Multiple sequence alignment - TraesCS7B01G119400

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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 TraesCS7B01G119400 chr7B 100.000 3080 0 0 1 3080 138752095 138755174 0.000000e+00 5688.0
1 TraesCS7B01G119400 chr7B 82.936 797 111 19 1033 1821 623795788 623796567 0.000000e+00 695.0
2 TraesCS7B01G119400 chr7B 80.137 876 138 18 1033 1887 623818069 623818929 3.370000e-174 621.0
3 TraesCS7B01G119400 chr7B 84.857 350 45 3 1819 2166 623798256 623798599 2.270000e-91 346.0
4 TraesCS7B01G119400 chr7B 85.965 285 33 2 1882 2166 623820114 623820391 6.460000e-77 298.0
5 TraesCS7B01G119400 chr7B 89.231 65 4 3 307 369 687409282 687409345 9.160000e-11 78.7
6 TraesCS7B01G119400 chr7D 92.525 2622 104 33 510 3080 174293218 174295798 0.000000e+00 3672.0
7 TraesCS7B01G119400 chr7D 83.392 1144 158 22 1033 2166 568257986 568259107 0.000000e+00 1031.0
8 TraesCS7B01G119400 chr7D 84.662 828 113 6 1342 2169 568273077 568273890 0.000000e+00 813.0
9 TraesCS7B01G119400 chr7D 83.791 401 24 16 1 367 107772812 107772419 2.940000e-90 342.0
10 TraesCS7B01G119400 chr7D 80.782 307 44 10 1033 1327 568272368 568272671 3.090000e-55 226.0
11 TraesCS7B01G119400 chr7D 97.872 47 1 0 363 409 107772402 107772356 7.080000e-12 82.4
12 TraesCS7B01G119400 chr7A 89.469 2241 180 21 867 3069 176274797 176277019 0.000000e+00 2780.0
13 TraesCS7B01G119400 chr6D 88.114 387 21 12 3 364 374112229 374112615 1.310000e-118 436.0
14 TraesCS7B01G119400 chr6D 97.959 49 1 0 363 411 374112635 374112683 5.470000e-13 86.1
15 TraesCS7B01G119400 chr4D 87.531 401 16 13 1 367 308826128 308826528 1.700000e-117 433.0
16 TraesCS7B01G119400 chr4D 87.531 401 16 13 1 367 477375302 477375702 1.700000e-117 433.0
17 TraesCS7B01G119400 chr4D 98.000 50 1 0 363 412 308826545 308826594 1.520000e-13 87.9
18 TraesCS7B01G119400 chr1B 86.035 401 21 11 1 367 130832735 130832336 6.190000e-107 398.0
19 TraesCS7B01G119400 chr3D 84.946 372 37 14 1 367 419603076 419603433 2.920000e-95 359.0
20 TraesCS7B01G119400 chr3D 97.727 44 1 0 363 406 419603450 419603493 3.290000e-10 76.8
21 TraesCS7B01G119400 chr4B 82.353 323 23 14 79 367 201801875 201801553 1.830000e-62 250.0
22 TraesCS7B01G119400 chr4B 96.078 51 2 0 363 413 201801536 201801486 1.970000e-12 84.2
23 TraesCS7B01G119400 chr2B 94.643 56 1 2 303 358 695682342 695682289 5.470000e-13 86.1
24 TraesCS7B01G119400 chr5D 94.340 53 1 2 306 358 379266984 379266934 2.550000e-11 80.5


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 TraesCS7B01G119400 chr7B 138752095 138755174 3079 False 5688.0 5688 100.0000 1 3080 1 chr7B.!!$F1 3079
1 TraesCS7B01G119400 chr7B 623795788 623798599 2811 False 520.5 695 83.8965 1033 2166 2 chr7B.!!$F3 1133
2 TraesCS7B01G119400 chr7B 623818069 623820391 2322 False 459.5 621 83.0510 1033 2166 2 chr7B.!!$F4 1133
3 TraesCS7B01G119400 chr7D 174293218 174295798 2580 False 3672.0 3672 92.5250 510 3080 1 chr7D.!!$F1 2570
4 TraesCS7B01G119400 chr7D 568257986 568259107 1121 False 1031.0 1031 83.3920 1033 2166 1 chr7D.!!$F2 1133
5 TraesCS7B01G119400 chr7D 568272368 568273890 1522 False 519.5 813 82.7220 1033 2169 2 chr7D.!!$F3 1136
6 TraesCS7B01G119400 chr7A 176274797 176277019 2222 False 2780.0 2780 89.4690 867 3069 1 chr7A.!!$F1 2202

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
507 508 0.039180 TGAGGGAGTAGTTGGCTCGA 59.961 55.0 0.00 0.0 34.0 4.04 F
509 510 0.039911 AGGGAGTAGTTGGCTCGAGT 59.960 55.0 15.13 0.0 34.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 5250 0.679002 GCATGCCTCCTTGAGAGCAA 60.679 55.0 6.36 0.0 41.74 3.91 R
2489 5808 0.951040 GCAGCAGGCACGTAAACTCT 60.951 55.0 0.00 0.0 43.97 3.24 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 1.840737 TGCTCTACAGACCTCCACTC 58.159 55.000 0.00 0.00 0.00 3.51
24 25 0.736053 GCTCTACAGACCTCCACTCG 59.264 60.000 0.00 0.00 0.00 4.18
25 26 0.736053 CTCTACAGACCTCCACTCGC 59.264 60.000 0.00 0.00 0.00 5.03
26 27 0.680280 TCTACAGACCTCCACTCGCC 60.680 60.000 0.00 0.00 0.00 5.54
27 28 1.994507 CTACAGACCTCCACTCGCCG 61.995 65.000 0.00 0.00 0.00 6.46
28 29 4.135153 CAGACCTCCACTCGCCGG 62.135 72.222 0.00 0.00 0.00 6.13
74 75 4.402528 CCGATCACCACGCCCCAA 62.403 66.667 0.00 0.00 0.00 4.12
75 76 3.124921 CGATCACCACGCCCCAAC 61.125 66.667 0.00 0.00 0.00 3.77
76 77 3.124921 GATCACCACGCCCCAACG 61.125 66.667 0.00 0.00 39.50 4.10
77 78 3.599285 GATCACCACGCCCCAACGA 62.599 63.158 0.00 0.00 36.70 3.85
78 79 3.894547 ATCACCACGCCCCAACGAC 62.895 63.158 0.00 0.00 36.70 4.34
86 87 3.361977 CCCCAACGACGCCCAAAG 61.362 66.667 0.00 0.00 0.00 2.77
87 88 4.038080 CCCAACGACGCCCAAAGC 62.038 66.667 0.00 0.00 38.52 3.51
88 89 2.978010 CCAACGACGCCCAAAGCT 60.978 61.111 0.00 0.00 40.39 3.74
89 90 2.252260 CAACGACGCCCAAAGCTG 59.748 61.111 0.00 0.00 40.39 4.24
90 91 2.203153 AACGACGCCCAAAGCTGT 60.203 55.556 0.00 0.00 40.39 4.40
91 92 2.251642 AACGACGCCCAAAGCTGTC 61.252 57.895 0.00 0.00 40.39 3.51
