Multiple sequence alignment - TraesCS5D01G339400

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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 TraesCS5D01G339400 chr5D 100.000 4126 0 0 1 4126 428495047 428499172 0.000000e+00 7620.0
1 TraesCS5D01G339400 chr5A 93.172 3398 118 37 770 4124 544152322 544155648 0.000000e+00 4885.0
2 TraesCS5D01G339400 chr5A 89.655 116 12 0 399 514 635453464 635453579 9.240000e-32 148.0
3 TraesCS5D01G339400 chr5B 89.674 1075 52 27 514 1555 517675931 517676979 0.000000e+00 1315.0
4 TraesCS5D01G339400 chr5B 88.283 862 61 19 2513 3372 517678776 517679599 0.000000e+00 996.0
5 TraesCS5D01G339400 chr5B 91.071 392 31 4 1 391 517675552 517675940 1.020000e-145 527.0
6 TraesCS5D01G339400 chr5B 90.722 388 31 5 1589 1974 517676979 517677363 2.840000e-141 512.0
7 TraesCS5D01G339400 chr5B 92.604 338 25 0 1979 2316 517678404 517678741 1.720000e-133 486.0
8 TraesCS5D01G339400 chr5B 84.038 213 15 8 3160 3372 517679718 517679911 1.960000e-43 187.0
9 TraesCS5D01G339400 chr5B 88.961 154 12 3 3439 3592 517679918 517680066 7.040000e-43 185.0
10 TraesCS5D01G339400 chr5B 94.059 101 5 1 4027 4126 517680469 517680569 7.140000e-33 152.0
11 TraesCS5D01G339400 chr5B 96.721 61 1 1 3771 3830 517680246 517680306 2.620000e-17 100.0
12 TraesCS5D01G339400 chr3A 91.667 120 10 0 391 510 265258822 265258941 2.550000e-37 167.0
13 TraesCS5D01G339400 chr7B 88.722 133 11 3 3256 3386 198951041 198951171 4.270000e-35 159.0
14 TraesCS5D01G339400 chr7B 89.286 112 9 3 3497 3606 27789946 27790056 2.000000e-28 137.0
15 TraesCS5D01G339400 chr2B 88.722 133 11 3 3256 3386 672094283 672094153 4.270000e-35 159.0
16 TraesCS5D01G339400 chr2B 88.636 44 3 2 2613 2655 614916583 614916625 7.000000e-03 52.8
17 TraesCS5D01G339400 chr4A 92.661 109 8 0 397 505 6932392 6932500 1.540000e-34 158.0
18 TraesCS5D01G339400 chr4A 91.150 113 10 0 397 509 707660725 707660837 1.990000e-33 154.0
19 TraesCS5D01G339400 chr3D 93.069 101 3 3 3503 3599 510332886 510332986 1.200000e-30 145.0
20 TraesCS5D01G339400 chrUn 91.346 104 5 3 3499 3598 48992705 48992808 5.560000e-29 139.0
21 TraesCS5D01G339400 chr3B 88.496 113 13 0 397 509 187550055 187550167 2.000000e-28 137.0
22 TraesCS5D01G339400 chr7D 91.919 99 4 3 3501 3598 44711115 44711210 7.190000e-28 135.0
23 TraesCS5D01G339400 chr7D 92.632 95 5 2 3503 3596 80201959 80202052 7.190000e-28 135.0
24 TraesCS5D01G339400 chr7D 91.176 102 5 3 3496 3593 263503839 263503940 7.190000e-28 135.0
25 TraesCS5D01G339400 chr7A 91.089 101 6 3 3501 3598 46777781 46777881 2.590000e-27 134.0


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 TraesCS5D01G339400 chr5D 428495047 428499172 4125 False 7620.000000 7620 100.000000 1 4126 1 chr5D.!!$F1 4125
1 TraesCS5D01G339400 chr5A 544152322 544155648 3326 False 4885.000000 4885 93.172000 770 4124 1 chr5A.!!$F1 3354
2 TraesCS5D01G339400 chr5B 517675552 517680569 5017 False 495.555556 1315 90.681444 1 4126 9 chr5B.!!$F1 4125

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
475 477 0.034767 CAGGCCCACATGTCAGTGAT 60.035 55.0 0.00 0.0 42.05 3.06 F
488 490 0.537188 CAGTGATAGAACGGCAGGGT 59.463 55.0 0.00 0.0 0.00 4.34 F
1389 1432 0.811616 GCTGGTTCGCGAATCCTGAT 60.812 55.0 31.41 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1619 1.342975 GGTAGGCCCCAATTCAACCAT 60.343 52.381 0.00 0.0 0.00 3.55 R
1834 1879 3.135348 TGGAAATTGGCCACAATGTTTCA 59.865 39.130 3.88 0.0 46.25 2.69 R
3383 4489 1.335964 CGTATACCATGAGACGGCTGG 60.336 57.143 0.00 0.0 36.09 4.85 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
42 43 4.204799 GGTACTTCCCCACATTTATGACC 58.795 47.826 0.00 0.00 0.00 4.02
43 44 3.382083 ACTTCCCCACATTTATGACCC 57.618 47.619 0.00 0.00 0.00 4.46
44 45 2.652348 ACTTCCCCACATTTATGACCCA 59.348 45.455 0.00 0.00 0.00 4.51
45 46 2.818751 TCCCCACATTTATGACCCAC 57.181 50.000 0.00 0.00 0.00 4.61
46 47 1.065053 TCCCCACATTTATGACCCACG 60.065 52.381 0.00 0.00 0.00 4.94
47 48 0.738389 CCCACATTTATGACCCACGC 59.262 55.000 0.00 0.00 0.00 5.34
