Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007069.1 Kokia drynarioides strain JFW-HI SEQ_121678, 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: 14461
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:2546 original size:28 final size:30
Alignment explanation
Indices: 2480--2550 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
2470 ACTCTCAATA
2480 TTAAAAAAAATCAAATATAATTATTAATCT
1 TTAAAAAAAATCAAATATAATTATTAATCT
* *
2510 TTGAAAAAAAGTCGAATATAATTATTAATCT
1 TT-AAAAAAAATCAAATATAATTATTAATCT
*
2541 TAAAAAAAAA
1 TTAAAAAAAA
2551 AAAATCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (30 bp):
TTAAAAAAAATCAAATATAATTATTAATCT
Found at i:3105 original size:49 final size:50
Alignment explanation
Indices: 3031--3132 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 50
3021 AACTAAAACC
*
3031 ATTAAATTATTAATAAATTTATATTTTAATTAATT-AAT-TTTAAAAAATT
1 ATTAAATTATTAATAAATTTATATTTAAATT-ATTAAATATTTAAAAAATT
* *
3080 ATTAAATTATTCAAT-AGTTTCTATTTAAATTATTGAAATATTTAAAAAATT
1 ATTAAATTATT-AATAAATTTATATTTAAATTATT-AAATATTTAAAAAATT
3131 AT
1 AT
3133 ACTTAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
48 3 0.07
49 24 0.52
50 6 0.13
51 13 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (50 bp):
ATTAAATTATTAATAAATTTATATTTAAATTATTAAATATTTAAAAAATT
Found at i:3352 original size:36 final size:37
Alignment explanation
Indices: 3288--3365 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 37
3278 TCAAATCGTG
* *
3288 ATTATAATTTTAATACTTTAATTTATTTT-AAAATTT
1 ATTATAATTTGAATACTTTAATTGATTTTGAAAATTT
* * *
3324 ATTATAATTTGAGTTCTTTCATTGATTTTGAAAATTT
1 ATTATAATTTGAATACTTTAATTGATTTTGAAAATTT
3361 -TTATA
1 ATTATA
3366 TCCATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 29 0.81
37 7 0.19
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (37 bp):
ATTATAATTTGAATACTTTAATTGATTTTGAAAATTT
Found at i:6002 original size:104 final size:105
Alignment explanation
Indices: 5814--6011 Score: 258
Period size: 104 Copynumber: 1.9 Consensus size: 105
5804 GTCGTTTGAC
* * **
5814 ATTATGCTCATGGGAATCCATTTGGAATTTACGCTTGAGGATGGTTCACCCTTAGAAGGCGGAGA
1 ATTATGCTCATGGGAATACATTTAGAATTTACGCTTGAGGATGGTTCACCCTTAGAAGGCAAAGA
* *
5879 GATGTAAGATTAAGCAATAAGTAATGAGCCACCATCCAGG
66 GACGTAAGATTAAGCAATAAGAAATGAGCCACCATCCAGG
* *
5919 ATTATGCTCGTGGGCAA-ACATTTAGAA-TTACGCTTGAGGATGGTTCACCCTT-GGAGAGCAAA
1 ATTATGCTCATGGG-AATACATTTAGAATTTACGCTTGAGGATGGTTCACCCTTAGAAG-GCAAA
* * *
5981 GAGCCGTAATATTGAGCAATAAGAAATGAGC
64 GAGACGTAAGATTAAGCAATAAGAAATGAGC
6012 GGTCGTGGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
103 3 0.04
104 54 0.68
105 21 0.26
106 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (105 bp):
ATTATGCTCATGGGAATACATTTAGAATTTACGCTTGAGGATGGTTCACCCTTAGAAGGCAAAGA
GACGTAAGATTAAGCAATAAGAAATGAGCCACCATCCAGG
Found at i:9041 original size:16 final size:16
Alignment explanation
Indices: 9016--9050 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
9006 CTGAGACGTG
*
9016 TGTCATGAAGGTTAGT
1 TGTCAAGAAGGTTAGT
9032 TGTCAAGAAGGTTAGT
1 TGTCAAGAAGGTTAGT
9048 TGT
1 TGT
9051 GAACAGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.31, T:0.37
Consensus pattern (16 bp):
TGTCAAGAAGGTTAGT
Found at i:9312 original size:12 final size:12
