Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012957.1 Kokia drynarioides strain JFW-HI SEQ_127975, 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: 68846
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:253 original size:23 final size:23
Alignment explanation
Indices: 215--318 Score: 136
Period size: 23 Copynumber: 4.4 Consensus size: 23
205 AGCACATCTC
215 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
* *
240 GTTCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
263 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
286 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
309 GTGCTCTCTG
1 GTGCTCTCTG
319 TTTCCCAGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
23 61 0.87
25 9 0.13
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:359 original size:69 final size:69
Alignment explanation
Indices: 218--367 Score: 198
Period size: 69 Copynumber: 2.1 Consensus size: 69
208 ACATCTCGTG
* * *
218 CTCTCTGTTATTAGCACTGTGTGTTCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAGCACCTTATGTGCTCTCTGATTAGTACTT
283 TGTGTA
64 TGTGTA
*
289 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTCCCAGC-CCTTATGTGCTCTCTG-TTAGTACT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT---AGCACCTTATGTGCTCTCTGATTAGTACT
352 TTG-GTA
63 TTGTGTA
358 CTCTCTGTTT
1 CTCTCTGTTT
368 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
69 36 0.50
70 12 0.17
71 21 0.29
72 3 0.04
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.46
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACCTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:4010 original size:42 final size:41
Alignment explanation
Indices: 3963--4093 Score: 122
Period size: 42 Copynumber: 3.1 Consensus size: 41
3953 TTAATATAAA
3963 TTATATTTATTATTATATTTTCTTGAAAATATTTATTTATTT
1 TTATATTTATTATTATATTTT-TTGAAAATATTTATTTATTT
* * * *
4005 TTATATATATTATTAT-TTATTGTCAACAATATTTTTTTA-TT
1 TTATATTTATTATTATATT-TTTTGAA-AATATTTATTTATTT
** * * * *
4046 TTAGGTTTCTTATTATATTTTTTTGATATTATTTATGTATTT
1 TTATATTTATTATTATA-TTTTTTGAAAATATTTATTTATTT
4088 TTATAT
1 TTATAT
4094 ATTCCTTTGA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
41 28 0.41
42 38 0.56
43 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (41 bp):
TTATATTTATTATTATATTTTTTGAAAATATTTATTTATTT
Found at i:4945 original size:29 final size:27
Alignment explanation
Indices: 4900--4976 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 27
4890 AAATTTTTAG
* *
4900 CTTTTAAAGACTCAAAATTTTTTACCAA
1 CTTTTAAAGACTTAAAATTTTCT-CCAA
4928 CTTTTAATAGACTTAAAAAAATTTTCTCCAA
1 CTTTTAA-AGACTT---AAAATTTTCTCCAA
*
4959 CTTTTAAGAGATTTAAAA
1 CTTTTAA-AGACTTAAAA
4977 CCCCCATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 11 0.27
29 5 0.12
31 16 0.39
32 9 0.22
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (27 bp):
CTTTTAAAGACTTAAAATTTTCTCCAA
Found at i:4962 original size:31 final size:32
Alignment explanation
Indices: 4913--4976 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
4903 TTAAAGACTC
* *
4913 AAAATTTTTTACCAACTTTTAATAGACTTAAA
1 AAAATTTTCTACCAACTTTTAAGAGACTTAAA
*
4945 AAAATTTTCT-CCAACTTTTAAGAGATTTAAA
1 AAAATTTTCTACCAACTTTTAAGAGACTTAAA
4976 A
1 A
4977 CCCCCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (32 bp):
AAAATTTTCTACCAACTTTTAAGAGACTTAAA
Found at i:7019 original size:17 final size:17
Alignment explanation
Indices: 6993--7042 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
6983 TTAGCTTAGG
*
6993 TTTTCATTTTTCATTTT-T
1 TTTTC-TTTTTC-TTTTCC
7011 TTTTCTTTTTCTTTTCC
1 TTTTCTTTTTCTTTTCC
7028 TTTTCTTTTCTCTTT
1 TTTTCTTTT-TCTTT
7043 ATTGTAGCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 15 0.52
18 10 0.34
