Multiple sequence alignment - TraesCS6B01G019500

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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 TraesCS6B01G019500 chr6B 100.000 2762 0 0 1 2762 11749290 11746529 0.000000e+00 5101.0
1 TraesCS6B01G019500 chr6B 96.318 2037 50 6 408 2443 11618936 11616924 0.000000e+00 3323.0
2 TraesCS6B01G019500 chr6B 96.988 332 2 1 2439 2762 11616892 11616561 4.020000e-153 551.0
3 TraesCS6B01G019500 chr6B 90.714 140 9 1 172 311 11619104 11618969 1.690000e-42 183.0
4 TraesCS6B01G019500 chr6B 76.056 213 49 2 1304 1515 19120098 19120309 2.910000e-20 110.0
5 TraesCS6B01G019500 chr5B 80.000 180 36 0 610 789 536910845 536910666 1.730000e-27 134.0
6 TraesCS6B01G019500 chr5D 79.330 179 37 0 611 789 441239155 441238977 2.890000e-25 126.0
7 TraesCS6B01G019500 chr6D 76.995 213 47 2 1304 1515 10344952 10344741 1.340000e-23 121.0
8 TraesCS6B01G019500 chr6D 89.189 74 8 0 623 696 10030306 10030379 2.930000e-15 93.5
9 TraesCS6B01G019500 chr7A 73.497 366 72 16 1431 1778 728055991 728055633 6.250000e-22 115.0
10 TraesCS6B01G019500 chr7A 75.185 270 44 16 1681 1945 728088776 728088525 3.760000e-19 106.0
11 TraesCS6B01G019500 chr7A 97.826 46 1 0 1 46 239425303 239425258 2.280000e-11 80.5
12 TraesCS6B01G019500 chr3B 83.784 111 17 1 635 744 749648332 749648442 1.350000e-18 104.0
13 TraesCS6B01G019500 chr7B 72.521 353 78 12 1431 1768 738817213 738817561 2.260000e-16 97.1
14 TraesCS6B01G019500 chr7D 76.437 174 38 3 621 793 618767156 618766985 1.050000e-14 91.6


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 TraesCS6B01G019500 chr6B 11746529 11749290 2761 True 5101.000000 5101 100.000000 1 2762 1 chr6B.!!$R1 2761
1 TraesCS6B01G019500 chr6B 11616561 11619104 2543 True 1352.333333 3323 94.673333 172 2762 3 chr6B.!!$R2 2590

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
393 408 0.103572 GCCATTGCTGAATGCCGATT 59.896 50.0 0.0 0.0 42.00 3.34 F
813 828 0.756815 GGGCATGGTTCTTCCCCATC 60.757 60.0 0.0 0.0 40.76 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1616 1.558294 AGAGCAAGCATCCACTCATCA 59.442 47.619 0.0 0.0 0.00 3.07 R
1950 1965 2.071688 ACGAAGTAAGAGCAGCACAG 57.928 50.000 0.0 0.0 41.94 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.977244 CGCCCTGGCCACAAACAC 61.977 66.667 0.00 0.00 37.98 3.32
40 41 2.521708 GCCCTGGCCACAAACACT 60.522 61.111 0.00 0.00 34.56 3.55
41 42 2.133641 GCCCTGGCCACAAACACTT 61.134 57.895 0.00 0.00 34.56 3.16
42 43 2.041153 CCCTGGCCACAAACACTTC 58.959 57.895 0.00 0.00 0.00 3.01
43 44 1.463553 CCCTGGCCACAAACACTTCC 61.464 60.000 0.00 0.00 0.00 3.46
44 45 1.463553 CCTGGCCACAAACACTTCCC 61.464 60.000 0.00 0.00 0.00 3.97
45 46 0.468029 CTGGCCACAAACACTTCCCT 60.468 55.000 0.00 0.00 0.00 4.20
46 47 0.847373 TGGCCACAAACACTTCCCTA 59.153 50.000 0.00 0.00 0.00 3.53
47 48 1.202879 TGGCCACAAACACTTCCCTAG 60.203 52.381 0.00 0.00 0.00 3.02
48 49 1.073284 GGCCACAAACACTTCCCTAGA 59.927 52.381 0.00 0.00 0.00 2.43
49 50 2.152016 GCCACAAACACTTCCCTAGAC 58.848 52.381 0.00 0.00 0.00 2.59
50 51 2.779506 CCACAAACACTTCCCTAGACC 58.220 52.381 0.00 0.00 0.00 3.85
51 52 2.105821 CCACAAACACTTCCCTAGACCA 59.894 50.000 0.00 0.00 0.00 4.02
52 53 3.434453 CCACAAACACTTCCCTAGACCAA 60.434 47.826 0.00 0.00 0.00 3.67
53 54 4.204012 CACAAACACTTCCCTAGACCAAA 58.796 43.478 0.00 0.00 0.00 3.28
54 55 4.036380 CACAAACACTTCCCTAGACCAAAC 59.964 45.833 0.00 0.00 0.00 2.93
55 56 2.833631 ACACTTCCCTAGACCAAACG 57.166 50.000 0.00 0.00 0.00 3.60
56 57 2.044758 ACACTTCCCTAGACCAAACGT 58.955 47.619 0.00 0.00 0.00 3.99
57 58 2.036862 ACACTTCCCTAGACCAAACGTC 59.963 50.000 0.00 0.00 42.32 4.34
58 59 1.622312 ACTTCCCTAGACCAAACGTCC 59.378 52.381 0.00 0.00 43.08 4.79
59 60 0.604578 TTCCCTAGACCAAACGTCCG 59.395 55.000 0.00 0.00 43.08 4.79
60 61 1.447314 CCCTAGACCAAACGTCCGC 60.447 63.158 0.00 0.00 43.08 5.54
61 62 1.804326 CCTAGACCAAACGTCCGCG 60.804 63.158 0.00 0.00 43.08 6.46
71 72 4.907034 CGTCCGCGTCCCAGATCG 62.907 72.222 4.92 0.00 0.00 3.69
72 73 4.570663 GTCCGCGTCCCAGATCGG 62.571 72.222 4.92 0.00 42.96 4.18
