Multiple sequence alignment - TraesCS7D01G222200

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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 TraesCS7D01G222200 chr7D 100.000 3914 0 0 430 4343 183330532 183326619 0.000000e+00 7228.0
1 TraesCS7D01G222200 chr7D 90.421 261 23 2 430 689 536598249 536597990 4.160000e-90 342.0
2 TraesCS7D01G222200 chr7D 89.655 261 26 1 430 689 166227656 166227396 9.000000e-87 331.0
3 TraesCS7D01G222200 chr7D 100.000 111 0 0 1 111 183330961 183330851 5.690000e-49 206.0
4 TraesCS7D01G222200 chr7A 95.446 3689 91 23 724 4343 187937857 187941537 0.000000e+00 5810.0
5 TraesCS7D01G222200 chr7B 95.303 3577 87 23 810 4343 152062016 152058478 0.000000e+00 5600.0
6 TraesCS7D01G222200 chr2D 92.015 263 19 2 430 691 324343906 324344167 6.860000e-98 368.0
7 TraesCS7D01G222200 chr2D 89.844 256 25 1 434 688 512097030 512097285 1.160000e-85 327.0
8 TraesCS7D01G222200 chr2D 94.595 111 6 0 1 111 155174770 155174880 5.770000e-39 172.0
9 TraesCS7D01G222200 chr2D 94.595 111 6 0 1 111 170417842 170417952 5.770000e-39 172.0
10 TraesCS7D01G222200 chr2D 93.694 111 7 0 1 111 166789753 166789863 2.690000e-37 167.0
11 TraesCS7D01G222200 chr2D 93.694 111 7 0 1 111 565306261 565306371 2.690000e-37 167.0
12 TraesCS7D01G222200 chr5D 90.840 262 23 1 430 690 440658995 440658734 2.490000e-92 350.0
13 TraesCS7D01G222200 chr5D 90.038 261 25 1 430 689 46688803 46688543 1.930000e-88 337.0
14 TraesCS7D01G222200 chr5D 89.354 263 27 1 430 691 393997777 393997515 3.240000e-86 329.0
15 TraesCS7D01G222200 chr5D 93.694 111 7 0 1 111 239948994 239948884 2.690000e-37 167.0
16 TraesCS7D01G222200 chr4A 89.655 261 26 1 430 689 3187653 3187393 9.000000e-87 331.0
17 TraesCS7D01G222200 chr4A 89.272 261 26 2 430 689 413249367 413249108 4.190000e-85 326.0
18 TraesCS7D01G222200 chr4A 100.000 30 0 0 4073 4102 543736275 543736246 6.070000e-04 56.5
19 TraesCS7D01G222200 chr3D 95.495 111 5 0 1 111 226627739 226627849 1.240000e-40 178.0
20 TraesCS7D01G222200 chr3D 95.495 111 5 0 1 111 485222618 485222728 1.240000e-40 178.0
21 TraesCS7D01G222200 chr1D 94.595 111 6 0 1 111 222719194 222719304 5.770000e-39 172.0
22 TraesCS7D01G222200 chr1D 93.694 111 7 0 1 111 467317474 467317364 2.690000e-37 167.0
23 TraesCS7D01G222200 chr1A 92.308 52 4 0 4051 4102 355336635 355336584 1.680000e-09 75.0


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 TraesCS7D01G222200 chr7D 183326619 183330961 4342 True 3717 7228 100.000 1 4343 2 chr7D.!!$R3 4342
1 TraesCS7D01G222200 chr7A 187937857 187941537 3680 False 5810 5810 95.446 724 4343 1 chr7A.!!$F1 3619
2 TraesCS7D01G222200 chr7B 152058478 152062016 3538 True 5600 5600 95.303 810 4343 1 chr7B.!!$R1 3533

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
611 612 0.171231 GGGCGCCACTCAAAAAGATC 59.829 55.000 30.85 0.98 0.00 2.75 F
612 613 0.881118 GGCGCCACTCAAAAAGATCA 59.119 50.000 24.80 0.00 0.00 2.92 F
613 614 1.135575 GGCGCCACTCAAAAAGATCAG 60.136 52.381 24.80 0.00 0.00 2.90 F
1584 1658 1.203013 GGCCAACCACCCTTAGAAGTT 60.203 52.381 0.00 0.00 35.26 2.66 F
1853 1939 0.539438 TCCACCCAGGCAAATGTCAC 60.539 55.000 0.00 0.00 37.29 3.67 F
2132 2219 4.104738 TGGAGACCTTTTCCTCATTTGACT 59.895 41.667 0.00 0.00 35.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1553 1.386525 CCAGTTTGCCCATCCATCCG 61.387 60.000 0.00 0.0 0.0 4.18 R
1654 1728 1.905637 CCACCCAACCCTTAAGTGAC 58.094 55.000 0.97 0.0 0.0 3.67 R
1769 1847 4.546829 AGGTCAGCGGTTTATACTTCAA 57.453 40.909 0.00 0.0 0.0 2.69 R
2914 3002 4.748701 GTAGATTACCAGGGTCCAGGATA 58.251 47.826 5.40 0.0 0.0 2.59 R
3069 3157 5.293079 GCCAAATTTTTACAGCAAAGTGACA 59.707 36.000 0.00 0.0 0.0 3.58 R
3960 4051 4.724074 ACAACGTCACTATTTCCGGATA 57.276 40.909 4.15 0.0 0.0 2.59 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
27 28 7.655236 TGAGCAATTTGTTCACATTAATTGG 57.345 32.000 11.37 2.88 35.87 3.16
28 29 7.440198 TGAGCAATTTGTTCACATTAATTGGA 58.560 30.769 11.37 0.00 35.87 3.53
29 30 8.095792 TGAGCAATTTGTTCACATTAATTGGAT 58.904 29.630 11.37 1.02 35.87 3.41
30 31 8.483307 AGCAATTTGTTCACATTAATTGGATC 57.517 30.769 14.60 0.00 35.87 3.36
31 32 8.095792 AGCAATTTGTTCACATTAATTGGATCA 58.904 29.630 14.60 0.00 35.87 2.92
32 33 8.719648 GCAATTTGTTCACATTAATTGGATCAA 58.280 29.630 14.60 5.90 35.87 2.57
36 37 9.605275 TTTGTTCACATTAATTGGATCAAAACA 57.395 25.926 14.25 7.45 30.20 2.83
37 38 9.605275 TTGTTCACATTAATTGGATCAAAACAA 57.395 25.926 0.00 0.00 0.00 2.83
38 39 9.258826 TGTTCACATTAATTGGATCAAAACAAG 57.741 29.630 0.00 0.00 0.00 3.16
39 40 8.711457 GTTCACATTAATTGGATCAAAACAAGG 58.289 33.333 0.00 0.00 0.00 3.61
40 41 7.385267 TCACATTAATTGGATCAAAACAAGGG 58.615 34.615 0.00 0.00 0.00 3.95
41 42 6.594937 CACATTAATTGGATCAAAACAAGGGG 59.405 38.462 0.00 0.00 0.00 4.79
42 43 6.500049 ACATTAATTGGATCAAAACAAGGGGA 59.500 34.615 0.00 0.00 0.00 4.81
43 44 7.182568 ACATTAATTGGATCAAAACAAGGGGAT 59.817 33.333 0.00 0.00 0.00 3.85
44 45 5.682234 AATTGGATCAAAACAAGGGGATC 57.318 39.130 0.00 0.00 36.33 3.36
45 46 2.722094 TGGATCAAAACAAGGGGATCG 58.278 47.619 0.00 0.00 37.59 3.69
