Multiple sequence alignment - TraesCS6B01G149000

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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 TraesCS6B01G149000 chr6B 100.000 2745 0 0 1 2745 149772307 149775051 0.000000e+00 5070
1 TraesCS6B01G149000 chr6B 84.615 442 48 14 1215 1642 149611142 149611577 3.270000e-114 422
2 TraesCS6B01G149000 chr6B 84.598 435 47 13 1215 1642 149551450 149551871 5.470000e-112 414
3 TraesCS6B01G149000 chr6B 91.509 212 17 1 1432 1642 149577340 149577551 9.620000e-75 291
4 TraesCS6B01G149000 chr6A 88.131 2199 144 58 424 2561 92053823 92055965 0.000000e+00 2507
5 TraesCS6B01G149000 chr6A 80.392 663 90 28 1001 1642 91924685 91925328 4.140000e-128 468
6 TraesCS6B01G149000 chr6D 90.194 1703 90 38 424 2094 76063791 76065448 0.000000e+00 2148
7 TraesCS6B01G149000 chr6D 84.654 593 41 20 2082 2654 76067284 76067846 1.860000e-151 545
8 TraesCS6B01G149000 chr6D 85.650 446 42 13 1215 1642 76042981 76043422 1.500000e-122 449
9 TraesCS6B01G149000 chr6D 85.520 442 45 12 1215 1642 75991670 75992106 6.980000e-121 444
10 TraesCS6B01G149000 chr6D 83.784 185 19 8 240 422 141974505 141974330 6.080000e-37 165
11 TraesCS6B01G149000 chr6D 83.708 178 23 3 247 424 426106898 426106727 2.190000e-36 163
12 TraesCS6B01G149000 chrUn 84.615 442 48 14 1215 1642 78112293 78111858 3.270000e-114 422
13 TraesCS6B01G149000 chr3A 86.391 169 17 3 254 422 238686371 238686209 2.170000e-41 180
14 TraesCS6B01G149000 chr1B 88.235 153 15 1 269 421 325812695 325812546 2.170000e-41 180
15 TraesCS6B01G149000 chr4D 84.492 187 22 4 236 421 117421172 117421352 7.810000e-41 178
16 TraesCS6B01G149000 chr1D 87.261 157 14 3 254 410 225704946 225704796 1.010000e-39 174
17 TraesCS6B01G149000 chr1D 84.659 176 16 4 253 421 371657549 371657720 6.080000e-37 165
18 TraesCS6B01G149000 chr3B 85.976 164 18 3 260 422 269251992 269252151 1.310000e-38 171
19 TraesCS6B01G149000 chr3D 85.542 166 17 4 245 410 549066961 549066803 1.690000e-37 167


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 TraesCS6B01G149000 chr6B 149772307 149775051 2744 False 5070.0 5070 100.000 1 2745 1 chr6B.!!$F4 2744
1 TraesCS6B01G149000 chr6A 92053823 92055965 2142 False 2507.0 2507 88.131 424 2561 1 chr6A.!!$F2 2137
2 TraesCS6B01G149000 chr6A 91924685 91925328 643 False 468.0 468 80.392 1001 1642 1 chr6A.!!$F1 641
3 TraesCS6B01G149000 chr6D 76063791 76067846 4055 False 1346.5 2148 87.424 424 2654 2 chr6D.!!$F3 2230

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
927 941 0.035739 TTGGCAGGTAACCTTCGACC 59.964 55.0 0.0 0.0 35.83 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2112 0.390735 GGTACGCCCATGAACGAACT 60.391 55.0 13.27 0.0 0.0 3.01 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
20 21 2.344093 ACCCTGGATCCAACTGTAGT 57.656 50.000 17.00 4.17 0.00 2.73
21 22 2.632537 ACCCTGGATCCAACTGTAGTT 58.367 47.619 17.00 0.00 39.12 2.24
44 45 8.766493 GTTGTTTTCGGTAAATAACTTTACGT 57.234 30.769 10.81 0.00 45.07 3.57
45 46 9.220635 GTTGTTTTCGGTAAATAACTTTACGTT 57.779 29.630 10.81 0.00 45.07 3.99
96 97 8.882415 AAAAGAATACAGTAAAACAGTCGAGA 57.118 30.769 0.00 0.00 0.00 4.04
97 98 8.882415 AAAGAATACAGTAAAACAGTCGAGAA 57.118 30.769 0.00 0.00 0.00 2.87
98 99 8.882415 AAGAATACAGTAAAACAGTCGAGAAA 57.118 30.769 0.00 0.00 0.00 2.52
99 100 8.295569 AGAATACAGTAAAACAGTCGAGAAAC 57.704 34.615 0.00 0.00 0.00 2.78
100 101 7.924412 AGAATACAGTAAAACAGTCGAGAAACA 59.076 33.333 0.00 0.00 0.00 2.83
101 102 5.968387 ACAGTAAAACAGTCGAGAAACAG 57.032 39.130 0.00 0.00 0.00 3.16
102 103 5.657474 ACAGTAAAACAGTCGAGAAACAGA 58.343 37.500 0.00 0.00 0.00 3.41
103 104 6.103997 ACAGTAAAACAGTCGAGAAACAGAA 58.896 36.000 0.00 0.00 0.00 3.02
104 105 6.592607 ACAGTAAAACAGTCGAGAAACAGAAA 59.407 34.615 0.00 0.00 0.00 2.52
105 106 6.900299 CAGTAAAACAGTCGAGAAACAGAAAC 59.100 38.462 0.00 0.00 0.00 2.78
106 107 6.817140 AGTAAAACAGTCGAGAAACAGAAACT 59.183 34.615 0.00 0.00 0.00 2.66
107 108 7.977853 AGTAAAACAGTCGAGAAACAGAAACTA 59.022 33.333 0.00 0.00 0.00 2.24
108 109 7.605410 AAAACAGTCGAGAAACAGAAACTAA 57.395 32.000 0.00 0.00 0.00 2.24
109 110 7.605410 AAACAGTCGAGAAACAGAAACTAAA 57.395 32.000 0.00 0.00 0.00 1.85
110 111 7.605410 AACAGTCGAGAAACAGAAACTAAAA 57.395 32.000 0.00 0.00 0.00 1.52
111 112 7.235430 ACAGTCGAGAAACAGAAACTAAAAG 57.765 36.000 0.00 0.00 0.00 2.27
112 113 6.258068 ACAGTCGAGAAACAGAAACTAAAAGG 59.742 38.462 0.00 0.00 0.00 3.11
113 114 6.479001 CAGTCGAGAAACAGAAACTAAAAGGA 59.521 38.462 0.00 0.00 0.00 3.36
114 115 7.011109 CAGTCGAGAAACAGAAACTAAAAGGAA 59.989 37.037 0.00 0.00 0.00 3.36
115 116 7.715686 AGTCGAGAAACAGAAACTAAAAGGAAT 59.284 33.333 0.00 0.00 0.00 3.01
116 117 7.798982 GTCGAGAAACAGAAACTAAAAGGAATG 59.201 37.037 0.00 0.00 0.00 2.67
