Multiple sequence alignment - TraesCS6A01G204900

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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 TraesCS6A01G204900 chr6A 100.000 3483 0 0 1 3483 357403769 357407251 0.000000e+00 6433.0
1 TraesCS6A01G204900 chr6A 81.457 604 75 28 2 593 33309530 33308952 8.810000e-126 460.0
2 TraesCS6A01G204900 chr6A 94.576 295 12 2 301 593 357374500 357374792 1.470000e-123 453.0
3 TraesCS6A01G204900 chr6A 83.753 437 46 18 999 1410 299717368 299717804 1.170000e-104 390.0
4 TraesCS6A01G204900 chr6D 92.839 2402 131 17 725 3118 262780979 262783347 0.000000e+00 3445.0
5 TraesCS6A01G204900 chr6D 94.024 251 11 2 3205 3451 262783544 262783794 9.130000e-101 377.0
6 TraesCS6A01G204900 chr6D 87.356 87 2 4 3170 3247 262783468 262783554 1.330000e-14 91.6
7 TraesCS6A01G204900 chr6B 92.179 2097 128 16 725 2809 347121224 347119152 0.000000e+00 2931.0
8 TraesCS6A01G204900 chr4A 93.355 602 30 3 1 593 374691539 374690939 0.000000e+00 881.0
9 TraesCS6A01G204900 chr4A 84.884 86 9 2 2808 2892 313696905 313696987 2.230000e-12 84.2
10 TraesCS6A01G204900 chr2A 92.893 605 28 6 1 596 166238918 166239516 0.000000e+00 865.0
11 TraesCS6A01G204900 chr2A 91.542 201 11 5 398 593 166234200 166234399 4.430000e-69 272.0
12 TraesCS6A01G204900 chr4D 86.333 600 61 14 2 593 74360446 74359860 4.900000e-178 634.0
13 TraesCS6A01G204900 chr4D 85.358 601 65 15 2 593 139503089 139502503 4.970000e-168 601.0
14 TraesCS6A01G204900 chr4D 82.274 299 34 12 301 593 74365413 74365128 1.250000e-59 241.0
15 TraesCS6A01G204900 chr4D 100.000 35 0 0 2895 2929 173276149 173276115 8.070000e-07 65.8
16 TraesCS6A01G204900 chr3D 86.213 602 61 16 2 594 614095699 614096287 1.760000e-177 632.0
17 TraesCS6A01G204900 chr3D 82.274 299 34 12 301 593 614090906 614091191 1.250000e-59 241.0
18 TraesCS6A01G204900 chr2B 82.724 602 74 19 2 593 61463705 61464286 3.100000e-140 508.0
19 TraesCS6A01G204900 chr7B 81.579 608 65 27 2 593 745384493 745385069 3.170000e-125 459.0
20 TraesCS6A01G204900 chr7B 80.395 607 72 36 2 595 111947990 111947418 5.380000e-113 418.0
21 TraesCS6A01G204900 chr7B 78.621 145 11 8 2801 2930 570579057 570579196 1.040000e-10 78.7
22 TraesCS6A01G204900 chr7B 79.612 103 17 4 2791 2892 432543860 432543761 1.730000e-08 71.3
23 TraesCS6A01G204900 chr2D 82.609 299 33 12 301 593 165334711 165334996 2.680000e-61 246.0
24 TraesCS6A01G204900 chr1A 88.235 85 7 1 2808 2892 584568917 584568998 7.960000e-17 99.0
25 TraesCS6A01G204900 chr1D 87.059 85 7 2 2808 2892 481404432 481404352 3.700000e-15 93.5
26 TraesCS6A01G204900 chr1D 83.721 86 9 2 2808 2892 389482762 389482681 3.730000e-10 76.8
27 TraesCS6A01G204900 chr3B 85.185 81 9 1 2808 2888 829460737 829460660 2.880000e-11 80.5
28 TraesCS6A01G204900 chr3B 94.286 35 2 0 2895 2929 449633916 449633950 2.000000e-03 54.7
29 TraesCS6A01G204900 chr1B 85.897 78 8 1 2815 2892 283289415 283289489 2.880000e-11 80.5
30 TraesCS6A01G204900 chr4B 81.915 94 13 4 2798 2890 263118944 263119034 3.730000e-10 76.8
31 TraesCS6A01G204900 chr5B 97.143 35 1 0 2895 2929 635010273 635010307 3.750000e-05 60.2
32 TraesCS6A01G204900 chr5A 97.143 35 1 0 2895 2929 375437694 375437660 3.750000e-05 60.2
33 TraesCS6A01G204900 chr3A 75.969 129 23 6 2808 2929 556683731 556683858 3.750000e-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 TraesCS6A01G204900 chr6A 357403769 357407251 3482 False 6433.000000 6433 100.000000 1 3483 1 chr6A.!!$F3 3482
1 TraesCS6A01G204900 chr6A 33308952 33309530 578 True 460.000000 460 81.457000 2 593 1 chr6A.!!$R1 591
2 TraesCS6A01G204900 chr6D 262780979 262783794 2815 False 1304.533333 3445 91.406333 725 3451 3 chr6D.!!$F1 2726
3 TraesCS6A01G204900 chr6B 347119152 347121224 2072 True 2931.000000 2931 92.179000 725 2809 1 chr6B.!!$R1 2084
4 TraesCS6A01G204900 chr4A 374690939 374691539 600 True 881.000000 881 93.355000 1 593 1 chr4A.!!$R1 592
5 TraesCS6A01G204900 chr2A 166238918 166239516 598 False 865.000000 865 92.893000 1 596 1 chr2A.!!$F2 595
6 TraesCS6A01G204900 chr4D 74359860 74360446 586 True 634.000000 634 86.333000 2 593 1 chr4D.!!$R1 591
7 TraesCS6A01G204900 chr4D 139502503 139503089 586 True 601.000000 601 85.358000 2 593 1 chr4D.!!$R3 591
8 TraesCS6A01G204900 chr3D 614095699 614096287 588 False 632.000000 632 86.213000 2 594 1 chr3D.!!$F2 592
9 TraesCS6A01G204900 chr2B 61463705 61464286 581 False 508.000000 508 82.724000 2 593 1 chr2B.!!$F1 591
10 TraesCS6A01G204900 chr7B 745384493 745385069 576 False 459.000000 459 81.579000 2 593 1 chr7B.!!$F2 591
11 TraesCS6A01G204900 chr7B 111947418 111947990 572 True 418.000000 418 80.395000 2 595 1 chr7B.!!$R1 593

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
844 895 0.040058 AGCCCAGCATCAAACATCCA 59.960 50.0 0.0 0.0 0.0 3.41 F
