Multiple sequence alignment - TraesCS7D01G184300

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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 TraesCS7D01G184300 chr7D 100.000 2646 0 0 525 3170 137872386 137869741 0.000000e+00 4887
1 TraesCS7D01G184300 chr7D 100.000 129 0 0 1 129 137872910 137872782 4.090000e-59 239
2 TraesCS7D01G184300 chr7D 76.538 439 77 24 968 1394 137790122 137789698 1.910000e-52 217
3 TraesCS7D01G184300 chr7A 96.514 2295 62 7 890 3170 137827362 137825072 0.000000e+00 3779
4 TraesCS7D01G184300 chr7A 89.286 280 24 4 533 808 137867276 137866999 2.340000e-91 346
5 TraesCS7D01G184300 chr7B 94.279 1678 70 13 819 2490 103117073 103115416 0.000000e+00 2543
6 TraesCS7D01G184300 chr7B 92.878 337 23 1 2596 2932 103115425 103115090 3.680000e-134 488
7 TraesCS7D01G184300 chrUn 100.000 390 0 0 1238 1627 480092364 480092753 0.000000e+00 721
8 TraesCS7D01G184300 chr2B 79.094 287 56 3 1133 1417 54016537 54016253 8.970000e-46 195
9 TraesCS7D01G184300 chr6A 77.895 285 50 8 1133 1415 15700857 15701130 7.030000e-37 165
10 TraesCS7D01G184300 chr6A 77.895 285 50 8 1133 1415 15906810 15906537 7.030000e-37 165
11 TraesCS7D01G184300 chr5A 81.500 200 37 0 1133 1332 456099767 456099568 7.030000e-37 165
12 TraesCS7D01G184300 chr6B 78.903 237 42 6 1133 1365 52574013 52573781 1.520000e-33 154
13 TraesCS7D01G184300 chr5D 80.500 200 39 0 1133 1332 356636935 356637134 1.520000e-33 154


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 TraesCS7D01G184300 chr7D 137869741 137872910 3169 True 2563.0 4887 100.0000 1 3170 2 chr7D.!!$R2 3169
1 TraesCS7D01G184300 chr7A 137825072 137827362 2290 True 3779.0 3779 96.5140 890 3170 1 chr7A.!!$R1 2280
2 TraesCS7D01G184300 chr7B 103115090 103117073 1983 True 1515.5 2543 93.5785 819 2932 2 chr7B.!!$R1 2113

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
742 743 0.034896 AACTTCCTCGCGTGGAATGT 59.965 50.0 34.96 29.58 44.17 2.71 F
745 746 0.174845 TTCCTCGCGTGGAATGTAGG 59.825 55.0 32.50 17.78 40.80 3.18 F
796 797 0.313672 GGTCAGCCGAATTTGCAACA 59.686 50.0 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1779 1.309499 CCAAGCGTCTCGAGGACTCT 61.309 60.000 13.56 7.1 41.20 3.24 R
1902 1919 1.340991 ACCGGCCTTTGAGCAATGTAT 60.341 47.619 0.00 0.0 0.00 2.29 R
2508 2538 1.902938 TGTTTCATCCCACGCATGAA 58.097 45.000 0.00 0.0 38.27 2.57 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
20 21 2.509336 GGCATCCACGTGACGAGG 60.509 66.667 19.30 15.36 38.87 4.63
21 22 3.188786 GCATCCACGTGACGAGGC 61.189 66.667 19.30 16.16 37.51 4.70
22 23 2.880879 CATCCACGTGACGAGGCG 60.881 66.667 19.30 6.46 37.51 5.52
23 24 3.060000 ATCCACGTGACGAGGCGA 61.060 61.111 19.30 3.75 37.51 5.54
24 25 3.338126 ATCCACGTGACGAGGCGAC 62.338 63.158 19.30 0.00 37.51 5.19
25 26 4.337060 CCACGTGACGAGGCGACA 62.337 66.667 19.30 0.00 30.30 4.35
26 27 2.126463 CACGTGACGAGGCGACAT 60.126 61.111 13.70 0.00 34.08 3.06
27 28 2.152699 CACGTGACGAGGCGACATC 61.153 63.158 13.70 0.00 34.08 3.06
28 29 2.579787 CGTGACGAGGCGACATCC 60.580 66.667 0.00 0.00 34.08 3.51
29 30 2.571757 GTGACGAGGCGACATCCA 59.428 61.111 0.00 0.00 34.08 3.41
30 31 1.805945 GTGACGAGGCGACATCCAC 60.806 63.158 0.00 0.00 34.08 4.02
31 32 2.202756 GACGAGGCGACATCCACC 60.203 66.667 0.00 0.00 0.00 4.61
32 33 3.718210 GACGAGGCGACATCCACCC 62.718 68.421 0.00 0.00 0.00 4.61
33 34 3.461773 CGAGGCGACATCCACCCT 61.462 66.667 0.00 0.00 0.00 4.34
34 35 2.501610 GAGGCGACATCCACCCTC 59.498 66.667 0.00 0.00 37.33 4.30
35 36 3.083997 AGGCGACATCCACCCTCC 61.084 66.667 0.00 0.00 0.00 4.30
36 37 4.176752 GGCGACATCCACCCTCCC 62.177 72.222 0.00 0.00 0.00 4.30
37 38 3.399181 GCGACATCCACCCTCCCA 61.399 66.667 0.00 0.00 0.00 4.37
38 39 2.746375 GCGACATCCACCCTCCCAT 61.746 63.158 0.00 0.00 0.00 4.00
39 40 1.447643 CGACATCCACCCTCCCATC 59.552 63.158 0.00 0.00 0.00 3.51
40 41 1.839894 GACATCCACCCTCCCATCC 59.160 63.158 0.00 0.00 0.00 3.51
41 42 0.695803 GACATCCACCCTCCCATCCT 60.696 60.000 0.00 0.00 0.00 3.24
42 43 0.647738 ACATCCACCCTCCCATCCTA 59.352 55.000 0.00 0.00 0.00 2.94
43 44 1.059913 CATCCACCCTCCCATCCTAC 58.940 60.000 0.00 0.00 0.00 3.18
44 45 0.471971 ATCCACCCTCCCATCCTACG 60.472 60.000 0.00 0.00 0.00 3.51
45 46 1.075525 CCACCCTCCCATCCTACGA 60.076 63.158 0.00 0.00 0.00 3.43
46 47 0.471971 CCACCCTCCCATCCTACGAT 60.472 60.000 0.00 0.00 0.00 3.73
47 48 1.424638 CACCCTCCCATCCTACGATT 58.575 55.000 0.00 0.00 0.00 3.34
48 49 1.768870 CACCCTCCCATCCTACGATTT 59.231 52.381 0.00 0.00 0.00 2.17
49 50 1.768870 ACCCTCCCATCCTACGATTTG 59.231 52.381 0.00 0.00 0.00 2.32
50 51 1.543429 CCCTCCCATCCTACGATTTGC 60.543 57.143 0.00 0.00 0.00 3.68
51 52 1.417890 CCTCCCATCCTACGATTTGCT 59.582 52.381 0.00 0.00 0.00 3.91
52 53 2.487934 CTCCCATCCTACGATTTGCTG 58.512 52.381 0.00 0.00 0.00 4.41
53 54 0.947244 CCCATCCTACGATTTGCTGC 59.053 55.000 0.00 0.00 0.00 5.25
54 55 0.583438 CCATCCTACGATTTGCTGCG 59.417 55.000 0.00 0.00 0.00 5.18
55 56 1.570813 CATCCTACGATTTGCTGCGA 58.429 50.000 0.00 0.00 0.00 5.10
56 57 2.138320 CATCCTACGATTTGCTGCGAT 58.862 47.619 0.00 0.00 0.00 4.58
57 58 1.852942 TCCTACGATTTGCTGCGATC 58.147 50.000 0.00 0.43 0.00 3.69
58 59 0.861837 CCTACGATTTGCTGCGATCC 59.138 55.000 9.35 0.00 0.00 3.36
59 60 0.861837 CTACGATTTGCTGCGATCCC 59.138 55.000 9.35 0.00 0.00 3.85
