Multiple sequence alignment - TraesCS6B01G016200

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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 TraesCS6B01G016200 chr6B 100.000 3165 0 0 650 3814 9876041 9872877 0.000000e+00 5845
1 TraesCS6B01G016200 chr6B 100.000 198 0 0 1 198 9876690 9876493 2.160000e-97 366
2 TraesCS6B01G016200 chr6D 96.747 3136 88 9 685 3814 13618924 13622051 0.000000e+00 5214


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 TraesCS6B01G016200 chr6B 9872877 9876690 3813 True 3105.5 5845 100.000 1 3814 2 chr6B.!!$R1 3813
1 TraesCS6B01G016200 chr6D 13618924 13622051 3127 False 5214.0 5214 96.747 685 3814 1 chr6D.!!$F1 3129

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
40 41 0.031616 AGATCTCCTCCACCTCCCAC 60.032 60.0 0.00 0.00 0.00 4.61 F
77 78 0.103208 CCTCTCGTTCAATCCCCTCG 59.897 60.0 0.00 0.00 0.00 4.63 F
82 83 0.178068 CGTTCAATCCCCTCGACCAT 59.822 55.0 0.00 0.00 0.00 3.55 F
86 87 0.179045 CAATCCCCTCGACCATCCAC 60.179 60.0 0.00 0.00 0.00 4.02 F
151 152 0.318275 GAAGATCTACTCTGCCGCGG 60.318 60.0 24.05 24.05 33.29 6.46 F
179 180 0.342313 TTCCTCCTCCCTACTTCCCC 59.658 60.0 0.00 0.00 0.00 4.81 F
1358 1359 0.401356 TGCCATGTTCAGGAGCTCAA 59.599 50.0 17.19 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1482 0.612732 TTCTTCCAATGCAGGGCAGG 60.613 55.000 6.94 0.0 43.65 4.85 R
1704 1705 2.803030 AACAGTCCTCGCCTAGACTA 57.197 50.000 0.00 0.0 41.38 2.59 R
1901 1902 3.788333 GCAAGAGCAAGGCAATATCAA 57.212 42.857 0.00 0.0 41.58 2.57 R
2443 2445 4.965042 GTTAGCAACCAAAAACCATTCG 57.035 40.909 0.00 0.0 0.00 3.34 R
2490 2492 4.647399 GCTCCTCTAGAATAGGTGAGTTGT 59.353 45.833 0.00 0.0 39.78 3.32 R
2514 2516 7.202011 GCCATACCTCTAAAAGTAGGAGATTCA 60.202 40.741 0.00 0.0 36.66 2.57 R
3222 3228 0.179032 TATATGTGGGGTTGGCGCAG 60.179 55.000 10.83 0.0 0.00 5.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.637663 CCCCCTCTCCCAGATCTC 57.362 66.667 0.00 0.00 0.00 2.75
28 29 1.152139 CCCCCTCTCCCAGATCTCC 60.152 68.421 0.00 0.00 0.00 3.71
29 30 1.673928 CCCCCTCTCCCAGATCTCCT 61.674 65.000 0.00 0.00 0.00 3.69
30 31 0.178935 CCCCTCTCCCAGATCTCCTC 60.179 65.000 0.00 0.00 0.00 3.71
31 32 0.178935 CCCTCTCCCAGATCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
32 33 0.560193 CCTCTCCCAGATCTCCTCCA 59.440 60.000 0.00 0.00 0.00 3.86
33 34 1.703411 CTCTCCCAGATCTCCTCCAC 58.297 60.000 0.00 0.00 0.00 4.02
34 35 0.263172 TCTCCCAGATCTCCTCCACC 59.737 60.000 0.00 0.00 0.00 4.61
35 36 0.264359 CTCCCAGATCTCCTCCACCT 59.736 60.000 0.00 0.00 0.00 4.00
36 37 0.263172 TCCCAGATCTCCTCCACCTC 59.737 60.000 0.00 0.00 0.00 3.85
37 38 0.762461 CCCAGATCTCCTCCACCTCC 60.762 65.000 0.00 0.00 0.00 4.30
38 39 0.762461 CCAGATCTCCTCCACCTCCC 60.762 65.000 0.00 0.00 0.00 4.30
39 40 0.031716 CAGATCTCCTCCACCTCCCA 60.032 60.000 0.00 0.00 0.00 4.37
40 41 0.031616 AGATCTCCTCCACCTCCCAC 60.032 60.000 0.00 0.00 0.00 4.61
41 42 1.381872 ATCTCCTCCACCTCCCACG 60.382 63.158 0.00 0.00 0.00 4.94
42 43 1.875422 ATCTCCTCCACCTCCCACGA 61.875 60.000 0.00 0.00 0.00 4.35
43 44 1.381872 CTCCTCCACCTCCCACGAT 60.382 63.158 0.00 0.00 0.00 3.73
44 45 0.106167 CTCCTCCACCTCCCACGATA 60.106 60.000 0.00 0.00 0.00 2.92
45 46 0.561184 TCCTCCACCTCCCACGATAT 59.439 55.000 0.00 0.00 0.00 1.63
46 47 1.062428 TCCTCCACCTCCCACGATATT 60.062 52.381 0.00 0.00 0.00 1.28
47 48 1.344763 CCTCCACCTCCCACGATATTC 59.655 57.143 0.00 0.00 0.00 1.75
48 49 2.320781 CTCCACCTCCCACGATATTCT 58.679 52.381 0.00 0.00 0.00 2.40
49 50 2.297597 CTCCACCTCCCACGATATTCTC 59.702 54.545 0.00 0.00 0.00 2.87
50 51 2.039418 CCACCTCCCACGATATTCTCA 58.961 52.381 0.00 0.00 0.00 3.27
51 52 2.434336 CCACCTCCCACGATATTCTCAA 59.566 50.000 0.00 0.00 0.00 3.02
52 53 3.458189 CACCTCCCACGATATTCTCAAC 58.542 50.000 0.00 0.00 0.00 3.18
53 54 2.434702 ACCTCCCACGATATTCTCAACC 59.565 50.000 0.00 0.00 0.00 3.77
54 55 2.700897 CCTCCCACGATATTCTCAACCT 59.299 50.000 0.00 0.00 0.00 3.50
55 56 3.243907 CCTCCCACGATATTCTCAACCTC 60.244 52.174 0.00 0.00 0.00 3.85
56 57 2.698797 TCCCACGATATTCTCAACCTCC 59.301 50.000 0.00 0.00 0.00 4.30
57 58 2.700897 CCCACGATATTCTCAACCTCCT 59.299 50.000 0.00 0.00 0.00 3.69
58 59 3.243907 CCCACGATATTCTCAACCTCCTC 60.244 52.174 0.00 0.00 0.00 3.71
59 60 3.243907 CCACGATATTCTCAACCTCCTCC 60.244 52.174 0.00 0.00 0.00 4.30
60 61 3.639094 CACGATATTCTCAACCTCCTCCT 59.361 47.826 0.00 0.00 0.00 3.69
61 62 3.892588 ACGATATTCTCAACCTCCTCCTC 59.107 47.826 0.00 0.00 0.00 3.71
62 63 4.148838 CGATATTCTCAACCTCCTCCTCT 58.851 47.826 0.00 0.00 0.00 3.69
63 64 4.217550 CGATATTCTCAACCTCCTCCTCTC 59.782 50.000 0.00 0.00 0.00 3.20
64 65 1.840737 TTCTCAACCTCCTCCTCTCG 58.159 55.000 0.00 0.00 0.00 4.04
65 66 0.699399 TCTCAACCTCCTCCTCTCGT 59.301 55.000 0.00 0.00 0.00 4.18
