Multiple sequence alignment - TraesCS4B01G304700

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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 TraesCS4B01G304700 chr4B 100.000 2575 0 0 1 2575 593133296 593135870 0.000000e+00 4756
1 TraesCS4B01G304700 chr4B 81.727 498 55 16 2094 2571 593155435 593155916 1.450000e-102 383
2 TraesCS4B01G304700 chr4B 91.386 267 23 0 2302 2568 593116360 593116626 1.460000e-97 366
3 TraesCS4B01G304700 chr4B 86.645 307 29 2 2281 2575 593197285 593197591 1.910000e-86 329
4 TraesCS4B01G304700 chr4B 80.587 443 67 10 2139 2575 593342180 593342609 8.890000e-85 324
5 TraesCS4B01G304700 chr4B 84.483 290 31 8 2292 2568 593347561 593347849 9.080000e-70 274
6 TraesCS4B01G304700 chr4D 91.125 1307 65 15 432 1714 471147406 471148685 0.000000e+00 1724
7 TraesCS4B01G304700 chr4D 89.084 513 19 13 1779 2279 471153027 471153514 1.020000e-168 603
8 TraesCS4B01G304700 chr4D 91.753 291 12 5 2285 2575 471153586 471153864 6.680000e-106 394
9 TraesCS4B01G304700 chr4D 92.135 267 21 0 2302 2568 470856439 470856705 6.730000e-101 377
10 TraesCS4B01G304700 chr4D 82.599 431 47 14 2161 2571 471212137 471212559 3.150000e-94 355
11 TraesCS4B01G304700 chr4D 82.247 445 44 11 2145 2575 471216273 471216696 4.080000e-93 351
12 TraesCS4B01G304700 chr4D 83.972 287 32 6 2292 2565 471265030 471265315 1.960000e-66 263
13 TraesCS4B01G304700 chr4A 93.162 1053 48 11 678 1714 678367401 678368445 0.000000e+00 1524
14 TraesCS4B01G304700 chr4A 89.494 771 39 18 1821 2575 678369327 678370071 0.000000e+00 937
15 TraesCS4B01G304700 chr4A 87.597 258 20 1 2311 2568 678340585 678340830 3.240000e-74 289
16 TraesCS4B01G304700 chr4A 79.464 448 53 27 2155 2568 678408306 678408748 5.420000e-72 281
17 TraesCS4B01G304700 chr5B 82.553 235 31 9 448 678 13202948 13202720 5.620000e-47 198
18 TraesCS4B01G304700 chr6D 74.376 441 98 12 1 432 365628910 365628476 9.470000e-40 174
19 TraesCS4B01G304700 chr7A 73.988 346 66 17 101 432 290931046 290930711 4.500000e-23 119
20 TraesCS4B01G304700 chr1B 89.011 91 9 1 588 677 669022060 669021970 7.530000e-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 TraesCS4B01G304700 chr4B 593133296 593135870 2574 False 4756.0 4756 100.0000 1 2575 1 chr4B.!!$F2 2574
1 TraesCS4B01G304700 chr4D 471147406 471148685 1279 False 1724.0 1724 91.1250 432 1714 1 chr4D.!!$F2 1282
2 TraesCS4B01G304700 chr4D 471153027 471153864 837 False 498.5 603 90.4185 1779 2575 2 chr4D.!!$F4 796
3 TraesCS4B01G304700 chr4D 471212137 471216696 4559 False 353.0 355 82.4230 2145 2575 2 chr4D.!!$F5 430
4 TraesCS4B01G304700 chr4A 678367401 678370071 2670 False 1230.5 1524 91.3280 678 2575 2 chr4A.!!$F3 1897

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
330 331 0.037139 CTGCTTGCTCTGCACTCTCT 60.037 55.0 0.0 0.0 38.71 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2553 0.250513 GGACTGCATCGAGGGAAAGT 59.749 55.0 0.0 0.0 0.0 2.66 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 4.840271 TCTCATGGTGTCGACTAGTTAGA 58.160 43.478 17.92 9.63 0.00 2.10
24 25 3.693085 TCATGGTGTCGACTAGTTAGACC 59.307 47.826 17.92 18.52 34.24 3.85
25 26 3.144657 TGGTGTCGACTAGTTAGACCA 57.855 47.619 17.92 18.65 34.24 4.02
26 27 2.816087 TGGTGTCGACTAGTTAGACCAC 59.184 50.000 17.92 17.59 34.24 4.16
27 28 2.163211 GGTGTCGACTAGTTAGACCACC 59.837 54.545 17.92 22.05 34.24 4.61
28 29 2.163211 GTGTCGACTAGTTAGACCACCC 59.837 54.545 17.92 9.62 34.24 4.61
31 32 3.021695 TCGACTAGTTAGACCACCCATG 58.978 50.000 0.00 0.00 0.00 3.66
32 33 2.481449 CGACTAGTTAGACCACCCATGC 60.481 54.545 0.00 0.00 0.00 4.06
34 35 2.501723 ACTAGTTAGACCACCCATGCTG 59.498 50.000 0.00 0.00 0.00 4.41
35 36 0.620556 AGTTAGACCACCCATGCTGG 59.379 55.000 6.18 6.18 37.25 4.85
36 37 0.618458 GTTAGACCACCCATGCTGGA 59.382 55.000 13.26 0.00 40.96 3.86
37 38 0.618458 TTAGACCACCCATGCTGGAC 59.382 55.000 13.26 7.99 40.96 4.02
40 41 2.124983 CCACCCATGCTGGACTCG 60.125 66.667 2.10 0.00 40.96 4.18
41 42 2.659063 CCACCCATGCTGGACTCGA 61.659 63.158 2.10 0.00 40.96 4.04
42 43 1.448540 CACCCATGCTGGACTCGAC 60.449 63.158 4.00 0.00 40.96 4.20
43 44 2.187946 CCCATGCTGGACTCGACC 59.812 66.667 4.00 0.00 40.96 4.79
45 46 2.887568 CATGCTGGACTCGACCGC 60.888 66.667 0.00 0.00 0.00 5.68
46 47 4.148825 ATGCTGGACTCGACCGCC 62.149 66.667 6.49 0.00 0.00 6.13
48 49 4.070552 GCTGGACTCGACCGCCTT 62.071 66.667 0.00 0.00 0.00 4.35
50 51 2.282958 TGGACTCGACCGCCTTCT 60.283 61.111 0.00 0.00 0.00 2.85
54 55 1.919956 GACTCGACCGCCTTCTTCGA 61.920 60.000 0.00 0.00 39.38 3.71
55 56 1.514443 CTCGACCGCCTTCTTCGAC 60.514 63.158 0.00 0.00 36.87 4.20
56 57 1.924320 CTCGACCGCCTTCTTCGACT 61.924 60.000 0.00 0.00 36.87 4.18
57 58 1.801913 CGACCGCCTTCTTCGACTG 60.802 63.158 0.00 0.00 34.62 3.51
60 61 1.738099 CCGCCTTCTTCGACTGGTG 60.738 63.158 0.00 0.00 0.00 4.17
62 63 2.035442 GCCTTCTTCGACTGGTGGC 61.035 63.158 0.00 0.00 0.00 5.01
63 64 1.674057 CCTTCTTCGACTGGTGGCT 59.326 57.895 0.00 0.00 0.00 4.75
64 65 0.390472 CCTTCTTCGACTGGTGGCTC 60.390 60.000 0.00 0.00 0.00 4.70
65 66 0.390472 CTTCTTCGACTGGTGGCTCC 60.390 60.000 0.00 0.00 0.00 4.70
78 79 2.359230 GCTCCAGGCCACAGTGTC 60.359 66.667 5.01 0.00 34.27 3.67
79 80 3.150949 CTCCAGGCCACAGTGTCA 58.849 61.111 5.01 0.00 0.00 3.58
81 82 0.392193 CTCCAGGCCACAGTGTCATC 60.392 60.000 5.01 0.00 0.00 2.92
