Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012648.1 Kokia drynarioides strain JFW-HI SEQ_127658, 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: 12457
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.34
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:9736 original size:17 final size:17
Alignment explanation
Indices: 9711--9787 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
9701 TCCAATCAGC
*
9711 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAT
* *
9728 TTAAGTTTATTCTAAAT
1 TTAAATTTATTTTAAAT
* *
9745 TTAAATTTAGTTGAAAT
1 TTAAATTTATTTTAAAT
*
9762 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
9779 TTAAATTTA
1 TTAAATTTA
9788 AAGTTTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:9749 original size:6 final size:6
Alignment explanation
Indices: 9711--9794 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
9701 TCCAATCAGC
* * * *
9711 TTAAAT TT-ATT TTAAAA TTAAGT TT--AT TCTAAAT TTAAAT TT-AGT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAAT
*
9756 TGAAAT TTAAAT TT--AT TATAAAT TTAAAT TTAAAGT TTA
1 TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAA-T TTA
9795 TTTTAAAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
4 5 0.08
5 9 0.15
6 35 0.59
7 10 0.17
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:11600 original size:30 final size:30
Alignment explanation
Indices: 11564--11821 Score: 231
Period size: 30 Copynumber: 8.8 Consensus size: 30
11554 AAGGTCCCTA
*
11564 AACCTTCCAAAAATCTTATTTTTAACCCCG
1 AACCTTCCAAAAATCTCATTTTTAACCCCG
* * *
11594 AACCTTCCAAAATTATCA-TTTTACCCCCG
1 AACCTTCCAAAAATCTCATTTTTAACCCCG
11623 AA-CTTCCAAAAAT-TCCATTTTTAACCCCG
1 AACCTTCCAAAAATCT-CATTTTTAACCCCG
*
11652 AACCTTCCAAAAAATATCA-TTTT-ACCCTCG
1 AACCTTCC-AAAAATCTCATTTTTAACCC-CG
*
11682 AA-CTTCCAAAAATC-CTATTTTTAACCCCA
1 AACCTTCCAAAAATCTC-ATTTTTAACCCCG
* *
11711 AACCTTCCAAAATTAC-CA-TTTT-ACCCCT
1 AACCTTCCAAAAAT-CTCATTTTTAACCCCG
* *
11739 AAACTTCCAAAAATC-CAATTTTTAACCTCG
1 AACCTTCCAAAAATCTC-ATTTTTAACCCCG
*
11769 AACCTTCCAAAAAT-TACCA-TTTTACCCCCG
1 AACCTTCCAAAAATCT--CATTTTTAACCCCG
*
11799 AA-CTTCC-AAAATCCCATTTTTAA
1 AACCTTCCAAAAATCTCATTTTTAA
11822 AATTACCATT
Statistics
Matches: 190, Mismatches: 19, Indels: 40
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.03
28 47 0.25
29 53 0.28
30 71 0.37
31 11 0.06
32 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (30 bp):
AACCTTCCAAAAATCTCATTTTTAACCCCG
Found at i:11657 original size:58 final size:58
Alignment explanation
Indices: 11567--11821 Score: 363
Period size: 58 Copynumber: 4.4 Consensus size: 58
11557 GTCCCTAAAC
* *
11567 CTTCCAAAAATCTTATTTTTAACCCCGAACCTTCC-AAAATTATCATTTTACCCCCGAA
1 CTTCCAAAAATC-CATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
* * *
11625 CTTCCAAAAATTCCATTTTTAACCCCGAACCTTCCAAAAAATATCATTTTACCCTCGAA
1 CTTCCAAAAA-TCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
* **
11684 CTTCCAAAAATCCTATTTTTAACCCCAAACCTTCC-AAAATTACCATTTTACCCCTAAA
1 CTTCCAAAAATCC-ATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
*
11742 CTTCCAAAAATCCAATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATCC-ATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
11801 CTTCC-AAAATCCCATTTTTAA
1 CTTCCAAAAAT-CCATTTTTAA
11822 AATTACCATT
Statistics
Matches: 178, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
58 97 0.54
59 81 0.46
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (58 bp):
CTTCCAAAAATCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:11773 original size:117 final size:117
Alignment explanation
Indices: 11567--11821 Score: 397
Period size: 117 Copynumber: 2.2 Consensus size: 117
11557 GTCCCTAAAC
* * * *
11567 CTTCCAAAAATCTTATTTTTAACCCCGAACCTTCCAAAATTATCATTTTACCCCCGAACTTCCAA
1 CTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAATTACCATTTTACCCCCAAACTTCCAA
