Multiple sequence alignment - TraesCS4D01G266500

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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 TraesCS4D01G266500 chr4D 100.000 3141 0 0 1 3141 437284505 437287645 0.000000e+00 5801.0
1 TraesCS4D01G266500 chr4D 96.819 1572 41 6 1519 3087 437248434 437249999 0.000000e+00 2617.0
2 TraesCS4D01G266500 chr4D 93.007 715 43 5 2376 3087 437157538 437158248 0.000000e+00 1037.0
3 TraesCS4D01G266500 chr4A 94.531 2834 99 22 281 3088 31169947 31167144 0.000000e+00 4324.0
4 TraesCS4D01G266500 chr4A 78.862 246 37 11 486 725 30306682 30306918 5.430000e-33 152.0
5 TraesCS4D01G266500 chr4B 93.222 841 45 9 1545 2377 539495877 539496713 0.000000e+00 1227.0
6 TraesCS4D01G266500 chr4B 92.885 773 44 9 2376 3141 539496807 539497575 0.000000e+00 1112.0
7 TraesCS4D01G266500 chr4B 81.996 561 84 10 987 1536 539488249 539488803 7.940000e-126 460.0
8 TraesCS4D01G266500 chr4B 81.905 525 67 16 459 975 539479109 539479613 4.850000e-113 418.0
9 TraesCS4D01G266500 chr2B 72.549 918 187 36 486 1380 639444728 639445603 4.050000e-59 239.0
10 TraesCS4D01G266500 chr2D 81.560 282 40 6 486 760 537320704 537320980 4.080000e-54 222.0
11 TraesCS4D01G266500 chr2D 90.196 51 5 0 559 609 72308847 72308797 2.020000e-07 67.6
12 TraesCS4D01G266500 chr3B 81.250 112 20 1 525 636 69620619 69620729 4.310000e-14 89.8
13 TraesCS4D01G266500 chr6B 100.000 28 0 0 584 611 567821320 567821347 6.000000e-03 52.8


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 TraesCS4D01G266500 chr4D 437284505 437287645 3140 False 5801.0 5801 100.0000 1 3141 1 chr4D.!!$F3 3140
1 TraesCS4D01G266500 chr4D 437248434 437249999 1565 False 2617.0 2617 96.8190 1519 3087 1 chr4D.!!$F2 1568
2 TraesCS4D01G266500 chr4D 437157538 437158248 710 False 1037.0 1037 93.0070 2376 3087 1 chr4D.!!$F1 711
3 TraesCS4D01G266500 chr4A 31167144 31169947 2803 True 4324.0 4324 94.5310 281 3088 1 chr4A.!!$R1 2807
4 TraesCS4D01G266500 chr4B 539495877 539497575 1698 False 1169.5 1227 93.0535 1545 3141 2 chr4B.!!$F3 1596
5 TraesCS4D01G266500 chr4B 539488249 539488803 554 False 460.0 460 81.9960 987 1536 1 chr4B.!!$F2 549
6 TraesCS4D01G266500 chr4B 539479109 539479613 504 False 418.0 418 81.9050 459 975 1 chr4B.!!$F1 516
7 TraesCS4D01G266500 chr2B 639444728 639445603 875 False 239.0 239 72.5490 486 1380 1 chr2B.!!$F1 894

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
408 421 0.033366 TGTGAAGCAGCGCTCTGTAA 59.967 50.0 7.13 0.00 42.29 2.41 F
448 461 0.237498 GGTTTTACAGGAGCACGTGC 59.763 55.0 32.79 32.79 42.49 5.34 F
679 703 0.596083 CTTCGTGGATAGCCTGCTCG 60.596 60.0 0.00 0.00 34.31 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1427 1.002468 CAAACCGAAGAAGCAGGTGTG 60.002 52.381 0.0 0.0 38.44 3.82 R
1391 1428 1.308998 CAAACCGAAGAAGCAGGTGT 58.691 50.000 0.0 0.0 38.44 4.16 R
2164 2209 3.222603 GGAATATGCCCGTTTCCAGAAT 58.777 45.455 0.0 0.0 39.00 2.40 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
27 28 5.011586 CCTATAGTTAGGTCTAGAGGCACC 58.988 50.000 0.00 0.00 40.79 5.01
28 29 2.162264 AGTTAGGTCTAGAGGCACCC 57.838 55.000 0.00 0.00 32.45 4.61
29 30 1.646977 AGTTAGGTCTAGAGGCACCCT 59.353 52.381 4.42 4.42 36.03 4.34
30 31 9.860997 CCTATAGTTAGGTCTAGAGGCACCCTC 62.861 51.852 2.24 3.04 43.73 4.30
37 38 4.792087 GAGGCACCCTCGACAAAA 57.208 55.556 0.00 0.00 41.08 2.44
38 39 3.249687 GAGGCACCCTCGACAAAAT 57.750 52.632 0.00 0.00 41.08 1.82
39 40 1.534729 GAGGCACCCTCGACAAAATT 58.465 50.000 0.00 0.00 41.08 1.82
40 41 1.200020 GAGGCACCCTCGACAAAATTG 59.800 52.381 0.00 0.00 41.08 2.32
41 42 0.388520 GGCACCCTCGACAAAATTGC 60.389 55.000 0.00 0.00 0.00 3.56
42 43 0.388520 GCACCCTCGACAAAATTGCC 60.389 55.000 0.00 0.00 0.00 4.52
43 44 0.243636 CACCCTCGACAAAATTGCCC 59.756 55.000 0.00 0.00 0.00 5.36
44 45 1.241315 ACCCTCGACAAAATTGCCCG 61.241 55.000 0.00 0.00 0.00 6.13
45 46 1.506262 CCTCGACAAAATTGCCCGG 59.494 57.895 0.00 0.00 0.00 5.73
46 47 1.154035 CTCGACAAAATTGCCCGGC 60.154 57.895 1.04 1.04 0.00 6.13
47 48 2.503809 CGACAAAATTGCCCGGCG 60.504 61.111 4.58 0.00 0.00 6.46
48 49 2.126110 GACAAAATTGCCCGGCGG 60.126 61.111 21.46 21.46 0.00 6.13
60 61 4.038080 CGGCGGGGCAACAAACTC 62.038 66.667 0.00 0.00 39.74 3.01
61 62 4.038080 GGCGGGGCAACAAACTCG 62.038 66.667 0.00 0.00 39.74 4.18
62 63 4.700365 GCGGGGCAACAAACTCGC 62.700 66.667 0.00 0.00 39.74 5.03
63 64 3.283684 CGGGGCAACAAACTCGCA 61.284 61.111 0.00 0.00 39.74 5.10
64 65 2.625823 CGGGGCAACAAACTCGCAT 61.626 57.895 0.00 0.00 39.74 4.73
65 66 1.212751 GGGGCAACAAACTCGCATC 59.787 57.895 0.00 0.00 39.74 3.91
66 67 1.212751 GGGCAACAAACTCGCATCC 59.787 57.895 0.00 0.00 39.74 3.51
