Multiple sequence alignment - TraesCS6D01G123800

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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 TraesCS6D01G123800 chr6D 100.000 2534 0 0 1 2534 88837368 88834835 0.000000e+00 4680
1 TraesCS6D01G123800 chr6D 80.430 1303 225 17 324 1618 88892013 88890733 0.000000e+00 966
2 TraesCS6D01G123800 chr6D 78.453 1267 230 26 321 1568 93524781 93526023 0.000000e+00 787
3 TraesCS6D01G123800 chr6A 91.994 2036 131 18 208 2218 106895511 106893483 0.000000e+00 2828
4 TraesCS6D01G123800 chr6A 80.784 1301 222 14 325 1618 106986213 106984934 0.000000e+00 992
5 TraesCS6D01G123800 chr6A 78.692 1300 223 38 330 1604 115281263 115279993 0.000000e+00 817
6 TraesCS6D01G123800 chr6B 92.992 1912 117 12 208 2110 169177123 169175220 0.000000e+00 2772
7 TraesCS6D01G123800 chr6B 80.186 1287 227 15 325 1604 169236505 169235240 0.000000e+00 939
8 TraesCS6D01G123800 chr6B 78.173 1292 238 27 333 1604 179469945 179468678 0.000000e+00 784
9 TraesCS6D01G123800 chr6B 84.161 322 23 13 2215 2534 169175178 169174883 1.150000e-73 287
10 TraesCS6D01G123800 chr3A 76.167 600 122 16 330 916 669765445 669766036 1.910000e-76 296
11 TraesCS6D01G123800 chr3B 75.466 644 125 25 296 916 705994057 705994690 1.480000e-72 283
12 TraesCS6D01G123800 chr4A 83.568 213 33 2 1 211 428260346 428260134 5.530000e-47 198
13 TraesCS6D01G123800 chr7D 83.663 202 28 5 11 210 528889855 528889657 4.300000e-43 185


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 TraesCS6D01G123800 chr6D 88834835 88837368 2533 True 4680.0 4680 100.0000 1 2534 1 chr6D.!!$R1 2533
1 TraesCS6D01G123800 chr6D 88890733 88892013 1280 True 966.0 966 80.4300 324 1618 1 chr6D.!!$R2 1294
2 TraesCS6D01G123800 chr6D 93524781 93526023 1242 False 787.0 787 78.4530 321 1568 1 chr6D.!!$F1 1247
3 TraesCS6D01G123800 chr6A 106893483 106895511 2028 True 2828.0 2828 91.9940 208 2218 1 chr6A.!!$R1 2010
4 TraesCS6D01G123800 chr6A 106984934 106986213 1279 True 992.0 992 80.7840 325 1618 1 chr6A.!!$R2 1293
5 TraesCS6D01G123800 chr6A 115279993 115281263 1270 True 817.0 817 78.6920 330 1604 1 chr6A.!!$R3 1274
6 TraesCS6D01G123800 chr6B 169174883 169177123 2240 True 1529.5 2772 88.5765 208 2534 2 chr6B.!!$R3 2326
7 TraesCS6D01G123800 chr6B 169235240 169236505 1265 True 939.0 939 80.1860 325 1604 1 chr6B.!!$R1 1279
8 TraesCS6D01G123800 chr6B 179468678 179469945 1267 True 784.0 784 78.1730 333 1604 1 chr6B.!!$R2 1271
9 TraesCS6D01G123800 chr3A 669765445 669766036 591 False 296.0 296 76.1670 330 916 1 chr3A.!!$F1 586
10 TraesCS6D01G123800 chr3B 705994057 705994690 633 False 283.0 283 75.4660 296 916 1 chr3B.!!$F1 620

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
36 37 0.030101 GCAGAGCGAGCTAGGTACAG 59.97 60.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1774 0.617935 TGGTCCTTCGGCATGATTGA 59.382 50.0 0.0 0.0 0.0 2.57 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
29 30 3.826754 CCACGGCAGAGCGAGCTA 61.827 66.667 0.00 0.00 0.00 3.32
30 31 2.278466 CACGGCAGAGCGAGCTAG 60.278 66.667 0.00 0.00 0.00 3.42
31 32 3.522731 ACGGCAGAGCGAGCTAGG 61.523 66.667 0.00 0.00 0.00 3.02
32 33 3.522731 CGGCAGAGCGAGCTAGGT 61.523 66.667 0.00 0.00 0.00 3.08
33 34 2.187493 CGGCAGAGCGAGCTAGGTA 61.187 63.158 0.00 0.00 0.00 3.08
34 35 1.360911 GGCAGAGCGAGCTAGGTAC 59.639 63.158 0.00 0.00 0.00 3.34
35 36 1.384989 GGCAGAGCGAGCTAGGTACA 61.385 60.000 0.00 0.00 0.00 2.90
36 37 0.030101 GCAGAGCGAGCTAGGTACAG 59.970 60.000 0.00 0.00 0.00 2.74
37 38 1.669604 CAGAGCGAGCTAGGTACAGA 58.330 55.000 0.00 0.00 0.00 3.41
38 39 1.332375 CAGAGCGAGCTAGGTACAGAC 59.668 57.143 0.00 0.00 0.00 3.51
39 40 0.305313 GAGCGAGCTAGGTACAGACG 59.695 60.000 0.00 0.00 0.00 4.18
40 41 1.298488 GCGAGCTAGGTACAGACGC 60.298 63.158 8.84 8.84 36.40 5.19
41 42 1.011019 CGAGCTAGGTACAGACGCG 60.011 63.158 3.53 3.53 0.00 6.01
42 43 1.298488 GAGCTAGGTACAGACGCGC 60.298 63.158 5.73 0.00 0.00 6.86
43 44 2.651232 GCTAGGTACAGACGCGCG 60.651 66.667 30.96 30.96 0.00 6.86
