Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015035.1 Kokia drynarioides strain JFW-HI SEQ_130079, 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: 108629
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 461 characters in sequence are not A, C, G, or T
Found at i:1073 original size:22 final size:22
Alignment explanation
Indices: 1016--1095 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
1006 GCTGGGGAAA
*
1016 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
1038 CCGGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
1061 CAGTAGGCGCACATAGAGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
1084 CAGTAGGCACAC
1 CAGTAGGCACAC
1096 GAAGTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 15 0.31
23 34 0.69
ACGTcount: A:0.36, C:0.28, G:0.24, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:1110 original size:23 final size:22
Alignment explanation
Indices: 1013--1111 Score: 92
Period size: 23 Copynumber: 4.4 Consensus size: 22
1003 AGTGCTGGGG
*
1013 AAACAGTAAGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
* *
1035 AATCCGGTAGGCACACACAGTGC
1 AA-ACAGTAGGCACACACAGTGC
* * * *
1058 AATCAGTAGGCGCACATAGAGC
1 AAACAGTAGGCACACACAGTGC
1080 AAATCAGTAGGCACACGA-AGTGC
1 AAA-CAGTAGGCACAC-ACAGTGC
1103 GAAACAGTA
1 -AAACAGTA
1112 AGCGCTAGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
22 19 0.31
23 39 0.63
24 4 0.06
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:6558 original size:19 final size:20
Alignment explanation
Indices: 6518--6580 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
6508 TTAAATATAA
*
6518 ATTTTAAATATTTATAAA-T
1 ATTTTAAATATTTAAAAATT
*
6537 ATTTTGAAT-TTTAAAAATT
1 ATTTTAAATATTTAAAAATT
* *
6556 ATTTTAAATCTTTGAAAATT
1 ATTTTAAATATTTAAAAATT
6576 ATTTT
1 ATTTT
6581 TATTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 7 0.18
19 17 0.45
20 14 0.37
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTTAAATATTTAAAAATT
Found at i:6888 original size:10 final size:11
Alignment explanation
Indices: 6870--6898 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
6860 TGTCATTTCG
6870 TTATTATTTTA
1 TTATTATTTTA
6881 TT-TTATTTTA
1 TTATTATTTTA
6891 TTATTATT
1 TTATTATT
6899 GTTTGGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:7566 original size:103 final size:103
Alignment explanation
Indices: 7387--7578 Score: 384
Period size: 103 Copynumber: 1.9 Consensus size: 103
7377 AGACTCCTAA
7387 AAGACAAGAAAGTAATAGTTGAGAGTGAGAGTAGGTTGCAGGTGCAGCTGTTGCTGATAGCTCAG
1 AAGACAAGAAAGTAATAGTTGAGAGTGAGAGTAGGTTGCAGGTGCAGCTGTTGCTGATAGCTCAG
7452 TGCAAACACCCACGCTCTGGCTTTAGCATGCGATTGAG
66 TGCAAACACCCACGCTCTGGCTTTAGCATGCGATTGAG
7490 AAGACAAGAAAGTAATAGTTGAGAGTGAGAGTAGGTTGCAGGTGCAGCTGTTGCTGATAGCTCAG
1 AAGACAAGAAAGTAATAGTTGAGAGTGAGAGTAGGTTGCAGGTGCAGCTGTTGCTGATAGCTCAG
7555 TGCAAACACCCACGCTCTGGCTTT
66 TGCAAACACCCACGCTCTGGCTTT
7579 GATCCGTAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (103 bp):
AAGACAAGAAAGTAATAGTTGAGAGTGAGAGTAGGTTGCAGGTGCAGCTGTTGCTGATAGCTCAG
TGCAAACACCCACGCTCTGGCTTTAGCATGCGATTGAG
Found at i:41030 original size:18 final size:19
Alignment explanation
Indices: 40981--41019 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40971 ATTTAAAATG
40981 AAAATTGCTTTTAGCATAT
1 AAAATTGCTTTTAGCATAT
41000 AAAATTGCTTTTAGCATAT
1 AAAATTGCTTTTAGCATAT
41019 A
1 A
41020 CTTTGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
AAAATTGCTTTTAGCATAT
Found at i:44091 original size:32 final size:30
Alignment explanation
Indices: 44034--44093 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
44024 ACTTTGTCCC
**
44034 TTTAAAAATGATAAAATTTTGATTTAATAT
1 TTTAAAAATGATAAAATTTCAATTTAATAT
*
44064 TTTAAAAATTATAAAAAATTTCAATTTAAT
1 TTTAAAAATGAT--AAAATTTCAATTTAAT
44094 TTCGACCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.44
32 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTAAAAATGATAAAATTTCAATTTAATAT
Found at i:47078 original size:21 final size:21
Alignment explanation
