Multiple sequence alignment - TraesCS5A01G391500

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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 TraesCS5A01G391500 chr5A 100.000 3455 0 0 1 3455 586670950 586667496 0.000000e+00 6381.0
1 TraesCS5A01G391500 chr5D 92.128 2744 121 45 629 3345 466571045 466568370 0.000000e+00 3783.0
2 TraesCS5A01G391500 chr5D 89.277 401 24 9 277 661 466571438 466571041 5.180000e-133 484.0
3 TraesCS5A01G391500 chr5B 93.396 1060 37 17 1400 2457 573408697 573407669 0.000000e+00 1539.0
4 TraesCS5A01G391500 chr5B 92.038 942 47 13 2487 3404 573407671 573406734 0.000000e+00 1299.0
5 TraesCS5A01G391500 chr5B 87.697 634 40 14 639 1243 573409338 573408714 0.000000e+00 704.0
6 TraesCS5A01G391500 chr1D 91.875 160 4 4 107 265 365226013 365225862 7.510000e-52 215.0
7 TraesCS5A01G391500 chr1D 82.331 266 14 12 1 265 452008668 452008435 2.100000e-47 200.0
8 TraesCS5A01G391500 chr1D 83.721 215 11 8 1 215 342192994 342192804 7.620000e-42 182.0
9 TraesCS5A01G391500 chr1D 79.310 145 14 8 129 267 22273856 22273990 1.710000e-13 87.9
10 TraesCS5A01G391500 chr1D 77.419 124 19 7 2266 2386 462091981 462091864 8.000000e-07 65.8
11 TraesCS5A01G391500 chr1A 82.310 277 15 12 1 275 12250567 12250323 3.490000e-50 209.0
12 TraesCS5A01G391500 chr1A 84.118 170 18 2 106 274 493946757 493946596 4.620000e-34 156.0
13 TraesCS5A01G391500 chr4D 90.625 160 6 3 107 265 484583620 484583771 1.630000e-48 204.0
14 TraesCS5A01G391500 chr4D 88.199 161 8 5 107 264 490014139 490013987 7.620000e-42 182.0
15 TraesCS5A01G391500 chr7D 82.397 267 9 13 1 266 154206741 154206970 7.560000e-47 198.0
16 TraesCS5A01G391500 chr7D 86.709 158 7 4 112 265 577930837 577930690 2.760000e-36 163.0
17 TraesCS5A01G391500 chr2B 80.702 285 22 14 1 284 676507942 676507690 1.270000e-44 191.0
18 TraesCS5A01G391500 chr2B 77.193 114 24 2 1866 1978 39093581 39093693 8.000000e-07 65.8
19 TraesCS5A01G391500 chr6D 81.509 265 17 6 1 265 423548453 423548221 4.550000e-44 189.0
20 TraesCS5A01G391500 chr6D 82.609 138 11 5 132 265 461509585 461509457 3.650000e-20 110.0
21 TraesCS5A01G391500 chr3A 87.879 165 12 1 111 275 26887068 26887224 1.640000e-43 187.0
22 TraesCS5A01G391500 chr3A 72.414 522 106 31 1870 2374 32100717 32100217 7.780000e-27 132.0
23 TraesCS5A01G391500 chr3A 93.333 75 4 1 2 76 26887002 26887075 3.650000e-20 110.0
24 TraesCS5A01G391500 chr2A 80.072 276 20 12 1 275 733388521 733388762 4.580000e-39 172.0
25 TraesCS5A01G391500 chr2A 88.889 108 7 5 16 123 778340905 778341007 1.010000e-25 128.0
26 TraesCS5A01G391500 chr4A 79.771 262 26 10 1 262 681105812 681106046 7.670000e-37 165.0
27 TraesCS5A01G391500 chr2D 85.526 152 8 6 126 275 498213488 498213349 2.780000e-31 147.0
28 TraesCS5A01G391500 chr3B 76.113 247 42 15 2132 2374 39580966 39580733 2.820000e-21 113.0
29 TraesCS5A01G391500 chr1B 83.962 106 12 2 18 123 660013876 660013776 2.840000e-16 97.1
30 TraesCS5A01G391500 chrUn 97.500 40 1 0 2157 2196 308272754 308272793 6.190000e-08 69.4


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 TraesCS5A01G391500 chr5A 586667496 586670950 3454 True 6381.000000 6381 100.000000 1 3455 1 chr5A.!!$R1 3454
1 TraesCS5A01G391500 chr5D 466568370 466571438 3068 True 2133.500000 3783 90.702500 277 3345 2 chr5D.!!$R1 3068
2 TraesCS5A01G391500 chr5B 573406734 573409338 2604 True 1180.666667 1539 91.043667 639 3404 3 chr5B.!!$R1 2765

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
957 1039 0.035725 GTAGCCTTACCACACACCCC 60.036 60.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2549 2636 0.317938 AGTCGATCGGATAAGCGTGC 60.318 55.0 16.41 0.0 0.0 5.34 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
32 33 4.770874 CCGACCCCGCCGTTTGAT 62.771 66.667 0.00 0.00 0.00 2.57
33 34 3.496131 CGACCCCGCCGTTTGATG 61.496 66.667 0.00 0.00 0.00 3.07
34 35 2.359478 GACCCCGCCGTTTGATGT 60.359 61.111 0.00 0.00 0.00 3.06
35 36 2.671619 ACCCCGCCGTTTGATGTG 60.672 61.111 0.00 0.00 0.00 3.21
36 37 2.671619 CCCCGCCGTTTGATGTGT 60.672 61.111 0.00 0.00 0.00 3.72
37 38 2.265182 CCCCGCCGTTTGATGTGTT 61.265 57.895 0.00 0.00 0.00 3.32
38 39 1.081509 CCCGCCGTTTGATGTGTTG 60.082 57.895 0.00 0.00 0.00 3.33
39 40 1.729131 CCGCCGTTTGATGTGTTGC 60.729 57.895 0.00 0.00 0.00 4.17
40 41 1.729131 CGCCGTTTGATGTGTTGCC 60.729 57.895 0.00 0.00 0.00 4.52
41 42 1.372872 GCCGTTTGATGTGTTGCCC 60.373 57.895 0.00 0.00 0.00 5.36
42 43 2.037053 CCGTTTGATGTGTTGCCCA 58.963 52.632 0.00 0.00 0.00 5.36
43 44 0.318614 CCGTTTGATGTGTTGCCCAC 60.319 55.000 0.00 0.00 44.78 4.61
51 52 4.555709 TGTTGCCCACGCGTCCTT 62.556 61.111 9.86 0.00 38.08 3.36
52 53 3.284449 GTTGCCCACGCGTCCTTT 61.284 61.111 9.86 0.00 38.08 3.11
53 54 2.975799 TTGCCCACGCGTCCTTTC 60.976 61.111 9.86 0.00 38.08 2.62
54 55 3.469863 TTGCCCACGCGTCCTTTCT 62.470 57.895 9.86 0.00 38.08 2.52
