Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001481.1 Kokia drynarioides strain JFW-HI SEQ_113012, 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: 4619
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Found at i:1025 original size:42 final size:41
Alignment explanation
Indices: 966--1118 Score: 164
Period size: 42 Copynumber: 3.6 Consensus size: 41
956 ATTATATTGT
*
966 TGTTTTGGTGTTGTTTTTATTGTTTTGGTTTCTATTTTTTGC
1 TGTTTTGGTGTT-TTTTTACTGTTTTGGTTTCTATTTTTTGC
* * * * *
1008 TGTTTTGGTGATTTTTTTATTGTTTTAGTTACTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTACTGTTTTGGTTTCTATTTTTTGC
* * *
1050 TGTTTTGATGTTTTTTTAACTGTTTTGGTTAT-TGTTTTTTGT
1 TGTTTTGGTGTTTTTTT-ACTGTTTTGGTT-TCTATTTTTTGC
*
1092 TGTTTTGGTTTTTTTTTTACTGTTTTG
1 TGTTTTGG-TGTTTTTTTACTGTTTTG
1119 ATGTTGTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
41 7 0.07
42 77 0.82
43 10 0.11
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (41 bp):
TGTTTTGGTGTTTTTTTACTGTTTTGGTTTCTATTTTTTGC
Found at i:1066 original size:62 final size:62
Alignment explanation
Indices: 1000--1135 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 62
990 TTGGTTTCTA
1000 TTTTTTGCTGTTTTGGTGA-T-TTTTTTATTGTTTTAGTTACTTTTTTTTACTGTTTTGATGTT
1 TTTTTTGCTGTTTTGGTGATTGTTTTTTATTGTTTTAGTT--TTTTTTTTACTGTTTTGATGTT
** * * *
1062 TTTTTAACTGTTTTGGTTATTGTTTTTTGTTGTTTTGGTTTTTTTTTTACTGTTTTGATGTT
1 TTTTTTGCTGTTTTGGTGATTGTTTTTTATTGTTTTAGTTTTTTTTTTACTGTTTTGATGTT
*
1124 GTTTTTGCTGTT
1 TTTTTTGCTGTT
1136 ATTTTTTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 47 0.73
63 1 0.02
64 16 0.25
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (62 bp):
TTTTTTGCTGTTTTGGTGATTGTTTTTTATTGTTTTAGTTTTTTTTTTACTGTTTTGATGTT
Found at i:1134 original size:20 final size:20
Alignment explanation
Indices: 966--1135 Score: 83
Period size: 20 Copynumber: 8.2 Consensus size: 20
956 ATTATATTGT
* *
966 TGTTTTGGTGTTGTTTTTAT
1 TGTTTTGATGTTGTTTTTAC
* * * *
986 TGTTTTGGTTTCTATTTTTTGC
1 TGTTTTGATGT-T-GTTTTTAC
* *
1008 TGTTTTGGTGATT-TTTTTAT
1 TGTTTTGATG-TTGTTTTTAC
* * *
1028 TGTTTTAGTTACTTTTTTTTAC
1 TGTTTT-GAT-GTTGTTTTTAC
1050 TGTTTTGATGTT-TTTTTAAC
1 TGTTTTGATGTTGTTTTT-AC
* * **
1070 TGTTTTGGTTATTGTTTTTTGT
1 TGTTTT-GATGTTG-TTTTTAC
* * *
1092 TGTTTTGGTTTTTTTTTTAC
1 TGTTTTGATGTTGTTTTTAC
*
1112 TGTTTTGATGTTGTTTTTGC
1 TGTTTTGATGTTGTTTTTAC
1132 TGTT
1 TGTT
1136 ATTTTTTTTG
Statistics
Matches: 115, Mismatches: 25, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
19 5 0.04
20 56 0.49
21 15 0.13
22 33 0.29
23 6 0.05
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (20 bp):
TGTTTTGATGTTGTTTTTAC
Found at i:1147 original size:12 final size:12
Alignment explanation
Indices: 1114--1170 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1104 TTTTTTACTG
* *
1114 TTTTGATGTTGT
1 TTTTGTTGTTAT
*
1126 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
