Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005077.1 Kokia drynarioides strain JFW-HI SEQ_118887, 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: 27644
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5973 original size:20 final size:20
Alignment explanation
Indices: 5948--5988 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5938 ATATATAGTA
5948 AGGGAGAGTTTAATCATGGT
1 AGGGAGAGTTTAATCATGGT
5968 AGGGAGAGTTTAATCATGGT
1 AGGGAGAGTTTAATCATGGT
5988 A
1 A
5989 CTTTCAGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (20 bp):
AGGGAGAGTTTAATCATGGT
Found at i:8973 original size:22 final size:22
Alignment explanation
Indices: 8942--8988 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
8932 TAATTGCTCC
8942 AACAACGAATGTGACATTTTGT
1 AACAACGAATGTGACATTTTGT
* *
8964 AACAATGAATGTGGCATTTTGT
1 AACAACGAATGTGACATTTTGT
8986 AAC
1 AAC
8989 TTGGACCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (22 bp):
AACAACGAATGTGACATTTTGT
Found at i:12994 original size:26 final size:26
Alignment explanation
Indices: 12952--13017 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
12942 TGAAATTTTC
* *
12952 TCGAATCGAGTCAAGTGTGATGGAAT
1 TCGAATCGAGTCGAGTGTGATGAAAT
*
12978 TTGAATCGAGTCGAGTGTGATGAAAT
1 TCGAATCGAGTCGAGTGTGATGAAAT
*
13004 TCGAATCGAATCGA
1 TCGAATCGAGTCGA
13018 ATATATTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (26 bp):
TCGAATCGAGTCGAGTGTGATGAAAT
Found at i:16030 original size:15 final size:15
Alignment explanation
Indices: 16010--16041 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16000 GCATTTTGTC
16010 ATTTTTTAAATAGTA
1 ATTTTTTAAATAGTA
*
16025 ATTTTTTAAATCGTA
1 ATTTTTTAAATAGTA
16040 AT
1 AT
16042 AAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTTTTTAAATAGTA
Found at i:18048 original size:6 final size:6
Alignment explanation
Indices: 18004--18065 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
17994 TAATAGGGAT
* * * * *
18004 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTCCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
18051 TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTT
18066 TGATCGCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 38 0.84
7 3 0.07
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTCAA
Found at i:20591 original size:26 final size:26
Alignment explanation
Indices: 20562--20614 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20552 ATAAATATGA
20562 CTCTATTTTCATTCTCGTAATTCTTC
1 CTCTATTTTCATTCTCGTAATTCTTC
20588 CTCTATTTTCATTCTCGTAATTCTTC
1 CTCTATTTTCATTCTCGTAATTCTTC
20614 C
1 C
20615 ATGCATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.28, G:0.04, T:0.53
Consensus pattern (26 bp):
CTCTATTTTCATTCTCGTAATTCTTC
Found at i:21141 original size:19 final size:18
Alignment explanation
Indices: 21119--21156 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 18
21109 TTAATAATCC
21119 AAAATAAAAATAATAATAAA
1 AAAAT-AAAATAAT-ATAAA
21139 AAAATAAAATAATATAAA
1 AAAATAAAATAATATAAA
21157 TTTGTAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAATAATATAAA
Found at i:22227 original size:14 final size:14
Alignment explanation
Indices: 22210--22252 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
22200 AAAGTCAACA
22210 GTCAACGATCAATG
1 GTCAACGATCAATG
*
22224 GTCAACGGTC---G
1 GTCAACGATCAATG
22235 GTCAACGATCAATG
1 GTCAACGATCAATG
22249 GTCA
1 GTCA
22253 GTCAATGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 10 0.42
14 14 0.58
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (14 bp):
GTCAACGATCAATG
Done.