Multiple sequence alignment - TraesCS6A01G195700

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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 TraesCS6A01G195700 chr6A 100.000 2834 0 0 1 2834 282152786 282149953 0.000000e+00 5234
1 TraesCS6A01G195700 chr3D 93.247 2621 129 22 247 2834 209668807 209671412 0.000000e+00 3816
2 TraesCS6A01G195700 chr2B 92.182 2622 151 37 250 2834 667802426 667805030 0.000000e+00 3657
3 TraesCS6A01G195700 chr2B 92.174 115 6 2 252 365 667814963 667814851 2.920000e-35 159
4 TraesCS6A01G195700 chr2A 91.436 1915 151 10 924 2833 25355088 25353182 0.000000e+00 2615
5 TraesCS6A01G195700 chr2A 87.958 191 23 0 252 442 25355643 25355453 2.840000e-55 226
6 TraesCS6A01G195700 chr1A 90.147 1969 159 16 893 2834 536289557 536291517 0.000000e+00 2529
7 TraesCS6A01G195700 chr1A 92.368 380 26 2 252 628 489318984 489318605 3.210000e-149 538
8 TraesCS6A01G195700 chr1A 91.453 117 7 2 250 365 489293120 489293234 1.050000e-34 158
9 TraesCS6A01G195700 chr2D 90.081 1845 169 10 995 2834 610422630 610420795 0.000000e+00 2381
10 TraesCS6A01G195700 chr5D 89.739 1842 182 5 996 2834 432780776 432778939 0.000000e+00 2348
11 TraesCS6A01G195700 chr5D 89.582 1843 184 6 995 2834 432776222 432774385 0.000000e+00 2333
12 TraesCS6A01G195700 chr7D 89.691 1843 180 7 995 2834 570675861 570674026 0.000000e+00 2342
13 TraesCS6A01G195700 chr6D 94.796 1422 59 12 646 2059 466379594 466381008 0.000000e+00 2202
14 TraesCS6A01G195700 chr6D 84.841 409 28 9 251 628 466379138 466379543 5.730000e-102 381
15 TraesCS6A01G195700 chr6D 90.310 258 14 4 1 248 219781103 219781359 7.570000e-86 327
16 TraesCS6A01G195700 chr4A 95.337 1351 57 4 1488 2834 616709737 616711085 0.000000e+00 2141
17 TraesCS6A01G195700 chr4A 94.885 391 14 3 244 628 553454250 553453860 8.680000e-170 606
18 TraesCS6A01G195700 chr6B 87.884 1271 141 9 995 2259 694394485 694395748 0.000000e+00 1482
19 TraesCS6A01G195700 chr6B 88.354 395 24 8 252 628 432496111 432495721 3.330000e-124 455
20 TraesCS6A01G195700 chr6B 95.327 107 5 0 97 203 331016928 331017034 1.350000e-38 171
21 TraesCS6A01G195700 chr1D 97.119 243 6 1 251 493 22597924 22597683 2.630000e-110 409


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 TraesCS6A01G195700 chr6A 282149953 282152786 2833 True 5234.0 5234 100.0000 1 2834 1 chr6A.!!$R1 2833
1 TraesCS6A01G195700 chr3D 209668807 209671412 2605 False 3816.0 3816 93.2470 247 2834 1 chr3D.!!$F1 2587
2 TraesCS6A01G195700 chr2B 667802426 667805030 2604 False 3657.0 3657 92.1820 250 2834 1 chr2B.!!$F1 2584
3 TraesCS6A01G195700 chr2A 25353182 25355643 2461 True 1420.5 2615 89.6970 252 2833 2 chr2A.!!$R1 2581
4 TraesCS6A01G195700 chr1A 536289557 536291517 1960 False 2529.0 2529 90.1470 893 2834 1 chr1A.!!$F2 1941
5 TraesCS6A01G195700 chr2D 610420795 610422630 1835 True 2381.0 2381 90.0810 995 2834 1 chr2D.!!$R1 1839
6 TraesCS6A01G195700 chr5D 432774385 432780776 6391 True 2340.5 2348 89.6605 995 2834 2 chr5D.!!$R1 1839
7 TraesCS6A01G195700 chr7D 570674026 570675861 1835 True 2342.0 2342 89.6910 995 2834 1 chr7D.!!$R1 1839
8 TraesCS6A01G195700 chr6D 466379138 466381008 1870 False 1291.5 2202 89.8185 251 2059 2 chr6D.!!$F2 1808
9 TraesCS6A01G195700 chr4A 616709737 616711085 1348 False 2141.0 2141 95.3370 1488 2834 1 chr4A.!!$F1 1346
10 TraesCS6A01G195700 chr6B 694394485 694395748 1263 False 1482.0 1482 87.8840 995 2259 1 chr6B.!!$F2 1264

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
162 163 0.105039 AACGATTCGGCCTGAGATCC 59.895 55.0 11.29 0.0 0.00 3.36 F
185 186 0.251121 TGCCAGGATCGCAAAGGAAA 60.251 50.0 0.00 0.0 32.05 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 6115 1.002366 CCTTTGACTCCGCATTCTCG 58.998 55.000 0.0 0.0 0.0 4.04 R
2067 6756 1.754226 TCCCTTTGCAAGCGTTCTTTT 59.246 42.857 0.0 0.0 0.0 2.27 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
18 19 2.862780 TTCTACACCTGGGGTTGCT 58.137 52.632 7.03 0.00 31.02 3.91
19 20 0.400213 TTCTACACCTGGGGTTGCTG 59.600 55.000 7.03 0.00 31.02 4.41
20 21 1.675641 CTACACCTGGGGTTGCTGC 60.676 63.158 7.03 0.00 31.02 5.25
21 22 3.204467 TACACCTGGGGTTGCTGCC 62.204 63.158 7.03 0.00 31.02 4.85
22 23 4.290622 CACCTGGGGTTGCTGCCT 62.291 66.667 0.00 0.00 31.02 4.75
23 24 3.511610 ACCTGGGGTTGCTGCCTT 61.512 61.111 0.00 0.00 27.29 4.35
24 25 2.203684 CCTGGGGTTGCTGCCTTT 60.204 61.111 0.00 0.00 0.00 3.11
25 26 1.838396 CCTGGGGTTGCTGCCTTTT 60.838 57.895 0.00 0.00 0.00 2.27
26 27 0.541764 CCTGGGGTTGCTGCCTTTTA 60.542 55.000 0.00 0.00 0.00 1.52
27 28 0.890683 CTGGGGTTGCTGCCTTTTAG 59.109 55.000 0.00 0.00 0.00 1.85
28 29 0.480690 TGGGGTTGCTGCCTTTTAGA 59.519 50.000 0.00 0.00 0.00 2.10
29 30 0.888619 GGGGTTGCTGCCTTTTAGAC 59.111 55.000 0.00 0.00 0.00 2.59
30 31 1.616159 GGGTTGCTGCCTTTTAGACA 58.384 50.000 0.00 0.00 0.00 3.41
31 32 1.269723 GGGTTGCTGCCTTTTAGACAC 59.730 52.381 0.00 0.00 0.00 3.67
