Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005410.1 Kokia drynarioides strain JFW-HI SEQ_119426, 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: 9790
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Found at i:2083 original size:10 final size:10
Alignment explanation
Indices: 2068--2093 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2058 AAGGGGAGAG
2068 GAAGAAAGAA
1 GAAGAAAGAA
2078 GAAGAAAGAA
1 GAAGAAAGAA
2088 GAAGAA
1 GAAGAA
2094 TAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:2710 original size:67 final size:67
Alignment explanation
Indices: 2625--2758 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
2615 TTATATAAAA
*
2625 ATAAATATTTATTTATATTATTTTGATCAGATCTTGTATCCTATATGAATATTTTATATTTATTT
1 ATAAATATTTATTTATATTATTTTGATCAGATCTTGTATCCTATATAAATATTTTATATTTATTT
2690 TT
66 TT
*
2692 ATAAATATTTATTTATATTATTTTGATCAGATTTTGTATCCTATATAAATATTTTATATTTATTT
1 ATAAATATTTATTTATATTATTTTGATCAGATCTTGTATCCTATATAAATATTTTATATTTATTT
2757 TT
66 TT
2759 CGCTAACGTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (67 bp):
ATAAATATTTATTTATATTATTTTGATCAGATCTTGTATCCTATATAAATATTTTATATTTATTT
TT
Found at i:3370 original size:15 final size:14
Alignment explanation
Indices: 3350--3390 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3340 AGTTGTGGCT
3350 TTAAATTGTGAAAGC
1 TTAAATTGTGAAA-C
3365 TTAAATTGT--AAC
1 TTAAATTGTGAAAC
3377 TTCAAATTGTGAAA
1 TT-AAATTGTGAAA
3391 TCAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 9 0.39
15 11 0.48
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
TTAAATTGTGAAAC
Found at i:4609 original size:19 final size:20
Alignment explanation
Indices: 4585--4626 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
4575 AAATTTCGAA
4585 GTGTTTGATATAGAC-TTAT
1 GTGTTTGATATAGACTTTAT
*
4604 GTGTTTGATATAGGCTTTAT
1 GTGTTTGATATAGACTTTAT
4624 GTG
1 GTG
4627 GGAATGGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (20 bp):
GTGTTTGATATAGACTTTAT
Found at i:6297 original size:50 final size:50
Alignment explanation
Indices: 6227--6344 Score: 218
Period size: 50 Copynumber: 2.4 Consensus size: 50
6217 AAATCTCATG
*
6227 TGATGTTTTAAATAAATATTTATATTTATTTAAAGTGATTTGTTTAAATC
1 TGATGTTTTAAATAAATATTTATATTTATTTAAAGTGATTTGTTTAAATA
6277 TGATGTTTTAAATAAATATTTATATTTATTTAAAGTGATTTGTTTAAATA
1 TGATGTTTTAAATAAATATTTATATTTATTTAAAGTGATTTGTTTAAATA
*
6327 TGATGTTTTATATAAATA
1 TGATGTTTTAAATAAATA
6345 AACATTTATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (50 bp):
TGATGTTTTAAATAAATATTTATATTTATTTAAAGTGATTTGTTTAAATA
Found at i:8999 original size:29 final size:28
Alignment explanation
Indices: 8894--9176 Score: 133
Period size: 30 Copynumber: 9.7 Consensus size: 28
8884 TGGATATTGG
* *
8894 GGGGT-AAAATGGTAATTTCAAGAAAGTTTA
1 GGGGTAAAAAT-GTAATTT-TAGAAAG-TTC
* * ** *
8924 GGGTTAAAAATGAAATTTTAGGTA-TCC
1 GGGGTAAAAATGTAATTTTAGAAAGTTC
*** * *
8951 GAGGGTAAAAGCATAATTTTTGGAAGTTC
1 G-GGGTAAAAATGTAATTTTAGAAAGTTC
* * *
8980 GGGGTCAAAATGTAATTTTTGGAAAAATT-
1 GGGGTAAAAATGTAA-TTTTAG-AAAGTTC
* * *
9009 GAGGTAAAAAATGGAATTTT-GAAAAGTTTA
1 GGGGT-AAAAATGTAATTTTAG-AAAG-TTC
* * *
9039 AGAGTAAAAATGTAATTTTTAAAAAGTTC
1 GGGGTAAAAATGTAA-TTTTAGAAAGTTC
* * *
9068 GAGGTCCAAAATATAATTTTAGAAAGTTC
1 GGGGT-AAAAATGTAATTTTAGAAAGTTC
9097 GGGGGTAAAAATGTAATTTTTAGAAAGTTC
1 -GGGGTAAAAATGTAA-TTTTAGAAAGTTC
* * *
9127 AGGGTTAAAAATATAATTTTAGAGAAGTTTG
1 -GGGGTAAAAATGTAATTTTAGA-AAG-TTC
* *
9158 GGGGTCAAAATATAATTTT
1 GGGGTAAAAATGTAATTTT
9177 TTGATAGTTT
Statistics
Matches: 191, Mismatches: 47, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.01
28 31 0.16
29 61 0.32
30 90 0.47
31 7 0.04
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTAGAAAGTTC
Found at i:9072 original size:59 final size:59
Alignment explanation
Indices: 8986--9155 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 59
8976 GTTCGGGGTC
* *
8986 AAAATGTAATTTTTGGAAAAA-TT-GAGGTAAAAAATGGAATTTT-GAAAAGTTTAAGAGTA
1 AAAATGTAATTTTT--AAAAAGTTCGAGGTAAAAAATAGAATTTTAG-AAAGTTCAAGAGTA
** * ** *
9045 AAAATGTAATTTTTAAAAAGTTCGAGGTCCAAAATATAATTTTAGAAAGTTCGGGGGTA
1 AAAATGTAATTTTTAAAAAGTTCGAGGTAAAAAATAGAATTTTAGAAAGTTCAAGAGTA
* * *
9104 AAAATGTAATTTTTAGAAAGTTC-AGGGTTAAAAATATAATTTTAGAGAAGTT
1 AAAATGTAATTTTTAAAAAGTTCGA-GGTAAAAAATAGAATTTTAGA-AAGTT
9156 TGGGGGTCAA
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
57 5 0.05
58 3 0.03
59 81 0.85
60 6 0.06
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (59 bp):
AAAATGTAATTTTTAAAAAGTTCGAGGTAAAAAATAGAATTTTAGAAAGTTCAAGAGTA
Found at i:9186 original size:30 final size:29
Alignment explanation
Indices: 9042--9176 Score: 146
Period size: 30 Copynumber: 4.6 Consensus size: 29
9032 AAGTTTAAGA
* * *
9042 GTAAAAATGTAATTTTTAAAAAGTTC-GAG
1 GTAAAAATATAA-TTTTAGAAAGTTCGGGG
*
9071 GTCCAAAATATAATTTTAGAAAGTTCGGGG
1 GT-AAAAATATAATTTTAGAAAGTTCGGGG
* *
9101 GTAAAAATGTAATTTTTAGAAAGTTCAGGG
1 GTAAAAATATAA-TTTTAGAAAGTTCGGGG
* *
9131 TTAAAAATATAATTTTAGAGAAGTTTGGGG
1 GTAAAAATATAATTTTAGA-AAGTTCGGGG
*
9161 GTCAAAATATAATTTT
1 GTAAAAATATAATTTT
9177 TTGATAGTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
29 29 0.33
30 60 0.67
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (29 bp):
GTAAAAATATAATTTTAGAAAGTTCGGGG
Done.