Multiple sequence alignment - TraesCS7B01G272000

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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 TraesCS7B01G272000 chr7B 100.000 2651 0 0 1 2651 498961980 498964630 0.000000e+00 4896
1 TraesCS7B01G272000 chr7B 97.143 70 2 0 2 71 230350244 230350175 4.640000e-23 119
2 TraesCS7B01G272000 chr7D 94.888 1291 37 9 381 1659 475155752 475157025 0.000000e+00 1991
3 TraesCS7B01G272000 chr7D 86.257 553 50 8 1733 2260 475160046 475160597 6.360000e-161 577
4 TraesCS7B01G272000 chr7D 86.094 489 42 9 1675 2138 475157090 475157577 1.100000e-138 503
5 TraesCS7B01G272000 chr7D 92.053 151 12 0 2135 2285 475159305 475159455 2.070000e-51 213
6 TraesCS7B01G272000 chr7D 95.699 93 4 0 177 269 475155615 475155707 1.640000e-32 150
7 TraesCS7B01G272000 chr7A 92.947 1347 53 23 324 1659 520873804 520872489 0.000000e+00 1923
8 TraesCS7B01G272000 chr7A 86.982 507 44 12 1824 2308 520872149 520871643 3.860000e-153 551
9 TraesCS7B01G272000 chr7A 89.083 229 24 1 2081 2308 520838660 520838432 1.550000e-72 283
10 TraesCS7B01G272000 chr6A 97.183 71 2 0 1 71 586572794 586572724 1.290000e-23 121
11 TraesCS7B01G272000 chr1B 92.857 84 5 1 1 84 200915181 200915099 1.290000e-23 121
12 TraesCS7B01G272000 chr6D 98.507 67 1 0 1 67 223047236 223047302 4.640000e-23 119
13 TraesCS7B01G272000 chr2B 97.143 70 2 0 1 70 144384152 144384083 4.640000e-23 119
14 TraesCS7B01G272000 chr2B 97.183 71 1 1 1 70 677342200 677342270 4.640000e-23 119
15 TraesCS7B01G272000 chr6B 95.775 71 3 0 1 71 706341229 706341299 6.000000e-22 115
16 TraesCS7B01G272000 chr3A 94.595 74 4 0 2 75 370186089 370186016 6.000000e-22 115
17 TraesCS7B01G272000 chr3B 91.463 82 6 1 2 83 798284775 798284695 7.760000e-21 111


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 TraesCS7B01G272000 chr7B 498961980 498964630 2650 False 4896.0 4896 100.0000 1 2651 1 chr7B.!!$F1 2650
1 TraesCS7B01G272000 chr7D 475155615 475160597 4982 False 686.8 1991 90.9982 177 2285 5 chr7D.!!$F1 2108
2 TraesCS7B01G272000 chr7A 520871643 520873804 2161 True 1237.0 1923 89.9645 324 2308 2 chr7A.!!$R2 1984

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
110 111 0.039035 GGTGGCATGTTACCTTGGGA 59.961 55.0 11.76 0.0 34.11 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1686 0.667792 AAGAAGGCTGAACTCGTCGC 60.668 55.0 0.0 0.0 0.0 5.19 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 5.283060 CTATAATTATGCGCCTTGGTCAC 57.717 43.478 4.18 0.00 0.00 3.67
23 24 1.102978 AATTATGCGCCTTGGTCACC 58.897 50.000 4.18 0.00 0.00 4.02
24 25 1.095228 ATTATGCGCCTTGGTCACCG 61.095 55.000 4.18 0.00 0.00 4.94
25 26 2.457743 TTATGCGCCTTGGTCACCGT 62.458 55.000 4.18 0.00 0.00 4.83
29 30 4.947147 GCCTTGGTCACCGTGCCA 62.947 66.667 9.74 9.74 0.00 4.92
30 31 2.203280 CCTTGGTCACCGTGCCAA 60.203 61.111 19.72 19.72 41.90 4.52
31 32 1.826054 CCTTGGTCACCGTGCCAAA 60.826 57.895 20.67 0.00 43.29 3.28
32 33 1.388065 CCTTGGTCACCGTGCCAAAA 61.388 55.000 20.67 7.24 43.29 2.44
33 34 0.457851 CTTGGTCACCGTGCCAAAAA 59.542 50.000 20.67 6.72 43.29 1.94
34 35 1.068434 CTTGGTCACCGTGCCAAAAAT 59.932 47.619 20.67 0.00 43.29 1.82
35 36 1.982660 TGGTCACCGTGCCAAAAATA 58.017 45.000 10.99 0.00 0.00 1.40
36 37 2.307768 TGGTCACCGTGCCAAAAATAA 58.692 42.857 10.99 0.00 0.00 1.40
37 38 2.894126 TGGTCACCGTGCCAAAAATAAT 59.106 40.909 10.99 0.00 0.00 1.28
38 39 4.079970 TGGTCACCGTGCCAAAAATAATA 58.920 39.130 10.99 0.00 0.00 0.98
39 40 4.082679 TGGTCACCGTGCCAAAAATAATAC 60.083 41.667 10.99 0.00 0.00 1.89
40 41 4.082679 GGTCACCGTGCCAAAAATAATACA 60.083 41.667 7.01 0.00 0.00 2.29
41 42 4.854839 GTCACCGTGCCAAAAATAATACAC 59.145 41.667 0.00 0.00 0.00 2.90
42 43 4.082679 TCACCGTGCCAAAAATAATACACC 60.083 41.667 0.00 0.00 0.00 4.16
43 44 4.082463 CACCGTGCCAAAAATAATACACCT 60.082 41.667 0.00 0.00 0.00 4.00
44 45 4.525100 ACCGTGCCAAAAATAATACACCTT 59.475 37.500 0.00 0.00 0.00 3.50
45 46 5.711036 ACCGTGCCAAAAATAATACACCTTA 59.289 36.000 0.00 0.00 0.00 2.69
46 47 6.031471 CCGTGCCAAAAATAATACACCTTAC 58.969 40.000 0.00 0.00 0.00 2.34
47 48 6.349445 CCGTGCCAAAAATAATACACCTTACA 60.349 38.462 0.00 0.00 0.00 2.41
48 49 7.254852 CGTGCCAAAAATAATACACCTTACAT 58.745 34.615 0.00 0.00 0.00 2.29
49 50 8.399425 CGTGCCAAAAATAATACACCTTACATA 58.601 33.333 0.00 0.00 0.00 2.29
65 66 6.253946 CTTACATAAAGGAATGGAGGGAGT 57.746 41.667 0.00 0.00 0.00 3.85
66 67 7.374975 CTTACATAAAGGAATGGAGGGAGTA 57.625 40.000 0.00 0.00 0.00 2.59
67 68 5.896073 ACATAAAGGAATGGAGGGAGTAG 57.104 43.478 0.00 0.00 0.00 2.57
68 69 5.289510 ACATAAAGGAATGGAGGGAGTAGT 58.710 41.667 0.00 0.00 0.00 2.73
69 70 6.449956 ACATAAAGGAATGGAGGGAGTAGTA 58.550 40.000 0.00 0.00 0.00 1.82
70 71 7.082972 ACATAAAGGAATGGAGGGAGTAGTAT 58.917 38.462 0.00 0.00 0.00 2.12
71 72 7.572861 ACATAAAGGAATGGAGGGAGTAGTATT 59.427 37.037 0.00 0.00 0.00 1.89
72 73 6.910259 AAAGGAATGGAGGGAGTAGTATTT 57.090 37.500 0.00 0.00 0.00 1.40
73 74 6.910259 AAGGAATGGAGGGAGTAGTATTTT 57.090 37.500 0.00 0.00 0.00 1.82
