Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011653.1 Kokia drynarioides strain JFW-HI SEQ_126645, 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: 56294
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:3129 original size:14 final size:15
Alignment explanation
Indices: 3110--3138 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3100 ATGGTTTTCC
3110 TTTTC-TTTTCTTTT
1 TTTTCTTTTTCTTTT
3124 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
3139 ACTTTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:3133 original size:20 final size:21
Alignment explanation
Indices: 3104--3146 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3094 CATAACATGG
3104 TTTTCCTTTTCTTTT-CTTTT
1 TTTTCCTTTTCTTTTACTTTT
*
3124 TTTTCTTTTTCTTTTACTTTT
1 TTTTCCTTTTCTTTTACTTTT
3145 TT
1 TT
3147 CCATGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTCCTTTTCTTTTACTTTT
Found at i:4151 original size:61 final size:61
Alignment explanation
Indices: 4077--4198 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
4067 GCGCCCAAGG
* * *
4077 TTAATTCCTGAAAAATAAATAAATTACGATTTTTCCAAAGACGCCAAGCAAATATTCCAAA
1 TTAATTCCTGAAAAACAAATAAATTACGATTTTTCCAAAAACGCCAAGCAAACATTCCAAA
* * *
4138 TTAATTCCTGAAAAACAAATAAATTACGGTTTTTTCAAAAACGCCAGGCAAACATTCCAAA
1 TTAATTCCTGAAAAACAAATAAATTACGATTTTTCCAAAAACGCCAAGCAAACATTCCAAA
4199 GAAACATTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (61 bp):
TTAATTCCTGAAAAACAAATAAATTACGATTTTTCCAAAAACGCCAAGCAAACATTCCAAA
Found at i:11875 original size:22 final size:22
Alignment explanation
Indices: 11847--11890 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11837 CTATACTTTC
*
11847 TTTCATAAGGGTCTTTTGAATG
1 TTTCATAAGGGTCTTTCGAATG
11869 TTTCATAAGGGTCTTTCGAATG
1 TTTCATAAGGGTCTTTCGAATG
11891 AATATTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (22 bp):
TTTCATAAGGGTCTTTCGAATG
Found at i:15633 original size:8 final size:8
Alignment explanation
Indices: 15622--15663 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
15612 TTTAATCTTT
15622 TAAAATTA
1 TAAAATTA
*
15630 TAAAAATA
1 TAAAATTA
15638 T-AAATTA
1 TAAAATTA
*
15645 TTAAAATAA
1 -TAAAATTA
15654 TAAAATTA
1 TAAAATTA
15662 TA
1 TA
15664 TTTTTAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:15642 original size:15 final size:17
Alignment explanation
Indices: 15622--15663 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
15612 TTTAATCTTT
15622 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
15638 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
15654 TAAAATTATA
1 TAAAATTATA
15664 TTTTTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:17380 original size:3 final size:3
Alignment explanation
Indices: 17372--17401 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17362 TTTAAACTGC
17372 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17402 GGAGAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17697 original size:29 final size:30
Alignment explanation
Indices: 17653--17709 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
17643 AATTAATAAA
*
17653 GATAAAATTATAATTTGA-TCTTTAAAATT
1 GATAAAATTATAATTTAATTCTTTAAAATT
* *
17682 GATAAAATTTTGATTTAATTCTTTAAAA
1 GATAAAATTATAATTTAATTCTTTAAAA
17710 AATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
GATAAAATTATAATTTAATTCTTTAAAATT
Found at i:21837 original size:23 final size:24
Alignment explanation
Indices: 21807--21854 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21797 AAGGCCTCAA
* *
21807 AAATTTATA-ATTTTAACTTTTTT
1 AAATTTATATAATTTAAATTTTTT
21830 AAATTTATATAATTTAAATTTTTT
1 AAATTTATATAATTTAAATTTTTT
21854 A
1 A
21855 TATTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTTATATAATTTAAATTTTTT
Found at i:21868 original size:30 final size:29
Alignment explanation
