Multiple sequence alignment - TraesCS3D01G226200

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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 TraesCS3D01G226200 chr3D 100.000 4064 0 0 1 4064 307942299 307938236 0.000000e+00 7505.0
1 TraesCS3D01G226200 chr3D 92.638 489 35 1 3200 3688 285115286 285114799 0.000000e+00 702.0
2 TraesCS3D01G226200 chr3D 93.158 380 16 4 3695 4064 285114752 285114373 2.140000e-152 549.0
3 TraesCS3D01G226200 chr3D 81.928 83 9 3 560 641 384005799 384005722 9.430000e-07 65.8
4 TraesCS3D01G226200 chr3A 97.619 2814 66 1 875 3688 427213371 427210559 0.000000e+00 4824.0
5 TraesCS3D01G226200 chr3A 93.456 489 31 1 3200 3688 373330255 373329768 0.000000e+00 725.0
6 TraesCS3D01G226200 chr3A 96.657 359 12 0 3687 4045 427210513 427210155 7.520000e-167 597.0
7 TraesCS3D01G226200 chr3A 88.703 478 39 5 1 478 427213981 427213519 1.640000e-158 569.0
8 TraesCS3D01G226200 chr3A 93.122 378 18 3 3695 4064 373329722 373329345 7.680000e-152 547.0
9 TraesCS3D01G226200 chr3A 78.113 265 37 17 587 837 620206310 620206567 9.100000e-32 148.0
10 TraesCS3D01G226200 chr3B 97.974 2567 50 2 875 3441 413802314 413804878 0.000000e+00 4451.0
11 TraesCS3D01G226200 chr3B 92.638 489 35 1 3200 3688 378138896 378139383 0.000000e+00 702.0
12 TraesCS3D01G226200 chr3B 92.689 383 18 4 3692 4064 378139427 378139809 9.930000e-151 544.0
13 TraesCS3D01G226200 chr3B 88.986 345 37 1 27 371 413764835 413765178 3.750000e-115 425.0
14 TraesCS3D01G226200 chr3B 96.825 252 8 0 3687 3938 413804928 413805179 4.860000e-114 422.0
15 TraesCS3D01G226200 chr7D 90.946 2209 188 4 988 3195 330439318 330437121 0.000000e+00 2961.0
16 TraesCS3D01G226200 chr5D 84.387 538 76 2 2 538 508630415 508629885 4.650000e-144 521.0
17 TraesCS3D01G226200 chr5B 84.416 385 54 3 1 383 546440015 546440395 1.380000e-99 374.0
18 TraesCS3D01G226200 chr5B 100.000 30 0 0 808 837 146280398 146280427 5.670000e-04 56.5
19 TraesCS3D01G226200 chr7B 90.826 109 10 0 372 480 713626336 713626444 3.270000e-31 147.0
20 TraesCS3D01G226200 chr4A 81.212 165 23 5 684 841 284646676 284646513 4.260000e-25 126.0
21 TraesCS3D01G226200 chr4B 76.277 274 42 15 578 835 494690216 494689950 1.530000e-24 124.0
22 TraesCS3D01G226200 chr1D 76.562 256 43 5 581 835 414495222 414494983 1.530000e-24 124.0
23 TraesCS3D01G226200 chr2A 77.083 240 37 16 586 818 149459428 149459656 5.520000e-24 122.0
24 TraesCS3D01G226200 chr2A 82.000 100 8 4 706 802 678036127 678036219 4.360000e-10 76.8


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 TraesCS3D01G226200 chr3D 307938236 307942299 4063 True 7505.000000 7505 100.000000 1 4064 1 chr3D.!!$R1 4063
1 TraesCS3D01G226200 chr3D 285114373 285115286 913 True 625.500000 702 92.898000 3200 4064 2 chr3D.!!$R3 864
2 TraesCS3D01G226200 chr3A 427210155 427213981 3826 True 1996.666667 4824 94.326333 1 4045 3 chr3A.!!$R2 4044
3 TraesCS3D01G226200 chr3A 373329345 373330255 910 True 636.000000 725 93.289000 3200 4064 2 chr3A.!!$R1 864
4 TraesCS3D01G226200 chr3B 413802314 413805179 2865 False 2436.500000 4451 97.399500 875 3938 2 chr3B.!!$F3 3063
5 TraesCS3D01G226200 chr3B 378138896 378139809 913 False 623.000000 702 92.663500 3200 4064 2 chr3B.!!$F2 864
6 TraesCS3D01G226200 chr7D 330437121 330439318 2197 True 2961.000000 2961 90.946000 988 3195 1 chr7D.!!$R1 2207
7 TraesCS3D01G226200 chr5D 508629885 508630415 530 True 521.000000 521 84.387000 2 538 1 chr5D.!!$R1 536

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
541 604 0.032416 GTAGGTGGGTGAGGGCTAGA 60.032 60.0 0.00 0.00 0.00 2.43 F
650 713 0.036388 TTTTGAGCCCGAGTGCTAGG 60.036 55.0 0.00 0.00 42.95 3.02 F
764 827 0.037605 CTGAAAACTAGGCCCGACGT 60.038 55.0 0.00 0.00 0.00 4.34 F
765 828 0.037975 TGAAAACTAGGCCCGACGTC 60.038 55.0 5.18 5.18 0.00 4.34 F
801 864 0.106015 AGGTTTTCTGCTGTGGGCTT 60.106 50.0 0.00 0.00 42.39 4.35 F
966 1029 0.106868 TCGCCATAGGTCGAAGAGGA 60.107 55.0 0.00 0.00 36.95 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1416 1.292242 AGGAGGTTGCAGGAGGATAGA 59.708 52.381 0.00 0.00 0.00 1.98 R
1827 1890 1.445716 CGGTCGTCTCGCCTATCCTT 61.446 60.000 0.00 0.00 0.00 3.36 R
2457 2521 2.092323 GCTACTGCTTCCGGGATTTTT 58.908 47.619 0.00 0.00 36.03 1.94 R
2734 2798 9.979578 GCATGCTGATATTAGAGTATTATAGCT 57.020 33.333 11.37 0.00 0.00 3.32 R
3027 3091 8.585471 ATGTGTCATAATCAATTGATATCCCC 57.415 34.615 21.00 10.12 33.73 4.81 R
3187 3251 3.122948 GCCTGTTGACGTTGTATGTGTAG 59.877 47.826 0.00 0.00 0.00 2.74 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
24 25 5.988310 TCAAGTTCTTTGGACCGTATCTA 57.012 39.130 0.00 0.00 37.39 1.98
34 35 2.502295 GACCGTATCTAGTGGTCCGAT 58.498 52.381 12.26 0.00 45.14 4.18
43 44 1.125093 AGTGGTCCGATGGGTGAACA 61.125 55.000 0.00 0.00 33.83 3.18
45 46 0.250553 TGGTCCGATGGGTGAACAAC 60.251 55.000 0.00 0.00 33.83 3.32
67 68 5.986530 ACGTGACGTATGAGCTGAAGCTAT 61.987 45.833 9.69 2.71 45.35 2.97
