Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011111.1 Kokia drynarioides strain JFW-HI SEQ_126084, 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: 60423
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:13997 original size:22 final size:21
Alignment explanation
Indices: 13967--14007 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
13957 ATGTCTAGCT
13967 AGATCAAATATATTTTGATAC
1 AGATCAAATATATTTTGATAC
13988 AGATCCAAATATATTTTGAT
1 AGAT-CAAATATATTTTGAT
14008 TATCAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
AGATCAAATATATTTTGATAC
Found at i:25187 original size:44 final size:44
Alignment explanation
Indices: 25137--25227 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
25127 AATTTATAAT
25137 ATTTTTATTATTTAAATTGAATTCGGGCTAACCCAAGGTGCAAA
1 ATTTTTATTATTTAAATTGAATTCGGGCTAACCCAAGGTGCAAA
25181 ATTTTTATTATTTAAATTGAATTCGGGCTAACCCAAGGTGCAAA
1 ATTTTTATTATTTAAATTGAATTCGGGCTAACCCAAGGTGCAAA
25225 ATT
1 ATT
25228 ACTTGTCCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (44 bp):
ATTTTTATTATTTAAATTGAATTCGGGCTAACCCAAGGTGCAAA
Found at i:26692 original size:41 final size:41
Alignment explanation
Indices: 26647--26779 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
26637 GAAAAAAGGT
*
26647 AGAGCAATAACGGCGCTTATGGGAAAGCGCCGCTAAAGATC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATC
* * * * * * *
26688 AGAGCAATAGTGACGCTTATAGGCAAGCGCTGCAAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATC
* * * * *
26729 AGACCAATAGCAGCACTTATGGGAAAGCGCCGTTAAA-AGTT
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGA-TC
26770 AGAGCAATAG
1 AGAGCAATAG
26780 AAGATTAGTG
Statistics
Matches: 70, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.17
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGATC
Found at i:30953 original size:43 final size:43
Alignment explanation
Indices: 30906--31004 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
30896 GACTATATTT
*
30906 TTTAGCGGCGTTTGT-ATGAACAGTGCCACTAAAAAACATGTTC
1 TTTAGCGGCGTTTGTGAGGAA-AGTGCCACTAAAAAACATGTTC
* * ** **
30949 TTTAGCGGTGTTTGTGGGGAAAGTGCCGTTAAAAATTATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGTGCCACTAAAAAACATGTTC
*
30992 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
31005 TTTCTAATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 43 0.93
44 3 0.07
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGGAAAGTGCCACTAAAAAACATGTTC
Found at i:31160 original size:22 final size:22
Alignment explanation
Indices: 31108--31161 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
31098 TATAAATGCA
* *
31108 GCTATAAACCCAAAAAAACGCC
1 GCTAAAAACCAAAAAAAACGCC
* *
31130 GCTATAAACCAAAAAAAACTCC
1 GCTAAAAACCAAAAAAAACGCC
*
31152 GTTAAAAACC
1 GCTAAAAACC
31162 TGTTTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.13
Consensus pattern (22 bp):
GCTAAAAACCAAAAAAAACGCC
Found at i:32060 original size:19 final size:19
Alignment explanation
Indices: 32018--32060 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
32008 TAGTTTTAAC
*
32018 TGTTAAGTACAGCTAGTAT
1 TGTTAAGTACAGCTACTAT
* * *
32037 AGTTAAGTACTGCTACTGT
1 TGTTAAGTACAGCTACTAT
32056 TGTTA
1 TGTTA
32061 GAGCAGTTAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (19 bp):
TGTTAAGTACAGCTACTAT
Found at i:38916 original size:60 final size:60
Alignment explanation
Indices: 38852--38967 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
38842 TAATTTGGTT
* *
38852 ACCATTTTGTAACATTTCATAGTT-ATCTGACCAAATA-ATAAATTTACTAATAGTTGAGTG
1 ACCATTTTGTAACATTTCATAATTAAT-TGACCAAA-AGAAAAATTTACTAATAGTTGAGTG
*
38912 ACCATTTTGTAATATTTCATAATTAATTGACCAAAAGAAAAATTTACTAATAGTTG
1 ACCATTTTGTAACATTTCATAATTAATTGACCAAAAGAAAAATTTACTAATAGTTG
38968 GATGACTACT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 1 0.02
60 48 0.94
