Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013630.1 Corchorus olitorius cultivar O-4 contig13663, 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: 12773
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:947 original size:30 final size:30
Alignment explanation
Indices: 913--1015 Score: 80
Period size: 33 Copynumber: 3.2 Consensus size: 30
903 TTGATTATGG
913 AATTTACCCTTAAAATAAAAATAAAATTTT
1 AATTTACCCTTAAAATAAAAATAAAATTTT
*** * * *
943 AATTTGGGGCTACTATAATAATAAATTATTAATATTG
1 AATTT-ACCCT--TAAAATAA-AAA-TA-AAAT-TTT
980 AATTTTACCCTTAAAATAAAAATAAAATTTT
1 AA-TTTACCCTTAAAATAAAAATAAAATTTT
1011 AATTT
1 AATTT
1016 GGGGTTAAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
30 8 0.15
31 6 0.11
32 3 0.06
33 9 0.17
34 6 0.11
35 9 0.17
36 3 0.06
37 6 0.11
38 3 0.06
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.40
Consensus pattern (30 bp):
AATTTACCCTTAAAATAAAAATAAAATTTT
Found at i:1308 original size:3 final size:3
Alignment explanation
Indices: 1300--1363 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
1290 CAAATTTTAG
**
1300 TAT TAT TAT TAT TAT TGC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1348 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
1364 CTGATATTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3977 original size:24 final size:24
Alignment explanation
Indices: 3945--3991 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3935 TTTTTTTAAG
3945 ATTTATTTTTGTAAAAGGATTAGT
1 ATTTATTTTTGTAAAAGGATTAGT
3969 ATTTATTTTTGTAAAAGGATTAG
1 ATTTATTTTTGTAAAAGGATTAG
3992 GGTATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (24 bp):
ATTTATTTTTGTAAAAGGATTAGT
Found at i:3999 original size:24 final size:24
Alignment explanation
Indices: 3948--3999 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3938 TTTTAAGATT
* *
3948 TATTTTTGTAAAAGGATTAGTATT
1 TATTTTTGTAAAAGGATTAGGATA
*
3972 TATTTTTGTAAAAGGATTAGGGTA
1 TATTTTTGTAAAAGGATTAGGATA
3996 TATT
1 TATT
4000 AAGAGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (24 bp):
TATTTTTGTAAAAGGATTAGGATA
Found at i:4829 original size:24 final size:24
Alignment explanation
Indices: 4800--4847 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4790 TTTTTTTAAA
*
4800 TATTTATTTTTATAAAATGATTAG
1 TATTTATTTTTATAAAAGGATTAG
*
4824 TATTTATTTTTGTAAAAGGATTAG
1 TATTTATTTTTATAAAAGGATTAG
4848 GGTATATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (24 bp):
TATTTATTTTTATAAAAGGATTAG
Found at i:4990 original size:6 final size:6
Alignment explanation
Indices: 4972--5006 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
4962 GTTTAGACTT
4972 ATATAG TATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATAT
5007 TAAGTTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:11055 original size:65 final size:61
Alignment explanation
Indices: 10983--11110 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 61
10973 CGAATGAAGC
** * *
10983 AAAACTTAATTCACCGTTAGTGGAAGAAAAACTAATTAATGAGATTCTTGCGGTAAAGAAATTAG
1 AAAACTTAATTCACAATTAGTGCAAGAAAAACT-A--AA-GAGATTCGTGCGGTAAAGAAATTAG
*
11048 AAAACTTAATTCACAATTAGTGCAAGACAAACTAAAGAGATTCGTGCGGTAAAGAAATTAG
1 AAAACTTAATTCACAATTAGTGCAAGAAAAACTAAAGAGATTCGTGCGGTAAAGAAATTAG
11109 AA
1 AA
11111 TTTTTTAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 26 0.45
62 2 0.03
64 1 0.02
65 29 0.50
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAACTTAATTCACAATTAGTGCAAGAAAAACTAAAGAGATTCGTGCGGTAAAGAAATTAG
Found at i:12248 original size:2 final size:2
Alignment explanation
Indices: 12241--12266 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12231 CATATGAAGC
12241 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12267 TCTCAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.