Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004361.1 Hibiscus syriacus cultivar Beakdansim tig00009554_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86984
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2883 original size:16 final size:15
Alignment explanation
Indices: 2858--2896 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2848 AAGCTCAAAT
2858 TACAAATATTAAATAA
1 TACAAATATTAAA-AA
*
2874 TACAAGTATTAAAAA
1 TACAAATATTAAAAA
*
2889 TAAAAATA
1 TACAAATA
2897 ACCCATAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (15 bp):
TACAAATATTAAAAA
Found at i:4390 original size:12 final size:12
Alignment explanation
Indices: 4373--4403 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4363 TGTAATTAGT
4373 AATAATAATATA
1 AATAATAATATA
4385 AATAATAATATA
1 AATAATAATATA
4397 AATAATA
1 AATAATA
4404 TAAATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATAATATA
Found at i:4862 original size:133 final size:132
Alignment explanation
Indices: 4606--4896 Score: 467
Period size: 133 Copynumber: 2.2 Consensus size: 132
4596 GAGTCGTCTA
* * * *
4606 AGGGTGACACGGTTCCTACGTGATGAGGAAATATAGTCGAGGATGACACTGCTCATACGTGATGA
1 AGGGTGACACGGCTCCTACGTGATGAAGAAATATAGTCGAGGATGACACGGATCATACGTGATGA
4671 AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTAT
4736 CT
131 CT
* * * *
4738 AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-AGGGATGACACGGATCATACGTGATG
1 AGGGTGACACGGCTCCTACGTGATGAAGAAATATAGTCGA-GGATGACACGGATCATACGTGATG
4802 AAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTT
65 AAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTT
4867 ATCT
129 ATCT
* *
4871 AGGGTGACACAGCTCCTACTTGATGA
1 AGGGTGACACGGCTCCTACGTGATGA
4897 GGAGGACTGG
Statistics
Matches: 146, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.01
132 62 0.42
133 83 0.57
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (132 bp):
AGGGTGACACGGCTCCTACGTGATGAAGAAATATAGTCGAGGATGACACGGATCATACGTGATGA
AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTAT
CT
Found at i:4929 original size:93 final size:93
Alignment explanation
Indices: 4829--5001 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
4819 TTTAGGAAGG
* * * *
4829 GTGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGTGACACAGCTCCTACTTGA
1 GTGATAACTCGATTCCTACACGATGAGGACGACTGGTTATCAAGGGTGACACAGCTCCTACGTGA
4894 TGAGGAGGACTGGTCGTTTAAAGGAAAT
66 TGAGGAGGACTGGTCGTTTAAAGGAAAT
* * * *
4922 GTGATAACTCGATTCCTACATGATGAGGACGTCTGGTTATCAAGGTTGACACGGCTCCTACGTGA
1 GTGATAACTCGATTCCTACACGATGAGGACGACTGGTTATCAAGGGTGACACAGCTCCTACGTGA
*
4987 TGAGGAGGTCTGGTC
66 TGAGGAGGACTGGTC
5002 AGGGATGACA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (93 bp):
GTGATAACTCGATTCCTACACGATGAGGACGACTGGTTATCAAGGGTGACACAGCTCCTACGTGA
TGAGGAGGACTGGTCGTTTAAAGGAAAT
Found at i:4998 original size:42 final size:39
Alignment explanation
Indices: 4935--5032 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 39
4925 ATAACTCGAT
* *
4935 TCCTACATGATGAGGACGTCTGGTTATCAAGGTTGACACGGC
1 TCCTACGTGATGAGGACGTCTGG---TCAAGGATGACACGGC
* * *
4977 TCCTACGTGATGAGGAGGTCTGGTCAGGGATGACACGGT
1 TCCTACGTGATGAGGACGTCTGGTCAAGGATGACACGGC
*
5016 TCCTATGTGATGAGGAC
1 TCCTACGTGATGAGGAC
5033 TGCTGGCCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 28 0.57
42 21 0.43
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (39 bp):
TCCTACGTGATGAGGACGTCTGGTCAAGGATGACACGGC
Found at i:5452 original size:34 final size:35
Alignment explanation
Indices: 5414--5480 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5404 TTTTCAAAAG
* *
5414 AAATTGTCTC-AAGAGAGACAAAATTTTGTTTTTA
1 AAATTGTATCTAAGAGAGAAAAAATTTTGTTTTTA
*
5448 AAATTGTATCTAAGTGAGAAAAAATTTTGTTTT
1 AAATTGTATCTAAGAGAGAAAAAATTTTGTTTT
5481 CAAAGAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (35 bp):
AAATTGTATCTAAGAGAGAAAAAATTTTGTTTTTA
Found at i:5742 original size:30 final size:29
Alignment explanation
Indices: 5699--5771 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
5689 GAAACAAAAT
* * * *
5699 TGTTTTAATAGAAACGATCTCAAAGGTGGG
1 TGTTTCAA-AGAAACGAACTCAAAGATAGG
*
5729 TGTTTCAAGAGAAACTAACTCAAAGATAGG
1 TGTTTCAA-AGAAACGAACTCAAAGATAGG
5759 TGTTTCAAAGAAA
1 TGTTTCAAAGAAA
5772 TTATCTCGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (29 bp):
TGTTTCAAAGAAACGAACTCAAAGATAGG
Found at i:6669 original size:36 final size:36
Alignment explanation
Indices: 6629--6731 Score: 156
Period size: 35 Copynumber: 2.9 Consensus size: 36
6619 GTCTCTAGCT
6629 AGACAAAATTTGTTTTTCAAGAAATTGTCTCAAACG
1 AGACAAAATTTGTTTTTCAAGAAATTGTCTCAAACG
*
6665 AGACAAAATTTGTTTTT--AGAAAATTGTCTCAAGCG
1 AGACAAAATTTGTTTTTCAAG-AAATTGTCTCAAACG
*
6700 AGACAAAATTTGTTTTTCAAAAGAATTGTCTC
1 AGACAAAATTTGTTTTTCAAGA-AATTGTCTC
6732 TAGCGAAACG
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
34 2 0.03