32 33 1.269723 GGTTGCTGCCTTTTAGACACC 59.730 52.381 0.00 0.00 0.00 4.16
33 34 2.230660 GTTGCTGCCTTTTAGACACCT 58.769 47.619 0.00 0.00 0.00 4.00
34 35 2.185004 TGCTGCCTTTTAGACACCTC 57.815 50.000 0.00 0.00 0.00 3.85
35 36 1.699634 TGCTGCCTTTTAGACACCTCT 59.300 47.619 0.00 0.00 0.00 3.69
36 37 2.903784 TGCTGCCTTTTAGACACCTCTA 59.096 45.455 0.00 0.00 0.00 2.43
37 38 3.519510 TGCTGCCTTTTAGACACCTCTAT 59.480 43.478 0.00 0.00 0.00 1.98
38 39 3.873952 GCTGCCTTTTAGACACCTCTATG 59.126 47.826 0.00 0.00 0.00 2.23
39 40 4.624125 GCTGCCTTTTAGACACCTCTATGT 60.624 45.833 0.00 0.00 34.78 2.29
40 41 4.832248 TGCCTTTTAGACACCTCTATGTG 58.168 43.478 0.00 0.00 42.05 3.21
41 42 4.530553 TGCCTTTTAGACACCTCTATGTGA 59.469 41.667 0.00 0.00 39.57 3.58
42 43 5.012664 TGCCTTTTAGACACCTCTATGTGAA 59.987 40.000 0.00 0.00 39.57 3.18
43 44 5.938125 GCCTTTTAGACACCTCTATGTGAAA 59.062 40.000 0.00 0.00 39.57 2.69
44 45 6.599638 GCCTTTTAGACACCTCTATGTGAAAT 59.400 38.462 0.00 0.00 39.57 2.17
45 46 7.414540 GCCTTTTAGACACCTCTATGTGAAATG 60.415 40.741 0.00 0.00 39.57 2.32
46 47 7.824289 CCTTTTAGACACCTCTATGTGAAATGA 59.176 37.037 0.00 0.00 39.57 2.57
47 48 9.219603 CTTTTAGACACCTCTATGTGAAATGAA 57.780 33.333 0.00 0.00 39.57 2.57
48 49 9.567776 TTTTAGACACCTCTATGTGAAATGAAA 57.432 29.630 0.00 0.00 39.57 2.69
49 50 9.567776 TTTAGACACCTCTATGTGAAATGAAAA 57.432 29.630 0.00 0.00 39.57 2.29
50 51 9.567776 TTAGACACCTCTATGTGAAATGAAAAA 57.432 29.630 0.00 0.00 39.57 1.94
79 80 6.192970 CCTAATGGGCCTGGGATATTATAG 57.807 45.833 4.53 0.00 0.00 1.31
80 81 5.672194 CCTAATGGGCCTGGGATATTATAGT 59.328 44.000 4.53 0.00 0.00 2.12
81 82 6.160459 CCTAATGGGCCTGGGATATTATAGTT 59.840 42.308 4.53 0.00 0.00 2.24
82 83 6.483888 AATGGGCCTGGGATATTATAGTTT 57.516 37.500 4.53 0.00 0.00 2.66
83 84 5.941146 TGGGCCTGGGATATTATAGTTTT 57.059 39.130 4.53 0.00 0.00 2.43
84 85 6.288096 TGGGCCTGGGATATTATAGTTTTT 57.712 37.500 4.53 0.00 0.00 1.94
108 109 5.379757 GCAATTGCAATTTTATCAGACGG 57.620 39.130 25.36 8.03 41.59 4.79
109 110 4.864247 GCAATTGCAATTTTATCAGACGGT 59.136 37.500 25.36 0.00 41.59 4.83
110 111 5.348451 GCAATTGCAATTTTATCAGACGGTT 59.652 36.000 25.36 0.00 41.59 4.44
111 112 6.670452 GCAATTGCAATTTTATCAGACGGTTG 60.670 38.462 25.36 8.43 41.59 3.77
112 113 5.697473 TTGCAATTTTATCAGACGGTTGA 57.303 34.783 0.00 0.00 0.00 3.18
113 114 5.295431 TGCAATTTTATCAGACGGTTGAG 57.705 39.130 0.00 0.00 0.00 3.02
114 115 4.155826 TGCAATTTTATCAGACGGTTGAGG 59.844 41.667 0.00 0.00 0.00 3.86
115 116 4.156008 GCAATTTTATCAGACGGTTGAGGT 59.844 41.667 0.00 0.00 0.00 3.85
116 117 5.335661 GCAATTTTATCAGACGGTTGAGGTT 60.336 40.000 0.00 0.00 0.00 3.50
117 118 5.880054 ATTTTATCAGACGGTTGAGGTTG 57.120 39.130 0.00 0.00 0.00 3.77
118 119 4.610605 TTTATCAGACGGTTGAGGTTGA 57.389 40.909 0.00 0.00 0.00 3.18
119 120 4.819105 TTATCAGACGGTTGAGGTTGAT 57.181 40.909 0.00 0.00 0.00 2.57
120 121 2.743636 TCAGACGGTTGAGGTTGATC 57.256 50.000 0.00 0.00 0.00 2.92
121 122 1.067846 TCAGACGGTTGAGGTTGATCG 60.068 52.381 0.00 0.00 0.00 3.69
122 123 0.246635 AGACGGTTGAGGTTGATCGG 59.753 55.000 0.00 0.00 0.00 4.18
123 124 0.739813 GACGGTTGAGGTTGATCGGG 60.740 60.000 0.00 0.00 0.00 5.14
124 125 1.295423 CGGTTGAGGTTGATCGGGT 59.705 57.895 0.00 0.00 0.00 5.28
125 126 0.533491 CGGTTGAGGTTGATCGGGTA 59.467 55.000 0.00 0.00 0.00 3.69
126 127 1.066716 CGGTTGAGGTTGATCGGGTAA 60.067 52.381 0.00 0.00 0.00 2.85
127 128 2.629051 GGTTGAGGTTGATCGGGTAAG 58.371 52.381 0.00 0.00 0.00 2.34
128 129 2.027469 GGTTGAGGTTGATCGGGTAAGT 60.027 50.000 0.00 0.00 0.00 2.24
129 130 3.196254 GGTTGAGGTTGATCGGGTAAGTA 59.804 47.826 0.00 0.00 0.00 2.24
130 131 4.141779 GGTTGAGGTTGATCGGGTAAGTAT 60.142 45.833 0.00 0.00 0.00 2.12
131 132 4.931661 TGAGGTTGATCGGGTAAGTATC 57.068 45.455 0.00 0.00 0.00 2.24
132 133 3.640029 TGAGGTTGATCGGGTAAGTATCC 59.360 47.826 0.00 0.00 0.00 2.59
133 134 3.640029 GAGGTTGATCGGGTAAGTATCCA 59.360 47.826 0.00 0.00 0.00 3.41
134 135 4.035112 AGGTTGATCGGGTAAGTATCCAA 58.965 43.478 0.00 0.00 0.00 3.53
135 136 4.124970 GGTTGATCGGGTAAGTATCCAAC 58.875 47.826 0.00 0.00 0.00 3.77
136 137 3.720949 TGATCGGGTAAGTATCCAACG 57.279 47.619 0.00 0.00 0.00 4.10
137 138 3.289836 TGATCGGGTAAGTATCCAACGA 58.710 45.455 0.00 0.00 0.00 3.85
138 139 3.067180 TGATCGGGTAAGTATCCAACGAC 59.933 47.826 0.00 0.00 0.00 4.34
139 140 2.726821 TCGGGTAAGTATCCAACGACT 58.273 47.619 0.00 0.00 0.00 4.18
140 141 2.684881 TCGGGTAAGTATCCAACGACTC 59.315 50.000 0.00 0.00 0.00 3.36
141 142 2.424601 CGGGTAAGTATCCAACGACTCA 59.575 50.000 0.00 0.00 0.00 3.41
142 143 3.733077 CGGGTAAGTATCCAACGACTCAC 60.733 52.174 0.00 0.00 0.00 3.51
143 144 3.194116 GGGTAAGTATCCAACGACTCACA 59.806 47.826 0.00 0.00 0.00 3.58
144 145 4.322198 GGGTAAGTATCCAACGACTCACAA 60.322 45.833 0.00 0.00 0.00 3.33
145 146 4.624452 GGTAAGTATCCAACGACTCACAAC 59.376 45.833 0.00 0.00 0.00 3.32
146 147 2.942710 AGTATCCAACGACTCACAACG 58.057 47.619 0.00 0.00 0.00 4.10