92 93 2.629051 GGAAATACCCGACTCCTTGTG 58.371 52.381 0.00 0.00 0.00 3.33
93 94 2.027469 GGAAATACCCGACTCCTTGTGT 60.027 50.000 0.00 0.00 0.00 3.72
94 95 3.259902 GAAATACCCGACTCCTTGTGTC 58.740 50.000 0.00 0.00 0.00 3.67
99 100 3.952811 GACTCCTTGTGTCGTGCC 58.047 61.111 0.00 0.00 0.00 5.01
100 101 1.668151 GACTCCTTGTGTCGTGCCC 60.668 63.158 0.00 0.00 0.00 5.36
101 102 2.377628 GACTCCTTGTGTCGTGCCCA 62.378 60.000 0.00 0.00 0.00 5.36
102 103 1.003355 CTCCTTGTGTCGTGCCCAT 60.003 57.895 0.00 0.00 0.00 4.00
103 104 1.003839 TCCTTGTGTCGTGCCCATC 60.004 57.895 0.00 0.00 0.00 3.51
104 105 2.390599 CCTTGTGTCGTGCCCATCG 61.391 63.158 0.00 0.00 0.00 3.84
105 106 3.027170 CTTGTGTCGTGCCCATCGC 62.027 63.158 0.00 0.00 38.31 4.58
106 107 3.529341 TTGTGTCGTGCCCATCGCT 62.529 57.895 0.00 0.00 38.78 4.93
107 108 2.742372 GTGTCGTGCCCATCGCTT 60.742 61.111 0.00 0.00 38.78 4.68
108 109 2.434185 TGTCGTGCCCATCGCTTC 60.434 61.111 0.00 0.00 38.78 3.86
109 110 2.125512 GTCGTGCCCATCGCTTCT 60.126 61.111 0.00 0.00 38.78 2.85
110 111 2.167861 GTCGTGCCCATCGCTTCTC 61.168 63.158 0.00 0.00 38.78 2.87
111 112 2.892425 CGTGCCCATCGCTTCTCC 60.892 66.667 0.00 0.00 38.78 3.71
112 113 2.892425 GTGCCCATCGCTTCTCCG 60.892 66.667 0.00 0.00 38.78 4.63
113 114 4.838152 TGCCCATCGCTTCTCCGC 62.838 66.667 0.00 0.00 38.78 5.54
115 116 3.854669 CCCATCGCTTCTCCGCCT 61.855 66.667 0.00 0.00 0.00 5.52
116 117 2.279784 CCATCGCTTCTCCGCCTC 60.280 66.667 0.00 0.00 0.00 4.70
117 118 2.790791 CCATCGCTTCTCCGCCTCT 61.791 63.158 0.00 0.00 0.00 3.69
118 119 1.299773 CATCGCTTCTCCGCCTCTC 60.300 63.158 0.00 0.00 0.00 3.20
119 120 2.840066 ATCGCTTCTCCGCCTCTCG 61.840 63.158 0.00 0.00 38.08 4.04
120 121 3.509757 CGCTTCTCCGCCTCTCGA 61.510 66.667 0.00 0.00 41.67 4.04
121 122 2.103340 GCTTCTCCGCCTCTCGAC 59.897 66.667 0.00 0.00 41.67 4.20
122 123 2.405594 CTTCTCCGCCTCTCGACG 59.594 66.667 0.00 0.00 41.67 5.12
130 131 4.477975 CCTCTCGACGGCGACACC 62.478 72.222 10.67 0.00 42.51 4.16
131 132 3.432588 CTCTCGACGGCGACACCT 61.433 66.667 10.67 0.00 42.51 4.00
132 133 2.979197 CTCTCGACGGCGACACCTT 61.979 63.158 10.67 0.00 42.51 3.50
133 134 2.504244 CTCGACGGCGACACCTTC 60.504 66.667 10.67 0.00 42.51 3.46
134 135 3.966026 CTCGACGGCGACACCTTCC 62.966 68.421 10.67 0.00 42.51 3.46
136 137 4.047059 GACGGCGACACCTTCCGA 62.047 66.667 16.62 0.00 45.53 4.55
137 138 4.353437 ACGGCGACACCTTCCGAC 62.353 66.667 16.62 0.00 45.53 4.79
170 171 3.917760 GACGGCCGGGGAGAGATG 61.918 72.222 31.76 0.00 0.00 2.90
237 238 0.394352 GTTTCCCGCTGGATCCATGT 60.394 55.000 16.63 0.00 41.40 3.21
238 239 1.134220 GTTTCCCGCTGGATCCATGTA 60.134 52.381 16.63 0.00 41.40 2.29
239 240 0.468226 TTCCCGCTGGATCCATGTAC 59.532 55.000 16.63 4.54 41.40 2.90
240 241 0.398522 TCCCGCTGGATCCATGTACT 60.399 55.000 16.63 0.00 35.03 2.73
257 258 9.261180 TCCATGTACTTATTTTCAGATCGATTC 57.739 33.333 0.00 0.00 0.00 2.52
298 299 2.231478 TGTTCCTCGGAGTGTTCTCATC 59.769 50.000 4.02 0.00 42.05 2.92
311 312 1.062364 TCTCATCAGCCCCATGATCC 58.938 55.000 0.00 0.00 37.84 3.36
312 313 0.769247 CTCATCAGCCCCATGATCCA 59.231 55.000 0.00 0.00 37.84 3.41
315 316 1.155323 ATCAGCCCCATGATCCATGT 58.845 50.000 0.00 0.00 39.94 3.21
316 317 0.928505 TCAGCCCCATGATCCATGTT 59.071 50.000 0.00 0.00 39.94 2.71
317 318 1.288633 TCAGCCCCATGATCCATGTTT 59.711 47.619 0.00 0.00 39.94 2.83
318 319 1.411246 CAGCCCCATGATCCATGTTTG 59.589 52.381 0.00 0.00 39.94 2.93
319 320 1.288633 AGCCCCATGATCCATGTTTGA 59.711 47.619 0.00 0.00 39.94 2.69
322 323 2.036733 CCCCATGATCCATGTTTGATGC 59.963 50.000 0.00 0.00 39.94 3.91
323 324 2.696187 CCCATGATCCATGTTTGATGCA 59.304 45.455 0.00 0.00 39.94 3.96
325 326 4.202315 CCCATGATCCATGTTTGATGCAAT 60.202 41.667 0.00 0.00 39.94 3.56
327 328 6.463190 CCCATGATCCATGTTTGATGCAATAA 60.463 38.462 0.00 0.00 39.94 1.40
328 329 6.645003 CCATGATCCATGTTTGATGCAATAAG 59.355 38.462 0.00 0.00 39.94 1.73
340 355 3.644966 TGCAATAAGATTCCGAACCCT 57.355 42.857 0.00 0.00 0.00 4.34
347 362 1.279271 AGATTCCGAACCCTTGGAGTG 59.721 52.381 0.00 0.00 35.26 3.51
348 363 1.003233 GATTCCGAACCCTTGGAGTGT 59.997 52.381 0.00 0.00 35.26 3.55
