Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012372.1 Kokia drynarioides strain JFW-HI SEQ_127376, 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: 124438
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6385 original size:12 final size:11
Alignment explanation
Indices: 6342--6392 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
6332 ATGGGTAGTA
6342 TAAAATAAATT
1 TAAAATAAATT
6353 T-AAATACAATT
1 TAAAATA-AATT
*
6364 TAAATTTAAATT
1 TAAA-ATAAATT
6376 TAATAATAAATT
1 TAA-AATAAATT
6388 ATAAA
1 -TAAA
6393 TTAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 5 0.15
11 6 0.18
12 16 0.48
13 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:12221 original size:30 final size:30
Alignment explanation
Indices: 12185--12249 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
12175 CAACTTAACA
* *
12185 AACAAATGTCTCTAAAATAGTAACAAAAAT
1 AACAAATGCCTCTAAAATAATAACAAAAAT
* *
12215 AACAAATGCCTCTAAAATAATTACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAAAT
12245 AACAA
1 AACAA
12250 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAAAT
Found at i:23523 original size:21 final size:21
Alignment explanation
Indices: 23484--23524 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23474 AAGTAGGATA
* **
23484 TAAAAAATTATTTTTTTATTT
1 TAAAAAATAATTTAATTATTT
23505 TAAAAAATAATTTAATTATT
1 TAAAAAATAATTTAATTATT
23525 CTTTTTTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAAAAATAATTTAATTATTT
Found at i:48222 original size:23 final size:22
Alignment explanation
Indices: 48180--48222 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
48170 ACATTCTCAG
**
48180 ATATTTTTATTTATTTAATAAT
1 ATATTTTTATTTATGAAATAAT
48202 ATATTTTTATTTTATGAAATA
1 ATATTTTTA-TTTATGAAATA
48223 TAAAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTTTTATTTATGAAATAAT
Found at i:51394 original size:22 final size:22
Alignment explanation
Indices: 51383--51424 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
51373 TATGTTTTTA
51383 TTTTTATATTTATATTTTATAG
1 TTTTTATATTTATATTTTATAG
* *
51405 TTTTTATAATTCTATTTTAT
1 TTTTTATATTTATATTTTAT
51425 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATATTTATATTTTATAG
Found at i:51420 original size:28 final size:28
Alignment explanation
Indices: 51367--51426 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
51357 TTTTAAACAA
**
51367 ATTTTATATGTTTTTATTTTTATATTTAT
1 ATTTTATATGTTTTTATAATTATATTT-T
*
51396 ATTTTATA-GTTTTTATAATTCTATTTT
1 ATTTTATATGTTTTTATAATTATATTTT
51423 ATTT
1 ATTT
51427 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 15 0.54
29 8 0.29
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
ATTTTATATGTTTTTATAATTATATTTT
Found at i:51423 original size:29 final size:29
Alignment explanation
Indices: 51367--51424 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
51357 TTTTAAACAA
*
51367 ATTTTATATGTTTTTATTTTTATATTTAT
1 ATTTTATATGTTTTTATTTCTATATTTAT
51396 ATTTTATA-GTTTTTATAATTCTAT-TTTAT
1 ATTTTATATGTTTTTAT--TTCTATATTTAT
51425 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.31
29 13 0.50
30 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (29 bp):
ATTTTATATGTTTTTATTTCTATATTTAT
Found at i:52096 original size:8 final size:7
Alignment explanation
Indices: 52078--52148 Score: 67
Period size: 7 Copynumber: 10.1 Consensus size: 7
52068 TTTTTATTAA
52078 ATAAAAT
1 ATAAAAT
*
52085 A-AAATT
1 ATAAAAT
52091 ATAAAAACT
1 AT-AAAA-T
52100 ATAAAAT
1 ATAAAAT
52107 ATAAAA-
1 ATAAAAT
52113 ATAAAACT
1 ATAAAA-T
*
52121 ATACAAT
1 ATAAAAT
52128 ATAAAAT
1 ATAAAAT
*
52135 A-AAAAA
1 ATAAAAT
52141 ATAAAAT
1 ATAAAAT
52148 A
1 A
52149 ACATGACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 16 0.31
7 21 0.40