86 87 5.827797 AGCTATCATAAGGATCCTCGATCTC 59.172 44.000 16.52 11.85 38.91 2.75
166 167 5.105023 TCCTCATCTCTTCCATCACTTTCTG 60.105 44.000 0.00 0.00 0.00 3.02
206 207 5.003160 TGTGGAGATATTGGACAAACACTG 58.997 41.667 0.00 0.00 0.00 3.66
229 230 2.401195 GCGGCTCGAACAAGATGC 59.599 61.111 0.00 0.00 0.00 3.91
251 252 0.179073 GAGCAAGGCCTGATTCGCTA 60.179 55.000 5.69 0.00 0.00 4.26
255 256 0.471617 AAGGCCTGATTCGCTAGCAT 59.528 50.000 16.45 0.59 0.00 3.79
272 273 1.200020 GCATGACAACCAAGCTACACC 59.800 52.381 0.00 0.00 36.61 4.16
273 274 2.503331 CATGACAACCAAGCTACACCA 58.497 47.619 0.00 0.00 0.00 4.17
303 304 2.498078 GGAGGACCTTGAAGATCTTCGT 59.502 50.000 26.32 19.34 42.28 3.85
308 309 2.557056 ACCTTGAAGATCTTCGTCGTCA 59.443 45.455 26.32 9.43 42.28 4.35
332 333 0.460311 CCTACTACTGCGACTTGGGG 59.540 60.000 0.00 0.00 0.00 4.96
354 355 3.467803 ACAAGTCTTGTCCGAAGAAAGG 58.532 45.455 12.62 0.00 40.56 3.11
356 357 1.348036 AGTCTTGTCCGAAGAAAGGGG 59.652 52.381 0.00 0.00 0.00 4.79
357 358 0.690762 TCTTGTCCGAAGAAAGGGGG 59.309 55.000 0.00 0.00 0.00 5.40
381 382 1.226030 GGTGTTGGCGACCACACTAC 61.226 60.000 23.41 5.89 36.51 2.73
389 390 0.391597 CGACCACACTACACAAGGGT 59.608 55.000 0.00 0.00 45.21 4.34
392 393 1.975680 ACCACACTACACAAGGGTAGG 59.024 52.381 13.59 5.64 41.08 3.18
415 416 1.903183 GAAGGAAGAGCTACACCAGGT 59.097 52.381 0.00 0.00 37.82 4.00
422 423 3.166434 CTACACCAGGTTGGCCCA 58.834 61.111 0.00 0.00 42.67 5.36
430 431 0.401738 CAGGTTGGCCCAAGAGAGAA 59.598 55.000 0.00 0.00 34.66 2.87
433 434 1.539157 GTTGGCCCAAGAGAGAAAGG 58.461 55.000 0.00 0.00 0.00 3.11
434 435 1.073923 GTTGGCCCAAGAGAGAAAGGA 59.926 52.381 0.00 0.00 0.00 3.36
436 437 0.254462 GGCCCAAGAGAGAAAGGAGG 59.746 60.000 0.00 0.00 0.00 4.30
437 438 0.393673 GCCCAAGAGAGAAAGGAGGC 60.394 60.000 0.00 0.00 0.00 4.70
482 545 4.567537 CCAATGGGTCTCCTACATGTTCAA 60.568 45.833 2.30 0.00 0.00 2.69
488 551 3.751698 GTCTCCTACATGTTCAACCCAAC 59.248 47.826 2.30 0.00 0.00 3.77
523 586 2.996249 CTCATATGAGCAGGTGTGGT 57.004 50.000 19.47 0.00 35.13 4.16
525 588 3.987547 CTCATATGAGCAGGTGTGGTAG 58.012 50.000 19.47 0.00 35.13 3.18
526 589 2.700371 TCATATGAGCAGGTGTGGTAGG 59.300 50.000 0.00 0.00 33.41 3.18
527 590 2.247699 TATGAGCAGGTGTGGTAGGT 57.752 50.000 0.00 0.00 33.41 3.08
528 591 0.615331 ATGAGCAGGTGTGGTAGGTG 59.385 55.000 0.00 0.00 33.41 4.00
529 592 1.296715 GAGCAGGTGTGGTAGGTGG 59.703 63.158 0.00 0.00 33.41 4.61
530 593 2.185310 GAGCAGGTGTGGTAGGTGGG 62.185 65.000 0.00 0.00 33.41 4.61
531 594 2.526046 GCAGGTGTGGTAGGTGGGT 61.526 63.158 0.00 0.00 0.00 4.51
532 595 1.374947 CAGGTGTGGTAGGTGGGTG 59.625 63.158 0.00 0.00 0.00 4.61
533 596 1.125093 CAGGTGTGGTAGGTGGGTGA 61.125 60.000 0.00 0.00 0.00 4.02
534 597 0.836400 AGGTGTGGTAGGTGGGTGAG 60.836 60.000 0.00 0.00 0.00 3.51
535 598 1.677552 GTGTGGTAGGTGGGTGAGG 59.322 63.158 0.00 0.00 0.00 3.86
536 599 1.537889 TGTGGTAGGTGGGTGAGGG 60.538 63.158 0.00 0.00 0.00 4.30
537 600 2.609610 TGGTAGGTGGGTGAGGGC 60.610 66.667 0.00 0.00 0.00 5.19
538 601 2.285442 GGTAGGTGGGTGAGGGCT 60.285 66.667 0.00 0.00 0.00 5.19
539 602 1.002533 GGTAGGTGGGTGAGGGCTA 59.997 63.158 0.00 0.00 0.00 3.93
540 603 1.049289 GGTAGGTGGGTGAGGGCTAG 61.049 65.000 0.00 0.00 0.00 3.42
541 604 0.032416 GTAGGTGGGTGAGGGCTAGA 60.032 60.000 0.00 0.00 0.00 2.43
542 605 0.032416 TAGGTGGGTGAGGGCTAGAC 60.032 60.000 0.00 0.00 0.00 2.59
543 606 2.368011 GGTGGGTGAGGGCTAGACC 61.368 68.421 6.47 6.47 37.93 3.85
544 607 1.306226 GTGGGTGAGGGCTAGACCT 60.306 63.158 20.19 20.19 45.57 3.85
545 608 1.306141 TGGGTGAGGGCTAGACCTG 60.306 63.158 26.06 0.00 42.10 4.00
546 609 2.066999 GGGTGAGGGCTAGACCTGG 61.067 68.421 26.06 0.00 42.10 4.45
547 610 2.736826 GGTGAGGGCTAGACCTGGC 61.737 68.421 26.06 14.41 42.10 4.85
553 616 3.647367 GCTAGACCTGGCCATGGA 58.353 61.111 23.24 0.00 0.00 3.41
554 617 1.915228 GCTAGACCTGGCCATGGAA 59.085 57.895 23.24 0.87 0.00 3.53
555 618 0.255890 GCTAGACCTGGCCATGGAAA 59.744 55.000 23.24 0.44 0.00 3.13
556 619 1.340991 GCTAGACCTGGCCATGGAAAA 60.341 52.381 23.24 0.00 0.00 2.29
557 620 2.369394 CTAGACCTGGCCATGGAAAAC 58.631 52.381 23.24 2.31 0.00 2.43
558 621 0.251787 AGACCTGGCCATGGAAAACC 60.252 55.000 23.24 7.65 0.00 3.27
559 622 1.229177 ACCTGGCCATGGAAAACCC 60.229 57.895 23.24 7.22 0.00 4.11
560 623 2.350458 CCTGGCCATGGAAAACCCG 61.350 63.158 18.40 3.07 37.93 5.28
561 624 2.283532 TGGCCATGGAAAACCCGG 60.284 61.111 18.40 0.00 37.93 5.73
562 625 3.770040 GGCCATGGAAAACCCGGC 61.770 66.667 18.40 0.00 39.78 6.13
563 626 3.770040 GCCATGGAAAACCCGGCC 61.770 66.667 18.40 0.00 35.96 6.13
564 627 2.037208 CCATGGAAAACCCGGCCT 59.963 61.111 5.56 0.00 37.93 5.19
565 628 1.304952 CCATGGAAAACCCGGCCTA 59.695 57.895 5.56 0.00 37.93 3.93
566 629 0.323908 CCATGGAAAACCCGGCCTAA 60.324 55.000 5.56 0.00 37.93 2.69
567 630 0.815095 CATGGAAAACCCGGCCTAAC 59.185 55.000 0.00 0.00 37.93 2.34
