Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001360.1 Kokia drynarioides strain JFW-HI SEQ_112817, 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: 58279
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:383 original size:10 final size:11
Alignment explanation
Indices: 362--392 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
352 TTCTGACTTT
362 GAAAAATCATA
1 GAAAAATCATA
373 GAAAAAT-ATA
1 GAAAAATCATA
383 GAAAAATCAT
1 GAAAAATCAT
393 TAGAGACGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (11 bp):
GAAAAATCATA
Found at i:886 original size:24 final size:24
Alignment explanation
Indices: 854--900 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
844 ATAATAGTGA
854 CATGCCATTAAGGAACACTAGCGG
1 CATGCCATTAAGGAACACTAGCGG
878 CATGCCATTAAGGAACACTAGCG
1 CATGCCATTAAGGAACACTAGCG
901 CGCCCTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (24 bp):
CATGCCATTAAGGAACACTAGCGG
Found at i:929 original size:23 final size:23
Alignment explanation
Indices: 899--963 Score: 114
Period size: 23 Copynumber: 2.8 Consensus size: 23
889 GGAACACTAG
899 CGCGCCCTCTGCTTAGCACGTTT
1 CGCGCCCTCTGCTTAGCACGTTT
922 CGCGCCCTCTGCTTAGCACGTTT
1 CGCGCCCTCTGCTTAGCACGTTT
945 CGCGCCCTCTG-TTCAGCAC
1 CGCGCCCTCTGCTT-AGCAC
964 TGTGTGTGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.05
23 39 0.95
ACGTcount: A:0.09, C:0.42, G:0.22, T:0.28
Consensus pattern (23 bp):
CGCGCCCTCTGCTTAGCACGTTT
Found at i:974 original size:23 final size:23
Alignment explanation
Indices: 948--1053 Score: 99
Period size: 25 Copynumber: 4.4 Consensus size: 23
938 CACGTTTCGC
*
948 GCCCTCTGTTCAGCACTGTGTGT
1 GCCCTCTGTTCAGCACTTTGTGT
* *
971 GCCCTTTGTTATTAGCACTTTGTGT
1 GCCCTCTG-T-TCAGCACTTTGTGT
*
996 GCCCTCTAATT-AGCACTTTGTGT
1 GCCCTCT-GTTCAGCACTTTGTGT
*
1019 GCCCTCTGTTACCCAGCAC-TTATGT
1 GCCCTCTGTT---CAGCACTTTGTGT
1044 GCCCTCTGTT
1 GCCCTCTGTT
1054 AAGTACTTCG
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.03
23 26 0.38
24 2 0.03
25 34 0.49
26 5 0.07
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (23 bp):
GCCCTCTGTTCAGCACTTTGTGT
Found at i:994 original size:25 final size:24
Alignment explanation
Indices: 959--1029 Score: 90
Period size: 23 Copynumber: 2.9 Consensus size: 24
949 CCCTCTGTTC
*
959 AGCACTGTGTGTGCCCTTTGTTATT
1 AGCACTTTGTGTGCCC-TTGTTATT
* *
984 AGCACTTTGTGTGCCC-TCTAATT
1 AGCACTTTGTGTGCCCTTGTTATT
1007 AGCACTTTGTGTGCCCTCTGTTA
1 AGCACTTTGTGTGCCCT-TGTTA
1030 CCCAGCACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 21 0.54
25 18 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (24 bp):
AGCACTTTGTGTGCCCTTGTTATT
Found at i:1001 original size:48 final size:47
Alignment explanation
Indices: 948--1054 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 47
938 CACGTTTCGC
* ** *
948 GCCCTCTGTTCAGCACTGTGTGTGCCCTTTGTTA-TTAGCACTTTGTGT
1 GCCCTCTGTT-AGCACTGTGTGTGCCCTCTGTTACCCAGCAC-TTATGT
* *
996 GCCCTCTAATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATGT
1 GCCCTCT-GTTAGCACTGTGTGTGCCCTCTGTTACCCAGCACTTATGT
1044 GCCCTCTGTTA
1 GCCCTCTGTTA
1055 AGTACTTCGA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
47 3 0.06
48 40 0.80
49 7 0.14
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (47 bp):
GCCCTCTGTTAGCACTGTGTGTGCCCTCTGTTACCCAGCACTTATGT
Found at i:8137 original size:29 final size:29
Alignment explanation
