Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014540.1 Kokia drynarioides strain JFW-HI SEQ_129579, 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: 18681
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:10752 original size:209 final size:209
Alignment explanation
Indices: 10359--12077 Score: 2334
Period size: 209 Copynumber: 8.2 Consensus size: 209
10349 AGCAATGCAA
10359 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * * * * *
10424 TCTTCAAAATCCCCAGCTTCCTGATGAGATATTAAGAAGAAGATCGAAGCAATAAAATGGTTAGC
66 TCTTC-GAA-CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACC
* * * * * * *
10489 TTCTTGAAGAGATACTA-AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
129 TTCCTGATGAGATAC-AGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
** *
10553 TGAAACAAGCGATGCGG
193 CAAAACAAGTGATGCGG
* * * * *
10570 TCACCTTCTTGATAAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * * * * * *
10635 TCATAGAACCCAAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAACAATAAAGTTGTTACCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * * *
10700 CCTGATGAGATACAAAGAAGTGAACCAGATCCATCTTCCTGATGAGATACAGAGAAGTTGATCAA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
10765 AACAAGTGATGCGG
196 AACAAGTGATGCGG
* * * * * *
10779 TCATCTTCTTGATAAGATACTGAGAAGTAGACCAAATCTACGAAACTAGGCTCCAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* *
10844 TCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * *
10909 CCTGATGAGATACAGATAAGTGAACCAGATCCGTCTTCCTCATGAGACACAGAAAAGTGGATCAA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
10974 AACAAGTGATGCGG
196 AACAAGTGATGCGG
* * * * * *
10988 TCATCTTCCTGATGAGATTCTGAGAAATAGACCAAATCAAAGAAATCAGGCTCAAAGCGAGCGAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * * * *
11053 TCTTCGAACCCCAGCATCCTGACGAGATACTGAGAAGCAGGTCAAAGCAATAAAATGGTCAGCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * * * * * * * **
11118 CTTGATAAGATATTA-AGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
131 CCTGATGAGATA-CAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
* *
11182 AAACAAGTGAGGTGG
195 AAACAAGTGATGCGG
* * * *
11197 TCATCTTCCTGATGAGATACTGAGAAATAGGCCAAATTAATGAAACCAGGTTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * * *
11262 TCATCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* *
11327 CCTGATGAGATACTGAGAAGTGAACCAGATTCGTCTTCCTGAT--GACACAGAGAAGTGGATCAA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
*
11390 AACAAGTGATTCGG
196 AACAAGTGATGCGG
* *
11404 TCATCTTCTTGATGAAATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
*
11469 TCTTCGAACCCCAGCTTCCTGAT-AGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * * * *
11533 CCTGATGAGATACTGACAAGTGAACTAGGTCCGTCTTCCTGATGAGACACAGAGAATTGGATCAA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
11598 AACAAGTGATGCGG
196 AACAAGTGATGCGG
* *
11612 TCATCTTCCTGATGAGATATTGAGAAGTAGACCAAATCAACGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * *
11677 TCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGTGGTTACCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * *
11742 CCAGATGAGATACAGAGAAGTGAACCAGGTCCATCTTCCTGATGAGACACAGAGAAGTGGATCAA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
*
11807 AATAAGTGATGCGG
196 AACAAGTGATGCGG
11821 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
* * * * * **
11886 TATTTGAACCCCAACATCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAGCGGTTACCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
* * * * * *
11951 CTTGATGAGATACAGAGAAGCGAACTAGATTCGTCTTCTTGATGAGACAC-GAAAAAGTGGATCA
131 CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAG-AGAAGTGGATCA
* * *
12015 AAACAAATGATACAG
195 AAACAAGTGATGCGG
* * *
12030 TCATCTTCTTGATGAGAAACTGAGAAGTAGACCAAATCAATGACACCA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
12078 AACCACTGAA
Statistics
Matches: 1335, Mismatches: 166, Indels: 16
0.88 0.11 0.01
Matches are distributed among these distances:
206 79 0.06
207 107 0.08
208 117 0.09
209 966 0.72
210 3 0.00
211 63 0.05
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (209 bp):
TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACCTT
CCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAA
AACAAGTGATGCGG
Found at i:12397 original size:11 final size:11
Alignment explanation
Indices: 12381--12409 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12371 CACTTTTGAT
12381 TTTAAATTAAG
1 TTTAAATTAAG
12392 TTTAAA-TAAG
1 TTTAAATTAAG
12402 TTTAAATT
1 TTTAAATT
12410 TATTTTTAAA
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:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAG
Found at i:12411 original size:6 final size:6
Alignment explanation
Indices: 12381--12511 Score: 101
Period size: 6 Copynumber: 22.7 Consensus size: 6
12371 CACTTTTGAT
* * ** *
12381 TTTAAA -TTAAG TTTAAA --TAAG TTTAAA TTTATT TTTAAA TTTAAC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * ** *
12426 TTT-AT TTTAAA TTTAAA TTTAGA TTTATT TTTAAA TTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** **
12473 TTTATT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
12512 GTTAAATGAA
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
4 3 0.03
5 11 0.12
6 81 0.85
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:12429 original size:18 final size:17
Alignment explanation
Indices: 12402--12511 Score: 104
Period size: 17 Copynumber: 6.6 Consensus size: 17