1582 1641 0.508641 CTCGCTCGTTTGGTTGTCTG 59.491 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2428 0.179065 CAGCATCGATGGCCTTCTGA 60.179 55.0 26.00 14.29 0.00 3.27 R
3090 3157 0.108186 TGATGCCTCACACATCCGTC 60.108 55.0 1.61 0.00 42.68 4.79 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
62 63 0.457851 CATGAGAGGACGGTCTCCAC 59.542 60.000 8.23 0.21 42.16 4.02
170 173 3.470888 CCGAGCCGATCCAACCCT 61.471 66.667 0.00 0.00 0.00 4.34
235 238 1.445871 GGTGGGTGTTACGGATCAAC 58.554 55.000 0.00 0.00 0.00 3.18
374 391 1.407989 GGGATGAGGTTGGCTTGAGAG 60.408 57.143 0.00 0.00 0.00 3.20
398 415 1.014352 GGTGAGCGAGAGAGAGAGAC 58.986 60.000 0.00 0.00 0.00 3.36
422 450 3.517500 GAGAGGTGGGAGAGAATTTCAGT 59.482 47.826 0.00 0.00 0.00 3.41
429 457 7.017254 AGGTGGGAGAGAATTTCAGTTTTACTA 59.983 37.037 0.00 0.00 0.00 1.82
489 529 2.550456 TACCCCACGTCCCCTCTGA 61.550 63.158 0.00 0.00 0.00 3.27
596 645 2.434884 CTGCCGCGGTGACAGATT 60.435 61.111 28.70 0.00 33.10 2.40
597 646 2.741985 TGCCGCGGTGACAGATTG 60.742 61.111 28.70 0.00 0.00 2.67
598 647 2.742372 GCCGCGGTGACAGATTGT 60.742 61.111 28.70 0.00 0.00 2.71
599 648 2.325082 GCCGCGGTGACAGATTGTT 61.325 57.895 28.70 0.00 0.00 2.83
600 649 1.497278 CCGCGGTGACAGATTGTTG 59.503 57.895 19.50 0.00 0.00 3.33
601 650 1.227999 CCGCGGTGACAGATTGTTGT 61.228 55.000 19.50 0.00 0.00 3.32
602 651 1.424403 CGCGGTGACAGATTGTTGTA 58.576 50.000 0.00 0.00 0.00 2.41
603 652 1.390123 CGCGGTGACAGATTGTTGTAG 59.610 52.381 0.00 0.00 0.00 2.74
604 653 2.683968 GCGGTGACAGATTGTTGTAGA 58.316 47.619 0.00 0.00 0.00 2.59
605 654 3.262420 GCGGTGACAGATTGTTGTAGAT 58.738 45.455 0.00 0.00 0.00 1.98
606 655 3.307242 GCGGTGACAGATTGTTGTAGATC 59.693 47.826 0.00 0.00 0.00 2.75
607 656 4.748892 CGGTGACAGATTGTTGTAGATCT 58.251 43.478 0.00 0.00 33.01 2.75
608 657 5.171476 CGGTGACAGATTGTTGTAGATCTT 58.829 41.667 0.00 0.00 30.43 2.40
609 658 5.639506 CGGTGACAGATTGTTGTAGATCTTT 59.360 40.000 0.00 0.00 30.43 2.52
610 659 6.811665 CGGTGACAGATTGTTGTAGATCTTTA 59.188 38.462 0.00 0.00 30.43 1.85
611 660 7.492669 CGGTGACAGATTGTTGTAGATCTTTAT 59.507 37.037 0.00 0.00 30.43 1.40
612 661 8.607459 GGTGACAGATTGTTGTAGATCTTTATG 58.393 37.037 0.00 0.00 30.43 1.90
613 662 9.155975 GTGACAGATTGTTGTAGATCTTTATGT 57.844 33.333 0.00 0.00 30.43 2.29
614 663 9.371136 TGACAGATTGTTGTAGATCTTTATGTC 57.629 33.333 0.00 4.21 30.43 3.06
615 664 9.371136 GACAGATTGTTGTAGATCTTTATGTCA 57.629 33.333 0.00 0.00 30.41 3.58
616 665 9.376075 ACAGATTGTTGTAGATCTTTATGTCAG 57.624 33.333 0.00 0.00 30.43 3.51
617 666 9.591792 CAGATTGTTGTAGATCTTTATGTCAGA 57.408 33.333 0.00 0.00 30.43 3.27
622 671 9.166173 TGTTGTAGATCTTTATGTCAGATTTGG 57.834 33.333 0.00 0.00 30.70 3.28
623 672 7.792374 TGTAGATCTTTATGTCAGATTTGGC 57.208 36.000 0.00 0.00 30.70 4.52
624 673 6.767902 TGTAGATCTTTATGTCAGATTTGGCC 59.232 38.462 0.00 0.00 30.70 5.36
625 674 6.011122 AGATCTTTATGTCAGATTTGGCCT 57.989 37.500 3.32 0.00 30.70 5.19
626 675 7.141758 AGATCTTTATGTCAGATTTGGCCTA 57.858 36.000 3.32 0.00 30.70 3.93
627 676 7.577303 AGATCTTTATGTCAGATTTGGCCTAA 58.423 34.615 3.32 2.09 30.70 2.69
628 677 8.223330 AGATCTTTATGTCAGATTTGGCCTAAT 58.777 33.333 12.50 12.50 30.70 1.73
629 678 7.572523 TCTTTATGTCAGATTTGGCCTAATG 57.427 36.000 17.50 5.68 0.00 1.90
630 679 7.118723 TCTTTATGTCAGATTTGGCCTAATGT 58.881 34.615 17.50 10.55 0.00 2.71
631 680 8.271458 TCTTTATGTCAGATTTGGCCTAATGTA 58.729 33.333 17.50 0.00 0.00 2.29
632 681 8.450578 TTTATGTCAGATTTGGCCTAATGTAG 57.549 34.615 17.50 8.31 0.00 2.74
633 682 4.199310 TGTCAGATTTGGCCTAATGTAGC 58.801 43.478 17.50 9.52 0.00 3.58
634 683 3.248602 GTCAGATTTGGCCTAATGTAGCG 59.751 47.826 17.50 2.14 0.00 4.26
635 684 2.031682 CAGATTTGGCCTAATGTAGCGC 60.032 50.000 17.50 0.00 0.00 5.92
636 685 1.266989 GATTTGGCCTAATGTAGCGCC 59.733 52.381 17.50 0.00 40.42 6.53
637 686 1.092921 TTTGGCCTAATGTAGCGCCG 61.093 55.000 2.29 0.00 41.87 6.46
638 687 2.665185 GGCCTAATGTAGCGCCGG 60.665 66.667 2.29 0.00 34.19 6.13
639 688 2.420043 GCCTAATGTAGCGCCGGA 59.580 61.111 5.05 0.00 0.00 5.14
640 689 1.004918 GCCTAATGTAGCGCCGGAT 60.005 57.895 5.05 0.00 0.00 4.18
641 690 0.602905 GCCTAATGTAGCGCCGGATT 60.603 55.000 5.05 1.83 0.00 3.01
642 691 1.878953 CCTAATGTAGCGCCGGATTT 58.121 50.000 5.05 0.00 0.00 2.17
643 692 2.218603 CCTAATGTAGCGCCGGATTTT 58.781 47.619 5.05 0.00 0.00 1.82
644 693 2.032030 CCTAATGTAGCGCCGGATTTTG 60.032 50.000 5.05 0.00 0.00 2.44
645 694 1.459450 AATGTAGCGCCGGATTTTGT 58.541 45.000 5.05 0.00 0.00 2.83
646 695 2.319136 ATGTAGCGCCGGATTTTGTA 57.681 45.000 5.05 0.00 0.00 2.41
647 696 2.096220 TGTAGCGCCGGATTTTGTAA 57.904 45.000 5.05 0.00 0.00 2.41
648 697 2.004017 TGTAGCGCCGGATTTTGTAAG 58.996 47.619 5.05 0.00 0.00 2.34
649 698 1.011333 TAGCGCCGGATTTTGTAAGC 58.989 50.000 5.05 0.00 0.00 3.09
