Multiple sequence alignment - TraesCS5A01G328200

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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 TraesCS5A01G328200 chr5A 100.000 3991 0 0 1 3991 537352532 537356522 0.000000e+00 7371
1 TraesCS5A01G328200 chr5B 93.876 3217 122 30 650 3827 511694935 511698115 0.000000e+00 4780
2 TraesCS5A01G328200 chr5B 85.641 195 18 4 3805 3991 511698140 511698332 3.150000e-46 196
3 TraesCS5A01G328200 chr5B 80.645 248 18 13 393 617 511694621 511694861 8.870000e-37 165
4 TraesCS5A01G328200 chr5B 82.653 196 21 5 3397 3586 511701831 511702019 1.150000e-35 161
5 TraesCS5A01G328200 chr5D 95.309 2494 71 16 650 3114 423858455 423860931 0.000000e+00 3916
6 TraesCS5A01G328200 chr5D 95.758 825 26 3 3175 3991 423861444 423862267 0.000000e+00 1321
7 TraesCS5A01G328200 chr5D 78.161 261 18 19 393 617 423858140 423858397 3.240000e-26 130
8 TraesCS5A01G328200 chr7D 83.996 931 134 9 1000 1927 262024012 262024930 0.000000e+00 880
9 TraesCS5A01G328200 chr7B 83.691 932 135 11 1000 1927 242356676 242355758 0.000000e+00 863


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 TraesCS5A01G328200 chr5A 537352532 537356522 3990 False 7371.0 7371 100.000000 1 3991 1 chr5A.!!$F1 3990
1 TraesCS5A01G328200 chr5B 511694621 511702019 7398 False 1325.5 4780 85.703750 393 3991 4 chr5B.!!$F1 3598
2 TraesCS5A01G328200 chr5D 423858140 423862267 4127 False 1789.0 3916 89.742667 393 3991 3 chr5D.!!$F1 3598
3 TraesCS5A01G328200 chr7D 262024012 262024930 918 False 880.0 880 83.996000 1000 1927 1 chr7D.!!$F1 927
4 TraesCS5A01G328200 chr7B 242355758 242356676 918 True 863.0 863 83.691000 1000 1927 1 chr7B.!!$R1 927

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
275 276 0.107214 CGGTGCACCCAACCTATCAT 60.107 55.0 29.95 0.0 0.00 2.45 F
585 628 0.111832 ACGCACGGAGATATAGGGGA 59.888 55.0 0.00 0.0 0.00 4.81 F
1281 1425 0.179045 GGGTCTTCACCATCATCCCG 60.179 60.0 0.00 0.0 45.94 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1425 0.035439 TCTTCTTGAATGACCCGGCC 60.035 55.000 0.0 0.0 0.00 6.13 R
2466 2616 0.738975 CATACTCGGCCTTCTCGACA 59.261 55.000 0.0 0.0 32.86 4.35 R
3103 3254 3.309121 CCTCCATGTACCAAGAACCCAAT 60.309 47.826 0.0 0.0 0.00 3.16 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
23 24 6.484364 TGGACTGCATATAGAATGAACAGA 57.516 37.500 0.00 0.00 0.00 3.41
24 25 6.283694 TGGACTGCATATAGAATGAACAGAC 58.716 40.000 0.00 0.00 0.00 3.51
25 26 6.127083 TGGACTGCATATAGAATGAACAGACA 60.127 38.462 0.00 0.00 0.00 3.41
26 27 6.933521 GGACTGCATATAGAATGAACAGACAT 59.066 38.462 0.00 0.00 0.00 3.06
27 28 7.117523 GGACTGCATATAGAATGAACAGACATC 59.882 40.741 0.00 0.00 0.00 3.06
28 29 6.644181 ACTGCATATAGAATGAACAGACATCG 59.356 38.462 0.00 0.00 0.00 3.84
29 30 6.515832 TGCATATAGAATGAACAGACATCGT 58.484 36.000 0.00 0.00 0.00 3.73
30 31 7.657336 TGCATATAGAATGAACAGACATCGTA 58.343 34.615 0.00 0.00 0.00 3.43
31 32 8.306761 TGCATATAGAATGAACAGACATCGTAT 58.693 33.333 0.00 0.00 0.00 3.06
32 33 9.144747 GCATATAGAATGAACAGACATCGTATT 57.855 33.333 0.00 0.00 0.00 1.89
37 38 8.553459 AGAATGAACAGACATCGTATTTTTCT 57.447 30.769 0.00 0.00 0.00 2.52
38 39 9.003658 AGAATGAACAGACATCGTATTTTTCTT 57.996 29.630 0.00 0.00 0.00 2.52
39 40 8.955061 AATGAACAGACATCGTATTTTTCTTG 57.045 30.769 0.00 0.00 0.00 3.02
40 41 7.722795 TGAACAGACATCGTATTTTTCTTGA 57.277 32.000 0.00 0.00 0.00 3.02
41 42 8.148807 TGAACAGACATCGTATTTTTCTTGAA 57.851 30.769 0.00 0.00 0.00 2.69
42 43 8.783093 TGAACAGACATCGTATTTTTCTTGAAT 58.217 29.630 0.00 0.00 0.00 2.57
43 44 8.955061 AACAGACATCGTATTTTTCTTGAATG 57.045 30.769 0.00 0.00 0.00 2.67
44 45 7.530010 ACAGACATCGTATTTTTCTTGAATGG 58.470 34.615 0.00 0.00 0.00 3.16
45 46 7.390440 ACAGACATCGTATTTTTCTTGAATGGA 59.610 33.333 0.00 0.00 0.00 3.41
46 47 7.907045 CAGACATCGTATTTTTCTTGAATGGAG 59.093 37.037 0.00 0.00 0.00 3.86
47 48 7.824289 AGACATCGTATTTTTCTTGAATGGAGA 59.176 33.333 0.00 0.00 0.00 3.71
48 49 7.978982 ACATCGTATTTTTCTTGAATGGAGAG 58.021 34.615 0.00 0.00 0.00 3.20
49 50 7.824289 ACATCGTATTTTTCTTGAATGGAGAGA 59.176 33.333 0.00 0.00 0.00 3.10
50 51 7.834068 TCGTATTTTTCTTGAATGGAGAGAG 57.166 36.000 0.00 0.00 0.00 3.20
51 52 7.386851 TCGTATTTTTCTTGAATGGAGAGAGT 58.613 34.615 0.00 0.00 0.00 3.24
52 53 8.528643 TCGTATTTTTCTTGAATGGAGAGAGTA 58.471 33.333 0.00 0.00 0.00 2.59
53 54 9.151471 CGTATTTTTCTTGAATGGAGAGAGTAA 57.849 33.333 0.00 0.00 0.00 2.24
82 83 7.675962 TTAATATGGCAAGTGTTTTACGAGT 57.324 32.000 0.00 0.00 0.00 4.18
83 84 3.896648 ATGGCAAGTGTTTTACGAGTG 57.103 42.857 0.00 0.00 0.00 3.51
84 85 1.332375 TGGCAAGTGTTTTACGAGTGC 59.668 47.619 0.00 0.00 36.40 4.40
85 86 1.332375 GGCAAGTGTTTTACGAGTGCA 59.668 47.619 0.00 0.00 37.84 4.57