67 68 1.212751 GGCAACAAACTCGCATCCC 59.787 57.895 0.00 0.00 0.00 3.85
68 69 1.212751 GCAACAAACTCGCATCCCC 59.787 57.895 0.00 0.00 0.00 4.81
69 70 1.883021 CAACAAACTCGCATCCCCC 59.117 57.895 0.00 0.00 0.00 5.40
70 71 0.893270 CAACAAACTCGCATCCCCCA 60.893 55.000 0.00 0.00 0.00 4.96
71 72 0.893727 AACAAACTCGCATCCCCCAC 60.894 55.000 0.00 0.00 0.00 4.61
72 73 2.046285 CAAACTCGCATCCCCCACC 61.046 63.158 0.00 0.00 0.00 4.61
73 74 2.231380 AAACTCGCATCCCCCACCT 61.231 57.895 0.00 0.00 0.00 4.00
74 75 2.198304 AAACTCGCATCCCCCACCTC 62.198 60.000 0.00 0.00 0.00 3.85
75 76 3.866582 CTCGCATCCCCCACCTCC 61.867 72.222 0.00 0.00 0.00 4.30
76 77 4.731853 TCGCATCCCCCACCTCCA 62.732 66.667 0.00 0.00 0.00 3.86
77 78 3.492353 CGCATCCCCCACCTCCAT 61.492 66.667 0.00 0.00 0.00 3.41
78 79 3.018901 GCATCCCCCACCTCCATT 58.981 61.111 0.00 0.00 0.00 3.16
79 80 1.152673 GCATCCCCCACCTCCATTC 60.153 63.158 0.00 0.00 0.00 2.67
80 81 1.538666 CATCCCCCACCTCCATTCC 59.461 63.158 0.00 0.00 0.00 3.01
81 82 1.086565 ATCCCCCACCTCCATTCCA 59.913 57.895 0.00 0.00 0.00 3.53
82 83 1.289244 ATCCCCCACCTCCATTCCAC 61.289 60.000 0.00 0.00 0.00 4.02
83 84 2.683475 CCCCACCTCCATTCCACC 59.317 66.667 0.00 0.00 0.00 4.61
84 85 2.272146 CCCACCTCCATTCCACCG 59.728 66.667 0.00 0.00 0.00 4.94
85 86 2.272146 CCACCTCCATTCCACCGG 59.728 66.667 0.00 0.00 0.00 5.28
86 87 2.602676 CCACCTCCATTCCACCGGT 61.603 63.158 0.00 0.00 0.00 5.28
87 88 1.078426 CACCTCCATTCCACCGGTC 60.078 63.158 2.59 0.00 0.00 4.79
88 89 2.186903 CCTCCATTCCACCGGTCG 59.813 66.667 2.59 0.00 0.00 4.79
89 90 2.656069 CCTCCATTCCACCGGTCGT 61.656 63.158 2.59 0.00 0.00 4.34
90 91 1.153628 CTCCATTCCACCGGTCGTC 60.154 63.158 2.59 0.00 0.00 4.20
91 92 2.508439 CCATTCCACCGGTCGTCG 60.508 66.667 2.59 0.00 38.88 5.12
92 93 2.569657 CATTCCACCGGTCGTCGA 59.430 61.111 2.59 0.00 42.43 4.20
93 94 1.516386 CATTCCACCGGTCGTCGAG 60.516 63.158 2.59 0.00 42.43 4.04
94 95 1.676635 ATTCCACCGGTCGTCGAGA 60.677 57.895 2.59 0.00 42.43 4.04
102 103 2.175322 GTCGTCGAGACCACGTCC 59.825 66.667 0.00 0.00 43.95 4.79
103 104 3.417224 TCGTCGAGACCACGTCCG 61.417 66.667 0.00 0.00 38.45 4.79
105 106 4.773117 GTCGAGACCACGTCCGCC 62.773 72.222 0.00 0.00 32.18 6.13
107 108 4.477975 CGAGACCACGTCCGCCTC 62.478 72.222 0.00 0.00 32.18 4.70
108 109 4.131088 GAGACCACGTCCGCCTCC 62.131 72.222 0.00 0.00 32.18 4.30
109 110 4.988716 AGACCACGTCCGCCTCCA 62.989 66.667 0.00 0.00 32.18 3.86
110 111 3.771160 GACCACGTCCGCCTCCAT 61.771 66.667 0.00 0.00 0.00 3.41
111 112 3.310860 GACCACGTCCGCCTCCATT 62.311 63.158 0.00 0.00 0.00 3.16
112 113 1.952102 GACCACGTCCGCCTCCATTA 61.952 60.000 0.00 0.00 0.00 1.90
113 114 1.227263 CCACGTCCGCCTCCATTAG 60.227 63.158 0.00 0.00 0.00 1.73
114 115 1.672854 CCACGTCCGCCTCCATTAGA 61.673 60.000 0.00 0.00 0.00 2.10
115 116 0.389391 CACGTCCGCCTCCATTAGAT 59.611 55.000 0.00 0.00 0.00 1.98
116 117 0.389391 ACGTCCGCCTCCATTAGATG 59.611 55.000 0.00 0.00 0.00 2.90
117 118 0.673985 CGTCCGCCTCCATTAGATGA 59.326 55.000 0.00 0.00 0.00 2.92
118 119 1.603172 CGTCCGCCTCCATTAGATGAC 60.603 57.143 0.00 0.00 0.00 3.06
119 120 0.673985 TCCGCCTCCATTAGATGACG 59.326 55.000 0.00 0.00 0.00 4.35
120 121 0.673985 CCGCCTCCATTAGATGACGA 59.326 55.000 0.00 0.00 0.00 4.20
121 122 1.068588 CCGCCTCCATTAGATGACGAA 59.931 52.381 0.00 0.00 0.00 3.85
122 123 2.128035 CGCCTCCATTAGATGACGAAC 58.872 52.381 0.00 0.00 0.00 3.95
123 124 2.484889 GCCTCCATTAGATGACGAACC 58.515 52.381 0.00 0.00 0.00 3.62
124 125 2.103263 GCCTCCATTAGATGACGAACCT 59.897 50.000 0.00 0.00 0.00 3.50
125 126 3.800604 GCCTCCATTAGATGACGAACCTC 60.801 52.174 0.00 0.00 0.00 3.85
126 127 3.551046 CCTCCATTAGATGACGAACCTCG 60.551 52.174 0.00 0.00 46.93 4.63
127 128 2.361119 TCCATTAGATGACGAACCTCGG 59.639 50.000 0.67 0.00 45.59 4.63
128 129 2.100916 CCATTAGATGACGAACCTCGGT 59.899 50.000 0.67 0.00 45.59 4.69
129 130 3.317149 CCATTAGATGACGAACCTCGGTA 59.683 47.826 0.67 0.00 45.59 4.02
130 131 4.022242 CCATTAGATGACGAACCTCGGTAT 60.022 45.833 0.67 0.00 45.59 2.73
131 132 4.563337 TTAGATGACGAACCTCGGTATG 57.437 45.455 0.67 0.00 45.59 2.39
132 133 2.376109 AGATGACGAACCTCGGTATGT 58.624 47.619 0.67 0.00 45.59 2.29
133 134 2.099263 AGATGACGAACCTCGGTATGTG 59.901 50.000 0.67 0.00 45.59 3.21
134 135 0.108992 TGACGAACCTCGGTATGTGC 60.109 55.000 0.67 0.00 45.59 4.57
135 136 0.804933 GACGAACCTCGGTATGTGCC 60.805 60.000 0.67 0.00 45.59 5.01
136 137 1.216977 CGAACCTCGGTATGTGCCA 59.783 57.895 0.00 0.00 36.00 4.92
137 138 0.806102 CGAACCTCGGTATGTGCCAG 60.806 60.000 0.00 0.00 36.00 4.85
138 139 1.078426 AACCTCGGTATGTGCCAGC 60.078 57.895 0.00 0.00 0.00 4.85