55 56 2.668550 GCCCACGCGTCCTTTCTT 60.669 61.111 9.86 0.00 0.00 2.52
56 57 2.258726 GCCCACGCGTCCTTTCTTT 61.259 57.895 9.86 0.00 0.00 2.52
57 58 1.792118 GCCCACGCGTCCTTTCTTTT 61.792 55.000 9.86 0.00 0.00 2.27
58 59 0.666374 CCCACGCGTCCTTTCTTTTT 59.334 50.000 9.86 0.00 0.00 1.94
78 79 3.779271 TTTTTGGTACGCCGAACTTTT 57.221 38.095 0.00 0.00 37.86 2.27
79 80 3.337301 TTTTGGTACGCCGAACTTTTC 57.663 42.857 0.00 0.00 37.86 2.29
80 81 1.950828 TTGGTACGCCGAACTTTTCA 58.049 45.000 0.00 0.00 37.67 2.69
81 82 2.172851 TGGTACGCCGAACTTTTCAT 57.827 45.000 0.00 0.00 37.67 2.57
82 83 2.070783 TGGTACGCCGAACTTTTCATC 58.929 47.619 0.00 0.00 37.67 2.92
83 84 1.395954 GGTACGCCGAACTTTTCATCC 59.604 52.381 0.00 0.00 0.00 3.51
84 85 1.060122 GTACGCCGAACTTTTCATCCG 59.940 52.381 0.00 0.00 0.00 4.18
85 86 0.320073 ACGCCGAACTTTTCATCCGA 60.320 50.000 0.00 0.00 0.00 4.55
86 87 1.006832 CGCCGAACTTTTCATCCGAT 58.993 50.000 0.00 0.00 0.00 4.18
87 88 1.004927 CGCCGAACTTTTCATCCGATC 60.005 52.381 0.00 0.00 0.00 3.69
88 89 1.004927 GCCGAACTTTTCATCCGATCG 60.005 52.381 8.51 8.51 0.00 3.69
89 90 1.004927 CCGAACTTTTCATCCGATCGC 60.005 52.381 10.32 0.00 0.00 4.58
90 91 1.004927 CGAACTTTTCATCCGATCGCC 60.005 52.381 10.32 0.00 0.00 5.54
91 92 2.006888 GAACTTTTCATCCGATCGCCA 58.993 47.619 10.32 0.00 0.00 5.69
92 93 2.107950 ACTTTTCATCCGATCGCCAA 57.892 45.000 10.32 0.00 0.00 4.52
93 94 2.432444 ACTTTTCATCCGATCGCCAAA 58.568 42.857 10.32 2.40 0.00 3.28
94 95 2.161609 ACTTTTCATCCGATCGCCAAAC 59.838 45.455 10.32 0.00 0.00 2.93
95 96 2.107950 TTTCATCCGATCGCCAAACT 57.892 45.000 10.32 0.00 0.00 2.66
96 97 1.368641 TTCATCCGATCGCCAAACTG 58.631 50.000 10.32 0.35 0.00 3.16
97 98 0.249120 TCATCCGATCGCCAAACTGT 59.751 50.000 10.32 0.00 0.00 3.55
98 99 0.374758 CATCCGATCGCCAAACTGTG 59.625 55.000 10.32 0.00 0.00 3.66
109 110 3.498927 CCAAACTGTGGCAAGATGATC 57.501 47.619 0.00 0.00 41.72 2.92
110 111 2.159476 CCAAACTGTGGCAAGATGATCG 60.159 50.000 0.00 0.00 41.72 3.69
111 112 1.089920 AACTGTGGCAAGATGATCGC 58.910 50.000 0.00 0.00 0.00 4.58
112 113 0.745845 ACTGTGGCAAGATGATCGCC 60.746 55.000 4.62 4.62 46.43 5.54
115 116 4.124910 GGCAAGATGATCGCCGAA 57.875 55.556 0.00 0.00 35.79 4.30
116 117 1.643832 GGCAAGATGATCGCCGAAC 59.356 57.895 0.00 0.00 35.79 3.95
117 118 0.811616 GGCAAGATGATCGCCGAACT 60.812 55.000 0.00 0.00 35.79 3.01
118 119 0.302890 GCAAGATGATCGCCGAACTG 59.697 55.000 0.00 0.00 0.00 3.16
119 120 1.645034 CAAGATGATCGCCGAACTGT 58.355 50.000 0.00 0.00 0.00 3.55
120 121 1.325640 CAAGATGATCGCCGAACTGTG 59.674 52.381 0.00 0.00 0.00 3.66
121 122 0.179100 AGATGATCGCCGAACTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
128 129 3.343972 CCGAACTGTGGCAAGGTG 58.656 61.111 0.00 0.00 0.00 4.00
129 130 1.227823 CCGAACTGTGGCAAGGTGA 60.228 57.895 0.00 0.00 0.00 4.02
130 131 0.606401 CCGAACTGTGGCAAGGTGAT 60.606 55.000 0.00 0.00 0.00 3.06
131 132 0.798776 CGAACTGTGGCAAGGTGATC 59.201 55.000 0.00 0.00 0.00 2.92
132 133 0.798776 GAACTGTGGCAAGGTGATCG 59.201 55.000 0.00 0.00 0.00 3.69
133 134 1.237285 AACTGTGGCAAGGTGATCGC 61.237 55.000 0.00 0.00 0.00 4.58
134 135 2.359850 TGTGGCAAGGTGATCGCC 60.360 61.111 18.01 18.01 46.43 5.54
137 138 2.435938 GGCAAGGTGATCGCCGAA 60.436 61.111 19.45 0.00 35.79 4.30
138 139 2.750888 GGCAAGGTGATCGCCGAAC 61.751 63.158 19.45 12.07 35.79 3.95
139 140 1.741770 GCAAGGTGATCGCCGAACT 60.742 57.895 19.45 0.00 0.00 3.01
140 141 1.970917 GCAAGGTGATCGCCGAACTG 61.971 60.000 19.45 15.40 0.00 3.16
141 142 1.079127 AAGGTGATCGCCGAACTGG 60.079 57.895 19.45 0.00 42.50 4.00
142 143 2.511600 GGTGATCGCCGAACTGGG 60.512 66.667 10.09 0.00 38.63 4.45
150 151 4.473520 CCGAACTGGGCCGCTGAT 62.474 66.667 0.00 0.00 0.00 2.90
151 152 2.892425 CGAACTGGGCCGCTGATC 60.892 66.667 0.00 0.00 0.00 2.92
152 153 2.892425 GAACTGGGCCGCTGATCG 60.892 66.667 0.00 0.00 38.08 3.69
162 163 2.125512 GCTGATCGCGGGACTTGT 60.126 61.111 6.13 0.00 0.00 3.16
163 164 2.456119 GCTGATCGCGGGACTTGTG 61.456 63.158 6.13 0.00 0.00 3.33
164 165 1.811266 CTGATCGCGGGACTTGTGG 60.811 63.158 6.13 0.00 0.00 4.17
165 166 3.195698 GATCGCGGGACTTGTGGC 61.196 66.667 6.13 0.00 0.00 5.01
166 167 3.665675 GATCGCGGGACTTGTGGCT 62.666 63.158 6.13 0.00 0.00 4.75
167 168 3.254024 ATCGCGGGACTTGTGGCTT 62.254 57.895 6.13 0.00 0.00 4.35
168 169 2.748058 ATCGCGGGACTTGTGGCTTT 62.748 55.000 6.13 0.00 0.00 3.51
169 170 2.551912 CGCGGGACTTGTGGCTTTT 61.552 57.895 0.00 0.00 0.00 2.27
170 171 1.739667 GCGGGACTTGTGGCTTTTT 59.260 52.632 0.00 0.00 0.00 1.94
188 189 3.848272 TTTTTGTGAGCGGGATTGATC 57.152 42.857 0.00 0.00 0.00 2.92
189 190 2.488204 TTTGTGAGCGGGATTGATCA 57.512 45.000 0.00 0.00 30.63 2.92
190 191 2.488204 TTGTGAGCGGGATTGATCAA 57.512 45.000 11.26 11.26 35.82 2.57
191 192 2.028420 TGTGAGCGGGATTGATCAAG 57.972 50.000 14.54 1.10 35.82 3.02
192 193 1.278985 TGTGAGCGGGATTGATCAAGT 59.721 47.619 14.54 2.33 35.82 3.16
