Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1412
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: 22167
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:11451 original size:8 final size:8
Alignment explanation
Indices: 11438--11463 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11428 TGGTCATTTG
11438 ATTTGTTA
1 ATTTGTTA
11446 ATTTGTTA
1 ATTTGTTA
11454 ATTTGTTA
1 ATTTGTTA
11462 AT
1 AT
11464 AGTAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATTTGTTA
Found at i:15192 original size:19 final size:18
Alignment explanation
Indices: 15159--15195 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15149 ATGAAAATTC
15159 ATAATAATGAATAATTTA
1 ATAATAATGAATAATTTA
*
15177 ATAATAAATTAATAATTTA
1 ATAAT-AATGAATAATTTA
15196 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAATAATGAATAATTTA
Found at i:18311 original size:19 final size:18
Alignment explanation
Indices: 18286--18324 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18276 TTAAATAGAA
* *
18286 AAATTTAAATAAAATTAG
1 AAATTTTAATAAAAATAG
18304 AAATTTTAATAAAAATAG
1 AAATTTTAATAAAAATAG
18322 AAA
1 AAA
18325 AATTATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
AAATTTTAATAAAAATAG
Found at i:18342 original size:12 final size:12
Alignment explanation
Indices: 18325--18349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18315 AAAATAGAAA
18325 AATTATCTAATT
1 AATTATCTAATT
18337 AATTATCTAATT
1 AATTATCTAATT
18349 A
1 A
18350 TATATAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATCTAATT
Found at i:20190 original size:21 final size:21
Alignment explanation
Indices: 20151--20190 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20141 TTATCTATAG
*
20151 AATAGAAATGATATAGAATAT
1 AATAGAAATGAAATAGAATAT
* *
20172 AATATAAATGAAATGGAAT
1 AATAGAAATGAAATAGAAT
20191 TACTGATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
AATAGAAATGAAATAGAATAT
Found at i:20224 original size:21 final size:21
Alignment explanation
Indices: 20198--20237 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20188 AATTACTGAT
20198 AAAAGTTCTATATATCTATAG
1 AAAAGTTCTATATATCTATAG
*
20219 AAAAGTTGTATATATCTAT
1 AAAAGTTCTATATATCTAT
20238 CTTCTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAAGTTCTATATATCTATAG
Found at i:20256 original size:13 final size:13
Alignment explanation
Indices: 20240--20265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20230 ATATCTATCT
20240 TCTATATAATAAA
1 TCTATATAATAAA
20253 TCTATATAATAAA
1 TCTATATAATAAA
20266 ATTAAGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TCTATATAATAAA
Found at i:20293 original size:21 final size:21
Alignment explanation
Indices: 20251--20294 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20241 CTATATAATA
* *
20251 AATCTATATAATAAAATTAAG
1 AATCTATATAACAAAATAAAG
*
20272 AATCTATATAACAAAGTAAAG
1 AATCTATATAACAAAATAAAG
20293 AA
1 AA
20295 GGGCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AATCTATATAACAAAATAAAG
Found at i:20795 original size:13 final size:13
Alignment explanation
Indices: 20777--20803 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20767 GAATTTTCAG
20777 AAATTAACTTGTA
1 AAATTAACTTGTA
20790 AAATTAACTTGTA
1 AAATTAACTTGTA
20803 A
1 A
20804 TAAGAGTTGA
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:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATTAACTTGTA
Found at i:21869 original size:17 final size:17
Alignment explanation
Indices: 21847--21880 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21837 GCGGATCTAT
21847 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
21864 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
21881 AGATGCAAGG
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:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:22030 original size:19 final size:19
Alignment explanation
Indices: 21970--22024 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
21960 TATTTCTTAT
21970 TAATTAGAATAGAAAAGTC
1 TAATTAGAATAGAAAAGTC
21989 TAATTAGAATAGAAAAGTC
1 TAATTAGAATAGAAAAGTC
22008 TAATTAGAATAGAAAAG
1 TAATTAGAATAGAAAAG
22025 GATAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (19 bp):
TAATTAGAATAGAAAAGTC
Done.