74 75 6.910259 AGGAATGGAGGGAGTAGTATTTTT 57.090 37.500 0.00 0.00 0.00 1.94
96 97 1.369321 TTTTTGCGGGATTGGTGGC 59.631 52.632 0.00 0.00 0.00 5.01
97 98 1.402896 TTTTTGCGGGATTGGTGGCA 61.403 50.000 0.00 0.00 0.00 4.92
98 99 1.190833 TTTTGCGGGATTGGTGGCAT 61.191 50.000 0.00 0.00 35.03 4.40
99 100 1.886253 TTTGCGGGATTGGTGGCATG 61.886 55.000 0.00 0.00 35.03 4.06
100 101 2.755469 GCGGGATTGGTGGCATGT 60.755 61.111 0.00 0.00 0.00 3.21
101 102 2.350458 GCGGGATTGGTGGCATGTT 61.350 57.895 0.00 0.00 0.00 2.71
102 103 1.034838 GCGGGATTGGTGGCATGTTA 61.035 55.000 0.00 0.00 0.00 2.41
103 104 0.738389 CGGGATTGGTGGCATGTTAC 59.262 55.000 0.00 0.00 0.00 2.50
104 105 1.111277 GGGATTGGTGGCATGTTACC 58.889 55.000 12.04 12.04 37.48 2.85
105 106 1.341976 GGGATTGGTGGCATGTTACCT 60.342 52.381 17.59 3.02 37.84 3.08
106 107 2.456577 GGATTGGTGGCATGTTACCTT 58.543 47.619 17.59 8.41 37.84 3.50
107 108 2.166254 GGATTGGTGGCATGTTACCTTG 59.834 50.000 17.59 0.00 37.84 3.61
108 109 1.626686 TTGGTGGCATGTTACCTTGG 58.373 50.000 17.59 0.00 37.84 3.61
109 110 0.251564 TGGTGGCATGTTACCTTGGG 60.252 55.000 17.59 0.00 37.84 4.12
110 111 0.039035 GGTGGCATGTTACCTTGGGA 59.961 55.000 11.76 0.00 34.11 4.37
111 112 1.463674 GTGGCATGTTACCTTGGGAG 58.536 55.000 0.00 0.00 0.00 4.30
112 113 1.004277 GTGGCATGTTACCTTGGGAGA 59.996 52.381 0.00 0.00 0.00 3.71
113 114 1.281867 TGGCATGTTACCTTGGGAGAG 59.718 52.381 0.00 0.00 0.00 3.20
114 115 1.383523 GCATGTTACCTTGGGAGAGC 58.616 55.000 0.00 0.00 0.00 4.09
115 116 2.019156 GCATGTTACCTTGGGAGAGCC 61.019 57.143 0.00 0.00 0.00 4.70
130 131 5.073311 GGAGAGCCCAAAGGAAAAATAAC 57.927 43.478 0.00 0.00 33.47 1.89
131 132 4.526650 GGAGAGCCCAAAGGAAAAATAACA 59.473 41.667 0.00 0.00 33.47 2.41
132 133 5.011635 GGAGAGCCCAAAGGAAAAATAACAA 59.988 40.000 0.00 0.00 33.47 2.83
133 134 6.463755 GGAGAGCCCAAAGGAAAAATAACAAA 60.464 38.462 0.00 0.00 33.47 2.83
134 135 6.524734 AGAGCCCAAAGGAAAAATAACAAAG 58.475 36.000 0.00 0.00 33.47 2.77
135 136 6.326323 AGAGCCCAAAGGAAAAATAACAAAGA 59.674 34.615 0.00 0.00 33.47 2.52
136 137 6.524734 AGCCCAAAGGAAAAATAACAAAGAG 58.475 36.000 0.00 0.00 33.47 2.85
137 138 5.179368 GCCCAAAGGAAAAATAACAAAGAGC 59.821 40.000 0.00 0.00 33.47 4.09
138 139 5.405269 CCCAAAGGAAAAATAACAAAGAGCG 59.595 40.000 0.00 0.00 33.47 5.03
139 140 5.405269 CCAAAGGAAAAATAACAAAGAGCGG 59.595 40.000 0.00 0.00 0.00 5.52
140 141 4.783764 AGGAAAAATAACAAAGAGCGGG 57.216 40.909 0.00 0.00 0.00 6.13
141 142 3.509967 AGGAAAAATAACAAAGAGCGGGG 59.490 43.478 0.00 0.00 0.00 5.73
142 143 3.250744 GAAAAATAACAAAGAGCGGGGC 58.749 45.455 0.00 0.00 0.00 5.80
143 144 1.917872 AAATAACAAAGAGCGGGGCA 58.082 45.000 0.00 0.00 0.00 5.36
144 145 1.917872 AATAACAAAGAGCGGGGCAA 58.082 45.000 0.00 0.00 0.00 4.52
145 146 1.463674 ATAACAAAGAGCGGGGCAAG 58.536 50.000 0.00 0.00 0.00 4.01
146 147 0.608035 TAACAAAGAGCGGGGCAAGG 60.608 55.000 0.00 0.00 0.00 3.61
147 148 3.752339 CAAAGAGCGGGGCAAGGC 61.752 66.667 0.00 0.00 0.00 4.35
151 152 4.770874 GAGCGGGGCAAGGCGTAA 62.771 66.667 0.00 0.00 0.00 3.18
152 153 4.338710 AGCGGGGCAAGGCGTAAA 62.339 61.111 0.00 0.00 0.00 2.01
153 154 3.138128 GCGGGGCAAGGCGTAAAT 61.138 61.111 0.00 0.00 0.00 1.40
154 155 2.706834 GCGGGGCAAGGCGTAAATT 61.707 57.895 0.00 0.00 0.00 1.82
155 156 1.138671 CGGGGCAAGGCGTAAATTG 59.861 57.895 0.00 0.00 0.00 2.32
156 157 1.309499 CGGGGCAAGGCGTAAATTGA 61.309 55.000 0.00 0.00 0.00 2.57
157 158 0.455815 GGGGCAAGGCGTAAATTGAG 59.544 55.000 0.00 0.00 0.00 3.02
158 159 1.459450 GGGCAAGGCGTAAATTGAGA 58.541 50.000 0.00 0.00 0.00 3.27
159 160 1.401905 GGGCAAGGCGTAAATTGAGAG 59.598 52.381 0.00 0.00 0.00 3.20
160 161 2.356135 GGCAAGGCGTAAATTGAGAGA 58.644 47.619 0.00 0.00 0.00 3.10
161 162 2.096013 GGCAAGGCGTAAATTGAGAGAC 59.904 50.000 0.00 0.00 0.00 3.36
162 163 2.742053 GCAAGGCGTAAATTGAGAGACA 59.258 45.455 0.00 0.00 0.00 3.41
163 164 3.188460 GCAAGGCGTAAATTGAGAGACAA 59.812 43.478 0.00 0.00 42.95 3.18
164 165 4.320202 GCAAGGCGTAAATTGAGAGACAAA 60.320 41.667 0.00 0.00 42.03 2.83
165 166 5.619981 GCAAGGCGTAAATTGAGAGACAAAT 60.620 40.000 0.00 0.00 42.03 2.32
166 167 6.403200 GCAAGGCGTAAATTGAGAGACAAATA 60.403 38.462 0.00 0.00 42.03 1.40
167 168 7.679638 GCAAGGCGTAAATTGAGAGACAAATAT 60.680 37.037 0.00 0.00 42.03 1.28
168 169 7.865706 AGGCGTAAATTGAGAGACAAATATT 57.134 32.000 0.00 0.00 42.03 1.28
169 170 8.281212 AGGCGTAAATTGAGAGACAAATATTT 57.719 30.769 0.00 0.00 42.03 1.40
170 171 8.739972 AGGCGTAAATTGAGAGACAAATATTTT 58.260 29.630 0.00 0.00 42.03 1.82
171 172 8.798153 GGCGTAAATTGAGAGACAAATATTTTG 58.202 33.333 0.00 0.00 42.03 2.44
172 173 9.554724 GCGTAAATTGAGAGACAAATATTTTGA 57.445 29.630 6.96 0.00 42.03 2.69
195 196 7.798071 TGAGGTTTAATCACGAATAACCCTAT 58.202 34.615 0.00 0.00 39.20 2.57
206 207 6.984474 CACGAATAACCCTATGTACTTGTCAT 59.016 38.462 0.00 0.00 0.00 3.06
261 262 1.079073 CCCTGGCCCCAATGAAACT 59.921 57.895 0.00 0.00 0.00 2.66
262 263 0.972471 CCCTGGCCCCAATGAAACTC 60.972 60.000 0.00 0.00 0.00 3.01
269 270 1.315257 CCCAATGAAACTCCGCCCTG 61.315 60.000 0.00 0.00 0.00 4.45
270 271 1.508088 CAATGAAACTCCGCCCTGC 59.492 57.895 0.00 0.00 0.00 4.85
