Multiple sequence alignment - TraesCS3A01G429100

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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 TraesCS3A01G429100 chr3A 100.000 3056 0 0 1 3056 672097938 672094883 0.000000e+00 5644
1 TraesCS3A01G429100 chr3A 93.949 314 18 1 365 678 518488739 518488427 9.920000e-130 473
2 TraesCS3A01G429100 chr3A 91.346 104 8 1 2433 2535 449437615 449437512 1.140000e-29 141
3 TraesCS3A01G429100 chr3D 93.641 1777 76 9 678 2441 536885860 536884108 0.000000e+00 2621
4 TraesCS3A01G429100 chr3D 96.008 476 15 3 2583 3056 536884108 536883635 0.000000e+00 771
5 TraesCS3A01G429100 chr3D 88.732 355 32 5 1 355 536886224 536885878 7.830000e-116 427
6 TraesCS3A01G429100 chr3B 93.136 1792 80 11 668 2441 709274025 709272259 0.000000e+00 2588
7 TraesCS3A01G429100 chr3B 89.918 486 26 11 2583 3049 709272259 709271778 3.370000e-169 604
8 TraesCS3A01G429100 chr3B 93.675 332 20 1 1 331 709274371 709274040 2.120000e-136 496
9 TraesCS3A01G429100 chr2A 94.586 314 17 0 362 675 482410117 482409804 1.270000e-133 486
10 TraesCS3A01G429100 chr2A 94.754 305 16 0 363 667 639969409 639969105 2.760000e-130 475
11 TraesCS3A01G429100 chr2A 94.175 309 18 0 362 670 745560854 745560546 3.570000e-129 472
12 TraesCS3A01G429100 chr2A 89.720 107 10 1 2427 2532 321005819 321005925 5.310000e-28 135
13 TraesCS3A01G429100 chr4A 95.098 306 15 0 362 667 219187839 219188144 1.650000e-132 483
14 TraesCS3A01G429100 chr4A 94.025 318 17 2 363 678 47646681 47646364 5.930000e-132 481
15 TraesCS3A01G429100 chr2B 95.066 304 15 0 364 667 700210642 700210339 2.130000e-131 479
16 TraesCS3A01G429100 chr1A 94.194 310 18 0 363 672 232326426 232326117 9.920000e-130 473
17 TraesCS3A01G429100 chr1A 93.103 319 21 1 350 667 57137972 57138290 1.660000e-127 466
18 TraesCS3A01G429100 chr2D 93.069 101 6 1 2433 2532 420523736 420523836 2.460000e-31 147
19 TraesCS3A01G429100 chr7D 92.079 101 7 1 2433 2532 575148425 575148325 1.140000e-29 141
20 TraesCS3A01G429100 chr6B 89.720 107 10 1 2427 2532 469042009 469042115 5.310000e-28 135
21 TraesCS3A01G429100 chr6A 91.089 101 8 1 2433 2532 140050658 140050758 5.310000e-28 135
22 TraesCS3A01G429100 chr5D 91.089 101 8 1 2433 2532 138394323 138394223 5.310000e-28 135
23 TraesCS3A01G429100 chr5A 90.385 104 9 1 2433 2535 181018185 181018082 5.310000e-28 135
24 TraesCS3A01G429100 chr1D 88.889 108 10 2 2433 2539 415400314 415400420 6.880000e-27 132


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 TraesCS3A01G429100 chr3A 672094883 672097938 3055 True 5644.000000 5644 100.000000 1 3056 1 chr3A.!!$R3 3055
1 TraesCS3A01G429100 chr3D 536883635 536886224 2589 True 1273.000000 2621 92.793667 1 3056 3 chr3D.!!$R1 3055
2 TraesCS3A01G429100 chr3B 709271778 709274371 2593 True 1229.333333 2588 92.243000 1 3049 3 chr3B.!!$R1 3048

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
618 620 0.106519 GCATGCCACTCCAACCCTAT 60.107 55.0 6.36 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2378 0.109086 CTAGGTCGCACCACAGTCAG 60.109 60.0 7.86 0.0 41.95 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
48 49 0.179078 AGTACGTCGGTTTTGGCACA 60.179 50.000 0.00 0.00 0.00 4.57
94 95 1.375396 TGGGATGACGCAAACTCCG 60.375 57.895 0.00 0.00 36.07 4.63
114 115 2.616376 CGTCTCCTAGATCAGTCACTGG 59.384 54.545 4.57 0.00 31.51 4.00
286 288 7.704472 ACACCAAATACCATACAAATTAATGCG 59.296 33.333 0.00 0.00 0.00 4.73
375 377 5.876651 AAAAAGTCAAGGGCTTCTTTGAT 57.123 34.783 0.00 0.00 32.41 2.57
376 378 5.876651 AAAAGTCAAGGGCTTCTTTGATT 57.123 34.783 0.00 0.00 32.41 2.57
377 379 5.459536 AAAGTCAAGGGCTTCTTTGATTC 57.540 39.130 0.00 0.00 32.41 2.52
378 380 4.104383 AGTCAAGGGCTTCTTTGATTCA 57.896 40.909 0.00 0.00 32.41 2.57
379 381 4.473444 AGTCAAGGGCTTCTTTGATTCAA 58.527 39.130 0.00 0.00 32.41 2.69
380 382 4.895297 AGTCAAGGGCTTCTTTGATTCAAA 59.105 37.500 11.19 11.19 32.41 2.69
446 448 7.610580 TTTTTCCTATGTTGGTCCTTTGATT 57.389 32.000 0.00 0.00 0.00 2.57
447 449 6.834168 TTTCCTATGTTGGTCCTTTGATTC 57.166 37.500 0.00 0.00 0.00 2.52
448 450 5.512942 TCCTATGTTGGTCCTTTGATTCA 57.487 39.130 0.00 0.00 0.00 2.57
449 451 6.078456 TCCTATGTTGGTCCTTTGATTCAT 57.922 37.500 0.00 0.00 0.00 2.57
450 452 7.206789 TCCTATGTTGGTCCTTTGATTCATA 57.793 36.000 0.00 0.00 0.00 2.15
451 453 7.282585 TCCTATGTTGGTCCTTTGATTCATAG 58.717 38.462 0.00 0.00 35.63 2.23
452 454 6.488006 CCTATGTTGGTCCTTTGATTCATAGG 59.512 42.308 14.95 14.95 43.47 2.57
453 455 5.512942 TGTTGGTCCTTTGATTCATAGGA 57.487 39.130 18.57 18.57 38.81 2.94
454 456 6.078456 TGTTGGTCCTTTGATTCATAGGAT 57.922 37.500 23.34 0.00 41.93 3.24
455 457 6.493166 TGTTGGTCCTTTGATTCATAGGATT 58.507 36.000 23.34 0.00 41.93 3.01
456 458 6.377996 TGTTGGTCCTTTGATTCATAGGATTG 59.622 38.462 23.34 1.66 41.93 2.67
457 459 5.448654 TGGTCCTTTGATTCATAGGATTGG 58.551 41.667 23.34 2.03 41.93 3.16
458 460 5.193527 TGGTCCTTTGATTCATAGGATTGGA 59.806 40.000 23.34 9.48 41.93 3.53
459 461 6.126097 TGGTCCTTTGATTCATAGGATTGGAT 60.126 38.462 23.34 0.00 41.93 3.41
460 462 6.779539 GGTCCTTTGATTCATAGGATTGGATT 59.220 38.462 23.34 0.00 41.93 3.01