147 148 2.555325 AGTATCCAACGACTCACAACGA 59.445 45.455 0.00 0.00 0.00 3.85
148 149 2.743636 ATCCAACGACTCACAACGAT 57.256 45.000 0.00 0.00 0.00 3.73
149 150 2.519377 TCCAACGACTCACAACGATT 57.481 45.000 0.00 0.00 0.00 3.34
150 151 2.400399 TCCAACGACTCACAACGATTC 58.600 47.619 0.00 0.00 0.00 2.52
153 154 1.702299 CGACTCACAACGATTCGGC 59.298 57.895 11.29 0.00 41.66 5.54
154 155 1.683790 CGACTCACAACGATTCGGCC 61.684 60.000 11.29 0.00 41.66 6.13
155 156 0.389948 GACTCACAACGATTCGGCCT 60.390 55.000 11.29 0.00 0.00 5.19
156 157 0.670546 ACTCACAACGATTCGGCCTG 60.671 55.000 11.29 7.20 0.00 4.85
157 158 0.389817 CTCACAACGATTCGGCCTGA 60.390 55.000 11.29 6.37 0.00 3.86
158 159 0.389817 TCACAACGATTCGGCCTGAG 60.390 55.000 11.29 3.99 0.00 3.35
159 160 0.389817 CACAACGATTCGGCCTGAGA 60.390 55.000 11.29 0.00 0.00 3.27
160 161 0.537188 ACAACGATTCGGCCTGAGAT 59.463 50.000 11.29 0.00 0.00 2.75
161 162 1.212616 CAACGATTCGGCCTGAGATC 58.787 55.000 11.29 5.65 0.00 2.75
162 163 0.105039 AACGATTCGGCCTGAGATCC 59.895 55.000 11.29 0.00 0.00 3.36
163 164 1.372251 CGATTCGGCCTGAGATCCG 60.372 63.158 0.00 6.76 46.52 4.18
164 165 1.005630 GATTCGGCCTGAGATCCGG 60.006 63.158 0.00 0.00 45.31 5.14
165 166 3.170490 ATTCGGCCTGAGATCCGGC 62.170 63.158 0.00 6.73 45.31 6.13
166 167 4.841617 TCGGCCTGAGATCCGGCT 62.842 66.667 13.95 0.00 45.57 5.52
167 168 4.598894 CGGCCTGAGATCCGGCTG 62.599 72.222 13.95 11.70 45.57 4.85
168 169 4.925861 GGCCTGAGATCCGGCTGC 62.926 72.222 13.95 0.00 45.57 5.25
169 170 4.925861 GCCTGAGATCCGGCTGCC 62.926 72.222 9.11 9.11 42.98 4.85
170 171 3.473647 CCTGAGATCCGGCTGCCA 61.474 66.667 20.29 0.00 0.00 4.92
171 172 2.108566 CTGAGATCCGGCTGCCAG 59.891 66.667 20.29 7.68 0.00 4.85
172 173 3.457625 CTGAGATCCGGCTGCCAGG 62.458 68.421 20.29 19.69 0.00 4.45
173 174 3.157252 GAGATCCGGCTGCCAGGA 61.157 66.667 26.40 26.40 41.30 3.86
176 177 3.933722 ATCCGGCTGCCAGGATCG 61.934 66.667 27.88 11.71 43.27 3.69
180 181 2.751436 GGCTGCCAGGATCGCAAA 60.751 61.111 15.17 0.00 35.40 3.68
181 182 2.768492 GGCTGCCAGGATCGCAAAG 61.768 63.158 15.17 0.00 35.40 2.77
182 183 2.768492 GCTGCCAGGATCGCAAAGG 61.768 63.158 0.00 0.00 35.40 3.11
183 184 1.078214 CTGCCAGGATCGCAAAGGA 60.078 57.895 0.00 0.00 35.40 3.36
184 185 0.677731 CTGCCAGGATCGCAAAGGAA 60.678 55.000 0.00 0.00 35.40 3.36
185 186 0.251121 TGCCAGGATCGCAAAGGAAA 60.251 50.000 0.00 0.00 32.05 3.13
186 187 1.106285 GCCAGGATCGCAAAGGAAAT 58.894 50.000 0.00 0.00 0.00 2.17
187 188 1.066152 GCCAGGATCGCAAAGGAAATC 59.934 52.381 0.00 0.00 0.00 2.17
188 189 1.331756 CCAGGATCGCAAAGGAAATCG 59.668 52.381 0.00 0.00 0.00 3.34
189 190 2.279741 CAGGATCGCAAAGGAAATCGA 58.720 47.619 0.00 0.00 35.34 3.59
190 191 2.677836 CAGGATCGCAAAGGAAATCGAA 59.322 45.455 0.00 0.00 34.50 3.71
191 192 3.313526 CAGGATCGCAAAGGAAATCGAAT 59.686 43.478 0.00 0.00 34.50 3.34
192 193 3.561725 AGGATCGCAAAGGAAATCGAATC 59.438 43.478 0.00 0.00 34.50 2.52
193 194 3.561725 GGATCGCAAAGGAAATCGAATCT 59.438 43.478 0.00 0.00 34.50 2.40
194 195 4.750098 GGATCGCAAAGGAAATCGAATCTA 59.250 41.667 0.00 0.00 34.50 1.98
195 196 5.236478 GGATCGCAAAGGAAATCGAATCTAA 59.764 40.000 0.00 0.00 34.50 2.10
196 197 5.464965 TCGCAAAGGAAATCGAATCTAAC 57.535 39.130 0.00 0.00 0.00 2.34
197 198 4.032445 TCGCAAAGGAAATCGAATCTAACG 59.968 41.667 0.00 0.00 0.00 3.18
198 199 4.032445 CGCAAAGGAAATCGAATCTAACGA 59.968 41.667 0.00 0.00 43.65 3.85
199 200 5.256352 GCAAAGGAAATCGAATCTAACGAC 58.744 41.667 0.00 0.00 42.37 4.34
200 201 5.726963 GCAAAGGAAATCGAATCTAACGACC 60.727 44.000 0.00 0.00 42.37 4.79
201 202 4.056092 AGGAAATCGAATCTAACGACCC 57.944 45.455 0.00 0.00 42.37 4.46
202 203 3.449737 AGGAAATCGAATCTAACGACCCA 59.550 43.478 0.00 0.00 42.37 4.51
203 204 4.101119 AGGAAATCGAATCTAACGACCCAT 59.899 41.667 0.00 0.00 42.37 4.00
204 205 5.303589 AGGAAATCGAATCTAACGACCCATA 59.696 40.000 0.00 0.00 42.37 2.74
205 206 6.014499 AGGAAATCGAATCTAACGACCCATAT 60.014 38.462 0.00 0.00 42.37 1.78
206 207 6.090898 GGAAATCGAATCTAACGACCCATATG 59.909 42.308 0.00 0.00 42.37 1.78
207 208 3.909430 TCGAATCTAACGACCCATATGC 58.091 45.455 0.00 0.00 34.85 3.14
208 209 3.572682 TCGAATCTAACGACCCATATGCT 59.427 43.478 0.00 0.00 34.85 3.79
209 210 3.921021 CGAATCTAACGACCCATATGCTC 59.079 47.826 0.00 0.00 0.00 4.26
210 211 4.321304 CGAATCTAACGACCCATATGCTCT 60.321 45.833 0.00 0.00 0.00 4.09
211 212 4.527509 ATCTAACGACCCATATGCTCTG 57.472 45.455 0.00 0.00 0.00 3.35
212 213 2.628178 TCTAACGACCCATATGCTCTGG 59.372 50.000 0.00 0.00 0.00 3.86
213 214 1.204146 AACGACCCATATGCTCTGGT 58.796 50.000 0.00 0.00 31.44 4.00
214 215 0.465705 ACGACCCATATGCTCTGGTG 59.534 55.000 6.15 2.71 31.44 4.17
215 216 0.752658 CGACCCATATGCTCTGGTGA 59.247 55.000 6.15 0.00 31.44 4.02
216 217 1.138859 CGACCCATATGCTCTGGTGAA 59.861 52.381 6.15 0.00 31.44 3.18
217 218 2.224378 CGACCCATATGCTCTGGTGAAT 60.224 50.000 6.15 0.00 31.44 2.57
218 219 3.144506 GACCCATATGCTCTGGTGAATG 58.855 50.000 6.15 0.00 31.44 2.67