8 12 0.23
9 3 0.06
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (7 bp):
ATAAAAT
Found at i:52120 original size:21 final size:20
Alignment explanation
Indices: 52094--52148 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
52084 TAAAATTATA
52094 AAAACTATAAAATATAAAAAT
1 AAAACTATAAAATAT-AAAAT
*
52115 AAAACTATACAATATAAAAT
1 AAAACTATAAAATATAAAAT
**
52135 AAAAAAATAAAATA
1 AAAACTATAAAATA
52149 ACATGACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAACTATAAAATATAAAAT
Found at i:52135 original size:28 final size:30
Alignment explanation
Indices: 52075--52146 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 30
52065 AGTTTTTTAT
*
52075 TAAATAAAATAAAATTATAAAAACTATAAAA
1 TAAA-AAAATAAAACTATAAAAACTATAAAA
* *
52106 TATAAAAATAAAACTAT-ACAA-TATAAAA
1 TAAAAAAATAAAACTATAAAAACTATAAAA
52134 TAAAAAAATAAAA
1 TAAAAAAATAAAA
52147 TAACATGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.51
29 3 0.08
30 12 0.32
31 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (30 bp):
TAAAAAAATAAAACTATAAAAACTATAAAA
Found at i:55848 original size:8 final size:8
Alignment explanation
Indices: 55821--55859 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
55811 TTGTAGGATG
*
55821 ATATATAT
1 ATATGTAT
* *
55829 ACATGCAT
1 ATATGTAT
55837 ATATGTAT
1 ATATGTAT
55845 ATATGTAT
1 ATATGTAT
55853 ATATGTA
1 ATATGTA
55860 GCTTGTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (8 bp):
ATATGTAT
Found at i:60176 original size:3 final size:3
Alignment explanation
Indices: 60168--60201 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
60158 ATACAGAAAT
60168 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
60202 AAATAATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:60504 original size:5 final size:5
Alignment explanation
Indices: 60489--60517 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
60479 ATGAGGCATG
60489 CAAAA -AAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
60518 AAACTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:77851 original size:22 final size:23
Alignment explanation
Indices: 77825--77868 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
77815 ATTCAATAAA
77825 ATATTAAAAATATTTT-TAATTG
1 ATATTAAAAATATTTTATAATTG
* *
77847 ATATTATATATATTTTATAATT
1 ATATTAAAAATATTTTATAATT
77869 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTAAAAATATTTTATAATTG
Found at i:80608 original size:83 final size:83
Alignment explanation
Indices: 80469--80638 Score: 315
Period size: 83 Copynumber: 2.0 Consensus size: 83
80459 TTGGGCTTTG
80469 TATATCATTAGCCTTGATCCCGAGATGCCATGTGCTGAGTTCTCATAAGAGGATAAAAAACAAGT
1 TATATCATTAGCCTTGATCCCGAGATGCCATGTGCTGAGTTCTCATAAGAGGATAAAAAACAAGT
*
80534 GGCCAAATAGTTTGTCAC
66 GGCCAAAAAGTTTGTCAC
80552 TATATCATTAGCCTT-AGTCCCGAGATGCCATGTGCTGAGTTCTCATAAGAGGATAAAAAACAAG
1 TATATCATTAGCCTTGA-TCCCGAGATGCCATGTGCTGAGTTCTCATAAGAGGATAAAAAACAAG
80616 TGGCCAAAAAGTTTGTCAC
65 TGGCCAAAAAGTTTGTCAC
80635 TATA
1 TATA
80639 GGCCTAAATA
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 1 0.01
83 84 0.99
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (83 bp):
TATATCATTAGCCTTGATCCCGAGATGCCATGTGCTGAGTTCTCATAAGAGGATAAAAAACAAGT
GGCCAAAAAGTTTGTCAC
Found at i:81491 original size:2 final size:2
Alignment explanation
Indices: 81484--81524 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
81474 TTTGGGAAGG
81484 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
81525 CTCTTTGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:99713 original size:27 final size:28
Alignment explanation
Indices: 99658--99713 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
99648 ATAATTTTTT
* * *
99658 TTATGAAATTAATATATTTTATAATTAA
