Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010460.1 Kokia drynarioides strain JFW-HI SEQ_125358, 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: 19149
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Found at i:203 original size:37 final size:38
Alignment explanation
Indices: 103--205 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
93 GATCTTGAGT
* * *
103 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATTGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGATC
* * ** *
144 CGATGAGATACTGAGTACCACTTTACTTCGGCTAGA-C
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGATC
181 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
206 TTGCTTCAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.42
38 14 0.28
41 15 0.30
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGATC
Found at i:1561 original size:2 final size:2
Alignment explanation
Indices: 1554--1578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1544 TTATTTTCTT
1554 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1579 TATTACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1973 original size:29 final size:26
Alignment explanation
Indices: 1912--1975 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1902 AATATGACAA
1912 TTAAAATAAAAAAATAAATTTAAATT
1 TTAAAATAAAAAAATAAATTTAAATT
* * *
1938 TAAAAAATAGAAAACTATAATATTAAATAT
1 T-TAAAATAAAAAAATA-AAT-TTAAAT-T
1968 TTAAAATA
1 TTAAAATA
1976 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.03
27 12 0.40
28 3 0.10
29 12 0.40
30 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAAAATAAAAAAATAAATTTAAATT
Found at i:3766 original size:19 final size:20
Alignment explanation
Indices: 3706--3776 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
3696 AATTTGACGG
*
3706 GTTTAGGGTTTAT-TATTTAA
1 GTTTAGGGTTT-TGTATTTAT
* * *
3726 GATTTAAGGTTTAGTGTTTAT
1 G-TTTAGGGTTTTGTATTTAT
3747 GTTTAGGGTTTTGT-TTTAT
1 GTTTAGGGTTTTGTATTTAT
3766 GTTTAGGGTTT
1 GTTTAGGGTTT
3777 AGGGTTTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.37
20 12 0.28
21 15 0.35
ACGTcount: A:0.18, C:0.00, G:0.25, T:0.56
Consensus pattern (20 bp):
GTTTAGGGTTTTGTATTTAT
Found at i:8910 original size:31 final size:29
Alignment explanation
Indices: 8846--8913 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
8836 ACGATAACGT
* *
8846 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATTGCAAACAA
* *
8875 AAGTGACTAAAATGTAACCTGATGCAAACAA
1 AAGTGACTAAAACGTAACAT--TGCAAACAA
8906 AAGTGACT
1 AAGTGACT
8914 GTTTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.55
31 15 0.45
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATTGCAAACAA
Found at i:16682 original size:20 final size:20
Alignment explanation
Indices: 16657--16700 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
16647 TATGGCCAAA
16657 GCCTATGATCAGGTTAAGTG
1 GCCTATGATCAGGTTAAGTG
16677 GCCTATGATCAGGTTAAGTG
1 GCCTATGATCAGGTTAAGTG
16697 GCCT
1 GCCT
16701 TTTTTAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (20 bp):
GCCTATGATCAGGTTAAGTG
Found at i:17849 original size:53 final size:53
Alignment explanation
Indices: 17769--17875 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
17759 TGGATCCCAT
17769 GCAATATTAATTTTAAGGTATCAAATCCACTTCCTCATTTAAGTTATATGAAA
1 GCAATATTAATTTTAAGGTATCAAATCCACTTCCTCATTTAAGTTATATGAAA
17822 GCAATATTAATTTTAAGGTATCAAATCCACTTCCTCATTTAAGTTATATGAAA
1 GCAATATTAATTTTAAGGTATCAAATCCACTTCCTCATTTAAGTTATATGAAA
17875 G
1 G
17876 TGGAGTATCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (53 bp):
GCAATATTAATTTTAAGGTATCAAATCCACTTCCTCATTTAAGTTATATGAAA
Found at i:17861 original size:27 final size:27
Alignment explanation
Indices: 17778--17861 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
17768 TGCAATATTA
17778 ATTTTAAGGTATCAAATCCACTTCCTC
1 ATTTTAAGGTATCAAATCCACTTCCTC
* ** * *
17805 A-TTTAAGTTAT-ATGAAAGCAATAT--TA
1 ATTTTAAGGTATCA--AATCCACT-TCCTC
17831 ATTTTAAGGTATCAAATCCACTTCCTC
1 ATTTTAAGGTATCAAATCCACTTCCTC
17858 ATTT
1 ATTT
17862 AAGTTATATG
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
25 2 0.05
26 16 0.40
27 20 0.50
28 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (27 bp):
ATTTTAAGGTATCAAATCCACTTCCTC
Done.