Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003384.1 Kokia drynarioides strain JFW-HI SEQ_116118, 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: 143200
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:15017 original size:53 final size:53
Alignment explanation
Indices: 14910--15025 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 53
14900 GGCTAAAATA
* *
14910 TTTTCAACTTGAGAGCAAGTTTTCCAATTATTTGTGCAAAAATTCCACCTTTT
1 TTTTCAACTTGAGAGCAAGTTTTCCAATTATTTGTGCAAAAAATCCAACTTTT
* * * * *
14963 TTTTCAATTTGAGAGCAAGTTTTCCATTTATTTTTGCAAAAAATCAATTATTTTT
1 TTTTCAACTTGAGAGCAAGTTTTCCAATTATTTGTGCAAAAAATCCA--ACTTTT
15018 TTTTCAAC
1 TTTTCAAC
15026 AAGGAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 42 0.79
55 11 0.21
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (53 bp):
TTTTCAACTTGAGAGCAAGTTTTCCAATTATTTGTGCAAAAAATCCAACTTTT
Found at i:27616 original size:16 final size:16
Alignment explanation
Indices: 27592--27625 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27582 TATTAATACA
*
27592 TATTTAATAATATTTT
1 TATTAAATAATATTTT
*
27608 TATTAAATAATTTTTT
1 TATTAAATAATATTTT
27624 TA
1 TA
27626 AAAATTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTAAATAATATTTT
Found at i:31209 original size:6 final size:6
Alignment explanation
Indices: 31198--31233 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
31188 TGAAACCCAA
* *
31198 TTATTT TTATTT TTATTT TTATTT CTATTT CTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
31234 CAGTCTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:32184 original size:22 final size:22
Alignment explanation
Indices: 32155--32206 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
32145 GGGCACCCCG
*
32155 TCTA-AATAGAGATTTATTTTT
1 TCTATAATAGAGATTTATTTTA
*
32176 TCTATAATATAGATTTATTTTA
1 TCTATAATAGAGATTTATTTTA
32198 TCATATAAT
1 TC-TATAAT
32207 TTATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (22 bp):
TCTATAATAGAGATTTATTTTA
Found at i:33916 original size:2 final size:2
Alignment explanation
Indices: 33909--33939 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33899 TCAAAACATC
33909 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 A
33940 ATAAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35284 original size:26 final size:26
Alignment explanation
Indices: 35251--35303 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35241 TTTAAAAATA
35251 TATATTTAAAAATATTTTTTATACTT
1 TATATTTAAAAATATTTTTTATACTT
35277 TATATTTAAAAATATTTTTTATACTT
1 TATATTTAAAAATATTTTTTATACTT
35303 T
1 T
35304 TTATACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATTTAAAAATATTTTTTATACTT
Found at i:44182 original size:21 final size:21
Alignment explanation
Indices: 44158--44197 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44148 TTTAATTTTT
* * *
44158 TTTAAGATGAAAATATTGAAA
1 TTTAAAATCAAAACATTGAAA
44179 TTTAAAATCAAAACATTGA
1 TTTAAAATCAAAACATTGA
44198 TGTGATAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTAAAATCAAAACATTGAAA
Found at i:44921 original size:19 final size:19
Alignment explanation
Indices: 44899--44959 Score: 50
Period size: 24 Copynumber: 2.9 Consensus size: 19
44889 ATATAAAATT
44899 ATTTTTTAATATATTTTCA
1 ATTTTTTAATATATTTTCA
* *
44918 ATTTGTTAAAAAATATATATTTTA
1 ATTT-TT---TAATATAT-TTTCA
44942 ATGTTTTTAATATATTTT
1 AT-TTTTTAATATATTTT
44960 ATATATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 7 0.21
23 7 0.21
24 8 0.24
25 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTTTAATATATTTTCA
Found at i:44965 original size:28 final size:28
Alignment explanation
Indices: 44931--44992 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
44921 TGTTAAAAAA
*
44931 TATATATTTTAATGTTTTT-AATATA-TTT
1 TATATATTAT-AT-TTTTTAAATATACTTT
*
44959 TATATATTATATTTTTTAAATTTACTTT
1 TATATATTATATTTTTTAAATATACTTT
44987 TATATA
1 TATATA
44993 AAAATTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 7 0.23
28 18 0.60
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TATATATTATATTTTTTAAATATACTTT
Found at i:64130 original size:31 final size:31
Alignment explanation
Indices: 64088--64176 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
64078 CGAAATTTAG
*
64088 AAAG-GTTTGAGCAAAAATATTAGGTCCAAA
1 AAAGAGTTTGAGCAAAAATATTAGGCCCAAA
64118 AAAGAGTTTGAGCAAAAATATTAGGCCCAAA
1 AAAGAGTTTGAGCAAAAATATTAGGCCCAAA
* *
64149 AAAGAGTTTGGGCAAAAATATTAAGCCC
1 AAAGAGTTTGAGCAAAAATATTAGGCCC
64177 GTTTAAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 4 0.07
31 51 0.93
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (31 bp):
AAAGAGTTTGAGCAAAAATATTAGGCCCAAA
Found at i:91761 original size:23 final size:23
