Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008366.1 Kokia drynarioides strain JFW-HI SEQ_123033, 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: 18341
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:3206 original size:13 final size:13
Alignment explanation
Indices: 3188--3212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3178 CAAAAAGGAT
3188 ACAAAGGGTAGCA
1 ACAAAGGGTAGCA
3201 ACAAAGGGTAGC
1 ACAAAGGGTAGC
3213 TATGCCTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (13 bp):
ACAAAGGGTAGCA
Found at i:5361 original size:13 final size:13
Alignment explanation
Indices: 5345--5369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5335 TATAAAAAAA
5345 ATTTATTTATTTT
1 ATTTATTTATTTT
5358 ATTTATTTATTT
1 ATTTATTTATTT
5370 AAAAATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:5536 original size:9 final size:8
Alignment explanation
Indices: 5508--5539 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5498 AATTAATTAA
5508 ATTTTTAT
1 ATTTTTAT
5516 ATTTTTAT
1 ATTTTTAT
5524 ATTTTTAT
1 ATTTTTAT
*
5532 AATTTTAT
1 ATTTTTAT
5540 GCTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:9032 original size:133 final size:133
Alignment explanation
Indices: 8794--9043 Score: 367
Period size: 133 Copynumber: 1.9 Consensus size: 133
8784 ATGAATTCGA
*
8794 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTTAAGCT
1 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
* * *
8859 AGTGTTAGCAACCCTAATCTGAAGCCAGTGTTAGTAGCCCGA-ATATGTCAACTTGTATAAACAA
66 AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATA-ATGTCAACTTGTATAAACAA
8923 ACGG
130 ACGG
* * * * * *
8927 GTGTTGTGATCAGGGATTAATTCGATGGCTTGAGATTCAATATATGTTGTGGATTCTCTGAAGCT
1 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
* * *
8992 AATGTTAGCAATCCTGATCCGAAGCTAGTGTTAGCAGCCCGATAATGTCAAC
66 AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATAATGTCAAC
9044 ATATGTAATC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
133 102 0.99
134 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (133 bp):
GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATAATGTCAACTTGTATAAACAAA
CGG
Found at i:11038 original size:82 final size:82
Alignment explanation
Indices: 10932--11098 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 82
10922 CCATCCCCGC
* *
10932 CCCGTGATTCGCAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
1 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
10997 ATCCCCGCTATATTCGT
66 ATCCCCGCTATATTCGT
11014 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
1 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
11079 ATCCCCGCTATATTCGT
66 ATCCCCGCTATATTCGT
11096 CCC
1 CCC
11099 ACGACCCACT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.27, C:0.44, G:0.11, T:0.17
Consensus pattern (82 bp):
CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
ATCCCCGCTATATTCGT
Found at i:12388 original size:18 final size:18
Alignment explanation
Indices: 12367--12410 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12357 TTAATTAAAA
*
12367 AATAAATAAATATAATAC-
1 AATAAA-AAACATAATACT
*
12385 AATAAAAAGCATAATACT
1 AATAAAAAACATAATACT
12403 AATAAAAA
1 AATAAAAA
12411 TAAAGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAAAAACATAATACT
Found at i:14911 original size:33 final size:34
Alignment explanation
Indices: 14827--14911 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
14817 TGTAAACACA
*
14827 GTATGGTCATAAGAGCT-ATCAAATCAAAACTCT
1 GTATGCTCATAAGAGCTAATCAAATCAAAACTCT
* *
14860 GTATGCTCATAAGAGCTAATC-AATCCATA-TACT
1 GTATGCTCATAAGAGCTAATCAAATCAAAACT-CT
14893 GTATGCTCATAAGAGCTAA
1 GTATGCTCATAAGAGCTAA
14912 CCAACCAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 43 0.91
34 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (34 bp):
GTATGCTCATAAGAGCTAATCAAATCAAAACTCT
Done.