Multiple sequence alignment - TraesCS1B01G051200

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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 TraesCS1B01G051200 chr1B 100.000 2315 0 0 1 2315 31124242 31126556 0.000000e+00 4276
1 TraesCS1B01G051200 chr1B 84.970 1324 186 3 991 2307 29898386 29899703 0.000000e+00 1330
2 TraesCS1B01G051200 chr1B 83.958 1334 197 11 991 2315 29823973 29825298 0.000000e+00 1262
3 TraesCS1B01G051200 chr1B 81.859 1334 219 16 991 2312 676851934 676853256 0.000000e+00 1101
4 TraesCS1B01G051200 chr1B 84.298 484 67 4 1832 2312 29085866 29086343 4.510000e-127 464
5 TraesCS1B01G051200 chrUn 94.335 2136 102 5 184 2315 116835885 116838005 0.000000e+00 3256
6 TraesCS1B01G051200 chrUn 84.790 1236 175 3 1079 2307 180337352 180338581 0.000000e+00 1229
7 TraesCS1B01G051200 chrUn 83.046 1333 210 7 991 2315 116819403 116820727 0.000000e+00 1195
8 TraesCS1B01G051200 chr1D 84.199 1329 190 12 991 2310 19807295 19808612 0.000000e+00 1273
9 TraesCS1B01G051200 chr1D 84.072 1331 199 6 992 2315 19341294 19342618 0.000000e+00 1271
10 TraesCS1B01G051200 chr1A 84.534 1235 176 7 992 2217 21075637 21076865 0.000000e+00 1208
11 TraesCS1B01G051200 chr1A 84.177 1087 159 5 1205 2284 21242771 21243851 0.000000e+00 1042


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 TraesCS1B01G051200 chr1B 31124242 31126556 2314 False 4276 4276 100.000 1 2315 1 chr1B.!!$F4 2314
1 TraesCS1B01G051200 chr1B 29898386 29899703 1317 False 1330 1330 84.970 991 2307 1 chr1B.!!$F3 1316
2 TraesCS1B01G051200 chr1B 29823973 29825298 1325 False 1262 1262 83.958 991 2315 1 chr1B.!!$F2 1324
3 TraesCS1B01G051200 chr1B 676851934 676853256 1322 False 1101 1101 81.859 991 2312 1 chr1B.!!$F5 1321
4 TraesCS1B01G051200 chrUn 116835885 116838005 2120 False 3256 3256 94.335 184 2315 1 chrUn.!!$F2 2131
5 TraesCS1B01G051200 chrUn 180337352 180338581 1229 False 1229 1229 84.790 1079 2307 1 chrUn.!!$F3 1228
6 TraesCS1B01G051200 chrUn 116819403 116820727 1324 False 1195 1195 83.046 991 2315 1 chrUn.!!$F1 1324
7 TraesCS1B01G051200 chr1D 19807295 19808612 1317 False 1273 1273 84.199 991 2310 1 chr1D.!!$F2 1319
8 TraesCS1B01G051200 chr1D 19341294 19342618 1324 False 1271 1271 84.072 992 2315 1 chr1D.!!$F1 1323
9 TraesCS1B01G051200 chr1A 21075637 21076865 1228 False 1208 1208 84.534 992 2217 1 chr1A.!!$F1 1225
10 TraesCS1B01G051200 chr1A 21242771 21243851 1080 False 1042 1042 84.177 1205 2284 1 chr1A.!!$F2 1079

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
136 137 0.030638 CCCACGAACCAAACAAGCTG 59.969 55.0 0.0 0.0 0.0 4.24 F
168 169 0.036388 CCTTGCTTCCACCTTCGCTA 60.036 55.0 0.0 0.0 0.0 4.26 F
170 171 0.321298 TTGCTTCCACCTTCGCTACC 60.321 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 1075 0.180171 CCATGCCGTCCATCACCTTA 59.820 55.000 0.00 0.0 29.71 2.69 R
1182 1183 0.647410 CTTCGAGCCAAGCACGTATG 59.353 55.000 6.32 0.0 42.61 2.39 R
2031 2049 1.071128 GGCCAGGCTCATCAGCTAG 59.929 63.158 12.43 0.0 46.03 3.42 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
23 24 5.819059 GATGTGAATTGCTCTCTGAATTCC 58.181 41.667 2.27 0.00 37.65 3.01
24 25 4.914983 TGTGAATTGCTCTCTGAATTCCT 58.085 39.130 2.27 0.00 37.65 3.36
25 26 6.053632 TGTGAATTGCTCTCTGAATTCCTA 57.946 37.500 2.27 0.00 37.65 2.94
26 27 6.656902 TGTGAATTGCTCTCTGAATTCCTAT 58.343 36.000 2.27 0.00 37.65 2.57
27 28 7.114754 TGTGAATTGCTCTCTGAATTCCTATT 58.885 34.615 2.27 0.00 37.65 1.73
28 29 7.281774 TGTGAATTGCTCTCTGAATTCCTATTC 59.718 37.037 2.27 5.43 37.65 1.75
29 30 7.498570 GTGAATTGCTCTCTGAATTCCTATTCT 59.501 37.037 2.27 0.00 40.68 2.40
30 31 7.714377 TGAATTGCTCTCTGAATTCCTATTCTC 59.286 37.037 2.27 0.00 40.68 2.87
31 32 5.543507 TGCTCTCTGAATTCCTATTCTCC 57.456 43.478 2.27 0.00 40.68 3.71
32 33 4.964897 TGCTCTCTGAATTCCTATTCTCCA 59.035 41.667 2.27 0.00 40.68 3.86
33 34 5.605908 TGCTCTCTGAATTCCTATTCTCCAT 59.394 40.000 2.27 0.00 40.68 3.41
34 35 6.165577 GCTCTCTGAATTCCTATTCTCCATC 58.834 44.000 2.27 0.00 40.68 3.51
35 36 6.678568 TCTCTGAATTCCTATTCTCCATCC 57.321 41.667 2.27 0.00 40.68 3.51
36 37 5.545723 TCTCTGAATTCCTATTCTCCATCCC 59.454 44.000 2.27 0.00 40.68 3.85
37 38 5.226803 TCTGAATTCCTATTCTCCATCCCA 58.773 41.667 2.27 0.00 40.68 4.37
38 39 5.072329 TCTGAATTCCTATTCTCCATCCCAC 59.928 44.000 2.27 0.00 40.68 4.61
39 40 4.977739 TGAATTCCTATTCTCCATCCCACT 59.022 41.667 2.27 0.00 40.68 4.00
40 41 5.433051 TGAATTCCTATTCTCCATCCCACTT 59.567 40.000 2.27 0.00 40.68 3.16
41 42 6.619437 TGAATTCCTATTCTCCATCCCACTTA 59.381 38.462 2.27 0.00 40.68 2.24
