Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_474 ID=scaffold_474-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: 8516
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.20
Warning! 1876 characters in sequence are not A, C, G, or T
Found at i:17 original size:8 final size:8
Alignment explanation
Indices: 5--93 Score: 80
Period size: 8 Copynumber: 11.6 Consensus size: 8
1 GCCC
5 AACCCCTA
1 AACCCCTA
*
13 AACCCCCA
1 AACCCCTA
* *
21 AATCCTTA
1 AACCCCTA
29 AACCCC-A
1 AACCCCTA
36 AACCCCTTA
1 AACCCC-TA
45 AA-CCCTA
1 AACCCCTA
*
52 AAGCCC--
1 AACCCCTA
58 AACCCCTA
1 AACCCCTA
*
66 AACCCCCA
1 AACCCCTA
*
74 AATCCCTA
1 AACCCCTA
82 AACCCC-A
1 AACCCCTA
89 AACCC
1 AACCC
94 TAACCCTAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
6 5 0.08
7 17 0.26
8 40 0.62
9 3 0.05
ACGTcount: A:0.38, C:0.49, G:0.01, T:0.11
Consensus pattern (8 bp):
AACCCCTA
Found at i:71 original size:30 final size:30
Alignment explanation
Indices: 2--96 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
1 G
*
2 CCCAACCCCTAAACCCCCAAAT-CCT-TA-
1 CCCAACCCCTAAACCCCCAAATCCCTAAAC
* *
29 ---AACCCC-AAACCCCTTAAA-CCCTAAAG
1 CCCAACCCCTAAACCCC-CAAATCCCTAAAC
55 CCCAACCCCTAAACCCCCAAATCCCTAAAC
1 CCCAACCCCTAAACCCCCAAATCCCTAAAC
*
85 CCCAAACCCTAA
1 CCCAACCCCTAA
97 CCCTAACCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
23 7 0.13
24 12 0.22
25 1 0.02
29 9 0.17
30 25 0.46
ACGTcount: A:0.38, C:0.49, G:0.01, T:0.12
Consensus pattern (30 bp):
CCCAACCCCTAAACCCCCAAATCCCTAAAC
Found at i:121 original size:7 final size:7
Alignment explanation
Indices: 8--138 Score: 76
Period size: 7 Copynumber: 18.4 Consensus size: 7
1 GCCCAAC
8 CCCTAAA
1 CCCTAAA
*
15 CCCCCAAA
1 -CCCTAAA
*
23 TCCTTAAA
1 -CCCTAAA
*
31 CCCCAAA
1 CCCTAAA
38 CCCCTTAAA
1 -CCC-TAAA
47 CCCTAAA
1 CCCTAAA
*
54 GCCC-AAC
1 -CCCTAAA
61 CCCTAAA
1 CCCTAAA
*
68 CCCCCAAA
1 -CCCTAAA
76 TCCCTAAA
1 -CCCTAAA
*
84 CCCCAAA
1 CCCTAAA
91 CCCT-AA
1 CCCTAAA
97 CCCT-AA
1 CCCTAAA
*
103 -CCTCAGA
1 CCCT-AAA
110 CCCTAAA
1 CCCTAAA
117 CCCTAAA
1 CCCTAAA
*
124 CCAT-AA
1 CCCTAAA
130 CCC-AAA
1 CCCTAAA
136 CCC
1 CCC
139 CTAACACCAA
Statistics
Matches: 96, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
5 3 0.03
6 20 0.21
7 35 0.36
8 35 0.36
9 3 0.03
ACGTcount: A:0.38, C:0.48, G:0.02, T:0.12
Consensus pattern (7 bp):
CCCTAAA
Found at i:143 original size:13 final size:13
Alignment explanation
Indices: 32--160 Score: 50
Period size: 14 Copynumber: 9.2 Consensus size: 13
22 ATCCTTAAAC
32 CCCAAACCCCTTAAA
1 CCCAAACCCC-T-AA
*
47 CCCTAAAGCCC-AA
1 CCC-AAACCCCTAA
*
60 CCCCTAAACCCCCAAA
1 -CCC-AAA-CCCCTAA
*
76 TCCCTAAACCCCAAA
1 -CCC-AAACCCCTAA
*
91 CCCTAA-CCCTAA
1 CCCAAACCCCTAA
*
103 CCTCAGA-CCCTAAA
1 CC-CAAACCCCT-AA
*
117 CCCTAAA-CCATAA
1 CCC-AAACCCCTAA
130 CCCAAACCCCTAA
1 CCCAAACCCCTAA
*
143 CACCAAACACCGTAA
1 C-CCAAAC-CCCTAA
158 CCC
1 CCC
161 CAAAATAGGA
Statistics
Matches: 93, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
12 10 0.11
13 22 0.24
14 27 0.29
15 19 0.20
16 15 0.16
ACGTcount: A:0.39, C:0.48, G:0.02, T:0.11
Consensus pattern (13 bp):
CCCAAACCCCTAA
Found at i:163 original size:15 final size:14
Alignment explanation
Indices: 5--164 Score: 62
Period size: 15 Copynumber: 11.1 Consensus size: 14
1 GCCC
5 AACCCCTAAACCCCCA
1 AACCCCT-AA-CCCCA
* *
21 AATCCTTAAACCCCA
1 AACCCCT-AACCCCA
*
36 AACCCCTTAAACCCTA
1 AACCCC-T-AACCCCA
*
52 AAGCCC-AACCCCTA
1 AACCCCTAACCCC-A
* *
66 AACCCCCAAATCCCTA
1 AA-CCCCTAA-CCCCA
* *
82 AACCCC-AAACCCT
1 AACCCCTAACCCCA
*
95 AA-CCCTAACCTCA
1 AACCCCTAACCCCA
* *
108 GA-CCCTAAACCCTA
1 AACCCCT-AACCCCA
*
122 AA-CCATAA-CCCA
1 AACCCCTAACCCCA
*
134 AACCCCTAACACCA
1 AACCCCTAACCCCA
*
148 AACACCGTAACCCCA
1 AAC-CCCTAACCCCA
163 AA
1 AA
165 ATAGGAACCT
Statistics
Matches: 109, Mismatches: 25, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
12 8 0.07
13 25 0.23
14 20 0.18
15 27 0.25
16 26 0.24
17 3 0.03
ACGTcount: A:0.40, C:0.47, G:0.02, T:0.11
Consensus pattern (14 bp):
AACCCCTAACCCCA
Found at i:7258 original size:31 final size:31
Alignment explanation
Indices: 7184--7264 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
7174 AAGAATGAAT
** * *
7184 TAAATTCAGTGCCCACTAAATCGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
*
7215 TAAATTTAGTGCTTATTAAAACGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
7246 TAAATTCAGTGCTTATTAA
1 TAAATTCAGTGCTTATTAA
7265 TACCCGGCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
TAAATTCAGTGCTTATTAAAACGTTGTAAAA
Done.