60 61 0.464036 TACGATTTGCTGCGATCCCT 59.536 50.000 9.35 0.38 0.00 4.20
61 62 1.091771 ACGATTTGCTGCGATCCCTG 61.092 55.000 9.35 0.97 0.00 4.45
62 63 1.358046 GATTTGCTGCGATCCCTGC 59.642 57.895 2.51 2.51 0.00 4.85
63 64 2.068277 GATTTGCTGCGATCCCTGCC 62.068 60.000 6.76 0.00 0.00 4.85
64 65 4.802051 TTGCTGCGATCCCTGCCC 62.802 66.667 6.76 0.00 0.00 5.36
67 68 4.899239 CTGCGATCCCTGCCCGTC 62.899 72.222 0.00 0.00 0.00 4.79
70 71 2.520982 CGATCCCTGCCCGTCCTA 60.521 66.667 0.00 0.00 0.00 2.94
71 72 2.565645 CGATCCCTGCCCGTCCTAG 61.566 68.421 0.00 0.00 0.00 3.02
72 73 2.844839 ATCCCTGCCCGTCCTAGC 60.845 66.667 0.00 0.00 0.00 3.42
81 82 3.885521 CGTCCTAGCCCCGACGTC 61.886 72.222 5.18 5.18 45.20 4.34
82 83 3.885521 GTCCTAGCCCCGACGTCG 61.886 72.222 30.33 30.33 39.44 5.12
83 84 4.100084 TCCTAGCCCCGACGTCGA 62.100 66.667 37.65 17.44 43.02 4.20
84 85 3.885521 CCTAGCCCCGACGTCGAC 61.886 72.222 37.65 25.14 43.02 4.20
85 86 3.129502 CTAGCCCCGACGTCGACA 61.130 66.667 37.65 16.40 43.02 4.35
86 87 3.392595 CTAGCCCCGACGTCGACAC 62.393 68.421 37.65 24.45 43.02 3.67
90 91 4.415332 CCCGACGTCGACACCCTG 62.415 72.222 37.65 19.12 43.02 4.45
91 92 4.415332 CCGACGTCGACACCCTGG 62.415 72.222 37.65 15.45 43.02 4.45
93 94 4.736896 GACGTCGACACCCTGGCC 62.737 72.222 17.16 0.00 0.00 5.36
99 100 3.792736 GACACCCTGGCCCGCATA 61.793 66.667 0.00 0.00 0.00 3.14
100 101 4.109675 ACACCCTGGCCCGCATAC 62.110 66.667 0.00 0.00 0.00 2.39
101 102 4.108299 CACCCTGGCCCGCATACA 62.108 66.667 0.00 0.00 0.00 2.29
102 103 3.334891 ACCCTGGCCCGCATACAA 61.335 61.111 0.00 0.00 0.00 2.41
103 104 2.516930 CCCTGGCCCGCATACAAG 60.517 66.667 0.00 0.00 0.00 3.16
104 105 3.211963 CCTGGCCCGCATACAAGC 61.212 66.667 0.00 0.00 0.00 4.01
105 106 2.438254 CTGGCCCGCATACAAGCA 60.438 61.111 0.00 0.00 0.00 3.91
106 107 2.438254 TGGCCCGCATACAAGCAG 60.438 61.111 0.00 0.00 0.00 4.24
107 108 3.211963 GGCCCGCATACAAGCAGG 61.212 66.667 0.00 0.00 35.13 4.85
108 109 2.438434 GCCCGCATACAAGCAGGT 60.438 61.111 0.00 0.00 34.50 4.00
109 110 2.764314 GCCCGCATACAAGCAGGTG 61.764 63.158 0.00 0.00 34.50 4.00
110 111 2.764314 CCCGCATACAAGCAGGTGC 61.764 63.158 0.00 0.00 42.49 5.01
111 112 2.039974 CCGCATACAAGCAGGTGCA 61.040 57.895 4.48 0.00 45.16 4.57
112 113 1.378882 CCGCATACAAGCAGGTGCAT 61.379 55.000 4.48 0.00 45.16 3.96
113 114 0.248336 CGCATACAAGCAGGTGCATG 60.248 55.000 4.48 5.12 44.42 4.06
114 115 0.526954 GCATACAAGCAGGTGCATGC 60.527 55.000 11.82 11.82 42.85 4.06
552 553 4.731612 CTCGCAGCAGCAGACGGT 62.732 66.667 0.82 0.00 42.27 4.83
553 554 4.724602 TCGCAGCAGCAGACGGTC 62.725 66.667 0.82 0.00 42.27 4.79
555 556 3.117171 GCAGCAGCAGACGGTCAG 61.117 66.667 11.27 3.23 41.58 3.51
556 557 3.117171 CAGCAGCAGACGGTCAGC 61.117 66.667 16.68 16.68 0.00 4.26
557 558 4.731612 AGCAGCAGACGGTCAGCG 62.732 66.667 18.03 14.13 33.83 5.18
573 574 4.986587 CGCCGTCGGTGACAACGA 62.987 66.667 20.30 12.49 34.74 3.85
574 575 3.103911 GCCGTCGGTGACAACGAG 61.104 66.667 17.48 6.82 41.50 4.18
575 576 3.103911 CCGTCGGTGACAACGAGC 61.104 66.667 17.48 10.35 41.50 5.03
576 577 2.050351 CGTCGGTGACAACGAGCT 60.050 61.111 17.48 0.00 41.50 4.09
577 578 2.081212 CGTCGGTGACAACGAGCTC 61.081 63.158 17.48 2.73 41.50 4.09
578 579 1.007734 GTCGGTGACAACGAGCTCA 60.008 57.895 17.48 0.00 41.50 4.26
579 580 0.388649 GTCGGTGACAACGAGCTCAT 60.389 55.000 17.48 0.00 41.50 2.90
580 581 0.109272 TCGGTGACAACGAGCTCATC 60.109 55.000 12.49 5.96 35.12 2.92
588 589 3.772636 CGAGCTCATCGTGTGGTG 58.227 61.111 15.40 0.00 46.62 4.17
589 590 1.807165 CGAGCTCATCGTGTGGTGG 60.807 63.158 15.40 0.00 46.62 4.61
590 591 1.293498 GAGCTCATCGTGTGGTGGT 59.707 57.895 9.40 0.00 0.00 4.16
591 592 1.004560 AGCTCATCGTGTGGTGGTG 60.005 57.895 0.00 0.00 0.00 4.17
592 593 2.034879 GCTCATCGTGTGGTGGTGG 61.035 63.158 0.00 0.00 0.00 4.61
593 594 1.375908 CTCATCGTGTGGTGGTGGG 60.376 63.158 0.00 0.00 0.00 4.61
594 595 3.055719 CATCGTGTGGTGGTGGGC 61.056 66.667 0.00 0.00 0.00 5.36
595 596 3.565214 ATCGTGTGGTGGTGGGCA 61.565 61.111 0.00 0.00 0.00 5.36
596 597 3.842925 ATCGTGTGGTGGTGGGCAC 62.843 63.158 0.00 0.00 0.00 5.01
598 599 4.555709 GTGTGGTGGTGGGCACGA 62.556 66.667 0.00 0.00 0.00 4.35
599 600 4.248842 TGTGGTGGTGGGCACGAG 62.249 66.667 0.00 0.00 0.00 4.18
603 604 3.717294 GTGGTGGGCACGAGGGAT 61.717 66.667 0.00 0.00 0.00 3.85
604 605 2.933287 TGGTGGGCACGAGGGATT 60.933 61.111 0.00 0.00 0.00 3.01
605 606 2.355115 GGTGGGCACGAGGGATTT 59.645 61.111 0.00 0.00 0.00 2.17
606 607 1.304134 GGTGGGCACGAGGGATTTT 60.304 57.895 0.00 0.00 0.00 1.82
607 608 1.595093 GGTGGGCACGAGGGATTTTG 61.595 60.000 0.00 0.00 0.00 2.44
608 609 0.608035 GTGGGCACGAGGGATTTTGA 60.608 55.000 0.00 0.00 0.00 2.69
609 610 0.331278 TGGGCACGAGGGATTTTGAT 59.669 50.000 0.00 0.00 0.00 2.57
610 611 0.740737 GGGCACGAGGGATTTTGATG 59.259 55.000 0.00 0.00 0.00 3.07
611 612 0.740737 GGCACGAGGGATTTTGATGG 59.259 55.000 0.00 0.00 0.00 3.51
612 613 1.681780 GGCACGAGGGATTTTGATGGA 60.682 52.381 0.00 0.00 0.00 3.41
613 614 1.672881 GCACGAGGGATTTTGATGGAG 59.327 52.381 0.00 0.00 0.00 3.86
614 615 1.672881 CACGAGGGATTTTGATGGAGC 59.327 52.381 0.00 0.00 0.00 4.70
615 616 1.281867 ACGAGGGATTTTGATGGAGCA 59.718 47.619 0.00 0.00 0.00 4.26
616 617 1.945394 CGAGGGATTTTGATGGAGCAG 59.055 52.381 0.00 0.00 0.00 4.24
617 618 1.680207 GAGGGATTTTGATGGAGCAGC 59.320 52.381 0.00 0.00 0.00 5.25
