Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019259.1 Corchorus olitorius cultivar O-4 contig19292, 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: 19444
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:86 original size:21 final size:19
Alignment explanation
Indices: 53--106 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
43 GAGAACAGAA
53 AAGAAAG-GAAAAATGTAAAG
1 AAGAAAGAGAAAAA-G-AAAG
73 AAGAAAGAGAAAAAGAAAG
1 AAGAAAGAGAAAAAGAAAG
92 AGAGGAAAGAGAAAA
1 A-A-GAAAGAGAAAA
107 GTTAAAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 17 0.55
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.04
Consensus pattern (19 bp):
AAGAAAGAGAAAAAGAAAG
Found at i:791 original size:23 final size:23
Alignment explanation
Indices: 761--869 Score: 157
Period size: 23 Copynumber: 4.7 Consensus size: 23
751 CACAATTGCT
761 TGGCGCCCGACCACTTCCAAACC
1 TGGCGCCCGACCACTTCCAAACC
784 TGGCGCCCGACCACTTCCAAACC
1 TGGCGCCCGACCACTTCCAAACC
*
807 TGGCGACCGACCACTTCCAAACC
1 TGGCGCCCGACCACTTCCAAACC
* *
830 TGGCGACCGACTACTTCCATAACGC
1 TGGCGCCCGACCACTTCCA-AAC-C
*
855 -GGCGCTCGACCACTT
1 TGGCGCCCGACCACTT
870 GTGACCACAA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
23 63 0.80
24 15 0.19
25 1 0.01
ACGTcount: A:0.22, C:0.43, G:0.19, T:0.16
Consensus pattern (23 bp):
TGGCGCCCGACCACTTCCAAACC
Found at i:1012 original size:26 final size:27
Alignment explanation
Indices: 951--1018 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
941 AACCAGCTGG
*
951 CACC-CCACACGTGACCTCCAAACGTA
1 CACCTCCACACGTGACCTCCAAACGGA
*
977 CGACCT-CACACGTGATCTCC-AACGGA
1 C-ACCTCCACACGTGACCTCCAAACGGA
*
1003 CACCTCCACATGTGAC
1 CACCTCCACACGTGAC
1019 ATCGCGCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.11
26 15 0.43
27 16 0.46
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.15
Consensus pattern (27 bp):
CACCTCCACACGTGACCTCCAAACGGA
Found at i:3649 original size:15 final size:15
Alignment explanation
Indices: 3629--3658 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3619 GCCGACTGTT
3629 GAAGAACTGAAGAAA
1 GAAGAACTGAAGAAA
*
3644 GAAGAAGTGAAGAAA
1 GAAGAACTGAAGAAA
3659 ATGGCGGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.30, T:0.07
Consensus pattern (15 bp):
GAAGAACTGAAGAAA
Found at i:6238 original size:45 final size:45
Alignment explanation
Indices: 6170--6260 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
6160 ACTGCTTAGA
* ** * * *
6170 CCCTATTGTTAAATGTGCCTTAAAGCAAGGAATTAACAATGCTGT
1 CCCTATTGATAAAAATGCCTTAAAGCAAAGAATAAACAATCCTGT
*
6215 CCCTATTGATAAAAATGCTTTAAAGCAAAGAATAAACAATCCTGT
1 CCCTATTGATAAAAATGCCTTAAAGCAAAGAATAAACAATCCTGT
6260 C
1 C
6261 TGCCAAACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (45 bp):
CCCTATTGATAAAAATGCCTTAAAGCAAAGAATAAACAATCCTGT
Found at i:14182 original size:2 final size:2
Alignment explanation
Indices: 14175--14209 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
14165 ACTAAAAATA
14175 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
14210 TGGAGAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15831 original size:2 final size:2
Alignment explanation
Indices: 15824--15857 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15814 AATTCACCAT
15824 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15858 CTTGAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16881 original size:26 final size:24
Alignment explanation
Indices: 16826--16881 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
16816 ATGAGTACCA
*
16826 ACCAAAGGCATACCGTAAACACCC
1 ACCAAAGGCATACCATAAACACCC
* *
16850 ATCAAAGGTATACCATAAACACACCC
1 ACCAAAGGCATACCAT-AA-ACACCC
16876 ACCAAA
1 ACCAAA
16882 TATTATACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 13 0.50
25 2 0.08
26 11 0.42
ACGTcount: A:0.46, C:0.34, G:0.09, T:0.11
Consensus pattern (24 bp):
ACCAAAGGCATACCATAAACACCC
Done.