Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020872.1 Corchorus olitorius cultivar O-4 contig20905, 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: 121002
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3912 original size:2 final size:2
Alignment explanation
Indices: 3905--3934 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3895 GTTAAAACTA
*
3905 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3935 GTGTGTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4144 original size:160 final size:160
Alignment explanation
Indices: 3969--4281 Score: 574
Period size: 160 Copynumber: 2.0 Consensus size: 160
3959 AATGCATTTT
3969 ATTTTTTTCGGCAGAACAATACATTTTATTTTTATATATGGGCTGTTTTTCAAAAGAGAAAAAAA
1 ATTTTTTTCGGCAGAACAATACATTTTATTTTTATATATGGGCTGTTTTTCAAAAGA-AAAAAAA
*
4034 AAGCATGGCTAAAAAA-TTTAAAAACTTATCAAAAGTTATAAACAATTATTGTAATTTTCTTTTA
65 AAGCATGGCTAAAAAACCTTAAAAACTTATCAAAAGTTATAAACAATTATTGTAATTTTCTTTTA
4098 AAAAATTAAAATACTGATTTACTAACAATGC
130 AAAAATTAAAATACTGATTTACTAACAATGC
* *
4129 ATTTTTTTTGGCAGAACAATGCATTTTATTTTTATATATGGGCTGTTTTTCAAAAGAAAAAAAAA
1 ATTTTTTTCGGCAGAACAATACATTTTATTTTTATATATGGGCTGTTTTTCAAAAGAAAAAAAAA
*
4194 AGCATGGCTAAAAAACCTTAAAAAGTTATCAAAAGTTATAAACAATTATTGTAATTTTCTTTTAA
66 AGCATGGCTAAAAAACCTTAAAAACTTATCAAAAGTTATAAACAATTATTGTAATTTTCTTTTAA
4259 AAAATTAAAATACTGATTTACTA
131 AAAATTAAAATACTGATTTACTA
4282 CTATTATTAG
Statistics
Matches: 148, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
159 23 0.16
160 125 0.84
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (160 bp):
ATTTTTTTCGGCAGAACAATACATTTTATTTTTATATATGGGCTGTTTTTCAAAAGAAAAAAAAA
AGCATGGCTAAAAAACCTTAAAAACTTATCAAAAGTTATAAACAATTATTGTAATTTTCTTTTAA
AAAATTAAAATACTGATTTACTAACAATGC
Found at i:5576 original size:76 final size:76
Alignment explanation
Indices: 5459--5599 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 76
5449 CCTCTTTCCG
*
5459 TTATGAATGTAAGCTCTAAAGGTATTTGTACTAGTAAGATAAGTGCAAAACTGGAAACTTTGCAT
1 TTATGAATGTAAGCTCTAAAGGTACTTGTACTAGTAAGATAAGTGCAAAACTGGAAACTTTGCAT
5524 ATCTCTTGTCA
66 ATCTCTTGTCA
* * * *
5535 TTATGAACT-TAAGCTCTGAAGGTACTTGTACTTA-TAAGATAAGTGGAAATCTGGAAGCTTTGC
1 TTATGAA-TGTAAGCTCTAAAGGTACTTGTAC-TAGTAAGATAAGTGCAAAACTGGAAACTTTGC
5598 AT
64 AT
5600 CTTACTTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
76 55 0.95
77 3 0.05
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (76 bp):
TTATGAATGTAAGCTCTAAAGGTACTTGTACTAGTAAGATAAGTGCAAAACTGGAAACTTTGCAT
ATCTCTTGTCA
Found at i:9272 original size:48 final size:48
Alignment explanation
Indices: 9201--9297 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
9191 CGAAATTTAA
9201 GGCCCAAGTAAGCGGATCACAAGATAAGATAAGACCCAGAAAACTGCG
1 GGCCCAAGTAAGCGGATCACAAGATAAGATAAGACCCAGAAAACTGCG
* *
9249 GGCCCAAGTAAGCGGATCACAAGATAAGATAAGACCCATAAGACTGCG
1 GGCCCAAGTAAGCGGATCACAAGATAAGATAAGACCCAGAAAACTGCG
9297 G
1 G
9298 TTTCATTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (48 bp):
GGCCCAAGTAAGCGGATCACAAGATAAGATAAGACCCAGAAAACTGCG
Found at i:15397 original size:40 final size:39
Alignment explanation
Indices: 15353--15758 Score: 638
Period size: 40 Copynumber: 10.2 Consensus size: 39
15343 TTGAGGGCCA
*
15353 ATGTGAATTAAGGCAAGTTCAATGTCTATTGGAAATTTGG
1 ATGTGAA-TAAGGCAAGTTCAATGTTTATTGGAAATTTGG
15393 ATGTGAATAAGGCAAGTTCAATG-TTATTTGGAAATGTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTA-TTGGAAAT-TTGG
15433 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGG
15472 ATGTGAATAAGGCAAGTTCAATG-TTATTTGGAAATTTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTA-TTGGAAA-TTTGG
15512 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGG
15551 ATGTGAATAAGGCAAGTTCAATG-TTATTTGGAAATTTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTA-TTGGAAA-TTTGG
15591 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGG
15631 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGG
**
15671 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGG
** *
15711 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTTGA
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGG
15751 ATGTGAAT
1 ATGTGAAT
15759 GTGCCGCGTA
Statistics
Matches: 352, Mismatches: 4, Indels: 20
0.94 0.01 0.05
Matches are distributed among these distances:
38 8 0.02
39 93 0.26
40 239 0.68
41 12 0.03
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (39 bp):
ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGG
Found at i:15676 original size:80 final size:79
Alignment explanation
Indices: 15353--15758 Score: 681
Period size: 79 Copynumber: 5.1 Consensus size: 79
15343 TTGAGGGCCA
*
15353 ATGTGAATTAAGGCAAGTTCAATGTCTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTT
1 ATGTGAA-TAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTT
15418 ATTTGG-AAATGTTGG
65 ATTTGGAAAAT-TTGG
15433 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTTA
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTTA
*
15498 TTTGGAAATTTTGG
66 TTTGGAAAATTTGG
15512 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTTA
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTTA
*
15577 TTTGGAAATTTTGG
66 TTTGGAAAATTTGG
15591 ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTT
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGGATGTGAATAAGGCAAGTTCAATGTT
15656 -TATTGGAAAATTTGG
65 AT-TTGGAAAATTTGG
** *
15671 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTTGGATGTGAATAAGGCAAGTTCAATGTC
1 ATGTGAATAAGGCAAGTTCAATGTTTATTGG-AAATTTGGATGTGAATAAGGCAAGTTCAATGTT
* *
15736 AATTGGAAAATTTGA
65 ATTTGGAAAATTTGG
15751 ATGTGAAT
1 ATGTGAAT
15759 GTGCCGCGTA
Statistics
Matches: 314, Mismatches: 8, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
79 177 0.56
80 137 0.44
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (79 bp):
ATGTGAATAAGGCAAGTTCAATGTTTATTGGAAATTTGGATGTGAATAAGGCAAGTTCAATGTTA
TTTGGAAAATTTGG
Found at i:15753 original size:20 final size:20
Alignment explanation
Indices: 15690--15754 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
15680 AGGCAAGTTC
15690 AATGTCAATTGGAAAATTTG
1 AATGTCAATTGGAAAATTTG
* * * * * *
15710 GATGTGAATAAGG-CAAGTTC
1 AATGTCAAT-TGGAAAATTTG
15730 AATGTCAATTGGAAAATTTG
1 AATGTCAATTGGAAAATTTG
15750 AATGT
1 AATGT
15755 GAATGTGCCG
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (20 bp):
AATGTCAATTGGAAAATTTG
Found at i:17173 original size:18 final size:18
Alignment explanation
Indices: 17150--17186 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17140 TAACACAGGG
17150 TGGGAATGTGCAAGAGTT
1 TGGGAATGTGCAAGAGTT
17168 TGGGAATGTGCAAGAGTT
1 TGGGAATGTGCAAGAGTT
17186 T
1 T
17187 ATGTGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30
Consensus pattern (18 bp):
TGGGAATGTGCAAGAGTT
Found at i:19045 original size:80 final size:82
Alignment explanation
Indices: 18904--19072 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 82
18894 ACACACGAGA
* * * * * *
18904 AGGACAACGGCTCTGAACAATGAGCCTCTCTCAAAACGGCTGCCGACTACGAGGCTTGCGGACAC
