Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000165.1 Corchorus olitorius cultivar O-4 contig00165, 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: 18063
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:3107 original size:13 final size:13
Alignment explanation
Indices: 3091--3124 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3081 TTGCATGCTT
3091 AATTTGAGGGGAA
1 AATTTGAGGGGAA
*
3104 AATTTGAGTGGAA
1 AATTTGAGGGGAA
*
3117 GATTTGAG
1 AATTTGAG
3125 AGAGAGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (13 bp):
AATTTGAGGGGAA
Found at i:3896 original size:28 final size:28
Alignment explanation
Indices: 3856--3920 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
3846 GTAAATTGAT
3856 CGGGTATCCCAGATACCCTTTTGCAGAG
1 CGGGTATCCCAGATACCCTTTTGCAGAG
*
3884 CGGGTATCCCAGATGCCCTTTTGCAGAG
1 CGGGTATCCCAGATACCCTTTTGCAGAG
*
3912 TGGGTATCC
1 CGGGTATCC
3921 TGATAAGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (28 bp):
CGGGTATCCCAGATACCCTTTTGCAGAG
Found at i:4547 original size:2 final size:2
Alignment explanation
Indices: 4540--4569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4530 TTGTATTTAT
4540 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
4570 GTCCTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5000 original size:16 final size:15
Alignment explanation
Indices: 4981--5037 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
4971 GACTTTTCCA
4981 GGTTCGGGCTTAGTCG
1 GGTTCGGG-TTAGTCG
**
4997 GGTTCGGGTATTTTCG
1 GGTTCGGGT-TAGTCG
*
5013 GGCTCGGGTTATGTCG
1 GGTTCGGGTTA-GTCG
5029 GGTTCGGGT
1 GGTTCGGGT
5038 ATTTTCGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 2 0.06
16 31 0.94
ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35
Consensus pattern (15 bp):
GGTTCGGGTTAGTCG
Found at i:5020 original size:32 final size:32
Alignment explanation
Indices: 4984--5045 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
4974 TTTTCCAGGT
4984 TCGGGCTTA-GTCGGGTTCGGGTATTTTCGGGC
1 TCGGG-TTATGTCGGGTTCGGGTATTTTCGGGC
5016 TCGGGTTATGTCGGGTTCGGGTATTTTCGG
1 TCGGGTTATGTCGGGTTCGGGTATTTTCGG
5046 TTTCGATCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.06, C:0.16, G:0.40, T:0.37
Consensus pattern (32 bp):
TCGGGTTATGTCGGGTTCGGGTATTTTCGGGC
Found at i:5045 original size:16 final size:16
Alignment explanation
Indices: 4994--5050 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
4984 TCGGGCTTAG
4994 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTT
* *
5010 TCGGGCTCGGGT-TATG
1 TCGGGTTCGGGTAT-TT
5026 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTT
*
5042 TCGGTTTCG
1 TCGGGTTCG
5051 ATCTCGGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.39, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTATTT
Found at i:5160 original size:3 final size:3
Alignment explanation
Indices: 5152--5186 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5142 AGTAATAGTA
5152 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5187 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5191 original size:2 final size:2
Alignment explanation
Indices: 5184--5217 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5174 TTATTATTAT
5184 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
5218 CTAAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7087 original size:27 final size:27
Alignment explanation
Indices: 7034--7087 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
7024 AATTTAATCA
*
7034 AATCCAAATTTATGTAATAGTACGTTG
1 AATCCAAATTTATGTAATACTACGTTG
*
7061 AATCCAAATTTATGTAATACTATGTTG
1 AATCCAAATTTATGTAATACTACGTTG
7088 CTAGGTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (27 bp):
AATCCAAATTTATGTAATACTACGTTG
Found at i:7270 original size:5 final size:5
Alignment explanation
Indices: 7260--7307 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
7250 TATAGATAAT
*
7260 ATATA ATATA ATAATA ATATA ATATA ACATA ATTATCA ATAT- ATATA
1 ATATA ATATA AT-ATA ATATA ATATA ATATA A-TAT-A ATATA ATATA
7307 A
1 A
7308 AGATTGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 21 0.57
6 10 0.27
7 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:7286 original size:21 final size:21
Alignment explanation
Indices: 7258--7307 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
7248 TTTATAGATA
*
7258 ATATATAATATAATAAT-AAT
1 ATATATAACATAATAATCAAT
*
7278 ATAATATAACATAATTATCAAT
1 AT-ATATAACATAATAATCAAT
7300 ATATATAA
1 ATATATAA
7308 AGATTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATAACATAATAATCAAT
Found at i:7292 original size:18 final size:15
Alignment explanation
Indices: 7250--7286 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
7240 TAGATAAGTT
7250 TATAGATAATATATAA
1 TATA-ATAATATATAA
7266 TATAATAATAATATAA
1 TATAATAAT-ATATAA
7282 TATAA
1 TATAA
7287 CATAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TATAATAATATATAA
Found at i:14117 original size:20 final size:20
Alignment explanation
Indices: 14092--14132 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
14082 GAGGTGAATT
14092 AGGCGGATAGATTATAAGGC
1 AGGCGGATAGATTATAAGGC
14112 AGGCGGATAGATTATAAGGC
1 AGGCGGATAGATTATAAGGC
14132 A
1 A
14133 AACCTGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.34, T:0.20
Consensus pattern (20 bp):
AGGCGGATAGATTATAAGGC
Done.