461 463 7.040132 GGTCCTTTGATTCATAGGATTGGATTC 60.040 40.741 23.34 11.96 41.93 2.52
462 464 7.006509 TCCTTTGATTCATAGGATTGGATTCC 58.993 38.462 18.57 0.00 36.84 3.01
463 465 6.779049 CCTTTGATTCATAGGATTGGATTCCA 59.221 38.462 15.80 0.00 35.14 3.53
464 466 7.453752 CCTTTGATTCATAGGATTGGATTCCAT 59.546 37.037 15.80 0.00 35.14 3.41
465 467 9.524496 CTTTGATTCATAGGATTGGATTCCATA 57.476 33.333 6.15 0.00 38.32 2.74
466 468 9.524496 TTTGATTCATAGGATTGGATTCCATAG 57.476 33.333 6.15 0.00 38.32 2.23
467 469 7.636579 TGATTCATAGGATTGGATTCCATAGG 58.363 38.462 6.15 0.00 38.32 2.57
468 470 7.462006 TGATTCATAGGATTGGATTCCATAGGA 59.538 37.037 6.15 0.31 38.32 2.94
469 471 7.646654 TTCATAGGATTGGATTCCATAGGAA 57.353 36.000 6.15 6.63 46.39 3.36
524 526 8.519799 TTCATAGGAAATTTAACATCCACTCC 57.480 34.615 0.00 0.00 35.62 3.85
525 527 7.638444 TCATAGGAAATTTAACATCCACTCCA 58.362 34.615 0.00 0.00 35.62 3.86
526 528 8.112822 TCATAGGAAATTTAACATCCACTCCAA 58.887 33.333 0.00 0.00 35.62 3.53
527 529 6.590234 AGGAAATTTAACATCCACTCCAAC 57.410 37.500 0.00 0.00 35.62 3.77
528 530 5.480422 AGGAAATTTAACATCCACTCCAACC 59.520 40.000 0.00 0.00 35.62 3.77
529 531 5.480422 GGAAATTTAACATCCACTCCAACCT 59.520 40.000 0.00 0.00 33.30 3.50
530 532 6.014584 GGAAATTTAACATCCACTCCAACCTT 60.015 38.462 0.00 0.00 33.30 3.50
531 533 6.994421 AATTTAACATCCACTCCAACCTTT 57.006 33.333 0.00 0.00 0.00 3.11
532 534 6.994421 ATTTAACATCCACTCCAACCTTTT 57.006 33.333 0.00 0.00 0.00 2.27
533 535 6.800072 TTTAACATCCACTCCAACCTTTTT 57.200 33.333 0.00 0.00 0.00 1.94
572 574 3.998099 TTTCGTGGCATCAAACAATCA 57.002 38.095 0.00 0.00 0.00 2.57
573 575 4.517952 TTTCGTGGCATCAAACAATCAT 57.482 36.364 0.00 0.00 0.00 2.45
574 576 4.517952 TTCGTGGCATCAAACAATCATT 57.482 36.364 0.00 0.00 0.00 2.57
575 577 3.835779 TCGTGGCATCAAACAATCATTG 58.164 40.909 0.00 0.00 0.00 2.82
576 578 2.346244 CGTGGCATCAAACAATCATTGC 59.654 45.455 0.00 0.00 0.00 3.56
577 579 3.592059 GTGGCATCAAACAATCATTGCT 58.408 40.909 0.00 0.00 0.00 3.91
578 580 4.674885 CGTGGCATCAAACAATCATTGCTA 60.675 41.667 0.00 0.00 0.00 3.49
579 581 5.170021 GTGGCATCAAACAATCATTGCTAA 58.830 37.500 0.00 0.00 0.00 3.09
580 582 5.813672 GTGGCATCAAACAATCATTGCTAAT 59.186 36.000 0.00 0.00 0.00 1.73
581 583 6.314400 GTGGCATCAAACAATCATTGCTAATT 59.686 34.615 0.00 0.00 0.00 1.40
582 584 6.535865 TGGCATCAAACAATCATTGCTAATTC 59.464 34.615 0.00 0.00 0.00 2.17
583 585 6.759827 GGCATCAAACAATCATTGCTAATTCT 59.240 34.615 0.00 0.00 0.00 2.40
584 586 7.922278 GGCATCAAACAATCATTGCTAATTCTA 59.078 33.333 0.00 0.00 0.00 2.10
585 587 9.472361 GCATCAAACAATCATTGCTAATTCTAT 57.528 29.630 0.00 0.00 0.00 1.98
599 601 8.868522 TGCTAATTCTATAGGATTCAAATGGG 57.131 34.615 9.67 0.00 0.00 4.00
600 602 7.394359 TGCTAATTCTATAGGATTCAAATGGGC 59.606 37.037 9.67 5.60 0.00 5.36
601 603 7.394359 GCTAATTCTATAGGATTCAAATGGGCA 59.606 37.037 9.67 0.00 0.00 5.36
602 604 9.471702 CTAATTCTATAGGATTCAAATGGGCAT 57.528 33.333 9.67 0.00 0.00 4.40
603 605 7.713734 ATTCTATAGGATTCAAATGGGCATG 57.286 36.000 0.00 0.00 0.00 4.06
604 606 5.012239 TCTATAGGATTCAAATGGGCATGC 58.988 41.667 9.90 9.90 0.00 4.06
605 607 1.125633 AGGATTCAAATGGGCATGCC 58.874 50.000 29.47 29.47 0.00 4.40
606 608 0.831966 GGATTCAAATGGGCATGCCA 59.168 50.000 36.56 23.14 37.98 4.92
607 609 1.473788 GGATTCAAATGGGCATGCCAC 60.474 52.381 36.56 25.50 37.98 5.01
608 610 1.483415 GATTCAAATGGGCATGCCACT 59.517 47.619 36.56 20.94 37.98 4.00
609 611 0.896923 TTCAAATGGGCATGCCACTC 59.103 50.000 36.56 20.78 37.98 3.51
610 612 0.971959 TCAAATGGGCATGCCACTCC 60.972 55.000 36.56 20.41 37.98 3.85
611 613 1.078891 AAATGGGCATGCCACTCCA 59.921 52.632 36.56 25.30 37.98 3.86
612 614 0.544833 AAATGGGCATGCCACTCCAA 60.545 50.000 36.56 15.42 37.98 3.53
613 615 1.259840 AATGGGCATGCCACTCCAAC 61.260 55.000 36.56 18.56 37.98 3.77
614 616 3.070576 GGGCATGCCACTCCAACC 61.071 66.667 36.56 14.15 37.98 3.77
615 617 3.070576 GGCATGCCACTCCAACCC 61.071 66.667 32.08 0.00 35.81 4.11
616 618 2.036256 GCATGCCACTCCAACCCT 59.964 61.111 6.36 0.00 0.00 4.34
617 619 1.302949 GCATGCCACTCCAACCCTA 59.697 57.895 6.36 0.00 0.00 3.53
618 620 0.106519 GCATGCCACTCCAACCCTAT 60.107 55.000 6.36 0.00 0.00 2.57
619 621 1.142870 GCATGCCACTCCAACCCTATA 59.857 52.381 6.36 0.00 0.00 1.31
620 622 2.224867 GCATGCCACTCCAACCCTATAT 60.225 50.000 6.36 0.00 0.00 0.86
621 623 3.751893 GCATGCCACTCCAACCCTATATT 60.752 47.826 6.36 0.00 0.00 1.28
622 624 4.473444 CATGCCACTCCAACCCTATATTT 58.527 43.478 0.00 0.00 0.00 1.40
623 625 4.601406 TGCCACTCCAACCCTATATTTT 57.399 40.909 0.00 0.00 0.00 1.82
624 626 4.941713 TGCCACTCCAACCCTATATTTTT 58.058 39.130 0.00 0.00 0.00 1.94
625 627 4.953579 TGCCACTCCAACCCTATATTTTTC 59.046 41.667 0.00 0.00 0.00 2.29
626 628 4.341235 GCCACTCCAACCCTATATTTTTCC 59.659 45.833 0.00 0.00 0.00 3.13
627 629 5.766590 CCACTCCAACCCTATATTTTTCCT 58.233 41.667 0.00 0.00 0.00 3.36
628 630 6.636336 GCCACTCCAACCCTATATTTTTCCTA 60.636 42.308 0.00 0.00 0.00 2.94
629 631 7.526918 CCACTCCAACCCTATATTTTTCCTAT 58.473 38.462 0.00 0.00 0.00 2.57
630 632 8.004801 CCACTCCAACCCTATATTTTTCCTATT 58.995 37.037 0.00 0.00 0.00 1.73
