Multiple sequence alignment - TraesCS3A01G043200

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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 TraesCS3A01G043200 chr3A 100.000 3629 0 0 1 3629 23446347 23449975 0.000000e+00 6702.0
1 TraesCS3A01G043200 chr3A 98.453 2909 24 2 721 3629 57277797 57274910 0.000000e+00 5103.0
2 TraesCS3A01G043200 chr3A 95.983 722 24 2 1 721 558589282 558589999 0.000000e+00 1168.0
3 TraesCS3A01G043200 chr3A 95.562 721 28 1 1 721 558581126 558581842 0.000000e+00 1151.0
4 TraesCS3A01G043200 chr4A 99.209 2909 17 1 721 3629 644772685 644769783 0.000000e+00 5240.0
5 TraesCS3A01G043200 chr5A 99.175 2909 18 1 721 3629 69232548 69229646 0.000000e+00 5234.0
6 TraesCS3A01G043200 chr1A 98.803 2924 13 3 721 3629 521287689 521284773 0.000000e+00 5186.0
7 TraesCS3A01G043200 chr1A 98.665 2922 16 4 724 3629 500074427 500071513 0.000000e+00 5158.0
8 TraesCS3A01G043200 chr7B 98.694 2909 17 2 721 3629 122624256 122627143 0.000000e+00 5142.0
9 TraesCS3A01G043200 chr7B 98.413 2458 18 2 721 3178 476795152 476792716 0.000000e+00 4303.0
10 TraesCS3A01G043200 chr2B 98.384 2909 22 7 721 3629 165276629 165279512 0.000000e+00 5088.0
11 TraesCS3A01G043200 chr5B 98.350 2909 27 2 721 3629 339081373 339084260 0.000000e+00 5086.0
12 TraesCS3A01G043200 chr5B 93.257 875 38 10 720 1593 434055864 434055010 0.000000e+00 1269.0
13 TraesCS3A01G043200 chr6A 98.958 2399 19 1 720 3118 97398565 97396173 0.000000e+00 4287.0
14 TraesCS3A01G043200 chr4B 97.740 2168 16 2 1480 3629 451450953 451448801 0.000000e+00 3701.0
15 TraesCS3A01G043200 chr4B 85.522 297 17 11 245 539 301095463 301095191 1.650000e-73 287.0
16 TraesCS3A01G043200 chr4B 93.701 127 7 1 245 371 301078886 301078761 4.780000e-44 189.0
17 TraesCS3A01G043200 chr4B 83.168 202 21 12 418 615 301078376 301078184 4.820000e-39 172.0
18 TraesCS3A01G043200 chr6B 93.279 863 47 7 720 1579 476708871 476709725 0.000000e+00 1262.0
19 TraesCS3A01G043200 chr6B 90.508 295 20 7 245 539 297931033 297930747 2.040000e-102 383.0
20 TraesCS3A01G043200 chr6B 84.973 366 31 14 245 606 297940007 297939662 2.070000e-92 350.0
21 TraesCS3A01G043200 chr7D 91.364 880 52 13 721 1593 151287715 151286853 0.000000e+00 1182.0
22 TraesCS3A01G043200 chr7D 91.136 880 53 14 721 1593 506650794 506649933 0.000000e+00 1170.0
23 TraesCS3A01G043200 chr2D 91.364 880 52 13 721 1593 499310618 499311480 0.000000e+00 1182.0
24 TraesCS3A01G043200 chr2D 91.023 880 54 14 721 1593 63947812 63946951 0.000000e+00 1164.0
25 TraesCS3A01G043200 chr2D 84.541 621 70 15 1 608 488028663 488028056 3.120000e-165 592.0
26 TraesCS3A01G043200 chr2D 83.876 614 68 20 1 608 318145789 318146377 1.140000e-154 556.0
27 TraesCS3A01G043200 chr6D 90.909 891 54 17 711 1593 57832579 57833450 0.000000e+00 1171.0
28 TraesCS3A01G043200 chr5D 90.827 883 53 14 720 1593 430991432 430990569 0.000000e+00 1157.0
29 TraesCS3A01G043200 chr5D 81.350 311 46 10 1 304 499810212 499809907 3.620000e-60 243.0
30 TraesCS3A01G043200 chr1D 90.530 887 59 14 714 1593 479819313 479818445 0.000000e+00 1149.0
31 TraesCS3A01G043200 chr1D 90.378 291 21 6 239 529 131454879 131455162 3.420000e-100 375.0
32 TraesCS3A01G043200 chr1D 92.490 253 13 3 239 491 131434610 131434856 1.240000e-94 357.0
33 TraesCS3A01G043200 chr1D 94.545 55 3 0 475 529 131440393 131440447 6.460000e-13 86.1
34 TraesCS3A01G043200 chr4D 86.842 380 34 12 239 615 219181929 219182295 9.380000e-111 411.0
35 TraesCS3A01G043200 chr4D 89.024 82 7 2 5 85 334376927 334376847 2.310000e-17 100.0
36 TraesCS3A01G043200 chr1B 82.883 111 18 1 2 111 396485051 396485161 8.290000e-17 99.0
37 TraesCS3A01G043200 chr1B 90.000 70 6 1 1 69 393562315 393562246 4.990000e-14 89.8


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 TraesCS3A01G043200 chr3A 23446347 23449975 3628 False 6702 6702 100.000 1 3629 1 chr3A.!!$F1 3628
1 TraesCS3A01G043200 chr3A 57274910 57277797 2887 True 5103 5103 98.453 721 3629 1 chr3A.!!$R1 2908
2 TraesCS3A01G043200 chr3A 558589282 558589999 717 False 1168 1168 95.983 1 721 1 chr3A.!!$F3 720
3 TraesCS3A01G043200 chr3A 558581126 558581842 716 False 1151 1151 95.562 1 721 1 chr3A.!!$F2 720
4 TraesCS3A01G043200 chr4A 644769783 644772685 2902 True 5240 5240 99.209 721 3629 1 chr4A.!!$R1 2908
5 TraesCS3A01G043200 chr5A 69229646 69232548 2902 True 5234 5234 99.175 721 3629 1 chr5A.!!$R1 2908
6 TraesCS3A01G043200 chr1A 521284773 521287689 2916 True 5186 5186 98.803 721 3629 1 chr1A.!!$R2 2908