618 619 1.006281 AGGGATTTTGATGGAGCAGCA 59.994 47.619 0.00 0.00 0.00 4.41
619 620 1.826720 GGGATTTTGATGGAGCAGCAA 59.173 47.619 0.00 0.00 38.00 3.91
620 621 2.417787 GGGATTTTGATGGAGCAGCAAC 60.418 50.000 0.00 0.00 39.50 4.17
621 622 2.231964 GGATTTTGATGGAGCAGCAACA 59.768 45.455 0.00 0.00 39.50 3.33
622 623 3.118884 GGATTTTGATGGAGCAGCAACAT 60.119 43.478 0.00 0.00 39.50 2.71
623 624 3.306917 TTTTGATGGAGCAGCAACATG 57.693 42.857 6.57 0.00 39.50 3.21
624 625 1.179152 TTGATGGAGCAGCAACATGG 58.821 50.000 6.57 0.00 34.77 3.66
625 626 1.317431 TGATGGAGCAGCAACATGGC 61.317 55.000 6.57 0.00 0.00 4.40
626 627 2.332362 GATGGAGCAGCAACATGGCG 62.332 60.000 6.57 0.00 39.27 5.69
627 628 2.747460 GGAGCAGCAACATGGCGA 60.747 61.111 0.00 0.00 39.27 5.54
628 629 2.758089 GGAGCAGCAACATGGCGAG 61.758 63.158 0.00 0.00 39.27 5.03
629 630 1.742880 GAGCAGCAACATGGCGAGA 60.743 57.895 0.00 0.00 39.27 4.04
630 631 1.703438 GAGCAGCAACATGGCGAGAG 61.703 60.000 0.00 0.00 39.27 3.20
631 632 1.742880 GCAGCAACATGGCGAGAGA 60.743 57.895 0.00 0.00 39.27 3.10
632 633 1.300971 GCAGCAACATGGCGAGAGAA 61.301 55.000 0.00 0.00 39.27 2.87
633 634 1.159285 CAGCAACATGGCGAGAGAAA 58.841 50.000 0.00 0.00 39.27 2.52
634 635 1.536766 CAGCAACATGGCGAGAGAAAA 59.463 47.619 0.00 0.00 39.27 2.29
635 636 2.030893 CAGCAACATGGCGAGAGAAAAA 60.031 45.455 0.00 0.00 39.27 1.94
650 651 1.210155 AAAAAGATGCGGTGCGAGC 59.790 52.632 0.00 0.00 0.00 5.03
651 652 2.513065 AAAAAGATGCGGTGCGAGCG 62.513 55.000 3.84 3.84 42.73 5.03
652 653 3.932580 AAAGATGCGGTGCGAGCGA 62.933 57.895 11.05 0.00 42.41 4.93
653 654 4.862092 AGATGCGGTGCGAGCGAG 62.862 66.667 11.05 0.00 42.41 5.03
658 659 4.406173 CGGTGCGAGCGAGTGACT 62.406 66.667 2.25 0.00 42.41 3.41
659 660 2.505118 GGTGCGAGCGAGTGACTC 60.505 66.667 1.65 1.65 0.00 3.36
668 669 2.202324 GAGTGACTCGGACGTCGC 60.202 66.667 9.92 10.96 43.03 5.19
669 670 3.664223 GAGTGACTCGGACGTCGCC 62.664 68.421 9.92 0.00 43.57 5.54
684 685 2.126071 GCCGTGCGTGCTTAGAGA 60.126 61.111 0.00 0.00 0.00 3.10
685 686 1.736645 GCCGTGCGTGCTTAGAGAA 60.737 57.895 0.00 0.00 0.00 2.87
686 687 1.687494 GCCGTGCGTGCTTAGAGAAG 61.687 60.000 0.00 0.00 35.60 2.85
687 688 1.078759 CCGTGCGTGCTTAGAGAAGG 61.079 60.000 0.00 0.00 32.84 3.46
688 689 1.078759 CGTGCGTGCTTAGAGAAGGG 61.079 60.000 0.00 0.00 32.84 3.95
689 690 0.741221 GTGCGTGCTTAGAGAAGGGG 60.741 60.000 0.00 0.00 32.84 4.79
690 691 1.815840 GCGTGCTTAGAGAAGGGGC 60.816 63.158 0.00 0.00 32.84 5.80
691 692 1.519455 CGTGCTTAGAGAAGGGGCG 60.519 63.158 0.00 0.00 32.84 6.13
692 693 1.597461 GTGCTTAGAGAAGGGGCGT 59.403 57.895 0.00 0.00 32.84 5.68
693 694 0.460459 GTGCTTAGAGAAGGGGCGTC 60.460 60.000 0.00 0.00 32.84 5.19
694 695 0.614979 TGCTTAGAGAAGGGGCGTCT 60.615 55.000 0.00 0.00 32.84 4.18
695 696 0.103390 GCTTAGAGAAGGGGCGTCTC 59.897 60.000 3.92 3.92 41.62 3.36
696 697 1.475403 CTTAGAGAAGGGGCGTCTCA 58.525 55.000 12.27 0.00 43.39 3.27
697 698 1.135333 CTTAGAGAAGGGGCGTCTCAC 59.865 57.143 12.27 0.00 43.39 3.51
698 699 0.331954 TAGAGAAGGGGCGTCTCACT 59.668 55.000 12.27 0.00 43.39 3.41
699 700 0.543174 AGAGAAGGGGCGTCTCACTT 60.543 55.000 12.27 0.00 43.39 3.16
700 701 0.390472 GAGAAGGGGCGTCTCACTTG 60.390 60.000 0.00 0.00 41.08 3.16
701 702 1.376037 GAAGGGGCGTCTCACTTGG 60.376 63.158 0.00 0.00 0.00 3.61
702 703 2.804828 GAAGGGGCGTCTCACTTGGG 62.805 65.000 0.00 0.00 0.00 4.12
707 708 3.636231 CGTCTCACTTGGGCCCCA 61.636 66.667 22.27 7.58 0.00 4.96
708 709 2.971598 CGTCTCACTTGGGCCCCAT 61.972 63.158 22.27 0.28 31.53 4.00
709 710 1.077429 GTCTCACTTGGGCCCCATC 60.077 63.158 22.27 0.00 31.53 3.51
710 711 1.541118 TCTCACTTGGGCCCCATCA 60.541 57.895 22.27 0.00 31.53 3.07
711 712 1.139498 TCTCACTTGGGCCCCATCAA 61.139 55.000 22.27 5.57 31.53 2.57
712 713 0.682209 CTCACTTGGGCCCCATCAAG 60.682 60.000 22.27 18.68 44.14 3.02
713 714 1.683365 CACTTGGGCCCCATCAAGG 60.683 63.158 22.27 2.32 43.20 3.61
720 721 2.751436 CCCCATCAAGGCACGTGG 60.751 66.667 18.88 0.00 38.64 4.94
721 722 3.443045 CCCATCAAGGCACGTGGC 61.443 66.667 32.77 32.77 38.64 5.01
730 731 2.594592 GCACGTGGCCAACTTCCT 60.595 61.111 18.88 0.00 36.11 3.36
731 732 2.617274 GCACGTGGCCAACTTCCTC 61.617 63.158 18.88 0.00 36.11 3.71
732 733 2.030562 ACGTGGCCAACTTCCTCG 59.969 61.111 7.24 7.72 43.71 4.63
733 734 3.423154 CGTGGCCAACTTCCTCGC 61.423 66.667 7.24 0.00 34.51 5.03
734 735 3.423154 GTGGCCAACTTCCTCGCG 61.423 66.667 7.24 0.00 0.00 5.87
735 736 3.936203 TGGCCAACTTCCTCGCGT 61.936 61.111 0.61 0.00 0.00 6.01
736 737 3.423154 GGCCAACTTCCTCGCGTG 61.423 66.667 5.77 2.75 0.00 5.34
737 738 3.423154 GCCAACTTCCTCGCGTGG 61.423 66.667 20.92 20.92 0.00 4.94
738 739 2.342279 CCAACTTCCTCGCGTGGA 59.658 61.111 25.07 25.07 0.00 4.02
739 740 1.301401 CCAACTTCCTCGCGTGGAA 60.301 57.895 33.30 33.30 43.16 3.53
740 741 0.673644 CCAACTTCCTCGCGTGGAAT 60.674 55.000 34.96 22.73 44.17 3.01
741 742 0.443869 CAACTTCCTCGCGTGGAATG 59.556 55.000 34.96 28.12 44.17 2.67
742 743 0.034896 AACTTCCTCGCGTGGAATGT 59.965 50.000 34.96 29.58 44.17 2.71
743 744 0.892755 ACTTCCTCGCGTGGAATGTA 59.107 50.000 34.96 18.64 44.17 2.29
744 745 1.135083 ACTTCCTCGCGTGGAATGTAG 60.135 52.381 34.96 27.05 44.17 2.74
745 746 0.174845 TTCCTCGCGTGGAATGTAGG 59.825 55.000 32.50 17.78 40.80 3.18
746 747 1.883084 CCTCGCGTGGAATGTAGGC 60.883 63.158 22.35 0.00 0.00 3.93
748 749 2.508439 CGCGTGGAATGTAGGCGT 60.508 61.111 0.00 0.00 44.50 5.68
