Multiple sequence alignment - TraesCS4D01G340900

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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 TraesCS4D01G340900 chr4D 100.000 4500 0 0 1 4500 497940191 497944690 0.000000e+00 8311.0
1 TraesCS4D01G340900 chr5A 94.520 2865 117 20 1646 4497 678265960 678268797 0.000000e+00 4385.0
2 TraesCS4D01G340900 chr5A 89.982 1118 75 19 566 1656 678264024 678265131 0.000000e+00 1410.0
3 TraesCS4D01G340900 chr5A 91.241 274 20 2 84 357 678262586 678262855 1.980000e-98 370.0
4 TraesCS4D01G340900 chr4B 96.603 2414 78 4 1646 4058 639844410 639846820 0.000000e+00 4000.0
5 TraesCS4D01G340900 chr4B 92.089 948 44 18 729 1649 639842657 639843600 0.000000e+00 1306.0
6 TraesCS4D01G340900 chr4B 92.439 410 19 4 4100 4500 639846822 639847228 3.900000e-160 575.0
7 TraesCS4D01G340900 chr7D 89.873 158 11 4 14 167 144010909 144010753 9.870000e-47 198.0
8 TraesCS4D01G340900 chr3D 89.691 97 10 0 440 536 323312789 323312693 1.700000e-24 124.0
9 TraesCS4D01G340900 chr2B 84.259 108 17 0 2596 2703 76087971 76087864 6.160000e-19 106.0
10 TraesCS4D01G340900 chr6B 83.333 108 10 3 440 539 217161336 217161229 4.790000e-15 93.5
11 TraesCS4D01G340900 chr2A 97.500 40 1 0 11 50 566857300 566857261 8.080000e-08 69.4


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 TraesCS4D01G340900 chr4D 497940191 497944690 4499 False 8311.000000 8311 100.000000 1 4500 1 chr4D.!!$F1 4499
1 TraesCS4D01G340900 chr5A 678262586 678268797 6211 False 2055.000000 4385 91.914333 84 4497 3 chr5A.!!$F1 4413
2 TraesCS4D01G340900 chr4B 639842657 639847228 4571 False 1960.333333 4000 93.710333 729 4500 3 chr4B.!!$F1 3771

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
72 73 0.041535 ATGGTGGTTGTCATGGCCAT 59.958 50.0 14.09 14.09 34.52 4.40 F
73 74 0.178938 TGGTGGTTGTCATGGCCATT 60.179 50.0 17.92 0.00 34.52 3.16 F
387 388 0.179097 GAAAGAGAGCGGGGCTACTG 60.179 60.0 0.00 0.00 39.88 2.74 F
1495 2584 0.319900 CGACCTCTTGTCTGGTGGTG 60.320 60.0 0.00 0.00 42.13 4.17 F
1558 2647 1.408969 TTGAACCACCCTTTTCTGCC 58.591 50.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 2397 0.312416 CCCAATTCGCAAAACACGGA 59.688 50.000 0.00 0.00 0.00 4.69 R
1999 4740 0.944386 CACCACACTTGCCACTACAC 59.056 55.000 0.00 0.00 0.00 2.90 R
2129 4870 1.665679 CGTCAATCTGGAATCCAACCG 59.334 52.381 2.61 0.00 30.80 4.44 R
2613 5355 0.323178 AATCAGAAGGGCAGTGGCAG 60.323 55.000 19.48 2.73 43.71 4.85 R
3514 6259 1.087771 GCCAACGAATACCACTCCGG 61.088 60.000 0.00 0.00 42.50 5.14 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
51 52 8.902540 TCAGTAAATCACACTGACTAACAATT 57.097 30.769 1.17 0.00 45.68 2.32
52 53 8.773645 TCAGTAAATCACACTGACTAACAATTG 58.226 33.333 3.24 3.24 45.68 2.32
53 54 8.773645 CAGTAAATCACACTGACTAACAATTGA 58.226 33.333 13.59 0.00 45.10 2.57
54 55 9.507329 AGTAAATCACACTGACTAACAATTGAT 57.493 29.630 13.59 2.25 0.00 2.57
55 56 9.546909 GTAAATCACACTGACTAACAATTGATG 57.453 33.333 13.59 4.12 0.00 3.07
56 57 6.748333 ATCACACTGACTAACAATTGATGG 57.252 37.500 13.59 4.81 0.00 3.51
57 58 5.620206 TCACACTGACTAACAATTGATGGT 58.380 37.500 13.59 8.63 0.00 3.55
58 59 5.469760 TCACACTGACTAACAATTGATGGTG 59.530 40.000 13.59 12.14 0.00 4.17
59 60 4.761739 ACACTGACTAACAATTGATGGTGG 59.238 41.667 13.59 6.37 32.53 4.61
60 61 4.761739 CACTGACTAACAATTGATGGTGGT 59.238 41.667 13.59 6.97 44.07 4.16
61 62 5.241506 CACTGACTAACAATTGATGGTGGTT 59.758 40.000 13.59 0.00 41.04 3.67
62 63 5.241506 ACTGACTAACAATTGATGGTGGTTG 59.758 40.000 13.59 1.41 41.04 3.77
63 64 5.136828 TGACTAACAATTGATGGTGGTTGT 58.863 37.500 13.59 0.00 41.04 3.32
64 65 5.240623 TGACTAACAATTGATGGTGGTTGTC 59.759 40.000 13.59 0.00 41.04 3.18
65 66 5.136828 ACTAACAATTGATGGTGGTTGTCA 58.863 37.500 13.59 0.00 37.06 3.58
66 67 5.774690 ACTAACAATTGATGGTGGTTGTCAT 59.225 36.000 13.59 0.00 37.06 3.06
67 68 4.524316 ACAATTGATGGTGGTTGTCATG 57.476 40.909 13.59 0.00 29.39 3.07
68 69 3.258872 ACAATTGATGGTGGTTGTCATGG 59.741 43.478 13.59 0.00 29.39 3.66
69 70 1.255882 TTGATGGTGGTTGTCATGGC 58.744 50.000 0.00 0.00 0.00 4.40
70 71 0.611618 TGATGGTGGTTGTCATGGCC 60.612 55.000 0.00 0.00 0.00 5.36
71 72 0.611618 GATGGTGGTTGTCATGGCCA 60.612 55.000 8.56 8.56 0.00 5.36
