Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014549.1 Kokia drynarioides strain JFW-HI SEQ_129588, 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: 16296
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:440 original size:29 final size:30
Alignment explanation
Indices: 394--629 Score: 221
Period size: 30 Copynumber: 7.9 Consensus size: 30
384 CCCAAGAGGT
* ** *
394 CCTTAAGCTTTTTAAAAATTACATTTTGAC
1 CCTTAAACTTTTCCAAAATCACATTTTGAC
* * * *
424 CCTTAAA-TTTTTCAAAATCATATTCT-AA
1 CCTTAAACTTTTCCAAAATCACATTTTGAC
* *
452 CCTCTAAATTTTTCCAAAATCACATTTTAAC
1 CCT-TAAACTTTTCCAAAATCACATTTTGAC
* ** *
483 CCCTAAACTTTTCCAAAATTGCATTTTAAC
1 CCTTAAACTTTTCCAAAATCACATTTTGAC
* *
513 CC-CAAACTTTTCCAAAATTACATTTTGAC
1 CCTTAAACTTTTCCAAAATCACATTTTGAC
542 ACC-TAAA-TTTTCCAAAAATCACATTTTGAC
1 -CCTTAAACTTTTCC-AAAATCACATTTTGAC
* **
572 ACCTCAAACTTTTTGAAAATCACATTTTGAC
1 -CCTTAAACTTTTCCAAAATCACATTTTGAC
*
603 CCTTAAACTTTTCCAAAATTACATTTT
1 CCTTAAACTTTTCCAAAATCACATTTT
630 CACCATAAAT
Statistics
Matches: 173, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.02
29 49 0.28
30 94 0.54
31 22 0.13
32 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
CCTTAAACTTTTCCAAAATCACATTTTGAC
Found at i:495 original size:59 final size:58
Alignment explanation
Indices: 408--621 Score: 220
Period size: 59 Copynumber: 3.6 Consensus size: 58
398 AAGCTTTTTA
* * *
408 AAAATTACATTTTGACCCTTAAA-TTTTTCAAAATCATATTCTAACCTCTAAATTTTTCC
1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAATCATATT-TAACCTC-AAATTTTTCC
* * *
467 AAAATCACATTTTAACCCCTAAACTTTTCCAAAATTGCAT-TTTAACCCCAAACTTTTCC
1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAA-T-CATATTTAACCTCAAATTTTTCC
* * * *
526 AAAATTACATTTTGACACCTAAA-TTTTCCAAAAATCACATTTTGACACCTCAAACTTTTT-G
1 AAAATCACATTTTGACCCCTAAACTTTTCC-AAAATCATA-TTT-A-ACCTCAAA-TTTTTCC
*
587 AAAATCACATTTTGACCCTTAAACTTTTCCAAAAT
1 AAAATCACATTTTGACCCCTAAACTTTTCCAAAAT
622 TACATTTTCA
Statistics
Matches: 129, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
57 2 0.02
58 7 0.05
59 56 0.43
60 16 0.12
61 35 0.27
62 13 0.10
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATCACATTTTGACCCCTAAACTTTTCCAAAATCATATTTAACCTCAAATTTTTCC
Found at i:5953 original size:13 final size:12
Alignment explanation
Indices: 5922--5952 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5912 AATCTCACCC
*
5922 AAAAAAATGAAA
1 AAAAAAAGGAAA
5934 AAAAAAAGGAAA
1 AAAAAAAGGAAA
5946 AAAAAAA
1 AAAAAAA
5953 ANNNNNNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAAAGGAAA
Found at i:7333 original size:90 final size:91
Alignment explanation
Indices: 7168--7344 Score: 259
Period size: 92 Copynumber: 2.0 Consensus size: 91
7158 AAGGAGAAAT
* * *
7168 AGATTGAAGCCGCAAAGGCGAATCTCAAAACAGTAAAGGGCTAGATTGAAGCTGCAAAGGTGAAT
1 AGATTAAAGCCGCAAAAGCGAATCTCAAAACAGTAAAGGGCTAGATTGAAACTGCAAAGGTGAAT
*
7233 CTTATATCCCTAAAGTTAAAAAGAAGA
66 CTTACATCCCT-AAGTTAAAAAGAAGA
* * *
7260 AGATTAAAGCCGTAAAAGCGAATCTCAAAGCTGTAAAGGG-T-GATTGAAACTGCAAAGGTGAAT
1 AGATTAAAGCCGCAAAAGCGAATCTCAAAACAGTAAAGGGCTAGATTGAAACTGCAAAGGTGAAT
*
7323 CTTACATCCCTAAGTTGAAAAG
66 CTTACATCCCTAAGTTAAAAAG
7345 GAGCAAATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
89 10 0.13
90 31 0.40
91 1 0.01
92 35 0.45
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (91 bp):
AGATTAAAGCCGCAAAAGCGAATCTCAAAACAGTAAAGGGCTAGATTGAAACTGCAAAGGTGAAT
CTTACATCCCTAAGTTAAAAAGAAGA
Found at i:8413 original size:21 final size:21
Alignment explanation
Indices: 8389--8440 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
8379 TGAGACAATA
*
8389 CTACCGATACAAG-TATGACTT
1 CTACCGATACAAGCCATG-CTT
* *
8410 CTACCGAAACATGCCATGCTT
1 CTACCGATACAAGCCATGCTT
8431 CTACCGATAC
1 CTACCGATAC
8441 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGCCATGCTT
Found at i:9252 original size:36 final size:36
Alignment explanation
Indices: 9154--9253 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
9144 CAATATTCGA
* * * * *
