Multiple sequence alignment - TraesCS3D01G215900

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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 TraesCS3D01G215900 chr3D 100.000 5075 0 0 1 5075 292030945 292025871 0.000000e+00 9372.0
1 TraesCS3D01G215900 chr3A 95.357 4932 112 40 178 5060 387295479 387300342 0.000000e+00 7731.0
2 TraesCS3D01G215900 chr3B 94.727 4779 123 30 374 5075 385467471 385462745 0.000000e+00 7310.0
3 TraesCS3D01G215900 chr2A 73.607 682 172 6 2485 3165 38966787 38967461 6.520000e-64 255.0
4 TraesCS3D01G215900 chr2D 72.328 683 182 5 2485 3165 35782822 35783499 1.850000e-49 207.0
5 TraesCS3D01G215900 chr1B 88.406 69 6 1 1 69 623195740 623195674 1.170000e-11 82.4
6 TraesCS3D01G215900 chr1D 97.297 37 1 0 3426 3462 18429087 18429123 4.240000e-06 63.9
7 TraesCS3D01G215900 chr6B 94.286 35 2 0 27 61 581573914 581573880 3.000000e-03 54.7
8 TraesCS3D01G215900 chr5D 94.118 34 2 0 27 60 80291463 80291430 9.000000e-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 TraesCS3D01G215900 chr3D 292025871 292030945 5074 True 9372 9372 100.000 1 5075 1 chr3D.!!$R1 5074
1 TraesCS3D01G215900 chr3A 387295479 387300342 4863 False 7731 7731 95.357 178 5060 1 chr3A.!!$F1 4882
2 TraesCS3D01G215900 chr3B 385462745 385467471 4726 True 7310 7310 94.727 374 5075 1 chr3B.!!$R1 4701
3 TraesCS3D01G215900 chr2A 38966787 38967461 674 False 255 255 73.607 2485 3165 1 chr2A.!!$F1 680
4 TraesCS3D01G215900 chr2D 35782822 35783499 677 False 207 207 72.328 2485 3165 1 chr2D.!!$F1 680

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
127 128 0.167908 CACACACACACACACACACC 59.832 55.0 0.00 0.0 0.00 4.16 F
133 134 0.179020 CACACACACACACCCTGGAT 60.179 55.0 0.00 0.0 0.00 3.41 F
1534 1556 0.184933 AGTACCAAAGCAGGCACCAA 59.815 50.0 0.00 0.0 0.00 3.67 F
2235 2293 1.696097 ATGATGCCAGTACCCCGGTC 61.696 60.0 0.00 0.0 0.00 4.79 F
3336 3400 1.172812 AGAAACAGAAAGGCGGCACC 61.173 55.0 13.08 0.0 39.61 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1684 0.389948 GTGGTTCACCTCCTGCTACG 60.390 60.0 0.00 0.0 36.82 3.51 R
2000 2058 0.825840 TTCAACCCCGCTTTTCCCAG 60.826 55.0 0.00 0.0 0.00 4.45 R
3316 3380 0.238553 GTGCCGCCTTTCTGTTTCTC 59.761 55.0 0.00 0.0 0.00 2.87 R
3717 3781 0.370273 CTCGCGGGTGAATTTCGAAG 59.630 55.0 6.13 0.0 0.00 3.79 R
4169 4233 0.824109 TCTCCCCTGCAGATAACACG 59.176 55.0 17.39 0.0 0.00 4.49 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
24 25 6.675987 CGTATGTAGTCTATAGTGGAAACCC 58.324 44.000 0.00 0.00 0.00 4.11
25 26 6.294397 CGTATGTAGTCTATAGTGGAAACCCC 60.294 46.154 0.00 0.00 0.00 4.95
26 27 4.950361 TGTAGTCTATAGTGGAAACCCCA 58.050 43.478 0.00 0.00 44.25 4.96
35 36 2.858787 TGGAAACCCCAAAAGGTCTT 57.141 45.000 0.00 0.00 43.29 3.01
36 37 3.975479 TGGAAACCCCAAAAGGTCTTA 57.025 42.857 0.00 0.00 43.29 2.10
37 38 4.479156 TGGAAACCCCAAAAGGTCTTAT 57.521 40.909 0.00 0.00 43.29 1.73
38 39 5.602291 TGGAAACCCCAAAAGGTCTTATA 57.398 39.130 0.00 0.00 43.29 0.98
39 40 6.160483 TGGAAACCCCAAAAGGTCTTATAT 57.840 37.500 0.00 0.00 43.29 0.86
40 41 6.566914 TGGAAACCCCAAAAGGTCTTATATT 58.433 36.000 0.00 0.00 43.29 1.28
41 42 7.020009 TGGAAACCCCAAAAGGTCTTATATTT 58.980 34.615 0.00 0.00 43.29 1.40
42 43 7.514473 TGGAAACCCCAAAAGGTCTTATATTTT 59.486 33.333 0.00 0.00 43.29 1.82
43 44 8.380099 GGAAACCCCAAAAGGTCTTATATTTTT 58.620 33.333 0.00 0.00 40.05 1.94
46 47 8.603898 ACCCCAAAAGGTCTTATATTTTTAGG 57.396 34.615 0.00 0.00 33.81 2.69
47 48 8.403474 ACCCCAAAAGGTCTTATATTTTTAGGA 58.597 33.333 0.00 0.00 33.81 2.94
48 49 9.262240 CCCCAAAAGGTCTTATATTTTTAGGAA 57.738 33.333 0.00 0.00 0.00 3.36
50 51 9.783256 CCAAAAGGTCTTATATTTTTAGGAACG 57.217 33.333 0.00 0.00 0.00 3.95
51 52 9.783256 CAAAAGGTCTTATATTTTTAGGAACGG 57.217 33.333 0.00 0.00 0.00 4.44
52 53 9.743581 AAAAGGTCTTATATTTTTAGGAACGGA 57.256 29.630 0.00 0.00 0.00 4.69
53 54 8.959705 AAGGTCTTATATTTTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
54 55 7.506971 AGGTCTTATATTTTTAGGAACGGAGG 58.493 38.462 0.00 0.00 0.00 4.30
55 56 6.709397 GGTCTTATATTTTTAGGAACGGAGGG 59.291 42.308 0.00 0.00 0.00 4.30
56 57 7.419403 GGTCTTATATTTTTAGGAACGGAGGGA 60.419 40.741 0.00 0.00 0.00 4.20
57 58 7.656542 GTCTTATATTTTTAGGAACGGAGGGAG 59.343 40.741 0.00 0.00 0.00 4.30
58 59 5.970501 ATATTTTTAGGAACGGAGGGAGT 57.029 39.130 0.00 0.00 0.00 3.85
59 60 8.551682 TTATATTTTTAGGAACGGAGGGAGTA 57.448 34.615 0.00 0.00 0.00 2.59
60 61 4.813750 TTTTTAGGAACGGAGGGAGTAG 57.186 45.455 0.00 0.00 0.00 2.57
61 62 2.449137 TTAGGAACGGAGGGAGTAGG 57.551 55.000 0.00 0.00 0.00 3.18
62 63 1.600058 TAGGAACGGAGGGAGTAGGA 58.400 55.000 0.00 0.00 0.00 2.94
63 64 0.259356 AGGAACGGAGGGAGTAGGAG 59.741 60.000 0.00 0.00 0.00 3.69
