Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002087.1 Kokia drynarioides strain JFW-HI SEQ_114000, 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: 5800
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Found at i:4914 original size:59 final size:58
Alignment explanation
Indices: 4826--4997 Score: 163
Period size: 59 Copynumber: 2.9 Consensus size: 58
4816 GGATTCTCGG
* * * ** ** *
4826 GGGTGAAACGGTAATTTTGGGAAAATTCGGGGTTAAAAATGGTTTTTTTAGACA-TCGAA
1 GGGTAAAATGGTAATTTTAGGAAGTTTCGGGGTTAAAAATGGAATTTTGAGA-AGTCG-A
* * *
4885 GGGTAAAATGGTAATTTTAGGAAGTTTCGGAGTCAAAAATGGAATTTTGGGAAGTTCGA
1 GGGTAAAATGGTAATTTTAGGAAGTTTCGGGGTTAAAAATGGAATTTTGAGAAG-TCGA
*
4944 GGCTAAAAATGG-AATTTTTA-GAAGTTTCGGGGTTAAAAATGGAATTTTG-GAAGT
1 GGGT-AAAATGGTAA-TTTTAGGAAGTTTCGGGGTTAAAAATGGAATTTTGAGAAGT
4998 TTTAAGGTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 5 0.05
59 74 0.78
60 15 0.16
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTAGGAAGTTTCGGGGTTAAAAATGGAATTTTGAGAAGTCGA
Found at i:4952 original size:29 final size:30
Alignment explanation
Indices: 4889--5296 Score: 273
Period size: 29 Copynumber: 13.8 Consensus size: 30
4879 ATCGAAGGGT
* *
4889 AAAATGGTAATTTTAGGAAGTTTCG-GAGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGAG-GTTA
* *
4920 AAAATGGAATTTTGGGAAG-TTCGAGGCTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* *
4949 AAAATGGAATTTTTAGAAGTTTCGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
**
4979 AAAATGGAA-TTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * * *
5008 AAAATGGGATTTTTAGAAGTTT-GGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* *
5037 AAAACGGGATTTTTGGAAGTTTCG-GGATTA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-TTA
* ** * * *
5067 AAAATGGTATTTTTATACG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * * *
5096 AAAATGGAATTTTTGGAGGTTTTGCGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * *
5126 AAAAT-GAGATTTTTGAAAGTTT-GGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGAGGTTA
* * *
5155 AAAACGGGATTTTTGGAAGTTTCG-GGATCA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-TTA
* * * *
5185 AAAATGGGATTTTTAGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * * * *
5214 AAGATGGAATTTTTGGAGGTTTTG-GGGTC
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
* * * * *
5243 AAAATTGAGGTTTTTGAAAGTTT-GGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGAGGTTA
*
5273 AAAATGGGATTTTTGGAAGTTTCG
1 AAAATGGAATTTTTGGAAGTTTCG
5297 GGACCCTCGA
Statistics
Matches: 298, Mismatches: 63, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
29 162 0.54
30 129 0.43
31 7 0.02
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTTA
Found at i:5010 original size:59 final size:59
Alignment explanation
Indices: 4889--5298 Score: 332
Period size: 59 Copynumber: 6.9 Consensus size: 59
4879 ATCGAAGGGT
* *
4889 AAAATGGTAA-TTTTAGGAAGTTTC-GGAGTCAAAAATGGAATTTTGGGAAG--TTCGAGGCTA
1 AAAATGG-AATTTTTA-GAAGTTTCGGGGGT-AAAAATGGAATTTT-GGAAGTTTTCG-GGTTA
* **
4949 AAAATGGAATTTTTAGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTAGAAGTTTCGGGGGTAAAAATGGAATTTTGGAAGTTTTCGGGTTA
* * *
5008 AAAATGGGATTTTTAGAAGTTT-GGGGGTAAAAACGGGATTTTTGGAAG-TTTCGGGATTA
1 AAAATGGAATTTTTAGAAGTTTCGGGGGTAAAAA-TGGAATTTTGGAAGTTTTCGGG-TTA
* * * * *
5067 AAAATGGTATTTTTATACG-TTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT-GCGGTCA
1 AAAATGGAATTTTTAGAAGTTTCGGGGGTAAAAATGGAA-TTTTGGAAGTTTTCG-GGTTA
* * *
5126 AAAAT-GAGATTTTT-GAAAGTTT-GGGGGTAAAAACGGGATTTTTGGAAG-TTTCGGGATCA
1 AAAATGGA-ATTTTTAG-AAGTTTCGGGGGTAAAAA-TGGAATTTTGGAAGTTTTCGGG-TTA
* * * * *
5185 AAAATGGGATTTTTAGAAG-TTCGGGGGTAAAGATGGAATTTTTGGAGGTTTT-GGGGTC
1 AAAATGGAATTTTTAGAAGTTTCGGGGGTAAAAATGGAA-TTTTGGAAGTTTTCGGGTTA
* * *
5243 AAAATTGAGGTTTTT-GAAAGTTT-GGGGGTAAAAATGGGATTTTTGGAAG-TTTCGGG
1 AAAATGGA-ATTTTTAG-AAGTTTCGGGGGTAAAAAT-GGAATTTTGGAAGTTTTCGGG
5299 ACCCTCGAGG
Statistics
Matches: 286, Mismatches: 38, Indels: 53
0.76 0.10 0.14
Matches are distributed among these distances:
58 46 0.16
59 203 0.71
60 37 0.13
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTAGAAGTTTCGGGGGTAAAAATGGAATTTTGGAAGTTTTCGGGTTA
Found at i:5010 original size:118 final size:116
Alignment explanation
Indices: 4883--5299 Score: 455
Period size: 118 Copynumber: 3.5 Consensus size: 116
4873 TTAGACATCG
* * * * * * *
4883 AAGGGTAAAATGGTAATTTTAGGAAGTTTCGGAGTCAAAAATGGAATTTTGGGAAG-TTCGAGGC
1 AAGGTTAAAATGG-AATTTTAGGAAGTTTGGGGGT-AAAAACGGGATTTTTGGAAGTTTCG-GGA
* *
4947 TAAAAATGGAATTTTTAGAAGTTTCGGGGTTAAAAATGGAA-TTTTGGAAGTTTT
63 TAAAAATGGAATTTTTAGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT
*
5001 AAGGTTAAAAATGGGATTTTTA-GAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGAT
1 AAGGTT-AAAAT-GGAATTTTAGGAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGA-
* * *
5065 TAAAAATGGTATTTTTATACGTTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT
63 TAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT
** * * *
5119 GCGGTCAAAAAT-GAGATTTTTGAAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGAT
1 AAGGT-TAAAATGGA-ATTTTAGGAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGAT
* *
5183 CAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAGATGGAATTTTTGGAGGTTTT
64 -AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT
** * * * * * *
5237 GGGGTCAAAATTGAGGTTTTTGAAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGA
1 AAGGTTAAAATGGA-ATTTTAGGAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGA
5300 CCCTCGAGGT
Statistics
Matches: 262, Mismatches: 27, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
116 2 0.01
117 47 0.18
118 200 0.76
119 11 0.04
120 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (116 bp):
AAGGTTAAAATGGAATTTTAGGAAGTTTGGGGGTAAAAACGGGATTTTTGGAAGTTTCGGGATAA
AAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTTGGAGGTTTT
Done.