Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2708
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: 25552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:103 original size:19 final size:20
Alignment explanation
Indices: 79--139 Score: 81
Period size: 19 Copynumber: 3.0 Consensus size: 20
69 TTATGTAAAA
79 TTTTATATATTA-ATATTTT
1 TTTTATATATTATATATTTT
98 TTTTATATATTTATATATTTT
1 TTTTATATA-TTATATATTTT
*
119 TATTATAT-TTATATCATTTT
1 TTTTATATATTATAT-ATTTT
139 T
1 T
140 ATGTTATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 15 0.39
20 9 0.24
21 14 0.37
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATATATTATATATTTT
Found at i:122 original size:27 final size:28
Alignment explanation
Indices: 80--137 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
70 TATGTAAAAT
* *
80 TTTATATATTAATATTTTTTTTATAT-A
1 TTTATATATTAATATTATATTTATATCA
**
107 TTTATATATTTTTATTATATTTATATCA
1 TTTATATATTAATATTATATTTATATCA
135 TTT
1 TTT
138 TTATGTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATATATTAATATTATATTTATATCA
Found at i:127 original size:11 final size:11
Alignment explanation
Indices: 86--169 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
76 AAATTTTATA
86 TATTAATATTTT
1 TATT-ATATTTT
* *
98 TTTTATATATT
1 TATTATATTTT
109 TA-TATATTTT
1 TATTATATTTT
119 TATTATA--TT
1 TATTATATTTT
128 TA-TATCATTTT
1 TATTAT-ATTTT
139 TATGT-TATTTT
1 TAT-TATATTTT
150 TAATTA-ATTTAT
1 T-ATTATATTT-T
162 T-TTATATT
1 TATTATATT
170 ATGCAATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
8 3 0.05
9 5 0.09
10 12 0.21
11 29 0.50
12 8 0.14
13 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (11 bp):
TATTATATTTT
Found at i:226 original size:17 final size:17
Alignment explanation
Indices: 204--237 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
194 TTTATATTGT
*
204 ATTCATACTATATTTTA
1 ATTCATAATATATTTTA
221 ATTCATAATATATTTTA
1 ATTCATAATATATTTTA
238 TATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTCATAATATATTTTA
Found at i:2962 original size:24 final size:24
Alignment explanation
Indices: 2925--2972 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2915 TATTTTATGT
2925 TATAATAATATTTAAAATATTATA
1 TATAATAATATTTAAAATATTATA
*
2949 TATACATAAT-TTTAATATATTATA
1 TATA-ATAATATTTAAAATATTATA
2973 ATTTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAATAATATTTAAAATATTATA
Found at i:2996 original size:14 final size:15
Alignment explanation
Indices: 2954--3014 Score: 70
Period size: 15 Copynumber: 3.8 Consensus size: 15
2944 TTATATATAC
2954 ATAATTTTAATATATT
1 ATAA-TTTAATATATT
2970 ATAATTTATATATATT
1 ATAATTTA-ATATATT
2986 A-AATTTAATATATTT
1 ATAATTTAATATA-TT
3001 ATATTATTTAATAT
1 ATA--ATTTAATAT
3015 TAATTTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 13 0.32
18 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATTTAATATATT
Found at i:3003 original size:31 final size:33
Alignment explanation
Indices: 2927--3008 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 33
2917 TTTTATGTTA
* *
2927 TAATAATATTTAAAATATTATATATACATAATTT
1 TAAT-ATATTTATAATATTATATATACATAAATT
*
2961 TAATATA-TTATAAT-TTATATATA-TTAAATT
1 TAATATATTTATAATATTATATATACATAAATT
*
2991 TAATATATTTATATTATT
1 TAATATATTTATAATATT
3009 TAATATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 12 0.29
31 15 0.36
32 8 0.19
33 3 0.07
34 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TAATATATTTATAATATTATATATACATAAATT
Found at i:3017 original size:24 final size:26
Alignment explanation
Indices: 2959--3018 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
2949 TATACATAAT
*
2959 TTTAATA-TATTATAATTTATATATA
1 TTTAATATTAATATAATTTATATATA
*
2984 TTAAAT-TTAATAT-ATTTATAT-TA
1 TTTAATATTAATATAATTTATATATA
3007 TTTAATATTAAT
1 TTTAATATTAAT
3019 TTTTAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 7 0.23
24 13 0.43
25 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTAATATTAATATAATTTATATATA
Found at i:3385 original size:3 final size:3
Alignment explanation
Indices: 3377--3411 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3367 GCAAGCACAA
*
3377 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3412 ATCAGCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7736 original size:54 final size:55
Alignment explanation
Indices: 7621--7750 Score: 192
Period size: 54 Copynumber: 2.4 Consensus size: 55
7611 CCTTAATTTA
* * *
7621 CCACAGTT-TGAGTCTCCAAATCAGTCCCAAGTACATAACAAAAAACCAAAATCTG
1 CCACA-TTCTGAGTCTCAAAACCAGCCCCAAGTACATAACAAAAAACCAAAATCTG
**
7676 CCACATTCTGAGTCTCAAAACCAGCCCCAAGTACATAA-TGAAAACCAAAATCTG
1 CCACATTCTGAGTCTCAAAACCAGCCCCAAGTACATAACAAAAAACCAAAATCTG
7730 CCACATTCTGAGTCTCAAAAC
1 CCACATTCTGAGTCTCAAAAC
7751 TAGGCTAAGT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 37 0.54
55 32 0.46
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (55 bp):
CCACATTCTGAGTCTCAAAACCAGCCCCAAGTACATAACAAAAAACCAAAATCTG
Found at i:15131 original size:36 final size:36
Alignment explanation
Indices: 15090--15165 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
15080 GGGGGACAAA
* *
15090 GGTAGTGACTCAGCCTAGTTTTGAGACTTAGATTGT
1 GGTAGTGACTCAGCCTAGTTTTGAGACTCAGAATGT
* * *
15126 GGTAGTGACTTAGCTTGGTTTTGAGACTCAGAATGT
1 GGTAGTGACTCAGCCTAGTTTTGAGACTCAGAATGT
15162 GGTA
1 GGTA
15166 ATGATAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (36 bp):
GGTAGTGACTCAGCCTAGTTTTGAGACTCAGAATGT
Found at i:20000 original size:2 final size:2
Alignment explanation
Indices: 19993--20059 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
19983 TTGTGGGTTT
19993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20035 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20060 TTTAGATATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20628 original size:16 final size:17
Alignment explanation
Indices: 20590--20631 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
20580 GATTCAATTA
20590 AAAATTATATATAAAAAT
1 AAAATT-TATATAAAAAT
* *
20608 CAAATTTA-ATAAATAT
1 AAAATTTATATAAAAAT
20624 AAAATTTA
1 AAAATTTA
20632 GGATGCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 14 0.67
17 2 0.10
18 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTTATATAAAAAT
Done.