66 67 1.075698 TCTCAACCTCCTCCTCTCGTT 59.924 52.381 0.00 0.00 0.00 3.85
67 68 1.474879 CTCAACCTCCTCCTCTCGTTC 59.525 57.143 0.00 0.00 0.00 3.95
68 69 1.203013 TCAACCTCCTCCTCTCGTTCA 60.203 52.381 0.00 0.00 0.00 3.18
69 70 1.618837 CAACCTCCTCCTCTCGTTCAA 59.381 52.381 0.00 0.00 0.00 2.69
70 71 2.234908 CAACCTCCTCCTCTCGTTCAAT 59.765 50.000 0.00 0.00 0.00 2.57
71 72 2.104170 ACCTCCTCCTCTCGTTCAATC 58.896 52.381 0.00 0.00 0.00 2.67
72 73 1.410882 CCTCCTCCTCTCGTTCAATCC 59.589 57.143 0.00 0.00 0.00 3.01
73 74 1.410882 CTCCTCCTCTCGTTCAATCCC 59.589 57.143 0.00 0.00 0.00 3.85
74 75 0.466124 CCTCCTCTCGTTCAATCCCC 59.534 60.000 0.00 0.00 0.00 4.81
75 76 1.490574 CTCCTCTCGTTCAATCCCCT 58.509 55.000 0.00 0.00 0.00 4.79
76 77 1.410882 CTCCTCTCGTTCAATCCCCTC 59.589 57.143 0.00 0.00 0.00 4.30
77 78 0.103208 CCTCTCGTTCAATCCCCTCG 59.897 60.000 0.00 0.00 0.00 4.63
78 79 1.103803 CTCTCGTTCAATCCCCTCGA 58.896 55.000 0.00 0.00 0.00 4.04
79 80 0.815734 TCTCGTTCAATCCCCTCGAC 59.184 55.000 0.00 0.00 0.00 4.20
80 81 0.179108 CTCGTTCAATCCCCTCGACC 60.179 60.000 0.00 0.00 0.00 4.79
81 82 0.901114 TCGTTCAATCCCCTCGACCA 60.901 55.000 0.00 0.00 0.00 4.02
82 83 0.178068 CGTTCAATCCCCTCGACCAT 59.822 55.000 0.00 0.00 0.00 3.55
83 84 1.806623 CGTTCAATCCCCTCGACCATC 60.807 57.143 0.00 0.00 0.00 3.51
84 85 0.837272 TTCAATCCCCTCGACCATCC 59.163 55.000 0.00 0.00 0.00 3.51
85 86 0.326143 TCAATCCCCTCGACCATCCA 60.326 55.000 0.00 0.00 0.00 3.41
86 87 0.179045 CAATCCCCTCGACCATCCAC 60.179 60.000 0.00 0.00 0.00 4.02
87 88 1.686325 AATCCCCTCGACCATCCACG 61.686 60.000 0.00 0.00 0.00 4.94
88 89 2.583298 ATCCCCTCGACCATCCACGA 62.583 60.000 0.00 0.00 37.03 4.35
89 90 2.134287 CCCCTCGACCATCCACGAT 61.134 63.158 0.00 0.00 37.86 3.73
90 91 1.364171 CCCTCGACCATCCACGATC 59.636 63.158 0.00 0.00 37.86 3.69
91 92 1.364171 CCTCGACCATCCACGATCC 59.636 63.158 0.00 0.00 37.86 3.36
92 93 1.364171 CTCGACCATCCACGATCCC 59.636 63.158 0.00 0.00 37.86 3.85
93 94 2.088674 CTCGACCATCCACGATCCCC 62.089 65.000 0.00 0.00 37.86 4.81
94 95 2.134287 CGACCATCCACGATCCCCT 61.134 63.158 0.00 0.00 0.00 4.79
95 96 1.447643 GACCATCCACGATCCCCTG 59.552 63.158 0.00 0.00 0.00 4.45
96 97 1.306997 ACCATCCACGATCCCCTGT 60.307 57.895 0.00 0.00 0.00 4.00
97 98 0.914417 ACCATCCACGATCCCCTGTT 60.914 55.000 0.00 0.00 0.00 3.16
98 99 1.128200 CCATCCACGATCCCCTGTTA 58.872 55.000 0.00 0.00 0.00 2.41
99 100 1.202651 CCATCCACGATCCCCTGTTAC 60.203 57.143 0.00 0.00 0.00 2.50
100 101 1.762957 CATCCACGATCCCCTGTTACT 59.237 52.381 0.00 0.00 0.00 2.24
101 102 2.832643 TCCACGATCCCCTGTTACTA 57.167 50.000 0.00 0.00 0.00 1.82
102 103 2.381911 TCCACGATCCCCTGTTACTAC 58.618 52.381 0.00 0.00 0.00 2.73
103 104 2.024655 TCCACGATCCCCTGTTACTACT 60.025 50.000 0.00 0.00 0.00 2.57
104 105 2.361438 CCACGATCCCCTGTTACTACTC 59.639 54.545 0.00 0.00 0.00 2.59
105 106 2.361438 CACGATCCCCTGTTACTACTCC 59.639 54.545 0.00 0.00 0.00 3.85
106 107 2.244252 ACGATCCCCTGTTACTACTCCT 59.756 50.000 0.00 0.00 0.00 3.69
107 108 2.885894 CGATCCCCTGTTACTACTCCTC 59.114 54.545 0.00 0.00 0.00 3.71
108 109 2.842645 TCCCCTGTTACTACTCCTCC 57.157 55.000 0.00 0.00 0.00 4.30
109 110 1.290130 TCCCCTGTTACTACTCCTCCC 59.710 57.143 0.00 0.00 0.00 4.30
110 111 1.691801 CCCCTGTTACTACTCCTCCCC 60.692 61.905 0.00 0.00 0.00 4.81
111 112 1.691801 CCCTGTTACTACTCCTCCCCC 60.692 61.905 0.00 0.00 0.00 5.40
127 128 4.371231 CCCTCCCCTCAACCCCCT 62.371 72.222 0.00 0.00 0.00 4.79
128 129 2.204306 CCTCCCCTCAACCCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
129 130 2.309504 CCTCCCCTCAACCCCCTTC 61.310 68.421 0.00 0.00 0.00 3.46
130 131 1.541368 CTCCCCTCAACCCCCTTCA 60.541 63.158 0.00 0.00 0.00 3.02
131 132 1.850755 TCCCCTCAACCCCCTTCAC 60.851 63.158 0.00 0.00 0.00 3.18
132 133 2.351276 CCCTCAACCCCCTTCACG 59.649 66.667 0.00 0.00 0.00 4.35
133 134 2.221299 CCCTCAACCCCCTTCACGA 61.221 63.158 0.00 0.00 0.00 4.35
134 135 1.758592 CCTCAACCCCCTTCACGAA 59.241 57.895 0.00 0.00 0.00 3.85
135 136 0.321653 CCTCAACCCCCTTCACGAAG 60.322 60.000 0.00 0.00 38.14 3.79
136 137 0.685097 CTCAACCCCCTTCACGAAGA 59.315 55.000 8.38 0.00 40.79 2.87
137 138 1.279271 CTCAACCCCCTTCACGAAGAT 59.721 52.381 8.38 0.00 40.79 2.40
138 139 1.278127 TCAACCCCCTTCACGAAGATC 59.722 52.381 8.38 0.00 40.79 2.75
139 140 1.279271 CAACCCCCTTCACGAAGATCT 59.721 52.381 8.38 0.00 40.79 2.75
140 141 2.500098 CAACCCCCTTCACGAAGATCTA 59.500 50.000 8.38 0.00 40.79 1.98
141 142 2.108970 ACCCCCTTCACGAAGATCTAC 58.891 52.381 8.38 0.00 40.79 2.59
142 143 2.292323 ACCCCCTTCACGAAGATCTACT 60.292 50.000 8.38 0.00 40.79 2.57
143 144 2.362717 CCCCCTTCACGAAGATCTACTC 59.637 54.545 8.38 0.00 40.79 2.59
144 145 3.292460 CCCCTTCACGAAGATCTACTCT 58.708 50.000 8.38 0.00 40.79 3.24
145 146 3.067461 CCCCTTCACGAAGATCTACTCTG 59.933 52.174 8.38 0.00 40.79 3.35
