Multiple sequence alignment - TraesCS3B01G382800

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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 TraesCS3B01G382800 chr3B 100.000 4263 0 0 1 4263 602473130 602468868 0.000000e+00 7873.0
1 TraesCS3B01G382800 chr3A 89.795 3802 225 64 546 4263 598904627 598900905 0.000000e+00 4721.0
2 TraesCS3B01G382800 chr3A 90.837 251 15 3 60 302 598905042 598904792 3.180000e-86 329.0
3 TraesCS3B01G382800 chr3A 89.781 137 10 2 300 436 598904762 598904630 5.670000e-39 172.0
4 TraesCS3B01G382800 chr3A 95.098 102 5 0 445 546 541219440 541219339 1.230000e-35 161.0
5 TraesCS3B01G382800 chr3A 100.000 45 0 0 2622 2666 598902536 598902492 2.730000e-12 84.2
6 TraesCS3B01G382800 chr3D 90.067 3443 202 57 891 4262 456010895 456007522 0.000000e+00 4335.0
7 TraesCS3B01G382800 chr3D 94.628 242 12 1 64 304 456011741 456011500 1.450000e-99 374.0
8 TraesCS3B01G382800 chr3D 89.492 295 8 8 546 818 456011337 456011044 6.780000e-93 351.0
9 TraesCS3B01G382800 chr3D 93.431 137 5 1 300 436 456011472 456011340 2.600000e-47 200.0
10 TraesCS3B01G382800 chr3D 97.778 45 1 0 2622 2666 456009182 456009138 1.270000e-10 78.7
11 TraesCS3B01G382800 chr5D 86.124 1117 106 24 2251 3355 491583647 491584726 0.000000e+00 1158.0
12 TraesCS3B01G382800 chr5D 91.075 493 24 11 533 1007 491583155 491583645 0.000000e+00 649.0
13 TraesCS3B01G382800 chr5D 94.472 199 8 2 3 201 491582739 491582934 1.930000e-78 303.0
14 TraesCS3B01G382800 chr5D 93.793 145 4 3 300 443 491583035 491583175 3.340000e-51 213.0
15 TraesCS3B01G382800 chr5D 100.000 45 0 0 2622 2666 491583972 491584016 2.730000e-12 84.2
16 TraesCS3B01G382800 chr5D 94.444 54 2 1 252 304 491582954 491583007 9.820000e-12 82.4
17 TraesCS3B01G382800 chr5B 95.192 104 5 0 443 546 271913673 271913570 9.480000e-37 165.0
18 TraesCS3B01G382800 chr7B 95.146 103 5 0 444 546 524879697 524879799 3.410000e-36 163.0
19 TraesCS3B01G382800 chrUn 93.137 102 7 0 445 546 191003549 191003448 2.660000e-32 150.0
20 TraesCS3B01G382800 chrUn 91.346 104 8 1 444 546 242486655 242486552 1.600000e-29 141.0
21 TraesCS3B01G382800 chr6B 93.137 102 7 0 445 546 432865901 432865800 2.660000e-32 150.0
22 TraesCS3B01G382800 chr4B 90.385 104 9 1 444 546 420427482 420427585 7.440000e-28 135.0
23 TraesCS3B01G382800 chr4A 89.623 106 8 1 444 546 725914341 725914446 9.620000e-27 132.0
24 TraesCS3B01G382800 chr1A 86.538 104 13 1 439 541 59948692 59948795 3.480000e-21 113.0


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 TraesCS3B01G382800 chr3B 602468868 602473130 4262 True 7873.000000 7873 100.00000 1 4263 1 chr3B.!!$R1 4262
1 TraesCS3B01G382800 chr3A 598900905 598905042 4137 True 1326.550000 4721 92.60325 60 4263 4 chr3A.!!$R2 4203
2 TraesCS3B01G382800 chr3D 456007522 456011741 4219 True 1067.740000 4335 93.07920 64 4262 5 chr3D.!!$R1 4198
3 TraesCS3B01G382800 chr5D 491582739 491584726 1987 False 414.933333 1158 93.31800 3 3355 6 chr5D.!!$F1 3352

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
516 558 0.179081 GTCGCTCCGCCTATTTCCTT 60.179 55.0 0.0 0.0 0.0 3.36 F
2240 2425 0.110419 TGCTCGCCGAATTTTTGACG 60.110 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2433 0.100503 GGGAAAAATGACGGCGGATG 59.899 55.0 13.24 0.0 0.00 3.51 R
3277 3520 0.747255 TCCAACGCTAGAGAGCCATC 59.253 55.0 0.00 0.0 46.86 3.51 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
32 33 9.823647 ATATTCTAAAGAGATGTACCACACTTG 57.176 33.333 0.00 0.00 0.00 3.16
56 57 4.400884 TGTGGGTTGACAATAATATGCACC 59.599 41.667 0.00 0.00 0.00 5.01
130 133 2.740055 GGGTGACGCTGCACTCTG 60.740 66.667 0.00 0.00 36.34 3.35
262 271 1.546923 TCGACCAGCAGAAAATCCGTA 59.453 47.619 0.00 0.00 0.00 4.02
346 388 3.435186 GCTCCAGCTTCGGTTGGC 61.435 66.667 0.00 0.00 44.51 4.52
347 389 2.747855 CTCCAGCTTCGGTTGGCC 60.748 66.667 0.00 0.00 44.51 5.36
348 390 3.249189 TCCAGCTTCGGTTGGCCT 61.249 61.111 3.32 0.00 44.51 5.19
349 391 3.058160 CCAGCTTCGGTTGGCCTG 61.058 66.667 3.32 0.00 39.36 4.85
350 392 2.281761 CAGCTTCGGTTGGCCTGT 60.282 61.111 3.32 0.00 0.00 4.00
351 393 2.281761 AGCTTCGGTTGGCCTGTG 60.282 61.111 3.32 0.00 0.00 3.66
353 395 1.896660 GCTTCGGTTGGCCTGTGAA 60.897 57.895 3.32 2.11 0.00 3.18
354 396 1.949257 CTTCGGTTGGCCTGTGAAC 59.051 57.895 3.32 0.00 0.00 3.18
355 397 1.841663 CTTCGGTTGGCCTGTGAACG 61.842 60.000 3.32 1.85 0.00 3.95
