Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015067.1 Kokia drynarioides strain JFW-HI SEQ_130111, 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: 30495
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1818 original size:16 final size:17
Alignment explanation
Indices: 1784--1830 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1774 TTTGGTTCAC
*
1784 TGTAATGGAATA-AGGT
1 TGTAATGGAATAGAGAT
1800 TGTAATGGAATAGA-AT
1 TGTAATGGAATAGAGAT
*
1816 TGTAATTGAATAGAG
1 TGTAATGGAATAGAG
1831 CTGTAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (17 bp):
TGTAATGGAATAGAGAT
Found at i:1835 original size:16 final size:16
Alignment explanation
Indices: 1800--1838 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1790 GGAATAAGGT
* *
1800 TGTAATGGAATAGAAT
1 TGTAATTGAATAGAAC
*
1816 TGTAATTGAATAGAGC
1 TGTAATTGAATAGAAC
1832 TGTAATT
1 TGTAATT
1839 AGTAATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (16 bp):
TGTAATTGAATAGAAC
Found at i:2162 original size:22 final size:21
Alignment explanation
Indices: 2122--2162 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2112 AAATTGAATT
*
2122 TAAAATAAATATTTTAATTGA
1 TAAAATAAATATTTCAATTGA
*
2143 TAAATTAATATATTTCAATT
1 TAAAATAA-ATATTTCAATT
2163 ATATTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAAATAAATATTTCAATTGA
Found at i:7537 original size:13 final size:13
Alignment explanation
Indices: 7519--7562 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
7509 TTATAGGTTA
7519 AATAAATTATATT
1 AATAAATTATATT
7532 AATAAA-TAT-TT
1 AATAAATTATATT
* *
7543 AATATATTATACT
1 AATAAATTATATT
7556 AATAAAT
1 AATAAAT
7563 ACTAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.27
12 6 0.23
13 13 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AATAAATTATATT
Found at i:8555 original size:3 final size:3
Alignment explanation
Indices: 8547--8571 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8537 AAGACTATTT
8547 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
8572 AGCTTTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10430 original size:12 final size:12
Alignment explanation
Indices: 10395--10424 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
10385 TGAATTATAG
10395 AAAAGAAAAAAAA
1 AAAAG-AAAAAAA
10408 AAAAGAAAAAAA
1 AAAAGAAAAAAA
10420 AAAAG
1 AAAAG
10425 GTAAAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:10430 original size:13 final size:13
Alignment explanation
Indices: 10395--10423 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10385 TGAATTATAG
10395 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
10408 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
10421 AAA
1 AAA
10424 GGTAAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:11950 original size:61 final size:63
Alignment explanation
Indices: 11870--11997 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 63
11860 ACGTCAACAA
* * *
11870 AGTTATTAAACTATAACTTCTTCATCTATTTTGAATAGATTTGA-TAAAATGTAAATTC-AAG
1 AGTTATCAAACTATAACTTCTTCATCTATTTTGAATAGATTTAACAAAAATGTAAATTCTAAG
* * *
11931 AGTTATCAAATTATAACTTCTTTATCTATTTTGAGTAGATTTAACAAAAATGTAAATTCTAAG
1 AGTTATCAAACTATAACTTCTTCATCTATTTTGAATAGATTTAACAAAAATGTAAATTCTAAG
11994 AGTT
1 AGTT
11998 TAAAAAAGCG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 39 0.66
62 13 0.22
63 7 0.12
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (63 bp):
AGTTATCAAACTATAACTTCTTCATCTATTTTGAATAGATTTAACAAAAATGTAAATTCTAAG
Found at i:19224 original size:17 final size:17
Alignment explanation
Indices: 19202--19235 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19192 ATGGAGGAAC
19202 TGAAGTCTAAGATAGTA
1 TGAAGTCTAAGATAGTA
19219 TGAAGTCTAAGATAGTA
1 TGAAGTCTAAGATAGTA
19236 CGCAATGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
TGAAGTCTAAGATAGTA
Found at i:23542 original size:23 final size:22
Alignment explanation
Indices: 23510--23642 Score: 108
Period size: 23 Copynumber: 5.9 Consensus size: 22
23500 AAGTACTTAA
23510 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
23532 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
23555 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
* * * *
23578 CAATAGGCACACGA-GGTGCAAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
*
23601 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
23624 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
23643 TGAACAGTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
22 17 0.18
23 76 0.81
24 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:23648 original size:23 final size:23
Alignment explanation
Indices: 23584--23654 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
23574 AAATCAATAG
* *
23584 GCACACGAGGTGCAAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
23607 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
23630 GCACAC-ACAGTGCTG-AACAGTAA
1 GCACACGA-AGTGC-GAAACAGTAA
23653 GC
1 GC
23655 GCGCTAGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.10
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAGTAA
Found at i:23755 original size:24 final size:26
Alignment explanation
Indices: 23717--23764 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
23707 TCTACATGGG
23717 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
23743 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
23765 ATATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:28240 original size:20 final size:20
Alignment explanation
Indices: 28217--28254 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28207 TCTCTCATTT
* *
28217 TTTTTTTTTTTTTACCCATG
1 TTTTTTATTTCTTACCCATG
28237 TTTTTTATTTCTTACCCA
1 TTTTTTATTTCTTACCCA
28255 ATTTTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTTATTTCTTACCCATG
Found at i:28259 original size:19 final size:20
Alignment explanation
Indices: 28217--28259 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28207 TCTCTCATTT
* * *
28217 TTTTTTTTTTTTTACCCATG
1 TTTTTTATTTCTTACCCATA
28237 TTTTTTATTTCTTACCCA-A
1 TTTTTTATTTCTTACCCATA
28256 TTTT
1 TTTT
28260 CTTTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTTATTTCTTACCCATA
Done.