82 83 1.377725 CCAGGCCACAGTGTCATCC 60.378 63.158 5.01 0.00 0.00 3.51
83 84 1.681666 CAGGCCACAGTGTCATCCT 59.318 57.895 5.01 0.00 0.00 3.24
84 85 0.392193 CAGGCCACAGTGTCATCCTC 60.392 60.000 5.01 0.00 0.00 3.71
85 86 1.448540 GGCCACAGTGTCATCCTCG 60.449 63.158 0.00 0.00 0.00 4.63
86 87 1.448540 GCCACAGTGTCATCCTCGG 60.449 63.158 0.00 0.00 0.00 4.63
88 89 0.108615 CCACAGTGTCATCCTCGGAC 60.109 60.000 0.00 0.00 35.83 4.79
89 90 0.603065 CACAGTGTCATCCTCGGACA 59.397 55.000 0.00 0.00 42.62 4.02
90 91 0.891373 ACAGTGTCATCCTCGGACAG 59.109 55.000 0.00 0.00 45.21 3.51
91 92 0.459237 CAGTGTCATCCTCGGACAGC 60.459 60.000 0.00 0.00 45.21 4.40
92 93 1.153549 GTGTCATCCTCGGACAGCC 60.154 63.158 0.00 0.00 45.21 4.85
93 94 1.305297 TGTCATCCTCGGACAGCCT 60.305 57.895 0.00 0.00 40.16 4.58
95 96 1.112113 GTCATCCTCGGACAGCCTTA 58.888 55.000 0.00 0.00 35.36 2.69
96 97 1.067821 GTCATCCTCGGACAGCCTTAG 59.932 57.143 0.00 0.00 35.36 2.18
115 116 1.440145 GGCGAGGCCTAAACTGCATC 61.440 60.000 4.42 0.00 46.69 3.91
116 117 0.744414 GCGAGGCCTAAACTGCATCA 60.744 55.000 4.42 0.00 39.36 3.07
117 118 1.959042 CGAGGCCTAAACTGCATCAT 58.041 50.000 4.42 0.00 39.36 2.45
119 120 1.869767 GAGGCCTAAACTGCATCATCG 59.130 52.381 4.42 0.00 39.22 3.84
120 121 0.308993 GGCCTAAACTGCATCATCGC 59.691 55.000 0.00 0.00 0.00 4.58
121 122 1.303309 GCCTAAACTGCATCATCGCT 58.697 50.000 0.00 0.00 0.00 4.93
122 123 1.262683 GCCTAAACTGCATCATCGCTC 59.737 52.381 0.00 0.00 0.00 5.03
123 124 2.831333 CCTAAACTGCATCATCGCTCT 58.169 47.619 0.00 0.00 0.00 4.09
126 127 1.649664 AACTGCATCATCGCTCTCAC 58.350 50.000 0.00 0.00 0.00 3.51
127 128 0.533951 ACTGCATCATCGCTCTCACA 59.466 50.000 0.00 0.00 0.00 3.58
128 129 1.209998 CTGCATCATCGCTCTCACAG 58.790 55.000 0.00 0.00 0.00 3.66
129 130 0.808847 TGCATCATCGCTCTCACAGC 60.809 55.000 0.00 0.00 45.85 4.40
136 137 3.123620 GCTCTCACAGCTTGGGCG 61.124 66.667 0.00 0.00 45.83 6.13
139 140 0.809241 CTCTCACAGCTTGGGCGATC 60.809 60.000 0.00 0.00 44.37 3.69
140 141 1.220206 CTCACAGCTTGGGCGATCT 59.780 57.895 0.00 0.00 44.37 2.75
141 142 1.078918 TCACAGCTTGGGCGATCTG 60.079 57.895 0.00 0.00 44.37 2.90
142 143 2.110967 CACAGCTTGGGCGATCTGG 61.111 63.158 0.00 0.00 44.37 3.86
143 144 2.293318 ACAGCTTGGGCGATCTGGA 61.293 57.895 0.00 0.00 44.37 3.86
144 145 1.078214 CAGCTTGGGCGATCTGGAA 60.078 57.895 0.00 0.00 44.37 3.53
145 146 1.094073 CAGCTTGGGCGATCTGGAAG 61.094 60.000 0.00 0.00 44.37 3.46
146 147 2.476320 GCTTGGGCGATCTGGAAGC 61.476 63.158 0.00 0.00 32.87 3.86
147 148 1.078214 CTTGGGCGATCTGGAAGCA 60.078 57.895 0.00 0.00 0.00 3.91
148 149 1.372087 CTTGGGCGATCTGGAAGCAC 61.372 60.000 0.00 0.00 34.36 4.40
149 150 2.514824 GGGCGATCTGGAAGCACC 60.515 66.667 0.00 0.00 39.54 5.01
150 151 2.892425 GGCGATCTGGAAGCACCG 60.892 66.667 0.00 0.00 42.61 4.94
152 153 1.447838 GCGATCTGGAAGCACCGAA 60.448 57.895 0.00 0.00 42.61 4.30
153 154 1.019278 GCGATCTGGAAGCACCGAAA 61.019 55.000 0.00 0.00 42.61 3.46
155 156 1.328680 CGATCTGGAAGCACCGAAATG 59.671 52.381 0.00 0.00 42.61 2.32
156 157 1.064654 GATCTGGAAGCACCGAAATGC 59.935 52.381 0.00 0.00 46.50 3.56
166 167 4.963815 CGAAATGCGGCCACTTTT 57.036 50.000 2.24 3.54 36.03 2.27
167 168 2.433637 CGAAATGCGGCCACTTTTG 58.566 52.632 9.18 2.53 36.03 2.44
168 169 0.039617 CGAAATGCGGCCACTTTTGA 60.040 50.000 9.18 0.00 36.03 2.69
169 170 1.418373 GAAATGCGGCCACTTTTGAC 58.582 50.000 9.18 0.00 0.00 3.18
170 171 0.318614 AAATGCGGCCACTTTTGACG 60.319 50.000 2.24 0.00 0.00 4.35
172 173 4.700365 GCGGCCACTTTTGACGGC 62.700 66.667 2.24 0.00 45.47 5.68
175 176 4.700365 GCCACTTTTGACGGCGCC 62.700 66.667 19.07 19.07 35.79 6.53
193 194 4.261888 CGACCTTCCACGGACAAG 57.738 61.111 0.00 0.00 0.00 3.16
195 196 1.371558 GACCTTCCACGGACAAGCT 59.628 57.895 0.00 0.00 0.00 3.74
196 197 0.670854 GACCTTCCACGGACAAGCTC 60.671 60.000 0.00 0.00 0.00 4.09
197 198 1.738099 CCTTCCACGGACAAGCTCG 60.738 63.158 0.00 0.00 0.00 5.03
198 199 1.006102 CTTCCACGGACAAGCTCGT 60.006 57.895 0.00 0.00 40.49 4.18
210 211 3.880591 GCTCGTGCAGCTGATCAA 58.119 55.556 20.43 0.00 45.83 2.57
213 214 1.718396 CTCGTGCAGCTGATCAAGAA 58.282 50.000 20.43 0.00 0.00 2.52
214 215 1.392853 CTCGTGCAGCTGATCAAGAAC 59.607 52.381 20.43 0.00 0.00 3.01
215 216 0.094216 CGTGCAGCTGATCAAGAACG 59.906 55.000 20.43 10.61 0.00 3.95
216 217 1.432514 GTGCAGCTGATCAAGAACGA 58.567 50.000 20.43 0.00 0.00 3.85
217 218 1.392853 GTGCAGCTGATCAAGAACGAG 59.607 52.381 20.43 0.00 0.00 4.18
218 219 1.005340 GCAGCTGATCAAGAACGAGG 58.995 55.000 20.43 0.00 0.00 4.63
219 220 1.005340 CAGCTGATCAAGAACGAGGC 58.995 55.000 8.42 0.00 0.00 4.70
223 224 3.144120 GATCAAGAACGAGGCGCGC 62.144 63.158 25.94 25.94 46.04 6.86
247 248 4.235762 GCCAAGGCCGGCGATAGA 62.236 66.667 22.54 0.00 43.52 1.98
248 249 2.029666 CCAAGGCCGGCGATAGAG 59.970 66.667 22.54 6.66 39.76 2.43
249 250 2.029666 CAAGGCCGGCGATAGAGG 59.970 66.667 22.54 1.08 38.27 3.69
250 251 2.123425 AAGGCCGGCGATAGAGGA 60.123 61.111 22.54 0.00 37.58 3.71
252 253 2.913060 GGCCGGCGATAGAGGACT 60.913 66.667 22.54 0.00 39.87 3.85
253 254 1.602888 GGCCGGCGATAGAGGACTA 60.603 63.158 22.54 0.00 39.87 2.59
254 255 1.587933 GGCCGGCGATAGAGGACTAG 61.588 65.000 22.54 0.00 39.87 2.57
255 256 0.605860 GCCGGCGATAGAGGACTAGA 60.606 60.000 12.58 0.00 37.58 2.43
