Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001503.1 Kokia drynarioides strain JFW-HI SEQ_113046, 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: 33431
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:415 original size:43 final size:43
Alignment explanation
Indices: 367--454 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
357 AATAGTATAC
* *
367 TTAGGTGTCTCTAATGAACATGTTACTAATATTGTTTTGAAAA
1 TTAGGTGTCCCTAATGAACAAGTTACTAATATTGTTTTGAAAA
*
410 TTAGGTGTCCCTAATGAACAAGTTATTAATATTGTTTTGAAAA
1 TTAGGTGTCCCTAATGAACAAGTTACTAATATTGTTTTGAAAA
453 TT
1 TT
455 TACATGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (43 bp):
TTAGGTGTCCCTAATGAACAAGTTACTAATATTGTTTTGAAAA
Found at i:11956 original size:31 final size:31
Alignment explanation
Indices: 11921--11992 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
11911 AAAAATAATT
*
11921 GTTCAGTGACTTAAACAAAAACTTT-TAACTA
1 GTTCAGTGACTTAAACAAAAACTTTCGAA-TA
* **
11952 GTTCAAT-ACTTAAATGAAAACTTTCGAATA
1 GTTCAGTGACTTAAACAAAAACTTTCGAATA
*
11982 GTTTAGTGACT
1 GTTCAGTGACT
11993 ATTTTGTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (31 bp):
GTTCAGTGACTTAAACAAAAACTTTCGAATA
Found at i:12409 original size:10 final size:10
Alignment explanation
Indices: 12394--12425 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12384 GGTTCTATTT
12394 CTCTCTCTCG
1 CTCTCTCTCG
12404 CTCTCTCTCG
1 CTCTCTCTCG
*
12414 CTCGCTCTCG
1 CTCTCTCTCG
12424 CT
1 CT
12426 GTTCAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.50, G:0.12, T:0.38
Consensus pattern (10 bp):
CTCTCTCTCG
Found at i:12410 original size:14 final size:14
Alignment explanation
Indices: 12393--12422 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12383 TGGTTCTATT
*
12393 TCTCTCTCTCGCTC
1 TCTCTCGCTCGCTC
12407 TCTCTCGCTCGCTC
1 TCTCTCGCTCGCTC
12421 TC
1 TC
12423 GCTGTTCAAA
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:0.00, C:0.50, G:0.10, T:0.40
Consensus pattern (14 bp):
TCTCTCGCTCGCTC
Found at i:14487 original size:24 final size:24
Alignment explanation
Indices: 14450--14497 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
14440 CCTGATGAAA
* *
14450 ACAATGCAATTGTTGAAACTAAAG
1 ACAATGCAAATGTTGAAAATAAAG
*
14474 ACAATGGAAATGTTGAAAATAAAG
1 ACAATGCAAATGTTGAAAATAAAG
14498 TCTCACTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (24 bp):
ACAATGCAAATGTTGAAAATAAAG
Found at i:20629 original size:17 final size:17
Alignment explanation
Indices: 20607--20641 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20597 ATAATTATAT
*
20607 TAATTATATATGTTAAA
1 TAATTATATATATTAAA
20624 TAATTATATATATTAAA
1 TAATTATATATATTAAA
20641 T
1 T
20642 TACTAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TAATTATATATATTAAA
Found at i:23827 original size:2 final size:2
Alignment explanation
Indices: 23799--23846 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
23789 GCATATTGAA
* * * *
23799 AT AT AT AC AT AC AT AT GT AT GT 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 AT AT AT AT AT
23841 AT AT AT
1 AT AT AT
23847 GGTTGGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26448 original size:15 final size:15
Alignment explanation
Indices: 26428--26457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26418 ACGTTTAGTA
26428 AACCTGGTATCATTT
1 AACCTGGTATCATTT
26443 AACCTGGTATCATTT
1 AACCTGGTATCATTT
26458 TTTAGCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
AACCTGGTATCATTT
Found at i:30095 original size:21 final size:20
Alignment explanation
Indices: 30052--30095 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30042 AAAAACAAAT
* *
30052 AATGTCTCAAATACATCATA
1 AATGTCTCAAATACAGCACA
30072 AATGTCTTCAAATACAGCACA
1 AATGTC-TCAAATACAGCACA
30093 AAT
1 AAT
30096 ACAAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.27
Consensus pattern (20 bp):
AATGTCTCAAATACAGCACA
Found at i:30312 original size:25 final size:26
Alignment explanation
Indices: 30258--30313 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
30248 TAAACATTAA
*
30258 ATTAAATTTAATATTAATATAATCAC
1 ATTAAATTTAATATTAATAAAATCAC
*
30284 ATTAATTTTAA-ATTAATAAAAT-AC
1 ATTAAATTTAATATTAATAAAATCAC
30308 TATTAA
1 -ATTAA
30314 GATAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 15 0.56
26 10 0.37
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTAAATTTAATATTAATAAAATCAC
Found at i:30997 original size:22 final size:22
Alignment explanation
Indices: 30969--31030 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
30959 TCAATTATGT
*
30969 TTATTTATAAAT-TATTTGTTTA
1 TTATTTATAAATATATTT-TTAA
30991 TTATTTATAAATATATTTTTAA
1 TTATTTATAAATATATTTTTAA
* *
31013 TTATTTGTAAAAATATTT
1 TTATTTATAAATATATTT
31031 AATTATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 31 0.86
23 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
TTATTTATAAATATATTTTTAA
Found at i:32846 original size:30 final size:31
Alignment explanation
Indices: 32785--32847 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
32775 AACATCCCAT
* *
32785 TGGTTTGAATTAAAACTTTTAAATAGTTCAA
1 TGGTTTAAATGAAAACTTTTAAATAGTTCAA
* *
32816 TGGTTTAAATGAAAA-TTTTGAATATTTCAA
1 TGGTTTAAATGAAAACTTTTAAATAGTTCAA
32846 TG
1 TG
32848 ACCAAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (31 bp):
TGGTTTAAATGAAAACTTTTAAATAGTTCAA
Done.