Multiple sequence alignment - TraesCS5B01G152600

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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 TraesCS5B01G152600 chr5B 100.000 4996 0 0 1 4996 281835969 281840964 0.000000e+00 9226
1 TraesCS5B01G152600 chr5B 97.238 362 8 2 1 361 436473897 436473537 3.310000e-171 612
2 TraesCS5B01G152600 chr5D 98.302 4298 54 9 716 4996 247610263 247614558 0.000000e+00 7515
3 TraesCS5B01G152600 chr5D 91.404 349 12 3 369 717 247609772 247610102 3.520000e-126 462
4 TraesCS5B01G152600 chr5A 96.826 3151 72 12 1869 4996 331400686 331403831 0.000000e+00 5240
5 TraesCS5B01G152600 chr5A 93.667 1279 56 12 614 1869 331399380 331400656 0.000000e+00 1890
6 TraesCS5B01G152600 chr5A 96.104 231 8 1 369 598 331398746 331398976 4.720000e-100 375
7 TraesCS5B01G152600 chr7A 98.066 362 6 1 1 361 121921431 121921792 3.280000e-176 628
8 TraesCS5B01G152600 chr2A 97.514 362 7 2 1 361 148617939 148618299 7.110000e-173 617
9 TraesCS5B01G152600 chr2A 96.961 362 9 2 1 361 752756238 752756598 1.540000e-169 606
10 TraesCS5B01G152600 chr4B 97.238 362 9 1 1 361 649620568 649620207 3.310000e-171 612
11 TraesCS5B01G152600 chr4B 96.685 362 11 1 1 361 655788321 655787960 7.160000e-168 601
12 TraesCS5B01G152600 chr2B 97.238 362 8 2 1 361 440601285 440600925 3.310000e-171 612
13 TraesCS5B01G152600 chr2B 96.961 362 10 1 1 361 364340044 364340405 1.540000e-169 606
14 TraesCS5B01G152600 chr7B 96.961 362 9 2 1 361 133435309 133435669 1.540000e-169 606
15 TraesCS5B01G152600 chr3A 76.772 917 143 54 2221 3083 47849893 47850793 2.740000e-122 449
16 TraesCS5B01G152600 chr3A 82.804 378 45 12 3544 3908 47851273 47851643 2.240000e-83 320
17 TraesCS5B01G152600 chr3A 88.837 215 24 0 1001 1215 47847920 47848134 1.070000e-66 265
18 TraesCS5B01G152600 chr3A 81.749 263 38 9 3185 3446 47850912 47851165 1.410000e-50 211
19 TraesCS5B01G152600 chr3D 82.114 369 49 13 3544 3908 37777978 37778333 2.920000e-77 300
20 TraesCS5B01G152600 chr3D 87.923 207 25 0 1001 1207 37774353 37774559 1.390000e-60 244
21 TraesCS5B01G152600 chr3D 82.510 263 36 9 3185 3446 37777617 37777870 6.510000e-54 222


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 TraesCS5B01G152600 chr5B 281835969 281840964 4995 False 9226.000000 9226 100.000000 1 4996 1 chr5B.!!$F1 4995
1 TraesCS5B01G152600 chr5D 247609772 247614558 4786 False 3988.500000 7515 94.853000 369 4996 2 chr5D.!!$F1 4627
2 TraesCS5B01G152600 chr5A 331398746 331403831 5085 False 2501.666667 5240 95.532333 369 4996 3 chr5A.!!$F1 4627
3 TraesCS5B01G152600 chr3A 47847920 47851643 3723 False 311.250000 449 82.540500 1001 3908 4 chr3A.!!$F1 2907
4 TraesCS5B01G152600 chr3D 37774353 37778333 3980 False 255.333333 300 84.182333 1001 3908 3 chr3D.!!$F1 2907

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
64 65 0.036577 GAGGCAGCAGCTCTTCTTCA 60.037 55.0 0.00 0.0 41.70 3.02 F
286 287 0.037975 GGACCTTAGCGTCACCGAAA 60.038 55.0 3.94 0.0 34.24 3.46 F
293 294 0.179067 AGCGTCACCGAAAAAGGTCA 60.179 50.0 0.00 0.0 43.89 4.02 F
294 295 0.234884 GCGTCACCGAAAAAGGTCAG 59.765 55.0 0.00 0.0 43.89 3.51 F
329 330 0.248289 GGAACGAGGTCAAATCGGGA 59.752 55.0 0.00 0.0 44.36 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 3421 0.543277 ACCATCCAGCATGTCGATGT 59.457 50.000 13.97 4.35 34.32 3.06 R
2250 3996 2.541556 GTCCGTCATAAGCCTCTTGAC 58.458 52.381 0.00 0.00 37.10 3.18 R
2336 4082 1.181098 CCTTTGTTCCTGCCAGGTGG 61.181 60.000 11.27 1.45 36.53 4.61 R
3437 5244 5.473039 AGAGGCAGCAATGTTTTTACATTC 58.527 37.500 0.00 0.00 38.16 2.67 R
4125 5964 4.522789 TGGAAGTTGCCAGAAAAGGATTAC 59.477 41.667 0.00 0.00 33.10 1.89 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 3.027533 TGGAGAGGATTTGAGGGGG 57.972 57.895 0.00 0.00 0.00 5.40
32 33 3.732849 GGGGGAGCTTGAGGGGTG 61.733 72.222 0.00 0.00 0.00 4.61
33 34 2.610859 GGGGAGCTTGAGGGGTGA 60.611 66.667 0.00 0.00 0.00 4.02
34 35 2.674220 GGGGAGCTTGAGGGGTGAG 61.674 68.421 0.00 0.00 0.00 3.51
35 36 1.613630 GGGAGCTTGAGGGGTGAGA 60.614 63.158 0.00 0.00 0.00 3.27
36 37 1.621672 GGGAGCTTGAGGGGTGAGAG 61.622 65.000 0.00 0.00 0.00 3.20
37 38 0.616111 GGAGCTTGAGGGGTGAGAGA 60.616 60.000 0.00 0.00 0.00 3.10
38 39 0.823460 GAGCTTGAGGGGTGAGAGAG 59.177 60.000 0.00 0.00 0.00 3.20
39 40 0.411452 AGCTTGAGGGGTGAGAGAGA 59.589 55.000 0.00 0.00 0.00 3.10
40 41 0.823460 GCTTGAGGGGTGAGAGAGAG 59.177 60.000 0.00 0.00 0.00 3.20
41 42 1.894978 GCTTGAGGGGTGAGAGAGAGT 60.895 57.143 0.00 0.00 0.00 3.24
