 41.59 2.83
135 136 2.545106 GGCAAATGCAACCTCAGTTTTG 59.455 45.455 7.80 0.00 44.36 2.44
136 137 2.802774 CGGCAAATGCAACCTCAGTTTT 60.803 45.455 7.80 0.00 44.36 2.43
137 138 1.269726 CGGCAAATGCAACCTCAGTTT 60.270 47.619 7.80 0.00 44.36 2.66
138 139 0.314935 CGGCAAATGCAACCTCAGTT 59.685 50.000 7.80 0.00 44.36 3.16
139 140 1.526575 CCGGCAAATGCAACCTCAGT 61.527 55.000 7.80 0.00 44.36 3.41
140 141 1.213537 CCGGCAAATGCAACCTCAG 59.786 57.895 7.80 0.00 44.36 3.35
141 142 0.825425 TTCCGGCAAATGCAACCTCA 60.825 50.000 7.80 0.00 44.36 3.86
142 143 0.316841 TTTCCGGCAAATGCAACCTC 59.683 50.000 7.80 0.00 44.36 3.85
143 144 0.975887 ATTTCCGGCAAATGCAACCT 59.024 45.000 7.80 0.00 44.36 3.50
144 145 2.165437 TCTATTTCCGGCAAATGCAACC 59.835 45.455 17.09 0.00 44.36 3.77
145 146 3.119495 AGTCTATTTCCGGCAAATGCAAC 60.119 43.478 17.09 12.96 44.36 4.17
146 147 3.088532 AGTCTATTTCCGGCAAATGCAA 58.911 40.909 17.09 0.00 44.36 4.08
147 148 2.722094 AGTCTATTTCCGGCAAATGCA 58.278 42.857 17.09 0.00 44.36 3.96
148 149 3.782889 AAGTCTATTTCCGGCAAATGC 57.217 42.857 17.09 0.00 35.34 3.56
149 150 5.737290 CGTTTAAGTCTATTTCCGGCAAATG 59.263 40.000 17.09 10.14 35.34 2.32
150 151 5.413523 ACGTTTAAGTCTATTTCCGGCAAAT 59.586 36.000 13.85 13.85 38.35 2.32
151 152 4.756135 ACGTTTAAGTCTATTTCCGGCAAA 59.244 37.500 0.00 0.00 0.00 3.68
152 153 4.317488 ACGTTTAAGTCTATTTCCGGCAA 58.683 39.130 0.00 0.00 0.00 4.52
153 154 3.929094 ACGTTTAAGTCTATTTCCGGCA 58.071 40.909 0.00 0.00 0.00 5.69
154 155 4.934075 AACGTTTAAGTCTATTTCCGGC 57.066 40.909 0.00 0.00 0.00 6.13
155 156 7.816945 TTCTAACGTTTAAGTCTATTTCCGG 57.183 36.000 5.91 0.00 0.00 5.14
171 172 9.490379 ACTAAGTCAATCAAGATTTTCTAACGT 57.510 29.630 0.00 0.00 0.00 3.99
178 179 9.944376 TGCTACTACTAAGTCAATCAAGATTTT 57.056 29.630 0.00 0.00 37.15 1.82
182 183 8.353684 GCTATGCTACTACTAAGTCAATCAAGA 58.646 37.037 0.00 0.00 37.15 3.02
183 184 7.324856 CGCTATGCTACTACTAAGTCAATCAAG 59.675 40.741 0.00 0.00 37.15 3.02
184 185 7.012989 TCGCTATGCTACTACTAAGTCAATCAA 59.987 37.037 0.00 0.00 37.15 2.57
185 186 6.485648 TCGCTATGCTACTACTAAGTCAATCA 59.514 38.462 0.00 0.00 37.15 2.57
186 187 6.900189 TCGCTATGCTACTACTAAGTCAATC 58.100 40.000 0.00 0.00 37.15 2.67
187 188 6.879276 TCGCTATGCTACTACTAAGTCAAT 57.121 37.500 0.00 0.00 37.15 2.57
188 189 6.711194 AGATCGCTATGCTACTACTAAGTCAA 59.289 38.462 0.00 0.00 37.15 3.18