42 43 7.128728 TGAATTCCTATTCTCCATCCCACTTAA 59.871 37.037 2.27 0.00 40.68 1.85
43 44 6.901615 TTCCTATTCTCCATCCCACTTAAA 57.098 37.500 0.00 0.00 0.00 1.52
44 45 7.465900 TTCCTATTCTCCATCCCACTTAAAT 57.534 36.000 0.00 0.00 0.00 1.40
45 46 7.079451 TCCTATTCTCCATCCCACTTAAATC 57.921 40.000 0.00 0.00 0.00 2.17
46 47 6.044404 TCCTATTCTCCATCCCACTTAAATCC 59.956 42.308 0.00 0.00 0.00 3.01
47 48 6.044871 CCTATTCTCCATCCCACTTAAATCCT 59.955 42.308 0.00 0.00 0.00 3.24
48 49 5.373812 TTCTCCATCCCACTTAAATCCTC 57.626 43.478 0.00 0.00 0.00 3.71
49 50 4.370776 TCTCCATCCCACTTAAATCCTCA 58.629 43.478 0.00 0.00 0.00 3.86
50 51 4.977739 TCTCCATCCCACTTAAATCCTCAT 59.022 41.667 0.00 0.00 0.00 2.90
51 52 5.433051 TCTCCATCCCACTTAAATCCTCATT 59.567 40.000 0.00 0.00 0.00 2.57
52 53 6.068853 TCTCCATCCCACTTAAATCCTCATTT 60.069 38.462 0.00 0.00 36.18 2.32
53 54 6.502138 TCCATCCCACTTAAATCCTCATTTT 58.498 36.000 0.00 0.00 33.95 1.82
54 55 6.607198 TCCATCCCACTTAAATCCTCATTTTC 59.393 38.462 0.00 0.00 33.95 2.29
55 56 6.608808 CCATCCCACTTAAATCCTCATTTTCT 59.391 38.462 0.00 0.00 33.95 2.52
56 57 7.201857 CCATCCCACTTAAATCCTCATTTTCTC 60.202 40.741 0.00 0.00 33.95 2.87
57 58 7.032598 TCCCACTTAAATCCTCATTTTCTCT 57.967 36.000 0.00 0.00 33.95 3.10
58 59 8.158025 TCCCACTTAAATCCTCATTTTCTCTA 57.842 34.615 0.00 0.00 33.95 2.43
59 60 8.611257 TCCCACTTAAATCCTCATTTTCTCTAA 58.389 33.333 0.00 0.00 33.95 2.10
60 61 9.413734 CCCACTTAAATCCTCATTTTCTCTAAT 57.586 33.333 0.00 0.00 33.95 1.73
69 70 8.954950 TCCTCATTTTCTCTAATCAATCAGAC 57.045 34.615 0.00 0.00 0.00 3.51
70 71 7.708322 TCCTCATTTTCTCTAATCAATCAGACG 59.292 37.037 0.00 0.00 0.00 4.18
71 72 7.708322 CCTCATTTTCTCTAATCAATCAGACGA 59.292 37.037 0.00 0.00 0.00 4.20
72 73 8.412608 TCATTTTCTCTAATCAATCAGACGAC 57.587 34.615 0.00 0.00 0.00 4.34
73 74 8.253810 TCATTTTCTCTAATCAATCAGACGACT 58.746 33.333 0.00 0.00 0.00 4.18
74 75 8.877779 CATTTTCTCTAATCAATCAGACGACTT 58.122 33.333 0.00 0.00 0.00 3.01
75 76 8.833231 TTTTCTCTAATCAATCAGACGACTTT 57.167 30.769 0.00 0.00 0.00 2.66
76 77 8.467402 TTTCTCTAATCAATCAGACGACTTTC 57.533 34.615 0.00 0.00 0.00 2.62
77 78 7.158099 TCTCTAATCAATCAGACGACTTTCA 57.842 36.000 0.00 0.00 0.00 2.69
78 79 7.602753 TCTCTAATCAATCAGACGACTTTCAA 58.397 34.615 0.00 0.00 0.00 2.69
79 80 8.253810 TCTCTAATCAATCAGACGACTTTCAAT 58.746 33.333 0.00 0.00 0.00 2.57
80 81 8.412608 TCTAATCAATCAGACGACTTTCAATC 57.587 34.615 0.00 0.00 0.00 2.67
81 82 8.253810 TCTAATCAATCAGACGACTTTCAATCT 58.746 33.333 0.00 0.00 0.00 2.40
82 83 6.900568 ATCAATCAGACGACTTTCAATCTC 57.099 37.500 0.00 0.00 0.00 2.75
83 84 5.171476 TCAATCAGACGACTTTCAATCTCC 58.829 41.667 0.00 0.00 0.00 3.71
84 85 5.047021 TCAATCAGACGACTTTCAATCTCCT 60.047 40.000 0.00 0.00 0.00 3.69
85 86 4.873746 TCAGACGACTTTCAATCTCCTT 57.126 40.909 0.00 0.00 0.00 3.36
86 87 5.977489 TCAGACGACTTTCAATCTCCTTA 57.023 39.130 0.00 0.00 0.00 2.69
87 88 5.710984 TCAGACGACTTTCAATCTCCTTAC 58.289 41.667 0.00 0.00 0.00 2.34
88 89 4.865365 CAGACGACTTTCAATCTCCTTACC 59.135 45.833 0.00 0.00 0.00 2.85
89 90 4.081586 AGACGACTTTCAATCTCCTTACCC 60.082 45.833 0.00 0.00 0.00 3.69
90 91 3.055312 ACGACTTTCAATCTCCTTACCCC 60.055 47.826 0.00 0.00 0.00 4.95
91 92 3.197983 CGACTTTCAATCTCCTTACCCCT 59.802 47.826 0.00 0.00 0.00 4.79
92 93 4.323562 CGACTTTCAATCTCCTTACCCCTT 60.324 45.833 0.00 0.00 0.00 3.95
93 94 5.105064 CGACTTTCAATCTCCTTACCCCTTA 60.105 44.000 0.00 0.00 0.00 2.69
94 95 6.575649 CGACTTTCAATCTCCTTACCCCTTAA 60.576 42.308 0.00 0.00 0.00 1.85
95 96 7.098845 ACTTTCAATCTCCTTACCCCTTAAA 57.901 36.000 0.00 0.00 0.00 1.52
96 97 7.709601 ACTTTCAATCTCCTTACCCCTTAAAT 58.290 34.615 0.00 0.00 0.00 1.40
97 98 7.834681 ACTTTCAATCTCCTTACCCCTTAAATC 59.165 37.037 0.00 0.00 0.00 2.17
98 99 6.262056 TCAATCTCCTTACCCCTTAAATCC 57.738 41.667 0.00 0.00 0.00 3.01
99 100 5.133830 TCAATCTCCTTACCCCTTAAATCCC 59.866 44.000 0.00 0.00 0.00 3.85
100 101 4.097017 TCTCCTTACCCCTTAAATCCCA 57.903 45.455 0.00 0.00 0.00 4.37
101 102 4.652628 TCTCCTTACCCCTTAAATCCCAT 58.347 43.478 0.00 0.00 0.00 4.00
102 103 5.050685 TCTCCTTACCCCTTAAATCCCATT 58.949 41.667 0.00 0.00 0.00 3.16
103 104 5.133830 TCTCCTTACCCCTTAAATCCCATTC 59.866 44.000 0.00 0.00 0.00 2.67
104 105 5.050685 TCCTTACCCCTTAAATCCCATTCT 58.949 41.667 0.00 0.00 0.00 2.40
105 106 5.133830 TCCTTACCCCTTAAATCCCATTCTC 59.866 44.000 0.00 0.00 0.00 2.87
106 107 3.973472 ACCCCTTAAATCCCATTCTCC 57.027 47.619 0.00 0.00 0.00 3.71
107 108 3.206464 ACCCCTTAAATCCCATTCTCCA 58.794 45.455 0.00 0.00 0.00 3.86