Indices: 47054--47101 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
47044 CGCCGCCGTT
*
47054 GCCACCTTTTCCACCACTTCC
1 GCCACCGTTTCCACCACTTCC
*
47075 GCCACCGTTTCCACCCCTTCC
1 GCCACCGTTTCCACCACTTCC
*
47096 ACCACC
1 GCCACC
47102 ATCTCTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.56, G:0.06, T:0.23
Consensus pattern (21 bp):
GCCACCGTTTCCACCACTTCC
Found at i:47083 original size:30 final size:30
Alignment explanation
Indices: 47042--47100 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
47032 TGATACTTTC
* **
47042 TCCGCCGCCGTTGCCACCTTTTCCACCACT
1 TCCGCCACCGTTGCCACCCCTTCCACCACT
*
47072 TCCGCCACCGTTTCCACCCCTTCCACCAC
1 TCCGCCACCGTTGCCACCCCTTCCACCAC
47101 CATCTCTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.54, G:0.10, T:0.24
Consensus pattern (30 bp):
TCCGCCACCGTTGCCACCCCTTCCACCACT
Found at i:48323 original size:15 final size:15
Alignment explanation
Indices: 48303--48332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48293 CACGCCAAGG
*
48303 GATGATGGTGATGGT
1 GATGATGATGATGGT
48318 GATGATGATGATGGT
1 GATGATGATGATGGT
48333 TTTTCACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (15 bp):
GATGATGATGATGGT
Found at i:50968 original size:16 final size:17
Alignment explanation
Indices: 50942--50973 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
50932 TCAGATTAGT
50942 TTTTATTTAAAAATATA
1 TTTTATTTAAAAATATA
50959 TTTT-TTTAAAAATAT
1 TTTTATTTAAAAATAT
50974 GATACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATTTAAAAATATA
Found at i:52581 original size:69 final size:69
Alignment explanation
Indices: 52470--52609 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
52460 CCTGGATTAG
52470 GAGTTAGATTATATTTTATCTCTTTCATCTAAAAATTATTATATTAGTCTCTGTACGTTAGATCA
1 GAGTTAGATTATATTTTATCTCTTTCATCTAAAAATTATTATATTAGTCTCTGTACGTTAGATCA
52535 TATA
66 TATA
52539 GAGTTAGATTATATTTTATCTCTTTCATCTAAAAATTATTATATTAGTCTCTGTACGTTAGATCA
1 GAGTTAGATTATATTTTATCTCTTTCATCTAAAAATTATTATATTAGTCTCTGTACGTTAGATCA
52604 TATA
66 TATA
52608 GA
1 GA
52610 AAATTGATAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (69 bp):
GAGTTAGATTATATTTTATCTCTTTCATCTAAAAATTATTATATTAGTCTCTGTACGTTAGATCA
TATA
Found at i:54116 original size:3 final size:3
Alignment explanation
Indices: 54108--54135 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54098 CAGTAGAAAA
54108 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
54136 GAAATCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55378 original size:118 final size:118
Alignment explanation
Indices: 55170--55403 Score: 441
Period size: 118 Copynumber: 2.0 Consensus size: 118
55160 GGCCTATAAC
*
55170 CGAAAACAATAGTGGGTAATTAATTTGTCACTTTTCGATAATTTTAGTAACTAATTTGTTATTTT
1 CGAAAACAATAGTGGGTAATTAATTTGTCACTTTTCGATAATTTTAGTAACTAATTTATTATTTT
*
55235 TTTTAAAGTTGAGTGGCAGAGTTGAAAGATAAGTGACTATGACTGACTGTTAT
66 TTTTAAAGTTGAGTGGCAGAATTGAAAGATAAGTGACTATGACTGACTGTTAT
*
55288 CGAAAACAATAGTGGGTAATTAATTTGTCACTTTTCGATAATTTTAGTGACTAATTTATTATTTT
1 CGAAAACAATAGTGGGTAATTAATTTGTCACTTTTCGATAATTTTAGTAACTAATTTATTATTTT
55353 TTTTAAAGTTGAGTGGCAGAATTGAAAGATAAGTGACTATGACTGACTGTT
66 TTTTAAAGTTGAGTGGCAGAATTGAAAGATAAGTGACTATGACTGACTGTT
55404 GGTGCACTTT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (118 bp):
CGAAAACAATAGTGGGTAATTAATTTGTCACTTTTCGATAATTTTAGTAACTAATTTATTATTTT
TTTTAAAGTTGAGTGGCAGAATTGAAAGATAAGTGACTATGACTGACTGTTAT
Found at i:56279 original size:18 final size:16
Alignment explanation
Indices: 56256--56297 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
56246 TATAATAATA
56256 TTAATAATTAATAAATGT
1 TTAATAATTAATAAA--T
*
56274 TTAAT-ATTAATGAAT
1 TTAATAATTAATAAAT
56289 TTAATAATT
1 TTAATAATT
56298 CTAAGTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 8 0.36
18 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (16 bp):
TTAATAATTAATAAAT
Found at i:58027 original size:16 final size:16
Alignment explanation
Indices: 58006--58038 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
57996 GAGGTTTGGT
58006 AAAAAAAAAT-CCAAA
1 AAAAAAAAATCCCAAA
58021 AAAAAAAAATCCCAAA
