Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013309.1 Kokia drynarioides strain JFW-HI SEQ_128331, 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: 54016
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:798 original size:23 final size:23
Alignment explanation
Indices: 769--926 Score: 142
Period size: 23 Copynumber: 6.6 Consensus size: 23
759 GAACACTAGC
*
769 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
791 CGTGCTCTCTGTTATTAGCACTTGTGT
1 -GTGCTCTCTG-T-TTAGCAC-TGTGT
* * *
818 GTGCTATCTGATTAGCACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
841 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
864 GTGCTCTCTGTTGTCCAGCACT-TAT
1 GTGCTCTCTGTT-T--AGCACTGTGT
*
889 GTGCTCTCTGTTGTCCAGCACT-TAT
1 GTGCTCTCTGTT-T--AGCACTGTGT
914 GTGCTCTCTGTTT
1 GTGCTCTCTGTTT
927 GTTCCGTATA
Statistics
Matches: 120, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
23 46 0.38
24 10 0.08
25 46 0.38
26 15 0.12
27 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:922 original size:27 final size:25
Alignment explanation
Indices: 854--925 Score: 126
Period size: 25 Copynumber: 2.8 Consensus size: 25
844 CTCTCTGATT
*
854 AGCACTGTGTGTGCTCTCTGTTGTCC
1 AGCACT-TATGTGCTCTCTGTTGTCC
880 AGCACTTATGTGCTCTCTGTTGTCC
1 AGCACTTATGTGCTCTCTGTTGTCC
905 AGCACTTATGTGCTCTCTGTT
1 AGCACTTATGTGCTCTCTGTT
926 TGTTCCGTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 39 0.87
26 6 0.13
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.40
Consensus pattern (25 bp):
AGCACTTATGTGCTCTCTGTTGTCC
Found at i:5031 original size:19 final size:19
Alignment explanation
Indices: 4993--5029 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4983 TTATATATTC
4993 TTTATATATTTTTTAAAAA
1 TTTATATATTTTTTAAAAA
5012 TTTATA-ATTTTTTAAAAA
1 TTTATATATTTTTTAAAAA
5030 ATATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATATTTTTTAAAAA
Found at i:5034 original size:17 final size:18
Alignment explanation
Indices: 4995--5035 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4985 ATATATTCTT
4995 TATAT-ATTTTTTAAAAA
1 TATATAATTTTTTAAAAA
*
5012 TTTATAATTTTTTAAAAA
1 TATATAATTTTTTAAAAA
5030 -ATATAA
1 TATATAA
5036 AATTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATAATTTTTTAAAAA
Found at i:5037 original size:26 final size:25
Alignment explanation
Indices: 5008--5076 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
4998 ATATTTTTTA
5008 AAAATTTATAATTTTTTAAAAAATAT
1 AAAATTTA-AATTTTTTAAAAAATAT
* *
5034 AAAATTTGAAATTTTTATAAATAATTT
1 AAAATTT-AAATTTTT-TAAAAAATAT
* *
5061 TAATTTTAAATTTTTT
1 AAAATTTAAATTTTTT
5077 TATAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.59
27 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
AAAATTTAAATTTTTTAAAAAATAT
Found at i:5039 original size:19 final size:18
Alignment explanation
Indices: 5000--5040 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4990 TTCTTTATAT
* *
5000 ATTTTTTAAAAATTTATA
1 ATTTTTTAAAAATATAAA
5018 ATTTTTTAAAAAATATAAA
1 ATTTTTT-AAAAATATAAA
5037 ATTT
1 ATTT
5041 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTTAAAAATATAAA
Found at i:10126 original size:17 final size:18
Alignment explanation
Indices: 10093--10126 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10083 TTCTCAGAAA
*
10093 CACTTTTGGGCCAAAAAG
1 CACTTTTGAGCCAAAAAG
10111 CACTTTTGAG-CAAAAA
1 CACTTTTGAGCCAAAAA
10127 CTAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (18 bp):
CACTTTTGAGCCAAAAAG
Found at i:30030 original size:20 final size:21
Alignment explanation
Indices: 29980--30043 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