139 140 1.553690 AACCTCGGTATGTGCCAGCT 61.554 55.000 0.00 0.00 0.00 4.24
140 141 1.227380 CCTCGGTATGTGCCAGCTC 60.227 63.158 0.00 0.00 0.00 4.09
141 142 1.227380 CTCGGTATGTGCCAGCTCC 60.227 63.158 0.00 0.00 0.00 4.70
142 143 1.960040 CTCGGTATGTGCCAGCTCCA 61.960 60.000 0.00 0.00 0.00 3.86
143 144 1.146930 CGGTATGTGCCAGCTCCAT 59.853 57.895 0.00 0.00 0.00 3.41
144 145 0.392706 CGGTATGTGCCAGCTCCATA 59.607 55.000 0.00 0.00 0.00 2.74
145 146 1.202639 CGGTATGTGCCAGCTCCATAA 60.203 52.381 0.00 0.00 0.00 1.90
146 147 2.498167 GGTATGTGCCAGCTCCATAAG 58.502 52.381 0.00 0.00 0.00 1.73
147 148 2.498167 GTATGTGCCAGCTCCATAAGG 58.502 52.381 0.00 0.00 0.00 2.69
150 151 3.833304 GCCAGCTCCATAAGGCAC 58.167 61.111 5.66 0.00 46.26 5.01
151 152 1.077501 GCCAGCTCCATAAGGCACA 60.078 57.895 5.66 0.00 46.26 4.57
152 153 0.680921 GCCAGCTCCATAAGGCACAA 60.681 55.000 5.66 0.00 46.26 3.33
153 154 1.386533 CCAGCTCCATAAGGCACAAG 58.613 55.000 0.00 0.00 33.74 3.16
154 155 0.737219 CAGCTCCATAAGGCACAAGC 59.263 55.000 0.00 0.00 41.10 4.01
155 156 0.622665 AGCTCCATAAGGCACAAGCT 59.377 50.000 0.00 0.00 41.70 3.74
156 157 0.737219 GCTCCATAAGGCACAAGCTG 59.263 55.000 0.00 0.00 41.70 4.24
157 158 0.737219 CTCCATAAGGCACAAGCTGC 59.263 55.000 0.00 0.00 46.31 5.25
164 165 2.177531 GCACAAGCTGCGACATGG 59.822 61.111 0.00 0.00 35.72 3.66
165 166 2.872557 CACAAGCTGCGACATGGG 59.127 61.111 0.00 0.00 0.00 4.00
166 167 2.360350 ACAAGCTGCGACATGGGG 60.360 61.111 0.00 0.00 0.00 4.96
167 168 3.136123 CAAGCTGCGACATGGGGG 61.136 66.667 0.00 0.00 0.00 5.40
184 185 3.283259 GGGGGATTTTGGACTAGAGTG 57.717 52.381 0.00 0.00 0.00 3.51
185 186 2.576648 GGGGGATTTTGGACTAGAGTGT 59.423 50.000 0.00 0.00 0.00 3.55
186 187 3.778629 GGGGGATTTTGGACTAGAGTGTA 59.221 47.826 0.00 0.00 0.00 2.90
187 188 4.141688 GGGGGATTTTGGACTAGAGTGTAG 60.142 50.000 0.00 0.00 0.00 2.74
188 189 4.141688 GGGGATTTTGGACTAGAGTGTAGG 60.142 50.000 0.00 0.00 0.00 3.18
189 190 4.715297 GGGATTTTGGACTAGAGTGTAGGA 59.285 45.833 0.00 0.00 0.00 2.94
190 191 5.367060 GGGATTTTGGACTAGAGTGTAGGAT 59.633 44.000 0.00 0.00 0.00 3.24
191 192 6.126739 GGGATTTTGGACTAGAGTGTAGGATT 60.127 42.308 0.00 0.00 0.00 3.01
192 193 7.339482 GGATTTTGGACTAGAGTGTAGGATTT 58.661 38.462 0.00 0.00 0.00 2.17
193 194 7.281100 GGATTTTGGACTAGAGTGTAGGATTTG 59.719 40.741 0.00 0.00 0.00 2.32
194 195 6.681729 TTTGGACTAGAGTGTAGGATTTGT 57.318 37.500 0.00 0.00 0.00 2.83
195 196 6.681729 TTGGACTAGAGTGTAGGATTTGTT 57.318 37.500 0.00 0.00 0.00 2.83
196 197 6.681729 TGGACTAGAGTGTAGGATTTGTTT 57.318 37.500 0.00 0.00 0.00 2.83
197 198 6.698380 TGGACTAGAGTGTAGGATTTGTTTC 58.302 40.000 0.00 0.00 0.00 2.78
198 199 6.497259 TGGACTAGAGTGTAGGATTTGTTTCT 59.503 38.462 0.00 0.00 0.00 2.52
199 200 7.036829 GGACTAGAGTGTAGGATTTGTTTCTC 58.963 42.308 0.00 0.00 0.00 2.87
200 201 6.937392 ACTAGAGTGTAGGATTTGTTTCTCC 58.063 40.000 0.00 0.00 0.00 3.71
201 202 5.167303 AGAGTGTAGGATTTGTTTCTCCC 57.833 43.478 0.00 0.00 31.49 4.30
202 203 3.933332 GAGTGTAGGATTTGTTTCTCCCG 59.067 47.826 0.00 0.00 31.49 5.14
203 204 2.418976 GTGTAGGATTTGTTTCTCCCGC 59.581 50.000 0.00 0.00 31.49 6.13
204 205 2.304761 TGTAGGATTTGTTTCTCCCGCT 59.695 45.455 0.00 0.00 31.49 5.52
205 206 1.826385 AGGATTTGTTTCTCCCGCTG 58.174 50.000 0.00 0.00 31.49 5.18
206 207 0.171231 GGATTTGTTTCTCCCGCTGC 59.829 55.000 0.00 0.00 0.00 5.25
207 208 0.881118 GATTTGTTTCTCCCGCTGCA 59.119 50.000 0.00 0.00 0.00 4.41
208 209 1.269448 GATTTGTTTCTCCCGCTGCAA 59.731 47.619 0.00 0.00 0.00 4.08
209 210 0.383949 TTTGTTTCTCCCGCTGCAAC 59.616 50.000 0.00 0.00 0.00 4.17
210 211 0.749818 TTGTTTCTCCCGCTGCAACA 60.750 50.000 0.00 0.00 0.00 3.33
211 212 1.282875 GTTTCTCCCGCTGCAACAC 59.717 57.895 0.00 0.00 0.00 3.32
212 213 1.153066 TTTCTCCCGCTGCAACACA 60.153 52.632 0.00 0.00 0.00 3.72
213 214 1.444119 TTTCTCCCGCTGCAACACAC 61.444 55.000 0.00 0.00 0.00 3.82
214 215 3.716006 CTCCCGCTGCAACACACG 61.716 66.667 0.00 0.00 0.00 4.49
219 220 4.629115 GCTGCAACACACGGGCAC 62.629 66.667 0.00 0.00 33.34 5.01
220 221 3.208383 CTGCAACACACGGGCACA 61.208 61.111 0.00 0.00 33.34 4.57
221 222 2.518112 TGCAACACACGGGCACAT 60.518 55.556 0.00 0.00 31.58 3.21
222 223 2.074230 CTGCAACACACGGGCACATT 62.074 55.000 0.00 0.00 33.34 2.71
223 224 1.067250 GCAACACACGGGCACATTT 59.933 52.632 0.00 0.00 0.00 2.32
224 225 1.214373 GCAACACACGGGCACATTTG 61.214 55.000 0.00 0.00 0.00 2.32
238 239 5.862924 GCACATTTGCTACTGAAGACTAA 57.137 39.130 0.00 0.00 46.17 2.24
239 240 5.862811 GCACATTTGCTACTGAAGACTAAG 58.137 41.667 0.00 0.00 46.17 2.18
240 241 5.639506 GCACATTTGCTACTGAAGACTAAGA 59.360 40.000 0.00 0.00 46.17 2.10
241 242 6.183360 GCACATTTGCTACTGAAGACTAAGAG 60.183 42.308 0.00 0.00 46.17 2.85