7 TraesCS3A01G043200 chr1A 500071513 500074427 2914 True 5158 5158 98.665 724 3629 1 chr1A.!!$R1 2905
8 TraesCS3A01G043200 chr7B 122624256 122627143 2887 False 5142 5142 98.694 721 3629 1 chr7B.!!$F1 2908
9 TraesCS3A01G043200 chr7B 476792716 476795152 2436 True 4303 4303 98.413 721 3178 1 chr7B.!!$R1 2457
10 TraesCS3A01G043200 chr2B 165276629 165279512 2883 False 5088 5088 98.384 721 3629 1 chr2B.!!$F1 2908
11 TraesCS3A01G043200 chr5B 339081373 339084260 2887 False 5086 5086 98.350 721 3629 1 chr5B.!!$F1 2908
12 TraesCS3A01G043200 chr5B 434055010 434055864 854 True 1269 1269 93.257 720 1593 1 chr5B.!!$R1 873
13 TraesCS3A01G043200 chr6A 97396173 97398565 2392 True 4287 4287 98.958 720 3118 1 chr6A.!!$R1 2398
14 TraesCS3A01G043200 chr4B 451448801 451450953 2152 True 3701 3701 97.740 1480 3629 1 chr4B.!!$R2 2149
15 TraesCS3A01G043200 chr6B 476708871 476709725 854 False 1262 1262 93.279 720 1579 1 chr6B.!!$F1 859
16 TraesCS3A01G043200 chr7D 151286853 151287715 862 True 1182 1182 91.364 721 1593 1 chr7D.!!$R1 872
17 TraesCS3A01G043200 chr7D 506649933 506650794 861 True 1170 1170 91.136 721 1593 1 chr7D.!!$R2 872
18 TraesCS3A01G043200 chr2D 499310618 499311480 862 False 1182 1182 91.364 721 1593 1 chr2D.!!$F2 872
19 TraesCS3A01G043200 chr2D 63946951 63947812 861 True 1164 1164 91.023 721 1593 1 chr2D.!!$R1 872
20 TraesCS3A01G043200 chr2D 488028056 488028663 607 True 592 592 84.541 1 608 1 chr2D.!!$R2 607
21 TraesCS3A01G043200 chr2D 318145789 318146377 588 False 556 556 83.876 1 608 1 chr2D.!!$F1 607
22 TraesCS3A01G043200 chr6D 57832579 57833450 871 False 1171 1171 90.909 711 1593 1 chr6D.!!$F1 882
23 TraesCS3A01G043200 chr5D 430990569 430991432 863 True 1157 1157 90.827 720 1593 1 chr5D.!!$R1 873
24 TraesCS3A01G043200 chr1D 479818445 479819313 868 True 1149 1149 90.530 714 1593 1 chr1D.!!$R1 879

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
690 696 0.034380 AGCGGTAGGAGAGCAGTACA 60.034 55.0 0.0 0.0 0.0 2.90 F
691 697 0.100861 GCGGTAGGAGAGCAGTACAC 59.899 60.0 0.0 0.0 0.0 2.90 F
693 699 0.100861 GGTAGGAGAGCAGTACACGC 59.899 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2037 3.538591 CAGACTGCAGATGCCTGAAATA 58.461 45.455 23.35 0.0 43.02 1.40 R
2227 2277 3.764434 TCCTGACACTTAGTTAGCTCTGG 59.236 47.826 0.00 0.0 32.77 3.86 R
3012 3137 2.568956 TCCTGACTCCAAGTGAAGATGG 59.431 50.000 0.00 0.0 38.09 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
215 221 1.236616 TGCCCAATCAGCAGTCAACG 61.237 55.000 0.00 0.00 34.69 4.10
248 254 1.278127 CGGTCATCTAACAAGTGGGGT 59.722 52.381 0.00 0.00 0.00 4.95
386 392 2.751436 GCCCCACACGTCATGCAT 60.751 61.111 0.00 0.00 0.00 3.96
387 393 3.055080 GCCCCACACGTCATGCATG 62.055 63.158 21.07 21.07 0.00 4.06
434 440 6.622833 GTCTACTAAGCTAGACTAACAGGG 57.377 45.833 7.05 0.00 39.69 4.45
435 441 5.008911 GTCTACTAAGCTAGACTAACAGGGC 59.991 48.000 7.05 0.00 39.69 5.19
436 442 3.032459 ACTAAGCTAGACTAACAGGGCC 58.968 50.000 0.00 0.00 0.00 5.80
437 443 1.952621 AAGCTAGACTAACAGGGCCA 58.047 50.000 6.18 0.00 0.00 5.36
438 444 1.490574 AGCTAGACTAACAGGGCCAG 58.509 55.000 6.18 0.00 0.00 4.85
439 445 0.179070 GCTAGACTAACAGGGCCAGC 60.179 60.000 6.18 0.00 0.00 4.85
440 446 0.466124 CTAGACTAACAGGGCCAGCC 59.534 60.000 6.18 0.00 0.00 4.85
441 447 0.042731 TAGACTAACAGGGCCAGCCT 59.957 55.000 6.18 0.00 36.10 4.58
442 448 1.222113 GACTAACAGGGCCAGCCTC 59.778 63.158 6.18 0.00 36.10 4.70
443 449 1.538876 ACTAACAGGGCCAGCCTCA 60.539 57.895 6.18 0.00 36.10 3.86
444 450 0.916358 ACTAACAGGGCCAGCCTCAT 60.916 55.000 6.18 0.00 36.10 2.90
445 451 0.179034 CTAACAGGGCCAGCCTCATC 60.179 60.000 6.18 0.00 36.10 2.92
446 452 1.635817 TAACAGGGCCAGCCTCATCC 61.636 60.000 6.18 0.00 36.10 3.51
447 453 3.414193 CAGGGCCAGCCTCATCCA 61.414 66.667 6.18 0.00 36.10 3.41
448 454 3.095163 AGGGCCAGCCTCATCCAG 61.095 66.667 6.18 0.00 36.10 3.86
449 455 3.092511 GGGCCAGCCTCATCCAGA 61.093 66.667 4.39 0.00 36.10 3.86
450 456 2.509916 GGCCAGCCTCATCCAGAG 59.490 66.667 0.00 0.00 44.31 3.35
458 464 3.157252 TCATCCAGAGAGCCGGCC 61.157 66.667 26.15 15.34 0.00 6.13
459 465 3.473647 CATCCAGAGAGCCGGCCA 61.474 66.667 26.15 0.00 0.00 5.36
460 466 3.160047 ATCCAGAGAGCCGGCCAG 61.160 66.667 26.15 8.60 0.00 4.85
465 471 4.925861 GAGAGCCGGCCAGCCATC 62.926 72.222 26.15 13.49 35.37 3.51
477 483 4.197498 GCCATCACACGGCCATGC 62.197 66.667 0.00 0.00 44.22 4.06
