Multiple sequence alignment - TraesCS6B01G135000

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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 TraesCS6B01G135000 chr6B 100.000 2543 0 0 1 2543 132307383 132309925 0.000000e+00 4697
1 TraesCS6B01G135000 chr6A 92.524 2167 114 25 373 2509 73979529 73981677 0.000000e+00 3061
2 TraesCS6B01G135000 chr6D 89.466 674 54 10 1870 2540 58689365 58690024 0.000000e+00 835
3 TraesCS6B01G135000 chr3B 94.361 266 13 1 20 283 507455143 507455408 8.470000e-110 407
4 TraesCS6B01G135000 chr4D 94.656 262 13 1 20 280 479154224 479154485 3.050000e-109 405
5 TraesCS6B01G135000 chr3D 94.677 263 11 2 19 279 447585145 447584884 3.050000e-109 405
6 TraesCS6B01G135000 chr3D 87.000 100 12 1 277 375 347516509 347516608 7.440000e-21 111
7 TraesCS6B01G135000 chr3D 82.500 120 17 4 276 392 575309020 575308902 4.480000e-18 102
8 TraesCS6B01G135000 chr1D 94.297 263 13 2 20 280 97740413 97740151 3.940000e-108 401
9 TraesCS6B01G135000 chr1B 94.275 262 13 2 21 280 211478859 211479120 1.420000e-107 399
10 TraesCS6B01G135000 chr4B 94.253 261 13 2 20 279 144006596 144006337 5.100000e-107 398
11 TraesCS6B01G135000 chr2B 94.275 262 12 2 21 280 357919559 357919819 5.100000e-107 398
12 TraesCS6B01G135000 chr2B 93.609 266 15 1 20 283 245948224 245947959 1.830000e-106 396
13 TraesCS6B01G135000 chr7A 93.893 262 15 1 20 280 44210820 44210559 6.590000e-106 394
14 TraesCS6B01G135000 chr1A 79.096 354 58 14 20 366 570043807 570044151 1.970000e-56 230
15 TraesCS6B01G135000 chr1A 86.869 99 12 1 278 375 134525965 134525867 2.670000e-20 110
16 TraesCS6B01G135000 chr4A 78.470 353 62 13 22 366 624013222 624013568 4.260000e-53 219
17 TraesCS6B01G135000 chr5B 87.129 101 10 3 278 376 6876074 6875975 7.440000e-21 111
18 TraesCS6B01G135000 chr5B 87.000 100 11 2 277 375 482316130 482316032 7.440000e-21 111
19 TraesCS6B01G135000 chr7B 86.869 99 12 1 278 375 516266983 516266885 2.670000e-20 110
20 TraesCS6B01G135000 chr2D 84.906 106 12 4 270 374 599889542 599889440 1.240000e-18 104


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 TraesCS6B01G135000 chr6B 132307383 132309925 2542 False 4697 4697 100.000 1 2543 1 chr6B.!!$F1 2542
1 TraesCS6B01G135000 chr6A 73979529 73981677 2148 False 3061 3061 92.524 373 2509 1 chr6A.!!$F1 2136
2 TraesCS6B01G135000 chr6D 58689365 58690024 659 False 835 835 89.466 1870 2540 1 chr6D.!!$F1 670

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
370 371 0.110104 TGGTCATGCATGTCACCACA 59.890 50.0 27.81 14.0 33.83 4.17 F
880 882 0.313987 TCGTGAGCGCAAGAAGAAGA 59.686 50.0 11.47 0.0 43.02 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1447 0.034767 CTCCTGGGAGCTTGAATGCA 60.035 55.0 3.52 0.0 35.31 3.96 R
2468 2495 0.742990 TAAAGAACGGCGCATGGAGG 60.743 55.0 10.83 0.0 0.00 4.30 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 2.777459 CTCCCCACTATGGAGGTACT 57.223 55.000 0.00 0.00 44.73 2.73
39 40 5.548181 AGGTACTCTCTCCGTTTCTTTTT 57.452 39.130 0.00 0.00 0.00 1.94
40 41 6.661304 AGGTACTCTCTCCGTTTCTTTTTA 57.339 37.500 0.00 0.00 0.00 1.52
41 42 6.689554 AGGTACTCTCTCCGTTTCTTTTTAG 58.310 40.000 0.00 0.00 0.00 1.85
42 43 6.267242 AGGTACTCTCTCCGTTTCTTTTTAGT 59.733 38.462 0.00 0.00 0.00 2.24
43 44 6.927936 GGTACTCTCTCCGTTTCTTTTTAGTT 59.072 38.462 0.00 0.00 0.00 2.24
44 45 7.440556 GGTACTCTCTCCGTTTCTTTTTAGTTT 59.559 37.037 0.00 0.00 0.00 2.66
45 46 7.247929 ACTCTCTCCGTTTCTTTTTAGTTTG 57.752 36.000 0.00 0.00 0.00 2.93
46 47 6.056428 TCTCTCCGTTTCTTTTTAGTTTGC 57.944 37.500 0.00 0.00 0.00 3.68
47 48 5.587043 TCTCTCCGTTTCTTTTTAGTTTGCA 59.413 36.000 0.00 0.00 0.00 4.08
48 49 6.262273 TCTCTCCGTTTCTTTTTAGTTTGCAT 59.738 34.615 0.00 0.00 0.00 3.96
49 50 7.442969 TCTCTCCGTTTCTTTTTAGTTTGCATA 59.557 33.333 0.00 0.00 0.00 3.14
50 51 8.106247 TCTCCGTTTCTTTTTAGTTTGCATAT 57.894 30.769 0.00 0.00 0.00 1.78
51 52 9.221933 TCTCCGTTTCTTTTTAGTTTGCATATA 57.778 29.630 0.00 0.00 0.00 0.86
52 53 9.834628 CTCCGTTTCTTTTTAGTTTGCATATAA 57.165 29.630 0.00 0.00 0.00 0.98
53 54 9.834628 TCCGTTTCTTTTTAGTTTGCATATAAG 57.165 29.630 0.00 0.00 0.00 1.73
54 55 9.834628 CCGTTTCTTTTTAGTTTGCATATAAGA 57.165 29.630 0.00 0.00 0.00 2.10
75 76 9.981114 ATAAGATTTGGTTAAAGTCAAACTTGG 57.019 29.630 15.23 0.00 38.66 3.61
76 77 7.418337 AGATTTGGTTAAAGTCAAACTTGGT 57.582 32.000 0.00 0.00 38.66 3.67
77 78 8.528044 AGATTTGGTTAAAGTCAAACTTGGTA 57.472 30.769 0.00 0.00 38.66 3.25
78 79 8.973182 AGATTTGGTTAAAGTCAAACTTGGTAA 58.027 29.630 0.00 0.00 38.66 2.85
79 80 9.589111 GATTTGGTTAAAGTCAAACTTGGTAAA 57.411 29.630 0.00 0.00 38.66 2.01
80 81 9.945904 ATTTGGTTAAAGTCAAACTTGGTAAAA 57.054 25.926 0.00 0.00 38.66 1.52
81 82 9.945904 TTTGGTTAAAGTCAAACTTGGTAAAAT 57.054 25.926 0.00 0.00 38.66 1.82
82 83 9.945904 TTGGTTAAAGTCAAACTTGGTAAAATT 57.054 25.926 0.00 0.00 38.66 1.82
83 84 9.945904 TGGTTAAAGTCAAACTTGGTAAAATTT 57.054 25.926 0.00 0.00 38.66 1.82
91 92 8.232913 TCAAACTTGGTAAAATTTGACTAGCT 57.767 30.769 5.64 0.00 36.42 3.32
92 93 8.691797 TCAAACTTGGTAAAATTTGACTAGCTT 58.308 29.630 5.64 0.00 36.42 3.74
93 94 9.313118 CAAACTTGGTAAAATTTGACTAGCTTT 57.687 29.630 5.64 0.00 34.62 3.51
