Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020386.1 Corchorus olitorius cultivar O-4 contig20419, 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: 19673
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:654 original size:16 final size:16
Alignment explanation
Indices: 633--664 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
623 TAAAACTAAT
633 TGGCAATAGGTGGAGA
1 TGGCAATAGGTGGAGA
*
649 TGGCAATAGTTGGAGA
1 TGGCAATAGGTGGAGA
665 GGCCCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.41, T:0.22
Consensus pattern (16 bp):
TGGCAATAGGTGGAGA
Found at i:11670 original size:31 final size:30
Alignment explanation
Indices: 11632--11797 Score: 139
Period size: 31 Copynumber: 5.6 Consensus size: 30
11622 TTAGGCTAAT
11632 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * **
11663 TGCTCAAA-AAGGGCCCGATCTTT--TAATT
1 TGCTCAAATAAGGG-CCTAACTTTGCCAAAA
11691 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * **
11722 TGCTCAAATAAGGGCCGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAACTTTGCCAAAA
11750 TGGC-CAAATAAGGGCCTAAGCTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAA-CTTTGCCAAAA
11781 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
11798 GACATCGAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 27 0.26
29 16 0.16
30 15 0.15
31 45 0.44
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:11728 original size:59 final size:59
Alignment explanation
Indices: 11636--11796 Score: 281
Period size: 59 Copynumber: 2.7 Consensus size: 59
11626 GCTAATTGCT
11636 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAA-AAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-TTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
11695 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGG-CCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-TTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
11754 CAAATAAGGGCCTAAGCTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAA-CTTTGCCAAAATGCTCAAATAAGGGCC
11797 TGACATCGAA
Statistics
Matches: 98, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
59 91 0.93
60 7 0.07
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (59 bp):
CAAATAAGGGCCTAACTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:11873 original size:31 final size:31
Alignment explanation
Indices: 11838--11943 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
11828 CTGATGCCAT
11838 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** * **
11869 GCCCTTATTTG-GCCAAATT---AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTGGCAAACG-TTAG
11898 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
11929 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
11944 ATTAGCCTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 2 0.03
31 32 0.54
32 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:13248 original size:85 final size:84
Alignment explanation
Indices: 13105--13277 Score: 310
Period size: 85 Copynumber: 2.0 Consensus size: 84
13095 AAAAAATCAC
* * *
13105 TCCTTTAGTAAATCAATTGCAGTTTTTTCAGCACCAAATCAAGTTAAATCCAGAATCATCAAATC
1 TCCTTTAGTAAATCAATTGCAATTTTTTCAACACAAAATCAAGTTAAATCCAGAATCATCAAATC
13170 GTTATATCAAGTTAATGGT
66 GTTATATCAAGTTAATGGT
13189 TCCTTTAGTAAATCAATTGCAATTTTTTCAAACACAAAATCAAGTTAAATCCAGAATCATCAAAT
1 TCCTTTAGTAAATCAATTGCAATTTTTTC-AACACAAAATCAAGTTAAATCCAGAATCATCAAAT
13254 CGTTATATCAAGTTAATGGT
65 CGTTATATCAAGTTAATGGT
13274 TCCT
1 TCCT
13278 CAAGCTTTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 28 0.33
85 57 0.67
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (84 bp):
TCCTTTAGTAAATCAATTGCAATTTTTTCAACACAAAATCAAGTTAAATCCAGAATCATCAAATC
GTTATATCAAGTTAATGGT
Found at i:14704 original size:7 final size:7
Alignment explanation
Indices: 14692--14725 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
14682 AGTCTCAAAT
14692 ATAAAAA
1 ATAAAAA
14699 ATAAAAA
1 ATAAAAA
14706 AT-AAAA
1 ATAAAAA
14712 ATAATAAA
1 ATAA-AAA
14720 ATAAAA
1 ATAAAA
14726 CAATTTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
ATAAAAA
Found at i:14711 original size:14 final size:15
Alignment explanation
Indices: 14692--14725 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
14682 AGTCTCAAAT
14692 ATAAAAAATAA-AAA
1 ATAAAAAATAATAAA
14706 AT-AAAAATAATAAA
1 ATAAAAAATAATAAA
14720 ATAAAA
1 ATAAAA
14726 CAATTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 7 0.39
15 3 0.17
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAAATAATAAA
Found at i:14717 original size:16 final size:16
Alignment explanation
Indices: 14688--14720 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14678 GATCAGTCTC
14688 AAATATAAAAAATAAA
1 AAATATAAAAAATAAA
14704 AAATA-AAAATAATAAA
1 AAATATAAAA-AATAAA
14720 A
1 A
14721 TAAAACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATATAAAAAATAAA
Found at i:15171 original size:25 final size:26
Alignment explanation
Indices: 15119--15190 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
15109 CCACTTTCTT
* *
15119 AAATCTTATTAAAATATATTCTCTAAAA
1 AAATCTTA-TACAATAT-TTCTCAAAAA
*
15147 GAATCTTATACAATATTTC-CAAAAA
1 AAATCTTATACAATATTTCTCAAAAA
15172 AAATCTTATACAAATATTT
1 AAATCTTATAC-AATATTT
15191 ATATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.38
26 10 0.26
27 7 0.18
28 7 0.18
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (26 bp):
AAATCTTATACAATATTTCTCAAAAA
Found at i:17672 original size:24 final size:24
Alignment explanation
Indices: 17631--17703 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
17621 AGGCATTGCC
* *
17631 CTGAGTTTTAGGCTTGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
*
17655 CTGGGGTTTAGGCATGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
*
17679 CTGAGTTTTAGGCATGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
17703 C
1 C
17704 CGTTAATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.45
Consensus pattern (24 bp):
CTGAGGTTTAGGCATGCTCTGTTT
Found at i:17826 original size:18 final size:18
Alignment explanation
Indices: 17803--17854 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
17793 ACCTTTCCAG
*
17803 TTTCCATACATAAACACC
1 TTTCCATACATAAACACA
* *
17821 TTTCCATACAAAAAGACA
1 TTTCCATACATAAACACA
17839 TTTCCATACATAAACA
1 TTTCCATACATAAACA
17855 TCCAGTAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (18 bp):
TTTCCATACATAAACACA
Done.