Multiple sequence alignment - TraesCS5B01G117800

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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 TraesCS5B01G117800 chr5B 100.000 5723 0 0 765 6487 208257545 208263267 0.000000e+00 10569.0
1 TraesCS5B01G117800 chr5B 100.000 378 0 0 1 378 208256781 208257158 0.000000e+00 699.0
2 TraesCS5B01G117800 chr5B 74.749 598 133 15 1475 2063 368486467 368487055 1.080000e-62 252.0
3 TraesCS5B01G117800 chr5B 85.864 191 25 2 6272 6461 412437497 412437308 1.100000e-47 202.0
4 TraesCS5B01G117800 chr5A 95.885 5735 150 35 788 6487 238694207 238699890 0.000000e+00 9204.0
5 TraesCS5B01G117800 chr5A 74.916 598 132 15 1475 2063 413041601 413042189 2.320000e-64 257.0
6 TraesCS5B01G117800 chr5A 93.651 63 4 0 141 203 238692724 238692786 1.930000e-15 95.3
7 TraesCS5B01G117800 chr5A 100.000 43 0 0 320 362 238694060 238694102 5.390000e-11 80.5
8 TraesCS5B01G117800 chr5A 94.595 37 2 0 6098 6134 238699463 238699499 2.530000e-04 58.4
9 TraesCS5B01G117800 chr5D 97.645 3142 61 4 765 3896 204074502 204077640 0.000000e+00 5380.0
10 TraesCS5B01G117800 chr5D 97.466 1934 31 4 3939 5868 204077640 204079559 0.000000e+00 3284.0
11 TraesCS5B01G117800 chr5D 86.217 711 45 25 5804 6487 204079560 204080244 0.000000e+00 721.0
12 TraesCS5B01G117800 chr5D 74.916 598 132 15 1475 2063 318442168 318442756 2.320000e-64 257.0
13 TraesCS5B01G117800 chr1D 85.714 231 32 1 6234 6463 50707188 50706958 6.500000e-60 243.0
14 TraesCS5B01G117800 chr1D 91.892 148 10 1 1 146 163461544 163461397 8.530000e-49 206.0
15 TraesCS5B01G117800 chr1D 79.585 289 56 3 4342 4628 430413539 430413826 3.070000e-48 204.0
16 TraesCS5B01G117800 chr4B 86.528 193 24 2 6272 6463 668409993 668409802 1.830000e-50 211.0
17 TraesCS5B01G117800 chr6B 97.297 111 3 0 195 305 551910552 551910662 8.590000e-44 189.0
18 TraesCS5B01G117800 chr2B 94.309 123 7 0 182 304 171459959 171460081 8.590000e-44 189.0
19 TraesCS5B01G117800 chr2B 97.248 109 3 0 197 305 182511806 182511914 1.110000e-42 185.0
20 TraesCS5B01G117800 chr2B 94.118 119 7 0 191 309 785073696 785073578 1.440000e-41 182.0
21 TraesCS5B01G117800 chr2B 78.744 207 41 2 6260 6463 699171973 699171767 1.130000e-27 135.0
22 TraesCS5B01G117800 chr7B 94.958 119 6 0 187 305 27494384 27494502 3.090000e-43 187.0
23 TraesCS5B01G117800 chr7B 94.167 120 7 0 198 317 271250783 271250902 3.990000e-42 183.0
24 TraesCS5B01G117800 chr3D 98.131 107 2 0 198 304 358788228 358788334 3.090000e-43 187.0
25 TraesCS5B01G117800 chr3B 97.273 110 3 0 198 307 22830625 22830516 3.090000e-43 187.0
26 TraesCS5B01G117800 chr3B 86.538 52 7 0 95 146 487202444 487202495 2.530000e-04 58.4
27 TraesCS5B01G117800 chr2D 98.131 107 2 0 198 304 13492461 13492567 3.090000e-43 187.0
28 TraesCS5B01G117800 chr6A 85.714 154 19 2 1 151 269005771 269005618 6.730000e-35 159.0
29 TraesCS5B01G117800 chr6A 92.857 42 3 0 95 136 464251294 464251253 1.950000e-05 62.1
30 TraesCS5B01G117800 chr7A 83.784 148 21 2 1 145 257274190 257274337 3.150000e-28 137.0
31 TraesCS5B01G117800 chr3A 78.182 220 40 5 6244 6463 640837496 640837707 4.080000e-27 134.0
32 TraesCS5B01G117800 chr3A 76.048 167 37 3 6295 6460 107977711 107977875 4.170000e-12 84.2
33 TraesCS5B01G117800 chr3A 87.692 65 7 1 82 145 373046714 373046650 2.510000e-09 75.0
34 TraesCS5B01G117800 chr2A 80.531 113 21 1 6352 6463 165102371 165102259 1.160000e-12 86.1


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 TraesCS5B01G117800 chr5B 208256781 208263267 6486 False 5634.000000 10569 100.00000 1 6487 2 chr5B.!!$F2 6486
1 TraesCS5B01G117800 chr5B 368486467 368487055 588 False 252.000000 252 74.74900 1475 2063 1 chr5B.!!$F1 588
2 TraesCS5B01G117800 chr5A 238692724 238699890 7166 False 2359.550000 9204 96.03275 141 6487 4 chr5A.!!$F2 6346
3 TraesCS5B01G117800 chr5A 413041601 413042189 588 False 257.000000 257 74.91600 1475 2063 1 chr5A.!!$F1 588
4 TraesCS5B01G117800 chr5D 204074502 204080244 5742 False 3128.333333 5380 93.77600 765 6487 3 chr5D.!!$F2 5722
5 TraesCS5B01G117800 chr5D 318442168 318442756 588 False 257.000000 257 74.91600 1475 2063 1 chr5D.!!$F1 588

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
53 54 0.037605 AAGGTGGTTTCGAGCCTACG 60.038 55.000 9.11 0.0 0.00 3.51 F
314 1216 0.101579 GAGGGAGTAGCTGCGAAGAC 59.898 60.000 0.00 0.0 0.00 3.01 F
1193 2361 0.181114 CCAATGGGAATCTCTCGGCA 59.819 55.000 0.00 0.0 35.59 5.69 F
1868 3036 0.322816 GATTCTTCCTGCACAGCCCA 60.323 55.000 0.00 0.0 0.00 5.36 F
2448 3616 1.967779 TGTCGAGTGTGGAAAGGATGA 59.032 47.619 0.00 0.0 0.00 2.92 F
3922 5100 0.251209 GGGAAACAGTGGGGGAGAAC 60.251 60.000 0.00 0.0 0.00 3.01 F