117 118 7.713507 TCGAGAAACAGAAACTAAAAGGAATGA 59.286 33.333 0.00 0.00 0.00 2.57
118 119 7.798982 CGAGAAACAGAAACTAAAAGGAATGAC 59.201 37.037 0.00 0.00 0.00 3.06
119 120 8.519799 AGAAACAGAAACTAAAAGGAATGACA 57.480 30.769 0.00 0.00 0.00 3.58
120 121 8.966868 AGAAACAGAAACTAAAAGGAATGACAA 58.033 29.630 0.00 0.00 0.00 3.18
121 122 9.581099 GAAACAGAAACTAAAAGGAATGACAAA 57.419 29.630 0.00 0.00 0.00 2.83
122 123 9.936759 AAACAGAAACTAAAAGGAATGACAAAA 57.063 25.926 0.00 0.00 0.00 2.44
123 124 9.936759 AACAGAAACTAAAAGGAATGACAAAAA 57.063 25.926 0.00 0.00 0.00 1.94
124 125 9.586435 ACAGAAACTAAAAGGAATGACAAAAAG 57.414 29.630 0.00 0.00 0.00 2.27
125 126 9.801873 CAGAAACTAAAAGGAATGACAAAAAGA 57.198 29.630 0.00 0.00 0.00 2.52
157 158 9.658799 ATTATCCTAATATTGATGTTCAGTCGG 57.341 33.333 0.00 0.00 0.00 4.79
158 159 6.724893 TCCTAATATTGATGTTCAGTCGGA 57.275 37.500 0.00 0.00 0.00 4.55
159 160 7.303182 TCCTAATATTGATGTTCAGTCGGAT 57.697 36.000 0.00 0.00 0.00 4.18
160 161 7.154656 TCCTAATATTGATGTTCAGTCGGATG 58.845 38.462 0.00 0.00 0.00 3.51
161 162 7.015195 TCCTAATATTGATGTTCAGTCGGATGA 59.985 37.037 0.00 0.00 0.00 2.92
162 163 7.330454 CCTAATATTGATGTTCAGTCGGATGAG 59.670 40.741 0.00 0.00 0.00 2.90
163 164 4.743057 ATTGATGTTCAGTCGGATGAGA 57.257 40.909 0.00 0.00 0.00 3.27
164 165 4.743057 TTGATGTTCAGTCGGATGAGAT 57.257 40.909 0.00 0.00 0.00 2.75
165 166 4.743057 TGATGTTCAGTCGGATGAGATT 57.257 40.909 0.00 0.00 0.00 2.40
166 167 5.089970 TGATGTTCAGTCGGATGAGATTT 57.910 39.130 0.00 0.00 0.00 2.17
167 168 5.491070 TGATGTTCAGTCGGATGAGATTTT 58.509 37.500 0.00 0.00 0.00 1.82
168 169 6.639563 TGATGTTCAGTCGGATGAGATTTTA 58.360 36.000 0.00 0.00 0.00 1.52
169 170 6.758416 TGATGTTCAGTCGGATGAGATTTTAG 59.242 38.462 0.00 0.00 0.00 1.85
170 171 6.037786 TGTTCAGTCGGATGAGATTTTAGT 57.962 37.500 0.00 0.00 0.00 2.24
171 172 6.464222 TGTTCAGTCGGATGAGATTTTAGTT 58.536 36.000 0.00 0.00 0.00 2.24
172 173 7.608153 TGTTCAGTCGGATGAGATTTTAGTTA 58.392 34.615 0.00 0.00 0.00 2.24
173 174 8.092068 TGTTCAGTCGGATGAGATTTTAGTTAA 58.908 33.333 0.00 0.00 0.00 2.01
174 175 8.381387 GTTCAGTCGGATGAGATTTTAGTTAAC 58.619 37.037 0.00 0.00 0.00 2.01
175 176 7.837863 TCAGTCGGATGAGATTTTAGTTAACT 58.162 34.615 13.68 13.68 0.00 2.24
176 177 7.974501 TCAGTCGGATGAGATTTTAGTTAACTC 59.025 37.037 12.39 0.00 0.00 3.01
177 178 7.976734 CAGTCGGATGAGATTTTAGTTAACTCT 59.023 37.037 12.39 2.41 0.00 3.24
178 179 8.192110 AGTCGGATGAGATTTTAGTTAACTCTC 58.808 37.037 12.39 12.50 40.89 3.20
192 193 7.639113 AGTTAACTCTCATCTAGACAAGAGG 57.361 40.000 25.81 15.76 39.64 3.69
193 194 7.179269 AGTTAACTCTCATCTAGACAAGAGGT 58.821 38.462 25.81 23.70 39.64 3.85
194 195 8.330247 AGTTAACTCTCATCTAGACAAGAGGTA 58.670 37.037 25.81 22.94 39.64 3.08
195 196 8.617809 GTTAACTCTCATCTAGACAAGAGGTAG 58.382 40.741 25.81 16.04 38.79 3.18
196 197 6.321821 ACTCTCATCTAGACAAGAGGTAGT 57.678 41.667 25.81 16.48 39.64 2.73
197 198 6.354130 ACTCTCATCTAGACAAGAGGTAGTC 58.646 44.000 25.81 0.00 39.64 2.59
198 199 6.069905 ACTCTCATCTAGACAAGAGGTAGTCA 60.070 42.308 25.81 6.70 39.64 3.41
199 200 6.905736 TCTCATCTAGACAAGAGGTAGTCAT 58.094 40.000 15.01 0.00 37.74 3.06
200 201 8.035448 TCTCATCTAGACAAGAGGTAGTCATA 57.965 38.462 15.01 0.00 37.74 2.15
201 202 7.934665 TCTCATCTAGACAAGAGGTAGTCATAC 59.065 40.741 15.01 0.00 37.74 2.39
263 264 7.801716 TTTTCAATTGATTATACTCCCTCCG 57.198 36.000 9.40 0.00 0.00 4.63
264 265 4.894784 TCAATTGATTATACTCCCTCCGC 58.105 43.478 3.38 0.00 0.00 5.54
265 266 4.593206 TCAATTGATTATACTCCCTCCGCT 59.407 41.667 3.38 0.00 0.00 5.52
266 267 4.810191 ATTGATTATACTCCCTCCGCTC 57.190 45.455 0.00 0.00 0.00 5.03
267 268 2.526432 TGATTATACTCCCTCCGCTCC 58.474 52.381 0.00 0.00 0.00 4.70
268 269 2.110188 TGATTATACTCCCTCCGCTCCT 59.890 50.000 0.00 0.00 0.00 3.69
269 270 2.289592 TTATACTCCCTCCGCTCCTC 57.710 55.000 0.00 0.00 0.00 3.71
270 271 0.404812 TATACTCCCTCCGCTCCTCC 59.595 60.000 0.00 0.00 0.00 4.30
271 272 1.365105 ATACTCCCTCCGCTCCTCCT 61.365 60.000 0.00 0.00 0.00 3.69
272 273 0.696826 TACTCCCTCCGCTCCTCCTA 60.697 60.000 0.00 0.00 0.00 2.94
273 274 1.230497 CTCCCTCCGCTCCTCCTAA 59.770 63.158 0.00 0.00 0.00 2.69
274 275 0.397254 CTCCCTCCGCTCCTCCTAAA 60.397 60.000 0.00 0.00 0.00 1.85
275 276 0.264955 TCCCTCCGCTCCTCCTAAAT 59.735 55.000 0.00 0.00 0.00 1.40
276 277 1.502039 TCCCTCCGCTCCTCCTAAATA 59.498 52.381 0.00 0.00 0.00 1.40
277 278 2.111972 TCCCTCCGCTCCTCCTAAATAT 59.888 50.000 0.00 0.00 0.00 1.28
278 279 3.335786 TCCCTCCGCTCCTCCTAAATATA 59.664 47.826 0.00 0.00 0.00 0.86
279 280 4.094476 CCCTCCGCTCCTCCTAAATATAA 58.906 47.826 0.00 0.00 0.00 0.98
280 281 4.160626 CCCTCCGCTCCTCCTAAATATAAG 59.839 50.000 0.00 0.00 0.00 1.73
281 282 4.773149 CCTCCGCTCCTCCTAAATATAAGT 59.227 45.833 0.00 0.00 0.00 2.24
