Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006740.1 Kokia drynarioides strain JFW-HI SEQ_121338, 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: 6664
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2939 original size:15 final size:15
Alignment explanation
Indices: 2919--2952 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2909 CAAAACACAT
2919 TAAATAAATAAATAA
1 TAAATAAATAAATAA
* *
2934 TAAATACATTAATAA
1 TAAATAAATAAATAA
2949 TAAA
1 TAAA
2953 AAAGGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATAAATAAATAA
Found at i:3927 original size:29 final size:28
Alignment explanation
Indices: 3872--4073 Score: 137
Period size: 29 Copynumber: 6.9 Consensus size: 28
3862 CCCAAAAGGT
* *
3872 CCTCAAACTTTCTAAAAATTATGTTTTGAC
1 CCTCAAACTTTC-CAAAATTATATTTT-AC
3902 CCTCAAACTTTCCAAAATTATATTTTAC
1 CCTCAAACTTTCCAAAATTATATTTTAC
* *
3930 CC-CTAAACTTCTCAAAAATTACATTTTCAC
1 CCTC-AAACTT-TCCAAAATTATATTTT-AC
* *
3960 CCTCGAA-TTTCTCTAAAATTACAATTTTAC
1 CCTCAAACTTTC-C-AAAATTA-TATTTTAC
* *
3990 CCTTAAAC-TTCCAAAAATCATAATTTTAC
1 CCTCAAACTTTCC-AAAATTAT-ATTTTAC
* *
4019 CC-CTAAAC-TTCCAAAAATCATATTTTCAT
1 CCTC-AAACTTTCC-AAAATTATATTTT-AC
*
4048 CC-CAAACTTTTCCAAAATTACATTTT
1 CCTCAAAC-TTTCCAAAATTATATTTT
4074 TGCCCCGAAC
Statistics
Matches: 143, Mismatches: 16, Indels: 27
0.77 0.09 0.15
Matches are distributed among these distances:
27 1 0.01
28 21 0.15
29 76 0.53
30 39 0.27
31 6 0.04
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (28 bp):
CCTCAAACTTTCCAAAATTATATTTTAC
Found at i:4089 original size:57 final size:58
Alignment explanation
Indices: 4018--4179 Score: 158
Period size: 58 Copynumber: 2.8 Consensus size: 58
4008 CATAATTTTA
* *
4018 CCCCTAAACTTCCAAAAATCATATTTTCATCC-CAAACTTTTCCAAAATTA-CATTTT-T
1 CCCC-AAACATCCAAAAATCACATTTTCA-CCTCAAACTTTTCCAAAATTACCATTTTGT
* * * *
4075 GCCCCGAACATCCAAAAATTACCATTTTGC-CCTCGAAC--ATCCAAAAATTACCATTTTGT
1 -CCCCAAACATCCAAAAATCA-CATTTT-CACCTCAAACTTTTCC-AAAATTACCATTTTGT
4134 CCCCAAACATCCAAAAATCACATTTTCAACCTCAAA-TTTTCCAAAA
1 CCCCAAACATCCAAAAATCACATTTTC-ACCTCAAACTTTTCCAAAA
4180 GTTCGATTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
56 4 0.05
57 28 0.33
58 47 0.56
59 5 0.06
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (58 bp):
CCCCAAACATCCAAAAATCACATTTTCACCTCAAACTTTTCCAAAATTACCATTTTGT
Found at i:4095 original size:28 final size:28
Alignment explanation
Indices: 4061--4159 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 28
4051 AAACTTTTCC
4061 AAAATTA-CATTTTTGCCCCGAACATCCA
1 AAAATTACCA-TTTTGCCCCGAACATCCA
4089 AAAATTACCATTTTGCCCTCGAACATCCA
1 AAAATTACCATTTTGCCC-CGAACATCCA
*
4118 AAAATTACCATTTTGTCCCCAAACATCCA
1 AAAATTACCATTTTG-CCCCGAACATCCA
*
4147 AAAATCA-CATTTT
1 AAAATTACCATTTT
4160 CAACCTCAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
28 21 0.32
29 42 0.64
30 3 0.05
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCGAACATCCA
Found at i:4147 original size:115 final size:117
Alignment explanation
Indices: 3915--4179 Score: 279
Period size: 115 Copynumber: 2.3 Consensus size: 117
3905 CAAACTTTCC
* * * * ** *
3915 AAAATTATATTTT-ACCCCTAAACTTCTCAAAAATTACATTTTCACCCTCGAATTTCTCTAAAAT
1 AAAATCATATTTTCAACCC-AAACTTTTCCAAAATTACATTTTCACCCTCGAACATCTCAAAAAT
* * * *
3979 TACAATTTTACCCTTAAACTTCCAAAAATCATAATTTTACCCCTAAACTTCCA
65 TACAATTTTACCCTCAAACATCCAAAAATCACAATTTTACCCCTAAACATCCA
* **
4032 AAAATCATATTTTCATCCCAAACTTTTCCAAAATTACATTTTTGCCC-CGAACATC-CAAAAATT
1 AAAATCATATTTTCAACCCAAACTTTTCCAAAATTACATTTTCACCCTCGAACATCTCAAAAATT
* * * * * *
4095 ACCATTTTGCCCTCGAACATCCAAAAATTACCATTTTGTCCCC-AAACATCCA
66 ACAATTTTACCCTCAAACATCCAAAAATCACAATTTT-ACCCCTAAACATCCA
*
4147 AAAATCACATTTTCAACCTCAAA-TTTTCCAAAA
1 AAAATCATATTTTCAACC-CAAACTTTTCCAAAA
4180 GTTCGATTTT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
115 70 0.56
116 14 0.11
117 36 0.29
118 4 0.03
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (117 bp):
AAAATCATATTTTCAACCCAAACTTTTCCAAAATTACATTTTCACCCTCGAACATCTCAAAAATT
ACAATTTTACCCTCAAACATCCAAAAATCACAATTTTACCCCTAAACATCCA
Found at i:4169 original size:29 final size:28
Alignment explanation
Indices: 4081--4169 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
4071 TTTTGCCCCG
*
4081 AACATCCAAAAATTACCATTTTGCCCTCG
1 AACATCCAAAAATTACCATTTT-CCCTCA
4110 AACATCCAAAAATTACCATTTTGTCCC-CA
1 AACATCCAAAAATTACCA-TTT-TCCCTCA
*
4139 AACATCCAAAAATCA-CATTTTCAACCTCA
1 AACATCCAAAAATTACCATTTTC--CCTCA
4168 AA
1 AA
4170 TTTTCCAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 4 0.08
29 37 0.70
30 6 0.11
31 1 0.02
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.26
Consensus pattern (28 bp):
AACATCCAAAAATTACCATTTTCCCTCA
Done.