64 65 0.258194 GGAACGGAGGGAGTAGGAGA 59.742 60.000 0.00 0.00 0.00 3.71
65 66 1.133419 GGAACGGAGGGAGTAGGAGAT 60.133 57.143 0.00 0.00 0.00 2.75
66 67 2.107901 GGAACGGAGGGAGTAGGAGATA 59.892 54.545 0.00 0.00 0.00 1.98
67 68 3.436180 GGAACGGAGGGAGTAGGAGATAA 60.436 52.174 0.00 0.00 0.00 1.75
68 69 4.409187 GAACGGAGGGAGTAGGAGATAAT 58.591 47.826 0.00 0.00 0.00 1.28
69 70 4.472690 ACGGAGGGAGTAGGAGATAATT 57.527 45.455 0.00 0.00 0.00 1.40
70 71 4.153411 ACGGAGGGAGTAGGAGATAATTG 58.847 47.826 0.00 0.00 0.00 2.32
71 72 3.511934 CGGAGGGAGTAGGAGATAATTGG 59.488 52.174 0.00 0.00 0.00 3.16
72 73 4.753186 GGAGGGAGTAGGAGATAATTGGA 58.247 47.826 0.00 0.00 0.00 3.53
73 74 4.528987 GGAGGGAGTAGGAGATAATTGGAC 59.471 50.000 0.00 0.00 0.00 4.02
74 75 5.399113 GAGGGAGTAGGAGATAATTGGACT 58.601 45.833 0.00 0.00 0.00 3.85
75 76 5.399113 AGGGAGTAGGAGATAATTGGACTC 58.601 45.833 0.00 0.00 0.00 3.36
76 77 5.137082 AGGGAGTAGGAGATAATTGGACTCT 59.863 44.000 0.00 0.00 33.84 3.24
77 78 5.841783 GGGAGTAGGAGATAATTGGACTCTT 59.158 44.000 0.00 0.00 33.84 2.85
78 79 7.011382 GGGAGTAGGAGATAATTGGACTCTTA 58.989 42.308 0.00 0.00 33.84 2.10
79 80 7.039574 GGGAGTAGGAGATAATTGGACTCTTAC 60.040 44.444 15.60 15.60 40.78 2.34
80 81 7.039574 GGAGTAGGAGATAATTGGACTCTTACC 60.040 44.444 17.73 12.86 41.11 2.85
81 82 5.793030 AGGAGATAATTGGACTCTTACCG 57.207 43.478 0.00 0.00 0.00 4.02
82 83 4.039366 AGGAGATAATTGGACTCTTACCGC 59.961 45.833 0.00 0.00 0.00 5.68
83 84 4.202223 GGAGATAATTGGACTCTTACCGCA 60.202 45.833 0.00 0.00 0.00 5.69
84 85 5.353394 AGATAATTGGACTCTTACCGCAA 57.647 39.130 0.00 0.00 0.00 4.85
85 86 5.741011 AGATAATTGGACTCTTACCGCAAA 58.259 37.500 0.00 0.00 0.00 3.68
86 87 5.585047 AGATAATTGGACTCTTACCGCAAAC 59.415 40.000 0.00 0.00 0.00 2.93
87 88 2.623878 TTGGACTCTTACCGCAAACA 57.376 45.000 0.00 0.00 0.00 2.83
88 89 2.163818 TGGACTCTTACCGCAAACAG 57.836 50.000 0.00 0.00 0.00 3.16
89 90 1.689813 TGGACTCTTACCGCAAACAGA 59.310 47.619 0.00 0.00 0.00 3.41
90 91 2.067013 GGACTCTTACCGCAAACAGAC 58.933 52.381 0.00 0.00 0.00 3.51
91 92 2.288886 GGACTCTTACCGCAAACAGACT 60.289 50.000 0.00 0.00 0.00 3.24
92 93 3.391049 GACTCTTACCGCAAACAGACTT 58.609 45.455 0.00 0.00 0.00 3.01
93 94 3.391049 ACTCTTACCGCAAACAGACTTC 58.609 45.455 0.00 0.00 0.00 3.01
94 95 3.069729 ACTCTTACCGCAAACAGACTTCT 59.930 43.478 0.00 0.00 0.00 2.85
95 96 3.650139 TCTTACCGCAAACAGACTTCTC 58.350 45.455 0.00 0.00 0.00 2.87
96 97 3.321111 TCTTACCGCAAACAGACTTCTCT 59.679 43.478 0.00 0.00 0.00 3.10
97 98 4.521639 TCTTACCGCAAACAGACTTCTCTA 59.478 41.667 0.00 0.00 0.00 2.43
98 99 3.027974 ACCGCAAACAGACTTCTCTAC 57.972 47.619 0.00 0.00 0.00 2.59
99 100 2.288886 ACCGCAAACAGACTTCTCTACC 60.289 50.000 0.00 0.00 0.00 3.18
100 101 2.028930 CCGCAAACAGACTTCTCTACCT 60.029 50.000 0.00 0.00 0.00 3.08
101 102 2.989840 CGCAAACAGACTTCTCTACCTG 59.010 50.000 0.00 0.00 0.00 4.00
102 103 3.330267 GCAAACAGACTTCTCTACCTGG 58.670 50.000 0.00 0.00 0.00 4.45
103 104 3.006967 GCAAACAGACTTCTCTACCTGGA 59.993 47.826 0.00 0.00 0.00 3.86
104 105 4.503296 GCAAACAGACTTCTCTACCTGGAA 60.503 45.833 0.00 0.00 0.00 3.53
105 106 5.611374 CAAACAGACTTCTCTACCTGGAAA 58.389 41.667 0.00 0.00 0.00 3.13
106 107 4.875561 ACAGACTTCTCTACCTGGAAAC 57.124 45.455 0.00 0.00 0.00 2.78
107 108 4.223953 ACAGACTTCTCTACCTGGAAACA 58.776 43.478 0.00 0.00 39.59 2.83
108 109 4.039366 ACAGACTTCTCTACCTGGAAACAC 59.961 45.833 0.00 0.00 35.60 3.32
109 110 4.039245 CAGACTTCTCTACCTGGAAACACA 59.961 45.833 0.00 0.00 35.60 3.72
110 111 4.039366 AGACTTCTCTACCTGGAAACACAC 59.961 45.833 0.00 0.00 35.60 3.82
111 112 3.709653 ACTTCTCTACCTGGAAACACACA 59.290 43.478 0.00 0.00 35.60 3.72
112 113 3.746045 TCTCTACCTGGAAACACACAC 57.254 47.619 0.00 0.00 35.60 3.82
113 114 3.035363 TCTCTACCTGGAAACACACACA 58.965 45.455 0.00 0.00 35.60 3.72
114 115 3.131396 CTCTACCTGGAAACACACACAC 58.869 50.000 0.00 0.00 35.60 3.82
115 116 2.502130 TCTACCTGGAAACACACACACA 59.498 45.455 0.00 0.00 35.60 3.72
116 117 1.459450 ACCTGGAAACACACACACAC 58.541 50.000 0.00 0.00 35.60 3.82
117 118 1.271652 ACCTGGAAACACACACACACA 60.272 47.619 0.00 0.00 35.60 3.72
118 119 1.132262 CCTGGAAACACACACACACAC 59.868 52.381 0.00 0.00 35.60 3.82
119 120 1.809547 CTGGAAACACACACACACACA 59.190 47.619 0.00 0.00 35.60 3.72
120 121 1.537638 TGGAAACACACACACACACAC 59.462 47.619 0.00 0.00 33.40 3.82
121 122 1.537638 GGAAACACACACACACACACA 59.462 47.619 0.00 0.00 0.00 3.72
122 123 2.580589 GAAACACACACACACACACAC 58.419 47.619 0.00 0.00 0.00 3.82
123 124 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
124 125 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
125 126 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
