Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024896.1 Corchorus olitorius cultivar O-4 contig24929, 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: 17036
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:126 original size:13 final size:13
Alignment explanation
Indices: 108--132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98 AAAACTTGAA
108 TTTCACAATTTTT
1 TTTCACAATTTTT
121 TTTCACAATTTT
1 TTTCACAATTTT
133 GTGCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCACAATTTTT
Found at i:1808 original size:130 final size:130
Alignment explanation
Indices: 1575--1827 Score: 461
Period size: 130 Copynumber: 1.9 Consensus size: 130
1565 GGACAAATGT
* *
1575 CAACAGGACAAAAGCCAAATGTTGAGCATACAACAGTTTGAGGATAACTTTAATAGTAAGGTATA
1 CAACAGGACAAAAGCCAAATGATGAGCATACAACAATTTGAGGATAACTTTAATAGTAAGGTATA
1640 GATTAACAAAAAAATTATATTACACAAGATGTAATTTAAAATAAGTTTTCATCAAACTGAGCATA
66 GATTAACAAAAAAATTATATTACACAAGATGTAATTTAAAATAAGTTTTCATCAAACTGAGCATA
* *
1705 CAACAGGAGAAATGCCAAATGATGAGCATACAACAATTTGAGGATAACTTTAATAGTAAGGTATA
1 CAACAGGACAAAAGCCAAATGATGAGCATACAACAATTTGAGGATAACTTTAATAGTAAGGTATA
*
1770 GATTAACAAAAAAATTATATTACACAAGATGTAATTTAAAATCAGTTTTCATCAAACT
66 GATTAACAAAAAAATTATATTACACAAGATGTAATTTAAAATAAGTTTTCATCAAACT
1828 TCAATCCCAC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 118 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (130 bp):
CAACAGGACAAAAGCCAAATGATGAGCATACAACAATTTGAGGATAACTTTAATAGTAAGGTATA
GATTAACAAAAAAATTATATTACACAAGATGTAATTTAAAATAAGTTTTCATCAAACTGAGCATA
Found at i:8910 original size:19 final size:19
Alignment explanation
Indices: 8886--8923 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8876 TATACAATAT
8886 TAAATAGACCGGCAATCGA
1 TAAATAGACCGGCAATCGA
8905 TAAATAGACCGGCAATCGA
1 TAAATAGACCGGCAATCGA
8924 AATCACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
TAAATAGACCGGCAATCGA
Found at i:10226 original size:8 final size:8
Alignment explanation
Indices: 10215--10287 Score: 74
Period size: 8 Copynumber: 8.4 Consensus size: 8
10205 TAGGAACTAA
10215 GTGGGAAT
1 GTGGGAAT
*
10223 GTGGAAAT
1 GTGGGAAT
10231 GTGGGAACT
1 GTGGGAA-T
10240 AAGTGGGAAT
1 --GTGGGAAT
10250 GTGGGAAT
1 GTGGGAAT
*
10258 GTGGAAAT
1 GTGGGAAT
10266 GTGGGAACT
1 GTGGGAA-T
10275 AAGTGGGAAT
1 --GTGGGAAT
10285 GTG
1 GTG
10288 CTGTTGGGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 37 0.67
9 2 0.04
10 2 0.04
11 14 0.25
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (8 bp):
GTGGGAAT
Found at i:10237 original size:27 final size:27
Alignment explanation
Indices: 10201--10261 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
10191 TGTAAGGGGG
*
10201 AATGTAGGAACTAAGTGGGAATGTGGA
1 AATGTGGGAACTAAGTGGGAATGTGGA
*
10228 AATGTGGGAACTAAGTGGGAATGTGGG
1 AATGTGGGAACTAAGTGGGAATGTGGA
10255 AATGTGG
1 AATGTGG
10262 AAATGTGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.41, T:0.23
Consensus pattern (27 bp):
AATGTGGGAACTAAGTGGGAATGTGGA
Found at i:10254 original size:35 final size:35
Alignment explanation
Indices: 10215--10287 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
10205 TAGGAACTAA
10215 GTGGGAATGTGGAAATGTGGGAACTAAGTGGGAAT
1 GTGGGAATGTGGAAATGTGGGAACTAAGTGGGAAT
10250 GTGGGAATGTGGAAATGTGGGAACTAAGTGGGAAT
1 GTGGGAATGTGGAAATGTGGGAACTAAGTGGGAAT
10285 GTG
1 GTG
10288 CTGTTGGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.30, C:0.03, G:0.44, T:0.23
Consensus pattern (35 bp):
GTGGGAATGTGGAAATGTGGGAACTAAGTGGGAAT
Found at i:12962 original size:19 final size:19
Alignment explanation
Indices: 12938--12975 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12928 TTTCTTCTTT
12938 TTACTTTGGACAAAAAATG
1 TTACTTTGGACAAAAAATG
12957 TTACTTTGGACAAAAAATG
1 TTACTTTGGACAAAAAATG
12976 AGAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
TTACTTTGGACAAAAAATG
Done.