Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013041.1 Kokia drynarioides strain JFW-HI SEQ_128059, 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: 10631
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:107 original size:6 final size:6
Alignment explanation
Indices: 61--146 Score: 65
Period size: 6 Copynumber: 14.5 Consensus size: 6
51 TTCTATTTAT
* * *
61 TTTAAA CTTTAAA TTTGAAA -ATAAG TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
109 TTTTGAAA --TAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 -TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
147 TTAAGCAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.05
5 12 0.19
6 34 0.53
7 12 0.19
8 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:147 original size:35 final size:35
Alignment explanation
Indices: 63--179 Score: 137
Period size: 35 Copynumber: 3.3 Consensus size: 35
53 CTATTTATTT
* * *
63 TAAACTTTAAA-TTTGAAAATAAGTTTAAACTTAAAT
1 TAAA-TTTAAATTTTG-AAATAAATTTAAATTTAAAA
99 TAAATTTAAATTTTGAAATAAATTTAAATTTAAAA
1 TAAATTTAAATTTTGAAATAAATTTAAATTTAAAA
* ** *
134 TAAATTTAAATTTTTAAGCAAATTTAATTTTTAAAA
1 TAAATTTAAATTTTGAAATAAATTTAA-ATTTAAAA
170 TAAATTTAAA
1 TAAATTTAAA
180 GAGAGTATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 47 0.65
36 25 0.35
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (35 bp):
TAAATTTAAATTTTGAAATAAATTTAAATTTAAAA
Found at i:157 original size:53 final size:53
Alignment explanation
Indices: 63--179 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
53 CTATTTATTT
* ** *
63 TAAACTTTAAATTTGAAAATAAGTTTAAACTTAAATTAAATTTAAATTTTGAAA
1 TAAA-TTTAAATTTGAAAATAAATTTAAACTTAAAGCAAATTTAAATTTTAAAA
* * *
117 TAAATTTAAATTT-AAAATAAATTTAAATTTTTAAGCAAATTTAATTTTTAAAA
1 TAAATTTAAATTTGAAAATAAATTTAAA-CTTAAAGCAAATTTAAATTTTAAAA
170 TAAATTTAAA
1 TAAATTTAAA
180 GAGAGTATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
52 13 0.24
53 38 0.69
54 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (53 bp):
TAAATTTAAATTTGAAAATAAATTTAAACTTAAAGCAAATTTAAATTTTAAAA
Found at i:158 original size:18 final size:18
Alignment explanation
Indices: 63--179 Score: 107
Period size: 18 Copynumber: 6.6 Consensus size: 18
53 CTATTTATTT
**
63 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTTAAA
* *
82 TAAGTTTAAA--CTTAAA
1 TAAATTTAAATTTTTAAA
*
98 TTAAATTTAAATTTTGAAA
1 -TAAATTTAAATTTTTAAA
*
117 TAAATTTAAA-TTTAAAA
1 TAAATTTAAATTTTTAAA
*
134 TAAATTTAAATTTTTAAG
1 TAAATTTAAATTTTTAAA
*
152 CAAATTT-AATTTTTAAAA
1 TAAATTTAAATTTTT-AAA
170 TAAATTTAAA
1 TAAATTTAAA
180 GAGAGTATGA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.04
17 32 0.41
18 35 0.44
19 9 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TAAATTTAAATTTTTAAA
Found at i:1166 original size:88 final size:88
Alignment explanation
Indices: 1012--1185 Score: 199
Period size: 88 Copynumber: 2.0 Consensus size: 88
1002 TCGCAAAAGA
* * * * *
1012 GAGATCGCGTGCTCTGCGGGCAACCCAAAGTGAAACACGTGTCTAGAAGACTTGAAGCCCGTTCA
1 GAGACCGCGTGCTCTGCAGGCAACCCAAAGTGAAACACGTGTCCAGAAGACCTGAAGCCCGCTCA
* *
1077 AAATATCAATCCCAAGAACAGAG
66 AAAAATCAATCCCAAAAACAGAG
* * * **
1100 GAGACCGCGTGCAT-TGCAGGCAATCCAGAGTGAAACACGTGTCCA-ATAGGCCTGAAGCTTGCT
1 GAGACCGCGTGC-TCTGCAGGCAACCCAAAGTGAAACACGTGTCCAGA-AGACCTGAAGCCCGCT
*
1163 CAAAAAATCAATCCTAAAAACAG
64 CAAAAAATCAATCCCAAAAACAG
1186 TGAGATCAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
87 1 0.01
88 69 0.97
89 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (88 bp):
GAGACCGCGTGCTCTGCAGGCAACCCAAAGTGAAACACGTGTCCAGAAGACCTGAAGCCCGCTCA
AAAAATCAATCCCAAAAACAGAG
Found at i:2048 original size:29 final size:30
