Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 27 of 27
Found at i:4028105 original size:15 final size:15
Alignment explanation
Indices: 4028085--4028130 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
4028075 GAATCCGTAC
4028085 AATGTATATATATAT
1 AATGTATATATATAT
4028100 AATGTATATATATAT
1 AATGTATATATATAT
*
4028115 -ATATATAATATATAT
1 AATGTAT-ATATATAT
4028130 A
1 A
4028131 GCCAACTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
AATGTATATATATAT
Found at i:4028115 original size:21 final size:21
Alignment explanation
Indices: 4028089--4028130 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4028079 CCGTACAATG
*
4028089 TATATATATATAATGTATATA
1 TATATATATATAATATATATA
4028110 TATATATATATAATATATATA
1 TATATATATATAATATATATA
4028131 GCCAACTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATATATATAATATATATA
Found at i:4029054 original size:2 final size:2
Alignment explanation
Indices: 4029047--4029072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4029037 ATTATAGATC
4029047 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
4029073 GAATAAAATA
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:4030077 original size:2 final size:2
Alignment explanation
Indices: 4030070--4030098 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4030060 AGTGTTAGTT
4030070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4030099 CTACGCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4034747 original size:2 final size:2
Alignment explanation
Indices: 4034736--4034779 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4034726 ATATCCTTAC
4034736 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4034777 TA T
1 TA T
4034780 GGGAATGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4039562 original size:19 final size:19
Alignment explanation
Indices: 4039538--4039577 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4039528 TGGATCCATC
4039538 ATCTATGCGGGTTCAGACT
1 ATCTATGCGGGTTCAGACT
4039557 ATCTATGCGGGTTCAGACT
1 ATCTATGCGGGTTCAGACT
4039576 AT
1 AT
4039578 AGACAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCTATGCGGGTTCAGACT
Found at i:4042494 original size:25 final size:25
Alignment explanation
Indices: 4042460--4042508 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4042450 TGTTTAAAAT
4042460 TAAAACTATCAGCAAATATCAAGGA
1 TAAAACTATCAGCAAATATCAAGGA
4042485 TAAAACTATCAGCAAATATCAAGG
1 TAAAACTATCAGCAAATATCAAGG
4042509 CAATACGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (25 bp):
TAAAACTATCAGCAAATATCAAGGA
Found at i:4045964 original size:17 final size:20
Alignment explanation
Indices: 4045921--4045967 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
4045911 ATAAATATAA
4045921 AAAATAATAATTTTTTGTTC
1 AAAATAATAATTTTTTGTTC
* *
4045941 AATATAA-AA-TTTTT-TTG
1 AAAATAATAATTTTTTGTTC
4045958 AAAATAATAA
1 AAAATAATAA
4045968 AAAGGAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 2 0.09
20 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (20 bp):
AAAATAATAATTTTTTGTTC
Found at i:4046306 original size:21 final size:21
Alignment explanation
Indices: 4046248--4046306 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
4046238 ATTCTTAACG
4046248 ATTTATATTTATATTTAAAATTA
1 ATTT-TATTTAT-TTTAAAATTA
* * *
4046271 ATTTTAATAATTTTTAAATTA
1 ATTTTATTTATTTTAAAATTA
4046292 ATTTTATTTACTTTT
1 ATTTTATTTA-TTTT
4046307 TTATATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.57
22 9 0.30
23 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTATTTATTTTAAAATTA
Found at i:4047092 original size:12 final size:12
Alignment explanation
Indices: 4047075--4047114 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