349 364 0.841289 TTCCGAACCCTTGGAGTGTT 59.159 50.000 0.00 0.00 35.26 3.32
350 365 0.841289 TCCGAACCCTTGGAGTGTTT 59.159 50.000 0.00 0.00 0.00 2.83
351 366 1.213430 TCCGAACCCTTGGAGTGTTTT 59.787 47.619 0.00 0.00 0.00 2.43
352 367 2.028876 CCGAACCCTTGGAGTGTTTTT 58.971 47.619 0.00 0.00 0.00 1.94
353 368 3.117963 TCCGAACCCTTGGAGTGTTTTTA 60.118 43.478 0.00 0.00 0.00 1.52
354 369 3.004002 CCGAACCCTTGGAGTGTTTTTAC 59.996 47.826 0.00 0.00 0.00 2.01
355 370 3.004002 CGAACCCTTGGAGTGTTTTTACC 59.996 47.826 0.00 0.00 0.00 2.85
356 371 3.673543 ACCCTTGGAGTGTTTTTACCA 57.326 42.857 0.00 0.00 0.00 3.25
357 372 3.293337 ACCCTTGGAGTGTTTTTACCAC 58.707 45.455 0.00 0.00 31.87 4.16
358 373 2.626266 CCCTTGGAGTGTTTTTACCACC 59.374 50.000 0.00 0.00 33.20 4.61
359 374 3.292460 CCTTGGAGTGTTTTTACCACCA 58.708 45.455 0.00 0.00 33.20 4.17
360 375 3.702045 CCTTGGAGTGTTTTTACCACCAA 59.298 43.478 0.00 0.00 36.66 3.67
361 376 4.160626 CCTTGGAGTGTTTTTACCACCAAA 59.839 41.667 0.00 0.00 37.20 3.28
362 377 5.163353 CCTTGGAGTGTTTTTACCACCAAAT 60.163 40.000 0.00 0.00 37.20 2.32
363 378 5.523438 TGGAGTGTTTTTACCACCAAATC 57.477 39.130 0.00 0.00 33.20 2.17
364 379 4.956700 TGGAGTGTTTTTACCACCAAATCA 59.043 37.500 0.00 0.00 33.20 2.57
365 380 5.068460 TGGAGTGTTTTTACCACCAAATCAG 59.932 40.000 0.00 0.00 33.20 2.90
366 381 5.300792 GGAGTGTTTTTACCACCAAATCAGA 59.699 40.000 0.00 0.00 33.20 3.27
367 382 6.183360 GGAGTGTTTTTACCACCAAATCAGAA 60.183 38.462 0.00 0.00 33.20 3.02
368 383 7.360113 AGTGTTTTTACCACCAAATCAGAAT 57.640 32.000 0.00 0.00 33.20 2.40
369 384 7.433680 AGTGTTTTTACCACCAAATCAGAATC 58.566 34.615 0.00 0.00 33.20 2.52
370 385 7.069331 AGTGTTTTTACCACCAAATCAGAATCA 59.931 33.333 0.00 0.00 33.20 2.57
371 386 7.169140 GTGTTTTTACCACCAAATCAGAATCAC 59.831 37.037 0.00 0.00 0.00 3.06
372 387 7.069331 TGTTTTTACCACCAAATCAGAATCACT 59.931 33.333 0.00 0.00 0.00 3.41
373 388 8.573035 GTTTTTACCACCAAATCAGAATCACTA 58.427 33.333 0.00 0.00 0.00 2.74
374 389 7.921786 TTTACCACCAAATCAGAATCACTAG 57.078 36.000 0.00 0.00 0.00 2.57
375 390 4.265073 ACCACCAAATCAGAATCACTAGC 58.735 43.478 0.00 0.00 0.00 3.42
376 391 3.629398 CCACCAAATCAGAATCACTAGCC 59.371 47.826 0.00 0.00 0.00 3.93
377 392 4.264253 CACCAAATCAGAATCACTAGCCA 58.736 43.478 0.00 0.00 0.00 4.75
378 393 4.885907 CACCAAATCAGAATCACTAGCCAT 59.114 41.667 0.00 0.00 0.00 4.40
379 394 5.359009 CACCAAATCAGAATCACTAGCCATT 59.641 40.000 0.00 0.00 0.00 3.16
380 395 5.359009 ACCAAATCAGAATCACTAGCCATTG 59.641 40.000 0.00 0.00 0.00 2.82
381 396 5.279384 CAAATCAGAATCACTAGCCATTGC 58.721 41.667 0.00 0.00 37.95 3.56
391 406 3.199551 GCCATTGCTGAATGCCGA 58.800 55.556 0.00 0.00 42.00 5.54
392 407 1.737816 GCCATTGCTGAATGCCGAT 59.262 52.632 0.00 0.00 42.00 4.18
393 408 0.103572 GCCATTGCTGAATGCCGATT 59.896 50.000 0.00 0.00 42.00 3.34
394 409 1.847818 CCATTGCTGAATGCCGATTG 58.152 50.000 0.00 0.00 42.00 2.67
395 410 1.135527 CCATTGCTGAATGCCGATTGT 59.864 47.619 0.00 0.00 42.00 2.71
396 411 2.417651 CCATTGCTGAATGCCGATTGTT 60.418 45.455 0.00 0.00 42.00 2.83
397 412 2.350899 TTGCTGAATGCCGATTGTTG 57.649 45.000 0.00 0.00 42.00 3.33
398 413 1.532523 TGCTGAATGCCGATTGTTGA 58.467 45.000 0.00 0.00 42.00 3.18
399 414 2.093890 TGCTGAATGCCGATTGTTGAT 58.906 42.857 0.00 0.00 42.00 2.57
400 415 2.492881 TGCTGAATGCCGATTGTTGATT 59.507 40.909 0.00 0.00 42.00 2.57
401 416 3.693578 TGCTGAATGCCGATTGTTGATTA 59.306 39.130 0.00 0.00 42.00 1.75
402 417 4.157472 TGCTGAATGCCGATTGTTGATTAA 59.843 37.500 0.00 0.00 42.00 1.40
403 418 5.163530 TGCTGAATGCCGATTGTTGATTAAT 60.164 36.000 0.00 0.00 42.00 1.40
404 419 5.400485 GCTGAATGCCGATTGTTGATTAATC 59.600 40.000 8.60 8.60 35.15 1.75
405 420 6.448207 TGAATGCCGATTGTTGATTAATCA 57.552 33.333 14.23 14.23 34.90 2.57
406 421 6.497437 TGAATGCCGATTGTTGATTAATCAG 58.503 36.000 17.28 6.29 38.19 2.90
407 422 6.318396 TGAATGCCGATTGTTGATTAATCAGA 59.682 34.615 17.28 8.99 38.19 3.27
408 423 6.889301 ATGCCGATTGTTGATTAATCAGAT 57.111 33.333 17.28 12.83 38.19 2.90
409 424 6.698008 TGCCGATTGTTGATTAATCAGATT 57.302 33.333 17.28 0.20 38.19 2.40
