Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010065.1 Kokia drynarioides strain JFW-HI SEQ_124839, 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: 10568
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:437 original size:205 final size:206
Alignment explanation
Indices: 1--563 Score: 858
Period size: 205 Copynumber: 2.7 Consensus size: 206
* * *
1 GAAGATGACCGCATCGCTTGTTTCAATCTGCTTCTCTGTATCTCATCAAGAAGGCAAATTTGGTT
1 GAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTT
* * * * * * **
66 CACTTCTCAGTATCTCATTAGGATGCTAATCATTTTATTACTTCGACCTACTTCTCAGTGTCTTG
66 CACTTCTCAGTATCTCATCAGGAAGCTAA-CCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
* * * ** * * *
131 TCAAGAAGTTGGAGTTTTTAAGATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTC
130 TCAGGAAGCTGG-GGTTCGAAGATTTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTC
196 AGTATCTCATCAG
194 AGTATCTCATCAG
* * *
209 GAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGATC
1 GAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTT
274 CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
66 CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
339 CAGGAAGCTGGGGTTCGAAGA-TTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
131 CAGGAAGCTGGGGTTCGAAGATTTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
403 TATCTCATCAG
196 TATCTCATCAG
* *
414 GAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTT
1 GAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTT
* *
479 CACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCC
66 CACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
544 TCAGGAAGCTGGGGTTCGAA
130 TCAGGAAGCTGGGGTTCGAA
564 NNNNNNNNNN
Statistics
Matches: 325, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
205 142 0.44
206 58 0.18
207 39 0.12
208 86 0.26
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (206 bp):
GAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTT
CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
TATCTCATCAG
Found at i:1383 original size:205 final size:207
Alignment explanation
Indices: 1014--1612 Score: 977
Period size: 205 Copynumber: 2.9 Consensus size: 207
1004 NNNNNNNNNN
* *
1014 TATCTCATCAAGAAGACAAATTTGGTTCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTAT
1 TATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * ** * *
1079 TACTTCGACCTACTTCTCAGTGTCTTGTCAAGAAGCTGGAGTTCGAAGATTTTGCTCGCTTTGAG
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAG
1144 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTGCAA
131 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTGCAA
1209 TCCGCTTCTCTG
196 TCCGCTTCTCTG
* * *
1221 TATCTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTAT
1 TATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * *
1285 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGA-TTTGCTCACATCGAG
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAG
* * *
1349 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAA
131 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTGCAA
1414 TCCGCTTCTCTG
196 TCCGCTTCTCTG
1426 TATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
1 TATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* *
1491 TGCTTCGACCTGCTTCTTAGTATCTCCTCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAG
66 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAG
* * *
1556 CGTGAGTTTGATTTGGTCTTCCTCTCAGTATCTCATCAGGAAGATGACTGCATCGCT
131 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCT
1613 GTTTGTGGAT
Statistics
Matches: 359, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
205 141 0.39
206 101 0.28
207 117 0.33
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (207 bp):
TATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAG
CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTGCAA
TCCGCTTCTCTG
Done.