Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014053.1 Kokia drynarioides strain JFW-HI SEQ_129084, 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: 69729
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 141 characters in sequence are not A, C, G, or T
Found at i:26306 original size:30 final size:30
Alignment explanation
Indices: 26272--26341 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
26262 CAAATTTTGG
26272 TTCATGTTCGTTTGTATATTTTTGAAGTTA
1 TTCATGTTCGTTTGTATATTTTTGAAGTTA
26302 TTCATGTTCGTTTGTATATTTTTGAAGTTA
1 TTCATGTTCGTTTGTATATTTTTGAAGTTA
26332 TTCATGTTCG
1 TTCATGTTCG
26342 GTTCGTGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.19, C:0.09, G:0.17, T:0.56
Consensus pattern (30 bp):
TTCATGTTCGTTTGTATATTTTTGAAGTTA
Found at i:26445 original size:23 final size:23
Alignment explanation
Indices: 26429--26534 Score: 160
Period size: 23 Copynumber: 4.6 Consensus size: 23
26419 TTAAAGTTCA
26429 CGAACATGTTCATTTAACATAAT
1 CGAACATGTTCATTTAACATAAT
26452 CGAACATGTTCATTTAACATAAT
1 CGAACATGTTCATTTAACATAAT
*
26475 CGAACATGTTCATTTAATATAAT
1 CGAACATGTTCATTTAACATAAT
*
26498 CGAACATGTTCA-TGAACATATAAT
1 CGAACATGTTCATTTAAC--ATAAT
*
26522 CGAATATGTTCAT
1 CGAACATGTTCAT
26535 GAACAATGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
22 3 0.04
23 57 0.75
24 16 0.21
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (23 bp):
CGAACATGTTCATTTAACATAAT
Found at i:26645 original size:12 final size:12
Alignment explanation
Indices: 26628--26662 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
26618 ATCATTACTA
*
26628 AATAAATGAGTC
1 AATAAACGAGTC
*
26640 AATAAACGAGCC
1 AATAAACGAGTC
26652 AATAAACGAGT
1 AATAAACGAGT
26663 TTGTTCATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:39357 original size:15 final size:15
Alignment explanation
Indices: 39337--39379 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39327 GGGTTCGTTT
39337 GTTTGACTGAAAATG
1 GTTTGACTGAAAATG
39352 GTTTGACTGAAAATG
1 GTTTGACTGAAAATG
* *
39367 ATTT-ATTGAAAAT
1 GTTTGACTGAAAAT
39380 AATTTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (15 bp):
GTTTGACTGAAAATG
Found at i:39378 original size:14 final size:14
Alignment explanation
Indices: 39342--39387 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
39332 CGTTTGTTTG
*
39342 ACTGAAAATGGTTT
1 ACTGAAAATGATTT
39356 GACTGAAAATGATTT
1 -ACTGAAAATGATTT
* *
39371 ATTGAAAATAATTT
1 ACTGAAAATGATTT
39385 ACT
1 ACT
39388 TTTCTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
ACTGAAAATGATTT
Found at i:52338 original size:19 final size:19
Alignment explanation
Indices: 52310--52354 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
52300 TATATAAACT
52310 AAAAATAAACCCAAA-TAA
1 AAAAATAAACCCAAATTAA
*
52328 AAAATATAAACCTAAATTAA
1 AAAA-ATAAACCCAAATTAA
52348 AAGAAAT
1 AA-AAAT
52355 CCAAAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 7 0.30
21 2 0.09
ACGTcount: A:0.69, C:0.11, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAATAAACCCAAATTAA
Found at i:54368 original size:14 final size:14
Alignment explanation
Indices: 54342--54371 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54332 TATATAAAAA
54342 TTATTGATTAAATT
1 TTATTGATTAAATT
*
54356 TTATTTATTAAATT
1 TTATTGATTAAATT
54370 TT
1 TT
54372 CTAAAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTATTGATTAAATT
Found at i:55224 original size:18 final size:17
Alignment explanation
Indices: 55201--55251 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
55191 TCCATATTTG
*
55201 ATTTTTTTTTTAAAATT
1 ATTTTTTTTTTAAAAAT
* *
55218 AATTTTTATTTAAAAAT
1 ATTTTTTTTTTAAAAAT
55235 A--TTTTTTTTAAAAAT
1 ATTTTTTTTTTAAAAAT
55250 AT
1 AT
55252 AATGCACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 14 0.48
17 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTTTTTTAAAAAT
Found at i:55229 original size:17 final size:15
Alignment explanation
Indices: 55204--55251 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
55194 ATATTTGATT
*
55204 TTTTTTTTAAAATTAA
1 TTTTTTTTAAAAAT-A
55220 TTTTTATTTAAAAATA
1 TTTTT-TTTAAAAATA
55236 TTTTTTTTAAAAATA
1 TTTTTTTTAAAAATA
55251 T
1 T
55252 AATGCACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.37
16 11 0.37
17 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTTTAAAAATA
Found at i:68903 original size:23 final size:23
Alignment explanation
Indices: 68830--68980 Score: 121
Period size: 23 Copynumber: 6.5 Consensus size: 23
68820 TATACGGAAC
* *
68830 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
68852 -AACAGAGAGCACATAAA-TGCT
1 AAACAGAGAGCACACAAAGTGCT
*
68873 GAGCAACAGAGAGCACACACAGTGCT
1 -A--AACAGAGAGCACACAAAGTGCT
* *
68899 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* * *
68922 GATCAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
68945 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
68970 AAACAGAGAGC
1 AAACAGAGAGC
68981 GCGCTAGTGT
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
21 14 0.14
22 3 0.03
23 47 0.46
24 1 0.01
25 32 0.31
26 5 0.05
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:68908 original size:25 final size:25
Alignment explanation
Indices: 68880--68979 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 25
68870 GCTGAGCAAC
68880 AGAGAGCACACACAGTGCTAAACAG
1 AGAGAGCACACACAGTGCTAAACAG
* * *
68905 AGAGTA-CACA-A-AGTACTGATC--
1 AGAG-AGCACACACAGTGCTAAACAG
* *
68926 AGAGAGCACACATAGTGCTAATA-AC
1 AGAGAGCACACACAGTGCTAA-ACAG
*
68951 AGAGAGCACGAGAC-GTGCTAAACAG
1 AGAGAGCAC-ACACAGTGCTAAACAG
68976 AGAG
1 AGAG
68980 CGCGCTAGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
20 1 0.02
21 8 0.14
22 1 0.02
23 13 0.23
24 2 0.04
25 29 0.51
26 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (25 bp):
AGAGAGCACACACAGTGCTAAACAG
Found at i:68952 original size:71 final size:69
Alignment explanation
Indices: 68830--68979 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 69
68820 TATACGGAAC
* *
68830 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAATGCTGAGCAACAGAGAGCAC-ACACA
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAATGCTGAACAACAGAGAGCACGACAC-
68894 GTGCT
65 GTGCT
* * * *
68899 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACACATAGTGCT-AATAACAGAGAGCACGAG
1 AAACAGAGAGTAC-CAAAGTACT-AACAGAGAGCACACA-AATGCTGAACAACAGAGAGCACGAC
68963 ACGTGCT
63 ACGTGCT
68970 AAACAGAGAG
1 AAACAGAGAG
68980 CGCGCTAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
69 13 0.18
70 9 0.13
71 41 0.58
72 8 0.11
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (69 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAATGCTGAACAACAGAGAGCACGACACG
TGCT
Done.