108 109 3.799578 ACCCCTTAAATCCCATTCTCCAT 59.200 43.478 0.00 0.00 0.00 3.41
109 110 4.140924 ACCCCTTAAATCCCATTCTCCATC 60.141 45.833 0.00 0.00 0.00 3.51
110 111 4.106987 CCCCTTAAATCCCATTCTCCATCT 59.893 45.833 0.00 0.00 0.00 2.90
111 112 5.320277 CCCTTAAATCCCATTCTCCATCTC 58.680 45.833 0.00 0.00 0.00 2.75
112 113 5.074239 CCCTTAAATCCCATTCTCCATCTCT 59.926 44.000 0.00 0.00 0.00 3.10
113 114 6.273260 CCCTTAAATCCCATTCTCCATCTCTA 59.727 42.308 0.00 0.00 0.00 2.43
114 115 7.202223 CCCTTAAATCCCATTCTCCATCTCTAA 60.202 40.741 0.00 0.00 0.00 2.10
115 116 8.389366 CCTTAAATCCCATTCTCCATCTCTAAT 58.611 37.037 0.00 0.00 0.00 1.73
116 117 9.804977 CTTAAATCCCATTCTCCATCTCTAATT 57.195 33.333 0.00 0.00 0.00 1.40
117 118 9.799106 TTAAATCCCATTCTCCATCTCTAATTC 57.201 33.333 0.00 0.00 0.00 2.17
118 119 5.832539 TCCCATTCTCCATCTCTAATTCC 57.167 43.478 0.00 0.00 0.00 3.01
119 120 4.599241 TCCCATTCTCCATCTCTAATTCCC 59.401 45.833 0.00 0.00 0.00 3.97
120 121 4.352001 CCCATTCTCCATCTCTAATTCCCA 59.648 45.833 0.00 0.00 0.00 4.37
121 122 5.312079 CCATTCTCCATCTCTAATTCCCAC 58.688 45.833 0.00 0.00 0.00 4.61
122 123 4.672587 TTCTCCATCTCTAATTCCCACG 57.327 45.455 0.00 0.00 0.00 4.94
123 124 3.910989 TCTCCATCTCTAATTCCCACGA 58.089 45.455 0.00 0.00 0.00 4.35
124 125 4.286707 TCTCCATCTCTAATTCCCACGAA 58.713 43.478 0.00 0.00 0.00 3.85
125 126 4.099573 TCTCCATCTCTAATTCCCACGAAC 59.900 45.833 0.00 0.00 0.00 3.95
126 127 3.134081 TCCATCTCTAATTCCCACGAACC 59.866 47.826 0.00 0.00 0.00 3.62
127 128 3.118408 CCATCTCTAATTCCCACGAACCA 60.118 47.826 0.00 0.00 0.00 3.67
128 129 4.513442 CATCTCTAATTCCCACGAACCAA 58.487 43.478 0.00 0.00 0.00 3.67
129 130 4.627284 TCTCTAATTCCCACGAACCAAA 57.373 40.909 0.00 0.00 0.00 3.28
130 131 4.320870 TCTCTAATTCCCACGAACCAAAC 58.679 43.478 0.00 0.00 0.00 2.93
131 132 4.069304 CTCTAATTCCCACGAACCAAACA 58.931 43.478 0.00 0.00 0.00 2.83
132 133 4.462133 TCTAATTCCCACGAACCAAACAA 58.538 39.130 0.00 0.00 0.00 2.83
133 134 3.726291 AATTCCCACGAACCAAACAAG 57.274 42.857 0.00 0.00 0.00 3.16
134 135 0.741915 TTCCCACGAACCAAACAAGC 59.258 50.000 0.00 0.00 0.00 4.01
135 136 0.106918 TCCCACGAACCAAACAAGCT 60.107 50.000 0.00 0.00 0.00 3.74
136 137 0.030638 CCCACGAACCAAACAAGCTG 59.969 55.000 0.00 0.00 0.00 4.24
137 138 0.594796 CCACGAACCAAACAAGCTGC 60.595 55.000 0.00 0.00 0.00 5.25
138 139 0.594796 CACGAACCAAACAAGCTGCC 60.595 55.000 0.00 0.00 0.00 4.85
139 140 0.751643 ACGAACCAAACAAGCTGCCT 60.752 50.000 0.00 0.00 0.00 4.75
140 141 1.234821 CGAACCAAACAAGCTGCCTA 58.765 50.000 0.00 0.00 0.00 3.93
141 142 1.606668 CGAACCAAACAAGCTGCCTAA 59.393 47.619 0.00 0.00 0.00 2.69
142 143 2.350772 CGAACCAAACAAGCTGCCTAAG 60.351 50.000 0.00 0.00 0.00 2.18
143 144 1.620822 ACCAAACAAGCTGCCTAAGG 58.379 50.000 0.00 0.00 0.00 2.69
144 145 1.133482 ACCAAACAAGCTGCCTAAGGT 60.133 47.619 0.00 0.00 38.63 3.50
146 147 2.365293 CCAAACAAGCTGCCTAAGGTTT 59.635 45.455 0.00 0.00 44.21 3.27
147 148 3.383761 CAAACAAGCTGCCTAAGGTTTG 58.616 45.455 13.64 13.64 44.21 2.93
148 149 1.620822 ACAAGCTGCCTAAGGTTTGG 58.379 50.000 0.00 0.00 44.21 3.28
149 150 0.244721 CAAGCTGCCTAAGGTTTGGC 59.755 55.000 8.09 8.09 44.21 4.52
150 151 0.900182 AAGCTGCCTAAGGTTTGGCC 60.900 55.000 11.88 0.00 44.21 5.36
159 160 3.869481 GGTTTGGCCTTGCTTCCA 58.131 55.556 3.32 0.00 0.00 3.53
160 161 1.367471 GGTTTGGCCTTGCTTCCAC 59.633 57.895 3.32 0.00 30.97 4.02
161 162 1.367471 GTTTGGCCTTGCTTCCACC 59.633 57.895 3.32 0.00 30.97 4.61
162 163 1.115326 GTTTGGCCTTGCTTCCACCT 61.115 55.000 3.32 0.00 30.97 4.00
163 164 0.398381 TTTGGCCTTGCTTCCACCTT 60.398 50.000 3.32 0.00 30.97 3.50
164 165 0.827507 TTGGCCTTGCTTCCACCTTC 60.828 55.000 3.32 0.00 30.97 3.46
165 166 2.335712 GGCCTTGCTTCCACCTTCG 61.336 63.158 0.00 0.00 0.00 3.79
166 167 2.982744 GCCTTGCTTCCACCTTCGC 61.983 63.158 0.00 0.00 0.00 4.70
167 168 1.302832 CCTTGCTTCCACCTTCGCT 60.303 57.895 0.00 0.00 0.00 4.93
168 169 0.036388 CCTTGCTTCCACCTTCGCTA 60.036 55.000 0.00 0.00 0.00 4.26
169 170 1.079503 CTTGCTTCCACCTTCGCTAC 58.920 55.000 0.00 0.00 0.00 3.58
170 171 0.321298 TTGCTTCCACCTTCGCTACC 60.321 55.000 0.00 0.00 0.00 3.18
171 172 1.449778 GCTTCCACCTTCGCTACCC 60.450 63.158 0.00 0.00 0.00 3.69
172 173 1.221021 CTTCCACCTTCGCTACCCC 59.779 63.158 0.00 0.00 0.00 4.95
173 174 2.253403 CTTCCACCTTCGCTACCCCC 62.253 65.000 0.00 0.00 0.00 5.40
174 175 2.687566 CCACCTTCGCTACCCCCT 60.688 66.667 0.00 0.00 0.00 4.79
175 176 2.732619 CCACCTTCGCTACCCCCTC 61.733 68.421 0.00 0.00 0.00 4.30
176 177 2.365237 ACCTTCGCTACCCCCTCC 60.365 66.667 0.00 0.00 0.00 4.30