146 147 3.490078 CCCTTCACGAAGATCTACTCTGC 60.490 52.174 8.38 0.00 40.79 4.26
147 148 3.490078 CCTTCACGAAGATCTACTCTGCC 60.490 52.174 8.38 0.00 40.79 4.85
148 149 1.671328 TCACGAAGATCTACTCTGCCG 59.329 52.381 0.00 0.00 37.09 5.69
149 150 0.382515 ACGAAGATCTACTCTGCCGC 59.617 55.000 0.00 0.00 35.49 6.53
150 151 0.658829 CGAAGATCTACTCTGCCGCG 60.659 60.000 0.00 0.00 33.29 6.46
151 152 0.318275 GAAGATCTACTCTGCCGCGG 60.318 60.000 24.05 24.05 33.29 6.46
152 153 1.038130 AAGATCTACTCTGCCGCGGT 61.038 55.000 28.70 9.01 33.29 5.68
153 154 1.299468 GATCTACTCTGCCGCGGTG 60.299 63.158 28.70 19.88 0.00 4.94
154 155 1.725557 GATCTACTCTGCCGCGGTGA 61.726 60.000 28.70 22.92 0.00 4.02
155 156 1.109920 ATCTACTCTGCCGCGGTGAT 61.110 55.000 28.70 14.98 0.00 3.06
156 157 1.299468 CTACTCTGCCGCGGTGATC 60.299 63.158 28.70 10.62 0.00 2.92
157 158 1.729470 CTACTCTGCCGCGGTGATCT 61.729 60.000 28.70 14.59 0.00 2.75
158 159 1.320344 TACTCTGCCGCGGTGATCTT 61.320 55.000 28.70 13.93 0.00 2.40
159 160 1.880340 CTCTGCCGCGGTGATCTTC 60.880 63.158 28.70 8.52 0.00 2.87
160 161 2.185350 CTGCCGCGGTGATCTTCT 59.815 61.111 28.70 0.00 0.00 2.85
161 162 1.448540 CTGCCGCGGTGATCTTCTT 60.449 57.895 28.70 0.00 0.00 2.52
162 163 1.424493 CTGCCGCGGTGATCTTCTTC 61.424 60.000 28.70 6.03 0.00 2.87
163 164 2.174319 GCCGCGGTGATCTTCTTCC 61.174 63.158 28.70 0.32 0.00 3.46
164 165 1.517832 CCGCGGTGATCTTCTTCCT 59.482 57.895 19.50 0.00 0.00 3.36
165 166 0.528684 CCGCGGTGATCTTCTTCCTC 60.529 60.000 19.50 0.00 0.00 3.71
166 167 0.528684 CGCGGTGATCTTCTTCCTCC 60.529 60.000 0.00 0.00 0.00 4.30
167 168 0.827368 GCGGTGATCTTCTTCCTCCT 59.173 55.000 0.00 0.00 0.00 3.69
168 169 1.202475 GCGGTGATCTTCTTCCTCCTC 60.202 57.143 0.00 0.00 0.00 3.71
169 170 1.410882 CGGTGATCTTCTTCCTCCTCC 59.589 57.143 0.00 0.00 0.00 4.30
170 171 1.765904 GGTGATCTTCTTCCTCCTCCC 59.234 57.143 0.00 0.00 0.00 4.30
171 172 2.628290 GGTGATCTTCTTCCTCCTCCCT 60.628 54.545 0.00 0.00 0.00 4.20
172 173 3.374318 GGTGATCTTCTTCCTCCTCCCTA 60.374 52.174 0.00 0.00 0.00 3.53
173 174 3.639561 GTGATCTTCTTCCTCCTCCCTAC 59.360 52.174 0.00 0.00 0.00 3.18
174 175 3.533907 TGATCTTCTTCCTCCTCCCTACT 59.466 47.826 0.00 0.00 0.00 2.57
175 176 4.016105 TGATCTTCTTCCTCCTCCCTACTT 60.016 45.833 0.00 0.00 0.00 2.24
176 177 3.983821 TCTTCTTCCTCCTCCCTACTTC 58.016 50.000 0.00 0.00 0.00 3.01
177 178 2.850695 TCTTCCTCCTCCCTACTTCC 57.149 55.000 0.00 0.00 0.00 3.46
178 179 1.291335 TCTTCCTCCTCCCTACTTCCC 59.709 57.143 0.00 0.00 0.00 3.97
179 180 0.342313 TTCCTCCTCCCTACTTCCCC 59.658 60.000 0.00 0.00 0.00 4.81
180 181 0.557907 TCCTCCTCCCTACTTCCCCT 60.558 60.000 0.00 0.00 0.00 4.79
181 182 1.242444 CCTCCTCCCTACTTCCCCTA 58.758 60.000 0.00 0.00 0.00 3.53
182 183 1.148236 CCTCCTCCCTACTTCCCCTAG 59.852 61.905 0.00 0.00 0.00 3.02
183 184 1.148236 CTCCTCCCTACTTCCCCTAGG 59.852 61.905 0.06 0.06 0.00 3.02
184 185 0.472161 CCTCCCTACTTCCCCTAGGC 60.472 65.000 2.05 0.00 30.78 3.93
185 186 0.472161 CTCCCTACTTCCCCTAGGCC 60.472 65.000 2.05 0.00 30.78 5.19
186 187 1.461655 CCCTACTTCCCCTAGGCCC 60.462 68.421 2.05 0.00 30.78 5.80
187 188 1.461655 CCTACTTCCCCTAGGCCCC 60.462 68.421 2.05 0.00 0.00 5.80
188 189 1.837499 CTACTTCCCCTAGGCCCCG 60.837 68.421 2.05 0.00 0.00 5.73
189 190 2.308118 CTACTTCCCCTAGGCCCCGA 62.308 65.000 2.05 0.00 0.00 5.14
190 191 1.671925 TACTTCCCCTAGGCCCCGAT 61.672 60.000 2.05 0.00 0.00 4.18
191 192 2.122547 TTCCCCTAGGCCCCGATC 60.123 66.667 2.05 0.00 0.00 3.69
192 193 3.786866 TTCCCCTAGGCCCCGATCC 62.787 68.421 2.05 0.00 0.00 3.36
194 195 4.574614 CCCTAGGCCCCGATCCCA 62.575 72.222 2.05 0.00 0.00 4.37
195 196 2.203998 CCTAGGCCCCGATCCCAT 60.204 66.667 0.00 0.00 0.00 4.00
196 197 2.294078 CCTAGGCCCCGATCCCATC 61.294 68.421 0.00 0.00 0.00 3.51
197 198 2.203938 TAGGCCCCGATCCCATCC 60.204 66.667 0.00 0.00 0.00 3.51
669 670 3.849064 CGAGATCTCGCCCCTTCT 58.151 61.111 30.41 0.00 46.50 2.85
670 671 1.657556 CGAGATCTCGCCCCTTCTC 59.342 63.158 30.41 0.00 46.50 2.87
671 672 1.801309 CGAGATCTCGCCCCTTCTCC 61.801 65.000 30.41 0.00 46.50 3.71
672 673 1.801309 GAGATCTCGCCCCTTCTCCG 61.801 65.000 7.04 0.00 30.61 4.63
673 674 3.507597 GATCTCGCCCCTTCTCCGC 62.508 68.421 0.00 0.00 0.00 5.54
675 676 3.854669 CTCGCCCCTTCTCCGCAT 61.855 66.667 0.00 0.00 0.00 4.73
676 677 2.443203 TCGCCCCTTCTCCGCATA 60.443 61.111 0.00 0.00 0.00 3.14
677 678 2.280186 CGCCCCTTCTCCGCATAC 60.280 66.667 0.00 0.00 0.00 2.39
678 679 2.111251 GCCCCTTCTCCGCATACC 59.889 66.667 0.00 0.00 0.00 2.73
679 680 2.829592 CCCCTTCTCCGCATACCC 59.170 66.667 0.00 0.00 0.00 3.69
680 681 2.819284 CCCCTTCTCCGCATACCCC 61.819 68.421 0.00 0.00 0.00 4.95
681 682 2.070039 CCCTTCTCCGCATACCCCA 61.070 63.158 0.00 0.00 0.00 4.96
682 683 1.632018 CCCTTCTCCGCATACCCCAA 61.632 60.000 0.00 0.00 0.00 4.12
