Multiple sequence alignment - TraesCS2D01G346900

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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 TraesCS2D01G346900 chr2D 100.000 4360 0 0 1 4360 444765602 444761243 0.000000e+00 8052.0
1 TraesCS2D01G346900 chr2D 80.252 238 33 13 5 240 468976855 468977080 2.700000e-37 167.0
2 TraesCS2D01G346900 chr2A 92.009 4092 155 59 354 4360 587277305 587273301 0.000000e+00 5587.0
3 TraesCS2D01G346900 chr2A 92.000 75 4 2 238 312 587277380 587277308 2.140000e-18 104.0
4 TraesCS2D01G346900 chr2B 97.960 1814 36 1 2548 4360 523086000 523084187 0.000000e+00 3144.0
5 TraesCS2D01G346900 chr2B 92.098 1835 70 31 765 2550 523087924 523086116 0.000000e+00 2516.0
6 TraesCS2D01G346900 chr2B 84.516 155 15 7 87 240 482190878 482191024 1.260000e-30 145.0
7 TraesCS2D01G346900 chr2B 91.026 78 5 2 163 240 174365356 174365281 2.140000e-18 104.0
8 TraesCS2D01G346900 chr2B 83.333 96 10 5 155 248 111083430 111083521 2.790000e-12 84.2
9 TraesCS2D01G346900 chr2B 83.146 89 11 4 154 241 773984264 773984349 1.300000e-10 78.7
10 TraesCS2D01G346900 chr2B 84.848 66 9 1 615 680 523088060 523087996 1.010000e-06 65.8
11 TraesCS2D01G346900 chr5B 84.454 238 27 7 6 241 497453989 497454218 4.390000e-55 226.0
12 TraesCS2D01G346900 chr3A 82.684 231 30 7 12 241 737345143 737344922 3.440000e-46 196.0
13 TraesCS2D01G346900 chr6D 85.443 158 14 9 87 242 297521245 297521395 5.840000e-34 156.0
14 TraesCS2D01G346900 chr3B 84.071 113 10 8 128 238 163164433 163164327 7.710000e-18 102.0


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 TraesCS2D01G346900 chr2D 444761243 444765602 4359 True 8052.0 8052 100.000000 1 4360 1 chr2D.!!$R1 4359
1 TraesCS2D01G346900 chr2A 587273301 587277380 4079 True 2845.5 5587 92.004500 238 4360 2 chr2A.!!$R1 4122
2 TraesCS2D01G346900 chr2B 523084187 523088060 3873 True 1908.6 3144 91.635333 615 4360 3 chr2B.!!$R2 3745

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
36 37 0.035439 ATGTAGGGCGTGAAAGGTGG 60.035 55.000 0.00 0.00 0.00 4.61 F
47 48 0.038310 GAAAGGTGGCAGGCCTACTT 59.962 55.000 3.98 12.21 34.81 2.24 F
185 186 0.107654 CGTGGAGGGGTTTCTCATCC 60.108 60.000 0.00 0.00 35.58 3.51 F
831 865 0.179029 AACACTAGCCCACACCACAC 60.179 55.000 0.00 0.00 0.00 3.82 F
1611 1700 1.078848 GCTCGGGCTCAGTGTCAAT 60.079 57.895 0.00 0.00 35.22 2.57 F
2684 2909 0.254178 ATGCTGTCACCCATCTCACC 59.746 55.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1643 0.034059 ACTGCTTCCTCGACTTGGTG 59.966 55.000 0.00 0.0 0.00 4.17 R
1688 1777 1.609841 GCATCGATCATCCATGCCTCA 60.610 52.381 5.96 0.0 37.54 3.86 R
1889 1978 2.673368 CTCTCCAATCACGTAAACCTGC 59.327 50.000 0.00 0.0 0.00 4.85 R
2351 2458 0.456995 GAAGGCGAGAGGAGTGAACG 60.457 60.000 0.00 0.0 0.00 3.95 R
2837 3066 0.749818 TTGAACCAAGAACAGCGCCA 60.750 50.000 2.29 0.0 0.00 5.69 R
3562 3791 2.103771 GTGGCTGCCATAGATCTTCTGA 59.896 50.000 26.22 0.0 35.28 3.27 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 7.278461 CATAGGATATCGGTAGAATGTAGGG 57.722 44.000 0.00 0.00 0.00 3.53
25 26 4.024670 AGGATATCGGTAGAATGTAGGGC 58.975 47.826 0.00 0.00 0.00 5.19
26 27 3.181489 GGATATCGGTAGAATGTAGGGCG 60.181 52.174 0.00 0.00 0.00 6.13
27 28 1.700955 ATCGGTAGAATGTAGGGCGT 58.299 50.000 0.00 0.00 0.00 5.68
28 29 0.742505 TCGGTAGAATGTAGGGCGTG 59.257 55.000 0.00 0.00 0.00 5.34
29 30 0.742505 CGGTAGAATGTAGGGCGTGA 59.257 55.000 0.00 0.00 0.00 4.35
30 31 1.135527 CGGTAGAATGTAGGGCGTGAA 59.864 52.381 0.00 0.00 0.00 3.18
31 32 2.417651 CGGTAGAATGTAGGGCGTGAAA 60.418 50.000 0.00 0.00 0.00 2.69
32 33 3.195661 GGTAGAATGTAGGGCGTGAAAG 58.804 50.000 0.00 0.00 0.00 2.62
33 34 2.403252 AGAATGTAGGGCGTGAAAGG 57.597 50.000 0.00 0.00 0.00 3.11
34 35 1.628846 AGAATGTAGGGCGTGAAAGGT 59.371 47.619 0.00 0.00 0.00 3.50
35 36 1.737793 GAATGTAGGGCGTGAAAGGTG 59.262 52.381 0.00 0.00 0.00 4.00
36 37 0.035439 ATGTAGGGCGTGAAAGGTGG 60.035 55.000 0.00 0.00 0.00 4.61
37 38 2.038837 GTAGGGCGTGAAAGGTGGC 61.039 63.158 0.00 0.00 0.00 5.01
38 39 2.521451 TAGGGCGTGAAAGGTGGCA 61.521 57.895 0.00 0.00 0.00 4.92
39 40 2.463589 TAGGGCGTGAAAGGTGGCAG 62.464 60.000 0.00 0.00 0.00 4.85
40 41 3.365265 GGCGTGAAAGGTGGCAGG 61.365 66.667 0.00 0.00 0.00 4.85
41 42 4.043200 GCGTGAAAGGTGGCAGGC 62.043 66.667 0.00 0.00 38.49 4.85
42 43 3.365265 CGTGAAAGGTGGCAGGCC 61.365 66.667 2.62 2.62 0.00 5.19
43 44 2.116125 GTGAAAGGTGGCAGGCCT 59.884 61.111 12.19 0.00 38.11 5.19
44 45 1.378762 GTGAAAGGTGGCAGGCCTA 59.621 57.895 3.98 0.00 34.81 3.93
45 46 0.960861 GTGAAAGGTGGCAGGCCTAC 60.961 60.000 3.98 0.00 34.81 3.18
46 47 1.133809 TGAAAGGTGGCAGGCCTACT 61.134 55.000 3.98 6.68 34.81 2.57
47 48 0.038310 GAAAGGTGGCAGGCCTACTT 59.962 55.000 3.98 12.21 34.81 2.24
48 49 1.280998 GAAAGGTGGCAGGCCTACTTA 59.719 52.381 3.98 0.00 34.81 2.24
49 50 1.368374 AAGGTGGCAGGCCTACTTAA 58.632 50.000 3.98 0.00 34.81 1.85
50 51 0.912486 AGGTGGCAGGCCTACTTAAG 59.088 55.000 3.98 0.00 33.97 1.85
63 64 4.192317 CCTACTTAAGGCAGACATGTTCC 58.808 47.826 7.53 2.04 38.97 3.62
64 65 2.699954 ACTTAAGGCAGACATGTTCCG 58.300 47.619 7.53 0.00 0.00 4.30
65 66 2.301870 ACTTAAGGCAGACATGTTCCGA 59.698 45.455 7.53 0.00 0.00 4.55
66 67 3.055094 ACTTAAGGCAGACATGTTCCGAT 60.055 43.478 7.53 0.33 0.00 4.18
67 68 2.496899 AAGGCAGACATGTTCCGATT 57.503 45.000 0.00 0.00 0.00 3.34
68 69 2.029838 AGGCAGACATGTTCCGATTC 57.970 50.000 0.00 0.00 0.00 2.52
