Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009250.1 Kokia drynarioides strain JFW-HI SEQ_123955, 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: 2760
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Found at i:1746 original size:29 final size:29
Alignment explanation
Indices: 1714--1963 Score: 206
Period size: 29 Copynumber: 8.4 Consensus size: 29
1704 TAACTGTTCG
* * *
1714 AAAATCCCATTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
*
1743 AAAATTACATTTTTACCCCCG-AACTTCCA
1 AAAATTCCATTTTTA-CCCCGAAACTTCCA
* * **
1772 AAGATTCCTTTTTTACCCTAAAACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
* *
1801 AAAATTACATTTTTATCCCCAAAACTTCCA
1 AAAATTCCATTTTTA-CCCCGAAACTTCCA
*
1831 AAAATTCCATTTTTAACCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
* *
1861 AAAATTACCA-TTTTGCCCCCAAA-TGTCCA
1 AAAATT-CCATTTTTACCCCGAAACT-TCCA
* *
1890 AAAATTCCATTTTTTAACCCCAAAACTTTCAAA
1 AAAATTCCA-TTTTT-ACCCCGAAAC-TTC-CA
* *
1923 AAAATACC-CTTTTACCCTCG-AA-TGTCCA
1 AAAATTCCATTTTTACCC-CGAAACT-TCCA
1951 AAAATTCCATTTT
1 AAAATTCCATTTT
1964 GATCTCGATT
Statistics
Matches: 178, Mismatches: 28, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
28 16 0.09
29 73 0.41
30 62 0.35
31 16 0.09
32 2 0.01
33 9 0.05
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAAACTTCCA
Found at i:1890 original size:59 final size:59
Alignment explanation
Indices: 1714--2022 Score: 274
Period size: 58 Copynumber: 5.2 Consensus size: 59
1704 TAACTGTTCG
* * *
1714 AAAATCCCA-TTTTGACCTCGAAACTTCCAAAAATTA-CATTTTTACCCCCGAACT-TCCA
1 AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCA-TTTTACCCCC-AAATGTCCA
* * * * *
1772 AAGATTCCTTTTTTACCCT-AAAACTTCCAAAAATTA-CATTTTTATCCCCAAAACT-TCCA
1 AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCA-TTTTA-CCCCCAAA-TGTCCA
*
1831 AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTGCCCCCAAATGTCCA
1 AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCCA
* * * * * * *
1890 AAAATTCCATTTTTTAACCCCAAAACTTTCAAAAAAATACCCTTTTACCCTCGAATGTCCA
1 AAAATTCCA-TTTTTAACCTCGAAAC-TTCCAAAAATTACCATTTTACCCCCAAATGTCCA
* * ** * **
1951 AAAATTCCA-TTTTGATCTCG-ATTTTCCTAAAAATTACCATTTTAACCCCGGATGTCCA
1 AAAATTCCATTTTTAACCTCGAAACTTCC-AAAAATTACCATTTTACCCCCAAATGTCCA
*
2009 AAAATTCCGTTTTT
1 AAAATTCCATTTTT
2023 CGATCCCAAT
Statistics
Matches: 206, Mismatches: 35, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
57 3 0.01
58 67 0.33
59 63 0.31
60 34 0.17
61 39 0.19
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCCA
Found at i:1955 original size:28 final size:29
Alignment explanation
Indices: 1827--2013 Score: 91
Period size: 30 Copynumber: 6.3 Consensus size: 29
1817 CCCCAAAACT
*
1827 TCCAAAAATTCCATTTTTAA-CCTCGAAACT-
1 TCCAAAAATACCA-TTTTAACCCTCG-AA-TG
* * *
1857 TCCAAAAATTACCATTTT-GCCCCCAAATG
1 TCCAAAAA-TACCATTTTAACCCTCGAATG
* * *
1886 TCCAAAAATTCCATTTTTTAACCC-CAAAACTT
1 TCCAAAAATACCA--TTTTAACCCTC-GAA-TG
* *
1918 TCAAAAAAATACCCTTTT-ACCCTCGAATG
1 TC-CAAAAATACCATTTTAACCCTCGAATG
* * * * *
1947 TCCAAAAATTCCATTTTGA-TCTCGATTT
1 TCCAAAAATACCATTTTAACCCTCGAATG
*
1975 TCCTAAAAATTACCATTTTAACCC-CGGATG
1 TCC-AAAAA-TACCATTTTAACCCTCGAATG
2005 TCCAAAAAT
1 TCCAAAAAT
2014 TCCGTTTTTC
Statistics
Matches: 119, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
28 27 0.23
29 24 0.20
30 41 0.34
31 16 0.13
32 3 0.03
33 8 0.07
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
TCCAAAAATACCATTTTAACCCTCGAATG
Found at i:1957 original size:61 final size:60
Alignment explanation
Indices: 1734--1963 Score: 213
Period size: 61 Copynumber: 3.9 Consensus size: 60
1724 TTTGACCTCG
* * * * *
1734 AAACTTCCAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAGATTCC-TTTTTT-ACCCTA
1 AAACTTCAAAAAAATACCA-TTTTACCCCC-AAATGTCCAAAAATTCCATTTTTTAACCCCA
* * * * *
1792 AAACTTCCAAAAATTA-CATTTTTATCCCCAAAACT-TCCAAAAATTCCA-TTTTTAACCTCG
1 AAACTTCAAAAAAATACCA-TTTTA-CCCCCAAA-TGTCCAAAAATTCCATTTTTTAACCCCA
* * *
1852 AAACTTCCAAAAATTACCATTTTGCCCCCAAATGTCCAAAAATTCCATTTTTTAACCCCA
1 AAACTTCAAAAAAATACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTTAACCCCA
* * *
1912 AAACTTTCAAAAAAATACCCTTTTACCCTCGAATGTCCAAAAATTCCATTTT
1 AAAC-TTCAAAAAAATACCATTTTACCCCCAAATGTCCAAAAATTCCATTTT
1964 GATCTCGATT
Statistics
Matches: 148, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
58 27 0.18
59 41 0.28
60 37 0.25
61 43 0.29
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (60 bp):
AAACTTCAAAAAAATACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTTAACCCCA
Found at i:2021 original size:28 final size:27
Alignment explanation
Indices: 1922--2021 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 27
1912 AAACTTTCAA
* * *
1922 AAAAATACCCTTTTACCCTCGAATGTCC
1 AAAAATTCCATTTTACCC-CGGATGTCC
* * *
1950 AAAAATTCCATTTTGATCTC-GATTTTCC
1 AAAAATTCCATTTT-ACCCCGGA-TGTCC
1978 TAAAAATTACCATTTTAACCCCGGATGTCC
1 -AAAAATT-CCATTTT-ACCCCGGATGTCC
*
2008 AAAAATTCCGTTTT
1 AAAAATTCCATTTT
2022 TCGATCCCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.02
28 23 0.41
29 16 0.29
30 14 0.25
31 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (27 bp):
AAAAATTCCATTTTACCCCGGATGTCC
Done.