271 272 1.678970 AATGAAACTCCGCCCTGCC 60.679 57.895 0.00 0.00 0.00 4.85
272 273 3.645268 ATGAAACTCCGCCCTGCCC 62.645 63.158 0.00 0.00 0.00 5.36
282 283 4.974721 CCCTGCCCCCACACACAC 62.975 72.222 0.00 0.00 0.00 3.82
283 284 4.202574 CCTGCCCCCACACACACA 62.203 66.667 0.00 0.00 0.00 3.72
284 285 2.906897 CTGCCCCCACACACACAC 60.907 66.667 0.00 0.00 0.00 3.82
285 286 3.712771 CTGCCCCCACACACACACA 62.713 63.158 0.00 0.00 0.00 3.72
286 287 3.216292 GCCCCCACACACACACAC 61.216 66.667 0.00 0.00 0.00 3.82
287 288 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
288 289 1.152777 CCCCCACACACACACACAT 60.153 57.895 0.00 0.00 0.00 3.21
289 290 1.172180 CCCCCACACACACACACATC 61.172 60.000 0.00 0.00 0.00 3.06
290 291 0.179020 CCCCACACACACACACATCT 60.179 55.000 0.00 0.00 0.00 2.90
291 292 1.229428 CCCACACACACACACATCTC 58.771 55.000 0.00 0.00 0.00 2.75
292 293 1.202687 CCCACACACACACACATCTCT 60.203 52.381 0.00 0.00 0.00 3.10
293 294 2.138320 CCACACACACACACATCTCTC 58.862 52.381 0.00 0.00 0.00 3.20
294 295 1.788886 CACACACACACACATCTCTCG 59.211 52.381 0.00 0.00 0.00 4.04
295 296 1.269778 ACACACACACACATCTCTCGG 60.270 52.381 0.00 0.00 0.00 4.63
296 297 0.319900 ACACACACACATCTCTCGGC 60.320 55.000 0.00 0.00 0.00 5.54
297 298 1.080501 ACACACACATCTCTCGGCG 60.081 57.895 0.00 0.00 0.00 6.46
298 299 1.212751 CACACACATCTCTCGGCGA 59.787 57.895 10.14 10.14 0.00 5.54
299 300 0.799917 CACACACATCTCTCGGCGAG 60.800 60.000 30.10 30.10 41.30 5.03
300 301 1.226802 CACACATCTCTCGGCGAGG 60.227 63.158 33.93 24.35 40.30 4.63
301 302 1.679305 ACACATCTCTCGGCGAGGT 60.679 57.895 33.93 21.82 40.30 3.85
302 303 1.064946 CACATCTCTCGGCGAGGTC 59.935 63.158 33.93 0.00 40.30 3.85
303 304 1.378646 ACATCTCTCGGCGAGGTCA 60.379 57.895 33.93 19.41 40.30 4.02
304 305 0.965866 ACATCTCTCGGCGAGGTCAA 60.966 55.000 33.93 18.25 40.30 3.18
305 306 0.173481 CATCTCTCGGCGAGGTCAAA 59.827 55.000 33.93 15.49 40.30 2.69
306 307 0.895530 ATCTCTCGGCGAGGTCAAAA 59.104 50.000 33.93 14.75 40.30 2.44
307 308 0.895530 TCTCTCGGCGAGGTCAAAAT 59.104 50.000 33.93 0.00 40.30 1.82
308 309 1.275291 TCTCTCGGCGAGGTCAAAATT 59.725 47.619 33.93 0.00 40.30 1.82
309 310 2.076863 CTCTCGGCGAGGTCAAAATTT 58.923 47.619 33.93 0.00 36.06 1.82
310 311 2.073816 TCTCGGCGAGGTCAAAATTTC 58.926 47.619 33.93 0.00 0.00 2.17
311 312 1.804151 CTCGGCGAGGTCAAAATTTCA 59.196 47.619 28.52 0.00 0.00 2.69
312 313 1.533731 TCGGCGAGGTCAAAATTTCAC 59.466 47.619 4.99 0.00 0.00 3.18
313 314 1.265635 CGGCGAGGTCAAAATTTCACA 59.734 47.619 0.00 0.00 0.00 3.58
314 315 2.095263 CGGCGAGGTCAAAATTTCACAT 60.095 45.455 0.00 0.00 0.00 3.21
315 316 3.501950 GGCGAGGTCAAAATTTCACATC 58.498 45.455 0.00 0.00 0.00 3.06
316 317 3.057596 GGCGAGGTCAAAATTTCACATCA 60.058 43.478 12.67 0.00 0.00 3.07
317 318 3.914364 GCGAGGTCAAAATTTCACATCAC 59.086 43.478 12.67 2.86 0.00 3.06
318 319 4.320494 GCGAGGTCAAAATTTCACATCACT 60.320 41.667 12.67 0.00 0.00 3.41
319 320 5.385617 CGAGGTCAAAATTTCACATCACTC 58.614 41.667 12.67 5.45 0.00 3.51
320 321 5.362556 AGGTCAAAATTTCACATCACTCG 57.637 39.130 0.00 0.00 0.00 4.18
321 322 3.914364 GGTCAAAATTTCACATCACTCGC 59.086 43.478 0.00 0.00 0.00 5.03
322 323 4.536065 GTCAAAATTTCACATCACTCGCA 58.464 39.130 0.00 0.00 0.00 5.10
364 365 6.505044 TCATTTCAAGAATGGATCACACAG 57.495 37.500 0.00 0.00 0.00 3.66
570 575 5.021033 TGCATTTCACAATCACCTTTTGT 57.979 34.783 0.00 0.00 37.79 2.83
575 580 5.867903 TTCACAATCACCTTTTGTCCATT 57.132 34.783 0.00 0.00 35.18 3.16
576 581 6.968263 TTCACAATCACCTTTTGTCCATTA 57.032 33.333 0.00 0.00 35.18 1.90
577 582 6.325919 TCACAATCACCTTTTGTCCATTAC 57.674 37.500 0.00 0.00 35.18 1.89
578 583 6.068010 TCACAATCACCTTTTGTCCATTACT 58.932 36.000 0.00 0.00 35.18 2.24
579 584 6.016360 TCACAATCACCTTTTGTCCATTACTG 60.016 38.462 0.00 0.00 35.18 2.74
580 585 5.243730 ACAATCACCTTTTGTCCATTACTGG 59.756 40.000 0.00 0.00 44.64 4.00
581 586 3.153919 TCACCTTTTGTCCATTACTGGC 58.846 45.455 0.00 0.00 42.80 4.85
582 587 2.890311 CACCTTTTGTCCATTACTGGCA 59.110 45.455 0.00 0.00 42.80 4.92
583 588 2.890945 ACCTTTTGTCCATTACTGGCAC 59.109 45.455 0.00 0.00 42.80 5.01
705 710 4.476628 AACTGGCCAATTCCATCAAATC 57.523 40.909 7.01 0.00 35.22 2.17
914 921 5.134202 TCGAAGCTTCTTATCACAGAACA 57.866 39.130 23.50 0.00 0.00 3.18
917 924 6.073765 TCGAAGCTTCTTATCACAGAACAAAC 60.074 38.462 23.50 0.00 0.00 2.93
920 927 4.451096 GCTTCTTATCACAGAACAAACCGA 59.549 41.667 0.00 0.00 0.00 4.69
921 928 5.049680 GCTTCTTATCACAGAACAAACCGAA 60.050 40.000 0.00 0.00 0.00 4.30
945 956 4.446371 GCCATCAGCTTGTAAGATACAGT 58.554 43.478 0.00 0.00 40.24 3.55
946 957 5.601662 GCCATCAGCTTGTAAGATACAGTA 58.398 41.667 0.00 0.00 40.24 2.74
954 969 7.170828 CAGCTTGTAAGATACAGTAACACACAA 59.829 37.037 0.00 6.92 40.24 3.33
959 974 7.929245 TGTAAGATACAGTAACACACAACACAT 59.071 33.333 0.00 0.00 34.06 3.21
961 981 6.759272 AGATACAGTAACACACAACACATCT 58.241 36.000 0.00 0.00 0.00 2.90
983 1003 4.743651 CTGCAAGAAACACCAAGAGGTAGA 60.744 45.833 0.00 0.00 41.88 2.59
994 1014 3.450457 CCAAGAGGTAGAGCACTCAGATT 59.550 47.826 0.00 0.00 36.20 2.40
