Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011756.1 Kokia drynarioides strain JFW-HI SEQ_126750, 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: 24702
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:17178 original size:96 final size:96
Alignment explanation
Indices: 17004--17188 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
16994 GCAAAGGATG
** *
17004 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
*
17069 AGATAAGGAAATATTACCTCGATTAAGGGTA
66 AGATAAAGAAATATTACCTCGATTAAGGGTA
* *
17100 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAA-TTTCTGAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TC
17164 GAA-ATAAA-AGAATATTACCTCGATT
64 GAAGATAAAGA-AATATTACCTCGATT
17189 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
95 6 0.08
96 69 0.86
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AGATAAAGAAATATTACCTCGATTAAGGGTA
Found at i:17450 original size:28 final size:28
Alignment explanation
Indices: 17405--17466 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
17395 AAATGAGACT
17405 TTTTGGATACCCGAGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
* * *
17433 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
17461 TTTTGG
1 TTTTGG
17467 GAAATTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:17696 original size:58 final size:58
Alignment explanation
Indices: 17540--17843 Score: 208
Period size: 58 Copynumber: 5.3 Consensus size: 58
17530 AATCAGGATA
* * * ** * * * *
17540 AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAGAGTTTGGGGGTC
1 AAAAATAGAATTTTTGAAAATTC-GGGGTAAAATTATAATTTTTGAAAGTTTCGAGGTT
* * * * *
17599 AAAAATGGAGTTTTTGGACATTCGGGG-AAAATTAGTAATTTTTGAAAGTTTCGATGTT
1 AAAAATAGAATTTTTGAAAATTCGGGGTAAAATTA-TAATTTTTGAAAGTTTCGAGGTT
* * * * *
17657 AAAAATAGAA-TTTTGCAAGTTCGAGGGTAAAATTATAATTTTT-ATAAGTTTTGGGGTC
1 AAAAATAGAATTTTTGAAAATTCG-GGGTAAAATTATAATTTTTGA-AAGTTTCGAGGTT
* * * * ** * *
17715 AAAAATGGAATTTTTGGAAATTAGGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGGT
1 AAAAATAGAATTTTTGAAAATTCGGGGTAAAATTATAATTTTTGAAAGTTTCGAGGTT
* * * * *
17772 AAAAATAGAATTTTTTAAACTTCGAGGTGAAAATGA-AATTTTTGAAAG-TTC-AGGGGT
1 AAAAATAGAATTTTTGAAAATTCGGGGT-AAAATTATAATTTTTGAAAGTTTCGA-GGTT
*
17829 AAAAATATAATTTTT
1 AAAAATAGAATTTTT
17844 AGATAGTTTA
Statistics
Matches: 197, Mismatches: 40, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
56 1 0.01
57 75 0.38
58 82 0.42
59 39 0.20
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAAATAGAATTTTTGAAAATTCGGGGTAAAATTATAATTTTTGAAAGTTTCGAGGTT
Found at i:17699 original size:29 final size:29
Alignment explanation
Indices: 17540--17843 Score: 184
Period size: 29 Copynumber: 10.5 Consensus size: 29
17530 AATCAGGATA
* * *
17540 AAAAATGGAATTTTTGGACA-TTCGGGGGT
1 AAAAATAGAATTTTT-GAAAGTTCGAGGGT
* * * *
17569 -AAAATGGTAATTTTTGAGAGTTTGGGGGT
1 AAAAATAG-AATTTTTGAAAGTTCGAGGGT
* * *
17598 CAAAAATGGAGTTTTTGGACA-TTCG-GGG-