35 31 0.51
36 18 0.30
37 10 0.16
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (36 bp):
AGACAAAATTTGTTTTTCAAGAAATTGTCTCAAACG
Found at i:7093 original size:4 final size:4
Alignment explanation
Indices: 7056--8186 Score: 2004
Period size: 4 Copynumber: 286.0 Consensus size: 4
7046 TTTATGTGTC
* * * * * *
7056 ATGT ATGT ACGT ACGT ACGT ACGT ACGT ACGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7104 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
7152 ATGT ATGT AGGT ATGT A-GT ATGT ATG- -TGT ATGT ATG- -TGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7195 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7243 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
7291 ATGT ATG- -TGT ATGT ATG- ATGT ATGT ATGT GTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7336 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7382 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7430 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7478 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7526 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7574 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7621 ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
7668 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGC ATGC ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
7716 ATGT ATGC ATGT ATGC ATGT ATGCGT ATG- -TGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT AT--GT ATGT ATGT ATGT ATGT ATGT ATGT
7764 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7811 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7859 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7907 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
7955 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8003 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8051 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8099 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8147 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8187 TTTTCTCAAT
Statistics
Matches: 1094, Mismatches: 16, Indels: 34
0.96 0.01 0.03
Matches are distributed among these distances:
2 10 0.01
3 15 0.01
4 1065 0.97
6 4 0.00
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:9044 original size:11 final size:10
Alignment explanation
Indices: 9015--9053 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
9005 TTTTATTGTT
9015 TTTGTTTTTC
1 TTTGTTTTTC
*
9025 ATTTATTTTTTC
1 -TTT-GTTTTTC
9037 TTTGTTTTTC
1 TTTGTTTTTC
9047 TTTGTTT
1 TTTGTTT
9054 CTTTTCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 13 0.52
11 6 0.24
12 6 0.24
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (10 bp):
TTTGTTTTTC
Found at i:13087 original size:16 final size:15
Alignment explanation
Indices: 13062--13100 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13052 AAGCTCAAAT
13062 TACAAATATTAAATAA
1 TACAAATATTAAA-AA
*
13078 TACAAGTATTAAAAA
1 TACAAATATTAAAAA
*
13093 TAAAAATA
1 TACAAATA
13101 ACCCATAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (15 bp):
TACAAATATTAAAAA
Found at i:14607 original size:3 final size:3
Alignment explanation
Indices: 14599--14635 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
14589 TTGTAATTAG
14599 TAA TAA TAA TAA TAA TAA T-A TAA -ATA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
14636 TAAATAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:14627 original size:17 final size:17
Alignment explanation
Indices: 14607--14641 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14597 AGTAATAATA
14607 ATAATAATAATATAAAT
1 ATAATAATAATATAAAT
14624 ATAATAATAATATAAAT
1 ATAATAATAATATAAAT
14641 A
1 A
14642 AATGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATATAAAT
Found at i:15441 original size:35 final size:35
Alignment explanation
Indices: 15366--15441 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 35
15356 GTGTTCGGTT
15366 GAGTCAAGTTAAAAATTTTGAGTGATTAAAGTTGAC
1 GAGTCAAGTTAAAAATTTTGAGTGATT-AAGTTGAC
* *
15402 GAGTCGAGTTAAAAATTTTCGAGTTATT-AGTTGAC
1 GAGTCAAGTTAAAAATTTT-GAGTGATTAAGTTGAC
15437 GAGTC
1 GAGTC
15442 TTATTTTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 12 0.32
36 18 0.49
37 7 0.19
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (35 bp):
GAGTCAAGTTAAAAATTTTGAGTGATTAAGTTGAC
Found at i:21862 original size:18 final size:18
Alignment explanation
Indices: 21833--21891 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
21823 ATAATATAAG
21833 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
21850 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
* *
21868 -TAATTATTATAAGCTATA
1 TTTA-TATTATAAACTATA
*
21886 TATATA
1 TTTATA
21892 AATTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 26 0.74
