Multiple sequence alignment - TraesCS7B01G225200

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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 TraesCS7B01G225200 chr7B 100.000 5484 0 0 1 5484 425708725 425714208 0.000000e+00 10128.0
1 TraesCS7B01G225200 chr7D 95.966 4512 136 19 226 4714 411301257 411305745 0.000000e+00 7282.0
2 TraesCS7B01G225200 chr7D 94.796 711 20 3 4776 5484 411306028 411306723 0.000000e+00 1092.0
3 TraesCS7B01G225200 chr7D 92.889 225 14 2 1 225 114449887 114449665 5.300000e-85 326.0
4 TraesCS7B01G225200 chr7A 95.214 2382 83 13 2189 4548 472190376 472192748 0.000000e+00 3738.0
5 TraesCS7B01G225200 chr7A 93.823 1878 86 13 227 2102 472188535 472190384 0.000000e+00 2798.0
6 TraesCS7B01G225200 chr7A 93.373 679 21 6 4810 5484 472194446 472195104 0.000000e+00 983.0
7 TraesCS7B01G225200 chr1D 93.043 230 15 1 1 230 57735254 57735026 8.800000e-88 335.0
8 TraesCS7B01G225200 chr1D 92.920 226 14 2 1 225 311219928 311219704 1.470000e-85 327.0
9 TraesCS7B01G225200 chr1D 86.806 144 14 2 2089 2231 54906481 54906620 7.360000e-34 156.0
10 TraesCS7B01G225200 chr1D 78.995 219 38 5 4555 4773 336373929 336374139 5.730000e-30 143.0
11 TraesCS7B01G225200 chr2D 93.333 225 14 1 1 225 164380965 164380742 1.140000e-86 331.0
12 TraesCS7B01G225200 chr2D 92.889 225 15 1 1 225 164290914 164290691 5.300000e-85 326.0
13 TraesCS7B01G225200 chr2D 96.053 76 3 0 5409 5484 637650001 637650076 2.070000e-24 124.0
14 TraesCS7B01G225200 chr2D 100.000 36 0 0 4555 4590 27783524 27783559 3.550000e-07 67.6
15 TraesCS7B01G225200 chr4D 92.275 233 17 1 1 233 18788498 18788729 4.100000e-86 329.0
16 TraesCS7B01G225200 chr4D 92.920 226 15 1 1 226 61295836 61296060 1.470000e-85 327.0
17 TraesCS7B01G225200 chr6D 92.889 225 15 1 1 225 120620070 120620293 5.300000e-85 326.0
18 TraesCS7B01G225200 chr1A 92.174 230 16 2 1 230 125086873 125087100 1.910000e-84 324.0
19 TraesCS7B01G225200 chr5B 82.301 226 28 8 4558 4776 243432994 243432774 9.380000e-43 185.0
20 TraesCS7B01G225200 chr5D 80.349 229 38 2 4555 4776 526122222 526121994 3.400000e-37 167.0
21 TraesCS7B01G225200 chr5D 87.778 90 11 0 4687 4776 464061163 464061252 7.510000e-19 106.0
22 TraesCS7B01G225200 chr4B 88.406 138 12 1 2094 2231 22850687 22850820 4.400000e-36 163.0
23 TraesCS7B01G225200 chr4B 83.436 163 22 3 2091 2253 535573447 535573604 4.430000e-31 147.0
24 TraesCS7B01G225200 chr4B 83.436 163 22 3 2091 2253 535576184 535576341 4.430000e-31 147.0
25 TraesCS7B01G225200 chr3A 88.406 138 12 1 2094 2231 528529312 528529445 4.400000e-36 163.0
26 TraesCS7B01G225200 chr2B 84.848 165 21 1 2086 2250 190547497 190547657 4.400000e-36 163.0
27 TraesCS7B01G225200 chr2B 96.053 76 3 0 5409 5484 795062864 795062939 2.070000e-24 124.0
28 TraesCS7B01G225200 chr6A 85.535 159 18 3 2092 2250 104117692 104117845 1.580000e-35 161.0
29 TraesCS7B01G225200 chr5A 83.051 177 16 9 2088 2258 237461520 237461688 1.230000e-31 148.0
30 TraesCS7B01G225200 chr2A 97.143 70 2 0 5415 5484 762293356 762293287 9.650000e-23 119.0
31 TraesCS7B01G225200 chr3B 76.316 228 48 2 4555 4776 620349554 620349327 3.470000e-22 117.0
32 TraesCS7B01G225200 chr1B 77.987 159 28 5 4555 4713 452304113 452304264 5.850000e-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 TraesCS7B01G225200 chr7B 425708725 425714208 5483 False 10128.000000 10128 100.000000 1 5484 1 chr7B.!!$F1 5483
1 TraesCS7B01G225200 chr7D 411301257 411306723 5466 False 4187.000000 7282 95.381000 226 5484 2 chr7D.!!$F1 5258
2 TraesCS7B01G225200 chr7A 472188535 472195104 6569 False 2506.333333 3738 94.136667 227 5484 3 chr7A.!!$F1 5257

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
175 176 0.035317 CCTACCTCTGTTGTGCTGCA 59.965 55.0 0.00 0.00 0.00 4.41 F
183 184 0.038599 TGTTGTGCTGCATCATCCCT 59.961 50.0 5.27 0.00 0.00 4.20 F
187 188 0.106819 GTGCTGCATCATCCCTTCCT 60.107 55.0 5.27 0.00 0.00 3.36 F
222 223 0.179073 AACATAGCTTCGAGCCGCAT 60.179 50.0 0.00 0.00 43.77 4.73 F
2233 2239 0.186386 ATCGCCTAGAGCCTAGGTGT 59.814 55.0 27.18 18.06 43.67 4.16 F
2595 2605 0.394625 ACCTCCTACGCCTCTCAGAC 60.395 60.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2115 0.725117 ACGCACAATTAACGCCTAGC 59.275 50.000 0.00 0.00 0.00 3.42 R
2178 2184 3.426695 GCGCTGAATTGTGCTTAATCTGT 60.427 43.478 0.00 0.00 40.01 3.41 R
2276 2282 4.456280 TGCTGACGTGTCTCTATTTGAT 57.544 40.909 0.00 0.00 0.00 2.57 R
2303 2309 4.504916 CGCTCTAGGCTGCGCAGT 62.505 66.667 35.80 21.44 45.50 4.40 R
3414 3437 0.098200 CATGCAGGCTGTCATGAACG 59.902 55.000 30.90 14.94 41.82 3.95 R
4556 4581 0.249741 GTACCTGACGTGTGGCACTT 60.250 55.000 19.83 2.72 31.34 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.815308 CCTATCTTGAGGCGCCGT 59.185 61.111 23.20 9.79 0.00 5.68
19 20 1.144057 CCTATCTTGAGGCGCCGTT 59.856 57.895 23.20 3.63 0.00 4.44
20 21 0.387929 CCTATCTTGAGGCGCCGTTA 59.612 55.000 23.20 8.69 0.00 3.18
21 22 1.488527 CTATCTTGAGGCGCCGTTAC 58.511 55.000 23.20 14.46 0.00 2.50
22 23 0.103572 TATCTTGAGGCGCCGTTACC 59.896 55.000 23.20 9.74 0.00 2.85
23 24 2.588856 ATCTTGAGGCGCCGTTACCC 62.589 60.000 23.20 7.87 0.00 3.69
24 25 4.745751 TTGAGGCGCCGTTACCCG 62.746 66.667 23.20 0.00 0.00 5.28
26 27 4.440127 GAGGCGCCGTTACCCGAA 62.440 66.667 23.20 0.00 39.56 4.30
