Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013369.1 Kokia drynarioides strain JFW-HI SEQ_128392, 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: 51467
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3936 original size:20 final size:20
Alignment explanation
Indices: 3911--3954 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3901 CATAAGATTT
3911 AAAAGA-AACAAGTAAAAGTA
1 AAAAGATAA-AAGTAAAAGTA
*
3931 AAAAGATAAAAGTAAATGTA
1 AAAAGATAAAAGTAAAAGTA
3951 AAAA
1 AAAA
3955 TGCATTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAGATAAAAGTAAAAGTA
Found at i:3942 original size:14 final size:14
Alignment explanation
Indices: 3910--3946 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3900 GCATAAGATT
3910 TAAAAG-AAACAAG
1 TAAAAGTAAACAAG
3923 TAAAAGTAAA-AAG
1 TAAAAGTAAACAAG
3936 ATAAAAGTAAA
1 -TAAAAGTAAA
3947 TGTAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.70, C:0.03, G:0.14, T:0.14
Consensus pattern (14 bp):
TAAAAGTAAACAAG
Found at i:7722 original size:18 final size:18
Alignment explanation
Indices: 7699--7737 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
7689 CTAATAATCC
7699 TTATCATGGTCTTTCTCT
1 TTATCATGGTCTTTCTCT
7717 TTATCATGGTCTTTCTCT
1 TTATCATGGTCTTTCTCT
7735 TTA
1 TTA
7738 AATCTATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.10, T:0.56
Consensus pattern (18 bp):
TTATCATGGTCTTTCTCT
Found at i:12886 original size:19 final size:19
Alignment explanation
Indices: 12845--12899 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
12835 ATTTTATCAT
* *
12845 AAAAATCATTAGAAAGTAA
1 AAAAATCATAAAAAAGTAA
*
12864 AAAAATCATAAAAAATTACAA
1 AAAAATCATAAAAAAGT--AA
12885 AAAAACTCATAAAAA
1 AAAAA-TCATAAAAA
12900 TATAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.47
21 7 0.23
22 9 0.30
ACGTcount: A:0.69, C:0.09, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAAATCATAAAAAAGTAA
Found at i:12916 original size:28 final size:28
Alignment explanation
Indices: 12885--12963 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 28
12875 AAAATTACAA
12885 AAAAACTCATAAAAATATAAAAATTATT
1 AAAAACTCATAAAAATATAAAAATTATT
*** *
12913 -AAAACTCAATATTCATAT-AAACTTATT
1 AAAAACTC-ATAAAAATATAAAAATTATT
*
12940 AAAAA-TTATAAATAATAATAAAAA
1 AAAAACTCATAAA-AAT-ATAAAAA
12964 CTTAAACTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 9
0.67 0.16 0.16
Matches are distributed among these distances:
26 3 0.08
27 18 0.49
28 13 0.35
29 3 0.08
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAACTCATAAAAATATAAAAATTATT
Found at i:13700 original size:10 final size:10
Alignment explanation
Indices: 13682--13921 Score: 53
Period size: 10 Copynumber: 24.8 Consensus size: 10
13672 CTAATAAATG
*
13682 ATTTATTATA
1 ATTTTTTATA
13692 ATTTTTTAT-
1 ATTTTTTATA
*
13701 ATTTGTTAT-
1 ATTTTTTATA
13710 A--TTTTATA
1 ATTTTTTATA
*
13718 ATTTAATTAAATA
1 ATTT--TT-TATA
13731 ATATTTTTATA
1 AT-TTTTTATA
* *
13742 ATTTATTAGA
1 ATTTTTTATA
* * *
13752 ACTTATTA-G
1 ATTTTTTATA
*
13761 ATTTATTATA
1 ATTTTTTATA
*
13771 A-TATTTATTA
1 ATTTTTTA-TA
* *
13781 AGTTTTTATG
1 ATTTTTTATA
*
13791 ACTTTTTATA
1 ATTTTTTATA
*
13801 ATTTATTATA
1 ATTTTTTATA
*
13811 A---TTAATA
1 ATTTTTTATA
* *
13818 A-ATTTTATC
1 ATTTTTTATA
13827 ATTTTTTAATA
1 ATTTTTT-ATA
13838 A-TTTTTATA
1 ATTTTTTATA
* *
13847 AGTTTATATCA
1 ATTTTTTAT-A
13858 A---TTT-TA
1 ATTTTTTATA
*
13864 ATTTTTAATA
1 ATTTTTTATA
*
13874 ATTTTGTA-A
1 ATTTTTTATA
* *
13883 ATTTTTATGTT
1 ATTTTT-TATA
* *
13894 TTTTTTTTTA
1 ATTTTTTATA
* *
13904 ATTTTTAATG
1 ATTTTTTATA
13914 ATTTTTTA
1 ATTTTTTA
13922 AGAAAATATA
Statistics
Matches: 167, Mismatches: 41, Indels: 44
0.66 0.16 0.17
Matches are distributed among these distances:
6 2 0.01
7 11 0.07
8 3 0.02
9 37 0.22
10 83 0.50
11 20 0.12
12 4 0.02
13 5 0.03
14 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:13833 original size:36 final size:36
Alignment explanation
Indices: 13784--13878 Score: 97
