Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012255.1 Kokia drynarioides strain JFW-HI SEQ_127256, 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: 72140
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:101 original size:37 final size:38
Alignment explanation
Indices: 4--110 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 38
1 CTT
** *
4 GAGTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATA
1 GAGTCGATGAGACACT-GG-GT-ACCACTTTACTTCGGATA
* * *
45 GATTCGATGAGATACTGGGTACCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
* **
83 G-GTCGATGAGACATTGGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTACCACTTTA
111 TTGCTTTGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
37 22 0.40
38 15 0.27
39 2 0.04
40 2 0.04
41 14 0.25
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTACCACTTTACTTCGGATA
Found at i:7660 original size:17 final size:17
Alignment explanation
Indices: 7621--7653 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7611 TACTTGTTGG
7621 ACAAGTATCGGTAGTAA
1 ACAAGTATCGGTAGTAA
7638 ACAAGTATCGGTAGTA
1 ACAAGTATCGGTAGTA
7654 GTCAAGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
ACAAGTATCGGTAGTAA
Found at i:11165 original size:16 final size:17
Alignment explanation
Indices: 11137--11168 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11127 CCCTTTTTTT
11137 TTTACATACCCAAATCC
1 TTTACATACCCAAATCC
11154 TTTACA-ACCCAAATC
1 TTTACATACCCAAATC
11169 ACCTAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (17 bp):
TTTACATACCCAAATCC
Found at i:12376 original size:2 final size:2
Alignment explanation
Indices: 12369--12396 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12359 ATGATCTCGC
12369 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12397 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12626 original size:2 final size:2
Alignment explanation
Indices: 12621--12648 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12611 TTCAATCCCC
12621 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
12649 TCAATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15438 original size:12 final size:12
Alignment explanation
Indices: 15405--15438 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15395 AATCCTCAGG
15405 TTTTTCTTTCTT
1 TTTTTCTTTCTT
*
15417 TTTTCCTTTCTT
1 TTTTTCTTTCTT
*
15429 TTTTTTTTTC
1 TTTTTCTTTC
15439 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:20456 original size:30 final size:30
Alignment explanation
Indices: 20422--20485 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
20412 ATTCATGTTA
20422 TATAGAATTTGATAGGTGTAGTTATTTATT
1 TATAGAATTTGATAGGTGTAGTTATTTATT
20452 TATAGAATTTGATAGGTGTAGTTATTTATT
1 TATAGAATTTGATAGGTGTAGTTATTTATT
20482 TATA
1 TATA
20486 TTATTGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (30 bp):
TATAGAATTTGATAGGTGTAGTTATTTATT
Found at i:21836 original size:30 final size:32
Alignment explanation
Indices: 21770--21843 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 32
21760 AATTTTAAAT
*
21770 AAATAATAGTAAAATTAAAATTTAATCTTCTTAA
1 AAATAATA--AAAATTAAAATTCAATCTTCTTAA
*
21804 AAATAATAAAAATT-TAATTCAATCTT-TTAA
1 AAATAATAAAAATTAAAATTCAATCTTCTTAA
21834 AAATAATAAA
1 AAATAATAAA
21844 GATAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 14 0.37
31 10 0.26
32 6 0.16
34 8 0.21
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (32 bp):
AAATAATAAAAATTAAAATTCAATCTTCTTAA
Found at i:55682 original size:19 final size:19
Alignment explanation
Indices: 55651--55691 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
55641 AATAAAAGAA
55651 AAAAACTTATAT-ATTAATT
1 AAAAACTTATATAATT-ATT
55670 AAAAA-TTACTATAATTATT
1 AAAAACTTA-TATAATTATT
55689 AAA
1 AAA
55692 TATTTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.15
19 14 0.70
20 3 0.15
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAACTTATATAATTATT
Found at i:55803 original size:26 final size:26
Alignment explanation
Indices: 55734--55822 Score: 80
Period size: 26 Copynumber: 3.6 Consensus size: 26
55724 TACATATTAA
* *
55734 ATATTGAATAATAATTATATTAAATT
1 ATATTTAATAATAATTTTATTAAATT
* * *
55760 ATGATTAAATTAT-TTTTTATTAAATT
1 AT-ATTTAATAATAATTTTATTAAATT
*
55786 ATATTTAATAATAGTTTT-TTAAA--
1 ATATTTAATAATAATTTTATTAAATT
55809 AT-TTTAATAATAAT
1 ATATTTAATAATAAT
55823 AACAATAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
22 11 0.21
23 2 0.04
25 13 0.25
26 19 0.36
27 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
ATATTTAATAATAATTTTATTAAATT
Found at i:56002 original size:16 final size:16
Alignment explanation
Indices: 55983--56026 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
55973 ATTATAGCTC
* *
55983 TATTTCATTACAACTT
1 TATTCCATTACAACTA
55999 TATTCCATTACAACTA
1 TATTCCATTACAACTA
*
56015 TATTCTATTACA
1 TATTCCATTACA
56027 GCCCTATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTCCATTACAACTA
Found at i:62878 original size:20 final size:20
Alignment explanation
Indices: 62853--62928 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
62843 TTGGTTATTG
62853 TTTGCACTTCGGTGCCCCTA
1 TTTGCACTTCGGTGCCCCTA
* **
62873 TTTGCATTTTAGTGCCCCTA
1 TTTGCACTTCGGTGCCCCTA
* * *
62893 TTTGTACTTTGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTA
*
62913 CTTGCACTTCGGTGCC
1 TTTGCACTTCGGTGCC
62929 TCTGTTTGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.09, C:0.30, G:0.21, T:0.39
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTA
Found at i:66917 original size:23 final size:22
Alignment explanation
Indices: 66886--66929 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
66876 AAAGAAATAA
*
66886 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
66908 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
66930 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:69564 original size:8 final size:8
Alignment explanation
Indices: 69551--69600 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
69541 CATATATTTA
69551 TTTTTTTC
1 TTTTTTTC
69559 TTTTTTTC
1 TTTTTTTC
* *
69567 TCTTTTCC
1 TTTTTTTC
69575 TATTTTTTC
1 T-TTTTTTC
69584 TTTCTTTTC
1 TTT-TTTTC
69593 TCTTTTTT
1 T-TTTTTT
69601 TTATAAGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 17 0.49
9 16 0.46
10 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:70655 original size:18 final size:18
Alignment explanation
Indices: 70634--70681 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
70624 CTTCTCTTCA
70634 TTCTTCTCCTC-TTTTTCC
1 TTCTTCTCCTCATTTTT-C
70652 TTC-TCTTCCTCATTTTTC
1 TTCTTC-TCCTCATTTTTC
*
70670 GTCTTCTCCTCA
1 TTCTTCTCCTCA
70682 GGTTTCGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 17 0.65
19 7 0.27
ACGTcount: A:0.04, C:0.38, G:0.02, T:0.56
Consensus pattern (18 bp):
TTCTTCTCCTCATTTTTC
Done.