631 633 9.067986 CACTCCAACCCTATATTTTTCCTATTC 57.932 37.037 0.00 0.00 0.00 1.75
632 634 8.225416 ACTCCAACCCTATATTTTTCCTATTCC 58.775 37.037 0.00 0.00 0.00 3.01
633 635 8.358082 TCCAACCCTATATTTTTCCTATTCCT 57.642 34.615 0.00 0.00 0.00 3.36
634 636 8.224720 TCCAACCCTATATTTTTCCTATTCCTG 58.775 37.037 0.00 0.00 0.00 3.86
635 637 7.039714 CCAACCCTATATTTTTCCTATTCCTGC 60.040 40.741 0.00 0.00 0.00 4.85
636 638 6.238648 ACCCTATATTTTTCCTATTCCTGCG 58.761 40.000 0.00 0.00 0.00 5.18
637 639 5.123979 CCCTATATTTTTCCTATTCCTGCGC 59.876 44.000 0.00 0.00 0.00 6.09
638 640 5.940470 CCTATATTTTTCCTATTCCTGCGCT 59.060 40.000 9.73 0.00 0.00 5.92
639 641 6.431234 CCTATATTTTTCCTATTCCTGCGCTT 59.569 38.462 9.73 0.00 0.00 4.68
640 642 6.715347 ATATTTTTCCTATTCCTGCGCTTT 57.285 33.333 9.73 0.00 0.00 3.51
641 643 4.864704 TTTTTCCTATTCCTGCGCTTTT 57.135 36.364 9.73 0.00 0.00 2.27
642 644 5.968528 TTTTTCCTATTCCTGCGCTTTTA 57.031 34.783 9.73 0.00 0.00 1.52
643 645 5.968528 TTTTCCTATTCCTGCGCTTTTAA 57.031 34.783 9.73 0.00 0.00 1.52
644 646 5.968528 TTTCCTATTCCTGCGCTTTTAAA 57.031 34.783 9.73 0.00 0.00 1.52
645 647 5.968528 TTCCTATTCCTGCGCTTTTAAAA 57.031 34.783 9.73 0.00 0.00 1.52
646 648 6.524101 TTCCTATTCCTGCGCTTTTAAAAT 57.476 33.333 9.73 2.81 0.00 1.82
647 649 6.131544 TCCTATTCCTGCGCTTTTAAAATC 57.868 37.500 9.73 0.00 0.00 2.17
648 650 5.067283 TCCTATTCCTGCGCTTTTAAAATCC 59.933 40.000 9.73 0.00 0.00 3.01
649 651 5.067805 CCTATTCCTGCGCTTTTAAAATCCT 59.932 40.000 9.73 0.00 0.00 3.24
650 652 6.262273 CCTATTCCTGCGCTTTTAAAATCCTA 59.738 38.462 9.73 0.00 0.00 2.94
651 653 6.715347 ATTCCTGCGCTTTTAAAATCCTAT 57.285 33.333 9.73 0.00 0.00 2.57
652 654 5.499139 TCCTGCGCTTTTAAAATCCTATG 57.501 39.130 9.73 0.00 0.00 2.23
653 655 5.189928 TCCTGCGCTTTTAAAATCCTATGA 58.810 37.500 9.73 0.00 0.00 2.15
654 656 5.650266 TCCTGCGCTTTTAAAATCCTATGAA 59.350 36.000 9.73 0.00 0.00 2.57
655 657 6.321181 TCCTGCGCTTTTAAAATCCTATGAAT 59.679 34.615 9.73 0.00 0.00 2.57
656 658 6.638468 CCTGCGCTTTTAAAATCCTATGAATC 59.362 38.462 9.73 0.00 0.00 2.52
657 659 7.094508 TGCGCTTTTAAAATCCTATGAATCA 57.905 32.000 9.73 0.00 0.00 2.57
658 660 7.542890 TGCGCTTTTAAAATCCTATGAATCAA 58.457 30.769 9.73 0.00 0.00 2.57
659 661 8.031864 TGCGCTTTTAAAATCCTATGAATCAAA 58.968 29.630 9.73 0.00 0.00 2.69
660 662 8.534778 GCGCTTTTAAAATCCTATGAATCAAAG 58.465 33.333 0.00 0.00 0.00 2.77
661 663 9.787532 CGCTTTTAAAATCCTATGAATCAAAGA 57.212 29.630 0.09 0.00 0.00 2.52
665 667 6.721704 AAAATCCTATGAATCAAAGAGGCC 57.278 37.500 0.00 0.00 0.00 5.19
666 668 3.864789 TCCTATGAATCAAAGAGGCCC 57.135 47.619 0.00 0.00 0.00 5.80
715 722 2.436115 GTAGGTGCACCGAAGCCC 60.436 66.667 29.68 9.37 42.08 5.19
716 723 2.925706 TAGGTGCACCGAAGCCCA 60.926 61.111 29.68 7.73 42.08 5.36
717 724 2.521451 TAGGTGCACCGAAGCCCAA 61.521 57.895 29.68 6.67 42.08 4.12
829 849 0.234106 GATGATGGATGCGCGAGTTG 59.766 55.000 12.10 0.00 0.00 3.16
939 960 3.513750 AAGCCACACCCAAGGGAGC 62.514 63.158 13.15 8.91 38.96 4.70
942 963 4.641645 CACACCCAAGGGAGCGCA 62.642 66.667 13.15 0.00 38.96 6.09
943 964 4.335647 ACACCCAAGGGAGCGCAG 62.336 66.667 13.15 0.00 38.96 5.18
944 965 4.020617 CACCCAAGGGAGCGCAGA 62.021 66.667 13.15 0.00 38.96 4.26
945 966 3.249189 ACCCAAGGGAGCGCAGAA 61.249 61.111 13.15 0.00 38.96 3.02
946 967 2.437359 CCCAAGGGAGCGCAGAAG 60.437 66.667 11.47 0.00 37.50 2.85
991 1012 2.116736 CTAGCGAGAGAGAGCGGCAG 62.117 65.000 1.45 0.00 38.61 4.85
1132 1159 4.771356 GCCAGCGCTACGTCGACA 62.771 66.667 10.99 0.00 0.00 4.35
1172 1199 4.410400 CCTCAACCAGGTCGGGGC 62.410 72.222 0.00 0.00 40.22 5.80
1532 1565 1.048601 AGGAAGCTGGAGAACACGAA 58.951 50.000 0.00 0.00 0.00 3.85
1709 1742 1.066858 GCTCGTCAAGGTCATGAAGGA 60.067 52.381 0.00 0.00 30.93 3.36
1711 1744 2.232452 CTCGTCAAGGTCATGAAGGACT 59.768 50.000 0.00 0.00 37.91 3.85
1728 1761 3.054287 AGGACTACCTCAGAGATGACGAA 60.054 47.826 0.00 0.00 44.13 3.85
1768 1801 0.671472 GATGATGATGATCGGCGCCA 60.671 55.000 28.98 14.46 0.00 5.69
1970 2003 2.202743 CATCCGCGACGTGTCCAT 60.203 61.111 8.23 0.00 0.00 3.41
2059 2092 1.003118 TGCTGTTCGGCCAGTAAGAAT 59.997 47.619 2.24 0.00 34.84 2.40
2066 2099 1.737793 CGGCCAGTAAGAATGGTGAAC 59.262 52.381 2.24 0.00 40.17 3.18
2067 2100 2.615493 CGGCCAGTAAGAATGGTGAACT 60.615 50.000 2.24 0.00 40.17 3.01
2120 2153 8.345565 AGCGATGTTGAATTCCTAATAATGTTC 58.654 33.333 2.27 0.00 0.00 3.18
2132 2165 9.781834 TTCCTAATAATGTTCTGCGTAAATTTG 57.218 29.630 0.00 0.00 0.00 2.32
2153 2186 0.310854 CAACAAAGTCGGCCTGGTTC 59.689 55.000 0.00 0.00 0.00 3.62
2204 2238 5.847670 AGCGTTATTGTTTCTCTTCAGTC 57.152 39.130 0.00 0.00 0.00 3.51
2234 2268 6.721571 AGTGTATGTGTTGTTTTCGATAGG 57.278 37.500 0.00 0.00 0.00 2.57
2236 2270 4.393680 TGTATGTGTTGTTTTCGATAGGCC 59.606 41.667 0.00 0.00 0.00 5.19
2249 2283 5.407407 TCGATAGGCCTCTATTTGGATTC 57.593 43.478 9.68 0.00 36.40 2.52
2251 2285 4.020218 CGATAGGCCTCTATTTGGATTCCA 60.020 45.833 9.68 0.00 36.40 3.53
2266 2300 6.367374 TGGATTCCATATTTGTATCCGCTA 57.633 37.500 0.00 0.00 36.02 4.26
2336 2374 2.949447 ACCAGAAGTTGAGCCATTGTT 58.051 42.857 0.00 0.00 0.00 2.83
2337 2375 2.624838 ACCAGAAGTTGAGCCATTGTTG 59.375 45.455 0.00 0.00 0.00 3.33
