Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012712.1 Kokia drynarioides strain JFW-HI SEQ_127723, 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: 100684
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 160 characters in sequence are not A, C, G, or T
Found at i:4978 original size:28 final size:28
Alignment explanation
Indices: 4934--4988 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4924 TGATCGACTG
* *
4934 ATATTTATCAAATTTTTTATATTTTTAT
1 ATATTTATCAAAATTTTAATATTTTTAT
4962 ATATTTAT-ATAAATTTTAATATTTTTA
1 ATATTTATCA-AAATTTTAATATTTTTA
4989 AATGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTTATCAAAATTTTAATATTTTTAT
Found at i:10793 original size:23 final size:24
Alignment explanation
Indices: 10749--10797 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
10739 TTGGAGAAAC
*
10749 TTTATGTAATTACTTTTAATTAAAT
1 TTTATGCAATTAC-TTTAATTAAAT
10774 TTTATGCAATTA-TTTAATTAAAT
1 TTTATGCAATTACTTTAATTAAAT
10797 T
1 T
10798 AACTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTATGCAATTACTTTAATTAAAT
Found at i:23865 original size:90 final size:88
Alignment explanation
Indices: 23770--23942 Score: 204
Period size: 90 Copynumber: 1.9 Consensus size: 88
23760 ATTATTAGGA
* ** *
23770 ACCAAATTAGAAAAAAAAATAAAGTTT-AGGTACCAAATTGGACCTCAAAAAGTTTAAGTACTAA
1 ACCAAAATAGAAAAAAAAATAAAGTTTGA-GTACCAAATTGGACCAAAAAAAGTTT-A-TACCAA
* *
23834 CTTAAGAAAAAATGTTAAGTTTAAGT
63 ATTAAGAAAAAATGTCAAGTTTAAGT
* *** *
23860 ACCAAAATAGGAAAAAGTGTCAAGTTTGAGTACCAAATTGGACCAAAAAAAGTTTATACCAAATT
1 ACCAAAATAGAAAAAAAAATAAAGTTTGAGTACCAAATTGGACCAAAAAAAGTTTATACCAAATT
*
23925 AAGAAAAAGTGTCAAGTT
66 AAGAAAAAATGTCAAGTT
23943 CAAATATAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
88 23 0.33
89 1 0.01
90 45 0.64
91 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (88 bp):
ACCAAAATAGAAAAAAAAATAAAGTTTGAGTACCAAATTGGACCAAAAAAAGTTTATACCAAATT
AAGAAAAAATGTCAAGTTTAAGT
Found at i:23874 original size:31 final size:31
Alignment explanation
Indices: 23819--23896 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
23809 GGACCTCAAA
* ** *
23819 AAGTTTAAGTACTAACTTAAGAAAAAATGTT
1 AAGTTTAAGTACCAAAATAAGAAAAAATGTC
* *
23850 AAGTTTAAGTACCAAAATAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAAATAAGAAAAAATGTC
*
23881 AAGTTTGAGTACCAAA
1 AAGTTTAAGTACCAAA
23897 TTGGACCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAAATAAGAAAAAATGTC
Found at i:27336 original size:29 final size:29
Alignment explanation
Indices: 27273--27336 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
27263 TTATACACTT
*
27273 GAAATTTAATCCATTTATTTTTATTTTCA
1 GAAATTTAATCCATTTATTTTTAATTTCA
* *
27302 GGAATTTAAT-CTTGTTATTTTTAGATTTCA
1 GAAATTTAATCCAT-TTATTTTTA-ATTTCA
27332 -AAATT
1 GAAATT
27337 CAAGTCCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.07
29 22 0.76
30 5 0.17
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (29 bp):
GAAATTTAATCCATTTATTTTTAATTTCA
Found at i:31515 original size:17 final size:16
Alignment explanation
Indices: 31493--31544 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
31483 TAATTAAAAA
31493 TAAATATAAATATTTTT
1 TAAATA-AAATATTTTT
* *
31510 TAAATAAACT-TTTTA
1 TAAATAAAATATTTTT
*
31525 TAATAAAAAATATTTTT
1 TAA-ATAAAATATTTTT
31542 TAA
1 TAA
31545 TCAAGTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
17 13 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAATAAAATATTTTT
Found at i:32310 original size:55 final size:55
Alignment explanation
Indices: 32249--32357 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
32239 GAGTATGTGC
32249 AATTCTTTTGTTGTATAGCACATAGGCTGTAGGAATATAGTCATGCATAATTTGA
1 AATTCTTTTGTTGTATAGCACATAGGCTGTAGGAATATAGTCATGCATAATTTGA
32304 AATTCTTTTGTTGTATAGCACATAGGCTGTAGGAATATAGTCATGCATAATTTG
1 AATTCTTTTGTTGTATAGCACATAGGCTGTAGGAATATAGTCATGCATAATTTG
32358 CCAAGCTGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (55 bp):
