Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2199
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: 37760
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Found at i:625 original size:21 final size:21
Alignment explanation
Indices: 601--644 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
591 TGATACGAGA
601 TCAAAGGCCCGACAAATGCGT
1 TCAAAGGCCCGACAAATGCGT
622 TCAAAGGCCCGACAAATGCGT
1 TCAAAGGCCCGACAAATGCGT
643 TC
1 TC
645 CAAACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
TCAAAGGCCCGACAAATGCGT
Found at i:10043 original size:46 final size:44
Alignment explanation
Indices: 9984--10098 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
9974 ACAGGACAGA
* *
9984 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
10030 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
10074 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
10099 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:10079 original size:44 final size:45
Alignment explanation
Indices: 9984--10117 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
9974 ACAGGACAGA
* *
9984 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
10030 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
10074 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
10118 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:17400 original size:46 final size:44
Alignment explanation
Indices: 17341--17455 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
17331 ACAGGACAGA
* *
17341 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
17387 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
17431 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
17456 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:17436 original size:44 final size:45
Alignment explanation
Indices: 17341--17474 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
17331 ACAGGACAGA
* *
17341 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
17387 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
17431 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
17475 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:24755 original size:46 final size:44
Alignment explanation
Indices: 24696--24810 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
24686 ACAGGACAGA
* *
24696 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
24742 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
24786 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
24811 GCCAAAGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:24791 original size:44 final size:45
Alignment explanation
Indices: 24696--24829 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
24686 ACAGGACAGA
* *
24696 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
24742 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** ***
24786 ACAGGAATAATTCATGTAAGTCCATGCCAAAGATATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
24830 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 35 0.47
45 1 0.01
46 38 0.51
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:36978 original size:18 final size:18
Alignment explanation
Indices: 36916--36979 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
36906 GCTCTGGTGA
*
36916 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGACTTCGG
* * *
36934 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TTAG-ACTT-CGG
36955 GCTTCAGTTAGACTTCGG
1 GCTTCAGTTAGACTTCGG
36973 GCTTCAG
1 GCTTCAG
36980 ATCACGATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 14 0.39
19 8 0.22
20 7 0.19
21 7 0.19
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (18 bp):
GCTTCAGTTAGACTTCGG
Done.