Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013650.1 Corchorus olitorius cultivar O-4 contig13683, 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: 75054
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:13095 original size:18 final size:16
Alignment explanation
Indices: 13072--13105 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
13062 TTTAGATTTT
13072 AATTATTGAAAATAATTA
1 AATTATT-AAAA-AATTA
13090 AATTATTAAAAAATTA
1 AATTATTAAAAAATTA
13106 TAAATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTATTAAAAAATTA
Found at i:17839 original size:28 final size:27
Alignment explanation
Indices: 17781--17842 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
17771 TCTTCCAGCC
* *
17781 TAAATAAAAAATAATAATTAATTCTAG
1 TAAATAAAAAATAATAAGTAATTCTAA
*
17808 TAAATTAAAAAT-ATAAGTAATTACATAA
1 TAAATAAAAAATAATAAGTAATT-C-TAA
17836 TAAATAA
1 TAAATAA
17843 TTATAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.31
27 12 0.41
28 8 0.28
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
TAAATAAAAAATAATAAGTAATTCTAA
Found at i:17854 original size:17 final size:17
Alignment explanation
Indices: 17834--17895 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
17824 GTAATTACAT
17834 AATAAATAATTATAGTA
1 AATAAATAATTATAGTA
*
17851 AATAATTAATTATAGTCA
1 AATAAATAATTATAGT-A
* * *
17869 AATAATTAAATA-ACTA
1 AATAAATAATTATAGTA
17885 AATAAA-AATTA
1 AATAAATAATTA
17896 ATAATTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
15 4 0.10
16 6 0.15
17 17 0.44
18 12 0.31
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAATAATTATAGTA
Found at i:18251 original size:19 final size:19
Alignment explanation
Indices: 18215--18286 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
18205 CATGATGTTC
18215 TTGAAGAAGTTTAT-AGAGT
1 TTGAAGAAGTTT-TGAGAGT
18234 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTTGAGAGT
*
18253 TAGAA-AA----TGA-AGT
1 TTGAAGAAGTTTTGAGAGT
*
18266 TTGAAGGAGTTTTGAGAGT
1 TTGAAGAAGTTTTGAGAGT
18285 TT
1 TT
18287 AAATATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
13 7 0.16
14 4 0.09
18 6 0.14
19 26 0.60
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTTGAGAGT
Found at i:21561 original size:17 final size:17
Alignment explanation
Indices: 21539--21583 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
21529 ATTCCAAAAG
*
21539 CAGGAATCGCGCAACAA
1 CAGGAATCACGCAACAA
**
21556 CAGGAATCACGTGACAA
1 CAGGAATCACGCAACAA
*
21573 CAGGATTCACG
1 CAGGAATCACG
21584 GAAGGACCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.27, G:0.24, T:0.11
Consensus pattern (17 bp):
CAGGAATCACGCAACAA
Found at i:23435 original size:12 final size:12
Alignment explanation
Indices: 23418--23459 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
23408 AAACAATGGT
23418 AATGATGAAGGA
1 AATGATGAAGGA
*
23430 AATGATGAAGGG
1 AATGATGAAGGA
* *
23442 CATGATGAAGGT
1 AATGATGAAGGA
23454 AATGAT
1 AATGAT
23460 TAAGTGCCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.21
Consensus pattern (12 bp):
AATGATGAAGGA
Found at i:23767 original size:27 final size:27
Alignment explanation
Indices: 23725--23776 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
23715 GTTGCTGGGA
23725 CTTCAAATGTCAGGGAT-AAGGCTGGAC
1 CTTCAAATGTCAGGGATGAA-GCTGGAC
**
23752 CTTCAAATGTTGGGGATGAAGCTGG
1 CTTCAAATGTCAGGGATGAAGCTGG
23777 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (27 bp):
CTTCAAATGTCAGGGATGAAGCTGGAC
Found at i:30763 original size:2 final size:2
Alignment explanation
Indices: 30756--30782 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30746 ACATAAAATA
30756 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
30783 AACATTATCC
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:35030 original size:2 final size:2
Alignment explanation
Indices: 35023--35056 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
35013 AGTTAGGATC
35023 AT AT AT AT AT AT -T 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 AT AT AT AT A
35057 CTAAATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48136 original size:1 final size:1
Alignment explanation
Indices: 48130--48154 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
48120 TTAGCTTCTG
48130 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
48155 AGTGATCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:48562 original size:3 final size:3
Alignment explanation
Indices: 48541--48578 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
48531 ATGATAAAGG
* *
48541 TAT TAT CAT TA- TCT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48579 CACCTATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:63995 original size:5 final size:5
Alignment explanation
Indices: 63987--64021 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
63977 TTTTTCCATC
*
63987 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTT TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
64022 AGAAATGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:64301 original size:5 final size:6
Alignment explanation
Indices: 64287--64316 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
64277 TAATTTTTTT
64287 AAAATA AAAATA AAAATA AAAATA TAAAAT
1 AAAATA AAAATA AAAATA AAAATA -AAAAT
64317 TTGCAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:70062 original size:9 final size:9
Alignment explanation
Indices: 70050--70080 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
70040 TCTTCTTCTT
70050 TTTTTTTTA
1 TTTTTTTTA
70059 TTTTTTTTTA
1 -TTTTTTTTA
70069 TTTTTTTTA
1 TTTTTTTTA
70078 TTT
1 TTT
70081 ATCTTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:70064 original size:10 final size:10
Alignment explanation
Indices: 70049--70080 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
70039 TTCTTCTTCT
70049 TTTTTTTTTA
1 TTTTTTTTTA
70059 TTTTTTTTTA
1 TTTTTTTTTA
70069 -TTTTTTTTA
1 TTTTTTTTTA
70078 TTT
1 TTT
70081 ATCTTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:70087 original size:19 final size:19
Alignment explanation
Indices: 70050--70088 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
70040 TCTTCTTCTT
* *
70050 TTTTTTTTATTTTTTTTTA
1 TTTTTTTTATTTATCTTTA
70069 TTTTTTTTATTTATCTTTA
1 TTTTTTTTATTTATCTTTA
70088 T
1 T
70089 CTTTATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTATTTATCTTTA
Found at i:74074 original size:13 final size:13
Alignment explanation
Indices: 74056--74083 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
74046 TCAAAGGGTG
74056 TTTAACACACCTC
1 TTTAACACACCTC
74069 TTTAACACACCTC
1 TTTAACACACCTC
74082 TT
1 TT
74084 GAGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAACACACCTC
Done.