Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013920.1 Kokia drynarioides strain JFW-HI SEQ_128950, 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: 67087
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:118 original size:20 final size:19
Alignment explanation
Indices: 67--119 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
57 ATTATTTGCC
*
67 TTATAAAAAATATAAATTAT
1 TTATATAAAATA-AAATTAT
* **
87 ATATATTTAATAAAATTATT
1 TTATATAAAATAAAATTA-T
107 TTATATAAAATAA
1 TTATATAAAATAA
120 TTAAAATGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATATAAAATAAAATTAT
Found at i:614 original size:36 final size:37
Alignment explanation
Indices: 564--639 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
554 ATAACTATTG
* *
564 ATGTTGTATATTTTATTA-ATATA-TAATCATTATATA
1 ATGTTATATATTTTATTAGATATATTAAT-AGTATATA
*
600 ATGTTATATCTTTTATTATGATATATTAATAGTATATA
1 ATGTTATATATTTTATTA-GATATATTAATAGTATATA
638 AT
1 AT
640 ATATTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 16 0.47
38 14 0.41
39 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (37 bp):
ATGTTATATATTTTATTAGATATATTAATAGTATATA
Found at i:11656 original size:70 final size:69
Alignment explanation
Indices: 11540--11675 Score: 166
Period size: 70 Copynumber: 2.0 Consensus size: 69
11530 ATTGTAATAT
* * * * * *
11540 AGTACTGAATTTGTTTTACACGTTTAAATGTTAGACAGTTTGTCTTAAATGTTGTTTCAAATTTT
1 AGTACTAAATTTGTCTTACACGTTTAAATATTAGACACTTTGTCTTAAACGTTGTTT-AAATATT
11605 AGTAC
65 AGTAC
* * *
11610 AGTACTAAATTTGTCTTATATGTTTAAATATTAGCCAC-TTGTTCTTAAACGTTGTTTAAATATT
1 AGTACTAAATTTGTCTTACACGTTTAAATATTAGACACTTTG-TCTTAAACGTTGTTTAAATATT
11674 AG
65 AG
11676 ATCGAAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
69 11 0.20
70 45 0.80
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (69 bp):
AGTACTAAATTTGTCTTACACGTTTAAATATTAGACACTTTGTCTTAAACGTTGTTTAAATATTA
GTAC
Found at i:17968 original size:41 final size:41
Alignment explanation
Indices: 17918--18098 Score: 195
Period size: 41 Copynumber: 4.4 Consensus size: 41
17908 TTATGGCTTT
* * *
17918 TTAGTGCCTAGCAGGCTTTATGCCGGTTTATTGTATCGGGCC
1 TTAGTGCCTAGCAGGCTTTATGCCGGTGTACTGTATCAGG-C
* * * * * *
17960 TTAG-GCCTAGCCGGTTTTATGCTGGTGGATTGTATCAAGC
1 TTAGTGCCTAGCAGGCTTTATGCCGGTGTACTGTATCAGGC
* * *
18000 TTAGTGTCTAGCAGACTTTATGCCGATGTACTGTATCAGGC
1 TTAGTGCCTAGCAGGCTTTATGCCGGTGTACTGTATCAGGC
* * * *
18041 TTAATGCCTA-TAGGTTTTATGCCGGTGTACTATATCAGGC
1 TTAGTGCCTAGCAGGCTTTATGCCGGTGTACTGTATCAGGC
18081 TTAGTGCCTAGCAGGCTT
1 TTAGTGCCTAGCAGGCTT
18099 CTTGTCGGTG
Statistics
Matches: 111, Mismatches: 26, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
40 39 0.35
41 68 0.61
42 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (41 bp):
TTAGTGCCTAGCAGGCTTTATGCCGGTGTACTGTATCAGGC
Found at i:19664 original size:27 final size:28
Alignment explanation
Indices: 19604--19665 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
19594 AATCACGTCA
* *
19604 ACAAGAAATTTAAAATTTATAAAAATATT
1 ACAA-AAATTCAAAATTCATAAAAATATT
19633 A-AAAAATTCAAAATTCA-AAATAA-ATT
1 ACAAAAATTCAAAATTCATAAA-AATATT
19659 ACAAAAA
1 ACAAAAA