568 631 0.323999 ATGGAAAACCCGGCCTAACC 60.324 55.000 0.00 0.00 37.93 2.85
569 632 1.679977 GGAAAACCCGGCCTAACCC 60.680 63.158 0.00 0.00 33.26 4.11
577 640 2.420466 GGCCTAACCCGATCCGAC 59.580 66.667 0.00 0.00 0.00 4.79
578 641 2.420466 GCCTAACCCGATCCGACC 59.580 66.667 0.00 0.00 0.00 4.79
579 642 2.726274 CCTAACCCGATCCGACCG 59.274 66.667 0.00 0.00 0.00 4.79
580 643 1.825191 CCTAACCCGATCCGACCGA 60.825 63.158 0.00 0.00 0.00 4.69
581 644 1.386525 CCTAACCCGATCCGACCGAA 61.387 60.000 0.00 0.00 0.00 4.30
582 645 0.457035 CTAACCCGATCCGACCGAAA 59.543 55.000 0.00 0.00 0.00 3.46
583 646 1.068127 CTAACCCGATCCGACCGAAAT 59.932 52.381 0.00 0.00 0.00 2.17
584 647 1.113788 AACCCGATCCGACCGAAATA 58.886 50.000 0.00 0.00 0.00 1.40
585 648 0.672342 ACCCGATCCGACCGAAATAG 59.328 55.000 0.00 0.00 0.00 1.73
586 649 0.666577 CCCGATCCGACCGAAATAGC 60.667 60.000 0.00 0.00 0.00 2.97
587 650 0.666577 CCGATCCGACCGAAATAGCC 60.667 60.000 0.00 0.00 0.00 3.93
588 651 0.666577 CGATCCGACCGAAATAGCCC 60.667 60.000 0.00 0.00 0.00 5.19
589 652 0.666577 GATCCGACCGAAATAGCCCG 60.667 60.000 0.00 0.00 0.00 6.13
590 653 1.111116 ATCCGACCGAAATAGCCCGA 61.111 55.000 0.00 0.00 0.00 5.14
591 654 1.590792 CCGACCGAAATAGCCCGAC 60.591 63.158 0.00 0.00 0.00 4.79
592 655 1.590792 CGACCGAAATAGCCCGACC 60.591 63.158 0.00 0.00 0.00 4.79
593 656 1.227468 GACCGAAATAGCCCGACCC 60.227 63.158 0.00 0.00 0.00 4.46
594 657 2.279918 CCGAAATAGCCCGACCCG 60.280 66.667 0.00 0.00 0.00 5.28
605 668 4.760047 CGACCCGGCCCTGTCTTG 62.760 72.222 15.24 0.18 0.00 3.02
606 669 3.637273 GACCCGGCCCTGTCTTGT 61.637 66.667 11.19 0.00 0.00 3.16
607 670 3.607370 GACCCGGCCCTGTCTTGTC 62.607 68.421 11.19 0.00 0.00 3.18
608 671 4.410400 CCCGGCCCTGTCTTGTCC 62.410 72.222 0.00 0.00 0.00 4.02
609 672 4.760047 CCGGCCCTGTCTTGTCCG 62.760 72.222 0.00 0.00 39.79 4.79
613 676 4.760047 CCCTGTCTTGTCCGCGGG 62.760 72.222 27.83 9.38 0.00 6.13
636 699 3.356814 GCCTGGGCCTAGTTTTTGA 57.643 52.632 15.86 0.00 34.56 2.69
637 700 1.177401 GCCTGGGCCTAGTTTTTGAG 58.823 55.000 15.86 0.00 34.56 3.02
638 701 1.177401 CCTGGGCCTAGTTTTTGAGC 58.823 55.000 15.86 0.00 0.00 4.26
639 702 1.177401 CTGGGCCTAGTTTTTGAGCC 58.823 55.000 8.21 0.00 43.09 4.70
641 704 2.180674 GGCCTAGTTTTTGAGCCCG 58.819 57.895 0.00 0.00 37.66 6.13
642 705 0.322187 GGCCTAGTTTTTGAGCCCGA 60.322 55.000 0.00 0.00 37.66 5.14
643 706 1.087501 GCCTAGTTTTTGAGCCCGAG 58.912 55.000 0.00 0.00 0.00 4.63
644 707 1.610886 GCCTAGTTTTTGAGCCCGAGT 60.611 52.381 0.00 0.00 0.00 4.18
645 708 2.076863 CCTAGTTTTTGAGCCCGAGTG 58.923 52.381 0.00 0.00 0.00 3.51
646 709 1.464997 CTAGTTTTTGAGCCCGAGTGC 59.535 52.381 0.00 0.00 0.00 4.40
647 710 0.179018 AGTTTTTGAGCCCGAGTGCT 60.179 50.000 0.00 0.00 46.37 4.40
648 711 1.071699 AGTTTTTGAGCCCGAGTGCTA 59.928 47.619 0.00 0.00 42.95 3.49
649 712 1.464997 GTTTTTGAGCCCGAGTGCTAG 59.535 52.381 0.00 0.00 42.95 3.42
650 713 0.036388 TTTTGAGCCCGAGTGCTAGG 60.036 55.000 0.00 0.00 42.95 3.02
651 714 1.192146 TTTGAGCCCGAGTGCTAGGT 61.192 55.000 0.00 0.00 42.95 3.08
652 715 1.605058 TTGAGCCCGAGTGCTAGGTC 61.605 60.000 0.00 0.00 42.95 3.85
653 716 3.127352 GAGCCCGAGTGCTAGGTCG 62.127 68.421 0.00 0.00 42.95 4.79
657 720 4.208686 CGAGTGCTAGGTCGGGCC 62.209 72.222 0.00 0.00 32.40 5.80
658 721 3.075005 GAGTGCTAGGTCGGGCCA 61.075 66.667 4.39 0.00 40.61 5.36
659 722 3.077556 AGTGCTAGGTCGGGCCAG 61.078 66.667 4.39 0.00 40.61 4.85
660 723 4.162690 GTGCTAGGTCGGGCCAGG 62.163 72.222 4.39 0.00 40.61 4.45
661 724 4.715130 TGCTAGGTCGGGCCAGGT 62.715 66.667 4.39 0.00 40.61 4.00
662 725 3.400054 GCTAGGTCGGGCCAGGTT 61.400 66.667 4.39 0.00 40.61 3.50
663 726 2.967946 GCTAGGTCGGGCCAGGTTT 61.968 63.158 4.39 0.00 40.61 3.27
664 727 1.078426 CTAGGTCGGGCCAGGTTTG 60.078 63.158 4.39 0.00 40.61 2.93
673 736 2.523902 CCAGGTTTGGGCTTGCCA 60.524 61.111 14.04 0.00 41.05 4.92
674 737 1.914764 CCAGGTTTGGGCTTGCCAT 60.915 57.895 14.04 0.00 41.05 4.40
675 738 1.482748 CCAGGTTTGGGCTTGCCATT 61.483 55.000 14.04 0.00 41.05 3.16
676 739 0.397564 CAGGTTTGGGCTTGCCATTT 59.602 50.000 14.04 0.00 0.00 2.32
677 740 1.622811 CAGGTTTGGGCTTGCCATTTA 59.377 47.619 14.04 0.00 0.00 1.40
678 741 2.236893 CAGGTTTGGGCTTGCCATTTAT 59.763 45.455 14.04 0.00 0.00 1.40
679 742 2.236893 AGGTTTGGGCTTGCCATTTATG 59.763 45.455 14.04 0.00 0.00 1.90
680 743 2.027285 GGTTTGGGCTTGCCATTTATGT 60.027 45.455 14.04 0.00 0.00 2.29
681 744 3.002102 GTTTGGGCTTGCCATTTATGTG 58.998 45.455 14.04 0.00 0.00 3.21
682 745 1.935799 TGGGCTTGCCATTTATGTGT 58.064 45.000 14.04 0.00 0.00 3.72
683 746 2.255406 TGGGCTTGCCATTTATGTGTT 58.745 42.857 14.04 0.00 0.00 3.32
684 747 2.636893 TGGGCTTGCCATTTATGTGTTT 59.363 40.909 14.04 0.00 0.00 2.83
685 748 3.072184 TGGGCTTGCCATTTATGTGTTTT 59.928 39.130 14.04 0.00 0.00 2.43
686 749 4.284490 TGGGCTTGCCATTTATGTGTTTTA 59.716 37.500 14.04 0.00 0.00 1.52
687 750 5.221722 TGGGCTTGCCATTTATGTGTTTTAA 60.222 36.000 14.04 0.00 0.00 1.52
