Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010323.1 Kokia drynarioides strain JFW-HI SEQ_125187, 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, 745
Length: 1242
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:872 original size:29 final size:29
Alignment explanation
Indices: 840--1110 Score: 178
Period size: 29 Copynumber: 9.2 Consensus size: 29
830 AAAAATTTTG
840 TTTTTACCCCTAAACTTCCAAAAATCTCA
1 TTTTTACCCCTAAACTTCCAAAAATCTCA
** * **
869 TTTTTGA-CCCTAAAACTTTTAAAAATTTTG
1 TTTTT-ACCCCT-AAACTTCCAAAAATCTCA
* * *
899 TTTTTACACCTGAACTTCCAAAAATCCCA
1 TTTTTACCCCTAAACTTCCAAAAATCTCA
* **
928 TTTTTGACCCCGAAACTTCTTAAAAT-TCTA
1 TTTTT-ACCCCTAAACTTCCAAAAATCTC-A
* * * ** * *
958 TTTTGACCTCAAAACTTCTTAAAATTTTA
1 TTTTTACCCCTAAACTTCCAAAAATCTCA
*
987 TTTTTACCCCCAAACTTCCAAAAATCTCA
1 TTTTTACCCCTAAACTTCCAAAAATCTCA
* *
1016 TTTTTTACCCCGAAACTTCAAAAAAT-TCTA
1 -TTTTTACCCCTAAACTTCCAAAAATCTC-A
* *
1046 TTTTTA-CCATCGAACTTCCAAAAAATC-CAA
1 TTTTTACCCCT-AAACTTCC-AAAAATCTC-A
*
1076 TTTTTA-CCCTCAAACTTTCAAAAAT-TCCA
1 TTTTTACCCCT-AAACTTCCAAAAATCT-CA
1105 TTTTTA
1 TTTTTA
1111 GCCACGAACT
Statistics
Matches: 189, Mismatches: 40, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.01
29 95 0.50
30 92 0.49
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTTTACCCCTAAACTTCCAAAAATCTCA
Found at i:915 original size:59 final size:60
Alignment explanation
Indices: 829--952 Score: 196
Period size: 59 Copynumber: 2.1 Consensus size: 60
819 CTAAATTGTC
* * *
829 TAAAAATTTTGTTTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCTAAAACTT-T
1 TAAAAATTTTGTTTTTACACCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCT
* *
888 TAAAAATTTTGTTTTTACACCTGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCT
1 TAAAAATTTTGTTTTTACACCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCT
948 TAAAA
1 TAAAA
953 TTCTATTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 53 0.90
60 6 0.10
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
TAAAAATTTTGTTTTTACACCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCT
Found at i:974 original size:59 final size:59
Alignment explanation
Indices: 851--975 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
841 TTTTACCCCT
* * * * * *
851 AAACTTCCAAAAATCTCATTTTTGACCCTAAAACTTTTAAAAATTTTGTTTTTACACCT
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTTAAAAATTCTATTTTGACACCA
* *
910 GAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTT-AAAATTCTATTTTGAC-CTCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT-TTAAAAATTCTATTTTGACAC-CA
969 AAACTTC
1 AAACTTC
976 TTAAAATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.02
59 52 0.95
60 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTTAAAAATTCTATTTTGACACCA
Found at i:982 original size:88 final size:86
Alignment explanation
Indices: 840--1049 Score: 255
Period size: 88 Copynumber: 2.4 Consensus size: 86
830 AAAAATTTTG
* *
840 TTTTTACCCCTAAACTTCCAAAAA-TCTCATTTTTGACCCTAAAACTTTTAAAAATTTTGTTTTT
1 TTTTTACCCCGAAACTT-CAAAAATTCT-A-TTTTGACCCTAAAACTTTTAAAAATTTTATTTTT
**
904 ACACCTGAACTTCCAAAAATCCCA
63 ACACCCAAACTTCCAAAAATCCCA
*
928 TTTTTGACCCCGAAACTTCTTAAAATTCTATTTTGA-CCTCAAAACTTCTT-AAAATTTTATTTT
1 TTTTT-ACCCCGAAACTTC-AAAAATTCTATTTTGACCCT-AAAACTT-TTAAAAATTTTATTTT
* *
991 TACCCCCAAACTTCCAAAAATCTCA
62 TACACCCAAACTTCCAAAAATCCCA
1016 TTTTTTACCCCGAAACTTCAAAAAATTCTATTTT
1 -TTTTTACCCCGAAACTTC-AAAAATTCTATTTT
1050 TACCATCGAA
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
87 3 0.03
88 78 0.73
89 23 0.21
90 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (86 bp):
TTTTTACCCCGAAACTTCAAAAATTCTATTTTGACCCTAAAACTTTTAAAAATTTTATTTTTACA
CCCAAACTTCCAAAAATCCCA
Found at i:1032 original size:59 final size:59
Alignment explanation
Indices: 964--1126 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 59
954 TCTATTTTGA
** * * *
964 CCTCAAAACTTCTTAAAATTTTATTTTTACCCCCAAACTTCC-AAAAATCTCATTTTTTAC
1 CCTC-AAACTTCAAAAAATTCTATTTTTACCACCAAACTTCCAAAAAATC-CAATTTTTAC
* *
1024 CC-CGAAACTTCAAAAAATTCTATTTTTACCATCGAACTTCCAAAAAATCCAATTTTTAC
1 CCTC-AAACTTCAAAAAATTCTATTTTTACCACCAAACTTCCAAAAAATCCAATTTTTAC
* *
1083 CCTCAAACTTTC-AAAAATTCCATTTTTAGCCA-CGAACTTCCAAA
1 CCTCAAAC-TTCAAAAAATTCTATTTTTA-CCACCAAACTTCCAAA
1127 CCCCAAAACT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
59 74 0.82
60 16 0.18
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
CCTCAAACTTCAAAAAATTCTATTTTTACCACCAAACTTCCAAAAAATCCAATTTTTAC
Done.