Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005240.1 Kokia drynarioides strain JFW-HI SEQ_119132, 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: 9303
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:4399 original size:9 final size:9
Alignment explanation
Indices: 4385--4453 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
4375 GCAAATGATT
4385 TTAAAATTA
1 TTAAAATTA
4394 TTAAAATTA
1 TTAAAATTA
4403 TT----TT-
1 TTAAAATTA
4407 TTAAAA-TA
1 TTAAAATTA
*
4415 -TAAAATAA
1 TTAAAATTA
4423 TTAAAATTA
1 TTAAAATTA
4432 TTTTAAAATTA
1 --TTAAAATTA
4443 TTAAAATTA
1 TTAAAATTA
4452 TT
1 TT
4454 TTTTTGAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.12
8 1 0.02
9 29 0.59
11 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:4405 original size:20 final size:20
Alignment explanation
Indices: 4377--4455 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
4367 CCACGTCAGC
*
4377 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
4397 AAATTATTTTTTAAAATATAAAATAATTA
1 AAATTA--TTTT-AAA-AT----TA-TTA
4426 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
4446 AAATTATTTT
1 AAATTATTTT
4456 TTTGAAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
20 18 0.37
21 2 0.04
22 4 0.08
23 3 0.06
24 2 0.04
25 2 0.04
26 3 0.06
27 4 0.08
28 2 0.04
29 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:4439 original size:11 final size:11
Alignment explanation
Indices: 4423--4455 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4413 TATAAAATAA
4423 TTAAAATTATT
1 TTAAAATTATT
4434 TTAAAATTA--
1 TTAAAATTATT
4443 TTAAAATTATT
1 TTAAAATTATT
4454 TT
1 TT
4456 TTTGAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:4447 original size:29 final size:29
Alignment explanation
Indices: 4385--4449 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
4375 GCAAATGATT
*
4385 TTAAAATTATTAAAATTATTTTTTAAAATA
1 TTAAAATAATTAAAATTA-TTTTTAAAATA
4415 -TAAAATAATTAAAATTA-TTTTAAAATTA
1 TTAAAATAATTAAAATTATTTTTAAAA-TA
4443 TTAAAAT
1 TTAAAAT
4450 TATTTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 8 0.25
28 2 0.06
29 22 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAAATAATTAAAATTATTTTTAAAATA
Found at i:4454 original size:49 final size:50
Alignment explanation
Indices: 4377--4487 Score: 174
Period size: 49 Copynumber: 2.2 Consensus size: 50
4367 CCACGTCAGC
*
4377 AAATGATTTTAAAATTATTAAAATTA-TTTTTT-AAA-ATATAAAATAATT
1 AAATTATTTTAAAATTATTAAAATTATTTTTTTGAAACA-ATAAAATAATT
4425 AAAATTATTTTAAAATTATTAAAATTATTTTTTTGAAACAATAAAATAATT
1 -AAATTATTTTAAAATTATTAAAATTATTTTTTTGAAACAATAAAATAATT
4476 AAATTATTTTAA
1 AAATTATTTTAA
4488 TTTCCAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
49 25 0.43
50 18 0.31
51 14 0.24
52 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (50 bp):
AAATTATTTTAAAATTATTAAAATTATTTTTTTGAAACAATAAAATAATT
Found at i:5981 original size:42 final size:42
Alignment explanation
Indices: 5934--6185 Score: 240
Period size: 42 Copynumber: 5.9 Consensus size: 42
5924 TGTGTGTGAC
* * *
5934 TTCAATCTACCCTTCTAGATTAAGGGTAAAAGACTGGACAGT
1 TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGATAGT
* ** * *
5976 TTCAATCTGCCCTTTTAGATTACAGGTAAAAGATTGGATGGTGGT
1 TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGA---TAGT
* * *
6021 TTCAATATGCCCCTT-TAGATTAGGGGTAAAAGATTGGAT-GAC
1 TTCAATCTG-CCCTTCTAGATTAGGGGTAAAAGACTGGATAG-T