193 194 2.290260 TGTGAGCGGGATTGATCAAGTT 60.290 45.455 14.54 0.00 35.82 2.66
194 195 2.749621 GTGAGCGGGATTGATCAAGTTT 59.250 45.455 14.54 0.00 35.82 2.66
195 196 2.749076 TGAGCGGGATTGATCAAGTTTG 59.251 45.455 14.54 5.36 30.08 2.93
196 197 3.009723 GAGCGGGATTGATCAAGTTTGA 58.990 45.455 14.54 0.00 42.14 2.69
197 198 3.420893 AGCGGGATTGATCAAGTTTGAA 58.579 40.909 14.54 0.00 41.13 2.69
198 199 4.019174 AGCGGGATTGATCAAGTTTGAAT 58.981 39.130 14.54 0.00 41.13 2.57
199 200 4.463891 AGCGGGATTGATCAAGTTTGAATT 59.536 37.500 14.54 0.00 41.13 2.17
200 201 5.047092 AGCGGGATTGATCAAGTTTGAATTT 60.047 36.000 14.54 0.00 41.13 1.82
201 202 5.062558 GCGGGATTGATCAAGTTTGAATTTG 59.937 40.000 14.54 0.00 41.13 2.32
202 203 5.062558 CGGGATTGATCAAGTTTGAATTTGC 59.937 40.000 14.54 0.00 41.13 3.68
203 204 5.352293 GGGATTGATCAAGTTTGAATTTGCC 59.648 40.000 14.54 4.60 41.13 4.52
204 205 5.062558 GGATTGATCAAGTTTGAATTTGCCG 59.937 40.000 14.54 0.00 41.13 5.69
205 206 3.316283 TGATCAAGTTTGAATTTGCCGC 58.684 40.909 0.00 0.00 41.13 6.53
206 207 1.764851 TCAAGTTTGAATTTGCCGCG 58.235 45.000 0.00 0.00 33.55 6.46
207 208 1.335182 TCAAGTTTGAATTTGCCGCGA 59.665 42.857 8.23 0.00 33.55 5.87
208 209 1.451651 CAAGTTTGAATTTGCCGCGAC 59.548 47.619 8.23 0.00 0.00 5.19
209 210 0.951558 AGTTTGAATTTGCCGCGACT 59.048 45.000 8.23 0.00 0.00 4.18
210 211 1.336755 AGTTTGAATTTGCCGCGACTT 59.663 42.857 8.23 0.00 0.00 3.01
211 212 1.451651 GTTTGAATTTGCCGCGACTTG 59.548 47.619 8.23 0.00 0.00 3.16
212 213 0.947960 TTGAATTTGCCGCGACTTGA 59.052 45.000 8.23 0.00 0.00 3.02
213 214 0.516877 TGAATTTGCCGCGACTTGAG 59.483 50.000 8.23 0.00 0.00 3.02
214 215 0.179189 GAATTTGCCGCGACTTGAGG 60.179 55.000 8.23 0.00 41.15 3.86
215 216 1.586154 AATTTGCCGCGACTTGAGGG 61.586 55.000 8.23 0.00 38.12 4.30
216 217 4.697756 TTGCCGCGACTTGAGGGG 62.698 66.667 8.23 0.00 43.62 4.79
219 220 4.148825 CCGCGACTTGAGGGGGAG 62.149 72.222 8.23 0.00 38.44 4.30
220 221 4.148825 CGCGACTTGAGGGGGAGG 62.149 72.222 0.00 0.00 0.00 4.30
221 222 3.787001 GCGACTTGAGGGGGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
222 223 3.083997 CGACTTGAGGGGGAGGGG 61.084 72.222 0.00 0.00 0.00 4.79
223 224 2.692741 GACTTGAGGGGGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
253 254 4.537433 GGCGTGGCTGGGAGCTAG 62.537 72.222 0.00 0.00 41.99 3.42
254 255 3.461773 GCGTGGCTGGGAGCTAGA 61.462 66.667 0.00 0.00 41.99 2.43
255 256 2.801631 GCGTGGCTGGGAGCTAGAT 61.802 63.158 0.00 0.00 41.99 1.98
256 257 1.365633 CGTGGCTGGGAGCTAGATC 59.634 63.158 0.00 0.00 41.99 2.75
257 258 1.365633 GTGGCTGGGAGCTAGATCG 59.634 63.158 1.16 0.00 41.99 3.69
258 259 2.341911 GGCTGGGAGCTAGATCGC 59.658 66.667 17.38 17.38 41.99 4.58
259 260 2.341911 GCTGGGAGCTAGATCGCC 59.658 66.667 20.75 14.13 38.45 5.54
260 261 3.055580 CTGGGAGCTAGATCGCCC 58.944 66.667 20.75 10.02 45.10 6.13
261 262 2.524394 TGGGAGCTAGATCGCCCC 60.524 66.667 20.75 9.29 44.37 5.80
262 263 3.315140 GGGAGCTAGATCGCCCCC 61.315 72.222 13.70 0.00 40.96 5.40
263 264 2.524394 GGAGCTAGATCGCCCCCA 60.524 66.667 1.16 0.00 0.00 4.96
264 265 2.578714 GGAGCTAGATCGCCCCCAG 61.579 68.421 1.16 0.00 0.00 4.45
265 266 1.531840 GAGCTAGATCGCCCCCAGA 60.532 63.158 0.00 0.00 0.00 3.86
266 267 1.531739 GAGCTAGATCGCCCCCAGAG 61.532 65.000 0.00 0.00 0.00 3.35
267 268 1.834822 GCTAGATCGCCCCCAGAGT 60.835 63.158 0.00 0.00 0.00 3.24
268 269 1.811645 GCTAGATCGCCCCCAGAGTC 61.812 65.000 0.00 0.00 0.00 3.36
269 270 0.178975 CTAGATCGCCCCCAGAGTCT 60.179 60.000 0.00 0.00 0.00 3.24
270 271 1.074084 CTAGATCGCCCCCAGAGTCTA 59.926 57.143 0.00 0.00 0.00 2.59
271 272 0.261991 AGATCGCCCCCAGAGTCTAA 59.738 55.000 0.00 0.00 0.00 2.10
272 273 1.120530 GATCGCCCCCAGAGTCTAAA 58.879 55.000 0.00 0.00 0.00 1.85
273 274 1.485066 GATCGCCCCCAGAGTCTAAAA 59.515 52.381 0.00 0.00 0.00 1.52
274 275 1.354101 TCGCCCCCAGAGTCTAAAAA 58.646 50.000 0.00 0.00 0.00 1.94
296 297 3.490890 CAGGCCTAAACTGCGAGC 58.509 61.111 3.98 0.00 0.00 5.03
365 372 3.085952 AGAGAGGAGAGAGGAAGTGTG 57.914 52.381 0.00 0.00 0.00 3.82
370 377 2.435059 GAGAGGAAGTGTGGCGGC 60.435 66.667 0.00 0.00 0.00 6.53
553 561 7.448777 ACAATAATACACATGTTGGGTTACACA 59.551 33.333 0.00 0.00 34.65 3.72
569 577 7.088272 GGGTTACACAAAATTGTATGGACTTC 58.912 38.462 0.00 0.00 39.91 3.01
571 579 8.021396 GGTTACACAAAATTGTATGGACTTCTC 58.979 37.037 0.00 0.00 39.91 2.87
577 585 7.926018 ACAAAATTGTATGGACTTCTCCAAAAC 59.074 33.333 0.00 0.00 40.81 2.43
586 594 7.687941 TGGACTTCTCCAAAACATATTCTTC 57.312 36.000 0.00 0.00 44.26 2.87
587 595 7.461749 TGGACTTCTCCAAAACATATTCTTCT 58.538 34.615 0.00 0.00 44.26 2.85
594 602 8.420222 TCTCCAAAACATATTCTTCTTTTTGCA 58.580 29.630 0.00 0.00 36.34 4.08
599 607 9.822185 AAAACATATTCTTCTTTTTGCAACTCT 57.178 25.926 0.00 0.00 0.00 3.24
604 612 5.998454 TCTTCTTTTTGCAACTCTCTCTG 57.002 39.130 0.00 0.00 0.00 3.35
