Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009862.1 Kokia drynarioides strain JFW-HI SEQ_124596, 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: 99856
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:257 original size:43 final size:43
Alignment explanation
Indices: 175--259 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
165 ATTAACATGT
* * * *
175 TAAATTTTATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC
* *
218 TAAATTATATTACTTTAATCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATGCTTG-CATGTTA
260 TTAATTTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC
Found at i:961 original size:45 final size:45
Alignment explanation
Indices: 829--962 Score: 178
Period size: 45 Copynumber: 3.0 Consensus size: 45
819 TAGCTCATCT
*
829 AGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATACTCA
1 AGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCA
* * *
874 AGCCAATGATATCAGCCTCAATTTGACGAGCCACCGCAATACTTA
1 AGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCA
** * * * *
919 AGGGAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATACTC
1 AGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
963 TATTCCTCCC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (45 bp):
AGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCA
Found at i:983 original size:21 final size:21
Alignment explanation
Indices: 957--999 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
947 AGCCATCGCG
*
957 ATACTCTATTCCTCCCGGGCA
1 ATACTCTACTCCTCCCGGGCA
* *
978 ATACTCTACTCCTTCGGGGCA
1 ATACTCTACTCCTCCCGGGCA
999 A
1 A
1000 ATGGACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (21 bp):
ATACTCTACTCCTCCCGGGCA
Found at i:1243 original size:21 final size:21
Alignment explanation
Indices: 1219--1258 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1209 TTCATAACAT
1219 TAAACCCTAAAACTT-AAATTA
1 TAAA-CCTAAAACTTGAAATTA
*
1240 TAAACCTTAAACTTGAAAT
1 TAAACCTAAAACTTGAAAT
1259 CCTAAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAACCTAAAACTTGAAATTA
Found at i:2755 original size:36 final size:36
Alignment explanation
Indices: 2708--2779 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2698 CTTTTCCTAG
2708 TTTGGTTCTTAAAGTTTTTTGGCTAACTCAATCCCT
1 TTTGGTTCTTAAAGTTTTTTGGCTAACTCAATCCCT
2744 TTTGGTTCTTAAAGTTTTTTGGCTAACTCAATCCCT
1 TTTGGTTCTTAAAGTTTTTTGGCTAACTCAATCCCT
2780 ACCGTTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (36 bp):
TTTGGTTCTTAAAGTTTTTTGGCTAACTCAATCCCT
Found at i:10752 original size:27 final size:26
Alignment explanation
Indices: 10722--10772 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
10712 GAGTTAAATA
*
10722 AATTTAAATTTAAATTGTATTGGATTG
1 AATTTAAACTTAAATTG-ATTGGATTG
*
10749 AATTTGAACTTAAATTGATTGGAT
1 AATTTAAACTTAAATTGATTGGAT
10773 CAAATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (26 bp):
AATTTAAACTTAAATTGATTGGATTG
Found at i:24688 original size:57 final size:57
Alignment explanation
Indices: 24600--24713 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
24590 TAATTGAGTG
*
24600 AAATGATGTTCAAAGTGTCTGCCAGAGCCAAGCCTATGCTTGGTCACTAGCTCAGCC
1 AAATGATGTTCAAAGTGTCTGCCAGAGCCAAGCCTATCCTTGGTCACTAGCTCAGCC
24657 AAATGATGTTCAAAGTGTCTGCCAGAGCCAAGCCTATCCTTGGTCACTAGCTCAGCC
1 AAATGATGTTCAAAGTGTCTGCCAGAGCCAAGCCTATCCTTGGTCACTAGCTCAGCC
24714 TTTGTTATGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (57 bp):
AAATGATGTTCAAAGTGTCTGCCAGAGCCAAGCCTATCCTTGGTCACTAGCTCAGCC
