Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012472.1 Kokia drynarioides strain JFW-HI SEQ_127476, 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: 20456
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4168 original size:50 final size:49
Alignment explanation
Indices: 4102--4199 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
4092 TAGACATCTA
* * * *
4102 GGGGTAAATGGTAATTTTTTGAAAAATTGAGGTTAAAAATGGAATTTTT
1 GGGGTAAATGGGAATTTTTAGAAAAATCGAGGTCAAAAATGGAATTTTT
*
4151 GGGGTAAAATGGGAATTTTTAGAGAAATCGAGGTCAAAAATGGAATTTT
1 GGGGT-AAATGGGAATTTTTAGAAAAATCGAGGTCAAAAATGGAATTTT
4200 GAAAAGTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 5 0.12
50 38 0.88
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.34
Consensus pattern (49 bp):
GGGGTAAATGGGAATTTTTAGAAAAATCGAGGTCAAAAATGGAATTTTT
Found at i:4240 original size:58 final size:60
Alignment explanation
Indices: 4151--4279 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 60
4141 TGGAATTTTT
4151 GGGGTAAAATGGGAATTTTTAGAGAAATCGAGGTCAAAAATGGAATTTT-GAAAAGTTTA
1 GGGGTAAAATGGGAATTTTTAGAGAAATCGAGGTCAAAAATGGAATTTTAGAAAAGTTTA
* * * *
4210 GTGGTAAAAT-GTAATTTTTA-A-AAAGTTCGAGGTCGAAAATGGTATTTTAGAAAAGTTTA
1 GGGGTAAAATGGGAATTTTTAGAGAAA--TCGAGGTCAAAAATGGAATTTTAGAAAAGTTTA
4269 GGGGTCAAAAT
1 GGGGT-AAAAT
4280 ATGATTTCTG
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
56 3 0.05
57 1 0.02
58 29 0.48
59 23 0.38
60 5 0.08
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.31
Consensus pattern (60 bp):
GGGGTAAAATGGGAATTTTTAGAGAAATCGAGGTCAAAAATGGAATTTTAGAAAAGTTTA
Found at i:4279 original size:30 final size:31
Alignment explanation
Indices: 4180--4278 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 31
4170 TAGAGAAATC
*
4180 GAGGTCAAAAATGGAATTTT-GAAAAGTTTA
1 GAGGTCAAAAATGGTATTTTAGAAAAGTTTA
* *
4210 GTGGT--AAAAT-GTAATTTTTA-AAAAG-TTC
1 GAGGTCAAAAATGGT-A-TTTTAGAAAAGTTTA
*
4238 GAGGTCGAAAATGGTATTTTAGAAAAGTTTA
1 GAGGTCAAAAATGGTATTTTAGAAAAGTTTA
*
4269 GGGGTCAAAA
1 GAGGTCAAAA
4279 TATGATTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
27 1 0.02
28 12 0.22
29 14 0.26
30 15 0.28
31 12 0.22
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.31
Consensus pattern (31 bp):
GAGGTCAAAAATGGTATTTTAGAAAAGTTTA
Found at i:5277 original size:16 final size:16
Alignment explanation
Indices: 5256--5293 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5246 TCATTTTTGT
*
5256 TTATTATTAATATTAA
1 TTATTATTAATAATAA
*
5272 TTATTATTATTAATAA
1 TTATTATTAATAATAA
5288 TTATTA
1 TTATTA
5294 ATGTTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTAATAATAA
Found at i:5293 original size:19 final size:19
Alignment explanation
Indices: 5256--5344 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
5246 TCATTTTTGT
5256 TTATTATTAAT-ATTAATTA
1 TTATTATTAATAATT-ATTA
5275 TTATTATTAATAATTATTA
1 TTATTATTAATAATTATTA
* * ** * **
5294 ATGTTATTTGTTACCATTA
1 TTATTATTAATAATTATTA
* *
5313 CTTATTATTTATCATTATTA
1 -TTATTATTAATAATTATTA
*
5333 ATATTATTAATA
1 TTATTATTAATA
5345 TATAACCTTA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
19 36 0.69
20 16 0.31
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAATAATTATTA
Found at i:5356 original size:55 final size:59
Alignment explanation
Indices: 5256--5368 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
5246 TCATTTTTGT
* ** *
5256 TTATTATTAATATTAATTATTATTATTAATAATTATTAATGTTATTTGTTA-CCATTAC
1 TTATTATTAATATTAATTAATATTATTAATAATTATTAACCTTATTTATTACCCATTAC
*
5314 TTATTATTTATCATT-ATTAATATTATTAAT-A-TA-TAACCTTATTTATTACCCATTA
1 TTATTATTAAT-ATTAATTAATATTATTAATAATTATTAACCTTATTTATTACCCATTA
5369 ATTTAATGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
55 12 0.25
56 8 0.17
57 1 0.02
58 24 0.50
59 3 0.06
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (59 bp):
TTATTATTAATATTAATTAATATTATTAATAATTATTAACCTTATTTATTACCCATTAC
Found at i:6141 original size:20 final size:18
Alignment explanation