126 127 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
127 128 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
128 129 0.958382 ACACACACACACACACACCC 60.958 55.000 0.00 0.00 0.00 4.61
129 130 0.676466 CACACACACACACACACCCT 60.676 55.000 0.00 0.00 0.00 4.34
130 131 0.676466 ACACACACACACACACCCTG 60.676 55.000 0.00 0.00 0.00 4.45
131 132 1.077787 ACACACACACACACCCTGG 60.078 57.895 0.00 0.00 0.00 4.45
132 133 1.223211 CACACACACACACCCTGGA 59.777 57.895 0.00 0.00 0.00 3.86
133 134 0.179020 CACACACACACACCCTGGAT 60.179 55.000 0.00 0.00 0.00 3.41
134 135 1.071542 CACACACACACACCCTGGATA 59.928 52.381 0.00 0.00 0.00 2.59
135 136 1.071699 ACACACACACACCCTGGATAC 59.928 52.381 0.00 0.00 0.00 2.24
136 137 1.347707 CACACACACACCCTGGATACT 59.652 52.381 0.00 0.00 37.61 2.12
137 138 2.054799 ACACACACACCCTGGATACTT 58.945 47.619 0.00 0.00 37.61 2.24
138 139 2.038557 ACACACACACCCTGGATACTTC 59.961 50.000 0.00 0.00 37.61 3.01
139 140 2.303022 CACACACACCCTGGATACTTCT 59.697 50.000 0.00 0.00 37.61 2.85
140 141 3.513912 CACACACACCCTGGATACTTCTA 59.486 47.826 0.00 0.00 37.61 2.10
141 142 4.020573 CACACACACCCTGGATACTTCTAA 60.021 45.833 0.00 0.00 37.61 2.10
142 143 4.595781 ACACACACCCTGGATACTTCTAAA 59.404 41.667 0.00 0.00 37.61 1.85
143 144 4.935808 CACACACCCTGGATACTTCTAAAC 59.064 45.833 0.00 0.00 37.61 2.01
144 145 4.844655 ACACACCCTGGATACTTCTAAACT 59.155 41.667 0.00 0.00 37.61 2.66
145 146 6.021030 ACACACCCTGGATACTTCTAAACTA 58.979 40.000 0.00 0.00 37.61 2.24
146 147 6.499350 ACACACCCTGGATACTTCTAAACTAA 59.501 38.462 0.00 0.00 37.61 2.24
147 148 7.042335 CACACCCTGGATACTTCTAAACTAAG 58.958 42.308 0.00 0.00 37.61 2.18
148 149 6.049790 CACCCTGGATACTTCTAAACTAAGC 58.950 44.000 0.00 0.00 37.61 3.09
149 150 5.965091 ACCCTGGATACTTCTAAACTAAGCT 59.035 40.000 0.00 0.00 37.61 3.74
150 151 6.444171 ACCCTGGATACTTCTAAACTAAGCTT 59.556 38.462 3.48 3.48 37.61 3.74
151 152 7.622479 ACCCTGGATACTTCTAAACTAAGCTTA 59.378 37.037 5.94 5.94 37.61 3.09
152 153 8.483758 CCCTGGATACTTCTAAACTAAGCTTAA 58.516 37.037 7.74 0.00 37.61 1.85
163 164 9.871238 TCTAAACTAAGCTTAATAGACAACTGG 57.129 33.333 7.74 0.00 0.00 4.00
164 165 9.871238 CTAAACTAAGCTTAATAGACAACTGGA 57.129 33.333 7.74 0.00 0.00 3.86
165 166 8.549338 AAACTAAGCTTAATAGACAACTGGAC 57.451 34.615 7.74 0.00 0.00 4.02
166 167 7.483580 ACTAAGCTTAATAGACAACTGGACT 57.516 36.000 7.74 0.00 0.00 3.85
167 168 7.548967 ACTAAGCTTAATAGACAACTGGACTC 58.451 38.462 7.74 0.00 0.00 3.36
168 169 6.613153 AAGCTTAATAGACAACTGGACTCT 57.387 37.500 0.00 0.00 0.00 3.24
169 170 7.719871 AAGCTTAATAGACAACTGGACTCTA 57.280 36.000 0.00 0.00 0.00 2.43
170 171 7.719871 AGCTTAATAGACAACTGGACTCTAA 57.280 36.000 0.00 0.00 0.00 2.10
171 172 7.777095 AGCTTAATAGACAACTGGACTCTAAG 58.223 38.462 0.00 0.00 0.00 2.18
172 173 7.616150 AGCTTAATAGACAACTGGACTCTAAGA 59.384 37.037 0.00 0.00 0.00 2.10
173 174 8.417884 GCTTAATAGACAACTGGACTCTAAGAT 58.582 37.037 0.00 0.00 0.00 2.40
174 175 9.743057 CTTAATAGACAACTGGACTCTAAGATG 57.257 37.037 0.00 0.00 0.00 2.90
175 176 7.726033 AATAGACAACTGGACTCTAAGATGT 57.274 36.000 0.00 0.00 32.73 3.06
176 177 5.652994 AGACAACTGGACTCTAAGATGTC 57.347 43.478 11.44 11.44 43.03 3.06
177 178 5.080337 AGACAACTGGACTCTAAGATGTCA 58.920 41.667 17.14 0.00 44.33 3.58
178 179 5.047660 AGACAACTGGACTCTAAGATGTCAC 60.048 44.000 17.14 2.18 44.33 3.67
179 180 4.588951 ACAACTGGACTCTAAGATGTCACA 59.411 41.667 0.00 0.00 35.11 3.58
180 181 5.070446 ACAACTGGACTCTAAGATGTCACAA 59.930 40.000 0.00 0.00 35.11 3.33
181 182 5.140747 ACTGGACTCTAAGATGTCACAAC 57.859 43.478 0.00 0.00 35.11 3.32
199 200 1.830279 ACATTGAGTGCCTGACATGG 58.170 50.000 0.00 0.00 0.00 3.66
239 240 5.866092 CCACTGTATCAAGATCCATCATACG 59.134 44.000 0.00 0.00 0.00 3.06
268 269 3.701040 CCTACCCAGTTCCATTCCAAATG 59.299 47.826 0.00 0.00 0.00 2.32
270 271 3.165071 ACCCAGTTCCATTCCAAATGAC 58.835 45.455 1.29 0.00 0.00 3.06
272 273 3.081061 CCAGTTCCATTCCAAATGACGA 58.919 45.455 1.29 0.00 0.00 4.20
347 348 2.623418 TAGTGTCCCCATCTCTGTGT 57.377 50.000 0.00 0.00 0.00 3.72
351 352 1.913262 TCCCCATCTCTGTGTGCGT 60.913 57.895 0.00 0.00 0.00 5.24
366 367 6.972901 TCTGTGTGCGTAGATTAATTAGTGAG 59.027 38.462 0.00 0.00 0.00 3.51
471 476 9.023962 TCTGACAGGCATTTAATTTGACTTTAT 57.976 29.630 1.81 0.00 26.83 1.40
657 670 2.425143 ACCTGCACATGATAACCAGG 57.575 50.000 0.00 9.65 46.53 4.45
658 671 1.027357 CCTGCACATGATAACCAGGC 58.973 55.000 0.00 0.00 36.94 4.85
660 673 1.945394 CTGCACATGATAACCAGGCTC 59.055 52.381 0.00 0.00 0.00 4.70
899 921 6.923199 ATTTGAGATTGTTTGAACAGGGAT 57.077 33.333 0.00 0.00 40.50 3.85
966 988 3.365868 GCATTTTATGTGAAGGCGTGTGA 60.366 43.478 0.00 0.00 0.00 3.58
