Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000936.1 Kokia drynarioides strain JFW-HI SEQ_112092, 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: 39505
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:5809 original size:29 final size:29
Alignment explanation
Indices: 5776--5840 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
5766 TAAGCTTTAG
5776 AGGAAAGCCCTTTGGAAGATATTGATGCA
1 AGGAAAGCCCTTTGGAAGATATTGATGCA
**
5805 AGGAAAAGGGCTTTGGAAGATATTGATGCA
1 AGG-AAAGCCCTTTGGAAGATATTGATGCA
*
5835 AAGAAA
1 AGGAAA
5841 AAGGCCTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (29 bp):
AGGAAAGCCCTTTGGAAGATATTGATGCA
Found at i:5820 original size:30 final size:30
Alignment explanation
Indices: 5785--5841 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
5775 GAGGAAAGCC
*
5785 CTTTGGAAGATATTGATGCAAGGAAAAGGG
1 CTTTGGAAGATATTGATGCAAAGAAAAGGG
5815 CTTTGGAAGATATTGATGCAAAGAAAA
1 CTTTGGAAGATATTGATGCAAAGAAAA
5842 AGGCCTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (30 bp):
CTTTGGAAGATATTGATGCAAAGAAAAGGG
Found at i:21056 original size:41 final size:41
Alignment explanation
Indices: 21009--21127 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 41
20999 TATTTCGCCT
* * *
21009 AAAAAAAGGATCGAGATGAAAACTCGTAAAGTGCATCTCGA
1 AAAAAAAGGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
*
21050 AAAAAAAGGATCGAGATGAAAACCCGCAAAGGGCATCTTGA
1 AAAAAAAGGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
* * * *
21091 AACCAAAAGGATTATGAGTTGAAAACCCGTAAAGGGC
1 AA-AAAAAGGA-T-CGAGATGAAAACCCGCAAAGGGC
21128 GACTCAAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 39 0.58
42 7 0.10
43 1 0.01
44 20 0.30
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (41 bp):
AAAAAAAGGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
Found at i:21713 original size:21 final size:21
Alignment explanation
Indices: 21687--21728 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
21677 GCCATGACAT
21687 CCTAACCATATGGCCTGCATA
1 CCTAACCATATGGCCTGCATA
21708 CCTAACCATATGGCCTGCATA
1 CCTAACCATATGGCCTGCATA
21729 GAGGTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (21 bp):
CCTAACCATATGGCCTGCATA
Found at i:22004 original size:47 final size:48
Alignment explanation
Indices: 21930--22025 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 48
21920 TTTCAAACCC
* * *
21930 TCATCTTCTTGATGAGATACAGAGAAGTGGATC-AAACAACGAAGCGA
1 TCATCTTCTTGATAAGATACAGAGAAGTAGACCAAAACAACGAAGCGA
* * * *
21977 TCATTTTCTTGATAATATATAGAGAAGTAGACCAAAACAATGAAGCGA
1 TCATCTTCTTGATAAGATACAGAGAAGTAGACCAAAACAACGAAGCGA
22025 T
1 T
22026 GCTCAATGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 27 0.66
48 14 0.34
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (48 bp):
TCATCTTCTTGATAAGATACAGAGAAGTAGACCAAAACAACGAAGCGA
Found at i:22048 original size:123 final size:123
Alignment explanation
Indices: 21761--22253 Score: 627
Period size: 123 Copynumber: 4.0 Consensus size: 123
21751 ATAGGACATG
* * * *
21761 GACCAAAACAACGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCTTTATCTTCCTGATGAGAT
1 GACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGAT
** * *
21826 ACAGAGAAGTGGATCAAACAACGAAGCCCT-ATTTTCTTGATGAGATATAGATAAGTG
66 ACAGAGAAGTGGATCAAACAACGAAGCGATCATTTTCTTGATGAGATATAGAGAAGTA
* * * * *
21883 GACTAAAACAATGAAGCGAATCTCAATATGAGTGAAATTTCAAACCCTCATCTTCTTGATGAGAT
