Multiple sequence alignment - TraesCS6D01G262300

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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 TraesCS6D01G262300 chr6D 100.000 2666 0 0 1 2666 370688162 370690827 0.000000e+00 4924.0
1 TraesCS6D01G262300 chr6D 90.620 597 53 3 1 597 27297459 27298052 0.000000e+00 789.0
2 TraesCS6D01G262300 chr6D 96.847 222 7 0 633 854 370688537 370688758 3.240000e-99 372.0
3 TraesCS6D01G262300 chr6D 92.174 230 18 0 633 862 27297831 27298060 2.560000e-85 326.0
4 TraesCS6D01G262300 chr6D 92.188 64 1 4 2396 2459 249956926 249956985 1.310000e-13 87.9
5 TraesCS6D01G262300 chr6D 100.000 45 0 0 598 642 370688709 370688753 1.700000e-12 84.2
6 TraesCS6D01G262300 chr6D 97.619 42 1 0 598 639 370688966 370689007 3.680000e-09 73.1
7 TraesCS6D01G262300 chr6A 94.727 1574 39 10 862 2399 511527824 511529389 0.000000e+00 2407.0
8 TraesCS6D01G262300 chr6A 95.714 210 9 0 2390 2599 511529455 511529664 3.290000e-89 339.0
9 TraesCS6D01G262300 chr6B 95.983 1195 28 3 952 2132 555805027 555806215 0.000000e+00 1923.0
10 TraesCS6D01G262300 chr6B 90.566 265 16 6 2135 2399 555806252 555806507 2.540000e-90 342.0
11 TraesCS6D01G262300 chr6B 95.238 168 8 0 2435 2602 555806508 555806675 1.570000e-67 267.0
12 TraesCS6D01G262300 chr6B 88.406 69 7 1 2594 2662 503898649 503898716 6.120000e-12 82.4
13 TraesCS6D01G262300 chr6B 90.385 52 4 1 902 952 555804945 555804996 1.710000e-07 67.6
14 TraesCS6D01G262300 chr3D 92.797 597 40 3 1 597 373942593 373942000 0.000000e+00 861.0
15 TraesCS6D01G262300 chr3D 88.648 599 60 7 1 597 262968297 262968889 0.000000e+00 723.0
16 TraesCS6D01G262300 chr3D 93.590 234 14 1 633 866 373942221 373941989 5.460000e-92 348.0
17 TraesCS6D01G262300 chr3D 92.511 227 16 1 633 858 262968667 262968893 9.210000e-85 324.0
18 TraesCS6D01G262300 chr3D 89.394 66 3 3 2373 2436 16052686 16052749 2.200000e-11 80.5
19 TraesCS6D01G262300 chr3D 97.778 45 1 0 598 642 373942049 373942005 7.910000e-11 78.7
20 TraesCS6D01G262300 chr2D 89.280 597 62 2 1 597 372640207 372640801 0.000000e+00 747.0
21 TraesCS6D01G262300 chr2D 86.789 598 65 12 4 597 188436129 188435542 0.000000e+00 654.0
22 TraesCS6D01G262300 chr2D 91.667 228 19 0 635 862 372640582 372640809 1.540000e-82 316.0
23 TraesCS6D01G262300 chr2D 88.608 79 6 3 2589 2666 486498509 486498433 2.830000e-15 93.5
24 TraesCS6D01G262300 chr2D 93.103 58 0 4 2391 2447 267707121 267707175 6.120000e-12 82.4
25 TraesCS6D01G262300 chr2D 95.556 45 2 0 598 642 54606514 54606470 3.680000e-09 73.1
26 TraesCS6D01G262300 chr2D 95.556 45 2 0 598 642 72340680 72340724 3.680000e-09 73.1
27 TraesCS6D01G262300 chr4D 89.149 599 57 8 1 597 86537184 86536592 0.000000e+00 739.0
28 TraesCS6D01G262300 chr4D 85.786 598 76 4 1 597 223525859 223525270 2.250000e-175 625.0
29 TraesCS6D01G262300 chr4D 92.952 227 14 2 633 857 86536815 86536589 1.980000e-86 329.0
30 TraesCS6D01G262300 chr4D 98.529 68 1 0 2599 2666 14981967 14982034 1.300000e-23 121.0
31 TraesCS6D01G262300 chr4B 89.573 585 55 6 14 597 123925802 123925223 0.000000e+00 737.0
32 TraesCS6D01G262300 chr4B 92.920 226 15 1 633 857 123925445 123925220 7.120000e-86 327.0
33 TraesCS6D01G262300 chr7D 88.462 598 64 5 1 597 586423007 586423600 0.000000e+00 717.0
34 TraesCS6D01G262300 chr7D 91.453 234 17 3 633 864 586423379 586423611 4.280000e-83 318.0
35 TraesCS6D01G262300 chr7D 91.429 70 4 2 2599 2666 2045395 2045464 7.860000e-16 95.3
36 TraesCS6D01G262300 chr7D 100.000 46 0 0 2391 2436 60588883 60588928 4.730000e-13 86.1
37 TraesCS6D01G262300 chr7D 96.154 52 2 0 2396 2447 101475419 101475470 4.730000e-13 86.1
38 TraesCS6D01G262300 chr7D 97.778 45 1 0 598 642 40736407 40736451 7.910000e-11 78.7
39 TraesCS6D01G262300 chr5D 92.920 226 16 0 633 858 305780530 305780755 1.980000e-86 329.0
40 TraesCS6D01G262300 chr5D 87.500 72 6 1 2598 2666 328252590 328252661 2.200000e-11 80.5
41 TraesCS6D01G262300 chr5D 97.778 45 1 0 598 642 305780702 305780746 7.910000e-11 78.7
42 TraesCS6D01G262300 chrUn 94.118 68 4 0 2599 2666 115235515 115235582 1.310000e-18 104.0
43 TraesCS6D01G262300 chrUn 87.838 74 9 0 2593 2666 16372860 16372933 1.310000e-13 87.9
44 TraesCS6D01G262300 chr5B 91.176 68 6 0 2599 2666 585809730 585809797 2.830000e-15 93.5
45 TraesCS6D01G262300 chr5B 98.000 50 1 0 2391 2440 285934833 285934784 1.310000e-13 87.9
46 TraesCS6D01G262300 chr1A 91.176 68 5 1 2599 2666 400957577 400957511 1.020000e-14 91.6
47 TraesCS6D01G262300 chr1B 94.737 57 1 2 2390 2444 305536608 305536664 1.310000e-13 87.9
48 TraesCS6D01G262300 chr2B 89.394 66 5 2 2374 2438 589297125 589297189 6.120000e-12 82.4
49 TraesCS6D01G262300 chr2B 97.368 38 1 0 1281 1318 573814522 573814485 6.160000e-07 65.8
50 TraesCS6D01G262300 chr1D 97.778 45 1 0 598 642 276753478 276753434 7.910000e-11 78.7
51 TraesCS6D01G262300 chr7B 95.556 45 2 0 598 642 145061837 145061793 3.680000e-09 73.1


