Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001929.1 Kokia drynarioides strain JFW-HI SEQ_113731, 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: 58268
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:20546 original size:51 final size:50
Alignment explanation
Indices: 20445--20642 Score: 261
Period size: 50 Copynumber: 3.9 Consensus size: 50
20435 TTAATAAATG
* * * * *
20445 CATGCATTATGTAACTTTCAAGTTAGTTAAGTATGGATCATAAATAATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATGA
* *
20495 CATGAATTATGTAACTTTCATGATTAGTTAAGTTTGCATCATAAATTATGA
1 CATGCATTATGTAACTCTCATG-TTAGTTAAGTTTGCATCATAAATTATGA
* * *
20546 CATGCAGTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATTATGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATGA
* *
20596 TATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAAT
1 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAAT
20643 CAAGTCATGC
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 71 0.54
51 55 0.42
52 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATGA
Found at i:20629 original size:101 final size:102
Alignment explanation
Indices: 20445--20642 Score: 267
Period size: 101 Copynumber: 2.0 Consensus size: 102
20435 TTAATAAATG
* * *
20445 CATGCATTATGTAACTTTCAAGTTAGTTAAGTATGGATCATAAATAATGACATGAATTATGTAAC
1 CATGCAGTATGTAACTCTCAAGTTAGTTAAGTATGCATCATAAATAATGACATGAATTATGTAAC
**
20510 TTTCATGATTAGTTAAGTTTGCATCA-TAAATTATGA
66 TCCCATGATTAGTTAAGTTTGCATCATTAAATTATGA
* * ** *
20546 CATGCAGTATGTAACTCTCATGTTAGTTAAG-ATTGCATCATAAATTATGTTATGCATTATGTAA
1 CATGCAGTATGTAACTCTCAAGTTAGTTAAGTA-TGCATCATAAATAATGACATGAATTATGTAA
20610 CTCCCATG-TTAGTTAAAGTTTGCATCATTAAAT
65 CTCCCATGATTAGTT-AAGTTTGCATCATTAAAT
20643 CAAGTCATGC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 7 0.08
101 72 0.86
102 5 0.06
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (102 bp):
CATGCAGTATGTAACTCTCAAGTTAGTTAAGTATGCATCATAAATAATGACATGAATTATGTAAC
TCCCATGATTAGTTAAGTTTGCATCATTAAATTATGA
Found at i:20995 original size:79 final size:78
Alignment explanation
Indices: 20856--21087 Score: 297
Period size: 79 Copynumber: 2.9 Consensus size: 78
20846 ATGCTTAATC
* * *
20856 AGGTGACTCTTCAAAAGACCAAGGGAAGACACTTCAAATACTGATCAGTTTTGGAACACTTAAAG
1 AGGTGACACTTCAAAAGACCAAGGGAA-ACTCTTCAAATGCTGATCAGTTTTGGAACACTTAAAG
* * *
20921 GTCACTTCAAGACA
65 GCCAATTCAAAACA
* * *
20935 AGTTGACACTTCAAAAGACCAATGGGAAACTCTTCAAATGCTGATTAGTTTTGGTACACTTAAAG
1 AGGTGACACTTCAAAAGACCAA-GGGAAACTCTTCAAATGCTGATCAGTTTTGGAACACTTAAAG
21000 GCCAATTCAAAACA
65 GCCAATTCAAAACA
* * *
21014 AGGTGA-ATCTTCAAAAGACCAAGGGGAAACTCTTAAAATGCTGATCGGTTTTTGG-GCACTTAA
1 AGGTGACA-CTTCAAAAGACCAA-GGGAAACTCTTCAAATGCTGATCAG-TTTTGGAACACTTAA
21077 AGGCCAATTCA
63 AGGCCAATTCA
21088 TGACACCAAT
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
78 1 0.01
79 123 0.91
80 11 0.08
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (78 bp):
AGGTGACACTTCAAAAGACCAAGGGAAACTCTTCAAATGCTGATCAGTTTTGGAACACTTAAAGG
CCAATTCAAAACA
Found at i:30130 original size:31 final size:30
Alignment explanation
Indices: 30087--30154 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
30077 CCCTAACCAT
* *
30087 ATTAAATTACCACAATAATTAATAAATCCC
1 ATTAAATGACCACAATAATTAATAAATCAC
* * *
30117 AATTAAATGACCACATTAGTTAATACATCAC
1 -ATTAAATGACCACAATAATTAATAAATCAC
30148 ATTAAAT
1 ATTAAAT
30155 AAAAAATTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (30 bp):
ATTAAATGACCACAATAATTAATAAATCAC
Found at i:30329 original size:25 final size:25
Alignment explanation
Indices: 30301--30348 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
30291 ATCATTACCA
*
30301 AAGCACAT-AAATATAATACAAAAGC
1 AAGCAAATCAAAT-TAATACAAAAGC
*
30326 AAGCAAATCAAATTAATAGAAAA
1 AAGCAAATCAAATTAATACAAAA
30349 ACAATATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.62, C:0.12, G:0.08, T:0.17
Consensus pattern (25 bp):
AAGCAAATCAAATTAATACAAAAGC
Found at i:34152 original size:6 final size:6
Alignment explanation
Indices: 34139--34173 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
34129 ACCGAAAAAA
* *
34139 GAAAGG GGAAGG GGAAGG GAAAGG GAAAGG GAAAG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
34174 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:34958 original size:4 final size:4
