Multiple sequence alignment - TraesCS5B01G427000

Loading Multiple Alignment...

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 TraesCS5B01G427000 chr5B 100.000 2175 0 0 1 2175 602842938 602845112 0.000000e+00 4017
1 TraesCS5B01G427000 chr5B 100.000 738 0 0 2406 3143 602845343 602846080 0.000000e+00 1363
2 TraesCS5B01G427000 chr5B 87.395 119 15 0 1186 1304 33756809 33756691 1.520000e-28 137
3 TraesCS5B01G427000 chr5A 84.754 1948 116 69 332 2175 610230326 610232196 0.000000e+00 1784
4 TraesCS5B01G427000 chr5A 86.070 402 27 14 2748 3143 610232795 610233173 3.770000e-109 405
5 TraesCS5B01G427000 chr5A 89.139 267 6 7 2481 2736 610232331 610232585 8.460000e-81 311
6 TraesCS5B01G427000 chr5A 89.916 119 12 0 1186 1304 27938355 27938473 1.510000e-33 154
7 TraesCS5B01G427000 chr5A 87.156 109 12 2 1196 1303 684316029 684315922 4.260000e-24 122
8 TraesCS5B01G427000 chr5D 84.063 1324 98 56 147 1412 489187586 489188854 0.000000e+00 1171
9 TraesCS5B01G427000 chr5D 90.548 730 20 17 2406 3131 489189664 489190348 0.000000e+00 920
10 TraesCS5B01G427000 chr5D 89.295 766 29 14 1440 2174 489188836 489189579 0.000000e+00 911
11 TraesCS5B01G427000 chr5D 87.395 119 15 0 1186 1304 40023828 40023946 1.520000e-28 137
12 TraesCS5B01G427000 chr4D 94.382 89 5 0 1176 1264 501675269 501675181 1.520000e-28 137
13 TraesCS5B01G427000 chr4D 88.288 111 13 0 1193 1303 501968480 501968590 1.970000e-27 134
14 TraesCS5B01G427000 chr4B 94.382 89 5 0 1176 1264 645897512 645897424 1.520000e-28 137


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 TraesCS5B01G427000 chr5B 602842938 602846080 3142 False 2690.000000 4017 100.000000 1 3143 2 chr5B.!!$F1 3142
1 TraesCS5B01G427000 chr5A 610230326 610233173 2847 False 833.333333 1784 86.654333 332 3143 3 chr5A.!!$F2 2811
2 TraesCS5B01G427000 chr5D 489187586 489190348 2762 False 1000.666667 1171 87.968667 147 3131 3 chr5D.!!$F2 2984

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
137 138 0.036388 ATGGTTGCACTAGTCGGGTG 60.036 55.0 0.00 0.0 37.70 4.61 F
218 219 0.039074 ACACAGAGAGACGCTTTCGG 60.039 55.0 0.00 0.0 40.69 4.30 F
763 833 0.179189 GAAAGGAAATGGCGCACTCG 60.179 55.0 10.83 0.0 39.07 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1613 0.465097 CCATGATGGAGCTGTGGGAC 60.465 60.000 5.27 0.00 40.96 4.46 R
2065 2180 1.012234 GCGGTACTACGTACGTCGG 60.012 63.158 26.53 20.34 44.69 4.79 R
2716 2863 0.662374 AGTACGTGCGTTGAGGTTCG 60.662 55.000 1.66 0.00 0.00 3.95 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
19 20 2.969628 AGGAGGACTTGATGCTAACG 57.030 50.000 0.00 0.00 0.00 3.18
20 21 2.457598 AGGAGGACTTGATGCTAACGA 58.542 47.619 0.00 0.00 0.00 3.85
21 22 2.428890 AGGAGGACTTGATGCTAACGAG 59.571 50.000 0.00 0.00 0.00 4.18
31 32 2.571757 CTAACGAGCAGCACGGGA 59.428 61.111 16.89 2.88 34.93 5.14
32 33 1.141881 CTAACGAGCAGCACGGGAT 59.858 57.895 16.89 5.09 34.93 3.85
33 34 0.872021 CTAACGAGCAGCACGGGATC 60.872 60.000 16.89 0.00 34.93 3.36
34 35 2.292794 TAACGAGCAGCACGGGATCC 62.293 60.000 16.89 1.92 34.93 3.36
35 36 3.842923 CGAGCAGCACGGGATCCT 61.843 66.667 12.58 0.00 0.00 3.24
36 37 2.586792 GAGCAGCACGGGATCCTT 59.413 61.111 12.58 0.00 0.00 3.36
37 38 1.522580 GAGCAGCACGGGATCCTTC 60.523 63.158 12.58 0.00 0.00 3.46
38 39 1.965754 GAGCAGCACGGGATCCTTCT 61.966 60.000 12.58 0.83 0.00 2.85
39 40 1.078143 GCAGCACGGGATCCTTCTT 60.078 57.895 12.58 0.00 0.00 2.52
40 41 0.678048 GCAGCACGGGATCCTTCTTT 60.678 55.000 12.58 0.00 0.00 2.52
41 42 1.826385 CAGCACGGGATCCTTCTTTT 58.174 50.000 12.58 0.00 0.00 2.27
42 43 2.162681 CAGCACGGGATCCTTCTTTTT 58.837 47.619 12.58 0.00 0.00 1.94
43 44 3.343617 CAGCACGGGATCCTTCTTTTTA 58.656 45.455 12.58 0.00 0.00 1.52
44 45 3.947834 CAGCACGGGATCCTTCTTTTTAT 59.052 43.478 12.58 0.00 0.00 1.40
45 46 3.947834 AGCACGGGATCCTTCTTTTTATG 59.052 43.478 12.58 0.00 0.00 1.90
46 47 3.945285 GCACGGGATCCTTCTTTTTATGA 59.055 43.478 12.58 0.00 0.00 2.15
47 48 4.035675 GCACGGGATCCTTCTTTTTATGAG 59.964 45.833 12.58 0.00 0.00 2.90
48 49 5.186198 CACGGGATCCTTCTTTTTATGAGT 58.814 41.667 12.58 0.00 0.00 3.41
49 50 5.648092 CACGGGATCCTTCTTTTTATGAGTT 59.352 40.000 12.58 0.00 0.00 3.01
50 51 5.880887 ACGGGATCCTTCTTTTTATGAGTTC 59.119 40.000 12.58 0.00 0.00 3.01
51 52 5.297029 CGGGATCCTTCTTTTTATGAGTTCC 59.703 44.000 12.58 0.00 0.00 3.62
52 53 5.297029 GGGATCCTTCTTTTTATGAGTTCCG 59.703 44.000 12.58 0.00 0.00 4.30
53 54 5.880887 GGATCCTTCTTTTTATGAGTTCCGT 59.119 40.000 3.84 0.00 0.00 4.69
54 55 7.046033 GGATCCTTCTTTTTATGAGTTCCGTA 58.954 38.462 3.84 0.00 0.00 4.02
55 56 7.011202 GGATCCTTCTTTTTATGAGTTCCGTAC 59.989 40.741 3.84 0.00 0.00 3.67
56 57 6.168389 TCCTTCTTTTTATGAGTTCCGTACC 58.832 40.000 0.00 0.00 0.00 3.34
