Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1773
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: 22395
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:2893 original size:13 final size:13
Alignment explanation
Indices: 2864--2910 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
2854 TTTAACTCTC
*
2864 ATAAAA-TATAAT
1 ATAAAATTAAAAT
*
2876 ATAAAATTAAATT
1 ATAAAATTAAAAT
*
2889 AT-AAATTAAAAA
1 ATAAAATTAAAAT
2901 ATAAAATTAA
1 ATAAAATTAA
2911 TAATTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:7396 original size:12 final size:13
Alignment explanation
Indices: 7379--7408 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7369 GCTGTGATCT
7379 AATTTTTT-TTTA
1 AATTTTTTATTTA
7391 AATTTTTTATTTA
1 AATTTTTTATTTA
7404 AATTT
1 AATTT
7409 GAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
AATTTTTTATTTA
Found at i:10522 original size:20 final size:21
Alignment explanation
Indices: 10471--10530 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
10461 TATTTATTTT
* *
10471 TATATATATTATAAATTAATAAAT
1 TATAT-TA-TATAAATT-TTAAAA
10495 TATATTATATAAATTTTAAAA
1 TATATTATATAAATTTTAAAA
*
10516 TAT-TTATATATATTT
1 TATATTATATAAATTT
10531 AATATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.33
21 7 0.21
22 8 0.24
23 2 0.06
24 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATATAAATTTTAAAA
Found at i:10539 original size:20 final size:20
Alignment explanation
Indices: 10480--10540 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
10470 TTATATATAT
*
10480 TATAAATTAATAAATTATATTA
1 TATAAATT-TTAAATTAT-TTA
*
10502 TATAAATTTTAAAATATTTA
1 TATAAATTTTAAATTATTTA
*
10522 TATATA-TTTAATATTATTT
1 TATAAATTTTAA-ATTATTT
10541 TTTATGACGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 7 0.21
22 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAAATTTTAAATTATTTA
Found at i:10916 original size:15 final size:17
Alignment explanation
Indices: 10875--10967 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 17
10865 TCGTAAAGTA
10875 TAAATTAATAAAAAATATT
1 TAAATTAAT--AAAATATT
10894 TAAATTAATAAAA-ATT
1 TAAATTAATAAAATATT
**
10910 T-AATTAA-AATTTTAATT
1 TAAATTAATAA-AAT-ATT
*
10927 T-AATTAGATTAAATTTATT
1 TAAATTA-A-TAAA-ATATT
10946 TAAATTAATAAAAATATT
1 TAAATTAAT-AAAATATT
10964 TAAA
1 TAAA
10968 ATTAGATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.03
15 6 0.10
16 4 0.07
17 13 0.21
18 10 0.16
19 17 0.28
20 9 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTAATAAAATATT
Found at i:10948 original size:19 final size:20
Alignment explanation
Indices: 10924--10982 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
10914 TAAAATTTTA
**
10924 ATTT-AATTAGATTAAATTT
1 ATTTAAATTAGATTAAAAAT
10943 ATTTAAATTA-A-TAAAAAT
1 ATTTAAATTAGATTAAAAAT
10961 ATTTAAAATTAGATTAAAAAT
1 ATTT-AAATTAGATTAAAAAT
10982 A
1 A
10983 AGATAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 9 0.26
19 11 0.32
20 6 0.18
21 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTAAATTAGATTAAAAAT
Found at i:10997 original size:21 final size:21
Alignment explanation
Indices: 10943--11015 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
10933 GATTAAATTT
10943 ATTTAAATTAAT--AAAAAT-
1 ATTTAAATTAATAAAAAAATA
10961 ATTTAAAATTAGATTAAAAATAAGATA
1 ATTT-AAATTA-A-T-AAAA-AA-ATA
*
10988 ATTTAAATTAATAAAAAAATT
1 ATTTAAATTAATAAAAAAATA
11009 ATTTAAA
1 ATTTAAA
11016 AAAATTAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
18 4 0.09
19 6 0.13
20 1 0.02
21 10 0.22
22 2 0.04
23 4 0.09
24 3 0.07
25 3 0.07
26 8 0.18
27 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
ATTTAAATTAATAAAAAAATA
Found at i:11015 original size:13 final size:13
Alignment explanation
Indices: 10992--11027 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10982 AAGATAATTT
10992 AAATTAA-TAAAA
1 AAATTAATTAAAA
*
11004 AAATTATTTAAAA
1 AAATTAATTAAAA
11017 AAATTAATTAA
1 AAATTAATTAA
11028 GTAAACTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTAATTAAAA
Found at i:13774 original size:19 final size:17
Alignment explanation
Indices: 13724--13779 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 17
13714 AAATAATTTT
13724 ATTTTTAAATTAATAAAA
1 ATTTTTAAATTAA-AAAA
*
13742 ATTTTAAAATATTATAAAAA
1 ATTTT-TAA-ATTA-AAAAA
13762 CATTTTTAAATTAAAAAA
1 -ATTTTTAAATTAAAAAA
13780 TTTATGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.31
19 6 0.19
20 10 0.31
21 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTTTAAATTAAAAAA
Found at i:14078 original size:22 final size:21
Alignment explanation
Indices: 14029--14087 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
14019 AAGTCATGCA
*
14029 TTTATGAAGTTTTATTTTATTAT
1 TTTAT-AA-TTTTATTTAATTAT
*
14052 ATTATAATTTTATTTAAATTAT
1 TTTATAATTTTATTT-AATTAT
14074 TTTAT-ATTTATATT
1 TTTATAATTT-TATT
14088 AATAGTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 12 0.39
22 15 0.48
23 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTATAATTTTATTTAATTAT
Found at i:14099 original size:20 final size:22
Alignment explanation
Indices: 14076--14124 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
14066 TAAATTATTT
14076 TATATTTAT-ATTAATAGTA-A
1 TATATTTATAATTAATAGTATA
* * *
14096 TATATTAATAATTTATATTATA
1 TATATTTATAATTAATAGTATA
14118 TATATTT
1 TATATTT
14125 TAAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATATTTATAATTAATAGTATA
Found at i:14213 original size:14 final size:14
Alignment explanation
Indices: 14175--14214 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
14165 ATATATATTG
* *
14175 TATTTATATAATCA
1 TATTTAAATTATCA
14189 TATTTAAAATTATCA
1 TATTT-AAATTATCA
14204 TATTTAAATTA
1 TATTTAAATTA
14215 ATTTTTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTAAATTATCA
Found at i:15181 original size:2 final size:2
Alignment explanation
Indices: 15174--15227 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
15164 TTTGAGTGCC
15174 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
15216 TA TA TA TA TA TA
1 TA TA TA TA TA TA
15228 AAGACTTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.