Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008498.1 Kokia drynarioides strain JFW-HI SEQ_123173, 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: 20416
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:1672 original size:15 final size:15
Alignment explanation
Indices: 1654--1713 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
1644 TGGCTTGTCA
1654 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
*
1669 TCTTTGGATTTGTT-G
1 TCTTTTGATTT-TTCG
* *
1684 TCTTTTGATTTGTCA
1 TCTTTTGATTTTTCG
1699 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
1714 CCATTGACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 34 0.92
16 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.63
Consensus pattern (15 bp):
TCTTTTGATTTTTCG
Found at i:7974 original size:25 final size:25
Alignment explanation
Indices: 7936--8000 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
7926 ATTCCAACAA
** *
7936 TAATATTATTTTAATAGT-ATTTTAT
1 TAATATTAAATTAA-AGTGATTATAT
*
7961 TAAT-TTAATATTAAAGTGATTATCT
1 TAATATTAA-ATTAAAGTGATTATAT
7986 TAATATTAAATTAAA
1 TAATATTAAATTAAA
8001 TTTAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 6 0.18
25 23 0.70
26 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (25 bp):
TAATATTAAATTAAAGTGATTATAT
Found at i:10114 original size:19 final size:18
Alignment explanation
Indices: 10090--10151 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
10080 TATATTCAGA
10090 CTTTTTGCCCCAAAATTTT
1 CTTTTTGCCCC-AAATTTT
*
10109 CTTTTTGCCCTAAATTTT
1 CTTTTTGCCCCAAATTTT
10127 CTTTTTGCCCCAAATTTT
1 CTTTTTGCCCCAAATTTT
10145 CTTTTTG
1 CTTTTTG
10152 TCTTCGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 31 0.76
19 10 0.24
ACGTcount: A:0.16, C:0.24, G:0.06, T:0.53
Consensus pattern (18 bp):
CTTTTTGCCCCAAATTTT
Found at i:14344 original size:8 final size:8
Alignment explanation
Indices: 14326--14392 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
14316 TGTATGTGAA
14326 TTATATATT
1 TTAT-TATT
14335 TTATTATT
1 TTATTATT
14343 TTATTA-T
1 TTATTATT
*
14350 GTATATATGAT
1 TTAT-TAT--T
**
14361 AAATTAATT
1 TTATT-ATT
14370 TTATTATT
1 TTATTATT
14378 TTATTATT
1 TTATTATT
14386 TTATTAT
1 TTATTAT
14393 GTGATTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.08
8 30 0.62
9 8 0.17
10 1 0.02
11 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTATTATT
Found at i:18728 original size:15 final size:15
Alignment explanation
Indices: 18708--18775 Score: 109
Period size: 15 Copynumber: 4.5 Consensus size: 15
18698 CAATGGCGAA
*
18708 AAATCAAAAGATGAC
1 AAATCAAAAGACGAC
18723 AAATCAAAAGACGAC
1 AAATCAAAAGACGAC
18738 AAATCAAAAGACGAC
1 AAATCAAAAGACGAC
*
18753 AAATCAAAAGATGAC
1 AAATCAAAAGACGAC
*
18768 AAGTCAAA
1 AAATCAAA
18776 GCATGAAGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.10
Consensus pattern (15 bp):
AAATCAAAAGACGAC
Done.