Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005832.1 Kokia drynarioides strain JFW-HI SEQ_120122, 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: 44110
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:11513 original size:18 final size:19
Alignment explanation
Indices: 11490--11563 Score: 87
Period size: 18 Copynumber: 3.8 Consensus size: 19
11480 AATAACAACT
*
11490 AAAACAATAAAAAAA-ACC
1 AAAACAATAAAAAAACACA
*
11508 AAAACAATAAAAAAACATA
1 AAAACAATAAAAAAACACA
11527 AAAACAATAAAAAACAGCAACA
1 AAAACAATAAAAAA-A-C-ACA
*
11549 AAAACACTAAAAAAA
1 AAAACAATAAAAAAA
11564 AAAAGTACCA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 15 0.31
19 15 0.31
20 1 0.02
21 2 0.04
22 15 0.31
ACGTcount: A:0.77, C:0.15, G:0.01, T:0.07
Consensus pattern (19 bp):
AAAACAATAAAAAAACACA
Found at i:16954 original size:3 final size:3
Alignment explanation
Indices: 16946--16971 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16936 TATATTAAAA
16946 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
16972 AATAACCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18105 original size:2 final size:2
Alignment explanation
Indices: 18100--18130 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18090 TTAAACACAC
18100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18131 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19889 original size:11 final size:11
Alignment explanation
Indices: 19873--19898 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19863 CTATTTTAAT
19873 TTTGGTGTCGG
1 TTTGGTGTCGG
19884 TTTGGTGTCGG
1 TTTGGTGTCGG
19895 TTTG
1 TTTG
19899 ATGGCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.42, T:0.50
Consensus pattern (11 bp):
TTTGGTGTCGG
Found at i:20365 original size:14 final size:14
Alignment explanation
Indices: 20324--20365 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20314 AAGTACAATT
*
20324 TTAATGTATATATA
1 TTAATATATATATA
20338 -T-ATATATATATA
1 TTAATATATATATA
*
20350 TTAATTTATATATA
1 TTAATATATATATA
20364 TT
1 TT
20366 TTTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TTAATATATATATA
Found at i:20688 original size:30 final size:30
Alignment explanation
Indices: 20654--20712 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
20644 CAAATAAGCC
* *
20654 TTTAAACTTTAATTTATATTCAAATAAATG
1 TTTAAACGTTAACTTATATTCAAATAAATG
* *
20684 TTTAATCGTTAACTTGTATTCAAATAAAT
1 TTTAAACGTTAACTTATATTCAAATAAAT
20713 TCTCAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTAAACGTTAACTTATATTCAAATAAATG
Found at i:26942 original size:2 final size:2
Alignment explanation
Indices: 26935--26960 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26925 TTATAAAACA
26935 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26961 GATTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28258 original size:31 final size:31
Alignment explanation
Indices: 28191--28258 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
28181 TTACAAAATG
* * *
28191 ATCACTAAATTATTTGAAAGTTTCCATTTAA
1 ATCACTAAATTATTCGAAAATTTCCACTTAA
**
28222 ATCACTAAATTATTCGAAAATTTTTACTTAA
1 ATCACTAAATTATTCGAAAATTTCCACTTAA
*
28253 GTCACT
1 ATCACT
28259 GGATTGATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (31 bp):
ATCACTAAATTATTCGAAAATTTCCACTTAA
Found at i:30526 original size:3 final size:3
Alignment explanation
Indices: 30518--30546 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30508 GTTATTTGGA
30518 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30547 AGCATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:43261 original size:29 final size:31
Alignment explanation
Indices: 43228--43285 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
43218 GTACATTTTG
*
43228 AATTTAGTCATCCT-A-TTTTTATTTTAAGA
1 AATTTAATCATCCTAATTTTTTATTTTAAGA
**
43257 AATTTAATCATTTTAATTTTTTATTTTAA
1 AATTTAATCATCCTAATTTTTTATTTTAA
43286 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.46
30 1 0.04
31 12 0.50
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (31 bp):
AATTTAATCATCCTAATTTTTTATTTTAAGA
Found at i:43651 original size:15 final size:15
Alignment explanation
Indices: 43631--43660 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43621 TATCTATAAA
43631 AAAAAATGCTTTACT
1 AAAAAATGCTTTACT
43646 AAAAAATGCTTTACT
1 AAAAAATGCTTTACT
43661 TGACGACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
AAAAAATGCTTTACT
Found at i:44059 original size:13 final size:13
Alignment explanation
Indices: 44043--44077 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
44033 GGGTTTTTTT
44043 CAAAAAAATACGA
1 CAAAAAAATACGA
44056 C--AAAAATACGA
1 CAAAAAAATACGA
44067 CAAAAAAATAC
1 CAAAAAAATAC
44078 CTGACACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAATACGA
Done.