Multiple sequence alignment - TraesCS5B01G397900

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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 TraesCS5B01G397900 chr5B 100.000 5054 0 0 1 5054 575524805 575519752 0.000000e+00 9334
1 TraesCS5B01G397900 chr5D 94.466 4861 148 46 293 5054 468692646 468687808 0.000000e+00 7374
2 TraesCS5B01G397900 chr5A 94.767 4529 167 35 589 5054 588876838 588872317 0.000000e+00 6986
3 TraesCS5B01G397900 chr1B 93.197 294 19 1 1 293 638012381 638012674 1.010000e-116 431


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 TraesCS5B01G397900 chr5B 575519752 575524805 5053 True 9334 9334 100.000 1 5054 1 chr5B.!!$R1 5053
1 TraesCS5B01G397900 chr5D 468687808 468692646 4838 True 7374 7374 94.466 293 5054 1 chr5D.!!$R1 4761
2 TraesCS5B01G397900 chr5A 588872317 588876838 4521 True 6986 6986 94.767 589 5054 1 chr5A.!!$R1 4465

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
166 167 0.036294 GTTTTCCCTCCGCAGCTAGT 60.036 55.000 0.00 0.0 0.00 2.57 F
1791 1880 0.031414 TACCCAGGGAGCTAGGGAAC 60.031 60.000 14.54 0.0 45.80 3.62 F
2168 2257 0.036732 TCAGGCTCAATTCCAGCGTT 59.963 50.000 0.00 0.0 37.81 4.84 F
2758 2847 1.003580 GGCAGTTGGAATCACTGGAGA 59.996 52.381 3.42 0.0 32.55 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2237 0.674895 ACGCTGGAATTGAGCCTGAC 60.675 55.000 0.00 0.00 32.41 3.51 R
3298 3393 0.394352 AACCTTCCAATAGCCAGCCG 60.394 55.000 0.00 0.00 0.00 5.52 R
3708 3803 2.797156 CGCATACTCTGGAGCAACATAC 59.203 50.000 0.00 0.00 0.00 2.39 R
4571 4675 3.189287 GGTTGCTAGTGATCACCAGTTTG 59.811 47.826 22.21 6.11 0.00 2.93 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 4.864334 GGCGGCACAGGGATGGAG 62.864 72.222 3.07 0.00 0.00 3.86
19 20 3.785859 GCGGCACAGGGATGGAGA 61.786 66.667 0.00 0.00 0.00 3.71
20 21 2.187946 CGGCACAGGGATGGAGAC 59.812 66.667 0.00 0.00 0.00 3.36
21 22 2.592308 GGCACAGGGATGGAGACC 59.408 66.667 0.00 0.00 0.00 3.85
22 23 1.997874 GGCACAGGGATGGAGACCT 60.998 63.158 0.00 0.00 37.66 3.85
23 24 0.691078 GGCACAGGGATGGAGACCTA 60.691 60.000 0.00 0.00 34.71 3.08
24 25 0.755686 GCACAGGGATGGAGACCTAG 59.244 60.000 0.00 0.00 34.71 3.02
25 26 1.689575 GCACAGGGATGGAGACCTAGA 60.690 57.143 0.00 0.00 34.71 2.43
26 27 2.315176 CACAGGGATGGAGACCTAGAG 58.685 57.143 0.00 0.00 34.71 2.43
27 28 1.933765 ACAGGGATGGAGACCTAGAGT 59.066 52.381 0.00 0.00 34.71 3.24
28 29 2.316372 ACAGGGATGGAGACCTAGAGTT 59.684 50.000 0.00 0.00 34.71 3.01
29 30 2.962421 CAGGGATGGAGACCTAGAGTTC 59.038 54.545 0.00 0.00 34.71 3.01
30 31 2.587777 AGGGATGGAGACCTAGAGTTCA 59.412 50.000 0.00 0.00 34.71 3.18
31 32 2.962421 GGGATGGAGACCTAGAGTTCAG 59.038 54.545 0.00 0.00 0.00 3.02
32 33 2.364002 GGATGGAGACCTAGAGTTCAGC 59.636 54.545 0.00 0.00 0.00 4.26
33 34 1.464734 TGGAGACCTAGAGTTCAGCG 58.535 55.000 0.00 0.00 0.00 5.18
34 35 1.004394 TGGAGACCTAGAGTTCAGCGA 59.996 52.381 0.00 0.00 0.00 4.93
35 36 1.402613 GGAGACCTAGAGTTCAGCGAC 59.597 57.143 0.00 0.00 0.00 5.19
36 37 2.361789 GAGACCTAGAGTTCAGCGACT 58.638 52.381 0.00 0.00 0.00 4.18
37 38 2.088423 AGACCTAGAGTTCAGCGACTG 58.912 52.381 0.00 0.00 0.00 3.51
38 39 1.133407 GACCTAGAGTTCAGCGACTGG 59.867 57.143 6.95 0.00 31.51 4.00
39 40 0.457851 CCTAGAGTTCAGCGACTGGG 59.542 60.000 6.95 0.00 31.51 4.45
40 41 1.464734 CTAGAGTTCAGCGACTGGGA 58.535 55.000 6.95 0.00 31.51 4.37
41 42 1.819288 CTAGAGTTCAGCGACTGGGAA 59.181 52.381 6.95 0.00 31.51 3.97
42 43 0.605589 AGAGTTCAGCGACTGGGAAG 59.394 55.000 6.95 0.00 31.51 3.46
43 44 0.603569 GAGTTCAGCGACTGGGAAGA 59.396 55.000 6.95 0.00 31.51 2.87
44 45 1.205893 GAGTTCAGCGACTGGGAAGAT 59.794 52.381 6.95 0.00 31.51 2.40
45 46 1.066573 AGTTCAGCGACTGGGAAGATG 60.067 52.381 6.95 0.00 31.51 2.90
46 47 1.066858 GTTCAGCGACTGGGAAGATGA 60.067 52.381 6.95 0.00 31.51 2.92
47 48 1.489481 TCAGCGACTGGGAAGATGAT 58.511 50.000 6.95 0.00 31.51 2.45
48 49 1.137675 TCAGCGACTGGGAAGATGATG 59.862 52.381 6.95 0.00 31.51 3.07
49 50 1.137675 CAGCGACTGGGAAGATGATGA 59.862 52.381 0.00 0.00 0.00 2.92
50 51 1.833630 AGCGACTGGGAAGATGATGAA 59.166 47.619 0.00 0.00 0.00 2.57
51 52 2.437281 AGCGACTGGGAAGATGATGAAT 59.563 45.455 0.00 0.00 0.00 2.57
52 53 2.805099 GCGACTGGGAAGATGATGAATC 59.195 50.000 0.00 0.00 35.29 2.52
64 65 6.423776 AGATGATGAATCTTCTCTCCTTCC 57.576 41.667 3.51 0.00 43.52 3.46
65 66 5.307716 AGATGATGAATCTTCTCTCCTTCCC 59.692 44.000 3.51 0.00 43.52 3.97
66 67 4.629122 TGATGAATCTTCTCTCCTTCCCT 58.371 43.478 0.00 0.00 0.00 4.20
67 68 4.653341 TGATGAATCTTCTCTCCTTCCCTC 59.347 45.833 0.00 0.00 0.00 4.30
68 69 4.344938 TGAATCTTCTCTCCTTCCCTCT 57.655 45.455 0.00 0.00 0.00 3.69
69 70 4.029520 TGAATCTTCTCTCCTTCCCTCTG 58.970 47.826 0.00 0.00 0.00 3.35
70 71 3.774842 ATCTTCTCTCCTTCCCTCTGT 57.225 47.619 0.00 0.00 0.00 3.41
71 72 3.551635 TCTTCTCTCCTTCCCTCTGTT 57.448 47.619 0.00 0.00 0.00 3.16
72 73 3.863086 TCTTCTCTCCTTCCCTCTGTTT 58.137 45.455 0.00 0.00 0.00 2.83
73 74 4.235372 TCTTCTCTCCTTCCCTCTGTTTT 58.765 43.478 0.00 0.00 0.00 2.43
74 75 4.284746 TCTTCTCTCCTTCCCTCTGTTTTC 59.715 45.833 0.00 0.00 0.00 2.29
75 76 2.563179 TCTCTCCTTCCCTCTGTTTTCG 59.437 50.000 0.00 0.00 0.00 3.46
76 77 2.300437 CTCTCCTTCCCTCTGTTTTCGT 59.700 50.000 0.00 0.00 0.00 3.85
77 78 2.299297 TCTCCTTCCCTCTGTTTTCGTC 59.701 50.000 0.00 0.00 0.00 4.20
