Multiple sequence alignment - TraesCS7D01G383800

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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 TraesCS7D01G383800 chr7D 100.000 2602 0 0 1 2602 497919966 497917365 0.000000e+00 4806
1 TraesCS7D01G383800 chr3D 98.508 1944 27 2 660 2602 609330387 609328445 0.000000e+00 3428
2 TraesCS7D01G383800 chr3D 96.254 1949 68 2 655 2602 98497434 98499378 0.000000e+00 3190
3 TraesCS7D01G383800 chr3D 98.601 786 10 1 1817 2602 31791281 31792065 0.000000e+00 1389
4 TraesCS7D01G383800 chr3D 80.243 658 111 8 1 656 432249502 432250142 6.510000e-131 477
5 TraesCS7D01G383800 chr2D 97.688 1946 44 1 657 2602 43889897 43891841 0.000000e+00 3343
6 TraesCS7D01G383800 chr2D 98.346 786 12 1 1817 2602 459777869 459778653 0.000000e+00 1378
7 TraesCS7D01G383800 chr4D 96.917 1946 59 1 657 2602 494026357 494028301 0.000000e+00 3260
8 TraesCS7D01G383800 chr4D 93.651 1953 103 11 656 2602 54409191 54407254 0.000000e+00 2900
9 TraesCS7D01G383800 chr5A 96.553 1944 66 1 660 2602 32051353 32049410 0.000000e+00 3217
10 TraesCS7D01G383800 chr1A 92.612 1949 101 13 661 2602 517188879 517190791 0.000000e+00 2761
11 TraesCS7D01G383800 chr6D 95.859 1135 47 0 657 1791 410085363 410086497 0.000000e+00 1836
12 TraesCS7D01G383800 chr6D 97.549 816 20 0 1787 2602 410096545 410097360 0.000000e+00 1397
13 TraesCS7D01G383800 chr5D 97.044 1015 30 0 656 1670 435192755 435193769 0.000000e+00 1709
14 TraesCS7D01G383800 chr5D 98.346 786 12 1 1817 2602 45352799 45352015 0.000000e+00 1378
15 TraesCS7D01G383800 chr2A 90.060 1167 74 21 1445 2601 123570719 123571853 0.000000e+00 1474
16 TraesCS7D01G383800 chr2A 84.932 657 98 1 1 657 90022217 90021562 0.000000e+00 664
17 TraesCS7D01G383800 chr1D 84.018 657 94 7 1 657 104014568 104013923 2.840000e-174 621
18 TraesCS7D01G383800 chr1B 77.997 659 139 6 1 657 629151480 629150826 2.410000e-110 409
19 TraesCS7D01G383800 chr5B 89.831 118 11 1 540 657 606008478 606008362 1.610000e-32 150


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 TraesCS7D01G383800 chr7D 497917365 497919966 2601 True 4806 4806 100.000 1 2602 1 chr7D.!!$R1 2601
1 TraesCS7D01G383800 chr3D 609328445 609330387 1942 True 3428 3428 98.508 660 2602 1 chr3D.!!$R1 1942
2 TraesCS7D01G383800 chr3D 98497434 98499378 1944 False 3190 3190 96.254 655 2602 1 chr3D.!!$F2 1947
3 TraesCS7D01G383800 chr3D 31791281 31792065 784 False 1389 1389 98.601 1817 2602 1 chr3D.!!$F1 785
4 TraesCS7D01G383800 chr3D 432249502 432250142 640 False 477 477 80.243 1 656 1 chr3D.!!$F3 655
5 TraesCS7D01G383800 chr2D 43889897 43891841 1944 False 3343 3343 97.688 657 2602 1 chr2D.!!$F1 1945
6 TraesCS7D01G383800 chr2D 459777869 459778653 784 False 1378 1378 98.346 1817 2602 1 chr2D.!!$F2 785
7 TraesCS7D01G383800 chr4D 494026357 494028301 1944 False 3260 3260 96.917 657 2602 1 chr4D.!!$F1 1945
8 TraesCS7D01G383800 chr4D 54407254 54409191 1937 True 2900 2900 93.651 656 2602 1 chr4D.!!$R1 1946
9 TraesCS7D01G383800 chr5A 32049410 32051353 1943 True 3217 3217 96.553 660 2602 1 chr5A.!!$R1 1942
10 TraesCS7D01G383800 chr1A 517188879 517190791 1912 False 2761 2761 92.612 661 2602 1 chr1A.!!$F1 1941
11 TraesCS7D01G383800 chr6D 410085363 410086497 1134 False 1836 1836 95.859 657 1791 1 chr6D.!!$F1 1134
12 TraesCS7D01G383800 chr6D 410096545 410097360 815 False 1397 1397 97.549 1787 2602 1 chr6D.!!$F2 815
13 TraesCS7D01G383800 chr5D 435192755 435193769 1014 False 1709 1709 97.044 656 1670 1 chr5D.!!$F1 1014
14 TraesCS7D01G383800 chr5D 45352015 45352799 784 True 1378 1378 98.346 1817 2602 1 chr5D.!!$R1 785
15 TraesCS7D01G383800 chr2A 123570719 123571853 1134 False 1474 1474 90.060 1445 2601 1 chr2A.!!$F1 1156
16 TraesCS7D01G383800 chr2A 90021562 90022217 655 True 664 664 84.932 1 657 1 chr2A.!!$R1 656
17 TraesCS7D01G383800 chr1D 104013923 104014568 645 True 621 621 84.018 1 657 1 chr1D.!!$R1 656
18 TraesCS7D01G383800 chr1B 629150826 629151480 654 True 409 409 77.997 1 657 1 chr1B.!!$R1 656

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
375 390 0.034616 CCGATCTGCTTGGGATCTCC 59.965 60.0 0.0 0.0 37.88 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2507 3.75485 CCAGTTCACTTCTGCATTCATGA 59.245 43.478 0.0 0.0 0.0 3.07 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
18 19 1.824658 TTTCTGGGTATACGGGGCG 59.175 57.895 0.00 0.00 0.00 6.13
24 25 1.767681 TGGGTATACGGGGCGTTTAAT 59.232 47.619 0.00 0.00 41.54 1.40
27 28 3.934579 GGGTATACGGGGCGTTTAATATG 59.065 47.826 0.00 0.00 41.54 1.78
36 37 5.460646 GGGGCGTTTAATATGTCATTCATG 58.539 41.667 0.00 0.00 37.91 3.07
67 68 0.834612 TTTGGTCGGAACTGTGTCCT 59.165 50.000 0.00 0.00 35.31 3.85
81 82 2.364973 TCCTGGACCTGCGCCATA 60.365 61.111 4.18 0.00 34.33 2.74
146 147 2.106566 GGTCAAGCTCTCCATCTCAGA 58.893 52.381 0.00 0.00 0.00 3.27
147 148 2.699846 GGTCAAGCTCTCCATCTCAGAT 59.300 50.000 0.00 0.00 0.00 2.90
175 176 1.004044 CTGTTGCCTGACCATCCTCTT 59.996 52.381 0.00 0.00 0.00 2.85
178 179 3.073798 TGTTGCCTGACCATCCTCTTTTA 59.926 43.478 0.00 0.00 0.00 1.52
