Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018943.1 Corchorus olitorius cultivar O-4 contig18976, 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: 48031
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:11242 original size:12 final size:12
Alignment explanation
Indices: 11219--11249 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
11209 TCATTTTCGT
11219 TATTATTATATTA
1 TATTA-TATATTA
11232 TATTATATATTA
1 TATTATATATTA
11244 TATTAT
1 TATTAT
11250 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATATTA
Found at i:11244 original size:17 final size:16
Alignment explanation
Indices: 11218--11249 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11208 CTCATTTTCG
11218 TTATTATTATATTATA
1 TTATTATTATATTATA
11234 TTATATATTATATTAT
1 TTAT-TATTATATTAT
11250 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTATTATATTATA
Found at i:16917 original size:12 final size:11
Alignment explanation
Indices: 16890--16965 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 11
16880 AATAGTTTAA
16890 TAATTATATAT
1 TAATTATATAT
16901 T-ATTATATAT
1 TAATTATATAT
16911 GTAATTATATA-
1 -TAATTATATAT
16922 T-ATCTA-ATAT
1 TAAT-TATATAT
*
16932 TATTTTATATAT
1 TA-ATTATATAT
*
16944 ATATTATATATATT
1 -TAAT-TATATA-T
16958 TAATTATA
1 TAATTATA
16966 AATATTACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
9 5 0.09
10 13 0.25
11 4 0.08
12 19 0.36
13 11 0.21
14 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATTATATAT
Found at i:16952 original size:21 final size:21
Alignment explanation
Indices: 16893--16972 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 21
16883 AGTTTAATAA
16893 TTATATAT-TATTATA-TATGT
1 TTATATATATATTATATTAT-T
* *
16913 AATTATATATATCTAATATTATT
1 --TTATATATATATTATATTATT
16936 TTATATATATATTATATATATT
1 TTATATATATATTATAT-TATT
* *
16958 TAATTATAAATATTA
1 TTA-TATATATATTA
16973 CTAAACGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 15 0.31
22 14 0.29
23 16 0.33
24 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTATATATATATTATATTATT
Found at i:16955 original size:32 final size:31
Alignment explanation
Indices: 16897--16961 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
16887 TAATAATTAT
*
16897 ATATTATTATATATGTAATTATATATATCTA
1 ATATTATTATATATATAATTATATATATCTA
* *
16928 ATATTATTTTATATATATATTATATATATTTA
1 ATATTATTATATATATA-ATTATATATATCTA
16960 AT
1 AT
16962 TATAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATATTATTATATATATAATTATATATATCTA
Found at i:16964 original size:25 final size:25
Alignment explanation
Indices: 16885--16970 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
16875 GTTTAAATAG
*
16885 TTTAATAAT-TATATATTATTATATA
1 TTTAATTATATATATATTA-TATATA
* * *
16910 TGTAATTATATATATCTAATAT-TA
1 TTTAATTATATATATATTATATATA
16934 -TT--TTATATATATATTATATATA
1 TTTAATTATATATATATTATATATA
*
16956 TTTAATTATAAATAT
1 TTTAATTATATATAT
16971 TACTAAACGG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 3 0.06
24 2 0.04
25 19 0.40
26 7 0.15
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTAATTATATATATATTATATATA
Found at i:36915 original size:13 final size:14
Alignment explanation
Indices: 36883--36919 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
36873 TGTATAGTAT
36883 TAATAAATACAACA
1 TAATAAATACAACA
*
36897 TTATAAATA-AACA
1 TAATAAATACAACA
36910 TAAT-AATACA
1 TAATAAATACA
36920 TATTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAAATACAACA
Found at i:37321 original size:22 final size:22
Alignment explanation
Indices: 37296--37340 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
37286 TTTCTAACAG
37296 GACATGCGCGTGTAATGCAGGC
1 GACATGCGCGTGTAATGCAGGC
37318 GACATGCGCGTGTAATGCAGGC
1 GACATGCGCGTGTAATGCAGGC
37340 G
1 G
37341 CCGTTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.18
Consensus pattern (22 bp):
GACATGCGCGTGTAATGCAGGC
Found at i:38646 original size:8 final size:9
Alignment explanation