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 TraesCS6D01G262300 chr6D 370688162 370690827 2665 False 1363.325000 4924 98.616500 1 2666 4 chr6D.!!$F3 2665
1 TraesCS6D01G262300 chr6D 27297459 27298060 601 False 557.500000 789 91.397000 1 862 2 chr6D.!!$F2 861
2 TraesCS6D01G262300 chr6A 511527824 511529664 1840 False 1373.000000 2407 95.220500 862 2599 2 chr6A.!!$F1 1737
3 TraesCS6D01G262300 chr6B 555804945 555806675 1730 False 649.900000 1923 93.043000 902 2602 4 chr6B.!!$F2 1700
4 TraesCS6D01G262300 chr3D 262968297 262968893 596 False 523.500000 723 90.579500 1 858 2 chr3D.!!$F2 857
5 TraesCS6D01G262300 chr3D 373941989 373942593 604 True 429.233333 861 94.721667 1 866 3 chr3D.!!$R1 865
6 TraesCS6D01G262300 chr2D 188435542 188436129 587 True 654.000000 654 86.789000 4 597 1 chr2D.!!$R2 593
7 TraesCS6D01G262300 chr2D 372640207 372640809 602 False 531.500000 747 90.473500 1 862 2 chr2D.!!$F3 861
8 TraesCS6D01G262300 chr4D 223525270 223525859 589 True 625.000000 625 85.786000 1 597 1 chr4D.!!$R1 596
9 TraesCS6D01G262300 chr4D 86536589 86537184 595 True 534.000000 739 91.050500 1 857 2 chr4D.!!$R2 856
10 TraesCS6D01G262300 chr4B 123925220 123925802 582 True 532.000000 737 91.246500 14 857 2 chr4B.!!$R1 843
11 TraesCS6D01G262300 chr7D 586423007 586423611 604 False 517.500000 717 89.957500 1 864 2 chr7D.!!$F5 863

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
520 533 0.03601 ATCTGCCTTCCCGTGTCAAG 60.036 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2437 0.675633 GTGGGCATGCCATTATCCAC 59.324 55.0 36.56 27.86 37.98 4.02 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
62 64 0.531753 GCCTGAATCTCGAGAAGGCC 60.532 60.000 32.93 20.80 46.31 5.19
84 86 0.477597 AGGGGAATGTGACCAGGGAA 60.478 55.000 0.00 0.00 0.00 3.97
114 117 2.037251 GCAGATTACGCAGGGAGGAATA 59.963 50.000 0.00 0.00 0.00 1.75
288 300 2.238701 GGATGGTGGGTTGGGGAGT 61.239 63.158 0.00 0.00 0.00 3.85
303 315 3.052944 TGGGGAGTTAATGAATGGGAAGG 60.053 47.826 0.00 0.00 0.00 3.46
353 366 1.330655 AATGGCGAGTCGTGGGAGAT 61.331 55.000 15.08 0.00 0.00 2.75
359 372 1.808411 GAGTCGTGGGAGATGCAAAA 58.192 50.000 0.00 0.00 0.00 2.44
399 412 4.719616 GCGCGACGGCAGTTTCAC 62.720 66.667 12.10 0.00 39.92 3.18
400 413 4.072088 CGCGACGGCAGTTTCACC 62.072 66.667 0.00 0.00 39.92 4.02
405 418 4.368808 CGGCAGTTTCACCGCACG 62.369 66.667 0.00 0.00 43.44 5.34
406 419 4.683334 GGCAGTTTCACCGCACGC 62.683 66.667 0.00 0.00 0.00 5.34
407 420 4.683334 GCAGTTTCACCGCACGCC 62.683 66.667 0.00 0.00 0.00 5.68
408 421 2.972505 CAGTTTCACCGCACGCCT 60.973 61.111 0.00 0.00 0.00 5.52
409 422 2.665185 AGTTTCACCGCACGCCTC 60.665 61.111 0.00 0.00 0.00 4.70
410 423 4.072088 GTTTCACCGCACGCCTCG 62.072 66.667 0.00 0.00 0.00 4.63
411 424 4.287781 TTTCACCGCACGCCTCGA 62.288 61.111 0.00 0.00 0.00 4.04
419 432 3.470567 CACGCCTCGACTCGCAAC 61.471 66.667 0.00 0.00 0.00 4.17
420 433 4.719369 ACGCCTCGACTCGCAACC 62.719 66.667 0.00 0.00 0.00 3.77
423 436 4.421479 CCTCGACTCGCAACCGCT 62.421 66.667 0.00 0.00 35.30 5.52
424 437 3.175240 CTCGACTCGCAACCGCTG 61.175 66.667 0.00 0.00 35.30 5.18
425 438 3.898627 CTCGACTCGCAACCGCTGT 62.899 63.158 0.00 0.00 35.30 4.40
426 439 3.470567 CGACTCGCAACCGCTGTC 61.471 66.667 0.00 0.00 35.72 3.51
427 440 3.470567 GACTCGCAACCGCTGTCG 61.471 66.667 0.00 0.00 35.30 4.35
428 441 4.280494 ACTCGCAACCGCTGTCGT 62.280 61.111 0.00 0.00 35.30 4.34
429 442 3.470567 CTCGCAACCGCTGTCGTC 61.471 66.667 0.00 0.00 35.30 4.20
433 446 2.805353 CAACCGCTGTCGTCCGAG 60.805 66.667 0.00 0.00 0.00 4.63
434 447 3.292936 AACCGCTGTCGTCCGAGT 61.293 61.111 0.00 0.00 0.00 4.18
435 448 3.553437 AACCGCTGTCGTCCGAGTG 62.553 63.158 0.00 0.00 0.00 3.51
436 449 3.733960 CCGCTGTCGTCCGAGTGA 61.734 66.667 0.00 0.00 0.00 3.41
437 450 2.202362 CGCTGTCGTCCGAGTGAG 60.202 66.667 0.00 0.00 0.00 3.51
438 451 2.677979 CGCTGTCGTCCGAGTGAGA 61.678 63.158 0.00 0.00 0.00 3.27
439 452 1.579932 GCTGTCGTCCGAGTGAGAA 59.420 57.895 0.00 0.00 0.00 2.87
440 453 0.039437 GCTGTCGTCCGAGTGAGAAA 60.039 55.000 0.00 0.00 0.00 2.52
441 454 1.687628 CTGTCGTCCGAGTGAGAAAC 58.312 55.000 0.00 0.00 0.00 2.78
442 455 0.040692 TGTCGTCCGAGTGAGAAACG 60.041 55.000 0.00 0.00 34.80 3.60
443 456 0.236711 GTCGTCCGAGTGAGAAACGA 59.763 55.000 0.00 0.00 39.77 3.85
444 457 0.236711 TCGTCCGAGTGAGAAACGAC 59.763 55.000 0.00 0.00 37.43 4.34
445 458 1.058590 CGTCCGAGTGAGAAACGACG 61.059 60.000 0.00 0.00 35.45 5.12
446 459 0.040603 GTCCGAGTGAGAAACGACGT 60.041 55.000 0.00 0.00 33.77 4.34
447 460 0.040692 TCCGAGTGAGAAACGACGTG 60.041 55.000 0.00 0.00 33.77 4.49
448 461 1.606350 CCGAGTGAGAAACGACGTGC 61.606 60.000 0.00 0.00 33.77 5.34
449 462 0.933047 CGAGTGAGAAACGACGTGCA 60.933 55.000 0.00 0.00 0.00 4.57
450 463 0.778815 GAGTGAGAAACGACGTGCAG 59.221 55.000 0.00 0.00 0.00 4.41