42 43 1.824230 CTTGAGGGGTGAGAGAGAGTG 59.176 57.143 0.00 0.00 0.00 3.51
43 44 0.040351 TGAGGGGTGAGAGAGAGTGG 59.960 60.000 0.00 0.00 0.00 4.00
44 45 0.686112 GAGGGGTGAGAGAGAGTGGG 60.686 65.000 0.00 0.00 0.00 4.61
45 46 1.687493 GGGGTGAGAGAGAGTGGGG 60.687 68.421 0.00 0.00 0.00 4.96
46 47 1.388531 GGGTGAGAGAGAGTGGGGA 59.611 63.158 0.00 0.00 0.00 4.81
47 48 0.686112 GGGTGAGAGAGAGTGGGGAG 60.686 65.000 0.00 0.00 0.00 4.30
48 49 0.686112 GGTGAGAGAGAGTGGGGAGG 60.686 65.000 0.00 0.00 0.00 4.30
49 50 1.000993 TGAGAGAGAGTGGGGAGGC 59.999 63.158 0.00 0.00 0.00 4.70
50 51 1.000993 GAGAGAGAGTGGGGAGGCA 59.999 63.158 0.00 0.00 0.00 4.75
51 52 1.001503 AGAGAGAGTGGGGAGGCAG 59.998 63.158 0.00 0.00 0.00 4.85
52 53 2.686835 AGAGAGTGGGGAGGCAGC 60.687 66.667 0.00 0.00 0.00 5.25
53 54 3.005539 GAGAGTGGGGAGGCAGCA 61.006 66.667 0.00 0.00 0.00 4.41
54 55 3.007920 AGAGTGGGGAGGCAGCAG 61.008 66.667 0.00 0.00 0.00 4.24
55 56 4.792804 GAGTGGGGAGGCAGCAGC 62.793 72.222 0.00 0.00 41.10 5.25
57 58 4.792804 GTGGGGAGGCAGCAGCTC 62.793 72.222 0.00 0.00 41.70 4.09
59 60 3.726144 GGGGAGGCAGCAGCTCTT 61.726 66.667 0.00 0.00 41.70 2.85
60 61 2.124778 GGGAGGCAGCAGCTCTTC 60.125 66.667 0.00 0.00 41.70 2.87
61 62 2.668120 GGGAGGCAGCAGCTCTTCT 61.668 63.158 0.00 0.00 41.70 2.85
62 63 1.299321 GGAGGCAGCAGCTCTTCTT 59.701 57.895 0.00 0.00 41.70 2.52
63 64 0.744057 GGAGGCAGCAGCTCTTCTTC 60.744 60.000 0.00 0.00 41.70 2.87
64 65 0.036577 GAGGCAGCAGCTCTTCTTCA 60.037 55.000 0.00 0.00 41.70 3.02
65 66 0.399454 AGGCAGCAGCTCTTCTTCAA 59.601 50.000 0.00 0.00 41.70 2.69
66 67 0.803740 GGCAGCAGCTCTTCTTCAAG 59.196 55.000 0.00 0.00 41.70 3.02
67 68 0.168568 GCAGCAGCTCTTCTTCAAGC 59.831 55.000 0.00 0.00 38.84 4.01
69 70 1.733360 CAGCAGCTCTTCTTCAAGCTC 59.267 52.381 0.00 0.00 45.57 4.09
70 71 0.720590 GCAGCTCTTCTTCAAGCTCG 59.279 55.000 0.00 0.00 45.57 5.03
71 72 1.357907 CAGCTCTTCTTCAAGCTCGG 58.642 55.000 0.00 0.00 45.57 4.63
72 73 0.248843 AGCTCTTCTTCAAGCTCGGG 59.751 55.000 0.00 0.00 45.57 5.14
73 74 1.365368 GCTCTTCTTCAAGCTCGGGC 61.365 60.000 0.00 0.00 35.60 6.13
83 84 4.883354 GCTCGGGCTGGATTGGGG 62.883 72.222 0.00 0.00 35.22 4.96
84 85 3.089874 CTCGGGCTGGATTGGGGA 61.090 66.667 0.00 0.00 0.00 4.81
85 86 2.612430 TCGGGCTGGATTGGGGAA 60.612 61.111 0.00 0.00 0.00 3.97
86 87 2.210144 CTCGGGCTGGATTGGGGAAA 62.210 60.000 0.00 0.00 0.00 3.13
87 88 1.754234 CGGGCTGGATTGGGGAAAG 60.754 63.158 0.00 0.00 0.00 2.62
88 89 1.388133 GGGCTGGATTGGGGAAAGT 59.612 57.895 0.00 0.00 0.00 2.66
89 90 0.972471 GGGCTGGATTGGGGAAAGTG 60.972 60.000 0.00 0.00 0.00 3.16
90 91 0.251787 GGCTGGATTGGGGAAAGTGT 60.252 55.000 0.00 0.00 0.00 3.55
91 92 0.890683 GCTGGATTGGGGAAAGTGTG 59.109 55.000 0.00 0.00 0.00 3.82
92 93 1.823250 GCTGGATTGGGGAAAGTGTGT 60.823 52.381 0.00 0.00 0.00 3.72
93 94 1.888512 CTGGATTGGGGAAAGTGTGTG 59.111 52.381 0.00 0.00 0.00 3.82
94 95 1.256812 GGATTGGGGAAAGTGTGTGG 58.743 55.000 0.00 0.00 0.00 4.17
95 96 1.256812 GATTGGGGAAAGTGTGTGGG 58.743 55.000 0.00 0.00 0.00 4.61
96 97 0.178935 ATTGGGGAAAGTGTGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
97 98 1.585651 TTGGGGAAAGTGTGTGGGGT 61.586 55.000 0.00 0.00 0.00 4.95
98 99 1.530655 GGGGAAAGTGTGTGGGGTG 60.531 63.158 0.00 0.00 0.00 4.61
99 100 1.530655 GGGAAAGTGTGTGGGGTGG 60.531 63.158 0.00 0.00 0.00 4.61
100 101 1.530655 GGAAAGTGTGTGGGGTGGG 60.531 63.158 0.00 0.00 0.00 4.61
101 102 1.534697 GAAAGTGTGTGGGGTGGGA 59.465 57.895 0.00 0.00 0.00 4.37
102 103 0.822121 GAAAGTGTGTGGGGTGGGAC 60.822 60.000 0.00 0.00 0.00 4.46
103 104 2.292785 AAAGTGTGTGGGGTGGGACC 62.293 60.000 0.00 0.00 37.60 4.46
114 115 3.885814 TGGGACCCACACACTCTC 58.114 61.111 9.95 0.00 0.00 3.20
115 116 1.841556 TGGGACCCACACACTCTCC 60.842 63.158 9.95 0.00 0.00 3.71
116 117 2.593956 GGGACCCACACACTCTCCC 61.594 68.421 5.33 0.00 33.97 4.30
117 118 2.657237 GACCCACACACTCTCCCG 59.343 66.667 0.00 0.00 0.00 5.14
118 119 2.923035 ACCCACACACTCTCCCGG 60.923 66.667 0.00 0.00 0.00 5.73
119 120 2.923035 CCCACACACTCTCCCGGT 60.923 66.667 0.00 0.00 0.00 5.28
120 121 2.343758 CCACACACTCTCCCGGTG 59.656 66.667 0.00 0.00 40.19 4.94
121 122 2.343758 CACACACTCTCCCGGTGG 59.656 66.667 0.00 0.00 38.83 4.61
122 123 2.923035 ACACACTCTCCCGGTGGG 60.923 66.667 0.00 0.00 46.11 4.61
138 139 1.205966 TGGGGTTATCCACTTACCGG 58.794 55.000 0.00 0.00 38.13 5.28
139 140 0.471191 GGGGTTATCCACTTACCGGG 59.529 60.000 6.32 0.00 37.22 5.73
140 141 0.471191 GGGTTATCCACTTACCGGGG 59.529 60.000 6.32 0.00 35.00 5.73