5341 6525 0.904649 AGGCATGATGAAGTCGTGGA 59.095 50.000 0.00 0.0 42.89 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 2889 1.136502 CGCTGCGAGAAGAGTTTGTTC 60.137 52.381 18.66 0.00 0.00 3.18 R
2168 3336 1.202806 CCAAGCAAGACAGTCTTCCCA 60.203 52.381 13.27 0.00 33.78 4.37 R
2745 3913 2.197283 TAGGCAACATCATGTGTGCA 57.803 45.000 19.87 4.83 41.14 4.57 R
3202 4370 5.221880 GCAAAGTCAATGCAAGACATGTTA 58.778 37.500 20.52 0.00 43.29 2.41 R
4045 5223 5.739752 TCAGCATGTTGTATAGTTGCATC 57.260 39.130 9.54 0.00 37.40 3.91 R
5342 6526 0.174389 GCTCTTCGACATCTCCTGCA 59.826 55.000 0.00 0.00 0.00 4.41 R
6392 7681 0.242286 CTCTCTCGAGTGGTGTGTGG 59.758 60.000 13.13 0.00 32.47 4.17 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
22 23 5.470845 CTTCGTGAGAGTGACTTTTGTTT 57.529 39.130 0.00 0.00 43.69 2.83
23 24 5.869350 CTTCGTGAGAGTGACTTTTGTTTT 58.131 37.500 0.00 0.00 43.69 2.43
24 25 5.873179 TCGTGAGAGTGACTTTTGTTTTT 57.127 34.783 0.00 0.00 34.84 1.94
25 26 5.864986 TCGTGAGAGTGACTTTTGTTTTTC 58.135 37.500 0.00 0.00 34.84 2.29
26 27 5.642063 TCGTGAGAGTGACTTTTGTTTTTCT 59.358 36.000 0.00 0.00 34.84 2.52
27 28 6.148811 TCGTGAGAGTGACTTTTGTTTTTCTT 59.851 34.615 0.00 0.00 34.84 2.52
28 29 6.801862 CGTGAGAGTGACTTTTGTTTTTCTTT 59.198 34.615 0.00 0.00 0.00 2.52
29 30 7.201266 CGTGAGAGTGACTTTTGTTTTTCTTTG 60.201 37.037 0.00 0.00 0.00 2.77
30 31 7.062255 GTGAGAGTGACTTTTGTTTTTCTTTGG 59.938 37.037 0.00 0.00 0.00 3.28
31 32 6.993079 AGAGTGACTTTTGTTTTTCTTTGGT 58.007 32.000 0.00 0.00 0.00 3.67
32 33 6.868339 AGAGTGACTTTTGTTTTTCTTTGGTG 59.132 34.615 0.00 0.00 0.00 4.17
33 34 6.521162 AGTGACTTTTGTTTTTCTTTGGTGT 58.479 32.000 0.00 0.00 0.00 4.16
34 35 7.662897 AGTGACTTTTGTTTTTCTTTGGTGTA 58.337 30.769 0.00 0.00 0.00 2.90
35 36 8.145122 AGTGACTTTTGTTTTTCTTTGGTGTAA 58.855 29.630 0.00 0.00 0.00 2.41
36 37 8.432359 GTGACTTTTGTTTTTCTTTGGTGTAAG 58.568 33.333 0.00 0.00 0.00 2.34
37 38 7.600752 TGACTTTTGTTTTTCTTTGGTGTAAGG 59.399 33.333 0.00 0.00 0.00 2.69
38 39 7.446769 ACTTTTGTTTTTCTTTGGTGTAAGGT 58.553 30.769 0.00 0.00 0.00 3.50
39 40 7.386573 ACTTTTGTTTTTCTTTGGTGTAAGGTG 59.613 33.333 0.00 0.00 0.00 4.00
40 41 5.331876 TGTTTTTCTTTGGTGTAAGGTGG 57.668 39.130 0.00 0.00 0.00 4.61
41 42 4.773149 TGTTTTTCTTTGGTGTAAGGTGGT 59.227 37.500 0.00 0.00 0.00 4.16
42 43 5.246429 TGTTTTTCTTTGGTGTAAGGTGGTT 59.754 36.000 0.00 0.00 0.00 3.67
43 44 6.167685 GTTTTTCTTTGGTGTAAGGTGGTTT 58.832 36.000 0.00 0.00 0.00 3.27
44 45 5.585820 TTTCTTTGGTGTAAGGTGGTTTC 57.414 39.130 0.00 0.00 0.00 2.78
45 46 3.207778 TCTTTGGTGTAAGGTGGTTTCG 58.792 45.455 0.00 0.00 0.00 3.46
46 47 3.118334 TCTTTGGTGTAAGGTGGTTTCGA 60.118 43.478 0.00 0.00 0.00 3.71
47 48 2.536761 TGGTGTAAGGTGGTTTCGAG 57.463 50.000 0.00 0.00 0.00 4.04
48 49 1.154197 GGTGTAAGGTGGTTTCGAGC 58.846 55.000 0.00 0.00 0.00 5.03
49 50 1.154197 GTGTAAGGTGGTTTCGAGCC 58.846 55.000 1.61 1.61 0.00 4.70
50 51 1.053424 TGTAAGGTGGTTTCGAGCCT 58.947 50.000 9.11 0.37 0.00 4.58
51 52 2.028748 GTGTAAGGTGGTTTCGAGCCTA 60.029 50.000 9.11 0.00 0.00 3.93
52 53 2.028748 TGTAAGGTGGTTTCGAGCCTAC 60.029 50.000 9.11 1.37 0.00 3.18
53 54 0.037605 AAGGTGGTTTCGAGCCTACG 60.038 55.000 9.11 0.00 0.00 3.51
54 55 1.183676 AGGTGGTTTCGAGCCTACGT 61.184 55.000 9.11 0.00 34.70 3.57
55 56 1.012486 GGTGGTTTCGAGCCTACGTG 61.012 60.000 0.00 0.00 34.70 4.49
56 57 1.012486 GTGGTTTCGAGCCTACGTGG 61.012 60.000 0.00 0.00 39.35 4.94
57 58 1.180456 TGGTTTCGAGCCTACGTGGA 61.180 55.000 0.00 0.00 38.35 4.02
58 59 0.175073 GGTTTCGAGCCTACGTGGAT 59.825 55.000 0.00 0.00 38.35 3.41
59 60 1.278238 GTTTCGAGCCTACGTGGATG 58.722 55.000 0.00 0.00 38.35 3.51
60 61 0.892755 TTTCGAGCCTACGTGGATGT 59.107 50.000 0.00 0.00 38.35 3.06
61 62 0.892755 TTCGAGCCTACGTGGATGTT 59.107 50.000 0.00 0.00 38.35 2.71
62 63 0.454600 TCGAGCCTACGTGGATGTTC 59.545 55.000 0.00 0.00 38.35 3.18
63 64 0.866061 CGAGCCTACGTGGATGTTCG 60.866 60.000 0.00 0.00 38.35 3.95
64 65 1.146358 GAGCCTACGTGGATGTTCGC 61.146 60.000 0.00 0.00 38.35 4.70
65 66 1.447140 GCCTACGTGGATGTTCGCA 60.447 57.895 0.00 0.00 38.35 5.10
66 67 0.810031 GCCTACGTGGATGTTCGCAT 60.810 55.000 0.00 0.00 41.22 4.73
79 80 3.183754 TGTTCGCATCTACAATACACCG 58.816 45.455 0.00 0.00 0.00 4.94
80 81 1.847818 TCGCATCTACAATACACCGC 58.152 50.000 0.00 0.00 0.00 5.68
81 82 1.407618 TCGCATCTACAATACACCGCT 59.592 47.619 0.00 0.00 0.00 5.52
82 83 1.787155 CGCATCTACAATACACCGCTC 59.213 52.381 0.00 0.00 0.00 5.03
83 84 2.543861 CGCATCTACAATACACCGCTCT 60.544 50.000 0.00 0.00 0.00 4.09
84 85 3.458189 GCATCTACAATACACCGCTCTT 58.542 45.455 0.00 0.00 0.00 2.85
85 86 4.617959 GCATCTACAATACACCGCTCTTA 58.382 43.478 0.00 0.00 0.00 2.10
86 87 5.230942 GCATCTACAATACACCGCTCTTAT 58.769 41.667 0.00 0.00 0.00 1.73
87 88 6.387465 GCATCTACAATACACCGCTCTTATA 58.613 40.000 0.00 0.00 0.00 0.98