* * * ** * *
6063 TTCAATTTGCCCCTCTATATTAGGGGTAAAAGACTAAATGGC
1 TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGATAGT
*
6105 TTCAATCTGCCCTTTTAGATTAGGGGTAAAAGACTGGATAGCT
1 TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGATAG-T
* *
6148 TT-AATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGAT
1 TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGAT
6186 GGTGATGTAA
Statistics
Matches: 174, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
41 5 0.03
42 130 0.75
43 3 0.02
45 31 0.18
46 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (42 bp):
TTCAATCTGCCCTTCTAGATTAGGGGTAAAAGACTGGATAGT
Found at i:6038 original size:45 final size:45
Alignment explanation
Indices: 5974--6060 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
5964 AGACTGGACA
* *
5974 GTTTCAATCTGCCCTTTTAGATTACAGGTAAAAGATTGGATGGTG
1 GTTTCAATATGCCCCTTTAGATTACAGGTAAAAGATTGGATGGTG
**
6019 GTTTCAATATGCCCCTTTAGATTAGGGGTAAAAGATTGGATG
1 GTTTCAATATGCCCCTTTAGATTACAGGTAAAAGATTGGATG
6061 ACTTCAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (45 bp):
GTTTCAATATGCCCCTTTAGATTACAGGTAAAAGATTGGATGGTG
Found at i:6136 original size:84 final size:84
Alignment explanation
Indices: 5943--6179 Score: 269
Period size: 84 Copynumber: 2.8 Consensus size: 84
5933 CTTCAATCTA
* * * * * **
5943 CCCTTCTAGATTAAGGGTAAAAGACTGGACAGTTTCAATCTGCCCTTTTAGATTACAGGTAAAAG
1 CCCTT-TAGATTAGGGGTAAAAGACTGGATAGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAG
* ** *
6008 ATTGGATGGTGGTTTCAATATGC
65 ACT--A-AATGGCTTCAATATGC
* * *
6031 CCCTTTAGATTAGGGGTAAAAGATTGGAT-GACTTCAATTTGCCCCTCTATATTAGGGGTAAAAG
1 CCCTTTAGATTAGGGGTAAAAGACTGGATAG-CTTCAATCTGCCCCTCTAGATTAGGGGTAAAAG
*
6095 ACTAAATGGCTTCAATCTGC
65 ACTAAATGGCTTCAATATGC
* *
6115 CCTTTTAGATTAGGGGTAAAAGACTGGATAGCTTTAATCTGCCCCTCTAGATTAGGGGTAAAAGA
1 CCCTTTAGATTAGGGGTAAAAGACTGGATAGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGA
6180 TTGGATGGTG
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
84 70 0.55
85 2 0.02
86 1 0.01
87 49 0.39
88 5 0.04
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (84 bp):
CCCTTTAGATTAGGGGTAAAAGACTGGATAGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGA
CTAAATGGCTTCAATATGC
Found at i:6659 original size:98 final size:97
Alignment explanation
Indices: 6391--6659 Score: 292
Period size: 98 Copynumber: 2.7 Consensus size: 97
6381 GGATCTGATG
* * * *
6391 CTTCACTCCATTCCACTGTAACCTTAGGGAAATTGAGATCTGCTTCGTCGTTTTAATTCGATCCA
1 CTTCTCTCCATT-CACTGTAACCTCAGGG-AATTGAGATCTGCTTCATCGTTTTAATCCGATCCA
* *
6456 CTGCAATTCAAAGGTATGAGATTTGTTATTGTAA
64 CTGCAACTCAAAGGTATGAGATTTGATATTGTAA
* * * *
6490 CTTCTCTCCATTCTATTGTAATCTCAGGGAATTGAGATCTGCTTCATTGTTTTAATCTGA-CCTA
1 CTTCTCTCCATTC-ACTGTAACCTCAGGGAATTGAGATCTGCTTCATCGTTTTAATCCGATCC-A
* * *
6554 CTACAACTCAAGGGTATGAGATTTGATGTTGTAA
64 CTGCAACTCAAAGGTATGAGATTTGATATTGTAA
* * * * *
6588 CTTCTCTCCATTACACTGTAACCTCAAGGATATTGAGATTTG-TT-ACTCATTTTGATCCAATCC
1 CTTCTCTCCATT-CACTGTAACCTCAGGGA-ATTGAGATCTGCTTCA-TCGTTTTAATCCGATCC
6651 ACTGCAACT
63 ACTGCAACT
6660 TCAGGGATAC
Statistics
Matches: 141, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
97 3 0.02
98 102 0.72
99 36 0.26
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (97 bp):
CTTCTCTCCATTCACTGTAACCTCAGGGAATTGAGATCTGCTTCATCGTTTTAATCCGATCCACT
GCAACTCAAAGGTATGAGATTTGATATTGTAA
Done.