Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000464.1 Kokia drynarioides strain JFW-HI SEQ_111336, 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: 104568
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 83 characters in sequence are not A, C, G, or T
Found at i:123 original size:4 final size:4
Alignment explanation
Indices: 116--154 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
106 TTCTTCCTTC
*
116 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
155 CTTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:143 original size:21 final size:20
Alignment explanation
Indices: 114--158 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
104 CCTTCTTCCT
114 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
135 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
155 -CTTC
1 TCTTC
159 ATTTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:151 original size:11 final size:11
Alignment explanation
Indices: 113--165 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
103 TCCTTCTTCC
*
113 TTCTTCTTTCT
1 TTCTTTTTTCT
124 TTCTTTCTTTC-
1 TTCTTT-TTTCT
135 -TCTTTTTTCT
1 TTCTTTTTTCT
*
145 TTCTTTTTTCC
1 TTCTTTTTTCT
*
156 TTCATTTTTC
1 TTCTTTTTTC
166 GTTGATCCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 23 0.64
12 4 0.11
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:163 original size:21 final size:21
Alignment explanation
Indices: 109--163 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
99 CTTCTCCTTC
109 TTCCTTCTTCTTTCTTTCTTTCT
1 TTCCTTC-T-TTTCTTTCTTTCT
132 TTCTCTT-TTTTCTTTCTTT-T
1 TTC-CTTCTTTTCTTTCTTTCT
152 TTCCTTCATTTT
1 TTCCTTC-TTTT
164 TCGTTGATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 15 0.52
22 1 0.03
23 3 0.10
24 3 0.10
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTTCTTTTCTTTCTTTCT
Found at i:356 original size:27 final size:28
Alignment explanation
Indices: 326--381 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
316 CCCTTAGTGC
326 CGCCAC-TTGATATTCCTCCATT-GGTGT
1 CGCCACTTTG-TATTCCTCCATTGGGTGT
*
353 CGCCACTTTGTGTTCCTCCATTGGGTGT
1 CGCCACTTTGTATTCCTCCATTGGGTGT
381 C
1 C
382 AGGTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (28 bp):
CGCCACTTTGTATTCCTCCATTGGGTGT
Found at i:3365 original size:4 final size:4
Alignment explanation
Indices: 3356--3395 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
3346 AATCTTATTT
3356 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3396 CACATTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:3890 original size:17 final size:17
Alignment explanation
Indices: 3863--3895 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
3853 AAGTGACCTT
3863 TGTTTGAGAC-AGAACA
1 TGTTTGAGACAAGAACA
3879 TGTTTCGAGACAAGAAC
1 TGTTT-GAGACAAGAAC
3896 CCCTTGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (17 bp):
TGTTTGAGACAAGAACA
Found at i:14621 original size:24 final size:24
Alignment explanation
Indices: 14575--14621 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
14565 CACATGGCAT
* * *
14575 TTTTTCAAATTAAATTATGTGGTA
1 TTTTTAAAATAAAAATATGTGGTA
*
14599 TTTTTAAAATAAAAATATTTGGT
1 TTTTTAAAATAAAAATATGTGGT
14622 CAACGGTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTTTAAAATAAAAATATGTGGTA
Found at i:15650 original size:20 final size:21
Alignment explanation
Indices: 15627--15672 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15617 TAAGATTTTT
15627 AAAAAT-ATTAAAAATTAATA
1 AAAAATAATTAAAAATTAATA
* * *
15647 AAAAATAATTAATATTTATTA
1 AAAAATAATTAAAAATTAATA
15668 AAAAA
1 AAAAA
15673 ACATCATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATAATTAAAAATTAATA
Found at i:17831 original size:26 final size:25