44 45 2.789917 CTAGGTACAGACGCGCGT 59.210 61.111 38.52 38.52 0.00 6.01
45 46 1.582937 CTAGGTACAGACGCGCGTG 60.583 63.158 42.90 29.09 0.00 5.34
46 47 2.914797 CTAGGTACAGACGCGCGTGG 62.915 65.000 42.90 32.17 0.00 4.94
47 48 4.712425 GGTACAGACGCGCGTGGT 62.712 66.667 42.90 35.66 0.00 4.16
48 49 2.732094 GTACAGACGCGCGTGGTT 60.732 61.111 42.90 24.83 0.00 3.67
49 50 1.442520 GTACAGACGCGCGTGGTTA 60.443 57.895 42.90 23.70 0.00 2.85
50 51 1.003262 GTACAGACGCGCGTGGTTAA 61.003 55.000 42.90 20.25 0.00 2.01
51 52 0.109179 TACAGACGCGCGTGGTTAAT 60.109 50.000 42.90 20.70 0.00 1.40
52 53 0.947180 ACAGACGCGCGTGGTTAATT 60.947 50.000 42.90 13.73 0.00 1.40
53 54 0.165079 CAGACGCGCGTGGTTAATTT 59.835 50.000 42.90 12.81 0.00 1.82
54 55 0.869730 AGACGCGCGTGGTTAATTTT 59.130 45.000 42.90 11.87 0.00 1.82
55 56 0.972013 GACGCGCGTGGTTAATTTTG 59.028 50.000 42.90 3.97 0.00 2.44
56 57 0.386226 ACGCGCGTGGTTAATTTTGG 60.386 50.000 37.37 0.15 0.00 3.28
57 58 0.110147 CGCGCGTGGTTAATTTTGGA 60.110 50.000 24.19 0.00 0.00 3.53
58 59 1.333115 GCGCGTGGTTAATTTTGGAC 58.667 50.000 8.43 0.00 0.00 4.02
59 60 1.597798 CGCGTGGTTAATTTTGGACG 58.402 50.000 0.00 0.00 0.00 4.79
60 61 1.069771 CGCGTGGTTAATTTTGGACGT 60.070 47.619 0.00 0.00 0.00 4.34
61 62 2.577450 GCGTGGTTAATTTTGGACGTC 58.423 47.619 7.13 7.13 0.00 4.34
62 63 2.031857 GCGTGGTTAATTTTGGACGTCA 60.032 45.455 18.91 0.27 0.00 4.35
63 64 3.805823 CGTGGTTAATTTTGGACGTCAG 58.194 45.455 18.91 0.00 0.00 3.51
64 65 3.249080 CGTGGTTAATTTTGGACGTCAGT 59.751 43.478 18.91 0.00 0.00 3.41
65 66 4.260866 CGTGGTTAATTTTGGACGTCAGTT 60.261 41.667 18.91 2.64 0.00 3.16
66 67 4.973663 GTGGTTAATTTTGGACGTCAGTTG 59.026 41.667 18.91 0.00 0.00 3.16
67 68 4.036971 TGGTTAATTTTGGACGTCAGTTGG 59.963 41.667 18.91 0.00 0.00 3.77
68 69 4.276431 GGTTAATTTTGGACGTCAGTTGGA 59.724 41.667 18.91 0.00 0.00 3.53
69 70 5.449304 GTTAATTTTGGACGTCAGTTGGAG 58.551 41.667 18.91 0.00 0.00 3.86
70 71 2.702592 TTTTGGACGTCAGTTGGAGT 57.297 45.000 18.91 0.00 0.00 3.85
71 72 2.702592 TTTGGACGTCAGTTGGAGTT 57.297 45.000 18.91 0.00 0.00 3.01
72 73 1.948104 TTGGACGTCAGTTGGAGTTG 58.052 50.000 18.91 0.00 0.00 3.16
73 74 0.531974 TGGACGTCAGTTGGAGTTGC 60.532 55.000 18.91 0.00 0.00 4.17
74 75 0.249911 GGACGTCAGTTGGAGTTGCT 60.250 55.000 18.91 0.00 0.00 3.91
75 76 1.000506 GGACGTCAGTTGGAGTTGCTA 59.999 52.381 18.91 0.00 0.00 3.49
76 77 2.059541 GACGTCAGTTGGAGTTGCTAC 58.940 52.381 11.55 0.00 0.00 3.58
77 78 1.687123 ACGTCAGTTGGAGTTGCTACT 59.313 47.619 0.00 0.00 37.31 2.57
78 79 2.061773 CGTCAGTTGGAGTTGCTACTG 58.938 52.381 5.27 8.46 39.41 2.74
79 80 2.545952 CGTCAGTTGGAGTTGCTACTGT 60.546 50.000 5.27 0.00 39.16 3.55
80 81 3.467803 GTCAGTTGGAGTTGCTACTGTT 58.532 45.455 5.27 0.00 39.16 3.16
81 82 3.248602 GTCAGTTGGAGTTGCTACTGTTG 59.751 47.826 5.27 0.00 39.16 3.33
82 83 2.031682 CAGTTGGAGTTGCTACTGTTGC 60.032 50.000 5.27 7.29 33.84 4.17
83 84 2.158755 AGTTGGAGTTGCTACTGTTGCT 60.159 45.455 14.81 0.00 33.84 3.91
84 85 3.071023 AGTTGGAGTTGCTACTGTTGCTA 59.929 43.478 14.81 5.09 33.84 3.49
85 86 3.319137 TGGAGTTGCTACTGTTGCTAG 57.681 47.619 14.81 0.00 33.84 3.42
86 87 2.003301 GGAGTTGCTACTGTTGCTAGC 58.997 52.381 8.10 8.10 37.68 3.42
87 88 2.354203 GGAGTTGCTACTGTTGCTAGCT 60.354 50.000 17.23 9.78 37.98 3.32
88 89 2.670414 GAGTTGCTACTGTTGCTAGCTG 59.330 50.000 17.23 6.20 37.98 4.24
89 90 1.734465 GTTGCTACTGTTGCTAGCTGG 59.266 52.381 17.23 0.00 37.98 4.85
90 91 1.266178 TGCTACTGTTGCTAGCTGGA 58.734 50.000 17.23 0.00 37.98 3.86
91 92 1.066858 TGCTACTGTTGCTAGCTGGAC 60.067 52.381 17.23 12.23 37.98 4.02
92 93 1.066858 GCTACTGTTGCTAGCTGGACA 60.067 52.381 17.23 15.91 34.82 4.02
93 94 2.886081 CTACTGTTGCTAGCTGGACAG 58.114 52.381 28.69 28.69 43.81 3.51
94 95 1.051812 ACTGTTGCTAGCTGGACAGT 58.948 50.000 29.59 29.59 45.62 3.55
96 97 3.533606 CTGTTGCTAGCTGGACAGTAT 57.466 47.619 25.24 0.00 35.84 2.12
97 98 4.655762 CTGTTGCTAGCTGGACAGTATA 57.344 45.455 25.24 0.31 35.84 1.47
98 99 5.207110 CTGTTGCTAGCTGGACAGTATAT 57.793 43.478 25.24 0.00 35.84 0.86
