Multiple sequence alignment - TraesCS5D01G155900

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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 TraesCS5D01G155900 chr5D 100.000 5231 0 0 1 5231 244211083 244205853 0.000000e+00 9660
1 TraesCS5D01G155900 chr5D 96.889 225 2 1 1345 1569 457642296 457642077 6.400000e-99 372
2 TraesCS5D01G155900 chr5A 94.202 2087 80 17 2053 4117 328659641 328657574 0.000000e+00 3145
3 TraesCS5D01G155900 chr5A 93.419 1717 100 7 317 2026 328661473 328659763 0.000000e+00 2532
4 TraesCS5D01G155900 chr5A 91.058 548 21 10 4119 4653 328657541 328657009 0.000000e+00 715
5 TraesCS5D01G155900 chr5A 94.949 99 4 1 207 304 328661630 328661532 2.520000e-33 154
6 TraesCS5D01G155900 chr5B 92.890 2180 92 33 1986 4117 277268055 277265891 0.000000e+00 3109
7 TraesCS5D01G155900 chr5B 93.950 1752 83 14 334 2067 277269771 277268025 0.000000e+00 2627
8 TraesCS5D01G155900 chr5B 89.243 502 21 12 4119 4600 277265858 277265370 9.700000e-167 597
9 TraesCS5D01G155900 chr7B 92.559 1989 89 26 1099 3049 22545642 22543675 0.000000e+00 2798
10 TraesCS5D01G155900 chr2B 92.428 1981 103 17 1099 3049 152135944 152133981 0.000000e+00 2784
11 TraesCS5D01G155900 chr2B 92.119 571 38 5 4663 5229 736859769 736860336 0.000000e+00 798
12 TraesCS5D01G155900 chr4B 92.794 1582 68 23 1498 3049 13274592 13276157 0.000000e+00 2248
13 TraesCS5D01G155900 chr4B 90.370 405 38 1 1096 1500 13233042 13233445 9.970000e-147 531
14 TraesCS5D01G155900 chr2D 92.453 583 40 2 4653 5231 594052829 594053411 0.000000e+00 830
15 TraesCS5D01G155900 chr2D 91.552 580 44 3 4654 5229 44916707 44916129 0.000000e+00 795
16 TraesCS5D01G155900 chr2D 89.863 582 49 8 4653 5229 619552861 619553437 0.000000e+00 739
17 TraesCS5D01G155900 chr2D 89.175 582 42 4 4654 5231 592145837 592146401 0.000000e+00 706
18 TraesCS5D01G155900 chr7A 91.176 578 46 3 4654 5227 732012657 732013233 0.000000e+00 780
19 TraesCS5D01G155900 chr1A 89.810 579 52 4 4654 5227 515283327 515282751 0.000000e+00 736
20 TraesCS5D01G155900 chr3B 89.175 582 59 2 4654 5231 759877409 759876828 0.000000e+00 723
21 TraesCS5D01G155900 chr3B 78.593 327 56 10 4892 5208 755695513 755695835 2.470000e-48 204
22 TraesCS5D01G155900 chr7D 88.021 576 50 4 4654 5228 603368917 603369474 0.000000e+00 664


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 TraesCS5D01G155900 chr5D 244205853 244211083 5230 True 9660.0 9660 100.000000 1 5231 1 chr5D.!!$R1 5230
1 TraesCS5D01G155900 chr5A 328657009 328661630 4621 True 1636.5 3145 93.407000 207 4653 4 chr5A.!!$R1 4446
2 TraesCS5D01G155900 chr5B 277265370 277269771 4401 True 2111.0 3109 92.027667 334 4600 3 chr5B.!!$R1 4266
3 TraesCS5D01G155900 chr7B 22543675 22545642 1967 True 2798.0 2798 92.559000 1099 3049 1 chr7B.!!$R1 1950
4 TraesCS5D01G155900 chr2B 152133981 152135944 1963 True 2784.0 2784 92.428000 1099 3049 1 chr2B.!!$R1 1950
5 TraesCS5D01G155900 chr2B 736859769 736860336 567 False 798.0 798 92.119000 4663 5229 1 chr2B.!!$F1 566
6 TraesCS5D01G155900 chr4B 13274592 13276157 1565 False 2248.0 2248 92.794000 1498 3049 1 chr4B.!!$F2 1551
7 TraesCS5D01G155900 chr2D 594052829 594053411 582 False 830.0 830 92.453000 4653 5231 1 chr2D.!!$F2 578
8 TraesCS5D01G155900 chr2D 44916129 44916707 578 True 795.0 795 91.552000 4654 5229 1 chr2D.!!$R1 575
9 TraesCS5D01G155900 chr2D 619552861 619553437 576 False 739.0 739 89.863000 4653 5229 1 chr2D.!!$F3 576
10 TraesCS5D01G155900 chr2D 592145837 592146401 564 False 706.0 706 89.175000 4654 5231 1 chr2D.!!$F1 577
11 TraesCS5D01G155900 chr7A 732012657 732013233 576 False 780.0 780 91.176000 4654 5227 1 chr7A.!!$F1 573
12 TraesCS5D01G155900 chr1A 515282751 515283327 576 True 736.0 736 89.810000 4654 5227 1 chr1A.!!$R1 573
13 TraesCS5D01G155900 chr3B 759876828 759877409 581 True 723.0 723 89.175000 4654 5231 1 chr3B.!!$R1 577
14 TraesCS5D01G155900 chr7D 603368917 603369474 557 False 664.0 664 88.021000 4654 5228 1 chr7D.!!$F1 574

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
24 25 0.033504 AAACATCGACGACACCAGCT 59.966 50.0 0.00 0.00 0.00 4.24 F
304 306 0.105039 CGGAGATGCCCTAACACCTC 59.895 60.0 0.00 0.00 0.00 3.85 F
867 930 0.169009 GGGCAGTCTCGTCATTTTGC 59.831 55.0 0.00 0.00 0.00 3.68 F
868 931 0.169009 GGCAGTCTCGTCATTTTGCC 59.831 55.0 0.00 0.00 43.54 4.52 F
2553 2769 0.322975 ACTCTTGCAGGTGCTCGATT 59.677 50.0 3.18 0.00 42.66 3.34 F
3263 3480 0.392729 AAGCTCTGTCTGGATGCAGC 60.393 55.0 9.76 5.56 33.09 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1496 1.186200 CATTGGAGAGGTCGAGGTCA 58.814 55.000 0.00 0.0 0.00 4.02 R
1710 1785 1.275666 TGGAACAGGACGTGATGGAT 58.724 50.000 0.00 0.0 0.00 3.41 R
2553 2769 2.158885 TGACATTCCGACAGGTTGACAA 60.159 45.455 0.00 0.0 39.05 3.18 R
2740 2956 3.072768 AGCATTTGGAAGCATTTTCCCAA 59.927 39.130 3.66 0.0 37.79 4.12 R
4117 4343 0.317269 CTGCAAAGACCACACGCTTG 60.317 55.000 0.00 0.0 0.00 4.01 R
4464 4737 0.527817 GACAGGCCGACAGGTAATCG 60.528 60.000 0.00 0.0 40.50 3.34 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
17 18 2.776072 CCGCCAAACATCGACGAC 59.224 61.111 0.00 0.00 0.00 4.34
18 19 2.024868 CCGCCAAACATCGACGACA 61.025 57.895 0.00 0.00 0.00 4.35
19 20 1.129809 CGCCAAACATCGACGACAC 59.870 57.895 0.00 0.00 0.00 3.67