29970 TTATATGTGA
* * *
29980 AATACAATAAAATAAACAAAT
1 AATACATTAAATTAAAAAAAT
30001 AATACATTAAATTAAAAAAAT
1 AATACATTAAATTAAAAAAAT
*
30022 AATTC-TT-AATATAAAAAAAT
1 AATACATTAAAT-TAAAAAAAT
30042 AA
1 AA
30044 CGTAATTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
21 22 0.58
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
AATACATTAAATTAAAAAAAT
Found at i:33499 original size:11 final size:11
Alignment explanation
Indices: 33483--33509 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33473 CCAAATAAAA
33483 TAAATTTATTT
1 TAAATTTATTT
33494 TAAATTTATTT
1 TAAATTTATTT
33505 TAAAT
1 TAAAT
33510 CCATAGTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TAAATTTATTT
Found at i:46546 original size:18 final size:18
Alignment explanation
Indices: 46525--46561 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46515 AAAAGAAAGC
*
46525 AAATAAATAAACGAAAAA
1 AAATAAACAAACGAAAAA
*
46543 AAATAAACAAATGAAAAA
1 AAATAAACAAACGAAAAA
46561 A
1 A
46562 GGGGAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (18 bp):
AAATAAACAAACGAAAAA
Found at i:46602 original size:17 final size:18
Alignment explanation
Indices: 46577--46618 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
46567 AAAGAGGGGG
*
46577 GGGAAAAAGGGGGAA-GA
1 GGGAGAAAGGGGGAAGGA
46594 GGGAGAAAGGGGGAAGGA
1 GGGAGAAAGGGGGAAGGA
46612 GGGAGAA
1 GGGAGAA
46619 TCCTAATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
GGGAGAAAGGGGGAAGGA
Found at i:46773 original size:31 final size:31
Alignment explanation
Indices: 46700--46783 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
46690 TTATTTTTTT
* *
46700 ATTAAATTATTTAAAAAATTTTATTTAAGTA
1 ATTAAATTATTTAAATATTTTTATTTAAGTA
*
46731 ATTAAACTATTTAAATATTTTTATTTTAA-TA
1 ATTAAATTATTTAAATATTTTTA-TTTAAGTA
** *
46762 ATTTGATTATTT-CATATTTTTA
1 ATTAAATTATTTAAATATTTTTA
46784 AGTTTGATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 9 0.20
31 31 0.69
32 5 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTAAATTATTTAAATATTTTTATTTAAGTA
Found at i:46956 original size:21 final size:21
Alignment explanation
Indices: 46918--46959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46908 TTTTAACATT
* * *
46918 TAAAATTGTTTCATAAAAAAA
1 TAAAATTGTATAAGAAAAAAA
46939 TAAAATTGTATAAGAAAAAAA
1 TAAAATTGTATAAGAAAAAAA
46960 GAACAAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
TAAAATTGTATAAGAAAAAAA
Found at i:48106 original size:76 final size:76
Alignment explanation
Indices: 47980--48132 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
47970 TCACAAATCC
47980 CGTGAAAACTTTTGGGGGAAAACAATTAAAATGCGGGTGGCATTATGGGGGGAGAATATGGGATT
1 CGTGAAAACTTTTGGGGGAAAACAATTAAAATGCGGGTGGCATTATGGGGGGAGAATATGGGATT
48045 GGTATGAAATT
66 GGTATGAAATT
*
48056 CGTGAAAACTTTTGGGGGAAAACAATTAAAATGCGGGTGGCATTATGGGGGGAGAATTTGGGATT
1 CGTGAAAACTTTTGGGGGAAAACAATTAAAATGCGGGTGGCATTATGGGGGGAGAATATGGGATT
48121 GGTATGAAATT
66 GGTATGAAATT
48132 C
1 C
48133 TTTAGAAATT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.27
Consensus pattern (76 bp):
CGTGAAAACTTTTGGGGGAAAACAATTAAAATGCGGGTGGCATTATGGGGGGAGAATATGGGATT
GGTATGAAATT
Found at i:48974 original size:29 final size:29
Alignment explanation
Indices: 48932--48997 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
48922 AATGAACATG
*
48932 ACAAAATTTGATTATAAGAAATTCCTTTA
1 ACAAAATTTGATTATAAGAAATGCCTTTA
48961 ACAAAATTTGATTATAAGAAATGCCTTTA
1 ACAAAATTTGATTATAAGAAATGCCTTTA
48990 ACAAAATT
1 ACAAAATT
48998 AAGCTTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (29 bp):
ACAAAATTTGATTATAAGAAATGCCTTTA
Done.