219 220 2.511218 ACCCATATGCTCTGGTGAATGT 59.489 45.455 0.00 0.00 31.44 2.71
220 221 2.882761 CCCATATGCTCTGGTGAATGTG 59.117 50.000 0.00 0.00 31.44 3.21
221 222 2.882761 CCATATGCTCTGGTGAATGTGG 59.117 50.000 0.00 0.00 0.00 4.17
222 223 2.715749 TATGCTCTGGTGAATGTGGG 57.284 50.000 0.00 0.00 0.00 4.61
223 224 0.994247 ATGCTCTGGTGAATGTGGGA 59.006 50.000 0.00 0.00 0.00 4.37
224 225 0.325933 TGCTCTGGTGAATGTGGGAG 59.674 55.000 0.00 0.00 0.00 4.30
225 226 1.028868 GCTCTGGTGAATGTGGGAGC 61.029 60.000 0.00 0.00 39.14 4.70
226 227 0.617413 CTCTGGTGAATGTGGGAGCT 59.383 55.000 0.00 0.00 0.00 4.09
227 228 0.615331 TCTGGTGAATGTGGGAGCTC 59.385 55.000 4.71 4.71 0.00 4.09
228 229 0.742281 CTGGTGAATGTGGGAGCTCG 60.742 60.000 7.83 0.00 0.00 5.03
229 230 1.450312 GGTGAATGTGGGAGCTCGG 60.450 63.158 7.83 0.00 0.00 4.63
230 231 1.296715 GTGAATGTGGGAGCTCGGT 59.703 57.895 7.83 0.00 0.00 4.69
231 232 0.321653 GTGAATGTGGGAGCTCGGTT 60.322 55.000 7.83 0.00 0.00 4.44
232 233 0.400213 TGAATGTGGGAGCTCGGTTT 59.600 50.000 7.83 0.00 0.00 3.27
233 234 1.202879 TGAATGTGGGAGCTCGGTTTT 60.203 47.619 7.83 0.00 0.00 2.43
234 235 2.039216 TGAATGTGGGAGCTCGGTTTTA 59.961 45.455 7.83 0.00 0.00 1.52
235 236 2.109425 ATGTGGGAGCTCGGTTTTAC 57.891 50.000 7.83 1.09 0.00 2.01
236 237 0.759959 TGTGGGAGCTCGGTTTTACA 59.240 50.000 7.83 3.69 0.00 2.41
237 238 1.154197 GTGGGAGCTCGGTTTTACAC 58.846 55.000 7.83 4.46 0.00 2.90
238 239 0.759959 TGGGAGCTCGGTTTTACACA 59.240 50.000 7.83 0.00 0.00 3.72
239 240 1.270625 TGGGAGCTCGGTTTTACACAG 60.271 52.381 7.83 0.00 0.00 3.66
240 241 0.796927 GGAGCTCGGTTTTACACAGC 59.203 55.000 7.83 0.00 0.00 4.40
241 242 1.608283 GGAGCTCGGTTTTACACAGCT 60.608 52.381 7.83 0.00 43.22 4.24
242 243 1.727335 GAGCTCGGTTTTACACAGCTC 59.273 52.381 0.00 11.26 46.85 4.09
243 244 1.344763 AGCTCGGTTTTACACAGCTCT 59.655 47.619 0.00 0.00 35.46 4.09
244 245 1.461127 GCTCGGTTTTACACAGCTCTG 59.539 52.381 0.00 0.00 0.00 3.35
245 246 2.755650 CTCGGTTTTACACAGCTCTGT 58.244 47.619 0.00 0.00 46.17 3.41
246 247 3.859627 GCTCGGTTTTACACAGCTCTGTA 60.860 47.826 1.79 0.00 42.83 2.74
247 248 4.304110 CTCGGTTTTACACAGCTCTGTAA 58.696 43.478 10.17 10.17 42.83 2.41
248 249 4.053295 TCGGTTTTACACAGCTCTGTAAC 58.947 43.478 13.39 6.64 42.83 2.50
337 338 2.797177 TGCCAATATACCACTGCACA 57.203 45.000 0.00 0.00 0.00 4.57
505 536 4.415150 CACCAGGAGCATGGCGGT 62.415 66.667 0.37 0.00 44.80 5.68
620 664 1.081092 CTCCTCCTCCCTGGGTTCA 59.919 63.158 13.56 0.00 36.20 3.18
628 672 2.757099 CCTGGGTTCATGGCTGGC 60.757 66.667 0.00 0.00 0.00 4.85
629 673 2.357836 CTGGGTTCATGGCTGGCT 59.642 61.111 2.00 0.00 0.00 4.75
630 674 1.751927 CTGGGTTCATGGCTGGCTC 60.752 63.158 2.00 0.00 0.00 4.70
631 675 2.440980 GGGTTCATGGCTGGCTCC 60.441 66.667 2.00 0.00 0.00 4.70
632 676 2.679716 GGTTCATGGCTGGCTCCT 59.320 61.111 2.00 0.00 0.00 3.69
635 679 2.683465 TTCATGGCTGGCTCCTCCC 61.683 63.158 2.00 0.00 0.00 4.30
636 680 3.095163 CATGGCTGGCTCCTCCCT 61.095 66.667 2.00 0.00 0.00 4.20
648 725 2.363018 CTCCCTCCCTCTGACGCA 60.363 66.667 0.00 0.00 0.00 5.24
656 733 2.780094 CCTCTGACGCATCGGCTCT 61.780 63.158 0.00 0.00 35.04 4.09
695 792 3.386237 GCAGCTCCGGTCAGAGGT 61.386 66.667 0.00 0.00 45.23 3.85
696 793 2.052690 GCAGCTCCGGTCAGAGGTA 61.053 63.158 0.00 0.00 42.56 3.08
697 794 1.395826 GCAGCTCCGGTCAGAGGTAT 61.396 60.000 0.00 0.00 42.56 2.73
698 795 0.671251 CAGCTCCGGTCAGAGGTATC 59.329 60.000 0.00 0.00 42.56 2.24
699 796 0.468400 AGCTCCGGTCAGAGGTATCC 60.468 60.000 0.00 0.00 42.63 2.59
700 797 1.797211 GCTCCGGTCAGAGGTATCCG 61.797 65.000 0.00 0.00 42.22 4.18
701 798 1.797211 CTCCGGTCAGAGGTATCCGC 61.797 65.000 0.00 0.00 41.38 5.54
702 799 2.728817 CGGTCAGAGGTATCCGCC 59.271 66.667 0.00 0.00 36.68 6.13
703 800 2.857744 CGGTCAGAGGTATCCGCCC 61.858 68.421 0.00 0.00 36.68 6.13
704 801 2.508751 GGTCAGAGGTATCCGCCCC 61.509 68.421 0.00 0.00 0.00 5.80
705 802 1.760875 GTCAGAGGTATCCGCCCCA 60.761 63.158 0.00 0.00 0.00 4.96
706 803 1.457643 TCAGAGGTATCCGCCCCAG 60.458 63.158 0.00 0.00 0.00 4.45
707 804 2.844839 AGAGGTATCCGCCCCAGC 60.845 66.667 0.00 0.00 0.00 4.85
708 805 2.844839 GAGGTATCCGCCCCAGCT 60.845 66.667 0.00 0.00 36.60 4.24
709 806 2.844839 AGGTATCCGCCCCAGCTC 60.845 66.667 0.00 0.00 36.60 4.09
710 807 4.301027 GGTATCCGCCCCAGCTCG 62.301 72.222 0.00 0.00 36.60 5.03
711 808 3.537874 GTATCCGCCCCAGCTCGT 61.538 66.667 0.00 0.00 36.60 4.18
712 809 3.224324 TATCCGCCCCAGCTCGTC 61.224 66.667 0.00 0.00 36.60 4.20
724 821 1.066573 CAGCTCGTCCCAGATCAGTTT 60.067 52.381 0.00 0.00 0.00 2.66
730 827 1.002134 CCCAGATCAGTTTGCCGGT 60.002 57.895 1.90 0.00 0.00 5.28
731 828 0.251916 CCCAGATCAGTTTGCCGGTA 59.748 55.000 1.90 0.00 0.00 4.02
793 890 1.654954 CGAGTTCGTCCCGGATCAGT 61.655 60.000 0.73 0.00 34.11 3.41
796 893 1.000019 TTCGTCCCGGATCAGTCCT 60.000 57.895 0.73 0.00 42.73 3.85
856 953 2.759795 GGCCTCCTCTGCAACCTT 59.240 61.111 0.00 0.00 0.00 3.50
