Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008138.1 Kokia drynarioides strain JFW-HI SEQ_122796, 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: 18372
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:3473 original size:33 final size:34
Alignment explanation
Indices: 3431--3515 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
3421 TGTTGGTTGG
3431 TTAGCTCTTATGAGCATACAGTA-TATGGA-TTGA
1 TTAGCTCTTATGAGCATACAG-AGTATGGATTTGA
* *
3464 TTAGCTCTTATGAGCATACAGAGTTTTGATTTGA
1 TTAGCTCTTATGAGCATACAGAGTATGGATTTGA
*
3498 -TAGCTCTTATGACCATAC
1 TTAGCTCTTATGAGCATAC
3516 TGTGTTTACA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 42 0.89
34 4 0.09
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (34 bp):
TTAGCTCTTATGAGCATACAGAGTATGGATTTGA
Found at i:5973 original size:18 final size:18
Alignment explanation
Indices: 5932--5975 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5922 TAAATCTTTA
*
5932 TTTTTATTAGTATTATGC
1 TTTTTATTAGTATTATAC
*
5950 TTTTTATT-GTATTATAT
1 TTTTTATTAGTATTATAC
5967 TTATTTATT
1 TT-TTTATT
5976 TTTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTTTATTAGTATTATAC
Found at i:7301 original size:41 final size:41
Alignment explanation
Indices: 7256--7386 Score: 101
Period size: 41 Copynumber: 3.2 Consensus size: 41
7246 GACGAATATA
7256 GCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGG
1 GCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGG
** * ** * ***
7297 GCGGGGA-T-GGTTTTAGTCTTGTGAATCGC--G-GGACGAATATA
1 GCGGGGATTAGG-TGGA-TCTGGTG-ATC-CATGTGGGTG-GTGGG
7338 GCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGG
1 GCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGG
7379 GCGGGGAT
1 GCGGGGAT
7387 GGTTTTAGTC
Statistics
Matches: 62, Mismatches: 18, Indels: 20
0.62 0.18 0.20
Matches are distributed among these distances:
39 3 0.05
40 9 0.15
41 38 0.61
42 9 0.15
43 3 0.05
ACGTcount: A:0.15, C:0.11, G:0.47, T:0.27
Consensus pattern (41 bp):
GCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGG
Found at i:7381 original size:82 final size:82
Alignment explanation
Indices: 7244--7410 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 82
7234 AGTGGGTCGT
7244 GGGACGAATATAGCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGGGCGGGGATGGTT
1 GGGACGAATATAGCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGGGCGGGGATGGTT
* *
7309 TTAGTCTTGTGAATCGC
66 TTAGTCTTGCGAATCAC
7326 GGGACGAATATAGCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGGGCGGGGATGGTT
1 GGGACGAATATAGCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGGGCGGGGATGGTT
7391 TTAGTCTTGCGAATCAC
66 TTAGTCTTGCGAATCAC
7408 GGG
1 GGG
7411 GCGGGGATGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.17, C:0.11, G:0.44, T:0.27
Consensus pattern (82 bp):
GGGACGAATATAGCGGGGATTAGGTGGATCTGGTGATCCATGTGGGTGGTGGGGCGGGGATGGTT
TTAGTCTTGCGAATCAC
Found at i:9537 original size:133 final size:133
Alignment explanation
Indices: 9299--9548 Score: 367
Period size: 133 Copynumber: 1.9 Consensus size: 133
9289 GATTACATAT
* * * *
9299 GTTGACATTATCGGGCTGCTAACACTAGCTTCGGATCAGGATTGCTAACATTAGCTTCAGAGAAT
1 GTTGACATTATCGGGCTACTAACACTAGCTTCAGATCAGGATTGCTAACACTAGCTTAAGAGAAT
9364 CCACAACATATATTGAATCTCAAGCCATCGAATTAATCCCTGATCACAACACCCGTTTGTTTATA
66 CCACAACATATATTGAATCTCAAGCCATCGAATTAATCCCTGATCACAACACCCGTTTGTTTATA
9429 CAA
131 CAA
* * *
9432 GTTGACA-TATTCGGGCTACTAACACTGGCTTCAGATTAGGGTTGCTAACACTAGCTTAAGAGAA
1 GTTGACATTA-TCGGGCTACTAACACTAGCTTCAGATCAGGATTGCTAACACTAGCTTAAGAGAA
* * * * * *
9496 TCCGCAACATATTTTGGATTTCAAGCCATTGTATTAATCCCTGATCACAACAC
65 TCCACAACATATATTGAATCTCAAGCCATCGAATTAATCCCTGATCACAACAC
9549 TCGAATTCAT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
132 2 0.02
133 101 0.98