48 49 0.376852 CCACATTTATGACCCACGCG 59.623 55.000 3.53 3.53 0.00 6.01
81 82 2.236146 AGGTATGCTTGTCGTGGATCAA 59.764 45.455 0.00 0.00 0.00 2.57
107 108 2.253610 ACCAGTGGACAACGATTCCTA 58.746 47.619 18.40 0.00 33.84 2.94
108 109 2.028385 ACCAGTGGACAACGATTCCTAC 60.028 50.000 18.40 0.00 33.84 3.18
111 112 3.927142 CAGTGGACAACGATTCCTACTTC 59.073 47.826 0.00 0.00 33.84 3.01
152 153 7.699566 TCAATTGGGTAAATTAATCTACGTGC 58.300 34.615 5.42 0.00 36.28 5.34
172 173 5.616645 CGTGCATGCAAAGTCACTTATGTTA 60.617 40.000 24.58 0.00 0.00 2.41
174 175 4.788100 GCATGCAAAGTCACTTATGTTACG 59.212 41.667 14.21 0.00 0.00 3.18
178 179 4.084013 GCAAAGTCACTTATGTTACGTGCT 60.084 41.667 0.00 0.00 35.41 4.40
257 259 6.932356 ATTGTATTGAGATAAGTGCACCAG 57.068 37.500 14.63 0.00 0.00 4.00
269 271 2.423538 AGTGCACCAGAAGTCACAAAAC 59.576 45.455 14.63 0.00 32.30 2.43
273 275 3.002759 GCACCAGAAGTCACAAAACTCTC 59.997 47.826 0.00 0.00 0.00 3.20
309 311 7.682021 GCACTTTGGTCACACTTCTTCTAAAAT 60.682 37.037 0.00 0.00 0.00 1.82
321 323 6.934645 ACTTCTTCTAAAATGTGATGAACCGA 59.065 34.615 0.00 0.00 0.00 4.69
332 334 3.325870 TGATGAACCGATCACAACACTC 58.674 45.455 0.00 0.00 41.93 3.51
350 352 6.932356 ACACTCCATATTATGAGCAAACAG 57.068 37.500 5.21 0.00 0.00 3.16
360 362 3.769739 TGAGCAAACAGGTGACATACT 57.230 42.857 0.00 0.00 0.00 2.12
362 364 2.744202 GAGCAAACAGGTGACATACTGG 59.256 50.000 12.82 0.04 39.00 4.00
374 376 0.824109 CATACTGGTTCGAGGAGCCA 59.176 55.000 1.24 1.24 40.50 4.75
381 383 0.670854 GTTCGAGGAGCCAAGGTGTC 60.671 60.000 0.00 0.00 0.00 3.67
382 384 1.827399 TTCGAGGAGCCAAGGTGTCC 61.827 60.000 2.39 2.39 0.00 4.02
383 385 2.286523 CGAGGAGCCAAGGTGTCCT 61.287 63.158 10.79 10.79 43.76 3.85
384 386 1.298014 GAGGAGCCAAGGTGTCCTG 59.702 63.158 14.60 0.00 41.00 3.86
385 387 2.360475 GGAGCCAAGGTGTCCTGC 60.360 66.667 3.22 0.00 32.13 4.85
386 388 2.753029 GAGCCAAGGTGTCCTGCT 59.247 61.111 1.18 1.18 35.91 4.24
387 389 1.673665 GAGCCAAGGTGTCCTGCTG 60.674 63.158 5.56 0.00 33.81 4.41
388 390 2.116983 GAGCCAAGGTGTCCTGCTGA 62.117 60.000 5.56 0.00 33.81 4.26
389 391 1.968540 GCCAAGGTGTCCTGCTGAC 60.969 63.158 0.00 0.00 44.72 3.51
390 392 1.757306 CCAAGGTGTCCTGCTGACT 59.243 57.895 8.16 0.00 44.75 3.41
391 393 0.604780 CCAAGGTGTCCTGCTGACTG 60.605 60.000 8.16 0.00 44.75 3.51
392 394 0.604780 CAAGGTGTCCTGCTGACTGG 60.605 60.000 8.16 0.00 44.75 4.00
393 395 0.764369 AAGGTGTCCTGCTGACTGGA 60.764 55.000 8.16 0.00 44.75 3.86
394 396 0.546267 AGGTGTCCTGCTGACTGGAT 60.546 55.000 8.16 0.00 44.73 3.41
395 397 0.392193 GGTGTCCTGCTGACTGGATG 60.392 60.000 8.16 0.00 44.73 3.51
396 398 1.023513 GTGTCCTGCTGACTGGATGC 61.024 60.000 8.16 0.00 44.73 3.91
397 399 1.812922 GTCCTGCTGACTGGATGCG 60.813 63.158 0.00 0.00 44.73 4.73
398 400 2.513204 CCTGCTGACTGGATGCGG 60.513 66.667 0.00 0.00 37.06 5.69
399 401 3.200593 CTGCTGACTGGATGCGGC 61.201 66.667 0.00 0.00 36.93 6.53
400 402 3.677284 CTGCTGACTGGATGCGGCT 62.677 63.158 0.00 0.00 37.30 5.52
401 403 2.894387 GCTGACTGGATGCGGCTC 60.894 66.667 0.00 0.00 33.67 4.70
402 404 2.202987 CTGACTGGATGCGGCTCC 60.203 66.667 0.00 6.53 35.74 4.70
403 405 2.685017 TGACTGGATGCGGCTCCT 60.685 61.111 16.01 1.50 36.20 3.69
404 406 2.107953 GACTGGATGCGGCTCCTC 59.892 66.667 16.01 5.06 36.20 3.71
405 407 2.364842 ACTGGATGCGGCTCCTCT 60.365 61.111 16.01 2.85 36.20 3.69
406 408 2.108566 CTGGATGCGGCTCCTCTG 59.891 66.667 16.01 6.32 36.20 3.35
408 410 4.925861 GGATGCGGCTCCTCTGCC 62.926 72.222 0.00 0.00 46.56 4.85
425 427 3.711842 CGTGCGCCATGTGACGTT 61.712 61.111 4.18 0.00 0.00 3.99
426 428 2.127270 GTGCGCCATGTGACGTTG 60.127 61.111 4.18 0.00 0.00 4.10
427 429 2.590291 TGCGCCATGTGACGTTGT 60.590 55.556 4.18 0.00 0.00 3.32
428 430 2.127270 GCGCCATGTGACGTTGTG 60.127 61.111 0.00 0.00 0.00 3.33
429 431 2.127270 CGCCATGTGACGTTGTGC 60.127 61.111 0.00 0.00 0.00 4.57
430 432 2.255252 GCCATGTGACGTTGTGCC 59.745 61.111 0.00 0.00 0.00 5.01
431 433 2.551006 GCCATGTGACGTTGTGCCA 61.551 57.895 0.00 0.00 0.00 4.92