20 21 1.495951 GCCAAACATCGACGACACC 59.504 57.895 0.00 0.00 0.00 4.16
21 22 1.225376 GCCAAACATCGACGACACCA 61.225 55.000 0.00 0.00 0.00 4.17
22 23 0.790207 CCAAACATCGACGACACCAG 59.210 55.000 0.00 0.00 0.00 4.00
23 24 0.163788 CAAACATCGACGACACCAGC 59.836 55.000 0.00 0.00 0.00 4.85
24 25 0.033504 AAACATCGACGACACCAGCT 59.966 50.000 0.00 0.00 0.00 4.24
25 26 0.388649 AACATCGACGACACCAGCTC 60.389 55.000 0.00 0.00 0.00 4.09
26 27 1.517257 CATCGACGACACCAGCTCC 60.517 63.158 0.00 0.00 0.00 4.70
27 28 1.977009 ATCGACGACACCAGCTCCA 60.977 57.895 0.00 0.00 0.00 3.86
28 29 1.532604 ATCGACGACACCAGCTCCAA 61.533 55.000 0.00 0.00 0.00 3.53
29 30 1.300620 CGACGACACCAGCTCCAAA 60.301 57.895 0.00 0.00 0.00 3.28
30 31 1.557443 CGACGACACCAGCTCCAAAC 61.557 60.000 0.00 0.00 0.00 2.93
31 32 0.249911 GACGACACCAGCTCCAAACT 60.250 55.000 0.00 0.00 0.00 2.66
32 33 0.532862 ACGACACCAGCTCCAAACTG 60.533 55.000 0.00 0.00 34.82 3.16
33 34 0.249868 CGACACCAGCTCCAAACTGA 60.250 55.000 0.00 0.00 37.32 3.41
34 35 1.517242 GACACCAGCTCCAAACTGAG 58.483 55.000 0.00 0.00 37.32 3.35
35 36 0.109342 ACACCAGCTCCAAACTGAGG 59.891 55.000 0.00 0.00 37.32 3.86
36 37 0.109342 CACCAGCTCCAAACTGAGGT 59.891 55.000 0.00 0.00 43.54 3.85
37 38 0.398318 ACCAGCTCCAAACTGAGGTC 59.602 55.000 0.00 0.00 40.94 3.85
38 39 0.689623 CCAGCTCCAAACTGAGGTCT 59.310 55.000 0.00 0.00 40.94 3.85
39 40 1.902508 CCAGCTCCAAACTGAGGTCTA 59.097 52.381 0.00 0.00 40.94 2.59
40 41 2.093764 CCAGCTCCAAACTGAGGTCTAG 60.094 54.545 0.00 0.00 40.94 2.43
41 42 1.552792 AGCTCCAAACTGAGGTCTAGC 59.447 52.381 0.00 0.00 38.69 3.42
42 43 1.406205 GCTCCAAACTGAGGTCTAGCC 60.406 57.143 0.00 0.00 32.81 3.93
43 44 1.902508 CTCCAAACTGAGGTCTAGCCA 59.097 52.381 6.07 0.00 40.61 4.75
44 45 1.902508 TCCAAACTGAGGTCTAGCCAG 59.097 52.381 6.07 0.00 40.61 4.85
45 46 1.625818 CCAAACTGAGGTCTAGCCAGT 59.374 52.381 6.07 0.00 42.34 4.00
46 47 2.832129 CCAAACTGAGGTCTAGCCAGTA 59.168 50.000 0.00 0.00 39.93 2.74
47 48 3.118956 CCAAACTGAGGTCTAGCCAGTAG 60.119 52.174 0.00 3.92 39.93 2.57
48 49 3.741245 AACTGAGGTCTAGCCAGTAGA 57.259 47.619 0.00 0.00 39.93 2.59
49 50 3.290948 ACTGAGGTCTAGCCAGTAGAG 57.709 52.381 6.07 0.00 38.52 2.43
50 51 2.847449 ACTGAGGTCTAGCCAGTAGAGA 59.153 50.000 6.07 0.00 38.52 3.10
51 52 3.118038 ACTGAGGTCTAGCCAGTAGAGAG 60.118 52.174 6.07 0.00 38.52 3.20
52 53 2.847449 TGAGGTCTAGCCAGTAGAGAGT 59.153 50.000 6.07 0.00 38.52 3.24
53 54 4.038633 TGAGGTCTAGCCAGTAGAGAGTA 58.961 47.826 6.07 0.00 38.52 2.59
54 55 4.101898 TGAGGTCTAGCCAGTAGAGAGTAG 59.898 50.000 6.07 0.00 38.52 2.57
55 56 3.393278 AGGTCTAGCCAGTAGAGAGTAGG 59.607 52.174 6.07 0.00 38.52 3.18
56 57 3.497227 GGTCTAGCCAGTAGAGAGTAGGG 60.497 56.522 0.00 0.00 38.52 3.53
57 58 3.391955 GTCTAGCCAGTAGAGAGTAGGGA 59.608 52.174 0.00 0.00 38.52 4.20
58 59 4.045736 TCTAGCCAGTAGAGAGTAGGGAA 58.954 47.826 0.00 0.00 32.36 3.97
59 60 3.306472 AGCCAGTAGAGAGTAGGGAAG 57.694 52.381 0.00 0.00 0.00 3.46
60 61 2.853707 AGCCAGTAGAGAGTAGGGAAGA 59.146 50.000 0.00 0.00 0.00 2.87
61 62 3.117663 AGCCAGTAGAGAGTAGGGAAGAG 60.118 52.174 0.00 0.00 0.00 2.85
62 63 3.827722 CCAGTAGAGAGTAGGGAAGAGG 58.172 54.545 0.00 0.00 0.00 3.69
63 64 3.435890 CCAGTAGAGAGTAGGGAAGAGGG 60.436 56.522 0.00 0.00 0.00 4.30
64 65 2.176148 AGTAGAGAGTAGGGAAGAGGGC 59.824 54.545 0.00 0.00 0.00 5.19
65 66 1.314895 AGAGAGTAGGGAAGAGGGCT 58.685 55.000 0.00 0.00 0.00 5.19
66 67 2.504905 AGAGAGTAGGGAAGAGGGCTA 58.495 52.381 0.00 0.00 0.00 3.93
67 68 2.860041 AGAGAGTAGGGAAGAGGGCTAA 59.140 50.000 0.00 0.00 0.00 3.09
68 69 3.272551 AGAGAGTAGGGAAGAGGGCTAAA 59.727 47.826 0.00 0.00 0.00 1.85
69 70 4.078278 AGAGAGTAGGGAAGAGGGCTAAAT 60.078 45.833 0.00 0.00 0.00 1.40
70 71 4.228010 AGAGTAGGGAAGAGGGCTAAATC 58.772 47.826 0.00 0.00 0.00 2.17
71 72 3.319220 AGTAGGGAAGAGGGCTAAATCC 58.681 50.000 0.00 0.00 0.00 3.01
72 73 2.286935 AGGGAAGAGGGCTAAATCCA 57.713 50.000 0.00 0.00 31.63 3.41
73 74 2.131023 AGGGAAGAGGGCTAAATCCAG 58.869 52.381 0.00 0.00 31.63 3.86
74 75 1.143889 GGGAAGAGGGCTAAATCCAGG 59.856 57.143 0.00 0.00 31.63 4.45
75 76 1.477740 GGAAGAGGGCTAAATCCAGGC 60.478 57.143 0.00 0.00 40.27 4.85
76 77 1.492599 GAAGAGGGCTAAATCCAGGCT 59.507 52.381 0.00 0.00 40.78 4.58
77 78 2.496679 AGAGGGCTAAATCCAGGCTA 57.503 50.000 0.00 0.00 40.78 3.93
78 79 2.776665 AGAGGGCTAAATCCAGGCTAA 58.223 47.619 0.00 0.00 40.78 3.09
79 80 3.331120 AGAGGGCTAAATCCAGGCTAAT 58.669 45.455 0.00 0.00 40.78 1.73
80 81 3.073650 AGAGGGCTAAATCCAGGCTAATG 59.926 47.826 0.00 0.00 40.78 1.90
81 82 2.785857 AGGGCTAAATCCAGGCTAATGT 59.214 45.455 0.00 0.00 40.78 2.71
82 83 3.149981 GGGCTAAATCCAGGCTAATGTC 58.850 50.000 0.00 0.00 40.78 3.06
83 84 2.808543 GGCTAAATCCAGGCTAATGTCG 59.191 50.000 0.00 0.00 38.06 4.35
84 85 2.224314 GCTAAATCCAGGCTAATGTCGC 59.776 50.000 0.00 0.00 0.00 5.19
85 86 1.299541 AAATCCAGGCTAATGTCGCG 58.700 50.000 0.00 0.00 0.00 5.87
86 87 0.178068 AATCCAGGCTAATGTCGCGT 59.822 50.000 5.77 0.00 0.00 6.01
87 88 0.249489 ATCCAGGCTAATGTCGCGTC 60.249 55.000 5.77 0.00 0.00 5.19
88 89 2.230940 CCAGGCTAATGTCGCGTCG 61.231 63.158 5.77 0.00 0.00 5.12
89 90 2.582498 AGGCTAATGTCGCGTCGC 60.582 61.111 7.29 7.29 0.00 5.19
90 91 2.582498 GGCTAATGTCGCGTCGCT 60.582 61.111 16.36 0.00 0.00 4.93
91 92 2.577785 GGCTAATGTCGCGTCGCTC 61.578 63.158 16.36 8.86 0.00 5.03
