Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004180.1 Kokia drynarioides strain JFW-HI SEQ_117412, 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: 6364
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:1734 original size:60 final size:62
Alignment explanation
Indices: 1667--1810 Score: 193
Period size: 62 Copynumber: 2.3 Consensus size: 62
1657 AGCCAATGCA
* *
1667 TGACCAACACCAAAAAAATTTA-TTTTTTTATCAGATAAAAA-AATGGTGTCGACCAAACAT
1 TGACCAACACCAAAAAAATTTATTTTTTTTATCAAATAAAAATAATGGCGTCGACCAAACAT
* * ** **
1727 TGGCCAACACCAAAAAATTTTATTTTTTTTATCAAATAAAAATGGTGGCGTCGACCAAGGAT
1 TGACCAACACCAAAAAAATTTATTTTTTTTATCAAATAAAAATAATGGCGTCGACCAAACAT
1789 TGACCAACACCAAAAAATATTT
1 TGACCAACACCAAAAAA-ATTT
1811 TTATCTGATA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
60 20 0.28
61 18 0.25
62 30 0.42
63 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (62 bp):
TGACCAACACCAAAAAAATTTATTTTTTTTATCAAATAAAAATAATGGCGTCGACCAAACAT
Found at i:1822 original size:56 final size:57
Alignment explanation
Indices: 1643--1912 Score: 200
Period size: 54 Copynumber: 4.7 Consensus size: 57
1633 TTTTTTGATA
* *
1643 AAAAAGGTAGTGTCAGCCAATGCA-TGACCAACACCAAAAAAATTTATTTTTTTATCAGAT
1 AAAAAGATGGTGTCAGCCAA-GCATTGACCAACACC-AAAAAA-TTA-TTTTTTATCAGAT
* * * *
1703 AAAAAAATGGTGTC-GACCAAACATTGGCCAACACCAAAAAATTTTATTTTTTTTATCAAAT
1 AAAAAGATGGTGTCAG-CCAAGCATTGACCAACACCAAAAAA--TTA--TTTTTTATCAGAT
* * * *
1764 AAAAATGGTGGCGTC-GACCAAGGATTGACCAACACCAAAAAA-TA-TTTTTATCTGAT
1 AAAAA-GATGGTGTCAG-CCAAGCATTGACCAACACCAAAAAATTATTTTTTATCAGAT
* * * * *
1820 AAAAAAGGTGGTGTCAGTCAATGCA-TGACCAATACC--AAAA-T-GTTTTTATCTGATT
1 -AAAAAGATGGTGTCAGCCAA-GCATTGACCAACACCAAAAAATTATTTTTTATCAGA-T
*
1875 AAAAAGATGGTGTCAGCCAAGCATTGATCAACACCAAA
1 AAAAAGATGGTGTCAGCCAAGCATTGACCAACACCAAA
1913 TTTTTTTATC
Statistics
Matches: 175, Mismatches: 22, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
53 3 0.02
54 43 0.25
55 1 0.01
56 32 0.18
57 8 0.05
59 11 0.06
60 29 0.17
61 18 0.10
62 30 0.17
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (57 bp):
AAAAAGATGGTGTCAGCCAAGCATTGACCAACACCAAAAAATTATTTTTTATCAGAT
Found at i:1880 original size:54 final size:54
Alignment explanation
Indices: 1750--1992 Score: 208
Period size: 54 Copynumber: 4.4 Consensus size: 54
1740 AAAATTTTAT
** * * * *
1750 TTTTTTTATCAAATAAAAATGGTGGCGTC-GACCAA-GGATTGACCAACACCAAAAAA
1 TTTTTTTATCTGATAAAAAAGGTGGTGTCAG-CCAATGCA-TGACCAATACC--AAAA
* *
1806 TATTTTTATCTGATAAAAAAGGTGGTGTCAGTCAATGCATGACCAATACCAAAA
1 TTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGCATGACCAATACCAAAA
* * * * *
1860 TGTTTTTATCTGATTAAAAAGATGGTGTCAGCCAA-GCATTGATCAACACC-AAA
1 TTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGCA-TGACCAATACCAAAA
* ** **
1913 TTTTTTTATCTAATAAAAAATATTGGTGTCTA-CCAATGCATGACCAATACCAATTT
1 TTTTTTTATCTGATAAAAAA-GGTGGTGTC-AGCCAATGCATGACCAATACCAA-AA
*
1969 TTTTTTTATCTGATCAAAAAGGTG
1 TTTTTTTATCTGATAAAAAAGGTG
1993 CTTGGCCAAC
Statistics
Matches: 152, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
53 23 0.15
54 64 0.42
55 7 0.05
56 55 0.36
57 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (54 bp):
TTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGCATGACCAATACCAAAA
Found at i:5936 original size:11 final size:11
Alignment explanation
Indices: 5922--5985 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
5912 AGCCCTTTTT
*
5922 AATTTATTTTA
1 AATTTAATTTA
*
5933 AATTTAAATT-
1 AATTTAATTTA
5943 AATCTTAAATTTA
1 AAT-TT-AATTTA
5956 AATTTAATTTA
1 AATTTAATTTA
5967 AATTTAAATTTA
1 AATTT-AATTTA
*
5979 ATTTTAA
1 AATTTAA
5986 AATTAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.07
11 23 0.51
12 16 0.36
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:5940 original size:6 final size:6
Alignment explanation
Indices: 5929--5992 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
5919 TTTAATTTAT
5929 TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
5975 TTTAAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
5993 AAGTCCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.14
6 39 0.76
7 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:5950 original size:17 final size:17
Alignment explanation
Indices: 5922--5992 Score: 99
Period size: 17 Copynumber: 4.1 Consensus size: 17
5912 AGCCCTTTTT
*
5922 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
5939 AA-TTAATCTTAAATTTA
1 AATTTAAT-TTAAATTTA
5956 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
5973 AATTTAATTTTAAAATTA
1 AATTTAA-TTTAAATTTA
5991 AA
1 AA
5993 AAGTCCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 4 0.08
17 29 0.59
18 16 0.33
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:5956 original size:23 final size:22
Alignment explanation
Indices: 5920--5991 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
5910 CGAGCCCTTT
*
5920 TTAATTT-ATTTTAAATTTAAA
1 TTAATTTAAATTTAAATTTAAA
*
5941 TTAATCTTAAATTTAAATTTAAT
1 TTAAT-TTAAATTTAAATTTAAA
*
5964 TTAAATTTAAATTTAATTTTAAAA
1 TT-AATTTAAATTTAAATTT-AAA
5988 TTAA
1 TTAA
5992 AAAGTCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 29 0.67
24 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTTAAATTTAAATTTAAA
Done.