478 484 2.751036 CCATCACACGGCCATGCA 60.751 61.111 0.00 0.00 0.00 3.96
479 485 2.486504 CATCACACGGCCATGCAC 59.513 61.111 0.00 0.00 0.00 4.57
480 486 2.033911 ATCACACGGCCATGCACA 59.966 55.556 0.00 0.00 0.00 4.57
481 487 1.603171 ATCACACGGCCATGCACAA 60.603 52.632 0.00 0.00 0.00 3.33
482 488 1.177895 ATCACACGGCCATGCACAAA 61.178 50.000 0.00 0.00 0.00 2.83
483 489 1.372004 CACACGGCCATGCACAAAG 60.372 57.895 0.00 0.00 0.00 2.77
484 490 2.259204 CACGGCCATGCACAAAGG 59.741 61.111 2.24 0.00 0.00 3.11
509 515 4.021559 CATGGCCATGGTCAGCAA 57.978 55.556 34.31 0.00 35.24 3.91
510 516 1.514087 CATGGCCATGGTCAGCAAC 59.486 57.895 34.31 0.00 35.24 4.17
511 517 1.077086 ATGGCCATGGTCAGCAACA 59.923 52.632 25.65 0.00 31.29 3.33
512 518 0.968901 ATGGCCATGGTCAGCAACAG 60.969 55.000 25.65 0.00 31.29 3.16
513 519 2.570181 GCCATGGTCAGCAACAGC 59.430 61.111 14.67 0.00 0.00 4.40
514 520 2.872557 CCATGGTCAGCAACAGCG 59.127 61.111 2.57 0.00 0.00 5.18
515 521 1.968017 CCATGGTCAGCAACAGCGT 60.968 57.895 2.57 0.00 0.00 5.07
516 522 0.673333 CCATGGTCAGCAACAGCGTA 60.673 55.000 2.57 0.00 0.00 4.42
517 523 1.372582 CATGGTCAGCAACAGCGTAT 58.627 50.000 0.00 0.00 0.00 3.06
518 524 2.549926 CATGGTCAGCAACAGCGTATA 58.450 47.619 0.00 0.00 0.00 1.47
519 525 2.753055 TGGTCAGCAACAGCGTATAA 57.247 45.000 0.00 0.00 0.00 0.98
520 526 3.260475 TGGTCAGCAACAGCGTATAAT 57.740 42.857 0.00 0.00 0.00 1.28
521 527 4.394439 TGGTCAGCAACAGCGTATAATA 57.606 40.909 0.00 0.00 0.00 0.98
522 528 4.368315 TGGTCAGCAACAGCGTATAATAG 58.632 43.478 0.00 0.00 0.00 1.73
523 529 3.184581 GGTCAGCAACAGCGTATAATAGC 59.815 47.826 0.00 0.00 0.00 2.97
524 530 3.802139 GTCAGCAACAGCGTATAATAGCA 59.198 43.478 0.00 0.00 35.48 3.49
525 531 4.051237 TCAGCAACAGCGTATAATAGCAG 58.949 43.478 0.00 0.00 35.48 4.24
526 532 2.802816 AGCAACAGCGTATAATAGCAGC 59.197 45.455 0.00 0.00 35.48 5.25
527 533 2.543848 GCAACAGCGTATAATAGCAGCA 59.456 45.455 0.00 0.00 35.48 4.41
528 534 3.363378 GCAACAGCGTATAATAGCAGCAG 60.363 47.826 0.00 0.00 35.48 4.24
529 535 2.408050 ACAGCGTATAATAGCAGCAGC 58.592 47.619 0.00 0.00 42.56 5.25
539 545 3.088044 GCAGCAGCTAAGCACGAG 58.912 61.111 0.00 0.00 37.91 4.18
540 546 2.459442 GCAGCAGCTAAGCACGAGG 61.459 63.158 0.00 0.00 37.91 4.63
541 547 1.216444 CAGCAGCTAAGCACGAGGA 59.784 57.895 0.00 0.00 36.85 3.71
542 548 0.805322 CAGCAGCTAAGCACGAGGAG 60.805 60.000 0.00 0.00 36.85 3.69
543 549 2.170434 GCAGCTAAGCACGAGGAGC 61.170 63.158 0.00 0.00 35.07 4.70
544 550 1.216444 CAGCTAAGCACGAGGAGCA 59.784 57.895 0.00 0.00 37.40 4.26
545 551 0.805322 CAGCTAAGCACGAGGAGCAG 60.805 60.000 0.00 0.00 37.40 4.24
546 552 1.216710 GCTAAGCACGAGGAGCAGT 59.783 57.895 0.00 0.00 34.96 4.40
547 553 0.456221 GCTAAGCACGAGGAGCAGTA 59.544 55.000 0.00 0.00 34.96 2.74
548 554 1.535015 GCTAAGCACGAGGAGCAGTAG 60.535 57.143 0.00 0.00 34.96 2.57
549 555 0.456221 TAAGCACGAGGAGCAGTAGC 59.544 55.000 0.00 0.00 42.56 3.58
566 572 4.511443 CGCAACGCAGCAGCTAGC 62.511 66.667 6.62 6.62 46.19 3.42
583 589 4.024698 CGAGCAGCATCAGTAGGC 57.975 61.111 0.00 0.00 0.00 3.93
584 590 1.948138 CGAGCAGCATCAGTAGGCG 60.948 63.158 0.00 0.00 37.52 5.52
585 591 1.439228 GAGCAGCATCAGTAGGCGA 59.561 57.895 0.00 0.00 37.52 5.54
586 592 0.597118 GAGCAGCATCAGTAGGCGAG 60.597 60.000 0.00 0.00 37.52 5.03
587 593 2.243264 GCAGCATCAGTAGGCGAGC 61.243 63.158 0.00 0.00 37.52 5.03
588 594 1.142531 CAGCATCAGTAGGCGAGCA 59.857 57.895 0.00 0.00 37.52 4.26
589 595 0.875040 CAGCATCAGTAGGCGAGCAG 60.875 60.000 0.00 0.00 37.52 4.24
610 616 4.528674 CGATTAGCAGCAGCACCT 57.471 55.556 3.17 0.00 45.49 4.00
611 617 3.667448 CGATTAGCAGCAGCACCTA 57.333 52.632 3.17 0.00 45.49 3.08
612 618 1.495878 CGATTAGCAGCAGCACCTAG 58.504 55.000 3.17 0.00 45.49 3.02
613 619 1.224965 GATTAGCAGCAGCACCTAGC 58.775 55.000 3.17 0.00 45.49 3.42
629 635 4.100981 GCAAGCAGCGTAGGAGAG 57.899 61.111 0.00 0.00 0.00 3.20
630 636 2.170434 GCAAGCAGCGTAGGAGAGC 61.170 63.158 0.00 0.00 0.00 4.09
631 637 1.216444 CAAGCAGCGTAGGAGAGCA 59.784 57.895 0.00 0.00 35.48 4.26
632 638 0.390340 CAAGCAGCGTAGGAGAGCAA 60.390 55.000 0.00 0.00 35.48 3.91
633 639 0.108424 AAGCAGCGTAGGAGAGCAAG 60.108 55.000 0.00 0.00 35.48 4.01
634 640 2.170434 GCAGCGTAGGAGAGCAAGC 61.170 63.158 0.00 0.00 35.48 4.01
635 641 1.216444 CAGCGTAGGAGAGCAAGCA 59.784 57.895 0.00 0.00 35.48 3.91
636 642 0.179089 CAGCGTAGGAGAGCAAGCAT 60.179 55.000 0.00 0.00 35.48 3.79
637 643 0.103937 AGCGTAGGAGAGCAAGCATC 59.896 55.000 0.00 0.00 35.48 3.91
