Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012018.1 Kokia drynarioides strain JFW-HI SEQ_127016, 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: 5075
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Found at i:71 original size:36 final size:36
Alignment explanation
Indices: 16--84 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
6 CACGCGCTAC
* *
16 ATTAAAATATGTTATGTGTAAAAATTTTATATACGT
1 ATTAAAATATATTACGTGTAAAAATTTTATATACGT
* * *
52 ATTAAATTATATTACGTGTAAATATTTTTTATA
1 ATTAAAATATATTACGTGTAAAAATTTTATATA
85 TAAAAATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.48
Consensus pattern (36 bp):
ATTAAAATATATTACGTGTAAAAATTTTATATACGT
Found at i:1042 original size:17 final size:17
Alignment explanation
Indices: 1012--1074 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
1002 GGCCCAAAAG
*
1012 AATTTGAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
1029 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
1046 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
1063 AATTTAAATTTA
1 AATTTAAATTTA
1075 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:1051 original size:6 final size:6
Alignment explanation
Indices: 1012--1080 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
1002 GGCCCAAAAG
* * * * *
1012 AATTTG AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1057 -ATTATA AATTTA AATTTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA
1081 TTTAAATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 36 0.71
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:1068 original size:23 final size:22
Alignment explanation
Indices: 1042--1087 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
1032 TTAAGTTTAT
1042 TTTAAATTTAAATTTATTATAAA
1 TTTAAATTTAAATTTATT-TAAA
1065 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTATTTAAA
1087 T
1 T
1088 AATGTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAAATTTATTTAAA
Found at i:1730 original size:3 final size:3
Alignment explanation
Indices: 1722--1752 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1712 TTAAATGAAA
1722 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1753 ATTTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2523 original size:12 final size:12
Alignment explanation
Indices: 2506--2530 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2496 CCCATGGCCA
2506 ACCCGAAATCCG
1 ACCCGAAATCCG
2518 ACCCGAAATCCG
1 ACCCGAAATCCG
2530 A
1 A
2531 TCTGACTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.16, T:0.08
Consensus pattern (12 bp):
ACCCGAAATCCG
Found at i:2984 original size:30 final size:30
Alignment explanation
Indices: 2924--3278 Score: 338
Period size: 30 Copynumber: 12.0 Consensus size: 30
2914 CCCTAATATG
* * *
2924 TCCAAAAATTTCATATTT-ACCTCG-AACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
*
2952 TCCAAAAATTCCATATTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
* *
2982 TCCAAAAATTTCATTTTT-ACCCTCG-AACC
1 TCCAAAAATTCCATTTTTGACCC-CGAAACT
* *
3011 TCCAAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
*
3041 TCCAAAAATTCCATTTTTTACCTCC-AAACT
1 TCCAAAAATTCCATTTTTGACC-CCGAAACT
* *
3071 TTCAAAAATTCCATTTTTGACCTCG-AACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
* *
3100 TCCAAAAAATT-AATTTTT-ACCCTCG-AACC
1 TCC-AAAAATTCCATTTTTGACCC-CGAAACT
* **
3129 TCAAAAAATTCTGTTTTTG-CCCCTGAAACT
1 TCCAAAAATTCCATTTTTGACCCC-GAAACT
* * *
3159 TCTAAAAATTCCATTTTTGACCCCAAAATT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
* *
3189 TCCAAAAATCCCATTTTTTACCCCTG-AACT
1 TCCAAAAATTCCATTTTTGACCCC-GAAACT
* *
3219 TCCAAAATTTCCATTTTTAACCCTC-AAACT
1 TCCAAAAATTCCATTTTTGACCC-CGAAACT
* *
3249 TCCAAAAATTCCATTTTCGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACT
3279 CTCAAAATTA
Statistics
Matches: 272, Mismatches: 37, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
28 28 0.10
29 60 0.22
30 177 0.65
31 7 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTGACCCCGAAACT
Found at i:3022 original size:59 final size:59
Alignment explanation
Indices: 2924--3278 Score: 373
Period size: 60 Copynumber: 6.0 Consensus size: 59
2914 CCCTAATATG
* * *
2924 TCCAAAAATTTCATATTTA-CCTCGAACTTCCAAAAATTCCATATTTGACCCCGAAACT
1 TCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * *
2982 TCCAAAAATTTCATTTTTACCCTCGAACCTCCAAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * *
3041 TCCAAAAATTCCATTTTTTA-CCTCCAAACTTTCAAAAATTCCATTTTTGACCTCG-AACT
1 TCCAAAAATTTCA-TTTTTACCCT-CAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
* * * * * **
3100 TCCAAAAAATTAATTTTTACCCTCGAACCTCAAAAAATTCTGTTTTTG-CCCCTGAAACT
