Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008591.1 Kokia drynarioides strain JFW-HI SEQ_123269, 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: 19606
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:153 original size:17 final size:17
Alignment explanation
Indices: 119--151 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
109 TTTTAAATTT
*
119 TTAATATTTTAGACAAA
1 TTAATATTTTAGAAAAA
136 TTAAT-TTTTAGAAAAA
1 TTAATATTTTAGAAAAA
152 ATATTACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAATATTTTAGAAAAA
Found at i:2839 original size:22 final size:21
Alignment explanation
Indices: 2814--2861 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2804 TAAATATTGT
*
2814 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
2836 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
2857 TTAAT
1 TTAAT
2862 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:3769 original size:42 final size:42
Alignment explanation
Indices: 3659--3887 Score: 196
Period size: 41 Copynumber: 5.5 Consensus size: 42
3649 GGTGTATAAA
* * * ** *
3659 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTG-TATA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGAT-TT
* *
3701 AATGGAATACTCATGTCTCGAAATGAGAATGAGATTTTGATTT
1 AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATTT
* * *
3744 AAGGAAGACTCATGTCTTGAGATGAGAATGAGATTATGA-GT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATTT
* * *
3785 AAGGAAGACTCATGTCTCGAAATAAGAATGATATTTTGA-TT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATTT
* * * * * * *
3826 AAGAAAGACTCATGGT-TTGAGATGGGAATGAGAATATGGTTA
1 AAGGAAGACTCAT-GTCTCGAGATGAGAATGAGATTTTGATTT
* *
3868 AAGGAAGACTTATGACTCGA
1 AAGGAAGACTCATGTCTCGA
3888 AAGAGCATAA
Statistics
Matches: 149, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
41 64 0.43
42 52 0.35
43 32 0.21
44 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (42 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATTT
Found at i:3815 original size:83 final size:83
Alignment explanation
Indices: 3681--3889 Score: 255
Period size: 83 Copynumber: 2.5 Consensus size: 83
3671 TGTCTCGGGT
* * * *
3681 TGAGCATGAGAA-ATTGTATAAATGGAATACTCATGTCTCGAAATGAGAATGAGATTTTGATTTA
1 TGAGAATGAGAATATGGT-TAAA-GGAAGACTCATGTCTCGAAATAAGAATGAGATTTTGA-TTA
*
3745 AGGAAGACTCAT-GTCTTGAGA
63 AGAAAGACTCATGGT-TTGAGA
* *
3766 TGAGAATGAGATTATGAG-T-AAGGAAGACTCATGTCTCGAAATAAGAATGATATTTTGATTAAG
1 TGAGAATGAGAATATG-GTTAAAGGAAGACTCATGTCTCGAAATAAGAATGAGATTTTGATTAAG
3829 AAAGACTCATGGTTTGAGA
65 AAAGACTCATGGTTTGAGA
* * *
3848 TGGGAATGAGAATATGGTTAAAGGAAGACTTATGACTCGAAA
1 TGAGAATGAGAATATGGTTAAAGGAAGACTCATGTCTCGAAA
3890 GAGCATAAGG
Statistics
Matches: 108, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
81 1 0.01
82 35 0.32
83 56 0.52
84 2 0.02
85 11 0.10
86 2 0.02
87 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (83 bp):
TGAGAATGAGAATATGGTTAAAGGAAGACTCATGTCTCGAAATAAGAATGAGATTTTGATTAAGA
AAGACTCATGGTTTGAGA
Found at i:8236 original size:50 final size:50
Alignment explanation
Indices: 8161--8400 Score: 186
Period size: 50 Copynumber: 5.0 Consensus size: 50
8151 CCCTCTTCGC
* *
8161 CATTGCTG-CTTCAATCTACCCCTCTATAGCTTTAGGTGTATAAGATTTGT
1 CATTGC-GACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGT
** *
8211 CATTGCGACTTCAATCTGTTCCTCTACAGCTTTA---G-----G--TCGT
1 CATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGT
* * * * * *
8251 CCTTGCGACTTCAATATGCCCCTCTACAGCTTTAGGTGAATGAGATTCGC
1 CATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGT
* * *
8301 CATTGCTG-CTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAGGTTT-T
1 CATTGC-GACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGT
** *
8350 CCATTGCGACTTCAATC-GTTCCTCTACAGCTTTAGAG-GTATAGGATTTGT
1 -CATTGCGACTTCAATCTGCCCCTCTACAGCTTTAG-GTGTATAAGATTTGT
8400 C
1 C
8401 GTTCTATCGC