410 425 6.728200 TGCCGATTGTTGATTAATCAGATTC 58.272 36.000 17.28 12.09 38.19 2.52
411 426 5.848036 GCCGATTGTTGATTAATCAGATTCG 59.152 40.000 17.28 20.33 38.19 3.34
412 427 5.848036 CCGATTGTTGATTAATCAGATTCGC 59.152 40.000 22.93 12.57 38.19 4.70
413 428 6.293081 CCGATTGTTGATTAATCAGATTCGCT 60.293 38.462 22.93 8.86 38.19 4.93
414 429 7.095649 CCGATTGTTGATTAATCAGATTCGCTA 60.096 37.037 22.93 7.15 38.19 4.26
415 430 8.275632 CGATTGTTGATTAATCAGATTCGCTAA 58.724 33.333 17.28 6.70 38.19 3.09
416 431 9.374960 GATTGTTGATTAATCAGATTCGCTAAC 57.625 33.333 17.28 10.39 38.19 2.34
417 432 7.246674 TGTTGATTAATCAGATTCGCTAACC 57.753 36.000 17.28 0.00 38.19 2.85
418 433 6.260050 TGTTGATTAATCAGATTCGCTAACCC 59.740 38.462 17.28 0.00 38.19 4.11
419 434 6.174720 TGATTAATCAGATTCGCTAACCCT 57.825 37.500 14.23 0.00 32.11 4.34
420 435 7.297936 TGATTAATCAGATTCGCTAACCCTA 57.702 36.000 14.23 0.00 32.11 3.53
421 436 7.378966 TGATTAATCAGATTCGCTAACCCTAG 58.621 38.462 14.23 0.00 32.11 3.02
422 437 6.971726 TTAATCAGATTCGCTAACCCTAGA 57.028 37.500 0.00 0.00 0.00 2.43
423 438 5.461032 AATCAGATTCGCTAACCCTAGAG 57.539 43.478 0.00 0.00 0.00 2.43
424 439 3.899726 TCAGATTCGCTAACCCTAGAGT 58.100 45.455 0.00 0.00 0.00 3.24
425 440 5.045012 TCAGATTCGCTAACCCTAGAGTA 57.955 43.478 0.00 0.00 0.00 2.59
426 441 5.632118 TCAGATTCGCTAACCCTAGAGTAT 58.368 41.667 0.00 0.00 0.00 2.12
537 552 3.714391 CGGTACTAATGCCCTGTTCTAC 58.286 50.000 0.00 0.00 0.00 2.59
548 563 3.761897 CCCTGTTCTACATTGTTTCCCA 58.238 45.455 0.00 0.00 0.00 4.37
574 589 4.516323 CCACAGATACCATCACAACATGA 58.484 43.478 0.00 0.00 43.13 3.07
579 594 2.270352 ACCATCACAACATGAACGGT 57.730 45.000 0.00 0.00 41.93 4.83
580 595 1.879380 ACCATCACAACATGAACGGTG 59.121 47.619 0.00 2.11 42.69 4.94
602 617 4.699522 GAAGCCGCCGGGAGTGTT 62.700 66.667 4.77 0.00 34.06 3.32
605 620 4.382320 GCCGCCGGGAGTGTTGTA 62.382 66.667 4.77 0.00 34.06 2.41
613 628 2.380410 GGAGTGTTGTACGCAGCCG 61.380 63.158 0.00 0.00 41.14 5.52
627 642 0.811616 CAGCCGTATGGAAGGTGCTC 60.812 60.000 4.73 0.00 37.49 4.26
628 643 1.220749 GCCGTATGGAAGGTGCTCA 59.779 57.895 4.73 0.00 37.49 4.26
663 678 0.891449 TCATCGAGATCCTCCTCCGC 60.891 60.000 0.00 0.00 0.00 5.54
667 682 1.152652 GAGATCCTCCTCCGCCTCA 60.153 63.158 0.00 0.00 0.00 3.86
713 728 1.005037 CCCTTGTGTGCAGACGCTA 60.005 57.895 9.70 0.00 39.64 4.26
719 734 2.275380 TGTGCAGACGCTAGCTCCA 61.275 57.895 13.93 0.00 39.64 3.86
726 741 2.590007 CGCTAGCTCCACCATGCC 60.590 66.667 13.93 0.00 0.00 4.40
753 768 2.241176 TCCGGCCTTCCTATGTCATTTT 59.759 45.455 0.00 0.00 0.00 1.82
754 769 2.618709 CCGGCCTTCCTATGTCATTTTC 59.381 50.000 0.00 0.00 0.00 2.29
799 814 1.344953 TGGCTTCTATCGTGGGGCAT 61.345 55.000 0.00 0.00 0.00 4.40
813 828 0.756815 GGGCATGGTTCTTCCCCATC 60.757 60.000 0.00 0.00 40.76 3.51
815 830 0.756815 GCATGGTTCTTCCCCATCCC 60.757 60.000 0.00 0.00 40.76 3.85
819 834 2.612430 TTCTTCCCCATCCCGCCA 60.612 61.111 0.00 0.00 0.00 5.69
838 853 2.650116 CCATATCCCCCGGAGCTCG 61.650 68.421 0.73 3.03 34.05 5.03
917 932 4.500837 CGCTATATCGATCAAGGATTTCCG 59.499 45.833 0.00 0.00 42.08 4.30
924 939 1.762708 TCAAGGATTTCCGGAATGGC 58.237 50.000 19.62 10.18 42.08 4.40
928 943 1.037030 GGATTTCCGGAATGGCTGCA 61.037 55.000 19.62 0.42 37.80 4.41
984 999 1.174078 TTCGAGTGCACCGTCCACTA 61.174 55.000 21.61 4.61 43.17 2.74
985 1000 0.963856 TCGAGTGCACCGTCCACTAT 60.964 55.000 21.61 0.00 43.17 2.12
1022 1037 2.125269 CATCGTCCCACCGTTCCC 60.125 66.667 0.00 0.00 0.00 3.97
1030 1045 3.055719 CACCGTTCCCGCAGCATT 61.056 61.111 0.00 0.00 0.00 3.56
1032 1047 1.743995 ACCGTTCCCGCAGCATTAC 60.744 57.895 0.00 0.00 0.00 1.89
1217 1232 3.244596 GCCACCACTAAAACCTCTTCTCT 60.245 47.826 0.00 0.00 0.00 3.10
1596 1611 4.142381 GGGGACAATGCTGAGTTTATGTTC 60.142 45.833 0.00 0.00 0.00 3.18
1597 1612 4.702131 GGGACAATGCTGAGTTTATGTTCT 59.298 41.667 0.00 0.00 0.00 3.01
1598 1613 5.183904 GGGACAATGCTGAGTTTATGTTCTT 59.816 40.000 0.00 0.00 0.00 2.52
1599 1614 6.088824 GGACAATGCTGAGTTTATGTTCTTG 58.911 40.000 0.00 0.00 0.00 3.02
