Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000008.1 Kokia drynarioides strain JFW-HI SEQ_11565, 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: 5109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3504 original size:28 final size:28
Alignment explanation
Indices: 3402--3506 Score: 90
Period size: 28 Copynumber: 3.7 Consensus size: 28
3392 TGGATACTTG
3402 GGGGGTAAAATGGTAATTTTGGAC-TCTC
1 GGGGGTAAAATGGTAATTTTGGACATC-C
* * *
3430 GAGGGTGAAATGGTAATTTTGGGA-AGTTC
1 GGGGGTAAAATGGTAATTTT-GGACA-TCC
** * *
3459 ATGGTTAAAAATGG-AATTTTAGACATCC
1 GGGGGT-AAAATGGTAATTTTGGACATCC
3487 GGGGGTAAAATGGTAATTTT
1 GGGGGTAAAATGGTAATTTT
3507 TGGAAAAATG
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
27 7 0.12
28 31 0.53
29 14 0.24
30 7 0.12
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGGGTAAAATGGTAATTTTGGACATCC
Found at i:3559 original size:58 final size:57
Alignment explanation
Indices: 3489--3650 Score: 170
Period size: 58 Copynumber: 2.8 Consensus size: 57
3479 AGACATCCGG
**
3489 GGGTAAAATGGTAATTTTTGGAAAAAT-GGGATCAAAAATGGAATTTTTGGA-AGTTT
1 GGGTAAAATGGTAATTTTTGGAAAAATAGGG-TCAAAAATGGAATTTTTAAAGAGTTT
** * *
3545 GATGGTAAAATGGTAATTTTTAAAAAAATCGAGGTCAAAAAT-GAAATTTTAAAGAGTTT
1 G--GGTAAAATGGTAATTTTTGGAAAAATAG-GGTCAAAAATGGAATTTTTAAAGAGTTT
*
3604 GGGCTAAAAAT-GTAATTTTTGGAAAAATTAGGGTAAAAAATGGAATT
1 GGG-T-AAAATGGTAATTTTTGGAAAAA-TAGGGTCAAAAATGGAATT
3651 CTAGAAAGTT
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 56 0.64
59 26 0.30
60 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGAAAAATAGGGTCAAAAATGGAATTTTTAAAGAGTTT
Found at i:3630 original size:59 final size:58
Alignment explanation
Indices: 3493--3682 Score: 162
Period size: 58 Copynumber: 3.3 Consensus size: 58
3483 ATCCGGGGGT
**
3493 AAAATGGTAATTTTTGG-AAAAATGGGATCAAAAATGGAATTTT-TGGAAGTTTGATGGT-
1 AAAATGGTAATTTTTGGAAAAAATGGG-TCAAAAATGGAATTTTAAAG-AGTTTGA-GGTA
* *
3551 AAAATGGTAATTTTT-AAAAAAATCGAGGTCAAAAATGAAATTTTAAAGAGTTTG-GGCTA
1 AAAATGGTAATTTTTGGAAAAAAT-G-GGTCAAAAATGGAATTTTAAAGAGTTTGAGG-TA
* * * *
3610 AAAAT-GTAATTTTTGGAAAAATTAGGGTAAAAAATGGAATTCTAGAA-AGTTCGAGGGTA
1 AAAATGGTAATTTTTGGAAAAAAT-GGGTCAAAAATGGAATTTTA-AAGAGTTTGA-GGTA
*
3669 AAAAT-GCAATTTTT
1 AAAATGGTAATTTTT
3683 ACAAAGTTTA
Statistics
Matches: 110, Mismatches: 12, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
57 2 0.02
58 52 0.47
59 51 0.46
60 5 0.05
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAAATGGGTCAAAAATGGAATTTTAAAGAGTTTGAGGTA
Found at i:3694 original size:59 final size:56
Alignment explanation
Indices: 3608--3920 Score: 182
Period size: 60 Copynumber: 5.2 Consensus size: 56
3598 GAGTTTGGGC
* *
3608 TAAAAATGTAATTTTTGGAAAA-ATTAGGGTAAAAAATGGAATTCTAGAAAGTTCGAGGG
1 TAAAAATGTAATTTTT--AAAAGTTTAGGGTAAAAAAT--AATTTTAGAAAGTTCGAGGG
* * *
3667 TAAAAATGCAATTTTTACAAAGTTTAGGGATAAAAATATAATTTTAGGGAAGTT-TAGGCG
1 TAAAAATGTAATTTTTA-AAAGTTTAGGG-TAAAAA-ATAATTTTA-GAAAGTTCGAGG-G
* * * *