688 751 5.351189 GGGCTTGCCATTTATGTGTTTTAAG 59.649 40.000 14.04 0.00 0.00 1.85
689 752 5.351189 GGCTTGCCATTTATGTGTTTTAAGG 59.649 40.000 6.79 0.00 0.00 2.69
690 753 6.162777 GCTTGCCATTTATGTGTTTTAAGGA 58.837 36.000 0.00 0.00 0.00 3.36
691 754 6.648725 GCTTGCCATTTATGTGTTTTAAGGAA 59.351 34.615 0.00 0.00 0.00 3.36
692 755 7.148590 GCTTGCCATTTATGTGTTTTAAGGAAG 60.149 37.037 0.00 0.00 0.00 3.46
693 756 6.696411 TGCCATTTATGTGTTTTAAGGAAGG 58.304 36.000 0.00 0.00 0.00 3.46
694 757 6.106003 GCCATTTATGTGTTTTAAGGAAGGG 58.894 40.000 0.00 0.00 0.00 3.95
695 758 6.639563 CCATTTATGTGTTTTAAGGAAGGGG 58.360 40.000 0.00 0.00 0.00 4.79
696 759 5.731957 TTTATGTGTTTTAAGGAAGGGGC 57.268 39.130 0.00 0.00 0.00 5.80
697 760 2.003937 TGTGTTTTAAGGAAGGGGCC 57.996 50.000 0.00 0.00 0.00 5.80
698 761 1.263356 GTGTTTTAAGGAAGGGGCCC 58.737 55.000 17.12 17.12 0.00 5.80
699 762 0.251430 TGTTTTAAGGAAGGGGCCCG 60.251 55.000 18.95 0.00 0.00 6.13
700 763 0.968901 GTTTTAAGGAAGGGGCCCGG 60.969 60.000 18.95 0.00 0.00 5.73
701 764 2.791613 TTTTAAGGAAGGGGCCCGGC 62.792 60.000 18.95 13.31 0.00 6.13
727 790 3.431725 CGGCGGGCTTTTCCACTC 61.432 66.667 0.00 0.00 36.21 3.51
729 792 1.678970 GGCGGGCTTTTCCACTCAT 60.679 57.895 0.00 0.00 36.21 2.90
741 804 1.746615 CACTCATGGACCGGGCTTG 60.747 63.158 7.57 5.74 0.00 4.01
756 819 1.177401 GCTTGGGCCTGAAAACTAGG 58.823 55.000 4.53 0.00 38.39 3.02
762 825 3.154589 CCTGAAAACTAGGCCCGAC 57.845 57.895 0.00 0.00 0.00 4.79
763 826 0.739813 CCTGAAAACTAGGCCCGACG 60.740 60.000 0.00 0.00 0.00 5.12
764 827 0.037605 CTGAAAACTAGGCCCGACGT 60.038 55.000 0.00 0.00 0.00 4.34
765 828 0.037975 TGAAAACTAGGCCCGACGTC 60.038 55.000 5.18 5.18 0.00 4.34
766 829 1.074872 GAAAACTAGGCCCGACGTCG 61.075 60.000 30.33 30.33 39.44 5.12
792 855 2.873797 CCTGGCCTAGGTTTTCTGC 58.126 57.895 11.31 0.00 42.00 4.26
793 856 0.329596 CCTGGCCTAGGTTTTCTGCT 59.670 55.000 11.31 0.00 42.00 4.24
794 857 1.457346 CTGGCCTAGGTTTTCTGCTG 58.543 55.000 11.31 0.00 0.00 4.41
795 858 0.771127 TGGCCTAGGTTTTCTGCTGT 59.229 50.000 11.31 0.00 0.00 4.40
796 859 1.168714 GGCCTAGGTTTTCTGCTGTG 58.831 55.000 11.31 0.00 0.00 3.66
797 860 1.168714 GCCTAGGTTTTCTGCTGTGG 58.831 55.000 11.31 0.00 0.00 4.17
798 861 1.826385 CCTAGGTTTTCTGCTGTGGG 58.174 55.000 0.00 0.00 0.00 4.61
799 862 1.168714 CTAGGTTTTCTGCTGTGGGC 58.831 55.000 0.00 0.00 42.22 5.36
800 863 0.771127 TAGGTTTTCTGCTGTGGGCT 59.229 50.000 0.00 0.00 42.39 5.19
801 864 0.106015 AGGTTTTCTGCTGTGGGCTT 60.106 50.000 0.00 0.00 42.39 4.35
802 865 1.144913 AGGTTTTCTGCTGTGGGCTTA 59.855 47.619 0.00 0.00 42.39 3.09
803 866 1.269723 GGTTTTCTGCTGTGGGCTTAC 59.730 52.381 0.00 0.00 42.39 2.34
804 867 1.069227 GTTTTCTGCTGTGGGCTTACG 60.069 52.381 0.00 0.00 42.39 3.18
805 868 0.107831 TTTCTGCTGTGGGCTTACGT 59.892 50.000 0.00 0.00 42.39 3.57
806 869 0.970640 TTCTGCTGTGGGCTTACGTA 59.029 50.000 0.00 0.00 42.39 3.57
807 870 0.530744 TCTGCTGTGGGCTTACGTAG 59.469 55.000 0.00 0.00 42.39 3.51
808 871 0.460284 CTGCTGTGGGCTTACGTAGG 60.460 60.000 0.00 0.00 42.39 3.18
814 877 2.203029 GGCTTACGTAGGCCCAGC 60.203 66.667 32.48 20.26 42.11 4.85
824 887 2.348998 GGCCCAGCCCGAGATATG 59.651 66.667 0.00 0.00 44.06 1.78
825 888 2.348998 GCCCAGCCCGAGATATGG 59.651 66.667 0.00 0.00 0.00 2.74
830 893 2.348998 GCCCGAGATATGGCCAGG 59.651 66.667 13.05 6.01 41.97 4.45
831 894 2.520536 GCCCGAGATATGGCCAGGT 61.521 63.158 13.05 0.88 41.97 4.00
832 895 1.192146 GCCCGAGATATGGCCAGGTA 61.192 60.000 13.05 0.00 41.97 3.08
833 896 1.573108 CCCGAGATATGGCCAGGTAT 58.427 55.000 13.05 4.82 0.00 2.73
834 897 2.747177 CCCGAGATATGGCCAGGTATA 58.253 52.381 13.05 0.00 0.00 1.47
835 898 2.695666 CCCGAGATATGGCCAGGTATAG 59.304 54.545 13.05 0.92 0.00 1.31
836 899 3.366396 CCGAGATATGGCCAGGTATAGT 58.634 50.000 13.05 0.00 0.00 2.12
837 900 3.131223 CCGAGATATGGCCAGGTATAGTG 59.869 52.174 13.05 0.00 0.00 2.74
838 901 4.017126 CGAGATATGGCCAGGTATAGTGA 58.983 47.826 13.05 0.00 0.00 3.41
839 902 4.097135 CGAGATATGGCCAGGTATAGTGAG 59.903 50.000 13.05 0.00 0.00 3.51
840 903 4.357325 AGATATGGCCAGGTATAGTGAGG 58.643 47.826 13.05 0.00 0.00 3.86
841 904 1.734655 ATGGCCAGGTATAGTGAGGG 58.265 55.000 13.05 0.00 0.00 4.30
842 905 1.054406 TGGCCAGGTATAGTGAGGGC 61.054 60.000 0.00 0.00 44.39 5.19
861 924 4.297891 CAGGCGTGTGTGCGTGTG 62.298 66.667 0.00 0.00 43.69 3.82
862 925 4.830765 AGGCGTGTGTGCGTGTGT 62.831 61.111 0.00 0.00 35.06 3.72
863 926 3.871574 GGCGTGTGTGCGTGTGTT 61.872 61.111 0.00 0.00 35.06 3.32
864 927 2.350760 GCGTGTGTGCGTGTGTTC 60.351 61.111 0.00 0.00 0.00 3.18
865 928 2.323105 CGTGTGTGCGTGTGTTCC 59.677 61.111 0.00 0.00 0.00 3.62
866 929 2.171079 CGTGTGTGCGTGTGTTCCT 61.171 57.895 0.00 0.00 0.00 3.36
867 930 1.641677 GTGTGTGCGTGTGTTCCTC 59.358 57.895 0.00 0.00 0.00 3.71
868 931 0.810031 GTGTGTGCGTGTGTTCCTCT 60.810 55.000 0.00 0.00 0.00 3.69
869 932 0.809636 TGTGTGCGTGTGTTCCTCTG 60.810 55.000 0.00 0.00 0.00 3.35