Indices: 6075--6158 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 18
6065 ATTCAGTTTT
*
6075 AAATCAATTTAAATTT--
1 AAATAAATTTAAATTTAA
* *
6091 AATTAAATTCAAATTT-A
1 AAATAAATTTAAATTTAA
** *
6108 AAGCAAATTAAAATTTAA
1 AAATAAATTTAAATTTAA
6126 AACGATAAATTTAAATTTAA
1 AA--ATAAATTTAAATTTAA
6146 AAATAAATTTAAA
1 AAATAAATTTAAA
6159 CCAATTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
16 13 0.24
17 13 0.24
18 14 0.25
20 15 0.27
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATAAATTTAAATTTAA
Found at i:6167 original size:22 final size:22
Alignment explanation
Indices: 6139--6184 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6129 GATAAATTTA
6139 AATTTAAAAATAAATTT-AAACC
1 AATTTAAAAAT-AATTTAAAACC
*
6161 AATTTAAAACTAATTTAAAACC
1 AATTTAAAAATAATTTAAAACC
6183 AA
1 AA
6185 AGGCTTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAAATAATTTAAAACC
Found at i:6175 original size:11 final size:11
Alignment explanation
Indices: 6139--6181 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
6129 GATAAATTTA
*
6139 AATTTAAAAAT
1 AATTTAAAACT
*
6150 AAATTT-AAACC
1 -AATTTAAAACT
6161 AATTTAAAACT
1 AATTTAAAACT
6172 AATTTAAAAC
1 AATTTAAAAC
6182 CAAAGGCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.19
11 17 0.63
12 5 0.19
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTTAAAACT
Found at i:11034 original size:13 final size:14
Alignment explanation
Indices: 11016--11045 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11006 CTTTAGCCAT
11016 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
11029 TTTTTATTTTATTA
1 TTTTTATTTTATTA
11043 TTT
1 TTT
11046 GCATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:14017 original size:5 final size:5
Alignment explanation
Indices: 13997--14048 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
13987 AATTAGTATA
*
13997 TTTAT TTTCAAT TTTAT TTTAT TTTAT CTTAT TTTAT TTTAAT TTTAT
1 TTTAT TTT--AT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT
14045 TTTA
1 TTTA
14049 GTTATGCACT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 32 0.76
6 5 0.12
7 5 0.12
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:15898 original size:23 final size:25
Alignment explanation
Indices: 15872--15917 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
15862 GCAATTAGGG
15872 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
15895 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
15918 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:16337 original size:15 final size:15
Alignment explanation
Indices: 16300--16338 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
16290 TTATGTGTGC
*
16300 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
16315 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
16329 TTAATTCTTG
1 TTAATTCTTG
16339 TTTGATGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:19712 original size:39 final size:39
Alignment explanation
Indices: 19649--20454 Score: 517
Period size: 39 Copynumber: 20.7 Consensus size: 39
19639 GAAGATCCCG
* * **
19649 ATCTCTTACCCCGATCCTAGGGCAGATCATCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * * * **
19688 ATCTCTTACCCCAAGCCTGAGGCAGATTA-CAGTCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TCAGTCA
* * ** * *
19727 ATCTCTTACCCCGAGCATGGGGTAGATCAGAACCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * * *
19766 ATCTCTTACCCCGAGCCGGGGGCAAAT--TGCAGCCA-TCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAGT-CA
*
19805 ATCTCTTACCCCGAGCCTGGGGTAGATCATCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTC-A
* * * * **
19844 ATCTCTTACCCCAAGCCTAGGGCAGAT--TGCAGCCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAGTCA
* * ** * * *
19883 ATCTCTTACACCGAGACTTTGGAAGATCATTATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * * * *
19922 ATCTCTTACCTCGAGCCTGGGGTAGAT--TGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAGTCA
*