19 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:21896 original size:20 final size:18
Alignment explanation
Indices: 21839--21897 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
21829 TAAGTTTATA
*
21839 TATAAACTATAT-TTATAT
1 TATAAACTATATAATA-AT
*
21857 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
21875 TATAAGCTATATATATAAAT
1 TATAAACTATATA-AT-AAT
21895 TAT
1 TAT
21898 GTTTATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:21952 original size:22 final size:21
Alignment explanation
Indices: 21907--21952 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
21897 TGTTTATATG
21907 AACTATATATATAAACTATGTA
1 AACTATATATATAAACTA-GTA
21929 AACTATATAGGTATAAACTA-TA
1 AACTATATA--TATAAACTAGTA
21951 AA
1 AA
21953 AAAATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTATATATATAAACTAGTA
Found at i:22198 original size:2 final size:2
Alignment explanation
Indices: 22191--22218 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22181 TCGTTGGCTA
22191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22219 TCACATGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22652 original size:14 final size:14
Alignment explanation
Indices: 22635--22677 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
22625 CACTTATGTT
22635 TAATTATATATATA
1 TAATTATATATATA
* *
22649 TAATTTTATGTATA
1 TAATTATATATATA
*
22663 TATTTATATATATA
1 TAATTATATATATA
22677 T
1 T
22678 TCTTCAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:22806 original size:26 final size:27
Alignment explanation
Indices: 22758--22809 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
22748 GGGAATTTAG
*
22758 AGGGAAATTGAGAAATTTTGAGAATAT
1 AGGGAAATTGAGAAATTTAGAGAATAT
22785 AGGGAAATTG-GAAATTTAGAGAATA
1 AGGGAAATTGAGAAATTTAGAGAATA
22810 GAAAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (27 bp):
AGGGAAATTGAGAAATTTAGAGAATAT
Found at i:23022 original size:2 final size:2
Alignment explanation
Indices: 23015--23171 Score: 80
Period size: 2 Copynumber: 80.0 Consensus size: 2
23005 TACTTTTAAT
* * *
23015 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA AA CTA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * *
23058 TA AA CTA TA TA -A AA TA TT TA GTT TT TA TA -A TT TA TA T- TA -A
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
23098 TA TA GTA TA TA TA TG TA TG TA TA -A CTA -A TA TA -A GTA -A TC
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
*
23137 TA TA GA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23172 GTTTATAGAA
Statistics
Matches: 117, Mismatches: 23, Indels: 30
0.69 0.14 0.18
Matches are distributed among these distances:
1 9 0.08
2 101 0.86
3 7 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:23059 original size:15 final size:15
Alignment explanation
Indices: 23019--23068 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
23009 TTTAATTATA
*
23019 TATATATATATATA-
1 TATATATATATAAAC
*
23033 TGTATATATATAAAC
1 TATATATATATAAAC
*
23048 TATATATGTATAAAC
1 TATATATATATAAAC
23063 TATATA
1 TATATA
23069 AAATATTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:23542 original size:13 final size:13
Alignment explanation
Indices: 23524--23548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23514 AATGAAAGAG
23524 TGGGCTTATGTAT
1 TGGGCTTATGTAT
23537 TGGGCTTATGTA
1 TGGGCTTATGTA
23549 AACTAATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (13 bp):
TGGGCTTATGTAT
Found at i:23859 original size:16 final size:15
Alignment explanation
Indices: 23840--23921 Score: 105
Period size: 14 Copynumber: 5.5 Consensus size: 15
23830 ATAAACCATG
23840 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
23856 TATATATATATATA-
1 TATATATATATAAAC
*
23870 TATATATATATATA-
1 TATATATATATAAAC
*
23884 TATATATATATAACC
1 TATATATATATAAAC
23899 TAATATATATATAAAC
1 T-ATATATATATAAAC
23915 TATATAT
1 TATATAT
23922 GGTAAACTAC
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
14 26 0.43
15 16 0.27
16 18 0.30
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:23938 original size:2 final size:2
Alignment explanation
Indices: 23840--23921 Score: 87
Period size: 2 Copynumber: 40.5 Consensus size: 2
23830 ATAAACCATG
*
23840 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** *
23884 TA TA TA TA TA TA -A CC TA -A TA TA TA TA TA AA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
23922 GGTAAACTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.03
2 62 0.91
3 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:24004 original size:7 final size:7
Alignment explanation
Indices: 23994--24059 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
23984 ATAGTTTATA
23994 TAAACCC
1 TAAACCC
24001 TAAACCC
1 TAAACCC
* *
24008 TAATCCA
1 TAAACCC
***
24015 TAAATAA
1 TAAACCC
24022 TAAACCC
1 TAAACCC
**
24029 TAAACTA
1 TAAACCC
24036 TAAACCC
