Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002061.1 Kokia drynarioides strain JFW-HI SEQ_113964, 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: 22371
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:138 original size:23 final size:23
Alignment explanation
Indices: 112--169 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
102 TCAATACTGT
**
112 GTGTGCTTACTGTTTCGCATTTC
1 GTGTGCTTACTGTTTCGCACCTC
*
135 GTGTGCTTACTGTTTTGCACCTC
1 GTGTGCTTACTGTTTCGCACCTC
158 GTGTGCTTACTG
1 GTGTGCTTACTG
170 ATTTGCGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.45
Consensus pattern (23 bp):
GTGTGCTTACTGTTTCGCACCTC
Found at i:1554 original size:16 final size:18
Alignment explanation
Indices: 1532--1575 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 18
1522 AATTTCAAGT
1532 TTCAAAAAGTATAAG-GA
1 TTCAAAAAGTATAAGCGA
1549 TT--AAAA-T-TAAGCGA
1 TTCAAAAAGTATAAGCGA
1563 TTCAAAAAGTATA
1 TTCAAAAAGTATA
1576 GGTACTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 4 0.18
16 4 0.18
17 3 0.14
18 2 0.09
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (18 bp):
TTCAAAAAGTATAAGCGA
Found at i:2719 original size:15 final size:15
Alignment explanation
Indices: 2699--2741 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2689 CTTTTAATTA
2699 ATATTTTTAGTTTTT
1 ATATTTTTAGTTTTT
2714 ATATTTTTA-TATTTT
1 ATATTTTTAGT-TTTT
*
2729 TTATTTTTTAGTT
1 ATA-TTTTTAGTT
2742 CTTACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 15 0.62
16 7 0.29
17 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
ATATTTTTAGTTTTT
Found at i:2720 original size:8 final size:8
Alignment explanation
Indices: 2699--2736 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2689 CTTTTAATTA
2699 ATATTTTT
1 ATATTTTT
*
2707 A-GTTTTT
1 ATATTTTT
2714 ATATTTTT
1 ATATTTTT
2722 ATATTTTT
1 ATATTTTT
2730 -TATTTTT
1 ATATTTTT
2737 TAGTTCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
ATATTTTT
Found at i:8874 original size:17 final size:18
Alignment explanation
Indices: 8847--8885 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
8837 TATATTATTT
*
8847 ATTTAGGTTAATTGATTA
1 ATTTAGGTTAATTAATTA
8865 ATTT-GGTTAATTAATTA
1 ATTTAGGTTAATTAATTA
8882 ATTT
1 ATTT
8886 CGAATCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (18 bp):
ATTTAGGTTAATTAATTA
Found at i:14724 original size:3 final size:3
Alignment explanation
Indices: 14716--14740 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14706 CCTCTAGCCT
14716 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
14741 ATATAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.