256 257 1.951424 GCCGGCGATAGAGGACTAGAT 60.951 57.143 12.58 0.00 37.58 1.98
257 258 2.680221 GCCGGCGATAGAGGACTAGATA 60.680 54.545 12.58 0.00 37.58 1.98
258 259 3.607741 CCGGCGATAGAGGACTAGATAA 58.392 50.000 9.30 0.00 37.58 1.75
259 260 4.008330 CCGGCGATAGAGGACTAGATAAA 58.992 47.826 9.30 0.00 37.58 1.40
260 261 4.458295 CCGGCGATAGAGGACTAGATAAAA 59.542 45.833 9.30 0.00 37.58 1.52
261 262 5.125739 CCGGCGATAGAGGACTAGATAAAAT 59.874 44.000 9.30 0.00 37.58 1.82
262 263 6.350277 CCGGCGATAGAGGACTAGATAAAATT 60.350 42.308 9.30 0.00 37.58 1.82
263 264 7.148120 CCGGCGATAGAGGACTAGATAAAATTA 60.148 40.741 9.30 0.00 37.58 1.40
264 265 8.407064 CGGCGATAGAGGACTAGATAAAATTAT 58.593 37.037 0.00 0.00 39.76 1.28
265 266 9.738832 GGCGATAGAGGACTAGATAAAATTATC 57.261 37.037 0.00 5.24 38.22 1.75
266 267 9.738832 GCGATAGAGGACTAGATAAAATTATCC 57.261 37.037 9.07 0.00 38.51 2.59
274 275 9.722184 GGACTAGATAAAATTATCCCTGTAACC 57.278 37.037 9.07 2.67 40.26 2.85
279 280 8.218488 AGATAAAATTATCCCTGTAACCTGACC 58.782 37.037 9.07 0.00 40.26 4.02
281 282 5.994416 AATTATCCCTGTAACCTGACCAT 57.006 39.130 0.00 0.00 0.00 3.55
282 283 4.771114 TTATCCCTGTAACCTGACCATG 57.229 45.455 0.00 0.00 0.00 3.66
283 284 2.038863 TCCCTGTAACCTGACCATGT 57.961 50.000 0.00 0.00 0.00 3.21
284 285 2.344592 TCCCTGTAACCTGACCATGTT 58.655 47.619 0.00 0.00 0.00 2.71
286 287 2.224769 CCCTGTAACCTGACCATGTTGT 60.225 50.000 0.00 0.00 0.00 3.32
288 289 4.324254 CCCTGTAACCTGACCATGTTGTAT 60.324 45.833 0.00 0.00 0.00 2.29
289 290 5.253330 CCTGTAACCTGACCATGTTGTATT 58.747 41.667 0.00 0.00 0.00 1.89
291 292 5.870706 TGTAACCTGACCATGTTGTATTGA 58.129 37.500 0.00 0.00 0.00 2.57
293 294 3.955471 ACCTGACCATGTTGTATTGAGG 58.045 45.455 0.00 0.00 0.00 3.86
294 295 3.330701 ACCTGACCATGTTGTATTGAGGT 59.669 43.478 0.00 0.00 0.00 3.85
295 296 4.202567 ACCTGACCATGTTGTATTGAGGTT 60.203 41.667 0.00 0.00 0.00 3.50
296 297 4.156556 CCTGACCATGTTGTATTGAGGTTG 59.843 45.833 0.00 0.00 0.00 3.77
297 298 4.979335 TGACCATGTTGTATTGAGGTTGA 58.021 39.130 0.00 0.00 0.00 3.18
298 299 5.569355 TGACCATGTTGTATTGAGGTTGAT 58.431 37.500 0.00 0.00 0.00 2.57
301 302 6.189859 ACCATGTTGTATTGAGGTTGATCAT 58.810 36.000 0.00 0.00 0.00 2.45
302 303 6.319658 ACCATGTTGTATTGAGGTTGATCATC 59.680 38.462 0.00 0.00 0.00 2.92
303 304 6.238842 CCATGTTGTATTGAGGTTGATCATCC 60.239 42.308 14.07 14.07 0.00 3.51
304 305 5.192927 TGTTGTATTGAGGTTGATCATCCC 58.807 41.667 17.57 10.89 0.00 3.85
305 306 5.192927 GTTGTATTGAGGTTGATCATCCCA 58.807 41.667 17.57 12.78 0.00 4.37
306 307 4.780815 TGTATTGAGGTTGATCATCCCAC 58.219 43.478 17.57 12.99 0.00 4.61
307 308 4.474651 TGTATTGAGGTTGATCATCCCACT 59.525 41.667 17.57 12.10 0.00 4.00
308 309 4.598036 ATTGAGGTTGATCATCCCACTT 57.402 40.909 17.57 0.00 0.00 3.16
309 310 3.634397 TGAGGTTGATCATCCCACTTC 57.366 47.619 17.57 9.33 0.00 3.01
310 311 2.093500 TGAGGTTGATCATCCCACTTCG 60.093 50.000 17.57 0.00 0.00 3.79
312 313 1.407437 GGTTGATCATCCCACTTCGCT 60.407 52.381 11.25 0.00 0.00 4.93
314 315 0.462581 TGATCATCCCACTTCGCTGC 60.463 55.000 0.00 0.00 0.00 5.25
315 316 0.179062 GATCATCCCACTTCGCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
316 317 0.254178 ATCATCCCACTTCGCTGCTT 59.746 50.000 0.00 0.00 0.00 3.91
318 319 2.042831 ATCCCACTTCGCTGCTTGC 61.043 57.895 0.00 0.00 38.57 4.01
319 320 2.475371 ATCCCACTTCGCTGCTTGCT 62.475 55.000 0.00 0.00 40.11 3.91
321 322 1.670406 CCACTTCGCTGCTTGCTCT 60.670 57.895 0.00 0.00 40.11 4.09
322 323 1.496393 CACTTCGCTGCTTGCTCTG 59.504 57.895 0.00 0.00 40.11 3.35
324 325 2.281002 TTCGCTGCTTGCTCTGCA 60.281 55.556 0.00 0.00 40.11 4.41
325 326 2.510190 CTTCGCTGCTTGCTCTGCAC 62.510 60.000 0.00 0.00 38.71 4.57
327 328 2.868920 GCTGCTTGCTCTGCACTC 59.131 61.111 0.00 0.00 38.71 3.51
328 329 1.671704 GCTGCTTGCTCTGCACTCT 60.672 57.895 0.00 0.00 38.71 3.24
329 330 1.637478 GCTGCTTGCTCTGCACTCTC 61.637 60.000 0.00 0.00 38.71 3.20
330 331 0.037139 CTGCTTGCTCTGCACTCTCT 60.037 55.000 0.00 0.00 38.71 3.10
331 332 0.037512 TGCTTGCTCTGCACTCTCTC 60.038 55.000 0.00 0.00 38.71 3.20
332 333 0.037512 GCTTGCTCTGCACTCTCTCA 60.038 55.000 0.00 0.00 38.71 3.27
334 335 1.545136 CTTGCTCTGCACTCTCTCAGA 59.455 52.381 0.00 0.00 38.71 3.27
336 337 0.179166 GCTCTGCACTCTCTCAGACG 60.179 60.000 0.00 0.00 35.66 4.18
337 338 0.179166 CTCTGCACTCTCTCAGACGC 60.179 60.000 0.00 0.00 35.66 5.19
338 339 1.153862 CTGCACTCTCTCAGACGCC 60.154 63.158 0.00 0.00 32.26 5.68
339 340 1.871126 CTGCACTCTCTCAGACGCCA 61.871 60.000 0.00 0.00 32.26 5.69
340 341 1.253593 TGCACTCTCTCAGACGCCAT 61.254 55.000 0.00 0.00 0.00 4.40
341 342 0.108424 GCACTCTCTCAGACGCCATT 60.108 55.000 0.00 0.00 0.00 3.16
342 343 1.638133 CACTCTCTCAGACGCCATTG 58.362 55.000 0.00 0.00 0.00 2.82
343 344 1.067283 CACTCTCTCAGACGCCATTGT 60.067 52.381 0.00 0.00 0.00 2.71
344 345 1.067283 ACTCTCTCAGACGCCATTGTG 60.067 52.381 0.00 0.00 0.00 3.33
345 346 0.969149 TCTCTCAGACGCCATTGTGT 59.031 50.000 0.00 0.00 38.09 3.72
347 348 0.392706 TCTCAGACGCCATTGTGTGT 59.607 50.000 0.00 0.00 34.74 3.72
348 349 1.616374 TCTCAGACGCCATTGTGTGTA 59.384 47.619 0.00 0.00 34.74 2.90
349 350 1.726791 CTCAGACGCCATTGTGTGTAC 59.273 52.381 0.00 0.00 34.74 2.90
350 351 0.438445 CAGACGCCATTGTGTGTACG 59.562 55.000 0.00 0.00 34.74 3.67
352 353 2.235536 GACGCCATTGTGTGTACGCC 62.236 60.000 3.51 0.00 34.74 5.68
