Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002930.1 Kokia drynarioides strain JFW-HI SEQ_115374, 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: 2991
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Found at i:809 original size:209 final size:209
Alignment explanation
Indices: 449--1033 Score: 884
Period size: 209 Copynumber: 2.8 Consensus size: 209
439 CAATGGAGAA
* * * ** *
449 AAGTGAACCAAATCCGTCTTTCTAATGAGATACAGAGAAAAGGATTAAAATAATGAGGCGGTCAT
1 AAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCAT
* *
514 CTTCCTGATGAGATATTGAGAAGTAGACCAATTCAATGAAA-CGAAGCTCAATGTAAGTGAAATT
66 CTTCCTGATGAGATATTGAGAAGTAGACCAATTCAA-AAAAGCGAAGCTCAATGTGAGTGAAATT
*
578 TCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGTTACCTTCC
130 TCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGCGGTTACCTTCC
643 AAATGAGATACAGAG
195 AAATGAGATACAGAG
* * * *
658 AAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAGGTGGATTAAAACAATGAGGAGATCAT
1 AAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCAT
* * * * *
723 CTTACTGATGAGATATTGAGAAGTAGACCAAATCAAAAAAGCAAAGCTCAATTTGAGTGAAACTT
66 CTTCCTGATGAGATATTGAGAAGTAGACCAATTCAAAAAAGCGAAGCTCAATGTGAGTGAAATTT
* **
788 CAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGTGGTTACCTTCTT
131 CAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGCGGTTACCTTCCA
*
853 GATGAGATACAGAG
196 AATGAGATACAGAG
867 AAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCAT
1 AAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCAT
* **
932 CTTCCTGATGAGATACTGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATGTGAGTGAAATTT
66 CTTCCTGATGAGATATTGAGAAGTAGACCAATTCAAAAAAGCGAAGCTCAATGTGAGTGAAATTT
* * * * *
997 CAAATCCCCATCTTCTTGATGAGCTATAGAGAAGTGA
131 CAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGA
1034 ACCGTCTTCA
Statistics
Matches: 336, Mismatches: 39, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
208 3 0.01
209 333 0.99
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
AAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCAT
CTTCCTGATGAGATATTGAGAAGTAGACCAATTCAAAAAAGCGAAGCTCAATGTGAGTGAAATTT
CAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGCGGTTACCTTCCA
AATGAGATACAGAG
Found at i:962 original size:85 final size:85
Alignment explanation
Indices: 795--955 Score: 216
Period size: 85 Copynumber: 1.9 Consensus size: 85
785 CTTCAAACCC
* * * *
795 CCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGTGGTTACCTTCTTGATGAGA
1 CCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAACAATAAAGCGGTCACCTTCCTGATGAGA
860 TACAGAGAAGTGAACCAAAT
66 TACAGAGAAGTGAACCAAAT
* * * * *
880 CCATCTTCCTGATGAGATACAGAGAAGTG-GATTAAAACAATGAGGCGGTCATCTTCCTGATGAG
1 CCATCTTCCTGATGAGATACAAAGAAGTGAG-TCAAAACAATAAAGCGGTCACCTTCCTGATGAG
*
944 ATACTGAGAAGT
65 ATACAGAGAAGT
956 AGACCAATTC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 1 0.02
85 64 0.98
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (85 bp):
CCATCTTCCTGATGAGATACAAAGAAGTGAGTCAAAACAATAAAGCGGTCACCTTCCTGATGAGA
TACAGAGAAGTGAACCAAAT
Found at i:2152 original size:24 final size:24
Alignment explanation
Indices: 2121--2166 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2111 TCAAAAAAAG
2121 GGGTTCATAGAAGACAGATTTTTA
1 GGGTTCATAGAAGACAGATTTTTA
*
2145 GGGTTCATAGAAGATAGATTTT
1 GGGTTCATAGAAGACAGATTTT
2167 AAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (24 bp):
GGGTTCATAGAAGACAGATTTTTA
Done.