605 613 5.431765 TCTTCTTTTTGCAACTCTCTCTGT 58.568 37.500 0.00 0.00 0.00 3.41
606 614 6.582636 TCTTCTTTTTGCAACTCTCTCTGTA 58.417 36.000 0.00 0.00 0.00 2.74
691 739 8.286996 ACAATGAGAGTATTTCGTAATCATCG 57.713 34.615 0.00 0.00 29.93 3.84
704 752 4.090066 CGTAATCATCGCTTACACATAGGC 59.910 45.833 0.00 0.00 0.00 3.93
728 776 6.398935 GCTCAAAACTCACATTCAAAATACGC 60.399 38.462 0.00 0.00 0.00 4.42
788 853 2.223386 GCATAGAGTGTGAGAGGACGTC 60.223 54.545 7.13 7.13 0.00 4.34
816 889 1.262417 GTGAGTGACGTCGTGAGTGTA 59.738 52.381 11.62 0.00 0.00 2.90
832 905 0.242825 TGTACTGCTAGTGTGGTCGC 59.757 55.000 0.00 0.00 0.00 5.19
869 951 1.344114 TGCACTTGAAAATCCTTGCCC 59.656 47.619 0.00 0.00 0.00 5.36
898 980 5.876357 TCCTTCTATATAAACCCATGCCAC 58.124 41.667 0.00 0.00 0.00 5.01
957 1039 0.035725 GTAGCCTTACCACACACCCC 60.036 60.000 0.00 0.00 0.00 4.95
958 1040 0.178885 TAGCCTTACCACACACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
959 1041 1.002502 GCCTTACCACACACCCCTC 60.003 63.158 0.00 0.00 0.00 4.30
960 1042 1.295423 CCTTACCACACACCCCTCG 59.705 63.158 0.00 0.00 0.00 4.63
990 1072 2.281761 CACTCCCACAGGCCACAC 60.282 66.667 5.01 0.00 0.00 3.82
991 1073 2.772191 ACTCCCACAGGCCACACA 60.772 61.111 5.01 0.00 0.00 3.72
992 1074 2.033141 CTCCCACAGGCCACACAG 59.967 66.667 5.01 0.00 0.00 3.66
993 1075 4.269523 TCCCACAGGCCACACAGC 62.270 66.667 5.01 0.00 0.00 4.40
1007 1089 0.529337 CACAGCCTAGCCATGTCTCG 60.529 60.000 0.00 0.00 0.00 4.04
1009 1091 1.381872 AGCCTAGCCATGTCTCGGT 60.382 57.895 0.00 0.00 0.00 4.69
1021 1103 1.887854 TGTCTCGGTCCACGTTAATCA 59.112 47.619 0.00 0.00 44.69 2.57
1024 1106 2.100252 TCTCGGTCCACGTTAATCATCC 59.900 50.000 0.00 0.00 44.69 3.51
1025 1107 2.100916 CTCGGTCCACGTTAATCATCCT 59.899 50.000 0.00 0.00 44.69 3.24
1026 1108 2.100252 TCGGTCCACGTTAATCATCCTC 59.900 50.000 0.00 0.00 44.69 3.71
1029 1111 1.754803 TCCACGTTAATCATCCTCGCT 59.245 47.619 0.00 0.00 0.00 4.93
1037 1119 1.523154 ATCATCCTCGCTCTCCTCGC 61.523 60.000 0.00 0.00 0.00 5.03
1127 1209 3.049674 CGACGCTGCCATGGTGTT 61.050 61.111 14.67 0.00 0.00 3.32
1245 1327 2.366584 CGACTCGTTTAACGCCGCA 61.367 57.895 13.06 0.00 42.21 5.69
1452 1534 2.359975 GGCGTCAAGGACCAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
1614 1696 8.744568 AAATGTTAAAAAGAATTTGCAAGGGA 57.255 26.923 0.00 0.00 39.02 4.20
1698 1782 3.057734 GGACCAGTCTACAAACAAGTCG 58.942 50.000 0.00 0.00 0.00 4.18
1699 1783 3.492137 GGACCAGTCTACAAACAAGTCGT 60.492 47.826 0.00 0.00 0.00 4.34
1700 1784 3.454375 ACCAGTCTACAAACAAGTCGTG 58.546 45.455 0.00 0.00 0.00 4.35
1701 1785 2.221055 CCAGTCTACAAACAAGTCGTGC 59.779 50.000 0.00 0.00 0.00 5.34
1702 1786 2.221055 CAGTCTACAAACAAGTCGTGCC 59.779 50.000 0.00 0.00 0.00 5.01
1703 1787 2.102588 AGTCTACAAACAAGTCGTGCCT 59.897 45.455 0.00 0.00 0.00 4.75
1704 1788 2.475487 GTCTACAAACAAGTCGTGCCTC 59.525 50.000 0.00 0.00 0.00 4.70
1705 1789 1.455786 CTACAAACAAGTCGTGCCTCG 59.544 52.381 0.00 0.00 41.41 4.63
1711 1795 4.702081 AGTCGTGCCTCGTGCGTC 62.702 66.667 0.00 0.00 45.60 5.19
1768 1853 9.282247 GTCAATGCTAACTTTACTTCAATGATG 57.718 33.333 0.00 0.00 0.00 3.07
1769 1854 9.230122 TCAATGCTAACTTTACTTCAATGATGA 57.770 29.630 3.02 0.00 0.00 2.92
1854 1939 9.559732 TTCATCATGTACTAATCCAATAACCTG 57.440 33.333 0.00 0.00 0.00 4.00
2359 2444 0.321564 CATGAAGAACTCGTGGGGCA 60.322 55.000 0.00 0.00 37.41 5.36
2489 2575 2.097038 GCACGTCACTAGCTGGCTG 61.097 63.158 5.25 0.00 0.00 4.85
2549 2636 0.244450 TAAGCACCGTACGTTCCTGG 59.756 55.000 15.21 0.00 0.00 4.45
2759 2855 8.537728 ACCATGATGAATTTGTACATATTGGT 57.462 30.769 15.15 12.55 37.20 3.67
2886 2994 1.549620 CCATTGCTGGTTTGCCATACA 59.450 47.619 0.00 0.00 45.05 2.29
2983 3096 0.532417 CTAGAGCCACTGGAGCATGC 60.532 60.000 10.51 10.51 0.00 4.06
3031 3144 2.300787 GCACGACACTCACACGTCC 61.301 63.158 0.00 0.00 38.18 4.79
3131 3244 1.085091 GCACTGCAACAGGATCAGAG 58.915 55.000 0.00 0.00 35.51 3.35
3134 3247 1.980765 ACTGCAACAGGATCAGAGGAA 59.019 47.619 0.00 0.00 35.51 3.36
3136 3249 1.338105 TGCAACAGGATCAGAGGAACG 60.338 52.381 0.00 0.00 0.00 3.95
3137 3250 1.338200 GCAACAGGATCAGAGGAACGT 60.338 52.381 0.00 0.00 0.00 3.99
3140 3253 1.186200 CAGGATCAGAGGAACGTGGA 58.814 55.000 0.00 0.00 30.73 4.02
3203 3316 1.228510 GGCCCCCTTGAGATGGAAG 59.771 63.158 0.00 0.00 0.00 3.46
3230 3348 0.588252 CGTACCGTACGTATCCTGGG 59.412 60.000 20.61 0.00 46.41 4.45
3351 3469 6.819649 CAGTATCTCTCCTTAGTATACGAGGG 59.180 46.154 21.12 15.49 32.55 4.30
3354 3472 5.619220 TCTCTCCTTAGTATACGAGGGTTC 58.381 45.833 21.12 0.00 0.00 3.62
3385 3503 3.434299 GCAAGATTTCAAATGGTTGGCAG 59.566 43.478 0.00 0.00 35.29 4.85
3388 3506 3.896888 AGATTTCAAATGGTTGGCAGACA 59.103 39.130 0.00 0.00 35.29 3.41
3389 3507 4.529377 AGATTTCAAATGGTTGGCAGACAT 59.471 37.500 0.00 0.78 35.29 3.06
3409 3527 9.630098 CAGACATGCAAGAAAAACATAGTAATT 57.370 29.630 0.00 0.00 0.00 1.40
