Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020166.1 Corchorus olitorius cultivar O-4 contig20199, 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: 18341
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:158 original size:22 final size:22
Alignment explanation
Indices: 130--173 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
120 CAAAATCAAC
*
130 TAAAGAAAGCAATCAAAAAGAT
1 TAAAGAAAACAATCAAAAAGAT
* *
152 TAAAGAAAACAATTAACAAGAT
1 TAAAGAAAACAATCAAAAAGAT
174 AGCAGTGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (22 bp):
TAAAGAAAACAATCAAAAAGAT
Found at i:3949 original size:60 final size:60
Alignment explanation
Indices: 3856--3968 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
3846 GACACCAGGG
** * *
3856 CCTTATTTGAGTATTTTCGCATACATTAGGACCCTATTTAACTAAATTAAAAGCATGGAC
1 CCTTATTTGAACATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAGCATGGAC
* *
3916 CCTTATTTGAACATTTTCACATACGTTAGGACCCTATTTGACCAAATTAAAAG
1 CCTTATTTGAACATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAG
3969 TATGAGACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (60 bp):
CCTTATTTGAACATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAGCATGGAC
Found at i:3991 original size:60 final size:59
Alignment explanation
Indices: 3856--3991 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 59
3846 GACACCAGGG
* * * *
3856 CCTTATTTGAGTATTTTCGCATACATTAGGACCCTATTTAACTAAATTAAAAGCATGGA
1 CCTTAATTGAGCATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAGCATGGA
* * * * *
3915 CCCTTATTTGAACATTTTCACATACGTTAGGACCCTATTTGACCAAATTAAAAGTATGAGA
1 -CCTTAATTGAGCATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAGCATG-GA
3976 -CTTAAATTGAGCATTT
1 CCTT-AATTGAGCATTT
3992 CAGTATTAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 60 0.92
61 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (59 bp):
CCTTAATTGAGCATTTTCACATACATTAGGACCCTATTTAACCAAATTAAAAGCATGGA
Found at i:6747 original size:21 final size:21
Alignment explanation
Indices: 6723--6763 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6713 GAAAAAGTGG
* *
6723 AAAAAGTGCTATAACGGCTAC
1 AAAAAGAGCTACAACGGCTAC
*
6744 AAAAAGAGCTCCAACGGCTA
1 AAAAAGAGCTACAACGGCTA
6764 GAAACTTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.15
Consensus pattern (21 bp):
AAAAAGAGCTACAACGGCTAC
Found at i:6922 original size:17 final size:17
Alignment explanation
Indices: 6896--6929 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6886 CCTACTAGTT
6896 TTGAGATAAAATTTGTA
1 TTGAGATAAAATTTGTA
*
6913 TTGAGCTAAAATTTGTA
1 TTGAGATAAAATTTGTA
6930 CTTGGGATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGAGATAAAATTTGTA
Found at i:11175 original size:180 final size:180
Alignment explanation
Indices: 10857--11221 Score: 660
Period size: 180 Copynumber: 2.0 Consensus size: 180
10847 AGGAACAAAC
*
10857 AAAAAATCTTGAACATAAAGACCCCCTTCTCTACGGCCTATCCCAATCTGCTTCCATGTATGTCG
1 AAAAAATCTAGAACATAAAGACCCCCTTCTCTACGGCCTATCCCAATCTGCTTCCATGTATGTCG
*
10922 ATCCTGTACAACACAAAAAATATCTGAAAACCAAATATCACAACCAAAATCAGCATGTTGTCCAA
66 ATCCTGTACAACACAAAAAATATCTGAAAACCAAATATCACAACCAAAATCAGCAAGTTGTCCAA
10987 TCGAAAGAAGGTTAACAGATAATTGGAGTGCATATAAAACATTAGGAACA
131 TCGAAAGAAGGTTAACAGATAATTGGAGTGCATATAAAACATTAGGAACA
**
11037 AAAAAATCTAGAACATAAAGACGTCCTTCTCTACGGCCTATCCCAATCTGCTTCCATGTATGTCG
1 AAAAAATCTAGAACATAAAGACCCCCTTCTCTACGGCCTATCCCAATCTGCTTCCATGTATGTCG
*
11102 ATCCTGTACAACACAAAAAATATCTGAAAACCAAATATCACAACCAAAATCAGCAAGTTGTTCAA
66 ATCCTGTACAACACAAAAAATATCTGAAAACCAAATATCACAACCAAAATCAGCAAGTTGTCCAA
*
11167 -CTGAAAGAAGGTTAACAGATAATTGGAGTGCATATAAAACATTATGAACA
131 TC-GAAAGAAGGTTAACAGATAATTGGAGTGCATATAAAACATTAGGAACA
11217 AAAAA
1 AAAAA
11222 TTTTCCAAGG
Statistics
Matches: 178, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
179 1 0.01
180 177 0.99
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (180 bp):
AAAAAATCTAGAACATAAAGACCCCCTTCTCTACGGCCTATCCCAATCTGCTTCCATGTATGTCG
ATCCTGTACAACACAAAAAATATCTGAAAACCAAATATCACAACCAAAATCAGCAAGTTGTCCAA
TCGAAAGAAGGTTAACAGATAATTGGAGTGCATATAAAACATTAGGAACA
Found at i:15454 original size:25 final size:25
Alignment explanation
Indices: 15420--15472 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
15410 GTAGATCTTA
15420 TAATTGAAGAGGTAATTTTGCAAAG
1 TAATTGAAGAGGTAATTTTGCAAAG
*
15445 TAATTGAAGAGGTAATTTTGTAAAG
1 TAATTGAAGAGGTAATTTTGCAAAG
15470 TAA
1 TAA
15473 AATAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (25 bp):
TAATTGAAGAGGTAATTTTGCAAAG
Found at i:17911 original size:13 final size:13
Alignment explanation
Indices: 17895--17920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17885 ATAATAATGA
17895 ATTATAACACATT
1 ATTATAACACATT
17908 ATTATAACACATT
1 ATTATAACACATT
17921 TGACACTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATAACACATT
Done.