1 TCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCC-GAAACT
* * * * *
3159 TCTAAAAATTCCATTTTTGACCC-CAAAATTTCCAAAAATCCCATTTTTTACCCCTG-AACT
1 TCCAAAAATTTCATTTTT-ACCCTC-AAACTTCCAAAAATTCCATTTTTGACCCC-GAAACT
* *
3219 TCC-AAAATTTCCATTTTTAACCCTCAAACTTCCAAAAATTCCATTTTCGACCTCGAAACT
1 TCCAAAAATTT-CATTTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
3279 CTCAAAATTA
Statistics
Matches: 243, Mismatches: 42, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
57 3 0.01
58 44 0.18
59 93 0.38
60 96 0.40
61 7 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
TCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
Found at i:3324 original size:29 final size:29
Alignment explanation
Indices: 2924--3324 Score: 298
Period size: 30 Copynumber: 13.6 Consensus size: 29
2914 CCCTAATATG
* * *
2924 TCCAAAAATTTCATATTTA-CCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
*
2952 TCCAAAAATTCCATATTTGA-CCCCGAAACT
1 TCCAAAAATTCCAT-TTTTACCCCCG-AACT
* * *
2982 TCCAAAAATTTCATTTTTACCCTCGAACC
1 TCCAAAAATTCCATTTTTACCCCCGAACT
**
3011 TCCAAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCGAACT
* *
3041 TCCAAAAATTCCATTTTTTACCTCCAAACT
1 TCCAAAAATTCCA-TTTTTACCCCCGAACT
* *
3071 TTCAAAAATTCCATTTTTGA-CCTCGAACT
1 TCCAAAAATTCCATTTTT-ACCCCCGAACT
* * *
3100 TCCAAAAAATT-AATTTTTACCCTCGAACC
1 TCC-AAAAATTCCATTTTTACCCCCGAACT
* ** * *
3129 TCAAAAAATTCTGTTTTTGCCCCTGAAACT
1 TCCAAAAATTCCATTTTTACCCCCG-AACT
* ** *
3159 TCTAAAAATTCCATTTTTGACCCCAAAATT
1 TCCAAAAATTCCATTTTT-ACCCCCGAACT
* *
3189 TCCAAAAATCCCATTTTTTACCCCTGAACT
1 TCCAAAAATTCCA-TTTTTACCCCCGAACT
* * *
3219 TCCAAAATTTCCATTTTTAACCCTCAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCGAACT
* *
3249 TCCAAAAATTCCATTTTCGA-CCTCGAAAC-
1 TCCAAAAATTCCATTTT-TACCCCCG-AACT
*
3278 TCTC-AAAATTACC-CTTTTACCCCCGAA-T
1 TC-CAAAAATT-CCATTTTTACCCCCGAACT
*
3306 GTCTAAAAATTCCATTTTT
1 -TCCAAAAATTCCATTTTT
3325 TAACCTTGAA
Statistics
Matches: 297, Mismatches: 54, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
28 26 0.09
29 105 0.35
30 152 0.51
31 14 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCGAACT
Found at i:3337 original size:148 final size:143
Alignment explanation
Indices: 2928--3329 Score: 400
Period size: 148 Copynumber: 2.7 Consensus size: 143
2918 AATATGTCCA
* *
2928 AAAATTT-CATATTTACCTCGAACTTCCAAAAATTCCATATTTGACCCCGAAACT-TCCAAAAAT
1 AAAATTTCCATTTTTACCTCGAACTTCCAAAAATTCCAT-TTTGACCTCGAAACTCT-C-AAAA-
* * * * *
2991 TTCATTTTTACCCTCGAACCTCCAAAAATTCCA-TTTTTAACCCCAAAACTTCCAAAAATTCCAT
62 TTCATTTTTACCCCCGAA-TTCTAAAAATTCCATTTTTTAA-CCCAAAATTTCCAAAAATCCCAT
*
3055 TTTTTACCTCCAAACTTTC
125 TTTTTACCTCCAAACTTCC
* * * * **
3074 AAAAATTCCATTTTTGACCTCGAACTTCCAAAAAATT-AATTTTTACCCTCGAACCTCAAAAAAT
1 AAAATTTCCATTTTT-ACCTCGAACTTCC-AAAAATTCCATTTTGA-CCTCGAAACTCTCAAAAT
* * * * *
3138 TCTGTTTTTGCCCCTGAAACTTCTAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAATCCCAT
63 TC-ATTTTTACCCCCG-AA-TTCTAAAAATTCCATTTTTTAACCCAAAATTTCCAAAAATCCCAT
*
3203 TTTTTACC-CCTGAACTTCC
125 TTTTTACCTCC-AAACTTCC
*
3222 AAAATTTCCATTTTTAACCCTCAAACTTCCAAAAATTCCATTTTCGACCTCGAAACTCTCAAAAT
1 AAAATTTCCATTTTT-A-CCTCGAACTTCCAAAAATTCCATTTT-GACCTCGAAACTCTCAAAAT
**
3287 TACCCTTTTACCCCCGAATGTCTAAAAATTCCATTTTTTAACC
63 T-CATTTTTACCCCCGAAT-TCTAAAAATTCCATTTTTTAACC
3330 TTGAATTTTC
Statistics
Matches: 208, Mismatches: 34, Indels: 26
0.78 0.13 0.10
Matches are distributed among these distances:
146 9 0.04
147 26 0.12
148 118 0.57
149 53 0.25
150 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (143 bp):
AAAATTTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTGACCTCGAAACTCTCAAAATTCA
TTTTTACCCCCGAATTCTAAAAATTCCATTTTTTAACCCAAAATTTCCAAAAATCCCATTTTTTA
CCTCCAAACTTCC
Found at i:3724 original size:96 final size:96
Alignment explanation
Indices: 3614--3798 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
3604 AAAATTTTAA
* ** *
3614 AATCGAGGCAATGTTAT-TTTAT-TTCGAGTT-TCAAAAATTTGTGCCTTAACTTACTAGGTGTA
1 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTCT-AAAAATTTGCACCTTAACTTACTAGGTGCA
** *
3676 ATTTTTCTTCAAATCGAAATAATCGAATACCCTT
63 ACCTTTCATCAAATCGAAATAATCGAATACCCTT
*
3710 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCACCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATGTTTCCTTATCTTCGATTCTAAAAATTTGCACCTTAACTTACTAGGTGCAACC
*
3775 TTTCATCAAATCGAGATAATCGAA
66 TTTCATCAAATCGAAATAATCGAA
3799 CATCCTTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 70 0.91
97 6 0.08
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATGTTTCCTTATCTTCGATTCTAAAAATTTGCACCTTAACTTACTAGGTGCAACC
TTTCATCAAATCGAAATAATCGAATACCCTT
Done.