1600 1615 6.072508 GGACAATGCTGAGTTTATGTTCTTGA 60.073 38.462 0.00 0.00 0.00 3.02
1601 1616 7.362401 GGACAATGCTGAGTTTATGTTCTTGAT 60.362 37.037 0.00 0.00 0.00 2.57
1602 1617 7.310664 ACAATGCTGAGTTTATGTTCTTGATG 58.689 34.615 0.00 0.00 0.00 3.07
1603 1618 7.175467 ACAATGCTGAGTTTATGTTCTTGATGA 59.825 33.333 0.00 0.00 0.00 2.92
1604 1619 7.876936 ATGCTGAGTTTATGTTCTTGATGAT 57.123 32.000 0.00 0.00 0.00 2.45
1605 1620 7.080353 TGCTGAGTTTATGTTCTTGATGATG 57.920 36.000 0.00 0.00 0.00 3.07
1606 1621 6.880529 TGCTGAGTTTATGTTCTTGATGATGA 59.119 34.615 0.00 0.00 0.00 2.92
1607 1622 7.065443 TGCTGAGTTTATGTTCTTGATGATGAG 59.935 37.037 0.00 0.00 0.00 2.90
1608 1623 7.065563 GCTGAGTTTATGTTCTTGATGATGAGT 59.934 37.037 0.00 0.00 0.00 3.41
1609 1624 8.260270 TGAGTTTATGTTCTTGATGATGAGTG 57.740 34.615 0.00 0.00 0.00 3.51
1610 1625 7.335171 TGAGTTTATGTTCTTGATGATGAGTGG 59.665 37.037 0.00 0.00 0.00 4.00
1611 1626 7.397221 AGTTTATGTTCTTGATGATGAGTGGA 58.603 34.615 0.00 0.00 0.00 4.02
1612 1627 8.051535 AGTTTATGTTCTTGATGATGAGTGGAT 58.948 33.333 0.00 0.00 0.00 3.41
1613 1628 7.797038 TTATGTTCTTGATGATGAGTGGATG 57.203 36.000 0.00 0.00 0.00 3.51
1704 1719 7.392673 CCTATCCATCCTTTTATGATGTTCTGG 59.607 40.741 0.00 0.00 38.32 3.86
1800 1815 3.239449 TCTTCTCTTGGCTGAGGTTACA 58.761 45.455 7.90 0.00 34.98 2.41
1890 1905 7.038302 AGGTATATGATTGGTTCCATACGTCAT 60.038 37.037 0.00 11.31 32.44 3.06
1950 1965 8.218338 TCTCTAAGATGATTTTGAAAGGATGC 57.782 34.615 0.00 0.00 0.00 3.91
2260 2275 2.957491 TTGTTTGGTGAGTTTGCAGG 57.043 45.000 0.00 0.00 0.00 4.85
2401 2416 5.357878 TCTGAAATAGCATCACAAACCCATC 59.642 40.000 0.00 0.00 0.00 3.51
2462 2513 0.178068 ACCGTTGAACTGTGACTGCT 59.822 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.977244 GTGTTTGTGGCCAGGGCG 61.977 66.667 5.11 0.00 43.06 6.13
23 24 2.087462 GAAGTGTTTGTGGCCAGGGC 62.087 60.000 5.11 5.91 41.06 5.19
24 25 1.463553 GGAAGTGTTTGTGGCCAGGG 61.464 60.000 5.11 0.00 0.00 4.45
25 26 1.463553 GGGAAGTGTTTGTGGCCAGG 61.464 60.000 5.11 0.00 0.00 4.45
26 27 0.468029 AGGGAAGTGTTTGTGGCCAG 60.468 55.000 5.11 0.00 0.00 4.85
27 28 0.847373 TAGGGAAGTGTTTGTGGCCA 59.153 50.000 0.00 0.00 0.00 5.36
28 29 1.073284 TCTAGGGAAGTGTTTGTGGCC 59.927 52.381 0.00 0.00 0.00 5.36
29 30 2.152016 GTCTAGGGAAGTGTTTGTGGC 58.848 52.381 0.00 0.00 0.00 5.01
30 31 2.105821 TGGTCTAGGGAAGTGTTTGTGG 59.894 50.000 0.00 0.00 0.00 4.17
31 32 3.485463 TGGTCTAGGGAAGTGTTTGTG 57.515 47.619 0.00 0.00 0.00 3.33
32 33 4.204799 GTTTGGTCTAGGGAAGTGTTTGT 58.795 43.478 0.00 0.00 0.00 2.83
33 34 3.250040 CGTTTGGTCTAGGGAAGTGTTTG 59.750 47.826 0.00 0.00 0.00 2.93
34 35 3.118149 ACGTTTGGTCTAGGGAAGTGTTT 60.118 43.478 0.00 0.00 0.00 2.83
35 36 2.436911 ACGTTTGGTCTAGGGAAGTGTT 59.563 45.455 0.00 0.00 0.00 3.32
36 37 2.036862 GACGTTTGGTCTAGGGAAGTGT 59.963 50.000 0.00 0.00 42.62 3.55
37 38 2.612221 GGACGTTTGGTCTAGGGAAGTG 60.612 54.545 0.00 0.00 45.35 3.16
38 39 1.622312 GGACGTTTGGTCTAGGGAAGT 59.378 52.381 0.00 0.00 45.35 3.01
39 40 1.403780 CGGACGTTTGGTCTAGGGAAG 60.404 57.143 0.00 0.00 45.35 3.46
40 41 0.604578 CGGACGTTTGGTCTAGGGAA 59.395 55.000 0.00 0.00 45.35 3.97
41 42 1.880819 GCGGACGTTTGGTCTAGGGA 61.881 60.000 0.00 0.00 45.35 4.20
42 43 1.447314 GCGGACGTTTGGTCTAGGG 60.447 63.158 0.00 0.00 45.35 3.53
43 44 1.804326 CGCGGACGTTTGGTCTAGG 60.804 63.158 0.00 0.00 45.35 3.02
44 45 3.763319 CGCGGACGTTTGGTCTAG 58.237 61.111 0.00 0.00 45.35 2.43
55 56 4.570663 CCGATCTGGGACGCGGAC 62.571 72.222 12.47 3.69 46.29 4.79
72 73 2.027469 ACACAAGGAGTCGGGTATTTCC 60.027 50.000 0.00 0.00 0.00 3.13
73 74 3.259902 GACACAAGGAGTCGGGTATTTC 58.740 50.000 0.00 0.00 0.00 2.17
74 75 3.329929 GACACAAGGAGTCGGGTATTT 57.670 47.619 0.00 0.00 0.00 1.40
82 83 1.668151 GGGCACGACACAAGGAGTC 60.668 63.158 0.00 0.00 0.00 3.36
83 84 1.768684 ATGGGCACGACACAAGGAGT 61.769 55.000 0.00 0.00 0.00 3.85
84 85 1.003355 ATGGGCACGACACAAGGAG 60.003 57.895 0.00 0.00 0.00 3.69
85 86 1.003839 GATGGGCACGACACAAGGA 60.004 57.895 0.00 0.00 0.00 3.36
86 87 2.390599 CGATGGGCACGACACAAGG 61.391 63.158 0.00 0.00 0.00 3.61
87 88 3.027170 GCGATGGGCACGACACAAG 62.027 63.158 0.00 0.00 42.87 3.16