69 70 1.278985 AGGCAGACATGTTCCGATTCA 59.721 47.619 0.00 0.00 0.00 2.57
70 71 2.092753 AGGCAGACATGTTCCGATTCAT 60.093 45.455 0.00 0.00 0.00 2.57
71 72 3.134623 AGGCAGACATGTTCCGATTCATA 59.865 43.478 0.00 0.00 0.00 2.15
72 73 3.496130 GGCAGACATGTTCCGATTCATAG 59.504 47.826 0.00 0.00 0.00 2.23
73 74 3.059325 GCAGACATGTTCCGATTCATAGC 60.059 47.826 0.00 0.00 0.00 2.97
74 75 3.183172 CAGACATGTTCCGATTCATAGCG 59.817 47.826 0.00 0.00 0.00 4.26
80 81 3.234390 CGATTCATAGCGGCCGTG 58.766 61.111 28.70 17.79 0.00 4.94
81 82 2.310233 CGATTCATAGCGGCCGTGG 61.310 63.158 28.70 13.83 0.00 4.94
82 83 1.069090 GATTCATAGCGGCCGTGGA 59.931 57.895 28.70 12.93 0.00 4.02
83 84 0.946221 GATTCATAGCGGCCGTGGAG 60.946 60.000 28.70 14.93 0.00 3.86
84 85 1.686325 ATTCATAGCGGCCGTGGAGT 61.686 55.000 28.70 12.78 0.00 3.85
85 86 2.572095 TTCATAGCGGCCGTGGAGTG 62.572 60.000 28.70 17.85 0.00 3.51
86 87 3.849951 ATAGCGGCCGTGGAGTGG 61.850 66.667 28.70 0.00 0.00 4.00
91 92 4.394712 GGCCGTGGAGTGGAGGTG 62.395 72.222 0.00 0.00 0.00 4.00
92 93 4.394712 GCCGTGGAGTGGAGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
93 94 3.706373 CCGTGGAGTGGAGGTGGG 61.706 72.222 0.00 0.00 0.00 4.61
94 95 2.923035 CGTGGAGTGGAGGTGGGT 60.923 66.667 0.00 0.00 0.00 4.51
95 96 2.943978 CGTGGAGTGGAGGTGGGTC 61.944 68.421 0.00 0.00 0.00 4.46
96 97 1.841556 GTGGAGTGGAGGTGGGTCA 60.842 63.158 0.00 0.00 0.00 4.02
97 98 1.160870 TGGAGTGGAGGTGGGTCAT 59.839 57.895 0.00 0.00 0.00 3.06
98 99 1.200760 TGGAGTGGAGGTGGGTCATG 61.201 60.000 0.00 0.00 0.00 3.07
99 100 0.909610 GGAGTGGAGGTGGGTCATGA 60.910 60.000 0.00 0.00 0.00 3.07
100 101 0.250513 GAGTGGAGGTGGGTCATGAC 59.749 60.000 17.91 17.91 0.00 3.06
101 102 1.079127 GTGGAGGTGGGTCATGACG 60.079 63.158 19.33 0.00 0.00 4.35
102 103 2.125106 GGAGGTGGGTCATGACGC 60.125 66.667 30.28 30.28 43.59 5.19
103 104 2.509336 GAGGTGGGTCATGACGCG 60.509 66.667 30.56 3.53 45.89 6.01
104 105 2.994995 AGGTGGGTCATGACGCGA 60.995 61.111 30.56 20.00 45.89 5.87
105 106 2.509336 GGTGGGTCATGACGCGAG 60.509 66.667 30.56 0.00 45.89 5.03
119 120 3.631145 ACGCGAGTAGTTAGTTTGTGA 57.369 42.857 15.93 0.00 46.88 3.58
120 121 4.170292 ACGCGAGTAGTTAGTTTGTGAT 57.830 40.909 15.93 0.00 46.88 3.06
121 122 5.300969 ACGCGAGTAGTTAGTTTGTGATA 57.699 39.130 15.93 0.00 46.88 2.15
122 123 5.330295 ACGCGAGTAGTTAGTTTGTGATAG 58.670 41.667 15.93 0.00 46.88 2.08
123 124 5.106396 ACGCGAGTAGTTAGTTTGTGATAGT 60.106 40.000 15.93 0.00 46.88 2.12
124 125 5.451662 CGCGAGTAGTTAGTTTGTGATAGTC 59.548 44.000 0.00 0.00 0.00 2.59
125 126 5.742926 GCGAGTAGTTAGTTTGTGATAGTCC 59.257 44.000 0.00 0.00 0.00 3.85
126 127 5.964168 CGAGTAGTTAGTTTGTGATAGTCCG 59.036 44.000 0.00 0.00 0.00 4.79
127 128 5.648572 AGTAGTTAGTTTGTGATAGTCCGC 58.351 41.667 0.00 0.00 0.00 5.54
128 129 3.508762 AGTTAGTTTGTGATAGTCCGCG 58.491 45.455 0.00 0.00 0.00 6.46
129 130 3.057033 AGTTAGTTTGTGATAGTCCGCGT 60.057 43.478 4.92 0.00 0.00 6.01
130 131 1.710013 AGTTTGTGATAGTCCGCGTG 58.290 50.000 4.92 0.00 0.00 5.34
131 132 0.719465 GTTTGTGATAGTCCGCGTGG 59.281 55.000 9.28 9.28 0.00 4.94
132 133 0.604073 TTTGTGATAGTCCGCGTGGA 59.396 50.000 15.21 15.21 43.88 4.02
135 136 0.172803 GTGATAGTCCGCGTGGAGTT 59.827 55.000 29.26 17.62 46.17 3.01
136 137 0.172578 TGATAGTCCGCGTGGAGTTG 59.827 55.000 29.26 0.00 46.17 3.16
137 138 0.527817 GATAGTCCGCGTGGAGTTGG 60.528 60.000 29.26 0.00 46.17 3.77
138 139 0.968901 ATAGTCCGCGTGGAGTTGGA 60.969 55.000 29.26 13.19 46.17 3.53
139 140 1.592400 TAGTCCGCGTGGAGTTGGAG 61.592 60.000 29.26 0.00 46.17 3.86
140 141 2.915659 TCCGCGTGGAGTTGGAGT 60.916 61.111 15.21 0.00 40.17 3.85
141 142 2.030562 CCGCGTGGAGTTGGAGTT 59.969 61.111 10.20 0.00 37.49 3.01
142 143 1.180456 TCCGCGTGGAGTTGGAGTTA 61.180 55.000 15.21 0.00 40.17 2.24
143 144 0.108329 CCGCGTGGAGTTGGAGTTAT 60.108 55.000 10.20 0.00 37.49 1.89
144 145 0.999406 CGCGTGGAGTTGGAGTTATG 59.001 55.000 0.00 0.00 0.00 1.90
145 146 1.671850 CGCGTGGAGTTGGAGTTATGT 60.672 52.381 0.00 0.00 0.00 2.29
146 147 2.416296 CGCGTGGAGTTGGAGTTATGTA 60.416 50.000 0.00 0.00 0.00 2.29
147 148 3.592059 GCGTGGAGTTGGAGTTATGTAA 58.408 45.455 0.00 0.00 0.00 2.41
148 149 3.370061 GCGTGGAGTTGGAGTTATGTAAC 59.630 47.826 0.00 0.00 36.46 2.50
149 150 4.562082 CGTGGAGTTGGAGTTATGTAACA 58.438 43.478 5.77 0.00 38.62 2.41
150 151 4.387862 CGTGGAGTTGGAGTTATGTAACAC 59.612 45.833 5.77 0.00 38.62 3.32
151 152 5.548406 GTGGAGTTGGAGTTATGTAACACT 58.452 41.667 5.77 0.59 38.62 3.55
152 153 6.570957 CGTGGAGTTGGAGTTATGTAACACTA 60.571 42.308 5.77 0.00 38.62 2.74
153 154 7.328737 GTGGAGTTGGAGTTATGTAACACTAT 58.671 38.462 5.77 0.00 38.62 2.12
154 155 7.822822 GTGGAGTTGGAGTTATGTAACACTATT 59.177 37.037 5.77 0.00 38.62 1.73
155 156 7.822334 TGGAGTTGGAGTTATGTAACACTATTG 59.178 37.037 5.77 0.00 38.62 1.90
156 157 7.822822 GGAGTTGGAGTTATGTAACACTATTGT 59.177 37.037 5.77 0.00 38.62 2.71
157 158 9.865321 GAGTTGGAGTTATGTAACACTATTGTA 57.135 33.333 5.77 0.00 38.62 2.41
161 162 9.647797 TGGAGTTATGTAACACTATTGTAACTG 57.352 33.333 5.77 0.00 38.62 3.16
162 163 8.601476 GGAGTTATGTAACACTATTGTAACTGC 58.399 37.037 5.77 3.35 38.62 4.40
163 164 8.488651 AGTTATGTAACACTATTGTAACTGCC 57.511 34.615 5.77 0.00 38.62 4.85
164 165 8.098286 AGTTATGTAACACTATTGTAACTGCCA 58.902 33.333 5.77 0.00 38.62 4.92
165 166 8.723311 GTTATGTAACACTATTGTAACTGCCAA 58.277 33.333 0.00 0.00 33.55 4.52