78 79 2.037251 CTCCTTCCCTCTGTTTTCGTCA 59.963 50.000 0.00 0.00 0.00 4.35
79 80 2.637872 TCCTTCCCTCTGTTTTCGTCAT 59.362 45.455 0.00 0.00 0.00 3.06
80 81 2.744202 CCTTCCCTCTGTTTTCGTCATG 59.256 50.000 0.00 0.00 0.00 3.07
81 82 3.403038 CTTCCCTCTGTTTTCGTCATGT 58.597 45.455 0.00 0.00 0.00 3.21
82 83 4.562757 CCTTCCCTCTGTTTTCGTCATGTA 60.563 45.833 0.00 0.00 0.00 2.29
83 84 4.610605 TCCCTCTGTTTTCGTCATGTAA 57.389 40.909 0.00 0.00 0.00 2.41
84 85 5.160607 TCCCTCTGTTTTCGTCATGTAAT 57.839 39.130 0.00 0.00 0.00 1.89
85 86 5.175859 TCCCTCTGTTTTCGTCATGTAATC 58.824 41.667 0.00 0.00 0.00 1.75
86 87 5.046591 TCCCTCTGTTTTCGTCATGTAATCT 60.047 40.000 0.00 0.00 0.00 2.40
87 88 5.643777 CCCTCTGTTTTCGTCATGTAATCTT 59.356 40.000 0.00 0.00 0.00 2.40
88 89 6.402550 CCCTCTGTTTTCGTCATGTAATCTTG 60.403 42.308 0.00 0.00 0.00 3.02
89 90 6.368791 CCTCTGTTTTCGTCATGTAATCTTGA 59.631 38.462 0.00 0.00 0.00 3.02
90 91 7.065085 CCTCTGTTTTCGTCATGTAATCTTGAT 59.935 37.037 0.00 0.00 31.98 2.57
91 92 8.996024 TCTGTTTTCGTCATGTAATCTTGATA 57.004 30.769 0.00 0.00 31.98 2.15
92 93 9.430623 TCTGTTTTCGTCATGTAATCTTGATAA 57.569 29.630 0.00 0.00 31.98 1.75
93 94 9.478019 CTGTTTTCGTCATGTAATCTTGATAAC 57.522 33.333 0.00 0.00 31.98 1.89
94 95 9.214957 TGTTTTCGTCATGTAATCTTGATAACT 57.785 29.630 0.00 0.00 31.98 2.24
97 98 8.771920 TTCGTCATGTAATCTTGATAACTTGT 57.228 30.769 0.00 0.00 31.98 3.16
98 99 9.863845 TTCGTCATGTAATCTTGATAACTTGTA 57.136 29.630 0.00 0.00 31.98 2.41
99 100 9.516314 TCGTCATGTAATCTTGATAACTTGTAG 57.484 33.333 0.00 0.00 31.98 2.74
100 101 9.516314 CGTCATGTAATCTTGATAACTTGTAGA 57.484 33.333 0.00 0.00 31.98 2.59
127 128 8.996271 AGTTTAAATAACTGTACTGGTGTAAGC 58.004 33.333 0.00 0.00 0.00 3.09
128 129 7.585286 TTAAATAACTGTACTGGTGTAAGCG 57.415 36.000 0.00 0.00 36.92 4.68
129 130 5.395682 AATAACTGTACTGGTGTAAGCGA 57.604 39.130 0.00 0.00 36.92 4.93
130 131 3.955650 AACTGTACTGGTGTAAGCGAT 57.044 42.857 4.66 0.00 36.92 4.58
131 132 3.232213 ACTGTACTGGTGTAAGCGATG 57.768 47.619 4.66 0.00 36.92 3.84
132 133 1.927174 CTGTACTGGTGTAAGCGATGC 59.073 52.381 0.00 0.00 36.92 3.91
133 134 1.273886 TGTACTGGTGTAAGCGATGCA 59.726 47.619 0.00 0.00 36.92 3.96
134 135 2.093711 TGTACTGGTGTAAGCGATGCAT 60.094 45.455 0.00 0.00 36.92 3.96
135 136 1.372582 ACTGGTGTAAGCGATGCATG 58.627 50.000 2.46 0.00 36.92 4.06
136 137 1.339055 ACTGGTGTAAGCGATGCATGT 60.339 47.619 2.46 0.00 36.92 3.21
137 138 1.328680 CTGGTGTAAGCGATGCATGTC 59.671 52.381 2.46 0.00 36.92 3.06
138 139 1.338579 TGGTGTAAGCGATGCATGTCA 60.339 47.619 2.46 0.00 36.92 3.58
139 140 1.942657 GGTGTAAGCGATGCATGTCAT 59.057 47.619 2.46 2.78 38.32 3.06
140 141 2.286595 GGTGTAAGCGATGCATGTCATG 60.287 50.000 2.46 8.56 35.05 3.07
141 142 2.352651 GTGTAAGCGATGCATGTCATGT 59.647 45.455 14.26 0.00 35.05 3.21
142 143 2.609002 TGTAAGCGATGCATGTCATGTC 59.391 45.455 14.26 7.37 35.05 3.06
143 144 2.034104 AAGCGATGCATGTCATGTCT 57.966 45.000 14.26 2.12 35.05 3.41
144 145 2.034104 AGCGATGCATGTCATGTCTT 57.966 45.000 14.26 5.28 35.05 3.01
145 146 2.362736 AGCGATGCATGTCATGTCTTT 58.637 42.857 14.26 0.00 35.05 2.52
146 147 2.751259 AGCGATGCATGTCATGTCTTTT 59.249 40.909 14.26 0.00 35.05 2.27
147 148 2.850060 GCGATGCATGTCATGTCTTTTG 59.150 45.455 14.26 2.90 35.05 2.44
148 149 3.671433 GCGATGCATGTCATGTCTTTTGT 60.671 43.478 14.26 0.00 35.05 2.83
149 150 4.478699 CGATGCATGTCATGTCTTTTGTT 58.521 39.130 14.26 0.00 35.05 2.83
150 151 4.919168 CGATGCATGTCATGTCTTTTGTTT 59.081 37.500 14.26 0.00 35.05 2.83
151 152 5.403166 CGATGCATGTCATGTCTTTTGTTTT 59.597 36.000 14.26 0.00 35.05 2.43
152 153 6.399249 CGATGCATGTCATGTCTTTTGTTTTC 60.399 38.462 14.26 0.00 35.05 2.29
153 154 5.049167 TGCATGTCATGTCTTTTGTTTTCC 58.951 37.500 14.26 0.00 0.00 3.13
154 155 4.448732 GCATGTCATGTCTTTTGTTTTCCC 59.551 41.667 14.26 0.00 0.00 3.97
155 156 5.739935 GCATGTCATGTCTTTTGTTTTCCCT 60.740 40.000 14.26 0.00 0.00 4.20
156 157 5.514274 TGTCATGTCTTTTGTTTTCCCTC 57.486 39.130 0.00 0.00 0.00 4.30
157 158 4.340950 TGTCATGTCTTTTGTTTTCCCTCC 59.659 41.667 0.00 0.00 0.00 4.30
158 159 3.568007 TCATGTCTTTTGTTTTCCCTCCG 59.432 43.478 0.00 0.00 0.00 4.63
159 160 1.679153 TGTCTTTTGTTTTCCCTCCGC 59.321 47.619 0.00 0.00 0.00 5.54
160 161 1.679153 GTCTTTTGTTTTCCCTCCGCA 59.321 47.619 0.00 0.00 0.00 5.69
161 162 1.953686 TCTTTTGTTTTCCCTCCGCAG 59.046 47.619 0.00 0.00 0.00 5.18
162 163 0.387565 TTTTGTTTTCCCTCCGCAGC 59.612 50.000 0.00 0.00 0.00 5.25
163 164 0.467290 TTTGTTTTCCCTCCGCAGCT 60.467 50.000 0.00 0.00 0.00 4.24
164 165 0.398696 TTGTTTTCCCTCCGCAGCTA 59.601 50.000 0.00 0.00 0.00 3.32
165 166 0.036388 TGTTTTCCCTCCGCAGCTAG 60.036 55.000 0.00 0.00 0.00 3.42
166 167 0.036294 GTTTTCCCTCCGCAGCTAGT 60.036 55.000 0.00 0.00 0.00 2.57
167 168 0.036388 TTTTCCCTCCGCAGCTAGTG 60.036 55.000 0.00 0.00 0.00 2.74
175 176 1.927895 CCGCAGCTAGTGGTCTTTAG 58.072 55.000 7.38 0.00 43.15 1.85
176 177 1.281899 CGCAGCTAGTGGTCTTTAGC 58.718 55.000 0.00 0.00 41.99 3.09
186 187 8.582433 GCTAGTGGTCTTTAGCTTAGATTAAG 57.418 38.462 0.00 0.00 39.30 1.85
187 188 7.654116 GCTAGTGGTCTTTAGCTTAGATTAAGG 59.346 40.741 0.00 0.00 39.30 2.69
188 189 7.497773 AGTGGTCTTTAGCTTAGATTAAGGT 57.502 36.000 0.00 5.92 46.97 3.50
