Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013617.1 Corchorus olitorius cultivar O-4 contig13650, 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: 28843
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:505 original size:13 final size:13
Alignment explanation
Indices: 487--516 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
477 ATAATTGAAT
487 TTTTCTAACATTA
1 TTTTCTAACATTA
*
500 TTTTCTAACTTTA
1 TTTTCTAACATTA
513 TTTT
1 TTTT
517 TATTACCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTCTAACATTA
Found at i:1973 original size:21 final size:21
Alignment explanation
Indices: 1937--1980 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1927 ATTTTCTCAT
** *
1937 TAAAGGTTATTGAGAAGATTA
1 TAAAGGTTATCAAGAACATTA
1958 TAAAGGTTATCAAGAACATTA
1 TAAAGGTTATCAAGAACATTA
1979 TA
1 TA
1981 CTATTATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (21 bp):
TAAAGGTTATCAAGAACATTA
Found at i:3423 original size:32 final size:32
Alignment explanation
Indices: 3331--3428 Score: 76
Period size: 32 Copynumber: 3.1 Consensus size: 32
3321 TTAATTATTA
3331 AATTGAATTTTACTCTGAAGCAAATGCTTAAC
1 AATTGAATTTTACTCTGAAGCAAATGCTTAAC
* * *** **
3363 AA-CG--TTTCACAATAACAAAAAAAGTGCTTAAC
1 AATTGAATTTTAC--TCTGAAGCAAA-TGCTTAAC
*
3395 AATTGAATTTTACTCTGAAGCAAATGCTTGAC
1 AATTGAATTTTACTCTGAAGCAAATGCTTAAC
3427 AA
1 AA
3429 CGTTTCACAA
Statistics
Matches: 45, Mismatches: 15, Indels: 12
0.62 0.21 0.17
Matches are distributed among these distances:
29 5 0.11
31 7 0.16
32 21 0.47
33 7 0.16
35 5 0.11
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (32 bp):
AATTGAATTTTACTCTGAAGCAAATGCTTAAC
Found at i:3432 original size:64 final size:63
Alignment explanation
Indices: 3331--3458 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 63
3321 TTAATTATTA
*
3331 AATTGAATTTTACTCTGAAGCAAATGCTTAACAACGTTTCACAATAACAAAAAAAGTGCTTAAC
1 AATTGAATTTTACTCTGAAGCAAATGCTTAACAACGTTTCACAACAACAAAAAAA-TGCTTAAC
*
3395 AATTGAATTTTACTCTGAAGCAAATGCTTGACAACGTTTCACAACAACAAAAAAATGCTTAAC
1 AATTGAATTTTACTCTGAAGCAAATGCTTAACAACGTTTCACAACAACAAAAAAATGCTTAAC
3458 A
1 A
3459 GCGTAAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 9 0.15
64 53 0.85
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (63 bp):
AATTGAATTTTACTCTGAAGCAAATGCTTAACAACGTTTCACAACAACAAAAAAATGCTTAAC
Found at i:3531 original size:25 final size:26
Alignment explanation
Indices: 3503--3554 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
3493 TTGCTTAAAC
3503 TAAAATTTTAAAATTAAAA-GGTATT
1 TAAAATTTTAAAATTAAAAGGGTATT
3528 TAAAATTTTAAAATTAAAAGGGTATT
1 TAAAATTTTAAAATTAAAAGGGTATT
3554 T
1 T
3555 TAGATATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (26 bp):
TAAAATTTTAAAATTAAAAGGGTATT
Found at i:3963 original size:12 final size:12
Alignment explanation
Indices: 3946--3971 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3936 ATTTTCAAAC
3946 TATATTTATTAT
1 TATATTTATTAT
3958 TATATTTATTAT
1 TATATTTATTAT
3970 TA
1 TA
3972 GGGTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTTATTAT
Found at i:7554 original size:14 final size:14
Alignment explanation
