Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020293.1 Corchorus olitorius cultivar O-4 contig20326, 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: 10503
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:2354 original size:28 final size:29
Alignment explanation
Indices: 2290--2366 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
2280 TGTAAAGGCA
*
2290 TAAAATTACCGTTTTACCCTAAGAATGAG
1 TAAAATTACCGTTTTACCCTTAGAATGAG
*
2319 T-AAGTTACCGTTTTACCCTTAGAA-G-G
1 TAAAATTACCGTTTTACCCTTAGAATGAG
* *
2345 TTAAATTTACAGTTTTACCCTT
1 -TAAAATTACCGTTTTACCCTT
2367 TTAACCTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 38 0.90
29 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (29 bp):
TAAAATTACCGTTTTACCCTTAGAATGAG
Found at i:2917 original size:37 final size:37
Alignment explanation
Indices: 2867--2951 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
2857 CCCGTTGAGG
* *
2867 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
2904 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
*
2941 AAAATATTTTA
1 AAAATGTTTTA
2952 ATAAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (37 bp):
AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
Found at i:5056 original size:3 final size:3
Alignment explanation
Indices: 5048--5074 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5038 AGATGAGGTG
5048 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
5075 AAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5229 original size:10 final size:10
Alignment explanation
Indices: 5190--5241 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
5180 GCCCTAGCCC
5190 AAAGAAAAAA
1 AAAGAAAAAA
*
5200 AAACAAAAAA
1 AAAGAAAAAA
5210 AAATGAAATAAA
1 AAA-GAAA-AAA
*
5222 AAAGAATAAGA
1 AAAGAA-AAAA
*
5233 AAGGAAAAA
1 AAAGAAAAA
5242 GGAAGAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 14 0.41
11 13 0.38
12 7 0.21
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:6324 original size:28 final size:29
Alignment explanation
Indices: 6260--6336 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
6250 TGTAAAGGCA
*
6260 TAAAATTACCGTTTTACCCTAAGAATGAG
1 TAAAATTACCGTTTTACCCTTAGAATGAG
*
6289 T-AAGTTACCGTTTTACCCTTAGAA-G-G
1 TAAAATTACCGTTTTACCCTTAGAATGAG
* *
6315 TTAAATTTACAGTTTTACCCTT
1 -TAAAATTACCGTTTTACCCTT
6337 TTAACCTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 38 0.90
29 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (29 bp):
TAAAATTACCGTTTTACCCTTAGAATGAG
Found at i:6886 original size:37 final size:37
Alignment explanation
Indices: 6836--6920 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
6826 CCCGTTGAGG
* *
6836 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
6873 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
*
6910 AAAATATTTTA
1 AAAATGTTTTA
6921 ATAAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (37 bp):
AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
Found at i:8923 original size:6 final size:6
Alignment explanation
Indices: 8905--8964 Score: 102
Period size: 6 Copynumber: 9.7 Consensus size: 6
8895 GTTTAGACTT
8905 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATAG TATATAG
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG -ATATAG
8955 ATATAG ATAT
1 ATATAG ATAT
8965 GTAACCTTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
6 40 0.77
7 12 0.23
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:10143 original size:39 final size:40
Alignment explanation
Indices: 10087--10167 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
10077 TTTAATTCCT
10087 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
10127 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
10166 AT
1 AT
10168 TTTAAGGTAT
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
Done.