1 TAAACCC
*
24043 TAAACCA
1 TAAACCC
24050 TAAACCC
1 TAAACCC
24057 TAA
1 TAA
24060 TGTAAATTGA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:24046 original size:21 final size:21
Alignment explanation
Indices: 23992--24054 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
23982 ATATAGTTTA
*
23992 TATAAACCCTAAACCCTAATC
1 TATAAACCCTAAACCCTAAAC
* ***
24013 CATAAATAATAAACCCTAAAC
1 TATAAACCCTAAACCCTAAAC
*
24034 TATAAACCCTAAACCATAAAC
1 TATAAACCCTAAACCCTAAAC
24055 CCTAATGTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
TATAAACCCTAAACCCTAAAC
Found at i:24046 original size:28 final size:28
Alignment explanation
Indices: 23993--24059 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
23983 TATAGTTTAT
* * *
23993 ATAAACCCTAAACCCTAATCCATAAATA
1 ATAAACCCTAAACCATAAACCATAAACA
* * *
24021 ATAAACCCTAAACTATAAACCCTAAACC
1 ATAAACCCTAAACCATAAACCATAAACA
24049 ATAAACCCTAA
1 ATAAACCCTAA
24060 TGTAAATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (28 bp):
ATAAACCCTAAACCATAAACCATAAACA
Found at i:25080 original size:16 final size:15
Alignment explanation
Indices: 25051--25091 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
25041 TTTCATCCAT
25051 GGTAATATATAAGTCA
1 GGTAA-ATATAAGTCA
25067 GGTAAATATCAAGTCA
1 GGTAAATAT-AAGTCA
*
25083 GATAAATAT
1 GGTAAATAT
25092 TAGATCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (15 bp):
GGTAAATATAAGTCA
Found at i:25529 original size:45 final size:45
Alignment explanation
Indices: 25463--25566 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
25453 TTACAACCCT
* *
25463 ACCCATATGCATTTCAATTATGGAATCCTTTCATGCCGATAATGC
1 ACCCATATGCATTTCAATTATGGAATCATTTCATACCGATAATGC
* *
25508 ACCCATATGCATTTCAGTTATGGCATCATTTCATACCGATAATGC
1 ACCCATATGCATTTCAATTATGGAATCATTTCATACCGATAATGC
*
25553 ACTCATATGCATTT
1 ACCCATATGCATTT
25567 TTTTTCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (45 bp):
ACCCATATGCATTTCAATTATGGAATCATTTCATACCGATAATGC
Found at i:26098 original size:20 final size:20
Alignment explanation
Indices: 26075--26156 Score: 103
Period size: 20 Copynumber: 4.0 Consensus size: 20
26065 ATGTAAATCC
26075 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
**
26095 CAACGCGATAAT-ACATAATCG
1 CAACGCGATTCTGAC-T-ATCG
26116 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
* *
26136 TAACGTGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
26156 C
1 C
26157 GTTGCGATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 33 0.63
21 15 0.29
22 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:26349 original size:22 final size:22
Alignment explanation
Indices: 26324--26381 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
26314 TCACTCTCTA
*
26324 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
26346 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
* *
26368 CGGCAAAATCCGTC
1 CGACGAAATCCGTC
26382 TATCTCCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.45, G:0.16, T:0.17
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:26865 original size:20 final size:19
Alignment explanation
Indices: 26813--26885 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
26803 GTTGCAATTT
*
26813 TCATTTCGAGTTGCGATAG
1 TCATTTCGTGTTGCGATAG
*
26832 TCAAATTT-GCGTTGCGATAG
1 TC--ATTTCGTGTTGCGATAG
* **
26852 TCATTTCCGTGTTGTGATTT
1 TCATTT-CGTGTTGCGATAG
26872 TCATTTTCGTGTTG
1 TCA-TTTCGTGTTG
26886 TGATTTTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 4 0.09
19 2 0.05
20 31 0.70
21 7 0.16
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.45
Consensus pattern (19 bp):
TCATTTCGTGTTGCGATAG
Found at i:26886 original size:20 final size:20
Alignment explanation
Indices: 26852--26892 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
26842 GTTGCGATAG
26852 TCATTTCCGTGTTGTGATTT
1 TCATTTCCGTGTTGTGATTT
*
26872 TCATTTTCGTGTTGTGATTT
1 TCATTTCCGTGTTGTGATTT
26892 T
1 T
26893 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (20 bp):
TCATTTCCGTGTTGTGATTT
Found at i:26899 original size:20 final size:20
Alignment explanation
Indices: 26859--26899 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
26849 TAGTCATTTC
* *
26859 CGTGTTGTGATTTTCATTTT
1 CGTGTTGTGATTTTAAGTTT
26879 CGTGTTGTGATTTTAAGTTT
1 CGTGTTGTGATTTTAAGTTT
26899 C
1 C
26900 AGAAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.10, G:0.22, T:0.56
Consensus pattern (20 bp):
CGTGTTGTGATTTTAAGTTT
Found at i:28831 original size:20 final size:20
Alignment explanation
Indices: 28808--28851 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28798 CTTAAAATCA
28808 CAACGCGAAAATGACTACCG
1 CAACGCGAAAATGACTACCG
** *
28828 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTACCG
28848 CAAC
1 CAAC
28852 AGGATAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAATGACTACCG
Found at i:28892 original size:19 final size:19
Alignment explanation
Indices: 28868--28909 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
28858 ATCACAATGC
*
28868 GAAATAAAAATTGCAACGT
1 GAAATAAAAATCGCAACGT
28887 GAAATAAAAATCGCAACGT
1 GAAATAAAAATCGCAACGT
28906 GAAA
1 GAAA
28910 ATCGCAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAATAAAAATCGCAACGT
Found at i:28928 original size:20 final size:20
Alignment explanation
Indices: 28905--28942 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28895 AATCGCAACG
*
28905 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
28925 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
28943 TTTAGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:28975 original size:19 final size:19
Alignment explanation
Indices: 28947--28983 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28937 CGCGAATTTA
28947 GTTTCACGTTGTGATTTTG
1 GTTTCACGTTGTGATTTTG
*
28966 GTTTCGCGTTGTGATTTT
1 GTTTCACGTTGTGATTTT
28984 CTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.11, G:0.27, T:0.54
Consensus pattern (19 bp):
GTTTCACGTTGTGATTTTG
Found at i:28996 original size:33 final size:33
Alignment explanation
Indices: 28948--29027 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
28938 GCGAATTTAG
* * * * *
28948 TTTCACGTTGTGATTTTGGTTTCGCGTTGTGAT
1 TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
*
28981 TTTCTCGTTGCGATTTTTATTTCGCATTGCGAT
1 TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
* *
29014 TATCTTGTTGCGAT
1 TTTCTCGTTGCGAT
29028 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
Found at i:29045 original size:20 final size:20
Alignment explanation
Indices: 29020--29084 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
29010 CGATTATCTT
**
29020 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
*
29040 GTTGCGATAGTCTTTTTCGC
1 GTTGCGATAGTCATTTTCGC
29060 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
29080 GTTGC
1 GTTGC
29085 AATTTTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:29097 original size:20 final size:20
Alignment explanation
Indices: 29074--29117 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29064 CGATAGTCAT
29074 TTTCGCGTTGCAATTTTAAG
1 TTTCGCGTTGCAATTTTAAG
* *
29094 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCAATTTTAAG
29114 TTTC
1 TTTC
29118 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCAATTTTAAG
Found at i:29680 original size:21 final size:21
Alignment explanation
Indices: 29618--29689 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
29608 TCTCCTATCA
*
29618 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTATCATCG
* * **
29639 CTCAAGAGTCCCCTCCCATCG
1 TTCAAGAGGCCCCTATCATCG
* *
29660 TTCATGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTATCATCG
*
29681 TTGAAGAGG
1 TTCAAGAGG
29690 TCACTCCCAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTATCATCG
Found at i:29688 original size:42 final size:41
Alignment explanation
Indices: 29587--29709 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
29577 GCCCGACTCA
* *
29587 CCTGTCATCGTTCAAGCAGCCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCGTTCAAG-AGCCCCTCCCATCATTCAAGAGGCC
* ** * *
29629 CCTATCATCCCTCAAGAGTCCCCTCCCATCGTTCATGAGGCC
1 CCTGTCATCGTTCAAGAG-CCCCTCCCATCATTCAAGAGGCC
* * * *
29671 CCTGTCATCGTTGAAGAGGTCACTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GCCCCTCCCATCATTCAAGAG
29710 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.95
43 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (41 bp):
CCTGTCATCGTTCAAGAGCCCCTCCCATCATTCAAGAGGCC
Found at i:30764 original size:90 final size:91
Alignment explanation
Indices: 30610--30788 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 91
30600 CCTAACACAC
* * *
30610 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
* *
30675 TATTTAATTAATTAGAATTTAATAAT
66 TATTTAATTAATTAAAATTAAATAAT
*
30701 CCTTTTATATCCAAGTTACCCTAATCATATCAGGG-ATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
30765 TATTTAATTAATTAAAATTAAATA
66 TATTTAATTAATTAAAATTAAATA
30789 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 50 0.61
91 32 0.39
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (91 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
TATTTAATTAATTAAAATTAAATAAT
Found at i:37536 original size:90 final size:90
Alignment explanation
Indices: 37382--37557 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
37372 CCTAACACAC
* * *
37382 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
*
37447 TATTTAATTAATTAGAATTTAATAAT
66 TATTTAATTAATT-GAAATTAATAAT
*
37473 CCTTTTATATCCAAGTTACCCTAATCATATCAGGG-ATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
37537 TATTTAATTAATTGAAATTAA
66 TATTTAATTAATTGAAATTAA
37558 ATATTCGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 7 0.09
