Multiple sequence alignment - TraesCS7D01G311600

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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 TraesCS7D01G311600 chr7D 100.000 1687 0 0 908 2594 394992211 394990525 0.000000e+00 3116.0
1 TraesCS7D01G311600 chr7D 100.000 588 0 0 1 588 394993118 394992531 0.000000e+00 1086.0
2 TraesCS7D01G311600 chr7B 92.899 1718 58 27 908 2594 394780718 394779034 0.000000e+00 2438.0
3 TraesCS7D01G311600 chr7B 93.258 267 5 4 322 588 394780980 394780727 5.240000e-102 381.0
4 TraesCS7D01G311600 chr7B 84.589 292 38 6 1 290 394806731 394806445 1.520000e-72 283.0
5 TraesCS7D01G311600 chr7A 95.043 1291 38 10 908 2185 448266497 448265220 0.000000e+00 2006.0
6 TraesCS7D01G311600 chr7A 91.321 265 8 6 327 588 448266758 448266506 5.310000e-92 348.0
7 TraesCS7D01G311600 chr7A 90.566 265 8 7 2333 2594 448264945 448264695 4.140000e-88 335.0
8 TraesCS7D01G311600 chr7A 79.670 182 34 3 1 180 126485648 126485828 7.530000e-26 128.0
9 TraesCS7D01G311600 chr7A 100.000 47 0 0 2179 2225 448265025 448264979 1.280000e-13 87.9
10 TraesCS7D01G311600 chr2B 81.667 180 31 2 1 178 681736368 681736189 5.780000e-32 148.0
11 TraesCS7D01G311600 chr2B 82.394 142 23 2 1 141 458070273 458070413 3.510000e-24 122.0
12 TraesCS7D01G311600 chr2D 81.111 180 29 5 2 179 576863969 576864145 3.480000e-29 139.0
13 TraesCS7D01G311600 chr5A 79.397 199 36 4 1 197 641058418 641058613 4.500000e-28 135.0
14 TraesCS7D01G311600 chr3A 80.447 179 33 2 1 177 589313054 589313232 4.500000e-28 135.0
15 TraesCS7D01G311600 chr4A 81.633 147 24 3 35 179 473764394 473764539 4.530000e-23 119.0
16 TraesCS7D01G311600 chr6D 76.111 180 41 2 2 179 416027286 416027107 2.750000e-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 TraesCS7D01G311600 chr7D 394990525 394993118 2593 True 2101.000 3116 100.0000 1 2594 2 chr7D.!!$R1 2593
1 TraesCS7D01G311600 chr7B 394779034 394780980 1946 True 1409.500 2438 93.0785 322 2594 2 chr7B.!!$R2 2272
2 TraesCS7D01G311600 chr7A 448264695 448266758 2063 True 694.225 2006 94.2325 327 2594 4 chr7A.!!$R1 2267

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
26 27 0.031178 CTGCAACAAGTGTTCCCAGC 59.969 55.0 7.88 3.78 35.83 4.85 F
309 310 0.179097 GAGATTGACTCCAGGACGGC 60.179 60.0 0.00 0.00 39.53 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 1058 1.518903 GGGTCTTGTTGAGCTGGTGC 61.519 60.0 0.0 0.0 42.4 5.01 R
2239 2474 0.318441 TCCAAGTCCTGTTCTGCTCG 59.682 55.0 0.0 0.0 0.0 5.03 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.492421 CTGTCAACTGCAACAAGTGTT 57.508 42.857 0.00 0.00 39.12 3.32
21 22 3.429085 CTGTCAACTGCAACAAGTGTTC 58.571 45.455 0.00 0.00 35.83 3.18
22 23 2.163412 TGTCAACTGCAACAAGTGTTCC 59.837 45.455 0.00 0.00 35.83 3.62
23 24 1.748493 TCAACTGCAACAAGTGTTCCC 59.252 47.619 0.00 0.00 35.83 3.97
24 25 1.476085 CAACTGCAACAAGTGTTCCCA 59.524 47.619 0.00 0.00 35.83 4.37
25 26 1.392589 ACTGCAACAAGTGTTCCCAG 58.607 50.000 14.96 14.96 38.92 4.45
26 27 0.031178 CTGCAACAAGTGTTCCCAGC 59.969 55.000 7.88 3.78 35.83 4.85
27 28 0.395586 TGCAACAAGTGTTCCCAGCT 60.396 50.000 0.00 0.00 35.83 4.24
28 29 0.746659 GCAACAAGTGTTCCCAGCTT 59.253 50.000 0.00 0.00 35.83 3.74
29 30 1.269257 GCAACAAGTGTTCCCAGCTTC 60.269 52.381 0.00 0.00 35.83 3.86
30 31 1.002468 CAACAAGTGTTCCCAGCTTCG 60.002 52.381 0.00 0.00 35.83 3.79
31 32 0.535102 ACAAGTGTTCCCAGCTTCGG 60.535 55.000 0.00 0.00 0.00 4.30
32 33 1.600916 AAGTGTTCCCAGCTTCGGC 60.601 57.895 0.00 0.00 42.17 5.54
33 34 2.281484 GTGTTCCCAGCTTCGGCA 60.281 61.111 0.00 0.00 44.74 5.69
34 35 1.896660 GTGTTCCCAGCTTCGGCAA 60.897 57.895 0.00 0.00 44.74 4.52
35 36 1.600636 TGTTCCCAGCTTCGGCAAG 60.601 57.895 0.00 0.00 44.74 4.01
36 37 1.600916 GTTCCCAGCTTCGGCAAGT 60.601 57.895 0.00 0.00 44.74 3.16
37 38 1.600636 TTCCCAGCTTCGGCAAGTG 60.601 57.895 0.00 0.00 44.74 3.16
38 39 2.032528 CCCAGCTTCGGCAAGTGA 59.967 61.111 0.00 0.00 44.74 3.41
39 40 2.037136 CCCAGCTTCGGCAAGTGAG 61.037 63.158 0.00 0.00 44.74 3.51
40 41 2.037136 CCAGCTTCGGCAAGTGAGG 61.037 63.158 0.00 0.00 44.74 3.86
41 42 2.037136 CAGCTTCGGCAAGTGAGGG 61.037 63.158 0.00 0.00 44.74 4.30
42 43 2.747855 GCTTCGGCAAGTGAGGGG 60.748 66.667 0.00 0.00 41.33 4.79
43 44 2.747855 CTTCGGCAAGTGAGGGGC 60.748 66.667 0.00 0.00 0.00 5.80
44 45 3.551496 CTTCGGCAAGTGAGGGGCA 62.551 63.158 0.00 0.00 0.00 5.36
45 46 3.126703 TTCGGCAAGTGAGGGGCAA 62.127 57.895 0.00 0.00 0.00 4.52
46 47 2.361610 CGGCAAGTGAGGGGCAAT 60.362 61.111 0.00 0.00 0.00 3.56
47 48 2.703798 CGGCAAGTGAGGGGCAATG 61.704 63.158 0.00 0.00 0.00 2.82
48 49 1.304381 GGCAAGTGAGGGGCAATGA 60.304 57.895 0.00 0.00 0.00 2.57
49 50 1.598701 GGCAAGTGAGGGGCAATGAC 61.599 60.000 0.00 0.00 0.00 3.06
50 51 1.926511 GCAAGTGAGGGGCAATGACG 61.927 60.000 0.00 0.00 0.00 4.35
51 52 0.321564 CAAGTGAGGGGCAATGACGA 60.322 55.000 0.00 0.00 0.00 4.20
52 53 0.321653 AAGTGAGGGGCAATGACGAC 60.322 55.000 0.00 0.00 0.00 4.34
53 54 2.100631 GTGAGGGGCAATGACGACG 61.101 63.158 0.00 0.00 0.00 5.12
54 55 2.511600 GAGGGGCAATGACGACGG 60.512 66.667 0.00 0.00 0.00 4.79
55 56 4.778143 AGGGGCAATGACGACGGC 62.778 66.667 0.00 0.00 0.00 5.68
57 58 3.799755 GGGCAATGACGACGGCAC 61.800 66.667 4.98 0.00 0.00 5.01