27 28 3.938019 GAGGCGCCGTTACCCGAAA 62.938 63.158 23.20 0.00 39.56 3.46
28 29 3.493440 GGCGCCGTTACCCGAAAG 61.493 66.667 12.58 0.00 39.56 2.62
42 43 1.173913 CGAAAGGGATTGACAACCCC 58.826 55.000 10.02 10.02 46.64 4.95
49 50 3.502356 GGGATTGACAACCCCTTTAACA 58.498 45.455 10.82 0.00 40.19 2.41
50 51 4.093743 GGGATTGACAACCCCTTTAACAT 58.906 43.478 10.82 0.00 40.19 2.71
51 52 4.081697 GGGATTGACAACCCCTTTAACATG 60.082 45.833 10.82 0.00 40.19 3.21
52 53 4.081697 GGATTGACAACCCCTTTAACATGG 60.082 45.833 0.00 0.00 0.00 3.66
53 54 2.243810 TGACAACCCCTTTAACATGGC 58.756 47.619 0.00 0.00 0.00 4.40
54 55 1.201414 GACAACCCCTTTAACATGGCG 59.799 52.381 0.00 0.00 0.00 5.69
55 56 0.530288 CAACCCCTTTAACATGGCGG 59.470 55.000 0.00 0.00 0.00 6.13
56 57 0.613572 AACCCCTTTAACATGGCGGG 60.614 55.000 0.00 0.00 36.55 6.13
57 58 1.000145 CCCCTTTAACATGGCGGGT 60.000 57.895 0.00 0.00 32.91 5.28
58 59 0.613572 CCCCTTTAACATGGCGGGTT 60.614 55.000 0.00 0.00 32.91 4.11
59 60 0.530288 CCCTTTAACATGGCGGGTTG 59.470 55.000 0.00 0.00 0.00 3.77
60 61 0.108851 CCTTTAACATGGCGGGTTGC 60.109 55.000 0.00 0.00 45.38 4.17
69 70 2.485122 GCGGGTTGCGAGGATTTG 59.515 61.111 0.00 0.00 0.00 2.32
70 71 2.332654 GCGGGTTGCGAGGATTTGT 61.333 57.895 0.00 0.00 0.00 2.83
71 72 1.862602 GCGGGTTGCGAGGATTTGTT 61.863 55.000 0.00 0.00 0.00 2.83
72 73 1.444836 CGGGTTGCGAGGATTTGTTA 58.555 50.000 0.00 0.00 0.00 2.41
73 74 2.014128 CGGGTTGCGAGGATTTGTTAT 58.986 47.619 0.00 0.00 0.00 1.89
74 75 2.031683 CGGGTTGCGAGGATTTGTTATC 59.968 50.000 0.00 0.00 0.00 1.75
75 76 3.279434 GGGTTGCGAGGATTTGTTATCT 58.721 45.455 0.00 0.00 0.00 1.98
76 77 3.065371 GGGTTGCGAGGATTTGTTATCTG 59.935 47.826 0.00 0.00 0.00 2.90
77 78 3.689649 GGTTGCGAGGATTTGTTATCTGT 59.310 43.478 0.00 0.00 0.00 3.41
78 79 4.437390 GGTTGCGAGGATTTGTTATCTGTG 60.437 45.833 0.00 0.00 0.00 3.66
79 80 3.937814 TGCGAGGATTTGTTATCTGTGT 58.062 40.909 0.00 0.00 0.00 3.72
80 81 3.684305 TGCGAGGATTTGTTATCTGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
81 82 3.063997 GCGAGGATTTGTTATCTGTGTGG 59.936 47.826 0.00 0.00 0.00 4.17
82 83 4.503910 CGAGGATTTGTTATCTGTGTGGA 58.496 43.478 0.00 0.00 0.00 4.02
83 84 4.568359 CGAGGATTTGTTATCTGTGTGGAG 59.432 45.833 0.00 0.00 0.00 3.86
84 85 4.848357 AGGATTTGTTATCTGTGTGGAGG 58.152 43.478 0.00 0.00 0.00 4.30
85 86 3.947834 GGATTTGTTATCTGTGTGGAGGG 59.052 47.826 0.00 0.00 0.00 4.30
86 87 3.433306 TTTGTTATCTGTGTGGAGGGG 57.567 47.619 0.00 0.00 0.00 4.79
87 88 2.038863 TGTTATCTGTGTGGAGGGGT 57.961 50.000 0.00 0.00 0.00 4.95
88 89 2.344592 TGTTATCTGTGTGGAGGGGTT 58.655 47.619 0.00 0.00 0.00 4.11
89 90 2.039746 TGTTATCTGTGTGGAGGGGTTG 59.960 50.000 0.00 0.00 0.00 3.77
90 91 2.038863 TATCTGTGTGGAGGGGTTGT 57.961 50.000 0.00 0.00 0.00 3.32
91 92 1.149101 ATCTGTGTGGAGGGGTTGTT 58.851 50.000 0.00 0.00 0.00 2.83
92 93 0.923358 TCTGTGTGGAGGGGTTGTTT 59.077 50.000 0.00 0.00 0.00 2.83
93 94 1.286553 TCTGTGTGGAGGGGTTGTTTT 59.713 47.619 0.00 0.00 0.00 2.43
94 95 2.510382 TCTGTGTGGAGGGGTTGTTTTA 59.490 45.455 0.00 0.00 0.00 1.52
95 96 3.139397 TCTGTGTGGAGGGGTTGTTTTAT 59.861 43.478 0.00 0.00 0.00 1.40
96 97 3.226777 TGTGTGGAGGGGTTGTTTTATG 58.773 45.455 0.00 0.00 0.00 1.90
97 98 3.227614 GTGTGGAGGGGTTGTTTTATGT 58.772 45.455 0.00 0.00 0.00 2.29
98 99 3.639561 GTGTGGAGGGGTTGTTTTATGTT 59.360 43.478 0.00 0.00 0.00 2.71
99 100 3.639094 TGTGGAGGGGTTGTTTTATGTTG 59.361 43.478 0.00 0.00 0.00 3.33
100 101 3.639561 GTGGAGGGGTTGTTTTATGTTGT 59.360 43.478 0.00 0.00 0.00 3.32
101 102 3.639094 TGGAGGGGTTGTTTTATGTTGTG 59.361 43.478 0.00 0.00 0.00 3.33
102 103 3.639561 GGAGGGGTTGTTTTATGTTGTGT 59.360 43.478 0.00 0.00 0.00 3.72
103 104 4.100344 GGAGGGGTTGTTTTATGTTGTGTT 59.900 41.667 0.00 0.00 0.00 3.32
104 105 5.017294 AGGGGTTGTTTTATGTTGTGTTG 57.983 39.130 0.00 0.00 0.00 3.33
105 106 3.558006 GGGGTTGTTTTATGTTGTGTTGC 59.442 43.478 0.00 0.00 0.00 4.17
106 107 4.438148 GGGTTGTTTTATGTTGTGTTGCT 58.562 39.130 0.00 0.00 0.00 3.91
107 108 4.873259 GGGTTGTTTTATGTTGTGTTGCTT 59.127 37.500 0.00 0.00 0.00 3.91
108 109 5.220567 GGGTTGTTTTATGTTGTGTTGCTTG 60.221 40.000 0.00 0.00 0.00 4.01
109 110 5.578727 GGTTGTTTTATGTTGTGTTGCTTGA 59.421 36.000 0.00 0.00 0.00 3.02
110 111 6.257630 GGTTGTTTTATGTTGTGTTGCTTGAT 59.742 34.615 0.00 0.00 0.00 2.57
111 112 7.201600 GGTTGTTTTATGTTGTGTTGCTTGATT 60.202 33.333 0.00 0.00 0.00 2.57
112 113 7.462109 TGTTTTATGTTGTGTTGCTTGATTC 57.538 32.000 0.00 0.00 0.00 2.52
113 114 7.264221 TGTTTTATGTTGTGTTGCTTGATTCT 58.736 30.769 0.00 0.00 0.00 2.40
114 115 7.434897 TGTTTTATGTTGTGTTGCTTGATTCTC 59.565 33.333 0.00 0.00 0.00 2.87
115 116 3.988379 TGTTGTGTTGCTTGATTCTCC 57.012 42.857 0.00 0.00 0.00 3.71
116 117 3.554934 TGTTGTGTTGCTTGATTCTCCT 58.445 40.909 0.00 0.00 0.00 3.69
117 118 4.713553 TGTTGTGTTGCTTGATTCTCCTA 58.286 39.130 0.00 0.00 0.00 2.94
118 119 4.515191 TGTTGTGTTGCTTGATTCTCCTAC 59.485 41.667 0.00 0.00 0.00 3.18
119 120 4.623932 TGTGTTGCTTGATTCTCCTACT 57.376 40.909 0.00 0.00 0.00 2.57
120 121 4.318332 TGTGTTGCTTGATTCTCCTACTG 58.682 43.478 0.00 0.00 0.00 2.74
121 122 3.686726 GTGTTGCTTGATTCTCCTACTGG 59.313 47.826 0.00 0.00 0.00 4.00
122 123 3.327757 TGTTGCTTGATTCTCCTACTGGT 59.672 43.478 0.00 0.00 34.23 4.00
123 124 4.202461 TGTTGCTTGATTCTCCTACTGGTT 60.202 41.667 0.00 0.00 34.23 3.67
