Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012038.1 Corchorus olitorius cultivar O-4 contig12071, 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: 15469
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1831 original size:3 final size:3
Alignment explanation
Indices: 1823--1874 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
1813 GAATTTGAAA
* * * *
1823 CTT CTT CTT CTT CTT CTT CTT CGT CTT CTT CGT CTT CGT CTT CGT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1871 CTT C
1 CTT C
1875 AGAATCAGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.35, G:0.08, T:0.58
Consensus pattern (3 bp):
CTT
Found at i:12537 original size:2 final size:2
Alignment explanation
Indices: 12530--12573 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
12520 ATAATGTATC
*
12530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
12573 A
1 A
12574 AGTCTAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12845 original size:39 final size:40
Alignment explanation
Indices: 12789--12869 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
12779 TTTAATTCCT
12789 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
12829 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
12868 AT
1 AT
12870 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:13224 original size:204 final size:201
Alignment explanation
Indices: 12986--13378 Score: 705
Period size: 204 Copynumber: 1.9 Consensus size: 201
12976 TTAATAATAA
*
12986 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
1 ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
* **
13051 AATAAATCAACCACTAATGTTTAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTAATG
66 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAACAATG
13116 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGACC
129 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGACC
13181 ATTGATAT
194 ATTGATAT
13189 ATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
1 ATAAATCAGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
*
13254 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAACAATGT
65 TAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAACAATGT
*
13319 GTTGTATCTTATTCACTGCAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
130 GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
13379 CATCATCGAT
Statistics
Matches: 183, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
202 75 0.41
203 12 0.07
204 96 0.52
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (201 bp):
ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAACAATGTG
TTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTGACCAT
TGATAT
Found at i:13955 original size:36 final size:36
Alignment explanation
Indices: 13908--13977 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
13898 GAGATTTTGG
* *
13908 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
13944 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
13978 GGTTAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:15357 original size:58 final size:58
Alignment explanation
Indices: 15256--15365 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
15246 ATCATGCCTC
* *
15256 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAATATGTCACTCGATAAGTTTT
1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGTTTT
* * *
15314 GGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
15366 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 30 0.65
59 16 0.35
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGTTTT
Done.