Indices: 21833--21895 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
21823 CTTTTTTAAA
*
21833 TTTATATA-ATTTAAATTTTTTATATTATTT
1 TTTATAAATATTTAAA-TTTTTATA-TATTT
*
21863 TTTATAAATATTTCAATTTTTATATATTT
1 TTTATAAATATTTAAATTTTTATATATTT
21892 TTTA
1 TTTA
21896 AAAGAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 9 0.30
30 15 0.50
31 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATAAATATTTAAATTTTTATATATTT
Found at i:21889 original size:16 final size:15
Alignment explanation
Indices: 21833--21891 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
21823 CTTTTTTAAA
21833 TTTATATAATTTAAATT
1 TTTATAT-ATTT-AATT
*
21850 TTT-TATA-TTATTT
1 TTTATATATTTAATT
21863 TTTATAAATATTTCAATT
1 TTTAT--ATATTT-AATT
21881 TTTATATATTT
1 TTTATATATTT
21892 TTTAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 6 0.17
14 3 0.09
15 1 0.03
16 12 0.34
17 5 0.14
18 8 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATATATTTAATT
Found at i:21905 original size:27 final size:30
Alignment explanation
Indices: 21849--21908 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
21839 TAATTTAAAT
* *
21849 TTTTTATATTATTTTTTATAAATATTTCAA
1 TTTTTATATTATTTTTTATAAAGATATCAA
21879 TTTTTATA-TATTTTTTA-AAAGA-ATCAA
1 TTTTTATATTATTTTTTATAAAGATATCAA
21906 TTT
1 TTT
21909 ACTCATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 4 0.14
29 9 0.32
30 8 0.29
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTTTATATTATTTTTTATAAAGATATCAA
Found at i:23805 original size:18 final size:17
Alignment explanation
Indices: 23765--23812 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
23755 AACGTCCTCA
23765 GTGA-AATGTAAC-AAT
1 GTGAGAATGTAACAAAT
*
23780 GAGAGAATGTAACAAATT
1 GTGAGAATGTAACAAA-T
23798 GTGAGAATGTAACAA
1 GTGAGAATGTAACAA
23813 TGCCTTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 8 0.29
17 2 0.07
18 15 0.54
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (17 bp):
GTGAGAATGTAACAAAT
Found at i:30253 original size:18 final size:18
Alignment explanation
Indices: 30227--30269 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30217 ACACTTTTTA
*
30227 TTAAATTTAA-ATTAATTT
1 TTAATTTTAATATTAA-TT
*
30245 TTAATTTTAATTTTAATT
1 TTAATTTTAATATTAATT
30263 TTAATTT
1 TTAATTT
30270 ATAACTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAATTTTAATATTAATT
Found at i:30258 original size:12 final size:12
Alignment explanation
Indices: 30238--30269 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
30228 TAAATTTAAA
30238 TTAATTTTTAATT
1 TTAA-TTTTAATT
30251 TTAATTTTAATT
1 TTAATTTTAATT
30263 TTAATTT
1 TTAATTT
30270 ATAACTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTTTAATT
Found at i:30746 original size:101 final size:101
Alignment explanation
Indices: 30520--30717 Score: 346
Period size: 99 Copynumber: 2.0 Consensus size: 101
30510 TACAAACGAT
*
30520 CATGATCACAAAATTAATTTATTACAAACCTTTTTTTTGGTAAATAATTTATTACAAACTTTTTT
1 CATGATCACAAAATTAATTTATTACAAACCTTTTTTCTGGTAAATAATTTATTACAAAC-TTTTT
*
30585 TTTTTTTGAAAGTACAAACTTTTAATTCTTACAAGAC
65 TTTTTTTGAAAGGACAAACTTTTAATTCTTACAAGAC
*
30622 CATGATCACAAAATTAATTTATTACAAATC-TTTTTCTGGTAAATAATTTATTACAAAC-TTTTT
1 CATGATCACAAAATTAATTTATTACAAACCTTTTTTCTGGTAAATAATTTATTACAAACTTTTTT
30685 TTTTTTGAAAGGACAAACTTTTAATTCTTACAA
66 TTTTTTGAAAGGACAAACTTTTAATTCTTACAA
30718 AGATATGTAT
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
99 37 0.40
101 27 0.29
102 29 0.31
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (101 bp):
CATGATCACAAAATTAATTTATTACAAACCTTTTTTCTGGTAAATAATTTATTACAAACTTTTTT
TTTTTTGAAAGGACAAACTTTTAATTCTTACAAGAC
Found at i:32782 original size:24 final size:25
Alignment explanation
Indices: 32755--32817 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
32745 AAGATTCATA
32755 ATTTGAAATT-TATTTTTA-TTAAAT
1 ATTT-AAATTATATTTTTACTTAAAT
