Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010919.1 Kokia drynarioides strain JFW-HI SEQ_125887, 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: 15736
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3688 original size:12 final size:12
Alignment explanation
Indices: 3671--3702 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3661 TGATTTACTA
3671 ACACCTCTATTG
1 ACACCTCTATTG
3683 ACACCTCTATTG
1 ACACCTCTATTG
3695 ACA-CTCTA
1 ACACCTCTA
3703 GACATCGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.31
Consensus pattern (12 bp):
ACACCTCTATTG
Found at i:4659 original size:18 final size:18
Alignment explanation
Indices: 4636--4678 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
4626 GAACCACTGA
4636 TTCCCCTCATAAATAAGT
1 TTCCCCTCATAAATAAGT
4654 TTCCCCTCATAAATAAGT
1 TTCCCCTCATAAATAAGT
4672 TTCCCCT
1 TTCCCCT
4679 TGTAGCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (18 bp):
TTCCCCTCATAAATAAGT
Found at i:6322 original size:41 final size:38
Alignment explanation
Indices: 6227--6325 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 38
6217 AGCAATAAAG
* * *
6227 TGACACCCAATGTCTCATCG-GTCTAGCCGAAGTAATG
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
** ** *
6264 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGT--AAT-A
6305 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
6326 CTCAAGGTCG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
37 15 0.33
38 11 0.24
40 3 0.07
41 17 0.37
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
Found at i:7592 original size:41 final size:38
Alignment explanation
Indices: 7497--7595 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 38
7487 AGCAATAAAG
* * *
7497 TGACACCCAATGTCTCATCG-GTCTAGCCGAAGTAATG
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
** ** *
7534 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGT--AAT-A
7575 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
7596 CTCAAGGTCG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
37 15 0.33
38 11 0.24
40 3 0.07
41 17 0.37
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
Found at i:12158 original size:12 final size:12
Alignment explanation
Indices: 12141--12172 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12131 TGATTTACTA
12141 ACACCTCTATTG
1 ACACCTCTATTG
12153 ACACCTCTATTG
1 ACACCTCTATTG
12165 ACA-CTCTA
1 ACACCTCTA
12173 GACATCGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.31
Consensus pattern (12 bp):
ACACCTCTATTG
Found at i:13129 original size:18 final size:18
Alignment explanation
Indices: 13106--13148 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
13096 GAACCACTGA
13106 TTCCCCTCATAAATAAGT
1 TTCCCCTCATAAATAAGT
13124 TTCCCCTCATAAATAAGT
1 TTCCCCTCATAAATAAGT
13142 TTCCCCT
1 TTCCCCT
13149 TGTAGCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (18 bp):
TTCCCCTCATAAATAAGT
Found at i:14792 original size:41 final size:38
Alignment explanation
Indices: 14697--14795 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 38
14687 AGCAATAAAG
* * *
14697 TGACACCCAATGTCTCATCG-GTCTAGCCGAAGTAATG
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
** ** *
14734 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAATCTAGCCGAAGT--AAT-A
14775 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
14796 CTCAAGGTCG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
37 15 0.33
38 11 0.24
40 3 0.07
41 17 0.37
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAATCTAGCCGAAGTAATA
Done.