166 167 6.548441 TGTAACACTATTGTAACTGCCAAC 57.452 37.500 0.00 0.00 33.55 3.77
167 168 4.742438 AACACTATTGTAACTGCCAACG 57.258 40.909 0.00 0.00 33.55 4.10
168 169 3.735591 ACACTATTGTAACTGCCAACGT 58.264 40.909 0.00 0.00 32.60 3.99
169 170 3.496884 ACACTATTGTAACTGCCAACGTG 59.503 43.478 0.00 0.00 32.60 4.49
170 171 3.071479 ACTATTGTAACTGCCAACGTGG 58.929 45.455 0.00 0.00 41.55 4.94
171 172 2.264005 ATTGTAACTGCCAACGTGGA 57.736 45.000 8.04 0.00 40.96 4.02
172 173 1.588674 TTGTAACTGCCAACGTGGAG 58.411 50.000 8.04 0.77 40.96 3.86
173 174 0.250124 TGTAACTGCCAACGTGGAGG 60.250 55.000 8.04 3.19 40.96 4.30
174 175 0.953960 GTAACTGCCAACGTGGAGGG 60.954 60.000 8.04 0.39 40.96 4.30
175 176 2.119484 TAACTGCCAACGTGGAGGGG 62.119 60.000 8.04 0.00 40.96 4.79
176 177 3.953775 CTGCCAACGTGGAGGGGT 61.954 66.667 8.04 0.00 40.96 4.95
177 178 3.491598 CTGCCAACGTGGAGGGGTT 62.492 63.158 8.04 0.00 40.96 4.11
178 179 2.203437 GCCAACGTGGAGGGGTTT 60.203 61.111 8.04 0.00 40.96 3.27
179 180 2.265904 GCCAACGTGGAGGGGTTTC 61.266 63.158 8.04 0.00 40.96 2.78
180 181 1.454539 CCAACGTGGAGGGGTTTCT 59.545 57.895 0.00 0.00 40.96 2.52
181 182 0.605589 CCAACGTGGAGGGGTTTCTC 60.606 60.000 0.00 0.00 40.96 2.87
182 183 0.107831 CAACGTGGAGGGGTTTCTCA 59.892 55.000 0.00 0.00 35.58 3.27
183 184 1.064825 AACGTGGAGGGGTTTCTCAT 58.935 50.000 0.00 0.00 35.58 2.90
184 185 0.613777 ACGTGGAGGGGTTTCTCATC 59.386 55.000 0.00 0.00 35.58 2.92
185 186 0.107654 CGTGGAGGGGTTTCTCATCC 60.108 60.000 0.00 0.00 35.58 3.51
186 187 0.256177 GTGGAGGGGTTTCTCATCCC 59.744 60.000 0.00 0.00 42.73 3.85
191 192 3.829577 GGGTTTCTCATCCCCCATC 57.170 57.895 0.00 0.00 37.89 3.51
192 193 0.186143 GGGTTTCTCATCCCCCATCC 59.814 60.000 0.00 0.00 37.89 3.51
193 194 1.226311 GGTTTCTCATCCCCCATCCT 58.774 55.000 0.00 0.00 0.00 3.24
194 195 1.143889 GGTTTCTCATCCCCCATCCTC 59.856 57.143 0.00 0.00 0.00 3.71
195 196 2.131023 GTTTCTCATCCCCCATCCTCT 58.869 52.381 0.00 0.00 0.00 3.69
196 197 2.511637 GTTTCTCATCCCCCATCCTCTT 59.488 50.000 0.00 0.00 0.00 2.85
197 198 2.109229 TCTCATCCCCCATCCTCTTC 57.891 55.000 0.00 0.00 0.00 2.87
198 199 1.582624 TCTCATCCCCCATCCTCTTCT 59.417 52.381 0.00 0.00 0.00 2.85
199 200 2.021639 TCTCATCCCCCATCCTCTTCTT 60.022 50.000 0.00 0.00 0.00 2.52
200 201 2.782341 CTCATCCCCCATCCTCTTCTTT 59.218 50.000 0.00 0.00 0.00 2.52
201 202 3.976654 CTCATCCCCCATCCTCTTCTTTA 59.023 47.826 0.00 0.00 0.00 1.85
202 203 4.379875 TCATCCCCCATCCTCTTCTTTAA 58.620 43.478 0.00 0.00 0.00 1.52
203 204 4.984268 TCATCCCCCATCCTCTTCTTTAAT 59.016 41.667 0.00 0.00 0.00 1.40
204 205 6.157536 TCATCCCCCATCCTCTTCTTTAATA 58.842 40.000 0.00 0.00 0.00 0.98
205 206 6.799582 TCATCCCCCATCCTCTTCTTTAATAT 59.200 38.462 0.00 0.00 0.00 1.28
206 207 7.967170 TCATCCCCCATCCTCTTCTTTAATATA 59.033 37.037 0.00 0.00 0.00 0.86
207 208 8.785859 CATCCCCCATCCTCTTCTTTAATATAT 58.214 37.037 0.00 0.00 0.00 0.86
209 210 9.507381 TCCCCCATCCTCTTCTTTAATATATAG 57.493 37.037 0.00 0.00 0.00 1.31
210 211 9.285359 CCCCCATCCTCTTCTTTAATATATAGT 57.715 37.037 0.00 0.00 0.00 2.12
233 234 2.610974 CACATTCGTGCGTATTCGAG 57.389 50.000 0.00 0.00 36.06 4.04
234 235 2.182014 CACATTCGTGCGTATTCGAGA 58.818 47.619 0.00 0.00 36.06 4.04
235 236 2.596862 CACATTCGTGCGTATTCGAGAA 59.403 45.455 0.00 0.00 36.06 2.87
236 237 3.060230 CACATTCGTGCGTATTCGAGAAA 59.940 43.478 0.00 0.00 36.06 2.52
320 321 8.106247 ACGTTTTGGATATTTCATTGTGTACT 57.894 30.769 0.00 0.00 0.00 2.73
321 322 8.020819 ACGTTTTGGATATTTCATTGTGTACTG 58.979 33.333 0.00 0.00 0.00 2.74
322 323 7.008266 CGTTTTGGATATTTCATTGTGTACTGC 59.992 37.037 0.00 0.00 0.00 4.40
323 324 7.459795 TTTGGATATTTCATTGTGTACTGCA 57.540 32.000 0.00 0.00 0.00 4.41
324 325 7.643569 TTGGATATTTCATTGTGTACTGCAT 57.356 32.000 0.00 0.00 0.00 3.96
325 326 8.744568 TTGGATATTTCATTGTGTACTGCATA 57.255 30.769 0.00 0.00 0.00 3.14
326 327 8.922931 TGGATATTTCATTGTGTACTGCATAT 57.077 30.769 0.00 0.00 0.00 1.78
332 333 8.424274 TTTCATTGTGTACTGCATATAGACTG 57.576 34.615 6.88 0.14 0.00 3.51
333 334 7.346751 TCATTGTGTACTGCATATAGACTGA 57.653 36.000 6.88 2.00 0.00 3.41
334 335 7.781056 TCATTGTGTACTGCATATAGACTGAA 58.219 34.615 6.88 0.00 0.00 3.02
335 336 8.257306 TCATTGTGTACTGCATATAGACTGAAA 58.743 33.333 6.88 0.00 0.00 2.69
336 337 9.049523 CATTGTGTACTGCATATAGACTGAAAT 57.950 33.333 6.88 0.00 0.00 2.17
337 338 8.424274 TTGTGTACTGCATATAGACTGAAATG 57.576 34.615 6.88 0.00 0.00 2.32
338 339 7.781056 TGTGTACTGCATATAGACTGAAATGA 58.219 34.615 6.88 0.00 0.00 2.57
339 340 7.706607 TGTGTACTGCATATAGACTGAAATGAC 59.293 37.037 6.88 0.00 0.00 3.06
340 341 7.923344 GTGTACTGCATATAGACTGAAATGACT 59.077 37.037 0.00 0.00 0.00 3.41
341 342 7.922811 TGTACTGCATATAGACTGAAATGACTG 59.077 37.037 0.00 0.00 0.00 3.51
342 343 7.117285 ACTGCATATAGACTGAAATGACTGA 57.883 36.000 0.00 0.00 0.00 3.41
343 344 7.559486 ACTGCATATAGACTGAAATGACTGAA 58.441 34.615 0.00 0.00 0.00 3.02
344 345 7.493971 ACTGCATATAGACTGAAATGACTGAAC 59.506 37.037 0.00 0.00 0.00 3.18
345 346 7.330262 TGCATATAGACTGAAATGACTGAACA 58.670 34.615 0.00 0.00 0.00 3.18
346 347 7.493645 TGCATATAGACTGAAATGACTGAACAG 59.506 37.037 0.00 0.00 35.14 3.16
347 348 7.042187 GCATATAGACTGAAATGACTGAACAGG 60.042 40.741 6.76 0.00 33.57 4.00
348 349 3.406764 AGACTGAAATGACTGAACAGGC 58.593 45.455 6.76 3.67 36.93 4.85
356 357 3.552132 TGACTGAACAGGCACACTAAA 57.448 42.857 6.23 0.00 42.59 1.85