683 684 0.474184 CCTTCTCCGCATACCCCAAT 59.526 55.000 0.00 0.00 0.00 3.16
684 685 1.543429 CCTTCTCCGCATACCCCAATC 60.543 57.143 0.00 0.00 0.00 2.67
685 686 0.472471 TTCTCCGCATACCCCAATCC 59.528 55.000 0.00 0.00 0.00 3.01
686 687 1.073199 CTCCGCATACCCCAATCCC 59.927 63.158 0.00 0.00 0.00 3.85
687 688 2.115266 CCGCATACCCCAATCCCC 59.885 66.667 0.00 0.00 0.00 4.81
688 689 2.460853 CCGCATACCCCAATCCCCT 61.461 63.158 0.00 0.00 0.00 4.79
702 703 2.432300 CCCCTCTACCGCCACGATT 61.432 63.158 0.00 0.00 0.00 3.34
716 717 0.736053 ACGATTCGCTCTGTCTCCTC 59.264 55.000 5.86 0.00 0.00 3.71
736 737 3.878667 CCCTCGCCCCTCCAATCC 61.879 72.222 0.00 0.00 0.00 3.01
757 758 3.634448 CCACTCCACCTAGATCTACACTG 59.366 52.174 0.00 0.00 0.00 3.66
765 766 4.830046 ACCTAGATCTACACTGCAATCGAT 59.170 41.667 0.00 0.00 0.00 3.59
785 786 5.072736 TCGATATCTTCTAGTGGGTGGTAGA 59.927 44.000 0.34 0.00 0.00 2.59
791 792 5.422331 TCTTCTAGTGGGTGGTAGATCTTTG 59.578 44.000 0.00 0.00 0.00 2.77
810 811 1.476891 TGCGTCATCTGACCTCCTAAC 59.523 52.381 4.81 0.00 41.86 2.34
860 861 2.170607 GGAGCAGCACTTACCCTAATCA 59.829 50.000 0.00 0.00 0.00 2.57
912 913 9.143631 GTTATTTTTCTCCACAATTTCATCCTG 57.856 33.333 0.00 0.00 0.00 3.86
1014 1015 8.152246 CCAATTTGCAGAATGGGTGATATAAAT 58.848 33.333 3.33 0.00 35.86 1.40
1099 1100 4.954875 GCTTGAGCACATAGTATCCTTCT 58.045 43.478 0.00 0.00 41.59 2.85
1178 1179 3.074687 TGGAAATTTGTGCCTACCCTACA 59.925 43.478 0.00 0.00 0.00 2.74
1192 1193 7.039011 TGCCTACCCTACATATTTCTGATACAG 60.039 40.741 0.00 0.00 0.00 2.74
1194 1195 8.307483 CCTACCCTACATATTTCTGATACAGTG 58.693 40.741 0.00 0.00 32.61 3.66
1208 1209 9.599866 TTCTGATACAGTGGATAAATGTAACAG 57.400 33.333 13.61 13.61 44.85 3.16
1239 1240 2.739784 TTTTTGCGTGGCCATGGG 59.260 55.556 26.22 11.81 0.00 4.00
1358 1359 0.401356 TGCCATGTTCAGGAGCTCAA 59.599 50.000 17.19 0.00 0.00 3.02
1376 1377 7.118496 AGCTCAAAGTCATTAGCTGTATAGT 57.882 36.000 0.00 0.00 43.46 2.12
1390 1391 7.618019 AGCTGTATAGTGGATGATTTCCTAA 57.382 36.000 0.00 0.00 45.68 2.69
1427 1428 3.523547 CTCTCATCTCCAAGCACTTGAG 58.476 50.000 11.94 7.53 42.93 3.02
1450 1451 5.129650 AGGAGGTTAGAGCTTGATAAGGTTC 59.870 44.000 0.00 0.00 39.77 3.62
1456 1457 4.434520 AGAGCTTGATAAGGTTCGCTTAC 58.565 43.478 0.00 0.00 39.77 2.34
1589 1590 6.198650 TGCAGTGGAATGTGAATTTGATAG 57.801 37.500 0.00 0.00 0.00 2.08
1590 1591 5.711506 TGCAGTGGAATGTGAATTTGATAGT 59.288 36.000 0.00 0.00 0.00 2.12
1740 1741 8.828688 AGGACTGTTTAGACTATTGTAACAAC 57.171 34.615 0.00 0.00 0.00 3.32
1836 1837 6.248433 TCTTCTGGAAGGTTTATCAAATGCT 58.752 36.000 10.01 0.00 38.88 3.79
1909 1910 4.261578 GGCATCCCCATTGTTGATATTG 57.738 45.455 0.00 0.00 0.00 1.90
2087 2088 5.405935 AGTGGGCTGTTATTTTGGATTTC 57.594 39.130 0.00 0.00 0.00 2.17
2132 2133 4.965200 AATCTATAGAGCCCTGAACACC 57.035 45.455 8.70 0.00 0.00 4.16
2329 2331 0.675633 ATGGCTTTCCACACTTGCAC 59.324 50.000 0.00 0.00 46.92 4.57
2333 2335 2.295909 GGCTTTCCACACTTGCACATAA 59.704 45.455 0.00 0.00 0.00 1.90
2347 2349 9.935682 CACTTGCACATAATTAATACACCTAAG 57.064 33.333 0.00 0.00 0.00 2.18
2443 2445 5.140747 ACTTGAGGACACTGATACTCAAC 57.859 43.478 7.09 0.00 42.95 3.18
2490 2492 1.495584 GGACTTGCACGCGTTCTTCA 61.496 55.000 10.22 2.11 0.00 3.02
2514 2516 4.806952 ACTCACCTATTCTAGAGGAGCT 57.193 45.455 3.61 0.00 37.53 4.09
2642 2644 0.822164 AGGTGGTCGAATCTAACGGG 59.178 55.000 0.00 0.00 0.00 5.28
2645 2647 0.819582 TGGTCGAATCTAACGGGGAC 59.180 55.000 0.00 0.00 0.00 4.46
2667 2669 4.230502 ACCATTATCAAGTGGAACATCCCT 59.769 41.667 0.00 0.00 44.52 4.20
2777 2782 9.817809 TTTGGTATATCGCCTGAGATAATTATC 57.182 33.333 16.35 16.35 36.77 1.75
2837 2842 6.330250 AGCTATTGGTATGTACCCTGAATTCT 59.670 38.462 7.05 0.00 45.87 2.40
2935 2940 6.580041 CGCAATAGCAATCTTAATGTTGATCC 59.420 38.462 4.63 0.00 42.27 3.36
2943 2948 8.223100 GCAATCTTAATGTTGATCCAAACAAAC 58.777 33.333 3.02 0.00 42.98 2.93
3040 3046 2.371306 TCATGTCAGAATGTGCCCATG 58.629 47.619 0.00 4.36 36.93 3.66
3067 3073 6.365520 ACTTTCCTGGTCATAAGTTGAAGTT 58.634 36.000 0.00 0.00 35.70 2.66
3099 3105 8.677148 TTGCATGTATTCCTTCTATTACCTTC 57.323 34.615 0.00 0.00 0.00 3.46
3130 3136 4.071961 ACTTGACATGACACTGCTACAA 57.928 40.909 0.00 0.00 0.00 2.41
3182 3188 7.201705 GGGTCTAAACATTTTTATAGCGCTTCT 60.202 37.037 18.68 6.28 0.00 2.85
3183 3189 8.182227 GGTCTAAACATTTTTATAGCGCTTCTT 58.818 33.333 18.68 3.47 0.00 2.52
3184 3190 9.211556 GTCTAAACATTTTTATAGCGCTTCTTC 57.788 33.333 18.68 0.00 0.00 2.87
3185 3191 8.114290 TCTAAACATTTTTATAGCGCTTCTTCG 58.886 33.333 18.68 0.00 0.00 3.79
3226 3232 3.118645 CGATGTCTTTATGATCGTCTGCG 59.881 47.826 0.00 0.00 35.38 5.18
3227 3233 2.193447 TGTCTTTATGATCGTCTGCGC 58.807 47.619 0.00 0.00 38.14 6.09
3231 3237 1.286501 TTATGATCGTCTGCGCCAAC 58.713 50.000 4.18 1.33 38.14 3.77
3270 3276 7.857734 ACACCATGTATATTTGTTTCGATCA 57.142 32.000 0.00 0.00 0.00 2.92
