Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010617.1 Kokia drynarioides strain JFW-HI SEQ_125550, 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: 11281
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:759 original size:15 final size:15
Alignment explanation
Indices: 739--781 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
729 CTAATATCAT
*
739 TAACAATATTAATGA
1 TAACAATAATAATGA
754 TAACAATAATAATGA
1 TAACAATAATAATGA
* *
769 CATCAATAATAAT
1 TAACAATAATAAT
782 ATTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (15 bp):
TAACAATAATAATGA
Found at i:797 original size:12 final size:12
Alignment explanation
Indices: 715--799 Score: 59
Period size: 12 Copynumber: 7.3 Consensus size: 12
705 TTGGCAATAA
*
715 TAATAATAATAT
1 TAATAATAACAT
* *
727 TACTAATATCAT
1 TAATAATAACAT
*
739 TAACAAT---AT
1 TAATAATAACAT
* *
748 TAATGATAACAA
1 TAATAATAACAT
*
760 TAATAATGACAT
1 TAATAATAACAT
* *
772 CAATAATAATAT
1 TAATAATAACAT
*
784 TAATAATAGCAT
1 TAATAATAACAT
796 TAAT
1 TAAT
800 TAAAAAAGAA
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
9 7 0.13
12 46 0.87
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (12 bp):
TAATAATAACAT
Found at i:1944 original size:29 final size:30
Alignment explanation
Indices: 1910--2254 Score: 217
Period size: 30 Copynumber: 11.6 Consensus size: 30
1900 CCTTAAATTG
1910 TCCAAAAATTACCATTTT-ACCCTCGAACT
1 TCCAAAAATTACCATTTTGACCCTCGAACT
* *
1939 TCCAAAAA-TCCCATTTTTGA-CCTCGAAACC
1 TCCAAAAATTACCA-TTTTGACCCTCG-AACT
* *
1969 TCCTAAAATTACCATTTT-ACCCCCGAACT
1 TCCAAAAATTACCATTTTGACCCTCGAACT
* *
1998 TCCAAAAA-TCCCATTTTTGACCGT-GAACCT
1 TCCAAAAATTACCA-TTTTGACCCTCGAA-CT
**
2028 TCCAAAAATTACCATTTT-ACCGC-AAAACT
1 TCCAAAAATTACCATTTTGACC-CTCGAACT
2057 TCCAAAAA-T-CCTATTTTTGACCC-CGAACCT
1 TCCAAAAATTACC-A-TTTTGACCCTCGAA-CT
*
2087 TCCAAAAATTA-CATTTT-ACCCCCGAACT
1 TCCAAAAATTACCATTTTGACCCTCGAACT
*** *
2115 TCCAAAAATCTAATTTTTTTAACCC-CGAACCT
1 TCCAAAAAT-T-ACCATTTTGACCCTCGAA-CT
** *
2147 TTTAAAAATTACCATTTT-ACCCTCAAACT
1 TCCAAAAATTACCATTTTGACCCTCGAACT
* * *
2176 T-CAAAAAATCCCATTTTTAACCCT-GAAACT
1 TCCAAAAATTACCA-TTTTGACCCTCG-AACT
*
2206 TCCAAAAATCTTA--TTTTTGA-CCTCGATACT
1 TCCAAAAA--TTACCATTTTGACCCTCGA-ACT
2236 TCCAAAAAATTACCATTTT
1 TCC-AAAAATTACCATTTT
2255 ACTCTCGGAT
Statistics
Matches: 249, Mismatches: 32, Indels: 68
0.71 0.09 0.19
Matches are distributed among these distances:
27 2 0.01
28 34 0.14
29 82 0.33
30 83 0.33
31 34 0.14
32 13 0.05
33 1 0.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTGACCCTCGAACT
Found at i:2006 original size:59 final size:59
Alignment explanation
Indices: 1910--2214 Score: 389
Period size: 59 Copynumber: 5.2 Consensus size: 59
1900 CCTTAAATTG
* *
1910 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACC-
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG-AACCT
* **
1969 TCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCGTGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* ** *
2028 TCCAAAAATTACCATTTTACCGCAAAACTTCCAAAAATCCTATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** *
2087 TCCAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATCTAATTTTTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTGACCCCGAACCT
** * * * * * *
2147 TTTAAAAATTACCATTTTACCCTCAAACTTCAAAAAATCCCATTTTTAACCCTGAAACT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
2206 TCCAAAAAT
1 TCCAAAAAT
2215 CTTATTTTTG
Statistics
Matches: 214, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
58 29 0.14
59 135 0.63
60 25 0.12
61 25 0.12
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:4360 original size:14 final size:15
Alignment explanation
Indices: 4316--4361 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
4306 TTATTGTAAA
4316 ATTTTAAATATAATTAT
1 ATTTTAAAT-TAA-TAT
*
4333 ATTTTTAATT-ATAT
1 ATTTTAAATTAATAT
4347 A-TTTAAATTAATAT
1 ATTTTAAATTAATAT
4361 A
1 A
4362 CACAATCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.27
14 9 0.35
15 1 0.04
16 1 0.04
17 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTAAATTAATAT
Found at i:10719 original size:22 final size:22
Alignment explanation
Indices: 10689--10739 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10679 AAGTAGCTAA
*
10689 AAAATAAAAGAAAACCAAAATAT
1 AAAA-AAAAGAAAAACAAAATAT
* *
10712 AAAAAAAATAAAAACTAAATAT
1 AAAAAAAAGAAAAACAAAATAT
10734 AAAAAA
1 AAAAAA
10740 TTATATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAAAAGAAAAACAAAATAT
Found at i:10724 original size:16 final size:18
Alignment explanation
Indices: 10685--10730 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
10675 ACAAAAGTAG
10685 CTAAAAAATAAAAGAAAA
1 CTAAAAAATAAAAGAAAA
* *
10703 CCAAAATATAAAA-AAAA
1 CTAAAAAATAAAAGAAAA
*
10720 -TAAAAACTAAA
1 CTAAAAAATAAA
10731 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 11 0.48
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.13
Consensus pattern (18 bp):
CTAAAAAATAAAAGAAAA
Done.