Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006650.1 Kokia drynarioides strain JFW-HI SEQ_121241, 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: 7419
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:3841 original size:28 final size:28
Alignment explanation
Indices: 3798--3887 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
3788 AAGGCTCAAG
*
3798 AGAGCGTTATTCTGTATTCTAGATCGAA
1 AGAGCGTTATTCTGTATTCTAGCTCGAA
* *
3826 AGAGCGTTATTTTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTATTCTAGCTCGAA
* *
3854 AGAGTGTTGTTCTGTATTCTAGCTCGAA
1 AGAGCGTTATTCTGTATTCTAGCTCGAA
3882 AGAGCG
1 AGAGCG
3888 ATAATTTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (28 bp):
AGAGCGTTATTCTGTATTCTAGCTCGAA
Found at i:3913 original size:56 final size:55
Alignment explanation
Indices: 3790--3913 Score: 151
Period size: 56 Copynumber: 2.2 Consensus size: 55
3780 GGGAATGAAA
* * *
3790 GGCTCAAGAGAGCGTTATTCTGTATTCTAGATCGAAAGAGCGTTATTTTGTATTCT
1 GGCTCAA-AGAGCGTTATTCTGTATTCTAGATCGAAAGAGCGTAATTTGGTACTCT
* * *
3846 GGCTCGAAAGAGTGTTGTTCTGTATTCTAGCTCGAAAGAGCGATAATTTGGT-CTCT
1 GGCTC-AAAGAGCGTTATTCTGTATTCTAGATCGAAAGAGCG-TAATTTGGTACTCT
3902 GGCTCATAAGAG
1 GGCTCA-AAGAG
3914 AAATATTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
55 1 0.02
56 49 0.83
57 9 0.15
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (55 bp):
GGCTCAAAGAGCGTTATTCTGTATTCTAGATCGAAAGAGCGTAATTTGGTACTCT
Found at i:3923 original size:28 final size:28
Alignment explanation
Indices: 3898--3952 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3888 ATAATTTGGT
3898 CTCTGGCTC-ATAAGAGAAATATTTTGAA
1 CTCTGGCTCAAT-AGAGAAATATTTTGAA
* *
3926 CTCTTGCTCAATAGAGAATTATTTTGA
1 CTCTGGCTCAATAGAGAAATATTTTGA
3953 TCTGGGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (28 bp):
CTCTGGCTCAATAGAGAAATATTTTGAA
Found at i:5685 original size:71 final size:71
Alignment explanation
Indices: 5540--5693 Score: 184
Period size: 71 Copynumber: 2.2 Consensus size: 71
5530 TTTTCAATCC
* * * *
5540 ACTACCTATACTTCAAATCACAATGAGCAAGACTAACTAGCCTGGAGGTTTCTACTGACACATCA
1 ACTACCAATACTTCAAATCACAATGAGCAAGACTAACTAACCTGGAGATTTCAACTGACACATCA
5605 ATTCTA
66 ATTCTA
* * * * * * **
5611 ACTACCGATACTTCAAATGACAGTGAGCAAGACTAACTAATCTGGTGATTTCAATTGATTCAT-A
1 ACTACCAATACTTCAAATCACAATGAGCAAGACTAACTAACCTGGAGATTTCAACTGACACATCA
5675 ATTCTCA
66 ATTCT-A
5682 ACTACCAATACT
1 ACTACCAATACT
5694 ACACACAAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
70 6 0.09
71 64 0.91
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (71 bp):
ACTACCAATACTTCAAATCACAATGAGCAAGACTAACTAACCTGGAGATTTCAACTGACACATCA
ATTCTA
Found at i:6625 original size:40 final size:39
Alignment explanation
Indices: 6570--6703 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 39
6560 CCATAGCTTG
* *
6570 GCTTGAATTCTATCACTGACTCGTAGTCTGCTAAGTCGAA
1 GCTTGAATTCTATCACTGACTCATAGCCTGCTAAG-CGAA
* * *
6610 GCTTGAATTTTATCAC-CAGCTCATAGCCTGCTAAGCCAAA
1 GCTTGAATTCTATCACTGA-CTCATAGCCTGCTAAG-CGAA
* *
6650 GCTTGAATTCTATCA-TCGGCTCATAGCCTACTAAGCTGAA
1 GCTTGAATTCTATCACT-GACTCATAGCCTGCTAAGC-GAA
6690 GCTTGAATTCTATC
1 GCTTGAATTCTATC
6704 CAAGATAACT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 77 0.97
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (39 bp):
GCTTGAATTCTATCACTGACTCATAGCCTGCTAAGCGAA
Done.