Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012118.1 Corchorus capsularis cultivar CVL-1 contig12139, 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: 105140
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6981 original size:39 final size:40
Alignment explanation
Indices: 6925--7002 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
6915 TTATAACTAT
* *
6925 GGGCTAAACCTGGATTTAATTTCTTACCTTAATGATTAGG
1 GGGCTAAACCTGAATTTAATTTATTACCTTAATGATTAGG
* *
6965 GGGCT-AACCTGAATTTAATTTATTTCCTTAATTATTAG
1 GGGCTAAACCTGAATTTAATTTATTACCTTAATGATTAG
7003 AATGGTCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (40 bp):
GGGCTAAACCTGAATTTAATTTATTACCTTAATGATTAGG
Found at i:8147 original size:18 final size:19
Alignment explanation
Indices: 8121--8161 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
8111 GTACAATTCT
8121 TATTATTTTTTTT-AGAAC
1 TATTATTTTTTTTGAGAAC
*
8139 TATTTTTTTTTTTGAGAAC
1 TATTATTTTTTTTGAGAAC
8158 TATT
1 TATT
8162 CTTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (19 bp):
TATTATTTTTTTTGAGAAC
Found at i:8205 original size:2 final size:2
Alignment explanation
Indices: 8198--8230 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8188 AGAAGGCTAG
8198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8231 ATTATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9691 original size:3 final size:3
Alignment explanation
Indices: 9679--9726 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
9669 CTTTAGGTAG
9679 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9726 T
1 T
9727 TCGAAAAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:15088 original size:12 final size:12
Alignment explanation
Indices: 15071--15099 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
15061 GTTACATATT
15071 GAAATATTTATG
1 GAAATATTTATG
15083 GAAATATTTATG
1 GAAATATTTATG
15095 GAAAT
1 GAAAT
15100 GAATGCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (12 bp):
GAAATATTTATG
Found at i:16988 original size:16 final size:16
Alignment explanation
Indices: 16967--17048 Score: 96
Period size: 16 Copynumber: 5.2 Consensus size: 16
16957 TTTAGGTCAT
16967 GTTAATTCGGGTTCGG
1 GTTAATTCGGGTTCGG
* *
16983 GTTAATTTGGG-TCAG
1 GTTAATTCGGGTTCGG
16998 GTTAATTCGGGTTCGG
1 GTTAATTCGGGTTCGG
* *
17014 GTTAAATTTGGG-TCAG
1 GTT-AATTCGGGTTCGG
*
17030 GTTAATTCGAGTTCGG
1 GTTAATTCGGGTTCGG
17046 GTT
1 GTT
17049 CTGTTTGGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
15 19 0.35
16 28 0.52
17 7 0.13
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.39
Consensus pattern (16 bp):
GTTAATTCGGGTTCGG
Found at i:17002 original size:31 final size:32
Alignment explanation
Indices: 16941--17048 Score: 164
Period size: 32 Copynumber: 3.4 Consensus size: 32
16931 CGAGATTGAG
** * *
16941 TCGGGTTCGGGTTGGATTTAGGTCATGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
16973 TCGGGTTCGGGTT-AATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
17004 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
*
17036 TCGAGTTCGGGTT
1 TCGGGTTCGGGTT
17049 CTGTTTGGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 28 0.39
32 43 0.61
