Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002837.1 Kokia drynarioides strain JFW-HI SEQ_115210, 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: 54670
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:285 original size:17 final size:16
Alignment explanation
Indices: 263--316 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
253 TATATATATT
263 TTTAAATGAATTTTAAA
1 TTTAAAT-AATTTTAAA
* **
280 TTTAAATTCATAATAAA
1 TTTAAA-TAATTTTAAA
*
297 TTTAAATAAATTTAAA
1 TTTAAATAATTTTAAA
313 TTTA
1 TTTA
317 TTGGGCCCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 10 0.34
17 18 0.62
18 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTAAATAATTTTAAA
Found at i:759 original size:23 final size:23
Alignment explanation
Indices: 729--774 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
719 GTCTGTGCTT
729 GTTAATCAAGTGTATAAGCATTA
1 GTTAATCAAGTGTATAAGCATTA
752 GTTAATCAAGTGTATAAGCATTA
1 GTTAATCAAGTGTATAAGCATTA
775 TCCAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
GTTAATCAAGTGTATAAGCATTA
Found at i:5617 original size:2 final size:2
Alignment explanation
Indices: 5600--5654 Score: 92
Period size: 2 Copynumber: 27.0 Consensus size: 2
5590 TTAAGAGCAC
*
5600 AT AT TT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5643 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5655 CCTTGTTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7978 original size:3 final size:3
Alignment explanation
Indices: 7970--7997 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7960 TACGGTTCCT
7970 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
7998 CTATATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:9087 original size:40 final size:39
Alignment explanation
Indices: 9032--9109 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
9022 GCTACTATTC
*
9032 CTTAAACCGCGCTTAAACGCATATATATCTCTCAATTTTG
1 CTTAAACCGCACTTAAACGCATA-ATATCTCTCAATTTTG
*
9072 CTTAAACCTCACTTAAACGCATAATATCTCTCAATTTT
1 CTTAAACCGCACTTAAACGCATAATATCTCTCAATTTT
9110 ATTTGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (39 bp):
CTTAAACCGCACTTAAACGCATAATATCTCTCAATTTTG
Found at i:10739 original size:2 final size:2
Alignment explanation
Indices: 10732--10761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10722 AAAAATTATT
10732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10762 AAGTAGCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13305 original size:69 final size:69
Alignment explanation
Indices: 13224--13362 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
13214 AAACCCTACG
*
13224 CATGTCATTTCCAACTTAACCAATAAGACCATTTCCTAAATAATTATTTTTAGTTCACTATCTAG
1 CATGTCATTTCCAACTTAACCAATAAGACCATTTCCTAAATAATTATTTTTAATTCACTATCTAG
13289 TTGT
66 TTGT
13293 CATGTCATTTCCAACTTAACCAATAAGACCATTTCCTAAATAATTATTTTTAATTCACTATCTAG
1 CATGTCATTTCCAACTTAACCAATAAGACCATTTCCTAAATAATTATTTTTAATTCACTATCTAG
13358 TTGT
66 TTGT
13362 C
1 C
13363 TAACTACTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (69 bp):
CATGTCATTTCCAACTTAACCAATAAGACCATTTCCTAAATAATTATTTTTAATTCACTATCTAG
TTGT
Found at i:13805 original size:17 final size:17
Alignment explanation
Indices: 13782--13903 Score: 181
Period size: 17 Copynumber: 7.1 Consensus size: 17
13772 CTAAACTCTC
13782 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* **
13799 ATTAAATTTATCTAAAAA
1 TTTAAATTTAT-TTTAAA
13817 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
13834 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
13851 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
13868 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
13886 TTTAAAATTATTTAAAA
1 TTTAAATTTATTTTAAA
13903 T
1 T
13904 AAATAAAGTT
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
17 66 0.69
18 29 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13821 original size:35 final size:34
Alignment explanation
Indices: 13782--13907 Score: 166
Period size: 35 Copynumber: 3.7 Consensus size: 34
13772 CTAAACTCTC
*
13782 TTTAAATTTATTTTAAAATTAAATTTATCTAAAAA
1 TTTAAATTTATTTTAAAATTAAATTTAT-TTAAAA
* *
