Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01745.N7
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: 9247
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Found at i:147 original size:13 final size:13
Alignment explanation
Indices: 131--157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
121 TTCGAGTCTC
131 TAATTCATATTAA
1 TAATTCATATTAA
144 TAATTCATATTAA
1 TAATTCATATTAA
157 T
1 T
158 TATGAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTCATATTAA
Found at i:586 original size:21 final size:23
Alignment explanation
Indices: 544--599 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
534 TTTATTTATC
544 TATTTA-ATATTATATTCAA-TT
1 TATTTATATATTATATTCAATTT
*
565 TATTTATATATTATA-TCTATTT
1 TATTTATATATTATATTCAATTT
587 TATTATATATATT
1 TATT-TATATATT
600 CTAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.29
22 14 0.45
23 8 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTATATATTATATTCAATTT
Found at i:619 original size:15 final size:15
Alignment explanation
Indices: 594--629 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
584 TTTTATTATA
594 TATATTCTAAATATTT
1 TATA-TCTAAATATTT
610 TATATCTAAATATTT
1 TATATCTAAATATTT
625 TATAT
1 TATAT
630 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATCTAAATATTT
Found at i:689 original size:34 final size:33
Alignment explanation
Indices: 567--713 Score: 117
Period size: 34 Copynumber: 4.5 Consensus size: 33
557 ATTCAATTTA
*
567 TTTATATATTATATCTAT-TTTATTATATATATT
1 TTTATATATTATATATATATTTATTATAT-TATT
** * * *
600 CTAAATATTTTATATCTAAATATT-TTATA-TATT
1 -TTTATATATTATATATATAT-TTATTATATTATT
*
633 TTTATAT-TTATATAT-TAATTATTAATATTATT
1 TTTATATATTATATATATATTTATT-ATATTATT
*
665 TTTATATATTATATATATATTTATTTCTATT-TT
1 TTTATATATTATATATATATTTA-TTATATTATT
*
698 TTGTATACATTATATA
1 TT-TATATATTATATA
714 CAATACAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.02
30 3 0.03
31 10 0.11
32 16 0.17
33 16 0.17
34 35 0.38
35 8 0.09
36 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTATATATTATATATATATTTATTATATTATT
Found at i:690 original size:49 final size:50
Alignment explanation
Indices: 533--690 Score: 125
Period size: 51 Copynumber: 3.2 Consensus size: 50
523 TTTTGGTTTA
* *
533 ATTTATTTATCTATTTAA-TATT-ATATTCAATTTATTTATATATTATATCTAT
1 ATTTATTTATATA-TTAATTATTAATATT--A-TTATTTATATATTATATATAT
* * * *
585 -TTTA-TTATATA-T-ATTCTAAATATT-TTATATCTAAATATTTTATATATT
1 ATTTATTTATATATTAATTATTAATATTATTAT-T-TATATATTATATATA-T
*
633 TTTATATTTATATATTAATTATTAATATTATT-TTTATATATTATATATAT
1 ATT-TATTTATATATTAATTATTAATATTATTATTTATATATTATATATAT
683 ATTTATTT
1 ATTTATTT
691 CTATTTTTTG
Statistics
Matches: 84, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
45 4 0.05
46 1 0.01
47 13 0.15
48 4 0.05
49 12 0.14
50 11 0.13
51 24 0.29
52 2 0.02
53 11 0.13
54 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (50 bp):
ATTTATTTATATATTAATTATTAATATTATTATTTATATATTATATATAT
Found at i:1974 original size:14 final size:14
Alignment explanation
Indices: 1952--1985 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1942 AATAGAAAAC
*
1952 TTTTCATCACTTTT
1 TTTTTATCACTTTT
1966 TTTTTATCACTTTT
1 TTTTTATCACTTTT
*
1980 TCTTTA
1 TTTTTA
1986 GCCTCCGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTATCACTTTT
Found at i:2727 original size:16 final size:17
Alignment explanation
Indices: 2706--2739 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2696 AATTAGAGAA
2706 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
2722 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
2739 T
1 T
2740 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:3431 original size:15 final size:15
Alignment explanation
Indices: 3413--3443 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3403 ATAACTAAAG
3413 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
3428 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
3443 A
1 A
3444 GATGAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:9112 original size:26 final size:26
Alignment explanation
Indices: 9083--9171 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 26
9073 AAATTACAAG
*
9083 TTATTAGCAATTAATATTAATTTATA
1 TTATTAGTAATTAATATTAATTTATA
* * **
9109 TTATTTGTTATTAATATTAA-GAATA
1 TTATTAGTAATTAATATTAATTTATA
*
9134 TTA--AGTAATTAATAAT-ATTTATA
1 TTATTAGTAATTAATATTAATTTATA
9157 TTATTA-T-ATTAATAT
1 TTATTAGTAATTAATAT
9172 ATTTCGATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
22 1 0.02
23 23 0.47
24 1 0.02
25 7 0.14
26 17 0.35
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (26 bp):
TTATTAGTAATTAATATTAATTTATA
Found at i:9228 original size:15 final size:14
Alignment explanation
Indices: 9195--9241 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
9185 AATCTATATT
9195 TCTA-TATTATTTA
1 TCTATTATTATTTA
9208 T-T-TTATTATTCTA
1 TCTATTATTATT-TA
9221 TCTATTATTATATTA
1 TCTATTATTAT-TTA
9236 TCTATT
1 TCTATT
9242 TATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 1 0.03
15 15 0.52
16 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTATTATTATTTA
Done.