Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007395.1 Kokia drynarioides strain JFW-HI SEQ_122014, 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: 24989
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4399 original size:93 final size:93
Alignment explanation
Indices: 4240--4426 Score: 347
Period size: 93 Copynumber: 2.0 Consensus size: 93
4230 GTTTCTGACA
*
4240 GGGAATCTAATAAGTTCAGGTGTACATCAATTGTTGTTTTAGTATTAAAATATTGAAGTATGGTT
1 GGGAATCTAATAAGTTCAGGTGTACATCAATTGTTGTTTTAGTATTAAAACATTGAAGTATGGTT
4305 GTAACACTATGTCCAGAATGTATGATGT
66 GTAACACTATGTCCAGAATGTATGATGT
4333 GGGAATCTAATAAGTTCAGGTGTACATCAATTGTTGTTTTAGTATTAAAACATTGAAGTATGGTT
1 GGGAATCTAATAAGTTCAGGTGTACATCAATTGTTGTTTTAGTATTAAAACATTGAAGTATGGTT
* *
4398 GTAACACTATGTTCGGAATGTATGATGT
66 GTAACACTATGTCCAGAATGTATGATGT
4426 G
1 G
4427 AGATGTGTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (93 bp):
GGGAATCTAATAAGTTCAGGTGTACATCAATTGTTGTTTTAGTATTAAAACATTGAAGTATGGTT
GTAACACTATGTCCAGAATGTATGATGT
Found at i:4774 original size:27 final size:27
Alignment explanation
Indices: 4706--4800 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
4696 AACATGTCAA
* * *
4706 GAAAAGAATGCCTTCGTAGCAATAAAT
1 GAAAAGAATGCCTTTGTGGCAATATAT
4733 GAAAAGAATGCCTTTGTGGCAATATAT
1 GAAAAGAATGCCTTTGTGGCAATATAT
* * *
4760 GAAAGGAATGTCTTTGTGGAAATATAT
1 GAAAAGAATGCCTTTGTGGCAATATAT
* *
4787 GAAAATAATACCTT
1 GAAAAGAATGCCTT
4801 AGTGACAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (27 bp):
GAAAAGAATGCCTTTGTGGCAATATAT
Found at i:6759 original size:8 final size:8
Alignment explanation
Indices: 6746--6772 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6736 AATTATCTCT
6746 CCCTCTTC
1 CCCTCTTC
6754 CCCTCTTC
1 CCCTCTTC
6762 CCCTCTTC
1 CCCTCTTC
6770 CCC
1 CCC
6773 ACCATCCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (8 bp):
CCCTCTTC
Found at i:7406 original size:41 final size:43
Alignment explanation
Indices: 7348--7428 Score: 139
Period size: 42 Copynumber: 1.9 Consensus size: 43
7338 TTTGTCTAGT
*
7348 CTTTCCCCCTCCCT-AAAATAAAGAAGTTGTATTAAATTTGGG
1 CTTTCCCCCTCCCTAAAAATAAAGAAGTTGTATGAAATTTGGG
7390 CTTT-CCCCTCCCTAAAAATAAAGAAGTTGTATGAAATTT
1 CTTTCCCCCTCCCTAAAAATAAAGAAGTTGTATGAAATTT
7429 AGGGGCGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 9 0.24
42 28 0.76
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (43 bp):
CTTTCCCCCTCCCTAAAAATAAAGAAGTTGTATGAAATTTGGG
Found at i:15939 original size:32 final size:33
Alignment explanation
Indices: 15898--15960 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
15888 CTTGTAACCT
15898 TCTGAATAATTGTCAGATGAT-ATGATAAGTAA
1 TCTGAATAATTGTCAGATGATGATGATAAGTAA
15930 TCTGAATAATTGTCAGATGATGATGATAAGT
1 TCTGAATAATTGTCAGATGATGATGATAAGT
15961 GGGTGTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (33 bp):
TCTGAATAATTGTCAGATGATGATGATAAGTAA
Found at i:18306 original size:31 final size:32
Alignment explanation
Indices: 18251--18316 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
18241 TATAATTAAA
18251 TATTTTTAGTAGAAAATAAATAAATA-AATAT
1 TATTTTTAGTAGAAAATAAATAAATATAATAT
* *
18282 TATTTTTAGATATAAAAT-ACTAAATATTAATAT
1 TATTTTTAG-TAGAAAATAAATAAATA-TAATAT
18315 TA
1 TA
18317 ATAATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 16 0.53
32 7 0.23
33 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (32 bp):
TATTTTTAGTAGAAAATAAATAAATATAATAT
Found at i:19284 original size:8 final size:9
Alignment explanation
Indices: 19257--19283 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19247 GTAGTGCACA
19257 TAATTTTTT
1 TAATTTTTT
19266 TAATTTTTT
1 TAATTTTTT
19275 TAATTTTTT
1 TAATTTTTT
19284 ATATTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TAATTTTTT
Found at i:22309 original size:26 final size:26
Alignment explanation
Indices: 22260--22309 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
22250 TCTATTTACA
**
22260 TTTGAATTTATTCAATAATTTTTATG
1 TTTGAATTTATTCAATAAGGTTTATG
* *
22286 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTCAATAAGGTTTA
22310 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (26 bp):
TTTGAATTTATTCAATAAGGTTTATG
Found at i:24853 original size:17 final size:18
Alignment explanation
Indices: 24801--24855 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
24791 TTAATTTGTC
*
24801 ATTTTAAAATTTTAAAAAT
1 ATTTTAATA-TTTAAAAAT
** *
24820 ATTTTTTTATTT-CAAAT
1 ATTTTAATATTTAAAAAT
24837 -TTTTAATATTTAAAAAT
1 ATTTTAATATTTAAAAAT
24854 AT
1 AT
24856 ATATTTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 4 0.15
19 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATATTTAAAAAT
Done.