183 184 4.323868 GCCTGACCATCCTCTTTTAGAAGT 60.324 45.833 0.00 0.00 34.41 3.01
214 215 0.698818 ATTTTTCCTCCTCCGCCTGT 59.301 50.000 0.00 0.00 0.00 4.00
216 217 0.250727 TTTTCCTCCTCCGCCTGTTG 60.251 55.000 0.00 0.00 0.00 3.33
267 270 1.455383 CCCCGTGCATTAGCCATTCC 61.455 60.000 0.00 0.00 41.13 3.01
268 271 0.751277 CCCGTGCATTAGCCATTCCA 60.751 55.000 0.00 0.00 41.13 3.53
269 272 1.321474 CCGTGCATTAGCCATTCCAT 58.679 50.000 0.00 0.00 41.13 3.41
270 273 2.503331 CCGTGCATTAGCCATTCCATA 58.497 47.619 0.00 0.00 41.13 2.74
271 274 2.226437 CCGTGCATTAGCCATTCCATAC 59.774 50.000 0.00 0.00 41.13 2.39
272 275 2.096268 CGTGCATTAGCCATTCCATACG 60.096 50.000 0.00 0.00 41.13 3.06
273 276 1.879380 TGCATTAGCCATTCCATACGC 59.121 47.619 0.00 0.00 41.13 4.42
274 277 1.879380 GCATTAGCCATTCCATACGCA 59.121 47.619 0.00 0.00 33.58 5.24
275 278 2.350772 GCATTAGCCATTCCATACGCAC 60.351 50.000 0.00 0.00 33.58 5.34
276 279 2.700722 TTAGCCATTCCATACGCACA 57.299 45.000 0.00 0.00 0.00 4.57
277 280 1.948104 TAGCCATTCCATACGCACAC 58.052 50.000 0.00 0.00 0.00 3.82
314 329 8.100135 AGGATCTCCTCTCTGTGAAATAATTT 57.900 34.615 0.00 0.00 44.77 1.82
357 372 9.617523 ATTTTTAATTCCACATGATTTGGATCC 57.382 29.630 4.20 4.20 42.88 3.36
358 373 4.924305 AATTCCACATGATTTGGATCCG 57.076 40.909 7.39 0.00 42.88 4.18
359 374 3.643199 TTCCACATGATTTGGATCCGA 57.357 42.857 7.39 1.27 42.88 4.55
360 375 3.862877 TCCACATGATTTGGATCCGAT 57.137 42.857 7.39 3.50 38.28 4.18
361 376 3.743521 TCCACATGATTTGGATCCGATC 58.256 45.455 16.99 16.99 38.28 3.69
362 377 3.392285 TCCACATGATTTGGATCCGATCT 59.608 43.478 21.74 6.83 38.28 2.75
363 378 3.501062 CCACATGATTTGGATCCGATCTG 59.499 47.826 21.74 18.94 36.02 2.90
364 379 3.058432 CACATGATTTGGATCCGATCTGC 60.058 47.826 21.74 6.69 0.00 4.26
365 380 3.181447 ACATGATTTGGATCCGATCTGCT 60.181 43.478 21.74 9.46 0.00 4.24
366 381 3.565764 TGATTTGGATCCGATCTGCTT 57.434 42.857 21.74 0.00 0.00 3.91
367 382 3.208594 TGATTTGGATCCGATCTGCTTG 58.791 45.455 21.74 0.00 0.00 4.01
368 383 2.042686 TTTGGATCCGATCTGCTTGG 57.957 50.000 7.39 0.00 0.00 3.61
369 384 0.181114 TTGGATCCGATCTGCTTGGG 59.819 55.000 7.39 0.00 0.00 4.12
370 385 0.690744 TGGATCCGATCTGCTTGGGA 60.691 55.000 7.39 0.00 0.00 4.37
371 386 0.689623 GGATCCGATCTGCTTGGGAT 59.310 55.000 8.29 0.00 41.83 3.85
372 387 2.091852 GATCCGATCTGCTTGGGATC 57.908 55.000 8.68 8.68 45.69 3.36
373 388 1.727062 ATCCGATCTGCTTGGGATCT 58.273 50.000 0.00 0.00 37.88 2.75
374 389 1.043816 TCCGATCTGCTTGGGATCTC 58.956 55.000 0.00 0.00 37.88 2.75
375 390 0.034616 CCGATCTGCTTGGGATCTCC 59.965 60.000 0.00 0.00 37.88 3.71
376 391 1.047002 CGATCTGCTTGGGATCTCCT 58.953 55.000 0.00 0.00 37.88 3.69
377 392 1.270199 CGATCTGCTTGGGATCTCCTG 60.270 57.143 0.00 0.00 37.88 3.86
378 393 1.767681 GATCTGCTTGGGATCTCCTGT 59.232 52.381 0.00 0.00 37.28 4.00
379 394 2.550277 TCTGCTTGGGATCTCCTGTA 57.450 50.000 0.00 0.00 36.20 2.74
380 395 2.832838 TCTGCTTGGGATCTCCTGTAA 58.167 47.619 0.00 0.00 36.20 2.41
381 396 2.501723 TCTGCTTGGGATCTCCTGTAAC 59.498 50.000 0.00 0.00 36.20 2.50
382 397 2.503356 CTGCTTGGGATCTCCTGTAACT 59.497 50.000 0.00 0.00 36.20 2.24
383 398 2.501723 TGCTTGGGATCTCCTGTAACTC 59.498 50.000 0.00 0.00 36.20 3.01
384 399 2.158885 GCTTGGGATCTCCTGTAACTCC 60.159 54.545 0.00 0.00 36.20 3.85
385 400 3.379452 CTTGGGATCTCCTGTAACTCCT 58.621 50.000 0.00 0.00 36.20 3.69
386 401 2.752030 TGGGATCTCCTGTAACTCCTG 58.248 52.381 0.00 0.00 36.20 3.86
387 402 2.044492 TGGGATCTCCTGTAACTCCTGT 59.956 50.000 0.00 0.00 36.20 4.00
388 403 3.271225 TGGGATCTCCTGTAACTCCTGTA 59.729 47.826 0.00 0.00 36.20 2.74
389 404 3.892588 GGGATCTCCTGTAACTCCTGTAG 59.107 52.174 0.00 0.00 35.95 2.74
390 405 3.319689 GGATCTCCTGTAACTCCTGTAGC 59.680 52.174 0.00 0.00 0.00 3.58
391 406 3.741245 TCTCCTGTAACTCCTGTAGCT 57.259 47.619 0.00 0.00 0.00 3.32
392 407 3.357203 TCTCCTGTAACTCCTGTAGCTG 58.643 50.000 0.00 0.00 0.00 4.24
393 408 3.093057 CTCCTGTAACTCCTGTAGCTGT 58.907 50.000 0.00 0.00 0.00 4.40
394 409 3.090037 TCCTGTAACTCCTGTAGCTGTC 58.910 50.000 0.00 0.00 0.00 3.51
395 410 3.093057 CCTGTAACTCCTGTAGCTGTCT 58.907 50.000 0.00 0.00 0.00 3.41
396 411 3.129638 CCTGTAACTCCTGTAGCTGTCTC 59.870 52.174 0.00 0.00 0.00 3.36
397 412 4.013728 CTGTAACTCCTGTAGCTGTCTCT 58.986 47.826 0.00 0.00 0.00 3.10
398 413 3.759086 TGTAACTCCTGTAGCTGTCTCTG 59.241 47.826 0.00 0.00 0.00 3.35
399 414 1.846007 ACTCCTGTAGCTGTCTCTGG 58.154 55.000 0.00 0.00 0.00 3.86
400 415 1.356059 ACTCCTGTAGCTGTCTCTGGA 59.644 52.381 0.00 2.82 0.00 3.86
401 416 2.023673 CTCCTGTAGCTGTCTCTGGAG 58.976 57.143 15.41 15.41 39.55 3.86
402 417 1.356059 TCCTGTAGCTGTCTCTGGAGT 59.644 52.381 0.00 0.00 0.00 3.85
403 418 2.175202 CCTGTAGCTGTCTCTGGAGTT 58.825 52.381 0.00 0.00 0.00 3.01
404 419 2.094286 CCTGTAGCTGTCTCTGGAGTTG 60.094 54.545 0.00 0.00 0.00 3.16
405 420 2.560542 CTGTAGCTGTCTCTGGAGTTGT 59.439 50.000 0.00 0.00 0.00 3.32
406 421 2.965831 TGTAGCTGTCTCTGGAGTTGTT 59.034 45.455 0.00 0.00 0.00 2.83
407 422 2.540265 AGCTGTCTCTGGAGTTGTTG 57.460 50.000 0.00 0.00 0.00 3.33
