Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1414
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: 12845
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1947 original size:24 final size:24
Alignment explanation
Indices: 1867--1948 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
1857 AATTAGTTGA
*
1867 ATTAAATTATTTAATTAAAACATATTAAT
1 ATTAAA-TATTTAATT-ATA-ATATT--T
* * *
1896 ATTAAATATTTAATTTTGATATTA
1 ATTAAATATTTAATTATAATATTT
1920 ATTAAATATTTAA-TATAATAATTT
1 ATTAAATATTTAATTATAAT-ATTT
1944 ATTAA
1 ATTAA
1949 TAAAATTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
23 4 0.09
24 21 0.47
26 5 0.11
28 9 0.20
29 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTAAATATTTAATTATAATATTT
Found at i:1986 original size:20 final size:22
Alignment explanation
Indices: 1945--1987 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1935 TAATAATTTA
1945 TTAATAAAATTATATATTTAAT
1 TTAATAAAATTATATATTTAAT
*
1967 TTAATAATATTAT-T-TTTAAT
1 TTAATAAAATTATATATTTAAT
1987 T
1 T
1988 AATGACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATAAAATTATATATTTAAT
Found at i:7919 original size:31 final size:31
Alignment explanation
Indices: 7884--7946 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
7874 AAGTTGATGA
* *
7884 TTTTTAAA-AAAAATTATTATTAATATATAAT
1 TTTTTAAATAAAAATAAATA-TAATATATAAT
*
7915 TTTTTAAATTAAAATAAATATAATATATAAT
1 TTTTTAAATAAAAATAAATATAATATATAAT
7946 T
1 T
7947 AAATAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTTTAAATAAAAATAAATATAATATATAAT
Found at i:8081 original size:22 final size:20
Alignment explanation
Indices: 8032--8081 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
8022 TTAAAATTTT
8032 TATTAA-TTTAAAAATAAAA
1 TATTAATTTTAAAAATAAAA
* *
8051 TATTTATTTTAAAAACATATAA
1 TATTAATTTT-AAAA-ATAAAA
8073 TATTAATTT
1 TATTAATTT
8082 ATCATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 4 0.16
22 13 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAATTTTAAAAATAAAA
Found at i:9328 original size:17 final size:17
Alignment explanation
Indices: 9284--9327 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
9274 GTAATCAATT
*
9284 AAATTAATTTGGACAAA
1 AAATTAATTTTGACAAA
9301 AAATTAATTTTGACAAA
1 AAATTAATTTTGACAAA
9318 AAATT-ATTTT
1 AAATTAATTTT
9328 TAAATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (17 bp):
AAATTAATTTTGACAAA
Found at i:10556 original size:13 final size:13
Alignment explanation
Indices: 10538--10563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10528 CAATTTTTTG
10538 TGTATCGATACAT
1 TGTATCGATACAT
10551 TGTATCGATACAT
1 TGTATCGATACAT
10564 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10628 original size:21 final size:21
Alignment explanation
Indices: 10602--10677 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
10592 CTGCCAAGAA
*
10602 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
10623 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
10643 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
10664 ATGTATCGATACAT
1 ATGTATCGATACAT
10678 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:10648 original size:20 final size:20
Alignment explanation
Indices: 10623--10695 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
10613 CATCTTTTTT
10623 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
10643 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
10664 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
10684 ATGTATCGATAC
1 ATGTATCGATAC
10696 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:10659 original size:41 final size:41
Alignment explanation
Indices: 10602--10695 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
10592 CTGCCAAGAA
*
10602 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
10643 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
10684 ATGTATCGATAC
1 ATGTATCGATAC
10696 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Done.