Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012237.1 Kokia drynarioides strain JFW-HI SEQ_127238, 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: 3665
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:889 original size:20 final size:18
Alignment explanation
Indices: 848--887 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
838 ATTAGAGGTG
848 AAATAAATACAAATAATT
1 AAATAAATACAAATAATT
866 AAATAAAATGACAAA-AATT
1 AAAT-AAAT-ACAAATAATT
885 AAA
1 AAA
888 ATGTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAAATACAAATAATT
Found at i:961 original size:27 final size:27
Alignment explanation
Indices: 897--962 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 27
887 AATGTCAAAA
897 AAATGAATAAAAATAATAAATACACATT
1 AAATGAAT-AAAATAATAAATACACATT
* *
925 AAAT-ATTAAAATGAAT-AATATA-ATAT
1 AAATGAATAAAAT-AATAAATACACAT-T
951 AAATGAATAAAA
1 AAATGAATAAAA
963 AAGGATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 2 0.06
26 15 0.47
27 11 0.34
28 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (27 bp):
AAATGAATAAAATAATAAATACACATT
Found at i:2557 original size:11 final size:11
Alignment explanation
Indices: 2541--2569 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2531 GAACTTTATA
2541 TTTTTTTTCTT
1 TTTTTTTTCTT
2552 TTTTTTTTCTT
1 TTTTTTTTCTT
2563 TTTTTTT
1 TTTTTTT
2570 GGGTCGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:2978 original size:101 final size:101
Alignment explanation
Indices: 2865--3051 Score: 241
Period size: 101 Copynumber: 1.9 Consensus size: 101
2855 TTCCACTACT
** * * * *
2865 ACTTTAAGGAGATTGAGATTCG-TTATTGTAACTTTAATTCGACCCACTACAGCTTCAGGGGTAT
1 ACTTTAAGGAGATAAAGATTCGCTT-TTGCAACTTTAATCCGACACACTACAACTTCAGGGGTAT
* *
2929 AGGATTTGATATTGTAGCTTCATCTTGCTCTATTGTA
65 AAGATTTGATATTGTAACTTCATCTTGCTCTATTGTA
* * *
2966 ACTTTAGGGAGATAAAGATTTGCTTTTGCAACTTTAATCCTACACACTACAACTTCAGGGGTATA
1 ACTTTAAGGAGATAAAGATTCGCTTTTGCAACTTTAATCCGACACACTACAACTTCAGGGGTATA
* *
3031 AGATTTGGTTTTGTAACTTCA
66 AGATTTGATATTGTAACTTCA
3052 ATCTACCTCT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 70 0.97
102 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (101 bp):
ACTTTAAGGAGATAAAGATTCGCTTTTGCAACTTTAATCCGACACACTACAACTTCAGGGGTATA
AGATTTGATATTGTAACTTCATCTTGCTCTATTGTA
Found at i:3099 original size:48 final size:47
Alignment explanation
Indices: 3024--3462 Score: 368
Period size: 48 Copynumber: 9.3 Consensus size: 47
3014 ACAACTTCAG
* * * * *
3024 GGGTATAAGATTTGG-TTTTGTAACTTCAATCTACCTCTTTGGATTTA
1 GGGTATAAGA-TTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
* * * * * **
3071 GTGGTATAAGATTTGATTTGGTGGCTTCAATTTGCCCTTTTATATTTAA
1 G-GGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTT-A
* * * * * *
3120 GGGAATAAGATAGGATGTGGCAGCTTCAATCTACCCCTCTGGATTTA
1 GGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
* * * * *
3167 TAGGTATAAGATTAGATATGGTGGCTTCAATCTGTCCCTTTAGATTTA
1 -GGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
* *** *
3215 GGCGTATAATATTGGATGCAGT-GACTTCAATCTACCCCTTTGGATTTA
1 GG-GTATAAGATTGGATATGGTAG-CTTCAATCTGCCCCTTTGGATTTA
3263 GGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCC-TTGGATTTA
1 -GGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
* * * * * *
3310 GGAGTATAAGATTGGATATGGTGGCTTTAATATGCCACTCTAGATTTAA
1 GG-GTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTT-A
* * * *
3359 GTGTATAAGATTTGATGTGGTAGCTTTAATCTGCCCCTTTGGATTTA
1 GGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
* * * *
3406 GAGGTATAAGATTAGATTTGGT---TTCAATCTGCCCCTCTAGATTTA
1 G-GGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
3451 GGGTATAAGATT
1 GGGTATAAGATT
3463 TAGTGATGTA
Statistics
Matches: 313, Mismatches: 67, Indels: 27
0.77 0.16 0.07
Matches are distributed among these distances:
44 11 0.04
45 21 0.07
46 2 0.01
47 49 0.16
48 223 0.71
49 7 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (47 bp):
GGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTTTGGATTTA
Found at i:3365 original size:143 final size:144
Alignment explanation
Indices: 3114--3462 Score: 408
Period size: 143 Copynumber: 2.5 Consensus size: 144
3104 GCCCTTTTAT
* * * * * * *
3114 ATTTAAGGGAATAAGATAGGATGTGGCAGCTTCAATCTACCCCTCTGGATTTA-TAGGTATAAGA
1 ATTTAGGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTCTGGATTTAGGA-GTATAAGA
* * * *
3178 TTAGATATGGTGGCTTCAATCTGTCCCTTTAGATTTAGGCGTATAATATTGGATGCAGT-GACTT
65 TTAGATATGGTGGCTTCAATATGTCCCTCTAGATTTAAGCGTATAAGATTGGATGCAGTAG-CTT
3242 CAATCTACCCCTTTGG
129 CAATCTACCCCTTTGG
3258 ATTTAGGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCT-TGGATTTAGGAGTATAAGAT
1 ATTTAGGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTCTGGATTTAGGAGTATAAGAT
* * * * ** *
3322 TGGATATGGTGGCTTTAATATG-CCACTCTAGATTTAAGTGTATAAGATTTGATGTGGTAGCTTT
66 TAGATATGGTGGCTTCAATATGTCC-CTCTAGATTTAAGCGTATAAGATTGGATGCAGTAGCTTC
*
3386 AATCTGCCCCTTTGG
130 AATCTACCCCTTTGG
* * * *
3401 ATTTAGAGGTATAAGATTAGATTTGGT---TTCAATCTGCCCCTCTAGATTTAGG-GTATAAGAT
1 ATTTAGGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTCTGGATTTAGGAGTATAAGAT
3462 T
66 T
3463 TAGTGATGTA
Statistics
Matches: 178, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
140 24 0.13
141 9 0.05
142 2 0.01
143 103 0.58
144 40 0.22
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (144 bp):
ATTTAGGGGTATAAGATTGGATATGGTAGCTTCAATCTGCCCCTCTGGATTTAGGAGTATAAGAT
TAGATATGGTGGCTTCAATATGTCCCTCTAGATTTAAGCGTATAAGATTGGATGCAGTAGCTTCA
ATCTACCCCTTTGG
Done.