189 190 7.919151 AGTGGTCTTTAGCTTAGATTAAGGTT 58.081 34.615 5.94 0.00 43.37 3.50
190 191 7.824779 AGTGGTCTTTAGCTTAGATTAAGGTTG 59.175 37.037 5.94 0.00 43.37 3.77
191 192 7.606839 GTGGTCTTTAGCTTAGATTAAGGTTGT 59.393 37.037 5.94 0.00 43.37 3.32
192 193 8.161425 TGGTCTTTAGCTTAGATTAAGGTTGTT 58.839 33.333 5.94 0.00 43.37 2.83
193 194 9.662947 GGTCTTTAGCTTAGATTAAGGTTGTTA 57.337 33.333 5.94 0.00 43.37 2.41
201 202 9.704098 GCTTAGATTAAGGTTGTTATCTTTTCG 57.296 33.333 0.00 0.00 36.31 3.46
205 206 8.727910 AGATTAAGGTTGTTATCTTTTCGAACC 58.272 33.333 0.00 0.00 34.29 3.62
206 207 5.700722 AAGGTTGTTATCTTTTCGAACCC 57.299 39.130 0.00 0.00 34.57 4.11
207 208 4.721132 AGGTTGTTATCTTTTCGAACCCA 58.279 39.130 0.00 0.00 34.57 4.51
208 209 5.134661 AGGTTGTTATCTTTTCGAACCCAA 58.865 37.500 0.00 0.00 34.57 4.12
209 210 5.773176 AGGTTGTTATCTTTTCGAACCCAAT 59.227 36.000 0.00 0.00 34.57 3.16
210 211 5.861787 GGTTGTTATCTTTTCGAACCCAATG 59.138 40.000 0.00 0.00 0.00 2.82
211 212 6.294286 GGTTGTTATCTTTTCGAACCCAATGA 60.294 38.462 0.00 0.00 0.00 2.57
212 213 6.249035 TGTTATCTTTTCGAACCCAATGAC 57.751 37.500 0.00 0.00 0.00 3.06
213 214 6.001460 TGTTATCTTTTCGAACCCAATGACT 58.999 36.000 0.00 0.00 0.00 3.41
214 215 6.072728 TGTTATCTTTTCGAACCCAATGACTG 60.073 38.462 0.00 0.00 0.00 3.51
215 216 3.146066 TCTTTTCGAACCCAATGACTGG 58.854 45.455 0.00 0.00 45.97 4.00
235 236 2.983592 GGGAGTGCCCGTGGTTTG 60.984 66.667 0.00 0.00 46.48 2.93
236 237 2.203294 GGAGTGCCCGTGGTTTGT 60.203 61.111 0.00 0.00 0.00 2.83
237 238 2.551912 GGAGTGCCCGTGGTTTGTG 61.552 63.158 0.00 0.00 0.00 3.33
238 239 2.518349 AGTGCCCGTGGTTTGTGG 60.518 61.111 0.00 0.00 0.00 4.17
239 240 2.831284 GTGCCCGTGGTTTGTGGT 60.831 61.111 0.00 0.00 0.00 4.16
240 241 2.517402 TGCCCGTGGTTTGTGGTC 60.517 61.111 0.00 0.00 0.00 4.02
241 242 3.656045 GCCCGTGGTTTGTGGTCG 61.656 66.667 0.00 0.00 0.00 4.79
242 243 2.109387 CCCGTGGTTTGTGGTCGA 59.891 61.111 0.00 0.00 0.00 4.20
243 244 1.302192 CCCGTGGTTTGTGGTCGAT 60.302 57.895 0.00 0.00 0.00 3.59
244 245 1.573829 CCCGTGGTTTGTGGTCGATG 61.574 60.000 0.00 0.00 0.00 3.84
245 246 0.882927 CCGTGGTTTGTGGTCGATGT 60.883 55.000 0.00 0.00 0.00 3.06
246 247 0.234625 CGTGGTTTGTGGTCGATGTG 59.765 55.000 0.00 0.00 0.00 3.21
247 248 0.591170 GTGGTTTGTGGTCGATGTGG 59.409 55.000 0.00 0.00 0.00 4.17
248 249 0.181587 TGGTTTGTGGTCGATGTGGT 59.818 50.000 0.00 0.00 0.00 4.16
249 250 1.314730 GGTTTGTGGTCGATGTGGTT 58.685 50.000 0.00 0.00 0.00 3.67
250 251 1.679153 GGTTTGTGGTCGATGTGGTTT 59.321 47.619 0.00 0.00 0.00 3.27
251 252 2.287368 GGTTTGTGGTCGATGTGGTTTC 60.287 50.000 0.00 0.00 0.00 2.78
252 253 1.222300 TTGTGGTCGATGTGGTTTCG 58.778 50.000 0.00 0.00 37.94 3.46
253 254 0.105224 TGTGGTCGATGTGGTTTCGT 59.895 50.000 0.00 0.00 37.82 3.85
254 255 1.223187 GTGGTCGATGTGGTTTCGTT 58.777 50.000 0.00 0.00 37.82 3.85
255 256 2.223994 TGTGGTCGATGTGGTTTCGTTA 60.224 45.455 0.00 0.00 37.82 3.18
256 257 2.801679 GTGGTCGATGTGGTTTCGTTAA 59.198 45.455 0.00 0.00 37.82 2.01
257 258 3.434299 GTGGTCGATGTGGTTTCGTTAAT 59.566 43.478 0.00 0.00 37.82 1.40
258 259 3.433957 TGGTCGATGTGGTTTCGTTAATG 59.566 43.478 0.00 0.00 37.82 1.90
259 260 3.680937 GGTCGATGTGGTTTCGTTAATGA 59.319 43.478 0.00 0.00 37.82 2.57
260 261 4.152759 GGTCGATGTGGTTTCGTTAATGAA 59.847 41.667 6.00 6.00 37.82 2.57
261 262 5.334260 GGTCGATGTGGTTTCGTTAATGAAA 60.334 40.000 17.06 17.06 37.82 2.69
262 263 6.311723 GTCGATGTGGTTTCGTTAATGAAAT 58.688 36.000 22.33 9.04 39.80 2.17
263 264 6.799925 GTCGATGTGGTTTCGTTAATGAAATT 59.200 34.615 22.33 8.50 39.80 1.82
264 265 6.799441 TCGATGTGGTTTCGTTAATGAAATTG 59.201 34.615 22.33 12.02 39.80 2.32
265 266 6.033407 CGATGTGGTTTCGTTAATGAAATTGG 59.967 38.462 22.33 7.62 39.80 3.16
266 267 6.392625 TGTGGTTTCGTTAATGAAATTGGA 57.607 33.333 22.33 8.01 39.80 3.53
267 268 6.442952 TGTGGTTTCGTTAATGAAATTGGAG 58.557 36.000 22.33 0.00 39.80 3.86
268 269 5.861787 GTGGTTTCGTTAATGAAATTGGAGG 59.138 40.000 22.33 0.00 39.80 4.30
269 270 5.047660 TGGTTTCGTTAATGAAATTGGAGGG 60.048 40.000 22.33 0.00 39.80 4.30
270 271 5.184287 GGTTTCGTTAATGAAATTGGAGGGA 59.816 40.000 22.33 0.00 39.80 4.20
271 272 6.294843 GGTTTCGTTAATGAAATTGGAGGGAA 60.295 38.462 22.33 0.00 39.80 3.97
272 273 6.902771 TTCGTTAATGAAATTGGAGGGAAA 57.097 33.333 7.67 0.00 36.99 3.13
273 274 6.262193 TCGTTAATGAAATTGGAGGGAAAC 57.738 37.500 0.00 0.00 36.99 2.78
274 275 5.184287 TCGTTAATGAAATTGGAGGGAAACC 59.816 40.000 0.00 0.00 45.42 3.27
320 321 1.865340 CCTACTTTTCTATTCCCGCGC 59.135 52.381 0.00 0.00 0.00 6.86
360 361 2.762745 GAAGAGGCCGTCACTGTTTAA 58.237 47.619 0.00 0.00 0.00 1.52
369 370 5.219633 GCCGTCACTGTTTAATCACAAAAT 58.780 37.500 0.00 0.00 0.00 1.82
370 371 5.689961 GCCGTCACTGTTTAATCACAAAATT 59.310 36.000 0.00 0.00 0.00 1.82
371 372 6.345723 GCCGTCACTGTTTAATCACAAAATTG 60.346 38.462 0.00 0.00 0.00 2.32
372 373 6.915300 CCGTCACTGTTTAATCACAAAATTGA 59.085 34.615 0.00 0.00 0.00 2.57
465 473 4.422057 TGATGTGTGAAACCCTCCTACTA 58.578 43.478 0.00 0.00 34.36 1.82
482 495 5.101529 CCTACTAATCCTAACCCCATCCAT 58.898 45.833 0.00 0.00 0.00 3.41
483 496 5.189934 CCTACTAATCCTAACCCCATCCATC 59.810 48.000 0.00 0.00 0.00 3.51
484 497 3.916989 ACTAATCCTAACCCCATCCATCC 59.083 47.826 0.00 0.00 0.00 3.51
485 498 2.531177 ATCCTAACCCCATCCATCCA 57.469 50.000 0.00 0.00 0.00 3.41