57 58 5.063060 CCTTCTTTTTATGAGTTCCGTACCG 59.937 44.000 0.00 0.00 0.00 4.02
58 59 5.389859 TCTTTTTATGAGTTCCGTACCGA 57.610 39.130 0.00 0.00 0.00 4.69
59 60 5.782047 TCTTTTTATGAGTTCCGTACCGAA 58.218 37.500 0.00 0.00 0.00 4.30
60 61 6.222389 TCTTTTTATGAGTTCCGTACCGAAA 58.778 36.000 0.00 0.00 0.00 3.46
61 62 6.366877 TCTTTTTATGAGTTCCGTACCGAAAG 59.633 38.462 0.00 0.00 0.00 2.62
62 63 5.389859 TTTATGAGTTCCGTACCGAAAGA 57.610 39.130 0.00 0.00 0.00 2.52
63 64 5.587388 TTATGAGTTCCGTACCGAAAGAT 57.413 39.130 0.00 0.00 0.00 2.40
64 65 3.226346 TGAGTTCCGTACCGAAAGATG 57.774 47.619 0.00 0.00 0.00 2.90
65 66 2.821378 TGAGTTCCGTACCGAAAGATGA 59.179 45.455 0.00 0.00 0.00 2.92
66 67 3.119602 TGAGTTCCGTACCGAAAGATGAG 60.120 47.826 0.00 0.00 0.00 2.90
67 68 2.824341 AGTTCCGTACCGAAAGATGAGT 59.176 45.455 0.00 0.00 0.00 3.41
68 69 2.921754 GTTCCGTACCGAAAGATGAGTG 59.078 50.000 0.00 0.00 0.00 3.51
69 70 1.475280 TCCGTACCGAAAGATGAGTGG 59.525 52.381 0.00 0.00 0.00 4.00
70 71 1.475280 CCGTACCGAAAGATGAGTGGA 59.525 52.381 0.00 0.00 0.00 4.02
71 72 2.479730 CCGTACCGAAAGATGAGTGGAG 60.480 54.545 0.00 0.00 0.00 3.86
72 73 2.163815 CGTACCGAAAGATGAGTGGAGT 59.836 50.000 0.00 0.00 0.00 3.85
73 74 3.376234 CGTACCGAAAGATGAGTGGAGTA 59.624 47.826 0.00 0.00 0.00 2.59
74 75 4.142534 CGTACCGAAAGATGAGTGGAGTAA 60.143 45.833 0.00 0.00 0.00 2.24
75 76 4.884668 ACCGAAAGATGAGTGGAGTAAA 57.115 40.909 0.00 0.00 0.00 2.01
76 77 4.566987 ACCGAAAGATGAGTGGAGTAAAC 58.433 43.478 0.00 0.00 0.00 2.01
77 78 3.933332 CCGAAAGATGAGTGGAGTAAACC 59.067 47.826 0.00 0.00 0.00 3.27
78 79 3.933332 CGAAAGATGAGTGGAGTAAACCC 59.067 47.826 0.00 0.00 0.00 4.11
79 80 4.262617 GAAAGATGAGTGGAGTAAACCCC 58.737 47.826 0.00 0.00 0.00 4.95
80 81 2.915869 AGATGAGTGGAGTAAACCCCA 58.084 47.619 0.00 0.00 0.00 4.96
81 82 3.256704 AGATGAGTGGAGTAAACCCCAA 58.743 45.455 0.00 0.00 33.69 4.12
82 83 3.852578 AGATGAGTGGAGTAAACCCCAAT 59.147 43.478 0.00 0.00 33.69 3.16
83 84 3.713826 TGAGTGGAGTAAACCCCAATC 57.286 47.619 4.37 4.37 44.95 2.67
84 85 2.307686 TGAGTGGAGTAAACCCCAATCC 59.692 50.000 8.37 0.00 44.33 3.01
85 86 1.639108 AGTGGAGTAAACCCCAATCCC 59.361 52.381 0.00 0.00 33.69 3.85
86 87 1.639108 GTGGAGTAAACCCCAATCCCT 59.361 52.381 0.00 0.00 33.69 4.20
87 88 1.920351 TGGAGTAAACCCCAATCCCTC 59.080 52.381 0.00 0.00 0.00 4.30
88 89 1.214673 GGAGTAAACCCCAATCCCTCC 59.785 57.143 0.00 0.00 0.00 4.30
89 90 2.206223 GAGTAAACCCCAATCCCTCCT 58.794 52.381 0.00 0.00 0.00 3.69
90 91 2.581246 GAGTAAACCCCAATCCCTCCTT 59.419 50.000 0.00 0.00 0.00 3.36
91 92 3.001086 AGTAAACCCCAATCCCTCCTTT 58.999 45.455 0.00 0.00 0.00 3.11
92 93 3.404769 AGTAAACCCCAATCCCTCCTTTT 59.595 43.478 0.00 0.00 0.00 2.27
93 94 2.325661 AACCCCAATCCCTCCTTTTG 57.674 50.000 0.00 0.00 0.00 2.44
94 95 1.466858 ACCCCAATCCCTCCTTTTGA 58.533 50.000 0.00 0.00 0.00 2.69
95 96 1.792651 ACCCCAATCCCTCCTTTTGAA 59.207 47.619 0.00 0.00 0.00 2.69
96 97 2.386811 ACCCCAATCCCTCCTTTTGAAT 59.613 45.455 0.00 0.00 0.00 2.57
97 98 3.181396 ACCCCAATCCCTCCTTTTGAATT 60.181 43.478 0.00 0.00 0.00 2.17
98 99 3.452264 CCCCAATCCCTCCTTTTGAATTC 59.548 47.826 0.00 0.00 0.00 2.17
99 100 3.452264 CCCAATCCCTCCTTTTGAATTCC 59.548 47.826 2.27 0.00 0.00 3.01
100 101 4.356436 CCAATCCCTCCTTTTGAATTCCT 58.644 43.478 2.27 0.00 0.00 3.36
101 102 4.161001 CCAATCCCTCCTTTTGAATTCCTG 59.839 45.833 2.27 0.00 0.00 3.86
102 103 2.807676 TCCCTCCTTTTGAATTCCTGC 58.192 47.619 2.27 0.00 0.00 4.85
103 104 2.109834 TCCCTCCTTTTGAATTCCTGCA 59.890 45.455 2.27 0.00 0.00 4.41
104 105 3.102204 CCCTCCTTTTGAATTCCTGCAT 58.898 45.455 2.27 0.00 0.00 3.96
105 106 3.516700 CCCTCCTTTTGAATTCCTGCATT 59.483 43.478 2.27 0.00 0.00 3.56
106 107 4.382362 CCCTCCTTTTGAATTCCTGCATTC 60.382 45.833 2.27 0.00 34.23 2.67
107 108 4.382362 CCTCCTTTTGAATTCCTGCATTCC 60.382 45.833 2.27 0.00 32.86 3.01
108 109 4.158786 TCCTTTTGAATTCCTGCATTCCA 58.841 39.130 2.27 0.00 32.86 3.53
109 110 4.221262 TCCTTTTGAATTCCTGCATTCCAG 59.779 41.667 2.27 0.00 41.41 3.86
110 111 4.020839 CCTTTTGAATTCCTGCATTCCAGT 60.021 41.667 2.27 0.00 40.06 4.00
111 112 5.511888 CCTTTTGAATTCCTGCATTCCAGTT 60.512 40.000 2.27 0.00 40.06 3.16
112 113 4.789012 TTGAATTCCTGCATTCCAGTTC 57.211 40.909 2.27 0.00 40.06 3.01
113 114 2.749076 TGAATTCCTGCATTCCAGTTCG 59.251 45.455 2.27 0.00 40.06 3.95
114 115 2.787473 ATTCCTGCATTCCAGTTCGA 57.213 45.000 0.00 0.00 40.06 3.71
115 116 2.099141 TTCCTGCATTCCAGTTCGAG 57.901 50.000 0.00 0.00 40.06 4.04
116 117 0.391661 TCCTGCATTCCAGTTCGAGC 60.392 55.000 0.00 0.00 40.06 5.03
117 118 0.392193 CCTGCATTCCAGTTCGAGCT 60.392 55.000 0.00 0.00 40.06 4.09
118 119 1.134699 CCTGCATTCCAGTTCGAGCTA 60.135 52.381 0.00 0.00 40.06 3.32
119 120 2.484417 CCTGCATTCCAGTTCGAGCTAT 60.484 50.000 0.00 0.00 40.06 2.97