889 992 1.614824 CCTCTGCCTCCAACCCTCT 60.615 63.158 0.00 0.00 0.00 3.69
898 1001 3.917300 CCTCCAACCCTCTAGTACATCT 58.083 50.000 0.00 0.00 0.00 2.90
937 1040 6.755542 ACAAAATTTCCCCCTGTTTTCATA 57.244 33.333 0.00 0.00 0.00 2.15
941 1044 8.371699 CAAAATTTCCCCCTGTTTTCATAGTTA 58.628 33.333 0.00 0.00 0.00 2.24
963 1066 8.850156 AGTTATTTTTCATTGTAAGTGCAGTCT 58.150 29.630 0.00 0.00 0.00 3.24
993 1101 5.219633 GTTGTGTTTGTGTGTTTCAGAGTT 58.780 37.500 0.00 0.00 0.00 3.01
1004 1112 3.436704 TGTTTCAGAGTTGATTCGATGGC 59.563 43.478 0.00 0.00 32.27 4.40
1049 1157 4.279922 TGTTCAGTCCTACTTGACGATTGA 59.720 41.667 0.00 0.00 40.26 2.57
1158 1269 2.635427 GGAGGAGAAGTTCAAGTGGTCT 59.365 50.000 5.50 0.00 0.00 3.85
1159 1270 3.306433 GGAGGAGAAGTTCAAGTGGTCTC 60.306 52.174 5.50 0.00 35.11 3.36
1160 1271 3.046968 GGAGAAGTTCAAGTGGTCTCC 57.953 52.381 5.50 2.45 45.58 3.71
1167 1278 3.648067 AGTTCAAGTGGTCTCCTGATCAA 59.352 43.478 0.00 0.00 34.75 2.57
1213 1324 5.134339 ACAGGATATAACACCATCCCATTGT 59.866 40.000 0.00 0.00 41.51 2.71
1321 5987 3.476552 CAACACAAGGAACAAGCTCCTA 58.523 45.455 0.00 0.00 45.59 2.94
1449 6115 3.437049 GTGAGGAGAACACCTATTTGCAC 59.563 47.826 0.00 0.00 40.73 4.57
1477 6146 2.426522 CGGAGTCAAAGGAGAATGCAA 58.573 47.619 0.00 0.00 0.00 4.08
1719 6405 7.430760 ACTAGCAATTAGAGAAGATTGGTCT 57.569 36.000 4.31 0.00 41.49 3.85
1751 6437 8.269424 CACGCAATATAGTGACACTAAAAGATC 58.731 37.037 18.89 6.71 40.56 2.75
1789 6475 1.216064 TGAGGATTGTCCATGGAGGG 58.784 55.000 16.81 0.00 39.61 4.30
1869 6555 2.036217 TGCTTCTTTCTTTGGCACATGG 59.964 45.455 0.00 0.00 39.30 3.66
2067 6756 1.225855 CGGTGAGTGCAAAACAGCTA 58.774 50.000 13.41 0.00 34.99 3.32
2275 6967 9.675464 CAACTACCAATAGTAAGGGTGAAATTA 57.325 33.333 6.41 0.00 41.00 1.40
2287 6979 5.410067 AGGGTGAAATTATGCATGTTTTCG 58.590 37.500 21.41 0.00 32.13 3.46
2378 7070 5.108517 GGTTGATGCAACTTTTCTTTGTGA 58.891 37.500 9.80 0.00 43.14 3.58
2465 7181 7.436376 GGTAGCATTTGGAATATTTGAGAAAGC 59.564 37.037 0.00 0.00 0.00 3.51
2466 7182 6.038356 AGCATTTGGAATATTTGAGAAAGCG 58.962 36.000 0.00 0.00 0.00 4.68
2506 7222 3.295093 TGGTTCATGGAGCAGTTGAAAA 58.705 40.909 0.48 0.00 31.66 2.29
2796 7513 1.603802 CGTGTGTGGACAAGAAGCAAT 59.396 47.619 0.00 0.00 33.77 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.400213 CAGCAACCCCAGGTGTAGAA 59.600 55.000 0.00 0.00 35.34 2.10
3 4 2.434331 GCAGCAACCCCAGGTGTA 59.566 61.111 0.00 0.00 35.34 2.90
5 6 3.815407 AAGGCAGCAACCCCAGGTG 62.815 63.158 0.00 0.00 35.34 4.00
7 8 0.541764 TAAAAGGCAGCAACCCCAGG 60.542 55.000 0.00 0.00 0.00 4.45
8 9 0.890683 CTAAAAGGCAGCAACCCCAG 59.109 55.000 0.00 0.00 0.00 4.45
9 10 0.480690 TCTAAAAGGCAGCAACCCCA 59.519 50.000 0.00 0.00 0.00 4.96
10 11 0.888619 GTCTAAAAGGCAGCAACCCC 59.111 55.000 0.00 0.00 0.00 4.95
11 12 1.269723 GTGTCTAAAAGGCAGCAACCC 59.730 52.381 0.00 0.00 25.72 4.11
12 13 1.269723 GGTGTCTAAAAGGCAGCAACC 59.730 52.381 5.88 0.00 46.62 3.77
13 14 2.706555 GGTGTCTAAAAGGCAGCAAC 57.293 50.000 5.88 0.00 46.62 4.17
17 18 4.872691 CACATAGAGGTGTCTAAAAGGCAG 59.127 45.833 0.00 0.00 38.82 4.85
18 19 4.530553 TCACATAGAGGTGTCTAAAAGGCA 59.469 41.667 0.00 0.00 38.82 4.75
19 20 5.086104 TCACATAGAGGTGTCTAAAAGGC 57.914 43.478 0.00 0.00 38.82 4.35
20 21 7.824289 TCATTTCACATAGAGGTGTCTAAAAGG 59.176 37.037 0.00 0.00 38.82 3.11
21 22 8.777865 TCATTTCACATAGAGGTGTCTAAAAG 57.222 34.615 0.00 0.00 38.82 2.27
22 23 9.567776 TTTCATTTCACATAGAGGTGTCTAAAA 57.432 29.630 0.00 0.00 38.82 1.52
23 24 9.567776 TTTTCATTTCACATAGAGGTGTCTAAA 57.432 29.630 0.00 0.00 38.82 1.85
24 25 9.567776 TTTTTCATTTCACATAGAGGTGTCTAA 57.432 29.630 0.00 0.00 38.82 2.10
56 57 5.672194 ACTATAATATCCCAGGCCCATTAGG 59.328 44.000 0.00 0.00 39.47 2.69
57 58 6.831664 ACTATAATATCCCAGGCCCATTAG 57.168 41.667 0.00 0.00 0.00 1.73
58 59 7.597850 AAACTATAATATCCCAGGCCCATTA 57.402 36.000 0.00 0.00 0.00 1.90
59 60 6.483888 AAACTATAATATCCCAGGCCCATT 57.516 37.500 0.00 0.00 0.00 3.16
60 61 6.483888 AAAACTATAATATCCCAGGCCCAT 57.516 37.500 0.00 0.00 0.00 4.00
61 62 5.941146 AAAACTATAATATCCCAGGCCCA 57.059 39.130 0.00 0.00 0.00 5.36
86 87 4.864247 ACCGTCTGATAAAATTGCAATTGC 59.136 37.500 24.74 23.69 42.50 3.56
87 88 6.585702 TCAACCGTCTGATAAAATTGCAATTG 59.414 34.615 24.74 11.48 0.00 2.32
88 89 6.686630 TCAACCGTCTGATAAAATTGCAATT 58.313 32.000 18.99 18.99 0.00 2.32
89 90 6.266168 TCAACCGTCTGATAAAATTGCAAT 57.734 33.333 5.99 5.99 0.00 3.56
90 91 5.335583 CCTCAACCGTCTGATAAAATTGCAA 60.336 40.000 0.00 0.00 0.00 4.08
91 92 4.155826 CCTCAACCGTCTGATAAAATTGCA 59.844 41.667 0.00 0.00 0.00 4.08
92 93 4.156008 ACCTCAACCGTCTGATAAAATTGC 59.844 41.667 0.00 0.00 0.00 3.56
93 94 5.880054 ACCTCAACCGTCTGATAAAATTG 57.120 39.130 0.00 0.00 0.00 2.32
94 95 6.001460 TCAACCTCAACCGTCTGATAAAATT 58.999 36.000 0.00 0.00 0.00 1.82
95 96 5.556915 TCAACCTCAACCGTCTGATAAAAT 58.443 37.500 0.00 0.00 0.00 1.82