141 142 0.179037 GGTTATCCACTTACCGGGGC 60.179 60.000 6.32 0.00 0.00 5.80
142 143 0.179037 GTTATCCACTTACCGGGGCC 60.179 60.000 6.32 0.00 0.00 5.80
143 144 0.620990 TTATCCACTTACCGGGGCCA 60.621 55.000 6.32 0.00 0.00 5.36
144 145 1.052124 TATCCACTTACCGGGGCCAG 61.052 60.000 6.32 0.00 0.00 4.85
145 146 2.833151 ATCCACTTACCGGGGCCAGA 62.833 60.000 6.32 0.00 0.00 3.86
146 147 2.267961 CACTTACCGGGGCCAGAC 59.732 66.667 6.32 0.00 0.00 3.51
147 148 2.203877 ACTTACCGGGGCCAGACA 60.204 61.111 6.32 0.00 0.00 3.41
148 149 2.267961 CTTACCGGGGCCAGACAC 59.732 66.667 6.32 0.00 0.00 3.67
149 150 3.324108 TTACCGGGGCCAGACACC 61.324 66.667 6.32 0.00 0.00 4.16
150 151 4.642488 TACCGGGGCCAGACACCA 62.642 66.667 6.32 0.00 0.00 4.17
155 156 4.035102 GGGCCAGACACCAGGGAC 62.035 72.222 4.39 0.00 0.00 4.46
156 157 3.249189 GGCCAGACACCAGGGACA 61.249 66.667 0.00 0.00 0.00 4.02
157 158 2.032681 GCCAGACACCAGGGACAC 59.967 66.667 0.00 0.00 0.00 3.67
158 159 2.520536 GCCAGACACCAGGGACACT 61.521 63.158 0.00 0.00 0.00 3.55
166 167 2.047844 CAGGGACACTGGCGTCTG 60.048 66.667 0.00 0.00 43.70 3.51
167 168 3.314331 AGGGACACTGGCGTCTGG 61.314 66.667 0.00 0.00 36.12 3.86
184 185 3.365265 GCCCCTTTGCCACGTCAG 61.365 66.667 0.00 0.00 0.00 3.51
185 186 3.365265 CCCCTTTGCCACGTCAGC 61.365 66.667 0.04 0.04 0.00 4.26
186 187 2.594303 CCCTTTGCCACGTCAGCA 60.594 61.111 5.70 5.70 38.81 4.41
187 188 2.620112 CCCTTTGCCACGTCAGCAG 61.620 63.158 9.53 0.58 42.17 4.24
188 189 2.620112 CCTTTGCCACGTCAGCAGG 61.620 63.158 9.53 5.63 42.17 4.85
189 190 1.893808 CTTTGCCACGTCAGCAGGT 60.894 57.895 9.53 0.00 42.17 4.00
190 191 1.845809 CTTTGCCACGTCAGCAGGTC 61.846 60.000 9.53 0.00 42.17 3.85
191 192 2.601194 TTTGCCACGTCAGCAGGTCA 62.601 55.000 9.53 0.00 42.17 4.02
192 193 2.280797 GCCACGTCAGCAGGTCAA 60.281 61.111 2.25 0.00 0.00 3.18
193 194 2.607892 GCCACGTCAGCAGGTCAAC 61.608 63.158 2.25 0.00 0.00 3.18
194 195 2.310233 CCACGTCAGCAGGTCAACG 61.310 63.158 3.15 3.15 40.77 4.10
195 196 2.029073 ACGTCAGCAGGTCAACGG 59.971 61.111 8.49 0.00 39.35 4.44
196 197 2.738521 CGTCAGCAGGTCAACGGG 60.739 66.667 0.00 0.00 0.00 5.28
197 198 3.050275 GTCAGCAGGTCAACGGGC 61.050 66.667 0.00 0.00 0.00 6.13
198 199 3.555324 TCAGCAGGTCAACGGGCA 61.555 61.111 0.00 0.00 0.00 5.36
199 200 3.052082 CAGCAGGTCAACGGGCAG 61.052 66.667 0.00 0.00 0.00 4.85
200 201 4.335647 AGCAGGTCAACGGGCAGG 62.336 66.667 0.00 0.00 0.00 4.85
253 254 4.124351 CCCGGCGTCTGCTTCGTA 62.124 66.667 6.01 0.00 42.25 3.43
254 255 2.126228 CCGGCGTCTGCTTCGTAA 60.126 61.111 6.01 0.00 42.25 3.18
255 256 2.442188 CCGGCGTCTGCTTCGTAAC 61.442 63.158 6.01 0.00 42.25 2.50
256 257 2.442188 CGGCGTCTGCTTCGTAACC 61.442 63.158 0.00 0.00 42.25 2.85
257 258 2.098831 GGCGTCTGCTTCGTAACCC 61.099 63.158 0.00 0.00 42.25 4.11
258 259 1.373748 GCGTCTGCTTCGTAACCCA 60.374 57.895 0.00 0.00 38.39 4.51
259 260 0.947180 GCGTCTGCTTCGTAACCCAA 60.947 55.000 0.00 0.00 38.39 4.12
260 261 1.504359 CGTCTGCTTCGTAACCCAAA 58.496 50.000 0.00 0.00 0.00 3.28
261 262 1.193874 CGTCTGCTTCGTAACCCAAAC 59.806 52.381 0.00 0.00 0.00 2.93
262 263 1.193874 GTCTGCTTCGTAACCCAAACG 59.806 52.381 0.00 0.00 41.64 3.60
263 264 0.110373 CTGCTTCGTAACCCAAACGC 60.110 55.000 0.00 0.00 40.12 4.84
264 265 1.208358 GCTTCGTAACCCAAACGCC 59.792 57.895 0.00 0.00 40.12 5.68
265 266 1.508808 GCTTCGTAACCCAAACGCCA 61.509 55.000 0.00 0.00 40.12 5.69
266 267 0.515564 CTTCGTAACCCAAACGCCAG 59.484 55.000 0.00 0.00 40.12 4.85
267 268 0.885596 TTCGTAACCCAAACGCCAGG 60.886 55.000 0.00 0.00 40.12 4.45
273 274 2.115266 CCAAACGCCAGGGACCTT 59.885 61.111 0.00 0.00 0.00 3.50
274 275 1.377229 CCAAACGCCAGGGACCTTA 59.623 57.895 0.00 0.00 0.00 2.69
275 276 0.676782 CCAAACGCCAGGGACCTTAG 60.677 60.000 0.00 0.00 0.00 2.18
276 277 1.002502 AAACGCCAGGGACCTTAGC 60.003 57.895 0.00 0.00 0.00 3.09
277 278 2.798148 AAACGCCAGGGACCTTAGCG 62.798 60.000 23.55 23.55 45.85 4.26
278 279 3.771160 CGCCAGGGACCTTAGCGT 61.771 66.667 19.25 0.00 39.76 5.07
279 280 2.187163 GCCAGGGACCTTAGCGTC 59.813 66.667 0.00 0.00 0.00 5.19
280 281 2.656069 GCCAGGGACCTTAGCGTCA 61.656 63.158 0.00 0.00 34.24 4.35
281 282 1.218316 CCAGGGACCTTAGCGTCAC 59.782 63.158 0.00 0.38 36.35 3.67
282 283 1.218316 CAGGGACCTTAGCGTCACC 59.782 63.158 0.00 0.00 36.81 4.02
283 284 2.183555 GGGACCTTAGCGTCACCG 59.816 66.667 0.00 0.00 34.24 4.94
284 285 2.345760 GGGACCTTAGCGTCACCGA 61.346 63.158 0.00 0.00 34.24 4.69
285 286 1.588082 GGACCTTAGCGTCACCGAA 59.412 57.895 3.94 0.00 34.24 4.30