1 AAAAAAAAATCCCAAA
58037 AA
1 AA
58039 CAGTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAAAAAATCCCAAA
Found at i:68186 original size:14 final size:13
Alignment explanation
Indices: 68155--68222 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 13
68145 AACTACTTAG
68155 AGTTTAGAGTTT-A
1 AGTTTAGA-TTTGA
68168 GAGTTTAAGATTTGA
1 -AGTTT-AGATTTGA
* *
68183 AGTTT-GAATTCA
1 AGTTTAGATTTGA
68195 AGGTTTAGATTTTGA
1 A-GTTTAGA-TTTGA
68210 AGTTTGAGATTTG
1 AGTTT-AGATTTG
68223 GATTCGAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.14
13 4 0.09
14 23 0.52
15 11 0.25
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.44
Consensus pattern (13 bp):
AGTTTAGATTTGA
Found at i:71649 original size:28 final size:31
Alignment explanation
Indices: 71596--71655 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
71586 ATATCATATT
71596 TGATACTTCTACTTTCATAAAATGTTCAATG
1 TGATACTTCTACTTTCATAAAATGTTCAATG
* *
71627 TGATACTTGTA-TTT-A-AAAATGTTTAATG
1 TGATACTTCTACTTTCATAAAATGTTCAATG
71655 T
1 T
71656 AGCTGAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 3 0.11
31 10 0.37
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (31 bp):
TGATACTTCTACTTTCATAAAATGTTCAATG
Found at i:78988 original size:15 final size:15
Alignment explanation
Indices: 78968--78999 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
78958 TTGAGGAGTT
*
78968 GGTTTTGGTGGTGGA
1 GGTTTTGATGGTGGA
78983 GGTTTTGATGGTGGA
1 GGTTTTGATGGTGGA
78998 GG
1 GG
79000 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.53, T:0.38
Consensus pattern (15 bp):
GGTTTTGATGGTGGA
Found at i:79254 original size:15 final size:15
Alignment explanation
Indices: 79234--79265 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
79224 TAAAAATAAT
*
79234 CCTCCACCATCAAAA
1 CCTCCACCACCAAAA
79249 CCTCCACCACCAAAA
1 CCTCCACCACCAAAA
79264 CC
1 CC
79266 AACTCCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.53, G:0.00, T:0.09
Consensus pattern (15 bp):
CCTCCACCACCAAAA
Found at i:85671 original size:40 final size:40
Alignment explanation
Indices: 85627--85708 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
85617 CTTAAACAAA
*
85627 TATAAAGTATACTAATATTATATTTAAACTCGACCCAATC
1 TATAAAATATACTAATATTATATTTAAACTCGACCCAATC
85667 TATAAAATATACTAATATTATATTTAAACTCGACCCAATC
1 TATAAAATATACTAATATTATATTTAAACTCGACCCAATC
85707 TA
1 TA
85709 ACTTATGAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (40 bp):
TATAAAATATACTAATATTATATTTAAACTCGACCCAATC
Found at i:85745 original size:8 final size:8
Alignment explanation
Indices: 85732--85760 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
85722 TCTACCCTCA
85732 CCCTCTCT
1 CCCTCTCT
85740 CCCTCTCT
1 CCCTCTCT
85748 CCCTCTCT
1 CCCTCTCT
85756 CCCTC
1 CCCTC
85761 ATATAGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (8 bp):
CCCTCTCT
Found at i:92232 original size:15 final size:15
Alignment explanation
Indices: 92208--92239 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
92198 TGTGATACGA
*
92208 AAATACATAAAAAAT
1 AAATAAATAAAAAAT
92223 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
92238 AA
1 AA
92240 GAAAACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:98132 original size:17 final size:17
Alignment explanation
Indices: 98112--98147 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
98102 CCACAATTTT
98112 CTTAACATAGAGTGGTC
1 CTTAACATAGAGTGGTC
98129 CTTAACATAGAGTGGTC
1 CTTAACATAGAGTGGTC
98146 CT
1 CT
98148 AAAAGGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (17 bp):
CTTAACATAGAGTGGTC
Found at i:99597 original size:14 final size:15
Alignment explanation
Indices: 99557--99597 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
99547 TCAAAAGTAC
99557 GTTTCTAACAAAATAT
1 GTTT-TAACAAAATAT
*
99573 GTTTTTA-AAAATAT
1 GTTTTAACAAAATAT
99587 -TTTTAACAAAA
1 GTTTTAACAAAA
99598 AATAGGAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 11 0.50
15 2 0.09
16 4 0.18
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (15 bp):
GTTTTAACAAAATAT
Done.