451 464 0.597637 AGTGAGAAACGACGTGCAGG 60.598 55.000 0.00 4.53 0.00 4.85
452 465 1.954146 TGAGAAACGACGTGCAGGC 60.954 57.895 6.26 0.00 0.00 4.85
459 472 4.255126 GACGTGCAGGCGAACTAA 57.745 55.556 6.26 0.00 35.59 2.24
460 473 1.779683 GACGTGCAGGCGAACTAAC 59.220 57.895 6.26 0.00 35.59 2.34
461 474 0.666577 GACGTGCAGGCGAACTAACT 60.667 55.000 6.26 0.00 35.59 2.24
462 475 0.599558 ACGTGCAGGCGAACTAACTA 59.400 50.000 6.26 0.00 35.59 2.24
463 476 0.989890 CGTGCAGGCGAACTAACTAC 59.010 55.000 0.00 0.00 0.00 2.73
464 477 1.667756 CGTGCAGGCGAACTAACTACA 60.668 52.381 0.00 0.00 0.00 2.74
465 478 1.725164 GTGCAGGCGAACTAACTACAC 59.275 52.381 0.00 0.00 0.00 2.90
466 479 1.341852 TGCAGGCGAACTAACTACACA 59.658 47.619 0.00 0.00 0.00 3.72
467 480 1.725164 GCAGGCGAACTAACTACACAC 59.275 52.381 0.00 0.00 0.00 3.82
468 481 2.334838 CAGGCGAACTAACTACACACC 58.665 52.381 0.00 0.00 0.00 4.16
469 482 1.965643 AGGCGAACTAACTACACACCA 59.034 47.619 0.00 0.00 0.00 4.17
470 483 2.064014 GGCGAACTAACTACACACCAC 58.936 52.381 0.00 0.00 0.00 4.16
471 484 2.546373 GGCGAACTAACTACACACCACA 60.546 50.000 0.00 0.00 0.00 4.17
472 485 2.473984 GCGAACTAACTACACACCACAC 59.526 50.000 0.00 0.00 0.00 3.82
473 486 3.708890 CGAACTAACTACACACCACACA 58.291 45.455 0.00 0.00 0.00 3.72
474 487 3.488310 CGAACTAACTACACACCACACAC 59.512 47.826 0.00 0.00 0.00 3.82
475 488 4.690122 GAACTAACTACACACCACACACT 58.310 43.478 0.00 0.00 0.00 3.55
476 489 4.054780 ACTAACTACACACCACACACTG 57.945 45.455 0.00 0.00 0.00 3.66
478 491 0.179056 ACTACACACCACACACTGGC 60.179 55.000 0.00 0.00 45.32 4.85
479 492 0.884704 CTACACACCACACACTGGCC 60.885 60.000 0.00 0.00 45.32 5.36
480 493 1.341913 TACACACCACACACTGGCCT 61.342 55.000 3.32 0.00 45.32 5.19
481 494 1.453745 CACACCACACACTGGCCTT 60.454 57.895 3.32 0.00 45.32 4.35
482 495 1.453745 ACACCACACACTGGCCTTG 60.454 57.895 3.32 3.47 45.32 3.61
483 496 1.453745 CACCACACACTGGCCTTGT 60.454 57.895 3.32 4.23 45.32 3.16
484 497 1.152963 ACCACACACTGGCCTTGTC 60.153 57.895 3.32 0.00 45.32 3.18
485 498 1.898574 CCACACACTGGCCTTGTCC 60.899 63.158 3.32 0.00 31.36 4.02
486 499 1.149174 CACACACTGGCCTTGTCCT 59.851 57.895 3.32 0.00 0.00 3.85
487 500 0.396435 CACACACTGGCCTTGTCCTA 59.604 55.000 3.32 0.00 0.00 2.94
488 501 0.396811 ACACACTGGCCTTGTCCTAC 59.603 55.000 3.32 0.00 0.00 3.18
489 502 0.670546 CACACTGGCCTTGTCCTACG 60.671 60.000 3.32 0.00 0.00 3.51
490 503 1.119574 ACACTGGCCTTGTCCTACGT 61.120 55.000 3.32 0.00 0.00 3.57
491 504 0.670546 CACTGGCCTTGTCCTACGTG 60.671 60.000 3.32 0.00 0.00 4.49
492 505 1.079127 CTGGCCTTGTCCTACGTGG 60.079 63.158 3.32 0.00 37.10 4.94
493 506 2.436115 GGCCTTGTCCTACGTGGC 60.436 66.667 0.00 0.00 38.02 5.01
494 507 2.345991 GCCTTGTCCTACGTGGCA 59.654 61.111 0.00 0.00 38.41 4.92
495 508 2.033194 GCCTTGTCCTACGTGGCAC 61.033 63.158 7.79 7.79 38.41 5.01
496 509 1.369692 CCTTGTCCTACGTGGCACA 59.630 57.895 19.09 0.00 35.26 4.57
510 523 2.070262 GGCACACAAAATCTGCCTTC 57.930 50.000 0.50 0.00 46.05 3.46
511 524 1.337167 GGCACACAAAATCTGCCTTCC 60.337 52.381 0.50 0.00 46.05 3.46
512 525 1.337167 GCACACAAAATCTGCCTTCCC 60.337 52.381 0.00 0.00 0.00 3.97
513 526 1.068333 CACACAAAATCTGCCTTCCCG 60.068 52.381 0.00 0.00 0.00 5.14
514 527 1.247567 CACAAAATCTGCCTTCCCGT 58.752 50.000 0.00 0.00 0.00 5.28
515 528 1.068333 CACAAAATCTGCCTTCCCGTG 60.068 52.381 0.00 0.00 0.00 4.94
516 529 1.247567 CAAAATCTGCCTTCCCGTGT 58.752 50.000 0.00 0.00 0.00 4.49
517 530 1.200020 CAAAATCTGCCTTCCCGTGTC 59.800 52.381 0.00 0.00 0.00 3.67
518 531 0.400213 AAATCTGCCTTCCCGTGTCA 59.600 50.000 0.00 0.00 0.00 3.58
519 532 0.400213 AATCTGCCTTCCCGTGTCAA 59.600 50.000 0.00 0.00 0.00 3.18
520 533 0.036010 ATCTGCCTTCCCGTGTCAAG 60.036 55.000 0.00 0.00 0.00 3.02
521 534 1.118965 TCTGCCTTCCCGTGTCAAGA 61.119 55.000 0.00 0.00 0.00 3.02
522 535 0.036010 CTGCCTTCCCGTGTCAAGAT 60.036 55.000 0.00 0.00 0.00 2.40
523 536 0.400213 TGCCTTCCCGTGTCAAGATT 59.600 50.000 0.00 0.00 0.00 2.40
524 537 1.087501 GCCTTCCCGTGTCAAGATTC 58.912 55.000 0.00 0.00 0.00 2.52
525 538 1.359848 CCTTCCCGTGTCAAGATTCG 58.640 55.000 0.00 0.00 0.00 3.34
526 539 1.337823 CCTTCCCGTGTCAAGATTCGT 60.338 52.381 0.00 0.00 0.00 3.85
527 540 1.726791 CTTCCCGTGTCAAGATTCGTG 59.273 52.381 0.00 0.00 0.00 4.35
528 541 0.669318 TCCCGTGTCAAGATTCGTGC 60.669 55.000 0.00 0.00 0.00 5.34
529 542 0.948623 CCCGTGTCAAGATTCGTGCA 60.949 55.000 0.00 0.00 0.00 4.57
530 543 0.865111 CCGTGTCAAGATTCGTGCAA 59.135 50.000 0.00 0.00 0.00 4.08
531 544 1.262950 CCGTGTCAAGATTCGTGCAAA 59.737 47.619 0.00 0.00 0.00 3.68
532 545 2.286713 CCGTGTCAAGATTCGTGCAAAA 60.287 45.455 0.00 0.00 0.00 2.44
533 546 3.554524 CGTGTCAAGATTCGTGCAAAAT 58.445 40.909 0.00 0.00 0.00 1.82
534 547 3.974401 CGTGTCAAGATTCGTGCAAAATT 59.026 39.130 0.00 0.00 0.00 1.82
535 548 5.143660 CGTGTCAAGATTCGTGCAAAATTA 58.856 37.500 0.00 0.00 0.00 1.40
536 549 5.623264 CGTGTCAAGATTCGTGCAAAATTAA 59.377 36.000 0.00 0.00 0.00 1.40
