Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2590
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: 26616
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2774 original size:18 final size:18
Alignment explanation
Indices: 2735--2778 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2725 CATATGATAC
2735 AATGCAATGTTAATACATG
1 AATGCAATG-TAATACATG
2754 AATGCAATG-AATACAATG
1 AATGCAATGTAATAC-ATG
2772 AATGCAA
1 AATGCAA
2779 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (18 bp):
AATGCAATGTAATACATG
Found at i:4797 original size:3 final size:3
Alignment explanation
Indices: 4789--4825 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
4779 AATGATAAAT
*
4789 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4826 AGGGACAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:8390 original size:20 final size:20
Alignment explanation
Indices: 8365--8414 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
8355 TGGCTTAAAA
8365 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
8385 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
8402 GTGGTAGTGGATT
1 TTGGTAGTGGATT
8415 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:13026 original size:20 final size:20
Alignment explanation
Indices: 13001--13050 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
12991 TGGCTTAAAA
13001 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
13021 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
13038 GTGGTAGTGGATT
1 TTGGTAGTGGATT
13051 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:16050 original size:18 final size:18
Alignment explanation
Indices: 16029--16066 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16019 ATAAAAGAAC
*
16029 TAAATTATTAAGGACTAT
1 TAAATTATTAAGGAATAT
16047 TAAATTATTAAGGAATAT
1 TAAATTATTAAGGAATAT
16065 TA
1 TA
16067 GTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAATTATTAAGGAATAT
Found at i:20845 original size:21 final size:21
Alignment explanation
Indices: 20819--20859 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20809 ATCTGCTCAA
* *
20819 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
20840 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
20860 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:26360 original size:156 final size:157
Alignment explanation
Indices: 26051--26356 Score: 380
Period size: 156 Copynumber: 2.0 Consensus size: 157
26041 TAAAGAATAT
* * * * *
26051 TAATTAGTTAAGAATTTTTATTAAATTATATATTTTTAATTATAATATATTAATAATAATTATGT
1 TAATTAGTTAAGAAATTTTATTAAATTATATATATTTAATTAGAAGATATTAATAATAATGATGT
*
26116 TTAAATAGATTAAAATTATTTATTATTGATATTAATAATCTTATTAAAAGTTAATAACAATACAA
66 TTAAATAGATTAAAATTATTTATTATTGATAATAATAATCTTATTAAAAGTTAATAACAATACAA
26181 TTAATAATTTACCAAAACAAATTTCTA
131 TTAATAATTTACCAAAACAAATTTCTA
26208 TAATTA-TTAAGAAATTTTATTAAATT-TATATATTTAATTAAGAAGATATTTAA-AATAATGAT
1 TAATTAGTTAAGAAATTTTATTAAATTATATATATTTAATT-AGAAGATA-TTAATAATAATGAT
* * *
26270 -TTTAAA-ATGAATT-AAATTACTTTA-TATATGATAATAATAATCTTATTTAAATTTAA-ATAT
64 GTTTAAATA-G-ATTAAAATTA-TTTATTAT-TGATAATAATAATCTTATTAAAAGTTAATA-AC
*
26330 AATAACAA-TAATCA-TTACCAAAACAAA
124 AAT-ACAATTAATAATTTACCAAAACAAA
26357 ATTTATGCTA
Statistics
Matches: 131, Mismatches: 10, Indels: 18
0.82 0.06 0.11
Matches are distributed among these distances:
154 1 0.01
155 42 0.32
156 74 0.56
157 14 0.11
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (157 bp):
TAATTAGTTAAGAAATTTTATTAAATTATATATATTTAATTAGAAGATATTAATAATAATGATGT
TTAAATAGATTAAAATTATTTATTATTGATAATAATAATCTTATTAAAAGTTAATAACAATACAA
TTAATAATTTACCAAAACAAATTTCTA
Found at i:26507 original size:16 final size:16
Alignment explanation
Indices: 26486--26549 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
26476 GTTGATTTGC
*
26486 ATACACCTCTAATCCA
1 ATACACCTCTAAGCCA
26502 ATACACCTCTAAGCCA
1 ATACACCTCTAAGCCA
* *
26518 ATACAGCTCTAATCCA
1 ATACACCTCTAAGCCA
26534 A-ACA-CTCTAAGCCA
1 ATACACCTCTAAGCCA
26548 AT
1 AT
26550 TACAGCGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
14 10 0.23
15 3 0.07
16 30 0.70
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.22
Consensus pattern (16 bp):
ATACACCTCTAAGCCA
Found at i:26544 original size:30 final size:32
Alignment explanation
Indices: 26486--26555 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
26476 GTTGATTTGC
*
26486 ATACACCTCTAATCCAATACACCTCTAAGCCA
1 ATACAGCTCTAATCCAATACACCTCTAAGCCA
26518 ATACAGCTCTAATCCAA-ACA-CTCTAAGCCA
1 ATACAGCTCTAATCCAATACACCTCTAAGCCA
26548 ATTACAGC
1 A-TACAGC
26556 GAACCAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 11 0.31
31 9 0.25
32 16 0.44
ACGTcount: A:0.39, C:0.34, G:0.06, T:0.21
Consensus pattern (32 bp):
ATACAGCTCTAATCCAATACACCTCTAAGCCA
Done.