Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011200.1 Kokia drynarioides strain JFW-HI SEQ_126177, 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: 5783
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Found at i:3572 original size:48 final size:47
Alignment explanation
Indices: 3510--3914 Score: 176
Period size: 49 Copynumber: 8.3 Consensus size: 47
3500 CAGAAGCATG
**
3510 AAGGGAAAGATTTAAGCCACAACGGTATATCTAGTACCACGAAGACAC
1 AAGGGAAAGATTTAAGCCGTAACGGTA-ATCTAGTACCACGAAGACAC
* * * * * *
3558 AAGGGAAAGGTTTAAGTCGTAATGGAGAACCTAGTATCTCA-G-AGACATG
1 AAGGGAAAGATTTAAGCCGTAACGG-TAATCTAGTA-C-CACGAAGACA-C
*
3607 AAGGGAAAGATTTAAGCCGTAACGATGAATCTAGTACCACGAAGACAC
1 AAGGGAAAGATTTAAGCCGTAACGGT-AATCTAGTACCACGAAGACAC
* * * * * *
3655 AAGGGAAAGATTCAAGTCGCAATGACG-AATCTAGTATTCCA--AAGATATG
1 AAGGGAAAGATTTAAGCCGTAACG--GTAATCTAGTA--CCACGAAGACA-C
* * * * * * *** * *
3704 AGAGGG-AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTTAAAAACATG
1 A-AGGGAAAGATTTAAGCCGTAACGG-TAATCTAGTACCACGAAGACA-C
* * * * *
3753 AAGGGAAAGATTTAACCCGTAATGGCGAATCCAGTACCACGAAGACAT
1 AAGGGAAAGATTTAAGCCGTAACGG-TAATCTAGTACCACGAAGACAC
* * * ** * * * * *
3801 AATGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTC-AGAGACATG
1 AAGGGAAAGATTTAAGCCGTAACGG-TAATCTAGTACCACGA-AGACA-C
* * *
3850 AAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCGCGAAGACAC
1 AAGGGAAAGATTTAAGCCGTAACGGT-AATCTAGTACCACGAAGACAC
*
3898 AAGAGGAAAGGTTTAAG
1 AAG-GGAAAGATTTAAG
3915 TCGCAATAGC
Statistics
Matches: 270, Mismatches: 64, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
47 6 0.02
48 111 0.41
49 143 0.53
50 10 0.04
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.19
Consensus pattern (47 bp):
AAGGGAAAGATTTAAGCCGTAACGGTAATCTAGTACCACGAAGACAC
Found at i:3613 original size:97 final size:98
Alignment explanation
Indices: 3446--3691 Score: 290
Period size: 97 Copynumber: 2.5 Consensus size: 98
3436 CAAGTCTCAA
* * * *
3446 TACCACGAA-ACACGGAAGGAAAAGGTTTAAGTCGCAACGGCA-AGCCTTGTA-CTTCAGAAGCA
1 TACCACGAAGACAC--AAGGGAAAGGTTTAAGTCGCAATGG-AGAACCTAGTATCTTCAGAAGCA
*
3508 TGAAGGGAAAGATTTAAGCCACAACGGT-ATATCTAG
63 TGAAGGGAAAGATTTAAGCCACAACGATGA-ATCTAG
*
3544 TACCACGAAGACACAAGGGAAAGGTTTAAGTCGTAATGGAGAACCTAGTATC-TCAG-AGACATG
1 TACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGGAGAACCTAGTATCTTCAGAAG-CATG
**
3607 AAGGGAAAGATTTAAGCCGTAACGATGAATCTAG
65 AAGGGAAAGATTTAAGCCACAACGATGAATCTAG
* * *
3641 TACCACGAAGACACAAGGGAAAGATTCAAGTCGCAAT-GACGAATCTAGTAT
1 TACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGGA-GAACCTAGTAT
3692 TCCAAAGATA
Statistics
Matches: 130, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
96 5 0.04
97 110 0.85
98 11 0.08
99 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (98 bp):
TACCACGAAGACACAAGGGAAAGGTTTAAGTCGCAATGGAGAACCTAGTATCTTCAGAAGCATGA
AGGGAAAGATTTAAGCCACAACGATGAATCTAG
Found at i:3621 original size:49 final size:48
Alignment explanation
Indices: 3460--3871 Score: 220
Period size: 49 Copynumber: 8.5 Consensus size: 48
3450 ACGAAACACG
* * * * *