93 94 2.665185 GACGCCCAAAGCTGTCGT 60.665 61.111 0.00 0.00 40.39 4.34
94 95 2.665185 ACGCCCAAAGCTGTCGTC 60.665 61.111 0.00 0.00 40.39 4.20
95 96 3.777925 CGCCCAAAGCTGTCGTCG 61.778 66.667 0.00 0.00 40.39 5.12
96 97 3.423154 GCCCAAAGCTGTCGTCGG 61.423 66.667 0.00 0.00 38.99 4.79
97 98 2.742372 CCCAAAGCTGTCGTCGGG 60.742 66.667 0.00 0.00 0.00 5.14
98 99 2.742372 CCAAAGCTGTCGTCGGGG 60.742 66.667 0.00 0.00 0.00 5.73
99 100 3.423154 CAAAGCTGTCGTCGGGGC 61.423 66.667 0.00 0.00 0.00 5.80
100 101 3.936203 AAAGCTGTCGTCGGGGCA 61.936 61.111 0.00 0.00 0.00 5.36
101 102 3.883744 AAAGCTGTCGTCGGGGCAG 62.884 63.158 4.87 4.87 0.00 4.85
108 109 4.899239 CGTCGGGGCAGCCAGATC 62.899 72.222 15.19 6.28 0.00 2.75
109 110 4.554036 GTCGGGGCAGCCAGATCC 62.554 72.222 15.19 3.80 0.00 3.36
138 139 3.827898 CTCGCCTCGGACCTCCAC 61.828 72.222 0.00 0.00 35.14 4.02
139 140 4.361971 TCGCCTCGGACCTCCACT 62.362 66.667 0.00 0.00 35.14 4.00
140 141 3.382832 CGCCTCGGACCTCCACTT 61.383 66.667 0.00 0.00 35.14 3.16
141 142 2.266055 GCCTCGGACCTCCACTTG 59.734 66.667 0.00 0.00 35.14 3.16
142 143 2.266055 CCTCGGACCTCCACTTGC 59.734 66.667 0.00 0.00 35.14 4.01
143 144 2.266055 CTCGGACCTCCACTTGCC 59.734 66.667 0.00 0.00 35.14 4.52
144 145 2.525629 TCGGACCTCCACTTGCCA 60.526 61.111 0.00 0.00 35.14 4.92
145 146 2.046892 CGGACCTCCACTTGCCAG 60.047 66.667 0.00 0.00 35.14 4.85
146 147 2.360475 GGACCTCCACTTGCCAGC 60.360 66.667 0.00 0.00 35.64 4.85
147 148 2.743928 GACCTCCACTTGCCAGCG 60.744 66.667 0.00 0.00 0.00 5.18
148 149 3.537206 GACCTCCACTTGCCAGCGT 62.537 63.158 0.00 0.00 0.00 5.07
149 150 2.743928 CCTCCACTTGCCAGCGTC 60.744 66.667 0.00 0.00 0.00 5.19
150 151 3.114616 CTCCACTTGCCAGCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
176 177 4.308458 CACCTCCGTGCCGACCAA 62.308 66.667 0.00 0.00 32.04 3.67
177 178 4.003788 ACCTCCGTGCCGACCAAG 62.004 66.667 0.00 0.00 0.00 3.61
243 244 2.675519 CTCTCGCCAGAGCATGAAC 58.324 57.895 0.00 0.00 44.02 3.18
244 245 0.809241 CTCTCGCCAGAGCATGAACC 60.809 60.000 0.00 0.00 44.02 3.62
245 246 1.817099 CTCGCCAGAGCATGAACCC 60.817 63.158 0.00 0.00 39.83 4.11
246 247 2.825836 CGCCAGAGCATGAACCCC 60.826 66.667 0.00 0.00 39.83 4.95
247 248 2.679716 GCCAGAGCATGAACCCCT 59.320 61.111 0.00 0.00 39.53 4.79
248 249 1.751927 GCCAGAGCATGAACCCCTG 60.752 63.158 0.00 0.00 39.53 4.45
249 250 1.751927 CCAGAGCATGAACCCCTGC 60.752 63.158 0.00 0.00 38.69 4.85
252 253 3.499406 AGCATGAACCCCTGCTGA 58.501 55.556 0.00 0.00 46.55 4.26
253 254 1.769665 AGCATGAACCCCTGCTGAA 59.230 52.632 0.00 0.00 46.55 3.02
254 255 0.333993 AGCATGAACCCCTGCTGAAT 59.666 50.000 0.00 0.00 46.55 2.57
255 256 0.743097 GCATGAACCCCTGCTGAATC 59.257 55.000 0.00 0.00 35.49 2.52
256 257 1.019673 CATGAACCCCTGCTGAATCG 58.980 55.000 0.00 0.00 0.00 3.34
257 258 0.911769 ATGAACCCCTGCTGAATCGA 59.088 50.000 0.00 0.00 0.00 3.59
258 259 0.250234 TGAACCCCTGCTGAATCGAG 59.750 55.000 0.00 0.00 0.00 4.04
259 260 1.078143 AACCCCTGCTGAATCGAGC 60.078 57.895 0.00 0.00 39.62 5.03
260 261 2.587194 CCCCTGCTGAATCGAGCG 60.587 66.667 0.00 0.00 42.32 5.03
261 262 2.587194 CCCTGCTGAATCGAGCGG 60.587 66.667 0.00 0.00 43.90 5.52
262 263 3.267860 CCTGCTGAATCGAGCGGC 61.268 66.667 13.34 13.34 43.08 6.53
263 264 3.267860 CTGCTGAATCGAGCGGCC 61.268 66.667 16.47 0.00 42.32 6.13
264 265 4.838152 TGCTGAATCGAGCGGCCC 62.838 66.667 16.47 0.00 42.32 5.80
265 266 4.838152 GCTGAATCGAGCGGCCCA 62.838 66.667 10.00 0.00 0.00 5.36
266 267 2.892425 CTGAATCGAGCGGCCCAC 60.892 66.667 0.00 0.00 0.00 4.61
281 282 4.939368 CACGCCACCCAAACCCGA 62.939 66.667 0.00 0.00 0.00 5.14
282 283 4.636435 ACGCCACCCAAACCCGAG 62.636 66.667 0.00 0.00 0.00 4.63
285 286 4.323477 CCACCCAAACCCGAGCGA 62.323 66.667 0.00 0.00 0.00 4.93
286 287 2.742372 CACCCAAACCCGAGCGAG 60.742 66.667 0.00 0.00 0.00 5.03
287 288 2.920912 ACCCAAACCCGAGCGAGA 60.921 61.111 0.00 0.00 0.00 4.04
288 289 2.125512 CCCAAACCCGAGCGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
289 290 2.125512 CCAAACCCGAGCGAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
290 291 2.646175 CCAAACCCGAGCGAGAGGA 61.646 63.158 0.00 0.00 0.00 3.71
291 292 1.153745 CAAACCCGAGCGAGAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
292 293 2.352032 AAACCCGAGCGAGAGGAGG 61.352 63.158 0.00 0.00 0.00 4.30
294 295 4.507916 CCCGAGCGAGAGGAGGGA 62.508 72.222 0.00 0.00 44.70 4.20
295 296 2.440430 CCGAGCGAGAGGAGGGAA 60.440 66.667 0.00 0.00 0.00 3.97
296 297 2.485795 CCGAGCGAGAGGAGGGAAG 61.486 68.421 0.00 0.00 0.00 3.46
297 298 2.485795 CGAGCGAGAGGAGGGAAGG 61.486 68.421 0.00 0.00 0.00 3.46
298 299 2.042435 AGCGAGAGGAGGGAAGGG 60.042 66.667 0.00 0.00 0.00 3.95
299 300 3.855853 GCGAGAGGAGGGAAGGGC 61.856 72.222 0.00 0.00 0.00 5.19
300 301 3.157949 CGAGAGGAGGGAAGGGCC 61.158 72.222 0.00 0.00 0.00 5.80
301 302 2.370633 GAGAGGAGGGAAGGGCCT 59.629 66.667 0.00 0.00 36.66 5.19
302 303 1.764454 GAGAGGAGGGAAGGGCCTC 60.764 68.421 6.46 0.00 46.75 4.70
