Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1689
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: 39520
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Found at i:2114 original size:29 final size:29
Alignment explanation
Indices: 2077--2132 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2067 AGCGAGAGAT
2077 GCATCAAATGAATACTAAATATGAAGAAG
1 GCATCAAATGAATACTAAATATGAAGAAG
* * *
2106 GCATGAAATGGATACTGAATATGAAGA
1 GCATCAAATGAATACTAAATATGAAGA
2133 GGGATGCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (29 bp):
GCATCAAATGAATACTAAATATGAAGAAG
Found at i:12737 original size:29 final size:29
Alignment explanation
Indices: 12700--12755 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12690 AGCGAGAGAT
12700 GCATCAAATGAATACTAAATATGAAGAAG
1 GCATCAAATGAATACTAAATATGAAGAAG
* * *
12729 GCATGAAATGGATACTGAATATGAAGA
1 GCATCAAATGAATACTAAATATGAAGA
12756 GGGATGCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (29 bp):
GCATCAAATGAATACTAAATATGAAGAAG
Found at i:15857 original size:21 final size:21
Alignment explanation
Indices: 15831--15871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15821 ATCTGCTCAA
* *
15831 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
15852 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
15872 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:19812 original size:17 final size:17
Alignment explanation
Indices: 19790--19840 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
19780 GACTAATCCC
*
19790 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
*
19807 TATACATTACCTAGGTA
1 TATACATTACTTAGGTA
*
19824 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
19841 CATGCCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:20625 original size:41 final size:40
Alignment explanation
Indices: 20518--20628 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 40
20508 TCGGATAGTT
* *
20518 CGAAGCAATAGTTGACACCCAGTGTCTCATCG-GCCAAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
** ** * * *
20557 CGAAGT-A-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
20595 CGAAGTAATAGTATGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT-TGACACCCAGTGTCTCATCGA
20629 CTCAAGGTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.35
38 10 0.18
39 6 0.11
40 3 0.05
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
Found at i:22023 original size:17 final size:17
Alignment explanation
Indices: 22001--22070 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
21991 CTTCCTTCCT
22001 TCTCTGTTTCGTTTTGC
1 TCTCTGTTTCGTTTTGC
* *
22018 TCTCTGTTTCTTTCTTTTCCC
1 TCTCTGTTTC---GTTTT-GC
*
22039 TTCTCTGTTTTGTTTTGC
1 -TCTCTGTTTCGTTTTGC
22057 TCTCTGTTTC-TTTT
1 TCTCTGTTTCGTTTT
22071 CTTTCTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.10
17 19 0.45
18 1 0.02
19 4 0.10
20 4 0.10
21 1 0.02
22 9 0.21
ACGTcount: A:0.00, C:0.24, G:0.11, T:0.64
Consensus pattern (17 bp):
TCTCTGTTTCGTTTTGC
Found at i:22054 original size:39 final size:40
Alignment explanation
Indices: 21998--22074 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
21988 TTCCTTCCTT
21998 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTC-TTTCTTTTC
1 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTTC
*
22037 CCTTCTCTGTTTTGTTTTGCTCTCTGTTTCTTTTCTTT
1 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTT
22075 CTTTCTTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.00, C:0.26, G:0.10, T:0.64
Consensus pattern (40 bp):
CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTTC
Found at i:22102 original size:3 final size:3
Alignment explanation
Indices: 22094--22144 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
22084 TCATATATAT
*
22094 ATA ATA AT- ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22137 AT- ATA ATA
1 ATA ATA ATA
22145 TAAACATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
2 12 0.30
3 28 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:22105 original size:8 final size:8
Alignment explanation