3460 GAAGGAAAAGGTTTAAGTCGCAACGGCA-AGCCTTGTACTTCAGA-AGCAT
1 GAAGGGAAAGATTTAAGTCGCAATGG-AGAACCTAGTAC-TCAGAGA-CAT
* * * * *
3509 GAAGGGAAAGATTTAAGCCACAACGGTA-TATCTAGTAC-CACGAAGACA-
1 GAAGGGAAAGATTTAAGTCGCAATGG-AGAACCTAGTACTCA-G-AGACAT
* * *
3557 CAAGGGAAAGGTTTAAGTCGTAATGGAGAACCTAGTATCTCAGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGAGAACCTAGTA-CTCAGAGACAT
* * * *
3606 GAAGGGAAAGATTTAAGCCGTAA-CGATGAATCTAGTAC-CACGAAGACA-
1 GAAGGGAAAGATTTAAGTCGCAATGGA-GAACCTAGTACTCA-G-AGACAT
* * * * * *
3654 CAAGGGAAAGATTCAAGTCGCAAT-GACGAATCTAGTATTCCAAAGATAT
1 GAAGGGAAAGATTTAAGTCGCAATGGA-GAACCTAGTACT-CAGAGACAT
* * * * * * *
3703 GAGAGGG-AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTTAAAAACAT
1 GA-AGGGAAAGATTTAAGTCGCAATGGAGAACCTAGTA-CTCAGAGACAT
** * *
3752 GAAGGGAAAGATTTAACCCGTAATGGCGAATCC-AGTAC-CACGAAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGAGAA-CCTAGTACTCA-G-AGACAT
* * * *
3801 -AATGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGAGAACCTAGTA-CTCAGAGACAT
*
3849 GAAGGGAAAGATTTAAGCCGCAA
1 GAAGGGAAAGATTTAAGTCGCAA
3872 CGGTGAATCC
Statistics
Matches: 278, Mismatches: 60, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
47 8 0.03
48 110 0.40
49 145 0.52
50 15 0.05
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (48 bp):
GAAGGGAAAGATTTAAGTCGCAATGGAGAACCTAGTACTCAGAGACAT
Found at i:3718 original size:97 final size:97
Alignment explanation
Indices: 3506--3719 Score: 274
Period size: 97 Copynumber: 2.2 Consensus size: 97
3496 ACTTCAGAAG
** * *
3506 CATGAAGGGAAAGATTTAAGCCACAACGGT-ATATCTAGTACCACGAAGACACAAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGTAACGATGA-ATCTAGTACCACGAAGACACAAGGGAAAGATT
* * *
3570 TAAGTCGTAATGGAGAACCTAGTATCTCAGAGA
65 CAAGTCGCAATGGAGAACCTAGTATCTCAAAGA
3603 CATGAAGGGAAAGATTTAAGCCGTAACGATGAATCTAGTACCACGAAGACACAAGGGAAAGATTC
1 CATGAAGGGAAAGATTTAAGCCGTAACGATGAATCTAGTACCACGAAGACACAAGGGAAAGATTC
*
3668 AAGTCGCAAT-GACGAATCTAGTAT-TCCAAAGA
66 AAGTCGCAATGGA-GAACCTAGTATCT-CAAAGA
* *
3700 TATGAGAGGG-AAGGTTTAAG
1 CATGA-AGGGAAAGATTTAAG
3720 TCGCAACGGC
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
96 3 0.03
97 95 0.92
98 5 0.05
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (97 bp):
CATGAAGGGAAAGATTTAAGCCGTAACGATGAATCTAGTACCACGAAGACACAAGGGAAAGATTC
AAGTCGCAATGGAGAACCTAGTATCTCAAAGA
Found at i:3752 original size:146 final size:147
Alignment explanation
Indices: 3559--3887 Score: 378
Period size: 146 Copynumber: 2.3 Consensus size: 147
3549 CGAAGACACA
* * * * * *
3559 AGGGAAAGGTTTAAGTCGTAATGGAGAACCTAGTATCTCAGAGACATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGAGAACCTAGTACCTCAAAAACATGAAGGGAAAGATTTAACC
* * * *
3624 CGTAACGATGAATCTAGTACCACGAAGACACAAGGGAAAGATTCAAGTCGCAATGACGAATCTAG
66 CGTAACGACGAATCCAGTACCACGAAGACACAAGGGAAAGATTCAAGTCACAATGACGAACCTAG
3689 TATTCCAAAGATATGAG
131 TATTCCAAAGATATGAG
* * *
3706 AGGG-AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTTAAAAACATGAAGGGAAAGATTTAACC
1 AGGGAAAGGTTTAAGTCGCAACGGAGAACCTAGTACCTCAAAAACATGAAGGGAAAGATTTAACC
* * * * * * *
