Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018148.1 Corchorus olitorius cultivar O-4 contig18181, 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: 8114
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Found at i:1143 original size:15 final size:14
Alignment explanation
Indices: 1125--1158 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1115 TTTTTTGGGC
*
1125 TTTTTATTTTTTTAT
1 TTTTTATTTATTT-T
1140 TTTTTATTTATTTT
1 TTTTTATTTATTTT
1154 TTTTT
1 TTTTT
1159 CCAGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTATTTATTTT
Found at i:6997 original size:32 final size:34
Alignment explanation
Indices: 6967--7058 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 34
6957 AATGTGAATG
6967 AAGGCAAGTTCAATGTCATTTGGGATTGAATGTGAA
1 AAGGCAAGTTCAATGTCATTTGGGATTGAA-GTG-A
*
7003 TAAGGCAAGTTCAATGTCATTTGGGAAATTGGATGTGAA
1 -AAGGCAAGTTCAATGTCATTTGGG--ATT-GAAGTG-A
7042 TAAGGCAAGTTCAATGT
1 -AAGGCAAGTTCAATGT
7059 TGATTGGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 24 0.47
39 25 0.49
40 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (34 bp):
AAGGCAAGTTCAATGTCATTTGGGATTGAAGTGA
Found at i:7137 original size:34 final size:34
Alignment explanation
Indices: 7099--7177 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 34
7089 TAGTTCAATG
7099 TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
1 TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
7133 TCAATGTTAATTGGAAAATTCAGATGTGAATAAGGCAAGT
1 TC------AATTGGAAAATTCAGATGTGAATAAGGCAAGT
7173 TCAAT
1 TCAAT
7178 GTTAATTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
34 5 0.13
40 34 0.87
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (34 bp):
TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
Found at i:7139 original size:40 final size:39
Alignment explanation
Indices: 6917--7285 Score: 420
Period size: 41 Copynumber: 9.2 Consensus size: 39
6907 TTGAGGGCCA
* *
6917 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTG
1 ATGTGAA-TAAGGCAAGTTCAATGTCAATTGGAAAATTAG
* *
6957 AATGTGAATGAAGGCAAGTTCAATGTCATTTGG--GATT-G
1 -ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGAAAATTAG
* * *
6995 AATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTGG
1 -ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTAG
** *
7035 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAA-TTAG
*
7075 ATGTGAATCAAGGCTAGTTCAATGTCAATTGGAAAATTCAG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGAAAATT-AG
*
7116 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTCAG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATT-AG
* *
7156 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTAG
* *
7195 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGTAAAGTTGG
1 -ATGTGAAT-AAGGCAAGTTCAATGTCAATTGG-AAAATTAG
** * *
7237 ATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTAA
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATT-GGAAAATTAG
7278 ATGTGAAT
1 ATGTGAAT
7286 GTGCCGTGTA
Statistics
Matches: 296, Mismatches: 21, Indels: 22
0.87 0.06 0.06
Matches are distributed among these distances:
37 23 0.08
38 10 0.03
39 38 0.13
40 91 0.31
41 126 0.43
42 8 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (39 bp):
ATGTGAATAAGGCAAGTTCAATGTCAATTGGAAAATTAG
Found at i:7187 original size:121 final size:119
Alignment explanation
Indices: 6917--7285 Score: 501
Period size: 121 Copynumber: 3.1 Consensus size: 119
6907 TTGAGGGCCA
* * *
6917 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGAATGTGAATGAAGGCAAGTTCAATG
1 ATGTGAA-TAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATG
* * * * * *
6982 TCATTTGG--GATT-GAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTGG
65 TCAATTGGAAAATTAG-ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTAG
* * *
7035 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGGATGTGAATCAAGGCTAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
7100 CAATTGGAAAATTCAGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTCAG
66 CAATTGGAAAATT-AGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATT-AG
7156 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
* * * * *
7221 CAATTGGTAAAGTTGGATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTAA
66 CAATTGG-AAAATTAGATGTGAAT-AAGGCAAGTTCAATGTTAATT-GGAAAATTAG
7278 ATGTGAAT
1 ATGTGAAT
7286 GTGCCGTGTA
Statistics
Matches: 223, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
117 58 0.26
118 7 0.03
119 3 0.01
120 34 0.15
121 80 0.36
122 34 0.15
123 7 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (119 bp):
ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
CAATTGGAAAATTAGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTAG
Done.