46 47 2.307392 TGGATCAAAACAAGGGGATCGA 59.693 45.455 0.00 0.00 37.59 3.59
47 48 3.245087 TGGATCAAAACAAGGGGATCGAA 60.245 43.478 0.00 0.00 37.59 3.71
48 49 3.378427 GGATCAAAACAAGGGGATCGAAG 59.622 47.826 0.00 0.00 37.59 3.79
49 50 3.780804 TCAAAACAAGGGGATCGAAGA 57.219 42.857 0.00 0.00 45.75 2.87
50 51 4.093472 TCAAAACAAGGGGATCGAAGAA 57.907 40.909 0.00 0.00 43.58 2.52
51 52 4.072131 TCAAAACAAGGGGATCGAAGAAG 58.928 43.478 0.00 0.00 43.58 2.85
52 53 4.072131 CAAAACAAGGGGATCGAAGAAGA 58.928 43.478 0.00 0.00 43.58 2.87
53 54 4.576330 AAACAAGGGGATCGAAGAAGAT 57.424 40.909 0.00 0.00 43.58 2.40
54 55 4.576330 AACAAGGGGATCGAAGAAGATT 57.424 40.909 0.00 0.00 43.58 2.40
55 56 5.693769 AACAAGGGGATCGAAGAAGATTA 57.306 39.130 0.00 0.00 43.58 1.75
56 57 5.024785 ACAAGGGGATCGAAGAAGATTAC 57.975 43.478 0.00 0.00 43.58 1.89
57 58 4.141688 ACAAGGGGATCGAAGAAGATTACC 60.142 45.833 0.00 0.00 43.58 2.85
58 59 3.930035 AGGGGATCGAAGAAGATTACCT 58.070 45.455 0.00 0.00 43.58 3.08
59 60 4.299485 AGGGGATCGAAGAAGATTACCTT 58.701 43.478 0.00 0.00 43.58 3.50
60 61 4.101741 AGGGGATCGAAGAAGATTACCTTG 59.898 45.833 0.00 0.00 43.58 3.61
61 62 4.101119 GGGGATCGAAGAAGATTACCTTGA 59.899 45.833 0.00 0.00 43.58 3.02
62 63 5.293560 GGGATCGAAGAAGATTACCTTGAG 58.706 45.833 0.00 0.00 43.58 3.02
63 64 5.293560 GGATCGAAGAAGATTACCTTGAGG 58.706 45.833 0.00 0.00 43.58 3.86
64 65 4.737855 TCGAAGAAGATTACCTTGAGGG 57.262 45.455 1.54 0.00 40.27 4.30
65 66 4.350245 TCGAAGAAGATTACCTTGAGGGA 58.650 43.478 1.54 0.00 40.27 4.20
66 67 4.402793 TCGAAGAAGATTACCTTGAGGGAG 59.597 45.833 1.54 0.00 40.27 4.30
67 68 4.442192 CGAAGAAGATTACCTTGAGGGAGG 60.442 50.000 1.54 0.00 42.75 4.30
68 69 3.388913 AGAAGATTACCTTGAGGGAGGG 58.611 50.000 1.54 0.00 41.31 4.30
69 70 2.972153 AGATTACCTTGAGGGAGGGT 57.028 50.000 1.54 0.00 41.31 4.34
70 71 3.222394 AGATTACCTTGAGGGAGGGTT 57.778 47.619 1.54 0.00 41.31 4.11
71 72 3.542604 AGATTACCTTGAGGGAGGGTTT 58.457 45.455 1.54 0.00 41.31 3.27
72 73 3.267031 AGATTACCTTGAGGGAGGGTTTG 59.733 47.826 1.54 0.00 41.31 2.93
73 74 2.426431 TACCTTGAGGGAGGGTTTGA 57.574 50.000 1.54 0.00 41.31 2.69
74 75 0.771755 ACCTTGAGGGAGGGTTTGAC 59.228 55.000 1.54 0.00 41.31 3.18
75 76 1.068121 CCTTGAGGGAGGGTTTGACT 58.932 55.000 0.00 0.00 37.23 3.41
76 77 1.425448 CCTTGAGGGAGGGTTTGACTT 59.575 52.381 0.00 0.00 37.23 3.01
77 78 2.553247 CCTTGAGGGAGGGTTTGACTTC 60.553 54.545 0.00 0.00 37.23 3.01
78 79 0.685097 TGAGGGAGGGTTTGACTTCG 59.315 55.000 0.00 0.00 0.00 3.79
79 80 0.974383 GAGGGAGGGTTTGACTTCGA 59.026 55.000 0.00 0.00 0.00 3.71
80 81 1.346722 GAGGGAGGGTTTGACTTCGAA 59.653 52.381 0.00 0.00 0.00 3.71
81 82 1.772453 AGGGAGGGTTTGACTTCGAAA 59.228 47.619 0.00 0.00 0.00 3.46
82 83 2.375509 AGGGAGGGTTTGACTTCGAAAT 59.624 45.455 0.00 0.00 0.00 2.17
83 84 2.747989 GGGAGGGTTTGACTTCGAAATC 59.252 50.000 0.00 0.00 0.00 2.17
84 85 3.408634 GGAGGGTTTGACTTCGAAATCA 58.591 45.455 4.98 4.98 0.00 2.57
85 86 3.818773 GGAGGGTTTGACTTCGAAATCAA 59.181 43.478 17.37 17.37 33.03 2.57
86 87 4.320275 GGAGGGTTTGACTTCGAAATCAAC 60.320 45.833 20.60 15.04 34.61 3.18
87 88 3.250040 AGGGTTTGACTTCGAAATCAACG 59.750 43.478 20.60 0.00 34.61 4.10
88 89 3.551551 GGTTTGACTTCGAAATCAACGG 58.448 45.455 20.60 0.00 34.61 4.44
89 90 3.249080 GGTTTGACTTCGAAATCAACGGA 59.751 43.478 20.60 4.91 34.61 4.69
90 91 4.209112 GTTTGACTTCGAAATCAACGGAC 58.791 43.478 20.60 13.09 34.61 4.79
91 92 3.100658 TGACTTCGAAATCAACGGACA 57.899 42.857 6.87 0.00 0.00 4.02
92 93 3.459145 TGACTTCGAAATCAACGGACAA 58.541 40.909 6.87 0.00 0.00 3.18
93 94 3.872182 TGACTTCGAAATCAACGGACAAA 59.128 39.130 6.87 0.00 0.00 2.83
94 95 4.333095 TGACTTCGAAATCAACGGACAAAA 59.667 37.500 6.87 0.00 0.00 2.44
95 96 5.008217 TGACTTCGAAATCAACGGACAAAAT 59.992 36.000 6.87 0.00 0.00 1.82
96 97 5.449304 ACTTCGAAATCAACGGACAAAATC 58.551 37.500 0.00 0.00 0.00 2.17
97 98 5.238650 ACTTCGAAATCAACGGACAAAATCT 59.761 36.000 0.00 0.00 0.00 2.40
98 99 5.682943 TCGAAATCAACGGACAAAATCTT 57.317 34.783 0.00 0.00 0.00 2.40
99 100 5.685841 TCGAAATCAACGGACAAAATCTTC 58.314 37.500 0.00 0.00 0.00 2.87
100 101 5.237561 TCGAAATCAACGGACAAAATCTTCA 59.762 36.000 0.00 0.00 0.00 3.02
101 102 5.912396 CGAAATCAACGGACAAAATCTTCAA 59.088 36.000 0.00 0.00 0.00 2.69
102 103 6.416455 CGAAATCAACGGACAAAATCTTCAAA 59.584 34.615 0.00 0.00 0.00 2.69
103 104 7.114811 CGAAATCAACGGACAAAATCTTCAAAT 59.885 33.333 0.00 0.00 0.00 2.32
104 105 8.661352 AAATCAACGGACAAAATCTTCAAATT 57.339 26.923 0.00 0.00 0.00 1.82
105 106 8.661352 AATCAACGGACAAAATCTTCAAATTT 57.339 26.923 0.00 0.00 0.00 1.82
106 107 7.462109 TCAACGGACAAAATCTTCAAATTTG 57.538 32.000 12.15 12.15 39.38 2.32
107 108 6.478344 TCAACGGACAAAATCTTCAAATTTGG 59.522 34.615 17.90 3.33 38.14 3.28
108 109 6.155475 ACGGACAAAATCTTCAAATTTGGA 57.845 33.333 17.90 8.77 38.14 3.53
109 110 6.578023 ACGGACAAAATCTTCAAATTTGGAA 58.422 32.000 17.90 9.89 38.14 3.53
110 111 6.701400 ACGGACAAAATCTTCAAATTTGGAAG 59.299 34.615 17.90 17.55 42.42 3.46
446 447 3.933722 ACAGACAGTGCAGCGCCT 61.934 61.111 2.29 0.00 0.00 5.52
447 448 2.262603 CAGACAGTGCAGCGCCTA 59.737 61.111 2.29 0.00 0.00 3.93