189 190 6.231951 AGATCGCTATGCTACTACTAAGTCA 58.768 40.000 0.00 0.00 37.15 3.41
190 191 6.592607 AGAGATCGCTATGCTACTACTAAGTC 59.407 42.308 0.00 0.00 37.15 3.01
191 192 6.469410 AGAGATCGCTATGCTACTACTAAGT 58.531 40.000 0.00 0.00 39.91 2.24
221 222 7.996385 ACACTATAATTTGCTAATGTCCCAAC 58.004 34.615 0.00 0.00 0.00 3.77
222 223 7.011950 CGACACTATAATTTGCTAATGTCCCAA 59.988 37.037 0.00 0.00 33.28 4.12
223 224 6.481976 CGACACTATAATTTGCTAATGTCCCA 59.518 38.462 0.00 0.00 33.28 4.37
224 225 6.073222 CCGACACTATAATTTGCTAATGTCCC 60.073 42.308 0.00 0.00 33.28 4.46
225 226 6.482308 ACCGACACTATAATTTGCTAATGTCC 59.518 38.462 0.00 0.00 33.28 4.02
226 227 7.345192 CACCGACACTATAATTTGCTAATGTC 58.655 38.462 0.00 0.00 33.48 3.06
227 228 6.260050 CCACCGACACTATAATTTGCTAATGT 59.740 38.462 0.00 0.00 0.00 2.71
228 229 6.260050 ACCACCGACACTATAATTTGCTAATG 59.740 38.462 0.00 0.00 0.00 1.90
229 230 6.354130 ACCACCGACACTATAATTTGCTAAT 58.646 36.000 0.00 0.00 0.00 1.73
230 231 5.736813 ACCACCGACACTATAATTTGCTAA 58.263 37.500 0.00 0.00 0.00 3.09
231 232 5.347620 ACCACCGACACTATAATTTGCTA 57.652 39.130 0.00 0.00 0.00 3.49
232 233 4.216411 ACCACCGACACTATAATTTGCT 57.784 40.909 0.00 0.00 0.00 3.91
233 234 4.957759 AACCACCGACACTATAATTTGC 57.042 40.909 0.00 0.00 0.00 3.68
234 235 9.498307 GAAAATAACCACCGACACTATAATTTG 57.502 33.333 0.00 0.00 0.00 2.32
235 236 8.392612 CGAAAATAACCACCGACACTATAATTT 58.607 33.333 0.00 0.00 0.00 1.82
236 237 7.466320 GCGAAAATAACCACCGACACTATAATT 60.466 37.037 0.00 0.00 0.00 1.40
237 238 6.018507 GCGAAAATAACCACCGACACTATAAT 60.019 38.462 0.00 0.00 0.00 1.28
238 239 5.291614 GCGAAAATAACCACCGACACTATAA 59.708 40.000 0.00 0.00 0.00 0.98
239 240 4.805192 GCGAAAATAACCACCGACACTATA 59.195 41.667 0.00 0.00 0.00 1.31
240 241 3.619929 GCGAAAATAACCACCGACACTAT 59.380 43.478 0.00 0.00 0.00 2.12
241 242 2.995258 GCGAAAATAACCACCGACACTA 59.005 45.455 0.00 0.00 0.00 2.74
242 243 1.802365 GCGAAAATAACCACCGACACT 59.198 47.619 0.00 0.00 0.00 3.55
243 244 1.532007 TGCGAAAATAACCACCGACAC 59.468 47.619 0.00 0.00 0.00 3.67
244 245 1.880271 TGCGAAAATAACCACCGACA 58.120 45.000 0.00 0.00 0.00 4.35
293 294 9.893305 GGATTATAACCATCCAAAATTTCTACG 57.107 33.333 0.00 0.00 40.21 3.51
338 339 4.900635 ATCCTATGAATCAAACAACCGC 57.099 40.909 0.00 0.00 0.00 5.68
339 340 6.435430 TCAATCCTATGAATCAAACAACCG 57.565 37.500 0.00 0.00 0.00 4.44
470 474 4.431809 TGCATCACTGGAAAAACAAAGTG 58.568 39.130 0.00 0.00 41.11 3.16
