Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2212
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: 27387
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:3157 original size:40 final size:41
Alignment explanation
Indices: 3050--3248 Score: 280
Period size: 41 Copynumber: 4.9 Consensus size: 41
3040 ATTGAAGTAA
3050 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
3091 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
3132 TTCAGACTTT-AGTCTAGCAGGCTTAATGCCGGTGATACAT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
* *
3172 TTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-T
1 TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT
* * * **
3211 GAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 --TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
3249 ATCTGTTTAA
Statistics
Matches: 144, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 45 0.31
41 96 0.67
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
Found at i:3188 original size:81 final size:82
Alignment explanation
Indices: 3050--3248 Score: 280
Period size: 81 Copynumber: 2.4 Consensus size: 82
3040 ATTGAAGTAA
*
3050 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAAGTCTAGCAGGCT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGC-
3115 TAA-TGCCGGTGATACAT
65 TAAGTGCCGGTGATACAT
*
3132 TTCAGACTTT-AGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGCT
3196 AAGTGCCGGTG-TAC-T
66 AAGTGCCGGTGATACAT
* * * **
3211 GAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 --TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
3249 ATCTGTTTAA
Statistics
Matches: 106, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
79 1 0.01
80 6 0.06
81 67 0.63
82 32 0.30
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (82 bp):
TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGCT
AAGTGCCGGTGATACAT
Found at i:10679 original size:41 final size:41
Alignment explanation
Indices: 10631--10789 Score: 200
Period size: 41 Copynumber: 3.9 Consensus size: 41
10621 ATTGAAGTAA
10631 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
10672 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
* *
10713 TTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-T
1 TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT
* * **
10752 GAATCA-AGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 --TTCAGA-CTTTAAGTCTAGCAGGCTTAATGCCGGTGA
10790 ATCTGTTTAA
Statistics
Matches: 105, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
39 1 0.01
40 7 0.07
41 95 0.90
42 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (41 bp):
TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACAT
Found at i:12800 original size:46 final size:46
Alignment explanation
Indices: 12724--12906 Score: 267
Period size: 46 Copynumber: 4.0 Consensus size: 46
12714 ATTGCTATAG
* * * *
12724 CTCAGTATGGTTTCCTTCACGGAAATACCATACCTACTTTTCACCA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
* *
12770 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTCCATAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
*
12816 CTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
* * * *
12862 GTCAGTATGGTTTTGTTTACCGAAACACCATACCTACTTTTCACA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACA
12907 TTTTGCCATG
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35
Consensus pattern (46 bp):
CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
Done.