Alignment explanation
Indices: 91709--91803 Score: 95
Period size: 23 Copynumber: 4.1 Consensus size: 23
91699 ACACTAGCGC
*
91709 GCTCTCTGTTTAGCACGTTTCGTG-
1 GCTCTCTGATTAGCAC-TTT-GTGT
*
91733 AC-CTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
91755 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * * *
91778 ACTTTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
91801 GCT
1 GCT
91804 TTCTATTGCC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
21 3 0.05
22 4 0.07
23 51 0.86
24 1 0.02
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:91805 original size:23 final size:23
Alignment explanation
Indices: 91736--91807 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
91726 TTTCGTGACC
*
91736 TCTGATTAGCACTTTGTGTGCTC
1 TCTGATTAGCACTTTGTGTGCTT
* *
91759 TCTGATTAGTACTTTGTGTACTT
1 TCTGATTAGCACTTTGTGTGCTT
* *
91782 TCTGTTTAGCACTGTGTGTGCTT
1 TCTGATTAGCACTTTGTGTGCTT
91805 TCT
1 TCT
91808 ATTGCCTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (23 bp):
TCTGATTAGCACTTTGTGTGCTT
Found at i:98276 original size:17 final size:19
Alignment explanation
Indices: 98242--98279 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
98232 ACCATAATTT
98242 TTTTCAAGTTCAATTTAAA
1 TTTTCAAGTTCAATTTAAA
98261 TTTTCAA-TTC-ATTTAAA
1 TTTTCAAGTTCAATTTAAA
98278 TT
1 TT
98280 ATTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTCAAGTTCAATTTAAA
Found at i:110141 original size:16 final size:16
Alignment explanation
Indices: 110111--110149 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
110101 ATTAACTGAA
110111 AATAATATAAAATTTAT
1 AATAA-ATAAAATTTAT
*
110128 AATAAATAACATTTAT
1 AATAAATAAAATTTAT
110144 AATAAA
1 AATAAA
110150 AAATCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAATAAAATTTAT
Found at i:116355 original size:13 final size:13
Alignment explanation
Indices: 116318--116355 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
116308 TTTTTTTTTC
*
116318 AATTTGATATTCA
1 AATTTGATATTTA
*
116331 AATTTGGTATTTA
1 AATTTGATATTTA
116344 AATTTGATATTT
1 AATTTGATATTT
116356 TTTGAAGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (13 bp):
AATTTGATATTTA
Found at i:116805 original size:32 final size:31
Alignment explanation
Indices: 116768--116847 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 31
116758 AATTTAGGTA
116768 CTAAATTAAAAAAATATATCTAAATTCAAGTAT
1 CTAAATTAAAAAAA-ATATCTAAATTCAAGT-T
*
116801 -TAAATTAAGAAAAAATATTTAAATTCAAGTT
1 CTAAATTAA-AAAAAATATCTAAATTCAAGTT
116832 CTAAATTAAAAAAAAT
1 CTAAATTAAAAAAAAT
116848 CAAACTCTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
31 8 0.18
32 31 0.70
33 5 0.11
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (31 bp):
CTAAATTAAAAAAAATATCTAAATTCAAGTT
Found at i:119226 original size:6 final size:6
Alignment explanation
Indices: 119215--119242 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
119205 ACATTAATGG
119215 CTGCCC CTGCCC CTGCCC CTGCCC CTGC
1 CTGCCC CTGCCC CTGCCC CTGCCC CTGC
119243 ATCTTCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.18, T:0.18
Consensus pattern (6 bp):
CTGCCC
Found at i:121896 original size:22 final size:22
Alignment explanation
Indices: 121871--121915 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
121861 TTCGAGTTAA
121871 ACCAAAAATTTTGATTTTATTT
1 ACCAAAAATTTTGATTTTATTT
121893 ACCAAAAATTTTGATTTTATTT
1 ACCAAAAATTTTGATTTTATTT
121915 A
1 A
121916 TTCGAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
ACCAAAAATTTTGATTTTATTT
Found at i:122092 original size:20 final size:21
Alignment explanation
Indices: 122067--122108 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
122057 TAATCATAAG
122067 AAAATAAATATGAAT-ATGAA
1 AAAATAAATATGAATAATGAA
* *
122087 AAAATATATATTAATAATGAA
1 AAAATAAATATGAATAATGAA
122108 A
1 A
122109 TGAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAATAAATATGAATAATGAA
Found at i:133063 original size:16 final size:17
Alignment explanation
Indices: 133033--133065 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
133023 AAAAAATATT
133033 TATATTATACCATTTTAA
1 TATATTATA-CATTTTAA
133051 TATATTATA-ATTTTA
1 TATATTATACATTTTA
133066 TATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTATACATTTTAA
Found at i:136917 original size:32 final size:32
Alignment explanation
Indices: 136875--136938 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
136865 AAGTAAGTAC
* * *
136875 TTGGTTTTCATTTGCATAATTCGAGTTCAATA
1 TTGGTCTTCATTCGCAGAATTCGAGTTCAATA
*
136907 TTGGTCTTCATTCGCAGAATTTGAGTTCAATA
1 TTGGTCTTCATTCGCAGAATTCGAGTTCAATA
136939 CGTGTAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (32 bp):
TTGGTCTTCATTCGCAGAATTCGAGTTCAATA
Done.