Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019821.1 Corchorus olitorius cultivar O-4 contig19854, 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: 12748
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:2843 original size:30 final size:31
Alignment explanation
Indices: 2809--2866 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2799 TCTTCTTTCT
2809 TTTTTTTTCAAA-AAAAGAAAA-GAAAAATGG
1 TTTTTTTTCAAACAAAA-AAAAGGAAAAATGG
*
2839 TTTTTTTTTAAACAAAAAAAAGGAAAAA
1 TTTTTTTTCAAACAAAAAAAAGGAAAAA
2867 ATGAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.31
Consensus pattern (31 bp):
TTTTTTTTCAAACAAAAAAAAGGAAAAATGG
Found at i:2843 original size:31 final size:31
Alignment explanation
Indices: 2808--2880 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
2798 TTCTTCTTTC
2808 TTTTTTTTTCAAA-AAAAGAAAA-GAAAAATGG
1 TTTTTTTTT-AAACAAAA-AAAAGGAAAAATGG
*
2839 TTTTTTTTTAAACAAAAAAAAGGAAAAAATGA
1 TTTTTTTTTAAACAAAAAAAAGG-AAAAATGG
*
2871 ATTTTTTTTA
1 TTTTTTTTTA
2881 TTTTTATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 7 0.19
31 14 0.38
32 16 0.43
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (31 bp):
TTTTTTTTTAAACAAAAAAAAGGAAAAATGG
Found at i:2856 original size:32 final size:31
Alignment explanation
Indices: 2808--2880 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2798 TTCTTCTTTC
* *
2808 TTTTTTTTTCAAAAAAAGAAAAG-AAAAATGG
1 TTTTTTTTT-AAAAAAAAAAAAGAAAAAATGA
*
2839 TTTTTTTTTAAACAAAAAAAAGGAAAAAATGA
1 TTTTTTTTTAAA-AAAAAAAAAGAAAAAATGA
*
2871 ATTTTTTTTA
1 TTTTTTTTTA
2881 TTTTTATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 17 0.47
32 16 0.44
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (31 bp):
TTTTTTTTTAAAAAAAAAAAAGAAAAAATGA
Found at i:5837 original size:238 final size:238
Alignment explanation
Indices: 5419--5883 Score: 921
Period size: 238 Copynumber: 2.0 Consensus size: 238
5409 TAAAAACAAT
5419 ATAGAAAAATCTTTCTAATATTTTCTTAGATTTCAGTTATAATAGGTGCAAAATTATTTTGGACA
1 ATAGAAAAATCTTTCTAATATTTTCTTAGATTTCAGTTATAATAGGTGCAAAATTATTTTGGACA
5484 TATTTTGAAGTACAAACTTTCTATTTGCTACTATAATTCGTGGAGTACTCTTTTTGAAGACACCT
66 TATTTTGAAGTACAAACTTTCTATTTGCTACTATAATTCGTGGAGTACTCTTTTTGAAGACACCT
5549 TCTAGTTTTGTTGTTACTAAGATTGAAGTATGATGGCAAAAAAAAAAAAAGATTGAAGTATTAAA
131 TCTAGTTTTGTTGTTACTAAGATTGAAGTATGATGGCAAAAAAAAAAAAAGATTGAAGTATTAAA
5614 ATTCTTTTTCCTACTCATGAATATATAATATTCATGAGTTATA
196 ATTCTTTTTCCTACTCATGAATATATAATATTCATGAGTTATA
5657 ATAGAAAAATCTTTCTAATATTTTCTTAGATTTCAGTTATAATAGGTGCAAAATTATTTTGGACA
1 ATAGAAAAATCTTTCTAATATTTTCTTAGATTTCAGTTATAATAGGTGCAAAATTATTTTGGACA
*
5722 TATTTTGAAGTACAAACTTTCTATTTGCTAGTATAATTCGTGGAGTACTCTTTTTGAAGACACCT
66 TATTTTGAAGTACAAACTTTCTATTTGCTACTATAATTCGTGGAGTACTCTTTTTGAAGACACCT
5787 TCTAGTTTTGTTGTTACTAAGATTGAAGTATGATGGCAAAAAAAAAAAAAGATTGAAGTATTAAA
131 TCTAGTTTTGTTGTTACTAAGATTGAAGTATGATGGCAAAAAAAAAAAAAGATTGAAGTATTAAA
5852 ATTCTTTTTCCTACTCATGAATATATAATATT
196 ATTCTTTTTCCTACTCATGAATATATAATATT
5884 ATTTTGTAAA
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
238 226 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (238 bp):
ATAGAAAAATCTTTCTAATATTTTCTTAGATTTCAGTTATAATAGGTGCAAAATTATTTTGGACA
TATTTTGAAGTACAAACTTTCTATTTGCTACTATAATTCGTGGAGTACTCTTTTTGAAGACACCT
TCTAGTTTTGTTGTTACTAAGATTGAAGTATGATGGCAAAAAAAAAAAAAGATTGAAGTATTAAA
ATTCTTTTTCCTACTCATGAATATATAATATTCATGAGTTATA
Found at i:6887 original size:2 final size:2
Alignment explanation
Indices: 6880--6906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6870 TAATATTTAG
6880 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6907 TATCCCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8089 original size:10 final size:10
Alignment explanation
Indices: 8074--8100 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8064 TTTTGTAACT
8074 GGACCGAACG
1 GGACCGAACG
8084 GGACCGAACG
1 GGACCGAACG
8094 GGACCGA
1 GGACCGA
8101 CCGGTCTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.41, T:0.00
Consensus pattern (10 bp):
GGACCGAACG
Found at i:10234 original size:27 final size:25
Alignment explanation
Indices: 10186--10235 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
10176 AGCTTTCTAA
*
10186 TACATATTTTTTTAAAATTAAATTT
1 TACATATTTTTTTAAAAATAAATTT
10211 TACATATTTTTTTTAATAAATAAAT
1 TACATA-TTTTTTTAA-AAATAAAT
10236 ATTGTGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TACATATTTTTTTAAAAATAAATTT
Found at i:10642 original size:14 final size:14
Alignment explanation
Indices: 10617--10660 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
10607 TTTATTTTAT
10617 AAGTTCTTTTAAGA
1 AAGTTCTTTTAAGA
* *
10631 AATTTTTTTTAA-A
1 AAGTTCTTTTAAGA
10644 GAAGTTCTTTTAAGA
1 -AAGTTCTTTTAAGA
10659 AA
1 AA
10661 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (14 bp):
AAGTTCTTTTAAGA
Found at i:10670 original size:28 final size:28
Alignment explanation
Indices: 10617--10670 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
10607 TTTATTTTAT
* ***
10617 AAGTTCTTTTAAGAAATTTTTTTTAAAG
1 AAGTTCTTTTAAGAAAATTAAGTTAAAG
10645 AAGTTCTTTTAAGAAAATTAAGTTAA
1 AAGTTCTTTTAAGAAAATTAAGTTAA
10671 GAAATGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (28 bp):
AAGTTCTTTTAAGAAAATTAAGTTAAAG
Found at i:11664 original size:5 final size:5
Alignment explanation
Indices: 11654--11680 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
11644 AAAGTGTTTA
11654 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
11681 CTATTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Done.