537 550 6.141527 CGTGTCAAGATTCGTGCAAAATTAAA 59.858 34.615 0.00 0.00 0.00 1.52
538 551 7.148983 CGTGTCAAGATTCGTGCAAAATTAAAT 60.149 33.333 0.00 0.00 0.00 1.40
539 552 8.155923 GTGTCAAGATTCGTGCAAAATTAAATC 58.844 33.333 0.00 0.00 0.00 2.17
540 553 7.060518 TGTCAAGATTCGTGCAAAATTAAATCG 59.939 33.333 0.00 0.00 0.00 3.34
541 554 7.270365 GTCAAGATTCGTGCAAAATTAAATCGA 59.730 33.333 0.00 0.00 0.00 3.59
542 555 7.270365 TCAAGATTCGTGCAAAATTAAATCGAC 59.730 33.333 0.00 0.00 0.00 4.20
543 556 5.732647 AGATTCGTGCAAAATTAAATCGACG 59.267 36.000 0.00 0.00 0.00 5.12
544 557 3.738399 TCGTGCAAAATTAAATCGACGG 58.262 40.909 0.00 0.00 0.00 4.79
545 558 2.275253 CGTGCAAAATTAAATCGACGGC 59.725 45.455 0.00 0.00 0.00 5.68
546 559 2.275253 GTGCAAAATTAAATCGACGGCG 59.725 45.455 2.87 2.87 39.35 6.46
570 583 4.980805 GCGTGTGGGCGAGTTGGA 62.981 66.667 0.00 0.00 0.00 3.53
571 584 2.738521 CGTGTGGGCGAGTTGGAG 60.739 66.667 0.00 0.00 0.00 3.86
572 585 2.741092 GTGTGGGCGAGTTGGAGA 59.259 61.111 0.00 0.00 0.00 3.71
573 586 1.070786 GTGTGGGCGAGTTGGAGAA 59.929 57.895 0.00 0.00 0.00 2.87
574 587 0.951040 GTGTGGGCGAGTTGGAGAAG 60.951 60.000 0.00 0.00 0.00 2.85
575 588 1.371558 GTGGGCGAGTTGGAGAAGT 59.628 57.895 0.00 0.00 0.00 3.01
576 589 0.951040 GTGGGCGAGTTGGAGAAGTG 60.951 60.000 0.00 0.00 0.00 3.16
577 590 2.035442 GGGCGAGTTGGAGAAGTGC 61.035 63.158 0.00 0.00 0.00 4.40
578 591 2.035442 GGCGAGTTGGAGAAGTGCC 61.035 63.158 0.00 0.00 0.00 5.01
579 592 1.301716 GCGAGTTGGAGAAGTGCCA 60.302 57.895 0.00 0.00 0.00 4.92
580 593 1.569479 GCGAGTTGGAGAAGTGCCAC 61.569 60.000 0.00 0.00 34.56 5.01
581 594 0.249868 CGAGTTGGAGAAGTGCCACA 60.250 55.000 0.00 0.00 34.56 4.17
582 595 1.230324 GAGTTGGAGAAGTGCCACAC 58.770 55.000 0.00 0.00 34.56 3.82
583 596 0.532862 AGTTGGAGAAGTGCCACACG 60.533 55.000 0.00 0.00 39.64 4.49
584 597 0.814010 GTTGGAGAAGTGCCACACGT 60.814 55.000 0.00 0.00 39.64 4.49
585 598 0.813610 TTGGAGAAGTGCCACACGTG 60.814 55.000 15.48 15.48 39.64 4.49
586 599 1.227556 GGAGAAGTGCCACACGTGT 60.228 57.895 17.22 17.22 39.64 4.49
587 600 1.498865 GGAGAAGTGCCACACGTGTG 61.499 60.000 36.13 36.13 45.23 3.82
595 608 3.240203 CACACGTGTGGGCGTTAG 58.760 61.111 35.65 12.08 43.83 2.34
596 609 1.593209 CACACGTGTGGGCGTTAGT 60.593 57.895 35.65 1.12 43.83 2.24
597 610 0.318869 CACACGTGTGGGCGTTAGTA 60.319 55.000 35.65 0.00 43.83 1.82
598 611 0.604578 ACACGTGTGGGCGTTAGTAT 59.395 50.000 22.71 0.00 43.83 2.12
599 612 1.274596 CACGTGTGGGCGTTAGTATC 58.725 55.000 7.58 0.00 43.83 2.24
600 613 0.179156 ACGTGTGGGCGTTAGTATCG 60.179 55.000 0.00 0.00 43.04 2.92
601 614 0.099259 CGTGTGGGCGTTAGTATCGA 59.901 55.000 4.81 0.00 0.00 3.59
602 615 1.836383 GTGTGGGCGTTAGTATCGAG 58.164 55.000 4.81 0.00 0.00 4.04
603 616 0.742505 TGTGGGCGTTAGTATCGAGG 59.257 55.000 4.81 0.00 0.00 4.63
604 617 0.596859 GTGGGCGTTAGTATCGAGGC 60.597 60.000 4.81 0.00 0.00 4.70
605 618 1.371389 GGGCGTTAGTATCGAGGCG 60.371 63.158 4.81 0.00 0.00 5.52
606 619 1.358046 GGCGTTAGTATCGAGGCGT 59.642 57.895 4.81 0.00 0.00 5.68
607 620 0.933509 GGCGTTAGTATCGAGGCGTG 60.934 60.000 4.81 0.00 0.00 5.34
608 621 0.248377 GCGTTAGTATCGAGGCGTGT 60.248 55.000 4.81 0.00 0.00 4.49
609 622 1.463805 CGTTAGTATCGAGGCGTGTG 58.536 55.000 0.00 0.00 0.00 3.82
610 623 1.836383 GTTAGTATCGAGGCGTGTGG 58.164 55.000 0.00 0.00 0.00 4.17
611 624 0.742505 TTAGTATCGAGGCGTGTGGG 59.257 55.000 0.00 0.00 0.00 4.61
612 625 1.731433 TAGTATCGAGGCGTGTGGGC 61.731 60.000 0.00 0.00 42.69 5.36
620 633 4.980805 GCGTGTGGGCGAGTTGGA 62.981 66.667 0.00 0.00 0.00 3.53
621 634 2.738521 CGTGTGGGCGAGTTGGAG 60.739 66.667 0.00 0.00 0.00 3.86
622 635 2.741092 GTGTGGGCGAGTTGGAGA 59.259 61.111 0.00 0.00 0.00 3.71
623 636 1.070786 GTGTGGGCGAGTTGGAGAA 59.929 57.895 0.00 0.00 0.00 2.87
624 637 0.951040 GTGTGGGCGAGTTGGAGAAG 60.951 60.000 0.00 0.00 0.00 2.85
625 638 1.371558 GTGGGCGAGTTGGAGAAGT 59.628 57.895 0.00 0.00 0.00 3.01
626 639 0.951040 GTGGGCGAGTTGGAGAAGTG 60.951 60.000 0.00 0.00 0.00 3.16
627 640 2.035442 GGGCGAGTTGGAGAAGTGC 61.035 63.158 0.00 0.00 0.00 4.40
628 641 2.035442 GGCGAGTTGGAGAAGTGCC 61.035 63.158 0.00 0.00 0.00 5.01
629 642 1.301716 GCGAGTTGGAGAAGTGCCA 60.302 57.895 0.00 0.00 0.00 4.92
630 643 1.569479 GCGAGTTGGAGAAGTGCCAC 61.569 60.000 0.00 0.00 34.56 5.01
631 644 0.249868 CGAGTTGGAGAAGTGCCACA 60.250 55.000 0.00 0.00 34.56 4.17
632 645 1.230324 GAGTTGGAGAAGTGCCACAC 58.770 55.000 0.00 0.00 34.56 3.82
633 646 0.532862 AGTTGGAGAAGTGCCACACG 60.533 55.000 0.00 0.00 39.64 4.49
634 647 0.814010 GTTGGAGAAGTGCCACACGT 60.814 55.000 0.00 0.00 39.64 4.49
635 648 0.813610 TTGGAGAAGTGCCACACGTG 60.814 55.000 15.48 15.48 39.64 4.49
636 649 1.227556 GGAGAAGTGCCACACGTGT 60.228 57.895 17.22 17.22 39.64 4.49
665 678 4.988598 CAGTTCCACCGCACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
691 705 3.292936 AACCGCTGTCGTCCGAGT 61.293 61.111 0.00 0.00 0.00 4.18
