Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012577.1 Kokia drynarioides strain JFW-HI SEQ_127586, 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: 33692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:3437 original size:16 final size:16
Alignment explanation
Indices: 3416--3465 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3406 TGATAGGGAT
3416 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
3432 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
3447 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
3462 ATTA
1 ATTA
3466 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:3751 original size:20 final size:21
Alignment explanation
Indices: 3726--3768 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3716 TACTTACTAC
3726 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
3746 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
3767 TA
1 TA
3769 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:4138 original size:25 final size:25
Alignment explanation
Indices: 4104--4152 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4094 AAACACATTA
*
4104 CCTTTTTTTCCTT-TCTCCTTCTTCC
1 CCTTCTTTTCCTTCT-TCCTTCTTCC
4129 CCTTCTTTTCCTTCTTCCTTCTTC
1 CCTTCTTTTCCTTCTTCCTTCTTC
4153 TTTCTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (25 bp):
CCTTCTTTTCCTTCTTCCTTCTTCC
Found at i:4157 original size:4 final size:4
Alignment explanation
Indices: 4150--4188 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
4140 TTCTTCCTTC
*
4150 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
4189 CTTCAATTTT
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:4161 original size:18 final size:18
Alignment explanation
Indices: 4130--4179 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4120 CCTTCTTCCC
*
4130 CTTCTTTTCCTTCTTCCTT
1 CTTC-TTTCTTTCTTCCTT
*
4149 CTTCTTTCTTTCTTTCTT
1 CTTCTTTCTTTCTTCCTT
4167 -TCTCTTT-TTTCTT
1 CT-TCTTTCTTTCTT
4180 TCTTTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.25
18 17 0.61
19 4 0.14
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTCTTTCTTTCTTCCTT
Found at i:4177 original size:21 final size:20
Alignment explanation
Indices: 4148--4192 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
4138 CCTTCTTCCT
4148 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
4169 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
4189 -CTTC
1 TCTTC
4193 AATTTTCGTT
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:4425 original size:69 final size:65
Alignment explanation
Indices: 4297--4439 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 65
4287 AATTAATTTC
* **
4297 CACCTCTTAAAAAACCTACACAAACACACACACACGGTACAATGGGATGCTGCCAAGTGGCAAAA
1 CACCTCTTAAAAAACCCACACAAACACACACACACGACACAATGGGATGCTGCCAAGTGGCAAAA
*
4362 CACCTCTTAAAAAACCCACACAAACACACACACACACACGACACAATGGGGTGCTGCCAAGTGGC
1 CACCTCTTAAAAAACCCACAC--A-A-ACACACACACACGACACAATGGGATGCTGCCAAGTGGC
4427 AAAA
62 AAAA
*
4431 CACCCCTTA
1 CACCTCTTA
4440 GTGCCGCCAC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
65 20 0.29
67 1 0.01
68 1 0.01
69 47 0.68
ACGTcount: A:0.41, C:0.33, G:0.14, T:0.13
Consensus pattern (65 bp):
CACCTCTTAAAAAACCCACACAAACACACACACACGACACAATGGGATGCTGCCAAGTGGCAAAA
Found at i:5949 original size:3 final size:3
Alignment explanation
Indices: 5943--5972 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5933 TTCGTCGTCG
5943 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5973 ACTTATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:11030 original size:17 final size:17
Alignment explanation
Indices: 11008--11041 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10998 TTTTTAAATG
11008 TTAAAAGTAC-AATACAA
1 TTAAAA-TACAAATACAA
11025 TTAAAATACAAATACAA
1 TTAAAATACAAATACAA
11042 GTACATGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAAAATACAAATACAA
Found at i:11345 original size:2 final size:2
Alignment explanation
Indices: 11338--11378 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11328 TTGAGAACTC
11338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11379 AAATTGCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13777 original size:28 final size:28
Alignment explanation
Indices: 13741--13821 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 28
13731 AAAAAATTAA
13741 AAAATATATATATAAATACATAAATATTT
1 AAAA-ATATATATAAATACATAAATATTT
13770 AAAAATATATAT--AT-CAT-AATAAGTTT
1 AAAAATATATATAAATACATAAAT-A-TTT
*
13796 AAAAATATATGTAAA-A-ATAAATATTT
1 AAAAATATATATAAATACATAAATATTT
13822 TTTTAAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 19 0.42
27 3 0.07
28 12 0.27
29 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAAATATATATAAATACATAAATATTT
Found at i:13814 original size:24 final size:25
Alignment explanation
Indices: 13750--13815 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
13740 AAAAATATAT
*
13750 ATATAAATACATAAAT-A-TTTAAAA
1 ATATATATACA-AAATAAGTTTAAAA
*
13774 ATATATATATCATAATAAGTTTAAAA
1 ATATATATA-CAAAATAAGTTTAAAA
*
13800 ATATATGTA-AAAATAA
1 ATATATATACAAAATAA
