Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012701.1 Kokia drynarioides strain JFW-HI SEQ_127712, 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: 23307
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 TCTTTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1092 original size:3 final size:3
Alignment explanation
Indices: 1084--1136 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
1074 GGGGCAATTC
1084 CTT CTT CTT CTT CCTT C-T CTT CTT -TT CTCT CTT CTT C-T CTT GCTT
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT -CTT
1129 CTT CTT CT
1 CTT CTT CT
1137 ACTACAATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.14
3 29 0.66
4 9 0.20
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:6857 original size:12 final size:12
Alignment explanation
Indices: 6842--6867 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6832 ACTGCAACTT
6842 CTCTGCAGTTTG
1 CTCTGCAGTTTG
6854 CTCTGCAGTTTG
1 CTCTGCAGTTTG
6866 CT
1 CT
6868 TTCCACTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.23, T:0.42
Consensus pattern (12 bp):
CTCTGCAGTTTG
Found at i:13406 original size:16 final size:16
Alignment explanation
Indices: 13385--13417 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13375 TGATTATTTT
*
13385 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
13401 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
13417 A
1 A
13418 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:13854 original size:18 final size:16
Alignment explanation
Indices: 13831--13866 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
13821 CTTAGTAAAT
13831 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
13849 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
13865 AT
1 AT
13867 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:14520 original size:51 final size:51
Alignment explanation
Indices: 14404--14533 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
14394 CGTAAATGCA
* * *
14404 AAAGGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATCCTTTACAAATT
* *
14455 ATGAGGTCCAATGACTATGTGTCATCGTGA-TAAATGAATCCTATTACAAATT
1 A-AAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATCCT-TTACAAATT
* **
14507 AAAGGTCTGATGACTCCGTGTCATCGT
1 AAAGGTCCGATGACTATGTGTCATCGT
14534 CAGTTACCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 33 0.49
52 34 0.51
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (51 bp):
AAAGGTCCGATGACTATGTGTCATCGTGAGTAAATGAATCCTTTACAAATT
Found at i:18526 original size:16 final size:16
Alignment explanation
Indices: 18505--18537 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18495 TGATGATTTT
*
18505 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
18521 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
18537 A
1 A
18538 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:19595 original size:52 final size:53
Alignment explanation
Indices: 19517--19753 Score: 304
Period size: 52 Copynumber: 4.6 Consensus size: 53
19507 GTAAATGCAA
*
19517 AAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTCTTACAGATTAT
* * *
19569 AAGGTCCAATGACTATGTGTCATCGTGAGTATATGGATCCT-TTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTCTTACAGATTAT
* * * *
19621 GAGGTCCGATGATTATGTGTCATCGTGAGTATATGAAT-CTGTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTCTTACAGATTAT
* * *
19673 GAGGTCCGATGACTATGTGTCATCGTGAG-AAATAAATCCTCTTACAGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTCTTACAGATTAT
* ***
19724 AAGGTCTGATGACTCCATGTCATCGTGAGT
1 AAGGTCCGATGACTATGTGTCATCGTGAGT
19754 TACCAAATGC
Statistics
Matches: 166, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
51 32 0.19
52 134 0.81
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (53 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTCTTACAGATTAT
Found at i:22119 original size:80 final size:80
Alignment explanation
Indices: 21980--22192 Score: 284
Period size: 80 Copynumber: 2.7 Consensus size: 80
21970 CAATTTAACT
** * * * * *
21980 AACTAGAGCTGGGCTCACTTTTACGGTTTATCCACTAGGTACTAGGTGTTAGGATTTGACGGATT
1 AACTAGAGCTGGGCTCACTTTTGTGGTTTATCCGCTAGGCACTAGGTGCTAGGACTTGACGGATA
22045 TTTGTTGGTTAAACC
66 TTTGTTGGTTAAACC
* *
22060 AACTAGAGCTGGGCTCACTTTTGTGGTTTATCCGCTAGGCAGTAGGTGCGAGGACTTGACGGATA
1 AACTAGAGCTGGGCTCACTTTTGTGGTTTATCCGCTAGGCACTAGGTGCTAGGACTTGACGGATA
*
22125 TTTGTTGGTTAATCC
66 TTTGTTGGTTAAACC
* * * * *
22140 AACTAGTGTTGGGCTCAC-TTCGTGGTTTATCTGCTAGGCATTAGGTGCTAGGA
1 AACTAGAGCTGGGCTCACTTTTGTGGTTTATCCGCTAGGCACTAGGTGCTAGGA
22193 TCATTGGTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 31 0.26
80 86 0.74
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (80 bp):
AACTAGAGCTGGGCTCACTTTTGTGGTTTATCCGCTAGGCACTAGGTGCTAGGACTTGACGGATA
TTTGTTGGTTAAACC
Done.