92 93 1.872234 GCTAATGTCGCGTCGCTCA 60.872 57.895 16.36 14.27 0.00 4.26
93 94 1.410737 GCTAATGTCGCGTCGCTCAA 61.411 55.000 16.36 0.02 0.00 3.02
94 95 1.200483 CTAATGTCGCGTCGCTCAAT 58.800 50.000 16.36 9.90 0.00 2.57
95 96 1.188138 CTAATGTCGCGTCGCTCAATC 59.812 52.381 16.36 1.76 0.00 2.67
96 97 1.421410 AATGTCGCGTCGCTCAATCC 61.421 55.000 16.36 0.00 0.00 3.01
97 98 2.506217 GTCGCGTCGCTCAATCCA 60.506 61.111 16.36 0.00 0.00 3.41
98 99 1.878522 GTCGCGTCGCTCAATCCAT 60.879 57.895 16.36 0.00 0.00 3.41
99 100 1.588932 TCGCGTCGCTCAATCCATC 60.589 57.895 16.36 0.00 0.00 3.51
100 101 1.589993 CGCGTCGCTCAATCCATCT 60.590 57.895 16.36 0.00 0.00 2.90
101 102 0.317854 CGCGTCGCTCAATCCATCTA 60.318 55.000 16.36 0.00 0.00 1.98
102 103 1.852942 GCGTCGCTCAATCCATCTAA 58.147 50.000 10.68 0.00 0.00 2.10
103 104 2.408050 GCGTCGCTCAATCCATCTAAT 58.592 47.619 10.68 0.00 0.00 1.73
104 105 2.802816 GCGTCGCTCAATCCATCTAATT 59.197 45.455 10.68 0.00 0.00 1.40
105 106 3.248602 GCGTCGCTCAATCCATCTAATTT 59.751 43.478 10.68 0.00 0.00 1.82
106 107 4.260784 GCGTCGCTCAATCCATCTAATTTT 60.261 41.667 10.68 0.00 0.00 1.82
107 108 5.435557 CGTCGCTCAATCCATCTAATTTTC 58.564 41.667 0.00 0.00 0.00 2.29
108 109 5.235186 CGTCGCTCAATCCATCTAATTTTCT 59.765 40.000 0.00 0.00 0.00 2.52
109 110 6.238211 CGTCGCTCAATCCATCTAATTTTCTT 60.238 38.462 0.00 0.00 0.00 2.52
110 111 7.475840 GTCGCTCAATCCATCTAATTTTCTTT 58.524 34.615 0.00 0.00 0.00 2.52
111 112 8.612619 GTCGCTCAATCCATCTAATTTTCTTTA 58.387 33.333 0.00 0.00 0.00 1.85
112 113 8.830580 TCGCTCAATCCATCTAATTTTCTTTAG 58.169 33.333 0.00 0.00 0.00 1.85
113 114 8.830580 CGCTCAATCCATCTAATTTTCTTTAGA 58.169 33.333 0.00 0.00 41.23 2.10
120 121 8.408601 TCCATCTAATTTTCTTTAGAAGCATGC 58.591 33.333 10.51 10.51 40.57 4.06
121 122 8.192774 CCATCTAATTTTCTTTAGAAGCATGCA 58.807 33.333 21.98 0.00 40.57 3.96
122 123 9.017669 CATCTAATTTTCTTTAGAAGCATGCAC 57.982 33.333 21.98 13.47 40.57 4.57
123 124 7.538575 TCTAATTTTCTTTAGAAGCATGCACC 58.461 34.615 21.98 10.90 35.73 5.01
124 125 3.829886 TTTCTTTAGAAGCATGCACCG 57.170 42.857 21.98 0.70 35.21 4.94
125 126 2.472695 TCTTTAGAAGCATGCACCGT 57.527 45.000 21.98 3.69 0.00 4.83
126 127 2.076100 TCTTTAGAAGCATGCACCGTG 58.924 47.619 21.98 3.73 0.00 4.94
127 128 1.131126 CTTTAGAAGCATGCACCGTGG 59.869 52.381 21.98 0.23 0.00 4.94
128 129 0.676466 TTAGAAGCATGCACCGTGGG 60.676 55.000 21.98 0.00 0.00 4.61
129 130 2.535485 TAGAAGCATGCACCGTGGGG 62.535 60.000 21.98 0.00 40.11 4.96
139 140 2.270850 CCGTGGGGGTATGTGGTG 59.729 66.667 0.00 0.00 0.00 4.17
140 141 2.294839 CCGTGGGGGTATGTGGTGA 61.295 63.158 0.00 0.00 0.00 4.02
141 142 1.632018 CCGTGGGGGTATGTGGTGAT 61.632 60.000 0.00 0.00 0.00 3.06
142 143 0.254747 CGTGGGGGTATGTGGTGATT 59.745 55.000 0.00 0.00 0.00 2.57
143 144 1.340600 CGTGGGGGTATGTGGTGATTT 60.341 52.381 0.00 0.00 0.00 2.17
144 145 2.815158 GTGGGGGTATGTGGTGATTTT 58.185 47.619 0.00 0.00 0.00 1.82
145 146 3.169908 GTGGGGGTATGTGGTGATTTTT 58.830 45.455 0.00 0.00 0.00 1.94
160 161 3.306902 TTTTTGGTTGGCTGGTGGA 57.693 47.368 0.00 0.00 0.00 4.02
161 162 0.827368 TTTTTGGTTGGCTGGTGGAC 59.173 50.000 0.00 0.00 0.00 4.02
162 163 1.388065 TTTTGGTTGGCTGGTGGACG 61.388 55.000 0.00 0.00 0.00 4.79
163 164 2.559922 TTTGGTTGGCTGGTGGACGT 62.560 55.000 0.00 0.00 0.00 4.34
164 165 2.668550 GGTTGGCTGGTGGACGTC 60.669 66.667 7.13 7.13 0.00 4.34
165 166 2.668550 GTTGGCTGGTGGACGTCC 60.669 66.667 28.17 28.17 0.00 4.79
166 167 4.308458 TTGGCTGGTGGACGTCCG 62.308 66.667 28.70 15.86 39.43 4.79
169 170 4.736896 GCTGGTGGACGTCCGGAC 62.737 72.222 28.70 25.28 39.43 4.79
170 171 2.989824 CTGGTGGACGTCCGGACT 60.990 66.667 30.92 18.49 39.43 3.85
171 172 2.987547 TGGTGGACGTCCGGACTC 60.988 66.667 30.92 24.56 39.43 3.36
172 173 3.756727 GGTGGACGTCCGGACTCC 61.757 72.222 30.76 30.76 39.43 3.85
173 174 2.987547 GTGGACGTCCGGACTCCA 60.988 66.667 33.77 33.77 39.43 3.86
174 175 2.675423 TGGACGTCCGGACTCCAG 60.675 66.667 33.77 22.62 39.43 3.86
175 176 4.131088 GGACGTCCGGACTCCAGC 62.131 72.222 31.68 18.63 32.51 4.85
176 177 3.371063 GACGTCCGGACTCCAGCA 61.371 66.667 30.92 0.00 0.00 4.41
177 178 2.915659 ACGTCCGGACTCCAGCAA 60.916 61.111 30.92 0.00 0.00 3.91
178 179 2.342279 CGTCCGGACTCCAGCAAA 59.658 61.111 30.92 0.00 0.00 3.68
179 180 2.027625 CGTCCGGACTCCAGCAAAC 61.028 63.158 30.92 2.61 0.00 2.93
180 181 1.671379 GTCCGGACTCCAGCAAACC 60.671 63.158 27.64 0.00 0.00 3.27
181 182 1.841556 TCCGGACTCCAGCAAACCT 60.842 57.895 0.00 0.00 0.00 3.50
182 183 1.073199 CCGGACTCCAGCAAACCTT 59.927 57.895 0.00 0.00 0.00 3.50
183 184 0.537371 CCGGACTCCAGCAAACCTTT 60.537 55.000 0.00 0.00 0.00 3.11
184 185 0.875059 CGGACTCCAGCAAACCTTTC 59.125 55.000 0.00 0.00 0.00 2.62
185 186 1.248486 GGACTCCAGCAAACCTTTCC 58.752 55.000 0.00 0.00 0.00 3.13
186 187 1.478654 GGACTCCAGCAAACCTTTCCA 60.479 52.381 0.00 0.00 0.00 3.53
187 188 1.882623 GACTCCAGCAAACCTTTCCAG 59.117 52.381 0.00 0.00 0.00 3.86
188 189 1.494721 ACTCCAGCAAACCTTTCCAGA 59.505 47.619 0.00 0.00 0.00 3.86
189 190 2.108952 ACTCCAGCAAACCTTTCCAGAT 59.891 45.455 0.00 0.00 0.00 2.90
190 191 3.160269 CTCCAGCAAACCTTTCCAGATT 58.840 45.455 0.00 0.00 0.00 2.40
191 192 3.575687 CTCCAGCAAACCTTTCCAGATTT 59.424 43.478 0.00 0.00 0.00 2.17
192 193 4.735369 TCCAGCAAACCTTTCCAGATTTA 58.265 39.130 0.00 0.00 0.00 1.40