484 488 4.669206 TGGTTTGTTTGATTGCATCACT 57.331 36.364 0.00 0.00 39.39 3.41
524 528 1.950472 CGGTGTCGTGCTCATTTTTC 58.050 50.000 0.00 0.00 0.00 2.29
598 603 1.892474 GGTTCACTGGCCATTTTAGCA 59.108 47.619 5.51 0.00 0.00 3.49
599 604 1.135402 CGGTTCACTGGCCATTTTAGC 60.135 52.381 5.51 1.26 0.00 3.09
602 607 1.247567 CTCGGTTCACTGGCCATTTT 58.752 50.000 5.51 0.00 0.00 1.82
639 644 0.764752 AAATGGGCCCACGGGAAAAA 60.765 50.000 31.51 0.00 37.50 1.94
673 678 4.453819 GCTCTAGTGCAAAGAAATGTGTCT 59.546 41.667 11.82 0.00 0.00 3.41
708 714 0.981183 ACGATGGTGGAGGCTGTTAA 59.019 50.000 0.00 0.00 0.00 2.01
760 766 4.684703 CGTGTTTTATAGGACGGATGGATC 59.315 45.833 0.00 0.00 0.00 3.36
801 807 0.041833 CTCCCCAGTTGAGAGAGGGA 59.958 60.000 0.00 0.00 44.30 4.20
1263 1276 2.280797 TGGAACTGTGACTGCGGC 60.281 61.111 0.00 0.00 0.00 6.53
1265 1278 2.320587 GCCTGGAACTGTGACTGCG 61.321 63.158 0.00 0.00 0.00 5.18
1354 1367 0.250038 CTGCATACCTGTATGGCGCT 60.250 55.000 16.71 0.00 42.32 5.92
1428 1441 1.652124 CAACGGAACATACGAACCTCG 59.348 52.381 0.00 0.00 46.93 4.63
1838 1858 9.273016 GCTTAATTAACAAGCATATCTAGGACA 57.727 33.333 15.43 0.00 46.17 4.02
2000 2021 9.396022 CAACAACTACTGGACTAATTTGGATAT 57.604 33.333 0.00 0.00 0.00 1.63
2083 2147 9.209048 TCCCTTGTATGCTAATAGAAGACTAAA 57.791 33.333 4.65 0.00 40.47 1.85
2108 2180 3.627577 AGTTGGTATGACGCCATTCAATC 59.372 43.478 0.00 0.00 35.71 2.67
2118 2190 3.595173 TGTGGAATGAGTTGGTATGACG 58.405 45.455 0.00 0.00 0.00 4.35
2182 2254 2.485814 GGTTGAAGAACTCACTCATGGC 59.514 50.000 0.00 0.00 32.21 4.40
2200 2272 0.877071 TCTACGCGACTTCGAAGGTT 59.123 50.000 27.86 9.11 43.02 3.50
2202 2274 1.973138 TTTCTACGCGACTTCGAAGG 58.027 50.000 27.86 13.02 43.02 3.46
2278 2350 3.938963 TCTTGACTTTCGTGTTCTTGCTT 59.061 39.130 0.00 0.00 0.00 3.91
2385 2457 1.478510 TCTGTCGGCTTCTCAATCCTC 59.521 52.381 0.00 0.00 0.00 3.71
2402 2474 3.188048 CAGCTTGTTGGCTACTTCTTCTG 59.812 47.826 0.01 0.00 41.00 3.02
2411 2483 2.857186 TGTCATCAGCTTGTTGGCTA 57.143 45.000 0.00 0.00 41.00 3.93
2412 2484 2.211250 ATGTCATCAGCTTGTTGGCT 57.789 45.000 0.00 0.00 44.10 4.75
2426 2498 1.198094 TGCCCTTCCCGAGAATGTCA 61.198 55.000 0.00 0.00 0.00 3.58
2445 2517 0.178903 TCCTACCCTGGCAAGTGACT 60.179 55.000 0.31 0.00 0.00 3.41
2460 2532 1.847328 TGTTGATCCTCACGCTCCTA 58.153 50.000 0.00 0.00 0.00 2.94
2496 2568 2.804090 GCGAACACGGTCCTCGAC 60.804 66.667 11.43 1.47 42.43 4.20
