Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010344.1 Kokia drynarioides strain JFW-HI SEQ_125211, 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: 1760
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.31
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:1016 original size:59 final size:59
Alignment explanation
Indices: 944--1367 Score: 677
Period size: 59 Copynumber: 7.2 Consensus size: 59
934 GTCTCTAAAC
* * *
944 CTTCCAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCTCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
** * *
1003 CTTCCAAAAATTACTATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
1062 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* *
1121 CTTCCAAAAATTACTATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* *
1180 CTTCCAAAAATTACTATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACCCTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * * *
1239 CTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTCGATCCTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * *
1298 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCTAAA
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1357 CTTCCAAAAAT
1 CTTCCAAAAAT
1368 CCCAATTTTG
Statistics
Matches: 339, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 339 1.00
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
Found at i:1422 original size:177 final size:175
Alignment explanation
Indices: 944--1426 Score: 666
Period size: 177 Copynumber: 2.7 Consensus size: 175
934 GTCTCTAAAC
* * *
944 CTTCCAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCTCATTTTTGACCCCGAATCTTCCA
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAATCTTCCA
* * * *
1009 AAAATTACTATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATT
65 AAAATTACTATTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCCCTAATCTTCCAAAAATT
*
1074 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
129 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCGAAT
*
1121 CTTCCAAAAATTACTATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-CGAATCTTCCA
1186 AAAATTACTATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGA-CCCTGAATCTTCCAAAAAT
65 AAAATTACTATTTTACC-CCGAACTTCCAAAAATCCCATTTTTGACCCCT-AATCTTCCAAAAAT
* * * *
1250 TACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTCGATCCTGAAT
128 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCGAAT
* *
1298 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCCTAAACTTCCA
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAATCTTCCA
** * * ** *
1363 AAAATCCCAATTTTGATCCCGAACCTTCCAAAAATTAC-TATTTT-ACCCCTAAACTTCCAAAAA
65 AAAATTACTATTTT-ACCCCGAA-CTTCCAAAAATCCCAT-TTTTGACCCCTAATCTTCCAAAAA
1426 T
127 T
1427 CTCATTTTTA
Statistics
Matches: 275, Mismatches: 23, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
176 4 0.01
177 245 0.89
178 26 0.09
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (175 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAATCTTCCAA
AAATTACTATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCTAATCTTCCAAAAATTAC
CATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCGAAT
Found at i:1552 original size:58 final size:57
Alignment explanation
Indices: 1354--1570 Score: 249
Period size: 58 Copynumber: 3.7 Consensus size: 57
1344 TTTGATCCCT
* *
1354 AAACTTCCAAAAATCCCAATTTTGATCCCGAACCTTCCAAAAATTACTATTTTACCCC
1 AAACTTCCAAAAATCCCATTTTTGA-CCTGAACCTTCCAAAAATTACTATTTTACCCC
* * ** *
1412 TAAACTTCCAAAAATCTCATTTTTAACCCTGAACCTTCTTAAAATTACCATTTTACCCC
1 -AAACTTCCAAAAATCCCATTTTTGA-CCTGAACCTTCCAAAAATTACTATTTTACCCC
* *
1471 AAACTTCCAACAATCCCATTTTTGACCTTGAATCTTCCAAAAATTACTA-TTTACCCTC
1 AAACTTCCAAAAATCCCATTTTTGACC-TGAACCTTCCAAAAATTACTATTTTACCC-C
* * *
1529 GAACTTCCAAAAATCCTATTTTTGATTCC-GAACATTCCAAAA
1 AAACTTCCAAAAATCCCATTTTTGA--CCTGAACCTTCCAAAA
1571 CTACCATTCT
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
57 9 0.07
58 73 0.54
59 50 0.37
60 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
AAACTTCCAAAAATCCCATTTTTGACCTGAACCTTCCAAAAATTACTATTTTACCCC
Done.