88 89 3.047280 GCGATGGGCACGACACAA 61.047 61.111 0.00 0.00 42.87 3.33
98 99 3.798954 GAGGCGGAGAAGCGATGGG 62.799 68.421 0.00 0.00 38.18 4.00
99 100 2.279784 GAGGCGGAGAAGCGATGG 60.280 66.667 0.00 0.00 38.18 3.51
100 101 1.299773 GAGAGGCGGAGAAGCGATG 60.300 63.158 0.00 0.00 38.18 3.84
101 102 2.840066 CGAGAGGCGGAGAAGCGAT 61.840 63.158 0.00 0.00 38.18 4.58
102 103 3.509757 CGAGAGGCGGAGAAGCGA 61.510 66.667 0.00 0.00 38.18 4.93
103 104 3.509757 TCGAGAGGCGGAGAAGCG 61.510 66.667 0.00 0.00 41.33 4.68
104 105 2.103340 GTCGAGAGGCGGAGAAGC 59.897 66.667 0.00 0.00 41.33 3.86
113 114 4.477975 GGTGTCGCCGTCGAGAGG 62.478 72.222 0.00 2.63 46.46 3.69
114 115 2.852431 GAAGGTGTCGCCGTCGAGAG 62.852 65.000 2.47 0.00 46.46 3.20
115 116 2.974489 GAAGGTGTCGCCGTCGAGA 61.974 63.158 2.47 0.00 46.46 4.04
116 117 2.504244 GAAGGTGTCGCCGTCGAG 60.504 66.667 2.47 0.00 46.46 4.04
117 118 4.047059 GGAAGGTGTCGCCGTCGA 62.047 66.667 11.56 0.00 45.10 4.20
119 120 4.047059 TCGGAAGGTGTCGCCGTC 62.047 66.667 9.64 9.64 45.02 4.79
120 121 4.353437 GTCGGAAGGTGTCGCCGT 62.353 66.667 0.00 0.00 45.02 5.68
153 154 3.917760 CATCTCTCCCCGGCCGTC 61.918 72.222 26.12 0.00 0.00 4.79
154 155 4.779733 ACATCTCTCCCCGGCCGT 62.780 66.667 26.12 0.00 0.00 5.68
155 156 3.917760 GACATCTCTCCCCGGCCG 61.918 72.222 21.04 21.04 0.00 6.13
156 157 3.551407 GGACATCTCTCCCCGGCC 61.551 72.222 0.00 0.00 0.00 6.13
157 158 3.551407 GGGACATCTCTCCCCGGC 61.551 72.222 0.00 0.00 44.12 6.13
160 161 3.551407 GGCGGGACATCTCTCCCC 61.551 72.222 0.00 0.00 46.90 4.81
161 162 3.917760 CGGCGGGACATCTCTCCC 61.918 72.222 0.00 0.00 46.19 4.30
162 163 3.917760 CCGGCGGGACATCTCTCC 61.918 72.222 20.56 0.00 34.06 3.71
163 164 2.833582 TCCGGCGGGACATCTCTC 60.834 66.667 27.98 0.00 37.43 3.20
178 179 1.128188 ACCTCAGTCCAGGTTGGTCC 61.128 60.000 0.00 0.00 45.24 4.46
183 184 1.433592 AGGAGTACCTCAGTCCAGGTT 59.566 52.381 0.00 0.00 45.24 3.50
227 228 7.657354 CGATCTGAAAATAAGTACATGGATCCA 59.343 37.037 18.88 18.88 0.00 3.41
231 232 9.261180 GAATCGATCTGAAAATAAGTACATGGA 57.739 33.333 0.00 0.00 0.00 3.41
238 239 8.781196 CATCCATGAATCGATCTGAAAATAAGT 58.219 33.333 0.00 0.00 0.00 2.24
239 240 7.749570 GCATCCATGAATCGATCTGAAAATAAG 59.250 37.037 0.00 0.00 0.00 1.73
240 241 7.308770 GGCATCCATGAATCGATCTGAAAATAA 60.309 37.037 0.00 0.00 0.00 1.40
298 299 1.411246 CAAACATGGATCATGGGGCTG 59.589 52.381 11.85 1.25 45.16 4.85
311 312 6.497437 TCGGAATCTTATTGCATCAAACATG 58.503 36.000 0.00 0.00 0.00 3.21
312 313 6.698008 TCGGAATCTTATTGCATCAAACAT 57.302 33.333 0.00 0.00 0.00 2.71
315 316 5.163561 GGGTTCGGAATCTTATTGCATCAAA 60.164 40.000 0.36 0.00 0.00 2.69
316 317 4.338118 GGGTTCGGAATCTTATTGCATCAA 59.662 41.667 0.36 0.00 0.00 2.57
317 318 3.882888 GGGTTCGGAATCTTATTGCATCA 59.117 43.478 0.36 0.00 0.00 3.07
318 319 4.137543 AGGGTTCGGAATCTTATTGCATC 58.862 43.478 0.36 0.00 0.00 3.91
319 320 4.170468 AGGGTTCGGAATCTTATTGCAT 57.830 40.909 0.36 0.00 0.00 3.96
322 323 4.523083 TCCAAGGGTTCGGAATCTTATTG 58.477 43.478 0.36 4.50 0.00 1.90
323 324 4.227527 ACTCCAAGGGTTCGGAATCTTATT 59.772 41.667 0.36 0.00 0.00 1.40
325 326 3.055385 CACTCCAAGGGTTCGGAATCTTA 60.055 47.826 0.36 0.00 0.00 2.10
327 328 1.279271 CACTCCAAGGGTTCGGAATCT 59.721 52.381 0.36 0.00 0.00 2.40
328 329 1.003233 ACACTCCAAGGGTTCGGAATC 59.997 52.381 0.00 0.00 0.00 2.52
340 355 5.422331 TGATTTGGTGGTAAAAACACTCCAA 59.578 36.000 0.00 0.00 38.83 3.53
347 362 7.433680 AGTGATTCTGATTTGGTGGTAAAAAC 58.566 34.615 0.00 0.00 0.00 2.43
348 363 7.595819 AGTGATTCTGATTTGGTGGTAAAAA 57.404 32.000 0.00 0.00 0.00 1.94
349 364 7.094377 GCTAGTGATTCTGATTTGGTGGTAAAA 60.094 37.037 0.00 0.00 0.00 1.52
350 365 6.374333 GCTAGTGATTCTGATTTGGTGGTAAA 59.626 38.462 0.00 0.00 0.00 2.01
351 366 5.880332 GCTAGTGATTCTGATTTGGTGGTAA 59.120 40.000 0.00 0.00 0.00 2.85
352 367 5.428253 GCTAGTGATTCTGATTTGGTGGTA 58.572 41.667 0.00 0.00 0.00 3.25
353 368 4.265073 GCTAGTGATTCTGATTTGGTGGT 58.735 43.478 0.00 0.00 0.00 4.16
354 369 3.629398 GGCTAGTGATTCTGATTTGGTGG 59.371 47.826 0.00 0.00 0.00 4.61