Statistics
Matches: 151, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
40 33 0.22
42 1 0.01
43 1 0.01
47 1 0.01
48 1 0.01
49 26 0.17
50 87 0.58
51 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (50 bp):
CATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGT
Found at i:8325 original size:90 final size:90
Alignment explanation
Indices: 8169--8337 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 90
8159 GCCATTGCTG
* * * * * **
8169 CTTCAATCTACCCCTCTATAGCTTTAGGTGTATAAGATTTGTCATTGCGACTTCAATCTGTTCCT
1 CTTCAATATACCCCTCTACAGCTTTAGGTGAATAAGATTCGCCATTGCGACTTCAATCTGCCCCT
8234 CTACAGCTTTAGGTCGTCCTTGCGA
66 CTACAGCTTTAGGTCGTCCTTGCGA
* *
8259 CTTCAATATGCCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTGCTG-CTTCAATCTGCCCC
1 CTTCAATATACCCCTCTACAGCTTTAGGTGAATAAGATTCGCCATTGC-GACTTCAATCTGCCCC
*
8323 TCTATAGCTTTAGGT
65 TCTACAGCTTTAGGT
8338 GTATGAGGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
90 67 0.99
91 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (90 bp):
CTTCAATATACCCCTCTACAGCTTTAGGTGAATAAGATTCGCCATTGCGACTTCAATCTGCCCCT
CTACAGCTTTAGGTCGTCCTTGCGA
Found at i:16603 original size:17 final size:18
Alignment explanation
Indices: 16581--16631 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
16571 ATTTACATGT
16581 ATACATAATAAAAAATA-
1 ATACATAATAAAAAATAC
*
16598 ATACAT-ACAAAAAATAC
1 ATACATAATAAAAAATAC
*
16615 A-ACAAAATAAAATAATA
1 ATACATAATAAAA-AATA
16632 TGCATATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.43
17 12 0.43
18 4 0.14
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (18 bp):
ATACATAATAAAAAATAC
Found at i:16615 original size:13 final size:13
Alignment explanation
Indices: 16592--16624 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16582 TACATAATAA
16592 AAAATAATACATAC
1 AAAATAATACA-AC
16606 AAAA-AATACAAC
1 AAAATAATACAAC
16618 AAAATAA
1 AAAATAA
16625 AATAATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 8 0.44
14 4 0.22
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAATACAAC
Found at i:16716 original size:30 final size:29
Alignment explanation
Indices: 16682--17016 Score: 193
Period size: 30 Copynumber: 11.4 Consensus size: 29
16672 CATTAAAATC
16682 GGGTCAAATTTGAATTTTTGAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGAAAA-TTTAA
** **
16712 GGGTCAAATAAGAATTTTTGGAAAATTTGG
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
* * *
16742 GGGTCAAATTAGAATTTTTTTTAAAATTTTA
1 GGGTCAAATTTGAA--TTTTTGAAAATTTAA
** * *
16773 GGGTCAAATTCAAATTTCTAGAAAGTTTAA
1 GGGTCAAATTTGAATTT-TTGAAAATTTAA
* * *
16803 GGGTC--A--T--ATTTTGGAAATTTTGA
1 GGGTCAAATTTGAATTTTTGAAAATTTAA
* * * *
16826 GGGTTAATTTTGAAGTTTTGGTAAATTT-A
1 GGGTCAAATTTGAA-TTTTTGAAAATTTAA
* * *
16855 GGTGTTAAATTTAAATTTTTGGAAAATTTAG
1 GG-GTCAAATTTGAATTTTT-GAAAATTTAA
* * *
16886 GGGTTAAATTGGAATTTTTGGAAAGTTT-A
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
* *
16915 GGGTTAAAATTTGAATTTTTAGAAAATTTAG
1 GGG-TCAAATTTGAATTTTT-GAAAATTTAA
* *
16946 GGGTTAAATTTGAATTTTTGGTAAATTT-A
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
* ** *
16975 GGGATTAAATTCAAATTTTTTGAAAATTTTA
1 GGG-TCAAATTTGAA-TTTTTGAAAATTTAA
17006 GGGTCAAATTT
1 GGGTCAAATTT
17017 AGCTTTTTGG
Statistics
Matches: 241, Mismatches: 45, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
23 13 0.05
24 4 0.02
27 1 0.00
28 1 0.00
29 17 0.07
30 162 0.67
31 38 0.16
32 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGAAAATTTAA
Found at i:16747 original size:60 final size:59
Alignment explanation
Indices: 16682--17033 Score: 243
Period size: 60 Copynumber: 6.0 Consensus size: 59
16672 CATTAAAATC
* *
16682 GGGTCAAATTTGAATTTTTGAAAACTTTAAGGGTCAAATAAGAATTTTTGGAAAATTTGG
1 GGGTCAAATTTGAATTTTTGAAAA-TTTAAGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * * * * * *
16742 GGGTCAAATTAGAATTTTTTTTAAAATTTTAGGGTCAAATTCA-AATTTCTAGAAAGTTTAA
1 GGGTCAAATTTGAA--TTTTTGAAAATTTAAGGGTCAAATT-AGAATTTTTGGAAAATTTAG
* * * * * * * *
16803 GGGTC--A--T--ATTTTGGAAATTTTGAGGGTTAATTTTGAAGTTTTGGTAAATTTAG
1 GGGTCAAATTTGAATTTTTGAAAATTTAAGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * * * * * *
16856 GTGTTAAATTTAAATTTTTGGAAAATTTAGGGGTTAAATTGGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTT-GAAAATTTAAGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * * * * *
16916 GGTTAAAATTTGAATTTTTAGAAAATTTAGGGGTTAAATTTGAATTTTTGGTAAATTTAG
1 GGGTCAAATTTGAATTTTT-GAAAATTTAAGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * ** * * *
16976 GGATTAAATTCAAATTTTTTGAAAATTTTAGGGTCAAATTTAG-CTTTTTGGATAATTT
1 GGGTCAAATTTGAA-TTTTTGAAAATTTAAGGGTCAAA-TTAGAATTTTTGGAAAATTT
17034 GGTGGTAAAA
Statistics
Matches: 226, Mismatches: 53, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
53 34 0.15
55 2 0.01
57 1 0.00
59 6 0.03
60 134 0.59
61 39 0.17
62 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (59 bp):
GGGTCAAATTTGAATTTTTGAAAATTTAAGGGTCAAATTAGAATTTTTGGAAAATTTAG
Found at i:16807 original size:61 final size:60
Alignment explanation
Indices: 16682--16808 Score: 132
Period size: 61 Copynumber: 2.1 Consensus size: 60
16672 CATTAAAATC
* * * **
16682 GGGTCAAATTTGAATTTTTGAAAACTTTAAGGGTCAAATAAGAATTTTTGGAAAATTTGG
1 GGGTCAAATTAGAATTTTTGAAAACTTTAAGGGTCAAATAAGAATTTCTAGAAAATTTAA
* * * *
16742 GGGTCAAATTAGAATTTTTTTTAAAA-TTTTAGGGTCAAATTCA-AATTTCTAGAAAGTTTAA
1 GGGTCAAATTAGAA--TTTTTGAAAACTTTAAGGGTCAAA-TAAGAATTTCTAGAAAATTTAA
16803 GGGTCA
1 GGGTCA
16809 TATTTTGGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
60 13 0.24
61 31 0.56
62 11 0.20
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (60 bp):
GGGTCAAATTAGAATTTTTGAAAACTTTAAGGGTCAAATAAGAATTTCTAGAAAATTTAA
Found at i:16819 original size:23 final size:22
Alignment explanation
Indices: 16793--16837 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
16783 CAAATTTCTA
16793 GAAAGTTTAAGGGTCATATTTTG
1 GAAAGTTTAAGGGTCA-ATTTTG
* * *
16816 GAAATTTTGAGGGTTAATTTTG
1 GAAAGTTTAAGGGTCAATTTTG
16838 AAGTTTTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (22 bp):
GAAAGTTTAAGGGTCAATTTTG
Found at i:16942 original size:90 final size:90
Alignment explanation
Indices: 16811--17016 Score: 270
Period size: 90 Copynumber: 2.3 Consensus size: 90
16801 AAGGGTCATA
* * * *
16811 TTTTGGAAATTTTGAGGGTTAATTTTGAAGTTTTGGTAAATTTAGGTGTTAAATTTAAATTTTTG
1 TTTTGGAAATTTT-AGGGTTAAATTTGAAGTTTTAGAAAATTTAGGGGTTAAATTTAAATTTTTG
* **
16876 GAAAATTTAGGGGTTAAATTGGAA-T
65 GAAAATTTAGGGATTAAATTCAAATT
* * *
16901 TTTTGGAAAGTTTAGGGTTAAAATTTGAATTTTTAGAAAATTTAGGGGTTAAATTTGAATTTTTG
1 TTTTGGAAATTTTAGGGTT-AAATTTGAAGTTTTAGAAAATTTAGGGGTTAAATTTAAATTTTTG
*
16966 GTAAATTTAGGGATTAAATTCAAATT
65 GAAAATTTAGGGATTAAATTCAAATT
* *
16992 TTTTGAAAATTTTAGGGTCAAATTT
1 TTTTGGAAATTTTAGGGTTAAATTT
17017 AGCTTTTTGG
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
89 6 0.06
90 77 0.77
91 17 0.17
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (90 bp):
TTTTGGAAATTTTAGGGTTAAATTTGAAGTTTTAGAAAATTTAGGGGTTAAATTTAAATTTTTGG
AAAATTTAGGGATTAAATTCAAATT
Found at i:18032 original size:18 final size:18
Alignment explanation
Indices: 18009--18049 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
17999 GTATTTATTT
* *
18009 ATAAATATAAATAGATAA
1 ATAAATAAAAATAAATAA
18027 ATAAATAAAAATAAATAA
1 ATAAATAAAAATAAATAA
18045 ATAAA
1 ATAAA
18050 GTTAAAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAATAAAAATAAATAA
Found at i:18055 original size:14 final size:14
Alignment explanation
Indices: 18023--18049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18013 ATATAAATAG
18023 ATAAATAAATAAAA
1 ATAAATAAATAAAA
18037 ATAAATAAATAAA
1 ATAAATAAATAAA
18050 GTTAAAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAATAAATAAAA
Done.