3727 TCAAAATGTAATTTTCAAAATGTTCAGGGTCAAAAATATAATTTTGGAGAAGTTCGAGGG
1 TAAAAATGTAATTTTTAAAA-GTTTAGGGT-AAAAA-ATAATTTTAGA-AAGTTCGAGGG
* ** * * * *
3787 TCAAAATGTAATTTTTGAAAAGGGTATGGTCAAAAATATAATTTTGGAGAAGTTTGAGTG
1 TAAAAATGTAATTTTT-AAAAGTTTAGGGT-AAAAA-ATAATTTTAGA-AAGTTCGAGGG
* * * * * * *
3847 TCAAAATATAATTTTCAGAAAG-TTCGAGGTCAAAAATATAATTTTGGAGAAGTTCGTGTG
1 TAAAAATGTAATTTTTA-AAAGTTTAG-GGT-AAAAA-ATAATTTTAGA-AAGTTCGAGGG
* *
3907 TCAAAATATAATTT
1 TAAAAATGTAATTT
3921 CTGGATAGTT
Statistics
Matches: 215, Mismatches: 26, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 3 0.01
59 37 0.17
60 165 0.77
61 9 0.04
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (56 bp):
TAAAAATGTAATTTTTAAAAGTTTAGGGTAAAAAATAATTTTAGAAAGTTCGAGGG
Found at i:3710 original size:30 final size:28
Alignment explanation
Indices: 3591--3891 Score: 119
Period size: 30 Copynumber: 10.1 Consensus size: 28
3581 AAAAATGAAA
*
3591 TTTTAAAGAGTTT-GGGCTAAAAATGTAAT
1 TTTTAAA-AGTTTAGGG-TAAAAATATAAT
*
3620 TTTTGGAAAA-ATTAGGGTAAAAA-ATGGAA-
1 TTTT--AAAAGTTTAGGGTAAAAATAT--AAT
* * **
3649 TTCTAGAAAGTTCGAGGGTAAAAATGCAAT
1 TTTTA-AAAGTT-TAGGGTAAAAATATAAT
3679 TTTTACAAAGTTTAGGGATAAAAATATAA-
1 TTTTA-AAAGTTTAGGG-TAAAAATATAAT
* * *
3708 TTTTAGGGAAGTTTAGGCGTCAAAATGTAAT
1 TTTTA--AAAGTTTAGG-GTAAAAATATAAT
* *
3739 TTTCAAAATGTTCAGGGTCAAAAATATAAT
1 TTTTAAAA-GTTTAGGGT-AAAAATATAAT
* * * * *
3769 TTTGGAGAAGTTCGAGGGTCAAAATGTAAT
1 TTT-TAAAAGTT-TAGGGTAAAAATATAAT
** *
3799 TTTTGAAAAGGGTATGGTCAAAAATATAAT
1 TTTT-AAAAGTTTAGGGT-AAAAATATAAT
* * * *
3829 TTTGGAGAAGTTTGAGTGTCAAAATATAAT
1 TTT-TAAAAGTTT-AGGGTAAAAATATAAT
* *
3859 TTTCAGAAAG-TTCGAGGTCAAAAATATAAT
1 TTTTA-AAAGTTTAG-GGT-AAAAATATAAT
3889 TTT
1 TTT
3892 GGAGAAGTTC
Statistics
Matches: 201, Mismatches: 46, Indels: 49
0.68 0.16 0.17
Matches are distributed among these distances:
27 1 0.00
28 5 0.02
29 40 0.20
30 136 0.68
31 19 0.09
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (28 bp):
TTTTAAAAGTTTAGGGTAAAAATATAAT
Found at i:3740 original size:60 final size:58
Alignment explanation
Indices: 3663--3900 Score: 257
Period size: 60 Copynumber: 4.0 Consensus size: 58
3653 AGAAAGTTCG
* * *
3663 AGGGTAAAAATGCAATTTTTACAAAGTTTAGGGAT-AAAAATATAATTTTAGG-GAAGTTT
1 AGGGTCAAAATGTAATTTTCA-AAAGTTTAGGG-TCAAAAATATAATTTT-GGAGAAGTTT
* *
3722 AGGCGTCAAAATGTAATTTTCAAAATGTTCAGGGTCAAAAATATAATTTTGGAGAAGTTCG
1 AGG-GTCAAAATGTAATTTTCAAAA-GTTTAGGGTCAAAAATATAATTTTGGAGAAGTT-T
* ** *
3783 AGGGTCAAAATGTAATTTTTGAAAAGGGTATGGTCAAAAATATAATTTTGGAGAAGTTT
1 AGGGTCAAAATGTAA-TTTTCAAAAGTTTAGGGTCAAAAATATAATTTTGGAGAAGTTT
* * *
3842 GAGTGTCAAAATATAATTTTCAGAAAG-TTCGAGGTCAAAAATATAATTTTGGAGAAGTT
1 -AGGGTCAAAATGTAATTTTCA-AAAGTTTAG-GGTCAAAAATATAATTTTGGAGAAGTT
3901 CGTGTGTCAA
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
59 15 0.10
60 127 0.83
61 11 0.07
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (58 bp):
AGGGTCAAAATGTAATTTTCAAAAGTTTAGGGTCAAAAATATAATTTTGGAGAAGTTT
Found at i:3800 original size:120 final size:120
