Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018199.1 Corchorus olitorius cultivar O-4 contig18232, 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: 9537
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Found at i:1218 original size:26 final size:24
Alignment explanation
Indices: 1189--1243 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
1179 TTTTTGCTAT
**
1189 GTATGGATTTTATTTTTTTGTGACTG
1 GTATGGATTTTATAGTTTT-TGA-TG
1215 GTATGGATTTTATAGTTTTTGATG
1 GTATGGATTTTATAGTTTTTGATG
1239 GTATG
1 GTATG
1244 CATTCGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 3 0.11
26 17 0.63
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (24 bp):
GTATGGATTTTATAGTTTTTGATG
Found at i:1330 original size:61 final size:60
Alignment explanation
Indices: 1265--1423 Score: 248
Period size: 61 Copynumber: 2.6 Consensus size: 60
1255 AGTATACAAT
*
1265 AAGTTGG-AATTTTTTATTTTGTTTTATGTGTTGGGTTTTGTATTCGCATATAATATATGGA
1 AAGTTGGTAA-TTTTT-TTTTGTTTTATGTGTTGGGTTTTGTATTCGAATATAATATATGGA
*
1326 AAGTTGGTAATTTTTGTTTTGTTTTATGTGTTGGGTTTTGTATTCGAATATAATATATGGG
1 AAGTTGGTAATTTTT-TTTTGTTTTATGTGTTGGGTTTTGTATTCGAATATAATATATGGA
* *
1387 AAGTTGGTAAATTTTCTTTGTTTTATGTGTTGGGTTT
1 AAGTTGGTAATTTTTTTTTGTTTTATGTGTTGGGTTT
1424 CTGACTTGGT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
60 21 0.23
61 69 0.75
62 2 0.02
ACGTcount: A:0.21, C:0.03, G:0.23, T:0.53
Consensus pattern (60 bp):
AAGTTGGTAATTTTTTTTTGTTTTATGTGTTGGGTTTTGTATTCGAATATAATATATGGA
Found at i:2018 original size:9 final size:9
Alignment explanation
Indices: 2004--2043 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1994 TGAGAATGCA
*
2004 AATGGTAAG
1 AATGGTGAG
2013 AATGGTGAG
1 AATGGTGAG
2022 AATGGTGAG
1 AATGGTGAG
*
2031 AATGTTGAG
1 AATGGTGAG
2040 AATG
1 AATG
2044 CCGATAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (9 bp):
AATGGTGAG
Found at i:2165 original size:21 final size:21
Alignment explanation
Indices: 2141--2213 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
2131 AGGTTGAAGA
2141 AGATGAAGAGAGGGTTCAGGT
1 AGATGAAGAGAGGGTTCAGGT
* * *
2162 AGATGAAGAGAGGGTTGAAGA
1 AGATGAAGAGAGGGTTCAGGT
*
2183 AGATGAAAAGAAGGGTTCAGGT
1 AGATGAAGAG-AGGGTTCAGGT
*
2205 AGAAGAAGA
1 AGATGAAGA
2214 TGATTCTGAG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 27 0.64
22 15 0.36
ACGTcount: A:0.42, C:0.03, G:0.40, T:0.15
Consensus pattern (21 bp):
AGATGAAGAGAGGGTTCAGGT
Found at i:2180 original size:42 final size:43
Alignment explanation
Indices: 2132--2213 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
2122 ATTTTGTTAA
* *
2132 GGTTGAAGAAGATGAAGAG-AGGGTTCAGGTAGATGAAGAGAG
1 GGTTGAAGAAGATGAAAAGAAGGGTTCAGGTAGAAGAAGAGAG
2174 GGTTGAAGAAGATGAAAAGAAGGGTTCAGGTAGAAGAAGA
1 GGTTGAAGAAGATGAAAAGAAGGGTTCAGGTAGAAGAAGA
2214 TGATTCTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 18 0.49
43 19 0.51
ACGTcount: A:0.41, C:0.02, G:0.40, T:0.16
Consensus pattern (43 bp):
GGTTGAAGAAGATGAAAAGAAGGGTTCAGGTAGAAGAAGAGAG
Found at i:6035 original size:21 final size:21
Alignment explanation
Indices: 6011--6081 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
6001 TGCTAGGAGA
6011 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
6032 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
** *
6053 TCATTGGAGAAGGTTTTAAGT
1 TCATTGGAGAAGGTTCCAAGC
6074 TCATTGGA
1 TCATTGGA
6082 ATTGCCTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:6987 original size:25 final size:24
Alignment explanation
Indices: 6951--6997 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
6941 TCCTTCTATT
6951 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
6974 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
6998 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Done.