177 178 3.537874 CCTTCGCTACCCCCTCCG 61.538 72.222 0.00 0.00 0.00 4.63
178 179 2.758737 CTTCGCTACCCCCTCCGT 60.759 66.667 0.00 0.00 0.00 4.69
179 180 3.072468 TTCGCTACCCCCTCCGTG 61.072 66.667 0.00 0.00 0.00 4.94
180 181 3.892104 TTCGCTACCCCCTCCGTGT 62.892 63.158 0.00 0.00 0.00 4.49
181 182 3.834799 CGCTACCCCCTCCGTGTC 61.835 72.222 0.00 0.00 0.00 3.67
182 183 2.682494 GCTACCCCCTCCGTGTCA 60.682 66.667 0.00 0.00 0.00 3.58
199 200 2.688446 TGTCAGTGTCAGTCTCGTCTTT 59.312 45.455 0.00 0.00 0.00 2.52
207 208 2.750166 TCAGTCTCGTCTTTGGCTAGAG 59.250 50.000 0.00 0.00 0.00 2.43
221 222 1.945394 GCTAGAGCCATTCACCATGTG 59.055 52.381 0.00 0.00 34.31 3.21
252 253 1.733041 ATGACAACCGCGACGTCAG 60.733 57.895 22.96 8.71 42.53 3.51
291 292 0.757561 TTGTCTGGTCCACACGAGGA 60.758 55.000 0.00 0.00 34.64 3.71
332 333 1.804748 GGTGGACGCGATTTTCTTTCT 59.195 47.619 15.93 0.00 0.00 2.52
338 339 2.031157 ACGCGATTTTCTTTCTGGTTGG 60.031 45.455 15.93 0.00 0.00 3.77
344 345 0.465460 TTCTTTCTGGTTGGTGCGCT 60.465 50.000 9.73 0.00 0.00 5.92
355 356 0.950555 TGGTGCGCTTGTCATGTCTC 60.951 55.000 9.73 0.00 0.00 3.36
523 524 2.275134 TGCCAGCATTCTCAAAGTGA 57.725 45.000 0.00 0.00 0.00 3.41
528 529 5.243507 TGCCAGCATTCTCAAAGTGAATTTA 59.756 36.000 0.00 0.00 32.47 1.40
582 583 1.870580 GCAAGCACACCACACGTACTA 60.871 52.381 0.00 0.00 0.00 1.82
613 614 3.151958 AACGCACGCTCTGTCCACT 62.152 57.895 0.00 0.00 0.00 4.00
634 635 2.358372 ACATCCCGCCCAAATTGCC 61.358 57.895 0.00 0.00 0.00 4.52
670 671 0.608582 ACTCCCTCTGCTACGTCGTT 60.609 55.000 1.78 0.00 0.00 3.85
718 719 0.768221 TTCCCCTCTCACTGCACCTT 60.768 55.000 0.00 0.00 0.00 3.50
742 743 4.144703 GCCTCGGTTCGGGTCTCC 62.145 72.222 0.00 0.00 0.00 3.71
774 775 4.043200 GGTGCGGCTGCTTGGTTC 62.043 66.667 20.27 2.32 43.34 3.62
785 786 3.569049 CTTGGTTCCCGTCGACGCT 62.569 63.158 31.73 0.00 38.18 5.07
830 831 2.204034 TGACAGGCTCCTCCACCA 59.796 61.111 0.00 0.00 37.29 4.17
855 856 3.133721 CAGGTATCCTTCTTCCACTCAGG 59.866 52.174 0.00 0.00 39.47 3.86
885 886 2.158561 AAAATCAGCGCCAGTTGCCC 62.159 55.000 2.29 0.00 36.24 5.36
886 887 3.574074 AATCAGCGCCAGTTGCCCT 62.574 57.895 2.29 0.00 36.24 5.19
887 888 3.984193 ATCAGCGCCAGTTGCCCTC 62.984 63.158 2.29 0.00 36.24 4.30
905 906 0.996583 TCAATCACCCCTAACCCCAC 59.003 55.000 0.00 0.00 0.00 4.61
920 921 1.075374 CCCCACACCATTTTCTCCTCA 59.925 52.381 0.00 0.00 0.00 3.86
938 939 1.748493 TCAGCAAGGTGGTTGTGTTTC 59.252 47.619 0.00 0.00 38.55 2.78
951 952 0.663153 GTGTTTCCCTGTGTCAGTGC 59.337 55.000 0.00 0.00 0.00 4.40
988 989 2.172505 TGGGAGCTGTGAAAGACTGAAA 59.827 45.455 0.00 0.00 0.00 2.69
989 990 2.550180 GGGAGCTGTGAAAGACTGAAAC 59.450 50.000 0.00 0.00 0.00 2.78
1023 1024 0.468029 CAGAGTTTGTGGTTGGGCCT 60.468 55.000 4.53 0.00 38.35 5.19
1053 1054 0.468226 TGTTGAAGGACAAGGCGTCT 59.532 50.000 0.00 0.00 44.70 4.18
1216 1217 2.670414 CTCGAAGCACTCAAGAATGTCC 59.330 50.000 0.00 0.00 0.00 4.02
1218 1219 2.613977 CGAAGCACTCAAGAATGTCCCT 60.614 50.000 0.00 0.00 0.00 4.20
1227 1228 3.782523 TCAAGAATGTCCCTTATGAGGCT 59.217 43.478 0.00 0.00 42.09 4.58
1358 1363 4.235360 CCATCGTGTTCCGTTATAGGATC 58.765 47.826 0.00 0.00 40.48 3.36
1370 1375 5.508489 CCGTTATAGGATCGGCAAGAAGTTA 60.508 44.000 0.00 0.00 37.90 2.24
1376 1381 3.058639 GGATCGGCAAGAAGTTATGCATC 60.059 47.826 0.19 9.10 44.32 3.91
1488 1494 6.566942 GCGCATTACGGATTCCATATTAAACA 60.567 38.462 0.30 0.00 43.93 2.83
1519 1525 5.364157 AGAAGGATATTGTGAGTAGGTCCAC 59.636 44.000 0.00 0.00 0.00 4.02
1598 1610 2.093500 TCTCATCGTCCTTCCCATTGTG 60.093 50.000 0.00 0.00 0.00 3.33
1695 1707 1.004862 TCCAAAGGTGGTGTTGTGTGA 59.995 47.619 0.00 0.00 46.11 3.58
1803 1815 6.326583 TCAGAAAGAAGTAAGTGGGAAGAGAA 59.673 38.462 0.00 0.00 0.00 2.87
1901 1914 1.745653 GCCAAGGGAAGTGCAATACTC 59.254 52.381 0.00 0.00 39.18 2.59
1947 1962 6.032094 GTGGCTCAAATTATGAAGATGTGTG 58.968 40.000 0.00 0.00 37.67 3.82
1952 1967 7.272084 GCTCAAATTATGAAGATGTGTGTTCAC 59.728 37.037 0.00 0.00 40.01 3.18
1965 1983 2.223782 TGTGTTCACAGCCAAAATCTGC 60.224 45.455 1.23 0.00 35.04 4.26
1969 1987 2.161855 TCACAGCCAAAATCTGCGAAT 58.838 42.857 0.00 0.00 35.04 3.34
2031 2049 2.032636 GCATTCTGTTTGCAAAAGCCAC 60.033 45.455 14.67 1.92 39.90 5.01
2055 2079 2.042464 CTGATGAGCCTGGCCTAAGTA 58.958 52.381 16.57 0.00 0.00 2.24
2077 2101 2.443255 AGGTGGTTGACAAGATTCTGGT 59.557 45.455 0.00 0.00 0.00 4.00
2090 2114 3.402681 CTGGTCAGATGCGGGGGT 61.403 66.667 0.00 0.00 0.00 4.95
2194 2218 5.343307 AGCAAAACTTTCAACAAGGACAT 57.657 34.783 0.00 0.00 0.00 3.06
