Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2694
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: 9967
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:4067 original size:16 final size:17
Alignment explanation
Indices: 4048--4083 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4038 TAAAAGGTTT
4048 GAAAT-TGAAAAAGCTC
1 GAAATCTGAAAAAGCTC
*
4064 GAAATCTGTAAAAGCTC
1 GAAATCTGAAAAAGCTC
4081 GAA
1 GAA
4084 TCCATGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.19
Consensus pattern (17 bp):
GAAATCTGAAAAAGCTC
Found at i:4120 original size:22 final size:22
Alignment explanation
Indices: 4095--4168 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
4085 CCATGCAATT
4095 TGAGCCCGAAACTAATTTGATC
1 TGAGCCCGAAACTAATTTGATC
** * *
4117 TGAGCCTTAAACTCCA-TTGCAATT
1 TGAGCCCGAAACT-AATTTG--ATC
4141 TGAGCCCGAAACTAATTTGATC
1 TGAGCCCGAAACTAATTTGATC
4163 TGAGCC
1 TGAGCC
4169 TTAAACTGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 22 0.55
23 2 0.05
24 16 0.40
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (22 bp):
TGAGCCCGAAACTAATTTGATC
Found at i:4138 original size:46 final size:45
Alignment explanation
Indices: 4084--4175 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 45
4074 AAAGCTCGAA
4084 TCCATGCAATTTGAGCCCGAAACTAATTTGATCTGAGCCTTAAAC
1 TCCATGCAATTTGAGCCCGAAACTAATTTGATCTGAGCCTTAAAC
4129 TCCATTGCAATTTGAGCCCGAAACTAATTTGATCTGAGCCTTAAAC
1 TCCA-TGCAATTTGAGCCCGAAACTAATTTGATCTGAGCCTTAAAC
4175 T
1 T
4176 GATCCAATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (45 bp):
TCCATGCAATTTGAGCCCGAAACTAATTTGATCTGAGCCTTAAAC
Found at i:4152 original size:24 final size:24
Alignment explanation
Indices: 4084--4153 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 24
4074 AAAGCTCGAA
4084 TCCA-TGCAATTTGAGCCCGAAAC
1 TCCATTGCAATTTGAGCCCGAAAC
* * **
4107 T-AATTTG--ATCTGAGCCTTAAAC
1 TCCA-TTGCAATTTGAGCCCGAAAC
4129 TCCATTGCAATTTGAGCCCGAAAC
1 TCCATTGCAATTTGAGCCCGAAAC
4153 T
1 T
4154 AATTTGATCT
Statistics
Matches: 34, Mismatches: 8, Indels: 9
0.67 0.16 0.18
Matches are distributed among these distances:
22 17 0.50
23 2 0.06
24 15 0.44
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (24 bp):
TCCATTGCAATTTGAGCCCGAAAC
Found at i:5943 original size:32 final size:29
Alignment explanation
Indices: 5888--5948 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
5878 ATATGTTTGC
*
5888 AATTATATTATAAATATTATAGATACAATA
1 AATTATATAATAAATATTATAGATA-AATA
*
5918 AATTATATAATATTATATTTATAGATAAATA
1 AATTATATAATA-AATA-TTATAGATAAATA
5949 TATTTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 11 0.41
31 7 0.26
32 9 0.33
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTATATAATAAATATTATAGATAAATA
Found at i:5950 original size:16 final size:16
Alignment explanation
Indices: 5904--5955 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5894 ATTATAAATA
*
5904 TTATAGATACAATAAAT
1 TTATAGATA-AATATAT
*
5921 TATATA-AT-ATTATAT
1 T-TATAGATAAATATAT
5936 TTATAGATAAATATAT
1 TTATAGATAAATATAT
5952 TTAT
1 TTAT
5956 GTTATACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 10 0.34
17 3 0.10
18 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (16 bp):
TTATAGATAAATATAT
Found at i:6640 original size:16 final size:16
Alignment explanation
Indices: 6621--6686 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
6611 GACTCAAAAC
*
6621 TAAAATAATCTAAATT
1 TAAAATAATTTAAATT