357 358 3.879998 TGACTGAACAGGCACACTAAAA 58.120 40.909 6.23 0.00 42.59 1.52
358 359 4.460263 TGACTGAACAGGCACACTAAAAT 58.540 39.130 6.23 0.00 42.59 1.82
359 360 4.275689 TGACTGAACAGGCACACTAAAATG 59.724 41.667 6.23 0.00 42.59 2.32
360 361 4.207165 ACTGAACAGGCACACTAAAATGT 58.793 39.130 6.76 0.00 0.00 2.71
429 434 8.364894 AGTTTTACCCCATTGTATTTTGAGTTC 58.635 33.333 0.00 0.00 0.00 3.01
433 438 6.790319 ACCCCATTGTATTTTGAGTTCTACT 58.210 36.000 0.00 0.00 0.00 2.57
440 445 7.416154 TGTATTTTGAGTTCTACTTTGACCG 57.584 36.000 0.00 0.00 0.00 4.79
531 536 8.365647 AGGTACTTTCCAATCATACTATTACGG 58.634 37.037 0.00 0.00 27.25 4.02
532 537 7.117379 GGTACTTTCCAATCATACTATTACGGC 59.883 40.741 0.00 0.00 0.00 5.68
555 561 9.950680 CGGCTAAATAAACTTACATTTCATGAT 57.049 29.630 0.00 0.00 0.00 2.45
573 579 9.834628 TTTCATGATTAAAATCTACGGTCAAAC 57.165 29.630 0.00 0.00 36.39 2.93
585 591 6.347696 TCTACGGTCAAACTTTCACCTAAAA 58.652 36.000 0.00 0.00 0.00 1.52
586 592 6.993902 TCTACGGTCAAACTTTCACCTAAAAT 59.006 34.615 0.00 0.00 0.00 1.82
587 593 8.149647 TCTACGGTCAAACTTTCACCTAAAATA 58.850 33.333 0.00 0.00 0.00 1.40
602 615 8.547173 TCACCTAAAATAACTAATAAACCCCGA 58.453 33.333 0.00 0.00 0.00 5.14
603 616 8.615211 CACCTAAAATAACTAATAAACCCCGAC 58.385 37.037 0.00 0.00 0.00 4.79
604 617 8.328014 ACCTAAAATAACTAATAAACCCCGACA 58.672 33.333 0.00 0.00 0.00 4.35
605 618 8.833493 CCTAAAATAACTAATAAACCCCGACAG 58.167 37.037 0.00 0.00 0.00 3.51
606 619 9.603921 CTAAAATAACTAATAAACCCCGACAGA 57.396 33.333 0.00 0.00 0.00 3.41
607 620 8.502105 AAAATAACTAATAAACCCCGACAGAG 57.498 34.615 0.00 0.00 0.00 3.35
608 621 4.482952 AACTAATAAACCCCGACAGAGG 57.517 45.455 0.00 0.00 0.00 3.69
609 622 3.716431 ACTAATAAACCCCGACAGAGGA 58.284 45.455 0.00 0.00 0.00 3.71
610 623 4.098894 ACTAATAAACCCCGACAGAGGAA 58.901 43.478 0.00 0.00 0.00 3.36
611 624 4.533311 ACTAATAAACCCCGACAGAGGAAA 59.467 41.667 0.00 0.00 0.00 3.13
612 625 4.586306 AATAAACCCCGACAGAGGAAAT 57.414 40.909 0.00 0.00 0.00 2.17
613 626 5.703730 AATAAACCCCGACAGAGGAAATA 57.296 39.130 0.00 0.00 0.00 1.40
614 627 5.906772 ATAAACCCCGACAGAGGAAATAT 57.093 39.130 0.00 0.00 0.00 1.28
615 628 4.586306 AAACCCCGACAGAGGAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
616 629 4.586306 AACCCCGACAGAGGAAATATTT 57.414 40.909 0.00 0.00 0.00 1.40
617 630 3.886123 ACCCCGACAGAGGAAATATTTG 58.114 45.455 5.17 0.00 0.00 2.32
618 631 3.265995 ACCCCGACAGAGGAAATATTTGT 59.734 43.478 5.17 0.00 0.00 2.83
619 632 3.627577 CCCCGACAGAGGAAATATTTGTG 59.372 47.826 5.17 0.70 0.00 3.33
620 633 4.513442 CCCGACAGAGGAAATATTTGTGA 58.487 43.478 5.17 0.00 0.00 3.58
621 634 4.941263 CCCGACAGAGGAAATATTTGTGAA 59.059 41.667 5.17 0.00 0.00 3.18
727 760 3.929094 AGTTATTAAGTCGGCGGTTTCA 58.071 40.909 7.21 0.00 0.00 2.69
742 776 5.008613 GGCGGTTTCATTTGCTCTATAATGA 59.991 40.000 0.00 0.00 38.59 2.57
748 782 4.515191 TCATTTGCTCTATAATGAACGGGC 59.485 41.667 0.00 0.00 37.71 6.13
755 789 2.568623 ATAATGAACGGGCCATCCTC 57.431 50.000 4.39 0.00 0.00 3.71
756 790 0.472471 TAATGAACGGGCCATCCTCC 59.528 55.000 4.39 0.00 0.00 4.30
757 791 2.284515 AATGAACGGGCCATCCTCCC 62.285 60.000 4.39 0.00 40.43 4.30
762 796 3.237741 GGGCCATCCTCCCGAGAG 61.238 72.222 4.39 0.00 40.09 3.20
763 797 2.444895 GGCCATCCTCCCGAGAGT 60.445 66.667 0.00 0.00 38.58 3.24
777 811 1.677942 GAGAGTCCCGACCTTCGTAT 58.322 55.000 0.00 0.00 38.40 3.06
778 812 1.334243 GAGAGTCCCGACCTTCGTATG 59.666 57.143 0.00 0.00 38.40 2.39
825 859 0.534877 CACAGCAACACTAGCCCACA 60.535 55.000 0.00 0.00 0.00 4.17
831 865 0.179029 AACACTAGCCCACACCACAC 60.179 55.000 0.00 0.00 0.00 3.82
837 871 2.525592 CCCACACCACACCCCAAT 59.474 61.111 0.00 0.00 0.00 3.16
985 1049 6.297353 CCGATCTTCAAAGAAAAACGTACTC 58.703 40.000 0.00 0.00 38.77 2.59
986 1050 6.073980 CCGATCTTCAAAGAAAAACGTACTCA 60.074 38.462 0.00 0.00 38.77 3.41
1259 1332 2.502080 CGACTGCGACGGTGAGAC 60.502 66.667 0.00 0.00 40.82 3.36
1389 1475 4.794439 CTGATCGACGGCGTGCCA 62.794 66.667 21.19 8.66 38.98 4.92
1451 1540 4.716784 ACTGTAATGGCTCTGGTAGATTCA 59.283 41.667 0.00 0.00 0.00 2.57
1554 1643 2.287368 GGTGTTCGTGACCAACAATTCC 60.287 50.000 0.00 0.00 35.53 3.01
1611 1700 1.078848 GCTCGGGCTCAGTGTCAAT 60.079 57.895 0.00 0.00 35.22 2.57
1621 1710 4.425520 GCTCAGTGTCAATGAGGTAGTAC 58.574 47.826 26.73 9.38 43.61 2.73
1688 1777 6.240894 TCCTCTAGTGCAAAATCAACTTGAT 58.759 36.000 0.00 0.00 39.09 2.57
1791 1880 4.783227 TCCCTAAAGACAAGAAGGTAGCAT 59.217 41.667 0.00 0.00 0.00 3.79
1852 1941 5.392919 GCATTGGTACACATGATTTAGCACA 60.393 40.000 0.00 0.00 39.29 4.57
1889 1978 7.766278 AGCACAGAGTTAAGTATTTCTATGGTG 59.234 37.037 0.00 0.00 29.23 4.17
2116 2211 2.481568 GACTTCCGAAAAGTTTACCCGG 59.518 50.000 14.28 14.28 41.36 5.73
2352 2459 7.966157 ACAAAGTTCAGTAAGTATATCGTCG 57.034 36.000 0.00 0.00 0.00 5.12
2353 2460 7.533426 ACAAAGTTCAGTAAGTATATCGTCGT 58.467 34.615 0.00 0.00 0.00 4.34
2354 2461 8.025445 ACAAAGTTCAGTAAGTATATCGTCGTT 58.975 33.333 0.00 0.00 0.00 3.85
2355 2462 8.521860 CAAAGTTCAGTAAGTATATCGTCGTTC 58.478 37.037 0.00 0.00 0.00 3.95
2356 2463 7.312657 AGTTCAGTAAGTATATCGTCGTTCA 57.687 36.000 0.00 0.00 0.00 3.18
2460 2567 8.870075 AAGACTGCTTAGGATTGTAGAAATTT 57.130 30.769 0.00 0.00 31.07 1.82
2466 2573 8.840321 TGCTTAGGATTGTAGAAATTTAGATGC 58.160 33.333 0.00 0.00 0.00 3.91
2482 2589 2.159156 AGATGCGCATTTGATTGCACAT 60.159 40.909 26.12 0.00 45.38 3.21