242 243 7.093354 CACATTTGCTACTGAAGACTAAGAGA 58.907 38.462 0.00 0.00 0.00 3.10
243 244 7.763528 CACATTTGCTACTGAAGACTAAGAGAT 59.236 37.037 0.00 0.00 0.00 2.75
244 245 8.972127 ACATTTGCTACTGAAGACTAAGAGATA 58.028 33.333 0.00 0.00 0.00 1.98
245 246 9.809096 CATTTGCTACTGAAGACTAAGAGATAA 57.191 33.333 0.00 0.00 0.00 1.75
247 248 9.640963 TTTGCTACTGAAGACTAAGAGATAAAC 57.359 33.333 0.00 0.00 0.00 2.01
248 249 7.773149 TGCTACTGAAGACTAAGAGATAAACC 58.227 38.462 0.00 0.00 0.00 3.27
249 250 7.616150 TGCTACTGAAGACTAAGAGATAAACCT 59.384 37.037 0.00 0.00 0.00 3.50
250 251 9.122779 GCTACTGAAGACTAAGAGATAAACCTA 57.877 37.037 0.00 0.00 0.00 3.08
253 254 9.536510 ACTGAAGACTAAGAGATAAACCTAAGT 57.463 33.333 0.00 0.00 0.00 2.24
254 255 9.796120 CTGAAGACTAAGAGATAAACCTAAGTG 57.204 37.037 0.00 0.00 0.00 3.16
255 256 8.750298 TGAAGACTAAGAGATAAACCTAAGTGG 58.250 37.037 0.00 0.00 42.93 4.00
265 266 2.579878 CCTAAGTGGTCGCTCTCCA 58.420 57.895 0.00 0.00 0.00 3.86
271 272 2.057830 TGGTCGCTCTCCACAATGT 58.942 52.632 0.00 0.00 0.00 2.71
272 273 1.262417 TGGTCGCTCTCCACAATGTA 58.738 50.000 0.00 0.00 0.00 2.29
273 274 1.621317 TGGTCGCTCTCCACAATGTAA 59.379 47.619 0.00 0.00 0.00 2.41
274 275 2.236146 TGGTCGCTCTCCACAATGTAAT 59.764 45.455 0.00 0.00 0.00 1.89
275 276 2.609459 GGTCGCTCTCCACAATGTAATG 59.391 50.000 0.00 0.00 0.00 1.90
276 277 3.262420 GTCGCTCTCCACAATGTAATGT 58.738 45.455 0.00 0.00 0.00 2.71
277 278 4.430007 GTCGCTCTCCACAATGTAATGTA 58.570 43.478 0.00 0.00 30.84 2.29
278 279 4.504461 GTCGCTCTCCACAATGTAATGTAG 59.496 45.833 0.00 0.00 30.84 2.74
279 280 3.246226 CGCTCTCCACAATGTAATGTAGC 59.754 47.826 0.00 0.00 31.11 3.58
280 281 3.246226 GCTCTCCACAATGTAATGTAGCG 59.754 47.826 0.00 0.00 30.84 4.26
281 282 3.194861 TCTCCACAATGTAATGTAGCGC 58.805 45.455 0.00 0.00 30.84 5.92
282 283 3.118775 TCTCCACAATGTAATGTAGCGCT 60.119 43.478 17.26 17.26 30.84 5.92
283 284 3.605634 TCCACAATGTAATGTAGCGCTT 58.394 40.909 18.68 0.00 30.84 4.68
284 285 3.373748 TCCACAATGTAATGTAGCGCTTG 59.626 43.478 18.68 6.85 30.84 4.01
285 286 3.126858 CCACAATGTAATGTAGCGCTTGT 59.873 43.478 18.68 7.63 30.84 3.16
286 287 4.379394 CCACAATGTAATGTAGCGCTTGTT 60.379 41.667 18.68 11.07 30.84 2.83
287 288 5.153513 CACAATGTAATGTAGCGCTTGTTT 58.846 37.500 18.68 9.48 30.84 2.83
302 303 5.516090 CGCTTGTTTAAAAGGCAGTTCTTA 58.484 37.500 0.00 0.00 0.00 2.10
306 307 8.661257 GCTTGTTTAAAAGGCAGTTCTTAAAAA 58.339 29.630 0.00 0.00 0.00 1.94
327 337 4.789012 AAAAGGGTATGACTTCGTACGA 57.211 40.909 15.28 15.28 38.81 3.43
356 366 1.278637 GCAAACGACCGTGAACCAG 59.721 57.895 0.00 0.00 0.00 4.00
361 371 2.741092 GACCGTGAACCAGCCTGA 59.259 61.111 0.00 0.00 0.00 3.86
366 376 1.078759 CGTGAACCAGCCTGATCGAC 61.079 60.000 0.00 0.00 0.00 4.20
379 389 3.181499 CCTGATCGACGGTGCCTATATAC 60.181 52.174 0.00 0.00 0.00 1.47
381 391 4.077108 TGATCGACGGTGCCTATATACTT 58.923 43.478 0.00 0.00 0.00 2.24
392 405 6.807230 GGTGCCTATATACTTTCTCGTATGTG 59.193 42.308 0.00 0.00 32.63 3.21
408 421 0.033366 TGTGAAGCAGCGCTCTGTAA 59.967 50.000 7.13 0.00 42.29 2.41
448 461 0.237498 GGTTTTACAGGAGCACGTGC 59.763 55.000 32.79 32.79 42.49 5.34
523 536 2.227089 CTCCCCAACGACCTTCTCCG 62.227 65.000 0.00 0.00 0.00 4.63
542 555 1.578206 GCCACGTGCTTTCCTTCCTC 61.578 60.000 10.91 0.00 36.87 3.71
679 703 0.596083 CTTCGTGGATAGCCTGCTCG 60.596 60.000 0.00 0.00 34.31 5.03
978 1002 3.711348 CTCGATTTCTCGGGCTGC 58.289 61.111 0.00 0.00 45.10 5.25
1119 1143 3.435026 GGATCTATTTGCCCAGCCTTGTA 60.435 47.826 0.00 0.00 0.00 2.41
1201 1225 6.073222 ACTGTTAACTTCGGCAATTGTTAGAG 60.073 38.462 7.40 3.73 0.00 2.43
1287 1316 7.283807 TGTGATGGATGTTATGAATCTGAAAGG 59.716 37.037 0.00 0.00 0.00 3.11
1347 1376 4.851639 AGGATTATCACAAGTTGCCTCT 57.148 40.909 1.81 0.00 0.00 3.69
1369 1398 1.073763 TGGAGTTGTGGGTTCATCCTG 59.926 52.381 0.00 0.00 36.25 3.86
1415 1452 3.244422 ACCTGCTTCTTCGGTTTGTGATA 60.244 43.478 0.00 0.00 0.00 2.15
1476 1514 1.153208 GCTGCTCATACAGGCTGCT 60.153 57.895 15.89 4.57 45.42 4.24
1613 1652 5.602561 AGCCAAAAAGTTTAACTCCCATTCT 59.397 36.000 0.00 0.00 0.00 2.40
2061 2105 3.628646 ATCGGTGGGCTCACAAGGC 62.629 63.158 20.52 0.00 45.32 4.35
2152 2197 7.397476 ACTTCTGGATCTTAATGTGAGTAGTGA 59.603 37.037 0.00 0.00 0.00 3.41
2164 2209 7.984422 ATGTGAGTAGTGATCAACAAATCAA 57.016 32.000 0.00 0.00 37.41 2.57
2532 2676 0.548031 AATCAGTGTGGGCGATGGAT 59.452 50.000 0.00 0.00 0.00 3.41
2744 2897 5.011023 TGACAAAAGAGATGTACAGCTGAGA 59.989 40.000 20.17 4.64 0.00 3.27
2770 2924 7.881232 AGAGTTTTTATCTCCGTGACCATTTAA 59.119 33.333 0.00 0.00 32.93 1.52
2777 2931 4.951715 TCTCCGTGACCATTTAAGCTAGTA 59.048 41.667 0.00 0.00 0.00 1.82
