Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014124.1 Kokia drynarioides strain JFW-HI SEQ_129157, 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: 35245
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:3214 original size:89 final size:89
Alignment explanation
Indices: 3063--3240 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
3053 GCATGAAATT
*
3063 CTTCCAAAATAATCTCATCCAACACGTCAATGTGGTGACATTGTTCATTAGATCCGGACGGTAAT
1 CTTCCAAAATAATCTCATCCAACACGTCAATGTGGTGACATTGTTCATTAGATCCGAACGGTAAT
3128 GCTTCAAACACACTGAAGGTTACC
66 GCTTCAAACACACTGAAGGTTACC
3152 CTTCCAAAATAATCTCATCCAACACGTCAATGTGGTGACATTGTTCATTAGATCCGAACGGTAAT
1 CTTCCAAAATAATCTCATCCAACACGTCAATGTGGTGACATTGTTCATTAGATCCGAACGGTAAT
3217 GCTTCAAACACACTGAAGGTTACC
66 GCTTCAAACACACTGAAGGTTACC
3241 TGATCATCAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (89 bp):
CTTCCAAAATAATCTCATCCAACACGTCAATGTGGTGACATTGTTCATTAGATCCGAACGGTAAT
GCTTCAAACACACTGAAGGTTACC
Found at i:16363 original size:33 final size:34
Alignment explanation
Indices: 16320--16395 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
16310 TGTTTTGTGT
* *
16320 TTACTATCCTAGTGAACTTATCTTTGTTCTAT-C
1 TTACTGTCCTAGTGAACTTATCTCTGTTCTATGC
* *
16353 TTACTGTCCTAGTGGACTTATCTCTGTTCTATGT
1 TTACTGTCCTAGTGAACTTATCTCTGTTCTATGC
16387 TTACTGTCC
1 TTACTGTCC
16396 CAACGTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.47
Consensus pattern (34 bp):
TTACTGTCCTAGTGAACTTATCTCTGTTCTATGC
Found at i:22445 original size:3 final size:3
Alignment explanation
Indices: 22437--22469 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
22427 GAATAAGTTA
22437 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22470 GATGATGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:26680 original size:23 final size:23
Alignment explanation
Indices: 26574--26681 Score: 69
Period size: 23 Copynumber: 4.6 Consensus size: 23
26564 TAGGGTTCGC
* *
26574 ACATATAGGGTTCACATGAGTAA
1 ACATATAGGGTTCGCATGAATAA
* *
26597 ACAGATAGGGTGT-GCATGTATGACA
1 ACATATAGGGT-TCGCATGAAT-A-A
* *
26622 TGTA-ATATAAGGTTCGCATGTAT-A
1 ---ACATATAGGGTTCGCATGAATAA
* *
26646 ACATGTAAGGTTCGCATGAATAA
1 ACATATAGGGTTCGCATGAATAA
26669 ACATATAGGGTTC
1 ACATATAGGGTTC
26682 ACATAACTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
21 1 0.02
22 17 0.26
23 27 0.41
24 3 0.05
25 1 0.02
26 1 0.02
27 15 0.23
28 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (23 bp):
ACATATAGGGTTCGCATGAATAA
Found at i:30915 original size:14 final size:14
Alignment explanation
Indices: 30891--31001 Score: 73
Period size: 14 Copynumber: 7.8 Consensus size: 14
30881 ACCTGTAGAC
*
30891 CCCCTTATATGTGAA
1 CCCC-TATATGCGAA
*
30906 CCCCTATATGTGAA
1 CCCCTATATGCGAA
30920 CCTCCGTATA--CGAA
1 CC-CC-TATATGCGAA
* *
30934 CCCCTATAAGCAAA
1 CCCCTATATGCGAA
*
30948 CCCTTATATGCGAA
1 CCCCTATATGCGAA
*
30962 CTCCCTATAGGCGAA
1 C-CCCTATATGCGAA
* * * *
30977 CACTTGTATGTGAA
1 CCCCTATATGCGAA
*
30991 TCCCTATATGC
1 CCCCTATATGC
31002 AAACTATAAC
Statistics
Matches: 74, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
12 4 0.05
13 2 0.03
14 46 0.62
15 18 0.24
16 4 0.05
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (14 bp):
CCCCTATATGCGAA
Found at i:30986 original size:29 final size:29
Alignment explanation
Indices: 30925--31005 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 29
30915 GTGAACCTCC
* *
30925 GTATACGAAC-CCCTATAAGCAAACCCTT
1 GTATGCGAACTCCCTATAAGCAAACACTT
* * *
30953 ATATGCGAACTCCCTATAGGCGAACACTT
1 GTATGCGAACTCCCTATAAGCAAACACTT
* *
30982 GTATGTGAA-TCCCTATATGCAAAC
1 GTATGCGAACTCCCTATAAGCAAAC
31006 TATAACAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (29 bp):
GTATGCGAACTCCCTATAAGCAAACACTT
Found at i:32151 original size:18 final size:18
Alignment explanation
Indices: 32128--32173 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
32118 CACAAAAGGA
32128 TGAGCATACTAGCTCATT
1 TGAGCATACTAGCTCATT
* * * *
32146 TGAGCACATTGGCTCGTT
1 TGAGCATACTAGCTCATT
32164 TGAGCATACT
1 TGAGCATACT
32174 TGATCGTAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
TGAGCATACTAGCTCATT
Found at i:32180 original size:18 final size:18
Alignment explanation
Indices: 32128--32180 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
32118 CACAAAAGGA
* *
32128 TGAGCATACTAGCTCATT
1 TGAGCATACTTGCTCGTT
*
32146 TGAGCACA-TTGGCTCGTT
1 TGAGCATACTT-GCTCGTT
*
32164 TGAGCATACTTGATCGT
1 TGAGCATACTTGCTCGT
32181 AAGAGTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.89
19 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (18 bp):
TGAGCATACTTGCTCGTT
Found at i:33634 original size:8 final size:8
Alignment explanation
Indices: 33621--33645 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33611 AATTAACGAA
33621 AGAAATTG
1 AGAAATTG
33629 AGAAATTG
1 AGAAATTG
33637 AGAAATTG
1 AGAAATTG
33645 A
1 A
33646 ACACAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Done.