303 304 3.157949 GAGGAGGGAAGGGCCTCG 61.158 72.222 6.46 0.00 38.88 4.63
358 359 4.593864 GCGGCGAGGAGGATGGAC 62.594 72.222 12.98 0.00 0.00 4.02
359 360 4.271816 CGGCGAGGAGGATGGACG 62.272 72.222 0.00 0.00 0.00 4.79
360 361 3.917760 GGCGAGGAGGATGGACGG 61.918 72.222 0.00 0.00 0.00 4.79
361 362 3.917760 GCGAGGAGGATGGACGGG 61.918 72.222 0.00 0.00 0.00 5.28
362 363 3.227276 CGAGGAGGATGGACGGGG 61.227 72.222 0.00 0.00 0.00 5.73
363 364 2.844839 GAGGAGGATGGACGGGGG 60.845 72.222 0.00 0.00 0.00 5.40
366 367 3.866582 GAGGATGGACGGGGGCTG 61.867 72.222 0.00 0.00 0.00 4.85
378 379 3.081409 GGGCTGGGTTCGCTCCTA 61.081 66.667 0.00 0.00 0.00 2.94
379 380 2.501610 GGCTGGGTTCGCTCCTAG 59.498 66.667 5.10 5.10 38.78 3.02
380 381 2.501610 GCTGGGTTCGCTCCTAGG 59.498 66.667 0.82 0.82 36.72 3.02
381 382 2.501610 CTGGGTTCGCTCCTAGGC 59.498 66.667 2.96 0.00 33.33 3.93
382 383 3.081409 TGGGTTCGCTCCTAGGCC 61.081 66.667 2.96 0.00 0.00 5.19
383 384 4.222847 GGGTTCGCTCCTAGGCCG 62.223 72.222 2.96 9.61 0.00 6.13
384 385 4.893601 GGTTCGCTCCTAGGCCGC 62.894 72.222 2.96 8.37 0.00 6.53
385 386 4.893601 GTTCGCTCCTAGGCCGCC 62.894 72.222 2.96 0.00 0.00 6.13
405 406 2.125512 CGGGAGCGACCAAAGGAG 60.126 66.667 5.45 0.00 41.20 3.69
406 407 2.436824 GGGAGCGACCAAAGGAGC 60.437 66.667 5.45 0.00 41.20 4.70
407 408 2.815647 GGAGCGACCAAAGGAGCG 60.816 66.667 0.00 0.00 38.79 5.03
408 409 2.048127 GAGCGACCAAAGGAGCGT 60.048 61.111 0.00 0.00 35.79 5.07
409 410 2.048127 AGCGACCAAAGGAGCGTC 60.048 61.111 0.00 0.00 35.79 5.19
410 411 2.048127 GCGACCAAAGGAGCGTCT 60.048 61.111 0.00 0.00 0.00 4.18
411 412 1.214589 GCGACCAAAGGAGCGTCTA 59.785 57.895 0.00 0.00 0.00 2.59
412 413 0.389426 GCGACCAAAGGAGCGTCTAA 60.389 55.000 0.00 0.00 0.00 2.10
413 414 1.347320 CGACCAAAGGAGCGTCTAAC 58.653 55.000 0.00 0.00 0.00 2.34
414 415 1.067776 CGACCAAAGGAGCGTCTAACT 60.068 52.381 0.00 0.00 0.00 2.24
415 416 2.338500 GACCAAAGGAGCGTCTAACTG 58.662 52.381 0.00 0.00 0.00 3.16
416 417 1.692519 ACCAAAGGAGCGTCTAACTGT 59.307 47.619 0.00 0.00 0.00 3.55
417 418 2.104281 ACCAAAGGAGCGTCTAACTGTT 59.896 45.455 0.00 0.00 0.00 3.16
418 419 3.139077 CCAAAGGAGCGTCTAACTGTTT 58.861 45.455 0.00 0.00 0.00 2.83
419 420 3.564225 CCAAAGGAGCGTCTAACTGTTTT 59.436 43.478 0.00 0.00 0.00 2.43
420 421 4.036380 CCAAAGGAGCGTCTAACTGTTTTT 59.964 41.667 0.00 0.00 0.00 1.94
441 442 7.696992 TTTTTAAGAGTTGTTTCCTCACTGT 57.303 32.000 0.00 0.00 0.00 3.55
442 443 8.795842 TTTTTAAGAGTTGTTTCCTCACTGTA 57.204 30.769 0.00 0.00 0.00 2.74
443 444 8.795842 TTTTAAGAGTTGTTTCCTCACTGTAA 57.204 30.769 0.00 0.00 0.00 2.41
444 445 7.781548 TTAAGAGTTGTTTCCTCACTGTAAC 57.218 36.000 0.00 0.00 0.00 2.50
445 446 4.704965 AGAGTTGTTTCCTCACTGTAACC 58.295 43.478 0.00 0.00 0.00 2.85
446 447 4.163458 AGAGTTGTTTCCTCACTGTAACCA 59.837 41.667 0.00 0.00 0.00 3.67
447 448 4.850680 AGTTGTTTCCTCACTGTAACCAA 58.149 39.130 0.00 0.00 0.00 3.67
448 449 5.258051 AGTTGTTTCCTCACTGTAACCAAA 58.742 37.500 0.00 0.00 0.00 3.28
449 450 5.712917 AGTTGTTTCCTCACTGTAACCAAAA 59.287 36.000 0.00 0.00 0.00 2.44
450 451 5.570234 TGTTTCCTCACTGTAACCAAAAC 57.430 39.130 0.00 0.00 0.00 2.43
451 452 5.258051 TGTTTCCTCACTGTAACCAAAACT 58.742 37.500 0.00 0.00 0.00 2.66
452 453 5.712917 TGTTTCCTCACTGTAACCAAAACTT 59.287 36.000 0.00 0.00 0.00 2.66
453 454 6.885376 TGTTTCCTCACTGTAACCAAAACTTA 59.115 34.615 0.00 0.00 0.00 2.24
454 455 7.558444 TGTTTCCTCACTGTAACCAAAACTTAT 59.442 33.333 0.00 0.00 0.00 1.73
455 456 9.059260 GTTTCCTCACTGTAACCAAAACTTATA 57.941 33.333 0.00 0.00 0.00 0.98
456 457 9.802039 TTTCCTCACTGTAACCAAAACTTATAT 57.198 29.630 0.00 0.00 0.00 0.86
457 458 9.802039 TTCCTCACTGTAACCAAAACTTATATT 57.198 29.630 0.00 0.00 0.00 1.28
458 459 9.802039 TCCTCACTGTAACCAAAACTTATATTT 57.198 29.630 0.00 0.00 0.00 1.40
493 494 7.718334 AAAACTTATATTTGGGAACTGAGGG 57.282 36.000 0.00 0.00 0.00 4.30
494 495 6.652205 AACTTATATTTGGGAACTGAGGGA 57.348 37.500 0.00 0.00 0.00 4.20
495 496 6.253946 ACTTATATTTGGGAACTGAGGGAG 57.746 41.667 0.00 0.00 0.00 4.30
496 497 5.731678 ACTTATATTTGGGAACTGAGGGAGT 59.268 40.000 0.00 0.00 35.94 3.85
497 498 6.906901 ACTTATATTTGGGAACTGAGGGAGTA 59.093 38.462 0.00 0.00 33.09 2.59
498 499 5.896073 ATATTTGGGAACTGAGGGAGTAG 57.104 43.478 0.00 0.00 33.09 2.57
499 500 2.715763 TTGGGAACTGAGGGAGTAGT 57.284 50.000 0.00 0.00 33.09 2.73
500 501 2.715763 TGGGAACTGAGGGAGTAGTT 57.284 50.000 0.00 0.00 39.67 2.24
501 502 2.257207 TGGGAACTGAGGGAGTAGTTG 58.743 52.381 0.00 0.00 37.27 3.16
502 503 1.555533 GGGAACTGAGGGAGTAGTTGG 59.444 57.143 0.00 0.00 37.27 3.77
503 504 1.066071 GGAACTGAGGGAGTAGTTGGC 60.066 57.143 0.00 0.00 37.27 4.52
504 505 1.903183 GAACTGAGGGAGTAGTTGGCT 59.097 52.381 0.00 0.00 37.27 4.75
505 506 1.562783 ACTGAGGGAGTAGTTGGCTC 58.437 55.000 0.00 0.00 30.86 4.70
506 507 0.457851 CTGAGGGAGTAGTTGGCTCG 59.542 60.000 0.00 0.00 34.00 5.03
507 508 0.039180 TGAGGGAGTAGTTGGCTCGA 59.961 55.000 0.00 0.00 34.00 4.04
