Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013636.1 Kokia drynarioides strain JFW-HI SEQ_128664, 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: 16909
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4816 original size:20 final size:21
Alignment explanation
Indices: 4791--4831 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4781 CTCGTAACCA
4791 CATTTT-TTTCGAA-TAACTTT
1 CATTTTCTTTC-AACTAACTTT
4811 CATTTTCTTTCAACTAACTTT
1 CATTTTCTTTCAACTAACTTT
4832 TGTCTCTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (21 bp):
CATTTTCTTTCAACTAACTTT
Found at i:9163 original size:21 final size:20
Alignment explanation
Indices: 9138--9189 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
9128 ATTGGTCTCG
9138 ATTTTACAAAACAATATCGAT
1 ATTTTACAAAA-AATATCGAT
**
9159 ATTTTTGAAAAAATATCGAT
1 ATTTTACAAAAAATATCGAT
**
9179 ACCTTACAAAA
1 ATTTTACAAAA
9190 GGCATCGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTTTACAAAAAATATCGAT
Found at i:12852 original size:9 final size:9
Alignment explanation
Indices: 12840--12991 Score: 92
Period size: 10 Copynumber: 15.7 Consensus size: 9
12830 TTTATGATTT
12840 TTTTTATAA
1 TTTTTATAA
*
12849 TTTTTAAAA
1 TTTTTATAA
*
12858 GTTTATATTAA
1 -TTTTTA-TAA
* *
12869 TTTTAATAC
1 TTTTTATAA
*
12878 TTTTAATAA
1 TTTTTATAA
12887 TTTTTA-AGA
1 TTTTTATA-A
*
12896 TGTTTTATGA
1 T-TTTTATAA
12906 TTTTTATAGTA
1 TTTTTATA--A
*
12917 TTTTAATACA
1 TTTTTATA-A
12927 TTTTTATAAA
1 TTTTTAT-AA
*
12937 TTTTTAAATA
1 TTTTTATA-A
12947 TGTTTTATTAA
1 T-TTTTA-TAA
12958 -TTTTATAA
1 TTTTTATAA
12966 TTTTTTATAA
1 -TTTTTATAA
*
12976 TTTATTAGAA
1 TTT-TTATAA
12986 TTTTTA
1 TTTTTA
12992 AACATGACAC
Statistics
Matches: 113, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
8 4 0.04
9 43 0.38
10 48 0.42
11 17 0.15
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12891 original size:19 final size:18
Alignment explanation
Indices: 12840--12932 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 18
12830 TTTATGATTT
* *
12840 TTTTTATAATTTTTAAAA
1 TTTTAATAATTTTTAATA
*
12858 GTTTATATTAA-TTTTAATA
1 -TTT-TAATAATTTTTAATA
*
12877 CTTTTAATAATTTTTAAGA
1 -TTTTAATAATTTTTAATA
* *
12896 TGTTTTATGATTTTTATAGTA
1 T-TTTAATAATTTTTA-A-TA
12917 TTTTAATACATTTTTA
1 TTTTAATA-ATTTTTA
12933 TAAATTTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
18 6 0.11
19 32 0.56
20 10 0.18
21 9 0.16
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTAATAATTTTTAATA
Found at i:12941 original size:21 final size:22
Alignment explanation
Indices: 12917--12966 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
12907 TTTTATAGTA
12917 TTTTAATACAT-TTTTATAAAT
1 TTTTAATACATGTTTTATAAAT
* *
12938 TTTTAA-ATATGTTTTATTAAT
1 TTTTAATACATGTTTTATAAAT
12959 TTTATAAT
1 TTT-TAAT
12967 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATACATGTTTTATAAAT
Found at i:15462 original size:11 final size:11
Alignment explanation
Indices: 15438--15471 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
15428 ATTTTTTTTC
* *
15438 TTTTACTATTT
1 TTTTAATATAT
15449 TTTTAATATAT
1 TTTTAATATAT
15460 TTTTAATATAT
1 TTTTAATATAT
15471 T
1 T
15472 GGTATGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTAATATAT
Done.