Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022563.1 Corchorus olitorius cultivar O-4 contig22596, 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: 32076
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9454 original size:35 final size:35
Alignment explanation
Indices: 9378--9510 Score: 131
Period size: 36 Copynumber: 3.7 Consensus size: 35
9368 TTGCTAAAGT
** * *
9378 TTTATTTCAATTGATCCAGGGCGATCTTTCCTTCAA
1 TTTATTTCAGCTGACCCAGGGCGATCTTT-CTTCAG
* * *
9414 TTTATTTTAGCTGACCCATGGCGGTCTTTCTTCAG
1 TTTATTTCAGCTGACCCAGGGCGATCTTTCTTCAG
* * *
9449 TTTATTTCAGTTGATCTAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGCTGACCCAGGGCGATC-TTTCTTCAG
* * *
9485 TTTATTTCAGTTGATCCAGCGCGATC
1 TTTATTTCAGCTGACCCAGGGCGATC
9511 CAGGATTATT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 25 0.31
36 56 0.69
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (35 bp):
TTTATTTCAGCTGACCCAGGGCGATCTTTCTTCAG
Found at i:17890 original size:21 final size:21
Alignment explanation
Indices: 17852--17897 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17842 TAAGATGCAT
* *
17852 AAAAAAGAAATCTTAAATCTA
1 AAAAAAGAAATCTGAAATCGA
17873 AAAACAAGAAAT-TGAAATCGA
1 AAAA-AAGAAATCTGAAATCGA
17894 AAAA
1 AAAA
17898 TCCTAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAAAAGAAATCTGAAATCGA
Found at i:20965 original size:76 final size:76
Alignment explanation
Indices: 20828--20979 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
20818 ACAAGGACCC
* * *
20828 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
20893 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
20904 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
20966 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
20980 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:26982 original size:21 final size:21
Alignment explanation
Indices: 26949--26997 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
26939 AAGAATTGTA
**
26949 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
26969 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
26990 GCATTCCT
1 GC-TTCCT
26998 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:28160 original size:17 final size:16
Alignment explanation
Indices: 28132--28173 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
28122 TAAGAAAAAT
*
28132 AAAAAGAAATA-AAAG
1 AAAAAGAAAAATAAAG
*
28147 AAAAAGAAAAATAACG
1 AAAAAGAAAAATAAAG
*
28163 AAAAATAAAAA
1 AAAAAGAAAAA
28174 GATAAGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (16 bp):
AAAAAGAAAAATAAAG
Found at i:28165 original size:16 final size:14
Alignment explanation
Indices: 28126--28173 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
28116 AGTAACTAAG
*
28126 AAAAATAAAAAGAA
1 AAAAAGAAAAAGAA
28140 ATAAAAGAAAAAGAA
1 A-AAAAGAAAAAGAA
*
28155 AAATAACGAAAAATAA
1 AAA-AA-GAAAAAGAA
28171 AAA
1 AAA
28174 GATAAGGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 3 0.10
15 15 0.52
16 11 0.38
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.08
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:28166 original size:21 final size:22
Alignment explanation
Indices: 28123--28175 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
28113 AAAAGTAACT
* *
28123 AAGAAAAATAAAAAGAAA-TAA
1 AAGAAAAAGAAAAAGAAAGAAA
* *
28144 AAGAAAAAGAAAAATAACGAAA
1 AAGAAAAAGAAAAAGAAAGAAA
*
28166 AATAAAAAGA
1 AAGAAAAAGA
28176 TAAGGGTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.08
Consensus pattern (22 bp):
AAGAAAAAGAAAAAGAAAGAAA
Found at i:29883 original size:76 final size:76
Alignment explanation
Indices: 29756--29897 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
29746 CGACTCTACT
* *
29756 TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGTGGGCAGTGTC
1 TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATGGGCAGTGTC
29821 ACGACTCCAGC
66 ACGACTCCAGC
* * ** *
29832 TGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAGATGGGCTGT
1 TGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCAGATGGGCAGT
29894 GTCA
63 GTCA
29898 TAGCTCATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
75 4 0.07
76 46 0.82
77 6 0.11
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.25
Consensus pattern (76 bp):
TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATGGGCAGTGTC
ACGACTCCAGC
Done.