3425 3543 9.915629 ACATAGTAATTATAGCAAGAGTACTGC 57.084 33.333 0.00 0.00 0.00 4.40
3428 3546 7.437748 AGTAATTATAGCAAGAGTACTGCTGG 58.562 38.462 16.13 5.58 39.46 4.85
3429 3547 2.611225 ATAGCAAGAGTACTGCTGGC 57.389 50.000 16.13 13.73 39.46 4.85
3430 3548 1.561643 TAGCAAGAGTACTGCTGGCT 58.438 50.000 20.84 20.84 39.46 4.75
3431 3549 1.561643 AGCAAGAGTACTGCTGGCTA 58.438 50.000 17.58 0.00 37.53 3.93
3432 3550 1.902508 AGCAAGAGTACTGCTGGCTAA 59.097 47.619 17.58 0.00 37.53 3.09
3433 3551 2.003301 GCAAGAGTACTGCTGGCTAAC 58.997 52.381 0.00 0.00 0.00 2.34
3434 3552 2.622436 CAAGAGTACTGCTGGCTAACC 58.378 52.381 0.00 0.00 0.00 2.85
3435 3553 2.234908 CAAGAGTACTGCTGGCTAACCT 59.765 50.000 0.00 0.00 36.63 3.50
3436 3554 2.541466 AGAGTACTGCTGGCTAACCTT 58.459 47.619 0.00 0.00 36.63 3.50
3437 3555 2.234908 AGAGTACTGCTGGCTAACCTTG 59.765 50.000 0.00 0.00 36.63 3.61
3438 3556 1.978580 AGTACTGCTGGCTAACCTTGT 59.021 47.619 0.00 0.00 36.63 3.16
3439 3557 2.372172 AGTACTGCTGGCTAACCTTGTT 59.628 45.455 0.00 0.00 36.63 2.83
3440 3558 2.364972 ACTGCTGGCTAACCTTGTTT 57.635 45.000 0.00 0.00 36.63 2.83
3441 3559 3.502123 ACTGCTGGCTAACCTTGTTTA 57.498 42.857 0.00 0.00 36.63 2.01
3442 3560 4.034285 ACTGCTGGCTAACCTTGTTTAT 57.966 40.909 0.00 0.00 36.63 1.40
3443 3561 5.174037 ACTGCTGGCTAACCTTGTTTATA 57.826 39.130 0.00 0.00 36.63 0.98
3444 3562 5.755849 ACTGCTGGCTAACCTTGTTTATAT 58.244 37.500 0.00 0.00 36.63 0.86
3445 3563 5.823045 ACTGCTGGCTAACCTTGTTTATATC 59.177 40.000 0.00 0.00 36.63 1.63
3446 3564 6.001449 TGCTGGCTAACCTTGTTTATATCT 57.999 37.500 0.00 0.00 36.63 1.98
3447 3565 6.055588 TGCTGGCTAACCTTGTTTATATCTC 58.944 40.000 0.00 0.00 36.63 2.75
3448 3566 6.126768 TGCTGGCTAACCTTGTTTATATCTCT 60.127 38.462 0.00 0.00 36.63 3.10
3449 3567 6.203723 GCTGGCTAACCTTGTTTATATCTCTG 59.796 42.308 0.00 0.00 36.63 3.35
3450 3568 6.055588 TGGCTAACCTTGTTTATATCTCTGC 58.944 40.000 0.00 0.00 36.63 4.26
3451 3569 6.126768 TGGCTAACCTTGTTTATATCTCTGCT 60.127 38.462 0.00 0.00 36.63 4.24
3452 3570 7.070696 TGGCTAACCTTGTTTATATCTCTGCTA 59.929 37.037 0.00 0.00 36.63 3.49
3453 3571 7.931948 GGCTAACCTTGTTTATATCTCTGCTAA 59.068 37.037 0.00 0.00 0.00 3.09
3454 3572 8.766151 GCTAACCTTGTTTATATCTCTGCTAAC 58.234 37.037 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.770874 ATCAAACGGCGGGGTCGG 62.771 66.667 13.24 0.00 33.75 4.79
16 17 3.496131 CATCAAACGGCGGGGTCG 61.496 66.667 13.24 0.00 36.42 4.79
17 18 2.359478 ACATCAAACGGCGGGGTC 60.359 61.111 13.24 0.00 0.00 4.46
18 19 2.671619 CACATCAAACGGCGGGGT 60.672 61.111 13.24 0.00 0.00 4.95
19 20 2.265182 AACACATCAAACGGCGGGG 61.265 57.895 13.24 0.00 0.00 5.73
20 21 1.081509 CAACACATCAAACGGCGGG 60.082 57.895 13.24 0.00 0.00 6.13
21 22 1.729131 GCAACACATCAAACGGCGG 60.729 57.895 13.24 0.00 0.00 6.13
22 23 1.729131 GGCAACACATCAAACGGCG 60.729 57.895 4.80 4.80 0.00 6.46
23 24 1.372872 GGGCAACACATCAAACGGC 60.373 57.895 0.00 0.00 39.74 5.68
24 25 2.037053 TGGGCAACACATCAAACGG 58.963 52.632 0.00 0.00 39.74 4.44
34 35 4.555709 AAGGACGCGTGGGCAACA 62.556 61.111 20.70 0.00 39.92 3.33
35 36 3.249973 GAAAGGACGCGTGGGCAAC 62.250 63.158 20.70 0.00 39.92 4.17
36 37 2.951475 AAGAAAGGACGCGTGGGCAA 62.951 55.000 20.70 0.00 39.92 4.52
37 38 2.951475 AAAGAAAGGACGCGTGGGCA 62.951 55.000 20.70 0.00 39.92 5.36
38 39 1.792118 AAAAGAAAGGACGCGTGGGC 61.792 55.000 20.70 0.86 0.00 5.36
39 40 0.666374 AAAAAGAAAGGACGCGTGGG 59.334 50.000 20.70 0.00 0.00 4.61
58 59 3.128242 TGAAAAGTTCGGCGTACCAAAAA 59.872 39.130 13.15 0.00 34.57 1.94
59 60 2.681848 TGAAAAGTTCGGCGTACCAAAA 59.318 40.909 13.15 0.00 34.57 2.44
60 61 2.286872 TGAAAAGTTCGGCGTACCAAA 58.713 42.857 13.15 0.00 34.57 3.28
61 62 1.950828 TGAAAAGTTCGGCGTACCAA 58.049 45.000 13.15 0.00 34.57 3.67
62 63 2.070783 GATGAAAAGTTCGGCGTACCA 58.929 47.619 13.15 4.54 34.57 3.25
63 64 1.395954 GGATGAAAAGTTCGGCGTACC 59.604 52.381 13.15 0.00 0.00 3.34
64 65 1.060122 CGGATGAAAAGTTCGGCGTAC 59.940 52.381 8.72 8.72 0.00 3.67
65 66 1.067706 TCGGATGAAAAGTTCGGCGTA 60.068 47.619 6.85 0.00 0.00 4.42
66 67 0.320073 TCGGATGAAAAGTTCGGCGT 60.320 50.000 6.85 0.00 0.00 5.68
67 68 1.004927 GATCGGATGAAAAGTTCGGCG 60.005 52.381 0.00 0.00 0.00 6.46
68 69 1.004927 CGATCGGATGAAAAGTTCGGC 60.005 52.381 7.38 0.00 0.00 5.54
69 70 1.004927 GCGATCGGATGAAAAGTTCGG 60.005 52.381 18.30 0.00 0.00 4.30
70 71 1.004927 GGCGATCGGATGAAAAGTTCG 60.005 52.381 18.30 0.00 0.00 3.95
71 72 2.006888 TGGCGATCGGATGAAAAGTTC 58.993 47.619 18.30 0.00 0.00 3.01
72 73 2.107950 TGGCGATCGGATGAAAAGTT 57.892 45.000 18.30 0.00 0.00 2.66
73 74 2.107950 TTGGCGATCGGATGAAAAGT 57.892 45.000 18.30 0.00 0.00 2.66
74 75 2.420022 AGTTTGGCGATCGGATGAAAAG 59.580 45.455 18.30 0.00 0.00 2.27
75 76 2.161410 CAGTTTGGCGATCGGATGAAAA 59.839 45.455 18.30 0.00 0.00 2.29
76 77 1.737236 CAGTTTGGCGATCGGATGAAA 59.263 47.619 18.30 0.00 0.00 2.69
77 78 1.338674 ACAGTTTGGCGATCGGATGAA 60.339 47.619 18.30 0.00 0.00 2.57