86 87 2.223386 GGCAAGTGTTTTACGAGTGCAA 60.223 45.455 0.00 0.00 37.84 4.08
87 88 2.781646 GCAAGTGTTTTACGAGTGCAAC 59.218 45.455 0.00 0.00 36.83 4.17
126 127 9.665264 AAAGAAAAAGAAAGCATAAGTTAGACG 57.335 29.630 0.00 0.00 0.00 4.18
127 128 8.603242 AGAAAAAGAAAGCATAAGTTAGACGA 57.397 30.769 0.00 0.00 0.00 4.20
128 129 9.220767 AGAAAAAGAAAGCATAAGTTAGACGAT 57.779 29.630 0.00 0.00 0.00 3.73
129 130 9.827411 GAAAAAGAAAGCATAAGTTAGACGATT 57.173 29.630 0.00 0.00 0.00 3.34
130 131 9.612620 AAAAAGAAAGCATAAGTTAGACGATTG 57.387 29.630 0.00 0.00 0.00 2.67
131 132 8.547967 AAAGAAAGCATAAGTTAGACGATTGA 57.452 30.769 0.00 0.00 0.00 2.57
132 133 7.527084 AGAAAGCATAAGTTAGACGATTGAC 57.473 36.000 0.00 0.00 0.00 3.18
134 135 5.244785 AGCATAAGTTAGACGATTGACGA 57.755 39.130 0.00 0.00 45.77 4.20
135 136 5.035443 AGCATAAGTTAGACGATTGACGAC 58.965 41.667 0.00 0.00 45.77 4.34
136 137 4.206609 GCATAAGTTAGACGATTGACGACC 59.793 45.833 0.00 0.00 45.77 4.79
137 138 3.928727 AAGTTAGACGATTGACGACCA 57.071 42.857 0.00 0.00 45.77 4.02
138 139 4.451629 AAGTTAGACGATTGACGACCAT 57.548 40.909 0.00 0.00 45.77 3.55
139 140 3.770666 AGTTAGACGATTGACGACCATG 58.229 45.455 0.00 0.00 45.77 3.66
140 141 3.442625 AGTTAGACGATTGACGACCATGA 59.557 43.478 0.00 0.00 45.77 3.07
141 142 4.082408 AGTTAGACGATTGACGACCATGAA 60.082 41.667 0.00 0.00 45.77 2.57
142 143 3.313012 AGACGATTGACGACCATGAAA 57.687 42.857 0.00 0.00 45.77 2.69
143 144 3.659786 AGACGATTGACGACCATGAAAA 58.340 40.909 0.00 0.00 45.77 2.29
144 145 4.062293 AGACGATTGACGACCATGAAAAA 58.938 39.130 0.00 0.00 45.77 1.94
160 161 1.379527 AAAAAGAATCTAGGCGGGCG 58.620 50.000 0.00 0.00 0.00 6.13
161 162 1.095807 AAAAGAATCTAGGCGGGCGC 61.096 55.000 0.00 0.00 41.06 6.53
162 163 3.792053 AAGAATCTAGGCGGGCGCG 62.792 63.158 20.05 20.05 43.06 6.86
180 181 4.944372 CATACGACGAGGGCGCCC 62.944 72.222 39.29 39.29 42.48 6.13
197 198 4.530857 CCGACACGGGCCATCTCC 62.531 72.222 4.39 0.00 44.15 3.71
198 199 4.530857 CGACACGGGCCATCTCCC 62.531 72.222 4.39 0.00 43.02 4.30
199 200 4.176752 GACACGGGCCATCTCCCC 62.177 72.222 4.39 0.00 43.56 4.81
217 218 1.497161 CCCCCTCCAATTACTCGTCT 58.503 55.000 0.00 0.00 0.00 4.18
218 219 1.413077 CCCCCTCCAATTACTCGTCTC 59.587 57.143 0.00 0.00 0.00 3.36
219 220 1.413077 CCCCTCCAATTACTCGTCTCC 59.587 57.143 0.00 0.00 0.00 3.71
220 221 2.389715 CCCTCCAATTACTCGTCTCCT 58.610 52.381 0.00 0.00 0.00 3.69
221 222 2.362717 CCCTCCAATTACTCGTCTCCTC 59.637 54.545 0.00 0.00 0.00 3.71
222 223 2.362717 CCTCCAATTACTCGTCTCCTCC 59.637 54.545 0.00 0.00 0.00 4.30
223 224 2.022195 TCCAATTACTCGTCTCCTCCG 58.978 52.381 0.00 0.00 0.00 4.63
224 225 1.749634 CCAATTACTCGTCTCCTCCGT 59.250 52.381 0.00 0.00 0.00 4.69
225 226 2.223525 CCAATTACTCGTCTCCTCCGTC 60.224 54.545 0.00 0.00 0.00 4.79
226 227 1.677942 ATTACTCGTCTCCTCCGTCC 58.322 55.000 0.00 0.00 0.00 4.79
227 228 0.325933 TTACTCGTCTCCTCCGTCCA 59.674 55.000 0.00 0.00 0.00 4.02
228 229 0.392193 TACTCGTCTCCTCCGTCCAC 60.392 60.000 0.00 0.00 0.00 4.02
229 230 2.745100 TCGTCTCCTCCGTCCACG 60.745 66.667 0.00 0.00 39.44 4.94
230 231 4.477975 CGTCTCCTCCGTCCACGC 62.478 72.222 0.00 0.00 38.18 5.34
231 232 3.371063 GTCTCCTCCGTCCACGCA 61.371 66.667 0.00 0.00 38.18 5.24
232 233 3.371063 TCTCCTCCGTCCACGCAC 61.371 66.667 0.00 0.00 38.18 5.34
233 234 4.778415 CTCCTCCGTCCACGCACG 62.778 72.222 0.00 0.00 39.61 5.34
237 238 4.673298 TCCGTCCACGCACGCAAT 62.673 61.111 0.00 0.00 38.52 3.56
238 239 4.147322 CCGTCCACGCACGCAATC 62.147 66.667 0.00 0.00 38.52 2.67
239 240 3.410516 CGTCCACGCACGCAATCA 61.411 61.111 0.00 0.00 31.96 2.57
240 241 2.476051 GTCCACGCACGCAATCAG 59.524 61.111 0.00 0.00 0.00 2.90
241 242 2.741985 TCCACGCACGCAATCAGG 60.742 61.111 0.00 0.00 0.00 3.86
242 243 4.465512 CCACGCACGCAATCAGGC 62.466 66.667 0.00 0.00 0.00 4.85
243 244 3.425713 CACGCACGCAATCAGGCT 61.426 61.111 0.00 0.00 0.00 4.58
244 245 2.100031 CACGCACGCAATCAGGCTA 61.100 57.895 0.00 0.00 0.00 3.93
245 246 1.811266 ACGCACGCAATCAGGCTAG 60.811 57.895 0.00 0.00 0.00 3.42
246 247 1.519234 CGCACGCAATCAGGCTAGA 60.519 57.895 0.00 0.00 0.00 2.43
247 248 1.756375 CGCACGCAATCAGGCTAGAC 61.756 60.000 0.00 0.00 0.00 2.59
248 249 0.740868 GCACGCAATCAGGCTAGACA 60.741 55.000 0.00 0.00 0.00 3.41
249 250 1.725641 CACGCAATCAGGCTAGACAA 58.274 50.000 0.00 0.00 0.00 3.18
250 251 2.076100 CACGCAATCAGGCTAGACAAA 58.924 47.619 0.00 0.00 0.00 2.83
251 252 2.094894 CACGCAATCAGGCTAGACAAAG 59.905 50.000 0.00 0.00 0.00 2.77
252 253 1.667724 CGCAATCAGGCTAGACAAAGG 59.332 52.381 0.00 0.00 0.00 3.11
253 254 2.677902 CGCAATCAGGCTAGACAAAGGA 60.678 50.000 0.00 0.00 0.00 3.36
254 255 2.941720 GCAATCAGGCTAGACAAAGGAG 59.058 50.000 0.00 0.00 0.00 3.69
255 256 2.941720 CAATCAGGCTAGACAAAGGAGC 59.058 50.000 0.00 0.00 35.39 4.70
