Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g02721.F10
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: 3006
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Found at i:653 original size:69 final size:69
Alignment explanation
Indices: 533--694 Score: 229
Period size: 69 Copynumber: 2.3 Consensus size: 69
523 CCTCTGCGAA
*
533 TCCTCATCCTAGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT
1 TCCTCATCCTTGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT
598 CGAG
66 CGAG
* * *
602 TCCTCATCCTTGCATTGACGAAAGG-AACATGGATAATGTTGTCT-ATTCTTCTGCTCAAGTCCC
1 TCCTCATCCTTGCACTGACG-AAGGAAACATGGATAATGTTGTATCA-GCTTCTGCTCAAGTCCC
*
665 TTCGAG
64 CTCGAG
* *
671 TCCTCATCCTTGCTCTGATGAAGG
1 TCCTCATCCTTGCACTGACGAAGG
695 GAATAGTATG
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
68 5 0.06
69 74 0.89
70 4 0.05
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (69 bp):
TCCTCATCCTTGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT
CGAG
Found at i:970 original size:69 final size:69
Alignment explanation
Indices: 855--986 Score: 167
Period size: 69 Copynumber: 1.9 Consensus size: 69
845 GCCGCTTACG
** * * * * *
855 GTGGATAATGTTGTCTCTGCTTCTGCTGAAGTTTCCCCAAGCCCTCACCCTTGCGCTGACAAAGG
1 GTGGATAATGTTACCTCTGCTGCTGCTCAAGTTCCCCCAAGCCCTCACCCTTGCACTAACAAAGG
920 GAAC
66 GAAC
* *
924 GTGGATAATGTTACCTCTGCTGCTGCTCAAG-TCCCCTCAAGTCCTCATCCTTGCACTAACAAA
1 GTGGATAATGTTACCTCTGCTGCTGCTCAAGTTCCCC-CAAGCCCTCACCCTTGCACTAACAAA
987 AAGAACAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 4 0.08
69 49 0.92
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (69 bp):
GTGGATAATGTTACCTCTGCTGCTGCTCAAGTTCCCCCAAGCCCTCACCCTTGCACTAACAAAGG
GAAC
Found at i:1936 original size:243 final size:243
Alignment explanation
Indices: 1508--1994 Score: 884
Period size: 243 Copynumber: 2.0 Consensus size: 243
1498 CAAGTGTTGT
*
1508 TGATTTGACAGCTTCTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
1 TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
*
1573 CTTTCATGGAAGCAGCTAAAAGTTTAAGTGCAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
66 CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
*
1638 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACGGGCTCAAGCTGAGAGGAGGGAACCTGA
131 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA
1703 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
196 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
* *
1751 TGATTTGACAGCTACTGTTGCTGATTCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
1 TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
* *
1816 CTTTCATGGCAGCAGCTAAAAGTTTAAGTACTGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
66 CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
*
1881 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGCACCTGA
131 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA
**
1946 CAAGGCCATCAGAGAAGACCAGGACAAGATGGGCAGGAGTGTTCCTGC
196 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
1994 T
1 T
1995 TCGTCTGTTG
Statistics
Matches: 234, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 234 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.24
Consensus pattern (243 bp):
TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA
CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
Done.