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTCC
Found at i:13930 original size:21 final size:21
Alignment explanation
Indices: 13891--13945 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
13881 ATTAACAGTT
* *
13891 TATTAAATATTAAT-TCTTAA
1 TATTATATATTTATCTCTTAA
*
13911 TATTATATTTTTATCTCTTAA
1 TATTATATATTTATCTCTTAA
*
13932 TGTTATATATTTAT
1 TATTATATATTTAT
13946 TAAAATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTATATATTTATCTCTTAA
Found at i:14176 original size:24 final size:24
Alignment explanation
Indices: 14144--14189 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
14134 ATTTGTATTT
14144 AAAAAAATACTAATATCATATTCA
1 AAAAAAATACTAATATCATATTCA
14168 AAAAAAATACTAATATCATATT
1 AAAAAAATACTAATATCATATT
14190 TATATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAAAATACTAATATCATATTCA
Found at i:23069 original size:14 final size:15
Alignment explanation
Indices: 23052--23080 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23042 ATAAATTTTG
23052 AATAT-TAAAATAAA
1 AATATATAAAATAAA
23066 AATATATAAAATAAA
1 AATATATAAAATAAA
23081 TTAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATATAAAATAAA
Found at i:30821 original size:28 final size:26
Alignment explanation
Indices: 30774--30828 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
30764 CCTAAAAGTA
30774 TTATTAAAAAAAAAACACCGTCTATT
1 TTATTAAAAAAAAAACACCGTCTATT
* *
30800 TTATATAAAAAAAATAATACCGTTTATT
1 TTAT-TAAAAAAAA-AACACCGTCTATT
30828 T
1 T
30829 ACTTTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 9 0.36
28 12 0.48
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (26 bp):
TTATTAAAAAAAAAACACCGTCTATT
Found at i:31164 original size:26 final size:27
Alignment explanation
Indices: 31109--31164 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
31099 GAACCAATTA
* *
31109 TTTAACTAGTAAACAAATTATAATATT
1 TTTAACTAATAAACAAATTATAATAGT
*
31136 TTTAACTACATAAAC-AA-TATAATGGT
1 TTTAACTA-ATAAACAAATTATAATAGT
31162 TTT
1 TTT
31165 GCCTTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 10 0.40
27 10 0.40
28 5 0.20
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (27 bp):
TTTAACTAATAAACAAATTATAATAGT
Found at i:32729 original size:21 final size:20
Alignment explanation
Indices: 32703--32758 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
32693 TTTCATGATT
32703 AAAAATAATTATATTTTATAA
1 AAAAATAATT-TATTTTATAA
* *
32724 AAAAATTATTTCTTTTATAA
1 AAAAATAATTTATTTTATAA
32744 AATAAA-AATATTATT
1 AA-AAATAAT-TTATT
32759 ATAAGATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATAATTTATTTTATAA
Found at i:32755 original size:22 final size:22
Alignment explanation
Indices: 32702--32757 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
32692 TTTTCATGAT
32702 TAAAAATAATTATATTTTATAAA
1 TAAAAAT-ATTATATTTTATAAA
* *
32725 -AAAATTATT-TCTTTTATAAAA
1 TAAAAATATTATATTTTAT-AAA
32746 TAAAAATATTAT
1 TAAAAATATTAT
32758 TATAAGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 13 0.48
23 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAATATTATATTTTATAAA
Found at i:57249 original size:5 final size:5
Alignment explanation
Indices: 57239--57263 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57229 TCTTGATTAA
57239 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
57264 TAATGGATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:60465 original size:19 final size:19
Alignment explanation
Indices: 60437--60480 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
60427 TGGCTTAAGG
*
60437 TTAAGTTAATTA-AATTTAA
1 TTAAGATAATTAGAA-TTAA
60456 TTAAGATAATTAGTAATTAA
1 TTAAGATAATTAG-AATTAA
60476 TTAAG
1 TTAAG
60481 TTTAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
TTAAGATAATTAGAATTAA
Done.