94 95 8.871686 AACTTGGTAAAATTTGACTAGCTTTG 57.128 30.769 5.64 0.00 0.00 2.77
95 96 8.007405 ACTTGGTAAAATTTGACTAGCTTTGT 57.993 30.769 5.64 0.00 0.00 2.83
96 97 9.127277 ACTTGGTAAAATTTGACTAGCTTTGTA 57.873 29.630 5.64 0.00 0.00 2.41
97 98 9.612620 CTTGGTAAAATTTGACTAGCTTTGTAG 57.387 33.333 5.64 0.00 0.00 2.74
98 99 8.106247 TGGTAAAATTTGACTAGCTTTGTAGG 57.894 34.615 5.64 0.00 0.00 3.18
99 100 7.940137 TGGTAAAATTTGACTAGCTTTGTAGGA 59.060 33.333 5.64 0.00 0.00 2.94
100 101 8.789762 GGTAAAATTTGACTAGCTTTGTAGGAA 58.210 33.333 5.64 0.00 0.00 3.36
103 104 9.750125 AAAATTTGACTAGCTTTGTAGGAAAAG 57.250 29.630 0.00 0.00 39.66 2.27
104 105 8.691661 AATTTGACTAGCTTTGTAGGAAAAGA 57.308 30.769 0.00 0.00 39.12 2.52
105 106 8.870075 ATTTGACTAGCTTTGTAGGAAAAGAT 57.130 30.769 0.00 0.00 39.12 2.40
106 107 9.959721 ATTTGACTAGCTTTGTAGGAAAAGATA 57.040 29.630 0.00 0.00 39.12 1.98
107 108 9.959721 TTTGACTAGCTTTGTAGGAAAAGATAT 57.040 29.630 0.00 0.00 37.39 1.63
108 109 9.601217 TTGACTAGCTTTGTAGGAAAAGATATC 57.399 33.333 0.00 0.00 37.39 1.63
109 110 8.758829 TGACTAGCTTTGTAGGAAAAGATATCA 58.241 33.333 5.32 3.18 37.39 2.15
110 111 9.601217 GACTAGCTTTGTAGGAAAAGATATCAA 57.399 33.333 5.32 0.00 37.39 2.57
111 112 9.384764 ACTAGCTTTGTAGGAAAAGATATCAAC 57.615 33.333 5.32 0.00 37.39 3.18
112 113 9.383519 CTAGCTTTGTAGGAAAAGATATCAACA 57.616 33.333 5.32 0.00 37.39 3.33
113 114 8.814038 AGCTTTGTAGGAAAAGATATCAACAT 57.186 30.769 5.32 0.00 39.12 2.71
114 115 8.897752 AGCTTTGTAGGAAAAGATATCAACATC 58.102 33.333 5.32 0.00 39.12 3.06
115 116 8.131731 GCTTTGTAGGAAAAGATATCAACATCC 58.868 37.037 5.32 7.06 39.12 3.51
116 117 9.177608 CTTTGTAGGAAAAGATATCAACATCCA 57.822 33.333 5.32 0.00 39.12 3.41
117 118 8.506168 TTGTAGGAAAAGATATCAACATCCAC 57.494 34.615 5.32 8.31 0.00 4.02
118 119 7.629157 TGTAGGAAAAGATATCAACATCCACA 58.371 34.615 5.32 10.27 0.00 4.17
119 120 7.552687 TGTAGGAAAAGATATCAACATCCACAC 59.447 37.037 5.32 9.15 0.00 3.82
120 121 6.725364 AGGAAAAGATATCAACATCCACACT 58.275 36.000 5.32 0.00 0.00 3.55
121 122 7.861629 AGGAAAAGATATCAACATCCACACTA 58.138 34.615 5.32 0.00 0.00 2.74
122 123 8.497745 AGGAAAAGATATCAACATCCACACTAT 58.502 33.333 5.32 0.00 0.00 2.12
123 124 8.562892 GGAAAAGATATCAACATCCACACTATG 58.437 37.037 5.32 0.00 0.00 2.23
124 125 9.330063 GAAAAGATATCAACATCCACACTATGA 57.670 33.333 5.32 0.00 0.00 2.15
125 126 9.685276 AAAAGATATCAACATCCACACTATGAA 57.315 29.630 5.32 0.00 0.00 2.57
126 127 9.685276 AAAGATATCAACATCCACACTATGAAA 57.315 29.630 5.32 0.00 0.00 2.69
127 128 9.857656 AAGATATCAACATCCACACTATGAAAT 57.142 29.630 5.32 0.00 0.00 2.17
128 129 9.499479 AGATATCAACATCCACACTATGAAATC 57.501 33.333 5.32 0.00 0.00 2.17
129 130 9.276590 GATATCAACATCCACACTATGAAATCA 57.723 33.333 0.00 0.00 0.00 2.57
130 131 7.943079 ATCAACATCCACACTATGAAATCAA 57.057 32.000 0.00 0.00 0.00 2.57
131 132 7.943079 TCAACATCCACACTATGAAATCAAT 57.057 32.000 0.00 0.00 0.00 2.57
132 133 9.631257 ATCAACATCCACACTATGAAATCAATA 57.369 29.630 0.00 0.00 0.00 1.90
133 134 9.460019 TCAACATCCACACTATGAAATCAATAA 57.540 29.630 0.00 0.00 0.00 1.40
276 277 8.888579 TGTAGACTAAAAAGAAACAGAAGGAG 57.111 34.615 0.00 0.00 0.00 3.69
277 278 8.483758 TGTAGACTAAAAAGAAACAGAAGGAGT 58.516 33.333 0.00 0.00 0.00 3.85
278 279 9.978044 GTAGACTAAAAAGAAACAGAAGGAGTA 57.022 33.333 0.00 0.00 0.00 2.59
279 280 8.890124 AGACTAAAAAGAAACAGAAGGAGTAC 57.110 34.615 0.00 0.00 0.00 2.73
280 281 8.706521 AGACTAAAAAGAAACAGAAGGAGTACT 58.293 33.333 0.00 0.00 0.00 2.73
281 282 9.978044 GACTAAAAAGAAACAGAAGGAGTACTA 57.022 33.333 0.00 0.00 0.00 1.82
282 283 9.761504 ACTAAAAAGAAACAGAAGGAGTACTAC 57.238 33.333 0.00 0.00 0.00 2.73
283 284 9.205719 CTAAAAAGAAACAGAAGGAGTACTACC 57.794 37.037 0.00 2.33 0.00 3.18
284 285 6.997942 AAAGAAACAGAAGGAGTACTACCT 57.002 37.500 0.00 4.79 39.69 3.08
285 286 6.593268 AAGAAACAGAAGGAGTACTACCTC 57.407 41.667 0.00 0.00 36.67 3.85
296 297 6.980416 GGAGTACTACCTCCTTCATGTTAT 57.020 41.667 0.00 0.00 46.34 1.89
298 299 8.653036 GGAGTACTACCTCCTTCATGTTATAT 57.347 38.462 0.00 0.00 46.34 0.86
299 300 9.091220 GGAGTACTACCTCCTTCATGTTATATT 57.909 37.037 0.00 0.00 46.34 1.28
300 301 9.915629 GAGTACTACCTCCTTCATGTTATATTG 57.084 37.037 0.00 0.00 0.00 1.90
301 302 9.656323 AGTACTACCTCCTTCATGTTATATTGA 57.344 33.333 0.00 0.00 0.00 2.57
304 305 8.598041 ACTACCTCCTTCATGTTATATTGATCC 58.402 37.037 0.00 0.00 0.00 3.36
305 306 6.784031 ACCTCCTTCATGTTATATTGATCCC 58.216 40.000 0.00 0.00 0.00 3.85
306 307 6.183347 CCTCCTTCATGTTATATTGATCCCC 58.817 44.000 0.00 0.00 0.00 4.81
307 308 6.240263 CCTCCTTCATGTTATATTGATCCCCA 60.240 42.308 0.00 0.00 0.00 4.96
308 309 7.347319 TCCTTCATGTTATATTGATCCCCAT 57.653 36.000 0.00 0.00 0.00 4.00
309 310 7.768643 TCCTTCATGTTATATTGATCCCCATT 58.231 34.615 0.00 0.00 0.00 3.16
310 311 7.670979 TCCTTCATGTTATATTGATCCCCATTG 59.329 37.037 0.00 0.00 0.00 2.82
311 312 7.452501 CCTTCATGTTATATTGATCCCCATTGT 59.547 37.037 0.00 0.00 0.00 2.71
312 313 9.519191 CTTCATGTTATATTGATCCCCATTGTA 57.481 33.333 0.00 0.00 0.00 2.41
316 317 8.877864 TGTTATATTGATCCCCATTGTATTCC 57.122 34.615 0.00 0.00 0.00 3.01
317 318 7.609918 TGTTATATTGATCCCCATTGTATTCCG 59.390 37.037 0.00 0.00 0.00 4.30
318 319 3.943671 TTGATCCCCATTGTATTCCGT 57.056 42.857 0.00 0.00 0.00 4.69
