Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3246
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: 46115
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5479 original size:40 final size:40
Alignment explanation
Indices: 5405--5626 Score: 340
Period size: 40 Copynumber: 5.6 Consensus size: 40
5395 AACCCAAGTT
* *
5405 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
5444 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
5484 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
5524 CCTTCGGGACTTAGCCCGTATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* * *
5564 CTTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
5604 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
5627 CATTCGAATA
Statistics
Matches: 166, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 12 0.07
40 151 0.91
41 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:14247 original size:16 final size:16
Alignment explanation
Indices: 14205--14247 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
14195 GTAGATCGGC
*
14205 AAAAGCTGAAATACAG
1 AAAAGCAGAAATACAG
* *
14221 AAAACCCGAAATACAG
1 AAAAGCAGAAATACAG
14237 AAAAGCAGAAA
1 AAAAGCAGAAA
14248 GTTTTGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAGCAGAAATACAG
Found at i:14514 original size:29 final size:29
Alignment explanation
Indices: 14461--14574 Score: 112
Period size: 28 Copynumber: 4.1 Consensus size: 29
14451 AGCATGACTG
*
14461 TAAATGTGATTGGGGCCT-A-GCGGCCATA
1 TAAATGTGATTTGGGCCTAATG-GGCCATA
* *
14489 TGAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
*
14518 TAAATGTGA-TTGGGCTTAATGGGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
* * * *
14546 TAAAAG-G-GTAGGGCCTAGTGGGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
14573 TA
1 TA
14575 CAGGTATGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
27 19 0.26
28 38 0.52
29 15 0.21
30 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
TAAATGTGATTTGGGCCTAATGGGCCATA
Found at i:17329 original size:27 final size:26
Alignment explanation
Indices: 17299--17356 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
17289 ATTTACTAAA
* *
17299 ATACTCCTAAGTATGAAAATTACCATT
1 ATACCCCTAAGTAT-AAAATGACCATT
* *
17326 ATACCCCTAGGTGTAAAATGACCATT
1 ATACCCCTAAGTATAAAATGACCATT
*
17352 TTACC
1 ATACC
17357 TCTAGGGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (26 bp):
ATACCCCTAAGTATAAAATGACCATT
Found at i:17498 original size:27 final size:27
Alignment explanation
Indices: 17464--17578 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
17454 TGGAGGAAGC
*
17464 GTTCTGGTGGCTATGCCACAAATATTT
1 GTTCTGGTGGCTATGCCACAAATATCT
* *
17491 GTTTTGGTGGCTATGCCACAATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
17518 GTTCTGGTGGCTCA-GCCAC-AATATCT
1 GTTCTGGTGGCT-ATGCCACAAATATCT
* ** * *
17544 CTATCTGGTAACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTATGCCACAAATATCT
17571 GTTCTGGT
1 GTTCTGGT
17579 AGCCATGTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 13 0.18
27 60 0.81
28 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (27 bp):
GTTCTGGTGGCTATGCCACAAATATCT
Found at i:25031 original size:27 final size:26
Alignment explanation
Indices: 25001--25114 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
24991 TGGAGGAAGC
25001 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
* *
25028 GTTCTAGTGGCTATGCCACAATTATAT
1 GTTCTGGTGGCTATGCCACAA-TATCT
25055 GTTCTGGTGGCTCA-GCCACAATATCT
1 GTTCTGGTGGCT-ATGCCACAATATCT
* * *
25081 GTATCTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
25108 GTTCTGG
1 GTTCTGG
25115 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
26 13 0.17
27 62 0.82
28 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:40186 original size:18 final size:19
Alignment explanation
Indices: 40148--40186 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40138 AGCTATGTGT
*
40148 TTATACGAATGAGTTACTG
1 TTATACGAATGAATTACTG
*
40167 TTAT-CGAATGAATTATTG
1 TTATACGAATGAATTACTG
40185 TT
1 TT
40187 CATGTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (19 bp):
TTATACGAATGAATTACTG
Found at i:40921 original size:19 final size:19
Alignment explanation
Indices: 40897--40935 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40887 GGGCGTGTGT
40897 CTCAGTCATGTGTGACATA
1 CTCAGTCATGTGTGACATA
40916 CTCAGTCATGTGTGACATA
1 CTCAGTCATGTGTGACATA
40935 C
1 C
40936 GGTCACGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
CTCAGTCATGTGTGACATA
Done.