124 125 4.207891 TGCTTGATTCTCCTACTGGTTC 57.792 45.455 0.00 0.00 34.23 3.62
125 126 3.190874 GCTTGATTCTCCTACTGGTTCG 58.809 50.000 0.00 0.00 34.23 3.95
126 127 3.119101 GCTTGATTCTCCTACTGGTTCGA 60.119 47.826 0.00 0.00 34.23 3.71
127 128 4.442192 GCTTGATTCTCCTACTGGTTCGAT 60.442 45.833 0.00 0.00 34.23 3.59
128 129 5.221263 GCTTGATTCTCCTACTGGTTCGATA 60.221 44.000 0.00 0.00 34.23 2.92
129 130 6.683110 GCTTGATTCTCCTACTGGTTCGATAA 60.683 42.308 0.00 0.00 34.23 1.75
130 131 6.978674 TGATTCTCCTACTGGTTCGATAAT 57.021 37.500 0.00 0.00 34.23 1.28
131 132 6.982852 TGATTCTCCTACTGGTTCGATAATC 58.017 40.000 0.00 0.00 34.23 1.75
132 133 6.778069 TGATTCTCCTACTGGTTCGATAATCT 59.222 38.462 0.00 0.00 34.23 2.40
133 134 7.287927 TGATTCTCCTACTGGTTCGATAATCTT 59.712 37.037 0.00 0.00 34.23 2.40
134 135 6.392625 TCTCCTACTGGTTCGATAATCTTG 57.607 41.667 0.00 0.00 34.23 3.02
135 136 5.302059 TCTCCTACTGGTTCGATAATCTTGG 59.698 44.000 0.00 0.00 34.23 3.61
136 137 4.960469 TCCTACTGGTTCGATAATCTTGGT 59.040 41.667 0.00 0.00 34.23 3.67
137 138 5.424252 TCCTACTGGTTCGATAATCTTGGTT 59.576 40.000 0.00 0.00 34.23 3.67
138 139 6.070424 TCCTACTGGTTCGATAATCTTGGTTT 60.070 38.462 0.00 0.00 34.23 3.27
139 140 6.258068 CCTACTGGTTCGATAATCTTGGTTTC 59.742 42.308 0.00 0.00 0.00 2.78
140 141 5.556915 ACTGGTTCGATAATCTTGGTTTCA 58.443 37.500 0.00 0.00 0.00 2.69
141 142 6.180472 ACTGGTTCGATAATCTTGGTTTCAT 58.820 36.000 0.00 0.00 0.00 2.57
142 143 7.335627 ACTGGTTCGATAATCTTGGTTTCATA 58.664 34.615 0.00 0.00 0.00 2.15
143 144 7.993183 ACTGGTTCGATAATCTTGGTTTCATAT 59.007 33.333 0.00 0.00 0.00 1.78
144 145 8.378172 TGGTTCGATAATCTTGGTTTCATATC 57.622 34.615 0.00 0.00 0.00 1.63
145 146 7.444183 TGGTTCGATAATCTTGGTTTCATATCC 59.556 37.037 0.00 0.00 0.00 2.59
146 147 7.360101 GGTTCGATAATCTTGGTTTCATATCCG 60.360 40.741 0.00 0.00 0.00 4.18
147 148 6.988522 TCGATAATCTTGGTTTCATATCCGA 58.011 36.000 0.00 0.00 0.00 4.55
148 149 7.090808 TCGATAATCTTGGTTTCATATCCGAG 58.909 38.462 0.00 0.00 36.76 4.63
149 150 6.311445 CGATAATCTTGGTTTCATATCCGAGG 59.689 42.308 0.00 0.00 36.26 4.63
150 151 3.838244 TCTTGGTTTCATATCCGAGGG 57.162 47.619 0.00 0.00 36.26 4.30
151 152 3.380393 TCTTGGTTTCATATCCGAGGGA 58.620 45.455 0.00 0.00 36.26 4.20
152 153 3.778075 TCTTGGTTTCATATCCGAGGGAA 59.222 43.478 0.00 0.00 36.26 3.97
153 154 4.226394 TCTTGGTTTCATATCCGAGGGAAA 59.774 41.667 0.00 0.00 36.26 3.13
154 155 4.788925 TGGTTTCATATCCGAGGGAAAT 57.211 40.909 0.00 0.00 34.34 2.17
155 156 5.897851 TGGTTTCATATCCGAGGGAAATA 57.102 39.130 0.00 0.00 34.34 1.40
156 157 5.617252 TGGTTTCATATCCGAGGGAAATAC 58.383 41.667 0.00 0.00 34.34 1.89
157 158 5.001874 GGTTTCATATCCGAGGGAAATACC 58.998 45.833 0.00 0.00 34.34 2.73
158 159 5.221864 GGTTTCATATCCGAGGGAAATACCT 60.222 44.000 0.00 0.00 45.57 3.08
159 160 6.013984 GGTTTCATATCCGAGGGAAATACCTA 60.014 42.308 0.00 0.00 42.10 3.08
160 161 6.600882 TTCATATCCGAGGGAAATACCTAC 57.399 41.667 0.00 0.00 42.10 3.18
161 162 5.021458 TCATATCCGAGGGAAATACCTACC 58.979 45.833 0.00 0.00 42.10 3.18
162 163 3.632420 ATCCGAGGGAAATACCTACCT 57.368 47.619 0.00 0.00 42.10 3.08
163 164 2.954792 TCCGAGGGAAATACCTACCTC 58.045 52.381 0.00 0.00 42.10 3.85
164 165 2.517127 TCCGAGGGAAATACCTACCTCT 59.483 50.000 7.83 0.00 45.71 3.69
165 166 2.628657 CCGAGGGAAATACCTACCTCTG 59.371 54.545 7.83 0.00 45.71 3.35
166 167 3.297736 CGAGGGAAATACCTACCTCTGT 58.702 50.000 7.83 0.00 45.71 3.41
167 168 3.705072 CGAGGGAAATACCTACCTCTGTT 59.295 47.826 7.83 0.00 45.71 3.16
168 169 4.441634 CGAGGGAAATACCTACCTCTGTTG 60.442 50.000 7.83 0.00 45.71 3.33
169 170 4.436079 AGGGAAATACCTACCTCTGTTGT 58.564 43.478 0.00 0.00 39.65 3.32
170 171 4.225267 AGGGAAATACCTACCTCTGTTGTG 59.775 45.833 0.00 0.00 39.65 3.33
171 172 3.939592 GGAAATACCTACCTCTGTTGTGC 59.060 47.826 0.00 0.00 35.41 4.57
172 173 4.323562 GGAAATACCTACCTCTGTTGTGCT 60.324 45.833 0.00 0.00 35.41 4.40
173 174 3.895232 ATACCTACCTCTGTTGTGCTG 57.105 47.619 0.00 0.00 0.00 4.41
174 175 0.035458 ACCTACCTCTGTTGTGCTGC 59.965 55.000 0.00 0.00 0.00 5.25
175 176 0.035317 CCTACCTCTGTTGTGCTGCA 59.965 55.000 0.00 0.00 0.00 4.41
176 177 1.339438 CCTACCTCTGTTGTGCTGCAT 60.339 52.381 5.27 0.00 0.00 3.96
177 178 2.005451 CTACCTCTGTTGTGCTGCATC 58.995 52.381 5.27 0.09 0.00 3.91
178 179 0.109153 ACCTCTGTTGTGCTGCATCA 59.891 50.000 5.27 3.06 0.00 3.07
179 180 1.271762 ACCTCTGTTGTGCTGCATCAT 60.272 47.619 5.27 0.00 0.00 2.45
180 181 1.400846 CCTCTGTTGTGCTGCATCATC 59.599 52.381 5.27 6.05 0.00 2.92
181 182 1.400846 CTCTGTTGTGCTGCATCATCC 59.599 52.381 5.27 0.00 0.00 3.51
182 183 0.454600 CTGTTGTGCTGCATCATCCC 59.545 55.000 5.27 0.00 0.00 3.85
183 184 0.038599 TGTTGTGCTGCATCATCCCT 59.961 50.000 5.27 0.00 0.00 4.20
184 185 1.180029 GTTGTGCTGCATCATCCCTT 58.820 50.000 5.27 0.00 0.00 3.95
185 186 1.133790 GTTGTGCTGCATCATCCCTTC 59.866 52.381 5.27 0.00 0.00 3.46
186 187 0.394762 TGTGCTGCATCATCCCTTCC 60.395 55.000 5.27 0.00 0.00 3.46
187 188 0.106819 GTGCTGCATCATCCCTTCCT 60.107 55.000 5.27 0.00 0.00 3.36
188 189 0.182061 TGCTGCATCATCCCTTCCTC 59.818 55.000 0.00 0.00 0.00 3.71
189 190 0.473326 GCTGCATCATCCCTTCCTCT 59.527 55.000 0.00 0.00 0.00 3.69
190 191 1.133853 GCTGCATCATCCCTTCCTCTT 60.134 52.381 0.00 0.00 0.00 2.85
191 192 2.686118 GCTGCATCATCCCTTCCTCTTT 60.686 50.000 0.00 0.00 0.00 2.52
