Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_434 ID=scaffold_434-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: 7067
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:2872 original size:28 final size:28
Alignment explanation
Indices: 2840--2900 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
2830 AAATACAGGT
2840 GGCCCATAGGCAGCAAGTAGGTAAATCC
1 GGCCCATAGGCAGCAAGTAGGTAAATCC
* *
2868 GGCCCATGGGCGGCAAGTAGGTAAATCC
1 GGCCCATAGGCAGCAAGTAGGTAAATCC
2896 GGCCC
1 GGCCC
2901 TGTTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.13
Consensus pattern (28 bp):
GGCCCATAGGCAGCAAGTAGGTAAATCC
Found at i:3066 original size:17 final size:17
Alignment explanation
Indices: 3041--3074 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3031 CTTTTTACGA
* *
3041 AATTTTTATGTTAATTT
1 AATTGTTATGTAAATTT
3058 AATTGTTATGTAAATTT
1 AATTGTTATGTAAATTT
3075 GACTTCCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
AATTGTTATGTAAATTT
Found at i:5920 original size:231 final size:231
Alignment explanation
Indices: 5505--6100 Score: 1070
Period size: 231 Copynumber: 2.6 Consensus size: 231
5495 CTATTAAACT
*
5505 GTGACTCGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
1 GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
**
5570 ACATTACAGTCA-ACGTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCAT
66 ACATTATGGTCACA-GTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCAT
*
5634 TTGGCGACACATGTTAACACTCTTTGAACATCTGAGGTATGAGTTCTGGAAATTTTGGCTATACT
130 TTGGCGACACATGTTAACACTCTTTGAACATCTGAGGTATGAGTTCTGAAAATTTTGGCTATACT
*
5699 TGGTTGCTAAACGCTACTT-AACAGTAAATGTTCAACA
195 TGGTTGCTAAACGCTA-TTGAACAGCAAATGTTCAACA
5736 GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
1 GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
* *
5801 ACATTATGGTCACAGTTGATTGCTAAATGCTACCAAACCATAGCTAAATGATCAGAAATTCCATT
66 ACATTATGGTCACAGTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCATT
5866 TGGCGACACATGTTAACACTCTTTGAACATCTGAGGTATGAGTTCTGAAAATTTTGGCTATACTT
131 TGGCGACACATGTTAACACTCTTTGAACATCTGAGGTATGAGTTCTGAAAATTTTGGCTATACTT
* * *
5931 GGTTGCTGAACGCTATTGAACAGCGAATGTTCAACG
196 GGTTGCTAAACGCTATTGAACAGCAAATGTTCAACA
5967 GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
1 GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
6032 ACATTATGGTCACAGTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCATT
66 ACATTATGGTCACAGTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCATT
6097 TGGC
131 TGGC
6101 ATAATGGAGA
Statistics
Matches: 351, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
230 2 0.01
231 348 0.99
232 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (231 bp):
GTGACTTGATGATAAAGAATGCCATAGGGCGACATTCCGCCGAAAGGCACCTGTGTGGGTTCTTT
ACATTATGGTCACAGTTGATTGCTAAACGCTACCAAACCATGGCTAAATGATCAGAAATTCCATT
TGGCGACACATGTTAACACTCTTTGAACATCTGAGGTATGAGTTCTGAAAATTTTGGCTATACTT
GGTTGCTAAACGCTATTGAACAGCAAATGTTCAACA
Done.