Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003265.1 Kokia drynarioides strain JFW-HI SEQ_115922, 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, 668
Length: 1114
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Found at i:412 original size:217 final size:213
Alignment explanation
Indices: 9--1114 Score: 1150
Period size: 217 Copynumber: 5.1 Consensus size: 213
1 GTTCTTGT
* * * * * * *
9 TTTAATGATCAAAACTCGTTTACAAAATTA-AGACCTATTTAGACTAAATGATGCGATTTCTCGA
1 TTTAAAGACCAAAACTTGTTTACAAAATGACA-AACTATTTAGACCAAATGATGCGATTTCCCGA
* * *
73 GAATGGAATGTTTAAAAATTCCTCA-AAGGAATGGAACGTCTTGAATACTTTAAGGAACCGAAGT
65 GCATGGAATG-TTAAAAATTGCT-AGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGT
* * *
137 TATAAATGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAT-CAATGAACAAAGAGAGAGAAAC
128 TATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAA-GAAC-CAGAGAGAGAAAC
201 AATTCTCACGTAAATAAGTTTTAAA
190 AATTCTCACGTAAATAAGTTTT-AA
* * ** *
226 TTTAAAGACCAAAACTTGTTTACAAAATGACAAACAATTTAGA-AAAATGATGCGATTTTTCTAG
1 TTTAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAG
* * *
290 CATAGAATGTTAAGAAAGTTGCTAGAAGGAATGCATCGTCTTGAATACTTTAAGGAACTGAAGTT
66 CATGGAATGTTAA-AAA-TTGCTAGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTT
* * * * *
355 ATAAAAGAACTTGTAAAAGTTTGACTAGTTCGAAAGTTTGTCCAAGAACC-GAGAGAGAAATAAT
129 ATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAACCAGAGAGAGAAACAAT
419 TCTCACGTAAATAAGTTTTAA
193 TCTCACGTAAATAAGTTTTAA
* * * * * * ** *
440 TTCAAGAAACTAAACCTT-TTTACAAAATGACAAACAATTTAGACCAAATGAAGTTATTTTCCGA
1 TTTAA-AGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
* * * *
504 GCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATTGTCTTGAATACTTTATGGAACTGTAA-
65 GCATGGAATGTT--AAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCG-AAG
* * *
568 TTACAAAAGAACTCGAAAAAGTTTGATAAGTTCGGAAGTTCGTCCAAGAACCA-AAAGAGAAACA
127 TTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAACCAGAGAGAGAAACA
632 ATTCTCACGTAAATAAGTATTTAA
191 ATTCTCACGTAAATAAGT-TTTAA
* * *
656 TTCAAAGACCAAAAGTTTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCG
1 TTTAAAGACCAAAA--CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCG
* * ** *
721 AGCATGGAATGTTCAGAAAATTGCTTGATA-AAATGGATCGTCTTGAATACTGCAAGGAA-CGGA
64 AGCATGGAATGTT-A-AAAATTGCTAGA-AGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
* * *
784 GTTATAAAAGAACTCGTAAAAGTTTGAAATGTTCTGAAGTTCGTCCAACAGCC--A-AGA-AAA-
126 GTTATAAAAGAACTCGTAAAAGTTTGAAA-GTTCGGAAGTTCGTCCAAGAACCAGAGAGAGAAAC
* * * * **
844 AATCCTCAGGAAAATATGTTCTTGT
190 AATTCTCACGTAAATAAGTT-TTAA
* * * * * *
869 TTTAATGATCAAAACTCGTTTACAAAATTA-AGACCTATTTAGACTAAATGATGCGATTTCCCGA
1 TTTAAAGACCAAAACTTGTTTACAAAATGACA-AACTATTTAGACCAAATGATGCGATTTCCCGA
* * *
933 GAATGGAATGTTCAAAAATTCCTCA-AAGGAATGGATCGTCTTGAATACTTTAAGGAACCGGAGT
65 GCATGGAATGTT-AAAAATTGCT-AGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGT
* * **
997 TATAAATGAACTCGTAAAAGTTTGAAAAG-TCTGGAAGTTCATCCAAGAATAAAGAGAGAGAAAC
128 TATAAAAGAACTCGTAAAAGTTTG-AAAGTTC-GGAAGTTCGTCCAAGAA-CCAGAGAGAGAAAC
1061 AATTCTCACGTAAATAAGTTTTAAA
190 AATTCTCACGTAAATAAGTTTT-AA
* *
1086 TTTAAATACCATAACTTGTTTACAAAATG
1 TTTAAAGACCAAAACTTGTTTACAAAATG
Statistics
Matches: 747, Mismatches: 109, Indels: 66
0.81 0.12 0.07
Matches are distributed among these distances:
209 1 0.00
210 38 0.05
211 98 0.13
212 4 0.01
213 28 0.04
214 35 0.05
215 192 0.26
216 53 0.07
217 204 0.27
218 93 0.12
219 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (213 bp):
TTTAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAG
CATGGAATGTTAAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTAT
AAAAGAACTCGTAAAAGTTTGAAAGTTCGGAAGTTCGTCCAAGAACCAGAGAGAGAAACAATTCT
CACGTAAATAAGTTTTAA
Found at i:548 original size:215 final size:211
Alignment explanation
Indices: 45--1114 Score: 1077
Period size: 215 Copynumber: 5.0 Consensus size: 211
35 ATTAAGACCT
* * * * * *
45 ATTTAGACTAAATGATGCGA-TTTCTCGAGAATGGAATGTTTAAAAATTCCTCAAAGGAATGGAA
1 ATTTAGACCAAATGATGCGATTTTC-CGAGCATGGAATGTTCAAAAATTGCTCGAAGGAATGGAT
*
109 CGTCTTGAATACTTTAAGGAACCGAAGTTATAAATGAACTCGTAAAAGTTTGACAAGTTCGGAAG
65 CGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAG
* * * *
174 TTCAT-CAATGAACAAAGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTAAAGACCAA
129 TTCGTCCAA-GAAC--CGAGAGAGAAACAATTCTCACGTAAATAAGTTTT-AATTCAAA-AACAA
238 AACTTGTTTACAAAATGACAAACA
189 AACTT-TTTACAAAATGACAAACA
* * * * * *
262 ATTTAGA-AAAATGATGCGATTTTTCTAGCATAGAATGTT-AAGAAAGTTGCTAGAAGGAATGCA
1 ATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAA-AAA-TTGCTCGAAGGAATGGA
* * * *
325 TCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTTGTAAAAGTTTGACTAGTTCGAAA
64 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAA
* * *
390 GTTTGTCCAAGAACCGAGAGAGAAATAATTCTCACGTAAATAAGTTTTAATTCAAGAAACTAAAC
128 GTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAA-AAAC-AAAA
455 CTTTTTACAAAATGACAAACA
191 CTTTTTACAAAATGACAAACA
* ** *
476 ATTTAGACCAAATGAAGTTATTTTCCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGAT
1 ATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTC-AAAAATTGCTCGAAGGAATGGAT
* * * * *
541 TGTCTTGAATACTTTATGGAACTGTAA-TTACAAAAGAACTCGAAAAAGTTTGATAAGTTCGGAA
65 CGTCTTGAATACTTTAAGGAACCG-AAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAA
* * *
605 GTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTATTTAATTCAAAGACCAAAA
128 GTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGT-TTTAATTCAAA-AACAAAA
* *
670 GTTTTTTTTACAAAATGACAAACT
191 ---CTTTTTACAAAATGACAAACA
* * *
694 ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGATA-AAATGGA
1 ATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCA-AAAATTGCTCGA-AGGAATGGA
** * *
758 TCGTCTTGAATACTGCAAGGAA-CGGAGTTATAAAAGAACTCGTAAAAGTTTGAAATGTTCTGAA
64 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAA-GTTCGGAA
* * * * * * ** * * *
822 GTTCGTCCAACAGCC-A-AGA-AAA-AATCCTCAGGAAAATATGTTCTTGTTTTAATGATCAAAA
128 GTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTT-TTAATTCAA-AAACAAAA
* * * *
883 CTCGTTTACAAAATTA-AGACCT
191 CT-TTTTACAAAATGACA-AACA
* * * * *
905 ATTTAGACTAAATGATGCGATTTCCCGAGAATGGAATGTTCAAAAATTCCTCAAAGGAATGGATC
1 ATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAAAAATTGCTCGAAGGAATGGATC
* *
970 GTCTTGAATACTTTAAGGAACCGGAGTTATAAATGAACTCGTAAAAGTTTGAAAAG-TCTGGAAG
66 GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTG-AAAGTTC-GGAAG
* ** * * *
1034 TTCATCCAAGAATAAAGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTAAATACCATA
129 TTCGTCCAAG-A-ACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTT-AATTCAAA-AACAAA
1099 ACTTGTTTACAAAATG
190 ACTT-TTTACAAAATG
Statistics
Matches: 715, Mismatches: 102, Indels: 72
0.80 0.11 0.08
Matches are distributed among these distances:
209 1 0.00
210 39 0.05
211 96 0.13
212 5 0.01
213 27 0.04
214 37 0.05
215 186 0.26
216 52 0.07
217 176 0.25
218 95 0.13
219 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (211 bp):
ATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAAAAATTGCTCGAAGGAATGGATC
GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGTTCGGAAGTT
CGTCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAAAAACAAAACTTTT
TACAAAATGACAAACA
Done.