Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014167.1 Kokia drynarioides strain JFW-HI SEQ_129200, 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: 27698
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4325 original size:44 final size:46
Alignment explanation
Indices: 4268--4360 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
4258 TACAACATCT
* *
4268 ATTCCATTCAACCAAACACA-AGAA-TGCT-ATTACAACTCTATTCC
1 ATTCCAATCAACCAAACA-ATAGAATTACTAATTACAACTCTATTCC
*
4312 ATTCCAATCAACCAAACAATTGAATTACTAATTACAACTCTATTCC
1 ATTCCAATCAACCAAACAATAGAATTACTAATTACAACTCTATTCC
4358 ATT
1 ATT
4361 ACAACTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 3 0.07
46 19 0.44
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (46 bp):
ATTCCAATCAACCAAACAATAGAATTACTAATTACAACTCTATTCC
Found at i:4363 original size:16 final size:16
Alignment explanation
Indices: 4342--4395 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
4332 TGAATTACTA
4342 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
4358 ATTACAACTATATTTC
1 ATTACAACTCTATTCC
*
4374 ATTACATCTCTATTCC
1 ATTACAACTCTATTCC
4390 ATTACA
1 ATTACA
4396 GCCCAATTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:5466 original size:35 final size:35
Alignment explanation
Indices: 5427--5496 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
5417 TGATTAATAC
5427 ATATTATTTTATTATTATTTGACCTATGAAATTAG
1 ATATTATTTTATTATTATTTGACCTATGAAATTAG
5462 ATATTATTTTATTATTATTTGACCTATGAAATTAG
1 ATATTATTTTATTATTATTTGACCTATGAAATTAG
5497 CTTATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (35 bp):
ATATTATTTTATTATTATTTGACCTATGAAATTAG
Found at i:5655 original size:17 final size:17
Alignment explanation
Indices: 5633--5675 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
5623 TTTATCTACA
5633 TCTTTTGTACTCTTCAT
1 TCTTTTGTACTCTTCAT
5650 TCTTTTGTACTCTTCAT
1 TCTTTTGTACTCTTCAT
5667 TCTTTTGTA
1 TCTTTTGTA
5676 ATTATAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.12, C:0.21, G:0.07, T:0.60
Consensus pattern (17 bp):
TCTTTTGTACTCTTCAT
Found at i:7464 original size:22 final size:22
Alignment explanation
Indices: 7424--7484 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
7414 CAATCTAAGG
*
7424 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
7445 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
7467 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
7485 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:7475 original size:15 final size:16
Alignment explanation
Indices: 7450--7479 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7440 GAATTAAAAA
7450 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
7466 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
7480 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:8290 original size:19 final size:19
Alignment explanation
Indices: 8266--8308 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8256 AAACATAAAT
8266 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
8285 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
8304 TAAAT
1 TAAAT
8309 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:9059 original size:105 final size:105
Alignment explanation
Indices: 8873--9063 Score: 271
Period size: 105 Copynumber: 1.8 Consensus size: 105
8863 TTTTGTCAAA
* * *
8873 TTTTTCTTTTTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACACCCAAG
1 TTTTTCTTTTTTTTTTCTGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCAAG
8938 CACTCCATCCCAGTTACTCAGCCCAACATGCTCTCAATTT
66 CACTCCATCCCAGTTACTCAGCCCAACATGCTCTCAATTT
* * *
8978 TTTTTCTTCTCTTTTTTT-TGT-AGAATGCATTAGCCCTTTTGACACGAAGTGAAATGACAACCA
1 TTTTTCTT-T-TTTTTTTCTGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCA
*
9041 AGCACTCCA-CCTCGGTTACTCAG
64 AGCACTCCATCC-CAGTTACTCAG
9064 TCTAACACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
104 2 0.03
105 64 0.84
106 3 0.04
107 7 0.09
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (105 bp):
TTTTTCTTTTTTTTTTCTGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCAAG
CACTCCATCCCAGTTACTCAGCCCAACATGCTCTCAATTT