444 486 2.840296 GCTTTCTGCAGGAGTTATGC 57.160 50.000 15.13 5.53 44.11 3.14
445 487 1.063174 GCTTTCTGCAGGAGTTATGCG 59.937 52.381 15.13 0.00 46.87 4.73
446 488 2.621338 CTTTCTGCAGGAGTTATGCGA 58.379 47.619 15.13 0.00 46.87 5.10
447 489 2.760634 TTCTGCAGGAGTTATGCGAA 57.239 45.000 15.13 0.00 46.87 4.70
448 490 2.760634 TCTGCAGGAGTTATGCGAAA 57.239 45.000 15.13 0.00 46.87 3.46
449 491 2.346803 TCTGCAGGAGTTATGCGAAAC 58.653 47.619 15.13 0.00 46.87 2.78
450 492 1.061131 CTGCAGGAGTTATGCGAAACG 59.939 52.381 5.57 0.00 46.87 3.60
451 493 1.337354 TGCAGGAGTTATGCGAAACGA 60.337 47.619 0.00 0.00 46.87 3.85
452 494 1.060698 GCAGGAGTTATGCGAAACGAC 59.939 52.381 0.00 0.00 34.46 4.34
453 495 2.607187 CAGGAGTTATGCGAAACGACT 58.393 47.619 0.00 0.00 34.46 4.18
454 496 2.599082 CAGGAGTTATGCGAAACGACTC 59.401 50.000 0.00 0.00 36.80 3.36
455 497 1.925185 GGAGTTATGCGAAACGACTCC 59.075 52.381 11.72 11.72 46.60 3.85
456 498 2.877335 GAGTTATGCGAAACGACTCCT 58.123 47.619 0.00 0.00 34.46 3.69
457 499 3.251571 GAGTTATGCGAAACGACTCCTT 58.748 45.455 0.00 0.00 34.46 3.36
458 500 2.993899 AGTTATGCGAAACGACTCCTTG 59.006 45.455 0.00 0.00 34.46 3.61
459 501 2.004583 TATGCGAAACGACTCCTTGG 57.995 50.000 0.00 0.00 0.00 3.61
460 502 1.298859 ATGCGAAACGACTCCTTGGC 61.299 55.000 0.00 0.00 0.00 4.52
468 510 3.187211 GACTCCTTGGCGATCGATC 57.813 57.895 21.57 15.68 0.00 3.69
486 528 2.027605 GCCGGAGCGATCGATTCA 59.972 61.111 21.57 0.00 0.00 2.57
487 529 2.018866 GCCGGAGCGATCGATTCAG 61.019 63.158 21.57 15.18 0.00 3.02
488 530 1.654774 CCGGAGCGATCGATTCAGA 59.345 57.895 21.57 0.00 0.00 3.27
489 531 0.242286 CCGGAGCGATCGATTCAGAT 59.758 55.000 21.57 0.00 0.00 2.90
490 532 1.612156 CGGAGCGATCGATTCAGATC 58.388 55.000 21.57 0.00 42.58 2.75
498 540 4.310672 GATTCAGATCGCGCTCGT 57.689 55.556 5.56 0.00 36.96 4.18
499 541 2.129025 GATTCAGATCGCGCTCGTC 58.871 57.895 5.56 0.03 36.96 4.20
500 542 1.592560 GATTCAGATCGCGCTCGTCG 61.593 60.000 5.56 0.00 42.12 5.12
510 552 3.967335 GCTCGTCGCTCCGCCTAT 61.967 66.667 0.00 0.00 35.14 2.57
511 553 2.722487 CTCGTCGCTCCGCCTATT 59.278 61.111 0.00 0.00 0.00 1.73
512 554 1.065928 CTCGTCGCTCCGCCTATTT 59.934 57.895 0.00 0.00 0.00 1.40
513 555 0.935366 CTCGTCGCTCCGCCTATTTC 60.935 60.000 0.00 0.00 0.00 2.17
514 556 1.949631 CGTCGCTCCGCCTATTTCC 60.950 63.158 0.00 0.00 0.00 3.13
515 557 1.442148 GTCGCTCCGCCTATTTCCT 59.558 57.895 0.00 0.00 0.00 3.36
516 558 0.179081 GTCGCTCCGCCTATTTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
517 559 0.539986 TCGCTCCGCCTATTTCCTTT 59.460 50.000 0.00 0.00 0.00 3.11
518 560 0.938008 CGCTCCGCCTATTTCCTTTC 59.062 55.000 0.00 0.00 0.00 2.62
519 561 1.309950 GCTCCGCCTATTTCCTTTCC 58.690 55.000 0.00 0.00 0.00 3.13
520 562 1.968704 CTCCGCCTATTTCCTTTCCC 58.031 55.000 0.00 0.00 0.00 3.97
521 563 1.490910 CTCCGCCTATTTCCTTTCCCT 59.509 52.381 0.00 0.00 0.00 4.20
522 564 1.920351 TCCGCCTATTTCCTTTCCCTT 59.080 47.619 0.00 0.00 0.00 3.95
523 565 2.310647 TCCGCCTATTTCCTTTCCCTTT 59.689 45.455 0.00 0.00 0.00 3.11
524 566 2.688446 CCGCCTATTTCCTTTCCCTTTC 59.312 50.000 0.00 0.00 0.00 2.62
525 567 3.621558 CGCCTATTTCCTTTCCCTTTCT 58.378 45.455 0.00 0.00 0.00 2.52
526 568 4.384868 CCGCCTATTTCCTTTCCCTTTCTA 60.385 45.833 0.00 0.00 0.00 2.10
527 569 4.816925 CGCCTATTTCCTTTCCCTTTCTAG 59.183 45.833 0.00 0.00 0.00 2.43
528 570 4.580995 GCCTATTTCCTTTCCCTTTCTAGC 59.419 45.833 0.00 0.00 0.00 3.42
529 571 5.133941 CCTATTTCCTTTCCCTTTCTAGCC 58.866 45.833 0.00 0.00 0.00 3.93
530 572 4.955693 ATTTCCTTTCCCTTTCTAGCCT 57.044 40.909 0.00 0.00 0.00 4.58
531 573 4.741928 TTTCCTTTCCCTTTCTAGCCTT 57.258 40.909 0.00 0.00 0.00 4.35
532 574 4.741928 TTCCTTTCCCTTTCTAGCCTTT 57.258 40.909 0.00 0.00 0.00 3.11
533 575 4.741928 TCCTTTCCCTTTCTAGCCTTTT 57.258 40.909 0.00 0.00 0.00 2.27
534 576 5.074746 TCCTTTCCCTTTCTAGCCTTTTT 57.925 39.130 0.00 0.00 0.00 1.94
535 577 5.077564 TCCTTTCCCTTTCTAGCCTTTTTC 58.922 41.667 0.00 0.00 0.00 2.29
536 578 4.220821 CCTTTCCCTTTCTAGCCTTTTTCC 59.779 45.833 0.00 0.00 0.00 3.13
537 579 4.741928 TTCCCTTTCTAGCCTTTTTCCT 57.258 40.909 0.00 0.00 0.00 3.36
538 580 4.741928 TCCCTTTCTAGCCTTTTTCCTT 57.258 40.909 0.00 0.00 0.00 3.36
539 581 5.074746 TCCCTTTCTAGCCTTTTTCCTTT 57.925 39.130 0.00 0.00 0.00 3.11
540 582 5.464069 TCCCTTTCTAGCCTTTTTCCTTTT 58.536 37.500 0.00 0.00 0.00 2.27
541 583 5.538813 TCCCTTTCTAGCCTTTTTCCTTTTC 59.461 40.000 0.00 0.00 0.00 2.29
