Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005377.1 Kokia drynarioides strain JFW-HI SEQ_119364, 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: 11995
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:908 original size:15 final size:15
Alignment explanation
Indices: 888--924 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
878 AAATTAAAAT
*
888 TATTTAATAATTTTA
1 TATTTAAAAATTTTA
903 TATTTAAAAATTTTA
1 TATTTAAAAATTTTA
918 TATTTAA
1 TATTTAA
925 GAAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTAAAAATTTTA
Found at i:2950 original size:22 final size:22
Alignment explanation
Indices: 2908--2951 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2898 TAATATGGAG
* *
2908 TGATCAATTAAATTAACAATAA
1 TGATCAATTAAATAAAAAATAA
2930 TGATCAAATT-AATAAAAAATAA
1 TGATC-AATTAAATAAAAAATAA
2952 AATAACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
TGATCAATTAAATAAAAAATAA
Found at i:6973 original size:20 final size:19
Alignment explanation
Indices: 6935--6982 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
6925 GTTTTCAAAT
* *
6935 TAAAAAATATGTTTGATAAA
1 TAAAATATATGTTTAAT-AA
*
6955 TAAAATATATTTTTAATAA
1 TAAAATATATGTTTAATAA
*
6974 TGAAATATA
1 TAAAATATA
6983 ATCCACATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TAAAATATATGTTTAATAA
Found at i:7728 original size:42 final size:40
Alignment explanation
Indices: 7681--7781 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 40
7671 TATGTCGTTA
7681 TTTTGGTGCTTTTTTTACTAATTTGATTGCTATTTTTTACAG
1 TTTTGGTGCTTTTTTTACTAATTTGA-TGCT-TTTTTTACAG
** * *
7723 TTTTGGTATTTTTTTTTTACTATTTTGATGCTTTTTTTACTG
1 TTTTGG--TGCTTTTTTTACTAATTTGATGCTTTTTTTACAG
*
7765 TTTTGATGCTGTTTTTT
1 TTTTGGTGCT-TTTTTT
7782 TTATTGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
40 2 0.04
41 6 0.12
42 20 0.41
43 4 0.08
44 17 0.35
ACGTcount: A:0.13, C:0.08, G:0.14, T:0.65
Consensus pattern (40 bp):
TTTTGGTGCTTTTTTTACTAATTTGATGCTTTTTTTACAG
Found at i:7757 original size:20 final size:20
Alignment explanation
Indices: 7679--7781 Score: 100
Period size: 20 Copynumber: 4.9 Consensus size: 20
7669 TTTATGTCGT
*
7679 TATTTTGGTGCTTTTTTTAC
1 TATTTTGATGCTTTTTTTAC
*
7699 TAATTTGATTGCTATTTTTTAC
1 TATTTTGA-TGCT-TTTTTTAC
**
7721 -AGTTTTGGTATTTTTTTTTTAC
1 TA-TTTT-G-ATGCTTTTTTTAC
7743 TATTTTGATGCTTTTTTTAC
1 TATTTTGATGCTTTTTTTAC
*
7763 TGTTTTGATGCTGTTTTTT
1 TATTTTGATGCT-TTTTTT
7782 TTATTGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
20 28 0.41
21 12 0.18
22 23 0.34
23 4 0.06
24 1 0.01
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.65
Consensus pattern (20 bp):
TATTTTGATGCTTTTTTTAC
Found at i:7783 original size:44 final size:44
Alignment explanation
Indices: 7690--7771 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
7680 ATTTTGGTGC
*
7690 TTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGGTATTT
1 TTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGATATTT
* *
7734 TTTTTTTACTATTTTGA-TGCT-TTTTTTACTGTTTTGAT
1 TTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGAT
7772 GCTGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 15 0.43
43 4 0.11
44 16 0.46
ACGTcount: A:0.16, C:0.07, G:0.11, T:0.66