78 79 0.249120 ACAGTTTGGCGATCGGATGA 59.751 50.000 18.30 0.00 0.00 2.92
79 80 0.374758 CACAGTTTGGCGATCGGATG 59.625 55.000 18.30 0.00 0.00 3.51
80 81 0.744414 CCACAGTTTGGCGATCGGAT 60.744 55.000 18.30 0.00 39.07 4.18
81 82 1.375396 CCACAGTTTGGCGATCGGA 60.375 57.895 18.30 0.00 39.07 4.55
82 83 3.177600 CCACAGTTTGGCGATCGG 58.822 61.111 18.30 0.02 39.07 4.18
90 91 2.730090 GCGATCATCTTGCCACAGTTTG 60.730 50.000 0.00 0.00 0.00 2.93
91 92 1.470098 GCGATCATCTTGCCACAGTTT 59.530 47.619 0.00 0.00 0.00 2.66
92 93 1.089920 GCGATCATCTTGCCACAGTT 58.910 50.000 0.00 0.00 0.00 3.16
93 94 2.772739 GCGATCATCTTGCCACAGT 58.227 52.632 0.00 0.00 0.00 3.55
99 100 0.302890 CAGTTCGGCGATCATCTTGC 59.697 55.000 19.04 0.09 0.00 4.01
100 101 1.325640 CACAGTTCGGCGATCATCTTG 59.674 52.381 19.04 11.10 0.00 3.02
101 102 1.645034 CACAGTTCGGCGATCATCTT 58.355 50.000 19.04 0.00 0.00 2.40
102 103 0.179100 CCACAGTTCGGCGATCATCT 60.179 55.000 19.04 9.18 0.00 2.90
103 104 1.766143 GCCACAGTTCGGCGATCATC 61.766 60.000 19.04 7.17 40.35 2.92
104 105 1.815421 GCCACAGTTCGGCGATCAT 60.815 57.895 19.04 5.01 40.35 2.45
105 106 2.434185 GCCACAGTTCGGCGATCA 60.434 61.111 19.04 0.00 40.35 2.92
111 112 0.606401 ATCACCTTGCCACAGTTCGG 60.606 55.000 0.00 0.00 0.00 4.30
112 113 0.798776 GATCACCTTGCCACAGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
113 114 0.798776 CGATCACCTTGCCACAGTTC 59.201 55.000 0.00 0.00 0.00 3.01
114 115 1.237285 GCGATCACCTTGCCACAGTT 61.237 55.000 0.00 0.00 0.00 3.16
115 116 1.672356 GCGATCACCTTGCCACAGT 60.672 57.895 0.00 0.00 0.00 3.55
116 117 3.181367 GCGATCACCTTGCCACAG 58.819 61.111 0.00 0.00 0.00 3.66
121 122 1.741770 AGTTCGGCGATCACCTTGC 60.742 57.895 19.04 0.00 0.00 4.01
122 123 1.361668 CCAGTTCGGCGATCACCTTG 61.362 60.000 19.04 8.90 0.00 3.61
123 124 1.079127 CCAGTTCGGCGATCACCTT 60.079 57.895 19.04 0.00 0.00 3.50
124 125 2.579201 CCAGTTCGGCGATCACCT 59.421 61.111 19.04 6.87 0.00 4.00
125 126 2.511600 CCCAGTTCGGCGATCACC 60.512 66.667 19.04 4.72 0.00 4.02
126 127 3.195698 GCCCAGTTCGGCGATCAC 61.196 66.667 19.04 11.84 39.64 3.06
133 134 4.473520 ATCAGCGGCCCAGTTCGG 62.474 66.667 0.00 0.00 0.00 4.30
134 135 2.892425 GATCAGCGGCCCAGTTCG 60.892 66.667 0.00 0.00 0.00 3.95
135 136 2.892425 CGATCAGCGGCCCAGTTC 60.892 66.667 0.00 0.00 36.03 3.01
145 146 2.125512 ACAAGTCCCGCGATCAGC 60.126 61.111 8.23 0.00 43.95 4.26
146 147 1.811266 CCACAAGTCCCGCGATCAG 60.811 63.158 8.23 0.00 0.00 2.90
147 148 2.264480 CCACAAGTCCCGCGATCA 59.736 61.111 8.23 0.00 0.00 2.92
148 149 3.195698 GCCACAAGTCCCGCGATC 61.196 66.667 8.23 0.00 0.00 3.69
149 150 2.748058 AAAGCCACAAGTCCCGCGAT 62.748 55.000 8.23 0.00 0.00 4.58
150 151 2.951475 AAAAGCCACAAGTCCCGCGA 62.951 55.000 8.23 0.00 0.00 5.87
151 152 2.070654 AAAAAGCCACAAGTCCCGCG 62.071 55.000 0.00 0.00 0.00 6.46
152 153 1.739667 AAAAAGCCACAAGTCCCGC 59.260 52.632 0.00 0.00 0.00 6.13
168 169 3.153130 TGATCAATCCCGCTCACAAAAA 58.847 40.909 0.00 0.00 0.00 1.94
169 170 2.789213 TGATCAATCCCGCTCACAAAA 58.211 42.857 0.00 0.00 0.00 2.44
170 171 2.488204 TGATCAATCCCGCTCACAAA 57.512 45.000 0.00 0.00 0.00 2.83
171 172 2.290260 ACTTGATCAATCCCGCTCACAA 60.290 45.455 8.96 0.00 0.00 3.33
172 173 1.278985 ACTTGATCAATCCCGCTCACA 59.721 47.619 8.96 0.00 0.00 3.58
173 174 2.029838 ACTTGATCAATCCCGCTCAC 57.970 50.000 8.96 0.00 0.00 3.51
174 175 2.749076 CAAACTTGATCAATCCCGCTCA 59.251 45.455 8.96 0.00 0.00 4.26
175 176 3.009723 TCAAACTTGATCAATCCCGCTC 58.990 45.455 8.96 0.00 31.01 5.03
176 177 3.071874 TCAAACTTGATCAATCCCGCT 57.928 42.857 8.96 0.00 31.01 5.52
177 178 3.848272 TTCAAACTTGATCAATCCCGC 57.152 42.857 8.96 0.00 37.00 6.13
178 179 5.062558 GCAAATTCAAACTTGATCAATCCCG 59.937 40.000 8.96 0.00 37.00 5.14
179 180 5.352293 GGCAAATTCAAACTTGATCAATCCC 59.648 40.000 8.96 0.00 37.00 3.85
180 181 5.062558 CGGCAAATTCAAACTTGATCAATCC 59.937 40.000 8.96 0.00 37.00 3.01
181 182 5.445010 GCGGCAAATTCAAACTTGATCAATC 60.445 40.000 8.96 0.00 37.00 2.67
182 183 4.389687 GCGGCAAATTCAAACTTGATCAAT 59.610 37.500 8.96 0.00 37.00 2.57
183 184 3.740321 GCGGCAAATTCAAACTTGATCAA 59.260 39.130 8.12 8.12 37.00 2.57
184 185 3.316283 GCGGCAAATTCAAACTTGATCA 58.684 40.909 0.00 0.00 37.00 2.92
185 186 2.342354 CGCGGCAAATTCAAACTTGATC 59.658 45.455 0.00 0.00 37.00 2.92
186 187 2.030363 TCGCGGCAAATTCAAACTTGAT 60.030 40.909 6.13 0.00 37.00 2.57
187 188 1.335182 TCGCGGCAAATTCAAACTTGA 59.665 42.857 6.13 0.00 34.92 3.02
188 189 1.451651 GTCGCGGCAAATTCAAACTTG 59.548 47.619 5.47 0.00 0.00 3.16
189 190 1.336755 AGTCGCGGCAAATTCAAACTT 59.663 42.857 15.58 0.00 0.00 2.66
190 191 0.951558 AGTCGCGGCAAATTCAAACT 59.048 45.000 15.58 0.00 0.00 2.66
191 192 1.451651 CAAGTCGCGGCAAATTCAAAC 59.548 47.619 15.58 0.00 0.00 2.93
192 193 1.335182 TCAAGTCGCGGCAAATTCAAA 59.665 42.857 15.58 0.00 0.00 2.69
193 194 0.947960 TCAAGTCGCGGCAAATTCAA 59.052 45.000 15.58 0.00 0.00 2.69
