Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005074.1 Kokia drynarioides strain JFW-HI SEQ_118881, 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: 113109
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:3323 original size:37 final size:38
Alignment explanation
Indices: 3280--3361 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
3270 GACATTTTAA
* *
3280 GATTGTTGA-TAATATTTTAATGTTCAACAATTTGTTT
1 GATTGTTGACTAATATTTTAACGTTCAACAACTTGTTT
* * *
3317 GGTTGTT-ACTAATATTTTAACGTTTAATAACTTGTTT
1 GATTGTTGACTAATATTTTAACGTTCAACAACTTGTTT
3354 GATTGTTG
1 GATTGTTG
3362 CGCATTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (38 bp):
GATTGTTGACTAATATTTTAACGTTCAACAACTTGTTT
Found at i:14167 original size:21 final size:21
Alignment explanation
Indices: 14141--14190 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
14131 TTTTTTTATT
14141 TTGAATTTCAAACCTCAAATC
1 TTGAATTTCAAACCTCAAATC
** * *
14162 TTGAATTTTGAATCTTAAATC
1 TTGAATTTCAAACCTCAAATC
14183 TTGAATTT
1 TTGAATTT
14191 AGGGTTCGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (21 bp):
TTGAATTTCAAACCTCAAATC
Found at i:39258 original size:21 final size:21
Alignment explanation
Indices: 39229--39269 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39219 CTACTCCAAC
39229 TTTTAAAATATATTAAAAAAG
1 TTTTAAAATATATTAAAAAAG
* * *
39250 TTTTTAAATTTTTTAAAAAA
1 TTTTAAAATATATTAAAAAA
39270 CAAAAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTAAAATATATTAAAAAAG
Found at i:39555 original size:27 final size:27
Alignment explanation
Indices: 39535--39586 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39525 AAAAATCATC
39535 AAATTTTAATAAAAATAAAAAATATTA
1 AAATTTTAATAAAAATAAAAAATATTA
* * *
39562 AAATTTTATTAAAAATTAGAAATAT
1 AAATTTTAATAAAAATAAAAAATAT
39587 ATATAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATTTTAATAAAAATAAAAAATATTA
Found at i:39629 original size:27 final size:26
Alignment explanation
Indices: 39543--39629 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
39533 TCAAATTTTA
* *
39543 ATAAAAATAAAAAATAT-TAAAATTTT
1 ATAAAAATAAAAAAAATATAAAA-ATT
* * * * *
39569 ATTAAAAATTAGAAATATATATAAATC
1 A-TAAAAATAAAAAAAATATAAAAATT
39596 ATAAAAAATAAAAAAAATCATAAAAATT
1 AT-AAAAATAAAAAAAAT-ATAAAAATT
39624 ATAAAA
1 ATAAAA
39630 TGAATAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
26 2 0.04
27 32 0.68
28 13 0.28
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (26 bp):
ATAAAAATAAAAAAAATATAAAAATT
Found at i:39931 original size:27 final size:30
Alignment explanation
Indices: 39862--39932 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 30
39852 TTCTTATGAC
39862 TTTATAATTTTTT-CGATATTTCTATATGT
1 TTTATAATTTTTTACGATATTTCTATATGT
** *
39891 TTTATAATCGTTTAC-A-ATTT-TATATTT
1 TTTATAATTTTTTACGATATTTCTATATGT
*
39918 TTTCTAATTTTTTAC
1 TTTATAATTTTTTAC
39933 TACATGTCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 18 0.51
28 4 0.11
29 12 0.34
30 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTATAATTTTTTACGATATTTCTATATGT
Found at i:45495 original size:17 final size:17
Alignment explanation
Indices: 45468--45510 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
45458 AGATATTTAT
45468 AATAA-AAAAGT-AAAA
1 AATAAGAAAAGTGAAAA
*
45483 AATAAAGAAAAGTGAATA
1 AAT-AAGAAAAGTGAAAA
45501 AATAAGAAAA
1 AATAAGAAAA
45511 ATACAACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 13 0.54
18 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (17 bp):
AATAAGAAAAGTGAAAA
Found at i:49137 original size:40 final size:40
Alignment explanation
Indices: 49071--49151 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
49061 GATGCTTTTC
49071 TGGCAAAAAAAAAAAAAAAAAAACATTAATTAATTTTATT
1 TGGCAAAAAAAAAAAAAAAAAAACATTAATTAATTTTATT
* * * *
49111 TGGCAAAAAAACAAACAAACACACATTAATTAATTTTATT
1 TGGCAAAAAAAAAAAAAAAAAAACATTAATTAATTTTATT
49151 T
1 T