319 320 3.207265 TGATCCCCATTGTATTCCGTG 57.793 47.619 0.00 0.00 0.00 4.94
320 321 2.507886 TGATCCCCATTGTATTCCGTGT 59.492 45.455 0.00 0.00 0.00 4.49
321 322 2.702592 TCCCCATTGTATTCCGTGTC 57.297 50.000 0.00 0.00 0.00 3.67
322 323 1.909986 TCCCCATTGTATTCCGTGTCA 59.090 47.619 0.00 0.00 0.00 3.58
323 324 2.306219 TCCCCATTGTATTCCGTGTCAA 59.694 45.455 0.00 0.00 0.00 3.18
324 325 3.085533 CCCCATTGTATTCCGTGTCAAA 58.914 45.455 0.00 0.00 0.00 2.69
325 326 3.699038 CCCCATTGTATTCCGTGTCAAAT 59.301 43.478 0.00 0.00 0.00 2.32
326 327 4.159506 CCCCATTGTATTCCGTGTCAAATT 59.840 41.667 0.00 0.00 0.00 1.82
327 328 5.337169 CCCCATTGTATTCCGTGTCAAATTT 60.337 40.000 0.00 0.00 0.00 1.82
328 329 6.162777 CCCATTGTATTCCGTGTCAAATTTT 58.837 36.000 0.00 0.00 0.00 1.82
329 330 6.090628 CCCATTGTATTCCGTGTCAAATTTTG 59.909 38.462 2.59 2.59 0.00 2.44
330 331 6.865726 CCATTGTATTCCGTGTCAAATTTTGA 59.134 34.615 7.74 7.74 37.33 2.69
331 332 7.545265 CCATTGTATTCCGTGTCAAATTTTGAT 59.455 33.333 14.54 0.44 42.47 2.57
332 333 8.586273 CATTGTATTCCGTGTCAAATTTTGATC 58.414 33.333 14.54 10.13 42.47 2.92
333 334 7.208225 TGTATTCCGTGTCAAATTTTGATCA 57.792 32.000 14.54 11.36 42.47 2.92
334 335 7.825681 TGTATTCCGTGTCAAATTTTGATCAT 58.174 30.769 14.54 4.66 42.47 2.45
335 336 8.951243 TGTATTCCGTGTCAAATTTTGATCATA 58.049 29.630 14.54 0.00 42.47 2.15
336 337 9.781834 GTATTCCGTGTCAAATTTTGATCATAA 57.218 29.630 14.54 0.00 42.47 1.90
338 339 9.874205 ATTCCGTGTCAAATTTTGATCATAAAT 57.126 25.926 14.54 9.59 42.47 1.40
339 340 9.703892 TTCCGTGTCAAATTTTGATCATAAATT 57.296 25.926 14.54 16.33 42.47 1.82
340 341 9.703892 TCCGTGTCAAATTTTGATCATAAATTT 57.296 25.926 22.18 22.18 42.72 1.82
361 362 9.723601 AAATTTAACTAACAAATGGTCATGCAT 57.276 25.926 0.00 0.00 0.00 3.96
362 363 8.706492 ATTTAACTAACAAATGGTCATGCATG 57.294 30.769 21.07 21.07 0.00 4.06
363 364 5.726980 AACTAACAAATGGTCATGCATGT 57.273 34.783 25.43 4.01 0.00 3.21
364 365 5.314923 ACTAACAAATGGTCATGCATGTC 57.685 39.130 25.43 19.92 0.00 3.06
365 366 4.766373 ACTAACAAATGGTCATGCATGTCA 59.234 37.500 25.43 22.88 0.00 3.58
366 367 3.581024 ACAAATGGTCATGCATGTCAC 57.419 42.857 25.43 17.06 0.00 3.67
367 368 2.231964 ACAAATGGTCATGCATGTCACC 59.768 45.455 25.43 24.69 0.00 4.02
368 369 2.219080 AATGGTCATGCATGTCACCA 57.781 45.000 31.37 31.37 43.10 4.17
369 370 1.466856 ATGGTCATGCATGTCACCAC 58.533 50.000 31.71 20.45 41.74 4.16
370 371 0.110104 TGGTCATGCATGTCACCACA 59.890 50.000 27.81 14.00 33.83 4.17
371 372 1.246649 GGTCATGCATGTCACCACAA 58.753 50.000 25.32 4.75 35.64 3.33
385 386 6.098679 TGTCACCACAAATTTCTTGTCAAAG 58.901 36.000 0.00 0.00 34.45 2.77
414 416 3.002862 GTGTGAATTTGCGACCTGTACAA 59.997 43.478 0.00 0.00 0.00 2.41
415 417 3.818210 TGTGAATTTGCGACCTGTACAAT 59.182 39.130 0.00 0.00 0.00 2.71
427 429 5.514274 ACCTGTACAATGTTTCCAAGTTG 57.486 39.130 0.00 0.00 0.00 3.16
431 433 2.397597 ACAATGTTTCCAAGTTGCCCT 58.602 42.857 0.00 0.00 0.00 5.19
450 452 6.841601 TGCCCTATGATTATAAGTTTCAGCT 58.158 36.000 0.00 0.00 0.00 4.24
481 483 8.947055 ACTTTTACTTGTCAGCATTCAATTTT 57.053 26.923 0.00 0.00 0.00 1.82
534 536 9.226345 GCACATTTTCTTTCTTATATACAGTGC 57.774 33.333 0.00 0.00 38.34 4.40
553 555 6.128445 ACAGTGCGAAACTTCTGATATTCTTG 60.128 38.462 0.00 0.00 36.83 3.02
555 557 6.091441 AGTGCGAAACTTCTGATATTCTTGAC 59.909 38.462 0.00 0.00 34.57 3.18
561 563 3.179443 TCTGATATTCTTGACCCGCAC 57.821 47.619 0.00 0.00 0.00 5.34
593 595 0.326048 ACCTGCTATGTGGAGCTCCT 60.326 55.000 32.28 16.00 43.27 3.69
617 619 4.481195 GGACAAGTCCTGCTGCAA 57.519 55.556 11.94 0.00 46.16 4.08
652 654 3.562141 AGTAGAGCGTATACTGCAGTCTG 59.438 47.826 25.56 12.62 32.27 3.51
672 674 1.205460 TCCAGGTCCTTTGCCCCTAC 61.205 60.000 0.00 0.00 0.00 3.18
766 768 2.821378 CCATGCTTCACTGGATCAAACA 59.179 45.455 0.00 0.00 34.24 2.83
770 772 3.953612 TGCTTCACTGGATCAAACAAAGT 59.046 39.130 0.00 0.00 0.00 2.66
812 814 3.275617 TGGGTTACCATCGGATTCTTG 57.724 47.619 2.98 0.00 43.37 3.02
813 815 1.947456 GGGTTACCATCGGATTCTTGC 59.053 52.381 2.98 0.00 36.50 4.01
816 818 1.934589 TACCATCGGATTCTTGCACG 58.065 50.000 0.00 0.00 0.00 5.34
817 819 1.353103 CCATCGGATTCTTGCACGC 59.647 57.895 0.00 0.00 0.00 5.34
836 838 5.455525 GCACGCTTGTTATCCAAAATGTATC 59.544 40.000 0.00 0.00 31.20 2.24
841 843 5.651172 TGTTATCCAAAATGTATCTCGCG 57.349 39.130 0.00 0.00 0.00 5.87
852 854 6.453643 AATGTATCTCGCGTCAATATCAAC 57.546 37.500 5.77 0.00 0.00 3.18
863 865 5.393452 GCGTCAATATCAACATCAACAATCG 59.607 40.000 0.00 0.00 0.00 3.34
868 870 3.811722 TCAACATCAACAATCGTGAGC 57.188 42.857 0.00 0.00 0.00 4.26
879 881 1.354040 ATCGTGAGCGCAAGAAGAAG 58.646 50.000 11.47 0.00 36.15 2.85
880 882 0.313987 TCGTGAGCGCAAGAAGAAGA 59.686 50.000 11.47 0.00 43.02 2.87
881 883 1.067565 TCGTGAGCGCAAGAAGAAGAT 60.068 47.619 11.47 0.00 43.02 2.40
893 895 6.564312 CGCAAGAAGAAGATGCATGATAAGAG 60.564 42.308 2.46 0.00 40.04 2.85
900 902 5.883685 AGATGCATGATAAGAGGAGTTCA 57.116 39.130 2.46 0.00 0.00 3.18
902 904 6.656902 AGATGCATGATAAGAGGAGTTCAAA 58.343 36.000 2.46 0.00 0.00 2.69
922 924 7.080353 TCAAATTGTGATAATCAGTGCTCAG 57.920 36.000 0.00 0.00 0.00 3.35
936 938 2.739913 GTGCTCAGCGGTAATTGTGTAA 59.260 45.455 0.00 0.00 0.00 2.41