120 121 2.543012 CTGCATTCCAGTTCGAGCTATG 59.457 50.000 0.00 3.82 36.79 2.23
121 122 1.869767 GCATTCCAGTTCGAGCTATGG 59.130 52.381 0.00 0.91 0.00 2.74
122 123 2.743183 GCATTCCAGTTCGAGCTATGGT 60.743 50.000 0.00 0.00 34.32 3.55
123 124 3.535561 CATTCCAGTTCGAGCTATGGTT 58.464 45.455 0.00 0.00 34.32 3.67
124 125 2.672961 TCCAGTTCGAGCTATGGTTG 57.327 50.000 0.00 0.00 34.32 3.77
125 126 1.009829 CCAGTTCGAGCTATGGTTGC 58.990 55.000 0.00 0.00 0.00 4.17
126 127 1.675714 CCAGTTCGAGCTATGGTTGCA 60.676 52.381 0.00 0.00 0.00 4.08
127 128 1.394917 CAGTTCGAGCTATGGTTGCAC 59.605 52.381 0.00 0.00 0.00 4.57
128 129 1.276421 AGTTCGAGCTATGGTTGCACT 59.724 47.619 0.00 0.00 0.00 4.40
129 130 2.496070 AGTTCGAGCTATGGTTGCACTA 59.504 45.455 0.00 0.00 0.00 2.74
130 131 2.860735 GTTCGAGCTATGGTTGCACTAG 59.139 50.000 0.00 0.00 0.00 2.57
131 132 2.100197 TCGAGCTATGGTTGCACTAGT 58.900 47.619 0.00 0.00 0.00 2.57
132 133 2.099263 TCGAGCTATGGTTGCACTAGTC 59.901 50.000 0.00 0.00 0.00 2.59
133 134 2.464865 GAGCTATGGTTGCACTAGTCG 58.535 52.381 0.00 0.00 0.00 4.18
134 135 1.137086 AGCTATGGTTGCACTAGTCGG 59.863 52.381 0.00 0.00 0.00 4.79
135 136 1.806623 GCTATGGTTGCACTAGTCGGG 60.807 57.143 0.00 0.00 0.00 5.14
136 137 1.480954 CTATGGTTGCACTAGTCGGGT 59.519 52.381 0.00 0.00 0.00 5.28
137 138 0.036388 ATGGTTGCACTAGTCGGGTG 60.036 55.000 0.00 0.00 37.70 4.61
138 139 1.375523 GGTTGCACTAGTCGGGTGG 60.376 63.158 0.00 0.00 35.47 4.61
139 140 1.375523 GTTGCACTAGTCGGGTGGG 60.376 63.158 0.00 0.00 35.47 4.61
140 141 3.248446 TTGCACTAGTCGGGTGGGC 62.248 63.158 0.00 0.00 35.47 5.36
141 142 3.702048 GCACTAGTCGGGTGGGCA 61.702 66.667 0.00 0.00 35.47 5.36
142 143 2.579201 CACTAGTCGGGTGGGCAG 59.421 66.667 0.00 0.00 0.00 4.85
143 144 2.683933 ACTAGTCGGGTGGGCAGG 60.684 66.667 0.00 0.00 0.00 4.85
144 145 4.162690 CTAGTCGGGTGGGCAGGC 62.163 72.222 0.00 0.00 0.00 4.85
170 171 4.439057 GGCTGTCGACAACTCCAAATATA 58.561 43.478 20.49 0.00 0.00 0.86
180 181 5.123344 ACAACTCCAAATATAGCACGAAACC 59.877 40.000 0.00 0.00 0.00 3.27
184 185 5.845103 TCCAAATATAGCACGAAACCGATA 58.155 37.500 0.00 0.00 0.00 2.92
209 210 0.764369 AAGGGTGCCACACAGAGAGA 60.764 55.000 0.00 0.00 35.86 3.10
217 218 1.056103 CACACAGAGAGACGCTTTCG 58.944 55.000 0.00 0.00 42.43 3.46
218 219 0.039074 ACACAGAGAGACGCTTTCGG 60.039 55.000 0.00 0.00 40.69 4.30
221 222 1.546476 ACAGAGAGACGCTTTCGGATT 59.454 47.619 5.08 0.00 40.69 3.01
222 223 1.923204 CAGAGAGACGCTTTCGGATTG 59.077 52.381 0.00 0.00 40.69 2.67
223 224 1.819288 AGAGAGACGCTTTCGGATTGA 59.181 47.619 0.00 0.00 40.69 2.57
224 225 2.231478 AGAGAGACGCTTTCGGATTGAA 59.769 45.455 0.00 0.00 40.69 2.69
226 227 2.028930 AGAGACGCTTTCGGATTGAACT 60.029 45.455 0.00 0.00 40.69 3.01
228 229 2.066262 GACGCTTTCGGATTGAACTGA 58.934 47.619 0.00 0.00 40.69 3.41
230 231 1.201812 CGCTTTCGGATTGAACTGACG 60.202 52.381 0.00 0.00 35.97 4.35
231 232 2.066262 GCTTTCGGATTGAACTGACGA 58.934 47.619 0.00 0.00 35.97 4.20
232 233 2.159827 GCTTTCGGATTGAACTGACGAC 60.160 50.000 0.00 0.00 35.97 4.34
233 234 1.693467 TTCGGATTGAACTGACGACG 58.307 50.000 0.00 0.00 32.85 5.12
234 235 0.876399 TCGGATTGAACTGACGACGA 59.124 50.000 0.00 0.00 0.00 4.20
235 236 1.267533 TCGGATTGAACTGACGACGAA 59.732 47.619 0.00 0.00 0.00 3.85
240 243 1.373873 GAACTGACGACGAACCCCC 60.374 63.158 0.00 0.00 0.00 5.40
253 256 4.748798 CCCCCTCCTGGCTCCTGT 62.749 72.222 0.00 0.00 0.00 4.00
254 257 3.406200 CCCCTCCTGGCTCCTGTG 61.406 72.222 0.00 0.00 0.00 3.66
255 258 4.106925 CCCTCCTGGCTCCTGTGC 62.107 72.222 0.00 0.00 0.00 4.57
304 321 0.969894 GCTGGACTACACACCTCACT 59.030 55.000 0.00 0.00 0.00 3.41
305 322 1.067495 GCTGGACTACACACCTCACTC 60.067 57.143 0.00 0.00 0.00 3.51
306 323 1.546476 CTGGACTACACACCTCACTCC 59.454 57.143 0.00 0.00 0.00 3.85
309 326 1.215647 CTACACACCTCACTCCGCC 59.784 63.158 0.00 0.00 0.00 6.13
310 327 1.532078 TACACACCTCACTCCGCCA 60.532 57.895 0.00 0.00 0.00 5.69
311 328 1.116536 TACACACCTCACTCCGCCAA 61.117 55.000 0.00 0.00 0.00 4.52
312 329 1.961277 CACACCTCACTCCGCCAAC 60.961 63.158 0.00 0.00 0.00 3.77
315 332 2.429930 CCTCACTCCGCCAACCAA 59.570 61.111 0.00 0.00 0.00 3.67
316 333 1.228124 CCTCACTCCGCCAACCAAA 60.228 57.895 0.00 0.00 0.00 3.28
317 334 0.821711 CCTCACTCCGCCAACCAAAA 60.822 55.000 0.00 0.00 0.00 2.44
318 335 1.028905 CTCACTCCGCCAACCAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
353 370 2.024022 GCGTGCTGCGTGAAACAA 59.976 55.556 0.00 0.00 43.66 2.83
354 371 1.585002 GCGTGCTGCGTGAAACAAA 60.585 52.632 0.00 0.00 43.66 2.83
355 372 1.797388 GCGTGCTGCGTGAAACAAAC 61.797 55.000 0.00 0.00 43.66 2.93
356 373 1.520133 CGTGCTGCGTGAAACAAACG 61.520 55.000 0.00 0.00 43.81 3.60
423 441 4.528039 CCATGGCCGCCCAATCCT 62.528 66.667 7.03 0.00 46.14 3.24
