Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020434.1 Corchorus olitorius cultivar O-4 contig20467, 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: 72802
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:5835 original size:21 final size:21
Alignment explanation
Indices: 5809--5848 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5799 CGCTGCTCTA
*
5809 ATAATCTCATATGTACAGTAC
1 ATAATCTAATATGTACAGTAC
*
5830 ATAATCTAATCTGTACAGT
1 ATAATCTAATATGTACAGT
5849 GTAATCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATCTAATATGTACAGTAC
Found at i:5855 original size:19 final size:19
Alignment explanation
Indices: 5831--5867 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5821 GTACAGTACA
*
5831 TAATCTAATCTGTACAGTG
1 TAATCTAATCTATACAGTG
*
5850 TAATCTCATCTATACAGT
1 TAATCTAATCTATACAGT
5868 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTATACAGTG
Found at i:7667 original size:2 final size:2
Alignment explanation
Indices: 7660--7687 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7650 AAAGACCAAG
7660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7688 TAATAGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18785 original size:41 final size:41
Alignment explanation
Indices: 18714--18955 Score: 308
Period size: 41 Copynumber: 5.9 Consensus size: 41
18704 GTTTGATTTG
* * *
18714 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * *
18754 ATCTAATTCAAGGGTCTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
18795 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* **
18839 ATTTAATTCAAGGGTCTCAATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
18880 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
18921 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
18956 CAAACGAAAA
Statistics
Matches: 179, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
40 12 0.07
41 127 0.71
42 4 0.02
43 1 0.01
44 35 0.20
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:23299 original size:61 final size:61
Alignment explanation
Indices: 23222--23336 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
23212 TATATACATA
*
23222 AACCCATACACATTGAATTTTTCCAACATTTTGTATAACCAATACTGAGAATTGGTTATAT
1 AACCAATACACATTGAATTTTTCCAACATTTTGTATAACCAATACTGAGAATTGGTTATAT
* *
23283 AACCAATACACGTTGAATTTTTCCAACATTTTGTATAACCAATACTGAGCATTG
1 AACCAATACACATTGAATTTTTCCAACATTTTGTATAACCAATACTGAGAATTG
23337 AGCTTTGTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (61 bp):
AACCAATACACATTGAATTTTTCCAACATTTTGTATAACCAATACTGAGAATTGGTTATAT
Found at i:25956 original size:20 final size:18
Alignment explanation
Indices: 25919--25958 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
25909 TTTCATTTAT
*
25919 CAAGCAAAAAATTAATTA
1 CAAGCAAAAAAATAATTA
25937 CAAGTCAAATAAAATAATTA
1 CAAG-CAAA-AAAATAATTA
25957 CA
1 CA
25959 CATTAGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (18 bp):
CAAGCAAAAAAATAATTA
Found at i:26381 original size:19 final size:19
Alignment explanation
Indices: 26357--26395 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26347 AGATAAGGGT
26357 TTGCATTTTATAGGATGTA
1 TTGCATTTTATAGGATGTA
26376 TTGCATTTTATAGGATGTA
1 TTGCATTTTATAGGATGTA
26395 T
1 T
26396 AATTAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (19 bp):
TTGCATTTTATAGGATGTA
Found at i:28887 original size:6 final size:6
Alignment explanation
Indices: 28876--28902 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28866 TATCAATGCA
28876 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
28903 TAATTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:32468 original size:9 final size:10
Alignment explanation
Indices: 32447--32472 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32437 TCTTATCATA
32447 TTTATAAATT
1 TTTATAAATT
32457 TTTATAAATT
1 TTTATAAATT
32467 TTTATA
1 TTTATA
32473 TATATCTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:43925 original size:93 final size:93
Alignment explanation
Indices: 43765--43951 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
43755 GCTGCTAGCA
* *
43765 TCAGTTTCTTGAAGGATTGTGTCTAACATACTTGTGTTGGTGTCATGCAACTCTGCATCCATTTT
1 TCAGTTTCTTGAAGGATTGTGTCTAACATACTTGTATTGGTGTCATGCAACTCTGCATCCATCTT
