Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004817.1 Kokia drynarioides strain JFW-HI SEQ_118451, 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: 15617
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:520 original size:100 final size:100
Alignment explanation
Indices: 347--545 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
337 CCTTTCCATA
347 CAAATGAATTCTAGAATACATAATCTGATTAGGTATTTCCACATTGGCATAACAGTGAATCACTA
1 CAAATGAATTCTAGAATACATAATCTGATTAGGTATTTCCACATTGGCATAACAGTGAATCACTA
412 GTCAAAATAGAATACAAATCAAACTAAAATATTGC
66 GTCAAAATAGAATACAAATCAAACTAAAATATTGC
* *
447 CAAATGAATTCTAGAATACATAATCTGATTAGGTGTTTCCACATTGGCATAAGAGTGAATCACTA
1 CAAATGAATTCTAGAATACATAATCTGATTAGGTATTTCCACATTGGCATAACAGTGAATCACTA
512 GTCAAAATAGAATACAAATCAAACTAAAATATTG
66 GTCAAAATAGAATACAAATCAAACTAAAATATTG
546 TCATATTTTT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (100 bp):
CAAATGAATTCTAGAATACATAATCTGATTAGGTATTTCCACATTGGCATAACAGTGAATCACTA
GTCAAAATAGAATACAAATCAAACTAAAATATTGC
Found at i:2051 original size:20 final size:19
Alignment explanation
Indices: 2028--2177 Score: 54
Period size: 21 Copynumber: 7.3 Consensus size: 19
2018 TTGCTTTTTT
2028 TTTTTGCTGTTTTTATGTTG
1 TTTTTGCTGTTTTT-TGTTG
*
2048 TTTTTTACTGTTTTGTTGCTT-
1 -TTTTTGCTGTTTT-TTG-TTG
* *
2069 CTTTTACTGTTTTGGTTGTTG
1 TTTTTGCTGTTTT--TTGTTG
* * *
2090 TTTTCGTGTTGTTTTTGCTTTTC
1 TTTT--TGCTGTTTTT--TGTTG
* * *
2113 TTTTTACTGTTTTTTTTTCTA
1 TTTTTGCTG-TTTTTTGT-TG
*
2134 TTTTTGTTGTTTTTAATGTTG
1 TTTTTGCTGTTTTT--TGTTG
*
2155 -TTTTGCTGTTATTT-TTG
1 TTTTTGCTGTTTTTTGTTG
2172 TTTTTG
1 TTTTTG
2178 TTTTGGTTGT
Statistics
Matches: 100, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
17 3 0.03
18 6 0.06
20 33 0.33
21 34 0.34
22 10 0.10
23 14 0.14
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (19 bp):
TTTTTGCTGTTTTTTGTTG
Found at i:2169 original size:23 final size:24
Alignment explanation
Indices: 2138--2194 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
2128 TTTCTATTTT
*
2138 TGTTGTTTTTAATGTTGTTTT-GC
1 TGTTATTTTTAATGTTGTTTTGGC
** * *
2161 TGTTATTTTTGTTTTTGTTTTGGT
1 TGTTATTTTTAATGTTGTTTTGGC
2185 TGTTATTTTT
1 TGTTATTTTT
2195 GTTGTTTGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.72
Consensus pattern (24 bp):
TGTTATTTTTAATGTTGTTTTGGC
Found at i:2170 original size:12 final size:12
Alignment explanation
Indices: 2155--2200 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2145 TTTAATGTTG
*
2155 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
2167 TTTTGTTTTTGT
1 TTTTGTTGTTAT
*
2179 TTTGGTTGTTAT
1 TTTTGTTGTTAT
2191 TTTTGTTGTT
1 TTTTGTTGTT
2201 TGGATGTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.04, C:0.02, G:0.20, T:0.74
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:2188 original size:24 final size:24
Alignment explanation
Indices: 2152--2202 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
2142 GTTTTTAATG
2152 TTGTTTTGCTGTTATTTTTGTT-T
1 TTGTTTTGCTGTTATTTTTGTTGT
*
2175 TTGTTTTGGTTGTTATTTTTGTTGT
1 TTGTTTT-GCTGTTATTTTTGTTGT
2200 TTG
1 TTG
2203 GATGTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.28
24 14 0.56
25 4 0.16
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.73
Consensus pattern (24 bp):
TTGTTTTGCTGTTATTTTTGTTGT
Found at i:2208 original size:20 final size:20
Alignment explanation
Indices: 2150--2212 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2140 TTGTTTTTAA
* *
2150 TGTTGTTTTGCTGTTATTTT
1 TGTTGTTTGGATGTTATTTT
*
2170 TGTTTTTGTTTTGGTTGTTATTTT
1 TG---TTG-TTTGGATGTTATTTT
2194 TGTTGTTTGGATGTTATTT
1 TGTTGTTTGGATGTTATTT
2213 GTATGCGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 15 0.42
21 3 0.08
23 3 0.08
24 15 0.42
ACGTcount: A:0.06, C:0.02, G:0.22, T:0.70
Consensus pattern (20 bp):
TGTTGTTTGGATGTTATTTT
Found at i:3859 original size:18 final size:19
Alignment explanation
Indices: 3823--3864 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3813 TAGTATTGGC
3823 CATTGTCAAGGCAAAATAT
1 CATTGTCAAGGCAAAATAT
*
3842 CATTGTCAATGC-AAATAT
1 CATTGTCAAGGCAAAATAT
3860 C-TTGT
1 CATTGT
3865 GTTCTTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (19 bp):
CATTGTCAAGGCAAAATAT
Found at i:8279 original size:24 final size:24
Alignment explanation
Indices: 8247--8301 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
8237 AATTATCAGG
** *
8247 ATGGTTAGCTGTTACGAGCCCAGA
1 ATGGTTAGCCCTTACGAGCCCAAA
8271 ATGGTTAGCCCTTACGAGCCCAAA
1 ATGGTTAGCCCTTACGAGCCCAAA
8295 ATGGTTA
1 ATGGTTA
8302 ACCAGTATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (24 bp):
ATGGTTAGCCCTTACGAGCCCAAA
Found at i:11020 original size:15 final size:16
Alignment explanation
Indices: 10996--11028 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10986 AGATTTTATC
*
10996 TTTATTTTTTAA-TAT
1 TTTATCTTTTAACTAT
11011 TTTATCTTTTAACTAT
1 TTTATCTTTTAACTAT
11027 TT
1 TT
11029 AAGGATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATCTTTTAACTAT
Done.