425 443 1.075482 CATGGCCGCCCAATCCTAT 59.925 57.895 7.03 0.00 46.14 2.57
495 513 3.807538 TCGCGACGGACTAGCCAC 61.808 66.667 3.71 0.00 35.94 5.01
496 514 4.849329 CGCGACGGACTAGCCACC 62.849 72.222 0.00 0.00 35.94 4.61
497 515 3.755628 GCGACGGACTAGCCACCA 61.756 66.667 0.00 0.00 35.94 4.17
498 516 2.181021 CGACGGACTAGCCACCAC 59.819 66.667 0.00 0.00 35.94 4.16
499 517 2.341101 CGACGGACTAGCCACCACT 61.341 63.158 0.00 0.00 35.94 4.00
500 518 1.215647 GACGGACTAGCCACCACTG 59.784 63.158 0.00 0.00 35.94 3.66
501 519 2.125512 CGGACTAGCCACCACTGC 60.126 66.667 0.00 0.00 35.94 4.40
502 520 2.125512 GGACTAGCCACCACTGCG 60.126 66.667 0.00 0.00 36.34 5.18
503 521 2.815647 GACTAGCCACCACTGCGC 60.816 66.667 0.00 0.00 0.00 6.09
504 522 3.302347 GACTAGCCACCACTGCGCT 62.302 63.158 9.73 0.00 36.63 5.92
505 523 2.816958 CTAGCCACCACTGCGCTG 60.817 66.667 13.23 13.23 34.03 5.18
506 524 4.393155 TAGCCACCACTGCGCTGG 62.393 66.667 18.98 16.34 37.33 4.85
542 560 1.300388 CCAACCAGTTGCTTGCTGC 60.300 57.895 4.96 0.00 39.16 5.25
543 561 1.300388 CAACCAGTTGCTTGCTGCC 60.300 57.895 0.00 0.00 42.00 4.85
544 562 1.456331 AACCAGTTGCTTGCTGCCT 60.456 52.632 0.00 0.00 42.00 4.75
545 563 1.741327 AACCAGTTGCTTGCTGCCTG 61.741 55.000 0.00 0.00 42.00 4.85
565 583 1.614583 GGCCTCCTTTTCCAAGTCCTC 60.615 57.143 0.00 0.00 0.00 3.71
588 606 0.531974 TTTCTCCCACTCGTGTGTGC 60.532 55.000 15.79 0.00 42.34 4.57
599 617 1.001597 TCGTGTGTGCGTGTGTGTATA 60.002 47.619 0.00 0.00 0.00 1.47
600 618 1.123576 CGTGTGTGCGTGTGTGTATAC 59.876 52.381 0.00 0.00 0.00 1.47
601 619 2.400399 GTGTGTGCGTGTGTGTATACT 58.600 47.619 4.17 0.00 0.00 2.12
602 620 3.567530 GTGTGTGCGTGTGTGTATACTA 58.432 45.455 4.17 0.00 0.00 1.82
603 621 3.606777 GTGTGTGCGTGTGTGTATACTAG 59.393 47.826 4.17 0.00 0.00 2.57
634 652 4.181578 CCGTAAACAGAATCCCACTACAG 58.818 47.826 0.00 0.00 0.00 2.74
635 653 4.322499 CCGTAAACAGAATCCCACTACAGT 60.322 45.833 0.00 0.00 0.00 3.55
638 656 6.869913 CGTAAACAGAATCCCACTACAGTTTA 59.130 38.462 0.00 0.00 31.33 2.01
653 684 7.601130 CACTACAGTTTAGCATTTGTGGTAGTA 59.399 37.037 0.00 0.00 37.42 1.82
695 739 1.018910 GAGAGTCGTAGGGCTGAGAC 58.981 60.000 0.00 0.00 0.00 3.36
696 740 0.394625 AGAGTCGTAGGGCTGAGACC 60.395 60.000 0.00 0.00 34.41 3.85
697 741 1.716826 GAGTCGTAGGGCTGAGACCG 61.717 65.000 0.00 0.00 34.63 4.79
698 742 1.748122 GTCGTAGGGCTGAGACCGA 60.748 63.158 0.00 0.00 34.63 4.69
700 744 1.451567 CGTAGGGCTGAGACCGAGA 60.452 63.158 0.00 0.00 34.63 4.04
701 745 1.440938 CGTAGGGCTGAGACCGAGAG 61.441 65.000 0.00 0.00 34.63 3.20
702 746 1.454111 TAGGGCTGAGACCGAGAGC 60.454 63.158 0.00 0.00 34.63 4.09
703 747 2.211468 TAGGGCTGAGACCGAGAGCA 62.211 60.000 0.00 0.00 34.63 4.26
709 769 3.005897 GGCTGAGACCGAGAGCATATAAA 59.994 47.826 0.00 0.00 34.20 1.40
714 774 7.547370 GCTGAGACCGAGAGCATATAAATTATT 59.453 37.037 0.00 0.00 32.70 1.40
731 794 0.472898 ATTAGTAGCGGAAAGGGGGC 59.527 55.000 0.00 0.00 0.00 5.80
740 803 1.000843 CGGAAAGGGGGCAAAAGAAAG 59.999 52.381 0.00 0.00 0.00 2.62
743 808 3.135712 GGAAAGGGGGCAAAAGAAAGAAA 59.864 43.478 0.00 0.00 0.00 2.52
763 833 0.179189 GAAAGGAAATGGCGCACTCG 60.179 55.000 10.83 0.00 39.07 4.18
775 845 4.320456 CACTCGGCCAGCCACAGT 62.320 66.667 9.78 6.96 35.37 3.55
776 846 2.603473 ACTCGGCCAGCCACAGTA 60.603 61.111 9.78 0.00 35.37 2.74
777 847 2.185350 CTCGGCCAGCCACAGTAG 59.815 66.667 9.78 0.00 35.37 2.57
778 848 2.603473 TCGGCCAGCCACAGTAGT 60.603 61.111 9.78 0.00 35.37 2.73
782 852 0.391263 GGCCAGCCACAGTAGTACAC 60.391 60.000 3.12 0.00 35.81 2.90
788 858 4.011023 CAGCCACAGTAGTACACTAGAGT 58.989 47.826 2.52 0.00 34.98 3.24
799 872 1.076192 ACTAGAGTGGTAGCCCCCG 60.076 63.158 0.00 0.00 0.00 5.73
806 879 2.767073 GGTAGCCCCCGGTTAGCT 60.767 66.667 13.79 13.79 40.66 3.32
807 880 1.458209 GGTAGCCCCCGGTTAGCTA 60.458 63.158 11.98 11.98 38.06 3.32
808 881 1.050421 GGTAGCCCCCGGTTAGCTAA 61.050 60.000 16.28 0.86 40.59 3.09
810 883 0.832626 TAGCCCCCGGTTAGCTAAAC 59.167 55.000 11.73 11.73 36.21 2.01
811 884 1.816679 GCCCCCGGTTAGCTAAACG 60.817 63.158 32.15 32.15 45.35 3.60
829 908 1.081376 GAAACTGCTGCTGCTGCTG 60.081 57.895 27.75 27.75 41.07 4.41
895 975 4.033776 CGCCTTTCTCCTGGGCCA 62.034 66.667 5.85 5.85 42.58 5.36
906 986 1.360852 TCCTGGGCCAAACCATACATT 59.639 47.619 8.04 0.00 40.36 2.71
952 1032 3.684628 TCGCTTCCCCCTCCCTCT 61.685 66.667 0.00 0.00 0.00 3.69
992 1083 2.882927 TCATATCCTTTCCCACGACG 57.117 50.000 0.00 0.00 0.00 5.12
993 1084 2.104967 TCATATCCTTTCCCACGACGT 58.895 47.619 0.00 0.00 0.00 4.34
1512 1613 2.807895 ACGACGTTCCCAATCGCG 60.808 61.111 0.00 0.00 39.47 5.87
1566 1667 4.485834 CAGTACTACGCGCCGCCA 62.486 66.667 5.73 0.00 0.00 5.69
1615 1716 4.735132 GCGACCTGTACAGCGGCA 62.735 66.667 17.86 0.00 0.00 5.69
