Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold946
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: 25556
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:467 original size:23 final size:23
Alignment explanation
Indices: 437--485 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
427 TTGACCAGCA
437 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
460 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
483 TTT
1 TTT
486 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTTTATTATGTTTCATGCATT
Found at i:492 original size:20 final size:21
Alignment explanation
Indices: 434--492 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 21
424 GCCTTGACCA
**
434 GCATTTTTTATTATGTTTCAT
1 GCATTTTTTAACATGTTTCAT
**
455 GCATTTTTTTTATTATGTTTCAT
1 GCA--TTTTTTAACATGTTTCAT
478 GCA-TTTTTAACATGT
1 GCATTTTTTAACATGT
493 CCAGCATCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 10 0.29
21 3 0.09
23 21 0.62
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
GCATTTTTTAACATGTTTCAT
Found at i:2043 original size:20 final size:20
Alignment explanation
Indices: 1996--2070 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1986 AAAAAGACAT
*
1996 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2015 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2036 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
2056 AATGCATCGATACAT
1 AATGTATCGATACAT
2071 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2065 original size:40 final size:39
Alignment explanation
Indices: 1993--2070 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1983 GGTAAAAAGA
* * *
1993 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
2032 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
2071 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:4148 original size:20 final size:20
Alignment explanation
Indices: 4085--4148 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
4075 AAAAGATATA
**
4085 TTTGGATGAAATGATGT-AT
1 TTTGGATGAAAAAATGTAAT
* * *
4104 TGGTTGGATGAAAGAATGCATT
1 T--TTGGATGAAAAAATGTAAT
4126 TTTGGATGAAAAAATGTAAT
1 TTTGGATGAAAAAATGTAAT
4146 TTT
1 TTT
4149 TAATAACCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 13 0.37
22 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (20 bp):
TTTGGATGAAAAAATGTAAT
Found at i:4149 original size:21 final size:20
Alignment explanation
Indices: 4085--4149 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
4075 AAAAGATATA
**
4085 TTTGGATGAAATGATGTATT
1 TTTGGATGAAAAAATGTATT
* * *
4105 GGTTGGATGAAAGAATGCATT
1 -TTTGGATGAAAAAATGTATT
4126 TTTGGATGAAAAAATGTAATT
1 TTTGGATGAAAAAATGT-ATT
4147 TTT
1 TTT
4150 AATAACCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTGGATGAAAAAATGTATT
Found at i:6871 original size:15 final size:15
Alignment explanation
Indices: 6849--6889 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
6839 AAAAATAAAA
6849 TAAAATAATATTTTT
1 TAAAATAATATTTTT
* *
6864 TGAAATAATTTTTTT
1 TAAAATAATATTTTT
*
6879 TAAAAAAATAT
1 TAAAATAATAT
6890 GTATAGAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TAAAATAATATTTTT
Found at i:8836 original size:16 final size:17
Alignment explanation
Indices: 8815--8847 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
8805 AGAAAAGTGT
*
8815 GAAAGAGAGAG-GAAAA
1 GAAAGAAAGAGAGAAAA
8831 GAAAGAAAGAGAGAAAA
1 GAAAGAAAGAGAGAAAA
8848 AGGAGCAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAGAGAAAA
Found at i:12041 original size:28 final size:27
Alignment explanation
Indices: 11999--12058 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
11989 AATCTCATGA
*
11999 TATTTAAGTAAATTATCAAAATAATAT
1 TATTTAAATAAATTATCAAAATAATAT
** *
12026 TATTTAAAATAAATTATTGAAATATTAT
1 TATTT-AAATAAATTATCAAAATAATAT
12054 TATTT
1 TATTT
12059 TGATATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TATTTAAATAAATTATCAAAATAATAT
Found at i:12428 original size:14 final size:13
Alignment explanation
Indices: 12411--12456 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
12401 ATATAATTAT
12411 TTTAAAATATTTAA
1 TTTAAAAT-TTTAA
**
12425 TTTAATTTGTTTAA
1 TTTAAAAT-TTTAA
12439 TTTAAAATTTTAA
1 TTTAAAATTTTAA
12452 TTTAA
1 TTTAA
12457 GTTGTAACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TTTAAAATTTTAA
Found at i:12870 original size:20 final size:20
Alignment explanation
Indices: 12813--12870 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
12803 TAATAAAAAC
12813 TATTATTATATT-TATAACAA
1 TATTATTAT-TTATATAACAA
* * * **
12833 TATTAATAATAACCTAACAA
1 TATTATTATTTATATAACAA
12853 TATTATTATTTATATAAC
1 TATTATTATTTATATAAC
12871 GCTAACCACT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTATTATTTATATAACAA
Found at i:18662 original size:23 final size:24
Alignment explanation
Indices: 18636--18683 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
18626 TTTTTAAATA
*
18636 ACTTTAAATTTCAT-AAAATTATT
1 ACTTGAAATTTCATAAAAATTATT
*
18659 ACTTGAATTTTCATAAAAATTATT
1 ACTTGAAATTTCATAAAAATTATT
18683 A
1 A
18684 TATATAGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
ACTTGAAATTTCATAAAAATTATT
Done.