408 423 1.071385 AGCTGTCTCTGGAGTTGTTGG 59.929 52.381 0.00 0.00 0.00 3.77
409 424 1.070758 GCTGTCTCTGGAGTTGTTGGA 59.929 52.381 0.00 0.00 0.00 3.53
410 425 2.289945 GCTGTCTCTGGAGTTGTTGGAT 60.290 50.000 0.00 0.00 0.00 3.41
411 426 3.594134 CTGTCTCTGGAGTTGTTGGATC 58.406 50.000 0.00 0.00 0.00 3.36
412 427 3.242867 TGTCTCTGGAGTTGTTGGATCT 58.757 45.455 0.00 0.00 0.00 2.75
413 428 3.259374 TGTCTCTGGAGTTGTTGGATCTC 59.741 47.826 0.00 0.00 0.00 2.75
414 429 2.493675 TCTCTGGAGTTGTTGGATCTCG 59.506 50.000 0.00 0.00 0.00 4.04
415 430 1.066858 TCTGGAGTTGTTGGATCTCGC 60.067 52.381 0.00 0.00 0.00 5.03
416 431 0.389817 TGGAGTTGTTGGATCTCGCG 60.390 55.000 0.00 0.00 0.00 5.87
417 432 1.696832 GGAGTTGTTGGATCTCGCGC 61.697 60.000 0.00 0.00 0.00 6.86
418 433 1.696832 GAGTTGTTGGATCTCGCGCC 61.697 60.000 0.00 0.00 0.00 6.53
419 434 2.813474 TTGTTGGATCTCGCGCCG 60.813 61.111 0.00 0.00 0.00 6.46
425 440 3.264897 GATCTCGCGCCGCACATT 61.265 61.111 10.75 0.00 0.00 2.71
426 441 3.497407 GATCTCGCGCCGCACATTG 62.497 63.158 10.75 0.00 0.00 2.82
432 447 2.355599 CGCCGCACATTGCCAAAA 60.356 55.556 0.00 0.00 41.12 2.44
433 448 1.737371 CGCCGCACATTGCCAAAAT 60.737 52.632 0.00 0.00 41.12 1.82
434 449 1.789116 GCCGCACATTGCCAAAATG 59.211 52.632 0.00 0.00 41.12 2.32
435 450 0.950071 GCCGCACATTGCCAAAATGT 60.950 50.000 0.00 0.00 41.12 2.71
441 456 2.753296 ACATTGCCAAAATGTGTTCGG 58.247 42.857 3.03 0.00 39.22 4.30
442 457 2.102252 ACATTGCCAAAATGTGTTCGGT 59.898 40.909 3.03 0.00 39.22 4.69
443 458 2.500509 TTGCCAAAATGTGTTCGGTC 57.499 45.000 0.00 0.00 0.00 4.79
444 459 0.671251 TGCCAAAATGTGTTCGGTCC 59.329 50.000 0.00 0.00 0.00 4.46
445 460 0.038618 GCCAAAATGTGTTCGGTCCC 60.039 55.000 0.00 0.00 0.00 4.46
446 461 1.323412 CCAAAATGTGTTCGGTCCCA 58.677 50.000 0.00 0.00 0.00 4.37
447 462 1.892474 CCAAAATGTGTTCGGTCCCAT 59.108 47.619 0.00 0.00 0.00 4.00
448 463 2.094752 CCAAAATGTGTTCGGTCCCATC 60.095 50.000 0.00 0.00 0.00 3.51
449 464 1.834188 AAATGTGTTCGGTCCCATCC 58.166 50.000 0.00 0.00 0.00 3.51
459 474 2.447920 TCCCATCCGGACAGGTCA 59.552 61.111 20.22 6.76 41.99 4.02
460 475 1.685765 TCCCATCCGGACAGGTCAG 60.686 63.158 20.22 8.19 41.99 3.51
461 476 1.685765 CCCATCCGGACAGGTCAGA 60.686 63.158 20.22 0.00 41.99 3.27
462 477 1.050988 CCCATCCGGACAGGTCAGAT 61.051 60.000 20.22 0.60 41.99 2.90
463 478 0.105593 CCATCCGGACAGGTCAGATG 59.894 60.000 6.12 17.85 41.99 2.90
464 479 1.114627 CATCCGGACAGGTCAGATGA 58.885 55.000 6.12 4.21 40.97 2.92
465 480 1.482182 CATCCGGACAGGTCAGATGAA 59.518 52.381 6.12 0.00 40.97 2.57
466 481 1.639722 TCCGGACAGGTCAGATGAAA 58.360 50.000 0.00 0.00 41.99 2.69
467 482 1.550524 TCCGGACAGGTCAGATGAAAG 59.449 52.381 0.00 0.00 41.99 2.62
468 483 1.363744 CGGACAGGTCAGATGAAAGC 58.636 55.000 1.41 0.00 0.00 3.51
469 484 1.363744 GGACAGGTCAGATGAAAGCG 58.636 55.000 1.41 0.00 0.00 4.68
470 485 1.066858 GGACAGGTCAGATGAAAGCGA 60.067 52.381 1.41 0.00 0.00 4.93
471 486 1.996191 GACAGGTCAGATGAAAGCGAC 59.004 52.381 0.00 0.00 0.00 5.19
472 487 1.338200 ACAGGTCAGATGAAAGCGACC 60.338 52.381 0.00 0.00 43.02 4.79
473 488 0.108615 AGGTCAGATGAAAGCGACCG 60.109 55.000 0.00 0.00 45.69 4.79
474 489 1.084370 GGTCAGATGAAAGCGACCGG 61.084 60.000 0.00 0.00 36.54 5.28
475 490 0.108804 GTCAGATGAAAGCGACCGGA 60.109 55.000 9.46 0.00 0.00 5.14
476 491 0.173481 TCAGATGAAAGCGACCGGAG 59.827 55.000 9.46 2.13 0.00 4.63
477 492 1.153549 AGATGAAAGCGACCGGAGC 60.154 57.895 9.46 14.12 0.00 4.70
504 519 3.742433 CTTATGGAGCTCACCGAATCT 57.258 47.619 17.19 0.00 0.00 2.40
505 520 3.648009 CTTATGGAGCTCACCGAATCTC 58.352 50.000 17.19 0.00 0.00 2.75
506 521 0.755686 ATGGAGCTCACCGAATCTCC 59.244 55.000 17.19 0.00 44.04 3.71
507 522 1.330655 TGGAGCTCACCGAATCTCCC 61.331 60.000 17.19 0.00 43.33 4.30
508 523 1.066587 GAGCTCACCGAATCTCCCG 59.933 63.158 9.40 0.00 0.00 5.14
509 524 2.586357 GCTCACCGAATCTCCCGC 60.586 66.667 0.00 0.00 0.00 6.13
510 525 3.082579 GCTCACCGAATCTCCCGCT 62.083 63.158 0.00 0.00 0.00 5.52
511 526 1.066587 CTCACCGAATCTCCCGCTC 59.933 63.158 0.00 0.00 0.00 5.03
512 527 2.107141 CACCGAATCTCCCGCTCC 59.893 66.667 0.00 0.00 0.00 4.70
513 528 2.363795 ACCGAATCTCCCGCTCCA 60.364 61.111 0.00 0.00 0.00 3.86
514 529 2.107141 CCGAATCTCCCGCTCCAC 59.893 66.667 0.00 0.00 0.00 4.02
515 530 2.427245 CCGAATCTCCCGCTCCACT 61.427 63.158 0.00 0.00 0.00 4.00
516 531 1.066587 CGAATCTCCCGCTCCACTC 59.933 63.158 0.00 0.00 0.00 3.51
517 532 1.667154 CGAATCTCCCGCTCCACTCA 61.667 60.000 0.00 0.00 0.00 3.41
518 533 0.179097 GAATCTCCCGCTCCACTCAC 60.179 60.000 0.00 0.00 0.00 3.51
519 534 1.617947 AATCTCCCGCTCCACTCACC 61.618 60.000 0.00 0.00 0.00 4.02
520 535 3.775654 CTCCCGCTCCACTCACCC 61.776 72.222 0.00 0.00 0.00 4.61
521 536 4.631740 TCCCGCTCCACTCACCCA 62.632 66.667 0.00 0.00 0.00 4.51
522 537 3.402681 CCCGCTCCACTCACCCAT 61.403 66.667 0.00 0.00 0.00 4.00
523 538 2.124983 CCGCTCCACTCACCCATG 60.125 66.667 0.00 0.00 0.00 3.66
524 539 2.821366 CGCTCCACTCACCCATGC 60.821 66.667 0.00 0.00 0.00 4.06
525 540 2.673523 GCTCCACTCACCCATGCT 59.326 61.111 0.00 0.00 0.00 3.79