432 434 1.282570 CCATGTGACGTTGTGCCAC 59.717 57.895 0.00 0.00 0.00 5.01
433 435 1.165907 CCATGTGACGTTGTGCCACT 61.166 55.000 5.99 0.00 0.00 4.00
434 436 0.041047 CATGTGACGTTGTGCCACTG 60.041 55.000 5.99 0.00 0.00 3.66
435 437 0.179059 ATGTGACGTTGTGCCACTGA 60.179 50.000 5.99 0.00 0.00 3.41
436 438 1.087202 TGTGACGTTGTGCCACTGAC 61.087 55.000 5.99 0.00 0.00 3.51
437 439 1.087202 GTGACGTTGTGCCACTGACA 61.087 55.000 0.00 0.00 0.00 3.58
438 440 0.179059 TGACGTTGTGCCACTGACAT 60.179 50.000 0.00 0.00 0.00 3.06
439 441 0.235665 GACGTTGTGCCACTGACATG 59.764 55.000 0.00 0.00 0.00 3.21
440 442 0.463654 ACGTTGTGCCACTGACATGT 60.464 50.000 0.00 0.00 0.00 3.21
441 443 0.041047 CGTTGTGCCACTGACATGTG 60.041 55.000 1.15 0.00 37.66 3.21
447 449 3.991999 CACTGACATGTGGGCCAG 58.008 61.111 6.40 6.93 34.56 4.85
448 450 1.676635 CACTGACATGTGGGCCAGG 60.677 63.158 6.40 1.59 34.56 4.45
449 451 2.156098 ACTGACATGTGGGCCAGGT 61.156 57.895 6.40 5.66 41.63 4.00
450 452 1.075482 CTGACATGTGGGCCAGGTT 59.925 57.895 6.40 0.00 38.40 3.50
451 453 0.540365 CTGACATGTGGGCCAGGTTT 60.540 55.000 6.40 0.00 38.40 3.27
452 454 0.539438 TGACATGTGGGCCAGGTTTC 60.539 55.000 6.40 1.88 38.40 2.78
453 455 1.228862 ACATGTGGGCCAGGTTTCC 60.229 57.895 6.40 0.00 33.45 3.13
454 456 1.228831 CATGTGGGCCAGGTTTCCA 60.229 57.895 6.40 0.00 0.00 3.53
455 457 0.831288 CATGTGGGCCAGGTTTCCAA 60.831 55.000 6.40 0.00 31.73 3.53
456 458 0.831711 ATGTGGGCCAGGTTTCCAAC 60.832 55.000 6.40 0.00 31.73 3.77
457 459 1.456705 GTGGGCCAGGTTTCCAACA 60.457 57.895 6.40 0.00 31.73 3.33
458 460 1.152567 TGGGCCAGGTTTCCAACAG 60.153 57.895 0.00 0.00 0.00 3.16
459 461 1.908299 GGGCCAGGTTTCCAACAGG 60.908 63.158 4.39 0.00 0.00 4.00
460 462 2.574018 GGCCAGGTTTCCAACAGGC 61.574 63.158 0.00 11.77 46.85 4.85
461 463 2.574018 GCCAGGTTTCCAACAGGCC 61.574 63.158 0.00 0.00 43.88 5.19
462 464 1.908299 CCAGGTTTCCAACAGGCCC 60.908 63.158 0.00 0.00 0.00 5.80
463 465 1.152567 CAGGTTTCCAACAGGCCCA 60.153 57.895 0.00 0.00 0.00 5.36
464 466 1.152546 AGGTTTCCAACAGGCCCAC 60.153 57.895 0.00 0.00 0.00 4.61
465 467 1.456705 GGTTTCCAACAGGCCCACA 60.457 57.895 0.00 0.00 0.00 4.17
466 468 0.831711 GGTTTCCAACAGGCCCACAT 60.832 55.000 0.00 0.00 0.00 3.21
467 469 0.318120 GTTTCCAACAGGCCCACATG 59.682 55.000 0.00 0.00 0.00 3.21
468 470 0.105760 TTTCCAACAGGCCCACATGT 60.106 50.000 0.00 0.00 0.00 3.21
469 471 0.539438 TTCCAACAGGCCCACATGTC 60.539 55.000 0.00 0.00 0.00 3.06
470 472 1.228521 CCAACAGGCCCACATGTCA 60.229 57.895 0.00 0.00 0.00 3.58
471 473 1.246056 CCAACAGGCCCACATGTCAG 61.246 60.000 0.00 0.00 0.00 3.51
472 474 0.538057 CAACAGGCCCACATGTCAGT 60.538 55.000 0.00 0.00 0.00 3.41
473 475 0.538057 AACAGGCCCACATGTCAGTG 60.538 55.000 0.00 0.00 39.21 3.66
474 476 1.376086 CAGGCCCACATGTCAGTGA 59.624 57.895 0.00 0.00 42.05 3.41
475 477 0.034767 CAGGCCCACATGTCAGTGAT 60.035 55.000 0.00 0.00 42.05 3.06
476 478 1.210234 CAGGCCCACATGTCAGTGATA 59.790 52.381 0.00 0.00 42.05 2.15
477 479 1.487976 AGGCCCACATGTCAGTGATAG 59.512 52.381 0.00 0.00 42.05 2.08
478 480 1.486310 GGCCCACATGTCAGTGATAGA 59.514 52.381 0.00 0.00 42.05 1.98
479 481 2.092968 GGCCCACATGTCAGTGATAGAA 60.093 50.000 0.00 0.00 42.05 2.10
480 482 2.939103 GCCCACATGTCAGTGATAGAAC 59.061 50.000 0.00 0.00 42.05 3.01
481 483 3.190079 CCCACATGTCAGTGATAGAACG 58.810 50.000 0.00 0.00 42.05 3.95
482 484 3.190079 CCACATGTCAGTGATAGAACGG 58.810 50.000 0.00 0.00 42.05 4.44
483 485 2.604914 CACATGTCAGTGATAGAACGGC 59.395 50.000 0.00 0.00 42.05 5.68
484 486 2.233676 ACATGTCAGTGATAGAACGGCA 59.766 45.455 0.00 0.00 0.00 5.69
485 487 2.654749 TGTCAGTGATAGAACGGCAG 57.345 50.000 0.00 0.00 0.00 4.85
486 488 1.204704 TGTCAGTGATAGAACGGCAGG 59.795 52.381 0.00 0.00 0.00 4.85
487 489 0.824109 TCAGTGATAGAACGGCAGGG 59.176 55.000 0.00 0.00 0.00 4.45
488 490 0.537188 CAGTGATAGAACGGCAGGGT 59.463 55.000 0.00 0.00 0.00 4.34
489 491 0.537188 AGTGATAGAACGGCAGGGTG 59.463 55.000 0.00 0.00 0.00 4.61
490 492 1.090052 GTGATAGAACGGCAGGGTGC 61.090 60.000 0.00 0.00 44.08 5.01
