Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001449.1 Kokia drynarioides strain JFW-HI SEQ_112965, 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: 1774
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Found at i:1411 original size:216 final size:216
Alignment explanation
Indices: 728--1774 Score: 1151
Period size: 216 Copynumber: 4.8 Consensus size: 216
718 AAATGCATGA
* * * * **
728 AACTTTCGAACTTGTTGAACTTTTACGAGTTCTTTTATTAACTTTGATTCCTTAACTTATTCAAG
1 AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTA-TAACTTCGGTTCCTTAAAGTATTCAAG
* * *
793 ACAATCCAATCCTTTGAGAAAATTTT-CGAACATTCCATGCTCGGGAAATCGCATC-ATTCGGTC
65 ACGATCCAATCCTTTGAG-CAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATT-GGTC
* * *
856 TAAATAGTTTTTCATTTTGTGAAACAAG-TTTGGTCTTTGAATTTAAAACTTATTTATGTAAGAA
128 TAAATAGTTTTTCATTTTGT-AAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAA
*
920 TTGTTTCTCTCTTGGATCTT-G--G
192 TTGTTTCTCTCTTGGTTCTTGGACG
* * * * *
942 -AC----GAACTTGTCGAATTTTTACGAGTTCTTCTATAACTTCGGTTACTTAATGTATTAAAGA
1 AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * *
1002 CGATCAAATCCTTTGAGCAATTTTCCGAACATTCCATGCGAGAGAAATCGCATCATTTGGCCT-A
66 CGATCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATTGGTCTAA
* *
1066 GTAGTTTTTCAATTTT-TAAACAAGTTTTGATCTTTGAATT-AAAACTTATTTACATAAGTTTAC
131 ATAGTTTTTC-ATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC----G-----
* *
1129 ATGAGAATTGTGTCTCTCTTGGTTCTTGAACG
186 -TGAGAATTGTTTCTCTCTTGGTTCTTGGACG
* *
1161 AACTTCTGAACTTGTCGAACTTTTATGAGTTCTTTTATAACTAT-GGTTCCTTAAAGTATTCAAG
1 AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTATAACT-TCGGTTCCTTAAAGTATTCAAG
* * * *
1225 ACGATCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTTGGGAAGTTGCATCAATTGGTCCA
65 ACGATCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATTGGTCTA
* * * *
1290 AAAAGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTTAATTAAAAACTTATTTACGTGAGAATTG
130 AATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG
* *
1355 TTTCTCTCTTGGTTGTTGGGCG
195 TTTCTCTCTTGGTTCTTGGACG
* * * *
1377 AACTTTTGAACTTGTCAAACTTTTATGAGTTCTTTTTTAACTTCTGTTCCTTAAAGTATTCAAGA
1 AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
* * * * * * *
1442 -TAGTCCATTCCTTTTAGTAGTTTTTCGAACATTCCATGCTCGGGAAATCGCATC-ATTCGGTCT
66 CGA-TCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATT-GGTCT
* * *
1505 AAATAGCTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATA
129 AAATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* *
1570 GATTCTCTCTTGGTTCTTAGACG
194 GTTTCTCTCTTGGTTCTTGGACG
** * * * * * *
1593 AACTTTTGAAAATGACTAACTTTT-CGAGTTCTTTTACAACTTCGGTTCCTTTACGTA-TCTAAC
1 AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTC-AAG
** * * * * *
1656 ACGATCCAATCCTTTGAGCAATTTTTTGCACATTACATGCGAGGGAAATTGCATCATTTGGTCTA
65 ACGATCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATTGGTCTA
*
1721 AATAGTTTTTCATTTTGTAAACAAGTTTTGATCTTTGAATTAAAAACTTATTTA
130 AATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA
Statistics
Matches: 702, Mismatches: 99, Indels: 63
0.81 0.11 0.07
Matches are distributed among these distances:
206 19 0.03
207 31 0.04
208 72 0.10
209 29 0.04
210 1 0.00
213 2 0.00
214 2 0.00
215 134 0.19
216 256 0.36
219 1 0.00
220 2 0.00
222 1 0.00
224 109 0.16
225 30 0.04
226 13 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (216 bp):
AACTTTTGAACTTGTCGAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
CGATCCAATCCTTTGAGCAATTTTCCGAACATTCCATGCTAGGGAAATCGCATCAATTGGTCTAA
ATAGTTTTTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
TTCTCTCTTGGTTCTTGGACG
Done.