638 644 1.211818 GCGTAGGAGAGCAAGCATCG 61.212 60.000 0.00 0.00 0.00 3.84
639 645 1.211818 CGTAGGAGAGCAAGCATCGC 61.212 60.000 0.00 0.00 0.00 4.58
640 646 0.179100 GTAGGAGAGCAAGCATCGCA 60.179 55.000 0.00 0.00 0.00 5.10
641 647 0.103755 TAGGAGAGCAAGCATCGCAG 59.896 55.000 0.00 0.00 0.00 5.18
642 648 2.178890 GGAGAGCAAGCATCGCAGG 61.179 63.158 0.00 0.00 0.00 4.85
643 649 1.153489 GAGAGCAAGCATCGCAGGA 60.153 57.895 0.00 0.00 0.00 3.86
644 650 1.152989 GAGAGCAAGCATCGCAGGAG 61.153 60.000 0.00 0.00 0.00 3.69
645 651 1.153489 GAGCAAGCATCGCAGGAGA 60.153 57.895 0.00 0.00 0.00 3.71
646 652 1.152989 GAGCAAGCATCGCAGGAGAG 61.153 60.000 0.00 0.00 0.00 3.20
647 653 2.821688 GCAAGCATCGCAGGAGAGC 61.822 63.158 0.00 0.00 0.00 4.09
648 654 1.449070 CAAGCATCGCAGGAGAGCA 60.449 57.895 0.00 0.00 31.61 4.26
649 655 1.153409 AAGCATCGCAGGAGAGCAG 60.153 57.895 0.00 0.00 31.61 4.24
650 656 3.270839 GCATCGCAGGAGAGCAGC 61.271 66.667 0.00 0.00 0.00 5.25
651 657 2.186125 CATCGCAGGAGAGCAGCA 59.814 61.111 0.00 0.00 0.00 4.41
652 658 1.883544 CATCGCAGGAGAGCAGCAG 60.884 63.158 0.00 0.00 0.00 4.24
653 659 3.736732 ATCGCAGGAGAGCAGCAGC 62.737 63.158 0.00 0.00 42.56 5.25
663 669 2.256158 GCAGCAGCGCATCAACAA 59.744 55.556 11.47 0.00 0.00 2.83
664 670 1.800315 GCAGCAGCGCATCAACAAG 60.800 57.895 11.47 0.00 0.00 3.16
665 671 1.871077 CAGCAGCGCATCAACAAGA 59.129 52.632 11.47 0.00 0.00 3.02
666 672 0.179197 CAGCAGCGCATCAACAAGAG 60.179 55.000 11.47 0.00 0.00 2.85
667 673 1.513586 GCAGCGCATCAACAAGAGC 60.514 57.895 11.47 0.00 0.00 4.09
668 674 1.871077 CAGCGCATCAACAAGAGCA 59.129 52.632 11.47 0.00 32.74 4.26
669 675 0.179197 CAGCGCATCAACAAGAGCAG 60.179 55.000 11.47 0.00 32.74 4.24
670 676 1.513586 GCGCATCAACAAGAGCAGC 60.514 57.895 0.30 0.00 0.00 5.25
671 677 1.871077 CGCATCAACAAGAGCAGCA 59.129 52.632 0.00 0.00 0.00 4.41
672 678 0.179197 CGCATCAACAAGAGCAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
673 679 0.456312 GCATCAACAAGAGCAGCAGC 60.456 55.000 0.00 0.00 42.56 5.25
683 689 2.105930 GCAGCAGCGGTAGGAGAG 59.894 66.667 0.00 0.00 0.00 3.20
684 690 2.105930 CAGCAGCGGTAGGAGAGC 59.894 66.667 0.00 0.00 0.00 4.09
685 691 2.363018 AGCAGCGGTAGGAGAGCA 60.363 61.111 0.00 0.00 0.00 4.26
686 692 2.105930 GCAGCGGTAGGAGAGCAG 59.894 66.667 0.00 0.00 0.00 4.24
687 693 2.716017 GCAGCGGTAGGAGAGCAGT 61.716 63.158 0.00 0.00 0.00 4.40
688 694 1.384989 GCAGCGGTAGGAGAGCAGTA 61.385 60.000 0.00 0.00 0.00 2.74
689 695 0.382515 CAGCGGTAGGAGAGCAGTAC 59.617 60.000 0.00 0.00 0.00 2.73
690 696 0.034380 AGCGGTAGGAGAGCAGTACA 60.034 55.000 0.00 0.00 0.00 2.90
691 697 0.100861 GCGGTAGGAGAGCAGTACAC 59.899 60.000 0.00 0.00 0.00 2.90
692 698 0.377554 CGGTAGGAGAGCAGTACACG 59.622 60.000 0.00 0.00 0.00 4.49
693 699 0.100861 GGTAGGAGAGCAGTACACGC 59.899 60.000 0.00 0.00 0.00 5.34
694 700 0.100861 GTAGGAGAGCAGTACACGCC 59.899 60.000 3.86 0.00 0.00 5.68
695 701 0.323087 TAGGAGAGCAGTACACGCCA 60.323 55.000 3.86 0.00 31.17 5.69
696 702 1.185618 AGGAGAGCAGTACACGCCAA 61.186 55.000 3.86 0.00 31.17 4.52
697 703 0.737715 GGAGAGCAGTACACGCCAAG 60.738 60.000 3.86 0.00 0.00 3.61
698 704 0.243907 GAGAGCAGTACACGCCAAGA 59.756 55.000 3.86 0.00 0.00 3.02
699 705 0.244994 AGAGCAGTACACGCCAAGAG 59.755 55.000 3.86 0.00 0.00 2.85
700 706 1.355066 GAGCAGTACACGCCAAGAGC 61.355 60.000 3.86 0.00 38.52 4.09
701 707 1.667830 GCAGTACACGCCAAGAGCA 60.668 57.895 0.00 0.00 44.04 4.26
702 708 1.630244 GCAGTACACGCCAAGAGCAG 61.630 60.000 0.00 0.00 44.04 4.24
703 709 1.374758 AGTACACGCCAAGAGCAGC 60.375 57.895 0.00 0.00 44.04 5.25
704 710 1.667830 GTACACGCCAAGAGCAGCA 60.668 57.895 0.00 0.00 44.04 4.41
705 711 1.374631 TACACGCCAAGAGCAGCAG 60.375 57.895 0.00 0.00 44.04 4.24
706 712 4.099170 CACGCCAAGAGCAGCAGC 62.099 66.667 0.00 0.00 44.04 5.25
707 713 4.631247 ACGCCAAGAGCAGCAGCA 62.631 61.111 3.17 0.00 45.49 4.41
708 714 3.800863 CGCCAAGAGCAGCAGCAG 61.801 66.667 3.17 0.00 45.49 4.24
709 715 4.117661 GCCAAGAGCAGCAGCAGC 62.118 66.667 3.17 0.46 45.49 5.25
710 716 2.671963 CCAAGAGCAGCAGCAGCA 60.672 61.111 12.92 0.00 45.49 4.41
711 717 2.561885 CAAGAGCAGCAGCAGCAC 59.438 61.111 12.92 5.78 45.49 4.40
712 718 2.112507 AAGAGCAGCAGCAGCACA 59.887 55.556 12.92 0.00 45.49 4.57
713 719 2.259439 AAGAGCAGCAGCAGCACAC 61.259 57.895 12.92 3.29 45.49 3.82
714 720 2.953247 AAGAGCAGCAGCAGCACACA 62.953 55.000 12.92 0.00 45.49 3.72
715 721 3.251318 GAGCAGCAGCAGCACACAC 62.251 63.158 12.92 0.00 45.49 3.82