257 258 4.522971 GGCTAGACAAAGGAGCCG 57.477 61.111 0.00 0.00 45.94 5.52
258 259 1.153349 GGCTAGACAAAGGAGCCGG 60.153 63.158 0.00 0.00 45.94 6.13
259 260 1.597461 GCTAGACAAAGGAGCCGGT 59.403 57.895 1.90 0.00 0.00 5.28
260 261 0.741221 GCTAGACAAAGGAGCCGGTG 60.741 60.000 1.90 0.00 0.00 4.94
261 262 0.741221 CTAGACAAAGGAGCCGGTGC 60.741 60.000 1.90 0.00 37.95 5.01
262 263 1.476845 TAGACAAAGGAGCCGGTGCA 61.477 55.000 1.90 0.00 41.13 4.57
263 264 2.594592 ACAAAGGAGCCGGTGCAC 60.595 61.111 8.80 8.80 41.13 4.57
271 272 4.338710 GCCGGTGCACCCAACCTA 62.339 66.667 29.95 0.00 37.47 3.08
272 273 2.674754 CCGGTGCACCCAACCTAT 59.325 61.111 29.95 0.00 0.00 2.57
273 274 1.451387 CCGGTGCACCCAACCTATC 60.451 63.158 29.95 1.88 0.00 2.08
274 275 1.298340 CGGTGCACCCAACCTATCA 59.702 57.895 29.95 0.00 0.00 2.15
275 276 0.107214 CGGTGCACCCAACCTATCAT 60.107 55.000 29.95 0.00 0.00 2.45
276 277 1.392589 GGTGCACCCAACCTATCATG 58.607 55.000 26.31 0.00 0.00 3.07
277 278 0.740737 GTGCACCCAACCTATCATGC 59.259 55.000 5.22 0.00 0.00 4.06
278 279 0.747644 TGCACCCAACCTATCATGCG 60.748 55.000 0.00 0.00 35.83 4.73
279 280 0.748005 GCACCCAACCTATCATGCGT 60.748 55.000 0.00 0.00 0.00 5.24
280 281 1.474320 GCACCCAACCTATCATGCGTA 60.474 52.381 0.00 0.00 0.00 4.42
281 282 2.810400 GCACCCAACCTATCATGCGTAT 60.810 50.000 0.00 0.00 0.00 3.06
282 283 3.067106 CACCCAACCTATCATGCGTATC 58.933 50.000 0.00 0.00 0.00 2.24
283 284 2.703536 ACCCAACCTATCATGCGTATCA 59.296 45.455 0.00 0.00 0.00 2.15
284 285 3.135712 ACCCAACCTATCATGCGTATCAA 59.864 43.478 0.00 0.00 0.00 2.57
285 286 4.202461 ACCCAACCTATCATGCGTATCAAT 60.202 41.667 0.00 0.00 0.00 2.57
286 287 4.154737 CCCAACCTATCATGCGTATCAATG 59.845 45.833 0.00 0.00 0.00 2.82
287 288 4.996758 CCAACCTATCATGCGTATCAATGA 59.003 41.667 0.00 0.00 0.00 2.57
288 289 5.469760 CCAACCTATCATGCGTATCAATGAA 59.530 40.000 0.00 0.00 0.00 2.57
289 290 6.149973 CCAACCTATCATGCGTATCAATGAAT 59.850 38.462 0.00 0.00 0.00 2.57
290 291 6.732531 ACCTATCATGCGTATCAATGAATG 57.267 37.500 0.00 0.00 0.00 2.67
291 292 5.122869 ACCTATCATGCGTATCAATGAATGC 59.877 40.000 0.00 0.00 28.70 3.56
292 293 3.902261 TCATGCGTATCAATGAATGCC 57.098 42.857 0.00 0.00 28.70 4.40
293 294 3.212685 TCATGCGTATCAATGAATGCCA 58.787 40.909 0.00 0.00 28.70 4.92
294 295 3.003585 TCATGCGTATCAATGAATGCCAC 59.996 43.478 0.00 0.00 28.70 5.01
295 296 2.363683 TGCGTATCAATGAATGCCACA 58.636 42.857 0.00 0.00 0.00 4.17
296 297 2.097304 TGCGTATCAATGAATGCCACAC 59.903 45.455 0.00 0.00 0.00 3.82
297 298 2.097304 GCGTATCAATGAATGCCACACA 59.903 45.455 0.00 0.00 0.00 3.72
298 299 3.683989 CGTATCAATGAATGCCACACAC 58.316 45.455 0.00 0.00 0.00 3.82
299 300 2.925578 ATCAATGAATGCCACACACG 57.074 45.000 0.00 0.00 0.00 4.49
300 301 1.889545 TCAATGAATGCCACACACGA 58.110 45.000 0.00 0.00 0.00 4.35
301 302 2.225467 TCAATGAATGCCACACACGAA 58.775 42.857 0.00 0.00 0.00 3.85
302 303 2.620585 TCAATGAATGCCACACACGAAA 59.379 40.909 0.00 0.00 0.00 3.46
303 304 3.067320 TCAATGAATGCCACACACGAAAA 59.933 39.130 0.00 0.00 0.00 2.29
304 305 3.724508 ATGAATGCCACACACGAAAAA 57.275 38.095 0.00 0.00 0.00 1.94
305 306 2.803451 TGAATGCCACACACGAAAAAC 58.197 42.857 0.00 0.00 0.00 2.43
306 307 2.164422 TGAATGCCACACACGAAAAACA 59.836 40.909 0.00 0.00 0.00 2.83
307 308 2.490328 ATGCCACACACGAAAAACAG 57.510 45.000 0.00 0.00 0.00 3.16
308 309 1.454201 TGCCACACACGAAAAACAGA 58.546 45.000 0.00 0.00 0.00 3.41
309 310 1.813178 TGCCACACACGAAAAACAGAA 59.187 42.857 0.00 0.00 0.00 3.02
310 311 2.425312 TGCCACACACGAAAAACAGAAT 59.575 40.909 0.00 0.00 0.00 2.40
311 312 2.788786 GCCACACACGAAAAACAGAATG 59.211 45.455 0.00 0.00 46.00 2.67
325 326 3.754188 CAGAATGTCAGCTGCTAAACC 57.246 47.619 9.47 0.00 0.00 3.27
326 327 2.421424 CAGAATGTCAGCTGCTAAACCC 59.579 50.000 9.47 0.00 0.00 4.11
327 328 1.745653 GAATGTCAGCTGCTAAACCCC 59.254 52.381 9.47 0.00 0.00 4.95
328 329 0.698238 ATGTCAGCTGCTAAACCCCA 59.302 50.000 9.47 0.00 0.00 4.96
329 330 0.476338 TGTCAGCTGCTAAACCCCAA 59.524 50.000 9.47 0.00 0.00 4.12
330 331 1.133637 TGTCAGCTGCTAAACCCCAAA 60.134 47.619 9.47 0.00 0.00 3.28
331 332 1.960689 GTCAGCTGCTAAACCCCAAAA 59.039 47.619 9.47 0.00 0.00 2.44
332 333 2.364002 GTCAGCTGCTAAACCCCAAAAA 59.636 45.455 9.47 0.00 0.00 1.94
353 354 3.356814 AAAAACTGGGGATCACCGG 57.643 52.632 22.05 22.05 41.60 5.28
354 355 0.898326 AAAAACTGGGGATCACCGGC 60.898 55.000 23.57 0.00 40.73 6.13
355 356 1.789576 AAAACTGGGGATCACCGGCT 61.790 55.000 23.57 8.04 40.73 5.52
356 357 2.198304 AAACTGGGGATCACCGGCTC 62.198 60.000 23.57 0.00 40.73 4.70
357 358 4.227134 CTGGGGATCACCGGCTCG 62.227 72.222 10.68 0.00 41.60 5.03
367 368 2.822701 CCGGCTCGGTTTTAGGCC 60.823 66.667 0.00 0.00 42.73 5.19
368 369 2.822701 CGGCTCGGTTTTAGGCCC 60.823 66.667 0.00 0.00 41.35 5.80
