Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006473.1 Kokia drynarioides strain JFW-HI SEQ_121056, 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: 52668
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:6767 original size:2 final size:2
Alignment explanation
Indices: 6760--6801 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6750 CCCTACAGCC
6760 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT
6802 CCATATACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9638 original size:2 final size:2
Alignment explanation
Indices: 9631--9663 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9621 CCACCGTGAG
9631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9664 CTTATTCGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12928 original size:22 final size:23
Alignment explanation
Indices: 12896--12938 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12886 ATAATGACAG
*
12896 CAAAACAGTGGTAA-AACAATAC
1 CAAAACAGTGGAAACAACAATAC
*
12918 CAAAACGGTGGAAACAACAAT
1 CAAAACAGTGGAAACAACAAT
12939 TTTTTTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.12
Consensus pattern (23 bp):
CAAAACAGTGGAAACAACAATAC
Found at i:19652 original size:21 final size:21
Alignment explanation
Indices: 19626--19667 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19616 ATAGATGTCT
*
19626 CAGTTTTCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCTA
*
19647 CAGTTTGCTTTTGAGAATCTA
1 CAGTTTGCTTTTGAAAATCTA
19668 TAGATTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCTA
Found at i:28773 original size:4 final size:4
Alignment explanation
Indices: 28764--28824 Score: 51
Period size: 4 Copynumber: 16.2 Consensus size: 4
28754 AAATAATAAT
* * *
28764 AATA AATA AATA AA-A AATA AA-A AATG AA-A ATTA AATA GAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
28808 AAT- AATA AATGA AATA A
1 AATA AATA AAT-A AATA A
28825 TAATAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
3 12 0.27
4 29 0.64
5 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:28781 original size:7 final size:7
Alignment explanation
Indices: 28753--28840 Score: 59
Period size: 7 Copynumber: 11.6 Consensus size: 7
28743 GGAAGATTGG
28753 AAAATAA
1 AAAATAA
28760 TAATAATAA
1 -AA-AATAA
28769 ATAAATAA
1 A-AAATAA
28777 AAAATAA
1 AAAATAA
*
28784 AAAATGA
1 AAAATAA
*
28791 AAATTAA
1 AAAATAA
*
28798 ATAGATAA
1 A-AAATAA
*
28806 TAAATAA
1 AAAATAA
*
28813 TAAATGAA
1 AAAAT-AA
*
28821 ATAATAA
1 AAAATAA
28828 TAAAATAA
1 -AAAATAA
28836 CAAAA
1 -AAAA
28841 AGAGAAAAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
7 30 0.47
8 28 0.44
9 6 0.09
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (7 bp):
AAAATAA
Found at i:28829 original size:29 final size:30
Alignment explanation
Indices: 28761--28840 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
28751 GGAAAATAAT
28761 AATAATAAATAAATAAAAAATAAAAAATGA
1 AATAATAAATAAATAAAAAATAAAAAATGA
* * * *
28791 AA-ATTAAATAGATAATAAATAATAAATGA
1 AATAATAAATAAATAAAAAATAAAAAATGA
28820 AATAAT-AATAAAATAACAAAA
1 AATAATAAAT-AAATAA-AAAA
28841 AGAGAAAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 28 0.70
30 9 0.22
31 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (30 bp):
AATAATAAATAAATAAAAAATAAAAAATGA
Found at i:28835 original size:11 final size:11
Alignment explanation
Indices: 28753--28835 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
28743 GGAAGATTGG
28753 AAAATAATAAT
1 AAAATAATAAT
*
28764 AATA-AATAAAT
1 AAAATAAT-AAT
28775 AAAA-AATAA-
1 AAAATAATAAT
28784 AAAATGAA-AAT
1 AAAAT-AATAAT
*
28795 TAAATAGATAAT
1 AAAATA-ATAAT
28807 -AAATAATAAAT
1 AAAATAAT-AAT
*
28818 GAAATAATAAT
1 AAAATAATAAT
28829 AAAATAA
1 AAAATAA
28836 CAAAAAGAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
9 4 0.07
10 10 0.17
11 36 0.60
12 10 0.17
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:32098 original size:49 final size:49
Alignment explanation
Indices: 32041--32139 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
32031 CAGGGACTCT
*
32041 ATATTAATTTTTTAGTCTGATGAATAGATTGCTTTGAAAAACCATTATC
1 ATATTAATTTTTTAGTCAGATGAATAGATTGCTTTGAAAAACCATTATC
*
32090 ATATTAATTTTTTAGTCAGATGAATAGCTTGCTTTGAAAAACCATTATC
1 ATATTAATTTTTTAGTCAGATGAATAGATTGCTTTGAAAAACCATTATC
32139 A
1 A
32140 GTCTGGATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (49 bp):
ATATTAATTTTTTAGTCAGATGAATAGATTGCTTTGAAAAACCATTATC