1 -AAAAATAGAATTTTT-GAAAGTTCGAGGGT
* * *
17626 AAAATTAGTAATTTTTGAAAGTTTCGATGTT
1 AAAAATAG-AATTTTTGAAAG-TTCGAGGGT
*
17657 AAAAATAGAA-TTTTGCAAGTTCGAGGGT
1 AAAAATAGAATTTTTGAAAGTTCGAGGGT
* * *
17685 AAAATTATAATTTTT-ATAAGTTTTG-GGGT
1 AAAAATAGAATTTTTGA-AAG-TTCGAGGGT
* *
17714 CAAAAATGGAATTTTTGGAAA-TTAG-GGGT
1 -AAAAATAGAATTTTT-GAAAGTTCGAGGGT
* *
17743 AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATAGAATTTTTGAAAGTTCGAGGGT
* *
17772 AAAAATAGAATTTTTTAAACTTCGA-GGT
1 AAAAATAGAATTTTTGAAAGTTCGAGGGT
*
17800 GAAAAT-GAAATTTTTGAAAGTTC-AGGGGT
1 AAAAATAG-AATTTTTGAAAGTTCGA-GGGT
*
17829 AAAAATATAATTTTT
1 AAAAATAGAATTTTT
17844 AGATAGTTTA
Statistics
Matches: 219, Mismatches: 34, Indels: 44
0.74 0.11 0.15
Matches are distributed among these distances:
27 14 0.06
28 70 0.32
29 88 0.40
30 27 0.12
31 19 0.09
32 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAAATAGAATTTTTGAAAGTTCGAGGGT
Found at i:17713 original size:116 final size:115
Alignment explanation
Indices: 17560--17843 Score: 308
Period size: 116 Copynumber: 2.5 Consensus size: 115
17550 TTTTTGGACA
* * * * * *
17560 TTCGGGGGTAAAATGGTAATTTTTGAGAGTTTGGGGGTCAAAAATGGAGTTTTTGGACATTCGGG
1 TTCGAGGGTAAAATGATAATTTTTGAAAGTTTGGGGGTCAAAAATGGAATTTTTGGAAATTAGGG
* * * *
17625 G-AAAATTAGTAATTTTTGAAAGTTTCGATGTTAAAAATAGAATTTTGCAAG
66 GTAAAAAT-GGAATTTTTGAAAG-TTCGAGGGTAAAAATAGAATTTTGCAAG
* *
17676 TTCGAGGGTAAAATTATAATTTTT-ATAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAATTAGG
1 TTCGAGGGTAAAATGATAATTTTTGA-AAGTTTGGGGGTCAAAAATGGAATTTTTGGAAATTAGG
* ** *
17740 GGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTTAAAC
65 GGTAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATAGAA-TTTTGCAAG
** **
17792 TTCGA-GGTGAAAATGA-AATTTTTGAAAGTTCAGGGGT-AAAAATATAATTTTT
1 TTCGAGGGT-AAAATGATAATTTTTGAAAGTTTGGGGGTCAAAAATGGAATTTTT
17844 AGATAGTTTA
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
114 13 0.09
115 38 0.27
116 86 0.61
117 5 0.04
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (115 bp):
TTCGAGGGTAAAATGATAATTTTTGAAAGTTTGGGGGTCAAAAATGGAATTTTTGGAAATTAGGG
GTAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAATAGAATTTTGCAAG
Found at i:18973 original size:22 final size:21
Alignment explanation
Indices: 18940--18998 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 21
18930 TATTTATACC
18940 TTATTAATATTATTAATAAAA
1 TTATTAATATTATTAATAAAA
18961 TTATTCAATATTATTAATAAAA
1 TTATT-AATATTATTAATAAAA
18983 TTATTTAATATGTATT
1 TTA-TTAATAT-TATT
18999 TAATGCATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.14
22 24 0.69
23 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTAATATTATTAATAAAA
Found at i:18975 original size:10 final size:9
Alignment explanation
Indices: 18910--18979 Score: 50
Period size: 9 Copynumber: 7.0 Consensus size: 9
18900 TGTTATTTAT
*
18910 TTATTATTA
1 TTATTAATA
*
18919 TTAATTATTA
1 TT-ATTAATA
*
18929 TTATTTATA
1 TTATTAATA