2340 2378 4.293415 CAGAAGTTGAGCCATTGTTGTTC 58.707 43.478 0.00 0.00 0.00 3.18
2350 2388 2.951642 CCATTGTTGTTCTGACTGTGGT 59.048 45.455 0.00 0.00 0.00 4.16
2366 2404 0.682209 TGGTGCGACCTAGGTACTCC 60.682 60.000 16.29 19.37 39.58 3.85
2447 2485 9.793252 ATTAGTATTGTGCAAAATGAGTGAATC 57.207 29.630 12.62 0.00 0.00 2.52
2448 2486 7.458409 AGTATTGTGCAAAATGAGTGAATCT 57.542 32.000 12.62 0.00 0.00 2.40
2449 2487 8.565896 AGTATTGTGCAAAATGAGTGAATCTA 57.434 30.769 12.62 0.00 0.00 1.98
2450 2488 8.454106 AGTATTGTGCAAAATGAGTGAATCTAC 58.546 33.333 12.62 0.00 0.00 2.59
2451 2489 5.627499 TGTGCAAAATGAGTGAATCTACC 57.373 39.130 0.00 0.00 0.00 3.18
2452 2490 4.458989 TGTGCAAAATGAGTGAATCTACCC 59.541 41.667 0.00 0.00 0.00 3.69
2453 2491 4.702131 GTGCAAAATGAGTGAATCTACCCT 59.298 41.667 0.00 0.00 0.00 4.34
2454 2492 4.943705 TGCAAAATGAGTGAATCTACCCTC 59.056 41.667 0.00 0.00 0.00 4.30
2455 2493 5.189180 GCAAAATGAGTGAATCTACCCTCT 58.811 41.667 0.00 0.00 0.00 3.69
2456 2494 6.070251 TGCAAAATGAGTGAATCTACCCTCTA 60.070 38.462 0.00 0.00 0.00 2.43
2457 2495 6.823689 GCAAAATGAGTGAATCTACCCTCTAA 59.176 38.462 0.00 0.00 0.00 2.10
2458 2496 7.336931 GCAAAATGAGTGAATCTACCCTCTAAA 59.663 37.037 0.00 0.00 0.00 1.85
2459 2497 9.231297 CAAAATGAGTGAATCTACCCTCTAAAA 57.769 33.333 0.00 0.00 0.00 1.52
2460 2498 9.981460 AAAATGAGTGAATCTACCCTCTAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
2461 2499 8.970859 AATGAGTGAATCTACCCTCTAAAATG 57.029 34.615 0.00 0.00 0.00 2.32
2462 2500 6.349300 TGAGTGAATCTACCCTCTAAAATGC 58.651 40.000 0.00 0.00 0.00 3.56
2463 2501 6.070251 TGAGTGAATCTACCCTCTAAAATGCA 60.070 38.462 0.00 0.00 0.00 3.96
2464 2502 6.904626 AGTGAATCTACCCTCTAAAATGCAT 58.095 36.000 0.00 0.00 0.00 3.96
2465 2503 6.995091 AGTGAATCTACCCTCTAAAATGCATC 59.005 38.462 0.00 0.00 0.00 3.91
2466 2504 6.995091 GTGAATCTACCCTCTAAAATGCATCT 59.005 38.462 0.00 0.00 0.00 2.90
2467 2505 8.150945 GTGAATCTACCCTCTAAAATGCATCTA 58.849 37.037 0.00 0.00 0.00 1.98
2468 2506 8.150945 TGAATCTACCCTCTAAAATGCATCTAC 58.849 37.037 0.00 0.00 0.00 2.59
2469 2507 7.618019 ATCTACCCTCTAAAATGCATCTACA 57.382 36.000 0.00 0.00 0.00 2.74
2470 2508 7.618019 TCTACCCTCTAAAATGCATCTACAT 57.382 36.000 0.00 0.00 0.00 2.29
2471 2509 8.721133 TCTACCCTCTAAAATGCATCTACATA 57.279 34.615 0.00 0.00 0.00 2.29
2472 2510 8.585881 TCTACCCTCTAAAATGCATCTACATAC 58.414 37.037 0.00 0.00 0.00 2.39
2473 2511 7.136822 ACCCTCTAAAATGCATCTACATACA 57.863 36.000 0.00 0.00 0.00 2.29
2474 2512 7.749666 ACCCTCTAAAATGCATCTACATACAT 58.250 34.615 0.00 0.00 0.00 2.29
2475 2513 7.880195 ACCCTCTAAAATGCATCTACATACATC 59.120 37.037 0.00 0.00 0.00 3.06
2476 2514 8.099537 CCCTCTAAAATGCATCTACATACATCT 58.900 37.037 0.00 0.00 0.00 2.90
2477 2515 8.933807 CCTCTAAAATGCATCTACATACATCTG 58.066 37.037 0.00 0.00 0.00 2.90
2478 2516 9.486497 CTCTAAAATGCATCTACATACATCTGT 57.514 33.333 0.00 0.00 0.00 3.41
2528 2566 9.730420 CAAAGACATATATTTAAAAACGGAGGG 57.270 33.333 0.00 0.00 0.00 4.30
2529 2567 9.689501 AAAGACATATATTTAAAAACGGAGGGA 57.310 29.630 0.00 0.00 0.00 4.20
2530 2568 8.904099 AGACATATATTTAAAAACGGAGGGAG 57.096 34.615 0.00 0.00 0.00 4.30
2531 2569 8.491958 AGACATATATTTAAAAACGGAGGGAGT 58.508 33.333 0.00 0.00 0.00 3.85
2532 2570 8.446599 ACATATATTTAAAAACGGAGGGAGTG 57.553 34.615 0.00 0.00 0.00 3.51
2533 2571 5.830000 ATATTTAAAAACGGAGGGAGTGC 57.170 39.130 0.00 0.00 0.00 4.40
2534 2572 2.943036 TTAAAAACGGAGGGAGTGCT 57.057 45.000 0.00 0.00 0.00 4.40
2535 2573 2.178912 TAAAAACGGAGGGAGTGCTG 57.821 50.000 0.00 0.00 0.00 4.41
2536 2574 1.172812 AAAAACGGAGGGAGTGCTGC 61.173 55.000 0.00 0.00 0.00 5.25
2537 2575 2.056906 AAAACGGAGGGAGTGCTGCT 62.057 55.000 0.00 0.00 0.00 4.24
2538 2576 1.192146 AAACGGAGGGAGTGCTGCTA 61.192 55.000 0.00 0.00 0.00 3.49
2539 2577 0.978146 AACGGAGGGAGTGCTGCTAT 60.978 55.000 0.00 0.00 0.00 2.97
2540 2578 1.365633 CGGAGGGAGTGCTGCTATC 59.634 63.158 0.00 0.00 0.00 2.08
2541 2579 1.112315 CGGAGGGAGTGCTGCTATCT 61.112 60.000 0.00 0.00 0.00 1.98
2542 2580 1.127343 GGAGGGAGTGCTGCTATCTT 58.873 55.000 0.00 0.00 0.00 2.40
2543 2581 1.488393 GGAGGGAGTGCTGCTATCTTT 59.512 52.381 0.00 0.00 0.00 2.52
2544 2582 2.092699 GGAGGGAGTGCTGCTATCTTTT 60.093 50.000 0.00 0.00 0.00 2.27
2545 2583 3.615155 GAGGGAGTGCTGCTATCTTTTT 58.385 45.455 0.00 0.00 0.00 1.94
2546 2584 3.350833 AGGGAGTGCTGCTATCTTTTTG 58.649 45.455 0.00 0.00 0.00 2.44
2547 2585 3.084786 GGGAGTGCTGCTATCTTTTTGT 58.915 45.455 0.00 0.00 0.00 2.83
2548 2586 3.507622 GGGAGTGCTGCTATCTTTTTGTT 59.492 43.478 0.00 0.00 0.00 2.83
2549 2587 4.479619 GGAGTGCTGCTATCTTTTTGTTG 58.520 43.478 0.00 0.00 0.00 3.33
2550 2588 4.216257 GGAGTGCTGCTATCTTTTTGTTGA 59.784 41.667 0.00 0.00 0.00 3.18
2551 2589 5.105997 GGAGTGCTGCTATCTTTTTGTTGAT 60.106 40.000 0.00 0.00 0.00 2.57
2552 2590 6.094048 GGAGTGCTGCTATCTTTTTGTTGATA 59.906 38.462 0.00 0.00 0.00 2.15
2553 2591 7.201767 GGAGTGCTGCTATCTTTTTGTTGATAT 60.202 37.037 0.00 0.00 0.00 1.63
2554 2592 8.059798 AGTGCTGCTATCTTTTTGTTGATATT 57.940 30.769 0.00 0.00 0.00 1.28
2555 2593 8.526147 AGTGCTGCTATCTTTTTGTTGATATTT 58.474 29.630 0.00 0.00 0.00 1.40
