Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_42 ID=scaffold_42-JGI_221_v2.0
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: 52286
ACGTcount: A:0.17, C:0.08, G:0.07, T:0.17
Warning! 26604 characters in sequence are not A, C, G, or T
Found at i:2935 original size:2 final size:2
Alignment explanation
Indices: 2928--2971 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2918 NNNNNNNNNN
2928 AT AT AT 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
2970 AT
1 AT
2972 TAGCTTCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6443 original size:20 final size:20
Alignment explanation
Indices: 6418--6456 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6408 AGAATCGTGA
6418 TAAGCTGGACAATGCATATG
1 TAAGCTGGACAATGCATATG
*
6438 TAAGCTGGACCATGCATAT
1 TAAGCTGGACAATGCATAT
6457 ATAGTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (20 bp):
TAAGCTGGACAATGCATATG
Found at i:6890 original size:65 final size:66
Alignment explanation
Indices: 6786--6917 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 66
6776 AGTGGGCAAA
6786 ACAAGGACGACGCCAAGGGAGCTGGTAGGGGTCAGGCCACCCTAAAACT-AAAAAAAATCACTTT
1 ACAAGGACGACGCCAAGGGAGCTGGTAGGGGTCAGGCCACCCTAAAACTAAAAAAAAATCACTTT
6850 G
66 G
6851 ACAAGGACGACGCCAAGGGAGCTGGTAGGGGTCAGGCCACCCTAAAACTAAAAAAAAATCACTTT
1 ACAAGGACGACGCCAAGGGAGCTGGTAGGGGTCAGGCCACCCTAAAACTAAAAAAAAATCACTTT
6916 G
66 G
6917 A
1 A
6918 TCCCCTTAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 49 0.74
66 17 0.26
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (66 bp):
ACAAGGACGACGCCAAGGGAGCTGGTAGGGGTCAGGCCACCCTAAAACTAAAAAAAAATCACTTT
G
Found at i:8431 original size:17 final size:17
Alignment explanation
Indices: 8384--8432 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
8374 AATAATTCAA
8384 AAAT-TATAAAAATATTT
1 AAATATATAAAAAT-TTT
* *
8401 AAACAAATAAAAATTTT
1 AAATATATAAAAATTTT
*
8418 AAATATATATAAATT
1 AAATATATAAAAATT
8433 CGAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATAAAAATTTT
Found at i:9868 original size:20 final size:20
Alignment explanation
Indices: 9825--9867 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
9815 TAAATAATTT
*
9825 AAATTATTAAAAAATTATAA
1 AAATTATTAAAAAATAATAA
*
9845 AAATTATTTAAAAAGTAATAA
1 AAATTA-TTAAAAAATAATAA
9866 AA
1 AA
9868 TCAGTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATTATTAAAAAATAATAA
Found at i:10712 original size:14 final size:14
Alignment explanation
Indices: 10693--10721 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10683 GATTTTGATC
10693 TAAAATAATTCAAA
1 TAAAATAATTCAAA
10707 TAAAATAATTCAAA
1 TAAAATAATTCAAA
10721 T
1 T
10722 TTAATCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAATAATTCAAA
Found at i:12959 original size:9 final size:9
Alignment explanation
Indices: 12945--13009 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
12935 TAACAATTAT
12945 TTTTAAAAA
1 TTTTAAAAA
12954 TTTT-AAAA
1 TTTTAAAAA
12962 TTTTGAAAAA
1 TTTT-AAAAA
*
12972 -TAT-AAAA
1 TTTTAAAAA
*
12979 TCATTTACAAA
1 T--TTTAAAAA
12990 TTTTAAAAA
1 TTTTAAAAA
12999 TTATTAAAAA
1 TT-TTAAAAA
13009 T
1 T
13010 ATAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 4 0.09
8 8 0.18
9 15 0.33
10 14 0.31
11 4 0.09
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:13008 original size:37 final size:36
Alignment explanation
Indices: 12946--13015 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
12936 AACAATTATT
12946 TTTAAAAATTTTAAAATTTTGAAAAATATAAAATCA
1 TTTAAAAATTTTAAAATTTTGAAAAATATAAAATCA
*
12982 TTTACAAATTTTAAAAATTATT-AAAAATATAAAA
1 TTTAAAAATTTT-AAAATT-TTGAAAAATATAAAA
13016 AATATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 11 0.35
37 18 0.58
38 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTTAAAAATTTTAAAATTTTGAAAAATATAAAATCA
Found at i:51949 original size:21 final size:20
Alignment explanation
Indices: 51925--51966 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
51915 AATTTAAATA
51925 TTTT-ATGGTGAACTTTATTTT
1 TTTTAATGGT-AACTTT-TTTT
*
51946 TTTTAATTGTAACTTTTTTT
1 TTTTAATGGTAACTTTTTTT
51966 T
1 T
51967 AATTGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTAATGGTAACTTTTTTT
Found at i:51964 original size:16 final size:17
Alignment explanation
Indices: 51942--51981 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
51932 GTGAACTTTA
51942 TTTTTTTTAATTGTAAC
1 TTTTTTTTAATTGTAAC
51959 TTTTTTTTAATTGTAAC
1 TTTTTTTTAATTGTAAC
51976 TATTTT
1 T-TTTT
51982 GAACAGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTTTTAATTGTAAC
Done.