508 509 0.741915 GAGGGAGTAGTTGGCTCGAG 59.258 60.000 8.45 8.45 34.00 4.04
509 510 0.039911 AGGGAGTAGTTGGCTCGAGT 59.960 55.000 15.13 0.00 34.00 4.18
510 511 0.173708 GGGAGTAGTTGGCTCGAGTG 59.826 60.000 15.13 0.00 34.00 3.51
511 512 0.173708 GGAGTAGTTGGCTCGAGTGG 59.826 60.000 15.13 0.00 34.00 4.00
512 513 0.173708 GAGTAGTTGGCTCGAGTGGG 59.826 60.000 15.13 0.00 0.00 4.61
513 514 1.448013 GTAGTTGGCTCGAGTGGGC 60.448 63.158 15.13 1.56 0.00 5.36
514 515 3.001902 TAGTTGGCTCGAGTGGGCG 62.002 63.158 15.13 0.00 0.00 6.13
515 516 4.681978 GTTGGCTCGAGTGGGCGT 62.682 66.667 15.13 0.00 0.00 5.68
516 517 4.680237 TTGGCTCGAGTGGGCGTG 62.680 66.667 15.13 0.00 0.00 5.34
520 521 4.717629 CTCGAGTGGGCGTGCGAA 62.718 66.667 3.62 0.00 31.89 4.70
540 541 3.420839 ACTGCGAAGGTGAAAACTTTG 57.579 42.857 0.00 0.00 33.41 2.77
560 563 1.077089 GGCGCGTTCTCTTCTGTACC 61.077 60.000 8.43 0.00 0.00 3.34
588 591 4.021894 CCTGAACGAAAGAGGAAGAGAAGA 60.022 45.833 0.00 0.00 0.00 2.87
589 592 5.509840 CCTGAACGAAAGAGGAAGAGAAGAA 60.510 44.000 0.00 0.00 0.00 2.52
590 593 5.914033 TGAACGAAAGAGGAAGAGAAGAAA 58.086 37.500 0.00 0.00 0.00 2.52
591 594 6.346096 TGAACGAAAGAGGAAGAGAAGAAAA 58.654 36.000 0.00 0.00 0.00 2.29
592 595 6.821665 TGAACGAAAGAGGAAGAGAAGAAAAA 59.178 34.615 0.00 0.00 0.00 1.94
663 667 2.203351 CCCAAATCCCTAGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
683 687 2.266055 CCACTCGACCAGCTTCCC 59.734 66.667 0.00 0.00 0.00 3.97
684 688 2.266055 CACTCGACCAGCTTCCCC 59.734 66.667 0.00 0.00 0.00 4.81
685 689 3.382832 ACTCGACCAGCTTCCCCG 61.383 66.667 0.00 0.00 0.00 5.73
686 690 4.821589 CTCGACCAGCTTCCCCGC 62.822 72.222 0.00 0.00 0.00 6.13
689 693 4.035102 GACCAGCTTCCCCGCCTT 62.035 66.667 0.00 0.00 0.00 4.35
690 694 3.978571 GACCAGCTTCCCCGCCTTC 62.979 68.421 0.00 0.00 0.00 3.46
691 695 3.721706 CCAGCTTCCCCGCCTTCT 61.722 66.667 0.00 0.00 0.00 2.85
692 696 2.352805 CAGCTTCCCCGCCTTCTT 59.647 61.111 0.00 0.00 0.00 2.52
693 697 1.746991 CAGCTTCCCCGCCTTCTTC 60.747 63.158 0.00 0.00 0.00 2.87
694 698 2.438614 GCTTCCCCGCCTTCTTCC 60.439 66.667 0.00 0.00 0.00 3.46
812 826 4.052229 CGTCGTTCCGCCACCTCT 62.052 66.667 0.00 0.00 0.00 3.69
853 867 2.473816 CATACACGATTCGTCCATGCT 58.526 47.619 9.11 0.00 38.32 3.79
857 871 0.736636 ACGATTCGTCCATGCTACGA 59.263 50.000 15.09 15.09 46.82 3.43
1096 1113 4.077184 TGTCCGGGTCGCATGTCC 62.077 66.667 0.00 0.00 0.00 4.02
1272 1295 3.632604 TCTCTGACCGAAGTGATGATACC 59.367 47.826 0.00 0.00 0.00 2.73
1284 1307 3.000322 GTGATGATACCGAAGTCAAAGCG 60.000 47.826 0.00 0.00 0.00 4.68
1406 1835 4.236935 GGCTTCGCTCAATTCATCAAAAA 58.763 39.130 0.00 0.00 0.00 1.94
1593 2022 0.965363 AGGCGGCCGATGTCAATTTT 60.965 50.000 33.48 0.00 0.00 1.82
1731 2160 2.363038 CGACGATATGGAACCCAAGGTA 59.637 50.000 0.00 0.00 36.95 3.08
1951 5261 0.249868 TGGTCGTGTTGCTCTCAAGG 60.250 55.000 0.00 0.00 31.93 3.61
2019 5329 2.820059 TGGCATCTGATGGATACGAC 57.180 50.000 18.60 0.73 42.51 4.34
2098 5410 7.116736 TCCTTGACCTCTTTGAGTTTAAACTT 58.883 34.615 21.40 6.19 39.88 2.66
2099 5411 7.614192 TCCTTGACCTCTTTGAGTTTAAACTTT 59.386 33.333 21.40 0.75 39.88 2.66
2100 5412 8.899771 CCTTGACCTCTTTGAGTTTAAACTTTA 58.100 33.333 21.40 11.47 39.88 1.85
2167 5480 9.727859 TCAGAAGTGATGATATCCTAGTACTAC 57.272 37.037 0.00 0.00 0.00 2.73
2168 5481 9.733556 CAGAAGTGATGATATCCTAGTACTACT 57.266 37.037 0.00 0.00 0.00 2.57
2222 5535 4.454678 TCTGTTTGAGCTCAGTTGTCATT 58.545 39.130 17.43 0.00 33.89 2.57
2223 5536 4.883585 TCTGTTTGAGCTCAGTTGTCATTT 59.116 37.500 17.43 0.00 33.89 2.32
2224 5537 6.054941 TCTGTTTGAGCTCAGTTGTCATTTA 58.945 36.000 17.43 0.00 33.89 1.40
2225 5538 6.712095 TCTGTTTGAGCTCAGTTGTCATTTAT 59.288 34.615 17.43 0.00 33.89 1.40
2350 5666 1.663643 TCTTTAAGTTAGCGGCGCATG 59.336 47.619 35.02 13.26 0.00 4.06
2361 5677 1.678360 CGGCGCATGCAATCTATTTC 58.322 50.000 19.57 0.00 45.35 2.17
2495 5814 8.519799 TTTTACAGAAGAATTGTCCAGAGTTT 57.480 30.769 0.00 0.00 0.00 2.66
2502 5821 1.873698 TTGTCCAGAGTTTACGTGCC 58.126 50.000 0.00 0.00 0.00 5.01
2545 5888 5.359009 AGGGCAATATGAATCAGAACAGTTG 59.641 40.000 0.00 0.00 0.00 3.16
2546 5889 5.126061 GGGCAATATGAATCAGAACAGTTGT 59.874 40.000 0.00 0.00 0.00 3.32
2547 5890 6.261118 GGCAATATGAATCAGAACAGTTGTC 58.739 40.000 0.00 0.00 0.00 3.18
2548 5891 6.094603 GGCAATATGAATCAGAACAGTTGTCT 59.905 38.462 0.00 0.00 0.00 3.41
2569 5912 4.224594 TCTTCTTCACTCAGCTGATCCATT 59.775 41.667 18.63 0.00 0.00 3.16
2592 5935 2.627699 GGTCCCAGAACTTTGCATTTGA 59.372 45.455 0.00 0.00 0.00 2.69
2597 5940 4.202141 CCCAGAACTTTGCATTTGAGAACA 60.202 41.667 0.00 0.00 0.00 3.18
2603 5946 4.021719 ACTTTGCATTTGAGAACATCCAGG 60.022 41.667 0.00 0.00 0.00 4.45
2608 5952 5.070180 TGCATTTGAGAACATCCAGGAAAAA 59.930 36.000 0.00 0.00 0.00 1.94
2612 5956 6.391227 TTGAGAACATCCAGGAAAAACTTC 57.609 37.500 0.00 0.00 0.00 3.01
2619 5963 7.365497 ACATCCAGGAAAAACTTCTTTTGAT 57.635 32.000 0.00 0.00 29.59 2.57
2661 6005 7.544511 GCTCGATGCTATATTTTTGTCAATG 57.455 36.000 0.00 0.00 38.95 2.82
