Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007617.1 Kokia drynarioides strain JFW-HI SEQ_122248, 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: 69877
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4353 original size:24 final size:24
Alignment explanation
Indices: 4308--4353 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4298 GTTTGATGAA
* *
4308 TTATTTATAAATAGTTCGATTTCT
1 TTATTTATAAATAATTAGATTTCT
* *
4332 TTATTTATTAATAATTATATTT
1 TTATTTATAAATAATTAGATTT
4354 AATTATCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATTTATAAATAATTAGATTTCT
Found at i:4368 original size:2 final size:2
Alignment explanation
Indices: 4361--4387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4351 TTTAATTATC
4361 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4388 AAGATAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15455 original size:33 final size:33
Alignment explanation
Indices: 15376--15458 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
15366 ACGAACTTAC
* * * *
15376 TTTT-TTTCGTGTTCACTGTCTCGATGGATTAT
1 TTTTGTTTCGTGTTTACTATCTCGATAGACTAT
* * * *
15408 CTCTGTTCCATGTTTACTATCTCGATAGACTAT
1 TTTTGTTTCGTGTTTACTATCTCGATAGACTAT
15441 TTTTGTTTCGTGTTTACT
1 TTTTGTTTCGTGTTTACT
15459 GTCTAGGGGG
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.52
Consensus pattern (33 bp):
TTTTGTTTCGTGTTTACTATCTCGATAGACTAT
Found at i:15804 original size:57 final size:57
Alignment explanation
Indices: 15653--15795 Score: 187
Period size: 57 Copynumber: 2.5 Consensus size: 57
15643 ACCTTGCCGT
* * *
15653 CATGTCATCTTTCATCCATGGTCTTGCGCCATATATCTTTATCGTGTACCATGCTGC
1 CATGACATCTTTCATCCATGGTCTTACGCCATATACCTTTATCGTGTACCATGCTGC
* * * * *
15710 CATGACATCTTTCACCCATGATCTTATGCCATATACCTTTATCGTGTACCATGTTGT
1 CATGACATCTTTCATCCATGGTCTTACGCCATATACCTTTATCGTGTACCATGCTGC
** *
15767 CATGATGTCTTTTATCCATGGTCTTACGC
1 CATGACATCTTTCATCCATGGTCTTACGC
15796 TACGTACCTC
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (57 bp):
CATGACATCTTTCATCCATGGTCTTACGCCATATACCTTTATCGTGTACCATGCTGC
Found at i:18168 original size:16 final size:16
Alignment explanation
Indices: 18147--18177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18137 TCCATGTCAA
*
18147 ATTAAATTGATTATAG
1 ATTAAATTAATTATAG
18163 ATTAAATTAATTATA
1 ATTAAATTAATTATA
18178 AGAACATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTAAATTAATTATAG
Found at i:21904 original size:24 final size:25
Alignment explanation
Indices: 21880--21950 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 25
21870 TTTATTATTC
*
21880 ATTAAGATGTTCGTGAACATGTTCA
1 ATTAAGATGTTCATGAACATGTTCA
* * *
21905 ATT-ATATTTTCATGAACATGTTCG
1 ATTAAGATGTTCATGAACATGTTCA
**
21929 ATTAAG-T-TAAATGAACATGTTC
1 ATTAAGATGTTCATGAACATGTTC
21951 GTGAACATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 13 0.34
24 21 0.55
25 4 0.11
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (25 bp):
ATTAAGATGTTCATGAACATGTTCA
Found at i:21946 original size:23 final size:24
Alignment explanation
Indices: 21893--21951 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
21883 AAGATGTTCG
* * **
21893 TGAACATGTTCAATTATATTTTCA
1 TGAACATGTTCGATTATAGTTAAA
21917 TGAACATGTTCGATTA-AGTTAAA
1 TGAACATGTTCGATTATAGTTAAA
21940 TGAACATGTTCG
1 TGAACATGTTCG
21952 TGAACATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (24 bp):
TGAACATGTTCGATTATAGTTAAA
Found at i:21961 original size:23 final size:23
Alignment explanation
Indices: 21916--21962 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
21906 TTATATTTTC
* *
21916 ATGAACATGTTCGATTAAGTTAA
1 ATGAACATGTTCGATGAAATTAA
21939 ATGAACATGTTCG-TGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
21962 A
1 A
