Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2026
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: 19059
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:949 original size:40 final size:40
Alignment explanation
Indices: 870--1051 Score: 273
Period size: 40 Copynumber: 4.6 Consensus size: 40
860 AACCCAAGTA
*
870 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
*
909 CCTTCGGGTCTTAGCCCGGATATAGC-ACTACTGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACT-C-GCACAAATG
*
949 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATG
*
989 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
1029 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
1052 CATCCGAATA
Statistics
Matches: 131, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
39 19 0.15
40 104 0.79
41 8 0.06
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
Found at i:6780 original size:27 final size:27
Alignment explanation
Indices: 6749--6926 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6739 TAAATTGTAC
6749 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
6776 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6802 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
6830 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
6858 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6885 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6912 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6927 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:6863 original size:82 final size:81
Alignment explanation
Indices: 6750--6905 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6740 AAATTGTACA
* *
6750 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
6814 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
6831 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
6896 TGCGAGTTGA
65 TGCGAATTGA
6906 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6917 original size:82 final size:81
Alignment explanation
Indices: 6746--6926 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
6736 GATTAAATTG
* *
6746 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
6811 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
6827 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
6891 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
6909 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
6927 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:14876 original size:27 final size:27
Alignment explanation
Indices: 14845--15022 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
14835 TAAATTGTAC
14845 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
14872 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
14898 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
14926 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
14954 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
14981 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
15008 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15023 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:14959 original size:82 final size:81
Alignment explanation
Indices: 14846--15001 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
14836 AAATTGTACA
* *
14846 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
14910 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
14927 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
14992 TGCGAGTTGA
65 TGCGAATTGA
15002 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:15013 original size:82 final size:81
Alignment explanation
Indices: 14842--15022 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
14832 GATTAAATTG
* *
14842 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
14907 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
14923 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
14987 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
15005 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
15023 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:17172 original size:21 final size:21
Alignment explanation
Indices: 17146--17185 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17136 ATCTTATCAC
*
17146 GACGACATGTACCTGACGTTT
1 GACGACATGTACCCGACGTTT
17167 GACGACATGTACCCGACGT
1 GACGACATGTACCCGACGT
17186 CGCGACGTGA
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:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (21 bp):
GACGACATGTACCCGACGTTT
Found at i:17602 original size:28 final size:26
Alignment explanation
Indices: 17571--17622 Score: 61
Period size: 28 Copynumber: 1.9 Consensus size: 26
17561 AATTAAATTG
17571 TTTA-GTTTTAGTTATTTATTGATTTTAA
1 TTTATGTTTTA-TTA-TTATT-ATTTTAA
*
17599 TTTATTTTTTATTATTATTATTTT
1 TTTATGTTTTATTATTATTATTTT
17623 GGTTACACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.23
27 5 0.23
28 7 0.32
29 5 0.23
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (26 bp):
TTTATGTTTTATTATTATTATTTTAA
Done.