2556 2594 9.787532 GTGCTGCTATCTTTTTGTTGATATTTA 57.212 29.630 0.00 0.00 0.00 1.40
2574 2612 9.425248 TGATATTTATCTTCCTCCAAAATTGCT 57.575 29.630 0.00 0.00 33.88 3.91
2575 2613 9.688592 GATATTTATCTTCCTCCAAAATTGCTG 57.311 33.333 0.00 0.00 0.00 4.41
2576 2614 7.722949 ATTTATCTTCCTCCAAAATTGCTGA 57.277 32.000 0.00 0.00 0.00 4.26
2577 2615 7.722949 TTTATCTTCCTCCAAAATTGCTGAT 57.277 32.000 0.00 0.00 0.00 2.90
2578 2616 8.821686 TTTATCTTCCTCCAAAATTGCTGATA 57.178 30.769 0.00 0.00 0.00 2.15
2579 2617 9.425248 TTTATCTTCCTCCAAAATTGCTGATAT 57.575 29.630 0.00 0.00 0.00 1.63
2580 2618 7.909485 ATCTTCCTCCAAAATTGCTGATATT 57.091 32.000 0.00 0.00 0.00 1.28
2581 2619 7.722949 TCTTCCTCCAAAATTGCTGATATTT 57.277 32.000 0.00 0.00 0.00 1.40
2582 2620 8.821686 TCTTCCTCCAAAATTGCTGATATTTA 57.178 30.769 0.00 0.00 0.00 1.40
2583 2621 9.425248 TCTTCCTCCAAAATTGCTGATATTTAT 57.575 29.630 0.00 0.00 0.00 1.40
2795 2838 5.355596 CCAAATTGTGTGTGCCTTAAAAGA 58.644 37.500 0.00 0.00 0.00 2.52
2942 2986 7.609760 TGTAGAATTACATCCACATGTCAAC 57.390 36.000 0.00 0.00 42.66 3.18
2948 2992 7.615582 ATTACATCCACATGTCAACTTAGTG 57.384 36.000 0.00 0.00 42.66 2.74
2950 2994 4.997395 ACATCCACATGTCAACTTAGTGAC 59.003 41.667 0.00 7.61 46.74 3.67
3014 3071 5.098211 GCATGTGCCTAATTCTGAAAGTTC 58.902 41.667 0.00 0.00 32.17 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.363807 GCTGGACTGTGCCAAAACC 59.636 57.895 0.00 0.00 37.52 3.27
48 49 1.302033 CTTTGGTCGCTGCTGGACT 60.302 57.895 7.45 0.00 34.82 3.85
94 95 2.360801 GCCAGTGACTGATCTAGGAGAC 59.639 54.545 15.33 0.00 32.44 3.36
114 115 0.251341 ATGGTCCCCTTCACAGTTGC 60.251 55.000 0.00 0.00 0.00 4.17
150 151 1.131315 GATGGCAACGAGGAAGAAAGC 59.869 52.381 0.00 0.00 42.51 3.51
226 228 0.889186 TGCAACGAGGAAGAAAGGCC 60.889 55.000 0.00 0.00 0.00 5.19
323 325 6.126997 ACGGTGTGGATAGTATAATTTGGTCA 60.127 38.462 0.00 0.00 0.00 4.02
356 358 4.473444 TGAATCAAAGAAGCCCTTGACTT 58.527 39.130 0.00 0.00 34.79 3.01
357 359 4.104383 TGAATCAAAGAAGCCCTTGACT 57.896 40.909 0.00 0.00 34.79 3.41
358 360 4.853924 TTGAATCAAAGAAGCCCTTGAC 57.146 40.909 0.00 0.00 34.79 3.18
422 424 7.288852 TGAATCAAAGGACCAACATAGGAAAAA 59.711 33.333 0.00 0.00 0.00 1.94
423 425 6.780031 TGAATCAAAGGACCAACATAGGAAAA 59.220 34.615 0.00 0.00 0.00 2.29
424 426 6.310941 TGAATCAAAGGACCAACATAGGAAA 58.689 36.000 0.00 0.00 0.00 3.13
425 427 5.886609 TGAATCAAAGGACCAACATAGGAA 58.113 37.500 0.00 0.00 0.00 3.36
426 428 5.512942 TGAATCAAAGGACCAACATAGGA 57.487 39.130 0.00 0.00 0.00 2.94
427 429 6.488006 CCTATGAATCAAAGGACCAACATAGG 59.512 42.308 0.33 0.33 44.75 2.57
428 430 7.282585 TCCTATGAATCAAAGGACCAACATAG 58.717 38.462 0.00 0.00 34.46 2.23
429 431 7.206789 TCCTATGAATCAAAGGACCAACATA 57.793 36.000 0.00 0.00 34.46 2.29
430 432 6.078456 TCCTATGAATCAAAGGACCAACAT 57.922 37.500 0.00 0.00 34.46 2.71
431 433 5.512942 TCCTATGAATCAAAGGACCAACA 57.487 39.130 0.00 0.00 34.46 3.33
432 434 6.183360 CCAATCCTATGAATCAAAGGACCAAC 60.183 42.308 0.00 0.00 42.08 3.77
433 435 5.893255 CCAATCCTATGAATCAAAGGACCAA 59.107 40.000 0.00 0.00 42.08 3.67
434 436 5.193527 TCCAATCCTATGAATCAAAGGACCA 59.806 40.000 0.00 0.00 42.08 4.02
435 437 5.694995 TCCAATCCTATGAATCAAAGGACC 58.305 41.667 0.00 0.00 42.08 4.46
436 438 7.040132 GGAATCCAATCCTATGAATCAAAGGAC 60.040 40.741 0.00 0.00 42.08 3.85
437 439 7.006509 GGAATCCAATCCTATGAATCAAAGGA 58.993 38.462 0.00 0.00 43.38 3.36
438 440 6.779049 TGGAATCCAATCCTATGAATCAAAGG 59.221 38.462 0.00 0.00 40.35 3.11
439 441 7.828508 TGGAATCCAATCCTATGAATCAAAG 57.171 36.000 0.00 0.00 40.35 2.77
440 442 9.524496 CTATGGAATCCAATCCTATGAATCAAA 57.476 33.333 5.89 0.00 40.35 2.69
441 443 8.111545 CCTATGGAATCCAATCCTATGAATCAA 58.888 37.037 5.89 0.00 40.35 2.57
442 444 7.462006 TCCTATGGAATCCAATCCTATGAATCA 59.538 37.037 5.89 0.00 40.35 2.57
443 445 7.865820 TCCTATGGAATCCAATCCTATGAATC 58.134 38.462 5.89 0.00 40.35 2.52
444 446 7.835728 TCCTATGGAATCCAATCCTATGAAT 57.164 36.000 5.89 0.00 40.35 2.57
445 447 7.646654 TTCCTATGGAATCCAATCCTATGAA 57.353 36.000 5.89 0.37 36.71 2.57
498 500 8.966868 GGAGTGGATGTTAAATTTCCTATGAAA 58.033 33.333 0.00 0.00 44.22 2.69
499 501 8.112822 TGGAGTGGATGTTAAATTTCCTATGAA 58.887 33.333 0.00 0.00 0.00 2.57
500 502 7.638444 TGGAGTGGATGTTAAATTTCCTATGA 58.362 34.615 0.00 0.00 0.00 2.15
501 503 7.880160 TGGAGTGGATGTTAAATTTCCTATG 57.120 36.000 0.00 0.00 0.00 2.23
502 504 7.342026 GGTTGGAGTGGATGTTAAATTTCCTAT 59.658 37.037 0.00 0.00 0.00 2.57
503 505 6.661805 GGTTGGAGTGGATGTTAAATTTCCTA 59.338 38.462 0.00 0.00 0.00 2.94
504 506 5.480422 GGTTGGAGTGGATGTTAAATTTCCT 59.520 40.000 0.00 0.00 0.00 3.36
505 507 5.480422 AGGTTGGAGTGGATGTTAAATTTCC 59.520 40.000 0.00 0.00 0.00 3.13
506 508 6.590234 AGGTTGGAGTGGATGTTAAATTTC 57.410 37.500 0.00 0.00 0.00 2.17
507 509 6.994421 AAGGTTGGAGTGGATGTTAAATTT 57.006 33.333 0.00 0.00 0.00 1.82
508 510 6.994421 AAAGGTTGGAGTGGATGTTAAATT 57.006 33.333 0.00 0.00 0.00 1.82
509 511 6.994421 AAAAGGTTGGAGTGGATGTTAAAT 57.006 33.333 0.00 0.00 0.00 1.40
510 512 6.800072 AAAAAGGTTGGAGTGGATGTTAAA 57.200 33.333 0.00 0.00 0.00 1.52
550 552 4.686972 TGATTGTTTGATGCCACGAAAAA 58.313 34.783 0.00 0.00 0.00 1.94