Found at i:36796 original size:6 final size:6
Alignment explanation
Indices: 36785--36809 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36775 TAATTCAACC
36785 AACCAG AACCAG AACCAG AACCAG A
1 AACCAG AACCAG AACCAG AACCAG A
36810 CATGACATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AACCAG
Found at i:44590 original size:16 final size:16
Alignment explanation
Indices: 44571--44630 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
44561 TGAAGAACAA
44571 TTATTTTAAATAATAG
1 TTATTTTAAATAATAG
*
44587 TTATTCTAAAT-ATAAG
1 TTATTTTAAATAAT-AG
*
44603 CTATTTTTAAATAATAG
1 TTA-TTTTAAATAATAG
* *
44620 TAACTTTAAAT
1 TTATTTTAAAT
44631 GATGAGATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.06
16 21 0.60
17 10 0.29
18 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (16 bp):
TTATTTTAAATAATAG
Found at i:53784 original size:14 final size:14
Alignment explanation
Indices: 53765--53792 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53755 ACTTTGTTAG
53765 GATTTTATCGAAGA
1 GATTTTATCGAAGA
53779 GATTTTATCGAAGA
1 GATTTTATCGAAGA
53793 CACTCTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GATTTTATCGAAGA
Found at i:58376 original size:20 final size:21
Alignment explanation
Indices: 58339--58378 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58329 AAAATCAAAG
58339 TTTTTAGAAAGATAATTAATT
1 TTTTTAGAAAGATAATTAATT
*
58360 TTTTTAGAATGAT-ATTAAT
1 TTTTTAGAAAGATAATTAAT
58379 ATCAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
TTTTTAGAAAGATAATTAATT
Found at i:59076 original size:25 final size:25
Alignment explanation
Indices: 59042--59092 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
59032 ATAGTCTTAG
* *
59042 CTTTACAATTATATTATTAAATGCC
1 CTTTAAAATTATACTATTAAATGCC
59067 CTTTAAAATTATACTATTAAATGCC
1 CTTTAAAATTATACTATTAAATGCC
59092 C
1 C
59093 ATTTTGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (25 bp):
CTTTAAAATTATACTATTAAATGCC
Found at i:59924 original size:13 final size:13
Alignment explanation
Indices: 59906--59930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59896 CTATTTTTAA
59906 TATAAAAAAATTT
1 TATAAAAAAATTT
59919 TATAAAAAAATT
1 TATAAAAAAATT
59931 AATTCACTTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAAAAAAATTT
Found at i:73399 original size:17 final size:18
Alignment explanation
Indices: 73379--73412 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
73369 GGATGGTGAA
73379 TTTAAAGGTTA-TGGGTC
1 TTTAAAGGTTATTGGGTC
*
73396 TTTAATGGTTATTGGGT
1 TTTAAAGGTTATTGGGT
73413 TTTCTTGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (18 bp):
TTTAAAGGTTATTGGGTC
Found at i:76905 original size:25 final size:26
Alignment explanation
Indices: 76848--76909 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
76838 AGCTTATGAT
*
76848 GATGATGATAATTTTGTTGGTATAGAA
1 GATGAT-ATAATCTTGTTGGTATAGAA
76875 GA-GATATAATACTTGTTGG-A-AGAA
1 GATGATATAAT-CTTGTTGGTATAGAA
76899 GATGATATAAT
1 GATGATATAAT
76910 TTTTAGTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.19
25 14 0.44
26 10 0.31
27 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (26 bp):
GATGATATAATCTTGTTGGTATAGAA
Found at i:77760 original size:6 final size:6
Alignment explanation
Indices: 77749--77774 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
77739 CCCAAGTACC
77749 AGAACT AGAACT AGAACT AGAACT AG
1 AGAACT AGAACT AGAACT AGAACT AG
77775 TACCCATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGAACT
Found at i:87090 original size:22 final size:22