650 699 0.676782 AGCGCCGGATTTTGTAAGCT 60.677 50.000 5.05 0.00 0.00 3.74
651 700 0.248094 GCGCCGGATTTTGTAAGCTC 60.248 55.000 5.05 0.00 0.00 4.09
652 701 0.377203 CGCCGGATTTTGTAAGCTCC 59.623 55.000 5.05 0.00 0.00 4.70
657 706 2.987232 GGATTTTGTAAGCTCCGACCT 58.013 47.619 0.00 0.00 0.00 3.85
658 707 2.678336 GGATTTTGTAAGCTCCGACCTG 59.322 50.000 0.00 0.00 0.00 4.00
659 708 2.178912 TTTTGTAAGCTCCGACCTGG 57.821 50.000 0.00 0.00 40.09 4.45
660 709 0.321298 TTTGTAAGCTCCGACCTGGC 60.321 55.000 0.00 0.00 37.80 4.85
661 710 2.180159 TTGTAAGCTCCGACCTGGCC 62.180 60.000 0.00 0.00 37.80 5.36
662 711 2.038975 TAAGCTCCGACCTGGCCT 59.961 61.111 3.32 0.00 37.80 5.19
663 712 2.058595 TAAGCTCCGACCTGGCCTC 61.059 63.158 3.32 0.00 37.80 4.70
664 713 2.516048 TAAGCTCCGACCTGGCCTCT 62.516 60.000 3.32 0.00 37.80 3.69
665 714 4.154347 GCTCCGACCTGGCCTCTG 62.154 72.222 3.32 0.00 37.80 3.35
666 715 2.363018 CTCCGACCTGGCCTCTGA 60.363 66.667 3.32 0.00 37.80 3.27
667 716 1.760086 CTCCGACCTGGCCTCTGAT 60.760 63.158 3.32 0.00 37.80 2.90
668 717 2.025767 CTCCGACCTGGCCTCTGATG 62.026 65.000 3.32 0.00 37.80 3.07
669 718 2.503061 CGACCTGGCCTCTGATGG 59.497 66.667 3.32 0.00 0.00 3.51
670 719 2.060383 CGACCTGGCCTCTGATGGA 61.060 63.158 3.32 0.00 0.00 3.41
671 720 1.828768 GACCTGGCCTCTGATGGAG 59.171 63.158 3.32 0.00 41.51 3.86
682 731 4.634184 CTCTGATGGAGGCATTTTTGAG 57.366 45.455 0.00 0.00 38.35 3.02
683 732 2.756760 TCTGATGGAGGCATTTTTGAGC 59.243 45.455 0.00 0.00 0.00 4.26
684 733 2.494471 CTGATGGAGGCATTTTTGAGCA 59.506 45.455 0.00 0.00 0.00 4.26
685 734 2.231964 TGATGGAGGCATTTTTGAGCAC 59.768 45.455 0.00 0.00 0.00 4.40
686 735 1.999648 TGGAGGCATTTTTGAGCACT 58.000 45.000 0.00 0.00 0.00 4.40
687 736 3.153369 TGGAGGCATTTTTGAGCACTA 57.847 42.857 0.00 0.00 0.00 2.74
688 737 3.495331 TGGAGGCATTTTTGAGCACTAA 58.505 40.909 0.00 0.00 0.00 2.24
689 738 3.894427 TGGAGGCATTTTTGAGCACTAAA 59.106 39.130 0.00 0.00 0.00 1.85
690 739 4.527816 TGGAGGCATTTTTGAGCACTAAAT 59.472 37.500 0.00 0.00 0.00 1.40
691 740 5.714333 TGGAGGCATTTTTGAGCACTAAATA 59.286 36.000 0.00 0.00 0.00 1.40
692 741 6.210385 TGGAGGCATTTTTGAGCACTAAATAA 59.790 34.615 0.00 0.00 0.00 1.40
693 742 7.096551 GGAGGCATTTTTGAGCACTAAATAAA 58.903 34.615 0.00 0.00 0.00 1.40
694 743 7.765819 GGAGGCATTTTTGAGCACTAAATAAAT 59.234 33.333 0.00 0.00 0.00 1.40
695 744 9.154847 GAGGCATTTTTGAGCACTAAATAAATT 57.845 29.630 0.00 0.00 0.00 1.82
698 747 9.906111 GCATTTTTGAGCACTAAATAAATTAGC 57.094 29.630 0.00 0.00 44.11 3.09
702 751 8.667987 TTTGAGCACTAAATAAATTAGCAACG 57.332 30.769 0.00 0.00 44.11 4.10
703 752 7.372451 TGAGCACTAAATAAATTAGCAACGT 57.628 32.000 0.00 0.00 44.11 3.99
704 753 7.461107 TGAGCACTAAATAAATTAGCAACGTC 58.539 34.615 0.00 0.00 44.11 4.34
705 754 6.782150 AGCACTAAATAAATTAGCAACGTCC 58.218 36.000 0.00 0.00 44.11 4.79
706 755 5.969435 GCACTAAATAAATTAGCAACGTCCC 59.031 40.000 0.00 0.00 44.11 4.46
707 756 6.492254 CACTAAATAAATTAGCAACGTCCCC 58.508 40.000 0.00 0.00 44.11 4.81
708 757 6.317893 CACTAAATAAATTAGCAACGTCCCCT 59.682 38.462 0.00 0.00 44.11 4.79
709 758 7.496591 CACTAAATAAATTAGCAACGTCCCCTA 59.503 37.037 0.00 0.00 44.11 3.53
710 759 8.048514 ACTAAATAAATTAGCAACGTCCCCTAA 58.951 33.333 0.00 0.00 44.11 2.69
711 760 7.706100 AAATAAATTAGCAACGTCCCCTAAA 57.294 32.000 0.00 0.00 0.00 1.85
712 761 7.706100 AATAAATTAGCAACGTCCCCTAAAA 57.294 32.000 0.00 0.00 0.00 1.52
713 762 5.638596 AAATTAGCAACGTCCCCTAAAAG 57.361 39.130 0.00 0.00 0.00 2.27
714 763 4.563140 ATTAGCAACGTCCCCTAAAAGA 57.437 40.909 0.00 0.00 0.00 2.52
715 764 2.943036 AGCAACGTCCCCTAAAAGAA 57.057 45.000 0.00 0.00 0.00 2.52
716 765 2.779506 AGCAACGTCCCCTAAAAGAAG 58.220 47.619 0.00 0.00 0.00 2.85
717 766 2.370849 AGCAACGTCCCCTAAAAGAAGA 59.629 45.455 0.00 0.00 0.00 2.87
718 767 3.143728 GCAACGTCCCCTAAAAGAAGAA 58.856 45.455 0.00 0.00 0.00 2.52
719 768 3.188667 GCAACGTCCCCTAAAAGAAGAAG 59.811 47.826 0.00 0.00 0.00 2.85
720 769 4.638304 CAACGTCCCCTAAAAGAAGAAGA 58.362 43.478 0.00 0.00 0.00 2.87
721 770 4.968971 ACGTCCCCTAAAAGAAGAAGAA 57.031 40.909 0.00 0.00 0.00 2.52
722 771 4.895961 ACGTCCCCTAAAAGAAGAAGAAG 58.104 43.478 0.00 0.00 0.00 2.85
723 772 4.591924 ACGTCCCCTAAAAGAAGAAGAAGA 59.408 41.667 0.00 0.00 0.00 2.87
743 792 6.866248 AGAAGAAGAAGAGAACAATCGAACTC 59.134 38.462 0.00 0.00 0.00 3.01
755 804 0.976641 TCGAACTCAGGGCAAGTGAT 59.023 50.000 0.00 0.00 0.00 3.06
767 816 2.159014 GGCAAGTGATGTGGTACCGATA 60.159 50.000 7.57 0.00 0.00 2.92
804 855 0.793861 CACGTACAATTCCACACGGG 59.206 55.000 0.00 0.00 38.67 5.28
805 856 0.952010 ACGTACAATTCCACACGGGC 60.952 55.000 0.00 0.00 38.67 6.13
806 857 0.672401 CGTACAATTCCACACGGGCT 60.672 55.000 0.00 0.00 36.21 5.19
807 858 1.084289 GTACAATTCCACACGGGCTC 58.916 55.000 0.00 0.00 36.21 4.70
808 859 0.981183 TACAATTCCACACGGGCTCT 59.019 50.000 0.00 0.00 36.21 4.09
