Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1652
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: 16625
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Found at i:3456 original size:30 final size:30
Alignment explanation
Indices: 3422--3482 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3412 TCCTTAACTC
3422 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
3452 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
3482 A
1 A
3483 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:7028 original size:30 final size:30
Alignment explanation
Indices: 6994--7054 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6984 TCCTTAACTC
6994 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
7024 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
7054 A
1 A
7055 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:8885 original size:28 final size:28
Alignment explanation
Indices: 8845--8946 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
8835 GAATCATTCG
* *
8845 ATATTTTGAACACTAAGTGTCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
* * *
8873 ATATCTCGCACACTAAGCGTCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
*
8901 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
8929 ATATTTCGTACACTAAGT
1 ATATTTCGTACACTAAGT
8947 ACCATATTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTCGTACACTAAGTGTCATTCTCA
Found at i:13916 original size:28 final size:28
Alignment explanation
Indices: 13885--14036 Score: 121
Period size: 29 Copynumber: 5.5 Consensus size: 28
13875 CAACCGACTT
*
13885 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGGTTACGGAACTC
**** * *
13913 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGGTTACGGAACTC
*
13942 GCACACACAGTGCTCGGTTACGAAACTC
1 GCACACACAGTGCTCGGTTACGGAACTC
**** * *
13970 GCACACACAGTGCCTCAACAACTGATCTC
1 GCACACACAGTG-CTCGGTTACGGAACTC
*
13999 GCACACACAATGCTC--TTAC-GAACTC
1 GCACACACAGTGCTCGGTTACGGAACTC
*
14024 ACACACACAGTGC
1 GCACACACAGTGC
14037 CTATGTTCAC
Statistics
Matches: 95, Mismatches: 27, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
25 16 0.17
26 2 0.02
28 36 0.38
29 41 0.43
ACGTcount: A:0.30, C:0.36, G:0.17, T:0.17
Consensus pattern (28 bp):
GCACACACAGTGCTCGGTTACGGAACTC
Found at i:13963 original size:57 final size:57
Alignment explanation
Indices: 13856--14038 Score: 257
Period size: 57 Copynumber: 3.2 Consensus size: 57
13846 GATCTCATTT
* * *
13856 CACACACTTAGTGCCCCAACAACCGA-CTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
*
13914 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGAAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
13971 CACACACAGTGCCTCAACAACTGATCTCGCACACACAATGCTC--TTAC-GAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
14025 CACACACAGTGCCT
1 CACACACAGTGCCT
14039 ATGTTCACTT
Statistics
Matches: 116, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
54 19 0.16
55 4 0.03
56 16 0.14
57 70 0.60
58 7 0.06
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.17
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:16047 original size:55 final size:56
Alignment explanation
Indices: 15979--16085 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 56
15969 GAATCATTCG
* * *
15979 ATATTTTGCACACTAAGTGTCATTCTCAATA-TTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCAATATTTCGCACACTAAGTACCATTCTCA
* *
16034 ATATTTCGTACACTAAGTGCCATTCTCAATATTTTCGTACACTAAGTACCAT
1 ATATTTCGCACACTAAGTGCCATTCTCAATA-TTTCGCACACTAAGTACCAT
16086 ATTTGAATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 28 0.62
57 17 0.38
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (56 bp):
ATATTTCGCACACTAAGTGCCATTCTCAATATTTCGCACACTAAGTACCATTCTCA
Found at i:16050 original size:28 final size:28
Alignment explanation
Indices: 15979--16085 Score: 153
Period size: 28 Copynumber: 3.8 Consensus size: 28
15969 GAATCATTCG
* *
15979 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
16007 ATA-TTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
16034 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
16062 ATATTTTCGTACACTAAGTACCAT
1 ATA-TTTCGCACACTAAGTGCCAT
16086 ATTTGAATTG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 25 0.34
28 29 0.40
29 19 0.26
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Done.