Multiple sequence alignment - TraesCS3A01G189100

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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 TraesCS3A01G189100 chr3A 100.000 3380 0 0 1 3380 231039019 231042398 0.000000e+00 6242.0
1 TraesCS3A01G189100 chr3D 95.747 1787 49 8 817 2593 182352245 182350476 0.000000e+00 2854.0
2 TraesCS3A01G189100 chr3D 79.249 559 71 26 2601 3121 182350435 182349884 6.940000e-92 348.0
3 TraesCS3A01G189100 chr3D 90.000 130 10 3 632 759 182352687 182352559 7.500000e-37 165.0
4 TraesCS3A01G189100 chr3D 94.737 95 5 0 543 637 182364641 182364547 7.560000e-32 148.0
5 TraesCS3A01G189100 chr3D 90.110 91 7 1 3290 3380 189816466 189816554 2.130000e-22 117.0
6 TraesCS3A01G189100 chr3D 100.000 38 0 0 3179 3216 182344925 182344888 1.680000e-08 71.3
7 TraesCS3A01G189100 chr3B 96.466 1528 48 3 1070 2592 260850053 260848527 0.000000e+00 2518.0
8 TraesCS3A01G189100 chr3B 91.160 362 22 7 2601 2958 260848485 260848130 1.820000e-132 483.0
9 TraesCS3A01G189100 chr3B 87.679 349 20 14 2944 3291 260848045 260847719 5.290000e-103 385.0
10 TraesCS3A01G189100 chr3B 91.209 91 7 1 3290 3380 406102488 406102399 4.580000e-24 122.0
11 TraesCS3A01G189100 chr4D 86.476 525 58 8 1 519 465073419 465072902 6.330000e-157 564.0
12 TraesCS3A01G189100 chr4D 85.347 505 59 11 1 492 67355769 67355267 3.010000e-140 508.0
13 TraesCS3A01G189100 chr4D 91.304 92 7 1 3289 3380 489840134 489840044 1.270000e-24 124.0
14 TraesCS3A01G189100 chr1D 85.551 526 66 7 1 519 292515194 292514672 2.970000e-150 542.0
15 TraesCS3A01G189100 chr1D 83.516 546 62 12 1 519 437470377 437470921 5.070000e-133 484.0
16 TraesCS3A01G189100 chr7A 84.183 569 57 12 1 543 500566186 500566747 3.860000e-144 521.0
17 TraesCS3A01G189100 chr7A 94.017 117 6 1 991 1106 706303706 706303822 3.470000e-40 176.0
18 TraesCS3A01G189100 chr7D 84.015 538 66 11 1 519 563346133 563346669 1.810000e-137 499.0
19 TraesCS3A01G189100 chr7D 94.872 117 5 1 991 1106 105206919 105206803 7.450000e-42 182.0
20 TraesCS3A01G189100 chr6D 83.619 525 80 4 1 519 13144628 13145152 3.920000e-134 488.0
21 TraesCS3A01G189100 chr1A 83.579 542 66 10 1 519 303848525 303849066 1.410000e-133 486.0
22 TraesCS3A01G189100 chr2A 81.937 537 75 8 1 519 47363108 47363640 5.180000e-118 435.0
23 TraesCS3A01G189100 chr7B 87.540 313 31 4 1 306 919192 918881 4.150000e-94 355.0
24 TraesCS3A01G189100 chr7B 91.453 117 9 1 991 1106 411385682 411385566 3.490000e-35 159.0
25 TraesCS3A01G189100 chr7B 90.110 91 8 1 3290 3380 186204687 186204598 2.130000e-22 117.0
26 TraesCS3A01G189100 chr2D 86.911 191 15 8 991 1172 85756407 85756218 4.420000e-49 206.0
27 TraesCS3A01G189100 chr2D 87.162 148 4 4 1355 1502 85756288 85756156 1.620000e-33 154.0
28 TraesCS3A01G189100 chr2D 90.110 91 7 1 3290 3380 366246682 366246770 2.130000e-22 117.0
29 TraesCS3A01G189100 chr2D 96.552 58 2 0 1656 1713 85755800 85755743 2.780000e-16 97.1
30 TraesCS3A01G189100 chr2D 97.727 44 1 0 476 519 618873827 618873870 3.620000e-10 76.8
31 TraesCS3A01G189100 chr5D 92.308 91 6 1 3290 3380 36865356 36865445 9.840000e-26 128.0
32 TraesCS3A01G189100 chr5D 92.308 91 6 1 3290 3380 494499777 494499866 9.840000e-26 128.0
33 TraesCS3A01G189100 chr5D 91.209 91 7 1 3290 3380 91300997 91301086 4.580000e-24 122.0
34 TraesCS3A01G189100 chr5D 90.110 91 7 1 3290 3380 296556737 296556649 2.130000e-22 117.0
35 TraesCS3A01G189100 chr1B 83.898 118 17 2 379 495 390871528 390871644 9.910000e-21 111.0
36 TraesCS3A01G189100 chr4A 90.909 44 4 0 476 519 600388640 600388597 3.640000e-05 60.2


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 TraesCS3A01G189100 chr3A 231039019 231042398 3379 False 6242.000000 6242 100.000000 1 3380 1 chr3A.!!$F1 3379
1 TraesCS3A01G189100 chr3D 182349884 182352687 2803 True 1122.333333 2854 88.332000 632 3121 3 chr3D.!!$R3 2489
2 TraesCS3A01G189100 chr3B 260847719 260850053 2334 True 1128.666667 2518 91.768333 1070 3291 3 chr3B.!!$R2 2221
3 TraesCS3A01G189100 chr4D 465072902 465073419 517 True 564.000000 564 86.476000 1 519 1 chr4D.!!$R2 518
4 TraesCS3A01G189100 chr4D 67355267 67355769 502 True 508.000000 508 85.347000 1 492 1 chr4D.!!$R1 491
5 TraesCS3A01G189100 chr1D 292514672 292515194 522 True 542.000000 542 85.551000 1 519 1 chr1D.!!$R1 518
6 TraesCS3A01G189100 chr1D 437470377 437470921 544 False 484.000000 484 83.516000 1 519 1 chr1D.!!$F1 518
7 TraesCS3A01G189100 chr7A 500566186 500566747 561 False 521.000000 521 84.183000 1 543 1 chr7A.!!$F1 542
8 TraesCS3A01G189100 chr7D 563346133 563346669 536 False 499.000000 499 84.015000 1 519 1 chr7D.!!$F1 518
9 TraesCS3A01G189100 chr6D 13144628 13145152 524 False 488.000000 488 83.619000 1 519 1 chr6D.!!$F1 518
10 TraesCS3A01G189100 chr1A 303848525 303849066 541 False 486.000000 486 83.579000 1 519 1 chr1A.!!$F1 518
11 TraesCS3A01G189100 chr2A 47363108 47363640 532 False 435.000000 435 81.937000 1 519 1 chr2A.!!$F1 518

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
576 653 0.036306 AAGCGACGTCCCATTTTCCT 59.964 50.0 10.58 0.0 0.00 3.36 F
578 655 0.672401 GCGACGTCCCATTTTCCTGA 60.672 55.0 10.58 0.0 0.00 3.86 F
1983 2341 0.873312 TCATTCAGATCGAGCAGCGC 60.873 55.0 2.38 0.0 40.61 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2396 0.745845 GTGTGCTCCTCATTGGCGAT 60.746 55.000 0.00 0.0 35.26 4.58 R
2329 2687 2.083774 GACAACGAATGGCTCCATCAA 58.916 47.619 1.31 0.0 35.31 2.57 R
