Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008447.1 Kokia drynarioides strain JFW-HI SEQ_123119, 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: 62926
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 159 characters in sequence are not A, C, G, or T
Found at i:17816 original size:5 final size:5
Alignment explanation
Indices: 17808--17842 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
17798 AAAAAAATGG
17808 GAAAA GAAAA GAAAA GAAAA GAAAAA GAAAGA GAA
1 GAAAA GAAAA GAAAA GAAAA G-AAAA GAAA-A GAA
17843 CGAGATGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 19 0.68
6 9 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:17826 original size:15 final size:17
Alignment explanation
Indices: 17808--17842 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17798 AAAAAAATGG
17808 GAAAAG-AAAAGAAA-A
1 GAAAAGAAAAAGAAAGA
17823 GAAAAGAAAAAGAAAGA
1 GAAAAGAAAAAGAAAGA
17840 GAA
1 GAA
17843 CGAGATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAGAAAGA
Found at i:18073 original size:4 final size:4
Alignment explanation
Indices: 18064--18097 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
18054 AGTATTTGAT
18064 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AG
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AG
18098 GTAGGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:19513 original size:27 final size:27
Alignment explanation
Indices: 19471--19526 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
19461 TGCCGCCTAT
*
19471 GCCGTGAAAGACTTGGAAAAGAAAGCA
1 GCCGTGAAAGAATTGGAAAAGAAAGCA
*
19498 GCCGTGAAAGAATTGGAAGAGAAAGCA
1 GCCGTGAAAGAATTGGAAAAGAAAGCA
19525 GC
1 GC
19527 GATAGTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.14, G:0.32, T:0.11
Consensus pattern (27 bp):
GCCGTGAAAGAATTGGAAAAGAAAGCA
Found at i:29087 original size:14 final size:15
Alignment explanation
Indices: 29055--29087 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29045 TTAAACACAT
29055 TTAAAAATTAAAAAA
1 TTAAAAATTAAAAAA
29070 -TAAAAA-TAAAAAA
1 TTAAAAATTAAAAAA
29083 TTAAA
1 TTAAA
29088 GTGTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TTAAAAATTAAAAAA
Found at i:30343 original size:18 final size:18
Alignment explanation
Indices: 30320--30391 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
30310 CATATGTGTC
30320 TATTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
*
30338 TATTGAAGATGCAAATGA
1 TATTGAAGATACAAATGA
30356 TATTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
30374 TATTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
30392 AACACAAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (18 bp):
TATTGAAGATACAAATGA
Found at i:43448 original size:3 final size:3
Alignment explanation
Indices: 43440--43465 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43430 AGGGTGAAAT
43440 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
43466 AACAAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:48970 original size:29 final size:30
Alignment explanation
Indices: 48937--49006 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
48927 AAATCAAAAT
48937 TTCATGTATAAAATTACACA-AAACCAAAC
1 TTCATGTATAAAATTACACATAAACCAAAC
* * * *
48966 TTCATGTATATAATTGCACATTAAACCATAG
1 TTCATGTATAAAATTACACA-TAAACCAAAC
48997 TTCATGTATA
1 TTCATGTATA
49007 GTCTTGAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TTCATGTATAAAATTACACATAAACCAAAC
Found at i:53436 original size:55 final size:55
Alignment explanation
Indices: 53352--53492 Score: 192
Period size: 55 Copynumber: 2.6 Consensus size: 55
53342 ATAGATAGAC
* * *
53352 AGAGCGTTAAGAATATGAACTATCATCAGTTTTGCTCTAAAGCTGAACCAAAAGT
1 AGAGCATTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGT
*
53407 AGAGCATTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
1 AGAGCATTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGT
* ** * * *
53462 AAAGCAAGACGACAATGAAATAACATCAGTT
1 AGAGCATTAAGACTATGAACTAACATCAGTT
53493 CAGCTCCAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 76 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (55 bp):
AGAGCATTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGT
Found at i:60783 original size:9 final size:8
Alignment explanation
Indices: 60758--60782 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
60748 AATTATAAAA
60758 TAATTTTT
1 TAATTTTT
60766 TAATTTTT
1 TAATTTTT
60774 TAATTTTT
1 TAATTTTT
60782 T
1 T
60783 TCACCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TAATTTTT
Done.