Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009920.1 Kokia drynarioides strain JFW-HI SEQ_124660, 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: 33679
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:8120 original size:18 final size:19
Alignment explanation
Indices: 8087--8122 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
8077 AATGAATGAA
*
8087 TAAATTAAATAATTAAATC
1 TAAAGTAAATAATTAAATC
8106 TAAAGTAAA-AATTAAAT
1 TAAAGTAAATAATTAAAT
8123 TATGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAGTAAATAATTAAATC
Found at i:9664 original size:13 final size:14
Alignment explanation
Indices: 9641--9672 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
9631 AATATATACC
9641 TTTTATTTTTATAA
1 TTTTATTTTTATAA
9655 TTTT-TTTTTATAA
1 TTTTATTTTTATAA
9668 TTTTA
1 TTTTA
9673 GCTAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTATAA
Found at i:11040 original size:14 final size:13
Alignment explanation
Indices: 11021--11055 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
11011 ATTTTTAACC
11021 AAACTTTTCAAAAA
1 AAACTTTTC-AAAA
*
11035 AAACTTCTCAAAA
1 AAACTTTTCAAAA
11048 AAACTTTT
1 AAACTTTT
11056 TCACTACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
AAACTTTTCAAAA
Found at i:11053 original size:13 final size:14
Alignment explanation
Indices: 11021--11050 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11011 ATTTTTAACC
*
11021 AAACTTTTCAAAAA
1 AAACTTCTCAAAAA
11035 AAACTTCTCAAAAA
1 AAACTTCTCAAAAA
11049 AA
1 AA
11051 CTTTTTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACTTCTCAAAAA
Found at i:14582 original size:89 final size:89
Alignment explanation
Indices: 14395--14584 Score: 219
Period size: 89 Copynumber: 2.1 Consensus size: 89
14385 TTAAAAAAGA
* * * *
14395 TTAGGTACCGAATTAGGAAAAAGAGTCAAGTTCAGGTATCAAATTGGACTCCAAAAAGTTTAAGT
1 TTAGGTACC-AATTAGGAAAAAGAGTCAAGTTCAAGTAACAAATTGGACTCAAAAAAATTTAAGT
*
14460 ACCAACTTAAAGAAAAGTGTCAAGC
65 ACCAAATTAAAGAAAAGTGTCAAGC
* * *
14485 TTAAGTACCATATTAGGAAAAATA-TCAAGTTTAAGTAACAAATTGGAC-CAAAAAAAATTT-AG
1 TTAGGTACCA-ATTAGGAAAAAGAGTCAAGTTCAAGTAACAAATTGGACTC-AAAAAAATTTAAG
14547 TCACCAAATT-AAGAAAAAGTGTCAAG-
64 T-ACCAAATTAAAG-AAAAGTGTCAAGC
14573 TTCAGGTACCAA
1 TT-AGGTACCAA
14585 ATATTATATT
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
88 10 0.12
89 56 0.65
90 20 0.23
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (89 bp):
TTAGGTACCAATTAGGAAAAAGAGTCAAGTTCAAGTAACAAATTGGACTCAAAAAAATTTAAGTA
CCAAATTAAAGAAAAGTGTCAAGC
Found at i:14902 original size:22 final size:21
Alignment explanation
Indices: 14860--14914 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
14850 TTTTTAAAAA
*
14860 ATTAAAATAAATTATAGAATTTT
1 ATTAAAA-AAA-TATAGAATTAT
*
14883 ATTAAAAAAATATTGAAATTAT
1 ATTAAAAAAATATAG-AATTAT
14905 -TTAAAAAAAT
1 ATTAAAAAAAT
14915 GGAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTAAAAAAATATAGAATTAT
Found at i:16028 original size:20 final size:20
Alignment explanation
Indices: 15988--16024 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
15978 TTATAATTTG
15988 ATTTTTAAACAATTTTAATA
1 ATTTTTAAACAATTTTAATA
*
16008 ATTTTTGAA-AATTTTAA
1 ATTTTTAAACAATTTTAA
16025 ATAACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTTTAAACAATTTTAATA
Found at i:16910 original size:45 final size:45
Alignment explanation
Indices: 16859--16946 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
16849 TGTGGCACAC
16859 AAAGTCGTAAGTCATGTCTGTGCTGTCAATTTTCCTTTATGCAAT
1 AAAGTCGTAAGTCATGTCTGTGCTGTCAATTTTCCTTTATGCAAT
16904 AAAGTCGTAAGTCATGTCTGTGCTGTCAATTTTCCTTTATGCA
1 AAAGTCGTAAGTCATGTCTGTGCTGTCAATTTTCCTTTATGCA
16947 GTCTAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (45 bp):
AAAGTCGTAAGTCATGTCTGTGCTGTCAATTTTCCTTTATGCAAT
Found at i:18915 original size:6 final size:6
Alignment explanation
Indices: 18904--18958 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
18894 AAATTTATTC
* *
18904 TAAATT TAAATT T-AGTT GAAATT TAAATT TATAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT
18950 TAAAATT TA
1 T-AAATT TA
18959 TTTTGAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
4 2 0.05
5 5 0.12
6 25 0.62