542 584 5.540337 CCCTTTCTAGCCTTTTTCCTTTTCT 59.460 40.000 0.00 0.00 0.00 2.52
543 585 6.450545 CCTTTCTAGCCTTTTTCCTTTTCTG 58.549 40.000 0.00 0.00 0.00 3.02
544 586 6.405278 TTTCTAGCCTTTTTCCTTTTCTGG 57.595 37.500 0.00 0.00 0.00 3.86
678 734 2.568100 GCAAGCGCTGATATCAAATCG 58.432 47.619 12.58 11.25 34.30 3.34
709 765 3.513515 AGAATATCTTGCGAGATCTCCCC 59.486 47.826 20.08 8.90 41.68 4.81
737 795 1.608055 TCATTATGGCCTCCATTGCG 58.392 50.000 3.32 0.00 42.23 4.85
829 904 3.222599 TACGACCCGTCCCCCTCAA 62.223 63.158 0.00 0.00 41.54 3.02
888 963 2.604174 CCCGCGGCGGCTATAAAAG 61.604 63.158 34.77 15.40 46.86 2.27
1015 1182 0.988145 CTCCATGGCTTACTCCCCCA 60.988 60.000 6.96 0.00 0.00 4.96
1016 1183 0.988145 TCCATGGCTTACTCCCCCAG 60.988 60.000 6.96 0.00 31.12 4.45
1081 1248 2.640302 GCAGTCTCCGAGGACAGCA 61.640 63.158 15.74 0.00 44.44 4.41
1136 1303 4.864334 CATGCCGCTCCCCTCCAC 62.864 72.222 0.00 0.00 0.00 4.02
1174 1341 1.446099 GCTCTGTTCGACCGCATGA 60.446 57.895 0.00 0.00 0.00 3.07
1441 1608 3.702048 CCGCGGAGGGTGAGGAAA 61.702 66.667 24.07 0.00 39.56 3.13
1573 1740 1.304464 GTGGGGCTTTTCTCTGGGG 60.304 63.158 0.00 0.00 0.00 4.96
1790 1957 4.717629 CGACAGCGGCGAGTGGAA 62.718 66.667 12.98 0.00 0.00 3.53
1854 2021 2.693074 TGACATTGCTCAGGTATCGCTA 59.307 45.455 0.00 0.00 0.00 4.26
2005 2189 7.938140 ATTTAGCAAAGGATAAGCACAAGTA 57.062 32.000 0.00 0.00 0.00 2.24
2066 2250 1.199327 GAGCGCCCTACCAAAAGTTTC 59.801 52.381 2.29 0.00 0.00 2.78
2098 2282 6.825610 ACCAAACTAAAGGCATGATCAAAAA 58.174 32.000 0.00 0.00 0.00 1.94
2194 2379 1.412079 TGGTTTGCAGCAAATGACCT 58.588 45.000 23.26 0.00 35.74 3.85
2219 2404 0.929366 CATGCATATTCGCGCGCAAA 60.929 50.000 32.61 21.61 38.01 3.68
2223 2408 0.157269 CATATTCGCGCGCAAATTGC 59.843 50.000 32.61 8.09 40.69 3.56
2237 2422 3.724277 CAAATTGCTCGCCGAATTTTTG 58.276 40.909 0.00 0.00 30.94 2.44
2238 2423 3.296322 AATTGCTCGCCGAATTTTTGA 57.704 38.095 0.00 0.00 0.00 2.69
2239 2424 2.044888 TTGCTCGCCGAATTTTTGAC 57.955 45.000 0.00 0.00 0.00 3.18
2240 2425 0.110419 TGCTCGCCGAATTTTTGACG 60.110 50.000 0.00 0.00 0.00 4.35
2241 2426 0.165079 GCTCGCCGAATTTTTGACGA 59.835 50.000 0.00 0.00 0.00 4.20
2243 2428 2.727916 GCTCGCCGAATTTTTGACGAAT 60.728 45.455 0.00 0.00 0.00 3.34
2244 2429 2.840176 CTCGCCGAATTTTTGACGAATG 59.160 45.455 0.00 0.00 0.00 2.67
2246 2431 2.667171 CGCCGAATTTTTGACGAATGGT 60.667 45.455 0.00 0.00 0.00 3.55
2248 2433 3.363724 GCCGAATTTTTGACGAATGGTTC 59.636 43.478 0.00 0.00 0.00 3.62
2249 2434 4.541779 CCGAATTTTTGACGAATGGTTCA 58.458 39.130 0.00 0.00 0.00 3.18
2273 2459 2.202427 GTCATTTTTCCCGCGCGG 60.202 61.111 41.00 41.00 0.00 6.46
2290 2476 0.594110 CGGTGGCCAAAATTACGTGT 59.406 50.000 7.24 0.00 0.00 4.49
2291 2477 1.664588 CGGTGGCCAAAATTACGTGTG 60.665 52.381 7.24 0.00 0.00 3.82
2295 2481 1.609555 GGCCAAAATTACGTGTGTGGA 59.390 47.619 0.00 0.00 0.00 4.02
2296 2482 2.351350 GGCCAAAATTACGTGTGTGGAG 60.351 50.000 0.00 0.00 0.00 3.86
2585 2787 3.619233 AAACCGAAAACGAAGGATGTG 57.381 42.857 0.00 0.00 0.00 3.21
2586 2788 1.519408 ACCGAAAACGAAGGATGTGG 58.481 50.000 0.00 0.00 0.00 4.17
2587 2789 0.802494 CCGAAAACGAAGGATGTGGG 59.198 55.000 0.00 0.00 0.00 4.61
2588 2790 0.802494 CGAAAACGAAGGATGTGGGG 59.198 55.000 0.00 0.00 0.00 4.96
2589 2791 1.880646 CGAAAACGAAGGATGTGGGGT 60.881 52.381 0.00 0.00 0.00 4.95
2590 2792 1.539827 GAAAACGAAGGATGTGGGGTG 59.460 52.381 0.00 0.00 0.00 4.61
2591 2793 0.251165 AAACGAAGGATGTGGGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
2592 2794 2.137177 AACGAAGGATGTGGGGTGGG 62.137 60.000 0.00 0.00 0.00 4.61
2593 2795 2.683475 GAAGGATGTGGGGTGGGG 59.317 66.667 0.00 0.00 0.00 4.96
2594 2796 2.946650 AAGGATGTGGGGTGGGGG 60.947 66.667 0.00 0.00 0.00 5.40
2595 2797 3.848200 AAGGATGTGGGGTGGGGGT 62.848 63.158 0.00 0.00 0.00 4.95
2596 2798 4.060667 GGATGTGGGGTGGGGGTG 62.061 72.222 0.00 0.00 0.00 4.61
2597 2799 4.759205 GATGTGGGGTGGGGGTGC 62.759 72.222 0.00 0.00 0.00 5.01
2600 2802 4.315264 GTGGGGTGGGGGTGCAAT 62.315 66.667 0.00 0.00 0.00 3.56
2601 2803 3.526428 TGGGGTGGGGGTGCAATT 61.526 61.111 0.00 0.00 0.00 2.32
2602 2804 2.170506 TGGGGTGGGGGTGCAATTA 61.171 57.895 0.00 0.00 0.00 1.40
2603 2805 1.684391 GGGGTGGGGGTGCAATTAC 60.684 63.158 0.00 0.00 0.00 1.89
2604 2806 1.077625 GGGTGGGGGTGCAATTACA 59.922 57.895 0.00 0.00 0.00 2.41
