Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000581.1 Kokia drynarioides strain JFW-HI SEQ_111507, 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: 119135
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:10902 original size:12 final size:12
Alignment explanation
Indices: 10864--10903 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
10854 CTTCATCAAA
10864 ATCCTTATCTTC
1 ATCCTTATCTTC
10876 ATCCATATGATCTTC
1 ATCC-T-T-ATCTTC
10891 ATCCTTATCTTC
1 ATCCTTATCTTC
10903 A
1 A
10904 CACTATTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 2 0.08
15 10 0.40
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (12 bp):
ATCCTTATCTTC
Found at i:24034 original size:14 final size:13
Alignment explanation
Indices: 24015--24046 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
24005 TTTGACCTGT
24015 TATATGTATGTTAA
1 TATATGTATGTT-A
24029 TATATGTATGTTA
1 TATATGTATGTTA
24042 TATAT
1 TATAT
24047 TTTACTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (13 bp):
TATATGTATGTTA
Found at i:38857 original size:16 final size:16
Alignment explanation
Indices: 38836--38868 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38826 TGAACTTTTA
38836 TCGATATTTGTAAATG
1 TCGATATTTGTAAATG
38852 TCGATATTTGTAAATG
1 TCGATATTTGTAAATG
38868 T
1 T
38869 TCATCAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TCGATATTTGTAAATG
Found at i:42867 original size:21 final size:21
Alignment explanation
Indices: 42838--42878 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42828 ATTTTTATTT
*
42838 AAATTTTTATAATATTAAAAC
1 AAATGTTTATAATATTAAAAC
* *
42859 AAATGTTTATATTTTTAAAA
1 AAATGTTTATAATATTAAAA
42879 GATGACTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATGTTTATAATATTAAAAC
Found at i:45431 original size:58 final size:58
Alignment explanation
Indices: 45369--45478 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 58
45359 TAGCCCGAAT
*
45369 ACACCGGCAAGAAGCCTACTAGGCACAAAGCCCAAAAACATCAGCACAAAGCTTGAAA
1 ACACCGGCAAGAAGCCTACTAGGCACAAAGCCCAAAAACATCAACACAAAGCTTGAAA
* * ** *
45427 ACACCGGCACGAAGTCTACTAGGCACAAAGCCTGAAAACATCAACACGAAGC
1 ACACCGGCAAGAAGCCTACTAGGCACAAAGCCCAAAAACATCAACACAAAGC
45479 CTACTAAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.43, C:0.30, G:0.18, T:0.09
Consensus pattern (58 bp):
ACACCGGCAAGAAGCCTACTAGGCACAAAGCCCAAAAACATCAACACAAAGCTTGAAA
Found at i:45463 original size:37 final size:37
Alignment explanation
Indices: 45411--45499 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
45401 CAAAAACATC
* ** *
45411 AGCACAAAGCTTGAAAACACCGGCACGAAGTCTACTA
1 AGCACAAAGCCTGAAAACACCAACACGAAGCCTACTA
* *
45448 GGCACAAAGCCTGAAAACATCAACACGAAGCCTACTA
1 AGCACAAAGCCTGAAAACACCAACACGAAGCCTACTA
45485 AGCACAAAGCCTGAA
1 AGCACAAAGCCTGAA
45500 TTTTTAGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.43, C:0.28, G:0.18, T:0.11
Consensus pattern (37 bp):
AGCACAAAGCCTGAAAACACCAACACGAAGCCTACTA
Found at i:53088 original size:37 final size:37
Alignment explanation
Indices: 53038--53118 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
53028 TGGACCACTA
* *
53038 GCACAAAGCTTGCTAGGCACATAGCCTGAATACACCG
1 GCACAAAGCTTGCTAGGCACACAGCCCGAATACACCG
*
53075 GCACAAAGCTTGCTAGGCACACAGCCCGAATACACTG
1 GCACAAAGCTTGCTAGGCACACAGCCCGAATACACCG
53112 GCACAAA
1 GCACAAA
53119 ACCTAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.14
Consensus pattern (37 bp):
GCACAAAGCTTGCTAGGCACACAGCCCGAATACACCG
Found at i:53160 original size:20 final size:20
Alignment explanation
Indices: 53053--53167 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
53043 AAGCTTGCTA
*
53053 GGCACATAGCCTGAATACACC
1 GGCACAAAGCCTG-ATACACC
* *
53074 GGCACAAAGCTTGCT--A--
1 GGCACAAAGCCTGATACACC
* * *
53090 GGCACACAGCCCGAATACACT
1 GGCACAAAGCCTG-ATACACC
* * *
53111 GGCACAAAACCTAATACATC