286 287 0.037975 GGACCTTAGCGTCACCGAAA 60.038 55.000 3.94 0.00 34.24 3.46
287 288 1.606224 GGACCTTAGCGTCACCGAAAA 60.606 52.381 3.94 0.00 34.24 2.29
288 289 2.137523 GACCTTAGCGTCACCGAAAAA 58.862 47.619 0.00 0.00 35.63 1.94
289 290 2.140717 ACCTTAGCGTCACCGAAAAAG 58.859 47.619 0.00 0.00 35.63 2.27
290 291 1.463444 CCTTAGCGTCACCGAAAAAGG 59.537 52.381 0.00 0.00 34.60 3.11
292 293 1.787012 TAGCGTCACCGAAAAAGGTC 58.213 50.000 0.00 0.00 43.89 3.85
293 294 0.179067 AGCGTCACCGAAAAAGGTCA 60.179 50.000 0.00 0.00 43.89 4.02
294 295 0.234884 GCGTCACCGAAAAAGGTCAG 59.765 55.000 0.00 0.00 43.89 3.51
295 296 1.860676 CGTCACCGAAAAAGGTCAGA 58.139 50.000 0.00 0.00 43.89 3.27
296 297 2.206750 CGTCACCGAAAAAGGTCAGAA 58.793 47.619 0.00 0.00 43.89 3.02
297 298 2.610374 CGTCACCGAAAAAGGTCAGAAA 59.390 45.455 0.00 0.00 43.89 2.52
298 299 3.303132 CGTCACCGAAAAAGGTCAGAAAG 60.303 47.826 0.00 0.00 43.89 2.62
299 300 3.875134 GTCACCGAAAAAGGTCAGAAAGA 59.125 43.478 0.00 0.00 43.89 2.52
300 301 4.334481 GTCACCGAAAAAGGTCAGAAAGAA 59.666 41.667 0.00 0.00 43.89 2.52
301 302 4.944930 TCACCGAAAAAGGTCAGAAAGAAA 59.055 37.500 0.00 0.00 43.89 2.52
302 303 5.416326 TCACCGAAAAAGGTCAGAAAGAAAA 59.584 36.000 0.00 0.00 43.89 2.29
303 304 6.071840 TCACCGAAAAAGGTCAGAAAGAAAAA 60.072 34.615 0.00 0.00 43.89 1.94
328 329 2.763651 GGAACGAGGTCAAATCGGG 58.236 57.895 0.00 0.00 44.36 5.14
329 330 0.248289 GGAACGAGGTCAAATCGGGA 59.752 55.000 0.00 0.00 44.36 5.14
330 331 1.134491 GGAACGAGGTCAAATCGGGAT 60.134 52.381 0.00 0.00 44.36 3.85
331 332 2.629051 GAACGAGGTCAAATCGGGATT 58.371 47.619 0.00 0.00 44.36 3.01
332 333 2.781681 ACGAGGTCAAATCGGGATTT 57.218 45.000 0.89 0.89 44.36 2.17
333 334 3.899052 ACGAGGTCAAATCGGGATTTA 57.101 42.857 6.34 0.00 44.36 1.40
334 335 3.793559 ACGAGGTCAAATCGGGATTTAG 58.206 45.455 6.34 2.80 44.36 1.85
335 336 3.197116 ACGAGGTCAAATCGGGATTTAGT 59.803 43.478 6.34 0.00 44.36 2.24
336 337 4.189231 CGAGGTCAAATCGGGATTTAGTT 58.811 43.478 6.34 0.00 38.84 2.24
337 338 4.634443 CGAGGTCAAATCGGGATTTAGTTT 59.366 41.667 6.34 0.00 38.84 2.66
338 339 5.447279 CGAGGTCAAATCGGGATTTAGTTTG 60.447 44.000 6.34 0.00 38.84 2.93
339 340 4.157840 AGGTCAAATCGGGATTTAGTTTGC 59.842 41.667 6.34 0.00 38.84 3.68
340 341 4.421058 GTCAAATCGGGATTTAGTTTGCC 58.579 43.478 6.34 0.00 38.84 4.52
341 342 4.157840 GTCAAATCGGGATTTAGTTTGCCT 59.842 41.667 6.34 0.00 38.84 4.75
342 343 4.770010 TCAAATCGGGATTTAGTTTGCCTT 59.230 37.500 6.34 0.00 38.84 4.35
343 344 5.946972 TCAAATCGGGATTTAGTTTGCCTTA 59.053 36.000 6.34 0.00 38.84 2.69
344 345 6.434652 TCAAATCGGGATTTAGTTTGCCTTAA 59.565 34.615 6.34 0.00 38.84 1.85
345 346 6.451064 AATCGGGATTTAGTTTGCCTTAAG 57.549 37.500 0.00 0.00 0.00 1.85
346 347 4.266714 TCGGGATTTAGTTTGCCTTAAGG 58.733 43.478 17.81 17.81 38.53 2.69
347 348 3.380320 CGGGATTTAGTTTGCCTTAAGGG 59.620 47.826 23.06 5.18 35.18 3.95
348 349 4.350245 GGGATTTAGTTTGCCTTAAGGGT 58.650 43.478 23.06 0.00 37.43 4.34
349 350 4.401519 GGGATTTAGTTTGCCTTAAGGGTC 59.598 45.833 23.06 7.88 37.43 4.46
350 351 5.014202 GGATTTAGTTTGCCTTAAGGGTCA 58.986 41.667 23.06 10.53 37.43 4.02
351 352 5.125578 GGATTTAGTTTGCCTTAAGGGTCAG 59.874 44.000 23.06 0.00 37.43 3.51
352 353 4.986054 TTAGTTTGCCTTAAGGGTCAGA 57.014 40.909 23.06 5.99 37.43 3.27
353 354 3.876309 AGTTTGCCTTAAGGGTCAGAA 57.124 42.857 23.06 7.80 37.43 3.02
354 355 3.487372 AGTTTGCCTTAAGGGTCAGAAC 58.513 45.455 23.06 16.72 37.43 3.01
355 356 3.117663 AGTTTGCCTTAAGGGTCAGAACA 60.118 43.478 23.06 7.59 37.43 3.18
356 357 2.859165 TGCCTTAAGGGTCAGAACAG 57.141 50.000 23.06 0.00 37.43 3.16
357 358 2.054799 TGCCTTAAGGGTCAGAACAGT 58.945 47.619 23.06 0.00 37.43 3.55
358 359 3.244582 TGCCTTAAGGGTCAGAACAGTA 58.755 45.455 23.06 0.00 37.43 2.74
359 360 3.649023 TGCCTTAAGGGTCAGAACAGTAA 59.351 43.478 23.06 0.00 37.43 2.24
360 361 4.288626 TGCCTTAAGGGTCAGAACAGTAAT 59.711 41.667 23.06 0.00 37.43 1.89
361 362 4.876679 GCCTTAAGGGTCAGAACAGTAATC 59.123 45.833 23.06 0.00 37.43 1.75
362 363 5.429130 CCTTAAGGGTCAGAACAGTAATCC 58.571 45.833 14.25 0.00 0.00 3.01
363 364 5.429130 CTTAAGGGTCAGAACAGTAATCCC 58.571 45.833 0.00 0.00 0.00 3.85
364 365 3.207044 AGGGTCAGAACAGTAATCCCT 57.793 47.619 0.00 0.00 38.91 4.20
365 366 3.108376 AGGGTCAGAACAGTAATCCCTC 58.892 50.000 0.00 0.00 39.44 4.30
366 367 2.170817 GGGTCAGAACAGTAATCCCTCC 59.829 54.545 0.00 0.00 0.00 4.30
367 368 2.170817 GGTCAGAACAGTAATCCCTCCC 59.829 54.545 0.00 0.00 0.00 4.30
488 489 1.758280 ACTCGTACCAATAATGCCGGA 59.242 47.619 5.05 0.00 0.00 5.14
