Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005234.1 Kokia drynarioides strain JFW-HI SEQ_119122, 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: 4629
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Found at i:170 original size:13 final size:13
Alignment explanation
Indices: 152--176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142 TGTTACACTT
152 TTTTTAATTAATG
1 TTTTTAATTAATG
165 TTTTTAATTAAT
1 TTTTTAATTAAT
177 AATATATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:548 original size:20 final size:21
Alignment explanation
Indices: 525--568 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
515 AAATTAATTG
*
525 ATAT-TTTAAAA-AAATA-AA
1 ATATATTTAAAATAAAGATAA
543 ATATATTTAAAATAAAGATAA
1 ATATATTTAAAATAAAGATAA
564 ATATA
1 ATATA
569 AAAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 4 0.18
21 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATATATTTAAAATAAAGATAA
Found at i:551 original size:19 final size:19
Alignment explanation
Indices: 501--568 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 19
491 TATATAAAGA
*
501 AAAATATA-TTACAAAAAT
1 AAAATATATTTAAAAAAAT
* *
519 TAATTGATATTTTAAAAAAAT
1 AAAAT-ATA-TTTAAAAAAAT
*
540 AAAATATATTTAAAATAAAG
1 AAAATATATTTAAAA-AAAT
560 ATAAATATA
1 A-AAATATA
569 AAAATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
18 3 0.08
19 10 0.26
20 7 0.18
21 19 0.49
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAATATATTTAAAAAAAT
Found at i:696 original size:25 final size:28
Alignment explanation
Indices: 652--725 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
642 TAACATAATG
* *
652 ATATATATAAAATAAATATT-TTT-ATT
1 ATATAAATAAAATAATTATTATTTGATT
* *
678 ATAT-AATTATATAATTATTATTTGATT
1 ATATAAATAAAATAATTATTATTTGATT
*
705 TTATAAATAAAATAATTATTA
1 ATATAAATAAAATAATTATTA
726 ATTAAAAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 11 0.29
26 7 0.18
27 6 0.16
28 14 0.37
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
ATATAAATAAAATAATTATTATTTGATT
Found at i:997 original size:142 final size:139
Alignment explanation
Indices: 771--1032 Score: 307
Period size: 142 Copynumber: 1.9 Consensus size: 139
761 ACAATATATT
* * **
771 TATTAATAAAAAAATAAAAAAACTTGAAACAACATGAAAAAAAATACAAATGTGCTTAAAAGAAT
1 TATTAATAAAAAAATAAAAAAACTCGAAACAACATGAAAAAAAATACAAATGCGAGTAAAAGAAT
* * * *
836 AATTAAACTTGAGACTTAAGGATGAAA-CACTATTATTTAATCATCTAACCAAAAAAAATGAATC
66 AATTAAACTGGAGACTTAAGGATAAAACCACTAATATTTAATCATCCAACCAAAAAAAATGAATC
900 TGTTAAAAA
131 TGTTAAAAA
* *
909 TATTAATTAAAAATAA-AACAAAAACTCGAAACAATATGAAATAAAAAATACAAATGCGAGTAGA
1 TATTAA-TAAAAA-AATAA-AAAAACTCGAAACAACATG-AA-AAAAAATACAAATGCGAGTAAA
* * * *
973 AGAGA-AATTGAACTCGGA-ATTTAAGGATAAAACCATTAATATTTAATCATCCAACTAAAA
61 AGA-ATAATTAAACT-GGAGACTTAAGGATAAAACCACTAATATTTAATCATCCAACCAAAA
1033 GAGTTTATGT
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
138 6 0.06
139 8 0.08
140 19 0.19
141 2 0.02
142 41 0.40
143 26 0.25
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (139 bp):
TATTAATAAAAAAATAAAAAAACTCGAAACAACATGAAAAAAAATACAAATGCGAGTAAAAGAAT
AATTAAACTGGAGACTTAAGGATAAAACCACTAATATTTAATCATCCAACCAAAAAAAATGAATC
TGTTAAAAA
Found at i:2279 original size:70 final size:70
Alignment explanation
Indices: 2169--2309 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
2159 TCGTTCAATG
2169 ATTTTTATTAAGATTTTGATGTGAATCATGAGATTTGAATTTGATAAATATCTATTTGTTAAAAA
1 ATTTTTATTAAGATTTTGATGTGAATCATGAGATTTGAATTTGATAAATATCTATTTGTTAAAAA
2234 AATTT
66 AATTT
2239 ATTTTTATTAAGATTTTGATGTGAATCATGAGATTTGAATTTGATAAATATCTATTTGTTAAAAA
1 ATTTTTATTAAGATTTTGATGTGAATCATGAGATTTGAATTTGATAAATATCTATTTGTTAAAAA
2304 AATTT
66 AATTT
2309 A
1 A
2310 ACATACCAAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (70 bp):
ATTTTTATTAAGATTTTGATGTGAATCATGAGATTTGAATTTGATAAATATCTATTTGTTAAAAA
AATTT
Done.