526 541 1.748122 GCTCCACTCACCCATGCTG 60.748 63.158 0.00 0.00 0.00 4.41
527 542 1.985614 CTCCACTCACCCATGCTGA 59.014 57.895 0.00 0.00 0.00 4.26
528 543 0.545171 CTCCACTCACCCATGCTGAT 59.455 55.000 0.00 0.00 0.00 2.90
529 544 0.994247 TCCACTCACCCATGCTGATT 59.006 50.000 0.00 0.00 0.00 2.57
530 545 1.100510 CCACTCACCCATGCTGATTG 58.899 55.000 0.00 0.00 0.00 2.67
531 546 0.454600 CACTCACCCATGCTGATTGC 59.545 55.000 0.00 0.00 43.25 3.56
541 556 2.260247 GCTGATTGCAACAGAGGCA 58.740 52.632 24.19 7.99 42.31 4.75
542 557 0.109412 GCTGATTGCAACAGAGGCAC 60.109 55.000 24.19 9.25 41.75 5.01
543 558 0.524862 CTGATTGCAACAGAGGCACC 59.475 55.000 18.50 0.00 41.75 5.01
544 559 0.178995 TGATTGCAACAGAGGCACCA 60.179 50.000 0.00 0.00 41.75 4.17
545 560 0.524862 GATTGCAACAGAGGCACCAG 59.475 55.000 0.00 0.00 41.75 4.00
546 561 0.111061 ATTGCAACAGAGGCACCAGA 59.889 50.000 0.00 0.00 41.75 3.86
547 562 0.819259 TTGCAACAGAGGCACCAGAC 60.819 55.000 0.00 0.00 41.75 3.51
548 563 1.968540 GCAACAGAGGCACCAGACC 60.969 63.158 0.00 0.00 0.00 3.85
549 564 1.669115 CAACAGAGGCACCAGACCG 60.669 63.158 0.00 0.00 0.00 4.79
550 565 2.883828 AACAGAGGCACCAGACCGG 61.884 63.158 0.00 0.00 42.50 5.28
551 566 4.087892 CAGAGGCACCAGACCGGG 62.088 72.222 6.32 0.00 40.22 5.73
558 573 4.265507 ACCAGACCGGGGTCCCTT 62.266 66.667 14.08 0.00 45.59 3.95
559 574 2.933834 CCAGACCGGGGTCCCTTT 60.934 66.667 14.08 0.00 45.59 3.11
560 575 2.669240 CAGACCGGGGTCCCTTTC 59.331 66.667 14.08 1.84 45.59 2.62
561 576 2.609921 AGACCGGGGTCCCTTTCC 60.610 66.667 14.08 0.00 45.59 3.13
562 577 3.725032 GACCGGGGTCCCTTTCCC 61.725 72.222 6.32 0.00 43.90 3.97
563 578 4.603097 ACCGGGGTCCCTTTCCCA 62.603 66.667 6.32 0.00 46.26 4.37
564 579 3.021263 CCGGGGTCCCTTTCCCAT 61.021 66.667 8.15 0.00 46.26 4.00
565 580 2.275418 CGGGGTCCCTTTCCCATG 59.725 66.667 8.15 0.00 46.26 3.66
566 581 2.042944 GGGGTCCCTTTCCCATGC 60.043 66.667 8.15 0.00 46.26 4.06
567 582 2.042944 GGGTCCCTTTCCCATGCC 60.043 66.667 0.00 0.00 44.05 4.40
568 583 2.770130 GGTCCCTTTCCCATGCCA 59.230 61.111 0.00 0.00 0.00 4.92
569 584 1.078347 GGTCCCTTTCCCATGCCAA 59.922 57.895 0.00 0.00 0.00 4.52
570 585 0.325577 GGTCCCTTTCCCATGCCAAT 60.326 55.000 0.00 0.00 0.00 3.16
571 586 1.571955 GTCCCTTTCCCATGCCAATT 58.428 50.000 0.00 0.00 0.00 2.32
572 587 1.482182 GTCCCTTTCCCATGCCAATTC 59.518 52.381 0.00 0.00 0.00 2.17
573 588 1.078490 TCCCTTTCCCATGCCAATTCA 59.922 47.619 0.00 0.00 0.00 2.57
574 589 2.121129 CCCTTTCCCATGCCAATTCAT 58.879 47.619 0.00 0.00 0.00 2.57
575 590 3.052262 TCCCTTTCCCATGCCAATTCATA 60.052 43.478 0.00 0.00 0.00 2.15
576 591 3.905591 CCCTTTCCCATGCCAATTCATAT 59.094 43.478 0.00 0.00 0.00 1.78
577 592 4.348754 CCCTTTCCCATGCCAATTCATATT 59.651 41.667 0.00 0.00 0.00 1.28
578 593 5.163174 CCCTTTCCCATGCCAATTCATATTT 60.163 40.000 0.00 0.00 0.00 1.40
579 594 6.043012 CCCTTTCCCATGCCAATTCATATTTA 59.957 38.462 0.00 0.00 0.00 1.40
580 595 7.419981 CCCTTTCCCATGCCAATTCATATTTAA 60.420 37.037 0.00 0.00 0.00 1.52
581 596 7.992033 CCTTTCCCATGCCAATTCATATTTAAA 59.008 33.333 0.00 0.00 0.00 1.52
582 597 9.393512 CTTTCCCATGCCAATTCATATTTAAAA 57.606 29.630 0.00 0.00 0.00 1.52
583 598 8.961294 TTCCCATGCCAATTCATATTTAAAAG 57.039 30.769 0.00 0.00 0.00 2.27
584 599 7.507829 TCCCATGCCAATTCATATTTAAAAGG 58.492 34.615 0.00 0.00 0.00 3.11
585 600 7.346698 TCCCATGCCAATTCATATTTAAAAGGA 59.653 33.333 0.00 0.00 0.00 3.36
586 601 7.992033 CCCATGCCAATTCATATTTAAAAGGAA 59.008 33.333 0.00 0.00 0.00 3.36
587 602 8.829612 CCATGCCAATTCATATTTAAAAGGAAC 58.170 33.333 0.00 0.00 0.00 3.62
588 603 8.542132 CATGCCAATTCATATTTAAAAGGAACG 58.458 33.333 0.00 0.00 0.00 3.95
589 604 6.533367 TGCCAATTCATATTTAAAAGGAACGC 59.467 34.615 0.00 1.53 0.00 4.84
590 605 6.291585 GCCAATTCATATTTAAAAGGAACGCG 60.292 38.462 3.53 3.53 0.00 6.01
591 606 6.198216 CCAATTCATATTTAAAAGGAACGCGG 59.802 38.462 12.47 0.00 0.00 6.46
592 607 4.886247 TCATATTTAAAAGGAACGCGGG 57.114 40.909 12.47 0.00 0.00 6.13
593 608 3.628487 TCATATTTAAAAGGAACGCGGGG 59.372 43.478 12.47 0.00 0.00 5.73
594 609 0.528924 ATTTAAAAGGAACGCGGGGC 59.471 50.000 12.47 0.00 0.00 5.80
595 610 1.525718 TTTAAAAGGAACGCGGGGCC 61.526 55.000 12.47 8.71 0.00 5.80
596 611 3.923782 TAAAAGGAACGCGGGGCCC 62.924 63.158 15.76 15.76 0.00 5.80
611 626 3.376078 CCCGCTTGCATGCAACCT 61.376 61.111 28.80 0.00 0.00 3.50
612 627 2.180017 CCGCTTGCATGCAACCTC 59.820 61.111 28.80 18.32 0.00 3.85
613 628 2.628696 CCGCTTGCATGCAACCTCA 61.629 57.895 28.80 9.03 0.00 3.86
614 629 1.509463 CGCTTGCATGCAACCTCAT 59.491 52.632 28.80 0.00 0.00 2.90
615 630 0.800683 CGCTTGCATGCAACCTCATG 60.801 55.000 28.80 18.46 44.93 3.07
623 638 2.840974 GCAACCTCATGCACGTACT 58.159 52.632 0.00 0.00 45.70 2.73
624 639 0.443869 GCAACCTCATGCACGTACTG 59.556 55.000 0.00 0.00 45.70 2.74
625 640 3.439241 GCAACCTCATGCACGTACTGC 62.439 57.143 9.52 9.52 45.70 4.40
647 662 5.890110 CACGTACAGTGGAATATGATCAC 57.110 43.478 0.00 0.00 46.77 3.06
648 663 5.592054 CACGTACAGTGGAATATGATCACT 58.408 41.667 0.00 0.00 46.77 3.41
649 664 6.042777 CACGTACAGTGGAATATGATCACTT 58.957 40.000 0.00 0.00 46.77 3.16