90 41 0.51
91 32 0.40
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTTTATTATTTCAAATTAATTAAATCTA
TATTTAATTAATTGAAATTAATAAT
Found at i:39392 original size:14 final size:14
Alignment explanation
Indices: 39373--39409 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39363 GCTTGTTTAA
39373 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
39387 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
39401 TTGATTTGT
1 TTGATTTGT
39410 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:39554 original size:20 final size:20
Alignment explanation
Indices: 39529--39601 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
39519 AGGTACACTT
*
39529 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
39549 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
39569 TTGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
39589 TCGCAACTCGAAA
1 TCGCAACGCGAAA
39602 GTCATTTCGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:39602 original size:20 final size:20
Alignment explanation
Indices: 39544--39594 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
39534 ACGCTAAACT
*
39544 CAAAATCGCAATGCGAAAGT
1 CAAAATCGCAATGCGAAAGC
*
39564 CAAAATTGCAATGCGAAAGC
1 CAAAATCGCAATGCGAAAGC
39584 CAAAATCGCAA
1 CAAAATCGCAA
39595 CTCGAAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.14
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGC
Found at i:39670 original size:20 final size:20
Alignment explanation
Indices: 39645--39795 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
39635 GCGATTTTCT
*
39645 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
39665 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
39685 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
39705 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
39725 CATTGCGAT--T---TTTC-
1 CGTTGCGATAGTCAAATTCG
* *
39739 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
39759 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
39779 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
39796 AAATGTGTAA
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.06
15 3 0.03
16 1 0.01
18 1 0.01
19 3 0.03
20 95 0.86
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:39734 original size:94 final size:94
Alignment explanation
Indices: 39607--39795 Score: 265
Period size: 94 Copynumber: 2.0 Consensus size: 94
39597 CGAAAGTCAT
* * *
39607 TTCGCGTTGTGCTAGTCTAATACGATTTGCGA-TTTTCTCGTTGCGATAGTCAAATTCCCGTTGC
1 TTCGCGTTGCGATAGTCAAATACGATTTGCGATTTTTCT-GTTGCGATAGTCAAATTCCCGTTGC
39671 GATAATCAAATTCACATTGCGATAGTCAAA
65 GATAATCAAATTCACATTGCGATAGTCAAA
* * *
39701 TTCGCGTTGCGATAGTCAAATTCGCA-TTGCGATTTTTCTGTTGCGATAGTCATATTCGCGTTGC
1 TTCGCGTTGCGATAGTCAAATACG-ATTTGCGATTTTTCTGTTGCGATAGTCAAATTCCCGTTGC
* * *
39765 GATAGTCAAATTCGCATTGCGATATTCAAA
65 GATAATCAAATTCACATTGCGATAGTCAAA
39795 T
1 T
39796 AAATGTGTAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 77 0.92
95 7 0.08
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (94 bp):
TTCGCGTTGCGATAGTCAAATACGATTTGCGATTTTTCTGTTGCGATAGTCAAATTCCCGTTGCG
ATAATCAAATTCACATTGCGATAGTCAAA
Found at i:39951 original size:140 final size:140
Alignment explanation
Indices: 39766--40188 Score: 774
Period size: 140 Copynumber: 3.0 Consensus size: 140
39756 TCGCGTTGCG
* * *
39766 ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTGTAATAAGTGATAAAAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
39831 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
39896 AATACATATA
131 AATACACATA
*
39906 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
39971 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
40036 AATACACATA
131 AATACACATA
*
40046 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
40111 TAGCAATGTTCAAACTCAAGTTAGTAATGCATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
40176 AATACACATA
131 AATACACATA
40186 ATA
1 ATA
40189 CAATGTTTGC
Statistics
Matches: 274, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 274 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:40269 original size:18 final size:18
Alignment explanation
Indices: 40246--40280 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40236 AAGCCGGGTG
*
40246 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
40264 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
40281 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:42587 original size:24 final size:24
Alignment explanation
Indices: 42536--42587 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42526 ATCCTAGTAT
** *
42536 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
42560 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
42584 TGAC
1 TGAC
42588 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:43427 original size:20 final size:21
