Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010758.1 Kokia drynarioides strain JFW-HI SEQ_125717, 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, 859
Length: 1433
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.38
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:459 original size:214 final size:216
Alignment explanation
Indices: 1--855 Score: 1072
Period size: 214 Copynumber: 4.0 Consensus size: 216
* * *
1 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTCAAGTATTCATGACGATCCATTCCTTCGAGCC
1 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
* * * * *
66 ATTTTTCGAACATTCCATGATCAGGAAATCGTATCATTTGGTCCAAATGGATTGT-ATTTTGTAA
66 ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAA
* * *
130 ACAACTTTTTGGTCTTTAAATTT--AA---A-TTACGTCAGATTGTTTCTTTTTTTGTACTTGGA
131 ACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGA
* * * *
189 CGAATTTCCAAACTTATCAAA
196 CGAACTTACGAACTTGTCAAA
* * *
210 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTAGTCACGACGATCCATTCCTTCGAGCC
1 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
* *
275 ATTTTTCGAACATTCCATGCTCGGGAAATCGTATCATTTGGTCCAAAT-GCTTTGTCATTTCGTA
66 ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAG-TTTGTCATTTTGTA
* * *
339 AAC-AC-TTTTGGCCTTTGAATTTAAAACTTATTTACGTCAGATTGTTTCTCATTTGGTTCTTGG
130 AACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGG
* *
402 ACGAACTTATGAACTTGTGAAA
195 ACGAACTTACGAACTTGTCAAA
* * * *
424 CTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTTTTCAAGATGATCCATTCCTTCGAGTA
1 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
*
489 ATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCA-TTTGTAA
66 ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAA
* * * * *
553 GCAAC-TTTAGGTTTTTAAATTTAAAACTTATTTATGTGAGACTTGTTTCTCTTTTGGTTCTTGG
131 ACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGA-TTGTTTCTCTTTTGGTTCTTGG
* *
617 ATGAACTTACGAGCTTGTCAAA
195 ACGAACTTACGAACTTGTCAAA
* * * * * * *
639 ATGTTACGAGTTCTTTTCTAACTTCGATTCCTTAAAGTATTCAAAACGATCCATTCCTTTGAGCA
1 CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
* * *
704 ATTTTTCCGAGCATTCCATGCTCGAGAAATCACATCATTTGGTCCAAAATAGTTTGTCATTTTGT
66 ATTTTT-CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCC-AAATAGTTTGTCATTTTGT
* * ** * *
769 CAACAACTTTTTGGTCTTTGAATAAAAAACTTATTTGCGTCAGAATTGTCTCTCTTTTGG-T-TT
129 AAACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAG-ATTGTTTCTCTTTTGGTTCTT
* *
832 GGACGAACTTCCAAACTTGTCAAA
193 GGACGAACTTACGAACTTGTCAAA
856 NNNNNNNNNN
Statistics
Matches: 559, Mismatches: 71, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
208 16 0.03
209 114 0.20
210 12 0.02
213 8 0.01
214 187 0.33
215 100 0.18
216 34 0.06
217 35 0.06
218 11 0.02
219 41 0.07
220 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (216 bp):
CTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAA
ACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGA
CGAACTTACGAACTTGTCAAA
Found at i:1360 original size:215 final size:214
Alignment explanation
Indices: 957--1433 Score: 666
Period size: 215 Copynumber: 2.2 Consensus size: 214
947 NNNNNNNNNN
*
957 TTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTAAATTTAAAACTTATTTAC
1 TTTGGTCCAAATGATTTGTCA-TTTGTAAACAAC-TTTTGGTCTTTAAATTTAAAACTTATTTAC
* * * * * *
1022 GTCAGATTGTTTCTTTTTTGGATCTTGGACGAATTTCCAAACTTGTCAAACTTTTACAAGTTCAT
64 GTCAGATTGTTCCTCTTTTGGATCTGGGACGAACTTACAAACTTCTCAAACTTTTACAAGTTCAT
* * * *
1087 TTATAACTTTGGTTCCTTAAAGTAGTCACGACGATCCATTCCTTCGAGCCATTTTTCGAACATTC
129 TTATAACTTTGGTTCCTTAAAGTAGTCAAGACGATCCATTCATTCGAGCAAATTTTCGAACATTC
* *
1152 CATGCTCGGTAAATCGTATCA
194 CATGCTCGGGAAATCGCATCA
* *
1173 TTTGGTTCAAATGATTTGTCATTTCGTAAACAACTTTTGGTCTTTGAATTTAAAACTTATTTACG
1 TTTGGTCCAAATGATTTGTCATTT-GTAAACAACTTTTGGTCTTTAAATTTAAAACTTATTTACG
* * ** * * *
1238 TCAGATTGTTCCTCTTTTGGTTCTGGGATGAACTTATGAACTTCTGAAAGTTTTACAAGTTCTTT
65 TCAGATTGTTCCTCTTTTGGATCTGGGACGAACTTACAAACTTCTCAAACTTTTACAAGTTCATT
* * *
1303 TATAACTTTGGTTCCTTAAAGTATTCAAGATGATCCATTCATTCGAGTAAATTTTCGAACATTCC
130 TATAACTTTGGTTCCTTAAAGTAGTCAAGACGATCCATTCATTCGAGCAAATTTTCGAACATTCC
*
1368 ATGCTTGGGAAATCGCATCA
195 ATGCTCGGGAAATCGCATCA
* * *
1388 TTTGGTCCAAATAATTTGTCATTTGTAAGCAACTTTTGGTTTTTAA
1 TTTGGTCCAAATGATTTGTCATTTGTAAACAACTTTTGGTCTTTAA
Statistics
Matches: 229, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
214 19 0.08
215 182 0.79
216 28 0.12
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (214 bp):
TTTGGTCCAAATGATTTGTCATTTGTAAACAACTTTTGGTCTTTAAATTTAAAACTTATTTACGT
CAGATTGTTCCTCTTTTGGATCTGGGACGAACTTACAAACTTCTCAAACTTTTACAAGTTCATTT
ATAACTTTGGTTCCTTAAAGTAGTCAAGACGATCCATTCATTCGAGCAAATTTTCGAACATTCCA
TGCTCGGGAAATCGCATCA
Done.