716 722 4.678269 GCAGCAGCAGCACACACG 62.678 66.667 4.63 0.00 45.49 4.49
717 723 3.274586 CAGCAGCAGCACACACGT 61.275 61.111 3.17 0.00 45.49 4.49
718 724 3.274586 AGCAGCAGCACACACGTG 61.275 61.111 15.48 15.48 46.56 4.49
784 790 4.034048 CAGATTGGTACCACGATTGCTAAC 59.966 45.833 16.04 0.00 0.00 2.34
1181 1210 0.966920 CAACGAGGTCAGTACAGGGT 59.033 55.000 0.00 0.00 0.00 4.34
1182 1211 1.343465 CAACGAGGTCAGTACAGGGTT 59.657 52.381 0.00 0.00 0.00 4.11
1183 1212 2.559668 CAACGAGGTCAGTACAGGGTTA 59.440 50.000 0.00 0.00 0.00 2.85
1184 1213 2.444421 ACGAGGTCAGTACAGGGTTAG 58.556 52.381 0.00 0.00 0.00 2.34
1987 2037 2.915869 TCCAGGAAGATAAGGTGGTGT 58.084 47.619 0.00 0.00 0.00 4.16
2227 2277 7.565323 AGTATGAATTTGGAGCTGAAGAATC 57.435 36.000 0.00 0.00 0.00 2.52
3109 3234 0.839277 TCACGCAGATCCCCAATGAT 59.161 50.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 221 2.431057 AGATGACCGGTCAATAGTCACC 59.569 50.000 39.04 19.58 42.89 4.02
248 254 6.585416 ACAGATTGTGCATATGACATGTAGA 58.415 36.000 6.97 0.00 0.00 2.59
386 392 9.914834 ACTAATTAATGTTTTGGTATAGCCTCA 57.085 29.630 0.00 0.00 38.35 3.86
428 434 2.679716 GATGAGGCTGGCCCTGTT 59.320 61.111 8.11 0.00 46.60 3.16
429 435 3.415087 GGATGAGGCTGGCCCTGT 61.415 66.667 8.11 0.00 46.60 4.00
430 436 3.414193 TGGATGAGGCTGGCCCTG 61.414 66.667 8.11 0.00 46.60 4.45
432 438 3.092511 TCTGGATGAGGCTGGCCC 61.093 66.667 8.11 0.85 36.58 5.80
433 439 2.042404 CTCTCTGGATGAGGCTGGCC 62.042 65.000 3.00 3.00 42.86 5.36
434 440 1.446791 CTCTCTGGATGAGGCTGGC 59.553 63.158 0.00 0.00 42.86 4.85
435 441 1.446791 GCTCTCTGGATGAGGCTGG 59.553 63.158 0.00 0.00 42.86 4.85
439 445 3.136750 CCGGCTCTCTGGATGAGG 58.863 66.667 0.00 0.00 42.86 3.86
440 446 2.420890 GCCGGCTCTCTGGATGAG 59.579 66.667 22.15 0.00 41.45 2.90
441 447 3.157252 GGCCGGCTCTCTGGATGA 61.157 66.667 28.56 0.00 41.45 2.92
442 448 3.457625 CTGGCCGGCTCTCTGGATG 62.458 68.421 28.56 2.25 41.45 3.51
443 449 3.160047 CTGGCCGGCTCTCTGGAT 61.160 66.667 28.56 0.00 41.45 3.41
448 454 4.925861 GATGGCTGGCCGGCTCTC 62.926 72.222 34.76 25.85 39.42 3.20
461 467 2.751036 TGCATGGCCGTGTGATGG 60.751 61.111 25.67 0.00 0.00 3.51
462 468 1.864725 TTGTGCATGGCCGTGTGATG 61.865 55.000 25.67 11.12 0.00 3.07
463 469 1.177895 TTTGTGCATGGCCGTGTGAT 61.178 50.000 25.67 0.00 0.00 3.06
464 470 1.794151 CTTTGTGCATGGCCGTGTGA 61.794 55.000 25.67 10.58 0.00 3.58
465 471 1.372004 CTTTGTGCATGGCCGTGTG 60.372 57.895 25.67 12.21 0.00 3.82
466 472 2.563798 CCTTTGTGCATGGCCGTGT 61.564 57.895 25.67 0.00 0.00 4.49
467 473 2.259204 CCTTTGTGCATGGCCGTG 59.741 61.111 21.33 21.33 0.00 4.94
468 474 3.683937 GCCTTTGTGCATGGCCGT 61.684 61.111 0.00 0.00 40.71 5.68
469 475 3.682885 TGCCTTTGTGCATGGCCG 61.683 61.111 16.48 0.00 45.56 6.13
470 476 2.047939 GTGCCTTTGTGCATGGCC 60.048 61.111 16.48 0.00 45.56 5.36
471 477 1.373748 CTGTGCCTTTGTGCATGGC 60.374 57.895 13.61 13.61 44.30 4.40
472 478 1.290955 CCTGTGCCTTTGTGCATGG 59.709 57.895 0.00 0.00 44.30 3.66
473 479 1.373748 GCCTGTGCCTTTGTGCATG 60.374 57.895 0.00 0.00 44.30 4.06
474 480 3.053828 GCCTGTGCCTTTGTGCAT 58.946 55.556 0.00 0.00 44.30 3.96
492 498 1.252215 TGTTGCTGACCATGGCCATG 61.252 55.000 34.82 34.82 38.51 3.66
493 499 0.968901 CTGTTGCTGACCATGGCCAT 60.969 55.000 14.09 14.09 0.00 4.40
494 500 1.604308 CTGTTGCTGACCATGGCCA 60.604 57.895 13.04 8.56 0.00 5.36
495 501 2.998279 GCTGTTGCTGACCATGGCC 61.998 63.158 13.04 0.00 36.03 5.36
496 502 2.570181 GCTGTTGCTGACCATGGC 59.430 61.111 13.04 5.35 36.03 4.40
497 503 0.673333 TACGCTGTTGCTGACCATGG 60.673 55.000 11.19 11.19 36.97 3.66
498 504 1.372582 ATACGCTGTTGCTGACCATG 58.627 50.000 0.00 0.00 36.97 3.66
499 505 2.979814 TATACGCTGTTGCTGACCAT 57.020 45.000 0.00 0.00 36.97 3.55
500 506 2.753055 TTATACGCTGTTGCTGACCA 57.247 45.000 0.00 0.00 36.97 4.02
501 507 3.184581 GCTATTATACGCTGTTGCTGACC 59.815 47.826 0.00 0.00 36.97 4.02
502 508 3.802139 TGCTATTATACGCTGTTGCTGAC 59.198 43.478 0.00 0.00 36.97 3.51
503 509 4.051237 CTGCTATTATACGCTGTTGCTGA 58.949 43.478 0.00 0.00 36.97 4.26
504 510 3.363378 GCTGCTATTATACGCTGTTGCTG 60.363 47.826 0.00 0.00 36.97 4.41
505 511 2.802816 GCTGCTATTATACGCTGTTGCT 59.197 45.455 0.00 0.00 36.97 3.91
506 512 2.543848 TGCTGCTATTATACGCTGTTGC 59.456 45.455 0.00 0.00 0.00 4.17
507 513 3.363378 GCTGCTGCTATTATACGCTGTTG 60.363 47.826 8.53 0.00 36.03 3.33
508 514 2.802816 GCTGCTGCTATTATACGCTGTT 59.197 45.455 8.53 0.00 36.03 3.16
509 515 2.408050 GCTGCTGCTATTATACGCTGT 58.592 47.619 8.53 0.00 36.03 4.40
