Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011955.1 Corchorus olitorius cultivar O-4 contig11988, 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: 37652
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1970 original size:2 final size:2
Alignment explanation
Indices: 1958--1988 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1948 CTGGTACTCC
1958 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1989 AAAGACCCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4209 original size:30 final size:30
Alignment explanation
Indices: 4169--4230 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4159 CTTTAGTAAA
* *
4169 TTGAATCATAAGCTTTATTATTTTATTT-TT
1 TTGAAACATAAACTTT-TTATTTTATTTATT
*
4199 TTGAAACATAAACTTTTTATTTTCTTTATT
1 TTGAAACATAAACTTTTTATTTTATTTATT
4229 TT
1 TT
4231 TTAGTGTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.60
Consensus pattern (30 bp):
TTGAAACATAAACTTTTTATTTTATTTATT
Found at i:4579 original size:21 final size:21
Alignment explanation
Indices: 4555--4602 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4545 TGAGATTGTG
4555 AGATTAAACACTGTACAGATC
1 AGATTAAACACTGTACAGATC
*** *
4576 AGATTAGGTACTGTACAGATG
1 AGATTAAACACTGTACAGATC
4597 AGATTA
1 AGATTA
4603 TAATCAGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
AGATTAAACACTGTACAGATC
Found at i:5056 original size:22 final size:21
Alignment explanation
Indices: 4996--5056 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
4986 AGAAGACAAG
* **
4996 AAAAAATAAAAGACAAAAAGGC
1 AAAAAAAAAAAGA-AAAAAGAA
5018 AAAAAAAAAAAGTAAAAAAGAA
1 AAAAAAAAAAAG-AAAAAAGAA
5040 AAAAAAAAGAAAGAAAA
1 AAAAAAAA-AAAGAAAA
5057 GGACATACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAAAAGAA
Found at i:8403 original size:2 final size:2
Alignment explanation
Indices: 8359--8383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8349 CCATTATGAG
8359 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 A
8384 GCCATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13596 original size:23 final size:22
Alignment explanation
Indices: 13530--13611 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
13520 TCAGAGGGAT
* *
13530 GTTATCAAAA-ATCATAAGAAG
1 GTTATCAAAATTTCATAGGAAG
*
13551 ATTA-CAAAATTTCATAGGAAG
1 GTTATCAAAATTTCATAGGAAG
* **
13572 GTTTATTAAAATTTCATAGTTAG
1 G-TTATCAAAATTTCATAGGAAG
*
13595 GTTATCAAAGTTTCATA
1 GTTATCAAAATTTCATA
13612 TATATATTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.10
21 12 0.24
22 17 0.35
23 15 0.31
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGAAG
Found at i:16476 original size:31 final size:31
Alignment explanation
Indices: 16439--16511 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
16429 GACCCGTAAT
16439 CCAGATGACCCGAGACCCGAATAAACATAAC
1 CCAGATGACCCGAGACCCGAATAAACATAAC
*
16470 CCAGATGACCCGAGACCCGAATAAACATGAC
1 CCAGATGACCCGAGACCCGAATAAACATAAC
16501 CC-G-TGACCCGA
1 CCAGATGACCCGA
16512 TTGACTCGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 8 0.20
30 1 0.02
31 32 0.78
ACGTcount: A:0.37, C:0.34, G:0.19, T:0.10
Consensus pattern (31 bp):
CCAGATGACCCGAGACCCGAATAAACATAAC
Found at i:36551 original size:25 final size:25
Alignment explanation
Indices: 36523--36573 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
36513 GCTTCAGCTC
*
36523 TTTTCCCCTATTGTTTGGCCTAAAG
1 TTTTCCCCTATTGTTTGACCTAAAG
*
36548 TTTTCCCCTTTTGTTTGACCTAAAG
1 TTTTCCCCTATTGTTTGACCTAAAG
36573 T
1 T
36574 GCCCATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.47
Consensus pattern (25 bp):
TTTTCCCCTATTGTTTGACCTAAAG
Done.