749 750 2.798501 CGCGTGGAATGTAGGCGTG 61.799 63.158 0.00 0.00 44.50 5.34
750 751 3.089784 CGTGGAATGTAGGCGTGC 58.910 61.111 0.00 0.00 0.00 5.34
751 752 2.798501 CGTGGAATGTAGGCGTGCG 61.799 63.158 0.00 0.00 0.00 5.34
752 753 1.447140 GTGGAATGTAGGCGTGCGA 60.447 57.895 0.00 0.00 0.00 5.10
753 754 1.017177 GTGGAATGTAGGCGTGCGAA 61.017 55.000 0.00 0.00 0.00 4.70
754 755 0.739462 TGGAATGTAGGCGTGCGAAG 60.739 55.000 0.00 0.00 0.00 3.79
755 756 1.429148 GGAATGTAGGCGTGCGAAGG 61.429 60.000 0.00 0.00 0.00 3.46
756 757 2.036764 GAATGTAGGCGTGCGAAGGC 62.037 60.000 0.00 0.00 40.52 4.35
758 759 4.789075 GTAGGCGTGCGAAGGCGA 62.789 66.667 1.21 0.00 44.10 5.54
759 760 4.789075 TAGGCGTGCGAAGGCGAC 62.789 66.667 1.21 0.00 44.10 5.19
767 768 4.831307 CGAAGGCGACCGACGGAG 62.831 72.222 23.38 15.04 42.83 4.63
795 796 3.107017 GGTCAGCCGAATTTGCAAC 57.893 52.632 0.00 0.00 0.00 4.17
796 797 0.313672 GGTCAGCCGAATTTGCAACA 59.686 50.000 0.00 0.00 0.00 3.33
797 798 1.408422 GTCAGCCGAATTTGCAACAC 58.592 50.000 0.00 0.00 0.00 3.32
798 799 1.001378 GTCAGCCGAATTTGCAACACT 60.001 47.619 0.00 0.00 0.00 3.55
799 800 1.680735 TCAGCCGAATTTGCAACACTT 59.319 42.857 0.00 0.00 0.00 3.16
800 801 2.100584 TCAGCCGAATTTGCAACACTTT 59.899 40.909 0.00 0.00 0.00 2.66
801 802 2.472488 CAGCCGAATTTGCAACACTTTC 59.528 45.455 0.00 0.00 0.00 2.62
802 803 1.792367 GCCGAATTTGCAACACTTTCC 59.208 47.619 0.00 0.00 0.00 3.13
803 804 2.801342 GCCGAATTTGCAACACTTTCCA 60.801 45.455 0.00 0.00 0.00 3.53
804 805 3.452474 CCGAATTTGCAACACTTTCCAA 58.548 40.909 0.00 0.00 0.00 3.53
805 806 3.868077 CCGAATTTGCAACACTTTCCAAA 59.132 39.130 0.00 0.00 0.00 3.28
806 807 4.025813 CCGAATTTGCAACACTTTCCAAAG 60.026 41.667 0.00 0.00 41.73 2.77
807 808 4.803088 CGAATTTGCAACACTTTCCAAAGA 59.197 37.500 0.00 0.00 39.31 2.52
808 809 5.290643 CGAATTTGCAACACTTTCCAAAGAA 59.709 36.000 0.00 0.00 39.31 2.52
809 810 6.183360 CGAATTTGCAACACTTTCCAAAGAAA 60.183 34.615 0.00 0.00 39.70 2.52
810 811 7.446001 AATTTGCAACACTTTCCAAAGAAAA 57.554 28.000 0.00 0.00 41.40 2.29
811 812 6.479095 TTTGCAACACTTTCCAAAGAAAAG 57.521 33.333 0.00 0.00 41.40 2.27
812 813 5.398603 TGCAACACTTTCCAAAGAAAAGA 57.601 34.783 6.05 0.00 41.40 2.52
813 814 5.788450 TGCAACACTTTCCAAAGAAAAGAA 58.212 33.333 6.05 0.00 41.40 2.52
814 815 5.637387 TGCAACACTTTCCAAAGAAAAGAAC 59.363 36.000 6.05 0.00 41.40 3.01
815 816 5.063438 GCAACACTTTCCAAAGAAAAGAACC 59.937 40.000 6.05 0.00 41.40 3.62
816 817 6.398095 CAACACTTTCCAAAGAAAAGAACCT 58.602 36.000 6.05 0.00 41.40 3.50
817 818 5.965922 ACACTTTCCAAAGAAAAGAACCTG 58.034 37.500 6.05 0.00 41.40 4.00
822 823 7.780271 ACTTTCCAAAGAAAAGAACCTGAGTAT 59.220 33.333 6.05 0.00 41.40 2.12
828 829 9.249457 CAAAGAAAAGAACCTGAGTATTTTTCC 57.751 33.333 4.45 0.00 38.23 3.13
867 868 2.287103 AGAACGTGACGAAAGAAAAGGC 59.713 45.455 13.70 0.00 0.00 4.35
902 908 7.363968 CCGTAGATAAGGAGATATTTTCCCTCC 60.364 44.444 0.00 0.00 45.16 4.30
940 946 3.440522 AGAGAAGATTTTAAACGCCCTGC 59.559 43.478 0.00 0.00 0.00 4.85
1015 1023 1.635663 CGCCATGTTCCAACTCCGAC 61.636 60.000 0.00 0.00 0.00 4.79
1023 1031 2.660552 CAACTCCGACCGCGTGTT 60.661 61.111 4.92 0.00 34.34 3.32
1082 1090 2.107141 CCGCGTCAATCCCCTCTC 59.893 66.667 4.92 0.00 0.00 3.20
1762 1779 3.067106 GAGAAGCTCACCGACAAAATCA 58.933 45.455 0.00 0.00 0.00 2.57
1902 1919 1.141657 GTTGCTGGGCTGGAGATATCA 59.858 52.381 5.32 0.00 0.00 2.15
1995 2012 0.608640 AGCTACTCAACACGAAGGGG 59.391 55.000 0.00 0.00 0.00 4.79
2007 2024 0.035056 CGAAGGGGTTGCTGGATCTT 60.035 55.000 0.00 0.00 0.00 2.40
2171 2188 7.748847 TCAGAGAACACAAAACAAAACTAGAC 58.251 34.615 0.00 0.00 0.00 2.59
2212 2242 1.312815 GTGAGCACCATAGGATTGCC 58.687 55.000 0.00 0.00 36.91 4.52
2213 2243 0.918258 TGAGCACCATAGGATTGCCA 59.082 50.000 0.00 0.00 36.91 4.92
2214 2244 1.496001 TGAGCACCATAGGATTGCCAT 59.504 47.619 0.00 0.00 36.91 4.40
2215 2245 1.884579 GAGCACCATAGGATTGCCATG 59.115 52.381 0.00 0.00 36.91 3.66
2216 2246 1.216175 AGCACCATAGGATTGCCATGT 59.784 47.619 0.00 0.00 36.91 3.21
2217 2247 2.034124 GCACCATAGGATTGCCATGTT 58.966 47.619 0.00 0.00 36.29 2.71
2218 2248 2.223876 GCACCATAGGATTGCCATGTTG 60.224 50.000 0.00 0.00 36.29 3.33
2219 2249 2.363038 CACCATAGGATTGCCATGTTGG 59.637 50.000 0.00 0.00 41.55 3.77
2358 2388 4.767578 TCATCTTGCCAGAAATAGAGCT 57.232 40.909 0.00 0.00 30.76 4.09
2392 2422 4.448720 TCTGGGAATGATCATGCTTGAT 57.551 40.909 14.48 14.48 45.39 2.57
2508 2538 1.840635 GGGGAACTGCTAGGAATCAGT 59.159 52.381 0.00 0.00 44.64 3.41
2521 2551 2.292267 GAATCAGTTCATGCGTGGGAT 58.708 47.619 5.98 2.16 34.41 3.85
2523 2553 0.612744 TCAGTTCATGCGTGGGATGA 59.387 50.000 5.98 5.04 0.00 2.92
2549 2579 2.100749 TGTATGGACGGTGCATGAGTAG 59.899 50.000 23.20 0.00 29.08 2.57
2554 2584 1.472878 GACGGTGCATGAGTAGTCTGA 59.527 52.381 0.00 0.00 0.00 3.27
2576 2606 7.065443 TCTGACGATTTCTTTCTATCAGACGTA 59.935 37.037 0.00 0.00 36.94 3.57
2687 2719 2.035066 GTGTTGGCTTCAGCTGTTCAAT 59.965 45.455 14.67 0.00 41.70 2.57
2756 2788 7.337942 CCAAGTTGAAATCATTTAGAGCCTACT 59.662 37.037 3.87 0.00 0.00 2.57
2831 2864 9.169592 GATGGAATGATTTTTGAAAATGGTGAT 57.830 29.630 6.44 0.00 38.64 3.06
2876 2909 9.354673 GAGATATTAATTTTGTCTTGATGGGGA 57.645 33.333 0.00 0.00 0.00 4.81
2998 3031 2.159142 ACAACCGAGTTCTCGTTTCTGT 60.159 45.455 18.59 13.00 0.00 3.41