2668 6012 9.816354 ATGCTATATTTTTGTCAATGTAAACCC 57.184 29.630 0.00 0.00 0.00 4.11
2672 6016 4.592485 TTTTGTCAATGTAAACCCGCAT 57.408 36.364 0.00 0.00 0.00 4.73
2675 6020 2.486203 TGTCAATGTAAACCCGCATGAC 59.514 45.455 0.00 0.00 0.00 3.06
2746 6091 4.037446 TGCAAAACAATCTTCAGTGGTACC 59.963 41.667 4.43 4.43 0.00 3.34
2747 6092 4.558697 GCAAAACAATCTTCAGTGGTACCC 60.559 45.833 10.07 0.32 0.00 3.69
2756 6101 1.839747 AGTGGTACCCGGCTTGACA 60.840 57.895 10.07 0.00 0.00 3.58
2758 6103 0.322187 GTGGTACCCGGCTTGACAAT 60.322 55.000 10.07 0.00 0.00 2.71
2760 6105 1.029947 GGTACCCGGCTTGACAATGG 61.030 60.000 0.00 0.00 0.00 3.16
2766 6111 1.134098 CCGGCTTGACAATGGAGGTAT 60.134 52.381 0.00 0.00 0.00 2.73
2789 6134 3.308438 TTTCTGTACTGGCGGAACTAC 57.692 47.619 0.00 0.00 33.90 2.73
2797 6142 2.442188 GGCGGAACTACACTTCGCG 61.442 63.158 0.00 0.00 46.22 5.87
2801 6146 1.623973 GGAACTACACTTCGCGGTGC 61.624 60.000 14.31 0.00 40.52 5.01
2810 6155 0.040514 CTTCGCGGTGCATCAACAAA 60.041 50.000 6.13 0.00 0.00 2.83
2813 6158 1.396648 TCGCGGTGCATCAACAAATAG 59.603 47.619 6.13 0.00 0.00 1.73
2820 6165 5.156355 GGTGCATCAACAAATAGTTCTGTG 58.844 41.667 0.00 0.00 38.74 3.66
2834 6179 5.948992 AGTTCTGTGGAGTTTTAGAATGC 57.051 39.130 0.00 0.00 32.44 3.56
2850 6195 7.776933 TTAGAATGCTGTGAAGACATATGTC 57.223 36.000 25.47 25.47 45.08 3.06
2863 6208 6.101650 AGACATATGTCGATGGCTAATGAA 57.898 37.500 26.13 0.00 43.74 2.57
2866 6211 5.928839 ACATATGTCGATGGCTAATGAAGAC 59.071 40.000 1.41 0.00 0.00 3.01
2939 6292 5.372547 ACGGACTCCAAAAGCTTTTTATC 57.627 39.130 21.70 15.11 0.00 1.75
2941 6294 5.154222 CGGACTCCAAAAGCTTTTTATCAC 58.846 41.667 21.70 12.70 0.00 3.06
2942 6295 5.470368 GGACTCCAAAAGCTTTTTATCACC 58.530 41.667 21.70 17.12 0.00 4.02
2944 6297 5.147767 ACTCCAAAAGCTTTTTATCACCCT 58.852 37.500 21.70 0.00 0.00 4.34
2945 6298 5.602561 ACTCCAAAAGCTTTTTATCACCCTT 59.397 36.000 21.70 0.00 0.00 3.95
2946 6299 6.096673 TCCAAAAGCTTTTTATCACCCTTC 57.903 37.500 21.70 0.00 0.00 3.46
2950 6306 7.254761 CCAAAAGCTTTTTATCACCCTTCAAAC 60.255 37.037 21.70 0.00 0.00 2.93
2951 6307 5.121221 AGCTTTTTATCACCCTTCAAACG 57.879 39.130 0.00 0.00 0.00 3.60
2973 6329 2.162208 CCCAACGAAACATCAGGTCATG 59.838 50.000 0.00 0.00 0.00 3.07
3009 6365 3.702048 GGACTGTGCCGGCTGGTA 61.702 66.667 29.70 5.63 37.67 3.25
3045 6401 7.419711 TTCGTAAAGGAAGATAACATCTCCT 57.580 36.000 0.00 0.00 39.08 3.69
3053 6409 4.851639 AGATAACATCTCCTGCTGGTTT 57.148 40.909 9.73 0.04 33.42 3.27
3061 6417 5.367937 ACATCTCCTGCTGGTTTCTATATGT 59.632 40.000 9.73 7.26 34.23 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.435515 GAGGTCTGTAGAGCAGCGG 59.564 63.158 12.97 0.00 44.66 5.52
1 2 1.315981 TGGAGGTCTGTAGAGCAGCG 61.316 60.000 12.97 0.00 44.66 5.18
4 5 1.840737 GAGTGGAGGTCTGTAGAGCA 58.159 55.000 12.97 0.00 44.42 4.26
5 6 0.736053 CGAGTGGAGGTCTGTAGAGC 59.264 60.000 2.98 2.98 42.47 4.09
6 7 0.736053 GCGAGTGGAGGTCTGTAGAG 59.264 60.000 0.00 0.00 0.00 2.43
7 8 0.680280 GGCGAGTGGAGGTCTGTAGA 60.680 60.000 0.00 0.00 0.00 2.59
8 9 1.810532 GGCGAGTGGAGGTCTGTAG 59.189 63.158 0.00 0.00 0.00 2.74
9 10 2.044555 CGGCGAGTGGAGGTCTGTA 61.045 63.158 0.00 0.00 0.00 2.74
10 11 3.374402 CGGCGAGTGGAGGTCTGT 61.374 66.667 0.00 0.00 0.00 3.41
57 58 4.402528 TTGGGGCGTGGTGATCGG 62.403 66.667 0.00 0.00 0.00 4.18
58 59 3.124921 GTTGGGGCGTGGTGATCG 61.125 66.667 0.00 0.00 0.00 3.69
59 60 3.124921 CGTTGGGGCGTGGTGATC 61.125 66.667 0.00 0.00 0.00 2.92
60 61 3.632080 TCGTTGGGGCGTGGTGAT 61.632 61.111 0.00 0.00 0.00 3.06
61 62 4.612412 GTCGTTGGGGCGTGGTGA 62.612 66.667 0.00 0.00 0.00 4.02
69 70 3.361977 CTTTGGGCGTCGTTGGGG 61.362 66.667 0.00 0.00 0.00 4.96
70 71 4.038080 GCTTTGGGCGTCGTTGGG 62.038 66.667 0.00 0.00 0.00 4.12
79 80 3.423154 CCGACGACAGCTTTGGGC 61.423 66.667 0.00 0.00 42.19 5.36
80 81 2.742372 CCCGACGACAGCTTTGGG 60.742 66.667 0.00 0.00 31.18 4.12
81 82 2.742372 CCCCGACGACAGCTTTGG 60.742 66.667 0.00 0.00 0.00 3.28
82 83 3.423154 GCCCCGACGACAGCTTTG 61.423 66.667 0.00 0.00 0.00 2.77
83 84 3.883744 CTGCCCCGACGACAGCTTT 62.884 63.158 0.00 0.00 0.00 3.51
84 85 4.379243 CTGCCCCGACGACAGCTT 62.379 66.667 0.00 0.00 0.00 3.74
91 92 4.899239 GATCTGGCTGCCCCGACG 62.899 72.222 17.53 0.00 35.87 5.12
92 93 4.554036 GGATCTGGCTGCCCCGAC 62.554 72.222 17.53 5.39 35.87 4.79
121 122 3.827898 GTGGAGGTCCGAGGCGAG 61.828 72.222 0.00 0.00 39.43 5.03
122 123 3.881019 AAGTGGAGGTCCGAGGCGA 62.881 63.158 0.00 0.00 39.43 5.54
123 124 3.382832 AAGTGGAGGTCCGAGGCG 61.383 66.667 0.00 0.00 39.43 5.52
124 125 2.266055 CAAGTGGAGGTCCGAGGC 59.734 66.667 0.00 0.00 39.43 4.70
125 126 2.266055 GCAAGTGGAGGTCCGAGG 59.734 66.667 0.00 0.00 39.43 4.63
126 127 2.266055 GGCAAGTGGAGGTCCGAG 59.734 66.667 0.00 0.00 39.43 4.63
127 128 2.525629 TGGCAAGTGGAGGTCCGA 60.526 61.111 0.00 0.00 39.43 4.55
128 129 2.046892 CTGGCAAGTGGAGGTCCG 60.047 66.667 0.00 0.00 39.43 4.79
129 130 2.360475 GCTGGCAAGTGGAGGTCC 60.360 66.667 0.00 0.00 0.00 4.46