Alignment explanation
Indices: 87059--87102 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
87049 TAATTGCACA
87059 ATATTAGTCTCGGTAACTAACC
1 ATATTAGTCTCGGTAACTAACC
*
87081 ATATTTGTCTCGGTAACTAACC
1 ATATTAGTCTCGGTAACTAACC
87103 TAGTGTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (22 bp):
ATATTAGTCTCGGTAACTAACC
Found at i:98368 original size:29 final size:28
Alignment explanation
Indices: 98314--98371 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
98304 ATTTTTTGTG
98314 TAAATTTAAAATTTAATCCTTATACTTT
1 TAAATTTAAAATTTAATCCTTATACTTT
*
98342 TAAATTTAAGAATTTAGTCCCTT-TACTTT
1 TAAATTTAA-AATTTAAT-CCTTATACTTT
98371 T
1 T
98372 TGAAATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 14 0.52
30 4 0.15
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.50
Consensus pattern (28 bp):
TAAATTTAAAATTTAATCCTTATACTTT
Found at i:98586 original size:69 final size:70
Alignment explanation
Indices: 98471--98613 Score: 200
Period size: 69 Copynumber: 2.1 Consensus size: 70
98461 CCAAGTAAGT
* * * * *
98471 ATTTCAATAAAAAAATAGTAGTGTTAACAATTCGACTTTAATTTTGAAATATGAAAAATACAAGG
1 ATTTCAATAAAAAAATAGCAATGTTAACAATTCGACTTAAACTTTGAAATATGAAAAATACAACG
98536 ACTAA
66 ACTAA
* *
98541 ATTTCAA-AAAAAATTAGCAATGTTAACAATTTC-ACTTAAACTTTGAAATATGAAAAGTACAAC
1 ATTTCAATAAAAAAATAGCAATGTTAACAA-TTCGACTTAAACTTTGAAATATGAAAAATACAAC
98604 GACTAA
65 GACTAA
98610 ATTT
1 ATTT
98614 GAAATATGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
69 55 0.85
70 10 0.15
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (70 bp):
ATTTCAATAAAAAAATAGCAATGTTAACAATTCGACTTAAACTTTGAAATATGAAAAATACAACG
ACTAA
Found at i:99712 original size:21 final size:20
Alignment explanation
Indices: 99686--99817 Score: 92
Period size: 21 Copynumber: 6.3 Consensus size: 20
99676 AAAAGTTCAA
*
99686 GGTTTAGGGTTTGGAGGTTAG
1 GGTTTAGGGTTT-GAGGTTTG
**
99707 GGTTTAAGGG-TTGAGGCGTG
1 GGTTT-AGGGTTTGAGGTTTG
*
99727 GGCCTTAGGGTTTGAGGTTTG
1 GG-TTTAGGGTTTGAGGTTTG
99748 TGGTTTAGGG-TTGAGGTTTG
1 -GGTTTAGGGTTTGAGGTTTG
* *
99768 GAGGTTAGGGTTTTG-TGTTTG
1 G-GTTTAGGG-TTTGAGGTTTG
*
99789 AGTTTTAGGGTTT-AGAGTTTG
1 -GGTTTAGGGTTTGAG-GTTTG
99810 AGGTTTAG
1 -GGTTTAG
99818 TTTAGGGTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
19 1 0.01
20 31 0.35
21 46 0.52
22 10 0.11
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (20 bp):
GGTTTAGGGTTTGAGGTTTG
Found at i:99776 original size:41 final size:40
Alignment explanation
Indices: 99689--99814 Score: 105
Period size: 41 Copynumber: 3.0 Consensus size: 40
99679 AGTTCAAGGT
* ** *
99689 TTAGGGTTTGGAGGTTAGGGTTTAAGGGTTGAGGCGTGG-GCC
1 TTAGGGTTT-GAGGTTTGGGTTT-AGGGTTGAGGTTTGGAG-G
99731 TTAGGGTTTGAGGTTTGTGGTTTAGGGTTGAGGTTTGGAGG
1 TTAGGGTTTGAGGTTTG-GGTTTAGGGTTGAGGTTTGGAGG
* * *
99772 TTAGGGTTTTG-TGTTTGAGTTTTAGGGTTTAGAGTTT-GAGG
1 TTAGGG-TTTGAGGTTTG-GGTTTAGGGTTGAG-GTTTGGAGG
99813 TT
1 TT
99815 TAGTTTAGGG
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
41 49 0.68
42 23 0.32
ACGTcount: A:0.13, C:0.02, G:0.43, T:0.41
Consensus pattern (40 bp):
TTAGGGTTTGAGGTTTGGGTTTAGGGTTGAGGTTTGGAGG
Found at i:99840 original size:26 final size:26
Alignment explanation
Indices: 99792--99842 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
99782 GTGTTTGAGT
* *
99792 TTTAGGGTTTAGAGTTTGAGGTTTAG
1 TTTAGGGTTTAAAGGTTGAGGTTTAG
99818 TTTAGGGTTTAAAGGTT-ATGGTTTA
1 TTTAGGGTTTAAAGGTTGA-GGTTTA
99843 AGGATTAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (26 bp):
TTTAGGGTTTAAAGGTTGAGGTTTAG
Done.