ACGTcount: A:0.16, C:0.10, G:0.35, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAATTTGGGTCAGGTTAAT
Found at i:17215 original size:15 final size:15
Alignment explanation
Indices: 17197--17321 Score: 108
Period size: 16 Copynumber: 8.1 Consensus size: 15
17187 TTTTCATAAA
*
17197 TTTTCGGATTCGGGT
1 TTTTCGGGTTCGGGT
*
17212 TTTTCGGG-TCTGAGCT
1 TTTTCGGGTTC-G-GGT
17228 TTTTCGGGTTCGGGT
1 TTTTCGGGTTCGGGT
* *
17243 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCG-GGT
*
17259 TTTTCGGGTTCGTGTT
1 TTTTCGGGTTCG-GGT
** *
17275 TTTTCGGGTTTAAGCT
1 TTTTCGGG-TTCGGGT
*
17291 TTTTCGAGTTCGGGT
1 TTTTCGGGTTCGGGT
*
17306 TTTTCGGGTTCAGGT
1 TTTTCGGGTTCGGGT
17321 T
1 T
17322 CAGGCGGGTT
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
14 2 0.02
15 39 0.44
16 43 0.49
17 4 0.05
ACGTcount: A:0.06, C:0.14, G:0.32, T:0.49
Consensus pattern (15 bp):
TTTTCGGGTTCGGGT
Found at i:17240 original size:31 final size:31
Alignment explanation
Indices: 17197--17315 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
17187 TTTTCATAAA
* *
17197 TTTTCGGATTCGGGTTTTTCGGGTCTGAGCT
1 TTTTCGGGTTCGGGTTTTTCGGGTTTGAGCT
17228 TTTTCGGGTTCGGGTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTCGGGTTTGAGCT
* *
17259 TTTTCGGGTTCGTGTTTTTTCGGGTTTAAGCT
1 TTTTCGGGTTCG-GGTTTTTCGGGTTTGAGCT
*
17291 TTTTCGAGTTCGGGTTTTTCGGGTT
1 TTTTCGGGTTCGGGTTTTTCGGGTT
17316 CAGGTTCAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 53 0.65
32 28 0.35
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (31 bp):
TTTTCGGGTTCGGGTTTTTCGGGTTTGAGCT
Found at i:17295 original size:63 final size:62
Alignment explanation
Indices: 17197--17315 Score: 184
Period size: 63 Copynumber: 1.9 Consensus size: 62
17187 TTTTCATAAA
* *
17197 TTTTCGGATTCGGGTTTTTCGGGTCTGAGCTTTTTCGGGTTCGGGTTTTTCGGGTTTGAGCT
1 TTTTCGGATTCGGGTTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTTTGAGCT
* * *
17259 TTTTCGGGTTCGTGTTTTTTCGGGTTTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTT
1 TTTTCGGATTCG-GGTTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTT
17316 CAGGTTCAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 11 0.22
63 40 0.78
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (62 bp):
TTTTCGGATTCGGGTTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTTTGAGCT
Found at i:17330 original size:63 final size:63
Alignment explanation
Indices: 17211--17333 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
17201 CGGATTCGGG
* * * ***
17211 TTTTTCGGGTCTGAGCTTTTTCGGGTTCGGGTTTTTCGGGTTTGAGCTTTTTCGGGTTCGTGT
1 TTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTTTCAGCTTAGGCGGGTTCGTGT
* *
17274 TTTTTCGGGTTTAAGCTTTTTCGAGTTCGGGTTTTTCGGG-TTCAGGTTCAGGCGGGTTCG
1 TTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTTTCAGCTT-AGGCGGGTTCG
17334 AATATTTGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 6 0.12
63 45 0.88
ACGTcount: A:0.06, C:0.15, G:0.33, T:0.46
Consensus pattern (63 bp):
TTTTTCGGGTCTAAGCTTTTTCGAGTTCGGGTTTTTCGGGTTTCAGCTTAGGCGGGTTCGTGT
Found at i:17890 original size:2 final size:2
Alignment explanation
Indices: 17883--17908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17873 GTTGTCAAAA
17883 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