Alignment explanation
Indices: 43402--43504 Score: 124
Period size: 21 Copynumber: 5.0 Consensus size: 21
43392 GCATTGCGAC
*
43402 AGTCAGAATCGCGTTGTGA-T
1 AGTCAGAATCGCGTTGCGATT
43422 AGTCAGAATCGCGTTGCGATT
1 AGTCAGAATCGCGTTGCGATT
**
43443 ATGT-ATTATCGCGTTGCGATT
1 A-GTCAGAATCGCGTTGCGATT
*
43464 ATGT-ATAATCGCGTTGCGA-T
1 A-GTCAGAATCGCGTTGCGATT
43484 AGTCAGAATCGCGTTGCGATT
1 AGTCAGAATCGCGTTGCGATT
43505 TACATATTCG
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.03
20 34 0.46
21 36 0.49
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (21 bp):
AGTCAGAATCGCGTTGCGATT
Found at i:43515 original size:20 final size:19
Alignment explanation
Indices: 43408--43525 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 19
43398 CGACAGTCAG
* * *
43408 AATCGCGTTGTGATAGTCAG
1 AATCGCGTTGCGAT-TTCAT
*
43428 AATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATT-T-CAT
* *
43449 TATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATT-T-CAT
* *
43470 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGAT-TTCAT
43490 AATCGCGTTGCGATTTACAT
1 AATCGCGTTGCGATTT-CAT
* *
43510 ATTCGCATTGCGATTT
1 AATCGCGTTGCGATTT
43526 TCTAAAATCG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.01
20 45 0.56
21 35 0.43
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (19 bp):
AATCGCGTTGCGATTTCAT
Found at i:43535 original size:41 final size:41
Alignment explanation
Indices: 43392--43581 Score: 120
Period size: 41 Copynumber: 4.6 Consensus size: 41
43382 TTGAAATTTA
* * * *
43392 GCATTGCGACAGTCAGAATCGCGTTGTGA-TAGT-CAGAATC
1 GCATTGCGATAGTCAAAATCGCGTTGCGATTA-TACATAATC
* ** **
43432 GCGTTGCGATTATGT-ATTATCGCGTTGCGATTATGTATAATC
1 GCATTGCGA-TA-GTCAAAATCGCGTTGCGATTATACATAATC
* * *
43474 GCGTTGCGATAGTCAGAATCGCGTTGCGATT-TACATATTC
1 GCATTGCGATAGTCAAAATCGCGTTGCGATTATACATAATC
** ** ** *
43514 GCATTGCGATTTTCTAAAATCGCAATGCGAATT-TGGAAAATC
1 GCATTGCGATAGTC-AAAATCGCGTTGCG-ATTATACATAATC
*
43556 GCAATGCGATAGTCAAAATCGCGTTG
1 GCATTGCGATAGTCAAAATCGCGTTG
43582 TGAATCTTGA
Statistics
Matches: 116, Mismatches: 27, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
40 27 0.23
41 52 0.45
42 37 0.32
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
GCATTGCGATAGTCAAAATCGCGTTGCGATTATACATAATC
Found at i:43536 original size:82 final size:82
Alignment explanation
Indices: 43375--43581 Score: 195
Period size: 82 Copynumber: 2.5 Consensus size: 82
43365 TAAAACCTGT
* * * * *
43375 TGCGAATTT-GAAATTTAGCATTGCGACAGTCAGAATCGCGTTGTGATAGTCAGAATCGCGTTGC
1 TGCGAATTTGGAAA-ATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGC
* ** **
43439 GATTATGTATTATCGCGT
65 GATTATCTAAAATCGCAA
* * * * * *
43457 TGCG-ATTATGTATAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT-TTACATATTCGCATTG
1 TGCGAATT-TGGAAAATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAATCGCATTG
*
43520 CGATTTTCTAAAATCGCAA
64 CGATTATCTAAAATCGCAA
* *
43539 TGCGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTG
1 TGCGAATTTGGAAAATCGCATTGCGATAGTCAGAATCGCGTTG
43582 TGAATCTTGA
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
81 4 0.04
82 90 0.91
83 5 0.05
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (82 bp):
TGCGAATTTGGAAAATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCG
ATTATCTAAAATCGCAA
Found at i:43542 original size:21 final size:21
Alignment explanation
Indices: 43512--43565 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
43502 ATTTACATAT
* *
43512 TCGCATTGCGATTTTCTAAAA
1 TCGCAATGCGATTTTCGAAAA
* *
43533 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGATTTTCGAAAA
43554 TCGCAATGCGAT
1 TCGCAATGCGAT
43566 AGTCAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (21 bp):
TCGCAATGCGATTTTCGAAAA
Found at i:43997 original size:94 final size:94
Alignment explanation
Indices: 43829--44001 Score: 235
Period size: 94 Copynumber: 1.8 Consensus size: 94
43819 CCCTGATATT
* * *
43829 GATACTTCTATACTATGGTACCGATACCCCTTTCAGTATCGAAACCATTTCTATATTCTGTGTTG
1 GATACTACTATACTATGGTACCGATACCCCTTTCAGTATCGAAACCATTTCTACATTCTGTGATG
*
43894 CCTGGTATCGATACCCTTCTCTCAGTATC
66 CCTGATATCGATACCCTTCTCTCAGTATC
* * *
43923 GATACTACTATACTATGGTACTGATACTCCGTTTCAGTATCGATACCATTT-TGACATTCTG-GA
1 GATACTACTATACTATGGTACCGATAC-CCCTTTCAGTATCGAAACCATTTCT-ACATTCTGTGA
43986 T-CCATGATATCGATAC
64 TGCC-TGATATCGATAC
44002 TTCCCCTTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
93 2 0.03
94 39 0.57
95 28 0.41
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (94 bp):
GATACTACTATACTATGGTACCGATACCCCTTTCAGTATCGAAACCATTTCTACATTCTGTGATG
CCTGATATCGATACCCTTCTCTCAGTATC
Found at i:44051 original size:15 final size:17
Alignment explanation
Indices: 44011--44056 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
44001 CTTCCCCTTG
*
44011 TTAGTATCGATACCCCA
1 TTAGTATCGATACCACA
