Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013798.1 Corchorus olitorius cultivar O-4 contig13831, 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: 3452
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:1503 original size:50 final size:50
Alignment explanation
Indices: 1444--1687 Score: 429
Period size: 50 Copynumber: 4.9 Consensus size: 50
1434 CGAATGTTTT
* *
1444 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1494 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
1544 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
1594 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
1644 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTC-ATT-TCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAA
1688 ACCTTGGTTT
Statistics
Matches: 188, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 4 0.02
49 3 0.02
50 181 0.96
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
Found at i:1915 original size:50 final size:50
Alignment explanation
Indices: 1737--2296 Score: 913
Period size: 50 Copynumber: 11.1 Consensus size: 50
1727 GCATTACCTT
1737 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * *
1787 TTTTATAGGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGATCC
1 TTTTA-A-GATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*** * * *
1839 TTTTTAAGATTGAACCAGAAGACAGTTCGAAGGATAAGCGAAAGACGGTCC
1 -TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1890 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
1940 TTTAAAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTT-TAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
1991 TTTTTAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2041 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2091 TTTTAAAGATTGAATTGTTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2142 TTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCC
1 -TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
2193 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2243 TTTCAAGATTGAATTGGTAGACAATTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
2293 TTTT
1 TTTT
2297 TTATTAGATT
Statistics
Matches: 473, Mismatches: 31, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
50 247 0.52
51 175 0.37
52 46 0.10
53 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:1950 original size:101 final size:100
Alignment explanation
Indices: 1741--2296 Score: 905
Period size: 101 Copynumber: 5.5 Consensus size: 100
1731 TACCTTTTTT
1741 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGGATTGAATTGG
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA-A-GATTGAATTGG
* * * *
1806 AAGACAGTTCAAAGGATAAGCGGAAGATGATCCTTTTT
64 TAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTC
*** * * *
1844 AAGATTGAACCAGAAGACAGTTCGAAGGATAAGCGAAAGACGGTCCTTTTAAGATTGAATTGGTA
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTA
*
1909 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTAA
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT-C
* *
1945 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAGATTGAATTGGTA
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTA
2010 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTC
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTC
*
2045 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGATTGAATTGTT
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT-AAGATTGAATTGGT
*
2110 AGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTT
65 AGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTC
*
2147 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTGAATTGGTA
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTA
2212 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTC
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTC
*
2247 AAGATTGAATTGGTAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
2297 TTATTAGATT
Statistics
Matches: 424, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
100 103 0.24
101 223 0.53
102 53 0.12
103 45 0.11
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (100 bp):
AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTA
GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTC
Found at i:1982 original size:23 final size:23
Alignment explanation
Indices: 1908--1985 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
1898 TTGAATTGGT
1908 AGACAGTTCAAAGGATAAGCGGA
1 AGACAGTTCAAAGGATAAGCGGA
* * * **
1931 AGACGGTCCTTTAAAAGATTGAATTGGA
1 AGACAG---TTCAAAGGA-T-AAGCGGA
1959 AGACAGTTCAAAGGATAAGCGGA
1 AGACAGTTCAAAGGATAAGCGGA
1982 AGAC
1 AGAC
1986 GGTCCTTTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
23 14 0.35
24 1 0.03
25 7 0.17
26 7 0.17
27 1 0.03
28 10 0.25
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.18
Consensus pattern (23 bp):
AGACAGTTCAAAGGATAAGCGGA
Done.