194 195 0.516877 CTCAAGTCGCGGCAAATTCA 59.483 50.000 15.58 0.00 0.00 2.57
195 196 0.179189 CCTCAAGTCGCGGCAAATTC 60.179 55.000 15.58 0.00 0.00 2.17
196 197 1.586154 CCCTCAAGTCGCGGCAAATT 61.586 55.000 15.58 0.00 0.00 1.82
197 198 2.040544 CCCTCAAGTCGCGGCAAAT 61.041 57.895 15.58 0.00 0.00 2.32
198 199 2.668212 CCCTCAAGTCGCGGCAAA 60.668 61.111 15.58 0.00 0.00 3.68
199 200 4.697756 CCCCTCAAGTCGCGGCAA 62.698 66.667 15.58 0.00 0.00 4.52
202 203 4.148825 CTCCCCCTCAAGTCGCGG 62.149 72.222 6.13 0.00 0.00 6.46
203 204 4.148825 CCTCCCCCTCAAGTCGCG 62.149 72.222 0.00 0.00 0.00 5.87
204 205 3.787001 CCCTCCCCCTCAAGTCGC 61.787 72.222 0.00 0.00 0.00 5.19
205 206 3.083997 CCCCTCCCCCTCAAGTCG 61.084 72.222 0.00 0.00 0.00 4.18
206 207 2.692741 CCCCCTCCCCCTCAAGTC 60.693 72.222 0.00 0.00 0.00 3.01
236 237 4.537433 CTAGCTCCCAGCCACGCC 62.537 72.222 0.00 0.00 43.77 5.68
237 238 2.707529 GATCTAGCTCCCAGCCACGC 62.708 65.000 0.00 0.00 43.77 5.34
238 239 1.365633 GATCTAGCTCCCAGCCACG 59.634 63.158 0.00 0.00 43.77 4.94
239 240 1.365633 CGATCTAGCTCCCAGCCAC 59.634 63.158 0.00 0.00 43.77 5.01
240 241 2.502492 GCGATCTAGCTCCCAGCCA 61.502 63.158 0.00 0.00 43.77 4.75
241 242 2.341911 GCGATCTAGCTCCCAGCC 59.658 66.667 0.00 0.00 43.77 4.85
242 243 2.341911 GGCGATCTAGCTCCCAGC 59.658 66.667 0.00 0.00 42.84 4.85
243 244 3.055580 GGGCGATCTAGCTCCCAG 58.944 66.667 1.03 0.00 38.62 4.45
247 248 1.531739 CTCTGGGGGCGATCTAGCTC 61.532 65.000 0.00 0.00 37.29 4.09
248 249 1.532794 CTCTGGGGGCGATCTAGCT 60.533 63.158 0.00 0.00 37.29 3.32
249 250 1.811645 GACTCTGGGGGCGATCTAGC 61.812 65.000 0.00 0.00 0.00 3.42
250 251 0.178975 AGACTCTGGGGGCGATCTAG 60.179 60.000 0.00 0.00 0.00 2.43
251 252 1.146452 TAGACTCTGGGGGCGATCTA 58.854 55.000 0.00 0.00 0.00 1.98
252 253 0.261991 TTAGACTCTGGGGGCGATCT 59.738 55.000 0.00 0.00 0.00 2.75
253 254 1.120530 TTTAGACTCTGGGGGCGATC 58.879 55.000 0.00 0.00 0.00 3.69
254 255 1.580059 TTTTAGACTCTGGGGGCGAT 58.420 50.000 0.00 0.00 0.00 4.58
255 256 1.354101 TTTTTAGACTCTGGGGGCGA 58.646 50.000 0.00 0.00 0.00 5.54
256 257 3.948735 TTTTTAGACTCTGGGGGCG 57.051 52.632 0.00 0.00 0.00 6.13
271 272 3.683365 CAGTTTAGGCCTGCCATTTTT 57.317 42.857 17.99 0.00 38.92 1.94
330 332 1.137872 CTCTCTAGCTTGGCCATTCGT 59.862 52.381 6.09 0.00 0.00 3.85
338 340 2.174639 TCCTCTCTCCTCTCTAGCTTGG 59.825 54.545 0.00 0.00 0.00 3.61
365 372 1.160329 AGTATGCTTGATTCGCCGCC 61.160 55.000 0.00 0.00 0.00 6.13
370 377 6.964677 CATGCTAAAAGTATGCTTGATTCG 57.035 37.500 0.00 0.00 31.86 3.34
425 432 3.194329 TCCAAGTCACTAGCATCACTCAG 59.806 47.826 0.00 0.00 0.00 3.35
474 481 1.617322 CATCATGCCATGGAAGGAGG 58.383 55.000 18.40 11.03 0.00 4.30
539 547 7.015682 TCCATACAATTTTGTGTAACCCAACAT 59.984 33.333 6.21 0.00 42.31 2.71
569 577 8.592105 TGCAAAAAGAAGAATATGTTTTGGAG 57.408 30.769 8.69 0.00 38.82 3.86
571 579 8.829612 AGTTGCAAAAAGAAGAATATGTTTTGG 58.170 29.630 0.00 0.00 38.82 3.28
577 585 8.728833 AGAGAGAGTTGCAAAAAGAAGAATATG 58.271 33.333 0.00 0.00 0.00 1.78
578 586 8.728833 CAGAGAGAGTTGCAAAAAGAAGAATAT 58.271 33.333 0.00 0.00 0.00 1.28
579 587 7.716998 ACAGAGAGAGTTGCAAAAAGAAGAATA 59.283 33.333 0.00 0.00 0.00 1.75
580 588 6.545298 ACAGAGAGAGTTGCAAAAAGAAGAAT 59.455 34.615 0.00 0.00 0.00 2.40
582 590 5.431765 ACAGAGAGAGTTGCAAAAAGAAGA 58.568 37.500 0.00 0.00 0.00 2.87
583 591 5.747951 ACAGAGAGAGTTGCAAAAAGAAG 57.252 39.130 0.00 0.00 0.00 2.85
584 592 7.336931 AGTTTACAGAGAGAGTTGCAAAAAGAA 59.663 33.333 0.00 0.00 0.00 2.52
586 594 7.020914 AGTTTACAGAGAGAGTTGCAAAAAG 57.979 36.000 0.00 0.00 0.00 2.27
587 595 8.500753 TTAGTTTACAGAGAGAGTTGCAAAAA 57.499 30.769 0.00 0.00 0.00 1.94
691 739 4.695455 TGAGTTTTGAGCCTATGTGTAAGC 59.305 41.667 0.00 0.00 0.00 3.09
704 752 6.088085 GGCGTATTTTGAATGTGAGTTTTGAG 59.912 38.462 0.00 0.00 0.00 3.02
788 853 1.467543 CGACGTCACTCACACCCATAG 60.468 57.143 17.16 0.00 0.00 2.23
816 889 1.239296 TACGCGACCACACTAGCAGT 61.239 55.000 15.93 0.00 0.00 4.40
832 905 9.767684 TTCAAGTGCATATTAAGAAAATGTACG 57.232 29.630 0.00 0.00 40.03 3.67
864 946 7.340999 GGTTTATATAGAAGGAAAGTTGGGCAA 59.659 37.037 0.00 0.00 0.00 4.52
869 951 8.352942 GCATGGGTTTATATAGAAGGAAAGTTG 58.647 37.037 0.00 0.00 0.00 3.16
898 980 3.777910 GCCCAAATGCTGCAGGGG 61.778 66.667 24.51 24.51 41.75 4.79
990 1072 1.068753 CCGAGACATGGCTAGGCTG 59.931 63.158 15.47 14.68 0.00 4.85
991 1073 1.381872 ACCGAGACATGGCTAGGCT 60.382 57.895 26.31 11.71 34.41 4.58
992 1074 1.068250 GACCGAGACATGGCTAGGC 59.932 63.158 26.31 15.61 34.41 3.93
993 1075 1.043116 TGGACCGAGACATGGCTAGG 61.043 60.000 24.96 24.96 36.80 3.02
1007 1089 2.470821 CGAGGATGATTAACGTGGACC 58.529 52.381 0.00 0.00 0.00 4.46
1009 1091 1.754803 AGCGAGGATGATTAACGTGGA 59.245 47.619 0.00 0.00 0.00 4.02
1021 1103 2.909965 GGCGAGGAGAGCGAGGAT 60.910 66.667 0.00 0.00 35.00 3.24