70 71 3.843985 GGCACGTCTTCGACTCAC 58.156 61.111 0.00 0.00 40.62 3.51
71 72 1.286260 GGCACGTCTTCGACTCACT 59.714 57.895 0.00 0.00 40.62 3.41
72 73 0.318784 GGCACGTCTTCGACTCACTT 60.319 55.000 0.00 0.00 40.62 3.16
73 74 1.053811 GCACGTCTTCGACTCACTTC 58.946 55.000 0.00 0.00 40.62 3.01
74 75 1.599667 GCACGTCTTCGACTCACTTCA 60.600 52.381 0.00 0.00 40.62 3.02
75 76 2.311462 CACGTCTTCGACTCACTTCAG 58.689 52.381 0.00 0.00 40.62 3.02
76 77 1.948145 ACGTCTTCGACTCACTTCAGT 59.052 47.619 0.00 0.00 40.62 3.41
77 78 2.287069 ACGTCTTCGACTCACTTCAGTG 60.287 50.000 0.02 0.02 42.59 3.66
78 79 2.055100 GTCTTCGACTCACTTCAGTGC 58.945 52.381 1.74 0.00 45.25 4.40
79 80 1.957177 TCTTCGACTCACTTCAGTGCT 59.043 47.619 1.74 0.00 45.25 4.40
80 81 2.362397 TCTTCGACTCACTTCAGTGCTT 59.638 45.455 1.74 0.00 45.25 3.91
81 82 2.140065 TCGACTCACTTCAGTGCTTG 57.860 50.000 1.74 0.00 45.25 4.01
82 83 1.409064 TCGACTCACTTCAGTGCTTGT 59.591 47.619 1.74 1.62 45.25 3.16
83 84 2.621526 TCGACTCACTTCAGTGCTTGTA 59.378 45.455 1.74 0.00 45.25 2.41
84 85 2.983136 CGACTCACTTCAGTGCTTGTAG 59.017 50.000 1.74 0.00 45.25 2.74
85 86 3.551046 CGACTCACTTCAGTGCTTGTAGT 60.551 47.826 1.74 0.39 45.25 2.73
86 87 3.983741 ACTCACTTCAGTGCTTGTAGTC 58.016 45.455 1.74 0.00 45.25 2.59
87 88 2.983136 CTCACTTCAGTGCTTGTAGTCG 59.017 50.000 1.74 0.00 45.25 4.18
88 89 2.361119 TCACTTCAGTGCTTGTAGTCGT 59.639 45.455 1.74 0.00 45.25 4.34
89 90 3.123804 CACTTCAGTGCTTGTAGTCGTT 58.876 45.455 0.00 0.00 35.50 3.85
90 91 3.060272 CACTTCAGTGCTTGTAGTCGTTG 60.060 47.826 0.00 0.00 35.50 4.10
91 92 1.497991 TCAGTGCTTGTAGTCGTTGC 58.502 50.000 0.00 0.00 0.00 4.17
92 93 1.068588 TCAGTGCTTGTAGTCGTTGCT 59.931 47.619 0.00 0.00 0.00 3.91
93 94 1.867233 CAGTGCTTGTAGTCGTTGCTT 59.133 47.619 0.00 0.00 0.00 3.91
94 95 2.287915 CAGTGCTTGTAGTCGTTGCTTT 59.712 45.455 0.00 0.00 0.00 3.51
95 96 2.287915 AGTGCTTGTAGTCGTTGCTTTG 59.712 45.455 0.00 0.00 0.00 2.77
96 97 2.031683 GTGCTTGTAGTCGTTGCTTTGT 59.968 45.455 0.00 0.00 0.00 2.83
97 98 2.031560 TGCTTGTAGTCGTTGCTTTGTG 59.968 45.455 0.00 0.00 0.00 3.33
98 99 2.602217 GCTTGTAGTCGTTGCTTTGTGG 60.602 50.000 0.00 0.00 0.00 4.17
99 100 2.319136 TGTAGTCGTTGCTTTGTGGT 57.681 45.000 0.00 0.00 0.00 4.16
100 101 2.634600 TGTAGTCGTTGCTTTGTGGTT 58.365 42.857 0.00 0.00 0.00 3.67
101 102 3.011119 TGTAGTCGTTGCTTTGTGGTTT 58.989 40.909 0.00 0.00 0.00 3.27
102 103 4.190001 TGTAGTCGTTGCTTTGTGGTTTA 58.810 39.130 0.00 0.00 0.00 2.01
103 104 4.817464 TGTAGTCGTTGCTTTGTGGTTTAT 59.183 37.500 0.00 0.00 0.00 1.40
104 105 4.223320 AGTCGTTGCTTTGTGGTTTATG 57.777 40.909 0.00 0.00 0.00 1.90
105 106 3.004315 AGTCGTTGCTTTGTGGTTTATGG 59.996 43.478 0.00 0.00 0.00 2.74
106 107 3.003897 GTCGTTGCTTTGTGGTTTATGGA 59.996 43.478 0.00 0.00 0.00 3.41
107 108 3.823873 TCGTTGCTTTGTGGTTTATGGAT 59.176 39.130 0.00 0.00 0.00 3.41
108 109 4.083003 TCGTTGCTTTGTGGTTTATGGATC 60.083 41.667 0.00 0.00 0.00 3.36
109 110 4.494484 GTTGCTTTGTGGTTTATGGATCC 58.506 43.478 4.20 4.20 0.00 3.36
110 111 3.772387 TGCTTTGTGGTTTATGGATCCA 58.228 40.909 18.88 18.88 0.00 3.41
116 117 3.378861 TGGTTTATGGATCCACATGCA 57.621 42.857 18.99 0.00 34.38 3.96
117 118 3.706183 TGGTTTATGGATCCACATGCAA 58.294 40.909 18.99 3.55 33.45 4.08
118 119 4.288398 TGGTTTATGGATCCACATGCAAT 58.712 39.130 18.99 1.07 33.45 3.56
119 120 4.715792 TGGTTTATGGATCCACATGCAATT 59.284 37.500 18.99 0.21 33.45 2.32
120 121 5.189342 TGGTTTATGGATCCACATGCAATTT 59.811 36.000 18.99 0.00 33.45 1.82
121 122 6.114767 GGTTTATGGATCCACATGCAATTTT 58.885 36.000 18.99 0.00 33.45 1.82
122 123 6.598850 GGTTTATGGATCCACATGCAATTTTT 59.401 34.615 18.99 0.00 33.45 1.94
123 124 7.768120 GGTTTATGGATCCACATGCAATTTTTA 59.232 33.333 18.99 0.00 33.45 1.52
124 125 9.328845 GTTTATGGATCCACATGCAATTTTTAT 57.671 29.630 18.99 0.00 33.45 1.40
125 126 9.902684 TTTATGGATCCACATGCAATTTTTATT 57.097 25.926 18.99 0.00 33.45 1.40
129 130 9.902684 TGGATCCACATGCAATTTTTATTATTT 57.097 25.926 11.44 0.00 0.00 1.40
133 134 9.716531 TCCACATGCAATTTTTATTATTTGTGA 57.283 25.926 9.22 0.00 34.22 3.58
149 150 8.942669 TTATTTGTGATGTTCGTTGTAATGTC 57.057 30.769 0.00 0.00 0.00 3.06
150 151 5.993106 TTGTGATGTTCGTTGTAATGTCA 57.007 34.783 0.00 0.00 0.00 3.58
151 152 6.552859 TTGTGATGTTCGTTGTAATGTCAT 57.447 33.333 0.00 0.00 0.00 3.06
152 153 5.925907 TGTGATGTTCGTTGTAATGTCATG 58.074 37.500 0.00 0.00 0.00 3.07
153 154 5.698545 TGTGATGTTCGTTGTAATGTCATGA 59.301 36.000 0.00 0.00 0.00 3.07
154 155 6.371271 TGTGATGTTCGTTGTAATGTCATGAT 59.629 34.615 0.00 0.00 0.00 2.45
155 156 7.094848 TGTGATGTTCGTTGTAATGTCATGATT 60.095 33.333 0.00 0.00 0.00 2.57
156 157 7.216881 GTGATGTTCGTTGTAATGTCATGATTG 59.783 37.037 0.00 0.00 0.00 2.67
157 158 6.793492 TGTTCGTTGTAATGTCATGATTGA 57.207 33.333 0.00 0.00 0.00 2.57
158 159 7.195839 TGTTCGTTGTAATGTCATGATTGAA 57.804 32.000 0.00 0.00 32.48 2.69
159 160 7.075121 TGTTCGTTGTAATGTCATGATTGAAC 58.925 34.615 0.00 1.12 32.48 3.18
160 161 7.041440 TGTTCGTTGTAATGTCATGATTGAACT 60.041 33.333 0.00 0.00 33.78 3.01
161 162 6.830736 TCGTTGTAATGTCATGATTGAACTG 58.169 36.000 0.00 0.00 32.48 3.16
162 163 6.648725 TCGTTGTAATGTCATGATTGAACTGA 59.351 34.615 0.00 0.00 32.48 3.41
163 164 7.172361 TCGTTGTAATGTCATGATTGAACTGAA 59.828 33.333 0.00 0.00 32.48 3.02