1616 1717 2.507102 CGACCTGTACAGCGGCAG 60.507 66.667 17.86 5.96 0.00 4.85
1617 1718 2.815647 GACCTGTACAGCGGCAGC 60.816 66.667 17.86 0.00 45.58 5.25
1887 1991 0.606604 ACTACAACAACGGCGAGGAT 59.393 50.000 16.62 0.00 0.00 3.24
2039 2154 2.224066 CCCTACAACTCCTATTCGGCTG 60.224 54.545 0.00 0.00 0.00 4.85
2065 2180 3.793888 CCCTACCGCCCTTCACCC 61.794 72.222 0.00 0.00 0.00 4.61
2435 2571 1.917273 TAGCTTCGTTTTCCGGATCG 58.083 50.000 4.15 11.41 37.11 3.69
2436 2572 0.245539 AGCTTCGTTTTCCGGATCGA 59.754 50.000 18.27 18.27 37.11 3.59
2437 2573 0.645868 GCTTCGTTTTCCGGATCGAG 59.354 55.000 20.16 16.44 37.11 4.04
2438 2574 1.734707 GCTTCGTTTTCCGGATCGAGA 60.735 52.381 20.16 10.38 37.11 4.04
2439 2575 2.602878 CTTCGTTTTCCGGATCGAGAA 58.397 47.619 20.16 15.67 37.11 2.87
2440 2576 2.953466 TCGTTTTCCGGATCGAGAAT 57.047 45.000 18.27 0.00 37.11 2.40
2441 2577 2.536365 TCGTTTTCCGGATCGAGAATG 58.464 47.619 18.27 9.28 37.11 2.67
2449 2585 2.146342 CGGATCGAGAATGGAAATGGG 58.854 52.381 0.00 0.00 0.00 4.00
2672 2816 1.147153 CGATTGAAGGCCCTCCTCC 59.853 63.158 0.00 0.00 43.40 4.30
2673 2817 1.341156 CGATTGAAGGCCCTCCTCCT 61.341 60.000 0.00 0.00 43.40 3.69
2674 2818 0.922626 GATTGAAGGCCCTCCTCCTT 59.077 55.000 0.00 0.00 45.98 3.36
2716 2863 5.354792 CCGATCCAGCTAGTAATAGTAGTCC 59.645 48.000 4.28 0.00 0.00 3.85
2819 3167 0.248377 GTAGTCCATCGGGTCGAACG 60.248 60.000 4.54 4.54 39.99 3.95
2908 3257 2.667199 GGTGGGGTGGAACGAACG 60.667 66.667 0.00 0.00 38.12 3.95
3004 3353 3.879682 GCATCGCCATCGCAGCAA 61.880 61.111 0.00 0.00 36.01 3.91
3038 3393 1.517832 GACGGACTGGACTGGATGG 59.482 63.158 0.00 0.00 0.00 3.51
3039 3394 0.970937 GACGGACTGGACTGGATGGA 60.971 60.000 0.00 0.00 0.00 3.41
3040 3395 0.325671 ACGGACTGGACTGGATGGAT 60.326 55.000 0.00 0.00 0.00 3.41
3041 3396 0.105593 CGGACTGGACTGGATGGATG 59.894 60.000 0.00 0.00 0.00 3.51
3117 3479 1.257055 GGTCCAGAGAGCAGAGCAGT 61.257 60.000 0.00 0.00 40.37 4.40
3131 3493 0.886043 AGCAGTGCAGTTCATTCGCA 60.886 50.000 19.20 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.428890 CTCGTTAGCATCAAGTCCTCCT 59.571 50.000 0.00 0.00 0.00 3.69
14 15 0.872021 GATCCCGTGCTGCTCGTTAG 60.872 60.000 20.67 10.55 0.00 2.34
15 16 1.141019 GATCCCGTGCTGCTCGTTA 59.859 57.895 20.67 10.05 0.00 3.18
16 17 2.125512 GATCCCGTGCTGCTCGTT 60.126 61.111 20.67 7.16 0.00 3.85
17 18 4.148825 GGATCCCGTGCTGCTCGT 62.149 66.667 20.67 4.54 0.00 4.18
18 19 3.376935 AAGGATCCCGTGCTGCTCG 62.377 63.158 16.35 16.35 0.00 5.03
19 20 1.522580 GAAGGATCCCGTGCTGCTC 60.523 63.158 8.55 0.00 0.00 4.26
20 21 1.557269 AAGAAGGATCCCGTGCTGCT 61.557 55.000 8.55 0.00 35.24 4.24
21 22 0.678048 AAAGAAGGATCCCGTGCTGC 60.678 55.000 8.55 0.00 0.00 5.25
22 23 1.826385 AAAAGAAGGATCCCGTGCTG 58.174 50.000 8.55 0.00 0.00 4.41
23 24 2.586648 AAAAAGAAGGATCCCGTGCT 57.413 45.000 8.55 0.00 0.00 4.40
24 25 3.945285 TCATAAAAAGAAGGATCCCGTGC 59.055 43.478 8.55 0.00 0.00 5.34
25 26 5.186198 ACTCATAAAAAGAAGGATCCCGTG 58.814 41.667 8.55 0.00 0.00 4.94
26 27 5.437191 ACTCATAAAAAGAAGGATCCCGT 57.563 39.130 8.55 0.00 0.00 5.28
27 28 5.297029 GGAACTCATAAAAAGAAGGATCCCG 59.703 44.000 8.55 0.00 0.00 5.14
28 29 5.297029 CGGAACTCATAAAAAGAAGGATCCC 59.703 44.000 8.55 0.00 0.00 3.85
29 30 5.880887 ACGGAACTCATAAAAAGAAGGATCC 59.119 40.000 2.48 2.48 0.00 3.36
30 31 6.986904 ACGGAACTCATAAAAAGAAGGATC 57.013 37.500 0.00 0.00 0.00 3.36
31 32 6.822170 GGTACGGAACTCATAAAAAGAAGGAT 59.178 38.462 0.00 0.00 0.00 3.24
32 33 6.168389 GGTACGGAACTCATAAAAAGAAGGA 58.832 40.000 0.00 0.00 0.00 3.36
33 34 6.418585 GGTACGGAACTCATAAAAAGAAGG 57.581 41.667 0.00 0.00 0.00 3.46
52 53 3.870633 ACTCCACTCATCTTTCGGTAC 57.129 47.619 0.00 0.00 0.00 3.34
53 54 5.337009 GGTTTACTCCACTCATCTTTCGGTA 60.337 44.000 0.00 0.00 0.00 4.02
54 55 4.562963 GGTTTACTCCACTCATCTTTCGGT 60.563 45.833 0.00 0.00 0.00 4.69
55 56 3.933332 GGTTTACTCCACTCATCTTTCGG 59.067 47.826 0.00 0.00 0.00 4.30
56 57 3.933332 GGGTTTACTCCACTCATCTTTCG 59.067 47.826 0.00 0.00 0.00 3.46
57 58 4.262617 GGGGTTTACTCCACTCATCTTTC 58.737 47.826 0.00 0.00 0.00 2.62
58 59 3.655777 TGGGGTTTACTCCACTCATCTTT 59.344 43.478 0.00 0.00 0.00 2.52
59 60 3.256704 TGGGGTTTACTCCACTCATCTT 58.743 45.455 0.00 0.00 0.00 2.40
60 61 2.915869 TGGGGTTTACTCCACTCATCT 58.084 47.619 0.00 0.00 0.00 2.90
61 62 3.713826 TTGGGGTTTACTCCACTCATC 57.286 47.619 0.00 0.00 32.00 2.92
62 63 3.053619 GGATTGGGGTTTACTCCACTCAT 60.054 47.826 17.70 3.31 35.30 2.90
63 64 2.307686 GGATTGGGGTTTACTCCACTCA 59.692 50.000 17.70 0.00 35.30 3.41
64 65 2.356844 GGGATTGGGGTTTACTCCACTC 60.357 54.545 9.93 9.93 33.57 3.51
65 66 1.639108 GGGATTGGGGTTTACTCCACT 59.361 52.381 0.00 0.00 32.00 4.00
66 67 1.639108 AGGGATTGGGGTTTACTCCAC 59.361 52.381 0.00 0.00 32.00 4.02
