Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006271.1 Kokia drynarioides strain JFW-HI SEQ_120842, 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: 6882
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:3149 original size:24 final size:24
Alignment explanation
Indices: 3114--3161 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3104 GATCTTTTGT
*
3114 TGGTAAAGACAGCTTCCAATGGAA
1 TGGTAAAAACAGCTTCCAATGGAA
3138 TGGTAAAAACAGCTTCCAATGGAA
1 TGGTAAAAACAGCTTCCAATGGAA
3162 GGGTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (24 bp):
TGGTAAAAACAGCTTCCAATGGAA
Found at i:4561 original size:208 final size:208
Alignment explanation
Indices: 4119--4923 Score: 1096
Period size: 208 Copynumber: 3.9 Consensus size: 208
4109 TCTACTTGTT
* * * *
4119 TGTATCTCATCAGGAAGACGAATTTGGTTAATTTCTCTGCATCTCATCAGGAAGATGACCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
* * *
4184 ATTGATTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGGAAGTTTCACTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* * * * *
4249 AGCTTCACTTCGTTGACTTGGTCTACTTCTTTGTATCTCATCAAGACGATGACCACTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CGCTTCATTGAT
*
4314 TTAATCCACTTCTA
195 TTAATCCACTTCTC
* * * * *
4328 TGTATCTCATCAGGAAGAAGGATTTGGTTCACTTCTCTACATCTCGTTAGGAAGATGACCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
*
4393 ATTGATTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGGAAG-TTCACTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* * * *
4457 AGCTTAACTTCGTTTAATTGGTCTACTTTTTTGTATCTCATCAGGAAGATGATCGCTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CGCTTCATTGAT
*
4522 TTAATCCCCTTCTC
195 TTAATCCACTTCTC
* * * * *
4536 TGTATCTCATCAAGAAGATGGATTTGGTTAACTTATCTGCATCTCGTCAGGAAGATGTCCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
* * *
4601 ATTGATTTGA-CCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAAGTTTCATTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* *
4665 AGCTTCACTTCGTTGAATTAGTCTACTTTTCTGTATCTCATCAGGAAGATGACTGCTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAC-GCTTCATTGAT
4730 TTAATCCACTTCTC
195 TTAATCCACTTCTC
* * *
4744 TGTATCTCATC-AGAAAGACGGATTT-GTTCTACTTCTCTATATCTCATCAGGAAGATGACCTCT
1 TGTATCTCATCAAG-AAGACGGATTTGGTT-AACTTCTCTACATCTCATCAGGAAGATGACCACT
* * * * **
4807 TAATTGCTTTGACCCACTTCTTTATATCTCATCAAGAAGATGGGGTTTCGAAGTTTCACTCGTAT
64 TTATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACAT
* * * ** *
4872 TGAGCTTCTCATCATTGTTTTGGTCTGCTTCTCTGTATCTCATCAGGAAGAT
129 TGAGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGAT
4924 TACCTTTTGA
Statistics
Matches: 531, Mismatches: 60, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
207 43 0.08
208 292 0.55
209 196 0.37
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACGCTTCATTGATT
TAATCCACTTCTC
Done.