282 283 5.105675 CCTCCGCTCCTCCTAAATATAAGTC 60.106 48.000 0.00 0.00 0.00 3.01
283 284 5.642165 TCCGCTCCTCCTAAATATAAGTCT 58.358 41.667 0.00 0.00 0.00 3.24
284 285 6.075984 TCCGCTCCTCCTAAATATAAGTCTT 58.924 40.000 0.00 0.00 0.00 3.01
285 286 6.553852 TCCGCTCCTCCTAAATATAAGTCTTT 59.446 38.462 0.00 0.00 0.00 2.52
286 287 7.070821 TCCGCTCCTCCTAAATATAAGTCTTTT 59.929 37.037 0.00 0.00 0.00 2.27
287 288 7.715686 CCGCTCCTCCTAAATATAAGTCTTTTT 59.284 37.037 0.00 0.00 0.00 1.94
317 318 9.179909 AGAGATTCCACTATGAACTATATACGG 57.820 37.037 0.00 0.00 0.00 4.02
318 319 9.175312 GAGATTCCACTATGAACTATATACGGA 57.825 37.037 0.00 0.00 0.00 4.69
319 320 9.179909 AGATTCCACTATGAACTATATACGGAG 57.820 37.037 0.00 0.00 0.00 4.63
320 321 6.754702 TCCACTATGAACTATATACGGAGC 57.245 41.667 0.00 0.00 0.00 4.70
321 322 6.243148 TCCACTATGAACTATATACGGAGCA 58.757 40.000 0.00 0.00 0.00 4.26
322 323 6.717997 TCCACTATGAACTATATACGGAGCAA 59.282 38.462 0.00 0.00 0.00 3.91
323 324 7.231925 TCCACTATGAACTATATACGGAGCAAA 59.768 37.037 0.00 0.00 0.00 3.68
324 325 7.870954 CCACTATGAACTATATACGGAGCAAAA 59.129 37.037 0.00 0.00 0.00 2.44
325 326 9.424319 CACTATGAACTATATACGGAGCAAAAT 57.576 33.333 0.00 0.00 0.00 1.82
326 327 9.424319 ACTATGAACTATATACGGAGCAAAATG 57.576 33.333 0.00 0.00 0.00 2.32
327 328 9.639601 CTATGAACTATATACGGAGCAAAATGA 57.360 33.333 0.00 0.00 0.00 2.57
328 329 7.946655 TGAACTATATACGGAGCAAAATGAG 57.053 36.000 0.00 0.00 0.00 2.90
329 330 7.497595 TGAACTATATACGGAGCAAAATGAGT 58.502 34.615 0.00 0.00 0.00 3.41
330 331 8.635328 TGAACTATATACGGAGCAAAATGAGTA 58.365 33.333 0.00 0.00 0.00 2.59
331 332 9.472361 GAACTATATACGGAGCAAAATGAGTAA 57.528 33.333 0.00 0.00 0.00 2.24
332 333 9.826574 AACTATATACGGAGCAAAATGAGTAAA 57.173 29.630 0.00 0.00 0.00 2.01
333 334 9.998106 ACTATATACGGAGCAAAATGAGTAAAT 57.002 29.630 0.00 0.00 0.00 1.40
337 338 6.663944 ACGGAGCAAAATGAGTAAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
338 339 6.170506 ACGGAGCAAAATGAGTAAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
339 340 6.092259 ACGGAGCAAAATGAGTAAATCTACAC 59.908 38.462 0.00 0.00 0.00 2.90
340 341 6.313905 CGGAGCAAAATGAGTAAATCTACACT 59.686 38.462 0.00 0.00 0.00 3.55
341 342 7.464710 CGGAGCAAAATGAGTAAATCTACACTC 60.465 40.741 0.00 0.00 41.31 3.51
342 343 7.550906 GGAGCAAAATGAGTAAATCTACACTCT 59.449 37.037 3.65 0.00 41.46 3.24
343 344 9.587772 GAGCAAAATGAGTAAATCTACACTCTA 57.412 33.333 3.65 0.00 41.46 2.43
344 345 9.944376 AGCAAAATGAGTAAATCTACACTCTAA 57.056 29.630 3.65 0.00 41.46 2.10
351 352 9.224267 TGAGTAAATCTACACTCTAAACTACGT 57.776 33.333 0.00 0.00 41.46 3.57
444 445 6.930667 TTAGTTAATTTATTCCTGCCCGAC 57.069 37.500 0.00 0.00 0.00 4.79
475 476 3.708451 TCACTACTTCCTACATGCAGGA 58.292 45.455 10.89 10.89 43.17 3.86
580 585 1.134175 AGCAGTTTTTGACCGTGTTGG 59.866 47.619 0.00 0.00 46.41 3.77
606 611 3.921767 TTGCGAGCGAGCCTGACAG 62.922 63.158 0.00 0.00 36.02 3.51
608 613 4.426112 CGAGCGAGCCTGACAGCA 62.426 66.667 0.00 0.00 34.23 4.41
609 614 2.508887 GAGCGAGCCTGACAGCAG 60.509 66.667 0.00 0.00 41.93 4.24
610 615 2.993840 AGCGAGCCTGACAGCAGA 60.994 61.111 0.00 0.00 45.17 4.26
611 616 2.508887 GCGAGCCTGACAGCAGAG 60.509 66.667 0.00 0.00 45.17 3.35
613 618 2.346541 CGAGCCTGACAGCAGAGGA 61.347 63.158 0.00 0.00 45.17 3.71
614 619 1.516892 GAGCCTGACAGCAGAGGAG 59.483 63.158 0.00 0.00 45.17 3.69
640 646 7.088905 AGTCTACCAGTGAAGTAATTACAACG 58.911 38.462 17.65 8.79 0.00 4.10
657 663 5.493133 ACAACGAAAACTGTCATGCTAAA 57.507 34.783 0.00 0.00 0.00 1.85
658 664 6.072112 ACAACGAAAACTGTCATGCTAAAT 57.928 33.333 0.00 0.00 0.00 1.40
659 665 7.197071 ACAACGAAAACTGTCATGCTAAATA 57.803 32.000 0.00 0.00 0.00 1.40
660 666 7.816640 ACAACGAAAACTGTCATGCTAAATAT 58.183 30.769 0.00 0.00 0.00 1.28
706 715 1.782569 TCGTAAGCGTTTGTTCACGAG 59.217 47.619 3.99 0.00 43.15 4.18
785 794 3.850273 CGAAGTAAACCTACGCAGTACTG 59.150 47.826 18.93 18.93 45.11 2.74
907 917 3.519370 AACCCCTACCATCCTAGGAAA 57.481 47.619 17.30 0.85 36.10 3.13
916 930 2.091665 CCATCCTAGGAAATTGGCAGGT 60.092 50.000 17.30 0.00 0.00 4.00
926 940 2.109425 ATTGGCAGGTAACCTTCGAC 57.891 50.000 0.00 0.00 37.17 4.20
927 941 0.035739 TTGGCAGGTAACCTTCGACC 59.964 55.000 0.00 0.00 35.83 4.79
929 943 0.108281 GGCAGGTAACCTTCGACCTC 60.108 60.000 0.00 0.00 44.54 3.85
930 944 0.896226 GCAGGTAACCTTCGACCTCT 59.104 55.000 0.00 0.00 44.54 3.69
931 945 1.135053 GCAGGTAACCTTCGACCTCTC 60.135 57.143 0.00 0.00 44.54 3.20
932 946 2.448453 CAGGTAACCTTCGACCTCTCT 58.552 52.381 0.00 0.00 44.54 3.10
933 947 2.424246 CAGGTAACCTTCGACCTCTCTC 59.576 54.545 0.00 0.00 44.54 3.20
934 948 2.309458 AGGTAACCTTCGACCTCTCTCT 59.691 50.000 0.00 0.00 42.69 3.10
935 949 2.684374 GGTAACCTTCGACCTCTCTCTC 59.316 54.545 0.00 0.00 32.58 3.20
