Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_665 ID=scaffold_665-JGI_221_v2.0
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: 5066
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.32
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:1400 original size:14 final size:14
Alignment explanation
Indices: 1381--1408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1371 CCCTTTGCGG
1381 GTTTTCACCTTAGC
1 GTTTTCACCTTAGC
1395 GTTTTCACCTTAGC
1 GTTTTCACCTTAGC
1409 CTCTCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
GTTTTCACCTTAGC
Found at i:1465 original size:23 final size:21
Alignment explanation
Indices: 1413--1465 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
1403 CTTAGCCTCT
*
1413 CCATTTTTACTTTTCCATTTT
1 CCATTTTTACTTTTCCATTTC
* *
1434 TCATTTTTTCACTTTTTCATTTC
1 CCA-TTTTT-ACTTTTCCATTTC
1457 CCATGTTTT
1 CCAT-TTTT
1466 TTTTTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 6 0.24
23 17 0.68
ACGTcount: A:0.13, C:0.23, G:0.02, T:0.62
Consensus pattern (21 bp):
CCATTTTTACTTTTCCATTTC
Found at i:1963 original size:1 final size:1
Alignment explanation
Indices: 1957--2062 Score: 59
Period size: 1 Copynumber: 106.0 Consensus size: 1
1947 CCGATAGAGG
* * * * * * * * * * * *
1957 TTTTTTTGTTTCTTTTTGTTTTTTGTTTTTTGTTCTTTTTTGTTCTCTTTTTTTCTTTTTTCTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
2022 TTTTTCTCTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2063 AAACTGAATC
Statistics
Matches: 71, Mismatches: 34, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.84
Consensus pattern (1 bp):
T
Found at i:1980 original size:17 final size:16
Alignment explanation
Indices: 1957--2062 Score: 85
Period size: 17 Copynumber: 6.4 Consensus size: 16
1947 CCGATAGAGG
1957 TTTTTTTGTTTCTTT-T
1 TTTTTTTGTTT-TTTGT
1973 TGTTTTTTGTTTTTTGT
1 T-TTTTTTGTTTTTTGT
*
1990 TCTTTTTTGTTCTCTT-T
1 T-TTTTTTGTT-TTTTGT
* * *
2007 TTTTCTT-TTTTCTAT
1 TTTTTTTGTTTTTTGT
2022 TTTTTCTCT-TTTTTTGT
1 TTTTT-T-TGTTTTTTGT
2039 TTTTTTTGTTTTTTTGT
1 TTTTTTTG-TTTTTTGT
2056 TTTTTTT
1 TTTTTTT
2063 AAACTGAATC
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
14 2 0.03
15 8 0.11
16 11 0.15
17 50 0.68
18 3 0.04
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.84
Consensus pattern (16 bp):
TTTTTTTGTTTTTTGT
Found at i:1987 original size:9 final size:9
Alignment explanation
Indices: 1957--2062 Score: 89
Period size: 9 Copynumber: 11.8 Consensus size: 9
1947 CCGATAGAGG
1957 TTTTTTTGT
1 TTTTTTTGT
1966 TTCTTTTTG-
1 TT-TTTTTGT
1975 -TTTTTTG-
1 TTTTTTTGT
1982 -TTTTTTGT
1 TTTTTTTGT
1990 TCTTTTTTGT
1 T-TTTTTTGT
2000 TCTCTTTTT-T
1 T-T-TTTTTGT
*
2010 TCTTTTTTCT
1 T-TTTTTTGT
* *
2020 ATTTTTTCT
1 TTTTTTTGT
2029 CTTTTTTTGT
1 -TTTTTTTGT
2039 TTTTTTTG-
1 TTTTTTTGT
2047 TTTTTTTGT
1 TTTTTTTGT
2056 TTTTTTT
1 TTTTTTT
2063 AAACTGAATC
Statistics
Matches: 86, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
7 13 0.15
8 9 0.10
9 30 0.35
10 29 0.34
11 5 0.06
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTGT
Done.