Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold386
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: 9626
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Found at i:6639 original size:42 final size:42
Alignment explanation
Indices: 6544--6651 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 42
6534 CTTGGTTGTG
* * * ** *
6544 CAGGAGCCTCGGTGACCATCAGCACCTTGTGTGCTCGGATGTG
1 CAGGAGCCTTGG-CACCATCGGCACCTTGTGTGCAAGGATGTA
6587 CAGGAGCCTTGGGCACCATCGGCACCTTG-GTGCAAGGATGTA
1 CAGGAGCCTT-GGCACCATCGGCACCTTGTGTGCAAGGATGTA
6629 C-GAGAGCCTTGGCACCATCGGCA
1 CAG-GAGCCTTGGCACCATCGGCA
6652 ACTTAGGCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
41 14 0.25
42 18 0.32
43 23 0.40
44 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.19
Consensus pattern (42 bp):
CAGGAGCCTTGGCACCATCGGCACCTTGTGTGCAAGGATGTA
Found at i:6692 original size:43 final size:43
Alignment explanation
Indices: 6639--7460 Score: 801
Period size: 43 Copynumber: 19.5 Consensus size: 43
6629 CGAGAGCCTT
* * *
6639 GGCACCATCGGCAACTTAGGCCCTTGGTCGTACGGGACCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
*
6682 GGCACCATCGGCAACCTAGGCCCTTGGTC--AC-GGAGCCTC-
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
*
6721 GGCACCATCCGCAACCTA-GCCCTTGGTCGTGC-GGAGCCTC-
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
*
6761 GGCACCATC-GCAACCTAGGCCCTTGGTCGTACGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * * *
6803 GACACCATCGGC-ACCTTGGCGCTTGGAT-GTACGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
* * *
6845 GACACCATCGGCAACCCAGGCCCTTGGAT-GTGCGGAAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
* * * *
6888 GACACCATCGGTAACCTAGGACACTTGGTCGTGCGGGAGTCTC-
1 GGCACCATCGGCAACCTAGG-CCCTTGGTCGTGCGGGAGCCTCG
* *
6931 GGCACCATCGGTAA-CTAGG-CCTTGGTCGTGCGAGAGCCTC-
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* *
6971 GGCACCATCGGCAACCTAGGCCCCTAGTCGTGCGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * ** *
7014 GGCACCATCGGTAACCTAGGCCCCTAATCGTGCGGGAGCGTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* ** * *
7057 GGCACCGTCGAAAACCTAGGCCCCTGGTCGTGCGGGATCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * **
7100 GGCACCATCGGCAACCTAGGCCCCTGGACGTGCGACAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* *
7143 GGCACCATCGGC-ACCTAGGCCCCTGGTCGTGCGGAAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * *
7185 GGCACCATCGGTAACCTAGGCCCCTGGTCGTCCGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * ** ** * *
7228 GGCACCATCGAC-GCCTTCGTGCTTGGAT-GTACGAGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
* *
7270 GACACCATCGGTAACCTAGGCCCTTGGTTC-TGCGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
* * * *
7313 GGCACCATCGGTAACCGAGGCCCTTGGTCATGCGAGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* * * *
7356 GGCACCATCGGC-ACCT-TGCTGCCTCGGAT-GTACGAGAGCCTCG
1 GGCACCATCGGCAACCTAGGC--CCTTGG-TCGTGCGGGAGCCTCG
* * * * **
7399 AGCAGCATTGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCG
1 GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
* *
7441 GACACCATAGGCAACCTAGG
1 GGCACCATCGGCAACCTAGG
7461 ACGTTGGATG
Statistics
Matches: 663, Mismatches: 93, Indels: 46
0.83 0.12 0.06
Matches are distributed among these distances:
38 10 0.02
39 25 0.04
40 69 0.10
41 17 0.03
42 167 0.25
43 356 0.54
44 19 0.03
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (43 bp):
GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
Found at i:6867 original size:85 final size:85
Alignment explanation
Indices: 6639--7460 Score: 775
Period size: 85 Copynumber: 9.7 Consensus size: 85
6629 CGAGAGCCTT
* * *
6639 GGCACCATCGGCAACTTAGGCCCTTGGTCGTACGGGACCCTCGGGCACCATCGGCAACCTAGGCC
1 GGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
*
6704 CTTGGTC--AC-GGAGCCTC-
65 CTTGGTCGTGCGGGAGCCTCG
*
6721 GGCACCATCCGCAACCTA-GCCCTTGGTCGTGC-GGAGCCTC-GGCACCATC-GCAACCTAGGCC
1 GGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
*
6782 CTTGGTCGTACGGGAGCCTCG
65 CTTGGTCGTGCGGGAGCCTCG
* * * * * *
6803 GACACCATCGGCACCTTGGCGCTTGGAT-GTACGGGAGCCTCGGACACCATCGGCAACCCAGGCC
1 GGCACCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
*
6867 CTTGGAT-GTGCGGAAGCCTCG
65 CTTGG-TCGTGCGGGAGCCTCG
* * * * *
6888 GACACCATCGGTAACCTAGGACACTTGGTCGTGCGGGAGTCTC-GGCACCATCGGTAA-CTAGG-
1 GGCACCATCGG-CACCTAGG-CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
*
6950 CCTTGGTCGTGCGAGAGCCTC-
64 CCTTGGTCGTGCGGGAGCCTCG