12392 TTTAAATAAG
12402 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
12420 TTTAACTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
12437 TTTAAATTTAGATTT--A
1 TTTAAATTTA-TTTTAAA
* *
12453 TTT---TTAAATTTAAA
1 TTTAAATTTATTTTAAA
*
12467 TTTAGATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
12485 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
12502 TTTAAATTTA
1 TTTAAATTTA
12512 GTTAAATGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.05
13 3 0.04
14 4 0.05
16 4 0.05
17 35 0.46
18 26 0.34
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:12462 original size:24 final size:24
Alignment explanation
Indices: 12414--12511 Score: 139
Period size: 24 Copynumber: 4.2 Consensus size: 24
12404 TAAATTTATT
12414 TTTAAATTTA-ACTTTA-TTTTAAA
1 TTTAAATTTAGA-TTTATTTTTAAA
12437 TTTAAATTTAGATTTATTTTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
12461 TTTAAATTTAGATTTATTTTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
* **
12485 TTTAAATTT-GTTTTAAATTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
12508 TTTA
1 TTTA
12512 GTTAAATGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 29 0.41
24 41 0.59
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTAAATTTAGATTTATTTTTAAA
Found at i:13231 original size:16 final size:16
Alignment explanation
Indices: 13212--13251 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
13202 ATATTAGGTA
13212 TAATTAATAAATATAT
1 TAATTAATAAATATAT
*
13228 TAATTAATAAATTTAT
1 TAATTAATAAATATAT
*
13244 TAAATAAT
1 TAATTAAT
13252 GTTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAATAAATATAT
Found at i:13904 original size:11 final size:11
Alignment explanation
Indices: 13888--13916 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
13878 CACTTTTGAT
13888 TTTAAATTAAG
1 TTTAAATTAAG
13899 TTTAAA-TAAG
1 TTTAAATTAAG
13909 TTTAAATT
1 TTTAAATT
13917 TATTTTTAAA
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:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAG
Found at i:13918 original size:6 final size:6
Alignment explanation
Indices: 13888--14018 Score: 101
Period size: 6 Copynumber: 22.7 Consensus size: 6
13878 CACTTTTGAT
* * ** *
13888 TTTAAA -TTAAG TTTAAA --TAAG TTTAAA TTTATT TTTAAA TTTAAC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * ** *
13933 TTT-AT TTTAAA TTTAAA TTTAGA TTTATT TTTAAA TTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** **
13980 TTTATT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
14019 GTTAAATGAA
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
4 3 0.03
5 11 0.12
6 81 0.85
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:13936 original size:18 final size:17
Alignment explanation
Indices: 13909--14018 Score: 104
Period size: 17 Copynumber: 6.6 Consensus size: 17
13899 TTTAAATAAG
13909 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
13927 TTTAACTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
13944 TTTAAATTTAGATTT--A
1 TTTAAATTTA-TTTTAAA
* *
13960 TTT---TTAAATTTAAA
1 TTTAAATTTATTTTAAA
*
13974 TTTAGATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
13992 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
14009 TTTAAATTTA
1 TTTAAATTTA
14019 GTTAAATGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.05
13 3 0.04
14 4 0.05
16 4 0.05
17 35 0.46
18 26 0.34
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13969 original size:24 final size:24
Alignment explanation
Indices: 13921--14018 Score: 139
Period size: 24 Copynumber: 4.2 Consensus size: 24
13911 TAAATTTATT
13921 TTTAAATTTA-ACTTTA-TTTTAAA
1 TTTAAATTTAGA-TTTATTTTTAAA
13944 TTTAAATTTAGATTTATTTTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
13968 TTTAAATTTAGATTTATTTTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
* **
13992 TTTAAATTT-GTTTTAAATTTAAA
1 TTTAAATTTAGATTTATTTTTAAA
14015 TTTA
1 TTTA
14019 GTTAAATGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 29 0.41
24 41 0.59
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTAAATTTAGATTTATTTTTAAA
Found at i:14738 original size:16 final size:16
Alignment explanation
Indices: 14719--14758 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
14709 ATATTAGGTA
14719 TAATTAATAAATATAT
1 TAATTAATAAATATAT
*
14735 TAATTAATAAATTTAT
1 TAATTAATAAATATAT
*
14751 TAAATAAT
1 TAATTAAT
14759 GTTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAATAAATATAT
Found at i:15365 original size:27 final size:28
Alignment explanation
Indices: 15322--15376 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
15312 ATCTAGAGAT
*
15322 AAAGAAACAGGAGGAAGCAAAA-AAGAA
1 AAAGAAACAGGAAGAAGCAAAAGAAGAA
15349 AAAGAAAGCA-GAAGAAGCAAAAGAAGAA
1 AAAGAAA-CAGGAAGAAGCAAAAGAAGAA
15377 GCAAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.67, C:0.07, G:0.25, T:0.00
Consensus pattern (28 bp):
AAAGAAACAGGAAGAAGCAAAAGAAGAA
Found at i:15388 original size:12 final size:13
Alignment explanation
Indices: 15335--15396 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
15325 GAAACAGGAG
15335 GAAGCAAAAAAGAA
1 GAAGC-AAAAAGAA
* *
15349 AAAG-AAAGCAGAA
1 GAAGCAAA-AAGAA
15362 GAAGC-AAAAGAA
1 GAAGCAAAAAGAA
15374 GAAGCAAAAAG-A
1 GAAGCAAAAAGAA
*
15386 GAAGAAAAAAG
1 GAAGCAAAAAG
15397 CCTTGGCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 23 0.57
13 14 0.35
14 3 0.08
ACGTcount: A:0.69, C:0.06, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGCAAAAAGAA
Done.