Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003791.1 Kokia drynarioides strain JFW-HI SEQ_116774, 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: 69873
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5100 original size:40 final size:40
Alignment explanation
Indices: 5056--5135 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
5046 TGCTAAACTA
* * *
5056 TAAATATCTATCTTCTCTGTAACTCTTCTCATTCGTCAAT
1 TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
*
5096 TAAATATCCATTTTCTCTGCAACTCTTCTCATTCATCAAT
1 TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
5136 CACCTTCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (40 bp):
TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
Found at i:13903 original size:21 final size:20
Alignment explanation
Indices: 13865--13903 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13855 AACTTTGTTT
*
13865 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGCA
*
13885 AAATTTATGAATAAAAAAG
1 AAATTTAAG-ATAAAAAAG
13904 AACAGAGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGCA
Found at i:24498 original size:25 final size:26
Alignment explanation
Indices: 24444--24500 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
24434 AATTTAAAAT
* * *
24444 AAAATATATAAAAATTATATATTTTT
1 AAAATATATAAAAATTATAAATTATA
24470 AAAATATA-AAAAATTATAAATTATA
1 AAAATATATAAAAATTATAAATTATA
24495 AAAATA
1 AAAATA
24501 AATGTATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATATATAAAAATTATAAATTATA
Found at i:25015 original size:31 final size:31
Alignment explanation
Indices: 24960--25028 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
24950 ATTTAACTGA
* * *
24960 GAGTGCCCAAAATAGAAACGATCTAAAACGT
1 GAGTGACCAAAATAGAAACAATCTAAAACAT
**
24991 GAGTGACCAAAATAGAATTAATCTAAAACAT
1 GAGTGACCAAAATAGAAACAATCTAAAACAT
*
25022 TAGTGAC
1 GAGTGAC
25029 TAAATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.20
Consensus pattern (31 bp):
GAGTGACCAAAATAGAAACAATCTAAAACAT
Found at i:41885 original size:29 final size:27
Alignment explanation
Indices: 41853--41930 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
41843 CAATTAAACT
* *
41853 TTAATTTTTAAATTTGAAAAATACAATGA
1 TTAATTTTTAAATAT-AAAAATAAAAT-A
*
41882 TTAAATTTTTAAATATAAAGATAAAATA
1 TT-AATTTTTAAATATAAAAATAAAATA
* * *
41910 TTAAATTTTAAACATATAAAT
1 TTAATTTTTAAATATAAAAAT
41931 GAAGACCTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 15 0.37
28 3 0.07
29 11 0.27
30 12 0.29
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (27 bp):
TTAATTTTTAAATATAAAAATAAAATA
Found at i:57940 original size:6 final size:6
Alignment explanation
Indices: 57929--57959 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
57919 CATCTTTTCT
*
57929 TTCCCA TTCCCA TTCCCA TTCCCA ATCCCA T
1 TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA T
57960 CCCTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
TTCCCA
Found at i:62378 original size:3 final size:3
Alignment explanation
Indices: 62372--62400 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62362 AAAAAAAAAC
62372 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62401 AATTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64794 original size:40 final size:40
Alignment explanation
Indices: 64739--64818 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
64729 TAAGAAGGTG
* * *
64739 ATTGATGAATGAGAAGAGTTGCAGAGAAAATGGATATTTA
1 ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
*
64779 ATTGACGAATGAGAAGAGTTACAGAGAAGATAGATATTTA
1 ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
64819 TAGTTTAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (40 bp):
ATTGACGAATGAGAAGAGTTACAGAGAAAATAGATATTTA
Done.