Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2741
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: 19983
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:901 original size:17 final size:17
Alignment explanation
Indices: 879--930 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
869 CTTTTTCTTT
879 AATAATTAATTATATTA
1 AATAATTAATTATATTA
896 AATAATT-A-TATA-TA
1 AATAATTAATTATATTA
910 ATATAATTAATTATATATA
1 A-ATAATTAATTATAT-TA
929 AA
1 AA
931 AATAAATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 2 0.07
17 11 0.37
18 1 0.03
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATTAATTATATTA
Found at i:903 original size:13 final size:14
Alignment explanation
Indices: 881--929 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
871 TTTTCTTTAA
881 TAAT-TAATTATAT
1 TAATATAATTATAT
894 TAA-ATAATTATAT
1 TAATATAATTATAT
907 ATAATATAATTA-AT
1 -TAATATAATTATAT
921 TATATATAA
1 TA-ATATAA
930 AAATAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 14 0.44
14 11 0.34
15 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATATAATTATAT
Found at i:1140 original size:2 final size:2
Alignment explanation
Indices: 1133--1157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1123 ATTTGTATGC
1133 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1158 CACATCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8515 original size:42 final size:38
Alignment explanation
Indices: 8449--8533 Score: 125
Period size: 42 Copynumber: 2.1 Consensus size: 38
8439 ACCGTCATCC
8449 TTTTATTAAAAATTTTAAAATAAATAAAATTAAGTTTTACT
1 TTTTATTAAAAATTTTAAAATAAATAAAA-TAA-TTTTA-T
*
8490 TTTTATTAAAATTTTTTAAAATAAATAAAATAATTTTAT
1 TTTTATTAAAA-ATTTTAAAATAAATAAAATAATTTTAT
8529 TTTTA
1 TTTTA
8534 ATGAATAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
39 6 0.14
40 5 0.12
41 14 0.33
42 17 0.40
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTTATTAAAAATTTTAAAATAAATAAAATAATTTTAT
Found at i:8698 original size:22 final size:22
Alignment explanation
Indices: 8663--8704 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
8653 ATAATTTATT
8663 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
8685 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
8705 ATTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:8886 original size:14 final size:13
Alignment explanation
Indices: 8869--8974 Score: 51
Period size: 16 Copynumber: 7.6 Consensus size: 13
8859 TAAATTTTTA
8869 ATATTAAATATATT
1 ATATTAAATATA-T
8883 ATATTAAA-ATA-
1 ATATTAAATATAT
*
8894 ATA-TAAATA-AA
1 ATATTAAATATAT
8905 ATAATTAAAATATAAT
1 AT-ATT-AAATAT-AT
8921 ATAATATAAATATAT
1 AT-AT-TAAATATAT
8936 AT-TTAAAATTTATAT
1 ATATT-AAA--TATAT
*
8951 AATATTAATTATTAAT
1 -ATATTAAATA-T-AT
8967 ATATTAAA
1 ATATTAAA
8975 ATTTATAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 29
0.70 0.03 0.27
Matches are distributed among these distances:
10 5 0.07
11 6 0.08
12 2 0.03
13 8 0.11
14 15 0.20
15 17 0.23
16 18 0.24
17 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:8927 original size:30 final size:28
Alignment explanation
Indices: 8885--8955 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
8875 AATATATTAT
*
8885 ATTAAAATAATATAAATAAAATAATTAAA
1 ATTAATATAATATAAAT-AAATAATTAAA
* *
8914 ATATAATATAATATAAATATATATTTAAA
1 AT-TAATATAATATAAATAAATAATTAAA
*
8943 ATTTATATAATAT
1 ATTAATATAATAT
8956 TAATTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 10 0.27
29 13 0.35
30 14 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTAATATAATATAAATAAATAATTAAA
Found at i:8949 original size:15 final size:15
Alignment explanation
Indices: 8931--8981 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
8921 ATAATATAAA
8931 TATATATTTAAAATT
1 TATATATTTAAAATT
*
8946 TATATAATATTAATTATT
1 TATAT-AT-TTAA-AATT
*
8964 AATATA-TTAAAATT
1 TATATATTTAAAATT
8978 TATA
1 TATA
8982 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.21
15 9 0.31
16 2 0.07
17 5 0.17
18 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATTTAAAATT
Found at i:8955 original size:18 final size:18
Alignment explanation
Indices: 8930--8997 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
8920 TATAATATAA
8930 ATAT-ATATTTAAAATTT
1 ATATAATATTTAAAATTT
8947 ATATAATA-TT--AA-TT
1 ATATAATATTTAAAATTT
8961 AT-TAATATATTAAAATTT
1 ATATAATAT-TTAAAATTT
*
8979 ATA-AAAATTTAAAAATTT
1 ATATAATATTT-AAAATTT
8997 A
1 A
8998 AAATATAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 5 0.12
14 4 0.10
15 4 0.10
17 10 0.24
18 19 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAATATTTAAAATTT
Found at i:10001 original size:2 final size:2
Alignment explanation
Indices: 9990--10038 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
9980 AAATTAAAAA
*
9990 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10032 AT AT AT A
1 AT AT AT A
10039 GTTGCATGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14553 original size:7 final size:7
Alignment explanation
Indices: 14541--14573 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
14531 CCTCGGTCGA
14541 TGTTGAT
1 TGTTGAT
*
14548 TGTTGAC
1 TGTTGAT
14555 T-TTGAT
1 TGTTGAT
14561 TGTTGAT
1 TGTTGAT
14568 TGTTGA
1 TGTTGA
14574 CTTTGACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.15, C:0.03, G:0.27, T:0.55
Consensus pattern (7 bp):
TGTTGAT
Found at i:14566 original size:20 final size:20
Alignment explanation
Indices: 14541--14579 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14531 CCTCGGTCGA
14541 TGTTGATTGTTGACTTTGAT
1 TGTTGATTGTTGACTTTGAT
14561 TGTTGATTGTTGACTTTGA
1 TGTTGATTGTTGACTTTGA
14580 CCAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.26, T:0.54
Consensus pattern (20 bp):
TGTTGATTGTTGACTTTGAT
Found at i:15752 original size:13 final size:14
Alignment explanation
Indices: 15724--15753 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15714 CCTAGAGGAC
15724 AAAAAGAAAGACAAA
1 AAAAAGAAAGA-AAA
15739 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
15753 A
1 A
15754 TAAGAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:19890 original size:21 final size:21
Alignment explanation
Indices: 19861--19917 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
19851 ATTTTTATCC
19861 AAATGTATCGATACATTTATA
1 AAATGTATCGATACATTTATA
* * *
19882 AAATATATCGATATATTTGTA
1 AAATGTATCGATACATTTATA
*
19903 GAATGTATCGATACA
1 AAATGTATCGATACA
19918 AGGTCCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATGTATCGATACATTTATA
Done.