193 194 4.522789 TCCAGCAAACCTTTCCAGATTTAC 59.477 41.667 0.00 0.00 0.00 2.01
194 195 4.524328 CCAGCAAACCTTTCCAGATTTACT 59.476 41.667 0.00 0.00 0.00 2.24
195 196 5.011023 CCAGCAAACCTTTCCAGATTTACTT 59.989 40.000 0.00 0.00 0.00 2.24
196 197 6.462909 CCAGCAAACCTTTCCAGATTTACTTT 60.463 38.462 0.00 0.00 0.00 2.66
197 198 6.642540 CAGCAAACCTTTCCAGATTTACTTTC 59.357 38.462 0.00 0.00 0.00 2.62
198 199 6.323739 AGCAAACCTTTCCAGATTTACTTTCA 59.676 34.615 0.00 0.00 0.00 2.69
199 200 6.642540 GCAAACCTTTCCAGATTTACTTTCAG 59.357 38.462 0.00 0.00 0.00 3.02
200 201 7.684428 GCAAACCTTTCCAGATTTACTTTCAGT 60.684 37.037 0.00 0.00 0.00 3.41
201 202 7.898014 AACCTTTCCAGATTTACTTTCAGTT 57.102 32.000 0.00 0.00 0.00 3.16
202 203 7.898014 ACCTTTCCAGATTTACTTTCAGTTT 57.102 32.000 0.00 0.00 0.00 2.66
203 204 8.306313 ACCTTTCCAGATTTACTTTCAGTTTT 57.694 30.769 0.00 0.00 0.00 2.43
204 205 9.416284 ACCTTTCCAGATTTACTTTCAGTTTTA 57.584 29.630 0.00 0.00 0.00 1.52
229 230 4.869215 CATTAATGCCGCACCATATTTGA 58.131 39.130 1.74 0.00 0.00 2.69
233 234 2.373224 TGCCGCACCATATTTGATGAA 58.627 42.857 0.00 0.00 0.00 2.57
236 237 4.180057 GCCGCACCATATTTGATGAAAAA 58.820 39.130 0.00 0.00 0.00 1.94
295 297 4.148825 ACGCAGTCGGAGATGCCC 62.149 66.667 8.96 0.00 29.74 5.36
304 306 0.105039 CGGAGATGCCCTAACACCTC 59.895 60.000 0.00 0.00 0.00 3.85
305 307 1.204146 GGAGATGCCCTAACACCTCA 58.796 55.000 0.00 0.00 0.00 3.86
306 308 1.134371 GGAGATGCCCTAACACCTCAC 60.134 57.143 0.00 0.00 0.00 3.51
307 309 1.555075 GAGATGCCCTAACACCTCACA 59.445 52.381 0.00 0.00 0.00 3.58
308 310 1.985159 AGATGCCCTAACACCTCACAA 59.015 47.619 0.00 0.00 0.00 3.33
309 311 2.375174 AGATGCCCTAACACCTCACAAA 59.625 45.455 0.00 0.00 0.00 2.83
310 312 2.738587 TGCCCTAACACCTCACAAAA 57.261 45.000 0.00 0.00 0.00 2.44
311 313 3.019799 TGCCCTAACACCTCACAAAAA 57.980 42.857 0.00 0.00 0.00 1.94
386 434 1.166531 GGAAGCAACTCCACGCAGTT 61.167 55.000 0.00 0.00 41.61 3.16
710 760 0.682209 GCCTGTACCTCCTCCGTACA 60.682 60.000 0.00 0.00 42.83 2.90
780 842 2.829458 GTACTCCCCTCGCGCTCT 60.829 66.667 5.56 0.00 0.00 4.09
807 869 1.526225 GGGGCAGATAGGGAAACGC 60.526 63.158 0.00 0.00 0.00 4.84
865 928 0.693049 AGGGGCAGTCTCGTCATTTT 59.307 50.000 0.00 0.00 0.00 1.82
866 929 0.804989 GGGGCAGTCTCGTCATTTTG 59.195 55.000 0.00 0.00 0.00 2.44
867 930 0.169009 GGGCAGTCTCGTCATTTTGC 59.831 55.000 0.00 0.00 0.00 3.68
868 931 0.169009 GGCAGTCTCGTCATTTTGCC 59.831 55.000 0.00 0.00 43.54 4.52
870 933 0.804989 CAGTCTCGTCATTTTGCCCC 59.195 55.000 0.00 0.00 0.00 5.80
947 1014 1.227674 GCCATTGCTACTCCCTCCG 60.228 63.158 0.00 0.00 33.53 4.63
969 1036 2.664851 TTCTTGGTGTCGCAGCGG 60.665 61.111 16.42 0.00 34.27 5.52
998 1066 4.974721 CCAACCTGCCTTGCCCGT 62.975 66.667 0.00 0.00 0.00 5.28
1060 1128 4.742201 TCTGCTCTGCCGCGGTTC 62.742 66.667 28.70 11.89 37.54 3.62
1104 1172 2.262915 CTGGCCGACGAGCTTCTT 59.737 61.111 0.00 0.00 0.00 2.52
1710 1785 4.408270 AGCCATGCTTCTTCTTGATCTCTA 59.592 41.667 0.00 0.00 33.89 2.43
1757 1832 3.117888 TGGATGAAGGGAGTTATGGCTTC 60.118 47.826 0.00 0.00 0.00 3.86
1884 1960 2.030457 CACGTGAATTTCTCCATACGGC 59.970 50.000 10.90 0.00 36.01 5.68
1888 1964 3.938963 GTGAATTTCTCCATACGGCTTGA 59.061 43.478 0.00 0.00 0.00 3.02
1890 1966 3.914426 ATTTCTCCATACGGCTTGACT 57.086 42.857 0.00 0.00 0.00 3.41
2004 2081 2.213499 GGAATTGGACTATCGCAGTGG 58.787 52.381 0.00 0.00 37.72 4.00
2086 2263 6.608808 CCTTTTGAGGATGGGAATCAGTAATT 59.391 38.462 0.00 0.00 0.00 1.40
2121 2298 2.811431 TGAGGTGCCAAATAGACAAACG 59.189 45.455 0.00 0.00 0.00 3.60
2209 2395 3.844211 AGCTACCCAATCTTGAGGTGTTA 59.156 43.478 11.19 0.00 34.80 2.41
2217 2403 1.160137 CTTGAGGTGTTAGCACTGGC 58.840 55.000 9.71 0.60 44.65 4.85
2249 2435 4.659115 TGGAATAGATGATGATGCCCTTG 58.341 43.478 0.00 0.00 0.00 3.61
2553 2769 0.322975 ACTCTTGCAGGTGCTCGATT 59.677 50.000 3.18 0.00 42.66 3.34
2740 2956 3.806949 TTTGGCAGGTTACTCCATCTT 57.193 42.857 0.00 0.00 39.02 2.40
2768 2984 4.996788 AATGCTTCCAAATGCTTCCTAG 57.003 40.909 0.00 0.00 0.00 3.02
2800 3016 2.559668 CTGAAATTGGAAGGCTGCAAGA 59.440 45.455 0.50 0.00 36.21 3.02
3021 3238 5.781827 TCCCTCATCTCTCTAAGAATGGAA 58.218 41.667 0.00 0.00 37.61 3.53
3069 3286 2.464459 CCGACTGATTGGGAAGCGC 61.464 63.158 0.00 0.00 0.00 5.92
3093 3310 3.173953 TGCCATTTGGAAGAGTTGGAT 57.826 42.857 0.00 0.00 37.39 3.41
3099 3316 5.887598 CCATTTGGAAGAGTTGGATATCACA 59.112 40.000 4.83 0.00 37.39 3.58
3135 3352 6.206634 TGGATGATGAAGGTTTGTACTGAAAC 59.793 38.462 0.00 0.00 35.45 2.78
3142 3359 8.062065 TGAAGGTTTGTACTGAAACTCAAATT 57.938 30.769 8.28 0.00 36.30 1.82
3146 3363 8.749354 AGGTTTGTACTGAAACTCAAATTTCTT 58.251 29.630 8.28 0.00 39.02 2.52
3172 3389 7.190871 ACTATTATTTTTGGTAAATGGACGCG 58.809 34.615 3.53 3.53 0.00 6.01
3231 3448 6.410540 AGTTAACAGTGATGAGATCTTTCCC 58.589 40.000 8.61 0.00 0.00 3.97
3232 3449 3.533606 ACAGTGATGAGATCTTTCCCG 57.466 47.619 0.00 0.00 0.00 5.14
3239 3456 1.078143 AGATCTTTCCCGTGCAGGC 60.078 57.895 0.00 0.00 39.21 4.85
3263 3480 0.392729 AAGCTCTGTCTGGATGCAGC 60.393 55.000 9.76 5.56 33.09 5.25
3273 3490 1.199327 CTGGATGCAGCAAACTGTCAG 59.801 52.381 3.51 0.00 46.30 3.51
3274 3491 1.242076 GGATGCAGCAAACTGTCAGT 58.758 50.000 3.51 0.00 46.30 3.41
3475 3692 5.569059 CAGAAATAACAGATGTTTCGTTGGC 59.431 40.000 3.14 0.00 42.21 4.52