*
32779 ATTTTAATTATATTTTTACTTAAA-
1 ATTTAAATTATATTTTTACTTAAAT
*
32803 ACTTAAATATATATT
1 ATTTAAAT-TATATT
32818 AAATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 4 0.12
24 18 0.55
25 11 0.33
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTAAATTATATTTTTACTTAAAT
Found at i:32808 original size:23 final size:24
Alignment explanation
Indices: 32761--32814 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
32751 CATAATTTGA
*
32761 AATT-TATTTTTATTAAATATTTT
1 AATTATATTTTTATTAAATATCTT
32784 AATTATATTTTTACTTAAA-A-CTT
1 AATTATATTTTTA-TTAAATATCTT
*
32807 AAATATAT
1 AATTATAT
32815 ATTAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 13 0.48
24 9 0.33
25 5 0.19
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
AATTATATTTTTATTAAATATCTT
Found at i:54039 original size:21 final size:21
Alignment explanation
Indices: 54013--54059 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54003 AAAGTAAGAA
*
54013 TTTAATTAATATTAAATTTAT
1 TTTAATTAATATTAAATTAAT
* *
54034 TTTAATTATTATTGAATTAAT
1 TTTAATTAATATTAAATTAAT
54055 TTTAA
1 TTTAA
54060 ATAACATAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATTAATATTAAATTAAT
Found at i:55938 original size:25 final size:25
Alignment explanation
Indices: 55910--55961 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
55900 CAAAGTACTA
*
55910 AACAGAGAG-CACATAAGTGCTGAGC
1 AACAGAGAGACACA-AAGTACTGAGC
55935 AACAGAGAGTACACAAAGTACTGAGC
1 AACAGAGAG-ACACAAAGTACTGAGC
55961 A
1 A
55962 CACAAAGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 11 0.46
27 4 0.17
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (25 bp):
AACAGAGAGACACAAAGTACTGAGC
Found at i:55959 original size:26 final size:26
Alignment explanation
Indices: 55888--55961 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 26
55878 AAACGGAACA
*
55888 AACAGATAGTAC-CAAAGTACT-A--
1 AACAGAGAGTACACAAAGTACTGAGC
*
55910 AACAGAGAG--CACATAAGTGCTGAGC
1 AACAGAGAGTACACA-AAGTACTGAGC
55935 AACAGAGAGTACACAAAGTACTGAGC
1 AACAGAGAGTACACAAAGTACTGAGC
55961 A
1 A
55962 CACAAAGTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 14 0.33
23 1 0.02
25 9 0.21
26 11 0.26
27 4 0.10
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (26 bp):
AACAGAGAGTACACAAAGTACTGAGC
Found at i:55986 original size:23 final size:23
Alignment explanation
Indices: 55957--56060 Score: 163
Period size: 23 Copynumber: 4.5 Consensus size: 23
55947 ACAAAGTACT
*
55957 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAAACAGA
*
55980 GAGCACACGAAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAACAGA
* *
56003 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAAACAGA
*
56026 GAGCACACACAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAACAGA
56049 GAGCACACAAAG
1 GAGCACACAAAG
56061 CGCGCTAGTG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAAACAGA
Found at i:56009 original size:46 final size:46
Alignment explanation
Indices: 55957--56060 Score: 183
Period size: 46 Copynumber: 2.3 Consensus size: 46
55947 ACAAAGTACT
55957 GAGCACACAAAGTGCTAATCAGAGAGCACACGA-AGTGCTAAACAGA
1 GAGCACACAAAGTGCTAATCAGAGAGCACAC-ACAGTGCTAAACAGA
*
56003 GAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAACAGA
56049 GAGCACACAAAG
1 GAGCACACAAAG
56061 CGCGCTAGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
45 1 0.02
46 54 0.98
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (46 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAACAGA
Found at i:56162 original size:24 final size:26
Alignment explanation
Indices: 56124--56171 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
56114 TCTACATGGG
56124 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
56150 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
56172 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.