Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004028.1 Kokia drynarioides strain JFW-HI SEQ_117155, 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: 11216
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:32 original size:17 final size:16
Alignment explanation
Indices: 10--98 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 16
1 TTGGACATT
10 ATTTAAATGAATTTTAA
1 ATTTAAAT-AATTTTAA
* **
27 ATTTAAATTTATAATAA
1 ATTTAAA-TAATTTTAA
*
44 ATTTAAATAAATTTAA
1 ATTTAAATAATTTTAA
**
60 ATTTAAAATAAACTTAA
1 ATTT-AAATAATTTTAA
* *
77 TTTTAAAAATAAATTTAA
1 ATTT--AAATAATTTTAA
95 ATTT
1 ATTT
99 GTTGGGCCCA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
16 9 0.16
17 33 0.57
18 16 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATTTAAATAATTTTAA
Found at i:33 original size:6 final size:6
Alignment explanation
Indices: 22--98 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
12 TTAAATGAAT
22 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * **
67 -ATAAA CTTAAT TTTAAA AATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
99 GTTGGGCCCA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
4 6 0.11
5 6 0.11
6 42 0.75
7 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:54 original size:10 final size:10
Alignment explanation
Indices: 10--61 Score: 59
Period size: 11 Copynumber: 4.8 Consensus size: 10
1 TTGGACATT
10 ATTTAAATGAA
1 ATTTAAAT-AA
*
21 TTTTAAATTTAA
1 ATTTAAA--TAA
33 ATTTATAATAA
1 ATTTA-AATAA
44 ATTTAAATAA
1 ATTTAAATAA
54 ATTTAAAT
1 ATTTAAAT
62 TTAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 13 0.36
11 14 0.39
12 6 0.17
13 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:54 original size:27 final size:27
Alignment explanation
Indices: 24--76 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
14 AAATGAATTT
* *
24 TAAATTTAAATTTATAATAAATTTAAA
1 TAAATTTAAATTTAAAATAAACTTAAA
51 TAAATTTAAATTTAAAATAAACTTAA
1 TAAATTTAAATTTAAAATAAACTTAA
77 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTTAAAATAAACTTAAA
Found at i:4058 original size:17 final size:16
Alignment explanation
Indices: 4036--4090 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 16
4026 ACCCATTTTA
4036 AAATTTATTTTAAGATT
1 AAATTTATTTTAA-ATT
*
4053 AAATTTATTTTGAATTT
1 AAATTTATTTT-AAATT
4070 AAATTTATTTTAAATTT
1 AAATTTATTTTAAA-TT
4087 AAAT
1 AAAT
4091 GTTTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 2 0.06
17 30 0.88
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
AAATTTATTTTAAATT
Found at i:4076 original size:6 final size:6
Alignment explanation
Indices: 4051--4129 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
4041 TATTTTAAGA
* * *
4051 TTAAAT TT-ATT TTGAAT TTAAAT TT-ATT TTAAAT TTAAATGTT TTAAATT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA---T TTAAA-T
* *
4101 TTAAAT TTAGAT TTATAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
4130 ACTTATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 8 0.13
6 39 0.65
7 7 0.12
9 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:4097 original size:15 final size:16
Alignment explanation
Indices: 4077--4106 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4067 TTTAAATTTA
4077 TTTTAAA-TTTAAATG
1 TTTTAAATTTTAAATG
4092 TTTTAAATTTTAAAT
1 TTTTAAATTTTAAAT
4107 TTAGATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTTAAATTTTAAATG
Found at i:6086 original size:59 final size:59
Alignment explanation
Indices: 5981--6156 Score: 201
Period size: 59 Copynumber: 2.9 Consensus size: 59
5971 GCCCTAAAGG
* * * *
5981 TCCCTAAACTATCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTAA
1 TCCCAAAACT-TCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTCAA
** *
6041 TCCCAAAACTTCCAAAAATTCCATTTTTACCCTTGAACTTTCAAAAATTCCATTTTCAA
1 TCCCAAAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTCAA
* * ** * *
6100 CCCCGAAACTTTTAAAAAATCTATTTTTGACCCTAAAACTTCCAAAAA-TCCAATTTT
1 TCCCAAAACTTCCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAAAATTCC-ATTTT
6157 TACCCTCGAA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 69 0.70
60 30 0.30
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (59 bp):
TCCCAAAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTCAA
Found at i:6181 original size:29 final size:29
Alignment explanation
Indices: 5982--6177 Score: 193
Period size: 30 Copynumber: 6.7 Consensus size: 29
5972 CCCTAAAGGT
5982 CCCT-AAACTATCCAAAAATTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
*
6011 CCCTCAAACTTCCAAAAATTTCATTTTTAA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
*
6041 TCCC-AAAACTTCCAAAAATTCCATTTTTA
1 -CCCTCAAACTTCCAAAAATTCCATTTTTA
** * *
6070 CCCTTGAACTTTCAAAAATTCCATTTTCAA
1 CCCTCAAACTTCCAAAAATTCCATTTT-TA
** * *
6100 CCC-CGAAACTTTTAAAAAATCTATTTTTGA
1 CCCTC-AAACTTCCAAAAATTCCATTTTT-A
*
6130 CCCTAAAACTTCCAAAAA-TCCAATTTTTA
1 CCCTCAAACTTCCAAAAATTCC-ATTTTTA
*
6159 CCCTCGAACTTCCAAAAAT
1 CCCTCAAACTTCCAAAAAT
6178 CCAAAAATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.02
29 61 0.44
30 71 0.51
31 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:6188 original size:29 final size:29
Alignment explanation
Indices: 6136--6191 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
6126 TTGACCCTAA
***
6136 AACTTCCAAAAATCCAATTTTTACCCTCG
1 AACTTCCAAAAATCCAAAAATTACCCTCG
6165 AACTTCCAAAAATCCAAAAATTACCCT
1 AACTTCCAAAAATCCAAAAATTACCCT
6192 AGATTGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.30, G:0.02, T:0.27
Consensus pattern (29 bp):
AACTTCCAAAAATCCAAAAATTACCCTCG
Found at i:11204 original size:21 final size:20
Alignment explanation
Indices: 11164--11206 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11154 AGAAATATAT
*
11164 AAAAATAAATAAATATTTTA
1 AAAAATAAATAAATAATTTA
11184 AAAAATATAAT-AATAAATTTA
1 AAAAATA-AATAAAT-AATTTA
11205 AA
1 AA
11207 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATAAATAAATAATTTA
Done.