Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000660.1 Kokia drynarioides strain JFW-HI SEQ_111642, 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: 20218
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:5849 original size:36 final size:36
Alignment explanation
Indices: 5794--5864 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
5784 CTAACAAATT
* *
5794 AGAATAGGACTACATAGGAACCTGACTTGGAGCTAC
1 AGAATAAGACTACACAGGAACCTGACTTGGAGCTAC
* *
5830 AGAATAAGACTGCACAGGAACGTGACTTGGAGCTA
1 AGAATAAGACTACACAGGAACCTGACTTGGAGCTA
5865 TAAGAGCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (36 bp):
AGAATAAGACTACACAGGAACCTGACTTGGAGCTAC
Found at i:6662 original size:13 final size:13
Alignment explanation
Indices: 6644--6668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6634 CAACTTACTA
6644 ACTTCAACAACTG
1 ACTTCAACAACTG
6657 ACTTCAACAACT
1 ACTTCAACAACT
6669 AACATTAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
ACTTCAACAACTG
Found at i:6871 original size:21 final size:21
Alignment explanation
Indices: 6847--6889 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6837 TCATCAACAC
6847 ATCACCTTCAATCACACTGTA
1 ATCACCTTCAATCACACTGTA
6868 ATCACCTTCAATCACACTGTA
1 ATCACCTTCAATCACACTGTA
6889 A
1 A
6890 ATATATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (21 bp):
ATCACCTTCAATCACACTGTA
Found at i:8276 original size:115 final size:112
Alignment explanation
Indices: 8155--8377 Score: 340
Period size: 115 Copynumber: 2.0 Consensus size: 112
8145 AATCTCTAAT
*
8155 TTTTTTATTTTTCTTATAAGT-AATAACAATAAAATTTATAATTATTATATTATTAAATGAAATT
1 TTTTTTATTTGTCTTATAAGTAAATAAC-ATAAAATTTATAATTATTATATTATTAAATGAAATT
* *
8219 AAGAAATTAAACATTTTATTATCTTATCCTCCAAATATTTAAGATATTCTA
65 AAGAAAATAAACATTTTATCATCTTAT-CT--AAATATTTAAGATATTCTA
* * *
8270 TTTTTTATTTGTCTTGTAAGTAAATAACATTAATTTTATAATTATTATATTATTAAATGAAATTA
1 TTTTTTATTTGTCTTATAAGTAAATAACATAAAATTTATAATTATTATATTATTAAATGAAATTA
*
8335 AGAAAATAAACATTTTATCATCTTATCTAAGTATTTAAGATAT
66 AGAAAATAAACATTTTATCATCTTATCTAAATATTTAAGATAT
8378 CTTGAAATTT
Statistics
Matches: 100, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
112 14 0.14
114 2 0.02
115 78 0.78
116 6 0.06
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (112 bp):
TTTTTTATTTGTCTTATAAGTAAATAACATAAAATTTATAATTATTATATTATTAAATGAAATTA
AGAAAATAAACATTTTATCATCTTATCTAAATATTTAAGATATTCTA
Found at i:13450 original size:15 final size:16
Alignment explanation
Indices: 13416--13450 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13406 AAATAATCCC
*
13416 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
*
13432 AAAATTAAAAGTCTTA
1 AAAATTAAAAGTCTCA
13448 AAA
1 AAA
13451 CCACTGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:15222 original size:25 final size:24
Alignment explanation
Indices: 15165--15222 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 24
15155 AAACTTGATG
*
15165 AAAATTAATAAAATAAACGAATAAT
1 AAAATTAA-AAAATAAACGAATAAA
*
15190 AAAA-TAAATAATAAA-GAACTAACA
1 AAAATTAAAAAATAAACGAA-TAA-A
15214 AAAATTAAA
1 AAAATTAAA
15223 CTAGGGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 7 0.25
25 8 0.29
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (24 bp):
AAAATTAAAAAATAAACGAATAAA
Found at i:17927 original size:40 final size:39
Alignment explanation
Indices: 17822--17910 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 39
17812 TGTCATGACG
* *
17822 TAGACATGCTATGTCTCATGACGAAAGGGGTTTGTTGTAACA
1 TAGACATTCTATG-C-CA-GACGAAGGGGGTTTGTTGTAACA
*
17864 TAGATATTCTATGCCATGACGAAGGGGGTTTGTTGTAACA
1 TAGACATTCTATGCCA-GACGAAGGGGGTTTGTTGTAACA
17904 TAGACAT
1 TAGACAT
17911 GTTATGTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 31 0.72
41 1 0.02
42 11 0.26
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (39 bp):
TAGACATTCTATGCCAGACGAAGGGGGTTTGTTGTAACA
Found at i:19150 original size:273 final size:275
Alignment explanation
Indices: 18662--19203 Score: 926
Period size: 273 Copynumber: 2.0 Consensus size: 275
18652 CTTTACAAAG
* * *
18662 CTCTTTATGGGCTGAAACAAGCTCCTAGAGCCTGGTATAATATAATTGACTCCTATTTACTACAA
1 CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
* *
18727 GAAAGGTTTATAAGAAGTGAAAGTGAAGCTACATTGTATGTTAAGAAGCTTGAGGATGAGAAGAA
66 GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
* * *
18792 ACTTATTGTTTCATTGTATGTTGATGATCTGCTTGTTATGGGAGATAATGAAGTGTCTATAGAGC
131 ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
* *
18857 AGTTCAAACAAAGAATGAAAAATATGTTTGAAATGTCTGATTT-GATAATATGAAGTGTTTTCTT
196 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
18921 GGGATGGAAATTCAC
261 GGGATGGAAATTCAC
* * *
18936 CTCTTTATGAGTTGAAACAAGCTCCTAAAGCCTGTTATATTAGAATTGACTCCTATTTACTACAA
1 CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
19001 G-AAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
66 GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
*
19065 ACTCATTGTTTGATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
131 ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
* *
19130 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGGTGATATGAAGTGTTTTCTT
196 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
19195 GGGATGGAA
261 GGGATGGAA
19204 CCAATATGAT
Statistics
Matches: 251, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
273 163 0.65
274 88 0.35
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (275 bp):
CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
GGGATGGAAATTCAC
Done.