164 165 7.964559 CGTTGTAATGTCATGATTGAACTGAAT 59.035 33.333 0.00 0.00 32.48 2.57
167 168 9.889128 TGTAATGTCATGATTGAACTGAATAGA 57.111 29.630 0.00 0.00 32.48 1.98
171 172 9.623000 ATGTCATGATTGAACTGAATAGATTGA 57.377 29.630 0.00 0.00 32.48 2.57
172 173 8.886719 TGTCATGATTGAACTGAATAGATTGAC 58.113 33.333 0.00 0.00 32.48 3.18
173 174 8.886719 GTCATGATTGAACTGAATAGATTGACA 58.113 33.333 0.00 0.00 32.48 3.58
174 175 9.106070 TCATGATTGAACTGAATAGATTGACAG 57.894 33.333 0.00 0.00 36.58 3.51
175 176 8.890718 CATGATTGAACTGAATAGATTGACAGT 58.109 33.333 0.00 0.00 43.92 3.55
214 215 7.637631 AAATAATGAGAAGAGGGAAAAGAGC 57.362 36.000 0.00 0.00 0.00 4.09
215 216 4.647564 AATGAGAAGAGGGAAAAGAGCA 57.352 40.909 0.00 0.00 0.00 4.26
216 217 3.409026 TGAGAAGAGGGAAAAGAGCAC 57.591 47.619 0.00 0.00 0.00 4.40
217 218 2.039084 TGAGAAGAGGGAAAAGAGCACC 59.961 50.000 0.00 0.00 0.00 5.01
218 219 1.352687 AGAAGAGGGAAAAGAGCACCC 59.647 52.381 0.00 0.00 43.55 4.61
219 220 1.073923 GAAGAGGGAAAAGAGCACCCA 59.926 52.381 0.00 0.00 45.43 4.51
220 221 1.149101 AGAGGGAAAAGAGCACCCAA 58.851 50.000 0.00 0.00 45.43 4.12
221 222 1.074566 AGAGGGAAAAGAGCACCCAAG 59.925 52.381 0.00 0.00 45.43 3.61
222 223 0.853530 AGGGAAAAGAGCACCCAAGT 59.146 50.000 0.00 0.00 45.43 3.16
223 224 1.202940 AGGGAAAAGAGCACCCAAGTC 60.203 52.381 0.00 0.00 45.43 3.01
224 225 1.478654 GGGAAAAGAGCACCCAAGTCA 60.479 52.381 0.00 0.00 42.81 3.41
225 226 2.306847 GGAAAAGAGCACCCAAGTCAA 58.693 47.619 0.00 0.00 0.00 3.18
226 227 2.693074 GGAAAAGAGCACCCAAGTCAAA 59.307 45.455 0.00 0.00 0.00 2.69
227 228 3.243535 GGAAAAGAGCACCCAAGTCAAAG 60.244 47.826 0.00 0.00 0.00 2.77
228 229 3.297134 AAAGAGCACCCAAGTCAAAGA 57.703 42.857 0.00 0.00 0.00 2.52
229 230 3.297134 AAGAGCACCCAAGTCAAAGAA 57.703 42.857 0.00 0.00 0.00 2.52
230 231 3.297134 AGAGCACCCAAGTCAAAGAAA 57.703 42.857 0.00 0.00 0.00 2.52
231 232 3.631250 AGAGCACCCAAGTCAAAGAAAA 58.369 40.909 0.00 0.00 0.00 2.29
232 233 4.023291 AGAGCACCCAAGTCAAAGAAAAA 58.977 39.130 0.00 0.00 0.00 1.94
233 234 4.098501 AGAGCACCCAAGTCAAAGAAAAAG 59.901 41.667 0.00 0.00 0.00 2.27
234 235 3.132824 AGCACCCAAGTCAAAGAAAAAGG 59.867 43.478 0.00 0.00 0.00 3.11
235 236 3.132111 GCACCCAAGTCAAAGAAAAAGGA 59.868 43.478 0.00 0.00 0.00 3.36
236 237 4.202253 GCACCCAAGTCAAAGAAAAAGGAT 60.202 41.667 0.00 0.00 0.00 3.24
237 238 5.010617 GCACCCAAGTCAAAGAAAAAGGATA 59.989 40.000 0.00 0.00 0.00 2.59
238 239 6.462347 GCACCCAAGTCAAAGAAAAAGGATAA 60.462 38.462 0.00 0.00 0.00 1.75
239 240 7.670364 CACCCAAGTCAAAGAAAAAGGATAAT 58.330 34.615 0.00 0.00 0.00 1.28
240 241 8.150296 CACCCAAGTCAAAGAAAAAGGATAATT 58.850 33.333 0.00 0.00 0.00 1.40
241 242 8.713971 ACCCAAGTCAAAGAAAAAGGATAATTT 58.286 29.630 0.00 0.00 0.00 1.82
242 243 9.559732 CCCAAGTCAAAGAAAAAGGATAATTTT 57.440 29.630 0.00 0.00 33.86 1.82
246 247 9.764363 AGTCAAAGAAAAAGGATAATTTTCACC 57.236 29.630 12.60 0.00 45.06 4.02
247 248 8.988934 GTCAAAGAAAAAGGATAATTTTCACCC 58.011 33.333 12.60 0.00 45.06 4.61
248 249 8.709308 TCAAAGAAAAAGGATAATTTTCACCCA 58.291 29.630 12.60 0.00 45.06 4.51
249 250 8.992073 CAAAGAAAAAGGATAATTTTCACCCAG 58.008 33.333 12.60 0.00 45.06 4.45
250 251 7.855784 AGAAAAAGGATAATTTTCACCCAGT 57.144 32.000 12.60 0.00 45.06 4.00
251 252 7.896811 AGAAAAAGGATAATTTTCACCCAGTC 58.103 34.615 12.60 0.00 45.06 3.51
252 253 7.730332 AGAAAAAGGATAATTTTCACCCAGTCT 59.270 33.333 12.60 0.00 45.06 3.24
253 254 8.950007 AAAAAGGATAATTTTCACCCAGTCTA 57.050 30.769 0.00 0.00 31.25 2.59
254 255 9.547279 AAAAAGGATAATTTTCACCCAGTCTAT 57.453 29.630 0.00 0.00 31.25 1.98
255 256 8.525290 AAAGGATAATTTTCACCCAGTCTATG 57.475 34.615 0.00 0.00 0.00 2.23
256 257 6.064717 AGGATAATTTTCACCCAGTCTATGC 58.935 40.000 0.00 0.00 0.00 3.14
257 258 5.827797 GGATAATTTTCACCCAGTCTATGCA 59.172 40.000 0.00 0.00 0.00 3.96
258 259 6.016777 GGATAATTTTCACCCAGTCTATGCAG 60.017 42.308 0.00 0.00 0.00 4.41
259 260 4.574674 ATTTTCACCCAGTCTATGCAGA 57.425 40.909 0.00 0.00 0.00 4.26
260 261 4.365514 TTTTCACCCAGTCTATGCAGAA 57.634 40.909 0.00 0.00 30.85 3.02
261 262 4.365514 TTTCACCCAGTCTATGCAGAAA 57.634 40.909 0.00 0.00 30.85 2.52
262 263 3.616956 TCACCCAGTCTATGCAGAAAG 57.383 47.619 0.00 0.00 30.85 2.62
263 264 2.906389 TCACCCAGTCTATGCAGAAAGT 59.094 45.455 0.00 0.00 30.85 2.66
264 265 4.093743 TCACCCAGTCTATGCAGAAAGTA 58.906 43.478 0.00 0.00 30.85 2.24
265 266 4.716784 TCACCCAGTCTATGCAGAAAGTAT 59.283 41.667 0.00 0.00 30.85 2.12
266 267 5.897250 TCACCCAGTCTATGCAGAAAGTATA 59.103 40.000 0.00 0.00 30.85 1.47
267 268 6.382859 TCACCCAGTCTATGCAGAAAGTATAA 59.617 38.462 0.00 0.00 30.85 0.98
268 269 7.071196 TCACCCAGTCTATGCAGAAAGTATAAT 59.929 37.037 0.00 0.00 30.85 1.28
269 270 7.716998 CACCCAGTCTATGCAGAAAGTATAATT 59.283 37.037 0.00 0.00 30.85 1.40
270 271 8.934697 ACCCAGTCTATGCAGAAAGTATAATTA 58.065 33.333 0.00 0.00 30.85 1.40
271 272 9.209175 CCCAGTCTATGCAGAAAGTATAATTAC 57.791 37.037 0.00 0.00 30.85 1.89
272 273 8.916654 CCAGTCTATGCAGAAAGTATAATTACG 58.083 37.037 0.00 0.00 30.78 3.18
273 274 8.428536 CAGTCTATGCAGAAAGTATAATTACGC 58.571 37.037 0.00 0.00 30.78 4.42
274 275 8.361139 AGTCTATGCAGAAAGTATAATTACGCT 58.639 33.333 0.00 0.00 30.78 5.07
