Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012525.1 Kokia drynarioides strain JFW-HI SEQ_127532, 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: 56797
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:551 original size:18 final size:18
Alignment explanation
Indices: 528--564 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
518 TTTGTGATCA
528 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
546 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
564 A
1 A
565 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:6242 original size:49 final size:49
Alignment explanation
Indices: 6110--6334 Score: 190
Period size: 49 Copynumber: 4.6 Consensus size: 49
6100 GACATGAAGG
* * ** *
6110 GAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCGCGAAGATAATTGAGG
1 GAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCACGAAGAT-ATAAAGA
* *
6160 GAAAGATTTAAG-CTGCAACGGCAAATCTAGTACCACGAAGATATAAAGA
1 GAAAGATTTAAGTC-GCAACGGCGAACCTAGTACCACGAAGATATAAAGA
* * * * *
6209 GAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATGAAGA
1 GAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAC-GAAGATATAAAGA
* * ** * * *
6258 GAAATATTTAAGTCGTAACAACAAATCTAGTACCACGAAGATACAAA-A
1 GAAAGATTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATAAAGA
6306 GGAAATG-TTTAAGTCGCAACGGCGAACCT
1 -GAAA-GATTTAAGTCGCAACGGCGAACCT
6335 TATACCCCAA
Statistics
Matches: 137, Mismatches: 31, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
48 5 0.04
49 92 0.67
50 40 0.29
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (49 bp):
GAAAGATTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATAAAGA
Found at i:6299 original size:98 final size:99
Alignment explanation
Indices: 6181--6426 Score: 320
Period size: 98 Copynumber: 2.5 Consensus size: 99
6171 GCTGCAACGG
* * *
6181 CAAATCTAGTACCACGAAGATATAAAGAGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
1 CAAATCTAGTACCACGAAGATATAAAGAGAAAAGTTTAAGTCGCAACGGCGAACCTTATACCCCA
* * * *
6246 GAAGCATGAA-GAGAAATATTTAAGTCGTAACA-A
66 AAAGCACGAAGGA-AAAAATTTAAGCCGTAACAGA
* *
6279 CAAATCTAGTACCACGAAGATACAAA-AGGAAATGTTTAAGTCGCAACGGCGAACCTTATACCCC
1 CAAATCTAGTACCACGAAGATATAAAGA-GAAAAGTTTAAGTCGCAACGGCGAACCTTATACCCC
6343 AAAAGCACGAAGGAAAAAATTTAAGCCGTAACAGA
65 AAAAGCACGAAGGAAAAAATTTAAGCCGTAACAGA
* * * * *
6378 -AAATCTAGTACCGCGAAGACATAAAGAGAAAAATTGAAGCCGCAACGGC
1 CAAATCTAGTACCACGAAGATATAAAGAGAAAAGTTTAAGTCGCAACGGC
6427 AAATTTTATA
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
97 1 0.01
98 124 0.96
99 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (99 bp):
CAAATCTAGTACCACGAAGATATAAAGAGAAAAGTTTAAGTCGCAACGGCGAACCTTATACCCCA
AAAGCACGAAGGAAAAAATTTAAGCCGTAACAGA
Found at i:6911 original size:30 final size:30
Alignment explanation
Indices: 6877--6967 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
6867 ATTTAATTTA
* *
6877 ATTTAATTTTACAAGTCCATTTACAAGCCC
1 ATTTAATTTGAGAAGTCCATTTACAAGCCC
6907 ATTTAATTTGAGAAGTCCATTTACAAGCCC
1 ATTTAATTTGAGAAGTCCATTTACAAGCCC
6937 ATTTAATTTGAGAAGTCCATTTACAAGCCC
1 ATTTAATTTGAGAAGTCCATTTACAAGCCC
6967 A
1 A
6968 AATCTCAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (30 bp):
ATTTAATTTGAGAAGTCCATTTACAAGCCC
Found at i:7101 original size:11 final size:11
Alignment explanation
Indices: 7085--7118 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
7075 ACGTCCGCAT
7085 CGCCATGTCAG
1 CGCCATGTCAG
7096 CGCCATGTCAG
1 CGCCATGTCAG
*
7107 CGCCACGTCAG
1 CGCCATGTCAG
7118 C
1 C
7119 CATGTGACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.41, G:0.26, T:0.15
Consensus pattern (11 bp):
CGCCATGTCAG
Found at i:10066 original size:3 final size:3
Alignment explanation
Indices: 10058--10087 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10048 GGTAAGGTAC
10058 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
10088 TGGTTGCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:11361 original size:36 final size:37
Alignment explanation
Indices: 11314--11391 Score: 149
Period size: 36 Copynumber: 2.1 Consensus size: 37
11304 ATAAAATTTT
11314 ACTCAAAACTATCCATATTTACAAAAGATTAACTT-A
1 ACTCAAAACTATCCATATTTACAAAAGATTAACTTAA
11350 ACTCAAAACTATCCATATTTACAAAAGATTAACTTAA
1 ACTCAAAACTATCCATATTTACAAAAGATTAACTTAA
11387 ACTCA
1 ACTCA
11392 TTTTAAGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 35 0.85