2666 2891 4.686191 TTTCATTGCAACAAACAGGGAT 57.314 36.364 0.00 0.00 0.00 3.85
2684 2909 0.254178 ATGCTGTCACCCATCTCACC 59.746 55.000 0.00 0.00 0.00 4.02
2767 2995 7.096884 ACAGAACTCTTTATACATACTGCGA 57.903 36.000 0.00 0.00 0.00 5.10
2837 3066 4.404098 GGTGGCGGGTCGATGGTT 62.404 66.667 0.00 0.00 0.00 3.67
2909 3138 4.550422 CGTCGACATTCATGATGGACTAT 58.450 43.478 17.16 0.00 40.21 2.12
2927 3156 6.013725 TGGACTATCTGGCAAAGAAGTAAGAA 60.014 38.462 0.00 0.00 38.79 2.52
2976 3205 4.280819 TCCATGAATCCATTTCCAGAACC 58.719 43.478 0.00 0.00 33.04 3.62
2977 3206 4.017222 TCCATGAATCCATTTCCAGAACCT 60.017 41.667 0.00 0.00 33.04 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.239064 GCCCTACATTCTACCGATATCCTATG 60.239 46.154 0.00 0.00 0.00 2.23
1 2 5.834204 GCCCTACATTCTACCGATATCCTAT 59.166 44.000 0.00 0.00 0.00 2.57
3 4 4.024670 GCCCTACATTCTACCGATATCCT 58.975 47.826 0.00 0.00 0.00 3.24
7 8 2.555325 CACGCCCTACATTCTACCGATA 59.445 50.000 0.00 0.00 0.00 2.92
8 9 1.340248 CACGCCCTACATTCTACCGAT 59.660 52.381 0.00 0.00 0.00 4.18
9 10 0.742505 CACGCCCTACATTCTACCGA 59.257 55.000 0.00 0.00 0.00 4.69
10 11 0.742505 TCACGCCCTACATTCTACCG 59.257 55.000 0.00 0.00 0.00 4.02
12 13 3.195661 CCTTTCACGCCCTACATTCTAC 58.804 50.000 0.00 0.00 0.00 2.59
15 16 1.737793 CACCTTTCACGCCCTACATTC 59.262 52.381 0.00 0.00 0.00 2.67
16 17 1.613255 CCACCTTTCACGCCCTACATT 60.613 52.381 0.00 0.00 0.00 2.71
18 19 1.373435 CCACCTTTCACGCCCTACA 59.627 57.895 0.00 0.00 0.00 2.74
19 20 2.038837 GCCACCTTTCACGCCCTAC 61.039 63.158 0.00 0.00 0.00 3.18
20 21 2.349755 GCCACCTTTCACGCCCTA 59.650 61.111 0.00 0.00 0.00 3.53
21 22 3.850098 CTGCCACCTTTCACGCCCT 62.850 63.158 0.00 0.00 0.00 5.19
22 23 3.365265 CTGCCACCTTTCACGCCC 61.365 66.667 0.00 0.00 0.00 6.13
23 24 3.365265 CCTGCCACCTTTCACGCC 61.365 66.667 0.00 0.00 0.00 5.68
24 25 4.043200 GCCTGCCACCTTTCACGC 62.043 66.667 0.00 0.00 0.00 5.34
25 26 2.463589 TAGGCCTGCCACCTTTCACG 62.464 60.000 17.99 0.00 38.81 4.35
26 27 0.960861 GTAGGCCTGCCACCTTTCAC 60.961 60.000 17.99 0.00 38.81 3.18
27 28 1.133809 AGTAGGCCTGCCACCTTTCA 61.134 55.000 17.99 0.00 38.81 2.69
28 29 0.038310 AAGTAGGCCTGCCACCTTTC 59.962 55.000 17.99 0.00 38.81 2.62
29 30 1.368374 TAAGTAGGCCTGCCACCTTT 58.632 50.000 17.99 6.51 38.81 3.11
30 31 1.282157 CTTAAGTAGGCCTGCCACCTT 59.718 52.381 17.99 13.15 38.81 3.50
31 32 0.912486 CTTAAGTAGGCCTGCCACCT 59.088 55.000 17.99 0.00 41.57 4.00
32 33 0.107165 CCTTAAGTAGGCCTGCCACC 60.107 60.000 17.99 0.00 37.17 4.61
33 34 3.478540 CCTTAAGTAGGCCTGCCAC 57.521 57.895 17.99 5.62 37.17 5.01
42 43 3.865745 CGGAACATGTCTGCCTTAAGTAG 59.134 47.826 0.00 0.00 0.00 2.57
43 44 3.512329 TCGGAACATGTCTGCCTTAAGTA 59.488 43.478 0.00 0.00 31.99 2.24
44 45 2.301870 TCGGAACATGTCTGCCTTAAGT 59.698 45.455 0.00 0.00 31.99 2.24
45 46 2.972625 TCGGAACATGTCTGCCTTAAG 58.027 47.619 0.00 0.00 31.99 1.85
46 47 3.627395 ATCGGAACATGTCTGCCTTAA 57.373 42.857 0.00 0.00 31.99 1.85
47 48 3.055458 TGAATCGGAACATGTCTGCCTTA 60.055 43.478 0.00 0.00 31.99 2.69
48 49 2.290260 TGAATCGGAACATGTCTGCCTT 60.290 45.455 0.00 0.00 31.99 4.35
49 50 1.278985 TGAATCGGAACATGTCTGCCT 59.721 47.619 0.00 0.00 31.99 4.75
50 51 1.737838 TGAATCGGAACATGTCTGCC 58.262 50.000 0.00 0.13 31.99 4.85
51 52 3.059325 GCTATGAATCGGAACATGTCTGC 60.059 47.826 0.00 0.00 31.99 4.26
52 53 3.183172 CGCTATGAATCGGAACATGTCTG 59.817 47.826 0.00 0.00 0.00 3.51
53 54 3.384668 CGCTATGAATCGGAACATGTCT 58.615 45.455 0.00 0.00 0.00 3.41
54 55 3.777807 CGCTATGAATCGGAACATGTC 57.222 47.619 0.00 0.00 0.00 3.06
63 64 2.310233 CCACGGCCGCTATGAATCG 61.310 63.158 28.58 0.00 0.00 3.34
64 65 0.946221 CTCCACGGCCGCTATGAATC 60.946 60.000 28.58 0.00 0.00 2.52
65 66 1.069765 CTCCACGGCCGCTATGAAT 59.930 57.895 28.58 0.00 0.00 2.57
66 67 2.355986 ACTCCACGGCCGCTATGAA 61.356 57.895 28.58 0.00 0.00 2.57
67 68 2.758327 ACTCCACGGCCGCTATGA 60.758 61.111 28.58 15.47 0.00 2.15
68 69 2.586079 CACTCCACGGCCGCTATG 60.586 66.667 28.58 16.82 0.00 2.23
69 70 3.849951 CCACTCCACGGCCGCTAT 61.850 66.667 28.58 1.81 0.00 2.97
74 75 4.394712 CACCTCCACTCCACGGCC 62.395 72.222 0.00 0.00 0.00 6.13
75 76 4.394712 CCACCTCCACTCCACGGC 62.395 72.222 0.00 0.00 0.00 5.68
76 77 3.706373 CCCACCTCCACTCCACGG 61.706 72.222 0.00 0.00 0.00 4.94
77 78 2.923035 ACCCACCTCCACTCCACG 60.923 66.667 0.00 0.00 0.00 4.94
78 79 1.201429 ATGACCCACCTCCACTCCAC 61.201 60.000 0.00 0.00 0.00 4.02
79 80 1.160870 ATGACCCACCTCCACTCCA 59.839 57.895 0.00 0.00 0.00 3.86
80 81 0.909610 TCATGACCCACCTCCACTCC 60.910 60.000 0.00 0.00 0.00 3.85
81 82 0.250513 GTCATGACCCACCTCCACTC 59.749 60.000 15.31 0.00 0.00 3.51
82 83 1.544825 CGTCATGACCCACCTCCACT 61.545 60.000 20.03 0.00 0.00 4.00
83 84 1.079127 CGTCATGACCCACCTCCAC 60.079 63.158 20.03 0.00 0.00 4.02
84 85 2.954684 GCGTCATGACCCACCTCCA 61.955 63.158 20.03 0.00 0.00 3.86
85 86 2.125106 GCGTCATGACCCACCTCC 60.125 66.667 20.03 0.00 0.00 4.30
86 87 2.509336 CGCGTCATGACCCACCTC 60.509 66.667 20.03 2.20 0.00 3.85
87 88 2.994995 TCGCGTCATGACCCACCT 60.995 61.111 20.03 0.00 0.00 4.00
88 89 1.940883 TACTCGCGTCATGACCCACC 61.941 60.000 20.03 5.47 0.00 4.61
89 90 0.525668 CTACTCGCGTCATGACCCAC 60.526 60.000 20.03 8.96 0.00 4.61
90 91 0.963856 ACTACTCGCGTCATGACCCA 60.964 55.000 20.03 3.23 0.00 4.51
91 92 0.172803 AACTACTCGCGTCATGACCC 59.827 55.000 20.03 10.42 0.00 4.46
92 93 2.097142 ACTAACTACTCGCGTCATGACC 59.903 50.000 20.03 11.62 0.00 4.02
