Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004055.1 Kokia drynarioides strain JFW-HI SEQ_117205, 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: 3128
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.23
Warning! 133 characters in sequence are not A, C, G, or T
Found at i:1949 original size:37 final size:37
Alignment explanation
Indices: 1908--2056 Score: 127
Period size: 37 Copynumber: 3.7 Consensus size: 37
1898 AAAAGGTTAG
* *
1908 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGC
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGC
* * *
1945 CTTCCTGAGGAGATACAGAGAAGCGAGTTGAAACAAACGACGCAGTC
1 CTTCCTGATGAGATACAGAG-A---AG-TGAACCAAA--TC-C-G-C
*
1992 ATCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGC
1 --CTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGC
*
2031 CTTCCTGATAAGATACAGAGAAGTGA
1 CTTCCTGATGAGATACAGAGAAGTGA
2057 GTTGAAACGA
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
37 42 0.47
38 1 0.01
39 1 0.01
40 1 0.01
41 3 0.03
42 9 0.10
44 8 0.09
45 3 0.03
46 1 0.01
47 1 0.01
48 1 0.01
49 18 0.20
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (37 bp):
CTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGC
Found at i:2008 original size:86 final size:86
Alignment explanation
Indices: 1908--2102 Score: 327
Period size: 86 Copynumber: 2.3 Consensus size: 86
1898 AAAAGGTTAG
* *
1908 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGAGGAGATACAGAGAAGCGAGT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGCCTTCCTGAGAAGATACAGAGAAGCGAGT
1973 TGAAACAAACGACGCAGTCAT
66 TGAAACAAACGACGCAGTCAT
* *
1994 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGCCTTCCTGATAAGATACAGAGAAGTGAGT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGCCTTCCTGAGAAGATACAGAGAAGCGAGT
* *
2059 TGAAACGAACGACGCGGTCAT
66 TGAAACAAACGACGCAGTCAT
*
2080 CTTCCTGATGAGACACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
2103 AAGACCCAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (86 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCGCCTTCCTGAGAAGATACAGAGAAGCGAGT
TGAAACAAACGACGCAGTCAT
Found at i:2299 original size:203 final size:203
Alignment explanation
Indices: 2076--2634 Score: 788
Period size: 203 Copynumber: 2.7 Consensus size: 203
2066 AACGACGCGG
*
2076 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAATGAGGCTCAAAGTGAGCAAAGTCTTTCA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAGTCTTTCA
2141 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATATAAGGTTAACTTCCTGATGA
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA-AAGGTTAACTTCCTGATGA
*
2206 GGTATTGAGAAGTGAACCAAATTCGTCTTTC-GAATGAGATACGGAGGAGCGAATT-AAAACAAA
130 GGTATTGAGAAGTGAACCAAATTCGTCTTCCAG-ATGAGATACGGAGGAGCGAATTGAAAA-AAA
*
2269 CAGTAATGTAA
193 CAGCAATGTAA
* *
2280 TCATC-TCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAGTGAGCAAAGTCTTTGA
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAGTCTTTCA
* *
2344 ACCCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAGGTTAACTTCCTGATGA
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAAGGTTAACTTCCTGATGA
*
2409 GGTACTT-AGAAGTGAACCAAATTCGTCTTCCAGATGATATACGGAGGAGCGAATTGAAAAAAAC
130 GGTA-TTGAGAAGTGAACCAAATTCGTCTTCCAGATGAGATACGGAGGAGCGAATTGAAAAAAAC
*
2473 AGCGATGTAA
194 AGCAATGTAA
* * * * **
2483 TCATCTTCCTGATGAGGCACTGAAAAAAATACCCAAACGAGGCTCAAAACGAGCAAA-TC-TTCT
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAGTCTTTC-
** * * **
2546 AACCCCAGCTTCCTGATGAGATGCTGAGAAGCAGGTCGAAGCCATAAAGTGGTTAGCCCCCTGAT
65 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA--GGTTAACTTCCTGAT
* **
2611 GAGATACCGAGAAGTGAACCAAAT
128 GAGGTATTGAGAAGTGAACCAAAT
2635 CCTGATGAAA
Statistics
Matches: 318, Mismatches: 28, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
202 5 0.02
203 224 0.70
204 89 0.28
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (203 bp):
TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAGTCTTTCA
ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAGGTTAACTTCCTGATGAG
GTATTGAGAAGTGAACCAAATTCGTCTTCCAGATGAGATACGGAGGAGCGAATTGAAAAAAACAG
CAATGTAA
Found at i:3085 original size:6 final size:6
Alignment explanation
Indices: 3074--3126 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
3064 ATTTGTGTAG
* *
3074 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
3120 -AATTT AA
1 AAATTT AA
3127 GT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.10
5 9 0.23
6 22 0.56
7 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:3096 original size:17 final size:17
Alignment explanation
Indices: 3074--3120 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
3064 ATTTGTGTAG
3074 AAATTTAAATTTATATT-
1 AAATTTAAATTTAT-TTC
3091 AAATTTAAATTTATTTC
1 AAATTTAAATTTATTTC
*
3108 GAATTTAAATTTA
1 AAATTTAAATTTA
3121 ATTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTC
Found at i:3123 original size:11 final size:12
Alignment explanation
Indices: 3074--3126 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
3064 ATTTGTGTAG
3074 AAATTTAAATTT
1 AAATTTAAATTT
*
3086 ATA-TTAAATTT
1 AAATTTAAATTT
3097 AAATTT--ATTT
1 AAATTTAAATTT
*
3107 CGAATTTAAATTT
1 -AAATTTAAATTT
3120 -AATTTAA
1 AAATTTAA
3127 GT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
10 4 0.12
11 22 0.65
12 4 0.12
13 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
AAATTTAAATTT
Done.