AATTCTTTTGTTGTATAGCACATAGGCTGTAGGAATATAGTCATGCATAATTTGA
Found at i:39476 original size:10 final size:10
Alignment explanation
Indices: 39452--39502 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
39442 AGAAGAGAAT
39452 AAAAAATAAAG
1 AAAAAA-AAAG
39463 -AAAAAAAAG
1 AAAAAAAAAG
39472 AAAAATTAAAAG
1 AAAAA--AAAAG
* *
39484 AACATAAAAG
1 AAAAAAAAAG
39494 AAAAAAAAA
1 AAAAAAAAA
39503 TTACTCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
9 4 0.12
10 21 0.64
12 8 0.24
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:61741 original size:45 final size:47
Alignment explanation
Indices: 61675--61768 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 47
61665 CAATTTGATC
** *
61675 TACTAAATATTTAACTAAATTATATATTATTTATTTTAAATTATTTA
1 TACTAAATATTTAACTAAATTATATAGCATTAATTTTAAATTATTTA
* *
61722 TACT-AAT-TTTAATTAAATTATATAGCATTAATTTTTAATTATTTA
1 TACTAAATATTTAACTAAATTATATAGCATTAATTTTAAATTATTTA
61767 TA
1 TA
61769 TTTAGCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 35 0.83
46 3 0.07
47 4 0.10
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (47 bp):
TACTAAATATTTAACTAAATTATATAGCATTAATTTTAAATTATTTA
Found at i:63019 original size:16 final size:17
Alignment explanation
Indices: 62998--63031 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62988 ATTAATTAAG
62998 TCAATT-AATTAATTTC
1 TCAATTAAATTAATTTC
*
63014 TCAATTAAATTACTTTC
1 TCAATTAAATTAATTTC
63031 T
1 T
63032 AAACCTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TCAATTAAATTAATTTC
Found at i:70370 original size:2 final size:2
Alignment explanation
Indices: 70363--70403 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
70353 TTAAGAGCCA
* *
70363 AG AG AG AG AG GG AG AG AG GG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70404 GGTGTTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:70585 original size:6 final size:6
Alignment explanation
Indices: 70574--70612 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
70564 TTATTTATCA
70574 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
70613 TGCATGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:71974 original size:29 final size:30
Alignment explanation
Indices: 71942--72004 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
71932 AAAAATTATG
* *
71942 AAATTTTAATAAAAAT-ATAAAAAATTCAA
1 AAATTTTAATAAAAATCATAAAAAAATAAA
* * *
71971 AAATTTTTATCAAAATCGTAAAAAAATAAA
1 AAATTTTAATAAAAATCATAAAAAAATAAA
72001 AAAT
1 AAAT
72005 CGTAAACTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATTTTAATAAAAATCATAAAAAAATAAA
Found at i:72016 original size:37 final size:38
Alignment explanation
Indices: 71950--72032 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 38
71940 TGAAATTTTA
* *
71950 ATAAAAATATAAAAAATTCAAAAATTTTTATCA-AAATC
1 ATAAAAAAATAAAAAATTCAAAAACTTTTAT-AGAAATC
* **
71988 GTAAAAAAATAAAAAA-TCGTAAACTTTTATAGAAATC
1 ATAAAAAAATAAAAAATTCAAAAACTTTTATAGAAATC
72025 ATAAAAAA
1 ATAAAAAA
72033 TTATAAATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.03
37 23 0.61
38 14 0.37
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (38 bp):
ATAAAAAAATAAAAAATTCAAAAACTTTTATAGAAATC
Found at i:73249 original size:39 final size:40
Alignment explanation
Indices: 73190--73265 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
73180 CACTAAATGG
73190 ACACATTTTGAAGAGTCACAACCC-TTTCAAATTGGATGA
1 ACACATTTTGAAGAGTCACAACCCTTTTCAAATTGGATGA
* *
73229 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
1 ACACATTTTGAAGAGTCACAACCCTTTTCAAATTGGA
73266 CATACCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 23 0.68
40 11 0.32
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (40 bp):
ACACATTTTGAAGAGTCACAACCCTTTTCAAATTGGATGA
Found at i:73281 original size:39 final size:38
Alignment explanation
Indices: 73190--73282 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
