Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008914.1 Kokia drynarioides strain JFW-HI SEQ_123603, 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: 2346
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Found at i:669 original size:3 final size:3
Alignment explanation
Indices: 656--710 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
646 ACATTGTTCG
* **
656 TAA TAAA TAA TAA TAA TAA TAA TAA CT-G TTT TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
702 TAA TAA TAA
1 TAA TAA TAA
711 CATTTATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 40 0.89
4 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1818 original size:30 final size:30
Alignment explanation
Indices: 1782--2070 Score: 220
Period size: 30 Copynumber: 9.6 Consensus size: 30
1772 AAACTGTCCA
*
1782 AAAATTATATTTTGACCCTCGAACTTCTCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* * *
1812 AAAATTATATTTTTGA-CCACAAACTTTTCA
1 AAAATTATA-TTTTGACCCTCAAACTTCTCC
*
1842 AAAATTATATTTTGA-CCTCCAAAGTTCTCC
1 AAAATTATATTTTGACCCT-CAAACTTCTCC
* * * **
1872 AAAATTATATTTTTGACTCT-GAACTTTTTG
1 AAAATTATA-TTTTGACCCTCAAACTTCTCC
* *
1902 AAAATTACATTTTCACCCTCAAACTTCTCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* * *
1932 AAAATTATATTTTTGA-CCTTAAACTTTTTCA
1 AAAATTATA-TTTTGACCCTCAAAC-TTCTCC
*
1963 AAAATT-TCATTTTGACCCATCAAACTTC-CTT
1 AAAATTAT-ATTTTGACCC-TCAAACTTCTC-C
*
1994 AAAATTATATTTTAACCCT-AAACTT-TCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* * * *
2022 AAAAATTACATTTTTACCCCCAAACTT-GCC
1 -AAAATTATATTTTGACCCTCAAACTTCTCC
2052 AAAATT-TCATTTTTGACCC
1 AAAATTAT-A-TTTTGACCC
2071 GATTTTCCTA
Statistics
Matches: 205, Mismatches: 37, Indels: 34
0.74 0.13 0.12
Matches are distributed among these distances:
29 46 0.22
30 104 0.51
31 47 0.23
32 8 0.04
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTCAAACTTCTCC
Found at i:1870 original size:60 final size:59
Alignment explanation
Indices: 1780--2125 Score: 307
Period size: 60 Copynumber: 5.8 Consensus size: 59
1770 CTAAACTGTC
*
1780 CAAAAATTATATTTTGACCCTCGAACTTCTCCAAAATTATATTTTTGACCACAAACTTTT
1 CAAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACC-CAAACTTTT
* **
1840 CAAAAATTATATTTTGA-CCTCCAAAGTTCTCCAAAATTATATTTTTGACTCTGAACTTTT
1 CAAAAATTATATTTTGACCCT-CAAACTTCTCCAAAATTATATTTTTGAC-CCAAACTTTT
** * * *
1900 TGAAAATTACATTTTCACCCTCAAACTTCTCCAAAATTATATTTTTGACCTTAAACTTTTT
1 CAAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACC-CAAAC-TTTT
* * *
1961 CAAAAATT-TCATTTTGACCCATCAAACTTC-CTTAAAATTATA-TTTTAACCCTAAACTTTC
1 CAAAAATTAT-ATTTTGACCC-TCAAACTTCTC-CAAAATTATATTTTTGACCC-AAACTTTT
* * * * *
2021 CAAAAATTACATTTTTACCCCCAAACTT-GCCAAAATT-TCATTTTTGACCC-GA-TTTT
1 CAAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTAT-ATTTTTGACCCAAACTTTT
* * * **
2077 CCTAAAAATTATCATTTT-ACCCCCGAACTTC-CAAAAATTCCATTTTTGA
1 -C-AAAAATTAT-ATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGA
2126 TCTTTTTCCA
Statistics
Matches: 239, Mismatches: 29, Indels: 38
0.78 0.09 0.12
Matches are distributed among these distances:
56 3 0.01
57 3 0.01
58 41 0.17
59 25 0.10
60 114 0.48
61 35 0.15
62 18 0.08
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
CAAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACCCAAACTTTT
Found at i:2084 original size:58 final size:55
Alignment explanation
Indices: 2017--2155 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 55
2007 AACCCTAAAC
*
2017 TTTCCAAAAATTA-CATTTTTACCCCCAAACTTGCC-AAAATTTCATTTTTGACCCGAT
1 TTTCCAAAAATTACCA-TTTTACCCCCAAACTT-CCAAAAATTCCATTTTTGA-CC-AT
* * * *
2074 TTTCCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCTT
1 TTTCC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
2130 TTTCCAAAAATTACCATTTTACCCCC
1 TTTCCAAAAATTACCATTTTACCCCC
2156 GAATGTTTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
55 20 0.27
56 6 0.08
57 8 0.11
58 38 0.51
59 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (55 bp):
TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
Found at i:2190 original size:27 final size:28
Alignment explanation
Indices: 2136--2207 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
2126 TCTTTTTCCA
* *
2136 AAAATTACCATTTTACCCCCGAATGTTT
1 AAAATTACCATTTTAACCACGAATGTTT
2164 AAAATT-CCATTTTTAACCACGAA-GTTT
1 AAAATTACCA-TTTTAACCACGAATGTTT
2191 CCCAAAATTACCATTTT
1 ---AAAATTACCATTTT
2208 GCCCTCGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 7 0.19
28 17 0.46
30 10 0.27
31 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTAACCACGAATGTTT
Done.