3328 3878 0.322456 TTACAGGATGGCAGGCACAC 60.322 55.000 0.00 0.0 43.62 3.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.654877 GACGAGTCCGCCCTCAAA 59.345 61.111 0.00 0.00 39.95 2.69
44 45 0.323360 CCCTCAAATGGGCGAAGGAA 60.323 55.000 0.00 0.00 40.84 3.36
159 160 2.282251 ACAGCGACGAGGAGGACA 60.282 61.111 0.00 0.00 0.00 4.02
313 383 0.889994 TGTAGACGGCGGCTTTTAGA 59.110 50.000 25.39 0.00 0.00 2.10
395 468 4.481930 TCGTCGAGTTCATGCAAAAATT 57.518 36.364 0.00 0.00 0.00 1.82
446 519 3.751246 CGAACCCGCGGTGACCTA 61.751 66.667 26.12 0.00 35.34 3.08
519 594 1.602237 CCCTCAGGCCGCTCTTTTA 59.398 57.895 0.00 0.00 0.00 1.52
523 598 0.249398 TCAGGCCGCTCTTTTAGACC 59.751 55.000 0.00 0.00 0.00 3.85
524 599 1.084370 CAGGCCGCTCTTTTAGACCG 61.084 60.000 0.00 0.00 0.00 4.79
525 600 1.217244 GGCCGCTCTTTTAGACCGA 59.783 57.895 0.00 0.00 0.00 4.69
539 616 2.227089 GACCGAACGGCTGGAGATGT 62.227 60.000 13.32 0.00 39.32 3.06
543 620 0.179097 GAACGGCTGGAGATGTCCTC 60.179 60.000 10.72 1.99 44.30 3.71
544 621 0.904865 AACGGCTGGAGATGTCCTCA 60.905 55.000 10.72 0.00 44.30 3.86
545 622 1.142748 CGGCTGGAGATGTCCTCAC 59.857 63.158 10.72 0.00 44.30 3.51
546 623 1.524482 GGCTGGAGATGTCCTCACC 59.476 63.158 10.72 5.15 44.30 4.02
547 624 1.267574 GGCTGGAGATGTCCTCACCA 61.268 60.000 10.72 0.00 44.30 4.17
548 625 0.107945 GCTGGAGATGTCCTCACCAC 60.108 60.000 10.72 0.00 44.30 4.16
549 626 0.539051 CTGGAGATGTCCTCACCACC 59.461 60.000 10.72 0.00 44.30 4.61
550 627 0.178906 TGGAGATGTCCTCACCACCA 60.179 55.000 10.72 0.00 44.30 4.17
551 628 0.539051 GGAGATGTCCTCACCACCAG 59.461 60.000 0.54 0.00 43.76 4.00
552 629 0.107945 GAGATGTCCTCACCACCAGC 60.108 60.000 0.00 0.00 41.58 4.85
553 630 1.448540 GATGTCCTCACCACCAGCG 60.449 63.158 0.00 0.00 0.00 5.18
554 631 2.172483 GATGTCCTCACCACCAGCGT 62.172 60.000 0.00 0.00 0.00 5.07
555 632 2.357517 GTCCTCACCACCAGCGTG 60.358 66.667 0.00 0.00 39.91 5.34
556 633 4.314440 TCCTCACCACCAGCGTGC 62.314 66.667 0.00 0.00 38.79 5.34
557 634 4.624364 CCTCACCACCAGCGTGCA 62.624 66.667 0.00 0.00 38.79 4.57
558 635 2.591429 CTCACCACCAGCGTGCAA 60.591 61.111 0.00 0.00 38.79 4.08
559 636 2.591429 TCACCACCAGCGTGCAAG 60.591 61.111 0.00 0.00 38.79 4.01
560 637 4.332637 CACCACCAGCGTGCAAGC 62.333 66.667 17.43 17.43 38.79 4.01
563 640 4.374702 CACCAGCGTGCAAGCGAC 62.375 66.667 18.93 1.41 43.00 5.19
566 643 4.415501 CAGCGTGCAAGCGACGTC 62.416 66.667 18.93 5.18 43.00 4.34
570 647 2.742372 GTGCAAGCGACGTCCCAT 60.742 61.111 10.58 0.00 0.00 4.00
571 648 2.031919 TGCAAGCGACGTCCCATT 59.968 55.556 10.58 0.00 0.00 3.16
572 649 1.599518 TGCAAGCGACGTCCCATTT 60.600 52.632 10.58 0.00 0.00 2.32
573 650 1.169661 TGCAAGCGACGTCCCATTTT 61.170 50.000 10.58 0.00 0.00 1.82
574 651 0.454452 GCAAGCGACGTCCCATTTTC 60.454 55.000 10.58 0.00 0.00 2.29
575 652 0.168128 CAAGCGACGTCCCATTTTCC 59.832 55.000 10.58 0.00 0.00 3.13
576 653 0.036306 AAGCGACGTCCCATTTTCCT 59.964 50.000 10.58 0.00 0.00 3.36
577 654 0.673644 AGCGACGTCCCATTTTCCTG 60.674 55.000 10.58 0.00 0.00 3.86
578 655 0.672401 GCGACGTCCCATTTTCCTGA 60.672 55.000 10.58 0.00 0.00 3.86
579 656 1.359848 CGACGTCCCATTTTCCTGAG 58.640 55.000 10.58 0.00 0.00 3.35
580 657 1.067142 CGACGTCCCATTTTCCTGAGA 60.067 52.381 10.58 0.00 0.00 3.27
581 658 2.418746 CGACGTCCCATTTTCCTGAGAT 60.419 50.000 10.58 0.00 0.00 2.75
582 659 2.939103 GACGTCCCATTTTCCTGAGATG 59.061 50.000 3.51 0.00 0.00 2.90
583 660 2.571653 ACGTCCCATTTTCCTGAGATGA 59.428 45.455 0.00 0.00 0.00 2.92
584 661 3.200825 ACGTCCCATTTTCCTGAGATGAT 59.799 43.478 0.00 0.00 0.00 2.45
585 662 4.408921 ACGTCCCATTTTCCTGAGATGATA 59.591 41.667 0.00 0.00 0.00 2.15
586 663 5.104527 ACGTCCCATTTTCCTGAGATGATAA 60.105 40.000 0.00 0.00 0.00 1.75
587 664 5.822519 CGTCCCATTTTCCTGAGATGATAAA 59.177 40.000 0.00 0.00 0.00 1.40
588 665 6.318648 CGTCCCATTTTCCTGAGATGATAAAA 59.681 38.462 0.00 0.00 0.00 1.52
589 666 7.013655 CGTCCCATTTTCCTGAGATGATAAAAT 59.986 37.037 0.00 0.00 31.67 1.82
590 667 8.699130 GTCCCATTTTCCTGAGATGATAAAATT 58.301 33.333 0.00 0.00 29.66 1.82
591 668 8.917088 TCCCATTTTCCTGAGATGATAAAATTC 58.083 33.333 0.00 0.00 29.66 2.17
592 669 8.921205 CCCATTTTCCTGAGATGATAAAATTCT 58.079 33.333 0.00 0.00 29.66 2.40
593 670 9.745880 CCATTTTCCTGAGATGATAAAATTCTG 57.254 33.333 0.00 0.00 29.66 3.02
598 675 9.519191 TTCCTGAGATGATAAAATTCTGAAACA 57.481 29.630 0.00 0.00 0.00 2.83
599 676 8.950210 TCCTGAGATGATAAAATTCTGAAACAC 58.050 33.333 0.00 0.00 0.00 3.32
600 677 8.186821 CCTGAGATGATAAAATTCTGAAACACC 58.813 37.037 0.00 0.00 0.00 4.16
601 678 8.868522 TGAGATGATAAAATTCTGAAACACCT 57.131 30.769 0.00 0.00 0.00 4.00
602 679 9.958180 TGAGATGATAAAATTCTGAAACACCTA 57.042 29.630 0.00 0.00 0.00 3.08
604 681 8.883731 AGATGATAAAATTCTGAAACACCTACG 58.116 33.333 0.00 0.00 0.00 3.51
605 682 8.786826 ATGATAAAATTCTGAAACACCTACGA 57.213 30.769 0.00 0.00 0.00 3.43
606 683 8.251750 TGATAAAATTCTGAAACACCTACGAG 57.748 34.615 0.00 0.00 0.00 4.18
607 684 8.092068 TGATAAAATTCTGAAACACCTACGAGA 58.908 33.333 0.00 0.00 0.00 4.04
608 685 9.099454 GATAAAATTCTGAAACACCTACGAGAT 57.901 33.333 0.00 0.00 0.00 2.75
610 687 8.842358 AAAATTCTGAAACACCTACGAGATAA 57.158 30.769 0.00 0.00 0.00 1.75
611 688 8.842358 AAATTCTGAAACACCTACGAGATAAA 57.158 30.769 0.00 0.00 0.00 1.40
612 689 8.842358 AATTCTGAAACACCTACGAGATAAAA 57.158 30.769 0.00 0.00 0.00 1.52
613 690 9.449719 AATTCTGAAACACCTACGAGATAAAAT 57.550 29.630 0.00 0.00 0.00 1.82
614 691 8.842358 TTCTGAAACACCTACGAGATAAAATT 57.158 30.769 0.00 0.00 0.00 1.82