2605 2807 0.325203 GGGTGGGGGTGCAATTACAT 60.325 55.000 0.00 0.00 0.00 2.29
2606 2808 0.823460 GGTGGGGGTGCAATTACATG 59.177 55.000 0.00 0.00 0.00 3.21
2607 2809 1.555967 GTGGGGGTGCAATTACATGT 58.444 50.000 2.69 2.69 0.00 3.21
2608 2810 1.899142 GTGGGGGTGCAATTACATGTT 59.101 47.619 2.30 0.00 0.00 2.71
2609 2811 2.301583 GTGGGGGTGCAATTACATGTTT 59.698 45.455 2.30 0.00 0.00 2.83
2610 2812 2.975489 TGGGGGTGCAATTACATGTTTT 59.025 40.909 2.30 0.00 0.00 2.43
2611 2813 3.392616 TGGGGGTGCAATTACATGTTTTT 59.607 39.130 2.30 0.00 0.00 1.94
2666 2868 8.318412 TGTTCTACTGCCATCAAATTCTAAGTA 58.682 33.333 0.00 0.00 0.00 2.24
2667 2869 8.821894 GTTCTACTGCCATCAAATTCTAAGTAG 58.178 37.037 0.00 0.00 38.01 2.57
2669 2871 8.198109 TCTACTGCCATCAAATTCTAAGTAGTC 58.802 37.037 0.00 0.00 37.92 2.59
2671 2873 8.079211 ACTGCCATCAAATTCTAAGTAGTCTA 57.921 34.615 0.00 0.00 0.00 2.59
2673 2875 8.893219 TGCCATCAAATTCTAAGTAGTCTATG 57.107 34.615 0.00 0.00 0.00 2.23
2674 2876 7.442364 TGCCATCAAATTCTAAGTAGTCTATGC 59.558 37.037 0.00 0.00 0.00 3.14
2676 2878 9.499479 CCATCAAATTCTAAGTAGTCTATGCAT 57.501 33.333 3.79 3.79 0.00 3.96
2688 2927 6.831353 AGTAGTCTATGCATCACTACTCAACT 59.169 38.462 29.38 18.31 46.50 3.16
2742 2981 1.019673 ATCACTGCATGATTGGTCGC 58.980 50.000 0.00 0.00 46.54 5.19
2783 3022 7.749126 CCACATAAATAAAACGAGACAAAGTCC 59.251 37.037 0.00 0.00 32.18 3.85
2788 3027 6.894339 ATAAAACGAGACAAAGTCCCAAAT 57.106 33.333 0.00 0.00 32.18 2.32
2790 3029 6.894339 AAAACGAGACAAAGTCCCAAATAT 57.106 33.333 0.00 0.00 32.18 1.28
2808 3047 7.326063 CCCAAATATCTCGTCTTTTGAAAACAC 59.674 37.037 0.00 0.00 32.17 3.32
2810 3049 9.232082 CAAATATCTCGTCTTTTGAAAACACAA 57.768 29.630 0.00 0.00 32.17 3.33
2813 3052 5.092781 TCTCGTCTTTTGAAAACACAAAGC 58.907 37.500 0.00 0.00 40.15 3.51
2818 3057 4.732923 TCTTTTGAAAACACAAAGCGATCG 59.267 37.500 11.69 11.69 40.15 3.69
2825 3068 5.545658 AAACACAAAGCGATCGTCATATT 57.454 34.783 17.81 2.32 0.00 1.28
2849 3092 5.337578 TTTTGCTGCAAAAGTACCTTTCT 57.662 34.783 30.53 0.00 38.24 2.52
2850 3093 5.337578 TTTGCTGCAAAAGTACCTTTCTT 57.662 34.783 24.24 0.00 31.99 2.52
2851 3094 5.337578 TTGCTGCAAAAGTACCTTTCTTT 57.662 34.783 13.51 0.00 36.81 2.52
2852 3095 5.337578 TGCTGCAAAAGTACCTTTCTTTT 57.662 34.783 0.00 0.00 43.14 2.27
2853 3096 6.458232 TGCTGCAAAAGTACCTTTCTTTTA 57.542 33.333 0.00 0.00 41.30 1.52
2854 3097 6.270064 TGCTGCAAAAGTACCTTTCTTTTAC 58.730 36.000 0.00 0.36 41.30 2.01
2855 3098 5.690409 GCTGCAAAAGTACCTTTCTTTTACC 59.310 40.000 0.00 0.83 41.30 2.85
2856 3099 6.461092 GCTGCAAAAGTACCTTTCTTTTACCT 60.461 38.462 0.00 0.00 41.30 3.08
3177 3420 1.562942 TGAGGATGGATGCAGCTTTCT 59.437 47.619 0.22 0.00 0.00 2.52
3182 3425 1.304282 GGATGCAGCTTTCTCCCCA 59.696 57.895 0.22 0.00 0.00 4.96
3191 3434 0.182299 CTTTCTCCCCATCTCCCTGC 59.818 60.000 0.00 0.00 0.00 4.85
3213 3456 4.388499 CTACGCGTGGGGGCTGTT 62.388 66.667 24.59 0.00 0.00 3.16
3268 3511 3.306502 CCCCGTACCGCATATGATTAAGT 60.307 47.826 6.97 0.00 0.00 2.24
3277 3520 5.123706 CGCATATGATTAAGTTCGTTCGTG 58.876 41.667 6.97 0.00 0.00 4.35
3361 3604 3.057526 TGTCATGTGGTCGTTCTCTAGTG 60.058 47.826 0.00 0.00 0.00 2.74
3362 3605 3.190744 GTCATGTGGTCGTTCTCTAGTGA 59.809 47.826 0.00 0.00 0.00 3.41
3363 3606 3.190744 TCATGTGGTCGTTCTCTAGTGAC 59.809 47.826 0.00 0.00 0.00 3.67
3365 3608 3.220110 TGTGGTCGTTCTCTAGTGACTT 58.780 45.455 0.00 0.00 0.00 3.01
3366 3609 3.635373 TGTGGTCGTTCTCTAGTGACTTT 59.365 43.478 0.00 0.00 0.00 2.66
3367 3610 3.982058 GTGGTCGTTCTCTAGTGACTTTG 59.018 47.826 0.00 0.00 0.00 2.77
3368 3611 3.635373 TGGTCGTTCTCTAGTGACTTTGT 59.365 43.478 0.00 0.00 0.00 2.83
3369 3612 4.098960 TGGTCGTTCTCTAGTGACTTTGTT 59.901 41.667 0.00 0.00 0.00 2.83
3370 3613 5.048507 GGTCGTTCTCTAGTGACTTTGTTT 58.951 41.667 0.00 0.00 0.00 2.83
3371 3614 5.050972 GGTCGTTCTCTAGTGACTTTGTTTG 60.051 44.000 0.00 0.00 0.00 2.93
3372 3615 4.506654 TCGTTCTCTAGTGACTTTGTTTGC 59.493 41.667 0.00 0.00 0.00 3.68
3373 3616 4.508124 CGTTCTCTAGTGACTTTGTTTGCT 59.492 41.667 0.00 0.00 0.00 3.91
3374 3617 5.557136 CGTTCTCTAGTGACTTTGTTTGCTG 60.557 44.000 0.00 0.00 0.00 4.41
3375 3618 3.809832 TCTCTAGTGACTTTGTTTGCTGC 59.190 43.478 0.00 0.00 0.00 5.25
3376 3619 2.878406 TCTAGTGACTTTGTTTGCTGCC 59.122 45.455 0.00 0.00 0.00 4.85
3414 3657 4.487019 GCCGTTGGCTTATATCTCTAGAC 58.513 47.826 0.00 0.00 46.69 2.59
3648 3897 4.379339 TTTGACACCAAAAACAGTAGGC 57.621 40.909 0.00 0.00 39.15 3.93
