Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3664
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: 38729
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:535 original size:13 final size:13
Alignment explanation
Indices: 512--564 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
502 AATTAAGGCA
*
512 GTTCACGATAGGG
1 GTTCACCATAGGG
*
525 GTTCGCCATAGGTG
1 GTTCACCATAGG-G
*
539 AGTTCACGATAGGG
1 -GTTCACCATAGGG
553 GTTCACCATAGG
1 GTTCACCATAGG
565 TGAGTTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (13 bp):
GTTCACCATAGGG
Found at i:551 original size:28 final size:28
Alignment explanation
Indices: 511--570 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
501 GAATTAAGGC
*
511 AGTTCACGATAGGGGTTCGCCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
539 AGTTCACGATAGGGGTTCACCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
567 AGTT
1 AGTT
571 TGCCATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
AGTTCACGATAGGGGTTCACCATAGGTG
Found at i:582 original size:28 final size:28
Alignment explanation
Indices: 523--601 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
513 TTCACGATAG
* * * *
523 GGGTTCGCCATAGGTGAGTTCACGATAG
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
551 GGGTTCACCATAGGTGAGTTTGCCATAA
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
579 GGGTT-ACTCATATGTGAGTTTAC
1 GGGTTCAC-CATAGGTGAGTTTAC
602 TAGACATAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGTTCACCATAGGTGAGTTTACCATAA
Found at i:8038 original size:26 final size:25
Alignment explanation
Indices: 7994--8042 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
7984 GATACGTTCT
*
7994 AACATTCAATTTTCAGTTTAATTAG
1 AACATTCAAATTTCAGTTTAATTAG
8019 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAA-ATTTCAGTTTAATT
8043 TGCATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (25 bp):
AACATTCAAATTTCAGTTTAATTAG
Found at i:9746 original size:26 final size:25
Alignment explanation
Indices: 9706--9754 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
9696 AATACGTTCT
**
9706 AACATTCAATTTTTCAGTTTAATTAG
1 AACATTCAAGATTTCAG-TTAATTAG
9732 AACATTCAAGATTTCAGTTAATT
1 AACATTCAAGATTTCAGTTAATT
9755 TGCATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (25 bp):
AACATTCAAGATTTCAGTTAATTAG
Found at i:13922 original size:26 final size:26
Alignment explanation
Indices: 13883--13932 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
13873 AATACGTTCT
*
13883 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
13909 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
13933 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:16013 original size:26 final size:25
Alignment explanation
Indices: 15974--16022 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
15964 AATACGTTCT
*
15974 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTT-AGTTTAATTAG
16000 AACATTCAAGATTTAGTTTAATT
1 AACATTCAAGATTTAGTTTAATT
16023 TGCATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (25 bp):
AACATTCAAGATTTAGTTTAATTAG
Found at i:18105 original size:24 final size:25
Alignment explanation
Indices: 18069--18115 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
18059 ATACGTTCTA
*
18069 ACATTCAATATTTCAG-TTAATTAG
1 ACATTCAAGATTTCAGTTTAATTAG
18093 ACATTCAAGATTTCAGTTTAATT
1 ACATTCAAGATTTCAGTTTAATT
18116 TGCATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (25 bp):
ACATTCAAGATTTCAGTTTAATTAG
Found at i:20201 original size:26 final size:26
Alignment explanation
Indices: 20162--20211 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20152 AATACGTTCT
*
20162 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
20188 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
20212 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:21957 original size:26 final size:26
Alignment explanation
Indices: 21918--21967 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
21908 AATACGTTCT
*
21918 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
21944 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
21968 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:24069 original size:26 final size:26
Alignment explanation
Indices: 24030--24079 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
24020 AATACGTTCT
*
24030 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
24056 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
24080 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:26180 original size:26 final size:26
Alignment explanation
Indices: 26141--26190 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
26131 AATACGTTCT
*
26141 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
26167 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
26191 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:28292 original size:26 final size:26
Alignment explanation
Indices: 28253--28302 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28243 AATACGTTCT
*
28253 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
28279 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
28303 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:30403 original size:26 final size:26
Alignment explanation
Indices: 30364--30413 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
30354 AATACGTTCT
*
30364 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
30390 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
30414 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:32511 original size:26 final size:26
Alignment explanation
Indices: 32472--32521 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
32462 AATACGTTCT
*
32472 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
32498 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
32522 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:34622 original size:26 final size:26
Alignment explanation
Indices: 34583--34632 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
34573 AATACGTTCT
*
34583 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
34609 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
34633 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Found at i:36714 original size:26 final size:26
Alignment explanation
Indices: 36675--36724 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
36665 AATACGTTCT
*
36675 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAAGATTTCAGTTTAATTAG
36701 AACATTCAAGATTTCAGTTTAATT
1 AACATTCAAGATTTCAGTTTAATT
36725 TGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAAGATTTCAGTTTAATTAG
Done.