615 692 8.475331 TCTGAAACACCTACGAGATAAAATTC 57.525 34.615 0.00 0.00 0.00 2.17
616 693 8.311836 TCTGAAACACCTACGAGATAAAATTCT 58.688 33.333 0.00 0.00 0.00 2.40
617 694 8.251750 TGAAACACCTACGAGATAAAATTCTG 57.748 34.615 0.00 0.00 0.00 3.02
618 695 8.092068 TGAAACACCTACGAGATAAAATTCTGA 58.908 33.333 0.00 0.00 0.00 3.27
619 696 8.480643 AAACACCTACGAGATAAAATTCTGAG 57.519 34.615 0.00 0.00 0.00 3.35
620 697 7.406031 ACACCTACGAGATAAAATTCTGAGA 57.594 36.000 0.00 0.00 0.00 3.27
621 698 7.837863 ACACCTACGAGATAAAATTCTGAGAA 58.162 34.615 0.00 0.00 0.00 2.87
622 699 7.760340 ACACCTACGAGATAAAATTCTGAGAAC 59.240 37.037 0.00 0.00 0.00 3.01
623 700 7.976734 CACCTACGAGATAAAATTCTGAGAACT 59.023 37.037 0.00 0.00 0.00 3.01
624 701 8.532819 ACCTACGAGATAAAATTCTGAGAACTT 58.467 33.333 0.00 0.00 0.00 2.66
625 702 8.812329 CCTACGAGATAAAATTCTGAGAACTTG 58.188 37.037 0.00 0.00 0.00 3.16
626 703 7.066374 ACGAGATAAAATTCTGAGAACTTGC 57.934 36.000 0.00 0.00 0.00 4.01
627 704 6.650807 ACGAGATAAAATTCTGAGAACTTGCA 59.349 34.615 0.00 0.00 0.00 4.08
628 705 6.958193 CGAGATAAAATTCTGAGAACTTGCAC 59.042 38.462 0.00 0.00 0.00 4.57
629 706 7.360353 CGAGATAAAATTCTGAGAACTTGCACA 60.360 37.037 0.00 0.00 0.00 4.57
630 707 8.169977 AGATAAAATTCTGAGAACTTGCACAA 57.830 30.769 0.00 0.00 0.00 3.33
673 751 3.677976 CGGATAGCCAAACCTACGAGTTT 60.678 47.826 0.00 0.00 40.57 2.66
713 791 8.166706 CGGCTCGATTAATGTGGTTATTATTAC 58.833 37.037 0.00 0.00 0.00 1.89
714 792 8.995220 GGCTCGATTAATGTGGTTATTATTACA 58.005 33.333 0.00 0.00 0.00 2.41
719 798 9.612620 GATTAATGTGGTTATTATTACAGCAGC 57.387 33.333 0.00 0.00 0.00 5.25
722 801 4.335315 TGTGGTTATTATTACAGCAGCAGC 59.665 41.667 0.00 0.00 42.56 5.25
725 804 4.531332 GTTATTATTACAGCAGCAGCAGC 58.469 43.478 3.17 0.46 45.49 5.25
759 838 7.201539 GGAGTTTTCCTTAGCTAAATCGAACTC 60.202 40.741 25.65 25.65 40.58 3.01
760 839 6.594547 AGTTTTCCTTAGCTAAATCGAACTCC 59.405 38.462 7.74 1.53 0.00 3.85
761 840 4.667519 TCCTTAGCTAAATCGAACTCCC 57.332 45.455 7.74 0.00 0.00 4.30
762 841 4.287552 TCCTTAGCTAAATCGAACTCCCT 58.712 43.478 7.74 0.00 0.00 4.20
763 842 4.099573 TCCTTAGCTAAATCGAACTCCCTG 59.900 45.833 7.74 0.00 0.00 4.45
764 843 2.990066 AGCTAAATCGAACTCCCTGG 57.010 50.000 0.00 0.00 0.00 4.45
765 844 2.188817 AGCTAAATCGAACTCCCTGGT 58.811 47.619 0.00 0.00 0.00 4.00
766 845 2.093447 AGCTAAATCGAACTCCCTGGTG 60.093 50.000 0.00 0.00 0.00 4.17
767 846 2.093658 GCTAAATCGAACTCCCTGGTGA 60.094 50.000 0.00 0.00 0.00 4.02
768 847 2.770164 AAATCGAACTCCCTGGTGAG 57.230 50.000 9.73 9.73 38.37 3.51
801 1149 6.461927 CCATTTGGGAAGTCCATATTGACATG 60.462 42.308 9.43 0.00 46.52 3.21
803 1151 3.202818 TGGGAAGTCCATATTGACATGCT 59.797 43.478 9.43 0.00 41.46 3.79
804 1152 4.411869 TGGGAAGTCCATATTGACATGCTA 59.588 41.667 9.43 0.00 41.46 3.49
805 1153 4.999950 GGGAAGTCCATATTGACATGCTAG 59.000 45.833 9.43 0.00 37.73 3.42
806 1154 5.455326 GGGAAGTCCATATTGACATGCTAGT 60.455 44.000 9.43 0.00 37.73 2.57
807 1155 5.698545 GGAAGTCCATATTGACATGCTAGTC 59.301 44.000 9.43 2.66 37.73 2.59
808 1156 4.876125 AGTCCATATTGACATGCTAGTCG 58.124 43.478 9.43 0.00 41.41 4.18
809 1157 4.584743 AGTCCATATTGACATGCTAGTCGA 59.415 41.667 9.43 2.23 41.41 4.20
810 1158 4.920340 GTCCATATTGACATGCTAGTCGAG 59.080 45.833 2.13 0.00 41.41 4.04
811 1159 4.584743 TCCATATTGACATGCTAGTCGAGT 59.415 41.667 0.00 0.00 41.41 4.18
812 1160 4.683320 CCATATTGACATGCTAGTCGAGTG 59.317 45.833 2.10 0.00 41.41 3.51
813 1161 5.507985 CCATATTGACATGCTAGTCGAGTGA 60.508 44.000 2.10 0.00 41.41 3.41
814 1162 3.934457 TTGACATGCTAGTCGAGTGAA 57.066 42.857 2.10 0.00 41.41 3.18
815 1163 3.934457 TGACATGCTAGTCGAGTGAAA 57.066 42.857 2.10 0.00 41.41 2.69
832 1180 6.249893 CGAGTGAAATATTGAACATTGCACAG 59.750 38.462 9.76 0.19 42.27 3.66
833 1181 6.392354 AGTGAAATATTGAACATTGCACAGG 58.608 36.000 9.76 0.00 42.27 4.00
834 1182 6.209192 AGTGAAATATTGAACATTGCACAGGA 59.791 34.615 9.76 0.00 42.27 3.86
835 1183 6.867816 GTGAAATATTGAACATTGCACAGGAA 59.132 34.615 2.49 0.00 40.37 3.36
836 1184 6.867816 TGAAATATTGAACATTGCACAGGAAC 59.132 34.615 0.00 0.00 0.00 3.62
837 1185 5.981088 ATATTGAACATTGCACAGGAACA 57.019 34.783 0.00 0.00 0.00 3.18
838 1186 3.435105 TTGAACATTGCACAGGAACAC 57.565 42.857 0.00 0.00 0.00 3.32
846 1194 1.400142 TGCACAGGAACACGAGTTTTG 59.600 47.619 0.00 4.87 38.30 2.44
856 1204 1.082104 CGAGTTTTGCAGGGAACGC 60.082 57.895 0.00 0.00 0.00 4.84
870 1218 1.060726 GAACGCGTGAGAGTGAGTCG 61.061 60.000 14.98 0.00 45.70 4.18
904 1252 2.513895 CACCACCAAACCCTCCGT 59.486 61.111 0.00 0.00 0.00 4.69
905 1253 1.896660 CACCACCAAACCCTCCGTG 60.897 63.158 0.00 0.00 0.00 4.94
906 1254 2.983592 CCACCAAACCCTCCGTGC 60.984 66.667 0.00 0.00 0.00 5.34
907 1255 3.353836 CACCAAACCCTCCGTGCG 61.354 66.667 0.00 0.00 0.00 5.34
909 1257 2.742372 CCAAACCCTCCGTGCGAG 60.742 66.667 0.00 0.00 38.46 5.03
1077 1435 4.463879 CTGGGCGAGGAGGTGCTG 62.464 72.222 0.00 0.00 0.00 4.41
1488 1846 2.971452 GGCGTCCTCTCCGTCTTT 59.029 61.111 0.00 0.00 0.00 2.52
1916 2274 3.019564 ACATGGCTACCTCAAATCAAGC 58.980 45.455 0.00 0.00 0.00 4.01
1949 2307 4.081406 CAGACATCAAATCAAGGTGGGAA 58.919 43.478 0.00 0.00 0.00 3.97
1950 2308 4.708421 CAGACATCAAATCAAGGTGGGAAT 59.292 41.667 0.00 0.00 0.00 3.01
1983 2341 0.873312 TCATTCAGATCGAGCAGCGC 60.873 55.000 2.38 0.00 40.61 5.92
1984 2342 1.948138 ATTCAGATCGAGCAGCGCG 60.948 57.895 12.95 12.95 40.61 6.86
1989 2347 4.263209 ATCGAGCAGCGCGAGGAG 62.263 66.667 25.48 0.00 39.20 3.69
2038 2396 1.302949 GCATCTGCCAACCCTACCA 59.697 57.895 0.00 0.00 34.31 3.25