3649 3898 2.303175 TGACACCAAAAACAGTAGGCC 58.697 47.619 0.00 0.00 0.00 5.19
3650 3899 2.092103 TGACACCAAAAACAGTAGGCCT 60.092 45.455 11.78 11.78 0.00 5.19
3651 3900 2.552743 GACACCAAAAACAGTAGGCCTC 59.447 50.000 9.68 0.21 0.00 4.70
3654 3905 2.224793 ACCAAAAACAGTAGGCCTCTCC 60.225 50.000 9.68 0.00 0.00 3.71
3674 3927 2.816087 CCTACTGTGCTGCATTCAAACT 59.184 45.455 5.27 0.00 0.00 2.66
3699 3952 9.250370 CTTATAGAAGAGTTGCGACAAGCCTTG 62.250 44.444 6.90 2.11 39.04 3.61
3721 3974 3.434984 GGAAGCAGAACAGAAAGCTACAG 59.565 47.826 0.00 0.00 36.07 2.74
3725 3978 3.807209 GCAGAACAGAAAGCTACAGGGAA 60.807 47.826 0.00 0.00 0.00 3.97
3775 4028 5.329035 TGCTTTTGAGCAAATAATCTCCC 57.671 39.130 0.00 0.00 42.40 4.30
3776 4029 5.018809 TGCTTTTGAGCAAATAATCTCCCT 58.981 37.500 0.00 0.00 42.40 4.20
3777 4030 5.481473 TGCTTTTGAGCAAATAATCTCCCTT 59.519 36.000 0.00 0.00 42.40 3.95
3778 4031 6.663093 TGCTTTTGAGCAAATAATCTCCCTTA 59.337 34.615 0.00 0.00 42.40 2.69
3779 4032 7.148018 TGCTTTTGAGCAAATAATCTCCCTTAG 60.148 37.037 0.00 0.00 42.40 2.18
3780 4033 7.148000 GCTTTTGAGCAAATAATCTCCCTTAGT 60.148 37.037 0.00 0.00 34.41 2.24
3816 4073 5.751586 CCACAAGGCTCTAATACCCTTAAA 58.248 41.667 0.00 0.00 36.86 1.52
4053 4312 5.581085 CCGAAAACGAGATCCAACTAATCTT 59.419 40.000 0.00 0.00 33.64 2.40
4118 4377 0.519175 GAGCACATGTTTAGCGCACG 60.519 55.000 11.47 0.00 0.00 5.34
4165 4424 6.266168 TGTTTGCATTAATCACCTACTTGG 57.734 37.500 0.00 0.00 42.93 3.61
4170 4429 6.125719 TGCATTAATCACCTACTTGGCATTA 58.874 36.000 0.00 0.00 40.22 1.90
4184 4443 3.587923 TGGCATTACACGTACTAACCAC 58.412 45.455 0.00 0.00 0.00 4.16
4185 4444 3.006644 TGGCATTACACGTACTAACCACA 59.993 43.478 0.00 0.00 0.00 4.17
4196 4469 4.332543 CGTACTAACCACACCGACTATGTA 59.667 45.833 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.639601 TGGTACATCTCTTTAGAATATTATGCG 57.360 33.333 0.00 0.00 34.73 4.73
31 32 5.012893 TGCATATTATTGTCAACCCACACA 58.987 37.500 0.00 0.00 0.00 3.72
32 33 5.339990 GTGCATATTATTGTCAACCCACAC 58.660 41.667 0.00 0.00 0.00 3.82
56 57 5.008415 GCTCTTGGATCATGGAAATGTGTAG 59.992 44.000 0.00 0.00 0.00 2.74
114 117 1.560860 GAACAGAGTGCAGCGTCACC 61.561 60.000 7.59 1.28 37.68 4.02
130 133 2.676076 TCGGTTAAACTAGTGCCGAAC 58.324 47.619 21.03 12.27 46.81 3.95
246 255 6.085555 TCTATAGTACGGATTTTCTGCTGG 57.914 41.667 0.00 0.00 0.00 4.85
250 259 8.568794 TCTCACATCTATAGTACGGATTTTCTG 58.431 37.037 0.00 0.00 0.00 3.02
262 271 5.049060 GCACGAGACATCTCACATCTATAGT 60.049 44.000 9.49 0.00 43.00 2.12
341 383 0.310854 CCTTTCGTTCACAGGCCAAC 59.689 55.000 5.01 0.00 0.00 3.77
342 384 1.452145 GCCTTTCGTTCACAGGCCAA 61.452 55.000 5.01 0.00 46.55 4.52
344 386 2.954611 GCCTTTCGTTCACAGGCC 59.045 61.111 0.00 0.00 46.55 5.19
346 388 1.151668 CAGAGCCTTTCGTTCACAGG 58.848 55.000 0.00 0.00 0.00 4.00
347 389 1.871080 ACAGAGCCTTTCGTTCACAG 58.129 50.000 0.00 0.00 0.00 3.66
348 390 1.939934 CAACAGAGCCTTTCGTTCACA 59.060 47.619 0.00 0.00 0.00 3.58
349 391 1.940613 ACAACAGAGCCTTTCGTTCAC 59.059 47.619 0.00 0.00 0.00 3.18
350 392 2.325583 ACAACAGAGCCTTTCGTTCA 57.674 45.000 0.00 0.00 0.00 3.18
351 393 3.312697 AGAAACAACAGAGCCTTTCGTTC 59.687 43.478 0.00 0.00 0.00 3.95
353 395 2.919228 AGAAACAACAGAGCCTTTCGT 58.081 42.857 0.00 0.00 0.00 3.85
354 396 4.307432 TCTAGAAACAACAGAGCCTTTCG 58.693 43.478 0.00 0.00 0.00 3.46
355 397 5.334491 GCTTCTAGAAACAACAGAGCCTTTC 60.334 44.000 6.63 0.00 0.00 2.62
439 481 2.343101 CCAAGGAGTCGTTTCGCATAA 58.657 47.619 0.00 0.00 0.00 1.90
440 482 2.004583 CCAAGGAGTCGTTTCGCATA 57.995 50.000 0.00 0.00 0.00 3.14
441 483 1.298859 GCCAAGGAGTCGTTTCGCAT 61.299 55.000 8.73 0.00 0.00 4.73
442 484 1.959226 GCCAAGGAGTCGTTTCGCA 60.959 57.895 8.73 0.00 0.00 5.10
443 485 2.861006 GCCAAGGAGTCGTTTCGC 59.139 61.111 0.00 0.00 0.00 4.70
444 486 0.736325 ATCGCCAAGGAGTCGTTTCG 60.736 55.000 9.46 9.46 0.00 3.46
445 487 1.000145 GATCGCCAAGGAGTCGTTTC 59.000 55.000 0.00 0.00 0.00 2.78
446 488 0.736325 CGATCGCCAAGGAGTCGTTT 60.736 55.000 0.26 0.00 0.00 3.60
447 489 1.153823 CGATCGCCAAGGAGTCGTT 60.154 57.895 0.26 0.00 0.00 3.85
448 490 1.384989 ATCGATCGCCAAGGAGTCGT 61.385 55.000 11.09 0.00 34.24 4.34
449 491 0.661780 GATCGATCGCCAAGGAGTCG 60.662 60.000 11.09 7.91 0.00 4.18
450 492 0.661780 CGATCGATCGCCAAGGAGTC 60.662 60.000 32.34 0.00 43.84 3.36
451 493 1.360551 CGATCGATCGCCAAGGAGT 59.639 57.895 32.34 0.00 43.84 3.85
