Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010825.1 Kokia drynarioides strain JFW-HI SEQ_125792, 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: 2065
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:33 original size:17 final size:16
Alignment explanation
Indices: 1--35 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1 TTAAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
17 TTAAATCTTATAATAAA
1 TTAAAT-TTAAAATAAA
34 TT
1 TT
36 TAAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:1050 original size:21 final size:20
Alignment explanation
Indices: 1013--1120 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 20
1003 AAAAACTCAT
* *
1013 AAAAATAACACCCAAACAAC
1 AAAAACAACACCAAAACAAC
1033 AAAAACAACAACCAAAACAATAAC
1 AAAAACAAC-ACCAAAAC---AAC
** **
1057 AAAAACAACAAAAATAACAGT
1 AAAAACAACACCAA-AACAAC
1078 AAAAACAACACCAAAACAA-
1 AAAAACAACACCAAAACAAC
*
1097 AAAAA-AA-ACCAGAAACAGC
1 AAAAACAACACCA-AAACAAC
1116 AAAAA
1 AAAAA
1121 AAATATATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
17 4 0.06
18 7 0.10
19 10 0.14
20 12 0.17
21 20 0.28
23 3 0.04
24 15 0.21
ACGTcount: A:0.71, C:0.22, G:0.03, T:0.04
Consensus pattern (20 bp):
AAAAACAACACCAAAACAAC
Found at i:1075 original size:24 final size:23
Alignment explanation
Indices: 1030--1093 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
1020 ACACCCAAAC
*
1030 AACAAAAACAACAACCAAAACAAT
1 AACAAAAACAACAA-AAAAACAAT
*
1054 AACAAAAACAACAAAAATAACAGT
1 AACAAAAACAACAAAAA-AACAAT
*
1078 AA-AAACAACACCAAAA
1 AACAAA-AACAACAAAA
1094 CAAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.14
24 30 0.86
ACGTcount: A:0.72, C:0.22, G:0.02, T:0.05
Consensus pattern (23 bp):
AACAAAAACAACAAAAAAACAAT
Found at i:1083 original size:33 final size:32
Alignment explanation
Indices: 1026--1102 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 32
1016 AATAACACCC
*
1026 AAACAACAAAAACAACAACCAAAACAATAACAA
1 AAACAACAAAAACAACAACAAAAACAA-AACAA
* ** * *
1059 AAACAACAAAAATAACAGTAAAAACAACACCA
1 AAACAACAAAAACAACAACAAAAACAAAACAA
*
1091 AAACAAAAAAAA
1 AAACAACAAAAA
1103 AACCAGAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 14 0.38
33 23 0.62
ACGTcount: A:0.74, C:0.21, G:0.01, T:0.04
Consensus pattern (32 bp):
AAACAACAAAAACAACAACAAAAACAAAACAA
Found at i:1093 original size:12 final size:12
Alignment explanation
Indices: 1027--1067 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1017 ATAACACCCA
1027 AACAACAAAAAC
1 AACAACAAAAAC
*
1039 AACAACCAAAAC
1 AACAACAAAAAC
*
1051 AATAACAAAAAC
1 AACAACAAAAAC
1063 AACAA
1 AACAA
1068 AAATAACAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.24, G:0.00, T:0.02
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:2064 original size:17 final size:18
Alignment explanation
Indices: 2032--2065 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2022 CAAACTCCCT
*
2032 TTAAATTTATTTTAAAAA
1 TTAAATTTAGTTTAAAAA
2050 TTAAATTT-GTTTAAAA
1 TTAAATTTAGTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAAATTTAGTTTAAAAA
Done.