3331 3337 2.094234 GTGTTGCCCCAATCCATAACAC 60.094 50.000 0.00 0.00 40.41 3.32
3433 3439 6.680874 ACATGCATTGAACACACAAAATTT 57.319 29.167 0.00 0.00 33.44 1.82
3617 3623 9.698309 ATTTGAGTTCACATCCTAAGATATACG 57.302 33.333 0.00 0.00 0.00 3.06
3618 3624 8.459911 TTGAGTTCACATCCTAAGATATACGA 57.540 34.615 0.00 0.00 0.00 3.43
3643 3649 9.349145 GAACTTCTCTTAGTACTGAAGTGAATC 57.651 37.037 20.82 13.84 45.45 2.52
3645 3651 8.301002 ACTTCTCTTAGTACTGAAGTGAATCAC 58.699 37.037 19.91 5.02 44.78 3.06
3732 3738 2.009774 AGAGCACGACCATAAACATGC 58.990 47.619 0.00 0.00 0.00 4.06
3759 3765 9.733556 ATATCACATACTGTTTAGAAACCACAA 57.266 29.630 2.80 0.00 38.11 3.33
3768 3774 7.093945 ACTGTTTAGAAACCACAACAAAGATGT 60.094 33.333 2.80 0.00 38.65 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.152139 GGAGATCTGGGAGAGGGGG 60.152 68.421 0.00 0.00 0.00 5.40
11 12 0.178935 GAGGAGATCTGGGAGAGGGG 60.179 65.000 0.00 0.00 0.00 4.79
12 13 0.178935 GGAGGAGATCTGGGAGAGGG 60.179 65.000 0.00 0.00 0.00 4.30
13 14 0.560193 TGGAGGAGATCTGGGAGAGG 59.440 60.000 0.00 0.00 0.00 3.69
14 15 1.703411 GTGGAGGAGATCTGGGAGAG 58.297 60.000 0.00 0.00 0.00 3.20
15 16 0.263172 GGTGGAGGAGATCTGGGAGA 59.737 60.000 0.00 0.00 0.00 3.71
16 17 0.264359 AGGTGGAGGAGATCTGGGAG 59.736 60.000 0.00 0.00 0.00 4.30
17 18 0.263172 GAGGTGGAGGAGATCTGGGA 59.737 60.000 0.00 0.00 0.00 4.37
18 19 0.762461 GGAGGTGGAGGAGATCTGGG 60.762 65.000 0.00 0.00 0.00 4.45
19 20 0.762461 GGGAGGTGGAGGAGATCTGG 60.762 65.000 0.00 0.00 0.00 3.86
20 21 0.031716 TGGGAGGTGGAGGAGATCTG 60.032 60.000 0.00 0.00 0.00 2.90
21 22 0.031616 GTGGGAGGTGGAGGAGATCT 60.032 60.000 0.00 0.00 0.00 2.75
22 23 1.395826 CGTGGGAGGTGGAGGAGATC 61.396 65.000 0.00 0.00 0.00 2.75
23 24 1.381872 CGTGGGAGGTGGAGGAGAT 60.382 63.158 0.00 0.00 0.00 2.75
24 25 1.875422 ATCGTGGGAGGTGGAGGAGA 61.875 60.000 0.00 0.00 0.00 3.71
25 26 0.106167 TATCGTGGGAGGTGGAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
26 27 0.561184 ATATCGTGGGAGGTGGAGGA 59.439 55.000 0.00 0.00 0.00 3.71
27 28 1.344763 GAATATCGTGGGAGGTGGAGG 59.655 57.143 0.00 0.00 0.00 4.30
28 29 2.297597 GAGAATATCGTGGGAGGTGGAG 59.702 54.545 0.00 0.00 0.00 3.86
29 30 2.317040 GAGAATATCGTGGGAGGTGGA 58.683 52.381 0.00 0.00 0.00 4.02
30 31 2.039418 TGAGAATATCGTGGGAGGTGG 58.961 52.381 0.00 0.00 0.00 4.61
31 32 3.458189 GTTGAGAATATCGTGGGAGGTG 58.542 50.000 0.00 0.00 0.00 4.00
32 33 2.434702 GGTTGAGAATATCGTGGGAGGT 59.565 50.000 0.00 0.00 0.00 3.85
33 34 2.700897 AGGTTGAGAATATCGTGGGAGG 59.299 50.000 0.00 0.00 0.00 4.30
34 35 3.243907 GGAGGTTGAGAATATCGTGGGAG 60.244 52.174 0.00 0.00 0.00 4.30
35 36 2.698797 GGAGGTTGAGAATATCGTGGGA 59.301 50.000 0.00 0.00 0.00 4.37
36 37 2.700897 AGGAGGTTGAGAATATCGTGGG 59.299 50.000 0.00 0.00 0.00 4.61
37 38 3.243907 GGAGGAGGTTGAGAATATCGTGG 60.244 52.174 0.00 0.00 0.00 4.94
38 39 3.639094 AGGAGGAGGTTGAGAATATCGTG 59.361 47.826 0.00 0.00 0.00 4.35
39 40 3.892588 GAGGAGGAGGTTGAGAATATCGT 59.107 47.826 0.00 0.00 0.00 3.73
40 41 4.148838 AGAGGAGGAGGTTGAGAATATCG 58.851 47.826 0.00 0.00 0.00 2.92
41 42 4.217550 CGAGAGGAGGAGGTTGAGAATATC 59.782 50.000 0.00 0.00 0.00 1.63
42 43 4.148838 CGAGAGGAGGAGGTTGAGAATAT 58.851 47.826 0.00 0.00 0.00 1.28
43 44 3.053544 ACGAGAGGAGGAGGTTGAGAATA 60.054 47.826 0.00 0.00 0.00 1.75
44 45 2.291930 ACGAGAGGAGGAGGTTGAGAAT 60.292 50.000 0.00 0.00 0.00 2.40
45 46 1.075698 ACGAGAGGAGGAGGTTGAGAA 59.924 52.381 0.00 0.00 0.00 2.87
46 47 0.699399 ACGAGAGGAGGAGGTTGAGA 59.301 55.000 0.00 0.00 0.00 3.27
47 48 1.474879 GAACGAGAGGAGGAGGTTGAG 59.525 57.143 0.00 0.00 0.00 3.02
48 49 1.203013 TGAACGAGAGGAGGAGGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
49 50 1.257743 TGAACGAGAGGAGGAGGTTG 58.742 55.000 0.00 0.00 0.00 3.77
50 51 2.011122 TTGAACGAGAGGAGGAGGTT 57.989 50.000 0.00 0.00 0.00 3.50
51 52 2.104170 GATTGAACGAGAGGAGGAGGT 58.896 52.381 0.00 0.00 0.00 3.85
52 53 1.410882 GGATTGAACGAGAGGAGGAGG 59.589 57.143 0.00 0.00 0.00 4.30
53 54 1.410882 GGGATTGAACGAGAGGAGGAG 59.589 57.143 0.00 0.00 0.00 3.69
54 55 1.486211 GGGATTGAACGAGAGGAGGA 58.514 55.000 0.00 0.00 0.00 3.71
55 56 0.466124 GGGGATTGAACGAGAGGAGG 59.534 60.000 0.00 0.00 0.00 4.30
56 57 1.410882 GAGGGGATTGAACGAGAGGAG 59.589 57.143 0.00 0.00 0.00 3.69
57 58 1.486211 GAGGGGATTGAACGAGAGGA 58.514 55.000 0.00 0.00 0.00 3.71
58 59 0.103208 CGAGGGGATTGAACGAGAGG 59.897 60.000 0.00 0.00 0.00 3.69
59 60 1.103803 TCGAGGGGATTGAACGAGAG 58.896 55.000 0.00 0.00 0.00 3.20
60 61 0.815734 GTCGAGGGGATTGAACGAGA 59.184 55.000 0.00 0.00 33.82 4.04
61 62 0.179108 GGTCGAGGGGATTGAACGAG 60.179 60.000 0.00 0.00 33.82 4.18
62 63 0.901114 TGGTCGAGGGGATTGAACGA 60.901 55.000 0.00 0.00 30.63 3.85
63 64 0.178068 ATGGTCGAGGGGATTGAACG 59.822 55.000 0.00 0.00 30.63 3.95
