Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006842.1 Kokia drynarioides strain JFW-HI SEQ_121441, 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: 1853
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Found at i:176 original size:18 final size:18
Alignment explanation
Indices: 153--190 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
143 TTAGTTCCCT
*
153 TTTTTATTATTATTAATA
1 TTTTTATTAATATTAATA
171 TTTTTATTAATATTAATA
1 TTTTTATTAATATTAATA
189 TT
1 TT
191 AATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTATTAATATTAATA
Found at i:177 original size:12 final size:12
Alignment explanation
Indices: 157--200 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
147 TTCCCTTTTT
157 TATTATTATTAA
1 TATTATTATTAA
*
169 TATTTTTATTAA
1 TATTATTATTAA
*
181 TATTAATATTAA
1 TATTATTATTAA
*
193 TTTTATTA
1 TATTATTA
201 ATACCTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:866 original size:17 final size:17
Alignment explanation
Indices: 848--957 Score: 123
Period size: 17 Copynumber: 6.4 Consensus size: 17
838 CTTTATTTAT
* *
848 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
865 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
883 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
900 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
917 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
935 TTT-AATCCTAAAATAAA
1 TTTAAAT-TTAAAATAAA
952 TTTAAA
1 TTTAAA
958 ATGAGTTTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 49 0.63
18 28 0.36
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:893 original size:6 final size:6
Alignment explanation
Indices: 848--925 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
838 CTTTATTTAT
* * *
848 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
895 -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
926 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.24
6 38 0.66
7 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:904 original size:11 final size:11
Alignment explanation
Indices: 866--924 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
856 TATAATAATT
866 TTAAATTTGAAA
1 TTAAATTT-AAA
*
878 ATAAATTTAAA
1 TTAAATTTAAA
889 CTTAAA-TTAAA
1 -TTAAATTTAAA
900 TTTAAATTTAAA
1 -TTAAATTTAAA
*
912 ATAAATTTAAA
1 TTAAATTTAAA
923 TT
1 TT
925 TTTAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:905 original size:52 final size:52
Alignment explanation
Indices: 848--957 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
838 CTTTATTTAT
* * * * *
848 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
** *
900 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATCCTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
952 TTTAAA
1 TTTAAA
958 ATGAGTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACCTAAAATAAA
Found at i:936 original size:35 final size:35
Alignment explanation
Indices: 848--957 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
838 CTTTATTTAT
* *
848 TTTAAATTTAT-AATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAATTT-AAAATAAA
*
883 TTTAAA--CTTAAATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTTTAAA-TAAATTTAAATTTAAAATAAA
* *
917 TTTAAATTTTTAAACAAATTT-AATCCTAAAATAAA
1 TTTAAATTTTTAAATAAATTTAAAT-TTAAAATAAA
952 TTTAAA
1 TTTAAA
958 ATGAGTTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 19 0.30
35 39 0.61
36 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTAAATTTTTAAATAAATTTAAATTTAAAATAAA
Found at i:1721 original size:158 final size:158
Alignment explanation
Indices: 1433--1771 Score: 579
Period size: 158 Copynumber: 2.1 Consensus size: 158
1423 CTTCGACTTG
* * *
1433 CTTCTCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTTCTCACATCGAGCGTGAGTTTGATT
1 CTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATT
*
1498 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTTGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGT
*
1563 ACCTCATCAGGAAGAAGAATTTGGTCCA
131 ACCTCATCAGGAAGAAGAATTTGATCCA
* * * *
1591 CTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGGGCGTGAGTTTAATT
1 CTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATT
1656 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGT
66 TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGT
* *
1721 ATCTCATCAGGAAGATGAATTTGATCCA
131 ACCTCATCAGGAAGAAGAATTTGATCCA
1749 CTTCTCAATATCTCATCAGGAAG
1 CTTCTCAATATCTCATCAGGAAG
1772 ATAACCACTT
Statistics
Matches: 168, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
158 168 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (158 bp):
CTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATT
TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGT
ACCTCATCAGGAAGAAGAATTTGATCCA
Done.