863 878 4.445385 GTGTGGACGTTAGTGTTTACGAAT 59.555 41.667 0.00 0.00 40.03 3.34
865 880 6.143758 GTGTGGACGTTAGTGTTTACGAATAA 59.856 38.462 0.00 0.00 40.03 1.40
1044 1091 3.522731 CTCCTGAGCCCCTCGACG 61.523 72.222 0.00 0.00 32.35 5.12
1614 1682 4.899239 CGGGTGCTCGCCATCTCC 62.899 72.222 1.60 0.00 0.00 3.71
1725 1793 7.774157 AGTGTCAGTATTCGAGGAATAAGACTA 59.226 37.037 20.64 11.98 39.62 2.59
1763 1831 7.694093 AGATTAGACCTTGGAACTCTGAAAAT 58.306 34.615 0.00 0.00 0.00 1.82
1768 1836 4.344968 ACCTTGGAACTCTGAAAATTTGGG 59.655 41.667 0.00 0.00 0.00 4.12
1994 2076 5.357878 TGCATTTTAGATTCCAGTTGCCTAG 59.642 40.000 0.00 0.00 0.00 3.02
2065 2147 6.499106 TGGCAACTTGGATAAGATCATCTA 57.501 37.500 0.00 0.00 37.36 1.98
2104 2186 3.072476 TCTTTATGCTGGGGTATGTAGGC 59.928 47.826 0.00 0.00 0.00 3.93
2106 2188 2.280865 GCTGGGGTATGTAGGCGC 60.281 66.667 0.00 0.00 0.00 6.53
2111 2193 1.440476 GGGTATGTAGGCGCGAGTT 59.560 57.895 12.10 0.00 0.00 3.01
2153 2269 0.672091 TTATGGCTTCGCAGTTCGCA 60.672 50.000 0.00 0.00 42.60 5.10
2168 2284 3.120199 AGTTCGCACCATCTGAAAAATCG 60.120 43.478 0.00 0.00 0.00 3.34
2187 2303 2.807967 TCGTGCCTTCAGAGTTCAATTG 59.192 45.455 0.00 0.00 0.00 2.32
2321 2437 4.281688 AGGTGGTGAAATTGGAGATGTTTG 59.718 41.667 0.00 0.00 0.00 2.93
2427 2618 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2452 2643 7.200434 AGGGAGTACATGACAATCTACATTT 57.800 36.000 0.00 0.00 0.00 2.32
2466 2657 9.155975 ACAATCTACATTTGTTTCTAGCAGTAG 57.844 33.333 0.00 0.00 33.64 2.57
2480 2671 3.905784 AGCAGTAGCACATTTTTCTTGC 58.094 40.909 0.00 0.00 45.49 4.01
2569 2760 8.318167 CGTTGACAAGTAAATTTTCAGAAAACC 58.682 33.333 10.62 0.28 32.37 3.27
2587 2778 5.559148 AAACCTAGATAGATCAGCTTGGG 57.441 43.478 12.57 7.61 39.54 4.12
2602 2793 5.046304 TCAGCTTGGGCCATATATCTTACTC 60.046 44.000 7.26 0.00 39.73 2.59
2603 2794 4.226168 AGCTTGGGCCATATATCTTACTCC 59.774 45.833 7.26 0.00 39.73 3.85
2604 2795 4.626529 GCTTGGGCCATATATCTTACTCCC 60.627 50.000 7.26 0.00 0.00 4.30
2605 2796 4.435977 TGGGCCATATATCTTACTCCCT 57.564 45.455 0.00 0.00 33.77 4.20
2606 2797 4.362677 TGGGCCATATATCTTACTCCCTC 58.637 47.826 0.00 0.00 33.77 4.30
2607 2798 4.047265 TGGGCCATATATCTTACTCCCTCT 59.953 45.833 0.00 0.00 33.77 3.69
2608 2799 4.407296 GGGCCATATATCTTACTCCCTCTG 59.593 50.000 4.39 0.00 0.00 3.35
2609 2800 5.026790 GGCCATATATCTTACTCCCTCTGT 58.973 45.833 0.00 0.00 0.00 3.41
2610 2801 6.195700 GGCCATATATCTTACTCCCTCTGTA 58.804 44.000 0.00 0.00 0.00 2.74
2611 2802 6.668283 GGCCATATATCTTACTCCCTCTGTAA 59.332 42.308 0.00 0.00 0.00 2.41
2612 2803 7.180408 GGCCATATATCTTACTCCCTCTGTAAA 59.820 40.741 0.00 0.00 30.72 2.01
2613 2804 8.035984 GCCATATATCTTACTCCCTCTGTAAAC 58.964 40.741 0.00 0.00 30.72 2.01
2614 2805 9.315363 CCATATATCTTACTCCCTCTGTAAACT 57.685 37.037 0.00 0.00 30.72 2.66
2625 2816 9.939424 ACTCCCTCTGTAAACTATTATAAGAGT 57.061 33.333 6.94 6.94 35.24 3.24
2627 2818 9.710818 TCCCTCTGTAAACTATTATAAGAGTGT 57.289 33.333 13.28 10.54 35.24 3.55
2646 2837 9.915629 AAGAGTGTTTAGATTACTGAAGTAGTG 57.084 33.333 0.00 0.00 40.65 2.74
2647 2838 9.298250 AGAGTGTTTAGATTACTGAAGTAGTGA 57.702 33.333 0.00 0.00 40.65 3.41
2656 2847 7.988904 ATTACTGAAGTAGTGATCTAAACGC 57.011 36.000 0.00 0.00 40.65 4.84
2657 2848 5.646577 ACTGAAGTAGTGATCTAAACGCT 57.353 39.130 0.00 0.00 38.49 5.07
2658 2849 5.642686 ACTGAAGTAGTGATCTAAACGCTC 58.357 41.667 0.00 0.00 38.49 5.03
2659 2850 5.416326 ACTGAAGTAGTGATCTAAACGCTCT 59.584 40.000 0.00 0.00 38.49 4.09
2660 2851 6.071840 ACTGAAGTAGTGATCTAAACGCTCTT 60.072 38.462 0.00 0.00 38.49 2.85
2661 2852 7.120873 ACTGAAGTAGTGATCTAAACGCTCTTA 59.879 37.037 0.00 0.00 38.49 2.10
2662 2853 7.249147 TGAAGTAGTGATCTAAACGCTCTTAC 58.751 38.462 0.00 0.00 0.00 2.34
2663 2854 6.754702 AGTAGTGATCTAAACGCTCTTACA 57.245 37.500 0.00 0.00 0.00 2.41
2664 2855 7.336161 AGTAGTGATCTAAACGCTCTTACAT 57.664 36.000 0.00 0.00 0.00 2.29
2665 2856 7.773149 AGTAGTGATCTAAACGCTCTTACATT 58.227 34.615 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 1.221840 CTGGTCACATTCCCCTCGG 59.778 63.158 0.00 0.00 0.00 4.63
93 96 0.178068 TTCCTCCCTGCGTAATCTGC 59.822 55.000 0.00 0.00 0.00 4.26
100 103 0.759346 GGTCATATTCCTCCCTGCGT 59.241 55.000 0.00 0.00 0.00 5.24
288 300 3.206464 ACTCCCCCTTCCCATTCATTAA 58.794 45.455 0.00 0.00 0.00 1.40
303 315 1.471287 GTTGCGGTTTCATTACTCCCC 59.529 52.381 0.00 0.00 0.00 4.81
353 366 1.136872 GCGCACAACTTCGTTTTGCA 61.137 50.000 15.43 0.00 45.78 4.08
382 395 4.719616 GTGAAACTGCCGTCGCGC 62.720 66.667 0.00 0.00 38.08 6.86
383 396 4.072088 GGTGAAACTGCCGTCGCG 62.072 66.667 0.00 0.00 38.08 5.87
384 397 4.072088 CGGTGAAACTGCCGTCGC 62.072 66.667 0.00 0.00 42.73 5.19
392 405 2.665185 GAGGCGTGCGGTGAAACT 60.665 61.111 0.00 0.00 36.74 2.66
393 406 4.072088 CGAGGCGTGCGGTGAAAC 62.072 66.667 0.00 0.00 0.00 2.78
394 407 4.287781 TCGAGGCGTGCGGTGAAA 62.288 61.111 0.00 0.00 0.00 2.69