996 1016 3.974719 AGAGGTAGAGCACTCAGATTCA 58.025 45.455 0.00 0.00 36.20 2.57
1089 1109 0.944311 ACATCAGCACCGACAACGTC 60.944 55.000 0.00 0.00 37.88 4.34
1373 1393 3.532501 GGAGGAGGCCGAGAAGAG 58.467 66.667 0.00 0.00 0.00 2.85
1659 1679 1.827681 TCAGCGACTAGACAGAGCTT 58.172 50.000 0.00 0.00 37.26 3.74
1660 1680 2.987232 TCAGCGACTAGACAGAGCTTA 58.013 47.619 0.00 0.00 37.26 3.09
1661 1681 3.344515 TCAGCGACTAGACAGAGCTTAA 58.655 45.455 0.00 0.00 37.26 1.85
1663 1683 4.399618 TCAGCGACTAGACAGAGCTTAATT 59.600 41.667 0.00 0.00 37.26 1.40
1664 1684 4.737765 CAGCGACTAGACAGAGCTTAATTC 59.262 45.833 0.00 0.00 37.26 2.17
1665 1685 4.399618 AGCGACTAGACAGAGCTTAATTCA 59.600 41.667 0.00 0.00 36.44 2.57
1666 1686 4.737765 GCGACTAGACAGAGCTTAATTCAG 59.262 45.833 0.00 0.00 0.00 3.02
1669 1689 3.876274 AGACAGAGCTTAATTCAGCGA 57.124 42.857 5.99 0.00 45.24 4.93
1670 1690 3.516615 AGACAGAGCTTAATTCAGCGAC 58.483 45.455 5.99 5.15 45.24 5.19
1672 1692 2.094700 ACAGAGCTTAATTCAGCGACGA 60.095 45.455 5.99 0.00 45.24 4.20
1673 1693 2.533535 CAGAGCTTAATTCAGCGACGAG 59.466 50.000 5.99 0.00 45.24 4.18
1676 1745 2.924290 AGCTTAATTCAGCGACGAGTTC 59.076 45.455 5.99 0.00 45.24 3.01
1698 1767 3.872771 CAGCCTTCTTGTTGCATGTTTTT 59.127 39.130 0.00 0.00 0.00 1.94
1740 1809 2.031157 GTGCATACTTCACACGCCTTTT 60.031 45.455 0.00 0.00 34.73 2.27
1741 1810 3.187637 GTGCATACTTCACACGCCTTTTA 59.812 43.478 0.00 0.00 34.73 1.52
1744 1813 1.892209 ACTTCACACGCCTTTTAGGG 58.108 50.000 0.00 0.00 35.37 3.53
1745 1814 1.142262 ACTTCACACGCCTTTTAGGGT 59.858 47.619 0.00 0.00 35.37 4.34
1746 1815 1.535462 CTTCACACGCCTTTTAGGGTG 59.465 52.381 7.13 7.13 40.28 4.61
1774 1843 4.128925 TGTTGCACCTCTAGCTTATCTG 57.871 45.455 0.00 0.00 0.00 2.90
1777 1846 3.374764 TGCACCTCTAGCTTATCTGGAA 58.625 45.455 0.00 0.00 31.56 3.53
1803 1876 1.072173 AGCATCACTGTAGCAACACCA 59.928 47.619 0.00 0.00 0.00 4.17
1808 1881 3.937814 TCACTGTAGCAACACCATAAGG 58.062 45.455 0.00 0.00 42.21 2.69
1822 2025 4.035675 CACCATAAGGCTTAAGCTTGTAGC 59.964 45.833 25.88 20.92 39.25 3.58
1833 2036 1.646189 GCTTGTAGCTAGTCACCAGC 58.354 55.000 0.00 0.00 38.45 4.85
1858 2061 6.593382 CCATGTTCTGTTTTTCCAAGTTCAAA 59.407 34.615 0.00 0.00 0.00 2.69
1862 2065 9.311916 TGTTCTGTTTTTCCAAGTTCAAATATG 57.688 29.630 0.00 0.00 0.00 1.78
1863 2066 9.313118 GTTCTGTTTTTCCAAGTTCAAATATGT 57.687 29.630 0.00 0.00 0.00 2.29
1864 2067 9.528018 TTCTGTTTTTCCAAGTTCAAATATGTC 57.472 29.630 0.00 0.00 0.00 3.06
1867 2070 9.883142 TGTTTTTCCAAGTTCAAATATGTCTTT 57.117 25.926 0.00 0.00 0.00 2.52
1892 2095 1.837439 TGGTGATCGGACAGCCTTAAT 59.163 47.619 8.79 0.00 37.46 1.40
1893 2096 2.238646 TGGTGATCGGACAGCCTTAATT 59.761 45.455 8.79 0.00 37.46 1.40
1895 2098 3.065371 GGTGATCGGACAGCCTTAATTTG 59.935 47.826 0.00 0.00 32.97 2.32
1896 2099 3.065371 GTGATCGGACAGCCTTAATTTGG 59.935 47.826 0.00 0.00 0.00 3.28
1911 2118 3.627395 ATTTGGCACTGATCTTCGGTA 57.373 42.857 0.00 0.00 33.46 4.02
1912 2119 3.410631 TTTGGCACTGATCTTCGGTAA 57.589 42.857 0.00 0.00 33.46 2.85
2013 2231 4.476297 CCCATCTTCCATTGATTCCATGA 58.524 43.478 0.00 0.00 0.00 3.07
2031 2255 5.124617 TCCATGAAAGTTTTATGCGTGCATA 59.875 36.000 13.49 10.37 37.82 3.14
2109 2336 6.976925 CCATCCTAAGAGAAATGCAATGAAAC 59.023 38.462 0.00 0.00 0.00 2.78
2138 4096 5.124617 TGTGATTAACTGCTTGTGTGTTTGA 59.875 36.000 0.00 0.00 0.00 2.69
2149 4107 6.645827 TGCTTGTGTGTTTGATCATTAATTGG 59.354 34.615 0.00 0.00 0.00 3.16
2224 4182 6.902224 AATTGTTTGCCTTGTGTTTAACTC 57.098 33.333 0.00 0.00 0.00 3.01
2268 4226 3.634397 TTCAGTCCAATCATCTCCACC 57.366 47.619 0.00 0.00 0.00 4.61
2275 4233 3.588842 TCCAATCATCTCCACCAACTCTT 59.411 43.478 0.00 0.00 0.00 2.85
2289 4247 7.559897 TCCACCAACTCTTTGTTATTCTTTTCT 59.440 33.333 0.00 0.00 37.07 2.52
2312 4271 9.474920 TTCTTATTGAAAAAGTACATTTGCCTG 57.525 29.630 0.00 0.00 0.00 4.85
2317 4315 6.634805 TGAAAAAGTACATTTGCCTGTGAAA 58.365 32.000 0.00 0.00 0.00 2.69
2323 4321 4.075963 ACATTTGCCTGTGAAAAGCATT 57.924 36.364 0.00 0.00 36.20 3.56
2338 4336 6.867816 TGAAAAGCATTATCCACACAATCAAC 59.132 34.615 0.00 0.00 0.00 3.18
2343 4341 4.740741 TTATCCACACAATCAACACGTG 57.259 40.909 15.48 15.48 36.70 4.49
2355 4353 2.094575 TCAACACGTGCAACACAACTAC 59.905 45.455 17.22 0.00 35.74 2.73
2357 4355 2.285083 ACACGTGCAACACAACTACAT 58.715 42.857 17.22 0.00 35.74 2.29
2358 4356 2.680841 ACACGTGCAACACAACTACATT 59.319 40.909 17.22 0.00 35.74 2.71
2359 4357 3.127895 ACACGTGCAACACAACTACATTT 59.872 39.130 17.22 0.00 35.74 2.32
2360 4358 4.101942 CACGTGCAACACAACTACATTTT 58.898 39.130 0.82 0.00 35.74 1.82
2361 4359 4.560819 CACGTGCAACACAACTACATTTTT 59.439 37.500 0.82 0.00 35.74 1.94
2391 4397 6.503589 TCAATAGTAAAAATGTTCACCCGG 57.496 37.500 0.00 0.00 0.00 5.73
2400 4406 0.841289 TGTTCACCCGGAAACCTTCT 59.159 50.000 0.73 0.00 37.23 2.85
2406 4413 0.825840 CCCGGAAACCTTCTTGCCAA 60.826 55.000 0.73 0.00 0.00 4.52
2417 4424 1.217244 CTTGCCAAATGCTCCAGCC 59.783 57.895 0.00 0.00 42.00 4.85
2418 4425 1.228956 TTGCCAAATGCTCCAGCCT 60.229 52.632 0.00 0.00 42.00 4.58