* *
11632 AAATTCCATTTTTAACCCCGAACCTTCCAAAAAATATCATTTTACCCTCGAA
66 AAATTCCATTTTTAACCCCGAACCTTCCAAAAAATACCATTTTACCCCCGAA
*
11684 CTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAATTACCATTTTACCCCTAAACTTCCAA
1 CTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAATTACCATTTTACCCCCAAACTTCCAA
* *
11749 AAA-TCCAATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
66 AAATTCC-ATTTTTAACCCCGAACCTTCCAAAAAATACCATTTTACCCCCGAA
*
11801 CTTCC-AAAATCCCATTTTTAA
1 CTTCCAAAAATCCTATTTTTAA
11822 AATTACCATT
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
116 18 0.14
117 109 0.86
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (117 bp):
CTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAATTACCATTTTACCCCCAAACTTCCAA
AAATTCCATTTTTAACCCCGAACCTTCCAAAAAATACCATTTTACCCCCGAA
Found at i:11837 original size:42 final size:43
Alignment explanation
Indices: 11778--11862 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 43
11768 GAACCTTCCA
*
11778 AAAATTACCATTTTACCCCCGAACTTCC-AAAATCCCATTTTT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
*
11820 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
11863 GACCCCGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 26 0.65
43 14 0.35
ACGTcount: A:0.35, C:0.29, G:0.01, T:0.34
Consensus pattern (43 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
Found at i:11877 original size:30 final size:29
Alignment explanation
Indices: 11830--11955 Score: 123
Period size: 30 Copynumber: 4.3 Consensus size: 29
11820 AAAATTACCA
*
11830 TTTTACCCCTAAACTTCCAAAAATCCCAT
1 TTTTACCCCGAAACTTCCAAAAATCCCAT
* *
11859 TTTTGACCCCGAACCTTCCAAAAATTACCA-
1 TTTT-ACCCCGAAACTTCCAAAAA-TCCCAT
11889 TTTTACCTCCG-AACTTCCAAAAATCCCAT
1 TTTTACC-CCGAAACTTCCAAAAATCCCAT
* * * *
11918 TTTCGACCTCGAAAC-TCTCAAAATTGCCAT
1 TTT-TACCCCGAAACTTC-CAAAAATCCCAT
11948 TTTTACCC
1 TTTTACCC
11956 TCAAATGTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
28 4 0.05
29 28 0.35
30 43 0.54
31 4 0.05
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (29 bp):
TTTTACCCCGAAACTTCCAAAAATCCCAT
Found at i:11894 original size:101 final size:102
Alignment explanation
Indices: 11719--11920 Score: 361
Period size: 101 Copynumber: 2.0 Consensus size: 102
11709 CAAACCTTCC
*
11719 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCAATTTTTAACCTCGAACCTTCCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCAATTTTTAACCCCGAACCTTCCAAAAATT
11784 ACCATTTTACCCCCGAACTTCC-AAAATCCCATTTTT
66 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
* *
11820 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCAATTTTTAACCCCGAACCTTCCAAAAATT
*
11885 ACCATTTTACCTCCGAACTTCCAAAAATCCCATTTT
66 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
11921 CGACCTCGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 83 0.86
102 13 0.14
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (102 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCAATTTTTAACCCCGAACCTTCCAAAAATT
ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
Found at i:11940 original size:59 final size:58
Alignment explanation
Indices: 11820--11955 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 58
11810 TCCCATTTTT
* *
11820 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
1 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTCGACCCCGAAACTTCC
* *
11878 AAAAATTACCATTTTACCTCC-GAACTTCCAAAAATCCCATTTTCGACCTCGAAAC-TCTC
1 -AAAATTACCATTTTACC-CCTAAACTTCCAAAAATCCCATTTTCGACCCCGAAACTTC-C
*
11937 AAAATTGCCATTTTTACCC
1 AAAATTACCA-TTTTACCC
11956 TCAAATGTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
58 12 0.17
59 55 0.80
60 2 0.03
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.30
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTCGACCCCGAAACTTCC
Done.