Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012812.1 Corchorus olitorius cultivar O-4 contig12845, 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: 9371
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:843 original size:11 final size:12
Alignment explanation
Indices: 814--866 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 12
804 TCATGCACCC
814 AAAACAATTTAATT
1 AAAAC-ATTTAA-T
828 AAAACATTT-AT
1 AAAACATTTAAT
839 AAAACAATTTAAT
1 AAAAC-ATTTAAT
*
852 AAAACA-GTAAT
1 AAAACATTTAAT
863 AAAA
1 AAAA
867 TAGTTCCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 14 0.39
12 6 0.17
13 11 0.31
14 5 0.14
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (12 bp):
AAAACATTTAAT
Found at i:853 original size:13 final size:13
Alignment explanation
Indices: 814--857 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
804 TCATGCACCC
814 AAAACAATTTAATT
1 AAAACAATTTAA-T
828 AAAAC-ATTT-AT
1 AAAACAATTTAAT
839 AAAACAATTTAAT
1 AAAACAATTTAAT
852 AAAACA
1 AAAACA
858 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 5 0.18
13 12 0.43
14 5 0.18
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:864 original size:24 final size:25
Alignment explanation
Indices: 814--866 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
804 TCATGCACCC
* *
814 AAAACAATTTAATTAAAACATTTAT
1 AAAACAATTTAATTAAAACAGTAAT
839 AAAACAATTTAA-TAAAACAGTAAT
1 AAAACAATTTAATTAAAACAGTAAT
863 AAAA
1 AAAA
867 TAGTTCCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAACAATTTAATTAAAACAGTAAT
Found at i:6413 original size:42 final size:42
Alignment explanation
Indices: 6366--6446 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
6356 TAAGGATCAG
6366 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* * *
6408 GATTTGAGTTGAGTATTTCTTATTTTGCAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
6447 AAGACTTAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:7190 original size:13 final size:13
Alignment explanation
Indices: 7172--7208 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
7162 ATCCACTTGT
*
7172 AAGTATTAATTTG
1 AAGTATTAATATG
7185 AAGTATTAATATG
1 AAGTATTAATATG
7198 AAGTATTAATA
1 AAGTATTAATA
7209 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (13 bp):
AAGTATTAATATG
Found at i:8052 original size:199 final size:198
Alignment explanation
Indices: 7634--8188 Score: 821
Period size: 198 Copynumber: 2.8 Consensus size: 198
7624 AATGAATATT
* **
7634 TATAAGCGGGTTAAGGAGTTGACACATACATCATTTCATAATTAATTAAATATTTAATATTAATA
1 TATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* * * *
7699 CATATTCCCTAAGCGGACACATGTCAACCCTTAAACTCGCG--CATGTAGTCTGCTAAACTCCAT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAAC-CCCGAACGTGTAGTCTGCTAAACT-CAC
* * *
7762 TGACGGTGTATTATATAATTTTTCTTATAAGATTATTATACAATACACTGTCATTGTAAATTTTG
129 TAACGGTGTATTGTATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTG
7827 GACTC
194 GACTC
* *
7832 CATAAGTGGGTTAAGAAGTTGACACATACCCCAGTTT-ATAATTAATTAAATATTTAATATTAAT
1 TATAAGCGGGTTAAGAAGTTGACACATACCCCA-TTTCATAATTAATTAAATATTTAATATTAAT
*
7896 ACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTGCTAAACTCTAC
65 ACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGTAGTCTGCTAAACTC-AC
* * *
7961 TAACGGTTTATTGTATAATTTTTCTTATGAGATTATTATACAATACACTGTTAGTGTAAATTTTG
129 TAACGGTGTATTGTATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTG
8026 GACTC
194 GACTC
* * *
8031 TATAAACGGGTTAATAAGTTGACACATA-CCCATTTCATAATTAATTAAATATTTAATACTAATA
1 TATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* * * *
8095 CATATTCCATAAGGAGACACATGTCAACCCTTAAACCCCAAACGTGTAGTCTGCTAAACTGCAGT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGTAGTCTGCTAAACT-CACT
*
8160 TACGGTGTATTGTATAATTTTTCTTATAA
130 AACGGTGTATTGTATAATTTTTCTTATAA
8189 TAAACTTACA
Statistics
Matches: 322, Mismatches: 29, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
197 6 0.02
198 207 0.64
199 109 0.34
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (198 bp):
TATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
CATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGAACGTGTAGTCTGCTAAACTCACTA
ACGGTGTATTGTATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGA
CTC
Done.