99 100 5.605534 CTGTTGCTAGCTGGACAGTATATT 58.394 41.667 25.24 0.00 35.84 1.28
100 101 5.989477 TGTTGCTAGCTGGACAGTATATTT 58.011 37.500 17.23 0.00 0.00 1.40
101 102 6.414732 TGTTGCTAGCTGGACAGTATATTTT 58.585 36.000 17.23 0.00 0.00 1.82
102 103 6.884295 TGTTGCTAGCTGGACAGTATATTTTT 59.116 34.615 17.23 0.00 0.00 1.94
103 104 8.044309 TGTTGCTAGCTGGACAGTATATTTTTA 58.956 33.333 17.23 0.00 0.00 1.52
104 105 8.889717 GTTGCTAGCTGGACAGTATATTTTTAA 58.110 33.333 17.23 0.00 0.00 1.52
105 106 9.627123 TTGCTAGCTGGACAGTATATTTTTAAT 57.373 29.630 17.23 0.00 0.00 1.40
127 128 1.671328 TCTGCTGAAGATACTCGGTCG 59.329 52.381 0.00 0.00 0.00 4.79
128 129 1.402259 CTGCTGAAGATACTCGGTCGT 59.598 52.381 0.00 0.00 0.00 4.34
129 130 1.816835 TGCTGAAGATACTCGGTCGTT 59.183 47.619 0.00 0.00 0.00 3.85
130 131 2.186076 GCTGAAGATACTCGGTCGTTG 58.814 52.381 0.00 0.00 0.00 4.10
131 132 2.798680 CTGAAGATACTCGGTCGTTGG 58.201 52.381 0.00 0.00 0.00 3.77
132 133 1.475280 TGAAGATACTCGGTCGTTGGG 59.525 52.381 0.00 0.00 0.00 4.12
133 134 0.175073 AAGATACTCGGTCGTTGGGC 59.825 55.000 0.00 0.00 0.00 5.36
134 135 1.588139 GATACTCGGTCGTTGGGCG 60.588 63.158 0.00 0.00 43.01 6.13
135 136 2.948840 GATACTCGGTCGTTGGGCGG 62.949 65.000 0.00 0.00 41.72 6.13
140 141 4.171103 GGTCGTTGGGCGGGCTAT 62.171 66.667 0.26 0.00 41.72 2.97
141 142 2.799452 GGTCGTTGGGCGGGCTATA 61.799 63.158 0.26 0.00 41.72 1.31
142 143 1.144496 GTCGTTGGGCGGGCTATAA 59.856 57.895 0.26 0.00 41.72 0.98
143 144 1.144496 TCGTTGGGCGGGCTATAAC 59.856 57.895 0.26 4.43 41.72 1.89
144 145 2.241880 CGTTGGGCGGGCTATAACG 61.242 63.158 18.21 18.21 38.21 3.18
154 155 4.385244 CGGGCTATAACGCTATTTTGAC 57.615 45.455 0.00 0.00 0.00 3.18
155 156 3.121126 CGGGCTATAACGCTATTTTGACG 60.121 47.826 0.00 0.00 0.00 4.35
156 157 3.363673 GGGCTATAACGCTATTTTGACGC 60.364 47.826 0.00 0.00 0.00 5.19
157 158 3.493503 GGCTATAACGCTATTTTGACGCT 59.506 43.478 0.00 0.00 0.00 5.07
158 159 4.446234 GCTATAACGCTATTTTGACGCTG 58.554 43.478 0.00 0.00 0.00 5.18
159 160 4.025979 GCTATAACGCTATTTTGACGCTGT 60.026 41.667 0.00 0.00 0.00 4.40
160 161 5.174398 GCTATAACGCTATTTTGACGCTGTA 59.826 40.000 0.00 0.00 0.00 2.74
161 162 6.291955 GCTATAACGCTATTTTGACGCTGTAA 60.292 38.462 0.00 0.00 0.00 2.41
162 163 4.735662 AACGCTATTTTGACGCTGTAAA 57.264 36.364 0.00 0.00 0.00 2.01
163 164 4.735662 ACGCTATTTTGACGCTGTAAAA 57.264 36.364 0.00 0.00 0.00 1.52
164 165 4.708601 ACGCTATTTTGACGCTGTAAAAG 58.291 39.130 0.00 0.00 0.00 2.27
165 166 4.449743 ACGCTATTTTGACGCTGTAAAAGA 59.550 37.500 0.00 0.00 0.00 2.52
166 167 5.049954 ACGCTATTTTGACGCTGTAAAAGAA 60.050 36.000 0.00 0.00 0.00 2.52
167 168 5.849081 CGCTATTTTGACGCTGTAAAAGAAA 59.151 36.000 0.00 0.00 0.00 2.52
168 169 6.183359 CGCTATTTTGACGCTGTAAAAGAAAC 60.183 38.462 0.00 0.00 0.00 2.78
169 170 6.856426 GCTATTTTGACGCTGTAAAAGAAACT 59.144 34.615 0.00 0.00 0.00 2.66
170 171 7.378728 GCTATTTTGACGCTGTAAAAGAAACTT 59.621 33.333 0.00 0.00 0.00 2.66
171 172 9.872757 CTATTTTGACGCTGTAAAAGAAACTTA 57.127 29.630 0.00 0.00 0.00 2.24
172 173 8.782533 ATTTTGACGCTGTAAAAGAAACTTAG 57.217 30.769 0.00 0.00 0.00 2.18
173 174 5.338614 TGACGCTGTAAAAGAAACTTAGC 57.661 39.130 0.00 0.00 0.00 3.09
175 176 3.153735 CGCTGTAAAAGAAACTTAGCGC 58.846 45.455 0.00 0.00 44.46 5.92
176 177 3.153735 GCTGTAAAAGAAACTTAGCGCG 58.846 45.455 0.00 0.00 0.00 6.86
177 178 3.153735 CTGTAAAAGAAACTTAGCGCGC 58.846 45.455 26.66 26.66 0.00 6.86
178 179 2.155802 GTAAAAGAAACTTAGCGCGCG 58.844 47.619 28.44 28.44 0.00 6.86
179 180 0.724785 AAAAGAAACTTAGCGCGCGC 60.725 50.000 45.10 45.10 42.33 6.86
199 200 2.967397 CGTAGGGCGTCTGTTGGA 59.033 61.111 0.00 0.00 35.54 3.53
200 201 1.153823 CGTAGGGCGTCTGTTGGAG 60.154 63.158 0.00 0.00 35.54 3.86
201 202 1.592400 CGTAGGGCGTCTGTTGGAGA 61.592 60.000 0.00 0.00 35.54 3.71
202 203 0.824759 GTAGGGCGTCTGTTGGAGAT 59.175 55.000 0.00 0.00 31.63 2.75
203 204 0.824109 TAGGGCGTCTGTTGGAGATG 59.176 55.000 0.00 0.00 40.33 2.90
268 269 4.070552 GCACTCTCCTTCCGCGGT 62.071 66.667 27.15 0.00 0.00 5.68