2250 2280 4.651778 TGACTTACCATCCCAGTTGAAAG 58.348 43.478 0.00 0.00 0.00 2.62
2279 2309 6.238456 GCTTTGCTTTTTGTGCTTTATTTCCT 60.238 34.615 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.589452 AGGAATTCAGAGAGCAATTCACATC 59.411 40.000 7.93 0.00 39.73 3.06
1 2 5.507637 AGGAATTCAGAGAGCAATTCACAT 58.492 37.500 7.93 0.00 39.73 3.21
2 3 4.914983 AGGAATTCAGAGAGCAATTCACA 58.085 39.130 7.93 0.00 39.73 3.58
3 4 7.498570 AGAATAGGAATTCAGAGAGCAATTCAC 59.501 37.037 7.93 0.00 43.44 3.18
4 5 7.571919 AGAATAGGAATTCAGAGAGCAATTCA 58.428 34.615 7.93 0.00 43.44 2.57
5 6 7.173047 GGAGAATAGGAATTCAGAGAGCAATTC 59.827 40.741 7.93 4.53 43.44 2.17
6 7 6.997476 GGAGAATAGGAATTCAGAGAGCAATT 59.003 38.462 7.93 0.00 43.44 2.32
7 8 6.100859 TGGAGAATAGGAATTCAGAGAGCAAT 59.899 38.462 7.93 0.00 43.44 3.56
8 9 5.426509 TGGAGAATAGGAATTCAGAGAGCAA 59.573 40.000 7.93 0.00 43.44 3.91
9 10 4.964897 TGGAGAATAGGAATTCAGAGAGCA 59.035 41.667 7.93 0.00 43.44 4.26
10 11 5.543507 TGGAGAATAGGAATTCAGAGAGC 57.456 43.478 7.93 0.00 43.44 4.09
11 12 6.295802 GGGATGGAGAATAGGAATTCAGAGAG 60.296 46.154 7.93 0.00 43.44 3.20
12 13 5.545723 GGGATGGAGAATAGGAATTCAGAGA 59.454 44.000 7.93 0.00 43.44 3.10
13 14 5.309020 TGGGATGGAGAATAGGAATTCAGAG 59.691 44.000 7.93 0.00 43.44 3.35
14 15 5.072329 GTGGGATGGAGAATAGGAATTCAGA 59.928 44.000 7.93 0.00 43.44 3.27
15 16 5.072872 AGTGGGATGGAGAATAGGAATTCAG 59.927 44.000 7.93 0.00 43.44 3.02
16 17 4.977739 AGTGGGATGGAGAATAGGAATTCA 59.022 41.667 7.93 0.00 43.44 2.57
17 18 5.574970 AGTGGGATGGAGAATAGGAATTC 57.425 43.478 0.00 0.00 41.65 2.17
18 19 7.465900 TTAAGTGGGATGGAGAATAGGAATT 57.534 36.000 0.00 0.00 0.00 2.17
19 20 7.465900 TTTAAGTGGGATGGAGAATAGGAAT 57.534 36.000 0.00 0.00 0.00 3.01
20 21 6.901615 TTTAAGTGGGATGGAGAATAGGAA 57.098 37.500 0.00 0.00 0.00 3.36
21 22 6.044404 GGATTTAAGTGGGATGGAGAATAGGA 59.956 42.308 0.00 0.00 0.00 2.94
22 23 6.044871 AGGATTTAAGTGGGATGGAGAATAGG 59.955 42.308 0.00 0.00 0.00 2.57
23 24 7.084268 AGGATTTAAGTGGGATGGAGAATAG 57.916 40.000 0.00 0.00 0.00 1.73
24 25 6.619437 TGAGGATTTAAGTGGGATGGAGAATA 59.381 38.462 0.00 0.00 0.00 1.75
25 26 5.433051 TGAGGATTTAAGTGGGATGGAGAAT 59.567 40.000 0.00 0.00 0.00 2.40
26 27 4.788075 TGAGGATTTAAGTGGGATGGAGAA 59.212 41.667 0.00 0.00 0.00 2.87
27 28 4.370776 TGAGGATTTAAGTGGGATGGAGA 58.629 43.478 0.00 0.00 0.00 3.71
28 29 4.778213 TGAGGATTTAAGTGGGATGGAG 57.222 45.455 0.00 0.00 0.00 3.86
29 30 5.732331 AATGAGGATTTAAGTGGGATGGA 57.268 39.130 0.00 0.00 0.00 3.41
30 31 6.608808 AGAAAATGAGGATTTAAGTGGGATGG 59.391 38.462 0.00 0.00 31.18 3.51
31 32 7.559170 AGAGAAAATGAGGATTTAAGTGGGATG 59.441 37.037 0.00 0.00 31.18 3.51
32 33 7.646884 AGAGAAAATGAGGATTTAAGTGGGAT 58.353 34.615 0.00 0.00 31.18 3.85
33 34 7.032598 AGAGAAAATGAGGATTTAAGTGGGA 57.967 36.000 0.00 0.00 31.18 4.37
34 35 8.807948 TTAGAGAAAATGAGGATTTAAGTGGG 57.192 34.615 0.00 0.00 31.18 4.61
43 44 9.558396 GTCTGATTGATTAGAGAAAATGAGGAT 57.442 33.333 0.00 0.00 0.00 3.24
44 45 7.708322 CGTCTGATTGATTAGAGAAAATGAGGA 59.292 37.037 0.00 0.00 0.00 3.71
45 46 7.708322 TCGTCTGATTGATTAGAGAAAATGAGG 59.292 37.037 0.00 0.00 0.00 3.86
46 47 8.538856 GTCGTCTGATTGATTAGAGAAAATGAG 58.461 37.037 0.00 0.00 0.00 2.90
47 48 8.253810 AGTCGTCTGATTGATTAGAGAAAATGA 58.746 33.333 0.00 0.00 0.00 2.57
48 49 8.417780 AGTCGTCTGATTGATTAGAGAAAATG 57.582 34.615 0.00 0.00 0.00 2.32
49 50 9.442047 AAAGTCGTCTGATTGATTAGAGAAAAT 57.558 29.630 0.00 0.00 0.00 1.82
50 51 8.833231 AAAGTCGTCTGATTGATTAGAGAAAA 57.167 30.769 0.00 0.00 0.00 2.29
51 52 8.088365 TGAAAGTCGTCTGATTGATTAGAGAAA 58.912 33.333 0.00 0.00 0.00 2.52
52 53 7.602753 TGAAAGTCGTCTGATTGATTAGAGAA 58.397 34.615 0.00 0.00 0.00 2.87
53 54 7.158099 TGAAAGTCGTCTGATTGATTAGAGA 57.842 36.000 0.00 0.00 0.00 3.10
54 55 7.818493 TTGAAAGTCGTCTGATTGATTAGAG 57.182 36.000 0.00 0.00 0.00 2.43
55 56 8.253810 AGATTGAAAGTCGTCTGATTGATTAGA 58.746 33.333 0.00 0.00 0.00 2.10
56 57 8.417780 AGATTGAAAGTCGTCTGATTGATTAG 57.582 34.615 0.00 0.00 0.00 1.73
57 58 7.492669 GGAGATTGAAAGTCGTCTGATTGATTA 59.507 37.037 0.00 0.00 0.00 1.75
58 59 6.314896 GGAGATTGAAAGTCGTCTGATTGATT 59.685 38.462 0.00 0.00 0.00 2.57
59 60 5.814705 GGAGATTGAAAGTCGTCTGATTGAT 59.185 40.000 0.00 0.00 0.00 2.57
60 61 5.047021 AGGAGATTGAAAGTCGTCTGATTGA 60.047 40.000 0.00 0.00 0.00 2.57
61 62 5.174395 AGGAGATTGAAAGTCGTCTGATTG 58.826 41.667 0.00 0.00 0.00 2.67
62 63 5.413309 AGGAGATTGAAAGTCGTCTGATT 57.587 39.130 0.00 0.00 0.00 2.57
63 64 5.413309 AAGGAGATTGAAAGTCGTCTGAT 57.587 39.130 0.00 0.00 0.00 2.90