452 494 4.235065 CGATCGATCGCCAAGGAG 57.765 61.111 32.34 6.58 43.84 3.69
469 511 2.018866 CTGAATCGATCGCTCCGGC 61.019 63.158 11.09 0.00 0.00 6.13
470 512 0.242286 ATCTGAATCGATCGCTCCGG 59.758 55.000 11.09 0.00 0.00 5.14
471 513 1.612156 GATCTGAATCGATCGCTCCG 58.388 55.000 11.09 6.21 31.43 4.63
481 523 1.592560 CGACGAGCGCGATCTGAATC 61.593 60.000 23.21 12.89 41.64 2.52
482 524 1.655654 CGACGAGCGCGATCTGAAT 60.656 57.895 23.21 4.85 41.64 2.57
483 525 2.277310 CGACGAGCGCGATCTGAA 60.277 61.111 23.21 0.00 41.64 3.02
501 543 1.490910 AGGGAAAGGAAATAGGCGGAG 59.509 52.381 0.00 0.00 0.00 4.63
502 544 1.591768 AGGGAAAGGAAATAGGCGGA 58.408 50.000 0.00 0.00 0.00 5.54
503 545 2.437085 AAGGGAAAGGAAATAGGCGG 57.563 50.000 0.00 0.00 0.00 6.13
504 546 3.621558 AGAAAGGGAAAGGAAATAGGCG 58.378 45.455 0.00 0.00 0.00 5.52
505 547 4.580995 GCTAGAAAGGGAAAGGAAATAGGC 59.419 45.833 0.00 0.00 0.00 3.93
506 548 5.103898 AGGCTAGAAAGGGAAAGGAAATAGG 60.104 44.000 0.00 0.00 0.00 2.57
507 549 6.007485 AGGCTAGAAAGGGAAAGGAAATAG 57.993 41.667 0.00 0.00 0.00 1.73
508 550 6.402981 AAGGCTAGAAAGGGAAAGGAAATA 57.597 37.500 0.00 0.00 0.00 1.40
509 551 4.955693 AGGCTAGAAAGGGAAAGGAAAT 57.044 40.909 0.00 0.00 0.00 2.17
510 552 4.741928 AAGGCTAGAAAGGGAAAGGAAA 57.258 40.909 0.00 0.00 0.00 3.13
511 553 4.741928 AAAGGCTAGAAAGGGAAAGGAA 57.258 40.909 0.00 0.00 0.00 3.36
512 554 4.741928 AAAAGGCTAGAAAGGGAAAGGA 57.258 40.909 0.00 0.00 0.00 3.36
513 555 4.220821 GGAAAAAGGCTAGAAAGGGAAAGG 59.779 45.833 0.00 0.00 0.00 3.11
514 556 5.080337 AGGAAAAAGGCTAGAAAGGGAAAG 58.920 41.667 0.00 0.00 0.00 2.62
515 557 5.074746 AGGAAAAAGGCTAGAAAGGGAAA 57.925 39.130 0.00 0.00 0.00 3.13
516 558 4.741928 AGGAAAAAGGCTAGAAAGGGAA 57.258 40.909 0.00 0.00 0.00 3.97
517 559 4.741928 AAGGAAAAAGGCTAGAAAGGGA 57.258 40.909 0.00 0.00 0.00 4.20
518 560 5.540337 AGAAAAGGAAAAAGGCTAGAAAGGG 59.460 40.000 0.00 0.00 0.00 3.95
519 561 6.450545 CAGAAAAGGAAAAAGGCTAGAAAGG 58.549 40.000 0.00 0.00 0.00 3.11
520 562 6.265422 TCCAGAAAAGGAAAAAGGCTAGAAAG 59.735 38.462 0.00 0.00 33.93 2.62
521 563 6.133356 TCCAGAAAAGGAAAAAGGCTAGAAA 58.867 36.000 0.00 0.00 33.93 2.52
522 564 5.701224 TCCAGAAAAGGAAAAAGGCTAGAA 58.299 37.500 0.00 0.00 33.93 2.10
523 565 5.319043 TCCAGAAAAGGAAAAAGGCTAGA 57.681 39.130 0.00 0.00 33.93 2.43
524 566 6.596309 AATCCAGAAAAGGAAAAAGGCTAG 57.404 37.500 0.00 0.00 41.92 3.42
525 567 7.893302 TCATAATCCAGAAAAGGAAAAAGGCTA 59.107 33.333 0.00 0.00 41.92 3.93
526 568 6.725834 TCATAATCCAGAAAAGGAAAAAGGCT 59.274 34.615 0.00 0.00 41.92 4.58
527 569 6.813649 GTCATAATCCAGAAAAGGAAAAAGGC 59.186 38.462 0.00 0.00 41.92 4.35
528 570 8.127150 AGTCATAATCCAGAAAAGGAAAAAGG 57.873 34.615 0.00 0.00 41.92 3.11
529 571 9.987272 AAAGTCATAATCCAGAAAAGGAAAAAG 57.013 29.630 0.00 0.00 41.92 2.27
530 572 9.981114 GAAAGTCATAATCCAGAAAAGGAAAAA 57.019 29.630 0.00 0.00 41.92 1.94
531 573 9.367160 AGAAAGTCATAATCCAGAAAAGGAAAA 57.633 29.630 0.00 0.00 41.92 2.29
532 574 8.940397 AGAAAGTCATAATCCAGAAAAGGAAA 57.060 30.769 0.00 0.00 41.92 3.13
533 575 8.940397 AAGAAAGTCATAATCCAGAAAAGGAA 57.060 30.769 0.00 0.00 41.92 3.36
537 579 9.884636 TCGATAAGAAAGTCATAATCCAGAAAA 57.115 29.630 0.00 0.00 0.00 2.29
538 580 9.534565 CTCGATAAGAAAGTCATAATCCAGAAA 57.465 33.333 0.00 0.00 0.00 2.52
539 581 8.144478 CCTCGATAAGAAAGTCATAATCCAGAA 58.856 37.037 0.00 0.00 0.00 3.02
540 582 7.661968 CCTCGATAAGAAAGTCATAATCCAGA 58.338 38.462 0.00 0.00 0.00 3.86
541 583 6.367422 GCCTCGATAAGAAAGTCATAATCCAG 59.633 42.308 0.00 0.00 0.00 3.86
542 584 6.223852 GCCTCGATAAGAAAGTCATAATCCA 58.776 40.000 0.00 0.00 0.00 3.41
543 585 5.639931 GGCCTCGATAAGAAAGTCATAATCC 59.360 44.000 0.00 0.00 0.00 3.01
544 586 6.223852 TGGCCTCGATAAGAAAGTCATAATC 58.776 40.000 3.32 0.00 0.00 1.75
576 618 4.713553 TCACTGCAAATTTCCAGAGTACA 58.286 39.130 16.08 0.00 33.40 2.90
709 765 9.811995 CAATGGAGGCCATAATGAATATTTATG 57.188 33.333 5.01 0.00 44.40 1.90
1066 1233 0.247736 AACATGCTGTCCTCGGAGAC 59.752 55.000 6.58 3.80 37.28 3.36
1081 1248 1.619669 GAGGGGGTCTGGGGAACAT 60.620 63.158 0.00 0.00 0.00 2.71
1174 1341 4.798682 AACCGGCGGGGAGAGGAT 62.799 66.667 31.78 2.61 39.97 3.24
1251 1418 1.228894 AGGGGAGTCGAGCAAGACA 60.229 57.895 12.94 0.00 43.24 3.41
1256 1423 1.228894 AAGTCAGGGGAGTCGAGCA 60.229 57.895 0.00 0.00 0.00 4.26
1294 1461 2.260434 GAAGTAGCCCACGTCGCA 59.740 61.111 6.89 0.00 0.00 5.10
