Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022150.1 Corchorus olitorius cultivar O-4 contig22183, 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: 21352
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:3933 original size:50 final size:50
Alignment explanation
Indices: 3866--3964 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
3856 ACCTGATGCA
3866 ATCTGTGCTTACTGTAAAGAAAAAGGCCATGTTGAAATGGTTTGCAAAGG
1 ATCTGTGCTTACTGTAAAGAAAAAGGCCATGTTGAAATGGTTTGCAAAGG
3916 ATCTGTGCTTACTGTAAAGAAAAAGGCCATGTTGAAATGGTTTGCAAAG
1 ATCTGTGCTTACTGTAAAGAAAAAGGCCATGTTGAAATGGTTTGCAAAG
3965 CAAAGTTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (50 bp):
ATCTGTGCTTACTGTAAAGAAAAAGGCCATGTTGAAATGGTTTGCAAAGG
Found at i:7879 original size:11 final size:11
Alignment explanation
Indices: 7863--7887 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7853 TAATAGGGTG
7863 GATACATGTTA
1 GATACATGTTA
7874 GATACATGTTA
1 GATACATGTTA
7885 GAT
1 GAT
7888 GATATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (11 bp):
GATACATGTTA
Found at i:8112 original size:15 final size:15
Alignment explanation
Indices: 8082--8133 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
8072 TTTAATTGTT
* *
8082 ACTTTCCTTAGTATC
1 ACTTTCCCTAGAATC
* * *
8097 ACTTTTCTTGGAATC
1 ACTTTCCCTAGAATC
8112 ACTTTCCCTAGAATC
1 ACTTTCCCTAGAATC
8127 ACTTTCC
1 ACTTTCC
8134 AGGGAAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (15 bp):
ACTTTCCCTAGAATC
Found at i:11002 original size:2 final size:2
Alignment explanation
Indices: 10989--11024 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
10979 TAATTAATTA
10989 AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11025 CACATTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11601 original size:5 final size:5
Alignment explanation
Indices: 11593--11617 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11583 ATATAATATT
11593 ATTAG ATTAG ATTAG ATTAG ATTAG
1 ATTAG ATTAG ATTAG ATTAG ATTAG
11618 CACCTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTAG
Found at i:14533 original size:29 final size:28
Alignment explanation
Indices: 14495--14596 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
14485 ATCAAAATGT
14495 TCAAATAAGGGTCCGATCTTTTAATTTGG
1 TCAAATAAGGG-CCGATCTTTTAATTTGG
* * * ** *
14524 TCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCGATC-TT-T-TAATTTGG
14555 TCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGG-CCGATCTTTTAATTTGG
14584 -CTAAATAAGGGCC
1 TC-AAATAAGGGCC
14597 TAACGTTATC
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
28 7 0.12
29 26 0.46
30 2 0.04
31 17 0.30
32 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (28 bp):
TCAAATAAGGGCCGATCTTTTAATTTGG
Found at i:14552 original size:60 final size:60
Alignment explanation
Indices: 14464--14622 Score: 241
Period size: 60 Copynumber: 2.6 Consensus size: 60
14454 AGCTAATTAC
* ** * *
14464 TCAAATAAGGACCTAATATTTATC-AAAATGTTCAAATAAGGGTCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAA-CGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
14524 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
14584 -CTAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAA
1 TC-AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAA
14623 AGACCTGGCG
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
59 6 0.07
60 86 0.93
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
Found at i:14562 original size:31 final size:31
Alignment explanation
Indices: 14524--14622 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
14514 TTTAATTTGG
14524 TCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTTATCGAAAATGC
* * * **
14555 TCAAATAAGGGCCCGATC-TT-T-TAATTTGGC
1 TCAAATAAGGG-CCTAACGTTATCGAAAAT-GC
14585 T-AAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTTATCGAAAATGC
14615 TCAAATAA
1 TCAAATAA
14623 AGACCTGGCG
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 4 0.08
29 14 0.27
30 8 0.15
31 22 0.42
32 4 0.08
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
TCAAATAAGGGCCTAACGTTATCGAAAATGC
Found at i:17090 original size:19 final size:20
Alignment explanation
Indices: 17066--17104 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
17056 ATTGTGAGGG
17066 AGTTTA-GAATTACTTACAC
1 AGTTTAGGAATTACTTACAC
17085 AGTTTAGGGAATTACTTACA
1 AGTTTA-GGAATTACTTACA
17105 GAATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
AGTTTAGGAATTACTTACAC
Found at i:19263 original size:2 final size:2
Alignment explanation
Indices: 19256--19283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19246 CCTATTAATA
19256 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
19284 TAAAGCACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.