Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013288.1 Kokia drynarioides strain JFW-HI SEQ_128310, 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: 2817
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2313 original size:816 final size:766
Alignment explanation
Indices: 742--2323 Score: 2151
Period size: 816 Copynumber: 2.0 Consensus size: 766
732 AATCCGGTTC
742 AAACACACGGATGTTACAATTCTTCCCCCCTTAAAATAAATTTCGTCCTCGAAATTTACCTGTAC
1 AAACACACGGATGTTACAATTCTTCCCCCCTTAAAATAAATTTCGTCCTCGAAATTTACCTGTAC
807 TGAACAACTGTGGATATTGCTGTTTCATCGTTTCCTCTCTTTCCCAAGTAGCTTCTTCTGAGTTA
66 TGAACAACTGTGGATATTGCTGTTTCATCGTTTCCTCTCTTTCCCAAGTAGCTTCTTCTGAGTTA
872 TGATGTCTCCATAGCACTTTTACCAGAAGAACTCTTTTATTTCTCAATTCTTTCACTTCTTGAGC
131 TGATGTCTCCATAGCACTTTTACCAGAAGAACTCTTTTATTTCTCAATTCTTTCACTTCTTGAGC
* *
937 TAGTATCTTTATTGGTTCCTCTTCATACGTCAAATCCGGTTGTATTTCAATACTCTCCGGAGTAA
196 TAGTATCTTTATTGGTTCCTCTTCATAAGTCAAATCCGGTTGTATTTCAATACTCTCCAGAGTAA
*
1002 TCACATGAGATGAGTCAGATCGGTACCTCCGTAGCATAGACACATGAAAAACATTATGAATCTTA
261 TCACATGAGATGAGTCAGATCGGTACCTCCGTAGCATAGACACATAAAAAACATTATGAATCTTA
* *
1067 TCTAATTCTGGAGGAAGAGCCAATTGATAAGCAACTGGACCAATTCTTTCCAATATCTCACATGG
326 TCTAATTCTGGAGGAAGAGCCAATCGATAAGCAACTGGACCAATTCTTTCCAAAATCTCACATGG
*
1132 CCCGATAAATCTTGGGTTCAATTTCCCTTTCTTACCAAATCGGAGAACTTTTTTCCACGGAGACA
391 CCCGATAAATCTTGGGTTCAATTTCCCTTTCTTACCAAATCGGAGAACTTTCTTCCACGGAGACA
* *
1197 CTTTTAAGAAAACCTTTTCACCAACATTAAACTCTATATCTTTCCTTTTCAAATCTGCATAGGAC
456 CTTTTAAGAAAACCTTTTCACCAACATTAAACTCTATATCTTTCCTTTTCAAATCAGCATAGAAC
*
1262 TTCTGTCTATCTGAAGCAGCCTTTAATCGCTCTCGGATCAACTTTACTTTTTCTTCAGTTTCTCG
521 TTCTATCTATCTGAAGCAGCCTTTAATCGCTCTCGGATCAACTTTACTTTTTCTTCAGTTTCTCG
1327 AATCAGATCAGGACCCACAAGCTTCTGTTCACTTAACTCTGTCCAACACACAGGAGTCCTACACT
586 AATCAGATCAGGACCCACAAGCTTCTGTTCACTTAACTCTGTCCAACACACAGGAGTCCTACACT
*
1392 TTCTTCCGTACAATGCTTCATACGGTGCCATCTGAATACTTGACTGATAACTGTTATTATAAGTA
651 TTCTTCCATACAATGCTTCATACGGTGCCATCTGAATACTTGACTGATAACTGTTATTATAAGTA
*
1457 AATTCAATCAACGGTAAATACCTTTCCCAATTACCTTCAAACTCAATAATA
716 AATTCAATCAACGGGAAATACCTTTCCCAATTACCTTCAAACTCAATAATA
************************* * * ** ***
1508 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAACACACGGATGTT
1 ----------------------------AAACACACGGATGTTACAATTCTTCCCCCCTTAAAAT
** ** ** ** *
1573 ACAATTCTTCCCCCCTTAAAATAAATTTCGTCCTCGAA-ATTTACCTGTACTGAACAACTGTGGA
38 A-AA-T-TT-CGTCCTCGAAATTTACCT-GTACT-GAACA---A-C-------------TGTGGA
1637 TATTGCTGTTTCATCGTTTCCTCTCTTTCCCAAGTAGCTTCTTCTGAGTTATGATGTCTCCATAG
80 TATTGCTGTTTCATCGTTTCCTCTCTTTCCCAAGTAGCTTCTTCTGAGTTATGATGTCTCCATAG