402 415 3.470567 GTTGCGAGTCGAGGCGTG 61.471 66.667 18.61 0.00 0.00 5.34
403 416 4.719369 GGTTGCGAGTCGAGGCGT 62.719 66.667 18.61 0.00 0.00 5.68
416 429 2.805353 CTCGGACGACAGCGGTTG 60.805 66.667 2.30 2.30 43.17 3.77
417 430 3.292936 ACTCGGACGACAGCGGTT 61.293 61.111 0.00 0.00 43.17 4.44
418 431 4.039357 CACTCGGACGACAGCGGT 62.039 66.667 0.00 0.00 43.17 5.68
419 432 3.669036 CTCACTCGGACGACAGCGG 62.669 68.421 0.00 0.00 43.17 5.52
420 433 2.183858 TTCTCACTCGGACGACAGCG 62.184 60.000 0.00 0.00 44.79 5.18
421 434 0.039437 TTTCTCACTCGGACGACAGC 60.039 55.000 0.00 0.00 0.00 4.40
422 435 1.687628 GTTTCTCACTCGGACGACAG 58.312 55.000 0.00 0.00 0.00 3.51
423 436 0.040692 CGTTTCTCACTCGGACGACA 60.041 55.000 0.00 0.00 35.90 4.35
424 437 0.236711 TCGTTTCTCACTCGGACGAC 59.763 55.000 0.00 0.00 37.76 4.34
425 438 0.236711 GTCGTTTCTCACTCGGACGA 59.763 55.000 0.00 0.00 40.03 4.20
426 439 1.058590 CGTCGTTTCTCACTCGGACG 61.059 60.000 0.00 0.00 35.24 4.79
427 440 0.040603 ACGTCGTTTCTCACTCGGAC 60.041 55.000 0.00 0.00 0.00 4.79
428 441 0.040692 CACGTCGTTTCTCACTCGGA 60.041 55.000 0.00 0.00 0.00 4.55
429 442 1.606350 GCACGTCGTTTCTCACTCGG 61.606 60.000 0.00 0.00 0.00 4.63
430 443 0.933047 TGCACGTCGTTTCTCACTCG 60.933 55.000 0.00 0.00 0.00 4.18
431 444 0.778815 CTGCACGTCGTTTCTCACTC 59.221 55.000 0.00 0.00 0.00 3.51
432 445 0.597637 CCTGCACGTCGTTTCTCACT 60.598 55.000 0.00 0.00 0.00 3.41
433 446 1.853319 CCTGCACGTCGTTTCTCAC 59.147 57.895 0.00 0.00 0.00 3.51
434 447 1.954146 GCCTGCACGTCGTTTCTCA 60.954 57.895 0.00 0.00 0.00 3.27
435 448 2.853914 GCCTGCACGTCGTTTCTC 59.146 61.111 0.00 0.00 0.00 2.87
436 449 2.964438 TTCGCCTGCACGTCGTTTCT 62.964 55.000 0.00 0.00 0.00 2.52
437 450 2.591311 TTCGCCTGCACGTCGTTTC 61.591 57.895 0.00 0.00 0.00 2.78
438 451 2.586635 TTCGCCTGCACGTCGTTT 60.587 55.556 0.00 0.00 0.00 3.60
439 452 2.410638 TAGTTCGCCTGCACGTCGTT 62.411 55.000 0.00 0.00 0.00 3.85
440 453 2.410638 TTAGTTCGCCTGCACGTCGT 62.411 55.000 0.00 0.00 0.00 4.34
441 454 1.731613 TTAGTTCGCCTGCACGTCG 60.732 57.895 0.00 0.00 0.00 5.12
442 455 0.666577 AGTTAGTTCGCCTGCACGTC 60.667 55.000 0.00 0.00 0.00 4.34
443 456 0.599558 TAGTTAGTTCGCCTGCACGT 59.400 50.000 0.00 0.00 0.00 4.49
444 457 0.989890 GTAGTTAGTTCGCCTGCACG 59.010 55.000 0.00 0.00 0.00 5.34
445 458 1.725164 GTGTAGTTAGTTCGCCTGCAC 59.275 52.381 0.00 0.00 35.29 4.57
446 459 1.341852 TGTGTAGTTAGTTCGCCTGCA 59.658 47.619 0.00 0.00 0.00 4.41
447 460 1.725164 GTGTGTAGTTAGTTCGCCTGC 59.275 52.381 0.00 0.00 0.00 4.85
448 461 2.288579 TGGTGTGTAGTTAGTTCGCCTG 60.289 50.000 0.00 0.00 0.00 4.85
449 462 1.965643 TGGTGTGTAGTTAGTTCGCCT 59.034 47.619 0.00 0.00 0.00 5.52
450 463 2.064014 GTGGTGTGTAGTTAGTTCGCC 58.936 52.381 0.00 0.00 0.00 5.54
451 464 2.473984 GTGTGGTGTGTAGTTAGTTCGC 59.526 50.000 0.00 0.00 0.00 4.70
452 465 3.488310 GTGTGTGGTGTGTAGTTAGTTCG 59.512 47.826 0.00 0.00 0.00 3.95
453 466 4.506654 CAGTGTGTGGTGTGTAGTTAGTTC 59.493 45.833 0.00 0.00 0.00 3.01
454 467 4.439057 CAGTGTGTGGTGTGTAGTTAGTT 58.561 43.478 0.00 0.00 0.00 2.24
455 468 3.181469 CCAGTGTGTGGTGTGTAGTTAGT 60.181 47.826 0.00 0.00 42.17 2.24
456 469 3.390135 CCAGTGTGTGGTGTGTAGTTAG 58.610 50.000 0.00 0.00 42.17 2.34
457 470 3.462483 CCAGTGTGTGGTGTGTAGTTA 57.538 47.619 0.00 0.00 42.17 2.24
458 471 2.325583 CCAGTGTGTGGTGTGTAGTT 57.674 50.000 0.00 0.00 42.17 2.24
468 481 0.396435 TAGGACAAGGCCAGTGTGTG 59.604 55.000 16.19 1.36 0.00 3.82
469 482 0.396811 GTAGGACAAGGCCAGTGTGT 59.603 55.000 16.19 8.81 0.00 3.72
470 483 0.670546 CGTAGGACAAGGCCAGTGTG 60.671 60.000 16.19 5.58 0.00 3.82
471 484 1.119574 ACGTAGGACAAGGCCAGTGT 61.120 55.000 11.62 11.62 0.00 3.55
472 485 0.670546 CACGTAGGACAAGGCCAGTG 60.671 60.000 5.01 4.97 0.00 3.66
473 486 1.671742 CACGTAGGACAAGGCCAGT 59.328 57.895 5.01 2.07 0.00 4.00
474 487 1.079127 CCACGTAGGACAAGGCCAG 60.079 63.158 5.01 0.00 41.22 4.85
475 488 3.065306 CCACGTAGGACAAGGCCA 58.935 61.111 5.01 0.00 41.22 5.36
476 489 2.436115 GCCACGTAGGACAAGGCC 60.436 66.667 0.00 0.00 41.22 5.19
477 490 2.033194 GTGCCACGTAGGACAAGGC 61.033 63.158 0.00 2.14 45.41 4.35
478 491 0.949105 GTGTGCCACGTAGGACAAGG 60.949 60.000 10.20 0.00 41.22 3.61
479 492 0.249699 TGTGTGCCACGTAGGACAAG 60.250 55.000 10.20 0.00 41.22 3.16
480 493 0.178301 TTGTGTGCCACGTAGGACAA 59.822 50.000 10.20 7.57 41.22 3.18
481 494 0.178301 TTTGTGTGCCACGTAGGACA 59.822 50.000 3.90 3.90 41.22 4.02
482 495 1.301423 TTTTGTGTGCCACGTAGGAC 58.699 50.000 0.00 0.00 41.22 3.85
483 496 2.147958 GATTTTGTGTGCCACGTAGGA 58.852 47.619 8.04 0.00 41.22 2.94
484 497 2.095768 CAGATTTTGTGTGCCACGTAGG 60.096 50.000 0.00 0.00 37.14 3.18
485 498 2.665519 GCAGATTTTGTGTGCCACGTAG 60.666 50.000 0.00 0.00 41.03 3.51
486 499 1.265635 GCAGATTTTGTGTGCCACGTA 59.734 47.619 0.00 0.00 41.03 3.57
487 500 0.030638 GCAGATTTTGTGTGCCACGT 59.969 50.000 0.00 0.00 41.03 4.49
488 501 2.800096 GCAGATTTTGTGTGCCACG 58.200 52.632 0.00 0.00 41.03 4.94
