Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2326
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: 24028
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Found at i:6213 original size:26 final size:26
Alignment explanation
Indices: 6175--6249 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
6165 CAACACACCA
*
6175 ATATCGCAGCAAAGCTGCCAGTAAAC
1 ATATCGCAACAAAGCTGCCAGTAAAC
6201 ATATCGCAACAAAGCTGCCAGT-AAC
1 ATATCGCAACAAAGCTGCCAGTAAAC
* *
6226 AGTAACACAA-ACAAGCTGCCAGTA
1 A-TATCGCAACA-AAGCTGCCAGTA
6250 TCAGTATATG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.12
26 38 0.88
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (26 bp):
ATATCGCAACAAAGCTGCCAGTAAAC
Found at i:12284 original size:43 final size:43
Alignment explanation
Indices: 12236--12358 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
12226 ATCACATGTA
*
12236 TCGCATCCATTACGAACTCGGACCACTCAACGAGTTCGAATGC
1 TCGCATCCATAACGAACTCGGACCACTCAACGAGTTCGAATGC
* * * *
12279 TCGCATCCATAATGAACTTGGACCACTCAACGAGCTCGGATGC
1 TCGCATCCATAACGAACTCGGACCACTCAACGAGTTCGAATGC
* ** * *
12322 -CACATATATCACGAACTCAGACCACTCAACGAGTTCG
1 TCGCATCCATAACGAACTCGGACCACTCAACGAGTTCG
12359 GACTTCTTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 29 0.43
43 38 0.57
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
TCGCATCCATAACGAACTCGGACCACTCAACGAGTTCGAATGC
Found at i:12350 original size:42 final size:43
Alignment explanation
Indices: 12247--12360 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 43
12237 CGCATCCATT
* * *
12247 ACGAACTCGGACCACTCAACGAGTTCGAATGCTCGCATCCATA
1 ACGAACTCGGACCACTCAACGAGTTCGGATGCTCACATACATA
* * * * *
12290 ATGAACTTGGACCACTCAACGAGCTCGGATGC-CACATATATC
1 ACGAACTCGGACCACTCAACGAGTTCGGATGCTCACATACATA
*
12332 ACGAACTCAGACCACTCAACGAGTTCGGA
1 ACGAACTCGGACCACTCAACGAGTTCGGA
12361 CTTCTTAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 31 0.53
43 28 0.47
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (43 bp):
ACGAACTCGGACCACTCAACGAGTTCGGATGCTCACATACATA
Found at i:16313 original size:86 final size:85
Alignment explanation
Indices: 16160--16317 Score: 203
Period size: 86 Copynumber: 1.8 Consensus size: 85
16150 AGCTTGTTCA
** * *
16160 ATGCCAACGTCCCAGACGTGGTCTTACATATAACCACATATCGATGCCACTATCCCAGACAGGGT
1 ATGCCAACGTCCCAGACACGATCTTACATATAACCACAAATCGATGCCACTATCCCAGACAGGGT
16225 CTTACACAAACTCATATATG
66 CTTACACAAACTCATATATG
* * * *
16245 ATGCCAATGTCCCAGACACGATCTTACATGTAAATCACAAATCGATGCCAAC-GTCCCAGAC-GT
1 ATGCCAACGTCCCAGACACGATCTTACATAT-AACCACAAATCGATGCC-ACTATCCCAGACAG-
16308 GGTCTTACAC
63 GGTCTTACAC
16318 GAAATCACAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
85 27 0.44
86 33 0.53
87 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACACGATCTTACATATAACCACAAATCGATGCCACTATCCCAGACAGGGT
CTTACACAAACTCATATATG
Found at i:16985 original size:13 final size:13
Alignment explanation
Indices: 16967--16991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16957 ACAAACAATA
16967 AAATTTTCACACG
1 AAATTTTCACACG
16980 AAATTTTCACAC
1 AAATTTTCACAC
16992 ATATCAATTT
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:22868 original size:11 final size:11
Alignment explanation
Indices: 22820--22874 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
22810 AATCATCATC
22820 ATAAAAAAAA-
1 ATAAAAAAAAT
*
22830 A-AAAAAAAAA
1 ATAAAAAAAAT
*
22840 ATCAAAAAAAT
1 ATAAAAAAAAT
*
22851 TTAAAAAAAAAT
1 AT-AAAAAAAAT
*
22863 ATAAAACAAAT
1 ATAAAAAAAAT
22874 A
1 A
22875 ACAAATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
9 8 0.22
10 2 0.06
11 17 0.47
12 9 0.25
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:22895 original size:16 final size:17
Alignment explanation
Indices: 22859--22900 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
22849 ATTTAAAAAA
22859 AAATATAAAACAAATAAC
1 AAATAT-AAACAAATAAC
*
22877 AAATATAAACATA-AAC
1 AAATATAAACAAATAAC
*
22893 AAAAATAA
1 AAATATAA
22901 CATCACAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 6 0.27
18 6 0.27
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATATAAACAAATAAC
Found at i:22898 original size:18 final size:17
Alignment explanation
Indices: 22852--22899 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
22842 CAAAAAAATT
22852 TAAAAAAAAATATAAAA
1 TAAAAAAAAATATAAAA
* *
22869 CAAATAACAAATATAAACA
1 TAAA-AAAAAATATAAA-A
*
22888 TAAACAAAAATA
1 TAAAAAAAAATA
22900 ACATCACAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 17 0.71
19 4 0.17
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAAAAAAAATATAAAA
Done.