*
6637 TAAAATTATTTAAA--
1 TAAAATAATTTAAATT
*
6651 TAAAA-AAATTAAATT
1 TAAAATAATTTAAATT
*
6666 TAAAATAATTTAAATC
1 TAAAATAATTTAAATT
6682 TAAAA
1 TAAAA
6687 ATATATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
13 6 0.15
14 5 0.12
15 5 0.12
16 25 0.61
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:6665 original size:29 final size:30
Alignment explanation
Indices: 6621--6680 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
6611 GACTCAAAAC
* *
6621 TAAAATAATCTAAATTTAAAATTATTTAAA
1 TAAAAAAATCTAAATTTAAAATAATTTAAA
6651 TAAAAAAAT-TAAATTTAAAATAATTTAAA
1 TAAAAAAATCTAAATTTAAAATAATTTAAA
6680 T
1 T
6681 CTAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAAAAAATCTAAATTTAAAATAATTTAAA
Found at i:6941 original size:20 final size:17
Alignment explanation
Indices: 6902--6943 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
6892 TTTGATTAAG
6902 TTTAATTTATTAAAAAT
1 TTTAATTTATTAAAAAT
6919 TTTAATTTTATTATAATAAT
1 TTTAA-TTTATTA-AA-AAT
6939 TTTAA
1 TTTAA
6944 AGAATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 2 0.09
20 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTTATTAAAAAT
Found at i:6951 original size:13 final size:13
Alignment explanation
Indices: 6933--6957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6923 ATTTTATTAT
6933 AATAATTTTAAAG
1 AATAATTTTAAAG
6946 AATAATTTTAAA
1 AATAATTTTAAA
6958 ATACTCATGA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AATAATTTTAAAG
Found at i:7113 original size:16 final size:17
Alignment explanation
Indices: 7050--7117 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 17
7040 TTTAACGATG
7050 TTAATATAAAATATTTAT
1 TTAATATAAAA-ATTTAT
* *
7068 AT-ATTTATAAAA-TTA-
1 TTAATATA-AAAATTTAT
7083 -TAATATAAAAATTTAT
1 TTAATATAAAAATTTAT
*
7099 TTAAT-TAAAATTTTAT
1 TTAATATAAAAATTTAT
7115 TTA
1 TTA
7118 CCTACTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 16 0.39
17 9 0.22
18 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATAAAAATTTAT
Found at i:7540 original size:14 final size:14
Alignment explanation
Indices: 7498--7546 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 14
7488 GAAAATATTT
7498 TAAAATTTAAAATATAA
1 TAAAATTT--AATA-AA
7515 TATAAATATTAATAAA
1 TA-AAAT-TTAATAAA
7531 TAAAATTTAATAAA
1 TAAAATTTAATAAA
7545 TA
1 TA
7547 TAAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.33
15 4 0.13
16 4 0.13
17 6 0.20
18 4 0.13
19 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATTTAATAAA
Found at i:7881 original size:16 final size:17
Alignment explanation
Indices: 7862--7896 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7852 AATTGATTAA
*
7862 TTTTATGAATTTT-ATT
1 TTTTAAGAATTTTAATT
7878 TTTTAAGAATTTTAATT
1 TTTTAAGAATTTTAATT
7895 TT
1 TT
7897 ATAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTTAAGAATTTTAATT
Found at i:7910 original size:31 final size:30
Alignment explanation
Indices: 7827--7910 Score: 73
Period size: 31 Copynumber: 2.7 Consensus size: 30
7817 AAGTTAGTCA
*
7827 AATTATTATTATAATAATGTTTTTAAATTGATT
1 AATT-TTATAATAATAAT-TTTTTAAATT-ATT
* *
7860 AATTTTATGAAT-TTTATTTTTTAAGAATT-TT
1 AATTTTAT-AATAATAATTTTTT-A-AATTATT
7891 AATTTTATAATAATAATTTT
1 AATTTTATAATAATAATTTT
7911 AAAGATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
30 3 0.07
31 21 0.50
32 8 0.19
33 10 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
AATTTTATAATAATAATTTTTTAAATTATT
Done.