938 940 2.095372 GCTCAGCGGTAATTGTGTAACC 59.905 50.000 0.00 0.00 34.36 2.85
940 942 3.331150 TCAGCGGTAATTGTGTAACCAG 58.669 45.455 0.00 0.00 34.36 4.00
951 953 9.442033 GTAATTGTGTAACCAGTGTAGAAAAAC 57.558 33.333 0.00 0.00 34.36 2.43
1005 1007 3.004629 TGACGCTTGTTTCTCAAATGCAT 59.995 39.130 0.00 0.00 35.48 3.96
1096 1098 5.172934 GTGTCAACCGTATCATTAAGGTGA 58.827 41.667 0.00 0.00 38.99 4.02
1148 1150 1.813753 CGGTGTTGTATGAGCGGGG 60.814 63.158 0.00 0.00 0.00 5.73
1161 1163 4.101448 CGGGGTGGCCAGAAGGAG 62.101 72.222 5.11 0.00 36.89 3.69
1215 1217 2.352421 GCGCTCTGAGGTACAAGTTACA 60.352 50.000 6.83 0.00 0.00 2.41
1219 1221 5.335426 CGCTCTGAGGTACAAGTTACACTTA 60.335 44.000 6.83 0.00 36.03 2.24
1239 1241 8.730680 ACACTTACAACAACCATCATATTTCTC 58.269 33.333 0.00 0.00 0.00 2.87
1244 1246 5.779529 ACAACCATCATATTTCTCCATGC 57.220 39.130 0.00 0.00 0.00 4.06
1276 1278 6.206634 GGGTCACTTTGTGAATGACTTGATAA 59.793 38.462 1.73 0.00 44.49 1.75
1322 1326 4.962362 TGTATAGATCTGTTTGGAGCCAGA 59.038 41.667 5.18 0.00 41.61 3.86
1323 1327 2.777832 AGATCTGTTTGGAGCCAGAC 57.222 50.000 0.00 3.40 40.30 3.51
1426 1430 2.559330 GCACTTTTGGGCCGTACG 59.441 61.111 8.69 8.69 44.67 3.67
1443 1447 2.284995 GGGGAGGAGACAGGCACT 60.285 66.667 0.00 0.00 43.88 4.40
1558 1562 2.564947 GGCTAGGTATGGACATCTCCTG 59.435 54.545 14.82 8.85 37.48 3.86
1615 1619 7.712639 CGGGATGCTATGTAATGCTTAATCTAT 59.287 37.037 0.00 0.00 0.00 1.98
1678 1682 2.358957 TGCTTCTGCTGTATCGCATTT 58.641 42.857 0.00 0.00 39.52 2.32
1708 1712 2.401583 TGATGAAGGAACATCCCGTG 57.598 50.000 0.00 0.00 43.96 4.94
1721 1725 1.271856 TCCCGTGGAGTGAATGCTAA 58.728 50.000 0.00 0.00 0.00 3.09
1767 1771 3.135994 GGTGCTCGTTTCCTAGTTTGAA 58.864 45.455 0.00 0.00 0.00 2.69
1774 1778 3.183775 CGTTTCCTAGTTTGAACGAGTGG 59.816 47.826 9.97 0.00 45.44 4.00
1780 1784 5.103000 CCTAGTTTGAACGAGTGGATGTAG 58.897 45.833 0.00 0.00 30.79 2.74
1816 1838 6.426980 TGCTACTGTTAAAGCATGAATCTG 57.573 37.500 0.00 0.00 43.56 2.90
1822 1844 6.435277 ACTGTTAAAGCATGAATCTGGAACAT 59.565 34.615 0.00 0.00 38.20 2.71
1858 1880 7.148356 TGCTGAATTGCTGATGTTCTAAACTAG 60.148 37.037 0.00 0.00 0.00 2.57
1958 1980 3.877801 CGCAGGTTCTTATCGCAAC 57.122 52.632 0.00 0.00 0.00 4.17
1959 1981 1.075542 CGCAGGTTCTTATCGCAACA 58.924 50.000 0.00 0.00 0.00 3.33
1960 1982 1.665679 CGCAGGTTCTTATCGCAACAT 59.334 47.619 0.00 0.00 0.00 2.71
1962 1984 2.420022 GCAGGTTCTTATCGCAACATGT 59.580 45.455 0.00 0.00 36.80 3.21
1964 1986 4.094294 GCAGGTTCTTATCGCAACATGTAA 59.906 41.667 0.00 0.00 36.80 2.41
1965 1987 5.727791 GCAGGTTCTTATCGCAACATGTAAG 60.728 44.000 0.00 0.00 36.80 2.34
1966 1988 5.580691 CAGGTTCTTATCGCAACATGTAAGA 59.419 40.000 0.00 0.00 31.26 2.10
1967 1989 6.258727 CAGGTTCTTATCGCAACATGTAAGAT 59.741 38.462 0.00 7.28 34.29 2.40
1968 1990 6.258727 AGGTTCTTATCGCAACATGTAAGATG 59.741 38.462 16.24 6.01 34.29 2.90
1969 1991 6.037172 GGTTCTTATCGCAACATGTAAGATGT 59.963 38.462 16.24 0.00 34.29 3.06
1970 1992 7.223971 GGTTCTTATCGCAACATGTAAGATGTA 59.776 37.037 16.24 7.33 34.29 2.29
1972 1994 8.352752 TCTTATCGCAACATGTAAGATGTAAG 57.647 34.615 16.24 13.35 30.53 2.34
1973 1995 8.194769 TCTTATCGCAACATGTAAGATGTAAGA 58.805 33.333 16.24 14.76 30.53 2.10
1974 1996 8.887036 TTATCGCAACATGTAAGATGTAAGAT 57.113 30.769 16.24 11.60 0.00 2.40
1975 1997 6.588348 TCGCAACATGTAAGATGTAAGATG 57.412 37.500 0.00 0.00 0.00 2.90
1976 1998 6.106003 TCGCAACATGTAAGATGTAAGATGT 58.894 36.000 0.00 0.00 0.00 3.06
1977 1999 7.262048 TCGCAACATGTAAGATGTAAGATGTA 58.738 34.615 0.00 0.00 0.00 2.29
1987 2014 6.932356 AGATGTAAGATGTAACTTGCATGG 57.068 37.500 14.38 0.00 46.93 3.66
1998 2025 4.913335 AACTTGCATGGCAGATCTTATG 57.087 40.909 4.44 0.00 40.61 1.90
2026 2053 4.202245 TGCCAGGTTCAGAGTGTATAAC 57.798 45.455 0.00 0.00 0.00 1.89
2092 2119 3.057946 GCTTCACCTCATTGTCCTTGAAC 60.058 47.826 0.00 0.00 0.00 3.18
2135 2162 1.959985 TGATCATCTCGAGGCTTCCTC 59.040 52.381 13.56 2.83 46.44 3.71
2198 2225 5.335426 GCAATGCTCTCAAATCTCAAGTTCA 60.335 40.000 0.00 0.00 0.00 3.18
2302 2329 3.537455 CTCTGGAGGAGGCAGATCT 57.463 57.895 0.00 0.00 38.35 2.75
2303 2330 1.792115 CTCTGGAGGAGGCAGATCTT 58.208 55.000 0.00 0.00 38.35 2.40
2304 2331 1.688197 CTCTGGAGGAGGCAGATCTTC 59.312 57.143 0.00 0.00 38.35 2.87
2305 2332 1.290431 TCTGGAGGAGGCAGATCTTCT 59.710 52.381 0.00 0.00 0.00 2.85
2306 2333 2.515853 TCTGGAGGAGGCAGATCTTCTA 59.484 50.000 0.00 0.00 0.00 2.10
2307 2334 3.141838 TCTGGAGGAGGCAGATCTTCTAT 59.858 47.826 0.00 0.00 0.00 1.98
2311 2338 5.162936 TGGAGGAGGCAGATCTTCTATCTTA 60.163 44.000 0.00 0.00 0.00 2.10
2333 2360 4.935495 CACACGTGCACCAGGGCT 62.935 66.667 17.22 0.00 34.04 5.19
2363 2390 2.152699 CGTCGTCAGCGTCATGTCC 61.153 63.158 0.00 0.00 39.49 4.02
2453 2480 1.166531 GGTCTTTGAACGGCAGTGCT 61.167 55.000 16.11 0.00 0.00 4.40
2462 2489 4.385405 GGCAGTGCTCACTCGCCT 62.385 66.667 23.62 0.00 44.60 5.52
2468 2495 2.817396 GCTCACTCGCCTGCCTTC 60.817 66.667 0.00 0.00 0.00 3.46
2474 2501 2.688666 TCGCCTGCCTTCCTCCAT 60.689 61.111 0.00 0.00 0.00 3.41
2475 2502 2.515523 CGCCTGCCTTCCTCCATG 60.516 66.667 0.00 0.00 0.00 3.66
