Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013614.1 Kokia drynarioides strain JFW-HI SEQ_128642, 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: 3483
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1040 original size:22 final size:21
Alignment explanation
Indices: 965--1039 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 21
955 AATGATATTG
*
965 TTGTTTTGGTGTTTTTTTTTTA
1 TTGTTTTGGT-TATTTTTTTTA
*
987 TTGTTTTGGTTGATTTTTTTTG
1 TTGTTTTGGTT-ATTTTTTTTA
*
1009 CTGTTTTTGAGTTATTTTTTTTA
1 TTG-TTTTG-GTTATTTTTTTTA
1032 TTGTTTTG
1 TTGTTTTG
1040 ATTGCTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.02
22 25 0.56
23 16 0.36
24 3 0.07
ACGTcount: A:0.07, C:0.01, G:0.19, T:0.73
Consensus pattern (21 bp):
TTGTTTTGGTTATTTTTTTTA
Found at i:1050 original size:23 final size:23
Alignment explanation
Indices: 962--1107 Score: 88
Period size: 23 Copynumber: 6.4 Consensus size: 23
952 AAAAATGATA
* * *
962 TTGTTGTTTTG-GTGTTTTTTTT
1 TTGTTGTTTTGATTGCTATTTTT
* * *
984 TTATTGTTTTGGTTGAT-TTTTT
1 TTGTTGTTTTGATTGCTATTTTT
* *
1006 TTGCTGTTTTTGA--GTTATTTTTT
1 TTGTTG-TTTTGATTGCTA-TTTTT
*
1029 TTATTGTTTTGATTGCTATTTTT
1 TTGTTGTTTTGATTGCTATTTTT
* * * *
1052 GTGTTATTTTTG-CTGTTATTTTT
1 TTGTT-GTTTTGATTGCTATTTTT
*
1075 ATTGTTGTTTTTATTGCTA-TTTT
1 -TTGTTGTTTTGATTGCTATTTTT
1098 TTGTTGTTTT
1 TTGTTGTTTT
1108 TAATGTTGTT
Statistics
Matches: 95, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
21 2 0.02
22 35 0.37
23 42 0.44
24 16 0.17
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (23 bp):
TTGTTGTTTTGATTGCTATTTTT
Found at i:1050 original size:47 final size:48
Alignment explanation
Indices: 978--1101 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 48
968 TTTTGGTGTT
* * *
978 TTTTTTTTATTGTTTTGGTTG--ATTTTTTTTGCTGTTTTTG-AGTTA
1 TTTTTTTTATTGTTTTGATTGCTATTTTTTGTGCTATTTTTGCAGTTA
* *
1023 TTTTTTTTATTGTTTTGATTGCTA-TTTTTGTGTTATTTTTGCTGTTA
1 TTTTTTTTATTGTTTTGATTGCTATTTTTTGTGCTATTTTTGCAGTTA
* * *
1070 TTTTTATTGTTGTTTTTATTGCTATTTTTTGT
1 TTTTTTTTATTGTTTTGATTGCTATTTTTTGT
1102 TGTTTTTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
45 20 0.30
46 14 0.21
47 26 0.39
48 7 0.10
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (48 bp):
TTTTTTTTATTGTTTTGATTGCTATTTTTTGTGCTATTTTTGCAGTTA
Found at i:1131 original size:12 final size:12
Alignment explanation
Indices: 1035--1161 Score: 84
Period size: 12 Copynumber: 10.8 Consensus size: 12
1025 TTTTTTATTG
*
1035 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
1048 TTTTG-TGTTAT
1 TTTTGTTGTTAT
*
1059 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
1071 TTTTATTGTTGT
1 TTTTGTTGTTAT
* *
1083 TTTTATTGCTA-
1 TTTTGTTGTTAT
*
1094 TTTT-TTGTTGT
1 TTTTGTTGTTAT
** *
1105 TTTTAATGTT-G
1 TTTTGTTGTTAT
1116 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
1128 TTTTGCTGCTT-T
1 TTTTGTTG-TTAT
* *
1140 TTTGGTTGCTAT
1 TTTTGTTGTTAT
1152 TTTTGTTGTT
1 TTTTGTTGTT
1162 TGGATAATGT
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
10 4 0.04
11 27 0.30
12 51 0.57
13 7 0.08