Indices: 22092--22147 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
22082 TGTCATATAT
22092 ATATAATA
1 ATATAATA
22100 ATATAATA
1 ATATAATA
22108 ATATAATATA
1 ATAT-A-ATA
22118 ATATAAT-
1 ATATAATA
22125 ATATTAATA
1 ATA-TAATA
22134 ATA-ATATA
1 ATATA-ATA
22142 ATATAA
1 ATATAA
22148 ACATAATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
7 4 0.10
8 25 0.60
9 6 0.14
10 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:22107 original size:5 final size:5
Alignment explanation
Indices: 22086--22147 Score: 67
Period size: 5 Copynumber: 12.2 Consensus size: 5
22076 TTTCTTTGTC
22086 ATATA TATATA ATA-A TATAATA ATATA ATATA ATATA ATAT- AT-TA
1 ATATA -ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA ATATA
22131 ATAATA ATATA ATATA A
1 AT-ATA ATATA ATATA A
22148 ACATAATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
3 1 0.02
4 5 0.10
5 31 0.62
6 12 0.24
7 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:22158 original size:29 final size:29
Alignment explanation
Indices: 22102--22159 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
22092 ATATAATAAT
*
22102 ATAATAATATAATATAATATAATATATTA
1 ATAATAATATAATATAACATAATATATTA
22131 ATAATAATATAATATAAACATAAT-TATTA
1 ATAATAATATAATAT-AACATAATATATTA
22160 CTTACGCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAATAATATAATATAACATAATATATTA
Found at i:23729 original size:24 final size:24
Alignment explanation
Indices: 23702--23776 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
23692 AAACTATACT
* *
23702 GAATTTCCGAGAGAAAATCCAAAA
1 GAATATCCCAGAGAAAATCCAAAA
*
23726 GAATATCCCAGAGAAAGTCCAAAA
1 GAATATCCCAGAGAAAATCCAAAA
*
23750 GAATATCCCAGAGAAAATCCACAA
1 GAATATCCCAGAGAAAATCCAAAA
23774 GAA
1 GAA
23777 GAATATCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (24 bp):
GAATATCCCAGAGAAAATCCAAAA
Found at i:23733 original size:12 final size:12
Alignment explanation
Indices: 23713--23776 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
23703 AATTTCCGAG
23713 AGAAAATCCAAA
1 AGAAAATCCAAA
* * *
23725 AGAATATCCCAG
1 AGAAAATCCAAA
*
23737 AGAAAGTCCAAA
1 AGAAAATCCAAA
* * *
23749 AGAATATCCCAG
1 AGAAAATCCAAA
*
23761 AGAAAATCCACA
1 AGAAAATCCAAA
23773 AGAA
1 AGAA
23777 GAATATCACT
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.55, C:0.20, G:0.14, T:0.11
Consensus pattern (12 bp):
AGAAAATCCAAA
Found at i:24089 original size:13 final size:13
Alignment explanation
Indices: 24071--24098 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24061 GATAAAAGAG
24071 CATATAGAATACC
1 CATATAGAATACC
24084 CATATAGAATACC
1 CATATAGAATACC
24097 CA
1 CA
24099 GAAGAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:25049 original size:22 final size:22
Alignment explanation
Indices: 25018--25063 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
25008 TATGCACTAT
*
25018 TAAACAGAGAGCACAAATGTGC
1 TAAACAGAGAGCACAAACGTGC
* *
25040 TAAACGGAGAGCACTAACGTGC
1 TAAACAGAGAGCACAAACGTGC
25062 TA
1 TA
25064 GTGATCAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (22 bp):
TAAACAGAGAGCACAAACGTGC
Found at i:25104 original size:25 final size:24
Alignment explanation
Indices: 25076--25169 Score: 102
Period size: 25 Copynumber: 3.9 Consensus size: 24
25066 GATCAGAGAG
25076 CGTGCTAATATTCAGAGAGCACTGA
1 CGTGCTAA-ATTCAGAGAGCACTGA
**
25101 CGTGCTAAATATCAGAGAGCACCAA
1 CGTGCTAAAT-TCAGAGAGCACTGA
*
25126 TGTGCTAAA--CAGAGAGCACTGA
1 CGTGCTAAATTCAGAGAGCACTGA
* *
25148 TGTGCTAATAATCAGAGAGCAC
1 CGTGCTAA-ATTCAGAGAGCAC
25170 GCTAAACTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
22 19 0.32
23 1 0.02
24 2 0.03
25 38 0.63
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (24 bp):
CGTGCTAAATTCAGAGAGCACTGA
Found at i:25153 original size:47 final size:47
Alignment explanation
Indices: 25022--25169 Score: 157
Period size: 47 Copynumber: 3.2 Consensus size: 47
25012 CACTATTAAA
* * * * *
25022 CAGAGAGCACAAATGTGCTAAACGGAGAGCACTAACGTGCTAGTGAT
1 CAGAGAGCACCAATGTGCTAAACAGAGAGCACTGACGTGCTAATAAT
25069 CAGAGAG---C---GTGCTAATATTCAGAGAGCACTGACGTGCTAA-ATAT