21963 CAGACGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:25471 original size:16 final size:16
Alignment explanation
Indices: 25452--25511 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
25442 AAAGAAATGT
25452 GAAAAAAAAAAGAGAA
1 GAAAAAAAAAAGAGAA
*
25468 GAAAAAAAAAAGTGAA
1 GAAAAAAAAAAGAGAA
* *
25484 TAATGAAAAAAATGA-AA
1 GAA--AAAAAAAAGAGAA
25501 GAAAAGAAAAA
1 GAAAA-AAAAA
25512 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 2 0.06
16 22 0.61
17 4 0.11
18 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
GAAAAAAAAAAGAGAA
Found at i:38360 original size:29 final size:30
Alignment explanation
Indices: 38325--38383 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
38315 TATAGTTTAA
38325 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
38354 TGTGCAATTTTATACTTGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
38384 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:38600 original size:29 final size:30
Alignment explanation
Indices: 38553--38631 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
38543 ATACATTTGA
* *
38553 ACCAATATTAGAATTTCATGTGTATAATT-AC
1 ACCAA-ATTA-AAGTTCATGTATATAATTCAC
38584 ACCAAATTAAAGTTCATGTATATAATTGCAC
1 ACCAAATTAAAGTTCATGTATATAATT-CAC
**
38615 ATTAAATTAAAGTTCAT
1 ACCAAATTAAAGTTCAT
38632 CCATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.38
30 4 0.10
31 22 0.52
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
ACCAAATTAAAGTTCATGTATATAATTCAC
Found at i:39128 original size:18 final size:18
Alignment explanation
Indices: 39105--39141 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39095 AATCAAAGTG
39105 GTTTCATAGTATATACAA
1 GTTTCATAGTATATACAA
39123 GTTTCATAGTATATACAA
1 GTTTCATAGTATATACAA
39141 G
1 G
39142 ATTGAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (18 bp):
GTTTCATAGTATATACAA
Found at i:40681 original size:18 final size:18
Alignment explanation
Indices: 40643--40680 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40633 CCAATCTGAA
40643 TTTAACAATATTTTTTGT
1 TTTAACAATATTTTTTGT
40661 TTTAA-AATATGTTTTT-T
1 TTTAACAATAT-TTTTTGT
40678 TTT
1 TTT
40681 TTGCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTAACAATATTTTTTGT
Found at i:44780 original size:13 final size:13
Alignment explanation
Indices: 44758--44790 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44748 CAAAATTTTT
*
44758 TAACTAATAATTA
1 TAACTTATAATTA
44771 TAACTTATAATTA
1 TAACTTATAATTA
44784 TAA-TTAT
1 TAACTTAT
44791 CATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (13 bp):
TAACTTATAATTA
Found at i:44948 original size:44 final size:44
Alignment explanation
Indices: 44885--44972 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
44875 ATAATTGTAA
* * * * *
44885 TTTAAGTTGTAATTATTTTTAAATTTGTAATTATCACAATTTCT
1 TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
*
44929 TTTAAATTATAATTATTTTTACATGTATAATTATCACAACTTCT
1 TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
44973 GTTTTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (44 bp):
TTTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCT
Found at i:62249 original size:3 final size:3
Alignment explanation
Indices: 62184--62238 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
62174 TACAATTTAC
62184 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62230 ATT ATT ATT
1 ATT ATT ATT
62239 TTGGATTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:67110 original size:20 final size:20
Alignment explanation
Indices: 67085--67125 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
67075 GATTGTGCAT
67085 TGTAATAAAACACATTAAAG
1 TGTAATAAAACACATTAAAG
* *
67105 TGTAATAAAATATATTAAAG
1 TGTAATAAAACACATTAAAG
67125 T
1 T
67126 CAATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (20 bp):
TGTAATAAAACACATTAAAG
Done.