Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006396.1 Kokia drynarioides strain JFW-HI SEQ_120973, 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: 4785
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Found at i:949 original size:28 final size:27
Alignment explanation
Indices: 926--1084 Score: 149
Period size: 28 Copynumber: 5.8 Consensus size: 27
916 CTTTTTTGTG
* *
926 AAGAATCCTTTGTGGTGATCTTTTTTA
1 AAGAAGCCTTTGTGGCGATCTTTTTTA
*
953 AAGAAAGCCTTTGTGACGATC-TTTTTA
1 AAG-AAGCCTTTGTGGCGATCTTTTTTA
*
980 AAGATAGCCTTTGTGGTGATCTTTTTTA
1 AAGA-AGCCTTTGTGGCGATCTTTTTTA
* * *
1008 AAGAAGCATTTGTGGCGATCTCTGTTA
1 AAGAAGCCTTTGTGGCGATCTTTTTTA
* * * * *
1035 AAGAAAGCATTTGTGGTGATCTCTGTGA
1 AAG-AAGCCTTTGTGGCGATCTTTTTTA
* *
1063 AAGAACGTCTTTGTGGCTATCT
1 AAGAA-GCCTTTGTGGCGATCT
1085 CTAGAAAAGA
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.01
27 50 0.45
28 61 0.54
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (27 bp):
AAGAAGCCTTTGTGGCGATCTTTTTTA
Found at i:957 original size:27 final size:27
Alignment explanation
Indices: 926--1056 Score: 156
Period size: 27 Copynumber: 4.8 Consensus size: 27
916 CTTTTTTGTG
*
926 AAGAATCCTTTGTGGTGATCTTTTTTA
1 AAGAAGCCTTTGTGGTGATCTTTTTTA
**
953 AAGAAAGCCTTTGTGACGATC-TTTTTA
1 AAG-AAGCCTTTGTGGTGATCTTTTTTA
980 AAGATAGCCTTTGTGGTGATCTTTTTTA
1 AAGA-AGCCTTTGTGGTGATCTTTTTTA
* * * *
1008 AAGAAGCATTTGTGGCGATCTCTGTTA
1 AAGAAGCCTTTGTGGTGATCTTTTTTA
*
1035 AAGAAAGCATTTGTGGTGATCT
1 AAG-AAGCCTTTGTGGTGATCT
1057 CTGTGAAAGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.01
27 48 0.53
28 41 0.46
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (27 bp):
AAGAAGCCTTTGTGGTGATCTTTTTTA
Found at i:993 original size:55 final size:55
Alignment explanation
Indices: 932--1056 Score: 189
Period size: 55 Copynumber: 2.3 Consensus size: 55
922 TGTGAAGAAT
* * *
932 CCTTTGTGGTGATCTTTTTTAAAGAAAGCCTTTGTGACGATCT-TTTTAAAGATAG
1 CCTTTGTGGTGATCTTTTTTAAAG-AAGCATTTGTGACGATCTCTGTTAAAGAAAG
*
987 CCTTTGTGGTGATCTTTTTTAAAGAAGCATTTGTGGCGATCTCTGTTAAAGAAAG
1 CCTTTGTGGTGATCTTTTTTAAAGAAGCATTTGTGACGATCTCTGTTAAAGAAAG
*
1042 CATTTGTGGTGATCT
1 CCTTTGTGGTGATCT
1057 CTGTGAAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 16 0.25
55 48 0.75
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (55 bp):
CCTTTGTGGTGATCTTTTTTAAAGAAGCATTTGTGACGATCTCTGTTAAAGAAAG
Found at i:1066 original size:55 final size:54
Alignment explanation
Indices: 934--1086 Score: 182
Period size: 55 Copynumber: 2.8 Consensus size: 54
924 TGAAGAATCC
* * * *
934 TTTGTGGTGATCTTTTTTAAAGAAAGCCTTTGTGACGATCT-TTTTAAAGATAGCC
1 TTTGTGGTGATCTTTTTTAAAG-AAG-CTTTGTGGCGATCTCTGTTAAAGAAAGCA
989 TTTGTGGTGATCTTTTTTAAAGAAGCATTTGTGGCGATCTCTGTTAAAGAAAGCA
1 TTTGTGGTGATCTTTTTTAAAGAAGC-TTTGTGGCGATCTCTGTTAAAGAAAGCA
* * * *
1044 TTTGTGGTGATCTCTGTGAAAGAACGTCTTTGTGGCTATCTCT
1 TTTGTGGTGATCTTTTTTAAAGAA-G-CTTTGTGGCGATCTCT
1087 AGAAAAGAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
53 1 0.01
54 15 0.17
55 54 0.63
56 15 0.17
57 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.41
Consensus pattern (54 bp):
TTTGTGGTGATCTTTTTTAAAGAAGCTTTGTGGCGATCTCTGTTAAAGAAAGCA
Found at i:4530 original size:29 final size:28
Alignment explanation
Indices: 4503--4770 Score: 139