2810 2964 1.876263 GTTGTGGGCGTGTGTTTGC 60.876 57.895 0.00 0.00 0.00 3.68
2853 3007 8.981647 CCAATTTTTCTTTGATTAACTGGACAG 58.018 33.333 0.00 0.00 0.00 3.51
2945 3100 4.951715 AGGGTCCCCGTTGAATTAATTTAC 59.048 41.667 3.51 3.61 41.95 2.01
2946 3101 4.705991 GGGTCCCCGTTGAATTAATTTACA 59.294 41.667 1.43 0.00 0.00 2.41
2950 3105 7.283807 GGTCCCCGTTGAATTAATTTACACTAT 59.716 37.037 1.43 0.00 0.00 2.12
2997 3156 9.727627 CTTGTCTTTCTAATGATATTCTTTGCC 57.272 33.333 0.00 0.00 0.00 4.52
3095 3254 5.026038 TGTAAGTTTCTCGTCCAAAAGGA 57.974 39.130 0.00 0.00 0.00 3.36
3107 3267 1.880027 CCAAAAGGACGGTGAAAGAGG 59.120 52.381 0.00 0.00 0.00 3.69
3113 3273 3.676093 AGGACGGTGAAAGAGGATTTTC 58.324 45.455 0.00 0.00 37.53 2.29
3118 3278 4.202367 ACGGTGAAAGAGGATTTTCAGTCT 60.202 41.667 1.74 0.00 45.00 3.24
3123 3283 7.391833 GGTGAAAGAGGATTTTCAGTCTTATGT 59.608 37.037 1.74 0.00 45.00 2.29
3125 3285 8.378565 TGAAAGAGGATTTTCAGTCTTATGTCT 58.621 33.333 0.00 0.00 40.95 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.668812 AGGGTGCCTCTAGACCTAACTATA 59.331 45.833 0.00 0.00 32.33 1.31
7 8 3.467863 AGGGTGCCTCTAGACCTAACTAT 59.532 47.826 0.00 0.00 32.33 2.12
8 9 2.857498 AGGGTGCCTCTAGACCTAACTA 59.143 50.000 0.00 0.00 32.33 2.24
9 10 1.646977 AGGGTGCCTCTAGACCTAACT 59.353 52.381 0.00 0.00 32.33 2.24
10 11 2.033372 GAGGGTGCCTCTAGACCTAAC 58.967 57.143 0.00 0.00 46.41 2.34
11 12 2.456073 GAGGGTGCCTCTAGACCTAA 57.544 55.000 0.00 0.00 46.41 2.69
20 21 1.200020 CAATTTTGTCGAGGGTGCCTC 59.800 52.381 0.00 0.00 46.44 4.70
21 22 1.247567 CAATTTTGTCGAGGGTGCCT 58.752 50.000 0.00 0.00 36.03 4.75
22 23 0.388520 GCAATTTTGTCGAGGGTGCC 60.389 55.000 0.00 0.00 0.00 5.01
23 24 0.388520 GGCAATTTTGTCGAGGGTGC 60.389 55.000 0.00 0.00 0.00 5.01
24 25 0.243636 GGGCAATTTTGTCGAGGGTG 59.756 55.000 0.00 0.00 32.44 4.61
25 26 1.241315 CGGGCAATTTTGTCGAGGGT 61.241 55.000 0.00 0.00 32.44 4.34
26 27 1.506262 CGGGCAATTTTGTCGAGGG 59.494 57.895 0.00 0.00 32.44 4.30
27 28 1.506262 CCGGGCAATTTTGTCGAGG 59.494 57.895 0.00 2.85 32.44 4.63
28 29 1.154035 GCCGGGCAATTTTGTCGAG 60.154 57.895 15.62 0.00 32.44 4.04
29 30 2.958576 GCCGGGCAATTTTGTCGA 59.041 55.556 15.62 0.00 32.44 4.20
30 31 2.503809 CGCCGGGCAATTTTGTCG 60.504 61.111 20.71 0.00 32.44 4.35
31 32 2.126110 CCGCCGGGCAATTTTGTC 60.126 61.111 20.71 0.00 0.00 3.18
32 33 3.690280 CCCGCCGGGCAATTTTGT 61.690 61.111 20.71 0.00 35.35 2.83
33 34 4.449568 CCCCGCCGGGCAATTTTG 62.450 66.667 19.21 0.00 44.50 2.44
43 44 4.038080 GAGTTTGTTGCCCCGCCG 62.038 66.667 0.00 0.00 0.00 6.46
44 45 4.038080 CGAGTTTGTTGCCCCGCC 62.038 66.667 0.00 0.00 0.00 6.13
45 46 4.700365 GCGAGTTTGTTGCCCCGC 62.700 66.667 0.00 0.00 35.91 6.13
46 47 2.527547 GATGCGAGTTTGTTGCCCCG 62.528 60.000 0.00 0.00 34.08 5.73
47 48 1.212751 GATGCGAGTTTGTTGCCCC 59.787 57.895 0.00 0.00 34.08 5.80
48 49 1.212751 GGATGCGAGTTTGTTGCCC 59.787 57.895 0.00 0.00 34.08 5.36
49 50 1.212751 GGGATGCGAGTTTGTTGCC 59.787 57.895 0.00 0.00 34.08 4.52
50 51 1.212751 GGGGATGCGAGTTTGTTGC 59.787 57.895 0.00 0.00 35.86 4.17
51 52 0.893270 TGGGGGATGCGAGTTTGTTG 60.893 55.000 0.00 0.00 0.00 3.33
52 53 0.893727 GTGGGGGATGCGAGTTTGTT 60.894 55.000 0.00 0.00 0.00 2.83
53 54 1.303317 GTGGGGGATGCGAGTTTGT 60.303 57.895 0.00 0.00 0.00 2.83
54 55 2.046285 GGTGGGGGATGCGAGTTTG 61.046 63.158 0.00 0.00 0.00 2.93
55 56 2.198304 GAGGTGGGGGATGCGAGTTT 62.198 60.000 0.00 0.00 0.00 2.66
56 57 2.610859 AGGTGGGGGATGCGAGTT 60.611 61.111 0.00 0.00 0.00 3.01
57 58 3.083997 GAGGTGGGGGATGCGAGT 61.084 66.667 0.00 0.00 0.00 4.18
58 59 3.866582 GGAGGTGGGGGATGCGAG 61.867 72.222 0.00 0.00 0.00 5.03
59 60 4.731853 TGGAGGTGGGGGATGCGA 62.732 66.667 0.00 0.00 0.00 5.10
60 61 2.965716 GAATGGAGGTGGGGGATGCG 62.966 65.000 0.00 0.00 0.00 4.73
61 62 1.152673 GAATGGAGGTGGGGGATGC 60.153 63.158 0.00 0.00 0.00 3.91
62 63 1.288508 TGGAATGGAGGTGGGGGATG 61.289 60.000 0.00 0.00 0.00 3.51
63 64 1.086565 TGGAATGGAGGTGGGGGAT 59.913 57.895 0.00 0.00 0.00 3.85
64 65 1.928567 GTGGAATGGAGGTGGGGGA 60.929 63.158 0.00 0.00 0.00 4.81
65 66 2.683475 GTGGAATGGAGGTGGGGG 59.317 66.667 0.00 0.00 0.00 5.40
66 67 2.683475 GGTGGAATGGAGGTGGGG 59.317 66.667 0.00 0.00 0.00 4.96
67 68 2.272146 CGGTGGAATGGAGGTGGG 59.728 66.667 0.00 0.00 0.00 4.61
68 69 2.272146 CCGGTGGAATGGAGGTGG 59.728 66.667 0.00 0.00 0.00 4.61
69 70 1.078426 GACCGGTGGAATGGAGGTG 60.078 63.158 14.63 0.00 35.00 4.00
70 71 2.656069 CGACCGGTGGAATGGAGGT 61.656 63.158 14.63 0.00 38.00 3.85
71 72 2.186903 CGACCGGTGGAATGGAGG 59.813 66.667 14.63 0.00 0.00 4.30
72 73 1.153628 GACGACCGGTGGAATGGAG 60.154 63.158 24.54 1.28 0.00 3.86