192 193 2.950309 CTGCATCATCCCTTCCTCTTTG 59.050 50.000 0.00 0.00 0.00 2.77
193 194 2.577563 TGCATCATCCCTTCCTCTTTGA 59.422 45.455 0.00 0.00 0.00 2.69
194 195 3.212685 GCATCATCCCTTCCTCTTTGAG 58.787 50.000 0.00 0.00 0.00 3.02
210 211 7.020914 CTCTTTGAGGAAATACCAACATAGC 57.979 40.000 0.00 0.00 42.04 2.97
211 212 6.721318 TCTTTGAGGAAATACCAACATAGCT 58.279 36.000 0.00 0.00 42.04 3.32
212 213 7.175104 TCTTTGAGGAAATACCAACATAGCTT 58.825 34.615 0.00 0.00 42.04 3.74
213 214 7.336931 TCTTTGAGGAAATACCAACATAGCTTC 59.663 37.037 0.00 0.00 42.04 3.86
214 215 5.116180 TGAGGAAATACCAACATAGCTTCG 58.884 41.667 0.00 0.00 42.04 3.79
215 216 5.105106 TGAGGAAATACCAACATAGCTTCGA 60.105 40.000 0.00 0.00 42.04 3.71
216 217 5.360591 AGGAAATACCAACATAGCTTCGAG 58.639 41.667 0.00 0.00 42.04 4.04
217 218 4.024809 GGAAATACCAACATAGCTTCGAGC 60.025 45.833 0.00 0.00 39.07 5.03
218 219 2.596904 TACCAACATAGCTTCGAGCC 57.403 50.000 0.00 0.00 43.77 4.70
219 220 0.460284 ACCAACATAGCTTCGAGCCG 60.460 55.000 0.00 0.00 43.77 5.52
220 221 1.638467 CAACATAGCTTCGAGCCGC 59.362 57.895 0.00 0.00 43.77 6.53
221 222 1.083806 CAACATAGCTTCGAGCCGCA 61.084 55.000 0.00 0.00 43.77 5.69
222 223 0.179073 AACATAGCTTCGAGCCGCAT 60.179 50.000 0.00 0.00 43.77 4.73
223 224 0.598680 ACATAGCTTCGAGCCGCATC 60.599 55.000 0.00 0.00 43.77 3.91
224 225 0.598419 CATAGCTTCGAGCCGCATCA 60.598 55.000 0.00 0.00 43.77 3.07
309 310 4.003788 CCCCGCGTGTCTTCCACT 62.004 66.667 4.92 0.00 42.20 4.00
341 342 1.887198 CTCCTCCACCGCTATTCGTAT 59.113 52.381 0.00 0.00 36.19 3.06
344 345 1.000163 CTCCACCGCTATTCGTATGCT 60.000 52.381 0.00 0.00 36.19 3.79
436 437 2.058595 GCCCTTACTCCTCTCCGCA 61.059 63.158 0.00 0.00 0.00 5.69
475 476 0.549902 TCACCCCACTGACCATCCAT 60.550 55.000 0.00 0.00 0.00 3.41
934 939 3.352748 TCACCCCCTCCGAGGCTA 61.353 66.667 9.17 0.00 32.73 3.93
947 952 3.459063 GGCTACGCTCCCGGTTCT 61.459 66.667 0.00 0.00 39.22 3.01
1145 1150 4.503314 CGACCCCGGAGCGGTAAC 62.503 72.222 0.73 0.00 46.80 2.50
1182 1187 3.249917 CCTGCTCGTCTTCTTTCTTCTC 58.750 50.000 0.00 0.00 0.00 2.87
1223 1228 3.019564 GTTGCAGTTGGAATATCTGGCT 58.980 45.455 0.00 0.00 0.00 4.75
1395 1400 7.161404 TCTACATAACTGAAAACTGTGCTCAT 58.839 34.615 0.00 0.00 0.00 2.90
1440 1445 1.604308 CAGCCTTGTGCCACCATCA 60.604 57.895 0.00 0.00 42.71 3.07
1535 1540 1.611965 GGAGGGCTTCCTGCAATCT 59.388 57.895 8.66 0.00 46.76 2.40
1603 1608 2.931969 CGCTCAGATACAATTGCTGTCA 59.068 45.455 5.05 0.00 39.64 3.58
1607 1612 5.505324 GCTCAGATACAATTGCTGTCAATCC 60.505 44.000 5.05 0.00 41.77 3.01
1709 1715 8.101309 TGATAGGAATTTCCCTGATAGTGAAA 57.899 34.615 11.92 0.00 37.19 2.69
2074 2080 9.300681 TCTCATTCATTCATTGGAAAAAGTAGT 57.699 29.630 0.00 0.00 36.43 2.73
2138 2144 1.285578 AATTGTGCGTGTGTTTTGCC 58.714 45.000 0.00 0.00 0.00 4.52
2198 2204 3.855950 GCACAGATTAAGCACAATTCAGC 59.144 43.478 0.00 0.00 0.00 4.26
2230 2236 1.099689 GCTATCGCCTAGAGCCTAGG 58.900 60.000 18.85 18.85 36.38 3.02
2231 2237 1.614850 GCTATCGCCTAGAGCCTAGGT 60.615 57.143 22.04 10.67 36.38 3.08
2233 2239 0.186386 ATCGCCTAGAGCCTAGGTGT 59.814 55.000 27.18 18.06 43.67 4.16
2303 2309 2.437413 AGAGACACGTCAGCATCACTA 58.563 47.619 0.00 0.00 0.00 2.74
2383 2392 3.190849 CCGTGGCATCTGTGAGCG 61.191 66.667 0.00 0.00 0.00 5.03
2401 2411 2.121009 GCGCACGTAAACCAAATTGTT 58.879 42.857 0.30 0.00 0.00 2.83
2406 2416 5.386933 CGCACGTAAACCAAATTGTTGAATC 60.387 40.000 0.00 0.00 36.83 2.52
2460 2470 7.496263 GGAGTATTAATCCAAGTGAGGAAGTTC 59.504 40.741 5.31 0.00 41.92 3.01
2571 2581 2.815503 TGTAGCTGTGTAGACGTTAGCA 59.184 45.455 0.00 0.00 36.87 3.49
2595 2605 0.394625 ACCTCCTACGCCTCTCAGAC 60.395 60.000 0.00 0.00 0.00 3.51
2621 2631 4.614284 CGTGTGCTGCTCTTCTTATTTTTG 59.386 41.667 0.00 0.00 0.00 2.44
2643 2653 5.316987 TGGTCTTTTCTCCTTTTCATCTCC 58.683 41.667 0.00 0.00 0.00 3.71
2811 2821 4.801330 TTCACGAGCTTCCTATCAGAAA 57.199 40.909 0.00 0.00 0.00 2.52
2841 2851 4.902448 AGTTTGCAGTTTTTACCCCCATAA 59.098 37.500 0.00 0.00 0.00 1.90
2899 2909 3.190118 AGCTGCTGTTGATGCTTAACTTC 59.810 43.478 0.00 0.00 30.96 3.01
3022 3033 3.660865 AGAGGTAATCGGTGTGTTTGTC 58.339 45.455 0.00 0.00 0.00 3.18
3028 3039 0.456628 TCGGTGTGTTTGTCGACAGA 59.543 50.000 19.11 12.05 0.00 3.41
3342 3353 5.954150 ACTCCATCCTGCTATGAAACAAATT 59.046 36.000 0.00 0.00 0.00 1.82
3345 3356 5.127519 CCATCCTGCTATGAAACAAATTCCA 59.872 40.000 0.00 0.00 37.22 3.53
3414 3437 2.192608 CTGCAGGCGCCAAGAAGAAC 62.193 60.000 31.54 8.60 37.32 3.01
3754 3777 3.702048 GGTACTGCCCCTCGTGCA 61.702 66.667 0.00 0.00 37.17 4.57
3843 3866 2.857186 ACCATGTGTACTGCATGACA 57.143 45.000 23.24 7.93 44.60 3.58
3888 3911 2.214216 TCACTGGTACTGCCCGCTT 61.214 57.895 0.00 0.00 36.04 4.68
4184 4207 5.188555 TGAATAGTTGAATCAGAGCCAGTCT 59.811 40.000 0.00 0.00 35.00 3.24
4454 4478 5.327891 GCAAACCGATTTTTCTTTTTGCAA 58.672 33.333 11.02 0.00 45.18 4.08
4496 4521 5.646793 GGGACCTTTTAAGACCATCTACAAC 59.353 44.000 0.00 0.00 0.00 3.32
4538 4563 4.022416 TGTTTGCGAAGAATGCACCTTTAT 60.022 37.500 4.87 0.00 43.10 1.40
4540 4565 5.888691 TTGCGAAGAATGCACCTTTATTA 57.111 34.783 4.87 0.00 43.10 0.98
4541 4566 6.449635 TTGCGAAGAATGCACCTTTATTAT 57.550 33.333 4.87 0.00 43.10 1.28
4601 4626 4.035441 GCACATGGCAACTTTGAATGTTTT 59.965 37.500 0.00 0.00 43.97 2.43
4626 4651 8.854979 TTTATGATAAATTTTGTGATGCGAGG 57.145 30.769 0.00 0.00 0.00 4.63
