Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012165.1 Kokia drynarioides strain JFW-HI SEQ_127166, 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: 4981
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1317 original size:119 final size:119
Alignment explanation
Indices: 1163--1424 Score: 409
Period size: 119 Copynumber: 2.2 Consensus size: 119
1153 ACTTCGACCT
* *
1163 GCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTCGTTCATCGCGTGTGGGTTTGATTT
1 GCTTCTCTGTATCTCATCAGGAAGCTAGGGTTCGAAGATTCGTTCATCGCGCGTGGGTTTGATTT
*
1228 GGTCTT-CTTCTCAATATCTCACCAGGAAGATGACCGTGTTGTTTGTTTCAATCC
66 GGTCTTAC-TCTCAATATCTCACCAGGAAGATGACCGCGTTGTTTGTTTCAATCC
* * * *
1282 GTTTCTCTGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCTTTCATCGCGCGTGGGTTTGATTT
1 GCTTCTCTGTATCTCATCAGGAAGCTAGGGTTCGAAGATTCGTTCATCGCGCGTGGGTTTGATTT
* * *
1347 GGTCTTACTCTCAGTATCTTATCAGGAAGATGACCGCGTTGTTTGTTTCAATCC
66 GGTCTTACTCTCAATATCTCACCAGGAAGATGACCGCGTTGTTTGTTTCAATCC
*
1401 GCTTGTCTGTATCTCATCAGGAAG
1 GCTTCTCTGTATCTCATCAGGAAG
1425 ACGAATTTGG
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
119 129 0.99
120 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (119 bp):
GCTTCTCTGTATCTCATCAGGAAGCTAGGGTTCGAAGATTCGTTCATCGCGCGTGGGTTTGATTT
GGTCTTACTCTCAATATCTCACCAGGAAGATGACCGCGTTGTTTGTTTCAATCC
Found at i:1771 original size:205 final size:205
Alignment explanation
Indices: 1284--2007 Score: 1012
Period size: 205 Copynumber: 3.5 Consensus size: 205
1274 TTCAATCCGT
* * * *
1284 TTCTCTGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCT-TT--CATCGCGCGTGGGTTTGATT
1 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT-TGTTCACATCGAGCGTGGGTTTGACT
* * * * *
1346 TGGTCTTAC-TCTCAGTATCTT-ATCAGGAAGATGACCGCGTTGTTTGTTTCAATCCGCTTGTCT
65 TGGTC-TACTTCTCAATAT-TTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCTGCTTCTCT
* * * * * * *
1409 GTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTTTCTCATCAGAAAGCTATCCATTTTA
128 ATGTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTA
* *
1474 TT-ATTTCGACCTGC
192 TTGCTTT-GACCTAC
* * * *
1488 TTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCTTGGGTTTAATTT
1 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
** *
1553 GGTCTTTTTCTCAATATTTCATCAGGAAGATGACTACGTCGTTTGTTTCAATCTGCTTCTCTATG
66 GGTCTACTTCTCAATATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCTGCTTCTCTATG
1618 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGC
131 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGC
1683 TTTGACCTAC
196 TTTGACCTAC
* *
1693 TTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
1 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
*
1758 GGTCTACTTCTCAATATTTCATCAGGAAGATGATTGCGTCGTTTGTTTCAATCTGCTTCTCTATG
66 GGTCTACTTCTCAATATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCTGCTTCTCTATG
* *
1823 TCTCATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATTAGGAAGCTAACC-TTTATTGC
131 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGC
*
1887 TTCGACCTAC
196 TTTGACCTAC
*
1897 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
1 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
* * * * * *
1962 GTTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAGTCGTTTGT
66 GGTCTACTTCTCAATATTTCATCAGGAAGATGACTGCGTCGTTTGT
2008 GGATAATCGC
Statistics
Matches: 470, Mismatches: 44, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
203 1 0.00
204 157 0.33
205 190 0.40
206 122 0.26
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (205 bp):
TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTT
GGTCTACTTCTCAATATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCTGCTTCTCTATG
TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGC
TTTGACCTAC
Done.