Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011939.1 Kokia drynarioides strain JFW-HI SEQ_126937, 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: 26629
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:1488 original size:9 final size:9
Alignment explanation
Indices: 1467--1499 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1457 CAAAATAAAT
1467 ATTAATT-A
1 ATTAATTAA
1475 ATTAATTAA
1 ATTAATTAA
*
1484 ATTAACTAA
1 ATTAATTAA
1493 ATTAATT
1 ATTAATT
1500 TTCCAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTAATTAA
Found at i:14802 original size:197 final size:197
Alignment explanation
Indices: 14467--14860 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
14457 TCAAAACACT
14467 ACAGAACTCAGAGAAAAAAACATCATATTCTTGCTGAAAATCACAATGCCATTGATTTACAAACC
1 ACAGAACTCAGAGAAAAAAACATCATATTCTTGCTGAAAATCACAATGCCATTGATTTACAAACC
14532 GAAAGGTTCAAACAAATGCACAAGTATACCAAGCTCTCAACGAGAAATTTAAAGCAAGGGTATCC
66 GAAAGGTTCAAACAAATGCACAAGTATACCAAGCTCTCAACGAGAAATTTAAAGCAAGGGTATCC
14597 ACAAACCGATCACAAATACCATCTATGCAGTCAGGCATCAAACGCTAACTAAGTTAGAAGCATGC
131 ACAAACCGATCACAAATACCATCTATGCAGTCAGGCATCAAACGCTAACTAAGTTAGAAGCATGC
14662 GA
196 GA
14664 ACAGAACTCAGAGAAAAAAACATCATATTCTTGCTGAAAATCACAATGCCATTGATTTACAAACC
1 ACAGAACTCAGAGAAAAAAACATCATATTCTTGCTGAAAATCACAATGCCATTGATTTACAAACC
14729 GAAAGGTTCAAACAAATGCACAAGTATACCAAGCTCTCAACGAGAAATTTAAAGCAAGGGTATCC
66 GAAAGGTTCAAACAAATGCACAAGTATACCAAGCTCTCAACGAGAAATTTAAAGCAAGGGTATCC
14794 ACAAACCGATCACAAATACCATCTATGCAGTCAGGCATCAAACGCTAACTAAGTTAGAAGCATGC
131 ACAAACCGATCACAAATACCATCTATGCAGTCAGGCATCAAACGCTAACTAAGTTAGAAGCATGC
14859 GA
196 GA
14861 CATAGGTGAC
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (197 bp):
ACAGAACTCAGAGAAAAAAACATCATATTCTTGCTGAAAATCACAATGCCATTGATTTACAAACC
GAAAGGTTCAAACAAATGCACAAGTATACCAAGCTCTCAACGAGAAATTTAAAGCAAGGGTATCC
ACAAACCGATCACAAATACCATCTATGCAGTCAGGCATCAAACGCTAACTAAGTTAGAAGCATGC
GA
Found at i:15631 original size:24 final size:25
Alignment explanation
Indices: 15597--15643 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
15587 ATTAGTTTTT
**
15597 TTATATAATTTTTTATTTTTTAAAA
1 TTATATAATTTTAAATTTTTTAAAA
15622 TTATAT-ATTTTAAATTTTTTAA
1 TTATATAATTTTAAATTTTTTAA
15644 TTGAGGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATATAATTTTAAATTTTTTAAAA
Found at i:18068 original size:23 final size:24
Alignment explanation
Indices: 18024--18068 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
18014 AAATTGGAAG
* *
18024 TTTTTTTTTTCAATTAAGTAATGC
1 TTTTTATTTTCAAGTAAGTAATGC
*
18048 TTTTTATTTT-AAGTAATTAAT
1 TTTTTATTTTCAAGTAAGTAAT
18069 ATGAAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTTTATTTTCAAGTAAGTAATGC
Found at i:18730 original size:38 final size:37
Alignment explanation
Indices: 18670--18771 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 37
18660 GTATAGACTC
* *
18670 ATCTAAGGCAACTTT-AAAAAGGTT-AAGATAGGCTTT
1 ATCTAAGGCAACTTTAAAAAAGGTTGAAG-TAGACCTT
* *
18706 ATCTAAGGTAACATTTAAAAAAGGTTGATGTAGACCTT
1 ATCTAAGGCAAC-TTTAAAAAAGGTTGAAGTAGACCTT
*
18744 ATCTAAGGCAACGTTTAAAAAATGTTGA
1 ATCTAAGGCAAC-TTTAAAAAAGGTTGA
18772 GAAGGTAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 11 0.20
37 3 0.05
38 40 0.71
39 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (37 bp):
ATCTAAGGCAACTTTAAAAAAGGTTGAAGTAGACCTT
Found at i:19095 original size:21 final size:20
Alignment explanation
Indices: 19042--19101 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
19032 AACTCATAAT
* *
19042 CATAAATCCTTGAATCCTAAA
