Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002483.1 Kokia drynarioides strain JFW-HI SEQ_114630, 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: 7969
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Found at i:616 original size:7 final size:7
Alignment explanation
Indices: 600--642 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
590 GCAACTTGAA
*
600 TTTCCCT
1 TTTCCTT
607 TTTCCTT
1 TTTCCTT
614 TTTCCTT
1 TTTCCTT
621 TTTCCTT
1 TTTCCTT
628 TTTCCTT
1 TTTCCTT
635 TTTCCTT
1 TTTCCTT
642 T
1 T
643 GTAACTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTCCTT
Found at i:887 original size:17 final size:17
Alignment explanation
Indices: 862--895 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
852 AAGGGTATGC
862 TTTTCTTTCTGTGTTTT
1 TTTTCTTTCTGTGTTTT
*
879 TTTTTTTTCTGTGTTTT
1 TTTTCTTTCTGTGTTTT
896 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (17 bp):
TTTTCTTTCTGTGTTTT
Found at i:901 original size:17 final size:17
Alignment explanation
Indices: 867--903 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
857 TATGCTTTTC
**
867 TTTCTGTGTTTTTTTTT
1 TTTCTGTGTTTTAATTT
884 TTTCTGTGTTTTAATTT
1 TTTCTGTGTTTTAATTT
901 TTT
1 TTT
904 AAGATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.78
Consensus pattern (17 bp):
TTTCTGTGTTTTAATTT
Found at i:6001 original size:172 final size:172
Alignment explanation
Indices: 5705--6017 Score: 378
Period size: 172 Copynumber: 1.8 Consensus size: 172
5695 CTTTTAGCTG
* *
5705 TGTCACAGTTTATGGATCATAGTGATGGTTATCAATATTGATGATGTGATATACTGCTTAGATAT
1 TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT
* * * * * *
5770 TCCACGTTAGTTTATGTTACCCGGACTTGAGGATGACCGCATATCATTTTCCCGATATGTGTCT-
66 GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATATCATTATCCAGATATGTGT-TG
*
5834 TACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA
130 CACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA
* ** **
5877 TGTCACAATTTATGGATCATGGTGATGGTTATCGTTATTGATGATCTGATATGTTGCTTAGATAT
1 TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT
**** * * *** *
5942 GCTGTTTTAATCTCTGTTACTCGGACTCGAGGATGAGTTCATATCCA-TATCTAGATATGTGTTG
66 GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATAT-CATTATCCAGATATGTGTTG
6006 CACATAGGTGTT
130 CACATAGGTGTT
6018 AGCCATGGGT
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
171 1 0.01
172 112 0.97
173 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (172 bp):
TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT
GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATATCATTATCCAGATATGTGTTGC
ACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA
Done.