650 665 6.019559 CACGTACAGTGGAATATGATCACTTG 60.020 42.308 0.00 0.00 46.77 3.16
651 666 6.042777 CGTACAGTGGAATATGATCACTTGT 58.957 40.000 0.00 0.00 39.43 3.16
652 667 6.535150 CGTACAGTGGAATATGATCACTTGTT 59.465 38.462 0.00 0.00 39.43 2.83
653 668 6.748333 ACAGTGGAATATGATCACTTGTTG 57.252 37.500 0.00 0.00 39.43 3.33
654 669 5.124457 ACAGTGGAATATGATCACTTGTTGC 59.876 40.000 0.00 0.00 39.43 4.17
658 673 4.516698 GGAATATGATCACTTGTTGCCGAT 59.483 41.667 0.00 0.00 0.00 4.18
696 711 2.282816 CATTTGGGGCGGTGGTGA 60.283 61.111 0.00 0.00 0.00 4.02
811 827 2.668632 GATGGAACTGACCGCCCA 59.331 61.111 0.00 0.00 0.00 5.36
940 959 2.038007 TGCCTTCCTCCTCGCTCT 59.962 61.111 0.00 0.00 0.00 4.09
951 970 2.436115 TCGCTCTTCTCTCGCCGA 60.436 61.111 0.00 0.00 0.00 5.54
958 977 1.924320 CTTCTCTCGCCGACCTCGTT 61.924 60.000 0.00 0.00 37.74 3.85
1052 1072 3.566853 CAGCCTGCCGTACATGCG 61.567 66.667 0.00 0.00 43.93 4.73
1246 1333 1.075659 GGGGCTTGAGCTGGAAACT 59.924 57.895 0.00 0.00 41.70 2.66
1910 2008 6.436218 TCTCAATTACCAGTGTAGCTTAGTGA 59.564 38.462 0.00 0.00 0.00 3.41
2312 2507 4.976864 TGCAGTCTGCCATTACATATCAT 58.023 39.130 21.99 0.00 44.23 2.45
2443 2638 1.565305 GCTCAAGCTACAGTCATCCG 58.435 55.000 0.00 0.00 38.21 4.18
2520 2715 4.644234 TGAACTTGGAGTTGAAGAATGCAA 59.356 37.500 0.00 0.00 38.80 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.752054 TAAACGCCCCGTATACCCAG 59.248 55.000 0.00 0.00 39.99 4.45
7 8 5.229423 TGACATATTAAACGCCCCGTATAC 58.771 41.667 0.00 0.00 39.99 1.47
18 19 7.220683 ACGCAAAGCATGAATGACATATTAAAC 59.779 33.333 0.00 0.00 37.46 2.01
24 25 3.688673 TCACGCAAAGCATGAATGACATA 59.311 39.130 0.00 0.00 37.46 2.29
27 28 2.095567 AGTCACGCAAAGCATGAATGAC 60.096 45.455 0.00 13.84 41.89 3.06
36 37 0.657368 CGACCAAAGTCACGCAAAGC 60.657 55.000 0.00 0.00 43.73 3.51
67 68 0.179048 CAAGATATGGCGCAGGTCCA 60.179 55.000 10.83 0.00 38.09 4.02
81 82 2.304180 CACAACAGAGGGAGTCCAAGAT 59.696 50.000 12.30 0.00 34.83 2.40
98 99 8.506437 CATCTTTTTATCAGAAGCTGTACACAA 58.494 33.333 0.00 0.00 32.61 3.33
107 108 6.500684 TGACCACATCTTTTTATCAGAAGC 57.499 37.500 0.00 0.00 0.00 3.86
110 111 6.240894 AGCTTGACCACATCTTTTTATCAGA 58.759 36.000 0.00 0.00 0.00 3.27
146 147 4.406456 TGGTCAGGCAACAGAAAATGTAT 58.594 39.130 0.00 0.00 43.00 2.29
147 148 3.826524 TGGTCAGGCAACAGAAAATGTA 58.173 40.909 0.00 0.00 43.00 2.29
183 184 7.283127 CGGAGGAGGAAAAATCAGATAAAATCA 59.717 37.037 0.00 0.00 0.00 2.57
214 215 0.185416 TTTTTCCACCTACGGGCCAA 59.815 50.000 4.39 0.00 35.63 4.52
216 217 4.826248 TTTTTCCACCTACGGGCC 57.174 55.556 0.00 0.00 35.63 5.80
239 242 1.663695 AATGCACGGGGATAAGAACG 58.336 50.000 0.00 0.00 0.00 3.95
273 276 2.620112 CCTTTGGAGGCAGCGTGTG 61.620 63.158 0.00 0.00 35.94 3.82
274 277 2.129555 ATCCTTTGGAGGCAGCGTGT 62.130 55.000 0.00 0.00 43.21 4.49
275 278 1.372087 GATCCTTTGGAGGCAGCGTG 61.372 60.000 0.00 0.00 43.21 5.34
276 279 1.078143 GATCCTTTGGAGGCAGCGT 60.078 57.895 0.00 0.00 43.21 5.07
277 280 0.813210 GAGATCCTTTGGAGGCAGCG 60.813 60.000 0.00 0.00 43.21 5.18
278 281 0.465278 GGAGATCCTTTGGAGGCAGC 60.465 60.000 0.00 0.00 43.21 5.25
341 356 3.501062 CAGATCGGATCCAAATCATGTGG 59.499 47.826 20.67 0.00 37.51 4.17
342 357 3.058432 GCAGATCGGATCCAAATCATGTG 60.058 47.826 20.67 13.64 33.21 3.21
343 358 3.144506 GCAGATCGGATCCAAATCATGT 58.855 45.455 20.67 3.65 33.21 3.21
344 359 3.409570 AGCAGATCGGATCCAAATCATG 58.590 45.455 20.67 16.67 33.21 3.07
345 360 3.784511 AGCAGATCGGATCCAAATCAT 57.215 42.857 20.67 8.13 33.21 2.45
346 361 3.208594 CAAGCAGATCGGATCCAAATCA 58.791 45.455 20.67 0.00 33.21 2.57
347 362 2.551459 CCAAGCAGATCGGATCCAAATC 59.449 50.000 13.41 13.66 0.00 2.17
348 363 2.579873 CCAAGCAGATCGGATCCAAAT 58.420 47.619 13.41 4.27 0.00 2.32
349 364 1.408683 CCCAAGCAGATCGGATCCAAA 60.409 52.381 13.41 0.00 0.00 3.28
350 365 0.181114 CCCAAGCAGATCGGATCCAA 59.819 55.000 13.41 0.00 0.00 3.53
351 366 0.690744 TCCCAAGCAGATCGGATCCA 60.691 55.000 13.41 0.00 0.00 3.41
352 367 0.689623 ATCCCAAGCAGATCGGATCC 59.310 55.000 14.19 0.00 28.64 3.36
353 368 2.091852 GATCCCAAGCAGATCGGATC 57.908 55.000 10.02 10.02 42.91 3.36
354 369 1.622811 GAGATCCCAAGCAGATCGGAT 59.377 52.381 0.00 0.00 44.02 4.18
355 370 1.043816 GAGATCCCAAGCAGATCGGA 58.956 55.000 0.00 0.00 44.02 4.55
356 371 0.034616 GGAGATCCCAAGCAGATCGG 59.965 60.000 0.00 0.00 44.02 4.18
357 372 1.047002 AGGAGATCCCAAGCAGATCG 58.953 55.000 0.00 0.00 44.02 3.69
358 373 1.767681 ACAGGAGATCCCAAGCAGATC 59.232 52.381 0.00 0.00 40.42 2.75
359 374 1.890552 ACAGGAGATCCCAAGCAGAT 58.109 50.000 0.00 0.00 37.41 2.90
360 375 2.501723 GTTACAGGAGATCCCAAGCAGA 59.498 50.000 0.00 0.00 37.41 4.26
361 376 2.503356 AGTTACAGGAGATCCCAAGCAG 59.497 50.000 0.00 0.00 37.41 4.24
362 377 2.501723 GAGTTACAGGAGATCCCAAGCA 59.498 50.000 0.00 0.00 37.41 3.91
363 378 2.158885 GGAGTTACAGGAGATCCCAAGC 60.159 54.545 0.00 0.00 37.41 4.01
364 379 3.133721 CAGGAGTTACAGGAGATCCCAAG 59.866 52.174 0.00 0.00 37.41 3.61
365 380 3.107601 CAGGAGTTACAGGAGATCCCAA 58.892 50.000 0.00 0.00 37.41 4.12