4047065 CTTTTGTTAC
4047075 TTATTATTTGTT
1 TTATTATTTGTT
4047087 TTATTA-TTGTT
1 TTATTATTTGTT
4047098 ATTATTATTTAGTT
1 -TTATTATTT-GTT
4047112 TTA
1 TTA
4047115 ATTTATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 12 0.48
13 5 0.20
14 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTATTATTTGTT
Found at i:4047792 original size:17 final size:18
Alignment explanation
Indices: 4047769--4047814 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
4047759 TTAATTTGAG
*
4047769 ATTATTTAATAGTTAAAT
1 ATTATTTAATAGATAAAT
*
4047787 -TTATTTGATA-ATAAAT
1 ATTATTTAATAGATAAAT
4047803 ATT-TTTAATAGA
1 ATTATTTAATAGA
4047815 AAAGAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTATTTAATAGATAAAT
Found at i:4059995 original size:14 final size:14
Alignment explanation
Indices: 4059978--4060014 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
4059968 AAATAATTTT
4059978 AAATAAATTTAAAC
1 AAATAAATTTAAAC
4059992 AAATAAA--TAAAC
1 AAATAAATTTAAAC
*
4060004 AAATATATTTA
1 AAATAAATTTA
4060015 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAATTTAAAC
Found at i:4060074 original size:36 final size:38
Alignment explanation
Indices: 4059992--4060076 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
4059982 AAATTTAAAC
4059992 AAATAAAT-AAACAAATATATTTATTAATTTTAATTAT
1 AAATAAATAAAACAAATATATTTATTAATTTTAATTAT
*
4060029 AAATTAATAAAACATAA-ATA-TTATT-A-TTTATATTAT
1 AAATAAATAAAACA-AATATATTTATTAATTTTA-ATTAT
4060065 AAATAAATAAAA
1 AAATAAATAAAA
4060077 AACTACATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 4 0.09
36 17 0.40
37 12 0.28
38 8 0.19
39 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (38 bp):
AAATAAATAAAACAAATATATTTATTAATTTTAATTAT
Found at i:4061856 original size:3 final size:3
Alignment explanation
Indices: 4061848--4061888 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4061838 CAGAAATATT
4061848 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4061889 CTGGATGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4062727 original size:2 final size:2
Alignment explanation
Indices: 4062720--4062745 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4062710 TGTGCGCGTG
4062720 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
4062746 TAAATTAGCA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4064843 original size:126 final size:126
Alignment explanation
Indices: 4064708--4064959 Score: 504
Period size: 126 Copynumber: 2.0 Consensus size: 126
4064698 GCAATGCAAG
4064708 GGACGTGTGATCCTCAAGGTCATGTAGCATAAAAACTTGTTTGGCAGCATTTATTTTCATATCTA
1 GGACGTGTGATCCTCAAGGTCATGTAGCATAAAAACTTGTTTGGCAGCATTTATTTTCATATCTA
4064773 TAACAGATCAGAAAAGTTGTAATAAAAATAGTTTAAAAAAAAAAATGTAGAAAACCACTTA
66 TAACAGATCAGAAAAGTTGTAATAAAAATAGTTTAAAAAAAAAAATGTAGAAAACCACTTA
4064834 GGACGTGTGATCCTCAAGGTCATGTAGCATAAAAACTTGTTTGGCAGCATTTATTTTCATATCTA
1 GGACGTGTGATCCTCAAGGTCATGTAGCATAAAAACTTGTTTGGCAGCATTTATTTTCATATCTA
4064899 TAACAGATCAGAAAAGTTGTAATAAAAATAGTTTAAAAAAAAAAATGTAGAAAACCACTTA
66 TAACAGATCAGAAAAGTTGTAATAAAAATAGTTTAAAAAAAAAAATGTAGAAAACCACTTA
4064960 ATTTCAAGAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (126 bp):
GGACGTGTGATCCTCAAGGTCATGTAGCATAAAAACTTGTTTGGCAGCATTTATTTTCATATCTA
TAACAGATCAGAAAAGTTGTAATAAAAATAGTTTAAAAAAAAAAATGTAGAAAACCACTTA
Found at i:4067684 original size:22 final size:22
Alignment explanation
Indices: 4067659--4067707 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
4067649 TAACTTGAGG
*
4067659 GATTTGGTTAGACAATCTTCAA
1 GATTTGATTAGACAATCTTCAA
4067681 GATTTGATTAGACAATCTTCAA
1 GATTTGATTAGACAATCTTCAA
4067703 GATTT
1 GATTT
4067708 ATGAATGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
GATTTGATTAGACAATCTTCAA
Done.