Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002081.1 Kokia drynarioides strain JFW-HI SEQ_113993, 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, 870
Length: 1450
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Found at i:845 original size:60 final size:59
Alignment explanation
Indices: 639--1011 Score: 558
Period size: 60 Copynumber: 6.3 Consensus size: 59
629 GTCCTTAAAC
* *
639 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCACCATTTTACCCCTAAA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
* * *
698 TTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCA-TTTACCCCTGAA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
756 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCTGAA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTA-CCCCTGAA
816 CTTCCAAAAATCCCATTTTT-ACCCTCGAACCTTCCAAAAATTACCATTTTACCCCTGAAA
1 CTTCCAAAAATCCCATTTTTAACCC-CGAACCTTCCAAAAATTACCATTTTACCCCTG-AA
* * *
876 C-TCAAAAAATCCCA-TTTTAACCCCGAACCTTCCAAAAATTACCAATTTACCCCTAAA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
* * * *
933 CTTCCAAAAATCCCATTTTTTTATCTCGAACCTTCCAAAAATTACCATTCTACCTCC-GAA
1 CTTCCAAAAATCCCA-TTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACC-CCTGAA
993 CTTCCAAAAATCCCATTTT
1 CTTCCAAAAATCCCATTTT
1012 CGACCTCAAA
Statistics
Matches: 289, Mismatches: 16, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
57 3 0.01
58 100 0.35
59 78 0.27
60 106 0.37
61 2 0.01
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (59 bp):
CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
Found at i:894 original size:118 final size:118
Alignment explanation
Indices: 639--1011 Score: 569
Period size: 118 Copynumber: 3.2 Consensus size: 118
629 GTCCTTAAAC
* *
639 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCACCATTTTACCCCTAAATTTCCA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
* *
704 AAAATCCCATTTTTAACCC-CAAACCTTCCAAAAATCACCA-TTTACCCCTGAA
66 AAAATCCCATTTTT-ACCCTCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
*
756 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCTGAACTTCC
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTA-CCCCTAAACTTCC
821 AAAAATCCCATTTTTACCCTCGAACCTTCCAAAAATTACCATTTTACCCCTGAAA
65 AAAAATCCCATTTTTACCCTCGAACCTTCCAAAAATTACCATTTTACCCCTG-AA
* *
876 C-TCAAAAAATCCCA-TTTTAACCCCGAACCTTCCAAAAATTACCAATTTACCCCTAAACTTCCA
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
* *
939 AAAATCCCATTTTTTTA-TCTCGAACCTTCCAAAAATTACCATTCTACCTCC-GAA
66 AAAATCCCA--TTTTTACCCTCGAACCTTCCAAAAATTACCATTTTACC-CCTGAA
993 CTTCCAAAAATCCCATTTT
1 CTTCCAAAAATCCCATTTT
1012 CGACCTCAAA
Statistics
Matches: 236, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
117 79 0.33
118 121 0.51
119 33 0.14
120 3 0.01
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (118 bp):
CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCA
AAAATCCCATTTTTACCCTCGAACCTTCCAAAAATTACCATTTTACCCCTGAA
Found at i:1018 original size:30 final size:28
Alignment explanation
Indices: 636--1011 Score: 366
Period size: 30 Copynumber: 12.8 Consensus size: 28
626 GAAGTCCTTA
636 AACCTTCCAAAAATCCCATTTTTAACCCCG
1 AACCTTCCAAAAATCCCA-TTTT-ACCCCG
*
666 AACCTTCCAAAAATCACCATTTTACCCCT
1 AACCTTCCAAAAATC-CCATTTTACCCCG
** *
695 AAATTTCCAAAAATCCCATTTTTAACCCCA
1 AACCTTCCAAAAATCCCA-TTTT-ACCCCG
725 AACCTTCCAAAAATCACCA-TTTACCCCTG
1 AACCTTCCAAAAATC-CCATTTTACCCC-G
754 AA-CTTCCAAAAATCCCATTTTTAACCCCG
1 AACCTTCCAAAAATCCCA-TTTT-ACCCCG
*
783 AACCTTCCAAAAATTACCATTTTACCCCCTG
1 AACCTTCCAAAAA-TCCCATTTTA-CCCC-G
814 AA-CTTCCAAAAATCCCATTTTTACCCTCG
1 AACCTTCCAAAAATCCCA-TTTTACCC-CG
*
843 AACCTTCCAAAAATTACCATTTTACCCCTG
1 AACCTTCCAAAAA-TCCCATTTTACCCC-G
* *
873 AAAC-TCAAAAAATCCCATTTTAACCCCG
1 AACCTTCCAAAAATCCCATTTT-ACCCCG
* * *
901 AACCTTCCAAAAATTACCAATTTACCCCT
1 AACCTTCCAAAAA-TCCCATTTTACCCCG
* * *
930 AAACTTCCAAAAATCCCATTTTTTTATCTCG
1 AACCTTCCAAAAATCCCA---TTTTACCCCG
* *
961 AACCTTCCAAAAATTACCATTCTACCTCCG
1 AACCTTCCAAAAA-TCCCATTTTACC-CCG
991 AA-CTTCCAAAAATCCCATTTT
1 AACCTTCCAAAAATCCCATTTT
1012 CGACCTCAAA
Statistics
Matches: 290, Mismatches: 31, Indels: 52
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.01
28 43 0.15
29 96 0.33
30 109 0.38
31 35 0.12
32 4 0.01
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (28 bp):
AACCTTCCAAAAATCCCATTTTACCCCG
Done.