Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005160.1 Kokia drynarioides strain JFW-HI SEQ_119007, 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: 8408
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:350 original size:25 final size:26
Alignment explanation
Indices: 322--407 Score: 68
Period size: 28 Copynumber: 3.2 Consensus size: 26
312 AAGTTAATGT
322 AATATTTT-TATTTTCTTTATAAAAA
1 AATATTTTATATTTTCTTTATAAAAA
* *
347 AATATTATTATACTTTTCTCTT-TACAAC
1 AATATT-TTATA-TTTTCT-TTATAAAAA
* * *
375 AATATTTTTCTGTTTTCTTTACATAAAA
1 AATA-TTTTATATTTTCTTTATA-AAAA
403 AATAT
1 AATAT
408 ATTCTTTACA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
25 6 0.13
26 4 0.09
27 10 0.21
28 23 0.49
29 4 0.09
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (26 bp):
AATATTTTATATTTTCTTTATAAAAA
Found at i:3436 original size:41 final size:40
Alignment explanation
Indices: 3402--3613 Score: 219
Period size: 40 Copynumber: 5.2 Consensus size: 40
3392 TATTCGCGAG
* *
3402 GCTTTCTTATAAGCACCGCTAAAGGTCAGTATATTAGCGGC
1 GCTTTCTCATAAGCGCCGCTAAAGGTCAGT-TATTAGCGGC
* * **
3443 ACTTTCTCATAAGCGCCACTAAAGGTCAGGCATTAGCGGC
1 GCTTTCTCATAAGCGCCGCTAAAGGTCAGTTATTAGCGGC
* * ** * *
3483 GCTTTCCCATAAGCGTCTATAAAGGTCAGTCATTAACGGC
1 GCTTTCTCATAAGCGCCGCTAAAGGTCAGTTATTAGCGGC
*
3523 GCTTTCCCATAAGCGCCGCTAAAGGTCAGGTTATTAGCGGC
1 GCTTTCTCATAAGCGCCGCTAAAGGTCA-GTTATTAGCGGC
* * * * **
3564 ACTTTTTTATAAGCACCGCTAAAGGTCAGGGCATTAGCGGC
1 GCTTTCTCATAAGCGCCGCTAAAGGTCA-GTTATTAGCGGC
3605 GC-TTCTCAT
1 GCTTTCTCAT
3614 TAGCATCGCT
Statistics
Matches: 142, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
40 72 0.51
41 70 0.49
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
GCTTTCTCATAAGCGCCGCTAAAGGTCAGTTATTAGCGGC
Found at i:3545 original size:121 final size:120
Alignment explanation
Indices: 3410--3664 Score: 327
Period size: 121 Copynumber: 2.1 Consensus size: 120
3400 AGGCTTTCTT
* *
3410 ATAAGCACCGCTAAAGGTCA-GTATATTAGCGGCACTTTCTCATAAGCGCCACTAAAGGTCA-GG
1 ATAAGCGCCGCTAAAGGTCAGGT-TATTAGCGGCACTTTCTCATAAGCACCACTAAAGGTCAGGG
* * * *
3473 CATTAGCGGCGCTTTCCCATAAGCGTCTATAAAGGTCA-GTCATTAACGGCGCTTTCCC
65 CATTAGCGGCGC-TTCCCATAAGCATCGATAAA-GTAATGT-ATTAACGACGCTTTCCC
* * *
3531 ATAAGCGCCGCTAAAGGTCAGGTTATTAGCGGCACTTTTTTATAAGCACCGCTAAAGGTCAGGGC
1 ATAAGCGCCGCTAAAGGTCAGGTTATTAGCGGCACTTTCTCATAAGCACCACTAAAGGTCAGGGC
* * * *
3596 ATTAGCGGCGCTTCTCATTAGCATCGCTAAATTAATGTATTAACGACGCTTTCCC
66 ATTAGCGGCGCTTCCCATAAGCATCGATAAAGTAATGTATTAACGACGCTTTCCC
*
3651 ATAAGCGTCGCTAA
1 ATAAGCGCCGCTAA
3665 TTTATTTAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
120 31 0.26
121 70 0.60
122 16 0.14
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (120 bp):
ATAAGCGCCGCTAAAGGTCAGGTTATTAGCGGCACTTTCTCATAAGCACCACTAAAGGTCAGGGC
ATTAGCGGCGCTTCCCATAAGCATCGATAAAGTAATGTATTAACGACGCTTTCCC
Found at i:3904 original size:17 final size:17
Alignment explanation
Indices: 3884--3970 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
3874 CCAATTTTAA
*
3884 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
3901 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
3918 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
3935 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
*
3953 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
3970 A
1 A
3971 AAATTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 47 0.77
18 14 0.23
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:3912 original size:6 final size:6
Alignment explanation
Indices: 3879--3978 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
3869 TGAACCCAAT
* * * *
3879 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * * *
3926 TTTAAA CTTATT TTTGAG TTTAAA TTT-AT TTTGAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
3974 TTTAA
1 TTTAA
3979 TTATAAATCC
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
5 12 0.17
6 47 0.66
7 12 0.17
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:3953 original size:35 final size:34
Alignment explanation
Indices: 3884--3966 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 34
3874 CCAATTTTAA
* *
3884 ATTTTAAATTTTAATTTATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTAAGTTTAAATTT
*
3918 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTA-TTTTAAGTTTAAATTT