96 97 4.963373 TCAACCTCAACCGTCTGATAAAA 58.037 39.130 0.00 0.00 0.00 1.52
97 98 4.610605 TCAACCTCAACCGTCTGATAAA 57.389 40.909 0.00 0.00 0.00 1.40
98 99 4.676986 CGATCAACCTCAACCGTCTGATAA 60.677 45.833 0.00 0.00 0.00 1.75
99 100 3.181490 CGATCAACCTCAACCGTCTGATA 60.181 47.826 0.00 0.00 0.00 2.15
100 101 2.417379 CGATCAACCTCAACCGTCTGAT 60.417 50.000 0.00 0.00 0.00 2.90
101 102 1.067846 CGATCAACCTCAACCGTCTGA 60.068 52.381 0.00 0.00 0.00 3.27
102 103 1.350193 CGATCAACCTCAACCGTCTG 58.650 55.000 0.00 0.00 0.00 3.51
103 104 0.246635 CCGATCAACCTCAACCGTCT 59.753 55.000 0.00 0.00 0.00 4.18
104 105 0.739813 CCCGATCAACCTCAACCGTC 60.740 60.000 0.00 0.00 0.00 4.79
105 106 1.295423 CCCGATCAACCTCAACCGT 59.705 57.895 0.00 0.00 0.00 4.83
106 107 0.533491 TACCCGATCAACCTCAACCG 59.467 55.000 0.00 0.00 0.00 4.44
107 108 2.027469 ACTTACCCGATCAACCTCAACC 60.027 50.000 0.00 0.00 0.00 3.77
108 109 3.329929 ACTTACCCGATCAACCTCAAC 57.670 47.619 0.00 0.00 0.00 3.18
109 110 4.100498 GGATACTTACCCGATCAACCTCAA 59.900 45.833 0.00 0.00 0.00 3.02
110 111 3.640029 GGATACTTACCCGATCAACCTCA 59.360 47.826 0.00 0.00 0.00 3.86
111 112 3.640029 TGGATACTTACCCGATCAACCTC 59.360 47.826 0.00 0.00 37.61 3.85
112 113 3.649843 TGGATACTTACCCGATCAACCT 58.350 45.455 0.00 0.00 37.61 3.50
113 114 4.124970 GTTGGATACTTACCCGATCAACC 58.875 47.826 0.00 0.00 37.61 3.77
114 115 3.800506 CGTTGGATACTTACCCGATCAAC 59.199 47.826 0.00 0.00 37.61 3.18
115 116 3.700539 TCGTTGGATACTTACCCGATCAA 59.299 43.478 0.00 0.00 37.61 2.57
116 117 3.067180 GTCGTTGGATACTTACCCGATCA 59.933 47.826 0.00 0.00 37.61 2.92
117 118 3.317430 AGTCGTTGGATACTTACCCGATC 59.683 47.826 0.00 0.00 37.61 3.69
118 119 3.294214 AGTCGTTGGATACTTACCCGAT 58.706 45.455 0.00 0.00 37.61 4.18
119 120 2.684881 GAGTCGTTGGATACTTACCCGA 59.315 50.000 0.00 0.00 37.61 5.14
120 121 2.424601 TGAGTCGTTGGATACTTACCCG 59.575 50.000 0.00 0.00 37.61 5.28
121 122 3.194116 TGTGAGTCGTTGGATACTTACCC 59.806 47.826 0.00 0.00 32.77 3.69
122 123 4.445452 TGTGAGTCGTTGGATACTTACC 57.555 45.455 0.00 0.00 32.77 2.85
123 124 4.322804 CGTTGTGAGTCGTTGGATACTTAC 59.677 45.833 0.00 0.00 33.96 2.34
124 125 4.216042 TCGTTGTGAGTCGTTGGATACTTA 59.784 41.667 0.00 0.00 37.61 2.24
125 126 3.005050 TCGTTGTGAGTCGTTGGATACTT 59.995 43.478 0.00 0.00 37.61 2.24
126 127 2.555325 TCGTTGTGAGTCGTTGGATACT 59.445 45.455 0.00 0.00 37.61 2.12
127 128 2.937591 TCGTTGTGAGTCGTTGGATAC 58.062 47.619 0.00 0.00 0.00 2.24
128 129 3.861276 ATCGTTGTGAGTCGTTGGATA 57.139 42.857 0.00 0.00 0.00 2.59
129 130 2.743636 ATCGTTGTGAGTCGTTGGAT 57.256 45.000 0.00 0.00 0.00 3.41
130 131 2.400399 GAATCGTTGTGAGTCGTTGGA 58.600 47.619 0.00 0.00 31.22 3.53
131 132 2.856091 GAATCGTTGTGAGTCGTTGG 57.144 50.000 0.00 0.00 31.22 3.77
136 137 0.389948 AGGCCGAATCGTTGTGAGTC 60.390 55.000 0.82 0.00 38.31 3.36
137 138 0.670546 CAGGCCGAATCGTTGTGAGT 60.671 55.000 0.82 0.00 0.00 3.41
138 139 0.389817 TCAGGCCGAATCGTTGTGAG 60.390 55.000 0.82 0.00 0.00 3.51
139 140 0.389817 CTCAGGCCGAATCGTTGTGA 60.390 55.000 0.82 0.10 0.00 3.58
140 141 0.389817 TCTCAGGCCGAATCGTTGTG 60.390 55.000 0.82 0.00 0.00 3.33
141 142 0.537188 ATCTCAGGCCGAATCGTTGT 59.463 50.000 0.82 0.00 0.00 3.32
142 143 1.212616 GATCTCAGGCCGAATCGTTG 58.787 55.000 0.82 0.00 0.00 4.10
143 144 0.105039 GGATCTCAGGCCGAATCGTT 59.895 55.000 0.82 0.00 0.00 3.85
144 145 1.742768 GGATCTCAGGCCGAATCGT 59.257 57.895 0.82 0.00 0.00 3.73
145 146 4.663444 GGATCTCAGGCCGAATCG 57.337 61.111 0.00 0.00 0.00 3.34
153 154 3.457625 CTGGCAGCCGGATCTCAGG 62.458 68.421 16.28 0.00 29.82 3.86
154 155 2.108566 CTGGCAGCCGGATCTCAG 59.891 66.667 16.28 4.81 29.82 3.35
155 156 3.473647 CCTGGCAGCCGGATCTCA 61.474 66.667 23.25 0.00 29.82 3.27
156 157 2.447586 GATCCTGGCAGCCGGATCTC 62.448 65.000 34.95 23.32 43.49 2.75
157 158 2.447379 ATCCTGGCAGCCGGATCT 60.447 61.111 23.25 7.18 33.88 2.75
158 159 2.031768 GATCCTGGCAGCCGGATC 59.968 66.667 32.05 32.05 41.98 3.36
159 160 3.933722 CGATCCTGGCAGCCGGAT 61.934 66.667 27.94 27.94 38.75 4.18
163 164 2.751436 TTTGCGATCCTGGCAGCC 60.751 61.111 9.56 3.66 42.12 4.85
164 165 2.768492 CCTTTGCGATCCTGGCAGC 61.768 63.158 9.56 0.00 42.12 5.25
165 166 0.677731 TTCCTTTGCGATCCTGGCAG 60.678 55.000 7.75 7.75 42.12 4.85
166 167 0.251121 TTTCCTTTGCGATCCTGGCA 60.251 50.000 0.00 0.00 38.93 4.92
167 168 1.066152 GATTTCCTTTGCGATCCTGGC 59.934 52.381 0.00 0.00 0.00 4.85
168 169 1.331756 CGATTTCCTTTGCGATCCTGG 59.668 52.381 0.00 0.00 0.00 4.45
169 170 2.279741 TCGATTTCCTTTGCGATCCTG 58.720 47.619 0.00 0.00 0.00 3.86
170 171 2.691409 TCGATTTCCTTTGCGATCCT 57.309 45.000 0.00 0.00 0.00 3.24
171 172 3.561725 AGATTCGATTTCCTTTGCGATCC 59.438 43.478 0.00 0.00 32.38 3.36
172 173 4.802876 AGATTCGATTTCCTTTGCGATC 57.197 40.909 0.00 0.00 32.38 3.69
173 174 5.276868 CGTTAGATTCGATTTCCTTTGCGAT 60.277 40.000 0.00 0.00 32.38 4.58
174 175 4.032445 CGTTAGATTCGATTTCCTTTGCGA 59.968 41.667 0.00 0.00 0.00 5.10
