Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004692.1 Kokia drynarioides strain JFW-HI SEQ_118250, 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: 3518
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Found at i:1787 original size:30 final size:29
Alignment explanation
Indices: 1753--1880 Score: 84
Period size: 29 Copynumber: 4.3 Consensus size: 29
1743 AAAATCCCGA
1753 TTTTAACCCTGTAACATCCAAAAAATCCAT
1 TTTTAACCCTG-AACATCCAAAAAATCCAT
** * **
1783 TTTT-ACCCCCAAAATATAAAAAATCCCAT
1 TTTTAACCCTGAACATCCAAAAAAT-CCAT
** *
1812 TTTTAACCCCAAAACTTCCAAAAAATTCCAT
1 TTTTAA-CCCTGAACATCCAAAAAA-TCCAT
*
1843 TTTT-ACCCTCGAAC-TACC-TAAAATCTCAT
1 TTTTAACCCT-GAACAT-CCAAAAAATC-CAT
1872 TTTTAACCC
1 TTTTAACCC
1881 CAAAACTTCC
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
28 13 0.17
29 27 0.36
30 15 0.20
31 20 0.26
32 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (29 bp):
TTTTAACCCTGAACATCCAAAAAATCCAT
Found at i:1804 original size:29 final size:29
Alignment explanation
Indices: 1771--2028 Score: 150
Period size: 29 Copynumber: 8.7 Consensus size: 29
1761 CTGTAACATC
1771 CAAAAAATCCATTTTTACCCCCAAAA-TAT
1 CAAAAAATCCATTTTTACCCCCAAAACT-T
*
1800 -AAAAAATCCCATTTTTAACCCCAAAACTT
1 CAAAAAAT-CCATTTTTACCCCCAAAACTT
* * *
1829 CCAAAAAATTCCATTTTTACCCTC-GAACTA
1 -CAAAAAA-TCCATTTTTACCCCCAAAACTT
** *
1859 CCTAAAATCTCATTTTTAACCCCAAAACTT
1 CAAAAAATC-CATTTTTACCCCCAAAACTT
* ** * * *
1889 CCAAGATTTCCATTTTTACCCCC-GAGCCT
1 -CAAAAAATCCATTTTTACCCCCAAAACTT
* * * *
1918 CCAAAAATCCCAATTTTGA-CCTCAAAACTA
1 CAAAAAAT-CC-ATTTTTACCCCCAAAACTT
* *
1948 CCAAAAATCCCATTTTTAACCCCAAAACTTT
1 CAAAAAAT-CCATTTTTACCCCCAAAAC-TT
** * *
1979 CAAAAGGTCCATTTTTACCCTC-GAACTT
1 CAAAAAATCCATTTTTACCCCCAAAACTT
* *
2007 CTAAAAATCCCATTTTGACCCC
1 CAAAAAAT-CCATTTTTACCCC
2029 GAATTTTCCC
Statistics
Matches: 171, Mismatches: 44, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
28 20 0.12
29 62 0.36
30 60 0.35
31 28 0.16
32 1 0.01
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.29
Consensus pattern (29 bp):
CAAAAAATCCATTTTTACCCCCAAAACTT
Found at i:1905 original size:30 final size:30
Alignment explanation
Indices: 1711--2022 Score: 183
Period size: 30 Copynumber: 10.5 Consensus size: 30
1701 CTAAATTGTT
* * ** *
1711 CAAAAATTCCATTTTTAACCTCGATGCTTT
1 CAAAAATTCCATTTTTAACCCCAAAACTTC
* * *** *
1741 TAAAAATCCCGA-TTTTAACCCTGTAACATC
1 CAAAAATTCC-ATTTTTAACCCCAAAACTTC
* *
1771 CAAAAAATCCATTTTTACCCCCAAAA-TAT-
1 CAAAAATTCCATTTTTAACCCCAAAACT-TC
* *
1800 AAAAAATCCCATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTC
* *
1830 CAAAAAATTCCATTTTT-ACCCTC-GAACTAC
1 C-AAAAATTCCATTTTTAACCC-CAAAACTTC
*
1860 CTAAAA-TCTCATTTTTAACCCCAAAACTTC
1 CAAAAATTC-CATTTTTAACCCCAAAACTTC
* * ** * *
1890 CAAGATTTCCATTTTT-ACCCCCGAGCCTC
1 CAAAAATTCCATTTTTAACCCCAAAACTTC
* * * * *
1919 CAAAAATCCCAATTTTGACCTCAAAACTAC