Alignment explanation
Indices: 9295--9325 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
9285 TAAACCACTT
9295 TTATTTTTTAAA
1 TTATTTTTTAAA
9307 TTA-TTTTTAAA
1 TTATTTTTTAAA
9318 TTATTTTT
1 TTATTTTT
9326 AATTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTTTAAA
Found at i:9329 original size:10 final size:11
Alignment explanation
Indices: 9299--9327 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9289 CCACTTTTAT
9299 TTTTTAAATTA
1 TTTTTAAATTA
9310 TTTTTAAATTA
1 TTTTTAAATTA
9321 TTTTTAA
1 TTTTTAA
9328 TTTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTAAATTA
Found at i:13057 original size:22 final size:23
Alignment explanation
Indices: 13022--13064 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13012 TTTAAAAATA
* *
13022 TAAAACTATTAAAATTATTTTTT
1 TAAAACTAATAAAATAATTTTTT
13045 TAAAA-TAATAAAATAATTTT
1 TAAAACTAATAAAATAATTTT
13065 ATTTCCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAACTAATAAAATAATTTTTT
Found at i:14300 original size:28 final size:28
Alignment explanation
Indices: 14252--14343 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
14242 AACGGGTCGA
* * * *
14252 AAAATG-AAGTTTCAAAGAATTCGGGGTG
1 AAAATGTAATTTTGAAA-AATTTGGGGTC
* *
14280 AAAATGTAATTTTGAAAAATTTAGGGTT
1 AAAATGTAATTTTGAAAAATTTGGGGTC
* * *
14308 AGAATGTAATTTTAGGAAATTTTGGGGTC
1 AAAATGTAATTTT-GAAAAATTTGGGGTC
14337 AAAATGT
1 AAAATGT
14344 GTTTTTGGGG
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGAAAAATTTGGGGTC
Found at i:14351 original size:19 final size:19
Alignment explanation
Indices: 14327--14370 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
14317 TTTTAGGAAA
14327 TTTTGGGGTCAAAATGTGT
1 TTTTGGGGTCAAAATGTGT
14346 TTTTGGGGTCAAAATGTGT
1 TTTTGGGGTCAAAATGTGT
14365 TTTTGG
1 TTTTGG
14371 AAAGTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTGT
Found at i:14396 original size:77 final size:76
Alignment explanation
Indices: 14274--14418 Score: 218
Period size: 77 Copynumber: 1.9 Consensus size: 76
14264 CAAAGAATTC
* * *
14274 GGGGTGAAAATGTAATTTTGAAAAATTTAGGGTTAGAATGTAATTTTAGGAAATTTTGGGGTCAA
1 GGGGTCAAAATGTAATTTTGAAAAATTTAGGGTTAAAATGTAATTTTAGGAAATTTAGGGGTCAA
14339 AATGTGTTTTT
66 AATGTGTTTTT
** * *
14350 GGGGTCAAAATGTGTTTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAATTTAGGGGTCA
1 GGGGTCAAAATGTAATTTTGAAAAATTT-AGGGTTAAAATGTAATTTTAGGAAATTTAGGGGTCA
14415 AAAT
65 AAAT
14419 CTAATTTTAG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
76 23 0.38
77 38 0.62
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (76 bp):
GGGGTCAAAATGTAATTTTGAAAAATTTAGGGTTAAAATGTAATTTTAGGAAATTTAGGGGTCAA
AATGTGTTTTT
Found at i:14397 original size:29 final size:29
Alignment explanation
Indices: 14351--14461 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 29
14341 TGTGTTTTTG
* *
14351 GGGTCAAAATGT-GTTTTTGGAAAGTTTAA
1 GGGTCAAAATGTAATTTTAGGAAA-TTTAA
* *
14380 GGGTTAAAATGTAATTTTAGGAAATTTAG
1 GGGTCAAAATGTAATTTTAGGAAATTTAA
* *
14409 GGGTCAAAATCTAATTTTAGGCAAATTTTA
1 GGGTCAAAATGTAATTTTAGG-AAATTTAA
*
14439 GGGTTAAAATGTAATTTT-GGAAA
1 GGGTCAAAATGTAATTTTAGGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.04
29 36 0.51
30 31 0.44
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAGGAAATTTAA
Done.