Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold609
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: 94972
ACGTcount: A:0.12, C:0.06, G:0.07, T:0.13
Warning! 59403 characters in sequence are not A, C, G, or T
Found at i:2743 original size:20 final size:20
Alignment explanation
Indices: 2718--2764 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2708 AGCTCATTTC
*
2718 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
2738 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
2758 CAGCTCA
1 CAGCTCA
2765 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:2767 original size:10 final size:10
Alignment explanation
Indices: 2708--2767 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
2698 AGCTCTGTTT
*
2708 AGCTCATTTCC
1 AGCTCAATT-C
* *
2719 AGCTCACTTG
1 AGCTCAATTC
*
2729 AGCTCAAGTC
1 AGCTCAATTC
2739 AGCTC-ATTC
1 AGCTCAATTC
*
2748 GAGATCAATTC
1 -AGCTCAATTC
2759 AGCTCAATT
1 AGCTCAATT
2768 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:7976 original size:70 final size:70
Alignment explanation
Indices: 7858--7994 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
7848 TTGCATGCCC
7858 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
7923 TGTTG
66 TGTTG
* *
7928 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
7993 TG
66 TG
7995 ATTTAATTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:8092 original size:22 final size:22
Alignment explanation
Indices: 8064--8110 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
8054 TAAATGCATT
*
8064 AATTACCTGCGGACACAAAATA
1 AATTACCTGCAGACACAAAATA
8086 AATTACCTGCAGACACAAAATA
1 AATTACCTGCAGACACAAAATA
8108 AAT
1 AAT
8111 GCATTAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (22 bp):
AATTACCTGCAGACACAAAATA
Found at i:42361 original size:10 final size:10
Alignment explanation
Indices: 42346--42387 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
42336 TTTGCAAGTT
42346 TTGAGCTAAA
1 TTGAGCTAAA
* *
42356 TTGAGCTGAT
1 TTGAGCTAAA
*
42366 TTGAGCT-CA
1 TTGAGCTAAA
42375 TTGAGCTAAA
1 TTGAGCTAAA
42385 TTG
1 TTG
42388 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:77076 original size:25 final size:25
Alignment explanation
Indices: 77038--77094 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
77028 TATTCTATGC
*
77038 TTTTTTTCTATTTTTTTCTTTTCTT
1 TTTTTTTCTATTTTGTTCTTTTCTT
77063 TTTTTATTCT-TTTTGTTCTTTTCTT
1 TTTTT-TTCTATTTTGTTCTTTTCTT
77088 TTTTTTT
1 TTTTTTT
77095 TACTTGCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.07
25 24 0.80
26 4 0.13
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.84
Consensus pattern (25 bp):
TTTTTTTCTATTTTGTTCTTTTCTT
Found at i:77081 original size:9 final size:8
Alignment explanation
Indices: 77037--77092 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
77027 CTATTCTATG
77037 CTTTTTTT
1 CTTTTTTT
*
77045 CTATTTTT
1 CTTTTTTT
*
77053 -TTCTTTT
1 CTTTTTTT
77060 CTTTTTTT
1 CTTTTTTT
*
77068 ATTCTTTTT
1 CTT-TTTTT
* *
77077 GTTCTTTT
1 CTTTTTTT
77085 CTTTTTTT
1 CTTTTTTT
77093 TTTACTTGCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
7 5 0.14
8 25 0.68
9 7 0.19
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (8 bp):
CTTTTTTT
Found at i:77093 original size:9 final size:9
Alignment explanation
Indices: 77038--77095 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
77028 TATTCTATGC
77038 TTTTTTTCT
1 TTTTTTTCT
77047 ATTTTTTTC-
1 -TTTTTTTCT
*
77056 TTTTCTT-T
1 TTTTTTTCT
*
77064 TTTTATTCT
1 TTTTTTTCT
*
77073 TTTTGTTCT
1 TTTTTTTCT
77082 TTTCTTTT-T
1 TTT-TTTTCT
77091 TTTTT
1 TTTTT
77096 ACTTGCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 14 0.34
9 16 0.39
10 11 0.27
ACGTcount: A:0.03, C:0.10, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:88997 original size:20 final size:19
Alignment explanation
Indices: 88972--89009 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
88962 AACATTTTTG
88972 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
88992 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
89010 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Done.