448 449 1.374631 CAGACAGTGCAGCGCCTAA 60.375 57.895 2.29 0.00 0.00 2.69
449 450 1.079543 AGACAGTGCAGCGCCTAAG 60.080 57.895 2.29 0.00 0.00 2.18
450 451 2.046892 ACAGTGCAGCGCCTAAGG 60.047 61.111 2.29 0.00 0.00 2.69
451 452 2.821366 CAGTGCAGCGCCTAAGGG 60.821 66.667 2.29 0.00 0.00 3.95
462 463 1.068250 CCTAAGGGCTAGACGCTGC 59.932 63.158 0.00 0.00 41.51 5.25
463 464 1.676678 CCTAAGGGCTAGACGCTGCA 61.677 60.000 0.00 0.00 41.51 4.41
464 465 0.528684 CTAAGGGCTAGACGCTGCAC 60.529 60.000 0.00 0.00 41.51 4.57
465 466 1.254975 TAAGGGCTAGACGCTGCACA 61.255 55.000 0.00 0.00 41.51 4.57
466 467 1.903877 AAGGGCTAGACGCTGCACAT 61.904 55.000 0.00 0.00 41.51 3.21
467 468 1.450312 GGGCTAGACGCTGCACATT 60.450 57.895 0.00 0.00 39.13 2.71
468 469 0.179084 GGGCTAGACGCTGCACATTA 60.179 55.000 0.00 0.00 39.13 1.90
469 470 0.931005 GGCTAGACGCTGCACATTAC 59.069 55.000 0.00 0.00 39.13 1.89
470 471 1.640428 GCTAGACGCTGCACATTACA 58.360 50.000 0.00 0.00 35.14 2.41
471 472 2.205074 GCTAGACGCTGCACATTACAT 58.795 47.619 0.00 0.00 35.14 2.29
472 473 2.033407 GCTAGACGCTGCACATTACATG 60.033 50.000 0.00 0.00 35.14 3.21
473 474 2.099141 AGACGCTGCACATTACATGT 57.901 45.000 2.69 2.69 46.22 3.21
481 482 2.179764 ACATTACATGTGTGGCGCC 58.820 52.632 22.73 22.73 43.01 6.53
482 483 0.322456 ACATTACATGTGTGGCGCCT 60.322 50.000 29.70 7.80 43.01 5.52
483 484 1.065782 ACATTACATGTGTGGCGCCTA 60.066 47.619 29.70 14.39 43.01 3.93
484 485 1.599071 CATTACATGTGTGGCGCCTAG 59.401 52.381 29.70 12.91 0.00 3.02
497 498 4.277593 CCTAGCTCGGAGGCGCTG 62.278 72.222 7.64 0.00 36.29 5.18
498 499 4.940593 CTAGCTCGGAGGCGCTGC 62.941 72.222 7.64 0.00 36.29 5.25
532 533 4.473520 CTAGGGGCTGCCACGGTG 62.474 72.222 22.05 8.71 28.26 4.94
538 539 4.314440 GCTGCCACGGTGGACAGA 62.314 66.667 35.00 17.24 40.96 3.41
539 540 2.047844 CTGCCACGGTGGACAGAG 60.048 66.667 30.87 18.24 40.96 3.35
540 541 3.596066 CTGCCACGGTGGACAGAGG 62.596 68.421 30.87 15.64 40.96 3.69
541 542 3.626924 GCCACGGTGGACAGAGGT 61.627 66.667 30.65 0.00 40.96 3.85
542 543 2.343758 CCACGGTGGACAGAGGTG 59.656 66.667 22.77 0.00 40.96 4.00
543 544 2.357517 CACGGTGGACAGAGGTGC 60.358 66.667 0.00 0.00 35.66 5.01
544 545 2.842462 ACGGTGGACAGAGGTGCA 60.842 61.111 0.00 0.00 43.61 4.57
548 549 2.280797 TGGACAGAGGTGCAACGC 60.281 61.111 0.00 0.00 42.81 4.84
549 550 3.050275 GGACAGAGGTGCAACGCC 61.050 66.667 0.31 0.00 38.12 5.68
555 556 2.345244 AGGTGCAACGCCTCAGAG 59.655 61.111 0.00 0.00 40.81 3.35
556 557 3.426568 GGTGCAACGCCTCAGAGC 61.427 66.667 0.00 0.00 38.12 4.09
557 558 2.358003 GTGCAACGCCTCAGAGCT 60.358 61.111 0.00 0.00 0.00 4.09
558 559 1.079819 GTGCAACGCCTCAGAGCTA 60.080 57.895 0.00 0.00 0.00 3.32
559 560 1.080995 GTGCAACGCCTCAGAGCTAG 61.081 60.000 0.00 0.00 0.00 3.42
560 561 2.170434 GCAACGCCTCAGAGCTAGC 61.170 63.158 6.62 6.62 0.00 3.42
571 572 3.449227 AGCTAGCGCTGCACCGTA 61.449 61.111 22.90 0.00 46.86 4.02
572 573 2.956964 GCTAGCGCTGCACCGTAG 60.957 66.667 22.90 8.64 0.00 3.51
585 586 3.454573 CGTAGGGTGTGGCGCCTA 61.455 66.667 29.70 14.39 33.98 3.93
586 587 2.186125 GTAGGGTGTGGCGCCTAC 59.814 66.667 29.70 24.84 35.45 3.18
587 588 3.454573 TAGGGTGTGGCGCCTACG 61.455 66.667 29.70 0.00 44.07 3.51
590 591 4.675029 GGTGTGGCGCCTACGTGT 62.675 66.667 29.70 0.00 42.83 4.49
591 592 3.110178 GTGTGGCGCCTACGTGTC 61.110 66.667 29.70 11.53 42.83 3.67
592 593 4.710695 TGTGGCGCCTACGTGTCG 62.711 66.667 29.70 0.00 42.83 4.35
604 605 4.980805 GTGTCGGGCGCCACTCAA 62.981 66.667 30.85 6.35 0.00 3.02
605 606 4.243008 TGTCGGGCGCCACTCAAA 62.243 61.111 30.85 5.09 0.00 2.69
606 607 2.975799 GTCGGGCGCCACTCAAAA 60.976 61.111 30.85 1.26 0.00 2.44
607 608 2.203224 TCGGGCGCCACTCAAAAA 60.203 55.556 30.85 0.05 0.00 1.94
608 609 2.255252 CGGGCGCCACTCAAAAAG 59.745 61.111 30.85 3.27 0.00 2.27
609 610 2.258013 CGGGCGCCACTCAAAAAGA 61.258 57.895 30.85 0.00 0.00 2.52
610 611 1.586154 CGGGCGCCACTCAAAAAGAT 61.586 55.000 30.85 0.00 0.00 2.40
611 612 0.171231 GGGCGCCACTCAAAAAGATC 59.829 55.000 30.85 0.98 0.00 2.75
612 613 0.881118 GGCGCCACTCAAAAAGATCA 59.119 50.000 24.80 0.00 0.00 2.92
613 614 1.135575 GGCGCCACTCAAAAAGATCAG 60.136 52.381 24.80 0.00 0.00 2.90
614 615 1.730446 GCGCCACTCAAAAAGATCAGC 60.730 52.381 0.00 0.00 0.00 4.26
615 616 1.808945 CGCCACTCAAAAAGATCAGCT 59.191 47.619 0.00 0.00 0.00 4.24
616 617 3.002791 CGCCACTCAAAAAGATCAGCTA 58.997 45.455 0.00 0.00 0.00 3.32
617 618 3.624861 CGCCACTCAAAAAGATCAGCTAT 59.375 43.478 0.00 0.00 0.00 2.97
618 619 4.495349 CGCCACTCAAAAAGATCAGCTATG 60.495 45.833 0.00 0.00 0.00 2.23
619 620 4.397417 GCCACTCAAAAAGATCAGCTATGT 59.603 41.667 0.00 0.00 0.00 2.29
620 621 5.675575 GCCACTCAAAAAGATCAGCTATGTG 60.676 44.000 0.00 0.00 0.00 3.21
621 622 5.645067 CCACTCAAAAAGATCAGCTATGTGA 59.355 40.000 0.00 0.00 0.00 3.58
622 623 6.149973 CCACTCAAAAAGATCAGCTATGTGAA 59.850 38.462 0.00 0.00 0.00 3.18
623 624 7.308770 CCACTCAAAAAGATCAGCTATGTGAAA 60.309 37.037 0.00 0.00 0.00 2.69
624 625 8.242053 CACTCAAAAAGATCAGCTATGTGAAAT 58.758 33.333 0.00 0.00 0.00 2.17
625 626 9.453572 ACTCAAAAAGATCAGCTATGTGAAATA 57.546 29.630 0.00 0.00 0.00 1.40