2419 4426 0.039472 TTGCCAAATGCTCCAGCCTA 59.961 50.000 0.00 0.00 42.00 3.93
2420 4427 0.394762 TGCCAAATGCTCCAGCCTAG 60.395 55.000 0.00 0.00 42.00 3.02
2423 4430 2.843701 CCAAATGCTCCAGCCTAGTAG 58.156 52.381 0.00 0.00 41.18 2.57
2439 4446 7.716998 CAGCCTAGTAGACACCATCATAAAAAT 59.283 37.037 0.00 0.00 0.00 1.82
2460 4467 9.720769 AAAAATGTCTTTATCTTTCGGTCTCTA 57.279 29.630 0.00 0.00 0.00 2.43
2463 4470 6.618811 TGTCTTTATCTTTCGGTCTCTACAC 58.381 40.000 0.00 0.00 0.00 2.90
2487 4494 7.061210 CACGATAGAATAAGTAAAGAGCCATCG 59.939 40.741 0.00 0.00 41.38 3.84
2492 4499 1.726853 AGTAAAGAGCCATCGCACAC 58.273 50.000 0.00 0.00 37.52 3.82
2493 4500 1.001974 AGTAAAGAGCCATCGCACACA 59.998 47.619 0.00 0.00 37.52 3.72
2517 4524 1.667236 TGAATAACATGCGCAGGAGG 58.333 50.000 30.79 14.14 34.40 4.30
2557 4564 2.628178 TCGATAACCACATCAGCCCTAG 59.372 50.000 0.00 0.00 0.00 3.02
2561 4568 3.629142 AACCACATCAGCCCTAGTAAC 57.371 47.619 0.00 0.00 0.00 2.50
2565 4572 3.525537 CACATCAGCCCTAGTAACACAG 58.474 50.000 0.00 0.00 0.00 3.66
2579 4586 8.038944 CCTAGTAACACAGAAAGCCTAACATAA 58.961 37.037 0.00 0.00 0.00 1.90
2584 4591 6.775708 ACACAGAAAGCCTAACATAAGGTTA 58.224 36.000 0.00 0.00 40.96 2.85
2587 4594 6.177610 CAGAAAGCCTAACATAAGGTTACCA 58.822 40.000 3.51 0.00 40.96 3.25
2600 4607 4.140575 AGGTTACCATCCCCACAAAAAT 57.859 40.909 3.51 0.00 0.00 1.82
2625 4632 9.769093 ATATGTGCAGAAAATCGTTTTTAGTAC 57.231 29.630 4.25 9.84 35.20 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.154195 GGTGACCAAGGCGCATAATTATAG 59.846 45.833 10.83 0.00 0.00 1.31
1 2 4.069304 GGTGACCAAGGCGCATAATTATA 58.931 43.478 10.83 0.00 0.00 0.98
2 3 2.884639 GGTGACCAAGGCGCATAATTAT 59.115 45.455 10.83 0.00 0.00 1.28
3 4 2.294074 GGTGACCAAGGCGCATAATTA 58.706 47.619 10.83 0.00 0.00 1.40
4 5 1.102978 GGTGACCAAGGCGCATAATT 58.897 50.000 10.83 0.00 0.00 1.40
5 6 1.095228 CGGTGACCAAGGCGCATAAT 61.095 55.000 10.83 0.00 0.00 1.28
6 7 1.743623 CGGTGACCAAGGCGCATAA 60.744 57.895 10.83 0.00 0.00 1.90
7 8 2.125310 CGGTGACCAAGGCGCATA 60.125 61.111 10.83 0.00 0.00 3.14
8 9 4.329545 ACGGTGACCAAGGCGCAT 62.330 61.111 10.83 0.00 0.00 4.73
12 13 4.947147 TGGCACGGTGACCAAGGC 62.947 66.667 12.26 6.15 31.46 4.35
13 14 1.388065 TTTTGGCACGGTGACCAAGG 61.388 55.000 25.13 0.00 46.20 3.61
14 15 0.457851 TTTTTGGCACGGTGACCAAG 59.542 50.000 25.13 0.00 46.20 3.61
15 16 1.115467 ATTTTTGGCACGGTGACCAA 58.885 45.000 23.78 23.78 44.11 3.67
16 17 1.982660 TATTTTTGGCACGGTGACCA 58.017 45.000 12.26 14.98 0.00 4.02
17 18 3.586100 ATTATTTTTGGCACGGTGACC 57.414 42.857 12.26 12.53 0.00 4.02
18 19 4.854839 GTGTATTATTTTTGGCACGGTGAC 59.145 41.667 13.29 10.30 0.00 3.67
19 20 4.082679 GGTGTATTATTTTTGGCACGGTGA 60.083 41.667 13.29 0.00 0.00 4.02
20 21 4.082463 AGGTGTATTATTTTTGGCACGGTG 60.082 41.667 3.15 3.15 0.00 4.94
21 22 4.083565 AGGTGTATTATTTTTGGCACGGT 58.916 39.130 0.00 0.00 0.00 4.83
22 23 4.712122 AGGTGTATTATTTTTGGCACGG 57.288 40.909 0.00 0.00 0.00 4.94
23 24 6.613233 TGTAAGGTGTATTATTTTTGGCACG 58.387 36.000 0.00 0.00 0.00 5.34
42 43 6.253946 ACTCCCTCCATTCCTTTATGTAAG 57.746 41.667 0.00 0.00 0.00 2.34
43 44 6.906901 ACTACTCCCTCCATTCCTTTATGTAA 59.093 38.462 0.00 0.00 0.00 2.41
44 45 6.449956 ACTACTCCCTCCATTCCTTTATGTA 58.550 40.000 0.00 0.00 0.00 2.29
45 46 5.289510 ACTACTCCCTCCATTCCTTTATGT 58.710 41.667 0.00 0.00 0.00 2.29
46 47 5.896073 ACTACTCCCTCCATTCCTTTATG 57.104 43.478 0.00 0.00 0.00 1.90
47 48 8.582891 AAATACTACTCCCTCCATTCCTTTAT 57.417 34.615 0.00 0.00 0.00 1.40
48 49 8.401955 AAAATACTACTCCCTCCATTCCTTTA 57.598 34.615 0.00 0.00 0.00 1.85
49 50 6.910259 AAATACTACTCCCTCCATTCCTTT 57.090 37.500 0.00 0.00 0.00 3.11
50 51 6.910259 AAAATACTACTCCCTCCATTCCTT 57.090 37.500 0.00 0.00 0.00 3.36
51 52 6.910259 AAAAATACTACTCCCTCCATTCCT 57.090 37.500 0.00 0.00 0.00 3.36
78 79 1.369321 GCCACCAATCCCGCAAAAA 59.631 52.632 0.00 0.00 0.00 1.94
79 80 1.190833 ATGCCACCAATCCCGCAAAA 61.191 50.000 0.00 0.00 34.38 2.44
80 81 1.608918 ATGCCACCAATCCCGCAAA 60.609 52.632 0.00 0.00 34.38 3.68
81 82 2.037049 ATGCCACCAATCCCGCAA 59.963 55.556 0.00 0.00 34.38 4.85
82 83 2.755064 CATGCCACCAATCCCGCA 60.755 61.111 0.00 0.00 35.35 5.69
83 84 1.034838 TAACATGCCACCAATCCCGC 61.035 55.000 0.00 0.00 0.00 6.13
84 85 0.738389 GTAACATGCCACCAATCCCG 59.262 55.000 0.00 0.00 0.00 5.14
85 86 1.111277 GGTAACATGCCACCAATCCC 58.889 55.000 10.68 0.00 34.77 3.85
86 87 2.143876 AGGTAACATGCCACCAATCC 57.856 50.000 16.41 0.00 37.28 3.01
87 88 2.166254 CCAAGGTAACATGCCACCAATC 59.834 50.000 16.41 0.00 37.28 2.67
88 89 2.178580 CCAAGGTAACATGCCACCAAT 58.821 47.619 16.41 4.50 37.28 3.16
89 90 1.626686 CCAAGGTAACATGCCACCAA 58.373 50.000 16.41 0.00 37.28 3.67
90 91 0.251564 CCCAAGGTAACATGCCACCA 60.252 55.000 16.41 0.00 37.28 4.17
91 92 0.039035 TCCCAAGGTAACATGCCACC 59.961 55.000 8.02 8.02 41.41 4.61
92 93 1.004277 TCTCCCAAGGTAACATGCCAC 59.996 52.381 0.00 0.00 41.41 5.01
93 94 1.281867 CTCTCCCAAGGTAACATGCCA 59.718 52.381 0.00 0.00 41.41 4.92
94 95 2.019156 GCTCTCCCAAGGTAACATGCC 61.019 57.143 0.00 0.00 41.41 4.40
