Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007298.1 Kokia drynarioides strain JFW-HI SEQ_121914, 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: 17456
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1082 original size:18 final size:21
Alignment explanation
Indices: 1046--1087 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1036 ATAATTTTTT
1046 TTTAAATATAGTTGCAAAT-A
1 TTTAAATATAGTTGCAAATGA
*
1066 TTTATATATA-TTG-AAATGA
1 TTTAAATATAGTTGCAAATGA
1085 TTT
1 TTT
1088 GAACATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTAAATATAGTTGCAAATGA
Found at i:4852 original size:17 final size:17
Alignment explanation
Indices: 4810--4853 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4800 TTATTATTCA
*
4810 TTAATT-TTTTATAATT
1 TTAATTATTTTAAAATT
**
4826 TTAACAATTTTAAAATT
1 TTAATTATTTTAAAATT
4843 TTAATTATTTT
1 TTAATTATTTT
4854 TCAATCAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATTATTTTAAAATT
Found at i:8430 original size:6 final size:6
Alignment explanation
Indices: 8419--8464 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
8409 TATTTTCATC
* *
8419 ATCTCT ATCTCT ATCTGT ATCTCT ATCTCT ATCTCT ATATCT ATCT
1 ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCT
8465 ACACCTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (6 bp):
ATCTCT
Found at i:13843 original size:20 final size:20
Alignment explanation
Indices: 13818--13884 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
13808 AATTCTAAAC
13818 CTCAAATCTTAAACCTCGAG
1 CTCAAATCTTAAACCTCGAG
* ** *
13838 CTCAAATCTTAAACTATAAAT
1 CTCAAATCTTAAAC-CTCGAG
* *
13859 CTCAAATCTTGAATCTCGAG
1 CTCAAATCTTAAACCTCGAG
13879 CTCAAA
1 CTCAAA
13885 CCTCAAATTT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (20 bp):
CTCAAATCTTAAACCTCGAG
Found at i:14980 original size:20 final size:20
Alignment explanation
Indices: 14941--14992 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
14931 AGTCTTCAAG
* *
14941 GTATCGGTAAAATTGAAGTT
1 GTATCGGTAGAAGTGAAGTT
*
14961 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGAAGTT
* *
14981 CTATCGATAGAA
1 GTATCGGTAGAA
14993 CTCCCAGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAAGTGAAGTT
Found at i:16557 original size:29 final size:28
Alignment explanation
Indices: 16466--16888 Score: 341
Period size: 29 Copynumber: 14.8 Consensus size: 28
16456 AAATCAGGGT
* **
16466 TAAAAATGAAATTTTTGGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
* *
16495 TCAAAATAGG-A-TTTTGGAAGTTTAGGGG
1 TAAAAAT-GGAATTTTTGGAAG-TTCGGGG
*
16523 TAAAAATGGAATTTTTGTAAGTTCGGTGG
1 TAAAAATGGAATTTTTGGAAGTTCGG-GG
* *
16552 TCAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTC-GGGG
16581 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
* *
16610 TCAAAAATGGGATTTTTGGAAATTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTCG-GGG
* * *
16640 TAAAAATGGGATTTTTGGAATTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGGG
*
16668 T-AAAATGGAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
*
16696 TTAAAAATGGGAA-TTTTGGAAGTTTGGGGG
1 -TAAAAAT-GGAATTTTTGGAAG-TTCGGGG
16726 TAAAAATGGAATTTTTAGG-A--TC----
1 TAAAAATGGAATTTTT-GGAAGTTCGGGG
* * * *
16748 -AAAAATGGGATTTTTGGAATTTTAGGTG
1 TAAAAATGGAATTTTTGGAA-GTTCGGGG
* *
16776 TAAAGATGGAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
* * *
16805 TCAAAAATTGGATTTTTTTGAAGTTTAGGGG
1 T-AAAAA-TGGAATTTTTGGAAG-TTCGGGG
*
16836 TAAAAATGGAATTTTTAGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
16865 TTAAAAAT-GAGATTTTTGGAAGTT