510 512 1.623163 CGAAGGGTAGAGGATCCTCC 58.377 60.000 33.81 21.70 37.91 4.30
537 539 2.489329 GCTGACTAGGCATCTTTTTGCA 59.511 45.455 0.00 0.00 44.59 4.08
620 622 2.084546 ACCTTAGTGCGGCATTTTCTC 58.915 47.619 5.72 0.00 0.00 2.87
657 659 6.308766 GTGATAAAGACCAAATGTGATGTTGC 59.691 38.462 0.00 0.00 0.00 4.17
683 686 5.066505 GGCGATATTTTGTCACTCCTTGATT 59.933 40.000 0.00 0.00 36.32 2.57
684 687 6.260050 GGCGATATTTTGTCACTCCTTGATTA 59.740 38.462 0.00 0.00 36.32 1.75
745 748 5.066375 CAGAGATCAAAAGGAACACACACAA 59.934 40.000 0.00 0.00 0.00 3.33
746 749 5.652014 AGAGATCAAAAGGAACACACACAAA 59.348 36.000 0.00 0.00 0.00 2.83
794 830 6.780706 AAAAGATAGGTAGAACAACACACG 57.219 37.500 0.00 0.00 0.00 4.49
795 831 5.717078 AAGATAGGTAGAACAACACACGA 57.283 39.130 0.00 0.00 0.00 4.35
817 853 5.505654 CGAGAAAAGGTTGCTAGCAAGAAAA 60.506 40.000 29.99 6.13 36.52 2.29
818 854 6.220726 AGAAAAGGTTGCTAGCAAGAAAAA 57.779 33.333 29.99 5.29 36.52 1.94
819 855 6.820335 AGAAAAGGTTGCTAGCAAGAAAAAT 58.180 32.000 29.99 14.76 36.52 1.82
1200 1242 5.249393 ACTGGAATCGGCCTGAGATTTATAT 59.751 40.000 0.00 0.00 38.32 0.86
1201 1243 6.126863 TGGAATCGGCCTGAGATTTATATT 57.873 37.500 0.00 0.00 38.32 1.28
1351 1394 3.568007 TGTTAGAATGTTTGTGCCTGACC 59.432 43.478 0.00 0.00 0.00 4.02
1354 1397 2.624838 AGAATGTTTGTGCCTGACCAAG 59.375 45.455 0.00 0.00 0.00 3.61
1364 1407 2.092968 TGCCTGACCAAGCCTACTTATG 60.093 50.000 0.00 0.00 33.74 1.90
1378 1421 2.350522 ACTTATGCTTCTGCTGGTTCG 58.649 47.619 0.00 0.00 40.48 3.95
1389 1432 0.811616 GCTGGTTCGCGAATCCTGAT 60.812 55.000 31.41 0.00 0.00 2.90
1434 1477 2.489329 CTGCACCCAAGTTAGTGGATTG 59.511 50.000 7.19 0.00 41.65 2.67
1436 1479 2.795329 CACCCAAGTTAGTGGATTGCT 58.205 47.619 0.00 0.00 41.65 3.91
1437 1480 2.749621 CACCCAAGTTAGTGGATTGCTC 59.250 50.000 0.00 0.00 41.65 4.26
1438 1481 2.009774 CCCAAGTTAGTGGATTGCTCG 58.990 52.381 0.00 0.00 41.65 5.03
1475 1518 7.855784 ATCTTCTTTACCAGGGAAAATTGTT 57.144 32.000 0.00 0.00 0.00 2.83
1503 1546 9.658475 TGATTGTAATCAAACTGAAAACTAACG 57.342 29.630 4.89 0.00 42.11 3.18
1506 1549 5.508200 AATCAAACTGAAAACTAACGGCA 57.492 34.783 0.00 0.00 0.00 5.69
1509 1552 4.396790 TCAAACTGAAAACTAACGGCAACT 59.603 37.500 0.00 0.00 0.00 3.16
1569 1614 7.745022 TTTATGTTTGAAGAGGTACGATACG 57.255 36.000 0.00 0.00 0.00 3.06
1574 1619 4.397481 TGAAGAGGTACGATACGAGAGA 57.603 45.455 0.00 0.00 0.00 3.10
1613 1658 3.129871 ACCATTTGATGTTTGTTTGCGG 58.870 40.909 0.00 0.00 0.00 5.69
1771 1816 6.698766 CAGGTCTGTTTCCTTTTTCAGATTTG 59.301 38.462 0.00 0.00 38.80 2.32
1819 1864 5.700722 AAGCATCATATACACTGCATTGG 57.299 39.130 9.06 0.00 37.09 3.16
1834 1879 6.375455 CACTGCATTGGTAATTTAGAGGACTT 59.625 38.462 0.00 0.00 0.00 3.01
1930 1976 7.469318 CGAATGAAGGACTCTTAGCTGATCTTA 60.469 40.741 0.00 0.00 32.52 2.10
2091 3173 9.959721 AAACATTACAGTAGTTGGTATGATCTT 57.040 29.630 0.00 0.00 0.00 2.40
2181 3263 6.785488 TTCCGCTGCATTATAATTCTACTG 57.215 37.500 0.00 0.00 0.00 2.74
2274 3356 5.819991 AGATGGCATCTTTCTGAAGGTTAA 58.180 37.500 24.01 0.00 35.76 2.01
2458 3556 3.170991 AGTGGAGCTCCTACTACAACA 57.829 47.619 32.28 6.94 30.46 3.33
2493 3591 7.497249 GCAATAGTATGATATCACTCCCAATCC 59.503 40.741 7.78 0.00 0.00 3.01
2494 3592 8.542926 CAATAGTATGATATCACTCCCAATCCA 58.457 37.037 7.78 0.00 0.00 3.41
2761 3860 9.547753 AGCTGTATGGTTCTTACTGTAATATTG 57.452 33.333 0.00 0.00 0.00 1.90
3225 4331 4.402829 TGATGCACTTTGGGTTAGCTAAA 58.597 39.130 7.99 0.00 0.00 1.85
3239 4345 8.110908 TGGGTTAGCTAAATGTTATACCTTGTT 58.889 33.333 7.99 0.00 0.00 2.83
3243 4349 7.303634 AGCTAAATGTTATACCTTGTTGACG 57.696 36.000 0.00 0.00 0.00 4.35
3281 4387 9.803130 GTAGATTTGTGATCATGTGAATATTCG 57.197 33.333 10.80 0.00 0.00 3.34
3396 4502 0.597568 TTTTTGCCAGCCGTCTCATG 59.402 50.000 0.00 0.00 0.00 3.07
3398 4504 2.410322 TTTGCCAGCCGTCTCATGGT 62.410 55.000 0.00 0.00 36.43 3.55
3421 4527 0.798776 CGCTGTTACTTTGGCTGGAG 59.201 55.000 0.00 0.00 0.00 3.86
3482 4867 5.705609 AAATGGAGTGCGTTACAAAGAAT 57.294 34.783 0.00 0.00 0.00 2.40