603 605 9.581289 CCCCTGACATACATATACCAAATAAAA 57.419 33.333 0.00 0.00 0.00 1.52
702 1092 1.136695 TGCAAAACCAGCAAGGAACAG 59.863 47.619 1.83 0.00 41.22 3.16
1044 1610 1.672030 CTGCGCTGATGACACCCAA 60.672 57.895 9.73 0.00 0.00 4.12
1065 1631 2.024319 GAAGAGAGTGCGCGTGCTT 61.024 57.895 23.16 10.48 43.34 3.91
1432 2000 5.645067 CAGCATTCAAATGTCAACTCTCCTA 59.355 40.000 4.76 0.00 38.65 2.94
1621 2601 3.408634 ACCACCGTAAACAGAGAAATGG 58.591 45.455 0.00 0.00 0.00 3.16
1627 2607 4.083484 CCGTAAACAGAGAAATGGTTCCAC 60.083 45.833 0.00 0.00 33.92 4.02
1742 3421 1.794714 GAGGAGCATGGGGAGAACTA 58.205 55.000 0.00 0.00 0.00 2.24
2250 3996 2.447244 AGTCTTCTTTCAGGCTGTCG 57.553 50.000 15.27 4.34 0.00 4.35
2336 4082 1.837538 TTGCAGCCGTTACAGTTCGC 61.838 55.000 0.00 0.00 0.00 4.70
2788 4556 1.267574 TGGTCATCTCTGGTGAGGGC 61.268 60.000 0.00 0.00 40.58 5.19
3165 4953 8.295288 TGTCTTCCTAGTTTCTACTTTTAGACG 58.705 37.037 0.00 0.00 33.81 4.18
3437 5244 1.590238 CTAAAGGCTCACGCAGAATCG 59.410 52.381 0.00 0.00 38.10 3.34
4476 6315 9.786224 CAACAAAACTTACTTTTAACACAACAC 57.214 29.630 0.00 0.00 30.39 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.027533 CCCCCTCAAATCCTCTCCA 57.972 57.895 0.00 0.00 0.00 3.86
15 16 3.732849 CACCCCTCAAGCTCCCCC 61.733 72.222 0.00 0.00 0.00 5.40
16 17 2.610859 TCACCCCTCAAGCTCCCC 60.611 66.667 0.00 0.00 0.00 4.81
17 18 1.613630 TCTCACCCCTCAAGCTCCC 60.614 63.158 0.00 0.00 0.00 4.30
18 19 0.616111 TCTCTCACCCCTCAAGCTCC 60.616 60.000 0.00 0.00 0.00 4.70
19 20 0.823460 CTCTCTCACCCCTCAAGCTC 59.177 60.000 0.00 0.00 0.00 4.09
20 21 0.411452 TCTCTCTCACCCCTCAAGCT 59.589 55.000 0.00 0.00 0.00 3.74
21 22 0.823460 CTCTCTCTCACCCCTCAAGC 59.177 60.000 0.00 0.00 0.00 4.01
22 23 1.824230 CACTCTCTCTCACCCCTCAAG 59.176 57.143 0.00 0.00 0.00 3.02
23 24 1.551099 CCACTCTCTCTCACCCCTCAA 60.551 57.143 0.00 0.00 0.00 3.02
24 25 0.040351 CCACTCTCTCTCACCCCTCA 59.960 60.000 0.00 0.00 0.00 3.86
25 26 0.686112 CCCACTCTCTCTCACCCCTC 60.686 65.000 0.00 0.00 0.00 4.30
26 27 1.390125 CCCACTCTCTCTCACCCCT 59.610 63.158 0.00 0.00 0.00 4.79
27 28 1.687493 CCCCACTCTCTCTCACCCC 60.687 68.421 0.00 0.00 0.00 4.95
28 29 0.686112 CTCCCCACTCTCTCTCACCC 60.686 65.000 0.00 0.00 0.00 4.61
29 30 0.686112 CCTCCCCACTCTCTCTCACC 60.686 65.000 0.00 0.00 0.00 4.02
30 31 1.326951 GCCTCCCCACTCTCTCTCAC 61.327 65.000 0.00 0.00 0.00 3.51
31 32 1.000993 GCCTCCCCACTCTCTCTCA 59.999 63.158 0.00 0.00 0.00 3.27
32 33 1.000993 TGCCTCCCCACTCTCTCTC 59.999 63.158 0.00 0.00 0.00 3.20
33 34 1.001503 CTGCCTCCCCACTCTCTCT 59.998 63.158 0.00 0.00 0.00 3.10
34 35 2.730524 GCTGCCTCCCCACTCTCTC 61.731 68.421 0.00 0.00 0.00 3.20
35 36 2.686835 GCTGCCTCCCCACTCTCT 60.687 66.667 0.00 0.00 0.00 3.10
36 37 3.005539 TGCTGCCTCCCCACTCTC 61.006 66.667 0.00 0.00 0.00 3.20
37 38 3.007920 CTGCTGCCTCCCCACTCT 61.008 66.667 0.00 0.00 0.00 3.24
38 39 4.792804 GCTGCTGCCTCCCCACTC 62.793 72.222 3.85 0.00 0.00 3.51
40 41 4.792804 GAGCTGCTGCCTCCCCAC 62.793 72.222 7.01 0.00 40.80 4.61
42 43 3.695747 GAAGAGCTGCTGCCTCCCC 62.696 68.421 7.01 0.00 40.80 4.81
43 44 2.124778 GAAGAGCTGCTGCCTCCC 60.125 66.667 7.01 0.00 40.80 4.30
44 45 0.744057 GAAGAAGAGCTGCTGCCTCC 60.744 60.000 7.01 2.17 40.80 4.30
45 46 0.036577 TGAAGAAGAGCTGCTGCCTC 60.037 55.000 7.01 9.12 40.80 4.70
46 47 0.399454 TTGAAGAAGAGCTGCTGCCT 59.601 50.000 7.01 6.37 40.80 4.75
47 48 0.803740 CTTGAAGAAGAGCTGCTGCC 59.196 55.000 7.01 4.03 40.80 4.85
48 49 0.168568 GCTTGAAGAAGAGCTGCTGC 59.831 55.000 7.01 7.62 36.01 5.25
49 50 1.810959 AGCTTGAAGAAGAGCTGCTG 58.189 50.000 7.01 0.00 46.82 4.41
54 55 1.365368 GCCCGAGCTTGAAGAAGAGC 61.365 60.000 1.22 0.00 39.17 4.09
55 56 2.761071 GCCCGAGCTTGAAGAAGAG 58.239 57.895 1.22 0.00 35.50 2.85
66 67 4.883354 CCCCAATCCAGCCCGAGC 62.883 72.222 0.00 0.00 40.32 5.03
67 68 2.210144 TTTCCCCAATCCAGCCCGAG 62.210 60.000 0.00 0.00 0.00 4.63
68 69 2.210144 CTTTCCCCAATCCAGCCCGA 62.210 60.000 0.00 0.00 0.00 5.14
69 70 1.754234 CTTTCCCCAATCCAGCCCG 60.754 63.158 0.00 0.00 0.00 6.13
70 71 0.972471 CACTTTCCCCAATCCAGCCC 60.972 60.000 0.00 0.00 0.00 5.19
71 72 0.251787 ACACTTTCCCCAATCCAGCC 60.252 55.000 0.00 0.00 0.00 4.85
72 73 0.890683 CACACTTTCCCCAATCCAGC 59.109 55.000 0.00 0.00 0.00 4.85
73 74 1.888512 CACACACTTTCCCCAATCCAG 59.111 52.381 0.00 0.00 0.00 3.86
74 75 1.480312 CCACACACTTTCCCCAATCCA 60.480 52.381 0.00 0.00 0.00 3.41
75 76 1.256812 CCACACACTTTCCCCAATCC 58.743 55.000 0.00 0.00 0.00 3.01
76 77 1.256812 CCCACACACTTTCCCCAATC 58.743 55.000 0.00 0.00 0.00 2.67