Indices: 7491--7554 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
7481 GAGTATTTTG
*
7491 TTTTTGCAATTCTA
1 TTTTTGTAATTCTA
*
7505 TTTTTGTAATTCTG
1 TTTTTGTAATTCTA
* * *
7519 TTTTGTTTAACTCAA
1 TTTT-TGTAATTCTA
*
7534 ATTTTGTAATTCTA
1 TTTTTGTAATTCTA
7548 TTTTTGT
1 TTTTTGT
7555 TTAGTTCAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
14 29 0.76
15 9 0.24
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTTTGTAATTCTA
Found at i:9767 original size:14 final size:14
Alignment explanation
Indices: 9748--9778 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9738 ATTGTTGTTG
9748 TTGAACTTGAATGT
1 TTGAACTTGAATGT
*
9762 TTGAACTTGGATGT
1 TTGAACTTGAATGT
9776 TTG
1 TTG
9779 TAATTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (14 bp):
TTGAACTTGAATGT
Found at i:15472 original size:22 final size:22
Alignment explanation
Indices: 15446--15490 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
15436 ATGGGCCACA
15446 TCATCAACATTAAGCAGTGATC
1 TCATCAACATTAAGCAGTGATC
**
15468 TCATCAACATTAAGTGGTGATC
1 TCATCAACATTAAGCAGTGATC
15490 T
1 T
15491 TCACTAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (22 bp):
TCATCAACATTAAGCAGTGATC
Found at i:21003 original size:42 final size:41
Alignment explanation
Indices: 20952--21036 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 41
20942 TGTTATATAC
*
20952 ATTTTATATATATCATAAATATGATT-TATATATTTTACACAT
1 ATTTTATATATATCATAAATA--ATTAAATATATTTTACACAT
*
20994 ATTTTATATATATCATAAATAATTAAATATATTTTATACAT
1 ATTTTATATATATCATAAATAATTAAATATATTTTACACAT
21035 AT
1 AT
21037 CATAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 3 0.08
41 16 0.40
42 21 0.52
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (41 bp):
ATTTTATATATATCATAAATAATTAAATATATTTTACACAT
Found at i:21006 original size:11 final size:11
Alignment explanation
Indices: 20944--21057 Score: 51
Period size: 11 Copynumber: 10.8 Consensus size: 11
20934 AAAAAATTTG
*
20944 TTATATACATT
1 TTATATATATT
20955 TTATATATA--
1 TTATATATATT
* * *
20964 TCATAAATATGA
1 TTATATATAT-T
20976 TT-TATATATT
1 TTATATATATT
* *
20986 TTACACATATT
1 TTATATATATT
20997 TTATATATA--
1 TTATATATATT
* * *
21006 TCATAAATA-A
1 TTATATATATT
*
21016 TTAAATATATT
1 TTATATATATT
* *
21027 TTATACATATC
1 TTATATATATT
* *
21038 ATAAATATATT
1 TTATATATATT
21049 TTATATATA
1 TTATATATA
21058 ATAGCATAAT
Statistics
Matches: 72, Mismatches: 25, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
9 14 0.19
10 8 0.11
11 49 0.68
12 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (11 bp):
TTATATATATT
Found at i:21046 original size:41 final size:41
Alignment explanation
Indices: 20959--21047 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
20949 TACATTTTAT
* ** *
20959 ATATATCATAAATATGATTTATATATTTTACACATATTTTAT
1 ATATATCATAAATA-GATTAATATATTTTACACATATCATAA
*
21001 ATATATCATAAATA-ATTAAATATATTTTATACATATCATAA
1 ATATATCATAAATAGATT-AATATATTTTACACATATCATAA
21042 ATATAT
1 ATATAT
21048 TTTATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.07
41 24 0.59
42 14 0.34
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (41 bp):
ATATATCATAAATAGATTAATATATTTTACACATATCATAA
Done.