355 370 4.264253 TGGCTAGTGATTCTGATTTGGTG 58.736 43.478 0.00 0.00 0.00 4.17
356 371 4.574674 TGGCTAGTGATTCTGATTTGGT 57.425 40.909 0.00 0.00 0.00 3.67
357 372 5.735354 GCAATGGCTAGTGATTCTGATTTGG 60.735 44.000 0.20 0.00 36.96 3.28
358 373 5.279384 GCAATGGCTAGTGATTCTGATTTG 58.721 41.667 0.20 0.00 36.96 2.32
359 374 5.511234 GCAATGGCTAGTGATTCTGATTT 57.489 39.130 0.20 0.00 36.96 2.17
379 394 9.233374 TGATTAATCAACAATCGGCATTCAGCA 62.233 37.037 15.82 0.00 38.37 4.41
380 395 2.857592 ATCAACAATCGGCATTCAGC 57.142 45.000 0.00 0.00 44.65 4.26
381 396 6.497437 TGATTAATCAACAATCGGCATTCAG 58.503 36.000 15.82 0.00 35.55 3.02
382 397 6.318396 TCTGATTAATCAACAATCGGCATTCA 59.682 34.615 18.47 0.00 38.25 2.57
383 398 6.728200 TCTGATTAATCAACAATCGGCATTC 58.272 36.000 18.47 0.00 38.25 2.67
384 399 6.698008 TCTGATTAATCAACAATCGGCATT 57.302 33.333 18.47 0.00 38.25 3.56
385 400 6.889301 ATCTGATTAATCAACAATCGGCAT 57.111 33.333 18.47 0.50 38.25 4.40
386 401 6.511605 CGAATCTGATTAATCAACAATCGGCA 60.512 38.462 18.47 0.00 38.25 5.69
387 402 5.848036 CGAATCTGATTAATCAACAATCGGC 59.152 40.000 18.47 3.51 38.25 5.54
388 403 5.848036 GCGAATCTGATTAATCAACAATCGG 59.152 40.000 26.49 14.30 39.25 4.18
389 404 6.653183 AGCGAATCTGATTAATCAACAATCG 58.347 36.000 23.96 23.96 36.18 3.34
390 405 9.374960 GTTAGCGAATCTGATTAATCAACAATC 57.625 33.333 18.47 12.81 36.18 2.67
391 406 8.345565 GGTTAGCGAATCTGATTAATCAACAAT 58.654 33.333 18.47 9.94 36.18 2.71
392 407 7.201696 GGGTTAGCGAATCTGATTAATCAACAA 60.202 37.037 18.47 8.18 36.18 2.83
393 408 6.260050 GGGTTAGCGAATCTGATTAATCAACA 59.740 38.462 18.47 9.07 36.18 3.33
394 409 6.483640 AGGGTTAGCGAATCTGATTAATCAAC 59.516 38.462 18.47 10.32 36.18 3.18
395 410 6.591935 AGGGTTAGCGAATCTGATTAATCAA 58.408 36.000 18.47 10.37 36.18 2.57
396 411 6.174720 AGGGTTAGCGAATCTGATTAATCA 57.825 37.500 17.07 17.07 35.16 2.57
397 412 7.603651 TCTAGGGTTAGCGAATCTGATTAATC 58.396 38.462 8.60 8.60 0.00 1.75
398 413 7.233757 ACTCTAGGGTTAGCGAATCTGATTAAT 59.766 37.037 2.28 0.00 0.00 1.40
399 414 6.550108 ACTCTAGGGTTAGCGAATCTGATTAA 59.450 38.462 2.28 0.00 0.00 1.40
400 415 6.069331 ACTCTAGGGTTAGCGAATCTGATTA 58.931 40.000 2.28 0.00 0.00 1.75
401 416 4.896482 ACTCTAGGGTTAGCGAATCTGATT 59.104 41.667 1.81 1.81 0.00 2.57
402 417 4.475345 ACTCTAGGGTTAGCGAATCTGAT 58.525 43.478 0.00 0.00 0.00 2.90
403 418 3.899726 ACTCTAGGGTTAGCGAATCTGA 58.100 45.455 0.00 0.00 0.00 3.27
404 419 5.968528 ATACTCTAGGGTTAGCGAATCTG 57.031 43.478 0.00 0.00 0.00 2.90
405 420 6.980416 AAATACTCTAGGGTTAGCGAATCT 57.020 37.500 0.00 0.00 0.00 2.40
406 421 8.358895 ACTAAAATACTCTAGGGTTAGCGAATC 58.641 37.037 0.00 0.00 0.00 2.52
407 422 8.247666 ACTAAAATACTCTAGGGTTAGCGAAT 57.752 34.615 0.00 0.00 0.00 3.34
408 423 7.201857 GGACTAAAATACTCTAGGGTTAGCGAA 60.202 40.741 0.00 0.00 0.00 4.70
409 424 6.264067 GGACTAAAATACTCTAGGGTTAGCGA 59.736 42.308 0.00 0.00 0.00 4.93
410 425 6.445475 GGACTAAAATACTCTAGGGTTAGCG 58.555 44.000 0.00 0.00 0.00 4.26
411 426 6.264067 TCGGACTAAAATACTCTAGGGTTAGC 59.736 42.308 0.00 0.00 0.00 3.09
412 427 7.814264 TCGGACTAAAATACTCTAGGGTTAG 57.186 40.000 0.00 0.00 0.00 2.34
413 428 8.773033 AATCGGACTAAAATACTCTAGGGTTA 57.227 34.615 0.00 0.00 0.00 2.85
414 429 7.672122 AATCGGACTAAAATACTCTAGGGTT 57.328 36.000 0.00 0.00 0.00 4.11
415 430 7.672122 AAATCGGACTAAAATACTCTAGGGT 57.328 36.000 0.00 0.00 0.00 4.34
416 431 8.959705 AAAAATCGGACTAAAATACTCTAGGG 57.040 34.615 0.00 0.00 0.00 3.53
443 458 7.345691 TGGCTAGTGAATTTCAATTAGATCCA 58.654 34.615 17.15 13.79 0.00 3.41
445 460 9.674824 CAATGGCTAGTGAATTTCAATTAGATC 57.325 33.333 17.15 11.27 0.00 2.75
446 461 9.193806 ACAATGGCTAGTGAATTTCAATTAGAT 57.806 29.630 3.97 5.89 0.00 1.98
447 462 8.579850 ACAATGGCTAGTGAATTTCAATTAGA 57.420 30.769 3.97 4.39 0.00 2.10
448 463 9.643693 AAACAATGGCTAGTGAATTTCAATTAG 57.356 29.630 3.97 9.14 0.00 1.73
450 465 9.643693 CTAAACAATGGCTAGTGAATTTCAATT 57.356 29.630 3.97 0.00 0.00 2.32
537 552 2.697751 TCTGTGGGTTTGGGAAACAATG 59.302 45.455 0.00 0.00 43.15 2.82
548 563 4.079253 GTTGTGATGGTATCTGTGGGTTT 58.921 43.478 0.00 0.00 0.00 3.27
