Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005319.1 Kokia drynarioides strain JFW-HI SEQ_119254, 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: 13296
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:6217 original size:20 final size:20
Alignment explanation
Indices: 6192--6230 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6182 TAGTCACAAG
6192 TTGCATTTCTTTGACCATCA
1 TTGCATTTCTTTGACCATCA
6212 TTGCATTTCTTTGACCATC
1 TTGCATTTCTTTGACCATC
6231 TCTTTGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.10, T:0.46
Consensus pattern (20 bp):
TTGCATTTCTTTGACCATCA
Found at i:8968 original size:8 final size:8
Alignment explanation
Indices: 8951--9004 Score: 99
Period size: 8 Copynumber: 6.8 Consensus size: 8
8941 ACCAAGTACC
*
8951 CTCTCTCT
1 CTCTCCCT
8959 CTCTCCCT
1 CTCTCCCT
8967 CTCTCCCT
1 CTCTCCCT
8975 CTCTCCCT
1 CTCTCCCT
8983 CTCTCCCT
1 CTCTCCCT
8991 CTCTCCCT
1 CTCTCCCT
8999 CTCTCC
1 CTCTCC
9005 TTTTCCTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (8 bp):
CTCTCCCT
Found at i:10383 original size:31 final size:33
Alignment explanation
Indices: 10347--10425 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 33
10337 TCCTTTTTTG
10347 ATTATTGATATTTATTAATAA-TAATATTAT-T-
1 ATTATTGATATTTATT-ATAATTAATATTATGTC
*
10378 ATTATTGTTATTTATTATAATTAATATTATGTC
1 ATTATTGATATTTATTATAATTAATATTATGTC
*
10411 ATTAATGATCATTTA
1 ATTATTGAT-ATTTA
10426 GTTCATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.10
31 24 0.59
32 1 0.02
33 7 0.17
34 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTATTGATATTTATTATAATTAATATTATGTC
Found at i:11095 original size:23 final size:24
Alignment explanation
Indices: 11064--11116 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
11054 AGCTTTGGAC
*
11064 ATTTTATTTGTAA-TTGGACTTTG
1 ATTTAATTTGTAATTTGGACTTTG
11087 ATTTAATTTGTAATTTGGACTTTG
1 ATTTAATTTGTAATTTGGACTTTG
11111 ATTTAA
1 ATTTAA
11117 ATAGATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (24 bp):
ATTTAATTTGTAATTTGGACTTTG
Found at i:11149 original size:17 final size:17
Alignment explanation
Indices: 11124--11186 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
11114 TAAATAGATT
*
11124 TAAACTTAAATTTATAA
1 TAAATTTAAATTTATAA
11141 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
11157 GTAAATTTAAACTTAAAA
1 -TAAATTTAAATTTATAA
11175 TAAATTTAAATT
1 TAAATTTAAATT
11187 CTGTTGGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.08
17 35 0.88
18 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:11150 original size:6 final size:6
Alignment explanation
Indices: 11121--11186 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
11111 ATTTAAATAG
* * *
11121 ATTTAA ACTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
11167 ACTTAA A-ATAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATT
11187 CTGTTGGGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.04
5 9 0.20
6 33 0.72
7 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:12009 original size:207 final size:202
Alignment explanation
Indices: 11527--12111 Score: 782
Period size: 207 Copynumber: 2.9 Consensus size: 202
11517 CTTGGCCTTT
* * * * * * *
11527 TTCTCAATATCTTATCAGGAAGATGATTGCATCACTTCTTTCAATTCGTTTCTCTATATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATC
* *
11592 AGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCC
66 AGGAAGACAAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCC
* * * * * * *
11657 CTGCTTCTCAGTATCTCATTAGGAGGCT-AGGGTTTAAAGATTCGCTCGCATTGATCGTGGAGTT
131 CTACTTCTCAGTATCTCATCAGGAAGCTGAGGGTTCAAAGATTTGCTCACATCGATCGTGGAGTT
11721 GGTATTC
196 GGTATTC
* * * * * *
11728 TTCTCTGTATCTCATTAGGAAGATGACCGCCTTACTTGTTTCAATCCGCTTCTTTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATC
* * *
11793 AGGAAGACAAATTTGGTGC-ACTTCTCAGTATCTAATCAAGAAGCTAACCATTTTATTGCTTCAC
66 AGGAAGACAAATTTGGT-CTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGC
* * * *
11857 CCTACTTCTCAGTATCTCATCAAGAAGTTGAGGGTTCGAAGATTTGCTCATATCGAGT-GTGGGT
130 CCTACTTCTCAGTATCTCATCAGGAAGCTGAGGGTTCAAAGATTTGCTCACATCGA-TCGT-GG-
* *
11921 TTGATTCGGTCTTC
192 -AG-TT-GGTATTC
11935 TTCTCAGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATC
*
12000 AGAAAGACAAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCC
66 AGGAAGACAAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCC
*
12065 CTACTTCTCAGTATTTCATCAGGAAGCTG-GGGTTCAAAGATTTGCTC
131 CTACTTCTCAGTATCTCATCAGGAAGCTGAGGGTTCAAAGATTTGCTC
12112 GCTTTGAGCC
Statistics
Matches: 330, Mismatches: 45, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
201 133 0.40
202 23 0.07
203 3 0.01
205 1 0.00
206 20 0.06
207 150 0.45
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (202 bp):
TTCTCAGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATC
AGGAAGACAAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGCC
CTACTTCTCAGTATCTCATCAGGAAGCTGAGGGTTCAAAGATTTGCTCACATCGATCGTGGAGTT
GGTATTC
Done.