353 354 2.032634 CGCCATTGTGTGTACGCCT 61.033 57.895 3.51 0.00 0.00 5.52
355 356 1.234615 GCCATTGTGTGTACGCCTGT 61.235 55.000 3.51 0.00 0.00 4.00
356 357 0.516877 CCATTGTGTGTACGCCTGTG 59.483 55.000 3.51 0.00 0.00 3.66
357 358 1.507562 CATTGTGTGTACGCCTGTGA 58.492 50.000 3.51 0.00 0.00 3.58
359 360 0.747852 TTGTGTGTACGCCTGTGAGA 59.252 50.000 3.51 0.00 0.00 3.27
360 361 0.313987 TGTGTGTACGCCTGTGAGAG 59.686 55.000 3.51 0.00 0.00 3.20
361 362 1.009389 GTGTGTACGCCTGTGAGAGC 61.009 60.000 3.51 0.00 0.00 4.09
362 363 1.179174 TGTGTACGCCTGTGAGAGCT 61.179 55.000 3.51 0.00 0.00 4.09
363 364 0.734253 GTGTACGCCTGTGAGAGCTG 60.734 60.000 0.00 0.00 0.00 4.24
364 365 1.807573 GTACGCCTGTGAGAGCTGC 60.808 63.158 0.00 0.00 0.00 5.25
365 366 2.275380 TACGCCTGTGAGAGCTGCA 61.275 57.895 1.02 0.00 0.00 4.41
366 367 2.492449 TACGCCTGTGAGAGCTGCAC 62.492 60.000 1.02 8.91 36.81 4.57
367 368 2.745492 GCCTGTGAGAGCTGCACC 60.745 66.667 12.36 0.00 35.43 5.01
369 370 2.591072 CCTGTGAGAGCTGCACCCT 61.591 63.158 12.36 0.00 35.43 4.34
370 371 1.374190 CTGTGAGAGCTGCACCCTT 59.626 57.895 12.36 0.00 35.43 3.95
371 372 0.610174 CTGTGAGAGCTGCACCCTTA 59.390 55.000 12.36 0.00 35.43 2.69
372 373 0.321671 TGTGAGAGCTGCACCCTTAC 59.678 55.000 12.36 3.78 35.43 2.34
373 374 0.610687 GTGAGAGCTGCACCCTTACT 59.389 55.000 1.02 0.00 0.00 2.24
374 375 0.898320 TGAGAGCTGCACCCTTACTC 59.102 55.000 1.02 0.00 0.00 2.59
375 376 1.190643 GAGAGCTGCACCCTTACTCT 58.809 55.000 1.02 0.00 40.33 3.24
376 377 1.552792 GAGAGCTGCACCCTTACTCTT 59.447 52.381 1.02 0.00 37.82 2.85
377 378 1.981495 AGAGCTGCACCCTTACTCTTT 59.019 47.619 1.02 0.00 34.06 2.52
378 379 2.373502 AGAGCTGCACCCTTACTCTTTT 59.626 45.455 1.02 0.00 34.06 2.27
379 380 3.149981 GAGCTGCACCCTTACTCTTTTT 58.850 45.455 1.02 0.00 0.00 1.94
408 409 4.393062 CCACCTATCAATGGAATGATACGC 59.607 45.833 0.00 0.00 40.44 4.42
409 410 5.240891 CACCTATCAATGGAATGATACGCT 58.759 41.667 0.00 0.00 40.44 5.07
410 411 5.121298 CACCTATCAATGGAATGATACGCTG 59.879 44.000 0.00 0.00 40.44 5.18
412 413 3.198409 TCAATGGAATGATACGCTGCT 57.802 42.857 0.00 0.00 0.00 4.24
413 414 3.133691 TCAATGGAATGATACGCTGCTC 58.866 45.455 0.00 0.00 0.00 4.26
414 415 2.874086 CAATGGAATGATACGCTGCTCA 59.126 45.455 0.00 0.00 0.00 4.26
416 417 1.482182 TGGAATGATACGCTGCTCAGT 59.518 47.619 0.00 0.00 0.00 3.41
417 418 1.863454 GGAATGATACGCTGCTCAGTG 59.137 52.381 8.73 8.73 44.11 3.66
486 487 3.935828 GCTGAAGTCAAGTCCCTTATGAC 59.064 47.826 0.00 0.00 42.91 3.06
491 492 5.776173 AGTCAAGTCCCTTATGACGATAG 57.224 43.478 0.00 0.00 46.19 2.08
497 498 5.938279 AGTCCCTTATGACGATAGAGTGTA 58.062 41.667 0.00 0.00 40.26 2.90
504 505 8.957466 CCTTATGACGATAGAGTGTATATTCCA 58.043 37.037 0.00 0.00 41.38 3.53
507 508 7.761038 TGACGATAGAGTGTATATTCCACAT 57.239 36.000 7.66 0.40 41.38 3.21
511 512 9.298250 ACGATAGAGTGTATATTCCACATAACT 57.702 33.333 7.66 0.00 41.38 2.24
535 536 7.651304 ACTTTCATAGATCTCAGAATAGCGTTG 59.349 37.037 0.00 0.00 0.00 4.10
542 543 5.262588 TCTCAGAATAGCGTTGCAGATTA 57.737 39.130 0.00 0.00 0.00 1.75
559 560 5.615289 CAGATTAGCTGGCAAGGTATAGTT 58.385 41.667 0.00 0.00 41.07 2.24
602 604 4.424711 GCTTGGCGGATGACCCCA 62.425 66.667 0.00 0.00 35.67 4.96
608 610 0.110486 GGCGGATGACCCCATGTATT 59.890 55.000 0.00 0.00 32.09 1.89
614 616 3.331889 GGATGACCCCATGTATTGAGGAT 59.668 47.826 0.00 0.00 32.09 3.24
633 635 5.141182 AGGATCTCTTGCCGAAAGATAGTA 58.859 41.667 0.00 0.00 44.02 1.82
637 639 5.408356 TCTCTTGCCGAAAGATAGTAACAC 58.592 41.667 1.62 0.00 44.02 3.32
638 640 5.185249 TCTCTTGCCGAAAGATAGTAACACT 59.815 40.000 1.62 0.00 44.02 3.55
639 641 6.376299 TCTCTTGCCGAAAGATAGTAACACTA 59.624 38.462 1.62 0.00 44.02 2.74
640 642 7.068348 TCTCTTGCCGAAAGATAGTAACACTAT 59.932 37.037 0.00 0.00 44.02 2.12
762 765 1.337354 TGAACGAATTAGCCTGCGACA 60.337 47.619 0.00 0.00 0.00 4.35
785 788 3.314080 ACATGACGAAATGGAAAACGTGT 59.686 39.130 0.00 0.00 39.04 4.49
911 914 4.673441 ACTCATAATGCTAGTGTGACGAC 58.327 43.478 0.00 0.00 0.00 4.34
966 969 0.538287 AACAGCAAAGCCTCCACCTC 60.538 55.000 0.00 0.00 0.00 3.85
980 983 0.323908 CACCTCTCTCTTCCTCCGGT 60.324 60.000 0.00 0.00 0.00 5.28
1048 1059 2.099098 GCCCCACTATCGAAACCATTTG 59.901 50.000 0.00 0.00 0.00 2.32
1051 1062 4.006989 CCCACTATCGAAACCATTTGTCA 58.993 43.478 0.00 0.00 0.00 3.58
1052 1063 4.457603 CCCACTATCGAAACCATTTGTCAA 59.542 41.667 0.00 0.00 0.00 3.18
1086 1102 8.579006 TCTGATTTAACTCTGCATTTGTTCATT 58.421 29.630 0.00 0.00 0.00 2.57
1207 1225 1.452145 TTGCAGAAACCAAGGACCGC 61.452 55.000 0.00 0.00 0.00 5.68
1210 1228 1.597027 AGAAACCAAGGACCGCGTG 60.597 57.895 4.92 0.00 0.00 5.34
1218 1236 2.413634 CCAAGGACCGCGTGTTTATTTC 60.414 50.000 4.92 0.00 0.00 2.17
1229 1247 4.215965 CGTGTTTATTTCCAAGTTCGTGG 58.784 43.478 0.00 0.00 40.33 4.94
1361 1379 3.284449 GCCAAGTTCACGGCGGTT 61.284 61.111 13.24 0.00 38.82 4.44
1612 1639 3.635331 CGAACTTCCGTGTTCACTTCTA 58.365 45.455 11.71 0.00 44.59 2.10
1717 1745 4.832823 GGAATTTCCCTTGGTTTCTCAAGA 59.167 41.667 3.89 0.00 44.98 3.02
1719 1747 2.568623 TCCCTTGGTTTCTCAAGAGC 57.431 50.000 6.21 0.00 44.98 4.09
1722 1750 1.543429 CCTTGGTTTCTCAAGAGCGGT 60.543 52.381 6.21 0.00 44.98 5.68
1723 1751 1.532868 CTTGGTTTCTCAAGAGCGGTG 59.467 52.381 0.00 0.00 44.98 4.94
1724 1752 0.756294 TGGTTTCTCAAGAGCGGTGA 59.244 50.000 0.00 0.00 0.00 4.02