64 65 1.475213 GGATGGTCGAGGGGATTGAAC 60.475 57.143 0.00 0.00 0.00 3.18
65 66 0.837272 GGATGGTCGAGGGGATTGAA 59.163 55.000 0.00 0.00 0.00 2.69
66 67 0.326143 TGGATGGTCGAGGGGATTGA 60.326 55.000 0.00 0.00 0.00 2.57
67 68 0.179045 GTGGATGGTCGAGGGGATTG 60.179 60.000 0.00 0.00 0.00 2.67
68 69 1.686325 CGTGGATGGTCGAGGGGATT 61.686 60.000 0.00 0.00 0.00 3.01
69 70 2.134287 CGTGGATGGTCGAGGGGAT 61.134 63.158 0.00 0.00 0.00 3.85
70 71 2.583298 ATCGTGGATGGTCGAGGGGA 62.583 60.000 0.00 0.00 39.38 4.81
71 72 2.088674 GATCGTGGATGGTCGAGGGG 62.089 65.000 0.00 0.00 39.38 4.79
72 73 1.364171 GATCGTGGATGGTCGAGGG 59.636 63.158 0.00 0.00 39.38 4.30
73 74 1.364171 GGATCGTGGATGGTCGAGG 59.636 63.158 0.00 0.00 39.38 4.63
74 75 1.364171 GGGATCGTGGATGGTCGAG 59.636 63.158 0.00 0.00 39.38 4.04
75 76 2.131709 GGGGATCGTGGATGGTCGA 61.132 63.158 0.00 0.00 40.28 4.20
76 77 2.134287 AGGGGATCGTGGATGGTCG 61.134 63.158 0.00 0.00 0.00 4.79
77 78 1.338136 ACAGGGGATCGTGGATGGTC 61.338 60.000 0.00 0.00 33.45 4.02
78 79 0.914417 AACAGGGGATCGTGGATGGT 60.914 55.000 0.00 0.00 33.45 3.55
79 80 1.128200 TAACAGGGGATCGTGGATGG 58.872 55.000 0.00 0.00 33.45 3.51
80 81 1.762957 AGTAACAGGGGATCGTGGATG 59.237 52.381 0.00 0.00 33.45 3.51
81 82 2.176247 AGTAACAGGGGATCGTGGAT 57.824 50.000 0.00 0.00 33.45 3.41
82 83 2.024655 AGTAGTAACAGGGGATCGTGGA 60.025 50.000 0.00 0.00 33.45 4.02
83 84 2.361438 GAGTAGTAACAGGGGATCGTGG 59.639 54.545 0.00 0.00 33.45 4.94
84 85 2.361438 GGAGTAGTAACAGGGGATCGTG 59.639 54.545 0.00 0.00 35.14 4.35
85 86 2.244252 AGGAGTAGTAACAGGGGATCGT 59.756 50.000 0.00 0.00 0.00 3.73
86 87 2.885894 GAGGAGTAGTAACAGGGGATCG 59.114 54.545 0.00 0.00 0.00 3.69
87 88 3.232662 GGAGGAGTAGTAACAGGGGATC 58.767 54.545 0.00 0.00 0.00 3.36
88 89 2.090663 GGGAGGAGTAGTAACAGGGGAT 60.091 54.545 0.00 0.00 0.00 3.85
89 90 1.290130 GGGAGGAGTAGTAACAGGGGA 59.710 57.143 0.00 0.00 0.00 4.81
90 91 1.691801 GGGGAGGAGTAGTAACAGGGG 60.692 61.905 0.00 0.00 0.00 4.79
91 92 1.691801 GGGGGAGGAGTAGTAACAGGG 60.692 61.905 0.00 0.00 0.00 4.45
92 93 1.790818 GGGGGAGGAGTAGTAACAGG 58.209 60.000 0.00 0.00 0.00 4.00
110 111 3.910646 AAGGGGGTTGAGGGGAGGG 62.911 68.421 0.00 0.00 0.00 4.30
111 112 2.204306 AAGGGGGTTGAGGGGAGG 60.204 66.667 0.00 0.00 0.00 4.30
112 113 1.541368 TGAAGGGGGTTGAGGGGAG 60.541 63.158 0.00 0.00 0.00 4.30
113 114 1.850755 GTGAAGGGGGTTGAGGGGA 60.851 63.158 0.00 0.00 0.00 4.81
114 115 2.763902 GTGAAGGGGGTTGAGGGG 59.236 66.667 0.00 0.00 0.00 4.79
115 116 1.774894 TTCGTGAAGGGGGTTGAGGG 61.775 60.000 0.00 0.00 0.00 4.30
116 117 0.321653 CTTCGTGAAGGGGGTTGAGG 60.322 60.000 1.57 0.00 34.87 3.86
117 118 0.685097 TCTTCGTGAAGGGGGTTGAG 59.315 55.000 9.58 0.00 38.88 3.02
118 119 1.278127 GATCTTCGTGAAGGGGGTTGA 59.722 52.381 9.58 0.00 38.88 3.18
119 120 1.279271 AGATCTTCGTGAAGGGGGTTG 59.721 52.381 9.58 0.00 38.88 3.77
120 121 1.657804 AGATCTTCGTGAAGGGGGTT 58.342 50.000 9.58 0.00 38.88 4.11
121 122 2.108970 GTAGATCTTCGTGAAGGGGGT 58.891 52.381 0.00 0.00 38.88 4.95
122 123 2.362717 GAGTAGATCTTCGTGAAGGGGG 59.637 54.545 0.00 0.00 38.88 5.40
123 124 3.067461 CAGAGTAGATCTTCGTGAAGGGG 59.933 52.174 0.00 0.00 35.47 4.79
124 125 3.490078 GCAGAGTAGATCTTCGTGAAGGG 60.490 52.174 0.00 0.00 35.47 3.95
125 126 3.490078 GGCAGAGTAGATCTTCGTGAAGG 60.490 52.174 0.00 0.00 35.47 3.46
126 127 3.701241 GGCAGAGTAGATCTTCGTGAAG 58.299 50.000 0.00 3.17 35.47 3.02
127 128 2.097629 CGGCAGAGTAGATCTTCGTGAA 59.902 50.000 0.00 0.00 35.47 3.18
128 129 1.671328 CGGCAGAGTAGATCTTCGTGA 59.329 52.381 0.00 0.00 35.47 4.35
129 130 1.862008 GCGGCAGAGTAGATCTTCGTG 60.862 57.143 0.00 0.36 35.47 4.35
130 131 0.382515 GCGGCAGAGTAGATCTTCGT 59.617 55.000 0.00 0.00 35.47 3.85
131 132 0.658829 CGCGGCAGAGTAGATCTTCG 60.659 60.000 0.00 0.00 35.47 3.79
132 133 0.318275 CCGCGGCAGAGTAGATCTTC 60.318 60.000 14.67 0.00 35.47 2.87
133 134 1.038130 ACCGCGGCAGAGTAGATCTT 61.038 55.000 28.58 0.00 35.47 2.40
134 135 1.454111 ACCGCGGCAGAGTAGATCT 60.454 57.895 28.58 0.00 39.56 2.75
135 136 1.299468 CACCGCGGCAGAGTAGATC 60.299 63.158 28.58 0.00 0.00 2.75
136 137 1.109920 ATCACCGCGGCAGAGTAGAT 61.110 55.000 28.58 13.94 0.00 1.98
137 138 1.725557 GATCACCGCGGCAGAGTAGA 61.726 60.000 28.58 12.16 0.00 2.59
138 139 1.299468 GATCACCGCGGCAGAGTAG 60.299 63.158 28.58 6.61 0.00 2.57
139 140 1.320344 AAGATCACCGCGGCAGAGTA 61.320 55.000 28.58 4.40 0.00 2.59
140 141 2.564553 GAAGATCACCGCGGCAGAGT 62.565 60.000 28.58 12.28 0.00 3.24
141 142 1.880340 GAAGATCACCGCGGCAGAG 60.880 63.158 28.58 13.39 0.00 3.35
142 143 1.888436 AAGAAGATCACCGCGGCAGA 61.888 55.000 28.58 24.33 0.00 4.26
143 144 1.424493 GAAGAAGATCACCGCGGCAG 61.424 60.000 28.58 19.22 0.00 4.85
144 145 1.447838 GAAGAAGATCACCGCGGCA 60.448 57.895 28.58 13.44 0.00 5.69
145 146 2.174319 GGAAGAAGATCACCGCGGC 61.174 63.158 28.58 9.08 0.00 6.53