Period size: 29 Copynumber: 9.2 Consensus size: 28
4493 GTAATTTTAT
4503 GAAAGTTTAAGGTTAAAATGTGATTTTAG
1 GAAAGTTTAAGGTTAAAATGTGATTTT-G
* * ** *
4532 G-AAGCTTTAGGGCTAAAACATGAATTTAAG
1 GAAAG-TTTAAGGTTAAAATGTG-ATTT-TG
* * *
4562 AAAAATTAAAGGGTTAAAATGTGATTTTG
1 GAAAGTTTAA-GGTTAAAATGTGATTTTG
* * *
4591 GAAAGTTTAGGGTCAAAATGTAATTTTG
1 GAAAGTTTAAGGTTAAAATGTGATTTTG
**
4619 GAAAAGTTT-AGGTGTCAAAATGCAATTTTG
1 G-AAAGTTTAAGGT-T-AAAATGTGATTTTG
* *
4649 GAGAAGCTTAAGTGTTAAAATGTAATTTTG
1 GA-AAGTTTAAG-GTTAAAATGTGATTTTG
* * *** *
4679 AAAAGTTTAGGGTTAAAATACAATTTTA
1 GAAAGTTTAAGGTTAAAATGTGATTTTG
* ** *
4707 GAGAAG-TTAAGGGCTAAAATGCAATTTAG
1 GA-AAGTTTAA-GGTTAAAATGTGATTTTG
* *
4736 AAAAGTTTAAGGGTT-AAATGTAATTTTG
1 GAAAGTTTAA-GGTTAAAATGTGATTTTG
4764 GAGAAGT
1 GA-AAGT
4771 GTGGGAGTCA
Statistics
Matches: 183, Mismatches: 41, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
28 56 0.31
29 66 0.36
30 45 0.25
31 14 0.08
32 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (28 bp):
GAAAGTTTAAGGTTAAAATGTGATTTTG
Found at i:4595 original size:88 final size:84
Alignment explanation
Indices: 4493--4770 Score: 267
Period size: 88 Copynumber: 3.2 Consensus size: 84
4483 GGGTCTAAAG
* * *
4493 GTAATTTTATGAAAGTTTAAGGTTAAAATGTGATTTTAGGAAGCTTTAGGGCTAAAACATG-AAT
1 GTAATTTT-GGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAG-TTTAGGGCT-AAA-ATGCAAT
4557 TTAAGAAAAATTAAAGGGTTAAAAT
62 TT-AGAAAAATT-AAGGGTTAAAAT
* *
4582 GTGATTTTGGAAAGTTTAGGGTCAAAATGTAATTTT-GGAAAAGTTTAGGTG-TCAAAATGCAAT
1 GTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGG--AAGTTTAGG-GCT-AAAATGCAA-
* ** *
4645 TTTGGAGAAGCTTAAGTGTTAAAAT
61 TTTAGA-AAAATTAAGGGTTAAAAT
* ** *
4670 GTAATTTTGAAAAGTTTAGGGTTAAAATACAATTTTAGAGAAGTTAAGGGCTAAAATGCAATTTA
1 GTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAG-GAAGTTTAGGGCTAAAATGCAATTTA
*
4735 GAAAAGTTTAAGGGTT-AAAT
65 GAAAA-ATTAAGGGTTAAAAT
4755 GTAATTTTGGAGAAGT
1 GTAATTTTGGA-AAGT
4771 GTGGGAGTCA
Statistics
Matches: 157, Mismatches: 21, Indels: 25
0.77 0.10 0.12
Matches are distributed among these distances:
85 16 0.10
86 17 0.11
87 15 0.10
88 89 0.57
89 19 0.12
90 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.34
Consensus pattern (84 bp):
GTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAGTTTAGGGCTAAAATGCAATTTAG
AAAAATTAAGGGTTAAAAT
Found at i:4647 original size:58 final size:56
Alignment explanation
Indices: 4571--4770 Score: 215
Period size: 57 Copynumber: 3.5 Consensus size: 56
4561 GAAAAATTAA
** *
4571 AGGGTTAAAATGTGATTTTGGA-AAGTTTAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 AGGG-TAAAATGCAATTTTGGAGAAGTTAAGGGTCAAAATGTAATTTT-GAAAAGTTT
* *
4628 AGGTGTCAAAATGCAATTTTGGAGAAGCTTAAGTGTTAAAATGTAATTTTGAAAAGTTT
1 AGG-GT-AAAATGCAATTTTGGAGAAG-TTAAGGGTCAAAATGTAATTTTGAAAAGTTT
* * * *
4687 AGGGTTAAAATACAATTTTAGAGAAGTTAAGGG-CTAAAATGCAATTTAGAAAAGTTT
1 AGGG-TAAAATGCAATTTTGGAGAAGTTAAGGGTC-AAAATGTAATTTTGAAAAGTTT
* *
4744 AAGGGTTAAATGTAATTTTGGAGAAGT
1 -AGGGTAAAATGCAATTTTGGAGAAGT
4771 GTGGGAGTCA
Statistics
Matches: 121, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
57 48 0.40
58 38 0.31
59 16 0.13
60 19 0.16
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (56 bp):
AGGGTAAAATGCAATTTTGGAGAAGTTAAGGGTCAAAATGTAATTTTGAAAAGTTT
Done.