Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2479
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: 17088
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1364 original size:2 final size:2
Alignment explanation
Indices: 1357--1395 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1347 AATACGTTGC
1357 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1396 GGGTTGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2152 original size:17 final size:18
Alignment explanation
Indices: 2130--2163 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2120 ATTATATTTT
*
2130 TATTTAA-AATTTTAATA
1 TATTTAACAATTATAATA
2147 TATTTAACAATTATAAT
1 TATTTAACAATTATAAT
2164 TTTATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTAACAATTATAATA
Found at i:3004 original size:2 final size:2
Alignment explanation
Indices: 2997--3021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2987 GATCTCTTTT
2997 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 T
3022 GAGATGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4214 original size:2 final size:2
Alignment explanation
Indices: 4207--4233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4197 TTTCGTATGA
4207 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4234 AAGAAGCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7043 original size:19 final size:19
Alignment explanation
Indices: 7008--7044 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6998 TTAAAAAAAA
*
7008 TTATATAATTTTAATTAAT
1 TTATATAATTATAATTAAT
*
7027 TTATATAATTATCATTAA
1 TTATATAATTATAATTAA
7045 AAAAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATAATTATAATTAAT
Found at i:7348 original size:8 final size:7
Alignment explanation
Indices: 7321--7347 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7311 ACAGGGAGGA
7321 AAAAAAG
1 AAAAAAG
7328 AAAAAAG
1 AAAAAAG
7335 AAAAAAG
1 AAAAAAG
7342 AAAAAA
1 AAAAAA
7348 AAATCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:9137 original size:13 final size:13
Alignment explanation
Indices: 9119--9147 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9109 ATAATAAGTT
9119 TATAATTAATAAA
1 TATAATTAATAAA
9132 TATAATTAATAAA
1 TATAATTAATAAA
9145 TAT
1 TAT
9148 GATATAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATAATTAATAAA
Found at i:11222 original size:13 final size:13
Alignment explanation
Indices: 11199--11231 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
11189 CTAAAATTAT
11199 TAAAT-TTAAATA
1 TAAATATTAAATA
11211 TAAATATTAAATA
1 TAAATATTAAATA
11224 TAAATATT
1 TAAATATT
11232 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:16978 original size:20 final size:20
Alignment explanation
Indices: 16953--16990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16943 CCTCCCTTTC
16953 CTCCTC-TTTCTTTTCTTTTT
1 CTCCTCTTTTC-TTTCTTTTT
16973 CTCCTCTTTTCTTTCTTT
1 CTCCTCTTTTCTTTCTTT
16991 GTCCTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCCTCTTTTCTTTCTTTTT
Done.