Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012736.1 Kokia drynarioides strain JFW-HI SEQ_127747, 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: 29260
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6710 original size:28 final size:28
Alignment explanation
Indices: 6667--6722 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
6657 AACTCATGTT
* * *
6667 GTAACAGTCCAGTTTTTCAGTGGTGTCG
1 GTAACAGCCCAATTTTTCAATGGTGTCG
6695 GTAACAGCCCAATTTTTCAATGGTGTCG
1 GTAACAGCCCAATTTTTCAATGGTGTCG
6723 AAAACAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (28 bp):
GTAACAGCCCAATTTTTCAATGGTGTCG
Found at i:6728 original size:28 final size:28
Alignment explanation
Indices: 6669--6729 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
6659 CTCATGTTGT
* * * **
6669 AACAGTCCAGTTTTTCAGTGGTGTCGGT
1 AACAGCCCAATTTTTCAATGGTGTCGAA
6697 AACAGCCCAATTTTTCAATGGTGTCGAA
1 AACAGCCCAATTTTTCAATGGTGTCGAA
6725 AACAG
1 AACAG
6730 TGATTTTGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (28 bp):
AACAGCCCAATTTTTCAATGGTGTCGAA
Found at i:7571 original size:35 final size:35
Alignment explanation
Indices: 7492--7575 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
7482 AAGTGGTTTT
*
7492 TGATGAAATTAGGGTTTAAAGATTAAAATGCTAAA
1 TGATGAAATTAGGGTTTAAAGACTAAAATGCTAAA
* *
7527 TGGTAAAATTAGGGTTTAAAGACTAAAATGCTAAA
1 TGATGAAATTAGGGTTTAAAGACTAAAATGCTAAA
7562 TGATGAAATT-GGGT
1 TGATGAAATTAGGGT
7576 GTACTTTAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 4 0.09
35 40 0.91
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.31
Consensus pattern (35 bp):
TGATGAAATTAGGGTTTAAAGACTAAAATGCTAAA
Found at i:8326 original size:24 final size:24
Alignment explanation
Indices: 8290--8344 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
8280 ATATACTAGT
*
8290 TAACTATTCTGGGCTC-ATAAGAGC
1 TAACCATTCTGGGCTCGA-AAGAGC
*
8314 TAACCATTTTGGGCTCGAAAGAGC
1 TAACCATTCTGGGCTCGAAAGAGC
8338 TAACCAT
1 TAACCAT
8345 CATGGGTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGAAAGAGC
Found at i:8350 original size:24 final size:24
Alignment explanation
Indices: 8299--8364 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
8289 TTAACTATTC
**
8299 TGGGCTC-ATAAGAGCTAACCATTT
1 TGGGCTCGA-AAGAGCTAACCATCA
8323 TGGGCTCGAAAGAGCTAACCATCA
1 TGGGCTCGAAAGAGCTAACCATCA
* **
8347 TGGGTTCGTGAGAGCTAA
1 TGGGCTCGAAAGAGCTAA
8365 TGTTTTCTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (24 bp):
TGGGCTCGAAAGAGCTAACCATCA
Found at i:8911 original size:21 final size:21
Alignment explanation
Indices: 8882--8921 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8872 TTGAATTTTG
*
8882 CATACTTGTTTCGATAGAACC
1 CATACTTGTATCGATAGAACC
* *
8903 CATAGTTGTATCGGTAGAA
1 CATACTTGTATCGATAGAA
8922 GTACAGGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
CATACTTGTATCGATAGAACC
Found at i:11425 original size:30 final size:29
Alignment explanation
Indices: 11384--11444 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
11374 ACCTCAATTT
*
11384 CATATCGAGGAGCTGCTGGTAACGCCACCA
1 CATATCCAGGAGCTGCTGGTAAC-CCACCA
*
11414 CATATCCAGGAGCTGCTTGTAACCCACCA
1 CATATCCAGGAGCTGCTGGTAACCCACCA
11443 CA
1 CA
11445 AGATTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (29 bp):
CATATCCAGGAGCTGCTGGTAACCCACCA
Found at i:16831 original size:6 final size:6
Alignment explanation
Indices: 16820--16846 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16810 GGAAGAAATT
16820 GATTAG GATTAG GATTAG GATTAG GAT
1 GATTAG GATTAG GATTAG GATTAG GAT
16847 CAGTTGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GATTAG
Found at i:27605 original size:15 final size:16
Alignment explanation
Indices: 27582--27614 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27572 CGAAATTAAA
27582 TTATAATTTTAATAAT
1 TTATAATTTTAATAAT
*
27598 TTAT-ATTTTTATAAT
1 TTATAATTTTAATAAT
27613 TT
1 TT
27615 TTAAAGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAATTTTAATAAT
Found at i:27668 original size:30 final size:30
Alignment explanation
Indices: 27602--27668 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
27592 AATAATTTAT
** *
27602 ATTTTTATAATTTTTAAAGGATTAAACTAA
1 ATTTTTATAATTTTTAAAGGAGCAAAATAA
* * * *
27632 AATTTTATCATTTTTAAGGGAGCAAAATAC
1 ATTTTTATAATTTTTAAAGGAGCAAAATAA
27662 ATTTTTA
1 ATTTTTA
27669 CTTTTACTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAGGAGCAAAATAA
Done.