1 AGGACAACGGCTCTCAACAATGAG-CGCTCTCAAAACAGCCGCCGACTACAAGGCTCGCGGACAC
*
18969 -ACACATGAACGTACACG
65 GACACACGAACGTACACG
* * * *
18986 AGGACAGCGGCTCTCAACAGTGAG-GCTCTCAAAACAGCCGCCTACTGCAAGGCTCGCGGACACG
1 AGGACAACGGCTCTCAACAATGAGCGCTCTCAAAACAGCCGCCGACTACAAGGCTCGCGGACACG
*
19050 ACACACGAAGGTACACG
66 ACACACGAACGTACACG
19067 AGGACA
1 AGGACA
19073 CAATCAAGCA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
80 32 0.43
81 21 0.28
82 21 0.28
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.12
Consensus pattern (82 bp):
AGGACAACGGCTCTCAACAATGAGCGCTCTCAAAACAGCCGCCGACTACAAGGCTCGCGGACACG
ACACACGAACGTACACG
Found at i:38916 original size:21 final size:20
Alignment explanation
Indices: 38892--38950 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
38882 GCTGTTCAAA
*
38892 TAATCTTATCTGTACAGTATC
1 TAATCTAATCTGTACAGT-TC
* *
38913 TAATCTAATATGTACAG-TG
1 TAATCTAATCTGTACAGTTC
*
38932 TAATCTCATCTGTACAGTT
1 TAATCTAATCTGTACAGTT
38951 GCTACACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.50
20 1 0.03
21 15 0.47
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
TAATCTAATCTGTACAGTTC
Found at i:42170 original size:24 final size:22
Alignment explanation
Indices: 42125--42170 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
42115 CATTGAACAA
**
42125 ATCTTTGAAATATAAATGCAAT
1 ATCTTTGAAATATAAAACCAAT
42147 ATCTTTGAAATATATACAACCAAT
1 ATCTTTGAAATATA-A-AACCAAT
42171 TTTTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 1 0.05
24 5 0.25
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (22 bp):
ATCTTTGAAATATAAAACCAAT
Found at i:54032 original size:3 final size:3
Alignment explanation
Indices: 54024--54050 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54014 CTGTCTATGC
54024 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
54051 GATAGTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:64218 original size:11 final size:11
Alignment explanation
Indices: 64204--64228 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
64194 CCTGATTAAT
64204 CCGAATCCAAC
1 CCGAATCCAAC
64215 CCGAATCCAAC
1 CCGAATCCAAC
64226 CCG
1 CCG
64229 TGTCGCGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.48, G:0.12, T:0.08
Consensus pattern (11 bp):
CCGAATCCAAC
Found at i:69868 original size:17 final size:19
Alignment explanation
Indices: 69843--69884 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
69833 TCATGCAACC
69843 TTTTATTTTC-A-TAGTCT
1 TTTTATTTTCTATTAGTCT
*
69860 TTTTTTTTTCTTATTAGTCT
1 TTTTATTTTC-TATTAGTCT
69880 TTTTA
1 TTTTA
69885 CCCCTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTATTTTCTATTAGTCT
Found at i:83133 original size:54 final size:56
Alignment explanation
Indices: 83058--83164 Score: 146
Period size: 54 Copynumber: 1.9 Consensus size: 56
83048 ATCTTAGTGC
* *
83058 TTTTTTTCATACATAACTTTATCCAAAT-T-TTTTATATCTTCGAAAATAATTACT
1 TTTTTTTCATACATAACTTTATCAAAATATCTTTTATATCTTCGAAAACAATTACT
** * *
83112 TTTTTTTGGTACATAATTTTATTAAAATATCTTTTATATCTTCGAAAACAATT
1 TTTTTTTCATACATAACTTTATCAAAATATCTTTTATATCTTCGAAAACAATT
83165 CTAATTATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 23 0.51
55 1 0.02
56 21 0.47
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (56 bp):
TTTTTTTCATACATAACTTTATCAAAATATCTTTTATATCTTCGAAAACAATTACT
Found at i:87904 original size:33 final size:33
Alignment explanation
Indices: 87862--87953 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
87852 TAATGGAAAC
*
87862 AACAATTGACTCTGGAATCAAAGATTCCATGGA
