Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019460.1 Corchorus olitorius cultivar O-4 contig19493, 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: 4048
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:278 original size:17 final size:18
Alignment explanation
Indices: 256--289 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
246 AAAGTTGCTT
256 AAAATTATTT-CTATTTG
1 AAAATTATTTCCTATTTG
*
273 AAAATTTTTTCCTATTT
1 AAAATTATTTCCTATTT
290 TAATTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAATTATTTCCTATTTG
Found at i:715 original size:27 final size:27
Alignment explanation
Indices: 685--772 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
675 GTGCCTGTTT
685 CTTCAGATTTTGGCTTGGATTAGTTGC
1 CTTCAGATTTTGGCTTGGATTAGTTGC
* ** *
712 CTTCAAGAAGTTTGTAG-TTGCGCCT-GTT-T
1 CTTC-AG-A-TTT-TGGCTTG-GATTAGTTGC
741 CTTCAGATTTTGGCTTGGATTAGTTGC
1 CTTCAGATTTTGGCTTGGATTAGTTGC
768 CTTCA
1 CTTCA
773 AGAATAAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 10 0.22
28 4 0.09
29 5 0.11
30 9 0.20
31 4 0.09
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
CTTCAGATTTTGGCTTGGATTAGTTGC
Found at i:737 original size:56 final size:56
Alignment explanation
Indices: 662--776 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
652 GCTATCATAT
* *
662 GAAGTTTGTCGTTGTGCCTGTTTCTTCAGATTTTGGCTTGGATTAGTTGCCTTCAA
1 GAAGTTTGTAGTTGCGCCTGTTTCTTCAGATTTTGGCTTGGATTAGTTGCCTTCAA
718 GAAGTTTGTAGTTGCGCCTGTTTCTTCAGATTTTGGCTTGGATTAGTTGCCTTCAA
1 GAAGTTTGTAGTTGCGCCTGTTTCTTCAGATTTTGGCTTGGATTAGTTGCCTTCAA
774 GAA
1 GAA
777 TAAACTTCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.43
Consensus pattern (56 bp):
GAAGTTTGTAGTTGCGCCTGTTTCTTCAGATTTTGGCTTGGATTAGTTGCCTTCAA
Found at i:1811 original size:6 final size:6
Alignment explanation
Indices: 1793--1828 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1783 GGGGGGCAAC
*
1793 CTAATA CTCATA CTAATA CTAATA CTAATA CTAATA
1 CTAATA CTAATA CTAATA CTAATA CTAATA CTAATA
1829 TGACGTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (6 bp):
CTAATA
Found at i:3067 original size:18 final size:17
Alignment explanation
Indices: 3044--3081 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3034 CCCAAATTAC
3044 TTATGGAAAATAGGGAAA
1 TTATGGAAAATA-GGAAA
*
3062 TTATGGAAATTAGGAAA
1 TTATGGAAAATAGGAAA
3079 TTA
1 TTA
3082 AATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (17 bp):
TTATGGAAAATAGGAAA
Found at i:3077 original size:8 final size:9
Alignment explanation
Indices: 3044--3081 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3034 CCCAAATTAC
3044 TTATGGAAA
1 TTATGGAAA
* *
3053 ATAGGGAAA
1 TTATGGAAA
3062 TTATGGAAA
1 TTATGGAAA
3071 TTA-GGAAA
1 TTATGGAAA
3079 TTA
1 TTA
3082 AATGAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (9 bp):
TTATGGAAA
Done.