72 73 0.041535 ATGGTGGTTGTCATGGCCAT 59.958 50.000 14.09 14.09 34.52 4.40
73 74 0.178938 TGGTGGTTGTCATGGCCATT 60.179 50.000 17.92 0.00 34.52 3.16
74 75 0.247185 GGTGGTTGTCATGGCCATTG 59.753 55.000 17.92 12.11 34.52 2.82
75 76 0.247185 GTGGTTGTCATGGCCATTGG 59.753 55.000 17.92 6.04 34.52 3.16
76 77 0.178938 TGGTTGTCATGGCCATTGGT 60.179 50.000 17.92 0.00 0.00 3.67
77 78 0.532115 GGTTGTCATGGCCATTGGTC 59.468 55.000 17.92 4.33 0.00 4.02
78 79 1.255882 GTTGTCATGGCCATTGGTCA 58.744 50.000 17.92 13.33 43.40 4.02
135 136 4.235939 TGAACGTAAAGCAATGCATGTT 57.764 36.364 8.35 4.60 0.00 2.71
179 180 7.839680 AAATCATACCAGAGGTCTTTTGTTT 57.160 32.000 0.00 0.00 37.09 2.83
187 188 6.605594 ACCAGAGGTCTTTTGTTTGATTTGTA 59.394 34.615 0.00 0.00 0.00 2.41
190 191 6.540914 AGAGGTCTTTTGTTTGATTTGTACGA 59.459 34.615 0.00 0.00 0.00 3.43
197 198 2.554893 GTTTGATTTGTACGAAGCCCCA 59.445 45.455 8.59 0.00 0.00 4.96
208 209 4.643387 AGCCCCACCTCAACGCAC 62.643 66.667 0.00 0.00 0.00 5.34
217 218 2.088423 ACCTCAACGCACTGTTTTTCA 58.912 42.857 0.00 0.00 39.29 2.69
291 292 6.041523 GTCTCAGCTTTGAATAGATAGTCCCT 59.958 42.308 0.00 0.00 0.00 4.20
315 316 0.392461 GGGTTGCTGGTTATCTCGCA 60.392 55.000 0.00 0.00 0.00 5.10
321 322 0.735978 CTGGTTATCTCGCACGTGCA 60.736 55.000 37.03 23.52 42.21 4.57
332 333 1.580256 CGCACGTGCATTTGATTCATG 59.420 47.619 37.03 14.62 42.21 3.07
339 340 1.841944 GCATTTGATTCATGTCGTGCG 59.158 47.619 0.00 0.00 0.00 5.34
347 348 3.706373 ATGTCGTGCGAAGGCCCT 61.706 61.111 0.00 0.00 38.85 5.19
349 350 2.202756 GTCGTGCGAAGGCCCTAG 60.203 66.667 0.00 0.00 38.85 3.02
357 358 0.464452 CGAAGGCCCTAGGTTCGAAT 59.536 55.000 22.22 0.00 44.61 3.34
358 359 1.538419 CGAAGGCCCTAGGTTCGAATC 60.538 57.143 22.22 0.00 44.61 2.52
359 360 0.837940 AAGGCCCTAGGTTCGAATCC 59.162 55.000 8.29 6.73 0.00 3.01
360 361 1.054978 AGGCCCTAGGTTCGAATCCC 61.055 60.000 8.29 0.05 0.00 3.85
361 362 1.450642 GCCCTAGGTTCGAATCCCC 59.549 63.158 8.29 0.00 0.00 4.81
362 363 2.053259 GCCCTAGGTTCGAATCCCCC 62.053 65.000 8.29 0.00 0.00 5.40
363 364 1.746517 CCTAGGTTCGAATCCCCCG 59.253 63.158 4.40 0.00 0.00 5.73
364 365 1.047034 CCTAGGTTCGAATCCCCCGT 61.047 60.000 4.40 0.00 0.00 5.28
365 366 1.696063 CTAGGTTCGAATCCCCCGTA 58.304 55.000 4.40 0.00 0.00 4.02
366 367 1.612463 CTAGGTTCGAATCCCCCGTAG 59.388 57.143 4.40 1.73 0.00 3.51
367 368 1.227468 GGTTCGAATCCCCCGTAGC 60.227 63.158 0.00 0.00 0.00 3.58
368 369 1.590792 GTTCGAATCCCCCGTAGCG 60.591 63.158 0.00 0.00 0.00 4.26
369 370 1.753848 TTCGAATCCCCCGTAGCGA 60.754 57.895 0.00 0.00 0.00 4.93
370 371 1.321805 TTCGAATCCCCCGTAGCGAA 61.322 55.000 0.00 0.00 35.69 4.70
371 372 1.142314 CGAATCCCCCGTAGCGAAA 59.858 57.895 0.00 0.00 0.00 3.46
372 373 0.874607 CGAATCCCCCGTAGCGAAAG 60.875 60.000 0.00 0.00 0.00 2.62
373 374 0.462789 GAATCCCCCGTAGCGAAAGA 59.537 55.000 0.00 0.00 0.00 2.52
374 375 0.464452 AATCCCCCGTAGCGAAAGAG 59.536 55.000 0.00 0.00 0.00 2.85
375 376 0.396695 ATCCCCCGTAGCGAAAGAGA 60.397 55.000 0.00 0.00 0.00 3.10
376 377 1.035932 TCCCCCGTAGCGAAAGAGAG 61.036 60.000 0.00 0.00 0.00 3.20
377 378 1.227002 CCCCGTAGCGAAAGAGAGC 60.227 63.158 0.00 0.00 0.00 4.09
378 379 1.586564 CCCGTAGCGAAAGAGAGCG 60.587 63.158 0.00 0.00 38.61 5.03
379 380 1.586564 CCGTAGCGAAAGAGAGCGG 60.587 63.158 0.00 0.00 38.61 5.52
380 381 1.586564 CGTAGCGAAAGAGAGCGGG 60.587 63.158 0.00 0.00 38.61 6.13
381 382 1.227002 GTAGCGAAAGAGAGCGGGG 60.227 63.158 0.00 0.00 38.61 5.73
382 383 3.077519 TAGCGAAAGAGAGCGGGGC 62.078 63.158 0.00 0.00 38.61 5.80
383 384 4.459089 GCGAAAGAGAGCGGGGCT 62.459 66.667 0.00 0.00 43.88 5.19
384 385 3.077519 GCGAAAGAGAGCGGGGCTA 62.078 63.158 0.00 0.00 39.88 3.93
385 386 1.227002 CGAAAGAGAGCGGGGCTAC 60.227 63.158 0.00 0.00 39.88 3.58
386 387 1.668101 CGAAAGAGAGCGGGGCTACT 61.668 60.000 0.00 0.00 39.88 2.57
387 388 0.179097 GAAAGAGAGCGGGGCTACTG 60.179 60.000 0.00 0.00 39.88 2.74
394 395 2.982130 CGGGGCTACTGCTGAAGT 59.018 61.111 0.00 0.00 43.40 3.01
395 396 1.296715 CGGGGCTACTGCTGAAGTT 59.703 57.895 0.00 0.00 40.56 2.66
396 397 0.535335 CGGGGCTACTGCTGAAGTTA 59.465 55.000 0.00 0.00 40.56 2.24
397 398 1.066430 CGGGGCTACTGCTGAAGTTAA 60.066 52.381 0.00 0.00 40.56 2.01
398 399 2.420129 CGGGGCTACTGCTGAAGTTAAT 60.420 50.000 0.00 0.00 40.56 1.40
