Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003472.1 Kokia drynarioides strain JFW-HI SEQ_116272, 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: 16874
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3324 original size:17 final size:16
Alignment explanation
Indices: 3296--3332 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3286 CATTTTACCA
*
3296 TTCATTTGCATTACAT
1 TTCATTTGCATTAAAT
3312 TTCATTATGCATTAAAT
1 TTCATT-TGCATTAAAT
3329 TTCA
1 TTCA
3333 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (16 bp):
TTCATTTGCATTAAAT
Found at i:4885 original size:7 final size:7
Alignment explanation
Indices: 4868--4930 Score: 65
Period size: 7 Copynumber: 8.4 Consensus size: 7
4858 ATTTCACCTA
4868 AAAAAAG
1 AAAAAAG
4875 AGAAAATAG
1 A-AAAA-AG
4884 AAAATAA-
1 AAAA-AAG
4891 AAGAAAAG
1 AA-AAAAG
*
4899 AAAAAGG
1 AAAAAAG
4906 AAAAAAG
1 AAAAAAG
4913 AAAGAAAG
1 AAA-AAAG
4921 AAAAAAG
1 AAAAAAG
4928 AAA
1 AAA
4931 GAAAAAGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
7 25 0.52
8 19 0.40
9 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:4900 original size:22 final size:21
Alignment explanation
Indices: 4866--4930 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
4856 GTATTTCACC
4866 TAAAA-AAAGAGAAAATAGAAAA
1 TAAAAGAAA-AGAAAA-AGAAAA
4888 TAAAAGAAAAGAAAAAGGAAAA
1 TAAAAGAAAAGAAAAA-GAAAA
*
4910 AAGAAAG-AAAGAAAAAAGAAA
1 TA-AAAGAAAAG-AAAAAGAAA
4931 GAAAAAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 1 0.03
22 25 0.66
23 12 0.32
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
TAAAAGAAAAGAAAAAGAAAA
Found at i:4918 original size:4 final size:4
Alignment explanation
Indices: 4890--4934 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
4880 ATAGAAAATA
*
4890 AAAG AAAAG AAA- AAGG AAA- AAAG AAAG AAAG AAA- AAAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
4935 AAGGAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
3 8 0.23
4 23 0.66
5 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4919 original size:11 final size:11
Alignment explanation
Indices: 4875--4941 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
4865 CTAAAAAAAG
*
4875 AGAAAATAGAA
1 AGAAAAAAGAA
*
4886 A-ATAAAAGAAA
1 AGAAAAAAG-AA
*
4897 AGAAAAAGGAA
1 AGAAAAAAGAA
4908 A-AAAGAAAGAA
1 AGAAA-AAAGAA
4919 AGAAAAAAGAA
1 AGAAAAAAGAA
*
4930 AGAAAAAGGAA
1 AGAAAAAAGAA
4941 A
1 A
4942 ATGGAGAGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 8 0.17
11 30 0.65
12 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:4925 original size:15 final size:15
Alignment explanation
Indices: 4894--4934 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
4884 AAAATAAAAG
*
4894 AAAAGAAA-AAGGAA
1 AAAAGAAAGAAAGAA
4908 AAAAGAAAGAAAGAA
1 AAAAGAAAGAAAGAA
4923 AAAAGAAAGAAA
1 AAAAGAAAGAAA
4935 AAGGAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAGAA
Found at i:5980 original size:49 final size:48
Alignment explanation
Indices: 5821--5984 Score: 186
Period size: 49 Copynumber: 3.4 Consensus size: 48
5811 AAAGACGTAA
* * * *
5821 AGGGAAATATTGAAGCCGCAATGGTGAATCTTATACCTTAGAGATATGG
1 AGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCTTAGAAATAT-G
* * * *
5870 AGGGAAAGACTAAAGCCGCAATTGCGGATCTTGTACCTTAGAAATATG
1 AGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCTTAGAAATATG
* * *
5918 AAGGGAAATATTGAAGTCGCAATGGCGAATCTTGTACCCTT-GAAATGTAG
1 -AGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTA-CCTTAGAAATAT-G
5968 AGGGAAAGATTGAAGCC
1 AGGGAAAGATTGAAGCC
5985 ACAACAAAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 89 0.94
50 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (48 bp):
AGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCTTAGAAATATG
Found at i:5999 original size:98 final size:98
Alignment explanation
Indices: 5820--6007 Score: 216
Period size: 98 Copynumber: 1.9 Consensus size: 98
5810 TAAAGACGTA
* * *
5820 AAGGGAAATATTGAAGCCGCAATGGTGAATCTTATACCTTAGAGATATGGAGGGAAAGACTAAAG
1 AAGGGAAATATTGAAGCCGCAATGGCGAATCTTATACCTTAGAAATATAGAGGGAAAGACTAAAG
* ****** *
5885 CCGCAATTGCGGATCTTGTACCTTAGAAATATG
66 CCACAACAAAAAATCTTATACCTTAGAAATATG
* * * * *
5918 AAGGGAAATATTGAAGTCGCAATGGCGAATCTTGTACCCTT-GAAATGTAGAGGGAAAGATTGAA
1 AAGGGAAATATTGAAGCCGCAATGGCGAATCTTATA-CCTTAGAAATATAGAGGGAAAGACTAAA
5982 GCCACAACAAAAAATCTTATACCTTA
65 GCCACAACAAAAAATCTTATACCTTA
6008 AAGACTGTAC
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
98 69 0.95
99 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (98 bp):
AAGGGAAATATTGAAGCCGCAATGGCGAATCTTATACCTTAGAAATATAGAGGGAAAGACTAAAG
CCACAACAAAAAATCTTATACCTTAGAAATATG
Found at i:6497 original size:44 final size:45
Alignment explanation
Indices: 6434--6524 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 45
6424 TTACATTGGG
** *
6434 CACCATCCAGTCTTTTACCCCTAATCCA-AAGGGCAGATTGAAGC
1 CACCATCCAACCTTTTACCCCTAATCCAGAAGGGCAAATTGAAGC
* *
6478 CACCATCCAACCTTTTACCCCTAATCTAGAGGGGCAAATTGAAGC
1 CACCATCCAACCTTTTACCCCTAATCCAGAAGGGCAAATTGAAGC
6523 CA
1 CA
6525 TCAGTCGATC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 25 0.61
45 16 0.39
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (45 bp):
CACCATCCAACCTTTTACCCCTAATCCAGAAGGGCAAATTGAAGC
Found at i:6538 original size:45 final size:45
Alignment explanation
Indices: 6437--6571 Score: 148
Period size: 45 Copynumber: 3.0 Consensus size: 45
6427 CATTGGGCAC
* * * *
6437 CATCCAGTCTTTTACCCCTAATCCA-AAGGGCAGATTGAAGCCAC
1 CATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCAT
* *
6481 CATCCAACCTTTTACCCCTAATCTAGAGGGGCAAATTGAAGCCAT
1 CATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCAT
* ** *
6526 CAGT-CGATCTTTTAATCTTAAATCTAGAGGGGCAGATTGAAGCCAT
1 CA-TCCAATCTTTTACCCCT-AATCTAGAGGGGCAGATTGAAGCCAT
6572 ACACATAACT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 22 0.29
45 28 0.37
46 26 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (45 bp):
CATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGCCAT
Found at i:15787 original size:30 final size:30
Alignment explanation
Indices: 15751--15844 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
15741 ACTCTGATGG
15751 GTTCTACCAATACCAAATGAAACCCTCAGA
1 GTTCTACCAATACCAAATGAAACCCTCAGA
* *
15781 GTTCTACCGATACTC---TG--A---T--GG
1 GTTCTACCAATAC-CAAATGAAACCCTCAGA
15802 GTTCTACCAATACCAAATGAAACCCTCAGA
1 GTTCTACCAATACCAAATGAAACCCTCAGA
*
15832 GTTCTACCGATAC
1 GTTCTACCAATAC
15845 AACGACTCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 22
0.64 0.07 0.29
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
23 3 0.06
25 1 0.02
26 1 0.02
28 3 0.06
30 25 0.52
31 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (30 bp):
GTTCTACCAATACCAAATGAAACCCTCAGA
Found at i:15793 original size:51 final size:51
Alignment explanation
Indices: 15731--15844 Score: 219
Period size: 51 Copynumber: 2.2 Consensus size: 51
15721 TCCTTTGCAC
*
15731 TTCTACTGATACTCTGATGGGTTCTACCAATACCAAATGAAACCCTCAGAG
1 TTCTACCGATACTCTGATGGGTTCTACCAATACCAAATGAAACCCTCAGAG
15782 TTCTACCGATACTCTGATGGGTTCTACCAATACCAAATGAAACCCTCAGAG
1 TTCTACCGATACTCTGATGGGTTCTACCAATACCAAATGAAACCCTCAGAG
15833 TTCTACCGATAC
1 TTCTACCGATAC
15845 AACGACTCCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
TTCTACCGATACTCTGATGGGTTCTACCAATACCAAATGAAACCCTCAGAG
Done.