49152 TAATATTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (40 bp):
TGGCAAAAAAAAAAAAAAAAAAACATTAATTAATTTTATT
Found at i:50901 original size:26 final size:25
Alignment explanation
Indices: 50845--50897 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
50835 TAAGGTGACT
*
50845 ATATATAACATTTTAATAAATAAAA
1 ATATATAAAATTTTAATAAATAAAA
*
50870 ATATATAAAATTATTAATTAA-AAAA
1 ATATATAAAATT-TTAATAAATAAAA
50895 ATA
1 ATA
50898 ATATGGACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATATAAAATTTTAATAAATAAAA
Found at i:56775 original size:20 final size:21
Alignment explanation
Indices: 56737--56775 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
56727 TCTCGACAAA
56737 TAAATTATATTATTAAATTGG
1 TAAATTATATTATTAAATTGG
56758 TAAATT-TATCTA-TAAATT
1 TAAATTATAT-TATTAAATT
56776 ATATTTACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (21 bp):
TAAATTATATTATTAAATTGG
Found at i:64072 original size:28 final size:29
Alignment explanation
Indices: 64029--64105 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
64019 GTGTTCCAAG
64029 TTTTTGTATATT-TAAAATTTAGTCCTTTTA
1 TTTTT-TATATTCTAAAATTT-GTCCTTTTA
*
64059 -TTTTTAT-TTCTAAAAGTTTGTCTTTTTA
1 TTTTTTATATTCTAAAA-TTTGTCCTTTTA
*
64087 TTTTTTATATTTTAAAATT
1 TTTTTTATATTCTAAAATT
64106 CGGATTCACT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 2 0.05
28 16 0.39
29 16 0.39
30 7 0.17
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTTTTATATTCTAAAATTTGTCCTTTTA
Found at i:68254 original size:21 final size:21
Alignment explanation
Indices: 68174--68254 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
68164 TATTTAAATA
* *
68174 TAAATATTTAATGATT-ATATT
1 TAAATAATTAAT-ATTAATTTT
* * *
68195 TAAATATTTAAAATATAATTTA
1 TAAATAATTAATAT-TAATTTT
*
68217 T-AA-AATCTAAT-TAAATTTT
1 TAAATAAT-TAATATTAATTTT
68236 TAAATAATTAATATTAATT
1 TAAATAATTAATATTAATT
68255 ACTTAGAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
19 6 0.13
20 11 0.24
21 25 0.54
22 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
TAAATAATTAATATTAATTTT
Found at i:69587 original size:31 final size:31
Alignment explanation
Indices: 69552--69610 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
69542 AGATGACTCT
*
69552 AATGAGAAGCACAATTACTCTCTCAATATCC
1 AATGAGAAACACAATTACTCTCTCAATATCC
69583 AATGAGAAACACAATTACTCTCTCAATA
1 AATGAGAAACACAATTACTCTCTCAATA
69611 GAATCATAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
AATGAGAAACACAATTACTCTCTCAATATCC
Found at i:78675 original size:7 final size:8
Alignment explanation
Indices: 78658--78687 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
78648 CCTAAAAATA
78658 TTTATTTT
1 TTTATTTT
78666 TTTATTTT
1 TTTATTTT
78674 TTTATTTT
1 TTTATTTT
78682 TTTATT
1 TTTATT
78688 GTGACATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTATTTT
Found at i:78998 original size:16 final size:16
Alignment explanation
Indices: 78965--79019 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
78955 TAGAAATATT
*
78965 ATTTATATTATTT-TTA
1 ATTTA-ATTATTTAATA
78981 ATTTAATTATTTAATA
1 ATTTAATTATTTAATA
*
78997 ATTTTATGTA-TTAATA
1 ATTTAAT-TATTTAATA
79013 ATCTTAA
1 AT-TTAA
79020 CAATTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 7 0.21
16 21 0.64
17 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTAATTATTTAATA
Found at i:85563 original size:132 final size:132
Alignment explanation
Indices: 85321--85716 Score: 720
Period size: 132 Copynumber: 3.0 Consensus size: 132
85311 TAATGTTGTA
* *
85321 ATTGGAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAAGAAGGGTATAATAGCT
1 ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
* * * *
85386 ATAAAATGAAGGGACCTTTTGTTTCCTGGTCATGTCCGCAAGTTGCGGTTTTGTGTGTTTTCAGC
66 ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGCGAGTTGCGGTTTTGTGTGTTTTCAGC
85451 TT
131 TT
85453 ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
1 ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
*