Consensus pattern (44 bp):
TTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGATATTT
Found at i:7789 original size:23 final size:23
Alignment explanation
Indices: 7733--7803 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
7723 TTTTGGTATT
*
7733 TTTTTTTTACTATTTTGATGC--
1 TTTTTTTTACTGTTTTGATGCTG
7754 -TTTTTTTACTGTTTTGATGCTG
1 TTTTTTTTACTGTTTTGATGCTG
* * *
7776 TTTTTTTTATTGTTTTGGTGTTG
1 TTTTTTTTACTGTTTTGATGCTG
7799 TTTTT
1 TTTTT
7804 GCTGTTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.44
23 24 0.56
ACGTcount: A:0.08, C:0.06, G:0.15, T:0.70
Consensus pattern (23 bp):
TTTTTTTTACTGTTTTGATGCTG
Found at i:7792 original size:43 final size:42
Alignment explanation
Indices: 7690--7784 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 42
7680 ATTTTGGTGC
* * * *
7690 TTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGGTATTT
1 TTTTTTTACTATTTTGA-TGCT-TTTTTTACTGTTTTGATATGT
*
7734 TTTTTTTACTATTTTGATGCTTTTTTTACTGTTTTGATGCTGT
1 TTTTTTTACTATTTTGATGCTTTTTTTACTGTTTTGAT-ATGT
7777 TTTTTTTA
1 TTTTTTTA
7785 TTGTTTTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 15 0.33
43 14 0.31
44 16 0.36
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (42 bp):
TTTTTTTACTATTTTGATGCTTTTTTTACTGTTTTGATATGT
Found at i:7797 original size:20 final size:20
Alignment explanation
Indices: 7681--7809 Score: 78
Period size: 20 Copynumber: 6.1 Consensus size: 20
7671 TATGTCGTTA
* *
7681 TTTTGGTGCTTTTTTTACTA
1 TTTTGGTGTTTTTTTTACTG
* * * *
7701 ATTTGATTGCTATTTTTTACAG
1 TTTTG-GTG-TTTTTTTTACTG
* *
7723 TTTTGGTATTTTTTTTTTACTA
1 TTTTGG--TGTTTTTTTTACTG
* *
7745 TTTTGATGCTTTTTTTACTG
1 TTTTGGTGTTTTTTTTACTG
*
7765 TTTTGATGCTGTTTTTTTTATTG
1 TTTTG--G-TGTTTTTTTTACTG
* *
7788 TTTTGGTGTTGTTTTTGCTG
1 TTTTGGTGTTTTTTTTACTG
7808 TT
1 TT
7810 GTTTTTATTG
Statistics
Matches: 80, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
20 33 0.41
21 3 0.04
22 26 0.32
23 18 0.22
ACGTcount: A:0.11, C:0.07, G:0.16, T:0.66
Consensus pattern (20 bp):
TTTTGGTGTTTTTTTTACTG
Found at i:7803 original size:12 final size:12
Alignment explanation
Indices: 7788--7860 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
7778 TTTTTTATTG
*
7788 TTTTGGTGTTGT
1 TTTTGCTGTTGT
7800 TTTTGCTGTTGT
1 TTTTGCTGTTGT
** * *
7812 TTTTATTGCTAT
1 TTTTGCTGTTGT
7824 TTTTG-TGTTG-
1 TTTTGCTGTTGT
* * *
7834 TTTTGTTATTAT
1 TTTTGCTGTTGT
7846 TTTTGCTGTTGT
1 TTTTGCTGTTGT
7858 TTT
1 TTT
7861 AATTGTTATT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
10 5 0.11
11 6 0.13
12 35 0.76
ACGTcount: A:0.05, C:0.04, G:0.21, T:0.70
Consensus pattern (12 bp):
TTTTGCTGTTGT
Found at i:7803 original size:64 final size:64
Alignment explanation
Indices: 7679--7803 Score: 146
Period size: 64 Copynumber: 2.0 Consensus size: 64
7669 TTTATGTCGT
* * *
7679 TATTTTGGTGCTTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGGTATTTTTTTTTTAC
1 TATTTTGATGCTTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGGTAGTTGTTTTTTAC
** * **
7743 TATTTTGATGCTTTTTTTACTGTTTTGA-TGCTGTTTTTTTTATTGTTTTGGT-GTTGTTTTT
1 TATTTTGATGCTTTTTTTACTAATTTGATTGC--TATTTTTTACAGTTTTGGTAGTTGTTTTT
7804 GCTGTTGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.06
