Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001379.1 Kokia drynarioides strain JFW-HI SEQ_112849, 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: 16312
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:5100 original size:15 final size:15
Alignment explanation
Indices: 5080--5114 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5070 TGGTCTTGGG
*
5080 TTTTCAAACAGAGGA
1 TTTTCAAACAGAGAA
*
5095 TTTTCACACAGAGAA
1 TTTTCAAACAGAGAA
5110 TTTTC
1 TTTTC
5115 CATTTTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTTTCAAACAGAGAA
Found at i:6436 original size:23 final size:24
Alignment explanation
Indices: 6385--6436 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
6375 CGAATTTTTT
6385 TCGAA-TTTCGAATTCGAATCAAA
1 TCGAATTTTCGAATTCGAATCAAA
* * *
6408 TTGAATTTTTGAATTCGAAT-AAC
1 TCGAATTTTCGAATTCGAATCAAA
6431 TCGAAT
1 TCGAAT
6437 AATTCGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (24 bp):
TCGAATTTTCGAATTCGAATCAAA
Found at i:11160 original size:36 final size:36
Alignment explanation
Indices: 11113--11444 Score: 212
Period size: 36 Copynumber: 9.3 Consensus size: 36
11103 CAGTGTACAT
*
11113 ACGTAAGACCATAGCTGGGCTATGACAGTTATTTAG
1 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
* * ** * * * *
11149 ACGTAAGACCATTGTTGAACCATGACAATGTA--TAT
1 ACGTAAGACCATAGCTGGGCTATGGCAGT-TATTTAG
* *
11184 ATGTAAGACCATAGATGGGCTATGGCAGTTATTTAG
1 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
* * * * * * *
11220 ACGTAAGACCATGGTTGGACCATTGCAATGTA--TAT
1 ACGTAAGACCATAGCTGGGCTATGGCAGT-TATTTAG
* *
11255 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTCAA
1 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
* * * *
11291 ACGTAAGACCATGGTTGGACCATGGCAGTGTATTT--
1 ACGTAAGACCATAGCTGGGCTATGGCAGT-TATTTAG
* *
11326 ACGTAAGACCATAGCTAGGCTATGGCAGTTATTCAG
1 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
* * * * * *
11362 ATGTAAGACCATGGTTGGACCATGGCAGTGTA--TAT
1 ACGTAAGACCATAGCTGGGCTATGGCAGT-TATTTAG
* * * ** * *
11397 ATGTAAGACCATAGTTAGGCTACAGCAGTTATTCAT
1 ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
*
11433 ATGTAAGACCAT
1 ACGTAAGACCAT
11445 GGTTGAACCA
Statistics
Matches: 226, Mismatches: 58, Indels: 24
0.73 0.19 0.08
Matches are distributed among these distances:
34 10 0.04
35 96 0.42
36 110 0.49
37 10 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (36 bp):
ACGTAAGACCATAGCTGGGCTATGGCAGTTATTTAG
Found at i:11194 original size:71 final size:71
Alignment explanation
Indices: 11072--11491 Score: 597
Period size: 71 Copynumber: 5.9 Consensus size: 71
11062 GATAGGCTGC
* *
11072 ATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTACATACGTAAGACCATAGCTGGGCTATG
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
*
11137 ACAGTT
66 GCAGTT
* * * * * * *
11143 ATTTAGACGTAAGACCATTGTTGAACCATGACAATGTATATATGTAAGACCATAGATGGGCTATG
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
11208 GCAGTT
66 GCAGTT
* * *
11214 ATTTAGACGTAAGACCATGGTTGGACCATTGCAATGTATATACGTAAGACCATAGCTGGGCTATG
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
11279 GCAGTT
66 GCAGTT
* * *
11285 ATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTATTTACGTAAGACCATAGCTAGGCTATG
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
11350 GCAGTT
66 GCAGTT
* * * * **
11356 ATTCAGATGTAAGACCATGGTTGGACCATGGCAGTGTATATATGTAAGACCATAGTTAGGCTACA
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
11421 GCAGTT
66 GCAGTT
* * * * *
11427 ATTCATATGTAAGACCATGGTTGAACCATGGCAGTGTATATATGTAAGACCATAGCTGGACTATG
1 ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
11492 CATTCTGATG
Statistics
Matches: 313, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 313 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (71 bp):
ATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTATATACGTAAGACCATAGCTGGGCTATG
GCAGTT
Found at i:13597 original size:17 final size:17
Alignment explanation
Indices: 13575--13652 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
13565 CCAATAGGAT
13575 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
13592 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
13609 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
13625 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
13643 TTAAAGTTTA
1 TTAAA-TTTA
13653 ATCTAGTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.08
17 38 0.76
18 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:13611 original size:6 final size:6
Alignment explanation
Indices: 13573--13653 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
13563 GCCCAATAGG
* * * *
13573 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
13618 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTTAA
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA A-TTTAA
13654 TCTAGTTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 34 0.60
7 8 0.14
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:13617 original size:34 final size:34
Alignment explanation
Indices: 13573--13652 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 34
13563 GCCCAATAGG
* *
13573 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
13607 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
13641 ATTTAAAGTTTA
1 ATTTAAA-TTTA
13653 ATCTAGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.15
34 30 0.75
35 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:15399 original size:29 final size:29
Alignment explanation
Indices: 15356--15539 Score: 164
Period size: 30 Copynumber: 6.3 Consensus size: 29
15346 AAATAGTAAT
15356 TTTTTGGAAGTTTCGGGGTCAAAAATGGGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
* *
15386 TTTTAGGAAG-TTCGAGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCG-GGGTAAAAATGG-GA
*
15415 TTTTTGGAAGTTTTGGGGTCAAAAATGGGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
*
15445 TTTTTGGAAG-TTCGGAGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGG-GGTAAAAATGG-GA
* * * *
15474 TTTGTAGAAGTTTTGGGGTCAAAAATGAGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
* *
15504 TTTTTGAAAGTTT-GGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGGGGTAAAAATGG-GA
15532 TTTTTGGA
1 TTTTTGGA
15540 CAGCCTAGGG
Statistics
Matches: 125, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
27 6 0.05
28 22 0.18
29 39 0.31
30 45 0.36
31 13 0.10
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (29 bp):
TTTTTGGAAGTTTCGGGGTAAAAATGGGA
Found at i:15436 original size:59 final size:58
Alignment explanation
Indices: 15338--15539 Score: 296
Period size: 59 Copynumber: 3.4 Consensus size: 58
15328 TTTGGACATC
* * *
15338 CGGGAGTAAAATAGTAATTTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTAGGAAGTT
1 CGGG-GTAAAATGGTAA-TTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
15398 CGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CG-GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
15457 CGGAGGTAAAATGGTAATTTGTAGAAGTTTTGGGGTCAAAAATGAGATTTTTGAAAGTT
1 CGG-GGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
*
15516 TGGGGTAAAATGGTAATTTTTGGA
1 CGGGGTAAAATGGTAATTTTTGGA
15540 CAGCCTAGGG
Statistics
Matches: 130, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
58 20 0.15
59 95 0.73
60 13 0.10
61 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (58 bp):
CGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
Done.