Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020917.1 Corchorus olitorius cultivar O-4 contig20950, 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: 20975
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:130 original size:51 final size:50
Alignment explanation
Indices: 29--130 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
19 GTTCTTCATA
* **
29 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCATACAGTGT
*
79 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-ATACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCATACA-GTGT
130 T
1 T
131 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCATACAGTGT
Found at i:4037 original size:13 final size:13
Alignment explanation
Indices: 4019--4043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4009 TGGTATTGTT
4019 TTGGAAAAATTAG
1 TTGGAAAAATTAG
4032 TTGGAAAAATTA
1 TTGGAAAAATTA
4044 AAGCATTACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
TTGGAAAAATTAG
Found at i:6009 original size:2 final size:2
Alignment explanation
Indices: 6002--6030 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5992 CAACAACTAG
6002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6031 GTGGTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15634 original size:21 final size:21
Alignment explanation
Indices: 15610--15677 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
15600 TTTAATGGTC
*
15610 AAACCCCAACATTTGATAGTG
1 AAACCCCAACGTTTGATAGTG
*
15631 AAACCCCAACGTTTGATTGTG
1 AAACCCCAACGTTTGATAGTG
* *
15652 AAACCCCAATGTTTGATAGTC
1 AAACCCCAACGTTTGATAGTG
15673 AAACC
1 AAACC
15678 ATGTTAAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
AAACCCCAACGTTTGATAGTG
Found at i:15639 original size:42 final size:42
Alignment explanation
Indices: 15593--15677 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
15583 ATTTCAGTCA
* *
15593 CCCAAATTTTAATGGTCAAACCCCAACATTTGATAGTGAAAC
1 CCCAAAGTTTAATGGTCAAACCCCAACATTTGATAGTCAAAC
* * * * **
15635 CCCAACGTTTGATTGTGAAACCCCAATGTTTGATAGTCAAAC
1 CCCAAAGTTTAATGGTCAAACCCCAACATTTGATAGTCAAAC
15677 C
1 C
15678 ATGTTAAATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
CCCAAAGTTTAATGGTCAAACCCCAACATTTGATAGTCAAAC
Found at i:15776 original size:21 final size:21
Alignment explanation
Indices: 15745--15864 Score: 168
Period size: 21 Copynumber: 5.7 Consensus size: 21
15735 TTGCCAAAAT
* *
15745 TTTGATGGTCAAACCTCAAAG
1 TTTGATAGTCAAACCCCAAAG
* *
15766 TTTAATAGTCAAACCCCAAAT
1 TTTGATAGTCAAACCCCAAAG
*
15787 TTTGATGGTCAAACCCCAAAG
1 TTTGATAGTCAAACCCCAAAG
*
15808 TTTGATTGTCAAACCCCAAAG
1 TTTGATAGTCAAACCCCAAAG
* *
15829 TTTGATGGTCAAACCCCAAAA
1 TTTGATAGTCAAACCCCAAAG
15850 TTTGATAGTCAAACC
1 TTTGATAGTCAAACC
15865 ATGTTAAACC
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (21 bp):
TTTGATAGTCAAACCCCAAAG
Found at i:15798 original size:42 final size:42
Alignment explanation
Indices: 15741--15864 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
15731 TTCTTTGCCA
* *
15741 AAATTTTGATGGTCAAACCTCAAAGTTTAATAGTCAAACCCC
1 AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCC
*
15783 AAATTTTGATGGTCAAACCCCAAAGTTTGATTGTCAAACCCC
1 AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCC
* *
15825 AAAGTTTGATGGTCAAACCCCAAAATTTGATAGTCAAACC
1 AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACC
15865 ATGTTAAACC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (42 bp):
AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCC
Found at i:15819 original size:63 final size:63
Alignment explanation
Indices: 15745--15864 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
15735 TTGCCAAAAT
* * *
15745 TTTGATGGTCAAACCTCAAAGTTTAATAGTCAAACCCCAAATTTTGATGGTCAAACCCCAAAG
1 TTTGATGGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAATTTGATAGTCAAACCCCAAAG
* * *
15808 TTTGATTGTCAAACCCCAAAGTTTGATGGTCAAACCCCAAAATTTGATAGTCAAACC
1 TTTGATGGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAATTTGATAGTCAAACC
15865 ATGTTAAACC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (63 bp):
TTTGATGGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAATTTGATAGTCAAACCCCAAAG
Found at i:15951 original size:21 final size:21
Alignment explanation
Indices: 15925--16049 Score: 187
Period size: 21 Copynumber: 6.0 Consensus size: 21
15915 TGTTTTTACG
*
15925 CAAATTTTGATAGTCAAACCC
1 CAAATTTTGATGGTCAAACCC
*
15946 CAAATTTTGATGATCAAACCC
1 CAAATTTTGATGGTCAAACCC
*
15967 TAAATTTTGATGGTCAAACCC
1 CAAATTTTGATGGTCAAACCC
*
15988 CAAAGTTTGATGGTCAAACCC
1 CAAATTTTGATGGTCAAACCC
*
16009 CAAAATTTGATGGTCAAACCC
1 CAAATTTTGATGGTCAAACCC
* *
16030 CAAAATTTGATAGTCAAACC
1 CAAATTTTGATGGTCAAACC
16050 ATGATAAATC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 96 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (21 bp):
CAAATTTTGATGGTCAAACCC
Found at i:16020 original size:185 final size:183
Alignment explanation
Indices: 15592--16104 Score: 735
Period size: 185 Copynumber: 2.8 Consensus size: 183
15582 CATTTCAGTC
* * * * *
15592 ACCCAAATTTTAATGGTCAAACCCCAACA-TTTGATAGTGAAACCCCAACGTTTGATTGTGAAAC
1 ACCCAAATTTTGATGGTCAAACCCCAA-AGTTTGATAGTCAAACCCCAAAGTTTGATGGTCAAAC
**
15656 CCCAATGTTTGATAGTCAAACCATGTTAAATCTTATCAATTGAAGCACCCACCACATTTTTTGCC
65 CCCAAAATTTGATAGTCAAACCATGTTAAATCTTATCAATTGAAGCACCCACCACA-TTTTTG-C
* * * *
15721 CAAAACTGTATTCTTTGCCAAAATTTTGATGGTCAAACCTCAAAGTTTAATAGTCAA
128 CAAAACTGTGTT-TTTACCAAAATTTTGATAGTCAAACCCCAAAGTTTAATAGTCAA
*
15778 ACCCCAAATTTTGATGGTCAAACCCCAAAGTTTGATTGTCAAACCCCAAAGTTTGATGGTCAAAC
1 A-CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGGTCAAAC
* *
15843 CCCAAAATTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAGCACCCACCACAATTTTGCTC
65 CCCAAAATTTGATAGTCAAACCATGTTAAATCTTATCAATTGAAGCACCCACCACATTTTTGC-C
* *
15908 AAAACTGTGTTTTTACGC-AAATTTTGATAGTCAAACCCCAAATTTTGAT-GATCAA
129 AAAACTGTGTTTTTAC-CAAAATTTTGATAGTCAAACCCCAAAGTTTAATAG-TCAA
* *
15963 ACCCTAAATTTTGATGGTCAAACCCCAAAGTTTGATGGTCAAACCCCAAAATTTGATGGTCAAAC
1 ACCC-AAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGGTCAAAC
* *
16028 CCCAAAATTTGATAGTCAAACCATGATAAATCTTATCAATTGAAGCACCCAACACATTTTTGCCT
65 CCCAAAATTTGATAGTCAAACCATGTTAAATCTTATCAATTGAAGCACCCACCACATTTTTGCC-
16093 AAAACTGTGTTT
129 AAAACTGTGTTT
16105 AAGGCAAATT
Statistics
Matches: 298, Mismatches: 22, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
184 5 0.02
185 166 0.56
186 19 0.06
187 108 0.36
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (183 bp):
ACCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAGTTTGATGGTCAAACC
CCAAAATTTGATAGTCAAACCATGTTAAATCTTATCAATTGAAGCACCCACCACATTTTTGCCAA
AACTGTGTTTTTACCAAAATTTTGATAGTCAAACCCCAAAGTTTAATAGTCAA
Found at i:20423 original size:13 final size:13
Alignment explanation
Indices: 20405--20429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20395 TTTGCCAAAA
20405 AATAATTTTAAGC
1 AATAATTTTAAGC
20418 AATAATTTTAAG
1 AATAATTTTAAG
20430 GTGGTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATAATTTTAAGC
Done.