77 78 0.178935 CCCCACACACTTTCCCCAAT 60.179 55.000 0.00 0.00 0.00 3.16
78 79 1.231641 CCCCACACACTTTCCCCAA 59.768 57.895 0.00 0.00 0.00 4.12
79 80 2.009882 ACCCCACACACTTTCCCCA 61.010 57.895 0.00 0.00 0.00 4.96
80 81 1.530655 CACCCCACACACTTTCCCC 60.531 63.158 0.00 0.00 0.00 4.81
81 82 1.530655 CCACCCCACACACTTTCCC 60.531 63.158 0.00 0.00 0.00 3.97
82 83 1.530655 CCCACCCCACACACTTTCC 60.531 63.158 0.00 0.00 0.00 3.13
83 84 0.822121 GTCCCACCCCACACACTTTC 60.822 60.000 0.00 0.00 0.00 2.62
84 85 1.229076 GTCCCACCCCACACACTTT 59.771 57.895 0.00 0.00 0.00 2.66
85 86 2.763645 GGTCCCACCCCACACACTT 61.764 63.158 0.00 0.00 30.04 3.16
86 87 3.175710 GGTCCCACCCCACACACT 61.176 66.667 0.00 0.00 30.04 3.55
97 98 1.841556 GGAGAGTGTGTGGGTCCCA 60.842 63.158 6.47 6.47 0.00 4.37
98 99 2.593956 GGGAGAGTGTGTGGGTCCC 61.594 68.421 0.00 0.00 40.27 4.46
99 100 2.943978 CGGGAGAGTGTGTGGGTCC 61.944 68.421 0.00 0.00 0.00 4.46
100 101 2.657237 CGGGAGAGTGTGTGGGTC 59.343 66.667 0.00 0.00 0.00 4.46
101 102 2.923035 CCGGGAGAGTGTGTGGGT 60.923 66.667 0.00 0.00 0.00 4.51
102 103 2.923035 ACCGGGAGAGTGTGTGGG 60.923 66.667 6.32 0.00 0.00 4.61
103 104 2.343758 CACCGGGAGAGTGTGTGG 59.656 66.667 6.32 0.00 0.00 4.17
104 105 2.343758 CCACCGGGAGAGTGTGTG 59.656 66.667 6.32 0.00 35.59 3.82
119 120 1.205966 CCGGTAAGTGGATAACCCCA 58.794 55.000 0.00 0.00 34.81 4.96
120 121 0.471191 CCCGGTAAGTGGATAACCCC 59.529 60.000 0.00 0.00 34.81 4.95
121 122 0.471191 CCCCGGTAAGTGGATAACCC 59.529 60.000 0.00 0.00 34.81 4.11
122 123 0.179037 GCCCCGGTAAGTGGATAACC 60.179 60.000 0.00 0.00 0.00 2.85
123 124 0.179037 GGCCCCGGTAAGTGGATAAC 60.179 60.000 0.00 0.00 0.00 1.89
124 125 0.620990 TGGCCCCGGTAAGTGGATAA 60.621 55.000 0.00 0.00 0.00 1.75
125 126 1.003182 TGGCCCCGGTAAGTGGATA 59.997 57.895 0.00 0.00 0.00 2.59
126 127 2.285818 TGGCCCCGGTAAGTGGAT 60.286 61.111 0.00 0.00 0.00 3.41
127 128 3.006728 CTGGCCCCGGTAAGTGGA 61.007 66.667 0.00 0.00 0.00 4.02
128 129 3.006728 TCTGGCCCCGGTAAGTGG 61.007 66.667 0.00 0.00 0.00 4.00
129 130 2.267961 GTCTGGCCCCGGTAAGTG 59.732 66.667 0.00 0.00 0.00 3.16
130 131 2.203877 TGTCTGGCCCCGGTAAGT 60.204 61.111 0.00 0.00 0.00 2.24
131 132 2.267961 GTGTCTGGCCCCGGTAAG 59.732 66.667 0.00 0.00 0.00 2.34
132 133 3.324108 GGTGTCTGGCCCCGGTAA 61.324 66.667 0.00 0.00 0.00 2.85
133 134 4.642488 TGGTGTCTGGCCCCGGTA 62.642 66.667 0.00 0.00 0.00 4.02
138 139 4.035102 GTCCCTGGTGTCTGGCCC 62.035 72.222 0.00 0.00 0.00 5.80
139 140 3.249189 TGTCCCTGGTGTCTGGCC 61.249 66.667 0.00 0.00 0.00 5.36
140 141 2.032681 GTGTCCCTGGTGTCTGGC 59.967 66.667 0.00 0.00 0.00 4.85
141 142 1.372683 CAGTGTCCCTGGTGTCTGG 59.627 63.158 0.00 0.00 37.54 3.86
149 150 2.047844 CAGACGCCAGTGTCCCTG 60.048 66.667 7.70 0.00 39.77 4.45
150 151 3.314331 CCAGACGCCAGTGTCCCT 61.314 66.667 7.70 0.00 39.77 4.20
167 168 3.365265 CTGACGTGGCAAAGGGGC 61.365 66.667 0.00 0.00 43.73 5.80
168 169 3.365265 GCTGACGTGGCAAAGGGG 61.365 66.667 0.00 0.00 0.00 4.79
169 170 2.594303 TGCTGACGTGGCAAAGGG 60.594 61.111 9.89 0.00 36.71 3.95
170 171 2.620112 CCTGCTGACGTGGCAAAGG 61.620 63.158 12.75 8.52 39.30 3.11
171 172 1.845809 GACCTGCTGACGTGGCAAAG 61.846 60.000 12.75 9.98 39.30 2.77
172 173 1.891919 GACCTGCTGACGTGGCAAA 60.892 57.895 12.75 0.00 39.30 3.68
173 174 2.280797 GACCTGCTGACGTGGCAA 60.281 61.111 12.75 0.09 39.30 4.52
174 175 3.100503 TTGACCTGCTGACGTGGCA 62.101 57.895 11.48 11.48 38.10 4.92
175 176 2.280797 TTGACCTGCTGACGTGGC 60.281 61.111 0.00 0.00 0.00 5.01
176 177 2.310233 CGTTGACCTGCTGACGTGG 61.310 63.158 0.00 0.00 0.00 4.94
177 178 2.310233 CCGTTGACCTGCTGACGTG 61.310 63.158 0.00 0.00 33.95 4.49
178 179 2.029073 CCGTTGACCTGCTGACGT 59.971 61.111 0.00 0.00 33.95 4.34
179 180 2.738521 CCCGTTGACCTGCTGACG 60.739 66.667 0.00 0.00 35.44 4.35
180 181 3.050275 GCCCGTTGACCTGCTGAC 61.050 66.667 0.00 0.00 0.00 3.51
181 182 3.535629 CTGCCCGTTGACCTGCTGA 62.536 63.158 0.00 0.00 0.00 4.26
182 183 3.052082 CTGCCCGTTGACCTGCTG 61.052 66.667 0.00 0.00 0.00 4.41
183 184 4.335647 CCTGCCCGTTGACCTGCT 62.336 66.667 0.00 0.00 0.00 4.24
236 237 3.636313 TTACGAAGCAGACGCCGGG 62.636 63.158 2.18 0.00 39.83 5.73
237 238 2.126228 TTACGAAGCAGACGCCGG 60.126 61.111 0.00 0.00 39.83 6.13
238 239 2.442188 GGTTACGAAGCAGACGCCG 61.442 63.158 0.00 0.00 39.83 6.46
239 240 2.098831 GGGTTACGAAGCAGACGCC 61.099 63.158 0.00 0.00 39.83 5.68
240 241 0.947180 TTGGGTTACGAAGCAGACGC 60.947 55.000 0.00 0.00 38.99 5.19