88 89 6.866770 GCATCTACAATACACCGCTCTTATAA 59.133 38.462 0.00 0.00 0.00 0.98
89 90 7.545965 GCATCTACAATACACCGCTCTTATAAT 59.454 37.037 0.00 0.00 0.00 1.28
90 91 9.424319 CATCTACAATACACCGCTCTTATAATT 57.576 33.333 0.00 0.00 0.00 1.40
94 95 8.951787 ACAATACACCGCTCTTATAATTAACA 57.048 30.769 0.00 0.00 0.00 2.41
95 96 9.555727 ACAATACACCGCTCTTATAATTAACAT 57.444 29.630 0.00 0.00 0.00 2.71
98 99 9.998106 ATACACCGCTCTTATAATTAACATTCT 57.002 29.630 0.00 0.00 0.00 2.40
99 100 8.366671 ACACCGCTCTTATAATTAACATTCTC 57.633 34.615 0.00 0.00 0.00 2.87
100 101 8.204836 ACACCGCTCTTATAATTAACATTCTCT 58.795 33.333 0.00 0.00 0.00 3.10
101 102 9.046296 CACCGCTCTTATAATTAACATTCTCTT 57.954 33.333 0.00 0.00 0.00 2.85
102 103 9.614792 ACCGCTCTTATAATTAACATTCTCTTT 57.385 29.630 0.00 0.00 0.00 2.52
124 125 8.767085 TCTTTTCTATAAAAATATGGTACGCCG 58.233 33.333 0.00 0.00 34.26 6.46
125 126 8.436046 TTTTCTATAAAAATATGGTACGCCGT 57.564 30.769 0.00 0.00 32.67 5.68
126 127 8.436046 TTTCTATAAAAATATGGTACGCCGTT 57.564 30.769 0.00 0.00 37.67 4.44
127 128 7.410800 TCTATAAAAATATGGTACGCCGTTG 57.589 36.000 0.00 0.00 37.67 4.10
128 129 3.768468 AAAAATATGGTACGCCGTTGG 57.232 42.857 0.00 0.00 37.67 3.77
129 130 2.406596 AAATATGGTACGCCGTTGGT 57.593 45.000 0.00 0.00 37.67 3.67
130 131 1.658994 AATATGGTACGCCGTTGGTG 58.341 50.000 0.00 0.00 39.41 4.17
132 133 1.180907 TATGGTACGCCGTTGGTGTA 58.819 50.000 0.00 5.19 45.32 2.90
136 137 3.984838 TACGCCGTTGGTGTACTTT 57.015 47.368 0.00 0.00 45.32 2.66
137 138 2.237393 TACGCCGTTGGTGTACTTTT 57.763 45.000 0.00 0.00 45.32 2.27
138 139 0.658897 ACGCCGTTGGTGTACTTTTG 59.341 50.000 0.00 0.00 45.32 2.44
139 140 0.938713 CGCCGTTGGTGTACTTTTGA 59.061 50.000 0.00 0.00 0.00 2.69
199 200 0.529119 CCACGGCCGTTATCACCTAC 60.529 60.000 32.11 0.00 0.00 3.18
203 204 0.391966 GGCCGTTATCACCTACTCCC 59.608 60.000 0.00 0.00 0.00 4.30
204 205 1.411041 GCCGTTATCACCTACTCCCT 58.589 55.000 0.00 0.00 0.00 4.20
205 206 1.340568 GCCGTTATCACCTACTCCCTC 59.659 57.143 0.00 0.00 0.00 4.30
206 207 1.962100 CCGTTATCACCTACTCCCTCC 59.038 57.143 0.00 0.00 0.00 4.30
209 210 3.029570 GTTATCACCTACTCCCTCCGTT 58.970 50.000 0.00 0.00 0.00 4.44
210 211 1.777941 ATCACCTACTCCCTCCGTTC 58.222 55.000 0.00 0.00 0.00 3.95
211 212 0.679002 TCACCTACTCCCTCCGTTCG 60.679 60.000 0.00 0.00 0.00 3.95
213 214 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
214 215 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
216 217 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
218 219 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
219 220 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
221 222 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
222 223 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
223 224 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
224 225 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
226 227 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
227 228 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
228 229 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
231 232 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
232 233 3.680789 GGAATTACTTGTCGCGGAAATG 58.319 45.455 6.13 0.00 0.00 2.32
233 234 3.486875 GGAATTACTTGTCGCGGAAATGG 60.487 47.826 6.13 0.00 0.00 3.16
234 235 2.459060 TTACTTGTCGCGGAAATGGA 57.541 45.000 6.13 0.00 0.00 3.41
236 237 1.086696 ACTTGTCGCGGAAATGGATG 58.913 50.000 6.13 0.00 0.00 3.51
237 238 1.086696 CTTGTCGCGGAAATGGATGT 58.913 50.000 6.13 0.00 0.00 3.06
238 239 2.276201 CTTGTCGCGGAAATGGATGTA 58.724 47.619 6.13 0.00 0.00 2.29
242 243 3.319689 TGTCGCGGAAATGGATGTATCTA 59.680 43.478 6.13 0.00 0.00 1.98
247 1149 4.558898 GCGGAAATGGATGTATCTAGACGT 60.559 45.833 0.00 0.00 0.00 4.34
248 1150 5.335426 GCGGAAATGGATGTATCTAGACGTA 60.335 44.000 0.00 0.00 0.00 3.57
251 1153 7.813148 CGGAAATGGATGTATCTAGACGTATTT 59.187 37.037 0.00 0.00 0.00 1.40
291 1193 7.158697 TCCATTTCTGAGACAAGTAATTTCGA 58.841 34.615 0.00 0.00 0.00 3.71
293 1195 7.746475 CCATTTCTGAGACAAGTAATTTCGAAC 59.254 37.037 0.00 0.00 0.00 3.95
294 1196 6.448053 TTCTGAGACAAGTAATTTCGAACG 57.552 37.500 0.00 0.00 0.00 3.95
295 1197 4.921515 TCTGAGACAAGTAATTTCGAACGG 59.078 41.667 0.00 0.00 0.00 4.44
296 1198 4.873817 TGAGACAAGTAATTTCGAACGGA 58.126 39.130 0.00 0.00 0.00 4.69
297 1199 4.921515 TGAGACAAGTAATTTCGAACGGAG 59.078 41.667 0.00 0.00 0.00 4.63
299 1201 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
304 1206 3.521947 AATTTCGAACGGAGGGAGTAG 57.478 47.619 0.00 0.00 0.00 2.57
307 1209 1.030488 TCGAACGGAGGGAGTAGCTG 61.030 60.000 0.00 0.00 0.00 4.24
310 1212 2.829003 CGGAGGGAGTAGCTGCGA 60.829 66.667 0.00 0.00 33.90 5.10
311 1213 2.415608 CGGAGGGAGTAGCTGCGAA 61.416 63.158 0.00 0.00 33.90 4.70