626 627 9.932699 CTCAAAAAGATCAGCTATGTGAAATAG 57.067 33.333 0.00 0.00 0.00 1.73
627 628 9.453572 TCAAAAAGATCAGCTATGTGAAATAGT 57.546 29.630 0.00 0.00 0.00 2.12
632 633 7.701445 AGATCAGCTATGTGAAATAGTTTTGC 58.299 34.615 0.00 0.00 0.00 3.68
633 634 5.868257 TCAGCTATGTGAAATAGTTTTGCG 58.132 37.500 0.00 0.00 0.00 4.85
634 635 5.030295 CAGCTATGTGAAATAGTTTTGCGG 58.970 41.667 0.00 0.00 0.00 5.69
635 636 4.941263 AGCTATGTGAAATAGTTTTGCGGA 59.059 37.500 0.00 0.00 0.00 5.54
636 637 5.028375 GCTATGTGAAATAGTTTTGCGGAC 58.972 41.667 0.00 0.00 0.00 4.79
637 638 5.391523 GCTATGTGAAATAGTTTTGCGGACA 60.392 40.000 0.00 0.00 0.00 4.02
638 639 4.902443 TGTGAAATAGTTTTGCGGACAA 57.098 36.364 0.00 0.00 0.00 3.18
639 640 5.446143 TGTGAAATAGTTTTGCGGACAAT 57.554 34.783 0.00 0.00 35.21 2.71
640 641 5.837437 TGTGAAATAGTTTTGCGGACAATT 58.163 33.333 0.00 0.00 35.21 2.32
641 642 6.276847 TGTGAAATAGTTTTGCGGACAATTT 58.723 32.000 0.00 0.00 35.21 1.82
642 643 7.426410 TGTGAAATAGTTTTGCGGACAATTTA 58.574 30.769 0.00 0.00 35.21 1.40
643 644 8.085296 TGTGAAATAGTTTTGCGGACAATTTAT 58.915 29.630 0.00 0.00 35.21 1.40
644 645 8.921670 GTGAAATAGTTTTGCGGACAATTTATT 58.078 29.630 0.00 0.00 35.21 1.40
645 646 9.482627 TGAAATAGTTTTGCGGACAATTTATTT 57.517 25.926 7.49 7.49 35.21 1.40
648 649 8.825667 ATAGTTTTGCGGACAATTTATTTTGT 57.174 26.923 0.00 0.00 42.37 2.83
649 650 6.942891 AGTTTTGCGGACAATTTATTTTGTG 58.057 32.000 0.00 0.00 39.85 3.33
650 651 6.758886 AGTTTTGCGGACAATTTATTTTGTGA 59.241 30.769 0.00 0.00 39.85 3.58
651 652 7.278868 AGTTTTGCGGACAATTTATTTTGTGAA 59.721 29.630 0.00 0.00 39.85 3.18
652 653 7.721286 TTTGCGGACAATTTATTTTGTGAAT 57.279 28.000 0.00 0.00 39.85 2.57
653 654 7.721286 TTGCGGACAATTTATTTTGTGAATT 57.279 28.000 0.00 0.00 39.85 2.17
654 655 7.344910 TGCGGACAATTTATTTTGTGAATTC 57.655 32.000 0.00 0.00 39.85 2.17
655 656 6.925718 TGCGGACAATTTATTTTGTGAATTCA 59.074 30.769 3.38 3.38 39.85 2.57
656 657 7.601886 TGCGGACAATTTATTTTGTGAATTCAT 59.398 29.630 12.12 0.00 39.85 2.57
657 658 8.442384 GCGGACAATTTATTTTGTGAATTCATT 58.558 29.630 12.12 0.00 39.85 2.57
671 672 9.460019 TTGTGAATTCATTACATTCATAGGTCA 57.540 29.630 12.12 0.00 41.55 4.02
672 673 9.460019 TGTGAATTCATTACATTCATAGGTCAA 57.540 29.630 12.12 0.00 41.55 3.18
687 688 8.309163 TCATAGGTCAAAATTGTCAAATTTGC 57.691 30.769 17.69 13.41 43.63 3.68
688 689 7.387397 TCATAGGTCAAAATTGTCAAATTTGCC 59.613 33.333 17.69 19.32 43.63 4.52
689 690 4.511082 AGGTCAAAATTGTCAAATTTGCCG 59.489 37.500 17.69 0.00 43.63 5.69
690 691 4.210629 GTCAAAATTGTCAAATTTGCCGC 58.789 39.130 17.69 6.77 43.63 6.53
691 692 4.024977 GTCAAAATTGTCAAATTTGCCGCT 60.025 37.500 17.69 0.00 43.63 5.52
692 693 4.574013 TCAAAATTGTCAAATTTGCCGCTT 59.426 33.333 17.69 2.25 43.63 4.68
693 694 5.755375 TCAAAATTGTCAAATTTGCCGCTTA 59.245 32.000 17.69 1.36 43.63 3.09
694 695 6.426328 TCAAAATTGTCAAATTTGCCGCTTAT 59.574 30.769 17.69 0.00 43.63 1.73
695 696 6.799926 AAATTGTCAAATTTGCCGCTTATT 57.200 29.167 13.54 4.62 42.97 1.40
696 697 6.407475 AATTGTCAAATTTGCCGCTTATTC 57.593 33.333 13.54 0.00 31.76 1.75
697 698 3.843999 TGTCAAATTTGCCGCTTATTCC 58.156 40.909 13.54 0.00 0.00 3.01
698 699 3.256879 TGTCAAATTTGCCGCTTATTCCA 59.743 39.130 13.54 0.00 0.00 3.53
699 700 3.612423 GTCAAATTTGCCGCTTATTCCAC 59.388 43.478 13.54 0.00 0.00 4.02
700 701 3.509575 TCAAATTTGCCGCTTATTCCACT 59.490 39.130 13.54 0.00 0.00 4.00
701 702 4.021544 TCAAATTTGCCGCTTATTCCACTT 60.022 37.500 13.54 0.00 0.00 3.16
702 703 4.535526 AATTTGCCGCTTATTCCACTTT 57.464 36.364 0.00 0.00 0.00 2.66
703 704 5.652994 AATTTGCCGCTTATTCCACTTTA 57.347 34.783 0.00 0.00 0.00 1.85
704 705 5.852282 ATTTGCCGCTTATTCCACTTTAT 57.148 34.783 0.00 0.00 0.00 1.40
705 706 5.652994 TTTGCCGCTTATTCCACTTTATT 57.347 34.783 0.00 0.00 0.00 1.40
706 707 4.893424 TGCCGCTTATTCCACTTTATTC 57.107 40.909 0.00 0.00 0.00 1.75
707 708 4.265893 TGCCGCTTATTCCACTTTATTCA 58.734 39.130 0.00 0.00 0.00 2.57
708 709 4.095782 TGCCGCTTATTCCACTTTATTCAC 59.904 41.667 0.00 0.00 0.00 3.18
709 710 4.335594 GCCGCTTATTCCACTTTATTCACT 59.664 41.667 0.00 0.00 0.00 3.41
710 711 5.163652 GCCGCTTATTCCACTTTATTCACTT 60.164 40.000 0.00 0.00 0.00 3.16
711 712 6.625081 GCCGCTTATTCCACTTTATTCACTTT 60.625 38.462 0.00 0.00 0.00 2.66
712 713 7.414762 GCCGCTTATTCCACTTTATTCACTTTA 60.415 37.037 0.00 0.00 0.00 1.85
713 714 8.621286 CCGCTTATTCCACTTTATTCACTTTAT 58.379 33.333 0.00 0.00 0.00 1.40
777 778 1.844357 CGTGCATAGCGTACAGTACAC 59.156 52.381 11.37 0.84 0.00 2.90
958 971 1.385206 GCCATTCCCCTCCTCTCCT 60.385 63.158 0.00 0.00 0.00 3.69
1174 1194 1.906824 GGTGTCGTCAGGGAGGTGA 60.907 63.158 0.00 0.00 0.00 4.02
1227 1247 2.230992 CGCTCCCTGGATCTAGATTCTG 59.769 54.545 12.38 11.28 0.00 3.02
1375 1424 4.225942 AGTGGAAAGACATCTTGCTGGATA 59.774 41.667 0.00 0.00 36.12 2.59
1378 1427 5.591472 TGGAAAGACATCTTGCTGGATATTG 59.409 40.000 0.00 0.00 36.12 1.90
1381 1430 3.881688 AGACATCTTGCTGGATATTGCAC 59.118 43.478 0.00 0.00 39.05 4.57
1584 1658 1.203013 GGCCAACCACCCTTAGAAGTT 60.203 52.381 0.00 0.00 35.26 2.66
1599 1673 3.445008 AGAAGTTACATCAGGGCAGAGA 58.555 45.455 0.00 0.00 0.00 3.10