574 589 2.657237 CGGCTTCCTCTCACCGTT 59.343 61.111 0.00 0.00 40.77 4.44
599 614 0.738063 CCATACGGCTGCGTACAACA 60.738 55.000 6.51 0.00 0.00 3.33
602 617 0.179121 CTTCCATACGGCTGCGTACA 60.179 55.000 6.51 0.00 0.00 2.90
605 620 2.186903 CCTTCCATACGGCTGCGT 59.813 61.111 0.00 0.00 0.00 5.24
613 628 4.009675 TCATTGTTGAGCACCTTCCATAC 58.990 43.478 0.00 0.00 0.00 2.39
627 642 2.455674 TGAGGAGGTCGTCATTGTTG 57.544 50.000 0.00 0.00 36.04 3.33
663 678 2.352805 GTGGTGGGGAAGCTGAGG 59.647 66.667 0.00 0.00 0.00 3.86
667 682 2.936032 GAGGGTGGTGGGGAAGCT 60.936 66.667 0.00 0.00 0.00 3.74
708 723 2.187946 GCATGGTGGAGCTAGCGT 59.812 61.111 9.55 0.00 0.00 5.07
713 728 0.987081 ATCAGAGGCATGGTGGAGCT 60.987 55.000 0.00 0.00 0.00 4.09
719 734 3.234349 CCGGATCAGAGGCATGGT 58.766 61.111 0.00 0.00 0.00 3.55
726 741 1.274728 CATAGGAAGGCCGGATCAGAG 59.725 57.143 5.05 0.00 39.96 3.35
753 768 1.605058 GAGGAGGGTGCAGCTTACGA 61.605 60.000 16.65 0.00 0.00 3.43
754 769 1.153549 GAGGAGGGTGCAGCTTACG 60.154 63.158 16.65 0.00 0.00 3.18
778 793 0.179018 GCCCCACGATAGAAGCCAAT 60.179 55.000 0.00 0.00 41.38 3.16
799 814 2.978946 GCGGGATGGGGAAGAACCA 61.979 63.158 0.00 0.00 43.22 3.67
813 828 3.966543 GGGGGATATGGTGGCGGG 61.967 72.222 0.00 0.00 0.00 6.13
815 830 4.329545 CCGGGGGATATGGTGGCG 62.330 72.222 0.00 0.00 0.00 5.69
819 834 1.536662 GAGCTCCGGGGGATATGGT 60.537 63.158 1.90 0.00 0.00 3.55
822 837 2.997897 GCGAGCTCCGGGGGATAT 60.998 66.667 1.90 0.00 39.04 1.63
840 855 2.202743 ACACGGCGGATGACATCG 60.203 61.111 13.24 6.20 0.00 3.84
917 932 0.743097 GGTGAAGATGCAGCCATTCC 59.257 55.000 0.00 0.00 0.00 3.01
924 939 2.777969 GCCTCTGGTGAAGATGCAG 58.222 57.895 0.00 0.00 43.79 4.41
928 943 2.971330 CTCCTATGCCTCTGGTGAAGAT 59.029 50.000 0.00 0.00 33.29 2.40
984 999 2.158696 GGACATGCTTCTCTTAGGGCAT 60.159 50.000 0.00 0.00 44.77 4.40
985 1000 1.210478 GGACATGCTTCTCTTAGGGCA 59.790 52.381 0.00 0.00 39.06 5.36
1022 1037 6.299023 TGGAGTAAATATTGTAATGCTGCG 57.701 37.500 0.00 0.00 0.00 5.18
1032 1047 8.266682 CGAGTGTCGTAAATGGAGTAAATATTG 58.733 37.037 0.00 0.00 34.72 1.90
1217 1232 7.303182 AGCATAGGTTTACTGTCATATAGCA 57.697 36.000 0.00 0.00 0.00 3.49
1596 1611 3.243101 GCAAGCATCCACTCATCATCAAG 60.243 47.826 0.00 0.00 0.00 3.02
1597 1612 2.686405 GCAAGCATCCACTCATCATCAA 59.314 45.455 0.00 0.00 0.00 2.57
1598 1613 2.092592 AGCAAGCATCCACTCATCATCA 60.093 45.455 0.00 0.00 0.00 3.07
1599 1614 2.548904 GAGCAAGCATCCACTCATCATC 59.451 50.000 0.00 0.00 0.00 2.92
1600 1615 2.172930 AGAGCAAGCATCCACTCATCAT 59.827 45.455 0.00 0.00 0.00 2.45
1601 1616 1.558294 AGAGCAAGCATCCACTCATCA 59.442 47.619 0.00 0.00 0.00 3.07
1602 1617 2.328819 AGAGCAAGCATCCACTCATC 57.671 50.000 0.00 0.00 0.00 2.92
1603 1618 3.647113 AGATAGAGCAAGCATCCACTCAT 59.353 43.478 0.00 0.00 0.00 2.90
1604 1619 3.036819 AGATAGAGCAAGCATCCACTCA 58.963 45.455 0.00 0.00 0.00 3.41
1605 1620 3.391965 CAGATAGAGCAAGCATCCACTC 58.608 50.000 0.00 0.00 0.00 3.51
1606 1621 2.104451 CCAGATAGAGCAAGCATCCACT 59.896 50.000 0.00 0.00 0.00 4.00
1607 1622 2.103771 TCCAGATAGAGCAAGCATCCAC 59.896 50.000 0.00 0.00 0.00 4.02
1608 1623 2.401568 TCCAGATAGAGCAAGCATCCA 58.598 47.619 0.00 0.00 0.00 3.41
1609 1624 3.699411 ATCCAGATAGAGCAAGCATCC 57.301 47.619 0.00 0.00 0.00 3.51
1610 1625 5.975282 TGATATCCAGATAGAGCAAGCATC 58.025 41.667 0.00 0.00 0.00 3.91
1611 1626 6.013553 ACTTGATATCCAGATAGAGCAAGCAT 60.014 38.462 10.64 6.44 36.01 3.79
1612 1627 5.306419 ACTTGATATCCAGATAGAGCAAGCA 59.694 40.000 10.64 0.00 36.01 3.91
1613 1628 5.638657 CACTTGATATCCAGATAGAGCAAGC 59.361 44.000 10.64 0.00 36.01 4.01
1890 1905 8.352201 CAATGATGTTGAACTGGTTCTCTAAAA 58.648 33.333 13.54 0.00 40.14 1.52
1950 1965 2.071688 ACGAAGTAAGAGCAGCACAG 57.928 50.000 0.00 0.00 41.94 3.66
2260 2275 2.094417 GTGATACAACAGAGCGAAAGGC 59.906 50.000 0.00 0.00 44.05 4.35
2401 2416 4.646572 AGGAAGCTAAAGTTTCAGACTGG 58.353 43.478 1.81 0.00 39.00 4.00
2462 2513 8.588472 ACTCACATACATAATAGCTTGAGCATA 58.412 33.333 5.70 0.00 45.16 3.14


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

AutoCloner maintained by Alex Coulton.