369 370 2.439701 GGCTCGGTTTTAGGCCCC 60.440 66.667 0.00 0.00 38.77 5.80
370 371 2.353573 GCTCGGTTTTAGGCCCCA 59.646 61.111 0.00 0.00 0.00 4.96
371 372 2.044555 GCTCGGTTTTAGGCCCCAC 61.045 63.158 0.00 0.00 0.00 4.61
372 373 1.377229 CTCGGTTTTAGGCCCCACA 59.623 57.895 0.00 0.00 0.00 4.17
373 374 0.676782 CTCGGTTTTAGGCCCCACAG 60.677 60.000 0.00 0.00 0.00 3.66
374 375 2.340328 CGGTTTTAGGCCCCACAGC 61.340 63.158 0.00 0.00 0.00 4.40
383 384 4.421515 CCCCACAGCCAGAGCCAG 62.422 72.222 0.00 0.00 41.25 4.85
384 385 3.324930 CCCACAGCCAGAGCCAGA 61.325 66.667 0.00 0.00 41.25 3.86
385 386 2.268280 CCACAGCCAGAGCCAGAG 59.732 66.667 0.00 0.00 41.25 3.35
386 387 2.436292 CACAGCCAGAGCCAGAGC 60.436 66.667 0.00 0.00 41.25 4.09
387 388 4.079850 ACAGCCAGAGCCAGAGCG 62.080 66.667 0.00 0.00 46.67 5.03
446 456 3.461773 ATCCCCACGTCGCCTCTG 61.462 66.667 0.00 0.00 0.00 3.35
447 457 4.988716 TCCCCACGTCGCCTCTGT 62.989 66.667 0.00 0.00 0.00 3.41
450 460 4.778415 CCACGTCGCCTCTGTCCG 62.778 72.222 0.00 0.00 0.00 4.79
518 537 4.961511 GGCGCATGGCATGGCATG 62.962 66.667 42.44 42.44 46.16 4.06
538 566 2.111043 ATAGCATTGACCCCGCGG 59.889 61.111 21.04 21.04 0.00 6.46
585 628 0.111832 ACGCACGGAGATATAGGGGA 59.888 55.000 0.00 0.00 0.00 4.81
586 629 0.811915 CGCACGGAGATATAGGGGAG 59.188 60.000 0.00 0.00 0.00 4.30
587 630 0.533032 GCACGGAGATATAGGGGAGC 59.467 60.000 0.00 0.00 0.00 4.70
589 632 0.323542 ACGGAGATATAGGGGAGCCG 60.324 60.000 0.00 0.00 42.64 5.52
592 635 0.335361 GAGATATAGGGGAGCCGGGA 59.665 60.000 2.18 0.00 0.00 5.14
593 636 0.790993 AGATATAGGGGAGCCGGGAA 59.209 55.000 2.18 0.00 0.00 3.97
596 639 2.127651 TATAGGGGAGCCGGGAAAAT 57.872 50.000 2.18 0.00 0.00 1.82
614 713 1.264045 ATGGCCCCCAAAAATCACCG 61.264 55.000 0.00 0.00 36.95 4.94
617 716 2.571231 CCCCAAAAATCACCGCGG 59.429 61.111 26.86 26.86 0.00 6.46
618 717 2.571231 CCCAAAAATCACCGCGGG 59.429 61.111 31.76 18.67 0.00 6.13
619 718 1.974343 CCCAAAAATCACCGCGGGA 60.974 57.895 31.76 23.50 35.57 5.14
634 733 3.706373 GGAGGGAGCACGAGCCAA 61.706 66.667 0.00 0.00 43.56 4.52
649 748 4.973055 CAAACGCACCCGACCCGA 62.973 66.667 0.00 0.00 38.29 5.14
650 749 4.974989 AAACGCACCCGACCCGAC 62.975 66.667 0.00 0.00 38.29 4.79
753 868 0.756070 GAGAGAGTAACCCCTCCCCG 60.756 65.000 0.00 0.00 31.53 5.73
791 907 0.707616 CCAATTTACTCCCCACCCCA 59.292 55.000 0.00 0.00 0.00 4.96
792 908 1.618616 CCAATTTACTCCCCACCCCAC 60.619 57.143 0.00 0.00 0.00 4.61
793 909 0.708209 AATTTACTCCCCACCCCACC 59.292 55.000 0.00 0.00 0.00 4.61
794 910 1.219131 ATTTACTCCCCACCCCACCC 61.219 60.000 0.00 0.00 0.00 4.61
795 911 3.895253 TTACTCCCCACCCCACCCC 62.895 68.421 0.00 0.00 0.00 4.95
838 959 2.040359 CCCCTTCCTCCTCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
841 962 2.652113 CCTTCCTCCTCCTCCCCCT 61.652 68.421 0.00 0.00 0.00 4.79
849 970 4.364686 TCCTCCCCCTCCCCCAAC 62.365 72.222 0.00 0.00 0.00 3.77
887 1008 2.041265 GGAGGCAGGGAGGAAGGA 59.959 66.667 0.00 0.00 0.00 3.36
888 1009 1.616628 GGAGGCAGGGAGGAAGGAA 60.617 63.158 0.00 0.00 0.00 3.36
896 1017 4.840005 GAGGAAGGAAGGCCGCCG 62.840 72.222 3.05 0.00 38.20 6.46
958 1094 2.360191 CCTCCACCCCACCCATTG 59.640 66.667 0.00 0.00 0.00 2.82
960 1096 4.358841 TCCACCCCACCCATTGCG 62.359 66.667 0.00 0.00 0.00 4.85
1170 1314 4.253257 GCCGACCTCTACGAGCGG 62.253 72.222 0.00 0.00 38.00 5.52
1281 1425 0.179045 GGGTCTTCACCATCATCCCG 60.179 60.000 0.00 0.00 45.94 5.14
1905 2049 3.084039 CACCTCCAAGTTGTGCATACAT 58.916 45.455 1.45 0.00 36.53 2.29
1970 2114 2.808523 CTCGAGGAGCATCAGCATAA 57.191 50.000 3.91 0.00 45.49 1.90
1976 2120 2.502947 AGGAGCATCAGCATAACACAGA 59.497 45.455 0.00 0.00 45.49 3.41
2084 2228 2.158608 CCTCCAACTCCAACTCCAACTT 60.159 50.000 0.00 0.00 0.00 2.66
2088 2238 3.891366 CCAACTCCAACTCCAACTTCAAT 59.109 43.478 0.00 0.00 0.00 2.57
2421 2571 1.526986 CGACGCTCAGCATTTAAACCG 60.527 52.381 0.00 0.00 0.00 4.44
2460 2610 1.230635 CCGTTGTTGACCAGCTCCTG 61.231 60.000 0.00 0.00 0.00 3.86
2466 2616 2.031163 GACCAGCTCCTGCGTGTT 59.969 61.111 0.00 0.00 45.42 3.32
3103 3254 6.016693 TGGCGAAAGTTGATTTACATCTTTGA 60.017 34.615 9.56 0.00 43.89 2.69
3182 3785 1.000233 TCGCGCGTACAGAACTTGAC 61.000 55.000 30.98 0.00 0.00 3.18
3198 3801 2.136298 TGACTTGCTTTGTGGTGGAA 57.864 45.000 0.00 0.00 0.00 3.53
3258 3861 9.325198 TGGTCTAAATGTTGTATCATGTACATC 57.675 33.333 5.07 0.00 31.25 3.06
3345 3948 4.654091 ACCTCATGGTTTTGTTTGACTG 57.346 40.909 0.00 0.00 46.05 3.51
3792 4405 4.345859 ACAAAACTGGAGGTACGATGAA 57.654 40.909 0.00 0.00 0.00 2.57
3835 4495 6.753913 ACATAACATGATCCATGACCTACT 57.246 37.500 13.22 0.00 43.81 2.57
3865 4525 7.565029 TGAAACTATAGGATCTCCATCTGTCAA 59.435 37.037 4.43 0.00 38.89 3.18
3871 4531 2.030027 TCTCCATCTGTCAACCACCT 57.970 50.000 0.00 0.00 0.00 4.00