13817 TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
* *
13851 TTTAAATTTATTTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAATTTA-TTTAAAA
*
13886 TTTAAAATTA-TTTAAAA-TAAAT
1 TTTAAATTTATTTTAAAATTAAAT
13908 AAAGTTCAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
33 5 0.06
34 37 0.44
35 42 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
Found at i:13833 original size:11 final size:11
Alignment explanation
Indices: 13815--13877 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
13805 TTTATCTAAA
13815 AATTTAAATTT
1 AATTTAAATTT
*
13826 ATTTTAAATTT
1 AATTTAAATTT
*
13837 AAATTT-ATTTT
1 -AATTTAAATTT
13848 AAATTTAAATTT
1 -AATTTAAATTT
*
13860 ATTTTAAATTT
1 AATTTAAATTT
13871 AAATTTA
1 -AATTTA
13878 TTTTCAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
11 30 0.70
12 13 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:13860 original size:52 final size:52
Alignment explanation
Indices: 13782--13903 Score: 183
Period size: 52 Copynumber: 2.3 Consensus size: 52
13772 CTAAACTCTC
*
13782 TTTAAATTTATTTTAAAATTAAATTTATCTAAAAATTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAATTTAAATTTAT-TAAAAATTTAAATTTATTTTCAAA
**
13834 TTTAAATTTATTTTAAATTTAAATTTATTTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTAAAAATTTAAATTTATTTTCAAA
* *
13886 TTTAAAATTATTTAAAAT
1 TTTAAATTTATTTTAAAT
13904 AAATAAAGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 18 0.28
52 46 0.72
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (52 bp):
TTTAAATTTATTTTAAATTTAAATTTATTAAAAATTTAAATTTATTTTCAAA
Found at i:15819 original size:29 final size:30
Alignment explanation
Indices: 15755--16065 Score: 312
Period size: 30 Copynumber: 10.5 Consensus size: 30
15745 AAGGGTCCCT
*
15755 AAACTATCCAAAAATTCCATTTTTGACCACC-
1 AAACT-TCCAAAAATCCCATTTTTGACC-CCA
* * * *
15786 GAACTTCTAAAAATCCCA-TTTTAACCCCT
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
15815 AAACTTCTAAAAATCCTATTTTTGCCCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
*
15845 AAACTTCCAAAAATCCCATTTTTAACCCTC-
1 AAACTTCCAAAAATCCCATTTTTGACCC-CA
** *
15875 AATGTTCTAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* *
15905 AAACTTCCAAAAATCCCA-TTTTAACCCCC
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
*
15934 AAACTTCTAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* *
15964 AAACTTCCAAGAATCCCATTTTT-ACCCCC
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* *
15993 AAACTTCCAAAAATTCCATTTTT-AGCCTC-
1 AAACTTCCAAAAATCCCATTTTTGA-CCCCA
* * * * *
16022 GAACTTCCCAAAATTCCATTTTTGACTCCG
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
*
16052 AAACTTCCTAAAAT
1 AAACTTCCAAAAAT
16066 TAACATTCTA
Statistics
Matches: 235, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.01
29 100 0.43
30 128 0.54
31 5 0.02
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (30 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:15850 original size:59 final size:58
Alignment explanation
Indices: 15751--16015 Score: 336
Period size: 59 Copynumber: 4.4 Consensus size: 58
15741 CCCCAAGGGT
* * *
15751 CCCTAAACTATCCAAAAATTCCATTTTTGACCACC-GAACTTCTAAAAATCCCATTTTAAC
1 CCCTAAACT-TCTAAAAA-TCCATTTTTGACC-CCAAAACTTCCAAAAATCCCATTTTAAC
*
15811 CCCTAAACTTCTAAAAATCCTATTTTTGCCCCCAAAACTTCCAAAAATCCCATTTTTAA-
1 CCCTAAACTTCTAAAAATCC-ATTTTTGACCCCAAAACTTCCAAAAATCCCA-TTTTAAC
**
15870 CCCTCAATGTTCTAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTAAC
1 CCCT-AAACTTCTAAAAAT-CCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTAAC
* * *
15930 CCCCAAACTTCTAAAAATCCCATTTTTGACCCCAAAACTTCCAAGAATCCCATTTTTAC
1 CCCTAAACTTCTAAAAAT-CCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTAAC
* *
15989 CCCCAAACTTCCAAAAATTCCATTTTT
1 CCCTAAACTTCTAAAAA-TCCATTTTT
16016 AGCCTCGAAC
Statistics
Matches: 185, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
58 5 0.03
59 117 0.63
60 61 0.33
61 2 0.01
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.31
Consensus pattern (58 bp):
CCCTAAACTTCTAAAAATCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTAAC
Found at i:16056 original size:59 final size:59