3770 CGTAATGGCGAATCCAGTACCACGAAGACATAATGGAAAGGTTTAAGTCACAATGGCGAACCTAG
66 CGTAACGACGAATCCAGTACCACGAAGACACAAGGGAAAGATTCAAGTCACAATGACGAACCTAG
* * *
3835 TA-CCTCAGAGACATGA-
131 TATTC-CAAAGATATGAG
* * *
3851 AGGGAAAGATTTAAGCCGCAACGGTGAATCC-AGTACC
1 AGGGAAAGGTTTAAGTCGCAACGGAGAA-CCTAGTACC
3888 GCGAAGACAC
Statistics
Matches: 152, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
145 5 0.03
146 141 0.93
147 6 0.04
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (147 bp):
AGGGAAAGGTTTAAGTCGCAACGGAGAACCTAGTACCTCAAAAACATGAAGGGAAAGATTTAACC
CGTAACGACGAATCCAGTACCACGAAGACACAAGGGAAAGATTCAAGTCACAATGACGAACCTAG
TATTCCAAAGATATGAG
Found at i:3782 original size:98 final size:95
Alignment explanation
Indices: 3655--3986 Score: 333
Period size: 98 Copynumber: 3.4 Consensus size: 95
3645 ACGAAGACAC
* * * * * * *
3655 AAGGGAAAGATTCAAGTCGCAATGACGAATCTAGTATTCCAAAGATATGAGAGGGAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTA--CCAAAGACAT-AGAGGAAAGGTTTAAG
* *
3720 TCGCAACGGCGAACCTTGTACCTTAAAAACATG
63 TCGCAATGGCGAACCTTGTACCTCAAAAACATG
* * *
3753 AAGGGAAAGATTTAACCCGTAATGGCGAATCCAGTACCACGAAGACATA-ATGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA--AAGACATAGA-GGAAAGGTTTAAG
* * * *
3817 TCACAATGGCGAACCTAGTACCTCAGAGACATG
63 TCGCAATGGCGAACCTTGTACCTCAAAAACATG
* * *
3850 AAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCGCGAAGACACAAGAGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTA-C-CAAAGACA-TAGAGGAAAGGTTTAAG
* * * *
3915 TCGCAATAGCGAAGCTTATACCTCAAAAGCATG
63 TCGCAATGGCGAACCTTGTACCTCAAAAACATG
* * **
3948 AAAGGAAAAATTTAAGCCGCAACGGCGAATTTAGTACCA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
3987 TGCGGATTGA
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
96 5 0.03
97 79 0.41
98 107 0.55
99 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (95 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAAGACATAGAGGAAAGGTTTAAGTCG
CAATGGCGAACCTTGTACCTCAAAAACATG
Found at i:3813 original size:97 final size:98
Alignment explanation
Indices: 3704--3986 Score: 361
Period size: 97 Copynumber: 2.9 Consensus size: 98
3694 CAAAGATATG
* * * *
3704 AGAGGGAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTTAAAAACATGAAGGGAAAGATTTAAC
1 AGAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGAAGGGAAAGATTTAAG
* * *
3769 CCGTAATGGCGAATCCAGTACCACGAAGACATA
66 CCGCAACGGCGAATCCAGTACCACGAAGACACA
* * * * *
3802 A-TGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAG
1 AGAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGAAGGGAAAGATTTAAG
* *
3866 CCGCAACGGTGAATCCAGTACCGCGAAGACACA
66 CCGCAACGGCGAATCCAGTACCACGAAGACACA
* * * * * *
3899 AGAGGAAAGGTTTAAGTCGCAATAGCGAAGCTTATACCTCAAAAGCATGAAAGGAAAAATTTAAG
1 AGAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGAAGGGAAAGATTTAAG
**
3964 CCGCAACGGCGAATTTAGTACCA
66 CCGCAACGGCGAATCCAGTACCA
3987 TGCGGATTGA
Statistics
Matches: 155, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
97 83 0.54
98 72 0.46
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
AGAGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGAAGGGAAAGATTTAAG
CCGCAACGGCGAATCCAGTACCACGAAGACACA
Found at i:3895 original size:243 final size:244
Alignment explanation
Indices: 3467--3921 Score: 675
Period size: 243 Copynumber: 1.9 Consensus size: 244
3457 ACGGAAGGAA
* * *
3467 AAGGTTTAAGTCGCAACGGCAAGCCTTGTACTTCAGAAGCATGAAGGGAAAGATTTAAGCCACAA
1 AAGGTTTAAGTCGCAACGGCAAGCCTTGTACTTCAAAAACATGAAGGGAAAGATTTAACCCACAA
* * ** *
3532 CGGTATATCTAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGTAATGGAGAACCTAGTATCT
66 CGGGATATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCACAATGGAGAACCTAGTACCT
* *
3597 CAGAGACATGAAGGGAAAGATTTAAGCCGTAACGATGAATCTAGTACCACGAAGACACAAG-GGA
131 CAGAGACATGAAGGGAAAGATTTAAGCCGCAACGATGAATCCAGTACCACGAAGACACAAGAGGA
3661 AAGATTCAAGTCGCAATGACGAATCTAGTATTCCAAAGATATGAGAGGG
196 AAGATTCAAGTCGCAATGACGAATCTAGTATTCCAAAGATATGAGAGGG
**
3710 AAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTT-AAAAACATGAAGGGAAAGATTTAACCCGT
1 AAGGTTTAAGTCGCAACGGC-AAGCCTTGTA-CTTCAAAAACATGAAGGGAAAGATTTAACCCAC
* * * *
3773 AATGGCGA-ATCCAGTACCACGAAGACATAATGGAAAGGTTTAAGTCACAATGGCGAACCTAGTA
64 AACGG-GATATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCACAATGGAGAACCTAGTA
* *
3837 CCTCAGAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCGCGAAGACACAAGA
128 CCTCAGAGACATGAAGGGAAAGATTTAAGCCGCAACGATGAATCCAGTACCACGAAGACACAAGA
* *
3902 GGAAAGGTTTAAGTCGCAAT
193 GGAAAGATTCAAGTCGCAAT
3922 AGCGAAGCTT
Statistics
Matches: 188, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
243 164 0.87
244 24 0.13
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (244 bp):
AAGGTTTAAGTCGCAACGGCAAGCCTTGTACTTCAAAAACATGAAGGGAAAGATTTAACCCACAA
CGGGATATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCACAATGGAGAACCTAGTACCT
CAGAGACATGAAGGGAAAGATTTAAGCCGCAACGATGAATCCAGTACCACGAAGACACAAGAGGA
AAGATTCAAGTCGCAATGACGAATCTAGTATTCCAAAGATATGAGAGGG
Found at i:4909 original size:17 final size:17
Alignment explanation
Indices: 4887--4952 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
4877 GGAATTGTTT
*
4887 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
4904 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* * *
4921 CTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
4938 TTTTAAATTAAAATT
1 TTTTAAATTTAAATT
4953 AAAAGTGTCC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:4977 original size:13 final size:13
Alignment explanation
Indices: 4959--4983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4949 AATTAAAAGT
4959 GTCCAATTACAAA
1 GTCCAATTACAAA
4972 GTCCAATTACAA
1 GTCCAATTACAA
4984 TTGAGCCTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:5621 original size:3 final size:3
Alignment explanation
Indices: 5608--5684 Score: 75
Period size: 3 Copynumber: 25.0 Consensus size: 3
5598 TAAATGAGTT
* * *
5608 TAA TAAA TAA TAA TAA TAT TAA TGA TAA TAA -ATA TAA TAC TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
5654 CAT TAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
5685 CAAAAAAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 52 0.87
4 7 0.12
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Done.