306 307 0.034089 GTGTAAAGCCATGGCCTCCT 60.034 55.000 33.14 16.93 43.17 3.69
455 463 2.207924 ACCTTCCTCAACGCCGTCT 61.208 57.895 0.00 0.00 0.00 4.18
585 593 4.436998 CCGCTCCGACCCTGACAC 62.437 72.222 0.00 0.00 0.00 3.67
628 636 2.030274 CGATTTCTTTTTCACCCGCCTT 60.030 45.455 0.00 0.00 0.00 4.35
699 722 1.518133 GCTACGTGCTCCTCTGCAG 60.518 63.158 7.63 7.63 44.20 4.41
912 950 4.717629 TGCCGCCGTCTTCTCGTG 62.718 66.667 0.00 0.00 0.00 4.35
924 962 2.681778 CTCGTGGGAGAGCAGGGT 60.682 66.667 0.00 0.00 43.27 4.34
927 965 2.883828 CGTGGGAGAGCAGGGTGTT 61.884 63.158 0.00 0.00 0.00 3.32
976 1014 1.301716 GCCACTGCCTGAAGACGAA 60.302 57.895 0.00 0.00 0.00 3.85
977 1015 1.569479 GCCACTGCCTGAAGACGAAC 61.569 60.000 0.00 0.00 0.00 3.95
1183 1221 1.110442 TTGCCCAGTTGACTTTGGTG 58.890 50.000 0.00 0.00 32.40 4.17
1201 1239 2.582052 GTGTCCATGTTTGGTTCTGGA 58.418 47.619 0.00 0.00 44.06 3.86
1314 1355 6.145858 CACTAGAAGATGTTGAGCTGCATATC 59.854 42.308 1.02 0.00 0.00 1.63
1344 1385 3.811083 TGTCGATGGGTTTGTGTACTTT 58.189 40.909 0.00 0.00 0.00 2.66
1681 1722 6.166982 GGACACTGGGCTATCTACATTTATC 58.833 44.000 0.00 0.00 0.00 1.75
1691 1732 6.089150 GCTATCTACATTTATCGGTTTCGTCC 59.911 42.308 0.00 0.00 37.69 4.79
1715 1756 6.636850 CCAATACTTGCTTGTGTTTTACTGAC 59.363 38.462 0.00 0.00 0.00 3.51
1802 1846 0.457035 GCATGTGTGGCAATACCCTG 59.543 55.000 0.00 0.00 37.83 4.45
1988 2032 5.653330 GTCTCAACTCCCTAGCTAAGTACTT 59.347 44.000 13.68 13.68 0.00 2.24
2007 2051 8.546597 AGTACTTGATTGTTTGTTTTGCTTTT 57.453 26.923 0.00 0.00 0.00 2.27
2064 2108 5.072329 CCCCATCTATCTACTTGGAACACAT 59.928 44.000 0.00 0.00 39.29 3.21
2093 2137 7.432350 TTGCATTTTAACCATTTTTAGGCAG 57.568 32.000 0.00 0.00 0.00 4.85
2116 2160 7.649306 GCAGGCTTCGATAATATTCAAAATGTT 59.351 33.333 0.00 0.00 0.00 2.71
2117 2161 9.520204 CAGGCTTCGATAATATTCAAAATGTTT 57.480 29.630 0.00 0.00 0.00 2.83
2162 2222 8.154649 AGTATATTAGTGCAAAGGATTTTCCG 57.845 34.615 0.00 0.00 42.75 4.30
2167 2227 4.119136 AGTGCAAAGGATTTTCCGTTTTG 58.881 39.130 0.00 4.67 42.75 2.44
2176 2236 8.549338 AAGGATTTTCCGTTTTGTTTGTTTTA 57.451 26.923 0.00 0.00 42.75 1.52
2202 2262 4.175962 ACTGATAAGTCTTTTCAGGGGGA 58.824 43.478 26.81 0.06 40.92 4.81
2273 2333 6.239317 GGTCTTTCTTTTACAAAGCTGGGATT 60.239 38.462 0.00 0.00 31.85 3.01
2283 2343 5.368989 ACAAAGCTGGGATTAGTATACTGC 58.631 41.667 15.90 8.20 0.00 4.40
2323 2383 4.968812 TGCAACTACAACATCATGGATG 57.031 40.909 4.74 4.74 44.71 3.51
2337 2397 2.899303 TGGATGAAAAGGGAAGGTCC 57.101 50.000 0.00 0.00 35.23 4.46
2338 2398 2.358258 TGGATGAAAAGGGAAGGTCCT 58.642 47.619 0.00 0.00 36.57 3.85
2341 2401 3.371702 GGATGAAAAGGGAAGGTCCTACC 60.372 52.174 4.66 4.66 36.57 3.18
2388 2448 9.929180 TTGTTTATATCTGATATACCAGCTGAC 57.071 33.333 17.39 0.00 34.28 3.51
2389 2449 9.088987 TGTTTATATCTGATATACCAGCTGACA 57.911 33.333 17.39 1.88 34.28 3.58
2392 2452 7.968014 ATATCTGATATACCAGCTGACATCA 57.032 36.000 17.39 15.52 34.28 3.07
2393 2453 6.676990 ATCTGATATACCAGCTGACATCAA 57.323 37.500 17.39 8.95 34.28 2.57
2394 2454 5.847304 TCTGATATACCAGCTGACATCAAC 58.153 41.667 17.39 1.63 34.28 3.18
2395 2455 5.363580 TCTGATATACCAGCTGACATCAACA 59.636 40.000 17.39 6.27 34.28 3.33
2396 2456 5.359756 TGATATACCAGCTGACATCAACAC 58.640 41.667 17.39 0.00 0.00 3.32
2397 2457 3.988976 ATACCAGCTGACATCAACACT 57.011 42.857 17.39 0.00 0.00 3.55
2398 2458 1.888215 ACCAGCTGACATCAACACTG 58.112 50.000 17.39 0.00 0.00 3.66
2399 2459 1.417517 ACCAGCTGACATCAACACTGA 59.582 47.619 17.39 0.00 35.56 3.41
2400 2460 2.039480 ACCAGCTGACATCAACACTGAT 59.961 45.455 17.39 0.00 43.40 2.90
2401 2461 3.079578 CCAGCTGACATCAACACTGATT 58.920 45.455 17.39 0.00 40.49 2.57
2402 2462 4.256110 CCAGCTGACATCAACACTGATTA 58.744 43.478 17.39 0.00 40.49 1.75
2403 2463 4.093998 CCAGCTGACATCAACACTGATTAC 59.906 45.833 17.39 0.00 40.49 1.89
2404 2464 4.934001 CAGCTGACATCAACACTGATTACT 59.066 41.667 8.42 0.00 40.49 2.24
2411 2471 2.029739 TCAACACTGATTACTTCCGCGA 60.030 45.455 8.23 0.00 0.00 5.87
2413 2473 1.271379 ACACTGATTACTTCCGCGACA 59.729 47.619 8.23 0.00 0.00 4.35