312 1214 1.439644 GGAGGGAGTAGCTGCGAAG 59.560 63.158 0.00 0.00 0.00 3.79
313 1215 1.038130 GGAGGGAGTAGCTGCGAAGA 61.038 60.000 0.00 0.00 0.00 2.87
314 1216 0.101579 GAGGGAGTAGCTGCGAAGAC 59.898 60.000 0.00 0.00 0.00 3.01
315 1217 1.226717 GGGAGTAGCTGCGAAGACG 60.227 63.158 0.00 0.00 42.93 4.18
318 1220 0.248296 GAGTAGCTGCGAAGACGAGG 60.248 60.000 0.00 0.00 42.66 4.63
362 1520 3.787001 CGTGCCTCCTTCCTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
363 1521 3.787001 GTGCCTCCTTCCTCCCCG 61.787 72.222 0.00 0.00 0.00 5.73
365 1523 2.687566 GCCTCCTTCCTCCCCGAA 60.688 66.667 0.00 0.00 0.00 4.30
367 1525 2.722201 CCTCCTTCCTCCCCGAACG 61.722 68.421 0.00 0.00 0.00 3.95
368 1526 2.682494 TCCTTCCTCCCCGAACGG 60.682 66.667 6.25 6.25 0.00 4.44
369 1527 2.682494 CCTTCCTCCCCGAACGGA 60.682 66.667 15.07 0.00 37.50 4.69
909 2067 5.212194 CGAATAAAATATCTGCCCCGTTTG 58.788 41.667 0.00 0.00 0.00 2.93
962 2120 3.086600 CCTCCCTGGGCTCTCACC 61.087 72.222 8.22 0.00 0.00 4.02
963 2121 2.040278 CTCCCTGGGCTCTCACCT 59.960 66.667 8.22 0.00 0.00 4.00
964 2122 1.311403 CTCCCTGGGCTCTCACCTA 59.689 63.158 8.22 0.00 0.00 3.08
965 2123 0.758685 CTCCCTGGGCTCTCACCTAG 60.759 65.000 8.22 0.00 38.01 3.02
1088 2256 1.240256 GGATCGATCCAGCTACTCGT 58.760 55.000 34.65 0.00 46.38 4.18
1098 2266 2.278013 CTACTCGTTCGAGGCGGC 60.278 66.667 22.90 0.00 36.64 6.53
1193 2361 0.181114 CCAATGGGAATCTCTCGGCA 59.819 55.000 0.00 0.00 35.59 5.69
1208 2376 3.066814 GCACTCGACTACGGGGGT 61.067 66.667 0.00 0.00 46.21 4.95
1433 2601 1.671742 GACCTTCTGCTGGGACGAA 59.328 57.895 0.00 0.00 0.00 3.85
1571 2739 2.260434 GACAGGTTCCGCTGCGTA 59.740 61.111 21.59 1.07 0.00 4.42
1721 2889 2.202756 GAGGCCTACGTCCTTGCG 60.203 66.667 4.42 0.00 33.24 4.85
1868 3036 0.322816 GATTCTTCCTGCACAGCCCA 60.323 55.000 0.00 0.00 0.00 5.36
2097 3265 2.455557 TGCCTGTTGGGATTAACATGG 58.544 47.619 0.00 0.00 39.60 3.66
2132 3300 3.684693 GCTCCAGCTTCCTGATCTC 57.315 57.895 0.00 0.00 41.77 2.75
2321 3489 3.087065 CCAAGGGGTGGTAGTGGG 58.913 66.667 0.00 0.00 43.20 4.61
2376 3544 4.636206 AGGAAAGTTGCACGAGGATTAATC 59.364 41.667 6.93 6.93 0.00 1.75
2418 3586 4.323562 GGTATAGTCCTGTGGAGCTTGTTT 60.324 45.833 0.00 0.00 29.39 2.83
2426 3594 4.323485 CCTGTGGAGCTTGTTTATAGGACA 60.323 45.833 0.00 0.00 0.00 4.02
2448 3616 1.967779 TGTCGAGTGTGGAAAGGATGA 59.032 47.619 0.00 0.00 0.00 2.92
2460 3628 7.011482 GTGTGGAAAGGATGACATATTACACTC 59.989 40.741 17.63 13.13 32.96 3.51
2591 3759 6.431234 CACCAAAGAGGAAAAGTATGCTAGTT 59.569 38.462 0.00 0.00 41.22 2.24
2745 3913 7.040494 CCATGAGAAGCATTATCGATATGTCT 58.960 38.462 5.84 4.99 39.67 3.41
2894 4062 3.129638 ACCGCAACTTCAAAAAGCTTACA 59.870 39.130 0.00 0.00 35.81 2.41
3029 4197 7.040201 ACTGTTGTTAACATCATGAATGCTCTT 60.040 33.333 17.45 0.00 41.26 2.85
3163 4331 6.578023 ACTTTATGAGGTATGCTCTCACTTC 58.422 40.000 4.59 0.00 43.07 3.01
3289 4457 9.810231 CAAGTATAAACAAATGCAAAATCAACC 57.190 29.630 0.00 0.00 0.00 3.77
3396 4574 7.665561 TCATAGAACGATCATTTGAACAACA 57.334 32.000 0.00 0.00 0.00 3.33
3440 4618 2.404559 TGTGGGGTACAGGATCATACC 58.595 52.381 10.26 10.26 40.25 2.73
3531 4709 7.821595 AAGTAACAACATGCATCATCAATTG 57.178 32.000 0.00 0.00 0.00 2.32
3613 4791 2.160721 TCAGTAGGGGAGCCTACAAG 57.839 55.000 2.25 0.00 43.49 3.16
3717 4895 6.986231 GGACCAATTCAAGAGTTCACAAAATT 59.014 34.615 0.00 0.00 0.00 1.82
3840 5018 6.155221 AGCTGTGATTACCATGAAGTCTCTTA 59.845 38.462 0.00 0.00 0.00 2.10
3922 5100 0.251209 GGGAAACAGTGGGGGAGAAC 60.251 60.000 0.00 0.00 0.00 3.01
4045 5223 4.184629 GGTGAAGTAAGACCAGTATGCAG 58.815 47.826 0.00 0.00 31.97 4.41
4259 5438 6.142320 CGTTCTTAATTTTCAGTTTGTGCCTC 59.858 38.462 0.00 0.00 0.00 4.70
4457 5638 5.303078 CCTGTATACAGAAGCTACTGATGGT 59.697 44.000 30.41 0.00 46.59 3.55
4925 6109 8.743714 AGTTCATTAAACAAATCCTGGATTCTC 58.256 33.333 21.57 3.25 40.56 2.87
5224 6408 5.211201 AGCAAGGCCAAGTATTATTTGGAT 58.789 37.500 19.10 6.30 46.42 3.41
5338 6522 1.137872 GAGGAGGCATGATGAAGTCGT 59.862 52.381 0.00 0.00 0.00 4.34
5339 6523 1.134580 AGGAGGCATGATGAAGTCGTG 60.135 52.381 0.00 0.00 44.99 4.35
5340 6524 1.293924 GAGGCATGATGAAGTCGTGG 58.706 55.000 0.00 0.00 42.89 4.94
5341 6525 0.904649 AGGCATGATGAAGTCGTGGA 59.095 50.000 0.00 0.00 42.89 4.02
5342 6526 1.487976 AGGCATGATGAAGTCGTGGAT 59.512 47.619 0.00 0.00 42.89 3.41
5343 6527 1.600957 GGCATGATGAAGTCGTGGATG 59.399 52.381 0.00 0.00 42.89 3.51
5344 6528 1.003116 GCATGATGAAGTCGTGGATGC 60.003 52.381 0.00 0.00 42.89 3.91
5345 6529 2.282407 CATGATGAAGTCGTGGATGCA 58.718 47.619 0.00 0.00 39.68 3.96
5346 6530 2.014335 TGATGAAGTCGTGGATGCAG 57.986 50.000 0.00 0.00 0.00 4.41
5347 6531 1.293924 GATGAAGTCGTGGATGCAGG 58.706 55.000 0.00 0.00 0.00 4.85
5348 6532 0.904649 ATGAAGTCGTGGATGCAGGA 59.095 50.000 5.43 5.43 0.00 3.86