Found at i:9082 original size:105 final size:106
Alignment explanation
Indices: 8872--9102 Score: 265
Period size: 105 Copynumber: 2.2 Consensus size: 106
8862 ATTTTGTCAA
* * *
8872 ATTTTTCTTT-TTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACACCCA
1 ATTTTTCTTTCTTTTTTT-TGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCA
**
8936 AGCACTCCATCCCAGTTACTCAGCCCAACATGCTCTCAATTT
65 AGCACTCCATCCCAGTTACTCAGCCCAACACACTCTCAATTT
* * *
8978 -TTTTTCTTCTCTTTTTTTTGT-AGAATGCATTAGCCCTTTTGACACGAAGTGAAATGACAACCA
1 ATTTTTCTT-TCTTTTTTTTGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCA
* * * *
9041 AGCACTCCA-CCTCGGTTACTCAGTCTAACACATTC-CGAATTT
65 AGCACTCCATCC-CAGTTACTCAGCCCAACACACTCTC-AATTT
*
9083 ATTTATTTTTTCTTTTTTTT
1 ATTT-TTCTTTCTTTTTTTT
9103 ATTTGGGTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
104 3 0.03
105 76 0.72
106 16 0.15
107 11 0.10
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (106 bp):
ATTTTTCTTTCTTTTTTTTGTAAGAATACATTAGACCTTTTGACACGAAATGAAATGACAACCAA
GCACTCCATCCCAGTTACTCAGCCCAACACACTCTCAATTT
Found at i:9854 original size:4 final size:4
Alignment explanation
Indices: 9845--9897 Score: 63
Period size: 4 Copynumber: 12.8 Consensus size: 4
9835 TCCTGGACAA
*
9845 AAAT AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAAA AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
9895 AAA
1 AAA
9898 AATAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 2 0.05
4 32 0.74
5 8 0.19
6 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:9898 original size:12 final size:12
Alignment explanation
Indices: 9845--9908 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
9835 TCCTGGACAA
*
9845 AAATAAATAAAT
1 AAATAAAAAAAT
9857 AAATAAATAAAAT
1 AAATAAA-AAAAT
*
9870 AAGATAGAAAAAT
1 AA-ATAAAAAAAT
9883 AAA-AAAATAAAT
1 AAATAAAA-AAAT
9895 AAA-AATAAAAAT
1 AAATAA-AAAAAT
9907 AA
1 AA
9909 TTGGGTTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 3 0.07
12 23 0.51
13 15 0.33
14 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:12523 original size:22 final size:22
Alignment explanation
Indices: 12467--12513 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
12457 CGATCTAAGG
* *
12467 AAAAATAAAA-TAAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
12488 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
12510 AAAA
1 AAAA
12514 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:12526 original size:16 final size:16
Alignment explanation
Indices: 12493--12522 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12483 GAATTAAAAA
12493 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
12509 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
12523 ATTAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:13355 original size:19 final size:19
Alignment explanation
Indices: 13331--13373 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13321 AAACATAAAT
13331 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13350 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13369 TAAAT
1 TAAAT
13374 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:13619 original size:24 final size:23
Alignment explanation
Indices: 13576--13620 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
13566 AGGATCATAC
13576 TCTAAAAATATATATATTTAATA
1 TCTAAAAATATATATATTTAATA
* *
13599 TCTAAAAGTATGTCATATTTAA
1 TCTAAAAATATAT-ATATTTAA
13621 GCATTATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
TCTAAAAATATATATATTTAATA
Found at i:16985 original size:35 final size:35
Alignment explanation
Indices: 16946--17014 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
16936 TAATTAACTA
** *
16946 ACTAAATTGCATAATATATCTTATAAATTATTTAC
1 ACTAAATTAAATAATATATATTATAAATTATTTAC
* *
16981 ACTAAATTAAATAATATTTATTATTAATTATTTA
1 ACTAAATTAAATAATATATATTATAAATTATTTA
17015 TATTTGGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (35 bp):
ACTAAATTAAATAATATATATTATAAATTATTTAC
Found at i:18272 original size:95 final size:96
Alignment explanation
Indices: 18085--18274 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 96
18075 CATTCTCAAT
* *