275 276 8.979574 GTCTATGCAGAAAGTATAATTACGCTT 58.020 33.333 0.00 0.00 30.78 4.68
276 277 9.542462 TCTATGCAGAAAGTATAATTACGCTTT 57.458 29.630 12.97 12.97 34.34 3.51
279 280 8.035165 TGCAGAAAGTATAATTACGCTTTTCA 57.965 30.769 13.83 10.76 32.14 2.69
280 281 7.960738 TGCAGAAAGTATAATTACGCTTTTCAC 59.039 33.333 13.83 8.99 32.14 3.18
281 282 7.162062 GCAGAAAGTATAATTACGCTTTTCACG 59.838 37.037 13.83 7.50 32.14 4.35
282 283 7.634817 CAGAAAGTATAATTACGCTTTTCACGG 59.365 37.037 13.83 3.73 32.14 4.94
283 284 6.973229 AAGTATAATTACGCTTTTCACGGT 57.027 33.333 0.00 0.00 33.32 4.83
284 285 8.477984 AAAGTATAATTACGCTTTTCACGGTA 57.522 30.769 9.17 0.00 33.32 4.02
285 286 8.652810 AAGTATAATTACGCTTTTCACGGTAT 57.347 30.769 0.00 0.00 33.32 2.73
286 287 8.652810 AGTATAATTACGCTTTTCACGGTATT 57.347 30.769 0.00 0.00 33.32 1.89
287 288 8.545420 AGTATAATTACGCTTTTCACGGTATTG 58.455 33.333 0.00 0.00 33.32 1.90
288 289 3.458779 TTACGCTTTTCACGGTATTGC 57.541 42.857 0.00 0.00 34.00 3.56
289 290 1.231221 ACGCTTTTCACGGTATTGCA 58.769 45.000 0.00 0.00 34.00 4.08
290 291 1.196808 ACGCTTTTCACGGTATTGCAG 59.803 47.619 0.00 0.00 34.00 4.41
291 292 1.463056 CGCTTTTCACGGTATTGCAGA 59.537 47.619 0.00 0.00 0.00 4.26
292 293 2.474526 CGCTTTTCACGGTATTGCAGAG 60.475 50.000 0.00 0.00 0.00 3.35
293 294 2.742053 GCTTTTCACGGTATTGCAGAGA 59.258 45.455 0.00 0.00 0.00 3.10
294 295 3.375299 GCTTTTCACGGTATTGCAGAGAT 59.625 43.478 0.00 0.00 0.00 2.75
295 296 4.142600 GCTTTTCACGGTATTGCAGAGATT 60.143 41.667 0.00 0.00 0.00 2.40
296 297 4.944962 TTTCACGGTATTGCAGAGATTG 57.055 40.909 0.00 0.00 0.00 2.67
297 298 3.885724 TCACGGTATTGCAGAGATTGA 57.114 42.857 0.00 0.00 0.00 2.57
298 299 3.521560 TCACGGTATTGCAGAGATTGAC 58.478 45.455 0.00 0.00 0.00 3.18
299 300 3.195610 TCACGGTATTGCAGAGATTGACT 59.804 43.478 0.00 0.00 0.00 3.41
300 301 3.553511 CACGGTATTGCAGAGATTGACTC 59.446 47.826 0.00 0.00 45.22 3.36
301 302 3.126831 CGGTATTGCAGAGATTGACTCC 58.873 50.000 0.00 0.00 45.96 3.85
302 303 3.430790 CGGTATTGCAGAGATTGACTCCA 60.431 47.826 0.00 0.00 45.96 3.86
303 304 4.125703 GGTATTGCAGAGATTGACTCCAG 58.874 47.826 0.00 0.00 45.96 3.86
304 305 2.775911 TTGCAGAGATTGACTCCAGG 57.224 50.000 0.00 0.00 45.96 4.45
305 306 1.942776 TGCAGAGATTGACTCCAGGA 58.057 50.000 0.00 0.00 45.96 3.86
306 307 1.552337 TGCAGAGATTGACTCCAGGAC 59.448 52.381 0.00 0.00 45.96 3.85
307 308 1.470632 GCAGAGATTGACTCCAGGACG 60.471 57.143 0.00 0.00 45.96 4.79
308 309 1.135915 CAGAGATTGACTCCAGGACGG 59.864 57.143 0.00 0.00 45.96 4.79
309 310 0.179097 GAGATTGACTCCAGGACGGC 60.179 60.000 0.00 0.00 39.53 5.68
310 311 1.519455 GATTGACTCCAGGACGGCG 60.519 63.158 4.80 4.80 33.14 6.46
311 312 3.665675 ATTGACTCCAGGACGGCGC 62.666 63.158 6.90 0.00 33.14 6.53
313 314 4.803426 GACTCCAGGACGGCGCTG 62.803 72.222 16.39 16.39 33.14 5.18
430 434 3.007635 CCAACTCCCACGTAATTCTTCC 58.992 50.000 0.00 0.00 0.00 3.46
497 502 2.748647 ACATTAACACGCGCCCCC 60.749 61.111 5.73 0.00 0.00 5.40
498 503 2.437716 CATTAACACGCGCCCCCT 60.438 61.111 5.73 0.00 0.00 4.79
499 504 2.124860 ATTAACACGCGCCCCCTC 60.125 61.111 5.73 0.00 0.00 4.30
1044 1058 1.351012 CTACGACGACTACCTGCGG 59.649 63.158 0.00 0.00 0.00 5.69
1693 1707 1.129917 TGTACACCGGGTTTTCTGGA 58.870 50.000 6.32 0.00 44.90 3.86
1711 1725 5.902681 TCTGGATCGATTTGTTACTGTAGG 58.097 41.667 0.00 0.00 0.00 3.18
1732 1746 7.675195 TGTAGGTAGGTAGTTGATTCTTTGGTA 59.325 37.037 0.00 0.00 0.00 3.25
1817 1833 8.970859 AGACAAGATATGAGAATTTTTCGGAT 57.029 30.769 0.00 0.00 34.02 4.18
1839 1856 8.031277 CGGATGAAAAGAAGATGAAGGAAAAAT 58.969 33.333 0.00 0.00 0.00 1.82
1840 1857 9.716531 GGATGAAAAGAAGATGAAGGAAAAATT 57.283 29.630 0.00 0.00 0.00 1.82
1997 2014 2.360801 GACTAGAGACACTGATGGAGCC 59.639 54.545 0.00 0.00 0.00 4.70
1999 2016 0.613292 AGAGACACTGATGGAGCCGT 60.613 55.000 0.00 0.00 0.00 5.68
2032 2049 2.675844 CGTGCAGGGTTCGAAAATGATA 59.324 45.455 0.00 0.00 0.00 2.15
2034 2051 3.065371 GTGCAGGGTTCGAAAATGATAGG 59.935 47.826 0.00 0.00 0.00 2.57
2035 2052 3.279434 GCAGGGTTCGAAAATGATAGGT 58.721 45.455 0.00 0.00 0.00 3.08
2036 2053 3.312697 GCAGGGTTCGAAAATGATAGGTC 59.687 47.826 0.00 0.00 0.00 3.85
2037 2054 3.555956 CAGGGTTCGAAAATGATAGGTCG 59.444 47.826 0.00 0.00 34.85 4.79
2038 2055 2.287103 GGGTTCGAAAATGATAGGTCGC 59.713 50.000 0.00 0.00 33.58 5.19
2043 2060 5.403897 TCGAAAATGATAGGTCGCATTTC 57.596 39.130 0.00 0.00 42.17 2.17
2044 2061 5.116180 TCGAAAATGATAGGTCGCATTTCT 58.884 37.500 0.00 0.00 42.17 2.52
2177 2210 8.404107 ACCATATAATGTGCTTAATTACCACC 57.596 34.615 11.09 0.00 0.00 4.61
2178 2211 8.224720 ACCATATAATGTGCTTAATTACCACCT 58.775 33.333 11.09 1.88 0.00 4.00
2239 2474 4.583073 GTCAGGGGAAGAGAGAAGATCTAC 59.417 50.000 0.00 0.00 38.84 2.59
2285 2520 3.198409 TGTCATATGTGGCACCTCATC 57.802 47.619 16.26 2.26 34.41 2.92
2287 2522 3.181462 TGTCATATGTGGCACCTCATCTC 60.181 47.826 16.26 1.28 34.41 2.75
2413 2660 2.103432 TCAGCTTTACCTTTCGTGTCCA 59.897 45.455 0.00 0.00 0.00 4.02
2430 2677 3.138283 TGTCCACTTTGGGAAGAGATTGT 59.862 43.478 0.00 0.00 39.05 2.71
2431 2678 4.349636 TGTCCACTTTGGGAAGAGATTGTA 59.650 41.667 0.00 0.00 39.05 2.41
2432 2679 4.695928 GTCCACTTTGGGAAGAGATTGTAC 59.304 45.833 0.00 0.00 39.05 2.90
2433 2680 3.684788 CCACTTTGGGAAGAGATTGTACG 59.315 47.826 0.00 0.00 36.69 3.67