2055 2413 1.442526 CCATCGCCAATGAGGAGCAC 61.443 60.000 0.00 0.00 41.22 4.40
2329 2687 1.338973 TCTACTTCTTGACGCGGTTGT 59.661 47.619 12.47 1.72 0.00 3.32
2399 2757 6.682746 TCTGAGTTCTGACTAATGTTCTGTC 58.317 40.000 0.00 0.00 35.88 3.51
2402 2760 5.844004 AGTTCTGACTAATGTTCTGTCGTT 58.156 37.500 0.00 0.00 33.32 3.85
2425 2783 4.201901 TGTTGTTACATGTGTGTCAAGCTG 60.202 41.667 9.11 0.00 39.77 4.24
2434 2792 2.854185 GTGTGTCAAGCTGAAAAGCAAC 59.146 45.455 0.00 0.00 37.25 4.17
2437 2795 2.754552 TGTCAAGCTGAAAAGCAACTGT 59.245 40.909 0.00 0.00 37.25 3.55
2476 2834 4.443394 GTGACTACTACTTTGTTGGTCACG 59.557 45.833 0.00 0.00 39.69 4.35
2543 2901 8.705594 TCATTGGGACTTTAGACTCTTATAAGG 58.294 37.037 12.54 6.10 0.00 2.69
2544 2902 8.487028 CATTGGGACTTTAGACTCTTATAAGGT 58.513 37.037 12.54 9.12 0.00 3.50
2547 2905 8.342270 TGGGACTTTAGACTCTTATAAGGTAGT 58.658 37.037 12.54 9.31 0.00 2.73
2593 2955 5.502153 AGTCCATGTCTTGTCGTATAGTC 57.498 43.478 0.00 0.00 0.00 2.59
2594 2956 4.948004 AGTCCATGTCTTGTCGTATAGTCA 59.052 41.667 0.00 0.00 0.00 3.41
2595 2957 5.066634 AGTCCATGTCTTGTCGTATAGTCAG 59.933 44.000 0.00 0.00 0.00 3.51
2596 2958 4.948004 TCCATGTCTTGTCGTATAGTCAGT 59.052 41.667 0.00 0.00 0.00 3.41
2598 2960 6.071560 TCCATGTCTTGTCGTATAGTCAGTTT 60.072 38.462 0.00 0.00 0.00 2.66
2599 2961 6.590292 CCATGTCTTGTCGTATAGTCAGTTTT 59.410 38.462 0.00 0.00 0.00 2.43
2632 3027 9.356929 GTTTCAATTTTTATTCTTGCGTTCTTG 57.643 29.630 0.00 0.00 0.00 3.02
2635 3030 9.092876 TCAATTTTTATTCTTGCGTTCTTGTTT 57.907 25.926 0.00 0.00 0.00 2.83
2664 3059 3.564644 TCTCGCGTTCTCCCTTAGATTAG 59.435 47.826 5.77 0.00 33.05 1.73
2665 3060 3.285484 TCGCGTTCTCCCTTAGATTAGT 58.715 45.455 5.77 0.00 33.05 2.24
2667 3062 3.066342 CGCGTTCTCCCTTAGATTAGTGA 59.934 47.826 0.00 0.00 33.05 3.41
2668 3063 4.261656 CGCGTTCTCCCTTAGATTAGTGAT 60.262 45.833 0.00 0.00 33.05 3.06
2670 3065 6.514541 CGCGTTCTCCCTTAGATTAGTGATAA 60.515 42.308 0.00 0.00 33.05 1.75
2710 3119 9.723601 ATCTGCCTGCAATTTTCTTTTATTTTA 57.276 25.926 0.00 0.00 0.00 1.52
2743 3152 9.214957 TGTCTGGTATTGTTTCTTACATTGTAG 57.785 33.333 0.00 0.00 36.44 2.74
2829 3260 4.119136 GTGCAGCACTTGGTAATTTTTGT 58.881 39.130 18.92 0.00 0.00 2.83
2871 3302 3.706594 GACTGACCATATTCCTCCTGTCA 59.293 47.826 0.00 0.00 0.00 3.58
2921 3372 5.961272 TGGTTTTGTTTGTCTTTTCTCCTC 58.039 37.500 0.00 0.00 0.00 3.71
2940 3391 5.419542 TCCTCGTATTCAAATTCAGGAGTG 58.580 41.667 0.00 0.00 0.00 3.51
2963 3512 2.540101 CGTTTTGAGTGAGTGTCCAGAC 59.460 50.000 0.00 0.00 0.00 3.51
2983 3532 6.016777 CCAGACAAGAGTAACAAAATCAAGCT 60.017 38.462 0.00 0.00 0.00 3.74
3019 3569 4.747810 AGGTGCTTATTTTACTGCATTGC 58.252 39.130 0.46 0.46 37.76 3.56
3025 3575 5.722051 GCTTATTTTACTGCATTGCGCTTTG 60.722 40.000 9.73 7.42 43.06 2.77
3044 3594 5.757886 CTTTGTGTTGTTTATCATGGACGT 58.242 37.500 0.00 0.00 0.00 4.34
3091 3641 7.813148 TGTATTTAGTTGTAGTGAGCAGAAGTC 59.187 37.037 0.00 0.00 0.00 3.01
3095 3645 1.813178 TGTAGTGAGCAGAAGTCCTCG 59.187 52.381 0.00 0.00 0.00 4.63
3096 3646 2.085320 GTAGTGAGCAGAAGTCCTCGA 58.915 52.381 0.00 0.00 0.00 4.04
3108 3658 3.926821 AGTCCTCGAGAGTCTTTTGTC 57.073 47.619 15.71 0.00 0.00 3.18
3111 3661 2.621998 TCCTCGAGAGTCTTTTGTCGTT 59.378 45.455 15.71 0.00 34.07 3.85
3112 3662 3.817084 TCCTCGAGAGTCTTTTGTCGTTA 59.183 43.478 15.71 0.00 34.07 3.18
3119 3669 3.537580 AGTCTTTTGTCGTTACCTTGCA 58.462 40.909 0.00 0.00 0.00 4.08
3125 3675 1.468127 TGTCGTTACCTTGCATGCATG 59.532 47.619 23.37 23.21 0.00 4.06
3167 3717 7.392393 ACATGCATGCATACATACATTCAGTAT 59.608 33.333 31.73 2.53 38.05 2.12
3198 3748 5.527951 CAGCGAATCTACTAGGAGTACTTGA 59.472 44.000 0.78 0.00 0.00 3.02
3199 3749 5.761234 AGCGAATCTACTAGGAGTACTTGAG 59.239 44.000 0.78 0.00 0.00 3.02
3211 3761 4.865365 GGAGTACTTGAGCTGTACATGTTC 59.135 45.833 2.30 0.00 41.76 3.18
3216 3766 4.516698 ACTTGAGCTGTACATGTTCTTTGG 59.483 41.667 2.30 0.00 0.00 3.28
3217 3767 3.411446 TGAGCTGTACATGTTCTTTGGG 58.589 45.455 2.30 0.00 0.00 4.12
3220 3770 0.878416 TGTACATGTTCTTTGGGCGC 59.122 50.000 2.30 0.00 0.00 6.53
3227 3777 1.600636 TTCTTTGGGCGCCTGTCTG 60.601 57.895 28.56 13.12 0.00 3.51
3256 3806 2.456119 CGGCTGGCTCAACGTCATC 61.456 63.158 0.00 0.00 0.00 2.92
3280 3830 4.023021 TGGTTAGGGTATTTGTTTTCGTGC 60.023 41.667 0.00 0.00 0.00 5.34
3286 3836 4.151512 GGGTATTTGTTTTCGTGCCATTTG 59.848 41.667 0.00 0.00 0.00 2.32
3287 3837 4.985409 GGTATTTGTTTTCGTGCCATTTGA 59.015 37.500 0.00 0.00 0.00 2.69
3288 3838 5.107645 GGTATTTGTTTTCGTGCCATTTGAC 60.108 40.000 0.00 0.00 0.00 3.18
3289 3839 3.510388 TTGTTTTCGTGCCATTTGACA 57.490 38.095 0.00 0.00 0.00 3.58
3290 3840 3.724508 TGTTTTCGTGCCATTTGACAT 57.275 38.095 0.00 0.00 0.00 3.06
3291 3841 3.637432 TGTTTTCGTGCCATTTGACATC 58.363 40.909 0.00 0.00 0.00 3.06
3292 3842 3.317711 TGTTTTCGTGCCATTTGACATCT 59.682 39.130 0.00 0.00 0.00 2.90
3293 3843 3.829886 TTTCGTGCCATTTGACATCTC 57.170 42.857 0.00 0.00 0.00 2.75
3294 3844 2.768253 TCGTGCCATTTGACATCTCT 57.232 45.000 0.00 0.00 0.00 3.10
3295 3845 3.057969 TCGTGCCATTTGACATCTCTT 57.942 42.857 0.00 0.00 0.00 2.85
3296 3846 3.411446 TCGTGCCATTTGACATCTCTTT 58.589 40.909 0.00 0.00 0.00 2.52
3297 3847 3.820467 TCGTGCCATTTGACATCTCTTTT 59.180 39.130 0.00 0.00 0.00 2.27
3298 3848 4.083324 TCGTGCCATTTGACATCTCTTTTC 60.083 41.667 0.00 0.00 0.00 2.29
3299 3849 4.083110 CGTGCCATTTGACATCTCTTTTCT 60.083 41.667 0.00 0.00 0.00 2.52
3300 3850 5.563475 CGTGCCATTTGACATCTCTTTTCTT 60.563 40.000 0.00 0.00 0.00 2.52
