Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004830.1 Kokia drynarioides strain JFW-HI SEQ_118473, 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: 36485
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:78 original size:23 final size:23
Alignment explanation
Indices: 46--99 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
36 ACGCTAGCGC
*
46 GCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
69 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
92 GCCTACTG
1 GCTTACTG
100 ATTAGAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:152 original size:23 final size:23
Alignment explanation
Indices: 110--167 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
100 ATTAGAGCTA
*
110 TGTGCGCCTACT-GATTGCACAG
1 TGTGTGCCTACTGGATTGCACAG
*
132 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACTGGATTGCACAG
*
155 TGTGTGCTTACTG
1 TGTGTGCCTACTG
168 TTTCCCAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.34
Consensus pattern (23 bp):
TGTGTGCCTACTGGATTGCACAG
Found at i:167 original size:45 final size:46
Alignment explanation
Indices: 65--167 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
55 TTCGCACTTC
* **
65 GTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGATTAGAGCTAT
1 GTGTGCTTACTGATTCGCACAGTGTGTGCCTACTGATTAGAGCTAT
* * *
111 GTGCGCCTACTGATT-GCACAGTGTGTGCCTACTGGATT-GCA-CTGT
1 GTGTGCTTACTGATTCGCACAGTGTGTGCCTACT-GATTAG-AGCTAT
156 GTGTGCTTACTG
1 GTGTGCTTACTG
168 TTTCCCAGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
45 30 0.64
46 17 0.36
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (46 bp):
GTGTGCTTACTGATTCGCACAGTGTGTGCCTACTGATTAGAGCTAT
Found at i:6916 original size:29 final size:29
Alignment explanation
Indices: 6874--6929 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
6864 GAACTTAATC
*
6874 AAATAAAATTTCATGTATGA-AATTGTATA
1 AAATAAAATTTCATATAT-ACAATTGTATA
6903 AAATCAAAA-TTCATATATACAATTGTA
1 AAAT-AAAATTTCATATATACAATTGTA
6930 AATTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 19 0.79
30 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATAAAATTTCATATATACAATTGTATA
Found at i:7160 original size:16 final size:16
Alignment explanation
Indices: 7139--7175 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
7129 CACCCCCTCC
7139 CCCCTTCTCTCTCTCT
1 CCCCTTCTCTCTCTCT
7155 CCCCTTCTCTCTCTCT
1 CCCCTTCTCTCTCTCT
7171 CCCCT
1 CCCCT
7176 CTTTGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (16 bp):
CCCCTTCTCTCTCTCT
Found at i:7597 original size:17 final size:19
Alignment explanation
Indices: 7564--7601 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
7554 TTTTGCTTTG
7564 TTTGTTGATTCAGTGTGTT
1 TTTGTTGATTCAGTGTGTT
7583 TTTGTTG-TTCA-TGTGTT
1 TTTGTTGATTCAGTGTGTT
7600 TT
1 TT
7602 CTTTGTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.08, C:0.05, G:0.24, T:0.63
Consensus pattern (19 bp):
TTTGTTGATTCAGTGTGTT
Found at i:21080 original size:22 final size:22
Alignment explanation
Indices: 21052--21094 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21042 ATCAATTGTT
*
21052 TTGCTACTGTTTTGTTATTATA
1 TTGCTACTATTTTGTTATTATA
*
21074 TTGCTACTATTTTGTTGTTAT
1 TTGCTACTATTTTGTTATTAT
21095 TGTTTAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.60
Consensus pattern (22 bp):
TTGCTACTATTTTGTTATTATA
Found at i:31018 original size:3 final size:3
Alignment explanation
Indices: 31010--31048 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31000 AAAATAAAGA
31010 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
31049 TGATAGAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33339 original size:16 final size:17
Alignment explanation
Indices: 33309--33340 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33299 TATTTTGTTT
33309 AAAATTTGTATATAAAC
1 AAAATTTGTATATAAAC
33326 AAAATTTG-ATATAAA
1 AAAATTTGTATATAAA
33341 AATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (17 bp):
AAAATTTGTATATAAAC
Done.