Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1106
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: 35681
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:274 original size:20 final size:20
Alignment explanation
Indices: 238--316 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
228 GAGCTAATAA
*
238 TGAGCT-GAATGAGCTGAAT
1 TGAGCTCGAATAAGCTGAAT
**
257 TGAGCTCGTGTAAGCTGACA-
1 TGAGCTCGAATAAGCTGA-AT
* *
277 TGAGCTCGAATAAGATGACT
1 TGAGCTCGAATAAGCTGAAT
*
297 TGAGCTC-AAGTGAGCTGAAT
1 TGAGCTCGAA-TAAGCTGAAT
317 CGCATGGAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
19 8 0.17
20 37 0.80
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
TGAGCTCGAATAAGCTGAAT
Found at i:313 original size:40 final size:39
Alignment explanation
Indices: 237--314 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 39
227 AGAGCTAATA
* * **
237 ATGAGCTGAATGAGCTGAATTGAGCTCGTGTAAGCTGAC
1 ATGAGCTGAATAAGATGAATTGAGCTCAAGTAAGCTGAC
* *
276 ATGAGCTCGAATAAGATGACTTGAGCTCAAGTGAGCTGA
1 ATGAGCT-GAATAAGATGAATTGAGCTCAAGTAAGCTGA
315 ATCGCATGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 7 0.22
40 25 0.78
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.24
Consensus pattern (39 bp):
ATGAGCTGAATAAGATGAATTGAGCTCAAGTAAGCTGAC
Found at i:1369 original size:21 final size:23
Alignment explanation
Indices: 1324--1370 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1314 TCACCTGTAA
* *
1324 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
1347 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
1368 TAA
1 TAA
1371 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:2098 original size:21 final size:20
Alignment explanation
Indices: 2035--2098 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
2025 ACGAAAGCTC
*
2035 TAAACGAACAGATCTGAAAAT
1 TAAACTAACAGATCT-AAAAT
* * *
2056 TAAAATAA-AGAAC-AAGAT
1 TAAACTAACAGATCTAAAAT
2074 TAAACTAATCAGATCTAAAAT
1 TAAACTAA-CAGATCTAAAAT
2095 TAAA
1 TAAA
2099 TCCCCAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 11 0.33
20 8 0.24
21 14 0.42
ACGTcount: A:0.58, C:0.11, G:0.09, T:0.22
Consensus pattern (20 bp):
TAAACTAACAGATCTAAAAT
Found at i:11890 original size:12 final size:12
Alignment explanation
Indices: 11873--11898 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11863 TAGTAGTTTC
11873 TTCAAAAAAAAA
1 TTCAAAAAAAAA
11885 TTCAAAAAAAAA
1 TTCAAAAAAAAA
11897 TT
1 TT
11899 TGGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:11979 original size:16 final size:15
Alignment explanation
Indices: 11936--11976 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
11926 GATATCAAGT
*
11936 TGAAAAAAAAATTTG
1 TGAAAAAAAAATTCG
11951 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
11966 TGAAAAAAAAA
1 TGAAAAAAAAA
11977 ATTTTCGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:11988 original size:16 final size:16
Alignment explanation
Indices: 11936--11991 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
11926 GATATCAAGT
11936 TGAAAAAAAAATTT-G
1 TGAAAAAAAAATTTCG
11951 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
11966 TGAAAAAAAAAATTTTCG
1 TG-AAAAAAAAA-TTTCG
11984 T-AAAAAAA
1 TGAAAAAAA
11992 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.05
15 14 0.38
16 16 0.43
18 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:19005 original size:46 final size:46
Alignment explanation
Indices: 18952--19044 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
18942 TGTGAAACGC
18952 TCAATCTGTTTGA-TCGTGATGGTAATGAAAATTTTTTAACTCTTAG
1 TCAATCTGTTTGATTCG-GATGGTAATGAAAATTTTTTAACTCTTAG
18998 TCAATCTGTTTGATTCGGATGGTAATGAAAATTTTTTAACTCTTAG
1 TCAATCTGTTTGATTCGGATGGTAATGAAAATTTTTTAACTCTTAG
19044 T
1 T
19045 GTGAGATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 43 0.93
47 3 0.07
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (46 bp):
TCAATCTGTTTGATTCGGATGGTAATGAAAATTTTTTAACTCTTAG
Found at i:19699 original size:62 final size:63
Alignment explanation
Indices: 19628--19752 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 63
19618 GAAAAGGTAA
19628 TACCAATTTCTATTTTTGATCCCGGCATTGATTCAT-TGTTGTTCTTTTGAGTTTATTTGCTC
1 TACCAATTTCTATTTTTGATCCCGGCATTGATTCATATGTTGTTCTTTTGAGTTTATTTGCTC
19690 TACCAATTTCTATTTTTGATCCCGGCATTGATTCATATGTTGTTCTTTTGAGTTTATTTGCTC
1 TACCAATTTCTATTTTTGATCCCGGCATTGATTCATATGTTGTTCTTTTGAGTTTATTTGCTC
19753 AAGTTGTGAC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 36 0.58
63 26 0.42
ACGTcount: A:0.17, C:0.18, G:0.14, T:0.51
Consensus pattern (63 bp):
TACCAATTTCTATTTTTGATCCCGGCATTGATTCATATGTTGTTCTTTTGAGTTTATTTGCTC
Found at i:35415 original size:23 final size:25
Alignment explanation
Indices: 35389--35439 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
35379 TTCAGTTCAT
35389 TTAT-TAAGTAAGT-TTAT-ATGGTG
1 TTATGTAA-TAAGTGTTATAATGGTG
*
35412 TTATGTAATAAGTGTTTTAATGGTG
1 TTATGTAATAAGTGTTATAATGGTG
35437 TTA
1 TTA
35440 ATAAACTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.38
24 6 0.25
25 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (25 bp):
TTATGTAATAAGTGTTATAATGGTG
Done.