95 96 1.383523 GCTCTCCCAAGGTAACATGC 58.616 55.000 0.00 0.00 41.41 4.06
96 97 2.044123 GGCTCTCCCAAGGTAACATG 57.956 55.000 0.00 0.00 41.41 3.21
108 109 4.526650 TGTTATTTTTCCTTTGGGCTCTCC 59.473 41.667 0.00 0.00 0.00 3.71
109 110 5.722021 TGTTATTTTTCCTTTGGGCTCTC 57.278 39.130 0.00 0.00 0.00 3.20
110 111 6.326323 TCTTTGTTATTTTTCCTTTGGGCTCT 59.674 34.615 0.00 0.00 0.00 4.09
111 112 6.521162 TCTTTGTTATTTTTCCTTTGGGCTC 58.479 36.000 0.00 0.00 0.00 4.70
112 113 6.493189 TCTTTGTTATTTTTCCTTTGGGCT 57.507 33.333 0.00 0.00 0.00 5.19
113 114 5.179368 GCTCTTTGTTATTTTTCCTTTGGGC 59.821 40.000 0.00 0.00 0.00 5.36
114 115 5.405269 CGCTCTTTGTTATTTTTCCTTTGGG 59.595 40.000 0.00 0.00 0.00 4.12
115 116 5.405269 CCGCTCTTTGTTATTTTTCCTTTGG 59.595 40.000 0.00 0.00 0.00 3.28
116 117 5.405269 CCCGCTCTTTGTTATTTTTCCTTTG 59.595 40.000 0.00 0.00 0.00 2.77
117 118 5.510690 CCCCGCTCTTTGTTATTTTTCCTTT 60.511 40.000 0.00 0.00 0.00 3.11
118 119 4.021456 CCCCGCTCTTTGTTATTTTTCCTT 60.021 41.667 0.00 0.00 0.00 3.36
119 120 3.509967 CCCCGCTCTTTGTTATTTTTCCT 59.490 43.478 0.00 0.00 0.00 3.36
120 121 3.845178 CCCCGCTCTTTGTTATTTTTCC 58.155 45.455 0.00 0.00 0.00 3.13
121 122 3.250744 GCCCCGCTCTTTGTTATTTTTC 58.749 45.455 0.00 0.00 0.00 2.29
122 123 2.630580 TGCCCCGCTCTTTGTTATTTTT 59.369 40.909 0.00 0.00 0.00 1.94
123 124 2.243810 TGCCCCGCTCTTTGTTATTTT 58.756 42.857 0.00 0.00 0.00 1.82
124 125 1.917872 TGCCCCGCTCTTTGTTATTT 58.082 45.000 0.00 0.00 0.00 1.40
125 126 1.818674 CTTGCCCCGCTCTTTGTTATT 59.181 47.619 0.00 0.00 0.00 1.40
126 127 1.463674 CTTGCCCCGCTCTTTGTTAT 58.536 50.000 0.00 0.00 0.00 1.89
127 128 0.608035 CCTTGCCCCGCTCTTTGTTA 60.608 55.000 0.00 0.00 0.00 2.41
128 129 1.903404 CCTTGCCCCGCTCTTTGTT 60.903 57.895 0.00 0.00 0.00 2.83
129 130 2.282462 CCTTGCCCCGCTCTTTGT 60.282 61.111 0.00 0.00 0.00 2.83
130 131 3.752339 GCCTTGCCCCGCTCTTTG 61.752 66.667 0.00 0.00 0.00 2.77
134 135 4.770874 TTACGCCTTGCCCCGCTC 62.771 66.667 0.00 0.00 0.00 5.03
135 136 3.638592 ATTTACGCCTTGCCCCGCT 62.639 57.895 0.00 0.00 0.00 5.52
136 137 2.706834 AATTTACGCCTTGCCCCGC 61.707 57.895 0.00 0.00 0.00 6.13
137 138 1.138671 CAATTTACGCCTTGCCCCG 59.861 57.895 0.00 0.00 0.00 5.73
138 139 0.455815 CTCAATTTACGCCTTGCCCC 59.544 55.000 0.00 0.00 0.00 5.80
139 140 1.401905 CTCTCAATTTACGCCTTGCCC 59.598 52.381 0.00 0.00 0.00 5.36
140 141 2.096013 GTCTCTCAATTTACGCCTTGCC 59.904 50.000 0.00 0.00 0.00 4.52
141 142 2.742053 TGTCTCTCAATTTACGCCTTGC 59.258 45.455 0.00 0.00 0.00 4.01
142 143 5.356882 TTTGTCTCTCAATTTACGCCTTG 57.643 39.130 0.00 0.00 35.84 3.61
143 144 7.865706 ATATTTGTCTCTCAATTTACGCCTT 57.134 32.000 0.00 0.00 35.84 4.35
144 145 7.865706 AATATTTGTCTCTCAATTTACGCCT 57.134 32.000 0.00 0.00 35.84 5.52
145 146 8.798153 CAAAATATTTGTCTCTCAATTTACGCC 58.202 33.333 0.39 0.00 35.84 5.68
146 147 9.554724 TCAAAATATTTGTCTCTCAATTTACGC 57.445 29.630 0.39 0.00 35.84 4.42
158 159 9.840427 CGTGATTAAACCTCAAAATATTTGTCT 57.160 29.630 0.39 0.00 0.00 3.41
159 160 9.834628 TCGTGATTAAACCTCAAAATATTTGTC 57.165 29.630 0.39 0.00 0.00 3.18
166 167 8.248253 GGGTTATTCGTGATTAAACCTCAAAAT 58.752 33.333 10.07 0.00 33.46 1.82
167 168 7.449086 AGGGTTATTCGTGATTAAACCTCAAAA 59.551 33.333 12.97 0.00 39.04 2.44
168 169 6.943718 AGGGTTATTCGTGATTAAACCTCAAA 59.056 34.615 12.97 0.00 39.04 2.69
169 170 6.478129 AGGGTTATTCGTGATTAAACCTCAA 58.522 36.000 12.97 0.00 39.04 3.02
170 171 6.057321 AGGGTTATTCGTGATTAAACCTCA 57.943 37.500 12.97 0.00 39.04 3.86
171 172 7.713942 ACATAGGGTTATTCGTGATTAAACCTC 59.286 37.037 19.23 6.63 41.11 3.85
172 173 7.571025 ACATAGGGTTATTCGTGATTAAACCT 58.429 34.615 19.47 19.47 43.15 3.50
173 174 7.797038 ACATAGGGTTATTCGTGATTAAACC 57.203 36.000 9.53 9.53 35.37 3.27
174 175 9.538508 AGTACATAGGGTTATTCGTGATTAAAC 57.461 33.333 0.00 0.00 0.00 2.01
195 196 6.567959 TGTGCATTTTTCAATGACAAGTACA 58.432 32.000 0.00 0.00 42.35 2.90
206 207 5.220815 GCTCCAACATTTGTGCATTTTTCAA 60.221 36.000 0.00 0.00 0.00 2.69
269 270 3.216292 GTGTGTGTGTGTGGGGGC 61.216 66.667 0.00 0.00 0.00 5.80
270 271 1.152777 ATGTGTGTGTGTGTGGGGG 60.153 57.895 0.00 0.00 0.00 5.40
271 272 0.179020 AGATGTGTGTGTGTGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
272 273 1.202687 AGAGATGTGTGTGTGTGTGGG 60.203 52.381 0.00 0.00 0.00 4.61
273 274 2.138320 GAGAGATGTGTGTGTGTGTGG 58.862 52.381 0.00 0.00 0.00 4.17
275 276 1.269778 CCGAGAGATGTGTGTGTGTGT 60.270 52.381 0.00 0.00 0.00 3.72
276 277 1.422388 CCGAGAGATGTGTGTGTGTG 58.578 55.000 0.00 0.00 0.00 3.82
278 279 1.347097 CGCCGAGAGATGTGTGTGTG 61.347 60.000 0.00 0.00 0.00 3.82
279 280 1.080501 CGCCGAGAGATGTGTGTGT 60.081 57.895 0.00 0.00 0.00 3.72
280 281 1.212751 TCGCCGAGAGATGTGTGTG 59.787 57.895 0.00 0.00 0.00 3.82
281 282 3.681473 TCGCCGAGAGATGTGTGT 58.319 55.556 0.00 0.00 0.00 3.72
289 290 1.726853 AATTTTGACCTCGCCGAGAG 58.273 50.000 17.19 8.36 46.44 3.20
290 291 2.073816 GAAATTTTGACCTCGCCGAGA 58.926 47.619 17.19 0.00 0.00 4.04
291 292 1.804151 TGAAATTTTGACCTCGCCGAG 59.196 47.619 7.25 7.25 0.00 4.63