3010 3043 8.674607 AGTTCTCGTTTCTGTTATGTTTTTCTT 58.325 29.630 0.00 0.00 0.00 2.52
3034 3067 5.584251 TCTTTCTTGAAACAAACAATTGGCC 59.416 36.000 10.83 0.00 41.01 5.36
3132 3165 8.206126 TGTTATATATCAGCTCCTCAAATGGA 57.794 34.615 0.00 0.00 34.52 3.41
3140 3173 2.751806 GCTCCTCAAATGGAAGAAGGTG 59.248 50.000 0.00 0.00 35.43 4.00
3151 3184 0.034059 AAGAAGGTGTGCAGACCTCG 59.966 55.000 33.55 0.00 46.29 4.63
3158 3191 2.418746 GGTGTGCAGACCTCGTGATAAT 60.419 50.000 25.15 0.00 32.69 1.28
3164 3197 5.581085 GTGCAGACCTCGTGATAATAAAACT 59.419 40.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.626680 CTCGTCACGTGGATGCCGT 62.627 63.158 17.00 0.00 39.52 5.68
2 3 2.880879 CTCGTCACGTGGATGCCG 60.881 66.667 17.00 10.45 32.27 5.69
3 4 2.509336 CCTCGTCACGTGGATGCC 60.509 66.667 17.00 0.00 42.19 4.40
4 5 3.188786 GCCTCGTCACGTGGATGC 61.189 66.667 22.33 10.70 42.19 3.91
5 6 2.880879 CGCCTCGTCACGTGGATG 60.881 66.667 22.33 9.34 42.19 3.51
6 7 3.060000 TCGCCTCGTCACGTGGAT 61.060 61.111 22.33 0.00 42.19 3.41
7 8 4.034258 GTCGCCTCGTCACGTGGA 62.034 66.667 22.33 4.94 42.19 4.02
8 9 3.626680 ATGTCGCCTCGTCACGTGG 62.627 63.158 17.00 14.11 42.44 4.94
9 10 2.126463 ATGTCGCCTCGTCACGTG 60.126 61.111 9.94 9.94 0.00 4.49
10 11 2.178521 GATGTCGCCTCGTCACGT 59.821 61.111 0.00 0.00 0.00 4.49
11 12 2.579787 GGATGTCGCCTCGTCACG 60.580 66.667 0.00 0.00 0.00 4.35
12 13 1.805945 GTGGATGTCGCCTCGTCAC 60.806 63.158 0.00 0.00 0.00 3.67
13 14 2.571757 GTGGATGTCGCCTCGTCA 59.428 61.111 0.00 0.00 0.00 4.35
14 15 2.202756 GGTGGATGTCGCCTCGTC 60.203 66.667 0.00 0.00 42.62 4.20
15 16 3.771160 GGGTGGATGTCGCCTCGT 61.771 66.667 0.00 0.00 45.18 4.18
16 17 3.432051 GAGGGTGGATGTCGCCTCG 62.432 68.421 0.00 0.00 45.18 4.63
17 18 2.501610 GAGGGTGGATGTCGCCTC 59.498 66.667 0.00 0.00 45.18 4.70
18 19 3.083997 GGAGGGTGGATGTCGCCT 61.084 66.667 0.00 0.00 45.18 5.52
19 20 4.176752 GGGAGGGTGGATGTCGCC 62.177 72.222 0.00 0.00 45.12 5.54
20 21 2.666596 GATGGGAGGGTGGATGTCGC 62.667 65.000 0.00 0.00 0.00 5.19
21 22 1.447643 GATGGGAGGGTGGATGTCG 59.552 63.158 0.00 0.00 0.00 4.35
22 23 0.695803 AGGATGGGAGGGTGGATGTC 60.696 60.000 0.00 0.00 0.00 3.06
23 24 0.647738 TAGGATGGGAGGGTGGATGT 59.352 55.000 0.00 0.00 0.00 3.06
24 25 1.059913 GTAGGATGGGAGGGTGGATG 58.940 60.000 0.00 0.00 0.00 3.51
25 26 0.471971 CGTAGGATGGGAGGGTGGAT 60.472 60.000 0.00 0.00 0.00 3.41
26 27 1.075525 CGTAGGATGGGAGGGTGGA 60.076 63.158 0.00 0.00 0.00 4.02
27 28 0.471971 ATCGTAGGATGGGAGGGTGG 60.472 60.000 0.00 0.00 0.00 4.61
28 29 1.424638 AATCGTAGGATGGGAGGGTG 58.575 55.000 0.00 0.00 31.83 4.61
29 30 1.768870 CAAATCGTAGGATGGGAGGGT 59.231 52.381 0.00 0.00 31.83 4.34
30 31 1.543429 GCAAATCGTAGGATGGGAGGG 60.543 57.143 0.00 0.00 31.83 4.30
31 32 1.417890 AGCAAATCGTAGGATGGGAGG 59.582 52.381 0.00 0.00 31.83 4.30
32 33 2.487934 CAGCAAATCGTAGGATGGGAG 58.512 52.381 0.00 0.00 31.83 4.30
33 34 1.475034 GCAGCAAATCGTAGGATGGGA 60.475 52.381 0.00 0.00 31.83 4.37
34 35 0.947244 GCAGCAAATCGTAGGATGGG 59.053 55.000 0.00 0.00 31.83 4.00
35 36 0.583438 CGCAGCAAATCGTAGGATGG 59.417 55.000 0.00 0.00 31.83 3.51
36 37 1.570813 TCGCAGCAAATCGTAGGATG 58.429 50.000 0.00 0.00 31.83 3.51
37 38 2.408050 GATCGCAGCAAATCGTAGGAT 58.592 47.619 0.00 0.00 0.00 3.24
38 39 1.538204 GGATCGCAGCAAATCGTAGGA 60.538 52.381 0.00 0.00 0.00 2.94
39 40 0.861837 GGATCGCAGCAAATCGTAGG 59.138 55.000 0.00 0.00 0.00 3.18
40 41 0.861837 GGGATCGCAGCAAATCGTAG 59.138 55.000 4.64 0.00 0.00 3.51
41 42 0.464036 AGGGATCGCAGCAAATCGTA 59.536 50.000 12.83 0.00 0.00 3.43
42 43 1.091771 CAGGGATCGCAGCAAATCGT 61.092 55.000 12.83 0.00 0.00 3.73
43 44 1.645455 CAGGGATCGCAGCAAATCG 59.355 57.895 12.83 0.00 0.00 3.34
44 45 1.358046 GCAGGGATCGCAGCAAATC 59.642 57.895 20.14 0.00 0.00 2.17
45 46 2.123428 GGCAGGGATCGCAGCAAAT 61.123 57.895 24.90 0.00 0.00 2.32
46 47 2.751436 GGCAGGGATCGCAGCAAA 60.751 61.111 24.90 0.00 0.00 3.68
47 48 4.802051 GGGCAGGGATCGCAGCAA 62.802 66.667 24.90 0.00 0.00 3.91
50 51 4.899239 GACGGGCAGGGATCGCAG 62.899 72.222 12.83 5.08 0.00 5.18
53 54 2.520982 TAGGACGGGCAGGGATCG 60.521 66.667 0.00 0.00 0.00 3.69
54 55 2.873525 GCTAGGACGGGCAGGGATC 61.874 68.421 0.00 0.00 0.00 3.36
55 56 2.844839 GCTAGGACGGGCAGGGAT 60.845 66.667 0.00 0.00 0.00 3.85
65 66 3.885521 CGACGTCGGGGCTAGGAC 61.886 72.222 29.70 0.00 35.37 3.85
66 67 4.100084 TCGACGTCGGGGCTAGGA 62.100 66.667 35.05 12.79 40.29 2.94
67 68 3.885521 GTCGACGTCGGGGCTAGG 61.886 72.222 35.05 7.30 40.29 3.02
68 69 3.129502 TGTCGACGTCGGGGCTAG 61.130 66.667 35.05 8.08 40.29 3.42
69 70 3.434319 GTGTCGACGTCGGGGCTA 61.434 66.667 35.05 15.12 40.29 3.93
73 74 4.415332 CAGGGTGTCGACGTCGGG 62.415 72.222 35.05 11.19 40.29 5.14
74 75 4.415332 CCAGGGTGTCGACGTCGG 62.415 72.222 35.05 18.23 40.29 4.79
76 77 4.736896 GGCCAGGGTGTCGACGTC 62.737 72.222 11.62 5.18 0.00 4.34
82 83 3.792736 TATGCGGGCCAGGGTGTC 61.793 66.667 4.39 0.00 0.00 3.67
83 84 4.109675 GTATGCGGGCCAGGGTGT 62.110 66.667 4.39 0.00 0.00 4.16
84 85 3.636929 TTGTATGCGGGCCAGGGTG 62.637 63.158 4.39 0.00 0.00 4.61
85 86 3.334891 TTGTATGCGGGCCAGGGT 61.335 61.111 4.39 0.00 0.00 4.34
86 87 2.516930 CTTGTATGCGGGCCAGGG 60.517 66.667 4.39 0.00 0.00 4.45
87 88 3.211963 GCTTGTATGCGGGCCAGG 61.212 66.667 4.39 0.00 0.00 4.45
88 89 2.438254 TGCTTGTATGCGGGCCAG 60.438 61.111 4.39 0.00 35.36 4.85
89 90 2.438254 CTGCTTGTATGCGGGCCA 60.438 61.111 4.39 0.00 35.80 5.36