3563 3780 4.744867 GCTGGGCTCTCAGAAATAGCAATA 60.745 45.833 0.04 0.00 38.01 1.90
3788 4014 3.139029 GGTCACCGACATTGGACTC 57.861 57.895 0.00 0.00 33.68 3.36
4021 4247 2.509964 AGGTATTCTACTTGCCCCCTTG 59.490 50.000 0.00 0.00 0.00 3.61
4214 4471 7.798596 ACGATGAGATTATGAGAAATGCTTT 57.201 32.000 0.00 0.00 0.00 3.51
4238 4495 0.591659 TCGTCGTCTTGACTGTCAGG 59.408 55.000 13.19 13.19 45.87 3.86
4328 4601 7.184800 TCGGAACAATGTTGTATATGTATGC 57.815 36.000 2.20 0.00 41.31 3.14
4348 4621 1.070134 CTTCGTTCAGTGGACTGGGAA 59.930 52.381 6.94 7.53 43.91 3.97
4401 4674 6.160576 AGAGAAGCAGGAGATAGATGAAAC 57.839 41.667 0.00 0.00 0.00 2.78
4410 4683 7.256119 GCAGGAGATAGATGAAACCATAGAGAA 60.256 40.741 0.00 0.00 0.00 2.87
4411 4684 8.646004 CAGGAGATAGATGAAACCATAGAGAAA 58.354 37.037 0.00 0.00 0.00 2.52
4412 4685 9.391227 AGGAGATAGATGAAACCATAGAGAAAT 57.609 33.333 0.00 0.00 0.00 2.17
4466 4739 8.687242 ACTTTACTGATCAATATGAGAGTTCGA 58.313 33.333 0.00 0.00 29.21 3.71
4467 4740 9.689976 CTTTACTGATCAATATGAGAGTTCGAT 57.310 33.333 0.00 0.00 29.21 3.59
4471 4744 8.085296 ACTGATCAATATGAGAGTTCGATTACC 58.915 37.037 0.00 0.00 0.00 2.85
4473 4746 8.084684 TGATCAATATGAGAGTTCGATTACCTG 58.915 37.037 0.00 0.00 0.00 4.00
4474 4747 7.348080 TCAATATGAGAGTTCGATTACCTGT 57.652 36.000 0.00 0.00 0.00 4.00
4475 4748 7.426410 TCAATATGAGAGTTCGATTACCTGTC 58.574 38.462 0.00 0.00 0.00 3.51
4476 4749 3.759527 TGAGAGTTCGATTACCTGTCG 57.240 47.619 0.00 0.00 40.30 4.35
4477 4750 2.422479 TGAGAGTTCGATTACCTGTCGG 59.578 50.000 0.00 0.00 39.45 4.79
4559 4833 8.469200 GTCCAATTCTCAAATCATGAATGGTTA 58.531 33.333 0.00 0.00 37.67 2.85
4585 4859 8.422577 TGGTATACTGCATGATACAACTAGAT 57.577 34.615 16.03 0.00 31.34 1.98
4622 4897 6.753107 GCTTTTGCTACCTCAGGTTAATTA 57.247 37.500 0.00 0.00 43.35 1.40
4628 4903 9.528489 TTTGCTACCTCAGGTTAATTATTCTTT 57.472 29.630 0.00 0.00 37.09 2.52
4629 4904 8.732746 TGCTACCTCAGGTTAATTATTCTTTC 57.267 34.615 0.00 0.00 37.09 2.62
4630 4905 8.548877 TGCTACCTCAGGTTAATTATTCTTTCT 58.451 33.333 0.00 0.00 37.09 2.52
4760 5035 0.830648 TCCATCGGGCTCCTTGTAAG 59.169 55.000 0.00 0.00 0.00 2.34
4765 5040 1.377333 GGGCTCCTTGTAAGCGCTT 60.377 57.895 27.97 27.97 46.04 4.68
4820 5096 6.127925 GGTGAATGAATGCACAGAGACAATTA 60.128 38.462 3.84 0.00 36.76 1.40
4935 5212 1.000993 GGGGACTCTCTCCAGCTCA 59.999 63.158 0.00 0.00 41.63 4.26
4941 5218 1.006998 ACTCTCTCCAGCTCATCCACT 59.993 52.381 0.00 0.00 0.00 4.00
4992 5269 0.036010 CCTTCATCTTCGGCACCACT 60.036 55.000 0.00 0.00 0.00 4.00
5025 5302 2.377810 TGGCTCATCCCCATCGCTT 61.378 57.895 0.00 0.00 0.00 4.68
5038 5315 0.610174 ATCGCTTGGCTCTCAGTTCA 59.390 50.000 0.00 0.00 0.00 3.18
5113 5392 1.910772 CCCCACCCCATTTTTCGCA 60.911 57.895 0.00 0.00 0.00 5.10
5136 5415 2.821378 CAGCATCCAGAACCACATCAAA 59.179 45.455 0.00 0.00 0.00 2.69
5152 5431 5.010922 CACATCAAATTTCTTCTCAACCCCA 59.989 40.000 0.00 0.00 0.00 4.96
5205 5487 2.482142 CCTCCTTGTTCTGATCCGCTAC 60.482 54.545 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.024868 TGTCGTCGATGTTTGGCGG 61.025 57.895 4.21 0.00 0.00 6.13
1 2 1.129809 GTGTCGTCGATGTTTGGCG 59.870 57.895 4.21 0.00 0.00 5.69
2 3 1.225376 TGGTGTCGTCGATGTTTGGC 61.225 55.000 4.21 0.00 0.00 4.52
3 4 0.790207 CTGGTGTCGTCGATGTTTGG 59.210 55.000 4.21 0.00 0.00 3.28
4 5 0.163788 GCTGGTGTCGTCGATGTTTG 59.836 55.000 4.21 0.00 0.00 2.93
5 6 0.033504 AGCTGGTGTCGTCGATGTTT 59.966 50.000 4.21 0.00 0.00 2.83
6 7 0.388649 GAGCTGGTGTCGTCGATGTT 60.389 55.000 4.21 0.00 0.00 2.71
7 8 1.213013 GAGCTGGTGTCGTCGATGT 59.787 57.895 4.21 0.00 0.00 3.06
8 9 1.517257 GGAGCTGGTGTCGTCGATG 60.517 63.158 0.00 0.00 0.00 3.84
9 10 1.532604 TTGGAGCTGGTGTCGTCGAT 61.533 55.000 0.00 0.00 0.00 3.59
10 11 1.740332 TTTGGAGCTGGTGTCGTCGA 61.740 55.000 0.00 0.00 0.00 4.20
11 12 1.300620 TTTGGAGCTGGTGTCGTCG 60.301 57.895 0.00 0.00 0.00 5.12
12 13 0.249911 AGTTTGGAGCTGGTGTCGTC 60.250 55.000 0.00 0.00 0.00 4.20
13 14 0.532862 CAGTTTGGAGCTGGTGTCGT 60.533 55.000 0.00 0.00 0.00 4.34
14 15 0.249868 TCAGTTTGGAGCTGGTGTCG 60.250 55.000 0.00 0.00 34.89 4.35
15 16 1.517242 CTCAGTTTGGAGCTGGTGTC 58.483 55.000 0.00 0.00 34.89 3.67
16 17 0.109342 CCTCAGTTTGGAGCTGGTGT 59.891 55.000 0.00 0.00 34.89 4.16
17 18 0.109342 ACCTCAGTTTGGAGCTGGTG 59.891 55.000 0.00 0.00 34.89 4.17
18 19 0.398318 GACCTCAGTTTGGAGCTGGT 59.602 55.000 0.00 0.00 34.89 4.00
19 20 0.689623 AGACCTCAGTTTGGAGCTGG 59.310 55.000 0.00 0.00 34.89 4.85
20 21 2.676463 GCTAGACCTCAGTTTGGAGCTG 60.676 54.545 0.00 0.00 33.47 4.24
21 22 1.552792 GCTAGACCTCAGTTTGGAGCT 59.447 52.381 0.00 0.00 33.47 4.09
22 23 1.406205 GGCTAGACCTCAGTTTGGAGC 60.406 57.143 0.00 0.00 33.47 4.70
23 24 1.902508 TGGCTAGACCTCAGTTTGGAG 59.097 52.381 0.00 0.00 40.22 3.86
24 25 1.902508 CTGGCTAGACCTCAGTTTGGA 59.097 52.381 0.00 0.00 40.22 3.53
25 26 1.625818 ACTGGCTAGACCTCAGTTTGG 59.374 52.381 3.17 0.00 38.44 3.28
26 27 3.764434 TCTACTGGCTAGACCTCAGTTTG 59.236 47.826 3.17 7.50 41.37 2.93
27 28 4.020543 CTCTACTGGCTAGACCTCAGTTT 58.979 47.826 3.17 0.00 41.37 2.66
28 29 3.267291 TCTCTACTGGCTAGACCTCAGTT 59.733 47.826 3.17 0.00 41.37 3.16
29 30 2.847449 TCTCTACTGGCTAGACCTCAGT 59.153 50.000 3.17 3.61 43.26 3.41
30 31 3.118038 ACTCTCTACTGGCTAGACCTCAG 60.118 52.174 3.17 0.00 40.22 3.35