1403 1570 1.004918 AACCCGAGCGTGGAAAGAG 60.005 57.895 0.00 0.00 0.00 2.85
1433 1600 2.106683 CCGGCGTCCATTTCCTCAC 61.107 63.158 6.01 0.00 0.00 3.51
1455 1622 0.601576 CGAACACCATGACGGGTTCA 60.602 55.000 14.85 0.00 41.46 3.18
1573 1740 2.600470 GAAACCCACCCCACCAGC 60.600 66.667 0.00 0.00 0.00 4.85
1717 1884 1.021390 CACTCGCAATGGAGTCCCAC 61.021 60.000 6.74 0.00 46.98 4.61
1755 1922 1.826024 GTCCATCACCCAGCTCGAT 59.174 57.895 0.00 0.00 0.00 3.59
1803 1970 1.812922 CAGGAGTGCACCATCGCTC 60.813 63.158 14.63 2.77 41.53 5.03
1809 1976 2.818169 GGTGACCAGGAGTGCACCA 61.818 63.158 14.63 0.00 42.03 4.17
1854 2021 5.505181 AAGTCAATAGAGATGGGTGTTGT 57.495 39.130 0.00 0.00 0.00 3.32
2005 2189 9.577110 CTTATGAATGAAATAGTTGTGCAATGT 57.423 29.630 0.00 0.00 0.00 2.71
2066 2250 5.493133 TGCCTTTAGTTTGGTTATATGCG 57.507 39.130 0.00 0.00 0.00 4.73
2119 2303 7.398024 AGCAGGTTCTAGAGTTACAATCAAAT 58.602 34.615 0.00 0.00 0.00 2.32
2160 2345 3.420893 CAAACCAAATGGAGACCAGCTA 58.579 45.455 6.42 0.00 36.75 3.32
2190 2375 4.031765 CGCGAATATGCATGTATGTAGGTC 59.968 45.833 10.16 0.00 34.15 3.85
2194 2379 2.344142 CGCGCGAATATGCATGTATGTA 59.656 45.455 28.94 0.00 34.15 2.29
2219 2404 2.595386 GTCAAAAATTCGGCGAGCAAT 58.405 42.857 10.46 0.00 0.00 3.56
2223 2408 2.587612 TTCGTCAAAAATTCGGCGAG 57.412 45.000 10.46 0.00 0.00 5.03
2237 2422 1.762222 CGGCGGATGAACCATTCGTC 61.762 60.000 9.09 5.90 43.93 4.20
2238 2423 1.813753 CGGCGGATGAACCATTCGT 60.814 57.895 9.09 0.00 43.93 3.85
2239 2424 1.762222 GACGGCGGATGAACCATTCG 61.762 60.000 13.24 3.43 44.77 3.34
2240 2425 0.742990 TGACGGCGGATGAACCATTC 60.743 55.000 13.24 0.00 38.90 2.67
2241 2426 0.107214 ATGACGGCGGATGAACCATT 60.107 50.000 13.24 0.00 38.90 3.16
2243 2428 0.322098 AAATGACGGCGGATGAACCA 60.322 50.000 13.24 0.00 38.90 3.67
2244 2429 0.808755 AAAATGACGGCGGATGAACC 59.191 50.000 13.24 0.00 0.00 3.62
2246 2431 1.470890 GGAAAAATGACGGCGGATGAA 59.529 47.619 13.24 0.00 0.00 2.57
2248 2433 0.100503 GGGAAAAATGACGGCGGATG 59.899 55.000 13.24 0.00 0.00 3.51
2249 2434 1.373590 CGGGAAAAATGACGGCGGAT 61.374 55.000 13.24 0.00 0.00 4.18
2273 2459 2.389998 CACACACGTAATTTTGGCCAC 58.610 47.619 3.88 0.00 0.00 5.01
2277 2463 2.351350 GGCTCCACACACGTAATTTTGG 60.351 50.000 0.00 0.00 0.00 3.28
2278 2464 2.292016 TGGCTCCACACACGTAATTTTG 59.708 45.455 0.00 0.00 0.00 2.44
2290 2476 2.360726 CAGCTGCATGGCTCCACA 60.361 61.111 0.00 0.00 41.00 4.17
2291 2477 2.360852 ACAGCTGCATGGCTCCAC 60.361 61.111 15.27 0.00 41.00 4.02
2315 2501 2.576847 GCGCCAATTTTCGCTCGG 60.577 61.111 12.32 0.00 46.92 4.63
2516 2711 0.110486 AACCGGCTCAACTGACCAAT 59.890 50.000 0.00 0.00 0.00 3.16
2518 2713 1.070786 GAACCGGCTCAACTGACCA 59.929 57.895 0.00 0.00 0.00 4.02
2558 2760 4.096682 TCCTTCGTTTTCGGTTTTGTTGAT 59.903 37.500 0.00 0.00 44.25 2.57
2559 2761 3.439476 TCCTTCGTTTTCGGTTTTGTTGA 59.561 39.130 0.00 0.00 44.25 3.18
2560 2762 3.760537 TCCTTCGTTTTCGGTTTTGTTG 58.239 40.909 0.00 0.00 44.25 3.33
2562 2764 3.379057 ACATCCTTCGTTTTCGGTTTTGT 59.621 39.130 0.00 0.00 44.25 2.83
2563 2765 3.728718 CACATCCTTCGTTTTCGGTTTTG 59.271 43.478 0.00 0.00 44.25 2.44
2567 2769 1.519408 CCACATCCTTCGTTTTCGGT 58.481 50.000 0.00 0.00 44.25 4.69
2569 2771 0.802494 CCCCACATCCTTCGTTTTCG 59.198 55.000 0.00 0.00 45.64 3.46
2570 2772 1.539827 CACCCCACATCCTTCGTTTTC 59.460 52.381 0.00 0.00 0.00 2.29
2585 2787 1.684391 GTAATTGCACCCCCACCCC 60.684 63.158 0.00 0.00 0.00 4.95
2586 2788 0.325203 ATGTAATTGCACCCCCACCC 60.325 55.000 0.00 0.00 0.00 4.61
2587 2789 0.823460 CATGTAATTGCACCCCCACC 59.177 55.000 0.00 0.00 0.00 4.61
2588 2790 1.555967 ACATGTAATTGCACCCCCAC 58.444 50.000 0.00 0.00 0.00 4.61
2589 2791 2.317371 AACATGTAATTGCACCCCCA 57.683 45.000 0.00 0.00 0.00 4.96
2590 2792 3.694043 AAAACATGTAATTGCACCCCC 57.306 42.857 0.00 0.00 0.00 5.40
2608 2810 7.139619 TCTCTCCTATCCCTCCTATTCAAAAA 58.860 38.462 0.00 0.00 0.00 1.94
2609 2811 6.693599 TCTCTCCTATCCCTCCTATTCAAAA 58.306 40.000 0.00 0.00 0.00 2.44
2610 2812 6.295041 TCTCTCCTATCCCTCCTATTCAAA 57.705 41.667 0.00 0.00 0.00 2.69
2611 2813 5.950320 TCTCTCCTATCCCTCCTATTCAA 57.050 43.478 0.00 0.00 0.00 2.69
2612 2814 5.617418 TCTTCTCTCCTATCCCTCCTATTCA 59.383 44.000 0.00 0.00 0.00 2.57
2613 2815 6.011981 TCTCTTCTCTCCTATCCCTCCTATTC 60.012 46.154 0.00 0.00 0.00 1.75
2614 2816 5.860666 TCTCTTCTCTCCTATCCCTCCTATT 59.139 44.000 0.00 0.00 0.00 1.73
