Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012590.1 Corchorus olitorius cultivar O-4 contig12623, 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: 5313
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:3899 original size:2 final size:2
Alignment explanation
Indices: 3892--3998 Score: 58
Period size: 2 Copynumber: 59.0 Consensus size: 2
3882 AACTGATGAA
3892 AT AT AT AT AT AT AT AT AT -T A- AT AT -T AT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3929 TT AT AT AT AT -T AT AG AT TT AT AT TT AT AT -T TT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3968 TT TT A- AT -T AGT -T AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
3999 CAGAAATAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
1 12 0.15
2 68 0.84
3 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:3920 original size:23 final size:23
Alignment explanation
Indices: 3893--3992 Score: 74
Period size: 23 Copynumber: 4.6 Consensus size: 23
3883 ACTGATGAAA
3893 TATATATATATATATATTAATAT
1 TATATATATATATATATTAATAT
3916 TATATATA-AT-TAT-TT-ATA-
1 TATATATATATATATATTAATAT
* * *
3934 TATATTATAGATTTATATTTATAT
1 TATA-TATATATATATATTAATAT
*
3958 T-T-TATAT-TAT-TTTTAATTAGT
1 TATATATATATATATATTAA-TA-T
3979 TATATATATATATA
1 TATATATATATATA
3993 ATATATCAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
18 4 0.07
19 11 0.18
20 8 0.13
21 12 0.20
22 5 0.08
23 17 0.28
24 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATATATATATATATTAATAT
Found at i:4098 original size:15 final size:15
Alignment explanation
Indices: 4079--4118 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4069 AATACCTAAA
4079 TAAAAACT-AAAAAC
1 TAAAAACTAAAAAAC
*
4093 TAAAAACTAAAAACC
1 TAAAAACTAAAAAAC
*
4108 TAAAGACTAAA
1 TAAAAACTAAA
4119 GTCAGCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (15 bp):
TAAAAACTAAAAAAC
Found at i:4119 original size:7 final size:7
Alignment explanation
Indices: 4079--4118 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
4069 AATACCTAAA
4079 TAAAAAC
1 TAAAAAC
4086 TAAAAAC
1 TAAAAAC
4093 TAAAAAC
1 TAAAAAC
4100 TAAAAACC
1 TAAAAA-C
*
4108 TAAAGAC
1 TAAAAAC
4115 TAAA
1 TAAA
4119 GTCAGCAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (7 bp):
TAAAAAC
Found at i:4916 original size:17 final size:17
Alignment explanation
Indices: 4896--4932 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4886 GCTCTGGATT
4896 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
4913 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
4930 TTA
1 TTA
4933 ATAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (17 bp):
TTATTTGTATAAGCATG
Done.