Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007241.1 Kokia drynarioides strain JFW-HI SEQ_121856, 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: 52428
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:365 original size:29 final size:29
Alignment explanation
Indices: 310--386 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
300 GATTTGGGAG
* *
310 GTCCTTATATTATGAGGATTGGATTAAATTA
1 GTCCTTATATTATTA--AATGGATTAAATTA
** * *
341 GTTTTTCTATTATTAAATGGATTAATTTA
1 GTCCTTATATTATTAAATGGATTAAATTA
370 GTCCTTATATTATTAAA
1 GTCCTTATATTATTAAA
387 AAGAATCAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 26 0.70
31 11 0.30
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (29 bp):
GTCCTTATATTATTAAATGGATTAAATTA
Found at i:18724 original size:41 final size:41
Alignment explanation
Indices: 18667--18748 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
18657 CTGGGAAGAA
18667 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
1 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
18708 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
1 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
18749 GTACTATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (41 bp):
TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
Found at i:19025 original size:41 final size:41
Alignment explanation
Indices: 18968--19049 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
18958 CTGGGAAGAA
18968 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
1 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
19009 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
1 TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
19050 GTACTATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (41 bp):
TCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATT
Found at i:19036 original size:301 final size:301
Alignment explanation
Indices: 18494--19309 Score: 1596
Period size: 301 Copynumber: 2.7 Consensus size: 301
18484 TCTCCTAAGT
* *
18494 TGCGCATTCTAATCACGAATTCACCAACACATTCTCTTATTTGTCTCATTTTCTCTTTTCCCTTC
1 TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
*
18559 CATTTCCCTTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
66 CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
18624 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
131 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
18689 GTGCAGTTCTTGAGAAATTTCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATTGTACT
196 GTGCAGTTCTTGAGAAATTTCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATTGTACT
18754 ATTAATTGTATTTATTACATTTTTATTCTTTTATTTATATC
261 ATTAATTGTATTTATTACATTTTTATTCTTTTATTTATATC
18795 TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
1 TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
18860 CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
66 CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
18925 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
131 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
18990 GTGCAGTTCTTGAGAAATTTCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATTGTACT
196 GTGCAGTTCTTGAGAAATTTCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATTGTACT
19055 ATTAATTGTATTTATTACATTTTTATTCTTTTATTTATATC
261 ATTAATTGTATTTATTACATTTTTATTCTTTTATTTATATC
19096 TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
1 TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
19161 CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
66 CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
19226 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
131 TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
*
19291 ATGCAGTTCTTGAGAAATT
196 GTGCAGTTCTTGAGAAATT
19310 GTACTATTAA
Statistics
Matches: 511, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 511 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (301 bp):
TGCGCATTCTAATCACGAATTCACCAACACGTTCTCTTATTTATCTCATTTTCTCTTTTCCCTTC
CATTTCCATTCCATTCTTTTGCCGATTTTCCCCTCTTGGGAAAGAGTGTTCTTCAACCTTGGAAA
TAGCTTCATTGGGTGTTCATCAAAGATCTTGATCTGGGAAGAATCGAGCAAGAAAGACGAAGAAC