Alignment explanation
Indices: 3656--3920 Score: 344
Period size: 120 Copynumber: 2.2 Consensus size: 120
3646 GAATTCTAGA
* * **
3656 AAGTTCGAGGGTAAAAATGCAATTTTT-ACAAAGTTTAGGGAT-AAAAATATAATTTTAGG-GAA
1 AAGTTCGAGGGTCAAAATGTAATTTTTGA-AAAGGGTAGGG-TCAAAAATATAATTTT-GGAGAA
*
3718 GTTT-AGGCGTCAAAATGTAATTTTCA-AAATGTTC-AGGGTCAAAAATATAATTTTGGAG
63 GTTTGA-GCGTCAAAATATAATTTTCAGAAA-GTTCGA-GGTCAAAAATATAATTTTGGAG
*
3776 AAGTTCGAGGGTCAAAATGTAATTTTTGAAAAGGGTATGGTCAAAAATATAATTTTGGAGAAGTT
1 AAGTTCGAGGGTCAAAATGTAATTTTTGAAAAGGGTAGGGTCAAAAATATAATTTTGGAGAAGTT
*
3841 TGAGTGTCAAAATATAATTTTCAGAAAGTTCGAGGTCAAAAATATAATTTTGGAG
66 TGAGCGTCAAAATATAATTTTCAGAAAGTTCGAGGTCAAAAATATAATTTTGGAG
* * *
3896 AAGTTCGTGTGTCAAAATATAATTT
1 AAGTTCGAGGGTCAAAATGTAATTT
3921 CTGGATAGTT
Statistics
Matches: 129, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
119 3 0.02
120 120 0.93
121 6 0.05
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (120 bp):
AAGTTCGAGGGTCAAAATGTAATTTTTGAAAAGGGTAGGGTCAAAAATATAATTTTGGAGAAGTT
TGAGCGTCAAAATATAATTTTCAGAAAGTTCGAGGTCAAAAATATAATTTTGGAG
Found at i:3900 original size:30 final size:29
Alignment explanation
Indices: 3699--3925 Score: 171
Period size: 30 Copynumber: 7.6 Consensus size: 29
3689 TTTAGGGATA
*
3699 AAAATATAATTTTAGG-GAAGTT-TAGGCGTC
1 AAAATATAATTTT-GGAGAAGTTCGA-G-GTC
* * *
3729 AAAATGTAATTTT-CAAAATGTTC-AGGGTC
1 AAAATATAATTTTGGAGAA-GTTCGA-GGTC
3758 AAAAATATAATTTTGGAGAAGTTCGAGGGTC
1 -AAAATATAATTTTGGAGAAGTTCGA-GGTC
* * * *
3789 AAAATGTAATTTTTGAAAAG--GGTATGGTC
1 AAAATATAATTTTGGAGAAGTTCG-A-GGTC
*
3818 AAAAATATAATTTTGGAGAAGTTTGAGTGTC
1 -AAAATATAATTTTGGAGAAGTTCGAG-GTC
*
3849 AAAATATAATTTT-CAGAAAGTTCGAGGTC
1 AAAATATAATTTTGGAG-AAGTTCGAGGTC
*
3878 AAAAATATAATTTTGGAGAAGTTCGTGTGTC
1 -AAAATATAATTTTGGAGAAGTTCGAG-GTC
3909 AAAATATAATTTCTGGA
1 AAAATATAATTT-TGGA
3926 TAGTTTAGGG
Statistics
Matches: 162, Mismatches: 19, Indels: 31
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.01
29 15 0.09
30 123 0.76
31 22 0.14
32 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (29 bp):
AAAATATAATTTTGGAGAAGTTCGAGGTC
Found at i:3913 original size:90 final size:91
Alignment explanation
Indices: 3759--3925 Score: 209
Period size: 90 Copynumber: 1.8 Consensus size: 91
3749 TTCAGGGTCA
* * * *
3759 AAAATATAATTTTGGAGAAGTTCGAGGGTCAAAATGTAATTTTTGAAAAGGGTATGGTCAAAAAT
1 AAAATATAATTTTAGAGAAGTTCGAGGGTCAAAATATAATTTTGGAAAAGCGTATGGTCAAAAAT
3824 ATAATTT-TGGAGAAGTTTGAGTGTC
66 ATAATTTCTGGAGAAGTTTGAGTGTC
* *
3849 AAAATATAATTTTCAGA-AAGTTCGA-GGTCAAAAATATAATTTTGGAGAAGTTCGTGT-GTC-A
1 AAAATATAATTTT-AGAGAAGTTCGAGGGTC-AAAATATAATTTTGGAAAAG--CGTATGGTCAA
3910 AAATATAATTTCTGGA
62 AAATATAATTTCTGGA
3926 TAGTTTAGGG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
89 4 0.06
90 50 0.76
91 9 0.14
92 3 0.05
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.34
Consensus pattern (91 bp):
AAAATATAATTTTAGAGAAGTTCGAGGGTCAAAATATAATTTTGGAAAAGCGTATGGTCAAAAAT
ATAATTTCTGGAGAAGTTTGAGTGTC
Done.