43830 GCAATCACCTTGGCCACCAAGCTCAACT
66 GCAATCACCTTGGCCACCAAGCTCAACT
43858 TCAGTTTCTTGAAGGATTGTGTCTAACATACTTGTATTGGTGTCATGCAACTCTGCATCCATCTT
1 TCAGTTTCTTGAAGGATTGTGTCTAACATACTTGTATTGGTGTCATGCAACTCTGCATCCATCTT
43923 GCAATCACCTTGGCCACCAAGCTCAACT
66 GCAATCACCTTGGCCACCAAGCTCAACT
43951 T
1 T
43952 TGAGGCCAGA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (93 bp):
TCAGTTTCTTGAAGGATTGTGTCTAACATACTTGTATTGGTGTCATGCAACTCTGCATCCATCTT
GCAATCACCTTGGCCACCAAGCTCAACT
Found at i:52403 original size:16 final size:16
Alignment explanation
Indices: 52382--52412 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52372 ATATTTCATT
52382 TATATATCAGAAATTA
1 TATATATCAGAAATTA
*
52398 TATATATTAGAAATT
1 TATATATCAGAAATT
52413 CTTTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
TATATATCAGAAATTA
Found at i:53085 original size:18 final size:19
Alignment explanation
Indices: 53057--53098 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
53047 GAAGTTTTGG
*
53057 GTGAGATTGGATACTTACT
1 GTGAGATTGGATACTTAAT
53076 GTGA-ATTGGATACTTAAT
1 GTGAGATTGGATACTTAAT
53094 GTGAG
1 GTGAG
53099 TTGATGGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (19 bp):
GTGAGATTGGATACTTAAT
Found at i:53157 original size:32 final size:32
Alignment explanation
Indices: 53121--53181 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
53111 TATGCTCTGG
*
53121 TTTGATTATTTGTTAGTTGATTTTTGCCTAGT
1 TTTGATCATTTGTTAGTTGATTTTTGCCTAGT
*
53153 TTTGATCATTTGTTTGTTGATTTTTGCCT
1 TTTGATCATTTGTTAGTTGATTTTTGCCT
53182 GAATACTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.13, C:0.08, G:0.18, T:0.61
Consensus pattern (32 bp):
TTTGATCATTTGTTAGTTGATTTTTGCCTAGT
Found at i:55474 original size:20 final size:20
Alignment explanation
Indices: 55436--55474 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55426 GTGATATTTG
* *
55436 TTATTGTTGAATTGGTTTCT
1 TTATTATTGAATTGCTTTCT
*
55456 TTATTATTGACTTGCTTTC
1 TTATTATTGAATTGCTTTC
55475 AATACTCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (20 bp):
TTATTATTGAATTGCTTTCT
Found at i:59032 original size:18 final size:20
Alignment explanation
Indices: 58995--59033 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
58985 TCAAGTCAAT
58995 GGTGGAACTGTTGCTGACAA
1 GGTGGAACTGTTGCTGACAA
*
59015 GGTGG-ACT-TTGCTTACAA
1 GGTGGAACTGTTGCTGACAA
59033 G
1 G
59034 TTCTTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (20 bp):
GGTGGAACTGTTGCTGACAA
Found at i:65293 original size:27 final size:27
Alignment explanation
Indices: 65230--65294 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
65220 GGTGAACTTA
* * **
65230 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATCCCCCTGAATGACC
65257 AAATGACTAAAATCCCCCTGAATGACC
1 AAATGACTAAAATCCCCCTGAATGACC
65284 TAAATG-CTAAA
1 -AAATGACTAAA
65295 TAAGAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.20
Consensus pattern (27 bp):
AAATGACTAAAATCCCCCTGAATGACC
Found at i:66899 original size:14 final size:14
Alignment explanation
Indices: 66880--66913 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
66870 TTTTATAATT
66880 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
66894 ATTTTATTTTTACT
1 ATTTTATTTTTACC
66908 ATTTTA
1 ATTTTA
66914 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:66959 original size:14 final size:15
Alignment explanation
Indices: 66940--66971 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
66930 TGATTAACCT
66940 GTTTTC-ATTTGATA
1 GTTTTCTATTTGATA
66954 GTTTTCTATTTGATA
1 GTTTTCTATTTGATA
66969 GTT
1 GTT
66972 AATGTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.59
Consensus pattern (15 bp):
GTTTTCTATTTGATA
Found at i:67805 original size:40 final size:40
Alignment explanation
Indices: 67747--67830 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
67737 AATTGTCCCT
*
67747 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGATAATAAATTAAATCCAGGTTTAGCCC
67787 CCTAATAATTAAGATAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGATAATAAATTAAATCCAGGTTTAGCCC
67827 CCTA
1 CCTA
67831 GTTATAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (40 bp):
CCTAATAATTAAGATAATAAATTAAATCCAGGTTTAGCCC
Done.