Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015225.1 Kokia drynarioides strain JFW-HI SEQ_130269, 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: 377715
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 333 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:355775 original size:44 final size:44
Alignment explanation
Indices: 355691--355777 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
355681 TCTTACTAAA
*
355691 AACCAACACAATAGATTAAGTTCTAGCAAAACCAAAAAAACAAT
1 AACCAACACAATAAATTAAGTTCTAGCAAAACCAAAAAAACAAT
* *
355735 AACCAACACAATAAATTGAAGTTGTAGCAAAA-CAAGAAAACAA
1 AACCAACACAATAAATT-AAGTTCTAGCAAAACCAAAAAAACAA
355778 GAATAATCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 26 0.67
45 13 0.33
ACGTcount: A:0.57, C:0.18, G:0.09, T:0.15
Consensus pattern (44 bp):
AACCAACACAATAAATTAAGTTCTAGCAAAACCAAAAAAACAAT
Found at i:357439 original size:8 final size:8
Alignment explanation
Indices: 357426--357455 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
357416 TTCCAGTAAA
357426 AGAAAATC
1 AGAAAATC
357434 AGAAAATC
1 AGAAAATC
357442 AGAAAATC
1 AGAAAATC
357450 A-AAAAT
1 AGAAAAT
357456 ATTAATGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (8 bp):
AGAAAATC
Found at i:357694 original size:40 final size:40
Alignment explanation
Indices: 357641--357732 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
357631 GCTGATAGGT
357641 TTTGGGTTTGGGAAATAGTAGGTTTAATAATTTGTAGGGG
1 TTTGGGTTTGGGAAATAGTAGGTTTAATAATTTGTAGGGG
357681 TTTGGGTTTGGGAAATAGTAGGTTTAATAATTTGTAGGGG
1 TTTGGGTTTGGGAAATAGTAGGTTTAATAATTTGTAGGGG
*
357721 TTTGGGCTTGGG
1 TTTGGGTTTGGG
357733 TTTGGAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.22, C:0.01, G:0.37, T:0.40
Consensus pattern (40 bp):
TTTGGGTTTGGGAAATAGTAGGTTTAATAATTTGTAGGGG
Found at i:369170 original size:2 final size:2
Alignment explanation
Indices: 369163--369209 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
369153 AACGAATTTA
369163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
369205 AT AT A
1 AT AT A
369210 ATTTTGATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:369933 original size:17 final size:18
Alignment explanation
Indices: 369911--369944 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
369901 CATTTTCAAA
369911 TATTTATATA-TATAAAT
1 TATTTATATATTATAAAT
369928 TATTTATATATTATAAA
1 TATTTATATATTATAAA
369945 ATGTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTATATATTATAAAT
Found at i:372644 original size:13 final size:14
Alignment explanation
Indices: 372626--372667 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
372616 TTTCAATTTT
372626 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
372639 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
372654 ATTTTAAATAATAT
1 ATTTT-AATAATAT
372668 TTATTACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:372652 original size:16 final size:16
Alignment explanation
Indices: 372630--372666 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
372620 AATTTTATTT
372630 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
372647 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
372662 TAATA
1 TAATA
372667 TTTATTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:373197 original size:14 final size:14
Alignment explanation
Indices: 373172--373207 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
373162 GAAAAATAAG
373172 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
* *
373186 TTATTTTTCAGAAA
1 TCATTTTCCAGAAA
373200 TCATTTTC
1 TCATTTTC
373208 AATGAAACAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Done.