Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011879.1 Kokia drynarioides strain JFW-HI SEQ_126876, 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: 14410
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Found at i:781 original size:21 final size:23
Alignment explanation
Indices: 752--795 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
742 TGGGAAAACC
*
752 GTTTAGATCTAGGC-TAGATCTG
1 GTTTAGATCTAGACTTAGATCTG
774 GTTT-GATCTAGACTTAGATCTG
1 GTTTAGATCTAGACTTAGATCTG
796 TTCTTGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (23 bp):
GTTTAGATCTAGACTTAGATCTG
Found at i:1633 original size:30 final size:30
Alignment explanation
Indices: 1597--1987 Score: 469
Period size: 30 Copynumber: 13.2 Consensus size: 30
1587 AAGGTCCTCG
*
1597 AAACTTCTAAAAATCTCATTTTTAACCCCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* *
1627 AAACTTCTTAAAATCTCATTTTT-ACCCTC-
1 AAACTTCTAAAAATCCCATTTTTAACCC-CA
1656 AAACTTCTAAAAATCCCATTTTTAACCCCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* * * *
1686 AAACTCCCAAAAATCTCATTTCT-ACCTCC-
1 AAACTTCTAAAAATCCCATTTTTAACC-CCA
* *
1715 GAACTTCTAAAAATCCCATTTCTAACCCCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* *
1745 AAACTTCCAAAAATCCCATTTTTACCCCCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* *
1775 AAA-TTCTAAAAATCCCATTTTTAACCTCG
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* *
1804 AAACTTCAAAAAATCCCATTTTAAACCCCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
* * *
1834 AAACTTCCAAAAAACCCATTTTTAACCTCA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
1864 AAACTT-TAAAAAATCCCATTTTTAACCCCA
1 AAACTTCT-AAAAATCCCATTTTTAACCCCA
*
1894 AAACTTCTAAAAATCACATTTTT-ACCCTC-
1 AAACTTCTAAAAATCCCATTTTTAACCC-CA
*
1923 GAACTTCTAAAAATCCCATTTTT-ACCCTC-
1 AAACTTCTAAAAATCCCATTTTTAACCC-CA
* *
1952 AAACTTCTAAAAGTCCCATTTTTAACCCTA
1 AAACTTCTAAAAATCCCATTTTTAACCCCA
1982 AAACTT
1 AAACTT
1988 TCAAAAGTTT
Statistics
Matches: 313, Mismatches: 36, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
29 127 0.41
30 185 0.59
31 1 0.00
ACGTcount: A:0.38, C:0.30, G:0.01, T:0.31
Consensus pattern (30 bp):
AAACTTCTAAAAATCCCATTTTTAACCCCA
Found at i:1669 original size:59 final size:59
Alignment explanation
Indices: 1592--2033 Score: 475
Period size: 59 Copynumber: 7.5 Consensus size: 59
1582 CCTTGAAGGT
* * *
1592 CCTCGAAACTTCTAAAAATCTCATTTTTAACCCCAAAACTTCTTAAAATCTCATTTTTAC
1 CCTC-AAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTTAC
* * * *
1652 CCTCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATCTCATTTCTA-
1 CCTCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTTAC
* * *
1710 CCTCCGAACTTCTAAAAATCCCATTTCTAACCCCAAAACTTCCAAAAATCCCATTTTTAC
1 CCT-CAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTTAC
* * * * * *
1770 CCCCAAAATTCTAAAAATCCCATTTTTAACCTCGAAACTTCAAAAAATCCCATTTTAAAC
1 CCTCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTT-TAC
* * *
1830 CC-CAAAACTTCCAAAAAACCCATTTTTAACCTCAAAACTT-TAAAAAATCCCATTTTTAAC
1 CCTC-AAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCT-AAAAATCCCATTTTT-AC
* *
1890 CC-CAAAACTTCTAAAAATCACATTTTT-ACCCTC-GAACTTCTAAAAATCCCATTTTTAC
1 CCTC-AAACTTCTAAAAATCCCATTTTTAACCC-CAAAACTTCTAAAAATCCCATTTTTAC
* * * **
1948 CCTCAAACTTCTAAAAGTCCCATTTTTAACCCTAAAACTT-TCAAAAGTTTCATTTTTAC
1 CCTCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCT-AAAAATCCCATTTTTAC
* * * * *
2007 CCCCGAACTCCTAAAGATCCCTTTTTT
1 CCTCAAACTTCTAAAAATCCCATTTTT
2034 TACCTCGAAT
Statistics
Matches: 328, Mismatches: 42, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
58 29 0.09
59 215 0.66
60 84 0.26
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (59 bp):
CCTCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTTAC
Found at i:1749 original size:89 final size:89
Alignment explanation
Indices: 1597--1987 Score: 445
Period size: 89 Copynumber: 4.4 Consensus size: 89
1587 AAGGTCCTCG
* * * * *
1597 AAACTTCTAAAAATCTCATTTTTAACCCCAAAACTTCTTAAAATCTCATTTTTACCCTCAAACTT
1 AAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTAACCCTCAAACTT
*
1662 CTAAAAATCCCATTTTTAACCCCA
66 CCAAAAATCCCATTTTTAACCCCA
* * * * *
1686 AAACTCCCAAAAATCTCATTTCT-ACCTCC-GAACTTCTAAAAATCCCATTTCTAACCC-CAAAA
1 AAACTTCAAAAAATCCCATTTTTAACC-CCAAAACTTCTAAAAATCCCATTT-TAACCCTC-AAA
*
1748 CTTCCAAAAATCCCATTTTTACCCCCA
63 CTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1775 AAA-TTCTAAAAATCCCATTTTTAACCTCGAAACTTCAAAAAATCCCATTTTAAACCC-CAAAAC
1 AAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTT-AACCCTC-AAAC
* *
1838 TTCCAAAAAACCCATTTTTAACCTCA
64 TTCCAAAAATCCCATTTTTAACCCCA
* * * *
1864 AAACTTTAAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCACATTTTTACCCTCGAACTT
1 AAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTAACCCTCAAACTT
*
1929 CTAAAAATCCCATTTTT-ACCCTC-
66 CCAAAAATCCCATTTTTAACCC-CA
* * *
1952 AAACTTCTAAAAGTCCCATTTTTAACCCTAAAACTT
1 AAACTTCAAAAAATCCCATTTTTAACCCCAAAACTT
1988 TCAAAAGTTT
Statistics
Matches: 259, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
88 74 0.29
89 142 0.55
90 43 0.17
ACGTcount: A:0.38, C:0.30, G:0.01, T:0.31
Consensus pattern (89 bp):
AAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATCCCATTTTAACCCTCAAACTT
CCAAAAATCCCATTTTTAACCCCA
Done.