2434 2681 4.315803 CACTTTGGGAAGAGATTGTACGT 58.684 43.478 0.00 0.00 36.69 3.57
2459 2706 2.932614 AGAGAATCAAAGATTGACGCCG 59.067 45.455 0.00 0.00 43.48 6.46
2479 2726 0.554792 CCCCATTCTGGCATTCTCCT 59.445 55.000 0.00 0.00 35.79 3.69
2480 2727 1.478288 CCCCATTCTGGCATTCTCCTC 60.478 57.143 0.00 0.00 35.79 3.71
2481 2728 1.478288 CCCATTCTGGCATTCTCCTCC 60.478 57.143 0.00 0.00 35.79 4.30
2482 2729 1.493871 CCATTCTGGCATTCTCCTCCT 59.506 52.381 0.00 0.00 0.00 3.69
2483 2730 2.091994 CCATTCTGGCATTCTCCTCCTT 60.092 50.000 0.00 0.00 0.00 3.36
2484 2731 2.795231 TTCTGGCATTCTCCTCCTTG 57.205 50.000 0.00 0.00 0.00 3.61
2487 2734 0.549902 TGGCATTCTCCTCCTTGGGA 60.550 55.000 0.00 0.00 36.20 4.37
2511 2760 2.030540 ACATGTCTGTTGCTGTGCATTC 60.031 45.455 0.00 0.00 38.76 2.67
2531 2789 2.978010 CCACTGTCCCGTGGCAAC 60.978 66.667 0.00 0.00 46.98 4.17
2532 2790 2.111043 CACTGTCCCGTGGCAACT 59.889 61.111 0.00 0.00 37.61 3.16
2533 2791 1.525995 CACTGTCCCGTGGCAACTT 60.526 57.895 0.00 0.00 37.61 2.66
2534 2792 1.101049 CACTGTCCCGTGGCAACTTT 61.101 55.000 0.00 0.00 37.61 2.66
2535 2793 0.818040 ACTGTCCCGTGGCAACTTTC 60.818 55.000 0.00 0.00 37.61 2.62
2536 2794 0.817634 CTGTCCCGTGGCAACTTTCA 60.818 55.000 0.00 0.00 37.61 2.69
2537 2795 0.179004 TGTCCCGTGGCAACTTTCAT 60.179 50.000 0.00 0.00 37.61 2.57
2538 2796 0.240945 GTCCCGTGGCAACTTTCATG 59.759 55.000 0.00 0.00 37.61 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.429085 GAACACTTGTTGCAGTTGACAG 58.571 45.455 0.00 0.00 38.56 3.51
1 2 2.163412 GGAACACTTGTTGCAGTTGACA 59.837 45.455 8.58 0.00 44.35 3.58
2 3 2.479560 GGGAACACTTGTTGCAGTTGAC 60.480 50.000 14.57 0.00 46.34 3.18
3 4 1.748493 GGGAACACTTGTTGCAGTTGA 59.252 47.619 14.57 0.00 46.34 3.18
4 5 1.476085 TGGGAACACTTGTTGCAGTTG 59.524 47.619 14.57 0.00 46.34 3.16
5 6 1.750778 CTGGGAACACTTGTTGCAGTT 59.249 47.619 14.57 0.00 46.34 3.16
6 7 1.392589 CTGGGAACACTTGTTGCAGT 58.607 50.000 14.57 0.00 46.34 4.40
7 8 0.031178 GCTGGGAACACTTGTTGCAG 59.969 55.000 14.57 10.81 46.34 4.41
8 9 0.395586 AGCTGGGAACACTTGTTGCA 60.396 50.000 14.57 0.00 46.34 4.08
9 10 0.746659 AAGCTGGGAACACTTGTTGC 59.253 50.000 5.11 5.11 44.24 4.17
10 11 1.002468 CGAAGCTGGGAACACTTGTTG 60.002 52.381 0.00 0.00 38.56 3.33
11 12 1.308998 CGAAGCTGGGAACACTTGTT 58.691 50.000 0.00 0.00 41.64 2.83
12 13 0.535102 CCGAAGCTGGGAACACTTGT 60.535 55.000 0.00 0.00 33.70 3.16
13 14 1.856265 GCCGAAGCTGGGAACACTTG 61.856 60.000 8.22 0.00 33.70 3.16
14 15 1.600916 GCCGAAGCTGGGAACACTT 60.601 57.895 8.22 0.00 35.39 3.16
15 16 2.032681 GCCGAAGCTGGGAACACT 59.967 61.111 8.22 0.00 35.60 3.55
16 17 1.856265 CTTGCCGAAGCTGGGAACAC 61.856 60.000 8.22 0.00 40.80 3.32
17 18 1.600636 CTTGCCGAAGCTGGGAACA 60.601 57.895 8.22 0.00 40.80 3.18
18 19 1.600916 ACTTGCCGAAGCTGGGAAC 60.601 57.895 8.22 0.00 40.80 3.62
19 20 1.600636 CACTTGCCGAAGCTGGGAA 60.601 57.895 8.22 2.65 40.80 3.97
20 21 2.032528 CACTTGCCGAAGCTGGGA 59.967 61.111 8.22 0.00 40.80 4.37
21 22 2.032528 TCACTTGCCGAAGCTGGG 59.967 61.111 0.00 0.00 40.80 4.45
22 23 2.037136 CCTCACTTGCCGAAGCTGG 61.037 63.158 0.00 0.00 40.80 4.85
23 24 2.037136 CCCTCACTTGCCGAAGCTG 61.037 63.158 0.00 0.00 40.80 4.24
24 25 2.348998 CCCTCACTTGCCGAAGCT 59.651 61.111 0.00 0.00 40.80 3.74
25 26 2.747855 CCCCTCACTTGCCGAAGC 60.748 66.667 0.00 0.00 40.48 3.86
26 27 2.747855 GCCCCTCACTTGCCGAAG 60.748 66.667 0.00 0.00 35.07 3.79
27 28 2.424842 ATTGCCCCTCACTTGCCGAA 62.425 55.000 0.00 0.00 0.00 4.30
28 29 2.905996 ATTGCCCCTCACTTGCCGA 61.906 57.895 0.00 0.00 0.00 5.54
29 30 2.361610 ATTGCCCCTCACTTGCCG 60.362 61.111 0.00 0.00 0.00 5.69
30 31 1.304381 TCATTGCCCCTCACTTGCC 60.304 57.895 0.00 0.00 0.00 4.52
31 32 1.885871 GTCATTGCCCCTCACTTGC 59.114 57.895 0.00 0.00 0.00 4.01
32 33 0.321564 TCGTCATTGCCCCTCACTTG 60.322 55.000 0.00 0.00 0.00 3.16
33 34 0.321653 GTCGTCATTGCCCCTCACTT 60.322 55.000 0.00 0.00 0.00 3.16
34 35 1.296715 GTCGTCATTGCCCCTCACT 59.703 57.895 0.00 0.00 0.00 3.41
35 36 2.100631 CGTCGTCATTGCCCCTCAC 61.101 63.158 0.00 0.00 0.00 3.51
36 37 2.264480 CGTCGTCATTGCCCCTCA 59.736 61.111 0.00 0.00 0.00 3.86
37 38 2.511600 CCGTCGTCATTGCCCCTC 60.512 66.667 0.00 0.00 0.00 4.30
38 39 4.778143 GCCGTCGTCATTGCCCCT 62.778 66.667 0.00 0.00 0.00 4.79
40 41 3.799755 GTGCCGTCGTCATTGCCC 61.800 66.667 0.00 0.00 0.00 5.36
41 42 4.147322 CGTGCCGTCGTCATTGCC 62.147 66.667 0.00 0.00 0.00 4.52
42 43 3.411351 ACGTGCCGTCGTCATTGC 61.411 61.111 0.00 0.00 40.04 3.56
69 70 3.123804 CAACGACTACAAGCACTGAAGT 58.876 45.455 0.00 0.00 0.00 3.01
70 71 2.096713 GCAACGACTACAAGCACTGAAG 60.097 50.000 0.00 0.00 0.00 3.02
71 72 1.864711 GCAACGACTACAAGCACTGAA 59.135 47.619 0.00 0.00 0.00 3.02
72 73 1.068588 AGCAACGACTACAAGCACTGA 59.931 47.619 0.00 0.00 0.00 3.41
73 74 1.502231 AGCAACGACTACAAGCACTG 58.498 50.000 0.00 0.00 0.00 3.66
74 75 2.240493 AAGCAACGACTACAAGCACT 57.760 45.000 0.00 0.00 0.00 4.40
75 76 2.031683 ACAAAGCAACGACTACAAGCAC 59.968 45.455 0.00 0.00 0.00 4.40
76 77 2.031560 CACAAAGCAACGACTACAAGCA 59.968 45.455 0.00 0.00 0.00 3.91
77 78 2.602217 CCACAAAGCAACGACTACAAGC 60.602 50.000 0.00 0.00 0.00 4.01
78 79 2.612212 ACCACAAAGCAACGACTACAAG 59.388 45.455 0.00 0.00 0.00 3.16