93 94 3.402058 ACTAACTACTCGCGTCATGAC 57.598 47.619 16.21 16.21 0.00 3.06
94 95 4.163552 CAAACTAACTACTCGCGTCATGA 58.836 43.478 5.77 0.00 0.00 3.07
95 96 3.918591 ACAAACTAACTACTCGCGTCATG 59.081 43.478 5.77 0.00 0.00 3.07
96 97 3.918591 CACAAACTAACTACTCGCGTCAT 59.081 43.478 5.77 0.00 0.00 3.06
97 98 3.003585 TCACAAACTAACTACTCGCGTCA 59.996 43.478 5.77 0.00 0.00 4.35
98 99 3.558505 TCACAAACTAACTACTCGCGTC 58.441 45.455 5.77 0.00 0.00 5.19
99 100 3.631145 TCACAAACTAACTACTCGCGT 57.369 42.857 5.77 0.00 0.00 6.01
100 101 5.330295 ACTATCACAAACTAACTACTCGCG 58.670 41.667 0.00 0.00 0.00 5.87
101 102 5.742926 GGACTATCACAAACTAACTACTCGC 59.257 44.000 0.00 0.00 0.00 5.03
102 103 5.964168 CGGACTATCACAAACTAACTACTCG 59.036 44.000 0.00 0.00 0.00 4.18
103 104 5.742926 GCGGACTATCACAAACTAACTACTC 59.257 44.000 0.00 0.00 0.00 2.59
104 105 5.648572 GCGGACTATCACAAACTAACTACT 58.351 41.667 0.00 0.00 0.00 2.57
105 106 4.498323 CGCGGACTATCACAAACTAACTAC 59.502 45.833 0.00 0.00 0.00 2.73
106 107 4.156556 ACGCGGACTATCACAAACTAACTA 59.843 41.667 12.47 0.00 0.00 2.24
107 108 3.057033 ACGCGGACTATCACAAACTAACT 60.057 43.478 12.47 0.00 0.00 2.24
108 109 3.060363 CACGCGGACTATCACAAACTAAC 59.940 47.826 12.47 0.00 0.00 2.34
109 110 3.247442 CACGCGGACTATCACAAACTAA 58.753 45.455 12.47 0.00 0.00 2.24
110 111 2.416296 CCACGCGGACTATCACAAACTA 60.416 50.000 12.47 0.00 0.00 2.24
111 112 1.671850 CCACGCGGACTATCACAAACT 60.672 52.381 12.47 0.00 0.00 2.66
112 113 0.719465 CCACGCGGACTATCACAAAC 59.281 55.000 12.47 0.00 0.00 2.93
113 114 0.604073 TCCACGCGGACTATCACAAA 59.396 50.000 12.47 0.00 35.91 2.83
114 115 0.172578 CTCCACGCGGACTATCACAA 59.827 55.000 12.47 0.00 35.91 3.33
115 116 0.963856 ACTCCACGCGGACTATCACA 60.964 55.000 12.47 0.00 35.91 3.58
116 117 0.172803 AACTCCACGCGGACTATCAC 59.827 55.000 12.47 0.00 35.91 3.06
117 118 0.172578 CAACTCCACGCGGACTATCA 59.827 55.000 12.47 0.00 35.91 2.15
118 119 0.527817 CCAACTCCACGCGGACTATC 60.528 60.000 12.47 0.00 35.91 2.08
119 120 0.968901 TCCAACTCCACGCGGACTAT 60.969 55.000 12.47 0.00 35.91 2.12
120 121 1.592400 CTCCAACTCCACGCGGACTA 61.592 60.000 12.47 0.00 35.91 2.59
121 122 2.915659 TCCAACTCCACGCGGACT 60.916 61.111 12.47 0.00 35.91 3.85
122 123 2.432628 CTCCAACTCCACGCGGAC 60.433 66.667 12.47 0.00 35.91 4.79
123 124 1.180456 TAACTCCAACTCCACGCGGA 61.180 55.000 12.47 0.00 39.79 5.54
124 125 0.108329 ATAACTCCAACTCCACGCGG 60.108 55.000 12.47 0.00 0.00 6.46
125 126 0.999406 CATAACTCCAACTCCACGCG 59.001 55.000 3.53 3.53 0.00 6.01
126 127 2.094762 ACATAACTCCAACTCCACGC 57.905 50.000 0.00 0.00 0.00 5.34
127 128 4.387862 GTGTTACATAACTCCAACTCCACG 59.612 45.833 3.58 0.00 37.12 4.94
128 129 5.548406 AGTGTTACATAACTCCAACTCCAC 58.452 41.667 3.58 0.00 37.12 4.02
129 130 5.818678 AGTGTTACATAACTCCAACTCCA 57.181 39.130 3.58 0.00 37.12 3.86
130 131 7.822822 ACAATAGTGTTACATAACTCCAACTCC 59.177 37.037 3.58 0.00 32.58 3.85
131 132 8.773404 ACAATAGTGTTACATAACTCCAACTC 57.227 34.615 3.58 0.00 32.58 3.01
135 136 9.647797 CAGTTACAATAGTGTTACATAACTCCA 57.352 33.333 14.04 0.00 39.28 3.86
136 137 8.601476 GCAGTTACAATAGTGTTACATAACTCC 58.399 37.037 14.04 0.00 39.28 3.85
137 138 8.601476 GGCAGTTACAATAGTGTTACATAACTC 58.399 37.037 14.04 6.19 39.28 3.01
138 139 8.098286 TGGCAGTTACAATAGTGTTACATAACT 58.902 33.333 14.04 8.56 39.28 2.24
139 140 8.259049 TGGCAGTTACAATAGTGTTACATAAC 57.741 34.615 14.04 6.52 39.28 1.89
140 141 8.723311 GTTGGCAGTTACAATAGTGTTACATAA 58.277 33.333 14.04 2.15 39.28 1.90
141 142 7.063662 CGTTGGCAGTTACAATAGTGTTACATA 59.936 37.037 14.04 0.00 39.28 2.29
142 143 6.128391 CGTTGGCAGTTACAATAGTGTTACAT 60.128 38.462 14.04 0.00 39.28 2.29
143 144 5.177881 CGTTGGCAGTTACAATAGTGTTACA 59.822 40.000 14.04 0.00 39.28 2.41
144 145 5.178067 ACGTTGGCAGTTACAATAGTGTTAC 59.822 40.000 0.00 2.19 39.30 2.50
145 146 5.177881 CACGTTGGCAGTTACAATAGTGTTA 59.822 40.000 0.00 0.00 39.30 2.41
146 147 4.024387 CACGTTGGCAGTTACAATAGTGTT 60.024 41.667 0.00 0.00 39.30 3.32
147 148 3.496884 CACGTTGGCAGTTACAATAGTGT 59.503 43.478 0.00 0.00 42.09 3.55
148 149 3.120338 CCACGTTGGCAGTTACAATAGTG 60.120 47.826 0.00 0.00 38.19 2.74
149 150 3.071479 CCACGTTGGCAGTTACAATAGT 58.929 45.455 0.00 0.00 0.00 2.12
150 151 3.331150 TCCACGTTGGCAGTTACAATAG 58.669 45.455 0.00 0.00 37.47 1.73
151 152 3.331150 CTCCACGTTGGCAGTTACAATA 58.669 45.455 0.00 0.00 37.47 1.90
152 153 2.151202 CTCCACGTTGGCAGTTACAAT 58.849 47.619 0.00 0.00 37.47 2.71
153 154 1.588674 CTCCACGTTGGCAGTTACAA 58.411 50.000 0.00 0.00 37.47 2.41
154 155 0.250124 CCTCCACGTTGGCAGTTACA 60.250 55.000 0.00 0.00 37.47 2.41
155 156 0.953960 CCCTCCACGTTGGCAGTTAC 60.954 60.000 0.00 0.00 37.47 2.50
156 157 1.373435 CCCTCCACGTTGGCAGTTA 59.627 57.895 0.00 0.00 37.47 2.24
157 158 2.113139 CCCTCCACGTTGGCAGTT 59.887 61.111 0.00 0.00 37.47 3.16
158 159 3.953775 CCCCTCCACGTTGGCAGT 61.954 66.667 0.00 0.00 37.47 4.40
159 160 2.976494 AAACCCCTCCACGTTGGCAG 62.976 60.000 0.00 0.00 37.47 4.85
160 161 2.969300 GAAACCCCTCCACGTTGGCA 62.969 60.000 0.00 0.00 37.47 4.92
161 162 2.203437 AAACCCCTCCACGTTGGC 60.203 61.111 0.00 0.00 37.47 4.52
162 163 0.605589 GAGAAACCCCTCCACGTTGG 60.606 60.000 0.00 0.00 39.43 3.77
163 164 0.107831 TGAGAAACCCCTCCACGTTG 59.892 55.000 0.00 0.00 32.32 4.10
164 165 1.003233 GATGAGAAACCCCTCCACGTT 59.997 52.381 0.00 0.00 32.32 3.99