73 74 2.975536 GACGACCGGTGGAATGGA 59.024 61.111 24.54 0.00 0.00 3.41
74 75 2.508439 CGACGACCGGTGGAATGG 60.508 66.667 24.54 5.18 33.91 3.16
75 76 1.516386 CTCGACGACCGGTGGAATG 60.516 63.158 24.54 11.85 39.14 2.67
76 77 1.676635 TCTCGACGACCGGTGGAAT 60.677 57.895 24.54 0.61 39.14 3.01
77 78 2.281692 TCTCGACGACCGGTGGAA 60.282 61.111 24.54 7.22 39.14 3.53
78 79 3.052082 GTCTCGACGACCGGTGGA 61.052 66.667 24.54 8.73 36.62 4.02
85 86 2.175322 GGACGTGGTCTCGACGAC 59.825 66.667 10.75 3.82 39.21 4.34
86 87 3.417224 CGGACGTGGTCTCGACGA 61.417 66.667 10.75 0.00 39.21 4.20
88 89 4.773117 GGCGGACGTGGTCTCGAC 62.773 72.222 0.00 4.43 31.51 4.20
90 91 4.477975 GAGGCGGACGTGGTCTCG 62.478 72.222 0.00 0.00 32.47 4.04
91 92 4.131088 GGAGGCGGACGTGGTCTC 62.131 72.222 8.85 8.85 32.47 3.36
92 93 4.988716 TGGAGGCGGACGTGGTCT 62.989 66.667 0.00 0.00 32.47 3.85
93 94 1.952102 TAATGGAGGCGGACGTGGTC 61.952 60.000 0.00 0.00 0.00 4.02
94 95 1.956629 CTAATGGAGGCGGACGTGGT 61.957 60.000 0.00 0.00 0.00 4.16
95 96 1.227263 CTAATGGAGGCGGACGTGG 60.227 63.158 0.00 0.00 0.00 4.94
96 97 0.389391 ATCTAATGGAGGCGGACGTG 59.611 55.000 0.00 0.00 0.00 4.49
97 98 0.389391 CATCTAATGGAGGCGGACGT 59.611 55.000 0.00 0.00 0.00 4.34
98 99 0.673985 TCATCTAATGGAGGCGGACG 59.326 55.000 0.00 0.00 0.00 4.79
99 100 1.603172 CGTCATCTAATGGAGGCGGAC 60.603 57.143 0.00 0.00 0.00 4.79
100 101 0.673985 CGTCATCTAATGGAGGCGGA 59.326 55.000 0.00 0.00 0.00 5.54
101 102 0.673985 TCGTCATCTAATGGAGGCGG 59.326 55.000 0.00 0.00 0.00 6.13
102 103 2.128035 GTTCGTCATCTAATGGAGGCG 58.872 52.381 0.00 0.00 0.00 5.52
103 104 2.103263 AGGTTCGTCATCTAATGGAGGC 59.897 50.000 0.00 0.00 0.00 4.70
104 105 3.551046 CGAGGTTCGTCATCTAATGGAGG 60.551 52.174 0.00 0.00 34.72 4.30
105 106 3.551046 CCGAGGTTCGTCATCTAATGGAG 60.551 52.174 0.00 0.00 38.40 3.86
106 107 2.361119 CCGAGGTTCGTCATCTAATGGA 59.639 50.000 0.00 0.00 38.40 3.41
107 108 2.100916 ACCGAGGTTCGTCATCTAATGG 59.899 50.000 0.00 0.00 38.40 3.16
108 109 3.438297 ACCGAGGTTCGTCATCTAATG 57.562 47.619 0.00 0.00 38.40 1.90
109 110 4.583489 ACATACCGAGGTTCGTCATCTAAT 59.417 41.667 0.00 0.00 38.40 1.73
110 111 3.949754 ACATACCGAGGTTCGTCATCTAA 59.050 43.478 0.00 0.00 38.40 2.10
111 112 3.314357 CACATACCGAGGTTCGTCATCTA 59.686 47.826 0.00 0.00 38.40 1.98
112 113 2.099263 CACATACCGAGGTTCGTCATCT 59.901 50.000 0.00 0.00 38.40 2.90
113 114 2.460918 CACATACCGAGGTTCGTCATC 58.539 52.381 0.00 0.00 38.40 2.92
114 115 1.470979 GCACATACCGAGGTTCGTCAT 60.471 52.381 0.00 0.00 38.40 3.06
115 116 0.108992 GCACATACCGAGGTTCGTCA 60.109 55.000 0.00 0.00 38.40 4.35
116 117 0.804933 GGCACATACCGAGGTTCGTC 60.805 60.000 0.00 0.00 38.40 4.20
117 118 1.217244 GGCACATACCGAGGTTCGT 59.783 57.895 0.00 0.00 38.40 3.85
118 119 0.806102 CTGGCACATACCGAGGTTCG 60.806 60.000 0.00 0.00 38.20 3.95
119 120 1.090052 GCTGGCACATACCGAGGTTC 61.090 60.000 0.00 0.00 38.20 3.62
120 121 1.078426 GCTGGCACATACCGAGGTT 60.078 57.895 0.00 0.00 38.20 3.50
121 122 1.961180 GAGCTGGCACATACCGAGGT 61.961 60.000 0.00 0.00 38.20 3.85
122 123 1.227380 GAGCTGGCACATACCGAGG 60.227 63.158 0.00 0.00 38.20 4.63
123 124 1.227380 GGAGCTGGCACATACCGAG 60.227 63.158 0.00 0.00 38.20 4.63
124 125 1.337384 ATGGAGCTGGCACATACCGA 61.337 55.000 0.00 0.00 38.20 4.69
125 126 0.392706 TATGGAGCTGGCACATACCG 59.607 55.000 0.00 0.00 38.20 4.02
126 127 2.498167 CTTATGGAGCTGGCACATACC 58.502 52.381 0.00 0.00 38.20 2.73
127 128 2.498167 CCTTATGGAGCTGGCACATAC 58.502 52.381 0.00 0.00 33.64 2.39
128 129 1.202806 GCCTTATGGAGCTGGCACATA 60.203 52.381 5.66 0.13 44.34 2.29
129 130 0.466922 GCCTTATGGAGCTGGCACAT 60.467 55.000 5.66 7.63 44.34 3.21
130 131 1.077501 GCCTTATGGAGCTGGCACA 60.078 57.895 5.66 0.00 44.34 4.57
131 132 3.833304 GCCTTATGGAGCTGGCAC 58.167 61.111 5.66 0.00 44.34 5.01
133 134 0.680921 TTGTGCCTTATGGAGCTGGC 60.681 55.000 3.59 3.59 45.10 4.85
134 135 1.386533 CTTGTGCCTTATGGAGCTGG 58.613 55.000 0.00 0.00 34.57 4.85
135 136 0.737219 GCTTGTGCCTTATGGAGCTG 59.263 55.000 0.00 0.00 34.57 4.24
136 137 0.622665 AGCTTGTGCCTTATGGAGCT 59.377 50.000 0.00 0.97 40.80 4.09
137 138 0.737219 CAGCTTGTGCCTTATGGAGC 59.263 55.000 0.00 0.00 40.80 4.70
148 149 2.693762 CCCCATGTCGCAGCTTGTG 61.694 63.158 0.00 0.00 0.00 3.33
149 150 2.360350 CCCCATGTCGCAGCTTGT 60.360 61.111 0.00 0.00 0.00 3.16
150 151 3.136123 CCCCCATGTCGCAGCTTG 61.136 66.667 0.00 0.00 0.00 4.01
164 165 2.576648 ACACTCTAGTCCAAAATCCCCC 59.423 50.000 0.00 0.00 0.00 5.40
165 166 4.141688 CCTACACTCTAGTCCAAAATCCCC 60.142 50.000 0.00 0.00 0.00 4.81
166 167 4.715297 TCCTACACTCTAGTCCAAAATCCC 59.285 45.833 0.00 0.00 0.00 3.85
167 168 5.934402 TCCTACACTCTAGTCCAAAATCC 57.066 43.478 0.00 0.00 0.00 3.01