870 933 0.810031 GTGTGCGTGTGTTCCTCTGT 60.810 55.000 0.00 0.00 0.00 3.41
871 934 0.747852 TGTGCGTGTGTTCCTCTGTA 59.252 50.000 0.00 0.00 0.00 2.74
872 935 1.343142 TGTGCGTGTGTTCCTCTGTAT 59.657 47.619 0.00 0.00 0.00 2.29
873 936 1.993370 GTGCGTGTGTTCCTCTGTATC 59.007 52.381 0.00 0.00 0.00 2.24
938 1001 4.069304 CCCCAAGTTGTACTCGAATCAAA 58.931 43.478 1.45 0.00 0.00 2.69
956 1019 4.693283 TCAAAGTCTGTAATCGCCATAGG 58.307 43.478 0.00 0.00 0.00 2.57
966 1029 0.106868 TCGCCATAGGTCGAAGAGGA 60.107 55.000 0.00 0.00 36.95 3.71
975 1038 1.673329 GGTCGAAGAGGAAGAACCAGC 60.673 57.143 0.00 0.00 42.04 4.85
983 1046 2.032681 AAGAACCAGCGAGTGCCC 59.967 61.111 0.00 0.00 44.31 5.36
1154 1217 1.454847 CACTCCTCCTCTCCTCCCG 60.455 68.421 0.00 0.00 0.00 5.14
1377 1440 1.621672 CCTCCTGCAACCTCCTCCTC 61.622 65.000 0.00 0.00 0.00 3.71
1636 1699 0.830444 AAGGGGTAGTGACGCTGTCA 60.830 55.000 7.20 7.20 40.50 3.58
2727 2791 7.872113 AAGAAATCATGGATTAACTCCTGAC 57.128 36.000 0.00 0.00 45.21 3.51
2734 2798 3.322541 TGGATTAACTCCTGACGTTGTCA 59.677 43.478 0.00 0.00 45.21 3.58
2784 2848 4.727507 CTACAGGAGCAACACTGATAGT 57.272 45.455 0.00 0.00 38.09 2.12
3027 3091 4.579869 TGAGGAAGGATTTCTCGGAAAAG 58.420 43.478 3.67 0.00 33.68 2.27
3086 3150 9.582431 TTAGTGTGAGTTGAATACAAGTATAGC 57.418 33.333 0.00 0.00 39.43 2.97
3087 3151 7.611770 AGTGTGAGTTGAATACAAGTATAGCA 58.388 34.615 0.00 0.00 39.43 3.49
3130 3194 4.584327 ATTTGTTGCTCAGTAACCCAAC 57.416 40.909 2.87 0.00 38.36 3.77
3310 3374 7.362662 CACTTGCATTCTGTACAAATACACTT 58.637 34.615 0.00 0.00 36.34 3.16
3381 3445 1.066858 TGAGAACTCCGGAGATTGTGC 60.067 52.381 37.69 15.15 0.00 4.57
3624 3688 7.808856 TGTTGACTACACCTTTGTTTGTTTAAC 59.191 33.333 0.00 0.00 37.15 2.01
3680 3744 8.190784 CCTTGACCCTGAAATTGTATCATTTAC 58.809 37.037 0.00 0.00 0.00 2.01
3803 3916 4.088823 GCAGCTTGCATTATATACAGGC 57.911 45.455 0.00 0.00 44.26 4.85
3840 3993 8.413309 TGGAGATCATTTGAAGTTGAAAGAAT 57.587 30.769 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.125093 TGTTCACCCATCGGACCACT 61.125 55.000 0.00 0.00 0.00 4.00
34 35 0.459078 TACGTCACGTTGTTCACCCA 59.541 50.000 8.85 0.00 41.54 4.51
43 44 2.596452 CTTCAGCTCATACGTCACGTT 58.404 47.619 8.85 0.00 41.54 3.99
45 46 0.917259 GCTTCAGCTCATACGTCACG 59.083 55.000 0.00 0.00 38.21 4.35
67 68 5.512942 AGAGAGATCGAGGATCCTTATGA 57.487 43.478 17.42 14.67 39.66 2.15
70 71 5.783360 AGACTAGAGAGATCGAGGATCCTTA 59.217 44.000 17.42 8.03 39.66 2.69
86 87 2.164422 TGCGACACATGGAAGACTAGAG 59.836 50.000 0.00 0.00 0.00 2.43
166 167 2.163010 CCACAGGAACATTCACAGCATC 59.837 50.000 0.00 0.00 0.00 3.91
170 171 3.407424 TCTCCACAGGAACATTCACAG 57.593 47.619 0.00 0.00 0.00 3.66
218 219 1.741401 TGCTCCCGCATCTTGTTCG 60.741 57.895 0.00 0.00 42.25 3.95
229 230 1.821332 GAATCAGGCCTTGCTCCCG 60.821 63.158 0.00 0.00 0.00 5.14
255 256 1.765904 TCTGGTGTAGCTTGGTTGTCA 59.234 47.619 0.00 0.00 0.00 3.58
272 273 1.765314 CAAGGTCCTCCCAGGTATCTG 59.235 57.143 0.00 0.00 40.59 2.90
273 274 1.651770 TCAAGGTCCTCCCAGGTATCT 59.348 52.381 0.00 0.00 36.53 1.98
287 288 2.557056 TGACGACGAAGATCTTCAAGGT 59.443 45.455 29.93 23.23 39.46 3.50
303 304 2.089980 GCAGTAGTAGGGAAGTGACGA 58.910 52.381 0.00 0.00 0.00 4.20
308 309 2.492484 CAAGTCGCAGTAGTAGGGAAGT 59.508 50.000 0.00 0.00 0.00 3.01
360 361 4.572571 TGTGGTCGCCAACACCCC 62.573 66.667 0.00 0.00 34.18 4.95
361 362 2.386064 TAGTGTGGTCGCCAACACCC 62.386 60.000 0.00 0.00 36.74 4.61
381 382 0.984230 TCCTTCTGCCTACCCTTGTG 59.016 55.000 0.00 0.00 0.00 3.33
389 390 2.761208 GTGTAGCTCTTCCTTCTGCCTA 59.239 50.000 0.00 0.00 0.00 3.93
392 393 1.276421 TGGTGTAGCTCTTCCTTCTGC 59.724 52.381 0.00 0.00 0.00 4.26
415 416 1.352352 CTCCTTTCTCTCTTGGGCCAA 59.648 52.381 19.68 19.68 0.00 4.52
422 423 1.064832 GCATGGCCTCCTTTCTCTCTT 60.065 52.381 3.32 0.00 0.00 2.85
436 437 0.038892 CAGTGAACTTGTGGCATGGC 60.039 55.000 13.29 13.29 0.00 4.40
437 438 0.599558 CCAGTGAACTTGTGGCATGG 59.400 55.000 0.00 0.00 0.00 3.66
482 545 0.765519 ACCTACGGGTTCAGTTGGGT 60.766 55.000 2.40 0.00 44.73 4.51
488 551 1.471119 TGAGCTACCTACGGGTTCAG 58.529 55.000 0.00 0.00 44.73 3.02
504 567 2.996249 ACCACACCTGCTCATATGAG 57.004 50.000 25.64 25.64 44.75 2.90
505 568 2.700371 CCTACCACACCTGCTCATATGA 59.300 50.000 5.07 5.07 0.00 2.15
506 569 2.435805 ACCTACCACACCTGCTCATATG 59.564 50.000 0.00 0.00 0.00 1.78
507 570 2.435805 CACCTACCACACCTGCTCATAT 59.564 50.000 0.00 0.00 0.00 1.78
508 571 1.831106 CACCTACCACACCTGCTCATA 59.169 52.381 0.00 0.00 0.00 2.15
509 572 0.615331 CACCTACCACACCTGCTCAT 59.385 55.000 0.00 0.00 0.00 2.90
510 573 1.480212 CCACCTACCACACCTGCTCA 61.480 60.000 0.00 0.00 0.00 4.26
511 574 1.296715 CCACCTACCACACCTGCTC 59.703 63.158 0.00 0.00 0.00 4.26
512 575 2.224159 CCCACCTACCACACCTGCT 61.224 63.158 0.00 0.00 0.00 4.24
513 576 2.351276 CCCACCTACCACACCTGC 59.649 66.667 0.00 0.00 0.00 4.85
514 577 1.125093 TCACCCACCTACCACACCTG 61.125 60.000 0.00 0.00 0.00 4.00
