Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1344
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: 13689
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Found at i:2072 original size:19 final size:19
Alignment explanation
Indices: 2048--2085 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2038 TGCACTTTAC
2048 AATCAGTAATTCAATGTAT
1 AATCAGTAATTCAATGTAT
2067 AATCAGTAATTCAATGTAT
1 AATCAGTAATTCAATGTAT
2086 CTTGACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
AATCAGTAATTCAATGTAT
Found at i:4416 original size:13 final size:13
Alignment explanation
Indices: 4398--4429 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4388 TTTCCAGCAA
4398 TTATGAATTTATT
1 TTATGAATTTATT
4411 TTATGAATTTATT
1 TTATGAATTTATT
*
4424 TGATGA
1 TTATGA
4430 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4668 original size:50 final size:50
Alignment explanation
Indices: 4521--4767 Score: 293
Period size: 50 Copynumber: 4.8 Consensus size: 50
4511 ATTTGGGTAA
* *
4521 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
*
4577 AGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
4626 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
4676 AGAGGTCCCCTATAAGACCATGT-TGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GACG
** *
4725 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4768 TGTTATCAGA
Statistics
Matches: 169, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
48 1 0.01
49 32 0.19
50 75 0.44
51 17 0.10
52 3 0.02
54 2 0.01
55 31 0.18
56 8 0.05
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:4757 original size:100 final size:102
Alignment explanation
Indices: 4525--4768 Score: 336
Period size: 100 Copynumber: 2.4 Consensus size: 102
4515 GGGTAAAGAG
*
4525 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCTGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCCTATA
* *
4590 AGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAG
63 AGACCATGTCTGGGACATGGCATGGGCACCGACACGAGAC
* * *
4630 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTATAAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGT-CCCTATAAG
4692 ACCATGT-TGGGACATGGCATGGGCACC-ATCACGAGAAC
65 ACCATGTCTGGGACATGGCATGGGCACCGA-CACGAG-AC
*
4730 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4769 GTTATCAGAA
Statistics
Matches: 127, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
98 1 0.01
99 34 0.27
100 54 0.43
104 2 0.02
105 36 0.28
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (102 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCTATAAGA
CCATGTCTGGGACATGGCATGGGCACCGACACGAGAC
Found at i:11741 original size:29 final size:30
Alignment explanation
Indices: 11682--11739 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11672 TCCGAGCCTT
*
11682 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
11712 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
11740 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:11969 original size:13 final size:13
Alignment explanation
Indices: 11951--11982 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11941 TTTCCAGCAA
11951 TTATGAATTTATT
1 TTATGAATTTATT
11964 TTATGAATTTATT
1 TTATGAATTTATT
*
11977 TGATGA
1 TTATGA
11983 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:12190 original size:50 final size:50
Alignment explanation
Indices: 12077--12318 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
12067 ATTTGGGTAA
* * *
12077 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
12133 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
12183 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
12233 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
12283 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
12319 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:12266 original size:100 final size:103
Alignment explanation
Indices: 12077--12326 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
12067 ATTTGGGTAA
12077 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
12142 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
12183 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
12245 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
12283 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
12327 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Done.