4643 4668 5.543714 TGCGAGGATGACAACTTTAGTTTA 58.456 37.500 0.00 0.00 35.83 2.01
4644 4669 6.170506 TGCGAGGATGACAACTTTAGTTTAT 58.829 36.000 0.00 0.00 35.83 1.40
4714 4746 7.078228 GTGTCACTGAAATTTGTCATCCTTAC 58.922 38.462 0.00 0.00 0.00 2.34
4715 4747 6.770303 TGTCACTGAAATTTGTCATCCTTACA 59.230 34.615 0.00 0.00 0.00 2.41
4716 4748 7.448161 TGTCACTGAAATTTGTCATCCTTACAT 59.552 33.333 0.00 0.00 0.00 2.29
4718 4750 7.665145 TCACTGAAATTTGTCATCCTTACATGA 59.335 33.333 0.00 0.00 0.00 3.07
4720 4752 9.028284 ACTGAAATTTGTCATCCTTACATGATT 57.972 29.630 0.00 0.00 35.23 2.57
4721 4753 9.297586 CTGAAATTTGTCATCCTTACATGATTG 57.702 33.333 0.00 0.00 35.23 2.67
4722 4754 8.252417 TGAAATTTGTCATCCTTACATGATTGG 58.748 33.333 0.00 0.00 35.23 3.16
4740 4969 3.574284 TGGAATTGCCATCAAAAGACG 57.426 42.857 0.00 0.00 43.33 4.18
4765 4994 2.104859 CCTGAGTGCCACGCATCTG 61.105 63.158 0.63 0.00 41.91 2.90
4767 4996 1.357258 CTGAGTGCCACGCATCTGAC 61.357 60.000 0.63 0.00 41.91 3.51
4768 4997 2.433145 AGTGCCACGCATCTGACG 60.433 61.111 0.00 0.00 41.91 4.35
4781 5034 2.238942 TCTGACGTGTGACAAGCATT 57.761 45.000 0.00 0.00 0.00 3.56
4889 6616 0.250793 TTCGGAGCGGCAAATCCTAA 59.749 50.000 1.45 0.00 33.12 2.69
5144 6871 4.982241 TCTTTCTCCCATCTCTTGTGTT 57.018 40.909 0.00 0.00 0.00 3.32
5229 6956 0.743345 AAGAACCGCCGATGCCTTAC 60.743 55.000 0.00 0.00 0.00 2.34
5270 6997 7.497249 AGAGAGGAGTTTTCGATGGATTAATTG 59.503 37.037 0.00 0.00 0.00 2.32
5271 6998 7.338710 AGAGGAGTTTTCGATGGATTAATTGA 58.661 34.615 0.00 0.00 0.00 2.57
5272 6999 7.995488 AGAGGAGTTTTCGATGGATTAATTGAT 59.005 33.333 0.00 0.00 0.00 2.57
5273 7000 8.525290 AGGAGTTTTCGATGGATTAATTGATT 57.475 30.769 0.00 0.00 0.00 2.57
5274 7001 9.627123 AGGAGTTTTCGATGGATTAATTGATTA 57.373 29.630 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.387929 TAACGGCGCCTCAAGATAGG 59.612 55.000 26.68 7.84 39.87 2.57
2 3 1.488527 GTAACGGCGCCTCAAGATAG 58.511 55.000 26.68 8.67 0.00 2.08
3 4 0.103572 GGTAACGGCGCCTCAAGATA 59.896 55.000 26.68 4.81 0.00 1.98
4 5 1.153429 GGTAACGGCGCCTCAAGAT 60.153 57.895 26.68 5.92 0.00 2.40
5 6 2.263540 GGTAACGGCGCCTCAAGA 59.736 61.111 26.68 1.62 0.00 3.02
6 7 2.818274 GGGTAACGGCGCCTCAAG 60.818 66.667 26.68 11.62 37.60 3.02
7 8 4.745751 CGGGTAACGGCGCCTCAA 62.746 66.667 26.68 6.07 39.42 3.02
9 10 3.938019 TTTCGGGTAACGGCGCCTC 62.938 63.158 26.68 11.81 44.45 4.70
10 11 3.945304 CTTTCGGGTAACGGCGCCT 62.945 63.158 26.68 9.55 44.45 5.52
11 12 3.493440 CTTTCGGGTAACGGCGCC 61.493 66.667 19.07 19.07 44.45 6.53
12 13 3.493440 CCTTTCGGGTAACGGCGC 61.493 66.667 6.90 0.00 44.45 6.53
13 14 2.816520 CCCTTTCGGGTAACGGCG 60.817 66.667 4.80 4.80 46.12 6.46
22 23 1.173913 GGGTTGTCAATCCCTTTCGG 58.826 55.000 3.15 0.00 40.48 4.30
23 24 1.173913 GGGGTTGTCAATCCCTTTCG 58.826 55.000 24.72 0.00 43.00 3.46
28 29 3.502356 TGTTAAAGGGGTTGTCAATCCC 58.498 45.455 24.64 24.64 42.73 3.85
29 30 4.081697 CCATGTTAAAGGGGTTGTCAATCC 60.082 45.833 6.29 6.29 0.00 3.01
30 31 4.620567 GCCATGTTAAAGGGGTTGTCAATC 60.621 45.833 0.00 0.00 0.00 2.67
31 32 3.260632 GCCATGTTAAAGGGGTTGTCAAT 59.739 43.478 0.00 0.00 0.00 2.57
32 33 2.630580 GCCATGTTAAAGGGGTTGTCAA 59.369 45.455 0.00 0.00 0.00 3.18
33 34 2.243810 GCCATGTTAAAGGGGTTGTCA 58.756 47.619 0.00 0.00 0.00 3.58
34 35 1.201414 CGCCATGTTAAAGGGGTTGTC 59.799 52.381 0.00 0.00 33.55 3.18
35 36 1.253100 CGCCATGTTAAAGGGGTTGT 58.747 50.000 0.00 0.00 33.55 3.32
36 37 0.530288 CCGCCATGTTAAAGGGGTTG 59.470 55.000 0.00 0.00 36.21 3.77
37 38 0.613572 CCCGCCATGTTAAAGGGGTT 60.614 55.000 0.00 0.00 38.44 4.11
38 39 1.000145 CCCGCCATGTTAAAGGGGT 60.000 57.895 0.00 0.00 38.44 4.95
39 40 0.613572 AACCCGCCATGTTAAAGGGG 60.614 55.000 3.73 4.60 46.10 4.79
41 42 0.108851 GCAACCCGCCATGTTAAAGG 60.109 55.000 0.00 0.00 32.94 3.11
42 43 0.455972 CGCAACCCGCCATGTTAAAG 60.456 55.000 0.00 0.00 37.30 1.85
43 44 0.889638 TCGCAACCCGCCATGTTAAA 60.890 50.000 0.00 0.00 37.30 1.52
44 45 1.302383 CTCGCAACCCGCCATGTTAA 61.302 55.000 0.00 0.00 37.30 2.01
45 46 1.743623 CTCGCAACCCGCCATGTTA 60.744 57.895 0.00 0.00 37.30 2.41
46 47 3.055719 CTCGCAACCCGCCATGTT 61.056 61.111 0.00 0.00 37.30 2.71
48 49 4.776322 TCCTCGCAACCCGCCATG 62.776 66.667 0.00 0.00 37.30 3.66
49 50 2.837031 AAATCCTCGCAACCCGCCAT 62.837 55.000 0.00 0.00 37.30 4.40
50 51 3.561120 AAATCCTCGCAACCCGCCA 62.561 57.895 0.00 0.00 37.30 5.69
51 52 2.750237 AAATCCTCGCAACCCGCC 60.750 61.111 0.00 0.00 37.30 6.13
52 53 1.862602 AACAAATCCTCGCAACCCGC 61.863 55.000 0.00 0.00 36.73 6.13
53 54 1.444836 TAACAAATCCTCGCAACCCG 58.555 50.000 0.00 0.00 38.61 5.28
54 55 3.065371 CAGATAACAAATCCTCGCAACCC 59.935 47.826 0.00 0.00 0.00 4.11
55 56 3.689649 ACAGATAACAAATCCTCGCAACC 59.310 43.478 0.00 0.00 0.00 3.77
56 57 4.154195 ACACAGATAACAAATCCTCGCAAC 59.846 41.667 0.00 0.00 0.00 4.17
57 58 4.154015 CACACAGATAACAAATCCTCGCAA 59.846 41.667 0.00 0.00 0.00 4.85
58 59 3.684305 CACACAGATAACAAATCCTCGCA 59.316 43.478 0.00 0.00 0.00 5.10
59 60 3.063997 CCACACAGATAACAAATCCTCGC 59.936 47.826 0.00 0.00 0.00 5.03
60 61 4.503910 TCCACACAGATAACAAATCCTCG 58.496 43.478 0.00 0.00 0.00 4.63
61 62 4.878397 CCTCCACACAGATAACAAATCCTC 59.122 45.833 0.00 0.00 0.00 3.71
62 63 4.324563 CCCTCCACACAGATAACAAATCCT 60.325 45.833 0.00 0.00 0.00 3.24
63 64 3.947834 CCCTCCACACAGATAACAAATCC 59.052 47.826 0.00 0.00 0.00 3.01