17909 TAATTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18155 original size:131 final size:131
Alignment explanation
Indices: 17921--18160 Score: 435
Period size: 131 Copynumber: 1.8 Consensus size: 131
17911 ATTTTCTTAC
*
17921 ATTTCCGGAGTTCTCGGCCTATTCTACGTTTTTAATAACTTCAACCTTTCAGAGGATTTGAAATT
1 ATTTCCGGAGTTCTCGGCCTATTCTACGTTTGTAATAACTTCAACCTTTCAGAGGATTTGAAATT
*
17986 TTAGAAAATAAAGCAAAGGGCAAAAGTGTCAAAAGTGTAAAAAAAAAATACGACACGTTATCGTC
66 TTAGAAAATAAAGCAAAGGGCAAAAATGTCAAAAGTGTAAAAAAAAAATACGACACGTTATCGTC
18051 T
131 T
* *
18052 ATTTCCGGAGTTCTCGGCTTATTCTACGTTTGTAATAACTTCAACCTTTTAGAGGATTTGAAATT
1 ATTTCCGGAGTTCTCGGCCTATTCTACGTTTGTAATAACTTCAACCTTTCAGAGGATTTGAAATT
*
18117 TTAGAAAATAAAGCAAATGGCAAAAATGTCAAAAGTGTAAAAAA
66 TTAGAAAATAAAGCAAAGGGCAAAAATGTCAAAAGTGTAAAAAA
18161 TGGGATGGTG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 104 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (131 bp):
ATTTCCGGAGTTCTCGGCCTATTCTACGTTTGTAATAACTTCAACCTTTCAGAGGATTTGAAATT
TTAGAAAATAAAGCAAAGGGCAAAAATGTCAAAAGTGTAAAAAAAAAATACGACACGTTATCGTC
T
Found at i:26368 original size:21 final size:21
Alignment explanation
Indices: 26340--26379 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
26330 AACTGGTACG
*
26340 TACAAATTAATTA-GAAATCC
1 TACAAATTAAGTATGAAATCC
26360 TACATAATTAAGTATGAAAT
1 TACA-AATTAAGTATGAAAT
26380 ATGCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (21 bp):
TACAAATTAAGTATGAAATCC
Found at i:32058 original size:12 final size:12
Alignment explanation
Indices: 32041--32066 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32031 AGGGTTAGAA
32041 AAAAATTCAAGT
1 AAAAATTCAAGT
32053 AAAAATTCAAGT
1 AAAAATTCAAGT
32065 AA
1 AA
32067 TAAACACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAATTCAAGT
Found at i:34669 original size:4 final size:4
Alignment explanation
Indices: 34660--34686 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
34650 GATATATGAT
34660 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
34687 TTGCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:46036 original size:21 final size:21
Alignment explanation
Indices: 46003--46042 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
45993 AAGCGGAGAA
46003 AACAGGAAGGAAAAAGAAAAG
1 AACAGGAAGGAAAAAGAAAAG
46024 AACAGTGAA-GAAAAAGAAA
1 AACAG-GAAGGAAAAAGAAA
46043 GAAGAGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.03
Consensus pattern (21 bp):
AACAGGAAGGAAAAAGAAAAG
Found at i:50138 original size:17 final size:18
Alignment explanation
Indices: 50116--50150 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
50106 AAAAATGTAG
50116 GCCAT-AAACAGAAACAT
1 GCCATAAAACAGAAACAT
50133 GCCATAAAACAGAAACAT
1 GCCATAAAACAGAAACAT
50151 ACTTGATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.54, C:0.23, G:0.11, T:0.11
Consensus pattern (18 bp):
GCCATAAAACAGAAACAT
Found at i:59237 original size:32 final size:31
Alignment explanation
Indices: 59175--59332 Score: 129
Period size: 31 Copynumber: 5.1 Consensus size: 31
59165 ACGGTGTCCG
* * *
59175 ACATGGCATGCCACGTGTACCAAAAAGTGAC
1 ACATGTCACGCCACATGTACCAAAAAGTGAC
* *
59206 ATATGAT-ACGTCACATGTACCAAAAAAGTGAC
1 ACATG-TCACGCCACATGTACC-AAAAAGTGAC