175 176 4.032445 TCGTTAGATTCGATTTCCTTTGCG 59.968 41.667 0.00 0.00 32.30 4.85
176 177 5.256352 GTCGTTAGATTCGATTTCCTTTGC 58.744 41.667 0.00 0.00 39.45 3.68
177 178 5.220605 GGGTCGTTAGATTCGATTTCCTTTG 60.221 44.000 0.00 0.00 39.45 2.77
178 179 4.874396 GGGTCGTTAGATTCGATTTCCTTT 59.126 41.667 0.00 0.00 39.45 3.11
179 180 4.081309 TGGGTCGTTAGATTCGATTTCCTT 60.081 41.667 0.00 0.00 39.45 3.36
180 181 3.449737 TGGGTCGTTAGATTCGATTTCCT 59.550 43.478 0.00 0.00 39.45 3.36
181 182 3.788937 TGGGTCGTTAGATTCGATTTCC 58.211 45.455 0.00 0.00 39.45 3.13
182 183 6.401153 GCATATGGGTCGTTAGATTCGATTTC 60.401 42.308 4.56 0.00 39.45 2.17
183 184 5.408604 GCATATGGGTCGTTAGATTCGATTT 59.591 40.000 4.56 0.00 39.45 2.17
184 185 4.929808 GCATATGGGTCGTTAGATTCGATT 59.070 41.667 4.56 0.00 39.45 3.34
185 186 4.220821 AGCATATGGGTCGTTAGATTCGAT 59.779 41.667 4.56 0.00 39.45 3.59
186 187 3.572682 AGCATATGGGTCGTTAGATTCGA 59.427 43.478 4.56 0.00 34.91 3.71
187 188 3.914312 AGCATATGGGTCGTTAGATTCG 58.086 45.455 4.56 0.00 0.00 3.34
197 198 3.144506 CATTCACCAGAGCATATGGGTC 58.855 50.000 4.56 0.88 42.48 4.46
198 199 2.511218 ACATTCACCAGAGCATATGGGT 59.489 45.455 4.56 0.00 42.48 4.51
199 200 2.882761 CACATTCACCAGAGCATATGGG 59.117 50.000 4.56 0.00 42.48 4.00
200 201 2.882761 CCACATTCACCAGAGCATATGG 59.117 50.000 4.56 0.70 43.87 2.74
201 202 2.882761 CCCACATTCACCAGAGCATATG 59.117 50.000 0.00 0.00 0.00 1.78
202 203 2.779430 TCCCACATTCACCAGAGCATAT 59.221 45.455 0.00 0.00 0.00 1.78
203 204 2.171237 CTCCCACATTCACCAGAGCATA 59.829 50.000 0.00 0.00 0.00 3.14
204 205 0.994247 TCCCACATTCACCAGAGCAT 59.006 50.000 0.00 0.00 0.00 3.79
205 206 0.325933 CTCCCACATTCACCAGAGCA 59.674 55.000 0.00 0.00 0.00 4.26
206 207 1.028868 GCTCCCACATTCACCAGAGC 61.029 60.000 0.00 0.00 39.86 4.09
207 208 0.617413 AGCTCCCACATTCACCAGAG 59.383 55.000 0.00 0.00 0.00 3.35
208 209 0.615331 GAGCTCCCACATTCACCAGA 59.385 55.000 0.87 0.00 0.00 3.86
209 210 0.742281 CGAGCTCCCACATTCACCAG 60.742 60.000 8.47 0.00 0.00 4.00
210 211 1.296392 CGAGCTCCCACATTCACCA 59.704 57.895 8.47 0.00 0.00 4.17
211 212 1.450312 CCGAGCTCCCACATTCACC 60.450 63.158 8.47 0.00 0.00 4.02
212 213 0.321653 AACCGAGCTCCCACATTCAC 60.322 55.000 8.47 0.00 0.00 3.18
213 214 0.400213 AAACCGAGCTCCCACATTCA 59.600 50.000 8.47 0.00 0.00 2.57
214 215 1.534729 AAAACCGAGCTCCCACATTC 58.465 50.000 8.47 0.00 0.00 2.67
215 216 2.224670 TGTAAAACCGAGCTCCCACATT 60.225 45.455 8.47 0.05 0.00 2.71
216 217 1.349688 TGTAAAACCGAGCTCCCACAT 59.650 47.619 8.47 0.00 0.00 3.21
217 218 0.759959 TGTAAAACCGAGCTCCCACA 59.240 50.000 8.47 0.62 0.00 4.17
218 219 1.154197 GTGTAAAACCGAGCTCCCAC 58.846 55.000 8.47 0.47 0.00 4.61
219 220 0.759959 TGTGTAAAACCGAGCTCCCA 59.240 50.000 8.47 0.00 0.00 4.37
220 221 1.439679 CTGTGTAAAACCGAGCTCCC 58.560 55.000 8.47 0.00 0.00 4.30
221 222 0.796927 GCTGTGTAAAACCGAGCTCC 59.203 55.000 8.47 0.00 0.00 4.70
222 223 1.727335 GAGCTGTGTAAAACCGAGCTC 59.273 52.381 2.73 2.73 46.41 4.09
223 224 1.344763 AGAGCTGTGTAAAACCGAGCT 59.655 47.619 0.00 0.00 42.69 4.09
224 225 1.461127 CAGAGCTGTGTAAAACCGAGC 59.539 52.381 1.91 0.00 0.00 5.03
225 226 2.755650 ACAGAGCTGTGTAAAACCGAG 58.244 47.619 15.99 0.00 43.11 4.63
226 227 2.902705 ACAGAGCTGTGTAAAACCGA 57.097 45.000 15.99 0.00 43.11 4.69
227 228 4.056050 AGTTACAGAGCTGTGTAAAACCG 58.944 43.478 31.25 0.00 42.99 4.44
228 229 6.453092 TCTAGTTACAGAGCTGTGTAAAACC 58.547 40.000 31.25 21.33 42.99 3.27
229 230 7.326547 GTCTCTAGTTACAGAGCTGTGTAAAAC 59.673 40.741 31.25 24.21 42.99 2.43
230 231 7.013942 TGTCTCTAGTTACAGAGCTGTGTAAAA 59.986 37.037 31.25 22.49 42.99 1.52
231 232 6.489022 TGTCTCTAGTTACAGAGCTGTGTAAA 59.511 38.462 31.25 19.26 42.99 2.01
232 233 6.002082 TGTCTCTAGTTACAGAGCTGTGTAA 58.998 40.000 27.42 27.42 44.63 2.41
233 234 5.557866 TGTCTCTAGTTACAGAGCTGTGTA 58.442 41.667 19.08 19.08 44.63 2.90
234 235 4.399219 TGTCTCTAGTTACAGAGCTGTGT 58.601 43.478 21.34 21.34 44.63 3.72
235 236 5.378292 TTGTCTCTAGTTACAGAGCTGTG 57.622 43.478 9.74 9.74 44.63 3.66
236 237 6.183360 GCTATTGTCTCTAGTTACAGAGCTGT 60.183 42.308 8.35 8.35 46.87 4.40
237 238 6.205784 GCTATTGTCTCTAGTTACAGAGCTG 58.794 44.000 18.23 0.00 41.61 4.24
238 239 5.300792 GGCTATTGTCTCTAGTTACAGAGCT 59.699 44.000 21.28 0.00 41.61 4.09
239 240 5.067936 TGGCTATTGTCTCTAGTTACAGAGC 59.932 44.000 17.76 17.76 41.61 4.09
240 241 6.701145 TGGCTATTGTCTCTAGTTACAGAG 57.299 41.667 5.78 5.78 42.96 3.35
241 242 7.476540 TTTGGCTATTGTCTCTAGTTACAGA 57.523 36.000 0.00 0.00 0.00 3.41
242 243 8.607459 CATTTTGGCTATTGTCTCTAGTTACAG 58.393 37.037 0.00 0.00 0.00 2.74
243 244 7.065803 GCATTTTGGCTATTGTCTCTAGTTACA 59.934 37.037 0.00 0.00 0.00 2.41
244 245 7.410485 GCATTTTGGCTATTGTCTCTAGTTAC 58.590 38.462 0.00 0.00 0.00 2.50
245 246 6.542370 GGCATTTTGGCTATTGTCTCTAGTTA 59.458 38.462 0.00 0.00 40.14 2.24
246 247 5.358160 GGCATTTTGGCTATTGTCTCTAGTT 59.642 40.000 0.00 0.00 40.14 2.24
