Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023995.1 Corchorus olitorius cultivar O-4 contig24028, 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: 7401
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Found at i:2620 original size:84 final size:84
Alignment explanation
Indices: 2495--2662 Score: 246
Period size: 84 Copynumber: 2.0 Consensus size: 84
2485 ACTAATGCTT
* * *
2495 CCTCTTCAGTGCGACTAATTCCACAGGAAAATAGTTTTGATTCTCTGACCACTCATGGTTATTTA
1 CCTCTCCAGTGCCACTAATTCCACAGGAAAATAGTTCTGATTCTCTGACCACTCATGGTTATTTA
*
2560 GTGCCACTAGCTCCACAGA
66 GTGCCACTAGATCCACAGA
* * * ** *
2579 CCTCTCCAGTGCCACTACTTCCACAGGCAAATTGTTCTGATTCTCTGGTCACTCATGGTTCTTTA
1 CCTCTCCAGTGCCACTAATTCCACAGGAAAATAGTTCTGATTCTCTGACCACTCATGGTTATTTA
2644 GTGCCACTAGATCCACAGA
66 GTGCCACTAGATCCACAGA
2663 ATAGTCGCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (84 bp):
CCTCTCCAGTGCCACTAATTCCACAGGAAAATAGTTCTGATTCTCTGACCACTCATGGTTATTTA
GTGCCACTAGATCCACAGA
Found at i:2777 original size:17 final size:17
Alignment explanation
Indices: 2737--2955 Score: 108
Period size: 18 Copynumber: 13.1 Consensus size: 17
2727 GTCAATCCTA
*
2737 GGGAACTAACTTTGAAT
1 GGGAACTGACTTTGAAT
*
2754 GGGGAACTGCCTTTGAAT
1 -GGGAACTGACTTTGAAT
2772 GGGAACT-AGCTTTGAAT
1 GGGAACTGA-CTTTGAAT
*
2789 GGAGAACTGACTTGGAAT
1 GG-GAACTGACTTTGAAT
*
2807 GAGAGACTGACTTTGAAT
1 GGGA-ACTGACTTTGAAT
2825 --G-A---ACTTTGAAT
1 GGGAACTGACTTTGAAT
* * *
2836 AGAGAATTGACTTGGAAT
1 -GGGAACTGACTTTGAAT
*
2854 GAGAAACTGACTTTGAAT
1 G-GGAACTGACTTTGAAT
*
2872 --G-A---ACTTTGAACG
1 GGGAACTGACTTTGAA-T
*
2884 GGGAACTGCCTTTGAAT
1 GGGAACTGACTTTGAAT
2901 GAGGAACT-AGCTTTGAAT
1 G-GGAACTGA-CTTTGAAT
* *
2919 GGAGAATTGACTTGGAAT
1 GG-GAACTGACTTTGAAT
*
2937 GAGAGAC-GAACTTTGAAT
1 GGGA-ACTG-ACTTTGAAT
2955 G
1 G
2956 ATCCTTAACA
Statistics
Matches: 155, Mismatches: 21, Indels: 50
0.69 0.09 0.22
Matches are distributed among these distances:
11 17 0.11
14 4 0.03
15 2 0.01
16 1 0.01
17 25 0.16
18 104 0.67
19 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.27
Consensus pattern (17 bp):
GGGAACTGACTTTGAAT
Found at i:2847 original size:47 final size:47
Alignment explanation
Indices: 2781--2919 Score: 181
Period size: 47 Copynumber: 3.0 Consensus size: 47
2771 TGGGAACTAG
* *
2781 CTTTGAATGGAGAACTGACTTGGAATGAGAGACTGACTTTGAATGAA
1 CTTTGAATAGAGAACTGACTTGGAATGAGAAACTGACTTTGAATGAA
*
2828 CTTTGAATAGAGAATTGACTTGGAATGAGAAACTGACTTTGAATGAA
1 CTTTGAATAGAGAACTGACTTGGAATGAGAAACTGACTTTGAATGAA
** * * * *
2875 CTTTGAACGGGGAACTGCCTTTGAATGAGGAACT-AGCTTTGAATG
1 CTTTGAATAGAGAACTGACTTGGAATGAGAAACTGA-CTTTGAATG
2920 GAGAATTGAC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 1 0.01
47 80 0.99
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (47 bp):
CTTTGAATAGAGAACTGACTTGGAATGAGAAACTGACTTTGAATGAA
Found at i:2877 original size:29 final size:29
Alignment explanation
Indices: 2845--2902 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2835 TAGAGAATTG
*
2845 ACTTGGAATGAGAAACTGACTTTGAATGA
1 ACTTGGAACGAGAAACTGACTTTGAATGA
* * * *
2874 ACTTTGAACGGGGAACTGCCTTTGAATGA
1 ACTTGGAACGAGAAACTGACTTTGAATGA
2903 GGAACTAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
ACTTGGAACGAGAAACTGACTTTGAATGA
Found at i:2919 original size:65 final size:65
Alignment explanation
Indices: 2744--2938 Score: 195
Period size: 65 Copynumber: 3.0 Consensus size: 65
2734 CTAGGGAACT
*
2744 AACTTTGAATGGGGAACTGCCTTTGAATG-GGAACTAGCTTTGAATGGAGAACTGACTTGGAATG
1 AACTTTGAACGGGGAACTGCCTTTGAATGAGGAACTAGCTTTGAATGGAGAACTGACTTGGAATG
*** *** * * * *
2808 AGAGACTG-ACTTTGAA-TGAACTTTGAAT-AGAGAA-TTGACTTGGAAT-GAGAAACTGACTTT
1 A-ACTTTGAACGGGGAACTG-CCTTTGAATGAG-GAACTAG-CTTTGAATGGAG-AACTGACTTG
2868 GAATG
61 GAATG
*
2873 AACTTTGAACGGGGAACTGCCTTTGAATGAGGAACTAGCTTTGAATGGAGAATTGACTTGGAATG
1 AACTTTGAACGGGGAACTGCCTTTGAATGAGGAACTAGCTTTGAATGGAGAACTGACTTGGAATG
2938 A
1 A
2939 GAGACGAACT
Statistics
Matches: 98, Mismatches: 22, Indels: 21
0.70 0.16 0.15
Matches are distributed among these distances:
63 2 0.02
64 22 0.22
65 65 0.66
66 9 0.09
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (65 bp):
AACTTTGAACGGGGAACTGCCTTTGAATGAGGAACTAGCTTTGAATGGAGAACTGACTTGGAATG
Found at i:5403 original size:2 final size:2
Alignment explanation
Indices: 5396--5427 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5386 AGACCCAATC
5396 AT AT AT 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 AT AT AT
5428 GCCCAACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.