3512 4897 7.936301 CCAAATGGACTGGGAAAAAGAATAAAA 59.064 33.333 0.00 0.00 37.39 1.52
3513 4898 9.336171 CAAATGGACTGGGAAAAAGAATAAAAA 57.664 29.630 0.00 0.00 0.00 1.94
3596 4981 2.551270 TCTGAGCTACATCCCCTTTGT 58.449 47.619 0.00 0.00 0.00 2.83
3604 4989 2.823959 ACATCCCCTTTGTGCATGAAT 58.176 42.857 0.00 0.00 0.00 2.57
3685 5078 3.423907 CCGTCGAAAGTATTTTGGAACGG 60.424 47.826 15.65 15.65 39.27 4.44
3768 5161 1.495951 GCGTCAAAGAAACCGCGAT 59.504 52.632 8.23 0.00 36.53 4.58
3772 5165 1.136057 GTCAAAGAAACCGCGATCACC 60.136 52.381 8.23 0.00 0.00 4.02
3883 5307 3.580731 GTGCTCTACTTGTTCAGAGTCC 58.419 50.000 0.00 0.00 40.40 3.85
3909 5333 5.144359 CCAACGGAAAATCAAAGAAGTACG 58.856 41.667 0.00 0.00 0.00 3.67
3941 5376 6.861065 TTGAACCAGATCTTGTACAAAGTC 57.139 37.500 10.03 10.27 0.00 3.01
3965 5400 5.296780 CAGACCAATTTACGGCTACATTGAT 59.703 40.000 0.00 0.00 0.00 2.57
3966 5401 5.885912 AGACCAATTTACGGCTACATTGATT 59.114 36.000 0.00 0.00 0.00 2.57
3967 5402 6.038271 AGACCAATTTACGGCTACATTGATTC 59.962 38.462 0.00 0.00 0.00 2.52
3968 5403 5.067283 ACCAATTTACGGCTACATTGATTCC 59.933 40.000 0.00 0.00 0.00 3.01
3969 5404 5.067153 CCAATTTACGGCTACATTGATTCCA 59.933 40.000 0.00 0.00 0.00 3.53
3970 5405 6.201517 CAATTTACGGCTACATTGATTCCAG 58.798 40.000 0.00 0.00 0.00 3.86
3971 5406 4.746535 TTACGGCTACATTGATTCCAGA 57.253 40.909 0.00 0.00 0.00 3.86
3972 5407 2.906354 ACGGCTACATTGATTCCAGAC 58.094 47.619 0.00 0.00 0.00 3.51
3973 5408 2.501723 ACGGCTACATTGATTCCAGACT 59.498 45.455 0.00 0.00 0.00 3.24
3974 5409 3.704566 ACGGCTACATTGATTCCAGACTA 59.295 43.478 0.00 0.00 0.00 2.59
3975 5410 4.345257 ACGGCTACATTGATTCCAGACTAT 59.655 41.667 0.00 0.00 0.00 2.12
3976 5411 5.163301 ACGGCTACATTGATTCCAGACTATT 60.163 40.000 0.00 0.00 0.00 1.73
4001 5436 4.444056 CCAGTCAAATTGGTAAAAGTTGCG 59.556 41.667 0.00 0.00 0.00 4.85
4010 5445 6.380095 TTGGTAAAAGTTGCGTCAAGTTAT 57.620 33.333 11.35 2.87 36.18 1.89
4011 5446 5.753744 TGGTAAAAGTTGCGTCAAGTTATG 58.246 37.500 11.35 0.00 36.18 1.90
4016 5451 9.769093 GTAAAAGTTGCGTCAAGTTATGAATAT 57.231 29.630 11.35 0.00 40.50 1.28
4043 5478 3.239449 TCCAGTCTCTAGCCAACTTTCA 58.761 45.455 0.00 0.00 0.00 2.69
4076 5512 4.698304 GGCAGCAAGTTTACTGGTACATTA 59.302 41.667 0.00 0.00 38.20 1.90
4107 5543 5.654650 TGCCAAGTTTGAAGGAGAAAAGTTA 59.345 36.000 0.00 0.00 29.87 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.353557 GAAGTACCCCAAACCTCCATTC 58.646 50.000 0.00 0.00 0.00 2.67
36 37 3.845259 GGGAGCGCGTGGGTCATA 61.845 66.667 8.43 0.00 45.03 2.15
44 45 4.827087 CTCATGCTGGGAGCGCGT 62.827 66.667 8.43 0.00 46.26 6.01
46 47 2.388890 ATACCTCATGCTGGGAGCGC 62.389 60.000 0.00 0.00 46.26 5.92
47 48 0.602106 CATACCTCATGCTGGGAGCG 60.602 60.000 8.97 0.00 46.26 5.03
48 49 3.319135 CATACCTCATGCTGGGAGC 57.681 57.895 8.97 0.00 42.82 4.70
71 72 3.056821 CACTGGTTAGAGTTGATCCACGA 60.057 47.826 0.00 0.00 0.00 4.35
75 76 3.260884 TGTCCACTGGTTAGAGTTGATCC 59.739 47.826 0.00 0.00 0.00 3.36
81 82 2.313317 TCGTTGTCCACTGGTTAGAGT 58.687 47.619 0.00 0.00 0.00 3.24
107 108 7.951347 ATTGAATTAGAATTGCAGAGGAAGT 57.049 32.000 0.00 0.00 0.00 3.01
108 109 7.705325 CCAATTGAATTAGAATTGCAGAGGAAG 59.295 37.037 7.12 0.04 38.81 3.46
111 112 6.127253 ACCCAATTGAATTAGAATTGCAGAGG 60.127 38.462 7.12 11.93 38.81 3.69
145 146 1.800586 AGTGACTTTGCATGCACGTAG 59.199 47.619 22.58 19.43 36.43 3.51
147 148 1.024271 AAGTGACTTTGCATGCACGT 58.976 45.000 22.58 20.28 36.43 4.49
152 153 5.790003 CACGTAACATAAGTGACTTTGCATG 59.210 40.000 1.97 4.04 39.98 4.06
172 173 6.160684 TGTGTAGTAAATTACATCAGCACGT 58.839 36.000 5.89 0.00 36.08 4.49
249 251 2.423538 AGTTTTGTGACTTCTGGTGCAC 59.576 45.455 8.80 8.80 0.00 4.57
257 259 4.950050 TCTCCTGAGAGTTTTGTGACTTC 58.050 43.478 0.00 0.00 41.26 3.01
273 275 2.289882 TGACCAAAGTGCTCATCTCCTG 60.290 50.000 0.00 0.00 0.00 3.86
286 288 7.645340 CACATTTTAGAAGAAGTGTGACCAAAG 59.355 37.037 7.26 0.00 44.95 2.77
296 298 6.934645 TCGGTTCATCACATTTTAGAAGAAGT 59.065 34.615 0.00 0.00 0.00 3.01
