Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012084.1 Kokia drynarioides strain JFW-HI SEQ_127083, 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: 4946
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:131 original size:26 final size:26
Alignment explanation
Indices: 95--148 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
85 TTTTGAATCA
95 ACATTTTAGTTGAACGTTTCCAATAT
1 ACATTTTAGTTGAACGTTTCCAATAT
*
121 ACATTTTAGTTGAATGTTTCCAATAT
1 ACATTTTAGTTGAACGTTTCCAATAT
147 AC
1 AC
149 GTATAGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (26 bp):
ACATTTTAGTTGAACGTTTCCAATAT
Found at i:1695 original size:29 final size:25
Alignment explanation
Indices: 1638--1691 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1628 GAGAAACTCT
*
1638 TTAT-TTTATTTAATATTAATAAAA
1 TTATATTTATTTAACATTAATAAAA
*
1662 TTATATTTATTTAACATTATATAATA
1 TTATATTTATTTAACATTA-ATAAAA
1688 TTAT
1 TTAT
1692 TATAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 4 0.15
25 13 0.50
26 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATTTATTTAACATTAATAAAA
Found at i:1794 original size:56 final size:54
Alignment explanation
Indices: 1723--1850 Score: 150
Period size: 56 Copynumber: 2.3 Consensus size: 54
1713 TTTTTGAAAA
* *
1723 TATTTATTTTCATATATTTTTAAAATTTATATATTATTTATTCTTGTCAATAATATT
1 TATTTATTTTTATATATTTTTAAAATTTAT-TATTATATATT-TTGTCAA-AATATT
* * * * *
1780 T-TTTATTTTTATATATTTTTTATATTTATTATTATATATTTTTTGAAATTATT
1 TATTTATTTTTATATATTTTTAAAATTTATTATTATATATTTTGTCAAAATATT
*
1833 TATGTATTTTTATATATT
1 TATTTATTTTTATATATT
1851 CCTTTTAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
53 6 0.10
54 20 0.32
55 10 0.16
56 25 0.40
57 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (54 bp):
TATTTATTTTTATATATTTTTAAAATTTATTATTATATATTTTGTCAAAATATT
Found at i:1797 original size:17 final size:17
Alignment explanation
Indices: 1725--1850 Score: 74
Period size: 17 Copynumber: 6.9 Consensus size: 17
1715 TTTGAAAATA
*
1725 TTTATTTTCATATATTT
1 TTTATTTTTATATATTT
* ** *
1742 TTAAAATTTATATATTA
1 TTTATTTTTATATATTT
1759 TTTATTCTTGTCAATAATATTT
1 TTTATT-TT-T--AT-ATATTT
1781 TTTATTTTTATATATTT
1 TTTATTTTTATATATTT
* *
1798 TTTATATTTAT-TATTA
1 TTTATTTTTATATATTT
* *
1814 TATATTTTTTGAAATTATTT
1 TTTA-TTTTT-ATA-TATTT
*
1834 ATGTATTTTTATATATT
1 -TTTATTTTTATATATT
1851 CCTTTTAGTT
Statistics
Matches: 82, Mismatches: 17, Indels: 19
0.69 0.14 0.16
Matches are distributed among these distances:
16 7 0.09
17 35 0.43
18 9 0.11
19 3 0.04
20 10 0.12
21 7 0.09
22 11 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTATTTTTATATATTT
Found at i:1798 original size:10 final size:10
Alignment explanation
Indices: 1783--1850 Score: 57
Period size: 10 Copynumber: 6.4 Consensus size: 10
1773 TAATATTTTT
1783 TATTTTTATA
1 TATTTTTATA
1793 TATTTTT-TA
1 TATTTTTATA
1802 TATTTATTATTA
1 TATTT-TTA-TA
*
1814 TATATTTTTTGA
1 TAT-TTTTAT-A
* *
1826 AATTATTTATG
1 TATT-TTTATA
1837 TATTTTTATA
1 TATTTTTATA
1847 TATT
1 TATT
1851 CCTTTTAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
9 7 0.15
10 18 0.39
11 5 0.11
12 14 0.30
13 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TATTTTTATA
Found at i:1822 original size:39 final size:40
Alignment explanation
Indices: 1722--1822 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 40
1712 TTTTTTGAAA
1722 ATATTTATT-TTCATATATTTTTAAAATTTATATATTATTT
1 ATATTTATTATT-ATATATTTTTAAAATTTATATATTATTT
* * * * ** *
1762 AT-TCTTGTCAATA-ATATTTTTTATTTTTATATATTTTTT
1 ATAT-TTATTATTATATATTTTTAAAATTTATATATTATTT
1801 ATATTTATTATTATATATTTTT
1 ATATTTATTATTATATATTTTT
1823 TGAAATTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
39 31 0.66
40 15 0.32
41 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (40 bp):
ATATTTATTATTATATATTTTTAAAATTTATATATTATTT
Found at i:1831 original size:23 final size:23
Alignment explanation
Indices: 1782--1848 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1772 ATAATATTTT
* *
1782 TTATTTTTATATATTTTTTATAT
1 TTATTATTATATATTTTTTATAA
1805 TTATTATTATATATTTTTTGA-AA
1 TTATTATTATATATTTTTT-ATAA
*
1828 TTA-T-TTATGTATTTTTATATA
1 TTATTATTATATATTTTT-TATA
1849 TTCCTTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 12 0.32
22 3 0.08
23 22 0.58
24 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (23 bp):
TTATTATTATATATTTTTTATAA
Done.