Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010175.1 Kokia drynarioides strain JFW-HI SEQ_124980, 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: 71027
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:196 original size:8 final size:9
Alignment explanation
Indices: 173--197 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
163 AAAAAATATT
173 TATTTTTAA
1 TATTTTTAA
182 TATTTTTAA
1 TATTTTTAA
191 TATTTTT
1 TATTTTT
198 GATGTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TATTTTTAA
Found at i:3993 original size:20 final size:22
Alignment explanation
Indices: 3954--3993 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3944 AACCATTTTT
*
3954 TTTTTAAGAGTTTCGAAAATTA
1 TTTTTAAGAATTTCGAAAATTA
3976 TTTTT-AGAATTT-GAAAAT
1 TTTTTAAGAATTTCGAAAAT
3994 GAGAGTCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (22 bp):
TTTTTAAGAATTTCGAAAATTA
Found at i:5045 original size:8 final size:8
Alignment explanation
Indices: 5034--5074 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
5024 ATTTTCTTAT
5034 TTATTTTA
1 TTATTTTA
5042 TTATTTTA
1 TTATTTTA
5050 TTATTTTGA
1 TTATTTT-A
5059 --ATTTTA
1 TTATTTTA
5065 TTTATTTTA
1 -TTATTTTA
5074 T
1 T
5075 AGCCCGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 1 0.03
7 5 0.17
8 16 0.55
9 7 0.24
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:5055 original size:16 final size:16
Alignment explanation
Indices: 5030--5075 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
5020 TAAAATTTTC
5030 TTATTTATTTTATTATT
1 TTATTTATTTTA-TATT
5047 TTA-TTATTTTGA-ATT
1 TTATTTATTTT-ATATT
5062 TTATTTATTTTATA
1 TTATTTATTTTATA
5076 GCCCGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.27
16 15 0.58
17 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTATTTTATATT
Found at i:6709 original size:25 final size:23
Alignment explanation
Indices: 6681--6726 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
6671 TAAGAAACTG
6681 TTAATTAATTAAAAATGAATATATT
1 TTAATT-ATTAAAAATG-ATATATT
*
6706 TTAATTATTAAATATGATATA
1 TTAATTATTAAAAATGATATA
6727 GACGGGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 9 0.45
25 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAATTATTAAAAATGATATATT
Found at i:8378 original size:23 final size:21
Alignment explanation
Indices: 8339--8385 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
8329 ATAATTTTAA
*
8339 AATGTAATAAAAGTATAATTT
1 AATGTAATAAAAATATAATTT
8360 AATGTGAATACAAAATATAATTT
1 AATGT-AATA-AAAATATAATTT
8383 AAT
1 AAT
8386 CTTTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (21 bp):
AATGTAATAAAAATATAATTT
Found at i:10847 original size:55 final size:55
Alignment explanation
Indices: 10763--10878 Score: 223
Period size: 55 Copynumber: 2.1 Consensus size: 55
10753 AAATGCACCT
10763 CTAGCAAGCTAGGTCTAGGTGGATTGTGTTGACTTTATTTGTTGCCATTTGCTGG
1 CTAGCAAGCTAGGTCTAGGTGGATTGTGTTGACTTTATTTGTTGCCATTTGCTGG
10818 CTAGCAAGCTAGGTCTAGGTGGATTGTGTTGACTTTATTTGTTGCCATTTGCTGG
1 CTAGCAAGCTAGGTCTAGGTGGATTGTGTTGACTTTATTTGTTGCCATTTGCTGG
*
10873 CAAGCA
1 CTAGCA
10879 TGCTTCTTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (55 bp):
CTAGCAAGCTAGGTCTAGGTGGATTGTGTTGACTTTATTTGTTGCCATTTGCTGG
Found at i:17021 original size:18 final size:18
Alignment explanation
Indices: 16998--17041 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
16988 TGTTATCATA
16998 AGCAACCAACTTGGGCGT
1 AGCAACCAACTTGGGCGT
17016 AGCAACCAACTTGGGCGT
1 AGCAACCAACTTGGGCGT
17034 AGCAACCA
1 AGCAACCA
17042 TGAGAGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.14
Consensus pattern (18 bp):
AGCAACCAACTTGGGCGT
Found at i:18758 original size:23 final size:23
Alignment explanation
Indices: 18728--18783 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
18718 GTTTGCAGCA
18728 CTTTCAGCTTAACACCAAGAATT
1 CTTTCAGCTTAACACCAAGAATT
18751 CTTTCAGCTTAACACCAAGAATT
1 CTTTCAGCTTAACACCAAGAATT
18774 CTTTCAGCTT
1 CTTTCAGCTT
18784 GTCTATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (23 bp):
CTTTCAGCTTAACACCAAGAATT
Found at i:25260 original size:21 final size:22
Alignment explanation
Indices: 25215--25266 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
25205 TACAAGGTCG
* *
25215 ACGTCGTGACGAGATTTTGTCC
1 ACGTTGTGACGAGATTTTCTCC
*
25237 ACGTTGTGACGATA-TTTCTCC
1 ACGTTGTGACGAGATTTTCTCC
25258 ACGTTGTGA
1 ACGTTGTGA
25267 TGACACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (22 bp):
