Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold25
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 471
Length: 786
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:266 original size:144 final size:144
Alignment explanation
Indices: 1--542 Score: 667
Period size: 144 Copynumber: 3.8 Consensus size: 144
* * *
1 ACCGACTCCGATGGCTTGTTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCTGGTTCGTT
1 ACCGACTCCGACGGCTTGCTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCCGGTTCGTT
* *
66 GACTGAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTACCACCGACTCAGGTC
66 GACTGAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTACTACCGACTCGGGTC
131 TTGTTGATGTGACC
131 TTGTTGATGTGACC
* *
145 ACCGACTCCGATGGCTTGTTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCCGGTTCGTT
1 ACCGACTCCGACGGCTTGCTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCCGGTTCGTT
* * * * *
210 GACTGAGTACACCACTACCTGGACCACTACTGGT-AGTGATGGTATGCCCACTACCGACTCGGGT
66 GACTGAGTACACCACCACCTGGACCACCACTGGTCA-CGATGGTAAGCCTACTACCGACTCGGGT
* * * *
274 ATTGTCGACT-TCACT
130 CTTGTTGA-TGTGACC
* * * * *
289 ACCGGCTCGGACGGCTTGCTGACAACTTCTAC--CC-TGACCTTCCCGC-----AC-TCCGGTCC
1 ACCGACTCCGACGGCTTGCTGACCACTTCGACGTCCGTG---TTCCCGCATTTGACGTCCGGT-T
* * *
345 CG-TGACTGAGTACACCACTACATGGACCACTACTGGTCACGATGGTAAGCCTACTACCGACTCG
62 CGTTGACTGAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTACTACCGACTCG
409 GGTCTTGTTGATGTGACC
127 GGTCTTGTTGATGTGACC
* * ** * *
427 ACCGACTCCAACGGCTCGCTGGGCACTTCGACGTCCGTGTTCCCTCATTTGACGTCTGGTTCGTT
1 ACCGACTCCGACGGCTTGCTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCCGGTTCGTT
*
492 GACTGAGTACACCACCACCTGGACCACCACTGGTGACGATGGTAAGCCTAC
66 GACTGAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTAC
543 NCACCTGGAC
Statistics
Matches: 338, Mismatches: 42, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
137 1 0.00
138 104 0.31
139 5 0.01
140 2 0.01
141 4 0.01
142 2 0.01
143 5 0.01
144 214 0.63
145 1 0.00
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.25
Consensus pattern (144 bp):
ACCGACTCCGACGGCTTGCTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCCGGTTCGTT
GACTGAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTACTACCGACTCGGGTC
TTGTTGATGTGACC
Left flanking sequence: None
Right flanking sequence: Indices 543 -- 786
NCACCTGGACCACCACTGGTGACGATGGTAAGCCTACCACCGACTCAGGTCTTGTTGATGTGACC
ACCGACTCCGATGGCTCGTTGACCACTTCTACCCTGACCTTCCCACACTCCGGTCCCGTGACTGA
GTACACCACCACCTGGACCACCACTGGTGACGATGGTAAGCCTACTACCGACTCGGGTCTTGTTG
ATGTGACCACCGACTCTAACGGCTCGCTGGGCACTTCGACGTCCGTGTT
Found at i:548 original size:37 final size:36
Alignment explanation
Indices: 505--583 Score: 149
Period size: 37 Copynumber: 2.2 Consensus size: 36
495 TGAGTACACC
505 ACCACCTGGACCACCACTGGTGACGATGGTAAGCCT
1 ACCACCTGGACCACCACTGGTGACGATGGTAAGCCT
541 ACNCACCTGGACCACCACTGGTGACGATGGTAAGCCT
1 AC-CACCTGGACCACCACTGGTGACGATGGTAAGCCT
578 ACCACC
1 ACCACC
584 GACTCAGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 6 0.14
37 36 0.86
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.15
Consensus pattern (36 bp):
ACCACCTGGACCACCACTGGTGACGATGGTAAGCCT
Left flanking sequence: Indices 5 -- 504
ACTCCGATGGCTTGTTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGTCTGGTTCGTTGACT
GAGTACACCACCACCTGGACCACCACTGGTCACGATGGTAAGCCTACCACCGACTCAGGTCTTGT
TGATGTGACCACCGACTCCGATGGCTTGTTGACCACTTCGACGTCCGTGTTCCCGCATTTGACGT
CCGGTTCGTTGACTGAGTACACCACTACCTGGACCACTACTGGTAGTGATGGTATGCCCACTACC
GACTCGGGTATTGTCGACTTCACTACCGGCTCGGACGGCTTGCTGACAACTTCTACCCTGACCTT
CCCGCACTCCGGTCCCGTGACTGAGTACACCACTACATGGACCACTACTGGTCACGATGGTAAGC
CTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCCAACGGCTCGCTGGGCACTTCGACG
TCCGTGTTCCCTCATTTGACGTCTGGTTCGTTGACTGAGTACACC
Right flanking sequence: Indices 584 -- 786
GACTCAGGTCTTGTTGATGTGACCACCGACTCCGATGGCTCGTTGACCACTTCTACCCTGACCTT
CCCACACTCCGGTCCCGTGACTGAGTACACCACCACCTGGACCACCACTGGTGACGATGGTAAGC
CTACTACCGACTCGGGTCTTGTTGATGTGACCACCGACTCTAACGGCTCGCTGGGCACTTCGACG
TCCGTGTT
Done.