Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004410.1 Kokia drynarioides strain JFW-HI SEQ_117790, 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: 82504
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:811 original size:6 final size:6
Alignment explanation
Indices: 802--864 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
792 CAATGATGAT
802 GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG
1 GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG GATCTG
* *
850 GATCCG GATCAG GAT
1 GATCTG GATCTG GAT
865 TTTTTGGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (6 bp):
GATCTG
Found at i:13982 original size:14 final size:14
Alignment explanation
Indices: 13965--13995 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13955 AAAAAGCATA
13965 AAAGTAAAAGAAAT
1 AAAGTAAAAGAAAT
*
13979 AAAGTAAAGGAAAT
1 AAAGTAAAAGAAAT
13993 AAA
1 AAA
13996 TGTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (14 bp):
AAAGTAAAAGAAAT
Found at i:14490 original size:13 final size:14
Alignment explanation
Indices: 14465--14501 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
14455 GTTTCCACAA
14465 AACAAAAATGAAAT-
1 AACAAAAA-GAAATG
14479 AACAAAAAGAAATG
1 AACAAAAAGAAATG
14493 AA-AAAAAGA
1 AACAAAAAGA
14502 CTAAACCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (14 bp):
AACAAAAAGAAATG
Found at i:35939 original size:61 final size:61
Alignment explanation
Indices: 35787--35919 Score: 239
Period size: 61 Copynumber: 2.2 Consensus size: 61
35777 GTAAATGCAA
35787 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTACAGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTACAGATT
* **
35848 AAAGGTCCTATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTACAGATT
35909 AAAGGTCCGAT
1 AAAGGTCCGAT
35920 ACCTTTACGG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (61 bp):
AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTACAGATT
Found at i:41553 original size:24 final size:24
Alignment explanation
Indices: 41501--41564 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
41491 ACTCTGTTTG
*
41501 GGCTCGTAAGAGCTAACCTTTCTA
1 GGCTCGTAAGAGCTAACCTGTCTA
* *
41525 TGCTCGTAAGAGCTAATTCTGTCT-
1 GGCTCGTAAGAGCTAA-CCTGTCTA
*
41549 GGCTCGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
41565 ATTATGGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCTGTCTA
Found at i:46814 original size:27 final size:28
Alignment explanation
Indices: 46783--46852 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
46773 TAGAAGGATC
*
46783 AAATTAATTTAAATTAATCTAC-CAAAA
1 AAATTAGTTTAAATTAATCTACACAAAA
*
46810 AAATTAGTTTAAATT-ATTTACACAAAA
1 AAATTAGTTTAAATTAATCTACACAAAA
*
46837 GAATTAGTTTAAATTA
1 AAATTAGTTTAAATTA
46853 TATTAATGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (28 bp):
AAATTAGTTTAAATTAATCTACACAAAA
Found at i:58481 original size:8 final size:8
Alignment explanation
Indices: 58468--58495 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
58458 ATCATTTTGG
58468 TTTTTATT
1 TTTTTATT
58476 TTTTTATT
1 TTTTTATT
58484 TTTTTATT
1 TTTTTATT
58492 TTTT
1 TTTT
58496 GTTTTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:78257 original size:14 final size:14
Alignment explanation
Indices: 78238--78266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
78228 GATCCATGCC
78238 ATTACTACACTTGA
1 ATTACTACACTTGA
78252 ATTACTACACTTGA
1 ATTACTACACTTGA
78266 A
1 A
78267 AATCTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ATTACTACACTTGA
Done.