Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014585.1 Kokia drynarioides strain JFW-HI SEQ_129624, 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: 20707
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4589 original size:33 final size:33
Alignment explanation
Indices: 4547--4613 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4537 AAATGAAAAG
4547 AACAAATTAGCATGATTGTGAACACGTCTATAA
1 AACAAATTAGCATGATTGTGAACACGTCTATAA
*
4580 AACAAATTAGCATGATTGTGAACATGTCTATAA
1 AACAAATTAGCATGATTGTGAACACGTCTATAA
4613 A
1 A
4614 GCCAGAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (33 bp):
AACAAATTAGCATGATTGTGAACACGTCTATAA
Found at i:6178 original size:29 final size:29
Alignment explanation
Indices: 6144--6424 Score: 134
Period size: 29 Copynumber: 9.6 Consensus size: 29
6134 TTTGACACCA
** *
6144 AAACTTTTGAAAATTATATTTTTACCCTC
1 AAACTTTCAAAAATTATATTTTGACCCTC
* * * *
6173 GAACTTTCAAAAAAAATCAAATTTTGACCCTA
1 AAACTTTC---AAAAATTATATTTTGACCCTC
*
6205 AAAC-TTCCAAAATTATATTTTGACCC-C
1 AAACTTTCAAAAATTATATTTTGACCCTC
* *
6232 AAAACTTTCAAAAATTACATTTTTACCCTC
1 -AAACTTTCAAAAATTATATTTTGACCCTC
* *
6262 GAACTTTCAAAAATTCCAT-TTTTAACCC-C
1 AAACTTTCAAAAATT--ATATTTTGACCCTC
* * *
6291 AAAACTTCCAAAAATTACATTTTTACCCT-
1 -AAACTTTCAAAAATTATATTTTGACCCTC
* *
6320 GAAC-CTCAAAAAATTCCAT-TTTTGA-CCTC
1 AAACTTTC-AAAAATT--ATATTTTGACCCTC
*
6349 AAAGATTTCAAAAATTATCATTTT-ACCC-C
1 AAA-CTTTCAAAAATTAT-ATTTTGACCCTC
* * * *
6378 AAGACATCCAAAAACTCCAT-TTTTGACCCTG
1 AA-ACTTTCAAAAA-T-TATATTTTGACCCTC
* *
6409 AAACTCTCTAAAATTA
1 AAACTTTCAAAAATTA
6425 CCATTTTACC
Statistics
Matches: 187, Mismatches: 40, Indels: 51
0.67 0.14 0.18
Matches are distributed among these distances:
27 1 0.01
28 37 0.20
29 71 0.38
30 49 0.26
31 10 0.05
32 19 0.10
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTTCAAAAATTATATTTTGACCCTC
Found at i:6340 original size:58 final size:59
Alignment explanation
Indices: 6222--6435 Score: 235
Period size: 59 Copynumber: 3.6 Consensus size: 59
6212 CAAAATTATA
*
6222 TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCCAT
1 TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTCTCAAAAATTCCAT
* *
6281 TTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCT-GAAC-CTCAAAAAATTCCAT
1 TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTCTC-AAAAATTCCAT
* * *
6339 TTTTGACCTCAAAGA-TTTCAAAAATTATCA-TTTTACCC-CAAGACATC-CAAAAACTCCAT
1 TTTTGACCCCAAA-ACTTTCAAAAATTA-CATTTTTACCCTCGA-AC-TCTCAAAAATTCCAT
** * *
6398 TTTTGACCCTGAAACTCTCTAAAATTACCA-TTTTACCC
1 TTTTGACCCCAAAACTTTCAAAAATTA-CATTTTTACCC
6436 CCTGGTATCC
Statistics
Matches: 133, Mismatches: 14, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
57 2 0.02
58 47 0.35
59 82 0.62
60 1 0.01
61 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (59 bp):
TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTCTCAAAAATTCCAT
Found at i:6413 original size:117 final size:117
Alignment explanation
Indices: 6222--6435 Score: 267
Period size: 117 Copynumber: 1.8 Consensus size: 117
6212 CAAAATTATA
* * * *
6222 TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTAA
1 TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAACATCCAAAAACTCCATTTTTAA
6287 CCCCAAAACT-TCCAAAAATTA-CATTTTTACCCTGAACCTCAAAAAATTCCAT
66 CCCCAAAACTCT-CAAAAATTACCA-TTTTACCCTGAACCTCAAAAAATTCCAT
*
6339 TTTTGACCTCAAAGA-TTTCAAAAATTATCA-TTTTACCC-CAAGACATCCAAAAACTCCATTTT
1 TTTTGACCCCAAA-ACTTTCAAAAATTA-CATTTTTACCCTCAA-ACATCCAAAAACTCCATTTT
* ** *
6401 TGACCCTGAAACTCTCTAAAATTACCATTTTACCC
63 TAACCCCAAAACTCTCAAAAATTACCATTTTACCC
6436 CCTGGTATCC
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
116 2 0.02
117 75 0.90
118 6 0.07
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (117 bp):
TTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTCAAACATCCAAAAACTCCATTTTTAA
CCCCAAAACTCTCAAAAATTACCATTTTACCCTGAACCTCAAAAAATTCCAT
Found at i:9622 original size:43 final size:42
Alignment explanation
Indices: 9568--9795 Score: 253
Period size: 43 Copynumber: 5.3 Consensus size: 42
9558 TTATGAGGAA
* * *
9568 AAACACCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-CAC
*
9611 AAATGCCGCTAAAGAACATGGTCTTTTAGCGGCGCTTTTCCAGC
1 AAACGCCGCTAAAGAACATGGTC-TTTAGCGGCGCTTTTCCA-C
* *
9655 AAATGCCGCTAAAGAACATGGTTTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCC-AC
* * * *
9698 AAAAGCCGCTAAAAAACATAGTATTTAGCGG-GACTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTTT-CCAC
* *
9741 AAACGCCGCTAAA-AAGCATGGTCTTTAACGACGCTTTTCTCAC
1 AAACGCCGCTAAAGAA-CATGGTCTTTAGCGGCGCTTTTC-CAC
*
9784 AAACGCCACTAA
1 AAACGCCGCTAA
9796 TATCAACAAA
Statistics
Matches: 162, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
42 4 0.02
43 116 0.72
44 42 0.26
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
Found at i:11537 original size:42 final size:41
Alignment explanation
Indices: 11490--11585 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
11480 AAATTAGACT
* * * * *
11490 TTTAGCGGCGTTTTTATTATAAACGCCGTTAATGCTCTGAGC
1 TTTAGCGGCG-CTTTATCATAAACACCGCTAATGCTCTGACC
* * *
11532 TTTAGCAGCGCTTTCTCATAAGCACCGCTAATGCTCTGACC
1 TTTAGCGGCGCTTTATCATAAACACCGCTAATGCTCTGACC
11573 TTTAGCGGCGCTT
1 TTTAGCGGCGCTT
11586 GCCCATAAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 36 0.80
42 9 0.20
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGCTTTATCATAAACACCGCTAATGCTCTGACC
Found at i:11608 original size:41 final size:41
Alignment explanation
Indices: 11515--11614 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
11505 ATTATAAACG
* * *
11515 CCGTTAATGCTCTGAGCTTTAGCAGCGCTTTCTCATAAGCA
1 CCGTTAATGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCA
* * *
11556 CCGCTAATGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCG
1 CCGTTAATGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCA
* * *
11597 TCGTTATTGCTCTAACCT
1 CCGTTAATGCTCTGACCT
11615 CAAGCACCGC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (41 bp):
CCGTTAATGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCA
Done.