2540 2568 0.383590 ACATCCAGATCTGCGAGTCG 59.616 55.000 17.76 8.54 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.178106 AGAGTACCTCCATAGTGGGGAG 59.822 54.545 0.00 1.44 41.85 4.30
5 6 2.177233 GAGAGTACCTCCATAGTGGGGA 59.823 54.545 0.00 0.00 41.85 4.81
6 7 2.178106 AGAGAGTACCTCCATAGTGGGG 59.822 54.545 7.50 0.00 42.97 4.96
7 8 3.492337 GAGAGAGTACCTCCATAGTGGG 58.508 54.545 7.50 0.00 42.97 4.61
15 16 2.725637 AGAAACGGAGAGAGTACCTCC 58.274 52.381 6.59 6.59 45.16 4.30
16 17 4.787260 AAAGAAACGGAGAGAGTACCTC 57.213 45.455 3.84 3.84 42.28 3.85
17 18 5.548181 AAAAAGAAACGGAGAGAGTACCT 57.452 39.130 0.00 0.00 0.00 3.08
18 19 6.453943 ACTAAAAAGAAACGGAGAGAGTACC 58.546 40.000 0.00 0.00 0.00 3.34
19 20 7.943413 AACTAAAAAGAAACGGAGAGAGTAC 57.057 36.000 0.00 0.00 0.00 2.73
20 21 7.042254 GCAAACTAAAAAGAAACGGAGAGAGTA 60.042 37.037 0.00 0.00 0.00 2.59
21 22 6.238402 GCAAACTAAAAAGAAACGGAGAGAGT 60.238 38.462 0.00 0.00 0.00 3.24
22 23 6.136743 GCAAACTAAAAAGAAACGGAGAGAG 58.863 40.000 0.00 0.00 0.00 3.20
23 24 5.587043 TGCAAACTAAAAAGAAACGGAGAGA 59.413 36.000 0.00 0.00 0.00 3.10
24 25 5.816919 TGCAAACTAAAAAGAAACGGAGAG 58.183 37.500 0.00 0.00 0.00 3.20
25 26 5.821516 TGCAAACTAAAAAGAAACGGAGA 57.178 34.783 0.00 0.00 0.00 3.71
26 27 9.834628 TTATATGCAAACTAAAAAGAAACGGAG 57.165 29.630 0.00 0.00 0.00 4.63
27 28 9.834628 CTTATATGCAAACTAAAAAGAAACGGA 57.165 29.630 0.00 0.00 0.00 4.69
28 29 9.834628 TCTTATATGCAAACTAAAAAGAAACGG 57.165 29.630 0.00 0.00 0.00 4.44
49 50 9.981114 CCAAGTTTGACTTTAACCAAATCTTAT 57.019 29.630 0.00 0.00 36.03 1.73
50 51 8.973182 ACCAAGTTTGACTTTAACCAAATCTTA 58.027 29.630 0.00 0.00 36.03 2.10
51 52 7.847096 ACCAAGTTTGACTTTAACCAAATCTT 58.153 30.769 0.00 0.00 36.03 2.40
52 53 7.418337 ACCAAGTTTGACTTTAACCAAATCT 57.582 32.000 0.00 0.00 36.03 2.40
53 54 9.589111 TTTACCAAGTTTGACTTTAACCAAATC 57.411 29.630 0.00 0.00 36.03 2.17
54 55 9.945904 TTTTACCAAGTTTGACTTTAACCAAAT 57.054 25.926 0.00 0.00 36.03 2.32
55 56 9.945904 ATTTTACCAAGTTTGACTTTAACCAAA 57.054 25.926 0.00 0.00 36.03 3.28
56 57 9.945904 AATTTTACCAAGTTTGACTTTAACCAA 57.054 25.926 0.00 0.00 36.03 3.67
57 58 9.945904 AAATTTTACCAAGTTTGACTTTAACCA 57.054 25.926 0.00 0.00 36.03 3.67
66 67 8.232913 AGCTAGTCAAATTTTACCAAGTTTGA 57.767 30.769 0.00 2.51 42.95 2.69
67 68 8.871686 AAGCTAGTCAAATTTTACCAAGTTTG 57.128 30.769 0.00 0.00 39.70 2.93
68 69 9.313118 CAAAGCTAGTCAAATTTTACCAAGTTT 57.687 29.630 0.00 0.27 0.00 2.66
69 70 8.474831 ACAAAGCTAGTCAAATTTTACCAAGTT 58.525 29.630 0.00 0.00 0.00 2.66
70 71 8.007405 ACAAAGCTAGTCAAATTTTACCAAGT 57.993 30.769 0.00 0.00 0.00 3.16
71 72 9.612620 CTACAAAGCTAGTCAAATTTTACCAAG 57.387 33.333 0.00 0.00 0.00 3.61
72 73 8.573035 CCTACAAAGCTAGTCAAATTTTACCAA 58.427 33.333 0.00 0.00 0.00 3.67
73 74 7.940137 TCCTACAAAGCTAGTCAAATTTTACCA 59.060 33.333 0.00 0.00 0.00 3.25
74 75 8.331730 TCCTACAAAGCTAGTCAAATTTTACC 57.668 34.615 0.00 0.00 0.00 2.85
77 78 9.750125 CTTTTCCTACAAAGCTAGTCAAATTTT 57.250 29.630 0.00 0.00 0.00 1.82
78 79 9.131791 TCTTTTCCTACAAAGCTAGTCAAATTT 57.868 29.630 0.00 0.00 34.26 1.82
79 80 8.691661 TCTTTTCCTACAAAGCTAGTCAAATT 57.308 30.769 0.00 0.00 34.26 1.82
80 81 8.870075 ATCTTTTCCTACAAAGCTAGTCAAAT 57.130 30.769 0.00 0.00 34.26 2.32
81 82 9.959721 ATATCTTTTCCTACAAAGCTAGTCAAA 57.040 29.630 0.00 0.00 34.26 2.69
82 83 9.601217 GATATCTTTTCCTACAAAGCTAGTCAA 57.399 33.333 0.00 0.00 34.26 3.18
83 84 8.758829 TGATATCTTTTCCTACAAAGCTAGTCA 58.241 33.333 3.98 0.00 34.26 3.41
84 85 9.601217 TTGATATCTTTTCCTACAAAGCTAGTC 57.399 33.333 3.98 0.00 34.26 2.59
85 86 9.384764 GTTGATATCTTTTCCTACAAAGCTAGT 57.615 33.333 3.98 0.00 34.26 2.57
86 87 9.383519 TGTTGATATCTTTTCCTACAAAGCTAG 57.616 33.333 3.98 0.00 34.26 3.42
87 88 9.905713 ATGTTGATATCTTTTCCTACAAAGCTA 57.094 29.630 3.98 0.00 34.26 3.32
88 89 8.814038 ATGTTGATATCTTTTCCTACAAAGCT 57.186 30.769 3.98 0.00 34.26 3.74
89 90 8.131731 GGATGTTGATATCTTTTCCTACAAAGC 58.868 37.037 3.98 0.00 34.26 3.51
90 91 9.177608 TGGATGTTGATATCTTTTCCTACAAAG 57.822 33.333 3.98 0.00 35.39 2.77
91 92 8.956426 GTGGATGTTGATATCTTTTCCTACAAA 58.044 33.333 3.98 0.00 0.00 2.83
92 93 8.106462 TGTGGATGTTGATATCTTTTCCTACAA 58.894 33.333 3.98 0.00 0.00 2.41
93 94 7.552687 GTGTGGATGTTGATATCTTTTCCTACA 59.447 37.037 3.98 8.97 0.00 2.74
94 95 7.770897 AGTGTGGATGTTGATATCTTTTCCTAC 59.229 37.037 3.98 8.53 0.00 3.18
95 96 7.861629 AGTGTGGATGTTGATATCTTTTCCTA 58.138 34.615 3.98 0.00 0.00 2.94
96 97 6.725364 AGTGTGGATGTTGATATCTTTTCCT 58.275 36.000 3.98 0.00 0.00 3.36
97 98 8.562892 CATAGTGTGGATGTTGATATCTTTTCC 58.437 37.037 3.98 6.04 0.00 3.13
98 99 9.330063 TCATAGTGTGGATGTTGATATCTTTTC 57.670 33.333 3.98 0.00 0.00 2.29
99 100 9.685276 TTCATAGTGTGGATGTTGATATCTTTT 57.315 29.630 3.98 0.00 0.00 2.27
100 101 9.685276 TTTCATAGTGTGGATGTTGATATCTTT 57.315 29.630 3.98 0.00 0.00 2.52
101 102 9.857656 ATTTCATAGTGTGGATGTTGATATCTT 57.142 29.630 3.98 0.00 0.00 2.40
102 103 9.499479 GATTTCATAGTGTGGATGTTGATATCT 57.501 33.333 3.98 0.00 0.00 1.98
103 104 9.276590 TGATTTCATAGTGTGGATGTTGATATC 57.723 33.333 0.00 0.00 0.00 1.63
104 105 9.631257 TTGATTTCATAGTGTGGATGTTGATAT 57.369 29.630 0.00 0.00 0.00 1.63
105 106 9.631257 ATTGATTTCATAGTGTGGATGTTGATA 57.369 29.630 0.00 0.00 0.00 2.15
106 107 7.943079 TTGATTTCATAGTGTGGATGTTGAT 57.057 32.000 0.00 0.00 0.00 2.57
