Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023760.1 Corchorus olitorius cultivar O-4 contig23793, 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: 8384
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Found at i:3832 original size:22 final size:21
Alignment explanation
Indices: 3807--3935 Score: 105
Period size: 22 Copynumber: 5.9 Consensus size: 21
3797 TTATATGGGA
3807 AGGTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATA-AG
* *
3829 AGGTTACCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATA-AG
* * * *
3851 AGGCTAACAAAATTTTATATG
1 AGGTTATCAAAATTTCATAAG
* * *
3872 AAGGTTATCGAAATTTTATATTG
1 -AGGTTATCAAAATTTCATA-AG
*
3895 TGGTTATCAAAATTTCATAAG
1 AGGTTATCAAAATTTCATAAG
* *
3916 AATGTTAACAAAATTTCATA
1 -AGGTTATCAAAATTTCATA
3936 GGGACTGAAG
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
21 2 0.02
22 83 0.95
23 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAAG
Found at i:3862 original size:44 final size:44
Alignment explanation
Indices: 3814--3939 Score: 128
Period size: 44 Copynumber: 2.9 Consensus size: 44
3804 GGAAGGTTAT
*
3814 CAAAATTTCATACAG-AGGTTACCAAAATTTCATAGGGAGGCTAA
1 CAAAATTTCATA-AGAAGGTTAACAAAATTTCATAGGGAGGCTAA
* * * * * ** * * *
3858 CAAAATTTTATATGAAGGTTATCGAAATTTTATATTGTGGTTAT
1 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAGGGAGGCTAA
*
3902 CAAAATTTCATAAGAATGTTAACAAAATTTCATAGGGA
1 CAAAATTTCATAAGAAGGTTAACAAAATTTCATAGGGA
3940 CTGAAGTTAT
Statistics
Matches: 62, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
43 1 0.02
44 61 0.98
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (44 bp):
CAAAATTTCATAAGAAGGTTAACAAAATTTCATAGGGAGGCTAA
Found at i:3879 original size:66 final size:66
Alignment explanation
Indices: 3805--3931 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
3795 AATTATATGG
* *
3805 GAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAGGGAGGCTAACAAAATTTTATA
1 GAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGCTAACAAAATTTTATA
3870 T
66 T
* * ** * * * *
3871 GAAGGTTATCGAAATTTTATATTGTGGTTATCAAAATTTCATAAGAATGTTAACAAAATTT
1 GAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGCTAACAAAATTT
3932 CATAGGGACT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (66 bp):
GAAGGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAGAAGGCTAACAAAATTTTATA
T
Found at i:4099 original size:22 final size:22
Alignment explanation
Indices: 4074--4280 Score: 145
Period size: 22 Copynumber: 9.5 Consensus size: 22
4064 TTCTCATAGG
* **
4074 GTGGTTATCGAAATTTTATGGT
1 GTGGTTATCAAAATTTTACAGT
*
4096 GTGGTTATCAAAATTTTA-AGAG
1 GTGGTTATCAAAATTTTACAG-T
*
4118 GAGGTTATCAAAATTTTCACAGT
1 GTGGTTATCAAAATTTT-ACAGT
* *
4141 ATGGTT-TC-CAATTTTACAGT
1 GTGGTTATCAAAATTTTACAGT
* * *
4161 GTGATTATCAAAATTTCACACT
1 GTGGTTATCAAAATTTTACAGT
* * *
4183 GAGGTTATCAAAATTTCATAGT
1 GTGGTTATCAAAATTTTACAGT
*
4205 GTGGTTATC-AAATTTT-CATTGG
1 GTGGTTATCAAAATTTTACA--GT
* * * *
4227 GTGGTTATCGAAATTTCATAAT
1 GTGGTTATCAAAATTTTACAGT
** * *
4249 AAGGTTATTAAATTTTTACAGT
1 GTGGTTATCAAAATTTTACAGT
4271 GTGGTTATCA
1 GTGGTTATCA
4281 CGTTGGAGCA
Statistics
Matches: 140, Mismatches: 36, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
20 10 0.07
21 15 0.11
22 101 0.72
23 11 0.08
24 3 0.02
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (22 bp):
GTGGTTATCAAAATTTTACAGT
Found at i:4262 original size:65 final size:66
Alignment explanation
Indices: 4074--4280 Score: 203
Period size: 66 Copynumber: 3.2 Consensus size: 66
4064 TTCTCATAGG
*
4074 GTGGTTATCGAAATTTT-ATGGTGTGGTTATCAAAATTT--TAAGAGGAGGTTATCAAAATTTTC
1 GTGGTTATC-AAATTTTCATGG-GTGGTTATCAAAATTTCATAATA--AGGTTATCAAAATTTTC
4136 ACAGT
62 ACAGT
* * * * * * * *
4141 ATGGTT-TCCAATTTTACA-GTGTGATTATCAAAATTTCACACTGAGGTTATCAAAA-TTTCATA
1 GTGGTTATCAAATTTT-CATGGGTGGTTATCAAAATTTCATAATAAGGTTATCAAAATTTTCACA
4203 GT
65 GT
* * *
4205 GTGGTTATCAAATTTTCATTGGGTGGTTATCGAAATTTCATAATAAGGTTAT-TAAATTTTTACA
1 GTGGTTATCAAATTTTCA-TGGGTGGTTATCAAAATTTCATAATAAGGTTATCAAAATTTTCACA
4269 GT
65 GT
4271 GTGGTTATCA
1 GTGGTTATCA
4281 CGTTGGAGCA
Statistics
Matches: 112, Mismatches: 20, Indels: 17
0.75 0.13 0.11
Matches are distributed among these distances:
64 15 0.13
65 44 0.39
66 46 0.41
67 7 0.06
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (66 bp):
GTGGTTATCAAATTTTCATGGGTGGTTATCAAAATTTCATAATAAGGTTATCAAAATTTTCACAG
T
Found at i:5806 original size:2 final size:2
Alignment explanation
Indices: 5799--5832 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5789 AGTGAGAGGG
5799 AT 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 AT
5833 GTATGGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.