1 CAAAAATTCCATTTTTAACCCCAAAACTTC
* *
1949 CAAAAATCCCATTTTTAACCCCAAAACTTT
1 CAAAAATTCCATTTTTAACCCCAAAACTTC
** *
1979 CAAAAGGTCCATTTTT-ACCCTC-GAACTTC
1 CAAAAATTCCATTTTTAACCC-CAAAACTTC
* *
2008 TAAAAATCCCATTTT
1 CAAAAATTCCATTTT
2023 GACCCCGAAT
Statistics
Matches: 210, Mismatches: 59, Indels: 27
0.71 0.20 0.09
Matches are distributed among these distances:
28 2 0.01
29 77 0.37
30 113 0.54
31 18 0.09
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (30 bp):
CAAAAATTCCATTTTTAACCCCAAAACTTC
Found at i:1910 original size:89 final size:87
Alignment explanation
Indices: 1742--2031 Score: 254
Period size: 89 Copynumber: 3.3 Consensus size: 87
1732 CGATGCTTTT
* *
1742 AAAAATCCCGATTTTAACCCT-GTAAC-ATCCAAAAAAT-CCATTTTTACCCCCAAAA-TAT--A
1 AAAAATCCC-ATTTTGACCCTCG-AACTA-CC-AAAAATCCCATTTTTAACCCCAAAACT-TCCA
** *
1801 AAAAATCCCATTTTTAACCCCAAAACTTCC
61 AAAGGT-CCATTTTT-ACCCC-GAACTTCC
* * * * * *
1831 AAAAAATTCCATTTTTACCCTCGAACTACCTAAAATCTCATTTTTAACCCCAAAACTTCCAAGAT
1 -AAAAATCCCATTTTGACCCTCGAACTACCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAG
* * *
1896 TTCCATTTTTACCCCCGAGCCTCC
65 GTCCATTTTTA-CCCCGAACTTCC
* *
1920 AAAAATCCCAATTTTGA-CCTCAAAACTACCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAA
1 AAAAATCCC-ATTTTGACCCTC-GAACTACCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAA
*
1984 GGTCCATTTTTACCCTCGAACTTCT
64 GGTCCATTTTTACCC-CGAACTTCC
2009 AAAAATCCCATTTTGACCC-CGAA
1 AAAAATCCCATTTTGACCCTCGAA
2032 TTTTCCCAAA
Statistics
Matches: 165, Mismatches: 24, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
87 2 0.01
88 28 0.17
89 108 0.65
90 23 0.14
91 4 0.02
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (87 bp):
AAAAATCCCATTTTGACCCTCGAACTACCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAGG
TCCATTTTTACCCCGAACTTCC
Found at i:1944 original size:59 final size:59
Alignment explanation
Indices: 1742--1970 Score: 228
Period size: 59 Copynumber: 3.9 Consensus size: 59
1732 CGATGCTTTT
*** * * * * **
1742 AAAAATCCCGA-TTTTAACCCTGTAACATCCAAAAAATCCATTTTTACCCCCAAAATATA
1 AAAAATCCC-ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTACC
*
1801 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAAATTCCATTTTTACCCTCGAACTACC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC-AAAAATTCCATTTTTACCCCCGAACTACC
* * * * *
1861 TAAAATCTCATTTTTAACCCCAAAACTTCCAAGATTTCCATTTTTACCCCCGAGCCT-CC
1 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGA-ACTACC
* * * * * *
1920 AAAAATCCCAATTTTGACCTCAAAACTACCAAAAATCCCATTTTTAACCCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
1971 AAAACTTTCA
Statistics
Matches: 141, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.01
59 87 0.62
60 53 0.38
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.28
Consensus pattern (59 bp):
AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTACC
Done.