Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022412.1 Corchorus olitorius cultivar O-4 contig22445, 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: 29028
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1696 original size:2 final size:2
Alignment explanation
Indices: 1689--1715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1679 TAACAATACA
1689 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 A
1716 AATAAGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8587 original size:18 final size:18
Alignment explanation
Indices: 8566--8609 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
8556 GCCACCGCCT
8566 CCTCCACCTCCACCACCA
1 CCTCCACCTCCACCACCA
* **
8584 CCTCCGCCTCCGTCACCA
1 CCTCCACCTCCACCACCA
*
8602 CCACCACC
1 CCTCCACC
8610 ACCGCCAACC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.66, G:0.05, T:0.11
Consensus pattern (18 bp):
CCTCCACCTCCACCACCA
Found at i:8592 original size:27 final size:27
Alignment explanation
Indices: 8560--8612 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
8550 GCTGCTGCCA
*
8560 CCGCCTCC-TCCACCTCCACCACCACCT
1 CCGCCTCCGT-CACCACCACCACCACCT
8587 CCGCCTCCGTCACCACCACCACCACC
1 CCGCCTCCGTCACCACCACCACCACC
8613 GCCAACCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.66, G:0.06, T:0.11
Consensus pattern (27 bp):
CCGCCTCCGTCACCACCACCACCACCT
Found at i:8593 original size:24 final size:24
Alignment explanation
Indices: 8566--8615 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
8556 GCCACCGCCT
* *
8566 CCTCCACCTCCACCACCACCTCCG
1 CCTCCACCACCACCACCACCACCG
**
8590 CCTCCGTCACCACCACCACCACCG
1 CCTCCACCACCACCACCACCACCG
8614 CC
1 CC
8616 AACCTCGGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.66, G:0.06, T:0.10
Consensus pattern (24 bp):
CCTCCACCACCACCACCACCACCG
Found at i:11204 original size:19 final size:20
Alignment explanation
Indices: 11152--11209 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
11142 GCTGCTCTAA
*
11152 TAATCTCATATGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* * *
11173 TATTCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
11192 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
11210 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:23353 original size:13 final size:13
Alignment explanation
Indices: 23335--23359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23325 AAAGCATGCA
23335 GCAGTGAAAAATT
1 GCAGTGAAAAATT
23348 GCAGTGAAAAAT
1 GCAGTGAAAAAT
23360 AAACTTATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
GCAGTGAAAAATT
Found at i:23867 original size:8 final size:8
Alignment explanation
Indices: 23847--23908 Score: 92
Period size: 8 Copynumber: 7.9 Consensus size: 8
23837 GCTGTCACCA
23847 TACACACAT
1 TACACA-AT
23856 TACACAAT
1 TACACAAT
*
23864 TACACAAC
1 TACACAAT
23872 TACACAAT
1 TACACAAT
23880 TACACAAT
1 TACACAAT
23888 TACAC-AT
1 TACACAAT
23895 TACAC-AT
1 TACACAAT
23902 TACACAA
1 TACACAA
23909 CACTATCACC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
7 14 0.28
8 30 0.60
9 6 0.12
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (8 bp):
TACACAAT
Found at i:28118 original size:3 final size:3
Alignment explanation
Indices: 28105--28188 Score: 141
Period size: 3 Copynumber: 27.7 Consensus size: 3
28095 ACTTCAACCT
*
28105 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
28153 TAA TAA TAA TAA TAA TAA TAA TAAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
28189 GTGCTAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 73 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.