1601 1675 2.540383 AGTTACATCAGGGCAGAGACA 58.460 47.619 0.00 0.00 0.00 3.41
1606 1680 2.437281 ACATCAGGGCAGAGACATTAGG 59.563 50.000 0.00 0.00 0.00 2.69
1633 1707 4.202284 ACTTGCCTTCGAAAAGTAGTACCA 60.202 41.667 11.13 0.00 32.48 3.25
1853 1939 0.539438 TCCACCCAGGCAAATGTCAC 60.539 55.000 0.00 0.00 37.29 3.67
1890 1976 8.281212 TCAAAGCTTTAGAAAATATCACCTCC 57.719 34.615 12.25 0.00 0.00 4.30
2132 2219 4.104738 TGGAGACCTTTTCCTCATTTGACT 59.895 41.667 0.00 0.00 35.67 3.41
2569 2657 6.487689 AGCTGCTAAATTCTCTTGTGTTAC 57.512 37.500 0.00 0.00 0.00 2.50
2570 2658 5.997746 AGCTGCTAAATTCTCTTGTGTTACA 59.002 36.000 0.00 0.00 0.00 2.41
2634 2722 5.809001 TCTGGATTTGCTTGAGTACTGATT 58.191 37.500 0.00 0.00 0.00 2.57
3664 3754 4.068599 TGATCGCTGTGAACCAAACAATA 58.931 39.130 0.00 0.00 0.00 1.90
3960 4051 7.174107 ACATTGCAAAAATGCTATTACCTCT 57.826 32.000 1.71 0.00 35.49 3.69
3990 4082 7.306983 CGGAAATAGTGACGTTGTTTTAGTTCT 60.307 37.037 0.00 0.00 0.00 3.01
4022 4116 4.829064 ATTGAACTAAAACAGCGCTCAA 57.171 36.364 7.13 6.12 0.00 3.02
4211 4306 5.843673 TCAAGATCTTGATTCTAGCTCGT 57.156 39.130 30.05 0.00 43.90 4.18
4337 4432 1.664151 GACGATCCCGACCAATTGTTC 59.336 52.381 4.43 0.00 39.50 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.723311 CCAATTAATGTGAACAAATTGCTCATT 58.277 29.630 2.22 6.57 34.86 2.57
2 3 8.095792 TCCAATTAATGTGAACAAATTGCTCAT 58.904 29.630 2.22 0.00 34.86 2.90
3 4 7.440198 TCCAATTAATGTGAACAAATTGCTCA 58.560 30.769 12.21 0.00 34.86 4.26
4 5 7.887996 TCCAATTAATGTGAACAAATTGCTC 57.112 32.000 12.21 0.00 34.86 4.26
5 6 8.095792 TGATCCAATTAATGTGAACAAATTGCT 58.904 29.630 12.21 5.15 34.86 3.91
6 7 8.254178 TGATCCAATTAATGTGAACAAATTGC 57.746 30.769 12.21 3.92 34.86 3.56
10 11 9.605275 TGTTTTGATCCAATTAATGTGAACAAA 57.395 25.926 13.97 13.97 33.50 2.83
11 12 9.605275 TTGTTTTGATCCAATTAATGTGAACAA 57.395 25.926 6.25 6.25 0.00 2.83
12 13 9.258826 CTTGTTTTGATCCAATTAATGTGAACA 57.741 29.630 0.00 0.00 0.00 3.18
13 14 8.711457 CCTTGTTTTGATCCAATTAATGTGAAC 58.289 33.333 0.00 0.00 0.00 3.18
14 15 7.877097 CCCTTGTTTTGATCCAATTAATGTGAA 59.123 33.333 0.00 0.00 0.00 3.18
15 16 7.385267 CCCTTGTTTTGATCCAATTAATGTGA 58.615 34.615 0.00 0.00 0.00 3.58
16 17 6.594937 CCCCTTGTTTTGATCCAATTAATGTG 59.405 38.462 0.00 0.00 0.00 3.21
17 18 6.500049 TCCCCTTGTTTTGATCCAATTAATGT 59.500 34.615 0.00 0.00 0.00 2.71
18 19 6.945218 TCCCCTTGTTTTGATCCAATTAATG 58.055 36.000 0.00 0.00 0.00 1.90
19 20 7.417797 CGATCCCCTTGTTTTGATCCAATTAAT 60.418 37.037 0.00 0.00 31.94 1.40
20 21 6.127479 CGATCCCCTTGTTTTGATCCAATTAA 60.127 38.462 0.00 0.00 31.94 1.40
21 22 5.359576 CGATCCCCTTGTTTTGATCCAATTA 59.640 40.000 0.00 0.00 31.94 1.40
22 23 4.160252 CGATCCCCTTGTTTTGATCCAATT 59.840 41.667 0.00 0.00 31.94 2.32
23 24 3.701040 CGATCCCCTTGTTTTGATCCAAT 59.299 43.478 0.00 0.00 31.94 3.16
24 25 3.088532 CGATCCCCTTGTTTTGATCCAA 58.911 45.455 0.00 0.00 31.94 3.53
25 26 2.307392 TCGATCCCCTTGTTTTGATCCA 59.693 45.455 0.00 0.00 31.94 3.41
26 27 2.999331 TCGATCCCCTTGTTTTGATCC 58.001 47.619 0.00 0.00 31.94 3.36
27 28 4.261801 TCTTCGATCCCCTTGTTTTGATC 58.738 43.478 0.00 0.00 0.00 2.92
28 29 4.301072 TCTTCGATCCCCTTGTTTTGAT 57.699 40.909 0.00 0.00 0.00 2.57
29 30 3.780804 TCTTCGATCCCCTTGTTTTGA 57.219 42.857 0.00 0.00 0.00 2.69
30 31 4.072131 TCTTCTTCGATCCCCTTGTTTTG 58.928 43.478 0.00 0.00 0.00 2.44
31 32 4.367039 TCTTCTTCGATCCCCTTGTTTT 57.633 40.909 0.00 0.00 0.00 2.43
32 33 4.576330 ATCTTCTTCGATCCCCTTGTTT 57.424 40.909 0.00 0.00 0.00 2.83
33 34 4.576330 AATCTTCTTCGATCCCCTTGTT 57.424 40.909 0.00 0.00 0.00 2.83
34 35 4.141688 GGTAATCTTCTTCGATCCCCTTGT 60.142 45.833 0.00 0.00 0.00 3.16
35 36 4.101741 AGGTAATCTTCTTCGATCCCCTTG 59.898 45.833 0.00 0.00 0.00 3.61
36 37 4.299485 AGGTAATCTTCTTCGATCCCCTT 58.701 43.478 0.00 0.00 0.00 3.95
37 38 3.930035 AGGTAATCTTCTTCGATCCCCT 58.070 45.455 0.00 0.00 0.00 4.79
38 39 4.101119 TCAAGGTAATCTTCTTCGATCCCC 59.899 45.833 0.00 0.00 32.41 4.81
39 40 5.277857 TCAAGGTAATCTTCTTCGATCCC 57.722 43.478 0.00 0.00 32.41 3.85
40 41 5.293560 CCTCAAGGTAATCTTCTTCGATCC 58.706 45.833 0.00 0.00 32.41 3.36
41 42 5.069251 TCCCTCAAGGTAATCTTCTTCGATC 59.931 44.000 0.00 0.00 36.75 3.69
42 43 4.962995 TCCCTCAAGGTAATCTTCTTCGAT 59.037 41.667 0.00 0.00 36.75 3.59
43 44 4.350245 TCCCTCAAGGTAATCTTCTTCGA 58.650 43.478 0.00 0.00 36.75 3.71
44 45 4.442192 CCTCCCTCAAGGTAATCTTCTTCG 60.442 50.000 0.00 0.00 36.75 3.79
45 46 4.141597 CCCTCCCTCAAGGTAATCTTCTTC 60.142 50.000 0.00 0.00 36.75 2.87
46 47 3.783082 CCCTCCCTCAAGGTAATCTTCTT 59.217 47.826 0.00 0.00 36.75 2.52
47 48 3.246535 ACCCTCCCTCAAGGTAATCTTCT 60.247 47.826 0.00 0.00 36.75 2.85
48 49 3.116174 ACCCTCCCTCAAGGTAATCTTC 58.884 50.000 0.00 0.00 36.75 2.87
49 50 3.222394 ACCCTCCCTCAAGGTAATCTT 57.778 47.619 0.00 0.00 36.75 2.40
50 51 2.972153 ACCCTCCCTCAAGGTAATCT 57.028 50.000 0.00 0.00 36.75 2.40
51 52 3.265995 TCAAACCCTCCCTCAAGGTAATC 59.734 47.826 0.00 0.00 36.75 1.75
52 53 3.010250 GTCAAACCCTCCCTCAAGGTAAT 59.990 47.826 0.00 0.00 36.75 1.89
53 54 2.374170 GTCAAACCCTCCCTCAAGGTAA 59.626 50.000 0.00 0.00 36.75 2.85
54 55 1.982958 GTCAAACCCTCCCTCAAGGTA 59.017 52.381 0.00 0.00 36.75 3.08