2420 2480 4.989797 TGATTACTTCCGCGACACTTTTAA 59.010 37.500 8.23 0.00 0.00 1.52
2426 2486 5.467735 ACTTCCGCGACACTTTTAATTAACT 59.532 36.000 8.23 0.00 0.00 2.24
2427 2487 6.646240 ACTTCCGCGACACTTTTAATTAACTA 59.354 34.615 8.23 0.00 0.00 2.24
2460 2521 8.154649 TCTCTTTGAAACTGGTGAATAAACTC 57.845 34.615 0.00 0.00 0.00 3.01
2518 2579 6.492087 CCCTCCAATTCCTGTTTTACACTTTA 59.508 38.462 0.00 0.00 0.00 1.85
2520 2581 7.865889 CCTCCAATTCCTGTTTTACACTTTAAC 59.134 37.037 0.00 0.00 0.00 2.01
2531 2592 5.726980 TTACACTTTAACGCTAGGAGGAA 57.273 39.130 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.764810 CTAGCTCGCTCTGCCGTGG 62.765 68.421 0.00 0.00 0.00 4.94
13 14 2.278466 CTAGCTCGCTCTGCCGTG 60.278 66.667 0.00 0.00 0.00 4.94
14 15 2.888464 TACCTAGCTCGCTCTGCCGT 62.888 60.000 0.00 0.00 0.00 5.68
15 16 2.187493 TACCTAGCTCGCTCTGCCG 61.187 63.158 0.00 0.00 0.00 5.69
16 17 1.360911 GTACCTAGCTCGCTCTGCC 59.639 63.158 0.00 0.00 0.00 4.85
17 18 0.030101 CTGTACCTAGCTCGCTCTGC 59.970 60.000 0.00 0.00 0.00 4.26
18 19 1.332375 GTCTGTACCTAGCTCGCTCTG 59.668 57.143 0.00 0.00 0.00 3.35
19 20 1.670791 GTCTGTACCTAGCTCGCTCT 58.329 55.000 0.00 0.00 0.00 4.09
20 21 0.305313 CGTCTGTACCTAGCTCGCTC 59.695 60.000 0.00 0.00 0.00 5.03
21 22 1.716826 GCGTCTGTACCTAGCTCGCT 61.717 60.000 0.00 0.00 37.57 4.93
22 23 1.298488 GCGTCTGTACCTAGCTCGC 60.298 63.158 0.00 0.00 35.26 5.03
23 24 1.011019 CGCGTCTGTACCTAGCTCG 60.011 63.158 0.00 0.00 0.00 5.03
24 25 1.298488 GCGCGTCTGTACCTAGCTC 60.298 63.158 8.43 0.00 0.00 4.09
25 26 2.799371 GCGCGTCTGTACCTAGCT 59.201 61.111 8.43 0.00 0.00 3.32
26 27 2.651232 CGCGCGTCTGTACCTAGC 60.651 66.667 24.19 0.00 0.00 3.42
27 28 1.582937 CACGCGCGTCTGTACCTAG 60.583 63.158 35.61 15.06 0.00 3.02
28 29 2.481919 CACGCGCGTCTGTACCTA 59.518 61.111 35.61 0.00 0.00 3.08
29 30 4.415332 CCACGCGCGTCTGTACCT 62.415 66.667 35.61 5.82 0.00 3.08
30 31 2.801113 TAACCACGCGCGTCTGTACC 62.801 60.000 35.61 0.00 0.00 3.34
31 32 1.003262 TTAACCACGCGCGTCTGTAC 61.003 55.000 35.61 0.00 0.00 2.90
32 33 0.109179 ATTAACCACGCGCGTCTGTA 60.109 50.000 35.61 21.21 0.00 2.74
33 34 0.947180 AATTAACCACGCGCGTCTGT 60.947 50.000 35.61 28.98 0.00 3.41
34 35 0.165079 AAATTAACCACGCGCGTCTG 59.835 50.000 35.61 28.27 0.00 3.51
35 36 0.869730 AAAATTAACCACGCGCGTCT 59.130 45.000 35.61 22.36 0.00 4.18
36 37 0.972013 CAAAATTAACCACGCGCGTC 59.028 50.000 35.61 0.00 0.00 5.19
37 38 0.386226 CCAAAATTAACCACGCGCGT 60.386 50.000 32.73 32.73 0.00 6.01
38 39 0.110147 TCCAAAATTAACCACGCGCG 60.110 50.000 30.96 30.96 0.00 6.86
39 40 1.333115 GTCCAAAATTAACCACGCGC 58.667 50.000 5.73 0.00 0.00 6.86
40 41 1.069771 ACGTCCAAAATTAACCACGCG 60.070 47.619 3.53 3.53 0.00 6.01
41 42 2.031857 TGACGTCCAAAATTAACCACGC 60.032 45.455 14.12 0.00 0.00 5.34
42 43 3.249080 ACTGACGTCCAAAATTAACCACG 59.751 43.478 14.12 0.00 0.00 4.94
43 44 4.823790 ACTGACGTCCAAAATTAACCAC 57.176 40.909 14.12 0.00 0.00 4.16
44 45 4.036971 CCAACTGACGTCCAAAATTAACCA 59.963 41.667 14.12 0.00 0.00 3.67
45 46 4.276431 TCCAACTGACGTCCAAAATTAACC 59.724 41.667 14.12 0.00 0.00 2.85
46 47 5.008316 ACTCCAACTGACGTCCAAAATTAAC 59.992 40.000 14.12 0.00 0.00 2.01
47 48 5.127491 ACTCCAACTGACGTCCAAAATTAA 58.873 37.500 14.12 0.00 0.00 1.40
48 49 4.710324 ACTCCAACTGACGTCCAAAATTA 58.290 39.130 14.12 0.00 0.00 1.40
49 50 3.551846 ACTCCAACTGACGTCCAAAATT 58.448 40.909 14.12 0.00 0.00 1.82
50 51 3.208747 ACTCCAACTGACGTCCAAAAT 57.791 42.857 14.12 0.00 0.00 1.82
51 52 2.680841 CAACTCCAACTGACGTCCAAAA 59.319 45.455 14.12 0.00 0.00 2.44
52 53 2.285083 CAACTCCAACTGACGTCCAAA 58.715 47.619 14.12 0.00 0.00 3.28
53 54 1.948104 CAACTCCAACTGACGTCCAA 58.052 50.000 14.12 0.00 0.00 3.53
54 55 0.531974 GCAACTCCAACTGACGTCCA 60.532 55.000 14.12 0.01 0.00 4.02
55 56 0.249911 AGCAACTCCAACTGACGTCC 60.250 55.000 14.12 0.00 0.00 4.79
56 57 2.059541 GTAGCAACTCCAACTGACGTC 58.940 52.381 9.11 9.11 0.00 4.34
57 58 1.687123 AGTAGCAACTCCAACTGACGT 59.313 47.619 0.00 0.00 0.00 4.34
