Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012619.1 Kokia drynarioides strain JFW-HI SEQ_127628, 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: 8235
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:191 original size:9 final size:9
Alignment explanation
Indices: 177--211 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
167 TTTTTCCTCT
177 CCTTCTTCC
1 CCTTCTTCC
*
186 CCTTCTTCT
1 CCTTCTTCC
195 CCTTCTTCC
1 CCTTCTTCC
204 TCCTTCTT
1 -CCTTCTT
212 TCTCTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (9 bp):
CCTTCTTCC
Found at i:222 original size:10 final size:10
Alignment explanation
Indices: 191--239 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
181 CTTCCCCTTC
*
191 TTCTCCTTCT
1 TTCTCTTTCT
* *
201 TCCTCCTTCT
1 TTCTCTTTCT
211 TTCTCTTTC-
1 TTCTCTTTCT
220 TT-TCTTTCT
1 TTCTCTTTCT
229 TT-TCTTTCT
1 TTCTCTTTCT
238 TT
1 TT
240 TTTCCTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 6 0.17
9 13 0.37
10 16 0.46
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTCTTTCT
Found at i:234 original size:9 final size:9
Alignment explanation
Indices: 207--240 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
197 TTCTTCCTCC
207 TTCTTTCTCT
1 TTCTTT-TCT
217 TTC-TTTCT
1 TTCTTTTCT
225 TTCTTTTCT
1 TTCTTTTCT
234 TTCTTTT
1 TTCTTTT
241 TTCCTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 14 0.61
10 3 0.13
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:234 original size:13 final size:14
Alignment explanation
Indices: 207--239 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
197 TTCTTCCTCC
207 TTCTTTCTCTTTCT
1 TTCTTTCTCTTTCT
221 TTCTTTCT-TTTCT
1 TTCTTTCTCTTTCT
234 TTCTTT
1 TTCTTT
240 TTTCCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTCTCTTTCT
Found at i:5794 original size:25 final size:25
Alignment explanation
Indices: 5766--5852 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
5756 CAGCACTGTG
5766 TGTGCCCTCTGTTATTAGCACTTCA
1 TGTGCCCTCTGTTATTAGCACTTCA
* *
5791 TGTGCCCTC--TAATTAGCACTTCG
1 TGTGCCCTCTGTTATTAGCACTTCA
**
5814 TGTGCCCTCTGTTACCCAGCACTT-A
1 TGTGCCCTCTGTTA-TTAGCACTTCA
5839 TGTGCCCTCTGTTA
1 TGTGCCCTCTGTTA
5853 AGTACTTTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 21 0.40
25 25 0.47
26 7 0.13
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.37
Consensus pattern (25 bp):
TGTGCCCTCTGTTATTAGCACTTCA
Found at i:5809 original size:23 final size:23
Alignment explanation
Indices: 5779--5823 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5769 GCCCTCTGTT
5779 ATTAGCACTTCATGTGCCCTCTA
1 ATTAGCACTTCATGTGCCCTCTA
*
5802 ATTAGCACTTCGTGTGCCCTCT
1 ATTAGCACTTCATGTGCCCTCT
5824 GTTACCCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTAGCACTTCATGTGCCCTCTA
Found at i:5809 original size:48 final size:48
Alignment explanation
Indices: 5757--5848 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
5747 CCCTCTGCTC
**
5757 AGCACTGT-GTGTGCCCTCTGTTA-TTAGCACTTCATGTGCCCTCTAATT
1 AGCACT-TCGTGTGCCCTCTGTTACCCAGCACTT-ATGTGCCCTCTAATT
5805 AGCACTTCGTGTGCCCTCTGTTACCCAGCACTTATGTGCCCTCT
1 AGCACTTCGTGTGCCCTCTGTTACCCAGCACTTATGTGCCCTCT
5849 GTTAAGTACT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 1 0.03
48 32 0.80
49 7 0.17
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (48 bp):
AGCACTTCGTGTGCCCTCTGTTACCCAGCACTTATGTGCCCTCTAATT
Found at i:8212 original size:2 final size:2
Alignment explanation
Indices: 8205--8235 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8195 TTTGAAACTT
8205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.