1 CAGAGAGCACCAATGTGCTAA-A--CAGAGAGCACTGACGTGCTAATA-AT
*
25113 CAGAGAGCACCAATGTGCTAAACAGAGAGCACTGATGTGCTAATAAT
1 CAGAGAGCACCAATGTGCTAAACAGAGAGCACTGACGTGCTAATAAT
25160 CAGAGAGCAC
1 CAGAGAGCAC
25170 GCTAAACTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
41 7 0.08
42 1 0.01
44 27 0.32
47 40 0.48
48 1 0.01
49 1 0.01
50 7 0.08
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (47 bp):
CAGAGAGCACCAATGTGCTAAACAGAGAGCACTGACGTGCTAATAAT
Found at i:26490 original size:17 final size:17
Alignment explanation
Indices: 26468--26518 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
26458 GACTAATCCC
*
26468 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
*
26485 TATACATTACCTAGGTA
1 TATACATTACTTAGGTA
*
26502 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
26519 CATGCCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:27301 original size:41 final size:40
Alignment explanation
Indices: 27194--27304 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 40
27184 TCGGATAGTT
* *
27194 CGAAGCAATAGTTGACACCCAGTGTCTCATCG-GCCAAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
** ** * * *
27233 CGAAGT-A-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
27271 CGAAGTAATAGTATGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT-TGACACCCAGTGTCTCATCGA
27305 CTCAAGGTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.35
38 10 0.18
39 6 0.11
40 3 0.05
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
Found at i:28699 original size:17 final size:17
Alignment explanation
Indices: 28677--28746 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
28667 CTTCCTTCCT
28677 TCTCTGTTTCGTTTTGC
1 TCTCTGTTTCGTTTTGC
* *
28694 TCTCTGTTTCTTTCTTTTCCC
1 TCTCTGTTTC---GTTTT-GC
*
28715 TTCTCTGTTTTGTTTTGC
1 -TCTCTGTTTCGTTTTGC
28733 TCTCTGTTTC-TTTT
1 TCTCTGTTTCGTTTT
28747 CTTTCTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.10
17 19 0.45
18 1 0.02
19 4 0.10
20 4 0.10
21 1 0.02
22 9 0.21
ACGTcount: A:0.00, C:0.24, G:0.11, T:0.64
Consensus pattern (17 bp):
TCTCTGTTTCGTTTTGC
Found at i:28730 original size:39 final size:40
Alignment explanation
Indices: 28674--28750 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
28664 TTCCTTCCTT
28674 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTC-TTTCTTTTC
1 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTTC
*
28713 CCTTCTCTGTTTTGTTTTGCTCTCTGTTTCTTTTCTTT
1 CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTT
28751 CTTTCTTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.00, C:0.26, G:0.10, T:0.64
Consensus pattern (40 bp):
CCTTCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTTC
Found at i:28778 original size:5 final size:5
Alignment explanation
Indices: 28762--28819 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
28752 TTTCTTTGTC
28762 ATATA TATATA ATATA ATAATA TATATA ATATA ATAT- AT-TA ATAATA
1 ATATA -ATATA ATATA AT-ATA -ATATA ATATA ATATA ATATA AT-ATA
28809 ATATA ATATA A
1 ATATA ATATA A
28820 AAACATAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 25 0.53
6 15 0.32
7 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:28786 original size:19 final size:18
Alignment explanation
Indices: 28762--28818 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 18
28752 TTTCTTTGTC
28762 ATATATATATAATATAAT
1 ATATATATATAATATAAT
28780 A-ATATATATAATATAAT
1 ATATATATATAATATAAT
28797 ATAT-TAATAATAATATAAT
1 ATATAT-AT-ATAATATAAT
28816 ATA
1 ATA
28819 AAAACATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 18 0.50
18 5 0.14
19 13 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATATATAATATAAT
Found at i:37589 original size:29 final size:29
Alignment explanation
Indices: 37552--37607 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
37542 AGCGAGAGAT
37552 GCATCAAATGAATACTAAATATGAAGAAG
1 GCATCAAATGAATACTAAATATGAAGAAG
* * *
37581 GCATGAAATGGATACTGAATATGAAGA
1 GCATCAAATGAATACTAAATATGAAGA
37608 GGGATGCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (29 bp):
GCATCAAATGAATACTAAATATGAAGAAG
Done.