515 578 0.836400 CTCACCCACCTACCACACCT 60.836 60.000 0.00 0.00 0.00 4.00
516 579 1.677552 CTCACCCACCTACCACACC 59.322 63.158 0.00 0.00 0.00 4.16
517 580 1.677552 CCTCACCCACCTACCACAC 59.322 63.158 0.00 0.00 0.00 3.82
518 581 1.537889 CCCTCACCCACCTACCACA 60.538 63.158 0.00 0.00 0.00 4.17
519 582 2.967946 GCCCTCACCCACCTACCAC 61.968 68.421 0.00 0.00 0.00 4.16
520 583 1.817572 TAGCCCTCACCCACCTACCA 61.818 60.000 0.00 0.00 0.00 3.25
521 584 1.002533 TAGCCCTCACCCACCTACC 59.997 63.158 0.00 0.00 0.00 3.18
522 585 0.032416 TCTAGCCCTCACCCACCTAC 60.032 60.000 0.00 0.00 0.00 3.18
523 586 0.032416 GTCTAGCCCTCACCCACCTA 60.032 60.000 0.00 0.00 0.00 3.08
524 587 1.306226 GTCTAGCCCTCACCCACCT 60.306 63.158 0.00 0.00 0.00 4.00
525 588 2.368011 GGTCTAGCCCTCACCCACC 61.368 68.421 0.00 0.00 0.00 4.61
526 589 1.306226 AGGTCTAGCCCTCACCCAC 60.306 63.158 0.00 0.00 38.26 4.61
527 590 1.306141 CAGGTCTAGCCCTCACCCA 60.306 63.158 0.00 0.00 38.26 4.51
528 591 2.066999 CCAGGTCTAGCCCTCACCC 61.067 68.421 0.00 0.00 38.26 4.61
529 592 2.736826 GCCAGGTCTAGCCCTCACC 61.737 68.421 0.00 0.00 38.26 4.02
530 593 2.736826 GGCCAGGTCTAGCCCTCAC 61.737 68.421 0.00 0.00 43.76 3.51
531 594 2.365635 GGCCAGGTCTAGCCCTCA 60.366 66.667 0.00 0.00 43.76 3.86
536 599 0.255890 TTTCCATGGCCAGGTCTAGC 59.744 55.000 17.55 0.00 0.00 3.42
537 600 2.369394 GTTTTCCATGGCCAGGTCTAG 58.631 52.381 17.55 0.22 0.00 2.43
538 601 1.005450 GGTTTTCCATGGCCAGGTCTA 59.995 52.381 17.55 0.00 40.31 2.59
539 602 0.251787 GGTTTTCCATGGCCAGGTCT 60.252 55.000 17.55 0.00 40.31 3.85
540 603 1.257750 GGGTTTTCCATGGCCAGGTC 61.258 60.000 17.55 7.89 42.91 3.85
541 604 1.229177 GGGTTTTCCATGGCCAGGT 60.229 57.895 17.55 0.00 42.91 4.00
542 605 2.350458 CGGGTTTTCCATGGCCAGG 61.350 63.158 13.05 12.17 42.91 4.45
543 606 2.350458 CCGGGTTTTCCATGGCCAG 61.350 63.158 13.05 2.90 42.91 4.85
544 607 2.283532 CCGGGTTTTCCATGGCCA 60.284 61.111 8.56 8.56 42.91 5.36
547 610 0.323908 TTAGGCCGGGTTTTCCATGG 60.324 55.000 4.97 4.97 42.91 3.66
548 611 0.815095 GTTAGGCCGGGTTTTCCATG 59.185 55.000 2.18 0.00 42.91 3.66
549 612 0.323999 GGTTAGGCCGGGTTTTCCAT 60.324 55.000 2.18 0.00 42.91 3.41
550 613 1.075305 GGTTAGGCCGGGTTTTCCA 59.925 57.895 2.18 0.00 42.91 3.53
551 614 1.679977 GGGTTAGGCCGGGTTTTCC 60.680 63.158 2.18 0.00 38.44 3.13
552 615 2.042259 CGGGTTAGGCCGGGTTTTC 61.042 63.158 2.18 0.00 38.44 2.29
553 616 1.855441 ATCGGGTTAGGCCGGGTTTT 61.855 55.000 2.18 0.00 38.06 2.43
554 617 2.261430 GATCGGGTTAGGCCGGGTTT 62.261 60.000 2.18 0.00 38.06 3.27
555 618 2.689771 ATCGGGTTAGGCCGGGTT 60.690 61.111 2.18 0.00 38.06 4.11
556 619 3.159347 GATCGGGTTAGGCCGGGT 61.159 66.667 2.18 0.00 38.06 5.28
557 620 3.937447 GGATCGGGTTAGGCCGGG 61.937 72.222 2.18 0.00 38.06 5.73
558 621 4.295119 CGGATCGGGTTAGGCCGG 62.295 72.222 0.00 0.00 38.40 6.13
559 622 3.221389 TCGGATCGGGTTAGGCCG 61.221 66.667 0.00 0.00 43.11 6.13
560 623 2.420466 GTCGGATCGGGTTAGGCC 59.580 66.667 0.00 0.00 0.00 5.19
561 624 2.420466 GGTCGGATCGGGTTAGGC 59.580 66.667 0.00 0.00 0.00 3.93
562 625 1.386525 TTCGGTCGGATCGGGTTAGG 61.387 60.000 11.21 0.00 0.00 2.69
563 626 0.457035 TTTCGGTCGGATCGGGTTAG 59.543 55.000 11.21 0.00 0.00 2.34
564 627 1.113788 ATTTCGGTCGGATCGGGTTA 58.886 50.000 11.21 0.00 0.00 2.85
565 628 1.068127 CTATTTCGGTCGGATCGGGTT 59.932 52.381 11.21 0.00 0.00 4.11
566 629 0.672342 CTATTTCGGTCGGATCGGGT 59.328 55.000 11.21 0.01 0.00 5.28
567 630 0.666577 GCTATTTCGGTCGGATCGGG 60.667 60.000 11.21 0.00 0.00 5.14
568 631 0.666577 GGCTATTTCGGTCGGATCGG 60.667 60.000 11.21 0.00 0.00 4.18
569 632 0.666577 GGGCTATTTCGGTCGGATCG 60.667 60.000 3.82 3.82 0.00 3.69
570 633 0.666577 CGGGCTATTTCGGTCGGATC 60.667 60.000 0.00 0.00 0.00 3.36
571 634 1.111116 TCGGGCTATTTCGGTCGGAT 61.111 55.000 0.00 0.00 0.00 4.18
572 635 1.753848 TCGGGCTATTTCGGTCGGA 60.754 57.895 0.00 0.00 0.00 4.55
573 636 1.590792 GTCGGGCTATTTCGGTCGG 60.591 63.158 0.00 0.00 0.00 4.79
574 637 1.590792 GGTCGGGCTATTTCGGTCG 60.591 63.158 0.00 0.00 0.00 4.79
575 638 1.227468 GGGTCGGGCTATTTCGGTC 60.227 63.158 0.00 0.00 0.00 4.79
576 639 2.905681 GGGTCGGGCTATTTCGGT 59.094 61.111 0.00 0.00 0.00 4.69
577 640 2.279918 CGGGTCGGGCTATTTCGG 60.280 66.667 0.00 0.00 0.00 4.30
578 641 2.279918 CCGGGTCGGGCTATTTCG 60.280 66.667 0.00 0.00 44.15 3.46
588 651 4.760047 CAAGACAGGGCCGGGTCG 62.760 72.222 20.63 8.28 39.01 4.79
589 652 3.607370 GACAAGACAGGGCCGGGTC 62.607 68.421 19.67 19.67 0.00 4.46
590 653 3.637273 GACAAGACAGGGCCGGGT 61.637 66.667 8.94 6.06 0.00 5.28
591 654 4.410400 GGACAAGACAGGGCCGGG 62.410 72.222 8.94 2.25 0.00 5.73
592 655 4.760047 CGGACAAGACAGGGCCGG 62.760 72.222 0.79 0.79 38.40 6.13
596 659 4.760047 CCCGCGGACAAGACAGGG 62.760 72.222 30.73 0.44 0.00 4.45
618 681 1.177401 CTCAAAAACTAGGCCCAGGC 58.823 55.000 2.40 0.00 41.06 4.85
619 682 1.177401 GCTCAAAAACTAGGCCCAGG 58.823 55.000 2.40 0.00 0.00 4.45
620 683 1.177401 GGCTCAAAAACTAGGCCCAG 58.823 55.000 0.00 0.00 37.12 4.45
