Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009709.1 Kokia drynarioides strain JFW-HI SEQ_124428, 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: 14783
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:56 original size:23 final size:22
Alignment explanation
Indices: 24--168 Score: 114
Period size: 23 Copynumber: 6.4 Consensus size: 22
14 GCTGGGGAAA
24 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
* *
46 CCAGTAGGCACACACAATGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
69 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
* * *
92 CAGTAGGCACACGA-GGTGCAAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
*
115 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
*
138 CAGTAAGCACACACAGTGCTAAA
1 CAGTAAGCACACACAGTGC-AAT
161 CAGTAAGC
1 CAGTAAGC
169 GCGCTAGCCT
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
22 16 0.15
23 88 0.84
24 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:201 original size:28 final size:28
Alignment explanation
Indices: 161--217 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
151 CAGTGCTAAA
161 CAGTAAGCGCGCTAGCCTTAATGGCATG
1 CAGTAAGCGCGCTAGCCTTAATGGCATG
189 CAGTAAGCGCGCTAGCCTTAATGGCATG
1 CAGTAAGCGCGCTAGCCTTAATGGCATG
217 C
1 C
218 CACTATTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (28 bp):
CAGTAAGCGCGCTAGCCTTAATGGCATG
Found at i:293 original size:24 final size:26
Alignment explanation
Indices: 255--302 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
245 TCTACATGGG
255 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
281 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
303 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:1692 original size:21 final size:23
Alignment explanation
Indices: 1668--1711 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1658 CCTTTTCATC
1668 AGTTCTTTTCT-TC-ATTTCTCT
1 AGTTCTTTTCTATCAATTTCTCT
*
1689 AGTTTTTTTCTATCAATTTCTCT
1 AGTTCTTTTCTATCAATTTCTCT
1712 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.14, C:0.20, G:0.05, T:0.61
Consensus pattern (23 bp):
AGTTCTTTTCTATCAATTTCTCT
Found at i:2228 original size:23 final size:24
Alignment explanation
Indices: 2184--2233 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2174 CCAACCCAAC
* *
2184 AATTAAATAATTTAAGTCATTT-T
1 AATTAAATAATTGAAGTAATTTAT
2207 AATTAAATAATTGATAG-AATTTAT
1 AATTAAATAATTGA-AGTAATTTAT
2231 AAT
1 AAT
2234 AGCATTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
AATTAAATAATTGAAGTAATTTAT
Found at i:3142 original size:18 final size:19
Alignment explanation
Indices: 3105--3156 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
3095 TTGGTAATTT
*
3105 TAACACAAATTAATTATTTTA
1 TAACATAAATT-A-TATTTTA
*
3126 TAA-ATAAATTATATTTTT
1 TAACATAAATTATATTTTA
*
3144 TAACATTAATTAT
1 TAACATAAATTAT
3157 TCAAAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.33
19 9 0.33
20 6 0.22
21 3 0.11
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
TAACATAAATTATATTTTA
Found at i:4832 original size:13 final size:13
Alignment explanation
Indices: 4790--4837 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
4780 AATTATTTCA
*
4790 TTAATAAATTGGG
1 TTAATTAATTGGG
*
4803 TTAATTAAAAT--G
1 TTAATT-AATTGGG
4815 TTAATTAATTGGG
1 TTAATTAATTGGG
4828 TTAATTAATT
1 TTAATTAATT
4838 AATTTGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 16 0.55
14 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAATTAATTGGG
Done.