64 65 3.947834 CCCCTCCACACAGATAACAAATC 59.052 47.826 0.00 0.00 0.00 2.17
65 66 3.333680 ACCCCTCCACACAGATAACAAAT 59.666 43.478 0.00 0.00 0.00 2.32
66 67 2.714250 ACCCCTCCACACAGATAACAAA 59.286 45.455 0.00 0.00 0.00 2.83
67 68 2.344592 ACCCCTCCACACAGATAACAA 58.655 47.619 0.00 0.00 0.00 2.83
68 69 2.038863 ACCCCTCCACACAGATAACA 57.961 50.000 0.00 0.00 0.00 2.41
69 70 2.039879 ACAACCCCTCCACACAGATAAC 59.960 50.000 0.00 0.00 0.00 1.89
70 71 2.344592 ACAACCCCTCCACACAGATAA 58.655 47.619 0.00 0.00 0.00 1.75
71 72 2.038863 ACAACCCCTCCACACAGATA 57.961 50.000 0.00 0.00 0.00 1.98
72 73 1.149101 AACAACCCCTCCACACAGAT 58.851 50.000 0.00 0.00 0.00 2.90
73 74 0.923358 AAACAACCCCTCCACACAGA 59.077 50.000 0.00 0.00 0.00 3.41
74 75 1.775385 AAAACAACCCCTCCACACAG 58.225 50.000 0.00 0.00 0.00 3.66
75 76 3.226777 CATAAAACAACCCCTCCACACA 58.773 45.455 0.00 0.00 0.00 3.72
76 77 3.227614 ACATAAAACAACCCCTCCACAC 58.772 45.455 0.00 0.00 0.00 3.82
77 78 3.603965 ACATAAAACAACCCCTCCACA 57.396 42.857 0.00 0.00 0.00 4.17
78 79 3.639561 ACAACATAAAACAACCCCTCCAC 59.360 43.478 0.00 0.00 0.00 4.02
79 80 3.639094 CACAACATAAAACAACCCCTCCA 59.361 43.478 0.00 0.00 0.00 3.86
80 81 3.639561 ACACAACATAAAACAACCCCTCC 59.360 43.478 0.00 0.00 0.00 4.30
81 82 4.929819 ACACAACATAAAACAACCCCTC 57.070 40.909 0.00 0.00 0.00 4.30
82 83 4.682050 GCAACACAACATAAAACAACCCCT 60.682 41.667 0.00 0.00 0.00 4.79
83 84 3.558006 GCAACACAACATAAAACAACCCC 59.442 43.478 0.00 0.00 0.00 4.95
84 85 4.438148 AGCAACACAACATAAAACAACCC 58.562 39.130 0.00 0.00 0.00 4.11
85 86 5.578727 TCAAGCAACACAACATAAAACAACC 59.421 36.000 0.00 0.00 0.00 3.77
86 87 6.639671 TCAAGCAACACAACATAAAACAAC 57.360 33.333 0.00 0.00 0.00 3.32
87 88 7.763528 AGAATCAAGCAACACAACATAAAACAA 59.236 29.630 0.00 0.00 0.00 2.83
88 89 7.264221 AGAATCAAGCAACACAACATAAAACA 58.736 30.769 0.00 0.00 0.00 2.83
89 90 7.096065 GGAGAATCAAGCAACACAACATAAAAC 60.096 37.037 0.00 0.00 36.25 2.43
90 91 6.922957 GGAGAATCAAGCAACACAACATAAAA 59.077 34.615 0.00 0.00 36.25 1.52
91 92 6.265196 AGGAGAATCAAGCAACACAACATAAA 59.735 34.615 0.00 0.00 36.25 1.40
92 93 5.769662 AGGAGAATCAAGCAACACAACATAA 59.230 36.000 0.00 0.00 36.25 1.90
93 94 5.316167 AGGAGAATCAAGCAACACAACATA 58.684 37.500 0.00 0.00 36.25 2.29
94 95 4.147321 AGGAGAATCAAGCAACACAACAT 58.853 39.130 0.00 0.00 36.25 2.71
95 96 3.554934 AGGAGAATCAAGCAACACAACA 58.445 40.909 0.00 0.00 36.25 3.33
96 97 4.757149 AGTAGGAGAATCAAGCAACACAAC 59.243 41.667 0.00 0.00 36.25 3.32
97 98 4.756642 CAGTAGGAGAATCAAGCAACACAA 59.243 41.667 0.00 0.00 36.25 3.33
98 99 4.318332 CAGTAGGAGAATCAAGCAACACA 58.682 43.478 0.00 0.00 36.25 3.72
99 100 3.686726 CCAGTAGGAGAATCAAGCAACAC 59.313 47.826 0.00 0.00 36.25 3.32
100 101 3.327757 ACCAGTAGGAGAATCAAGCAACA 59.672 43.478 0.00 0.00 38.69 3.33
101 102 3.944087 ACCAGTAGGAGAATCAAGCAAC 58.056 45.455 0.00 0.00 38.69 4.17
102 103 4.579869 GAACCAGTAGGAGAATCAAGCAA 58.420 43.478 0.00 0.00 38.69 3.91
103 104 3.368427 CGAACCAGTAGGAGAATCAAGCA 60.368 47.826 0.00 0.00 38.69 3.91
104 105 3.119101 TCGAACCAGTAGGAGAATCAAGC 60.119 47.826 0.00 0.00 38.69 4.01
105 106 4.720649 TCGAACCAGTAGGAGAATCAAG 57.279 45.455 0.00 0.00 38.69 3.02
106 107 6.785337 TTATCGAACCAGTAGGAGAATCAA 57.215 37.500 0.00 0.00 38.69 2.57
107 108 6.778069 AGATTATCGAACCAGTAGGAGAATCA 59.222 38.462 15.07 0.00 38.69 2.57
108 109 7.222000 AGATTATCGAACCAGTAGGAGAATC 57.778 40.000 0.00 8.92 38.69 2.52
109 110 7.437748 CAAGATTATCGAACCAGTAGGAGAAT 58.562 38.462 0.00 0.00 38.69 2.40
110 111 6.183360 CCAAGATTATCGAACCAGTAGGAGAA 60.183 42.308 0.00 0.00 38.69 2.87
111 112 5.302059 CCAAGATTATCGAACCAGTAGGAGA 59.698 44.000 0.00 0.00 38.69 3.71
112 113 5.069251 ACCAAGATTATCGAACCAGTAGGAG 59.931 44.000 0.00 0.00 38.69 3.69
113 114 4.960469 ACCAAGATTATCGAACCAGTAGGA 59.040 41.667 0.00 0.00 38.69 2.94
114 115 5.277857 ACCAAGATTATCGAACCAGTAGG 57.722 43.478 0.00 0.00 42.21 3.18
115 116 6.816640 TGAAACCAAGATTATCGAACCAGTAG 59.183 38.462 0.00 0.00 0.00 2.57
116 117 6.703319 TGAAACCAAGATTATCGAACCAGTA 58.297 36.000 0.00 0.00 0.00 2.74
117 118 5.556915 TGAAACCAAGATTATCGAACCAGT 58.443 37.500 0.00 0.00 0.00 4.00
118 119 6.683974 ATGAAACCAAGATTATCGAACCAG 57.316 37.500 0.00 0.00 0.00 4.00
119 120 7.444183 GGATATGAAACCAAGATTATCGAACCA 59.556 37.037 0.00 0.00 0.00 3.67
120 121 7.360101 CGGATATGAAACCAAGATTATCGAACC 60.360 40.741 0.00 0.00 0.00 3.62
121 122 7.384115 TCGGATATGAAACCAAGATTATCGAAC 59.616 37.037 0.00 0.00 0.00 3.95
122 123 7.438564 TCGGATATGAAACCAAGATTATCGAA 58.561 34.615 0.00 0.00 0.00 3.71
123 124 6.988522 TCGGATATGAAACCAAGATTATCGA 58.011 36.000 0.00 0.00 0.00 3.59
124 125 6.311445 CCTCGGATATGAAACCAAGATTATCG 59.689 42.308 0.00 0.00 0.00 2.92
125 126 6.595716 CCCTCGGATATGAAACCAAGATTATC 59.404 42.308 0.00 0.00 0.00 1.75
126 127 6.272324 TCCCTCGGATATGAAACCAAGATTAT 59.728 38.462 0.00 0.00 0.00 1.28
127 128 5.605069 TCCCTCGGATATGAAACCAAGATTA 59.395 40.000 0.00 0.00 0.00 1.75
128 129 4.412199 TCCCTCGGATATGAAACCAAGATT 59.588 41.667 0.00 0.00 0.00 2.40
129 130 3.973973 TCCCTCGGATATGAAACCAAGAT 59.026 43.478 0.00 0.00 0.00 2.40
130 131 3.380393 TCCCTCGGATATGAAACCAAGA 58.620 45.455 0.00 0.00 0.00 3.02
131 132 3.838244 TCCCTCGGATATGAAACCAAG 57.162 47.619 0.00 0.00 0.00 3.61