5349 6533 0.247460 TGAAGTCGTGGATGCAGGAG 59.753 55.000 10.06 0.00 0.00 3.69
5350 6534 0.532573 GAAGTCGTGGATGCAGGAGA 59.467 55.000 10.06 0.00 0.00 3.71
5495 6679 5.104235 ACCTAGTGTTGGTCTAGTTTTGGTT 60.104 40.000 0.00 0.00 34.72 3.67
5777 6963 3.967332 TTTACTCCCTCCGTACCAAAG 57.033 47.619 0.00 0.00 0.00 2.77
5901 7153 4.008933 GCCTCCCCATAGCGCGAT 62.009 66.667 12.10 5.99 0.00 4.58
5948 7212 3.612247 CTCCAGGCCGTGAACCAGG 62.612 68.421 0.00 0.00 35.22 4.45
5954 7218 3.052082 CCGTGAACCAGGCTGCTG 61.052 66.667 9.56 0.00 0.00 4.41
5955 7219 3.730761 CGTGAACCAGGCTGCTGC 61.731 66.667 9.56 7.10 38.76 5.25
5956 7220 3.730761 GTGAACCAGGCTGCTGCG 61.731 66.667 9.56 0.00 40.82 5.18
6007 7271 4.457496 CAGGCCGCGATCCAGTGT 62.457 66.667 8.23 0.00 0.00 3.55
6008 7272 2.758327 AGGCCGCGATCCAGTGTA 60.758 61.111 8.23 0.00 0.00 2.90
6009 7273 2.585247 GGCCGCGATCCAGTGTAC 60.585 66.667 8.23 0.00 0.00 2.90
6165 7450 7.938140 TTTGTCAAAAAGAAGAAGAAGAGGA 57.062 32.000 0.00 0.00 0.00 3.71
6166 7451 7.938140 TTGTCAAAAAGAAGAAGAAGAGGAA 57.062 32.000 0.00 0.00 0.00 3.36
6167 7452 7.559590 TGTCAAAAAGAAGAAGAAGAGGAAG 57.440 36.000 0.00 0.00 0.00 3.46
6168 7453 7.338710 TGTCAAAAAGAAGAAGAAGAGGAAGA 58.661 34.615 0.00 0.00 0.00 2.87
6169 7454 7.995488 TGTCAAAAAGAAGAAGAAGAGGAAGAT 59.005 33.333 0.00 0.00 0.00 2.40
6170 7455 8.288913 GTCAAAAAGAAGAAGAAGAGGAAGATG 58.711 37.037 0.00 0.00 0.00 2.90
6171 7456 6.816134 AAAAGAAGAAGAAGAGGAAGATGC 57.184 37.500 0.00 0.00 0.00 3.91
6172 7457 5.495926 AAGAAGAAGAAGAGGAAGATGCA 57.504 39.130 0.00 0.00 0.00 3.96
6173 7458 4.831107 AGAAGAAGAAGAGGAAGATGCAC 58.169 43.478 0.00 0.00 0.00 4.57
6208 7493 2.159156 TGCAAATCAAGATCATGCAGGC 60.159 45.455 15.31 0.00 38.09 4.85
6264 7549 5.324409 TCTTTGAAATGGCAGTTATCCTGT 58.676 37.500 0.00 0.00 43.55 4.00
6270 7555 6.543465 TGAAATGGCAGTTATCCTGTATTCAG 59.457 38.462 0.00 0.00 43.55 3.02
6277 7562 7.439655 GGCAGTTATCCTGTATTCAGTAAGAAG 59.560 40.741 0.00 0.00 43.55 2.85
6278 7563 8.198109 GCAGTTATCCTGTATTCAGTAAGAAGA 58.802 37.037 0.00 0.00 43.55 2.87
6291 7579 5.692204 TCAGTAAGAAGAAAAGAGTTGCTCG 59.308 40.000 0.00 0.00 35.36 5.03
6293 7581 2.147150 AGAAGAAAAGAGTTGCTCGGC 58.853 47.619 0.00 0.00 35.36 5.54
6299 7587 4.762251 AGAAAAGAGTTGCTCGGCTAATTT 59.238 37.500 0.00 0.00 35.36 1.82
6300 7588 4.686839 AAAGAGTTGCTCGGCTAATTTC 57.313 40.909 0.00 0.00 35.36 2.17
6308 7596 2.477357 GCTCGGCTAATTTCGGAAAACC 60.477 50.000 7.33 6.25 0.00 3.27
6365 7654 2.544903 CCGGACAAAAACCATCACAACC 60.545 50.000 0.00 0.00 0.00 3.77
6366 7655 2.099921 CGGACAAAAACCATCACAACCA 59.900 45.455 0.00 0.00 0.00 3.67
6367 7656 3.243704 CGGACAAAAACCATCACAACCAT 60.244 43.478 0.00 0.00 0.00 3.55
6371 7660 5.927819 ACAAAAACCATCACAACCATTGAT 58.072 33.333 0.00 0.00 33.81 2.57
6373 7662 5.804944 AAAACCATCACAACCATTGATCA 57.195 34.783 0.00 0.00 30.98 2.92
6375 7664 4.038271 ACCATCACAACCATTGATCAGT 57.962 40.909 0.00 0.00 30.98 3.41
6392 7681 5.542635 TGATCAGTACACATAAGATACCCCC 59.457 44.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.470845 AAACAAAAGTCACTCTCACGAAG 57.529 39.130 0.00 0.00 0.00 3.79
1 2 5.873179 AAAACAAAAGTCACTCTCACGAA 57.127 34.783 0.00 0.00 0.00 3.85
2 3 5.642063 AGAAAAACAAAAGTCACTCTCACGA 59.358 36.000 0.00 0.00 0.00 4.35
3 4 5.869350 AGAAAAACAAAAGTCACTCTCACG 58.131 37.500 0.00 0.00 0.00 4.35
4 5 7.062255 CCAAAGAAAAACAAAAGTCACTCTCAC 59.938 37.037 0.00 0.00 0.00 3.51
5 6 7.090173 CCAAAGAAAAACAAAAGTCACTCTCA 58.910 34.615 0.00 0.00 0.00 3.27
6 7 7.062255 CACCAAAGAAAAACAAAAGTCACTCTC 59.938 37.037 0.00 0.00 0.00 3.20
7 8 6.868339 CACCAAAGAAAAACAAAAGTCACTCT 59.132 34.615 0.00 0.00 0.00 3.24
8 9 6.645003 ACACCAAAGAAAAACAAAAGTCACTC 59.355 34.615 0.00 0.00 0.00 3.51
9 10 6.521162 ACACCAAAGAAAAACAAAAGTCACT 58.479 32.000 0.00 0.00 0.00 3.41
10 11 6.779115 ACACCAAAGAAAAACAAAAGTCAC 57.221 33.333 0.00 0.00 0.00 3.67
11 12 7.600752 CCTTACACCAAAGAAAAACAAAAGTCA 59.399 33.333 0.00 0.00 0.00 3.41
12 13 7.601130 ACCTTACACCAAAGAAAAACAAAAGTC 59.399 33.333 0.00 0.00 0.00 3.01
13 14 7.386573 CACCTTACACCAAAGAAAAACAAAAGT 59.613 33.333 0.00 0.00 0.00 2.66
14 15 7.148490 CCACCTTACACCAAAGAAAAACAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
15 16 6.651225 CCACCTTACACCAAAGAAAAACAAAA 59.349 34.615 0.00 0.00 0.00 2.44
16 17 6.166982 CCACCTTACACCAAAGAAAAACAAA 58.833 36.000 0.00 0.00 0.00 2.83
17 18 5.246429 ACCACCTTACACCAAAGAAAAACAA 59.754 36.000 0.00 0.00 0.00 2.83
18 19 4.773149 ACCACCTTACACCAAAGAAAAACA 59.227 37.500 0.00 0.00 0.00 2.83
19 20 5.333299 ACCACCTTACACCAAAGAAAAAC 57.667 39.130 0.00 0.00 0.00 2.43
20 21 6.361768 AAACCACCTTACACCAAAGAAAAA 57.638 33.333 0.00 0.00 0.00 1.94
21 22 5.393243 CGAAACCACCTTACACCAAAGAAAA 60.393 40.000 0.00 0.00 0.00 2.29