1 GACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGAT
* *
21948 ACAGAGAAGTGGATCAAACAACGAAGCGATCATTTTCTTGATAATATATAGAGAAGTA
66 ACAGAGAAGTGGATCAAACAACGAAGCGATCATTTTCTTGATGAGATATAGAGAAGTA
* *
22006 GACCAAAACAATGAAGCGATGCTCAATGTGAGTGAAACTTCAAACCC-CAATCTTCTTGATGAGA
1 GACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTC-ATCTTCCTGATGAGA
* * *
22070 TACTA-AGAAGTGGATTAAACAACGAAGCGATCATCTTCTTGATGAGATATAGAGAAATA
65 TAC-AGAGAAGTGGATCAAACAACGAAGCGATCATTTTCTTGATGAGATATAGAGAAGTA
* * * * *
22129 GACCAAAACAATTAAGCAAAGCTCCATGTGAGTAAAACTTCAAA-CCTCATCTTCCCGATGAGAT
1 GACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGAT
* * * * * * *
22193 ACAGAGAAATGGTTCAGAGCGACGAAGCGGTCATCTTT-TTTATGAGATACAGAGAAGTA
66 ACAGAGAAGTGGATCA-AACAACGAAGCGATCAT-TTTCTTGATGAGATATAGAGAAGTA
22252 GA
1 GA
22254 TCGAAATATG
Statistics
Matches: 322, Mismatches: 42, Indels: 13
0.85 0.11 0.03
Matches are distributed among these distances:
121 1 0.00
122 112 0.35
123 206 0.64
124 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (123 bp):
GACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGAT
ACAGAGAAGTGGATCAAACAACGAAGCGATCATTTTCTTGATGAGATATAGAGAAGTA
Found at i:22191 original size:245 final size:246
Alignment explanation
Indices: 21761--22253 Score: 634
Period size: 245 Copynumber: 2.0 Consensus size: 246
21751 ATAGGACATG
* ***
21761 GACCAAAACAACGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCTTTATCTTCCTGATGAGAT
1 GACCAAAACAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCAATCTTCCTGATGAGAT
* * * * * *
21826 ACAGAGAAGTGGATCAAACAACGAAGCCCTATTTTCTTGATGAGATATAGATAAGTGGACTAAAA
66 ACAGAGAAGTGGATCAAACAACGAAGCCATATCTTCTTGATGAGATATAGAGAAATAGACCAAAA
* * * * **
21891 CAATGAAGCGAATCTCAATATGAGTGAAATTTCAAACCCTCATCTTCTTGATGAGATACAGAGAA
131 CAATGAAGCAAAGCTCAATATGAGTAAAACTTCAAACCCTCATCTTCCCGATGAGATACAGAGAA
* * *
21956 GTGGATCA-AACAACGAAGCGATCAT-TTTCTTGATAATATATAGAGAAGTA
196 ATGGATCAGAACAACGAAGCGATCATCTTT-TTGATAAGATACAGAGAAGTA
* * *
22006 GACCAAAACAATGAAGCGATGCTCAATGTGAGTGAAACTTCAAACCCCAATCTTCTTGATGAGAT
1 GACCAAAACAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCAATCTTCCTGATGAGAT
* *
22071 ACTA-AGAAGTGGATTAAACAACGAAGCGATCATCTTCTTGATGAGATATAGAGAAATAGACCAA
66 AC-AGAGAAGTGGATCAAACAACGAAGCCAT-ATCTTCTTGATGAGATATAGAGAAATAGACCAA
* * *
22135 AACAATTAAGCAAAGCTCCATGTGAGTAAAACTTCAAA-CCTCATCTTCCCGATGAGATACAGAG
129 AACAATGAAGCAAAGCTCAATATGAGTAAAACTTCAAACCCTCATCTTCCCGATGAGATACAGAG
* * * * * *
22199 AAATGGTTCAGAGCGACGAAGCGGTCATCTTTTTTATGAGATACAGAGAAGTA
194 AAATGGATCAGAACAACGAAGCGATCATCTTTTTGATAAGATACAGAGAAGTA
22252 GA
1 GA
22254 TCGAAATATG
Statistics
Matches: 211, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
245 115 0.55
246 93 0.44
247 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (246 bp):
GACCAAAACAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCAATCTTCCTGATGAGAT
ACAGAGAAGTGGATCAAACAACGAAGCCATATCTTCTTGATGAGATATAGAGAAATAGACCAAAA
CAATGAAGCAAAGCTCAATATGAGTAAAACTTCAAACCCTCATCTTCCCGATGAGATACAGAGAA
ATGGATCAGAACAACGAAGCGATCATCTTTTTGATAAGATACAGAGAAGTA
Found at i:24184 original size:28 final size:29
Alignment explanation
Indices: 24152--24305 Score: 172
Period size: 28 Copynumber: 5.3 Consensus size: 29
24142 AATATTTGGA
24152 TTGACCCTTGAACTTTCCAAAAATTAAG-
1 TTGACCCTTGAACTTTCCAAAAATTAAGT
*
24180 TTGACTCTTGAACTTTCCAAAAATTAAGT
