Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold934
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: 23017
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Found at i:1739 original size:28 final size:28
Alignment explanation
Indices: 1676--1801 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
1666 ATATTAAGTC
*
1676 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
1703 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
1731 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1759 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1788 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1802 CAATCTCATG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.24
28 49 0.54
29 19 0.21
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:9658 original size:28 final size:28
Alignment explanation
Indices: 9595--9720 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
9585 ATATTAAGTC
*
9595 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
9622 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
9650 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
9678 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
9707 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9721 CAATCTCATG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.24
28 51 0.55
29 19 0.21
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:17530 original size:27 final size:26
Alignment explanation
Indices: 17513--17582 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
17503 ATATTAAGTC
17513 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
17540 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
17568 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
17583 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 (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:17576 original size:28 final size:28
Alignment explanation
Indices: 17513--17610 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
17503 ATATTAAGTC
*
17513 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
17540 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
17568 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
17597 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17611 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:22547 original size:18 final size:18
Alignment explanation
Indices: 22507--22551 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
22497 GCGTTAGAAA
***
22507 AAAAAAAAATTATTTTTT
1 AAAAAAAAATTATAAATT
*
22525 TAAAAAAAATTATAAATT
1 AAAAAAAAATTATAAATT
22543 AAAAAAAAA
1 AAAAAAAAA
22552 AGAAATTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAAAAATTATAAATT
Found at i:22577 original size:18 final size:18
Alignment explanation
Indices: 22547--22590 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
22537 TAAATTAAAA
*
22547 AAAAAAGAAATTTATTTTT
1 AAAAAA-AATTTTATTTTT
22566 ATAAAAAAATTTTATTTTT
1 A-AAAAAAATTTTATTTTT
22585 AAAAAA
1 AAAAAA
22591 TTTTAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAAAAAATTTTATTTTT
Done.