Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011145.1 Kokia drynarioides strain JFW-HI SEQ_126118, 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: 34791
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4470 original size:20 final size:20
Alignment explanation
Indices: 4440--4485 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
4430 GACATTTGAT
4440 ACTTCATTGTCGAAGGACCAG
1 ACTT-ATTGTCGAAGGACCAG
4461 ACTTATTGTCGAAGGACCAG
1 ACTTATTGTCGAAGGACCAG
4481 ACTTA
1 ACTTA
4486 CAATGACTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (20 bp):
ACTTATTGTCGAAGGACCAG
Found at i:9865 original size:21 final size:21
Alignment explanation
Indices: 9841--9890 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
9831 GAATTTCAGC
*
9841 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
* *
9862 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
9883 AGAAAACT
1 AGCAAACT
9891 GAGGCATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:9891 original size:21 final size:21
Alignment explanation
Indices: 9852--9891 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9842 GCAATCTATA
*
9852 GATTTTCAAAAGCAAACTGTG
1 GATTTTCAAAAGAAAACTGTG
9873 GATTTTCAAAAGAAAACTG
1 GATTTTCAAAAGAAAACTG
9892 AGGCATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACTGTG
Found at i:13942 original size:8 final size:8
Alignment explanation
Indices: 13929--13983 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
13919 ACCCAATTAT
13929 TTTTTTTA
1 TTTTTTTA
13937 TTTTTTTA
1 TTTTTTTA
*
13945 TTTTTCTA
1 TTTTTTTA
13953 TCTTATTTTA
1 T-TT-TTTTA
*
13963 TTTATTTA
1 TTTTTTTA
*
13971 TTTATTTA
1 TTTTTTTA
13979 TTTTT
1 TTTTT
13984 GTCCAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 32 0.78
9 4 0.10
10 5 0.12
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:13968 original size:4 final size:4
Alignment explanation
Indices: 13933--13981 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
13923 AATTATTTTT
*
13933 TTTA TTTT TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA TTT
13982 TTGTCCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 29 0.74
5 6 0.15
6 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:14921 original size:89 final size:90
Alignment explanation
Indices: 14761--14930 Score: 245
Period size: 89 Copynumber: 1.9 Consensus size: 90
14751 ATTTGGAGTG
* * *
14761 TGTTAGACTGAGTAACCGGGGTGGAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGGCTAAC
1 TGTTAGACTGAGTAACCGGGATGAAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGGCCAAC
*
14826 GCATTC-TACAAAAAATTGAGAGCA
66 GCATTCTTAAAAAAAATTGAGAGCA
* *
14850 TGTTAGGCTGAGTAACCGGGATGAAGTGCTTGAG-TGTCATTTCATTTCGCGTCAAAAGGTCCAA
1 TGTTAGACTGAGTAACCGGGATGAAGTGCTTG-GTTGTCATTTCATTTCGCGTCAAAAGGGCCAA
* *
14914 TGTATTCTTAAAAAAAA
65 CGCATTCTTAAAAAAAA
14931 AAAAAAGGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
89 62 0.87
90 9 0.13
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (90 bp):
TGTTAGACTGAGTAACCGGGATGAAGTGCTTGGTTGTCATTTCATTTCGCGTCAAAAGGGCCAAC
GCATTCTTAAAAAAAATTGAGAGCA
Found at i:15527 original size:19 final size:19
Alignment explanation
Indices: 15505--15549 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15495 TTATATTAGG
15505 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
15524 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
15543 ATTTAAT
1 ATTTAAT
15550 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:16403 original size:21 final size:22
Alignment explanation
Indices: 16361--16407 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
16351 TTTCTATTTC
*
16361 TTTTAATTCTATTTTTTGTTAT
1 TTTTAATTCTATTTCTTGTTAT
* *
16383 TTTTAATTTTGTTTCTT-TTAT
1 TTTTAATTCTATTTCTTGTTAT
16404 TTTT
1 TTTT
16408 CCTTAGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTAATTCTATTTCTTGTTAT
Found at i:28345 original size:19 final size:19
Alignment explanation
Indices: 28323--28360 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28313 ATGTATAATA
28323 TATTATATCATT-TTATATT
