Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010251.1 Kokia drynarioides strain JFW-HI SEQ_125086, 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: 4076
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:1002 original size:382 final size:372
Alignment explanation
Indices: 296--1036 Score: 1392
Period size: 382 Copynumber: 2.0 Consensus size: 372
286 NNNNNNNNNN
296 TTTAAAAAAAAAAGGAGAACAATCTTTTTCTTTTTTCGTCGAAAAAAAGACCGAACCCTTTTGGA
1 TTTAAAAAAAAAAGGAGAACAATCTTTTTCTTTTTTCGTCGAAAAAAAGACCGAACCCTTTTGGA
361 TCTAGGCTAGATCGGGTTCAATCTAGACCTAGACCCTTTTTTTTTAAAAAAAGGATGAAAAGAGA
66 TCTAGGCTAGATCGGGTTCAATCTAGACCTAGACCCTTTTTTTTTAAAAAAAGGATGAAAAGAGA
426 AAGATTGAAACTTTTCTTACCAAGAACTACGGTGCGTGAACGGCGAAACCCAGCGAACAGAGAGC
131 AAGATTGAAACTTTTCTTACCAAGAACTACGGTGCGTGAACGGCGAAACCCAGCGAACAGAGAGC
491 GGTGCAGGCCATTGGGGTACCCGGTGACCGTGCGTGGCTGTGGGTGAAGCATGTGTGACGGGGGT
196 GGTGCAGGCCATTGGGGTACCCGGTGACCGTGCGTGGCTGTGGGTGAAGCATGTGTGACGGGGGT
556 CGACAACGCGCATGACTGGTGAAGGCAGCGGTGCGCACACCGGAGAACCCAGGTAACGACTCGCG
261 CGACAACGCGCATGACTGGTGAAGGCAGCGGTGCGCACACCGGAGAACCCAGGTAACGACTCGCG
621 AGGGCCACGCGTGGGGATCGTCGACGCGCGTGGGCCCNNNNNNNNNNTCTGGAGATT
326 AGGGCCACGCGTGGGGATCGTCGACGCGCGTGGGCCC----------TCTGGAGATT
678 TTTAAAAAAAAAAGGAGAACAATCTTTTTCTTTTTTCGTCGAAAAAAAGACCGAACCCTTTTGGA
1 TTTAAAAAAAAAAGGAGAACAATCTTTTTCTTTTTTCGTCGAAAAAAAGACCGAACCCTTTTGGA
743 TCTAGGCTAGATCGGGTTCAATCTAGACCTAGACCCTTTTTTTTTAAAAAAAGGATGAAAAGAGA
66 TCTAGGCTAGATCGGGTTCAATCTAGACCTAGACCCTTTTTTTTTAAAAAAAGGATGAAAAGAGA
808 AAGATTGAAACTTTTCTTACCAAGAACTACGGTGCGTGAACGGCGAAACCCAGCGAACAGAGAGC
131 AAGATTGAAACTTTTCTTACCAAGAACTACGGTGCGTGAACGGCGAAACCCAGCGAACAGAGAGC
873 GGTGCAGGCCATTGGGGTACCCGGTGACCGTGCGTGGCTGTGGGTGAAGCATGTGTGACGGGGGT
196 GGTGCAGGCCATTGGGGTACCCGGTGACCGTGCGTGGCTGTGGGTGAAGCATGTGTGACGGGGGT
938 CGACAACGCGCATGACTGGTGAAGGCAGCGGTGCGCACACCGGAGAACCCAGGTAACGACTCGCG
261 CGACAACGCGCATGACTGGTGAAGGCAGCGGTGCGCACACCGGAGAACCCAGGTAACGACTCGCG
1003 AGGGCCACGCGTGGGGATCGTCGACGCGCGTGGG
326 AGGGCCACGCGTGGGGATCGTCGACGCGCGTGGG
1037 NGCGACGGAT
Statistics
Matches: 359, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
382 359 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (372 bp):
TTTAAAAAAAAAAGGAGAACAATCTTTTTCTTTTTTCGTCGAAAAAAAGACCGAACCCTTTTGGA
TCTAGGCTAGATCGGGTTCAATCTAGACCTAGACCCTTTTTTTTTAAAAAAAGGATGAAAAGAGA
AAGATTGAAACTTTTCTTACCAAGAACTACGGTGCGTGAACGGCGAAACCCAGCGAACAGAGAGC
GGTGCAGGCCATTGGGGTACCCGGTGACCGTGCGTGGCTGTGGGTGAAGCATGTGTGACGGGGGT
CGACAACGCGCATGACTGGTGAAGGCAGCGGTGCGCACACCGGAGAACCCAGGTAACGACTCGCG
AGGGCCACGCGTGGGGATCGTCGACGCGCGTGGGCCCTCTGGAGATT
Found at i:1697 original size:30 final size:29
Alignment explanation
Indices: 1663--1781 Score: 113
Period size: 30 Copynumber: 4.1 Consensus size: 29
1653 CCCCGGAGGT
**
1663 CCCTGAACCTTCCAAAAATTACTGTTTTAC
1 CCCTGAA-CTTCCAAAAATTACCATTTTAC
*
1693 CCCTGAA-TTCCCAAAAA-TCCCATTTTTGAC
1 CCCTGAACTT-CCAAAAATTACCA-TTTT-AC
1723 CCC-GAACCTTCCAAAAATTACCATTTTA-
1 CCCTGAA-CTTCCAAAAATTACCATTTTAC
*
1751 TCCTCGAACTTCC-AAAATTACCATTTTAC
1 CCCT-GAACTTCCAAAAATTACCATTTTAC
1780 CC
1 CC
1782 TCGAGTTGCT
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
28 21 0.28
29 21 0.28
30 26 0.35
31 6 0.08
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATTACCATTTTAC
Found at i:1772 original size:28 final size:30
Alignment explanation
Indices: 1663--1785 Score: 118
Period size: 28 Copynumber: 4.2 Consensus size: 30
1653 CCCCGGAGGT
**
1663 CCCT-GAACCTTCCAAAAATTACTGTTTTA
1 CCCTCGAACCTTCCAAAAATTACCATTTTA
*
1692 CCC-CTGAA--TTCCCAAAAA-TCCCATTTTTGA
1 CCCTC-GAACCTT-CCAAAAATTACCA-TTTT-A
1722 CCC-CGAACCTTCCAAAAATTACCATTTTA
1 CCCTCGAACCTTCCAAAAATTACCATTTTA
*
1751 TCCTCGAA-CTTCC-AAAATTACCATTTTA
1 CCCTCGAACCTTCCAAAAATTACCATTTTA
1779 CCCTCGA
1 CCCTCGA
1786 GTTGCTAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
28 25 0.32
29 25 0.32
30 23 0.29
31 6 0.08
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (30 bp):
CCCTCGAACCTTCCAAAAATTACCATTTTA
Done.