1 GGCACAAAGCCTGATACACC
* *
53131 GGCACTAAGCTTGATACACC
1 GGCACAAAGCCTGATACACC
53151 GGCACAAAGCCTGATAC
1 GGCACAAAGCCTGATAC
53168 TTAGATGCAA
Statistics
Matches: 69, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
16 10 0.14
17 1 0.01
18 1 0.01
19 1 0.01
20 36 0.52
21 20 0.29
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (20 bp):
GGCACAAAGCCTGATACACC
Found at i:58513 original size:37 final size:37
Alignment explanation
Indices: 58463--58546 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 37
58453 ATATTTGGAC
58463 TTAAATTTTTTAGTC-TCTGCTACTCGTTTTCCTTAAT
1 TTAAATTTTTTAGTCTTC-GCTACTCGTTTTCCTTAAT
* *
58500 TTAAATTTTTTAGTCTTCGTTACTCTTTTTCCTTAAT
1 TTAAATTTTTTAGTCTTCGCTACTCGTTTTCCTTAAT
58537 TGTAACATTT
1 T-TAA-ATTT
58547 CCTATTGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 33 0.79
38 5 0.12
39 4 0.10
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (37 bp):
TTAAATTTTTTAGTCTTCGCTACTCGTTTTCCTTAAT
Found at i:58915 original size:7 final size:7
Alignment explanation
Indices: 58903--58936 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
58893 TCTCCCAGTC
58903 GCAACTT
1 GCAACTT
58910 GCAACTT
1 GCAACTT
58917 GCAACTT
1 GCAACTT
58924 GCAACTT
1 GCAACTT
58931 GCAACT
1 GCAACT
58937 CAACTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (7 bp):
GCAACTT
Found at i:66864 original size:23 final size:25
Alignment explanation
Indices: 66819--66866 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
66809 TCAATTCCTC
**
66819 CAAAAAAAAAAAAACTCTCAAATTA
1 CAAAAAAAAAAAAACTCAAAAATTA
66844 CAAAAAAAAAAAAA-T-AAAAATTA
1 CAAAAAAAAAAAAACTCAAAAATTA
66867 TCAGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (25 bp):
CAAAAAAAAAAAAACTCAAAAATTA
Found at i:70142 original size:9 final size:9
Alignment explanation
Indices: 70128--70165 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
70118 AAATTTTGGA
70128 TTTTTAATT
1 TTTTTAATT
70137 TTTTTAA-T
1 TTTTTAATT
*
70145 TTTTAAATT
1 TTTTTAATT
70154 TTTTTAAATT
1 TTTTT-AATT
70164 TT
1 TT
70166 AAATAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTAATT
Found at i:70148 original size:17 final size:18
Alignment explanation
Indices: 70127--70169 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
70117 TAAATTTTGG
70127 ATTTTT-AATTTTTTT-A
1 ATTTTTAAATTTTTTTAA
70143 ATTTTTAAATTTTTTTAA
1 ATTTTTAAATTTTTTTAA
70161 A-TTTTAAAT
1 ATTTTTAAAT
70170 AGTTTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.24
17 17 0.68
18 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAAATTTTTTTAA
Found at i:70175 original size:18 final size:17
Alignment explanation
Indices: 70127--70176 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
70117 TAAATTTTGG
* *
70127 ATTTTTAATTTTTTTAA
1 ATTTTAAATGTTTTTAA
* *
70144 TTTTTAAATTTTTTTAA
1 ATTTTAAATGTTTTTAA
70161 ATTTTAAATAGTTTTT
1 ATTTTAAAT-GTTTTT
70177 CATATGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTAAATGTTTTTAA
Found at i:70692 original size:18 final size:18
Alignment explanation
Indices: 70662--70698 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
70652 TTTTAAGCTT
70662 TTAATATTTTATATTATG
1 TTAATATTTTATATTATG
70680 TTAAT-TTTATATATTATG
1 TTAATATTT-TATATTATG
70698 T
1 T
70699 AACTTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTAATATTTTATATTATG
Found at i:71554 original size:39 final size:36
Alignment explanation
Indices: 71474--71546 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
71464 GATGACAAAT
71474 ATTCACCAATGGAATCATTTTTAGAAGAAGAAGAAG
1 ATTCACCAATGGAATCATTTTTAGAAGAAGAAGAAG
*
71510 ATTCACCAATGGGATCATTTTTAGAAGAAGAAGAAG
1 ATTCACCAATGGAATCATTTTTAGAAGAAGAAGAAG
71546 A
1 A
71547 AGATTCACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (36 bp):
ATTCACCAATGGAATCATTTTTAGAAGAAGAAGAAG
Found at i:71695 original size:63 final size:67
Alignment explanation