165 166 0.613777 GATGAGAAACCCCTCCACGT 59.386 55.000 0.00 0.00 32.32 4.49
166 167 0.107654 GGATGAGAAACCCCTCCACG 60.108 60.000 0.00 0.00 32.32 4.94
167 168 0.256177 GGGATGAGAAACCCCTCCAC 59.744 60.000 0.00 0.00 40.19 4.02
168 169 2.709992 GGGATGAGAAACCCCTCCA 58.290 57.895 0.00 0.00 40.19 3.86
173 174 0.186143 GGATGGGGGATGAGAAACCC 59.814 60.000 0.00 0.00 44.89 4.11
174 175 1.143889 GAGGATGGGGGATGAGAAACC 59.856 57.143 0.00 0.00 0.00 3.27
175 176 2.131023 AGAGGATGGGGGATGAGAAAC 58.869 52.381 0.00 0.00 0.00 2.78
176 177 2.594536 AGAGGATGGGGGATGAGAAA 57.405 50.000 0.00 0.00 0.00 2.52
177 178 2.021639 AGAAGAGGATGGGGGATGAGAA 60.022 50.000 0.00 0.00 0.00 2.87
178 179 1.582624 AGAAGAGGATGGGGGATGAGA 59.417 52.381 0.00 0.00 0.00 3.27
179 180 2.115337 AGAAGAGGATGGGGGATGAG 57.885 55.000 0.00 0.00 0.00 2.90
180 181 2.594536 AAGAAGAGGATGGGGGATGA 57.405 50.000 0.00 0.00 0.00 2.92
181 182 4.796110 TTAAAGAAGAGGATGGGGGATG 57.204 45.455 0.00 0.00 0.00 3.51
182 183 8.956356 ATATATTAAAGAAGAGGATGGGGGAT 57.044 34.615 0.00 0.00 0.00 3.85
183 184 9.507381 CTATATATTAAAGAAGAGGATGGGGGA 57.493 37.037 0.00 0.00 0.00 4.81
184 185 9.285359 ACTATATATTAAAGAAGAGGATGGGGG 57.715 37.037 0.00 0.00 0.00 5.40
215 216 2.554806 TCTCGAATACGCACGAATGT 57.445 45.000 0.00 0.00 38.05 2.71
216 217 3.899835 TTTCTCGAATACGCACGAATG 57.100 42.857 0.00 0.00 38.05 2.67
217 218 4.914312 TTTTTCTCGAATACGCACGAAT 57.086 36.364 0.00 0.00 38.05 3.34
236 237 7.556733 AGCAAATGTTGTGATTGATGTTTTT 57.443 28.000 0.00 0.00 0.00 1.94
294 295 9.221933 AGTACACAATGAAATATCCAAAACGTA 57.778 29.630 0.00 0.00 0.00 3.57
296 297 7.008266 GCAGTACACAATGAAATATCCAAAACG 59.992 37.037 0.00 0.00 0.00 3.60
312 313 8.257306 TCATTTCAGTCTATATGCAGTACACAA 58.743 33.333 0.00 0.00 0.00 3.33
314 315 7.923344 AGTCATTTCAGTCTATATGCAGTACAC 59.077 37.037 0.00 0.00 0.00 2.90
315 316 7.922811 CAGTCATTTCAGTCTATATGCAGTACA 59.077 37.037 0.00 0.00 0.00 2.90
316 317 8.138074 TCAGTCATTTCAGTCTATATGCAGTAC 58.862 37.037 0.00 0.00 0.00 2.73
317 318 8.237811 TCAGTCATTTCAGTCTATATGCAGTA 57.762 34.615 0.00 0.00 0.00 2.74
320 321 7.330262 TGTTCAGTCATTTCAGTCTATATGCA 58.670 34.615 0.00 0.00 0.00 3.96
321 322 7.042187 CCTGTTCAGTCATTTCAGTCTATATGC 60.042 40.741 0.00 0.00 0.00 3.14
322 323 7.042187 GCCTGTTCAGTCATTTCAGTCTATATG 60.042 40.741 0.00 0.00 0.00 1.78
323 324 6.989169 GCCTGTTCAGTCATTTCAGTCTATAT 59.011 38.462 0.00 0.00 0.00 0.86
324 325 6.070824 TGCCTGTTCAGTCATTTCAGTCTATA 60.071 38.462 0.00 0.00 0.00 1.31
325 326 5.181748 GCCTGTTCAGTCATTTCAGTCTAT 58.818 41.667 0.00 0.00 0.00 1.98
326 327 4.040339 TGCCTGTTCAGTCATTTCAGTCTA 59.960 41.667 0.00 0.00 0.00 2.59
327 328 3.181451 TGCCTGTTCAGTCATTTCAGTCT 60.181 43.478 0.00 0.00 0.00 3.24
328 329 3.058639 GTGCCTGTTCAGTCATTTCAGTC 60.059 47.826 0.00 0.00 0.00 3.51
329 330 2.880890 GTGCCTGTTCAGTCATTTCAGT 59.119 45.455 0.00 0.00 0.00 3.41
330 331 2.880268 TGTGCCTGTTCAGTCATTTCAG 59.120 45.455 0.00 0.00 0.00 3.02
331 332 2.618241 GTGTGCCTGTTCAGTCATTTCA 59.382 45.455 0.00 0.00 0.00 2.69
332 333 2.880890 AGTGTGCCTGTTCAGTCATTTC 59.119 45.455 0.00 0.00 0.00 2.17
333 334 2.936202 AGTGTGCCTGTTCAGTCATTT 58.064 42.857 0.00 0.00 0.00 2.32
334 335 2.645838 AGTGTGCCTGTTCAGTCATT 57.354 45.000 0.00 0.00 0.00 2.57
335 336 3.769739 TTAGTGTGCCTGTTCAGTCAT 57.230 42.857 0.00 0.00 0.00 3.06
336 337 3.552132 TTTAGTGTGCCTGTTCAGTCA 57.448 42.857 0.00 0.00 0.00 3.41
337 338 4.275936 ACATTTTAGTGTGCCTGTTCAGTC 59.724 41.667 0.00 0.00 0.00 3.51
338 339 4.036734 CACATTTTAGTGTGCCTGTTCAGT 59.963 41.667 0.00 0.00 42.51 3.41
339 340 4.539870 CACATTTTAGTGTGCCTGTTCAG 58.460 43.478 0.00 0.00 42.51 3.02
340 341 4.566545 CACATTTTAGTGTGCCTGTTCA 57.433 40.909 0.00 0.00 42.51 3.18
392 397 9.541884 ACAATGGGGTAAAACTATAAGATGTTT 57.458 29.630 0.00 0.00 37.92 2.83
404 409 8.364894 AGAACTCAAAATACAATGGGGTAAAAC 58.635 33.333 0.00 0.00 0.00 2.43
408 413 7.924541 AGTAGAACTCAAAATACAATGGGGTA 58.075 34.615 0.00 0.00 0.00 3.69
415 420 7.496591 ACGGTCAAAGTAGAACTCAAAATACAA 59.503 33.333 0.00 0.00 0.00 2.41
416 421 6.987992 ACGGTCAAAGTAGAACTCAAAATACA 59.012 34.615 0.00 0.00 0.00 2.29
417 422 7.417496 ACGGTCAAAGTAGAACTCAAAATAC 57.583 36.000 0.00 0.00 0.00 1.89
488 493 8.438676 AAAGTACCTTCAAATATGAATCTCGG 57.561 34.615 0.00 0.00 44.29 4.63
489 494 8.552034 GGAAAGTACCTTCAAATATGAATCTCG 58.448 37.037 6.55 0.00 44.29 4.04
490 495 9.396022 TGGAAAGTACCTTCAAATATGAATCTC 57.604 33.333 6.55 0.00 44.29 2.75
506 511 7.117379 GCCGTAATAGTATGATTGGAAAGTACC 59.883 40.741 0.00 0.00 0.00 3.34
529 534 9.950680 ATCATGAAATGTAAGTTTATTTAGCCG 57.049 29.630 0.00 0.00 46.80 5.52
553 559 9.326339 GTGAAAGTTTGACCGTAGATTTTAATC 57.674 33.333 0.00 0.00 35.64 1.75
555 561 7.499895 AGGTGAAAGTTTGACCGTAGATTTTAA 59.500 33.333 17.17 0.00 34.72 1.52
557 563 5.826208 AGGTGAAAGTTTGACCGTAGATTTT 59.174 36.000 17.17 0.00 34.72 1.82
562 568 6.607735 TTTTAGGTGAAAGTTTGACCGTAG 57.392 37.500 17.17 0.00 34.72 3.51
565 571 7.645402 AGTTATTTTAGGTGAAAGTTTGACCG 58.355 34.615 17.17 0.00 34.72 4.79
577 583 8.615211 GTCGGGGTTTATTAGTTATTTTAGGTG 58.385 37.037 0.00 0.00 0.00 4.00
585 591 5.901276 TCCTCTGTCGGGGTTTATTAGTTAT 59.099 40.000 0.00 0.00 0.00 1.89
586 592 5.271598 TCCTCTGTCGGGGTTTATTAGTTA 58.728 41.667 0.00 0.00 0.00 2.24
587 593 4.098894 TCCTCTGTCGGGGTTTATTAGTT 58.901 43.478 0.00 0.00 0.00 2.24
602 615 5.556915 TCCGTTCACAAATATTTCCTCTGT 58.443 37.500 0.00 0.00 0.00 3.41