1024 1106 4.544689 CACGGCGAGGAGAGCGAG 62.545 72.222 16.62 0.00 35.00 5.03
1026 1108 4.544689 CTCACGGCGAGGAGAGCG 62.545 72.222 22.27 2.66 38.18 5.03
1127 1209 0.247460 CATCCACTTCTCGTGCCTCA 59.753 55.000 0.00 0.00 42.42 3.86
1170 1252 2.802106 GCCTTCTCCTCCTCGTCG 59.198 66.667 0.00 0.00 0.00 5.12
1245 1327 3.699894 CGGTGGCTGCTGTCCTCT 61.700 66.667 0.00 0.00 0.00 3.69
1398 1480 2.503061 CTCCAGTCCATGCTCCCG 59.497 66.667 0.00 0.00 0.00 5.14
1452 1534 2.598589 TGATTGTACGTACCGCAAGAC 58.401 47.619 22.43 9.47 43.02 3.01
1698 1782 4.664677 AGTGGACGCACGAGGCAC 62.665 66.667 0.00 0.00 45.17 5.01
1699 1783 2.933878 AAAAGTGGACGCACGAGGCA 62.934 55.000 0.00 0.00 45.17 4.75
1700 1784 2.171489 GAAAAGTGGACGCACGAGGC 62.171 60.000 0.00 0.00 39.90 4.70
1701 1785 1.860078 GAAAAGTGGACGCACGAGG 59.140 57.895 0.00 0.00 0.00 4.63
1702 1786 1.487231 CGAAAAGTGGACGCACGAG 59.513 57.895 0.00 0.00 0.00 4.18
1703 1787 1.952133 CCGAAAAGTGGACGCACGA 60.952 57.895 0.00 0.00 0.00 4.35
1704 1788 2.154427 GACCGAAAAGTGGACGCACG 62.154 60.000 0.00 0.00 0.00 5.34
1705 1789 1.155424 TGACCGAAAAGTGGACGCAC 61.155 55.000 0.00 0.00 0.00 5.34
1711 1795 0.951558 CTGGGTTGACCGAAAAGTGG 59.048 55.000 0.00 0.00 44.64 4.00
1804 1889 4.202264 ACAGAGGCCATTAAGATTAGGACG 60.202 45.833 5.01 0.00 33.20 4.79
1812 1897 5.178096 TGATGAAACAGAGGCCATTAAGA 57.822 39.130 5.01 0.00 0.00 2.10
1819 1904 3.878778 AGTACATGATGAAACAGAGGCC 58.121 45.455 0.00 0.00 0.00 5.19
1852 1937 0.956633 GCATATGCATGTCACCCCAG 59.043 55.000 22.84 0.00 41.59 4.45
2470 2555 3.181967 GCCAGCTAGTGACGTGCG 61.182 66.667 0.00 0.00 0.00 5.34
2489 2575 0.463833 AACCATACGCCAAGCTAGCC 60.464 55.000 12.13 0.00 0.00 3.93
2499 2585 3.423907 CGAACCAAACACTAACCATACGC 60.424 47.826 0.00 0.00 0.00 4.42
2549 2636 0.317938 AGTCGATCGGATAAGCGTGC 60.318 55.000 16.41 0.00 0.00 5.34
2643 2737 6.571520 GTCGTCGTTACAGTACCTATTTATCG 59.428 42.308 0.00 0.00 0.00 2.92
2759 2855 7.121463 ACATGTTCTGTGGTTACAACTTACAAA 59.879 33.333 0.00 0.00 36.48 2.83
2886 2994 1.135373 CCATCACTGTCGACGTAGCTT 60.135 52.381 11.62 0.00 0.00 3.74
3031 3144 3.332409 AACGTCGTTTGTCCGCCG 61.332 61.111 4.40 0.00 0.00 6.46
3131 3244 1.597461 CTCTTCCCCTCCACGTTCC 59.403 63.158 0.00 0.00 0.00 3.62
3134 3247 3.003763 GGCTCTTCCCCTCCACGT 61.004 66.667 0.00 0.00 0.00 4.49
3136 3249 3.787001 CCGGCTCTTCCCCTCCAC 61.787 72.222 0.00 0.00 0.00 4.02
3137 3250 3.984186 CTCCGGCTCTTCCCCTCCA 62.984 68.421 0.00 0.00 0.00 3.86
3140 3253 3.684628 TCCTCCGGCTCTTCCCCT 61.685 66.667 0.00 0.00 0.00 4.79
3230 3348 1.959085 CCATTCATATGCCCACCGC 59.041 57.895 0.00 0.00 38.31 5.68
3287 3405 6.147864 GCCAAGCCAAATATGTCAATTCTA 57.852 37.500 0.00 0.00 0.00 2.10
3351 3469 6.991485 TTGAAATCTTGCGAATCAAAGAAC 57.009 33.333 0.38 0.00 33.65 3.01
3354 3472 6.366877 ACCATTTGAAATCTTGCGAATCAAAG 59.633 34.615 5.61 0.00 39.86 2.77
3404 3522 6.146347 GCCAGCAGTACTCTTGCTATAATTAC 59.854 42.308 7.69 0.00 37.11 1.89
3405 3523 6.042093 AGCCAGCAGTACTCTTGCTATAATTA 59.958 38.462 14.86 0.00 37.11 1.40
3406 3524 5.059833 GCCAGCAGTACTCTTGCTATAATT 58.940 41.667 7.69 0.00 37.11 1.40
3407 3525 4.346418 AGCCAGCAGTACTCTTGCTATAAT 59.654 41.667 14.86 0.11 37.11 1.28
3408 3526 3.706594 AGCCAGCAGTACTCTTGCTATAA 59.293 43.478 14.86 0.00 37.11 0.98
3409 3527 3.300388 AGCCAGCAGTACTCTTGCTATA 58.700 45.455 14.86 0.00 37.11 1.31
3410 3528 2.114616 AGCCAGCAGTACTCTTGCTAT 58.885 47.619 14.86 2.00 37.11 2.97
3411 3529 1.561643 AGCCAGCAGTACTCTTGCTA 58.438 50.000 14.86 0.00 37.11 3.49
3412 3530 1.561643 TAGCCAGCAGTACTCTTGCT 58.438 50.000 18.23 18.23 39.79 3.91
3413 3531 2.003301 GTTAGCCAGCAGTACTCTTGC 58.997 52.381 0.00 1.54 0.00 4.01
3414 3532 2.234908 AGGTTAGCCAGCAGTACTCTTG 59.765 50.000 0.00 0.00 37.19 3.02
3415 3533 2.541466 AGGTTAGCCAGCAGTACTCTT 58.459 47.619 0.00 0.00 37.19 2.85
3416 3534 2.234908 CAAGGTTAGCCAGCAGTACTCT 59.765 50.000 0.00 0.00 37.19 3.24
3417 3535 2.028020 ACAAGGTTAGCCAGCAGTACTC 60.028 50.000 0.00 0.00 37.19 2.59
3418 3536 1.978580 ACAAGGTTAGCCAGCAGTACT 59.021 47.619 0.00 0.00 37.19 2.73
3419 3537 2.474410 ACAAGGTTAGCCAGCAGTAC 57.526 50.000 0.00 0.00 37.19 2.73
3420 3538 3.502123 AAACAAGGTTAGCCAGCAGTA 57.498 42.857 0.00 0.00 37.19 2.74
3421 3539 2.364972 AAACAAGGTTAGCCAGCAGT 57.635 45.000 0.00 0.00 37.19 4.40
3422 3540 6.058183 AGATATAAACAAGGTTAGCCAGCAG 58.942 40.000 0.00 0.00 37.19 4.24
3423 3541 6.001449 AGATATAAACAAGGTTAGCCAGCA 57.999 37.500 0.00 0.00 37.19 4.41
3424 3542 6.203723 CAGAGATATAAACAAGGTTAGCCAGC 59.796 42.308 0.00 0.00 37.19 4.85
3425 3543 6.203723 GCAGAGATATAAACAAGGTTAGCCAG 59.796 42.308 0.00 0.00 37.19 4.85
3426 3544 6.055588 GCAGAGATATAAACAAGGTTAGCCA 58.944 40.000 0.00 0.00 37.19 4.75
3427 3545 6.292150 AGCAGAGATATAAACAAGGTTAGCC 58.708 40.000 0.00 0.00 0.00 3.93
3428 3546 8.766151 GTTAGCAGAGATATAAACAAGGTTAGC 58.234 37.037 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.