64 65 4.873746 AAGGAGATTGAAAGTCGTCTGA 57.126 40.909 0.00 0.00 0.00 3.27
65 66 4.865365 GGTAAGGAGATTGAAAGTCGTCTG 59.135 45.833 0.00 0.00 0.00 3.51
66 67 4.081586 GGGTAAGGAGATTGAAAGTCGTCT 60.082 45.833 0.00 0.00 0.00 4.18
67 68 4.182339 GGGTAAGGAGATTGAAAGTCGTC 58.818 47.826 0.00 0.00 0.00 4.20
68 69 3.055312 GGGGTAAGGAGATTGAAAGTCGT 60.055 47.826 0.00 0.00 0.00 4.34
69 70 3.197983 AGGGGTAAGGAGATTGAAAGTCG 59.802 47.826 0.00 0.00 0.00 4.18
70 71 4.846168 AGGGGTAAGGAGATTGAAAGTC 57.154 45.455 0.00 0.00 0.00 3.01
71 72 6.713731 TTAAGGGGTAAGGAGATTGAAAGT 57.286 37.500 0.00 0.00 0.00 2.66
72 73 7.285629 GGATTTAAGGGGTAAGGAGATTGAAAG 59.714 40.741 0.00 0.00 0.00 2.62
73 74 7.123383 GGATTTAAGGGGTAAGGAGATTGAAA 58.877 38.462 0.00 0.00 0.00 2.69
74 75 6.354477 GGGATTTAAGGGGTAAGGAGATTGAA 60.354 42.308 0.00 0.00 0.00 2.69
75 76 5.133830 GGGATTTAAGGGGTAAGGAGATTGA 59.866 44.000 0.00 0.00 0.00 2.57
76 77 5.103686 TGGGATTTAAGGGGTAAGGAGATTG 60.104 44.000 0.00 0.00 0.00 2.67
77 78 5.050685 TGGGATTTAAGGGGTAAGGAGATT 58.949 41.667 0.00 0.00 0.00 2.40
78 79 4.652628 TGGGATTTAAGGGGTAAGGAGAT 58.347 43.478 0.00 0.00 0.00 2.75
79 80 4.097017 TGGGATTTAAGGGGTAAGGAGA 57.903 45.455 0.00 0.00 0.00 3.71
80 81 5.134509 AGAATGGGATTTAAGGGGTAAGGAG 59.865 44.000 0.00 0.00 0.00 3.69
81 82 5.050685 AGAATGGGATTTAAGGGGTAAGGA 58.949 41.667 0.00 0.00 0.00 3.36
82 83 5.386060 GAGAATGGGATTTAAGGGGTAAGG 58.614 45.833 0.00 0.00 0.00 2.69
83 84 5.103686 TGGAGAATGGGATTTAAGGGGTAAG 60.104 44.000 0.00 0.00 0.00 2.34
84 85 4.796816 TGGAGAATGGGATTTAAGGGGTAA 59.203 41.667 0.00 0.00 0.00 2.85
85 86 4.385386 TGGAGAATGGGATTTAAGGGGTA 58.615 43.478 0.00 0.00 0.00 3.69
86 87 3.206464 TGGAGAATGGGATTTAAGGGGT 58.794 45.455 0.00 0.00 0.00 4.95
87 88 3.971468 TGGAGAATGGGATTTAAGGGG 57.029 47.619 0.00 0.00 0.00 4.79
88 89 5.074239 AGAGATGGAGAATGGGATTTAAGGG 59.926 44.000 0.00 0.00 0.00 3.95
89 90 6.198237 AGAGATGGAGAATGGGATTTAAGG 57.802 41.667 0.00 0.00 0.00 2.69
90 91 9.804977 AATTAGAGATGGAGAATGGGATTTAAG 57.195 33.333 0.00 0.00 0.00 1.85
91 92 9.799106 GAATTAGAGATGGAGAATGGGATTTAA 57.201 33.333 0.00 0.00 0.00 1.52
92 93 8.386264 GGAATTAGAGATGGAGAATGGGATTTA 58.614 37.037 0.00 0.00 0.00 1.40
93 94 7.237255 GGAATTAGAGATGGAGAATGGGATTT 58.763 38.462 0.00 0.00 0.00 2.17
94 95 6.240409 GGGAATTAGAGATGGAGAATGGGATT 60.240 42.308 0.00 0.00 0.00 3.01
95 96 5.252630 GGGAATTAGAGATGGAGAATGGGAT 59.747 44.000 0.00 0.00 0.00 3.85
96 97 4.599241 GGGAATTAGAGATGGAGAATGGGA 59.401 45.833 0.00 0.00 0.00 4.37
97 98 4.352001 TGGGAATTAGAGATGGAGAATGGG 59.648 45.833 0.00 0.00 0.00 4.00
98 99 5.312079 GTGGGAATTAGAGATGGAGAATGG 58.688 45.833 0.00 0.00 0.00 3.16
99 100 4.993584 CGTGGGAATTAGAGATGGAGAATG 59.006 45.833 0.00 0.00 0.00 2.67
100 101 4.901849 TCGTGGGAATTAGAGATGGAGAAT 59.098 41.667 0.00 0.00 0.00 2.40
101 102 4.286707 TCGTGGGAATTAGAGATGGAGAA 58.713 43.478 0.00 0.00 0.00 2.87
102 103 3.910989 TCGTGGGAATTAGAGATGGAGA 58.089 45.455 0.00 0.00 0.00 3.71
103 104 4.372656 GTTCGTGGGAATTAGAGATGGAG 58.627 47.826 0.00 0.00 34.05 3.86
104 105 3.134081 GGTTCGTGGGAATTAGAGATGGA 59.866 47.826 0.00 0.00 34.05 3.41
105 106 3.118408 TGGTTCGTGGGAATTAGAGATGG 60.118 47.826 0.00 0.00 34.05 3.51
106 107 4.137116 TGGTTCGTGGGAATTAGAGATG 57.863 45.455 0.00 0.00 34.05 2.90
107 108 4.837093 TTGGTTCGTGGGAATTAGAGAT 57.163 40.909 0.00 0.00 34.05 2.75
108 109 4.202377 TGTTTGGTTCGTGGGAATTAGAGA 60.202 41.667 0.00 0.00 34.05 3.10
109 110 4.069304 TGTTTGGTTCGTGGGAATTAGAG 58.931 43.478 0.00 0.00 34.05 2.43
110 111 4.088056 TGTTTGGTTCGTGGGAATTAGA 57.912 40.909 0.00 0.00 34.05 2.10
111 112 4.794169 CTTGTTTGGTTCGTGGGAATTAG 58.206 43.478 0.00 0.00 34.05 1.73
112 113 3.004944 GCTTGTTTGGTTCGTGGGAATTA 59.995 43.478 0.00 0.00 34.05 1.40
113 114 2.223947 GCTTGTTTGGTTCGTGGGAATT 60.224 45.455 0.00 0.00 34.05 2.17
114 115 1.339929 GCTTGTTTGGTTCGTGGGAAT 59.660 47.619 0.00 0.00 34.05 3.01
115 116 0.741915 GCTTGTTTGGTTCGTGGGAA 59.258 50.000 0.00 0.00 0.00 3.97
116 117 0.106918 AGCTTGTTTGGTTCGTGGGA 60.107 50.000 0.00 0.00 0.00 4.37
117 118 0.030638 CAGCTTGTTTGGTTCGTGGG 59.969 55.000 0.00 0.00 0.00 4.61
118 119 0.594796 GCAGCTTGTTTGGTTCGTGG 60.595 55.000 0.00 0.00 0.00 4.94
119 120 0.594796 GGCAGCTTGTTTGGTTCGTG 60.595 55.000 0.00 0.00 0.00 4.35
120 121 0.751643 AGGCAGCTTGTTTGGTTCGT 60.752 50.000 0.00 0.00 0.00 3.85
121 122 1.234821 TAGGCAGCTTGTTTGGTTCG 58.765 50.000 0.00 0.00 0.00 3.95
122 123 2.029918 CCTTAGGCAGCTTGTTTGGTTC 60.030 50.000 0.00 0.00 0.00 3.62