22 23 4.096682 CGAAACCACCTTACACCAAAGAAA 59.903 41.667 0.00 0.00 0.00 2.52
23 24 3.628487 CGAAACCACCTTACACCAAAGAA 59.372 43.478 0.00 0.00 0.00 2.52
24 25 3.118334 TCGAAACCACCTTACACCAAAGA 60.118 43.478 0.00 0.00 0.00 2.52
25 26 3.207778 TCGAAACCACCTTACACCAAAG 58.792 45.455 0.00 0.00 0.00 2.77
26 27 3.207778 CTCGAAACCACCTTACACCAAA 58.792 45.455 0.00 0.00 0.00 3.28
27 28 2.841215 CTCGAAACCACCTTACACCAA 58.159 47.619 0.00 0.00 0.00 3.67
28 29 1.541670 GCTCGAAACCACCTTACACCA 60.542 52.381 0.00 0.00 0.00 4.17
29 30 1.154197 GCTCGAAACCACCTTACACC 58.846 55.000 0.00 0.00 0.00 4.16
30 31 1.154197 GGCTCGAAACCACCTTACAC 58.846 55.000 0.00 0.00 0.00 2.90
31 32 1.053424 AGGCTCGAAACCACCTTACA 58.947 50.000 6.89 0.00 0.00 2.41
32 33 2.614779 GTAGGCTCGAAACCACCTTAC 58.385 52.381 6.89 0.00 33.60 2.34
33 34 1.203052 CGTAGGCTCGAAACCACCTTA 59.797 52.381 6.89 0.00 33.60 2.69
34 35 0.037605 CGTAGGCTCGAAACCACCTT 60.038 55.000 6.89 0.00 33.60 3.50
35 36 1.183676 ACGTAGGCTCGAAACCACCT 61.184 55.000 12.16 2.05 36.27 4.00
36 37 1.012486 CACGTAGGCTCGAAACCACC 61.012 60.000 12.16 0.00 34.70 4.61
37 38 1.012486 CCACGTAGGCTCGAAACCAC 61.012 60.000 12.16 2.82 34.70 4.16
38 39 1.180456 TCCACGTAGGCTCGAAACCA 61.180 55.000 12.16 0.00 37.29 3.67
39 40 0.175073 ATCCACGTAGGCTCGAAACC 59.825 55.000 12.16 0.00 37.29 3.27
40 41 1.278238 CATCCACGTAGGCTCGAAAC 58.722 55.000 12.16 0.00 37.29 2.78
41 42 0.892755 ACATCCACGTAGGCTCGAAA 59.107 50.000 12.16 0.02 37.29 3.46
42 43 0.892755 AACATCCACGTAGGCTCGAA 59.107 50.000 12.16 0.31 37.29 3.71
43 44 0.454600 GAACATCCACGTAGGCTCGA 59.545 55.000 12.16 0.00 37.29 4.04
44 45 0.866061 CGAACATCCACGTAGGCTCG 60.866 60.000 0.00 0.00 37.29 5.03
45 46 1.146358 GCGAACATCCACGTAGGCTC 61.146 60.000 0.00 0.00 37.29 4.70
46 47 1.153628 GCGAACATCCACGTAGGCT 60.154 57.895 0.00 0.00 37.29 4.58
47 48 0.810031 ATGCGAACATCCACGTAGGC 60.810 55.000 0.00 0.00 37.29 3.93
48 49 1.209128 GATGCGAACATCCACGTAGG 58.791 55.000 0.00 0.00 45.94 3.18
57 58 3.802139 CGGTGTATTGTAGATGCGAACAT 59.198 43.478 0.00 0.00 39.98 2.71
58 59 3.183754 CGGTGTATTGTAGATGCGAACA 58.816 45.455 0.00 0.00 0.00 3.18
59 60 2.034001 GCGGTGTATTGTAGATGCGAAC 60.034 50.000 0.00 0.00 0.00 3.95
60 61 2.159156 AGCGGTGTATTGTAGATGCGAA 60.159 45.455 0.00 0.00 0.00 4.70
61 62 1.407618 AGCGGTGTATTGTAGATGCGA 59.592 47.619 0.00 0.00 0.00 5.10
62 63 1.787155 GAGCGGTGTATTGTAGATGCG 59.213 52.381 0.00 0.00 0.00 4.73
63 64 3.099267 AGAGCGGTGTATTGTAGATGC 57.901 47.619 0.00 0.00 0.00 3.91
64 65 8.988064 ATTATAAGAGCGGTGTATTGTAGATG 57.012 34.615 0.00 0.00 0.00 2.90
69 70 8.951787 TGTTAATTATAAGAGCGGTGTATTGT 57.048 30.769 0.00 0.00 0.00 2.71
72 73 9.998106 AGAATGTTAATTATAAGAGCGGTGTAT 57.002 29.630 0.00 0.00 0.00 2.29
73 74 9.472361 GAGAATGTTAATTATAAGAGCGGTGTA 57.528 33.333 0.00 0.00 0.00 2.90
74 75 8.204836 AGAGAATGTTAATTATAAGAGCGGTGT 58.795 33.333 0.00 0.00 0.00 4.16
75 76 8.594881 AGAGAATGTTAATTATAAGAGCGGTG 57.405 34.615 0.00 0.00 0.00 4.94
76 77 9.614792 AAAGAGAATGTTAATTATAAGAGCGGT 57.385 29.630 0.00 0.00 0.00 5.68
98 99 8.767085 CGGCGTACCATATTTTTATAGAAAAGA 58.233 33.333 0.00 0.00 33.93 2.52
99 100 8.553696 ACGGCGTACCATATTTTTATAGAAAAG 58.446 33.333 12.58 0.00 33.93 2.27
100 101 8.436046 ACGGCGTACCATATTTTTATAGAAAA 57.564 30.769 12.58 0.00 34.57 2.29
101 102 8.336806 CAACGGCGTACCATATTTTTATAGAAA 58.663 33.333 15.20 0.00 34.57 2.52
102 103 7.041916 CCAACGGCGTACCATATTTTTATAGAA 60.042 37.037 15.20 0.00 34.57 2.10
103 104 6.424509 CCAACGGCGTACCATATTTTTATAGA 59.575 38.462 15.20 0.00 34.57 1.98
104 105 6.203338 ACCAACGGCGTACCATATTTTTATAG 59.797 38.462 15.20 0.00 34.57 1.31
105 106 6.018098 CACCAACGGCGTACCATATTTTTATA 60.018 38.462 15.20 0.00 34.57 0.98
106 107 4.883006 ACCAACGGCGTACCATATTTTTAT 59.117 37.500 15.20 0.00 34.57 1.40
107 108 4.094590 CACCAACGGCGTACCATATTTTTA 59.905 41.667 15.20 0.00 34.57 1.52
108 109 3.083293 ACCAACGGCGTACCATATTTTT 58.917 40.909 15.20 0.00 34.57 1.94
109 110 2.420722 CACCAACGGCGTACCATATTTT 59.579 45.455 15.20 0.00 34.57 1.82
110 111 2.011222 CACCAACGGCGTACCATATTT 58.989 47.619 15.20 0.00 34.57 1.40
111 112 1.065998 ACACCAACGGCGTACCATATT 60.066 47.619 15.20 0.00 34.57 1.28
112 113 0.538118 ACACCAACGGCGTACCATAT 59.462 50.000 15.20 0.00 34.57 1.78
113 114 1.135141 GTACACCAACGGCGTACCATA 60.135 52.381 15.20 0.00 35.80 2.74
114 115 0.390209 GTACACCAACGGCGTACCAT 60.390 55.000 15.20 0.00 35.80 3.55
115 116 1.006337 GTACACCAACGGCGTACCA 60.006 57.895 15.20 0.00 35.80 3.25
116 117 0.319813 AAGTACACCAACGGCGTACC 60.320 55.000 15.20 0.00 40.79 3.34
117 118 1.501169 AAAGTACACCAACGGCGTAC 58.499 50.000 15.20 6.62 40.36 3.67
118 119 1.865970 CAAAAGTACACCAACGGCGTA 59.134 47.619 15.20 0.00 0.00 4.42
119 120 0.658897 CAAAAGTACACCAACGGCGT 59.341 50.000 6.77 6.77 0.00 5.68