GTGCAGTTCTTGAGAAATTTCGAGCAAGAAAGACGAAGAACGTGCAGTTCTTGAGAAATTGTACT
ATTAATTGTATTTATTACATTTTTATTCTTTTATTTATATC
Found at i:20949 original size:25 final size:24
Alignment explanation
Indices: 20902--20950 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
20892 AAATTGTCAT
20902 TAATTTTTTTAAAAAAAGTATCTCC
1 TAATTTTTTTAAAAAAAG-ATCTCC
20927 TAATTTTTTAATAAAAAAA-ATCTC
1 TAATTTTTT--TAAAAAAAGATCTC
20951 ATTAAACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.64
27 8 0.36
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATTTTTTTAAAAAAAGATCTCC
Found at i:23851 original size:14 final size:14
Alignment explanation
Indices: 23832--23860 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23822 GAGGAACTCA
23832 GTGGGCCTAAAGTT
1 GTGGGCCTAAAGTT
23846 GTGGGCCTAAAGTT
1 GTGGGCCTAAAGTT
23860 G
1 G
23861 AGAAAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.28
Consensus pattern (14 bp):
GTGGGCCTAAAGTT
Found at i:27971 original size:15 final size:15
Alignment explanation
Indices: 27951--27988 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27941 AGTCTTTTTA
27951 AAAATTATAAATTA-T
1 AAAATTATAAA-TAGT
*
27966 AAAATTATATATAGT
1 AAAATTATAAATAGT
27981 AAAATTAT
1 AAAATTAT
27989 GCTTTAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATTATAAATAGT
Found at i:28068 original size:15 final size:15
Alignment explanation
Indices: 28048--28086 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28038 AGTCTTTTTA
28048 AAAATTATAAATTA-T
1 AAAATTATAAA-TAGT
*
28063 AAAATTATATATAGT
1 AAAATTATAAATAGT
28078 AAAATTATA
1 AAAATTATA
28087 CTTTTAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAAATTATAAATAGT
Found at i:28291 original size:15 final size:15
Alignment explanation
Indices: 28271--28305 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
28261 ATATCGATTT
28271 TATTTAT-TTATTTAA
1 TATTTATATT-TTTAA
28286 TATTTATATTTTTAA
1 TATTTATATTTTTAA
28301 TATTT
1 TATTT
28306 TCAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTATATTTTTAA
Found at i:38692 original size:8 final size:8
Alignment explanation
Indices: 38679--38712 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
38669 TTAAATTTTA
38679 ATATATTT
1 ATATATTT
38687 ATATATTT
1 ATATATTT
38695 ATATATTT
1 ATATATTT
38703 ATATATTT
1 ATATATTT
38711 AT
1 AT
38713 GTTGTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:38720 original size:24 final size:23
Alignment explanation
Indices: 38679--38726 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
38669 TTAAATTTTA
38679 ATATATTTATATATTTATATATTT
1 ATATATTTATATATTTAT-TATTT
*
38703 ATATATTTATGT-TGTTATTATTT
1 ATATATTTATATAT-TTATTATTT
38726 A
1 A
38727 GTATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATATTTATATATTTATTATTT
Found at i:48883 original size:31 final size:30
Alignment explanation
Indices: 48839--48900 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
48829 CCCTAACATC
* *
48839 TTAATTACATAAATAAAAAATTTTGAATAGT
1 TTAATGACATAAAT-AAAAATTTTAAATAGT
* * *
48870 TTAATGACTTAAATGACAATTTTAAATAGT
1 TTAATGACATAAATAAAAATTTTAAATAGT
48900 T
1 T
48901 AAAAGAATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (30 bp):
TTAATGACATAAATAAAAATTTTAAATAGT
Found at i:51104 original size:21 final size:20
Alignment explanation
Indices: 51065--51114 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
51055 AACATCACTC
*
51065 TTTAAATAATTTACCTTTAAAAT
1 TTTAAA-AATTTACATTT--AAT
51088 TTTAAAAA-TTACATTTAAT
1 TTTAAAAATTTACATTTAAT
51107 TTTAAAAA
1 TTTAAAAA
51115 AATACCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 11 0.42
21 7 0.27
22 2 0.08
23 6 0.23
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAAAATTTACATTTAAT
Found at i:51923 original size:23 final size:22
Alignment explanation
Indices: 51896--51946 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
51886 AAAATATAAA
*
51896 AATATATTA-AAAATGTTATGATG
1 AATATATTATAAAA-GTT-TAATG
51919 AATATA-TATAAAAGTTTAATG
1 AATATATTATAAAAGTTTAATG
51940 AATATAT
1 AATATAT
51947 ATTAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.40
22 5 0.20
23 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
AATATATTATAAAAGTTTAATG
Done.