Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023298.1 Corchorus olitorius cultivar O-4 contig23331, 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: 34666
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:225 original size:2 final size:2
Alignment explanation
Indices: 218--257 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
208 TGTGTAAGTA
218 AT AT AT 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 AT AT AT
258 GCCGCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1972 original size:13 final size:13
Alignment explanation
Indices: 1954--1983 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1944 GGGAGTATTG
*
1954 TATAATAATATAA
1 TATAATAAAATAA
1967 TATAATAAAATAA
1 TATAATAAAATAA
1980 TATA
1 TATA
1984 TATAGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAATAAAATAA
Found at i:7888 original size:2 final size:2
Alignment explanation
Indices: 7881--7909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7871 ATTTATTGCA
7881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7910 CTAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11949 original size:26 final size:26
Alignment explanation
Indices: 11913--11992 Score: 133
Period size: 26 Copynumber: 3.1 Consensus size: 26
11903 TTTAAAATGC
11913 ATGTAAAAAATAACTAGTAGAATACT
1 ATGTAAAAAATAACTAGTAGAATACT
11939 ATGTAAAAAATAACTAGTAGAATACT
1 ATGTAAAAAATAACTAGTAGAATACT
* * *
11965 ATGTCAAAAATAATTAGTAGAATGCT
1 ATGTAAAAAATAACTAGTAGAATACT
11991 AT
1 AT
11993 ATATTTTGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (26 bp):
ATGTAAAAAATAACTAGTAGAATACT
Found at i:20487 original size:64 final size:64
Alignment explanation
Indices: 20414--20535 Score: 244
Period size: 64 Copynumber: 1.9 Consensus size: 64
20404 ACTTGATAGA
20414 ATAGTTTATAAAACTATAAATTGTGGTTGAATACTATTGGATCACAATGGGTACATGTTTTGAT
1 ATAGTTTATAAAACTATAAATTGTGGTTGAATACTATTGGATCACAATGGGTACATGTTTTGAT
20478 ATAGTTTATAAAACTATAAATTGTGGTTGAATACTATTGGATCACAATGGGTACATGT
1 ATAGTTTATAAAACTATAAATTGTGGTTGAATACTATTGGATCACAATGGGTACATGT
20536 GAATACATCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (64 bp):
ATAGTTTATAAAACTATAAATTGTGGTTGAATACTATTGGATCACAATGGGTACATGTTTTGAT
Found at i:26343 original size:42 final size:43
Alignment explanation
Indices: 26292--26385 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
26282 AGTGCATTAT
*
26292 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
26333 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
26378 CTAATATT
1 CTAATATT
26386 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:29267 original size:41 final size:41
Alignment explanation
Indices: 29222--29314 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
29212 TCCTCCATTG
*
29222 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATAGTTTTTAAAGGATTTATTT
*
29263 TTGAAGGATATTTAAGAATGTAGTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATAGTTTTTAAAGGATTTATTT
*
29304 TTGAAAGATAT
1 TTGAAGGATAT
29315 ATTATGATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (41 bp):
TTGAAGGATATTTAAGAATATAGTTTTTAAAGGATTTATTT
Found at i:29310 original size:16 final size:15
Alignment explanation
Indices: 29245--29310 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
29235 AAGAATATAT
29245 TTTTTAAAGGATTTA
1 TTTTTAAAGGATTTA
*
29260 TTTTTGAAGGA--TA
1 TTTTTAAAGGATTTA
* *
29273 --TTT-AAGAATGTA
1 TTTTTAAAGGATTTA
29285 GTTTTTAAAGGATTTA
1 -TTTTTAAAGGATTTA
29301 TTTTTGAAAG
1 TTTTT-AAAG
29311 ATATATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
10 4 0.10
11 3 0.08
12 2 0.05
13 2 0.05
15 18 0.45