37 6 0.15
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (37 bp):
ACTCAAAACTATCCATATTTACAAAAGATTAACTTAA
Found at i:14783 original size:21 final size:22
Alignment explanation
Indices: 14740--14783 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14730 TTTTAAATTT
**
14740 TTTTAATATTTAAATTGTTTTA
1 TTTTAATATTTAAATAATTTTA
14762 TTTTAATATTT-AATAATTTTA
1 TTTTAATATTTAAATAATTTTA
14783 T
1 T
14784 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAATATTTAAATAATTTTA
Found at i:16239 original size:3 final size:3
Alignment explanation
Indices: 16231--16257 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16221 TAAGGATCAT
16231 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
16258 AAAGAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27878 original size:2 final size:2
Alignment explanation
Indices: 27865--27896 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
27855 TAATGTTGTC
*
27865 AT AT AC 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 AT AT AT
27897 TAAACATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29884 original size:23 final size:24
Alignment explanation
Indices: 29841--29886 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
29831 TTATTAATCG
*
29841 AATTGAATTAGTATTACTTAAATT
1 AATTGAATTAGTAATACTTAAATT
29865 AATTGAA-TAGTAAT-CTTTAAAT
1 AATTGAATTAGTAATAC-TTAAAT
29887 CGTTAATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 12 0.60
24 7 0.35
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (24 bp):
AATTGAATTAGTAATACTTAAATT
Found at i:31317 original size:22 final size:24
Alignment explanation
Indices: 31292--31344 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
31282 TAAGTTTAAT
31292 TATAAAAT-A-TATAAAATATTAG
1 TATAAAATAATTATAAAATATTAG
* *
31314 TATAAAATAATTTTTAAATATTAG
1 TATAAAATAATTATAAAATATTAG
31338 TATAAAA
1 TATAAAA
31345 CAATCTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 8 0.30
23 1 0.04
24 18 0.67
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TATAAAATAATTATAAAATATTAG
Found at i:36062 original size:19 final size:19
Alignment explanation
Indices: 36038--36077 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
36028 TAGTTAATAT
*
36038 AACCTAATTTAATTTCGTA
1 AACCTAATATAATTTCGTA
36057 AACCTAATATAATTTCGTA
1 AACCTAATATAATTTCGTA
36076 AA
1 AA
36078 TGACATAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
AACCTAATATAATTTCGTA
Found at i:36517 original size:21 final size:21
Alignment explanation
Indices: 36492--36532 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
36482 AATGTATATG
36492 ACTTACTAACAAAATAAAATT
1 ACTTACTAACAAAATAAAATT
36513 ACTTACTAACAAAATAAAAT
1 ACTTACTAACAAAATAAAAT
36533 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (21 bp):
ACTTACTAACAAAATAAAATT
Found at i:36853 original size:12 final size:12
Alignment explanation
Indices: 36823--36847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36813 CTAACAAATT
36823 AAATAAATTTAA
1 AAATAAATTTAA
36835 AAATAAATTTAA
1 AAATAAATTTAA
36847 A
1 A
36848 TTTAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:37313 original size:13 final size:15
Alignment explanation
Indices: 37282--37328 Score: 71
Period size: 14 Copynumber: 3.2 Consensus size: 15
37272 CCATTTTTAT
37282 AATTTTTTAATATTA
1 AATTTTTTAATATTA
37297 AA-TTTTTAATATT-
1 AATTTTTTAATATTA
37310 AATTTTTTAATATATA
1 AATTTTTTAATAT-TA
37326 AAT
1 AAT
37329 ACAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.07
14 21 0.72
15 3 0.10
16 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTTTAATATTA
Found at i:51350 original size:18 final size:18
Alignment explanation
Indices: 51324--51358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51314 TAAATAATAA
* *
51324 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
51342 AATAATATTATTAATTA
1 AATAATATTATTAATTA
51359 ATATATCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:51350 original size:21 final size:20
Alignment explanation
Indices: 51320--51363 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
51310 AATATAAATA
* *
51320 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
51340 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
51361 ATA
1 ATA
51364 TCATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Done.