Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013837.1 Corchorus olitorius cultivar O-4 contig13870, 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: 19438
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9296 original size:72 final size:72
Alignment explanation
Indices: 9174--9309 Score: 218
Period size: 72 Copynumber: 1.9 Consensus size: 72
9164 TTGGTCTCTG
* * *
9174 CACTTAAGGATTAGATATATTTTGGCTGCAAAAGACAGGTGTTGGGCAGGCAAAAAACAGGTGTC
1 CACTTAAGGATTAGATATATTTAGGCTACAAAAGACAGGTGTTGGACAGGCAAAAAACAGGTGTC
9239 GTTTTCT
66 GTTTTCT
* * *
9246 CACTTAGGGTTTAGATATATTTAGGCTACAAAAGACAGGTGTTGGACAGGCAAAAAATAGGTGT
1 CACTTAAGGATTAGATATATTTAGGCTACAAAAGACAGGTGTTGGACAGGCAAAAAACAGGTGT
9310 TAAATAGATC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (72 bp):
CACTTAAGGATTAGATATATTTAGGCTACAAAAGACAGGTGTTGGACAGGCAAAAAACAGGTGTC
GTTTTCT
Found at i:10671 original size:24 final size:24
Alignment explanation
Indices: 10644--10691 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10634 CAAATCTATG
* *
10644 GAATTGAAAGGTTTGTCATATATT
1 GAATTAAAACGTTTGTCATATATT
*
10668 GAATTAAAACGTTTGTTATATATT
1 GAATTAAAACGTTTGTCATATATT
10692 AGAGTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (24 bp):
GAATTAAAACGTTTGTCATATATT
Found at i:13031 original size:18 final size:19
Alignment explanation
Indices: 13010--13062 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
13000 TAAAAATCAG
13010 GCAACACATGTTCATTA-A
1 GCAACACATGTTCATTATA
*
13028 GCAACACATGTTC-TTATTG
1 GCAACACATGTTCATTA-TA
13047 GTCAACACATGTTCAT
1 G-CAACACATGTTCAT
13063 CTTCTATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 13 0.43
19 1 0.03
20 12 0.40
21 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (19 bp):
GCAACACATGTTCATTATA
Found at i:15580 original size:18 final size:18
Alignment explanation
Indices: 15557--15592 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15547 AGATTTACAC
* *
15557 TACCCGCTAACTACCCGA
1 TACCCGATAACAACCCGA
15575 TACCCGATAACAACCCGA
1 TACCCGATAACAACCCGA
15593 AGTGAGTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.42, G:0.11, T:0.14
Consensus pattern (18 bp):
TACCCGATAACAACCCGA
Found at i:15657 original size:30 final size:30
Alignment explanation
Indices: 15618--15714 Score: 185
Period size: 30 Copynumber: 3.2 Consensus size: 30
15608 AAATCATCCC
15618 AAAGTTCCAAATTTCATAGTAAACATTACAG
1 AAAG-TCCAAATTTCATAGTAAACATTACAG
15649 AAAGTCCAAATTTCATAGTAAACATTACAG
1 AAAGTCCAAATTTCATAGTAAACATTACAG
15679 AAAGTCCAAATTTCATAGTAAACATTACAG
1 AAAGTCCAAATTTCATAGTAAACATTACAG
15709 AAAGTC
1 AAAGTC
15715 AGAAATTCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
30 62 0.94
31 4 0.06
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.27
Consensus pattern (30 bp):
AAAGTCCAAATTTCATAGTAAACATTACAG
Found at i:18854 original size:22 final size:23
Alignment explanation
Indices: 18828--18872 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18818 AATGAGTTTG
18828 TTGAAATCA-GCGGATAGTGTGT
1 TTGAAATCAGGCGGATAGTGTGT
18850 TTGAAATCAGGCGGATAGTGTGT
1 TTGAAATCAGGCGGATAGTGTGT
18873 CAGAAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.31
Consensus pattern (23 bp):
TTGAAATCAGGCGGATAGTGTGT
Found at i:18878 original size:23 final size:22
Alignment explanation
Indices: 18830--18878 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
18820 TGAGTTTGTT
**
18830 GAAATCAGCGGATAGTGTGTTT
1 GAAATCAGCGGATAGTGTGTCA
18852 GAAATCAGGCGGATAGTGTGTCA
1 GAAATCA-GCGGATAGTGTGTCA
18875 GAAA
1 GAAA
18879 GAGATTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (22 bp):
GAAATCAGCGGATAGTGTGTCA
Found at i:19006 original size:18 final size:18
Alignment explanation
Indices: 18985--19028 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
18975 CTTGGACGGC
*
18985 GATGAAGAAGAAGATTGA
1 GATGAAGAAGAAGATCGA
19003 GATGAAGAAGAAGATCGA
1 GATGAAGAAGAAGATCGA
*
19021 GAAGAAGA
1 GATGAAGA
19029 TAAAAACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.34, T:0.11
Consensus pattern (18 bp):
GATGAAGAAGAAGATCGA
Done.