936 950 2.891191 AACCTTCGACCTCTCTCTCT 57.109 50.000 0.00 0.00 0.00 3.10
937 951 2.891191 ACCTTCGACCTCTCTCTCTT 57.109 50.000 0.00 0.00 0.00 2.85
938 952 3.163616 ACCTTCGACCTCTCTCTCTTT 57.836 47.619 0.00 0.00 0.00 2.52
939 953 3.086282 ACCTTCGACCTCTCTCTCTTTC 58.914 50.000 0.00 0.00 0.00 2.62
962 986 3.120165 TCGAGTCTCGATCAACACAAGAG 60.120 47.826 20.85 0.00 44.82 2.85
963 987 3.120165 CGAGTCTCGATCAACACAAGAGA 60.120 47.826 17.52 0.00 43.74 3.10
964 988 4.411327 GAGTCTCGATCAACACAAGAGAG 58.589 47.826 0.00 0.00 38.46 3.20
976 1000 4.338879 ACACAAGAGAGCCAGCAAATTAT 58.661 39.130 0.00 0.00 0.00 1.28
987 1011 3.242739 CCAGCAAATTATCTTCGGGTTCG 60.243 47.826 0.00 0.00 37.82 3.95
989 1013 3.374058 AGCAAATTATCTTCGGGTTCGTG 59.626 43.478 0.00 0.00 37.69 4.35
1020 1050 3.318275 TCATGTCTAGCCTTACGACCATC 59.682 47.826 0.00 0.00 0.00 3.51
1043 1073 4.473520 CGGCGCCATGGAGGAGTT 62.474 66.667 28.98 0.00 41.22 3.01
1194 1236 1.070786 GGGACAAGAGAACGGTGCA 59.929 57.895 0.00 0.00 0.00 4.57
1226 1268 3.273434 CTGCTACTTCAAGGCAGCATAA 58.727 45.455 14.43 0.00 45.04 1.90
1248 1290 3.842925 GAGGGCCAAGACGGTGCAA 62.843 63.158 6.18 0.00 36.97 4.08
1249 1291 2.909965 GGGCCAAGACGGTGCAAA 60.910 61.111 4.39 0.00 36.97 3.68
1313 1367 0.608640 GGGACGAGGAAGAAGCTCAA 59.391 55.000 0.00 0.00 0.00 3.02
1392 1451 3.558829 TCTCTCACGTACGTCCATACATC 59.441 47.826 19.94 0.00 0.00 3.06
1449 1511 4.508662 AGAAGATTCTGACCGGATTGTTC 58.491 43.478 9.46 0.00 35.89 3.18
1650 1712 4.544689 CGCCGAGACGCTCTCCTG 62.545 72.222 8.73 3.45 40.34 3.86
1684 1746 2.685017 TCCAGGCTCACGATGGCT 60.685 61.111 0.00 0.00 41.11 4.75
1713 1775 1.835483 GCTGTGTGTTCGTCCTGCAG 61.835 60.000 6.78 6.78 0.00 4.41
1773 1835 1.734748 GGGAGACTACTACTGCCGC 59.265 63.158 0.00 0.00 36.27 6.53
1775 1837 1.734748 GAGACTACTACTGCCGCCC 59.265 63.158 0.00 0.00 0.00 6.13
1776 1838 0.752376 GAGACTACTACTGCCGCCCT 60.752 60.000 0.00 0.00 0.00 5.19
1777 1839 0.549950 AGACTACTACTGCCGCCCTA 59.450 55.000 0.00 0.00 0.00 3.53
1787 1855 0.395586 TGCCGCCCTAGAAATGCATT 60.396 50.000 5.99 5.99 0.00 3.56
1846 1915 7.221450 AGTCAGTTAGCTTTATGTTTGGTACA 58.779 34.615 0.00 0.00 41.97 2.90
1862 1931 1.945394 GTACATGCATGAGCTTCAGGG 59.055 52.381 32.75 2.55 42.74 4.45
1870 1939 2.550830 TGAGCTTCAGGGAACAAGAC 57.449 50.000 0.00 0.00 0.00 3.01
1879 1948 6.072893 GCTTCAGGGAACAAGACGTTTATAAA 60.073 38.462 0.00 0.00 38.19 1.40
1880 1949 7.361799 GCTTCAGGGAACAAGACGTTTATAAAT 60.362 37.037 0.31 0.00 38.19 1.40
1881 1950 7.989416 TCAGGGAACAAGACGTTTATAAATT 57.011 32.000 0.31 0.00 38.19 1.82
1882 1951 9.504708 TTCAGGGAACAAGACGTTTATAAATTA 57.495 29.630 0.31 0.00 38.19 1.40
1883 1952 9.675464 TCAGGGAACAAGACGTTTATAAATTAT 57.325 29.630 0.31 0.00 38.19 1.28
1961 2036 8.276252 TGTTTAAGGAGCAAAATATCTACACC 57.724 34.615 0.00 0.00 0.00 4.16
1963 2038 9.609346 GTTTAAGGAGCAAAATATCTACACCTA 57.391 33.333 0.00 0.00 0.00 3.08
2000 2075 3.084988 CGATAACTATCTGACGATCGCG 58.915 50.000 16.60 0.00 44.79 5.87
2042 2118 3.300032 TCCAGCCAGGATAGTTCGT 57.700 52.632 0.00 0.00 43.07 3.85
2046 2122 2.158900 CCAGCCAGGATAGTTCGTTCAT 60.159 50.000 0.00 0.00 41.22 2.57
2049 2125 2.838736 CCAGGATAGTTCGTTCATGGG 58.161 52.381 0.00 0.00 39.52 4.00
2080 2159 4.345286 AGGTCCCCTCAGCTGCCT 62.345 66.667 9.47 5.59 0.00 4.75
2096 4023 2.659016 CTGGGAGCAGAGCGACAA 59.341 61.111 0.00 0.00 0.00 3.18
2110 4037 1.303643 GACAAGGGCCAGGTCCAAG 60.304 63.158 14.32 6.55 0.00 3.61
2331 4260 5.260027 ACAAGTTCGCGTATAACAAAGAC 57.740 39.130 5.77 0.00 0.00 3.01
2336 4265 6.717413 AGTTCGCGTATAACAAAGACAAAAA 58.283 32.000 5.77 0.00 0.00 1.94
2337 4266 6.849305 AGTTCGCGTATAACAAAGACAAAAAG 59.151 34.615 5.77 0.00 0.00 2.27
2391 4323 1.926510 GACCATAAAAATGCCGCTTGC 59.073 47.619 0.00 0.00 41.77 4.01
2404 4337 2.878406 GCCGCTTGCTGGATAGAAAATA 59.122 45.455 7.46 0.00 36.87 1.40
2482 4419 9.244799 GTCGATAGTTTTGTTCTTTGGAAAATT 57.755 29.630 0.00 0.00 32.95 1.82
2550 4499 8.797266 ATTTCCTAAAAATCAACGTCAAAGAC 57.203 30.769 0.00 0.00 0.00 3.01
2553 4502 8.610248 TCCTAAAAATCAACGTCAAAGACATA 57.390 30.769 0.00 0.00 32.09 2.29
2554 4503 8.717821 TCCTAAAAATCAACGTCAAAGACATAG 58.282 33.333 0.00 0.00 32.09 2.23
2555 4504 8.504005 CCTAAAAATCAACGTCAAAGACATAGT 58.496 33.333 0.00 0.00 32.09 2.12
2594 4543 5.897377 AGTAGTGGCATGGTGAAATTTAC 57.103 39.130 0.00 0.00 0.00 2.01
2596 4545 3.153919 AGTGGCATGGTGAAATTTACGT 58.846 40.909 0.00 0.00 0.00 3.57
2599 4548 2.490115 GGCATGGTGAAATTTACGTGGA 59.510 45.455 0.00 0.00 0.00 4.02
2600 4549 3.057174 GGCATGGTGAAATTTACGTGGAA 60.057 43.478 0.00 0.00 0.00 3.53
2601 4550 4.551388 GCATGGTGAAATTTACGTGGAAA 58.449 39.130 0.00 0.00 0.00 3.13
2618 4571 5.464168 GTGGAAATGTTCTCCAGAAACATG 58.536 41.667 2.53 0.00 43.68 3.21