168 169 7.824779 ACAAATCCTACACTCTAGTCCAAAATC 59.175 37.037 0.00 0.00 0.00 2.17
169 170 7.690256 ACAAATCCTACACTCTAGTCCAAAAT 58.310 34.615 0.00 0.00 0.00 1.82
170 171 7.074653 ACAAATCCTACACTCTAGTCCAAAA 57.925 36.000 0.00 0.00 0.00 2.44
171 172 6.681729 ACAAATCCTACACTCTAGTCCAAA 57.318 37.500 0.00 0.00 0.00 3.28
172 173 6.681729 AACAAATCCTACACTCTAGTCCAA 57.318 37.500 0.00 0.00 0.00 3.53
173 174 6.497259 AGAAACAAATCCTACACTCTAGTCCA 59.503 38.462 0.00 0.00 0.00 4.02
174 175 6.937392 AGAAACAAATCCTACACTCTAGTCC 58.063 40.000 0.00 0.00 0.00 3.85
175 176 7.036829 GGAGAAACAAATCCTACACTCTAGTC 58.963 42.308 0.00 0.00 32.51 2.59
176 177 6.070710 GGGAGAAACAAATCCTACACTCTAGT 60.071 42.308 0.00 0.00 35.80 2.57
177 178 6.342111 GGGAGAAACAAATCCTACACTCTAG 58.658 44.000 0.00 0.00 35.80 2.43
178 179 5.105473 CGGGAGAAACAAATCCTACACTCTA 60.105 44.000 0.00 0.00 35.80 2.43
179 180 4.322801 CGGGAGAAACAAATCCTACACTCT 60.323 45.833 0.00 0.00 35.80 3.24
180 181 3.933332 CGGGAGAAACAAATCCTACACTC 59.067 47.826 0.00 0.00 35.80 3.51
181 182 3.868754 GCGGGAGAAACAAATCCTACACT 60.869 47.826 0.00 0.00 35.80 3.55
182 183 2.418976 GCGGGAGAAACAAATCCTACAC 59.581 50.000 0.00 0.00 35.80 2.90
183 184 2.304761 AGCGGGAGAAACAAATCCTACA 59.695 45.455 0.00 0.00 35.80 2.74
184 185 2.678336 CAGCGGGAGAAACAAATCCTAC 59.322 50.000 0.00 0.00 35.80 3.18
185 186 2.939640 GCAGCGGGAGAAACAAATCCTA 60.940 50.000 0.00 0.00 35.80 2.94
186 187 1.826385 CAGCGGGAGAAACAAATCCT 58.174 50.000 0.00 0.00 35.80 3.24
187 188 0.171231 GCAGCGGGAGAAACAAATCC 59.829 55.000 0.00 0.00 34.64 3.01
188 189 0.881118 TGCAGCGGGAGAAACAAATC 59.119 50.000 0.00 0.00 0.00 2.17
189 190 1.000274 GTTGCAGCGGGAGAAACAAAT 60.000 47.619 0.00 0.00 0.00 2.32
190 191 0.383949 GTTGCAGCGGGAGAAACAAA 59.616 50.000 0.00 0.00 0.00 2.83
191 192 0.749818 TGTTGCAGCGGGAGAAACAA 60.750 50.000 0.00 0.00 0.00 2.83
192 193 1.153066 TGTTGCAGCGGGAGAAACA 60.153 52.632 0.00 0.00 0.00 2.83
193 194 1.282875 GTGTTGCAGCGGGAGAAAC 59.717 57.895 0.00 0.00 0.00 2.78
194 195 1.153066 TGTGTTGCAGCGGGAGAAA 60.153 52.632 0.00 0.00 0.00 2.52
195 196 1.891919 GTGTGTTGCAGCGGGAGAA 60.892 57.895 0.00 0.00 0.00 2.87
196 197 2.280797 GTGTGTTGCAGCGGGAGA 60.281 61.111 0.00 0.00 0.00 3.71
197 198 3.716006 CGTGTGTTGCAGCGGGAG 61.716 66.667 0.00 0.00 0.00 4.30
202 203 4.629115 GTGCCCGTGTGTTGCAGC 62.629 66.667 0.00 0.00 35.33 5.25
203 204 2.074230 AATGTGCCCGTGTGTTGCAG 62.074 55.000 0.00 0.00 35.33 4.41
204 205 1.670949 AAATGTGCCCGTGTGTTGCA 61.671 50.000 0.00 0.00 0.00 4.08
205 206 1.067250 AAATGTGCCCGTGTGTTGC 59.933 52.632 0.00 0.00 0.00 4.17
206 207 1.214373 GCAAATGTGCCCGTGTGTTG 61.214 55.000 0.00 0.00 45.68 3.33
207 208 1.067250 GCAAATGTGCCCGTGTGTT 59.933 52.632 0.00 0.00 45.68 3.32
208 209 2.727544 GCAAATGTGCCCGTGTGT 59.272 55.556 0.00 0.00 45.68 3.72
217 218 7.093354 TCTCTTAGTCTTCAGTAGCAAATGTG 58.907 38.462 0.00 0.00 0.00 3.21
218 219 7.233389 TCTCTTAGTCTTCAGTAGCAAATGT 57.767 36.000 0.00 0.00 0.00 2.71
219 220 9.809096 TTATCTCTTAGTCTTCAGTAGCAAATG 57.191 33.333 0.00 0.00 0.00 2.32
221 222 9.640963 GTTTATCTCTTAGTCTTCAGTAGCAAA 57.359 33.333 0.00 0.00 0.00 3.68
222 223 8.251721 GGTTTATCTCTTAGTCTTCAGTAGCAA 58.748 37.037 0.00 0.00 0.00 3.91
223 224 7.616150 AGGTTTATCTCTTAGTCTTCAGTAGCA 59.384 37.037 0.00 0.00 0.00 3.49
224 225 8.002984 AGGTTTATCTCTTAGTCTTCAGTAGC 57.997 38.462 0.00 0.00 0.00 3.58
227 228 9.536510 ACTTAGGTTTATCTCTTAGTCTTCAGT 57.463 33.333 0.00 0.00 0.00 3.41
228 229 9.796120 CACTTAGGTTTATCTCTTAGTCTTCAG 57.204 37.037 0.00 0.00 0.00 3.02
229 230 8.750298 CCACTTAGGTTTATCTCTTAGTCTTCA 58.250 37.037 0.00 0.00 0.00 3.02
247 248 2.579878 TGGAGAGCGACCACTTAGG 58.420 57.895 0.00 0.00 45.67 2.69
253 254 1.262417 TACATTGTGGAGAGCGACCA 58.738 50.000 0.00 0.00 34.84 4.02
254 255 2.380084 TTACATTGTGGAGAGCGACC 57.620 50.000 0.00 0.00 0.00 4.79
255 256 3.262420 ACATTACATTGTGGAGAGCGAC 58.738 45.455 0.00 0.00 0.00 5.19
256 257 3.610040 ACATTACATTGTGGAGAGCGA 57.390 42.857 0.00 0.00 0.00 4.93
257 258 3.246226 GCTACATTACATTGTGGAGAGCG 59.754 47.826 0.00 0.00 30.27 5.03
258 259 3.246226 CGCTACATTACATTGTGGAGAGC 59.754 47.826 0.00 1.62 31.21 4.09
259 260 3.246226 GCGCTACATTACATTGTGGAGAG 59.754 47.826 0.00 0.00 31.21 3.20
260 261 3.118775 AGCGCTACATTACATTGTGGAGA 60.119 43.478 8.99 0.00 31.21 3.71
261 262 3.198068 AGCGCTACATTACATTGTGGAG 58.802 45.455 8.99 0.00 32.44 3.86
262 263 3.260475 AGCGCTACATTACATTGTGGA 57.740 42.857 8.99 0.00 30.27 4.02
263 264 3.126858 ACAAGCGCTACATTACATTGTGG 59.873 43.478 12.05 0.00 0.00 4.17
264 265 4.340894 ACAAGCGCTACATTACATTGTG 57.659 40.909 12.05 2.50 0.00 3.33