9154 TTTACTCTCTATTGTCCCAAAGGTCAAGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGACGCTCAT
*
9190 TTTACTCCCTGTTGACGCAAAGGTCATGACGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGACGCTCAT
*
9226 TTTACTCCTTGTTGACCCAAAGGTCATG
1 TTTACTCCCTGTTGACCCAAAGGTCATG
9254 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (36 bp):
TTTACTCCCTGTTGACCCAAAGGTCATGACGCTCAT
Found at i:11441 original size:85 final size:85
Alignment explanation
Indices: 11298--11464 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
11288 CAAACCCTAT
* * *
11298 CTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCATATTCCTGATGAGATACA
* *
11363 GAGAAGTGGACCAAATCCGC
66 AAGAAGTAGACCAAATCCGC
* * * * * *
11383 CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATATTCTTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCATATTCCTGATGAGATACA
11448 AAGAAGTAGACCAAATC
66 AAGAAGTAGACCAAATC
11465 AACGAAGCGA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCATATTCCTGATGAGATACA
AAGAAGTAGACCAAATCCGC
Found at i:11622 original size:208 final size:208
Alignment explanation
Indices: 11252--11991 Score: 913
Period size: 208 Copynumber: 3.6 Consensus size: 208
11242 GACTGTTACA
** * * *
11252 AAATCAATGAAATGAAACTCAATACGAATGAGACTTCAAACCCTATCTTCCTGATGAGATATAGA
1 AAATCAATGAAGCGAAACTCAATACGAATAAGACTTCAAACCCCATCTTCCTGATGAGATACAGA
* * *
11317 GAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCG
66 GAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCCG
* *
11382 CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATATTCTTGATGAGATAC
131 CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATAC
*
11447 AAAGAAGTAGACC
196 AGAGAAGTAGACC
* *
11460 AAATCAACGAAGCGAAACTCAATACGAATAAGACTTCAAACCCCATCTTCTTGATGAGATACAGA
1 AAATCAATGAAGCGAAACTCAATACGAATAAGACTTCAAACCCCATCTTCCTGATGAGATACAGA
* * ** ***
11525 GAAGTGGGTCAAAGCAATAAAGC-AGTTATCTTTCAAATTTTATACAGAGAAGTAGATCAAATCC
66 GAAGTGGGTCAAAGCAATAAAGCGA-TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCC
* * * * * * *
11589 GCCTTCTTGATGAGATACAAATAAGTAGATTAAATCAATAAAGTGGTCATCTTCCTAATGAGATA
130 GCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATA
* *
11654 CAGATAAGTAAACC
195 CAGAGAAGTAGACC
* * ** *
11668 AAATCGATGAAGCGAAGCTCAATGTGAAT-GGA--T-AAACCCCATCTTCCTGATGAGATACAGA
1 AAATCAATGAAGCGAAACTCAATACGAATAAGACTTCAAACCCCATCTTCCTGATGAGATACAGA
* *
11729 GAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATTCA
66 GAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCCG
* * *
11794 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCGTCTTCCTGTTGAGATAC
131 CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATAC
11859 AGAGAAGTAGACC
196 AGAGAAGTAGACC
* * * * * *
11872 AAATCAAATGTAGC-AAAGTTCAATTCGAGAGAA-ACTTCAAACCTCTATCTTTCTGATGAGATA
1 AAATC-AATGAAGCGAAA-CTCAATACGA-ATAAGACTTCAAACC-CCATCTTCCTGATGAGATA
* * * *
11935 CAGAGAAGTGGGTCGAAA-CAATAAAGC-AGCTATCTTCTTGGTGAGATACAAAGAAGT
62 CAGAGAAGTGGGTC-AAAGCAATAAAGCGATC-ATCTTCCTGATGAGATACAGAGAAGT
11992 GGACCAAGAG
Statistics
Matches: 449, Mismatches: 71, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
204 154 0.34
205 15 0.03
206 2 0.00
207 3 0.01
208 202 0.45
209 7 0.02
210 63 0.14
211 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (208 bp):
AAATCAATGAAGCGAAACTCAATACGAATAAGACTTCAAACCCCATCTTCCTGATGAGATACAGA
GAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCCG
CCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACC
Found at i:11759 original size:48 final size:45
Alignment explanation
Indices: 11707--11866 Score: 165
Period size: 48 Copynumber: 3.6 Consensus size: 45
11697 GGATAAACCC
*
11707 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAA-CAAT-AAGCG-T
*
11755 CATCTTCCTGATGAGATACAGAGAAGTAGATC--A-AAT-----T
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAATAAGCGT
*
11792 CATCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAA-CAAT-AAGC-GT
* *
11840 CGTCTTCCTGTTGAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAGAGAAGT
