Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024816.1 Corchorus olitorius cultivar O-4 contig24849, 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: 24301
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:3882 original size:76 final size:76
Alignment explanation
Indices: 3744--4061 Score: 431
Period size: 76 Copynumber: 4.2 Consensus size: 76
3734 ACAGAATGGT
* * *
3744 GCCCCCGTTCGTCCACCTGTAAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
1 GCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
3809 CCTAGATTGGC
66 CCTAGATTGGC
* * * * * *
3820 GCCTCCGTTCGCCCACCAGTGAGACGGAGCGTCCTCGCAGACGACGCTCACTCGACGGCTGAGTG
1 GCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
*
3885 CCTAGATTAGC
66 CCTAGATTGGC
* * **
3896 GCCCCCGTTCGCCCACCAGTGAGACGGAGCGTCCACGCAGACGCCGCTCACT-AACGGCTGAGCA
1 GCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
* * *
3960 CCTATAATGGT
66 CCTAGATTGGC
* * *
3971 GCCCCCGTTCGTCCACCCGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGGGTG
1 GCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
*
4036 CCTAGACTGGC
66 CCTAGATTGGC
*
4047 GCCCCCGTCCGCCCA
1 GCCCCCGTTCGCCCA
4062 TGTCGACATG
Statistics
Matches: 209, Mismatches: 32, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
75 65 0.31
76 144 0.69
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.15
Consensus pattern (76 bp):
GCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
CCTAGATTGGC
Found at i:4019 original size:151 final size:152
Alignment explanation
Indices: 3744--4061 Score: 431
Period size: 151 Copynumber: 2.1 Consensus size: 152
3734 ACAGAATGGT
* * **
3744 GCCCCCGTTCGTCCACCTGTAAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGTG
1 GCCCCCGTTCGCCCACCAGTAAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGCA
* * * * *
3809 CCTAGATTGGCGCCTCCGTTCGCCCACCAGTGAGACGGAGCGTCCTCGCAGACGACGCTCACTCG
66 CCTAGAATGGCGCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGACGCTCACTCA
* *
3874 ACGGCTGAGTGCCTAGATTAGC
131 ACGACTGAGTGCCTAGACTAGC
* * *
3896 GCCCCCGTTCGCCCACCAGTGAGACGGAGCGTCCACGCAGACGCCGCTCACT-AACGGCTGAGCA
1 GCCCCCGTTCGCCCACCAGTAAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGCA
* * * * *
3960 CCTATAATGGTGCCCCCGTTCGTCCACCCGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCA
66 CCTAGAATGGCGCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGACGCTCACTCA
* *
4025 ACGACTGGGTGCCTAGACTGGC
131 ACGACTGAGTGCCTAGACTAGC
*
4047 GCCCCCGTCCGCCCA
1 GCCCCCGTTCGCCCA
4062 TGTCGACATG
Statistics
Matches: 144, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
151 96 0.67
152 48 0.33
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.15
Consensus pattern (152 bp):
GCCCCCGTTCGCCCACCAGTAAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGACTGAGCA
CCTAGAATGGCGCCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACGCAGACGACGCTCACTCA
ACGACTGAGTGCCTAGACTAGC
Found at i:4260 original size:2 final size:2
Alignment explanation
Indices: 4255--4291 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4245 CGACACATAA
4255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4292 AATACACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8759 original size:13 final size:14
Alignment explanation
Indices: 8741--8784 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
8731 CCAACTTCCG
8741 GAATTTAAAATTT-
1 GAATTTAAAATTTC
*
8754 GAATTTCAAATTTC
1 GAATTTAAAATTTC
8768 GAATTTCAAAAATTTC
1 GAATTT--AAAATTTC
8784 G
1 G
8785 CGCCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 12 0.46
14 6 0.23
16 8 0.31
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (14 bp):
GAATTTAAAATTTC
Found at i:8773 original size:14 final size:13
Alignment explanation
Indices: 8741--8777 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8731 CCAACTTCCG
*
8741 GAATTTAAAATTT
1 GAATTTCAAATTT
8754 GAATTTCAAATTT
1 GAATTTCAAATTT
8767 CGAATTTCAAA
1 -GAATTTCAAA
8778 AATTTCGCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (13 bp):
GAATTTCAAATTT
Found at i:10707 original size:16 final size:16
Alignment explanation
Indices: 10686--10747 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
10676 GGCAGTTTTC
10686 TCAGGTCATTCGGGTT
1 TCAGGTCATTCGGGTT
10702 TCAGGTCA-TCTGGG-T
1 TCAGGTCATTC-GGGTT
* *
10717 TC-GACTTATTCGGGTT
1 TCAG-GTCATTCGGGTT
*
10733 TCGGGTCATTCGGGT
1 TCAGGTCATTCGGGT
10748 CTCGGGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 1 0.03
15 10 0.27
16 25 0.68
17 1 0.03
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.37
Consensus pattern (16 bp):
TCAGGTCATTCGGGTT
Found at i:10752 original size:16 final size:16
Alignment explanation
Indices: 10684--10754 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
10674 CAGGCAGTTT
*
10684 TCTCAGGTCATTCGGG
1 TCTCGGGTCATTCGGG
* *
10700 TTTCAGGTCA-TCTGGG
1 TCTCGGGTCATTC-GGG
** *
10716 T-TCGACTTATTCGGG
1 TCTCGGGTCATTCGGG
*
10731 TTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
10747 TCTCGGGT
1 TCTCGGGT
10755 ATACCAGGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
15 10 0.23
16 33 0.77
ACGTcount: A:0.10, C:0.21, G:0.32, T:0.37
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:11607 original size:23 final size:23
Alignment explanation
Indices: 11563--11607 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
11553 TCGGGTTTCG
* *
11563 GGTCATACGGGTCTTGGATCACA
1 GGTCATACGAGTCTCGGATCACA
* *
11586 GGTCATTCGAGTCTCGGGTCAC
1 GGTCATACGAGTCTCGGATCAC
11608 TCGGGTTACG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (23 bp):
GGTCATACGAGTCTCGGATCACA
Found at i:11638 original size:16 final size:16
Alignment explanation
Indices: 11584--11639 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
11574 TCTTGGATCA
* *
11584 CAGGTCATTCGAGTCT
1 CAGGTCATTCGGGTTT
* * *
11600 CGGGTCACTCGGGTTA
1 CAGGTCATTCGGGTTT
11616 C-GAGTCATTCGGGTTT
1 CAG-GTCATTCGGGTTT
11632 CAGGTCAT
1 CAGGTCAT
11640 CTGAGTCATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (16 bp):
CAGGTCATTCGGGTTT
Done.