Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019708.1 Corchorus olitorius cultivar O-4 contig19741, 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: 10659
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:4464 original size:14 final size:15
Alignment explanation
Indices: 4445--4473 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4435 AAAGGAGGAG
4445 TTTT-GGTTTGGGTT
1 TTTTGGGTTTGGGTT
4459 TTTTGGGTTTGGGTT
1 TTTTGGGTTTGGGTT
4474 AGGCTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (15 bp):
TTTTGGGTTTGGGTT
Found at i:5087 original size:26 final size:26
Alignment explanation
Indices: 5052--5102 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5042 ATTTTTCTCC
*
5052 CCCTCGGTCAAATCCCTCATCTTTCT
1 CCCTCAGTCAAATCCCTCATCTTTCT
**
5078 CCCTCAGTCAAATCTTTCATCTTTC
1 CCCTCAGTCAAATCCCTCATCTTTC
5103 CTGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.39, G:0.06, T:0.37
Consensus pattern (26 bp):
CCCTCAGTCAAATCCCTCATCTTTCT
Found at i:5468 original size:31 final size:30
Alignment explanation
Indices: 5433--5495 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5423 ACTTAGATTG
* *
5433 ACATTAGAGTCTGAATTGAACTGATTTTGCA
1 ACATTAGAGACTG-ATTGAACCGATTTTGCA
* *
5464 ACATTAGGGACTGATTGAGCCGATTTTGCA
1 ACATTAGAGACTGATTGAACCGATTTTGCA
5494 AC
1 AC
5496 GCTAAGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (30 bp):
ACATTAGAGACTGATTGAACCGATTTTGCA
Found at i:5679 original size:15 final size:15
Alignment explanation
Indices: 5655--5687 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5645 TTGCTTACTC
5655 TTTTTCTTTT-CTTT
1 TTTTTCTTTTCCTTT
5669 TTTTTCTTTTTCCTTT
1 TTTTTC-TTTTCCTTT
5685 TTT
1 TTT
5688 AGGCCTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTCCTTT
Found at i:7966 original size:39 final size:39
Alignment explanation
Indices: 7912--8021 Score: 211
Period size: 39 Copynumber: 2.8 Consensus size: 39
7902 CAATCGCTGC
7912 TCTAATAATCTCATTTGTACACATTTGTACAGTACCTAA
1 TCTAATAATCTCATTTGTACACATTTGTACAGTACCTAA
7951 TCTAATAATCTCATTTGTACACATTTGTACAGTACCTAA
1 TCTAATAATCTCATTTGTACACATTTGTACAGTACCTAA
7990 TCTAATAATCTTCATTTGTACACATTTGTACA
1 TCTAATAATC-TCATTTGTACACATTTGTACA
8022 CATTTGTACA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
39 49 0.70
40 21 0.30
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (39 bp):
TCTAATAATCTCATTTGTACACATTTGTACAGTACCTAA
Found at i:8017 original size:10 final size:10
Alignment explanation
Indices: 8002--8031 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
7992 TAATAATCTT
8002 CATTTGTACA
1 CATTTGTACA
8012 CATTTGTACA
1 CATTTGTACA
8022 CATTTGTACA
1 CATTTGTACA
8032 GTACCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (10 bp):
CATTTGTACA
Found at i:8070 original size:50 final size:50
Alignment explanation
Indices: 7956--8126 Score: 161
Period size: 50 Copynumber: 3.3 Consensus size: 50
7946 CCTAATCTAA
* * * *
7956 TAATCTCATTTGTACACATTTGTACAGTACCTAATCTAATAATCTTCATTTG
1 TAATCTCATCTGTACACATTTGTACAGTACCTAATCTAAT-ATATACA-GTG
* *
8008 T-A-CACATTTGTACACATTTGTACAGTACCTAATCTAATATATACAGTG
1 TAATCTCATCTGTACACATTTGTACAGTACCTAATCTAATATATACAGTG
* *
8056 TAATCTCATCTGTACA-GTTACTAAACAG-ACAGTACCTAATCTAATATGTACAGTG
1 TAATCTCATCTGTACACATT--T-----GTACAGTACCTAATCTAATATATACAGTG
8111 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
8127 GTTACTAAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
48 3 0.03
49 8 0.08
50 45 0.44
51 2 0.02
52 1 0.01
55 42 0.41
56 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (50 bp):
TAATCTCATCTGTACACATTTGTACAGTACCTAATCTAATATATACAGTG
Found at i:8095 original size:55 final size:55
Alignment explanation
Indices: 8029--8138 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
8019 ACACATTTGT
8029 ACAGTACCTAATCTAATATATACAGTGTAATCTCATCTGTACAGTTACTAAACAG
1 ACAGTACCTAATCTAATATATACAGTGTAATCTCATCTGTACAGTTACTAAACAG
*
8084 ACAGTACCTAATCTAATATGTACAGTGTAATCTCATCTGTACAGTTACTAAACAG
1 ACAGTACCTAATCTAATATATACAGTGTAATCTCATCTGTACAGTTACTAAACAG
8139 TGTCAATCAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (55 bp):
ACAGTACCTAATCTAATATATACAGTGTAATCTCATCTGTACAGTTACTAAACAG
Found at i:8124 original size:19 final size:19
Alignment explanation
Indices: 8037--8128 Score: 66
Period size: 19 Copynumber: 4.9 Consensus size: 19
8027 GTACAGTACC
* *
8037 TAATCTAATATATACAGTG
1 TAATCTAATCTGTACAGTG
*
8056 TAATCTCATCTGTACAGT-
1 TAATCTAATCTGTACAGTG
* * *
8074 T-A-CTAAACAG-ACAGTACC
1 TAATCTAATCTGTACAGT--G
*
8092 TAATCTAATATGTACAGTG
1 TAATCTAATCTGTACAGTG
*
8111 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
8129 TACTAAACAG
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.09
16 5 0.09
17 1 0.02
18 2 0.04
19 32 0.58
20 5 0.09
21 5 0.09
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Done.