487 500 1.221635 CCTAACCCCATCCATCCACA 58.778 55.000 0.00 0.00 0.00 4.17
488 501 1.782752 CCTAACCCCATCCATCCACAT 59.217 52.381 0.00 0.00 0.00 3.21
490 503 1.612035 AACCCCATCCATCCACATCT 58.388 50.000 0.00 0.00 0.00 2.90
502 515 5.653769 TCCATCCACATCTCCAAAGAAAATC 59.346 40.000 0.00 0.00 34.49 2.17
520 533 3.145551 GGAGCATGGCAGGCAAGG 61.146 66.667 27.04 0.00 0.00 3.61
627 641 1.227263 CCGAGGGCAATACGGTCAG 60.227 63.158 0.00 0.00 41.47 3.51
628 642 1.672854 CCGAGGGCAATACGGTCAGA 61.673 60.000 0.00 0.00 41.47 3.27
730 779 1.518903 AAAGTGCAGCGAAGGAAGCC 61.519 55.000 0.00 0.00 34.64 4.35
770 829 4.314440 GACCGGCACCAGCAGTCA 62.314 66.667 0.00 0.00 44.61 3.41
771 830 4.320456 ACCGGCACCAGCAGTCAG 62.320 66.667 0.00 0.00 44.61 3.51
772 831 4.320456 CCGGCACCAGCAGTCAGT 62.320 66.667 0.00 0.00 44.61 3.41
773 832 2.740055 CGGCACCAGCAGTCAGTC 60.740 66.667 0.00 0.00 44.61 3.51
792 851 0.530431 CCAGCAGCACCAACCAAAAC 60.530 55.000 0.00 0.00 0.00 2.43
816 876 0.951040 GGGAGACAACAGACAAGGCG 60.951 60.000 0.00 0.00 0.00 5.52
817 877 1.569479 GGAGACAACAGACAAGGCGC 61.569 60.000 0.00 0.00 0.00 6.53
818 878 0.880278 GAGACAACAGACAAGGCGCA 60.880 55.000 10.83 0.00 0.00 6.09
819 879 0.882042 AGACAACAGACAAGGCGCAG 60.882 55.000 10.83 0.00 0.00 5.18
907 967 0.541764 TTCCCCATGTGAGTTTGCCC 60.542 55.000 0.00 0.00 0.00 5.36
908 968 1.984026 CCCCATGTGAGTTTGCCCC 60.984 63.158 0.00 0.00 0.00 5.80
909 969 1.077265 CCCATGTGAGTTTGCCCCT 59.923 57.895 0.00 0.00 0.00 4.79
913 973 1.142688 ATGTGAGTTTGCCCCTCCCT 61.143 55.000 0.00 0.00 0.00 4.20
914 974 1.002011 GTGAGTTTGCCCCTCCCTC 60.002 63.158 0.00 0.00 0.00 4.30
915 975 1.151810 TGAGTTTGCCCCTCCCTCT 60.152 57.895 0.00 0.00 0.00 3.69
916 976 1.201429 TGAGTTTGCCCCTCCCTCTC 61.201 60.000 0.00 0.00 0.00 3.20
917 977 1.916206 GAGTTTGCCCCTCCCTCTCC 61.916 65.000 0.00 0.00 0.00 3.71
918 978 2.614013 TTTGCCCCTCCCTCTCCC 60.614 66.667 0.00 0.00 0.00 4.30
919 979 4.760220 TTGCCCCTCCCTCTCCCC 62.760 72.222 0.00 0.00 0.00 4.81
1054 1131 3.388703 CTGCTCCTGCTCCTGCTCC 62.389 68.421 0.00 0.00 40.48 4.70
1056 1133 3.847602 CTCCTGCTCCTGCTCCCG 61.848 72.222 0.00 0.00 40.48 5.14
1059 1136 4.834453 CTGCTCCTGCTCCCGCTG 62.834 72.222 0.00 0.00 40.48 5.18
1088 1171 4.351938 CTCGTCGAACCGTGGCCA 62.352 66.667 0.00 0.00 0.00 5.36
1094 1177 4.329545 GAACCGTGGCCAGGAGCA 62.330 66.667 26.78 0.00 46.50 4.26
1327 1416 1.994507 CAGCTCTCCTTGCCCTCCT 60.995 63.158 0.00 0.00 0.00 3.69
1329 1418 1.077858 GCTCTCCTTGCCCTCCTTG 60.078 63.158 0.00 0.00 0.00 3.61
1518 1607 1.571460 CAGCTGCACGGAGTTGAAC 59.429 57.895 0.00 0.00 41.61 3.18
1620 1709 1.674651 GTCCCGGAACCTTCTTGCC 60.675 63.158 0.73 0.00 0.00 4.52
1773 1862 1.557099 ACAGATTGAGCGGTCTGGTA 58.443 50.000 16.64 0.00 44.72 3.25
1791 1880 0.031414 TACCCAGGGAGCTAGGGAAC 60.031 60.000 14.54 0.00 45.80 3.62
1845 1934 2.288395 CCAGTTTGATGCAGTGAAACCC 60.288 50.000 12.14 0.00 34.88 4.11
1884 1973 2.811799 GGAGAGCTTCCGGAGAGC 59.188 66.667 23.13 23.13 40.43 4.09
2142 2231 2.957680 TGTGTTTGATGTCAGTGGCAAT 59.042 40.909 0.00 0.00 0.00 3.56
2143 2232 3.243468 TGTGTTTGATGTCAGTGGCAATG 60.243 43.478 8.96 8.96 0.00 2.82
2148 2237 2.815503 TGATGTCAGTGGCAATGAACTG 59.184 45.455 20.20 7.48 44.23 3.16
2168 2257 0.036732 TCAGGCTCAATTCCAGCGTT 59.963 50.000 0.00 0.00 37.81 4.84
2181 2270 1.532921 CCAGCGTTTGCGAACAAAGAA 60.533 47.619 16.98 0.00 46.17 2.52
2243 2332 1.741028 TCTTCACCCTTCATGTCCCA 58.259 50.000 0.00 0.00 0.00 4.37
2393 2482 2.493278 ACAGGACCTTGCATGCATTAAC 59.507 45.455 23.37 13.32 0.00 2.01
2415 2504 9.554395 TTAACTCTTGATCACAATAACTTCACA 57.446 29.630 0.00 0.00 35.37 3.58
2758 2847 1.003580 GGCAGTTGGAATCACTGGAGA 59.996 52.381 3.42 0.00 32.55 3.71
2775 2864 7.015098 TCACTGGAGATTTTAGATCTCTCATCC 59.985 40.741 11.68 1.63 43.00 3.51
2874 2963 1.734465 CTCTCTGGAAACATTGCCGAC 59.266 52.381 0.00 0.00 41.51 4.79
2890 2982 1.411612 CCGACCTTACCCCAGTATCAC 59.588 57.143 0.00 0.00 0.00 3.06
2992 3087 5.069781 GCTAGTCCAGAACCTGAGAATACAT 59.930 44.000 0.00 0.00 32.44 2.29
3147 3242 4.262506 CGTTCTAACAGGAGAAGGGAAGTT 60.263 45.833 0.00 0.00 37.57 2.66
3298 3393 2.543641 GCATTCTGGTGGCAATAAAGC 58.456 47.619 0.00 0.00 0.00 3.51
3303 3398 1.139520 GGTGGCAATAAAGCGGCTG 59.860 57.895 1.81 0.00 34.64 4.85
3471 3566 5.121768 CGGTAACTTGGAAAGGTTCATACAG 59.878 44.000 0.00 0.00 45.56 2.74
3708 3803 1.301874 TGTCGCGGGTACTTTTGGG 60.302 57.895 6.13 0.00 0.00 4.12
3780 3875 3.398406 TGTGTACAGCTATGGTGTTGTG 58.602 45.455 7.70 0.00 41.72 3.33
3874 3969 2.951101 GCCTGGGCTTGCATGCTTT 61.951 57.895 22.27 0.00 38.26 3.51
3972 4067 0.973632 TGCACCTCGGTATCAAGTGT 59.026 50.000 0.00 0.00 0.00 3.55
4066 4161 5.586643 CCCTCTTACTAGAATTTGCAACTCC 59.413 44.000 0.00 0.00 0.00 3.85
4079 4174 4.817318 TGCAACTCCAGTATGACATACA 57.183 40.909 24.08 6.22 39.69 2.29
4200 4296 3.122948 GGTGGTGCAGTATTTATATCGCG 59.877 47.826 0.00 0.00 0.00 5.87
4314 4412 9.979578 TTTGAATGCTGTTAATTTATGTTGTCT 57.020 25.926 0.00 0.00 0.00 3.41
4347 4445 7.284261 TGGTGATATTGTTTTCTCTTGTCAACA 59.716 33.333 0.00 0.00 0.00 3.33
4453 4557 5.000012 AGCTTTCTGGTAGAAGTATGTCG 58.000 43.478 0.00 0.00 35.37 4.35
4570 4674 5.897377 ACTTCAACAAACTTAGTGCACTT 57.103 34.783 27.06 3.70 0.00 3.16