492 505 1.337167 GGGAAGGCAGATTTTGTGTGC 60.337 52.381 0.00 0.00 45.83 4.57
493 506 1.068333 CGGGAAGGCAGATTTTGTGTG 60.068 52.381 0.00 0.00 0.00 3.82
494 507 1.247567 CGGGAAGGCAGATTTTGTGT 58.752 50.000 0.00 0.00 0.00 3.72
495 508 1.068333 CACGGGAAGGCAGATTTTGTG 60.068 52.381 0.00 0.00 0.00 3.33
496 509 1.247567 CACGGGAAGGCAGATTTTGT 58.752 50.000 0.00 0.00 0.00 2.83
497 510 1.200020 GACACGGGAAGGCAGATTTTG 59.800 52.381 0.00 0.00 0.00 2.44
498 511 1.202879 TGACACGGGAAGGCAGATTTT 60.203 47.619 0.00 0.00 0.00 1.82
499 512 0.400213 TGACACGGGAAGGCAGATTT 59.600 50.000 0.00 0.00 0.00 2.17
500 513 0.400213 TTGACACGGGAAGGCAGATT 59.600 50.000 0.00 0.00 0.00 2.40
501 514 0.036010 CTTGACACGGGAAGGCAGAT 60.036 55.000 0.00 0.00 0.00 2.90
502 515 1.118965 TCTTGACACGGGAAGGCAGA 61.119 55.000 0.00 0.00 0.00 4.26
503 516 0.036010 ATCTTGACACGGGAAGGCAG 60.036 55.000 0.00 0.00 0.00 4.85
504 517 0.400213 AATCTTGACACGGGAAGGCA 59.600 50.000 0.00 0.00 0.00 4.75
505 518 1.087501 GAATCTTGACACGGGAAGGC 58.912 55.000 0.00 0.00 0.00 4.35
506 519 1.337823 ACGAATCTTGACACGGGAAGG 60.338 52.381 0.00 0.00 0.00 3.46
507 520 1.726791 CACGAATCTTGACACGGGAAG 59.273 52.381 0.00 0.00 0.00 3.46
508 521 1.790755 CACGAATCTTGACACGGGAA 58.209 50.000 0.00 0.00 0.00 3.97
509 522 0.669318 GCACGAATCTTGACACGGGA 60.669 55.000 0.00 0.00 0.00 5.14
510 523 0.948623 TGCACGAATCTTGACACGGG 60.949 55.000 0.00 0.00 0.00 5.28
511 524 0.865111 TTGCACGAATCTTGACACGG 59.135 50.000 0.00 0.00 0.00 4.94
512 525 2.661504 TTTGCACGAATCTTGACACG 57.338 45.000 0.00 0.00 0.00 4.49
513 526 6.984740 TTAATTTTGCACGAATCTTGACAC 57.015 33.333 0.00 0.00 0.00 3.67
514 527 7.060518 CGATTTAATTTTGCACGAATCTTGACA 59.939 33.333 0.00 0.00 0.00 3.58
515 528 7.270365 TCGATTTAATTTTGCACGAATCTTGAC 59.730 33.333 0.00 0.00 0.00 3.18
516 529 7.270365 GTCGATTTAATTTTGCACGAATCTTGA 59.730 33.333 0.00 0.00 0.00 3.02
517 530 7.375781 GTCGATTTAATTTTGCACGAATCTTG 58.624 34.615 0.00 0.00 0.00 3.02
518 531 6.248420 CGTCGATTTAATTTTGCACGAATCTT 59.752 34.615 0.00 0.00 0.00 2.40
519 532 5.732647 CGTCGATTTAATTTTGCACGAATCT 59.267 36.000 0.00 0.00 0.00 2.40
520 533 5.053286 CCGTCGATTTAATTTTGCACGAATC 60.053 40.000 0.00 0.00 0.00 2.52
521 534 4.791163 CCGTCGATTTAATTTTGCACGAAT 59.209 37.500 0.00 0.00 0.00 3.34
522 535 4.152526 CCGTCGATTTAATTTTGCACGAA 58.847 39.130 0.00 0.00 0.00 3.85
523 536 3.738399 CCGTCGATTTAATTTTGCACGA 58.262 40.909 0.00 0.00 0.00 4.35
524 537 2.275253 GCCGTCGATTTAATTTTGCACG 59.725 45.455 0.00 0.00 0.00 5.34
525 538 2.275253 CGCCGTCGATTTAATTTTGCAC 59.725 45.455 0.00 0.00 38.10 4.57
526 539 2.159824 TCGCCGTCGATTTAATTTTGCA 59.840 40.909 0.00 0.00 40.21 4.08
527 540 2.776330 TCGCCGTCGATTTAATTTTGC 58.224 42.857 0.00 0.00 40.21 3.68
550 563 4.681978 AACTCGCCCACACGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
551 564 4.988598 CAACTCGCCCACACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
553 566 4.980805 TCCAACTCGCCCACACGC 62.981 66.667 0.00 0.00 0.00 5.34
554 567 2.709125 TTCTCCAACTCGCCCACACG 62.709 60.000 0.00 0.00 0.00 4.49
555 568 0.951040 CTTCTCCAACTCGCCCACAC 60.951 60.000 0.00 0.00 0.00 3.82
556 569 1.371183 CTTCTCCAACTCGCCCACA 59.629 57.895 0.00 0.00 0.00 4.17
557 570 0.951040 CACTTCTCCAACTCGCCCAC 60.951 60.000 0.00 0.00 0.00 4.61
558 571 1.371183 CACTTCTCCAACTCGCCCA 59.629 57.895 0.00 0.00 0.00 5.36
559 572 2.035442 GCACTTCTCCAACTCGCCC 61.035 63.158 0.00 0.00 0.00 6.13
560 573 2.035442 GGCACTTCTCCAACTCGCC 61.035 63.158 0.00 0.00 0.00 5.54
561 574 1.301716 TGGCACTTCTCCAACTCGC 60.302 57.895 0.00 0.00 0.00 5.03
562 575 0.249868 TGTGGCACTTCTCCAACTCG 60.250 55.000 19.83 0.00 35.01 4.18
563 576 1.230324 GTGTGGCACTTCTCCAACTC 58.770 55.000 19.83 0.00 35.01 3.01
564 577 0.532862 CGTGTGGCACTTCTCCAACT 60.533 55.000 19.83 0.00 35.01 3.16
565 578 0.814010 ACGTGTGGCACTTCTCCAAC 60.814 55.000 19.83 5.57 35.01 3.77
566 579 0.813610 CACGTGTGGCACTTCTCCAA 60.814 55.000 19.83 0.00 35.01 3.53
567 580 1.227527 CACGTGTGGCACTTCTCCA 60.228 57.895 19.83 0.00 31.34 3.86
568 581 1.227556 ACACGTGTGGCACTTCTCC 60.228 57.895 22.71 0.84 34.19 3.71
569 582 1.934463 CACACGTGTGGCACTTCTC 59.066 57.895 35.65 5.98 42.10 2.87
570 583 4.124910 CACACGTGTGGCACTTCT 57.875 55.556 35.65 1.93 42.10 2.85
582 595 0.099259 TCGATACTAACGCCCACACG 59.901 55.000 0.00 0.00 39.50 4.49
583 596 1.535437 CCTCGATACTAACGCCCACAC 60.535 57.143 0.00 0.00 0.00 3.82
584 597 0.742505 CCTCGATACTAACGCCCACA 59.257 55.000 0.00 0.00 0.00 4.17
585 598 0.596859 GCCTCGATACTAACGCCCAC 60.597 60.000 0.00 0.00 0.00 4.61
586 599 1.737816 GCCTCGATACTAACGCCCA 59.262 57.895 0.00 0.00 0.00 5.36
587 600 1.371389 CGCCTCGATACTAACGCCC 60.371 63.158 0.00 0.00 0.00 6.13
588 601 0.933509 CACGCCTCGATACTAACGCC 60.934 60.000 0.00 0.00 0.00 5.68
589 602 0.248377 ACACGCCTCGATACTAACGC 60.248 55.000 0.00 0.00 0.00 4.84
590 603 1.463805 CACACGCCTCGATACTAACG 58.536 55.000 0.00 0.00 0.00 3.18