1 CATAAA-CCTTGAATCTTGAA
*
19063 CATAAACATTGAATCTTGAA
1 CATAAACCTTGAATCTTGAA
* *
19083 CCTCAAACCTTGAACCTTG
1 CAT-AAACCTTGAATCTTG
19102 TATCTCGATC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.28
Consensus pattern (20 bp):
CATAAACCTTGAATCTTGAA
Found at i:19869 original size:30 final size:29
Alignment explanation
Indices: 19834--19896 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
19824 TTAACTATTG
* *
19834 ATTTTTTTTAA-TTATTATTGAAATTTAA
1 ATTTTTTGTAATTTAATATTGAAATTTAA
*
19862 TATTTTTTGTAATTTAATATTTAAATTTAA
1 -ATTTTTTGTAATTTAATATTGAAATTTAA
19892 ATTTT
1 ATTTT
19897 GTTAAGGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTTTTGTAATTTAATATTGAAATTTAA
Found at i:20165 original size:7 final size:7
Alignment explanation
Indices: 20153--20184 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
20143 TAAAAACCCA
20153 TTCCTAT
1 TTCCTAT
20160 TTCCTAT
1 TTCCTAT
20167 TTCCTAT
1 TTCCTAT
20174 TTCCTAT
1 TTCCTAT
20181 TTCC
1 TTCC
20185 CATCCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCCTAT
Found at i:20558 original size:3 final size:3
Alignment explanation
Indices: 20550--20574 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20540 GGTAAGCTTA
20550 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
20575 GAAAATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20996 original size:52 final size:52
Alignment explanation
Indices: 20918--21025 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
20908 TTCTATTATG
*
20918 TAAACTTTTCCCGAAATATTTACTCTAAAGATGTGGAATTCTGCGAAGAATT
1 TAAACTTTTCCCGAAATATTTACTCTAAAGATGAGGAATTCTGCGAAGAATT
20970 TAAACTTTTCCCGAAATATTTACTCTAAAGATGAGGAATTCTGCGAAGAATT
1 TAAACTTTTCCCGAAATATTTACTCTAAAGATGAGGAATTCTGCGAAGAATT
21022 TAAA
1 TAAA
21026 GATTAGGTCG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (52 bp):
TAAACTTTTCCCGAAATATTTACTCTAAAGATGAGGAATTCTGCGAAGAATT
Found at i:23252 original size:38 final size:38
Alignment explanation
Indices: 23208--23294 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
23198 CTATTCTAAG
*
23208 CTTTTTAAAAGGTTATCTTAGACAAGATTCATCTCAA-
1 CTTTTTAAAAGATTATCTTAGACAAGATTCATCTCAAT
* * * *
23245 CTTTTTTAAAAGATTGTCTTAGATAAGGTTTATCTCAAT
1 C-TTTTTAAAAGATTATCTTAGACAAGATTCATCTCAAT
23284 CTTTTTAAAAG
1 CTTTTTAAAAG
23295 CATGCCTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 1 0.02
38 41 0.95
39 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (38 bp):
CTTTTTAAAAGATTATCTTAGACAAGATTCATCTCAAT
Found at i:23304 original size:38 final size:38
Alignment explanation
Indices: 23209--23307 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 38
23199 TATTCTAAGC
* **
23209 TTTTTAAAAGGTTATCTTAGACAAGATTCATCTCAACT
1 TTTTTAAAAGATTGCCTTAGACAAGATTCATCTCAACT
* * * *
23247 TTTTTAAAAGATTGTCTTAGATAAGGTTTATCTCAA-T
1 TTTTTAAAAGATTGCCTTAGACAAGATTCATCTCAACT
23284 CTTTTTAAAAGCA-TGCCTTAGACA
1 -TTTTTAAAAG-ATTGCCTTAGACA
23308 TGTCTATTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.02
38 50 0.96
39 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (38 bp):
TTTTTAAAAGATTGCCTTAGACAAGATTCATCTCAACT
Found at i:23400 original size:36 final size:35
Alignment explanation
Indices: 23342--23452 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 35
23332 GTTGTCGTAA
*
23342 ACAAAGTATATCTCAATCTTTTTAAGATTGTTTTAG
1 ACAAAGTATATCCCAA-CTTTTTAAGATTGTTTTAG
* *
23378 ACAAAGTTTATCCCAACATTTTTTAAAAGTTGTTTTAG
1 ACAAAGTATATCCCAAC--TTTTTAAGA-TTGTTTTAG
* * * * * *
23416 ATAGAGTCTATTCTAACTTTTTTAAGGTTGTTTTAG
