Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008100.1 Kokia drynarioides strain JFW-HI SEQ_122758, 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: 46305
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:247 original size:43 final size:43
Alignment explanation
Indices: 196--364 Score: 225
Period size: 43 Copynumber: 4.0 Consensus size: 43
186 TTTAGCGGCA
** *
196 TTTGTGGGAAAAGCATCGCTAAAGATCATGTTCTTTAGTGATG
1 TTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGATG
239 TTTGTGGGAAAAGCGCCGCTAAAGA-CGATGTTCTTTAGCGATG
1 TTTGTGGGAAAAGCGCCGCTAAAGATC-ATGTTCTTTAGCGATG
* * * * **
282 TTTGTGGAAAAAGTGCCGCTAAAGACCATGTTATTTAGCGGCG
1 TTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGATG
*
325 TTTGTGGG-AAAGCGCCGCTAAAGATCATGTTCTATAGCGA
1 TTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGA
365 CTTTTTTCCT
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
42 28 0.25
43 81 0.74
44 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (43 bp):
TTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGATG
Found at i:3636 original size:16 final size:16
Alignment explanation
Indices: 3615--3669 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
3605 GACTCCACCA
3615 TATTATTTTTATTTTT
1 TATTATTTTTATTTTT
3631 TATTATTTCTT-TTTATT
1 TATTATTT-TTATTT-TT
3648 T-TTACTTATTTATCTTTT
1 TATTA-TT-TTTAT-TTTT
3666 TATT
1 TATT
3670 TACCTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 14 0.44
17 9 0.28
18 5 0.16
19 4 0.12
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTATTTTTATTTTT
Found at i:3643 original size:13 final size:13
Alignment explanation
Indices: 3617--3665 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
3607 CTCCACCATA
*
3617 TTATTTTTATTTT
1 TTATTTTTACTTT
3630 TTATTATTT-CTTT
1 TTATT-TTTACTTT
3643 TTATTTTTACTTAT
1 TTATTTTTACTT-T
3657 TTATCTTTT
1 TTAT-TTTT
3666 TATTTACCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 3 0.10
13 16 0.52
14 8 0.26
15 4 0.13
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATTTTTACTTT
Found at i:3670 original size:12 final size:12
Alignment explanation
Indices: 3622--3694 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
3612 CCATATTATT
3622 TTTAT-TTTTTA
1 TTTATCTTTTTA
*
3633 TTATTTCTTTTTA
1 TT-TATCTTTTTA
**
3646 TTT-T-TACTTA
1 TTTATCTTTTTA
3656 TTTATCTTTTTA
1 TTTATCTTTTTA
*
3668 TTTACCTTTTTA
1 TTTATCTTTTTA
*
3680 TTTACCTTTTTA
1 TTTATCTTTTTA
3692 TTT
1 TTT
3695 TATTTTCTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
10 7 0.13
11 4 0.08
12 33 0.63
13 8 0.15
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATCTTTTTA
Found at i:5050 original size:15 final size:15
Alignment explanation
Indices: 5032--5061 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5022 TTCTATTTTG
5032 CATAATTTACTTTAA
1 CATAATTTACTTTAA
5047 CATAATTTACTTTAA
1 CATAATTTACTTTAA
5062 TTTTTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
CATAATTTACTTTAA
Found at i:6046 original size:24 final size:24
Alignment explanation
Indices: 6019--6065 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6009 AATCTTAATT
* *
6019 CTAATCAATGTTAAATATATTATG
1 CTAATAAATGCTAAATATATTATG
6043 CTAATAAATGCTAAATATATTAT
1 CTAATAAATGCTAAATATATTAT
6066 ACAAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATG
Found at i:6074 original size:24 final size:24
Alignment explanation
Indices: 6019--6075 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
6009 AATCTTAATT
* * *
6019 CTAATCAATGTTAAATATATTATG
1 CTAATAAATGCTAAATATATTATA
6043 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
6067 C-AAGTAAAT
1 CTAA-TAAAT
6076 CTTCTAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:7356 original size:24 final size:25
Alignment explanation
Indices: 7301--7356 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
7291 AGGATTATAG
*
7301 TTTCTTCTTTTATCTTTCTCTCTCT
1 TTTCTTCTTTCATCTTTCTCTCTCT
*
7326 TTT-TTCTTTCA-CTTT-TCTTTCTT
1 TTTCTTCTTTCATCTTTCTCTCTC-T
7349 TTTCTTCT
1 TTTCTTCT
7357 CTTCTCCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 8 0.30
24 11 0.41
25 3 0.11
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTCTTCTTTCATCTTTCTCTCTCT
Found at i:38433 original size:28 final size:28
Alignment explanation
Indices: 38398--38452 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
38388 GCAGAATTAC
38398 AACCATAATCCTCAAGTGCAGGCACATT
1 AACCATAATCCTCAAGTGCAGGCACATT
38426 AACCATAATCCTCAAGTGCAGGCACAT
1 AACCATAATCCTCAAGTGCAGGCACAT
38453 CATGATCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.29, G:0.15, T:0.20
Consensus pattern (28 bp):
AACCATAATCCTCAAGTGCAGGCACATT
Found at i:42755 original size:5 final size:5
Alignment explanation
Indices: 42745--42781 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
42735 TGTCATCACA
*
42745 TTTAT TTTA- TTTAC TTT-T TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
42782 ACTCTATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Done.