2619 4572 5.010012 GTGGAAATGTTCTCCAGAAACATGT 59.990 40.000 0.00 0.00 43.68 3.21
2621 4574 5.241506 GGAAATGTTCTCCAGAAACATGTCA 59.758 40.000 16.75 0.00 34.79 3.58
2632 4585 6.811170 TCCAGAAACATGTCAAAGTTTGAAAC 59.189 34.615 19.63 9.85 42.15 2.78
2723 4676 5.981088 ATTTTTGTGATAGTGACATGGCA 57.019 34.783 0.00 0.00 0.00 4.92
2724 4677 5.781210 TTTTTGTGATAGTGACATGGCAA 57.219 34.783 0.58 0.00 0.00 4.52
2725 4678 5.781210 TTTTGTGATAGTGACATGGCAAA 57.219 34.783 0.58 0.00 0.00 3.68
2726 4679 5.981088 TTTGTGATAGTGACATGGCAAAT 57.019 34.783 0.58 0.00 0.00 2.32
2727 4680 5.981088 TTGTGATAGTGACATGGCAAATT 57.019 34.783 0.58 0.00 0.00 1.82
2728 4681 5.313520 TGTGATAGTGACATGGCAAATTG 57.686 39.130 0.58 0.00 0.00 2.32
2729 4682 5.008980 TGTGATAGTGACATGGCAAATTGA 58.991 37.500 0.58 0.00 0.00 2.57
2730 4683 5.124297 TGTGATAGTGACATGGCAAATTGAG 59.876 40.000 0.58 0.00 0.00 3.02
2731 4684 4.641541 TGATAGTGACATGGCAAATTGAGG 59.358 41.667 0.58 0.00 0.00 3.86
2732 4685 2.173519 AGTGACATGGCAAATTGAGGG 58.826 47.619 0.58 0.00 0.00 4.30
2733 4686 1.205417 GTGACATGGCAAATTGAGGGG 59.795 52.381 0.58 0.00 0.00 4.79
2734 4687 0.826062 GACATGGCAAATTGAGGGGG 59.174 55.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.484953 ACTACAGTTGGATCCAGGGTA 57.515 47.619 15.53 16.22 0.00 3.69
1 2 2.344093 ACTACAGTTGGATCCAGGGT 57.656 50.000 15.53 15.96 0.00 4.34
12 13 9.112725 AGTTATTTACCGAAAACAACTACAGTT 57.887 29.630 5.43 0.00 34.54 3.16
13 14 8.667076 AGTTATTTACCGAAAACAACTACAGT 57.333 30.769 5.43 0.00 34.54 3.55
14 15 9.940166 AAAGTTATTTACCGAAAACAACTACAG 57.060 29.630 7.13 0.00 34.91 2.74
18 19 8.611757 ACGTAAAGTTATTTACCGAAAACAACT 58.388 29.630 5.54 2.28 45.31 3.16
19 20 8.766493 ACGTAAAGTTATTTACCGAAAACAAC 57.234 30.769 5.54 0.00 45.31 3.32
70 71 9.321562 TCTCGACTGTTTTACTGTATTCTTTTT 57.678 29.630 0.00 0.00 30.17 1.94
71 72 8.882415 TCTCGACTGTTTTACTGTATTCTTTT 57.118 30.769 0.00 0.00 30.17 2.27
72 73 8.882415 TTCTCGACTGTTTTACTGTATTCTTT 57.118 30.769 0.00 0.00 30.17 2.52
73 74 8.762426 GTTTCTCGACTGTTTTACTGTATTCTT 58.238 33.333 0.00 0.00 30.17 2.52
74 75 7.924412 TGTTTCTCGACTGTTTTACTGTATTCT 59.076 33.333 0.00 0.00 30.17 2.40
75 76 8.068893 TGTTTCTCGACTGTTTTACTGTATTC 57.931 34.615 0.00 0.00 30.17 1.75
76 77 7.924412 TCTGTTTCTCGACTGTTTTACTGTATT 59.076 33.333 0.00 0.00 30.17 1.89
77 78 7.431249 TCTGTTTCTCGACTGTTTTACTGTAT 58.569 34.615 0.00 0.00 30.17 2.29
78 79 6.798482 TCTGTTTCTCGACTGTTTTACTGTA 58.202 36.000 0.00 0.00 30.17 2.74
79 80 5.657474 TCTGTTTCTCGACTGTTTTACTGT 58.343 37.500 0.00 0.00 32.79 3.55
80 81 6.583912 TTCTGTTTCTCGACTGTTTTACTG 57.416 37.500 0.00 0.00 0.00 2.74
81 82 6.817140 AGTTTCTGTTTCTCGACTGTTTTACT 59.183 34.615 0.00 0.00 0.00 2.24
82 83 7.001695 AGTTTCTGTTTCTCGACTGTTTTAC 57.998 36.000 0.00 0.00 0.00 2.01
83 84 8.706492 TTAGTTTCTGTTTCTCGACTGTTTTA 57.294 30.769 0.00 0.00 0.00 1.52
84 85 7.605410 TTAGTTTCTGTTTCTCGACTGTTTT 57.395 32.000 0.00 0.00 0.00 2.43
85 86 7.605410 TTTAGTTTCTGTTTCTCGACTGTTT 57.395 32.000 0.00 0.00 0.00 2.83
86 87 7.201617 CCTTTTAGTTTCTGTTTCTCGACTGTT 60.202 37.037 0.00 0.00 0.00 3.16
87 88 6.258068 CCTTTTAGTTTCTGTTTCTCGACTGT 59.742 38.462 0.00 0.00 0.00 3.55
88 89 6.479001 TCCTTTTAGTTTCTGTTTCTCGACTG 59.521 38.462 0.00 0.00 0.00 3.51
89 90 6.579865 TCCTTTTAGTTTCTGTTTCTCGACT 58.420 36.000 0.00 0.00 0.00 4.18
90 91 6.839820 TCCTTTTAGTTTCTGTTTCTCGAC 57.160 37.500 0.00 0.00 0.00 4.20
91 92 7.713507 TCATTCCTTTTAGTTTCTGTTTCTCGA 59.286 33.333 0.00 0.00 0.00 4.04
92 93 7.798982 GTCATTCCTTTTAGTTTCTGTTTCTCG 59.201 37.037 0.00 0.00 0.00 4.04
93 94 8.621286 TGTCATTCCTTTTAGTTTCTGTTTCTC 58.379 33.333 0.00 0.00 0.00 2.87
94 95 8.519799 TGTCATTCCTTTTAGTTTCTGTTTCT 57.480 30.769 0.00 0.00 0.00 2.52
95 96 9.581099 TTTGTCATTCCTTTTAGTTTCTGTTTC 57.419 29.630 0.00 0.00 0.00 2.78
96 97 9.936759 TTTTGTCATTCCTTTTAGTTTCTGTTT 57.063 25.926 0.00 0.00 0.00 2.83
97 98 9.936759 TTTTTGTCATTCCTTTTAGTTTCTGTT 57.063 25.926 0.00 0.00 0.00 3.16
98 99 9.586435 CTTTTTGTCATTCCTTTTAGTTTCTGT 57.414 29.630 0.00 0.00 0.00 3.41
99 100 9.801873 TCTTTTTGTCATTCCTTTTAGTTTCTG 57.198 29.630 0.00 0.00 0.00 3.02
131 132 9.658799 CCGACTGAACATCAATATTAGGATAAT 57.341 33.333 0.00 0.00 0.00 1.28
132 133 8.866093 TCCGACTGAACATCAATATTAGGATAA 58.134 33.333 0.00 0.00 0.00 1.75
133 134 8.417273 TCCGACTGAACATCAATATTAGGATA 57.583 34.615 0.00 0.00 0.00 2.59
134 135 7.303182 TCCGACTGAACATCAATATTAGGAT 57.697 36.000 0.00 0.00 0.00 3.24
135 136 6.724893 TCCGACTGAACATCAATATTAGGA 57.275 37.500 0.00 0.00 0.00 2.94
136 137 7.154656 TCATCCGACTGAACATCAATATTAGG 58.845 38.462 0.00 0.00 0.00 2.69
137 138 8.084684 TCTCATCCGACTGAACATCAATATTAG 58.915 37.037 0.00 0.00 0.00 1.73
138 139 7.951591 TCTCATCCGACTGAACATCAATATTA 58.048 34.615 0.00 0.00 0.00 0.98