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:1142 original size:34 final size:36
Alignment explanation
Indices: 1047--1135 Score: 114
Period size: 34 Copynumber: 2.6 Consensus size: 36
1037 TTGATTGCTA
*
1047 TTTTTG-TGTTATTTTTGCTGTTATTTTTATTGTTG
1 TTTTTGTTGTTATTTTTGCTGTTATTTTTAATGTTG
* * *
1082 TTTTTATTGCTATTTTT--TGTTGTTTTTAATGTTG
1 TTTTTGTTGTTATTTTTGCTGTTATTTTTAATGTTG
1116 -TTTTGTTGTTATTTTTGCTG
1 TTTTTGTTGTTATTTTTGCTG
1136 CTTTTTTGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
33 14 0.31
34 15 0.33
35 7 0.16
36 9 0.20
ACGTcount: A:0.09, C:0.03, G:0.17, T:0.71
Consensus pattern (36 bp):
TTTTTGTTGTTATTTTTGCTGTTATTTTTAATGTTG
Found at i:1213 original size:21 final size:21
Alignment explanation
Indices: 1171--1213 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1161 TTGGATAATG
* * *
1171 TTTTTACTATTGTTTCACTAT
1 TTTTTAATATTATTTCAATAT
*
1192 TTTTTAATATTATTTGAATAT
1 TTTTTAATATTATTTCAATAT
1213 T
1 T
1214 GTAGAACTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTTAATATTATTTCAATAT
Found at i:3158 original size:20 final size:20
Alignment explanation
Indices: 3133--3202 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
3123 TTTACATTGT
*
3133 TGTTTTGATGCTTTTTTTAC
1 TGTTTTGATGTTTTTTTTAC
* * *
3153 TGTTTTGGTTTTTTTTTTGC
1 TGTTTTGATGTTTTTTTTAC
*
3173 TGTTTTTGA-GTTATTTTTTAT
1 TG-TTTTGATGTT-TTTTTTAC
3194 TGTTTTGAT
1 TGTTTTGAT
3203 TGCTATTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (20 bp):
TGTTTTGATGTTTTTTTTAC
Found at i:3223 original size:12 final size:12
Alignment explanation
Indices: 3214--3247 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3204 GCTATTTTCG
3214 TGTTATTTTTGC
1 TGTTATTTTTGC
*
3226 TGTTATTTTTGT
1 TGTTATTTTTGC
*
3238 TGTTGTTTTT
1 TGTTATTTTT
3248 ATTGCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.03, G:0.18, T:0.74
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:3241 original size:24 final size:24
Alignment explanation
Indices: 3203--3265 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
3193 TTGTTTTGAT
* *
3203 TGCTATTTTCG-TGTTATTTTTGC
1 TGCTATTTTTGTTGTTATTTTTAC
* * *
3226 TGTTATTTTTGTTGTTGTTTTTAT
1 TGCTATTTTTGTTGTTATTTTTAC
3250 TGCTATTTTTGTTGTT
1 TGCTATTTTTGTTGTT
3266 TTTAATGTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.68
Consensus pattern (24 bp):
TGCTATTTTTGTTGTTATTTTTAC
Found at i:3336 original size:56 final size:57
Alignment explanation
Indices: 3214--3338 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 57
3204 GCTATTTTCG
* * * * *
3214 TGTTATTTTTGCTGTTATTTTTGTTGTTGTTTTTATTGCTATTTTTGTTGTTTTTAA
1 TGTTATTTTTACTGTTATTTTTGTTGCTGTTTTGATAGCTATTTTTGTTGTTTTGAA
* * *
3271 TGTT-GTTTTACTGTTATTTTTGTTGCTGTTTTGGTAGCTATTTTTGTTG-TTTGGA
1 TGTTATTTTTACTGTTATTTTTGTTGCTGTTTTGATAGCTATTTTTGTTGTTTTGAA
3326 TGTTATTTTTACT
1 TGTTATTTTTACT
3339 ATTGTTTCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
55 8 0.14
56 46 0.79
57 4 0.07
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.66
Consensus pattern (57 bp):
TGTTATTTTTACTGTTATTTTTGTTGCTGTTTTGATAGCTATTTTTGTTGTTTTGAA
Done.