146 147 0.528684 GAGGAAGAAGATCACCGCGG 60.529 60.000 26.86 26.86 0.00 6.46
147 148 0.528684 GGAGGAAGAAGATCACCGCG 60.529 60.000 0.00 0.00 0.00 6.46
148 149 0.827368 AGGAGGAAGAAGATCACCGC 59.173 55.000 0.00 0.00 0.00 5.68
149 150 1.410882 GGAGGAGGAAGAAGATCACCG 59.589 57.143 0.00 0.00 0.00 4.94
150 151 1.765904 GGGAGGAGGAAGAAGATCACC 59.234 57.143 0.00 0.00 0.00 4.02
151 152 2.758130 AGGGAGGAGGAAGAAGATCAC 58.242 52.381 0.00 0.00 0.00 3.06
152 153 3.533907 AGTAGGGAGGAGGAAGAAGATCA 59.466 47.826 0.00 0.00 0.00 2.92
153 154 4.193240 AGTAGGGAGGAGGAAGAAGATC 57.807 50.000 0.00 0.00 0.00 2.75
154 155 4.552674 GAAGTAGGGAGGAGGAAGAAGAT 58.447 47.826 0.00 0.00 0.00 2.40
155 156 3.309994 GGAAGTAGGGAGGAGGAAGAAGA 60.310 52.174 0.00 0.00 0.00 2.87
156 157 3.035363 GGAAGTAGGGAGGAGGAAGAAG 58.965 54.545 0.00 0.00 0.00 2.85
157 158 2.292984 GGGAAGTAGGGAGGAGGAAGAA 60.293 54.545 0.00 0.00 0.00 2.52
158 159 1.291335 GGGAAGTAGGGAGGAGGAAGA 59.709 57.143 0.00 0.00 0.00 2.87
159 160 1.693083 GGGGAAGTAGGGAGGAGGAAG 60.693 61.905 0.00 0.00 0.00 3.46
160 161 0.342313 GGGGAAGTAGGGAGGAGGAA 59.658 60.000 0.00 0.00 0.00 3.36
161 162 0.557907 AGGGGAAGTAGGGAGGAGGA 60.558 60.000 0.00 0.00 0.00 3.71
162 163 1.148236 CTAGGGGAAGTAGGGAGGAGG 59.852 61.905 0.00 0.00 0.00 4.30
163 164 1.148236 CCTAGGGGAAGTAGGGAGGAG 59.852 61.905 0.00 0.00 34.42 3.69
164 165 1.242444 CCTAGGGGAAGTAGGGAGGA 58.758 60.000 0.00 0.00 34.42 3.71
165 166 0.472161 GCCTAGGGGAAGTAGGGAGG 60.472 65.000 11.72 0.00 38.03 4.30
166 167 0.472161 GGCCTAGGGGAAGTAGGGAG 60.472 65.000 11.72 0.00 38.03 4.30
167 168 1.630442 GGCCTAGGGGAAGTAGGGA 59.370 63.158 11.72 0.00 38.03 4.20
168 169 1.461655 GGGCCTAGGGGAAGTAGGG 60.462 68.421 11.72 0.00 38.03 3.53
169 170 1.461655 GGGGCCTAGGGGAAGTAGG 60.462 68.421 11.72 0.00 40.25 3.18
170 171 1.837499 CGGGGCCTAGGGGAAGTAG 60.837 68.421 11.72 0.00 33.58 2.57
171 172 1.671925 ATCGGGGCCTAGGGGAAGTA 61.672 60.000 11.72 0.00 33.58 2.24
172 173 2.967063 GATCGGGGCCTAGGGGAAGT 62.967 65.000 11.72 0.00 33.58 3.01
173 174 2.122369 ATCGGGGCCTAGGGGAAG 60.122 66.667 11.72 0.00 33.58 3.46
174 175 2.122547 GATCGGGGCCTAGGGGAA 60.123 66.667 11.72 0.00 33.58 3.97
175 176 4.250170 GGATCGGGGCCTAGGGGA 62.250 72.222 11.72 0.00 33.58 4.81
177 178 3.872487 ATGGGATCGGGGCCTAGGG 62.872 68.421 11.72 0.00 0.00 3.53
178 179 2.203998 ATGGGATCGGGGCCTAGG 60.204 66.667 3.67 3.67 0.00 3.02
179 180 2.294078 GGATGGGATCGGGGCCTAG 61.294 68.421 0.84 0.00 0.00 3.02
180 181 2.203938 GGATGGGATCGGGGCCTA 60.204 66.667 0.84 0.00 0.00 3.93
653 654 1.801309 CGGAGAAGGGGCGAGATCTC 61.801 65.000 13.05 13.05 38.04 2.75
654 655 1.830408 CGGAGAAGGGGCGAGATCT 60.830 63.158 0.00 0.00 0.00 2.75
655 656 2.731374 CGGAGAAGGGGCGAGATC 59.269 66.667 0.00 0.00 0.00 2.75
656 657 3.541713 GCGGAGAAGGGGCGAGAT 61.542 66.667 0.00 0.00 0.00 2.75
657 658 2.921853 TATGCGGAGAAGGGGCGAGA 62.922 60.000 0.00 0.00 0.00 4.04
658 659 2.498941 TATGCGGAGAAGGGGCGAG 61.499 63.158 0.00 0.00 0.00 5.03
659 660 2.443203 TATGCGGAGAAGGGGCGA 60.443 61.111 0.00 0.00 0.00 5.54
660 661 2.280186 GTATGCGGAGAAGGGGCG 60.280 66.667 0.00 0.00 0.00 6.13
661 662 2.111251 GGTATGCGGAGAAGGGGC 59.889 66.667 0.00 0.00 0.00 5.80
662 663 2.819284 GGGGTATGCGGAGAAGGGG 61.819 68.421 0.00 0.00 0.00 4.79
663 664 1.632018 TTGGGGTATGCGGAGAAGGG 61.632 60.000 0.00 0.00 0.00 3.95
664 665 0.474184 ATTGGGGTATGCGGAGAAGG 59.526 55.000 0.00 0.00 0.00 3.46
665 666 1.543429 GGATTGGGGTATGCGGAGAAG 60.543 57.143 0.00 0.00 0.00 2.85
666 667 0.472471 GGATTGGGGTATGCGGAGAA 59.528 55.000 0.00 0.00 0.00 2.87
667 668 1.415672 GGGATTGGGGTATGCGGAGA 61.416 60.000 0.00 0.00 0.00 3.71
668 669 1.073199 GGGATTGGGGTATGCGGAG 59.927 63.158 0.00 0.00 0.00 4.63
669 670 2.457323 GGGGATTGGGGTATGCGGA 61.457 63.158 0.00 0.00 0.00 5.54
670 671 2.115266 GGGGATTGGGGTATGCGG 59.885 66.667 0.00 0.00 0.00 5.69
671 672 1.073199 GAGGGGATTGGGGTATGCG 59.927 63.158 0.00 0.00 0.00 4.73
672 673 1.351350 GTAGAGGGGATTGGGGTATGC 59.649 57.143 0.00 0.00 0.00 3.14
673 674 1.985895 GGTAGAGGGGATTGGGGTATG 59.014 57.143 0.00 0.00 0.00 2.39
674 675 1.484446 CGGTAGAGGGGATTGGGGTAT 60.484 57.143 0.00 0.00 0.00 2.73
675 676 0.105349 CGGTAGAGGGGATTGGGGTA 60.105 60.000 0.00 0.00 0.00 3.69
676 677 1.384082 CGGTAGAGGGGATTGGGGT 60.384 63.158 0.00 0.00 0.00 4.95
677 678 2.819284 GCGGTAGAGGGGATTGGGG 61.819 68.421 0.00 0.00 0.00 4.96
678 679 2.819284 GGCGGTAGAGGGGATTGGG 61.819 68.421 0.00 0.00 0.00 4.12
679 680 2.070039 TGGCGGTAGAGGGGATTGG 61.070 63.158 0.00 0.00 0.00 3.16
680 681 1.146263 GTGGCGGTAGAGGGGATTG 59.854 63.158 0.00 0.00 0.00 2.67
681 682 2.432300 CGTGGCGGTAGAGGGGATT 61.432 63.158 0.00 0.00 0.00 3.01
682 683 2.658321 ATCGTGGCGGTAGAGGGGAT 62.658 60.000 0.00 0.00 0.00 3.85