1 AACAATTGACCCTGGAATCAAAGATTCCATGGA
* *
87895 AACAATTGACCCTGCAATCAAAGATTCGATGGA
1 AACAATTGACCCTGGAATCAAAGATTCCATGGA
87928 AACAATTGACCCTGCG-ATCAAAGATT
1 AACAATTGACCCTG-GAATCAAAGATT
87954 TAAGTGAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (33 bp):
AACAATTGACCCTGGAATCAAAGATTCCATGGA
Found at i:87975 original size:24 final size:24
Alignment explanation
Indices: 87943--88000 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
87933 TTGACCCTGC
*
87943 GATCAAAGATTTAA-GTGAATCTGG
1 GATCAAAGATTTAATG-GAAACTGG
87967 GATCAAAGATTTAATGGAAACTGG
1 GATCAAAGATTTAATGGAAACTGG
87991 GATCAAAGAT
1 GATCAAAGAT
88001 GCAATAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (24 bp):
GATCAAAGATTTAATGGAAACTGG
Found at i:88010 original size:24 final size:24
Alignment explanation
Indices: 87963--88011 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
87953 TTAAGTGAAT
** *
87963 CTGGGATCAAAGATTTAATGGAAA
1 CTGGGATCAAAGATGCAATAGAAA
87987 CTGGGATCAAAGATGCAATAGAAA
1 CTGGGATCAAAGATGCAATAGAAA
88011 C
1 C
88012 AATTGAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (24 bp):
CTGGGATCAAAGATGCAATAGAAA
Found at i:88141 original size:24 final size:24
Alignment explanation
Indices: 88114--88162 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
88104 TTCCCGAGCG
88114 TAAGCCTCCTATTTCCGGGTCAAT
1 TAAGCCTCCTATTTCCGGGTCAAT
*
88138 TAAGCCTCCTATTTCCTGGTCAAT
1 TAAGCCTCCTATTTCCGGGTCAAT
88162 T
1 T
88163 TCCGAGCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (24 bp):
TAAGCCTCCTATTTCCGGGTCAAT
Found at i:88968 original size:31 final size:31
Alignment explanation
Indices: 88930--88991 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
88920 ATTTGTTAAT
88930 TTTGAATTTTGGATATTAAACTTTCTGAGTG
1 TTTGAATTTTGGATATTAAACTTTCTGAGTG
88961 TTTGAATTTTGGATATTAAACTTTCTGAGTG
1 TTTGAATTTTGGATATTAAACTTTCTGAGTG
88992 ATGTTGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (31 bp):
TTTGAATTTTGGATATTAAACTTTCTGAGTG
Found at i:89005 original size:26 final size:29
Alignment explanation
Indices: 88931--89005 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
88921 TTTGTTAATT
*
88931 TTGAATTTTGGATATTAAACTTTCTGAGTG
1 TTGAATGTTGGATATTAAACTTTCTGAG-G
*
88961 TTTGAATTTTGGATATTAAACTTTCTGA-G
1 -TTGAATGTTGGATATTAAACTTTCTGAGG
88990 -TG-ATGTTGGATATTAA
1 TTGAATGTTGGATATTAA
89006 GTGTTTTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 13 0.30
27 2 0.05
29 1 0.02
31 27 0.63
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (29 bp):
TTGAATGTTGGATATTAAACTTTCTGAGG
Found at i:99325 original size:45 final size:44
Alignment explanation
Indices: 99269--99357 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
99259 GAGTCTGATG
99269 AAAAAGCAATTGAAGATGCTCTAAAAGTGAAAAG-GGAGATGGAAC
1 AAAAAGCAATTGAAGATGCTCTAAAAGT--AAAGTGGAGATGGAAC
* *
99314 AAAAGGCAATTGAAGATGCTCTGAAAGTAAAGTTGGAGATGGAA
1 AAAAAGCAATTGAAGATGCTCTAAAAGTAAAG-TGGAGATGGAA
99358 GCTAATTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 4 0.10
45 36 0.90
ACGTcount: A:0.46, C:0.08, G:0.28, T:0.18
Consensus pattern (44 bp):
AAAAAGCAATTGAAGATGCTCTAAAAGTAAAGTGGAGATGGAAC
Found at i:116676 original size:18 final size:18
Alignment explanation
Indices: 116653--116687 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
116643 ATATACATTT
116653 TTCATCCAA-ATTTTCGAA
1 TTCAT-CAATATTTTCGAA
116671 TTCATCAATATTTTCGA
1 TTCATCAATATTTTCGA
116688 TCCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (18 bp):
TTCATCAATATTTTCGAA
Done.