399 400 3.181469 CGGGGCTACTGCTGAAGTTAATA 60.181 47.826 0.00 0.00 40.56 0.98
400 401 4.381411 GGGGCTACTGCTGAAGTTAATAG 58.619 47.826 0.00 0.00 40.56 1.73
401 402 4.101119 GGGGCTACTGCTGAAGTTAATAGA 59.899 45.833 0.00 0.00 40.56 1.98
402 403 5.396436 GGGGCTACTGCTGAAGTTAATAGAA 60.396 44.000 0.00 0.00 40.56 2.10
403 404 6.113411 GGGCTACTGCTGAAGTTAATAGAAA 58.887 40.000 0.00 0.00 40.56 2.52
404 405 6.598064 GGGCTACTGCTGAAGTTAATAGAAAA 59.402 38.462 0.00 0.00 40.56 2.29
405 406 7.283354 GGGCTACTGCTGAAGTTAATAGAAAAT 59.717 37.037 0.00 0.00 40.56 1.82
406 407 9.326413 GGCTACTGCTGAAGTTAATAGAAAATA 57.674 33.333 0.00 0.00 40.56 1.40
410 411 9.088512 ACTGCTGAAGTTAATAGAAAATAGACG 57.911 33.333 0.00 0.00 34.57 4.18
411 412 8.420374 TGCTGAAGTTAATAGAAAATAGACGG 57.580 34.615 0.00 0.00 0.00 4.79
412 413 7.011109 TGCTGAAGTTAATAGAAAATAGACGGC 59.989 37.037 0.00 0.00 0.00 5.68
413 414 7.011109 GCTGAAGTTAATAGAAAATAGACGGCA 59.989 37.037 0.00 0.00 0.00 5.69
414 415 8.958119 TGAAGTTAATAGAAAATAGACGGCAT 57.042 30.769 0.00 0.00 0.00 4.40
415 416 8.826710 TGAAGTTAATAGAAAATAGACGGCATG 58.173 33.333 0.00 0.00 0.00 4.06
416 417 8.732746 AAGTTAATAGAAAATAGACGGCATGT 57.267 30.769 0.00 0.00 0.00 3.21
417 418 8.142994 AGTTAATAGAAAATAGACGGCATGTG 57.857 34.615 0.00 0.00 0.00 3.21
418 419 7.769044 AGTTAATAGAAAATAGACGGCATGTGT 59.231 33.333 0.00 0.00 0.00 3.72
419 420 6.604735 AATAGAAAATAGACGGCATGTGTC 57.395 37.500 11.01 11.01 36.60 3.67
429 430 3.051606 CGGCATGTGTCGGATTTAAAG 57.948 47.619 0.00 0.00 39.84 1.85
430 431 2.223249 CGGCATGTGTCGGATTTAAAGG 60.223 50.000 0.00 0.00 39.84 3.11
431 432 3.013921 GGCATGTGTCGGATTTAAAGGA 58.986 45.455 0.00 0.00 0.00 3.36
432 433 3.442273 GGCATGTGTCGGATTTAAAGGAA 59.558 43.478 0.00 0.00 0.00 3.36
433 434 4.097892 GGCATGTGTCGGATTTAAAGGAAT 59.902 41.667 0.00 0.00 0.00 3.01
434 435 5.036737 GCATGTGTCGGATTTAAAGGAATG 58.963 41.667 0.00 0.00 0.00 2.67
435 436 5.393027 GCATGTGTCGGATTTAAAGGAATGT 60.393 40.000 0.00 0.00 0.00 2.71
436 437 6.620678 CATGTGTCGGATTTAAAGGAATGTT 58.379 36.000 0.00 0.00 0.00 2.71
437 438 7.627513 GCATGTGTCGGATTTAAAGGAATGTTA 60.628 37.037 0.00 0.00 0.00 2.41
438 439 7.931578 TGTGTCGGATTTAAAGGAATGTTAT 57.068 32.000 0.00 0.00 0.00 1.89
439 440 8.343168 TGTGTCGGATTTAAAGGAATGTTATT 57.657 30.769 0.00 0.00 0.00 1.40
440 441 9.451002 TGTGTCGGATTTAAAGGAATGTTATTA 57.549 29.630 0.00 0.00 0.00 0.98
469 470 7.824779 ACATTCTGTTAGATAAGTTGAAGGACC 59.175 37.037 0.00 0.00 0.00 4.46
512 513 5.940470 AGTTCTTGTATGATTCTGTTCCCAC 59.060 40.000 0.00 0.00 0.00 4.61
514 515 4.288366 TCTTGTATGATTCTGTTCCCACCA 59.712 41.667 0.00 0.00 0.00 4.17
515 516 3.950397 TGTATGATTCTGTTCCCACCAC 58.050 45.455 0.00 0.00 0.00 4.16
516 517 3.587061 TGTATGATTCTGTTCCCACCACT 59.413 43.478 0.00 0.00 0.00 4.00
517 518 4.780554 TGTATGATTCTGTTCCCACCACTA 59.219 41.667 0.00 0.00 0.00 2.74
518 519 3.695830 TGATTCTGTTCCCACCACTAC 57.304 47.619 0.00 0.00 0.00 2.73
520 521 3.392947 TGATTCTGTTCCCACCACTACAA 59.607 43.478 0.00 0.00 0.00 2.41
522 523 2.404559 TCTGTTCCCACCACTACAAGT 58.595 47.619 0.00 0.00 0.00 3.16
523 524 2.775384 TCTGTTCCCACCACTACAAGTT 59.225 45.455 0.00 0.00 0.00 2.66
524 525 3.201266 TCTGTTCCCACCACTACAAGTTT 59.799 43.478 0.00 0.00 0.00 2.66
525 526 3.547746 TGTTCCCACCACTACAAGTTTC 58.452 45.455 0.00 0.00 0.00 2.78
526 527 3.201266 TGTTCCCACCACTACAAGTTTCT 59.799 43.478 0.00 0.00 0.00 2.52
527 528 3.485463 TCCCACCACTACAAGTTTCTG 57.515 47.619 0.00 0.00 0.00 3.02
528 529 2.775384 TCCCACCACTACAAGTTTCTGT 59.225 45.455 0.00 0.00 0.00 3.41
529 530 3.968649 TCCCACCACTACAAGTTTCTGTA 59.031 43.478 0.00 0.00 0.00 2.74
530 531 4.062991 CCCACCACTACAAGTTTCTGTAC 58.937 47.826 0.00 0.00 0.00 2.90
531 532 4.202326 CCCACCACTACAAGTTTCTGTACT 60.202 45.833 0.00 0.00 0.00 2.73
537 635 9.623000 ACCACTACAAGTTTCTGTACTATTTTT 57.377 29.630 0.00 0.00 0.00 1.94
562 660 8.556213 TTTGAGTGTTTACAAGTTTCTGTACT 57.444 30.769 0.00 0.00 31.52 2.73
563 661 8.556213 TTGAGTGTTTACAAGTTTCTGTACTT 57.444 30.769 0.00 0.00 38.87 2.24
564 662 8.556213 TGAGTGTTTACAAGTTTCTGTACTTT 57.444 30.769 0.00 0.00 36.24 2.66
569 1620 9.968870 TGTTTACAAGTTTCTGTACTTTTTGTT 57.031 25.926 0.00 0.00 36.24 2.83
663 1715 3.758931 GCCCGTGTGATTTGGCCC 61.759 66.667 0.00 0.00 37.94 5.80