61 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (60 bp):
ACCATTTTGTAACATTTCATAATTAATTGACCAAAAGAAAAATTTACTAATAGTTGAGTG
Found at i:39006 original size:46 final size:46
Alignment explanation
Indices: 38951--39119 Score: 135
Period size: 46 Copynumber: 3.4 Consensus size: 46
38941 ACCAAAAGAA
38951 AAATTTACTAATAGTTGGATGACTACTAGTTATCTGACCAAATAAT
1 AAATTTACTAATAGTTGGATGACTACTAGTTATCTGACCAAATAAT
* * * * *
38997 AAATTTACTAATAGTT-GAGTGACCATTTTGTAATATTTCATAATTAATTGACCAAA-ATAA
1 AAATTTACTAATAGTTGGA-TGA-C------TACTAGTT-AT--CT--G--ACCAAATA-AT
39057 AAATTTACTAATAGTTGGATGACTACTAGTTATCTGACCAAATAAT
1 AAATTTACTAATAGTTGGATGACTACTAGTTATCTGACCAAATAAT
39103 AAATTTACTAATAGTTG
1 AAATTTACTAATAGTTG
39120 AGTGGCCATT
Statistics
Matches: 95, Mismatches: 10, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
45 2 0.02
46 43 0.45
47 2 0.02
50 1 0.01
52 2 0.02
53 12 0.13
54 2 0.02
56 1 0.01
59 2 0.02
60 26 0.27
61 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (46 bp):
AAATTTACTAATAGTTGGATGACTACTAGTTATCTGACCAAATAAT
Found at i:39059 original size:106 final size:106
Alignment explanation
Indices: 38871--39192 Score: 626
Period size: 106 Copynumber: 3.0 Consensus size: 106
38861 TAACATTTCA
38871 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
1 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
38936 AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
66 AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
38977 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
1 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
*
39042 AATTGACCAAAATAAAAATTTACTAATAGTTGGATGACTAC
66 AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
*
39083 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGGCCATTTTGTAATATTTCATAATT
1 TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
39148 AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
66 AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
39189 TAGT
1 TAGT
39193 GTATTTTACC
Statistics
Matches: 213, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 213 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (106 bp):
TAGTTATCTGACCAAATAATAAATTTACTAATAGTTGAGTGACCATTTTGTAATATTTCATAATT
AATTGACCAAAAGAAAAATTTACTAATAGTTGGATGACTAC
Found at i:55425 original size:24 final size:24
Alignment explanation
Indices: 55333--55423 Score: 146
Period size: 24 Copynumber: 3.8 Consensus size: 24
55323 GAAATAATCA
55333 TTCAGTTAAACTCTGTTTAATTGT
1 TTCAGTTAAACTCTGTTTAATTGT
55357 TTCAGTTAAACTCTGTTTAATTGT
1 TTCAGTTAAACTCTGTTTAATTGT
* *
55381 TTCAGTTAAACTCTGTTTATTTAT
1 TTCAGTTAAACTCTGTTTAATTGT
* *
55405 TTCAATTAAACTTTGTTTA
1 TTCAGTTAAACTCTGTTTA
55424 TTGGTTTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (24 bp):
TTCAGTTAAACTCTGTTTAATTGT
Found at i:55439 original size:24 final size:24
Alignment explanation
Indices: 55388--55442 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
55378 TGTTTCAGTT
* * * *
55388 AAACTCTGTTTATTTATTTCAATT
1 AAACTTTGTTTATTGATTTAAATC
*
55412 AAACTTTGTTTATTGGTTTAAATC
1 AAACTTTGTTTATTGATTTAAATC
55436 AAACTTT
1 AAACTTT
55443 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (24 bp):
AAACTTTGTTTATTGATTTAAATC
Found at i:55440 original size:48 final size:48
Alignment explanation
Indices: 55340--55440 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
55330 TCATTCAGTT
* * * * *
55340 AAACTCTGTTTAATTGTTTCAGTTAAACTCTGTTTAATTGTTTCAGTT
1 AAACTCTGTTTAATTATTTCAATTAAACTCTGTTTAATTGTTTAAATC
* *
55388 AAACTCTGTTTATTTATTTCAATTAAACTTTGTTT-ATTGGTTTAAATC
1 AAACTCTGTTTAATTATTTCAATTAAACTCTGTTTAATT-GTTTAAATC
55436 AAACT
1 AAACT
55441 TTTATTAGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 3 0.07
48 42 0.93
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (48 bp):
AAACTCTGTTTAATTATTTCAATTAAACTCTGTTTAATTGTTTAAATC
Done.