551 553 4.313277 TGATTGTTTGATGCCACGAAAA 57.687 36.364 0.00 0.00 0.00 2.29
552 554 3.998099 TGATTGTTTGATGCCACGAAA 57.002 38.095 0.00 0.00 0.00 3.46
553 555 4.236147 CAATGATTGTTTGATGCCACGAA 58.764 39.130 0.00 0.00 0.00 3.85
554 556 3.835779 CAATGATTGTTTGATGCCACGA 58.164 40.909 0.00 0.00 0.00 4.35
555 557 2.346244 GCAATGATTGTTTGATGCCACG 59.654 45.455 7.05 0.00 0.00 4.94
556 558 3.592059 AGCAATGATTGTTTGATGCCAC 58.408 40.909 7.05 0.00 34.44 5.01
557 559 3.965379 AGCAATGATTGTTTGATGCCA 57.035 38.095 7.05 0.00 34.44 4.92
558 560 6.759827 AGAATTAGCAATGATTGTTTGATGCC 59.240 34.615 7.05 0.00 34.44 4.40
559 561 7.766219 AGAATTAGCAATGATTGTTTGATGC 57.234 32.000 7.05 0.00 0.00 3.91
573 575 9.300681 CCCATTTGAATCCTATAGAATTAGCAA 57.699 33.333 0.00 0.00 0.00 3.91
574 576 7.394359 GCCCATTTGAATCCTATAGAATTAGCA 59.606 37.037 0.00 0.00 0.00 3.49
575 577 7.394359 TGCCCATTTGAATCCTATAGAATTAGC 59.606 37.037 0.00 0.00 0.00 3.09
576 578 8.868522 TGCCCATTTGAATCCTATAGAATTAG 57.131 34.615 0.00 0.00 0.00 1.73
577 579 9.246670 CATGCCCATTTGAATCCTATAGAATTA 57.753 33.333 0.00 0.00 0.00 1.40
578 580 7.310237 GCATGCCCATTTGAATCCTATAGAATT 60.310 37.037 6.36 0.00 0.00 2.17
579 581 6.154021 GCATGCCCATTTGAATCCTATAGAAT 59.846 38.462 6.36 0.00 0.00 2.40
580 582 5.477984 GCATGCCCATTTGAATCCTATAGAA 59.522 40.000 6.36 0.00 0.00 2.10
581 583 5.012239 GCATGCCCATTTGAATCCTATAGA 58.988 41.667 6.36 0.00 0.00 1.98
582 584 4.159135 GGCATGCCCATTTGAATCCTATAG 59.841 45.833 27.24 0.00 0.00 1.31
583 585 4.088634 GGCATGCCCATTTGAATCCTATA 58.911 43.478 27.24 0.00 0.00 1.31
584 586 2.901839 GGCATGCCCATTTGAATCCTAT 59.098 45.455 27.24 0.00 0.00 2.57
585 587 2.318908 GGCATGCCCATTTGAATCCTA 58.681 47.619 27.24 0.00 0.00 2.94
586 588 1.125633 GGCATGCCCATTTGAATCCT 58.874 50.000 27.24 0.00 0.00 3.24
587 589 0.831966 TGGCATGCCCATTTGAATCC 59.168 50.000 33.44 4.70 39.18 3.01
596 598 2.283101 GTTGGAGTGGCATGCCCA 60.283 61.111 33.44 20.96 42.79 5.36
597 599 3.070576 GGTTGGAGTGGCATGCCC 61.071 66.667 33.44 23.56 34.56 5.36
598 600 2.210144 TAGGGTTGGAGTGGCATGCC 62.210 60.000 30.54 30.54 0.00 4.40
599 601 0.106519 ATAGGGTTGGAGTGGCATGC 60.107 55.000 9.90 9.90 0.00 4.06
600 602 3.795688 ATATAGGGTTGGAGTGGCATG 57.204 47.619 0.00 0.00 0.00 4.06
601 603 4.814224 AAATATAGGGTTGGAGTGGCAT 57.186 40.909 0.00 0.00 0.00 4.40
602 604 4.601406 AAAATATAGGGTTGGAGTGGCA 57.399 40.909 0.00 0.00 0.00 4.92
603 605 4.341235 GGAAAAATATAGGGTTGGAGTGGC 59.659 45.833 0.00 0.00 0.00 5.01
604 606 5.766590 AGGAAAAATATAGGGTTGGAGTGG 58.233 41.667 0.00 0.00 0.00 4.00
605 607 8.996651 AATAGGAAAAATATAGGGTTGGAGTG 57.003 34.615 0.00 0.00 0.00 3.51
606 608 8.225416 GGAATAGGAAAAATATAGGGTTGGAGT 58.775 37.037 0.00 0.00 0.00 3.85
607 609 8.448816 AGGAATAGGAAAAATATAGGGTTGGAG 58.551 37.037 0.00 0.00 0.00 3.86
608 610 8.224720 CAGGAATAGGAAAAATATAGGGTTGGA 58.775 37.037 0.00 0.00 0.00 3.53
609 611 7.039714 GCAGGAATAGGAAAAATATAGGGTTGG 60.040 40.741 0.00 0.00 0.00 3.77
610 612 7.308589 CGCAGGAATAGGAAAAATATAGGGTTG 60.309 40.741 0.00 0.00 0.00 3.77
611 613 6.715264 CGCAGGAATAGGAAAAATATAGGGTT 59.285 38.462 0.00 0.00 0.00 4.11
612 614 6.238648 CGCAGGAATAGGAAAAATATAGGGT 58.761 40.000 0.00 0.00 0.00 4.34
613 615 5.123979 GCGCAGGAATAGGAAAAATATAGGG 59.876 44.000 0.30 0.00 0.00 3.53
614 616 5.940470 AGCGCAGGAATAGGAAAAATATAGG 59.060 40.000 11.47 0.00 0.00 2.57
615 617 7.440523 AAGCGCAGGAATAGGAAAAATATAG 57.559 36.000 11.47 0.00 0.00 1.31
616 618 7.817418 AAAGCGCAGGAATAGGAAAAATATA 57.183 32.000 11.47 0.00 0.00 0.86
617 619 6.715347 AAAGCGCAGGAATAGGAAAAATAT 57.285 33.333 11.47 0.00 0.00 1.28
618 620 6.524101 AAAAGCGCAGGAATAGGAAAAATA 57.476 33.333 11.47 0.00 0.00 1.40
619 621 5.405935 AAAAGCGCAGGAATAGGAAAAAT 57.594 34.783 11.47 0.00 0.00 1.82
620 622 4.864704 AAAAGCGCAGGAATAGGAAAAA 57.135 36.364 11.47 0.00 0.00 1.94
621 623 5.968528 TTAAAAGCGCAGGAATAGGAAAA 57.031 34.783 11.47 0.00 0.00 2.29
622 624 5.968528 TTTAAAAGCGCAGGAATAGGAAA 57.031 34.783 11.47 0.00 0.00 3.13
623 625 5.968528 TTTTAAAAGCGCAGGAATAGGAA 57.031 34.783 11.47 0.00 0.00 3.36
624 626 5.067283 GGATTTTAAAAGCGCAGGAATAGGA 59.933 40.000 11.47 0.00 0.00 2.94
625 627 5.067805 AGGATTTTAAAAGCGCAGGAATAGG 59.932 40.000 11.47 0.00 0.00 2.57
626 628 6.136541 AGGATTTTAAAAGCGCAGGAATAG 57.863 37.500 11.47 0.00 0.00 1.73
627 629 7.500892 TCATAGGATTTTAAAAGCGCAGGAATA 59.499 33.333 11.47 0.00 0.00 1.75
628 630 6.321181 TCATAGGATTTTAAAAGCGCAGGAAT 59.679 34.615 11.47 0.37 0.00 3.01
629 631 5.650266 TCATAGGATTTTAAAAGCGCAGGAA 59.350 36.000 11.47 0.00 0.00 3.36
630 632 5.189928 TCATAGGATTTTAAAAGCGCAGGA 58.810 37.500 11.47 4.84 0.00 3.86
631 633 5.499139 TCATAGGATTTTAAAAGCGCAGG 57.501 39.130 11.47 2.68 0.00 4.85
632 634 7.195646 TGATTCATAGGATTTTAAAAGCGCAG 58.804 34.615 11.47 1.13 0.00 5.18
633 635 7.094508 TGATTCATAGGATTTTAAAAGCGCA 57.905 32.000 11.47 1.00 0.00 6.09
634 636 7.985634 TTGATTCATAGGATTTTAAAAGCGC 57.014 32.000 9.89 0.00 0.00 5.92
635 637 9.787532 TCTTTGATTCATAGGATTTTAAAAGCG 57.212 29.630 9.89 0.00 0.00 4.68
639 641 8.695456 GGCCTCTTTGATTCATAGGATTTTAAA 58.305 33.333 12.17 0.00 0.00 1.52