123 124 1.963515 CCTTAGGCAGCTTGTTTGGTT 59.036 47.619 0.00 0.00 0.00 3.67
124 125 1.133482 ACCTTAGGCAGCTTGTTTGGT 60.133 47.619 0.00 0.00 0.00 3.67
125 126 1.620822 ACCTTAGGCAGCTTGTTTGG 58.379 50.000 0.00 0.00 0.00 3.28
126 127 3.383761 CAAACCTTAGGCAGCTTGTTTG 58.616 45.455 0.00 5.04 37.36 2.93
127 128 2.365293 CCAAACCTTAGGCAGCTTGTTT 59.635 45.455 0.00 0.00 0.00 2.83
128 129 1.963515 CCAAACCTTAGGCAGCTTGTT 59.036 47.619 0.00 0.00 0.00 2.83
129 130 1.620822 CCAAACCTTAGGCAGCTTGT 58.379 50.000 0.00 0.00 0.00 3.16
142 143 1.367471 GTGGAAGCAAGGCCAAACC 59.633 57.895 5.01 0.00 35.63 3.27
143 144 1.115326 AGGTGGAAGCAAGGCCAAAC 61.115 55.000 5.01 0.00 35.63 2.93
144 145 0.398381 AAGGTGGAAGCAAGGCCAAA 60.398 50.000 5.01 0.00 35.63 3.28
145 146 0.827507 GAAGGTGGAAGCAAGGCCAA 60.828 55.000 5.01 0.00 35.63 4.52
146 147 1.228552 GAAGGTGGAAGCAAGGCCA 60.229 57.895 5.01 0.00 36.26 5.36
147 148 2.335712 CGAAGGTGGAAGCAAGGCC 61.336 63.158 0.00 0.00 36.26 5.19
148 149 2.982744 GCGAAGGTGGAAGCAAGGC 61.983 63.158 0.00 0.00 36.26 4.35
149 150 0.036388 TAGCGAAGGTGGAAGCAAGG 60.036 55.000 0.00 0.00 40.22 3.61
150 151 1.079503 GTAGCGAAGGTGGAAGCAAG 58.920 55.000 0.00 0.00 40.22 4.01
151 152 0.321298 GGTAGCGAAGGTGGAAGCAA 60.321 55.000 0.00 0.00 40.22 3.91
152 153 1.295423 GGTAGCGAAGGTGGAAGCA 59.705 57.895 0.00 0.00 40.22 3.91
153 154 1.449778 GGGTAGCGAAGGTGGAAGC 60.450 63.158 0.00 0.00 40.22 3.86
154 155 1.221021 GGGGTAGCGAAGGTGGAAG 59.779 63.158 0.00 0.00 40.22 3.46
155 156 2.295602 GGGGGTAGCGAAGGTGGAA 61.296 63.158 0.00 0.00 40.22 3.53
156 157 2.686106 GGGGGTAGCGAAGGTGGA 60.686 66.667 0.00 0.00 40.22 4.02
157 158 2.687566 AGGGGGTAGCGAAGGTGG 60.688 66.667 0.00 0.00 40.22 4.61
158 159 2.732619 GGAGGGGGTAGCGAAGGTG 61.733 68.421 0.00 0.00 40.22 4.00
159 160 2.365237 GGAGGGGGTAGCGAAGGT 60.365 66.667 0.00 0.00 44.89 3.50
160 161 3.537874 CGGAGGGGGTAGCGAAGG 61.538 72.222 0.00 0.00 0.00 3.46
161 162 2.758737 ACGGAGGGGGTAGCGAAG 60.759 66.667 0.00 0.00 0.00 3.79
162 163 3.072468 CACGGAGGGGGTAGCGAA 61.072 66.667 0.00 0.00 0.00 4.70
163 164 4.371417 ACACGGAGGGGGTAGCGA 62.371 66.667 0.00 0.00 0.00 4.93
164 165 3.834799 GACACGGAGGGGGTAGCG 61.835 72.222 0.00 0.00 0.00 4.26
165 166 2.682494 TGACACGGAGGGGGTAGC 60.682 66.667 0.00 0.00 0.00 3.58
166 167 1.305046 ACTGACACGGAGGGGGTAG 60.305 63.158 0.00 0.00 0.00 3.18
167 168 1.608336 CACTGACACGGAGGGGGTA 60.608 63.158 0.00 0.00 0.00 3.69
168 169 2.923035 CACTGACACGGAGGGGGT 60.923 66.667 0.00 0.00 0.00 4.95
169 170 2.923035 ACACTGACACGGAGGGGG 60.923 66.667 0.00 0.00 0.00 5.40
170 171 2.159819 CTGACACTGACACGGAGGGG 62.160 65.000 0.00 0.00 0.00 4.79
171 172 1.290324 CTGACACTGACACGGAGGG 59.710 63.158 0.00 0.00 0.00 4.30
172 173 0.039074 GACTGACACTGACACGGAGG 60.039 60.000 0.00 0.00 0.00 4.30
173 174 0.955178 AGACTGACACTGACACGGAG 59.045 55.000 0.00 0.00 0.00 4.63
174 175 0.952280 GAGACTGACACTGACACGGA 59.048 55.000 0.00 0.00 0.00 4.69
175 176 0.386100 CGAGACTGACACTGACACGG 60.386 60.000 0.00 0.00 0.00 4.94
176 177 0.308068 ACGAGACTGACACTGACACG 59.692 55.000 0.00 0.00 0.00 4.49
177 178 1.604755 AGACGAGACTGACACTGACAC 59.395 52.381 0.00 0.00 0.00 3.67
178 179 1.968704 AGACGAGACTGACACTGACA 58.031 50.000 0.00 0.00 0.00 3.58
179 180 3.046390 CAAAGACGAGACTGACACTGAC 58.954 50.000 0.00 0.00 0.00 3.51
180 181 2.034685 CCAAAGACGAGACTGACACTGA 59.965 50.000 0.00 0.00 0.00 3.41
181 182 2.398498 CCAAAGACGAGACTGACACTG 58.602 52.381 0.00 0.00 0.00 3.66
182 183 1.269831 GCCAAAGACGAGACTGACACT 60.270 52.381 0.00 0.00 0.00 3.55
207 208 1.952102 CTGCCCACATGGTGAATGGC 61.952 60.000 0.00 7.81 40.94 4.40
221 222 3.064324 GTCATGGTGGTGCTGCCC 61.064 66.667 0.00 0.00 36.04 5.36
236 237 3.764049 GCTGACGTCGCGGTTGTC 61.764 66.667 11.62 12.61 0.00 3.18
262 263 2.048503 CCAGACAACGACCGGGTC 60.049 66.667 17.38 17.38 0.00 4.46
263 264 2.841044 ACCAGACAACGACCGGGT 60.841 61.111 6.32 0.00 0.00 5.28
264 265 2.048503 GACCAGACAACGACCGGG 60.049 66.667 6.32 0.00 0.00 5.73
265 266 2.048503 GGACCAGACAACGACCGG 60.049 66.667 0.00 0.00 0.00 5.28
266 267 1.663702 GTGGACCAGACAACGACCG 60.664 63.158 0.00 0.00 0.00 4.79
267 268 0.878961 GTGTGGACCAGACAACGACC 60.879 60.000 16.63 0.00 0.00 4.79
268 269 1.213094 CGTGTGGACCAGACAACGAC 61.213 60.000 20.78 0.00 0.00 4.34
269 270 1.066752 CGTGTGGACCAGACAACGA 59.933 57.895 20.78 0.00 0.00 3.85
270 271 0.939577 CTCGTGTGGACCAGACAACG 60.940 60.000 20.78 15.42 0.00 4.10
271 272 0.600255 CCTCGTGTGGACCAGACAAC 60.600 60.000 20.78 4.77 0.00 3.32
272 273 0.757561 TCCTCGTGTGGACCAGACAA 60.758 55.000 20.78 2.11 0.00 3.18