Alignment explanation
Indices: 2016--2074 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
2006 TATGGTTTAA
2016 TGTGTAATTATATACATG-AACTTTGATTT
1 TGTGTAATTATATACATGAAACTTTGATTT
* *
2045 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTATATACATGAAACTTTGATTT
2075 AATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTGTAATTATATACATGAAACTTTGATTT
Found at i:4385 original size:25 final size:24
Alignment explanation
Indices: 4343--4389 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
4333 TAAAGGAAGA
4343 AGAAATAATAATAAAAAAATAATG
1 AGAAATAATAATAAAAAAATAATG
**
4367 AGAAATAAATAATCTAAAAATAA
1 AGAAAT-AATAATAAAAAAATAA
4390 AATAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (24 bp):
AGAAATAATAATAAAAAAATAATG
Found at i:5117 original size:4 final size:4
Alignment explanation
Indices: 5104--5149 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
5094 AACGGGCACC
* *
5104 AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAGG AGAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5150 TTAGTAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5823 original size:4 final size:4
Alignment explanation
Indices: 5814--5882 Score: 68
Period size: 4 Copynumber: 17.0 Consensus size: 4
5804 AAAGAAACGG
* * * *
5814 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAT GAAT GAAT GAGAG GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
*
5864 GAAA G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA
5883 TGTAATGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 3 0.05
4 47 0.82
5 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:5845 original size:25 final size:27
Alignment explanation
Indices: 5814--5882 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 27
5804 AAAGAAACGG
*
5814 GAAAGAAAGAAAGAAAAGAAAGAAAGAAA
1 GAAAGAAAGAAAG-AAAG-AGGAAAGAAA
* * *
5843 GAATGAATGAATG--AGAGGAAAGAAA
1 GAAAGAAAGAAAGAAAGAGGAAAGAAA
*
5868 G-AAGAAGGAAAGAAA
1 GAAAGAAAGAAAGAAA
5883 TGTAATGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
24 8 0.26
25 10 0.32
26 3 0.10
29 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (27 bp):
GAAAGAAAGAAAGAAAGAGGAAAGAAA
Found at i:5884 original size:29 final size:30
Alignment explanation
Indices: 5818--5884 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
5808 AAACGGGAAA
*
5818 GAAAGAAA-GAAAAGAAAGAAAGAAAGAAT
1 GAAAGAAATGAAAAGAAAGAAAGAAAGAAG
* * *
5847 GAATG-AATGAGAGGAAAGAAAG-AAGAAG
1 GAAAGAAATGAAAAGAAAGAAAGAAAGAAG
5875 GAAAGAAATG
1 GAAAGAAATG
5885 TAATGTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (30 bp):
GAAAGAAATGAAAAGAAAGAAAGAAAGAAG
Found at i:6365 original size:24 final size:24
Alignment explanation
Indices: 6338--6398 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
6328 GTACAAAATA
*
6338 AAGATCCAACTCCATTAGAAAAAG
1 AAGATTCAACTCCATTAGAAAAAG
*
6362 AAGATTCAACTCCATTAGAAAATG
1 AAGATTCAACTCCATTAGAAAAAG
6386 AAGATTCAACTCC
1 AAGATTCAACTCC
6399 GTGTATGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (24 bp):
AAGATTCAACTCCATTAGAAAAAG
Found at i:10591 original size:47 final size:47
Alignment explanation
Indices: 10539--10628 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
10529 AATACATAAG
*
10539 TTTACCAATATAATACAAAA-ATAATAATTAAATACCAAAATGGGTTA
1 TTTACCAAAATAATACAAAATAT-ATAATTAAATACCAAAATGGGTTA
** * *
10586 TTTACCAAAATGGTACAAAATATATATTTATATACCAAAATGG
1 TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGG
10629 TAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 35 0.95
48 2 0.05
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (47 bp):
TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGGGTTA
Done.