55 56 0.771755 GTCAAACCCTCCCTCAAGGT 59.228 55.000 0.00 0.00 36.75 3.50
56 57 1.068121 AGTCAAACCCTCCCTCAAGG 58.932 55.000 0.00 0.00 36.08 3.61
57 58 2.784347 GAAGTCAAACCCTCCCTCAAG 58.216 52.381 0.00 0.00 0.00 3.02
58 59 1.071699 CGAAGTCAAACCCTCCCTCAA 59.928 52.381 0.00 0.00 0.00 3.02
59 60 0.685097 CGAAGTCAAACCCTCCCTCA 59.315 55.000 0.00 0.00 0.00 3.86
60 61 0.974383 TCGAAGTCAAACCCTCCCTC 59.026 55.000 0.00 0.00 0.00 4.30
61 62 1.430992 TTCGAAGTCAAACCCTCCCT 58.569 50.000 0.00 0.00 0.00 4.20
62 63 2.265589 TTTCGAAGTCAAACCCTCCC 57.734 50.000 0.00 0.00 0.00 4.30
63 64 3.408634 TGATTTCGAAGTCAAACCCTCC 58.591 45.455 19.66 0.00 0.00 4.30
64 65 4.610680 CGTTGATTTCGAAGTCAAACCCTC 60.611 45.833 30.22 19.27 36.23 4.30
65 66 3.250040 CGTTGATTTCGAAGTCAAACCCT 59.750 43.478 30.22 0.00 36.23 4.34
66 67 3.551551 CGTTGATTTCGAAGTCAAACCC 58.448 45.455 30.22 19.85 36.23 4.11
67 68 3.249080 TCCGTTGATTTCGAAGTCAAACC 59.751 43.478 30.22 20.42 36.23 3.27
68 69 4.209112 GTCCGTTGATTTCGAAGTCAAAC 58.791 43.478 30.22 22.70 36.23 2.93
69 70 3.872182 TGTCCGTTGATTTCGAAGTCAAA 59.128 39.130 30.22 16.98 36.23 2.69
70 71 3.459145 TGTCCGTTGATTTCGAAGTCAA 58.541 40.909 26.47 26.47 32.31 3.18
71 72 3.100658 TGTCCGTTGATTTCGAAGTCA 57.899 42.857 18.27 18.27 0.00 3.41
72 73 4.461992 TTTGTCCGTTGATTTCGAAGTC 57.538 40.909 13.30 13.30 0.00 3.01
73 74 4.886247 TTTTGTCCGTTGATTTCGAAGT 57.114 36.364 0.00 0.00 0.00 3.01
74 75 5.689819 AGATTTTGTCCGTTGATTTCGAAG 58.310 37.500 0.00 0.00 0.00 3.79
75 76 5.682943 AGATTTTGTCCGTTGATTTCGAA 57.317 34.783 0.00 0.00 0.00 3.71
76 77 5.237561 TGAAGATTTTGTCCGTTGATTTCGA 59.762 36.000 0.00 0.00 0.00 3.71
77 78 5.448438 TGAAGATTTTGTCCGTTGATTTCG 58.552 37.500 0.00 0.00 0.00 3.46
78 79 7.692908 TTTGAAGATTTTGTCCGTTGATTTC 57.307 32.000 0.00 0.00 0.00 2.17
79 80 8.661352 AATTTGAAGATTTTGTCCGTTGATTT 57.339 26.923 0.00 0.00 0.00 2.17
80 81 8.550376 CAAATTTGAAGATTTTGTCCGTTGATT 58.450 29.630 13.08 0.00 0.00 2.57
81 82 7.171337 CCAAATTTGAAGATTTTGTCCGTTGAT 59.829 33.333 19.86 0.00 30.36 2.57
82 83 6.478344 CCAAATTTGAAGATTTTGTCCGTTGA 59.522 34.615 19.86 0.00 30.36 3.18
83 84 6.478344 TCCAAATTTGAAGATTTTGTCCGTTG 59.522 34.615 19.86 0.00 30.36 4.10
84 85 6.578023 TCCAAATTTGAAGATTTTGTCCGTT 58.422 32.000 19.86 0.00 30.36 4.44
85 86 6.155475 TCCAAATTTGAAGATTTTGTCCGT 57.845 33.333 19.86 0.00 30.36 4.69
86 87 7.109006 CTTCCAAATTTGAAGATTTTGTCCG 57.891 36.000 19.86 0.00 30.36 4.79
429 430 2.099652 TTAGGCGCTGCACTGTCTGT 62.100 55.000 7.64 0.00 0.00 3.41
430 431 1.357258 CTTAGGCGCTGCACTGTCTG 61.357 60.000 7.64 0.00 0.00 3.51
431 432 1.079543 CTTAGGCGCTGCACTGTCT 60.080 57.895 7.64 0.00 0.00 3.41
432 433 2.103042 CCTTAGGCGCTGCACTGTC 61.103 63.158 7.64 0.00 0.00 3.51
433 434 2.046892 CCTTAGGCGCTGCACTGT 60.047 61.111 7.64 0.00 0.00 3.55
434 435 2.821366 CCCTTAGGCGCTGCACTG 60.821 66.667 7.64 0.00 0.00 3.66
450 451 5.127274 CATGTAATGTGCAGCGTCTAGCC 62.127 52.174 0.00 0.00 43.26 3.93
451 452 2.033407 CATGTAATGTGCAGCGTCTAGC 60.033 50.000 0.00 0.00 42.81 3.42
452 453 3.848846 CATGTAATGTGCAGCGTCTAG 57.151 47.619 0.00 0.00 40.20 2.43
465 466 1.953559 CTAGGCGCCACACATGTAAT 58.046 50.000 31.54 5.89 0.00 1.89
466 467 0.742990 GCTAGGCGCCACACATGTAA 60.743 55.000 31.54 0.72 0.00 2.41
467 468 1.153449 GCTAGGCGCCACACATGTA 60.153 57.895 31.54 9.35 0.00 2.29
468 469 2.436646 GCTAGGCGCCACACATGT 60.437 61.111 31.54 8.51 0.00 3.21
469 470 2.124983 AGCTAGGCGCCACACATG 60.125 61.111 31.54 12.28 40.39 3.21
470 471 2.187946 GAGCTAGGCGCCACACAT 59.812 61.111 31.54 10.27 40.39 3.21
471 472 4.435436 CGAGCTAGGCGCCACACA 62.435 66.667 31.54 9.67 40.39 3.72
474 475 4.577246 CTCCGAGCTAGGCGCCAC 62.577 72.222 31.54 17.93 40.39 5.01
480 481 4.277593 CAGCGCCTCCGAGCTAGG 62.278 72.222 6.52 6.52 44.07 3.02
481 482 4.940593 GCAGCGCCTCCGAGCTAG 62.941 72.222 2.29 0.00 44.07 3.42
515 516 4.473520 CACCGTGGCAGCCCCTAG 62.474 72.222 9.64 0.00 0.00 3.02
521 522 4.314440 TCTGTCCACCGTGGCAGC 62.314 66.667 25.37 14.67 39.70 5.25
522 523 2.047844 CTCTGTCCACCGTGGCAG 60.048 66.667 24.71 24.71 40.56 4.85
523 524 3.625897 CCTCTGTCCACCGTGGCA 61.626 66.667 13.19 12.68 37.47 4.92
524 525 3.626924 ACCTCTGTCCACCGTGGC 61.627 66.667 13.19 8.69 37.47 5.01
525 526 2.343758 CACCTCTGTCCACCGTGG 59.656 66.667 11.73 11.73 39.43 4.94
526 527 2.357517 GCACCTCTGTCCACCGTG 60.358 66.667 0.00 0.00 0.00 4.94
527 528 2.439960 TTGCACCTCTGTCCACCGT 61.440 57.895 0.00 0.00 0.00 4.83
528 529 1.961277 GTTGCACCTCTGTCCACCG 60.961 63.158 0.00 0.00 0.00 4.94
529 530 1.961277 CGTTGCACCTCTGTCCACC 60.961 63.158 0.00 0.00 0.00 4.61
530 531 2.607892 GCGTTGCACCTCTGTCCAC 61.608 63.158 0.00 0.00 0.00 4.02
531 532 2.280797 GCGTTGCACCTCTGTCCA 60.281 61.111 0.00 0.00 0.00 4.02
532 533 3.050275 GGCGTTGCACCTCTGTCC 61.050 66.667 0.00 0.00 0.00 4.02
533 534 2.031163 AGGCGTTGCACCTCTGTC 59.969 61.111 0.00 0.00 28.76 3.51
538 539 2.345244 CTCTGAGGCGTTGCACCT 59.655 61.111 0.00 0.00 41.41 4.00
539 540 2.507110 TAGCTCTGAGGCGTTGCACC 62.507 60.000 6.83 0.00 37.29 5.01
540 541 1.079819 TAGCTCTGAGGCGTTGCAC 60.080 57.895 6.83 0.00 37.29 4.57