7 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:18961 original size:17 final size:16
Alignment explanation
Indices: 18893--18951 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 16
18883 CTGAGCCAAA
18893 TAAATTTATTCTAAATT
1 TAAATTTATT-TAAATT
*
18910 TAAATTTAGTTGAAATT
1 TAAATTTA-TTTAAATT
*
18927 TAAATTTATAATAAATT
1 TAAATTTAT-TTAAATT
18944 TAAATTTA
1 TAAATTTA
18952 AAATTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 1 0.03
17 34 0.92
18 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAATTTATTTAAATT
Found at i:19190 original size:15 final size:15
Alignment explanation
Indices: 19172--19200 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19162 CACCTGCCAC
19172 CACCGTCGCTGCAAT
1 CACCGTCGCTGCAAT
19187 CACCGTCGCTGCAA
1 CACCGTCGCTGCAA
19201 CCTGCAAAAG
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:0.21, C:0.41, G:0.21, T:0.17
Consensus pattern (15 bp):
CACCGTCGCTGCAAT
Found at i:21109 original size:17 final size:16
Alignment explanation
Indices: 21075--21133 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
21065 TAACTGGATT
*
21075 TTTTTAATT-AATTAAA
1 TTTTAAATTAAATT-AA
21091 TTTTAAATTCAAATTAA
1 TTTTAAATT-AAATTAA
*
21108 TTTTAAACTTAATTTAA
1 TTTTAAA-TTAAATTAA
*
21125 ATTTAAATT
1 TTTTAAATT
21134 TAAACTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.27
17 21 0.57
18 6 0.16
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATTAAATTAA
Found at i:21130 original size:23 final size:22
Alignment explanation
Indices: 21096--21142 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
21086 TTAAATTTTA
*
21096 AATTCAAATTAATTTTAAACTT
1 AATTCAAATTAAATTTAAACTT
*
21118 AATTTAAATTTAAATTTAAACTT
1 AATTCAAA-TTAAATTTAAACTT
21141 AA
1 AA
21143 AAGAAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTCAAATTAAATTTAAACTT
Found at i:21135 original size:6 final size:6
Alignment explanation
Indices: 21086--21174 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
21076 TTTTAATTAA
* * *
21086 TTAAATT TTAAAT TCAAA- TTAATT TTAAAC TT-AAT TTAAAT TTAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * ** *
21133 TTAAAC TTAAAA GAAAACT TTAAACT TTAAA- CTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA-T TTAAA-T TTAAAT TTAAAT TTAAA
21175 CCCAAAATGA
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
5 11 0.17
6 37 0.59
7 15 0.24
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:21143 original size:12 final size:12
Alignment explanation
Indices: 21093--21175 Score: 73
Period size: 11 Copynumber: 7.0 Consensus size: 12
21083 TAATTAAATT
*
21093 TTAAATTCAAA-
1 TTAAATTTAAAC
*
21104 TTAATTTTAAAC
1 TTAAATTTAAAC
*
21116 TT-AATTTAAAT
1 TTAAATTTAAAC
21127 TTAAATTTAAAC
1 TTAAATTTAAAC
***
21139 TTAAAAGAAAAC
1 TTAAATTTAAAC
21151 TTTAAACTTTAAAC
1 -TTAAA-TTTAAAC
21165 -TAAATTTAAAC
1 TTAAATTTAAAC
21176 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 25 0.44
12 23 0.40
13 5 0.09
14 4 0.07
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:29362 original size:2 final size:2
Alignment explanation
Indices: 29355--29380 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29345 CTATCGATTA
29355 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29381 TTTAAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31237 original size:30 final size:28
Alignment explanation
Indices: 31203--31273 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 28
31193 TTTAATGAAT
31203 AAATTAAAATTTTTAAACTA-AAATAATTGA
1 AAATTAAAATTTTTAAA-TATAAA-AATT-A
**
31233 AAATTTTAATTTTTAAATATAAAAATTA
1 AAATTAAAATTTTTAAATATAAAAATTA
* *
31261 AATTTCAAATTTT
1 AAATTAAAATTTT
31274 ATTAAAATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.31
29 6 0.17
30 18 0.51
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTAAAATTTTTAAATATAAAAATTA
Found at i:33663 original size:17 final size:17
Alignment explanation
Indices: 33641--33679 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
33631 ATGAAGGAAA
33641 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
33658 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
33675 AAAGA
1 AAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Done.