120 121 0.938713 TCAAAAGTACACCAACGGCG 59.061 50.000 4.80 4.80 0.00 6.46
121 122 3.423996 TTTCAAAAGTACACCAACGGC 57.576 42.857 0.00 0.00 0.00 5.68
150 151 0.532196 GCATAAGCCCACGTACTCCC 60.532 60.000 0.00 0.00 33.58 4.30
188 189 2.664015 ACGGAGGGAGTAGGTGATAAC 58.336 52.381 0.00 0.00 0.00 1.89
194 195 1.379576 CCGAACGGAGGGAGTAGGT 60.380 63.158 7.53 0.00 37.50 3.08
199 200 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
203 204 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
204 205 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
205 206 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
206 207 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
209 210 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
210 211 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
211 212 3.486875 CCATTTCCGCGACAAGTAATTCC 60.487 47.826 8.23 0.00 0.00 3.01
213 214 3.340034 TCCATTTCCGCGACAAGTAATT 58.660 40.909 8.23 0.00 0.00 1.40
214 215 2.980568 TCCATTTCCGCGACAAGTAAT 58.019 42.857 8.23 0.00 0.00 1.89
216 217 2.276201 CATCCATTTCCGCGACAAGTA 58.724 47.619 8.23 0.00 0.00 2.24
218 219 1.086696 ACATCCATTTCCGCGACAAG 58.913 50.000 8.23 0.00 0.00 3.16
219 220 2.388310 TACATCCATTTCCGCGACAA 57.612 45.000 8.23 0.00 0.00 3.18
221 222 2.755650 AGATACATCCATTTCCGCGAC 58.244 47.619 8.23 0.00 0.00 5.19
222 223 3.824443 TCTAGATACATCCATTTCCGCGA 59.176 43.478 8.23 0.00 0.00 5.87
223 224 3.921021 GTCTAGATACATCCATTTCCGCG 59.079 47.826 0.00 0.00 0.00 6.46
224 225 3.921021 CGTCTAGATACATCCATTTCCGC 59.079 47.826 0.00 0.00 0.00 5.54
226 227 9.490379 AAAATACGTCTAGATACATCCATTTCC 57.510 33.333 0.00 0.00 0.00 3.13
264 1166 9.098355 CGAAATTACTTGTCTCAGAAATGGATA 57.902 33.333 0.00 0.00 0.00 2.59
265 1167 7.824289 TCGAAATTACTTGTCTCAGAAATGGAT 59.176 33.333 0.00 0.00 0.00 3.41
269 1171 7.360101 CCGTTCGAAATTACTTGTCTCAGAAAT 60.360 37.037 0.00 0.00 0.00 2.17
270 1172 6.073980 CCGTTCGAAATTACTTGTCTCAGAAA 60.074 38.462 0.00 0.00 0.00 2.52
271 1173 5.404366 CCGTTCGAAATTACTTGTCTCAGAA 59.596 40.000 0.00 0.00 0.00 3.02
273 1175 4.921515 TCCGTTCGAAATTACTTGTCTCAG 59.078 41.667 0.00 0.00 0.00 3.35
274 1176 4.873817 TCCGTTCGAAATTACTTGTCTCA 58.126 39.130 0.00 0.00 0.00 3.27
275 1177 4.326548 CCTCCGTTCGAAATTACTTGTCTC 59.673 45.833 0.00 0.00 0.00 3.36
276 1178 4.243270 CCTCCGTTCGAAATTACTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
277 1179 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
278 1180 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
279 1181 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
280 1182 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
281 1183 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
282 1184 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
285 1187 1.136500 GCTACTCCCTCCGTTCGAAAT 59.864 52.381 0.00 0.00 0.00 2.17
286 1188 0.529378 GCTACTCCCTCCGTTCGAAA 59.471 55.000 0.00 0.00 0.00 3.46
287 1189 0.323178 AGCTACTCCCTCCGTTCGAA 60.323 55.000 0.00 0.00 0.00 3.71
289 1191 1.433879 CAGCTACTCCCTCCGTTCG 59.566 63.158 0.00 0.00 0.00 3.95
291 1193 2.711922 CGCAGCTACTCCCTCCGTT 61.712 63.158 0.00 0.00 0.00 4.44
293 1195 2.343163 CTTCGCAGCTACTCCCTCCG 62.343 65.000 0.00 0.00 0.00 4.63
294 1196 1.038130 TCTTCGCAGCTACTCCCTCC 61.038 60.000 0.00 0.00 0.00 4.30
295 1197 0.101579 GTCTTCGCAGCTACTCCCTC 59.898 60.000 0.00 0.00 0.00 4.30
296 1198 1.658686 CGTCTTCGCAGCTACTCCCT 61.659 60.000 0.00 0.00 0.00 4.20
297 1199 1.226717 CGTCTTCGCAGCTACTCCC 60.227 63.158 0.00 0.00 0.00 4.30
299 1201 0.248296 CCTCGTCTTCGCAGCTACTC 60.248 60.000 0.00 0.00 36.96 2.59
304 1206 3.184683 CAGCCTCGTCTTCGCAGC 61.185 66.667 0.00 0.00 36.96 5.25
307 1209 0.944311 TGAAACAGCCTCGTCTTCGC 60.944 55.000 0.00 0.00 36.96 4.70
962 2120 1.076632 AGGAGGTGACGAGGGCTAG 60.077 63.158 0.00 0.00 0.00 3.42
963 2121 1.379977 CAGGAGGTGACGAGGGCTA 60.380 63.158 0.00 0.00 0.00 3.93
964 2122 2.681778 CAGGAGGTGACGAGGGCT 60.682 66.667 0.00 0.00 0.00 5.19
965 2123 4.459089 GCAGGAGGTGACGAGGGC 62.459 72.222 0.00 0.00 0.00 5.19
1193 2361 1.680314 GGAACCCCCGTAGTCGAGT 60.680 63.158 0.00 0.00 39.71 4.18
1523 2691 2.258591 GCGACGTCTTCCTGCTCA 59.741 61.111 14.70 0.00 0.00 4.26
1571 2739 4.995058 TTGGGGAGGAAGGCCGGT 62.995 66.667 1.90 0.00 39.96 5.28
1721 2889 1.136502 CGCTGCGAGAAGAGTTTGTTC 60.137 52.381 18.66 0.00 0.00 3.18
1766 2934 1.947456 TGGATCCAGATGTAGTCGTCG 59.053 52.381 11.44 0.00 35.01 5.12
1868 3036 1.727062 AGAGCTCCGATGATGGGAAT 58.273 50.000 10.93 0.00 32.02 3.01
2132 3300 2.710971 CTCTGCAACACGCGACTCG 61.711 63.158 15.93 0.00 46.97 4.18
2166 3334 2.486472 AGCAAGACAGTCTTCCCATG 57.514 50.000 13.27 3.86 33.78 3.66
2168 3336 1.202806 CCAAGCAAGACAGTCTTCCCA 60.203 52.381 13.27 0.00 33.78 4.37