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (133 bp):
GTTGACATTATCGGGCTACTAACACTAGCTTCAGATCAGGATTGCTAACACTAGCTTAAGAGAAT
CCACAACATATATTGAATCTCAAGCCATCGAATTAATCCCTGATCACAACACCCGTTTGTTTATA
CAA
Found at i:12082 original size:304 final size:297
Alignment explanation
Indices: 11641--12224 Score: 647
Period size: 300 Copynumber: 1.9 Consensus size: 297
11631 TTTGTATAAC
* ** * *
11641 TATACTATTTAAAGTGTTTTATTGAGTTGGTGTCACCCTCAATCGGGTCACCAACTCAGTTAGAA
1 TATACTATTTAAAGTGTTTTATTGAGTTGGTATCACCCTCAATCGAATCACAAACTCAATTAGAA
* * * * * * *
11706 AAATTACGAAAACAATCTTCCGTAATTAAAATTAATTTATATTATTCGAGTGTAATTTAGTCTTT
66 AAATTACGAAAAC-ACCTTCCATAATCAAAATTAAGTTAGATTATTCAAGGGTAATTTAGTCTTT
* * * ** *
11771 TATTTAAAAACCAATGAAAAAAAATGTATATGGTGGGATTTGAAC-C-TTAGCTAATTGGGTTAG
130 TATTTAAAAA-C-A--AAAAAAAATGCATATGATGAGATTTGAACTCAAAAGATAATTGGGTT--
* *
11834 AAAAAAAAAATTAATTTATCACTCAACTAAAATTTTATTTTAATAATTT-TAAATATTTCAATTT
189 AAAAAAAAAATTAATTTATCACTAAACTAAAACTTTATTTTAAT-ATTTCTAAATATTTCAATTT
*
11898 TTATTATGCACACTTTATTATCACCATTATATATATATATATATA
253 TTACTATGCACACTTTATTATCACCATTATATATATATATATATA
** ** *
11943 TATACTATTTATTAAGTGTTTTATTGAGTTGGTATCACTTTCGTTCGAATCATAAACTCAATTAG
1 TATACTATTTA--AAGTGTTTTATTGAGTTGGTATCACCCTCAATCGAATCACAAACTCAATTAG
* *
12008 AAAAATTACAGAAATGC-CCTTTCATAATCAAAA-TAAGTTAGATTATTCAAGGGTAATTTAGTC
64 AAAAATTAC-GAAA-ACACCTTCCATAATCAAAATTAAGTTAGATTATTCAAGGGTAATTTAGTC
* *
12071 TTTTCATTTAAAAACAAATAAAAATGCATATGATGAGATTTGAACTCAAAATATAATTGGGTTAA
127 TTTT-ATTTAAAAACAAAAAAAAATGCATATGATGAGATTTGAACTCAAAAGATAATTGGGTTAA
* *** * * * * *
12136 CAAAACTTTTAATTTATCGCTAAATTAAAACTTTATTTTGATGTTTCTATATATTTCAATTTTTA
191 AAAAAAAATTAATTTATCACTAAACTAAAACTTTATTTTAATATTTCTAAATATTTCAATTTTTA
* *
12201 CTATGCACAGTTTATTATCTCCAT
256 CTATGCACACTTTATTATCACCAT
12225 CAATTGTACA
Statistics
Matches: 233, Mismatches: 41, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
299 3 0.01
300 98 0.42
301 1 0.00
302 23 0.10
303 31 0.13
304 72 0.31
305 4 0.02
306 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (297 bp):
TATACTATTTAAAGTGTTTTATTGAGTTGGTATCACCCTCAATCGAATCACAAACTCAATTAGAA
AAATTACGAAAACACCTTCCATAATCAAAATTAAGTTAGATTATTCAAGGGTAATTTAGTCTTTT
ATTTAAAAACAAAAAAAAATGCATATGATGAGATTTGAACTCAAAAGATAATTGGGTTAAAAAAA
AAATTAATTTATCACTAAACTAAAACTTTATTTTAATATTTCTAAATATTTCAATTTTTACTATG
CACACTTTATTATCACCATTATATATATATATATATA
Found at i:12817 original size:9 final size:8
Alignment explanation
Indices: 12803--12834 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
12793 TTTAAAAAGC
*
12803 ATAAAATT
1 ATAAAAAT
12811 ATAAAAAT
1 ATAAAAAT
12819 ATAAAAAT
1 ATAAAAAT
12827 ATAAAAAT
1 ATAAAAAT
12835 TTAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
ATAAAAAT
Found at i:12817 original size:17 final size:16
Alignment explanation
Indices: 12795--12833 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12785 TAACATTATT
*
12795 TAAAAAGCATAAAATTA
1 TAAAAA-CATAAAAATA
*
12812 TAAAAATATAAAAATA
1 TAAAAACATAAAAATA
12828 TAAAAA
1 TAAAAA
12834 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAAACATAAAAATA
Found at i:12991 original size:13 final size:13
Alignment explanation
Indices: 12973--12997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12963 GAAAATTTTT
12973 AAATAAATAAATA
1 AAATAAATAAATA
12986 AAATAAATAAAT
1 AAATAAATAAAT
12998 TTTTTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:15148 original size:13 final size:13
Alignment explanation
Indices: 15130--15154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15120 ACAAGGCATA
15130 GCTACCCTTTGTT
1 GCTACCCTTTGTT
15143 GCTACCCTTTGT
1 GCTACCCTTTGT
15155 ATCCTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.16, T:0.44
Consensus pattern (13 bp):
GCTACCCTTTGTT
Done.