Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1620
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: 27153
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:1712 original size:30 final size:30
Alignment explanation
Indices: 1656--1713 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1646 GTATCACGAG
* *
1656 TTATTTAAATAAAAAATTCAATTAATAAAA
1 TTATTTAAATAAAAAATTAAAGTAATAAAA
*
1686 TTATTTAAA-AACATAATTAAAGTAATAA
1 TTATTTAAATAA-AAAATTAAAGTAATAA
1714 TTTTGGGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (30 bp):
TTATTTAAATAAAAAATTAAAGTAATAAAA
Found at i:3920 original size:18 final size:18
Alignment explanation
Indices: 3899--3956 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3889 AAATATTTAA
3899 AATTTATATAATATAAAT
1 AATTTATATAATATAAAT
* *
3917 AATTAATATATTAT-AAT
1 AATTTATATAATATAAAT
* *
3934 ATTTTAAATAATTATAATAT
1 AATTTATATAA-TATAA-AT
3954 AAT
1 AAT
3957 AAAATAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 10 0.33
18 15 0.50
19 1 0.03
20 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTATATAATATAAAT
Found at i:3935 original size:23 final size:23
Alignment explanation
Indices: 3885--3965 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 23
3875 ATAAATAAAT
* *
3885 ATATAAATATTTAAAATTTATATA
1 ATATAAATAATTAAAATAT-TATA
*
3909 ATATAAATAATTAATATATTATA
1 ATATAAATAATTAAAATATTATA
* *
3932 ATATTTTAAATAATTATAATATAATA
1 ATA---TAAATAATTAAAATATTATA
*
3958 AAATAAAT
1 ATATAAAT
3966 TAAAATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
23 12 0.26
24 16 0.34
26 19 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATAAATAATTAAAATATTATA
Found at i:3959 original size:18 final size:18
Alignment explanation
Indices: 3906--3981 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
3896 TAAAATTTAT
*
3906 ATAA-TATAA-ATAATTA
1 ATAATTATAATATAATAA
**
3922 ATATATTATAATATTTTAA
1 ATA-ATTATAATATAATAA
3941 ATAATTATAATATAATAAA
1 ATAATTATAATATAAT-AA
*
3960 ATAAATTAAAATA-ATATAA
1 AT-AATTATAATATA-ATAA
3979 ATA
1 ATA
3982 TATAAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.06
17 1 0.02
18 17 0.35
19 16 0.33
20 11 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTATAATATAATAA
Found at i:3986 original size:23 final size:23
Alignment explanation
Indices: 3874--3990 Score: 64
Period size: 23 Copynumber: 5.0 Consensus size: 23
3864 TAAAATCAAT
3874 AATAA-ATAAATATATAAATATTTAA
1 AATAATATAAATATAT-AA-A-TTAA
* *
3899 AAT-TTATATAATATAAATAATTAA
1 AATAATATA-AATATATA-AATTAA
* * *
3923 TATATTAT-AATATTTTAAA-TAA
1 AATAATATAAATA-TATAAATTAA
* *
3945 TTATAATAT-AATAAAATAAATTAA
1 -AATAATATAAAT-ATATAAATTAA
3969 AATAATATAAATATATAAATTA
1 AATAATATAAATATATAAATTA
3991 TTAGAATTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
22 3 0.04
23 36 0.49
24 15 0.21
25 12 0.16
26 7 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAATATAAATATATAAATTAA
Found at i:3987 original size:18 final size:18
Alignment explanation
Indices: 3881--3987 Score: 57
Period size: 17 Copynumber: 6.1 Consensus size: 18
3871 AATAATAAAT
*
3881 AAAT-ATATAAATATTTA
1 AAATAATATAAATATATA
* *
3898 AAAT-TTATATA-ATAT-
1 AAATAATATAAATATATA
3913 AAATAAT-T-AATATATTA
1 AAATAATATAAATATA-TA
* * *
3930 TAATATTTTAAATAATTATA
1 AAATAATATAAAT-A-TATA
* *
3950 ATATAATA-AAATAAATTA
1 AAATAATATAAATATA-TA
3968 AAATAATATAAATATATA
1 AAATAATATAAATATATA
3986 AA
1 AA
3988 TTATTAGAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 19
0.67 0.14 0.19
Matches are distributed among these distances:
14 1 0.02
15 8 0.12
16 5 0.08
17 15 0.23
18 15 0.23
19 13 0.20
20 7 0.11
21 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAATATAAATATATA
Found at i:5815 original size:16 final size:15
Alignment explanation
Indices: 5795--5924 Score: 72
Period size: 15 Copynumber: 8.3 Consensus size: 15
5785 AGATCTAATT
5795 ATATAATATAATAAA
1 ATATAATATAATAAA
*
5810 TATATAA-AAAATAAA
1 -ATATAATATAATAAA
5825 ATTATAATATAATAAA
1 A-TATAATATAATAAA
*
5841 ATA-AATATATTTAAA
1 ATATAATATA-ATAAA
**
5856 AT-TTTTATAACATCAAA
1 ATATAATAT-A-AT-AAA
5873 AT-TAATATAAATAAA
1 ATATAATAT-AATAAA
* *
5888 A-ATTATTTTTAATATAA
1 ATA-TA-ATATAATA-AA
*
5905 TTATAATATAATAAA
1 ATATAATATAATAAA
5920 ATATA
1 ATATA
5925 TAAATATTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
14 7 0.08
15 33 0.38
16 30 0.34
17 17 0.19
18 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAATATAATAAA
Found at i:6163 original size:16 final size:16
Alignment explanation
Indices: 6111--6165 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
6101 TGAATATAAA
6111 AATTTAAA-CTAAAAT
1 AATTTAAATCTAAAAT
* **
6126 AATTTAAATTTAATTT