522 528 2.459442 CCTCGTGCTTAGCTGCTGC 61.459 63.158 13.43 7.62 40.05 5.25
523 529 0.805322 CTCCTCGTGCTTAGCTGCTG 60.805 60.000 13.43 0.00 0.00 4.41
524 530 1.515020 CTCCTCGTGCTTAGCTGCT 59.485 57.895 7.57 7.57 0.00 4.24
525 531 2.170434 GCTCCTCGTGCTTAGCTGC 61.170 63.158 5.60 0.00 32.18 5.25
526 532 0.805322 CTGCTCCTCGTGCTTAGCTG 60.805 60.000 5.60 0.00 35.95 4.24
527 533 1.254284 ACTGCTCCTCGTGCTTAGCT 61.254 55.000 5.60 0.00 35.95 3.32
528 534 0.456221 TACTGCTCCTCGTGCTTAGC 59.544 55.000 0.00 0.00 35.51 3.09
529 535 1.535015 GCTACTGCTCCTCGTGCTTAG 60.535 57.143 0.00 0.00 36.03 2.18
530 536 0.456221 GCTACTGCTCCTCGTGCTTA 59.544 55.000 0.00 0.00 36.03 3.09
531 537 1.216710 GCTACTGCTCCTCGTGCTT 59.783 57.895 0.00 0.00 36.03 3.91
532 538 2.888863 GCTACTGCTCCTCGTGCT 59.111 61.111 0.00 0.00 36.03 4.40
533 539 2.580867 CGCTACTGCTCCTCGTGC 60.581 66.667 0.00 0.00 36.97 5.34
534 540 2.580867 GCGCTACTGCTCCTCGTG 60.581 66.667 0.00 0.00 36.97 4.35
535 541 2.636412 TTGCGCTACTGCTCCTCGT 61.636 57.895 9.73 0.00 36.97 4.18
536 542 2.161486 GTTGCGCTACTGCTCCTCG 61.161 63.158 14.88 0.00 36.97 4.63
537 543 2.161486 CGTTGCGCTACTGCTCCTC 61.161 63.158 19.36 0.00 36.97 3.71
538 544 2.125912 CGTTGCGCTACTGCTCCT 60.126 61.111 19.36 0.00 36.97 3.69
549 555 4.511443 GCTAGCTGCTGCGTTGCG 62.511 66.667 13.43 0.00 45.42 4.85
550 556 4.511443 CGCTAGCTGCTGCGTTGC 62.511 66.667 26.72 13.68 46.09 4.17
562 568 1.335780 CCTACTGATGCTGCTCGCTAG 60.336 57.143 0.00 0.00 40.11 3.42
563 569 0.670706 CCTACTGATGCTGCTCGCTA 59.329 55.000 0.00 0.00 40.11 4.26
564 570 1.440893 CCTACTGATGCTGCTCGCT 59.559 57.895 0.00 0.00 40.11 4.93
565 571 2.243264 GCCTACTGATGCTGCTCGC 61.243 63.158 0.00 0.00 39.77 5.03
566 572 1.948138 CGCCTACTGATGCTGCTCG 60.948 63.158 0.00 0.00 0.00 5.03
567 573 0.597118 CTCGCCTACTGATGCTGCTC 60.597 60.000 0.00 0.00 0.00 4.26
568 574 1.440893 CTCGCCTACTGATGCTGCT 59.559 57.895 0.00 0.00 0.00 4.24
569 575 2.243264 GCTCGCCTACTGATGCTGC 61.243 63.158 0.00 0.00 0.00 5.25
570 576 0.875040 CTGCTCGCCTACTGATGCTG 60.875 60.000 0.00 0.00 0.00 4.41
571 577 1.440893 CTGCTCGCCTACTGATGCT 59.559 57.895 0.00 0.00 0.00 3.79
572 578 2.243264 GCTGCTCGCCTACTGATGC 61.243 63.158 0.00 0.00 0.00 3.91
573 579 0.875040 CTGCTGCTCGCCTACTGATG 60.875 60.000 0.00 0.00 38.05 3.07
574 580 1.440893 CTGCTGCTCGCCTACTGAT 59.559 57.895 0.00 0.00 38.05 2.90
575 581 2.888111 CTGCTGCTCGCCTACTGA 59.112 61.111 0.00 0.00 38.05 3.41
576 582 2.889503 GCTGCTGCTCGCCTACTG 60.890 66.667 8.53 0.00 38.05 2.74
577 583 4.504916 CGCTGCTGCTCGCCTACT 62.505 66.667 14.03 0.00 38.05 2.57
578 584 3.781770 ATCGCTGCTGCTCGCCTAC 62.782 63.158 14.03 0.00 38.05 3.18
579 585 1.734388 TAATCGCTGCTGCTCGCCTA 61.734 55.000 14.03 0.00 38.05 3.93
580 586 2.967929 CTAATCGCTGCTGCTCGCCT 62.968 60.000 14.03 0.00 38.05 5.52
581 587 2.586079 TAATCGCTGCTGCTCGCC 60.586 61.111 14.03 0.00 38.05 5.54
582 588 2.926855 CTAATCGCTGCTGCTCGC 59.073 61.111 14.03 2.71 36.97 5.03
583 589 1.819226 CTGCTAATCGCTGCTGCTCG 61.819 60.000 14.03 4.86 40.11 5.03
584 590 1.933005 CTGCTAATCGCTGCTGCTC 59.067 57.895 14.03 0.00 40.11 4.26
585 591 4.121691 CTGCTAATCGCTGCTGCT 57.878 55.556 14.03 0.00 40.11 4.24
590 596 1.351012 GTGCTGCTGCTAATCGCTG 59.649 57.895 17.00 0.00 40.48 5.18
591 597 1.817099 GGTGCTGCTGCTAATCGCT 60.817 57.895 17.00 0.00 40.48 4.93
592 598 0.530650 TAGGTGCTGCTGCTAATCGC 60.531 55.000 17.00 0.00 40.48 4.58
593 599 1.495878 CTAGGTGCTGCTGCTAATCG 58.504 55.000 17.00 0.00 40.48 3.34
594 600 1.224965 GCTAGGTGCTGCTGCTAATC 58.775 55.000 17.00 0.00 40.48 1.75
595 601 0.543277 TGCTAGGTGCTGCTGCTAAT 59.457 50.000 17.00 4.87 43.37 1.73
596 602 0.324614 TTGCTAGGTGCTGCTGCTAA 59.675 50.000 17.00 0.00 43.37 3.09
597 603 0.107993 CTTGCTAGGTGCTGCTGCTA 60.108 55.000 17.00 0.16 43.37 3.49
598 604 1.376942 CTTGCTAGGTGCTGCTGCT 60.377 57.895 17.00 0.00 43.37 4.24
599 605 3.048941 GCTTGCTAGGTGCTGCTGC 62.049 63.158 8.89 8.89 43.37 5.25
600 606 1.645704 CTGCTTGCTAGGTGCTGCTG 61.646 60.000 0.00 0.00 43.37 4.41
601 607 1.376942 CTGCTTGCTAGGTGCTGCT 60.377 57.895 0.00 0.00 43.37 4.24
602 608 3.048941 GCTGCTTGCTAGGTGCTGC 62.049 63.158 0.00 0.00 43.37 5.25
603 609 2.747822 CGCTGCTTGCTAGGTGCTG 61.748 63.158 0.00 0.00 43.37 4.41
604 610 1.888436 TACGCTGCTTGCTAGGTGCT 61.888 55.000 0.00 0.00 43.37 4.40
605 611 1.424493 CTACGCTGCTTGCTAGGTGC 61.424 60.000 0.00 0.00 40.11 5.01
606 612 0.807667 CCTACGCTGCTTGCTAGGTG 60.808 60.000 0.00 0.00 37.57 4.00