19666 AATTCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 7 0.24
27 19 0.66
28 2 0.07
29 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (28 bp):
ACAAAAATTCAAAATTCATAAAAATATT
Found at i:19670 original size:22 final size:21
Alignment explanation
Indices: 19642--19688 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19632 TAAAAAATTC
19642 AAAATTCAAAATAAATTACAAA
1 AAAATTCAAAA-AAATTACAAA
* * *
19664 AAAATTCATAAAATTTTCAAA
1 AAAATTCAAAAAAATTACAAA
19685 AAAA
1 AAAA
19689 AAAAAGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATTCAAAAAAATTACAAA
Found at i:19818 original size:31 final size:32
Alignment explanation
Indices: 19783--19851 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
19773 AAAAAAAACA
* *
19783 AAATTTCAATTCTTTTT-TAAAG-TTGATGGTC
1 AAATTTCAATT-TTTTTGAAAAGATTGAGGGTC
* *
19814 AAATTTGAGTTTTTTTGAAAAGATTGAGGGTC
1 AAATTTCAATTTTTTTGAAAAGATTGAGGGTC
19846 AAATTT
1 AAATTT
19852 AACTCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.16
31 13 0.41
32 14 0.44
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (32 bp):
AAATTTCAATTTTTTTGAAAAGATTGAGGGTC
Found at i:20393 original size:22 final size:22
Alignment explanation
Indices: 20367--20409 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20357 ACACTACTCG
*
20367 AGGTATCGCGATATCTACTTCT
1 AGGTATCGCGATATCAACTTCT
20389 AGGTATCGCGATATCAACTTC
1 AGGTATCGCGATATCAACTTC
20410 GTCAATGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (22 bp):
AGGTATCGCGATATCAACTTCT
Found at i:22649 original size:18 final size:18
Alignment explanation
Indices: 22628--22662 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22618 TAGCCGCCAT
*
22628 GTAATATATTTTAAATTC
1 GTAATATATTTAAAATTC
22646 GTAATATATTTAAAATT
1 GTAATATATTTAAAATT
22663 TATTTCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
GTAATATATTTAAAATTC
Found at i:23164 original size:15 final size:15
Alignment explanation
Indices: 23126--23172 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
23116 ACAAAACGAT
23126 AATATAAATAATTAA
1 AATATAAATAATTAA
* * *
23141 AAT-TTAATATTTTA
1 AATATAAATAATTAA
23155 AATATAAATAATTAA
1 AATATAAATAATTAA
23170 AAT
1 AAT
23173 GTAATATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:23178 original size:14 final size:14
Alignment explanation
Indices: 23126--23178 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
23116 ACAAAACGAT
23126 AATATAAATAATTAA
1 AATAT-AATAATTAA
* * *
23141 AATTTAATATTTTA
1 AATATAATAATTAA
23155 AATATAAATAATTAA
1 AATAT-AATAATTAA
*
23170 AATGTAATA
1 AATATAATA
23179 TAAAGTAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:23178 original size:20 final size:21
Alignment explanation
Indices: 23155--23193 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23145 TAATATTTTA
*
23155 AATATAAA-TAATTAAAATGT
1 AATATAAAGTAATAAAAATGT
23175 AATATAAAGTAATAAAAAT
1 AATATAAAGTAATAAAAAT
23194 AATTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
AATATAAAGTAATAAAAATGT
Found at i:37435 original size:18 final size:18
Alignment explanation
Indices: 37356--37444 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 18
37346 GGAGGTGGCG
* *
