Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012632.1 Kokia drynarioides strain JFW-HI SEQ_127641, 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: 5313
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:1335 original size:19 final size:19
Alignment explanation
Indices: 1308--1347 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1298 GAAATTACTG
1308 TACTAGCTCGTAAAAGCAA
1 TACTAGCTCGTAAAAGCAA
*
1327 TACTGGCTCGTAAAAGCAA
1 TACTAGCTCGTAAAAGCAA
1346 TA
1 TA
1348 TACTACACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (19 bp):
TACTAGCTCGTAAAAGCAA
Found at i:1549 original size:27 final size:27
Alignment explanation
Indices: 1519--1572 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1509 TGCATTATAT
1519 TGTAAGTTAAATATTCTTGCGAACTTA
1 TGTAAGTTAAATATTCTTGCGAACTTA
1546 TGTAAGTTAAATATTCTTGCGAACTTA
1 TGTAAGTTAAATATTCTTGCGAACTTA
1573 CTAAGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (27 bp):
TGTAAGTTAAATATTCTTGCGAACTTA
Found at i:4704 original size:213 final size:213
Alignment explanation
Indices: 4337--4762 Score: 825
Period size: 213 Copynumber: 2.0 Consensus size: 213
4327 ATAATTTTAG
4337 TTGAGAACTAATTTTGAAAAGTTCTGAATTGTATTCACTTACAATCTTAAAATCTTGCAATCATA
1 TTGAGAACTAATTTTGAAAAGTTCTGAATTGTATTCACTTACAATCTTAAAATCTTGCAATCATA
4402 AGTGCGTCCAGTCATAACAAGCTTTAGGGAGTACCACCGTTTTCTGATGATCAAATCTTTCTTTC
66 AGTGCGTCCAGTCATAACAAGCTTTAGGGAGTACCACCGTTTTCTGATGATCAAATCTTTCTTTC
*
4467 AAATCATTCCACAATTTAAGAGGGTCTTTCGCAGTGAAATATTCCACTTTTAATCCTTCATGTAG
131 AAATCATTCCACAATTTAAGAGGGTCTTTCACAGTGAAATATTCCACTTTTAATCCTTCATGTAG
4532 ATGATGACGGATGAAAAT
196 ATGATGACGGATGAAAAT
4550 TTGAGAACTAATTTTGAAAAGTTCTGAATTGTATTCACTTACAATCTTAAAATCTTGCAATCATA
1 TTGAGAACTAATTTTGAAAAGTTCTGAATTGTATTCACTTACAATCTTAAAATCTTGCAATCATA
* *
4615 AGTGCGTCCAGTCATAACAAGCTTTAGGGAGTACCACTGTTTTTTGATGATCAAATCTTTCTTTC
66 AGTGCGTCCAGTCATAACAAGCTTTAGGGAGTACCACCGTTTTCTGATGATCAAATCTTTCTTTC
4680 AAATCATTCCACAATTTAAGAGGGTCTTTCACAGTGAAATATTCCACTTTTAATCCTTCATGTAG
131 AAATCATTCCACAATTTAAGAGGGTCTTTCACAGTGAAATATTCCACTTTTAATCCTTCATGTAG
4745 ATGATGACGGATGAAAAT
196 ATGATGACGGATGAAAAT
4763 CATTGCTTTT
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 210 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (213 bp):
TTGAGAACTAATTTTGAAAAGTTCTGAATTGTATTCACTTACAATCTTAAAATCTTGCAATCATA
AGTGCGTCCAGTCATAACAAGCTTTAGGGAGTACCACCGTTTTCTGATGATCAAATCTTTCTTTC
AAATCATTCCACAATTTAAGAGGGTCTTTCACAGTGAAATATTCCACTTTTAATCCTTCATGTAG
ATGATGACGGATGAAAAT
Done.