Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010594.1 Kokia drynarioides strain JFW-HI SEQ_125522, 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: 4917
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2645 original size:820 final size:767
Alignment explanation
Indices: 1068--2654 Score: 2463
Period size: 820 Copynumber: 2.0 Consensus size: 767
1058 ATTTCGTGGT
1068 CAAACAATTAAATCCAAAGATAAAAAGTGAAGGAAGATTGAAATAGATATCATACTTGATCTGAA
1 CAAACAATTAAATCCAAAGATAAAAAGTGAAGGAAGATTGAAATAGATATCATACTTGATCTGAA
* * *
1133 ATTAAATTGTACTTCCATAAAAATTCAATTAATTAAAAATTCATCAACGTTTAAAGTGAGAATAC
66 ATTAAATTGTACTTCCATAAAAATTAAATTAATTAAAAATTCATCAACATTTAAAGTGAGAATAA
1198 AAGAATGAATTGAAGCATCCTATTCCTAGCCTACTAGAACCATTCCCTTACACTCTTGCGTCGCA
131 AAGAATGAATTGAAGCATCCTATTCCTAGCCTACTAGAACCATTCCCTTACACTCTTGCGTCGCA
1263 ATTAAGCATGCTCCTCGTCAGGAGCAAATTTGTCTTTTTGTCACAGTCAGGTCGCCCTCAATGAA
196 ATTAAGCATGCTCCTCGTCAGGAGCAAATTTGTCTTTTTGTCACAGTCAGGTCGCCCTCAATGAA
1328 GTTAAGCTACCATGGAAGCAAGCTTAAGAAAATGTTGAAGAGGAAGTTTTTATGCGTAAAAAATA
261 GTTAAGCTACCATGGAAGCAAGCTTAAGAAAATGTTGAAGAGGAAGTTTTTATGCGTAAAAAATA
*
1393 TGGAAGATGAAGCTTGAAGAATATCCTCTCTCATCAGTATTTATCAACAATTGCCAAGTACAGGT
326 TGGAAGATGAAGCTTGAAGAATATCCTCTCTCATCAGTATTTATCAACAATTGCCAAGTACAGGA
1458 GTCCTTTCTTTTAGATCCAACTTCCTCTAGCTGTACAAGTTGGTTATACCAGTTATACATTCACG
391 GTCCTTTCTTTTAGATCCAACTTCCTCTAGCTGTACAAGTTGGTTATACCAGTTATACATTCACG
*
1523 CAGATCTGGTGTGTTCATCAGACAGTCATTGGTTATGGTGACATTTCTGAGCACAAATTTGGATT
456 CAGATCTGGTGTGTTCATCAGACAGTCATTGGTTATGGCGACATTTCTGAGCACAAATTTGGATT
1588 CTATTTTGTGGCGACAACCCTAAATACCTTCATGCGTTGATCTTTTTGGACAGACTCCTGCACTG
521 CTATTTTGTGGCGACAACCCTAAATACCTTCATGCGTTGATCTTTTTGGACAGACTCCTGCACTG
1653 AACTTTGGATGCAATACTGAACATTAATTGTGGCGACATTAGTAGCAAAAACAGGAGAAAAAATA
586 AACTTTGGATGCAATACTGAACATTAATTGTGGCGACATTAGTAGCAAAAACAGGAGAAAAAATA
*
1718 AAGAAAATTAAACCTAGCATCACTGAATTTGATAATGCAATTACTAAGTTAAAAATGCTAAAAAT
651 AAGAAAATTAAACCTAGCATCACTGAATTTGAAAATGCAATTACTAAGTTAAAAATGCTAAAAAT
1783 GCATGCTAAAAAATGATAAAATGGGAACAAATTACACCCTAAGTAAGGAGAA
716 GCATGCTAAAAAATGATAAAATGGGAACAAATTACACCCTAAGTAAGGAGAA
************** *
1835 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAACAATTAAATCC
1 ------------------------------------CAAACAATTAAATCCAAA-GA-T--A---
1900 AAAGATAAACAGTGAAGGAAGATTGAAATAGATATCATACTTGATCTGAAATTAAATTGTACTTC
23 ------AAA-AGTGAAGGAAGATTGAAATAGATATCATACTTGATCTGAAATTAAATTGTACTTC
1965 CATAAAAATTAAATTAATTAAAAATTCATCAACATTTAAAGTGAGAATAAAAGAATGAATTGAAG
81 CATAAAAATTAAATTAATTAAAAATTCATCAACATTTAAAGTGAGAATAAAAGAATGAATTGAAG