Alignment explanation
Indices: 17775--17829 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
17765 TGATCAGTTC
*
17775 AAAATAAATATATTATTAAAAAATTT
1 AAAATAAAAATATTA-TAAAAAATTT
17801 AAAATAAAAATATTA-AAAAAATTAT
1 AAAATAAAAATATTATAAAAAATT-T
17826 AAAA
1 AAAA
17830 ATCGATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 5 0.19
26 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAATAAAAATATTATAAAAAATTT
Found at i:19685 original size:31 final size:31
Alignment explanation
Indices: 19590--19701 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
19580 TTAATATAAC
** * * *
19590 ATTTGGTACTTGAACTTGACACTCTTTCTTA
1 ATTTGGTACTCAAACTTGATACTTTTTCCTA
* *
19621 ATTTGGTAGTTAAACTT--T--TTTTAGTCC-A
1 ATTTGGTACTCAAACTTGATACTTTT--TCCTA
19649 ATTTGGTACTCAAACTTGATACTTTTTCCTA
1 ATTTGGTACTCAAACTTGATACTTTTTCCTA
19680 ATTTGGTAC-CTAAACTTGATAC
1 ATTTGGTACTC-AAACTTGATAC
19702 AGTTTTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
27 3 0.05
28 16 0.24
29 2 0.03
30 5 0.08
31 36 0.55
32 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTGGTACTCAAACTTGATACTTTTTCCTA
Found at i:19726 original size:32 final size:30
Alignment explanation
Indices: 19592--19728 Score: 86
Period size: 31 Copynumber: 4.5 Consensus size: 30
19582 AATATAACAT
* * * *
19592 TTGGTACTTGAACTTGACACTCTTTCTTAAT
1 TTGGTACTTAAACTTGATACTTTTTC-TAAG
* * *
19623 TTGGTAGTTAAACTT--T--TTTTAGTCCAAT
1 TTGGTACTTAAACTTGATACTTTT--TCTAAG
* *
19651 TTGGTACTCAAACTTGATACTTTTTCCTAAT
1 TTGGTACTTAAACTTGATACTTTTT-CTAAG
*
19682 TTGGTACCTAAACTTGATACAGTTTTT-TAAAG
1 TTGGTACTTAAACTTGATAC--TTTTTCT-AAG
19714 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
19729 TTTGGGATCC
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.04
28 16 0.19
29 2 0.02
30 2 0.02
31 36 0.43
32 20 0.24
33 5 0.06
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (30 bp):
TTGGTACTTAAACTTGATACTTTTTCTAAG
Found at i:20007 original size:33 final size:33
Alignment explanation
Indices: 19964--20053 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 33
19954 AAAAAAGCTT
19964 AGGTACCAAATTAGGAAAAAAATTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAAATTGTCAAGTTC
* *
19997 AGGTATCAAATTAGG--AAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAAATTGTCAAGTTC
* *
20028 ATGTACCAAATTGAGTCAAAAAAATT
1 AGGTACCAAATT-AG-GAAAAAAATT
20054 TAGATACCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 25 0.53
32 2 0.04
33 14 0.30
35 6 0.13
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.26
Consensus pattern (33 bp):
AGGTACCAAATTAGGAAAAAAATTGTCAAGTTC
Found at i:30073 original size:20 final size:19
Alignment explanation
Indices: 30050--30087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
30040 TAAAAATAAA
*
30050 TAAAAATTATAGAAAAATAG
1 TAAAAATTA-AAAAAAATAG
30070 TAAAAATTAAAAAAAATA
1 TAAAAATTAAAAAAAATA
30088 ACCCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
TAAAAATTAAAAAAAATAG
Found at i:45744 original size:19 final size:20
Alignment explanation
Indices: 45708--45749 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
45698 AATAAATTTT
45708 ATATATTTATTATGTAA-TA
1 ATATATTTATTATGTAATTA
45727 ATATATTTATTTAT-TAATTA
1 ATATATTTA-TTATGTAATTA
45747 ATA
1 ATA
45750 CATAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATATTTATTATGTAATTA
Found at i:54030 original size:25 final size:22
Alignment explanation
Indices: 53998--54045 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
53988 TTCACCCACC
53998 TTTTTTTTTA-AATTTTTTATATT
1 TTTTTTTTTATAA--TTTTATATT
54021 TTTTTGTTTTATAATTTTATATT
1 TTTTT-TTTTATAATTTTATATT
54044 TT
1 TT
54046 ATAGTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 16 0.70