85518 ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGTGAGTTGCGGTTTTGTGTGTTTTCAGC
66 ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGCGAGTTGCGGTTTTGTGTGTTTTCAGC
85583 TT
131 TT
85585 ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
1 ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
*
85650 ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGCGAGTTGTGGTTTTGTGTGTTTTCAGC
66 ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGCGAGTTGCGGTTTTGTGTGTTTTCAGC
85715 TT
131 TT
85717 GGTGTCGGGT
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 255 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (132 bp):
ATTGAAAAGCTGTTACATAGTTTTCTTTGAAGTTTTCTAATGATGTAAGGAAGGGTATAATAGCT
ACAAAATGAAGGGACCTTCTGTTTCCCGGTCATGTCCGCGAGTTGCGGTTTTGTGTGTTTTCAGC
TT
Found at i:95384 original size:15 final size:15
Alignment explanation
Indices: 95360--95389 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
95350 GGGTTAACTT
*
95360 CCTTTTTATAAACCA
1 CCTTTGTATAAACCA
95375 CCTTTGTATAAACCA
1 CCTTTGTATAAACCA
95390 ATCACAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (15 bp):
CCTTTGTATAAACCA
Found at i:99841 original size:10 final size:10
Alignment explanation
Indices: 99826--99855 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
99816 TTCATAGGTT
*
99826 GGGCTGTGCC
1 GGGCTGGGCC
99836 GGGCTGGGCC
1 GGGCTGGGCC
99846 GGGCTGGGCC
1 GGGCTGGGCC
99856 ATGGCTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.57, T:0.13
Consensus pattern (10 bp):
GGGCTGGGCC
Found at i:109229 original size:22 final size:19
Alignment explanation
Indices: 109176--109232 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 19
109166 TATAGGTAGT
109176 ATTGTGTCAAAAAAAAATAG
1 ATTGT-TCAAAAAAAAATAG
109196 ATATGATT-AAAAATAATAATGAG
1 AT-TG-TTCAAAAA-AA-AAT-AG
109219 ATTGTTCAAAAAAA
1 ATTGTTCAAAAAAA
109233 TCTTTGATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 7 0.23
21 9 0.29
22 11 0.35
23 4 0.13
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (19 bp):
ATTGTTCAAAAAAAAATAG
Found at i:109745 original size:29 final size:28
Alignment explanation
Indices: 109677--109769 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
109667 TTCTTGTATT
* * *
109677 TTTTTTATTAATTTAGAATTTAATTAATATA
1 TTTTTTATT-TTTTAAAATTTAA-AAAT-TA
* *
109708 ATTTTTA-TTTTTAAAATTTAAAATTTTA
1 TTTTTTATTTTTTAAAATTTAAAA-ATTA
*
109736 TTTTTCTATTTTTTAAATTTTAAAAATTA
1 TTTTT-TATTTTTTAAAATTTAAAAATTA
109765 TTTTT
1 TTTTT
109770 AATTATTAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.14
29 22 0.43
30 16 0.31
31 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTTTATTTTTTAAAATTTAAAAATTA
Found at i:109768 original size:21 final size:22
Alignment explanation
Indices: 109742--109791 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
109732 TTTATTTTTC
109742 TATTTTTTAAATT-TTAA-AAAT
1 TATTTTTT-AATTATTAAGAAAT
*
109763 TA-TTTTTAATTATTAAGTAAT
1 TATTTTTTAATTATTAAGAAAT
109784 TATTTTTT
1 TATTTTTT
109792 TTTAAATGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 7 0.28
22 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTTTTAATTATTAAGAAAT
Found at i:109778 original size:20 final size:21
Alignment explanation
Indices: 109745--109790 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
109735 ATTTTTCTAT
109745 TTTTTAAATTTTAA-AAATTA
1 TTTTTAAATTTTAAGAAATTA
*
109765 TTTTT-AATTATTAAGTAATTA
1 TTTTTAAATT-TTAAGAAATTA
109786 TTTTT
1 TTTTT
109791 TTTTAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTAAATTTTAAGAAATTA
Found at i:111413 original size:21 final size:21
Alignment explanation
Indices: 111374--111415 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
111364 TTTTTAATAG
111374 TATTAAAAAAATTAAATTAATC
1 TATTAAAAAAA-TAAATTAATC
111396 TATTAAATAAAA-AAATTAAT
1 TATTAAA-AAAATAAATTAAT
111416 TTAATCCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATTAAAAAAATAAATTAATC
Done.