Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2383
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: 9063
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Found at i:1985 original size:30 final size:30
Alignment explanation
Indices: 1954--2022 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
1944 TTCAATATTT
* *
1954 AAAAGAGTTTGAATAAAATATTAAATTTTTA
1 AAAAAAGTTTGAATAAAA-AATAAATTTTTA
*
1985 AAAAAATTTTGAATAAAAAATAAATTTGTTTA
1 AAAAAAGTTTGAATAAAAAATAAA-TT-TTTA
2017 AAAAAA
1 AAAAAA
2023 TAAGTTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 5 0.15
31 18 0.55
32 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (30 bp):
AAAAAAGTTTGAATAAAAAATAAATTTTTA
Found at i:1998 original size:31 final size:32
Alignment explanation
Indices: 1961--2023 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
1951 TTTAAAAGAG
*
1961 TTTGAATAAAATATTAAA-TT-TTTAAAAAAAT
1 TTTGAATAAAA-AATAAATTTGTTTAAAAAAAT
1992 TTTGAATAAAAAATAAATTTGTTTAAAAAAAT
1 TTTGAATAAAAAATAAATTTGTTTAAAAAAAT
2024 AAGTTTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.17
31 13 0.45
32 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (32 bp):
TTTGAATAAAAAATAAATTTGTTTAAAAAAAT
Found at i:2267 original size:6 final size:6
Alignment explanation
Indices: 2248--2283 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2238 AATCTATTTA
*
2248 TAAATT TAAAATT TATATT TAAATT TAAATT TAAAT
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAAT
2284 AAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:2830 original size:14 final size:14
Alignment explanation
Indices: 2813--2847 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2803 TTAACTTTAT
2813 TAATTTTTATATAA
1 TAATTTTTATATAA
*
2827 TAATTGTTATATAA
1 TAATTTTTATATAA
2841 TAATTTT
1 TAATTTT
2848 ATTTTATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TAATTTTTATATAA
Found at i:2969 original size:2 final size:2
Alignment explanation
Indices: 2962--2998 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2952 TTAAGGTTCC
2962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2999 CTGAGAGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3320 original size:22 final size:22
Alignment explanation
Indices: 3295--3338 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3285 AAATTATCAT
*
3295 TTAATA-ATATAAAATATTTTTA
1 TTAATATATA-AAAATAATTTTA
*
3317 TTAATTTATAAAAATAATTTTA
1 TTAATATATAAAAATAATTTTA
3339 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATATATAAAAATAATTTTA
Found at i:3352 original size:21 final size:22
Alignment explanation
Indices: 3265--3345 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 22
3255 TATAATTTTT
*
3265 TAATTTGAATAATTTAATAAAAA
1 TAATTTTAATAATTT-ATAAAAA
*
3288 TTATCATTTAATAA--TAT-AAAA
1 TAAT--TTTAATAATTTATAAAAA
* *
3309 TATTTTTATTAATTTATAAAAA
1 TAATTTTAATAATTTATAAAAA
3331 TAATTTTAAT-ATTTA
1 TAATTTTAATAATTTA
3346 AATAAATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 7 0.15
21 14 0.30
22 14 0.30
23 4 0.09
25 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATTTTAATAATTTATAAAAA
Found at i:6425 original size:13 final size:13
Alignment explanation
Indices: 6400--6434 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
6390 GGTAATTTTT
6400 TTTTAATAATTATA
1 TTTTAA-AATTATA
6414 TTTTAAAATTATA
1 TTTTAAAATTATA
6427 TTTTAAAA
1 TTTTAAAA
6435 AAATTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAAATTATA
Found at i:6466 original size:26 final size:27
Alignment explanation
Indices: 6417--6467 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
6407 AATTATATTT
6417 TAAAATTATATTTTAAAAAAATTAAGA
1 TAAAATTATATTTTAAAAAAATTAAGA
* *
6444 TAAAATT-TATTTTAATAATATTAA
1 TAAAATTATATTTTAAAAAAATTAA
6468 ATTTATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAAATTATATTTTAAAAAAATTAAGA
Found at i:7645 original size:24 final size:24
Alignment explanation
Indices: 7600--7646 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
7590 TATATATTTT
**
7600 TAAATACAAATTATTATTTTAAAC
1 TAAATACAAATTATTAAGTTAAAC
7624 TAAATA-AAATTTATTAAGTTAAA
1 TAAATACAAA-TTATTAAGTTAAA
7647 TAATTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATACAAATTATTAAGTTAAAC
Found at i:8957 original size:16 final size:16
Alignment explanation
Indices: 8919--8957 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
8909 AATAATAAAT
*
8919 ATAAATAAATTTATAA
1 ATAAATTAATTTATAA
8935 ACT-AATTAATTTATAA
1 A-TAAATTAATTTATAA
8951 ATAAATT
1 ATAAATT
8958 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATTAATTTATAA
Done.