*
3953 ATTTTGAATTTAAA
1 ATTTTAAATTTAAA
3967 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 16 0.36
35 28 0.64
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTAAGTTTAAATTT
Found at i:4972 original size:17 final size:18
Alignment explanation
Indices: 4952--4998 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
4942 TTCATTTTGG
*
4952 GTTTAAATTTAGTTT-AA
1 GTTTAAATTTAATTTGAA
4969 GTTTAAATTTAATTTGAA
1 GTTTAAATTTAATTTGAA
4987 -TTTAAAATTTAA
1 GTTT-AAATTTAA
4999 ATTAATTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
GTTTAAATTTAATTTGAA
Found at i:5005 original size:17 final size:18
Alignment explanation
Indices: 4973--5010 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4963 GTTTAAGTTT
* *
4973 AAATTTAATTTGAATTTA
1 AAATTTAAATTGAATTGA
4991 AAATTTAAATT-AATTGA
1 AAATTTAAATTGAATTGA
5008 AAA
1 AAA
5011 GGTCCAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AAATTTAAATTGAATTGA
Found at i:6928 original size:30 final size:29
Alignment explanation
Indices: 6880--7120 Score: 251
Period size: 29 Copynumber: 8.2 Consensus size: 29
6870 CCAAGAATTT
**
6880 CATTTTTACCTCCGAACTTCCAAAAATCC
1 CATTTTTACCTCAAAACTTCCAAAAATCC
*
6909 CATTTTTGACCTCAAAACTTCCAAAAATTC
1 CATTTTT-ACCTCAAAACTTCCAAAAATCC
*
6939 CATTTTTACCCTC-GAACTTCCAAAAATCC
1 CATTTTTA-CCTCAAAACTTCCAAAAATCC
*
6968 CATTTTTAACC-CTAAAACTTCCAAAAATTC
1 CATTTTT-ACCTC-AAAACTTCCAAAAATCC
* * *
6998 CATTTTTACCACCAAACTTTCAAAAA-CTC
1 CATTTTTACCTCAAAACTTCCAAAAATC-C
*
7027 CATTTTTAACCTCGAAACTTCC-AAAATCC
1 CATTTTT-ACCTCAAAACTTCCAAAAATCC
* * *
7056 TATTTTGACCCCAAAACTTCTC-AAAATCC
1 CATTTTTACCTCAAAACTTC-CAAAAATCC
*
7085 CATTTTTACCCTC-GAACTTCCAAAAATCC
1 CATTTTTA-CCTCAAAACTTCCAAAAATCC
7114 CATTTTT
1 CATTTTT
7121 GACCCCGAAA
Statistics
Matches: 179, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
28 13 0.07
29 98 0.55
30 68 0.38
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (29 bp):
CATTTTTACCTCAAAACTTCCAAAAATCC
Found at i:6961 original size:59 final size:58
Alignment explanation
Indices: 6863--7129 Score: 303
Period size: 59 Copynumber: 4.5 Consensus size: 58
6853 GGAGGTCCCT
* * *
6863 AAACTATCCAAGAATTTCATTTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACT-TCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATCCCATTTTTAACCTCA
6923 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTAACCTC-A
* * *
6982 AAACTTCCAAAAATTCCATTTTTACCACCAAACTTTCAAAAA-CTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATC-CCATTTTTAACCTCA
* * *
7041 AAACTTCC-AAAA-TCCTATTTTGACCCCAAAACTTCTC-AAAATCCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCC-ATTTTTACCCC-GAACTTC-CAAAAATCCCATTTTTAACCTCA
* *
7098 GAACTTCCAAAAATCCCATTTTTGACCCCGAA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCGAA
7130 ATTTCAAAGA
Statistics
Matches: 182, Mismatches: 13, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
57 12 0.07
58 49 0.27
59 114 0.63
60 7 0.04
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
Found at i:7150 original size:58 final size:59
Alignment explanation
Indices: 6880--7182 Score: 274
Period size: 59 Copynumber: 5.2 Consensus size: 59
6870 CCAAGAATTT
* * *
6880 CATTTTT-ACCTCCG-AACTTCCAAAAATCCCATTTTTGA-CCTCAAAACTTCCAAAAATTC
1 CATTTTTGACC-CCGAAACTTTCAAAAATCCCATTTTT-ACCCTC-GAACTTCCAAAAATCC
* ** *
6939 CATTTTT-ACCCTCG-AACTTCCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTC
1 CATTTTTGACCC-CGAAACTTTCAAAAATCCCATTTTT-ACCCTCGAACTTCCAAAAATCC
*
6998 CATTTTT-ACCACC-AAACTTTCAAAAA-CTCCATTTTTAACCTCGAAACTTCC-AAAATCC
1 CATTTTTGACC-CCGAAACTTTCAAAAATC-CCATTTTTACCCTCG-AACTTCCAAAAATCC
* *
7056 TA-TTTTGACCCCAAAACTTCTC-AAAATCCCATTTTTACCCTCGAACTTCCAAAAATCC
1 CATTTTTGACCCCGAAACTT-TCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCC
* * * *
7114 CATTTTTGACCCCGAAA-TTTCAAAGAAT-TCACTTTTACCCTCGAACCT-CTAAAATCTC
1 CATTTTTGACCCCGAAACTTTCAAA-AATCCCATTTTTACCCTCGAACTTCCAAAAATC-C
*
7172 TATTTTTGACC
1 CATTTTTGACC
7183 TCAAAACCCT
Statistics
Matches: 213, Mismatches: 16, Indels: 31
0.82 0.06 0.12
Matches are distributed among these distances:
57 22 0.10
58 80 0.38
59 107 0.50
60 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CATTTTTGACCCCGAAACTTTCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCC
Done.