67 68 1.920351 GAGGGATTGGGGTTTACTCCA 59.080 52.381 0.00 0.00 0.00 3.86
68 69 1.214673 GGAGGGATTGGGGTTTACTCC 59.785 57.143 0.00 0.00 36.60 3.85
69 70 2.206223 AGGAGGGATTGGGGTTTACTC 58.794 52.381 0.00 0.00 0.00 2.59
70 71 2.378308 AGGAGGGATTGGGGTTTACT 57.622 50.000 0.00 0.00 0.00 2.24
71 72 3.468071 AAAGGAGGGATTGGGGTTTAC 57.532 47.619 0.00 0.00 0.00 2.01
72 73 3.403051 TCAAAAGGAGGGATTGGGGTTTA 59.597 43.478 0.00 0.00 0.00 2.01
73 74 2.181196 TCAAAAGGAGGGATTGGGGTTT 59.819 45.455 0.00 0.00 0.00 3.27
74 75 1.792651 TCAAAAGGAGGGATTGGGGTT 59.207 47.619 0.00 0.00 0.00 4.11
75 76 1.466858 TCAAAAGGAGGGATTGGGGT 58.533 50.000 0.00 0.00 0.00 4.95
76 77 2.621556 TTCAAAAGGAGGGATTGGGG 57.378 50.000 0.00 0.00 0.00 4.96
77 78 3.452264 GGAATTCAAAAGGAGGGATTGGG 59.548 47.826 7.93 0.00 0.00 4.12
78 79 4.161001 CAGGAATTCAAAAGGAGGGATTGG 59.839 45.833 7.93 0.00 0.00 3.16
79 80 4.382362 GCAGGAATTCAAAAGGAGGGATTG 60.382 45.833 7.93 0.00 0.00 2.67
80 81 3.771479 GCAGGAATTCAAAAGGAGGGATT 59.229 43.478 7.93 0.00 0.00 3.01
81 82 3.245730 TGCAGGAATTCAAAAGGAGGGAT 60.246 43.478 7.93 0.00 0.00 3.85
82 83 2.109834 TGCAGGAATTCAAAAGGAGGGA 59.890 45.455 7.93 0.00 0.00 4.20
83 84 2.528564 TGCAGGAATTCAAAAGGAGGG 58.471 47.619 7.93 0.00 0.00 4.30
84 85 4.382362 GGAATGCAGGAATTCAAAAGGAGG 60.382 45.833 7.93 0.00 38.14 4.30
85 86 4.221262 TGGAATGCAGGAATTCAAAAGGAG 59.779 41.667 7.93 0.00 38.14 3.69
86 87 4.158786 TGGAATGCAGGAATTCAAAAGGA 58.841 39.130 7.93 0.00 38.14 3.36
87 88 4.020839 ACTGGAATGCAGGAATTCAAAAGG 60.021 41.667 6.73 0.00 38.14 3.11
88 89 5.143376 ACTGGAATGCAGGAATTCAAAAG 57.857 39.130 6.73 0.18 38.14 2.27
89 90 5.540911 GAACTGGAATGCAGGAATTCAAAA 58.459 37.500 6.73 0.00 38.14 2.44
90 91 4.321156 CGAACTGGAATGCAGGAATTCAAA 60.321 41.667 6.73 0.00 38.14 2.69
91 92 3.191162 CGAACTGGAATGCAGGAATTCAA 59.809 43.478 6.73 0.00 38.14 2.69
92 93 2.749076 CGAACTGGAATGCAGGAATTCA 59.251 45.455 6.73 0.00 38.14 2.57
93 94 3.009723 TCGAACTGGAATGCAGGAATTC 58.990 45.455 6.73 0.00 36.08 2.17
94 95 3.012518 CTCGAACTGGAATGCAGGAATT 58.987 45.455 6.73 0.00 0.00 2.17
95 96 2.636830 CTCGAACTGGAATGCAGGAAT 58.363 47.619 6.73 0.00 0.00 3.01
96 97 1.945819 GCTCGAACTGGAATGCAGGAA 60.946 52.381 6.73 0.00 0.00 3.36
97 98 0.391661 GCTCGAACTGGAATGCAGGA 60.392 55.000 6.73 0.00 0.00 3.86
98 99 0.392193 AGCTCGAACTGGAATGCAGG 60.392 55.000 6.73 0.00 0.00 4.85
99 100 2.299993 TAGCTCGAACTGGAATGCAG 57.700 50.000 0.00 0.00 0.00 4.41
100 101 2.554142 CATAGCTCGAACTGGAATGCA 58.446 47.619 0.00 0.00 0.00 3.96
101 102 1.869767 CCATAGCTCGAACTGGAATGC 59.130 52.381 0.00 0.00 0.00 3.56
102 103 3.185246 ACCATAGCTCGAACTGGAATG 57.815 47.619 0.00 0.00 32.92 2.67
103 104 3.535561 CAACCATAGCTCGAACTGGAAT 58.464 45.455 0.00 0.00 32.92 3.01
104 105 2.935238 GCAACCATAGCTCGAACTGGAA 60.935 50.000 0.00 0.00 32.92 3.53
105 106 1.405526 GCAACCATAGCTCGAACTGGA 60.406 52.381 0.00 0.00 32.92 3.86
106 107 1.009829 GCAACCATAGCTCGAACTGG 58.990 55.000 0.00 0.00 34.84 4.00
107 108 1.394917 GTGCAACCATAGCTCGAACTG 59.605 52.381 0.00 0.00 0.00 3.16
108 109 1.276421 AGTGCAACCATAGCTCGAACT 59.724 47.619 0.00 0.00 37.80 3.01
109 110 1.726853 AGTGCAACCATAGCTCGAAC 58.273 50.000 0.00 0.00 37.80 3.95
110 111 2.496070 ACTAGTGCAACCATAGCTCGAA 59.504 45.455 0.00 0.00 37.80 3.71
111 112 2.099263 GACTAGTGCAACCATAGCTCGA 59.901 50.000 0.00 0.00 37.80 4.04
112 113 2.464865 GACTAGTGCAACCATAGCTCG 58.535 52.381 0.00 0.00 37.80 5.03
113 114 2.464865 CGACTAGTGCAACCATAGCTC 58.535 52.381 0.00 0.00 37.80 4.09
114 115 1.137086 CCGACTAGTGCAACCATAGCT 59.863 52.381 0.00 0.00 37.80 3.32
115 116 1.571919 CCGACTAGTGCAACCATAGC 58.428 55.000 0.00 0.00 37.80 2.97
116 117 1.480954 ACCCGACTAGTGCAACCATAG 59.519 52.381 0.00 0.00 37.80 2.23
117 118 1.206132 CACCCGACTAGTGCAACCATA 59.794 52.381 0.00 0.00 37.80 2.74
118 119 0.036388 CACCCGACTAGTGCAACCAT 60.036 55.000 0.00 0.00 37.80 3.55
119 120 1.369692 CACCCGACTAGTGCAACCA 59.630 57.895 0.00 0.00 37.80 3.67
120 121 1.375523 CCACCCGACTAGTGCAACC 60.376 63.158 0.00 0.00 37.80 3.77
121 122 1.375523 CCCACCCGACTAGTGCAAC 60.376 63.158 0.00 0.00 33.75 4.17
122 123 3.065306 CCCACCCGACTAGTGCAA 58.935 61.111 0.00 0.00 33.75 4.08
123 124 3.702048 GCCCACCCGACTAGTGCA 61.702 66.667 0.00 0.00 33.75 4.57
124 125 3.665675 CTGCCCACCCGACTAGTGC 62.666 68.421 0.00 0.00 33.75 4.40
125 126 2.579201 CTGCCCACCCGACTAGTG 59.421 66.667 0.00 0.00 34.91 2.74
126 127 2.683933 CCTGCCCACCCGACTAGT 60.684 66.667 0.00 0.00 0.00 2.57
127 128 4.162690 GCCTGCCCACCCGACTAG 62.163 72.222 0.00 0.00 0.00 2.57
140 141 4.767255 GTCGACAGCCCAGGCCTG 62.767 72.222 26.87 26.87 43.17 4.85
142 143 4.329545 TTGTCGACAGCCCAGGCC 62.330 66.667 19.11 0.00 43.17 5.19
143 144 3.050275 GTTGTCGACAGCCCAGGC 61.050 66.667 20.48 0.00 42.33 4.85