79 80 2.634600 ACCACAAAGCAACGACTACAA 58.365 42.857 0.00 0.00 0.00 2.41
80 81 2.319136 ACCACAAAGCAACGACTACA 57.681 45.000 0.00 0.00 0.00 2.74
81 82 3.685836 AAACCACAAAGCAACGACTAC 57.314 42.857 0.00 0.00 0.00 2.73
82 83 4.214545 CCATAAACCACAAAGCAACGACTA 59.785 41.667 0.00 0.00 0.00 2.59
83 84 3.004315 CCATAAACCACAAAGCAACGACT 59.996 43.478 0.00 0.00 0.00 4.18
84 85 3.003897 TCCATAAACCACAAAGCAACGAC 59.996 43.478 0.00 0.00 0.00 4.34
85 86 3.215151 TCCATAAACCACAAAGCAACGA 58.785 40.909 0.00 0.00 0.00 3.85
86 87 3.634568 TCCATAAACCACAAAGCAACG 57.365 42.857 0.00 0.00 0.00 4.10
87 88 4.021544 TGGATCCATAAACCACAAAGCAAC 60.022 41.667 11.44 0.00 0.00 4.17
88 89 4.155709 TGGATCCATAAACCACAAAGCAA 58.844 39.130 11.44 0.00 0.00 3.91
89 90 3.772387 TGGATCCATAAACCACAAAGCA 58.228 40.909 11.44 0.00 0.00 3.91
96 97 3.378861 TGCATGTGGATCCATAAACCA 57.621 42.857 19.62 11.25 0.00 3.67
97 98 4.942761 ATTGCATGTGGATCCATAAACC 57.057 40.909 19.62 4.90 0.00 3.27
98 99 7.614124 AAAAATTGCATGTGGATCCATAAAC 57.386 32.000 19.62 12.10 0.00 2.01
99 100 9.902684 AATAAAAATTGCATGTGGATCCATAAA 57.097 25.926 19.62 7.15 0.00 1.40
103 104 9.902684 AAATAATAAAAATTGCATGTGGATCCA 57.097 25.926 11.44 11.44 0.00 3.41
107 108 9.716531 TCACAAATAATAAAAATTGCATGTGGA 57.283 25.926 8.01 0.00 36.14 4.02
123 124 9.554724 GACATTACAACGAACATCACAAATAAT 57.445 29.630 0.00 0.00 0.00 1.28
124 125 8.560374 TGACATTACAACGAACATCACAAATAA 58.440 29.630 0.00 0.00 0.00 1.40
125 126 8.089115 TGACATTACAACGAACATCACAAATA 57.911 30.769 0.00 0.00 0.00 1.40
126 127 6.964908 TGACATTACAACGAACATCACAAAT 58.035 32.000 0.00 0.00 0.00 2.32
127 128 6.364945 TGACATTACAACGAACATCACAAA 57.635 33.333 0.00 0.00 0.00 2.83
128 129 5.993106 TGACATTACAACGAACATCACAA 57.007 34.783 0.00 0.00 0.00 3.33
129 130 5.698545 TCATGACATTACAACGAACATCACA 59.301 36.000 0.00 0.00 0.00 3.58
130 131 6.164408 TCATGACATTACAACGAACATCAC 57.836 37.500 0.00 0.00 0.00 3.06
131 132 6.983474 ATCATGACATTACAACGAACATCA 57.017 33.333 0.00 0.00 0.00 3.07
132 133 7.463544 TCAATCATGACATTACAACGAACATC 58.536 34.615 0.00 0.00 0.00 3.06
133 134 7.376435 TCAATCATGACATTACAACGAACAT 57.624 32.000 0.00 0.00 0.00 2.71
134 135 6.793492 TCAATCATGACATTACAACGAACA 57.207 33.333 0.00 0.00 0.00 3.18
135 136 7.269084 CAGTTCAATCATGACATTACAACGAAC 59.731 37.037 0.00 0.00 34.61 3.95
136 137 7.172361 TCAGTTCAATCATGACATTACAACGAA 59.828 33.333 0.00 0.00 34.61 3.85
137 138 6.648725 TCAGTTCAATCATGACATTACAACGA 59.351 34.615 0.00 0.00 34.61 3.85
138 139 6.830736 TCAGTTCAATCATGACATTACAACG 58.169 36.000 0.00 0.00 34.61 4.10
141 142 9.889128 TCTATTCAGTTCAATCATGACATTACA 57.111 29.630 0.00 0.00 34.61 2.41
145 146 9.623000 TCAATCTATTCAGTTCAATCATGACAT 57.377 29.630 0.00 0.00 34.61 3.06
146 147 8.886719 GTCAATCTATTCAGTTCAATCATGACA 58.113 33.333 0.00 0.00 34.61 3.58
147 148 8.886719 TGTCAATCTATTCAGTTCAATCATGAC 58.113 33.333 0.00 0.00 34.61 3.06
148 149 9.106070 CTGTCAATCTATTCAGTTCAATCATGA 57.894 33.333 0.00 0.00 0.00 3.07
149 150 8.890718 ACTGTCAATCTATTCAGTTCAATCATG 58.109 33.333 0.00 0.00 37.81 3.07
150 151 9.458727 AACTGTCAATCTATTCAGTTCAATCAT 57.541 29.630 0.00 0.00 44.36 2.45
151 152 8.853077 AACTGTCAATCTATTCAGTTCAATCA 57.147 30.769 0.00 0.00 44.36 2.57
188 189 8.526978 GCTCTTTTCCCTCTTCTCATTATTTTT 58.473 33.333 0.00 0.00 0.00 1.94
189 190 7.671398 TGCTCTTTTCCCTCTTCTCATTATTTT 59.329 33.333 0.00 0.00 0.00 1.82
190 191 7.121907 GTGCTCTTTTCCCTCTTCTCATTATTT 59.878 37.037 0.00 0.00 0.00 1.40
191 192 6.601217 GTGCTCTTTTCCCTCTTCTCATTATT 59.399 38.462 0.00 0.00 0.00 1.40
192 193 6.118852 GTGCTCTTTTCCCTCTTCTCATTAT 58.881 40.000 0.00 0.00 0.00 1.28
193 194 5.491982 GTGCTCTTTTCCCTCTTCTCATTA 58.508 41.667 0.00 0.00 0.00 1.90
194 195 4.331108 GTGCTCTTTTCCCTCTTCTCATT 58.669 43.478 0.00 0.00 0.00 2.57
195 196 3.308046 GGTGCTCTTTTCCCTCTTCTCAT 60.308 47.826 0.00 0.00 0.00 2.90
196 197 2.039084 GGTGCTCTTTTCCCTCTTCTCA 59.961 50.000 0.00 0.00 0.00 3.27
197 198 2.616765 GGGTGCTCTTTTCCCTCTTCTC 60.617 54.545 0.00 0.00 38.29 2.87
198 199 1.352687 GGGTGCTCTTTTCCCTCTTCT 59.647 52.381 0.00 0.00 38.29 2.85
199 200 1.073923 TGGGTGCTCTTTTCCCTCTTC 59.926 52.381 0.00 0.00 41.58 2.87
200 201 1.149101 TGGGTGCTCTTTTCCCTCTT 58.851 50.000 0.00 0.00 41.58 2.85
201 202 1.074566 CTTGGGTGCTCTTTTCCCTCT 59.925 52.381 0.00 0.00 41.58 3.69
202 203 1.202940 ACTTGGGTGCTCTTTTCCCTC 60.203 52.381 0.00 0.00 41.58 4.30
203 204 0.853530 ACTTGGGTGCTCTTTTCCCT 59.146 50.000 0.00 0.00 41.58 4.20
204 205 1.248486 GACTTGGGTGCTCTTTTCCC 58.752 55.000 0.00 0.00 41.41 3.97
205 206 1.981256 TGACTTGGGTGCTCTTTTCC 58.019 50.000 0.00 0.00 0.00 3.13
206 207 3.632145 TCTTTGACTTGGGTGCTCTTTTC 59.368 43.478 0.00 0.00 0.00 2.29
207 208 3.631250 TCTTTGACTTGGGTGCTCTTTT 58.369 40.909 0.00 0.00 0.00 2.27
208 209 3.297134 TCTTTGACTTGGGTGCTCTTT 57.703 42.857 0.00 0.00 0.00 2.52
209 210 3.297134 TTCTTTGACTTGGGTGCTCTT 57.703 42.857 0.00 0.00 0.00 2.85
210 211 3.297134 TTTCTTTGACTTGGGTGCTCT 57.703 42.857 0.00 0.00 0.00 4.09
211 212 4.363138 CTTTTTCTTTGACTTGGGTGCTC 58.637 43.478 0.00 0.00 0.00 4.26
212 213 3.132824 CCTTTTTCTTTGACTTGGGTGCT 59.867 43.478 0.00 0.00 0.00 4.40
213 214 3.132111 TCCTTTTTCTTTGACTTGGGTGC 59.868 43.478 0.00 0.00 0.00 5.01