Indices: 71588--71879 Score: 378
Period size: 72 Copynumber: 4.2 Consensus size: 67
71578 GAAGAAGAAG
*
71588 AAGAAGAAGAATATGATGATGATGATGATGATGATAACGACAAAAATTCATCAATGGGATCATCG
1 AAGAAGAAGAAGA-GATGATGATGATGATGATG--AACGACAAAAATTCATCAATGGGATCATCG
71653 TTTTC
63 TTTTC
71658 -AGAAGAAGAAGA-A-GATGATGATGATGATG-ACGACAAAAATTCATCAATGGGATCATCGTTT
1 AAGAAGAAGAAGAGATGATGATGATGATGATGAACGACAAAAATTCATCAATGGGATCATCGTTT
71719 TC
66 TC
71721 AGAAGAAGAAGAAGAAGATGATGATGATGATGATGATAACGACAAAAATTCATCAATGGGATCAT
1 --AAGAAGAAGAAG-AGATGATGATGATGATGATG--AACGACAAAAATTCATCAATGGGATCAT
71786 CGTTTTC
61 CGTTTTC
71793 AGAAGAAGAAGATGATGATGATGATGATGATGATGATGACAACGACAAAAATTCATCAATGGGAT
1 --AAGAAGAAGA--A-GA-GATGATGATGATGATGATG--AACGACAAAAATTCATCAATGGGAT
* *
71858 CACCATTTTC
58 CATCGTTTTC
71868 -AGAAGAAGAAGA
1 AAGAAGAAGAAGA
71880 AGAACACTCA
Statistics
Matches: 205, Mismatches: 4, Indels: 27
0.87 0.02 0.11
Matches are distributed among these distances:
63 34 0.17
66 27 0.13
67 2 0.01
68 1 0.00
69 29 0.14
70 1 0.00
72 55 0.27
74 2 0.01
75 54 0.26
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (67 bp):
AAGAAGAAGAAGAGATGATGATGATGATGATGAACGACAAAAATTCATCAATGGGATCATCGTTT
TC
Found at i:71809 original size:3 final size:3
Alignment explanation
Indices: 71803--71831 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
71793 AGAAGAAGAA
71803 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
71832 CAACGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:71961 original size:3 final size:3
Alignment explanation
Indices: 71953--71979 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
71943 ATCAACACTT
71953 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
71980 AGCGAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:89041 original size:40 final size:40
Alignment explanation
Indices: 88986--89073 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 40
88976 CTAAAAAAGT
* *
88986 AATTTTACTTAGCATAAGCCCGTTTGAAATCTCACTGTCG
1 AATTTTTCTTAGCATAAGCCCGTTTGAAATCTCACTGACG
89026 AATTTTTCTTAGCATAAGCCCGTTTGAAATCTCACTGACG
1 AATTTTTCTTAGCATAAGCCCGTTTGAAATCTCACTGACG
89066 AATTTTTC
1 AATTTTTC
89074 AGCTTTTCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (40 bp):
AATTTTTCTTAGCATAAGCCCGTTTGAAATCTCACTGACG
Found at i:98246 original size:6 final size:6
Alignment explanation
Indices: 98210--98244 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
98200 AGAGAAGAGA
*
98210 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAA AGGGA
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGA
98245 AAAAGGAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:103715 original size:23 final size:22
Alignment explanation
Indices: 103668--103715 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
103658 AGTAAAAATA
* *
103668 TAATTTTATTATTTTAATAGTT
1 TAATTTTATGATTTTAATAGAT
103690 TAATATTTATGATTTTAA-ATGAT
1 TAAT-TTTATGATTTTAATA-GAT
103713 TAA
1 TAA
103716 ATTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
TAATTTTATGATTTTAATAGAT
Found at i:111019 original size:30 final size:29
Alignment explanation
Indices: 110985--111049 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
110975 ATTAATAAAA
*
110985 ATAAAATTACGTTTTAATT-TCTTAAAAATT
1 ATAAAATTACG-ATTAATTAT-TTAAAAATT
**
111015 ATAAAATTTTGATTAATTATTTAAAAATT
1 ATAAAATTACGATTAATTATTTAAAAATT
111044 ATAAAA
1 ATAAAA
111050 ATATTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
ATAAAATTACGATTAATTATTTAAAAATT
Found at i:111590 original size:15 final size:15
Alignment explanation
Indices: 111570--111598 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
111560 TTATAGATTA
111570 AAATATAAATTTATT
1 AAATATAAATTTATT
111585 AAATATAAATTTAT
1 AAATATAAATTTAT
111599 AATTTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATAAATTTATT
Done.