Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1859
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: 27004
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:2216 original size:16 final size:16
Alignment explanation
Indices: 2166--2216 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2156 TTAAAGTATT
2166 TTTTAT-TTATAT-AA
1 TTTTATATTATATAAA
2180 TTTTGATA-TAT-TAATA
1 TTTT-ATATTATATAA-A
2196 TTTTATATTATATAAA
1 TTTTATATTATATAAA
2212 TTTTA
1 TTTTA
2217 AAAATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 14 0.45
17 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTATATTATATAAA
Found at i:3918 original size:21 final size:19
Alignment explanation
Indices: 3885--3923 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3875 AATAGATAGG
*
3885 ATAAATTATTTAATTTAAA
1 ATAAATTATTTAAGTTAAA
3904 ATAAATTAAATTTAAGTTAA
1 ATAAATT--ATTTAAGTTAA
3924 TTTATATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAAATTATTTAAGTTAAA
Found at i:3948 original size:25 final size:26
Alignment explanation
Indices: 3913--3969 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
3903 AATAAATTAA
* *
3913 ATTTAAGTTAATTTATA-TGTTATGT
1 ATTTAAATTAATTTATATTATTATGT
*
3938 ATTTAAATTAATTTATATTATTATTT
1 ATTTAAATTAATTTATATTATTATGT
3964 ATTTAA
1 ATTTAA
3970 TAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (26 bp):
ATTTAAATTAATTTATATTATTATGT
Found at i:4212 original size:28 final size:27
Alignment explanation
Indices: 4177--4235 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
4167 ATATTTTCTT
*
4177 AAAA-TTTAGATATAAAAAATAACTTTA
1 AAAATTTTAAATAT-AAAAATAACTTTA
* *
4204 AAAATTTTAAATATATAAATAATTTTA
1 AAAATTTTAAATATAAAAATAACTTTA
4231 AAAAT
1 AAAAT
4236 AAAATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAATTTTAAATATAAAAATAACTTTA
Found at i:4247 original size:17 final size:18
Alignment explanation
Indices: 4202--4246 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4192 AAAATAACTT
*
4202 TAAA-AATTTTAAATATA
1 TAAATAATTTTAAAAATA
4219 TAAATAATTTTAAAAATA
1 TAAATAATTTTAAAAATA
4237 -AAATATATTT
1 TAAATA-ATTT
4247 ATATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATAATTTTAAAAATA
Found at i:5620 original size:3 final size:3
Alignment explanation
Indices: 5612--5649 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5602 TTGGGATACC
5612 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5650 GGATGAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6953 original size:15 final size:15
Alignment explanation
Indices: 6935--6987 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
6925 TTTAAATAAA
6935 TAAATTAATTTTATT
1 TAAATTAATTTTATT
6950 TAAATT-ATTTT-TT
1 TAAATTAATTTTATT
**
6963 ATAAAAAAATTTTTATT
1 -TAAATTAA-TTTTATT
6980 TAAATTAA
1 TAAATTAA
6988 ATTATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.07
14 9 0.30
15 7 0.23
16 10 0.33
17 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTAATTTTATT
Found at i:7028 original size:18 final size:18
Alignment explanation
Indices: 7007--7058 Score: 63
Period size: 16 Copynumber: 3.0 Consensus size: 18
6997 ATTTATATTT
*
7007 TAATATTATTTTAAATAA
1 TAATATAATTTTAAATAA
*
7025 TAATAAAATTTTAAAT--
1 TAATATAATTTTAAATAA
*
7041 TAATATAAATTTAAATAA
1 TAATATAATTTTAAATAA
7059 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATAATTTTAAATAA
Found at i:7685 original size:8 final size:8
Alignment explanation
Indices: 7669--7730 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
7659 AAATATAATA
*
7669 ATTTGTAT
1 ATTTATAT
7677 ATTTATAT
1 ATTTATAT
7685 ATTT-TATT
1 ATTTATA-T
7693 ATATTATA-
1 AT-TTATAT
7701 A-TTATAT
1 ATTTATAT
*
7708 -TTTAAAT
1 ATTTATAT
7715 ATTT-TAT
1 ATTTATAT
7722 ATTTATAT
1 ATTTATAT
7730 A
1 A
7731 AATTTTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
6 5 0.11
7 13 0.30
8 22 0.50
9 2 0.05
10 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:7731 original size:30 final size:29
Alignment explanation
Indices: 7674--7728 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
7664 TAATAATTTG
*
7674 TATATTTATATATTTTATTATATTATAAT
1 TATATTTAAATATTTTATTATATTATAAT
7703 TATATTTTAAATATTTTA-TAT-TTATA
1 TATA-TTTAAATATTTTATTATATTATA
7729 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 7 0.29
30 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTTAAATATTTTATTATATTATAAT
Found at i:14583 original size:15 final size:16
Alignment explanation
Indices: 14563--14592 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14553 ATCTCTTGAA
14563 TTTTT-AATAAAATAT
1 TTTTTAAATAAAATAT
14578 TTTTTAAATAAAATA
1 TTTTTAAATAAAATA
14593 CATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTAAATAAAATAT
Found at i:15931 original size:15 final size:16
Alignment explanation
Indices: 15898--15931 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15888 TTTAACACAC
15898 TTATAATTTATTTTCT
1 TTATAATTTATTTTCT
*
15914 TTATAATTT-TTTTTT
1 TTATAATTTATTTTCT
15929 TTA
1 TTA
15932 ACAATTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATAATTTATTTTCT
Found at i:16543 original size:18 final size:17
Alignment explanation
Indices: 16508--16593 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
16498 GATTAAATTT
16508 AATATAATTAAATAAAA
1 AATATAATTAAATAAAA
*
16525 AATACTAATTTAATTAAAA
1 AATA-TAA-TTAAATAAAA
*
16544 ATTGATAA--AAATAAAAA
1 AAT-ATAATTAAAT-AAAA
* *
16561 AATATTATTAAA-AATTTA
1 AATATAATTAAATAA--AA
16579 AA-ATAATTAAATAAA
1 AATATAATTAAATAAA
16594 TACATATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 19
0.66 0.10 0.24
Matches are distributed among these distances:
16 8 0.15
17 18 0.35
18 11 0.21
19 14 0.27
20 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AATATAATTAAATAAAA
Found at i:24721 original size:2 final size:2
Alignment explanation
Indices: 24714--24748 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24704 TTTCCCTTTT
24714 TA TA TA TA TA 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 TA TA TA TA TA T
24749 CCGAGAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25466 original size:22 final size:22
Alignment explanation
Indices: 25422--25467 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
25412 ATGAATTATT
**
25422 ATTTAATAATAAAAATATTTAA
1 ATTTAATAATAAAAATAAATAA
* *
25444 ATTTAATTATACAAATAAATAA
1 ATTTAATAATAAAAATAAATAA
25466 AT
1 AT
25468 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTAATAATAAAAATAAATAA
Done.