19961 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATTAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTC-A
* * *
20000 ATCTCTTACCCCGAGCCT-GGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-C-ATCAGTCA
* * * *
20038 ATCTCTTACCTCGAACCTGGGGAATATCATCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTC-A
* * ** * * *
20077 ATCTCTTACCCCGAGCTTGGGGTAGATTGT-AGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TCAGTCA
* * * * *
20116 ATCTCTTACCCCAAGCTTGGGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * * **
20155 ATCTCTTACCCCGAGTCTGGGGCAGATTA-CAATCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGTCA
* * *
20194 ATCACTTACCCTGAGCCTAGGGCAGATCA-CAATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGTC-A
* *
20233 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGT-A
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * *
20271 GATCTCTTACCCCGAGCCTGGGGCAGAT--TGCAGCTATTCG
1 -ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CATC-AGTCA
* *
20311 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
* * *
20350 ATCTCTTACCCCGAGCTTGGGGCAGAT--TGCAGT-TGTTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAG-TCA
* *
20389 ATCTCCTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
*
20428 ATCTCTTACCCCGAGCCTGAGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
20455 TG
Statistics
Matches: 583, Mismatches: 139, Indels: 90
0.72 0.17 0.11
Matches are distributed among these distances:
36 1 0.00
37 3 0.01
38 45 0.08
39 513 0.88
40 16 0.03
41 5 0.01
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGTCA
Found at i:19777 original size:78 final size:78
Alignment explanation
Indices: 19647--20376 Score: 748
Period size: 78 Copynumber: 9.4 Consensus size: 78
19637 TTGAAGATCC
* * * * * *
19647 CGATCTCTTACCCCGATCCTAGGGCAGATCATCATCAACCAATCTCTTACCCCAAGCCTGAGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
* *
19712 GATTACAGTCATT
66 GATTGCAGCCATT
* * * ** * * *
19725 TGATCTCTTACCCCGAGCATGGGGTAGATCAGAACCAGTAAATCTCTTACCCCGAGCCGGGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
* *
19790 AATTGCAGCCATC
66 GATTGCAGCCATT
* * *
19803 CGATCTCTTACCCCGAGCCTGGGGTAGATCATCATCAGCAAATCTCTTACCCCAAGCCTAGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
19868 GATTGCAGCCATT
66 GATTGCAGCCATT
* * * ** * * * * *
19881 TGATCTCTTACACCGAGACTTTGGAAGATCATTATCAGTAAATCTCTTACCTCGAGCCTGGGGTA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
19946 GATTGCAGCCATT
66 GATTGCAGCCATT
*
19959 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATTAGCAAATCTCTTACCCCGAGCCT-GGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
*
20023 GATTGCAACCATT
66 GATTGCAGCCATT
* * * * * *
20036 CGATCTCTTACCTCGAACCTGGGGAATATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGTA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
*
20101 GATTGTAGCCATT
66 GATTGCAGCCATT
* * * * * *
20114 CGATCTCTTACCCCAAGCTTGGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGTCTGGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
* **
20179 GATTACAATCATT
66 GATTGCAGCCATT
* * * * *
20192 TGATCACTTACCCTGAGCCTAGGGCAGATCA-CAATCAGCAAATCTCTTACCCCGAGCCTAGGGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGCAAATCTCTTACCCCGAGCCTGGGGC
20256 AGA-T-CA-CCATCAGT
65 AGATTGCAGCCAT---T
* *
20270 AGATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCTATTC-G---ATCTCTTACCCCGAGCCTGG
1 CGATCTCTTACCCCGAGCCTGGGGCAGA-T-CATC-A-TCAGCAAATCTCTTACCCCGAGCCTGG
20331 GGCAGA-T-CA-CCA-T
62 GGCAGATTGCAGCCATT
*
20344 CAGCCAATCTCTTACCCCGAGCTTGGGGCAGAT
1 C-G---ATCTCTTACCCCGAGCCTGGGGCAGAT
20377 TGCAGTTGTT
Statistics
Matches: 542, Mismatches: 97, Indels: 27
0.81 0.15 0.04
Matches are distributed among these distances:
74 1 0.00
75 4 0.01
76 2 0.00
77 72 0.13
78 455 0.84
79 1 0.00
80 2 0.00
81 3 0.01
82 2 0.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (78 bp):
CGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCA
GATTGCAGCCATT
Done.