1 -TAAAAATGGA-ATTTTTGGAAGTT
16889 AGGGACCTCC
Statistics
Matches: 330, Mismatches: 36, Indels: 56
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.01
21 15 0.05
24 1 0.00
26 1 0.00
27 19 0.06
28 40 0.12
29 150 0.45
30 77 0.23
31 25 0.08
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTCGGGG
Found at i:16594 original size:58 final size:57
Alignment explanation
Indices: 16466--16888 Score: 354
Period size: 59 Copynumber: 7.4 Consensus size: 57
16456 AAATCAGGGT
* * * **
16466 TAAAAATGAAATTTTTGGAAGTTTTAGGGTCAAAATAGGA-TTTTGGAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGAAG-TTTGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGG
* *
16523 TAAAAATGGAATTTTTGTAAGTTCGGTGGTCAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTGG-GGTCAAAATGGGATTTTTGGAAGTTCGGGGG
* *
16581 TAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAATTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTT-GGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGG
* * * *
16640 TAAAAATGGGATTTTTGGAA-TTTGGGGGT-AAAATGGAATTTTTGGAAGTTTTGGGGT
1 TAAAAATGGAATTTTTGGAAGTTT-GGGGTCAAAATGGGATTTTTGGAAG-TTCGGGGG
* *
16697 TAAAAATGGGAA-TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTAGG-A--TC-----
1 TAAAAAT-GGAATTTTTGGAAGTTT-GGGGTCAAAATGGGATTTTT-GGAAGTTCGGGGG
* * * * **
16748 -AAAAATGGGATTTTTGGAATTTTAGGTGT-AAAGATGGAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTT-GGGGTCAAA-ATGGGATTTTTGGAAGTTCGGGGG
* * * * * *
16805 TCAAAAATTGGATTTTTTTGAAGTTTAGGGGTAAAAATGGAATTTTTAGAAGTTTCGGGGT
1 T-AAAAA-TGGAATTTTTGGAAGTTT-GGGGTCAAAATGGGATTTTTGGAAG-TTCGGGGG
16866 TAAAAAT-GAGATTTTTGGAAGTT
1 TAAAAATGGA-ATTTTTGGAAGTT
16889 AGGGACCTCC
Statistics
Matches: 305, Mismatches: 36, Indels: 48
0.78 0.09 0.12
Matches are distributed among these distances:
49 8 0.03
50 33 0.11
52 1 0.00
56 21 0.07
57 51 0.17
58 63 0.21
59 78 0.26
60 41 0.13
61 9 0.03
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (57 bp):
TAAAAATGGAATTTTTGGAAGTTTGGGGTCAAAATGGGATTTTTGGAAGTTCGGGGG
Found at i:16736 original size:50 final size:50
Alignment explanation
Indices: 16682--16793 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
16672 ATGGAATTTT
* * * *
16682 TGGAAGTTTTGGGGTTAAAAATGGGAATTTTGGAAGTTTGGGGGTAAAAA
1 TGGAATTTTTGGGATCAAAAATGGGAATTTTGGAAGTTTAGGGGTAAAAA
* * * * *
16732 TGGAATTTTTAGGATCAAAAATGGGATTTTTGGAATTTTAGGTGTAAAGA
1 TGGAATTTTTGGGATCAAAAATGGGAATTTTGGAAGTTTAGGGGTAAAAA
16782 TGGAATTTTTGG
1 TGGAATTTTTGG
16794 AAGTTTTGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.31, C:0.01, G:0.31, T:0.37
Consensus pattern (50 bp):
TGGAATTTTTGGGATCAAAAATGGGAATTTTGGAAGTTTAGGGGTAAAAA
Found at i:16851 original size:60 final size:60
Alignment explanation
Indices: 16732--16892 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 60
16722 GGGGTAAAAA
* * * * * * *
16732 TGGAATTTTTAGGATCAAAAATGGGA-TTTTTGGAATTTTAGGTGTAAAGATGGAATTTT
1 TGGAAGTTTTGGGGTCAAAAATTGGATTTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
*
16791 TGGAAGTTTTGGGGTCAAAAATTGGATTTTTTTGAAGTTTAGGGGTAAAAATGGAATTTT
1 TGGAAGTTTTGGGGTCAAAAATTGGATTTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
* * *
16851 TAGAAGTTTCGGGGTTAAAAA-TGAGA-TTTTTGGAAG-TTAGGG
1 TGGAAGTTTTGGGGTCAAAAATTG-GATTTTTTGGAAGTTTAGGG
16893 ACCTCCAGGG
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 6 0.07
59 33 0.38
60 49 0.56
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.39
Consensus pattern (60 bp):
TGGAAGTTTTGGGGTCAAAAATTGGATTTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
Done.