672 1724 2.364970 TGTGATTTGGCCCAACTTTCTG 59.635 45.455 0.00 0.00 0.00 3.02
674 1726 3.069443 GTGATTTGGCCCAACTTTCTGAA 59.931 43.478 0.00 0.00 0.00 3.02
675 1727 3.069443 TGATTTGGCCCAACTTTCTGAAC 59.931 43.478 0.00 0.00 0.00 3.18
676 1728 1.408969 TTGGCCCAACTTTCTGAACC 58.591 50.000 0.00 0.00 0.00 3.62
677 1729 0.555769 TGGCCCAACTTTCTGAACCT 59.444 50.000 0.00 0.00 0.00 3.50
678 1730 1.063266 TGGCCCAACTTTCTGAACCTT 60.063 47.619 0.00 0.00 0.00 3.50
679 1731 2.039418 GGCCCAACTTTCTGAACCTTT 58.961 47.619 0.00 0.00 0.00 3.11
680 1732 2.434336 GGCCCAACTTTCTGAACCTTTT 59.566 45.455 0.00 0.00 0.00 2.27
681 1733 3.118408 GGCCCAACTTTCTGAACCTTTTT 60.118 43.478 0.00 0.00 0.00 1.94
700 1752 2.149606 TTTCCGTTCTTTCGCGACGC 62.150 55.000 9.15 10.49 35.60 5.19
1026 2094 2.496341 TCGCAGGCGAATCTGGAG 59.504 61.111 14.68 0.00 46.01 3.86
1127 2195 4.829518 GAAAATCGCCGGTGCCGC 62.830 66.667 11.05 0.30 38.24 6.53
1166 2240 0.465824 TCTCTCCCTCGTCGATTCCC 60.466 60.000 0.00 0.00 0.00 3.97
1355 2438 3.603385 TGGGTTAGGGTTATGGGGATTTT 59.397 43.478 0.00 0.00 0.00 1.82
1407 2491 2.634600 TGTGTTGTTTCGTTACCAGCT 58.365 42.857 0.00 0.00 0.00 4.24
1454 2543 4.530946 AGTACTAGGTGGCAGTTATGTGTT 59.469 41.667 0.00 0.00 0.00 3.32
1455 2544 5.718130 AGTACTAGGTGGCAGTTATGTGTTA 59.282 40.000 0.00 0.00 0.00 2.41
1456 2545 5.086104 ACTAGGTGGCAGTTATGTGTTAG 57.914 43.478 0.00 0.00 0.00 2.34
1466 2555 7.276218 TGGCAGTTATGTGTTAGTATTTCGTAC 59.724 37.037 0.00 0.00 0.00 3.67
1495 2584 0.319900 CGACCTCTTGTCTGGTGGTG 60.320 60.000 0.00 0.00 42.13 4.17
1558 2647 1.408969 TTGAACCACCCTTTTCTGCC 58.591 50.000 0.00 0.00 0.00 4.85
1575 2664 3.070015 TCTGCCTGATCTGCGATGAATTA 59.930 43.478 0.00 0.00 0.00 1.40
1611 2700 5.417894 GTGAATTAGGTTGGGTTTAAGGGAG 59.582 44.000 0.00 0.00 0.00 4.30
1675 4416 7.440856 GTGGGTTCTAAAAATGAAATGCTCAAA 59.559 33.333 0.00 0.00 37.67 2.69
1750 4491 4.162131 GGTGGCATTGGGTTCATAGATTTT 59.838 41.667 0.00 0.00 0.00 1.82
2118 4859 6.292923 TCTCACTATACCTCTCTTAGCTGAC 58.707 44.000 0.00 0.00 0.00 3.51
2129 4870 4.568359 TCTCTTAGCTGACGATTTTGATGC 59.432 41.667 0.00 0.00 0.00 3.91
2142 4883 1.462616 TTGATGCGGTTGGATTCCAG 58.537 50.000 5.36 0.00 33.81 3.86
2212 4953 3.411446 TGATGCGGTTGGATTCCATATC 58.589 45.455 6.15 6.80 31.53 1.63
2325 5066 7.001674 TGGAGTTTTTGTATTTCTAGGCTCAA 58.998 34.615 0.00 0.00 0.00 3.02
2494 5236 4.497473 TTTTCAACCAATTAGCGTGAGG 57.503 40.909 0.00 0.00 0.00 3.86
2570 5312 8.655970 CGAACAGAACAATACACATTTGATCTA 58.344 33.333 0.00 0.00 34.98 1.98
2599 5341 6.587226 TGATGTGAAGTGCAAATTTTCATAGC 59.413 34.615 0.00 0.00 33.82 2.97
2601 5343 5.921976 TGTGAAGTGCAAATTTTCATAGCTG 59.078 36.000 0.00 0.00 33.82 4.24
2613 5355 9.578439 AAATTTTCATAGCTGAACTTCTAATGC 57.422 29.630 0.00 0.00 41.05 3.56
2618 5360 2.086869 GCTGAACTTCTAATGCTGCCA 58.913 47.619 0.00 0.00 0.00 4.92
2997 5742 2.626743 TGCTCGTAAGGCTCTTATACCC 59.373 50.000 0.00 0.00 35.07 3.69
3503 6248 4.081807 AGGGCTACTACGGAAAGTAAAGTG 60.082 45.833 0.00 0.00 34.45 3.16
3533 6278 1.087771 CCGGAGTGGTATTCGTTGGC 61.088 60.000 0.00 0.00 0.00 4.52
3550 6295 1.291132 GGCGAGGCAACAGAAGTATC 58.709 55.000 0.00 0.00 41.41 2.24
3632 6378 2.489938 TATTGGTCTGGGTGCTGAAC 57.510 50.000 0.00 0.00 0.00 3.18
3720 6466 1.926510 TCAACTATGAACTGCATCGCG 59.073 47.619 0.00 0.00 38.44 5.87
3798 6544 3.585862 TCTCCGAATAAATATGAGCGGC 58.414 45.455 0.00 0.00 38.68 6.53
3839 6585 1.021202 TGCAGTGTTGGAAGGTTTCG 58.979 50.000 0.00 0.00 0.00 3.46
3851 6597 5.235516 TGGAAGGTTTCGTCTAAATCTGAC 58.764 41.667 0.00 0.00 37.56 3.51
3925 6671 1.242076 GAGCCTGAATGCTGTGTGTT 58.758 50.000 0.00 0.00 42.95 3.32
3927 6673 2.154462 AGCCTGAATGCTGTGTGTTAC 58.846 47.619 0.00 0.00 40.90 2.50
3935 6681 2.531771 TGCTGTGTGTTACCTAGGCTA 58.468 47.619 9.30 0.00 0.00 3.93
3949 6695 8.476447 GTTACCTAGGCTATACCCTGATATTTC 58.524 40.741 9.30 0.00 40.58 2.17
3953 6699 4.223032 AGGCTATACCCTGATATTTCACCG 59.777 45.833 0.00 0.00 40.58 4.94
3973 6719 1.301953 GGGCTTTGGCTTTTGGCTG 60.302 57.895 0.00 0.00 46.20 4.85
4009 6755 6.289064 AGGCCTACAGTTTGCATAACTATAC 58.711 40.000 1.29 3.88 0.00 1.47
4023 6769 4.608948 AACTATACTCTGCACCATAGCC 57.391 45.455 0.00 0.00 0.00 3.93
4037 6783 2.417924 CCATAGCCGCCTAGATGATGAC 60.418 54.545 0.00 0.00 0.00 3.06