366 381 2.044492 ACAGGAGTTACAGGAGATCCCA 59.956 50.000 0.00 0.00 37.41 4.37
367 382 2.753247 ACAGGAGTTACAGGAGATCCC 58.247 52.381 0.00 0.00 36.42 3.85
368 383 3.319689 GCTACAGGAGTTACAGGAGATCC 59.680 52.174 0.00 0.00 0.00 3.36
369 384 4.037446 CAGCTACAGGAGTTACAGGAGATC 59.963 50.000 0.00 0.00 0.00 2.75
370 385 3.957497 CAGCTACAGGAGTTACAGGAGAT 59.043 47.826 0.00 0.00 0.00 2.75
371 386 3.245300 ACAGCTACAGGAGTTACAGGAGA 60.245 47.826 0.00 0.00 0.00 3.71
372 387 3.093057 ACAGCTACAGGAGTTACAGGAG 58.907 50.000 0.00 0.00 0.00 3.69
373 388 3.090037 GACAGCTACAGGAGTTACAGGA 58.910 50.000 0.00 0.00 0.00 3.86
374 389 3.093057 AGACAGCTACAGGAGTTACAGG 58.907 50.000 0.00 0.00 0.00 4.00
375 390 4.013728 AGAGACAGCTACAGGAGTTACAG 58.986 47.826 0.00 0.00 0.00 2.74
376 391 3.759086 CAGAGACAGCTACAGGAGTTACA 59.241 47.826 0.00 0.00 0.00 2.41
377 392 3.129638 CCAGAGACAGCTACAGGAGTTAC 59.870 52.174 0.00 0.00 0.00 2.50
378 393 3.010250 TCCAGAGACAGCTACAGGAGTTA 59.990 47.826 0.00 0.00 0.00 2.24
379 394 2.175202 CCAGAGACAGCTACAGGAGTT 58.825 52.381 0.00 0.00 0.00 3.01
380 395 1.356059 TCCAGAGACAGCTACAGGAGT 59.644 52.381 0.00 0.00 0.00 3.85
381 396 2.023673 CTCCAGAGACAGCTACAGGAG 58.976 57.143 0.00 0.00 33.21 3.69
382 397 1.356059 ACTCCAGAGACAGCTACAGGA 59.644 52.381 0.70 0.00 0.00 3.86
383 398 1.846007 ACTCCAGAGACAGCTACAGG 58.154 55.000 0.70 0.00 0.00 4.00
384 399 2.560542 ACAACTCCAGAGACAGCTACAG 59.439 50.000 0.70 0.00 0.00 2.74
385 400 2.598565 ACAACTCCAGAGACAGCTACA 58.401 47.619 0.70 0.00 0.00 2.74
386 401 3.321497 CAACAACTCCAGAGACAGCTAC 58.679 50.000 0.70 0.00 0.00 3.58
387 402 2.300152 CCAACAACTCCAGAGACAGCTA 59.700 50.000 0.70 0.00 0.00 3.32
388 403 1.071385 CCAACAACTCCAGAGACAGCT 59.929 52.381 0.70 0.00 0.00 4.24
389 404 1.070758 TCCAACAACTCCAGAGACAGC 59.929 52.381 0.70 0.00 0.00 4.40
390 405 3.260380 AGATCCAACAACTCCAGAGACAG 59.740 47.826 0.70 0.00 0.00 3.51
391 406 3.242867 AGATCCAACAACTCCAGAGACA 58.757 45.455 0.70 0.00 0.00 3.41
392 407 3.674682 CGAGATCCAACAACTCCAGAGAC 60.675 52.174 0.70 0.00 0.00 3.36
393 408 2.493675 CGAGATCCAACAACTCCAGAGA 59.506 50.000 0.70 0.00 0.00 3.10
394 409 2.886081 CGAGATCCAACAACTCCAGAG 58.114 52.381 0.00 0.00 0.00 3.35
395 410 1.066858 GCGAGATCCAACAACTCCAGA 60.067 52.381 0.00 0.00 0.00 3.86
396 411 1.363744 GCGAGATCCAACAACTCCAG 58.636 55.000 0.00 0.00 0.00 3.86
397 412 0.389817 CGCGAGATCCAACAACTCCA 60.390 55.000 0.00 0.00 0.00 3.86
398 413 1.696832 GCGCGAGATCCAACAACTCC 61.697 60.000 12.10 0.00 0.00 3.85
399 414 1.696832 GGCGCGAGATCCAACAACTC 61.697 60.000 12.10 0.00 0.00 3.01
400 415 1.741770 GGCGCGAGATCCAACAACT 60.742 57.895 12.10 0.00 0.00 3.16
401 416 2.785258 GGCGCGAGATCCAACAAC 59.215 61.111 12.10 0.00 0.00 3.32
402 417 2.813474 CGGCGCGAGATCCAACAA 60.813 61.111 12.10 0.00 0.00 2.83
408 423 3.264897 AATGTGCGGCGCGAGATC 61.265 61.111 28.09 14.59 0.00 2.75
409 424 3.566853 CAATGTGCGGCGCGAGAT 61.567 61.111 28.09 16.69 0.00 2.75
415 430 1.737371 ATTTTGGCAATGTGCGGCG 60.737 52.632 0.51 0.51 46.21 6.46
416 431 0.950071 ACATTTTGGCAATGTGCGGC 60.950 50.000 0.00 0.00 46.21 6.53
417 432 3.214045 ACATTTTGGCAATGTGCGG 57.786 47.368 0.00 0.00 46.21 5.69
421 436 2.102252 ACCGAACACATTTTGGCAATGT 59.898 40.909 0.00 0.00 41.18 2.71
422 437 2.730928 GACCGAACACATTTTGGCAATG 59.269 45.455 0.00 0.00 0.00 2.82
423 438 2.288763 GGACCGAACACATTTTGGCAAT 60.289 45.455 0.00 0.00 0.00 3.56
424 439 1.067821 GGACCGAACACATTTTGGCAA 59.932 47.619 0.00 0.00 0.00 4.52
425 440 0.671251 GGACCGAACACATTTTGGCA 59.329 50.000 0.00 0.00 0.00 4.92
426 441 0.038618 GGGACCGAACACATTTTGGC 60.039 55.000 0.00 0.00 0.00 4.52
427 442 1.323412 TGGGACCGAACACATTTTGG 58.677 50.000 0.00 0.00 0.00 3.28
428 443 2.094752 GGATGGGACCGAACACATTTTG 60.095 50.000 0.00 0.00 33.77 2.44
429 444 2.167662 GGATGGGACCGAACACATTTT 58.832 47.619 0.00 0.00 33.77 1.82
430 445 1.834188 GGATGGGACCGAACACATTT 58.166 50.000 0.00 0.00 33.77 2.32
431 446 3.569873 GGATGGGACCGAACACATT 57.430 52.632 0.00 0.00 33.77 2.71
442 457 1.685765 CTGACCTGTCCGGATGGGA 60.686 63.158 25.80 13.67 44.68 4.37
443 458 1.050988 ATCTGACCTGTCCGGATGGG 61.051 60.000 24.30 22.13 36.31 4.00
444 459 0.105593 CATCTGACCTGTCCGGATGG 59.894 60.000 20.62 20.62 36.32 3.51
445 460 1.114627 TCATCTGACCTGTCCGGATG 58.885 55.000 7.81 16.99 38.71 3.51
446 461 1.866015 TTCATCTGACCTGTCCGGAT 58.134 50.000 7.81 0.00 36.31 4.18
447 462 1.550524 CTTTCATCTGACCTGTCCGGA 59.449 52.381 0.00 0.00 36.31 5.14
448 463 2.009042 GCTTTCATCTGACCTGTCCGG 61.009 57.143 0.00 0.00 39.35 5.14
449 464 1.363744 GCTTTCATCTGACCTGTCCG 58.636 55.000 0.00 0.00 0.00 4.79
450 465 1.066858 TCGCTTTCATCTGACCTGTCC 60.067 52.381 0.00 0.00 0.00 4.02
451 466 1.996191 GTCGCTTTCATCTGACCTGTC 59.004 52.381 0.00 0.00 0.00 3.51
452 467 1.338200 GGTCGCTTTCATCTGACCTGT 60.338 52.381 3.09 0.00 45.86 4.00
453 468 1.363744 GGTCGCTTTCATCTGACCTG 58.636 55.000 3.09 0.00 45.86 4.00
454 469 0.108615 CGGTCGCTTTCATCTGACCT 60.109 55.000 8.44 0.00 46.88 3.85
455 470 1.084370 CCGGTCGCTTTCATCTGACC 61.084 60.000 0.00 0.18 45.87 4.02
456 471 0.108804 TCCGGTCGCTTTCATCTGAC 60.109 55.000 0.00 0.00 0.00 3.51