241 242 1.193874 GTTTGGGTTACGAAGCAGACG 59.806 52.381 0.00 0.00 0.00 4.18
242 243 1.193874 CGTTTGGGTTACGAAGCAGAC 59.806 52.381 0.00 0.00 41.33 3.51
243 244 1.504359 CGTTTGGGTTACGAAGCAGA 58.496 50.000 0.00 0.00 41.33 4.26
244 245 0.110373 GCGTTTGGGTTACGAAGCAG 60.110 55.000 0.00 0.00 41.33 4.24
245 246 1.508808 GGCGTTTGGGTTACGAAGCA 61.509 55.000 0.00 0.00 41.33 3.91
246 247 1.208358 GGCGTTTGGGTTACGAAGC 59.792 57.895 0.00 0.00 41.33 3.86
247 248 0.515564 CTGGCGTTTGGGTTACGAAG 59.484 55.000 0.00 0.00 41.33 3.79
248 249 0.885596 CCTGGCGTTTGGGTTACGAA 60.886 55.000 0.00 0.00 41.33 3.85
249 250 1.301874 CCTGGCGTTTGGGTTACGA 60.302 57.895 0.00 0.00 41.33 3.43
250 251 2.329614 CCCTGGCGTTTGGGTTACG 61.330 63.158 0.00 0.00 41.71 3.18
251 252 1.073548 TCCCTGGCGTTTGGGTTAC 59.926 57.895 8.23 0.00 43.74 2.50
252 253 1.073548 GTCCCTGGCGTTTGGGTTA 59.926 57.895 8.23 0.00 43.74 2.85
253 254 2.203437 GTCCCTGGCGTTTGGGTT 60.203 61.111 8.23 0.00 43.74 4.11
254 255 4.280019 GGTCCCTGGCGTTTGGGT 62.280 66.667 8.23 0.00 43.74 4.51
255 256 2.132089 TAAGGTCCCTGGCGTTTGGG 62.132 60.000 2.94 2.94 44.66 4.12
256 257 0.676782 CTAAGGTCCCTGGCGTTTGG 60.677 60.000 0.00 0.00 0.00 3.28
257 258 1.305930 GCTAAGGTCCCTGGCGTTTG 61.306 60.000 0.00 0.00 0.00 2.93
258 259 1.002502 GCTAAGGTCCCTGGCGTTT 60.003 57.895 0.00 0.00 0.00 3.60
259 260 2.669240 GCTAAGGTCCCTGGCGTT 59.331 61.111 0.00 0.00 0.00 4.84
260 261 3.771160 CGCTAAGGTCCCTGGCGT 61.771 66.667 19.22 0.00 40.97 5.68
261 262 3.718210 GACGCTAAGGTCCCTGGCG 62.718 68.421 23.20 23.20 46.36 5.69
262 263 2.187163 GACGCTAAGGTCCCTGGC 59.813 66.667 0.00 0.00 0.00 4.85
263 264 1.218316 GTGACGCTAAGGTCCCTGG 59.782 63.158 0.00 0.00 36.07 4.45
264 265 1.218316 GGTGACGCTAAGGTCCCTG 59.782 63.158 0.00 0.00 36.07 4.45
265 266 3.709567 GGTGACGCTAAGGTCCCT 58.290 61.111 0.00 0.00 36.07 4.20
277 278 3.875134 TCTTTCTGACCTTTTTCGGTGAC 59.125 43.478 0.00 0.00 37.42 3.67
278 279 4.145365 TCTTTCTGACCTTTTTCGGTGA 57.855 40.909 0.00 0.00 37.42 4.02
279 280 4.893424 TTCTTTCTGACCTTTTTCGGTG 57.107 40.909 0.00 0.00 37.42 4.94
280 281 5.907866 TTTTCTTTCTGACCTTTTTCGGT 57.092 34.783 0.00 0.00 40.80 4.69
302 303 4.904253 TTTGACCTCGTTCCGAATTTTT 57.096 36.364 0.00 0.00 34.74 1.94
303 304 4.378046 CGATTTGACCTCGTTCCGAATTTT 60.378 41.667 0.00 0.00 34.74 1.82
304 305 3.124636 CGATTTGACCTCGTTCCGAATTT 59.875 43.478 0.00 0.00 34.74 1.82
305 306 2.671396 CGATTTGACCTCGTTCCGAATT 59.329 45.455 0.00 0.00 34.74 2.17
306 307 2.268298 CGATTTGACCTCGTTCCGAAT 58.732 47.619 0.00 0.00 34.74 3.34
307 308 1.670674 CCGATTTGACCTCGTTCCGAA 60.671 52.381 0.00 0.00 34.74 4.30
308 309 0.108992 CCGATTTGACCTCGTTCCGA 60.109 55.000 0.00 0.00 34.36 4.55
309 310 1.082117 CCCGATTTGACCTCGTTCCG 61.082 60.000 0.00 0.00 34.36 4.30
310 311 0.248289 TCCCGATTTGACCTCGTTCC 59.752 55.000 0.00 0.00 34.36 3.62
311 312 2.311124 ATCCCGATTTGACCTCGTTC 57.689 50.000 0.00 0.00 34.36 3.95
312 313 2.781681 AATCCCGATTTGACCTCGTT 57.218 45.000 0.00 0.00 34.36 3.85
313 314 2.781681 AAATCCCGATTTGACCTCGT 57.218 45.000 1.89 0.00 39.36 4.18
314 315 3.793559 ACTAAATCCCGATTTGACCTCG 58.206 45.455 11.99 0.00 40.83 4.63
315 316 5.676331 GCAAACTAAATCCCGATTTGACCTC 60.676 44.000 11.99 0.00 40.83 3.85
316 317 4.157840 GCAAACTAAATCCCGATTTGACCT 59.842 41.667 11.99 0.00 40.83 3.85
317 318 4.421058 GCAAACTAAATCCCGATTTGACC 58.579 43.478 11.99 0.00 40.83 4.02
318 319 4.157840 AGGCAAACTAAATCCCGATTTGAC 59.842 41.667 11.99 0.09 40.83 3.18
319 320 4.340617 AGGCAAACTAAATCCCGATTTGA 58.659 39.130 11.99 0.00 40.83 2.69
320 321 4.718940 AGGCAAACTAAATCCCGATTTG 57.281 40.909 11.99 5.77 40.83 2.32
321 322 6.127451 CCTTAAGGCAAACTAAATCCCGATTT 60.127 38.462 9.00 7.74 42.95 2.17
322 323 5.359860 CCTTAAGGCAAACTAAATCCCGATT 59.640 40.000 9.00 0.00 0.00 3.34
323 324 4.887655 CCTTAAGGCAAACTAAATCCCGAT 59.112 41.667 9.00 0.00 0.00 4.18
324 325 4.266714 CCTTAAGGCAAACTAAATCCCGA 58.733 43.478 9.00 0.00 0.00 5.14
325 326 3.380320 CCCTTAAGGCAAACTAAATCCCG 59.620 47.826 16.70 0.00 0.00 5.14
326 327 4.350245 ACCCTTAAGGCAAACTAAATCCC 58.650 43.478 16.70 0.00 40.58 3.85
327 328 5.014202 TGACCCTTAAGGCAAACTAAATCC 58.986 41.667 16.70 0.00 40.58 3.01
328 329 5.944007 TCTGACCCTTAAGGCAAACTAAATC 59.056 40.000 16.70 2.75 40.58 2.17
329 330 5.887754 TCTGACCCTTAAGGCAAACTAAAT 58.112 37.500 16.70 0.00 40.58 1.40
330 331 5.313280 TCTGACCCTTAAGGCAAACTAAA 57.687 39.130 16.70 0.00 40.58 1.85
331 332 4.986054 TCTGACCCTTAAGGCAAACTAA 57.014 40.909 16.70 0.00 40.58 2.24