809 860 0.110486 ACAATTCCACACGGGCTCTT 59.890 50.000 0.00 0.00 36.21 2.85
810 861 1.247567 CAATTCCACACGGGCTCTTT 58.752 50.000 0.00 0.00 36.21 2.52
811 862 1.068333 CAATTCCACACGGGCTCTTTG 60.068 52.381 0.00 0.00 36.21 2.77
812 863 0.400213 ATTCCACACGGGCTCTTTGA 59.600 50.000 0.00 0.00 36.21 2.69
813 864 0.250295 TTCCACACGGGCTCTTTGAG 60.250 55.000 0.00 0.00 36.21 3.02
844 895 0.040058 AGCCCAGCATCAAACATCCA 59.960 50.000 0.00 0.00 0.00 3.41
890 941 1.488705 TTTCCATCCACCTCCACGCT 61.489 55.000 0.00 0.00 0.00 5.07
915 966 2.660094 GCACACATATAAGCATGCGACG 60.660 50.000 13.01 1.58 0.00 5.12
997 1048 2.066999 GCCTCGACCCAAGGGATCT 61.067 63.158 13.15 0.00 38.96 2.75
1217 1268 2.011617 AAGCCCACCAAGCTCAGGTT 62.012 55.000 8.01 0.00 40.49 3.50
1222 1273 1.006102 ACCAAGCTCAGGTTCGTCG 60.006 57.895 5.03 0.00 35.33 5.12
1273 1325 2.238898 CCGGGGACTTTAGGTTGAGATT 59.761 50.000 0.00 0.00 0.00 2.40
1446 1498 0.617413 CTGAGATGCACCCAGTCCTT 59.383 55.000 0.00 0.00 0.00 3.36
1452 1504 4.040755 AGATGCACCCAGTCCTTATAACT 58.959 43.478 0.00 0.00 0.00 2.24
1455 1507 3.585289 TGCACCCAGTCCTTATAACTCAA 59.415 43.478 0.00 0.00 0.00 3.02
1486 1541 4.111916 GTCTTCACATTGTTGGTTTGTGG 58.888 43.478 2.80 0.00 40.82 4.17
1497 1552 9.487790 CATTGTTGGTTTGTGGATTTAGTTATT 57.512 29.630 0.00 0.00 0.00 1.40
1500 1555 6.031751 TGGTTTGTGGATTTAGTTATTGGC 57.968 37.500 0.00 0.00 0.00 4.52
1527 1586 4.592485 ACTCGAAGTAGCTATTCATGGG 57.408 45.455 0.00 0.00 0.00 4.00
1538 1597 3.570975 GCTATTCATGGGTTGATGCATGA 59.429 43.478 2.46 0.00 33.34 3.07
1582 1641 0.508641 CTCGCTCGTTTGGTTGTCTG 59.491 55.000 0.00 0.00 0.00 3.51
1603 1662 4.389576 CCAGCCTGTTCGTTGCGC 62.390 66.667 0.00 0.00 0.00 6.09
1649 1711 5.105917 CCATTTGGGTTCGCTGTTTAGTAAT 60.106 40.000 0.00 0.00 0.00 1.89
1690 1753 1.371635 GCGGTGCATTTGGTGTGTC 60.372 57.895 0.00 0.00 0.00 3.67
1691 1754 1.795170 GCGGTGCATTTGGTGTGTCT 61.795 55.000 0.00 0.00 0.00 3.41
1741 1804 4.870426 ACTACACTAAAATGCCATCGAGTG 59.130 41.667 10.42 10.42 40.09 3.51
1794 1857 4.456911 AGCATCTGTTGGTGTCATTGTTAG 59.543 41.667 0.00 0.00 33.95 2.34
1804 1867 4.079253 GTGTCATTGTTAGTGGTTCCCAT 58.921 43.478 0.00 0.00 35.28 4.00
1814 1877 2.899256 AGTGGTTCCCATTGGATGTTTG 59.101 45.455 3.62 0.00 41.40 2.93
1825 1888 9.942131 TCCCATTGGATGTTTGGAACAACAAAC 62.942 40.741 13.23 13.23 46.10 2.93
1948 2013 5.319043 TCTGTGAAACCTGGGAATTTAGT 57.681 39.130 0.00 0.00 34.36 2.24
1967 2032 9.853177 AATTTAGTATGCCTAATGCTTCTAACT 57.147 29.630 0.00 0.00 42.00 2.24
1982 2047 4.614555 TCTAACTGCAACCAAATATGCG 57.385 40.909 0.00 0.00 45.47 4.73
2001 2066 2.543653 GCGGTTGGGCTAATTGCTTATG 60.544 50.000 3.39 0.00 42.39 1.90
2004 2069 3.243068 GGTTGGGCTAATTGCTTATGTCG 60.243 47.826 0.00 0.00 42.39 4.35
2012 2077 4.685169 AATTGCTTATGTCGTGGTCTTG 57.315 40.909 0.00 0.00 0.00 3.02
2055 2120 2.005451 CGCTGATGTTTCTCTTCAGGG 58.995 52.381 11.13 11.13 46.26 4.45
2145 2210 4.642429 AGGTTGACATCTCTGGTGTTAAC 58.358 43.478 9.24 9.24 42.16 2.01
2157 2222 3.875134 CTGGTGTTAACGTGGAGAAGTTT 59.125 43.478 0.26 0.00 0.00 2.66
2220 2285 1.439543 AGACTGAAGGGGAGCTGTTT 58.560 50.000 0.00 0.00 0.00 2.83
2290 2355 6.839124 ATGTTTATGTCATTCTTTGCTCCA 57.161 33.333 0.00 0.00 0.00 3.86
2319 2384 8.475639 ACTTAGTTCTGTCTCTTGTCTGTTAAA 58.524 33.333 0.00 0.00 0.00 1.52
2347 2413 1.425066 ACCACCAAGAATCTGCCAGAA 59.575 47.619 0.00 0.00 0.00 3.02
2350 2416 3.512724 CCACCAAGAATCTGCCAGAATTT 59.487 43.478 0.00 0.00 0.00 1.82
2434 2500 5.248477 TGACCTTAAGAACTATCTTGGTGCT 59.752 40.000 3.36 0.00 45.47 4.40
2676 2742 5.122554 ACAGTTTGTCGTGTGTTATTTGTGA 59.877 36.000 0.00 0.00 0.00 3.58
2680 2746 3.812609 TGTCGTGTGTTATTTGTGATGCT 59.187 39.130 0.00 0.00 0.00 3.79
2718 2784 6.053632 TCATTCCTTCTGCTGATGTTTCTA 57.946 37.500 0.00 0.00 0.00 2.10
2720 2786 5.489792 TTCCTTCTGCTGATGTTTCTACT 57.510 39.130 0.00 0.00 0.00 2.57
2724 2790 4.623932 TCTGCTGATGTTTCTACTGGTT 57.376 40.909 0.00 0.00 0.00 3.67
2766 2833 7.224753 AGGTCAATATAGTGTTGATGTTTAGCG 59.775 37.037 0.00 0.00 37.84 4.26
2797 2864 3.173953 TCTGGGATTTCAGCCATTTGT 57.826 42.857 0.00 0.00 34.91 2.83
2813 2880 5.390567 GCCATTTGTCTTTAGTGTTACTCCG 60.391 44.000 0.00 0.00 0.00 4.63
2821 2888 0.600057 AGTGTTACTCCGTCCGTTCC 59.400 55.000 0.00 0.00 0.00 3.62
2824 2891 2.228822 GTGTTACTCCGTCCGTTCCTAA 59.771 50.000 0.00 0.00 0.00 2.69
2829 2896 6.545666 TGTTACTCCGTCCGTTCCTAAATATA 59.454 38.462 0.00 0.00 0.00 0.86
2830 2897 7.068103 TGTTACTCCGTCCGTTCCTAAATATAA 59.932 37.037 0.00 0.00 0.00 0.98
2831 2898 6.081872 ACTCCGTCCGTTCCTAAATATAAG 57.918 41.667 0.00 0.00 0.00 1.73
2892 2959 8.843262 TGGAGCAAAATGATTGAATCTATACTG 58.157 33.333 6.73 0.00 0.00 2.74
2906 2973 9.077885 TGAATCTATACTGCACATCTGTATGTA 57.922 33.333 5.95 0.00 44.70 2.29
2965 3032 5.163602 ACCTGTGAATTTCGTTGTAGCAAAA 60.164 36.000 0.00 0.00 0.00 2.44
