Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1539
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: 20817
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:5840 original size:27 final size:27
Alignment explanation
Indices: 5807--6011 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
5797 TAAATTGTAC
5807 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
5834 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5861 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5887 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5915 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5943 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5970 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5997 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6012 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5975 original size:109 final size:108
Alignment explanation
Indices: 5808--6011 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
5798 AAATTGTACA
* *
5808 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
5873 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
5916 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
5981 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
6012 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Found at i:7750 original size:29 final size:27
Alignment explanation
Indices: 7732--7801 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
7722 ATATTAAGTC
7732 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
7759 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
7787 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
7802 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:7795 original size:28 final size:28
Alignment explanation
Indices: 7732--7829 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
7722 ATATTAAGTC
*
7732 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
7759 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
7787 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
7816 CGCACACTTAGTGC
1 CGCACACTTAGTGC
7830 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:15036 original size:29 final size:29
Alignment explanation
Indices: 14967--15101 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 29
14957 GCCCACTGAC
* **
14967 CGATCTCGCACACATAGTG-CTCGGTTGAA
1 CGATCTCGCACACACAGTGCCTCAATT-AA
* * *
14996 -GAACTCGCACACACAATGCCTCAATTAT
1 CGATCTCGCACACACAGTGCCTCAATTAA
* ***
15024 CGATCTCGCACACATAGTG-CTTGGTTAAA
1 CGATCTCGCACACACAGTGCCTCAATT-AA
* *
15053 GGAAT-TCGCACACACAGTGCCTCAATTAC
1 CG-ATCTCGCACACACAGTGCCTCAATTAA
*
15082 CGATCTCGCACACATAGTGC
1 CGATCTCGCACACACAGTGC
15102 TCGGTTAAAG
Statistics
Matches: 79, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
28 22 0.28
29 51 0.65
30 6 0.08
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (29 bp):
CGATCTCGCACACACAGTGCCTCAATTAA
Found at i:15079 original size:58 final size:57
Alignment explanation
Indices: 14967--15155 Score: 262
Period size: 58 Copynumber: 3.4 Consensus size: 57
14957 GCCCACTGAC
* * *
14967 CGATCTCGCACACATAGTGCTCGGTTGAAGAACTCGCACACACAATGCCTCAATTAT
1 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAGTGCCTCAATTAT
* *
15024 CGATCTCGCACACATAGTGCTTGGTTAAAGGAATTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAA-GAATTCGCACACACAGTGCCTCAATTAT
* *
15082 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTTGCACACA-AGTGCCTC--TAAT
1 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAGTGCCTCAATTAT
*
15136 C-AT-TCGCACACATAATGCTC
1 CGATCTCGCACACATAGTGCTC
15156 ATATTCATTG
Statistics
Matches: 121, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
52 16 0.13
53 2 0.02
54 3 0.02
56 8 0.07
57 39 0.32
58 53 0.44
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (57 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAGTGCCTCAATTAT
Found at i:15388 original size:43 final size:43
Alignment explanation
Indices: 15284--15417 Score: 227
Period size: 43 Copynumber: 3.2 Consensus size: 43
15274 CCTTGCTCGA
** *
15284 ATCACCGGCATTAAGCCTGCTAGGCAC-AAGACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
15326 ATCA-CGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
15368 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
15411 ATCACCG
1 ATCACCG
15418 AGTTTCATGC
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
41 20 0.23
42 22 0.25
43 45 0.52
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.11
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:17032 original size:38 final size:38
Alignment explanation
Indices: 16945--17108 Score: 168
Period size: 38 Copynumber: 4.3 Consensus size: 38
16935 CGAGGTATAA
* * * *
16945 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT
* ** * *
16984 AAACTAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
17022 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
* * * **
17060 AACCCGGATATAATTCTAGCA-TATAGCCTGCGGTCTTT
1 AACCCGGATATAATACCAGCACGA-AGCCTGCGGGATTT
17098 AAGCCCGGATA
1 AA-CCCGGATA
17109 CACATCAAAT
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
37 1 0.01
38 69 0.66
39 34 0.33
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT
Found at i:17106 original size:77 final size:77
Alignment explanation
Indices: 16945--17108 Score: 188
Period size: 77 Copynumber: 2.1 Consensus size: 77
16935 CGAGGTATAA
* * * *
16945 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTTAAACTAGATATAATACCAGCACTAGG
1 AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCAGATATAATACCAGCACTAAG
17010 CCTGCGGGATTT
66 CCTGCGGGATTT
* * * * * *
17022 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTTAACCCGGATATAATTCTAGCA-TATA
1 AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCAGATATAATACCAGCACTA-A
**
17085 GCCTGCGGTCTTT
65 GCCTGCGGGATTT
17098 AAGCCCGGATA
1 AA-CCCGGATA
17109 CACATCAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
75 2 0.03
76 32 0.44
77 39 0.53
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (77 bp):
AACCCGGATATAACACCAGCACGAAGCCTACGGGACTTTAAACCAGATATAATACCAGCACTAAG
CCTGCGGGATTT
Found at i:20681 original size:25 final size:26
Alignment explanation
Indices: 20647--20722 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 26
20637 CACTGACGAT
20647 CTCGCACACATAGTGCTCGGTT-GAA
1 CTCGCACACATAGTGCTCGGTTCGAA
* ** *
20672 CTCGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACATAGTG-CTCGGTT--CGAA
20701 CTCGCACACATAGTGCTCGGTT
1 CTCGCACACATAGTGCTCGGTT
20723 AAAGAATTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 14 0.35
26 5 0.12
28 5 0.12
29 16 0.40
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (26 bp):
CTCGCACACATAGTGCTCGGTTCGAA
Found at i:20704 original size:29 final size:29
Alignment explanation
Indices: 20672--20772 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 29
20662 CTCGGTTGAA
20672 CTCGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACACAGTGCCTCAATTACCGAT
* ** **
20701 CTCGCACACATAGTG-CTCGGTTAAAGAAT
1 CTCGCACACACAGTGCCTCAATTACCG-AT
*
20730 -TCGCACA-ACAATGCCTCAATTACCGAT
1 CTCGCACACACAGTGCCTCAATTACCGAT
* *
20757 CTCGTACACATAGTGC
1 CTCGCACACACAGTGC
20773 TCGGTTAAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
27 6 0.11
28 27 0.50
29 21 0.39
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAATTACCGAT
Found at i:20767 original size:56 final size:57
Alignment explanation
Indices: 20643--20797 Score: 237
Period size: 56 Copynumber: 2.8 Consensus size: 57
20633 TGCCCACTGA
* *
20643 CGATCTCGCACACATAGTGCTCGGTT---GAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAATGCCTCAATTAC
20697 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACA-ACAATGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAATGCCTCAATTAC
* *
20753 CGATCTCGTACACATAGTGCTCGGTTAAAGGAATTTGCACACACA
1 CGATCTCGCACACATAGTGCTCGGTTAAA-GAATTCGCACACACA
20798 GTGCTCTAAT
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
54 26 0.28
56 43 0.47
57 20 0.22
58 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (57 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAGAATTCGCACACACAATGCCTCAATTAC
Done.