132 133 4.577988 TTTCCCTCGGATATGAAACCAA 57.422 40.909 0.00 0.00 0.00 3.67
133 134 4.788925 ATTTCCCTCGGATATGAAACCA 57.211 40.909 0.00 0.00 30.27 3.67
134 135 5.001874 GGTATTTCCCTCGGATATGAAACC 58.998 45.833 0.00 0.00 30.27 3.27
135 136 5.866207 AGGTATTTCCCTCGGATATGAAAC 58.134 41.667 0.00 0.00 36.75 2.78
136 137 6.013984 GGTAGGTATTTCCCTCGGATATGAAA 60.014 42.308 0.00 0.00 35.97 2.69
137 138 5.482878 GGTAGGTATTTCCCTCGGATATGAA 59.517 44.000 0.00 0.00 35.97 2.57
138 139 5.021458 GGTAGGTATTTCCCTCGGATATGA 58.979 45.833 0.00 0.00 35.97 2.15
139 140 5.024118 AGGTAGGTATTTCCCTCGGATATG 58.976 45.833 0.00 0.00 35.97 1.78
140 141 5.016459 AGAGGTAGGTATTTCCCTCGGATAT 59.984 44.000 0.00 0.00 46.53 1.63
141 142 4.356190 AGAGGTAGGTATTTCCCTCGGATA 59.644 45.833 0.00 0.00 46.53 2.59
142 143 3.142407 AGAGGTAGGTATTTCCCTCGGAT 59.858 47.826 0.00 0.00 46.53 4.18
143 144 2.517127 AGAGGTAGGTATTTCCCTCGGA 59.483 50.000 0.00 0.00 46.53 4.55
144 145 2.628657 CAGAGGTAGGTATTTCCCTCGG 59.371 54.545 0.00 0.00 46.53 4.63
145 146 3.297736 ACAGAGGTAGGTATTTCCCTCG 58.702 50.000 0.00 0.00 46.53 4.63
146 147 4.470304 ACAACAGAGGTAGGTATTTCCCTC 59.530 45.833 0.00 0.00 43.14 4.30
147 148 4.225267 CACAACAGAGGTAGGTATTTCCCT 59.775 45.833 0.00 0.00 38.70 4.20
148 149 4.514401 CACAACAGAGGTAGGTATTTCCC 58.486 47.826 0.00 0.00 36.75 3.97
149 150 3.939592 GCACAACAGAGGTAGGTATTTCC 59.060 47.826 0.00 0.00 0.00 3.13
150 151 4.631813 CAGCACAACAGAGGTAGGTATTTC 59.368 45.833 0.00 0.00 0.00 2.17
151 152 4.579869 CAGCACAACAGAGGTAGGTATTT 58.420 43.478 0.00 0.00 0.00 1.40
152 153 3.619979 GCAGCACAACAGAGGTAGGTATT 60.620 47.826 0.00 0.00 0.00 1.89
153 154 2.093447 GCAGCACAACAGAGGTAGGTAT 60.093 50.000 0.00 0.00 0.00 2.73
154 155 1.275291 GCAGCACAACAGAGGTAGGTA 59.725 52.381 0.00 0.00 0.00 3.08
155 156 0.035458 GCAGCACAACAGAGGTAGGT 59.965 55.000 0.00 0.00 0.00 3.08
156 157 0.035317 TGCAGCACAACAGAGGTAGG 59.965 55.000 0.00 0.00 0.00 3.18
157 158 2.005451 GATGCAGCACAACAGAGGTAG 58.995 52.381 0.00 0.00 0.00 3.18
158 159 1.347378 TGATGCAGCACAACAGAGGTA 59.653 47.619 0.00 0.00 0.00 3.08
159 160 0.109153 TGATGCAGCACAACAGAGGT 59.891 50.000 0.00 0.00 0.00 3.85
160 161 1.400846 GATGATGCAGCACAACAGAGG 59.599 52.381 6.89 0.00 34.17 3.69
161 162 1.400846 GGATGATGCAGCACAACAGAG 59.599 52.381 6.89 0.00 34.17 3.35
162 163 1.456296 GGATGATGCAGCACAACAGA 58.544 50.000 6.89 0.00 34.17 3.41
163 164 0.454600 GGGATGATGCAGCACAACAG 59.545 55.000 6.89 0.00 34.17 3.16
164 165 0.038599 AGGGATGATGCAGCACAACA 59.961 50.000 6.89 0.00 35.29 3.33
165 166 1.133790 GAAGGGATGATGCAGCACAAC 59.866 52.381 6.89 1.52 0.00 3.32
166 167 1.466856 GAAGGGATGATGCAGCACAA 58.533 50.000 6.89 0.00 0.00 3.33
167 168 0.394762 GGAAGGGATGATGCAGCACA 60.395 55.000 6.89 0.00 0.00 4.57
168 169 0.106819 AGGAAGGGATGATGCAGCAC 60.107 55.000 6.89 0.81 0.00 4.40
169 170 0.182061 GAGGAAGGGATGATGCAGCA 59.818 55.000 7.31 7.31 0.00 4.41
170 171 0.473326 AGAGGAAGGGATGATGCAGC 59.527 55.000 0.00 0.00 0.00 5.25
171 172 2.950309 CAAAGAGGAAGGGATGATGCAG 59.050 50.000 0.00 0.00 0.00 4.41
172 173 2.577563 TCAAAGAGGAAGGGATGATGCA 59.422 45.455 0.00 0.00 0.00 3.96
173 174 3.212685 CTCAAAGAGGAAGGGATGATGC 58.787 50.000 0.00 0.00 0.00 3.91
186 187 6.825721 AGCTATGTTGGTATTTCCTCAAAGAG 59.174 38.462 0.00 0.00 37.07 2.85
187 188 6.721318 AGCTATGTTGGTATTTCCTCAAAGA 58.279 36.000 0.00 0.00 37.07 2.52
188 189 7.396540 AAGCTATGTTGGTATTTCCTCAAAG 57.603 36.000 0.00 0.00 37.07 2.77
189 190 6.093495 CGAAGCTATGTTGGTATTTCCTCAAA 59.907 38.462 0.00 0.00 37.07 2.69
190 191 5.584649 CGAAGCTATGTTGGTATTTCCTCAA 59.415 40.000 0.00 0.00 37.07 3.02
191 192 5.105106 TCGAAGCTATGTTGGTATTTCCTCA 60.105 40.000 0.00 0.00 37.07 3.86
192 193 5.357257 TCGAAGCTATGTTGGTATTTCCTC 58.643 41.667 0.00 0.00 37.07 3.71
193 194 5.353394 TCGAAGCTATGTTGGTATTTCCT 57.647 39.130 0.00 0.00 37.07 3.36
194 195 4.024809 GCTCGAAGCTATGTTGGTATTTCC 60.025 45.833 0.00 0.00 38.45 3.13
195 196 4.024809 GGCTCGAAGCTATGTTGGTATTTC 60.025 45.833 6.78 0.00 41.99 2.17
196 197 3.877508 GGCTCGAAGCTATGTTGGTATTT 59.122 43.478 6.78 0.00 41.99 1.40
197 198 3.467803 GGCTCGAAGCTATGTTGGTATT 58.532 45.455 6.78 0.00 41.99 1.89
198 199 2.545952 CGGCTCGAAGCTATGTTGGTAT 60.546 50.000 6.78 0.00 41.99 2.73
199 200 1.202371 CGGCTCGAAGCTATGTTGGTA 60.202 52.381 6.78 0.00 41.99 3.25
200 201 0.460284 CGGCTCGAAGCTATGTTGGT 60.460 55.000 6.78 0.00 41.99 3.67
201 202 1.766143 GCGGCTCGAAGCTATGTTGG 61.766 60.000 6.78 0.00 41.99 3.77
202 203 1.083806 TGCGGCTCGAAGCTATGTTG 61.084 55.000 0.00 0.00 41.99 3.33
203 204 0.179073 ATGCGGCTCGAAGCTATGTT 60.179 50.000 0.00 0.00 41.99 2.71
204 205 0.598680 GATGCGGCTCGAAGCTATGT 60.599 55.000 0.00 0.00 41.99 2.29
205 206 0.598419 TGATGCGGCTCGAAGCTATG 60.598 55.000 0.00 0.00 41.99 2.23
206 207 0.319383 CTGATGCGGCTCGAAGCTAT 60.319 55.000 0.00 1.86 41.99 2.97
207 208 1.066422 CTGATGCGGCTCGAAGCTA 59.934 57.895 0.00 0.00 41.99 3.32
208 209 2.202851 CTGATGCGGCTCGAAGCT 60.203 61.111 0.00 0.00 41.99 3.74
209 210 3.934684 GCTGATGCGGCTCGAAGC 61.935 66.667 0.00 1.69 41.46 3.86
210 211 2.202851 AGCTGATGCGGCTCGAAG 60.203 61.111 0.00 0.00 43.23 3.79
211 212 2.510012 CAGCTGATGCGGCTCGAA 60.510 61.111 8.42 0.00 43.23 3.71
221 222 4.827087 CTCGCGGTGGCAGCTGAT 62.827 66.667 20.43 0.00 39.92 2.90
267 268 2.878429 GCTCGCGACTGAAGAGGA 59.122 61.111 3.71 0.00 32.96 3.71
