Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022943.1 Corchorus olitorius cultivar O-4 contig22976, 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: 17840
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:2429 original size:26 final size:27
Alignment explanation
Indices: 2400--2450 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2390 TTTACACCTT
* *
2400 TAACACGAA-CAATTGTTTTTTTTTTC
1 TAACACAAATCAATTGTTGTTTTTTTC
*
2426 TAACACAAATCAGTTGTTGTTTTTT
1 TAACACAAATCAATTGTTGTTTTTT
2451 CTTATCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (27 bp):
TAACACAAATCAATTGTTGTTTTTTTC
Found at i:2529 original size:2 final size:2
Alignment explanation
Indices: 2522--2557 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2512 GAAAATAATA
2522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2558 GGAGGAAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3036 original size:2 final size:2
Alignment explanation
Indices: 3024--3064 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3014 CAGAAGAAGT
*
3024 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3065 CAACAGAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7253 original size:26 final size:26
Alignment explanation
Indices: 7224--7276 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
7214 TGTTTATCAA
*
7224 TCTGTATGCACTTTGCTTATGCCTCT
1 TCTGTATGCAATTTGCTTATGCCTCT
* *
7250 TCTGTATGCAATTTGCTTTTGTCTCT
1 TCTGTATGCAATTTGCTTATGCCTCT
7276 T
1 T
7277 TGATGTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (26 bp):
TCTGTATGCAATTTGCTTATGCCTCT
Found at i:14904 original size:7 final size:7
Alignment explanation
Indices: 14892--14922 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
14882 CTTACGTTGA
14892 AATTGTG
1 AATTGTG
14899 AATTGTG
1 AATTGTG
14906 AATTGTG
1 AATTGTG
14913 AATTGTG
1 AATTGTG
14920 AAT
1 AAT
14923 CTACATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (7 bp):
AATTGTG
Found at i:15151 original size:8 final size:8
Alignment explanation
Indices: 15138--15162 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15128 TACCAACCAA
15138 GGGTGAAG
1 GGGTGAAG
15146 GGGTGAAG
1 GGGTGAAG
15154 GGGTGAAG
1 GGGTGAAG
15162 G
1 G
15163 CTTGATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.64, T:0.12
Consensus pattern (8 bp):
GGGTGAAG
Found at i:16979 original size:21 final size:21
Alignment explanation
Indices: 16955--17018 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 21
16945 GTAATATATA
*
16955 TAATAACTAAAATACTTACAT
1 TAATAACTGAAATACTTACAT
* *
16976 TAATTAAATGTAATA-TT--A-
1 TAA-TAACTGAAATACTTACAT
16994 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTACAT
17015 TAAT
1 TAAT
17019 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 1 0.03
20 1 0.03
21 9 0.27
22 8 0.24
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAACTGAAATACTTACAT
Found at i:17000 original size:39 final size:40
Alignment explanation
Indices: 16943--17023 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
16933 TTTAATTCCT
16943 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
16983 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
17022 AT
1 AT
17024 TCTTAGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:17041 original size:24 final size:25
Alignment explanation
Indices: 17014--17060 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
17004 AATACTTACA
17014 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
17038 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
17061 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Done.