Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014002.1 Kokia drynarioides strain JFW-HI SEQ_129033, 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: 14753
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Found at i:2031 original size:205 final size:205
Alignment explanation
Indices: 1716--2285 Score: 852
Period size: 205 Copynumber: 2.8 Consensus size: 205
1706 GGTTTTAGTT
* * * *
1716 CACTTCTCTGTATTTCATCAGGAAGCTAACCGTTTTATTACTTCGACTTGCTTCTCAGTATCTCA
1 CACTTCTCAGTATTTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCA
* * * *
1781 TCAGGAAGCTGGGGTTCGAGGATTTGCTCACATCGAGCATGGGTTTAATTTGGTCTTCTTCTCAG
65 TCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
* *
1846 TATCTCATCAGGAAGATGACCGCGTCGTTTATTTTAATTCGCTTCTCTGTATCTCATCAGGAAGA
130 TATCTCATCAGGAAGATGACCGCGTCGTTTATTTAAATTCGCTTCTCTGTATCTCATCAAGAAGA
1911 CAAATTTGGTC
195 CAAATTTGGTC
* *
1922 CACTTCTCAGTATTTTATCAGGAAACTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
1 CACTTCTCAGTATTTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
* * * *
1987 TAGGAAGCTAGAGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGTCTTCTTCTCAAT
66 CAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
* * * * *
2052 ATCTCATCAGAAATATGACCGCGTCATTTGTTTAAATTCGCTTCTTTGTATCTCATCAAGAAGAC
131 ATCTCATCAGGAAGATGACCGCGTCGTTTATTTAAATTCGCTTCTCTGTATCTCATCAAGAAGAC
*
2117 GAATTTGGTC
196 AAATTTGGTC
* * * * *
2127 CACTTCTCAGTATCTCGTCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTTTTAGTGTCTCAT
1 CACTTCTCAGTATTTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
* *
2192 CAGGAAGCTAGGGTTCGAATATTTGCTCACATCGAACGTGGGTTTGATTTGGTCTTCTTCTCAGT
66 CAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
* *
2257 ATCTTATCAGGAAGATGACTGCGTCGTTT
131 ATCTCATCAGGAAGATGACCGCGTCGTTT
2286 GTGGATAATC
Statistics
Matches: 324, Mismatches: 40, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
205 296 0.91
206 28 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (205 bp):
CACTTCTCAGTATTTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
CAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
ATCTCATCAGGAAGATGACCGCGTCGTTTATTTAAATTCGCTTCTCTGTATCTCATCAAGAAGAC
AAATTTGGTC
Found at i:13807 original size:96 final size:96
Alignment explanation
Indices: 13618--13809 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
13608 ATTTTGGGAA
** *
13618 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
**
13683 AAATCGAAGATAAAGAAACATTGTCTCGATT
66 AAATCGAAGATAAAGAAACATTACCTCGATT
* *
13714 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* * *
13778 GAAACTTGAA-ATAAA-AGAATATTACCTCGATT
65 -AAAATCGAAGATAAAGA-AACATTACCTCGATT
13810 TTAAAGTCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 2 0.02
96 74 0.89
97 7 0.08
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTACCTCGATT
Found at i:14224 original size:29 final size:30
Alignment explanation
Indices: 14174--14433 Score: 293
Period size: 29 Copynumber: 8.8 Consensus size: 30
14164 TTTGGACACC
*
14174 CGAGGG-AAAAATAGTAATTTTTGGAAGTTT
1 CGAGGGTAAAAAT-GGAATTTTTGGAAGTTT
14204 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
* * *
14234 TG-GGGTTAAAATGGGA-TTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
*
14262 TGAGGGTAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
* *
14292 TG-GGGTCAAAATGGAATTTTTGGAAG-TT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
* *
14320 CGAGGGTGAAAAGGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTTT
*
14350 -TAGGGTCAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGTTT
* * *
14380 -AAGGGTCAAAATTAGAATTTTTGGAAG-TT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGTTT
* * *
14409 CGGGGGTGAAAATGGAAATTTTGGA
1 CGAGGGTAAAAATGGAATTTTTGGA
14434 CAGATTAGGG
Statistics
Matches: 201, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
28 17 0.08
29 90 0.45
30 88 0.44
31 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (30 bp):
CGAGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:14253 original size:117 final size:115
Alignment explanation
Indices: 14093--14433 Score: 318
Period size: 117 Copynumber: 2.9 Consensus size: 115
14083 ATTTTGTGTT
* * * *
14093 TAAAAATGGAATTTTTAGACA-TTTAAGGG-TAAAA-GGGTAATTTT-GAGAGTTTTAAGGTTGA
1 TAAAAATGGAATTTTTGGA-AGTTTTAGGGTTAAAATGGG--ATTTTGGA-AGTTTTAAGGGTAA
* *
14154 AAATGGAGTTTTTGGACA-CCCGAGGG-AAAAATAGTAATTTTTGGAAGTTTCGAGGG
62 AAATGGAATTTTTGGA-AGCCCG-GGGTAAAAAT-GGAATTTTTGGAAG-TTCGAGGG
* *
14210 TAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTGGAAGTTTTGAGGGTAAAAAT
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAATGGGATTTTGGAAGTTTTAAGGGTAAAAAT
*** *
14275 GGAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGG
66 GGAATTTTTGGAAG-CCCGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGG
* * * *
14326 TGAAAAGGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAG-TTTAAGGGTCAAA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGT-TAAAATGGGA-TTTTGGAAGTTTTAAGGGT-AAA
* * * * * *
14390 ATTAGAATTTTTGGAAGTTCGGGGGTGAAAATGGAAATTTTGGA
63 AATGGAATTTTTGGAAG-CCCGGGGTAAAAATGGAATTTTTGGA
14434 CAGATTAGGG
Statistics
Matches: 190, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
116 37 0.19
117 87 0.46
118 63 0.33
119 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (115 bp):
TAAAAATGGAATTTTTGGAAGTTTTAGGGTTAAAATGGGATTTTGGAAGTTTTAAGGGTAAAAAT
GGAATTTTTGGAAGCCCGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGG
Done.