58 59 2.061773 CAGTAGCAACTCCAACTGACG 58.938 52.381 0.00 0.00 41.47 4.35
59 60 3.113260 ACAGTAGCAACTCCAACTGAC 57.887 47.619 8.21 0.00 41.47 3.51
60 61 3.466836 CAACAGTAGCAACTCCAACTGA 58.533 45.455 8.21 0.00 41.47 3.41
61 62 2.031682 GCAACAGTAGCAACTCCAACTG 60.032 50.000 0.00 0.00 43.90 3.16
62 63 2.158755 AGCAACAGTAGCAACTCCAACT 60.159 45.455 0.00 0.00 31.97 3.16
63 64 2.222027 AGCAACAGTAGCAACTCCAAC 58.778 47.619 0.00 0.00 31.97 3.77
64 65 2.638480 AGCAACAGTAGCAACTCCAA 57.362 45.000 0.00 0.00 31.97 3.53
65 66 2.612972 GCTAGCAACAGTAGCAACTCCA 60.613 50.000 10.63 0.00 42.21 3.86
66 67 2.003301 GCTAGCAACAGTAGCAACTCC 58.997 52.381 10.63 0.00 42.21 3.85
67 68 2.670414 CAGCTAGCAACAGTAGCAACTC 59.330 50.000 18.83 0.00 44.62 3.01
68 69 2.613977 CCAGCTAGCAACAGTAGCAACT 60.614 50.000 18.83 0.00 44.62 3.16
69 70 1.734465 CCAGCTAGCAACAGTAGCAAC 59.266 52.381 18.83 0.00 44.62 4.17
70 71 1.623311 TCCAGCTAGCAACAGTAGCAA 59.377 47.619 18.83 0.00 44.62 3.91
71 72 1.066858 GTCCAGCTAGCAACAGTAGCA 60.067 52.381 18.83 0.00 44.62 3.49
72 73 1.066858 TGTCCAGCTAGCAACAGTAGC 60.067 52.381 18.83 0.00 42.85 3.58
73 74 2.886081 CTGTCCAGCTAGCAACAGTAG 58.114 52.381 25.17 11.62 35.51 2.57
75 76 1.051812 ACTGTCCAGCTAGCAACAGT 58.948 50.000 29.71 29.71 45.55 3.55
76 77 3.533606 ATACTGTCCAGCTAGCAACAG 57.466 47.619 28.78 28.78 43.69 3.16
77 78 5.614324 AATATACTGTCCAGCTAGCAACA 57.386 39.130 18.83 16.16 0.00 3.33
78 79 6.927294 AAAATATACTGTCCAGCTAGCAAC 57.073 37.500 18.83 12.33 0.00 4.17
79 80 9.627123 ATTAAAAATATACTGTCCAGCTAGCAA 57.373 29.630 18.83 0.00 0.00 3.91
98 99 9.261180 CCGAGTATCTTCAGCAGATATTAAAAA 57.739 33.333 0.00 0.00 44.80 1.94
99 100 8.421784 ACCGAGTATCTTCAGCAGATATTAAAA 58.578 33.333 0.00 0.00 44.80 1.52
100 101 7.952671 ACCGAGTATCTTCAGCAGATATTAAA 58.047 34.615 0.00 0.00 44.80 1.52
101 102 7.526142 ACCGAGTATCTTCAGCAGATATTAA 57.474 36.000 0.00 0.00 44.80 1.40
102 103 6.128254 CGACCGAGTATCTTCAGCAGATATTA 60.128 42.308 0.00 0.00 44.80 0.98
103 104 5.335269 CGACCGAGTATCTTCAGCAGATATT 60.335 44.000 0.00 0.00 44.80 1.28
104 105 4.155099 CGACCGAGTATCTTCAGCAGATAT 59.845 45.833 0.00 0.00 44.80 1.63
105 106 3.498777 CGACCGAGTATCTTCAGCAGATA 59.501 47.826 0.00 0.00 40.85 1.98
106 107 2.292016 CGACCGAGTATCTTCAGCAGAT 59.708 50.000 0.00 0.00 45.08 2.90
107 108 1.671328 CGACCGAGTATCTTCAGCAGA 59.329 52.381 0.00 0.00 35.33 4.26
108 109 1.402259 ACGACCGAGTATCTTCAGCAG 59.598 52.381 0.00 0.00 0.00 4.24
109 110 1.460504 ACGACCGAGTATCTTCAGCA 58.539 50.000 0.00 0.00 0.00 4.41
110 111 2.186076 CAACGACCGAGTATCTTCAGC 58.814 52.381 0.00 0.00 0.00 4.26
111 112 2.479730 CCCAACGACCGAGTATCTTCAG 60.480 54.545 0.00 0.00 0.00 3.02
112 113 1.475280 CCCAACGACCGAGTATCTTCA 59.525 52.381 0.00 0.00 0.00 3.02
113 114 1.801765 GCCCAACGACCGAGTATCTTC 60.802 57.143 0.00 0.00 0.00 2.87
114 115 0.175073 GCCCAACGACCGAGTATCTT 59.825 55.000 0.00 0.00 0.00 2.40
115 116 1.814527 GCCCAACGACCGAGTATCT 59.185 57.895 0.00 0.00 0.00 1.98
116 117 4.414732 GCCCAACGACCGAGTATC 57.585 61.111 0.00 0.00 0.00 2.24
126 127 2.241880 CGTTATAGCCCGCCCAACG 61.242 63.158 4.40 4.40 43.15 4.10
127 128 2.540228 GCGTTATAGCCCGCCCAAC 61.540 63.158 0.00 0.00 43.96 3.77
128 129 2.203098 GCGTTATAGCCCGCCCAA 60.203 61.111 0.00 0.00 43.96 4.12
133 134 3.121126 CGTCAAAATAGCGTTATAGCCCG 60.121 47.826 0.00 0.00 38.01 6.13
134 135 3.363673 GCGTCAAAATAGCGTTATAGCCC 60.364 47.826 0.00 0.00 38.01 5.19
135 136 3.493503 AGCGTCAAAATAGCGTTATAGCC 59.506 43.478 0.00 0.00 38.01 3.93
136 137 4.025979 ACAGCGTCAAAATAGCGTTATAGC 60.026 41.667 0.00 0.00 35.78 2.97
137 138 5.637104 ACAGCGTCAAAATAGCGTTATAG 57.363 39.130 0.00 0.00 35.78 1.31
138 139 7.522901 TTTACAGCGTCAAAATAGCGTTATA 57.477 32.000 0.00 0.00 35.78 0.98
139 140 6.411630 TTTACAGCGTCAAAATAGCGTTAT 57.588 33.333 0.00 0.00 35.78 1.89
140 141 5.842619 TTTACAGCGTCAAAATAGCGTTA 57.157 34.783 0.00 0.00 35.78 3.18
141 142 4.735662 TTTACAGCGTCAAAATAGCGTT 57.264 36.364 0.00 0.00 35.78 4.84
142 143 4.449743 TCTTTTACAGCGTCAAAATAGCGT 59.550 37.500 0.00 0.00 35.78 5.07