139 140 6.820335 TCTCATCCGACTGAACATCAATATT 58.180 36.000 0.00 0.00 0.00 1.28
140 141 6.410942 TCTCATCCGACTGAACATCAATAT 57.589 37.500 0.00 0.00 0.00 1.28
141 142 5.852282 TCTCATCCGACTGAACATCAATA 57.148 39.130 0.00 0.00 0.00 1.90
142 143 4.743057 TCTCATCCGACTGAACATCAAT 57.257 40.909 0.00 0.00 0.00 2.57
143 144 4.743057 ATCTCATCCGACTGAACATCAA 57.257 40.909 0.00 0.00 0.00 2.57
144 145 4.743057 AATCTCATCCGACTGAACATCA 57.257 40.909 0.00 0.00 0.00 3.07
145 146 6.758886 ACTAAAATCTCATCCGACTGAACATC 59.241 38.462 0.00 0.00 0.00 3.06
146 147 6.644347 ACTAAAATCTCATCCGACTGAACAT 58.356 36.000 0.00 0.00 0.00 2.71
147 148 6.037786 ACTAAAATCTCATCCGACTGAACA 57.962 37.500 0.00 0.00 0.00 3.18
148 149 6.969828 AACTAAAATCTCATCCGACTGAAC 57.030 37.500 0.00 0.00 0.00 3.18
149 150 8.311836 AGTTAACTAAAATCTCATCCGACTGAA 58.688 33.333 6.26 0.00 0.00 3.02
150 151 7.837863 AGTTAACTAAAATCTCATCCGACTGA 58.162 34.615 6.26 0.00 0.00 3.41
151 152 7.976734 AGAGTTAACTAAAATCTCATCCGACTG 59.023 37.037 8.42 0.00 38.05 3.51
152 153 8.068892 AGAGTTAACTAAAATCTCATCCGACT 57.931 34.615 8.42 0.00 38.05 4.18
166 167 9.179909 CCTCTTGTCTAGATGAGAGTTAACTAA 57.820 37.037 23.13 0.00 35.08 2.24
167 168 8.330247 ACCTCTTGTCTAGATGAGAGTTAACTA 58.670 37.037 23.13 0.00 35.08 2.24
168 169 7.179269 ACCTCTTGTCTAGATGAGAGTTAACT 58.821 38.462 23.13 8.13 35.08 2.24
169 170 7.399245 ACCTCTTGTCTAGATGAGAGTTAAC 57.601 40.000 23.13 0.00 35.08 2.01
170 171 8.330247 ACTACCTCTTGTCTAGATGAGAGTTAA 58.670 37.037 23.13 13.17 35.08 2.01
171 172 7.863722 ACTACCTCTTGTCTAGATGAGAGTTA 58.136 38.462 23.13 16.86 35.08 2.24
172 173 6.727394 ACTACCTCTTGTCTAGATGAGAGTT 58.273 40.000 23.13 16.70 35.08 3.01
173 174 6.069905 TGACTACCTCTTGTCTAGATGAGAGT 60.070 42.308 23.13 17.07 35.08 3.24
174 175 6.353323 TGACTACCTCTTGTCTAGATGAGAG 58.647 44.000 20.36 20.36 33.72 3.20
175 176 6.314899 TGACTACCTCTTGTCTAGATGAGA 57.685 41.667 16.78 12.42 34.57 3.27
176 177 7.174253 GGTATGACTACCTCTTGTCTAGATGAG 59.826 44.444 0.00 4.69 43.62 2.90
177 178 6.999272 GGTATGACTACCTCTTGTCTAGATGA 59.001 42.308 0.00 0.00 43.62 2.92
178 179 7.209471 GGTATGACTACCTCTTGTCTAGATG 57.791 44.000 0.00 0.00 43.62 2.90
238 239 7.201785 GCGGAGGGAGTATAATCAATTGAAAAA 60.202 37.037 13.09 1.13 0.00 1.94
239 240 6.262273 GCGGAGGGAGTATAATCAATTGAAAA 59.738 38.462 13.09 3.82 0.00 2.29
240 241 5.763204 GCGGAGGGAGTATAATCAATTGAAA 59.237 40.000 13.09 4.21 0.00 2.69
241 242 5.071788 AGCGGAGGGAGTATAATCAATTGAA 59.928 40.000 13.09 0.00 0.00 2.69
242 243 4.593206 AGCGGAGGGAGTATAATCAATTGA 59.407 41.667 11.26 11.26 0.00 2.57
243 244 4.899502 AGCGGAGGGAGTATAATCAATTG 58.100 43.478 0.00 0.00 0.00 2.32
244 245 4.020128 GGAGCGGAGGGAGTATAATCAATT 60.020 45.833 2.18 0.00 0.00 2.32
245 246 3.515901 GGAGCGGAGGGAGTATAATCAAT 59.484 47.826 2.18 0.00 0.00 2.57
246 247 2.897969 GGAGCGGAGGGAGTATAATCAA 59.102 50.000 2.18 0.00 0.00 2.57
247 248 2.110188 AGGAGCGGAGGGAGTATAATCA 59.890 50.000 2.18 0.00 0.00 2.57
248 249 2.756207 GAGGAGCGGAGGGAGTATAATC 59.244 54.545 0.00 0.00 0.00 1.75
249 250 2.557901 GGAGGAGCGGAGGGAGTATAAT 60.558 54.545 0.00 0.00 0.00 1.28
250 251 1.203025 GGAGGAGCGGAGGGAGTATAA 60.203 57.143 0.00 0.00 0.00 0.98
251 252 0.404812 GGAGGAGCGGAGGGAGTATA 59.595 60.000 0.00 0.00 0.00 1.47
252 253 1.154221 GGAGGAGCGGAGGGAGTAT 59.846 63.158 0.00 0.00 0.00 2.12
253 254 0.696826 TAGGAGGAGCGGAGGGAGTA 60.697 60.000 0.00 0.00 0.00 2.59
254 255 1.581923 TTAGGAGGAGCGGAGGGAGT 61.582 60.000 0.00 0.00 0.00 3.85
255 256 0.397254 TTTAGGAGGAGCGGAGGGAG 60.397 60.000 0.00 0.00 0.00 4.30
256 257 0.264955 ATTTAGGAGGAGCGGAGGGA 59.735 55.000 0.00 0.00 0.00 4.20
257 258 2.011122 TATTTAGGAGGAGCGGAGGG 57.989 55.000 0.00 0.00 0.00 4.30
258 259 4.773149 ACTTATATTTAGGAGGAGCGGAGG 59.227 45.833 0.00 0.00 0.00 4.30
259 260 5.712917 AGACTTATATTTAGGAGGAGCGGAG 59.287 44.000 0.00 0.00 0.00 4.63
260 261 5.642165 AGACTTATATTTAGGAGGAGCGGA 58.358 41.667 0.00 0.00 0.00 5.54
261 262 5.986501 AGACTTATATTTAGGAGGAGCGG 57.013 43.478 0.00 0.00 0.00 5.52
262 263 8.664211 AAAAAGACTTATATTTAGGAGGAGCG 57.336 34.615 0.00 0.00 0.00 5.03
291 292 9.179909 CCGTATATAGTTCATAGTGGAATCTCT 57.820 37.037 0.00 0.00 0.00 3.10
292 293 9.175312 TCCGTATATAGTTCATAGTGGAATCTC 57.825 37.037 0.00 0.00 0.00 2.75
293 294 9.179909 CTCCGTATATAGTTCATAGTGGAATCT 57.820 37.037 0.00 0.00 0.00 2.40
294 295 7.916450 GCTCCGTATATAGTTCATAGTGGAATC 59.084 40.741 0.00 0.00 0.00 2.52
295 296 7.396339 TGCTCCGTATATAGTTCATAGTGGAAT 59.604 37.037 0.00 0.00 0.00 3.01
296 297 6.717997 TGCTCCGTATATAGTTCATAGTGGAA 59.282 38.462 0.00 0.00 0.00 3.53
297 298 6.243148 TGCTCCGTATATAGTTCATAGTGGA 58.757 40.000 0.00 0.00 0.00 4.02
298 299 6.510879 TGCTCCGTATATAGTTCATAGTGG 57.489 41.667 0.00 0.00 0.00 4.00