3927 4595 3.873952 GCCCTGTAGACTTCATTTGCTAG 59.126 47.826 0.00 0.00 0.00 3.42
3950 4618 1.067776 ACTCGACTAACTTTGCTCCCG 60.068 52.381 0.00 0.00 0.00 5.14
3959 4627 1.151668 CTTTGCTCCCGTCTTCAGTG 58.848 55.000 0.00 0.00 0.00 3.66
3976 4644 1.490490 AGTGACCTTGTTTCTGGCTCA 59.510 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.127083 TGTCTGTTCATTCTATATGCAGTCCA 60.127 38.462 0.00 0.00 0.00 4.02
1 2 6.283694 TGTCTGTTCATTCTATATGCAGTCC 58.716 40.000 0.00 0.00 0.00 3.85
2 3 7.148836 CGATGTCTGTTCATTCTATATGCAGTC 60.149 40.741 0.00 0.00 0.00 3.51
3 4 6.644181 CGATGTCTGTTCATTCTATATGCAGT 59.356 38.462 0.00 0.00 0.00 4.40
4 5 6.644181 ACGATGTCTGTTCATTCTATATGCAG 59.356 38.462 0.00 0.00 0.00 4.41
5 6 6.515832 ACGATGTCTGTTCATTCTATATGCA 58.484 36.000 0.00 0.00 0.00 3.96
6 7 8.694975 ATACGATGTCTGTTCATTCTATATGC 57.305 34.615 0.00 0.00 0.00 3.14
11 12 9.653287 AGAAAAATACGATGTCTGTTCATTCTA 57.347 29.630 0.00 0.00 0.00 2.10
12 13 8.553459 AGAAAAATACGATGTCTGTTCATTCT 57.447 30.769 0.00 0.00 0.00 2.40
13 14 9.055248 CAAGAAAAATACGATGTCTGTTCATTC 57.945 33.333 0.00 0.00 0.00 2.67
14 15 8.783093 TCAAGAAAAATACGATGTCTGTTCATT 58.217 29.630 0.00 0.00 0.00 2.57
15 16 8.322906 TCAAGAAAAATACGATGTCTGTTCAT 57.677 30.769 0.00 0.00 0.00 2.57
16 17 7.722795 TCAAGAAAAATACGATGTCTGTTCA 57.277 32.000 0.00 0.00 0.00 3.18
17 18 9.055248 CATTCAAGAAAAATACGATGTCTGTTC 57.945 33.333 0.00 0.00 0.00 3.18
18 19 8.023128 CCATTCAAGAAAAATACGATGTCTGTT 58.977 33.333 0.00 0.00 0.00 3.16
19 20 7.390440 TCCATTCAAGAAAAATACGATGTCTGT 59.610 33.333 0.00 0.00 0.00 3.41
20 21 7.751732 TCCATTCAAGAAAAATACGATGTCTG 58.248 34.615 0.00 0.00 0.00 3.51
21 22 7.824289 TCTCCATTCAAGAAAAATACGATGTCT 59.176 33.333 0.00 0.00 0.00 3.41
22 23 7.974675 TCTCCATTCAAGAAAAATACGATGTC 58.025 34.615 0.00 0.00 0.00 3.06
23 24 7.824289 TCTCTCCATTCAAGAAAAATACGATGT 59.176 33.333 0.00 0.00 0.00 3.06
24 25 8.201554 TCTCTCCATTCAAGAAAAATACGATG 57.798 34.615 0.00 0.00 0.00 3.84
25 26 8.043710 ACTCTCTCCATTCAAGAAAAATACGAT 58.956 33.333 0.00 0.00 0.00 3.73
26 27 7.386851 ACTCTCTCCATTCAAGAAAAATACGA 58.613 34.615 0.00 0.00 0.00 3.43
27 28 7.602517 ACTCTCTCCATTCAAGAAAAATACG 57.397 36.000 0.00 0.00 0.00 3.06
56 57 8.736244 ACTCGTAAAACACTTGCCATATTAATT 58.264 29.630 0.00 0.00 0.00 1.40
57 58 8.181573 CACTCGTAAAACACTTGCCATATTAAT 58.818 33.333 0.00 0.00 0.00 1.40
58 59 7.523219 CACTCGTAAAACACTTGCCATATTAA 58.477 34.615 0.00 0.00 0.00 1.40
59 60 6.402766 GCACTCGTAAAACACTTGCCATATTA 60.403 38.462 0.00 0.00 0.00 0.98
60 61 5.619086 GCACTCGTAAAACACTTGCCATATT 60.619 40.000 0.00 0.00 0.00 1.28
61 62 4.142687 GCACTCGTAAAACACTTGCCATAT 60.143 41.667 0.00 0.00 0.00 1.78
62 63 3.187637 GCACTCGTAAAACACTTGCCATA 59.812 43.478 0.00 0.00 0.00 2.74
63 64 2.031157 GCACTCGTAAAACACTTGCCAT 60.031 45.455 0.00 0.00 0.00 4.40
64 65 1.332375 GCACTCGTAAAACACTTGCCA 59.668 47.619 0.00 0.00 0.00 4.92
65 66 1.332375 TGCACTCGTAAAACACTTGCC 59.668 47.619 0.00 0.00 0.00 4.52
66 67 2.748461 TGCACTCGTAAAACACTTGC 57.252 45.000 0.00 0.00 0.00 4.01
67 68 4.273005 AGTTGCACTCGTAAAACACTTG 57.727 40.909 0.00 0.00 0.00 3.16
68 69 4.957759 AAGTTGCACTCGTAAAACACTT 57.042 36.364 0.00 0.00 0.00 3.16
69 70 4.957759 AAAGTTGCACTCGTAAAACACT 57.042 36.364 0.00 0.00 0.00 3.55
70 71 5.090083 TCAAAAGTTGCACTCGTAAAACAC 58.910 37.500 0.00 0.00 0.00 3.32
71 72 5.298197 TCAAAAGTTGCACTCGTAAAACA 57.702 34.783 0.00 0.00 0.00 2.83
72 73 5.968848 TCATCAAAAGTTGCACTCGTAAAAC 59.031 36.000 0.00 0.00 0.00 2.43
73 74 6.125327 TCATCAAAAGTTGCACTCGTAAAA 57.875 33.333 0.00 0.00 0.00 1.52
74 75 5.743026 TCATCAAAAGTTGCACTCGTAAA 57.257 34.783 0.00 0.00 0.00 2.01
75 76 5.743026 TTCATCAAAAGTTGCACTCGTAA 57.257 34.783 0.00 0.00 0.00 3.18
76 77 5.743026 TTTCATCAAAAGTTGCACTCGTA 57.257 34.783 0.00 0.00 0.00 3.43
77 78 4.630894 TTTCATCAAAAGTTGCACTCGT 57.369 36.364 0.00 0.00 0.00 4.18
78 79 5.947503 TTTTTCATCAAAAGTTGCACTCG 57.052 34.783 0.00 0.00 32.96 4.18
100 101 9.665264 CGTCTAACTTATGCTTTCTTTTTCTTT 57.335 29.630 0.00 0.00 0.00 2.52
101 102 9.052759 TCGTCTAACTTATGCTTTCTTTTTCTT 57.947 29.630 0.00 0.00 0.00 2.52
102 103 8.603242 TCGTCTAACTTATGCTTTCTTTTTCT 57.397 30.769 0.00 0.00 0.00 2.52
103 104 9.827411 AATCGTCTAACTTATGCTTTCTTTTTC 57.173 29.630 0.00 0.00 0.00 2.29
104 105 9.612620 CAATCGTCTAACTTATGCTTTCTTTTT 57.387 29.630 0.00 0.00 0.00 1.94
105 106 8.999431 TCAATCGTCTAACTTATGCTTTCTTTT 58.001 29.630 0.00 0.00 0.00 2.27
106 107 8.443937 GTCAATCGTCTAACTTATGCTTTCTTT 58.556 33.333 0.00 0.00 0.00 2.52
107 108 7.201444 CGTCAATCGTCTAACTTATGCTTTCTT 60.201 37.037 0.00 0.00 34.52 2.52
108 109 6.253727 CGTCAATCGTCTAACTTATGCTTTCT 59.746 38.462 0.00 0.00 34.52 2.52
109 110 6.252869 TCGTCAATCGTCTAACTTATGCTTTC 59.747 38.462 0.00 0.00 40.80 2.62