1 TATTATAT-ATTCTTATATT
*
28342 TATTTTATATTCTTATATT
1 TATTATATATTCTTATATT
28361 ATATAAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTATATATTCTTATATT
Found at i:28647 original size:59 final size:59
Alignment explanation
Indices: 28526--28685 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 59
28516 CTTAATATAA
* * * * * * **
28526 CAATTTA-TATCTGAACTTGACAATTTTTTCTAATTTGATATTTAAATTTTTATTGATT
1 CAATTTAGTACCTGAACTTGATATTTTTTTTTAATTTGGTATTTAAATTTTTATTAACC
*
28584 CAATTTGGTACCTGAACTTGATATTTTTTTTTAATTTGGTATTTAAACTTTTT-TTAACC
1 CAATTTAGTACCTGAACTTGATATTTTTTTTTAATTTGGTATTTAAA-TTTTTATTAACC
* *
28643 CAATTTAGTACCTAAACTAAGCAT-TTTTTTTCTTAATTTGGTA
1 CAATTTAGTACCTGAACT-TG-ATATTTTTTT-TTAATTTGGTA
28686 CCTAATTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
58 6 0.07
59 53 0.62
60 13 0.15
61 13 0.15
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (59 bp):
CAATTTAGTACCTGAACTTGATATTTTTTTTTAATTTGGTATTTAAATTTTTATTAACC
Found at i:28963 original size:32 final size:31
Alignment explanation
Indices: 28926--29051 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
28916 CTTAAAAAGT
*
28926 TTTAAGT-TCCAACTTA-GAAAGAAAGTGTCAAG
1 TTTAAGTAT-CAAATTAGGAAA-AAA-TGTCAAG
28958 TTTAAGTATCAAATTAGGAAAAAATGTCAAG
1 TTTAAGTATCAAATTAGGAAAAAATGTCAAG
**
28989 TTTAAGTATCAAATT-GGACCAAAAAAAT--AG
1 TTTAAGTATCAAATTAGGA--AAAAATGTCAAG
* * *
29019 TTTAAGTACCAAATTAGGAAAAAGTATCAAG
1 TTTAAGTATCAAATTAGGAAAAAATGTCAAG
29050 TT
1 TT
29052 CAGGTACCAA
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
29 6 0.07
30 19 0.23
31 29 0.36
32 22 0.27
33 5 0.06
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
TTTAAGTATCAAATTAGGAAAAAATGTCAAG
Found at i:28988 original size:31 final size:31
Alignment explanation
Indices: 28953--29051 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
28943 AAAGAAAGTG
*
28953 TCAAGTTTAAGTATCAAATTAGGAAAAAATG
1 TCAAGTTTAAGTATCAAATTAGGAAAAAATA
*
28984 TCAAGTTTAAGTATCAAATT-GGACCAAAAAAA
1 TCAAGTTTAAGTATCAAATTAGGA--AAAAATA
* *
29016 T--AGTTTAAGTACCAAATTAGGAAAAAGTA
1 TCAAGTTTAAGTATCAAATTAGGAAAAAATA
29045 TCAAGTT
1 TCAAGTT
29052 CAGGTACCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 6 0.10
30 19 0.33
31 27 0.47
32 6 0.10
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (31 bp):
TCAAGTTTAAGTATCAAATTAGGAAAAAATA
Found at i:29063 original size:92 final size:92
Alignment explanation
Indices: 28869--29063 Score: 216
Period size: 92 Copynumber: 2.1 Consensus size: 92
28859 AAAAAATATT
* ** *
28869 AGGTACCAAATTAGAAAAAAAAATCAAGTTCAGGTACTAAATTGGACCTTAAAAAGTTTTAAGTT
1 AGGTACCAAATTAGAAAAAAAAATCAAGTTCAAGTACTAAATTGGACCAAAAAAAGTTTTAAGTA
* * *
28934 CCAACTTAGAAAGAAAGTGTCAAGTTT
66 CCAAATTAGAAAGAAAGTATCAAGTTC
* * * ** *
28961 AAGTATCAAATTAGGAAAAAATGTCAAGTTTAAGTA-TCAAATTGGACCAAAAAAA-TAGTTTAA
1 AGGTACCAAATTAGAAAAAAAAATCAAGTTCAAGTACT-AAATTGGACCAAAAAAAGT--TTTAA
*
29024 GTACCAAATTAGGAA-AAAGTATCAAGTTC
63 GTACCAAATTAGAAAGAAAGTATCAAGTTC
29053 AGGTACCAAAT
1 AGGTACCAAAT
29064 ATTATATTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
91 2 0.02
92 65 0.77
93 17 0.20
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (92 bp):
AGGTACCAAATTAGAAAAAAAAATCAAGTTCAAGTACTAAATTGGACCAAAAAAAGTTTTAAGTA
CCAAATTAGAAAGAAAGTATCAAGTTC
Found at i:29540 original size:17 final size:19
Alignment explanation
Indices: 29518--29561 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
29508 AAAAAATATA
29518 TTATTAAATTTA-T-TTAT
1 TTATTAAATTTATTATTAT
*
29535 TTATTATTATTTATTATTAT
1 TTATTA-AATTTATTATTAT
29555 TTATTAA
1 TTATTAA
29562 CCCAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 1 0.05
20 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTAAATTTATTATTAT
Found at i:29546 original size:10 final size:10
Alignment explanation
Indices: 29531--29560 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
29521 TTAAATTTAT
29531 TTATTTATTA
1 TTATTTATTA
29541 TTATTTATTA
1 TTATTTATTA
29551 TTATTTATTA
1 TTATTTATTA
29561 ACCCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTATTA
Done.