18938 CCTTATTAATA
1 --TTATTAATA
18949 TTATTAATAAAA
1 TTATTAAT---A
18961 TTATTCAATA
1 TTATT-AATA
18971 TTATTAATA
1 TTATTAATA
18980 AAATTATTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
9 19 0.37
10 15 0.29
11 8 0.16
12 6 0.12
13 3 0.06
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATTAATA
Found at i:19505 original size:78 final size:78
Alignment explanation
Indices: 19372--19528 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
19362 TCCGTAACCT
*
19372 TTCAACAGGTTTCTCATCTGGCTTTATAGCCATATCCCCCATAATTACAATCTGTTTTTTCATTT
1 TTCAACAGGTTTCTCATCTGGCTTTATAGCCATATCCCCCATAATTACAAACTGTTTTTTCATTT
19437 AATGCTTGTCCAG
66 AATGCTTGTCCAG
*
19450 TTCAACAGGTTTCTCATCTGGCTTTATAGCCATATCTCCCATAATTACAAACTGTTTTTTCATTT
1 TTCAACAGGTTTCTCATCTGGCTTTATAGCCATATCCCCCATAATTACAAACTGTTTTTTCATTT
19515 AATGCTTGTCCAG
66 AATGCTTGTCCAG
19528 T
1 T
19529 CCTTCCTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (78 bp):
TTCAACAGGTTTCTCATCTGGCTTTATAGCCATATCCCCCATAATTACAAACTGTTTTTTCATTT
AATGCTTGTCCAG
Found at i:21018 original size:30 final size:30
Alignment explanation
Indices: 20956--21149 Score: 182
Period size: 30 Copynumber: 6.5 Consensus size: 30
20946 AACATTGAAC
* * *
20956 TTTTGGAAAA-TTT-GAGGTCAAAAATGTGA
1 TTTTGGAAAAGTTTAGGGGTC-AAAATATAA
* *
20985 TTTTGGAGAAGTTTAGGGGTTAAAATATAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATATAA
* *
21015 TTTTGGAAAAGTTTTGGGGT-AAAATTTTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAA-TATAA
*
21045 TTTTGGAAAAGTTTAGGGATCAAAATATAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATATAA
* ** * *
21075 TTTTGGAGAAG-TTACAAGGTCAAAATGTGAT
1 TTTTGGAAAAGTTTA-GGGGTCAAAATAT-AA
21106 TTTTGG-AAAGTTTAGGGGTCAAAATATAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATATAA
**
21135 TTTTTAAAAAGTTTA
1 TTTTGGAAAAGTTTA
21150 AGGGCCTCAT
Statistics
Matches: 133, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
29 21 0.16
30 94 0.71
31 18 0.14
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAGGGGTCAAAATATAA
Found at i:21059 original size:60 final size:61
Alignment explanation
Indices: 20956--21152 Score: 217
Period size: 60 Copynumber: 3.3 Consensus size: 61
20946 AACATTGAAC
* * *
20956 TTTTGGAAAA-TTT-GAGGTCAAAAATGTG-ATTTTGGAGAAGTTTAGGGGTTAAAATATAA
1 TTTTGGAAAAGTTTCAAGGTC-AAAATGTGAATTTTGGAAAAGTTTAGGGGTCAAAATATAA
*** * * *
21015 TTTTGGAAAAGTTTTGGGGT-AAAATTTTAATTTTGGAAAAGTTTAGGGATCAAAATATAA
1 TTTTGGAAAAGTTTCAAGGTCAAAATGTGAATTTTGGAAAAGTTTAGGGGTCAAAATATAA
* * *
21075 TTTTGGAGAAGTTACAAGGTCAAAATGTGATTTTTGG-AAAGTTTAGGGGTCAAAATATAA
1 TTTTGGAAAAGTTTCAAGGTCAAAATGTGAATTTTGGAAAAGTTTAGGGGTCAAAATATAA
**
21135 TTTTTAAAAAGTTT-AAGG
1 TTTTGGAAAAGTTTCAAGG
21153 GCCTCATTAG
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 20 0.17
60 78 0.68
61 17 0.15
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (61 bp):
TTTTGGAAAAGTTTCAAGGTCAAAATGTGAATTTTGGAAAAGTTTAGGGGTCAAAATATAA
