Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003782.1 Kokia drynarioides strain JFW-HI SEQ_116762, 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, 617
Length: 1029
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Found at i:127 original size:48 final size:48
Alignment explanation
Indices: 14--222 Score: 210
Period size: 49 Copynumber: 4.3 Consensus size: 48
4 GAAGACACAA
* * * * *
14 AAGGGAAAGGTTTAAGTCGTAATGGCGAA-CCTAATACC-TCAGAGACAT
1 AAGGGAAAGGTTTAAGCCGCAACGGCGAATCC-AGTACCATGA-AGACAT
*
62 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACAT
1 -AAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACAT
* * * *
111 ATGGGAAAGGTTTAAGCCGCAACAGCGAATCCAGTACCATTAA-AGGA-
1 AAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCATGAAGA-CAT
* * * * *
158 AAGGGAAAGATTTAAGCCGCAACGACGAATTCAGTACCATGAAAACACA
1 AAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACA-T
207 AAGGGAAAGGTTTAAG
1 AAGGGAAAGGTTTAAG
223 TCGTAATGGC
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
47 39 0.29
48 41 0.30
49 51 0.38
50 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (48 bp):
AAGGGAAAGGTTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACAT
Found at i:187 original size:47 final size:47
Alignment explanation
Indices: 63--222 Score: 182
Period size: 48 Copynumber: 3.3 Consensus size: 47
53 CAGAGACATG
* *
63 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-TGAAGAC
1 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATTAAAGAC
*
109 ATATGGGAAAGGTTTAAGCCGCAAC-AGCGAATCCAGTACCATTAAAGGA-
1 A-A-GGGAAAGATTTAAGCCGCAACGA-CGAATCCAGTACCATTAAA-GAC
* * *
158 AAGGGAAAGATTTAAGCCGCAACGACGAATTCAGTACCATGAAAACAC
1 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCAT-TAAAGAC
*
206 AAAGGGAAAGGTTTAAG
1 -AAGGGAAAGATTTAAG
223 TCGTAATGGC
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
46 1 0.01
47 36 0.37
48 39 0.40
49 19 0.20
50 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (47 bp):
AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATTAAAGAC
Found at i:737 original size:6 final size:6
Alignment explanation
Indices: 716--795 Score: 64
Period size: 6 Copynumber: 14.2 Consensus size: 6
706 TTAAATTGGT
** *
716 TTTAAA TTTATT TTTAAA TTTAAA TTTATA TTT--- TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
761 TTT-GC TTTAAA TTTAAA TTT-AA -TTAAA TTTGAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T
796 GATTTTAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.05
4 2 0.03
5 7 0.12
6 42 0.72
7 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:771 original size:17 final size:15
Alignment explanation
Indices: 734--809 Score: 71
Period size: 17 Copynumber: 4.7 Consensus size: 15
724 TATTTTTAAA
*
734 TTTAAATTTATATTT
1 TTTAAATTTAAATTT
749 TTTAAATTTAAATTT
1 TTTAAATTTAAATTT
764 GCTTTAAATTTAAATTT
1 --TTTAAATTTAAATTT
* *
781 AATTAAATTTGAAATGAT
1 -TTTAAATTT-AAAT-TT
*
799 TTTAAACTTAA
1 TTTAAATTTAA
810 TATAAAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.27
16 10 0.20
17 26 0.51
18 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTAAATTTAAATTT
Found at i:802 original size:50 final size:50
Alignment explanation
Indices: 705--809 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
695 TTAAATTAGG
* ** * *
705 TTTAAATTGGTTTTAAATTTATTTTTAAATTTAAATTTATATTTTTTAAA
1 TTTAAATTGGCTTTAAATTTAAATTTAAATTTAAATTTAAATATTTTAAA
*
755 TTTAAATTTGCTTTAAATTTAAATTT-AA-TTAAATTTGAAATGATTTTAAA
1 TTTAAATTGGCTTTAAATTTAAATTTAAATTTAAATTT-AAAT-ATTTTAAA
*
805 CTTAA
1 TTTAA
810 TATAAAATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 8 0.17
49 5 0.11
50 33 0.72
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (50 bp):
TTTAAATTGGCTTTAAATTTAAATTTAAATTTAAATTTAAATATTTTAAA
Done.