Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005327.1 Kokia drynarioides strain JFW-HI SEQ_119276, 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: 51294
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1003 original size:26 final size:25
Alignment explanation
Indices: 945--1013 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
935 ATTTCATATG
*
945 CTTATTTTTATTTTAATTTAACTCGAA
1 CTTA-TTTTATTTT-ATTCAACTCGAA
*
972 C-AATTTTATTTTATTCAACTCGAAA
1 CTTATTTTATTTTATTCAACTCG-AA
*
997 CTTATTTTATTTGATTC
1 CTTATTTTATTTTATTC
1014 GATTTGAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.25
25 12 0.33
26 14 0.39
27 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (25 bp):
CTTATTTTATTTTATTCAACTCGAA
Found at i:11965 original size:25 final size:23
Alignment explanation
Indices: 11937--11990 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
11927 TATTTTAGAG
11937 TTTTAAAT-TTAATTTGAAAAATGAA
1 TTTTAAATATT-ATTTGAAAAA--AA
* *
11962 TTTTGAATATTATTTGATAAAAA
1 TTTTAAATATTATTTGAAAAAAA
11985 TTTTAA
1 TTTTAA
11991 CGTTTTCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
25 16 0.64
26 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTTAAATATTATTTGAAAAAAA
Found at i:18854 original size:29 final size:29
Alignment explanation
Indices: 18821--18878 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
18811 ATTTTTTTTT
18821 GTCATCCAACTATAAAAATTTATAAAATG
1 GTCATCCAACTATAAAAATTTATAAAATG
*
18850 GTCATCCAACTATAAAAATTTATAGAATG
1 GTCATCCAACTATAAAAATTTATAAAATG
18879 ATTGTCCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (29 bp):
GTCATCCAACTATAAAAATTTATAAAATG
Found at i:18886 original size:29 final size:29
Alignment explanation
Indices: 18822--18890 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
18812 TTTTTTTTTG
*
18822 TCATCCAACTATAAAAATTTATAAAATGG
1 TCATCCAACTATAAAAATTTATAAAATGA
*
18851 TCATCCAACTATAAAAATTTATAGAATGA
1 TCATCCAACTATAAAAATTTATAAAATGA
**
18880 TTGTCCAACTA
1 TCATCCAACTA
18891 CTTAATTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (29 bp):
TCATCCAACTATAAAAATTTATAAAATGA
Found at i:19402 original size:55 final size:58
Alignment explanation
Indices: 19343--19451 Score: 136
Period size: 55 Copynumber: 1.9 Consensus size: 58
19333 AGTTGGGTAG
* *
19343 TCATTTTTTAACTT-TTTATAATTGGGTGA-C-AAAAAAATT-ACTAATAGTTAAAAGA
1 TCATTTTGTAA-TTCTTTATAATTGGATGACCAAAAAAAATTCACTAATAGTTAAAAGA
*
19398 TCATTTTGTAATTCTTTATAGTTGGATGACCAATAAAAAAATTCACTAATAGTT
1 TCATTTTGTAATTCTTTATAATTGGATGACC-A-AAAAAAATTCACTAATAGTT
19452 GGGTGACTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
54 2 0.04
55 23 0.51
56 1 0.02
59 9 0.20
60 10 0.22
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (58 bp):
TCATTTTGTAATTCTTTATAATTGGATGACCAAAAAAAATTCACTAATAGTTAAAAGA
Found at i:29678 original size:24 final size:24
Alignment explanation
Indices: 29644--29692 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29634 TTTCACGAAC
* * *
29644 AAGCTCGTTTATTGACTTGTTTAT
1 AAGCTCATTTATTAACTCGTTTAT
29668 AAGCTCATTTATTAACTCGTTTAT
1 AAGCTCATTTATTAACTCGTTTAT
29692 A
1 A
29693 GCTTGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (24 bp):
AAGCTCATTTATTAACTCGTTTAT
Found at i:29854 original size:23 final size:23
Alignment explanation
Indices: 29795--29871 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
29785 ATTAACATTA
* * *
29795 TTCGTGAACGTGTTCAATTATATG
1 TTCGTGATCATGTTCGATTA-ATG
* * *
29819 TTCATGAAT-ATGTTCGTTTATTG
1 TTCGTG-ATCATGTTCGATTAATG
29842 TTCGTGATCATGTTCGATTAATG
1 TTCGTGATCATGTTCGATTAATG
29865 TTCGTGA
1 TTCGTGA
29872 ACATTAAACA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.05
23 26 0.62
24 13 0.31
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (23 bp):
TTCGTGATCATGTTCGATTAATG
Found at i:38763 original size:37 final size:37
Alignment explanation
Indices: 38694--38764 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
38684 AAATGCATAA
* *** **
38694 ATCTAATAGTTACAGTTTTTTTTTTTTTTTTGAATGG
1 ATCTAATAGTTACAGTTTTATCACTTAGTTTGAATGG
38731 ATCTAATAGTTACAGTTTTATCACTTAGTTTGAA
1 ATCTAATAGTTACAGTTTTATCACTTAGTTTGAA
38765 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (37 bp):
ATCTAATAGTTACAGTTTTATCACTTAGTTTGAATGG
Found at i:46896 original size:2 final size:2
Alignment explanation
Indices: 46889--46920 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
46879 CAAAATTTTA
*
46889 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46921 CCAAAAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.