Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_469 ID=scaffold_469-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: 6773
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:190 original size:108 final size:109
Alignment explanation
Indices: 1--288 Score: 506
Period size: 108 Copynumber: 2.6 Consensus size: 109
* *
1 TTTGCGTTTGGAAGTTCGAGAAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTCTCGTTCAACC
1 TTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACC
66 AAATAGCTTAATATCCTTTTAAAA-TTTTAAAATAAGGCAATGT
66 AAATAGCTTAATATCCTTTTAAAATTTTTAAAATAAGGCAATGT
*
109 TTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTTGATTTTTCTCGTTCAACC
1 TTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACC
*
174 AAATGGCTTAATATCCTTTTAAAATTTTTAAAATAAGGCAATGT
66 AAATAGCTTAATATCCTTTTAAAATTTTTAAAATAAGGCAATGT
* *
218 TTTACGTTTGGAAATTCGAAAAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAAC
1 TTTGCGTTTGGAAATTCG-AGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAAC
283 CAAATA
65 CAAATA
289 ACTAAAGATC
Statistics
Matches: 170, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
108 85 0.50
109 36 0.21
110 49 0.29
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
TTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACC
AAATAGCTTAATATCCTTTTAAAATTTTTAAAATAAGGCAATGT
Found at i:3010 original size:26 final size:27
Alignment explanation
Indices: 2955--3003 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
2945 ATAAAATACA
*
2955 TCTTTGCATTCCTTTTTGAGCTAATAT
1 TCTTTGCATTCCTTTTTGAGATAATAT
2982 TCTTT-CATT-CTTTTTGA-ATAAT
1 TCTTTGCATTCCTTTTTGAGATAAT
3004 TATTTCTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 4 0.19
27 5 0.24
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (27 bp):
TCTTTGCATTCCTTTTTGAGATAATAT
Found at i:3695 original size:6 final size:6
Alignment explanation
Indices: 3676--3759 Score: 62
Period size: 6 Copynumber: 13.7 Consensus size: 6
3666 AGAAAAAGAA
* * * * * *
3676 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* *
3724 AAAATG AAAATGAA AAAATC AAAAATC AAAAT- AAAA
1 AAAATC AAAAT--C AAAATC -AAAATC AAAATC AAAA
3760 AAAACAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
5 4 0.06
6 55 0.79
7 6 0.09
8 5 0.07
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:3754 original size:21 final size:21
Alignment explanation
Indices: 3724--3769 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3714 AATGAAAATG
* * *
3724 AAAATGAAAATGAAAAAATCA
1 AAAATCAAAATAAAAAAAACA
3745 AAAATCAAAATAAAAAAAACA
1 AAAATCAAAATAAAAAAAACA
3766 AAAA
1 AAAA
3770 GAAGAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAATCAAAATAAAAAAAACA
Found at i:3760 original size:6 final size:6
Alignment explanation
Indices: 3694--3739 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
3684 AATCAAAGTC
3694 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
3740 AATCAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:3784 original size:51 final size:53
Alignment explanation
Indices: 3682--3844 Score: 126
Period size: 51 Copynumber: 3.1 Consensus size: 53
3672 AGAAAAAATC
* * *
3682 AAAATCAAAGTCAAAATGAAAATGAAAA-TGAAAATGAAAATGAAA-ATGAAAATGAA
1 AAAATCAAAATCAAAATGAAAAT-AAAACT-AAAA--AGAA-GAAAGAAGAAAATGAA
*
3738 AAAATCAAAAATCAAAAT-AAAA-AAAAC-AAAAAGAAGAAAGAAGAAAA-AAA
1 AAAATC-AAAATCAAAATGAAAATAAAACTAAAAAGAAGAAAGAAGAAAATGAA
* * * *
3788 TTAAAATCAAGATCAAAATGAAAATGAAACTGAGAAGAAGAAAGAAG--AATGAA
1 --AAAATCAAAATCAAAATGAAAATAAAACTAAAAAGAAGAAAGAAGAAAATGAA
3841 AAAA
1 AAAA
3845 GAGAAATCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
50 6 0.07
51 23 0.26
52 12 0.13
53 10 0.11
54 18 0.20
56 10 0.11
57 10 0.11
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.12
Consensus pattern (53 bp):
AAAATCAAAATCAAAATGAAAATAAAACTAAAAAGAAGAAAGAAGAAAATGAA
Found at i:6067 original size:46 final size:45
Alignment explanation
Indices: 5991--6324 Score: 370
Period size: 46 Copynumber: 7.6 Consensus size: 45
5981 ATAAAATAGA
* *
5991 ACATACAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG
1 ACAT-CAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* * *
6037 ACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
1 AC-ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* * *
