Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003642.1 Kokia drynarioides strain JFW-HI SEQ_116541, 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, 812
Length: 1354
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Found at i:581 original size:209 final size:210
Alignment explanation
Indices: 174--1354 Score: 1446
Period size: 209 Copynumber: 5.6 Consensus size: 210
164 GGTGTTATTT
* * * *
174 ATTTGGTCTACTTCTCAATATCTCATCAGCAAGATGACTGCATCACTTT-TTTTGATCCACTTCT
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC-GTTTGTTTTGATCCACTTCT
* * * * * *
238 ATGTGTCTCATCAAGAAGAAGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTT
65 CTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACAGCTT
* *
303 TATTGCTTTGACCTGCTT-TTAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTG
130 TATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTG
*
367 AGCTTTGGCTTAATTG
195 AGCTTTGGCTTCATTG
* * *
383 ATTTGGTCTACTTATTAGTATCTCATCAGGAAGATAACCGCATC-TTTGTTTTGATCCACTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTTGATCCACTTCTC
* ** * * * *
447 TGTATCTCATCAGGAAGACGGATCCAGTTCACTTCTTTGTATCTAATCAGGAAGGTAACAGTTTT
66 TGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACAGCTTT
* * * * ** * * * *
512 ATTGCTTCGACCTACATCTTAGTATCTCATAAAAAAGATGGGGTTCAAAGATTCACTCACATCGA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTGA
*
577 GCTTTCGCTTCATTG
196 GCTTTGGCTTCATTG
* * *
592 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC-TCTATTTTGATCCACTTCTT
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTTGATCCACTTCTC
* * * * *
656 TGTATCTCATCAGGAAGACGGATCCGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGATTT
66 TGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACAGCTTT
* * * **
721 ATTGCTTCGATCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGTTTCACTCACATCAA
131 ATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTGA
* *
786 GCTTT-GTTTCATTA
196 GCTTTGGCTTCATTG
* * * * *
800 AGTTGGTGTACTTCTCTA-TATCTCATCAGGAAGATGACCGCTTCGCTTCTTTTGATCCACTTCT
1 ATTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTTGATCCACTTCT
** * *
864 CTGTGTCTCATCAGGAAGACTAATCTGGTTCACTTCTTTGTATCTCATCAGGAAGCTATCTA-CT
65 CTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAAC-AGCT
* * * * *
928 TTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACTTT
129 TTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATT
* **
993 GAG-TCTGATTTCATTG
194 GAGCTTTGGCTTCATTG
* * ** *
1009 ATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTTTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTTGATCCACTTCTC
* * * ** * *
1074 TGTGTCTCATCAGGAAAACGGATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTGACCA-TTT
66 TGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCT-AACAGCTT
* ** * *
1138 TATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGAGTTTAAAGTTTTGCTCACATTG
130 TATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTG
*
1203 AGCTTTGGCTTCTTTG
195 AGCTTTGGCTTCATTG
* *
1219 ATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATCGTC-TCGTTTGTTTTGATCCACTTCT
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG-CATCGTTTGTTTTGATCCACTTCT
* **
1283 CTGTGTCTCATCAGGAAGATGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCTCTT
65 CTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACAGCTT
1348 TATTGCT
130 TATTGCT
Statistics
Matches: 835, Mismatches: 126, Indels: 21
0.85 0.13 0.02
Matches are distributed among these distances:
207 3 0.00
208 135 0.16
209 570 0.68
210 126 0.15
211 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (210 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTTGATCCACTTCTC
TGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACAGCTTT
ATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTCGCTCACATTGA
GCTTTGGCTTCATTG
Found at i:746 original size:85 final size:85
Alignment explanation
Indices: 601--757 Score: 194
Period size: 85 Copynumber: 1.8 Consensus size: 85
591 GATTTGGTCT
* **
601 ACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTCTATTTTGATCCACTTCTTTGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGATAACCGCATCTCTATTTTGATCCACTTCTCAGTATCTCAT
666 CAGGAAGACGGATCCGGTTC
66 CAGGAAGACGGATCCGGTTC
* * **
686 ACTTCTCTGTATCTCATCAGGAAGGTAACCG-AT-T-TATTGCTTCGATCTGCTTCTCAGTATCT
1 ACTTCTCAGTATCTCATCAGGAAGATAACCGCATCTCTATT--TT-GATCCACTTCTCAGTATCT
*
748 CATTAGGAAG
63 CATCAGGAAG
758 CTGGGGTTCG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 4 0.07
83 1 0.02
84 4 0.07
85 52 0.85
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (85 bp):
ACTTCTCAGTATCTCATCAGGAAGATAACCGCATCTCTATTTTGATCCACTTCTCAGTATCTCAT
CAGGAAGACGGATCCGGTTC
Done.