4571 4675 5.880341 ACTTCAACAAACTTAGTGCACTTC 58.120 37.500 27.06 0.00 0.00 3.01
4651 4769 5.044846 AGACTGTTCTATGGCCCTTTGTTAT 60.045 40.000 0.00 0.00 0.00 1.89
4658 4776 4.806640 ATGGCCCTTTGTTATGAAACAG 57.193 40.909 0.00 0.00 45.99 3.16
4730 4848 3.744660 GCAGTATCGGAGGGATGAATTT 58.255 45.455 0.00 0.00 36.55 1.82
4760 4878 2.857592 ATCAACCGATGATTTGCTGC 57.142 45.000 0.00 0.00 46.85 5.25
4878 4999 6.958752 GCCAATTTTCGGTTGCATTATTTTAC 59.041 34.615 0.00 0.00 0.00 2.01
4925 5046 6.795144 TGGAATGGAAAACTATGAATGCAT 57.205 33.333 0.00 0.00 38.54 3.96
5036 5157 3.486383 TGTTGAGGATTCTGTTTGACCC 58.514 45.455 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.864334 CTCCATCCCTGTGCCGCC 62.864 72.222 0.00 0.00 0.00 6.13
2 3 3.785859 TCTCCATCCCTGTGCCGC 61.786 66.667 0.00 0.00 0.00 6.53
3 4 2.187946 GTCTCCATCCCTGTGCCG 59.812 66.667 0.00 0.00 0.00 5.69
4 5 0.691078 TAGGTCTCCATCCCTGTGCC 60.691 60.000 0.00 0.00 32.08 5.01
5 6 0.755686 CTAGGTCTCCATCCCTGTGC 59.244 60.000 0.00 0.00 32.08 4.57
6 7 2.315176 CTCTAGGTCTCCATCCCTGTG 58.685 57.143 0.00 0.00 32.08 3.66
7 8 1.933765 ACTCTAGGTCTCCATCCCTGT 59.066 52.381 0.00 0.00 32.08 4.00
8 9 2.765689 ACTCTAGGTCTCCATCCCTG 57.234 55.000 0.00 0.00 32.08 4.45
9 10 2.587777 TGAACTCTAGGTCTCCATCCCT 59.412 50.000 0.00 0.00 34.74 4.20
10 11 2.962421 CTGAACTCTAGGTCTCCATCCC 59.038 54.545 0.00 0.00 0.00 3.85
11 12 2.364002 GCTGAACTCTAGGTCTCCATCC 59.636 54.545 0.00 0.00 0.00 3.51
12 13 2.034053 CGCTGAACTCTAGGTCTCCATC 59.966 54.545 0.00 0.00 0.00 3.51
13 14 2.028130 CGCTGAACTCTAGGTCTCCAT 58.972 52.381 0.00 0.00 0.00 3.41
14 15 1.004394 TCGCTGAACTCTAGGTCTCCA 59.996 52.381 0.00 0.00 0.00 3.86
15 16 1.402613 GTCGCTGAACTCTAGGTCTCC 59.597 57.143 0.00 0.00 0.00 3.71
16 17 2.096819 CAGTCGCTGAACTCTAGGTCTC 59.903 54.545 1.18 0.00 32.44 3.36
17 18 2.088423 CAGTCGCTGAACTCTAGGTCT 58.912 52.381 1.18 0.00 32.44 3.85
18 19 1.133407 CCAGTCGCTGAACTCTAGGTC 59.867 57.143 8.20 0.00 32.44 3.85
19 20 1.178276 CCAGTCGCTGAACTCTAGGT 58.822 55.000 8.20 0.00 32.44 3.08
20 21 0.457851 CCCAGTCGCTGAACTCTAGG 59.542 60.000 8.20 0.00 32.44 3.02
21 22 1.464734 TCCCAGTCGCTGAACTCTAG 58.535 55.000 8.20 0.00 32.44 2.43
22 23 1.819288 CTTCCCAGTCGCTGAACTCTA 59.181 52.381 8.20 0.00 32.44 2.43
23 24 0.605589 CTTCCCAGTCGCTGAACTCT 59.394 55.000 8.20 0.00 32.44 3.24
24 25 0.603569 TCTTCCCAGTCGCTGAACTC 59.396 55.000 8.20 0.00 32.44 3.01
25 26 1.066573 CATCTTCCCAGTCGCTGAACT 60.067 52.381 8.20 0.00 32.44 3.01
26 27 1.066858 TCATCTTCCCAGTCGCTGAAC 60.067 52.381 8.20 0.00 32.44 3.18
27 28 1.266178 TCATCTTCCCAGTCGCTGAA 58.734 50.000 8.20 0.00 32.44 3.02
28 29 1.137675 CATCATCTTCCCAGTCGCTGA 59.862 52.381 8.20 0.00 32.44 4.26
29 30 1.137675 TCATCATCTTCCCAGTCGCTG 59.862 52.381 0.52 0.52 0.00 5.18
30 31 1.489481 TCATCATCTTCCCAGTCGCT 58.511 50.000 0.00 0.00 0.00 4.93
31 32 2.315925 TTCATCATCTTCCCAGTCGC 57.684 50.000 0.00 0.00 0.00 5.19
32 33 4.333913 AGATTCATCATCTTCCCAGTCG 57.666 45.455 0.00 0.00 39.47 4.18
41 42 5.307716 GGGAAGGAGAGAAGATTCATCATCT 59.692 44.000 0.00 0.00 45.03 2.90
42 43 5.307716 AGGGAAGGAGAGAAGATTCATCATC 59.692 44.000 0.00 0.00 0.00 2.92
43 44 5.226015 AGGGAAGGAGAGAAGATTCATCAT 58.774 41.667 0.00 0.00 0.00 2.45
44 45 4.629122 AGGGAAGGAGAGAAGATTCATCA 58.371 43.478 0.00 0.00 0.00 3.07
45 46 4.901250 AGAGGGAAGGAGAGAAGATTCATC 59.099 45.833 0.00 0.00 0.00 2.92
46 47 4.655186 CAGAGGGAAGGAGAGAAGATTCAT 59.345 45.833 0.00 0.00 0.00 2.57
47 48 4.029520 CAGAGGGAAGGAGAGAAGATTCA 58.970 47.826 0.00 0.00 0.00 2.57
48 49 4.030216 ACAGAGGGAAGGAGAGAAGATTC 58.970 47.826 0.00 0.00 0.00 2.52
49 50 4.073425 ACAGAGGGAAGGAGAGAAGATT 57.927 45.455 0.00 0.00 0.00 2.40
50 51 3.774842 ACAGAGGGAAGGAGAGAAGAT 57.225 47.619 0.00 0.00 0.00 2.40
51 52 3.551635 AACAGAGGGAAGGAGAGAAGA 57.448 47.619 0.00 0.00 0.00 2.87
52 53 4.574892 GAAAACAGAGGGAAGGAGAGAAG 58.425 47.826 0.00 0.00 0.00 2.85
53 54 3.006967 CGAAAACAGAGGGAAGGAGAGAA 59.993 47.826 0.00 0.00 0.00 2.87
54 55 2.563179 CGAAAACAGAGGGAAGGAGAGA 59.437 50.000 0.00 0.00 0.00 3.10
55 56 2.300437 ACGAAAACAGAGGGAAGGAGAG 59.700 50.000 0.00 0.00 0.00 3.20
56 57 2.299297 GACGAAAACAGAGGGAAGGAGA 59.701 50.000 0.00 0.00 0.00 3.71
57 58 2.037251 TGACGAAAACAGAGGGAAGGAG 59.963 50.000 0.00 0.00 0.00 3.69
58 59 2.043992 TGACGAAAACAGAGGGAAGGA 58.956 47.619 0.00 0.00 0.00 3.36
59 60 2.543777 TGACGAAAACAGAGGGAAGG 57.456 50.000 0.00 0.00 0.00 3.46
60 61 3.403038 ACATGACGAAAACAGAGGGAAG 58.597 45.455 0.00 0.00 0.00 3.46
61 62 3.485463 ACATGACGAAAACAGAGGGAA 57.515 42.857 0.00 0.00 0.00 3.97
62 63 4.610605 TTACATGACGAAAACAGAGGGA 57.389 40.909 0.00 0.00 0.00 4.20
63 64 5.178797 AGATTACATGACGAAAACAGAGGG 58.821 41.667 0.00 0.00 0.00 4.30
64 65 6.368791 TCAAGATTACATGACGAAAACAGAGG 59.631 38.462 0.00 0.00 0.00 3.69
65 66 7.351414 TCAAGATTACATGACGAAAACAGAG 57.649 36.000 0.00 0.00 0.00 3.35
66 67 7.905604 ATCAAGATTACATGACGAAAACAGA 57.094 32.000 0.00 0.00 0.00 3.41
67 68 9.478019 GTTATCAAGATTACATGACGAAAACAG 57.522 33.333 0.00 0.00 0.00 3.16
68 69 9.214957 AGTTATCAAGATTACATGACGAAAACA 57.785 29.630 0.00 0.00 0.00 2.83
71 72 9.214957 ACAAGTTATCAAGATTACATGACGAAA 57.785 29.630 0.00 0.00 0.00 3.46
72 73 8.771920 ACAAGTTATCAAGATTACATGACGAA 57.228 30.769 0.00 0.00 0.00 3.85