ACGTTGTGACGAGATTTTCTCC
Found at i:26354 original size:18 final size:18
Alignment explanation
Indices: 26333--26386 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
26323 TTCTTTATTT
26333 TTTTTGAAATTTTTATAA
1 TTTTTGAAATTTTTATAA
* ** *
26351 TTTTTAAAAAATATATAA
1 TTTTTGAAATTTTTATAA
* *
26369 ATTTTGGAATTTTTATAA
1 TTTTTGAAATTTTTATAA
26387 ATATTTTGAT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTTGAAATTTTTATAA
Found at i:29048 original size:21 final size:24
Alignment explanation
Indices: 28993--29056 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
28983 GGTGATCAAC
*
28993 AACAGCAGGAGCTGCAACATGAGG
1 AACAGCAGCAGCTGCAACATGAGG
29017 AACAGCAGCAGCTGCAACATGAGG
1 AACAGCAGCAGCTGCAACATGAGG
29041 AACAGCAGCAGCTGCA
1 AACAGCAGCAGCTGCA
29057 TCAGCAACAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.25, G:0.30, T:0.08
Consensus pattern (24 bp):
AACAGCAGCAGCTGCAACATGAGG
Found at i:29065 original size:21 final size:22
Alignment explanation
Indices: 28987--29066 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
28977 TGGCAAGGTG
* *
28987 ATCAACAACAGCAGGAGCTGCAAC
1 ATCAGCAACAGCAGCAGCTG--AC
* *
29011 ATGAGGAACAGCAGCAGCTGCAAC
1 ATCAGCAACAGCAGCAGCTG--AC
* *
29035 ATGAGGAACAGCAGCAGCTG-C
1 ATCAGCAACAGCAGCAGCTGAC
29056 ATCAGCAACAG
1 ATCAGCAACAG
29067 AATGATTCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.20
24 40 0.80
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.09
Consensus pattern (22 bp):
ATCAGCAACAGCAGCAGCTGAC
Found at i:31722 original size:3 final size:3
Alignment explanation
Indices: 31714--31744 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31704 AAGAAAACAG
31714 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
31745 ACCTTGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:37393 original size:6 final size:6
Alignment explanation
Indices: 37384--37425 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
37374 GAGTTGGCTC
37384 TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT
1 TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT
37426 GTTTCTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TGGCAT
Found at i:41302 original size:26 final size:26
Alignment explanation
Indices: 41257--41313 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
41247 TTTTTGATAA
* *
41257 TTTAAAATTTAATCTTTTTACTTTTAT
1 TTTAAAATATAATCTATTTACTTTT-T
41284 TTTAAAATATAAT-TATTTACTTTTT
1 TTTAAAATATAATCTATTTACTTTTT
41309 TTTAA
1 TTTAA
41314 TTTCAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 10 0.36
27 12 0.43
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTAAAATATAATCTATTTACTTTTT
Found at i:59426 original size:13 final size:13
Alignment explanation
Indices: 59408--59433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59398 ATATATATAT
59408 ATAAAAAAAAACA
1 ATAAAAAAAAACA
59421 ATAAAAAAAAACA
1 ATAAAAAAAAACA
59434 GAGGCTGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
ATAAAAAAAAACA
Found at i:67911 original size:31 final size:31
Alignment explanation
Indices: 67872--67951 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
67862 TTATAGTAAG
*
67872 GCATGGAAATTGAAGCAATAA-GGAGGTATAA
1 GCATGGAAATTGAAGCAATAATGG-GGCATAA
*
67903 TCATGGAAATTGAAGCAATAATGGGGCATAA
1 GCATGGAAATTGAAGCAATAATGGGGCATAA
*
67934 GCATAGAAATTGAAGCAA
1 GCATGGAAATTGAAGCAA
67952 ATGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (31 bp):
GCATGGAAATTGAAGCAATAATGGGGCATAA
Found at i:70211 original size:6 final size:6
Alignment explanation
Indices: 70202--70305 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
70192 TCGGCGTCGG
* * ** **
70202 CTTCAT CTTCGT CTTCTT CTTCAT CATCCTCAT CTTCAT CCCCAT CCCCAT
1 CTTCAT CTTCAT CTTCAT CTTCAT C-T--TCAT CTTCAT CTTCAT CTTCAT
* * * * *
70253 CTCCAT CTTCAT CCTCAT TTTCAT CTTCAT CTTCAT CTTCAG CTTCAG
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT
70301 CTTCA
1 CTTCA
70306 GGCTCAGTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
6 76 0.92
7 1 0.01
8 1 0.01
9 5 0.06
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (6 bp):
CTTCAT
Found at i:70729 original size:17 final size:18
Alignment explanation
Indices: 70696--70730 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
70686 CCGGTAACTA
*
70696 AATTCACAATTTTTTTAT
1 AATTCACAATTTGTTTAT
70714 AATTCA-AATTTGTTTAT
1 AATTCACAATTTGTTTAT
70731 TATTATGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTCACAATTTGTTTAT
Done.