1733 1761 6.465439 TCTCAAGAGCGGTGAGAATAATTA 57.535 37.500 12.75 0.00 46.57 1.40
1734 1762 6.873997 TCTCAAGAGCGGTGAGAATAATTAA 58.126 36.000 12.75 0.00 46.57 1.40
1737 1765 6.757010 TCAAGAGCGGTGAGAATAATTAAGTC 59.243 38.462 0.00 0.00 0.00 3.01
1739 1767 4.369182 AGCGGTGAGAATAATTAAGTCCG 58.631 43.478 0.00 0.00 38.67 4.79
1740 1768 4.710528 CGGTGAGAATAATTAAGTCCGC 57.289 45.455 0.00 0.00 0.00 5.54
1741 1769 4.369182 CGGTGAGAATAATTAAGTCCGCT 58.631 43.478 0.00 0.00 0.00 5.52
1743 2037 5.602628 GGTGAGAATAATTAAGTCCGCTCT 58.397 41.667 0.00 0.00 0.00 4.09
1760 2054 5.540337 TCCGCTCTAATTATTCTCATGTCCT 59.460 40.000 0.00 0.00 0.00 3.85
1761 2055 5.866633 CCGCTCTAATTATTCTCATGTCCTC 59.133 44.000 0.00 0.00 0.00 3.71
1764 2058 7.309133 CGCTCTAATTATTCTCATGTCCTCTCT 60.309 40.741 0.00 0.00 0.00 3.10
1800 2533 5.509840 GCTGTCATCGACCCACTCTAATTAT 60.510 44.000 0.00 0.00 0.00 1.28
1820 2553 1.956869 TCTCATGCCCTCTCCAAGAA 58.043 50.000 0.00 0.00 0.00 2.52
1821 2554 1.556911 TCTCATGCCCTCTCCAAGAAC 59.443 52.381 0.00 0.00 0.00 3.01
1822 2555 1.558756 CTCATGCCCTCTCCAAGAACT 59.441 52.381 0.00 0.00 0.00 3.01
1823 2556 1.988107 TCATGCCCTCTCCAAGAACTT 59.012 47.619 0.00 0.00 0.00 2.66
2034 2848 5.934402 ATTTAAGAAAGGCGAGTCTCCTA 57.066 39.130 1.10 0.00 32.65 2.94
2124 2938 9.155975 TCAGATAATAAGCTGAGAAAAACAGAC 57.844 33.333 0.00 0.00 43.05 3.51
2236 4232 7.694388 TTACATAGCAATGTCGTGTAATCTC 57.306 36.000 0.00 0.00 42.92 2.75
2239 4235 4.142609 AGCAATGTCGTGTAATCTCCAT 57.857 40.909 0.00 0.00 0.00 3.41
2279 4275 7.475840 AGAATCCGCAGAAACAATCTAAATTC 58.524 34.615 0.00 0.00 36.32 2.17
2283 4345 7.919690 TCCGCAGAAACAATCTAAATTCTATG 58.080 34.615 0.00 0.00 36.32 2.23
2463 4540 2.183046 GCTGAGGGAGCGTCAGTC 59.817 66.667 0.00 0.00 44.88 3.51
2464 4541 2.487428 CTGAGGGAGCGTCAGTCG 59.513 66.667 0.00 0.00 40.25 4.18
2465 4542 3.057547 CTGAGGGAGCGTCAGTCGG 62.058 68.421 0.00 0.00 40.25 4.79
2466 4543 4.500116 GAGGGAGCGTCAGTCGGC 62.500 72.222 0.00 0.00 40.26 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.634883 GTCTAACTAGTCGACACCATGAGA 59.365 45.833 19.50 9.85 0.00 3.27
1 2 4.201930 GGTCTAACTAGTCGACACCATGAG 60.202 50.000 19.50 7.62 0.00 2.90
2 3 3.693085 GGTCTAACTAGTCGACACCATGA 59.307 47.826 19.50 5.75 0.00 3.07
3 4 3.442625 TGGTCTAACTAGTCGACACCATG 59.557 47.826 19.50 5.13 0.00 3.66
5 6 2.816087 GTGGTCTAACTAGTCGACACCA 59.184 50.000 19.50 17.15 0.00 4.17
6 7 2.163211 GGTGGTCTAACTAGTCGACACC 59.837 54.545 19.50 14.66 0.00 4.16
8 9 2.224843 TGGGTGGTCTAACTAGTCGACA 60.225 50.000 19.50 2.84 0.00 4.35
9 10 2.440409 TGGGTGGTCTAACTAGTCGAC 58.560 52.381 7.70 7.70 0.00 4.20
10 11 2.885135 TGGGTGGTCTAACTAGTCGA 57.115 50.000 0.00 0.00 0.00 4.20
11 12 2.481449 GCATGGGTGGTCTAACTAGTCG 60.481 54.545 0.00 0.00 0.00 4.18
12 13 2.766828 AGCATGGGTGGTCTAACTAGTC 59.233 50.000 0.00 0.00 0.00 2.59
14 15 3.185246 CAGCATGGGTGGTCTAACTAG 57.815 52.381 0.00 0.00 32.81 2.57
28 29 2.887568 GCGGTCGAGTCCAGCATG 60.888 66.667 0.00 0.00 0.00 4.06
31 32 3.991536 GAAGGCGGTCGAGTCCAGC 62.992 68.421 0.00 0.00 0.00 4.85
32 33 1.878656 AAGAAGGCGGTCGAGTCCAG 61.879 60.000 0.00 0.00 0.00 3.86
34 35 1.153804 GAAGAAGGCGGTCGAGTCC 60.154 63.158 0.00 0.00 0.00 3.85
35 36 1.514443 CGAAGAAGGCGGTCGAGTC 60.514 63.158 0.00 0.00 36.92 3.36
36 37 1.970114 TCGAAGAAGGCGGTCGAGT 60.970 57.895 0.00 0.00 38.78 4.18
37 38 1.514443 GTCGAAGAAGGCGGTCGAG 60.514 63.158 5.37 0.00 43.85 4.04
40 41 1.446272 CCAGTCGAAGAAGGCGGTC 60.446 63.158 0.00 0.00 39.69 4.79
41 42 2.207924 ACCAGTCGAAGAAGGCGGT 61.208 57.895 0.00 0.00 39.69 5.68
42 43 1.738099 CACCAGTCGAAGAAGGCGG 60.738 63.158 0.00 0.00 39.69 6.13
43 44 1.738099 CCACCAGTCGAAGAAGGCG 60.738 63.158 0.00 0.00 39.69 5.52
45 46 0.390472 GAGCCACCAGTCGAAGAAGG 60.390 60.000 0.00 0.00 39.69 3.46
46 47 0.390472 GGAGCCACCAGTCGAAGAAG 60.390 60.000 0.00 0.00 37.04 2.85
48 49 1.533033 TGGAGCCACCAGTCGAAGA 60.533 57.895 0.00 0.00 44.64 2.87
62 63 0.392193 GATGACACTGTGGCCTGGAG 60.392 60.000 11.84 0.00 0.00 3.86
63 64 1.679311 GATGACACTGTGGCCTGGA 59.321 57.895 11.84 0.00 0.00 3.86
64 65 1.377725 GGATGACACTGTGGCCTGG 60.378 63.158 11.84 0.00 0.00 4.45
65 66 0.392193 GAGGATGACACTGTGGCCTG 60.392 60.000 11.84 0.00 0.00 4.85
67 68 1.448540 CGAGGATGACACTGTGGCC 60.449 63.158 11.84 7.12 0.00 5.36
68 69 1.448540 CCGAGGATGACACTGTGGC 60.449 63.158 13.09 10.15 0.00 5.01
69 70 0.108615 GTCCGAGGATGACACTGTGG 60.109 60.000 13.09 0.00 32.91 4.17
70 71 0.603065 TGTCCGAGGATGACACTGTG 59.397 55.000 6.19 6.19 37.80 3.66
71 72 0.891373 CTGTCCGAGGATGACACTGT 59.109 55.000 0.00 0.00 37.80 3.55
73 74 1.608717 GGCTGTCCGAGGATGACACT 61.609 60.000 0.00 0.00 37.80 3.55
74 75 1.153549 GGCTGTCCGAGGATGACAC 60.154 63.158 0.00 0.00 37.80 3.67
75 76 0.904865 AAGGCTGTCCGAGGATGACA 60.905 55.000 0.00 0.00 40.28 3.58
76 77 1.067821 CTAAGGCTGTCCGAGGATGAC 59.932 57.143 0.00 0.00 37.47 3.06
77 78 1.403814 CTAAGGCTGTCCGAGGATGA 58.596 55.000 0.00 0.00 37.47 2.92
78 79 0.390860 CCTAAGGCTGTCCGAGGATG 59.609 60.000 0.00 0.00 40.72 3.51
79 80 1.403687 GCCTAAGGCTGTCCGAGGAT 61.404 60.000 0.00 0.00 46.69 3.24
81 82 2.501610 GCCTAAGGCTGTCCGAGG 59.498 66.667 0.00 0.00 46.69 4.63
98 99 1.869767 GATGATGCAGTTTAGGCCTCG 59.130 52.381 9.68 0.00 0.00 4.63