273 274 1.152631 TCCTCGTGTGGACCAGACA 60.153 57.895 20.78 7.91 0.00 3.41
291 292 0.820891 GATGGATCATTGCCGCCAGT 60.821 55.000 0.00 0.00 33.26 4.00
293 294 1.893335 CGATGGATCATTGCCGCCA 60.893 57.895 0.00 0.00 34.45 5.69
318 319 2.031157 ACCAACCAGAAAGAAAATCGCG 60.031 45.455 0.00 0.00 0.00 5.87
322 323 2.545742 GCGCACCAACCAGAAAGAAAAT 60.546 45.455 0.30 0.00 0.00 1.82
324 325 0.383949 GCGCACCAACCAGAAAGAAA 59.616 50.000 0.30 0.00 0.00 2.52
332 333 1.528076 ATGACAAGCGCACCAACCA 60.528 52.632 11.47 0.00 0.00 3.67
338 339 1.127582 GAAGAGACATGACAAGCGCAC 59.872 52.381 11.47 0.00 0.00 5.34
344 345 7.094248 CCAAACCATAATGAAGAGACATGACAA 60.094 37.037 0.00 0.00 0.00 3.18
355 356 5.297776 CAGGCTAGTCCAAACCATAATGAAG 59.702 44.000 6.07 0.00 37.29 3.02
392 393 3.425359 CGACATCTCAACCATCTTTGTGC 60.425 47.826 0.00 0.00 0.00 4.57
425 426 1.002900 ACACGAAAACAACGCCTCATG 60.003 47.619 0.00 0.00 0.00 3.07
463 464 2.326550 GCGTCGTGTTGTTGGGTG 59.673 61.111 0.00 0.00 0.00 4.61
523 524 9.520515 AGTGTGGATGATGTTTCTTAGTAAATT 57.479 29.630 0.00 0.00 0.00 1.82
528 529 8.982723 AGTATAGTGTGGATGATGTTTCTTAGT 58.017 33.333 0.00 0.00 0.00 2.24
582 583 0.389166 GTGCGTTCTCTGCAGTAGCT 60.389 55.000 14.67 0.00 44.21 3.32
613 614 1.608918 AATTTGGGCGGGATGTGCA 60.609 52.632 0.00 0.00 0.00 4.57
725 726 4.144703 GGAGACCCGAACCGAGGC 62.145 72.222 0.00 0.00 0.00 4.70
757 758 4.043200 GAACCAAGCAGCCGCACC 62.043 66.667 0.00 0.00 42.27 5.01
801 802 3.767230 CTGTCACGGAAGCACGCG 61.767 66.667 3.53 3.53 37.37 6.01
812 813 2.217038 TGGTGGAGGAGCCTGTCAC 61.217 63.158 0.00 2.60 37.63 3.67
813 814 2.204034 TGGTGGAGGAGCCTGTCA 59.796 61.111 0.00 0.00 37.63 3.58
830 831 4.027437 GAGTGGAAGAAGGATACCTGAGT 58.973 47.826 0.00 0.00 32.13 3.41
885 886 1.064685 GTGGGGTTAGGGGTGATTGAG 60.065 57.143 0.00 0.00 0.00 3.02
886 887 0.996583 GTGGGGTTAGGGGTGATTGA 59.003 55.000 0.00 0.00 0.00 2.57
887 888 0.701731 TGTGGGGTTAGGGGTGATTG 59.298 55.000 0.00 0.00 0.00 2.67
905 906 3.844577 CTTGCTGAGGAGAAAATGGTG 57.155 47.619 0.00 0.00 0.00 4.17
920 921 1.111277 GGAAACACAACCACCTTGCT 58.889 50.000 0.00 0.00 32.41 3.91
938 939 1.665916 CTCACGCACTGACACAGGG 60.666 63.158 0.00 0.00 38.04 4.45
951 952 1.151668 CCCAACTGAAAGAGCTCACG 58.848 55.000 17.77 1.41 37.43 4.35
988 989 0.035317 TCTGCCATTGTTGCTCTCGT 59.965 50.000 0.00 0.00 0.00 4.18
989 990 0.725686 CTCTGCCATTGTTGCTCTCG 59.274 55.000 0.00 0.00 0.00 4.04
1023 1024 2.303022 GTCCTTCAACATGGAGACCAGA 59.697 50.000 0.00 0.00 36.75 3.86
1074 1075 0.180171 CCATGCCGTCCATCACCTTA 59.820 55.000 0.00 0.00 29.71 2.69
1182 1183 0.647410 CTTCGAGCCAAGCACGTATG 59.353 55.000 6.32 0.00 42.61 2.39
1183 1184 1.084370 GCTTCGAGCCAAGCACGTAT 61.084 55.000 6.32 0.00 46.93 3.06
1216 1217 5.235186 CGAAGACATTGTTAGCCTCATAAGG 59.765 44.000 0.00 0.00 46.44 2.69
1218 1219 5.972935 TCGAAGACATTGTTAGCCTCATAA 58.027 37.500 0.00 0.00 0.00 1.90
1358 1363 3.976793 ATGATGCATAACTTCTTGCCG 57.023 42.857 0.00 0.00 38.08 5.69
1370 1375 5.795972 TCAATGGTTTTCACAATGATGCAT 58.204 33.333 0.00 0.00 0.00 3.96
1472 1478 6.990349 TCTCGGAGTTGTTTAATATGGAATCC 59.010 38.462 4.69 0.00 0.00 3.01
1519 1525 3.248495 TCTGCTTCTTCTCTGCATCTG 57.752 47.619 0.00 0.00 36.07 2.90
1598 1610 2.038813 CCCAACCCACCCATTCCC 59.961 66.667 0.00 0.00 0.00 3.97
1695 1707 6.392354 TCTTAGTAACGTCAAAATCATCGGT 58.608 36.000 0.00 0.00 0.00 4.69
1803 1815 4.400251 CACATCATCCAGCACAATAAGGTT 59.600 41.667 0.00 0.00 0.00 3.50
1874 1887 2.429930 CTTCCCTTGGCACCGTGA 59.570 61.111 1.65 0.00 0.00 4.35
1901 1914 1.374885 TGCATTACGGGTGGTCGTG 60.375 57.895 0.00 0.00 43.70 4.35
1947 1962 1.266718 TCGCAGATTTTGGCTGTGAAC 59.733 47.619 0.00 0.00 46.41 3.18
1952 1967 1.135199 AGCATTCGCAGATTTTGGCTG 60.135 47.619 0.00 0.00 42.27 4.85
1965 1983 9.430838 CTTCAGAAAATCTTTATGTAGCATTCG 57.569 33.333 0.00 0.00 0.00 3.34
1969 1987 8.862325 TTCCTTCAGAAAATCTTTATGTAGCA 57.138 30.769 0.00 0.00 0.00 3.49
2031 2049 1.071128 GGCCAGGCTCATCAGCTAG 59.929 63.158 12.43 0.00 46.03 3.42
2038 2062 1.771255 CCTTACTTAGGCCAGGCTCAT 59.229 52.381 12.43 0.04 37.17 2.90
2055 2079 3.117512 ACCAGAATCTTGTCAACCACCTT 60.118 43.478 0.00 0.00 0.00 3.50
2077 2101 2.367202 GGAGAACCCCCGCATCTGA 61.367 63.158 0.00 0.00 0.00 3.27
2090 2114 2.162681 GCTTTGGCAGCTAAAGGAGAA 58.837 47.619 27.19 0.00 46.27 2.87
2194 2218 9.251440 TGAGCTTGAGTATAGGTAAAGTTTCTA 57.749 33.333 0.00 0.00 0.00 2.10
2250 2280 2.543641 AGCACAAAAAGCAAAGCACTC 58.456 42.857 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.