Alignment explanation
Indices: 15755--16066 Score: 319
Period size: 59 Copynumber: 5.3 Consensus size: 59
15745 AAGGGTCCCT
* ** * *
15755 AAACTATCCAAAAATTCCATTTTTGACCACC-GAACTTCTAAAAATCCCATTTTAACCCCT
1 AAACT-TCCAAAAATTCCATTTTTGACC-CCAAAACTTCCCAAAATCCCATTTTTACCCCC
* * * *
15815 AAACTTCTAAAAA-TCCTATTTTTGCCCCCAAAACTTCCAAAAATCCCATTTTTAACCCTC
1 AAACTTCCAAAAATTCC-ATTTTTGACCCCAAAACTTCCCAAAATCCCATTTTT-ACCCCC
** * * * *
15875 AATGTTCTAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTAACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCCAAAATCCCATTTTTACCCCC
* *
15934 AAACTTCTAAAAATCCCATTTTTGACCCCAAAACTT-CCAAGAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCCAA-AATCCCATTTTTACCCCC
* * * * *
15993 AAACTTCCAAAAATTCCATTTTT-AGCCTC-GAACTTCCCAAAATTCCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTTGA-CCCCAAAACTTCCCAAAATCCCATTTTT-ACCCCC
*
16052 AAACTTCCTAAAATT
1 AAACTTCCAAAAATT
16067 AACATTCTAC
Statistics
Matches: 219, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
58 25 0.11
59 138 0.63
60 54 0.25
61 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCCAAAATCCCATTTTTACCCCC
Found at i:26402 original size:24 final size:24
Alignment explanation
Indices: 26354--26403 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
26344 TTCTTCACCC
* * *
26354 TCTTCATCATCACCTTCATCTTCT
1 TCTTCATCATCACCCTCAGCCTCT
*
26378 TCTTCATCTTCACCCTCAGCCTCT
1 TCTTCATCATCACCCTCAGCCTCT
26402 TC
1 TC
26404 ATCACCCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.14, C:0.42, G:0.02, T:0.42
Consensus pattern (24 bp):
TCTTCATCATCACCCTCAGCCTCT
Found at i:30227 original size:9 final size:9
Alignment explanation
Indices: 30215--30240 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30205 GGTAAATAAA
30215 AAGAGAAAT
1 AAGAGAAAT
30224 AAGAGAAAT
1 AAGAGAAAT
30233 AAGAGAAA
1 AAGAGAAA
30241 AAATGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (9 bp):
AAGAGAAAT
Found at i:33127 original size:15 final size:15
Alignment explanation
Indices: 33107--33135 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33097 TCAAATCCGT
33107 CATCATAATCACCAC
1 CATCATAATCACCAC
33122 CATCATAATCACCA
1 CATCATAATCACCA
33136 TCTTCAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
CATCATAATCACCAC
Found at i:37841 original size:22 final size:23
Alignment explanation
Indices: 37794--37845 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
37784 TAATTTTTTT
*
37794 TAAAATTATGTTTATTAAAATAA
1 TAAAATTATATTTATTAAAATAA
**
37817 TAAAATTATATTT-TTATCATAA
1 TAAAATTATATTTATTAAAATAA
37839 TAAAATT
1 TAAAATT
37846 TACAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAAATTATATTTATTAAAATAA
Found at i:40962 original size:21 final size:22
Alignment explanation
Indices: 40925--40981 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
40915 ATATAATAAT
40925 CGAATAATAAACT-AGTTT-TAAA
1 CGAAT-ATAAA-TGAGTTTGTAAA
**
40947 CGAATATAAATGAGTTTGTTCA
1 CGAATATAAATGAGTTTGTAAA
*
40969 TGAATATAAATGA
1 CGAATATAAATGA
40982 ACTAAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 10 0.33
22 19 0.63
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (22 bp):
CGAATATAAATGAGTTTGTAAA
Found at i:42675 original size:14 final size:13
Alignment explanation
Indices: 42624--42675 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 13
42614 TCAAGTAATC
42624 ATTTTATAATA-AA
1 ATTTTA-AATATAA
42637 ATTTT-AATATAA
1 ATTTTAAATATAA
42649 ATTATTAAAATATAA
1 ATT-TT-AAATATAA
42664 TATTTTAAATAT
1 -ATTTTAAATAT
42676 TAATGAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.12
12 5 0.15
13 7 0.21
14 6 0.18
15 9 0.26
16 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAAATATAA
Found at i:42686 original size:29 final size:28
Alignment explanation
Indices: 42632--42693 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
42622 TCATTTTATA
* * *
42632 ATAAAATTTTAATATAAATTATTAAAAT
1 ATAATATTTTAATATAAATGAGTAAAAT
*
42660 ATAATATTTTAAATATTAATGAGTAAAAT
1 ATAATATTTT-AATATAAATGAGTAAAAT
*
42689 GTAAT
1 ATAAT
42694 CTGATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
ATAATATTTTAATATAAATGAGTAAAAT
Done.