144 145 1.374758 GAGTTGTCGACAGCCCAGG 60.375 63.158 26.19 0.00 0.00 4.45
145 146 1.374758 GGAGTTGTCGACAGCCCAG 60.375 63.158 26.19 0.00 0.00 4.45
146 147 1.691195 TTGGAGTTGTCGACAGCCCA 61.691 55.000 26.77 26.77 0.00 5.36
147 148 0.534203 TTTGGAGTTGTCGACAGCCC 60.534 55.000 26.19 24.64 0.00 5.19
148 149 1.523758 ATTTGGAGTTGTCGACAGCC 58.476 50.000 26.19 23.11 0.00 4.85
149 150 4.025647 GCTATATTTGGAGTTGTCGACAGC 60.026 45.833 23.14 23.14 0.00 4.40
150 151 5.005779 GTGCTATATTTGGAGTTGTCGACAG 59.994 44.000 19.11 3.31 0.00 3.51
151 152 4.868171 GTGCTATATTTGGAGTTGTCGACA 59.132 41.667 15.76 15.76 0.00 4.35
152 153 4.026804 CGTGCTATATTTGGAGTTGTCGAC 60.027 45.833 9.11 9.11 0.00 4.20
153 154 4.109766 CGTGCTATATTTGGAGTTGTCGA 58.890 43.478 0.00 0.00 0.00 4.20
157 158 5.569413 GGTTTCGTGCTATATTTGGAGTTG 58.431 41.667 0.00 0.00 0.00 3.16
170 171 1.153429 GGGCTATCGGTTTCGTGCT 60.153 57.895 0.00 0.00 37.69 4.40
203 204 1.819288 TCAATCCGAAAGCGTCTCTCT 59.181 47.619 0.00 0.00 35.23 3.10
209 210 1.798813 GTCAGTTCAATCCGAAAGCGT 59.201 47.619 0.00 0.00 34.69 5.07
217 218 1.725164 GGTTCGTCGTCAGTTCAATCC 59.275 52.381 0.00 0.00 0.00 3.01
218 219 1.725164 GGGTTCGTCGTCAGTTCAATC 59.275 52.381 0.00 0.00 0.00 2.67
221 222 1.364901 GGGGTTCGTCGTCAGTTCA 59.635 57.895 0.00 0.00 0.00 3.18
222 223 1.373873 GGGGGTTCGTCGTCAGTTC 60.374 63.158 0.00 0.00 0.00 3.01
223 224 1.813728 GAGGGGGTTCGTCGTCAGTT 61.814 60.000 0.00 0.00 0.00 3.16
224 225 2.203596 AGGGGGTTCGTCGTCAGT 60.204 61.111 0.00 0.00 0.00 3.41
226 227 2.993264 GGAGGGGGTTCGTCGTCA 60.993 66.667 0.00 0.00 0.00 4.35
228 229 2.995574 CAGGAGGGGGTTCGTCGT 60.996 66.667 0.00 0.00 0.00 4.34
230 231 4.097361 GCCAGGAGGGGGTTCGTC 62.097 72.222 0.00 0.00 37.04 4.20
231 232 4.658786 AGCCAGGAGGGGGTTCGT 62.659 66.667 0.00 0.00 34.27 3.85
232 233 3.787001 GAGCCAGGAGGGGGTTCG 61.787 72.222 0.00 0.00 39.15 3.95
233 234 3.412408 GGAGCCAGGAGGGGGTTC 61.412 72.222 0.00 0.00 39.15 3.62
234 235 3.960313 AGGAGCCAGGAGGGGGTT 61.960 66.667 0.00 0.00 39.15 4.11
235 236 4.748798 CAGGAGCCAGGAGGGGGT 62.749 72.222 0.00 0.00 42.44 4.95
318 335 8.334632 GCAGCACGCCATTATTTTATTTTTATT 58.665 29.630 0.00 0.00 32.94 1.40
319 336 7.306515 CGCAGCACGCCATTATTTTATTTTTAT 60.307 33.333 0.00 0.00 37.30 1.40
320 337 6.020281 CGCAGCACGCCATTATTTTATTTTTA 60.020 34.615 0.00 0.00 37.30 1.52
321 338 5.220378 CGCAGCACGCCATTATTTTATTTTT 60.220 36.000 0.00 0.00 37.30 1.94
322 339 4.267452 CGCAGCACGCCATTATTTTATTTT 59.733 37.500 0.00 0.00 37.30 1.82
323 340 3.796178 CGCAGCACGCCATTATTTTATTT 59.204 39.130 0.00 0.00 37.30 1.40
324 341 3.371168 CGCAGCACGCCATTATTTTATT 58.629 40.909 0.00 0.00 37.30 1.40
325 342 2.998772 CGCAGCACGCCATTATTTTAT 58.001 42.857 0.00 0.00 37.30 1.40
326 343 2.466870 CGCAGCACGCCATTATTTTA 57.533 45.000 0.00 0.00 37.30 1.52
327 344 3.327464 CGCAGCACGCCATTATTTT 57.673 47.368 0.00 0.00 37.30 1.82
341 358 1.730176 CACTCGTTTGTTTCACGCAG 58.270 50.000 0.00 0.00 37.57 5.18
423 441 3.876236 GGGGCCCCGGCGTAAATA 61.876 66.667 29.50 0.00 43.06 1.40
542 560 0.113190 ACTTGGAAAAGGAGGCCAGG 59.887 55.000 5.01 0.00 35.18 4.45
543 561 1.539157 GACTTGGAAAAGGAGGCCAG 58.461 55.000 5.01 0.00 32.47 4.85
544 562 0.112412 GGACTTGGAAAAGGAGGCCA 59.888 55.000 5.01 0.00 0.00 5.36
545 563 0.405973 AGGACTTGGAAAAGGAGGCC 59.594 55.000 0.00 0.00 0.00 5.19
565 583 2.408050 CACACGAGTGGGAGAAAAGAG 58.592 52.381 4.94 0.00 42.13 2.85
588 606 3.125829 ACCACGTCTAGTATACACACACG 59.874 47.826 5.50 9.84 32.51 4.49
599 617 3.146066 TGTTTACGGTACCACGTCTAGT 58.854 45.455 13.54 2.00 45.08 2.57
600 618 3.436704 TCTGTTTACGGTACCACGTCTAG 59.563 47.826 13.54 3.41 45.08 2.43
601 619 3.407698 TCTGTTTACGGTACCACGTCTA 58.592 45.455 13.54 0.00 45.08 2.59
602 620 2.229792 TCTGTTTACGGTACCACGTCT 58.770 47.619 13.54 0.00 45.08 4.18
603 621 2.704725 TCTGTTTACGGTACCACGTC 57.295 50.000 13.54 0.00 45.08 4.34
634 652 7.601508 ACTGTAGTACTACCACAAATGCTAAAC 59.398 37.037 26.41 2.82 35.26 2.01
635 653 7.673180 ACTGTAGTACTACCACAAATGCTAAA 58.327 34.615 26.41 5.78 35.26 1.85
638 656 5.740290 ACTGTAGTACTACCACAAATGCT 57.260 39.130 26.41 0.10 35.26 3.79
653 684 6.296026 TCACTTGGAAATGCTAAACTGTAGT 58.704 36.000 0.00 0.00 0.00 2.73
695 739 8.959058 CGCTACTAATAATTTATATGCTCTCGG 58.041 37.037 0.00 0.00 0.00 4.63
696 740 8.959058 CCGCTACTAATAATTTATATGCTCTCG 58.041 37.037 0.00 0.00 0.00 4.04
703 747 9.901172 CCCCTTTCCGCTACTAATAATTTATAT 57.099 33.333 0.00 0.00 0.00 0.86
709 769 3.244805 GCCCCCTTTCCGCTACTAATAAT 60.245 47.826 0.00 0.00 0.00 1.28
714 774 0.910566 TTGCCCCCTTTCCGCTACTA 60.911 55.000 0.00 0.00 0.00 1.82
717 777 0.610785 CTTTTGCCCCCTTTCCGCTA 60.611 55.000 0.00 0.00 0.00 4.26
