Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002928.1 Kokia drynarioides strain JFW-HI SEQ_115372, 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: 54521
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:1815 original size:254 final size:250
Alignment explanation
Indices: 1290--1910 Score: 775
Period size: 254 Copynumber: 2.5 Consensus size: 250
1280 ATTGTCAGAA
* * * *
1290 ATTGCTCAAGGTAATGATGATCCAAGATGAATGCCCT-TTCGTTTACCAGTGCCTGCCATATAGT
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAGT
* * *
1354 GTTGTGTGCATTTATTCATAAAGTAGTGAATTGGAAAGGAAAAGAAATACATAAACTTGTTTTAT
65 GTTGTGT--ATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTAT
* ** *
1419 TTTTTACCTCCAACAAATCTAGCACTTGCGGCTGTTTAAACTTCTTTTCCTTTAGAACGTCCTGC
128 TTTTTACCTCCAACAAATCTAGCACTTACGGCCATTT-AACTTCTTTTCCTGTAGAACGTCCTGC
* *
1484 AACGTTTAAAATGTTGGATTTTAAGCTCAAACATTATATGTTATAAACCTTGGAAAGAC
192 AACGTTTAAAATGTTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
* * *
1543 ATTGCTCAAAGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCAATATGGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
* *
1608 TTGTGTATGTATTCATAAAATAGTTAATTTGAAAGG-AAAGAAATACATAAACTTGTTTTCTTTT
66 TTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTATTTT
* * * * * * * * *
1672 TTACCTTCAA-AGACTCTGGCCCTTCTAACTGGCCCATTT-CCTTTTTTTTCTGTGGATTC-TCC
131 TTACCTCCAACA-AATCTAGCAC-T-T-AC-GG-CCATTTAACTTCTTTTCCTGTAGA-ACGTCC
* * *
1734 TGCAACGTTTAAAATTTTTGGATTCTAAGCTCGAACATTATATGTTATAAACCTAGGAAAGAG
189 TGCAACGTTTAAAA-TGTTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
* * *
1797 ATTGCTCATGGCAATGGTGATCCAAGATGAATGCCCTACTGGCTTCCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
* * *
1862 TTATGCATGTATTCATAAAGTAGTTAAATTGAAAGGAAAAGAAATACAT
66 TTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACAT
1911 CTCTCTCCAA
Statistics
Matches: 318, Mismatches: 40, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
249 1 0.00
250 43 0.14
251 27 0.08
252 1 0.00
253 88 0.28
254 142 0.45
255 16 0.05
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (250 bp):
ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
TTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTATTTT
TTACCTCCAACAAATCTAGCACTTACGGCCATTTAACTTCTTTTCCTGTAGAACGTCCTGCAACG
TTTAAAATGTTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
Found at i:20313 original size:19 final size:19
Alignment explanation
Indices: 20291--20338 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
20281 TCTTATTCCC
*
20291 TCTTTTTTTTTTTTCTTAT
1 TCTTTTTTTTTTCTCTTAT
* * *
20310 TCTTCTCTATTTCTCTTAT
1 TCTTTTTTTTTTCTCTTAT
20329 TCTTCTTTTT
1 TCTT-TTTTT
20339 ATCCTTAACT
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTTTTTTTTTTCTCTTAT
Found at i:20915 original size:37 final size:37
Alignment explanation
Indices: 20865--20938 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
20855 ACTTGGACAT
*
20865 ACATGAAATATGCTTATATGAAGCAGTTTTTATTAGA
1 ACATGAAATATGCTTATATGAAGAAGTTTTTATTAGA
*
20902 ACATGGAATATGCTTATATGAAGAAGTTTTTATTAGA
1 ACATGAAATATGCTTATATGAAGAAGTTTTTATTAGA
20939 GTATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (37 bp):
ACATGAAATATGCTTATATGAAGAAGTTTTTATTAGA
Found at i:21916 original size:16 final size:16
Alignment explanation
Indices: 21895--21932 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
21885 CACTGGAATT
21895 GAATAGGGTTATAATA
1 GAATAGGGTTATAATA
*
21911 GAATAGGGTTGTAATA
1 GAATAGGGTTATAATA
21927 GAATAG
1 GAATAG
21933 AGCTGTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
GAATAGGGTTATAATA
Found at i:21939 original size:16 final size:16
Alignment explanation
Indices: 21906--21957 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
21896 AATAGGGTTA
* *
21906 TAATAGAATAGGGTTG
1 TAATAGAATAGAGCTG
21922 TAATAGAATAGAGCTG
1 TAATAGAATAGAGCTG
* *
21938 TAATGGAATAAAGCTG
1 TAATAGAATAGAGCTG
21954 TAAT
1 TAAT
21958 CAGTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (16 bp):
TAATAGAATAGAGCTG
Found at i:21987 original size:45 final size:44
Alignment explanation
Indices: 21936--22030 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
21926 AGAATAGAGC
*
21936 TGTAATGGAATA-AAGCTGTAATCAGTAATTAAT-TGTTTGGTTAAA
1 TGTAATGGAATAGAA-CTATAAT-AGT-ATTAATGTGTTTGGTTAAA
* *
21981 TGTAATGGAATAGAACTATAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAACTATAATAGTATTAATGTGTTTGGTTAAA
*
22025 TATAAT
1 TGTAAT
22031 AGATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
43 5 0.11
44 19 0.43
45 18 0.41
46 2 0.05
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (44 bp):
TGTAATGGAATAGAACTATAATAGTATTAATGTGTTTGGTTAAA
Found at i:22175 original size:61 final size:60
Alignment explanation
Indices: 22122--22240 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 60
22112 ATTGTTCTTA
* *
22122 AATATATTAGAATTATTATTAAATATAATTTAATAAAAATGATAATAAATTATTTAATCAT
1 AATATAATAGAATTATTATTAAATATAATTTAATAAAAATAATAATAAATTATTT-ATCAT
* * *
22183 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATATAATT-TTTAT
1 AATATAATAGAATTATTATTAAATATAATTTAATAAAAATAAT-AATA-AATTATTTAT
22241 ATTAAATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 40 0.78
62 7 0.14
63 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (60 bp):
AATATAATAGAATTATTATTAAATATAATTTAATAAAAATAATAATAAATTATTTATCAT
Found at i:22252 original size:10 final size:10
Alignment explanation
Indices: 22237--22289 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
22227 AATATAATTT
22237 TTATATTAAA
1 TTATATTAAA
22247 TTATATTAAAA
1 TTATATT-AAA
* * *
22258 TGTTTTTTATAT
1 T-TATATTA-AA
22270 TTATATTAAA
1 TTATATTAAA
22280 TTATATTAAA
1 TTATATTAAA
22290 ATATTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 18 0.53
11 10 0.29
12 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TTATATTAAA
Found at i:22303 original size:33 final size:33
Alignment explanation
Indices: 22236--22304 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
22226 AAATATAATT
* ***
22236 TTTATATTAAATTATATTAAAATGTTTTTTATA
1 TTTATATTAAATTATATTAAAATATTTCAAATA
22269 TTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTATATTAAATTATATTAAAATATTTCAAATA
22302 TTT
1 TTT
22305 TGTTTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TTTATATTAAATTATATTAAAATATTTCAAATA
Found at i:23905 original size:31 final size:29
Alignment explanation
Indices: 23849--23907 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
23839 GCAGAAAAGG
23849 TAATATATTTTTTTTATAAATTTTAAAAA
1 TAATATATTTTTTTTATAAATTTTAAAAA
* *
23878 TAATTTATTTTATTTTATTTAATTTTAAAA
1 TAATATATTTT-TTTTA-TAAATTTTAAAA
23908 TTATGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
31 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TAATATATTTTTTTTATAAATTTTAAAAA
Found at i:28308 original size:33 final size:34
Alignment explanation
Indices: 28233--28308 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
28223 TCAAAACTTA
*
28233 TTTGCTGCTTGATACTGCGGAAAAAATTTGGGAT
1 TTTGCTGCTTGATACTGCGGAAAAAATTTGGAAT
* * *
28267 GTTACTGCTTGATACTGCGG-AATAATTTGGAAT
1 TTTGCTGCTTGATACTGCGGAAAAAATTTGGAAT
28300 TTTGCTGCT
1 TTTGCTGCT
28309 CTCACCTACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 18 0.50
34 18 0.50
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (34 bp):
TTTGCTGCTTGATACTGCGGAAAAAATTTGGAAT
Found at i:35934 original size:34 final size:34
Alignment explanation
Indices: 35896--35969 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
35886 GATGTATTGT
*
35896 GTCCGAGCAACACCTCAACTATTTGAGGGTCCAA
1 GTCCGAGCAACACCTCAACTATTTAAGGGTCCAA
*
35930 GTCCGAGCAATACCTCAACTATTTAAGGGTCCAA
1 GTCCGAGCAACACCTCAACTATTTAAGGGTCCAA
*
35964 GACCGA
1 GTCCGA
35970 CCTCCCCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (34 bp):
GTCCGAGCAACACCTCAACTATTTAAGGGTCCAA
Found at i:46633 original size:24 final size:24
Alignment explanation
Indices: 46601--46660 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
46591 GGTTTTGTCA
46601 GAAAACGCTTTCCACGCGCTTCCT
1 GAAAACGCTTTCCACGCGCTTCCT
46625 GAAAACGCTTTCCACGCGCTTCCT
1 GAAAACGCTTTCCACGCGCTTCCT
46649 GAAAACGCTTTC
1 GAAAACGCTTTC
46661 TACAAAACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (24 bp):
GAAAACGCTTTCCACGCGCTTCCT
Found at i:52526 original size:21 final size:21
Alignment explanation
Indices: 52486--52527 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52476 TGGTGAAATA
*
52486 TTAAAATTTGATTTAGTAATT
1 TTAAAATTTGATTAAGTAATT
* *
52507 TTAATATTTGATTAATTAATT
1 TTAAAATTTGATTAAGTAATT
52528 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
TTAAAATTTGATTAAGTAATT
Done.