621 684 3.356814 GGCTCAAAAACTAGGCCCA 57.643 52.632 0.00 0.00 37.12 5.36
624 687 1.087501 CTCGGGCTCAAAAACTAGGC 58.912 55.000 0.00 0.00 37.55 3.93
625 688 2.076863 CACTCGGGCTCAAAAACTAGG 58.923 52.381 0.00 0.00 0.00 3.02
626 689 1.464997 GCACTCGGGCTCAAAAACTAG 59.535 52.381 0.00 0.00 0.00 2.57
627 690 1.071699 AGCACTCGGGCTCAAAAACTA 59.928 47.619 0.00 0.00 41.05 2.24
628 691 0.179018 AGCACTCGGGCTCAAAAACT 60.179 50.000 0.00 0.00 41.05 2.66
629 692 1.464997 CTAGCACTCGGGCTCAAAAAC 59.535 52.381 0.00 0.00 44.54 2.43
630 693 1.610624 CCTAGCACTCGGGCTCAAAAA 60.611 52.381 0.00 0.00 44.54 1.94
631 694 0.036388 CCTAGCACTCGGGCTCAAAA 60.036 55.000 0.00 0.00 44.54 2.44
632 695 1.192146 ACCTAGCACTCGGGCTCAAA 61.192 55.000 0.00 0.00 44.54 2.69
633 696 1.605058 GACCTAGCACTCGGGCTCAA 61.605 60.000 0.00 0.00 44.54 3.02
634 697 2.037367 ACCTAGCACTCGGGCTCA 59.963 61.111 0.00 0.00 44.54 4.26
635 698 2.809010 GACCTAGCACTCGGGCTC 59.191 66.667 0.00 0.00 44.54 4.70
637 700 4.208686 CCGACCTAGCACTCGGGC 62.209 72.222 11.90 0.00 44.84 6.13
640 703 4.208686 GGCCCGACCTAGCACTCG 62.209 72.222 0.00 0.00 34.51 4.18
641 704 3.075005 TGGCCCGACCTAGCACTC 61.075 66.667 0.00 0.00 40.22 3.51
642 705 3.077556 CTGGCCCGACCTAGCACT 61.078 66.667 0.00 0.00 40.22 4.40
643 706 4.162690 CCTGGCCCGACCTAGCAC 62.163 72.222 0.00 0.00 40.22 4.40
644 707 4.715130 ACCTGGCCCGACCTAGCA 62.715 66.667 0.00 0.00 40.22 3.49
645 708 2.967946 AAACCTGGCCCGACCTAGC 61.968 63.158 0.00 0.00 40.22 3.42
646 709 1.078426 CAAACCTGGCCCGACCTAG 60.078 63.158 0.00 0.00 40.22 3.02
647 710 2.598787 CCAAACCTGGCCCGACCTA 61.599 63.158 0.00 0.00 40.22 3.08
648 711 3.966543 CCAAACCTGGCCCGACCT 61.967 66.667 0.00 0.00 40.22 3.85
656 719 2.523902 TGGCAAGCCCAAACCTGG 60.524 61.111 8.89 0.00 41.82 4.45
664 727 3.333029 AAACACATAAATGGCAAGCCC 57.667 42.857 8.89 0.00 34.56 5.19
665 728 5.351189 CCTTAAAACACATAAATGGCAAGCC 59.649 40.000 3.61 3.61 0.00 4.35
666 729 6.162777 TCCTTAAAACACATAAATGGCAAGC 58.837 36.000 0.00 0.00 0.00 4.01
667 730 7.331687 CCTTCCTTAAAACACATAAATGGCAAG 59.668 37.037 0.00 0.00 0.00 4.01
668 731 7.158021 CCTTCCTTAAAACACATAAATGGCAA 58.842 34.615 0.00 0.00 0.00 4.52
669 732 6.295575 CCCTTCCTTAAAACACATAAATGGCA 60.296 38.462 0.00 0.00 0.00 4.92
670 733 6.106003 CCCTTCCTTAAAACACATAAATGGC 58.894 40.000 0.00 0.00 0.00 4.40
671 734 6.639563 CCCCTTCCTTAAAACACATAAATGG 58.360 40.000 0.00 0.00 0.00 3.16
672 735 6.106003 GCCCCTTCCTTAAAACACATAAATG 58.894 40.000 0.00 0.00 0.00 2.32
673 736 5.188948 GGCCCCTTCCTTAAAACACATAAAT 59.811 40.000 0.00 0.00 0.00 1.40
674 737 4.528987 GGCCCCTTCCTTAAAACACATAAA 59.471 41.667 0.00 0.00 0.00 1.40
675 738 4.090819 GGCCCCTTCCTTAAAACACATAA 58.909 43.478 0.00 0.00 0.00 1.90
676 739 3.564790 GGGCCCCTTCCTTAAAACACATA 60.565 47.826 12.23 0.00 0.00 2.29
677 740 2.536066 GGCCCCTTCCTTAAAACACAT 58.464 47.619 0.00 0.00 0.00 3.21
678 741 1.481615 GGGCCCCTTCCTTAAAACACA 60.482 52.381 12.23 0.00 0.00 3.72
679 742 1.263356 GGGCCCCTTCCTTAAAACAC 58.737 55.000 12.23 0.00 0.00 3.32
680 743 0.251430 CGGGCCCCTTCCTTAAAACA 60.251 55.000 18.66 0.00 0.00 2.83
681 744 0.968901 CCGGGCCCCTTCCTTAAAAC 60.969 60.000 18.66 0.00 0.00 2.43
682 745 1.384975 CCGGGCCCCTTCCTTAAAA 59.615 57.895 18.66 0.00 0.00 1.52
683 746 3.092624 CCGGGCCCCTTCCTTAAA 58.907 61.111 18.66 0.00 0.00 1.52
684 747 3.735097 GCCGGGCCCCTTCCTTAA 61.735 66.667 18.66 0.00 0.00 1.85
710 773 3.431725 GAGTGGAAAAGCCCGCCG 61.432 66.667 0.00 0.00 37.42 6.46
711 774 1.678970 ATGAGTGGAAAAGCCCGCC 60.679 57.895 0.00 0.00 37.42 6.13
723 786 1.746615 CAAGCCCGGTCCATGAGTG 60.747 63.158 0.00 0.00 0.00 3.51
724 787 2.671070 CAAGCCCGGTCCATGAGT 59.329 61.111 0.00 0.00 0.00 3.41
745 808 0.037605 ACGTCGGGCCTAGTTTTCAG 60.038 55.000 0.84 0.00 0.00 3.02
746 809 0.037975 GACGTCGGGCCTAGTTTTCA 60.038 55.000 0.84 0.00 0.00 2.69
747 810 1.074872 CGACGTCGGGCCTAGTTTTC 61.075 60.000 29.70 0.00 35.37 2.29
748 811 1.080298 CGACGTCGGGCCTAGTTTT 60.080 57.895 29.70 0.00 35.37 2.43
749 812 2.570181 CGACGTCGGGCCTAGTTT 59.430 61.111 29.70 0.00 35.37 2.66
775 838 1.271597 ACAGCAGAAAACCTAGGCCAG 60.272 52.381 9.30 0.00 0.00 4.85
776 839 0.771127 ACAGCAGAAAACCTAGGCCA 59.229 50.000 9.30 0.00 0.00 5.36
777 840 1.168714 CACAGCAGAAAACCTAGGCC 58.831 55.000 9.30 0.00 0.00 5.19
778 841 1.168714 CCACAGCAGAAAACCTAGGC 58.831 55.000 9.30 0.00 0.00 3.93
779 842 1.826385 CCCACAGCAGAAAACCTAGG 58.174 55.000 7.41 7.41 0.00 3.02
780 843 1.168714 GCCCACAGCAGAAAACCTAG 58.831 55.000 0.00 0.00 42.97 3.02
781 844 3.339547 GCCCACAGCAGAAAACCTA 57.660 52.632 0.00 0.00 42.97 3.08
782 845 4.181051 GCCCACAGCAGAAAACCT 57.819 55.556 0.00 0.00 42.97 3.50
791 854 1.814169 GCCTACGTAAGCCCACAGC 60.814 63.158 4.76 0.00 45.62 4.40
792 855 1.153429 GGCCTACGTAAGCCCACAG 60.153 63.158 22.39 0.00 43.76 3.66
793 856 2.983791 GGCCTACGTAAGCCCACA 59.016 61.111 22.39 0.00 43.76 4.17