31 32 2.847449 ACTCTCTACTGGCTAGACCTCA 59.153 50.000 3.17 0.00 40.22 3.86
32 33 3.570912 ACTCTCTACTGGCTAGACCTC 57.429 52.381 3.17 0.00 40.22 3.85
33 34 3.393278 CCTACTCTCTACTGGCTAGACCT 59.607 52.174 3.17 0.00 40.22 3.85
34 35 3.497227 CCCTACTCTCTACTGGCTAGACC 60.497 56.522 3.17 0.00 39.84 3.85
35 36 3.391955 TCCCTACTCTCTACTGGCTAGAC 59.608 52.174 3.17 0.00 0.00 2.59
36 37 3.666568 TCCCTACTCTCTACTGGCTAGA 58.333 50.000 3.17 0.00 0.00 2.43
37 38 4.103469 TCTTCCCTACTCTCTACTGGCTAG 59.897 50.000 0.00 0.00 0.00 3.42
38 39 4.045736 TCTTCCCTACTCTCTACTGGCTA 58.954 47.826 0.00 0.00 0.00 3.93
39 40 2.853707 TCTTCCCTACTCTCTACTGGCT 59.146 50.000 0.00 0.00 0.00 4.75
40 41 3.219281 CTCTTCCCTACTCTCTACTGGC 58.781 54.545 0.00 0.00 0.00 4.85
41 42 3.435890 CCCTCTTCCCTACTCTCTACTGG 60.436 56.522 0.00 0.00 0.00 4.00
42 43 3.827722 CCCTCTTCCCTACTCTCTACTG 58.172 54.545 0.00 0.00 0.00 2.74
43 44 2.176148 GCCCTCTTCCCTACTCTCTACT 59.824 54.545 0.00 0.00 0.00 2.57
44 45 2.176148 AGCCCTCTTCCCTACTCTCTAC 59.824 54.545 0.00 0.00 0.00 2.59
45 46 2.504905 AGCCCTCTTCCCTACTCTCTA 58.495 52.381 0.00 0.00 0.00 2.43
46 47 1.314895 AGCCCTCTTCCCTACTCTCT 58.685 55.000 0.00 0.00 0.00 3.10
47 48 3.315880 TTAGCCCTCTTCCCTACTCTC 57.684 52.381 0.00 0.00 0.00 3.20
48 49 3.778622 TTTAGCCCTCTTCCCTACTCT 57.221 47.619 0.00 0.00 0.00 3.24
49 50 3.325425 GGATTTAGCCCTCTTCCCTACTC 59.675 52.174 0.00 0.00 0.00 2.59
50 51 3.311402 TGGATTTAGCCCTCTTCCCTACT 60.311 47.826 0.00 0.00 0.00 2.57
51 52 3.046374 TGGATTTAGCCCTCTTCCCTAC 58.954 50.000 0.00 0.00 0.00 3.18
52 53 3.318313 CTGGATTTAGCCCTCTTCCCTA 58.682 50.000 0.00 0.00 0.00 3.53
53 54 2.131023 CTGGATTTAGCCCTCTTCCCT 58.869 52.381 0.00 0.00 0.00 4.20
54 55 1.143889 CCTGGATTTAGCCCTCTTCCC 59.856 57.143 0.00 0.00 0.00 3.97
55 56 1.477740 GCCTGGATTTAGCCCTCTTCC 60.478 57.143 0.00 0.00 0.00 3.46
56 57 1.492599 AGCCTGGATTTAGCCCTCTTC 59.507 52.381 0.00 0.00 0.00 2.87
57 58 1.601248 AGCCTGGATTTAGCCCTCTT 58.399 50.000 0.00 0.00 0.00 2.85
58 59 2.496679 TAGCCTGGATTTAGCCCTCT 57.503 50.000 0.00 0.00 0.00 3.69
59 60 3.181439 ACATTAGCCTGGATTTAGCCCTC 60.181 47.826 0.00 0.00 0.00 4.30
60 61 2.785857 ACATTAGCCTGGATTTAGCCCT 59.214 45.455 0.00 0.00 0.00 5.19
61 62 3.149981 GACATTAGCCTGGATTTAGCCC 58.850 50.000 0.00 0.00 0.00 5.19
62 63 2.808543 CGACATTAGCCTGGATTTAGCC 59.191 50.000 0.00 0.00 0.00 3.93
63 64 2.224314 GCGACATTAGCCTGGATTTAGC 59.776 50.000 0.00 0.00 0.00 3.09
64 65 2.476619 CGCGACATTAGCCTGGATTTAG 59.523 50.000 0.00 0.00 0.00 1.85
65 66 2.159014 ACGCGACATTAGCCTGGATTTA 60.159 45.455 15.93 0.00 0.00 1.40
66 67 1.299541 CGCGACATTAGCCTGGATTT 58.700 50.000 0.00 0.00 0.00 2.17
67 68 0.178068 ACGCGACATTAGCCTGGATT 59.822 50.000 15.93 0.00 0.00 3.01
68 69 0.249489 GACGCGACATTAGCCTGGAT 60.249 55.000 15.93 0.00 0.00 3.41
69 70 1.141019 GACGCGACATTAGCCTGGA 59.859 57.895 15.93 0.00 0.00 3.86
70 71 2.230940 CGACGCGACATTAGCCTGG 61.231 63.158 15.93 0.00 0.00 4.45
71 72 2.860628 GCGACGCGACATTAGCCTG 61.861 63.158 15.93 0.00 0.00 4.85
72 73 2.582498 GCGACGCGACATTAGCCT 60.582 61.111 15.93 0.00 0.00 4.58
73 74 2.577785 GAGCGACGCGACATTAGCC 61.578 63.158 15.93 0.00 0.00 3.93
74 75 1.410737 TTGAGCGACGCGACATTAGC 61.411 55.000 15.93 5.47 0.00 3.09
75 76 1.188138 GATTGAGCGACGCGACATTAG 59.812 52.381 15.93 0.00 0.00 1.73
76 77 1.197055 GATTGAGCGACGCGACATTA 58.803 50.000 15.93 5.64 0.00 1.90
77 78 1.421410 GGATTGAGCGACGCGACATT 61.421 55.000 15.93 14.29 0.00 2.71
78 79 1.878522 GGATTGAGCGACGCGACAT 60.879 57.895 15.93 7.29 0.00 3.06
79 80 2.506217 GGATTGAGCGACGCGACA 60.506 61.111 15.93 15.71 0.00 4.35
80 81 1.812214 GATGGATTGAGCGACGCGAC 61.812 60.000 15.93 5.54 0.00 5.19
81 82 1.588932 GATGGATTGAGCGACGCGA 60.589 57.895 15.93 5.08 0.00 5.87
82 83 0.317854 TAGATGGATTGAGCGACGCG 60.318 55.000 15.18 3.53 0.00 6.01
83 84 1.852942 TTAGATGGATTGAGCGACGC 58.147 50.000 13.03 13.03 0.00 5.19
84 85 5.235186 AGAAAATTAGATGGATTGAGCGACG 59.765 40.000 0.00 0.00 0.00 5.12
85 86 6.610741 AGAAAATTAGATGGATTGAGCGAC 57.389 37.500 0.00 0.00 0.00 5.19
86 87 7.630242 AAAGAAAATTAGATGGATTGAGCGA 57.370 32.000 0.00 0.00 0.00 4.93
87 88 8.830580 TCTAAAGAAAATTAGATGGATTGAGCG 58.169 33.333 0.00 0.00 37.07 5.03
94 95 8.408601 GCATGCTTCTAAAGAAAATTAGATGGA 58.591 33.333 11.37 8.48 40.57 3.41
95 96 8.192774 TGCATGCTTCTAAAGAAAATTAGATGG 58.807 33.333 20.33 3.99 40.57 3.51
96 97 9.017669 GTGCATGCTTCTAAAGAAAATTAGATG 57.982 33.333 20.33 2.59 40.57 2.90
97 98 8.193438 GGTGCATGCTTCTAAAGAAAATTAGAT 58.807 33.333 20.33 0.00 40.57 1.98
98 99 7.538575 GGTGCATGCTTCTAAAGAAAATTAGA 58.461 34.615 20.33 0.00 39.51 2.10
99 100 6.470235 CGGTGCATGCTTCTAAAGAAAATTAG 59.530 38.462 20.33 0.00 34.79 1.73
100 101 6.072175 ACGGTGCATGCTTCTAAAGAAAATTA 60.072 34.615 20.33 0.00 33.07 1.40
101 102 5.163513 CGGTGCATGCTTCTAAAGAAAATT 58.836 37.500 20.33 0.00 33.07 1.82
102 103 4.218417 ACGGTGCATGCTTCTAAAGAAAAT 59.782 37.500 20.33 0.00 33.07 1.82
103 104 3.568007 ACGGTGCATGCTTCTAAAGAAAA 59.432 39.130 20.33 0.00 33.07 2.29
104 105 3.058293 CACGGTGCATGCTTCTAAAGAAA 60.058 43.478 20.33 0.00 33.07 2.52
105 106 2.483877 CACGGTGCATGCTTCTAAAGAA 59.516 45.455 20.33 0.00 0.00 2.52
106 107 2.076100 CACGGTGCATGCTTCTAAAGA 58.924 47.619 20.33 0.00 0.00 2.52