640 642 7.287696 GGGCCTCTTTGATTCATAGGATTTTAA 59.712 37.037 0.84 0.00 0.00 1.52
641 643 6.777580 GGGCCTCTTTGATTCATAGGATTTTA 59.222 38.462 0.84 0.00 0.00 1.52
642 644 5.600069 GGGCCTCTTTGATTCATAGGATTTT 59.400 40.000 0.84 0.00 0.00 1.82
643 645 5.143369 GGGCCTCTTTGATTCATAGGATTT 58.857 41.667 0.84 0.00 0.00 2.17
644 646 4.448347 GGGGCCTCTTTGATTCATAGGATT 60.448 45.833 0.84 0.00 0.00 3.01
645 647 3.075134 GGGGCCTCTTTGATTCATAGGAT 59.925 47.826 0.84 0.00 0.00 3.24
646 648 2.443255 GGGGCCTCTTTGATTCATAGGA 59.557 50.000 0.84 0.85 0.00 2.94
647 649 2.175499 TGGGGCCTCTTTGATTCATAGG 59.825 50.000 3.07 5.38 0.00 2.57
648 650 3.582998 TGGGGCCTCTTTGATTCATAG 57.417 47.619 3.07 0.00 0.00 2.23
649 651 4.329638 TTTGGGGCCTCTTTGATTCATA 57.670 40.909 3.07 0.00 0.00 2.15
650 652 2.925966 TTGGGGCCTCTTTGATTCAT 57.074 45.000 3.07 0.00 0.00 2.57
651 653 2.692709 TTTGGGGCCTCTTTGATTCA 57.307 45.000 3.07 0.00 0.00 2.57
652 654 4.507710 GAAATTTGGGGCCTCTTTGATTC 58.492 43.478 3.07 0.00 0.00 2.52
653 655 3.055891 CGAAATTTGGGGCCTCTTTGATT 60.056 43.478 3.07 0.00 0.00 2.57
654 656 2.497273 CGAAATTTGGGGCCTCTTTGAT 59.503 45.455 3.07 0.00 0.00 2.57
655 657 1.892474 CGAAATTTGGGGCCTCTTTGA 59.108 47.619 3.07 0.00 0.00 2.69
656 658 1.892474 TCGAAATTTGGGGCCTCTTTG 59.108 47.619 3.07 0.00 0.00 2.77
657 659 1.893137 GTCGAAATTTGGGGCCTCTTT 59.107 47.619 3.07 0.00 0.00 2.52
658 660 1.545841 GTCGAAATTTGGGGCCTCTT 58.454 50.000 3.07 0.00 0.00 2.85
659 661 0.676782 CGTCGAAATTTGGGGCCTCT 60.677 55.000 3.07 0.00 0.00 3.69
660 662 1.654023 CCGTCGAAATTTGGGGCCTC 61.654 60.000 0.84 0.00 0.00 4.70
661 663 1.677633 CCGTCGAAATTTGGGGCCT 60.678 57.895 0.84 0.00 0.00 5.19
662 664 2.882132 CCGTCGAAATTTGGGGCC 59.118 61.111 0.00 0.00 0.00 5.80
663 665 2.180769 GCCGTCGAAATTTGGGGC 59.819 61.111 0.00 0.00 0.00 5.80
664 666 1.211709 GTGCCGTCGAAATTTGGGG 59.788 57.895 0.00 0.00 0.00 4.96
665 667 1.211709 GGTGCCGTCGAAATTTGGG 59.788 57.895 0.00 0.00 0.00 4.12
666 668 1.211709 GGGTGCCGTCGAAATTTGG 59.788 57.895 0.00 0.00 0.00 3.28
734 741 1.178276 CAAGTGCCGAGAGACCTACT 58.822 55.000 0.00 0.00 0.00 2.57
735 742 0.889306 ACAAGTGCCGAGAGACCTAC 59.111 55.000 0.00 0.00 0.00 3.18
736 743 1.629043 AACAAGTGCCGAGAGACCTA 58.371 50.000 0.00 0.00 0.00 3.08
737 744 0.759346 AAACAAGTGCCGAGAGACCT 59.241 50.000 0.00 0.00 0.00 3.85
738 745 1.149148 GAAACAAGTGCCGAGAGACC 58.851 55.000 0.00 0.00 0.00 3.85
858 878 1.774110 TTTATAGACCCGTGGCCGTA 58.226 50.000 0.00 0.00 0.00 4.02
940 961 2.400896 TTTCGGGTTTGCGCTTCTGC 62.401 55.000 9.73 0.00 0.00 4.26
941 962 0.660300 GTTTCGGGTTTGCGCTTCTG 60.660 55.000 9.73 0.48 0.00 3.02
942 963 1.652563 GTTTCGGGTTTGCGCTTCT 59.347 52.632 9.73 0.00 0.00 2.85
943 964 1.371267 GGTTTCGGGTTTGCGCTTC 60.371 57.895 9.73 0.00 0.00 3.86
944 965 1.668101 TTGGTTTCGGGTTTGCGCTT 61.668 50.000 9.73 0.00 0.00 4.68
945 966 1.668101 TTTGGTTTCGGGTTTGCGCT 61.668 50.000 9.73 0.00 0.00 5.92
946 967 0.598942 ATTTGGTTTCGGGTTTGCGC 60.599 50.000 0.00 0.00 0.00 6.09
993 1014 4.778143 ACGTCGCCCATTGCTCCC 62.778 66.667 0.00 0.00 38.05 4.30
994 1015 3.195698 GACGTCGCCCATTGCTCC 61.196 66.667 0.00 0.00 38.05 4.70
995 1016 3.554692 CGACGTCGCCCATTGCTC 61.555 66.667 26.59 0.00 38.05 4.26
1132 1159 4.070552 GCGCCACTCGGAGGACTT 62.071 66.667 10.23 0.00 38.94 3.01
1437 1470 1.735198 GTCGTCGATGCCGTGGAAA 60.735 57.895 0.00 0.00 37.05 3.13
1510 1543 1.066573 CGTGTTCTCCAGCTTCCTGAT 60.067 52.381 0.00 0.00 41.77 2.90
1709 1742 3.283751 CCTTCGTCATCTCTGAGGTAGT 58.716 50.000 4.59 0.00 38.23 2.73
1711 1744 2.025155 GCCTTCGTCATCTCTGAGGTA 58.975 52.381 4.59 0.00 38.23 3.08
1719 1752 3.376935 CTGCCCGCCTTCGTCATCT 62.377 63.158 0.00 0.00 0.00 2.90
1851 1884 2.676822 TTCTCCAGCCTCGTCGCT 60.677 61.111 0.00 0.00 40.65 4.93
2007 2040 3.633065 GCTGGTAGAGGTCCTTGTAGTAG 59.367 52.174 0.00 0.00 0.00 2.57
2059 2092 4.993705 ACTTCCTTCCATAAGTTCACCA 57.006 40.909 0.00 0.00 32.00 4.17
2066 2099 7.609532 AGTCTTGATCAAACTTCCTTCCATAAG 59.390 37.037 9.88 0.00 0.00 1.73
2067 2100 7.461749 AGTCTTGATCAAACTTCCTTCCATAA 58.538 34.615 9.88 0.00 0.00 1.90
2120 2153 3.801594 ACTTTGTTGCCAAATTTACGCAG 59.198 39.130 10.87 4.09 39.72 5.18
2132 2165 2.644992 CAGGCCGACTTTGTTGCC 59.355 61.111 0.00 0.00 44.35 4.52
2153 2186 6.572119 GCCTAGAGTTGATCTCATATGGACAG 60.572 46.154 2.13 0.00 44.98 3.51
2204 2238 6.183359 CGAAAACAACACATACACTAAATGCG 60.183 38.462 0.00 0.00 0.00 4.73
2234 2268 7.530426 ACAAATATGGAATCCAAATAGAGGC 57.470 36.000 5.89 0.00 36.95 4.70
2249 2283 5.390885 GCACACATAGCGGATACAAATATGG 60.391 44.000 0.00 0.00 32.84 2.74
2251 2285 5.304778 TGCACACATAGCGGATACAAATAT 58.695 37.500 0.00 0.00 33.85 1.28
2266 2300 6.886459 AGATAAAAGTACAAGGATGCACACAT 59.114 34.615 0.00 0.00 39.98 3.21
2328 2366 2.287788 CCACAGTCAGAACAACAATGGC 60.288 50.000 0.00 0.00 0.00 4.40
2329 2367 2.951642 ACCACAGTCAGAACAACAATGG 59.048 45.455 0.00 0.00 32.81 3.16
2330 2368 3.793129 GCACCACAGTCAGAACAACAATG 60.793 47.826 0.00 0.00 0.00 2.82
2331 2369 2.358898 GCACCACAGTCAGAACAACAAT 59.641 45.455 0.00 0.00 0.00 2.71
2332 2370 1.742831 GCACCACAGTCAGAACAACAA 59.257 47.619 0.00 0.00 0.00 2.83