2992 3059 6.317140 ACAACCGATTACTATTCTGACGTAGA 59.683 38.462 0.00 0.00 0.00 2.59
3004 3071 6.598753 TTCTGACGTAGAAAAACTCCAAAG 57.401 37.500 0.00 0.00 42.31 2.77
3005 3072 5.909477 TCTGACGTAGAAAAACTCCAAAGA 58.091 37.500 0.00 0.00 30.84 2.52
3007 3074 5.054477 TGACGTAGAAAAACTCCAAAGAGG 58.946 41.667 0.00 0.00 45.11 3.69
3008 3075 4.386711 ACGTAGAAAAACTCCAAAGAGGG 58.613 43.478 0.00 0.00 45.11 4.30
3009 3076 3.188667 CGTAGAAAAACTCCAAAGAGGGC 59.811 47.826 0.00 0.00 45.11 5.19
3013 3080 1.986882 AAACTCCAAAGAGGGCACAG 58.013 50.000 0.00 0.00 45.11 3.66
3060 3127 1.401148 CGAAGGTCGTTGATGTCGAGT 60.401 52.381 0.00 0.00 37.99 4.18
3086 3153 2.182791 CTCGATGGCGCTGTGTCT 59.817 61.111 7.64 0.00 37.46 3.41
3088 3155 2.887568 CGATGGCGCTGTGTCTCC 60.888 66.667 7.64 0.00 0.00 3.71
3090 3157 4.457496 ATGGCGCTGTGTCTCCGG 62.457 66.667 7.64 0.00 0.00 5.14
3097 3164 1.139734 CTGTGTCTCCGGACGGATG 59.860 63.158 14.50 8.64 44.24 3.51
3098 3165 1.595993 CTGTGTCTCCGGACGGATGT 61.596 60.000 14.50 0.00 44.24 3.06
3099 3166 1.153823 GTGTCTCCGGACGGATGTG 60.154 63.158 14.50 2.99 44.24 3.21
3118 3203 1.627329 TGTGAGGCATCAAGAAGCTCT 59.373 47.619 0.92 0.00 37.14 4.09
3133 3218 4.700365 TCTGACACGGCAGCGACG 62.700 66.667 2.24 2.24 41.40 5.12
3217 3396 3.518998 CGACGGCCATCTCCTCGT 61.519 66.667 2.24 0.00 38.62 4.18
3221 3400 2.556459 CGGCCATCTCCTCGTCGAT 61.556 63.158 2.24 0.00 0.00 3.59
3299 3478 1.135344 GCTCGAAGGTTAGCTCGTCTT 60.135 52.381 0.00 0.00 36.46 3.01
3303 3482 4.918037 TCGAAGGTTAGCTCGTCTTAATC 58.082 43.478 0.00 0.00 36.46 1.75
3305 3484 3.712091 AGGTTAGCTCGTCTTAATCCG 57.288 47.619 0.00 0.00 0.00 4.18
3316 3495 0.474184 CTTAATCCGGGCCTGGTGAT 59.526 55.000 30.31 14.91 0.00 3.06
3345 3524 0.821517 TGCGAGCTAGGGATTTTCGA 59.178 50.000 0.00 0.00 33.38 3.71
3375 3554 1.673665 CTGCTTGGACAGTGGGAGC 60.674 63.158 0.00 0.00 32.78 4.70
3408 3587 1.069513 GTAAGGTTTTGGGGTGTTGGC 59.930 52.381 0.00 0.00 0.00 4.52
3451 3633 0.861837 GGAGCGGCGAATATGTGAAG 59.138 55.000 12.98 0.00 0.00 3.02
3452 3634 0.861837 GAGCGGCGAATATGTGAAGG 59.138 55.000 12.98 0.00 0.00 3.46
3453 3635 0.532862 AGCGGCGAATATGTGAAGGG 60.533 55.000 12.98 0.00 0.00 3.95
3454 3636 1.941812 CGGCGAATATGTGAAGGGC 59.058 57.895 0.00 0.00 0.00 5.19
3455 3637 0.813610 CGGCGAATATGTGAAGGGCA 60.814 55.000 0.00 0.00 0.00 5.36
3456 3638 0.947244 GGCGAATATGTGAAGGGCAG 59.053 55.000 0.00 0.00 0.00 4.85
3457 3639 0.308993 GCGAATATGTGAAGGGCAGC 59.691 55.000 0.00 0.00 0.00 5.25
3458 3640 1.667236 CGAATATGTGAAGGGCAGCA 58.333 50.000 0.00 0.00 0.00 4.41
3459 3641 1.331756 CGAATATGTGAAGGGCAGCAC 59.668 52.381 0.00 0.00 35.63 4.40
3460 3642 2.648059 GAATATGTGAAGGGCAGCACT 58.352 47.619 0.00 0.00 36.05 4.40
3461 3643 2.814805 ATATGTGAAGGGCAGCACTT 57.185 45.000 10.56 10.56 36.05 3.16
3462 3644 2.584835 TATGTGAAGGGCAGCACTTT 57.415 45.000 12.34 0.00 36.05 2.66
3463 3645 0.963962 ATGTGAAGGGCAGCACTTTG 59.036 50.000 12.34 0.00 36.05 2.77
3464 3646 1.006922 GTGAAGGGCAGCACTTTGC 60.007 57.895 12.34 3.81 45.46 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 238 0.449388 GCTTCCACAATCTCTTGGCG 59.551 55.000 0.00 0.00 36.64 5.69
374 391 2.043852 TCTCTCGCTCACCCCCTC 60.044 66.667 0.00 0.00 0.00 4.30
398 415 3.517100 TGAAATTCTCTCCCACCTCTCTG 59.483 47.826 0.00 0.00 0.00 3.35
429 457 7.042119 GCATTGTAGCAAACAGGTTGTTATTTT 60.042 33.333 0.00 0.00 40.14 1.82
438 468 3.077359 GAGAGCATTGTAGCAAACAGGT 58.923 45.455 0.00 0.00 39.87 4.00
489 529 2.842462 TGTGTGGCCGGAGTGAGT 60.842 61.111 5.05 0.00 0.00 3.41
596 645 9.166173 CCAAATCTGACATAAAGATCTACAACA 57.834 33.333 0.00 0.00 33.17 3.33
597 646 8.125448 GCCAAATCTGACATAAAGATCTACAAC 58.875 37.037 0.00 0.00 33.17 3.32
598 647 7.283127 GGCCAAATCTGACATAAAGATCTACAA 59.717 37.037 0.00 0.00 33.17 2.41
599 648 6.767902 GGCCAAATCTGACATAAAGATCTACA 59.232 38.462 0.00 0.00 33.17 2.74
600 649 6.995091 AGGCCAAATCTGACATAAAGATCTAC 59.005 38.462 5.01 0.00 33.17 2.59
601 650 7.141758 AGGCCAAATCTGACATAAAGATCTA 57.858 36.000 5.01 0.00 33.17 1.98
602 651 6.011122 AGGCCAAATCTGACATAAAGATCT 57.989 37.500 5.01 0.00 33.17 2.75
603 652 7.807977 TTAGGCCAAATCTGACATAAAGATC 57.192 36.000 5.01 0.00 33.17 2.75
604 653 7.781693 ACATTAGGCCAAATCTGACATAAAGAT 59.218 33.333 5.01 0.00 35.89 2.40
605 654 7.118723 ACATTAGGCCAAATCTGACATAAAGA 58.881 34.615 5.01 0.00 0.00 2.52
606 655 7.338800 ACATTAGGCCAAATCTGACATAAAG 57.661 36.000 5.01 0.00 0.00 1.85
607 656 7.013274 GCTACATTAGGCCAAATCTGACATAAA 59.987 37.037 5.01 0.00 0.00 1.40
608 657 6.486657 GCTACATTAGGCCAAATCTGACATAA 59.513 38.462 5.01 0.00 0.00 1.90
609 658 5.997746 GCTACATTAGGCCAAATCTGACATA 59.002 40.000 5.01 0.00 0.00 2.29
610 659 4.823989 GCTACATTAGGCCAAATCTGACAT 59.176 41.667 5.01 0.00 0.00 3.06
611 660 4.199310 GCTACATTAGGCCAAATCTGACA 58.801 43.478 5.01 0.00 0.00 3.58