64 32 0.63
65 16 0.31
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.66
Consensus pattern (64 bp):
TATTTTGATGCTTTTTTTACTAATTTGATTGCTATTTTTTACAGTTTTGGTAGTTGTTTTTTAC
Found at i:7811 original size:23 final size:23
Alignment explanation
Indices: 7785--7893 Score: 109
Period size: 23 Copynumber: 4.8 Consensus size: 23
7775 GTTTTTTTTA
* *
7785 TTGTTTTGGTGTTGTTTTTGCTG
1 TTGTTTTGTTGTTATTTTTGCTG
* *
7808 TTGTTTTTATTGCTATTTTTG-TG
1 TTG-TTTTGTTGTTATTTTTGCTG
*
7831 TTGTTTTGTTATTATTTTTGCTG
1 TTGTTTTGTTGTTATTTTTGCTG
*
7854 TTGTTTTAATTGTTA-TTTTG--G
1 TTGTTTT-GTTGTTATTTTTGCTG
*
7875 TTGTTTTGATGTTATTTTT
1 TTGTTTTGTTGTTATTTTT
7894 ATGCGTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
20 5 0.07
21 12 0.17
22 14 0.20
23 22 0.31
24 18 0.25
ACGTcount: A:0.08, C:0.03, G:0.20, T:0.69
Consensus pattern (23 bp):
TTGTTTTGTTGTTATTTTTGCTG
Found at i:7814 original size:46 final size:46
Alignment explanation
Indices: 7763--7893 Score: 124
Period size: 46 Copynumber: 2.9 Consensus size: 46
7753 CTTTTTTTAC
* * * *
7763 TGTTTTGA-TGCTGTTTTTTTTATTGTTTTGGTGTTGTTTTTGCTGT
1 TGTTTTGATTGCT-ATTTTTGTATTGTTTTGGTATTATTTTTGCTGT
* * *
7809 TGTTTTTATTGCTATTTTTGTGTTGTTTTGTTATTATTTTTGCTGT
1 TGTTTTGATTGCTATTTTTGTATTGTTTTGGTATTATTTTTGCTGT
* * * * *
7855 TGTTTTAATTGTTA-TTTTG-GTTGTTTTGATGTTATTTTT
1 TGTTTTGATTGCTATTTTTGTATTGTTTTGGTATTATTTTT
7894 ATGCGTTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 18 0.25
45 5 0.07
46 46 0.63
47 4 0.05
ACGTcount: A:0.08, C:0.03, G:0.20, T:0.69
Consensus pattern (46 bp):
TGTTTTGATTGCTATTTTTGTATTGTTTTGGTATTATTTTTGCTGT
Found at i:7832 original size:35 final size:32
Alignment explanation
Indices: 7771--7837 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
7761 ACTGTTTTGA
*
7771 TGCTGTTTTTTTTATTGTTTTGGTGTTGTTTT
1 TGCTGTTGTTTTTATTGTTTTGGTGTTGTTTT
*
7803 TGCTGTTGTTTTTATTGCTATTTTTGTGTTGTTTT
1 TGCTGTTGTTTTTATTG---TTTTGGTGTTGTTTT
7838 GTTATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 16 0.53
35 14 0.47
ACGTcount: A:0.04, C:0.04, G:0.21, T:0.70
Consensus pattern (32 bp):
TGCTGTTGTTTTTATTGTTTTGGTGTTGTTTT
Found at i:8234 original size:13 final size:13
Alignment explanation
Indices: 8216--8241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8206 TTTTCGGATC
8216 AAACCTAAAATTT
1 AAACCTAAAATTT
8229 AAACCTAAAATTT
1 AAACCTAAAATTT
8242 TGTTAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAACCTAAAATTT
Found at i:8533 original size:6 final size:6
Alignment explanation
Indices: 8483--8529 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
8473 ACAAACAAGT
* *
8483 GCAACC GCAACC GCAACC GCAACC GCAACC GCAACC GTAACA GCAAC
1 GCAACC GCAACC GCAACC GCAACC GCAACC GCAACC GCAACC GCAAC
8530 AGCATCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.36, C:0.45, G:0.17, T:0.02
Consensus pattern (6 bp):
GCAACC
Found at i:8585 original size:6 final size:6
Alignment explanation
Indices: 8574--8598 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8564 ATATCCTCTG
8574 CCATCT CCATCT CCATCT CCATCT C
1 CCATCT CCATCT CCATCT CCATCT C
8599 TTGTATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCATCT
Done.