Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022296.1 Corchorus olitorius cultivar O-4 contig22329, 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: 7089
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3771 original size:29 final size:29
Alignment explanation
Indices: 3639--3852 Score: 266
Period size: 29 Copynumber: 7.4 Consensus size: 29
3629 TATAGCATTC
** * *
3639 AAAATGACCAAAACACCCCTAAAGGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* *
3668 AAAATGACCAAAATACCCCTGAAAGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
**
3697 AAAATGACCAAAATGCCATTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
3726 AAAATGACCAGAGTGCCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
*
3755 AAAATGACCAAAATGCCCCTGAGTGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
3784 AAAATAACCAAAATGCCCCTGAGTGTGTA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* *
3813 AAAATGACCAAAATGCCCCTGGATGTTCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
*
3842 AATATGACCAA
1 AAAATGACCAA
3853 TTAAGAAATA
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 161 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATGTGCA
Found at i:4396 original size:62 final size:60
Alignment explanation
Indices: 4134--4597 Score: 438
Period size: 60 Copynumber: 7.8 Consensus size: 60
4124 TTTAAAAATA
* * * * ** * *
4134 GAAAACTCTCTACTAGAGACCTCGAACAGGGTTTT-AAAAGCAAGATGCGATTTTGAATC
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGATAAGATTTAGAATT
* * * * * *
4193 GAAAACTCTCTACTAGAGACCTCGATCAAGATTTTAAAAGACAACACAGGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGATAAGATTTAGAATT
* *
4253 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTTTTTTAAAAAAAAAAACAAGACAAGATTTG
1 GAAAACTCTCTACCAGAGACCTCGATCAGGA-----TTTT-----AAAAAACAAGATAAGATTTA
4318 GAATT
56 GAATT
*
4323 GAAAACTCTCTACCAGAGGCCTCGATCAGGATTTTCAGAAAAACAAGATAAGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTT-A-AAAAACAAGATAAGATTTAGAATT
* *
4385 GAAAACTCTCTACTAGAGACCTCGAAT-AGGATTTTAGAAAACAAGATAAGATTTAGAATT
1 GAAAACTCTCTACCAGAGACCTCG-ATCAGGATTTTAAAAAACAAGATAAGATTTAGAATT
*
4445 GAAAACTCTCTACCAGAGACCTCGAACAGGATTTT-AAAAACAAGAT--G----A-AATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGATAAGATTTAGAATT
* * * * * *
4497 -AATA--CTCTACCATAGACCTCGAACAGGATGTT-AAAAACAAGATGAA-ATTTTGGATT
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGAT-AAGATTTAGAATT
* *
4553 GAAAACTCTCTACCAGACACCTCGATAAGGATTTT-AAAAACAAGA
1 GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGA
4598 CAAAATTTGA
Statistics
Matches: 342, Mismatches: 38, Indels: 50
0.80 0.09 0.12
Matches are distributed among these distances:
49 37 0.11
51 3 0.01
52 4 0.01
53 1 0.00
56 3 0.01
57 4 0.01
59 76 0.22
60 99 0.29
61 2 0.01
62 52 0.15
63 2 0.01
65 8 0.02
70 51 0.15
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (60 bp):
GAAAACTCTCTACCAGAGACCTCGATCAGGATTTTAAAAAACAAGATAAGATTTAGAATT
Found at i:4514 original size:49 final size:49
Alignment explanation
Indices: 4452--4545 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
4442 ATTGAAAACT
*
4452 CTCTACCAGAGACCTCGAACAGGATTTTAAAAACAAGATGAAATTAATA
1 CTCTACCAGAGACCTCGAACAGGATGTTAAAAACAAGATGAAATTAATA
*
4501 CTCTACCATAGACCTCGAACAGGATGTTAAAAACAAGATGAAATT
1 CTCTACCAGAGACCTCGAACAGGATGTTAAAAACAAGATGAAATT
4546 TTGGATTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (49 bp):
CTCTACCAGAGACCTCGAACAGGATGTTAAAAACAAGATGAAATTAATA
Found at i:4584 original size:108 final size:109
Alignment explanation
Indices: 4392--4597 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 109
4382 ATTGAAAACT
* * *
4392 CTCTACTAGAGACCTCGAATAGGATTTTAGAAAACAAGATAAGATTTAGAATTGAAAACTCTCTA
1 CTCTACCAGAGACCTCGAACAGGATGTTAGAAAACAAGATAAGATTTAGAATTGAAAACTCTCTA
*
4457 CCAGAGACCTCGAACAGGATTTTAAAAACAAGATGAAATTAATA
66 CCAGACACCTCGAACAGGATTTTAAAAACAAGATGAAATTAATA
* * *
4501 CTCTACCATAGACCTCGAACAGGATGTTA-AAAACAAGATGAA-ATTTTGGATTGAAAACTCTCT
1 CTCTACCAGAGACCTCGAACAGGATGTTAGAAAACAAGAT-AAGATTTAGAATTGAAAACTCTCT
4564 ACCAGACACCTCGATA-AGGATTTTAAAAACAAGA
65 ACCAGACACCTCGA-ACAGGATTTTAAAAACAAGA
4598 CAAAATTTGA
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
108 60 0.68
109 28 0.32
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (109 bp):
CTCTACCAGAGACCTCGAACAGGATGTTAGAAAACAAGATAAGATTTAGAATTGAAAACTCTCTA
CCAGACACCTCGAACAGGATTTTAAAAACAAGATGAAATTAATA
Done.