37356 GAGCCGGAGCCGGAG-TC
1 GAGCTGGAGCTGGAGCTC
* *
37373 GGAGCAGGAGCTGGAGCTG
1 -GAGCTGGAGCTGGAGCTC
*
37392 GAGCTGGAGCTGGAGCTG
1 GAGCTGGAGCTGGAGCTC
37410 GAGCTGGAGCTGGAGC-C
1 GAGCTGGAGCTGGAGCTC
* *
37427 GATGGTGGAGGTGGAGCT
1 GA-GCTGGAGCTGGAGCT
37445 GGCTGCTCTG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
17 2 0.03
18 58 0.95
19 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.51, T:0.13
Consensus pattern (18 bp):
GAGCTGGAGCTGGAGCTC
Found at i:37442 original size:6 final size:6
Alignment explanation
Indices: 37355--37425 Score: 99
Period size: 6 Copynumber: 11.8 Consensus size: 6
37345 TGGAGGTGGC
* * *
37355 GGAGCC GGAGCC GGAG-T CGGAGCA GGAGCT GGAGCT GGAGCT GGAGCT
1 GGAGCT GGAGCT GGAGCT -GGAGCT GGAGCT GGAGCT GGAGCT GGAGCT
37403 GGAGCT GGAGCT GGAGCT GGAGC
1 GGAGCT GGAGCT GGAGCT GGAGC
37426 CGATGGTGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.18, C:0.20, G:0.51, T:0.11
Consensus pattern (6 bp):
GGAGCT
Found at i:58708 original size:19 final size:18
Alignment explanation
Indices: 58655--58711 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
58645 AGAAAGTTCA
* *
58655 AAAATATTTTCAAAAATTC
1 AAAATATTTT-AAAATTTT
58674 AAAATAATTGTT-AAATTTT
1 AAAAT-ATT-TTAAAATTTT
58693 AAAATATTTATAAAATTTT
1 AAAATATTT-TAAAATTTT
58712 CATTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 22 0.69
20 3 0.09
21 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATATTTTAAAATTTT
Found at i:59072 original size:18 final size:17
Alignment explanation
Indices: 59046--59081 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
59036 TAAACCATAT
*
59046 AAATTTTAAAAATATAAA
1 AAATATTAAAAATA-AAA
59064 AAATATTAAAAATAAAA
1 AAATATTAAAAATAAAA
59081 A
1 A
59082 TTCAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATTAAAAATAAAA
Found at i:64583 original size:17 final size:17
Alignment explanation
Indices: 64497--64573 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
64487 CCCAATCAGC
* *
64497 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
64514 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
64531 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
64548 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
64565 TTAAATTTA
1 TTAAATTTA
64574 AAGTTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:65273 original size:30 final size:31
Alignment explanation
Indices: 65237--65295 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
65227 TAAATGAGAT
* * *
65237 TTATTATTATTTAA-AATATTATTAAAAACA
1 TTATTATTAATTAATAATAATAATAAAAACA
65267 TTATTATTAATTAATAATAATAATAAAAA
1 TTATTATTAATTAATAATAATAATAAAAA
65296 ATGAAGAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATTAATTAATAATAATAATAAAAACA
Found at i:66457 original size:58 final size:59
Alignment explanation
Indices: 66383--66704 Score: 451
Period size: 58 Copynumber: 5.5 Consensus size: 59
66373 GAGGTCCCTA
66383 AACCTTCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * *
66441 AACCTTCCAAATATTACCATTTTACCCTCGAACTTACAAAAATCCCA-TTTTAACCCCA
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
*
66499 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCC-AAAATCCCA-TTTTAACCCCT