110 111 6.034683 GTCGTCAATCGTCTAACTTATGCTTT 59.965 38.462 0.00 0.00 40.80 3.51
111 112 5.515626 GTCGTCAATCGTCTAACTTATGCTT 59.484 40.000 0.00 0.00 40.80 3.91
112 113 5.035443 GTCGTCAATCGTCTAACTTATGCT 58.965 41.667 0.00 0.00 40.80 3.79
113 114 4.206609 GGTCGTCAATCGTCTAACTTATGC 59.793 45.833 0.00 0.00 40.80 3.14
114 115 5.337554 TGGTCGTCAATCGTCTAACTTATG 58.662 41.667 0.00 0.00 40.80 1.90
115 116 5.571784 TGGTCGTCAATCGTCTAACTTAT 57.428 39.130 0.00 0.00 40.80 1.73
116 117 5.124297 TCATGGTCGTCAATCGTCTAACTTA 59.876 40.000 0.00 0.00 40.80 2.24
117 118 3.928727 TGGTCGTCAATCGTCTAACTT 57.071 42.857 0.00 0.00 40.80 2.66
118 119 3.442625 TCATGGTCGTCAATCGTCTAACT 59.557 43.478 0.00 0.00 40.80 2.24
119 120 3.766151 TCATGGTCGTCAATCGTCTAAC 58.234 45.455 0.00 0.00 40.80 2.34
120 121 4.443913 TTCATGGTCGTCAATCGTCTAA 57.556 40.909 0.00 0.00 40.80 2.10
121 122 4.443913 TTTCATGGTCGTCAATCGTCTA 57.556 40.909 0.00 0.00 40.80 2.59
122 123 3.313012 TTTCATGGTCGTCAATCGTCT 57.687 42.857 0.00 0.00 40.80 4.18
123 124 4.398549 TTTTTCATGGTCGTCAATCGTC 57.601 40.909 0.00 0.00 40.80 4.20
141 142 1.379527 CGCCCGCCTAGATTCTTTTT 58.620 50.000 0.00 0.00 0.00 1.94
142 143 1.095807 GCGCCCGCCTAGATTCTTTT 61.096 55.000 0.00 0.00 34.56 2.27
143 144 1.523938 GCGCCCGCCTAGATTCTTT 60.524 57.895 0.00 0.00 34.56 2.52
144 145 2.109181 GCGCCCGCCTAGATTCTT 59.891 61.111 0.00 0.00 34.56 2.52
145 146 4.286320 CGCGCCCGCCTAGATTCT 62.286 66.667 0.00 0.00 37.98 2.40
163 164 4.944372 GGGCGCCCTCGTCGTATG 62.944 72.222 38.76 0.00 42.10 2.39
181 182 4.530857 GGGAGATGGCCCGTGTCG 62.531 72.222 0.00 0.00 38.58 4.35
198 199 1.413077 GAGACGAGTAATTGGAGGGGG 59.587 57.143 0.00 0.00 0.00 5.40
199 200 1.413077 GGAGACGAGTAATTGGAGGGG 59.587 57.143 0.00 0.00 0.00 4.79
200 201 2.362717 GAGGAGACGAGTAATTGGAGGG 59.637 54.545 0.00 0.00 0.00 4.30
201 202 2.362717 GGAGGAGACGAGTAATTGGAGG 59.637 54.545 0.00 0.00 0.00 4.30
202 203 2.033550 CGGAGGAGACGAGTAATTGGAG 59.966 54.545 0.00 0.00 0.00 3.86
203 204 2.022195 CGGAGGAGACGAGTAATTGGA 58.978 52.381 0.00 0.00 0.00 3.53
204 205 1.749634 ACGGAGGAGACGAGTAATTGG 59.250 52.381 0.00 0.00 34.93 3.16
205 206 2.223525 GGACGGAGGAGACGAGTAATTG 60.224 54.545 0.00 0.00 34.93 2.32
206 207 2.022934 GGACGGAGGAGACGAGTAATT 58.977 52.381 0.00 0.00 34.93 1.40
207 208 1.064906 TGGACGGAGGAGACGAGTAAT 60.065 52.381 0.00 0.00 34.93 1.89
208 209 0.325933 TGGACGGAGGAGACGAGTAA 59.674 55.000 0.00 0.00 34.93 2.24
209 210 0.392193 GTGGACGGAGGAGACGAGTA 60.392 60.000 0.00 0.00 34.93 2.59
210 211 1.674980 GTGGACGGAGGAGACGAGT 60.675 63.158 0.00 0.00 34.93 4.18
211 212 2.751913 CGTGGACGGAGGAGACGAG 61.752 68.421 0.00 0.00 35.37 4.18
212 213 2.745100 CGTGGACGGAGGAGACGA 60.745 66.667 0.00 0.00 35.37 4.20
213 214 4.477975 GCGTGGACGGAGGAGACG 62.478 72.222 0.71 0.00 40.23 4.18
214 215 3.371063 TGCGTGGACGGAGGAGAC 61.371 66.667 0.71 0.00 40.23 3.36
215 216 3.371063 GTGCGTGGACGGAGGAGA 61.371 66.667 0.71 0.00 41.17 3.71
216 217 4.778415 CGTGCGTGGACGGAGGAG 62.778 72.222 7.51 0.00 45.90 3.69
220 221 4.673298 ATTGCGTGCGTGGACGGA 62.673 61.111 15.51 10.10 39.81 4.69
221 222 4.147322 GATTGCGTGCGTGGACGG 62.147 66.667 15.51 0.00 39.81 4.79
222 223 3.353114 CTGATTGCGTGCGTGGACG 62.353 63.158 9.65 9.65 42.42 4.79
223 224 2.476051 CTGATTGCGTGCGTGGAC 59.524 61.111 0.00 0.00 0.00 4.02
224 225 2.741985 CCTGATTGCGTGCGTGGA 60.742 61.111 0.00 0.00 0.00 4.02
225 226 4.465512 GCCTGATTGCGTGCGTGG 62.466 66.667 0.00 0.00 0.00 4.94
226 227 2.028766 CTAGCCTGATTGCGTGCGTG 62.029 60.000 0.00 0.00 36.02 5.34
227 228 1.811266 CTAGCCTGATTGCGTGCGT 60.811 57.895 0.00 0.00 36.02 5.24
228 229 1.519234 TCTAGCCTGATTGCGTGCG 60.519 57.895 0.00 0.00 36.02 5.34
229 230 0.740868 TGTCTAGCCTGATTGCGTGC 60.741 55.000 0.00 0.00 36.02 5.34
230 231 1.725641 TTGTCTAGCCTGATTGCGTG 58.274 50.000 0.00 0.00 36.02 5.34
231 232 2.350522 CTTTGTCTAGCCTGATTGCGT 58.649 47.619 0.00 0.00 36.02 5.24
232 233 1.667724 CCTTTGTCTAGCCTGATTGCG 59.332 52.381 0.00 0.00 36.02 4.85
233 234 2.941720 CTCCTTTGTCTAGCCTGATTGC 59.058 50.000 0.00 0.00 0.00 3.56
234 235 2.941720 GCTCCTTTGTCTAGCCTGATTG 59.058 50.000 0.00 0.00 0.00 2.67
235 236 3.274095 GCTCCTTTGTCTAGCCTGATT 57.726 47.619 0.00 0.00 0.00 2.57
236 237 2.998316 GCTCCTTTGTCTAGCCTGAT 57.002 50.000 0.00 0.00 0.00 2.90
241 242 0.741221 CACCGGCTCCTTTGTCTAGC 60.741 60.000 0.00 0.00 35.47 3.42
242 243 0.741221 GCACCGGCTCCTTTGTCTAG 60.741 60.000 0.00 0.00 36.96 2.43
243 244 1.295423 GCACCGGCTCCTTTGTCTA 59.705 57.895 0.00 0.00 36.96 2.59
244 245 2.032681 GCACCGGCTCCTTTGTCT 59.967 61.111 0.00 0.00 36.96 3.41
245 246 2.281484 TGCACCGGCTCCTTTGTC 60.281 61.111 0.00 0.00 41.91 3.18
246 247 2.594592 GTGCACCGGCTCCTTTGT 60.595 61.111 5.22 0.00 41.91 2.83