73 74 9.516314 CTACAAGTTATCAAGATTACATGACGA 57.484 33.333 0.00 0.00 0.00 4.20
74 75 9.516314 TCTACAAGTTATCAAGATTACATGACG 57.484 33.333 0.00 3.07 0.00 4.35
101 102 8.996271 GCTTACACCAGTACAGTTATTTAAACT 58.004 33.333 0.00 0.00 0.00 2.66
102 103 7.953710 CGCTTACACCAGTACAGTTATTTAAAC 59.046 37.037 0.00 0.00 0.00 2.01
103 104 7.871973 TCGCTTACACCAGTACAGTTATTTAAA 59.128 33.333 0.00 0.00 0.00 1.52
104 105 7.377398 TCGCTTACACCAGTACAGTTATTTAA 58.623 34.615 0.00 0.00 0.00 1.52
105 106 6.923012 TCGCTTACACCAGTACAGTTATTTA 58.077 36.000 0.00 0.00 0.00 1.40
106 107 5.786311 TCGCTTACACCAGTACAGTTATTT 58.214 37.500 0.00 0.00 0.00 1.40
107 108 5.395682 TCGCTTACACCAGTACAGTTATT 57.604 39.130 0.00 0.00 0.00 1.40
108 109 5.348986 CATCGCTTACACCAGTACAGTTAT 58.651 41.667 0.00 0.00 0.00 1.89
109 110 4.740268 CATCGCTTACACCAGTACAGTTA 58.260 43.478 0.00 0.00 0.00 2.24
110 111 3.585862 CATCGCTTACACCAGTACAGTT 58.414 45.455 0.00 0.00 0.00 3.16
111 112 2.674177 GCATCGCTTACACCAGTACAGT 60.674 50.000 0.00 0.00 0.00 3.55
112 113 1.927174 GCATCGCTTACACCAGTACAG 59.073 52.381 0.00 0.00 0.00 2.74
113 114 1.273886 TGCATCGCTTACACCAGTACA 59.726 47.619 0.00 0.00 0.00 2.90
114 115 2.004583 TGCATCGCTTACACCAGTAC 57.995 50.000 0.00 0.00 0.00 2.73
115 116 2.093711 ACATGCATCGCTTACACCAGTA 60.094 45.455 0.00 0.00 0.00 2.74
116 117 1.339055 ACATGCATCGCTTACACCAGT 60.339 47.619 0.00 0.00 0.00 4.00
117 118 1.328680 GACATGCATCGCTTACACCAG 59.671 52.381 0.00 0.00 0.00 4.00
118 119 1.338579 TGACATGCATCGCTTACACCA 60.339 47.619 0.00 0.00 0.00 4.17
119 120 1.368641 TGACATGCATCGCTTACACC 58.631 50.000 0.00 0.00 0.00 4.16
120 121 2.352651 ACATGACATGCATCGCTTACAC 59.647 45.455 15.49 0.00 34.15 2.90
121 122 2.609002 GACATGACATGCATCGCTTACA 59.391 45.455 15.49 0.00 34.15 2.41
122 123 2.868583 AGACATGACATGCATCGCTTAC 59.131 45.455 15.49 0.00 34.15 2.34
123 124 3.183793 AGACATGACATGCATCGCTTA 57.816 42.857 15.49 0.00 34.15 3.09
124 125 2.034104 AGACATGACATGCATCGCTT 57.966 45.000 15.49 0.00 34.15 4.68
125 126 2.034104 AAGACATGACATGCATCGCT 57.966 45.000 15.49 2.92 34.15 4.93
126 127 2.838386 AAAGACATGACATGCATCGC 57.162 45.000 15.49 0.69 34.15 4.58
127 128 4.087510 ACAAAAGACATGACATGCATCG 57.912 40.909 15.49 2.46 34.15 3.84
128 129 6.128742 GGAAAACAAAAGACATGACATGCATC 60.129 38.462 15.49 6.64 34.15 3.91
129 130 5.697633 GGAAAACAAAAGACATGACATGCAT 59.302 36.000 15.49 0.00 37.85 3.96
130 131 5.049167 GGAAAACAAAAGACATGACATGCA 58.951 37.500 15.49 0.00 0.00 3.96
131 132 4.448732 GGGAAAACAAAAGACATGACATGC 59.551 41.667 15.49 8.35 0.00 4.06
132 133 5.846203 AGGGAAAACAAAAGACATGACATG 58.154 37.500 14.02 14.02 0.00 3.21
133 134 5.011023 GGAGGGAAAACAAAAGACATGACAT 59.989 40.000 0.00 0.00 0.00 3.06
134 135 4.340950 GGAGGGAAAACAAAAGACATGACA 59.659 41.667 0.00 0.00 0.00 3.58
135 136 4.556699 CGGAGGGAAAACAAAAGACATGAC 60.557 45.833 0.00 0.00 0.00 3.06
136 137 3.568007 CGGAGGGAAAACAAAAGACATGA 59.432 43.478 0.00 0.00 0.00 3.07
137 138 3.857010 GCGGAGGGAAAACAAAAGACATG 60.857 47.826 0.00 0.00 0.00 3.21
138 139 2.296190 GCGGAGGGAAAACAAAAGACAT 59.704 45.455 0.00 0.00 0.00 3.06
139 140 1.679153 GCGGAGGGAAAACAAAAGACA 59.321 47.619 0.00 0.00 0.00 3.41
140 141 1.679153 TGCGGAGGGAAAACAAAAGAC 59.321 47.619 0.00 0.00 0.00 3.01
141 142 1.953686 CTGCGGAGGGAAAACAAAAGA 59.046 47.619 0.00 0.00 0.00 2.52
142 143 1.602920 GCTGCGGAGGGAAAACAAAAG 60.603 52.381 5.93 0.00 0.00 2.27
143 144 0.387565 GCTGCGGAGGGAAAACAAAA 59.612 50.000 5.93 0.00 0.00 2.44
144 145 0.467290 AGCTGCGGAGGGAAAACAAA 60.467 50.000 5.93 0.00 0.00 2.83
145 146 0.398696 TAGCTGCGGAGGGAAAACAA 59.601 50.000 5.93 0.00 0.00 2.83
146 147 0.036388 CTAGCTGCGGAGGGAAAACA 60.036 55.000 5.93 0.00 0.00 2.83
147 148 0.036294 ACTAGCTGCGGAGGGAAAAC 60.036 55.000 5.93 0.00 0.00 2.43
148 149 0.036388 CACTAGCTGCGGAGGGAAAA 60.036 55.000 5.93 0.00 0.00 2.29
149 150 1.596934 CACTAGCTGCGGAGGGAAA 59.403 57.895 5.93 0.00 0.00 3.13
150 151 2.359169 CCACTAGCTGCGGAGGGAA 61.359 63.158 5.93 0.00 0.00 3.97
151 152 2.759973 CCACTAGCTGCGGAGGGA 60.760 66.667 5.93 0.00 0.00 4.20
152 153 3.077556 ACCACTAGCTGCGGAGGG 61.078 66.667 5.93 0.00 0.00 4.30
153 154 1.608717 AAGACCACTAGCTGCGGAGG 61.609 60.000 5.93 9.29 0.00 4.30
154 155 0.247736 AAAGACCACTAGCTGCGGAG 59.752 55.000 0.00 0.00 0.00 4.63
155 156 1.476891 CTAAAGACCACTAGCTGCGGA 59.523 52.381 0.00 0.00 0.00 5.54
156 157 1.927895 CTAAAGACCACTAGCTGCGG 58.072 55.000 0.00 0.00 0.00 5.69
157 158 1.134965 AGCTAAAGACCACTAGCTGCG 60.135 52.381 0.00 0.00 43.44 5.18
158 159 2.682155 AGCTAAAGACCACTAGCTGC 57.318 50.000 0.00 0.00 43.44 5.25
159 160 5.584253 TCTAAGCTAAAGACCACTAGCTG 57.416 43.478 0.00 0.00 44.21 4.24
160 161 6.800072 AATCTAAGCTAAAGACCACTAGCT 57.200 37.500 0.99 0.00 46.63 3.32
161 162 7.654116 CCTTAATCTAAGCTAAAGACCACTAGC 59.346 40.741 0.99 0.00 34.46 3.42
162 163 8.697292 ACCTTAATCTAAGCTAAAGACCACTAG 58.303 37.037 0.99 0.00 34.46 2.57
163 164 8.605325 ACCTTAATCTAAGCTAAAGACCACTA 57.395 34.615 0.99 0.00 34.46 2.74
164 165 7.497773 ACCTTAATCTAAGCTAAAGACCACT 57.502 36.000 0.99 0.00 34.46 4.00
165 166 7.606839 ACAACCTTAATCTAAGCTAAAGACCAC 59.393 37.037 0.99 0.00 34.46 4.16
166 167 7.686434 ACAACCTTAATCTAAGCTAAAGACCA 58.314 34.615 0.99 0.00 34.46 4.02
