Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005706.1 Kokia drynarioides strain JFW-HI SEQ_119924, 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: 3300
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Found at i:391 original size:134 final size:134
Alignment explanation
Indices: 144--429 Score: 448
Period size: 134 Copynumber: 2.1 Consensus size: 134
134 ATTCAGTCTT
* * *
144 CTTCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
209 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTTATCAAGAAACTAACCATTTTATTGCTTCGA
66 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCAACAAGAAACTAACCATTTTATTACTTCGA
274 CCTG
131 CCTG
* * * *
278 CTTCTCAGTATCTCATCAGGAAGATGTCCACCTCATTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
343 CAGGAAGA-AGAATTTGGTCCACTTCTCAGTATCTCAACAGGAAGCTAACCATTTTATTACTTCG
66 CAGGAAGACA-AATTTGGTCCACTTCTCAGTATCTCAACAAGAAACTAACCATTTTATTACTTCG
407 ACCTG
130 ACCTG
412 CTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATCA
430 AGCAGCTGAG
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 1 0.01
134 138 0.99
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (134 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCAACAAGAAACTAACCATTTTATTACTTCGA
CCTG
Found at i:650 original size:201 final size:201
Alignment explanation
Indices: 278--721 Score: 669
Period size: 201 Copynumber: 2.2 Consensus size: 201
268 CTTCGACCTG
* * * *
278 CTTCTCAGTATCTCATCAGGAAGATG-TCCACCTCATTTGTTTCAATCCGCTTCTTTGTATCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGCT-CGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCA
*
342 TCAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCAACAGGAAGCTAACCATTTTATTACTTCG
65 TCAGGAAGAAGAATTTGGTCCACTTCTCAATATCTCAACAGGAAGCTAACCATTTTATTACTTCG
* *
407 ACCTGCTTCTCAGTATCTCATCAAGCAGCTGAGGTACGAAGATTTGCTCGTATTGAGCCCTGAGT
130 ACCTGCTTCTCAGTATCTCATCAAGAAGCTGAGGTACGAAGATTTGCTCGCATTGAGCCCTGAGT
472 TGGTATA
195 TGGTATA
* *
479 CTTCTCTGTACCTCATCAGGAAAATGCTCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGCTCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
544 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGAAGAATTTGGTCCACTTCTCAATATCTCAACAGGAAGCTAACCATTTTATTACTTCGA
* * * * * *
609 CCTGCTTCTCCGTATCTCATCAGGAATCTGGGGTTCGAAGATTTGCTCGCATTGATCCCTGAGTT
131 CCTGCTTCTCAGTATCTCATCAAGAAGCTGAGGTACGAAGATTTGCTCGCATTGAGCCCTGAGTT
674 GGTATA
196 GGTATA
*
680 TTTCGT-TGTATCTCATCAGGAAGATGAC-CGCCTCACTTGTTT
1 CTTC-TCTGTATCTCATCAGGAAGATG-CTCGCCTCACTTGTTT
722 TAGGTAATTG
Statistics
Matches: 219, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
201 216 0.99
202 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGCTCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGAAGAATTTGGTCCACTTCTCAATATCTCAACAGGAAGCTAACCATTTTATTACTTCGA
CCTGCTTCTCAGTATCTCATCAAGAAGCTGAGGTACGAAGATTTGCTCGCATTGAGCCCTGAGTT
GGTATA
Done.