93 94 1.378882 ATGCACCTGCTTGTATGCGG 61.379 55.000 0.00 0.00 41.07 5.69
94 95 0.248336 CATGCACCTGCTTGTATGCG 60.248 55.000 0.00 0.00 41.07 4.73
95 96 3.635433 CATGCACCTGCTTGTATGC 57.365 52.632 0.00 0.00 42.66 3.14
96 97 0.248336 CGCATGCACCTGCTTGTATG 60.248 55.000 19.57 7.07 44.86 2.39
97 98 1.996786 GCGCATGCACCTGCTTGTAT 61.997 55.000 19.57 0.00 44.86 2.29
98 99 2.689785 GCGCATGCACCTGCTTGTA 61.690 57.895 19.57 0.00 44.86 2.41
99 100 4.047059 GCGCATGCACCTGCTTGT 62.047 61.111 19.57 0.00 44.86 3.16
100 101 4.789075 GGCGCATGCACCTGCTTG 62.789 66.667 17.66 8.45 45.35 4.01
535 536 4.731612 ACCGTCTGCTGCTGCGAG 62.732 66.667 18.84 9.43 43.34 5.03
536 537 4.724602 GACCGTCTGCTGCTGCGA 62.725 66.667 18.84 8.36 43.34 5.10
538 539 3.117171 CTGACCGTCTGCTGCTGC 61.117 66.667 8.89 8.89 40.20 5.25
539 540 3.117171 GCTGACCGTCTGCTGCTG 61.117 66.667 19.91 0.00 38.17 4.41
540 541 4.731612 CGCTGACCGTCTGCTGCT 62.732 66.667 23.14 0.00 38.90 4.24
556 557 4.986587 TCGTTGTCACCGACGGCG 62.987 66.667 15.39 1.94 46.42 6.46
557 558 3.103911 CTCGTTGTCACCGACGGC 61.104 66.667 15.39 0.00 46.42 5.68
558 559 3.103911 GCTCGTTGTCACCGACGG 61.104 66.667 13.61 13.61 46.42 4.79
560 561 0.388649 ATGAGCTCGTTGTCACCGAC 60.389 55.000 9.64 0.00 0.00 4.79
561 562 0.109272 GATGAGCTCGTTGTCACCGA 60.109 55.000 10.42 0.00 0.00 4.69
562 563 1.406219 CGATGAGCTCGTTGTCACCG 61.406 60.000 10.42 3.94 42.56 4.94
563 564 2.363807 CGATGAGCTCGTTGTCACC 58.636 57.895 10.42 0.00 42.56 4.02
572 573 1.016130 CACCACCACACGATGAGCTC 61.016 60.000 6.82 6.82 0.00 4.09
573 574 1.004560 CACCACCACACGATGAGCT 60.005 57.895 0.00 0.00 0.00 4.09
574 575 2.034879 CCACCACCACACGATGAGC 61.035 63.158 0.00 0.00 0.00 4.26
575 576 1.375908 CCCACCACCACACGATGAG 60.376 63.158 0.00 0.00 0.00 2.90
576 577 2.747022 CCCACCACCACACGATGA 59.253 61.111 0.00 0.00 0.00 2.92
577 578 3.055719 GCCCACCACCACACGATG 61.056 66.667 0.00 0.00 0.00 3.84
578 579 3.565214 TGCCCACCACCACACGAT 61.565 61.111 0.00 0.00 0.00 3.73
579 580 4.555709 GTGCCCACCACCACACGA 62.556 66.667 0.00 0.00 38.55 4.35
581 582 4.555709 TCGTGCCCACCACCACAC 62.556 66.667 0.00 0.00 41.53 3.82
582 583 4.248842 CTCGTGCCCACCACCACA 62.249 66.667 0.00 0.00 41.53 4.17
586 587 2.764637 AAATCCCTCGTGCCCACCAC 62.765 60.000 0.00 0.00 41.15 4.16
587 588 2.075355 AAAATCCCTCGTGCCCACCA 62.075 55.000 0.00 0.00 0.00 4.17
588 589 1.304134 AAAATCCCTCGTGCCCACC 60.304 57.895 0.00 0.00 0.00 4.61
589 590 0.608035 TCAAAATCCCTCGTGCCCAC 60.608 55.000 0.00 0.00 0.00 4.61
590 591 0.331278 ATCAAAATCCCTCGTGCCCA 59.669 50.000 0.00 0.00 0.00 5.36
591 592 0.740737 CATCAAAATCCCTCGTGCCC 59.259 55.000 0.00 0.00 0.00 5.36
592 593 0.740737 CCATCAAAATCCCTCGTGCC 59.259 55.000 0.00 0.00 0.00 5.01
593 594 1.672881 CTCCATCAAAATCCCTCGTGC 59.327 52.381 0.00 0.00 0.00 5.34
594 595 1.672881 GCTCCATCAAAATCCCTCGTG 59.327 52.381 0.00 0.00 0.00 4.35
595 596 1.281867 TGCTCCATCAAAATCCCTCGT 59.718 47.619 0.00 0.00 0.00 4.18
596 597 1.945394 CTGCTCCATCAAAATCCCTCG 59.055 52.381 0.00 0.00 0.00 4.63
597 598 1.680207 GCTGCTCCATCAAAATCCCTC 59.320 52.381 0.00 0.00 0.00 4.30
598 599 1.006281 TGCTGCTCCATCAAAATCCCT 59.994 47.619 0.00 0.00 0.00 4.20
599 600 1.477553 TGCTGCTCCATCAAAATCCC 58.522 50.000 0.00 0.00 0.00 3.85
600 601 2.231964 TGTTGCTGCTCCATCAAAATCC 59.768 45.455 0.00 0.00 0.00 3.01
601 602 3.581024 TGTTGCTGCTCCATCAAAATC 57.419 42.857 0.00 0.00 0.00 2.17
602 603 3.369052 CCATGTTGCTGCTCCATCAAAAT 60.369 43.478 0.00 0.00 0.00 1.82
603 604 2.028839 CCATGTTGCTGCTCCATCAAAA 60.029 45.455 0.00 0.00 0.00 2.44
604 605 1.546923 CCATGTTGCTGCTCCATCAAA 59.453 47.619 0.00 0.00 0.00 2.69
605 606 1.179152 CCATGTTGCTGCTCCATCAA 58.821 50.000 0.00 0.00 0.00 2.57
606 607 1.317431 GCCATGTTGCTGCTCCATCA 61.317 55.000 0.00 0.00 0.00 3.07
607 608 1.436336 GCCATGTTGCTGCTCCATC 59.564 57.895 0.00 0.00 0.00 3.51
608 609 2.412323 CGCCATGTTGCTGCTCCAT 61.412 57.895 0.00 0.00 0.00 3.41
609 610 3.057548 CGCCATGTTGCTGCTCCA 61.058 61.111 0.00 0.00 0.00 3.86
610 611 2.747460 TCGCCATGTTGCTGCTCC 60.747 61.111 0.00 0.00 0.00 4.70
611 612 1.703438 CTCTCGCCATGTTGCTGCTC 61.703 60.000 0.00 0.00 0.00 4.26
612 613 1.744368 CTCTCGCCATGTTGCTGCT 60.744 57.895 0.00 0.00 0.00 4.24
613 614 1.300971 TTCTCTCGCCATGTTGCTGC 61.301 55.000 0.00 0.00 0.00 5.25
614 615 1.159285 TTTCTCTCGCCATGTTGCTG 58.841 50.000 0.00 0.00 0.00 4.41
615 616 1.896220 TTTTCTCTCGCCATGTTGCT 58.104 45.000 0.00 0.00 0.00 3.91
616 617 2.704725 TTTTTCTCTCGCCATGTTGC 57.295 45.000 0.00 0.00 0.00 4.17
632 633 1.210155 GCTCGCACCGCATCTTTTT 59.790 52.632 0.00 0.00 0.00 1.94
633 634 2.870372 GCTCGCACCGCATCTTTT 59.130 55.556 0.00 0.00 0.00 2.27
634 635 3.490759 CGCTCGCACCGCATCTTT 61.491 61.111 0.00 0.00 0.00 2.52
635 636 4.435436 TCGCTCGCACCGCATCTT 62.435 61.111 0.00 0.00 0.00 2.40
636 637 4.862092 CTCGCTCGCACCGCATCT 62.862 66.667 0.00 0.00 0.00 2.90
641 642 4.406173 AGTCACTCGCTCGCACCG 62.406 66.667 0.00 0.00 0.00 4.94
642 643 2.505118 GAGTCACTCGCTCGCACC 60.505 66.667 0.00 0.00 0.00 5.01
643 644 2.872001 CGAGTCACTCGCTCGCAC 60.872 66.667 15.62 0.00 46.75 5.34
651 652 2.202324 GCGACGTCCGAGTCACTC 60.202 66.667 10.58 0.00 40.98 3.51
652 653 3.735029 GGCGACGTCCGAGTCACT 61.735 66.667 10.58 0.00 40.98 3.41
667 668 1.687494 CTTCTCTAAGCACGCACGGC 61.687 60.000 0.00 0.00 0.00 5.68
