Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013846.1 Kokia drynarioides strain JFW-HI SEQ_128874, 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: 10733
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:9497 original size:97 final size:96
Alignment explanation
Indices: 9312--9504 Score: 232
Period size: 97 Copynumber: 2.0 Consensus size: 96
9302 TTTTTGCGAA
* * * *
9312 AAGGATATTCGATTATCTTGATTTGAAAAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTTA
1 AAGGATATTCGATTATCTCGATTTGAAAAAAAATTGCACCTAATAAGTTAAGGCACAATATTTTA
*
9377 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
9408 AAGGGTATTCGATTAAT-TCGATTTGAAGAAAAAATTGCACCTAATGAGTTAAGGCACAA-ATTT
1 AAGGATATTCGATT-ATCTCGATTTGAA-AAAAAATTGCACCTAATAAGTTAAGGCACAATATTT
* *
9471 TTGAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 TAG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
9505 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
96 29 0.35
97 49 0.59
98 5 0.06
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAAAATTGCACCTAATAAGTTAAGGCACAATATTTTA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:9799 original size:29 final size:29
Alignment explanation
Indices: 9752--10208 Score: 278
Period size: 29 Copynumber: 15.7 Consensus size: 29
9742 AGGGAAATTT
*
9752 AGGGTTAAAATGGAA-TTTTAGACA-TTCG
1 AGGGTAAAAATGGAATTTTTAGA-AGTTCG
* *
9780 AGAGTAAAAATGGAATTTTT-GGAGTATCG
1 AGGGTAAAAATGGAATTTTTAGAAGT-TCG
* * * *
9809 A-GGTCGAAAATAGAGTTTTTAGACA-TCCG
1 AGGGT-AAAAATGGAATTTTTAGA-AGTTCG
* *
9838 GGGGTAAAAATGGAA-TTTTAGGAGTTTCG
1 AGGGTAAAAATGGAATTTTTAGAAG-TTCG
* *
9867 -GGGTTATAAATGGAATTTTTGGAAGTTCG
1 AGGG-TAAAAATGGAATTTTTAGAAGTTCG
* * * *
9896 GGGGTGAAAATGGAATTTTTGGAAGTTTTG
1 AGGGTAAAAATGGAATTTTTAGAAG-TTCG
* * *
9926 -GGGTCAAAATAGG-GTTTTTGGAAGTTCG
1 AGGGTAAAAAT-GGAATTTTTAGAAGTTCG
9954 AGGGTAAAAATGGAATTTTTAGAAGTTCG
1 AGGGTAAAAATGGAATTTTTAGAAGTTCG
* * * *
9983 AGTGTAAAAATGGAATTTGTGGAAGTTTTG
1 AGGGTAAAAATGGAATTTTTAGAAG-TTCG
*
10013 -GGGTTAAAAATGGAATTTTTGGAAGTTCG
1 AGGG-TAAAAATGGAATTTTTAGAAGTTCG
**
10042 AGGGTAAAAAT-GAGA-TTTTAGGAA-TTTT
1 AGGGTAAAAATGGA-ATTTTTA-GAAGTTCG
* **
10070 AGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 A-GGGTAAAAATGGAATTTTTAGAAGTTCG
* **
10100 AGGGTTAAAAATGGGATTTTT-GAAAGTTTT
1 AGGG-TAAAAATGGAATTTTTAG-AAGTTCG
* * * * *
10130 AGGGCAAAAATAGAATATTTGGAAGTTTTG
1 AGGGTAAAAATGGAATTTTTAGAAG-TTCG
* * *
10160 AGGTTAAAAATAGG-ATTTTTGGAAGTTTG
1 AGGGTAAAAAT-GGAATTTTTAGAAGTTCG
* * *
10189 AAGGCAAAAATGTAATTTTT
1 AGGGTAAAAATGGAATTTTT
10209 GGACAGCTTA
Statistics
Matches: 346, Mismatches: 52, Indels: 61
0.75 0.11 0.13
Matches are distributed among these distances:
27 2 0.01
28 41 0.12
29 195 0.56
30 106 0.31
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTTAGAAGTTCG
Found at i:10038 original size:59 final size:60
Alignment explanation
Indices: 9838--10211 Score: 357
Period size: 59 Copynumber: 6.4 Consensus size: 60
9828 TAGACATCCG
* * **
9838 GGGGTAAAAATGGAATTTTAGG-AGTTTCG-GGGTTATAAATGGAATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTT
* * * * *
9896 GGGGTGAAAATGGAATTTTTGGAAGTTTTG-GGG-TCAAAATAGG-GTTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAAT-GGAATTTTTGGAAGTTTT
* * *
9953 GAGGGTAAAAATGGAATTTTTAGAAG-TTCGAGTG-TAAAAATGGAATTTGTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTT
*
10012 GGGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGG-TAAAAAT-GAGATTTTAGGAA-TTTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGA-ATTTTTGGAAGTTTT
* * *
10070 AGGGGTAAAAATGGAATTTTTGGAAGTTT-TAGGGTTAAAAATGGGATTTTTGAAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTT
* * * * *
10130 AGGGCAAAAATAGAATATTTGGAAGTTTTGA-GGTTAAAAATAGG-ATTTTTGGAAG-TTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAAT-GGAATTTTTGGAAGTTTT
* * *
10188 GAAGGCAAAAATGTAATTTTTGGA
1 G-GGGTAAAAATGGAATTTTTGGA
10212 CAGCTTAGGG
Statistics
Matches: 265, Mismatches: 35, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
57 7 0.03
58 111 0.42
59 139 0.52
60 8 0.03
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (60 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTTGGAAGTTTT
Found at i:10209 original size:29 final size:29
Alignment explanation
Indices: 9839--10211 Score: 357
Period size: 29 Copynumber: 12.8 Consensus size: 29
9829 AGACATCCGG
*
9839 GGGTAAAAATGGAATTTTAGG-AGTTTCG-
1 GGGTAAAAATGGAATTTTTGGAAGTTT-GA
* * *
9867 GGGTTATAAATGGAATTTTTGGAAGTTCGG
1 GGG-TAAAAATGGAATTTTTGGAAGTTTGA
*
9897 GGGTGAAAATGGAATTTTTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAG-TTTGA
* * *
9926 GGGTCAAAATAGG-GTTTTTGGAAGTTCGA
1 GGGTAAAAAT-GGAATTTTTGGAAGTTTGA
* *
9955 GGGTAAAAATGGAATTTTTAGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTGA
* *
9984 GTGTAAAAATGGAATTTGTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAG-TTTGA
*
10013 GGGTTAAAAATGGAATTTTTGGAAGTTCGA
1 GGG-TAAAAATGGAATTTTTGGAAGTTTGA
* *
10043 GGGTAAAAAT-GAGATTTTAGGAA-TTTTA
1 GGGTAAAAATGGA-ATTTTTGGAAGTTTGA
*
10071 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGAATTTTTGGAAGTTTGA
* * *
10101 GGGTTAAAAATGGGATTTTTGAAAGTTTTA
1 GGG-TAAAAATGGAATTTTTGGAAGTTTGA
* * *
10131 GGGCAAAAATAGAATATTTGGAAGTTTTGA
1 GGGTAAAAATGGAATTTTTGGAAG-TTTGA
*
10161 GGTTAAAAATAGG-ATTTTTGGAAGTTTGA
1 GGGTAAAAAT-GGAATTTTTGGAAGTTTGA
* * *
10190 AGGCAAAAATGTAATTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
10212 CAGCTTAGGG
Statistics
Matches: 288, Mismatches: 39, Indels: 35
0.80 0.11 0.10
Matches are distributed among these distances:
28 14 0.05
29 179 0.62
30 94 0.33
31 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTGA
Done.