11867 AGACCAAATC
Statistics
Matches: 95, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
37 31 0.33
39 1 0.01
41 3 0.03
44 3 0.03
46 1 0.01
48 56 0.59
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (45 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAATAAGCGT
Found at i:11804 original size:37 final size:37
Alignment explanation
Indices: 11754--11827 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
11744 AATAAAGCGA
11754 TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAAT
1 TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAAT
* *
11791 TCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAT
1 TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAAT
11828 CAATGAAGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (37 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAAT
Found at i:11855 original size:85 final size:85
Alignment explanation
Indices: 11707--11875 Score: 266
Period size: 85 Copynumber: 2.0 Consensus size: 85
11697 GGATAAACCC
*
11707 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTGATGAGAT
*
11772 ACAGAGAAGTAGATCAAATT
66 ACAGAGAAGTAGACCAAATT
* * * * * *
11792 CATCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCGTCTTCCTGTTGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTGATGAGAT
11857 ACAGAGAAGTAGACCAAAT
66 ACAGAGAAGTAGACCAAAT
11876 CAAATGTAGC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (85 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCCTGATGAGAT
ACAGAGAAGTAGACCAAATT
Found at i:13585 original size:29 final size:29
Alignment explanation
Indices: 13517--13675 Score: 194
Period size: 29 Copynumber: 5.3 Consensus size: 29
13507 GGTCCCTTAA
13517 TTTCTCAAAATCACATTTTGACCCCTAAACT
1 TTTCT-AAAATCACATTTTGACCCC-AAACT
*
13548 TTTCTAAAATTACATTTTGACCCCAAACT
1 TTTCTAAAATCACATTTTGACCCCAAACT
* * *
13577 TTTCTAAAATTACATTTTAACCCCAAAAT
1 TTTCTAAAATCACATTTTGACCCCAAACT
*
13606 TTTCCAAATATCACATTTTGACCCCAAAC-
1 TTTCTAAA-ATCACATTTTGACCCCAAACT
* **
13635 TTTCTAAAAATCACATTTTAACCTTAAAACT
1 TTTCT-AAAATCACATTTTGACC-CCAAACT
13666 TTTCTAAAAT
1 TTTCTAAAAT
13676 TTCATTTAAC
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
29 56 0.50
30 47 0.42
31 10 0.09
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
TTTCTAAAATCACATTTTGACCCCAAACT
Found at i:13682 original size:59 final size:59
Alignment explanation
Indices: 13517--13682 Score: 212
Period size: 59 Copynumber: 2.8 Consensus size: 59
13507 GGTCCCTTAA
*
13517 TTTCTCAAAATCACATTTTGACCCCT-AAACTTTTCTAAAATTACATTTTGACCCCAAACT
1 TTTCT-AAAATCACATTTT-AACCCTAAAACTTTTCTAAAATTACATTTTGACCCCAAACT
* * * *
13577 TTTCTAAAATTACATTTTAACCCCAAAA-TTTTCCAAATATCACATTTTGACCCCAAAC-
1 TTTCTAAAATCACATTTTAACCCTAAAACTTTTCTAAA-ATTACATTTTGACCCCAAACT
* *
13635 TTTCTAAAAATCACATTTTAACCTTAAAACTTTTCTAAAATTTCATTT
1 TTTCT-AAAATCACATTTTAACCCTAAAACTTTTCTAAAATTACATTT
13683 AACCCTAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
58 17 0.19
59 61 0.67
60 13 0.14
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (59 bp):
TTTCTAAAATCACATTTTAACCCTAAAACTTTTCTAAAATTACATTTTGACCCCAAACT
Found at i:15226 original size:11 final size:10
Alignment explanation
Indices: 15173--15225 Score: 58
Period size: 9 Copynumber: 5.6 Consensus size: 10
15163 TTTAAAATTT
*
15173 TAAAAAAATA
1 TAAAAATATA
15183 TAAAAAT-TA
1 TAAAAATATA
* *
15192 TAACATTAT-
1 TAAAAATATA
15201 TAAAAATATA
1 TAAAAATATA
15211 T-AAAATATA
1 TAAAAATATA
15220 TAAAAA
1 TAAAAA
15226 AAAAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 23 0.66
10 12 0.34
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAATATA
Found at i:15537 original size:20 final size:20
Alignment explanation
Indices: 15514--15551 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15504 TTCAAAACTA
*
15514 AATTAAAACCTCATTAATGG
1 AATTAAAACCTAATTAATGG
15534 AATTAAAACCTAATTAAT
1 AATTAAAACCTAATTAAT
15552 TAGTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (20 bp):
AATTAAAACCTAATTAATGG
Done.