2321 3489 3.127030 CCTTTAATCCTTGCACGTCCTTC 59.873 47.826 0.00 0.00 0.00 3.46
2376 3544 2.637025 CGACCGCCCAAACTGTTG 59.363 61.111 0.00 0.00 34.25 3.33
2418 3586 4.274978 TCCACACTCGACAATGTCCTATA 58.725 43.478 7.91 0.00 0.00 1.31
2426 3594 3.007940 TCATCCTTTCCACACTCGACAAT 59.992 43.478 0.00 0.00 0.00 2.71
2460 3628 2.356313 AACGACGCACTCAGCCAG 60.356 61.111 0.00 0.00 41.38 4.85
2579 3747 7.161404 TGAATTCTGACACAACTAGCATACTT 58.839 34.615 7.05 0.00 0.00 2.24
2591 3759 4.910195 AGCAACCTATGAATTCTGACACA 58.090 39.130 7.05 0.00 0.00 3.72
2745 3913 2.197283 TAGGCAACATCATGTGTGCA 57.803 45.000 19.87 4.83 41.14 4.57
2894 4062 7.112122 TGTAATCAGCAACAATAGAATCCACT 58.888 34.615 0.00 0.00 0.00 4.00
3029 4197 6.882610 ACAACATTCTTCTTATCAGCACAA 57.117 33.333 0.00 0.00 0.00 3.33
3202 4370 5.221880 GCAAAGTCAATGCAAGACATGTTA 58.778 37.500 20.52 0.00 43.29 2.41
3531 4709 7.926018 ACCTTCAGAACCAACATTCAAATTTAC 59.074 33.333 0.00 0.00 0.00 2.01
3717 4895 6.126273 TGAGAACTATTAGGGTACAGCCTCTA 60.126 42.308 2.61 0.00 37.43 2.43
3867 5045 6.260700 TCCATGGTAAATGCCTAACAGTAT 57.739 37.500 12.58 0.00 0.00 2.12
3922 5100 7.162082 ACTCAGTAGAAAAATTGACAGTAGGG 58.838 38.462 0.00 0.00 0.00 3.53
3935 5113 7.446769 TGCAATGGTAAGTACTCAGTAGAAAA 58.553 34.615 0.00 0.00 0.00 2.29
3936 5114 6.999950 TGCAATGGTAAGTACTCAGTAGAAA 58.000 36.000 0.00 0.00 0.00 2.52
3937 5115 6.599356 TGCAATGGTAAGTACTCAGTAGAA 57.401 37.500 0.00 0.00 0.00 2.10
4045 5223 5.739752 TCAGCATGTTGTATAGTTGCATC 57.260 39.130 9.54 0.00 37.40 3.91
4925 6109 5.180868 CCAGACAAGAAATCAGTTTCCAGAG 59.819 44.000 0.00 0.00 43.82 3.35
5338 6522 1.137675 CTTCGACATCTCCTGCATCCA 59.862 52.381 0.00 0.00 0.00 3.41
5339 6523 1.410517 TCTTCGACATCTCCTGCATCC 59.589 52.381 0.00 0.00 0.00 3.51
5340 6524 2.741612 CTCTTCGACATCTCCTGCATC 58.258 52.381 0.00 0.00 0.00 3.91
5341 6525 1.202510 GCTCTTCGACATCTCCTGCAT 60.203 52.381 0.00 0.00 0.00 3.96
5342 6526 0.174389 GCTCTTCGACATCTCCTGCA 59.826 55.000 0.00 0.00 0.00 4.41
5343 6527 0.174389 TGCTCTTCGACATCTCCTGC 59.826 55.000 0.00 0.00 0.00 4.85
5344 6528 2.886862 ATGCTCTTCGACATCTCCTG 57.113 50.000 0.00 0.00 0.00 3.86
5345 6529 4.406456 AGATATGCTCTTCGACATCTCCT 58.594 43.478 0.00 0.00 0.00 3.69
5346 6530 4.217334 TGAGATATGCTCTTCGACATCTCC 59.783 45.833 6.87 0.00 44.27 3.71
5347 6531 5.369685 TGAGATATGCTCTTCGACATCTC 57.630 43.478 0.00 0.00 44.27 2.75
5348 6532 5.981088 ATGAGATATGCTCTTCGACATCT 57.019 39.130 0.00 0.00 44.27 2.90
5349 6533 6.851609 ACTATGAGATATGCTCTTCGACATC 58.148 40.000 0.00 0.00 44.27 3.06
5350 6534 6.127758 GGACTATGAGATATGCTCTTCGACAT 60.128 42.308 0.00 0.00 44.27 3.06
5495 6679 3.249080 CGAGAAGGCAAACGGTAAAAGAA 59.751 43.478 0.00 0.00 0.00 2.52
5612 6798 6.185511 ACATACACTACCTGCTACTAACAGA 58.814 40.000 0.00 0.00 37.32 3.41
5682 6868 3.721575 TGGCCCAAATGGTCATCTACTAT 59.278 43.478 0.00 0.00 46.23 2.12
5901 7153 2.966732 CGGTAGGGAGGCAAAGGCA 61.967 63.158 0.00 0.00 43.71 4.75
5956 7220 4.329545 TGGTTCACGGCCTGGAGC 62.330 66.667 0.00 3.35 42.60 4.70
5957 7221 2.046892 CTGGTTCACGGCCTGGAG 60.047 66.667 0.00 0.00 0.00 3.86
5958 7222 3.636231 CCTGGTTCACGGCCTGGA 61.636 66.667 0.00 0.00 44.79 3.86
6007 7271 2.549198 CGCCGGCGTGGATCTAGTA 61.549 63.158 39.71 0.00 42.00 1.82
6008 7272 3.900892 CGCCGGCGTGGATCTAGT 61.901 66.667 39.71 0.00 42.00 2.57
6208 7493 4.693283 TCTCTGGTTGTGTACTCAAGTTG 58.307 43.478 10.50 0.00 0.00 3.16
6239 7524 5.649395 CAGGATAACTGCCATTTCAAAGAGA 59.351 40.000 0.00 0.00 40.97 3.10
6240 7525 5.888105 CAGGATAACTGCCATTTCAAAGAG 58.112 41.667 0.00 0.00 40.97 2.85
6241 7526 5.902613 CAGGATAACTGCCATTTCAAAGA 57.097 39.130 0.00 0.00 40.97 2.52
6264 7549 9.209175 GAGCAACTCTTTTCTTCTTACTGAATA 57.791 33.333 0.00 0.00 33.71 1.75
6270 7555 4.377533 GCCGAGCAACTCTTTTCTTCTTAC 60.378 45.833 0.00 0.00 0.00 2.34
6277 7562 4.686839 AATTAGCCGAGCAACTCTTTTC 57.313 40.909 0.00 0.00 0.00 2.29
6278 7563 4.378459 CGAAATTAGCCGAGCAACTCTTTT 60.378 41.667 0.00 0.00 0.00 2.27
6279 7564 3.125316 CGAAATTAGCCGAGCAACTCTTT 59.875 43.478 0.00 0.00 0.00 2.52
6318 7606 6.662755 TCTCCATAATTAACTGGCAATCTGT 58.337 36.000 0.82 0.00 32.30 3.41
6365 7654 7.604164 GGGGTATCTTATGTGTACTGATCAATG 59.396 40.741 0.00 0.00 0.00 2.82
6366 7655 7.256691 GGGGGTATCTTATGTGTACTGATCAAT 60.257 40.741 0.00 0.00 0.00 2.57
6367 7656 6.042781 GGGGGTATCTTATGTGTACTGATCAA 59.957 42.308 0.00 0.00 0.00 2.57
6392 7681 0.242286 CTCTCTCGAGTGGTGTGTGG 59.758 60.000 13.13 0.00 32.47 4.17
6405 7694 2.116827 TCTTGACGAGACCCTCTCTC 57.883 55.000 0.00 0.00 41.26 3.20
6431 7720 3.129109 GAGTGATGACGATGATGCATGT 58.871 45.455 2.46 0.00 0.00 3.21
6437 7726 1.967066 GGGAGGAGTGATGACGATGAT 59.033 52.381 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.