254 255 3.638592 ATAGGTTGGGTGCACCGGC 62.639 63.158 29.08 19.99 44.64 6.13
255 256 1.451387 GATAGGTTGGGTGCACCGG 60.451 63.158 29.08 0.00 44.64 5.28
256 257 0.107214 ATGATAGGTTGGGTGCACCG 60.107 55.000 29.08 0.00 44.64 4.94
257 258 1.392589 CATGATAGGTTGGGTGCACC 58.607 55.000 28.57 28.57 40.81 5.01
258 259 0.740737 GCATGATAGGTTGGGTGCAC 59.259 55.000 8.80 8.80 33.09 4.57
259 260 0.747644 CGCATGATAGGTTGGGTGCA 60.748 55.000 0.00 0.00 33.09 4.57
260 261 0.748005 ACGCATGATAGGTTGGGTGC 60.748 55.000 0.00 0.00 37.59 5.01
261 262 2.613026 TACGCATGATAGGTTGGGTG 57.387 50.000 0.00 0.00 39.11 4.61
262 263 2.703536 TGATACGCATGATAGGTTGGGT 59.296 45.455 0.00 0.00 41.29 4.51
263 264 3.401033 TGATACGCATGATAGGTTGGG 57.599 47.619 0.00 0.00 0.00 4.12
264 265 4.996758 TCATTGATACGCATGATAGGTTGG 59.003 41.667 0.00 0.00 0.00 3.77
265 266 6.544038 TTCATTGATACGCATGATAGGTTG 57.456 37.500 0.00 0.00 0.00 3.77
266 267 6.348786 GCATTCATTGATACGCATGATAGGTT 60.349 38.462 0.00 0.00 0.00 3.50
267 268 5.122869 GCATTCATTGATACGCATGATAGGT 59.877 40.000 0.00 0.00 0.00 3.08
268 269 5.448225 GGCATTCATTGATACGCATGATAGG 60.448 44.000 0.00 0.00 0.00 2.57
269 270 5.122711 TGGCATTCATTGATACGCATGATAG 59.877 40.000 0.00 0.00 0.00 2.08
270 271 5.002516 TGGCATTCATTGATACGCATGATA 58.997 37.500 0.00 0.00 0.00 2.15
271 272 3.822167 TGGCATTCATTGATACGCATGAT 59.178 39.130 0.00 0.00 0.00 2.45
272 273 3.003585 GTGGCATTCATTGATACGCATGA 59.996 43.478 0.00 0.00 0.00 3.07
273 274 3.243134 TGTGGCATTCATTGATACGCATG 60.243 43.478 0.00 0.00 0.00 4.06
274 275 2.950975 TGTGGCATTCATTGATACGCAT 59.049 40.909 0.00 0.00 0.00 4.73
275 276 2.097304 GTGTGGCATTCATTGATACGCA 59.903 45.455 0.00 0.00 0.00 5.24
276 277 2.097304 TGTGTGGCATTCATTGATACGC 59.903 45.455 0.00 0.00 0.00 4.42
277 278 3.683989 GTGTGTGGCATTCATTGATACG 58.316 45.455 0.00 0.00 0.00 3.06
278 279 3.373748 TCGTGTGTGGCATTCATTGATAC 59.626 43.478 0.00 0.00 0.00 2.24
279 280 3.604582 TCGTGTGTGGCATTCATTGATA 58.395 40.909 0.00 0.00 0.00 2.15
280 281 2.435422 TCGTGTGTGGCATTCATTGAT 58.565 42.857 0.00 0.00 0.00 2.57
281 282 1.889545 TCGTGTGTGGCATTCATTGA 58.110 45.000 0.00 0.00 0.00 2.57
282 283 2.702898 TTCGTGTGTGGCATTCATTG 57.297 45.000 0.00 0.00 0.00 2.82
283 284 3.724508 TTTTCGTGTGTGGCATTCATT 57.275 38.095 0.00 0.00 0.00 2.57
284 285 3.181482 TGTTTTTCGTGTGTGGCATTCAT 60.181 39.130 0.00 0.00 0.00 2.57
285 286 2.164422 TGTTTTTCGTGTGTGGCATTCA 59.836 40.909 0.00 0.00 0.00 2.57
286 287 2.788786 CTGTTTTTCGTGTGTGGCATTC 59.211 45.455 0.00 0.00 0.00 2.67
287 288 2.425312 TCTGTTTTTCGTGTGTGGCATT 59.575 40.909 0.00 0.00 0.00 3.56
288 289 2.020720 TCTGTTTTTCGTGTGTGGCAT 58.979 42.857 0.00 0.00 0.00 4.40
289 290 1.454201 TCTGTTTTTCGTGTGTGGCA 58.546 45.000 0.00 0.00 0.00 4.92
290 291 2.553079 TTCTGTTTTTCGTGTGTGGC 57.447 45.000 0.00 0.00 0.00 5.01
291 292 4.027572 ACATTCTGTTTTTCGTGTGTGG 57.972 40.909 0.00 0.00 0.00 4.17
292 293 4.657055 TGACATTCTGTTTTTCGTGTGTG 58.343 39.130 0.00 0.00 0.00 3.82
293 294 4.730613 GCTGACATTCTGTTTTTCGTGTGT 60.731 41.667 0.00 0.00 0.00 3.72
294 295 3.725740 GCTGACATTCTGTTTTTCGTGTG 59.274 43.478 0.00 0.00 0.00 3.82
295 296 3.627577 AGCTGACATTCTGTTTTTCGTGT 59.372 39.130 0.00 0.00 0.00 4.49
296 297 3.970610 CAGCTGACATTCTGTTTTTCGTG 59.029 43.478 8.42 0.00 0.00 4.35
297 298 3.548818 GCAGCTGACATTCTGTTTTTCGT 60.549 43.478 20.43 0.00 33.09 3.85
298 299 2.975851 GCAGCTGACATTCTGTTTTTCG 59.024 45.455 20.43 0.00 33.09 3.46
299 300 4.234530 AGCAGCTGACATTCTGTTTTTC 57.765 40.909 20.43 0.00 33.09 2.29
300 301 5.772825 TTAGCAGCTGACATTCTGTTTTT 57.227 34.783 20.43 0.00 33.09 1.94
301 302 5.507985 GGTTTAGCAGCTGACATTCTGTTTT 60.508 40.000 20.43 0.00 33.09 2.43
302 303 4.022849 GGTTTAGCAGCTGACATTCTGTTT 60.023 41.667 20.43 0.00 33.09 2.83
303 304 3.503748 GGTTTAGCAGCTGACATTCTGTT 59.496 43.478 20.43 3.96 33.09 3.16
304 305 3.077359 GGTTTAGCAGCTGACATTCTGT 58.923 45.455 20.43 0.00 33.09 3.41
305 306 2.421424 GGGTTTAGCAGCTGACATTCTG 59.579 50.000 20.43 0.00 0.00 3.02
306 307 2.619074 GGGGTTTAGCAGCTGACATTCT 60.619 50.000 20.43 6.99 0.00 2.40
307 308 1.745653 GGGGTTTAGCAGCTGACATTC 59.254 52.381 20.43 3.98 0.00 2.67
308 309 1.075374 TGGGGTTTAGCAGCTGACATT 59.925 47.619 20.43 1.55 0.00 2.71
309 310 0.698238 TGGGGTTTAGCAGCTGACAT 59.302 50.000 20.43 4.69 0.00 3.06
310 311 0.476338 TTGGGGTTTAGCAGCTGACA 59.524 50.000 20.43 0.00 0.00 3.58
311 312 1.616159 TTTGGGGTTTAGCAGCTGAC 58.384 50.000 20.43 9.11 0.00 3.51
312 313 2.373335 TTTTGGGGTTTAGCAGCTGA 57.627 45.000 20.43 0.00 0.00 4.26
335 336 0.898326 GCCGGTGATCCCCAGTTTTT 60.898 55.000 1.90 0.00 0.00 1.94
336 337 1.304134 GCCGGTGATCCCCAGTTTT 60.304 57.895 1.90 0.00 0.00 2.43
337 338 2.198304 GAGCCGGTGATCCCCAGTTT 62.198 60.000 1.90 0.00 0.00 2.66
338 339 2.610859 AGCCGGTGATCCCCAGTT 60.611 61.111 1.90 0.00 0.00 3.16