4075 6823 5.755409 TGTGTATGTGGTTGAGACCTTAT 57.245 39.130 0.00 0.00 46.66 1.73
4076 6824 6.860790 TGTGTATGTGGTTGAGACCTTATA 57.139 37.500 0.00 0.00 46.66 0.98
4077 6825 6.873997 TGTGTATGTGGTTGAGACCTTATAG 58.126 40.000 0.00 0.00 46.66 1.31
4078 6826 6.666113 TGTGTATGTGGTTGAGACCTTATAGA 59.334 38.462 0.00 0.00 46.66 1.98
4079 6827 7.179516 TGTGTATGTGGTTGAGACCTTATAGAA 59.820 37.037 0.00 0.00 46.66 2.10
4080 6828 8.038944 GTGTATGTGGTTGAGACCTTATAGAAA 58.961 37.037 0.00 0.00 46.66 2.52
4090 6838 5.908341 AGACCTTATAGAAAGAAGGCTTCG 58.092 41.667 20.78 5.83 46.27 3.79
4095 6843 8.265764 ACCTTATAGAAAGAAGGCTTCGTTATT 58.734 33.333 24.81 18.60 46.27 1.40
4133 6881 1.795170 CTTTGTCTTGTGGCGGTGGG 61.795 60.000 0.00 0.00 0.00 4.61
4235 6983 1.405821 AGCACTAGAGATTCCGTTCCG 59.594 52.381 0.00 0.00 0.00 4.30
4311 7061 7.049754 AGCATCCTTTGAAAGTTGAAACAAAT 58.950 30.769 4.02 0.00 33.01 2.32
4375 7125 2.095364 GCAGAGGTGCACATCTCTTTTG 60.095 50.000 29.85 20.03 46.19 2.44
4399 7149 0.864797 GGTCATTCGAGACGCCGTAC 60.865 60.000 0.00 0.00 39.42 3.67
4414 7164 1.800681 GTACAAGGCCATGGAACGC 59.199 57.895 18.40 0.00 0.00 4.84
4498 7254 8.628630 AAAAACCACAAGAATTTTCCTTTTGA 57.371 26.923 0.00 0.00 0.00 2.69
4499 7255 7.848223 AAACCACAAGAATTTTCCTTTTGAG 57.152 32.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.773645 TCAATTGTTAGTCAGTGTGATTTACTG 58.226 33.333 5.13 0.00 45.30 2.74
28 29 8.902540 TCAATTGTTAGTCAGTGTGATTTACT 57.097 30.769 5.13 0.00 0.00 2.24
29 30 9.546909 CATCAATTGTTAGTCAGTGTGATTTAC 57.453 33.333 5.13 0.00 0.00 2.01
30 31 8.729756 CCATCAATTGTTAGTCAGTGTGATTTA 58.270 33.333 5.13 0.00 0.00 1.40
31 32 7.231317 ACCATCAATTGTTAGTCAGTGTGATTT 59.769 33.333 5.13 0.00 0.00 2.17
32 33 6.716628 ACCATCAATTGTTAGTCAGTGTGATT 59.283 34.615 5.13 0.00 0.00 2.57
33 34 6.149973 CACCATCAATTGTTAGTCAGTGTGAT 59.850 38.462 5.13 0.00 0.00 3.06
34 35 5.469760 CACCATCAATTGTTAGTCAGTGTGA 59.530 40.000 5.13 0.00 0.00 3.58
35 36 5.335113 CCACCATCAATTGTTAGTCAGTGTG 60.335 44.000 5.13 2.25 0.00 3.82
36 37 4.761739 CCACCATCAATTGTTAGTCAGTGT 59.238 41.667 5.13 0.00 0.00 3.55
37 38 4.761739 ACCACCATCAATTGTTAGTCAGTG 59.238 41.667 5.13 5.22 0.00 3.66
38 39 4.985538 ACCACCATCAATTGTTAGTCAGT 58.014 39.130 5.13 0.00 0.00 3.41
39 40 5.241506 ACAACCACCATCAATTGTTAGTCAG 59.758 40.000 5.13 0.00 31.27 3.51
40 41 5.136828 ACAACCACCATCAATTGTTAGTCA 58.863 37.500 5.13 0.00 31.27 3.41
41 42 5.240623 TGACAACCACCATCAATTGTTAGTC 59.759 40.000 5.13 3.48 35.47 2.59
42 43 5.136828 TGACAACCACCATCAATTGTTAGT 58.863 37.500 5.13 0.00 35.47 2.24
43 44 5.703978 TGACAACCACCATCAATTGTTAG 57.296 39.130 5.13 0.00 35.47 2.34
44 45 5.047448 CCATGACAACCACCATCAATTGTTA 60.047 40.000 5.13 0.00 35.47 2.41
45 46 4.262549 CCATGACAACCACCATCAATTGTT 60.263 41.667 5.13 0.00 35.47 2.83
46 47 3.258872 CCATGACAACCACCATCAATTGT 59.741 43.478 5.13 0.00 37.97 2.71
47 48 3.852286 CCATGACAACCACCATCAATTG 58.148 45.455 0.00 0.00 0.00 2.32
48 49 2.234414 GCCATGACAACCACCATCAATT 59.766 45.455 0.00 0.00 0.00 2.32
49 50 1.826720 GCCATGACAACCACCATCAAT 59.173 47.619 0.00 0.00 0.00 2.57
50 51 1.255882 GCCATGACAACCACCATCAA 58.744 50.000 0.00 0.00 0.00 2.57
51 52 0.611618 GGCCATGACAACCACCATCA 60.612 55.000 0.00 0.00 0.00 3.07
52 53 0.611618 TGGCCATGACAACCACCATC 60.612 55.000 0.00 0.00 0.00 3.51
53 54 0.041535 ATGGCCATGACAACCACCAT 59.958 50.000 20.04 0.00 35.99 3.55
54 55 0.178938 AATGGCCATGACAACCACCA 60.179 50.000 21.63 0.00 35.99 4.17
55 56 0.247185 CAATGGCCATGACAACCACC 59.753 55.000 21.63 0.00 35.99 4.61
56 57 0.247185 CCAATGGCCATGACAACCAC 59.753 55.000 21.63 0.00 35.99 4.16
57 58 0.178938 ACCAATGGCCATGACAACCA 60.179 50.000 21.63 0.00 37.99 3.67
58 59 0.532115 GACCAATGGCCATGACAACC 59.468 55.000 21.63 3.14 0.00 3.77
59 60 1.255882 TGACCAATGGCCATGACAAC 58.744 50.000 21.63 10.78 0.00 3.32
60 61 2.234896 ATGACCAATGGCCATGACAA 57.765 45.000 21.63 4.84 0.00 3.18
61 62 3.598693 ATATGACCAATGGCCATGACA 57.401 42.857 21.63 14.60 0.00 3.58
62 63 4.942761 AAATATGACCAATGGCCATGAC 57.057 40.909 21.63 8.82 0.00 3.06
63 64 5.210430 AGAAAATATGACCAATGGCCATGA 58.790 37.500 21.63 1.28 0.00 3.07
64 65 5.540400 AGAAAATATGACCAATGGCCATG 57.460 39.130 21.63 10.60 0.00 3.66