607 613 0.970937 TCCTACGCTGCTTGCTAGGT 60.971 55.000 17.57 6.92 40.37 3.08
608 614 0.249238 CTCCTACGCTGCTTGCTAGG 60.249 60.000 0.00 14.80 40.60 3.02
609 615 0.741326 TCTCCTACGCTGCTTGCTAG 59.259 55.000 0.00 0.00 40.11 3.42
610 616 0.741326 CTCTCCTACGCTGCTTGCTA 59.259 55.000 0.00 0.00 40.11 3.49
611 617 1.515020 CTCTCCTACGCTGCTTGCT 59.485 57.895 0.00 0.00 40.11 3.91
612 618 2.170434 GCTCTCCTACGCTGCTTGC 61.170 63.158 0.00 0.00 38.57 4.01
613 619 0.390340 TTGCTCTCCTACGCTGCTTG 60.390 55.000 0.00 0.00 0.00 4.01
614 620 0.108424 CTTGCTCTCCTACGCTGCTT 60.108 55.000 0.00 0.00 0.00 3.91
615 621 1.515020 CTTGCTCTCCTACGCTGCT 59.485 57.895 0.00 0.00 0.00 4.24
616 622 2.170434 GCTTGCTCTCCTACGCTGC 61.170 63.158 0.00 0.00 0.00 5.25
617 623 0.179089 ATGCTTGCTCTCCTACGCTG 60.179 55.000 0.00 0.00 0.00 5.18
618 624 0.103937 GATGCTTGCTCTCCTACGCT 59.896 55.000 0.00 0.00 0.00 5.07
619 625 1.211818 CGATGCTTGCTCTCCTACGC 61.212 60.000 0.00 0.00 0.00 4.42
620 626 1.211818 GCGATGCTTGCTCTCCTACG 61.212 60.000 0.00 0.00 0.00 3.51
621 627 0.179100 TGCGATGCTTGCTCTCCTAC 60.179 55.000 0.00 0.00 0.00 3.18
622 628 0.103755 CTGCGATGCTTGCTCTCCTA 59.896 55.000 0.00 0.00 0.00 2.94
623 629 1.153409 CTGCGATGCTTGCTCTCCT 60.153 57.895 0.00 0.00 0.00 3.69
624 630 2.178890 CCTGCGATGCTTGCTCTCC 61.179 63.158 0.00 0.00 0.00 3.71
625 631 1.152989 CTCCTGCGATGCTTGCTCTC 61.153 60.000 0.00 0.00 0.00 3.20
626 632 1.153409 CTCCTGCGATGCTTGCTCT 60.153 57.895 0.00 0.00 0.00 4.09
627 633 1.152989 CTCTCCTGCGATGCTTGCTC 61.153 60.000 0.00 0.00 0.00 4.26
628 634 1.153409 CTCTCCTGCGATGCTTGCT 60.153 57.895 0.00 0.00 0.00 3.91
629 635 2.821688 GCTCTCCTGCGATGCTTGC 61.822 63.158 0.00 0.00 0.00 4.01
630 636 1.429927 CTGCTCTCCTGCGATGCTTG 61.430 60.000 0.00 0.00 35.36 4.01
631 637 1.153409 CTGCTCTCCTGCGATGCTT 60.153 57.895 0.00 0.00 35.36 3.91
632 638 2.500165 CTGCTCTCCTGCGATGCT 59.500 61.111 0.00 0.00 35.36 3.79
633 639 3.270839 GCTGCTCTCCTGCGATGC 61.271 66.667 0.00 0.00 35.36 3.91
634 640 1.883544 CTGCTGCTCTCCTGCGATG 60.884 63.158 0.00 0.00 40.88 3.84
635 641 2.500165 CTGCTGCTCTCCTGCGAT 59.500 61.111 0.00 0.00 40.88 4.58
636 642 4.447989 GCTGCTGCTCTCCTGCGA 62.448 66.667 8.53 0.00 40.88 5.10
639 645 4.754667 TGCGCTGCTGCTCTCCTG 62.755 66.667 9.73 0.00 36.97 3.86
640 646 3.736732 GATGCGCTGCTGCTCTCCT 62.737 63.158 9.73 0.00 36.97 3.69
641 647 3.270839 GATGCGCTGCTGCTCTCC 61.271 66.667 9.73 0.00 36.97 3.71
642 648 2.104859 TTGATGCGCTGCTGCTCTC 61.105 57.895 9.73 7.78 36.97 3.20
643 649 2.046604 TTGATGCGCTGCTGCTCT 60.047 55.556 9.73 0.00 36.97 4.09
644 650 2.099831 GTTGATGCGCTGCTGCTC 59.900 61.111 9.73 6.30 36.97 4.26
645 651 2.196382 CTTGTTGATGCGCTGCTGCT 62.196 55.000 9.73 0.00 36.97 4.24
646 652 1.800315 CTTGTTGATGCGCTGCTGC 60.800 57.895 9.73 5.34 0.00 5.25
647 653 0.179197 CTCTTGTTGATGCGCTGCTG 60.179 55.000 9.73 0.00 0.00 4.41
648 654 1.919956 GCTCTTGTTGATGCGCTGCT 61.920 55.000 9.73 0.00 0.00 4.24
649 655 1.513586 GCTCTTGTTGATGCGCTGC 60.514 57.895 9.73 0.13 0.00 5.25
650 656 0.179197 CTGCTCTTGTTGATGCGCTG 60.179 55.000 9.73 0.00 0.00 5.18
651 657 1.919956 GCTGCTCTTGTTGATGCGCT 61.920 55.000 9.73 0.00 0.00 5.92
652 658 1.513586 GCTGCTCTTGTTGATGCGC 60.514 57.895 0.00 0.00 0.00 6.09
653 659 0.179197 CTGCTGCTCTTGTTGATGCG 60.179 55.000 0.00 0.00 0.00 4.73
654 660 0.456312 GCTGCTGCTCTTGTTGATGC 60.456 55.000 8.53 0.00 36.03 3.91
655 661 0.179197 CGCTGCTGCTCTTGTTGATG 60.179 55.000 14.03 0.00 36.97 3.07
656 662 1.303799 CCGCTGCTGCTCTTGTTGAT 61.304 55.000 14.03 0.00 36.97 2.57
657 663 1.962822 CCGCTGCTGCTCTTGTTGA 60.963 57.895 14.03 0.00 36.97 3.18
658 664 0.950555 TACCGCTGCTGCTCTTGTTG 60.951 55.000 14.03 0.00 36.97 3.33
659 665 0.671781 CTACCGCTGCTGCTCTTGTT 60.672 55.000 14.03 0.00 36.97 2.83
660 666 1.079543 CTACCGCTGCTGCTCTTGT 60.080 57.895 14.03 7.85 36.97 3.16
661 667 1.812922 CCTACCGCTGCTGCTCTTG 60.813 63.158 14.03 2.32 36.97 3.02
662 668 1.954362 CTCCTACCGCTGCTGCTCTT 61.954 60.000 14.03 0.18 36.97 2.85
663 669 2.363018 TCCTACCGCTGCTGCTCT 60.363 61.111 14.03 0.78 36.97 4.09
664 670 2.105930 CTCCTACCGCTGCTGCTC 59.894 66.667 14.03 0.00 36.97 4.26
665 671 2.363018 TCTCCTACCGCTGCTGCT 60.363 61.111 14.03 0.00 36.97 4.24
666 672 2.105930 CTCTCCTACCGCTGCTGC 59.894 66.667 5.34 5.34 0.00 5.25
667 673 2.105930 GCTCTCCTACCGCTGCTG 59.894 66.667 0.00 0.00 0.00 4.41
668 674 2.363018 TGCTCTCCTACCGCTGCT 60.363 61.111 0.00 0.00 0.00 4.24