101 102 0.308993 GCGATGATGCAGTTTAGGCC 59.691 55.000 0.00 0.00 34.15 5.19
102 103 1.262683 GAGCGATGATGCAGTTTAGGC 59.737 52.381 0.00 0.00 37.31 3.93
103 104 2.799412 GAGAGCGATGATGCAGTTTAGG 59.201 50.000 0.00 0.00 37.31 2.69
104 105 3.244814 GTGAGAGCGATGATGCAGTTTAG 59.755 47.826 0.00 0.00 37.31 1.85
105 106 3.190079 GTGAGAGCGATGATGCAGTTTA 58.810 45.455 0.00 0.00 37.31 2.01
120 121 0.809241 GATCGCCCAAGCTGTGAGAG 60.809 60.000 0.00 0.00 36.60 3.20
121 122 1.219124 GATCGCCCAAGCTGTGAGA 59.781 57.895 0.00 0.00 36.60 3.27
122 123 1.088340 CAGATCGCCCAAGCTGTGAG 61.088 60.000 0.00 0.00 36.60 3.51
123 124 1.078918 CAGATCGCCCAAGCTGTGA 60.079 57.895 0.00 0.00 36.60 3.58
126 127 1.078214 TTCCAGATCGCCCAAGCTG 60.078 57.895 0.00 0.00 36.60 4.24
127 128 1.222936 CTTCCAGATCGCCCAAGCT 59.777 57.895 0.00 0.00 36.60 3.74
128 129 2.476320 GCTTCCAGATCGCCCAAGC 61.476 63.158 6.13 6.13 33.21 4.01
129 130 1.078214 TGCTTCCAGATCGCCCAAG 60.078 57.895 0.00 0.00 0.00 3.61
130 131 1.377202 GTGCTTCCAGATCGCCCAA 60.377 57.895 0.00 0.00 0.00 4.12
131 132 2.268920 GTGCTTCCAGATCGCCCA 59.731 61.111 0.00 0.00 0.00 5.36
133 134 2.852495 TTCGGTGCTTCCAGATCGCC 62.852 60.000 0.00 0.00 35.57 5.54
134 135 1.019278 TTTCGGTGCTTCCAGATCGC 61.019 55.000 0.00 0.00 35.57 4.58
135 136 1.328680 CATTTCGGTGCTTCCAGATCG 59.671 52.381 0.00 0.00 35.57 3.69
136 137 1.064654 GCATTTCGGTGCTTCCAGATC 59.935 52.381 1.90 0.00 41.82 2.75
139 140 1.135315 CGCATTTCGGTGCTTCCAG 59.865 57.895 6.75 0.00 42.88 3.86
140 141 3.262936 CGCATTTCGGTGCTTCCA 58.737 55.556 6.75 0.00 42.88 3.53
149 150 0.039617 TCAAAAGTGGCCGCATTTCG 60.040 50.000 20.59 13.34 38.08 3.46
150 151 1.418373 GTCAAAAGTGGCCGCATTTC 58.582 50.000 20.59 4.51 0.00 2.17
152 153 1.285641 CGTCAAAAGTGGCCGCATT 59.714 52.632 20.59 10.56 0.00 3.56
153 154 2.625823 CCGTCAAAAGTGGCCGCAT 61.626 57.895 20.59 2.72 0.00 4.73
155 156 4.700365 GCCGTCAAAAGTGGCCGC 62.700 66.667 8.71 8.71 43.06 6.53
156 157 4.383602 CGCCGTCAAAAGTGGCCG 62.384 66.667 0.00 0.00 46.12 6.13
157 158 4.700365 GCGCCGTCAAAAGTGGCC 62.700 66.667 0.00 0.00 46.12 5.36
158 159 4.700365 GGCGCCGTCAAAAGTGGC 62.700 66.667 12.58 0.00 45.39 5.01
159 160 4.038080 GGGCGCCGTCAAAAGTGG 62.038 66.667 22.54 0.00 0.00 4.00
160 161 4.383602 CGGGCGCCGTCAAAAGTG 62.384 66.667 22.54 0.00 42.73 3.16
173 174 4.754667 GTCCGTGGAAGGTCGGGC 62.755 72.222 3.85 0.00 45.79 6.13
174 175 2.781595 CTTGTCCGTGGAAGGTCGGG 62.782 65.000 3.85 0.00 45.79 5.14
175 176 1.374252 CTTGTCCGTGGAAGGTCGG 60.374 63.158 0.00 0.00 46.93 4.79
177 178 0.670854 GAGCTTGTCCGTGGAAGGTC 60.671 60.000 4.54 4.54 38.96 3.85
178 179 1.371558 GAGCTTGTCCGTGGAAGGT 59.628 57.895 0.00 0.00 32.68 3.50
180 181 1.006102 ACGAGCTTGTCCGTGGAAG 60.006 57.895 0.00 0.00 37.64 3.46
181 182 3.134879 ACGAGCTTGTCCGTGGAA 58.865 55.556 0.00 0.00 37.64 3.53
185 186 2.356313 CTGCACGAGCTTGTCCGT 60.356 61.111 2.72 0.00 42.74 4.69
195 196 1.432514 GTTCTTGATCAGCTGCACGA 58.567 50.000 9.47 2.46 0.00 4.35
196 197 0.094216 CGTTCTTGATCAGCTGCACG 59.906 55.000 9.47 0.00 0.00 5.34
197 198 1.392853 CTCGTTCTTGATCAGCTGCAC 59.607 52.381 9.47 5.92 0.00 4.57
198 199 1.673923 CCTCGTTCTTGATCAGCTGCA 60.674 52.381 9.47 0.00 0.00 4.41
199 200 1.005340 CCTCGTTCTTGATCAGCTGC 58.995 55.000 9.47 0.00 0.00 5.25
200 201 1.005340 GCCTCGTTCTTGATCAGCTG 58.995 55.000 7.63 7.63 0.00 4.24
201 202 0.459237 CGCCTCGTTCTTGATCAGCT 60.459 55.000 0.00 0.00 0.00 4.24
204 205 1.805539 CGCGCCTCGTTCTTGATCA 60.806 57.895 0.00 0.00 0.00 2.92
206 207 3.188786 GCGCGCCTCGTTCTTGAT 61.189 61.111 23.24 0.00 41.07 2.57
231 232 2.029666 CTCTATCGCCGGCCTTGG 59.970 66.667 23.46 10.76 0.00 3.61
232 233 2.029666 CCTCTATCGCCGGCCTTG 59.970 66.667 23.46 7.26 0.00 3.61
233 234 2.123425 TCCTCTATCGCCGGCCTT 60.123 61.111 23.46 11.31 0.00 4.35
236 237 0.605860 TCTAGTCCTCTATCGCCGGC 60.606 60.000 19.07 19.07 0.00 6.13
237 238 2.116827 ATCTAGTCCTCTATCGCCGG 57.883 55.000 0.00 0.00 0.00 6.13
239 240 9.738832 GATAATTTTATCTAGTCCTCTATCGCC 57.261 37.037 3.56 0.00 37.23 5.54
240 241 9.738832 GGATAATTTTATCTAGTCCTCTATCGC 57.261 37.037 9.53 0.00 39.53 4.58
248 249 9.722184 GGTTACAGGGATAATTTTATCTAGTCC 57.278 37.037 9.53 3.69 39.53 3.85
253 254 8.218488 GGTCAGGTTACAGGGATAATTTTATCT 58.782 37.037 9.53 0.00 39.53 1.98
254 255 7.996644 TGGTCAGGTTACAGGGATAATTTTATC 59.003 37.037 2.32 2.32 39.01 1.75
255 256 7.878495 TGGTCAGGTTACAGGGATAATTTTAT 58.122 34.615 0.00 0.00 0.00 1.40
256 257 7.273457 TGGTCAGGTTACAGGGATAATTTTA 57.727 36.000 0.00 0.00 0.00 1.52
257 258 6.147437 TGGTCAGGTTACAGGGATAATTTT 57.853 37.500 0.00 0.00 0.00 1.82
258 259 5.789574 TGGTCAGGTTACAGGGATAATTT 57.210 39.130 0.00 0.00 0.00 1.82
259 260 5.193728 ACATGGTCAGGTTACAGGGATAATT 59.806 40.000 0.00 0.00 0.00 1.40
260 261 4.726825 ACATGGTCAGGTTACAGGGATAAT 59.273 41.667 0.00 0.00 0.00 1.28
261 262 4.108570 ACATGGTCAGGTTACAGGGATAA 58.891 43.478 0.00 0.00 0.00 1.75
262 263 3.731431 ACATGGTCAGGTTACAGGGATA 58.269 45.455 0.00 0.00 0.00 2.59
263 264 2.562296 ACATGGTCAGGTTACAGGGAT 58.438 47.619 0.00 0.00 0.00 3.85
264 265 2.038863 ACATGGTCAGGTTACAGGGA 57.961 50.000 0.00 0.00 0.00 4.20
265 266 2.224769 ACAACATGGTCAGGTTACAGGG 60.225 50.000 0.00 0.00 33.15 4.45
266 267 3.140325 ACAACATGGTCAGGTTACAGG 57.860 47.619 0.00 0.00 33.15 4.00