130 131 2.743928 CGCTGGCAAGTGGAGGTC 60.744 66.667 0.00 0.00 0.00 3.85
131 132 3.537206 GACGCTGGCAAGTGGAGGT 62.537 63.158 6.61 0.00 38.30 3.85
132 133 2.743928 GACGCTGGCAAGTGGAGG 60.744 66.667 6.61 0.00 38.30 4.30
133 134 3.114616 CGACGCTGGCAAGTGGAG 61.115 66.667 6.61 0.00 38.30 3.86
226 227 1.219124 GGTTCATGCTCTGGCGAGA 59.781 57.895 9.91 0.00 39.74 4.04
227 228 1.817099 GGGTTCATGCTCTGGCGAG 60.817 63.158 0.00 0.00 42.25 5.03
228 229 2.268920 GGGTTCATGCTCTGGCGA 59.731 61.111 0.00 0.00 42.25 5.54
229 230 2.825836 GGGGTTCATGCTCTGGCG 60.826 66.667 0.00 0.00 42.25 5.69
230 231 1.751927 CAGGGGTTCATGCTCTGGC 60.752 63.158 0.00 0.00 39.26 4.85
231 232 1.751927 GCAGGGGTTCATGCTCTGG 60.752 63.158 1.51 0.00 46.01 3.86
232 233 3.915575 GCAGGGGTTCATGCTCTG 58.084 61.111 0.00 0.00 46.01 3.35
237 238 1.019673 CGATTCAGCAGGGGTTCATG 58.980 55.000 0.00 0.00 0.00 3.07
238 239 0.911769 TCGATTCAGCAGGGGTTCAT 59.088 50.000 0.00 0.00 0.00 2.57
239 240 0.250234 CTCGATTCAGCAGGGGTTCA 59.750 55.000 0.00 0.00 0.00 3.18
240 241 1.092345 GCTCGATTCAGCAGGGGTTC 61.092 60.000 0.00 0.00 39.43 3.62
241 242 1.078143 GCTCGATTCAGCAGGGGTT 60.078 57.895 0.00 0.00 39.43 4.11
242 243 2.586792 GCTCGATTCAGCAGGGGT 59.413 61.111 0.00 0.00 39.43 4.95
243 244 2.587194 CGCTCGATTCAGCAGGGG 60.587 66.667 8.24 0.00 39.62 4.79
244 245 2.587194 CCGCTCGATTCAGCAGGG 60.587 66.667 8.24 0.73 39.62 4.45
245 246 3.267860 GCCGCTCGATTCAGCAGG 61.268 66.667 8.24 9.81 39.62 4.85
246 247 3.267860 GGCCGCTCGATTCAGCAG 61.268 66.667 0.00 0.13 39.62 4.24
247 248 4.838152 GGGCCGCTCGATTCAGCA 62.838 66.667 0.00 0.00 39.62 4.41
248 249 4.838152 TGGGCCGCTCGATTCAGC 62.838 66.667 0.00 0.00 35.90 4.26
249 250 2.892425 GTGGGCCGCTCGATTCAG 60.892 66.667 10.52 0.00 0.00 3.02
250 251 4.812476 CGTGGGCCGCTCGATTCA 62.812 66.667 16.24 0.00 0.00 2.57
264 265 4.939368 TCGGGTTTGGGTGGCGTG 62.939 66.667 0.00 0.00 0.00 5.34
265 266 4.636435 CTCGGGTTTGGGTGGCGT 62.636 66.667 0.00 0.00 0.00 5.68
268 269 4.323477 TCGCTCGGGTTTGGGTGG 62.323 66.667 0.00 0.00 0.00 4.61
269 270 2.742372 CTCGCTCGGGTTTGGGTG 60.742 66.667 0.00 0.00 0.00 4.61
270 271 2.920912 TCTCGCTCGGGTTTGGGT 60.921 61.111 0.00 0.00 0.00 4.51
271 272 2.125512 CTCTCGCTCGGGTTTGGG 60.126 66.667 0.00 0.00 0.00 4.12
272 273 2.125512 CCTCTCGCTCGGGTTTGG 60.126 66.667 0.00 0.00 0.00 3.28
273 274 1.153745 CTCCTCTCGCTCGGGTTTG 60.154 63.158 0.00 0.00 0.00 2.93
274 275 2.352032 CCTCCTCTCGCTCGGGTTT 61.352 63.158 0.00 0.00 0.00 3.27
275 276 2.756283 CCTCCTCTCGCTCGGGTT 60.756 66.667 0.00 0.00 0.00 4.11
276 277 4.824515 CCCTCCTCTCGCTCGGGT 62.825 72.222 0.00 0.00 0.00 5.28
277 278 4.507916 TCCCTCCTCTCGCTCGGG 62.508 72.222 0.00 0.00 36.21 5.14
278 279 2.440430 TTCCCTCCTCTCGCTCGG 60.440 66.667 0.00 0.00 0.00 4.63
279 280 2.485795 CCTTCCCTCCTCTCGCTCG 61.486 68.421 0.00 0.00 0.00 5.03
280 281 2.131067 CCCTTCCCTCCTCTCGCTC 61.131 68.421 0.00 0.00 0.00 5.03
281 282 2.042435 CCCTTCCCTCCTCTCGCT 60.042 66.667 0.00 0.00 0.00 4.93
282 283 3.855853 GCCCTTCCCTCCTCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
283 284 3.157949 GGCCCTTCCCTCCTCTCG 61.158 72.222 0.00 0.00 0.00 4.04
284 285 1.764454 GAGGCCCTTCCCTCCTCTC 60.764 68.421 0.00 0.00 44.60 3.20
285 286 2.370633 GAGGCCCTTCCCTCCTCT 59.629 66.667 0.00 0.00 44.60 3.69
341 342 4.593864 GTCCATCCTCCTCGCCGC 62.594 72.222 0.00 0.00 0.00 6.53
342 343 4.271816 CGTCCATCCTCCTCGCCG 62.272 72.222 0.00 0.00 0.00 6.46
343 344 3.917760 CCGTCCATCCTCCTCGCC 61.918 72.222 0.00 0.00 0.00 5.54
344 345 3.917760 CCCGTCCATCCTCCTCGC 61.918 72.222 0.00 0.00 0.00 5.03
345 346 3.227276 CCCCGTCCATCCTCCTCG 61.227 72.222 0.00 0.00 0.00 4.63
346 347 2.844839 CCCCCGTCCATCCTCCTC 60.845 72.222 0.00 0.00 0.00 3.71
349 350 3.866582 CAGCCCCCGTCCATCCTC 61.867 72.222 0.00 0.00 0.00 3.71
361 362 3.081409 TAGGAGCGAACCCAGCCC 61.081 66.667 0.00 0.00 34.64 5.19
362 363 2.501610 CTAGGAGCGAACCCAGCC 59.498 66.667 0.00 0.00 34.64 4.85
363 364 2.501610 CCTAGGAGCGAACCCAGC 59.498 66.667 1.05 0.00 0.00 4.85
364 365 2.501610 GCCTAGGAGCGAACCCAG 59.498 66.667 14.75 0.00 0.00 4.45
365 366 3.081409 GGCCTAGGAGCGAACCCA 61.081 66.667 14.75 0.00 0.00 4.51
366 367 4.222847 CGGCCTAGGAGCGAACCC 62.223 72.222 14.75 0.47 0.00 4.11
367 368 4.893601 GCGGCCTAGGAGCGAACC 62.894 72.222 14.75 1.30 0.00 3.62
368 369 4.893601 GGCGGCCTAGGAGCGAAC 62.894 72.222 14.75 0.91 0.00 3.95
387 388 4.388499 TCCTTTGGTCGCTCCCGC 62.388 66.667 0.00 0.00 34.77 6.13
388 389 2.125512 CTCCTTTGGTCGCTCCCG 60.126 66.667 0.00 0.00 34.77 5.14
389 390 2.436824 GCTCCTTTGGTCGCTCCC 60.437 66.667 0.00 0.00 34.77 4.30
390 391 2.815647 CGCTCCTTTGGTCGCTCC 60.816 66.667 0.00 0.00 0.00 4.70
391 392 2.048127 ACGCTCCTTTGGTCGCTC 60.048 61.111 0.00 0.00 0.00 5.03
392 393 1.248785 TAGACGCTCCTTTGGTCGCT 61.249 55.000 0.00 0.00 35.87 4.93
393 394 0.389426 TTAGACGCTCCTTTGGTCGC 60.389 55.000 0.00 0.00 35.87 5.19