292 293 1.533731 GTGAAATTTTGACCTCGCCGA 59.466 47.619 0.00 0.00 0.00 5.54
293 294 1.265635 TGTGAAATTTTGACCTCGCCG 59.734 47.619 0.00 0.00 0.00 6.46
294 295 3.057596 TGATGTGAAATTTTGACCTCGCC 60.058 43.478 0.00 0.00 0.00 5.54
295 296 3.914364 GTGATGTGAAATTTTGACCTCGC 59.086 43.478 0.00 2.92 0.00 5.03
296 297 5.362556 AGTGATGTGAAATTTTGACCTCG 57.637 39.130 0.00 0.00 0.00 4.63
297 298 5.385617 CGAGTGATGTGAAATTTTGACCTC 58.614 41.667 0.00 0.00 0.00 3.85
298 299 4.320494 GCGAGTGATGTGAAATTTTGACCT 60.320 41.667 0.00 0.00 0.00 3.85
299 300 3.914364 GCGAGTGATGTGAAATTTTGACC 59.086 43.478 0.00 0.00 0.00 4.02
300 301 4.536065 TGCGAGTGATGTGAAATTTTGAC 58.464 39.130 0.00 0.00 0.00 3.18
301 302 4.827304 TGCGAGTGATGTGAAATTTTGA 57.173 36.364 0.00 0.00 0.00 2.69
302 303 5.886715 TTTGCGAGTGATGTGAAATTTTG 57.113 34.783 0.00 0.00 0.00 2.44
303 304 6.900568 TTTTTGCGAGTGATGTGAAATTTT 57.099 29.167 0.00 0.00 0.00 1.82
327 328 7.111247 TCTTGAAATGAATGTGTGGAGTTTT 57.889 32.000 0.00 0.00 0.00 2.43
364 365 9.903682 CATATTCATGGTGTTAAAATGAGGATC 57.096 33.333 0.00 0.00 32.23 3.36
367 368 7.490840 TGCATATTCATGGTGTTAAAATGAGG 58.509 34.615 0.00 0.00 32.23 3.86
369 370 8.476447 ACATGCATATTCATGGTGTTAAAATGA 58.524 29.630 17.85 0.00 46.02 2.57
570 575 0.541392 ATCTGCGTGCCAGTAATGGA 59.459 50.000 14.70 0.00 42.38 3.41
575 580 1.804151 GTTGAAATCTGCGTGCCAGTA 59.196 47.619 0.00 0.00 42.38 2.74
576 581 0.593128 GTTGAAATCTGCGTGCCAGT 59.407 50.000 0.00 0.00 42.38 4.00
577 582 0.109597 GGTTGAAATCTGCGTGCCAG 60.110 55.000 0.00 0.00 43.17 4.85
578 583 1.523154 GGGTTGAAATCTGCGTGCCA 61.523 55.000 0.00 0.00 0.00 4.92
579 584 1.212751 GGGTTGAAATCTGCGTGCC 59.787 57.895 0.00 0.00 0.00 5.01
580 585 1.130561 GTAGGGTTGAAATCTGCGTGC 59.869 52.381 0.00 0.00 0.00 5.34
581 586 2.699954 AGTAGGGTTGAAATCTGCGTG 58.300 47.619 0.00 0.00 0.00 5.34
582 587 3.418684 AAGTAGGGTTGAAATCTGCGT 57.581 42.857 0.00 0.00 0.00 5.24
583 588 3.751175 TGAAAGTAGGGTTGAAATCTGCG 59.249 43.478 0.00 0.00 0.00 5.18
705 710 8.791327 AAGGGATTACAAATTTTGGCATAAAG 57.209 30.769 13.42 0.00 34.12 1.85
802 809 6.015940 CCATGCATGATACTACTGAGTACTGA 60.016 42.308 28.31 0.00 41.01 3.41
803 810 6.015940 TCCATGCATGATACTACTGAGTACTG 60.016 42.308 28.31 4.86 41.01 2.74
804 811 6.015856 GTCCATGCATGATACTACTGAGTACT 60.016 42.308 28.31 0.00 41.01 2.73
805 812 6.153067 GTCCATGCATGATACTACTGAGTAC 58.847 44.000 28.31 4.24 41.01 2.73
806 813 5.048713 CGTCCATGCATGATACTACTGAGTA 60.049 44.000 28.31 0.00 42.41 2.59
807 814 4.261783 CGTCCATGCATGATACTACTGAGT 60.262 45.833 28.31 0.00 39.92 3.41
808 815 4.233005 CGTCCATGCATGATACTACTGAG 58.767 47.826 28.31 7.07 0.00 3.35
809 816 3.552890 GCGTCCATGCATGATACTACTGA 60.553 47.826 28.31 10.87 34.15 3.41
941 952 3.312421 GCAGATGTGTTGTGTGTTACTGT 59.688 43.478 0.00 0.00 0.00 3.55
942 953 3.312146 TGCAGATGTGTTGTGTGTTACTG 59.688 43.478 0.00 0.00 0.00 2.74
943 954 3.540617 TGCAGATGTGTTGTGTGTTACT 58.459 40.909 0.00 0.00 0.00 2.24
944 955 3.961477 TGCAGATGTGTTGTGTGTTAC 57.039 42.857 0.00 0.00 0.00 2.50
945 956 4.195416 TCTTGCAGATGTGTTGTGTGTTA 58.805 39.130 0.00 0.00 0.00 2.41
946 957 3.016031 TCTTGCAGATGTGTTGTGTGTT 58.984 40.909 0.00 0.00 0.00 3.32
954 969 2.653726 TGGTGTTTCTTGCAGATGTGT 58.346 42.857 0.00 0.00 0.00 3.72
959 974 2.092429 ACCTCTTGGTGTTTCTTGCAGA 60.092 45.455 0.00 0.00 46.51 4.26
961 981 2.435372 ACCTCTTGGTGTTTCTTGCA 57.565 45.000 0.00 0.00 46.51 4.08
975 995 3.953612 CTGAATCTGAGTGCTCTACCTCT 59.046 47.826 0.68 0.00 0.00 3.69
983 1003 3.054875 TGCCATAACTGAATCTGAGTGCT 60.055 43.478 0.00 0.00 0.00 4.40
987 1007 3.209410 GGGTGCCATAACTGAATCTGAG 58.791 50.000 0.00 0.00 0.00 3.35
990 1010 2.684927 GCTGGGTGCCATAACTGAATCT 60.685 50.000 0.00 0.00 35.15 2.40
994 1014 0.035152 CTGCTGGGTGCCATAACTGA 60.035 55.000 0.00 0.00 42.00 3.41
996 1016 0.254178 CTCTGCTGGGTGCCATAACT 59.746 55.000 0.00 0.00 42.00 2.24
1659 1679 2.259618 GCTGAACTCGTCGCTGAATTA 58.740 47.619 0.00 0.00 0.00 1.40
1660 1680 1.071605 GCTGAACTCGTCGCTGAATT 58.928 50.000 0.00 0.00 0.00 2.17
1661 1681 0.737715 GGCTGAACTCGTCGCTGAAT 60.738 55.000 0.00 0.00 0.00 2.57
1663 1683 1.806461 AAGGCTGAACTCGTCGCTGA 61.806 55.000 0.00 0.00 0.00 4.26
1664 1684 1.347817 GAAGGCTGAACTCGTCGCTG 61.348 60.000 0.00 0.00 0.00 5.18
1665 1685 1.080434 GAAGGCTGAACTCGTCGCT 60.080 57.895 0.00 0.00 0.00 4.93
1666 1686 0.667792 AAGAAGGCTGAACTCGTCGC 60.668 55.000 0.00 0.00 0.00 5.19
1669 1689 2.213499 CAACAAGAAGGCTGAACTCGT 58.787 47.619 0.00 0.00 0.00 4.18
1670 1690 1.069636 GCAACAAGAAGGCTGAACTCG 60.070 52.381 0.00 0.00 0.00 4.18
1672 1692 2.057137 TGCAACAAGAAGGCTGAACT 57.943 45.000 0.00 0.00 0.00 3.01
1673 1693 2.035066 ACATGCAACAAGAAGGCTGAAC 59.965 45.455 0.00 0.00 0.00 3.18
1676 1745 2.806608 AACATGCAACAAGAAGGCTG 57.193 45.000 0.00 0.00 0.00 4.85
1753 1822 3.118629 CCAGATAAGCTAGAGGTGCAACA 60.119 47.826 3.64 0.00 39.98 3.33
1774 1843 3.126000 GCTACAGTGATGCTCAAGTTTCC 59.874 47.826 0.00 0.00 0.00 3.13
1777 1846 3.407424 TGCTACAGTGATGCTCAAGTT 57.593 42.857 0.00 0.00 0.00 2.66
1789 1862 2.305927 AGCCTTATGGTGTTGCTACAGT 59.694 45.455 0.00 0.00 34.24 3.55
