Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018329.1 Corchorus olitorius cultivar O-4 contig18362, 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: 15713
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:3332 original size:12 final size:12
Alignment explanation
Indices: 3315--3345 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3305 TGCAATTTTC
3315 AAAAAAAAAGAA
1 AAAAAAAAAGAA
3327 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
3339 AAGAAAA
1 AAAAAAA
3346 GAAAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:3340 original size:17 final size:17
Alignment explanation
Indices: 3315--3354 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3305 TGCAATTTTC
3315 AAAAA-AAAAGAAAAAA
1 AAAAAGAAAAGAAAAAA
*
3331 AAAAAGAAAAGAAAAGA
1 AAAAAGAAAAGAAAAAA
3348 AAAAAGA
1 AAAAAGA
3355 GAACAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAA
Found at i:3354 original size:12 final size:11
Alignment explanation
Indices: 3315--3352 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3305 TGCAATTTTC
3315 AAAAAAAAAGA
1 AAAAAAAAAGA
3326 AAAAAAAAA-A
1 AAAAAAAAAGA
*
3336 GAAAAGAAAAGA
1 -AAAAAAAAAGA
3348 AAAAA
1 AAAAA
3353 GAGAACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:5036 original size:6 final size:6
Alignment explanation
Indices: 5018--5062 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
5008 AATAATATCT
* * *
5018 GAAAAA AAAAAA GATAAA GAAAAA GAAAAA G-AAAA GGAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
5063 GATATAGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:5042 original size:12 final size:11
Alignment explanation
Indices: 5020--5062 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5010 TAATATCTGA
*
5020 AAAAAAAAAAG
1 AAAAAGAAAAG
*
5031 ATAAAGAAAAAG
1 AAAAAG-AAAAG
5043 AAAAAGAAAAG
1 AAAAAGAAAAG
*
5054 GAAAAGAAA
1 AAAAAGAAA
5063 GATATAGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:5046 original size:17 final size:17
Alignment explanation
Indices: 5020--5066 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5010 TAATATCTGA
*
5020 AAAAAAAAAAGATAAAG
1 AAAAAGAAAAGATAAAG
5037 AAAAAGAAAAAGA-AAAG
1 AAAAAG-AAAAGATAAAG
*
5054 GAAAAG-AAAGATA
1 AAAAAGAAAAGATA
5067 TAGCAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 14 0.54
18 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (17 bp):
AAAAAGAAAAGATAAAG
Found at i:5366 original size:20 final size:20
Alignment explanation
Indices: 5341--5380 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5331 AATTACAAAC
5341 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
5361 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
5381 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:7160 original size:21 final size:21
Alignment explanation
Indices: 7134--7175 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7124 AAAGTAGGTA
7134 GTTTATTAAGGTAAATTGCTT
1 GTTTATTAAGGTAAATTGCTT
7155 GTTTATTAAGGTAAATTGCTT
1 GTTTATTAAGGTAAATTGCTT
7176 ATTTTGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48
Consensus pattern (21 bp):
GTTTATTAAGGTAAATTGCTT
Found at i:10979 original size:3 final size:3
Alignment explanation
Indices: 10973--11036 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
10963 TTTCCCTAGT
* * *
10973 GAA GAA GATA TGAG GAA GAG GAA GAA GAA GATA TGAA GAA GAG GAA GAA
1 GAA GAA GA-A -GAA GAA GAA GAA GAA GAA GA-A -GAA GAA GAA GAA GAA
*
11022 GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA
11037 AGATTGAAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 42 0.86
4 3 0.06
5 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:11003 original size:23 final size:23
Alignment explanation
Indices: 10973--11026 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
10963 TTTCCCTAGT
*
10973 GAAGAAGATATGAGGAAGAGGAA
1 GAAGAAGATATGAAGAAGAGGAA
10996 GAAGAAGATATGAAGAAGAGGAA
1 GAAGAAGATATGAAGAAGAGGAA
11019 GAAGAAGA
1 GAAGAAGA
11027 AAAAGAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (23 bp):
GAAGAAGATATGAAGAAGAGGAA
Found at i:15679 original size:2 final size:2
Alignment explanation
Indices: 15672--15713 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15662 TAAGTTGATT
15672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.