267 268 5.937540 TCAATACAACATGGTCAGGTTACAG 59.062 40.000 0.00 0.00 33.15 2.74
268 269 5.870706 TCAATACAACATGGTCAGGTTACA 58.129 37.500 0.00 0.00 33.15 2.41
270 271 5.013704 ACCTCAATACAACATGGTCAGGTTA 59.986 40.000 0.00 0.00 33.15 2.85
271 272 4.202567 ACCTCAATACAACATGGTCAGGTT 60.203 41.667 0.00 0.00 35.51 3.50
272 273 3.330701 ACCTCAATACAACATGGTCAGGT 59.669 43.478 0.00 0.00 0.00 4.00
274 275 5.003160 TCAACCTCAATACAACATGGTCAG 58.997 41.667 0.00 0.00 0.00 3.51
275 276 4.979335 TCAACCTCAATACAACATGGTCA 58.021 39.130 0.00 0.00 0.00 4.02
277 278 5.569355 TGATCAACCTCAATACAACATGGT 58.431 37.500 0.00 0.00 0.00 3.55
278 279 6.238842 GGATGATCAACCTCAATACAACATGG 60.239 42.308 14.49 0.00 0.00 3.66
279 280 6.238842 GGGATGATCAACCTCAATACAACATG 60.239 42.308 20.25 0.00 0.00 3.21
281 282 5.192927 GGGATGATCAACCTCAATACAACA 58.807 41.667 20.25 0.00 0.00 3.33
282 283 5.066505 GTGGGATGATCAACCTCAATACAAC 59.933 44.000 20.25 4.85 0.00 3.32
283 284 5.044919 AGTGGGATGATCAACCTCAATACAA 60.045 40.000 20.25 0.00 0.00 2.41
284 285 4.474651 AGTGGGATGATCAACCTCAATACA 59.525 41.667 20.25 7.07 0.00 2.29
286 287 5.684704 GAAGTGGGATGATCAACCTCAATA 58.315 41.667 20.25 1.61 0.00 1.90
288 289 3.619733 CGAAGTGGGATGATCAACCTCAA 60.620 47.826 20.25 5.41 0.00 3.02
289 290 2.093500 CGAAGTGGGATGATCAACCTCA 60.093 50.000 20.25 13.87 0.00 3.86
291 292 1.407437 GCGAAGTGGGATGATCAACCT 60.407 52.381 20.25 1.64 0.00 3.50
293 294 1.667724 CAGCGAAGTGGGATGATCAAC 59.332 52.381 0.00 0.00 0.00 3.18
294 295 2.013563 GCAGCGAAGTGGGATGATCAA 61.014 52.381 0.00 0.00 0.00 2.57
295 296 0.462581 GCAGCGAAGTGGGATGATCA 60.463 55.000 0.00 0.00 0.00 2.92
296 297 0.179062 AGCAGCGAAGTGGGATGATC 60.179 55.000 0.00 0.00 0.00 2.92
297 298 0.254178 AAGCAGCGAAGTGGGATGAT 59.746 50.000 0.00 0.00 0.00 2.45
298 299 0.674581 CAAGCAGCGAAGTGGGATGA 60.675 55.000 0.00 0.00 0.00 2.92
301 302 2.669569 GCAAGCAGCGAAGTGGGA 60.670 61.111 0.00 0.00 0.00 4.37
310 311 1.637478 GAGAGTGCAGAGCAAGCAGC 61.637 60.000 0.00 0.00 43.63 5.25
312 313 0.037512 GAGAGAGTGCAGAGCAAGCA 60.038 55.000 0.00 0.00 41.47 3.91
314 315 1.545136 TCTGAGAGAGTGCAGAGCAAG 59.455 52.381 0.00 0.00 41.47 4.01
315 316 1.271934 GTCTGAGAGAGTGCAGAGCAA 59.728 52.381 0.00 0.00 41.47 3.91
316 317 0.887247 GTCTGAGAGAGTGCAGAGCA 59.113 55.000 0.00 0.00 41.42 4.26
318 319 0.179166 GCGTCTGAGAGAGTGCAGAG 60.179 60.000 0.00 0.00 41.42 3.35
319 320 1.590610 GGCGTCTGAGAGAGTGCAGA 61.591 60.000 0.00 0.00 38.72 4.26
321 322 1.253593 ATGGCGTCTGAGAGAGTGCA 61.254 55.000 0.00 0.00 30.73 4.57
322 323 0.108424 AATGGCGTCTGAGAGAGTGC 60.108 55.000 0.00 0.00 0.00 4.40
324 325 1.067283 CACAATGGCGTCTGAGAGAGT 60.067 52.381 0.00 0.00 0.00 3.24
325 326 1.067283 ACACAATGGCGTCTGAGAGAG 60.067 52.381 0.00 0.00 0.00 3.20
327 328 1.073964 CACACAATGGCGTCTGAGAG 58.926 55.000 0.00 0.00 0.00 3.20
328 329 0.392706 ACACACAATGGCGTCTGAGA 59.607 50.000 0.00 0.00 0.00 3.27
329 330 1.726791 GTACACACAATGGCGTCTGAG 59.273 52.381 0.00 0.00 0.00 3.35
330 331 1.790755 GTACACACAATGGCGTCTGA 58.209 50.000 0.00 0.00 0.00 3.27
331 332 0.438445 CGTACACACAATGGCGTCTG 59.562 55.000 0.00 0.00 0.00 3.51
332 333 1.289109 GCGTACACACAATGGCGTCT 61.289 55.000 0.00 0.00 34.57 4.18
334 335 2.322081 GGCGTACACACAATGGCGT 61.322 57.895 0.00 0.00 34.57 5.68
336 337 1.234615 ACAGGCGTACACACAATGGC 61.235 55.000 0.00 0.00 0.00 4.40
337 338 0.516877 CACAGGCGTACACACAATGG 59.483 55.000 0.00 0.00 0.00 3.16
338 339 1.460743 CTCACAGGCGTACACACAATG 59.539 52.381 0.00 0.00 0.00 2.82
339 340 1.343142 TCTCACAGGCGTACACACAAT 59.657 47.619 0.00 0.00 0.00 2.71
340 341 0.747852 TCTCACAGGCGTACACACAA 59.252 50.000 0.00 0.00 0.00 3.33
341 342 0.313987 CTCTCACAGGCGTACACACA 59.686 55.000 0.00 0.00 0.00 3.72
342 343 1.009389 GCTCTCACAGGCGTACACAC 61.009 60.000 0.00 0.00 0.00 3.82
343 344 1.179174 AGCTCTCACAGGCGTACACA 61.179 55.000 0.00 0.00 0.00 3.72
344 345 0.734253 CAGCTCTCACAGGCGTACAC 60.734 60.000 0.00 0.00 0.00 2.90
345 346 1.586541 CAGCTCTCACAGGCGTACA 59.413 57.895 0.00 0.00 0.00 2.90
347 348 2.275380 TGCAGCTCTCACAGGCGTA 61.275 57.895 0.00 0.00 0.00 4.42
348 349 3.619767 TGCAGCTCTCACAGGCGT 61.620 61.111 0.00 0.00 0.00 5.68
349 350 3.117171 GTGCAGCTCTCACAGGCG 61.117 66.667 9.99 0.00 34.73 5.52
350 351 2.745492 GGTGCAGCTCTCACAGGC 60.745 66.667 9.07 0.95 36.22 4.85
352 353 0.610174 TAAGGGTGCAGCTCTCACAG 59.390 55.000 16.65 0.00 36.22 3.66
353 354 0.321671 GTAAGGGTGCAGCTCTCACA 59.678 55.000 16.65 0.00 36.22 3.58
355 356 0.898320 GAGTAAGGGTGCAGCTCTCA 59.102 55.000 16.65 0.00 0.00 3.27
356 357 1.190643 AGAGTAAGGGTGCAGCTCTC 58.809 55.000 16.65 16.55 31.65 3.20
357 358 1.650528 AAGAGTAAGGGTGCAGCTCT 58.349 50.000 16.65 7.33 38.06 4.09
359 360 2.959465 AAAAGAGTAAGGGTGCAGCT 57.041 45.000 16.65 0.00 0.00 4.24
384 385 5.793817 CGTATCATTCCATTGATAGGTGGA 58.206 41.667 6.17 0.00 42.55 4.02
385 386 4.393062 GCGTATCATTCCATTGATAGGTGG 59.607 45.833 12.85 0.00 42.39 4.61
386 387 5.121298 CAGCGTATCATTCCATTGATAGGTG 59.879 44.000 12.85 10.12 42.39 4.00
387 388 5.240891 CAGCGTATCATTCCATTGATAGGT 58.759 41.667 12.85 4.16 42.39 3.08
388 389 4.093998 GCAGCGTATCATTCCATTGATAGG 59.906 45.833 8.89 8.89 42.88 2.57
389 390 4.934001 AGCAGCGTATCATTCCATTGATAG 59.066 41.667 0.00 0.00 38.83 2.08
390 391 4.898320 AGCAGCGTATCATTCCATTGATA 58.102 39.130 0.00 0.00 37.51 2.15