24 5 0.22
25 2 0.09
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTTTTTATAATTTTATATT
Found at i:54032 original size:15 final size:15
Alignment explanation
Indices: 54012--54070 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
54002 TTTTTAAATT
* *
54012 TTTTATATTTTTTTG
1 TTTTATATTTTTATA
*
54027 TTTTATAATTTTATA
1 TTTTATATTTTTATA
*
54042 TTTTATAGTTTTCATA
1 TTTTATA-TTTTTATA
*
54058 ATTTA-ATTTTTAT
1 TTTTATATTTTTAT
54071 CTCATAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 6 0.17
15 20 0.56
16 10 0.28
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTATATTTTTATA
Found at i:54038 original size:23 final size:24
Alignment explanation
Indices: 54012--54068 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
54002 TTTTTAAATT
*
54012 TTTTATATTTTTTTGTTTT-ATAA
1 TTTTATATTTTTTAGTTTTCATAA
*
54035 TTTTATATTTTATAGTTTTCATAA
1 TTTTATATTTTTTAGTTTTCATAA
54059 -TTTA-ATTTTT
1 TTTTATATTTTT
54069 ATCTCATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 21 0.70
24 4 0.13
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTATATTTTTTAGTTTTCATAA
Found at i:64955 original size:7 final size:7
Alignment explanation
Indices: 64945--64973 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
64935 AAAACAAAGG
64945 GTCTCAT
1 GTCTCAT
64952 GTCTCAT
1 GTCTCAT
64959 GTCTCAT
1 GTCTCAT
64966 GTCTCAT
1 GTCTCAT
64973 G
1 G
64974 CTAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.17, T:0.41
Consensus pattern (7 bp):
GTCTCAT
Found at i:71287 original size:18 final size:19
Alignment explanation
Indices: 71252--71312 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
71242 AACTTTTATC
71252 TAAAATTATTAAAATAATA
1 TAAAATTATTAAAATAATA
71271 TAAAA-TATTATATTAATAATA
1 TAAAATTATTA-A--AATAATA
71292 TTAAAATTA-TAAAATAA-A
1 -TAAAATTATTAAAATAATA
71310 TAA
1 TAA
71313 TTTTCAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 11 0.30
21 8 0.22
22 7 0.19
23 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATTATTAAAATAATA
Found at i:71288 original size:21 final size:20
Alignment explanation
Indices: 71264--71302 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
71254 AAATTATTAA
71264 AATAATATAAAATATTATATT
1 AATAATATAAAA-ATTATATT
*
71285 AATAATATTAAAATTATA
1 AATAATATAAAAATTATA
71303 AAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATATAAAAATTATATT
Found at i:74925 original size:16 final size:16
Alignment explanation
Indices: 74882--74933 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
74872 TATGATTTGA
*
74882 AAAAACATATTGCGGT
1 AAAAACATATTGTGGT
*
74898 AAACAGACATATTGTGTT
1 AAA-A-ACATATTGTGGT
74916 AAAAACATATTGTGGT
1 AAAAACATATTGTGGT
74932 AA
1 AA
74934 GACTTTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 16 0.52
17 2 0.06
18 13 0.42
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (16 bp):
AAAAACATATTGTGGT
Found at i:74974 original size:13 final size:13
Alignment explanation
Indices: 74956--74981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74946 ACCTTTTCTC
74956 TGTCTTTTCTTTT
1 TGTCTTTTCTTTT
74969 TGTCTTTTCTTTT
1 TGTCTTTTCTTTT
74982 CCTTTCTTTT
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:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (13 bp):
TGTCTTTTCTTTT
Found at i:74975 original size:24 final size:23
Alignment explanation
Indices: 74948--74992 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
74938 TTACTTGTAC
*
74948 CTTTTCTCTGTCTTTTCTTTTTGT
1 CTTTTCT-TGTCCTTTCTTTTTGT
*
74972 CTTTTCTTTTCCTTTCTTTTT
1 CTTTTCTTGTCCTTTCTTTTT
74993 TACATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.73
Consensus pattern (23 bp):
CTTTTCTTGTCCTTTCTTTTTGT
Done.