Found at i:21100 original size:90 final size:90
Alignment explanation
Indices: 20984--21149 Score: 203
Period size: 90 Copynumber: 1.8 Consensus size: 90
20974 CAAAAATGTG
** * * *
20984 ATTTTGGAGAAGTTTAGGGGTTAAAATAT-AATTTTGGAAAAGTTTTGGGGT-AAAATTTTAATT
1 ATTTTGGAGAAGTTTAAAGGTCAAAATATGAATTTTGG-AAAGTTTAGGGGTCAAAA-TATAATT
*
21047 TTGGAAAAGTTTAGGGATCAAAATATA
64 TTGAAAAAGTTTAGGGATCAAAATATA
* *
21074 ATTTTGGAGAAG-TTACAAGGTCAAAATGTGATTTTTGGAAAGTTTAGGGGTCAAAATATAATTT
1 ATTTTGGAGAAGTTTA-AAGGTCAAAATATGAATTTTGGAAAGTTTAGGGGTCAAAATATAATTT
*
21138 TTAAAAAGTTTA
65 TGAAAAAGTTTA
21150 AGGGCCTCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
89 3 0.05
90 50 0.78
91 11 0.17
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (90 bp):
ATTTTGGAGAAGTTTAAAGGTCAAAATATGAATTTTGGAAAGTTTAGGGGTCAAAATATAATTTT
GAAAAAGTTTAGGGATCAAAATATA
Found at i:22141 original size:20 final size:18
Alignment explanation
Indices: 22103--22158 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
22093 TTGAATTTTT
22103 TTTA-TTAATATTTATTA
1 TTTATTTAATATTTATTA
22120 TTTATTTAATATTATAATTA
1 TTTATTTAATATT-T-ATTA
*
22140 TTTA-TTATGTATTTATTA
1 TTTATTTA-ATATTTATTA
22158 T
1 T
22159 AAATGTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 5 0.15
20 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATTTAATATTTATTA
Found at i:23160 original size:39 final size:37
Alignment explanation
Indices: 23117--23239 Score: 106
Period size: 39 Copynumber: 3.2 Consensus size: 37
23107 AATGGTTGTA
* *
23117 ATCTGCACTAAGCTCGAGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATT-G-TGATGGTG
* * * *
23156 ATCTGCCCCAGGCTAGGGGTAAGAGATTG-AATGGTTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATTGTGATGG-TG
23193 CAATCTGCCCCAAGCTC-AGGGTAAGAGATTGGTTGATGGTG
1 --ATCTGCCCCAAGCTCGA-GGTAAGAGATT-G-TGATGGTG
23234 ATCTGC
1 ATCTGC
23240 TCTATGATCG
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 1 0.01
39 53 0.79
40 1 0.01
41 2 0.03
42 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (37 bp):
ATCTGCCCCAAGCTCGAGGTAAGAGATTGTGATGGTG
Found at i:23253 original size:78 final size:78
Alignment explanation
Indices: 23098--23271 Score: 215
Period size: 78 Copynumber: 2.2 Consensus size: 78
23088 GTTCTTTTTA
* *
23098 AAGAGATTGAATGGTTGTAATCTGCACTAAGCTCGAGGTAAGAGATTAGCTGATGGTGATCTGCC
1 AAGAGATTGAATGGTTGCAATCTGCACCAAGCTCGAGGTAAGAGATTAGCTGATGGTGATCTGCC
*
23163 CCAGGCTAGGGGT
66 CCAGGATAGGGGT
* * *
23176 AAGAGATTGAATGGTTGCAATCTGCCCCAAGCTC-AGGGTAAGAGATTGGTTGATGGTGATCTGC
1 AAGAGATTGAATGGTTGCAATCTGCACCAAGCTCGA-GGTAAGAGATTAGCTGATGGTGATCTGC
* * * *
23240 TCTATGATCGGGGT
65 CCCAGGATAGGGGT
* * *
23254 AAAAGATCGAATAGTTGC
1 AAGAGATTGAATGGTTGC
23272 TGTAGAGACC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 1 0.01
78 81 0.99
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (78 bp):
AAGAGATTGAATGGTTGCAATCTGCACCAAGCTCGAGGTAAGAGATTAGCTGATGGTGATCTGCC
CCAGGATAGGGGT
Done.