1521 1543 0.537143 CCAAGCAGGCAACAGTACCA 60.537 55.000 0.00 0.00 41.41 3.25
1530 1552 1.317613 CAACAGTACCAAAGCAGGCA 58.682 50.000 0.00 0.00 0.00 4.75
1531 1553 1.001378 CAACAGTACCAAAGCAGGCAC 60.001 52.381 0.00 0.00 0.00 5.01
1534 1556 0.184933 AGTACCAAAGCAGGCACCAA 59.815 50.000 0.00 0.00 0.00 3.67
1626 1684 3.610911 ACCTGGTGCAAATAGAAGTAGC 58.389 45.455 0.00 0.00 0.00 3.58
2235 2293 1.696097 ATGATGCCAGTACCCCGGTC 61.696 60.000 0.00 0.00 0.00 4.79
2307 2365 8.129211 GCTGACACTAGTTGTAAGAAAATGTTT 58.871 33.333 11.80 0.00 38.93 2.83
2308 2366 9.438291 CTGACACTAGTTGTAAGAAAATGTTTG 57.562 33.333 0.00 0.00 38.93 2.93
2309 2367 9.168451 TGACACTAGTTGTAAGAAAATGTTTGA 57.832 29.630 0.00 0.00 39.17 2.69
2323 2384 9.715121 AGAAAATGTTTGATGATAATGTTGCTT 57.285 25.926 0.00 0.00 0.00 3.91
2430 2491 6.490381 ACCAGGAAAGTGTTAAGAAAGAATCC 59.510 38.462 0.00 0.00 0.00 3.01
2493 2554 2.237893 ACAATTAACCTACCCTGACCCG 59.762 50.000 0.00 0.00 0.00 5.28
2907 2971 9.403110 GATAACCATAAAACATACGAGTACGAT 57.597 33.333 0.00 0.00 42.66 3.73
3229 3293 5.018539 TGCCAGTGATATTAGTACACCAC 57.981 43.478 0.00 0.00 35.47 4.16
3316 3380 1.963515 CCCTTGAACAAACCCCAAGAG 59.036 52.381 0.00 0.00 39.55 2.85
3336 3400 1.172812 AGAAACAGAAAGGCGGCACC 61.173 55.000 13.08 0.00 39.61 5.01
3370 3434 5.104982 CCTGGTTCTTCTTCTCAGCTATTCT 60.105 44.000 0.00 0.00 0.00 2.40
3537 3601 4.764823 GTGACCAAAGTTGATATGGAACCA 59.235 41.667 0.00 0.00 37.66 3.67
3678 3742 7.537715 TCAAGTATGATTCAAATGACGCATTT 58.462 30.769 10.67 10.67 43.71 2.32
3717 3781 0.735978 GCCAAGTTAATGGGCAACGC 60.736 55.000 9.37 0.00 46.92 4.84
3816 3880 3.249320 GTGATGATGCGTGTGAATATGCT 59.751 43.478 0.00 0.00 33.75 3.79
3892 3956 2.415625 CCAGTAGACGGTTACACAGCTC 60.416 54.545 0.00 0.00 0.00 4.09
3915 3979 5.885352 TCTGTTCAGGTTTGACAATGAAAGA 59.115 36.000 4.65 7.22 33.74 2.52
3987 4051 2.557490 ACCTTCTTACCGTCTGACAGAC 59.443 50.000 23.28 23.28 41.71 3.51
4023 4087 1.137872 CTCCGTGGCTTCTATGAGCTT 59.862 52.381 0.00 0.00 42.32 3.74
4137 4201 1.476891 TCAAGTAGTCATCTGGTCGCC 59.523 52.381 0.00 0.00 0.00 5.54
4169 4233 9.774742 GATCTGGTTATTAATCACACTTTGAAC 57.225 33.333 2.38 0.00 37.92 3.18
4222 4286 7.120051 TCAGTTAGGCTCTCTGTATTTCTAGT 58.880 38.462 15.16 0.00 0.00 2.57
4283 4348 5.009631 CCATTTCTGTTGTGGACCTTATGA 58.990 41.667 0.00 0.00 34.94 2.15
4298 4363 4.288626 ACCTTATGAAAGCTAGGTGTGGAA 59.711 41.667 2.72 0.00 39.47 3.53
4332 4397 3.073274 GGTGTGGACCTTATGAAAGCT 57.927 47.619 0.00 0.00 39.47 3.74
4333 4398 4.216411 GGTGTGGACCTTATGAAAGCTA 57.784 45.455 0.00 0.00 39.47 3.32
4334 4399 4.192317 GGTGTGGACCTTATGAAAGCTAG 58.808 47.826 0.00 0.00 39.47 3.42
4335 4400 3.623510 GTGTGGACCTTATGAAAGCTAGC 59.376 47.826 6.62 6.62 0.00 3.42
4336 4401 3.519510 TGTGGACCTTATGAAAGCTAGCT 59.480 43.478 12.68 12.68 0.00 3.32
4337 4402 3.873952 GTGGACCTTATGAAAGCTAGCTG 59.126 47.826 20.16 5.38 0.00 4.24
4338 4403 3.519510 TGGACCTTATGAAAGCTAGCTGT 59.480 43.478 20.16 14.01 0.00 4.40
4339 4404 3.873952 GGACCTTATGAAAGCTAGCTGTG 59.126 47.826 20.16 1.67 0.00 3.66
4340 4405 3.873952 GACCTTATGAAAGCTAGCTGTGG 59.126 47.826 20.16 12.31 0.00 4.17
4341 4406 3.519510 ACCTTATGAAAGCTAGCTGTGGA 59.480 43.478 20.16 1.33 0.00 4.02
4342 4407 3.873952 CCTTATGAAAGCTAGCTGTGGAC 59.126 47.826 20.16 8.75 0.00 4.02
4343 4408 2.409948 ATGAAAGCTAGCTGTGGACC 57.590 50.000 20.16 0.61 0.00 4.46
4344 4409 1.352083 TGAAAGCTAGCTGTGGACCT 58.648 50.000 20.16 0.00 0.00 3.85
4345 4410 1.699634 TGAAAGCTAGCTGTGGACCTT 59.300 47.619 20.16 6.64 0.00 3.50
4346 4411 2.903784 TGAAAGCTAGCTGTGGACCTTA 59.096 45.455 20.16 0.00 0.00 2.69
4347 4412 3.519510 TGAAAGCTAGCTGTGGACCTTAT 59.480 43.478 20.16 0.00 0.00 1.73
4348 4413 3.550437 AAGCTAGCTGTGGACCTTATG 57.450 47.619 20.16 0.00 0.00 1.90
4349 4414 2.752030 AGCTAGCTGTGGACCTTATGA 58.248 47.619 18.57 0.00 0.00 2.15
4350 4415 3.107601 AGCTAGCTGTGGACCTTATGAA 58.892 45.455 18.57 0.00 0.00 2.57
4351 4416 3.713764 AGCTAGCTGTGGACCTTATGAAT 59.286 43.478 18.57 0.00 0.00 2.57
4352 4417 3.812053 GCTAGCTGTGGACCTTATGAATG 59.188 47.826 7.70 0.00 0.00 2.67
4353 4418 4.443457 GCTAGCTGTGGACCTTATGAATGA 60.443 45.833 7.70 0.00 0.00 2.57
4354 4419 3.878778 AGCTGTGGACCTTATGAATGAC 58.121 45.455 0.00 0.00 0.00 3.06
4355 4420 3.521126 AGCTGTGGACCTTATGAATGACT 59.479 43.478 0.00 0.00 0.00 3.41
4356 4421 3.624861 GCTGTGGACCTTATGAATGACTG 59.375 47.826 0.00 0.00 0.00 3.51
4448 4514 1.661178 CGCGCATGCATTATTCTGGTC 60.661 52.381 19.57 0.00 42.97 4.02
4554 4621 8.292444 AGATAAATTGCTTAACATTGCTACCA 57.708 30.769 0.00 0.00 0.00 3.25
4555 4622 8.190784 AGATAAATTGCTTAACATTGCTACCAC 58.809 33.333 0.00 0.00 0.00 4.16
