Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold779
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: 32228
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:7150 original size:27 final size:27
Alignment explanation
Indices: 7133--7310 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
7123 ATATTAAGTC
7133 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
7160 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
7188 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *** ** *
7215 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
7242 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
7269 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
7296 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
7311 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 104 0.79
28 27 0.21
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:7272 original size:54 final size:54
Alignment explanation
Indices: 7133--7309 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
7123 ATATTAAGTC
* * *
7133 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAA-T
* ** * *
7188 CGCACACTTAGTGC-TACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
7242 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
7296 CGCACACTTAGTGC
1 CGCACACTTAGTGC
7310 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 44 0.42
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:7299 original size:81 final size:82
Alignment explanation
Indices: 7154--7309 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
7144 TGCTATATAA
* *
7154 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
7219 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
7236 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
7299 ACACTTAGTGC
65 ACACTTAGTGC
7310 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:15568 original size:21 final size:20
Alignment explanation
Indices: 15542--15582 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
15532 ATTTAATTAT
* *
15542 TTATATTTATTAATATATTTA
1 TTATATTAATAAAT-TATTTA
15563 TTATATTAATAAATTATTTA
1 TTATATTAATAAATTATTTA
15583 ATTTTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTAATAAATTATTTA
Found at i:15569 original size:17 final size:18
Alignment explanation
Indices: 15530--15573 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
15520 TTAAACATAC
15530 ATAT-TTAAT-TATTTAT
1 ATATATTAATATATTTAT
*
15546 ATTTATTAATATATTTAT
1 ATATATTAATATATTTAT
15564 -TATATTAATA
1 ATATATTAATA
15574 AATTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.58
18 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTAATATATTTAT
Found at i:15597 original size:34 final size:38
Alignment explanation
Indices: 15536--15611 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 38
15526 ATACATATTT
*
15536 AATTATTTATATTTATTAATATATTTATTATATTAATA
1 AATTATTTATATTTATTAATATATTTATTATAATAATA
* *
15574 AATTATTTA-ATTT-TTCA-AT-TTTATTTTAATAATA
1 AATTATTTATATTTATTAATATATTTATTATAATAATA
15608 AATT
1 AATT
15612 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 17 0.49
35 2 0.06
36 3 0.09
37 4 0.11
38 9 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
AATTATTTATATTTATTAATATATTTATTATAATAATA
Found at i:15612 original size:13 final size:14
Alignment explanation
Indices: 15596--15637 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
15586 TTTCAATTTT
15596 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
15609 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
15624 ATTTTAAATAATAT
1 ATTTT-AATAATAT
15638 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:15622 original size:16 final size:16
Alignment explanation
Indices: 15600--15636 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
15590 AATTTTATTT
15600 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
15617 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
15632 TAATA
1 TAATA
15637 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:16209 original size:14 final size:14
Alignment explanation
Indices: 16187--16225 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
16177 CCAGAAAAGT
16187 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
16201 AAATTATTTTCCA-
1 AAATCATTTTCCAG
16214 AAAGTCATTTTC
1 AAA-TCATTTTC
16226 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:22889 original size:24 final size:24
Alignment explanation
Indices: 22868--22919 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
22858 AATCAATGTC
*
22868 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
22892 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
22916 AAAT
1 AAAT
22920 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:25375 original size:38 final size:38
Alignment explanation
Indices: 25324--25402 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
25314 TTATAAGGCT
*
25324 CTACGAGACCTTAAAACATGCTTGTATGAGGTTTGGGA
1 CTACGAGACCTTAAAACATGCTTGTACGAGGTTTGGGA
25362 CTACGAGACCTTAAAACATGCTTGTACGAGGTTTGGGA
1 CTACGAGACCTTAAAACATGCTTGTACGAGGTTTGGGA
25400 CTA
1 CTA
25403 AACCGATAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (38 bp):
CTACGAGACCTTAAAACATGCTTGTACGAGGTTTGGGA
Found at i:26808 original size:43 final size:43
Alignment explanation
Indices: 26692--26841 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 43
26682 TATCTTGGAT
* * * * *
26692 ATGGTCTTACATGTTATCAC-ATATCGATGCCACTATCCCAGAC
1 ATGGTCTTACACGTAATCACAATA-CAATGCCAATGTCCCAGAC
* * * *
26735 AAGGTCTTATACGAAATCA-TATA-ATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACA--ATGCCAATGTCCCAGAC
26778 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
* *
26821 ATGGTCTTTCATGTAATCACA
1 ATGGTCTTACACGTAATCACA
26842 TCTCGGCAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
43 84 0.95
44 3 0.03
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
Done.