Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022181.1 Corchorus olitorius cultivar O-4 contig22214, 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: 8230
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:1029 original size:17 final size:17
Alignment explanation
Indices: 1007--1039 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
997 AAAAAGCTCC
*
1007 AAAATACACCTATTTCA
1 AAAATACACCCATTTCA
1024 AAAATACACCCATTTC
1 AAAATACACCCATTTC
1040 CATCACAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATACACCCATTTCA
Found at i:2819 original size:57 final size:56
Alignment explanation
Indices: 2713--2820 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 56
2703 TTCCTTTCAG
*
2713 ACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTCCAC
1 ACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTCTTCCAC
*
2769 ACAATAAATGTTATAATAAATCATATTCTCCCTATCTCTACTTAATTATTCT
1 ACAATAAATGTTATAATAAATCATA-TCCCCCTATCTCTACTTAATTATTCT
2821 ACAAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 24 0.49
57 25 0.51
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (56 bp):
ACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTCTTCCAC
Found at i:2897 original size:31 final size:31
Alignment explanation
Indices: 2859--2921 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2849 TAGAACAAAG
2859 TTGTTAGATAAGATAACTAAGGATTAGGATT
1 TTGTTAGATAAGATAACTAAGGATTAGGATT
2890 TTGTTAGATAAGATAACTAAGGATTAGGATT
1 TTGTTAGATAAGATAACTAAGGATTAGGATT
2921 T
1 T
2922 GAGTTGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (31 bp):
TTGTTAGATAAGATAACTAAGGATTAGGATT
Found at i:2976 original size:42 final size:42
Alignment explanation
Indices: 2917--2997 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
2907 TAAGGATTAG
2917 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
2959 GATTTGAGTTGAGTATTTCTTCATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
2998 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:4840 original size:25 final size:25
Alignment explanation
Indices: 4812--4860 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4802 TGTTAGTTTG
4812 TAGAGACCGAGCGAGAGTGCTCAAT
1 TAGAGACCGAGCGAGAGTGCTCAAT
4837 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
4861 GATTGTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAT
Found at i:6682 original size:21 final size:21
Alignment explanation
Indices: 6647--6688 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6637 TGGGTGTGTG
*
6647 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
6669 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
6689 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Done.