1 TTATAAAATAAATATATTTTATAAGTAA
*
99686 TTATAAAATAAATAT-TTTTATTAGTAA
1 TTATAAAATAAATATATTTTATAAGTAA
99713 T
1 T
99714 AAAAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTATAAAATAAATATATTTTATAAGTAA
Found at i:103915 original size:27 final size:28
Alignment explanation
Indices: 103879--103938 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
103869 TATTTTTATT
* *
103879 TGTTTAAAAT-TATATTTTAGTTATTTA
1 TGTTTAAAATATATATTTTAATCATTTA
* *
103906 TGTTTGAAATGATATGTTTTAATCATTTA
1 TGTTTAAAAT-ATATATTTTAATCATTTA
103935 TGTT
1 TGTT
103939 ATCGTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.33
29 18 0.67
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (28 bp):
TGTTTAAAATATATATTTTAATCATTTA
Found at i:104089 original size:18 final size:18
Alignment explanation
Indices: 104066--104108 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
104056 GAATAATTTT
104066 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
104084 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
104102 TTAATTA
1 TTAATTA
104109 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:105749 original size:26 final size:25
Alignment explanation
Indices: 105698--105749 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
105688 AAGCCTTATC
* ***
105698 AAACTTTTACGGGAGTAAATTGATA
1 AAACTTTTACGGGAATAAAAAAATA
105723 AAACATTTTACGGGAATAAAAAAATA
1 AAAC-TTTTACGGGAATAAAAAAATA
105749 A
1 A
105750 TTTTACGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (25 bp):
AAACTTTTACGGGAATAAAAAAATA
Found at i:105773 original size:21 final size:22
Alignment explanation
Indices: 105742--105782 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
105732 ACGGGAATAA
*
105742 AAAAATAATTTTACGTTGATTG
1 AAAAATAATTTTACATTGATTG
105764 AAAAAT-ATTTTACATTGAT
1 AAAAATAATTTTACATTGAT
105783 CATTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAAATAATTTTACATTGATTG
Found at i:111814 original size:21 final size:21
Alignment explanation
Indices: 111789--111831 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
111779 TGTCTAACCA
*
111789 ATTACAAAGTAGAATCAAACT
1 ATTACAAAGTAGAAACAAACT
*
111810 ATTACAAAGTATAAACAAACT
1 ATTACAAAGTAGAAACAAACT
111831 A
1 A
111832 AGAATCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (21 bp):
ATTACAAAGTAGAAACAAACT
Found at i:120011 original size:17 final size:17
Alignment explanation
Indices: 119988--120026 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
119978 AGGTGGAGAA
*
119988 CTTGTTCGTTGAGAATT
1 CTTGTTCGTAGAGAATT
*
120005 TTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
120022 CTTGT
1 CTTGT
120027 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.23, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:120109 original size:41 final size:41
Alignment explanation
Indices: 120016--120111 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
120006 TTGTTCGTAG
* *
120016 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTTGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
*
120057 AGAATTCTTGTTTAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
120098 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
120112 AATAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.27, C:0.06, G:0.28, T:0.39
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
Found at i:121097 original size:24 final size:24
Alignment explanation
Indices: 121070--121122 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
121060 AATTTTTTTT
*
121070 AAATATATTTAGATAAATT-TTATA
1 AAATATA-TTAAATAAATTATTATA
* *
121094 AAATTTATTAAATAATTTATTATA
1 AAATATATTAAATAAATTATTATA
121118 AAATA
1 AAATA
121123 AAAAGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATATATTAAATAAATTATTATA
Done.