107 108 1.131126 CCACGGTGCATGCTTCTAAAG 59.869 52.381 20.33 5.86 0.00 1.85
108 109 1.164411 CCACGGTGCATGCTTCTAAA 58.836 50.000 20.33 0.00 0.00 1.85
109 110 0.676466 CCCACGGTGCATGCTTCTAA 60.676 55.000 20.33 0.00 0.00 2.10
110 111 1.078497 CCCACGGTGCATGCTTCTA 60.078 57.895 20.33 0.00 0.00 2.10
111 112 2.360350 CCCACGGTGCATGCTTCT 60.360 61.111 20.33 0.00 0.00 2.85
112 113 3.443045 CCCCACGGTGCATGCTTC 61.443 66.667 20.33 11.78 0.00 3.86
122 123 1.632018 ATCACCACATACCCCCACGG 61.632 60.000 0.00 0.00 37.81 4.94
123 124 0.254747 AATCACCACATACCCCCACG 59.745 55.000 0.00 0.00 0.00 4.94
124 125 2.525105 AAATCACCACATACCCCCAC 57.475 50.000 0.00 0.00 0.00 4.61
125 126 3.551635 AAAAATCACCACATACCCCCA 57.448 42.857 0.00 0.00 0.00 4.96
142 143 0.827368 GTCCACCAGCCAACCAAAAA 59.173 50.000 0.00 0.00 0.00 1.94
143 144 1.388065 CGTCCACCAGCCAACCAAAA 61.388 55.000 0.00 0.00 0.00 2.44
144 145 1.826054 CGTCCACCAGCCAACCAAA 60.826 57.895 0.00 0.00 0.00 3.28
145 146 2.203280 CGTCCACCAGCCAACCAA 60.203 61.111 0.00 0.00 0.00 3.67
146 147 3.469863 GACGTCCACCAGCCAACCA 62.470 63.158 3.51 0.00 0.00 3.67
147 148 2.668550 GACGTCCACCAGCCAACC 60.669 66.667 3.51 0.00 0.00 3.77
148 149 2.668550 GGACGTCCACCAGCCAAC 60.669 66.667 29.75 0.00 35.64 3.77
149 150 4.308458 CGGACGTCCACCAGCCAA 62.308 66.667 32.80 0.00 35.14 4.52
152 153 4.736896 GTCCGGACGTCCACCAGC 62.737 72.222 32.80 14.47 35.14 4.85
153 154 2.989824 AGTCCGGACGTCCACCAG 60.990 66.667 32.80 18.29 36.20 4.00
154 155 2.987547 GAGTCCGGACGTCCACCA 60.988 66.667 32.80 13.91 36.20 4.17
155 156 3.756727 GGAGTCCGGACGTCCACC 61.757 72.222 31.68 24.59 36.20 4.61
156 157 2.987547 TGGAGTCCGGACGTCCAC 60.988 66.667 33.77 23.89 35.34 4.02
157 158 2.675423 CTGGAGTCCGGACGTCCA 60.675 66.667 34.30 34.30 36.77 4.02
158 159 4.131088 GCTGGAGTCCGGACGTCC 62.131 72.222 30.76 30.76 36.20 4.79
159 160 2.430382 TTTGCTGGAGTCCGGACGTC 62.430 60.000 28.26 23.31 36.20 4.34
160 161 2.504274 TTTGCTGGAGTCCGGACGT 61.504 57.895 28.26 16.89 36.20 4.34
161 162 2.027625 GTTTGCTGGAGTCCGGACG 61.028 63.158 28.26 15.45 36.20 4.79
162 163 1.671379 GGTTTGCTGGAGTCCGGAC 60.671 63.158 27.67 27.67 29.82 4.79
163 164 1.415672 AAGGTTTGCTGGAGTCCGGA 61.416 55.000 22.95 0.00 29.82 5.14
164 165 0.537371 AAAGGTTTGCTGGAGTCCGG 60.537 55.000 14.25 14.25 0.00 5.14
165 166 0.875059 GAAAGGTTTGCTGGAGTCCG 59.125 55.000 4.30 0.44 0.00 4.79
166 167 1.248486 GGAAAGGTTTGCTGGAGTCC 58.752 55.000 0.73 0.73 0.00 3.85
167 168 1.882623 CTGGAAAGGTTTGCTGGAGTC 59.117 52.381 0.00 0.00 0.00 3.36
168 169 1.494721 TCTGGAAAGGTTTGCTGGAGT 59.505 47.619 1.96 0.00 0.00 3.85
169 170 2.276732 TCTGGAAAGGTTTGCTGGAG 57.723 50.000 1.96 0.00 0.00 3.86
170 171 2.978156 ATCTGGAAAGGTTTGCTGGA 57.022 45.000 1.96 0.00 0.00 3.86
171 172 4.524328 AGTAAATCTGGAAAGGTTTGCTGG 59.476 41.667 1.90 0.00 0.00 4.85
172 173 5.712152 AGTAAATCTGGAAAGGTTTGCTG 57.288 39.130 1.90 0.00 0.00 4.41
173 174 6.323739 TGAAAGTAAATCTGGAAAGGTTTGCT 59.676 34.615 0.00 0.00 0.00 3.91
174 175 6.512297 TGAAAGTAAATCTGGAAAGGTTTGC 58.488 36.000 0.00 0.00 0.00 3.68
236 237 4.770010 TGAACCAAGGTGTTCTCACTTTTT 59.230 37.500 5.61 0.00 43.96 1.94
326 374 7.004555 TCCGGTTATCACTGCATAGAATATT 57.995 36.000 0.00 0.00 0.00 1.28
330 378 3.704566 ACTCCGGTTATCACTGCATAGAA 59.295 43.478 0.00 0.00 0.00 2.10
441 489 2.231380 TGGTGAGAAAGGGGGAGGC 61.231 63.158 0.00 0.00 0.00 4.70
449 499 1.003696 GGAGGGAAGGTGGTGAGAAAG 59.996 57.143 0.00 0.00 0.00 2.62
792 854 0.107654 ACCTGCGTTTCCCTATCTGC 60.108 55.000 0.00 0.00 0.00 4.26
793 855 1.656652 CACCTGCGTTTCCCTATCTG 58.343 55.000 0.00 0.00 0.00 2.90
795 857 0.463833 CCCACCTGCGTTTCCCTATC 60.464 60.000 0.00 0.00 0.00 2.08
827 889 2.960129 CGTCGCCTTATCACGGCC 60.960 66.667 0.00 0.00 44.73 6.13
859 922 0.975887 GCAAGGAAGGGGCAAAATGA 59.024 50.000 0.00 0.00 0.00 2.57
865 928 1.047801 GAAAAAGCAAGGAAGGGGCA 58.952 50.000 0.00 0.00 0.00 5.36
866 929 0.321671 GGAAAAAGCAAGGAAGGGGC 59.678 55.000 0.00 0.00 0.00 5.80
867 930 0.976641 GGGAAAAAGCAAGGAAGGGG 59.023 55.000 0.00 0.00 0.00 4.79
868 931 1.895798 GAGGGAAAAAGCAAGGAAGGG 59.104 52.381 0.00 0.00 0.00 3.95
870 933 2.822561 GGAGAGGGAAAAAGCAAGGAAG 59.177 50.000 0.00 0.00 0.00 3.46
947 1014 1.557443 CTGCGACACCAAGAACGGAC 61.557 60.000 0.00 0.00 0.00 4.79
969 1036 0.385390 CAGGTTGGCAGTTGGTTGTC 59.615 55.000 0.00 0.00 0.00 3.18
998 1066 4.545706 GGATCGCCGTGGCCATGA 62.546 66.667 27.13 14.01 37.98 3.07
1275 1343 3.403558 GGGCAGAGGGTGAGGTCC 61.404 72.222 0.00 0.00 0.00 4.46
1320 1388 4.841617 ATGGGCGCGGAGGAGAGA 62.842 66.667 8.83 0.00 0.00 3.10
1428 1496 1.186200 CATTGGAGAGGTCGAGGTCA 58.814 55.000 0.00 0.00 0.00 4.02
1710 1785 1.275666 TGGAACAGGACGTGATGGAT 58.724 50.000 0.00 0.00 0.00 3.41
1884 1960 4.757149 AGATCGAAAGGGAAAACAGTCAAG 59.243 41.667 0.00 0.00 0.00 3.02
1888 1964 4.887655 ACAAAGATCGAAAGGGAAAACAGT 59.112 37.500 0.00 0.00 0.00 3.55
1890 1966 5.472137 CCTACAAAGATCGAAAGGGAAAACA 59.528 40.000 0.00 0.00 0.00 2.83
2086 2263 2.810400 GCACCTCAACAGAAAGTAGCCA 60.810 50.000 0.00 0.00 0.00 4.75
2144 2330 4.021229 TCTTTGGAGATCTGCAATGCAAT 58.979 39.130 27.54 6.00 40.52 3.56
2209 2395 3.196207 AACACATCCCGCCAGTGCT 62.196 57.895 0.00 0.00 36.76 4.40
2217 2403 4.071961 TCATCTATTCCAACACATCCCG 57.928 45.455 0.00 0.00 0.00 5.14