591 604 1.535437 CCCACACGCCTCGATACTAAC 60.535 57.143 0.00 0.00 0.00 2.34
592 605 0.742505 CCCACACGCCTCGATACTAA 59.257 55.000 0.00 0.00 0.00 2.24
593 606 1.731433 GCCCACACGCCTCGATACTA 61.731 60.000 0.00 0.00 0.00 1.82
594 607 3.077519 GCCCACACGCCTCGATACT 62.078 63.158 0.00 0.00 0.00 2.12
595 608 2.585247 GCCCACACGCCTCGATAC 60.585 66.667 0.00 0.00 0.00 2.24
596 609 4.201679 CGCCCACACGCCTCGATA 62.202 66.667 0.00 0.00 0.00 2.92
600 613 4.681978 AACTCGCCCACACGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
601 614 4.988598 CAACTCGCCCACACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
603 616 4.980805 TCCAACTCGCCCACACGC 62.981 66.667 0.00 0.00 0.00 5.34
604 617 2.709125 TTCTCCAACTCGCCCACACG 62.709 60.000 0.00 0.00 0.00 4.49
605 618 0.951040 CTTCTCCAACTCGCCCACAC 60.951 60.000 0.00 0.00 0.00 3.82
606 619 1.371183 CTTCTCCAACTCGCCCACA 59.629 57.895 0.00 0.00 0.00 4.17
607 620 0.951040 CACTTCTCCAACTCGCCCAC 60.951 60.000 0.00 0.00 0.00 4.61
608 621 1.371183 CACTTCTCCAACTCGCCCA 59.629 57.895 0.00 0.00 0.00 5.36
609 622 2.035442 GCACTTCTCCAACTCGCCC 61.035 63.158 0.00 0.00 0.00 6.13
610 623 2.035442 GGCACTTCTCCAACTCGCC 61.035 63.158 0.00 0.00 0.00 5.54
611 624 1.301716 TGGCACTTCTCCAACTCGC 60.302 57.895 0.00 0.00 0.00 5.03
612 625 0.249868 TGTGGCACTTCTCCAACTCG 60.250 55.000 19.83 0.00 35.01 4.18
613 626 1.230324 GTGTGGCACTTCTCCAACTC 58.770 55.000 19.83 0.00 35.01 3.01
614 627 0.532862 CGTGTGGCACTTCTCCAACT 60.533 55.000 19.83 0.00 35.01 3.16
615 628 0.814010 ACGTGTGGCACTTCTCCAAC 60.814 55.000 19.83 5.57 35.01 3.77
616 629 0.813610 CACGTGTGGCACTTCTCCAA 60.814 55.000 19.83 0.00 35.01 3.53
617 630 1.227527 CACGTGTGGCACTTCTCCA 60.228 57.895 19.83 0.00 31.34 3.86
618 631 1.227556 ACACGTGTGGCACTTCTCC 60.228 57.895 22.71 0.84 34.19 3.71
619 632 1.934463 CACACGTGTGGCACTTCTC 59.066 57.895 35.65 5.98 42.10 2.87
620 633 4.124910 CACACGTGTGGCACTTCT 57.875 55.556 35.65 1.93 42.10 2.85
807 822 2.022129 CAACTCGCCCACACGTCTC 61.022 63.158 0.00 0.00 0.00 3.36
858 873 5.445964 AGCACCTTCCCAATTATTATTCGT 58.554 37.500 0.00 0.00 0.00 3.85
863 878 5.430417 TCACCTAGCACCTTCCCAATTATTA 59.570 40.000 0.00 0.00 0.00 0.98
865 880 3.785887 TCACCTAGCACCTTCCCAATTAT 59.214 43.478 0.00 0.00 0.00 1.28
976 1023 2.766400 CGTGGGAGGAGAGACGCTC 61.766 68.421 0.00 0.00 43.17 5.03
1101 1148 2.822255 GGGTTTCGCGCATAGGCA 60.822 61.111 8.75 0.00 41.24 4.75
1614 1682 4.803426 GACACTCCGAGGGCGCAG 62.803 72.222 10.83 0.00 35.83 5.18
1725 1793 7.928706 CCAAGGTCTAATCTCATATCTCGTTTT 59.071 37.037 0.00 0.00 0.00 2.43
1763 1831 2.402564 TCAACATCCAAAAGCCCCAAA 58.597 42.857 0.00 0.00 0.00 3.28
1768 1836 3.383761 CACACTTCAACATCCAAAAGCC 58.616 45.455 0.00 0.00 0.00 4.35
1994 2076 2.611518 AGCAATACGAGAGCAACTCAC 58.388 47.619 10.61 0.00 45.14 3.51
2104 2186 2.298300 CAACTTGCAAGTAAACTCGCG 58.702 47.619 31.31 0.00 38.57 5.87
2153 2269 2.795329 AGGCACGATTTTTCAGATGGT 58.205 42.857 0.00 0.00 0.00 3.55
2168 2284 4.836125 TTCAATTGAACTCTGAAGGCAC 57.164 40.909 16.91 0.00 0.00 5.01
2321 2437 0.675633 GTGGGCATGCCATTATCCAC 59.324 55.000 36.56 27.86 37.98 4.02
2372 2488 9.293404 ACTACTAGTACAGAGACAACAAATGTA 57.707 33.333 0.00 0.00 44.12 2.29
2427 2618 5.854010 TGTAGATTGTCATGTACTCCCTC 57.146 43.478 0.00 0.00 31.62 4.30
2452 2643 6.486657 AGAAAAATGTGCTACTGCTAGAAACA 59.513 34.615 0.00 0.00 40.48 2.83
2466 2657 5.063817 AGTGAAAACAGCAAGAAAAATGTGC 59.936 36.000 0.00 0.00 38.59 4.57
2569 2760 2.902486 TGGCCCAAGCTGATCTATCTAG 59.098 50.000 0.00 0.00 39.73 2.43
2587 2778 7.719871 TTACAGAGGGAGTAAGATATATGGC 57.280 40.000 0.00 0.00 0.00 4.40
2620 2811 9.915629 CACTACTTCAGTAATCTAAACACTCTT 57.084 33.333 0.00 0.00 34.98 2.85
2621 2812 9.298250 TCACTACTTCAGTAATCTAAACACTCT 57.702 33.333 0.00 0.00 34.98 3.24
2630 2821 7.916450 GCGTTTAGATCACTACTTCAGTAATCT 59.084 37.037 0.00 5.42 34.98 2.40
2631 2822 7.916450 AGCGTTTAGATCACTACTTCAGTAATC 59.084 37.037 0.00 0.00 34.98 1.75
2632 2823 7.773149 AGCGTTTAGATCACTACTTCAGTAAT 58.227 34.615 0.00 0.00 34.98 1.89
2633 2824 7.120873 AGAGCGTTTAGATCACTACTTCAGTAA 59.879 37.037 0.00 0.00 37.82 2.24
2634 2825 6.598457 AGAGCGTTTAGATCACTACTTCAGTA 59.402 38.462 0.00 0.00 37.82 2.74
2635 2826 5.416326 AGAGCGTTTAGATCACTACTTCAGT 59.584 40.000 0.00 0.00 37.82 3.41
2636 2827 5.885881 AGAGCGTTTAGATCACTACTTCAG 58.114 41.667 0.00 0.00 37.82 3.02
2637 2828 5.899120 AGAGCGTTTAGATCACTACTTCA 57.101 39.130 0.00 0.00 37.82 3.02
2638 2829 7.249147 TGTAAGAGCGTTTAGATCACTACTTC 58.751 38.462 0.00 0.00 37.82 3.01
2639 2830 7.154435 TGTAAGAGCGTTTAGATCACTACTT 57.846 36.000 0.00 0.00 37.82 2.24
2640 2831 6.754702 TGTAAGAGCGTTTAGATCACTACT 57.245 37.500 0.00 0.00 37.82 2.57
2641 2832 7.988904 AATGTAAGAGCGTTTAGATCACTAC 57.011 36.000 0.00 0.00 37.82 2.73


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

AutoCloner maintained by Alex Coulton.