Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011655.1 Kokia drynarioides strain JFW-HI SEQ_126647, 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: 9198
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2295 original size:27 final size:26
Alignment explanation
Indices: 2245--2304 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
2235 CAATTTTCAA
*
2245 TTAATGATTGTTTCCTTTGACCTCCCT
1 TTAAT-ATTGTTTCCTTCGACCTCCCT
**
2272 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGA-CCTCCCT
2299 TTAATA
1 TTAATA
2305 GAATTCTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.52
Consensus pattern (26 bp):
TTAATATTGTTTCCTTCGACCTCCCT
Found at i:3727 original size:29 final size:30
Alignment explanation
Indices: 3682--3926 Score: 136
Period size: 30 Copynumber: 8.4 Consensus size: 30
3672 ACGGTCAAAG
*
3682 AAATT-CCATTTTAACCCTAAACTTTCTAA
1 AAATTACCATTTTAACCCTAAACTTTCCAA
* *
3711 AAATTATCATTTTACCCCTAAA-TTTCCAA
1 AAATTACCATTTTAACCCTAAACTTTCCAA
*
3740 AAA-T-CCAATTTTGACCCTAAACTTTCCAA
1 AAATTACC-ATTTTAACCCTAAACTTTCCAA
* **
3769 AAATTACCATTTTACCCCCGAAC-TTCCAA
1 AAATTACCATTTTAACCCTAAACTTTCCAA
* ** * *
3798 AAA-T-CTCATTTTTGACCCCGAACCTTCTAA
1 AAATTAC-CA-TTTTAACCCTAAACTTTCCAA
* * **
3828 AAATTACTATTTTACCCCCGAAC--TCC-A
1 AAATTACCATTTTAACCCTAAACTTTCCAA
* * * * * *
3855 AAAGTCCCATTTTTTACCCTGAACCTTCTAA
1 AAATTACCA-TTTTAACCCTAAACTTTCCAA
* **
3886 AAATTACCATTTTACCCCCGAAC-TTCCAA
1 AAATTACCATTTTAACCCTAAACTTTCCAA
*
3915 AAA-TCCCATTTT
1 AAATTACCATTTT
3927 TGACCCCGAA
Statistics
Matches: 171, Mismatches: 31, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
27 9 0.05
28 37 0.22
29 53 0.31
30 59 0.35
31 12 0.07
32 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
AAATTACCATTTTAACCCTAAACTTTCCAA
Found at i:3893 original size:117 final size:117
Alignment explanation
Indices: 3705--4047 Score: 519
Period size: 117 Copynumber: 2.9 Consensus size: 117
3695 ACCCTAAACT
** * * * * * *
3705 TTCTAAAAATTA-TCATTTTACCCCTAAATTTCCAAAAAT-CCAATTTTGACCCTAAACTTTCCA
1 TTCTAAAAATTACT-ATTTTACCCCCGAA-CTCCAAAAGTCCCATTTTTGACCCTGAACCTTCTA
*
3768 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACC
64 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
3822 TTCTAAAAATTACTATTTTACCCCCGAACTCCAAAAGTCCCATTTTTTACCCTGAACCTTCTAAA
1 TTCTAAAAATTACTATTTTACCCCCGAACTCCAAAAGTCCCATTTTTGACCCTGAACCTTCTAAA
*
3887 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATC
66 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
3939 TTCTAGAAATTACCATTTTACCCCCGAACTCCCAAAAGTCCCATTTTTGACCCCGAACCTTCTAA
1 TTCTAAAAATTACTATTTTACCCCCGAACT-CCAAAAGTCCCATTTTTGACCCTGAACCTTCTAA
4004 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
65 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
4048 TTTCGAGCCT
Statistics
Matches: 208, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
116 8 0.04
117 123 0.59
118 77 0.37
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (117 bp):
TTCTAAAAATTACTATTTTACCCCCGAACTCCAAAAGTCCCATTTTTGACCCTGAACCTTCTAAA
AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:3927 original size:29 final size:29
Alignment explanation
Indices: 3720--4045 Score: 242
Period size: 29 Copynumber: 11.1 Consensus size: 29
3710 AAAATTATCA
** * *
3720 TTTTACCCCTAAATTTCCAAAAATCCAAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
* ** *
3749 TTTGA-CCCTAAACTTTCCAAAAATTACCA-
1 TTTTACCCCCGAAC-TTCCAAAAA-TCCCAT
*
3778 TTTTACCCCCGAACTTCCAAAAATCTCAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
* **
3807 TTTTGA-CCCCGAACCTTCTAAAAATTAC-T
1 TTTT-ACCCCCGAA-CTTCCAAAAATCCCAT
*
3836 ATTTTACCCCCGAAC-TCCAAAAGTCCCATT
1 -TTTTACCCCCGAACTTCCAAAAATCCCA-T
* * *
3866 TTTTA-CCCTGAACCTTCTAAAAATTACCA-
1 TTTTACCCCCGAA-CTTCCAAAAA-TCCCAT
3895 TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
* * *
3924 TTTTGA-CCCCGAATCTTCTAGAAATTACCA-
1 TTTT-ACCCCCGAA-CTTCCA-AAAATCCCAT
* *
3954 TTTTACCCCCGAACTCCCAAAAGTCCCAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
* *
3983 TTTTGA-CCCCGAACCTTCTAAAAATTACCA-
1 TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCAT
4013 TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTACCCCCGAACTTCCAAAAATCCCAT
4042 TTTT
1 TTTT
4046 GATTTCGAGC
Statistics
Matches: 236, Mismatches: 36, Indels: 50
0.73 0.11 0.16
Matches are distributed among these distances:
28 39 0.17
29 101 0.43
30 81 0.34
31 15 0.06
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (29 bp):
TTTTACCCCCGAACTTCCAAAAATCCCAT
Found at i:4081 original size:59 final size:59
Alignment explanation
Indices: 3705--4047 Score: 510
Period size: 59 Copynumber: 5.8 Consensus size: 59
3695 ACCCTAAACT
* ** * * ** *
3705 TTCTAAAAATTATCATTTTACCCCTAAATTTCCAAAAAT-CCAATTTTGACCCTAAACT
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
3763 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
3822 TTCTAAAAATTACTATTTTACCCCCGAAC-TCCAAAAGTCCCATTTTTTACCCTGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
3880 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
3939 TTCTAGAAATTACCATTTTACCCCCGAACTCCCAAAAGTCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
3998 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
4048 TTTCGAGCCT
Statistics
Matches: 255, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
58 87 0.34
59 168 0.66
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Done.