2249 2435 3.084039 TGCATTCATTCTCAAGACCACC 58.916 45.455 0.00 0.00 0.00 4.61
2553 2769 2.158885 TGACATTCCGACAGGTTGACAA 60.159 45.455 0.00 0.00 39.05 3.18
2740 2956 3.072768 AGCATTTGGAAGCATTTTCCCAA 59.927 39.130 3.66 0.00 37.79 4.12
2768 2984 3.091545 TCCAATTTCAGGGTCTGCAATC 58.908 45.455 0.00 0.00 27.05 2.67
2841 3057 5.788450 CTCAGGCTCAACTCTCTTAAAGAA 58.212 41.667 0.00 0.00 32.23 2.52
3021 3238 8.043710 CCTTCACTAGAAAAATGACTACAGGAT 58.956 37.037 0.00 0.00 32.35 3.24
3099 3316 5.191426 CCTTCATCATCCAAATCACTGTCT 58.809 41.667 0.00 0.00 0.00 3.41
3114 3331 6.353323 TGAGTTTCAGTACAAACCTTCATCA 58.647 36.000 5.45 1.20 37.01 3.07
3146 3363 8.336806 CGCGTCCATTTACCAAAAATAATAGTA 58.663 33.333 0.00 0.00 0.00 1.82
3147 3364 7.190871 CGCGTCCATTTACCAAAAATAATAGT 58.809 34.615 0.00 0.00 0.00 2.12
3148 3365 6.635239 CCGCGTCCATTTACCAAAAATAATAG 59.365 38.462 4.92 0.00 0.00 1.73
3149 3366 6.318144 TCCGCGTCCATTTACCAAAAATAATA 59.682 34.615 4.92 0.00 0.00 0.98
3172 3389 5.103290 TGTTGCGAGAAACAGTTAATTCC 57.897 39.130 0.00 0.00 35.16 3.01
3195 3412 6.039781 TCACTGTTAACTTTTTGTAGTCGC 57.960 37.500 7.22 0.00 0.00 5.19
3196 3413 7.847487 TCATCACTGTTAACTTTTTGTAGTCG 58.153 34.615 7.22 0.00 0.00 4.18
3200 3417 9.778741 AGATCTCATCACTGTTAACTTTTTGTA 57.221 29.630 7.22 0.00 0.00 2.41
3208 3425 5.292101 CGGGAAAGATCTCATCACTGTTAAC 59.708 44.000 0.00 0.00 0.00 2.01
3239 3456 2.419324 GCATCCAGACAGAGCTTTCAAG 59.581 50.000 0.00 0.00 0.00 3.02
3263 3480 8.925161 TTCCAATTTTTAAGACTGACAGTTTG 57.075 30.769 10.01 7.40 0.00 2.93
3269 3486 9.807649 ATGCATATTCCAATTTTTAAGACTGAC 57.192 29.630 0.00 0.00 0.00 3.51
3273 3490 9.252962 CCTCATGCATATTCCAATTTTTAAGAC 57.747 33.333 0.00 0.00 0.00 3.01
3274 3491 9.199645 TCCTCATGCATATTCCAATTTTTAAGA 57.800 29.630 0.00 0.00 0.00 2.10
3475 3692 0.512518 TGCACATTTTGAGAGCGACG 59.487 50.000 0.00 0.00 0.00 5.12
3563 3780 4.972875 GCAAGTAGCCTGCATCCT 57.027 55.556 0.00 0.00 37.23 3.24
3711 3929 8.755018 GCAATGTTAAATTATGTGCAAGGTATC 58.245 33.333 0.00 0.00 0.00 2.24
3717 3935 5.930569 TGCAGCAATGTTAAATTATGTGCAA 59.069 32.000 0.00 0.00 34.44 4.08
3720 3938 7.758613 TGATGCAGCAATGTTAAATTATGTG 57.241 32.000 0.00 0.00 0.00 3.21
3721 3939 9.467258 GTATGATGCAGCAATGTTAAATTATGT 57.533 29.630 9.54 0.00 0.00 2.29
3788 4014 3.257873 CACATATGCTAGAGAGGGACAGG 59.742 52.174 1.58 0.00 0.00 4.00
4021 4247 3.828875 ATCTTCTACACCTAGGCTTGC 57.171 47.619 9.30 0.00 0.00 4.01
4117 4343 0.317269 CTGCAAAGACCACACGCTTG 60.317 55.000 0.00 0.00 0.00 4.01
4238 4495 5.359756 TCTACACCATCATGTTCATGTAGC 58.640 41.667 17.54 0.00 39.44 3.58
4328 4601 0.679505 TCCCAGTCCACTGAACGAAG 59.320 55.000 8.36 0.00 46.59 3.79
4348 4621 3.252458 GGATACGGCACAACAAAAGAACT 59.748 43.478 0.00 0.00 0.00 3.01
4410 4683 6.817140 GTCGACCTCCAGTAATTTGACTAATT 59.183 38.462 3.51 0.65 39.69 1.40
4411 4684 6.338937 GTCGACCTCCAGTAATTTGACTAAT 58.661 40.000 3.51 0.00 0.00 1.73
4412 4685 5.337009 GGTCGACCTCCAGTAATTTGACTAA 60.337 44.000 27.64 0.00 0.00 2.24
4413 4686 4.159135 GGTCGACCTCCAGTAATTTGACTA 59.841 45.833 27.64 0.00 0.00 2.59
4414 4687 3.056035 GGTCGACCTCCAGTAATTTGACT 60.056 47.826 27.64 0.00 0.00 3.41
4415 4688 3.056035 AGGTCGACCTCCAGTAATTTGAC 60.056 47.826 31.69 0.00 44.77 3.18
4416 4689 3.056107 CAGGTCGACCTCCAGTAATTTGA 60.056 47.826 34.28 0.00 46.65 2.69
4417 4690 3.262420 CAGGTCGACCTCCAGTAATTTG 58.738 50.000 34.28 15.91 46.65 2.32
4463 4736 0.968901 ACAGGCCGACAGGTAATCGA 60.969 55.000 0.00 0.00 42.25 3.59
4464 4737 0.527817 GACAGGCCGACAGGTAATCG 60.528 60.000 0.00 0.00 40.50 3.34
4466 4739 0.907704 TGGACAGGCCGACAGGTAAT 60.908 55.000 0.00 0.00 40.66 1.89
4467 4740 1.122632 TTGGACAGGCCGACAGGTAA 61.123 55.000 0.00 0.00 40.66 2.85
4468 4741 0.907704 ATTGGACAGGCCGACAGGTA 60.908 55.000 0.00 0.00 40.66 3.08
4470 4743 1.746615 CATTGGACAGGCCGACAGG 60.747 63.158 0.00 0.00 40.66 4.00
4471 4744 1.003355 ACATTGGACAGGCCGACAG 60.003 57.895 0.00 0.00 40.66 3.51
4473 4746 0.889186 AACACATTGGACAGGCCGAC 60.889 55.000 0.00 0.00 40.66 4.79
4474 4747 0.605319 GAACACATTGGACAGGCCGA 60.605 55.000 0.00 0.00 40.66 5.54
4475 4748 0.606401 AGAACACATTGGACAGGCCG 60.606 55.000 0.00 0.00 40.66 6.13
4476 4749 1.620822 AAGAACACATTGGACAGGCC 58.379 50.000 0.00 0.00 37.10 5.19
4477 4750 5.163513 CAAATAAGAACACATTGGACAGGC 58.836 41.667 0.00 0.00 0.00 4.85
4559 4833 8.422577 TCTAGTTGTATCATGCAGTATACCAT 57.577 34.615 15.12 0.00 0.00 3.55
4659 4934 7.762159 CACATACATACACAGGTACAATACACA 59.238 37.037 0.00 0.00 30.94 3.72
4760 5035 3.448686 AGATATACACACACTGAAGCGC 58.551 45.455 0.00 0.00 0.00 5.92
4765 5040 6.183360 CCGAGTACAAGATATACACACACTGA 60.183 42.308 0.00 0.00 0.00 3.41
4820 5096 7.345653 TGGAGTCTGATACCAAGTAGAATGATT 59.654 37.037 3.87 0.00 0.00 2.57
4886 5163 3.249189 AGCTGGTGGCCGGAGAAA 61.249 61.111 5.05 0.00 43.05 2.52
4992 5269 2.224159 GCCACTGTGGGAAGAGGGA 61.224 63.158 27.02 0.00 38.19 4.20
5025 5302 2.224159 GGGGGTGAACTGAGAGCCA 61.224 63.158 0.00 0.00 0.00 4.75
5113 5392 2.224843 TGATGTGGTTCTGGATGCTGTT 60.225 45.455 0.00 0.00 0.00 3.16
5136 5415 3.502123 TCGTTGGGGTTGAGAAGAAAT 57.498 42.857 0.00 0.00 0.00 2.17
5152 5431 3.807622 CACTTGTGGTAGTTGTGATCGTT 59.192 43.478 0.00 0.00 0.00 3.85
5205 5487 1.406219 CGATGAACTGAGTGACGCCG 61.406 60.000 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.