1 TTGACCCTTGAACTTTCCAAAAATTAAGT
* ** *
24209 TGGTTCC-TAAACTTTCCAAAAATTAAGTT
1 TTGACCCTTGAACTTTCCAAAAATTAAG-T
*
24238 TTGACCCTTGAACTTTCC-AAAATTTAGT
1 TTGACCCTTGAACTTTCCAAAAATTAAGT
* *
24266 TTGACCCTCGAAC-TTCACAAAAATTCAGAT
1 TTGACCCTTGAACTTTC-CAAAAATTAAG-T
*
24296 TTAACCCTTG
1 TTGACCCTTG
24306 GACATCCATA
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
27 3 0.03
28 60 0.57
29 24 0.23
30 18 0.17
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (29 bp):
TTGACCCTTGAACTTTCCAAAAATTAAGT
Found at i:24280 original size:58 final size:57
Alignment explanation
Indices: 24152--24305 Score: 170
Period size: 58 Copynumber: 2.7 Consensus size: 57
24142 AATATTTGGA
*
24152 TTGACCCTTGAACTTTCCAAAAATTAAG-TTGACTCTTGAACTTTCCAAAAATTAAGT
1 TTGACCC-TGAACTTTCCAAAAATTAAGTTTGACCCTTGAACTTTCCAAAAATTAAGT
* ** * *
24209 TGGTTCCTAAACTTTCCAAAAATTAAGTTTTGACCCTTGAACTTTCC-AAAATTTAGT
1 TTGACCCTGAACTTTCCAAAAATTAAG-TTTGACCCTTGAACTTTCCAAAAATTAAGT
* *
24266 TTGACCCTCGAAC-TTCACAAAAATTCAGATTTAACCCTTG
1 TTGACCCT-GAACTTTC-CAAAAATTAAG-TTTGACCCTTG
24306 GACATCCATA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
56 19 0.24
57 21 0.26
58 40 0.50
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (57 bp):
TTGACCCTGAACTTTCCAAAAATTAAGTTTGACCCTTGAACTTTCCAAAAATTAAGT
Found at i:25998 original size:34 final size:34
Alignment explanation
Indices: 25931--26000 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
25921 AAAAAAAAAA
* * * *
25931 AACATGATAAGCTTGATGTGGATGTGTTGAATAT
1 AACATGATAACCTTGATGTGAATGTATTCAATAT
*
25965 AACATGATAACCTTGATGTTAATGTATTCAATAT
1 AACATGATAACCTTGATGTGAATGTATTCAATAT
25999 AA
1 AA
26001 AATATAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (34 bp):
AACATGATAACCTTGATGTGAATGTATTCAATAT
Found at i:31494 original size:26 final size:26
Alignment explanation
Indices: 31439--31514 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
31429 GTTAAACCTC
**
31439 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
31465 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
31491 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
31515 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:38057 original size:17 final size:17
Alignment explanation
Indices: 38047--38087 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
38037 AAAGAAGTAG
38047 AGAAGAAAAAGAAAAAA
1 AGAAGAAAAAGAAAAAA
38064 AGAAGAAAAAGAAAAAAA
1 AGAAGAAAAAG-AAAAAA
38082 AGAAGA
1 AGAAGA
38088 GAAGGAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AGAAGAAAAAGAAAAAA
Found at i:38064 original size:9 final size:9
Alignment explanation
Indices: 38047--38085 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
38037 AAAGAAGTAG
*
38047 AGAAGAAAA
1 AGAAAAAAA
38056 AG-AAAAAA
1 AGAAAAAAA
*
38064 AGAAGAAAA
1 AGAAAAAAA
38073 AGAAAAAAA
1 AGAAAAAAA
38082 AGAA
1 AGAA
38086 GAGAAGGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:38737 original size:29 final size:29
Alignment explanation
Indices: 38691--38753 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
38681 AAAAAGAAGT
38691 ATAAATATATTAGATCATTTA-CAAATAAA
1 ATAAATATATTAGATCATTTATCAAA-AAA
* * *
38720 ATAAATATATTGGGTCATTTATTAAAAAA
1 ATAAATATATTAGATCATTTATCAAAAAA
38749 ATAAA
1 ATAAA
38754 AAAAGGACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (29 bp):
ATAAATATATTAGATCATTTATCAAAAAA
Done.