2685 2757 6.246919 AGTTATCAGCTACACCTACCGATAT 58.753 40.000 0.00 0.00 0.00 1.63
2706 2778 5.127031 ACAAAGCAGAACAACATACCAAGTT 59.873 36.000 0.00 0.00 0.00 2.66
2709 2781 4.736168 GCACAAAGCAGAACAACATACCAA 60.736 41.667 0.00 0.00 44.79 3.67
2904 2976 3.088259 TTGCTGTAACCTGCAACGT 57.912 47.368 3.33 0.00 46.52 3.99
3032 3104 4.519350 GGAACCTTTGGAGTTTTGGTAGAG 59.481 45.833 0.00 0.00 0.00 2.43
3095 3167 2.223735 GCTCCTCGACATCGTCCATTAA 60.224 50.000 0.54 0.00 40.80 1.40
3834 3909 1.134965 ACAGAAGCGTCAGCCTCATAC 60.135 52.381 1.61 0.00 46.67 2.39
3846 3921 4.452455 AGAACACCTGAATAAACAGAAGCG 59.548 41.667 0.00 0.00 39.94 4.68
3934 4009 7.637511 AGGGAGTTAGAATGATGTTTCTGATT 58.362 34.615 0.00 0.00 36.63 2.57
3955 4030 3.325716 AGCGAAGTACCTTGTAAAAGGGA 59.674 43.478 16.40 4.25 44.27 4.20
4117 4195 9.713740 CTTGACAAACATTTAGCTTCTATCATC 57.286 33.333 0.00 0.00 0.00 2.92
4120 4198 9.548208 GAACTTGACAAACATTTAGCTTCTATC 57.452 33.333 0.00 0.00 0.00 2.08
4315 4394 4.097892 GTGTTTGTTCACCCATTTCAGTCT 59.902 41.667 0.00 0.00 32.81 3.24
4326 4405 4.206200 CGCATTTTAGTGTGTTTGTTCACC 59.794 41.667 0.00 0.00 37.51 4.02
4378 4459 7.931948 CCCTCCGTTCACTATTATAAGATGTTT 59.068 37.037 0.00 0.00 0.00 2.83
4473 4554 8.691797 GGTACCTATTTTCCAGCAAATCATTAA 58.308 33.333 4.06 0.00 0.00 1.40
4513 4594 6.427441 TGTAATAACATGCCAGGTATTCCAA 58.573 36.000 0.00 0.00 35.89 3.53
4653 4734 5.069318 TGTGGCAAGTCATGTTCAATCTTA 58.931 37.500 0.00 0.00 0.00 2.10
4717 4798 9.158233 CAGGACAACCGTAATAATAAGAAAGAA 57.842 33.333 0.00 0.00 41.83 2.52
4798 4879 0.319211 TTGCTGACACGTACTTCCCG 60.319 55.000 0.00 0.00 0.00 5.14
5335 5420 4.323028 CCAGCCTGACAGAGAAGTTATTCA 60.323 45.833 3.32 0.00 37.94 2.57
5339 5424 2.828520 CTCCAGCCTGACAGAGAAGTTA 59.171 50.000 3.32 0.00 0.00 2.24
5436 5521 0.676782 GACGCCCCATGCTGTTAGTT 60.677 55.000 0.00 0.00 38.05 2.24
5600 5685 9.851686 TGTTATTATTTGCATATCACTTCTCCT 57.148 29.630 0.00 0.00 0.00 3.69
5601 5686 9.884465 GTGTTATTATTTGCATATCACTTCTCC 57.116 33.333 0.00 0.00 29.58 3.71
5676 5764 9.865321 GACTTCAGTTTACATTATACCAGTACA 57.135 33.333 0.00 0.00 0.00 2.90
6174 6269 6.105657 TGCAACATCAACAATCTGTATACG 57.894 37.500 0.00 0.00 0.00 3.06
6204 6299 7.310664 CAAAGAAGACACAATGCTAATGTCAT 58.689 34.615 6.40 0.00 44.26 3.06



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

AutoCloner maintained by Alex Coulton.