394 395 1.067776 AGTTAGACGCTCCTTTGGTCG 60.068 52.381 0.00 0.00 35.87 4.79
395 396 2.288886 ACAGTTAGACGCTCCTTTGGTC 60.289 50.000 0.00 0.00 0.00 4.02
396 397 1.692519 ACAGTTAGACGCTCCTTTGGT 59.307 47.619 0.00 0.00 0.00 3.67
397 398 2.457366 ACAGTTAGACGCTCCTTTGG 57.543 50.000 0.00 0.00 0.00 3.28
398 399 4.813296 AAAACAGTTAGACGCTCCTTTG 57.187 40.909 0.00 0.00 0.00 2.77
417 418 7.696992 ACAGTGAGGAAACAACTCTTAAAAA 57.303 32.000 0.00 0.00 35.98 1.94
418 419 8.671028 GTTACAGTGAGGAAACAACTCTTAAAA 58.329 33.333 0.00 0.00 35.98 1.52
419 420 7.281549 GGTTACAGTGAGGAAACAACTCTTAAA 59.718 37.037 0.00 0.00 35.98 1.52
420 421 6.764560 GGTTACAGTGAGGAAACAACTCTTAA 59.235 38.462 0.00 0.00 35.98 1.85
421 422 6.126997 TGGTTACAGTGAGGAAACAACTCTTA 60.127 38.462 0.00 0.00 35.98 2.10
422 423 5.123936 GGTTACAGTGAGGAAACAACTCTT 58.876 41.667 0.00 0.00 35.98 2.85
423 424 4.163458 TGGTTACAGTGAGGAAACAACTCT 59.837 41.667 0.00 0.00 35.98 3.24
424 425 4.448210 TGGTTACAGTGAGGAAACAACTC 58.552 43.478 0.00 0.00 35.55 3.01
425 426 4.497291 TGGTTACAGTGAGGAAACAACT 57.503 40.909 0.00 0.00 0.00 3.16
426 427 5.570234 TTTGGTTACAGTGAGGAAACAAC 57.430 39.130 0.00 0.00 29.76 3.32
427 428 5.712917 AGTTTTGGTTACAGTGAGGAAACAA 59.287 36.000 0.00 0.25 0.00 2.83
428 429 5.258051 AGTTTTGGTTACAGTGAGGAAACA 58.742 37.500 0.00 0.00 0.00 2.83
429 430 5.830000 AGTTTTGGTTACAGTGAGGAAAC 57.170 39.130 0.00 0.00 0.00 2.78
430 431 9.802039 ATATAAGTTTTGGTTACAGTGAGGAAA 57.198 29.630 0.00 0.00 0.00 3.13
431 432 9.802039 AATATAAGTTTTGGTTACAGTGAGGAA 57.198 29.630 0.00 0.00 0.00 3.36
432 433 9.802039 AAATATAAGTTTTGGTTACAGTGAGGA 57.198 29.630 0.00 0.00 0.00 3.71
468 469 7.953493 TCCCTCAGTTCCCAAATATAAGTTTTT 59.047 33.333 0.00 0.00 0.00 1.94
469 470 7.475299 TCCCTCAGTTCCCAAATATAAGTTTT 58.525 34.615 0.00 0.00 0.00 2.43
470 471 7.039722 TCCCTCAGTTCCCAAATATAAGTTT 57.960 36.000 0.00 0.00 0.00 2.66
471 472 6.217693 ACTCCCTCAGTTCCCAAATATAAGTT 59.782 38.462 0.00 0.00 26.56 2.66
472 473 5.731678 ACTCCCTCAGTTCCCAAATATAAGT 59.268 40.000 0.00 0.00 26.56 2.24
473 474 6.253946 ACTCCCTCAGTTCCCAAATATAAG 57.746 41.667 0.00 0.00 26.56 1.73
474 475 6.906901 ACTACTCCCTCAGTTCCCAAATATAA 59.093 38.462 0.00 0.00 36.43 0.98
475 476 6.449956 ACTACTCCCTCAGTTCCCAAATATA 58.550 40.000 0.00 0.00 36.43 0.86
476 477 5.289510 ACTACTCCCTCAGTTCCCAAATAT 58.710 41.667 0.00 0.00 36.43 1.28
477 478 4.695606 ACTACTCCCTCAGTTCCCAAATA 58.304 43.478 0.00 0.00 36.43 1.40
478 479 3.532102 ACTACTCCCTCAGTTCCCAAAT 58.468 45.455 0.00 0.00 36.43 2.32
479 480 2.986050 ACTACTCCCTCAGTTCCCAAA 58.014 47.619 0.00 0.00 36.43 3.28
480 481 2.637872 CAACTACTCCCTCAGTTCCCAA 59.362 50.000 0.00 0.00 36.43 4.12
481 482 2.257207 CAACTACTCCCTCAGTTCCCA 58.743 52.381 0.00 0.00 36.43 4.37
482 483 1.555533 CCAACTACTCCCTCAGTTCCC 59.444 57.143 0.00 0.00 36.43 3.97
483 484 1.066071 GCCAACTACTCCCTCAGTTCC 60.066 57.143 0.00 0.00 36.43 3.62
484 485 1.903183 AGCCAACTACTCCCTCAGTTC 59.097 52.381 0.00 0.00 36.43 3.01
485 486 1.903183 GAGCCAACTACTCCCTCAGTT 59.097 52.381 0.00 0.00 36.43 3.16
486 487 1.562783 GAGCCAACTACTCCCTCAGT 58.437 55.000 0.00 0.00 39.41 3.41
487 488 0.457851 CGAGCCAACTACTCCCTCAG 59.542 60.000 0.00 0.00 0.00 3.35
488 489 0.039180 TCGAGCCAACTACTCCCTCA 59.961 55.000 0.00 0.00 0.00 3.86
489 490 0.741915 CTCGAGCCAACTACTCCCTC 59.258 60.000 0.00 0.00 0.00 4.30
490 491 0.039911 ACTCGAGCCAACTACTCCCT 59.960 55.000 13.61 0.00 0.00 4.20
491 492 0.173708 CACTCGAGCCAACTACTCCC 59.826 60.000 13.61 0.00 0.00 4.30
492 493 0.173708 CCACTCGAGCCAACTACTCC 59.826 60.000 13.61 0.00 0.00 3.85
493 494 0.173708 CCCACTCGAGCCAACTACTC 59.826 60.000 13.61 0.00 0.00 2.59
494 495 1.889530 GCCCACTCGAGCCAACTACT 61.890 60.000 13.61 0.00 0.00 2.57
495 496 1.448013 GCCCACTCGAGCCAACTAC 60.448 63.158 13.61 0.00 0.00 2.73
496 497 2.978824 GCCCACTCGAGCCAACTA 59.021 61.111 13.61 0.00 0.00 2.24
497 498 4.379243 CGCCCACTCGAGCCAACT 62.379 66.667 13.61 0.00 0.00 3.16
498 499 4.681978 ACGCCCACTCGAGCCAAC 62.682 66.667 13.61 0.00 0.00 3.77
499 500 4.680237 CACGCCCACTCGAGCCAA 62.680 66.667 13.61 0.00 0.00 4.52
503 504 4.717629 TTCGCACGCCCACTCGAG 62.718 66.667 11.84 11.84 32.31 4.04
506 507 3.414700 CAGTTCGCACGCCCACTC 61.415 66.667 0.00 0.00 0.00 3.51
511 512 4.430423 CTTCGCAGTTCGCACGCC 62.430 66.667 0.00 0.00 42.60 5.68
512 513 4.430423 CCTTCGCAGTTCGCACGC 62.430 66.667 0.00 0.00 42.60 5.34
513 514 3.036084 ACCTTCGCAGTTCGCACG 61.036 61.111 0.00 0.00 42.60 5.34
514 515 1.495584 TTCACCTTCGCAGTTCGCAC 61.496 55.000 0.00 0.00 42.60 5.34
515 516 0.812014 TTTCACCTTCGCAGTTCGCA 60.812 50.000 0.00 0.00 42.60 5.10
516 517 0.306533 TTTTCACCTTCGCAGTTCGC 59.693 50.000 0.00 0.00 38.27 4.70
517 518 1.597663 AGTTTTCACCTTCGCAGTTCG 59.402 47.619 0.00 0.00 40.15 3.95
518 519 3.692791 AAGTTTTCACCTTCGCAGTTC 57.307 42.857 0.00 0.00 0.00 3.01
519 520 3.428862 CCAAAGTTTTCACCTTCGCAGTT 60.429 43.478 0.00 0.00 0.00 3.16
520 521 2.099098 CCAAAGTTTTCACCTTCGCAGT 59.901 45.455 0.00 0.00 0.00 4.40
