Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012781.1 Kokia drynarioides strain JFW-HI SEQ_127793, 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: 10710
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:3877 original size:31 final size:29
Alignment explanation
Indices: 3839--3908 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
3829 ATCTTAAAAC
*
3839 TATACATGAACTATGGTTTAATGTGTAATTG
1 TATACATGAACTATGATTT--TGTGTAATTG
* * *
3870 TATACATGAATTTTGATTTTGTGTAATTT
1 TATACATGAACTATGATTTTGTGTAATTG
3899 TATACATGAA
1 TATACATGAA
3909 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.46
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGTAATTG
Found at i:3902 original size:29 final size:30
Alignment explanation
Indices: 3860--3918 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
3850 TATGGTTTAA
3860 TGTGTAATTGTATACATG-AATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
*
3889 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
3919 GATCCAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTGATTT
Found at i:4026 original size:21 final size:21
Alignment explanation
Indices: 3985--4026 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3975 ATATATTGTA
*
3985 ATAATAAATAATTAATCTATT
1 ATAATAAATAATTAATATATT
*
4006 ATAA-AAATAAATTGATATATT
1 ATAATAAAT-AATTAATATATT
4027 TATTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATAAATAATTAATATATT
Found at i:4722 original size:12 final size:12
Alignment explanation
Indices: 4705--4750 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4695 TCATTTAAAA
4705 GCTCGTTTATTG
1 GCTCGTTTATTG
* **
4717 GTTCGTTTATAA
1 GCTCGTTTATTG
4729 GCTCGTTTATTG
1 GCTCGTTTATTG
*
4741 ACTCGTTTAT
1 GCTCGTTTAT
4751 GACTCATTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:4730 original size:24 final size:24
Alignment explanation
Indices: 4698--4750 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
4688 AACAAGCTCA
* **
4698 TTTAAAAGCTCGTTTATTGGTTCG
1 TTTATAAGCTCGTTTATTGACTCG
4722 TTTATAAGCTCGTTTATTGACTCG
1 TTTATAAGCTCGTTTATTGACTCG
4746 TTTAT
1 TTTAT
4751 GACTCATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (24 bp):
TTTATAAGCTCGTTTATTGACTCG
Found at i:4755 original size:11 final size:11
Alignment explanation
Indices: 4719--4761 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
4709 GTTTATTGGT
*
4719 TCGTTTATAAGC
1 TCGTTTATGA-C
4731 TCGTTTATTGAC
1 TCGTTTA-TGAC
4743 TCGTTTATGAC
1 TCGTTTATGAC
*
4754 TCATTTAT
1 TCGTTTAT
4762 TTATTAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 11 0.39
12 15 0.54
13 2 0.07
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (11 bp):
TCGTTTATGAC
Found at i:4950 original size:23 final size:23
Alignment explanation
Indices: 4907--4952 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4897 TTAATGTTCG
*
4907 TGAACATATTCGATTAAATTAAA
1 TGAACATATTCGATGAAATTAAA
4930 TGAACATATTCG-TGAACATTAAA
1 TGAACATATTCGATGAA-ATTAAA
4953 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (23 bp):
TGAACATATTCGATGAAATTAAA
Found at i:8260 original size:19 final size:19
Alignment explanation
Indices: 8236--8293 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
8226 ACCGATCCGA
8236 CCGAAATCATTCGGTTAAT
1 CCGAAATCATTCGGTTAAT
8255 CCGAAATCATTCGGTTAAT
1 CCGAAATCATTCGGTTAAT
8274 CCGAAATCATTCGGTTAAT
1 CCGAAATCATTCGGTTAAT
8293 C
1 C
8294 GATCGATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (19 bp):
CCGAAATCATTCGGTTAAT
Done.