1 AATTTAAATCTAAAAT
6142 AATTTAAATCTAAAAT
1 AATTTAAATCTAAAAT
*
6158 ATTTTAAA
1 AATTTAAA
6166 ATAATGAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAATCTAAAAT
Found at i:6271 original size:27 final size:28
Alignment explanation
Indices: 6212--6278 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
6202 AACATATAAA
* *
6212 ATAAATATTTATATTTATATTTTAGAGT
1 ATAAATATTTATATTTATATTTTAAAAT
* *
6240 TTAAATATTTTTATTTA-ATTTTAAAAT
1 ATAAATATTTATATTTATATTTTAAAAT
6267 ATAAATAATTTA
1 ATAAAT-ATTTA
6279 ACATATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
ATAAATATTTATATTTATATTTTAAAAT
Found at i:6277 original size:28 final size:28
Alignment explanation
Indices: 6188--6277 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 28
6178 ATATCTTTAT
* *
6188 TTTTTAATTAA-TTTAACATATAAAATAAA
1 TTTTTATTTAATTTTAAAATAT-AAAT-AA
* * *
6217 TATTTATATTTATATTTTAGAGTTTAAAT-A
1 T-TTT-TATTTA-ATTTTAAAATATAAATAA
6247 TTTTTATTTAATTTTAAAATATAAATAA
1 TTTTTATTTAATTTTAAAATATAAATAA
6275 TTT
1 TTT
6278 AACATATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
27 13 0.27
28 10 0.21
29 4 0.08
30 5 0.10
31 5 0.10
32 5 0.10
33 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTTTATTTAATTTTAAAATATAAATAA
Found at i:6562 original size:1 final size:1
Alignment explanation
Indices: 6556--6581 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6546 TCTCTCTGTG
6556 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
6582 ACGCCTCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:11650 original size:2 final size:2
Alignment explanation
Indices: 11643--11694 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
11633 TTTTGATTGG
11643 TA TA TA 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
*
11685 TG TA TA -A TA T
1 TA TA TA TA TA T
11695 GTATTATGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14076 original size:27 final size:25
Alignment explanation
Indices: 14046--14119 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
14036 TTTAAATTTT
14046 TATTTTATTATTTAAAATATATTAA
1 TATTTTATTATTTAAAATATATTAA
* * * **
14071 AATATTATATAATTAATTTTATATTAA
1 TATTTTAT-TATTTAA-AATATATTAA
14098 TATTTTATTAAATTTAAAATAT
1 TATTTTATT--ATTTAAAATAT
14120 TTTATTTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
25 6 0.17
26 7 0.20
27 17 0.49
28 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTTATTATTTAAAATATATTAA
Found at i:14943 original size:2 final size:2
Alignment explanation
Indices: 14938--14969 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
14928 TATATAATGG
14938 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14970 GCAATCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17980 original size:24 final size:23
Alignment explanation
Indices: 17953--17998 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
17943 ATCATTTTTA
17953 AAATCATTATGATA-ATTTAATTAT
1 AAAT-ATT-TGATATATTTAATTAT
17977 AAATATTTGATATTATTTAATT
1 AAATATTTGATA-TATTTAATT
17999 TAGTAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
AAATATTTGATATATTTAATTAT
Found at i:18558 original size:16 final size:17
Alignment explanation
Indices: 18527--18566 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
18517 ATGTATTTTG
18527 AAATAATTATTTTAAATT
1 AAAT-ATTATTTTAAATT
18545 AAATATTA-TTTAAATT
1 AAATATTATTTTAAATT
*
18561 ACATAT
1 AAATAT
18567 GATTAGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 4 0.19
18 4 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTATTTTAAATT
Found at i:20210 original size:6 final size:6
Alignment explanation
Indices: 20201--20228 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20191 TGAAAATTAT
20201 GGCTCA GGCTCA GGCTCA GGCTCA GGCT
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCT
20229 GCCCATTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (6 bp):
GGCTCA
Found at i:21959 original size:2 final size:2
Alignment explanation
Indices: 21952--21979 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21942 GTTTGATCAG
21952 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
21980 GTATCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24896 original size:25 final size:23
Alignment explanation
Indices: 24868--24916 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
24858 TACTAGATTT
*
24868 ACAATATTATTATCTCAAAGGAAAC
1 ACAATAGTATTA-CTCAAA-GAAAC
*
24893 ACAATAGTATTACTTAAAGAAAC
1 ACAATAGTATTACTCAAAGAAAC
24916 A
1 A
24917 ATAAATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 5 0.23
25 11 0.50
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (23 bp):
ACAATAGTATTACTCAAAGAAAC
Done.