Found at i:42107 original size:28 final size:29
Alignment explanation
Indices: 42060--42116 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
42050 ATGCCACCTA
*
42060 AAAATAATATAAATTATAAATTAT-AAAT
1 AAAATAATATAAATTATAAAATATCAAAT
42088 AAAATAA-ATAAAAGTT-TAAAATATCAAAT
1 AAAATAATAT-AAA-TTATAAAATATCAAAT
42117 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATAATATAAATTATAAAATATCAAAT
Found at i:45615 original size:12 final size:12
Alignment explanation
Indices: 45598--45640 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
45588 CAAATCTAGC
45598 AAATGTATGTGT
1 AAATGTATGTGT
*
45610 AAATGTA---GA
1 AAATGTATGTGT
45619 AAATGTATGTGT
1 AAATGTATGTGT
45631 AAATGTATGT
1 AAATGTATGT
45641 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.31
12 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (12 bp):
AAATGTATGTGT
Found at i:45635 original size:21 final size:21
Alignment explanation
Indices: 45589--45637 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
45579 AATAACTCAC
* *
45589 AAATCTAGCAAATGTATGTGT
1 AAATGTAGAAAATGTATGTGT
45610 AAATGTAGAAAATGTATGTGT
1 AAATGTAGAAAATGTATGTGT
45631 AAATGTA
1 AAATGTA
45638 TGTTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (21 bp):
AAATGTAGAAAATGTATGTGT
Found at i:45779 original size:21 final size:21
Alignment explanation
Indices: 45753--45828 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 21
45743 CACAGTACAT
45753 TAAATGTAGCAATTGTATGTG
1 TAAATGTAGCAATTGTATGTG
*
45774 TAAATGTATGTTTCATAATT-AATGTG
1 TAAATGTA-G---C--AATTGTATGTG
*
45800 TAAATGTAGCAACTGTATGTG
1 TAAATGTAGCAATTGTATGTG
45821 TAAATGTA
1 TAAATGTA
45829 TGTTTCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
20 3 0.07
21 21 0.47
22 2 0.04
25 2 0.04
26 13 0.29
27 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TAAATGTAGCAATTGTATGTG
Found at i:45783 original size:12 final size:12
Alignment explanation
Indices: 45766--45831 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
45756 ATGTAGCAAT
45766 TGTATGTGTAAA
1 TGTATGTGTAAA
*
45778 TGTATGTTTCATAA
1 TGTATGTGT-A-AA
45792 T-TAATGTGTAAA
1 TGT-ATGTGTAAA
* *
45804 TGTA---GCAAC
1 TGTATGTGTAAA
45813 TGTATGTGTAAA
1 TGTATGTGTAAA
45825 TGTATGT
1 TGTATGT
45832 TTCATAATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
9 7 0.17
12 22 0.54
13 4 0.10
14 8 0.20
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (12 bp):
TGTATGTGTAAA
Found at i:45798 original size:26 final size:26
Alignment explanation
Indices: 45766--45839 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
45756 ATGTAGCAAT
45766 TGTATGTGTAAATGTATGTTTCATAA
1 TGTATGTGTAAATGTATGTTTCATAA
*
45792 T-TAATGTGTAAATGTA-G---CA-AC
1 TGT-ATGTGTAAATGTATGTTTCATAA
45813 TGTATGTGTAAATGTATGTTTCATAA
1 TGTATGTGTAAATGTATGTTTCATAA
45839 T
1 T
45840 CAATATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
21 15 0.38
22 4 0.10
25 4 0.10
26 16 0.41
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (26 bp):
TGTATGTGTAAATGTATGTTTCATAA
Found at i:46643 original size:48 final size:48
Alignment explanation
Indices: 46587--46680 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
46577 GTTGGCAGTA
*
46587 AAGGTGGTGAGGGTTTAGATGCTAGCAATAAGGGTGGTGAGGGTGATG
1 AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGATG
* * * *
46635 AAGGTGGTGAGGGTTTGGAAGCTGGTAGTAAGGGTGGTGAGGGTGA
1 AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGA
46681 GGGAGATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.24
Consensus pattern (48 bp):
AAGGTGGTGAGGGTTTAGAAGCTAGCAATAAGGGTGGTGAGGGTGATG
Found at i:50708 original size:31 final size:32
Alignment explanation
Indices: 50673--50735 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
50663 TTCAACTCAT
50673 CGATTAAAC-AAACAGCAATATCGATTAAACA
1 CGATTAAACAAAACAGCAATATCGATTAAACA
*
50704 CGATTAAACAAAACAGTAATATCGATTAAACA
1 CGATTAAACAAAACAGCAATATCGATTAAACA
50736 AAATATCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (32 bp):
CGATTAAACAAAACAGCAATATCGATTAAACA
Found at i:50732 original size:22 final size:22
Alignment explanation
Indices: 50700--50757 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
50690 ATATCGATTA
50700 AACA-CGATTAAACAAAACAGT-
1 AACATCGATTAAACAAAACA-TC
* *
50721 AATATCGATTAAACAAAATATC
1 AACATCGATTAAACAAAACATC
50743 AACATCGATTAAACA
1 AACATCGATTAAACA
50758 TGATTAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (22 bp):
AACATCGATTAAACAAAACATC
Done.