Alignment explanation
Indices: 34949--35027 Score: 58
Period size: 4 Copynumber: 20.5 Consensus size: 4
34939 AACGGGTATT
* * *
34949 GAAA GAAA GAAA GAAA GGAA G-AA GGAA GAAA GAAA -AAA G-AA GGAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* * * *
34994 GAAG GAGAA GAAA TAAA -AGA GAAA GAGA GAAA GA
1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GA
35028 TAATGTATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
3 11 0.18
4 46 0.77
5 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:35011 original size:25 final size:25
Alignment explanation
Indices: 34949--35006 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 25
34939 AACGGGTATT
34949 GAAAGAAAGAAAGAAAGGAAGAAGGAA
1 GAAAGAAA-AAAG-AAGGAAGAAGGAA
34976 GAAAGAAAAAAGAAGGAAGAAGG-A
1 GAAAGAAAAAAGAAGGAAGAAGGAA
35000 G-AAGAAA
1 GAAAGAAA
35007 TAAAAGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 6 0.19
24 2 0.06
25 11 0.35
26 4 0.13
27 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
GAAAGAAAAAAGAAGGAAGAAGGAA
Found at i:35063 original size:14 final size:12
Alignment explanation
Indices: 35034--35058 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35024 AAGATAATGT
35034 ATTTATTTTTAA
1 ATTTATTTTTAA
35046 ATTTATTTTTAA
1 ATTTATTTTTAA
35058 A
1 A
35059 AATTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:35805 original size:30 final size:30
Alignment explanation
Indices: 35771--35865 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
35761 AAATGGTACA
*
35771 AAATAAATATTTATTTTGTATCATTTTGGT
1 AAATAAATATTTATTTTGTACCATTTTGGT
* * *
35801 AAAT-AATGA--TGTGTGGATACCATTTTGGT
1 AAATAAAT-ATTTATTTTG-TACCATTTTGGT
* *
35830 ATATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTGGT
35860 AAATAA
1 AAATAA
35866 CTCATTTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 4 0.08
29 18 0.36
30 24 0.48
31 4 0.08
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTGGT
Found at i:37115 original size:43 final size:42
Alignment explanation
Indices: 37034--37125 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 42
37024 TTAACATGTC
* *
37034 AAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTACT
1 AAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTA-T
* *
37077 AAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTAT
1 AAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTAT
*
37119 TAATTAT
1 AAATTAT
37126 GTAGTTCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 10 0.23
43 33 0.77
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (42 bp):
AAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAT
Found at i:37434 original size:14 final size:16
Alignment explanation
Indices: 37410--37441 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37400 ACAATCGGAT
37410 GATGCGAGTAC-CTCC
1 GATGCGAGTACACTCC
37425 GATG-GAGTACACTCC
1 GATGCGAGTACACTCC
37440 GA
1 GA
37442 ATTTGCAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (16 bp):
GATGCGAGTACACTCC
Found at i:37595 original size:6 final size:6
Alignment explanation
Indices: 37586--37637 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
37576 AGCTAAAGCT
* * * * * *
37586 AGAGCC AGAGCC AGAGCA AGAGCA AGAGGA AGAGGA AGAGGA AGAGGA
1 AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA
37634 AGAG
1 AGAG
37638 GCATTAGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.46, C:0.12, G:0.42, T:0.00
Consensus pattern (6 bp):
AGAGCA
Found at i:37638 original size:6 final size:6
Alignment explanation
Indices: 37598--37638 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
37588 AGCCAGAGCC
* *
37598 AGAGCA AGAGCA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
37639 CATTAGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.05, G:0.46, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:37769 original size:45 final size:45
Alignment explanation
Indices: 37701--37792 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
37691 GCCTACCTCA
* ** *
37701 TCAAGCCAAAGATATCAATCTCAGTTTGATGAGTCACCACAATAC
1 TCAAGCCAAAGATATCAACCTCAGTTTGACAAGCCACCACAATAC
*
37746 TCAAGCCAAGGATATCAACCTCAGTTTGACAAGCCACCACAATAC
1 TCAAGCCAAAGATATCAACCTCAGTTTGACAAGCCACCACAATAC
37791 TC
1 TC
