Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017471.1 Corchorus olitorius cultivar O-4 contig17504, 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: 31657
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:14131 original size:74 final size:73
Alignment explanation
Indices: 13999--14144 Score: 213
Period size: 74 Copynumber: 2.0 Consensus size: 73
13989 TTCATTACGT
* *
13999 CATTTTATTGTTACTAAAAGAATTATATTTTACGCAACAATATTGAGTTGCTGCGTAAAATATTT
1 CATTTTATTGTTACTAAAAGAATTATATTTTACGCAACAATAAT-ACTTGCTGCGTAAAATATTT
14064 TAACAACGC
65 TAACAACGC
* * *
14073 CATTTTATTGTTACTAAAAGAATTATATTTTGCGCAACAACTCAAT-CTTGTTGTGTAAAATATT
1 CATTTTATTGTTACTAAAAGAATTATATTTTACGCAACAA-T-AATACTTGCTGCGTAAAATATT
14137 TTAACAAC
64 TTAACAAC
14145 ACTATATATT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 62 0.95
75 1 0.02
76 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (73 bp):
CATTTTATTGTTACTAAAAGAATTATATTTTACGCAACAATAATACTTGCTGCGTAAAATATTTT
AACAACGC
Found at i:18802 original size:11 final size:11
Alignment explanation
Indices: 18786--18833 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
18776 CAGCGCAACA
18786 AAAACAAAACG
1 AAAACAAAACG
*
18797 AAAACAAAACA
1 AAAACAAAACG
18808 AAAACAAAA--
1 AAAACAAAACG
*
18817 AACAAAAAAACG
1 AA-AACAAAACG
18829 AAAAC
1 AAAAC
18834 GATGCCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 21 0.68
12 2 0.06
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAACAAAACG
Found at i:18832 original size:7 final size:6
Alignment explanation
Indices: 18782--18824 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
18772 TTGACAGCGC
*
18782 AACAAA AAC-AA AACGAA AAC-AA AACAAA AACAAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AACAAA AA
18825 AACGAAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 6 0.18
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:18832 original size:22 final size:21
Alignment explanation
Indices: 18782--18833 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
18772 TTGACAGCGC
*
18782 AACAAAAACAAAACGAAAACAA
1 AACAAAAACAAAAC-AAAAAAA
18804 AACAAAAACAAAA-AACAAAAA
1 AACAAAAACAAAACAA-AAAAA
*
18825 AACGAAAAC
1 AACAAAAAC
18834 GATGCCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 13 0.48
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (21 bp):
AACAAAAACAAAACAAAAAAA
Found at i:21316 original size:25 final size:25
Alignment explanation
Indices: 21282--21329 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
21272 ATTGGTTTGT
21282 AGAGACCGAGCGAGAGTGCTCAAAA
1 AGAGACCGAGCGAGAGTGCTCAAAA
21307 AGAGACCGAGCGAGAGTGCTCAA
1 AGAGACCGAGCGAGAGTGCTCAA
21330 GATTGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.33, T:0.08
Consensus pattern (25 bp):
AGAGACCGAGCGAGAGTGCTCAAAA
Found at i:24719 original size:27 final size:27
Alignment explanation
Indices: 24653--24721 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
24643 AGAGTTATCC
* * *
24653 AGGGGCATTTTGATCATTTGCACGTTT
1 AGGGGCATTTTGGTCATTTGAACATTT
*
24680 GGGGGCATTTTGGTCATTTGAACATTT
1 AGGGGCATTTTGGTCATTTGAACATTT
*
24707 AGGGGTATTTTGGTC
1 AGGGGCATTTTGGTC
24722 CTTTTCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.12, G:0.30, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGAACATTT
Found at i:28179 original size:21 final size:21
Alignment explanation
Indices: 28139--28179 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28129 GTAATCAAGA
*
28139 GTTTTCAAGATTTAAATAGAG
1 GTTTTCAAGATTCAAATAGAG
28160 GTTTTCAA-ATTCAAACTAGA
1 GTTTTCAAGATTCAAA-TAGA
28180 CTTAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
GTTTTCAAGATTCAAATAGAG
Found at i:29573 original size:16 final size:15
Alignment explanation
Indices: 29535--29576 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
29525 ACAGAGATTG
29535 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
29550 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
29565 ACTAGAAAACAA
1 AC-AGAAAACAA
29577 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.