2030 CATCCTATTCCTAGCCTACTAGAACCATTCCCTTACACTCCTCTTGCGTCGCAATTAAGCATGCT
146 CATCCTATTCCTAGCCTACTAGAACCATTCCCTTACA---CTCTTGCGTCGCAATTAAGCATGCT
*
2095 CCTCGTCAGGAGCAAATTTGTCTTTTTGTCACAGTCAGGTCTCCCTCAATGAAGTTAAGCTACCA
208 CCTCGTCAGGAGCAAATTTGTCTTTTTGTCACAGTCAGGTCGCCCTCAATGAAGTTAAGCTACCA
2160 TGGAAGCAAGCTTAAGAAAATGTTGAAGAGGAAGTTTTTATGCGTAAAAAATATGGAAGATGAAG
273 TGGAAGCAAGCTTAAGAAAATGTTGAAGAGGAAGTTTTTATGCGTAAAAAATATGGAAGATGAAG
2225 CTTGAAGAATATCCTCTCTCATCAGTATTTATCAACAATTGCCAAGTACAGGAGTCCTTTCTTTT
338 CTTGAAGAATATCCTCTCTCATCAGTATTTATCAACAATTGCCAAGTACAGGAGTCCTTTCTTTT
*
2290 AGATCCAACTTCCTCTAGCTGTACAAGTTGGTTATACCAGTTATATATTCACGCAGATCTGGTGT
403 AGATCCAACTTCCTCTAGCTGTACAAGTTGGTTATACCAGTTATACATTCACGCAGATCTGGTGT
*
2355 GTTCATTAGACAGTCATTGGTTATGGCGACATTTCTGAGCACAAATTTGGATTCTATTTTGTGGC
468 GTTCATCAGACAGTCATTGGTTATGGCGACATTTCTGAGCACAAATTTGGATTCTATTTTGTGGC
*
2420 GACAACCCTAAATACCTTCATGCGTTGATCTTTTTGGACAGACTCCTGCATTGAACTTTGGATGC
533 GACAACCCTAAATACCTTCATGCGTTGATCTTTTTGGACAGACTCCTGCACTGAACTTTGGATGC
*
2485 AATACTGAACATTAATTGTGGCGACATTAGTAGCAAAAATAGGAGAAAAAATAAAGAAAATTAAA
598 AATACTGAACATTAATTGTGGCGACATTAGTAGCAAAAACAGGAGAAAAAATAAAGAAAATTAAA
2550 CCTAGCATCACTGAATTTGAAAATGCAATTACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAA
663 CCTAGCATCACTGAATTTGAAAATGCAATTACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAA
2615 ATGATAAAATGGGAACAAATTACACCCTAAGTAAGGAGAA
728 ATGATAAAATGGGAACAAATTACACCCTAAGTAAGGAGAA
2655 ATCAATAGTC
Statistics
Matches: 741, Mismatches: 26, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
803 4 0.01
804 1 0.00
805 1 0.00
807 1 0.00
816 3 0.00
817 154 0.21
820 577 0.78
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.28
Consensus pattern (767 bp):
CAAACAATTAAATCCAAAGATAAAAAGTGAAGGAAGATTGAAATAGATATCATACTTGATCTGAA
ATTAAATTGTACTTCCATAAAAATTAAATTAATTAAAAATTCATCAACATTTAAAGTGAGAATAA
AAGAATGAATTGAAGCATCCTATTCCTAGCCTACTAGAACCATTCCCTTACACTCTTGCGTCGCA
ATTAAGCATGCTCCTCGTCAGGAGCAAATTTGTCTTTTTGTCACAGTCAGGTCGCCCTCAATGAA
GTTAAGCTACCATGGAAGCAAGCTTAAGAAAATGTTGAAGAGGAAGTTTTTATGCGTAAAAAATA
TGGAAGATGAAGCTTGAAGAATATCCTCTCTCATCAGTATTTATCAACAATTGCCAAGTACAGGA
GTCCTTTCTTTTAGATCCAACTTCCTCTAGCTGTACAAGTTGGTTATACCAGTTATACATTCACG
CAGATCTGGTGTGTTCATCAGACAGTCATTGGTTATGGCGACATTTCTGAGCACAAATTTGGATT
CTATTTTGTGGCGACAACCCTAAATACCTTCATGCGTTGATCTTTTTGGACAGACTCCTGCACTG
AACTTTGGATGCAATACTGAACATTAATTGTGGCGACATTAGTAGCAAAAACAGGAGAAAAAATA
AAGAAAATTAAACCTAGCATCACTGAATTTGAAAATGCAATTACTAAGTTAAAAATGCTAAAAAT
GCATGCTAAAAAATGATAAAATGGGAACAAATTACACCCTAAGTAAGGAGAA
Done.