669 675 1.384989 TACTGCTCTCCTACCGCTGC 61.385 60.000 0.00 0.00 0.00 5.25
670 676 0.382515 GTACTGCTCTCCTACCGCTG 59.617 60.000 0.00 0.00 0.00 5.18
671 677 0.034380 TGTACTGCTCTCCTACCGCT 60.034 55.000 0.00 0.00 0.00 5.52
672 678 0.100861 GTGTACTGCTCTCCTACCGC 59.899 60.000 0.00 0.00 0.00 5.68
673 679 0.377554 CGTGTACTGCTCTCCTACCG 59.622 60.000 0.00 0.00 0.00 4.02
674 680 0.100861 GCGTGTACTGCTCTCCTACC 59.899 60.000 0.00 0.00 0.00 3.18
675 681 0.100861 GGCGTGTACTGCTCTCCTAC 59.899 60.000 9.91 0.00 0.00 3.18
676 682 0.323087 TGGCGTGTACTGCTCTCCTA 60.323 55.000 9.91 0.00 0.00 2.94
677 683 1.185618 TTGGCGTGTACTGCTCTCCT 61.186 55.000 9.91 0.00 0.00 3.69
678 684 0.737715 CTTGGCGTGTACTGCTCTCC 60.738 60.000 9.91 0.00 0.00 3.71
679 685 0.243907 TCTTGGCGTGTACTGCTCTC 59.756 55.000 9.91 0.00 0.00 3.20
680 686 0.244994 CTCTTGGCGTGTACTGCTCT 59.755 55.000 9.91 0.00 0.00 4.09
681 687 1.355066 GCTCTTGGCGTGTACTGCTC 61.355 60.000 9.91 2.64 0.00 4.26
682 688 1.374758 GCTCTTGGCGTGTACTGCT 60.375 57.895 9.91 0.00 0.00 4.24
683 689 1.630244 CTGCTCTTGGCGTGTACTGC 61.630 60.000 0.00 0.00 45.43 4.40
684 690 1.630244 GCTGCTCTTGGCGTGTACTG 61.630 60.000 0.00 0.00 45.43 2.74
685 691 1.374758 GCTGCTCTTGGCGTGTACT 60.375 57.895 0.00 0.00 45.43 2.73
686 692 1.630244 CTGCTGCTCTTGGCGTGTAC 61.630 60.000 0.00 0.00 45.43 2.90
687 693 1.374631 CTGCTGCTCTTGGCGTGTA 60.375 57.895 0.00 0.00 45.43 2.90
688 694 2.667536 CTGCTGCTCTTGGCGTGT 60.668 61.111 0.00 0.00 45.43 4.49
689 695 4.099170 GCTGCTGCTCTTGGCGTG 62.099 66.667 8.53 0.00 45.43 5.34
690 696 4.631247 TGCTGCTGCTCTTGGCGT 62.631 61.111 17.00 0.00 45.43 5.68
691 697 3.800863 CTGCTGCTGCTCTTGGCG 61.801 66.667 17.00 0.00 45.43 5.69
692 698 4.117661 GCTGCTGCTGCTCTTGGC 62.118 66.667 22.10 9.14 40.48 4.52
693 699 2.671963 TGCTGCTGCTGCTCTTGG 60.672 61.111 27.67 3.49 40.48 3.61
694 700 2.258726 TGTGCTGCTGCTGCTCTTG 61.259 57.895 27.67 5.75 40.48 3.02
695 701 2.112507 TGTGCTGCTGCTGCTCTT 59.887 55.556 27.67 0.00 40.48 2.85
696 702 2.668889 GTGTGCTGCTGCTGCTCT 60.669 61.111 27.67 0.00 40.48 4.09
697 703 2.976350 TGTGTGCTGCTGCTGCTC 60.976 61.111 27.67 24.51 40.48 4.26
698 704 3.285215 GTGTGTGCTGCTGCTGCT 61.285 61.111 27.67 0.00 40.48 4.24
699 705 4.678269 CGTGTGTGCTGCTGCTGC 62.678 66.667 22.51 22.51 40.48 5.25
700 706 3.274586 ACGTGTGTGCTGCTGCTG 61.275 61.111 17.00 0.77 40.48 4.41
701 707 3.274586 CACGTGTGTGCTGCTGCT 61.275 61.111 17.00 0.00 39.67 4.24
702 708 3.232645 CTCACGTGTGTGCTGCTGC 62.233 63.158 16.51 8.89 46.01 5.25
703 709 1.554891 CTCTCACGTGTGTGCTGCTG 61.555 60.000 16.51 0.00 46.01 4.41
704 710 1.300465 CTCTCACGTGTGTGCTGCT 60.300 57.895 16.51 0.00 46.01 4.24
705 711 1.154205 AACTCTCACGTGTGTGCTGC 61.154 55.000 16.51 0.00 46.01 5.25
706 712 2.134201 TAACTCTCACGTGTGTGCTG 57.866 50.000 16.51 8.01 46.01 4.41
707 713 2.882927 TTAACTCTCACGTGTGTGCT 57.117 45.000 16.51 8.05 46.01 4.40
708 714 3.799035 CAATTAACTCTCACGTGTGTGC 58.201 45.455 16.51 0.00 46.01 4.57
710 716 3.247648 GTGCAATTAACTCTCACGTGTGT 59.752 43.478 16.51 10.32 0.00 3.72
711 717 3.247411 TGTGCAATTAACTCTCACGTGTG 59.753 43.478 16.51 13.78 0.00 3.82
712 718 3.462982 TGTGCAATTAACTCTCACGTGT 58.537 40.909 16.51 0.00 0.00 4.49
713 719 3.740832 TCTGTGCAATTAACTCTCACGTG 59.259 43.478 9.94 9.94 0.00 4.49
714 720 3.990092 TCTGTGCAATTAACTCTCACGT 58.010 40.909 0.00 0.00 0.00 4.49
715 721 4.449068 ACTTCTGTGCAATTAACTCTCACG 59.551 41.667 0.00 0.00 0.00 4.35
716 722 5.931441 ACTTCTGTGCAATTAACTCTCAC 57.069 39.130 0.00 0.00 0.00 3.51
717 723 5.932303 GGTACTTCTGTGCAATTAACTCTCA 59.068 40.000 0.00 0.00 0.00 3.27
718 724 5.932303 TGGTACTTCTGTGCAATTAACTCTC 59.068 40.000 0.00 0.00 0.00 3.20
784 790 2.353269 TGTTGGTACTGACACGCAAAAG 59.647 45.455 0.00 0.00 0.00 2.27
1181 1210 4.511304 TGAAACCCTAACCCTAACCCTAA 58.489 43.478 0.00 0.00 0.00 2.69
1182 1211 4.159104 TGAAACCCTAACCCTAACCCTA 57.841 45.455 0.00 0.00 0.00 3.53
1183 1212 3.008340 TGAAACCCTAACCCTAACCCT 57.992 47.619 0.00 0.00 0.00 4.34
1184 1213 5.658198 ATATGAAACCCTAACCCTAACCC 57.342 43.478 0.00 0.00 0.00 4.11
1987 2037 3.538591 CAGACTGCAGATGCCTGAAATA 58.461 45.455 23.35 0.00 43.02 1.40
2227 2277 3.764434 TCCTGACACTTAGTTAGCTCTGG 59.236 47.826 0.00 0.00 32.77 3.86
3012 3137 2.568956 TCCTGACTCCAAGTGAAGATGG 59.431 50.000 0.00 0.00 38.09 3.51
3109 3234 0.615331 GCCCACATTCTGGAGTGAGA 59.385 55.000 0.27 0.00 43.95 3.27


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

AutoCloner maintained by Alex Coulton.