16 11 0.28
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
TTTTTAAAGGATTTA
Found at i:30833 original size:15 final size:15
Alignment explanation
Indices: 30815--30887 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
30805 AAGAATATAT
30815 TTTTTAAAGGATTTA
1 TTTTTAAAGGATTTA
30830 TTTTTGAAA-GA--TA
1 TTTTT-AAAGGATTTA
* *
30843 --TTT-AAGAATGTA
1 TTTTTAAAGGATTTA
30855 TTGTTTAAAGGATTTA
1 TT-TTTAAAGGATTTA
* *
30871 TTTTTTAAGGATATA
1 TTTTTAAAGGATTTA
30886 TT
1 TT
30888 ATGATGATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 16
0.68 0.08 0.24
Matches are distributed among these distances:
9 2 0.04
10 1 0.02
11 3 0.07
12 2 0.04
13 2 0.04
15 23 0.51
16 12 0.27
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (15 bp):
TTTTTAAAGGATTTA
Found at i:30833 original size:16 final size:16
Alignment explanation
Indices: 30812--30887 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
30802 ATTAAGAATA
30812 TATTTTTTAAAGGATT
1 TATTTTTTAAAGGATT
*
30828 TATTTTTGAAA-GA--
1 TATTTTTTAAAGGATT
* *
30841 TA---TTT-AAGAATG
1 TATTTTTTAAAGGATT
*
30853 TATTGTTTAAAGGATT
1 TATTTTTTAAAGGATT
*
30869 TATTTTTT-AAGGATA
1 TATTTTTTAAAGGATT
30884 TATT
1 TATT
30888 ATGATGATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 15
0.68 0.10 0.22
Matches are distributed among these distances:
9 2 0.04
10 3 0.07
12 2 0.04
13 2 0.04
15 15 0.33
16 22 0.48
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
TATTTTTTAAAGGATT
Found at i:30862 original size:41 final size:41
Alignment explanation
Indices: 30803--30884 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
30793 TGTTGAAGGA
*
30803 TTAAGAATATATTTTTTAAAGGATTTATTTTTGAAAGATAT
1 TTAAGAATATATTGTTTAAAGGATTTATTTTTGAAAGATAT
* * *
30844 TTAAGAATGTATTGTTTAAAGGATTTATTTTTTAAGGATAT
1 TTAAGAATATATTGTTTAAAGGATTTATTTTTGAAAGATAT
30885 ATTATGATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (41 bp):
TTAAGAATATATTGTTTAAAGGATTTATTTTTGAAAGATAT
Found at i:33209 original size:41 final size:41
Alignment explanation
Indices: 33152--33230 Score: 142
Period size: 41 Copynumber: 1.9 Consensus size: 41
33142 ATAACTAGGA
33152 GCTAAACCTGGATTTAATTT-TTTACCTTAATTATTAGGGGG
1 GCTAAACCTGGATTTAATTTATTT-CCTTAATTATTAGGGGG
33193 GCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
1 GCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
33231 AGGGTCAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 34 0.92
42 3 0.08
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (41 bp):
GCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGGGGG
Found at i:33247 original size:13 final size:13
Alignment explanation
Indices: 33229--33265 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
33219 TTAATTATTA
*
33229 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
33242 GGAGGGACAAATT
1 GGAGGGTCAAATT
33255 GGAGGGTCAAA
1 GGAGGGTCAAA
33266 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:34262 original size:3 final size:3
Alignment explanation
Indices: 34248--34277 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
34238 GGAGTAACAA
*
34248 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34278 CATCATCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34590 original size:14 final size:15
Alignment explanation
Indices: 34568--34609 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
34558 GCTTTTTTGA
34568 TTGAAAAATATATTT
1 TTGAAAAATATATTT
*
34583 TT-AAAAATATGTTT
1 TTGAAAAATATATTT
*
34597 TTGAAAAAAATAT
1 TTGAAAAATATAT
34610 ATTATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TTGAAAAATATATTT
Done.