107 108 7.943079 ATTGATTTCATAGTGTGGATGTTGA 57.057 32.000 0.00 0.00 0.00 3.18
250 251 9.495572 CTCCTTCTGTTTCTTTTTAGTCTACAT 57.504 33.333 0.00 0.00 0.00 2.29
251 252 8.483758 ACTCCTTCTGTTTCTTTTTAGTCTACA 58.516 33.333 0.00 0.00 0.00 2.74
252 253 8.890124 ACTCCTTCTGTTTCTTTTTAGTCTAC 57.110 34.615 0.00 0.00 0.00 2.59
253 254 9.978044 GTACTCCTTCTGTTTCTTTTTAGTCTA 57.022 33.333 0.00 0.00 0.00 2.59
254 255 8.706521 AGTACTCCTTCTGTTTCTTTTTAGTCT 58.293 33.333 0.00 0.00 0.00 3.24
255 256 8.890124 AGTACTCCTTCTGTTTCTTTTTAGTC 57.110 34.615 0.00 0.00 0.00 2.59
256 257 9.761504 GTAGTACTCCTTCTGTTTCTTTTTAGT 57.238 33.333 0.00 0.00 0.00 2.24
257 258 9.205719 GGTAGTACTCCTTCTGTTTCTTTTTAG 57.794 37.037 0.00 0.00 0.00 1.85
258 259 8.931568 AGGTAGTACTCCTTCTGTTTCTTTTTA 58.068 33.333 0.00 0.00 30.18 1.52
259 260 7.803131 AGGTAGTACTCCTTCTGTTTCTTTTT 58.197 34.615 0.00 0.00 30.18 1.94
260 261 7.376335 AGGTAGTACTCCTTCTGTTTCTTTT 57.624 36.000 0.00 0.00 30.18 2.27
261 262 6.995364 GAGGTAGTACTCCTTCTGTTTCTTT 58.005 40.000 13.14 0.00 35.20 2.52
262 263 6.593268 GAGGTAGTACTCCTTCTGTTTCTT 57.407 41.667 13.14 0.00 35.20 2.52
274 275 9.915629 CAATATAACATGAAGGAGGTAGTACTC 57.084 37.037 0.00 0.00 36.76 2.59
275 276 9.656323 TCAATATAACATGAAGGAGGTAGTACT 57.344 33.333 0.00 0.00 0.00 2.73
278 279 8.598041 GGATCAATATAACATGAAGGAGGTAGT 58.402 37.037 0.00 0.00 0.00 2.73
279 280 8.043710 GGGATCAATATAACATGAAGGAGGTAG 58.956 40.741 0.00 0.00 0.00 3.18
280 281 7.037586 GGGGATCAATATAACATGAAGGAGGTA 60.038 40.741 0.00 0.00 0.00 3.08
281 282 6.240292 GGGGATCAATATAACATGAAGGAGGT 60.240 42.308 0.00 0.00 0.00 3.85
282 283 6.183347 GGGGATCAATATAACATGAAGGAGG 58.817 44.000 0.00 0.00 0.00 4.30
283 284 6.782986 TGGGGATCAATATAACATGAAGGAG 58.217 40.000 0.00 0.00 0.00 3.69
284 285 6.778542 TGGGGATCAATATAACATGAAGGA 57.221 37.500 0.00 0.00 0.00 3.36
285 286 7.452501 ACAATGGGGATCAATATAACATGAAGG 59.547 37.037 0.00 0.00 0.00 3.46
286 287 8.413309 ACAATGGGGATCAATATAACATGAAG 57.587 34.615 0.00 0.00 0.00 3.02
290 291 9.479549 GGAATACAATGGGGATCAATATAACAT 57.520 33.333 0.00 0.00 0.00 2.71
291 292 7.609918 CGGAATACAATGGGGATCAATATAACA 59.390 37.037 0.00 0.00 0.00 2.41
292 293 7.610305 ACGGAATACAATGGGGATCAATATAAC 59.390 37.037 0.00 0.00 0.00 1.89
293 294 7.609918 CACGGAATACAATGGGGATCAATATAA 59.390 37.037 0.00 0.00 0.00 0.98
294 295 7.109501 CACGGAATACAATGGGGATCAATATA 58.890 38.462 0.00 0.00 0.00 0.86
295 296 5.945784 CACGGAATACAATGGGGATCAATAT 59.054 40.000 0.00 0.00 0.00 1.28
296 297 5.163141 ACACGGAATACAATGGGGATCAATA 60.163 40.000 0.00 0.00 0.00 1.90
297 298 4.144297 CACGGAATACAATGGGGATCAAT 58.856 43.478 0.00 0.00 0.00 2.57
298 299 3.053991 ACACGGAATACAATGGGGATCAA 60.054 43.478 0.00 0.00 0.00 2.57
299 300 2.507886 ACACGGAATACAATGGGGATCA 59.492 45.455 0.00 0.00 0.00 2.92
300 301 3.139077 GACACGGAATACAATGGGGATC 58.861 50.000 0.00 0.00 0.00 3.36
301 302 2.507886 TGACACGGAATACAATGGGGAT 59.492 45.455 0.00 0.00 0.00 3.85
302 303 1.909986 TGACACGGAATACAATGGGGA 59.090 47.619 0.00 0.00 0.00 4.81
303 304 2.411628 TGACACGGAATACAATGGGG 57.588 50.000 0.00 0.00 0.00 4.96
304 305 4.981806 ATTTGACACGGAATACAATGGG 57.018 40.909 0.00 0.00 0.00 4.00
305 306 6.865726 TCAAAATTTGACACGGAATACAATGG 59.134 34.615 4.03 0.00 34.08 3.16
306 307 7.865875 TCAAAATTTGACACGGAATACAATG 57.134 32.000 4.03 0.00 34.08 2.82
307 308 8.303156 TGATCAAAATTTGACACGGAATACAAT 58.697 29.630 10.91 0.00 43.48 2.71
308 309 7.652727 TGATCAAAATTTGACACGGAATACAA 58.347 30.769 10.91 0.00 43.48 2.41
309 310 7.208225 TGATCAAAATTTGACACGGAATACA 57.792 32.000 10.91 0.00 43.48 2.29
310 311 9.781834 TTATGATCAAAATTTGACACGGAATAC 57.218 29.630 10.91 0.00 43.48 1.89
312 313 9.874205 ATTTATGATCAAAATTTGACACGGAAT 57.126 25.926 10.91 6.60 43.48 3.01
313 314 9.703892 AATTTATGATCAAAATTTGACACGGAA 57.296 25.926 10.91 4.65 43.48 4.30
314 315 9.703892 AAATTTATGATCAAAATTTGACACGGA 57.296 25.926 24.59 0.00 42.19 4.69
335 336 9.723601 ATGCATGACCATTTGTTAGTTAAATTT 57.276 25.926 0.00 0.00 0.00 1.82
336 337 9.153721 CATGCATGACCATTTGTTAGTTAAATT 57.846 29.630 22.59 0.00 0.00 1.82
337 338 8.313292 ACATGCATGACCATTTGTTAGTTAAAT 58.687 29.630 32.75 0.22 0.00 1.40
338 339 7.665690 ACATGCATGACCATTTGTTAGTTAAA 58.334 30.769 32.75 0.00 0.00 1.52
339 340 7.040132 TGACATGCATGACCATTTGTTAGTTAA 60.040 33.333 32.75 2.97 0.00 2.01
340 341 6.432472 TGACATGCATGACCATTTGTTAGTTA 59.568 34.615 32.75 3.41 0.00 2.24
341 342 5.243507 TGACATGCATGACCATTTGTTAGTT 59.756 36.000 32.75 4.97 0.00 2.24
342 343 4.766373 TGACATGCATGACCATTTGTTAGT 59.234 37.500 32.75 5.45 0.00 2.24
343 344 5.097529 GTGACATGCATGACCATTTGTTAG 58.902 41.667 32.75 1.77 0.00 2.34
344 345 4.082300 GGTGACATGCATGACCATTTGTTA 60.082 41.667 32.75 3.29 0.00 2.41
345 346 3.306225 GGTGACATGCATGACCATTTGTT 60.306 43.478 32.75 7.05 0.00 2.83
346 347 2.231964 GGTGACATGCATGACCATTTGT 59.768 45.455 32.75 9.56 0.00 2.83
347 348 2.231721 TGGTGACATGCATGACCATTTG 59.768 45.455 32.75 5.86 31.90 2.32
348 349 2.231964 GTGGTGACATGCATGACCATTT 59.768 45.455 31.67 13.16 46.14 2.32
349 350 1.820519 GTGGTGACATGCATGACCATT 59.179 47.619 31.67 13.82 46.14 3.16