339 340 3.083997 GAGCCGGTGATCCCCAGT 61.084 66.667 1.90 0.00 0.00 4.00
340 341 4.227134 CGAGCCGGTGATCCCCAG 62.227 72.222 1.90 0.00 0.00 4.45
351 352 2.822701 GGGCCTAAAACCGAGCCG 60.823 66.667 0.84 0.00 46.75 5.52
352 353 2.439701 GGGGCCTAAAACCGAGCC 60.440 66.667 0.84 0.00 44.99 4.70
353 354 2.044555 GTGGGGCCTAAAACCGAGC 61.045 63.158 0.84 0.00 0.00 5.03
354 355 0.676782 CTGTGGGGCCTAAAACCGAG 60.677 60.000 0.84 0.00 0.00 4.63
355 356 1.377229 CTGTGGGGCCTAAAACCGA 59.623 57.895 0.84 0.00 0.00 4.69
356 357 2.340328 GCTGTGGGGCCTAAAACCG 61.340 63.158 0.84 0.00 0.00 4.44
357 358 3.694746 GCTGTGGGGCCTAAAACC 58.305 61.111 0.84 0.00 0.00 3.27
366 367 4.421515 CTGGCTCTGGCTGTGGGG 62.422 72.222 0.00 0.00 38.73 4.96
367 368 3.324930 TCTGGCTCTGGCTGTGGG 61.325 66.667 0.00 0.00 38.73 4.61
368 369 2.268280 CTCTGGCTCTGGCTGTGG 59.732 66.667 0.00 0.00 38.73 4.17
369 370 2.436292 GCTCTGGCTCTGGCTGTG 60.436 66.667 0.00 0.00 38.73 3.66
370 371 4.079850 CGCTCTGGCTCTGGCTGT 62.080 66.667 0.00 0.00 38.73 4.40
518 537 2.555547 GCGGGGTCAATGCTATGCC 61.556 63.158 0.00 0.00 0.00 4.40
547 587 1.200839 GCGTCGTTTTCAGTCGTGG 59.799 57.895 0.00 0.00 0.00 4.94
550 590 1.155087 CGTGCGTCGTTTTCAGTCG 60.155 57.895 0.00 0.00 34.52 4.18
587 630 3.914551 TTGGGGGCCATTTTCCCGG 62.915 63.158 4.39 0.00 44.86 5.73
589 632 0.774276 TTTTTGGGGGCCATTTTCCC 59.226 50.000 4.39 5.98 43.15 3.97
592 635 2.224992 GGTGATTTTTGGGGGCCATTTT 60.225 45.455 4.39 0.00 31.53 1.82
593 636 1.354031 GGTGATTTTTGGGGGCCATTT 59.646 47.619 4.39 0.00 31.53 2.32
596 639 1.910772 CGGTGATTTTTGGGGGCCA 60.911 57.895 4.39 0.00 0.00 5.36
601 700 1.933115 CTCCCGCGGTGATTTTTGGG 61.933 60.000 26.12 0.99 38.02 4.12
617 716 3.254024 TTTGGCTCGTGCTCCCTCC 62.254 63.158 9.61 0.00 39.59 4.30
618 717 2.035442 GTTTGGCTCGTGCTCCCTC 61.035 63.158 9.61 0.00 39.59 4.30
619 718 2.032681 GTTTGGCTCGTGCTCCCT 59.967 61.111 9.61 0.00 39.59 4.20
625 724 4.025401 GGGTGCGTTTGGCTCGTG 62.025 66.667 0.00 0.00 44.05 4.35
628 727 3.723348 GTCGGGTGCGTTTGGCTC 61.723 66.667 0.00 0.00 44.05 4.70
632 731 4.973055 TCGGGTCGGGTGCGTTTG 62.973 66.667 0.00 0.00 0.00 2.93
633 732 4.974989 GTCGGGTCGGGTGCGTTT 62.975 66.667 0.00 0.00 0.00 3.60
677 776 4.903010 ACGACACGCACCACCCAC 62.903 66.667 0.00 0.00 0.00 4.61
678 777 4.901123 CACGACACGCACCACCCA 62.901 66.667 0.00 0.00 0.00 4.51
679 778 4.903010 ACACGACACGCACCACCC 62.903 66.667 0.00 0.00 0.00 4.61
680 779 3.636043 CACACGACACGCACCACC 61.636 66.667 0.00 0.00 0.00 4.61
753 868 2.365941 TGGGAATCGGTTTGGGTTTTTC 59.634 45.455 0.00 0.00 0.00 2.29
905 1041 2.642254 TTGCTACTCCCCGTCGGTG 61.642 63.158 11.06 0.00 0.00 4.94
994 1130 1.320344 TTGAGGTCGTCCATCTCGGG 61.320 60.000 0.51 0.00 35.89 5.14
1263 1407 0.179045 CCGGGATGATGGTGAAGACC 60.179 60.000 0.00 0.00 43.48 3.85
1281 1425 0.035439 TCTTCTTGAATGACCCGGCC 60.035 55.000 0.00 0.00 0.00 6.13
1287 1431 3.119352 GGTTGGCCATCTTCTTGAATGAC 60.119 47.826 6.09 0.00 34.09 3.06
1290 1434 3.094572 CTGGTTGGCCATCTTCTTGAAT 58.905 45.455 6.09 0.00 45.05 2.57
1809 1953 3.803082 CGGATGGCGTTGTGCTGG 61.803 66.667 0.00 0.00 45.43 4.85
1905 2049 2.242047 TTTTGTCCATGACGACGGAA 57.758 45.000 0.00 0.00 34.95 4.30
1970 2114 2.888447 GCAGGGTGCCTCTCTGTGT 61.888 63.158 7.53 0.00 45.80 3.72
1976 2120 4.031129 CAGCAGCAGGGTGCCTCT 62.031 66.667 18.77 0.00 46.52 3.69
2460 2610 2.668280 GGCCTTCTCGACAACACGC 61.668 63.158 0.00 0.00 0.00 5.34
2466 2616 0.738975 CATACTCGGCCTTCTCGACA 59.261 55.000 0.00 0.00 32.86 4.35
3103 3254 3.309121 CCTCCATGTACCAAGAACCCAAT 60.309 47.826 0.00 0.00 0.00 3.16
3182 3785 4.853924 AACTATTCCACCACAAAGCAAG 57.146 40.909 0.00 0.00 0.00 4.01
3198 3801 5.760253 CACGATGCTAATCTCCCAAAACTAT 59.240 40.000 0.00 0.00 0.00 2.12
3258 3861 8.713737 TTTCTCTGATAGATGAGTGAAATGTG 57.286 34.615 3.18 0.00 31.81 3.21
3336 3939 7.697352 CATAATTTGCAGAAACAGTCAAACA 57.303 32.000 0.00 0.00 32.17 2.83
3648 4252 4.852388 GAGGCCCCTCTTTTGCTT 57.148 55.556 0.00 0.00 39.80 3.91
3767 4380 5.872617 TCATCGTACCTCCAGTTTTGTAATG 59.127 40.000 0.00 0.00 0.00 1.90
3792 4405 3.181455 TGTTCATGTTGTGAGCTGGTAGT 60.181 43.478 0.00 0.00 38.70 2.73
3835 4495 7.395772 CAGATGGAGATCCTATAGTTTCAGCTA 59.604 40.741 0.00 0.00 36.82 3.32
3865 4525 2.108970 GGAGTTCTTCGGATAGGTGGT 58.891 52.381 0.00 0.00 0.00 4.16
3871 4531 1.397390 GGCCGGGAGTTCTTCGGATA 61.397 60.000 2.18 0.00 45.96 2.59
3904 4564 1.398390 GCAAATGAAGTCTACAGGGCG 59.602 52.381 0.00 0.00 0.00 6.13
3927 4595 2.987821 GGAGCAAAGTTAGTCGAGTGAC 59.012 50.000 7.06 7.06 45.86 3.67
3950 4618 3.561725 CCAGAAACAAGGTCACTGAAGAC 59.438 47.826 0.00 0.00 37.80 3.01
3959 4627 3.319122 ACAAATGAGCCAGAAACAAGGTC 59.681 43.478 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.