Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023842.1 Corchorus olitorius cultivar O-4 contig23875, 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: 30726
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:1820 original size:18 final size:19
Alignment explanation
Indices: 1781--1820 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1771 GTACTCCCGT
1781 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
1802 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
1820 T
1 T
1821 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:8069 original size:7 final size:7
Alignment explanation
Indices: 8057--8083 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
8047 GAGGGCATAC
8057 TCCCCAG
1 TCCCCAG
8064 TCCCCAG
1 TCCCCAG
8071 TCCCCAG
1 TCCCCAG
8078 TCCCCA
1 TCCCCA
8084 ACTTGGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.59, G:0.11, T:0.15
Consensus pattern (7 bp):
TCCCCAG
Found at i:14007 original size:21 final size:22
Alignment explanation
Indices: 13972--14015 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
13962 ATCACATGTC
13972 GAAATCTCTTTTTCCTTTAAAA
1 GAAATCTCTTTTTCCTTTAAAA
13994 GAAATCTC-TTTTCCTTTAAAA
1 GAAATCTCTTTTTCCTTTAAAA
14015 G
1 G
14016 TGTATCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (22 bp):
GAAATCTCTTTTTCCTTTAAAA
Found at i:19288 original size:31 final size:29
Alignment explanation
Indices: 19237--19300 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
19227 AATTTGAGCT
*
19237 TAAACCTTTAAATTGAACCAAATTGAGTC
1 TAAACCTTTAAAATGAACCAAATTGAGTC
* *
19266 TAAACCTTATTAAAATGTACCAACTTGAGTC
1 TAAACC-T-TTAAAATGAACCAAATTGAGTC
19297 TAAA
1 TAAA
19301 TTTGACTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
31 23 0.77
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (29 bp):
TAAACCTTTAAAATGAACCAAATTGAGTC
Found at i:28674 original size:4 final size:4
Alignment explanation
Indices: 28665--28691 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28655 CTTAAGCTCT
28665 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
28692 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29181 original size:40 final size:41
Alignment explanation
Indices: 29126--29203 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
29116 AAACCGAATT
29126 ACTTATCTTTGTACTCA-AAAGGTTAAAATTTCCTTTTGGA
1 ACTTATCTTTGTACTCAGAAAGGTTAAAATTTCCTTTTGGA
* *
29166 ACTTATCTTTGTACTCAGAGAGGTTAAATTTTCCTTTT
1 ACTTATCTTTGTACTCAGAAAGGTTAAAATTTCCTTTT
29204 TTTTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 17 0.49
41 18 0.51
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (41 bp):
ACTTATCTTTGTACTCAGAAAGGTTAAAATTTCCTTTTGGA
Found at i:29266 original size:45 final size:45
Alignment explanation
Indices: 29202--29290 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
29192 AATTTTCCTT
*
29202 TTTTTTTTTCAATCTCTCTAAATCCAATTGTGATATTGGATTCCA
1 TTTTTTTTTCAATCCCTCTAAATCCAATTGTGATATTGGATTCCA
*
29247 TTTTTTTTTCAATCCCTCTAGATCCAATTGTGATATTGGATTCC
1 TTTTTTTTTCAATCCCTCTAAATCCAATTGTGATATTGGATTCC
29291 GACTAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (45 bp):
TTTTTTTTTCAATCCCTCTAAATCCAATTGTGATATTGGATTCCA
Found at i:29659 original size:52 final size:52
Alignment explanation
Indices: 29597--29703 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
29587 GTCAGAACAA
*
29597 ATATAGAACTATTGATAGATGAAAAACACGATTGTGCCATGATACAACATCG
1 ATATAGAACTATTGATAAATGAAAAACACGATTGTGCCATGATACAACATCG
29649 ATATAGAACTATTGATAAATGAAAAACACGATTGTGCCATGATACAACATCG
1 ATATAGAACTATTGATAAATGAAAAACACGATTGTGCCATGATACAACATCG
29701 ATA
1 ATA
29704 GTTGGGTATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (52 bp):
ATATAGAACTATTGATAAATGAAAAACACGATTGTGCCATGATACAACATCG
Done.