Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004302.1 Kokia drynarioides strain JFW-HI SEQ_117608, 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, 635
Length: 1059
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Found at i:406 original size:216 final size:215
Alignment explanation
Indices: 1--1059 Score: 1124
Period size: 216 Copynumber: 5.0 Consensus size: 215
* ** *
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAAATTGTAAAACTTTTA-TGA
1 TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACT-A
* * ** * *
65 GTTATTTTTTAACTTCAGTTTCC-TAAAGTATTCAACAAGATCCATTCCTTCGAGCAATTTT-TC
65 GTTATTTTATAACTT-TGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCT-
* * * *
128 GAACATTCCATGCTCTGGAAATCGCATCATTTGGTCTAAATAGTTTGTAATTTTGTAAACAAGTT
128 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAAGTT
*
193 TTGGTCTTTGAATTAAAAACTTA
193 TTGGTCTTTAAATTAAAAACTTA
* * * * *
216 TTTACATGAGAATTGTTTCTCTCTTTGTTGTTGGACAAAGTTCCGAACCTATCAAACTTTTACTA
1 -TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACTA
* * * * *
281 GTTCTTTTATAACTTTGGATCCTTAAAGTATTCAATACGATCTATTCTTTCGAGCAATTTTCTGA
65 GTTATTTTATAACTTTGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCTGA
* *
346 ACATTCCATGCTCGGGAAATCGCACCATTTGGTCAAAATAATTTGTCATTTTGCAAACAAGTTTT
130 ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAAGTTTT
411 GGTCTTTAAATTAAAAACTTA
195 GGTCTTTAAATTAAAAACTTA
* *
432 TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTG-CAAACTTTTACGAG
1 TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACTAG
* ** * * * * * *
496 TTATTTTTTAACTTCAGTTCCCTAAACTATTCAACAAGATCCATTTTTTAGAACAATTTTTTGAA
66 TTATTTTATAACTTTGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCTGAA
* * * * * * *
561 CATTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTG
131 CATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAAGTTTTG
*
626 GTCTTTGAATTAAAAACTTA
196 GTCTTTAAATTAAAAACTTA
* * * * * *
646 TTTA-AGTGAGGATTGTTTCTCTCTTCGATCTTGGACGAAGTGTCAAACCTGTCAAACTTTTACT
1 -TTACA-TGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACT
* * * * * * *
710 AGTTCTTTTATAACTTTGGATCCTTAAAGTATTTAAGACGATCTATTCTTTTGAACAATTTTCTA
64 AGTTATTTTATAACTTTGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCTG
* *
775 AAAATTCCATGCTCTGGG-AATCGCATCATTTGGTCTAAATAAATTT-TCATTCTGCAAACAAGT
129 AACATTCCATGCTC-GGGAAATCGCATCATTTGGTCTAAAT-AATTTGTCATTTTGCAAACAAGT
*
838 TTTGGTCTTTAAATGAAAAACTTA
192 TTTGGTCTTTAAATTAAAAACTTA
* *
862 TTACGTGAGAATTGTTTCTCTCTTTGTTCTT----G-------G-A-C-G---AACTTTTACGAG
1 TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACTAG
* ** * * * * *
910 TTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTT-TCGA
66 TTATTTTATAACTTTGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCT-GA
* * * * * * * * *
974 ATATTCTATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACCAGTTTT
130 ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAAGTTTT
*
1039 GGTCTTTGAATTAAAAACTTA
195 GGTCTTTAAATTAAAAACTTA
Statistics
Matches: 709, Mismatches: 122, Indels: 42
0.81 0.14 0.05
Matches are distributed among these distances:
197 8 0.01
198 124 0.17
201 1 0.00
202 1 0.00
203 1 0.00
211 1 0.00
214 140 0.20
215 115 0.16
216 309 0.44
217 9 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (215 bp):
TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACCTGTCAAACTTTTACTAG
TTATTTTATAACTTTGGATCCTTAAAGTATTCAACAAGATCCATTCTTTCGAACAATTTTCTGAA
CATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGCAAACAAGTTTTG
GTCTTTAAATTAAAAACTTA
Found at i:859 original size:430 final size:429
Alignment explanation
Indices: 1--1059 Score: 1591
Period size: 430 Copynumber: 2.5 Consensus size: 429
* *
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAAATTGTAAAACTTTTATGAG
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTG--AAACTTTTACGAG
* ** *
66 TTATTTTTTAACTTCAGTTTCCTAAAGTATTCAACAAGATCCATTCCTTCGAGCAATTTTTCGAA
64 TTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTTTCGAA
* * * *
131 CATTCCATGCTCT-GGAAATCGCATCATTTGGTCTAAATAGTTTGTAATTTTGTAAACAAGTTTT
129 CATTCCATCCT-TGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTT
* * *
195 GGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTTGTTGTTGGACAAAGTTCC
193 GGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTCGATCTTGGACAAAGTTCC
* *
260 GAACCTATCAAACTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAATACGATCTA
258 AAACCTATCAAACTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCTA
* * *
325 TTCTTTCGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCACCATTTGGTCAAAATAATTT
323 TTCTTTCGAACAATTTTCTAAAAATTCCATGCTCGGGAAATCGCACCATTTGGTCAAAATAATTT
* *
390 GTCATTTTGCAAACAAGTTTTGGTCTTTAAATTAAAAACTTA
388 GTCATTCTGCAAACAAGTTTTGGTCTTTAAATGAAAAACTTA
*
432 TTACATGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGCAAACTTTTACGAGT
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTG-AAACTTTTACGAGT
* * *
497 TATTTTTTAACTTCAGTTCCCTAAACTATTCAACAAGATCCATTTTTTAGAACAATTTTTTGAAC
65 TATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTTTCGAAC
*
562 ATTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGG
130 ATTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGG
* *
627 TCTTTGAATTAAAAACTTATTTA-AGTGAGGATTGTTTCTCTCTTCGATCTTGGACGAAGTGT-C
195 TCTTTGAATTAAAAACTTATTTACA-TGAGAATTGTTTCTCTCTTCGATCTTGGACAAAGT-TCC
* *
690 AAACCTGTCAAACTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTTAAGACGATCTA
258 AAACCTATCAAACTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCTA
* * *
755 TTCTTTTGAACAATTTTCTAAAAATTCCATGCTCTGGG-AATCGCATCATTTGGTCTAAATAAAT
323 TTCTTTCGAACAATTTTCTAAAAATTCCATGCTC-GGGAAATCGCACCATTTGGTCAAAAT-AAT
819 TT-TCATTCTGCAAACAAGTTTTGGTCTTTAAATGAAAAACTTA
386 TTGTCATTCTGCAAACAAGTTTTGGTCTTTAAATGAAAAACTTA
862 TTACGTGAGAATTGTTTCTCTCTTTGTTCTT----G-------G-AC--G-AACTTTTACGAGTT
1 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGAAACTTTTACGAGTT
*
912 ATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTTTCGAATA
66 ATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTTTCGAACA
* *
977 TTCTATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACCAGTTTTGGT
131 TTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGT
1042 CTTTGAATTAAAAACTTA
196 CTTTGAATTAAAAACTTA
Statistics
Matches: 582, Mismatches: 41, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
414 155 0.27
416 1 0.00
418 2 0.00
419 1 0.00
426 1 0.00
429 2 0.00
430 363 0.62
431 57 0.10
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (429 bp):
TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGAAACTTTTACGAGTT
ATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTTTTTAGAGCAATTTTTCGAACA
TTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGT
CTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTCGATCTTGGACAAAGTTCCAAA
CCTATCAAACTTTTACTAGTTCTTTTATAACTTTGGATCCTTAAAGTATTCAAGACGATCTATTC
TTTCGAACAATTTTCTAAAAATTCCATGCTCGGGAAATCGCACCATTTGGTCAAAATAATTTGTC
ATTCTGCAAACAAGTTTTGGTCTTTAAATGAAAAACTTA
Done.