65 66 7.673641 TTAAGAAAATATGACCAATGGCCAT 57.326 32.000 14.09 14.09 0.00 4.40
66 67 7.673641 ATTAAGAAAATATGACCAATGGCCA 57.326 32.000 8.56 8.56 0.00 5.36
135 136 0.682292 TCCTGTGCGTTACCATGACA 59.318 50.000 0.00 0.00 0.00 3.58
179 180 1.612199 GGTGGGGCTTCGTACAAATCA 60.612 52.381 0.00 0.00 0.00 2.57
187 188 2.430367 GTTGAGGTGGGGCTTCGT 59.570 61.111 0.00 0.00 0.00 3.85
190 191 3.884774 TGCGTTGAGGTGGGGCTT 61.885 61.111 0.00 0.00 0.00 4.35
197 198 2.088423 TGAAAAACAGTGCGTTGAGGT 58.912 42.857 0.00 0.00 38.07 3.85
264 265 7.268586 GGACTATCTATTCAAAGCTGAGACAA 58.731 38.462 0.00 0.00 31.69 3.18
266 267 6.041523 AGGGACTATCTATTCAAAGCTGAGAC 59.958 42.308 0.00 0.00 36.02 3.36
269 270 6.814954 AAGGGACTATCTATTCAAAGCTGA 57.185 37.500 0.00 0.00 38.49 4.26
291 292 3.686016 GAGATAACCAGCAACCCTGAAA 58.314 45.455 0.00 0.00 44.64 2.69
298 299 0.370273 CGTGCGAGATAACCAGCAAC 59.630 55.000 0.00 0.00 41.56 4.17
315 316 2.483877 ACGACATGAATCAAATGCACGT 59.516 40.909 0.00 0.00 36.91 4.49
321 322 3.181507 CCTTCGCACGACATGAATCAAAT 60.182 43.478 0.00 0.00 0.00 2.32
332 333 2.202756 CTAGGGCCTTCGCACGAC 60.203 66.667 13.45 0.00 46.01 4.34
339 340 1.202663 GGATTCGAACCTAGGGCCTTC 60.203 57.143 13.45 7.13 0.00 3.46
347 348 1.696063 CTACGGGGGATTCGAACCTA 58.304 55.000 0.00 0.00 0.00 3.08
349 350 1.227468 GCTACGGGGGATTCGAACC 60.227 63.158 0.00 4.00 0.00 3.62
357 358 1.000521 TCTCTTTCGCTACGGGGGA 60.001 57.895 0.00 0.00 35.02 4.81
358 359 1.437986 CTCTCTTTCGCTACGGGGG 59.562 63.158 0.00 0.00 0.00 5.40
359 360 1.227002 GCTCTCTTTCGCTACGGGG 60.227 63.158 0.00 0.00 0.00 5.73
360 361 1.586564 CGCTCTCTTTCGCTACGGG 60.587 63.158 0.00 0.00 0.00 5.28
361 362 1.586564 CCGCTCTCTTTCGCTACGG 60.587 63.158 0.00 0.00 0.00 4.02
362 363 1.586564 CCCGCTCTCTTTCGCTACG 60.587 63.158 0.00 0.00 0.00 3.51
363 364 1.227002 CCCCGCTCTCTTTCGCTAC 60.227 63.158 0.00 0.00 0.00 3.58
364 365 3.077519 GCCCCGCTCTCTTTCGCTA 62.078 63.158 0.00 0.00 0.00 4.26
365 366 4.459089 GCCCCGCTCTCTTTCGCT 62.459 66.667 0.00 0.00 0.00 4.93
366 367 3.077519 TAGCCCCGCTCTCTTTCGC 62.078 63.158 0.00 0.00 40.44 4.70
367 368 1.227002 GTAGCCCCGCTCTCTTTCG 60.227 63.158 0.00 0.00 40.44 3.46
368 369 0.179097 CAGTAGCCCCGCTCTCTTTC 60.179 60.000 0.00 0.00 40.44 2.62
369 370 1.901085 CAGTAGCCCCGCTCTCTTT 59.099 57.895 0.00 0.00 40.44 2.52
370 371 2.726351 GCAGTAGCCCCGCTCTCTT 61.726 63.158 0.00 0.00 40.44 2.85
371 372 3.151022 GCAGTAGCCCCGCTCTCT 61.151 66.667 0.00 0.00 40.44 3.10
372 373 3.151022 AGCAGTAGCCCCGCTCTC 61.151 66.667 0.00 0.00 43.56 3.20
373 374 3.465403 CAGCAGTAGCCCCGCTCT 61.465 66.667 0.00 0.00 43.56 4.09
374 375 2.914777 CTTCAGCAGTAGCCCCGCTC 62.915 65.000 0.00 0.00 43.56 5.03
375 376 3.003173 TTCAGCAGTAGCCCCGCT 61.003 61.111 0.00 0.00 43.56 5.52
376 377 2.512515 CTTCAGCAGTAGCCCCGC 60.513 66.667 0.00 0.00 43.56 6.13
377 378 0.535335 TAACTTCAGCAGTAGCCCCG 59.465 55.000 0.00 0.00 43.56 5.73
378 379 2.781681 TTAACTTCAGCAGTAGCCCC 57.218 50.000 0.00 0.00 43.56 5.80
379 380 5.277857 TCTATTAACTTCAGCAGTAGCCC 57.722 43.478 0.00 0.00 43.56 5.19
380 381 7.611213 TTTTCTATTAACTTCAGCAGTAGCC 57.389 36.000 0.00 0.00 43.56 3.93
384 385 9.088512 CGTCTATTTTCTATTAACTTCAGCAGT 57.911 33.333 0.00 0.00 37.30 4.40
385 386 8.543774 CCGTCTATTTTCTATTAACTTCAGCAG 58.456 37.037 0.00 0.00 0.00 4.24
386 387 7.011109 GCCGTCTATTTTCTATTAACTTCAGCA 59.989 37.037 0.00 0.00 0.00 4.41
387 388 7.011109 TGCCGTCTATTTTCTATTAACTTCAGC 59.989 37.037 0.00 0.00 0.00 4.26
388 389 8.420374 TGCCGTCTATTTTCTATTAACTTCAG 57.580 34.615 0.00 0.00 0.00 3.02
389 390 8.826710 CATGCCGTCTATTTTCTATTAACTTCA 58.173 33.333 0.00 0.00 0.00 3.02
390 391 8.827677 ACATGCCGTCTATTTTCTATTAACTTC 58.172 33.333 0.00 0.00 0.00 3.01
391 392 8.612619 CACATGCCGTCTATTTTCTATTAACTT 58.387 33.333 0.00 0.00 0.00 2.66
392 393 7.769044 ACACATGCCGTCTATTTTCTATTAACT 59.231 33.333 0.00 0.00 0.00 2.24
393 394 7.916552 ACACATGCCGTCTATTTTCTATTAAC 58.083 34.615 0.00 0.00 0.00 2.01
394 395 7.042992 CGACACATGCCGTCTATTTTCTATTAA 60.043 37.037 12.56 0.00 0.00 1.40
395 396 6.419710 CGACACATGCCGTCTATTTTCTATTA 59.580 38.462 12.56 0.00 0.00 0.98
396 397 5.234329 CGACACATGCCGTCTATTTTCTATT 59.766 40.000 12.56 0.00 0.00 1.73
397 398 4.745125 CGACACATGCCGTCTATTTTCTAT 59.255 41.667 12.56 0.00 0.00 1.98