668 669 1.078759 CCTTCTCTAAGCACGCACGG 61.079 60.000 0.00 0.00 0.00 4.94
669 670 1.078759 CCCTTCTCTAAGCACGCACG 61.079 60.000 0.00 0.00 0.00 5.34
670 671 0.741221 CCCCTTCTCTAAGCACGCAC 60.741 60.000 0.00 0.00 0.00 5.34
671 672 1.596934 CCCCTTCTCTAAGCACGCA 59.403 57.895 0.00 0.00 0.00 5.24
672 673 1.815840 GCCCCTTCTCTAAGCACGC 60.816 63.158 0.00 0.00 0.00 5.34
673 674 1.519455 CGCCCCTTCTCTAAGCACG 60.519 63.158 0.00 0.00 0.00 5.34
674 675 0.460459 GACGCCCCTTCTCTAAGCAC 60.460 60.000 0.00 0.00 0.00 4.40
675 676 0.614979 AGACGCCCCTTCTCTAAGCA 60.615 55.000 0.00 0.00 0.00 3.91
676 677 0.103390 GAGACGCCCCTTCTCTAAGC 59.897 60.000 0.00 0.00 37.18 3.09
677 678 1.135333 GTGAGACGCCCCTTCTCTAAG 59.865 57.143 2.19 0.00 40.30 2.18
678 679 1.183549 GTGAGACGCCCCTTCTCTAA 58.816 55.000 2.19 0.00 40.30 2.10
679 680 0.331954 AGTGAGACGCCCCTTCTCTA 59.668 55.000 2.19 0.00 40.30 2.43
680 681 0.543174 AAGTGAGACGCCCCTTCTCT 60.543 55.000 2.19 0.00 40.30 3.10
681 682 0.390472 CAAGTGAGACGCCCCTTCTC 60.390 60.000 0.00 0.00 40.10 2.87
682 683 1.674057 CAAGTGAGACGCCCCTTCT 59.326 57.895 0.00 0.00 0.00 2.85
683 684 1.376037 CCAAGTGAGACGCCCCTTC 60.376 63.158 0.00 0.00 0.00 3.46
684 685 2.750350 CCAAGTGAGACGCCCCTT 59.250 61.111 0.00 0.00 0.00 3.95
685 686 3.322466 CCCAAGTGAGACGCCCCT 61.322 66.667 0.00 0.00 0.00 4.79
690 691 2.876368 GATGGGGCCCAAGTGAGACG 62.876 65.000 32.57 0.00 36.95 4.18
691 692 1.077429 GATGGGGCCCAAGTGAGAC 60.077 63.158 32.57 11.11 36.95 3.36
692 693 1.139498 TTGATGGGGCCCAAGTGAGA 61.139 55.000 32.57 9.85 36.95 3.27
693 694 0.682209 CTTGATGGGGCCCAAGTGAG 60.682 60.000 32.57 20.35 36.95 3.51
694 695 1.383799 CTTGATGGGGCCCAAGTGA 59.616 57.895 32.57 14.91 36.95 3.41
695 696 1.683365 CCTTGATGGGGCCCAAGTG 60.683 63.158 32.57 19.10 38.39 3.16
696 697 2.772924 CCTTGATGGGGCCCAAGT 59.227 61.111 32.57 15.35 38.39 3.16
697 698 2.761213 GCCTTGATGGGGCCCAAG 60.761 66.667 32.57 22.56 43.49 3.61
703 704 2.751436 CCACGTGCCTTGATGGGG 60.751 66.667 10.91 0.00 36.00 4.96
704 705 3.443045 GCCACGTGCCTTGATGGG 61.443 66.667 10.91 0.00 36.00 4.00
713 714 2.594592 AGGAAGTTGGCCACGTGC 60.595 61.111 3.88 4.71 40.16 5.34
714 715 2.317609 CGAGGAAGTTGGCCACGTG 61.318 63.158 3.88 9.08 35.27 4.49
715 716 2.030562 CGAGGAAGTTGGCCACGT 59.969 61.111 3.88 0.00 35.27 4.49
716 717 3.423154 GCGAGGAAGTTGGCCACG 61.423 66.667 3.88 4.82 41.48 4.94
717 718 3.423154 CGCGAGGAAGTTGGCCAC 61.423 66.667 3.88 0.00 0.00 5.01
718 719 3.936203 ACGCGAGGAAGTTGGCCA 61.936 61.111 15.93 0.00 0.00 5.36
719 720 3.423154 CACGCGAGGAAGTTGGCC 61.423 66.667 15.93 0.00 0.00 5.36
720 721 3.423154 CCACGCGAGGAAGTTGGC 61.423 66.667 18.51 0.00 0.00 4.52
721 722 1.301401 TTCCACGCGAGGAAGTTGG 60.301 57.895 30.41 17.63 42.56 3.77
722 723 4.354155 TTCCACGCGAGGAAGTTG 57.646 55.556 30.41 8.76 42.56 3.16
727 728 1.813859 CCTACATTCCACGCGAGGA 59.186 57.895 21.89 21.89 35.41 3.71
728 729 1.883084 GCCTACATTCCACGCGAGG 60.883 63.158 17.19 17.19 0.00 4.63
729 730 2.230940 CGCCTACATTCCACGCGAG 61.231 63.158 15.93 4.16 45.41 5.03
730 731 2.202690 CGCCTACATTCCACGCGA 60.203 61.111 15.93 0.00 45.41 5.87
732 733 3.089784 CACGCCTACATTCCACGC 58.910 61.111 0.00 0.00 0.00 5.34
733 734 2.798501 CGCACGCCTACATTCCACG 61.799 63.158 0.00 0.00 0.00 4.94
734 735 1.017177 TTCGCACGCCTACATTCCAC 61.017 55.000 0.00 0.00 0.00 4.02
735 736 0.739462 CTTCGCACGCCTACATTCCA 60.739 55.000 0.00 0.00 0.00 3.53
736 737 1.429148 CCTTCGCACGCCTACATTCC 61.429 60.000 0.00 0.00 0.00 3.01
737 738 2.006772 CCTTCGCACGCCTACATTC 58.993 57.895 0.00 0.00 0.00 2.67
738 739 2.106683 GCCTTCGCACGCCTACATT 61.107 57.895 0.00 0.00 34.03 2.71
739 740 2.511600 GCCTTCGCACGCCTACAT 60.512 61.111 0.00 0.00 34.03 2.29
741 742 4.789075 TCGCCTTCGCACGCCTAC 62.789 66.667 0.00 0.00 35.26 3.18
742 743 4.789075 GTCGCCTTCGCACGCCTA 62.789 66.667 0.00 0.00 35.26 3.93
750 751 4.831307 CTCCGTCGGTCGCCTTCG 62.831 72.222 11.88 0.00 38.35 3.79
764 765 4.980805 TGACCGGTTGTGCGCTCC 62.981 66.667 9.42 5.19 0.00 4.70
765 766 3.414700 CTGACCGGTTGTGCGCTC 61.415 66.667 9.42 5.51 0.00 5.03
777 778 0.313672 TGTTGCAAATTCGGCTGACC 59.686 50.000 0.00 0.00 0.00 4.02
778 779 1.001378 AGTGTTGCAAATTCGGCTGAC 60.001 47.619 0.00 3.88 0.00 3.51
779 780 1.317613 AGTGTTGCAAATTCGGCTGA 58.682 45.000 0.00 0.00 0.00 4.26
780 781 2.138596 AAGTGTTGCAAATTCGGCTG 57.861 45.000 0.00 0.00 0.00 4.85
781 782 2.545742 GGAAAGTGTTGCAAATTCGGCT 60.546 45.455 0.00 0.00 0.00 5.52
782 783 1.792367 GGAAAGTGTTGCAAATTCGGC 59.208 47.619 0.00 0.00 0.00 5.54
783 784 3.090952 TGGAAAGTGTTGCAAATTCGG 57.909 42.857 0.00 0.00 31.30 4.30
789 790 5.788450 TCTTTTCTTTGGAAAGTGTTGCAA 58.212 33.333 0.00 0.00 42.60 4.08
790 791 5.398603 TCTTTTCTTTGGAAAGTGTTGCA 57.601 34.783 0.00 0.00 41.66 4.08
791 792 5.063438 GGTTCTTTTCTTTGGAAAGTGTTGC 59.937 40.000 0.00 0.00 41.66 4.17
792 793 6.311200 CAGGTTCTTTTCTTTGGAAAGTGTTG 59.689 38.462 0.00 0.00 41.66 3.33
793 794 6.210584 TCAGGTTCTTTTCTTTGGAAAGTGTT 59.789 34.615 0.00 0.00 41.66 3.32
794 795 5.714806 TCAGGTTCTTTTCTTTGGAAAGTGT 59.285 36.000 0.00 0.00 41.66 3.55
795 796 6.127619 ACTCAGGTTCTTTTCTTTGGAAAGTG 60.128 38.462 0.00 0.00 41.66 3.16
796 797 5.952347 ACTCAGGTTCTTTTCTTTGGAAAGT 59.048 36.000 0.00 0.00 41.66 2.66
797 798 6.456795 ACTCAGGTTCTTTTCTTTGGAAAG 57.543 37.500 0.00 0.00 41.66 2.62