683 684 2.866523 AATCGTGGCGGTAGAGGGGA 62.867 60.000 0.00 0.00 0.00 4.81
684 685 2.365095 GAATCGTGGCGGTAGAGGGG 62.365 65.000 0.00 0.00 0.00 4.79
685 686 1.067582 GAATCGTGGCGGTAGAGGG 59.932 63.158 0.00 0.00 0.00 4.30
686 687 1.299165 CGAATCGTGGCGGTAGAGG 60.299 63.158 0.00 0.00 0.00 3.69
687 688 1.944676 GCGAATCGTGGCGGTAGAG 60.945 63.158 4.07 0.00 0.00 2.43
688 689 2.103538 GCGAATCGTGGCGGTAGA 59.896 61.111 4.07 0.00 0.00 2.59
702 703 1.077357 GGAGGAGGAGACAGAGCGA 60.077 63.158 0.00 0.00 0.00 4.93
736 737 3.067461 GCAGTGTAGATCTAGGTGGAGTG 59.933 52.174 1.64 0.35 0.00 3.51
757 758 4.926238 CACCCACTAGAAGATATCGATTGC 59.074 45.833 1.71 0.00 0.00 3.56
765 766 6.532119 AGATCTACCACCCACTAGAAGATA 57.468 41.667 0.00 0.00 0.00 1.98
785 786 2.419297 GGAGGTCAGATGACGCAAAGAT 60.419 50.000 6.87 0.00 45.65 2.40
791 792 1.202428 GGTTAGGAGGTCAGATGACGC 60.202 57.143 6.87 2.04 45.65 5.19
810 811 1.940613 GTAGCTCCAAAAGTATGCCGG 59.059 52.381 0.00 0.00 0.00 6.13
912 913 2.103263 GGGGAGGTGTGATAGTGATGAC 59.897 54.545 0.00 0.00 0.00 3.06
1014 1015 5.730550 TCTTGCGCTAATTTCTTCCTCTTA 58.269 37.500 9.73 0.00 0.00 2.10
1099 1100 4.129380 CTCACGGCCTCATTCAATGATAA 58.871 43.478 0.00 0.00 38.85 1.75
1235 1236 1.477700 CAATGATTGCGGTGTTCCCAT 59.522 47.619 0.00 0.00 0.00 4.00
1239 1240 3.182173 CACAAACAATGATTGCGGTGTTC 59.818 43.478 4.84 0.00 33.18 3.18
1358 1359 7.603180 TCATCCACTATACAGCTAATGACTT 57.397 36.000 0.00 0.00 0.00 3.01
1390 1391 2.909006 TGAGAGCTTGATCCCTGAACTT 59.091 45.455 0.00 0.00 0.00 2.66
1427 1428 5.360649 AACCTTATCAAGCTCTAACCTCC 57.639 43.478 0.00 0.00 0.00 4.30
1456 1457 5.946298 TGAGAAATCAACAATGCTAGCTTG 58.054 37.500 17.23 18.42 0.00 4.01
1468 1469 2.229784 CAGGGCAGGTTGAGAAATCAAC 59.770 50.000 11.71 11.71 46.60 3.18
1481 1482 0.612732 TTCTTCCAATGCAGGGCAGG 60.613 55.000 6.94 0.00 43.65 4.85
1704 1705 2.803030 AACAGTCCTCGCCTAGACTA 57.197 50.000 0.00 0.00 41.38 2.59
1740 1741 8.863086 ACATTATCACATCCCCAAGATTTATTG 58.137 33.333 0.00 0.00 30.59 1.90
1836 1837 6.659745 TCACTTAGCAACTCCAAGTAACTA 57.340 37.500 0.00 0.00 31.46 2.24
1891 1892 4.203342 AGGCAATATCAACAATGGGGAT 57.797 40.909 0.00 0.00 0.00 3.85
1896 1897 5.258456 AGAGCAAGGCAATATCAACAATG 57.742 39.130 0.00 0.00 0.00 2.82
1901 1902 3.788333 GCAAGAGCAAGGCAATATCAA 57.212 42.857 0.00 0.00 41.58 2.57
2443 2445 4.965042 GTTAGCAACCAAAAACCATTCG 57.035 40.909 0.00 0.00 0.00 3.34
2490 2492 4.647399 GCTCCTCTAGAATAGGTGAGTTGT 59.353 45.833 0.00 0.00 39.78 3.32
2514 2516 7.202011 GCCATACCTCTAAAAGTAGGAGATTCA 60.202 40.741 0.00 0.00 36.66 2.57
2642 2644 4.580580 GGATGTTCCACTTGATAATGGTCC 59.419 45.833 0.00 0.00 36.28 4.46
2645 2647 4.796606 AGGGATGTTCCACTTGATAATGG 58.203 43.478 0.00 0.00 38.64 3.16
2655 2657 4.200092 GTCTCCAATAAGGGATGTTCCAC 58.800 47.826 0.00 0.00 38.64 4.02
2667 2669 5.788533 TGACTTCCTTAAGGGTCTCCAATAA 59.211 40.000 21.53 4.16 37.01 1.40
2777 2782 1.536766 TGCATTTGGCTCTCTTTGACG 59.463 47.619 0.00 0.00 45.15 4.35
2977 2982 3.144506 CACCACTTGCATATCATCCTCC 58.855 50.000 0.00 0.00 0.00 4.30
2989 2994 5.385509 AAACCATATTGTACACCACTTGC 57.614 39.130 0.00 0.00 0.00 4.01
3016 3022 3.193903 TGGGCACATTCTGACATGATTTG 59.806 43.478 0.00 0.00 0.00 2.32
3040 3046 7.824779 ACTTCAACTTATGACCAGGAAAGTATC 59.175 37.037 0.00 0.00 37.92 2.24
3067 3073 9.466497 AATAGAAGGAATACATGCAAGAAGAAA 57.534 29.630 0.00 0.00 0.00 2.52
3099 3105 7.042858 GCAGTGTCATGTCAAGTTCTATCTATG 60.043 40.741 0.00 0.00 0.00 2.23
3182 3188 7.716768 TCGATTTATAAATATGGTGCACGAA 57.283 32.000 11.45 1.45 0.00 3.85
3183 3189 7.386573 ACATCGATTTATAAATATGGTGCACGA 59.613 33.333 18.65 7.55 0.00 4.35
3184 3190 7.518161 ACATCGATTTATAAATATGGTGCACG 58.482 34.615 18.65 12.60 0.00 5.34
3185 3191 8.721478 AGACATCGATTTATAAATATGGTGCAC 58.279 33.333 18.65 8.80 0.00 4.57
3220 3226 2.813226 TATGTGGGGTTGGCGCAGAC 62.813 60.000 10.83 6.81 0.00 3.51
3222 3228 0.179032 TATATGTGGGGTTGGCGCAG 60.179 55.000 10.83 0.00 0.00 5.18
3226 3232 5.221362 GGTGTTATTTATATGTGGGGTTGGC 60.221 44.000 0.00 0.00 0.00 4.52
3227 3233 5.894393 TGGTGTTATTTATATGTGGGGTTGG 59.106 40.000 0.00 0.00 0.00 3.77
3231 3237 8.877864 ATACATGGTGTTATTTATATGTGGGG 57.122 34.615 0.00 0.00 31.84 4.96
3617 3623 9.349145 GATTCACTTCAGTACTAAGAGAAGTTC 57.651 37.037 18.72 12.77 46.02 3.01
3618 3624 8.861086 TGATTCACTTCAGTACTAAGAGAAGTT 58.139 33.333 18.72 8.98 46.02 2.66
3629 3635 7.426929 AAGACATTGTGATTCACTTCAGTAC 57.573 36.000 17.26 4.26 35.11 2.73
3709 3715 1.278238 GTTTATGGTCGTGCTCTCCG 58.722 55.000 0.00 0.00 0.00 4.63
3759 3765 2.020720 TGGTTCGCAACACATCTTTGT 58.979 42.857 2.28 0.00 36.15 2.83
3768 3774 4.998033 TCTAACAACATATGGTTCGCAACA 59.002 37.500 7.80 0.00 37.72 3.33


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

AutoCloner maintained by Alex Coulton.