Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006903.1 Kokia drynarioides strain JFW-HI SEQ_121504, 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: 44340
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 GCACATTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8201 original size:14 final size:15
Alignment explanation
Indices: 8173--8202 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8163 ATTGACTTTT
8173 TAAATATTATTTTAA
1 TAAATATTATTTTAA
8188 TAAATATT-TTTTAA
1 TAAATATTATTTTAA
8202 T
1 T
8203 GAGATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAATATTATTTTAA
Found at i:12483 original size:28 final size:28
Alignment explanation
Indices: 12451--12506 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12441 ATTGAGTAAC
*
12451 AATAAAATGTAAAT-TT-AGATACTAAATT
1 AATAAAA-G-AAATCTTAAGATACCAAATT
12479 AATAAAAGAAATCTTAAGATACCAAATT
1 AATAAAAGAAATCTTAAGATACCAAATT
12507 CATTATTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 4 0.16
27 3 0.12
28 18 0.72
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAAAAGAAATCTTAAGATACCAAATT
Found at i:17711 original size:22 final size:22
Alignment explanation
Indices: 17681--17723 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17671 TGATTTAAAT
17681 TATAATTTTA-TATTAATATTTA
1 TATAATTTTATTATTAA-ATTTA
*
17703 TATATTTTTATTATTAAATTT
1 TATAATTTTATTATTAAATTT
17724 GATTTCGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATAATTTTATTATTAAATTTA
Found at i:18551 original size:14 final size:14
Alignment explanation
Indices: 18532--18558 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18522 AATAATTTTG
18532 AATTTAATAAAATA
1 AATTTAATAAAATA
18546 AATTTAATAAAAT
1 AATTTAATAAAAT
18559 TAATAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTAATAAAATA
Found at i:18604 original size:22 final size:21
Alignment explanation
Indices: 18578--18618 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18568 ACCCTAAATT
18578 TTAAAATCTAAAAAATAAAAAA
1 TTAAAATCT-AAAAATAAAAAA
* *
18600 TTAAATTCTTAAAATAAAA
1 TTAAAATCTAAAAATAAAA
18619 GTACAAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAAAATCTAAAAATAAAAAA
Found at i:20491 original size:19 final size:18
Alignment explanation
Indices: 20439--20491 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
20429 CATGGCCATC
20439 AAAT-TTAATAATTAGTAA
1 AAATATTAATAATTA-TAA
* *
20457 AAAAATTAAAAATTATAGA
1 AAATATTAATAATTATA-A
*
20476 AAATATTAATACTTAT
1 AAATATTAATAATTAT
20492 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
AAATATTAATAATTATAA
Found at i:21253 original size:11 final size:9
Alignment explanation
Indices: 21202--21244 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
21192 GGGCAATATT
21202 ATTTTTAATA
1 ATTTTT-ATA
*
21212 ATTATTA-A
1 ATTTTTATA
21220 TATTTTTATA
1 -ATTTTTATA
21230 ATTTTTATA
1 ATTTTTATA
21239 ATTTTT
1 ATTTTT
21245 CACTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 1 0.03
9 22 0.76
10 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:21419 original size:19 final size:18
Alignment explanation
Indices: 21397--21450 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
21387 CATATTTGAA
*
21397 AATTTGTAATAATTTTATT
1 AATTTTTAATAATTTTA-T
*
21416 AATTTTTAATAAATTGTAT
1 AATTTTTAAT-AATTTTAT
*
21435 AATTTTTTATAATTTT
1 AATTTTTAATAATTTT
21451 GCACTCACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 19 0.63
20 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATTTTTAATAATTTTAT
Found at i:21563 original size:20 final size:20
Alignment explanation
Indices: 21538--21576 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21528 AATGTATATA
*
21538 TTTTTATTAATTTTAAAATG
1 TTTTTAATAATTTTAAAATG
21558 TTTTTAATAATTTTAAAAT
1 TTTTTAATAATTTTAAAAT
21577 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATTTTAAAATG
Found at i:22053 original size:17 final size:18
Alignment explanation
Indices: 22018--22053 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22008 TGCGTGAACT
22018 AATTAATTGATTCAATTA
1 AATTAATTGATTCAATTA
*
22036 AATTAATTG-TTGAATTA
1 AATTAATTGATTCAATTA
22053 A
1 A
22054 CTTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (18 bp):
AATTAATTGATTCAATTA
Found at i:30776 original size:29 final size:28
Alignment explanation
Indices: 30718--30781 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
30708 TAAATCTCAA
*
30718 AATTATAAATGAACTTTGATTTAATGTGC
1 AATTATAAATGAACTTTAATTTAA-GTGC
*
30747 AATTATATACATGAACTTTAATTTGA-TGC
1 AATTATA-A-ATGAACTTTAATTTAAGTGC
30776 AATTAT
1 AATTAT
30782 GCACGTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 16 0.52
30 1 0.03
31 14 0.45
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (28 bp):
AATTATAAATGAACTTTAATTTAAGTGC
Found at i:34936 original size:115 final size:115
Alignment explanation
Indices: 34766--34992 Score: 375
Period size: 115 Copynumber: 2.0 Consensus size: 115
34756 GCAGGCTGGG
* *
34766 GTTAATCCTTTGGCAGGTATCCTTTTGATTAATTACTTCAGATTGTATGTTTATTTTTCATGTTC
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGTATGGTTATTTTTCATGTTC
34831 AATTAAATTTAGCTTCTTTTGAAAAATGGGTTTTTGCTTCGTTGGTATGAT
66 AATTAAATTTAGCTTCTTTTGAAAAATGGG-TTTTGCTTCGTTGGTATGAT
* *
34882 GTTAATCCTATGGCAGGTATCC-TTTGATTAATTACTTCAGATTGTATGGTTATTTTTCATTTTT
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGTATGGTTATTTTTCATGTTC
** *
34946 AATTAAATTTAGCTTCTTTTGAATGATGGGTTTTGTTTCGTTGGTAT
66 AATTAAATTTAGCTTCTTTTGAAAAATGGGTTTTGCTTCGTTGGTAT
34993 CTAGCTTATA
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 16 0.15
115 67 0.64
116 21 0.20
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.50
Consensus pattern (115 bp):
GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGTATGGTTATTTTTCATGTTC
AATTAAATTTAGCTTCTTTTGAAAAATGGGTTTTGCTTCGTTGGTATGAT
Done.