Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007022.1 Kokia drynarioides strain JFW-HI SEQ_121629, whole genome shotgun sequence
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: 2966
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Found at i:1516 original size:23 final size:22
Alignment explanation
Indices: 1490--1578 Score: 65
Period size: 23 Copynumber: 4.0 Consensus size: 22
1480 AAAAACGCAT
*
1490 AAAAAAATAACATCTAAACAACA
1 AAAAAAATAACA-CAAAACAACA
* * * *
1513 AAAATAACAAC-CAAAATAGCA
1 AAAAAAATAACACAAAACAACA
* *
1534 ACAAAAATAATAGCAAAACAACA
1 AAAAAAATAACA-CAAAACAACA
* *
1557 ACAAAAATAACAGAAAA-AACA
1 AAAAAAATAACACAAAACAACA
1578 A
1 A
1579 CACTAAAACA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
21 19 0.37
22 4 0.08
23 28 0.55
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.09
Consensus pattern (22 bp):
AAAAAAATAACACAAAACAACA
Found at i:1523 original size:12 final size:12
Alignment explanation
Indices: 1506--1568 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
1496 ATAACATCTA
1506 AACAACAAAAAT
1 AACAACAAAAAT
*
1518 AACAACCAAAAT
1 AACAACAAAAAT
*
1530 AGCAACAAAAAT
1 AACAACAAAAAT
* * *
1542 AATAGC-AAAAC
1 AACAACAAAAAT
1553 AACAACAAAAAT
1 AACAACAAAAAT
1565 AACA
1 AACA
1569 GAAAAAACAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 8 0.20
12 32 0.80
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:1564 original size:35 final size:35
Alignment explanation
Indices: 1505--1608 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 35
1495 AATAACATCT
* *
1505 AAACAACA--AAAATAACAACCAAAATAGCAACAA
1 AAACAACACTAAAACAACAACAAAAATAGCAACAA
* * *
1538 AAATAATAGC-AAAACAACAACAAAAATAACAGA-AA
1 AAACAACA-CTAAAACAACAACAAAAATAGCA-ACAA
* *
1573 AAACAACACTAAAACAATAA-AAAAATAGCATCAA
1 AAACAACACTAAAACAACAACAAAAATAGCAACAA
1607 AA
1 AA
1609 CAGCAACCGA
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
33 6 0.11
34 14 0.25
35 35 0.62
36 1 0.02
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.09
Consensus pattern (35 bp):
AAACAACACTAAAACAACAACAAAAATAGCAACAA
Found at i:1575 original size:24 final size:24
Alignment explanation
Indices: 1506--1580 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
1496 ATAACATCTA
*
1506 AACAACAAAAATAACA-ACCAAAAT
1 AACAACAAAAATAACAGA-CAAAAC
* *
1530 AGCAACAAAAATAATAG-CAAAAC
1 AACAACAAAAATAACAGACAAAAC
*
1553 AACAACAAAAATAACAGAAAAAAC
1 AACAACAAAAATAACAGACAAAAC
1577 AACA
1 AACA
1581 CTAAAACAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
23 20 0.47
24 23 0.53
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAGACAAAAC
Found at i:1649 original size:21 final size:20
Alignment explanation
Indices: 1624--1682 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
1614 ACCGAAACAA
*
1624 TAAAAAAAGCACCAAAATAG
1 TAAAAAAAACACCAAAATAG
*
1644 TAAAAACAACAACCAAAATAG
1 TAAAAAAAAC-ACCAAAATAG
1665 TAAAAAAAAACACCAAAA
1 T-AAAAAAAACACCAAAA
1683 CAACAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 18 0.53
22 8 0.24
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.08
Consensus pattern (20 bp):
TAAAAAAAACACCAAAATAG
Done.