Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007306.1 Kokia drynarioides strain JFW-HI SEQ_121922, 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: 12976
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:4002 original size:8 final size:7
Alignment explanation
Indices: 3983--4080 Score: 54
Period size: 7 Copynumber: 14.9 Consensus size: 7
3973 AATGGAACCC
3983 AATTTTA
1 AATTTTA
3990 AATTTTA
1 AATTTTA
*
3997 AAATTTA
1 AATTTTA
*
4004 AATTATTT
1 AATT-TTA
*
4012 AAGTTTA
1 AATTTTA
4019 AA-TTT-
1 AATTTTA
4024 -ATTTTA
1 AATTTTA
4030 AATTTTA
1 AATTTTA
4037 ACTTATTTT-
1 A---ATTTTA
*
4046 AAGTTTA
1 AATTTTA
4053 AA-TTT-
1 AATTTTA
4058 -ATTTTA
1 AATTTTA
4064 AA--TTA
1 AATTTTA
4069 AA-TTTA
1 AATTTTA
4075 AATTTT
1 AATTTT
4081 TAAAAAAAGG
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
4 2 0.03
5 11 0.15
6 15 0.21
7 33 0.46
8 5 0.07
9 1 0.01
10 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:4011 original size:17 final size:18
Alignment explanation
Indices: 3991--4074 Score: 92
Period size: 17 Copynumber: 5.1 Consensus size: 18
3981 CCAATTTTAA
*
3991 ATTTTAAAATTTAAA-TT
1 ATTTTAAAGTTTAAATTT
4008 A-TTT-AAGTTTAAATTT
1 ATTTTAAAGTTTAAATTT
* *
4024 ATTTTAAA-TTTTAACTT
1 ATTTTAAAGTTTAAATTT
4041 ATTTT-AAGTTTAAATTT
1 ATTTTAAAGTTTAAATTT
4058 ATTTTAAA--TTAAATTT
1 ATTTTAAAGTTTAAATTT
4074 A
1 A
4075 AATTTTTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
15 8 0.14
16 17 0.30
17 28 0.49
18 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTAAAGTTTAAATTT
Found at i:4018 original size:6 final size:6
Alignment explanation
Indices: 3986--4079 Score: 58
Period size: 6 Copynumber: 16.5 Consensus size: 6
3976 GGAACCCAAT
* *
3986 TTTAAA TTTTAAAA TTTAAA -TT--A TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
4032 TTTTAA CTT-AT TTTAAG TTTAAA TTT-AT TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4077 TTT
1 TTT
4080 TTAAAAAAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 18 0.27
6 37 0.55
7 6 0.09
8 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:4025 original size:16 final size:17
Alignment explanation
Indices: 4000--4074 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
3990 AATTTTAAAA
4000 TTTAAA-TTA-TTTAAG
1 TTTAAATTTATTTTAAG
*
4015 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
* *
4032 TTTTAACTTATTTTAAG
1 TTTAAATTTATTTTAAG
4049 TTTAAATTTATTTTAA-
1 TTTAAATTTATTTTAAG
*
4065 ATTAAATTTA
1 TTTAAATTTA
4075 AATTTTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 6 0.12
16 12 0.24
17 33 0.65
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:4031 original size:11 final size:11
Alignment explanation
Indices: 4008--4079 Score: 65
Period size: 11 Copynumber: 6.4 Consensus size: 11
3998 AATTTAAATT
4008 ATTTAAGTTTAA
1 ATTTAA-TTTAA
*
4020 ATTTATTTTAA
1 ATTTAATTTAA
*
4031 ATTTTAACTT-A
1 A-TTTAATTTAA
*
4042 TTTTAAGTTTAA
1 ATTTAA-TTTAA
*
4054 ATTTATTTTAA
1 ATTTAATTTAA
*
4065 ATTAAATTTAA
1 ATTTAATTTAA
4076 ATTT
1 ATTT
4080 TTAAAAAAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
10 5 0.11
11 26 0.55
12 16 0.34
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:4037 original size:33 final size:34
Alignment explanation
Indices: 3991--4067 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
3981 CCAATTTTAA
*
3991 ATTTTAAAATTTAAATTA-TTTAAGTTTAAATTT
1 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
*
4024 ATTTTAAATTTTAACTTATTTTAAGTTTAAATTT
1 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
4058 ATTTTAAATT
1 ATTTTAAATT
4068 AAATTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 16 0.39
34 25 0.61
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
Found at i:5465 original size:30 final size:29
Alignment explanation
Indices: 5394--5675 Score: 174
Period size: 29 Copynumber: 9.7 Consensus size: 29
5384 GGTCTCCGAG
* **
5394 CTTTCCAAAAATCACATTTTAACCCCCCGAA
1 CTTTCCAAAAATTACATTTT-A-CCCCTAAA
* *
5425 C-TT-CACAAAATTATAGTTTTACCCCTAAG
1 CTTTCCA-AAAATTACA-TTTTACCCCTAAA
* * * *
5454 CTTTCCAAAAATCACGCTTTAACCCTTAAA
1 CTTTCCAAAAATTAC-ATTTTACCCCTAAA
5484 CTTTCC-AAAATTACATTTTACCCCT-AA