457 472 0.173481 CTCCGGTCGCTTTCATCTGA 59.827 55.000 0.00 0.00 0.00 3.27
458 473 1.424493 GCTCCGGTCGCTTTCATCTG 61.424 60.000 0.00 0.00 0.00 2.90
459 474 1.153549 GCTCCGGTCGCTTTCATCT 60.154 57.895 0.00 0.00 0.00 2.90
460 475 0.741221 AAGCTCCGGTCGCTTTCATC 60.741 55.000 22.15 0.00 44.76 2.92
461 476 1.021390 CAAGCTCCGGTCGCTTTCAT 61.021 55.000 24.27 7.55 44.76 2.57
462 477 1.667830 CAAGCTCCGGTCGCTTTCA 60.668 57.895 24.27 0.00 44.76 2.69
463 478 1.627550 GACAAGCTCCGGTCGCTTTC 61.628 60.000 24.27 20.35 44.76 2.62
464 479 1.668151 GACAAGCTCCGGTCGCTTT 60.668 57.895 24.27 17.50 44.76 3.51
484 499 3.553922 GGAGATTCGGTGAGCTCCATAAG 60.554 52.174 12.15 0.00 44.91 1.73
485 500 2.365617 GGAGATTCGGTGAGCTCCATAA 59.634 50.000 12.15 0.69 44.91 1.90
486 501 1.964223 GGAGATTCGGTGAGCTCCATA 59.036 52.381 12.15 0.00 44.91 2.74
487 502 0.755686 GGAGATTCGGTGAGCTCCAT 59.244 55.000 12.15 0.00 44.91 3.41
488 503 1.330655 GGGAGATTCGGTGAGCTCCA 61.331 60.000 12.15 0.00 46.84 3.86
489 504 1.443828 GGGAGATTCGGTGAGCTCC 59.556 63.158 12.15 9.28 44.84 4.70
490 505 1.066587 CGGGAGATTCGGTGAGCTC 59.933 63.158 6.82 6.82 0.00 4.09
491 506 3.082579 GCGGGAGATTCGGTGAGCT 62.083 63.158 0.00 0.00 0.00 4.09
492 507 2.586357 GCGGGAGATTCGGTGAGC 60.586 66.667 0.00 0.00 0.00 4.26
493 508 1.066587 GAGCGGGAGATTCGGTGAG 59.933 63.158 0.00 0.00 38.50 3.51
494 509 2.423898 GGAGCGGGAGATTCGGTGA 61.424 63.158 0.00 0.00 38.50 4.02
495 510 2.107141 GGAGCGGGAGATTCGGTG 59.893 66.667 0.00 0.00 38.50 4.94
496 511 2.363795 TGGAGCGGGAGATTCGGT 60.364 61.111 0.00 0.00 41.19 4.69
497 512 2.107141 GTGGAGCGGGAGATTCGG 59.893 66.667 0.00 0.00 0.00 4.30
498 513 1.066587 GAGTGGAGCGGGAGATTCG 59.933 63.158 0.00 0.00 0.00 3.34
499 514 0.179097 GTGAGTGGAGCGGGAGATTC 60.179 60.000 0.00 0.00 0.00 2.52
500 515 1.617947 GGTGAGTGGAGCGGGAGATT 61.618 60.000 0.00 0.00 0.00 2.40
501 516 2.060980 GGTGAGTGGAGCGGGAGAT 61.061 63.158 0.00 0.00 0.00 2.75
502 517 2.680352 GGTGAGTGGAGCGGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
503 518 3.775654 GGGTGAGTGGAGCGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
504 519 3.924013 ATGGGTGAGTGGAGCGGGA 62.924 63.158 0.00 0.00 0.00 5.14
505 520 3.402681 ATGGGTGAGTGGAGCGGG 61.403 66.667 0.00 0.00 0.00 6.13
506 521 2.124983 CATGGGTGAGTGGAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
507 522 2.821366 GCATGGGTGAGTGGAGCG 60.821 66.667 0.00 0.00 0.00 5.03
508 523 1.748122 CAGCATGGGTGAGTGGAGC 60.748 63.158 0.00 0.00 32.22 4.70
509 524 0.545171 ATCAGCATGGGTGAGTGGAG 59.455 55.000 4.38 0.00 43.30 3.86
510 525 0.994247 AATCAGCATGGGTGAGTGGA 59.006 50.000 4.38 0.00 43.30 4.02
511 526 3.583054 AATCAGCATGGGTGAGTGG 57.417 52.632 4.38 0.00 43.30 4.00
513 528 2.877975 GCAATCAGCATGGGTGAGT 58.122 52.632 4.38 0.00 43.30 3.41
523 538 0.109412 GTGCCTCTGTTGCAATCAGC 60.109 55.000 18.50 11.63 41.06 4.26
524 539 0.524862 GGTGCCTCTGTTGCAATCAG 59.475 55.000 17.67 17.67 41.06 2.90
525 540 0.178995 TGGTGCCTCTGTTGCAATCA 60.179 50.000 0.59 1.80 41.06 2.57
526 541 0.524862 CTGGTGCCTCTGTTGCAATC 59.475 55.000 0.59 0.00 41.06 2.67
527 542 0.111061 TCTGGTGCCTCTGTTGCAAT 59.889 50.000 0.59 0.00 41.06 3.56
528 543 0.819259 GTCTGGTGCCTCTGTTGCAA 60.819 55.000 0.00 0.00 41.06 4.08
529 544 1.227943 GTCTGGTGCCTCTGTTGCA 60.228 57.895 0.00 0.00 36.12 4.08
530 545 1.968540 GGTCTGGTGCCTCTGTTGC 60.969 63.158 0.00 0.00 0.00 4.17
531 546 1.669115 CGGTCTGGTGCCTCTGTTG 60.669 63.158 0.00 0.00 0.00 3.33
532 547 2.743718 CGGTCTGGTGCCTCTGTT 59.256 61.111 0.00 0.00 0.00 3.16
533 548 3.314331 CCGGTCTGGTGCCTCTGT 61.314 66.667 0.00 0.00 0.00 3.41
534 549 4.087892 CCCGGTCTGGTGCCTCTG 62.088 72.222 0.00 0.00 35.15 3.35
541 556 3.805151 AAAGGGACCCCGGTCTGGT 62.805 63.158 7.00 0.00 44.04 4.00
542 557 2.933834 AAAGGGACCCCGGTCTGG 60.934 66.667 7.00 0.00 44.04 3.86
543 558 2.669240 GAAAGGGACCCCGGTCTG 59.331 66.667 7.00 0.00 44.04 3.51
544 559 2.609921 GGAAAGGGACCCCGGTCT 60.610 66.667 7.00 0.00 44.04 3.85
545 560 3.725032 GGGAAAGGGACCCCGGTC 61.725 72.222 7.00 5.23 41.38 4.79
546 561 3.902927 ATGGGAAAGGGACCCCGGT 62.903 63.158 7.00 0.00 46.21 5.28
547 562 3.021263 ATGGGAAAGGGACCCCGG 61.021 66.667 7.00 0.00 46.21 5.73
548 563 2.275418 CATGGGAAAGGGACCCCG 59.725 66.667 7.00 0.00 46.21 5.73
549 564 2.042944 GCATGGGAAAGGGACCCC 60.043 66.667 7.00 1.17 46.21 4.95
550 565 2.042944 GGCATGGGAAAGGGACCC 60.043 66.667 0.59 0.59 46.87 4.46
551 566 0.325577 ATTGGCATGGGAAAGGGACC 60.326 55.000 0.00 0.00 0.00 4.46
552 567 1.482182 GAATTGGCATGGGAAAGGGAC 59.518 52.381 0.00 0.00 0.00 4.46
553 568 1.078490 TGAATTGGCATGGGAAAGGGA 59.922 47.619 0.00 0.00 0.00 4.20
554 569 1.570803 TGAATTGGCATGGGAAAGGG 58.429 50.000 0.00 0.00 0.00 3.95
555 570 5.556006 AATATGAATTGGCATGGGAAAGG 57.444 39.130 0.00 0.00 0.00 3.11
556 571 8.961294 TTTAAATATGAATTGGCATGGGAAAG 57.039 30.769 0.00 0.00 0.00 2.62
557 572 9.393512 CTTTTAAATATGAATTGGCATGGGAAA 57.606 29.630 0.00 0.00 0.00 3.13
558 573 7.992033 CCTTTTAAATATGAATTGGCATGGGAA 59.008 33.333 0.00 0.00 0.00 3.97