265 266 5.371115 AAACAAGCGCTACATTACATTGT 57.629 34.783 12.05 4.80 0.00 2.71
266 267 7.789341 TTTAAACAAGCGCTACATTACATTG 57.211 32.000 12.05 4.01 0.00 2.82
267 268 7.540745 CCTTTTAAACAAGCGCTACATTACATT 59.459 33.333 12.05 0.29 0.00 2.71
268 269 7.027161 CCTTTTAAACAAGCGCTACATTACAT 58.973 34.615 12.05 0.00 0.00 2.29
269 270 6.375377 CCTTTTAAACAAGCGCTACATTACA 58.625 36.000 12.05 0.37 0.00 2.41
270 271 5.285370 GCCTTTTAAACAAGCGCTACATTAC 59.715 40.000 12.05 0.00 0.00 1.89
271 272 5.048643 TGCCTTTTAAACAAGCGCTACATTA 60.049 36.000 12.05 7.50 0.00 1.90
272 273 4.234574 GCCTTTTAAACAAGCGCTACATT 58.765 39.130 12.05 8.61 0.00 2.71
273 274 3.254657 TGCCTTTTAAACAAGCGCTACAT 59.745 39.130 12.05 0.00 0.00 2.29
274 275 2.619177 TGCCTTTTAAACAAGCGCTACA 59.381 40.909 12.05 0.00 0.00 2.74
275 276 3.234386 CTGCCTTTTAAACAAGCGCTAC 58.766 45.455 12.05 0.00 0.00 3.58
276 277 2.882137 ACTGCCTTTTAAACAAGCGCTA 59.118 40.909 12.05 0.00 0.00 4.26
277 278 1.681264 ACTGCCTTTTAAACAAGCGCT 59.319 42.857 2.64 2.64 0.00 5.92
278 279 2.134201 ACTGCCTTTTAAACAAGCGC 57.866 45.000 0.00 0.00 0.00 5.92
279 280 3.964909 AGAACTGCCTTTTAAACAAGCG 58.035 40.909 0.00 0.00 0.00 4.68
280 281 7.764695 TTTAAGAACTGCCTTTTAAACAAGC 57.235 32.000 0.00 0.00 0.00 4.01
306 307 4.488879 GTCGTACGAAGTCATACCCTTTT 58.511 43.478 21.39 0.00 43.93 2.27
310 311 2.096799 CGTCGTACGAAGTCATACCC 57.903 55.000 21.39 2.97 46.05 3.69
327 337 1.663388 TCGTTTGCGTGCATCTCGT 60.663 52.632 0.00 0.00 39.49 4.18
337 347 2.247267 GGTTCACGGTCGTTTGCG 59.753 61.111 0.00 0.00 39.92 4.85
356 366 2.088674 ATAGGCACCGTCGATCAGGC 62.089 60.000 0.00 0.86 0.00 4.85
361 371 4.765856 AGAAAGTATATAGGCACCGTCGAT 59.234 41.667 0.00 0.00 0.00 3.59
366 376 4.500603 ACGAGAAAGTATATAGGCACCG 57.499 45.455 0.00 0.00 0.00 4.94
379 389 2.028523 CGCTGCTTCACATACGAGAAAG 59.971 50.000 0.00 0.00 31.29 2.62
381 391 1.629013 CGCTGCTTCACATACGAGAA 58.371 50.000 0.00 0.00 31.29 2.87
392 405 2.224314 ACTTTTTACAGAGCGCTGCTTC 59.776 45.455 18.48 0.00 46.26 3.86
408 421 1.078426 CGATCGAGGGGGCACTTTT 60.078 57.895 10.26 0.00 0.00 2.27
437 450 3.775654 GCTAGGGCACGTGCTCCT 61.776 66.667 36.36 36.36 44.25 3.69
510 523 2.342648 GTGGCGGAGAAGGTCGTT 59.657 61.111 0.00 0.00 0.00 3.85
523 536 1.578206 GAGGAAGGAAAGCACGTGGC 61.578 60.000 18.88 9.78 45.30 5.01
725 749 0.386478 GAAGTCGTCGCCGTAGTTGT 60.386 55.000 0.00 0.00 35.01 3.32
978 1002 4.749310 AGACGAAGCAGCGCAGGG 62.749 66.667 11.47 0.00 33.86 4.45
1119 1143 0.106619 AACCGTCTAGCTCGAGGGAT 60.107 55.000 27.99 16.90 40.50 3.85
1201 1225 6.738200 CGACAACAATCAAGACATGTATTGAC 59.262 38.462 32.00 18.86 42.61 3.18
1287 1316 2.279517 CGCCTATCGTGAGCACCC 60.280 66.667 0.00 0.00 0.00 4.61
1347 1376 2.176798 AGGATGAACCCACAACTCCAAA 59.823 45.455 0.00 0.00 40.05 3.28
1390 1427 1.002468 CAAACCGAAGAAGCAGGTGTG 60.002 52.381 0.00 0.00 38.44 3.82
1391 1428 1.308998 CAAACCGAAGAAGCAGGTGT 58.691 50.000 0.00 0.00 38.44 4.16
1459 1497 2.835580 ATAGCAGCCTGTATGAGCAG 57.164 50.000 0.00 0.00 36.31 4.24
1462 1500 8.783833 ATAAATTGTATAGCAGCCTGTATGAG 57.216 34.615 0.00 0.00 0.00 2.90
2061 2105 5.491070 TGAAGGTACTCAAGATGTCCAATG 58.509 41.667 0.00 0.00 38.49 2.82
2152 2197 6.158598 CCGTTTCCAGAATTGATTTGTTGAT 58.841 36.000 0.00 0.00 0.00 2.57
2164 2209 3.222603 GGAATATGCCCGTTTCCAGAAT 58.777 45.455 0.00 0.00 39.00 2.40
2532 2676 3.491792 GGAACCGGCACATTTTTGAGAAA 60.492 43.478 0.00 0.00 0.00 2.52
2676 2828 3.476552 TGGTTTAAGCTCAGTTGGTCTG 58.523 45.455 0.00 0.00 44.85 3.51
2744 2897 4.884668 TGGTCACGGAGATAAAAACTCT 57.115 40.909 0.00 0.00 35.10 3.24
2770 2924 2.171840 CACCACAGGTCACTACTAGCT 58.828 52.381 0.00 0.00 31.02 3.32
2777 2931 1.134401 CACAACTCACCACAGGTCACT 60.134 52.381 0.00 0.00 31.02 3.41
2853 3007 9.744468 TTTTCTATTAGTTCAAAAGAAGTTGGC 57.256 29.630 0.00 0.00 0.00 4.52
2892 3047 5.996644 TCCTCACTCTGTTTTTAACCAAGA 58.003 37.500 0.00 0.00 0.00 3.02
3095 3254 4.065789 GACTGAAAATCCTCTTTCACCGT 58.934 43.478 0.00 0.00 39.74 4.83
3097 3256 7.391833 ACATAAGACTGAAAATCCTCTTTCACC 59.608 37.037 0.00 0.00 39.74 4.02
3099 3258 8.378565 AGACATAAGACTGAAAATCCTCTTTCA 58.621 33.333 0.00 0.00 41.80 2.69
3100 3259 8.663911 CAGACATAAGACTGAAAATCCTCTTTC 58.336 37.037 0.00 0.00 39.43 2.62
3107 3267 5.448360 GGCAGCAGACATAAGACTGAAAATC 60.448 44.000 1.63 0.00 39.43 2.17
3113 3273 2.277969 CTGGCAGCAGACATAAGACTG 58.722 52.381 0.00 0.00 39.94 3.51
3118 3278 0.393402 CTGGCTGGCAGCAGACATAA 60.393 55.000 37.49 14.41 44.75 1.90
3123 3283 2.033141 GTTCTGGCTGGCAGCAGA 59.967 61.111 37.49 31.34 44.75 4.26


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

AutoCloner maintained by Alex Coulton.