1 CTTTCCAAAAATTACATTTTACCCCTAAA
* * *
5511 CTTTTCAATAATCACATTTTGACCCCTAAA
1 CTTTCCAAAAATTACATTTT-ACCCCTAAA
*
5541 CTTTCC-AAAATTACATTTTTATCCCTAAA
1 CTTTCCAAAAATTACA-TTTTACCCCTAAA
* *
5570 CTTTTCC-AAAATTACATTTT-GCCCTCGAA
1 C-TTTCCAAAAATTACATTTTACCCCT-AAA
* * *
5599 C-ATCC-AAAATTCACCACTTT-CCCCTCGAA
1 CTTTCCAAAAATT-A-CATTTTACCCCT-AAA
* * *
5628 C-ATCCAAAAATTATCATTTTGCCCCCAAA
1 CTTTCCAAAAATTA-CATTTTACCCCTAAA
5657 -TTTCCAAAAATTACATTTT
1 CTTTCCAAAAATTACATTTT
5676 CAACTTCAAA
Statistics
Matches: 203, Mismatches: 32, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
27 16 0.08
28 30 0.15
29 81 0.40
30 69 0.34
31 7 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CTTTCCAAAAATTACATTTTACCCCTAAA
Found at i:5609 original size:57 final size:57
Alignment explanation
Indices: 5394--5590 Score: 173
Period size: 57 Copynumber: 3.4 Consensus size: 57
5384 GGTCTCCGAG
* * * ** *
5394 CTTTCCAAAAATCACATTTTAACCCCCCGAACT-TCACAAAATTATAGTTTTACCCCTAA
1 CTTTTCAATAATCACATTTTGA-CCCCTAAACTATC-CAAAATTACA-TTTTACCCCTAA
* * ** * * *
5453 GCTTTCCAAAAATCACGCTTTAACCCTTAAACTTTCCAAAATTACATTTTACCCCTAA
1 -CTTTTCAATAATCACATTTTGACCCCTAAACTATCCAAAATTACATTTTACCCCTAA
* *
5511 CTTTTCAATAATCACATTTTGACCCCTAAACTTTCCAAAATTACATTTTTATCCCTAAA
1 CTTTTCAATAATCACATTTTGACCCCTAAACTATCCAAAATTACA-TTTTACCCCT-AA
*
5570 CTTTTCCAA-AATTACATTTTG
1 CTTTT-CAATAATCACATTTTG
5591 CCCTCGAACA
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
57 39 0.33
58 21 0.18
59 34 0.29
60 25 0.21
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (57 bp):
CTTTTCAATAATCACATTTTGACCCCTAAACTATCCAAAATTACATTTTACCCCTAA
Found at i:5685 original size:29 final size:31
Alignment explanation
Indices: 5653--5768 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 31
5643 ATTTTGCCCC
5653 CAAA-TTTCCAAAAATTAC-ATTTTCAACTT
1 CAAATTTTCCAAAAATTACAATTTTCAACTT
* * *
5682 CAAATTTTCCAAAAGTT-CGA-TTTGAA-TCT
1 CAAATTTTCCAAAAATTACAATTTTCAACT-T
* * *
5711 CAAATTTTCCAAAAATTTCAATTTTGACCTT
1 CAAATTTTCCAAAAATTACAATTTTCAACTT
* *
5742 -AAA-TTCCTCAAAAATTAC-GTTTTCAAC
1 CAAATTTTC-CAAAAATTACAATTTTCAAC
5769 CCTGATTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.01
29 36 0.51
30 26 0.37
31 6 0.09
32 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (31 bp):
CAAATTTTCCAAAAATTACAATTTTCAACTT
Found at i:7556 original size:15 final size:15
Alignment explanation
Indices: 7536--7571 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
7526 ATAAAATTTT
7536 AAATTAGTAATAGTA
1 AAATTAGTAATAGTA
7551 AAATTAGTAATAGTA
1 AAATTAGTAATAGTA
7566 AAATTA
1 AAATTA
7572 TATTTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (15 bp):
AAATTAGTAATAGTA
Found at i:8288 original size:20 final size:20
Alignment explanation
Indices: 8251--8306 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
8241 CTACCCTGAG
* *
8251 ACTTCTACATG-TAGAACTCC
1 ACTTCTAC-TGATACAACTAC
8271 ACTTCTACTGATACAACTAC
1 ACTTCTACTGATACAACTAC
* *
8291 AATTCTACCGATACAA
1 ACTTCTACTGATACAA
8307 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (20 bp):
ACTTCTACTGATACAACTAC
Found at i:10804 original size:38 final size:38
Alignment explanation
Indices: 10753--10830 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
10743 AGTTTTATTT
10753 GTTTATTTTTTATCTAATAAAAGGAGAAGAAGAGAAAG
1 GTTTATTTTTTATCTAATAAAAGGAGAAGAAGAGAAAG
*
10791 GTTTATTTTTTATCTAATAAAAGGAGGAGAAGAGAAAG
1 GTTTATTTTTTATCTAATAAAAGGAGAAGAAGAGAAAG
10829 GT
1 GT
10831 AAATTTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (38 bp):
GTTTATTTTTTATCTAATAAAAGGAGAAGAAGAGAAAG
Found at i:10915 original size:28 final size:34
Alignment explanation
Indices: 10882--10951 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
10872 TTTGTAAAGA
10882 AAAATTAATG-T-CAAAT-TTTA-G-CTT-ATTG
1 AAAATTAATGCTCCAAATATTTATGCCTTAATTG
*
10910 AAAATTTATGCTCCAAATATTTATGCCTTAAATTG
1 AAAATTAATGCTCCAAATATTTATGCCTT-AATTG
10945 AAAATTA
1 AAAATTA
10952 TTTTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 9 0.27
29 1 0.03
30 5 0.15
31 4 0.12
32 1 0.03
33 3 0.09
35 10 0.30
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (34 bp):
AAAATTAATGCTCCAAATATTTATGCCTTAATTG
Done.