73180 CACTAAATGG
* *
73190 ACACATTTTGAAGAGTCACAACCCTTTCAAATTGGATGA
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GA
* * *
73229 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGA
*
73267 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
73283 ACTTGTCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGA
Found at i:78186 original size:39 final size:38
Alignment explanation
Indices: 78097--78187 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 38
78087 CTCAATGAAC
* * *
78097 ACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGGAT
1 ACCTTTGGAAGAGTCACAACCCTTTCAAATTAGA-GCAT
* *
78136 ACCTTTTGAAGAGTCACAACCCTTTTCATATTAGA-CAT
1 ACCTTTGGAAGAGTCACAACCC-TTTCAAATTAGAGCAT
78174 ACCTCTTGGAAGAG
1 ACCT-TTGGAAGAG
78188 ACTTGTCTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 6 0.13
39 30 0.65
40 10 0.22
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (38 bp):
ACCTTTGGAAGAGTCACAACCCTTTCAAATTAGAGCAT
Found at i:85587 original size:80 final size:79
Alignment explanation
Indices: 85490--85661 Score: 319
Period size: 80 Copynumber: 2.2 Consensus size: 79
85480 AAAAACTTGA
85490 TATAAATTATAAATTGTAAATTCTAAACTCAAACTTTAATCTTGATATGAATCATAAATTCGAAA
1 TATAAATTATAAATTGTAAATTCTAAACTCAAACTTTAATCTTGAT-TGAATCATAAATTCGAAA
85555 CTCTAAATTTTATAT
65 CTCTAAATTTTATAT
*
85570 TATAAATTATAAATTGTAAATTCTAAACTCAAACTTTAATCTTGATTGAATCATAATTTCGAAAC
1 TATAAATTATAAATTGTAAATTCTAAACTCAAACTTTAATCTTGATTGAATCATAAATTCGAAAC
85635 TCTAAATTTTATAT
66 TCTAAATTTTATAT
85649 TATAAATT-TAAAT
1 TATAAATTATAAAT
85662 CTAGAACCTA
Statistics
Matches: 91, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
78 5 0.05
79 40 0.44
80 46 0.51
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (79 bp):
TATAAATTATAAATTGTAAATTCTAAACTCAAACTTTAATCTTGATTGAATCATAAATTCGAAAC
TCTAAATTTTATAT
Found at i:90686 original size:30 final size:30
Alignment explanation
Indices: 90629--90718 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
90619 ATACATATTA
* *
90629 CATTTTCATACCTTGTATCATTCACATTTG
1 CATTATCATACCCTGTATCATTCACATTTG
90659 CA-TATCATACCCTGTAATC-TATCACATTTG
1 CATTATCATACCCTGT-ATCAT-TCACATTTG
* * * *
90689 CATTTTCATACCTTGGAATCATTCATATTT
1 CATTATCATACCCT-GTATCATTCACATTT
90719 TCGCATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
29 12 0.24
30 16 0.33
31 19 0.39
32 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (30 bp):
CATTATCATACCCTGTATCATTCACATTTG
Found at i:90741 original size:60 final size:59
Alignment explanation
Indices: 90629--90752 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
90619 ATACATATTA
*
90629 CATTTTCATACCTTGTATCATTCACATTTGCATATCATACCCTGTAATCTATCACATTT
1 CATTTTCATACCTTGAATCATTCACATTTGCATATCATACCCTGTAATCTATCACATTT
* * **
90688 GCATTTTCATACCTTGGAATCATTCATATTTTCGCAT-TTATACTTTGT-A-CTATCACATTT
1 -CATTTTCATACCTT-GAATCATTCACA-TTT-GCATATCATACCCTGTAATCTATCACATTT
90748 CATTT
1 CATTT
90753 CAATTCAATC
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
59 5 0.09
60 25 0.45
61 11 0.20
62 11 0.20
63 4 0.07
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (59 bp):
CATTTTCATACCTTGAATCATTCACATTTGCATATCATACCCTGTAATCTATCACATTT
Found at i:93242 original size:82 final size:82
Alignment explanation
Indices: 93142--93305 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 82
93132 ACAAGCTCCA
93142 TCAACACAATAAAAGTTTCATCTTCAGCCTCAATAGAACATTTTGACACGTTGGCAATTGATTCT
1 TCAACACAATAAAAGTTTCATCTTCAGCCTCAATAGAACATTTTGACACGTTGGCAATTGATTCT
*
93207 ATCGTAACTCAAGCACG
66 ATCATAACTCAAGCACG
93224 TCAACACAATAAAAGTTTCATCTTCAGCCTCAATAGAACATTTTGACACGTTGGCAATTGATTCT
1 TCAACACAATAAAAGTTTCATCTTCAGCCTCAATAGAACATTTTGACACGTTGGCAATTGATTCT
*
93289 ATCATGACTCAAGCACG
66 ATCATAACTCAAGCACG
93306 ACATATCTGG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (82 bp):
TCAACACAATAAAAGTTTCATCTTCAGCCTCAATAGAACATTTTGACACGTTGGCAATTGATTCT
ATCATAACTCAAGCACG
Done.