Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008096.1 Kokia drynarioides strain JFW-HI SEQ_122754, 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: 3553
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Found at i:112 original size:11 final size:11
Alignment explanation
Indices: 98--159 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
88 AAAGAGCAAA
*
98 AGAAGAATAAG
1 AGAAGAAGAAG
* *
109 AGAACAA-ATG
1 AGAAGAAGAAG
119 GAGAAGAAGAAG
1 -AGAAGAAGAAG
*
131 AAAAGAAGAAG
1 AGAAGAAGAAG
*
142 AGGAGAAGAAG
1 AGAAGAAGAAG
153 AAGAAGA
1 -AGAAGA
160 GAAAATGGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
10 2 0.05
11 31 0.77
12 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.03
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:125 original size:25 final size:25
Alignment explanation
Indices: 81--162 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
71 ACTGGGTAGT
* *
81 AGAAGA-AA-AAGAGCAAAAGAAGA
1 AGAAGAGAACAAGAGGAGAAGAAGA
*
104 ATAAGAGAACAA-ATGGAGAAGAAGA
1 AGAAGAGAACAAGA-GGAGAAGAAGA
* *
129 AGAAAAGAAGAAGAGGAGAAGAAGA
1 AGAAGAGAACAAGAGGAGAAGAAGA
154 AGAAGAGAA
1 AGAAGAGAA
163 AATGGAAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 5 0.10
24 3 0.06
25 39 0.81
26 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.30, T:0.02
Consensus pattern (25 bp):
AGAAGAGAACAAGAGGAGAAGAAGA
Found at i:128 original size:3 final size:3
Alignment explanation
Indices: 120--159 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
110 GAACAAATGG
*
120 AGA AGA AGA AGA A-A AGA AGA AG- AGG AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
160 GAAAATGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:140 original size:17 final size:17
Alignment explanation
Indices: 81--159 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
71 ACTGGGTAGT
* *
81 AGAAGAAAAAGAGCAAA
1 AGAAGAAGAAGAGAAAA
*
98 AGAAGAATAAGAGAACAA
1 AGAAGAAGAAGAGAA-AA
*
116 ATGGAGAAGAAGA-AGAAA
1 A-GAAGAAGAAGAGA-AAA
* *
134 AGAAGAAGAGGAGAAGA
1 AGAAGAAGAAGAGAAAA
151 AGAAGAAGA
1 AGAAGAAGA
160 GAAAATGGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 33 0.65
18 8 0.16
19 10 0.20
ACGTcount: A:0.65, C:0.03, G:0.30, T:0.03
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAAA
Found at i:161 original size:14 final size:14
Alignment explanation
Indices: 120--162 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
110 GAACAAATGG
*
120 AGAAGAAGAAGAAA
1 AGAAGAAGAAGAGA
*
134 AGAAGAAGAGGAGA
1 AGAAGAAGAAGAGA
148 AGAAGAAGAAGAGA
1 AGAAGAAGAAGAGA
162 A
1 A
163 AATGGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAGA
Found at i:162 original size:11 final size:11
Alignment explanation
Indices: 119--159 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
109 AGAACAAATG
119 GAGAAGAAGAA
1 GAGAAGAAGAA
*
130 GAAAAGAAGAA
1 GAGAAGAAGAA
*
141 GAGGAGAAGAA
1 GAGAAGAAGAA
152 GAAGAAGA
1 G-AGAAGA
160 GAAAATGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (11 bp):
GAGAAGAAGAA
Found at i:2801 original size:29 final size:29
Alignment explanation
Indices: 2750--2805 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2740 TAACTATTTG
* *
2750 AACTGATTAATTACACTACAAAAATATTA
1 AACTAATTAATAACACTACAAAAATATTA
* *
2779 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACACTACAAAAATAT
2806 AGAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (29 bp):
AACTAATTAATAACACTACAAAAATATTA
Found at i:3422 original size:18 final size:19
Alignment explanation
Indices: 3399--3457 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 19
3389 GGCGTTTAAT
3399 ATTTATATTTT-TTTGTTA
1 ATTTATATTTTATTTGTTA
* *
3417 ATTTATTTTTTATTTTTTA
1 ATTTATATTTTATTTGTTA
* *
3436 A-TTAAATTTTATCT-TTA
1 ATTTATATTTTATTTGTTA
3453 ATTTA
1 ATTTA
3458 AAAAAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.12
18 23 0.68
19 7 0.21
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTATATTTTATTTGTTA
Done.