398 399 4.109766 CGACACATGCCGTCTATTTTCTA 58.890 43.478 12.56 0.00 0.00 2.10
399 400 2.930040 CGACACATGCCGTCTATTTTCT 59.070 45.455 12.56 0.00 0.00 2.52
400 401 2.030457 CCGACACATGCCGTCTATTTTC 59.970 50.000 12.56 0.00 0.00 2.29
401 402 2.006888 CCGACACATGCCGTCTATTTT 58.993 47.619 12.56 0.00 0.00 1.82
402 403 1.206132 TCCGACACATGCCGTCTATTT 59.794 47.619 12.56 0.00 0.00 1.40
403 404 0.821517 TCCGACACATGCCGTCTATT 59.178 50.000 12.56 0.00 0.00 1.73
404 405 1.040646 ATCCGACACATGCCGTCTAT 58.959 50.000 12.56 5.08 0.00 1.98
405 406 0.821517 AATCCGACACATGCCGTCTA 59.178 50.000 12.56 3.28 0.00 2.59
406 407 0.036388 AAATCCGACACATGCCGTCT 60.036 50.000 12.56 0.00 0.00 4.18
407 408 1.647346 TAAATCCGACACATGCCGTC 58.353 50.000 5.91 5.91 0.00 4.79
408 409 2.102070 TTAAATCCGACACATGCCGT 57.898 45.000 0.00 0.00 0.00 5.68
409 410 2.223249 CCTTTAAATCCGACACATGCCG 60.223 50.000 0.00 0.00 0.00 5.69
410 411 3.013921 TCCTTTAAATCCGACACATGCC 58.986 45.455 0.00 0.00 0.00 4.40
411 412 4.695217 TTCCTTTAAATCCGACACATGC 57.305 40.909 0.00 0.00 0.00 4.06
412 413 6.194796 ACATTCCTTTAAATCCGACACATG 57.805 37.500 0.00 0.00 0.00 3.21
413 414 6.834168 AACATTCCTTTAAATCCGACACAT 57.166 33.333 0.00 0.00 0.00 3.21
414 415 7.931578 ATAACATTCCTTTAAATCCGACACA 57.068 32.000 0.00 0.00 0.00 3.72
444 445 7.824289 TGGTCCTTCAACTTATCTAACAGAATG 59.176 37.037 0.00 0.00 46.00 2.67
445 446 7.824779 GTGGTCCTTCAACTTATCTAACAGAAT 59.175 37.037 0.00 0.00 0.00 2.40
446 447 7.016268 AGTGGTCCTTCAACTTATCTAACAGAA 59.984 37.037 0.00 0.00 0.00 3.02
447 448 6.497259 AGTGGTCCTTCAACTTATCTAACAGA 59.503 38.462 0.00 0.00 0.00 3.41
448 449 6.702329 AGTGGTCCTTCAACTTATCTAACAG 58.298 40.000 0.00 0.00 0.00 3.16
492 493 4.396166 GTGGTGGGAACAGAATCATACAAG 59.604 45.833 0.00 0.00 44.46 3.16
494 495 3.587061 AGTGGTGGGAACAGAATCATACA 59.413 43.478 0.00 0.00 44.46 2.29
495 496 4.222124 AGTGGTGGGAACAGAATCATAC 57.778 45.455 0.00 0.00 44.46 2.39
501 502 2.775384 ACTTGTAGTGGTGGGAACAGAA 59.225 45.455 0.00 0.00 44.46 3.02
508 509 3.208747 ACAGAAACTTGTAGTGGTGGG 57.791 47.619 0.00 0.00 0.00 4.61
537 635 8.556213 AGTACAGAAACTTGTAAACACTCAAA 57.444 30.769 0.00 0.00 35.47 2.69
540 638 9.836076 AAAAAGTACAGAAACTTGTAAACACTC 57.164 29.630 0.00 0.00 39.62 3.51
541 639 9.620660 CAAAAAGTACAGAAACTTGTAAACACT 57.379 29.630 0.00 0.00 39.62 3.55
610 1661 1.614241 GGCCGTACATCTGGTGGACT 61.614 60.000 1.14 0.00 39.70 3.85
657 1709 1.063266 AGGTTCAGAAAGTTGGGCCAA 60.063 47.619 16.66 16.66 0.00 4.52
658 1710 0.555769 AGGTTCAGAAAGTTGGGCCA 59.444 50.000 0.00 0.00 0.00 5.36
679 1731 1.332202 CGTCGCGAAAGAACGGAAAAA 60.332 47.619 12.06 0.00 37.89 1.94
680 1732 0.230260 CGTCGCGAAAGAACGGAAAA 59.770 50.000 12.06 0.00 37.89 2.29
681 1733 1.847975 CGTCGCGAAAGAACGGAAA 59.152 52.632 12.06 0.00 37.89 3.13
700 1752 1.128692 GATGTTCAGAAACGAAGGCCG 59.871 52.381 0.00 0.00 45.44 6.13
708 1760 2.092211 CAGCCGTACGATGTTCAGAAAC 59.908 50.000 18.76 0.00 35.85 2.78
709 1761 2.333926 CAGCCGTACGATGTTCAGAAA 58.666 47.619 18.76 0.00 0.00 2.52
767 1821 2.285069 TCCGCCCACATACCTGGT 60.285 61.111 4.05 4.05 0.00 4.00
771 1825 2.202837 GTCGTCCGCCCACATACC 60.203 66.667 0.00 0.00 0.00 2.73
772 1826 2.581409 CGTCGTCCGCCCACATAC 60.581 66.667 0.00 0.00 0.00 2.39
773 1827 3.829044 CCGTCGTCCGCCCACATA 61.829 66.667 0.00 0.00 34.38 2.29
1317 2397 0.312416 CCCAATTCGCAAAACACGGA 59.688 50.000 0.00 0.00 0.00 4.69
1355 2438 4.806481 GAGCGCGCGTACTCGTCA 62.806 66.667 32.35 0.00 39.49 4.35
1407 2491 6.114187 ACGAATCTAGGCATTTCCATGATA 57.886 37.500 0.00 0.00 37.29 2.15
1466 2555 4.001017 GACAAGAGGTCGTCGTTAGTAG 57.999 50.000 0.00 0.00 36.65 2.57
1495 2584 2.423898 TTCGGGTCAGGGATCGCTC 61.424 63.158 9.74 0.00 0.00 5.03
1558 2647 4.091075 CACGGATAATTCATCGCAGATCAG 59.909 45.833 0.00 0.00 45.12 2.90
1575 2664 4.320870 ACCTAATTCACGAAAACACGGAT 58.679 39.130 0.00 0.00 37.61 4.18
1611 2700 4.514066 AGTTCCCGTGTATTCTGTCAAAAC 59.486 41.667 0.00 0.00 0.00 2.43
1946 4687 1.837051 ACACAGAAGCACGGAGGGA 60.837 57.895 0.00 0.00 0.00 4.20
1999 4740 0.944386 CACCACACTTGCCACTACAC 59.056 55.000 0.00 0.00 0.00 2.90
2118 4859 2.849880 ATCCAACCGCATCAAAATCG 57.150 45.000 0.00 0.00 0.00 3.34
2129 4870 1.665679 CGTCAATCTGGAATCCAACCG 59.334 52.381 2.61 0.00 30.80 4.44