612 661 3.248602 CGCTACATTAGGCCAAATCTGAC 59.751 47.826 5.01 0.00 0.00 3.51
613 662 3.466836 CGCTACATTAGGCCAAATCTGA 58.533 45.455 5.01 0.00 0.00 3.27
614 663 2.031682 GCGCTACATTAGGCCAAATCTG 60.032 50.000 5.01 0.00 0.00 2.90
615 664 2.222027 GCGCTACATTAGGCCAAATCT 58.778 47.619 5.01 0.00 0.00 2.40
616 665 1.266989 GGCGCTACATTAGGCCAAATC 59.733 52.381 7.64 0.00 40.03 2.17
617 666 1.318576 GGCGCTACATTAGGCCAAAT 58.681 50.000 7.64 0.00 40.03 2.32
618 667 1.092921 CGGCGCTACATTAGGCCAAA 61.093 55.000 7.64 0.00 40.18 3.28
619 668 1.522806 CGGCGCTACATTAGGCCAA 60.523 57.895 7.64 0.00 40.18 4.52
620 669 2.108157 CGGCGCTACATTAGGCCA 59.892 61.111 7.64 0.00 40.18 5.36
621 670 2.450479 ATCCGGCGCTACATTAGGCC 62.450 60.000 7.64 0.00 38.19 5.19
622 671 0.602905 AATCCGGCGCTACATTAGGC 60.603 55.000 7.64 0.00 0.00 3.93
623 672 1.878953 AAATCCGGCGCTACATTAGG 58.121 50.000 7.64 0.00 0.00 2.69
624 673 2.612212 ACAAAATCCGGCGCTACATTAG 59.388 45.455 7.64 2.56 0.00 1.73
625 674 2.634600 ACAAAATCCGGCGCTACATTA 58.365 42.857 7.64 0.00 0.00 1.90
626 675 1.459450 ACAAAATCCGGCGCTACATT 58.541 45.000 7.64 0.00 0.00 2.71
627 676 2.319136 TACAAAATCCGGCGCTACAT 57.681 45.000 7.64 0.00 0.00 2.29
628 677 2.004017 CTTACAAAATCCGGCGCTACA 58.996 47.619 7.64 0.00 0.00 2.74
629 678 1.267882 GCTTACAAAATCCGGCGCTAC 60.268 52.381 7.64 0.00 0.00 3.58
630 679 1.011333 GCTTACAAAATCCGGCGCTA 58.989 50.000 7.64 0.00 0.00 4.26
631 680 0.676782 AGCTTACAAAATCCGGCGCT 60.677 50.000 7.64 0.00 0.00 5.92
632 681 0.248094 GAGCTTACAAAATCCGGCGC 60.248 55.000 0.00 0.00 0.00 6.53
633 682 0.377203 GGAGCTTACAAAATCCGGCG 59.623 55.000 0.00 0.00 0.00 6.46
637 686 2.678336 CAGGTCGGAGCTTACAAAATCC 59.322 50.000 7.04 0.00 0.00 3.01
638 687 2.678336 CCAGGTCGGAGCTTACAAAATC 59.322 50.000 7.04 0.00 36.56 2.17
639 688 2.711542 CCAGGTCGGAGCTTACAAAAT 58.288 47.619 7.04 0.00 36.56 1.82
640 689 1.880646 GCCAGGTCGGAGCTTACAAAA 60.881 52.381 7.04 0.00 36.56 2.44
641 690 0.321298 GCCAGGTCGGAGCTTACAAA 60.321 55.000 7.04 0.00 36.56 2.83
642 691 1.295423 GCCAGGTCGGAGCTTACAA 59.705 57.895 7.04 0.00 36.56 2.41
643 692 2.656069 GGCCAGGTCGGAGCTTACA 61.656 63.158 7.04 0.00 36.56 2.41
644 693 2.187163 GGCCAGGTCGGAGCTTAC 59.813 66.667 7.04 2.40 36.56 2.34
645 694 2.038975 AGGCCAGGTCGGAGCTTA 59.961 61.111 5.01 0.00 36.56 3.09
646 695 3.394836 GAGGCCAGGTCGGAGCTT 61.395 66.667 5.01 0.00 36.56 3.74
647 696 4.390556 AGAGGCCAGGTCGGAGCT 62.391 66.667 5.01 3.41 36.56 4.09
648 697 4.154347 CAGAGGCCAGGTCGGAGC 62.154 72.222 5.01 0.00 36.56 4.70
649 698 1.760086 ATCAGAGGCCAGGTCGGAG 60.760 63.158 5.01 0.00 36.56 4.63
650 699 2.060383 CATCAGAGGCCAGGTCGGA 61.060 63.158 5.01 0.00 36.56 4.55
651 700 2.503061 CATCAGAGGCCAGGTCGG 59.497 66.667 5.01 0.00 38.11 4.79
652 701 2.025767 CTCCATCAGAGGCCAGGTCG 62.026 65.000 5.01 0.00 39.13 4.79
653 702 1.828768 CTCCATCAGAGGCCAGGTC 59.171 63.158 5.01 0.00 39.13 3.85
654 703 4.063335 CTCCATCAGAGGCCAGGT 57.937 61.111 5.01 0.00 39.13 4.00
661 710 3.181489 GCTCAAAAATGCCTCCATCAGAG 60.181 47.826 0.00 0.00 42.83 3.35
662 711 2.756760 GCTCAAAAATGCCTCCATCAGA 59.243 45.455 0.00 0.00 0.00 3.27
663 712 2.494471 TGCTCAAAAATGCCTCCATCAG 59.506 45.455 0.00 0.00 0.00 2.90
664 713 2.231964 GTGCTCAAAAATGCCTCCATCA 59.768 45.455 0.00 0.00 0.00 3.07
665 714 2.494870 AGTGCTCAAAAATGCCTCCATC 59.505 45.455 0.00 0.00 0.00 3.51
666 715 2.532843 AGTGCTCAAAAATGCCTCCAT 58.467 42.857 0.00 0.00 0.00 3.41
667 716 1.999648 AGTGCTCAAAAATGCCTCCA 58.000 45.000 0.00 0.00 0.00 3.86
668 717 4.519540 TTTAGTGCTCAAAAATGCCTCC 57.480 40.909 0.00 0.00 0.00 4.30
669 718 8.707938 ATTTATTTAGTGCTCAAAAATGCCTC 57.292 30.769 8.52 0.00 0.00 4.70
672 721 9.906111 GCTAATTTATTTAGTGCTCAAAAATGC 57.094 29.630 8.52 0.00 39.67 3.56
676 725 9.123709 CGTTGCTAATTTATTTAGTGCTCAAAA 57.876 29.630 0.00 0.00 39.67 2.44
677 726 8.293867 ACGTTGCTAATTTATTTAGTGCTCAAA 58.706 29.630 0.00 0.00 39.67 2.69
678 727 7.812648 ACGTTGCTAATTTATTTAGTGCTCAA 58.187 30.769 0.00 0.00 39.67 3.02
679 728 7.372451 ACGTTGCTAATTTATTTAGTGCTCA 57.628 32.000 0.00 0.00 39.67 4.26
680 729 6.905609 GGACGTTGCTAATTTATTTAGTGCTC 59.094 38.462 0.00 0.00 39.67 4.26
681 730 6.183360 GGGACGTTGCTAATTTATTTAGTGCT 60.183 38.462 0.00 0.00 39.67 4.40
682 731 5.969435 GGGACGTTGCTAATTTATTTAGTGC 59.031 40.000 0.00 0.00 39.67 4.40
683 732 6.317893 AGGGGACGTTGCTAATTTATTTAGTG 59.682 38.462 0.00 0.00 39.67 2.74
684 733 6.420638 AGGGGACGTTGCTAATTTATTTAGT 58.579 36.000 0.00 0.00 39.67 2.24
685 734 6.937436 AGGGGACGTTGCTAATTTATTTAG 57.063 37.500 0.00 0.00 40.34 1.85
686 735 8.804912 TTTAGGGGACGTTGCTAATTTATTTA 57.195 30.769 0.00 0.00 0.00 1.40
687 736 7.706100 TTTAGGGGACGTTGCTAATTTATTT 57.294 32.000 0.00 0.00 0.00 1.40
688 737 7.612633 TCTTTTAGGGGACGTTGCTAATTTATT 59.387 33.333 0.00 0.00 0.00 1.40
