Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5345.1
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: 25801
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.19
Warning! 9807 characters in sequence are not A, C, G, or T
Found at i:11546 original size:27 final size:27
Alignment explanation
Indices: 11529--12008 Score: 474
Period size: 27 Copynumber: 17.6 Consensus size: 27
11519 ATATTAAGTC
11529 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
11556 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11584 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11611 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11638 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11666 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11694 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11722 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11750 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11777 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
11804 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
11832 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11859 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11886 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11913 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
11940 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * * *
11967 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
*
11994 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
12009 GCACAATTTA
Statistics
Matches: 444, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
27 281 0.63
28 163 0.37
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:11659 original size:54 final size:54
Alignment explanation
Indices: 11529--12008 Score: 852
Period size: 54 Copynumber: 8.8 Consensus size: 54
11519 ATATTAAGTC
* * * *
11529 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTC-AACT
11584 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
11638 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTC-AACT
11694 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTC-AACT
11750 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
*
11804 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAACT
11859 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
11913 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
*
11967 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
12009 GCACAATTTA
Statistics
Matches: 415, Mismatches: 7, Indels: 7
0.97 0.02 0.02
Matches are distributed among these distances:
54 179 0.43
55 153 0.37
56 83 0.20
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
Found at i:11666 original size:82 final size:82
Alignment explanation
Indices: 11529--12008 Score: 874
Period size: 82 Copynumber: 5.9 Consensus size: 82
11519 ATATTAAGTC
* * * *
11529 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
11594 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
11611 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
11676 GTGCTACATAGTCAAACT
66 GTGCTACATAGTC-AACT
11694 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
11759 AGTGCTACATAGTCAACT
65 AGTGCTACATAGTCAACT
*
11777 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
11842 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
11859 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTC-AACTCGCACACTTA
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
11923 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
*
11940 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTC-AATTCGCACACTTA
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
12004 GTGCT
66 GTGCT
12009 GCACAATTTA
Statistics
Matches: 389, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
81 99 0.25
82 181 0.47
83 54 0.14
84 55 0.14
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:21653 original size:46 final size:46
Alignment explanation
Indices: 21581--21681 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
21571 GACAGGACAG
* * *
21581 GACAGAAATGAGCCATGTATGTCCATATCAGT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTATGCCCATATCA-TATATATGGCATTGGA
*
21627 GACAGGAATGAGCCATGTAAT-CCCATATTATATATATGGCATTGGA
1 GACAGGAATGAGCCATGT-ATGCCCATATCATATATATGGCATTGGA
21673 GACAGGAAT
1 GACAGGAAT
21682 AATTCATGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 1 0.02
46 46 0.94
47 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (46 bp):
GACAGGAATGAGCCATGTATGCCCATATCATATATATGGCATTGGA
Done.