Indices: 8088--8164 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
8078 AAATTGAATC
* *
8088 AAATTAAAATTTATCTGTAAAATTACAAA
1 AAATTAAAATTTATATATAAAATTACAAA
* * * *
8117 AAATTAAAATTTATTTATAAATTTAGATA
1 AAATTAAAATTTATATATAAAATTACAAA
* *
8146 AGATTCAAATTTATATATA
1 AAATTAAAATTTATATATA
8165 GTTTTGAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (29 bp):
AAATTAAAATTTATATATAAAATTACAAA
Found at i:19047 original size:31 final size:31
Alignment explanation
Indices: 19012--19070 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
19002 ATTAGATGCG
*
19012 TTTTCGAAAAAACTCGTCCAGTTGGACATGT
1 TTTTCAAAAAAACTCGTCCAGTTGGACATGT
*
19043 TTTTCAAAAAAACTCGTCTAGTTGGACA
1 TTTTCAAAAAAACTCGTCCAGTTGGACA
19071 AAATTTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (31 bp):
TTTTCAAAAAAACTCGTCCAGTTGGACATGT
Found at i:22189 original size:3 final size:3
Alignment explanation
Indices: 22181--22218 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
22171 CAAGAATATC
22181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22219 TATGATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:33059 original size:34 final size:34
Alignment explanation
Indices: 33020--33107 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
33010 AAATTTGATT
* * *
33020 AATTATAAAATATTTTAATTATTATTA-AATTATA
1 AATTATAATATATTTTAATTATAATTATAAGT-TA
*
33054 AATTATATTATATTTTAA-TATAATTATAAGTTA
1 AATTATAATATATTTTAATTATAATTATAAGTTA
33087 AA-TATAATATATTTTTAATTA
1 AATTATAATATA-TTTTAATTA
33108 ATTTATGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
32 8 0.17
33 17 0.37
34 21 0.46
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
AATTATAATATATTTTAATTATAATTATAAGTTA
Found at i:57338 original size:23 final size:23
Alignment explanation
Indices: 57264--57457 Score: 100
Period size: 23 Copynumber: 8.7 Consensus size: 23
57254 TAAACGGAAC
* *
57264 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTACT
* ***
57286 AAACAGAGAGCACATAAATGTTGGG
1 AAACAGAGAGCACACAAA-G-TACT
* *
57311 CAACAGAGAGCACCCAAAGTACT
1 AAACAGAGAGCACACAAAGTACT
*
57334 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTACT
* **
57357 -------GAGCAAACAAAGTGTT
1 AAACAGAGAGCACACAAAGTACT
* * *
57373 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTACT
* * * *
57396 AATCAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTACT
* *
57419 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTACT
*
57442 AATCAGAGAGCACACA
1 AAACAGAGAGCACACA
57458 GTGCTAATTA
Statistics
Matches: 132, Mismatches: 28, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
16 12 0.09
22 13 0.10
23 88 0.67
24 3 0.02
25 16 0.12
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTACT
Found at i:57472 original size:23 final size:21
Alignment explanation
Indices: 57367--57473 Score: 124
Period size: 23 Copynumber: 4.8 Consensus size: 21
57357 GAGCAAACAA
*
57367 AGTGTTAATCAGAGAGCACAC
1 AGTGCTAATCAGAGAGCACAC
*
57388 GAAGTGCTAATCAGAGAGCACGAG
1 --AGTGCTAATCAGAGAGCAC-AC
*
57412 ACGTGCTAAACAGAGAGCACACAC
1 A-GTGCTAATCAGAGAG--CACAC
57436 AGTGCTAATCAGAGAGCACAC
1 AGTGCTAATCAGAGAGCACAC
*
57457 AGTGCTAATTAGAGAGC
1 AGTGCTAATCAGAGAGC
57474 GTGCTAGTGT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
21 21 0.28
22 1 0.01
23 46 0.62
24 3 0.04
25 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (21 bp):
AGTGCTAATCAGAGAGCACAC
Done.