391 392 3.748083 AGCAGCGTATCATTCCATTGAT 58.252 40.909 0.00 0.00 39.60 2.57
392 393 3.133691 GAGCAGCGTATCATTCCATTGA 58.866 45.455 0.00 0.00 0.00 2.57
393 394 2.874086 TGAGCAGCGTATCATTCCATTG 59.126 45.455 0.00 0.00 0.00 2.82
394 395 3.136763 CTGAGCAGCGTATCATTCCATT 58.863 45.455 0.00 0.00 0.00 3.16
395 396 2.103771 ACTGAGCAGCGTATCATTCCAT 59.896 45.455 0.00 0.00 0.00 3.41
396 397 1.482182 ACTGAGCAGCGTATCATTCCA 59.518 47.619 0.00 0.00 0.00 3.53
398 399 2.544685 ACACTGAGCAGCGTATCATTC 58.455 47.619 0.00 0.00 0.00 2.67
400 401 4.202151 TGAATACACTGAGCAGCGTATCAT 60.202 41.667 10.55 0.00 36.10 2.45
403 404 3.448686 GTGAATACACTGAGCAGCGTAT 58.551 45.455 5.56 5.56 42.99 3.06
405 406 1.714794 GTGAATACACTGAGCAGCGT 58.285 50.000 0.00 0.00 42.99 5.07
406 407 0.642291 CGTGAATACACTGAGCAGCG 59.358 55.000 0.00 0.00 43.99 5.18
408 409 4.990543 TTTTCGTGAATACACTGAGCAG 57.009 40.909 0.00 0.00 43.99 4.24
427 428 8.953313 CCATAAACCGGTCTATCTAAACTTTTT 58.047 33.333 8.04 0.00 0.00 1.94
428 429 8.105197 ACCATAAACCGGTCTATCTAAACTTTT 58.895 33.333 8.04 0.00 27.30 2.27
429 430 7.627311 ACCATAAACCGGTCTATCTAAACTTT 58.373 34.615 8.04 0.00 27.30 2.66
443 444 6.987992 TCAGCTACTAAATAACCATAAACCGG 59.012 38.462 0.00 0.00 0.00 5.28
450 451 8.322091 ACTTGACTTCAGCTACTAAATAACCAT 58.678 33.333 0.00 0.00 0.00 3.55
507 508 8.851145 ACGCTATTCTGAGATCTATGAAAGTTA 58.149 33.333 12.12 2.96 0.00 2.24
511 512 6.422100 GCAACGCTATTCTGAGATCTATGAAA 59.578 38.462 12.12 0.00 0.00 2.69
530 531 1.063166 GCCAGCTAATCTGCAACGC 59.937 57.895 0.00 0.00 41.50 4.84
535 536 2.332063 TACCTTGCCAGCTAATCTGC 57.668 50.000 0.00 0.00 41.50 4.26
542 543 1.561542 AGCAACTATACCTTGCCAGCT 59.438 47.619 6.72 0.00 44.36 4.24
592 593 3.146104 CCTCAATACATGGGGTCATCC 57.854 52.381 0.00 0.00 45.55 3.51
602 604 3.643320 TCGGCAAGAGATCCTCAATACAT 59.357 43.478 0.00 0.00 32.06 2.29
608 610 2.179427 TCTTTCGGCAAGAGATCCTCA 58.821 47.619 0.00 0.00 36.51 3.86
614 616 5.185249 AGTGTTACTATCTTTCGGCAAGAGA 59.815 40.000 0.00 0.00 45.11 3.10
762 765 4.201970 ACACGTTTTCCATTTCGTCATGTT 60.202 37.500 0.00 0.00 34.30 2.71
785 788 2.907634 TGTTCGGTGCACTACAGAAAA 58.092 42.857 17.98 9.77 43.44 2.29
793 796 1.000506 ACTCGTTATGTTCGGTGCACT 59.999 47.619 17.98 0.00 0.00 4.40
980 983 5.018149 ACATGGTGATTGGTGATCAATGAA 58.982 37.500 0.00 0.00 45.96 2.57
1048 1059 8.386606 CAGAGTTAAATCAGAGTTAGCATTGAC 58.613 37.037 5.62 0.00 0.00 3.18
1051 1062 6.881065 TGCAGAGTTAAATCAGAGTTAGCATT 59.119 34.615 5.62 0.00 0.00 3.56
1052 1063 6.409704 TGCAGAGTTAAATCAGAGTTAGCAT 58.590 36.000 5.62 0.00 0.00 3.79
1165 1183 2.076207 TATGCGTACCTGGGAGCTTA 57.924 50.000 0.00 0.64 0.00 3.09
1207 1225 4.215965 CCACGAACTTGGAAATAAACACG 58.784 43.478 0.00 0.00 39.24 4.49
1210 1228 4.211794 TCGACCACGAACTTGGAAATAAAC 59.788 41.667 4.40 0.00 45.74 2.01
1229 1247 1.594862 GCATTACAGCTGATGGTCGAC 59.405 52.381 23.35 7.13 0.00 4.20
1598 1625 6.954944 TCAGAAAAATTAGAAGTGAACACGG 58.045 36.000 0.00 0.00 36.20 4.94
1717 1745 4.369182 CGGACTTAATTATTCTCACCGCT 58.631 43.478 0.00 0.00 0.00 5.52
1719 1747 4.369182 AGCGGACTTAATTATTCTCACCG 58.631 43.478 0.00 0.00 40.60 4.94
1730 1758 9.429359 CATGAGAATAATTAGAGCGGACTTAAT 57.571 33.333 0.00 0.00 0.00 1.40
1731 1759 8.421784 ACATGAGAATAATTAGAGCGGACTTAA 58.578 33.333 0.00 0.00 0.00 1.85
1733 1761 6.821388 ACATGAGAATAATTAGAGCGGACTT 58.179 36.000 0.00 0.00 0.00 3.01
1734 1762 6.412362 ACATGAGAATAATTAGAGCGGACT 57.588 37.500 0.00 0.00 0.00 3.85
1737 1765 5.788450 AGGACATGAGAATAATTAGAGCGG 58.212 41.667 0.00 0.00 0.00 5.52
1739 1767 7.895759 AGAGAGGACATGAGAATAATTAGAGC 58.104 38.462 0.00 0.00 0.00 4.09
1764 2058 1.266718 GATGACAGCCACGCTCAAAAA 59.733 47.619 0.00 0.00 36.40 1.94
1766 2060 1.291184 CGATGACAGCCACGCTCAAA 61.291 55.000 0.00 0.00 36.40 2.69
1767 2061 1.737735 CGATGACAGCCACGCTCAA 60.738 57.895 0.00 0.00 36.40 3.02
1800 2533 1.956869 TCTTGGAGAGGGCATGAGAA 58.043 50.000 0.00 0.00 0.00 2.87
1820 2553 0.250513 GGACTGCATCGAGGGAAAGT 59.749 55.000 0.00 0.00 0.00 2.66
1821 2554 0.539051 AGGACTGCATCGAGGGAAAG 59.461 55.000 0.00 0.00 0.00 2.62
1822 2555 0.537188 GAGGACTGCATCGAGGGAAA 59.463 55.000 0.00 0.00 0.00 3.13
1823 2556 0.324738 AGAGGACTGCATCGAGGGAA 60.325 55.000 0.00 0.00 0.00 3.97
2005 2819 9.962783 GAGACTCGCCTTTCTTAAATTAGTATA 57.037 33.333 0.00 0.00 0.00 1.47
2006 2820 7.927092 GGAGACTCGCCTTTCTTAAATTAGTAT 59.073 37.037 0.00 0.00 0.00 2.12
2034 2848 0.885879 TCGACGGCTGTAGAACACAT 59.114 50.000 5.96 0.00 36.29 3.21
2103 2917 7.497579 TGTGTGTCTGTTTTTCTCAGCTTATTA 59.502 33.333 0.00 0.00 33.48 0.98
2123 2937 2.359531 CCCGTGGTTTTTGTATGTGTGT 59.640 45.455 0.00 0.00 0.00 3.72
2124 2938 2.619177 TCCCGTGGTTTTTGTATGTGTG 59.381 45.455 0.00 0.00 0.00 3.82
2218 4214 3.610040 TGGAGATTACACGACATTGCT 57.390 42.857 0.00 0.00 0.00 3.91
2236 4232 6.366332 CGGATTCTTTATTAGAGACCGAATGG 59.634 42.308 7.22 0.00 46.49 3.16
2239 4235 5.163488 TGCGGATTCTTTATTAGAGACCGAA 60.163 40.000 14.01 4.41 46.49 4.30
2279 4275 3.119316 ACTCTGCTTCGTCTTGTCCATAG 60.119 47.826 0.00 0.00 0.00 2.23
2283 4345 1.704070 GACTCTGCTTCGTCTTGTCC 58.296 55.000 0.00 0.00 0.00 4.02
2448 4525 3.062466 CCGACTGACGCTCCCTCA 61.062 66.667 0.00 0.00 41.07 3.86


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

AutoCloner maintained by Alex Coulton.