44028 TTAGTATCGATACCAC-
1 TTAGTATCGATACCACA
*
44044 TT-GTATCGGTACC
1 TTAGTATCGATACC
44057 GATACTGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 15 0.56
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAGTATCGATACCACA
Found at i:44604 original size:3 final size:3
Alignment explanation
Indices: 44596--44621 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44586 CCACGTGAAT
44596 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
44622 GAAATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47009 original size:20 final size:21
Alignment explanation
Indices: 46961--47010 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
46951 AATAAAGGAT
46961 AATAATATAAGTAATGAAAAAA
1 AATAA-ATAAGTAATGAAAAAA
**
46983 AAT-AATAAG-AATGAAATGA
1 AATAAATAAGTAATGAAAAAA
47002 AATAAATAA
1 AATAAATAA
47011 AAGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 10 0.40
21 1 0.04
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
AATAAATAAGTAATGAAAAAA
Found at i:51140 original size:5 final size:5
Alignment explanation
Indices: 51130--51164 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
51120 GAACTTCTCT
*
51130 TTTTC TTTTC TTTTC TTTTC TTTTT TTCTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTT
51165 TTGATTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:51143 original size:11 final size:11
Alignment explanation
Indices: 51127--51165 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
51117 TTTGAACTTC
51127 TCTTTTTCTTT
1 TCTTTTTCTTT
51138 TC-TTTTCTTT
1 TCTTTTTCTTT
51148 TCTTTTT-TTCT
1 TCTTTTTCTT-T
51159 TCTTTTT
1 TCTTTTT
51166 TGATTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:58055 original size:18 final size:18
Alignment explanation
Indices: 58010--58070 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
58000 TGGAGACTAG
58010 GAGAAT-AAGAAAAT-AA
1 GAGAATAAAGAAAATGAA
**
58026 GAGAAGGGAAGAAAATGAA
1 GAGAA-TAAAGAAAATGAA
* *
58045 GAGAATAAAGAGACTGAA
1 GAGAATAAAGAAAATGAA
58063 GAG-ATAAA
1 GAGAATAAA
58071 AAGCCTAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.14
17 5 0.14
18 20 0.54
19 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.28, T:0.10
Consensus pattern (18 bp):
GAGAATAAAGAAAATGAA
Found at i:60414 original size:16 final size:15
Alignment explanation
Indices: 60393--60422 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
60383 ACCGAAACGA
60393 TTAATATGTTATTTTG
1 TTAATATGTT-TTTTG
60409 TTAATATGTTTTTT
1 TTAATATGTTTTTT
60423 ATAATCTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
TTAATATGTTTTTTG
Found at i:61277 original size:21 final size:21
Alignment explanation
Indices: 61251--61297 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
61241 GCCCCGTTAA
61251 GGCTTCGATCGAAATTGTGTG
1 GGCTTCGATCGAAATTGTGTG
*
61272 GGCTTCGATCGATATTGTGTG
1 GGCTTCGATCGAAATTGTGTG
61293 GGCTT
1 GGCTT
61298 TGCCAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.36
Consensus pattern (21 bp):
GGCTTCGATCGAAATTGTGTG
Found at i:79169 original size:19 final size:20
Alignment explanation
Indices: 79134--79175 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
79124 TTTTCTTCTG
*
79134 AAAGCAAAATTGGA-TTTGA
1 AAAGCAAAATTGAATTTTGA
79153 AAAGCAAAA-TGAAATTTTGA
1 AAAGCAAAATTG-AATTTTGA
79173 AAA
1 AAA
79176 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (20 bp):
AAAGCAAAATTGAATTTTGA
Found at i:79233 original size:21 final size:23
Alignment explanation
Indices: 79192--79233 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
79182 TTGAGCTTTC
79192 AAAAATTAAAATCAATGATTTGG
1 AAAAATTAAAATCAATGATTTGG
*
79215 AAAAA-TAAAAT-ATTGATTT
1 AAAAATTAAAATCAATGATTT
79234 TAAAGTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (23 bp):
AAAAATTAAAATCAATGATTTGG
Found at i:84646 original size:21 final size:21
Alignment explanation
Indices: 84620--84659 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
84610 GACTATCAAC
*
84620 ATTTCATGGCCTCGACAAAAG
1 ATTTCATGGCCTCAACAAAAG
84641 ATTTCATGGCCTCAACAAA
1 ATTTCATGGCCTCAACAAA
84660 TTACAGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
ATTTCATGGCCTCAACAAAAG
Found at i:84684 original size:38 final size:37
Alignment explanation
Indices: 84578--84685 Score: 103
Period size: 38 Copynumber: 2.9 Consensus size: 37
84568 AACAATCAAG
*
84578 CAACAAATTACAGGCCACAACAAAATAATTC-TGACT
1 CAACAAATTACAGGCCACAACAAAATATTTCATGACT
* * * * * *
84614 -ATCAACATTTCATGGCCTCGACAAAAGATTTCATGGCCT
1 CAACAA-ATTACA-GGCCACAACAAAATATTTCAT-GACT
*
84653 CAACAAATTACAGGCCACAACAAAATTTTTCAT
1 CAACAAATTACAGGCCACAACAAAATATTTCAT
84686 AGTAGCCCTG
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
35 4 0.07
36 5 0.09
37 15 0.28
38 18 0.33
39 8 0.15
40 4 0.07
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (37 bp):
CAACAAATTACAGGCCACAACAAAATATTTCATGACT
Done.