Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010179.1 Kokia drynarioides strain JFW-HI SEQ_124985, 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: 9117
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:328 original size:18 final size:18
Alignment explanation
Indices: 300--383 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 18
290 CCCTTTTTTA
300 TATTAATTATTAATAATAT
1 TATT-ATTATTAATAATAT
*
319 TATTATTATTAATAA-AA
1 TATTATTATTAATAATAT
* **
336 CATTTATTATTAATGCCT-T
1 TA-TTATTATTAAT-AATAT
*
355 TATTAATATTAATAATA-
1 TATTATTATTAATAATAT
372 -ATT-TTATTAATA
1 TATTATTATTAATA
384 CCTATTAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 8 0.16
16 3 0.06
17 3 0.06
18 32 0.63
19 5 0.10
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (18 bp):
TATTATTATTAATAATAT
Found at i:364 original size:21 final size:21
Alignment explanation
Indices: 340--393 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
330 ATAAAACATT
*
340 TATTATTAATGCCTTTATTAA
1 TATTATTAATGACTTTATTAA
* * *
361 TATTAATAATAATTTTATTAA
1 TATTATTAATGACTTTATTAA
*
382 TACCTATTAATG
1 TA-TTATTAATG
394 TCAATATTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (21 bp):
TATTATTAATGACTTTATTAA
Found at i:1066 original size:5 final size:6
Alignment explanation
Indices: 1047--1094 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
1037 GGACCTTTTC
* * *
1047 AATTAA AATTTA AA-TTA AATTTA AATTTA AACTTA AA-CTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1093 AA
1 AA
1095 CCCAAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:1072 original size:17 final size:18
Alignment explanation
Indices: 1047--1095 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
1037 GGACCTTTTC
*
1047 AATTAAAATTTAAA-TTA
1 AATTTAAATTTAAACTTA
1064 AATTTAAATTTAAACTTA
1 AATTTAAATTTAAACTTA
*
1082 AA-CTAAATTTAAAC
1 AATTTAAATTTAAAC
1096 CCAAAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTTAAATTTAAACTTA
Found at i:1082 original size:23 final size:23
Alignment explanation
Indices: 1047--1094 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1037 GGACCTTTTC
* *
1047 AATTAAAATTTAAATTAAATTTA
1 AATTAAAACTTAAACTAAATTTA
*
1070 AATTTAAACTTAAACTAAATTTA
1 AATTAAAACTTAAACTAAATTTA
1093 AA
1 AA
1095 CCCAAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTAAAACTTAAACTAAATTTA
Found at i:1095 original size:11 final size:11
Alignment explanation
Indices: 1052--1095 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1042 TTTTCAATTA
*
1052 AAATTTAAATT
1 AAATTTAAACT
*
1063 AAATTTAAATTT
1 AAATTTAAA-CT
*
1075 AAACTTAAACT
1 AAATTTAAACT
1086 AAATTTAAAC
1 AAATTTAAAC
1096 CCAAAATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTTAAACT
Found at i:1885 original size:24 final size:24
Alignment explanation
Indices: 1832--1885 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1822 TTATTTTTAT
* * *
1832 ATATTATATAATTTGTATTGTATA
1 ATATTATATAATTTATAATGTAGA
*
1856 AAATTATATAATATTATAATGT-GA
1 ATATTATATAAT-TTATAATGTAGA
1880 ATATTA
1 ATATTA
1886 AAAATACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (24 bp):
ATATTATATAATTTATAATGTAGA
Found at i:4061 original size:14 final size:15
Alignment explanation
Indices: 4042--4072 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4032 TTTTACTTTA
4042 TTTTATTTTTAT-CT
1 TTTTATTTTTATGCT
4056 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
4071 TT
1 TT
4073 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Done.