4563 4630 1.065418 ACATTGCTACCACCTACCAGC 60.065 52.381 0.00 0.00 34.56 4.85
4594 4661 7.011499 AGATCGGAGAGTAGAAGCTAAGATA 57.989 40.000 0.00 0.00 43.63 1.98
4656 4724 8.931385 AATATGCAAGTATGTTGTTGGATTTC 57.069 30.769 0.00 0.00 36.31 2.17
4657 4725 5.132897 TGCAAGTATGTTGTTGGATTTCC 57.867 39.130 0.00 0.00 0.00 3.13
4663 4731 8.764287 CAAGTATGTTGTTGGATTTCCTTTTTC 58.236 33.333 0.00 0.00 36.82 2.29
4665 4733 8.704668 AGTATGTTGTTGGATTTCCTTTTTCTT 58.295 29.630 0.00 0.00 36.82 2.52
4666 4734 9.325198 GTATGTTGTTGGATTTCCTTTTTCTTT 57.675 29.630 0.00 0.00 36.82 2.52
4667 4735 8.806429 ATGTTGTTGGATTTCCTTTTTCTTTT 57.194 26.923 0.00 0.00 36.82 2.27
4668 4736 9.898152 ATGTTGTTGGATTTCCTTTTTCTTTTA 57.102 25.926 0.00 0.00 36.82 1.52
4832 4907 6.871492 GGAATACCATTGTTTTTCGGAATTGT 59.129 34.615 0.00 0.00 35.97 2.71
4929 5004 4.149511 TGGCATGGAATTCATCGTAGAA 57.850 40.909 7.93 0.00 43.58 2.10
4948 5023 4.874970 AGAATTGCAAAATTCTTGACGCT 58.125 34.783 1.71 0.00 44.63 5.07
4950 5025 3.988379 TTGCAAAATTCTTGACGCTCT 57.012 38.095 0.00 0.00 0.00 4.09
5063 5162 1.135112 TCATTAGTGATGCAGACGCGT 60.135 47.619 13.85 13.85 42.97 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.294397 GGGGTTTCCACTATAGACTACATACG 60.294 46.154 6.78 0.00 35.00 3.06
1 2 6.552350 TGGGGTTTCCACTATAGACTACATAC 59.448 42.308 6.78 0.00 41.46 2.39
2 3 6.685541 TGGGGTTTCCACTATAGACTACATA 58.314 40.000 6.78 0.00 41.46 2.29
3 4 5.535029 TGGGGTTTCCACTATAGACTACAT 58.465 41.667 6.78 0.00 41.46 2.29
4 5 4.950361 TGGGGTTTCCACTATAGACTACA 58.050 43.478 6.78 0.00 41.46 2.74
16 17 2.858787 AAGACCTTTTGGGGTTTCCA 57.141 45.000 0.00 0.00 46.08 3.53
17 18 7.490657 AAATATAAGACCTTTTGGGGTTTCC 57.509 36.000 0.00 0.00 46.08 3.13
20 21 9.042450 CCTAAAAATATAAGACCTTTTGGGGTT 57.958 33.333 3.64 0.00 46.08 4.11
21 22 8.403474 TCCTAAAAATATAAGACCTTTTGGGGT 58.597 33.333 9.33 0.00 46.08 4.95
22 23 8.832458 TCCTAAAAATATAAGACCTTTTGGGG 57.168 34.615 9.33 4.32 46.08 4.96
25 26 9.783256 CCGTTCCTAAAAATATAAGACCTTTTG 57.217 33.333 0.00 0.00 0.00 2.44
26 27 9.743581 TCCGTTCCTAAAAATATAAGACCTTTT 57.256 29.630 0.00 0.00 0.00 2.27
27 28 9.392259 CTCCGTTCCTAAAAATATAAGACCTTT 57.608 33.333 0.00 0.00 0.00 3.11
28 29 7.991460 CCTCCGTTCCTAAAAATATAAGACCTT 59.009 37.037 0.00 0.00 0.00 3.50
29 30 7.419865 CCCTCCGTTCCTAAAAATATAAGACCT 60.420 40.741 0.00 0.00 0.00 3.85
30 31 6.709397 CCCTCCGTTCCTAAAAATATAAGACC 59.291 42.308 0.00 0.00 0.00 3.85
31 32 7.503549 TCCCTCCGTTCCTAAAAATATAAGAC 58.496 38.462 0.00 0.00 0.00 3.01
32 33 7.346436 ACTCCCTCCGTTCCTAAAAATATAAGA 59.654 37.037 0.00 0.00 0.00 2.10
33 34 7.506971 ACTCCCTCCGTTCCTAAAAATATAAG 58.493 38.462 0.00 0.00 0.00 1.73
34 35 7.441903 ACTCCCTCCGTTCCTAAAAATATAA 57.558 36.000 0.00 0.00 0.00 0.98
35 36 7.234166 CCTACTCCCTCCGTTCCTAAAAATATA 59.766 40.741 0.00 0.00 0.00 0.86
36 37 5.970501 ACTCCCTCCGTTCCTAAAAATAT 57.029 39.130 0.00 0.00 0.00 1.28
37 38 5.364735 CCTACTCCCTCCGTTCCTAAAAATA 59.635 44.000 0.00 0.00 0.00 1.40
38 39 4.163649 CCTACTCCCTCCGTTCCTAAAAAT 59.836 45.833 0.00 0.00 0.00 1.82
39 40 3.516700 CCTACTCCCTCCGTTCCTAAAAA 59.483 47.826 0.00 0.00 0.00 1.94
40 41 3.102204 CCTACTCCCTCCGTTCCTAAAA 58.898 50.000 0.00 0.00 0.00 1.52
41 42 2.312741 TCCTACTCCCTCCGTTCCTAAA 59.687 50.000 0.00 0.00 0.00 1.85
42 43 1.925255 TCCTACTCCCTCCGTTCCTAA 59.075 52.381 0.00 0.00 0.00 2.69
43 44 1.493871 CTCCTACTCCCTCCGTTCCTA 59.506 57.143 0.00 0.00 0.00 2.94
44 45 0.259356 CTCCTACTCCCTCCGTTCCT 59.741 60.000 0.00 0.00 0.00 3.36
45 46 0.258194 TCTCCTACTCCCTCCGTTCC 59.742 60.000 0.00 0.00 0.00 3.62
46 47 2.368311 ATCTCCTACTCCCTCCGTTC 57.632 55.000 0.00 0.00 0.00 3.95
47 48 3.967467 TTATCTCCTACTCCCTCCGTT 57.033 47.619 0.00 0.00 0.00 4.44
48 49 4.153411 CAATTATCTCCTACTCCCTCCGT 58.847 47.826 0.00 0.00 0.00 4.69
49 50 3.511934 CCAATTATCTCCTACTCCCTCCG 59.488 52.174 0.00 0.00 0.00 4.63
50 51 4.528987 GTCCAATTATCTCCTACTCCCTCC 59.471 50.000 0.00 0.00 0.00 4.30
51 52 5.399113 AGTCCAATTATCTCCTACTCCCTC 58.601 45.833 0.00 0.00 0.00 4.30
52 53 5.137082 AGAGTCCAATTATCTCCTACTCCCT 59.863 44.000 0.00 0.00 33.91 4.20
53 54 5.399113 AGAGTCCAATTATCTCCTACTCCC 58.601 45.833 0.00 0.00 33.91 4.30
54 55 6.987403 AAGAGTCCAATTATCTCCTACTCC 57.013 41.667 0.00 0.00 33.91 3.85
55 56 7.308710 CGGTAAGAGTCCAATTATCTCCTACTC 60.309 44.444 0.00 0.00 30.49 2.59
56 57 6.490721 CGGTAAGAGTCCAATTATCTCCTACT 59.509 42.308 0.00 0.00 30.49 2.57
57 58 6.679843 CGGTAAGAGTCCAATTATCTCCTAC 58.320 44.000 0.00 0.00 0.00 3.18
58 59 5.243283 GCGGTAAGAGTCCAATTATCTCCTA 59.757 44.000 0.00 0.00 0.00 2.94
59 60 4.039366 GCGGTAAGAGTCCAATTATCTCCT 59.961 45.833 0.00 0.00 0.00 3.69