689 738 7.114095 TCTTTTAGGGGACGTTGCTAATTTAT 58.886 34.615 0.00 0.00 0.00 1.40
690 739 6.474630 TCTTTTAGGGGACGTTGCTAATTTA 58.525 36.000 0.00 0.00 0.00 1.40
691 740 5.318630 TCTTTTAGGGGACGTTGCTAATTT 58.681 37.500 0.00 0.00 0.00 1.82
692 741 4.913784 TCTTTTAGGGGACGTTGCTAATT 58.086 39.130 0.00 0.00 0.00 1.40
693 742 4.563140 TCTTTTAGGGGACGTTGCTAAT 57.437 40.909 0.00 0.00 0.00 1.73
694 743 4.040706 TCTTCTTTTAGGGGACGTTGCTAA 59.959 41.667 0.00 0.00 0.00 3.09
695 744 3.579586 TCTTCTTTTAGGGGACGTTGCTA 59.420 43.478 0.00 0.00 0.00 3.49
696 745 2.370849 TCTTCTTTTAGGGGACGTTGCT 59.629 45.455 0.00 0.00 0.00 3.91
697 746 2.774687 TCTTCTTTTAGGGGACGTTGC 58.225 47.619 0.00 0.00 0.00 4.17
698 747 4.638304 TCTTCTTCTTTTAGGGGACGTTG 58.362 43.478 0.00 0.00 0.00 4.10
699 748 4.968971 TCTTCTTCTTTTAGGGGACGTT 57.031 40.909 0.00 0.00 0.00 3.99
700 749 4.591924 TCTTCTTCTTCTTTTAGGGGACGT 59.408 41.667 0.00 0.00 0.00 4.34
701 750 5.148651 TCTTCTTCTTCTTTTAGGGGACG 57.851 43.478 0.00 0.00 0.00 4.79
702 751 6.770542 TCTTCTTCTTCTTCTTTTAGGGGAC 58.229 40.000 0.00 0.00 0.00 4.46
703 752 7.292591 TCTTCTTCTTCTTCTTCTTTTAGGGGA 59.707 37.037 0.00 0.00 0.00 4.81
704 753 7.454225 TCTTCTTCTTCTTCTTCTTTTAGGGG 58.546 38.462 0.00 0.00 0.00 4.79
705 754 8.371699 TCTCTTCTTCTTCTTCTTCTTTTAGGG 58.628 37.037 0.00 0.00 0.00 3.53
706 755 9.771534 TTCTCTTCTTCTTCTTCTTCTTTTAGG 57.228 33.333 0.00 0.00 0.00 2.69
709 758 9.454859 TTGTTCTCTTCTTCTTCTTCTTCTTTT 57.545 29.630 0.00 0.00 0.00 2.27
710 759 9.625747 ATTGTTCTCTTCTTCTTCTTCTTCTTT 57.374 29.630 0.00 0.00 0.00 2.52
711 760 9.271828 GATTGTTCTCTTCTTCTTCTTCTTCTT 57.728 33.333 0.00 0.00 0.00 2.52
712 761 7.598493 CGATTGTTCTCTTCTTCTTCTTCTTCT 59.402 37.037 0.00 0.00 0.00 2.85
713 762 7.596995 TCGATTGTTCTCTTCTTCTTCTTCTTC 59.403 37.037 0.00 0.00 0.00 2.87
714 763 7.437748 TCGATTGTTCTCTTCTTCTTCTTCTT 58.562 34.615 0.00 0.00 0.00 2.52
715 764 6.987386 TCGATTGTTCTCTTCTTCTTCTTCT 58.013 36.000 0.00 0.00 0.00 2.85
716 765 7.383843 AGTTCGATTGTTCTCTTCTTCTTCTTC 59.616 37.037 0.00 0.00 0.00 2.87
717 766 7.213678 AGTTCGATTGTTCTCTTCTTCTTCTT 58.786 34.615 0.00 0.00 0.00 2.52
718 767 6.754193 AGTTCGATTGTTCTCTTCTTCTTCT 58.246 36.000 0.00 0.00 0.00 2.85
719 768 6.642950 TGAGTTCGATTGTTCTCTTCTTCTTC 59.357 38.462 0.00 0.00 0.00 2.87
720 769 6.516718 TGAGTTCGATTGTTCTCTTCTTCTT 58.483 36.000 0.00 0.00 0.00 2.52
721 770 6.090483 TGAGTTCGATTGTTCTCTTCTTCT 57.910 37.500 0.00 0.00 0.00 2.85
722 771 5.347364 CCTGAGTTCGATTGTTCTCTTCTTC 59.653 44.000 0.00 0.00 0.00 2.87
723 772 5.233988 CCTGAGTTCGATTGTTCTCTTCTT 58.766 41.667 0.00 0.00 0.00 2.52
743 792 1.453155 GTACCACATCACTTGCCCTG 58.547 55.000 0.00 0.00 0.00 4.45
755 804 4.744259 GCCCATTTGTATATCGGTACCACA 60.744 45.833 13.54 5.24 0.00 4.17
767 816 3.020984 CGTGTTTAGGGCCCATTTGTAT 58.979 45.455 27.56 2.98 0.00 2.29
805 856 0.739112 GAGTGCTCGGGCTCAAAGAG 60.739 60.000 9.62 0.00 39.59 2.85
806 857 1.293498 GAGTGCTCGGGCTCAAAGA 59.707 57.895 9.62 0.00 39.59 2.52
807 858 1.004560 TGAGTGCTCGGGCTCAAAG 60.005 57.895 9.62 0.00 38.61 2.77
808 859 1.004560 CTGAGTGCTCGGGCTCAAA 60.005 57.895 9.62 0.00 40.68 2.69
809 860 2.659016 CTGAGTGCTCGGGCTCAA 59.341 61.111 9.62 0.00 40.68 3.02
810 861 4.074526 GCTGAGTGCTCGGGCTCA 62.075 66.667 9.62 3.47 39.17 4.26
817 868 1.818785 GATGCTGGGCTGAGTGCTC 60.819 63.158 0.00 0.00 44.01 4.26
818 869 2.133359 TTGATGCTGGGCTGAGTGCT 62.133 55.000 0.00 0.00 42.39 4.40
858 909 5.077564 GTGGATGGAAACCCTAACTTTCTT 58.922 41.667 0.00 0.00 0.00 2.52
890 941 2.033675 GCATGCTTATATGTGTGCAGCA 59.966 45.455 11.37 0.00 44.32 4.41
915 966 2.420058 AGAATGGACGATGGGGTTTC 57.580 50.000 0.00 0.00 0.00 2.78
997 1048 4.467084 GGAGGTCGGCGCCATTGA 62.467 66.667 28.98 13.41 0.00 2.57
1217 1268 3.807538 GAGGCGGTAGTGCGACGA 61.808 66.667 0.00 0.00 35.06 4.20
1259 1311 6.071728 ACAGCCAAATCAATCTCAACCTAAAG 60.072 38.462 0.00 0.00 0.00 1.85
1273 1325 0.961019 GACCTGCAACAGCCAAATCA 59.039 50.000 0.00 0.00 0.00 2.57
1446 1498 7.283807 TGTGAAGACCTACGCTATTGAGTTATA 59.716 37.037 0.00 0.00 0.00 0.98
1452 1504 5.109210 CAATGTGAAGACCTACGCTATTGA 58.891 41.667 0.00 0.00 0.00 2.57
1455 1507 4.737855 ACAATGTGAAGACCTACGCTAT 57.262 40.909 0.00 0.00 0.00 2.97
1486 1541 6.479001 TCGAGTAAGCAGCCAATAACTAAATC 59.521 38.462 0.00 0.00 0.00 2.17
1497 1552 1.135083 GCTACTTCGAGTAAGCAGCCA 60.135 52.381 9.33 0.00 45.41 4.75
1500 1555 5.822278 TGAATAGCTACTTCGAGTAAGCAG 58.178 41.667 14.77 0.00 38.93 4.24
1527 1586 3.728076 ATGCTTCCATCATGCATCAAC 57.272 42.857 0.00 0.00 40.99 3.18
1554 1613 1.719780 CAAACGAGCGAGAACCTACAC 59.280 52.381 0.00 0.00 0.00 2.90
1582 1641 1.949257 CAACGAACAGGCTGGAACC 59.051 57.895 20.34 3.67 0.00 3.62
1603 1662 6.464222 TGGTAGTTAGTCCAAGTCTGATTTG 58.536 40.000 5.97 5.97 0.00 2.32