521 522 2.543653 CCCAAAGTTTTCACCTTCGCAG 60.544 50.000 0.00 0.00 0.00 5.18
540 541 1.077089 GTACAGAAGAGAACGCGCCC 61.077 60.000 5.73 0.00 0.00 6.13
560 563 1.151668 CCTCTTTCGTTCAGGCACAG 58.848 55.000 0.00 0.00 0.00 3.66
600 603 3.828875 AGACGAGATTGGGGATTCTTC 57.171 47.619 0.00 0.00 0.00 2.87
602 605 2.436173 GGAAGACGAGATTGGGGATTCT 59.564 50.000 0.00 0.00 0.00 2.40
683 687 4.840005 GCGGGAGGAAGAAGGCGG 62.840 72.222 0.00 0.00 0.00 6.13
685 689 4.083862 ACGCGGGAGGAAGAAGGC 62.084 66.667 12.47 0.00 0.00 4.35
686 690 2.184579 GACGCGGGAGGAAGAAGG 59.815 66.667 12.47 0.00 0.00 3.46
687 691 2.202623 CGACGCGGGAGGAAGAAG 60.203 66.667 12.47 0.00 0.00 2.85
688 692 4.430765 GCGACGCGGGAGGAAGAA 62.431 66.667 12.47 0.00 0.00 2.52
812 826 0.895530 CTAACCCTCAGTTGGAGCGA 59.104 55.000 0.00 0.00 42.62 4.93
853 867 2.267426 CTGGTCGCATTGTGATTCGTA 58.733 47.619 2.78 0.00 0.00 3.43
857 871 2.425143 ATCCTGGTCGCATTGTGATT 57.575 45.000 2.78 0.00 0.00 2.57
1006 1020 1.378778 CGGGAGACGGAGAAGAGGT 60.379 63.158 0.00 0.00 39.42 3.85
1096 1113 2.554893 GGGAGTAGCCGTCTATCTTGAG 59.445 54.545 0.00 0.00 37.63 3.02
1272 1295 3.245284 TCTTGAACTTCGCTTTGACTTCG 59.755 43.478 0.00 0.00 0.00 3.79
1284 1307 5.631096 GCCAAGCAAACTTATCTTGAACTTC 59.369 40.000 3.09 0.00 39.48 3.01
1406 1835 5.433051 TGAAGGGATTCCTCCAAGTCATATT 59.567 40.000 0.00 0.00 44.07 1.28
1408 1837 4.164221 GTGAAGGGATTCCTCCAAGTCATA 59.836 45.833 0.00 0.00 44.07 2.15
1593 2022 3.371063 GTCTCCGCACCGACCTCA 61.371 66.667 0.00 0.00 0.00 3.86
1731 2160 2.299326 AGTGGAGCAAAGCCTTGAAT 57.701 45.000 0.00 0.00 34.14 2.57
1936 5246 1.294659 GCCTCCTTGAGAGCAACACG 61.295 60.000 0.00 0.00 41.74 4.49
1940 5250 0.679002 GCATGCCTCCTTGAGAGCAA 60.679 55.000 6.36 0.00 41.74 3.91
1951 5261 1.471684 CAGGAACTTGAAGCATGCCTC 59.528 52.381 15.66 12.33 34.60 4.70
2489 5808 0.951040 GCAGCAGGCACGTAAACTCT 60.951 55.000 0.00 0.00 43.97 3.24
2502 5821 4.934602 GCCCTCTATTTATTCTAGCAGCAG 59.065 45.833 0.00 0.00 0.00 4.24
2545 5888 3.056250 TGGATCAGCTGAGTGAAGAAGAC 60.056 47.826 22.96 3.26 0.00 3.01
2546 5889 3.168292 TGGATCAGCTGAGTGAAGAAGA 58.832 45.455 22.96 0.00 0.00 2.87
2547 5890 3.606595 TGGATCAGCTGAGTGAAGAAG 57.393 47.619 22.96 0.00 0.00 2.85
2548 5891 4.564782 AATGGATCAGCTGAGTGAAGAA 57.435 40.909 22.96 3.68 0.00 2.52
2569 5912 2.380064 ATGCAAAGTTCTGGGACCAA 57.620 45.000 0.00 0.00 0.00 3.67
2592 5935 7.124147 TCAAAAGAAGTTTTTCCTGGATGTTCT 59.876 33.333 0.00 0.00 33.35 3.01
2619 5963 7.919690 CATCGAGCTTTTCTGGATGTTATTTA 58.080 34.615 8.22 0.00 46.55 1.40
2647 5991 6.692486 TGCGGGTTTACATTGACAAAAATAT 58.308 32.000 0.00 0.00 0.00 1.28
2660 6004 1.201181 GCATTGTCATGCGGGTTTACA 59.799 47.619 0.00 0.00 46.45 2.41
2661 6005 1.908065 GCATTGTCATGCGGGTTTAC 58.092 50.000 0.00 0.00 46.45 2.01
2672 6016 2.942804 TCCAACAAGGAAGCATTGTCA 58.057 42.857 0.00 0.00 45.65 3.58
2746 6091 0.251916 TACCTCCATTGTCAAGCCGG 59.748 55.000 0.00 0.00 0.00 6.13
2747 6092 2.332063 ATACCTCCATTGTCAAGCCG 57.668 50.000 0.00 0.00 0.00 5.52
2782 6127 1.623973 GCACCGCGAAGTGTAGTTCC 61.624 60.000 8.23 0.00 40.04 3.62
2789 6134 1.154413 GTTGATGCACCGCGAAGTG 60.154 57.895 8.23 9.76 40.88 3.16
2797 6142 5.156355 CACAGAACTATTTGTTGATGCACC 58.844 41.667 0.00 0.00 39.30 5.01
2801 6146 6.808008 ACTCCACAGAACTATTTGTTGATG 57.192 37.500 0.00 0.00 39.30 3.07
2810 6155 7.335422 CAGCATTCTAAAACTCCACAGAACTAT 59.665 37.037 0.00 0.00 30.28 2.12
2813 6158 5.239525 ACAGCATTCTAAAACTCCACAGAAC 59.760 40.000 0.00 0.00 30.28 3.01
2820 6165 5.470098 TGTCTTCACAGCATTCTAAAACTCC 59.530 40.000 0.00 0.00 0.00 3.85
2834 6179 3.492383 GCCATCGACATATGTCTTCACAG 59.508 47.826 28.51 14.99 42.66 3.66
2850 6195 3.186909 TGAACGTCTTCATTAGCCATCG 58.813 45.455 0.00 0.00 31.00 3.84
2863 6208 2.154462 CCTGGAAAGCAATGAACGTCT 58.846 47.619 0.00 0.00 0.00 4.18
2866 6211 2.351738 GGAACCTGGAAAGCAATGAACG 60.352 50.000 0.00 0.00 0.00 3.95
2916 6269 5.300792 TGATAAAAAGCTTTTGGAGTCCGTT 59.699 36.000 24.50 8.51 0.00 4.44
2919 6272 5.470368 GGTGATAAAAAGCTTTTGGAGTCC 58.530 41.667 24.50 18.76 0.00 3.85
2939 6292 1.362355 GTTGGGCGTTTGAAGGGTG 59.638 57.895 0.00 0.00 0.00 4.61
2941 6294 1.448922 TTCGTTGGGCGTTTGAAGGG 61.449 55.000 0.00 0.00 42.13 3.95
2942 6295 0.382515 TTTCGTTGGGCGTTTGAAGG 59.617 50.000 0.00 0.00 42.13 3.46
2944 6297 0.809385 TGTTTCGTTGGGCGTTTGAA 59.191 45.000 0.00 0.00 42.13 2.69
2945 6298 1.002251 GATGTTTCGTTGGGCGTTTGA 60.002 47.619 0.00 0.00 42.13 2.69
2946 6299 1.268794 TGATGTTTCGTTGGGCGTTTG 60.269 47.619 0.00 0.00 42.13 2.93
2950 6306 1.234615 ACCTGATGTTTCGTTGGGCG 61.235 55.000 0.00 0.00 43.01 6.13
2951 6307 0.521735 GACCTGATGTTTCGTTGGGC 59.478 55.000 0.00 0.00 0.00 5.36
2958 6314 4.764172 AGCTACTCATGACCTGATGTTTC 58.236 43.478 0.00 0.00 32.10 2.78
3009 6365 8.842358 TCTTCCTTTACGAAAGAAACATATGT 57.158 30.769 1.41 1.41 41.02 2.29


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

AutoCloner maintained by Alex Coulton.