1702 CACTTTTACCAGAAGAACTCTTTTATTTCTCAATTCTTTCACTTCTTGAGCTAGTATCTTTATTG
145 CACTTTTACCAGAAGAACTCTTTTATTTCTCAATTCTTTCACTTCTTGAGCTAGTATCTTTATTG
* *
1767 GTTCCTCTTCATAAGTCAAATCCGGTTGTATTTCAATACTCTCCATAGTAATCACATGGGATGAG
210 GTTCCTCTTCATAAGTCAAATCCGGTTGTATTTCAATACTCTCCAGAGTAATCACATGAGATGAG
1832 TCAGATCGGTACCTCCGTAGCATAGACACATAAAAAACATTATGAATCTTATCTAATTCTGGAGG
275 TCAGATCGGTACCTCCGTAGCATAGACACATAAAAAACATTATGAATCTTATCTAATTCTGGAGG
*
1897 AAGAGCCAATCGATAAGCAACTGGACCAATTCTTTCCAAAATCTCATATGGCCCGATAAATCTTG
340 AAGAGCCAATCGATAAGCAACTGGACCAATTCTTTCCAAAATCTCACATGGCCCGATAAATCTTG
*
1962 GGCTT-AATTTCCCTTTCTTGCCAAATCGGAGAACTTTCTTCCACGGAGACACTTTTAAGAAAAC
405 GG-TTCAATTTCCCTTTCTTACCAAATCGGAGAACTTTCTTCCACGGAGACACTTTTAAGAAAAC
*
2026 CTTTTCACCAACATTGAACTCTATATCTTTCCTTTTCAAATCAGCATAGAACTTCTATCTATCTG
469 CTTTTCACCAACATTAAACTCTATATCTTTCCTTTTCAAATCAGCATAGAACTTCTATCTATCTG
*
2091 AAGCAGCCTTTAATCGCTCTTGGATCAACTTTACTTTTTCTTCAGTTTCTCGAATCAGATCAGGA
534 AAGCAGCCTTTAATCGCTCTCGGATCAACTTTACTTTTTCTTCAGTTTCTCGAATCAGATCAGGA
2156 CCCACAAGCTTCTGTTCACTTAACTCTGTCCAACACACAGGAGTCCTACACTTTCTTCCATACAA
599 CCCACAAGCTTCTGTTCACTTAACTCTGTCCAACACACAGGAGTCCTACACTTTCTTCCATACAA
2221 TGCTTCATACGGTGCCATCTGAATACTTGACTGATAACTGTTATTATAAGTAAATTCAATCAACG
664 TGCTTCATACGGTGCCATCTGAATACTTGACTGATAACTGTTATTATAAGTAAATTCAATCAACG
*
2286 GGAAATACCTTTCCGAATTACCTTCAAACTCAATAATA
729 GGAAATACCTTTCCCAATTACCTTCAAACTCAATAATA
2324 CAGCTTCTCA
Statistics
Matches: 705, Mismatches: 59, Indels: 26
0.89 0.07 0.03
Matches are distributed among these distances:
794 6 0.01
795 2 0.00
796 1 0.00
797 2 0.00
798 10 0.01
799 5 0.01
800 3 0.00
802 1 0.00
803 1 0.00
816 672 0.95
817 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.33
Consensus pattern (766 bp):
AAACACACGGATGTTACAATTCTTCCCCCCTTAAAATAAATTTCGTCCTCGAAATTTACCTGTAC
TGAACAACTGTGGATATTGCTGTTTCATCGTTTCCTCTCTTTCCCAAGTAGCTTCTTCTGAGTTA
TGATGTCTCCATAGCACTTTTACCAGAAGAACTCTTTTATTTCTCAATTCTTTCACTTCTTGAGC
TAGTATCTTTATTGGTTCCTCTTCATAAGTCAAATCCGGTTGTATTTCAATACTCTCCAGAGTAA
TCACATGAGATGAGTCAGATCGGTACCTCCGTAGCATAGACACATAAAAAACATTATGAATCTTA
TCTAATTCTGGAGGAAGAGCCAATCGATAAGCAACTGGACCAATTCTTTCCAAAATCTCACATGG
CCCGATAAATCTTGGGTTCAATTTCCCTTTCTTACCAAATCGGAGAACTTTCTTCCACGGAGACA
CTTTTAAGAAAACCTTTTCACCAACATTAAACTCTATATCTTTCCTTTTCAAATCAGCATAGAAC
TTCTATCTATCTGAAGCAGCCTTTAATCGCTCTCGGATCAACTTTACTTTTTCTTCAGTTTCTCG
AATCAGATCAGGACCCACAAGCTTCTGTTCACTTAACTCTGTCCAACACACAGGAGTCCTACACT
TTCTTCCATACAATGCTTCATACGGTGCCATCTGAATACTTGACTGATAACTGTTATTATAAGTA
AATTCAATCAACGGGAAATACCTTTCCCAATTACCTTCAAACTCAATAATA
Done.