Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015808.1 Corchorus olitorius cultivar O-4 contig15841, 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: 29036
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:3621 original size:107 final size:103
Alignment explanation
Indices: 3501--3701 Score: 294
Period size: 105 Copynumber: 1.9 Consensus size: 103
3491 GTTCTGGCCT
*
3501 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
1 TTTTAAGGGTAAATTCCAAAATTAATAA--TATTATTATAGGGTTTTAGAAATAAAATACAAAAC
3566 TAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTA
64 TAA-TTCACTAAGTTT-ACCCCAAATTAAAATTTTATTTTTA
** * * *
3608 TTTTAAGGGTAAATTCCATCATTAATAATATTGTTATAGGGTTTTAGAAATAAAATATATAACTA
1 TTTTAAGGGTAAATTCCAAAATTAATAATATTATTATAGGGTTTTAGAAATAAAATACAAAACTA
**
3673 ATTCACTAAGTTTAGTCCAAATTAAAATT
66 ATTCACTAAGTTTACCCCAAATTAAAATT
3702 AAAATTAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
103 14 0.16
104 12 0.14
105 35 0.41
107 25 0.29
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (103 bp):
TTTTAAGGGTAAATTCCAAAATTAATAATATTATTATAGGGTTTTAGAAATAAAATACAAAACTA
ATTCACTAAGTTTACCCCAAATTAAAATTTTATTTTTA
Found at i:6356 original size:15 final size:15
Alignment explanation
Indices: 6338--6368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6328 TAAGGGCTGA
*
6338 AATTAATTAATTATT
1 AATTAAATAATTATT
6353 AATTAAATAATTATT
1 AATTAAATAATTATT
6368 A
1 A
6369 TTTTATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:6363 original size:19 final size:18
Alignment explanation
Indices: 6341--6391 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
6331 GGGCTGAAAT
6341 TAATTAATTATTAATTAAA
1 TAATT-ATTATTAATTAAA
* *
6360 TAATTATTATTTTATTGAA
1 TAATTATTA-TTAATTAAA
6379 TAATTATTATTAA
1 TAATTATTATTAA
6392 AAATTCTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTATTAATTAAA
Found at i:7843 original size:51 final size:50
Alignment explanation
Indices: 7742--7843 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
7732 GTTCTTCATA
* **
7742 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
7792 TTTTCTCTTGTTTCA-ATCTTGTCTCAGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
7843 T
1 T
7844 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
50 9 0.20
51 35 0.78
52 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:9504 original size:6 final size:6
Alignment explanation
Indices: 9468--9522 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
9458 TTTCCTTTAG
* * *
9468 TTTTGT TTTTAT TTTTAGT ATTTTGT TTTTGT TTTTG- TGTT-T TTGTGT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9516 TTTTGT T
1 TTTTGT T
9523 AATTTTGCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.13
6 27 0.69
7 3 0.08
8 4 0.10
ACGTcount: A:0.05, C:0.00, G:0.16, T:0.78
Consensus pattern (6 bp):
TTTTGT
Found at i:9508 original size:8 final size:8
Alignment explanation
Indices: 9493--9521 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9483 TAGTATTTTG
9493 TTTT-TGT
1 TTTTGTGT
9500 TTTTGTGT
1 TTTTGTGT
9508 TTTTGTGT
1 TTTTGTGT
9516 TTTTGT
1 TTTTGT
9522 TAATTTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (8 bp):
TTTTGTGT
Found at i:14927 original size:13 final size:13
Alignment explanation
Indices: 14909--14957 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
14899 CCTCAAGTAC
14909 AAAAAGAAGAAGA
1 AAAAAGAAGAAGA
14922 AAAAAGAA-AAGA
1 AAAAAGAAGAAGA
*
14934 CAAAAAAAAGAGAGA
1 -AAAAAGAAGA-AGA
14949 AAACAAGAA
1 AAA-AAGAA
14958 AATAAGCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 4 0.13
13 15 0.50
14 4 0.13
15 7 0.23
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAAGA
Found at i:14954 original size:18 final size:17
Alignment explanation
Indices: 14918--14959 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
14908 CAAAAAGAAG
*
14918 AAGAAAAAAGAAAAGAC
1 AAGAAAAAAGAAAAAAC
14935 AA-AAAAAAGAGAGAAAAC
1 AAGAAAAAAGA-A-AAAAC
14953 AAGAAAA
1 AAGAAAA
14960 TAAGCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 6 0.29
19 4 0.19
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAC
Found at i:17896 original size:31 final size:31
Alignment explanation
Indices: 17861--17934 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
17851 ATTTTTATAA
*
17861 ATGAAAATTACATTTTCTT-AAAAAAAAAGTT
1 ATGAAAA-TAAATTTTCTTCAAAAAAAAAGTT
*
17892 ATG--AATAAATTTTGTTGCAAAAAAAAAGTT
1 ATGAAAATAAATTTTCTT-CAAAAAAAAAGTT
17922 ATG--AATAAATTTT
1 ATGAAAATAAATTTT
17935 TTTAATACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 9 0.23
29 2 0.05
30 25 0.64
31 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.36
Consensus pattern (31 bp):
ATGAAAATAAATTTTCTTCAAAAAAAAAGTT
Found at i:17904 original size:28 final size:28
Alignment explanation
Indices: 17872--17939 Score: 100
Period size: 30 Copynumber: 2.4 Consensus size: 28
17862 TGAAAATTAC
17872 ATTTTCTTAAAAAAAAAGTTATGAATAA
1 ATTTTCTTAAAAAAAAAGTTATGAATAA
*
17900 ATTTTGTTGCAAAAAAAAAGTTATGAATAA
1 ATTTTCTT--AAAAAAAAAGTTATGAATAA
*
17930 ATTTTTTTAA
1 ATTTTCTTAA
17940 TACTATAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 9 0.25
30 27 0.75
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (28 bp):
ATTTTCTTAAAAAAAAAGTTATGAATAA
Found at i:19694 original size:23 final size:25
Alignment explanation
Indices: 19668--19718 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
19658 AATTTTCAAC
19668 TAATATATTTT-AT-TACAATCGCG
1 TAATATATTTTCATATACAATCGCG
*
19691 TAATATATTTTCTTATACAATCGCG
1 TAATATATTTTCATATACAATCGCG
19716 TAA
1 TAA
19719 AATTTCGACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 1 0.04
25 13 0.52
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (25 bp):
TAATATATTTTCATATACAATCGCG
Done.