350 351 1.272037 TGTGGTGACATGCATGACCAT 60.272 47.619 31.67 14.17 46.14 3.55
351 352 0.110104 TGTGGTGACATGCATGACCA 59.890 50.000 32.75 29.92 46.14 4.02
352 353 1.246649 TTGTGGTGACATGCATGACC 58.753 50.000 32.75 27.83 46.14 4.02
353 354 3.581024 ATTTGTGGTGACATGCATGAC 57.419 42.857 32.75 26.17 46.14 3.06
354 355 4.281435 AGAAATTTGTGGTGACATGCATGA 59.719 37.500 32.75 9.00 46.14 3.07
355 356 4.562082 AGAAATTTGTGGTGACATGCATG 58.438 39.130 25.09 25.09 46.14 4.06
356 357 4.877378 AGAAATTTGTGGTGACATGCAT 57.123 36.364 0.00 0.00 46.14 3.96
357 358 4.141981 ACAAGAAATTTGTGGTGACATGCA 60.142 37.500 0.00 0.00 46.14 3.96
358 359 4.370917 ACAAGAAATTTGTGGTGACATGC 58.629 39.130 0.00 0.00 46.14 4.06
359 360 5.590145 TGACAAGAAATTTGTGGTGACATG 58.410 37.500 0.00 0.00 46.14 3.21
360 361 5.850557 TGACAAGAAATTTGTGGTGACAT 57.149 34.783 0.00 0.00 46.14 3.06
361 362 5.651387 TTGACAAGAAATTTGTGGTGACA 57.349 34.783 0.00 0.00 38.70 3.58
362 363 5.005682 GCTTTGACAAGAAATTTGTGGTGAC 59.994 40.000 0.00 0.00 31.96 3.67
363 364 5.108517 GCTTTGACAAGAAATTTGTGGTGA 58.891 37.500 0.00 0.00 31.96 4.02
364 365 4.869297 TGCTTTGACAAGAAATTTGTGGTG 59.131 37.500 0.00 0.00 31.96 4.17
365 366 5.083533 TGCTTTGACAAGAAATTTGTGGT 57.916 34.783 0.00 0.00 31.96 4.16
366 367 6.258287 TGAATGCTTTGACAAGAAATTTGTGG 59.742 34.615 0.00 0.00 31.96 4.17
367 368 7.010738 ACTGAATGCTTTGACAAGAAATTTGTG 59.989 33.333 0.00 0.00 31.96 3.33
368 369 7.010738 CACTGAATGCTTTGACAAGAAATTTGT 59.989 33.333 0.00 0.00 34.97 2.83
369 370 7.010738 ACACTGAATGCTTTGACAAGAAATTTG 59.989 33.333 0.00 0.00 30.57 2.32
370 371 7.010738 CACACTGAATGCTTTGACAAGAAATTT 59.989 33.333 0.00 0.00 30.57 1.82
371 372 6.477688 CACACTGAATGCTTTGACAAGAAATT 59.522 34.615 0.00 0.00 30.57 1.82
385 386 2.658325 GTCGCAAATTCACACTGAATGC 59.342 45.455 0.00 0.33 45.57 3.56
414 416 4.046286 TCATAGGGCAACTTGGAAACAT 57.954 40.909 0.00 0.00 42.32 2.71
415 417 3.517296 TCATAGGGCAACTTGGAAACA 57.483 42.857 0.00 0.00 39.83 2.83
427 429 9.454859 AATAGCTGAAACTTATAATCATAGGGC 57.545 33.333 0.00 0.00 0.00 5.19
461 463 9.979578 ATTTGTAAAATTGAATGCTGACAAGTA 57.020 25.926 0.00 0.00 0.00 2.24
493 495 8.159344 AGAAAATGTGCTATACTTTATGAGCC 57.841 34.615 0.00 0.00 33.87 4.70
534 536 5.005779 CGGGTCAAGAATATCAGAAGTTTCG 59.994 44.000 0.00 0.00 0.00 3.46
553 555 0.591659 GAACAAAGAAGGTGCGGGTC 59.408 55.000 0.00 0.00 0.00 4.46
555 557 0.882927 TCGAACAAAGAAGGTGCGGG 60.883 55.000 0.00 0.00 37.88 6.13
561 563 1.884235 AGCAGGTCGAACAAAGAAGG 58.116 50.000 1.87 0.00 0.00 3.46
593 595 0.687354 GCAGGACTTGTCCTTCTCCA 59.313 55.000 18.72 0.00 38.22 3.86
601 603 1.845809 CGGTTGCAGCAGGACTTGTC 61.846 60.000 2.05 0.00 0.00 3.18
652 654 1.205460 TAGGGGCAAAGGACCTGGAC 61.205 60.000 0.00 0.00 44.19 4.02
672 674 3.264897 GTGCAGCCATACTCCGCG 61.265 66.667 0.00 0.00 0.00 6.46
801 803 0.729116 CAAGCGTGCAAGAATCCGAT 59.271 50.000 2.99 0.00 0.00 4.18
807 809 2.499197 TGGATAACAAGCGTGCAAGAA 58.501 42.857 2.99 0.00 0.00 2.52
812 814 3.574614 ACATTTTGGATAACAAGCGTGC 58.425 40.909 0.00 0.00 40.82 5.34
813 815 6.785191 AGATACATTTTGGATAACAAGCGTG 58.215 36.000 0.00 0.00 40.82 5.34
816 818 5.909610 GCGAGATACATTTTGGATAACAAGC 59.090 40.000 0.00 0.00 40.82 4.01
817 819 6.129393 CGCGAGATACATTTTGGATAACAAG 58.871 40.000 0.00 0.00 40.82 3.16
836 838 4.032786 TGTTGATGTTGATATTGACGCGAG 59.967 41.667 15.93 0.00 0.00 5.03
841 843 7.463544 TCACGATTGTTGATGTTGATATTGAC 58.536 34.615 0.00 0.00 0.00 3.18
852 854 0.443478 TGCGCTCACGATTGTTGATG 59.557 50.000 9.73 0.00 43.93 3.07
863 865 1.202009 GCATCTTCTTCTTGCGCTCAC 60.202 52.381 9.73 0.00 0.00 3.51
868 870 3.965292 ATCATGCATCTTCTTCTTGCG 57.035 42.857 0.00 0.00 39.23 4.85
879 881 6.932356 TTTGAACTCCTCTTATCATGCATC 57.068 37.500 0.00 0.00 0.00 3.91
880 882 7.341256 ACAATTTGAACTCCTCTTATCATGCAT 59.659 33.333 2.79 0.00 0.00 3.96
881 883 6.660521 ACAATTTGAACTCCTCTTATCATGCA 59.339 34.615 2.79 0.00 0.00 3.96
893 895 6.749118 GCACTGATTATCACAATTTGAACTCC 59.251 38.462 2.79 0.00 37.92 3.85
900 902 5.448225 CGCTGAGCACTGATTATCACAATTT 60.448 40.000 4.88 0.00 0.00 1.82
902 904 3.558829 CGCTGAGCACTGATTATCACAAT 59.441 43.478 4.88 0.00 0.00 2.71
922 924 2.809696 ACACTGGTTACACAATTACCGC 59.190 45.455 0.00 0.00 34.62 5.68
936 938 7.852263 AGCTATCATAGTTTTTCTACACTGGT 58.148 34.615 0.00 0.00 0.00 4.00
938 940 9.371136 TGAAGCTATCATAGTTTTTCTACACTG 57.629 33.333 0.00 0.00 31.50 3.66
951 953 6.339730 CCTAGCCAGATTGAAGCTATCATAG 58.660 44.000 0.00 0.00 38.37 2.23
1005 1007 1.323412 CCATTTTCACAACCGACCCA 58.677 50.000 0.00 0.00 0.00 4.51
1123 1125 2.676750 GCTCATACAACACCGACATGGA 60.677 50.000 0.00 0.00 42.00 3.41
1148 1150 0.035915 GGTCTTCTCCTTCTGGCCAC 60.036 60.000 0.00 0.00 0.00 5.01
1161 1163 0.322008 CTCCCCACAGCTTGGTCTTC 60.322 60.000 12.18 0.00 45.25 2.87
1215 1217 7.888021 TGGAGAAATATGATGGTTGTTGTAAGT 59.112 33.333 0.00 0.00 0.00 2.24
1219 1221 6.406177 GCATGGAGAAATATGATGGTTGTTGT 60.406 38.462 0.00 0.00 0.00 3.32
1244 1246 0.960364 CACAAAGTGACCCCCATCCG 60.960 60.000 0.00 0.00 35.23 4.18
1252 1254 5.695851 ATCAAGTCATTCACAAAGTGACC 57.304 39.130 0.00 0.00 42.60 4.02
1290 1292 7.560991 TCCAAACAGATCTATACATGCCAAAAT 59.439 33.333 0.00 0.00 0.00 1.82