320 321 0.683504 ACGAATAGCGGTGGAGGAGT 60.684 55.000 0.00 0.00 46.49 3.85
387 388 2.203070 GAGCGGCGGTCAATGGAT 60.203 61.111 31.62 0.00 0.00 3.41
597 600 1.887797 ATTTGTATCCCCTCCGGTGA 58.112 50.000 4.76 0.00 0.00 4.02
1145 1150 1.325355 CAGGCTAGGGATTGCAATGG 58.675 55.000 18.59 0.00 0.00 3.16
1191 1196 1.134753 CAACTGCAACAGCAACAAGGA 59.865 47.619 0.00 0.00 37.91 3.36
1223 1228 1.669115 GCGCCAGAGAGCAAAGACA 60.669 57.895 0.00 0.00 38.88 3.41
1395 1400 2.431782 AGAGCAAGCAAAGGAAAAGCAA 59.568 40.909 0.00 0.00 0.00 3.91
1535 1540 2.578940 CCCACCCTTATTTACACCTGGA 59.421 50.000 0.00 0.00 0.00 3.86
1603 1608 5.705609 ATTACTGACTTTTTGCACGGATT 57.294 34.783 0.00 0.00 0.00 3.01
1607 1612 6.086222 AGCATTATTACTGACTTTTTGCACG 58.914 36.000 0.00 0.00 0.00 5.34
1709 1715 2.309755 TGCCCTGGAAATCACAGAGAAT 59.690 45.455 0.00 0.00 38.20 2.40
1712 1718 1.815003 GTTGCCCTGGAAATCACAGAG 59.185 52.381 0.00 0.00 38.20 3.35
2074 2080 9.309516 GAACTATGGTAATAATCAAGAACACGA 57.690 33.333 0.00 0.00 0.00 4.35
2109 2115 0.725117 ACGCACAATTAACGCCTAGC 59.275 50.000 0.00 0.00 0.00 3.42
2178 2184 3.426695 GCGCTGAATTGTGCTTAATCTGT 60.427 43.478 0.00 0.00 40.01 3.41
2272 2278 5.457148 GCTGACGTGTCTCTATTTGATACTG 59.543 44.000 0.00 0.00 0.00 2.74
2273 2279 5.125578 TGCTGACGTGTCTCTATTTGATACT 59.874 40.000 0.00 0.00 0.00 2.12
2274 2280 5.340803 TGCTGACGTGTCTCTATTTGATAC 58.659 41.667 0.00 0.00 0.00 2.24
2275 2281 5.576447 TGCTGACGTGTCTCTATTTGATA 57.424 39.130 0.00 0.00 0.00 2.15
2276 2282 4.456280 TGCTGACGTGTCTCTATTTGAT 57.544 40.909 0.00 0.00 0.00 2.57
2303 2309 4.504916 CGCTCTAGGCTGCGCAGT 62.505 66.667 35.80 21.44 45.50 4.40
2320 2329 2.423538 CACTACAGTGCATAAAAGGCCC 59.576 50.000 0.00 0.00 39.39 5.80
2383 2392 5.460419 TGATTCAACAATTTGGTTTACGTGC 59.540 36.000 0.00 0.00 33.06 5.34
2401 2411 4.365899 GCACATGCAGAAGAATGATTCA 57.634 40.909 8.03 0.00 41.59 2.57
2460 2470 8.782339 TTTAGTAACGGAAAGGAGGAAAATAG 57.218 34.615 0.00 0.00 0.00 1.73
2595 2605 0.941463 AAGAAGAGCAGCACACGTCG 60.941 55.000 0.00 0.00 0.00 5.12
2621 2631 5.565509 AGGAGATGAAAAGGAGAAAAGACC 58.434 41.667 0.00 0.00 0.00 3.85
2811 2821 6.334989 GGGTAAAAACTGCAAACTTACTTGT 58.665 36.000 0.00 0.00 0.00 3.16
2841 2851 6.884832 TGTCCGGAAATACATGTCTCTTAAT 58.115 36.000 5.23 0.00 0.00 1.40
2899 2909 7.446625 ACCAGCATAAAGAGGAATTATAGCAAG 59.553 37.037 0.00 0.00 0.00 4.01
3022 3033 0.957395 AAGTGGCCAGCAATCTGTCG 60.957 55.000 5.11 0.00 38.66 4.35
3028 3039 4.202451 ACCATTTTAAAAGTGGCCAGCAAT 60.202 37.500 5.11 0.00 36.47 3.56
3345 3356 0.107456 CAGGACAGTGCCAGTTGTCT 59.893 55.000 8.62 0.00 42.52 3.41
3414 3437 0.098200 CATGCAGGCTGTCATGAACG 59.902 55.000 30.90 14.94 41.82 3.95
4084 4107 3.244805 CGTCCCTTCCTTTTCCTTTACCT 60.245 47.826 0.00 0.00 0.00 3.08
4541 4566 9.203421 CGTGTGGCACTTATATCAGAATAATAA 57.797 33.333 19.83 0.00 31.34 1.40
4555 4580 1.000060 GTACCTGACGTGTGGCACTTA 60.000 52.381 19.83 0.00 31.34 2.24
4556 4581 0.249741 GTACCTGACGTGTGGCACTT 60.250 55.000 19.83 2.72 31.34 3.16
4601 4626 8.681806 TCCTCGCATCACAAAATTTATCATAAA 58.318 29.630 0.00 0.00 0.00 1.40
4608 4633 5.414144 TGTCATCCTCGCATCACAAAATTTA 59.586 36.000 0.00 0.00 0.00 1.40
4611 4636 3.346315 TGTCATCCTCGCATCACAAAAT 58.654 40.909 0.00 0.00 0.00 1.82
4615 4640 1.276138 AGTTGTCATCCTCGCATCACA 59.724 47.619 0.00 0.00 0.00 3.58
4681 4713 4.955925 AATTTCAGTGACACACGACAAA 57.044 36.364 8.59 0.00 39.64 2.83
4686 4718 4.271590 TGACAAATTTCAGTGACACACG 57.728 40.909 8.59 0.00 39.64 4.49
4687 4719 5.009010 AGGATGACAAATTTCAGTGACACAC 59.991 40.000 8.59 0.00 34.10 3.82
4721 4753 3.575965 ACGTCTTTTGATGGCAATTCC 57.424 42.857 0.00 0.00 39.68 3.01
4722 4754 5.516339 CCATTACGTCTTTTGATGGCAATTC 59.484 40.000 0.00 0.00 39.68 2.17
4733 4962 3.074412 CACTCAGGCCATTACGTCTTTT 58.926 45.455 5.01 0.00 0.00 2.27
4734 4963 2.699954 CACTCAGGCCATTACGTCTTT 58.300 47.619 5.01 0.00 0.00 2.52
4737 4966 2.384203 GCACTCAGGCCATTACGTC 58.616 57.895 5.01 0.00 0.00 4.34
4762 4991 1.866601 CAATGCTTGTCACACGTCAGA 59.133 47.619 0.00 0.00 0.00 3.27
4765 4994 0.944386 ACCAATGCTTGTCACACGTC 59.056 50.000 0.00 0.00 0.00 4.34
4767 4996 0.662619 ACACCAATGCTTGTCACACG 59.337 50.000 0.00 0.00 0.00 4.49
4768 4997 2.869233 AACACCAATGCTTGTCACAC 57.131 45.000 0.00 0.00 0.00 3.82
4772 5001 4.846779 TCCTTAAACACCAATGCTTGTC 57.153 40.909 0.00 0.00 0.00 3.18
5105 6832 1.847088 AGAAGAGAATACCAAGGCCCC 59.153 52.381 0.00 0.00 0.00 5.80
5106 6833 3.653835 AAGAAGAGAATACCAAGGCCC 57.346 47.619 0.00 0.00 0.00 5.80
5229 6956 1.135915 CTCTCTGGACGACCCATTCTG 59.864 57.143 0.34 0.00 45.57 3.02
5271 6998 9.620660 GCGTTCCGGAATCAATTAATTAATAAT 57.379 29.630 22.04 5.80 35.69 1.28
5272 6999 8.077386 GGCGTTCCGGAATCAATTAATTAATAA 58.923 33.333 22.04 3.75 0.00 1.40
5273 7000 7.586747 GGCGTTCCGGAATCAATTAATTAATA 58.413 34.615 22.04 0.00 0.00 0.98
5274 7001 6.443792 GGCGTTCCGGAATCAATTAATTAAT 58.556 36.000 22.04 4.81 0.00 1.40
5275 7002 5.823353 GGCGTTCCGGAATCAATTAATTAA 58.177 37.500 22.04 0.00 0.00 1.40
5276 7003 5.427036 GGCGTTCCGGAATCAATTAATTA 57.573 39.130 22.04 0.00 0.00 1.40
5277 7004 4.301637 GGCGTTCCGGAATCAATTAATT 57.698 40.909 22.04 0.00 0.00 1.40
5278 7005 3.982576 GGCGTTCCGGAATCAATTAAT 57.017 42.857 22.04 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.