143 144 4.953269 TCTTTTACAGCGTCAAAATAGCG 58.047 39.130 0.00 0.00 35.78 4.26
144 145 6.856426 AGTTTCTTTTACAGCGTCAAAATAGC 59.144 34.615 0.00 0.00 0.00 2.97
145 146 8.782533 AAGTTTCTTTTACAGCGTCAAAATAG 57.217 30.769 0.00 0.00 0.00 1.73
146 147 9.872757 CTAAGTTTCTTTTACAGCGTCAAAATA 57.127 29.630 0.00 0.00 0.00 1.40
147 148 7.378728 GCTAAGTTTCTTTTACAGCGTCAAAAT 59.621 33.333 0.00 0.00 0.00 1.82
148 149 6.689669 GCTAAGTTTCTTTTACAGCGTCAAAA 59.310 34.615 0.00 0.00 0.00 2.44
149 150 6.196571 GCTAAGTTTCTTTTACAGCGTCAAA 58.803 36.000 0.00 0.00 0.00 2.69
150 151 5.557514 CGCTAAGTTTCTTTTACAGCGTCAA 60.558 40.000 12.95 0.00 38.27 3.18
151 152 4.084745 CGCTAAGTTTCTTTTACAGCGTCA 60.085 41.667 12.95 0.00 38.27 4.35
152 153 4.383679 CGCTAAGTTTCTTTTACAGCGTC 58.616 43.478 12.95 0.00 38.27 5.19
153 154 3.363673 GCGCTAAGTTTCTTTTACAGCGT 60.364 43.478 18.62 0.00 43.82 5.07
154 155 3.153735 GCGCTAAGTTTCTTTTACAGCG 58.846 45.455 15.41 15.41 44.60 5.18
155 156 3.153735 CGCGCTAAGTTTCTTTTACAGC 58.846 45.455 5.56 0.00 0.00 4.40
156 157 3.153735 GCGCGCTAAGTTTCTTTTACAG 58.846 45.455 26.67 0.00 0.00 2.74
157 158 2.410517 CGCGCGCTAAGTTTCTTTTACA 60.411 45.455 30.48 0.00 0.00 2.41
158 159 2.155802 CGCGCGCTAAGTTTCTTTTAC 58.844 47.619 30.48 0.00 0.00 2.01
159 160 1.462869 GCGCGCGCTAAGTTTCTTTTA 60.463 47.619 44.38 0.00 38.26 1.52
160 161 0.724785 GCGCGCGCTAAGTTTCTTTT 60.725 50.000 44.38 0.00 38.26 2.27
161 162 1.154469 GCGCGCGCTAAGTTTCTTT 60.154 52.632 44.38 0.00 38.26 2.52
162 163 2.474712 GCGCGCGCTAAGTTTCTT 59.525 55.556 44.38 0.00 38.26 2.52
183 184 0.824759 ATCTCCAACAGACGCCCTAC 59.175 55.000 0.00 0.00 32.26 3.18
184 185 0.824109 CATCTCCAACAGACGCCCTA 59.176 55.000 0.00 0.00 32.26 3.53
185 186 1.599047 CATCTCCAACAGACGCCCT 59.401 57.895 0.00 0.00 32.26 5.19
186 187 2.109126 GCATCTCCAACAGACGCCC 61.109 63.158 0.00 0.00 33.99 6.13
187 188 0.175760 TAGCATCTCCAACAGACGCC 59.824 55.000 0.00 0.00 41.57 5.68
188 189 2.231215 ATAGCATCTCCAACAGACGC 57.769 50.000 0.00 0.00 40.90 5.19
189 190 4.051922 GGTAATAGCATCTCCAACAGACG 58.948 47.826 0.00 0.00 32.26 4.18
190 191 4.141711 TGGGTAATAGCATCTCCAACAGAC 60.142 45.833 0.00 0.00 32.26 3.51
191 192 4.037222 TGGGTAATAGCATCTCCAACAGA 58.963 43.478 0.00 0.00 34.78 3.41
192 193 4.141620 ACTGGGTAATAGCATCTCCAACAG 60.142 45.833 0.00 0.00 0.00 3.16
193 194 3.780294 ACTGGGTAATAGCATCTCCAACA 59.220 43.478 0.00 0.00 0.00 3.33
194 195 4.130118 CACTGGGTAATAGCATCTCCAAC 58.870 47.826 0.00 0.00 0.00 3.77
195 196 3.136443 CCACTGGGTAATAGCATCTCCAA 59.864 47.826 0.00 0.00 0.00 3.53
196 197 2.705658 CCACTGGGTAATAGCATCTCCA 59.294 50.000 0.00 0.00 0.00 3.86
197 198 2.972713 TCCACTGGGTAATAGCATCTCC 59.027 50.000 0.00 0.00 34.93 3.71
198 199 4.323104 GGATCCACTGGGTAATAGCATCTC 60.323 50.000 6.95 0.00 34.93 2.75
199 200 3.584848 GGATCCACTGGGTAATAGCATCT 59.415 47.826 6.95 0.00 34.93 2.90
200 201 3.327757 TGGATCCACTGGGTAATAGCATC 59.672 47.826 11.44 0.00 34.93 3.91
201 202 3.326521 TGGATCCACTGGGTAATAGCAT 58.673 45.455 11.44 0.00 34.93 3.79
202 203 2.705658 CTGGATCCACTGGGTAATAGCA 59.294 50.000 11.44 0.00 34.93 3.49
203 204 2.972713 TCTGGATCCACTGGGTAATAGC 59.027 50.000 11.44 0.00 34.93 2.97
204 205 4.483950 TCTCTGGATCCACTGGGTAATAG 58.516 47.826 11.44 0.00 34.93 1.73
205 206 4.170053 TCTCTCTGGATCCACTGGGTAATA 59.830 45.833 11.44 0.00 34.93 0.98
206 207 3.051803 TCTCTCTGGATCCACTGGGTAAT 60.052 47.826 11.44 0.00 34.93 1.89
616 624 3.243053 TCGGGAAGGCGGGTGAAA 61.243 61.111 0.00 0.00 0.00 2.69
802 825 0.178068 AGCAATCAAGGCCGTACGAT 59.822 50.000 18.76 0.00 0.00 3.73
804 827 0.373716 GAAGCAATCAAGGCCGTACG 59.626 55.000 8.69 8.69 0.00 3.67
805 828 1.448985 TGAAGCAATCAAGGCCGTAC 58.551 50.000 0.00 0.00 34.30 3.67
806 829 2.288666 GATGAAGCAATCAAGGCCGTA 58.711 47.619 0.00 0.00 42.54 4.02
912 950 2.360475 GCAACACCCTGCTCTCCC 60.360 66.667 0.00 0.00 39.34 4.30
924 962 0.321564 CCACGGGAAGATCTGCAACA 60.322 55.000 2.29 0.00 0.00 3.33
927 965 1.596934 GACCACGGGAAGATCTGCA 59.403 57.895 2.29 0.00 0.00 4.41