731 794 7.517259 CGCCATTTCCTTTCTTTCTTTCTTTTG 60.517 37.037 0.00 0.00 0.00 2.44
740 803 2.029918 AGTGCGCCATTTCCTTTCTTTC 60.030 45.455 4.18 0.00 0.00 2.62
743 808 1.168714 GAGTGCGCCATTTCCTTTCT 58.831 50.000 4.18 0.00 0.00 2.52
763 833 0.391263 GTGTACTACTGTGGCTGGCC 60.391 60.000 4.43 4.43 0.00 5.36
772 842 4.575645 GGCTACCACTCTAGTGTACTACTG 59.424 50.000 9.17 0.00 44.21 2.74
773 843 4.385088 GGGCTACCACTCTAGTGTACTACT 60.385 50.000 9.17 0.00 44.21 2.57
774 844 3.882288 GGGCTACCACTCTAGTGTACTAC 59.118 52.174 9.17 0.00 44.21 2.73
775 845 3.117738 GGGGCTACCACTCTAGTGTACTA 60.118 52.174 9.17 0.00 44.21 1.82
776 846 2.357986 GGGGCTACCACTCTAGTGTACT 60.358 54.545 9.17 0.00 44.21 2.73
777 847 2.030371 GGGGCTACCACTCTAGTGTAC 58.970 57.143 9.17 0.00 44.21 2.90
778 848 1.063417 GGGGGCTACCACTCTAGTGTA 60.063 57.143 9.17 1.93 44.21 2.90
782 852 1.833049 CCGGGGGCTACCACTCTAG 60.833 68.421 0.00 0.00 42.91 2.43
788 858 2.241043 TAGCTAACCGGGGGCTACCA 62.241 60.000 17.24 2.81 42.91 3.25
799 872 3.667166 GCAGCAGTTTCGTTTAGCTAACC 60.667 47.826 5.45 0.00 33.59 2.85
806 879 1.264020 CAGCAGCAGCAGTTTCGTTTA 59.736 47.619 3.17 0.00 45.49 2.01
807 880 0.029834 CAGCAGCAGCAGTTTCGTTT 59.970 50.000 3.17 0.00 45.49 3.60
808 881 1.650912 CAGCAGCAGCAGTTTCGTT 59.349 52.632 3.17 0.00 45.49 3.85
810 883 2.126965 GCAGCAGCAGCAGTTTCG 60.127 61.111 4.63 0.00 45.49 3.46
811 884 1.081376 CAGCAGCAGCAGCAGTTTC 60.081 57.895 12.92 0.00 45.49 2.78
812 885 3.039988 CAGCAGCAGCAGCAGTTT 58.960 55.556 12.92 0.00 45.49 2.66
829 908 0.527385 CGCAGGAGAAGAGTAGCAGC 60.527 60.000 0.00 0.00 0.00 5.25
832 911 0.248296 CGACGCAGGAGAAGAGTAGC 60.248 60.000 0.00 0.00 0.00 3.58
834 913 1.199327 CAACGACGCAGGAGAAGAGTA 59.801 52.381 0.00 0.00 0.00 2.59
895 975 4.335416 CACTGGAGTGGAATGTATGGTTT 58.665 43.478 0.00 0.00 42.10 3.27
906 986 3.545574 TGCGTGCACTGGAGTGGA 61.546 61.111 16.19 2.76 45.72 4.02
934 1014 3.157949 GAGGGAGGGGGAAGCGAG 61.158 72.222 0.00 0.00 0.00 5.03
935 1015 3.680920 GAGAGGGAGGGGGAAGCGA 62.681 68.421 0.00 0.00 0.00 4.93
936 1016 3.157949 GAGAGGGAGGGGGAAGCG 61.158 72.222 0.00 0.00 0.00 4.68
952 1032 5.231552 TGATTATATCCACAAAGGGGGAGA 58.768 41.667 0.00 0.00 36.45 3.71
992 1083 1.244352 GGCGACGCGATTAAACAAAC 58.756 50.000 15.93 0.00 0.00 2.93
993 1084 0.166379 GGGCGACGCGATTAAACAAA 59.834 50.000 15.93 0.00 0.00 2.83
1075 1176 4.452733 GAGGTCGGTCCGCTTGGG 62.453 72.222 6.34 0.00 41.99 4.12
1167 1268 4.680237 TCCTTGCCGTCGGTGCAG 62.680 66.667 13.94 6.34 40.35 4.41
1171 1272 4.657824 CACGTCCTTGCCGTCGGT 62.658 66.667 13.94 0.00 36.17 4.69
1497 1598 3.078560 GACGCGATTGGGAACGTC 58.921 61.111 15.93 0.00 46.64 4.34
1512 1613 0.465097 CCATGATGGAGCTGTGGGAC 60.465 60.000 5.27 0.00 40.96 4.46
1684 1788 3.488978 CTCGCTGCTGCTGCTGAC 61.489 66.667 25.43 14.22 40.01 3.51
1870 1974 1.017177 GCATCCTCGCCGTTGTTGTA 61.017 55.000 0.00 0.00 0.00 2.41
1887 1991 4.382541 TCCAGCTCCTCCTCGGCA 62.383 66.667 0.00 0.00 0.00 5.69
2039 2154 1.153229 GGCGGTAGGGGACATGAAC 60.153 63.158 0.00 0.00 0.00 3.18
2065 2180 1.012234 GCGGTACTACGTACGTCGG 60.012 63.158 26.53 20.34 44.69 4.79
2084 2216 2.513897 GCTAATCTTGGCGGGCGT 60.514 61.111 0.00 0.00 0.00 5.68
2435 2571 4.443978 TCCATCTCCCATTTCCATTCTC 57.556 45.455 0.00 0.00 0.00 2.87
2436 2572 4.886755 TTCCATCTCCCATTTCCATTCT 57.113 40.909 0.00 0.00 0.00 2.40
2437 2573 4.217118 CGATTCCATCTCCCATTTCCATTC 59.783 45.833 0.00 0.00 0.00 2.67
2438 2574 4.147321 CGATTCCATCTCCCATTTCCATT 58.853 43.478 0.00 0.00 0.00 3.16
2439 2575 3.499202 CCGATTCCATCTCCCATTTCCAT 60.499 47.826 0.00 0.00 0.00 3.41
2440 2576 2.158623 CCGATTCCATCTCCCATTTCCA 60.159 50.000 0.00 0.00 0.00 3.53
2441 2577 2.508526 CCGATTCCATCTCCCATTTCC 58.491 52.381 0.00 0.00 0.00 3.13
2449 2585 1.958205 CTGGCGCCGATTCCATCTC 60.958 63.158 23.90 0.00 0.00 2.75
2672 2816 4.122776 CGGTGATGATGAAAGGTAGGAAG 58.877 47.826 0.00 0.00 0.00 3.46
2673 2817 3.772572 TCGGTGATGATGAAAGGTAGGAA 59.227 43.478 0.00 0.00 0.00 3.36
2674 2818 3.371034 TCGGTGATGATGAAAGGTAGGA 58.629 45.455 0.00 0.00 0.00 2.94
2675 2819 3.819564 TCGGTGATGATGAAAGGTAGG 57.180 47.619 0.00 0.00 0.00 3.18
2716 2863 0.662374 AGTACGTGCGTTGAGGTTCG 60.662 55.000 1.66 0.00 0.00 3.95
2791 3139 2.417651 CCCGATGGACTACGCAAAGTTA 60.418 50.000 0.00 0.00 0.00 2.24
2799 3147 0.248377 GTTCGACCCGATGGACTACG 60.248 60.000 0.00 0.00 35.23 3.51
2819 3167 0.107703 TCCATGCCAGATTCGACACC 60.108 55.000 0.00 0.00 0.00 4.16
3085 3440 3.537874 GGACCATCTCCCGTCCCG 61.538 72.222 0.00 0.00 42.39 5.14
3107 3469 0.036448 ATGAACTGCACTGCTCTGCT 59.964 50.000 1.98 0.00 38.07 4.24
3117 3479 1.159285 CTTCCTGCGAATGAACTGCA 58.841 50.000 0.00 0.00 37.07 4.41


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

AutoCloner maintained by Alex Coulton.