60 61 4.202223 TGCGGTAAGAGTCCAATTATCTCC 60.202 45.833 0.00 0.00 0.00 3.71
61 62 4.945246 TGCGGTAAGAGTCCAATTATCTC 58.055 43.478 0.00 0.00 0.00 2.75
62 63 5.353394 TTGCGGTAAGAGTCCAATTATCT 57.647 39.130 0.00 0.00 0.00 1.98
63 64 5.353123 TGTTTGCGGTAAGAGTCCAATTATC 59.647 40.000 0.00 0.00 0.00 1.75
64 65 5.250200 TGTTTGCGGTAAGAGTCCAATTAT 58.750 37.500 0.00 0.00 0.00 1.28
65 66 4.643463 TGTTTGCGGTAAGAGTCCAATTA 58.357 39.130 0.00 0.00 0.00 1.40
66 67 3.482436 TGTTTGCGGTAAGAGTCCAATT 58.518 40.909 0.00 0.00 0.00 2.32
67 68 3.074412 CTGTTTGCGGTAAGAGTCCAAT 58.926 45.455 0.00 0.00 0.00 3.16
68 69 2.103432 TCTGTTTGCGGTAAGAGTCCAA 59.897 45.455 0.00 0.00 0.00 3.53
69 70 1.689813 TCTGTTTGCGGTAAGAGTCCA 59.310 47.619 0.00 0.00 0.00 4.02
70 71 2.067013 GTCTGTTTGCGGTAAGAGTCC 58.933 52.381 0.00 0.00 0.00 3.85
71 72 3.027974 AGTCTGTTTGCGGTAAGAGTC 57.972 47.619 0.00 0.00 0.00 3.36
72 73 3.069729 AGAAGTCTGTTTGCGGTAAGAGT 59.930 43.478 0.00 0.00 0.00 3.24
73 74 3.654414 AGAAGTCTGTTTGCGGTAAGAG 58.346 45.455 0.00 0.00 0.00 2.85
74 75 3.321111 AGAGAAGTCTGTTTGCGGTAAGA 59.679 43.478 0.00 0.00 0.00 2.10
75 76 3.654414 AGAGAAGTCTGTTTGCGGTAAG 58.346 45.455 0.00 0.00 0.00 2.34
76 77 3.746045 AGAGAAGTCTGTTTGCGGTAA 57.254 42.857 0.00 0.00 0.00 2.85
77 78 3.057033 GGTAGAGAAGTCTGTTTGCGGTA 60.057 47.826 0.00 0.00 33.84 4.02
78 79 2.288886 GGTAGAGAAGTCTGTTTGCGGT 60.289 50.000 0.00 0.00 33.84 5.68
79 80 2.028930 AGGTAGAGAAGTCTGTTTGCGG 60.029 50.000 0.00 0.00 33.84 5.69
80 81 2.989840 CAGGTAGAGAAGTCTGTTTGCG 59.010 50.000 0.00 0.00 33.84 4.85
81 82 3.006967 TCCAGGTAGAGAAGTCTGTTTGC 59.993 47.826 0.00 0.00 33.84 3.68
82 83 4.873746 TCCAGGTAGAGAAGTCTGTTTG 57.126 45.455 0.00 0.00 33.84 2.93
83 84 5.130477 TGTTTCCAGGTAGAGAAGTCTGTTT 59.870 40.000 0.00 0.00 33.84 2.83
84 85 4.654262 TGTTTCCAGGTAGAGAAGTCTGTT 59.346 41.667 0.00 0.00 33.84 3.16
85 86 4.039366 GTGTTTCCAGGTAGAGAAGTCTGT 59.961 45.833 0.00 0.00 33.84 3.41
86 87 4.039245 TGTGTTTCCAGGTAGAGAAGTCTG 59.961 45.833 0.00 0.00 33.84 3.51
87 88 4.039366 GTGTGTTTCCAGGTAGAGAAGTCT 59.961 45.833 0.00 0.00 36.75 3.24
88 89 4.202223 TGTGTGTTTCCAGGTAGAGAAGTC 60.202 45.833 0.00 0.00 0.00 3.01
89 90 3.709653 TGTGTGTTTCCAGGTAGAGAAGT 59.290 43.478 0.00 0.00 0.00 3.01
90 91 4.058817 GTGTGTGTTTCCAGGTAGAGAAG 58.941 47.826 0.00 0.00 0.00 2.85
91 92 3.452990 TGTGTGTGTTTCCAGGTAGAGAA 59.547 43.478 0.00 0.00 0.00 2.87
92 93 3.035363 TGTGTGTGTTTCCAGGTAGAGA 58.965 45.455 0.00 0.00 0.00 3.10
93 94 3.131396 GTGTGTGTGTTTCCAGGTAGAG 58.869 50.000 0.00 0.00 0.00 2.43
94 95 2.502130 TGTGTGTGTGTTTCCAGGTAGA 59.498 45.455 0.00 0.00 0.00 2.59
95 96 2.612212 GTGTGTGTGTGTTTCCAGGTAG 59.388 50.000 0.00 0.00 0.00 3.18
96 97 2.027100 TGTGTGTGTGTGTTTCCAGGTA 60.027 45.455 0.00 0.00 0.00 3.08
97 98 1.271652 TGTGTGTGTGTGTTTCCAGGT 60.272 47.619 0.00 0.00 0.00 4.00
98 99 1.132262 GTGTGTGTGTGTGTTTCCAGG 59.868 52.381 0.00 0.00 0.00 4.45
99 100 1.809547 TGTGTGTGTGTGTGTTTCCAG 59.190 47.619 0.00 0.00 0.00 3.86
100 101 1.537638 GTGTGTGTGTGTGTGTTTCCA 59.462 47.619 0.00 0.00 0.00 3.53
101 102 1.537638 TGTGTGTGTGTGTGTGTTTCC 59.462 47.619 0.00 0.00 0.00 3.13
102 103 2.031595 TGTGTGTGTGTGTGTGTGTTTC 60.032 45.455 0.00 0.00 0.00 2.78
103 104 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
104 105 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
105 106 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
106 107 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
107 108 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
108 109 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
109 110 0.958382 GGGTGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
110 111 0.676466 AGGGTGTGTGTGTGTGTGTG 60.676 55.000 0.00 0.00 0.00 3.82
111 112 0.676466 CAGGGTGTGTGTGTGTGTGT 60.676 55.000 0.00 0.00 0.00 3.72
112 113 1.375853 CCAGGGTGTGTGTGTGTGTG 61.376 60.000 0.00 0.00 0.00 3.82
113 114 1.077787 CCAGGGTGTGTGTGTGTGT 60.078 57.895 0.00 0.00 0.00 3.72
114 115 0.179020 ATCCAGGGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
115 116 1.071699 GTATCCAGGGTGTGTGTGTGT 59.928 52.381 0.00 0.00 0.00 3.72
116 117 1.347707 AGTATCCAGGGTGTGTGTGTG 59.652 52.381 0.00 0.00 0.00 3.82
117 118 1.729586 AGTATCCAGGGTGTGTGTGT 58.270 50.000 0.00 0.00 0.00 3.72
118 119 2.303022 AGAAGTATCCAGGGTGTGTGTG 59.697 50.000 0.00 0.00 0.00 3.82
119 120 2.621070 AGAAGTATCCAGGGTGTGTGT 58.379 47.619 0.00 0.00 0.00 3.72
120 121 4.819105 TTAGAAGTATCCAGGGTGTGTG 57.181 45.455 0.00 0.00 0.00 3.82
121 122 4.844655 AGTTTAGAAGTATCCAGGGTGTGT 59.155 41.667 0.00 0.00 0.00 3.72
122 123 5.422214 AGTTTAGAAGTATCCAGGGTGTG 57.578 43.478 0.00 0.00 0.00 3.82