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * *
66556 AACCTTCCAAAAATTACCATTTTACCCTCGGACTTCCAAAAATCCCATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * ** *
66615 AACCTTCCAAAAATTACCATTTCA-CCTCCGAACTTTCAAAAATCCCATTTTCGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCT-CGAACTTCCAAAAATCCCATTTTTAACCCCG
* *
66674 AAAC-TCTC-AAAATTGCCATTTTACCCTCGAA
1 AACCTTC-CAAAAATTACCATTTTACCCTCGAA
66705 TGTTTTAAGT
Statistics
Matches: 241, Mismatches: 17, Indels: 12
0.89 0.06 0.04
Matches are distributed among these distances:
57 55 0.23
58 102 0.42
59 84 0.35
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:66666 original size:29 final size:27
Alignment explanation
Indices: 66386--66665 Score: 265
Period size: 29 Copynumber: 9.7 Consensus size: 27
66376 GTCCCTAAAC
66386 CTTCCAAAAATTACCATTTTACCCCGAA
1 CTTCCAAAAA-TACCATTTTACCCCGAA
*
66414 CTTCCAAAAATCCCATTTTTAACCCCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
*
66443 CCTTCCAAATATTACCATTTTACCCTCGAA
1 -CTTCCAAA-AATACCATTTTACCC-CGAA
* * *
66473 CTTACAAAAATCCCATTTTAACCCCAAA
1 CTTCCAAAAATACCATTTT-ACCCCGAA
66501 CCTTCCAAAAATTACCATTTTACCCTCGAA
1 -CTTCCAAAAA-TACCATTTTACCC-CGAA
* *
66531 CTTCC-AAAATCCCATTTTAACCCCTAA
1 CTTCCAAAAATACCATTTT-ACCCCGAA
*
66558 CCTTCCAAAAATTACCATTTTACCCTCGGA
1 -CTTCCAAAAA-TACCATTTTACCC-CGAA
* *
66588 CTTCCAAAAATCCCATTTTTGACCTCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
*
66617 CCTTCCAAAAATTACCATTTCACCTCCGAA
1 -CTTCCAAAAA-TACCATTTTACC-CCGAA
* *
66647 CTTTCAAAAATCCCATTTT
1 CTTCCAAAAATACCATTTT
66666 CGACCTCGAA
Statistics
Matches: 209, Mismatches: 24, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
27 15 0.07
28 50 0.24
29 78 0.37
30 57 0.27
31 9 0.04
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (27 bp):
CTTCCAAAAATACCATTTTACCCCGAA
Found at i:66675 original size:29 final size:27
Alignment explanation
Indices: 66386--66704 Score: 246
Period size: 30 Copynumber: 11.0 Consensus size: 27
66376 GTCCCTAAAC
* *
66386 CTTCCAAAAATTACCATTTTACCCCGAA
1 CTTCCAAAAA-TCCCATTTTACCTCGAA
*
66414 CTTCCAAAAATCCCATTTTTAACCCCGAA
1 CTTCCAAAAATCCCA-TTTT-ACCTCGAA
* *
66443 CCTTCCAAATATTACCATTTTACCCTCGAA
1 -CTTCCAAA-AATCCCATTTTA-CCTCGAA
* * *
66473 CTTACAAAAATCCCATTTTAACCCCAAA
1 CTTCCAAAAATCCCATTTT-ACCTCGAA
*
66501 CCTTCCAAAAATTACCATTTTACCCTCGAA
1 -CTTCCAAAAA-TCCCATTTTA-CCTCGAA
* *
66531 CTTCC-AAAATCCCATTTTAACCCCTAA
1 CTTCCAAAAATCCCATTTT-ACCTCGAA
* *
66558 CCTTCCAAAAATTACCATTTTACCCTCGGA
1 -CTTCCAAAAA-TCCCATTTTA-CCTCGAA
66588 CTTCCAAAAATCCCATTTTTGACCTCGAA
1 CTTCCAAAAATCCCA-TTTT-ACCTCGAA
* *
66617 CCTTCCAAAAATTACCATTTCACCTCCGAA
1 -CTTCCAAAAA-TCCCATTTTACCT-CGAA
*
66647 CTTTCAAAAATCCCATTTTCGACCTCGAAA
1 CTTCCAAAAATCCCATTTT--ACCTCG-AA
* *
66677 C-TCTCAAAATTGCCATTTTACCCTCGAA
1 CTTC-CAAAAATCCCATTTTA-CCTCGAA
66705 TGTTTTAAGT
Statistics
Matches: 237, Mismatches: 30, Indels: 48
0.75 0.10 0.15
Matches are distributed among these distances:
27 17 0.07
28 52 0.22
29 78 0.33
30 81 0.34
31 9 0.04
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (27 bp):
CTTCCAAAAATCCCATTTTACCTCGAA
Done.