*
59238 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACATGTCACGCCACATGTACCAAAAAGTGAC
* * * * **
59269 ACGTGGCATGCCACGTGTTTCAAAAAGTGAC
1 ACATGTCACGCCACATGTACCAAAAAGTGAC
* * * * **
59300 ACGTGACATGCCACACGTTTCAAAAAGTGAC
1 ACATGTCACGCCACATGTACCAAAAAGTGAC
59331 AC
1 AC
59333 GTGGTATGCC
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
31 82 0.76
32 26 0.24
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (31 bp):
ACATGTCACGCCACATGTACCAAAAAGTGAC
Found at i:59333 original size:31 final size:31
Alignment explanation
Indices: 59258--59344 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
59248 CCACGTGTAC
**
59258 CAAAAAGTGACACGTGGCATGCCACGTGTTT
1 CAAAAAGTGACACGTGGCATGCCACACGTTT
*
59289 CAAAAAGTGACACGTGACATGCCACACGTTT
1 CAAAAAGTGACACGTGGCATGCCACACGTTT
*
59320 CAAAAAGTGACACGTGGTATGCCAC
1 CAAAAAGTGACACGTGGCATGCCAC
59345 GTGCACAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (31 bp):
CAAAAAGTGACACGTGGCATGCCACACGTTT
Found at i:65680 original size:23 final size:23
Alignment explanation
Indices: 65653--65700 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
65643 ATCATCTTGA
* *
65653 ATGTTATATGCGAGGGAGTTTGT
1 ATGTTATATGCGAGAGAGTTCGT
*
65676 ATGTTATATGGGAGAGAGTTCGT
1 ATGTTATATGCGAGAGAGTTCGT
65699 AT
1 AT
65701 AATGTCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.04, G:0.33, T:0.38
Consensus pattern (23 bp):
ATGTTATATGCGAGAGAGTTCGT
Found at i:76975 original size:30 final size:30
Alignment explanation
Indices: 76941--77004 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
76931 CGTCAGCAGG
76941 TTCAGCAT-CTTCAGCCCCAT-GGACAGCACC
1 TTCAGC-TCCTTCAGCCCCATCGG-CAGCACC
* *
76971 TTCAGCTCCTTTAGCCCCTTCGGCAGCACC
1 TTCAGCTCCTTCAGCCCCATCGGCAGCACC
77001 TTCA
1 TTCA
77005 ACAGCCTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 27 0.90
31 2 0.07
ACGTcount: A:0.19, C:0.41, G:0.16, T:0.25
Consensus pattern (30 bp):
TTCAGCTCCTTCAGCCCCATCGGCAGCACC
Found at i:78015 original size:35 final size:35
Alignment explanation
Indices: 77966--78056 Score: 164
Period size: 35 Copynumber: 2.6 Consensus size: 35
77956 ACGAATAATC
* *
77966 CTTATCGAATGGCTGGTAGCGGCTAATCCGTTTAT
1 CTTATCGAACGGCTGATAGCGGCTAATCCGTTTAT
78001 CTTATCGAACGGCTGATAGCGGCTAATCCGTTTAT
1 CTTATCGAACGGCTGATAGCGGCTAATCCGTTTAT
78036 CTTATCGAACGGCTGATAGCG
1 CTTATCGAACGGCTGATAGCG
78057 TGAGTAATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (35 bp):
CTTATCGAACGGCTGATAGCGGCTAATCCGTTTAT
Found at i:78540 original size:18 final size:18
Alignment explanation
Indices: 78517--78553 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
78507 GTTTAAACAT
78517 CAGGTTCAACACCTTCAG
1 CAGGTTCAACACCTTCAG
* *
78535 CAGGTTCAGCCCCTTCAG
1 CAGGTTCAACACCTTCAG
78553 C
1 C
78554 CCCTTCGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (18 bp):
CAGGTTCAACACCTTCAG
Found at i:84780 original size:18 final size:18
Alignment explanation
Indices: 84757--84793 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
84747 GTTCAAACAT
84757 CAGGTTCAACACCTTCAG
1 CAGGTTCAACACCTTCAG
84775 CAGGTTCAACACCTTCAG
1 CAGGTTCAACACCTTCAG
84793 C
1 C
84794 CCCTTCGACA
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:0.35, G:0.16, T:0.22