1790 1863 2.991250 AGCCTTATGGTGTTGCTACAG 58.009 47.619 0.00 0.00 34.24 2.74
1794 1867 2.755103 GCTTAAGCCTTATGGTGTTGCT 59.245 45.455 17.00 0.00 35.27 3.91
1822 2025 2.027745 ACAGAACATGGCTGGTGACTAG 60.028 50.000 18.36 0.00 37.69 2.57
1829 2032 2.364970 TGGAAAAACAGAACATGGCTGG 59.635 45.455 18.36 0.00 37.69 4.85
1833 2036 5.659463 TGAACTTGGAAAAACAGAACATGG 58.341 37.500 0.00 0.00 0.00 3.66
1858 2061 7.773224 TGTCCGATCACCAAATTAAAGACATAT 59.227 33.333 0.00 0.00 0.00 1.78
1862 2065 5.673818 GCTGTCCGATCACCAAATTAAAGAC 60.674 44.000 0.00 0.00 0.00 3.01
1863 2066 4.394920 GCTGTCCGATCACCAAATTAAAGA 59.605 41.667 0.00 0.00 0.00 2.52
1864 2067 4.438744 GGCTGTCCGATCACCAAATTAAAG 60.439 45.833 0.00 0.00 0.00 1.85
1867 2070 2.238646 AGGCTGTCCGATCACCAAATTA 59.761 45.455 0.00 0.00 37.47 1.40
1868 2071 1.004745 AGGCTGTCCGATCACCAAATT 59.995 47.619 0.00 0.00 37.47 1.82
1892 2095 3.334691 CTTACCGAAGATCAGTGCCAAA 58.665 45.455 0.00 0.00 34.25 3.28
1893 2096 2.354704 CCTTACCGAAGATCAGTGCCAA 60.355 50.000 0.00 0.00 34.25 4.52
1895 2098 1.207329 ACCTTACCGAAGATCAGTGCC 59.793 52.381 0.00 0.00 34.25 5.01
1896 2099 2.674796 ACCTTACCGAAGATCAGTGC 57.325 50.000 0.00 0.00 34.25 4.40
1897 2100 5.962433 TCTAAACCTTACCGAAGATCAGTG 58.038 41.667 0.00 0.00 34.25 3.66
1898 2101 6.210984 ACTTCTAAACCTTACCGAAGATCAGT 59.789 38.462 0.00 0.00 36.04 3.41
2013 2231 5.181245 ACAGTCTATGCACGCATAAAACTTT 59.819 36.000 17.62 12.28 38.30 2.66
2031 2255 5.480422 TCAACACATACATACTCCACAGTCT 59.520 40.000 0.00 0.00 33.62 3.24
2079 2306 3.317430 GCATTTCTCTTAGGATGGCAAGG 59.683 47.826 0.00 0.00 0.00 3.61
2084 2311 6.704289 TTCATTGCATTTCTCTTAGGATGG 57.296 37.500 0.00 0.00 0.00 3.51
2109 2336 4.036734 ACACAAGCAGTTAATCACAGTTGG 59.963 41.667 0.00 0.00 0.00 3.77
2187 4145 4.272261 GCAAACAATTAAACACAACAGGGG 59.728 41.667 0.00 0.00 0.00 4.79
2250 4208 3.012518 GTTGGTGGAGATGATTGGACTG 58.987 50.000 0.00 0.00 0.00 3.51
2289 4247 8.417106 TCACAGGCAAATGTACTTTTTCAATAA 58.583 29.630 4.09 0.00 0.00 1.40
2294 4252 7.532682 TTTTCACAGGCAAATGTACTTTTTC 57.467 32.000 4.09 0.20 0.00 2.29
2308 4267 3.193267 TGTGGATAATGCTTTTCACAGGC 59.807 43.478 9.88 0.00 32.36 4.85
2309 4268 4.218200 TGTGTGGATAATGCTTTTCACAGG 59.782 41.667 12.58 0.00 36.07 4.00
2310 4269 5.375417 TGTGTGGATAATGCTTTTCACAG 57.625 39.130 12.58 0.00 36.07 3.66
2312 4271 6.389091 TGATTGTGTGGATAATGCTTTTCAC 58.611 36.000 0.00 0.00 0.00 3.18
2317 4315 5.619757 CGTGTTGATTGTGTGGATAATGCTT 60.620 40.000 0.00 0.00 0.00 3.91
2323 4321 2.482336 GCACGTGTTGATTGTGTGGATA 59.518 45.455 18.38 0.00 36.04 2.59
2338 4336 3.332761 AATGTAGTTGTGTTGCACGTG 57.667 42.857 12.28 12.28 37.14 4.49
2368 4374 6.239396 TCCGGGTGAACATTTTTACTATTGA 58.761 36.000 0.00 0.00 0.00 2.57
2386 4392 1.228459 GGCAAGAAGGTTTCCGGGT 60.228 57.895 0.00 0.00 0.00 5.28
2387 4393 0.825840 TTGGCAAGAAGGTTTCCGGG 60.826 55.000 0.00 0.00 0.00 5.73
2388 4394 1.036707 TTTGGCAAGAAGGTTTCCGG 58.963 50.000 0.00 0.00 0.00 5.14
2406 4413 2.432510 GTGTCTACTAGGCTGGAGCATT 59.567 50.000 4.33 0.00 44.36 3.56
2417 4424 9.823647 AGACATTTTTATGATGGTGTCTACTAG 57.176 33.333 4.19 0.00 43.02 2.57
2419 4426 9.520515 AAAGACATTTTTATGATGGTGTCTACT 57.479 29.630 6.29 0.00 43.77 2.57
2439 4446 6.618811 GTGTAGAGACCGAAAGATAAAGACA 58.381 40.000 0.00 0.00 0.00 3.41
2446 4453 5.366460 TCTATCGTGTAGAGACCGAAAGAT 58.634 41.667 0.00 0.00 33.78 2.40
2452 4459 6.542574 ACTTATTCTATCGTGTAGAGACCG 57.457 41.667 1.74 0.00 0.00 4.79
2460 4467 7.108841 TGGCTCTTTACTTATTCTATCGTGT 57.891 36.000 0.00 0.00 0.00 4.49
2463 4470 6.034044 GCGATGGCTCTTTACTTATTCTATCG 59.966 42.308 0.00 0.00 36.55 2.92
2497 4504 2.224606 CCTCCTGCGCATGTTATTCAT 58.775 47.619 12.24 0.00 37.22 2.57
2499 4506 1.331756 CACCTCCTGCGCATGTTATTC 59.668 52.381 12.24 0.00 0.00 1.75
2531 4538 3.438781 GGCTGATGTGGTTATCGACAAAA 59.561 43.478 0.00 0.00 36.04 2.44
2534 4541 1.134521 GGGCTGATGTGGTTATCGACA 60.135 52.381 0.00 0.00 36.78 4.35
2535 4542 1.139058 AGGGCTGATGTGGTTATCGAC 59.861 52.381 0.00 0.00 0.00 4.20
2536 4543 1.496060 AGGGCTGATGTGGTTATCGA 58.504 50.000 0.00 0.00 0.00 3.59
2537 4544 2.365617 ACTAGGGCTGATGTGGTTATCG 59.634 50.000 0.00 0.00 0.00 2.92
2538 4545 5.163343 TGTTACTAGGGCTGATGTGGTTATC 60.163 44.000 0.00 0.00 0.00 1.75
2540 4547 4.081309 GTGTTACTAGGGCTGATGTGGTTA 60.081 45.833 0.00 0.00 0.00 2.85
2557 4564 6.653740 ACCTTATGTTAGGCTTTCTGTGTTAC 59.346 38.462 0.00 0.00 38.99 2.50
2561 4568 6.093633 GGTAACCTTATGTTAGGCTTTCTGTG 59.906 42.308 0.00 0.00 40.05 3.66
2565 4572 6.262496 GGATGGTAACCTTATGTTAGGCTTTC 59.738 42.308 0.00 0.00 40.05 2.62
2579 4586 3.621682 TTTTTGTGGGGATGGTAACCT 57.378 42.857 0.00 0.00 0.00 3.50
2584 4591 3.197549 GCACATATTTTTGTGGGGATGGT 59.802 43.478 6.70 0.00 45.69 3.55
2587 4594 4.352009 TCTGCACATATTTTTGTGGGGAT 58.648 39.130 6.70 0.00 45.69 3.85
2600 4607 8.231837 GGTACTAAAAACGATTTTCTGCACATA 58.768 33.333 6.67 0.00 39.42 2.29
2614 4621 1.197492 GGTTGCGGGGTACTAAAAACG 59.803 52.381 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.