3301 3851 6.348458 CGTGCCATTTGACATCTCTTTTCTTA 60.348 38.462 0.00 0.00 0.00 2.10
3302 3852 7.542025 GTGCCATTTGACATCTCTTTTCTTAT 58.458 34.615 0.00 0.00 0.00 1.73
3303 3853 8.677300 GTGCCATTTGACATCTCTTTTCTTATA 58.323 33.333 0.00 0.00 0.00 0.98
3304 3854 9.241919 TGCCATTTGACATCTCTTTTCTTATAA 57.758 29.630 0.00 0.00 0.00 0.98
3327 3877 4.627611 AAAAGCGGAGTTGATGATGATG 57.372 40.909 0.00 0.00 0.00 3.07
3328 3878 2.251409 AGCGGAGTTGATGATGATGG 57.749 50.000 0.00 0.00 0.00 3.51
3329 3879 1.487976 AGCGGAGTTGATGATGATGGT 59.512 47.619 0.00 0.00 0.00 3.55
3330 3880 1.600957 GCGGAGTTGATGATGATGGTG 59.399 52.381 0.00 0.00 0.00 4.17
3331 3881 2.910199 CGGAGTTGATGATGATGGTGT 58.090 47.619 0.00 0.00 0.00 4.16
3332 3882 2.610833 CGGAGTTGATGATGATGGTGTG 59.389 50.000 0.00 0.00 0.00 3.82
3333 3883 2.357009 GGAGTTGATGATGATGGTGTGC 59.643 50.000 0.00 0.00 0.00 4.57
3334 3884 2.357009 GAGTTGATGATGATGGTGTGCC 59.643 50.000 0.00 0.00 0.00 5.01
3335 3885 2.025605 AGTTGATGATGATGGTGTGCCT 60.026 45.455 0.00 0.00 35.27 4.75
3336 3886 2.047002 TGATGATGATGGTGTGCCTG 57.953 50.000 0.00 0.00 35.27 4.85
3337 3887 0.666913 GATGATGATGGTGTGCCTGC 59.333 55.000 0.00 0.00 35.27 4.85
3338 3888 0.754217 ATGATGATGGTGTGCCTGCC 60.754 55.000 0.00 0.00 35.27 4.85
3339 3889 1.378911 GATGATGGTGTGCCTGCCA 60.379 57.895 0.00 0.00 39.33 4.92
3342 3892 2.043652 ATGGTGTGCCTGCCATCC 60.044 61.111 0.00 0.00 41.24 3.51
3343 3893 2.619446 ATGGTGTGCCTGCCATCCT 61.619 57.895 0.00 0.00 41.24 3.24
3344 3894 2.753043 GGTGTGCCTGCCATCCTG 60.753 66.667 0.00 0.00 0.00 3.86
3345 3895 2.034687 GTGTGCCTGCCATCCTGT 59.965 61.111 0.00 0.00 0.00 4.00
3346 3896 1.299648 GTGTGCCTGCCATCCTGTA 59.700 57.895 0.00 0.00 0.00 2.74
3347 3897 0.322456 GTGTGCCTGCCATCCTGTAA 60.322 55.000 0.00 0.00 0.00 2.41
3348 3898 0.625316 TGTGCCTGCCATCCTGTAAT 59.375 50.000 0.00 0.00 0.00 1.89
3349 3899 1.843206 TGTGCCTGCCATCCTGTAATA 59.157 47.619 0.00 0.00 0.00 0.98
3350 3900 2.442878 TGTGCCTGCCATCCTGTAATAT 59.557 45.455 0.00 0.00 0.00 1.28
3351 3901 3.650461 TGTGCCTGCCATCCTGTAATATA 59.350 43.478 0.00 0.00 0.00 0.86
3352 3902 4.256920 GTGCCTGCCATCCTGTAATATAG 58.743 47.826 0.00 0.00 0.00 1.31
3353 3903 4.020218 GTGCCTGCCATCCTGTAATATAGA 60.020 45.833 0.00 0.00 0.00 1.98
3354 3904 4.020218 TGCCTGCCATCCTGTAATATAGAC 60.020 45.833 0.00 0.00 0.00 2.59
3355 3905 4.223923 GCCTGCCATCCTGTAATATAGACT 59.776 45.833 0.00 0.00 0.00 3.24
3356 3906 5.728471 CCTGCCATCCTGTAATATAGACTG 58.272 45.833 0.00 0.00 0.00 3.51
3357 3907 5.247110 CCTGCCATCCTGTAATATAGACTGT 59.753 44.000 0.00 0.00 0.00 3.55
3358 3908 6.346477 TGCCATCCTGTAATATAGACTGTC 57.654 41.667 0.00 0.00 0.00 3.51
3359 3909 5.246203 TGCCATCCTGTAATATAGACTGTCC 59.754 44.000 3.76 0.00 0.00 4.02
3360 3910 5.622460 GCCATCCTGTAATATAGACTGTCCG 60.622 48.000 3.76 0.00 0.00 4.79
3361 3911 5.710567 CCATCCTGTAATATAGACTGTCCGA 59.289 44.000 3.76 0.00 0.00 4.55
3362 3912 6.378564 CCATCCTGTAATATAGACTGTCCGAT 59.621 42.308 3.76 1.21 0.00 4.18
3363 3913 7.093727 CCATCCTGTAATATAGACTGTCCGATT 60.094 40.741 3.76 4.66 0.00 3.34
3364 3914 7.834881 TCCTGTAATATAGACTGTCCGATTT 57.165 36.000 3.76 0.00 0.00 2.17
3365 3915 8.929260 TCCTGTAATATAGACTGTCCGATTTA 57.071 34.615 3.76 0.00 0.00 1.40
3366 3916 9.529823 TCCTGTAATATAGACTGTCCGATTTAT 57.470 33.333 3.76 0.00 0.00 1.40
3374 3924 6.003234 AGACTGTCCGATTTATATCTCACG 57.997 41.667 3.76 0.00 0.00 4.35
3375 3925 5.048643 AGACTGTCCGATTTATATCTCACGG 60.049 44.000 3.76 0.00 41.39 4.94
3376 3926 4.825634 ACTGTCCGATTTATATCTCACGGA 59.174 41.667 0.00 0.00 45.36 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.103263 GACATAGTCTTCCTTCGCCCAT 59.897 50.000 0.00 0.00 0.00 4.00
44 45 0.743688 CCTGCTCGCAGACATAGTCT 59.256 55.000 19.78 0.00 46.30 3.24
117 118 2.893398 GATGACGTCGCCCTCCTT 59.107 61.111 11.62 0.00 0.00 3.36
302 320 1.003866 CTACGCCAATCTAAAAGCCGC 60.004 52.381 0.00 0.00 0.00 6.53
313 383 0.461339 CCACGCCTAACTACGCCAAT 60.461 55.000 0.00 0.00 0.00 3.16
372 444 3.454042 TTTTGCATGAACTCGACGATG 57.546 42.857 0.00 0.00 0.00 3.84
395 468 6.024049 CGTTTAAATTTTTGCAAACTTGGCA 58.976 32.000 12.39 0.00 40.00 4.92
415 488 1.292992 GGTTCGGCGATATTCCGTTT 58.707 50.000 11.76 0.00 46.49 3.60
440 513 2.043752 TCGTCGGCCCATAGGTCA 60.044 61.111 0.00 0.00 37.79 4.02
474 547 1.077068 CGCTAAATTGGCCCCTGGA 60.077 57.895 0.00 0.00 0.00 3.86
519 594 1.682684 ATCTCCAGCCGTTCGGTCT 60.683 57.895 12.81 7.58 0.00 3.85
523 598 1.519455 GGACATCTCCAGCCGTTCG 60.519 63.158 0.00 0.00 36.42 3.95
524 599 0.179097 GAGGACATCTCCAGCCGTTC 60.179 60.000 0.00 0.00 39.39 3.95
525 600 0.904865 TGAGGACATCTCCAGCCGTT 60.905 55.000 0.00 0.00 41.76 4.44
539 616 4.314440 GCACGCTGGTGGTGAGGA 62.314 66.667 0.00 0.00 44.54 3.71
543 620 4.332637 GCTTGCACGCTGGTGGTG 62.333 66.667 8.12 0.00 44.54 4.17
549 626 4.415501 GACGTCGCTTGCACGCTG 62.416 66.667 13.78 7.11 41.10 5.18
553 630 1.852067 AAATGGGACGTCGCTTGCAC 61.852 55.000 29.62 5.71 0.00 4.57
554 631 1.169661 AAAATGGGACGTCGCTTGCA 61.170 50.000 29.62 12.90 0.00 4.08
555 632 0.454452 GAAAATGGGACGTCGCTTGC 60.454 55.000 29.62 14.26 0.00 4.01
556 633 0.168128 GGAAAATGGGACGTCGCTTG 59.832 55.000 29.62 0.00 0.00 4.01
557 634 0.036306 AGGAAAATGGGACGTCGCTT 59.964 50.000 29.62 22.16 0.00 4.68
558 635 0.673644 CAGGAAAATGGGACGTCGCT 60.674 55.000 29.62 12.57 0.00 4.93
559 636 0.672401 TCAGGAAAATGGGACGTCGC 60.672 55.000 24.41 24.41 0.00 5.19
560 637 1.067142 TCTCAGGAAAATGGGACGTCG 60.067 52.381 9.92 0.00 0.00 5.12