1302 1306 3.181471 CGTCTGGCTCCAAACAGATCTAT 60.181 47.826 0.00 0.00 44.65 1.98
1322 1326 2.545526 CTGATGTTTGTCAAGTGCTCGT 59.454 45.455 0.00 0.00 0.00 4.18
1323 1327 2.802247 TCTGATGTTTGTCAAGTGCTCG 59.198 45.455 0.00 0.00 0.00 5.03
1377 1381 3.006430 TCACAAAAGTGAGCGACCTGATA 59.994 43.478 0.00 0.00 0.00 2.15
1426 1430 2.284995 AGTGCCTGTCTCCTCCCC 60.285 66.667 0.00 0.00 0.00 4.81
1443 1447 0.034767 CTCCTGGGAGCTTGAATGCA 60.035 55.000 3.52 0.00 35.31 3.96
1558 1562 0.621862 ATCCCCTCCCCAGTCTTGAC 60.622 60.000 0.00 0.00 0.00 3.18
1562 1566 2.021042 TCAAATATCCCCTCCCCAGTCT 60.021 50.000 0.00 0.00 0.00 3.24
1615 1619 6.540995 ACAGAGTTCAGAGTAAGTACCTACA 58.459 40.000 4.50 0.00 0.00 2.74
1622 1626 7.526142 TCACATAACAGAGTTCAGAGTAAGT 57.474 36.000 0.00 0.00 0.00 2.24
1678 1682 2.874014 TCCTTCATCAACCAACATGCA 58.126 42.857 0.00 0.00 0.00 3.96
1708 1712 8.718102 TCTAGTTTATGTTTAGCATTCACTCC 57.282 34.615 0.00 0.00 38.94 3.85
1721 1725 7.094205 CCAGGTTTCAAGCATCTAGTTTATGTT 60.094 37.037 0.00 0.00 0.00 2.71
1767 1771 2.229062 CACAGTCACTACATCCACTCGT 59.771 50.000 0.00 0.00 0.00 4.18
1774 1778 3.809832 AGCAAACACACAGTCACTACATC 59.190 43.478 0.00 0.00 0.00 3.06
1780 1784 2.936498 ACAGTAGCAAACACACAGTCAC 59.064 45.455 0.00 0.00 0.00 3.67
1813 1835 2.766313 CACGAACCAGAATGTTCCAGA 58.234 47.619 0.00 0.00 41.24 3.86
1816 1838 1.197721 CAGCACGAACCAGAATGTTCC 59.802 52.381 0.00 0.00 41.24 3.62
1822 1844 1.266718 GCAATTCAGCACGAACCAGAA 59.733 47.619 0.00 0.00 36.12 3.02
1858 1880 1.146263 CATCAGCCGGAACCCCTAC 59.854 63.158 5.05 0.00 0.00 3.18
1945 1967 7.005062 ACATCTTACATGTTGCGATAAGAAC 57.995 36.000 2.30 0.00 37.25 3.01
1947 1969 8.194769 TCTTACATCTTACATGTTGCGATAAGA 58.805 33.333 2.30 6.29 37.88 2.10
1949 1971 8.764287 CATCTTACATCTTACATGTTGCGATAA 58.236 33.333 2.30 0.00 33.76 1.75
1950 1972 7.926018 ACATCTTACATCTTACATGTTGCGATA 59.074 33.333 2.30 0.00 33.76 2.92
1952 1974 6.106003 ACATCTTACATCTTACATGTTGCGA 58.894 36.000 2.30 0.00 33.76 5.10
1953 1975 6.349973 ACATCTTACATCTTACATGTTGCG 57.650 37.500 2.30 0.00 33.76 4.85
1954 1976 8.883731 AGTTACATCTTACATCTTACATGTTGC 58.116 33.333 2.30 0.00 33.76 4.17
1958 1980 8.882736 TGCAAGTTACATCTTACATCTTACATG 58.117 33.333 0.00 0.00 0.00 3.21
1959 1981 9.618890 ATGCAAGTTACATCTTACATCTTACAT 57.381 29.630 0.00 0.00 28.74 2.29
1960 1982 8.882736 CATGCAAGTTACATCTTACATCTTACA 58.117 33.333 0.00 0.00 31.47 2.41
1962 1984 7.012327 GCCATGCAAGTTACATCTTACATCTTA 59.988 37.037 0.00 0.00 31.47 2.10
1964 1986 5.297776 GCCATGCAAGTTACATCTTACATCT 59.702 40.000 0.00 0.00 31.47 2.90
1965 1987 5.066375 TGCCATGCAAGTTACATCTTACATC 59.934 40.000 0.00 0.00 34.76 3.06
1966 1988 4.949238 TGCCATGCAAGTTACATCTTACAT 59.051 37.500 0.00 0.00 34.76 2.29
1967 1989 4.331108 TGCCATGCAAGTTACATCTTACA 58.669 39.130 0.00 0.00 34.76 2.41
1968 1990 4.635765 TCTGCCATGCAAGTTACATCTTAC 59.364 41.667 0.00 0.00 38.41 2.34
1969 1991 4.842574 TCTGCCATGCAAGTTACATCTTA 58.157 39.130 0.00 0.00 38.41 2.10
1970 1992 3.689347 TCTGCCATGCAAGTTACATCTT 58.311 40.909 0.00 0.00 38.41 2.40
1972 1994 3.881688 AGATCTGCCATGCAAGTTACATC 59.118 43.478 0.00 0.00 38.41 3.06
1973 1995 3.894759 AGATCTGCCATGCAAGTTACAT 58.105 40.909 0.00 0.00 38.41 2.29
1974 1996 3.354948 AGATCTGCCATGCAAGTTACA 57.645 42.857 0.00 0.00 38.41 2.41
1975 1997 5.278169 CCATAAGATCTGCCATGCAAGTTAC 60.278 44.000 0.00 0.00 38.41 2.50
1976 1998 4.823442 CCATAAGATCTGCCATGCAAGTTA 59.177 41.667 0.00 0.00 38.41 2.24
1977 1999 3.635373 CCATAAGATCTGCCATGCAAGTT 59.365 43.478 0.00 0.00 38.41 2.66
1987 2014 3.009301 GCATGTTGCCATAAGATCTGC 57.991 47.619 0.00 0.00 37.42 4.26
2005 2032 3.055385 GGTTATACACTCTGAACCTGGCA 60.055 47.826 0.00 0.00 38.65 4.92
2026 2053 4.435121 GCGTACTTTTAGATCAAACACCGG 60.435 45.833 0.00 0.00 0.00 5.28
2135 2162 1.375396 TTGTCAAGGATGTCGGCCG 60.375 57.895 22.12 22.12 0.00 6.13
2137 2164 1.464997 GAAGTTGTCAAGGATGTCGGC 59.535 52.381 0.00 0.00 0.00 5.54
2140 2167 3.251004 GTGTGGAAGTTGTCAAGGATGTC 59.749 47.826 0.00 0.00 0.00 3.06
2198 2225 4.813697 GCTCTTCAGAAGAATTAAGCGGAT 59.186 41.667 14.01 0.00 37.02 4.18
2255 2282 1.742768 CTACGGGGGAGCACATCTC 59.257 63.158 0.00 0.00 41.15 2.75
2293 2320 6.013812 GTGGGAATAAGATAGAAGATCTGCCT 60.014 42.308 0.00 0.00 0.00 4.75
2301 2328 4.508124 GCACGTGTGGGAATAAGATAGAAG 59.492 45.833 18.38 0.00 0.00 2.85
2302 2329 4.081365 TGCACGTGTGGGAATAAGATAGAA 60.081 41.667 18.38 0.00 0.00 2.10
2303 2330 3.449377 TGCACGTGTGGGAATAAGATAGA 59.551 43.478 18.38 0.00 0.00 1.98
2304 2331 3.555956 GTGCACGTGTGGGAATAAGATAG 59.444 47.826 18.38 0.00 0.00 2.08
2305 2332 3.527533 GTGCACGTGTGGGAATAAGATA 58.472 45.455 18.38 0.00 0.00 1.98
2306 2333 2.356135 GTGCACGTGTGGGAATAAGAT 58.644 47.619 18.38 0.00 0.00 2.40
2307 2334 1.609580 GGTGCACGTGTGGGAATAAGA 60.610 52.381 18.38 0.00 0.00 2.10
2311 2338 1.600636 CTGGTGCACGTGTGGGAAT 60.601 57.895 18.38 0.00 0.00 3.01
2347 2374 2.178273 CGGACATGACGCTGACGA 59.822 61.111 0.00 0.00 43.93 4.20
2453 2480 2.604686 AGGAAGGCAGGCGAGTGA 60.605 61.111 0.00 0.00 0.00 3.41
2462 2489 4.802051 GGCGCATGGAGGAAGGCA 62.802 66.667 10.83 0.00 0.00 4.75
2468 2495 0.742990 TAAAGAACGGCGCATGGAGG 60.743 55.000 10.83 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.