18085 TCTTTTTCTGAAAATTTTTAATACAAAATAAATTTATATTTAATGCAATTTTTTTTATTTTCACA
1 TCTTTTTCTGAAAACTTTTAATACAAAATAAATTTATATTTAATGCAATTTTCTTTATTTTCACA
18150 TATAAATCTGCAAAACATAACCCAAAGCAAA
66 TATAAATCTGCAAAACATAACCCAAAGCAAA
* *
18181 TCTTTTTCT-AAACACTTTTAATGCAAAATAAATTTATATTTGATGC-ATTTTCTTTATTTTCAC
1 TCTTTTTCTGAAA-ACTTTTAATACAAAATAAATTTATATTTAATGCAATTTTCTTTATTTTCAC
18244 ATATAAAT-T-CACACAACATAACCCAAAGCAA
65 ATATAAATCTGCA-A-AACATAACCCAAAGCAA
18275 TTTGTTTGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
93 2 0.02
94 2 0.02
95 44 0.51
96 39 0.45
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (96 bp):
TCTTTTTCTGAAAACTTTTAATACAAAATAAATTTATATTTAATGCAATTTTCTTTATTTTCACA
TATAAATCTGCAAAACATAACCCAAAGCAAA
Found at i:20396 original size:20 final size:20
Alignment explanation
Indices: 20371--20415 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
20361 TACAAGGTTG
20371 TAAGAAATTTAATAATCTTA
1 TAAGAAATTTAATAATCTTA
* *
20391 TAAGAAGTTTAATAATTTTA
1 TAAGAAATTTAATAATCTTA
20411 TAAGA
1 TAAGA
20416 TATTCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (20 bp):
TAAGAAATTTAATAATCTTA
Found at i:22172 original size:30 final size:31
Alignment explanation
Indices: 22136--22196 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
22126 CTGTCAATGG
22136 GTCTCAACTAACCTCTTA-TTCCATGTGAAT
1 GTCTCAACTAACCTCTTATTTCCATGTGAAT
22166 GTCTCAACTAACCTCTTATTTCCATGTGAAT
1 GTCTCAACTAACCTCTTATTTCCATGTGAAT
22197 TGATCATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (31 bp):
GTCTCAACTAACCTCTTATTTCCATGTGAAT
Found at i:22762 original size:73 final size:73
Alignment explanation
Indices: 22676--22940 Score: 309
Period size: 73 Copynumber: 3.6 Consensus size: 73
22666 GCGGATTATT
* * * *
22676 TATGATGTCGTAGCATCATTCAACTATGGTCTTACACGATGTAACCCTGTGTTTACCATCTCGAC
1 TATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTACCATCTCGAC
22741 GAACTATC
66 GAACTATC
* * *
22749 TTTGATGTTGTAGCATCTTTCAACTATGGTCTTACACAATATAA-CTTCATGTTTACCATCTCGA
1 TATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCT-ATGTTTACCATCTCGA
* *
22813 CGGATTATC
65 CGAACTATC
* * * ** * *
22822 TATGATGTCGTAGCTTCTTTCAATTATGGTCTTACACAATATAACCCCATGTTTACTGTCTTGGC
1 TATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTACCATCTCGAC
*
22887 AAACTATC
66 GAACTATC
* ** *
22895 TATGATGTCATAG-AGTCTTTCAGTTATGGTCTTACATAATATAACC
1 TATGATGTCGTAGCA-TCTTTCAACTATGGTCTTACACAATATAACC
22941 TTGTGTTTGT
Statistics
Matches: 163, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
72 2 0.01
73 160 0.98
74 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (73 bp):
TATGATGTCGTAGCATCTTTCAACTATGGTCTTACACAATATAACCCTATGTTTACCATCTCGAC
GAACTATC
Found at i:22948 original size:146 final size:146
Alignment explanation
Indices: 22667--22939 Score: 359
Period size: 146 Copynumber: 1.9 Consensus size: 146
22657 ATGTTTCAGG
* * * **
22667 CGGATTATTTATGATGTCGTAGCATCATTCAACTATGGTCTTACACGATGTAACCCTGTGTTTAC
1 CGGATTATCTATGATGTCGTAGCATCATTCAACTATGGTCTTACACAATATAACCCCATGTTTAC
* * **
22732 CATCTCGACGAACTATCTTTGATGTTGTAGCATCTTTCAACTATGGTCTTACACAATATAACTTC
66 CATCTCGACAAACTATCTATGATGTCATAGCATCTTTCAACTATGGTCTTACACAATATAACTTC
22797 ATGTTTACCATCTCGA
131 ATGTTTACCATCTCGA
* * *
22813 CGGATTATCTATGATGTCGTAGCTTCTTTCAATTATGGTCTTACACAATATAACCCCATGTTTAC
1 CGGATTATCTATGATGTCGTAGCATCATTCAACTATGGTCTTACACAATATAACCCCATGTTTAC
** * * ** *
22878 TGTCTTGGCAAACTATCTATGATGTCATAG-AGTCTTTCAGTTATGGTCTTACATAATATAAC
66 CATCTCGACAAACTATCTATGATGTCATAGCA-TCTTTCAACTATGGTCTTACACAATATAAC
22940 CTTGTGTTTG
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
145 1 0.01
146 106 0.99
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (146 bp):
CGGATTATCTATGATGTCGTAGCATCATTCAACTATGGTCTTACACAATATAACCCCATGTTTAC
CATCTCGACAAACTATCTATGATGTCATAGCATCTTTCAACTATGGTCTTACACAATATAACTTC
ATGTTTACCATCTCGA
Found at i:24168 original size:17 final size:14
Alignment explanation
Indices: 24133--24160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24123 AGAAAGTTGA
24133 AATAAGTAGTATGT
1 AATAAGTAGTATGT
24147 AATAAGTAGTATGT
1 AATAAGTAGTATGT
24161 TTTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
AATAAGTAGTATGT
Done.