299 300 8.812147 TTTTGCTCCGTATATAGTTCATAGTG 57.188 34.615 0.00 0.00 0.00 2.74
300 301 9.424319 CATTTTGCTCCGTATATAGTTCATAGT 57.576 33.333 0.00 0.00 0.00 2.12
301 302 9.639601 TCATTTTGCTCCGTATATAGTTCATAG 57.360 33.333 0.00 0.00 0.00 2.23
302 303 9.639601 CTCATTTTGCTCCGTATATAGTTCATA 57.360 33.333 0.00 0.00 0.00 2.15
303 304 8.150945 ACTCATTTTGCTCCGTATATAGTTCAT 58.849 33.333 0.00 0.00 0.00 2.57
304 305 7.497595 ACTCATTTTGCTCCGTATATAGTTCA 58.502 34.615 0.00 0.00 0.00 3.18
305 306 7.948278 ACTCATTTTGCTCCGTATATAGTTC 57.052 36.000 0.00 0.00 0.00 3.01
306 307 9.826574 TTTACTCATTTTGCTCCGTATATAGTT 57.173 29.630 0.00 0.00 0.00 2.24
307 308 9.998106 ATTTACTCATTTTGCTCCGTATATAGT 57.002 29.630 0.00 0.00 0.00 2.12
311 312 9.472361 GTAGATTTACTCATTTTGCTCCGTATA 57.528 33.333 0.00 0.00 0.00 1.47
312 313 7.985184 TGTAGATTTACTCATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
313 314 7.277098 GTGTAGATTTACTCATTTTGCTCCGTA 59.723 37.037 0.00 0.00 0.00 4.02
314 315 6.092259 GTGTAGATTTACTCATTTTGCTCCGT 59.908 38.462 0.00 0.00 0.00 4.69
315 316 6.313905 AGTGTAGATTTACTCATTTTGCTCCG 59.686 38.462 0.00 0.00 0.00 4.63
316 317 7.550906 AGAGTGTAGATTTACTCATTTTGCTCC 59.449 37.037 7.09 0.00 44.41 4.70
317 318 8.485976 AGAGTGTAGATTTACTCATTTTGCTC 57.514 34.615 7.09 0.00 44.41 4.26
318 319 9.944376 TTAGAGTGTAGATTTACTCATTTTGCT 57.056 29.630 7.09 0.00 44.41 3.91
325 326 9.224267 ACGTAGTTTAGAGTGTAGATTTACTCA 57.776 33.333 7.09 0.00 41.72 3.41
413 414 8.989980 GCAGGAATAAATTAACTAATACTCGCT 58.010 33.333 0.00 0.00 0.00 4.93
414 415 8.228464 GGCAGGAATAAATTAACTAATACTCGC 58.772 37.037 0.00 0.00 0.00 5.03
415 416 8.718734 GGGCAGGAATAAATTAACTAATACTCG 58.281 37.037 0.00 0.00 0.00 4.18
416 417 8.718734 CGGGCAGGAATAAATTAACTAATACTC 58.281 37.037 0.00 0.00 0.00 2.59
417 418 8.434392 TCGGGCAGGAATAAATTAACTAATACT 58.566 33.333 0.00 0.00 0.00 2.12
418 419 8.501580 GTCGGGCAGGAATAAATTAACTAATAC 58.498 37.037 0.00 0.00 0.00 1.89
419 420 8.212312 TGTCGGGCAGGAATAAATTAACTAATA 58.788 33.333 0.00 0.00 0.00 0.98
420 421 7.012989 GTGTCGGGCAGGAATAAATTAACTAAT 59.987 37.037 0.00 0.00 0.00 1.73
421 422 6.316890 GTGTCGGGCAGGAATAAATTAACTAA 59.683 38.462 0.00 0.00 0.00 2.24
422 423 5.818857 GTGTCGGGCAGGAATAAATTAACTA 59.181 40.000 0.00 0.00 0.00 2.24
444 445 8.873830 CATGTAGGAAGTAGTGAACTAATTGTG 58.126 37.037 7.82 0.00 36.94 3.33
510 512 1.745232 TCAACAGTGTTGGCGTTTCT 58.255 45.000 30.57 0.00 0.00 2.52
580 585 0.367210 GCTCGCTCGCAAAAGTCTAC 59.633 55.000 0.00 0.00 0.00 2.59
606 611 1.748493 CACTGGTAGACTCTCCTCTGC 59.252 57.143 0.00 0.00 0.00 4.26
607 612 3.358111 TCACTGGTAGACTCTCCTCTG 57.642 52.381 0.00 0.00 0.00 3.35
608 613 3.332485 ACTTCACTGGTAGACTCTCCTCT 59.668 47.826 0.00 0.00 0.00 3.69
609 614 3.692690 ACTTCACTGGTAGACTCTCCTC 58.307 50.000 0.00 0.00 0.00 3.71
610 615 3.818295 ACTTCACTGGTAGACTCTCCT 57.182 47.619 0.00 0.00 0.00 3.69
611 616 6.532988 AATTACTTCACTGGTAGACTCTCC 57.467 41.667 0.00 0.00 0.00 3.71
613 618 8.305317 GTTGTAATTACTTCACTGGTAGACTCT 58.695 37.037 16.33 0.00 0.00 3.24
614 619 7.272948 CGTTGTAATTACTTCACTGGTAGACTC 59.727 40.741 16.33 0.00 0.00 3.36
684 690 1.519758 CGTGAACAAACGCTTACGAGT 59.480 47.619 0.00 0.00 43.93 4.18
739 748 5.234752 GGTGATTAATGTTTTGGTTGGACC 58.765 41.667 0.00 0.00 39.22 4.46
785 794 1.060122 CGCGGGTTAAACGAGACAATC 59.940 52.381 0.00 0.00 32.84 2.67
821 830 3.876198 CGGTCGTACCCGTACCGG 61.876 72.222 0.00 0.00 45.47 5.28
907 917 1.339727 GGTCGAAGGTTACCTGCCAAT 60.340 52.381 3.99 0.00 32.13 3.16
916 930 4.304048 AAGAGAGAGAGGTCGAAGGTTA 57.696 45.455 0.00 0.00 0.00 2.85
926 940 3.871594 GAGACTCGAGAAAGAGAGAGAGG 59.128 52.174 21.68 0.00 40.57 3.69
927 941 3.551890 CGAGACTCGAGAAAGAGAGAGAG 59.448 52.174 21.68 0.00 43.74 3.20
928 942 3.193903 TCGAGACTCGAGAAAGAGAGAGA 59.806 47.826 23.27 2.97 44.82 3.10
929 943 3.517602 TCGAGACTCGAGAAAGAGAGAG 58.482 50.000 23.27 0.58 44.82 3.20
930 944 3.596310 TCGAGACTCGAGAAAGAGAGA 57.404 47.619 23.27 6.05 44.82 3.10
962 986 2.291741 CCCGAAGATAATTTGCTGGCTC 59.708 50.000 0.00 0.00 0.00 4.70
963 987 2.301346 CCCGAAGATAATTTGCTGGCT 58.699 47.619 0.00 0.00 0.00 4.75
964 988 2.024414 ACCCGAAGATAATTTGCTGGC 58.976 47.619 0.00 0.00 0.00 4.85
976 1000 1.267806 GACAGTACACGAACCCGAAGA 59.732 52.381 0.00 0.00 39.50 2.87
987 1011 4.098654 AGGCTAGACATGATGACAGTACAC 59.901 45.833 0.00 0.00 0.00 2.90
989 1013 4.927978 AGGCTAGACATGATGACAGTAC 57.072 45.455 0.00 0.00 0.00 2.73
1043 1073 1.479709 GAGCTCCTCTACTTCCTGCA 58.520 55.000 0.87 0.00 0.00 4.41
1226 1268 2.147387 ACCGTCTTGGCCCTCTTGT 61.147 57.895 0.00 0.00 43.94 3.16
1248 1290 2.027024 TCGACGTCGCTGCTGTTT 59.973 55.556 32.19 0.00 39.60 2.83
1249 1291 2.729862 GTCGACGTCGCTGCTGTT 60.730 61.111 32.19 0.00 39.60 3.16
