Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007036.1 Kokia drynarioides strain JFW-HI SEQ_121644, 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: 5086
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:4198 original size:312 final size:312
Alignment explanation
Indices: 3633--4568 Score: 1631
Period size: 312 Copynumber: 3.0 Consensus size: 312
3623 AGGTTCAAAG
* *
3633 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATACAGCAATGCAGTGAATCC
1 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
** * *
3698 TAAAACCGAGACGAGCAAATCTAATCTGCCGAAAGAAGAATGGGAGAAAGCGATACCAACGACTA
66 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
*
3763 ATATGGTGGGAAATAATGTAAAATCAAGTGAAAAGGTACAAGGGAAGCAGCAACAGGTAGGGAAG
131 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGAAGCAGCAACAGGTAGGGAAG
*
3828 GAACATGGTAAGACTAAAATTCCACAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
196 GAACATGGTAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
3893 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTCAA
261 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTCAA
3945 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
1 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
4010 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
66 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
*
4075 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGAAGAAGCAACAGGTAGGGAAG
131 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGAAGCAGCAACAGGTAGGGAAG
*
4140 GAACATGATAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
196 GAACATGGTAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
4205 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTCAA
261 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTCAA
4257 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
1 AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
4322 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
66 TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
* * *
4387 ATATGGTGGGAAATCATGTAAAATCAAGT------G--CATGGGTAGCAGCAACAGGTTGGGAAG
131 ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGAAGCAGCAACAGGTAGGGAAG
* ** *
4444 GAACATGGTAAGACTAAAATCCCTCAATTTAGGTGTACTATATGCGACATAACTTGCGGTCGATC
196 GAACATGGTAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
*
4509 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGAC-AATATTCAG
261 AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAG-CTAATATTCAA
4561 AAAC-TGAA
1 AAACATGAA
4569 TAATCATGGA
Statistics
Matches: 603, Mismatches: 20, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
303 4 0.01
304 136 0.23
305 1 0.00
306 1 0.00
312 461 0.76
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (312 bp):
AAACATGAACCTCCCAAAGGCCAAGTATCTGCTTCGTCAGCAGCATGCAGCAAAGCAGTGAATCC
TAAAACCGAGACGAGTGAATCTAATCTGCCGAAAGAAGAATGGAAGAAGGCGATACCAACGACTA
ATATGGTGGGAAATCATGTAAAATCAAGTGAAAAGGTACAAGGGAAGCAGCAACAGGTAGGGAAG
GAACATGGTAAGACTAAAATTCCTCAATTTAGGTGTACTATATGTAACATAACCTGCGGTCGATC
AGAGGATTTGAATTCTCATCTATGGGGAAAGAAGCACTTAGCTAATATTCAA
Done.