Period size: 36 Copynumber: 2.6 Consensus size: 36
13774 TTTATTAAGT
*
13784 TTTTATGACTTTTTATAATTTATTATAA-TTA-ATAAA
1 TTTTAT-ATTTTTTATAATTT-TTATAAGTTATATAAA
*
13820 TTTTATCATTTTTTAATAATTTTTATAAGTTTATATCAA
1 TTTTAT-ATTTTTT-ATAATTTTTATAAG-TTATATAAA
*
13859 TTTTA-ATTTTTAATAATTTT
1 TTTTATATTTTTTATAATTTT
13879 GTAAATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 26 0.51
37 13 0.25
38 3 0.06
39 9 0.18
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (36 bp):
TTTTATATTTTTTATAATTTTTATAAGTTATATAAA
Found at i:13909 original size:22 final size:22
Alignment explanation
Indices: 13875--13920 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
13865 TTTTTAATAA
* *
13875 TTTTGTAAATTTTTATGTTTTT
1 TTTTGTAAATTTTAATGATTTT
* *
13897 TTTTTTAATTTTTAATGATTTT
1 TTTTGTAAATTTTAATGATTTT
13919 TT
1 TT
13921 AAGAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (22 bp):
TTTTGTAAATTTTAATGATTTT
Found at i:13989 original size:11 final size:10
Alignment explanation
Indices: 13973--14011 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
13963 TTTTACTTGT
13973 ATAATACAAAA
1 ATAATA-AAAA
13984 ATAATAAAAA
1 ATAATAAAAA
*
13994 ATTATAAAAA
1 ATAATAAAAA
14004 TATAATAA
1 -ATAATAA
14012 TTTTTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 13 0.52
11 12 0.48
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:22317 original size:13 final size:13
Alignment explanation
Indices: 22299--22323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22289 GCTGCTACTT
22299 TGAATTTCAGCAC
1 TGAATTTCAGCAC
22312 TGAATTTCAGCA
1 TGAATTTCAGCA
22324 ATTCATGTAA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGAATTTCAGCAC
Found at i:33040 original size:22 final size:23
Alignment explanation
Indices: 32992--33050 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
32982 TTATAAGCTG
*
32992 CATGTCTAGAGACA-TTAGCTAG
1 CATGTCTAGAGACATTTAGCTAA
* *
33014 TATGTCTAGAGACATTTGGC-AA
1 CATGTCTAGAGACATTTAGCTAA
*
33036 CATGTCTCGAGACAT
1 CATGTCTAGAGACAT
33051 AACCTACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (23 bp):
CATGTCTAGAGACATTTAGCTAA
Found at i:34477 original size:23 final size:23
Alignment explanation
Indices: 34451--34508 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
34441 TTTACACATT
*
34451 AATCATATTAACTATTAAGCATA
1 AATCACATTAACTATTAAGCATA
* *
34474 AATCACATTAACTTTTAAGCGTA
1 AATCACATTAACTATTAAGCATA
*
34497 AATTACATTAAC
1 AATCACATTAAC
34509 ACATATAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (23 bp):
AATCACATTAACTATTAAGCATA
Found at i:34537 original size:25 final size:25
Alignment explanation
Indices: 34518--34617 Score: 141
Period size: 25 Copynumber: 4.1 Consensus size: 25
34508 CACATATAAG
*
34518 CATATAAGTATATATTACATTAACA
1 CATATAAGTATATATCACATTAACA
* *
34543 C--ATAAGCATATACCACATTAACA
1 CATATAAGTATATATCACATTAACA
**
34566 CATATGGGTATATATCACATTAACA
1 CATATAAGTATATATCACATTAACA
34591 CATATAAGTATATATCACATTAACA
1 CATATAAGTATATATCACATTAACA
34616 CA
1 CA
34618 CAATTGAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
23 20 0.31
25 44 0.69
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (25 bp):
CATATAAGTATATATCACATTAACA
Found at i:37797 original size:29 final size:29
Alignment explanation
Indices: 37755--37827 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
37745 TACAAAACTC
*
37755 AACTCATCTCGTCAAAATTATTTCTTT-AG
1 AACTCATCTCGTCAAAATCATTT-TTTCAG
*
37784 AACTCATCTTGTCAAAATCATTTTTTCAG
1 AACTCATCTCGTCAAAATCATTTTTTCAG
37813 AA-TCCATCTCGTCAA
1 AACT-CATCTCGTCAA
37828 TTTTTTTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (29 bp):
AACTCATCTCGTCAAAATCATTTTTTCAG
Found at i:41126 original size:8 final size:8
Alignment explanation
Indices: 41113--41137 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41103 TGGATGAGTA
41113 GGAATGTT
1 GGAATGTT
41121 GGAATGTT
1 GGAATGTT
41129 GGAATGTT
1 GGAATGTT
41137 G
1 G
41138 TGCTGAAGAG
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:0.40, T:0.36