123 124 6.351966 GCTTAGTTTAGAAGTATCCAGGGTGT 60.352 42.308 0.00 0.00 0.00 4.16
124 125 6.049790 GCTTAGTTTAGAAGTATCCAGGGTG 58.950 44.000 0.00 0.00 0.00 4.61
125 126 5.965091 AGCTTAGTTTAGAAGTATCCAGGGT 59.035 40.000 0.00 0.00 0.00 4.34
126 127 6.487299 AGCTTAGTTTAGAAGTATCCAGGG 57.513 41.667 0.00 0.00 0.00 4.45
137 138 9.871238 CCAGTTGTCTATTAAGCTTAGTTTAGA 57.129 33.333 6.82 11.48 0.00 2.10
138 139 9.871238 TCCAGTTGTCTATTAAGCTTAGTTTAG 57.129 33.333 6.82 9.59 0.00 1.85
139 140 9.649167 GTCCAGTTGTCTATTAAGCTTAGTTTA 57.351 33.333 6.82 0.57 0.00 2.01
140 141 8.376270 AGTCCAGTTGTCTATTAAGCTTAGTTT 58.624 33.333 6.82 0.00 0.00 2.66
141 142 7.908453 AGTCCAGTTGTCTATTAAGCTTAGTT 58.092 34.615 6.82 1.83 0.00 2.24
142 143 7.397761 AGAGTCCAGTTGTCTATTAAGCTTAGT 59.602 37.037 6.24 6.50 0.00 2.24
143 144 7.777095 AGAGTCCAGTTGTCTATTAAGCTTAG 58.223 38.462 6.24 0.00 0.00 2.18
144 145 7.719871 AGAGTCCAGTTGTCTATTAAGCTTA 57.280 36.000 0.86 0.86 0.00 3.09
145 146 6.613153 AGAGTCCAGTTGTCTATTAAGCTT 57.387 37.500 3.48 3.48 0.00 3.74
146 147 7.616150 TCTTAGAGTCCAGTTGTCTATTAAGCT 59.384 37.037 0.00 0.00 0.00 3.74
147 148 7.773149 TCTTAGAGTCCAGTTGTCTATTAAGC 58.227 38.462 0.00 0.00 0.00 3.09
148 149 9.743057 CATCTTAGAGTCCAGTTGTCTATTAAG 57.257 37.037 0.00 0.00 0.00 1.85
149 150 9.256228 ACATCTTAGAGTCCAGTTGTCTATTAA 57.744 33.333 0.00 0.00 0.00 1.40
150 151 8.824756 ACATCTTAGAGTCCAGTTGTCTATTA 57.175 34.615 0.00 0.00 0.00 0.98
151 152 7.397476 TGACATCTTAGAGTCCAGTTGTCTATT 59.603 37.037 21.11 0.00 39.20 1.73
152 153 6.892456 TGACATCTTAGAGTCCAGTTGTCTAT 59.108 38.462 21.11 0.00 39.20 1.98
153 154 6.151312 GTGACATCTTAGAGTCCAGTTGTCTA 59.849 42.308 21.11 11.79 39.20 2.59
154 155 5.047660 GTGACATCTTAGAGTCCAGTTGTCT 60.048 44.000 21.11 0.00 39.20 3.41
155 156 5.164954 GTGACATCTTAGAGTCCAGTTGTC 58.835 45.833 17.12 17.12 39.03 3.18
156 157 4.588951 TGTGACATCTTAGAGTCCAGTTGT 59.411 41.667 8.54 4.14 33.89 3.32
157 158 5.139435 TGTGACATCTTAGAGTCCAGTTG 57.861 43.478 8.54 0.00 33.89 3.16
158 159 5.070446 TGTTGTGACATCTTAGAGTCCAGTT 59.930 40.000 8.54 0.00 33.89 3.16
159 160 4.588951 TGTTGTGACATCTTAGAGTCCAGT 59.411 41.667 8.54 0.00 33.89 4.00
160 161 5.139435 TGTTGTGACATCTTAGAGTCCAG 57.861 43.478 8.54 0.00 33.89 3.86
161 162 5.745312 ATGTTGTGACATCTTAGAGTCCA 57.255 39.130 8.54 5.02 42.83 4.02
162 163 6.166279 TCAATGTTGTGACATCTTAGAGTCC 58.834 40.000 8.54 3.21 45.58 3.85
163 164 6.870965 ACTCAATGTTGTGACATCTTAGAGTC 59.129 38.462 5.18 5.35 45.58 3.36
164 165 6.648310 CACTCAATGTTGTGACATCTTAGAGT 59.352 38.462 5.18 5.18 45.58 3.24
165 166 6.401903 GCACTCAATGTTGTGACATCTTAGAG 60.402 42.308 11.65 0.00 45.58 2.43
166 167 5.409520 GCACTCAATGTTGTGACATCTTAGA 59.590 40.000 11.65 0.00 45.58 2.10
167 168 5.391310 GGCACTCAATGTTGTGACATCTTAG 60.391 44.000 11.65 0.00 45.58 2.18
168 169 4.455533 GGCACTCAATGTTGTGACATCTTA 59.544 41.667 11.65 0.00 45.58 2.10
169 170 3.254166 GGCACTCAATGTTGTGACATCTT 59.746 43.478 11.65 0.00 45.58 2.40
170 171 2.816087 GGCACTCAATGTTGTGACATCT 59.184 45.455 11.65 0.00 45.58 2.90
171 172 2.816087 AGGCACTCAATGTTGTGACATC 59.184 45.455 14.62 0.00 45.58 3.06
172 173 2.555325 CAGGCACTCAATGTTGTGACAT 59.445 45.455 14.62 0.00 44.14 3.06
173 174 1.948834 CAGGCACTCAATGTTGTGACA 59.051 47.619 14.62 0.00 44.14 3.58
174 175 2.031682 GTCAGGCACTCAATGTTGTGAC 60.032 50.000 11.65 9.31 42.18 3.67
175 176 2.221169 GTCAGGCACTCAATGTTGTGA 58.779 47.619 11.65 0.00 34.60 3.58
176 177 1.948834 TGTCAGGCACTCAATGTTGTG 59.051 47.619 5.20 5.20 34.60 3.33
177 178 2.346766 TGTCAGGCACTCAATGTTGT 57.653 45.000 0.00 0.00 34.60 3.32
178 179 2.094906 CCATGTCAGGCACTCAATGTTG 60.095 50.000 0.00 0.00 34.60 3.33
179 180 2.165167 CCATGTCAGGCACTCAATGTT 58.835 47.619 0.00 0.00 34.60 2.71
180 181 1.074405 ACCATGTCAGGCACTCAATGT 59.926 47.619 0.00 0.00 34.60 2.71
181 182 1.471287 CACCATGTCAGGCACTCAATG 59.529 52.381 0.00 0.00 34.60 2.82
268 269 6.856426 TGATGATACACGATACTGATTTCGTC 59.144 38.462 0.00 0.00 46.06 4.20
270 271 7.027686 GTGATGATACACGATACTGATTTCG 57.972 40.000 0.00 0.00 41.04 3.46
347 348 9.459640 GTACAATCTCACTAATTAATCTACGCA 57.540 33.333 0.00 0.00 0.00 5.24
471 476 6.000246 TCAAACTAGTGCATGGATGGAATA 58.000 37.500 0.00 0.00 0.00 1.75
561 566 6.962182 AGATCACTACAGATTTGGGATTTGA 58.038 36.000 0.00 0.00 0.00 2.69
636 641 3.884895 CCTGGTTATCATGTGCAGGTTA 58.115 45.455 0.00 0.00 0.00 2.85
642 647 1.945394 CTGAGCCTGGTTATCATGTGC 59.055 52.381 0.00 0.00 0.00 4.57
660 673 4.394300 CACCCTTTTCTCAGTAGCAATCTG 59.606 45.833 0.00 0.00 0.00 2.90
925 947 2.238144 TGCTATGAGCTGAAGAAGGCTT 59.762 45.455 0.00 0.00 42.97 4.35
1173 1195 4.828939 TCCAACAACTCATTGATCTTTGCT 59.171 37.500 0.00 0.00 39.30 3.91