214 215 5.535753 ATCCTTTTTCTTTGACTTGGGTG 57.464 39.130 0.00 0.00 0.00 4.61
215 216 7.855784 ATTATCCTTTTTCTTTGACTTGGGT 57.144 32.000 0.00 0.00 0.00 4.51
216 217 9.559732 AAAATTATCCTTTTTCTTTGACTTGGG 57.440 29.630 0.00 0.00 0.00 4.12
220 221 9.764363 GGTGAAAATTATCCTTTTTCTTTGACT 57.236 29.630 9.50 0.00 41.49 3.41
221 222 8.988934 GGGTGAAAATTATCCTTTTTCTTTGAC 58.011 33.333 9.50 1.40 41.49 3.18
222 223 8.709308 TGGGTGAAAATTATCCTTTTTCTTTGA 58.291 29.630 9.50 0.00 41.49 2.69
223 224 8.900983 TGGGTGAAAATTATCCTTTTTCTTTG 57.099 30.769 9.50 0.00 41.49 2.77
224 225 8.713971 ACTGGGTGAAAATTATCCTTTTTCTTT 58.286 29.630 9.50 0.00 41.49 2.52
225 226 8.262601 ACTGGGTGAAAATTATCCTTTTTCTT 57.737 30.769 9.50 0.00 41.49 2.52
226 227 7.730332 AGACTGGGTGAAAATTATCCTTTTTCT 59.270 33.333 9.50 0.00 41.49 2.52
227 228 7.896811 AGACTGGGTGAAAATTATCCTTTTTC 58.103 34.615 2.72 2.72 41.36 2.29
228 229 7.855784 AGACTGGGTGAAAATTATCCTTTTT 57.144 32.000 0.00 0.00 0.00 1.94
229 230 8.971073 CATAGACTGGGTGAAAATTATCCTTTT 58.029 33.333 0.00 0.00 0.00 2.27
230 231 7.068716 GCATAGACTGGGTGAAAATTATCCTTT 59.931 37.037 0.00 0.00 0.00 3.11
231 232 6.547510 GCATAGACTGGGTGAAAATTATCCTT 59.452 38.462 0.00 0.00 0.00 3.36
232 233 6.064717 GCATAGACTGGGTGAAAATTATCCT 58.935 40.000 0.00 0.00 0.00 3.24
233 234 5.827797 TGCATAGACTGGGTGAAAATTATCC 59.172 40.000 0.00 0.00 0.00 2.59
234 235 6.767902 TCTGCATAGACTGGGTGAAAATTATC 59.232 38.462 0.00 0.00 0.00 1.75
235 236 6.662755 TCTGCATAGACTGGGTGAAAATTAT 58.337 36.000 0.00 0.00 0.00 1.28
236 237 6.061022 TCTGCATAGACTGGGTGAAAATTA 57.939 37.500 0.00 0.00 0.00 1.40
237 238 4.922206 TCTGCATAGACTGGGTGAAAATT 58.078 39.130 0.00 0.00 0.00 1.82
238 239 4.574674 TCTGCATAGACTGGGTGAAAAT 57.425 40.909 0.00 0.00 0.00 1.82
239 240 4.365514 TTCTGCATAGACTGGGTGAAAA 57.634 40.909 0.00 0.00 31.21 2.29
240 241 4.202461 ACTTTCTGCATAGACTGGGTGAAA 60.202 41.667 0.00 0.00 31.21 2.69
241 242 3.327757 ACTTTCTGCATAGACTGGGTGAA 59.672 43.478 0.00 0.00 31.21 3.18
242 243 2.906389 ACTTTCTGCATAGACTGGGTGA 59.094 45.455 0.00 0.00 31.21 4.02
243 244 3.340814 ACTTTCTGCATAGACTGGGTG 57.659 47.619 0.00 0.00 31.21 4.61
244 245 6.808321 TTATACTTTCTGCATAGACTGGGT 57.192 37.500 0.00 0.00 31.21 4.51
245 246 9.209175 GTAATTATACTTTCTGCATAGACTGGG 57.791 37.037 0.00 0.00 31.21 4.45
246 247 8.916654 CGTAATTATACTTTCTGCATAGACTGG 58.083 37.037 0.00 0.00 31.21 4.00
247 248 8.428536 GCGTAATTATACTTTCTGCATAGACTG 58.571 37.037 0.00 0.00 31.21 3.51
248 249 8.361139 AGCGTAATTATACTTTCTGCATAGACT 58.639 33.333 0.00 0.00 31.21 3.24
249 250 8.522178 AGCGTAATTATACTTTCTGCATAGAC 57.478 34.615 0.00 0.00 31.21 2.59
250 251 9.542462 AAAGCGTAATTATACTTTCTGCATAGA 57.458 29.630 8.93 0.00 0.00 1.98
253 254 8.673711 TGAAAAGCGTAATTATACTTTCTGCAT 58.326 29.630 13.13 2.04 31.37 3.96
254 255 7.960738 GTGAAAAGCGTAATTATACTTTCTGCA 59.039 33.333 13.13 10.26 31.37 4.41
255 256 7.162062 CGTGAAAAGCGTAATTATACTTTCTGC 59.838 37.037 13.13 8.61 31.37 4.26
256 257 7.634817 CCGTGAAAAGCGTAATTATACTTTCTG 59.365 37.037 13.13 6.57 31.37 3.02
257 258 7.332678 ACCGTGAAAAGCGTAATTATACTTTCT 59.667 33.333 13.13 6.76 31.37 2.52
258 259 7.458677 ACCGTGAAAAGCGTAATTATACTTTC 58.541 34.615 13.13 9.31 31.37 2.62
259 260 7.368480 ACCGTGAAAAGCGTAATTATACTTT 57.632 32.000 8.93 8.93 33.92 2.66
260 261 6.973229 ACCGTGAAAAGCGTAATTATACTT 57.027 33.333 0.00 0.00 0.00 2.24
261 262 8.545420 CAATACCGTGAAAAGCGTAATTATACT 58.455 33.333 0.00 0.00 0.00 2.12
262 263 7.319615 GCAATACCGTGAAAAGCGTAATTATAC 59.680 37.037 0.00 0.00 0.00 1.47
263 264 7.011202 TGCAATACCGTGAAAAGCGTAATTATA 59.989 33.333 0.00 0.00 0.00 0.98
264 265 6.183360 TGCAATACCGTGAAAAGCGTAATTAT 60.183 34.615 0.00 0.00 0.00 1.28
265 266 5.121925 TGCAATACCGTGAAAAGCGTAATTA 59.878 36.000 0.00 0.00 0.00 1.40
266 267 4.083217 TGCAATACCGTGAAAAGCGTAATT 60.083 37.500 0.00 0.00 0.00 1.40
267 268 3.437395 TGCAATACCGTGAAAAGCGTAAT 59.563 39.130 0.00 0.00 0.00 1.89
268 269 2.806818 TGCAATACCGTGAAAAGCGTAA 59.193 40.909 0.00 0.00 0.00 3.18
269 270 2.413796 CTGCAATACCGTGAAAAGCGTA 59.586 45.455 0.00 0.00 0.00 4.42
270 271 1.196808 CTGCAATACCGTGAAAAGCGT 59.803 47.619 0.00 0.00 0.00 5.07
271 272 1.463056 TCTGCAATACCGTGAAAAGCG 59.537 47.619 0.00 0.00 0.00 4.68
272 273 2.742053 TCTCTGCAATACCGTGAAAAGC 59.258 45.455 0.00 0.00 0.00 3.51
273 274 5.122239 TCAATCTCTGCAATACCGTGAAAAG 59.878 40.000 0.00 0.00 0.00 2.27
274 275 5.000591 TCAATCTCTGCAATACCGTGAAAA 58.999 37.500 0.00 0.00 0.00 2.29
275 276 4.391830 GTCAATCTCTGCAATACCGTGAAA 59.608 41.667 0.00 0.00 0.00 2.69
276 277 3.932710 GTCAATCTCTGCAATACCGTGAA 59.067 43.478 0.00 0.00 0.00 3.18
277 278 3.195610 AGTCAATCTCTGCAATACCGTGA 59.804 43.478 0.00 0.00 0.00 4.35
278 279 3.525537 AGTCAATCTCTGCAATACCGTG 58.474 45.455 0.00 0.00 0.00 4.94
279 280 3.430929 GGAGTCAATCTCTGCAATACCGT 60.431 47.826 0.00 0.00 42.40 4.83
280 281 3.126831 GGAGTCAATCTCTGCAATACCG 58.873 50.000 0.00 0.00 42.40 4.02
281 282 4.125703 CTGGAGTCAATCTCTGCAATACC 58.874 47.826 0.00 0.00 42.40 2.73
282 283 4.125703 CCTGGAGTCAATCTCTGCAATAC 58.874 47.826 0.00 0.00 42.40 1.89
283 284 4.033009 TCCTGGAGTCAATCTCTGCAATA 58.967 43.478 0.00 0.00 42.40 1.90