1290 1341 1.511768 CTTCTTCCTCGTCCCGTCC 59.488 63.158 0.00 0.00 0.00 4.79
1449 1511 1.471684 GCTTCTCACCCTGCAATTCAG 59.528 52.381 0.00 0.00 42.49 3.02
1540 1602 1.572085 CCGTCTGCTTGAGCTTGGTG 61.572 60.000 4.44 0.00 42.66 4.17
1650 1712 4.699522 ACAAGAAGGCCGGCGACC 62.700 66.667 22.54 6.17 0.00 4.79
1684 1746 3.247442 CGAACACACAGCCTTATCGTTA 58.753 45.455 0.00 0.00 0.00 3.18
1756 1818 1.734748 GGCGGCAGTAGTAGTCTCC 59.265 63.158 3.07 0.00 0.00 3.71
1773 1835 2.821546 TCGACGAATGCATTTCTAGGG 58.178 47.619 14.33 1.94 31.73 3.53
1775 1837 5.835911 ATGATCGACGAATGCATTTCTAG 57.164 39.130 14.33 8.30 31.73 2.43
1776 1838 6.037062 ACAAATGATCGACGAATGCATTTCTA 59.963 34.615 22.65 0.44 37.14 2.10
1777 1839 5.163723 ACAAATGATCGACGAATGCATTTCT 60.164 36.000 22.65 14.75 37.14 2.52
1842 1911 1.945394 CCCTGAAGCTCATGCATGTAC 59.055 52.381 25.43 18.09 42.74 2.90
1846 1915 1.005097 TGTTCCCTGAAGCTCATGCAT 59.995 47.619 0.00 0.00 42.74 3.96
1887 1956 9.778741 TCATTCAAGAAAAACTATAGACACTGT 57.221 29.630 6.78 0.00 0.00 3.55
1942 2017 7.676683 TTCTAGGTGTAGATATTTTGCTCCT 57.323 36.000 0.00 0.00 35.12 3.69
1943 2018 9.425577 GTATTCTAGGTGTAGATATTTTGCTCC 57.574 37.037 0.00 0.00 35.12 4.70
1944 2019 9.425577 GGTATTCTAGGTGTAGATATTTTGCTC 57.574 37.037 0.00 0.00 35.12 4.26
1957 2032 2.764572 CCGTCCTTGGTATTCTAGGTGT 59.235 50.000 0.00 0.00 0.00 4.16
1960 2035 1.269621 CGCCGTCCTTGGTATTCTAGG 60.270 57.143 0.00 0.00 0.00 3.02
1961 2036 1.679680 TCGCCGTCCTTGGTATTCTAG 59.320 52.381 0.00 0.00 0.00 2.43
1963 2038 1.120530 ATCGCCGTCCTTGGTATTCT 58.879 50.000 0.00 0.00 0.00 2.40
2036 2112 0.390735 GGTACGCCCATGAACGAACT 60.391 55.000 13.27 0.00 0.00 3.01
2040 2116 1.876714 CGAGGTACGCCCATGAACG 60.877 63.158 0.00 0.00 34.66 3.95
2080 2159 2.659016 CTTGTCGCTCTGCTCCCA 59.341 61.111 0.00 0.00 0.00 4.37
2096 4023 0.770557 TGTAACTTGGACCTGGCCCT 60.771 55.000 0.00 0.00 0.00 5.19
2110 4037 2.007608 GCCCGAATCAGGAAGTGTAAC 58.992 52.381 0.00 0.00 0.00 2.50
2227 4155 3.808466 TGGCAACTTTTTGTGTGCATA 57.192 38.095 0.00 0.00 35.73 3.14
2303 4231 4.212911 GTTATACGCGAACTTGTTTTGCA 58.787 39.130 15.93 0.00 44.13 4.08
2369 4301 3.181491 GCAAGCGGCATTTTTATGGTCTA 60.181 43.478 1.45 0.00 43.97 2.59
2370 4302 2.417243 GCAAGCGGCATTTTTATGGTCT 60.417 45.455 1.45 0.00 43.97 3.85
2565 4514 4.720046 TCACCATGCCACTACTTTTACAA 58.280 39.130 0.00 0.00 0.00 2.41
2566 4515 4.359434 TCACCATGCCACTACTTTTACA 57.641 40.909 0.00 0.00 0.00 2.41
2567 4516 5.699097 TTTCACCATGCCACTACTTTTAC 57.301 39.130 0.00 0.00 0.00 2.01
2594 4543 3.563808 TGTTTCTGGAGAACATTTCCACG 59.436 43.478 0.00 0.00 39.74 4.94
2596 4545 5.139727 ACATGTTTCTGGAGAACATTTCCA 58.860 37.500 0.00 0.00 42.30 3.53
2599 4548 6.713762 TTGACATGTTTCTGGAGAACATTT 57.286 33.333 0.00 0.00 33.13 2.32
2600 4549 6.322201 ACTTTGACATGTTTCTGGAGAACATT 59.678 34.615 0.00 0.00 33.13 2.71
2601 4550 5.829924 ACTTTGACATGTTTCTGGAGAACAT 59.170 36.000 0.00 0.00 33.13 2.71
2618 4571 7.581476 TCATTAGATCCGTTTCAAACTTTGAC 58.419 34.615 3.56 0.00 39.87 3.18
2619 4572 7.737972 TCATTAGATCCGTTTCAAACTTTGA 57.262 32.000 0.00 0.00 38.04 2.69
2697 4650 9.183368 TGCCATGTCACTATCACAAAAATATTA 57.817 29.630 0.00 0.00 0.00 0.98
2698 4651 8.065473 TGCCATGTCACTATCACAAAAATATT 57.935 30.769 0.00 0.00 0.00 1.28
2699 4652 7.643569 TGCCATGTCACTATCACAAAAATAT 57.356 32.000 0.00 0.00 0.00 1.28
2700 4653 7.459795 TTGCCATGTCACTATCACAAAAATA 57.540 32.000 0.00 0.00 0.00 1.40
2701 4654 5.981088 TGCCATGTCACTATCACAAAAAT 57.019 34.783 0.00 0.00 0.00 1.82
2702 4655 5.781210 TTGCCATGTCACTATCACAAAAA 57.219 34.783 0.00 0.00 0.00 1.94
2703 4656 5.781210 TTTGCCATGTCACTATCACAAAA 57.219 34.783 0.00 0.00 0.00 2.44
2704 4657 5.981088 ATTTGCCATGTCACTATCACAAA 57.019 34.783 0.00 0.00 0.00 2.83
2705 4658 5.476254 TCAATTTGCCATGTCACTATCACAA 59.524 36.000 0.00 0.00 0.00 3.33
2706 4659 5.008980 TCAATTTGCCATGTCACTATCACA 58.991 37.500 0.00 0.00 0.00 3.58
2707 4660 5.449588 CCTCAATTTGCCATGTCACTATCAC 60.450 44.000 0.00 0.00 0.00 3.06
2708 4661 4.641541 CCTCAATTTGCCATGTCACTATCA 59.358 41.667 0.00 0.00 0.00 2.15
2709 4662 4.037208 CCCTCAATTTGCCATGTCACTATC 59.963 45.833 0.00 0.00 0.00 2.08
2710 4663 3.956199 CCCTCAATTTGCCATGTCACTAT 59.044 43.478 0.00 0.00 0.00 2.12
2711 4664 3.355378 CCCTCAATTTGCCATGTCACTA 58.645 45.455 0.00 0.00 0.00 2.74
2712 4665 2.173519 CCCTCAATTTGCCATGTCACT 58.826 47.619 0.00 0.00 0.00 3.41
2713 4666 1.205417 CCCCTCAATTTGCCATGTCAC 59.795 52.381 0.00 0.00 0.00 3.67
2714 4667 1.559368 CCCCTCAATTTGCCATGTCA 58.441 50.000 0.00 0.00 0.00 3.58
2715 4668 0.826062 CCCCCTCAATTTGCCATGTC 59.174 55.000 0.00 0.00 0.00 3.06
2716 4669 2.995480 CCCCCTCAATTTGCCATGT 58.005 52.632 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.