561 638 2.762535 TCTCAGGAAAATGGGACGTC 57.237 50.000 7.13 7.13 0.00 4.34
562 639 2.571653 TCATCTCAGGAAAATGGGACGT 59.428 45.455 0.00 0.00 30.90 4.34
563 640 3.266510 TCATCTCAGGAAAATGGGACG 57.733 47.619 0.00 0.00 30.90 4.79
564 641 7.645058 TTTTATCATCTCAGGAAAATGGGAC 57.355 36.000 0.00 0.00 30.90 4.46
565 642 8.843308 AATTTTATCATCTCAGGAAAATGGGA 57.157 30.769 0.00 0.00 33.22 4.37
566 643 8.921205 AGAATTTTATCATCTCAGGAAAATGGG 58.079 33.333 0.00 0.00 31.77 4.00
567 644 9.745880 CAGAATTTTATCATCTCAGGAAAATGG 57.254 33.333 0.00 0.00 31.77 3.16
572 649 9.519191 TGTTTCAGAATTTTATCATCTCAGGAA 57.481 29.630 0.00 0.00 0.00 3.36
573 650 8.950210 GTGTTTCAGAATTTTATCATCTCAGGA 58.050 33.333 0.00 0.00 0.00 3.86
574 651 8.186821 GGTGTTTCAGAATTTTATCATCTCAGG 58.813 37.037 0.00 0.00 0.00 3.86
575 652 8.954350 AGGTGTTTCAGAATTTTATCATCTCAG 58.046 33.333 0.00 0.00 0.00 3.35
576 653 8.868522 AGGTGTTTCAGAATTTTATCATCTCA 57.131 30.769 0.00 0.00 0.00 3.27
578 655 8.883731 CGTAGGTGTTTCAGAATTTTATCATCT 58.116 33.333 0.00 0.00 0.00 2.90
579 656 8.879759 TCGTAGGTGTTTCAGAATTTTATCATC 58.120 33.333 0.00 0.00 0.00 2.92
580 657 8.786826 TCGTAGGTGTTTCAGAATTTTATCAT 57.213 30.769 0.00 0.00 0.00 2.45
581 658 8.092068 TCTCGTAGGTGTTTCAGAATTTTATCA 58.908 33.333 0.00 0.00 0.00 2.15
582 659 8.475331 TCTCGTAGGTGTTTCAGAATTTTATC 57.525 34.615 0.00 0.00 0.00 1.75
584 661 9.932207 TTATCTCGTAGGTGTTTCAGAATTTTA 57.068 29.630 0.00 0.00 0.00 1.52
585 662 8.842358 TTATCTCGTAGGTGTTTCAGAATTTT 57.158 30.769 0.00 0.00 0.00 1.82
586 663 8.842358 TTTATCTCGTAGGTGTTTCAGAATTT 57.158 30.769 0.00 0.00 0.00 1.82
587 664 8.842358 TTTTATCTCGTAGGTGTTTCAGAATT 57.158 30.769 0.00 0.00 0.00 2.17
588 665 9.449719 AATTTTATCTCGTAGGTGTTTCAGAAT 57.550 29.630 0.00 0.00 0.00 2.40
589 666 8.842358 AATTTTATCTCGTAGGTGTTTCAGAA 57.158 30.769 0.00 0.00 0.00 3.02
590 667 8.311836 AGAATTTTATCTCGTAGGTGTTTCAGA 58.688 33.333 0.00 0.00 0.00 3.27
591 668 8.383619 CAGAATTTTATCTCGTAGGTGTTTCAG 58.616 37.037 0.00 0.00 0.00 3.02
592 669 8.092068 TCAGAATTTTATCTCGTAGGTGTTTCA 58.908 33.333 0.00 0.00 0.00 2.69
593 670 8.475331 TCAGAATTTTATCTCGTAGGTGTTTC 57.525 34.615 0.00 0.00 0.00 2.78
594 671 8.311836 TCTCAGAATTTTATCTCGTAGGTGTTT 58.688 33.333 0.00 0.00 0.00 2.83
595 672 7.837863 TCTCAGAATTTTATCTCGTAGGTGTT 58.162 34.615 0.00 0.00 0.00 3.32
596 673 7.406031 TCTCAGAATTTTATCTCGTAGGTGT 57.594 36.000 0.00 0.00 0.00 4.16
597 674 7.976734 AGTTCTCAGAATTTTATCTCGTAGGTG 59.023 37.037 0.00 0.00 0.00 4.00
598 675 8.068892 AGTTCTCAGAATTTTATCTCGTAGGT 57.931 34.615 0.00 0.00 0.00 3.08
599 676 8.812329 CAAGTTCTCAGAATTTTATCTCGTAGG 58.188 37.037 0.00 0.00 0.00 3.18
600 677 8.324567 GCAAGTTCTCAGAATTTTATCTCGTAG 58.675 37.037 0.00 0.00 0.00 3.51
601 678 7.817478 TGCAAGTTCTCAGAATTTTATCTCGTA 59.183 33.333 0.00 0.00 0.00 3.43
602 679 6.650807 TGCAAGTTCTCAGAATTTTATCTCGT 59.349 34.615 0.00 0.00 0.00 4.18
603 680 6.958193 GTGCAAGTTCTCAGAATTTTATCTCG 59.042 38.462 0.00 0.00 0.00 4.04
604 681 7.810658 TGTGCAAGTTCTCAGAATTTTATCTC 58.189 34.615 0.00 0.00 0.00 2.75
605 682 7.750229 TGTGCAAGTTCTCAGAATTTTATCT 57.250 32.000 0.00 0.00 0.00 1.98
606 683 8.801715 TTTGTGCAAGTTCTCAGAATTTTATC 57.198 30.769 0.00 0.00 0.00 1.75
607 684 9.034544 GTTTTGTGCAAGTTCTCAGAATTTTAT 57.965 29.630 0.00 0.00 0.00 1.40
608 685 8.031864 TGTTTTGTGCAAGTTCTCAGAATTTTA 58.968 29.630 0.00 0.00 0.00 1.52
609 686 6.873076 TGTTTTGTGCAAGTTCTCAGAATTTT 59.127 30.769 0.00 0.00 0.00 1.82
610 687 6.397272 TGTTTTGTGCAAGTTCTCAGAATTT 58.603 32.000 0.00 0.00 0.00 1.82
611 688 5.964758 TGTTTTGTGCAAGTTCTCAGAATT 58.035 33.333 0.00 0.00 0.00 2.17
612 689 5.581126 TGTTTTGTGCAAGTTCTCAGAAT 57.419 34.783 0.00 0.00 0.00 2.40
613 690 5.384063 TTGTTTTGTGCAAGTTCTCAGAA 57.616 34.783 0.00 0.00 0.00 3.02
614 691 5.384063 TTTGTTTTGTGCAAGTTCTCAGA 57.616 34.783 0.00 0.00 0.00 3.27
615 692 5.443170 CGTTTTGTTTTGTGCAAGTTCTCAG 60.443 40.000 0.00 0.00 0.00 3.35
616 693 4.384247 CGTTTTGTTTTGTGCAAGTTCTCA 59.616 37.500 0.00 0.00 0.00 3.27
617 694 4.720946 GCGTTTTGTTTTGTGCAAGTTCTC 60.721 41.667 0.00 0.00 0.00 2.87
618 695 3.122780 GCGTTTTGTTTTGTGCAAGTTCT 59.877 39.130 0.00 0.00 0.00 3.01
619 696 3.403670 GCGTTTTGTTTTGTGCAAGTTC 58.596 40.909 0.00 0.00 0.00 3.01
620 697 2.159907 CGCGTTTTGTTTTGTGCAAGTT 60.160 40.909 0.00 0.00 0.00 2.66
621 698 1.388431 CGCGTTTTGTTTTGTGCAAGT 59.612 42.857 0.00 0.00 0.00 3.16
622 699 1.388431 ACGCGTTTTGTTTTGTGCAAG 59.612 42.857 5.58 0.00 0.00 4.01
623 700 1.125021 CACGCGTTTTGTTTTGTGCAA 59.875 42.857 10.22 0.00 0.00 4.08
624 701 0.710567 CACGCGTTTTGTTTTGTGCA 59.289 45.000 10.22 0.00 0.00 4.57
625 702 0.985549 TCACGCGTTTTGTTTTGTGC 59.014 45.000 10.22 0.00 0.00 4.57
626 703 3.898005 ATTCACGCGTTTTGTTTTGTG 57.102 38.095 10.22 0.00 0.00 3.33
627 704 3.921021 TCAATTCACGCGTTTTGTTTTGT 59.079 34.783 10.22 0.00 0.00 2.83
628 705 4.491554 TCAATTCACGCGTTTTGTTTTG 57.508 36.364 10.22 8.31 0.00 2.44
629 706 4.085822 CGATCAATTCACGCGTTTTGTTTT 60.086 37.500 10.22 4.27 0.00 2.43
630 707 3.420576 CGATCAATTCACGCGTTTTGTTT 59.579 39.130 10.22 6.63 0.00 2.83
673 751 1.305201 GAGCCGGTGTTTCAGTTCAA 58.695 50.000 1.90 0.00 0.00 2.69
719 798 0.036577 AACTCCTACTGCTGCTGCTG 60.037 55.000 18.66 18.66 42.70 4.41
722 801 2.079925 GGAAAACTCCTACTGCTGCTG 58.920 52.381 4.89 4.89 0.00 4.41
725 804 3.935828 GCTAAGGAAAACTCCTACTGCTG 59.064 47.826 0.00 0.00 39.65 4.41
728 807 7.222999 CGATTTAGCTAAGGAAAACTCCTACTG 59.777 40.741 6.24 0.00 39.65 2.74
