Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2469
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: 48663
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4900 original size:27 final size:26
Alignment explanation
Indices: 4856--4909 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
4846 GAGTCAACCA
**
4856 TCAGAATTAATGCCTTGTTAT-TTTCC
1 TCAGAATTAATGAATTGTT-TGTTTCC
4882 TCAGAAATTAATGAATTGTTTGTTTCC
1 TCAG-AATTAATGAATTGTTTGTTTCC
4909 T
1 T
4910 TGTAGTAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (26 bp):
TCAGAATTAATGAATTGTTTGTTTCC
Found at i:8486 original size:21 final size:21
Alignment explanation
Indices: 8461--8515 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
8451 GGATGATGAG
*
8461 GATGAGGAAGATGAAGCA-GGA
1 GATGAGGAAGATGAAG-ATGCA
**
8482 GATGATCAAGATGAAGATGCA
1 GATGAGGAAGATGAAGATGCA
*
8503 GATGAGGAGGATG
1 GATGAGGAAGATG
8516 CATCTGGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.40, T:0.15
Consensus pattern (21 bp):
GATGAGGAAGATGAAGATGCA
Found at i:8601 original size:15 final size:15
Alignment explanation
Indices: 8581--8609 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8571 TGCCAGTGGA
8581 GACGAGGATGATGAG
1 GACGAGGATGATGAG
8596 GACGAGGATGATGA
1 GACGAGGATGATGA
8610 CGATGACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14
Consensus pattern (15 bp):
GACGAGGATGATGAG
Found at i:8646 original size:9 final size:9
Alignment explanation
Indices: 8635--8681 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
8625 TGATGGTGAG
*
8635 GAAGAGGAG
1 GAAGAGGAA
*
8644 GAAGAAGAA
1 GAAGAGGAA
8653 GAAGAGGAA
1 GAAGAGGAA
* *
8662 GATGAGGAT
1 GAAGAGGAA
8671 GAAGAGGAA
1 GAAGAGGAA
8680 GA
1 GA
8682 GCTTCAGCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.04
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:8668 original size:24 final size:24
Alignment explanation
Indices: 8632--8682 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
8622 CGATGATGGT
8632 GAGGAAGAGGAGGAAGAAGAAGAA
1 GAGGAAGAGGAGGAAGAAGAAGAA
* * *
8656 GAGGAAGATGAGGATGAAGAGGAA
1 GAGGAAGAGGAGGAAGAAGAAGAA
8680 GAG
1 GAG
8683 CTTCAGCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (24 bp):
GAGGAAGAGGAGGAAGAAGAAGAA
Found at i:13623 original size:29 final size:29
Alignment explanation
Indices: 13581--13636 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
13571 TCAATTGGTT
13581 ATCCTGAATAACTATAGAGTTAAAACACA
1 ATCCTGAATAACTATAGAGTTAAAACACA
13610 ATCCTGAATAACTATAGAGTTAAAACA
1 ATCCTGAATAACTATAGAGTTAAAACA
13637 TTATTTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (29 bp):
ATCCTGAATAACTATAGAGTTAAAACACA
Found at i:20690 original size:20 final size:20
Alignment explanation
Indices: 20667--20706 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20657 AAGTATTTCA
*
20667 ATTAAATTCATGTTATTAAC
1 ATTAAATTCATATTATTAAC
* *
20687 ATTAATTTTATATTATTAAC
1 ATTAAATTCATATTATTAAC
20707 TCAGTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTAAATTCATATTATTAAC
Found at i:23556 original size:24 final size:24
Alignment explanation
Indices: 23528--23576 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23518 AAAACATCAC
23528 TAATTTACTAAATACAAATTTAAT
1 TAATTTACTAAATACAAATTTAAT
23552 TAATTTACTAAATACAAATTTAAT
1 TAATTTACTAAATACAAATTTAAT
23576 T
1 T
23577 TTTTGGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATTTACTAAATACAAATTTAAT
Found at i:25031 original size:2 final size:2
Alignment explanation
Indices: 25024--25063 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25014 ACTCTTATAG
25024 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
25064 AGAGATCGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:27867 original size:60 final size:60
Alignment explanation
Indices: 27739--27858 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
27729 TTTTTTTTTT
27739 AAAAGTTAATATTTTTGTTCGTCAAATTTATATTTTATATATGTGTATGTCATACGCAAA
1 AAAAGTTAATATTTTTGTTCGTCAAATTTATATTTTATATATGTGTATGTCATACGCAAA
27799 AAAAGTTAATATTTTTGTTCGTCAAATTTATATTTTATATATGTGTATGTCATACGCAAA
1 AAAAGTTAATATTTTTGTTCGTCAAATTTATATTTTATATATGTGTATGTCATACGCAAA
27859 GGAGGTTAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (60 bp):
AAAAGTTAATATTTTTGTTCGTCAAATTTATATTTTATATATGTGTATGTCATACGCAAA
Found at i:38497 original size:13 final size:13
Alignment explanation
Indices: 38479--38503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38469 TTAAATAGAC
38479 AGGACTTTTTTAT
1 AGGACTTTTTTAT
38492 AGGACTTTTTTA
1 AGGACTTTTTTA
38504 AAGAAGTATA
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
AGGACTTTTTTAT
Done.