37793 TACATCTCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAACCTCAGTTTGACAAGCCACCACAATAC
Found at i:38065 original size:21 final size:21
Alignment explanation
Indices: 38036--38081 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
38026 CATACCTCTA
* * *
38036 AACCTTAAATCATAAACCCTT
1 AACCCTAAATCAGAAACCATT
*
38057 AACCCTAAATTAGAAACCATT
1 AACCCTAAATCAGAAACCATT
38078 AACC
1 AACC
38082 TCAATTTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (21 bp):
AACCCTAAATCAGAAACCATT
Found at i:41434 original size:35 final size:36
Alignment explanation
Indices: 41364--41436 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
41354 TATTTTTATT
*
41364 AAATTAATAATTTTTTAATATTACTTTAGTCAAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
*
41400 AAATAAATAATTTTTGT-ATATTATTTTAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTTAGTCAAATA
41435 AA
1 AA
41437 TCTTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 26 0.76
37 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:41468 original size:30 final size:31
Alignment explanation
Indices: 41410--41468 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
41400 AAATAAATAA
* *
41410 TTTTTGTATATTATTTTAGTAAATAAATCTT
1 TTTTTATATATTATTTTAGTAAAGAAATCTT
* *
41441 TTTTTATATTTTATTTTGGT-AAGAAATC
1 TTTTTATATATTATTTTAGTAAAGAAATC
41469 AAAACCCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTTATATATTATTTTAGTAAAGAAATCTT
Found at i:43948 original size:15 final size:15
Alignment explanation
Indices: 43900--43958 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
43890 TTTAATATAA
*
43900 TTTAAAATAAAATAT
1 TTTAATATAAAATAT
* *
43915 TTTATTTTAAATTATAT
1 TTTAATATAAA--ATAT
43932 TTTGAA-ATAAAATAT
1 TTT-AATATAAAATAT
43947 TTTAATATAAAA
1 TTTAATATAAAA
43959 ATAATTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.06
15 21 0.60
17 11 0.31
18 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTTAATATAAAATAT
Found at i:44741 original size:65 final size:65
Alignment explanation
Indices: 44637--44762 Score: 225
Period size: 65 Copynumber: 1.9 Consensus size: 65
44627 TGATCAAACG
* *
44637 ACTACAATTTCCTCATTTTTGTCTTTTTAACACGCATACACACTATCAATTACATAAAACAAATT
1 ACTACAATCTCCTCATTTTCGTCTTTTTAACACGCATACACACTATCAATTACATAAAACAAATT
*
44702 ACTACAATCTCCTCATTTTCGTCTTTTTAACACGCATACACACTATCAGTTACATAAAACA
1 ACTACAATCTCCTCATTTTCGTCTTTTTAACACGCATACACACTATCAATTACATAAAACA
44763 GAGTCTAGCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (65 bp):
ACTACAATCTCCTCATTTTCGTCTTTTTAACACGCATACACACTATCAATTACATAAAACAAATT
Found at i:53030 original size:35 final size:35
Alignment explanation
Indices: 52991--53060 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
52981 ATCTAAATAA
52991 TATTATAAGTCACAAAACCTTGACATCTTAATAGT
1 TATTATAAGTCACAAAACCTTGACATCTTAATAGT
53026 TATTATAAGTCACAAAACCTTGACATCTTAATAGT
1 TATTATAAGTCACAAAACCTTGACATCTTAATAGT
53061 CTTCCTCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (35 bp):
TATTATAAGTCACAAAACCTTGACATCTTAATAGT
Found at i:53308 original size:12 final size:12
Alignment explanation
Indices: 53291--53315 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53281 GGTACTAGAG
53291 TCTCAAATTAAA
1 TCTCAAATTAAA
53303 TCTCAAATTAAA
1 TCTCAAATTAAA
53315 T
1 T
53316 TTCCAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTCAAATTAAA
Found at i:54791 original size:13 final size:13
Alignment explanation
Indices: 54773--54839 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
54763 TTGGTCAAGA
54773 AAAGTCAACAGTC
1 AAAGTCAACAGTC
*
54786 AAAGTCAAC-GATT
1 AAAGTCAACAG-TC
* *
54799 AAGGTCAACAGTT
1 AAAGTCAACAGTC
*
54812 AACGGTCAA-AGTC
1 AA-AGTCAACAGTC
54825 AAAGATCAA-AGTC
1 AAAG-TCAACAGTC
54838 AA
1 AA
54840 CGGTCAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.04
13 37 0.80
14 7 0.15
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (13 bp):
AAAGTCAACAGTC
Found at i:54846 original size:13 final size:13
Alignment explanation
Indices: 54801--54846 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
54791 CAACGATTAA
*
54801 GGTCAACAGTTAAC
1 GGTCAA-AGTCAAC
*
54815 GGTCAAAGTCAAA
1 GGTCAAAGTCAAC
*
54828 GATCAAAGTCAAC
1 GGTCAAAGTCAAC
54841 GGTCAA
1 GGTCAA
54847 GTTCGACGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Done.