559 574 7.346698 TCCTTTTAAATATGAATTGGCATGGGA 59.653 33.333 0.00 0.00 0.00 4.37
560 575 7.507829 TCCTTTTAAATATGAATTGGCATGGG 58.492 34.615 0.00 0.00 0.00 4.00
561 576 8.829612 GTTCCTTTTAAATATGAATTGGCATGG 58.170 33.333 0.00 0.00 0.00 3.66
562 577 8.542132 CGTTCCTTTTAAATATGAATTGGCATG 58.458 33.333 0.00 0.00 0.00 4.06
563 578 7.224557 GCGTTCCTTTTAAATATGAATTGGCAT 59.775 33.333 0.00 0.00 0.00 4.40
564 579 6.533367 GCGTTCCTTTTAAATATGAATTGGCA 59.467 34.615 0.00 0.00 0.00 4.92
565 580 6.291585 CGCGTTCCTTTTAAATATGAATTGGC 60.292 38.462 0.00 0.00 0.00 4.52
566 581 6.198216 CCGCGTTCCTTTTAAATATGAATTGG 59.802 38.462 4.92 0.00 0.00 3.16
567 582 6.198216 CCCGCGTTCCTTTTAAATATGAATTG 59.802 38.462 4.92 0.00 0.00 2.32
568 583 6.270064 CCCGCGTTCCTTTTAAATATGAATT 58.730 36.000 4.92 0.00 0.00 2.17
569 584 5.221165 CCCCGCGTTCCTTTTAAATATGAAT 60.221 40.000 4.92 0.00 0.00 2.57
570 585 4.096682 CCCCGCGTTCCTTTTAAATATGAA 59.903 41.667 4.92 0.00 0.00 2.57
571 586 3.628487 CCCCGCGTTCCTTTTAAATATGA 59.372 43.478 4.92 0.00 0.00 2.15
572 587 3.794138 GCCCCGCGTTCCTTTTAAATATG 60.794 47.826 4.92 0.00 0.00 1.78
573 588 2.359848 GCCCCGCGTTCCTTTTAAATAT 59.640 45.455 4.92 0.00 0.00 1.28
574 589 1.744522 GCCCCGCGTTCCTTTTAAATA 59.255 47.619 4.92 0.00 0.00 1.40
575 590 0.528924 GCCCCGCGTTCCTTTTAAAT 59.471 50.000 4.92 0.00 0.00 1.40
576 591 1.525718 GGCCCCGCGTTCCTTTTAAA 61.526 55.000 4.92 0.00 0.00 1.52
577 592 1.972752 GGCCCCGCGTTCCTTTTAA 60.973 57.895 4.92 0.00 0.00 1.52
578 593 2.360225 GGCCCCGCGTTCCTTTTA 60.360 61.111 4.92 0.00 0.00 1.52
605 620 0.443869 CAGTACGTGCATGAGGTTGC 59.556 55.000 14.17 0.00 43.07 4.17
620 635 4.399934 TCATATTCCACTGTACGTGCAGTA 59.600 41.667 33.95 21.88 46.81 2.74
622 637 3.780902 TCATATTCCACTGTACGTGCAG 58.219 45.455 28.94 28.94 42.42 4.41
623 638 3.878160 TCATATTCCACTGTACGTGCA 57.122 42.857 6.10 6.10 42.42 4.57
624 639 4.209288 GTGATCATATTCCACTGTACGTGC 59.791 45.833 0.00 0.00 42.42 5.34
625 640 5.592054 AGTGATCATATTCCACTGTACGTG 58.408 41.667 0.00 9.86 39.43 4.49
626 641 5.854010 AGTGATCATATTCCACTGTACGT 57.146 39.130 0.00 0.00 39.43 3.57
627 642 6.042777 ACAAGTGATCATATTCCACTGTACG 58.957 40.000 0.00 0.00 40.61 3.67
628 643 7.677276 GCAACAAGTGATCATATTCCACTGTAC 60.677 40.741 0.00 0.00 40.61 2.90
629 644 6.316140 GCAACAAGTGATCATATTCCACTGTA 59.684 38.462 0.00 0.00 40.61 2.74
630 645 5.124457 GCAACAAGTGATCATATTCCACTGT 59.876 40.000 0.00 0.00 40.61 3.55
631 646 5.449588 GGCAACAAGTGATCATATTCCACTG 60.450 44.000 0.00 0.00 40.61 3.66
632 647 4.641989 GGCAACAAGTGATCATATTCCACT 59.358 41.667 0.00 0.00 42.34 4.00
633 648 4.496341 CGGCAACAAGTGATCATATTCCAC 60.496 45.833 0.00 0.00 0.00 4.02
634 649 3.627123 CGGCAACAAGTGATCATATTCCA 59.373 43.478 0.00 0.00 0.00 3.53
635 650 3.876914 TCGGCAACAAGTGATCATATTCC 59.123 43.478 0.00 0.00 0.00 3.01
636 651 5.679734 ATCGGCAACAAGTGATCATATTC 57.320 39.130 0.00 0.00 0.00 1.75
637 652 8.846943 TTATATCGGCAACAAGTGATCATATT 57.153 30.769 0.00 0.00 0.00 1.28
638 653 9.453572 AATTATATCGGCAACAAGTGATCATAT 57.546 29.630 0.00 0.00 0.00 1.78
639 654 8.846943 AATTATATCGGCAACAAGTGATCATA 57.153 30.769 0.00 0.00 0.00 2.15
640 655 7.750229 AATTATATCGGCAACAAGTGATCAT 57.250 32.000 0.00 0.00 0.00 2.45
641 656 7.713073 TGTAATTATATCGGCAACAAGTGATCA 59.287 33.333 0.00 0.00 0.00 2.92
642 657 8.009974 GTGTAATTATATCGGCAACAAGTGATC 58.990 37.037 0.00 0.00 0.00 2.92
643 658 7.307160 CGTGTAATTATATCGGCAACAAGTGAT 60.307 37.037 0.00 0.00 0.00 3.06
644 659 6.019398 CGTGTAATTATATCGGCAACAAGTGA 60.019 38.462 0.00 0.00 0.00 3.41
645 660 6.019398 TCGTGTAATTATATCGGCAACAAGTG 60.019 38.462 0.00 0.00 0.00 3.16
646 661 6.044046 TCGTGTAATTATATCGGCAACAAGT 58.956 36.000 0.00 0.00 0.00 3.16
647 662 6.519353 TCGTGTAATTATATCGGCAACAAG 57.481 37.500 0.00 0.00 0.00 3.16
648 663 7.868922 ACTATCGTGTAATTATATCGGCAACAA 59.131 33.333 0.00 0.00 0.00 2.83
649 664 7.372714 ACTATCGTGTAATTATATCGGCAACA 58.627 34.615 0.00 0.00 0.00 3.33
650 665 7.807687 ACTATCGTGTAATTATATCGGCAAC 57.192 36.000 0.00 0.00 0.00 4.17
651 666 7.970061 GGTACTATCGTGTAATTATATCGGCAA 59.030 37.037 0.00 0.00 0.00 4.52
652 667 7.121020 TGGTACTATCGTGTAATTATATCGGCA 59.879 37.037 0.00 0.00 0.00 5.69
653 668 7.430502 GTGGTACTATCGTGTAATTATATCGGC 59.569 40.741 0.00 0.00 0.00 5.54
654 669 8.453320 TGTGGTACTATCGTGTAATTATATCGG 58.547 37.037 0.00 0.00 0.00 4.18
696 711 3.822940 TCCAAAAGTGGTACCAATTCGT 58.177 40.909 26.51 15.44 46.11 3.85
795 811 2.671070 CTGGGCGGTCAGTTCCAT 59.329 61.111 0.00 0.00 0.00 3.41
940 959 1.970114 AACGAGGTCGGCGAGAGAA 60.970 57.895 11.20 0.00 44.95 2.87
1052 1072 2.105128 CCGTGGATGAGGTCGAGC 59.895 66.667 6.48 6.48 0.00 5.03
2016 2116 3.805971 CCTTCCTGCAAAAAGAGCAAAAG 59.194 43.478 8.87 0.00 42.17 2.27
2312 2507 3.754850 CCAGTTCACTTCTGCATTCATGA 59.245 43.478 0.00 0.00 0.00 3.07
2443 2638 5.904362 AATATGCTTCAACTTCAGGTTCC 57.096 39.130 0.00 0.00 35.74 3.62
2520 2715 2.968574 TCTCCTCAGACTTTGTGAGCTT 59.031 45.455 0.00 0.00 40.22 3.74


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

AutoCloner maintained by Alex Coulton.