Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016968.1 Corchorus olitorius cultivar O-4 contig17001, 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: 25152
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:75 original size:19 final size:19
Alignment explanation
Indices: 53--103 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
43 GGGCTGAAAT
53 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
** *
72 TAA-TAATTACTTTTTTGAA
1 TAATTAATTA-TTAATTAAA
91 TAATT-ATTATTAA
1 TAATTAATTATTAA
104 ATTTCTAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:6790 original size:42 final size:42
Alignment explanation
Indices: 6743--6877 Score: 127
Period size: 42 Copynumber: 3.2 Consensus size: 42
6733 GTGAAACTTG
6743 GAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATT
1 GAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATT
* * * ** *
6785 GAGTTAAATGTT-CAGATACA-G-TTC-T-TACATACAGTGAAACTT
1 GAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTAC--T--AA-TT
6827 GGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATT
1 -GAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATT
6870 GAGTTAAA
1 GAGTTAAA
6878 TGTTCAGATA
Statistics
Matches: 70, Mismatches: 12, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
37 6 0.09
38 1 0.01
39 2 0.03
40 1 0.01
41 8 0.11
42 21 0.30
43 13 0.19
44 8 0.11
45 1 0.01
46 2 0.03
47 1 0.01
48 6 0.09
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (42 bp):
GAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATT
Found at i:6866 original size:85 final size:85
Alignment explanation
Indices: 6723--6892 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
6713 TCAGATTAAA
6723 CTTACATACAGTGAAACTTGGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATTGAG
1 CTTACATACAGTGAAACTTGGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATTGAG
6788 TTAAATGTTCAGATACAGTT
66 TTAAATGTTCAGATACAGTT
6808 CTTACATACAGTGAAACTTGGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATTGAG
1 CTTACATACAGTGAAACTTGGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATTGAG
6873 TTAAATGTTCAGATACAGTT
66 TTAAATGTTCAGATACAGTT
6893 TATGAGTAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (85 bp):
CTTACATACAGTGAAACTTGGAGTTAAAAGTTGAAGATTCAGGAAACATGTACCTACTAATTGAG
TTAAATGTTCAGATACAGTT
Found at i:9449 original size:45 final size:45
Alignment explanation
Indices: 9385--9475 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
9375 GCGTCGTGCA
9385 CCTGATTTTGATGGATAAGTCTACCAACGAGGACAGCTGCGTACG
1 CCTGATTTTGATGGATAAGTCTACCAACGAGGACAGCTGCGTACG
*
9430 CCTGATTTTGGTGGATAAGTCTACCAACGAGGACAGCTGCGTACG
1 CCTGATTTTGATGGATAAGTCTACCAACGAGGACAGCTGCGTACG
9475 C
1 C
9476 AAGATCTCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (45 bp):
CCTGATTTTGATGGATAAGTCTACCAACGAGGACAGCTGCGTACG
Found at i:9655 original size:64 final size:66
Alignment explanation
Indices: 9536--9667 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 66
9526 CATCAGTCTT
9536 ACTATGTTACTACTATATATTATTCTACACAAAAATGGATGATGTAAATTTCTACTATTTCTTTC
1 ACTATGTTACTACTATATATTATTCTACACAAAAATGGA-GATGTAAATTTCTACTATTTCTTTC
9601 CC
65 CC
9603 ACTATGTTACTACTATATATTATTCTACACAAAAAT-G-GATGTAAATTTCTACTATTTCTTTCC
1 ACTATGTTACTACTATATATTATTCTACACAAAAATGGAGATGTAAATTTCTACTATTTCTTTCC
9666 C
66 C
9667 A
1 A
9668 AATTTTTTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
64 28 0.43
66 1 0.02
67 36 0.55
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (66 bp):
ACTATGTTACTACTATATATTATTCTACACAAAAATGGAGATGTAAATTTCTACTATTTCTTTCC
C
Found at i:15497 original size:27 final size:28
Alignment explanation
Indices: 15459--15516 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
15449 TAATATTAAG
15459 TTATTTTTAGTGCTAAATGCCAGC-TTC
1 TTATTTTTAGTGCTAAATGCCAGCTTTC
15486 TTATTTTTAGTGCTAAATGCCAGCTTTC
1 TTATTTTTAGTGCTAAATGCCAGCTTTC
15514 TTA
1 TTA
15517 ATCCAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (28 bp):
TTATTTTTAGTGCTAAATGCCAGCTTTC
Found at i:25045 original size:3 final size:3
Alignment explanation
Indices: 25039--25115 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
25029 TAATAACATC
25039 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25087 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25116 TGTATTCATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.