Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006866.1 Corchorus capsularis cultivar CVL-1 contig06887, 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: 15834
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:491 original size:17 final size:17
Alignment explanation
Indices: 449--482 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
439 GGGTCAAGTT
* *
449 ATTCTGGTTCGGGTTGA
1 ATTCGGGTTCGGGTTCA
466 ATTCGGGTTCGGGTTCA
1 ATTCGGGTTCGGGTTCA
483 GTTTGGGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.35, T:0.38
Consensus pattern (17 bp):
ATTCGGGTTCGGGTTCA
Found at i:676 original size:16 final size:16
Alignment explanation
Indices: 655--687 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
645 CGGTTAGATC
655 TTTTTCGGATTCGGGT
1 TTTTTCGGATTCGGGT
*
671 TTTTTCGGGTTCGGGT
1 TTTTTCGGATTCGGGT
687 T
1 T
688 CGGGTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.33, T:0.52
Consensus pattern (16 bp):
TTTTTCGGATTCGGGT
Found at i:1915 original size:14 final size:14
Alignment explanation
Indices: 1896--1922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1886 TATGGACCGA
1896 TTTACTTAGATAGG
1 TTTACTTAGATAGG
1910 TTTACTTAGATAG
1 TTTACTTAGATAG
1923 AGAGGGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (14 bp):
TTTACTTAGATAGG
Found at i:2002 original size:21 final size:21
Alignment explanation
Indices: 1977--2033 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 21
1967 TTCTTTTTAC
1977 TAAATTTTATTTATAGTTATT
1 TAAATTTTATTTATAGTTATT
* *
1998 TAAA--TTA-TTA-AATTAAT
1 TAAATTTTATTTATAGTTATT
2015 T--ATTTTATTTATAGTTATT
1 TAAATTTTATTTATAGTTATT
2034 CAAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 1 0.04
17 9 0.32
18 6 0.21
19 8 0.29
21 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TAAATTTTATTTATAGTTATT
Found at i:2132 original size:14 final size:14
Alignment explanation
Indices: 2113--2140 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2103 ATAATTTGTA
2113 GTGTGTGTGTATAT
1 GTGTGTGTGTATAT
2127 GTGTGTGTGTATAT
1 GTGTGTGTGTATAT
2141 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (14 bp):
GTGTGTGTGTATAT
Found at i:6644 original size:21 final size:21
Alignment explanation
Indices: 6618--6659 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6608 AATACAGTAA
6618 GCCCCAATCACTCAAACAAAC
1 GCCCCAATCACTCAAACAAAC
*
6639 GCCCCAATCACTCAAATAAAC
1 GCCCCAATCACTCAAACAAAC
6660 ATACTAGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.40, G:0.05, T:0.12
Consensus pattern (21 bp):
GCCCCAATCACTCAAACAAAC
Found at i:7966 original size:16 final size:16
Alignment explanation
Indices: 7930--8019 Score: 87
Period size: 16 Copynumber: 5.8 Consensus size: 16
7920 ATTGGGCGGG
* *
7930 TTCGGGTTCGAGTA-C
1 TTCGGGTTCGGGTATT
* *
7945 TTCGGGTTTGGGTTTT
1 TTCGGGTTCGGGTATT
7961 TTCGGGTTCGGGT-TCT
1 TTCGGGTTCGGGTAT-T
* * *
7977 GTCGAGTTCGGATATT
1 TTCGGGTTCGGGTATT
7993 TT-GGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
8008 TTCGGGTTCGGG
1 TTCGGGTTCGGG
8020 CTCGGATCGG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
15 25 0.42
16 34 0.57
17 1 0.02
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:8017 original size:6 final size:6
Alignment explanation
Indices: 8008--8062 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
7998 TTCGGGTATT
* * ** *
8008 TTCGGG TTCGGG CTC-GG ATCGGG TTCGGG CCCGGG -TGGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
8054 TTCGGG TTC
1 TTCGGG TTC
8063 ACTTTCGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 7 0.18
6 32 0.82
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.27
Consensus pattern (6 bp):
TTCGGG
Found at i:8035 original size:23 final size:23
Alignment explanation
Indices: 8008--8062 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
7998 TTCGGGTATT
8008 TTCGGGTTCGGGCT-CGGATCGGG
1 TTCGGGTTCGGG-TGCGGATCGGG
** * *
8031 TTCGGGCCCGGGTGGGGTTCGGG
1 TTCGGGTTCGGGTGCGGATCGGG
8054 TTCGGGTTC
1 TTCGGGTTC
8063 ACTTTCGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.27
Consensus pattern (23 bp):
TTCGGGTTCGGGTGCGGATCGGG
Found at i:8059 original size:17 final size:17
Alignment explanation
Indices: 8009--8060 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
7999 TCGGGTATTT
*
8009 TCGGGTTCGGGCTCGGA
1 TCGGGTTCGGGCTCGGG
*
8026 TCGGGTTCGGGCCCGGG
1 TCGGGTTCGGGCTCGGG
* *
8043 TGGGGTTCGGGTTCGGG
1 TCGGGTTCGGGCTCGGG
8060 T
1 T
8061 TCACTTTCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.02, C:0.21, G:0.52, T:0.25
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:8827 original size:16 final size:16
Alignment explanation
Indices: 8806--8850 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
8796 CGGGCTCGGG
*
8806 TCGGGTTCGGGTTGTC
1 TCGGGTTCGGGTTATC
* *
8822 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTTATC
8838 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
8851 CGGGCGGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.04, C:0.16, G:0.42, T:0.38
Consensus pattern (16 bp):
TCGGGTTCGGGTTATC
Found at i:10838 original size:8 final size:8
Alignment explanation
Indices: 10825--10859 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
10815 CCTTCTCCAC
10825 ATATAATA
1 ATATAATA
10833 ATATAATA
1 ATATAATA
10841 ATATAATA
1 ATATAATA
10849 ATATAATA
1 ATATAATA
10857 ATA
1 ATA
10860 CAATTTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAATA
Done.