976 1014 1.681264 GCCAACTTTAAGCCAGTGTGT 59.319 47.619 0.00 0.00 0.00 3.72
977 1015 1.680735 TGCCAACTTTAAGCCAGTGTG 59.319 47.619 0.00 0.00 0.00 3.82
1054 1092 1.203313 GTAGCGTTGCGGTGTTCAC 59.797 57.895 3.41 0.00 38.30 3.18
1183 1221 3.077359 CTCTCCAGAACCAAACATGGAC 58.923 50.000 1.10 0.00 36.92 4.02
1221 1259 3.894427 TCTTGTCTAGCATCCATCTCTCC 59.106 47.826 0.00 0.00 0.00 3.71
1314 1355 0.744874 ACCCATCGACAGTATCCACG 59.255 55.000 0.00 0.00 0.00 4.94
1344 1385 1.411977 TGGAACGTTTCACCGGTAGAA 59.588 47.619 6.87 11.17 0.00 2.10
1620 1661 8.669243 CACAGTCTAAGATAAAAATGGACTTCC 58.331 37.037 0.00 0.00 31.40 3.46
1658 1699 5.864474 CGATAAATGTAGATAGCCCAGTGTC 59.136 44.000 0.00 0.00 0.00 3.67
1660 1701 5.171476 CCGATAAATGTAGATAGCCCAGTG 58.829 45.833 0.00 0.00 0.00 3.66
1715 1756 6.091169 GCATGATTGACAAAAACACCTAATGG 59.909 38.462 0.00 0.00 39.83 3.16
1731 1774 0.617935 TGGTCCTTCGGCATGATTGA 59.382 50.000 0.00 0.00 0.00 2.57
1802 1846 5.064198 CCAGACGTATAGACTATAGAGCTGC 59.936 48.000 6.78 0.00 0.00 5.25
1958 2002 1.746220 CTAGGGAGTTGAGACAGTCCG 59.254 57.143 0.00 0.00 0.00 4.79
1988 2032 7.446001 AAAGGAAAAGCAAAACAAACAATCA 57.554 28.000 0.00 0.00 0.00 2.57
2036 2080 4.344978 TCCAAGTAGATAGATGGGGATCG 58.655 47.826 0.00 0.00 33.66 3.69
2135 2195 9.120538 GGAAAATCCTTTGCACTAATATACTCA 57.879 33.333 0.00 0.00 33.34 3.41
2159 2219 7.313646 TCAGTTCATAAAACAAACAAAACGGA 58.686 30.769 0.00 0.00 0.00 4.69
2176 2236 6.183347 CCCCTGAAAAGACTTATCAGTTCAT 58.817 40.000 0.87 0.00 39.10 2.57
2245 2305 6.406961 CCCAGCTTTGTAAAAGAAAGACCTTT 60.407 38.462 3.95 0.00 37.94 3.11
2255 2315 9.614792 AGTATACTAATCCCAGCTTTGTAAAAG 57.385 33.333 2.75 0.00 0.00 2.27
2261 2321 4.757149 GGCAGTATACTAATCCCAGCTTTG 59.243 45.833 4.74 0.00 0.00 2.77
2265 2325 4.223923 AGATGGCAGTATACTAATCCCAGC 59.776 45.833 4.74 11.99 0.00 4.85
2315 2375 3.309121 GGACCTTCCCTTTTCATCCATGA 60.309 47.826 0.00 0.00 34.44 3.07
2372 2432 5.464722 GTGTTGATGTCAGCTGGTATATCAG 59.535 44.000 15.13 8.76 37.79 2.90
2382 2442 5.157940 AGTAATCAGTGTTGATGTCAGCT 57.842 39.130 0.00 0.00 43.20 4.24
2383 2443 5.163814 GGAAGTAATCAGTGTTGATGTCAGC 60.164 44.000 0.00 0.00 43.20 4.26
2384 2444 5.062683 CGGAAGTAATCAGTGTTGATGTCAG 59.937 44.000 0.00 0.00 43.20 3.51
2385 2445 4.929211 CGGAAGTAATCAGTGTTGATGTCA 59.071 41.667 0.00 0.00 43.20 3.58
2386 2446 4.201724 GCGGAAGTAATCAGTGTTGATGTC 60.202 45.833 0.00 0.00 43.20 3.06
2387 2447 3.684788 GCGGAAGTAATCAGTGTTGATGT 59.315 43.478 0.00 0.00 43.20 3.06
2388 2448 3.242091 CGCGGAAGTAATCAGTGTTGATG 60.242 47.826 0.00 0.00 43.20 3.07
2389 2449 2.930040 CGCGGAAGTAATCAGTGTTGAT 59.070 45.455 0.00 0.00 45.92 2.57
2390 2450 2.029739 TCGCGGAAGTAATCAGTGTTGA 60.030 45.455 6.13 0.00 35.55 3.18
2391 2451 2.092211 GTCGCGGAAGTAATCAGTGTTG 59.908 50.000 6.13 0.00 35.55 3.33
2392 2452 2.288579 TGTCGCGGAAGTAATCAGTGTT 60.289 45.455 6.13 0.00 35.55 3.32
2393 2453 1.271379 TGTCGCGGAAGTAATCAGTGT 59.729 47.619 6.13 0.00 35.55 3.55
2394 2454 1.654105 GTGTCGCGGAAGTAATCAGTG 59.346 52.381 6.13 0.00 35.39 3.66
2395 2455 1.544691 AGTGTCGCGGAAGTAATCAGT 59.455 47.619 6.13 0.00 0.00 3.41
2396 2456 2.279582 AGTGTCGCGGAAGTAATCAG 57.720 50.000 6.13 0.00 0.00 2.90
2397 2457 2.736144 AAGTGTCGCGGAAGTAATCA 57.264 45.000 6.13 0.00 0.00 2.57
2398 2458 5.520022 TTAAAAGTGTCGCGGAAGTAATC 57.480 39.130 6.13 0.00 0.00 1.75
2399 2459 6.490566 AATTAAAAGTGTCGCGGAAGTAAT 57.509 33.333 6.13 0.00 0.00 1.89
2400 2460 5.927954 AATTAAAAGTGTCGCGGAAGTAA 57.072 34.783 6.13 0.00 0.00 2.24
2401 2461 6.646240 AGTTAATTAAAAGTGTCGCGGAAGTA 59.354 34.615 6.13 0.00 0.00 2.24
2402 2462 5.467735 AGTTAATTAAAAGTGTCGCGGAAGT 59.532 36.000 6.13 0.00 0.00 3.01
2403 2463 5.923665 AGTTAATTAAAAGTGTCGCGGAAG 58.076 37.500 6.13 0.00 0.00 3.46
2404 2464 5.927954 AGTTAATTAAAAGTGTCGCGGAA 57.072 34.783 6.13 0.00 0.00 4.30
2460 2521 2.677875 GGGTGCCCAAGGAGCAAG 60.678 66.667 1.66 0.00 43.02 4.01
2481 2542 0.260230 TTGGAGGGCACAAAACAGGA 59.740 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.