Indices: 38620--38648 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
38610 CCTAAATTAC
38620 TTATGGAAA
1 TTATGGAAA
38629 TTATGGAAA
1 TTATGGAAA
38638 TTA-GGAAA
1 TTATGGAAA
38646 TTA
1 TTA
38649 AAGAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:38654 original size:17 final size:17
Alignment explanation
Indices: 38624--38657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38614 AATTACTTAT
**
38624 GGAAATTATGGAAATTA
1 GGAAATTAAAGAAATTA
38641 GGAAATTAAAGAAATTA
1 GGAAATTAAAGAAATTA
38658 AATGTGTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
GGAAATTAAAGAAATTA
Found at i:39992 original size:48 final size:47
Alignment explanation
Indices: 39863--39992 Score: 163
Period size: 48 Copynumber: 2.7 Consensus size: 47
39853 TACTTTTTAC
* *
39863 TGCACTTTTTCTCAATTTTTACT-ACAAAATTGAACCTTTATTTTTCT
1 TGCACTTTTTCTCAATTTTTA-TGACAAAATTGATCCTTTAATTTTCT
* * *
39910 CGCAACTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCAT
1 TGC-ACTTTTTCTCAATTTTTATGACAAAATTGATCCTTTAATTTTC-T
* *
39959 TGCACTTTTTATCAATTTTTTTGACAAAATTGAT
1 TGCACTTTTTCTCAATTTTTATGACAAAATTGAT
39993 TGGCACGCTC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
47 2 0.03
48 66 0.93
49 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (47 bp):
TGCACTTTTTCTCAATTTTTATGACAAAATTGATCCTTTAATTTTCT
Found at i:40121 original size:17 final size:18
Alignment explanation
Indices: 40095--40133 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
40085 CTGTTTTTGG
40095 AAAACTGAAAACG-AAACA
1 AAAACTG-AAACGAAAACA
40113 AAAAC-GAAACGAAAACA
1 AAAACTGAAACGAAAACA
40130 AAAA
1 AAAA
40134 AACAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.72, C:0.15, G:0.10, T:0.03
Consensus pattern (18 bp):
AAAACTGAAACGAAAACA
Found at i:43439 original size:225 final size:225
Alignment explanation
Indices: 43048--43722 Score: 1235
Period size: 225 Copynumber: 3.0 Consensus size: 225
43038 TAGATTCGAG
* *
43048 TCTTATGAATAGAGAAAATAGCACAGAAGAACTTCCTCTATTAAGGGATAAACGAGACTCAATCC
1 TCTTATGAATAGAGAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAACGAGACTCAATCC
* * *
43113 AAATTAGTGAGGATTAAATATAACTATCAGAGATATCAAGAGATTCTTACCAAAATAAAAAAGAT
66 AAATTAGTGAGGATTCAATATAACTATCAGAGATATCAGGAGATTCTTACAAAAATAAAAAAGAT
43178 GTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATGC
131 GTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATGC
43243 ATATGATTTATAATGTTTTTAAGGGGAGAA
196 ATATGATTTATAATGTTTTTAAGGGGAGAA
*
43273 TCTTATGAATAGAGAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAACGAGACTCGATCC
1 TCTTATGAATAGAGAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAACGAGACTCAATCC
*
43338 AAATTAGTGAGGATTCAATATAACTATCAAAGATATCAGGAGATTCTTACAAAAATAAAAAAGAT
66 AAATTAGTGAGGATTCAATATAACTATCAGAGATATCAGGAGATTCTTACAAAAATAAAAAAGAT
43403 GTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATGC
131 GTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATGC
*
43468 ATATAATTTATAATGTTTTTAAGGGGAGAA
196 ATATGATTTATAATGTTTTTAAGGGGAGAA
* * *
43498 TCTTATGAATAGAAAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAATGAGATTCAATCC
1 TCTTATGAATAGAGAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAACGAGACTCAATCC
43563 AAATTAGTGAGGATTCAATATAACTATCAGAGATATCAGGAGATTCTTA-ACAAAATAAAAAAGA
66 AAATTAGTGAGGATTCAATATAACTATCAGAGATATCAGGAGATTCTTACA-AAAATAAAAAAGA
43627 TGTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATG
130 TGTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATG
43692 CATATGATTTATAATGTTTTTAAGGGGAGAA
195 CATATGATTTATAATGTTTTTAAGGGGAGAA
43723 AACTATTATT
Statistics
Matches: 435, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
224 1 0.00
225 434 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (225 bp):
TCTTATGAATAGAGAAAATAGCACAGAAGAGCTTCCTCTATTCAGGGATAAACGAGACTCAATCC
AAATTAGTGAGGATTCAATATAACTATCAGAGATATCAGGAGATTCTTACAAAAATAAAAAAGAT
GTTTGTTTTTGGCCATATAAAACACATGTAACCCTTTTGTTTGTGTATAAATAATATATGTATGC
ATATGATTTATAATGTTTTTAAGGGGAGAA
Done.