603 616 5.065218 CCTCCGTTCACAAATATTTCCTCTG 59.935 44.000 0.00 0.00 0.00 3.35
604 617 5.186198 CCTCCGTTCACAAATATTTCCTCT 58.814 41.667 0.00 0.00 0.00 3.69
605 618 4.335594 CCCTCCGTTCACAAATATTTCCTC 59.664 45.833 0.00 0.00 0.00 3.71
606 619 4.018779 TCCCTCCGTTCACAAATATTTCCT 60.019 41.667 0.00 0.00 0.00 3.36
607 620 4.266714 TCCCTCCGTTCACAAATATTTCC 58.733 43.478 0.00 0.00 0.00 3.13
608 621 4.941873 ACTCCCTCCGTTCACAAATATTTC 59.058 41.667 0.00 0.00 0.00 2.17
609 622 4.700213 CACTCCCTCCGTTCACAAATATTT 59.300 41.667 0.00 0.00 0.00 1.40
610 623 4.261801 CACTCCCTCCGTTCACAAATATT 58.738 43.478 0.00 0.00 0.00 1.28
611 624 3.263425 ACACTCCCTCCGTTCACAAATAT 59.737 43.478 0.00 0.00 0.00 1.28
612 625 2.635915 ACACTCCCTCCGTTCACAAATA 59.364 45.455 0.00 0.00 0.00 1.40
613 626 1.420138 ACACTCCCTCCGTTCACAAAT 59.580 47.619 0.00 0.00 0.00 2.32
614 627 0.834612 ACACTCCCTCCGTTCACAAA 59.165 50.000 0.00 0.00 0.00 2.83
615 628 0.834612 AACACTCCCTCCGTTCACAA 59.165 50.000 0.00 0.00 0.00 3.33
616 629 0.391597 GAACACTCCCTCCGTTCACA 59.608 55.000 0.00 0.00 39.06 3.58
617 630 0.680061 AGAACACTCCCTCCGTTCAC 59.320 55.000 0.00 0.00 41.17 3.18
618 631 1.891150 GTAGAACACTCCCTCCGTTCA 59.109 52.381 0.00 0.00 41.17 3.18
619 632 1.891150 TGTAGAACACTCCCTCCGTTC 59.109 52.381 0.00 0.00 39.44 3.95
620 633 2.005370 TGTAGAACACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
621 634 1.617357 GTTGTAGAACACTCCCTCCGT 59.383 52.381 0.00 0.00 31.78 4.69
715 748 0.454452 GAGCAAATGAAACCGCCGAC 60.454 55.000 0.00 0.00 0.00 4.79
727 760 3.821033 GGCCCGTTCATTATAGAGCAAAT 59.179 43.478 0.00 0.00 0.00 2.32
748 782 1.834822 GGGACTCTCGGGAGGATGG 60.835 68.421 18.47 0.00 43.46 3.51
755 789 2.362632 AAGGTCGGGACTCTCGGG 60.363 66.667 0.00 0.00 0.00 5.14
756 790 2.762234 CGAAGGTCGGGACTCTCGG 61.762 68.421 0.00 0.00 36.00 4.63
757 791 0.742281 TACGAAGGTCGGGACTCTCG 60.742 60.000 16.12 16.12 45.59 4.04
758 792 1.334243 CATACGAAGGTCGGGACTCTC 59.666 57.143 2.38 0.00 45.59 3.20
759 793 1.064906 TCATACGAAGGTCGGGACTCT 60.065 52.381 2.38 0.00 45.59 3.24
760 794 1.334243 CTCATACGAAGGTCGGGACTC 59.666 57.143 2.38 0.00 45.59 3.36
761 795 1.340795 ACTCATACGAAGGTCGGGACT 60.341 52.381 2.38 0.00 45.59 3.85
762 796 1.101331 ACTCATACGAAGGTCGGGAC 58.899 55.000 2.38 0.00 45.59 4.46
763 797 1.100510 CACTCATACGAAGGTCGGGA 58.899 55.000 2.38 0.00 45.59 5.14
825 859 0.178935 CAAAGGGATTGGGGTGTGGT 60.179 55.000 0.00 0.00 35.27 4.16
831 865 1.902765 GCAAGGCAAAGGGATTGGGG 61.903 60.000 0.00 0.00 39.54 4.96
835 869 1.547472 GCTGGCAAGGCAAAGGGATT 61.547 55.000 0.00 0.00 0.00 3.01
837 871 2.601367 GCTGGCAAGGCAAAGGGA 60.601 61.111 0.00 0.00 0.00 4.20
904 944 3.618019 GCTGTGCCATGGATGAACATTTT 60.618 43.478 18.40 0.00 0.00 1.82
1131 1204 3.118454 CTGACGGCGCAATTCGGT 61.118 61.111 10.83 0.00 38.94 4.69
1259 1332 6.525121 TTAAACCTTAGCGATCGATCAATG 57.475 37.500 24.40 10.03 0.00 2.82
1389 1475 2.360600 AGCAGGTCGAGCGTCTCT 60.361 61.111 9.28 2.28 37.01 3.10
1451 1540 6.719301 AGTTTGAGAAGATGATCCATTCTGT 58.281 36.000 8.43 0.00 33.53 3.41
1554 1643 0.034059 ACTGCTTCCTCGACTTGGTG 59.966 55.000 0.00 0.00 0.00 4.17
1621 1710 1.952296 GCAGTTCATGGCAGGAATAGG 59.048 52.381 18.27 11.23 0.00 2.57
1688 1777 1.609841 GCATCGATCATCCATGCCTCA 60.610 52.381 5.96 0.00 37.54 3.86
1791 1880 6.358974 TTTCTGAAGATGGTGACTGATGTA 57.641 37.500 0.00 0.00 0.00 2.29
1889 1978 2.673368 CTCTCCAATCACGTAAACCTGC 59.327 50.000 0.00 0.00 0.00 4.85
2116 2211 4.213270 TGAGCACGGCAATATAATGTAAGC 59.787 41.667 0.00 0.00 0.00 3.09
2345 2452 1.931841 CGAGAGGAGTGAACGACGATA 59.068 52.381 0.00 0.00 0.00 2.92
2346 2453 0.727970 CGAGAGGAGTGAACGACGAT 59.272 55.000 0.00 0.00 0.00 3.73
2347 2454 1.909141 GCGAGAGGAGTGAACGACGA 61.909 60.000 0.00 0.00 0.00 4.20
2348 2455 1.512310 GCGAGAGGAGTGAACGACG 60.512 63.158 0.00 0.00 0.00 5.12
2349 2456 1.153997 GGCGAGAGGAGTGAACGAC 60.154 63.158 0.00 0.00 0.00 4.34
2350 2457 0.894184 AAGGCGAGAGGAGTGAACGA 60.894 55.000 0.00 0.00 0.00 3.85
2351 2458 0.456995 GAAGGCGAGAGGAGTGAACG 60.457 60.000 0.00 0.00 0.00 3.95
2352 2459 0.603569 TGAAGGCGAGAGGAGTGAAC 59.396 55.000 0.00 0.00 0.00 3.18
2353 2460 1.338107 TTGAAGGCGAGAGGAGTGAA 58.662 50.000 0.00 0.00 0.00 3.18
2354 2461 1.273606 CTTTGAAGGCGAGAGGAGTGA 59.726 52.381 0.00 0.00 0.00 3.41
2355 2462 1.001406 ACTTTGAAGGCGAGAGGAGTG 59.999 52.381 0.00 0.00 0.00 3.51
2356 2463 1.343069 ACTTTGAAGGCGAGAGGAGT 58.657 50.000 0.00 0.00 0.00 3.85
2443 2550 7.497579 TGCGCATCTAAATTTCTACAATCCTAA 59.502 33.333 5.66 0.00 0.00 2.69
2666 2891 1.679311 GGTGAGATGGGTGACAGCA 59.321 57.895 7.01 0.00 38.15 4.41
2744 2972 7.987268 TTCGCAGTATGTATAAAGAGTTCTG 57.013 36.000 0.00 0.00 39.31 3.02
2767 2995 5.745227 CAAGGGACTGTGTATGTATCCTTT 58.255 41.667 0.00 0.00 40.86 3.11
2837 3066 0.749818 TTGAACCAAGAACAGCGCCA 60.750 50.000 2.29 0.00 0.00 5.69
2909 3138 4.357918 AGCTTCTTACTTCTTTGCCAGA 57.642 40.909 0.00 0.00 0.00 3.86
2976 3205 4.543692 CTTCACACATTCTTCCTTGCAAG 58.456 43.478 19.93 19.93 0.00 4.01
2977 3206 3.243501 GCTTCACACATTCTTCCTTGCAA 60.244 43.478 0.00 0.00 0.00 4.08
3562 3791 2.103771 GTGGCTGCCATAGATCTTCTGA 59.896 50.000 26.22 0.00 35.28 3.27
3948 4186 9.035607 CCATCTGTACAGTACATTATTCTTGTC 57.964 37.037 21.99 0.00 38.15 3.18
4041 4283 6.002062 AGAAATCAGAAAAGTAAAGCCACG 57.998 37.500 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.