Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2317
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: 24084
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3999 original size:99 final size:99
Alignment explanation
Indices: 3828--4020 Score: 386
Period size: 99 Copynumber: 1.9 Consensus size: 99
3818 CCCAAAGTAA
3828 TTTATGAATTGGAAGGCATGCTTTTAAAAAAAACAAATGCACATCATCATTTAAACCAGAATAAT
1 TTTATGAATTGGAAGGCATGCTTTTAAAAAAAACAAATGCACATCATCATTTAAACCAGAATAAT
3893 TAATGAAGCTTTCTGTATTAACTATCTAATTTAC
66 TAATGAAGCTTTCTGTATTAACTATCTAATTTAC
3927 TTTATGAATTGGAAGGCATGCTTTTAAAAAAAACAAATGCACATCATCATTTAAACCAGAATAAT
1 TTTATGAATTGGAAGGCATGCTTTTAAAAAAAACAAATGCACATCATCATTTAAACCAGAATAAT
3992 TAATGAAGCTTTCTGTATTAACTATCTAA
66 TAATGAAGCTTTCTGTATTAACTATCTAA
4021 CGATATTATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (99 bp):
TTTATGAATTGGAAGGCATGCTTTTAAAAAAAACAAATGCACATCATCATTTAAACCAGAATAAT
TAATGAAGCTTTCTGTATTAACTATCTAATTTAC
Found at i:8653 original size:17 final size:17
Alignment explanation
Indices: 8631--8665 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8621 GAACGCTTCT
8631 CAATGGCGAATCCCACG
1 CAATGGCGAATCCCACG
8648 CAATGGCGAATCCCACG
1 CAATGGCGAATCCCACG
8665 C
1 C
8666 CATTTTGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.23, T:0.11
Consensus pattern (17 bp):
CAATGGCGAATCCCACG
Found at i:9170 original size:27 final size:26
Alignment explanation
Indices: 9140--9201 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
9130 AGATAATTAA
9140 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
9167 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
9194 AATAAAAT
1 AATAAAAT
9202 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:12785 original size:26 final size:26
Alignment explanation
Indices: 12756--12837 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
12746 TGATACAAAT
12756 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12782 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12808 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12834 TGAT
1 TGAT
12838 TGGAATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17723 original size:60 final size:60
Alignment explanation
Indices: 17630--17751 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
17620 TTTGAATTTT
17630 TTGTATCTAAATAAATAAATTTAACCATCAATTTAATACATTTCATATTCATATGCAACA
1 TTGTATCTAAATAAATAAATTTAACCATCAATTTAATACATTTCATATTCATATGCAACA
17690 TTGTATCTAAATAAATAAATTTAACCATCAATTTAATACATTTCATATTCATATGCAACA
1 TTGTATCTAAATAAATAAATTTAACCATCAATTTAATACATTTCATATTCATATGCAACA
17750 TT
1 TT
17752 CTCTATAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (60 bp):
TTGTATCTAAATAAATAAATTTAACCATCAATTTAATACATTTCATATTCATATGCAACA
Done.