Consensus pattern (8 bp):
GGAATGTT
Found at i:42937 original size:60 final size:59
Alignment explanation
Indices: 42816--42951 Score: 173
Period size: 60 Copynumber: 2.3 Consensus size: 59
42806 TTCATACTTT
* ** * * *
42816 AACTTGATAATTTTTTTAATTTTGTATTTGAACTTTTTTTGGATCCAATTTGATACCTG
1 AACTTGATATTTTTTTTAATTTAATACTTGAACTTTTTTTGGACCCAATTTGATACATG
* *
42875 AACTTGATATTTTTTCTTAATTTAATACTTGAACTTTTTTTGGACCCAATTTGGTTCATG
1 AACTTGATATTTTTT-TTAATTTAATACTTGAACTTTTTTTGGACCCAATTTGATACATG
* *
42935 AACTTAACATTTTTTTT
1 AACTTGATATTTTTTTT
42952 TCTAATTTGG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 16 0.24
60 50 0.76
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (59 bp):
AACTTGATATTTTTTTTAATTTAATACTTGAACTTTTTTTGGACCCAATTTGATACATG
Found at i:42966 original size:62 final size:60
Alignment explanation
Indices: 42826--42976 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
42816 AACTTGATAA
* * * * * *
42826 TTTTTTTAATTTTGTATTTGAACTTTTTTTGGATCCAATTTGATACCTGAACTTGATATT
1 TTTTTTTAATTTAGTACTTGAACTTTTTTTGGACCCAATTTGATACATGAACTTAACATT
* * * *
42886 TTTTCTTAATTTAATACTTGAACTTTTTTTGGACCCAATTTGGTTCATGAACTTAACATTT
1 TTTTTTTAATTTAGTACTTGAACTTTTTTTGGACCCAATTTGATACATGAACTTAACA-TT
* *
42947 TTTTTTCTAATTTGGTACTT-AAGTTTTTTT
1 TTTTTT-TAATTTAGTACTTGAACTTTTTTT
42977 TTAAGATTCA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
60 48 0.64
61 16 0.21
62 11 0.15
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (60 bp):
TTTTTTTAATTTAGTACTTGAACTTTTTTTGGACCCAATTTGATACATGAACTTAACATT
Found at i:43258 original size:31 final size:31
Alignment explanation
Indices: 43197--43334 Score: 115
Period size: 31 Copynumber: 4.5 Consensus size: 31
43187 CGACCCCAAA
* *
43197 AAGTTTAAGTACCAACTTA-AAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
* * *
43227 AAGTTTAGGTAGCAAATTAGGAAAAATTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
***
43258 AAGTTTAAGTACCAAATT--GAACTAAA--AAA
1 AAGTTTAAGTACCAAATTAGGAA--AAAGTGTC
* *
43287 AAGTTTAAGTACCAAATTAAGAAAAAGTATC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
* *
43318 AAGTTCAAATACCAAAT
1 AAGTTTAAGTACCAAAT
43335 GTTATATTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
29 24 0.28
30 16 0.18
31 47 0.54
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
Found at i:43625 original size:31 final size:30
Alignment explanation
Indices: 43565--43632 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
43555 AGCTGAGGTA
*
43565 ACTTGTGTAATGAAATATACTTTAAGTACC
1 ACTTGTGTAATGAAATATAATTTAAGTACC
**
43595 ACTTGATGTAAT-ATAATATAATTTGGGTACC
1 ACTTG-TGTAATGA-AATATAATTTAAGTACC
*
43626 ATTTGTG
1 ACTTGTG
43633 ACAAAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (30 bp):
ACTTGTGTAATGAAATATAATTTAAGTACC
Found at i:46021 original size:19 final size:19
Alignment explanation
Indices: 45997--46041 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45987 GTATTTCATA
*
45997 AAAAATTTTATAAATATTT-
1 AAAAATTTAATAAAT-TTTC
*
46016 AAAAATTTAATGAATTTTC
1 AAAAATTTAATAAATTTTC
46035 AAAAATT
1 AAAAATT
46042 CATAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAAATTTAATAAATTTTC
Found at i:48085 original size:21 final size:23
Alignment explanation
Indices: 48045--48090 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
48035 TTTTCTCTCA
*
48045 TTTTCTCTCTTGCCAAACACCAT
1 TTTTCTCTCTTGCAAAACACCAT
48068 TTTTCT-TCTT-CAAAACACCAT
1 TTTTCTCTCTTGCAAAACACCAT
48089 TT
1 TT
48091 ATAAAAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTCTCTCTTGCAAAACACCAT
Found at i:50691 original size:24 final size:24
Alignment explanation
Indices: 50634--50695 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
50624 TGCATAGTAG
* *
50634 GTATCGCTAGATCTATTCATAGAA
1 GTATCGGTAGATCTGTTCATAGAA
*
50658 GTATCAGTAGATCTGTTCATAGAA
1 GTATCGGTAGATCTGTTCATAGAA
50682 GTATCGGTAG-TCTG
1 GTATCGGTAGATCTG
50696 GGTGCTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (24 bp):
GTATCGGTAGATCTGTTCATAGAA
Done.