541 542 1.216444 CTAGCTCTGAGGCGTTGCA 59.784 57.895 6.83 0.00 37.29 4.08
542 543 2.170434 GCTAGCTCTGAGGCGTTGC 61.170 63.158 7.70 3.39 37.29 4.17
543 544 1.875813 CGCTAGCTCTGAGGCGTTG 60.876 63.158 13.93 0.00 42.23 4.10
544 545 2.492090 CGCTAGCTCTGAGGCGTT 59.508 61.111 13.93 0.00 42.23 4.84
555 556 2.956964 CTACGGTGCAGCGCTAGC 60.957 66.667 35.78 17.19 45.58 3.42
556 557 2.278857 CCTACGGTGCAGCGCTAG 60.279 66.667 35.78 30.14 0.00 3.42
557 558 3.833645 CCCTACGGTGCAGCGCTA 61.834 66.667 35.78 24.33 0.00 4.26
568 569 3.454573 TAGGCGCCACACCCTACG 61.455 66.667 31.54 0.00 32.65 3.51
569 570 2.186125 GTAGGCGCCACACCCTAC 59.814 66.667 31.54 17.29 44.70 3.18
570 571 3.454573 CGTAGGCGCCACACCCTA 61.455 66.667 31.54 8.16 32.65 3.53
573 574 4.675029 ACACGTAGGCGCCACACC 62.675 66.667 31.54 11.93 42.83 4.16
574 575 3.110178 GACACGTAGGCGCCACAC 61.110 66.667 31.54 24.06 42.83 3.82
575 576 4.710695 CGACACGTAGGCGCCACA 62.711 66.667 31.54 13.75 42.83 4.17
588 589 3.758973 TTTTGAGTGGCGCCCGACA 62.759 57.895 26.77 17.83 0.00 4.35
589 590 2.458006 CTTTTTGAGTGGCGCCCGAC 62.458 60.000 26.77 17.18 0.00 4.79
590 591 2.203224 TTTTTGAGTGGCGCCCGA 60.203 55.556 26.77 2.06 0.00 5.14
591 592 1.586154 ATCTTTTTGAGTGGCGCCCG 61.586 55.000 26.77 0.76 0.00 6.13
592 593 0.171231 GATCTTTTTGAGTGGCGCCC 59.829 55.000 26.77 15.80 0.00 6.13
593 594 0.881118 TGATCTTTTTGAGTGGCGCC 59.119 50.000 22.73 22.73 0.00 6.53
594 595 1.730446 GCTGATCTTTTTGAGTGGCGC 60.730 52.381 0.00 0.00 0.00 6.53
595 596 1.808945 AGCTGATCTTTTTGAGTGGCG 59.191 47.619 0.00 0.00 0.00 5.69
596 597 4.397417 ACATAGCTGATCTTTTTGAGTGGC 59.603 41.667 0.00 0.00 0.00 5.01
597 598 5.645067 TCACATAGCTGATCTTTTTGAGTGG 59.355 40.000 0.00 0.00 0.00 4.00
598 599 6.732531 TCACATAGCTGATCTTTTTGAGTG 57.267 37.500 0.00 0.00 0.00 3.51
599 600 7.750229 TTTCACATAGCTGATCTTTTTGAGT 57.250 32.000 0.00 0.00 0.00 3.41
600 601 9.932699 CTATTTCACATAGCTGATCTTTTTGAG 57.067 33.333 0.00 0.00 0.00 3.02
601 602 9.453572 ACTATTTCACATAGCTGATCTTTTTGA 57.546 29.630 0.00 0.00 0.00 2.69
606 607 8.186821 GCAAAACTATTTCACATAGCTGATCTT 58.813 33.333 0.00 0.00 0.00 2.40
607 608 7.466455 CGCAAAACTATTTCACATAGCTGATCT 60.466 37.037 0.00 0.00 0.00 2.75
608 609 6.630443 CGCAAAACTATTTCACATAGCTGATC 59.370 38.462 0.00 0.00 0.00 2.92
609 610 6.458751 CCGCAAAACTATTTCACATAGCTGAT 60.459 38.462 0.00 0.00 0.00 2.90
610 611 5.163764 CCGCAAAACTATTTCACATAGCTGA 60.164 40.000 0.00 0.00 0.00 4.26
611 612 5.030295 CCGCAAAACTATTTCACATAGCTG 58.970 41.667 0.00 0.00 0.00 4.24
612 613 4.941263 TCCGCAAAACTATTTCACATAGCT 59.059 37.500 0.00 0.00 0.00 3.32
613 614 5.028375 GTCCGCAAAACTATTTCACATAGC 58.972 41.667 0.00 0.00 0.00 2.97
614 615 6.176975 TGTCCGCAAAACTATTTCACATAG 57.823 37.500 0.00 0.00 0.00 2.23
615 616 6.561737 TTGTCCGCAAAACTATTTCACATA 57.438 33.333 0.00 0.00 0.00 2.29
616 617 5.446143 TTGTCCGCAAAACTATTTCACAT 57.554 34.783 0.00 0.00 0.00 3.21
617 618 4.902443 TTGTCCGCAAAACTATTTCACA 57.098 36.364 0.00 0.00 0.00 3.58
618 619 6.763303 AAATTGTCCGCAAAACTATTTCAC 57.237 33.333 0.00 0.00 38.21 3.18
619 620 9.482627 AAATAAATTGTCCGCAAAACTATTTCA 57.517 25.926 6.03 0.00 38.21 2.69
622 623 9.267084 ACAAAATAAATTGTCCGCAAAACTATT 57.733 25.926 0.00 0.00 39.23 1.73
623 624 8.707839 CACAAAATAAATTGTCCGCAAAACTAT 58.292 29.630 0.00 0.00 41.44 2.12
624 625 7.921214 TCACAAAATAAATTGTCCGCAAAACTA 59.079 29.630 0.00 0.00 41.44 2.24
625 626 6.758886 TCACAAAATAAATTGTCCGCAAAACT 59.241 30.769 0.00 0.00 41.44 2.66
626 627 6.938542 TCACAAAATAAATTGTCCGCAAAAC 58.061 32.000 0.00 0.00 41.44 2.43
627 628 7.539712 TTCACAAAATAAATTGTCCGCAAAA 57.460 28.000 0.00 0.00 41.44 2.44
628 629 7.721286 ATTCACAAAATAAATTGTCCGCAAA 57.279 28.000 0.00 0.00 41.44 3.68
629 630 7.439356 TGAATTCACAAAATAAATTGTCCGCAA 59.561 29.630 3.38 0.00 41.44 4.85
630 631 6.925718 TGAATTCACAAAATAAATTGTCCGCA 59.074 30.769 3.38 0.00 41.44 5.69
631 632 7.344910 TGAATTCACAAAATAAATTGTCCGC 57.655 32.000 3.38 0.00 41.44 5.54
645 646 9.460019 TGACCTATGAATGTAATGAATTCACAA 57.540 29.630 11.07 0.00 44.51 3.33
646 647 9.460019 TTGACCTATGAATGTAATGAATTCACA 57.540 29.630 11.07 4.92 44.51 3.58
661 662 8.772705 GCAAATTTGACAATTTTGACCTATGAA 58.227 29.630 27.56 0.00 40.09 2.57
662 663 7.387397 GGCAAATTTGACAATTTTGACCTATGA 59.613 33.333 27.56 0.00 40.09 2.15
663 664 7.520686 GGCAAATTTGACAATTTTGACCTATG 58.479 34.615 27.56 10.22 40.09 2.23
664 665 6.368516 CGGCAAATTTGACAATTTTGACCTAT 59.631 34.615 27.56 0.00 40.09 2.57
665 666 5.694006 CGGCAAATTTGACAATTTTGACCTA 59.306 36.000 27.56 0.00 40.09 3.08
666 667 4.511082 CGGCAAATTTGACAATTTTGACCT 59.489 37.500 27.56 0.56 40.09 3.85
667 668 4.771360 CGGCAAATTTGACAATTTTGACC 58.229 39.130 27.56 24.76 40.09 4.02
668 669 4.024977 AGCGGCAAATTTGACAATTTTGAC 60.025 37.500 27.56 25.28 40.09 3.18
669 670 4.125703 AGCGGCAAATTTGACAATTTTGA 58.874 34.783 27.56 0.07 40.09 2.69
670 671 4.471157 AGCGGCAAATTTGACAATTTTG 57.529 36.364 23.49 22.48 40.09 2.44
671 672 6.799926 ATAAGCGGCAAATTTGACAATTTT 57.200 29.167 23.49 13.10 40.09 1.82
672 673 6.128309 GGAATAAGCGGCAAATTTGACAATTT 60.128 34.615 23.49 15.32 42.37 1.82