* * *
6971 GGCACCATCGGCAACCTAGGCCCCTAGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCC
1 GGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* ** *
7036 CCTAATCGTGCGGGAGCGTCG
65 CTTGGTCGTGCGGGAGCCTCG
* ** * *
7057 GGCACCGTCGAAAACCTAGGCCCCTGGTCGTGCGGGATCCTCGGGCACCATCGGCAACCTAGGCC
1 GGCACCATCG-GCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* * **
7122 CCTGGACGTGCGACAGCCTCG
65 CTTGGTCGTGCGGGAGCCTCG
* * *
7143 GGCACCATCGGCACCTAGGCCCCTGGTCGTGCGGAAGCCTCGGGCACCATCGGTAACCTAGGCCC
1 GGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCC
* *
7208 CTGGTCGTCCGGGAGCCTCG
66 TTGGTCGTGCGGGAGCCTCG
* * ** ** * * * *
7228 GGCACCATCGACGCCTTCGTGCTTGGAT-GTACGAGAGCCTCGGACACCATCGGTAACCTAGGCC
1 GGCACCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
7292 CTTGGTTC-TGCGGGAGCCTCG
65 CTTGG-TCGTGCGGGAGCCTCG
* * * * *
7313 GGCACCATCGGTAACCGAGGCCCTTGGTCATGCGAGAGCCTCGGGCACCATCGGC-ACCT-TGCT
1 GGCACCATCGG-CACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC-
* * *
7376 GCCTCGGAT-GTACGAGAGCCTCG
64 -CCTTGG-TCGTGCGGGAGCCTCG
* * * * ** * *
7399 AGCAGCATTGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGACACCATAGGCAACCTAGG
1 GGCACCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
7461 ACGTTGGATG
Statistics
Matches: 611, Mismatches: 99, Indels: 55
0.80 0.13 0.07
Matches are distributed among these distances:
78 19 0.03
79 9 0.01
80 9 0.01
81 25 0.04
82 54 0.09
83 41 0.07
84 32 0.05
85 239 0.39
86 165 0.27
87 18 0.03
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (85 bp):
GGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCC
TTGGTCGTGCGGGAGCCTCG
Found at i:7201 original size:128 final size:129
Alignment explanation
Indices: 6584--7460 Score: 821
Period size: 128 Copynumber: 6.9 Consensus size: 129
6574 GTGCTCGGAT
* * * ** ** * * *
6584 GTGCAGGAGCCTTGGGCACCATCGGC-ACCTTGGTGCAAGGATGTACGAGAGCCT-TGGCACCAT
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
* * * * *
6647 CGGCAACTTAGGCCCTTGGTCGTACGGGACCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTC
66 CGGTAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTC
* * *
6711 --AC-GGAGCCTC-GGCACCATCCGCAACCTA-GCCCTTGGTCGTGCG-GAGCCTC-GGCACCAT
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
* * * * * *
6769 C-GCAACCTAGGCCCTTGGTCGTACGGGAGCCTCGGACACCATCGG-CACCTTGGCGCTTGGAT-
66 CGGTAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGG-TC
* * * * *
6831 GTACGGGAGCCTCGGACACCATCGGCAACCCAGGCCCTTGGATGTGCG-GAAGCCTCGGACACCA
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAG-AGCCTCGGGCACCA
* *
6895 TCGGTAACCTAGGACACTTGGTCGTGCGGGAGTCTC-GGCACCATCGGTAA-CTAGG-CCTTGGT
65 TCGGTAACCTAGG-CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGT
6957 C
129 C
* * * * *
6958 GTGCGAGAGCCTC-GGCACCATCGGCAACCTAGGCCCCTAGTCGTGCGGGAGCCTCGGGCACCAT
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
* ** * * ** *
7022 CGGTAACCTAGGCCCCTAATCGTGCGGGAGCGTCGGGCACCGTCGAAAACCTAGGCCCCTGGTC
66 CGGTAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTC
* * *
7086 GTGCGGGATCCTCGGGCACCATCGGCAACCTAGGCCCCTGGACGTGCGACAGCCTCGGGCACCAT
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
* * * *
7151 CGG-CACCTAGGCCCCTGGTCGTGCGGAAGCCTCGGGCACCATCGGTAACCTAGGCCCCTGGTC
66 CGGTAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTC
* * * ** ** * * *
7214 GTCCGGGAGCCTCGGGCACCATCGAC-GCCTTCGTGCTTGGATGTACGAGAGCCTCGGACACCAT
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
*
7278 CGGTAACCTAGGCCCTTGGTTC-TGCGGGAGCCTCGGGCACCATCGGTAACCGAGGCCCTTGGTC
66 CGGTAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTC
* * * * * * * *
7342 ATGCGAGAGCCTCGGGCACCATCGGC-ACCT-TGCTGCCTCGGATGTACGAGAGCCTCGAGCAGC
1 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC--CCTTGGACGTGCGAGAGCCTCGGGCACC
* * * ** * * *
7405 ATTGG-CACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGACACCATAGGCAACCTAGG
64 ATCGGTAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGG
7461 ACGTTGGATG
Statistics
Matches: 622, Mismatches: 104, Indels: 47
0.80 0.13 0.06
Matches are distributed among these distances:
120 12 0.02
121 42 0.07
122 17 0.03
123 27 0.04
124 26 0.04
125 31 0.05
126 72 0.12
127 62 0.10
128 234 0.38
129 99 0.16
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (129 bp):
GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGACGTGCGAGAGCCTCGGGCACCAT
CGGTAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTC
Done.