731 810 7.414222 TCGATTTAGCTAAGGAAAACTCCTA 57.586 36.000 6.24 0.00 39.65 2.94
745 824 2.093447 CACCAGGGAGTTCGATTTAGCT 60.093 50.000 0.00 0.00 0.00 3.32
759 838 0.692476 TGGACAATGACTCACCAGGG 59.308 55.000 0.00 0.00 0.00 4.45
760 839 2.795231 ATGGACAATGACTCACCAGG 57.205 50.000 0.00 0.00 34.08 4.45
761 840 3.192001 CCAAATGGACAATGACTCACCAG 59.808 47.826 0.00 0.00 37.39 4.00
762 841 3.156293 CCAAATGGACAATGACTCACCA 58.844 45.455 0.00 0.00 37.39 4.17
763 842 2.493278 CCCAAATGGACAATGACTCACC 59.507 50.000 0.00 0.00 37.39 4.02
764 843 3.420893 TCCCAAATGGACAATGACTCAC 58.579 45.455 0.00 0.00 38.61 3.51
765 844 3.805066 TCCCAAATGGACAATGACTCA 57.195 42.857 0.00 0.00 38.61 3.41
766 845 4.082125 ACTTCCCAAATGGACAATGACTC 58.918 43.478 0.00 0.00 45.11 3.36
767 846 4.082125 GACTTCCCAAATGGACAATGACT 58.918 43.478 0.00 0.00 45.11 3.41
768 847 3.193479 GGACTTCCCAAATGGACAATGAC 59.807 47.826 0.00 0.00 45.11 3.06
769 848 3.181424 TGGACTTCCCAAATGGACAATGA 60.181 43.478 0.00 0.00 45.11 2.57
801 1149 6.887376 TGTTCAATATTTCACTCGACTAGC 57.113 37.500 0.00 0.00 0.00 3.42
803 1151 7.333174 TGCAATGTTCAATATTTCACTCGACTA 59.667 33.333 0.00 0.00 0.00 2.59
804 1152 6.149308 TGCAATGTTCAATATTTCACTCGACT 59.851 34.615 0.00 0.00 0.00 4.18
805 1153 6.249260 GTGCAATGTTCAATATTTCACTCGAC 59.751 38.462 3.01 0.00 31.77 4.20
806 1154 6.072783 TGTGCAATGTTCAATATTTCACTCGA 60.073 34.615 10.17 0.00 34.31 4.04
807 1155 6.085573 TGTGCAATGTTCAATATTTCACTCG 58.914 36.000 10.17 0.00 34.31 4.18
808 1156 6.529125 CCTGTGCAATGTTCAATATTTCACTC 59.471 38.462 10.17 0.00 34.31 3.51
809 1157 6.209192 TCCTGTGCAATGTTCAATATTTCACT 59.791 34.615 10.17 0.00 34.31 3.41
810 1158 6.389091 TCCTGTGCAATGTTCAATATTTCAC 58.611 36.000 3.24 3.24 33.97 3.18
811 1159 6.587206 TCCTGTGCAATGTTCAATATTTCA 57.413 33.333 0.00 0.00 0.00 2.69
812 1160 6.867816 TGTTCCTGTGCAATGTTCAATATTTC 59.132 34.615 0.00 0.00 0.00 2.17
813 1161 6.646240 GTGTTCCTGTGCAATGTTCAATATTT 59.354 34.615 0.00 0.00 0.00 1.40
814 1162 6.158598 GTGTTCCTGTGCAATGTTCAATATT 58.841 36.000 0.00 0.00 0.00 1.28
815 1163 5.619757 CGTGTTCCTGTGCAATGTTCAATAT 60.620 40.000 0.00 0.00 0.00 1.28
832 1180 0.310854 CCCTGCAAAACTCGTGTTCC 59.689 55.000 2.94 0.00 34.96 3.62
833 1181 1.305201 TCCCTGCAAAACTCGTGTTC 58.695 50.000 2.94 0.00 34.96 3.18
834 1182 1.404035 GTTCCCTGCAAAACTCGTGTT 59.596 47.619 0.00 0.00 38.16 3.32
835 1183 1.021968 GTTCCCTGCAAAACTCGTGT 58.978 50.000 0.00 0.00 0.00 4.49
836 1184 0.041312 CGTTCCCTGCAAAACTCGTG 60.041 55.000 0.00 0.00 0.00 4.35
837 1185 1.782028 GCGTTCCCTGCAAAACTCGT 61.782 55.000 0.00 0.00 0.00 4.18
838 1186 1.082104 GCGTTCCCTGCAAAACTCG 60.082 57.895 0.00 0.00 0.00 4.18
846 1194 2.811317 CTCTCACGCGTTCCCTGC 60.811 66.667 10.22 0.00 0.00 4.85
856 1204 1.531578 TCAGTTCGACTCACTCTCACG 59.468 52.381 0.00 0.00 0.00 4.35
870 1218 1.605753 GTGGGTGTCCCTTTCAGTTC 58.394 55.000 6.38 0.00 45.70 3.01
931 1288 4.593864 GATCTCGGCCTGGGTCGC 62.594 72.222 8.91 0.00 43.58 5.19
1041 1399 4.736896 GTGTCGAGGACGGTGGCC 62.737 72.222 0.00 0.00 40.21 5.36
1733 2091 2.750135 GCATAGGAGGAGGAAGTCTCGA 60.750 54.545 0.00 0.00 43.34 4.04
1916 2274 2.768253 TGATGTCTGCCCTGTTACAG 57.232 50.000 5.22 5.22 35.15 2.74
1983 2341 1.134175 GCTGTCTCTTCTTCCTCCTCG 59.866 57.143 0.00 0.00 0.00 4.63
1984 2342 2.427095 GAGCTGTCTCTTCTTCCTCCTC 59.573 54.545 0.00 0.00 36.42 3.71
1989 2347 3.269178 CAATGGAGCTGTCTCTTCTTCC 58.731 50.000 0.00 0.00 39.31 3.46
2038 2396 0.745845 GTGTGCTCCTCATTGGCGAT 60.746 55.000 0.00 0.00 35.26 4.58
2055 2413 6.742109 AGGTTCTGATGAAGAAATTTGTGTG 58.258 36.000 0.00 0.00 46.51 3.82
2329 2687 2.083774 GACAACGAATGGCTCCATCAA 58.916 47.619 1.31 0.00 35.31 2.57
2399 2757 4.265949 TGACACACATGTAACAACAACG 57.734 40.909 0.00 0.00 39.95 4.10
2402 2760 3.944650 AGCTTGACACACATGTAACAACA 59.055 39.130 0.00 0.00 39.95 3.33
2425 2783 5.174398 CACATGATGTTCACAGTTGCTTTTC 59.826 40.000 0.00 0.00 0.00 2.29
2434 2792 2.745821 CACTCCCACATGATGTTCACAG 59.254 50.000 0.00 0.00 0.00 3.66
2437 2795 2.639347 AGTCACTCCCACATGATGTTCA 59.361 45.455 0.00 0.00 0.00 3.18
2476 2834 5.646577 ACATGACTGTCTACCTACAAGAC 57.353 43.478 9.51 0.00 43.04 3.01
2543 2901 9.262358 GTTGATCCCAGATAAAACTGATACTAC 57.738 37.037 0.00 0.00 39.94 2.73
2544 2902 9.213777 AGTTGATCCCAGATAAAACTGATACTA 57.786 33.333 0.00 0.00 39.94 1.82
2547 2905 9.213777 ACTAGTTGATCCCAGATAAAACTGATA 57.786 33.333 12.22 0.00 39.94 2.15
2642 3037 2.054232 ATCTAAGGGAGAACGCGAGA 57.946 50.000 15.93 1.02 37.85 4.04
2645 3040 3.066342 TCACTAATCTAAGGGAGAACGCG 59.934 47.826 3.53 3.53 37.85 6.01
2668 3063 9.353431 TGCAGGCAGATTGATAGATTTATTTTA 57.647 29.630 0.00 0.00 0.00 1.52
2670 3065 7.828508 TGCAGGCAGATTGATAGATTTATTT 57.171 32.000 0.00 0.00 0.00 1.40
2710 3119 6.877611 AGAAACAATACCAGACACGAAAAT 57.122 33.333 0.00 0.00 0.00 1.82
2777 3205 7.174599 TGAATTGCCCATAAATGGTTTTCAAAG 59.825 33.333 8.16 0.00 46.65 2.77
2829 3260 8.037758 GTCAGTCCTAGATTCAAATGAGAAAGA 58.962 37.037 0.00 0.00 0.00 2.52
2843 3274 5.077159 AGGAGGAATATGGTCAGTCCTAGAT 59.923 44.000 0.00 0.00 40.67 1.98
2871 3302 3.682696 TCTCAGCTTGTCAATTCATGCT 58.317 40.909 2.70 2.70 45.29 3.79
2921 3372 3.242413 CGCCACTCCTGAATTTGAATACG 60.242 47.826 0.00 0.00 0.00 3.06
2940 3391 0.586802 GGACACTCACTCAAAACGCC 59.413 55.000 0.00 0.00 0.00 5.68
2983 3532 4.705337 AAGCACCTACAACGAACAAAAA 57.295 36.364 0.00 0.00 0.00 1.94
2991 3540 5.106869 TGCAGTAAAATAAGCACCTACAACG 60.107 40.000 0.00 0.00 31.05 4.10
3019 3569 4.616802 GTCCATGATAAACAACACAAAGCG 59.383 41.667 0.00 0.00 0.00 4.68