797 860 3.752088 GGCTGGGCCTACGTAAGCC 62.752 68.421 24.39 24.39 46.69 4.35
798 861 2.203029 GGCTGGGCCTACGTAAGC 60.203 66.667 7.67 7.67 46.69 3.09
808 871 2.348998 CCATATCTCGGGCTGGGC 59.651 66.667 0.00 0.00 0.00 5.36
809 872 2.348998 GCCATATCTCGGGCTGGG 59.651 66.667 0.00 0.00 46.74 4.45
814 877 1.573108 ATACCTGGCCATATCTCGGG 58.427 55.000 5.51 4.26 0.00 5.14
815 878 3.131223 CACTATACCTGGCCATATCTCGG 59.869 52.174 5.51 5.16 0.00 4.63
816 879 4.017126 TCACTATACCTGGCCATATCTCG 58.983 47.826 5.51 0.00 0.00 4.04
817 880 4.404073 CCTCACTATACCTGGCCATATCTC 59.596 50.000 5.51 0.00 0.00 2.75
818 881 4.357325 CCTCACTATACCTGGCCATATCT 58.643 47.826 5.51 0.00 0.00 1.98
819 882 3.452627 CCCTCACTATACCTGGCCATATC 59.547 52.174 5.51 0.00 0.00 1.63
820 883 3.454858 CCCTCACTATACCTGGCCATAT 58.545 50.000 5.51 4.77 0.00 1.78
821 884 2.902608 CCCTCACTATACCTGGCCATA 58.097 52.381 5.51 0.00 0.00 2.74
822 885 1.734655 CCCTCACTATACCTGGCCAT 58.265 55.000 5.51 0.00 0.00 4.40
823 886 1.054406 GCCCTCACTATACCTGGCCA 61.054 60.000 4.71 4.71 32.74 5.36
824 887 1.755384 GCCCTCACTATACCTGGCC 59.245 63.158 0.00 0.00 32.74 5.36
825 888 1.367840 CGCCCTCACTATACCTGGC 59.632 63.158 0.00 0.00 35.55 4.85
826 889 1.367840 GCGCCCTCACTATACCTGG 59.632 63.158 0.00 0.00 0.00 4.45
827 890 0.032678 CTGCGCCCTCACTATACCTG 59.967 60.000 4.18 0.00 0.00 4.00
828 891 1.115930 CCTGCGCCCTCACTATACCT 61.116 60.000 4.18 0.00 0.00 3.08
829 892 1.367840 CCTGCGCCCTCACTATACC 59.632 63.158 4.18 0.00 0.00 2.73
830 893 1.301009 GCCTGCGCCCTCACTATAC 60.301 63.158 4.18 0.00 0.00 1.47
831 894 2.856628 CGCCTGCGCCCTCACTATA 61.857 63.158 4.18 0.00 0.00 1.31
832 895 4.227134 CGCCTGCGCCCTCACTAT 62.227 66.667 4.18 0.00 0.00 2.12
856 919 2.755655 AGGAGATACAGAGGAACACACG 59.244 50.000 0.00 0.00 0.00 4.49
857 920 4.020543 AGAGGAGATACAGAGGAACACAC 58.979 47.826 0.00 0.00 0.00 3.82
858 921 4.019858 CAGAGGAGATACAGAGGAACACA 58.980 47.826 0.00 0.00 0.00 3.72
859 922 4.020543 ACAGAGGAGATACAGAGGAACAC 58.979 47.826 0.00 0.00 0.00 3.32
860 923 4.323569 ACAGAGGAGATACAGAGGAACA 57.676 45.455 0.00 0.00 0.00 3.18
861 924 5.180492 CGATACAGAGGAGATACAGAGGAAC 59.820 48.000 0.00 0.00 0.00 3.62
862 925 5.071923 TCGATACAGAGGAGATACAGAGGAA 59.928 44.000 0.00 0.00 0.00 3.36
863 926 4.593634 TCGATACAGAGGAGATACAGAGGA 59.406 45.833 0.00 0.00 0.00 3.71
864 927 4.900684 TCGATACAGAGGAGATACAGAGG 58.099 47.826 0.00 0.00 0.00 3.69
865 928 4.391830 GCTCGATACAGAGGAGATACAGAG 59.608 50.000 0.00 0.00 38.63 3.35
866 929 4.041075 AGCTCGATACAGAGGAGATACAGA 59.959 45.833 0.00 0.00 38.63 3.41
867 930 4.154015 CAGCTCGATACAGAGGAGATACAG 59.846 50.000 0.00 0.00 38.63 2.74
868 931 4.068599 CAGCTCGATACAGAGGAGATACA 58.931 47.826 0.00 0.00 38.63 2.29
869 932 3.119990 GCAGCTCGATACAGAGGAGATAC 60.120 52.174 0.00 0.00 38.63 2.24
870 933 3.078097 GCAGCTCGATACAGAGGAGATA 58.922 50.000 0.00 0.00 38.63 1.98
871 934 1.885887 GCAGCTCGATACAGAGGAGAT 59.114 52.381 0.00 0.00 38.63 2.75
872 935 1.313772 GCAGCTCGATACAGAGGAGA 58.686 55.000 0.00 0.00 38.63 3.71
873 936 0.040514 CGCAGCTCGATACAGAGGAG 60.041 60.000 0.00 0.00 41.67 3.69
938 1001 2.293677 CGACCTATGGCGATTACAGACT 59.706 50.000 0.00 0.00 0.00 3.24
956 1019 1.715993 GCTGGTTCTTCCTCTTCGAC 58.284 55.000 0.00 0.00 37.07 4.20
966 1029 2.032681 GGGCACTCGCTGGTTCTT 59.967 61.111 0.00 0.00 38.60 2.52
975 1038 4.742201 CCGTCTGTGGGGCACTCG 62.742 72.222 0.00 0.00 35.11 4.18
983 1046 2.996621 GACATTTCTTCTCCGTCTGTGG 59.003 50.000 0.00 0.00 0.00 4.17
1309 1372 1.331399 GCGAGGAGGGAAAGTAGCCT 61.331 60.000 0.00 0.00 0.00 4.58
1353 1416 1.292242 AGGAGGTTGCAGGAGGATAGA 59.708 52.381 0.00 0.00 0.00 1.98
1575 1638 4.260375 GCGATGACCACATTGTATGAGAAC 60.260 45.833 0.00 0.00 39.41 3.01
1636 1699 5.602145 TCTTTCCCATTTCATCAAACACCTT 59.398 36.000 0.00 0.00 0.00 3.50
1827 1890 1.445716 CGGTCGTCTCGCCTATCCTT 61.446 60.000 0.00 0.00 0.00 3.36
1848 1911 3.922240 GTGACATCATTTCATGCAACACC 59.078 43.478 0.00 0.00 0.00 4.16
2185 2249 3.173151 TGTGATCTGGACTAAGAAGGCA 58.827 45.455 0.00 0.00 29.10 4.75
2191 2255 6.662865 ATAGGTGATGTGATCTGGACTAAG 57.337 41.667 0.00 0.00 0.00 2.18
2457 2521 2.092323 GCTACTGCTTCCGGGATTTTT 58.908 47.619 0.00 0.00 36.03 1.94
2734 2798 9.979578 GCATGCTGATATTAGAGTATTATAGCT 57.020 33.333 11.37 0.00 0.00 3.32
3027 3091 8.585471 ATGTGTCATAATCAATTGATATCCCC 57.415 34.615 21.00 10.12 33.73 4.81
3086 3150 6.639671 TTCAACGTTTTGAAATTGGACTTG 57.360 33.333 0.00 0.00 46.59 3.16
3187 3251 3.122948 GCCTGTTGACGTTGTATGTGTAG 59.877 47.826 0.00 0.00 0.00 2.74
3381 3445 4.469883 CTCCCCATTCGGAGCATG 57.530 61.111 0.00 0.00 43.01 4.06
3655 3719 7.910162 CGTAAATGATACAATTTCAGGGTCAAG 59.090 37.037 0.00 0.00 32.16 3.02
3803 3916 1.337167 TGATCTCCAGTGCACAAGACG 60.337 52.381 21.04 8.96 0.00 4.18
3840 3993 7.273320 TGAATAATACGGTCAAAAACACCAA 57.727 32.000 0.00 0.00 32.89 3.67


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

AutoCloner maintained by Alex Coulton.