247 248 4.884164 GGCATTTTGGCTATTGTCTCTAGT 59.116 41.667 0.00 0.00 40.14 2.57
248 249 4.883585 TGGCATTTTGGCTATTGTCTCTAG 59.116 41.667 2.66 0.00 44.10 2.43
337 338 9.353999 GTGTTATTTTGACAAGAAAAACTGAGT 57.646 29.630 8.06 0.00 29.78 3.41
387 388 1.141254 TGCCTCCGGTTTGACTAACAA 59.859 47.619 0.00 0.00 38.55 2.83
425 426 4.219919 CCACGGGGGTAATTTTGGAATAT 58.780 43.478 0.00 0.00 0.00 1.28
479 510 2.108976 CTCCTGGTGTGTGCGTGT 59.891 61.111 0.00 0.00 0.00 4.49
505 536 4.373116 GACGGCTGGTTCCTCGCA 62.373 66.667 0.00 0.00 0.00 5.10
543 577 1.547755 AGGGTCAGAGGGAGGGAGA 60.548 63.158 0.00 0.00 0.00 3.71
547 583 1.075600 GGAGAGGGTCAGAGGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
593 629 4.467107 GAGGAGGAGGAGGGCGGT 62.467 72.222 0.00 0.00 0.00 5.68
600 644 2.182858 GAACCCAGGGAGGAGGAGGA 62.183 65.000 14.54 0.00 41.22 3.71
620 664 2.771762 GAGGGAGGAGCCAGCCAT 60.772 66.667 0.00 0.00 38.95 4.40
628 672 1.454847 CGTCAGAGGGAGGGAGGAG 60.455 68.421 0.00 0.00 0.00 3.69
629 673 2.684104 CGTCAGAGGGAGGGAGGA 59.316 66.667 0.00 0.00 0.00 3.71
630 674 3.151022 GCGTCAGAGGGAGGGAGG 61.151 72.222 0.00 0.00 32.04 4.30
631 675 1.743321 GATGCGTCAGAGGGAGGGAG 61.743 65.000 0.00 0.00 35.17 4.30
632 676 1.758514 GATGCGTCAGAGGGAGGGA 60.759 63.158 0.00 0.00 36.16 4.20
635 679 2.415010 CCGATGCGTCAGAGGGAG 59.585 66.667 6.75 0.00 0.00 4.30
636 680 3.838271 GCCGATGCGTCAGAGGGA 61.838 66.667 6.75 0.00 0.00 4.20
638 682 2.279120 GAGCCGATGCGTCAGAGG 60.279 66.667 6.75 0.12 44.33 3.69
695 792 3.224324 GACGAGCTGGGGCGGATA 61.224 66.667 0.00 0.00 44.37 2.59
701 798 2.765807 ATCTGGGACGAGCTGGGG 60.766 66.667 0.00 0.00 0.00 4.96
702 799 2.025767 CTGATCTGGGACGAGCTGGG 62.026 65.000 0.00 0.00 0.00 4.45
703 800 1.326213 ACTGATCTGGGACGAGCTGG 61.326 60.000 0.00 0.00 0.00 4.85
704 801 0.534412 AACTGATCTGGGACGAGCTG 59.466 55.000 0.00 0.00 0.00 4.24
705 802 1.066573 CAAACTGATCTGGGACGAGCT 60.067 52.381 4.49 0.00 0.00 4.09
706 803 1.363744 CAAACTGATCTGGGACGAGC 58.636 55.000 4.49 0.00 0.00 5.03
707 804 1.363744 GCAAACTGATCTGGGACGAG 58.636 55.000 4.49 0.00 0.00 4.18
708 805 0.036388 GGCAAACTGATCTGGGACGA 60.036 55.000 4.49 0.00 0.00 4.20
709 806 1.361668 CGGCAAACTGATCTGGGACG 61.362 60.000 4.49 3.63 0.00 4.79
710 807 1.026718 CCGGCAAACTGATCTGGGAC 61.027 60.000 4.49 0.00 0.00 4.46
711 808 1.299648 CCGGCAAACTGATCTGGGA 59.700 57.895 4.49 0.00 0.00 4.37
712 809 0.251916 TACCGGCAAACTGATCTGGG 59.748 55.000 0.00 0.00 0.00 4.45
713 810 2.213499 GATACCGGCAAACTGATCTGG 58.787 52.381 0.00 0.00 0.00 3.86
714 811 2.158900 AGGATACCGGCAAACTGATCTG 60.159 50.000 0.00 0.00 37.17 2.90
715 812 2.103263 GAGGATACCGGCAAACTGATCT 59.897 50.000 0.00 0.00 37.17 2.75
724 821 2.134287 GGAGCAGAGGATACCGGCA 61.134 63.158 0.00 0.00 32.22 5.69
730 827 2.421952 GGTTGCAATGGAGCAGAGGATA 60.422 50.000 0.59 0.00 46.54 2.59
731 828 1.684248 GGTTGCAATGGAGCAGAGGAT 60.684 52.381 0.59 0.00 46.54 3.24
889 992 1.480789 TTGCCGCTGGAGATGTACTA 58.519 50.000 0.00 0.00 0.00 1.82
898 1001 0.179015 TTGTACCTTTTGCCGCTGGA 60.179 50.000 0.00 0.00 0.00 3.86
937 1040 8.850156 AGACTGCACTTACAATGAAAAATAACT 58.150 29.630 0.00 0.00 0.00 2.24
961 1064 8.594881 AAACACACAAACACAACAAATTTAGA 57.405 26.923 0.00 0.00 0.00 2.10
962 1065 8.491152 TGAAACACACAAACACAACAAATTTAG 58.509 29.630 0.00 0.00 0.00 1.85
963 1066 8.365399 TGAAACACACAAACACAACAAATTTA 57.635 26.923 0.00 0.00 0.00 1.40
1004 1112 9.922305 GAACATCTATTTCTACTTTGAAATCGG 57.078 33.333 5.85 2.56 43.21 4.18
1049 1157 4.448210 TCTGTAAACTCTTTTGCCGTCTT 58.552 39.130 0.00 0.00 0.00 3.01
1260 5926 5.278315 GGTCACACCAAACCTCACTATTTTC 60.278 44.000 0.00 0.00 38.42 2.29
1288 5954 3.509575 TCCTTGTGTTGCTGTTTGTTCTT 59.490 39.130 0.00 0.00 0.00 2.52
1321 5987 1.956869 TCCATATCCTCGGCCATGAT 58.043 50.000 2.24 3.53 0.00 2.45
1449 6115 1.002366 CCTTTGACTCCGCATTCTCG 58.998 55.000 0.00 0.00 0.00 4.04
1477 6146 5.278022 GCTCGACATTTTTCTCCTTTGACTT 60.278 40.000 0.00 0.00 0.00 3.01
1719 6405 5.699001 AGTGTCACTATATTGCGTGTCAAAA 59.301 36.000 2.87 0.00 38.34 2.44
1751 6437 2.257409 ATCGGTGCAACTAGCCCTGG 62.257 60.000 0.00 0.00 44.83 4.45
1789 6475 2.093869 TCGGTAACTTGGAGGCATGTAC 60.094 50.000 0.00 0.00 0.00 2.90
2067 6756 1.754226 TCCCTTTGCAAGCGTTCTTTT 59.246 42.857 0.00 0.00 0.00 2.27
2275 6967 5.182950 TGAACAACCTATCGAAAACATGCAT 59.817 36.000 0.00 0.00 0.00 3.96
2287 6979 5.643379 TTGAAGGCAATGAACAACCTATC 57.357 39.130 0.00 0.00 0.00 2.08
2465 7181 6.693315 ACCATACCCAATTTTCTGTATTCG 57.307 37.500 0.00 0.00 0.00 3.34
2466 7182 8.062065 TGAACCATACCCAATTTTCTGTATTC 57.938 34.615 0.00 0.00 0.00 1.75
2506 7222 3.624777 CTTGTGGTTCTCCAATAGCCAT 58.375 45.455 0.00 0.00 46.15 4.40
2747 7464 7.501892 TGTGATGCATGTTCAAATAGGCTATTA 59.498 33.333 19.53 4.74 0.00 0.98
2796 7513 6.873076 ACTCAACTTTTGTCATTGCTGAAAAA 59.127 30.769 0.00 0.00 36.92 1.94


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

AutoCloner maintained by Alex Coulton.