2336 2374 0.529773 GTCGCACCACAGTCAGAACA 60.530 55.000 0.00 0.00 0.00 3.18
2337 2375 1.222115 GGTCGCACCACAGTCAGAAC 61.222 60.000 1.01 0.00 38.42 3.01
2340 2378 0.109086 CTAGGTCGCACCACAGTCAG 60.109 60.000 7.86 0.00 41.95 3.51
2350 2388 1.452651 CCGGAGTACCTAGGTCGCA 60.453 63.158 20.32 0.00 0.00 5.10
2366 2404 4.635765 TCAGCAATCAAAAGTAAGGATCCG 59.364 41.667 5.98 0.00 0.00 4.18
2438 2476 6.070251 TGCATTTTAGAGGGTAGATTCACTCA 60.070 38.462 0.00 0.00 40.03 3.41
2441 2479 6.995091 AGATGCATTTTAGAGGGTAGATTCAC 59.005 38.462 0.00 0.00 0.00 3.18
2443 2481 8.150945 TGTAGATGCATTTTAGAGGGTAGATTC 58.849 37.037 0.00 0.00 0.00 2.52
2444 2482 8.034313 TGTAGATGCATTTTAGAGGGTAGATT 57.966 34.615 0.00 0.00 0.00 2.40
2445 2483 7.618019 TGTAGATGCATTTTAGAGGGTAGAT 57.382 36.000 0.00 0.00 0.00 1.98
2446 2484 7.618019 ATGTAGATGCATTTTAGAGGGTAGA 57.382 36.000 0.00 0.00 0.00 2.59
2447 2485 8.367911 TGTATGTAGATGCATTTTAGAGGGTAG 58.632 37.037 0.00 0.00 0.00 3.18
2448 2486 8.257602 TGTATGTAGATGCATTTTAGAGGGTA 57.742 34.615 0.00 0.00 0.00 3.69
2449 2487 7.136822 TGTATGTAGATGCATTTTAGAGGGT 57.863 36.000 0.00 0.00 0.00 4.34
2450 2488 8.099537 AGATGTATGTAGATGCATTTTAGAGGG 58.900 37.037 0.00 0.00 35.26 4.30
2451 2489 8.933807 CAGATGTATGTAGATGCATTTTAGAGG 58.066 37.037 0.00 0.00 35.26 3.69
2452 2490 9.486497 ACAGATGTATGTAGATGCATTTTAGAG 57.514 33.333 0.00 0.00 35.26 2.43
2502 2540 9.730420 CCCTCCGTTTTTAAATATATGTCTTTG 57.270 33.333 0.00 0.00 0.00 2.77
2503 2541 9.689501 TCCCTCCGTTTTTAAATATATGTCTTT 57.310 29.630 0.00 0.00 0.00 2.52
2504 2542 9.338622 CTCCCTCCGTTTTTAAATATATGTCTT 57.661 33.333 0.00 0.00 0.00 3.01
2505 2543 8.491958 ACTCCCTCCGTTTTTAAATATATGTCT 58.508 33.333 0.00 0.00 0.00 3.41
2506 2544 8.557029 CACTCCCTCCGTTTTTAAATATATGTC 58.443 37.037 0.00 0.00 0.00 3.06
2507 2545 7.012989 GCACTCCCTCCGTTTTTAAATATATGT 59.987 37.037 0.00 0.00 0.00 2.29
2508 2546 7.228706 AGCACTCCCTCCGTTTTTAAATATATG 59.771 37.037 0.00 0.00 0.00 1.78
2509 2547 7.228706 CAGCACTCCCTCCGTTTTTAAATATAT 59.771 37.037 0.00 0.00 0.00 0.86
2510 2548 6.540914 CAGCACTCCCTCCGTTTTTAAATATA 59.459 38.462 0.00 0.00 0.00 0.86
2511 2549 5.357032 CAGCACTCCCTCCGTTTTTAAATAT 59.643 40.000 0.00 0.00 0.00 1.28
2512 2550 4.698304 CAGCACTCCCTCCGTTTTTAAATA 59.302 41.667 0.00 0.00 0.00 1.40
2513 2551 3.506067 CAGCACTCCCTCCGTTTTTAAAT 59.494 43.478 0.00 0.00 0.00 1.40
2514 2552 2.882137 CAGCACTCCCTCCGTTTTTAAA 59.118 45.455 0.00 0.00 0.00 1.52
2515 2553 2.500229 CAGCACTCCCTCCGTTTTTAA 58.500 47.619 0.00 0.00 0.00 1.52
2516 2554 1.880646 GCAGCACTCCCTCCGTTTTTA 60.881 52.381 0.00 0.00 0.00 1.52
2517 2555 1.172812 GCAGCACTCCCTCCGTTTTT 61.173 55.000 0.00 0.00 0.00 1.94
2518 2556 1.600916 GCAGCACTCCCTCCGTTTT 60.601 57.895 0.00 0.00 0.00 2.43
2519 2557 1.192146 TAGCAGCACTCCCTCCGTTT 61.192 55.000 0.00 0.00 0.00 3.60
2520 2558 0.978146 ATAGCAGCACTCCCTCCGTT 60.978 55.000 0.00 0.00 0.00 4.44
2521 2559 1.381872 ATAGCAGCACTCCCTCCGT 60.382 57.895 0.00 0.00 0.00 4.69
2522 2560 1.112315 AGATAGCAGCACTCCCTCCG 61.112 60.000 0.00 0.00 0.00 4.63
2523 2561 1.127343 AAGATAGCAGCACTCCCTCC 58.873 55.000 0.00 0.00 0.00 4.30
2524 2562 2.998316 AAAGATAGCAGCACTCCCTC 57.002 50.000 0.00 0.00 0.00 4.30
2525 2563 3.245052 ACAAAAAGATAGCAGCACTCCCT 60.245 43.478 0.00 0.00 0.00 4.20
2526 2564 3.084786 ACAAAAAGATAGCAGCACTCCC 58.915 45.455 0.00 0.00 0.00 4.30
2527 2565 4.216257 TCAACAAAAAGATAGCAGCACTCC 59.784 41.667 0.00 0.00 0.00 3.85
2528 2566 5.362556 TCAACAAAAAGATAGCAGCACTC 57.637 39.130 0.00 0.00 0.00 3.51
2529 2567 5.972107 ATCAACAAAAAGATAGCAGCACT 57.028 34.783 0.00 0.00 0.00 4.40
2530 2568 8.693542 AAATATCAACAAAAAGATAGCAGCAC 57.306 30.769 0.00 0.00 30.91 4.40
2548 2586 9.425248 AGCAATTTTGGAGGAAGATAAATATCA 57.575 29.630 3.45 0.00 35.17 2.15
2549 2587 9.688592 CAGCAATTTTGGAGGAAGATAAATATC 57.311 33.333 0.00 0.00 0.00 1.63
2550 2588 9.425248 TCAGCAATTTTGGAGGAAGATAAATAT 57.575 29.630 0.00 0.00 0.00 1.28
2551 2589 8.821686 TCAGCAATTTTGGAGGAAGATAAATA 57.178 30.769 0.00 0.00 0.00 1.40
2552 2590 7.722949 TCAGCAATTTTGGAGGAAGATAAAT 57.277 32.000 0.00 0.00 0.00 1.40
2553 2591 7.722949 ATCAGCAATTTTGGAGGAAGATAAA 57.277 32.000 0.00 0.00 0.00 1.40
2554 2592 9.425248 AATATCAGCAATTTTGGAGGAAGATAA 57.575 29.630 0.00 0.00 0.00 1.75
2555 2593 9.425248 AAATATCAGCAATTTTGGAGGAAGATA 57.575 29.630 0.00 0.00 0.00 1.98
2556 2594 7.909485 AATATCAGCAATTTTGGAGGAAGAT 57.091 32.000 0.00 0.00 0.00 2.40
2557 2595 7.722949 AAATATCAGCAATTTTGGAGGAAGA 57.277 32.000 0.00 0.00 0.00 2.87
2766 2809 2.493278 GGCACACACAATTTGGCTAGAT 59.507 45.455 0.78 0.00 33.19 1.98
2806 2850 5.799936 CACATACAAAATTAACTCGGGCTTG 59.200 40.000 0.00 0.00 0.00 4.01
2942 2986 8.075574 TGTTTGCAATGTTGATAAGTCACTAAG 58.924 33.333 0.00 0.00 33.11 2.18
2948 2992 9.571810 TCAATATGTTTGCAATGTTGATAAGTC 57.428 29.630 0.00 0.00 0.00 3.01
2950 2994 8.525876 CGTCAATATGTTTGCAATGTTGATAAG 58.474 33.333 12.09 5.77 31.27 1.73
2984 3028 7.408756 TCAGAATTAGGCACATGCTTTTAAT 57.591 32.000 3.48 3.96 41.70 1.40


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

AutoCloner maintained by Alex Coulton.