Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_432 ID=scaffold_432-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: 7084
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Found at i:6749 original size:27 final size:28
Alignment explanation
Indices: 6709--6762 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
6699 CGAATGATTC
6709 GGGGAATCAACACTTAGCAA-CCCCTTA
1 GGGGAATCAACACTTAGCAAGCCCCTTA
*
6736 GGGGAATCAGCACTTAGCAAGCCCCTT
1 GGGGAATCAACACTTAGCAAGCCCCTT
6763 CACATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (28 bp):
GGGGAATCAACACTTAGCAAGCCCCTTA
Found at i:6817 original size:103 final size:102
Alignment explanation
Indices: 6633--6864 Score: 356
Period size: 103 Copynumber: 2.3 Consensus size: 102
6623 CCACTGATTC
* * *
6633 GGGGGATCAGCACTTAGCAATCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAA-CCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
6698 ACGAATGATTCGGGGAATCAACACTTAGCAACCCCTTA
65 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTA
*
6736 GGGGAATCAGCACTTAGCAAGCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAA-CCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
* * *
6801 ACCAATGAATCGGGGAATCAGCACTTAGCAAGCCCTTG
65 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTA
*
6839 GGGGATTCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
6865 GGGGGATTCA
Statistics
Matches: 118, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 6 0.05
103 112 0.95
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTA
Found at i:6848 original size:27 final size:27
Alignment explanation
Indices: 6812--6889 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
6802 CCAATGAATC
* *
6812 GGGGAATCAGCACTTAGCAAGCCCTTG
1 GGGGATTCAGCACTTAGCAACCCCTTG
6839 GGGGATTCAGCACTTAGCAACCCCTTG
1 GGGGATTCAGCACTTAGCAACCCCTTG
6866 GGGGATTCAGCACTTAGCAACCCC
1 GGGGATTCAGCACTTAGCAACCCC
6890 CTTTATATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.19
Consensus pattern (27 bp):
GGGGATTCAGCACTTAGCAACCCCTTG
Found at i:6877 original size:130 final size:130
Alignment explanation
Indices: 6709--6992 Score: 478
Period size: 130 Copynumber: 2.2 Consensus size: 130
6699 CGAATGATTC
*
6709 GGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAGCACTTAGCAAGCCCCTTCACATTTAAAG
1 GGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAG
*
6774 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAAGCCCTTG
66 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* * * * * * *
6839 GGGGATTCAGCACTTAGCAACCCCTTGGGGGATTCAGCACTTAGCAACCCCCTTTATATTTAAGG
1 GGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAG
*
6904 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGTGAATCAGCACTTAGCAACCCCTTG
66 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
6969 GGGGAATCAACACTTAGCAACCCC
1 GGGGAATCAACACTTAGCAACCCC
6993 CTTTATATTT
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 142 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (130 bp):
GGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAG
ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:6952 original size:103 final size:103
Alignment explanation
Indices: 6839--7070 Score: 410
Period size: 103 Copynumber: 2.3 Consensus size: 103
6829 CAAGCCCTTG
* * *
6839 GGGGATTCAGCACTTAGCAACCCCTTGGGGGATTCAGCACTTAGCAACCCCCTTTATATTTAAGG
1 GGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCCTTTATATTTAAGG
6904 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATC
66 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATC
*
6942 GGTGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCCTTTATATTTAAGG
1 GGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCCTTTATATTTAAGG
* *
7007 ATACGGTGGAATCAGCACTTAGCAACCACTAATGATTC
66 ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATC
7045 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
7071 CATATTCAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 122 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCCTTTATATTTAAGG
ATACGGTGGAATCAGCACTTAGCAACCACCAATGAATC
Found at i:7049 original size:233 final size:232
Alignment explanation
Indices: 6633--7070 Score: 689
Period size: 233 Copynumber: 1.9 Consensus size: 232
6623 CCACTGATTC
* *
6633 GGGGGATCAGCACTTAGCAATCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGGATCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
* * * *
6698 ACGAATGATTCGGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAGCACTTAGCAAGCCCCTT
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAACACTTAGCAACCCCCTT
6763 CACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTA
131 CACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTA
*
6828 GCAAGCCCTTGGGGGATTCAGCACTTAGCAACCCCTT
196 GCAACCCCTTGGGGGATTCAGCACTTAGCAACCCCTT
* * *
6865 GGGGGATTCAGCACTTAGCAACCCCCTTT-ATATTTAAGGATACGGTGGAATCAGCACTTAGCAA
1 GGGGGA-TCAGCACTTAGCAA-CCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAA
* * *
6929 CCACCAATGAATCGGTGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAACCCCC
64 CCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAACACTTAGCAACCCCC
* * * * *
6994 TTTATATTTAAGGATACGGTGGAATCAGCACTTAGCAACCACTAATGATTCGGGGAATCAGCACT
129 TTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACT
7059 TAGCAACCCCTT
194 TAGCAACCCCTT
7071 CATATTCAAT
Statistics
Matches: 186, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
232 6 0.03
233 174 0.94
234 6 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (232 bp):
GGGGGATCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTAGGGGAATCAACACTTAGCAACCCCCTT
CACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTA
GCAACCCCTTGGGGGATTCAGCACTTAGCAACCCCTT
Done.