Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009112.1 Kokia drynarioides strain JFW-HI SEQ_123813, 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: 62648
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:25637 original size:20 final size:21
Alignment explanation
Indices: 25609--25649 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
25599 TTAAAATTGT
25609 TTTATAAAC-ATTAAAAAAAAA
1 TTTATAAACTA-TAAAAAAAAA
25630 TTTA-AAACTATAAAAAAAAA
1 TTTATAAACTATAAAAAAAAA
25650 AGAATTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
TTTATAAACTATAAAAAAAAA
Found at i:26496 original size:13 final size:13
Alignment explanation
Indices: 26480--26504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26470 ATGAAATCCC
26480 AAAATAAAATAAT
1 AAAATAAAATAAT
26493 AAAATAAAATAA
1 AAAATAAAATAA
26505 ATCTATAAAT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:30010 original size:53 final size:54
Alignment explanation
Indices: 29933--30034 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
29923 TGGACTGTAA
* * *
29933 TATTGTTGATGTCGTGACATCAACTTGTAGG-TCGCGACATTGAGCCTGACTTGT
1 TATTGTTGAGGTCATGACATCAACTTGT-GGATCGCGACATCGAGCCTGACTTGT
*
29987 TATTGTT-AGGTCATGACATCAACTTGTGGATCTCGACATCGAGCCTGA
1 TATTGTTGAGGTCATGACATCAACTTGTGGATCGCGACATCGAGCCTGA
30035 TATTGAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 2 0.05
53 34 0.79
54 7 0.16
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (54 bp):
TATTGTTGAGGTCATGACATCAACTTGTGGATCGCGACATCGAGCCTGACTTGT
Found at i:34750 original size:32 final size:33
Alignment explanation
Indices: 34694--34772 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 33
34684 TAAAATAATA
34694 TAATAATTTTATATTTAAAAAAAAATTTAATAATTT
1 TAATAATTTTATATTT--AAAAAAA-TTAATAATTT
34730 TAATAATTTTATATTT-AAAAAATTAATAATTT
1 TAATAATTTTATATTTAAAAAAATTAATAATTT
34762 TAA-AATCTTTA
1 TAATAAT-TTTA
34773 CGGATCACGT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
31 3 0.07
32 17 0.40
33 6 0.14
36 16 0.38
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
TAATAATTTTATATTTAAAAAAATTAATAATTT
Found at i:34765 original size:17 final size:17
Alignment explanation
Indices: 34713--34766 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
34703 TATATTTAAA
34713 AAAAAATTTAATAATTTT
1 AAAAAA-TTAATAATTTT
* * *
34731 AATAATTTTAT-A-TTT
1 AAAAAATTAATAATTTT
34746 AAAAAATTAATAATTTT
1 AAAAAATTAATAATTTT
34763 AAAA
1 AAAA
34767 TCTTTACGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 11 0.39
18 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAAATTAATAATTTT
Found at i:38544 original size:16 final size:18
Alignment explanation
Indices: 38508--38542 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38498 TATTATTAAA
*
38508 AAAAATTACATAATATAT
1 AAAAATAACATAATATAT
38526 AAAAATAACATAATATA
1 AAAAATAACATAATATA
38543 AAGTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAACATAATATAT
Found at i:38751 original size:22 final size:22
Alignment explanation
Indices: 38723--38766 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38713 CGAGTCTGAG
*
38723 CGAATAA-TCCAACCCATCAACA
1 CGAATAACT-CAACACATCAACA
38745 CGAATAACTCAACACATCAACA
1 CGAATAACTCAACACATCAACA
38767 AATTTAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.48, C:0.34, G:0.05, T:0.14
Consensus pattern (22 bp):
CGAATAACTCAACACATCAACA
Found at i:53803 original size:20 final size:21
Alignment explanation
Indices: 53762--53805 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
53752 ACTCTCATGA
53762 TTAACTTAATTAATTGCCTAT
1 TTAACTTAATTAATTGCCTAT
53783 TTAACCTTAATTAA-T-CCTAT
1 TTAA-CTTAATTAATTGCCTAT
53803 TTA
1 TTA
53806 TAATCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACTTAATTAATTGCCTAT
Found at i:58124 original size:27 final size:27
Alignment explanation
Indices: 58086--58141 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
58076 ATCACTAACT
58086 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
58113 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
58140 AA
1 AA
58142 AAAATAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:58126 original size:5 final size:6
Alignment explanation
Indices: 58083--58133 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
58073 GGGATCACTA
* *
58083 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
58127 ACTAAT A
1 ACTAAT A
58134 GAATAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (6 bp):
ACTAAT
Found at i:58149 original size:14 final size:14
Alignment explanation
Indices: 58130--58157 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58120 ATCTAATACT
58130 AATAGAATAGAAAA
1 AATAGAATAGAAAA
58144 AATAGAATAGAAAA
1 AATAGAATAGAAAA
58158 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:58695 original size:15 final size:15
Alignment explanation
Indices: 58654--58696 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58644 AGAATAATGG
58654 AAGGGAATAAAAAAA
1 AAGGGAATAAAAAAA
* *
58669 AAAGAAATAAAAAAA
1 AAGGGAATAAAAAAA
58684 AGAGGGAA-AAAAA
1 A-AGGGAATAAAAA
58697 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AAGGGAATAAAAAAA
Found at i:62253 original size:15 final size:17
Alignment explanation
Indices: 62223--62254 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
62213 GTCAAAATCT
62223 TTTTATGCATTTATATA
1 TTTTATGCATTTATATA
62240 TTTTAT-CA-TTATATA
1 TTTTATGCATTTATATA
62255 AATGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTATGCATTTATATA
Done.