321 323 6.594744 TGCTCATAATATGGAGTGTTGTGAT 58.405 36.000 0.00 0.00 30.85 3.06
327 329 5.824624 CCTGTTTGCTCATAATATGGAGTGT 59.175 40.000 0.00 0.00 33.66 3.55
332 334 5.589855 TGTCACCTGTTTGCTCATAATATGG 59.410 40.000 0.00 0.00 0.00 2.74
350 352 1.822990 TCCTCGAACCAGTATGTCACC 59.177 52.381 0.00 0.00 0.00 4.02
360 362 1.841556 ACCTTGGCTCCTCGAACCA 60.842 57.895 0.00 0.00 0.00 3.67
362 364 0.670854 GACACCTTGGCTCCTCGAAC 60.671 60.000 0.00 0.00 0.00 3.95
381 383 2.513204 CCGCATCCAGTCAGCAGG 60.513 66.667 0.00 0.00 0.00 4.85
382 384 3.200593 GCCGCATCCAGTCAGCAG 61.201 66.667 0.00 0.00 0.00 4.24
383 385 3.670637 GAGCCGCATCCAGTCAGCA 62.671 63.158 0.00 0.00 0.00 4.41
384 386 2.894387 GAGCCGCATCCAGTCAGC 60.894 66.667 0.00 0.00 0.00 4.26
385 387 2.202987 GGAGCCGCATCCAGTCAG 60.203 66.667 0.00 0.00 39.34 3.51
386 388 2.685017 AGGAGCCGCATCCAGTCA 60.685 61.111 10.36 0.00 42.26 3.41
387 389 2.107953 GAGGAGCCGCATCCAGTC 59.892 66.667 10.36 0.00 42.26 3.51
388 390 2.364842 AGAGGAGCCGCATCCAGT 60.365 61.111 10.36 0.00 42.26 4.00
389 391 2.108566 CAGAGGAGCCGCATCCAG 59.891 66.667 10.36 0.00 42.26 3.86
390 392 4.166888 GCAGAGGAGCCGCATCCA 62.167 66.667 10.36 0.00 42.26 3.41
391 393 4.925861 GGCAGAGGAGCCGCATCC 62.926 72.222 0.00 0.00 46.12 3.51
413 415 2.255252 GGCACAACGTCACATGGC 59.745 61.111 0.00 0.00 0.00 4.40
414 416 3.743208 TGGCACAACGTCACATGG 58.257 55.556 0.00 0.00 31.92 3.66
419 421 0.179059 ATGTCAGTGGCACAACGTCA 60.179 50.000 21.41 11.63 44.16 4.35
420 422 0.235665 CATGTCAGTGGCACAACGTC 59.764 55.000 21.41 6.24 44.16 4.34
421 423 0.463654 ACATGTCAGTGGCACAACGT 60.464 50.000 21.41 15.35 44.16 3.99
422 424 0.041047 CACATGTCAGTGGCACAACG 60.041 55.000 21.41 7.90 44.16 4.10
423 425 3.851620 CACATGTCAGTGGCACAAC 57.148 52.632 21.41 17.24 44.16 3.32
430 432 1.676635 CCTGGCCCACATGTCAGTG 60.677 63.158 0.00 0.00 39.21 3.66
431 433 1.719063 AACCTGGCCCACATGTCAGT 61.719 55.000 0.00 0.00 0.00 3.41
432 434 0.540365 AAACCTGGCCCACATGTCAG 60.540 55.000 0.00 0.00 0.00 3.51
433 435 0.539438 GAAACCTGGCCCACATGTCA 60.539 55.000 0.00 0.00 0.00 3.58
434 436 1.250840 GGAAACCTGGCCCACATGTC 61.251 60.000 0.00 0.00 0.00 3.06
435 437 1.228862 GGAAACCTGGCCCACATGT 60.229 57.895 0.00 0.00 0.00 3.21
436 438 0.831288 TTGGAAACCTGGCCCACATG 60.831 55.000 0.00 0.00 0.00 3.21
437 439 0.831711 GTTGGAAACCTGGCCCACAT 60.832 55.000 0.00 0.00 42.21 3.21
438 440 1.456705 GTTGGAAACCTGGCCCACA 60.457 57.895 0.00 0.00 42.21 4.17
439 441 3.455152 GTTGGAAACCTGGCCCAC 58.545 61.111 0.00 0.00 42.21 4.61
449 451 0.105760 ACATGTGGGCCTGTTGGAAA 60.106 50.000 4.53 0.00 34.57 3.13
450 452 0.539438 GACATGTGGGCCTGTTGGAA 60.539 55.000 1.15 0.00 34.57 3.53
451 453 1.074775 GACATGTGGGCCTGTTGGA 59.925 57.895 1.15 0.00 34.57 3.53
452 454 1.228521 TGACATGTGGGCCTGTTGG 60.229 57.895 1.15 0.00 0.00 3.77
453 455 0.538057 ACTGACATGTGGGCCTGTTG 60.538 55.000 1.15 1.57 0.00 3.33
454 456 0.538057 CACTGACATGTGGGCCTGTT 60.538 55.000 1.15 0.00 34.56 3.16
455 457 1.073722 CACTGACATGTGGGCCTGT 59.926 57.895 1.15 0.00 34.56 4.00
456 458 0.034767 ATCACTGACATGTGGGCCTG 60.035 55.000 1.15 0.00 38.40 4.85
457 459 1.487976 CTATCACTGACATGTGGGCCT 59.512 52.381 1.15 0.00 38.40 5.19
458 460 1.486310 TCTATCACTGACATGTGGGCC 59.514 52.381 1.15 0.00 38.40 5.80
459 461 2.939103 GTTCTATCACTGACATGTGGGC 59.061 50.000 1.15 0.00 38.40 5.36
460 462 3.190079 CGTTCTATCACTGACATGTGGG 58.810 50.000 1.15 0.00 38.40 4.61
461 463 3.190079 CCGTTCTATCACTGACATGTGG 58.810 50.000 1.15 0.00 38.40 4.17
462 464 2.604914 GCCGTTCTATCACTGACATGTG 59.395 50.000 1.15 0.00 39.15 3.21
463 465 2.233676 TGCCGTTCTATCACTGACATGT 59.766 45.455 0.00 0.00 0.00 3.21
464 466 2.862536 CTGCCGTTCTATCACTGACATG 59.137 50.000 0.00 0.00 0.00 3.21
465 467 2.159043 CCTGCCGTTCTATCACTGACAT 60.159 50.000 0.00 0.00 0.00 3.06
466 468 1.204704 CCTGCCGTTCTATCACTGACA 59.795 52.381 0.00 0.00 0.00 3.58
467 469 1.471676 CCCTGCCGTTCTATCACTGAC 60.472 57.143 0.00 0.00 0.00 3.51
468 470 0.824109 CCCTGCCGTTCTATCACTGA 59.176 55.000 0.00 0.00 0.00 3.41