6083 ACAT--GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G
1 ACATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* *
6123 -CATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG
1 ACATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* * *
6167 ACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
1 AC-ATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* * *
6213 ACAT--GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G
1 ACATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
* *
6253 -CATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG
1 ACATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
6297 A-ATTTCAGATCTTATCTCCCTGAGGTTA
1 ACA--TCAGATCTTATCTCCCTGAGGTTA
6325 NNNNNNNNNN
Statistics
Matches: 239, Mismatches: 33, Indels: 32
0.79 0.11 0.11
Matches are distributed among these distances:
39 6 0.03
40 2 0.01
41 60 0.25
43 60 0.25
44 3 0.01
45 3 0.01
46 104 0.44
47 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (45 bp):
ACATCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG
Found at i:6142 original size:84 final size:85
Alignment explanation
Indices: 6000--6324 Score: 341
Period size: 84 Copynumber: 3.7 Consensus size: 85
5990 AACATACAGG
*
6000 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG----TCAGATCTTATCTCCCTGAGGTTA
* *
6065 CAGCGGAGCAGATCGAAGACATGA
62 CAGTGGAGTAGATCGAAGACATGA
* * * * *
6089 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTACAGT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
* *
6153 GGAGTAGACCGAAGACTTTCAGA
66 GGAGTAGATCGAAGAC-AT--GA
* * * * *
6176 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGTCA-GATCTTATCTCCCTGAGGTTACAG
* * * *
6241 TAGAGTAGATCGCA-TCA-GG
65 TGGAGTAGATCGAAGACATGA
*
6260 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG----TCAGATCTTATCTCCCTGAGGTTA
6325 NNNNNNNNNN
Statistics
Matches: 195, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
84 75 0.38
85 1 0.01
87 51 0.26
88 5 0.03
89 63 0.32
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (85 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
GGAGTAGATCGAAGACATGA
Found at i:6229 original size:130 final size:130
Alignment explanation
Indices: 5996--6324 Score: 649
Period size: 130 Copynumber: 2.5 Consensus size: 130
5986 ATAGAACATA
5996 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
6061 GTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 GTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
6126 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
6191 GTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 GTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
*
6256 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
6321 GTTA
66 GTTA
6325 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 198 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (130 bp):
CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAG
GTTACAGCGGAGCAGATCGAAGACATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:6628 original size:89 final size:89
Alignment explanation
Indices: 6434--6769 Score: 377
Period size: 89 Copynumber: 3.9 Consensus size: 89
6424 NAGCCTTTCA
* * * * * * *
6434 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAC-AT--GGTCTTATCTCTCTGAAGT
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
* ** * *
6496 TATAGTAGAGTAGATCGCA-TCA-
66 TACAGCGGAGTAGATCGAAGACAT
* * *
6518 GGTCTCATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
*
6583 TACAGCGGAGCAGATCGAAGACAT
66 TACAGCGGAGTAGATCGAAGACAT
*
6607 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGCCTTTCAGATCTTATCTCCCTGAGGT
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
6672 TACAGCGGAGTAGATCGAAGACAT
66 TACAGCGGAGTAGATCGAAGACAT
* * * * * * *
6696 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G-C-ATCAGGTCTTATCTCACTGAGGT
1 GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
*
6756 TACAGGGGAGTAGA
66 TACAGCGGAGTAGA
6770 CCGA
Statistics
Matches: 218, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
84 68 0.31
85 2 0.01
86 1 0.00
87 30 0.14
88 2 0.01
89 115 0.53
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (89 bp):
GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGT
TACAGCGGAGTAGATCGAAGACAT
Done.