Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007762.1 Corchorus capsularis cultivar CVL-1 contig07783, 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: 2903
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Found at i:1795 original size:24 final size:25
Alignment explanation
Indices: 1735--1793 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
1725 TTCAAAACCT
*
1735 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
1760 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
1784 AAA-TTCATTT
1 AAACTTCATTT
1794 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:1832 original size:26 final size:26
Alignment explanation
Indices: 1803--1870 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
1793 TTCCTTCATT
1803 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
1829 TTAATCATAAACTAATTAAATATTAA
1 TTAATCATAAACTAATTAAATACTAA
*
1855 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
1871 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:1833 original size:15 final size:15
Alignment explanation
Indices: 1803--1847 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1793 TTCCTTCATT
1803 TTAATCATAAACTAA
1 TTAATCATAAACTAA
1818 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
1829 TTAATCATAAACTAA
1 TTAATCATAAACTAA
1844 TTAA
1 TTAA
1848 ATATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.35
13 4 0.15
15 13 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:1939 original size:9 final size:9
Alignment explanation
Indices: 1925--1954 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1915 AATTAATATT
1925 AAAAAATTA
1 AAAAAATTA
1934 AAAAAATTAA
1 AAAAAATT-A
1944 AAAAAATTA
1 AAAAAATTA
1953 AA
1 AA
1955 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:1946 original size:10 final size:10
Alignment explanation
Indices: 1925--1954 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1915 AATTAATATT
1925 AAAAAATT-A
1 AAAAAATTAA
1934 AAAAAATTAA
1 AAAAAATTAA
1944 AAAAAATTAA
1 AAAAAATTAA
1954 A
1 A
1955 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:2055 original size:14 final size:14
Alignment explanation
Indices: 2036--2067 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2026 AAAAAAAATT
2036 AAAAATACTTTTTA
1 AAAAATACTTTTTA
*
2050 AAAAATATTTTTTA
1 AAAAATACTTTTTA
2064 AAAA
1 AAAA
2068 TGGGGCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATACTTTTTA
Found at i:2259 original size:20 final size:21
Alignment explanation
Indices: 2234--2272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2224 AAAAATTATA
2234 AAAAGGGG-GCAGTATTTAGC
1 AAAAGGGGAGCAGTATTTAGC
*
2254 AAAAGGGGAGCAGTGTTTA
1 AAAAGGGGAGCAGTATTTA
2273 TGAAATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.21
Consensus pattern (21 bp):
AAAAGGGGAGCAGTATTTAGC
Done.