469 471 0.537188 ACCCTGCCGTTCTATCACTG 59.463 55.000 0.00 0.00 0.00 3.66
470 472 0.537188 CACCCTGCCGTTCTATCACT 59.463 55.000 0.00 0.00 0.00 3.41
471 473 1.090052 GCACCCTGCCGTTCTATCAC 61.090 60.000 0.00 0.00 37.42 3.06
472 474 1.220749 GCACCCTGCCGTTCTATCA 59.779 57.895 0.00 0.00 37.42 2.15
473 475 4.126524 GCACCCTGCCGTTCTATC 57.873 61.111 0.00 0.00 37.42 2.08
482 484 3.682292 CTACCCTTCGGCACCCTGC 62.682 68.421 0.00 0.00 44.08 4.85
483 485 1.961180 CTCTACCCTTCGGCACCCTG 61.961 65.000 0.00 0.00 0.00 4.45
484 486 1.686110 CTCTACCCTTCGGCACCCT 60.686 63.158 0.00 0.00 0.00 4.34
485 487 2.732619 CCTCTACCCTTCGGCACCC 61.733 68.421 0.00 0.00 0.00 4.61
486 488 1.049289 ATCCTCTACCCTTCGGCACC 61.049 60.000 0.00 0.00 0.00 5.01
487 489 0.389757 GATCCTCTACCCTTCGGCAC 59.610 60.000 0.00 0.00 0.00 5.01
488 490 0.759436 GGATCCTCTACCCTTCGGCA 60.759 60.000 3.84 0.00 0.00 5.69
489 491 0.470268 AGGATCCTCTACCCTTCGGC 60.470 60.000 9.02 0.00 0.00 5.54
490 492 1.623163 GAGGATCCTCTACCCTTCGG 58.377 60.000 31.11 0.00 39.80 4.30
503 505 0.398381 AGTCAGCAGGGAGGAGGATC 60.398 60.000 0.00 0.00 0.00 3.36
504 506 0.937441 TAGTCAGCAGGGAGGAGGAT 59.063 55.000 0.00 0.00 0.00 3.24
505 507 0.260230 CTAGTCAGCAGGGAGGAGGA 59.740 60.000 0.00 0.00 0.00 3.71
506 508 0.758685 CCTAGTCAGCAGGGAGGAGG 60.759 65.000 0.00 0.00 0.00 4.30
507 509 1.398958 GCCTAGTCAGCAGGGAGGAG 61.399 65.000 0.00 0.00 33.44 3.69
508 510 1.381872 GCCTAGTCAGCAGGGAGGA 60.382 63.158 0.00 0.00 33.44 3.71
509 511 1.053264 ATGCCTAGTCAGCAGGGAGG 61.053 60.000 0.00 0.00 44.90 4.30
510 512 0.392336 GATGCCTAGTCAGCAGGGAG 59.608 60.000 0.00 0.00 44.90 4.30
511 513 0.031716 AGATGCCTAGTCAGCAGGGA 60.032 55.000 0.00 0.00 44.90 4.20
512 514 0.835941 AAGATGCCTAGTCAGCAGGG 59.164 55.000 0.00 0.00 44.90 4.45
572 574 1.606668 GTTGACCCAACATCTCGCAAA 59.393 47.619 5.08 0.00 43.09 3.68
606 608 0.039256 TGCTTGAGAAAATGCCGCAC 60.039 50.000 0.00 0.00 0.00 5.34
609 611 0.883833 AGGTGCTTGAGAAAATGCCG 59.116 50.000 0.00 0.00 0.00 5.69
657 659 1.597663 GGAGTGACAAAATATCGCCCG 59.402 52.381 0.00 0.00 0.00 6.13
759 762 8.177119 TCTACCTATCTTTTTGTGTGCATTTT 57.823 30.769 0.00 0.00 0.00 1.82
763 766 6.058833 TGTTCTACCTATCTTTTTGTGTGCA 58.941 36.000 0.00 0.00 0.00 4.57
764 767 6.554334 TGTTCTACCTATCTTTTTGTGTGC 57.446 37.500 0.00 0.00 0.00 4.57
765 768 7.855904 GTGTTGTTCTACCTATCTTTTTGTGTG 59.144 37.037 0.00 0.00 0.00 3.82
778 781 4.395959 TTTCTCGTGTGTTGTTCTACCT 57.604 40.909 0.00 0.00 0.00 3.08
794 830 5.438761 TTTCTTGCTAGCAACCTTTTCTC 57.561 39.130 26.06 0.00 0.00 2.87
795 831 5.852282 TTTTCTTGCTAGCAACCTTTTCT 57.148 34.783 26.06 0.00 0.00 2.52
1200 1242 1.745827 GCCACGGCCTAGCAATTAGAA 60.746 52.381 0.00 0.00 34.56 2.10
1201 1243 0.179056 GCCACGGCCTAGCAATTAGA 60.179 55.000 0.00 0.00 34.56 2.10
1354 1397 2.216898 CCAGCAGAAGCATAAGTAGGC 58.783 52.381 0.00 0.00 45.49 3.93
1364 1407 1.639298 ATTCGCGAACCAGCAGAAGC 61.639 55.000 26.00 0.00 42.56 3.86
1378 1421 6.748198 GCTACTACTACATTATCAGGATTCGC 59.252 42.308 0.00 0.00 0.00 4.70
1389 1432 6.038356 GCAAACGAAGGCTACTACTACATTA 58.962 40.000 0.00 0.00 0.00 1.90
1451 1494 7.290014 ACAACAATTTTCCCTGGTAAAGAAGAT 59.710 33.333 0.00 0.00 0.00 2.40
1457 1500 6.739331 ATCACAACAATTTTCCCTGGTAAA 57.261 33.333 0.00 0.00 0.00 2.01
1567 1612 2.356125 CCCCAATTCAACCATCTCTCGT 60.356 50.000 0.00 0.00 0.00 4.18
1569 1614 2.027385 GCCCCAATTCAACCATCTCTC 58.973 52.381 0.00 0.00 0.00 3.20
1574 1619 1.342975 GGTAGGCCCCAATTCAACCAT 60.343 52.381 0.00 0.00 0.00 3.55
1613 1658 3.243401 CCCTGACTGGTTACAAACAAAGC 60.243 47.826 0.00 0.00 0.00 3.51
1771 1816 5.912955 AGCAATGAAACGCAAACTAACTAAC 59.087 36.000 0.00 0.00 0.00 2.34
1819 1864 9.612620 CACAATGTTTCAAGTCCTCTAAATTAC 57.387 33.333 0.00 0.00 0.00 1.89
1834 1879 3.135348 TGGAAATTGGCCACAATGTTTCA 59.865 39.130 3.88 0.00 46.25 2.69
1862 1908 8.598041 TGGTGTAACTAATGGGCAAAATAAAAT 58.402 29.630 0.00 0.00 36.74 1.82
1930 1976 5.733620 ATGTTGCACTCCATGAAAGAAAT 57.266 34.783 0.00 0.00 0.00 2.17