332 333 4.103469 TGTTCTGACCCTTAAGGCAAACTA 59.897 41.667 16.70 0.00 40.58 2.24
333 334 3.117663 TGTTCTGACCCTTAAGGCAAACT 60.118 43.478 16.70 0.00 40.58 2.66
334 335 3.219281 TGTTCTGACCCTTAAGGCAAAC 58.781 45.455 16.70 13.84 40.58 2.93
335 336 3.117663 ACTGTTCTGACCCTTAAGGCAAA 60.118 43.478 16.70 2.18 40.58 3.68
336 337 2.441750 ACTGTTCTGACCCTTAAGGCAA 59.558 45.455 16.70 2.55 40.58 4.52
337 338 2.054799 ACTGTTCTGACCCTTAAGGCA 58.945 47.619 16.70 8.73 40.58 4.75
338 339 2.861147 ACTGTTCTGACCCTTAAGGC 57.139 50.000 16.70 4.03 40.58 4.35
339 340 5.429130 GGATTACTGTTCTGACCCTTAAGG 58.571 45.833 15.14 15.14 43.78 2.69
340 341 5.189934 AGGGATTACTGTTCTGACCCTTAAG 59.810 44.000 0.00 0.00 42.84 1.85
341 342 5.098663 AGGGATTACTGTTCTGACCCTTAA 58.901 41.667 0.00 0.00 42.84 1.85
342 343 4.695606 AGGGATTACTGTTCTGACCCTTA 58.304 43.478 0.00 0.00 42.84 2.69
343 344 3.519913 GAGGGATTACTGTTCTGACCCTT 59.480 47.826 0.00 0.00 44.99 3.95
344 345 3.207044 AGGGATTACTGTTCTGACCCT 57.793 47.619 0.00 0.00 40.97 4.34
345 346 2.170817 GGAGGGATTACTGTTCTGACCC 59.829 54.545 0.00 0.00 36.47 4.46
346 347 2.170817 GGGAGGGATTACTGTTCTGACC 59.829 54.545 0.00 0.00 0.00 4.02
347 348 2.170817 GGGGAGGGATTACTGTTCTGAC 59.829 54.545 0.00 0.00 0.00 3.51
348 349 2.225779 TGGGGAGGGATTACTGTTCTGA 60.226 50.000 0.00 0.00 0.00 3.27
349 350 2.171448 CTGGGGAGGGATTACTGTTCTG 59.829 54.545 0.00 0.00 0.00 3.02
350 351 2.045885 TCTGGGGAGGGATTACTGTTCT 59.954 50.000 0.00 0.00 0.00 3.01
351 352 2.436173 CTCTGGGGAGGGATTACTGTTC 59.564 54.545 0.00 0.00 36.03 3.18
352 353 2.225908 ACTCTGGGGAGGGATTACTGTT 60.226 50.000 0.00 0.00 43.46 3.16
353 354 1.366435 ACTCTGGGGAGGGATTACTGT 59.634 52.381 0.00 0.00 43.46 3.55
354 355 1.765314 CACTCTGGGGAGGGATTACTG 59.235 57.143 0.00 0.00 45.36 2.74
355 356 1.344496 CCACTCTGGGGAGGGATTACT 60.344 57.143 0.00 0.00 45.36 2.24
356 357 1.132500 CCACTCTGGGGAGGGATTAC 58.868 60.000 0.00 0.00 45.36 1.89
357 358 1.023719 TCCACTCTGGGGAGGGATTA 58.976 55.000 0.00 0.00 45.36 1.75
358 359 0.348370 ATCCACTCTGGGGAGGGATT 59.652 55.000 0.00 0.00 45.36 3.01
359 360 1.132689 GTATCCACTCTGGGGAGGGAT 60.133 57.143 15.12 15.12 45.36 3.85
360 361 0.264955 GTATCCACTCTGGGGAGGGA 59.735 60.000 0.00 2.08 45.36 4.20
361 362 0.031111 TGTATCCACTCTGGGGAGGG 60.031 60.000 0.00 0.00 43.46 4.30
362 363 1.765314 CTTGTATCCACTCTGGGGAGG 59.235 57.143 0.00 0.00 43.46 4.30
363 364 2.472029 ACTTGTATCCACTCTGGGGAG 58.528 52.381 0.00 0.00 44.62 4.30
364 365 2.642171 ACTTGTATCCACTCTGGGGA 57.358 50.000 0.00 0.00 38.32 4.81
365 366 3.721087 AAACTTGTATCCACTCTGGGG 57.279 47.619 0.00 0.00 38.32 4.96
366 367 4.321230 GCAAAAACTTGTATCCACTCTGGG 60.321 45.833 0.00 0.00 38.32 4.45
367 368 4.278170 TGCAAAAACTTGTATCCACTCTGG 59.722 41.667 0.00 0.00 39.43 3.86
511 513 1.215655 CTGCCCATCGCTTACGTAGC 61.216 60.000 0.00 1.21 46.83 3.58
603 605 2.596346 TCTGGTGGCATTGTTGAACAT 58.404 42.857 0.00 0.00 0.00 2.71
615 1005 5.049828 GCATTTGGTTATTATTCTGGTGGC 58.950 41.667 0.00 0.00 0.00 5.01
674 1064 2.161855 TGCTGGTTTTGCATCCTACTG 58.838 47.619 0.00 0.00 35.31 2.74
675 1065 2.584835 TGCTGGTTTTGCATCCTACT 57.415 45.000 0.00 0.00 35.31 2.57
676 1066 2.094545 CCTTGCTGGTTTTGCATCCTAC 60.095 50.000 0.00 0.00 40.34 3.18
677 1067 2.170166 CCTTGCTGGTTTTGCATCCTA 58.830 47.619 0.00 0.00 40.34 2.94
678 1068 0.971386 CCTTGCTGGTTTTGCATCCT 59.029 50.000 0.00 0.00 40.34 3.24
702 1092 9.748708 TGCATTATTGATTAGTTTATTGCTTCC 57.251 29.630 0.00 0.00 0.00 3.46
730 1286 2.268920 GACCGCCTTGCCATCTCA 59.731 61.111 0.00 0.00 0.00 3.27
1044 1610 2.992114 ACGCGCACTCTCTTCCCT 60.992 61.111 5.73 0.00 0.00 4.20
1265 1833 7.803279 AGGAGTACTTGTTTTAACAGAAAGG 57.197 36.000 0.00 0.00 40.50 3.11
1621 2601 4.693566 TCTCATTTATTGGTGACGTGGAAC 59.306 41.667 0.00 0.00 0.00 3.62
1627 2607 8.289618 TCTTCTTTTTCTCATTTATTGGTGACG 58.710 33.333 0.00 0.00 0.00 4.35
1742 3421 0.543277 ACCATCCAGCATGTCGATGT 59.457 50.000 13.97 4.35 34.32 3.06
2250 3996 2.541556 GTCCGTCATAAGCCTCTTGAC 58.458 52.381 0.00 0.00 37.10 3.18
2336 4082 1.181098 CCTTTGTTCCTGCCAGGTGG 61.181 60.000 11.27 1.45 36.53 4.61
3437 5244 5.473039 AGAGGCAGCAATGTTTTTACATTC 58.527 37.500 0.00 0.00 38.16 2.67
4119 5944 5.309323 TGCCAGAAAAGGATTACAAATCG 57.691 39.130 0.00 0.00 0.00 3.34
4125 5964 4.522789 TGGAAGTTGCCAGAAAAGGATTAC 59.477 41.667 0.00 0.00 33.10 1.89
4469 6308 1.668628 GGCCTTAATTGCCGTGTTGTG 60.669 52.381 0.00 0.00 39.48 3.33


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

AutoCloner maintained by Alex Coulton.