3025 3575 4.214545 TCCAACGTCCATGATAAACAACAC 59.785 41.667 0.00 0.00 0.00 3.32
3091 3641 2.708386 ACGACAAAAGACTCTCGAGG 57.292 50.000 13.56 5.96 0.00 4.63
3095 3645 4.084485 GCAAGGTAACGACAAAAGACTCTC 60.084 45.833 0.00 0.00 46.39 3.20
3096 3646 3.808174 GCAAGGTAACGACAAAAGACTCT 59.192 43.478 0.00 0.00 46.39 3.24
3145 3695 8.037382 AGAATACTGAATGTATGTATGCATGC 57.963 34.615 11.82 11.82 40.69 4.06
3146 3696 8.663025 GGAGAATACTGAATGTATGTATGCATG 58.337 37.037 10.16 0.00 40.69 4.06
3147 3697 8.600668 AGGAGAATACTGAATGTATGTATGCAT 58.399 33.333 3.79 3.79 40.69 3.96
3148 3698 7.966812 AGGAGAATACTGAATGTATGTATGCA 58.033 34.615 0.00 0.00 40.69 3.96
3149 3699 8.090831 TGAGGAGAATACTGAATGTATGTATGC 58.909 37.037 0.00 0.00 40.69 3.14
3150 3700 9.636879 CTGAGGAGAATACTGAATGTATGTATG 57.363 37.037 0.00 0.00 40.69 2.39
3151 3701 8.310382 GCTGAGGAGAATACTGAATGTATGTAT 58.690 37.037 0.00 0.00 40.69 2.29
3152 3702 7.522236 CGCTGAGGAGAATACTGAATGTATGTA 60.522 40.741 0.00 0.00 40.69 2.29
3153 3703 6.520272 GCTGAGGAGAATACTGAATGTATGT 58.480 40.000 0.00 0.00 40.69 2.29
3154 3704 5.632764 CGCTGAGGAGAATACTGAATGTATG 59.367 44.000 0.00 0.00 40.69 2.39
3155 3705 5.536538 TCGCTGAGGAGAATACTGAATGTAT 59.463 40.000 0.00 0.00 43.19 2.29
3156 3706 4.887655 TCGCTGAGGAGAATACTGAATGTA 59.112 41.667 0.00 0.00 35.37 2.29
3157 3707 3.701542 TCGCTGAGGAGAATACTGAATGT 59.298 43.478 0.00 0.00 0.00 2.71
3167 3717 4.138290 CCTAGTAGATTCGCTGAGGAGAA 58.862 47.826 0.00 0.00 35.86 2.87
3198 3748 2.162681 GCCCAAAGAACATGTACAGCT 58.837 47.619 0.00 0.00 0.00 4.24
3199 3749 1.135689 CGCCCAAAGAACATGTACAGC 60.136 52.381 0.00 0.00 0.00 4.40
3211 3761 1.898574 AACAGACAGGCGCCCAAAG 60.899 57.895 26.15 13.75 0.00 2.77
3216 3766 2.591715 ACACAACAGACAGGCGCC 60.592 61.111 21.89 21.89 0.00 6.53
3217 3767 1.835483 CTCACACAACAGACAGGCGC 61.835 60.000 0.00 0.00 0.00 6.53
3220 3770 1.491670 CGTCTCACACAACAGACAGG 58.508 55.000 0.00 0.00 39.29 4.00
3227 3777 2.607892 GCCAGCCGTCTCACACAAC 61.608 63.158 0.00 0.00 0.00 3.32
3256 3806 5.695818 CACGAAAACAAATACCCTAACCAG 58.304 41.667 0.00 0.00 0.00 4.00
3305 3855 4.142315 CCATCATCATCAACTCCGCTTTTT 60.142 41.667 0.00 0.00 0.00 1.94
3306 3856 3.379372 CCATCATCATCAACTCCGCTTTT 59.621 43.478 0.00 0.00 0.00 2.27
3307 3857 2.947652 CCATCATCATCAACTCCGCTTT 59.052 45.455 0.00 0.00 0.00 3.51
3308 3858 2.092753 ACCATCATCATCAACTCCGCTT 60.093 45.455 0.00 0.00 0.00 4.68
3309 3859 1.487976 ACCATCATCATCAACTCCGCT 59.512 47.619 0.00 0.00 0.00 5.52
3310 3860 1.600957 CACCATCATCATCAACTCCGC 59.399 52.381 0.00 0.00 0.00 5.54
3311 3861 2.610833 CACACCATCATCATCAACTCCG 59.389 50.000 0.00 0.00 0.00 4.63
3312 3862 2.357009 GCACACCATCATCATCAACTCC 59.643 50.000 0.00 0.00 0.00 3.85
3313 3863 2.357009 GGCACACCATCATCATCAACTC 59.643 50.000 0.00 0.00 35.26 3.01
3314 3864 2.025605 AGGCACACCATCATCATCAACT 60.026 45.455 0.00 0.00 39.06 3.16
3315 3865 2.098607 CAGGCACACCATCATCATCAAC 59.901 50.000 0.00 0.00 39.06 3.18
3316 3866 2.371306 CAGGCACACCATCATCATCAA 58.629 47.619 0.00 0.00 39.06 2.57
3317 3867 2.020181 GCAGGCACACCATCATCATCA 61.020 52.381 0.00 0.00 39.06 3.07
3318 3868 0.666913 GCAGGCACACCATCATCATC 59.333 55.000 0.00 0.00 39.06 2.92
3319 3869 0.754217 GGCAGGCACACCATCATCAT 60.754 55.000 0.00 0.00 39.06 2.45
3320 3870 1.378911 GGCAGGCACACCATCATCA 60.379 57.895 0.00 0.00 39.06 3.07
3321 3871 0.754217 ATGGCAGGCACACCATCATC 60.754 55.000 0.00 0.00 42.69 2.92
3322 3872 1.308666 ATGGCAGGCACACCATCAT 59.691 52.632 0.00 0.00 42.69 2.45
3323 3873 2.765279 ATGGCAGGCACACCATCA 59.235 55.556 0.00 0.00 42.69 3.07
3326 3876 3.259314 AGGATGGCAGGCACACCA 61.259 61.111 19.51 0.00 41.01 4.17
3327 3877 2.196997 TACAGGATGGCAGGCACACC 62.197 60.000 12.37 12.37 43.62 4.16
3328 3878 0.322456 TTACAGGATGGCAGGCACAC 60.322 55.000 0.00 0.00 43.62 3.82
3329 3879 0.625316 ATTACAGGATGGCAGGCACA 59.375 50.000 0.00 0.00 43.62 4.57
3330 3880 2.638480 TATTACAGGATGGCAGGCAC 57.362 50.000 0.00 0.00 43.62 5.01
3331 3881 4.020218 GTCTATATTACAGGATGGCAGGCA 60.020 45.833 0.00 0.00 43.62 4.75
3332 3882 4.223923 AGTCTATATTACAGGATGGCAGGC 59.776 45.833 0.00 0.00 43.62 4.85
3333 3883 5.247110 ACAGTCTATATTACAGGATGGCAGG 59.753 44.000 0.00 0.00 43.62 4.85
3334 3884 6.352016 ACAGTCTATATTACAGGATGGCAG 57.648 41.667 0.00 0.00 43.62 4.85
3335 3885 5.246203 GGACAGTCTATATTACAGGATGGCA 59.754 44.000 0.00 0.00 43.62 4.92
3336 3886 5.622460 CGGACAGTCTATATTACAGGATGGC 60.622 48.000 0.00 0.00 43.62 4.40
3337 3887 5.710567 TCGGACAGTCTATATTACAGGATGG 59.289 44.000 0.00 0.00 43.62 3.51
3338 3888 6.819397 TCGGACAGTCTATATTACAGGATG 57.181 41.667 0.00 0.00 46.00 3.51
3339 3889 8.423906 AAATCGGACAGTCTATATTACAGGAT 57.576 34.615 0.00 0.00 0.00 3.24
3340 3890 7.834881 AAATCGGACAGTCTATATTACAGGA 57.165 36.000 0.00 0.00 0.00 3.86
3348 3898 8.880750 CGTGAGATATAAATCGGACAGTCTATA 58.119 37.037 0.00 0.00 37.19 1.31
3349 3899 7.148222 CCGTGAGATATAAATCGGACAGTCTAT 60.148 40.741 0.00 0.00 40.29 1.98
3350 3900 6.148976 CCGTGAGATATAAATCGGACAGTCTA 59.851 42.308 0.00 0.00 40.29 2.59
3351 3901 5.048643 CCGTGAGATATAAATCGGACAGTCT 60.049 44.000 0.00 0.00 40.29 3.24
3352 3902 5.048921 TCCGTGAGATATAAATCGGACAGTC 60.049 44.000 0.00 0.00 41.45 3.51
3353 3903 4.825634 TCCGTGAGATATAAATCGGACAGT 59.174 41.667 0.00 0.00 41.45 3.55
3354 3904 5.372547 TCCGTGAGATATAAATCGGACAG 57.627 43.478 0.00 0.00 41.45 3.51


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

AutoCloner maintained by Alex Coulton.