Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019301.1 Corchorus olitorius cultivar O-4 contig19334, 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: 6493
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Found at i:895 original size:50 final size:50
Alignment explanation
Indices: 813--964 Score: 196
Period size: 50 Copynumber: 3.0 Consensus size: 50
803 GAAGTTTTAT
* * * *
813 AATAAGATTTGCATTCCATTTGCGAGTTCAAGATCAAAATTCAATTTTCAA
1 AATAAGA-TTGCATTCCATTTGTGAGTCCAAGATCAAAGTTCACTTTTCAA
* * *
864 AATAAGATCGCATTCGATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAGTTCACTTTTCAA
* * * *
914 AATAAGATTGCATTCTATTTGTGAGACCAAGACCAAAGTTCTCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAGTTCACTTTTCAA
964 A
1 A
965 GAGCATTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 82 0.92
51 7 0.08
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAGTTCACTTTTCAA
Found at i:1697 original size:68 final size:69
Alignment explanation
Indices: 1569--2050 Score: 650
Period size: 69 Copynumber: 7.0 Consensus size: 69
1559 CCGTAAGTCA
* *
1569 AAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGC--CACGTAGGCTTTTCCA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA-G-GGGCTTTTCCA
1632 CAAGCC
64 CAAGCC
* * *
1638 AAACTCGTTTCCATATGAGTCAGTT-AAGCATTGGTTCCATCCAAGCAGCGGGGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
*
1702 AGCT
66 AGCC
* *
1706 AAACTCGTTTCCATACGAGTCAGTT-ATGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
1770 AGCC
66 AGCC
* * * * * *
1774 AAACTCGTTTTCATGCGAGTCACTT-AAGTCTTGGTTCCATCTAAGCAACAGGGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
*
1838 AGCA
66 AGCC
* * *** * *
1842 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCTATCCAAGCAGTTTGTGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
*
1907 AGTC
66 AGCC
* * * * *
1911 AAACTTGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATGTGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
1976 AGCC
66 AGCC
*
1980 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
2045 AGCC
66 AGCC
2049 AA
1 AA
2051 GTTCATTTCT
Statistics
Matches: 366, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
68 178 0.49
69 187 0.51
70 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (69 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
AGCC
Found at i:1778 original size:136 final size:136
Alignment explanation
Indices: 1552--2050 Score: 655
Period size: 136 Copynumber: 3.6 Consensus size: 136
1542 CGAATGTTTC
** *
1552 GGCTTTTCCGTAAGTCAAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGC-
1 GGCTTTTCCACAAG-CAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
*
1616 -CACGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCAGTTAAGCATTGGTTCCATCC
65 GCA-G-AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGC-TTGGTTCCATCC
*
1680 AAGCAGCGGG
127 AAGCAGCAGG
* *
1690 GGCTTTTCCACAAGCTAAACTCGTTTCCATACGAGTCAGTT-ATGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* * * *
1754 CAGAGGCTTTTCCACAAGCCAAACTCGTTTTCATGCGAGTCACTTAAGTCTTGGTTCCATCTAAG
66 CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAG-CTTGGTTCCATCCAAG
*
1819 CAACAGG
130 CAGCAGG
* *
1826 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCTATCCAAGCAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
** * * * * *
1891 TTTG-TGCTTTTCCATAAGTCAAACTTGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCA
66 -CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT--AAGCTTGGTTCCATCCA
*
1955 AGCAGCATG
128 AGCAGCAGG
* * *
1964 TGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* *
2029 CAGGGGCTTTTCCATAAGCCAA
66 CAGAGGCTTTTCCACAAGCCAA
2051 GTTCATTTCT
Statistics
Matches: 316, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
136 120 0.38
137 83 0.26
138 111 0.35
139 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (136 bp):
GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCTTGGTTCCATCCAAGC
AGCAGG
Found at i:3040 original size:2 final size:2
Alignment explanation
Indices: 3033--3058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3023 TTAGCATTAC
3033 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3059 TATGTGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.