1138 TTTTTTTGTT-T
1 TTTTGTTGTTAT
* *
1149 TTTGGTTGCTAT
1 TTTTGTTGTTAT
1161 TTTTGTTGTT
1 TTTTGTTGTT
1171 TGTGTTGTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:1150 original size:42 final size:42
Alignment explanation
Indices: 1060--1151 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 42
1050 TGTTTTGATG
* *
1060 TTTTTTTAACTGTTTTGGTTATTGTTTTTTGTTGTTTTGGTTT
1 TTTTTTTAACTGTTTTGGATATTGTTTTTTGTTATTTT-GTTT
*
1103 TTTTTTT-ACTGTTTT-GATGTTGTTTTTGCTGTTATTTT-TTT
1 TTTTTTTAACTGTTTTGGATATTGTTTTT--TGTTATTTTGTTT
1144 TGTTTTTT
1 T-TTTTTT
1152 GGTTGCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 14 0.33
42 14 0.33
43 15 0.35
ACGTcount: A:0.07, C:0.03, G:0.16, T:0.74
Consensus pattern (42 bp):
TTTTTTTAACTGTTTTGGATATTGTTTTTTGTTATTTTGTTT
Found at i:1150 original size:84 final size:84
Alignment explanation
Indices: 966--1135 Score: 195
Period size: 84 Copynumber: 2.0 Consensus size: 84
956 ATTATATTGT
* * *
966 TGTTTTGGTGTTGTTTTTATTGTTTTGGTTTCTATTTTTTGCTGTTTTGGTGATTTTTTTATTGT
1 TGTTTTGATGTTGTTTTTACTGTTTTGGTTTCTATTTTTTGCTGTTTTGGTGATTTTTTTACTGT
* *
1031 TTTAGTTACTTTTTTTTAC
66 TTTAGATACTTGTTTTTAC
* * **
1050 TGTTTTGATGTT-TTTTTAACTGTTTTGGTTAT-TGTTTTTTGTTGTTTTGGTTTTTTTTTTACT
1 TGTTTTGATGTTGTTTTT-ACTGTTTTGGTT-TCTATTTTTTGCTGTTTTGGTGATTTTTTTACT
* *
1113 GTTTT-GAT-GTTGTTTTTGC
64 GTTTTAGATACTTGTTTTTAC
1132 TGTT
1 TGTT
1136 ATTTTTTTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 12 0.16
83 7 0.10
84 53 0.73
85 1 0.01
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (84 bp):
TGTTTTGATGTTGTTTTTACTGTTTTGGTTTCTATTTTTTGCTGTTTTGGTGATTTTTTTACTGT
TTTAGATACTTGTTTTTAC
Found at i:1151 original size:23 final size:23
Alignment explanation
Indices: 1120--1171 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1110 ACTGTTTTGA
*
1120 TGTTG-TTTTT-GCTGTTATTTT
1 TGTTGTTTTTTGGCTGCTATTTT
* *
1141 TTTTGTTTTTTGGTTGCTATTTT
1 TGTTGTTTTTTGGCTGCTATTTT
1164 TGTTGTTT
1 TGTTGTTT
1172 GTGTTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
23 16 0.64
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.73
Consensus pattern (23 bp):
TGTTGTTTTTTGGCTGCTATTTT
Found at i:1177 original size:53 final size:53
Alignment explanation
Indices: 1115--1236 Score: 131
Period size: 52 Copynumber: 2.3 Consensus size: 53
1105 TTTTTACTGT
*
1115 TTTGATGTTGTTTTTGCTGTTATTTTTTTTGTTTTTTGGTTGCTATTTTTGTTG
1 TTTGATGTTG-TTTTGCTGTTATTTTTTTTGTTTTTTGGTTGTTATTTTTGTTG
* * * * *
1169 TTTG-TGTTGTTTTGCTATTACTTTTTCTGCTATTTTGGTAGTTA-TTTTGATTG
1 TTTGATGTTGTTTTGCTGTTATTTTTTTTG-TTTTTTGGTTGTTATTTTTG-TTG
*
1222 TTTGGATGTTATTTT
1 TTT-GATGTTGTTTT
1237 TATGTGTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
52 22 0.39
53 22 0.39
54 5 0.09
55 8 0.14
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (53 bp):
TTTGATGTTGTTTTGCTGTTATTTTTTTTGTTTTTTGGTTGTTATTTTTGTTG
Done.