284 285 2.842496 TCCTGGAGTCAATCTCTGCAAT 59.158 45.455 0.00 0.00 42.40 3.56
285 286 2.027745 GTCCTGGAGTCAATCTCTGCAA 60.028 50.000 0.00 0.00 42.40 4.08
286 287 1.552337 GTCCTGGAGTCAATCTCTGCA 59.448 52.381 0.00 0.00 42.40 4.41
287 288 1.470632 CGTCCTGGAGTCAATCTCTGC 60.471 57.143 0.00 0.00 42.40 4.26
288 289 1.135915 CCGTCCTGGAGTCAATCTCTG 59.864 57.143 0.00 0.00 42.40 3.35
289 290 1.479709 CCGTCCTGGAGTCAATCTCT 58.520 55.000 0.00 0.00 42.40 3.10
290 291 0.179097 GCCGTCCTGGAGTCAATCTC 60.179 60.000 0.00 0.00 42.00 2.75
291 292 1.901085 GCCGTCCTGGAGTCAATCT 59.099 57.895 0.00 0.00 42.00 2.40
292 293 1.519455 CGCCGTCCTGGAGTCAATC 60.519 63.158 0.00 0.00 42.00 2.67
293 294 2.579201 CGCCGTCCTGGAGTCAAT 59.421 61.111 0.00 0.00 42.00 2.57
294 295 4.373116 GCGCCGTCCTGGAGTCAA 62.373 66.667 0.00 0.00 42.00 3.18
296 297 4.803426 CAGCGCCGTCCTGGAGTC 62.803 72.222 2.29 0.00 42.00 3.36
308 309 4.436448 GAGCTCAACACGCAGCGC 62.436 66.667 16.61 0.00 40.84 5.92
309 310 4.126390 CGAGCTCAACACGCAGCG 62.126 66.667 14.82 14.82 40.84 5.18
314 315 3.470567 GACCGCGAGCTCAACACG 61.471 66.667 15.40 11.14 35.25 4.49
315 316 2.049063 AGACCGCGAGCTCAACAC 60.049 61.111 15.40 0.77 0.00 3.32
316 317 2.258591 GAGACCGCGAGCTCAACA 59.741 61.111 15.40 0.00 0.00 3.33
317 318 2.507324 GGAGACCGCGAGCTCAAC 60.507 66.667 23.17 3.93 32.83 3.18
318 319 4.116328 CGGAGACCGCGAGCTCAA 62.116 66.667 23.17 0.00 41.17 3.02
430 434 3.716601 GGTGGTTTTGTTCTGTTGGATG 58.283 45.455 0.00 0.00 0.00 3.51
562 567 0.622154 TCGAGAGGAGGAGGAGGAGT 60.622 60.000 0.00 0.00 0.00 3.85
563 568 0.771127 ATCGAGAGGAGGAGGAGGAG 59.229 60.000 0.00 0.00 0.00 3.69
564 569 0.768622 GATCGAGAGGAGGAGGAGGA 59.231 60.000 0.00 0.00 0.00 3.71
565 570 0.251165 GGATCGAGAGGAGGAGGAGG 60.251 65.000 0.00 0.00 0.00 4.30
1044 1058 1.518903 GGGTCTTGTTGAGCTGGTGC 61.519 60.000 0.00 0.00 42.40 5.01
1285 1299 2.266055 GTGGAAGTCGCCCCTGAG 59.734 66.667 0.00 0.00 0.00 3.35
1693 1707 6.786967 ACCTACCTACAGTAACAAATCGAT 57.213 37.500 0.00 0.00 0.00 3.59
1711 1725 5.816258 GCCTACCAAAGAATCAACTACCTAC 59.184 44.000 0.00 0.00 0.00 3.18
1839 1856 6.214819 ACCTACTCACTGCTTTATCCCTTTAA 59.785 38.462 0.00 0.00 0.00 1.52
1840 1857 5.724854 ACCTACTCACTGCTTTATCCCTTTA 59.275 40.000 0.00 0.00 0.00 1.85
1997 2014 3.817960 GCACGGGCACAATTATACG 57.182 52.632 3.77 0.00 40.72 3.06
2022 2039 5.409643 AGAAATGCGACCTATCATTTTCG 57.590 39.130 0.00 0.00 41.40 3.46
2032 2049 3.006967 ACTGTCTTGTAGAAATGCGACCT 59.993 43.478 0.00 0.00 0.00 3.85
2034 2051 5.162075 AGTACTGTCTTGTAGAAATGCGAC 58.838 41.667 0.00 0.00 0.00 5.19
2035 2052 5.386958 AGTACTGTCTTGTAGAAATGCGA 57.613 39.130 0.00 0.00 0.00 5.10
2036 2053 6.552629 TCTAGTACTGTCTTGTAGAAATGCG 58.447 40.000 5.39 0.00 0.00 4.73
2037 2054 7.009723 GCTTCTAGTACTGTCTTGTAGAAATGC 59.990 40.741 5.39 2.24 31.13 3.56
2038 2055 8.029522 TGCTTCTAGTACTGTCTTGTAGAAATG 58.970 37.037 5.39 0.00 31.13 2.32
2043 2060 6.503589 AGTGCTTCTAGTACTGTCTTGTAG 57.496 41.667 5.39 0.00 39.72 2.74
2044 2061 8.459635 CAATAGTGCTTCTAGTACTGTCTTGTA 58.540 37.037 5.39 0.00 41.31 2.41
2239 2474 0.318441 TCCAAGTCCTGTTCTGCTCG 59.682 55.000 0.00 0.00 0.00 5.03
2285 2520 3.577667 TCGCAATGCTGAAAATTTGGAG 58.422 40.909 2.94 0.00 0.00 3.86
2287 2522 4.389382 TCAATCGCAATGCTGAAAATTTGG 59.611 37.500 2.94 0.00 0.00 3.28
2407 2654 2.930826 TCTCTTCCCAAAGTGGACAC 57.069 50.000 0.00 0.00 40.96 3.67
2413 2660 4.618920 ACGTACAATCTCTTCCCAAAGT 57.381 40.909 0.00 0.00 33.95 2.66
2430 2677 7.696872 CGTCAATCTTTGATTCTCTTCTACGTA 59.303 37.037 0.00 0.00 42.47 3.57
2431 2678 6.528423 CGTCAATCTTTGATTCTCTTCTACGT 59.472 38.462 0.00 0.00 42.47 3.57
2432 2679 6.507141 GCGTCAATCTTTGATTCTCTTCTACG 60.507 42.308 0.00 0.00 42.47 3.51
2433 2680 6.237969 GGCGTCAATCTTTGATTCTCTTCTAC 60.238 42.308 0.00 0.00 42.47 2.59
2434 2681 5.812642 GGCGTCAATCTTTGATTCTCTTCTA 59.187 40.000 0.00 0.00 42.47 2.10
2479 2726 2.338809 ACAGACATGTTCTCCCAAGGA 58.661 47.619 0.00 0.00 35.63 3.36
2480 2727 2.816087 CAACAGACATGTTCTCCCAAGG 59.184 50.000 0.00 0.00 46.90 3.61
2481 2728 2.227388 GCAACAGACATGTTCTCCCAAG 59.773 50.000 0.00 0.00 46.90 3.61
2482 2729 2.158623 AGCAACAGACATGTTCTCCCAA 60.159 45.455 0.00 0.00 46.90 4.12
2483 2730 1.421268 AGCAACAGACATGTTCTCCCA 59.579 47.619 0.00 0.00 46.90 4.37
2484 2731 1.808945 CAGCAACAGACATGTTCTCCC 59.191 52.381 0.00 0.00 46.90 4.30
2487 2734 1.605710 GCACAGCAACAGACATGTTCT 59.394 47.619 0.00 0.00 46.90 3.01
2491 2740 2.228103 AGAATGCACAGCAACAGACATG 59.772 45.455 0.00 0.00 43.62 3.21
2530 2788 0.035056 CCGGGAAGAGGCATGAAAGT 60.035 55.000 0.00 0.00 0.00 2.66
2531 2789 0.253044 TCCGGGAAGAGGCATGAAAG 59.747 55.000 0.00 0.00 0.00 2.62
2532 2790 0.035439 GTCCGGGAAGAGGCATGAAA 60.035 55.000 0.00 0.00 0.00 2.69
2533 2791 1.198094 TGTCCGGGAAGAGGCATGAA 61.198 55.000 0.00 0.00 0.00 2.57
2534 2792 0.982852 ATGTCCGGGAAGAGGCATGA 60.983 55.000 0.00 0.00 0.00 3.07
2535 2793 0.107017 AATGTCCGGGAAGAGGCATG 60.107 55.000 0.00 0.00 0.00 4.06
2536 2794 0.107017 CAATGTCCGGGAAGAGGCAT 60.107 55.000 0.00 0.00 0.00 4.40
2537 2795 1.299648 CAATGTCCGGGAAGAGGCA 59.700 57.895 0.00 0.00 0.00 4.75
2538 2796 0.322546 AACAATGTCCGGGAAGAGGC 60.323 55.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.