673 674 5.351189 GGAATAAGCGGCAAATTTGACAATT 59.649 36.000 23.49 17.97 35.35 2.32
674 675 4.869861 GGAATAAGCGGCAAATTTGACAAT 59.130 37.500 23.49 11.04 35.35 2.71
675 676 4.241681 GGAATAAGCGGCAAATTTGACAA 58.758 39.130 23.49 6.35 35.35 3.18
676 677 3.256879 TGGAATAAGCGGCAAATTTGACA 59.743 39.130 23.49 4.50 35.35 3.58
677 678 3.612423 GTGGAATAAGCGGCAAATTTGAC 59.388 43.478 22.31 18.50 0.00 3.18
678 679 3.509575 AGTGGAATAAGCGGCAAATTTGA 59.490 39.130 22.31 0.00 0.00 2.69
679 680 3.848726 AGTGGAATAAGCGGCAAATTTG 58.151 40.909 14.03 14.03 0.00 2.32
680 681 4.535526 AAGTGGAATAAGCGGCAAATTT 57.464 36.364 1.45 0.00 0.00 1.82
681 682 4.535526 AAAGTGGAATAAGCGGCAAATT 57.464 36.364 1.45 0.68 0.00 1.82
682 683 5.852282 ATAAAGTGGAATAAGCGGCAAAT 57.148 34.783 1.45 0.00 0.00 2.32
683 684 5.184096 TGAATAAAGTGGAATAAGCGGCAAA 59.816 36.000 1.45 0.00 0.00 3.68
684 685 4.702612 TGAATAAAGTGGAATAAGCGGCAA 59.297 37.500 1.45 0.00 0.00 4.52
685 686 4.095782 GTGAATAAAGTGGAATAAGCGGCA 59.904 41.667 1.45 0.00 0.00 5.69
686 687 4.335594 AGTGAATAAAGTGGAATAAGCGGC 59.664 41.667 0.00 0.00 0.00 6.53
687 688 6.436843 AAGTGAATAAAGTGGAATAAGCGG 57.563 37.500 0.00 0.00 0.00 5.52
710 711 9.485206 GGACCGAATTTAGAGCAAGTATAATAA 57.515 33.333 0.00 0.00 0.00 1.40
711 712 7.811236 CGGACCGAATTTAGAGCAAGTATAATA 59.189 37.037 8.64 0.00 0.00 0.98
712 713 6.645415 CGGACCGAATTTAGAGCAAGTATAAT 59.355 38.462 8.64 0.00 0.00 1.28
713 714 5.981315 CGGACCGAATTTAGAGCAAGTATAA 59.019 40.000 8.64 0.00 0.00 0.98
714 715 5.300034 TCGGACCGAATTTAGAGCAAGTATA 59.700 40.000 15.79 0.00 31.06 1.47
715 716 4.098960 TCGGACCGAATTTAGAGCAAGTAT 59.901 41.667 15.79 0.00 31.06 2.12
716 717 3.444742 TCGGACCGAATTTAGAGCAAGTA 59.555 43.478 15.79 0.00 31.06 2.24
717 718 2.232941 TCGGACCGAATTTAGAGCAAGT 59.767 45.455 15.79 0.00 31.06 3.16
718 719 2.860735 CTCGGACCGAATTTAGAGCAAG 59.139 50.000 18.93 0.00 34.74 4.01
719 720 2.494471 TCTCGGACCGAATTTAGAGCAA 59.506 45.455 18.93 0.00 34.74 3.91
720 721 2.097036 TCTCGGACCGAATTTAGAGCA 58.903 47.619 18.93 0.00 34.74 4.26
721 722 2.865343 TCTCGGACCGAATTTAGAGC 57.135 50.000 18.93 0.00 34.74 4.09
722 723 3.130693 ACCTTCTCGGACCGAATTTAGAG 59.869 47.826 18.93 4.30 34.74 2.43
734 735 4.069232 CGGCTGCACCTTCTCGGA 62.069 66.667 0.50 0.00 35.61 4.55
758 759 2.190981 GGTGTACTGTACGCTATGCAC 58.809 52.381 25.45 11.39 39.11 4.57
760 761 2.159282 AGTGGTGTACTGTACGCTATGC 60.159 50.000 25.45 12.58 38.49 3.14
958 971 1.228003 GGATCTCTCGGAGCTCGGA 60.228 63.158 21.29 21.29 39.77 4.55
1127 1147 1.614824 CCACTGAAGGCTCCCCTCT 60.615 63.158 0.00 0.00 41.90 3.69
1156 1176 1.878656 CTCACCTCCCTGACGACACC 61.879 65.000 0.00 0.00 0.00 4.16
1174 1194 1.751162 CGGGAGAAGAGCGAGGACT 60.751 63.158 0.00 0.00 0.00 3.85
1227 1247 8.230486 CAGTATATATCAAGCACCGAAAATTCC 58.770 37.037 0.00 0.00 0.00 3.01
1288 1337 5.432645 TCCGCCAAGAAAACATATGATACA 58.567 37.500 10.38 0.00 0.00 2.29
1375 1424 1.135527 CGAGCATCCCATTTGTGCAAT 59.864 47.619 0.00 0.00 41.19 3.56
1378 1427 0.810648 TTCGAGCATCCCATTTGTGC 59.189 50.000 0.00 0.00 39.10 4.57
1381 1430 3.450578 CCAATTTCGAGCATCCCATTTG 58.549 45.455 0.00 0.00 0.00 2.32
1423 1472 2.362169 ACAAATAATTGCCGTGGTGC 57.638 45.000 0.00 0.00 40.34 5.01
1424 1473 4.427096 TGTACAAATAATTGCCGTGGTG 57.573 40.909 0.00 0.00 40.34 4.17
1479 1553 1.386525 CCAGTTTGCCCATCCATCCG 61.387 60.000 0.00 0.00 0.00 4.18
1584 1658 3.643320 CCTAATGTCTCTGCCCTGATGTA 59.357 47.826 0.00 0.00 0.00 2.29
1599 1673 2.615493 CGAAGGCAAGTCCACCTAATGT 60.615 50.000 0.00 0.00 34.31 2.71
1601 1675 1.906574 TCGAAGGCAAGTCCACCTAAT 59.093 47.619 0.00 0.00 34.31 1.73
1606 1680 1.947456 ACTTTTCGAAGGCAAGTCCAC 59.053 47.619 7.71 0.00 37.29 4.02
1654 1728 1.905637 CCACCCAACCCTTAAGTGAC 58.094 55.000 0.97 0.00 0.00 3.67
1769 1847 4.546829 AGGTCAGCGGTTTATACTTCAA 57.453 40.909 0.00 0.00 0.00 2.69
2534 2622 7.212274 AGAATTTAGCAGCTTTCACAAAACAT 58.788 30.769 0.00 0.00 0.00 2.71
2569 2657 5.541953 TGAGGTGTCAGATGAGGATAATG 57.458 43.478 0.00 0.00 0.00 1.90
2570 2658 6.465464 CCAATGAGGTGTCAGATGAGGATAAT 60.465 42.308 0.00 0.00 35.66 1.28
2914 3002 4.748701 GTAGATTACCAGGGTCCAGGATA 58.251 47.826 5.40 0.00 0.00 2.59
3069 3157 5.293079 GCCAAATTTTTACAGCAAAGTGACA 59.707 36.000 0.00 0.00 0.00 3.58
3070 3158 5.556194 CGCCAAATTTTTACAGCAAAGTGAC 60.556 40.000 0.00 0.00 0.00 3.67
3664 3754 7.622893 ACCAAATGTTGCAAGTAAACAAAAT 57.377 28.000 0.00 0.00 40.69 1.82
3677 3768 6.737254 ATGTGTAGTACTACCAAATGTTGC 57.263 37.500 26.41 8.81 35.26 4.17
3844 3935 9.916397 CGGTAAGTTATCTCAAAACATATCAAC 57.084 33.333 0.00 0.00 0.00 3.18
3960 4051 4.724074 ACAACGTCACTATTTCCGGATA 57.276 40.909 4.15 0.00 0.00 2.59
4016 4110 5.687285 AGCTGTTTTAGTTCAAATTTGAGCG 59.313 36.000 23.85 12.41 42.34 5.03
4211 4306 5.339008 AGAAATCTAGCCAATGACGTACA 57.661 39.130 0.00 0.00 0.00 2.90
4254 4349 8.617290 TCATAGTTGTTAAAGAAACTTCCCTC 57.383 34.615 5.15 0.00 38.99 4.30
4289 4384 1.964223 ACTTGATCCGCATCCGACTAT 59.036 47.619 0.00 0.00 36.29 2.12


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

AutoCloner maintained by Alex Coulton.