1690 1753 7.273381 CCCAAGTCAAAATTCTACGCATTTAAG 59.727 37.037 0.00 0.00 0.00 1.85
1691 1754 7.040340 TCCCAAGTCAAAATTCTACGCATTTAA 60.040 33.333 0.00 0.00 0.00 1.52
1762 1825 5.804639 ACACCAACAGATGCTAACAGATAA 58.195 37.500 0.00 0.00 0.00 1.75
1825 1888 5.289434 GCCTGCCTCGAATTCATTTTAAAAG 59.711 40.000 6.79 0.00 0.00 2.27
1880 1943 5.305644 GCAAGGAGGGAATTCTCATAGACTA 59.694 44.000 8.33 0.00 35.58 2.59
1881 1944 4.102367 GCAAGGAGGGAATTCTCATAGACT 59.898 45.833 8.33 0.00 35.58 3.24
1882 1945 4.141620 TGCAAGGAGGGAATTCTCATAGAC 60.142 45.833 8.33 0.00 35.58 2.59
1883 1946 4.040047 TGCAAGGAGGGAATTCTCATAGA 58.960 43.478 8.33 0.00 35.58 1.98
1884 1947 4.428294 TGCAAGGAGGGAATTCTCATAG 57.572 45.455 8.33 0.00 35.58 2.23
1885 1948 4.166725 ACATGCAAGGAGGGAATTCTCATA 59.833 41.667 8.33 0.00 35.58 2.15
1886 1949 3.053095 ACATGCAAGGAGGGAATTCTCAT 60.053 43.478 8.33 0.00 35.58 2.90
1899 1964 1.067635 GGTGTAGCCAAACATGCAAGG 60.068 52.381 0.00 0.00 37.17 3.61
1930 1995 4.953579 GGCATACTAAATTCCCAGGTTTCA 59.046 41.667 0.00 0.00 0.00 2.69
1966 2031 2.652941 AACCGCATATTTGGTTGCAG 57.347 45.000 7.43 0.00 46.41 4.41
2001 2066 5.287992 GCATACTAACTTACAAGACCACGAC 59.712 44.000 0.00 0.00 0.00 4.34
2004 2069 8.888579 ATATGCATACTAACTTACAAGACCAC 57.111 34.615 8.99 0.00 0.00 4.16
2055 2120 3.841643 CACACCATTGATCTTGAAAGGC 58.158 45.455 0.00 0.00 0.00 4.35
2145 2210 3.809832 ACTTGTCATCAAACTTCTCCACG 59.190 43.478 0.00 0.00 32.87 4.94
2157 2222 2.353704 CCTGGCGAAGTACTTGTCATCA 60.354 50.000 14.14 3.55 0.00 3.07
2220 2285 3.808834 TGTACCTCCTTCTCAGTCTCA 57.191 47.619 0.00 0.00 0.00 3.27
2290 2355 6.127310 ACAGACAAGAGACAGAACTAAGTTGT 60.127 38.462 0.00 0.00 0.00 3.32
2319 2384 0.773644 ATTCTTGGTGGTCTGCAGGT 59.226 50.000 15.13 0.00 0.00 4.00
2362 2428 0.179065 CAGCATCGATGGCCTTCTGA 60.179 55.000 26.00 14.29 0.00 3.27
2434 2500 1.686428 CCATCCCTGAGAGAGAACCGA 60.686 57.143 0.00 0.00 0.00 4.69
2662 2728 8.519492 AACAAATAGCATCACAAATAACACAC 57.481 30.769 0.00 0.00 0.00 3.82
2665 2731 9.755804 TGAAAACAAATAGCATCACAAATAACA 57.244 25.926 0.00 0.00 0.00 2.41
2676 2742 9.729281 AGGAATGAAAATGAAAACAAATAGCAT 57.271 25.926 0.00 0.00 0.00 3.79
2766 2833 1.620822 AATCCCAGAACAACCAGCAC 58.379 50.000 0.00 0.00 0.00 4.40
2813 2880 7.724287 AGGTCTTCTTATATTTAGGAACGGAC 58.276 38.462 0.00 0.00 0.00 4.79
2856 2923 7.774625 TCAATCATTTTGCTCCATATGTAGTCA 59.225 33.333 1.24 0.00 0.00 3.41
2858 2925 8.523915 TTCAATCATTTTGCTCCATATGTAGT 57.476 30.769 1.24 0.00 0.00 2.73
2868 2935 8.347771 TGCAGTATAGATTCAATCATTTTGCTC 58.652 33.333 0.00 0.00 0.00 4.26
2870 2937 7.916977 TGTGCAGTATAGATTCAATCATTTTGC 59.083 33.333 0.00 3.93 0.00 3.68
2892 2959 6.870439 TCAATATGAGCTACATACAGATGTGC 59.130 38.462 7.69 3.35 46.11 4.57
2906 2973 8.277918 ACCCTTTTAGAGATTTCAATATGAGCT 58.722 33.333 0.00 0.00 0.00 4.09
2965 3032 5.125097 ACGTCAGAATAGTAATCGGTTGTCT 59.875 40.000 0.00 0.00 0.00 3.41
2992 3059 2.695147 CTGTGCCCTCTTTGGAGTTTTT 59.305 45.455 0.00 0.00 37.86 1.94
3008 3075 2.221906 CTCCAATGCAAGGCCTGTGC 62.222 60.000 24.52 24.52 42.55 4.57
3009 3076 0.609957 TCTCCAATGCAAGGCCTGTG 60.610 55.000 5.69 8.39 0.00 3.66
3013 3080 2.421399 GCCTCTCCAATGCAAGGCC 61.421 63.158 12.96 0.00 46.97 5.19
3016 3083 1.318158 GGGTGCCTCTCCAATGCAAG 61.318 60.000 0.00 0.00 36.65 4.01
3050 3117 2.434185 GCCGCCAACTCGACATCA 60.434 61.111 0.00 0.00 0.00 3.07
3051 3118 3.554692 CGCCGCCAACTCGACATC 61.555 66.667 0.00 0.00 0.00 3.06
3088 3155 2.509336 GCCTCACACATCCGTCCG 60.509 66.667 0.00 0.00 0.00 4.79
3090 3157 0.108186 TGATGCCTCACACATCCGTC 60.108 55.000 1.61 0.00 42.68 4.79
3097 3164 1.736681 GAGCTTCTTGATGCCTCACAC 59.263 52.381 5.11 0.00 0.00 3.82
3098 3165 1.627329 AGAGCTTCTTGATGCCTCACA 59.373 47.619 5.11 0.00 0.00 3.58
3099 3166 2.008329 CAGAGCTTCTTGATGCCTCAC 58.992 52.381 5.11 0.00 0.00 3.51
3118 3203 4.994201 GACGTCGCTGCCGTGTCA 62.994 66.667 8.62 0.00 38.92 3.58
3133 3218 1.130561 GGCTCAAATTAGTGCACGGAC 59.869 52.381 12.01 0.00 0.00 4.79
3217 3396 0.250166 CATGGCATGGCTGAGATCGA 60.250 55.000 19.80 0.00 0.00 3.59
3299 3478 1.705002 CCATCACCAGGCCCGGATTA 61.705 60.000 13.45 0.00 0.00 1.75
3303 3482 4.489771 GTCCATCACCAGGCCCGG 62.490 72.222 2.45 2.45 0.00 5.73
3331 3510 2.603560 CTGTCGTTCGAAAATCCCTAGC 59.396 50.000 0.00 0.00 0.00 3.42
3345 3524 0.957395 CCAAGCAGCCATCTGTCGTT 60.957 55.000 0.00 0.00 42.29 3.85
3375 3554 3.983044 AACCTTACCTCTAAGCCACTG 57.017 47.619 0.00 0.00 0.00 3.66
3408 3587 1.653151 GCCTTGACTAAAGTAGGCCG 58.347 55.000 11.40 0.00 41.62 6.13
3451 3633 4.389576 CGACGCAAAGTGCTGCCC 62.390 66.667 0.00 0.00 42.25 5.36
3452 3634 4.389576 CCGACGCAAAGTGCTGCC 62.390 66.667 0.00 0.00 42.25 4.85
3454 3636 4.724697 CGCCGACGCAAAGTGCTG 62.725 66.667 0.00 0.00 42.25 4.41


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

AutoCloner maintained by Alex Coulton.