1 ACAAAGTATATCCCAAC-TTTTTAAGATTGTTTTAG
23452 A
1 A
23453 TGGGTTTATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
35 1 0.02
36 24 0.39
37 16 0.26
38 21 0.34
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (35 bp):
ACAAAGTATATCCCAACTTTTTAAGATTGTTTTAG
Found at i:23438 original size:38 final size:37
Alignment explanation
Indices: 23360--23514 Score: 104
Period size: 38 Copynumber: 4.2 Consensus size: 37
23350 TATCTCAATC
* * * * * *
23360 TTTTTAAGA-TTGTTTTAGACAAAGTTTATCCCAACAT
1 TTTTTAAAAGTTGTTTTAGATAGAGTCTATTCTAAC-T
23397 TTTTTAAAAGTTGTTTTAGATAGAGTCTATTCTAACT
1 TTTTTAAAAGTTGTTTTAGATAGAGTCTATTCTAACT
* * * *
23434 TTTTT-AAGGTTGTTTTAGAT-GGGTTTA-TCTTAATT
1 TTTTTAAAAGTTGTTTTAGATAGAGTCTATTC-TAACT
** * *
23469 TATTTTAAAAGGTTACTTTAGATATAGTCTA-TCTTAACC
1 T-TTTTAAAA-GTTGTTTTAGATAGAGTCTATTC-TAACT
23508 TTTTTAA
1 TTTTTAA
23515 GGATGTCTTA
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
34 2 0.02
35 10 0.11
36 18 0.19
37 16 0.17
38 37 0.39
39 11 0.12
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (37 bp):
TTTTTAAAAGTTGTTTTAGATAGAGTCTATTCTAACT
Found at i:23453 original size:36 final size:37
Alignment explanation
Indices: 23360--23453 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 37
23350 TATCTCAATC
* * *
23360 TTTTTAAGATTGTTTTAGACAAAGTTTATCCCAACAT
1 TTTTTAAGGTTGTTTTAGATAAAGTCTATCCCAACAT
* * * *
23397 TTTTTAAAAGTTGTTTTAGATAGAGTCTATTCTAAC-T
1 TTTTT-AAGGTTGTTTTAGATAAAGTCTATCCCAACAT
23434 TTTTTAAGGTTGTTTTAGAT
1 TTTTTAAGGTTGTTTTAGAT
23454 GGGTTTATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
36 14 0.29
37 11 0.23
38 23 0.48
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (37 bp):
TTTTTAAGGTTGTTTTAGATAAAGTCTATCCCAACAT
Found at i:23489 original size:74 final size:73
Alignment explanation
Indices: 23397--23564 Score: 198
Period size: 74 Copynumber: 2.3 Consensus size: 73
23387 ATCCCAACAT
** * * * * *
23397 TTTTTAAAAGTTGTTTTAGATAGAGTCTAT-TCTAACTTTTTTAAGGTTGTTTTAGATGGGTTTA
1 TTTTTAAAAGTTACTTTAGATAGAGTCTATCT-TAACCTTTTTAAGGATGTCTTAAATAGGTTTA
23461 TCTT-AATT-
65 T-TTCAATTC
*
23469 TATTTTAAAAGGTTACTTTAGATATAGTCTATCTTAACCTTTTTAAGGATGTCTTAAATAGGTTT
1 T-TTTTAAAA-GTTACTTTAGATAGAGTCTATCTTAACCTTTTTAAGGATGTCTTAAATAGGTTT
23534 ATTTCAATTC
64 ATTTCAATTC
23544 TTTTTAAAAAGTTACTTTAGA
1 TTTTT-AAAAGTTACTTTAGA
23565 CGAGACTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
72 1 0.01
73 10 0.12
74 65 0.79
75 6 0.07
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (73 bp):
TTTTTAAAAGTTACTTTAGATAGAGTCTATCTTAACCTTTTTAAGGATGTCTTAAATAGGTTTAT
TTCAATTC
Found at i:23576 original size:74 final size:74
Alignment explanation
Indices: 23397--23586 Score: 172
Period size: 74 Copynumber: 2.6 Consensus size: 74
23387 ATCCCAACAT
* ** * * * * * * *
23397 TTTTTAAAAGTTGTTTTAGATAGAGTCTAT-TCTAACTTTTTTAAGGTTGTTTTAGATGGGTTTA
1 TTTTAAAAAGTTACTTTAGAGAGACTCTATCT-TAACATTTTTAAGGATGTCTTAAATAGGTTTA
23461 TCTTAATTTA
65 TCTTAATTTA
* * * * *
23471 TTTTAAAAGGTTACTTTAGATATAGTCTATCTTAACCTTTTTAAGGATGTCTTAAATAGGTTTAT
1 TTTTAAAAAGTTACTTTAGAGAGACTCTATCTTAACATTTTTAAGGATGTCTTAAATAGGTTTAT
23536 -TTCAATTCT-
66 CTT-AATT-TA
*
23545 TTTTAAAAAGTTACTTTAGACGAGACT-TATCTCAACATTTTT
1 TTTTAAAAAGTTACTTTAGA-GAGACTCTATCTTAACATTTTT
23587 TAAAGGTCGG
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
73 2 0.02
74 89 0.93
75 5 0.05
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.48
Consensus pattern (74 bp):
TTTTAAAAAGTTACTTTAGAGAGACTCTATCTTAACATTTTTAAGGATGTCTTAAATAGGTTTAT
CTTAATTTA
Done.