2615 2817 5.429518 TCTCTTCTCTCCTATCCCTCCTAT 58.570 45.833 0.00 0.00 0.00 2.57
2616 2818 4.845541 TCTCTTCTCTCCTATCCCTCCTA 58.154 47.826 0.00 0.00 0.00 2.94
2617 2819 3.687045 TCTCTTCTCTCCTATCCCTCCT 58.313 50.000 0.00 0.00 0.00 3.69
2618 2820 4.675063 ATCTCTTCTCTCCTATCCCTCC 57.325 50.000 0.00 0.00 0.00 4.30
2619 2821 5.393866 ACAATCTCTTCTCTCCTATCCCTC 58.606 45.833 0.00 0.00 0.00 4.30
2620 2822 5.417170 ACAATCTCTTCTCTCCTATCCCT 57.583 43.478 0.00 0.00 0.00 4.20
2666 2868 6.153510 TCAAGTTGAGTAGTGATGCATAGACT 59.846 38.462 13.82 13.82 0.00 3.24
2667 2869 6.333416 TCAAGTTGAGTAGTGATGCATAGAC 58.667 40.000 0.00 0.00 0.00 2.59
2669 2871 6.036517 GGTTCAAGTTGAGTAGTGATGCATAG 59.963 42.308 5.56 0.00 0.00 2.23
2671 2873 4.697352 GGTTCAAGTTGAGTAGTGATGCAT 59.303 41.667 0.00 0.00 0.00 3.96
2673 2875 3.123621 CGGTTCAAGTTGAGTAGTGATGC 59.876 47.826 5.56 0.00 0.00 3.91
2674 2876 3.679980 CCGGTTCAAGTTGAGTAGTGATG 59.320 47.826 5.56 0.00 0.00 3.07
2676 2878 2.036733 CCCGGTTCAAGTTGAGTAGTGA 59.963 50.000 5.56 0.00 0.00 3.41
2678 2917 2.036862 GACCCGGTTCAAGTTGAGTAGT 59.963 50.000 5.56 1.21 0.00 2.73
2688 2927 2.871096 AATTAGCTGACCCGGTTCAA 57.129 45.000 2.35 0.00 0.00 2.69
2765 3004 6.894339 ATTTGGGACTTTGTCTCGTTTTAT 57.106 33.333 0.00 0.00 35.49 1.40
2766 3005 7.881232 AGATATTTGGGACTTTGTCTCGTTTTA 59.119 33.333 0.00 0.00 35.49 1.52
2771 3010 4.504461 CGAGATATTTGGGACTTTGTCTCG 59.496 45.833 7.00 7.00 44.86 4.04
2783 3022 7.860373 TGTGTTTTCAAAAGACGAGATATTTGG 59.140 33.333 5.74 0.00 34.39 3.28
2788 3027 6.910433 GCTTTGTGTTTTCAAAAGACGAGATA 59.090 34.615 14.05 0.00 36.96 1.98
2790 3029 5.092781 GCTTTGTGTTTTCAAAAGACGAGA 58.907 37.500 14.05 0.00 36.96 4.04
3122 3365 2.024369 AGACCTCCTCCTTCTCCTTCTC 60.024 54.545 0.00 0.00 0.00 2.87
3125 3368 2.007636 AGAGACCTCCTCCTTCTCCTT 58.992 52.381 0.00 0.00 42.97 3.36
3177 3420 1.383664 CTCTGCAGGGAGATGGGGA 60.384 63.158 8.28 0.00 35.52 4.81
3182 3425 2.424474 CGTAGCTCTGCAGGGAGAT 58.576 57.895 20.53 8.53 35.52 2.75
3213 3456 2.190538 TGGACTCAAGCTGATCATGGA 58.809 47.619 0.00 0.00 0.00 3.41
3268 3511 0.888619 AGAGAGCCATCACGAACGAA 59.111 50.000 0.14 0.00 0.00 3.85
3277 3520 0.747255 TCCAACGCTAGAGAGCCATC 59.253 55.000 0.00 0.00 46.86 3.51
3361 3604 1.202452 AGCAAGGCAGCAAACAAAGTC 60.202 47.619 4.78 0.00 36.85 3.01
3362 3605 0.826062 AGCAAGGCAGCAAACAAAGT 59.174 45.000 4.78 0.00 36.85 2.66
3363 3606 1.214367 CAGCAAGGCAGCAAACAAAG 58.786 50.000 4.78 0.00 36.85 2.77
3365 3608 1.329171 ACCAGCAAGGCAGCAAACAA 61.329 50.000 4.78 0.00 43.14 2.83
3366 3609 1.757731 ACCAGCAAGGCAGCAAACA 60.758 52.632 4.78 0.00 43.14 2.83
3367 3610 1.300388 CACCAGCAAGGCAGCAAAC 60.300 57.895 4.78 0.00 43.14 2.93
3368 3611 3.131155 CACCAGCAAGGCAGCAAA 58.869 55.556 4.78 0.00 43.14 3.68
3369 3612 3.608662 GCACCAGCAAGGCAGCAA 61.609 61.111 4.78 0.00 43.14 3.91
3411 3654 2.693591 TCGTTCTGACCAACTCAAGTCT 59.306 45.455 0.00 0.00 34.02 3.24
3412 3655 2.795470 GTCGTTCTGACCAACTCAAGTC 59.205 50.000 0.00 0.00 42.04 3.01
3648 3897 0.829333 ATGCAGCACAGTAGGAGAGG 59.171 55.000 0.00 0.00 0.00 3.69
3649 3898 2.093816 TGAATGCAGCACAGTAGGAGAG 60.094 50.000 0.00 0.00 0.00 3.20
3650 3899 1.901833 TGAATGCAGCACAGTAGGAGA 59.098 47.619 0.00 0.00 0.00 3.71
3651 3900 2.391616 TGAATGCAGCACAGTAGGAG 57.608 50.000 0.00 0.00 0.00 3.69
3654 3905 4.494350 AAGTTTGAATGCAGCACAGTAG 57.506 40.909 0.00 0.00 0.00 2.57
3674 3927 4.081642 AGGCTTGTCGCAACTCTTCTATAA 60.082 41.667 0.00 0.00 41.67 0.98
3699 3952 3.403038 TGTAGCTTTCTGTTCTGCTTCC 58.597 45.455 0.00 0.00 37.02 3.46
3900 4157 8.940397 ATTTAATATCCAATGGTCTCCGAATT 57.060 30.769 0.00 0.00 0.00 2.17
3944 4201 9.669887 AGCATTTAATCTTTTATTTGCATCCAA 57.330 25.926 0.00 0.00 32.27 3.53
4031 4289 7.254488 GGCTAAGATTAGTTGGATCTCGTTTTC 60.254 40.741 1.82 0.00 32.86 2.29
4053 4312 3.459227 TGATTGACAGGGATTGATGGCTA 59.541 43.478 0.00 0.00 0.00 3.93
4165 4424 3.368843 GGTGTGGTTAGTACGTGTAATGC 59.631 47.826 0.00 0.00 0.00 3.56
4170 4429 1.001378 GTCGGTGTGGTTAGTACGTGT 60.001 52.381 0.00 0.00 0.00 4.49
4184 4443 4.982916 GCTATTCCAACTACATAGTCGGTG 59.017 45.833 0.00 0.00 34.99 4.94
4185 4444 4.038883 GGCTATTCCAACTACATAGTCGGT 59.961 45.833 0.00 0.00 34.99 4.69
4196 4469 2.270434 TCCAGGAGGCTATTCCAACT 57.730 50.000 0.00 0.00 39.84 3.16


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

AutoCloner maintained by Alex Coulton.