798 799 8.533569 AATACTCAGGTTCTTTTCTTTGGAAA 57.466 30.769 0.00 0.00 39.38 3.13
799 800 8.533569 AAATACTCAGGTTCTTTTCTTTGGAA 57.466 30.769 0.00 0.00 0.00 3.53
800 801 8.533569 AAAATACTCAGGTTCTTTTCTTTGGA 57.466 30.769 0.00 0.00 0.00 3.53
801 802 9.249457 GAAAAATACTCAGGTTCTTTTCTTTGG 57.751 33.333 0.00 0.00 34.96 3.28
802 803 9.249457 GGAAAAATACTCAGGTTCTTTTCTTTG 57.751 33.333 0.00 0.00 36.34 2.77
803 804 8.977412 TGGAAAAATACTCAGGTTCTTTTCTTT 58.023 29.630 0.00 0.00 36.34 2.52
804 805 8.533569 TGGAAAAATACTCAGGTTCTTTTCTT 57.466 30.769 0.00 0.00 36.34 2.52
805 806 8.712228 ATGGAAAAATACTCAGGTTCTTTTCT 57.288 30.769 0.00 0.00 36.34 2.52
806 807 9.411801 GAATGGAAAAATACTCAGGTTCTTTTC 57.588 33.333 0.00 0.00 35.90 2.29
807 808 9.147732 AGAATGGAAAAATACTCAGGTTCTTTT 57.852 29.630 0.00 0.00 0.00 2.27
808 809 8.712228 AGAATGGAAAAATACTCAGGTTCTTT 57.288 30.769 0.00 0.00 0.00 2.52
809 810 7.944554 TGAGAATGGAAAAATACTCAGGTTCTT 59.055 33.333 0.00 0.00 32.04 2.52
810 811 7.461749 TGAGAATGGAAAAATACTCAGGTTCT 58.538 34.615 0.00 0.00 32.04 3.01
811 812 7.687941 TGAGAATGGAAAAATACTCAGGTTC 57.312 36.000 0.00 0.00 32.04 3.62
812 813 8.477419 TTTGAGAATGGAAAAATACTCAGGTT 57.523 30.769 0.00 0.00 36.13 3.50
813 814 8.477419 TTTTGAGAATGGAAAAATACTCAGGT 57.523 30.769 0.00 0.00 36.13 4.00
814 815 8.796475 TCTTTTGAGAATGGAAAAATACTCAGG 58.204 33.333 0.00 0.00 36.13 3.86
842 843 5.798434 CCTTTTCTTTCGTCACGTTCTTTTT 59.202 36.000 0.00 0.00 0.00 1.94
846 847 2.287103 GCCTTTTCTTTCGTCACGTTCT 59.713 45.455 0.00 0.00 0.00 3.01
847 848 2.601504 GGCCTTTTCTTTCGTCACGTTC 60.602 50.000 0.00 0.00 0.00 3.95
849 850 0.942252 GGCCTTTTCTTTCGTCACGT 59.058 50.000 0.00 0.00 0.00 4.49
850 851 1.194772 GAGGCCTTTTCTTTCGTCACG 59.805 52.381 6.77 0.00 0.00 4.35
851 852 1.535896 GGAGGCCTTTTCTTTCGTCAC 59.464 52.381 6.77 0.00 0.00 3.67
852 853 1.420138 AGGAGGCCTTTTCTTTCGTCA 59.580 47.619 6.77 0.00 0.00 4.35
853 854 1.807142 CAGGAGGCCTTTTCTTTCGTC 59.193 52.381 6.77 0.00 0.00 4.20
854 855 1.545651 CCAGGAGGCCTTTTCTTTCGT 60.546 52.381 6.77 0.00 0.00 3.85
855 856 1.168714 CCAGGAGGCCTTTTCTTTCG 58.831 55.000 6.77 0.00 0.00 3.46
856 857 1.550327 CCCAGGAGGCCTTTTCTTTC 58.450 55.000 6.77 0.00 0.00 2.62
857 858 3.774144 CCCAGGAGGCCTTTTCTTT 57.226 52.632 6.77 0.00 0.00 2.52
867 868 0.969894 CTTATCTACGGCCCAGGAGG 59.030 60.000 0.00 0.00 39.47 4.30
902 908 9.468532 AAATCTTCTCTTCTTTTCCGATTTTTG 57.531 29.630 0.00 0.00 0.00 2.44
1015 1023 0.038159 AGGAAAGAGAGAACACGCGG 60.038 55.000 12.47 1.27 0.00 6.46
1023 1031 2.224793 TGAGTGGACGAGGAAAGAGAGA 60.225 50.000 0.00 0.00 0.00 3.10
1072 1080 2.042930 AAGGGCGGAGAGGGGATT 59.957 61.111 0.00 0.00 0.00 3.01
1073 1081 2.446802 GAAGGGCGGAGAGGGGAT 60.447 66.667 0.00 0.00 0.00 3.85
1762 1779 1.309499 CCAAGCGTCTCGAGGACTCT 61.309 60.000 13.56 7.10 41.20 3.24
1804 1821 1.735700 CGGCATCGTCTTCACAGCTAA 60.736 52.381 0.00 0.00 0.00 3.09
1902 1919 1.340991 ACCGGCCTTTGAGCAATGTAT 60.341 47.619 0.00 0.00 0.00 2.29
1995 2012 4.889832 ATCAAATCGAAGATCCAGCAAC 57.110 40.909 0.00 0.00 45.12 4.17
2007 2024 2.032799 GGCGGCATTGTAATCAAATCGA 59.967 45.455 3.07 0.00 37.11 3.59
2171 2188 2.636830 CAGGACAGGCAAGGTAGATTG 58.363 52.381 0.00 0.00 0.00 2.67
2207 2237 4.041938 ACTTTTTCCATCCAACATGGCAAT 59.958 37.500 0.00 0.00 37.47 3.56
2208 2238 3.390639 ACTTTTTCCATCCAACATGGCAA 59.609 39.130 0.00 0.00 37.47 4.52
2209 2239 2.971330 ACTTTTTCCATCCAACATGGCA 59.029 40.909 0.00 0.00 37.47 4.92
2210 2240 3.683365 ACTTTTTCCATCCAACATGGC 57.317 42.857 0.00 0.00 37.47 4.40
2211 2241 6.165577 CCTTAACTTTTTCCATCCAACATGG 58.834 40.000 0.00 0.00 40.48 3.66
2212 2242 6.758254 ACCTTAACTTTTTCCATCCAACATG 58.242 36.000 0.00 0.00 0.00 3.21
2213 2243 6.994421 ACCTTAACTTTTTCCATCCAACAT 57.006 33.333 0.00 0.00 0.00 2.71
2214 2244 6.800072 AACCTTAACTTTTTCCATCCAACA 57.200 33.333 0.00 0.00 0.00 3.33
2215 2245 7.045416 ACAAACCTTAACTTTTTCCATCCAAC 58.955 34.615 0.00 0.00 0.00 3.77
2216 2246 7.093289 TGACAAACCTTAACTTTTTCCATCCAA 60.093 33.333 0.00 0.00 0.00 3.53
2217 2247 6.381420 TGACAAACCTTAACTTTTTCCATCCA 59.619 34.615 0.00 0.00 0.00 3.41
2218 2248 6.811954 TGACAAACCTTAACTTTTTCCATCC 58.188 36.000 0.00 0.00 0.00 3.51
2219 2249 7.598869 GGATGACAAACCTTAACTTTTTCCATC 59.401 37.037 0.00 0.00 0.00 3.51
2358 2388 9.033711 TGATCATTCCCAGAAATTTCATTACAA 57.966 29.630 19.99 6.52 0.00 2.41
2392 2422 5.240623 ACAATAAAACCGACTGCAGATGAAA 59.759 36.000 23.35 0.00 0.00 2.69
2508 2538 1.902938 TGTTTCATCCCACGCATGAA 58.097 45.000 0.00 0.00 38.27 2.57
2521 2551 2.080693 GCACCGTCCATACATGTTTCA 58.919 47.619 2.30 0.00 0.00 2.69
2523 2553 2.192664 TGCACCGTCCATACATGTTT 57.807 45.000 2.30 0.00 0.00 2.83
2549 2579 7.444558 GTCTGATAGAAAGAAATCGTCAGAC 57.555 40.000 19.77 19.77 46.65 3.51
2554 2584 7.704271 TCATACGTCTGATAGAAAGAAATCGT 58.296 34.615 0.00 0.00 31.45 3.73
2576 2606 9.981460 ATTTAGAAGGGAAACACTTTCTATCAT 57.019 29.630 0.00 0.00 39.59 2.45
2588 2618 4.864704 TGCAACCATTTAGAAGGGAAAC 57.135 40.909 0.00 0.00 35.48 2.78
2790 2823 9.996554 AATCATTCCATCGTCTTGTATAATGTA 57.003 29.630 0.00 0.00 0.00 2.29
2831 2864 5.833406 TCTCTTCAAAACAAGATTGCACA 57.167 34.783 0.00 0.00 31.84 4.57
3010 3043 5.584251 GGCCAATTGTTTGTTTCAAGAAAGA 59.416 36.000 4.43 0.00 0.00 2.52
3140 3173 5.581085 AGTTTTATTATCACGAGGTCTGCAC 59.419 40.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.