167 168 8.563123 AACAACCTTAATCTAAGCTAAAGACC 57.437 34.615 0.99 0.00 34.46 3.85
175 176 9.704098 CGAAAAGATAACAACCTTAATCTAAGC 57.296 33.333 0.00 0.00 34.46 3.09
179 180 8.727910 GGTTCGAAAAGATAACAACCTTAATCT 58.272 33.333 0.00 0.00 32.16 2.40
180 181 7.966753 GGGTTCGAAAAGATAACAACCTTAATC 59.033 37.037 0.00 0.00 34.79 1.75
181 182 7.449086 TGGGTTCGAAAAGATAACAACCTTAAT 59.551 33.333 0.00 0.00 34.79 1.40
182 183 6.771749 TGGGTTCGAAAAGATAACAACCTTAA 59.228 34.615 0.00 0.00 34.79 1.85
183 184 6.297582 TGGGTTCGAAAAGATAACAACCTTA 58.702 36.000 0.00 0.00 34.79 2.69
184 185 5.134661 TGGGTTCGAAAAGATAACAACCTT 58.865 37.500 0.00 0.00 34.79 3.50
185 186 4.721132 TGGGTTCGAAAAGATAACAACCT 58.279 39.130 0.00 0.00 34.79 3.50
186 187 5.441709 TTGGGTTCGAAAAGATAACAACC 57.558 39.130 0.00 0.00 33.80 3.77
187 188 6.581166 GTCATTGGGTTCGAAAAGATAACAAC 59.419 38.462 0.00 0.00 0.00 3.32
188 189 6.488683 AGTCATTGGGTTCGAAAAGATAACAA 59.511 34.615 0.00 0.00 0.00 2.83
189 190 6.001460 AGTCATTGGGTTCGAAAAGATAACA 58.999 36.000 0.00 0.00 0.00 2.41
190 191 6.314784 CAGTCATTGGGTTCGAAAAGATAAC 58.685 40.000 0.00 0.00 0.00 1.89
191 192 5.414454 CCAGTCATTGGGTTCGAAAAGATAA 59.586 40.000 0.00 0.00 43.75 1.75
192 193 4.941263 CCAGTCATTGGGTTCGAAAAGATA 59.059 41.667 0.00 0.00 43.75 1.98
193 194 3.758554 CCAGTCATTGGGTTCGAAAAGAT 59.241 43.478 0.00 0.00 43.75 2.40
194 195 3.146066 CCAGTCATTGGGTTCGAAAAGA 58.854 45.455 0.00 0.00 43.75 2.52
195 196 3.559238 CCAGTCATTGGGTTCGAAAAG 57.441 47.619 0.00 0.00 43.75 2.27
206 207 1.021390 GCACTCCCGTCCAGTCATTG 61.021 60.000 0.00 0.00 0.00 2.82
207 208 1.296715 GCACTCCCGTCCAGTCATT 59.703 57.895 0.00 0.00 0.00 2.57
208 209 2.660064 GGCACTCCCGTCCAGTCAT 61.660 63.158 0.00 0.00 0.00 3.06
209 210 3.311110 GGCACTCCCGTCCAGTCA 61.311 66.667 0.00 0.00 0.00 3.41
210 211 4.083862 GGGCACTCCCGTCCAGTC 62.084 72.222 0.00 0.00 43.94 3.51
219 220 2.203294 ACAAACCACGGGCACTCC 60.203 61.111 0.00 0.00 0.00 3.85
220 221 2.551912 CCACAAACCACGGGCACTC 61.552 63.158 0.00 0.00 0.00 3.51
221 222 2.518349 CCACAAACCACGGGCACT 60.518 61.111 0.00 0.00 0.00 4.40
222 223 2.831284 ACCACAAACCACGGGCAC 60.831 61.111 0.00 0.00 0.00 5.01
223 224 2.517402 GACCACAAACCACGGGCA 60.517 61.111 0.00 0.00 0.00 5.36
224 225 3.656045 CGACCACAAACCACGGGC 61.656 66.667 0.00 0.00 0.00 6.13
225 226 1.302192 ATCGACCACAAACCACGGG 60.302 57.895 0.00 0.00 0.00 5.28
226 227 0.882927 ACATCGACCACAAACCACGG 60.883 55.000 0.00 0.00 0.00 4.94
227 228 0.234625 CACATCGACCACAAACCACG 59.765 55.000 0.00 0.00 0.00 4.94
228 229 0.591170 CCACATCGACCACAAACCAC 59.409 55.000 0.00 0.00 0.00 4.16
229 230 0.181587 ACCACATCGACCACAAACCA 59.818 50.000 0.00 0.00 0.00 3.67
230 231 1.314730 AACCACATCGACCACAAACC 58.685 50.000 0.00 0.00 0.00 3.27
231 232 2.601266 CGAAACCACATCGACCACAAAC 60.601 50.000 0.00 0.00 42.76 2.93
232 233 1.600013 CGAAACCACATCGACCACAAA 59.400 47.619 0.00 0.00 42.76 2.83
233 234 1.222300 CGAAACCACATCGACCACAA 58.778 50.000 0.00 0.00 42.76 3.33
234 235 0.105224 ACGAAACCACATCGACCACA 59.895 50.000 2.65 0.00 42.76 4.17
235 236 1.223187 AACGAAACCACATCGACCAC 58.777 50.000 2.65 0.00 42.76 4.16
236 237 2.816204 TAACGAAACCACATCGACCA 57.184 45.000 2.65 0.00 42.76 4.02
237 238 3.680937 TCATTAACGAAACCACATCGACC 59.319 43.478 2.65 0.00 42.76 4.79
238 239 4.914312 TCATTAACGAAACCACATCGAC 57.086 40.909 2.65 0.00 42.76 4.20
239 240 5.926214 TTTCATTAACGAAACCACATCGA 57.074 34.783 2.65 0.00 42.76 3.59
240 241 6.033407 CCAATTTCATTAACGAAACCACATCG 59.967 38.462 0.00 0.00 45.47 3.84
241 242 7.087639 TCCAATTTCATTAACGAAACCACATC 58.912 34.615 0.00 0.00 37.69 3.06
242 243 6.987386 TCCAATTTCATTAACGAAACCACAT 58.013 32.000 0.00 0.00 37.69 3.21
243 244 6.392625 TCCAATTTCATTAACGAAACCACA 57.607 33.333 0.00 0.00 37.69 4.17
244 245 5.861787 CCTCCAATTTCATTAACGAAACCAC 59.138 40.000 0.00 0.00 37.69 4.16
245 246 5.047660 CCCTCCAATTTCATTAACGAAACCA 60.048 40.000 0.00 0.00 37.69 3.67
246 247 5.184287 TCCCTCCAATTTCATTAACGAAACC 59.816 40.000 0.00 0.00 37.69 3.27
247 248 6.262193 TCCCTCCAATTTCATTAACGAAAC 57.738 37.500 0.00 0.00 37.69 2.78
248 249 6.902771 TTCCCTCCAATTTCATTAACGAAA 57.097 33.333 0.00 0.00 39.13 3.46
249 250 6.294843 GGTTTCCCTCCAATTTCATTAACGAA 60.295 38.462 0.00 0.00 0.00 3.85
250 251 5.184287 GGTTTCCCTCCAATTTCATTAACGA 59.816 40.000 0.00 0.00 0.00 3.85
251 252 5.185056 AGGTTTCCCTCCAATTTCATTAACG 59.815 40.000 0.00 0.00 35.62 3.18
252 253 6.605471 AGGTTTCCCTCCAATTTCATTAAC 57.395 37.500 0.00 0.00 35.62 2.01
295 296 6.164176 CGCGGGAATAGAAAAGTAGGAATAT 58.836 40.000 0.00 0.00 0.00 1.28
305 306 1.091537 CCAAGCGCGGGAATAGAAAA 58.908 50.000 15.06 0.00 0.00 2.29
351 352 9.904647 CAGTTTCAATTTTGTGATTAAACAGTG 57.095 29.630 0.00 0.00 0.00 3.66
465 473 2.447047 GTGGATGGATGGGGTTAGGATT 59.553 50.000 0.00 0.00 0.00 3.01
482 495 4.009675 CCGATTTTCTTTGGAGATGTGGA 58.990 43.478 0.00 0.00 0.00 4.02
483 496 4.009675 TCCGATTTTCTTTGGAGATGTGG 58.990 43.478 0.00 0.00 0.00 4.17
484 497 4.437930 GCTCCGATTTTCTTTGGAGATGTG 60.438 45.833 11.12 0.00 46.50 3.21
485 498 3.691609 GCTCCGATTTTCTTTGGAGATGT 59.308 43.478 11.12 0.00 46.50 3.06
487 500 3.955471 TGCTCCGATTTTCTTTGGAGAT 58.045 40.909 11.12 0.00 46.50 2.75
488 501 3.417069 TGCTCCGATTTTCTTTGGAGA 57.583 42.857 11.12 0.00 46.50 3.71