13816 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 17 0.49
25 3 0.09
26 15 0.43
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATATATACAAAATAAGTTTAAAA
Found at i:13912 original size:6 final size:6
Alignment explanation
Indices: 13901--13940 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
13891 CCCACTCTCA
13901 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC -CCCT
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCT
13941 ACCACGTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCCTC
Found at i:19309 original size:32 final size:31
Alignment explanation
Indices: 19273--19335 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
19263 ATGATAGAGC
*
19273 ATAAAAAAATTGATGGTTCAGTCTTTATCATT
1 ATAAAAAAATTAATGGTTCAGTC-TTATCATT
**
19305 ATAAAAATGTTAATGGTTCAGTCTTATCATT
1 ATAAAAAAATTAATGGTTCAGTCTTATCATT
19336 GTAATTCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (31 bp):
ATAAAAAAATTAATGGTTCAGTCTTATCATT
Found at i:23066 original size:7 final size:7
Alignment explanation
Indices: 23054--23082 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
23044 AGCTGCACCG
23054 TGTTGTC
1 TGTTGTC
23061 TGTTGTC
1 TGTTGTC
23068 TGTTGTC
1 TGTTGTC
23075 TGTTGTC
1 TGTTGTC
23082 T
1 T
23083 TGTCCCCTGT
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:0.00, C:0.14, G:0.28, T:0.59
Consensus pattern (7 bp):
TGTTGTC
Found at i:27565 original size:20 final size:17
Alignment explanation
Indices: 27540--27578 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
27530 ATCATGTATG
27540 AAATTAAATAACATAAATGA
1 AAATTAAA-AA-AT-AATGA
27560 AAATTAAAAAATAATGA
1 AAATTAAAAAATAATGA
27577 AA
1 AA
27579 TAAAACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 2 0.11
20 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAATAATGA
Found at i:32112 original size:23 final size:23
Alignment explanation
Indices: 32082--32148 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
32072 CGCTAGCGCA
32082 CTTACTGTTTCGCATTTTGTGTG
1 CTTACTGTTTCGCATTTTGTGTG
*
32105 CTTACTGTTTCGCACTTTGTGTG
1 CTTACTGTTTCGCATTTTGTGTG
* *
32128 CTTCCTGATTT-GCATTATGTG
1 CTTACTG-TTTCGCATTTTGTG
32149 CTCCTACTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 36 0.92
24 3 0.08
ACGTcount: A:0.10, C:0.19, G:0.21, T:0.49
Consensus pattern (23 bp):
CTTACTGTTTCGCATTTTGTGTG
Found at i:32187 original size:23 final size:22
Alignment explanation
Indices: 32099--32194 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 22
32089 TTTCGCATTT
* * *
32099 TGTGTGCTTACTGTTTCGCACTT
1 TGTGTGCCTACTGATT-GCACTG
* * * *
32122 TGTGTGCTTCCTGATTTGCATTA
1 TGTGTGCCTACTGA-TTGCACTG
32145 TGTGCT-CCTACTGATTGCACTG
1 TGTG-TGCCTACTGATTGCACTG
32167 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
32190 TGTGT
1 TGTGT
32195 ACTTACTGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 16 0.26
23 41 0.67
24 3 0.05
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:32201 original size:23 final size:23
Alignment explanation
Indices: 32151--32202 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
32141 ATTATGTGCT
*
32151 CCTACT-GATTGCACTGTGTGTG
1 CCTACTGGATTGCACTGTGTGTA
32173 CCTACTGGATTGCACTGTGTGTA
1 CCTACTGGATTGCACTGTGTGTA
*
32196 CTTACTG
1 CCTACTG
32203 TTTCTCCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (23 bp):
CCTACTGGATTGCACTGTGTGTA
Found at i:33119 original size:12 final size:12
Alignment explanation
Indices: 33102--33158 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
33092 GATGGGTCTA
33102 ATAAACGAGCTT
1 ATAAACGAGCTT
33114 ATAAAC-AGGCTT
1 ATAAACGA-GCTT
33126 -TAAACGAGCTT
1 ATAAACGAGCTT
* * *
33137 -TATACAAGCTA
1 ATAAACGAGCTT
33148 ATAAACGAGCT
1 ATAAACGAGCT
33159 AGTAAATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:33133 original size:23 final size:23
Alignment explanation
Indices: 33099--33158 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
33089 TCTGATGGGT
*
33099 CTAATAAACGAGCTTATAAACAGG
1 CTAATAAACGAGCTT-TAAACAAG
* *
33123 CT-TTAAACGAGCTTTATACAAG
1 CTAATAAACGAGCTTTAAACAAG
33145 CTAATAAACGAGCT
1 CTAATAAACGAGCT
33159 AGTAAATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 8 0.26
23 21 0.68
24 2 0.06
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (23 bp):
CTAATAAACGAGCTTTAAACAAG
Found at i:33136 original size:11 final size:11
Alignment explanation
Indices: 33103--33158 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
33093 ATGGGTCTAA
33103 TAAACGAGCTT
1 TAAACGAGCTT
33114 ATAAAC-AGGCTT
1 -TAAACGA-GCTT
33126 TAAACGAGCTT
1 TAAACGAGCTT
* * *
33137 TATACAAGCTAA
1 TAAACGAGCT-T
33149 TAAACGAGCT
1 TAAACGAGCT
33159 AGTAAATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (11 bp):
TAAACGAGCTT
Found at i:33198 original size:22 final size:22
Alignment explanation
Indices: 33170--33232 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
33160 GTAAATGAAT
33170 CATAAACGAGCTTGTTCGTAAA
1 CATAAACGAGCTTGTTCGTAAA
*
33192 CATAAACGAGCTTGTTCGTGAA
1 CATAAACGAGCTTGTTCGTAAA
33214 CATAAACGAGCTTGTTCGT
1 CATAAACGAGCTTGTTCGT
33233 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (22 bp):
CATAAACGAGCTTGTTCGTAAA
Done.