Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000343.1 Kokia drynarioides strain JFW-HI SEQ_111118, 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: 24074
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:93 original size:4 final size:4
Alignment explanation
Indices: 86--131 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
76 TCTTCCTTCC
* *
86 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT T
132 CATTTTTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 34 0.92
5 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTCT
Found at i:137 original size:11 final size:12
Alignment explanation
Indices: 89--138 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
79 TCCTTCCTTC
89 TTTCTTTC-TTT
1 TTTCTTTCATTT
*
100 CTTTCTTTCTCTTT
1 -TTTCTTTC-ATTT
*
114 TTTCTTTCTTTT
1 TTTCTTTCATTT
126 TTTC-TTCATTT
1 TTTCTTTCATTT
137 TT
1 TT
139 CGTTGGTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 8 0.24
12 15 0.44
13 8 0.24
14 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTCATTT
Found at i:2611 original size:6 final size:6
Alignment explanation
Indices: 2600--2628 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2590 ACACCTCTCT
2600 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
2629 TTCCTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:16627 original size:6 final size:6
Alignment explanation
Indices: 16616--16658 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
16606 CTAAAGTAAA
16616 AAAAAG AAAAAG --AAA- AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
16659 TATTTGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 3 0.09
5 3 0.09
6 28 0.82
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16633 original size:15 final size:15
Alignment explanation
Indices: 16608--16658 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
16598 TTTACCACCT
16608 AAAGTAAAAAAAAGAA
1 AAAG-AAAAAAAAGAA
16624 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
16639 AAAG---AAAAAGAA
1 AAAGAAAAAAAAGAA
16651 AAAGAAAA
1 AAAGAAAA
16659 TATTTGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.38
15 16 0.50
16 4 0.12
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAAAGAA
Found at i:18689 original size:2 final size:2
Alignment explanation
Indices: 18682--18712 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18672 TCTGAAACGC
*
18682 CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
18713 GCCTCATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Done.