Consensus pattern (18 bp):
CAGGTTCAACACCTTCAG
Found at i:88053 original size:72 final size:72
Alignment explanation
Indices: 87968--88117 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 72
87958 TGAAGGTCTT
* * *
87968 GGTTTGTGGGATTCTAGTTTTGATGC-AAAGTTTTCTGCTGAAGTCTTGAGGTTGTCAAAAATTG
1 GGTTTGTGGGATTCTAGTTTGGATGCGAAA-TTTTCTGCTGAAATCTTGAGATTGTCAAAAATTG
88032 A-CTTTGAA
65 ATC-TTGAA
* * *
88040 GGTTTGTGGGATTCTGGTTTGGATGCGAAATTTTCTGCTGAAATTTTTAGATTGTCAAAAATTGA
1 GGTTTGTGGGATTCTAGTTTGGATGCGAAATTTTCTGCTGAAATCTTGAGATTGTCAAAAATTGA
*
88105 TCTTGAT
66 TCTTGAA
88112 GGTTTG
1 GGTTTG
88118 CTTGCAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 65 0.94
73 4 0.06
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.42
Consensus pattern (72 bp):
GGTTTGTGGGATTCTAGTTTGGATGCGAAATTTTCTGCTGAAATCTTGAGATTGTCAAAAATTGA
TCTTGAA
Found at i:89534 original size:72 final size:72
Alignment explanation
Indices: 89435--89585 Score: 171
Period size: 72 Copynumber: 2.1 Consensus size: 72
89425 TGAAGATCTT
* * * * *
89435 GGTTTGTGGGATATTAGTTTTGATGCAAAGTTTTATGCT-AAAGTCTTGAGATTGTCAAAAATTG
1 GGTTTGTGCGATATTAGTTTGGATGCAAAATTTTATACTGAAA-TCTTGAAATTGTCAAAAATTG
89499 A-CTTTGAA
65 ATC-TTGAA
* * * * *
89507 GGTTTGTGCGATTTTGGTTTGGATGCAAAATTTTCTACTGAAATTTTTAAATTGTCAAAAATTGA
1 GGTTTGTGCGATATTAGTTTGGATGCAAAATTTTATACTGAAATCTTGAAATTGTCAAAAATTGA
*
89572 TCTTGAT
66 TCTTGAA
89579 GGTTTGT
1 GGTTTGT
89586 TTGCAAAAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
72 62 0.94
73 4 0.06
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (72 bp):
GGTTTGTGCGATATTAGTTTGGATGCAAAATTTTATACTGAAATCTTGAAATTGTCAAAAATTGA
TCTTGAA
Found at i:90438 original size:23 final size:23
Alignment explanation
Indices: 90408--90506 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 23
90398 CCTACATCTT
* *
90408 ATCTTTGCGCTTTTTTCTTTCCG
1 ATCTTTGCGCTTTTTTCTCTCCC
90431 ATCTTT--GCTTTTTTCTCTCCC
1 ATCTTTGCGCTTTTTTCTCTCCC
90452 ATC-TTGCG---TTTTCTCT-CC
1 ATCTTTGCGCTTTTTTCTCTCCC
*
90470 ATC-TTGCGTTTATTTTCTCTCCC
1 ATCTTTGCGCTT-TTTTCTCTCCC
90493 AT-TTTGC-CTTTTTT
1 ATCTTTGCGCTTTTTT
90507 GCCTTCCGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
18 10 0.15
19 8 0.12
20 2 0.03
21 20 0.31
22 11 0.17
23 14 0.22
ACGTcount: A:0.06, C:0.28, G:0.09, T:0.57
Consensus pattern (23 bp):
ATCTTTGCGCTTTTTTCTCTCCC
Found at i:90473 original size:18 final size:19
Alignment explanation
Indices: 90441--90480 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
90431 ATCTTTGCTT
90441 TTTTCTCTCCCATCTTGCG
1 TTTTCTCTCCCATCTTGCG
90460 TTTTCTCT-CCATCTTGCG
1 TTTTCTCTCCCATCTTGCG
90478 TTT
1 TTT
90481 ATTTTCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.05, C:0.33, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTTCTCTCCCATCTTGCG
Found at i:90631 original size:24 final size:24
Alignment explanation
Indices: 90599--90646 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
90589 GCTGCAATCC
*
90599 GCATCAAATTTACGTTTTTGCAAG
1 GCATCAAATTTACATTTTTGCAAG
90623 GCATCAAATTTACATTTTTGCAAG
1 GCATCAAATTTACATTTTTGCAAG
90647 TACGTCGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (24 bp):
GCATCAAATTTACATTTTTGCAAG
Done.