1521 1543 2.008242 TTGGTATTGGTGCCTGCTTT 57.992 45.000 0.00 0.00 0.00 3.51
1530 1552 0.965363 CCGCCTGCTTTGGTATTGGT 60.965 55.000 0.00 0.00 0.00 3.67
1531 1553 1.809207 CCGCCTGCTTTGGTATTGG 59.191 57.895 0.00 0.00 0.00 3.16
1534 1556 1.750399 CTGCCGCCTGCTTTGGTAT 60.750 57.895 0.00 0.00 42.00 2.73
1552 1610 2.671619 TGCCGCCTGCTTTGGTAC 60.672 61.111 0.00 0.00 42.00 3.34
1626 1684 0.389948 GTGGTTCACCTCCTGCTACG 60.390 60.000 0.00 0.00 36.82 3.51
1790 1848 3.550437 ATACAGAAGGCACATCCTGTC 57.450 47.619 0.00 0.00 46.94 3.51
1967 2025 2.637872 TGGTTAACCTTCTCCTCACCAG 59.362 50.000 24.78 0.00 36.82 4.00
2000 2058 0.825840 TTCAACCCCGCTTTTCCCAG 60.826 55.000 0.00 0.00 0.00 4.45
2307 2365 4.701171 TCAGCACAAGCAACATTATCATCA 59.299 37.500 0.00 0.00 45.49 3.07
2308 2366 5.239359 TCAGCACAAGCAACATTATCATC 57.761 39.130 0.00 0.00 45.49 2.92
2309 2367 5.126545 ACATCAGCACAAGCAACATTATCAT 59.873 36.000 0.00 0.00 45.49 2.45
2323 2384 4.203226 TCACCAGTTTTTACATCAGCACA 58.797 39.130 0.00 0.00 0.00 4.57
2508 2569 5.505173 AATTCACATTCCTGCCTTTATCG 57.495 39.130 0.00 0.00 0.00 2.92
2611 2672 4.821805 CCGAATAGTGGATTTGGTAGCATT 59.178 41.667 0.00 0.00 42.39 3.56
2907 2971 3.646162 AGTCTGACATAACCTCCACAACA 59.354 43.478 10.88 0.00 0.00 3.33
3229 3293 2.226437 CACTTGGTTCATTTCCAGGACG 59.774 50.000 0.00 0.00 35.92 4.79
3316 3380 0.238553 GTGCCGCCTTTCTGTTTCTC 59.761 55.000 0.00 0.00 0.00 2.87
3336 3400 3.414700 GAACCAGGCACACTCGCG 61.415 66.667 0.00 0.00 0.00 5.87
3370 3434 3.369471 GCAATAGTACTTGGAGAGGTGCA 60.369 47.826 0.00 0.00 0.00 4.57
3537 3601 6.290294 AGCCAAGTTAAATGCAATCTGAAT 57.710 33.333 0.00 0.00 0.00 2.57
3678 3742 8.594550 ACTTGGCTAGTTTCTACTAAATGAGAA 58.405 33.333 0.00 0.00 36.46 2.87
3717 3781 0.370273 CTCGCGGGTGAATTTCGAAG 59.630 55.000 6.13 0.00 0.00 3.79
3816 3880 1.132453 CGCTCAGTAATCTCACCGACA 59.868 52.381 0.00 0.00 0.00 4.35
3892 3956 6.135290 TCTTTCATTGTCAAACCTGAACAG 57.865 37.500 0.55 0.00 31.88 3.16
3915 3979 3.387962 TGCAGGAATCTCCAGAATACCT 58.612 45.455 0.00 0.00 39.61 3.08
4023 4087 2.259917 TCAGGAACAGAAGCTGGATCA 58.740 47.619 0.00 0.00 35.51 2.92
4075 4139 2.626266 TGTTAGCTTCCAAGTCAGTCGA 59.374 45.455 0.00 0.00 0.00 4.20
4169 4233 0.824109 TCTCCCCTGCAGATAACACG 59.176 55.000 17.39 0.00 0.00 4.49
4222 4286 5.846203 AGCACTAGAAGTACGGTAAAACAA 58.154 37.500 0.00 0.00 0.00 2.83
4283 4348 5.499004 TCATAAGTTCCACACCTAGCTTT 57.501 39.130 0.00 0.00 0.00 3.51
4298 4363 4.323562 GGTCCACACCTAGCTTTCATAAGT 60.324 45.833 0.00 0.00 40.00 2.24
4331 4396 5.053145 GTCATTCATAAGGTCCACAGCTAG 58.947 45.833 0.00 0.00 0.00 3.42
4332 4397 4.716784 AGTCATTCATAAGGTCCACAGCTA 59.283 41.667 0.00 0.00 0.00 3.32
4333 4398 3.521126 AGTCATTCATAAGGTCCACAGCT 59.479 43.478 0.00 0.00 0.00 4.24
4334 4399 3.624861 CAGTCATTCATAAGGTCCACAGC 59.375 47.826 0.00 0.00 0.00 4.40
4335 4400 4.194640 CCAGTCATTCATAAGGTCCACAG 58.805 47.826 0.00 0.00 0.00 3.66
4336 4401 3.054434 CCCAGTCATTCATAAGGTCCACA 60.054 47.826 0.00 0.00 0.00 4.17
4337 4402 3.199946 TCCCAGTCATTCATAAGGTCCAC 59.800 47.826 0.00 0.00 0.00 4.02
4338 4403 3.459828 TCCCAGTCATTCATAAGGTCCA 58.540 45.455 0.00 0.00 0.00 4.02
4339 4404 4.503714 TTCCCAGTCATTCATAAGGTCC 57.496 45.455 0.00 0.00 0.00 4.46
4340 4405 6.834168 TTTTTCCCAGTCATTCATAAGGTC 57.166 37.500 0.00 0.00 0.00 3.85
4365 4431 5.301805 CCAAACTAACAACCATCAAGTTCCT 59.698 40.000 0.00 0.00 30.37 3.36
4448 4514 1.021202 TGCCGAAAACCTGAACACAG 58.979 50.000 0.00 0.00 0.00 3.66
4549 4616 3.362706 TCTTAGTGCTGGTAGGTGGTAG 58.637 50.000 0.00 0.00 0.00 3.18
4550 4617 3.010920 TCTCTTAGTGCTGGTAGGTGGTA 59.989 47.826 0.00 0.00 0.00 3.25
4551 4618 2.180276 CTCTTAGTGCTGGTAGGTGGT 58.820 52.381 0.00 0.00 0.00 4.16
4552 4619 2.457598 TCTCTTAGTGCTGGTAGGTGG 58.542 52.381 0.00 0.00 0.00 4.61
4553 4620 3.243234 CGATCTCTTAGTGCTGGTAGGTG 60.243 52.174 0.00 0.00 0.00 4.00
4554 4621 2.952978 CGATCTCTTAGTGCTGGTAGGT 59.047 50.000 0.00 0.00 0.00 3.08
4555 4622 2.294791 CCGATCTCTTAGTGCTGGTAGG 59.705 54.545 0.00 0.00 0.00 3.18
4563 4630 5.049680 GCTTCTACTCTCCGATCTCTTAGTG 60.050 48.000 0.00 0.00 0.00 2.74
4594 4661 2.503356 TGTGGTTGTGCTGGGAAATTTT 59.497 40.909 0.00 0.00 0.00 1.82
4636 4704 5.391312 AGGAAATCCAACAACATACTTGC 57.609 39.130 1.67 0.00 38.89 4.01
4872 4947 9.241919 TCAATATGAATTGTGATTGTTGTAGGT 57.758 29.630 0.00 0.00 42.66 3.08
4929 5004 4.022935 TGAGAGCGTCAAGAATTTTGCAAT 60.023 37.500 0.00 0.00 29.64 3.56
4948 5023 6.430308 GGAGTTCTGGTACATACGATATGAGA 59.570 42.308 10.64 2.70 38.20 3.27
4950 5025 6.206829 CAGGAGTTCTGGTACATACGATATGA 59.793 42.308 10.64 0.00 39.76 2.15


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

AutoCloner maintained by Alex Coulton.