2181 3263 9.455847 GGCTTATCATCAATAACTGAAATGAAC 57.544 33.333 0.00 0.00 37.67 3.18
2304 3386 4.037222 TGTACTTGATAAGGGGCAGATCA 58.963 43.478 0.00 0.00 0.00 2.92
2493 3591 3.837578 GCCTCATCACTGGCCATG 58.162 61.111 5.51 7.41 43.11 3.66
2510 3608 7.678194 TCAGAACGCAAAAGAAAATACAAAG 57.322 32.000 0.00 0.00 0.00 2.77
2698 3797 2.894765 TCACCCACGAGTAGATTTGACA 59.105 45.455 0.00 0.00 0.00 3.58
2761 3860 3.312146 CCAAAAGGGTGTGCAATGTTTTC 59.688 43.478 0.00 0.00 0.00 2.29
3225 4331 3.374058 GCAGCGTCAACAAGGTATAACAT 59.626 43.478 0.00 0.00 0.00 2.71
3239 4345 1.877576 CTACCAGGACAGCAGCGTCA 61.878 60.000 16.01 0.00 37.66 4.35
3243 4349 2.012673 CAAATCTACCAGGACAGCAGC 58.987 52.381 0.00 0.00 0.00 5.25
3281 4387 7.511959 AAGGAACCACTCTTATTGTTCTTTC 57.488 36.000 0.00 0.00 33.44 2.62
3383 4489 1.335964 CGTATACCATGAGACGGCTGG 60.336 57.143 0.00 0.00 36.09 4.85
3396 4502 3.308866 CAGCCAAAGTAACAGCGTATACC 59.691 47.826 0.00 0.00 0.00 2.73
3398 4504 3.196039 TCCAGCCAAAGTAACAGCGTATA 59.804 43.478 0.00 0.00 0.00 1.47
3461 4844 4.759693 TGATTCTTTGTAACGCACTCCATT 59.240 37.500 0.00 0.00 0.00 3.16
3482 4867 3.320610 TTTCCCAGTCCATTTGGTTGA 57.679 42.857 0.00 0.00 36.34 3.18
3512 4897 0.611896 CCCCGCATCTCCACCTTTTT 60.612 55.000 0.00 0.00 0.00 1.94
3513 4898 1.000896 CCCCGCATCTCCACCTTTT 60.001 57.895 0.00 0.00 0.00 2.27
3517 4902 1.371558 GATACCCCGCATCTCCACC 59.628 63.158 0.00 0.00 0.00 4.61
3596 4981 8.969260 ATTACTTACAATCTGAGATTCATGCA 57.031 30.769 4.39 0.00 0.00 3.96
3604 4989 9.587772 GCTTCAGTAATTACTTACAATCTGAGA 57.412 33.333 15.60 3.45 39.81 3.27
3720 5113 8.469200 TGACAAAGATTTCTCTGTGACAATTTT 58.531 29.630 0.00 0.00 38.10 1.82
3768 5161 3.971305 TCTTTCCTACACAAAGGAGGTGA 59.029 43.478 0.00 0.00 46.29 4.02
3772 5165 5.120830 CGTTCATCTTTCCTACACAAAGGAG 59.879 44.000 0.00 0.00 46.29 3.69
3840 5264 1.597663 GAGTAAACAGCACACAACGCT 59.402 47.619 0.00 0.00 41.47 5.07
3883 5307 1.268352 TCTTTGATTTTCCGTTGGGCG 59.732 47.619 0.00 0.00 40.95 6.13
3941 5376 4.634004 TCAATGTAGCCGTAAATTGGTCTG 59.366 41.667 0.00 0.00 35.33 3.51
3965 5400 6.434028 CCAATTTGACTGGAAATAGTCTGGAA 59.566 38.462 7.35 1.51 45.70 3.53
3966 5401 5.945784 CCAATTTGACTGGAAATAGTCTGGA 59.054 40.000 7.35 0.00 45.70 3.86
3967 5402 5.711976 ACCAATTTGACTGGAAATAGTCTGG 59.288 40.000 7.35 8.37 45.70 3.86
3968 5403 6.824305 ACCAATTTGACTGGAAATAGTCTG 57.176 37.500 7.35 0.00 45.70 3.51
3969 5404 8.934023 TTTACCAATTTGACTGGAAATAGTCT 57.066 30.769 7.35 0.00 45.70 3.24
3970 5405 9.626045 CTTTTACCAATTTGACTGGAAATAGTC 57.374 33.333 0.00 0.00 45.71 2.59
3971 5406 9.143155 ACTTTTACCAATTTGACTGGAAATAGT 57.857 29.630 0.00 0.00 37.40 2.12
3972 5407 9.981114 AACTTTTACCAATTTGACTGGAAATAG 57.019 29.630 0.00 0.00 37.40 1.73
3973 5408 9.757227 CAACTTTTACCAATTTGACTGGAAATA 57.243 29.630 0.00 0.00 37.40 1.40
3974 5409 7.226523 GCAACTTTTACCAATTTGACTGGAAAT 59.773 33.333 0.00 0.00 37.40 2.17
3975 5410 6.536941 GCAACTTTTACCAATTTGACTGGAAA 59.463 34.615 0.00 0.00 37.40 3.13
3976 5411 6.045955 GCAACTTTTACCAATTTGACTGGAA 58.954 36.000 0.00 0.00 37.40 3.53
4010 5445 9.547279 TGGCTAGAGACTGGAAATATATATTCA 57.453 33.333 8.42 3.07 0.00 2.57
4016 5451 7.676683 AAGTTGGCTAGAGACTGGAAATATA 57.323 36.000 0.00 0.00 0.00 0.86
4019 5454 4.917906 AAGTTGGCTAGAGACTGGAAAT 57.082 40.909 0.00 0.00 0.00 2.17
4020 5455 4.102524 TGAAAGTTGGCTAGAGACTGGAAA 59.897 41.667 0.00 0.00 0.00 3.13
4021 5456 3.646162 TGAAAGTTGGCTAGAGACTGGAA 59.354 43.478 0.00 0.00 0.00 3.53
4022 5457 3.006967 GTGAAAGTTGGCTAGAGACTGGA 59.993 47.826 0.00 0.00 0.00 3.86
4023 5458 3.007398 AGTGAAAGTTGGCTAGAGACTGG 59.993 47.826 0.00 0.00 0.00 4.00
4024 5459 4.264460 AGTGAAAGTTGGCTAGAGACTG 57.736 45.455 0.00 0.00 0.00 3.51
4025 5460 7.719871 TTATAGTGAAAGTTGGCTAGAGACT 57.280 36.000 0.00 0.00 0.00 3.24
4043 5478 7.362920 CCAGTAAACTTGCTGCCAATTTATAGT 60.363 37.037 0.00 0.00 39.23 2.12
4076 5512 2.310538 CTTCAAACTTGGCAGGGAGTT 58.689 47.619 0.44 0.00 37.69 3.01


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

AutoCloner maintained by Alex Coulton.