490 503 2.754552 CCATGCTCCGATTTTCTTTGGA 59.245 45.455 0.00 0.00 0.00 3.53
502 515 3.515286 CTTGCCTGCCATGCTCCG 61.515 66.667 0.00 0.00 0.00 4.63
520 533 1.810031 GCTTTTGGGTTTTGACCAGGC 60.810 52.381 0.00 0.00 39.57 4.85
674 707 4.310769 CCGTCCTCCACTGATAATTCATC 58.689 47.826 0.00 0.00 0.00 2.92
680 713 1.286849 TCTCCCGTCCTCCACTGATAA 59.713 52.381 0.00 0.00 0.00 1.75
681 714 0.924090 TCTCCCGTCCTCCACTGATA 59.076 55.000 0.00 0.00 0.00 2.15
683 716 1.000771 CTCTCCCGTCCTCCACTGA 60.001 63.158 0.00 0.00 0.00 3.41
684 717 2.055042 CCTCTCCCGTCCTCCACTG 61.055 68.421 0.00 0.00 0.00 3.66
685 718 2.360980 CCTCTCCCGTCCTCCACT 59.639 66.667 0.00 0.00 0.00 4.00
686 719 3.462678 GCCTCTCCCGTCCTCCAC 61.463 72.222 0.00 0.00 0.00 4.02
688 721 4.816984 TCGCCTCTCCCGTCCTCC 62.817 72.222 0.00 0.00 0.00 4.30
730 779 1.078848 CTCTGCTTCCCCTTCCGTG 60.079 63.158 0.00 0.00 0.00 4.94
770 829 2.113986 GGTTGGTGCTGCTGGACT 59.886 61.111 14.56 0.00 34.78 3.85
771 830 1.391157 TTTGGTTGGTGCTGCTGGAC 61.391 55.000 6.70 6.70 0.00 4.02
772 831 0.685785 TTTTGGTTGGTGCTGCTGGA 60.686 50.000 0.00 0.00 0.00 3.86
773 832 0.530431 GTTTTGGTTGGTGCTGCTGG 60.530 55.000 0.00 0.00 0.00 4.85
792 851 1.185618 TGTCTGTTGTCTCCCTCCGG 61.186 60.000 0.00 0.00 0.00 5.14
907 967 4.179599 GGGGAGGGGAGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
908 968 3.039526 AGGGGAGGGGAGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
909 969 3.036959 GAGGGGAGGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
913 973 3.036959 GAGGGAGGGGAGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
914 974 4.548513 CGAGGGAGGGGAGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
916 976 4.862823 GACGAGGGAGGGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
919 979 4.444081 ACCGACGAGGGAGGGGAG 62.444 72.222 0.00 0.00 46.96 4.30
920 980 4.437587 GACCGACGAGGGAGGGGA 62.438 72.222 0.00 0.00 46.96 4.81
1066 1143 3.745803 ACGGTTCGACGAGGAGGC 61.746 66.667 2.12 0.00 37.61 4.70
1068 1145 2.178521 CCACGGTTCGACGAGGAG 59.821 66.667 6.10 0.00 45.62 3.69
1072 1155 4.351938 CTGGCCACGGTTCGACGA 62.352 66.667 0.00 0.00 37.61 4.20
1078 1161 4.335647 CTGCTCCTGGCCACGGTT 62.336 66.667 17.55 0.00 40.92 4.44
1088 1171 2.430610 GCCGATCTGTCCTGCTCCT 61.431 63.158 0.00 0.00 0.00 3.69
1094 1177 2.010582 GAGAAGCGCCGATCTGTCCT 62.011 60.000 12.10 0.00 0.00 3.85
1518 1607 2.113860 TGCCGGAAAGATCCAAGAAG 57.886 50.000 5.05 0.00 46.97 2.85
1773 1862 1.307084 GTTCCCTAGCTCCCTGGGT 60.307 63.158 13.56 0.00 41.58 4.51
1791 1880 0.868406 GAACCGACAAACCTGAGCAG 59.132 55.000 0.00 0.00 0.00 4.24
1884 1973 3.168628 CTTTGGCAAAGCTGTCACG 57.831 52.632 25.46 2.20 36.73 4.35
2142 2231 2.106338 TGGAATTGAGCCTGACAGTTCA 59.894 45.455 0.93 2.43 36.29 3.18
2143 2232 2.746362 CTGGAATTGAGCCTGACAGTTC 59.254 50.000 0.93 0.00 34.70 3.01
2148 2237 0.674895 ACGCTGGAATTGAGCCTGAC 60.675 55.000 0.00 0.00 32.41 3.51
2168 2257 2.859526 TGCACATTCTTTGTTCGCAA 57.140 40.000 0.00 0.00 35.12 4.85
2181 2270 0.890542 ACGGTTGCTGTGATGCACAT 60.891 50.000 0.20 0.00 43.71 3.21
2243 2332 4.637534 CCAATGATAGTTGTGCTACAGCTT 59.362 41.667 9.98 1.39 40.24 3.74
2383 2472 9.229784 GTTATTGTGATCAAGAGTTAATGCATG 57.770 33.333 0.00 0.00 36.97 4.06
2393 2482 6.875726 TCCTGTGAAGTTATTGTGATCAAGAG 59.124 38.462 0.00 0.00 36.97 2.85
2415 2504 4.543689 ACAGAATTGCATCCAATGATCCT 58.456 39.130 0.00 0.00 40.69 3.24
2758 2847 9.781633 CAGAGAATTGGATGAGAGATCTAAAAT 57.218 33.333 0.00 0.00 0.00 1.82
2775 2864 3.944015 GGACATTCCCAGACAGAGAATTG 59.056 47.826 0.00 0.00 0.00 2.32
2931 3026 1.532505 GCTCGCACATTCGAATGCAAT 60.533 47.619 32.70 14.99 42.17 3.56
3147 3242 5.772672 AGCACCAATATCCACAAAAACAGTA 59.227 36.000 0.00 0.00 0.00 2.74
3298 3393 0.394352 AACCTTCCAATAGCCAGCCG 60.394 55.000 0.00 0.00 0.00 5.52
3471 3566 4.827284 TCAATTGGTCTCTTTGTCCTTTCC 59.173 41.667 5.42 0.00 0.00 3.13
3609 3704 3.551890 GGTATGCAGTGTACTCATTGTCG 59.448 47.826 0.00 0.00 34.46 4.35
3708 3803 2.797156 CGCATACTCTGGAGCAACATAC 59.203 50.000 0.00 0.00 0.00 2.39
3774 3869 4.916983 AATAAGTTCAAGCAGCACAACA 57.083 36.364 0.00 0.00 0.00 3.33
3780 3875 5.362556 TGTCTGAAATAAGTTCAAGCAGC 57.637 39.130 0.00 0.00 45.67 5.25
3874 3969 3.612247 GAGCTCGGCCCTTCTGCAA 62.612 63.158 0.00 0.00 0.00 4.08
3972 4067 5.946972 CCTAGAAGAAAGAGAGTCCACAGTA 59.053 44.000 0.00 0.00 0.00 2.74
4066 4161 7.710896 TCAGTCTTGAGATGTATGTCATACTG 58.289 38.462 20.91 18.72 41.09 2.74
4200 4296 4.215399 TCACAGCCTAAAATACAGTTGCAC 59.785 41.667 0.00 0.00 0.00 4.57
4353 4451 6.469782 AACAATTTAATAGGGGCAGACATG 57.530 37.500 0.00 0.00 0.00 3.21
4423 4527 4.551702 TCTACCAGAAAGCTATTGTGCA 57.448 40.909 0.00 0.00 34.99 4.57
4570 4674 4.065088 GTTGCTAGTGATCACCAGTTTGA 58.935 43.478 22.21 3.52 0.00 2.69
4571 4675 3.189287 GGTTGCTAGTGATCACCAGTTTG 59.811 47.826 22.21 6.11 0.00 2.93
4747 4865 6.111768 ACTTACTTTAGCAGCAAATCATCG 57.888 37.500 0.00 0.00 0.00 3.84
4760 4878 8.926710 CATGCGGAAGGAATATACTTACTTTAG 58.073 37.037 2.01 0.00 32.68 1.85
4885 5006 6.150976 TCCATTCCAAATAACTAACAGCACTG 59.849 38.462 0.00 0.00 0.00 3.66
4886 5007 6.245408 TCCATTCCAAATAACTAACAGCACT 58.755 36.000 0.00 0.00 0.00 4.40
4977 5098 9.771534 GGAAATCAGAGCTTCAGTACTTAATAT 57.228 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.