2142 4883 4.657436 AGAGGGAACTGATACGTCAATC 57.343 45.455 0.00 0.00 44.43 2.67
2212 4953 9.476202 TCCACATGAAAACTATTAGATATGTCG 57.524 33.333 0.00 0.00 0.00 4.35
2325 5066 8.319143 ACATGCAACGAAATAACTAAGTTAGT 57.681 30.769 9.85 9.85 41.73 2.24
2489 5231 3.323403 AGCTAGCTTATGGATCACCTCAC 59.677 47.826 12.68 0.00 37.04 3.51
2494 5236 6.874288 AATCAAAGCTAGCTTATGGATCAC 57.126 37.500 29.52 0.00 34.84 3.06
2534 5276 2.063266 TGTTCTGTTCGATAACGGTGC 58.937 47.619 0.00 0.00 41.86 5.01
2570 5312 8.211116 TGAAAATTTGCACTTCACATCATTTT 57.789 26.923 0.00 0.00 0.00 1.82
2599 5341 3.126514 CAGTGGCAGCATTAGAAGTTCAG 59.873 47.826 5.50 0.00 0.00 3.02
2601 5343 2.159462 GCAGTGGCAGCATTAGAAGTTC 60.159 50.000 0.00 0.00 40.72 3.01
2613 5355 0.323178 AATCAGAAGGGCAGTGGCAG 60.323 55.000 19.48 2.73 43.71 4.85
2618 5360 3.728385 AAGCTAAATCAGAAGGGCAGT 57.272 42.857 0.00 0.00 0.00 4.40
2664 5409 3.489229 GCACAGAAACACCTGAAAAGACC 60.489 47.826 0.00 0.00 37.59 3.85
2665 5410 3.378427 AGCACAGAAACACCTGAAAAGAC 59.622 43.478 0.00 0.00 37.59 3.01
2666 5411 3.620488 AGCACAGAAACACCTGAAAAGA 58.380 40.909 0.00 0.00 37.59 2.52
2997 5742 5.157940 TGTGGAGAAGAGAAAAGATCAGG 57.842 43.478 0.00 0.00 0.00 3.86
3514 6259 1.087771 GCCAACGAATACCACTCCGG 61.088 60.000 0.00 0.00 42.50 5.14
3533 6278 1.920574 CACGATACTTCTGTTGCCTCG 59.079 52.381 0.00 0.00 0.00 4.63
3550 6295 5.227908 AGTCCTACTGTTTACATGTTCACG 58.772 41.667 2.30 1.13 0.00 4.35
3632 6378 1.595093 GACCCAAATGCGGTTCCCAG 61.595 60.000 0.00 0.00 32.27 4.45
3720 6466 2.249139 ACACCCAGAGGAACTACAGAC 58.751 52.381 0.00 0.00 41.55 3.51
3798 6544 1.459592 GCACAGCTTAGTAACACACCG 59.540 52.381 0.00 0.00 0.00 4.94
3839 6585 7.693951 CCAACAAATTCATCGTCAGATTTAGAC 59.306 37.037 0.00 0.00 34.23 2.59
3851 6597 3.557577 TCTGCACCAACAAATTCATCG 57.442 42.857 0.00 0.00 0.00 3.84
3925 6671 7.618512 GTGAAATATCAGGGTATAGCCTAGGTA 59.381 40.741 22.80 16.77 35.88 3.08
3927 6673 6.127026 GGTGAAATATCAGGGTATAGCCTAGG 60.127 46.154 22.80 12.10 35.88 3.02
3935 6681 3.072476 CCCACGGTGAAATATCAGGGTAT 59.928 47.826 10.28 0.00 35.88 2.73
3949 6695 2.026945 AAAAGCCAAAGCCCACGGTG 62.027 55.000 0.00 0.00 41.25 4.94
3953 6699 1.597854 GCCAAAAGCCAAAGCCCAC 60.598 57.895 0.00 0.00 41.25 4.61
3973 6719 1.271163 TGTAGGCCTTACTGGTGCAAC 60.271 52.381 12.58 0.00 38.35 4.17
4009 6755 1.748329 TAGGCGGCTATGGTGCAGAG 61.748 60.000 15.70 0.00 34.04 3.35
4023 6769 1.336240 TGCATCGTCATCATCTAGGCG 60.336 52.381 0.00 0.00 0.00 5.52
4037 6783 7.011189 CACATACACATATATGTTGTGCATCG 58.989 38.462 25.23 12.66 46.65 3.84
4075 6823 4.565564 GCGAATAACGAAGCCTTCTTTCTA 59.434 41.667 2.49 0.00 45.77 2.10
4076 6824 3.371285 GCGAATAACGAAGCCTTCTTTCT 59.629 43.478 2.49 0.00 45.77 2.52
4077 6825 3.371285 AGCGAATAACGAAGCCTTCTTTC 59.629 43.478 2.49 0.61 45.77 2.62
4078 6826 3.125316 CAGCGAATAACGAAGCCTTCTTT 59.875 43.478 2.49 2.02 45.77 2.52
4079 6827 2.673368 CAGCGAATAACGAAGCCTTCTT 59.327 45.455 2.49 0.00 45.77 2.52
4080 6828 2.271800 CAGCGAATAACGAAGCCTTCT 58.728 47.619 2.49 0.00 45.77 2.85
4090 6838 3.127030 CCCAGACTTTTCCAGCGAATAAC 59.873 47.826 0.00 0.00 0.00 1.89
4095 6843 0.034896 GTCCCAGACTTTTCCAGCGA 59.965 55.000 0.00 0.00 0.00 4.93
4158 6906 1.726791 CTTGAATTGGACGACGACTGG 59.273 52.381 0.00 0.00 0.00 4.00
4235 6983 1.340465 CGTACGCGTCTTGATGCAC 59.660 57.895 18.63 4.42 0.00 4.57
4255 7003 3.131240 GGTGATAACATTCAACGGTGC 57.869 47.619 0.00 0.00 0.00 5.01
4311 7061 0.173481 GTGCTGTCGTCCATAGCTGA 59.827 55.000 0.00 0.00 39.94 4.26
4364 7114 5.563475 CGAATGACCAAAGCAAAAGAGATGT 60.563 40.000 0.00 0.00 0.00 3.06
4375 7125 0.095417 GCGTCTCGAATGACCAAAGC 59.905 55.000 0.00 0.00 33.70 3.51
4399 7149 1.243342 TTGAGCGTTCCATGGCCTTG 61.243 55.000 6.96 11.68 0.00 3.61
4448 7200 5.177326 GTTGTGGGTACATACGTTTCCATA 58.823 41.667 0.00 0.00 36.53 2.74
4449 7201 3.985019 TGTGGGTACATACGTTTCCAT 57.015 42.857 0.00 0.00 31.51 3.41
4450 7202 3.181457 TGTTGTGGGTACATACGTTTCCA 60.181 43.478 0.00 0.00 36.53 3.53
4452 7204 5.421212 TTTGTTGTGGGTACATACGTTTC 57.579 39.130 0.00 0.00 36.53 2.78
4453 7205 5.831702 TTTTGTTGTGGGTACATACGTTT 57.168 34.783 0.00 0.00 36.53 3.60


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

AutoCloner maintained by Alex Coulton.